#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
PPFIBP2	8495	hgsc.bcm.edu	37	11	7661048	7661050	+	In_Frame_Del	DEL	CTC	CTC	-	rs375552735|rs143023559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7661048_7661050delCTC	ENST00000299492.4	+	15	1710_1712	c.1322_1324delCTC	c.(1321-1326)tctcct>tct	p.P443del	PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000530181.1_In_Frame_Del_p.P300del|PPFIBP2_ENST00000533792.1_In_Frame_Del_p.P285del|PPFIBP2_ENST00000528883.1_In_Frame_Del_p.P331del	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	443					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)	p.P442S(1)		breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		GCTGCCAAATCTCCTCCCACCAT	0.596														226	0.0451278	0.0129	0.0576	5008	,	,		18604	0.0933		0.0477	False		,,,				2504	0.0276				p.441_441del		Pindel,Atlas-Indel	.											.	PPFIBP2	87	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.1321_1323del						PASS	.			85,4179		1,83,2048						1.4	0.0		dbSNP_134	94	316,7928		9,298,3815	no	coding	PPFIBP2	NM_003621.2		10,381,5863	A1A1,A1R,RR		3.8331,1.9934,3.2059				401,12107				SO:0001651	inframe_deletion	8495	exon15			.	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.1322_1324delCTC	11.37:g.7661051_7661053delCTC	ENSP00000299492:p.Pro443del	Somatic	152	.	.		WXS	Illumina HiSeq	Phase_I	174	52	0.299	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	In_Frame_Del	DEL	ENST00000299492.4	37	CCDS31419.1																																																																																			CTC|0.944;-|0.056	0.056	strong		0.596	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
OVGP1	5016	hgsc.bcm.edu	37	1	111957502	111957525	+	In_Frame_Del	DEL	TCACAGACTGATGACTCACAGGGG	TCACAGACTGATGACTCACAGGGG	-	rs3767610|rs201350653|rs111600994|rs3767609|rs3767608|rs549398942|rs113843251|rs568931117|rs61742558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCACAGACTGATGACTCACAGGGG	TCACAGACTGATGACTCACAGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111957502_111957525delTCACAGACTGATGACTCACAGGGG	ENST00000369732.3	-	11	1653_1676	c.1598_1621delCCCCTGTGAGTCATCAGTCTGTGA	c.(1597-1623)acccctgtgagtcatcagtctgtgagc>agc	p.TPVSHQSV533del		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	533					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)		CCTCCAGGGCTCACAGACTGATGACTCACAGGGGTCACAGACTG	0.545																																					p.533_541del		Pindel,Atlas-Indel	.											.	OVGP1	177	.	4	Deletion - In frame(4)	haematopoietic_and_lymphoid_tissue(2)|stomach(2)	c.1599_1622del						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.1598_1621delCCCCTGTGAGTCATCAGTCTGTGA	1.37:g.111957502_111957525delTCACAGACTGATGACTCACAGGGG	ENSP00000358747:p.Thr533_Val540del	Somatic	155	.	.		WXS	Illumina HiSeq	Phase_I	156	35	0.224	NM_002557	A0AV19|B9EGE1|Q15841	In_Frame_Del	DEL	ENST00000369732.3	37	CCDS834.1																																																																																			.	.	weak		0.545	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
ORM1	5004	hgsc.bcm.edu	37	9	117088618	117088620	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117088618_117088620delAGG	ENST00000259396.8	+	6	665_667	c.587_589delAGG	c.(586-591)caggag>cag	p.E198del		NM_000607.2	NP_000598.2	P02763	A1AG1_HUMAN	orosomucoid 1	198					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(2)|large_intestine(4)|lung(2)	8		Myeloproliferative disorder(63;0.163)			Abiraterone(DB05812)|Acenocoumarol(DB01418)|Ajmaline(DB01426)|Alfentanil(DB00802)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aprindine(DB01429)|Bupropion(DB01156)|Canagliflozin(DB08907)|Celecoxib(DB00482)|Chlorpromazine(DB00477)|Desipramine(DB01151)|Disopyramide(DB00280)|Doxazosin(DB00590)|Doxepin(DB01142)|Erlotinib(DB00530)|Fluoxetine(DB00472)|Gefitinib(DB00317)|Imatinib(DB00619)|Imipramine(DB00458)|Ivacaftor(DB08820)|Maprotiline(DB00934)|Mirabegron(DB08893)|Nateglinide(DB00731)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxycodone(DB00497)|Penbutolol(DB01359)|Pethidine(DB00454)|Phenprocoumon(DB00946)|Pitavastatin(DB08860)|Prazosin(DB00457)|Propranolol(DB00571)|Quinidine(DB00908)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Tamsulosin(DB00706)|Telaprevir(DB05521)|Thalidomide(DB01041)|Trazodone(DB00656)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Vismodegib(DB08828)|Warfarin(DB00682)	GAGAGGAAACAGGAGGAGGGGGA	0.581																																					p.196_196del		Atlas-Indel	.											.	ORM1	20	.	0			c.586_588del						PASS	.																																			SO:0001651	inframe_deletion	5004	exon6			.		CCDS6803.1	9q32	2013-09-19			ENSG00000229314	ENSG00000229314		"""Lipocalins"""	8498	protein-coding gene	gene with protein product		138600					Standard	NM_000607		Approved		uc004bik.4	P02763	OTTHUMG00000021012	ENST00000259396.8:c.587_589delAGG	9.37:g.117088624_117088626delAGG	ENSP00000259396:p.Glu198del	Somatic	915	0	0		WXS	Illumina HiSeq	Phase_I	979	178	0.181818	NM_000607	B7ZKQ5|Q5T539|Q5U067|Q8TC16	In_Frame_Del	DEL	ENST00000259396.8	37	CCDS6803.1																																																																																			.	.	none		0.581	ORM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055426.1		
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382374	24382385	+	IGR	DEL	TGCTGCTGCTGC	TGCTGCTGCTGC	-	rs371342199		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGCTGCTGCTGC	TGCTGCTGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24382374_24382385delTGCTGCTGCTGC								AC004552.1 (15351 upstream) : PDK3 (100952 downstream)																							ctgctgctattgctgctgctgctgctgctgct	0.575																																					p.499_503del		Atlas-Indel	.											.	.	.	.	0			c.1496_1507del						PASS	.																																			SO:0001628	intergenic_variant	100130302	exon1			.																													X.37:g.24382374_24382385delTGCTGCTGCTGC		Somatic	393	0	0		WXS	Illumina HiSeq	Phase_I	418	131	0.313397	NM_001136234		In_Frame_Del	DEL		37																																																																																				.	.	alt	0	0.575								
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31913982	31913982	+	Frame_Shift_Del	DEL	G	G	-	rs5843453|rs201420116|rs570064399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31913982delG	ENST00000334046.5	-	1	201	c.171delC	c.(169-171)ttcfs	p.F57fs		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	57						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						TTTTTTAGTAGAATCCAGAGA	0.463													?|G|-|unsure	3942	0.787141	0.9266	0.7421	5008	,	,		17489	0.7034		0.7127	False		,,,				2504	0.7935				p.Y58fs		Pindel,Atlas-Indel	.											.	KRTAP19-6	16	.	0			c.172delT						PASS	.						33.0	58.0	51.0					21																	31913982		1069	2843	3912	SO:0001589	frameshift_variant	337973	exon1			.	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"""Keratin associated proteins"""	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.171delC	21.37:g.31913982delG	ENSP00000375107:p.Phe57fs	Somatic	65	.	.		WXS	Illumina HiSeq	Phase_I	70	43	0.614	NM_181612	Q3LI71	Frame_Shift_Del	DEL	ENST00000334046.5	37	CCDS13598.1																																																																																			-|0.758;G|0.242	0.758	strong		0.463	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4		
LRRC37A2	474170	hgsc.bcm.edu	37	17	44590963	44590965	+	In_Frame_Del	DEL	CAA	CAA	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:44590963_44590965delCAA	ENST00000576629.1	+	2	1380_1382	c.885_887delCAA	c.(883-888)cccaac>ccc	p.N296del	LRRC37A2_ENST00000333412.3_In_Frame_Del_p.N296del			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	296						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)		ATCACTTGCCCAACATTACAGTT	0.473																																					p.295_296del		Atlas-Indel	.											.	LRRC37A2	37	.	0			c.884_886del						PASS	.																																			SO:0001651	inframe_deletion	474170	exon1			.	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.885_887delCAA	17.37:g.44590963_44590965delCAA	ENSP00000459551:p.Asn296del	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	305	20	0.0655738	NM_001006607	B7ZMC3	In_Frame_Del	DEL	ENST00000576629.1	37	CCDS42353.1																																																																																			.	.	none		0.473	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607	
AK9	221264	hgsc.bcm.edu	37	6	109906330	109906332	+	In_Frame_Del	DEL	CTT	CTT	-	rs71770197|rs73519211|rs568921203|rs141134529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	51	.	.		WXS	Illumina HiSeq	Phase_I	60	27	0.450	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	
FOXD4L6	653404	hgsc.bcm.edu	37	9	69201361	69201362	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:69201361_69201362delTG	ENST00000377473.1	-	1	842_843	c.251_252delCA	c.(250-252)tcafs	p.S84fs		NM_001085476.1	NP_001078945.1	Q3SYB3	FX4L6_HUMAN	forkhead box D4-like 6	84					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGCCAAACTCTGAGGGGTCGCT	0.698																																					p.84_85del		Atlas-Indel	.											.	.	.	.	0			c.252_253del						PASS	.																																			SO:0001589	frameshift_variant	653404	exon1			.		CCDS43826.1	9q12	2014-05-06			ENSG00000204793	ENSG00000273514			31986	protein-coding gene	gene with protein product							Standard	NM_001085476		Approved	OTTHUMG00000066822	uc004afi.2	Q3SYB3	OTTHUMG00000188618	ENST00000377473.1:c.251_252delCA	9.37:g.69201361_69201362delTG	ENSP00000366693:p.Ser84fs	Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	547	86	0.157221	NM_001085476	B2RPC4|Q4V336	Frame_Shift_Del	DEL	ENST00000377473.1	37	CCDS43826.1																																																																																			.	.	none		0.698	FOXD4L6-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143174.1	NM_001085476	
TTN	7273	hgsc.bcm.edu	37	2	179514942	179514959	+	In_Frame_Del	DEL	TTTCCTCTTCAGGAGCAA	TTTCCTCTTCAGGAGCAA	-	rs374976705|rs139512154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTTCCTCTTCAGGAGCAA	TTTCCTCTTCAGGAGCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179514942_179514959delTTTCCTCTTCAGGAGCAA	ENST00000591111.1	-	165	35452_35469	c.35228_35245delTTGCTCCTGAAGAGGAAA	c.(35227-35247)attgctcctgaagaggaaaag>aag	p.IAPEEE11743del	TTN_ENST00000589042.1_In_Frame_Del_p.IAPEEE13250del|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_In_Frame_Del_p.IAPEEE10816del|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	11743	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGAACTGGCTTTTCCTCTTCAGGAGCAATTTCCTCTTC	0.381														166	0.033147	0.084	0.0173	5008	,	,		20291	0.0119		0.0139	False		,,,				2504	0.0174				p.13250_13256del		Pindel,Atlas-Indel	.											.	TTN	18412	.	0			c.39750_39767del						PASS	.		,,,	109,3367		6,97,1635					,,,	1.6	1.0		dbSNP_134	28	38,7756		1,36,3860	no	intron,intron,coding,intron	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	,,,	7,133,5495	A1A1,A1R,RR		0.4876,3.1358,1.3043	,,,	,,,		147,11123				SO:0001651	inframe_deletion	7273	exon210			.	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.35228_35245delTTGCTCCTGAAGAGGAAA	2.37:g.179514942_179514959delTTTCCTCTTCAGGAGCAA	ENSP00000465570:p.Ile11743_Glu11748del	Somatic	220	.	.		WXS	Illumina HiSeq	Phase_I	197	39	0.198	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	In_Frame_Del	DEL	ENST00000591111.1	37																																																																																				TTTCCTCTTCAGGAGCAA|0.972;-|0.028	0.028	strong		0.381	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
NPR2	4882	hgsc.bcm.edu	37	9	35811486	35811497	+	IGR	DEL	CCAGGACCAGAG	CCAGGACCAGAG	-	rs59748329|rs555852229|rs141090907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCAGGACCAGAG	CCAGGACCAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35811486_35811497delCCAGGACCAGAG	ENST00000342694.2	+	0	3686				SPAG8_ENST00000484764.1_In_Frame_Del_p.180_184GSGPG>G|TMEM8B_ENST00000377996.1_5'Flank|SPAG8_ENST00000396638.2_In_Frame_Del_p.182_186GSGPG>G|SPAG8_ENST00000479751.1_5'Flank|AL133410.1_ENST00000582432.1_RNA|HINT2_ENST00000474908.1_5'Flank|SPAG8_ENST00000340291.2_In_Frame_Del_p.182_186GSGPG>G	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		Pindel,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	53	.	.		WXS	Illumina HiSeq	Phase_I	46	29	0.630	NM_172312	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		
LCNL1	401562	hgsc.bcm.edu	37	9	139879429	139879429	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139879429delT	ENST00000408973.2	+	3	1055	c.461delT	c.(460-462)ctcfs	p.L154fs	LCNL1_ENST00000432827.1_Intron	NM_207510.3	NP_997393.3	Q6ZST4	LCNL1_HUMAN	lipocalin-like 1	154																	tgcccctctctccctctcttc	0.682																																					p.L154fs		Atlas-Indel	.											.	LCNL1	4	.	0			c.460delC						PASS	.						8.0	11.0	10.0					9																	139879429		1791	3853	5644	SO:0001589	frameshift_variant	401562	exon3			.		CCDS43908.1	9q34.3	2014-01-22			ENSG00000214402	ENSG00000214402		"""Lipocalins"""	34436	protein-coding gene	gene with protein product							Standard	NM_207510		Approved	FLJ45224	uc004ckh.1	Q6ZST4	OTTHUMG00000159546	ENST00000408973.2:c.461delT	9.37:g.139879429delT	ENSP00000386162:p.Leu154fs	Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	209	15	0.0717703	NM_207510		Frame_Shift_Del	DEL	ENST00000408973.2	37	CCDS43908.1																																																																																			.	.	none		0.682	LCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356128.1	NM_207510	
MIR517C	574492	hgsc.bcm.edu	37	19	54245839	54245840	+	RNA	INS	-	-	GT	rs370992581|rs111745142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54245839_54245840insGT	ENST00000385103.1	+	0	95				MIR520H_ENST00000385126.1_RNA|RNU6-982P_ENST00000516216.1_RNA	NR_030214.1				microRNA 517c																		TTCCCTTTAGAGTTACTGTTTG	0.421														37	0.00738818	0.0076	0.0	5008	,	,		20005	0.0109		0.0119	False		,,,				2504	0.0041				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																					574493	.			.			19q13.42	2011-09-12		2008-12-18	ENSG00000207838	ENSG00000207838		"""ncRNAs / Micro RNAs"""	32124	non-coding RNA	RNA, micro				MIRN517C			Standard	NR_030214		Approved	hsa-mir-517c	uc021var.1				19.37:g.54245840_54245841dupGT		Somatic	172	.	.		WXS	Illumina HiSeq	Phase_I	129	21	0.163	.		RNA	INS	ENST00000385103.1	37																																																																																				-|0.978;GT|0.022	0.022	strong		0.421	MIR517C-201	KNOWN	basic	miRNA	miRNA		NR_030214	
C6orf48	50854	hgsc.bcm.edu	37	6	31807372	31807373	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31807372_31807373insA	ENST00000375640.3	+	4	887_888	c.160_161insA	c.(160-162)tacfs	p.Y54fs	C6orf48_ENST00000395789.1_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000395788.3_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375642.2_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375638.3_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375639.2_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375633.1_Frame_Shift_Ins_p.Y54fs|SNORD52_ENST00000364884.1_RNA|C6orf48_ENST00000375641.2_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375635.2_Frame_Shift_Ins_p.Y54fs	NM_001040438.1	NP_001035528.1	Q9UBA6	G8_HUMAN	chromosome 6 open reading frame 48	54										breast(1)|large_intestine(1)|lung(1)|skin(1)	4						CCTAAGAACTTACAACTTTCCT	0.391																																					p.Y54_N55delinsX		Pindel,Atlas-Indel	.											.	C6orf48	8	.	0			c.160_161insA						PASS	.																																			SO:0001589	frameshift_variant	50854	exon5			.	AJ249732	CCDS34416.1	6p21.33	2011-12-13			ENSG00000204387	ENSG00000204387			19078	protein-coding gene	gene with protein product		605447				8096093	Standard	NM_001287483		Approved	D6S57, G8	uc003rjy.2	Q9UBA6	OTTHUMG00000031175	ENST00000375640.3:c.161dupA	6.37:g.31807373_31807373dupA	ENSP00000364791:p.Tyr54fs	Somatic	119	.	.		WXS	Illumina HiSeq	Phase_I	120	41	0.342	NM_001040437	Q9BW21|Q9UBA7|Q9UBA8	Frame_Shift_Ins	INS	ENST00000375640.3	37	CCDS34416.1																																																																																			.	.	none		0.391	C6orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076332.2	NM_001040437	
PRDM2	7799	hgsc.bcm.edu	37	1	14106394	14106395	+	In_Frame_Ins	INS	-	-	CTC	rs2308040|rs148293494|rs59028030		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:14106394_14106395insCTC	ENST00000235372.7	+	8	2960_2961	c.2104_2105insCTC	c.(2104-2106)act>aCTCct	p.703_704insP	PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000311066.5_In_Frame_Ins_p.703_704insP|PRDM2_ENST00000343137.4_In_Frame_Ins_p.502_503insP|PRDM2_ENST00000413440.1_In_Frame_Ins_p.502_503insP|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000503842.1_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	703				P -> PP (in Ref. 1 and 7). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P703_A704insP(1)		endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		AGATAAACTAACTCCTGCAGGG	0.401																																					p.T702delinsTP		Pindel,Atlas-Indel	.											.	PRDM2	147	.	1	Insertion - In frame(1)	ovary(1)	c.2104_2105insCTC						PASS	.		,,,	2438,1826		699,1040,393					,,,	0.5	0.2		dbSNP_100	80	3443,4811		676,2091,1360	no	coding,coding,intron,coding	PRDM2	NM_015866.4,NM_012231.4,NM_001135610.1,NM_001007257.2	,,,	1375,3131,1753	A1A1,A1R,RR		41.7131,42.8236,46.9803	,,,	,,,		5881,6637				SO:0001652	inframe_insertion	7799	exon8			.	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.2105_2107dupCTC	1.37:g.14106395_14106397dupCTC	ENSP00000235372:p.Pro703_Pro703dup	Somatic	110	.	.		WXS	Illumina HiSeq	Phase_I	131	48	0.366	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	In_Frame_Ins	INS	ENST00000235372.7	37	CCDS150.1																																																																																			-|0.492;CTC|0.508	0.508	strong		0.401	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786761	75786761	+	Frame_Shift_Del	DEL	C	C	-	rs145576551		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75786761delC	ENST00000478296.1	-	4	2139	c.1863delG	c.(1861-1863)gggfs	p.G621fs	ZNF717_ENST00000422325.1_Frame_Shift_Del_p.G671fs|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Frame_Shift_Del_p.G664fs|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	661					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TACGGTTTTTCCCCGTGTGAG	0.408																																					p.K672fs		Pindel,Atlas-Indel	.											.	ZNF717	160	.	0			c.2014delA						PASS	.			1106,1664		310,486,589	12.0	11.0	11.0			0.3	0.0	3	dbSNP_134	19	3067,3341		691,1685,828	no	frameshift	ZNF717	NM_001128223.1		1001,2171,1417	A1A1,A1R,RR		47.862,39.9278,45.4674			75786761	4173,5005	587	1452	2039	SO:0001589	frameshift_variant	100131827	exon5			.	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1863delG	3.37:g.75786761delC	ENSP00000419377:p.Gly621fs	Somatic	22	.	.		WXS	Illumina HiSeq	Phase_I	57	16	0.281	NM_001128223		Frame_Shift_Del	DEL	ENST00000478296.1	37																																																																																				.	.	weak		0.408	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
OR6C4	341418	hgsc.bcm.edu	37	12	55945585	55945588	+	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs59693527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCTT	TCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55945585_55945588delTCTT	ENST00000394256.2	+	1	603_606	c.575_578delTCTT	c.(574-579)ctcttafs	p.LL192fs	RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	192						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(3)|lung(5)|skin(1)	11						GACACAAGCCTCTTAGAACTGATG	0.466														289	0.0577077	0.2095	0.0173	5008	,	,		21072	0.0		0.0	False		,,,				2504	0.0				p.192_193del		Pindel,Atlas-Indel	.											.	OR6C4	34	.	0			c.574_577del						PASS	.			740,3524		60,620,1452						-8.3	0.0		dbSNP_129	152	13,8241		0,13,4114	no	frameshift	OR6C4	NM_001005494.1		60,633,5566	A1A1,A1R,RR		0.1575,17.3546,6.0153				753,11765				SO:0001589	frameshift_variant	341418	exon1			.	BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"""GPCR / Class A : Olfactory receptors"""	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.575_578delTCTT	12.37:g.55945585_55945588delTCTT	ENSP00000377799:p.Leu192fs	Somatic	249	.	.		WXS	Illumina HiSeq	Phase_I	235	72	0.306	NM_001005494	A8MZG7|B2RNN2|Q6IFK1	Frame_Shift_Del	DEL	ENST00000394256.2	37	CCDS31827.1																																																																																			TCTT|0.950;-|0.050	0.050	strong		0.466	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1		
TIGD6	81789	hgsc.bcm.edu	37	5	149374880	149374880	+	Frame_Shift_Del	DEL	T	T	-	rs397756704|rs3832324|rs201139146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149374880delT	ENST00000296736.3	-	2	1806	c.1032delA	c.(1030-1032)caafs	p.Q344fs	TIGD6_ENST00000515406.2_Frame_Shift_Del_p.Q344fs	NM_030953.3	NP_112215.1	Q17RP2	TIGD6_HUMAN	tigger transposable element derived 6	344	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|stomach(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCACCTCTTCTTGATCCTCAC	0.502													TT|TT|T|deletion	2598	0.51877	0.3616	0.4813	5008	,	,		23962	0.5853		0.6074	False		,,,				2504	0.5982				p.E345fs		Pindel,Atlas-Indel	.											.	TIGD6	29	.	0			c.1033delG						PASS	.			1735,2529		362,1011,759	98.0	51.0	67.0			2.2	0.0	5	dbSNP_130	135	5379,2875		1759,1861,507	yes	frameshift	TIGD6	NM_030953.3		2121,2872,1266	A1A1,A1R,RR		34.8316,40.6895,43.1698			149374880	7114,5404	2168	4015	6183	SO:0001589	frameshift_variant	81789	exon2			.	AK056604	CCDS4301.1	5q33.1	2008-02-05			ENSG00000164296	ENSG00000164296			18332	protein-coding gene	gene with protein product						11230166	Standard	NM_030953		Approved	DKFZp761E2110	uc003lrj.3	Q17RP2	OTTHUMG00000130045	ENST00000296736.3:c.1032delA	5.37:g.149374880delT	ENSP00000296736:p.Gln344fs	Somatic	226	.	.		WXS	Illumina HiSeq	Phase_I	276	73	0.264	NM_030953	B3KTZ8|Q96MQ4|Q9H0X7	Frame_Shift_Del	DEL	ENST00000296736.3	37	CCDS4301.1																																																																																			T|0.470;-|0.530	0.530	strong		0.502	TIGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252324.1	NM_030953	
NAP1L5	266812	hgsc.bcm.edu	37	4	89618415	89618426	+	In_Frame_Del	DEL	GCAGCCTCTGCC	GCAGCCTCTGCC	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCAGCCTCTGCC	GCAGCCTCTGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:89618415_89618426delGCAGCCTCTGCC	ENST00000323061.5	-	1	960_971	c.480_491delGGCAGAGGCTGC	c.(478-492)gcggcagaggctgcc>gcc	p.160_164AAEAA>A	HERC3_ENST00000543130.1_Intron|HERC3_ENST00000264345.3_Intron|HERC3_ENST00000402738.1_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	160	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(123;0.000181)		GGCCCCCGCGGCAGCCTCTGCCGCAGcctcct	0.608																																					p.161_164del		Pindel,Atlas-Indel	.											.	NAP1L5	23	.	0			c.481_492del						PASS	.		,	4,4262		1,2,2130					,	-3.3	0.0			93	0,8252		0,0,4126	no	coding,intron	HERC3,NAP1L5	NM_153757.2,NM_014606.1	,	1,2,6256	A1A1,A1R,RR		0.0,0.0938,0.032	,	,		4,12514				SO:0001651	inframe_deletion	266812	exon1			.	NM_153757	CCDS3632.1	4q21-q22	2006-04-12			ENSG00000177432	ENSG00000177432			19968	protein-coding gene	gene with protein product		612203				12383514	Standard	NM_153757		Approved	DRLM	uc003hrx.3	Q96NT1	OTTHUMG00000130950	ENST00000323061.5:c.480_491delGGCAGAGGCTGC	4.37:g.89618415_89618426delGCAGCCTCTGCC	ENSP00000320488:p.Ala160_Ala163del	Somatic	279	.	.		WXS	Illumina HiSeq	Phase_I	285	66	0.232	NM_153757		In_Frame_Del	DEL	ENST00000323061.5	37	CCDS3632.1																																																																																			.	.	none		0.608	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757	
LRRC37A	9884	hgsc.bcm.edu	37	17	44373384	44373386	+	In_Frame_Del	DEL	CAA	CAA	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:44373384_44373386delCAA	ENST00000320254.5	+	1	888_890	c.885_887delCAA	c.(883-888)cccaac>ccc	p.N296del	LRRC37A_ENST00000496930.1_Intron|ARL17B_ENST00000570618.1_Intron|LRRC37A_ENST00000393465.3_In_Frame_Del_p.N296del	NM_014834.4	NP_055649.4	A6NMS7	L37A1_HUMAN	leucine rich repeat containing 37A	296						integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|pancreas(6)|prostate(1)|skin(1)	11		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		ATCACTTGCCCAACATTACAGTT	0.473																																					p.295_296del		Atlas-Indel	.											.	LRRC37A	19	.	0			c.884_886del						PASS	.																																			SO:0001651	inframe_deletion	9884	exon1			.	BC040501	CCDS11504.2	17q21.31	2014-04-01			ENSG00000176681	ENSG00000176681			29069	protein-coding gene	gene with protein product						9628581, 15533724	Standard	NM_014834		Approved	KIAA0563	uc031rbr.1	A6NMS7	OTTHUMG00000149841	ENST00000320254.5:c.885_887delCAA	17.37:g.44373384_44373386delCAA	ENSP00000326324:p.Asn296del	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	305	21	0.0688525	NM_014834	Q68DY2|Q8IWC7	In_Frame_Del	DEL	ENST00000320254.5	37	CCDS11504.2																																																																																			.	.	none		0.473	LRRC37A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313519.3	NM_014834	
GIGYF2	26058	hgsc.bcm.edu	37	2	233712227	233712229	+	In_Frame_Del	DEL	ACA	ACA	-	rs7563724|rs398061180|rs527464858|rs58340018|rs376678075|rs10555297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233712227_233712229delACA	ENST00000409547.1	+	29	3941_3943	c.3630_3632delACA	c.(3628-3633)ccacag>ccg	p.Q1216del	GIGYF2_ENST00000409451.3_In_Frame_Del_p.Q1237del|GIGYF2_ENST00000409480.1_In_Frame_Del_p.Q1238del|GIGYF2_ENST00000373566.3_In_Frame_Del_p.Q1238del|GIGYF2_ENST00000409196.3_In_Frame_Del_p.Q1210del|GIGYF2_ENST00000373563.4_In_Frame_Del_p.Q1216del	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1216	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.Q1216delQ(2)|p.Q1237delQ(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		agcagctgccacagcagcagcag	0.547														2800	0.559105	0.6021	0.6138	5008	,	,		10978	0.6022		0.6302	False		,,,				2504	0.3446				p.1231_1232del		Atlas-Indel	.											.	GIGYF2	288	.	3	Deletion - In frame(3)	breast(2)|ovary(1)	c.3692_3694del						PASS	.																																			SO:0001651	inframe_deletion	26058	exon29			.	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3630_3632delACA	2.37:g.233712227_233712229delACA	ENSP00000386537:p.Gln1216del	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	In_Frame_Del	DEL	ENST00000409547.1	37	CCDS33401.1																																																																																			ACA|0.358;-|0.642	0.642	strong		0.547	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643073	1643073	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1643073delC	ENST00000399682.1	-	1	295	c.251delG	c.(250-252)tgtfs	p.C84fs		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GGAACCCCCACAAGAGCCATA	0.667																																					p.C84fs		Atlas-Indel	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	0			c.252delT						PASS	.						9.0	15.0	13.0					11																	1643073		682	1575	2257	SO:0001589	frameshift_variant	387267	exon1			.	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.251delG	11.37:g.1643073delC	ENSP00000382590:p.Cys84fs	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	284	23	0.0809859	NM_001012709		Frame_Shift_Del	DEL	ENST00000399682.1	37																																																																																				.	.	none		0.667	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
FANCE	2178	hgsc.bcm.edu	37	6	35424008	35424010	+	In_Frame_Del	DEL	GGA	GGA	-	rs45451605|rs397897540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35424008_35424010delGGA	ENST00000229769.2	+	2	918_920	c.733_735delGGA	c.(733-735)ggadel	p.G246del		NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	246	Interaction with FANCC.				DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						CCTGGCAGATGGAGGAAGTGCAT	0.507			"""N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia					17	0.00339457	0.0113	0.0014	5008	,	,		22003	0.0		0.0	False		,,,				2504	0.001				p.244_245del		Pindel,Atlas-Indel	.	yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	"""Fanconi anemia, complementation group E"""		L	.	FANCE	45	.	0			c.732_734del						PASS	.			70,4194		2,66,2064						-4.1	0.0		dbSNP_127	120	5,8249		0,5,4122	no	coding	FANCE	NM_021922.2		2,71,6186	A1A1,A1R,RR		0.0606,1.6417,0.5991				75,12443				SO:0001651	inframe_deletion	2178	exon2	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039		"""Fanconi anemia, complementation groups"""	3586	protein-coding gene	gene with protein product		613976		FACE		7662964, 11001585	Standard	XM_005248885		Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.733_735delGGA	6.37:g.35424011_35424013delGGA	ENSP00000229769:p.Gly246del	Somatic	138	.	.		WXS	Illumina HiSeq	Phase_I	142	42	0.296	NM_021922	A8K907|Q4ZGH2	In_Frame_Del	DEL	ENST00000229769.2	37	CCDS4805.1																																																																																			GGA|0.979;-|0.021	0.021	strong		0.507	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040282.1		
FERMT1	55612	hgsc.bcm.edu	37	20	6091083	6091085	+	In_Frame_Del	DEL	ATG	ATG	-	rs150175364		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:6091083_6091085delATG	ENST00000217289.4	-	5	1394_1396	c.606_608delCAT	c.(604-609)accatg>acg	p.M203del	FERMT1_ENST00000536936.1_Intron	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	203	FERM.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						GAACCAAGTCATGGTGGATGATG	0.498																																					p.203_203del		Pindel,Atlas-Indel	.											.	FERMT1	106	.	0			c.607_609del						PASS	.			23,4241		0,23,2109						1.5	1.0		dbSNP_134	224	0,8254		0,0,4127	no	coding	FERMT1	NM_017671.4		0,23,6236	A1A1,A1R,RR		0.0,0.5394,0.1837				23,12495				SO:0001651	inframe_deletion	55612	exon5			.	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.606_608delCAT	20.37:g.6091083_6091085delATG	ENSP00000217289:p.Met203del	Somatic	221	.	.		WXS	Illumina HiSeq	Phase_I	209	68	0.325	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	In_Frame_Del	DEL	ENST00000217289.4	37	CCDS13098.1																																																																																			.	.	strong		0.498	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
HYDIN	54768	hgsc.bcm.edu	37	16	71007312	71007312	+	Frame_Shift_Del	DEL	G	G	-	rs373616607		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71007312delG	ENST00000393567.2	-	35	5463	c.5313delC	c.(5311-5313)cccfs	p.P1771fs		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1771					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)				CTCCAGAAATGGGCTGGATTT	0.403																																					p.I1772fs		Pindel,Atlas-Indel	.											.	HYDIN	788	.	0			c.5314delA						PASS	.						1.0	1.0	1.0					16																	71007312		454	1000	1454	SO:0001589	frameshift_variant	54768	exon35			.	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.5313delC	16.37:g.71007312delG	ENSP00000377197:p.Pro1771fs	Somatic	101	.	.		WXS	Illumina HiSeq	Phase_I	140	25	0.179	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Frame_Shift_Del	DEL	ENST00000393567.2	37	CCDS59269.1																																																																																			.	.	weak		0.403	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
PIEZO1	9780	hgsc.bcm.edu	37	16	88780635	88780636	+	IGR	INS	-	-	GTGT	rs397761749|rs149847195|rs571090098|rs562672342|rs11278302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88780635_88780636insGTGT	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Splice_Site_p.R366fs|CTU2_ENST00000567949.1_Splice_Site_p.R437fs|CTU2_ENST00000378384.3_Splice_Site_p.R279fs|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Splice_Site_p.R366fs	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						ACtgtgtacaggtgtgggtgtg	0.644																																					p.R366fs		Pindel,Atlas-Indel	.											.	CTU2	66	.	0			c.1097_1098insGTGT						PASS	.																																			SO:0001628	intergenic_variant	348180	exon10			.	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.88780636_88780639dupGTGT		Somatic	115	.	.		WXS	Illumina HiSeq	Phase_I	62	10	0.161	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Frame_Shift_Ins	INS	ENST00000301015.9	37	CCDS54058.1																																																																																			.	.	weak		0.644	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
SSPO	23145	hgsc.bcm.edu	37	7	149480091	149480092	+	RNA	INS	-	-	C	rs144883973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149480091_149480092insC	ENST00000378016.2	+	0	2057_2058							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)			ATCACCCTGGACCCCCGCCATG	0.653													CCCCC|CCCCC|CCCCCC|insertion	131	0.0261581	0.0946	0.0086	5008	,	,		17227	0.0		0.0	False		,,,				2504	0.0				p.D686fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.2057_2058insC						PASS	.			263,3523		27,209,1657						4.2	1.0		dbSNP_134	31	27,7833		1,25,3904	no	frameshift	SSPO	NM_198455.2		28,234,5561	A1A1,A1R,RR		0.3435,6.9466,2.4901				290,11356						23145	exon15			.	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.149480096_149480096dupC		Somatic	217	.	.		WXS	Illumina HiSeq	Phase_I	217	71	0.327	NM_198455	Q76B61	Frame_Shift_Ins	INS	ENST00000378016.2	37																																																																																				-|0.979;C|0.021	0.021	strong		0.653	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
TIGD6	81789	hgsc.bcm.edu	37	5	149375721	149375721	+	Frame_Shift_Del	DEL	C	C	-	rs33910807|rs575130996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149375721delC	ENST00000296736.3	-	2	965	c.191delG	c.(190-192)ggafs	p.G64fs	TIGD6_ENST00000515406.2_Frame_Shift_Del_p.G64fs	NM_030953.3	NP_112215.1	Q17RP2	TIGD6_HUMAN	tigger transposable element derived 6	64						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|stomach(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCGCTGGGGTCCCACGGATGC	0.433													CCC|CCC|CC|deletion	476	0.0950479	0.3449	0.0231	5008	,	,		21862	0.0		0.004	False		,,,				2504	0.0				p.G64fs		Pindel,Atlas-Indel	.											.	TIGD6	29	.	0			c.192delA						PASS	.			1204,3060		171,862,1099	71.0	98.0	89.0			-2.9	0.2	5	dbSNP_126	99	16,8222		2,12,4105	yes	frameshift	TIGD6	NM_030953.3		173,874,5204	A1A1,A1R,RR		0.1942,28.2364,9.7584			149375721	1220,11282	2188	4300	6488	SO:0001589	frameshift_variant	81789	exon2			.	AK056604	CCDS4301.1	5q33.1	2008-02-05			ENSG00000164296	ENSG00000164296			18332	protein-coding gene	gene with protein product						11230166	Standard	NM_030953		Approved	DKFZp761E2110	uc003lrj.3	Q17RP2	OTTHUMG00000130045	ENST00000296736.3:c.191delG	5.37:g.149375721delC	ENSP00000296736:p.Gly64fs	Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	82	32	0.390	NM_030953	B3KTZ8|Q96MQ4|Q9H0X7	Frame_Shift_Del	DEL	ENST00000296736.3	37	CCDS4301.1																																																																																			C|0.913;-|0.087	0.087	strong		0.433	TIGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252324.1	NM_030953	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350728	50350729	+	In_Frame_Ins	INS	-	-	TCC	rs6614552|rs375199494|rs143151534		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:50350728_50350729insTCC	ENST00000289292.7	-	6	3696_3697	c.3413_3414insGGA	c.(3412-3414)gaa>gaGGAa	p.1138_1138E>EE	SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1022_1022E>EE|SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1138_1138E>EE			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1138	Glu-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)					cttcttcttcttcctcctcctc	0.559														968	0.256424	0.1286	0.1614	3775	,	,		11689	0.1885		0.2127	False		,,,				2504	0.2883				p.E1138delinsEE		Atlas-Indel	.											.	SHROOM4	171	.	0			c.3414_3415insGGA						PASS	.																																			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.3411_3413dupGGA	X.37:g.50350735_50350737dupTCC	ENSP00000289292:p.Glu1151dup	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	71	12	0.169014	NM_020717	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	ENST00000289292.7	37	CCDS35277.1																																																																																			-|0.700;TCC|0.300	0.300	strong		0.559	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
SCARA5	286133	hgsc.bcm.edu	37	8	27779652	27779672	+	In_Frame_Del	DEL	GCAGCGGAGCCTGCAGCAGCC	GCAGCGGAGCCTGCAGCAGCC	-	rs556775167|rs370651084|rs544481270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCAGCGGAGCCTGCAGCAGCC	GCAGCGGAGCCTGCAGCAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27779652_27779672delGCAGCGGAGCCTGCAGCAGCC	ENST00000354914.3	-	4	817_837	c.332_352delGGCTGCTGCAGGCTCCGCTGC	c.(331-354)cggctgctgcaggctccgctgcaa>caa	p.RLLQAPL111del	SCARA5_ENST00000524352.1_In_Frame_Del_p.RLLQAPL111del|SCARA5_ENST00000518030.1_In_Frame_Del_p.RLLQAPL68del|SCARA5_ENST00000301906.4_In_Frame_Del_p.RLLQAPL68del|SCARA5_ENST00000380385.2_Intron	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	111					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)		AGGTCCGCTTGCAGCGGAGCCTGCAGCAGCCGCAGCTGCAA	0.67														4	0.000798722	0.003	0.0	5008	,	,		20679	0.0		0.0	False		,,,				2504	0.0				p.111_118del		Pindel,Atlas-Indel	.											.	SCARA5	53	.	0			c.333_353del						PASS	.			5,4237		1,3,2117						3.1	1.0			13	9,8227		3,3,4112	no	coding	SCARA5	NM_173833.5		4,6,6229	A1A1,A1R,RR		0.1093,0.1179,0.1122				14,12464				SO:0001651	inframe_deletion	286133	exon4			.	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.332_352delGGCTGCTGCAGGCTCCGCTGC	8.37:g.27779652_27779672delGCAGCGGAGCCTGCAGCAGCC	ENSP00000346990:p.Arg111_Leu117del	Somatic	97	.	.		WXS	Illumina HiSeq	Phase_I	53	26	0.491	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	In_Frame_Del	DEL	ENST00000354914.3	37	CCDS6064.1																																																																																			.	.	none		0.670	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833	
DEFB126	81623	hgsc.bcm.edu	37	20	126156	126159	+	Frame_Shift_Del	DEL	CAAA	CAAA	-	rs200807952|rs397788846|rs11467497		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAAA	CAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	152	.	.		WXS	Illumina HiSeq	Phase_I	110	44	0.400	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	
SLC39A8	64116	hgsc.bcm.edu	37	4	103188834	103188836	+	Intron	DEL	AGA	AGA	-	rs370986625|rs71813938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:103188834_103188836delAGA	ENST00000394833.2	-	7	1525				SLC39A8_ENST00000424970.2_Intron|SLC39A8_ENST00000356736.4_Intron	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8						transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		AAAGTCTCCTAGAAGAAGAAGAA	0.369														302	0.0603035	0.2179	0.0173	5008	,	,		19711	0.0		0.002	False		,,,				2504	0.0				.		Atlas-Indel	.											SLC39A8,NS,carcinoma,0,1	SLC39A8	24	1	0			.						PASS	.		,,,	882,3384		101,680,1352					,,,	4.9	1.0		dbSNP_130	74	16,8232		0,16,4108	no	intron,intron,intron,intron	SLC39A8	NM_022154.5,NM_001135148.1,NM_001135147.1,NM_001135146.1	,,,	101,696,5460	A1A1,A1R,RR		0.194,20.6751,7.176	,,,	,,,		898,11616				SO:0001627	intron_variant	64116	.			.		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"""Solute carriers"""	20862	protein-coding gene	gene with protein product		608732	"""solute carrier family 39 (metal ion transporter), member 8"""			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.1049-3TCT>-	4.37:g.103188843_103188845delAGA		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	160	55	0.34375	.	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Splice_Site	DEL	ENST00000394833.2	37	CCDS3656.1																																																																																			AGA|0.950;-|0.050	0.050	strong		0.369	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154	
NBPF3	84224	hgsc.bcm.edu	37	1	21801436	21801444	+	Splice_Site	DEL	GTCTCCCAG	GTCTCCCAG	-	rs139002241|rs570380722|rs372317136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GTCTCCCAG	GTCTCCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21801436_21801444delGTCTCCCAG	ENST00000318249.5	+	8	1334_1342	c.984_992delGTCTCCCAG	c.(982-993)gtgtctcccagg>gtg	p.SPR329del	NBPF3_ENST00000454000.2_Splice_Site_p.SPR259del|NBPF3_ENST00000342104.5_Splice_Site_p.SPR329del|NBPF3_ENST00000318220.6_Splice_Site_p.SPR273del	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	329	NBPF 2. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AAGGGCCAGTGTCTCCCAGGTAATGCCAT	0.388														277	0.0553115	0.1551	0.0937	5008	,	,		21818	0.001		0.002	False		,,,				2504	0.0041				p.328_331del		Pindel,Atlas-Indel	.											.	NBPF3	55	.	0			c.983_991del						PASS	.			506,3760		32,442,1659						-1.6	0.0		dbSNP_134	214	59,8193		1,57,4068	no	coding-near-splice	NBPF3	NM_032264.2		33,499,5727	A1A1,A1R,RR		0.715,11.8612,4.5135				565,11953				SO:0001630	splice_region_variant	84224	exon8			.	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.992+1GTCTCCCAG>-	1.37:g.21801436_21801444delGTCTCCCAG		Somatic	85	.	.		WXS	Illumina HiSeq	Phase_I	88	17	0.193	NM_032264	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	In_Frame_Del	DEL	ENST00000318249.5	37	CCDS216.1																																																																																			GTCTCCCAG|0.948;-|0.052	0.052	strong		0.388	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	In_Frame_Del
PHRF1	57661	hgsc.bcm.edu	37	11	608503	608514	+	In_Frame_Del	DEL	GGACGCGCTCTG	GGACGCGCTCTG	-	rs553793466|rs144630030|rs370880150|rs376527396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGACGCGCTCTG	GGACGCGCTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:608503_608514delGGACGCGCTCTG	ENST00000264555.5	+	14	3175_3186	c.3047_3058delGGACGCGCTCTG	c.(3046-3060)cggacgcgctctggg>cgg	p.TRSG1017del	PHRF1_ENST00000533464.1_In_Frame_Del_p.TRSG1013del|PHRF1_ENST00000413872.2_In_Frame_Del_p.TRSG1015del|PHRF1_ENST00000416188.2_In_Frame_Del_p.TRSG1016del	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1017	Arg-rich.				mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)	p.G1020_S1023delGTRS(2)|p.R1023L(1)|p.R1018L(1)|p.G1025_S1028delGTRS(1)		breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GAGCACGGACGGACGCGCTCTGGGACGCGCTC	0.675														425	0.0848642	0.2368	0.0519	5008	,	,		20295	0.001		0.0527	False		,,,				2504	0.0225				p.1015_1018del		Pindel,Atlas-Indel	.											.	PHRF1	188	.	5	Deletion - In frame(3)|Substitution - Missense(2)	lung(2)|breast(2)|ovary(1)	c.3043_3054del						PASS	.			711,3413		97,517,1448						-2.3	0.0		dbSNP_132	33	442,7712		38,366,3673	no	coding	PHRF1	NM_020901.2		135,883,5121	A1A1,A1R,RR		5.4207,17.2405,9.3908				1153,11125				SO:0001651	inframe_deletion	57661	exon14			.	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.3047_3058delGGACGCGCTCTG	11.37:g.608503_608514delGGACGCGCTCTG	ENSP00000264555:p.Thr1017_Gly1020del	Somatic	100	.	.		WXS	Illumina HiSeq	Phase_I	107	31	0.290	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	In_Frame_Del	DEL	ENST00000264555.5	37																																																																																				-|1.000;|0.000	1.000	weak		0.675	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
REXO1	57455	hgsc.bcm.edu	37	19	1825928	1825930	+	In_Frame_Del	DEL	CTC	CTC	-	rs149465929|rs75443592|rs199696044	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1825928_1825930delCTC	ENST00000170168.4	-	3	2018_2020	c.1924_1926delGAG	c.(1924-1926)gagdel	p.E642del	REXO1_ENST00000587524.1_5'Flank|CTB-31O20.4_ENST00000593201.1_RNA|CTB-31O20.4_ENST00000590531.1_RNA|CTB-31O20.4_ENST00000587741.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	642						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|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)		CCTCACTCTTCTCTTCCTTGGGG	0.606														1503	0.30012	0.2844	0.4135	5008	,	,		15520	0.3829		0.2087	False		,,,				2504	0.2495				p.642_643del		Pindel,Atlas-Indel	.											.	REXO1	55	.	0			c.1925_1927del						PASS	.			1300,2964		203,894,1035						3.2	0.0		dbSNP_106	100	1727,6527		175,1377,2575	no	coding	REXO1	NM_020695.3		378,2271,3610	A1A1,A1R,RR		20.9232,30.4878,24.1812				3027,9491				SO:0001651	inframe_deletion	57455	exon3			.	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.1924_1926delGAG	19.37:g.1825928_1825930delCTC	ENSP00000170168:p.Glu642del	Somatic	162	.	.		WXS	Illumina HiSeq	Phase_I	186	56	0.301	NM_020695	Q9ULT2	In_Frame_Del	DEL	ENST00000170168.4	37	CCDS32866.1																																																																																			CTC|0.704;-|0.296	0.296	strong		0.606	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
THAP2	83591	hgsc.bcm.edu	37	12	72070506	72070508	+	In_Frame_Del	DEL	GTT	GTT	-	rs140783391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72070506_72070508delGTT	ENST00000308086.2	+	3	1806_1808	c.305_307delGTT	c.(304-309)agttgt>agt	p.C103del	RP11-293I14.2_ENST00000548802.1_Intron	NM_031435.3	NP_113623.1	Q9H0W7	THAP2_HUMAN	THAP domain containing, apoptosis associated protein 2	103						nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	10						AAAAACAACAGTTGTTCTCCAGC	0.34														202	0.0403355	0.0113	0.0591	5008	,	,		19109	0.003		0.0507	False		,,,				2504	0.0941				p.102_102del		Pindel,Atlas-Indel	.											.	THAP2	29	.	0			c.304_306del						PASS	.			82,4182		2,78,2052						2.0	1.0		dbSNP_134	46	567,7685		14,539,3573	no	coding	THAP2	NM_031435.3		16,617,5625	A1A1,A1R,RR		6.8711,1.9231,5.1854				649,11867				SO:0001651	inframe_deletion	83591	exon3			.	BC008358	CCDS9001.1	12q21.1	2013-01-25				ENSG00000173451		"""THAP (C2CH-type zinc finger) domain containing"""	20854	protein-coding gene	gene with protein product		612531				12575992	Standard	NM_031435		Approved	DKFZP564I0422	uc001swq.3	Q9H0W7	OTTHUMG00000169556	ENST00000308086.2:c.305_307delGTT	12.37:g.72070509_72070511delGTT	ENSP00000310796:p.Cys103del	Somatic	95	.	.		WXS	Illumina HiSeq	Phase_I	118	46	0.390	NM_031435	B2R8P3	In_Frame_Del	DEL	ENST00000308086.2	37	CCDS9001.1																																																																																			GTT|0.969;-|0.031	0.031	strong		0.340	THAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404796.1	NM_031435	
ING3	54556	hgsc.bcm.edu	37	7	120610847	120610849	+	In_Frame_Del	DEL	AAC	AAC	-	rs539687500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:120610847_120610849delAAC	ENST00000315870.5	+	10	1162_1164	c.1014_1016delAAC	c.(1012-1017)caaaca>caa	p.T340del	ING3_ENST00000431467.1_In_Frame_Del_p.T325del	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3	340					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|positive regulation of apoptotic process (GO:0043065)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	12	all_neural(327;0.117)					TCTCTCAACAAACAACTGTAGTG	0.394														6	0.00119808	0.0045	0.0	5008	,	,		17162	0.0		0.0	False		,,,				2504	0.0				p.338_339del		Pindel,Atlas-Indel	.											.	ING3	36	.	0			c.1013_1015del						PASS	.																																			SO:0001651	inframe_deletion	54556	exon10			.	AF074968	CCDS5778.1, CCDS35497.1	7q31	2013-01-28			ENSG00000071243	ENSG00000071243		"""Zinc fingers, PHD-type"""	14587	protein-coding gene	gene with protein product		607493				12080476	Standard	NM_019071		Approved	p47ING3, FLJ20089, Eaf4, MEAF4	uc003vjn.3	Q9NXR8	OTTHUMG00000141270	ENST00000315870.5:c.1014_1016delAAC	7.37:g.120610850_120610852delAAC	ENSP00000320566:p.Thr340del	Somatic	112	.	.		WXS	Illumina HiSeq	Phase_I	92	37	0.402	NM_019071	A8K790|O60394|Q567P3|Q6GMT3|Q7Z762|Q969G0|Q96DT4|Q9HC99|Q9P081	In_Frame_Del	DEL	ENST00000315870.5	37	CCDS5778.1																																																																																			.	.	none		0.394	ING3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280453.2	NM_019071	
FOXD4L4	349334	hgsc.bcm.edu	37	9	70427685	70427685	+	Frame_Shift_Del	DEL	G	G	-	rs59364037		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:70427685delG	ENST00000377413.1	-	1	2046	c.1215delC	c.(1213-1215)tgcfs	p.C405fs		NM_199244.2	NP_954714.2	Q8WXT5	FX4L4_HUMAN	forkhead box D4-like 4	405					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)								GBM - Glioblastoma multiforme(29;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		TGCCCGCCCAGCACCGCGCCC	0.677																																					p.W406fs		Atlas-Indel	.											.	FOXD4L4	5	.	0			c.1216delT						PASS	.																																			SO:0001589	frameshift_variant	349334	exon1			.		CCDS75845.1	9q13	2007-03-19			ENSG00000184659	ENSG00000184659			23762	protein-coding gene	gene with protein product		611085					Standard	NM_199244		Approved	bA460E7.2, OTTHUMG00000013337		Q8WXT5	OTTHUMG00000013337	ENST00000377413.1:c.1215delC	9.37:g.70427685delG	ENSP00000366630:p.Cys405fs	Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	344	56	0.162791	NM_199244	Q5RIB4	Frame_Shift_Del	DEL	ENST00000377413.1	37	CCDS6621.1																																																																																			.	.	weak		0.677	FOXD4L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037143.2		
NAIP	4671	hgsc.bcm.edu	37	5	70281620	70281621	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70281620_70281621delAT	ENST00000517649.1	-	12	1545_1546	c.1255_1256delAT	c.(1255-1257)atgfs	p.M419fs	NAIP_ENST00000503719.2_Frame_Shift_Del_p.M257fs|NAIP_ENST00000194097.4_Frame_Shift_Del_p.M419fs|NAIP_ENST00000508426.2_Frame_Shift_Del_p.M419fs|NAIP_ENST00000523981.1_Frame_Shift_Del_p.M257fs	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	419					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		AAGCAAAGACATGTGGCGGAAA	0.5																																					p.419_419del		Atlas-Indel	.											.	NAIP	38	.	0			c.1256_1257del						PASS	.																																			SO:0001589	frameshift_variant	4671	exon12			.	U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"""Baculoviral IAP repeat containing"", ""Nucleotide-binding domain and leucine rich repeat containing"""	7634	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1"", ""NLR family, BIR domain containing 1"""	600355	"""baculoviral IAP repeat-containing 1"""	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.1255_1256delAT	5.37:g.70281620_70281621delAT	ENSP00000428657:p.Met419fs	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	205	32	0.156098	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Del	DEL	ENST00000517649.1	37	CCDS4009.1																																																																																			.	.	none		0.500	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536	
PIEZO1	9780	hgsc.bcm.edu	37	16	88800373	88800375	+	In_Frame_Del	DEL	TCC	TCC	-	rs572934641|rs59446030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88800373_88800375delTCC	ENST00000301015.9	-	17	2514_2516	c.2268_2270delGGA	c.(2266-2271)gaggac>gac	p.E756del	RP5-1142A6.2_ENST00000567968.1_RNA|RP5-1142A6.2_ENST00000440406.2_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	756					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						GTCCCTGGAGtcctcctcctcct	0.685														256	0.0511182	0.1785	0.0187	5008	,	,		22177	0.001		0.001	False		,,,				2504	0.0051				p.757_757del		Atlas-Indel	.											.	PIEZO1	79	.	0			c.2269_2271del						PASS	.																																			SO:0001651	inframe_deletion	9780	exon17			.	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.2268_2270delGGA	16.37:g.88800382_88800384delTCC	ENSP00000301015:p.Glu756del	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	60	12	0.2	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	In_Frame_Del	DEL	ENST00000301015.9	37	CCDS54058.1																																																																																			.	.	weak		0.685	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
MYO5B	4645	hgsc.bcm.edu	37	18	47405425	47405426	+	In_Frame_Ins	INS	-	-	GAG	rs33910398|rs3841750|rs200219597|rs397841722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47405425_47405426insGAG	ENST00000285039.7	-	24	3464_3465	c.3165_3166insCTC	c.(3163-3168)ctcatg>ctcCTCatg	p.1055_1056insL	MYO5B_ENST00000587895.1_5'Flank|MYO5B_ENST00000324581.6_In_Frame_Ins_p.196_197insL	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1055			L -> LL (in dbSNP:rs72530399). {ECO:0000269|PubMed:10574461, ECO:0000269|Ref.4}.		endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)	p.M1056L(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TCTTTCTTCATGAGATTTTCCT	0.45														2027	0.404752	0.3638	0.268	5008	,	,		21517	0.5685		0.3002	False		,,,				2504	0.4959				p.M1056delinsLM		Pindel,Atlas-Indel	.											MYO5B,NS,carcinoma,0,1	MYO5B	178	1	1	Substitution - Missense(1)	pancreas(1)	c.3166_3167insCTC						PASS	.			1273,2303		242,789,757						2.8	0.9		dbSNP_119	77	2176,5680		316,1544,2068	no	coding	MYO5B	NM_001080467.2		558,2333,2825	A1A1,A1R,RR		27.6986,35.5984,30.1697				3449,7983				SO:0001652	inframe_insertion	4645	exon24			.	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.3163_3165dupCTC	18.37:g.47405426_47405428dupGAG	ENSP00000285039:p.Leu1055_Leu1055dup	Somatic	173	.	.		WXS	Illumina HiSeq	Phase_I	176	88	0.500	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	In_Frame_Ins	INS	ENST00000285039.7	37	CCDS42436.1																																																																																			-|0.623;GAG|0.377	0.377	strong		0.450	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
FOXD4L5	653427	hgsc.bcm.edu	37	9	70176769	70176769	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:70176769delG	ENST00000377420.1	-	1	2046	c.1215delC	c.(1213-1215)tgcfs	p.C405fs		NM_001126334.1	NP_001119806.1	Q5VV16	FX4L5_HUMAN	forkhead box D4-like 5	405					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|lung(2)	7						TGCCCGCCCAGCACCGCGCCC	0.677																																					p.W406fs		Atlas-Indel	.											.	FOXD4L5	27	.	0			c.1216delT						PASS	.			10,4		5,0,2	0.0	1.0	1.0			1.1	0.1	9		1	16,8		8,0,4	no	frameshift	FOXD4L5	NM_001126334.1		13,0,6	A1A1,A1R,RR		33.3333,28.5714,31.5789			70176769	26,12	0	3	3	SO:0001589	frameshift_variant	653427	exon1			.		CCDS47977.1	9q13	2008-07-21			ENSG00000204779	ENSG00000204779			18522	protein-coding gene	gene with protein product						12234674	Standard	NM_001126334		Approved	bA15J10.2, OTTHUMG00000013332	uc010moc.3	Q5VV16	OTTHUMG00000013332	ENST00000377420.1:c.1215delC	9.37:g.70176769delG	ENSP00000366637:p.Cys405fs	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	356	48	0.134831	NM_001126334		Frame_Shift_Del	DEL	ENST00000377420.1	37	CCDS47977.1																																																																																			.	.	weak		0.677	FOXD4L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037122.1	NM_001126334	
CHDC2	286464	hgsc.bcm.edu	37	X	36162684	36162685	+	Frame_Shift_Ins	INS	-	-	TG	rs372871921|rs112700338		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:36162684_36162685insTG	ENST00000313548.4	+	11	1453_1454	c.1267_1268insTG	c.(1267-1269)ctgfs	p.L423fs		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	423	CH.					integral component of membrane (GO:0016021)											ctaggtgtgtctgagggtgttt	0.436														1488	0.394172	0.5832	0.2752	3775	,	,		11883	0.2272		0.0616	False		,,,				2504	0.2403				p.L423fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1267_1268insTG						PASS	.			2585,1136		761,686,377,145,160						0.7	0.1		dbSNP_130	111	478,6006		11,322,134,2024,1636	no	frameshift	CXorf59	NM_173695.2		772,1008,511,2169,1796	A1A1,A1R,A1,RR,R		7.372,30.5294,30.0147				3063,7142				SO:0001589	frameshift_variant	286464	exon11			.	AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"""chromosome X open reading frame 59"""	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.1268_1269dupTG	X.37:g.36162685_36162686dupTG	ENSP00000324767:p.Leu423fs	Somatic	106	.	.		WXS	Illumina HiSeq	Phase_I	87	54	0.621	NM_173695		Frame_Shift_Ins	INS	ENST00000313548.4	37	CCDS14238.1																																																																																			TG|1.000;|0.000	1.000	weak		0.436	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695	
ZNF233	353355	hgsc.bcm.edu	37	19	44778796	44778796	+	Frame_Shift_Del	DEL	G	G	-	rs386809644|rs59660444|rs75921463|rs386809645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44778796delG	ENST00000391958.2	+	5	2110	c.1983delG	c.(1981-1983)tcgfs	p.S661fs	ZNF235_ENST00000589799.1_Intron|ZNF233_ENST00000592581.1_3'UTR|ZNF233_ENST00000334152.1_Frame_Shift_Del_p.S643fs	NM_181756.2	NP_861421.2	A6NK53	ZN233_HUMAN	zinc finger protein 233	661					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)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|skin(3)|urinary_tract(1)	20		Prostate(69;0.0435)|all_neural(266;0.226)				GTAAGAGTTCGTTGTCTTCAG	0.418													?|G|-|unsure	1594	0.318291	0.6536	0.3372	5008	,	,		19999	0.2579		0.1322	False		,,,				2504	0.1053				p.S661fs		Atlas-Indel	.											.	ZNF233	73	.	0			c.1982delC						PASS	.						39.0	73.0	61.0					19																	44778796		2094	4294	6388	SO:0001589	frameshift_variant	353355	exon5			.	AY166792	CCDS33047.1	19q13.31	2013-01-08				ENSG00000159915		"""Zinc fingers, C2H2-type"", ""-"""	30946	protein-coding gene	gene with protein product						12743021	Standard	NM_001207005		Approved	FLJ38032	uc021uvi.1	A6NK53		ENST00000391958.2:c.1983delG	19.37:g.44778796delG	ENSP00000375820:p.Ser661fs	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	51	0.894737	NM_001207005	B2RN78|B2RN79|Q86WL8	Frame_Shift_Del	DEL	ENST00000391958.2	37	CCDS33047.1																																																																																			G|0.700;-|0.300	0.300	strong		0.418	ZNF233-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460737.1	NM_181756	
ARID4B	51742	hgsc.bcm.edu	37	1	235377279	235377281	+	In_Frame_Del	DEL	TCC	TCC	-	rs113894806|rs10588817|rs113458177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235377279_235377281delTCC	ENST00000264183.3	-	17	2141_2143	c.1644_1646delGGA	c.(1642-1647)gaggaa>gaa	p.548_549EE>E	ARID4B_ENST00000366603.2_In_Frame_Del_p.548_549EE>E|ARID4B_ENST00000349213.3_Intron	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	548	Glu-rich.				histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E548E(2)		NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			ttcttcttcttcctcctcctcct	0.414														183	0.0365415	0.1203	0.0144	5008	,	,		17403	0.001		0.008	False		,,,				2504	0.0051				p.549_549del		Pindel,Atlas-Indel	.											.	ARID4B	142	.	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)	c.1645_1647del						PASS	.																																			SO:0001651	inframe_deletion	51742	exon17			.	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.1644_1646delGGA	1.37:g.235377288_235377290delTCC	ENSP00000264183:p.Glu553del	Somatic	137	.	.		WXS	Illumina HiSeq	Phase_I	176	28	0.159	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	In_Frame_Del	DEL	ENST00000264183.3	37	CCDS31061.1																																																																																			TCC|0.967;-|0.033	0.033	strong		0.414	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	
SIRPA	140885	hgsc.bcm.edu	37	20	1896052	1896054	+	In_Frame_Del	DEL	CGA	CGA	-	rs139878822|rs202172737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1896052_1896054delCGA	ENST00000358771.4	+	2	539_541	c.387_389delCGA	c.(385-390)cccgat>cct	p.D131del	SIRPA_ENST00000400068.3_In_Frame_Del_p.D131del|SIRPA_ENST00000356025.3_In_Frame_Del_p.D131del	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	131	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.D131delD(2)|p.D130A(1)|p.P129P(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		AAGGGAGCCCCGATGACGTGGAG	0.527														1950	0.389377	0.264	0.4063	5008	,	,		16040	0.5933		0.2932	False		,,,				2504	0.4356				p.129_130del	GBM(155;1668 1920 5945 42733 48121)	Atlas-Indel	.											SIRPA,NS,carcinoma,-1,1	SIRPA	83	1	4	Deletion - In frame(2)|Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)|upper_aerodigestive_tract(1)|large_intestine(1)	c.386_388del						PASS	.		,,	1147,3105		167,813,1146					,,	2.0	0.0		dbSNP_134	106	2654,5494		452,1750,1872	no	coding,coding,coding	SIRPA	NM_080792.2,NM_001040023.1,NM_001040022.1	,,	619,2563,3018	A1A1,A1R,RR		32.5724,26.9755,30.6532	,,	,,		3801,8599				SO:0001651	inframe_deletion	140885	exon3			.	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.387_389delCGA	20.37:g.1896052_1896054delCGA	ENSP00000351621:p.Asp131del	Somatic	470	0	0		WXS	Illumina HiSeq	Phase_I	281	42	0.149466	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	In_Frame_Del	DEL	ENST00000358771.4	37	CCDS13022.1																																																																																			.	.	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT	rs201922875|rs553160982		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	121	.	.		WXS	Illumina HiSeq	Phase_I	84	32	0.381	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	
C14orf177	283598	hgsc.bcm.edu	37	14	99182527	99182535	+	Start_Codon_Del	DEL	GGATGCATC	GGATGCATC	-	rs17097718|rs373583218|rs139827156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGATGCATC	GGATGCATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:99182527_99182535delGGATGCATC	ENST00000325812.2	+	0	418_426					NM_182560.2	NP_872366.2	Q52M58	CN177_HUMAN	chromosome 14 open reading frame 177											endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	13		Melanoma(154;0.128)				CAGTACGACTGGATGCATCGGAAAGAGCC	0.569														134	0.0267572	0.0356	0.0245	5008	,	,		21205	0.004		0.0567	False		,,,				2504	0.0092				.		Pindel,Atlas-Indel	.											.	C14orf177	37	.	0			.						PASS	.			127,4135		2,123,2006						1.8	0.0		dbSNP_134	53	465,7787		31,403,3692	no	coding	C14orf177	NM_182560.2		33,526,5698	A1A1,A1R,RR		5.635,2.9798,4.7307				592,11922				SO:0001582	initiator_codon_variant	283598	wholegene			.	AK098639	CCDS9948.1	14q32.2	2012-05-30			ENSG00000176605	ENSG00000176605			26375	protein-coding gene	gene with protein product						12477932	Standard	NM_182560		Approved	FLJ25773	uc001yfz.2	Q52M58	OTTHUMG00000167745		14.37:g.99182527_99182535delGGATGCATC		Somatic	78	.	.		WXS	Illumina HiSeq	Phase_I	68	20	0.294	NM_182560	Q8N7D2	Frame_Shift_Del	DEL	ENST00000325812.2	37	CCDS9948.1																																																																																			GGATGCATC|0.963;-|0.037	0.037	strong		0.569	C14orf177-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396078.1	NM_182560	
CACNA1B	774	hgsc.bcm.edu	37	9	140918171	140918185	+	In_Frame_Del	DEL	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	-	rs145816559|rs11137342|rs370787788|rs551405755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140918171_140918185delGGAGAAGGAGACCAC	ENST00000371372.1	+	19	3121_3135	c.2976_2990delGGAGAAGGAGACCAC	c.(2974-2991)gtggagaaggagaccacg>gtg	p.EKETT993del	CACNA1B_ENST00000371367.5_5'UTR|CACNA1B_ENST00000371357.1_In_Frame_Del_p.EKETT994del|CACNA1B_ENST00000371355.4_In_Frame_Del_p.EKETT994del|CACNA1B_ENST00000371363.1_In_Frame_Del_p.EKETT993del|CACNA1B_ENST00000277549.5_In_Frame_Del_p.EKETT185del|CACNA1B_ENST00000277551.2_In_Frame_Del_p.EKETT993del|CACNA1B_ENST00000545473.1_5'Flank	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	993					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.T996_E1000delTTEKE(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	ACGAGGCTGTGGAGAAGGAGACCACGGAGAAGGAG	0.735														1990	0.397364	0.6225	0.1282	5008	,	,		9031	0.6349		0.1521	False		,,,				2504	0.2914				p.992_997del		Pindel,Atlas-Indel	.											.	CACNA1B	266	.	1	Deletion - In frame(1)	breast(1)	c.2975_2989del						PASS	.			1091,1197		364,363,417						-1.3	0.0		dbSNP_134	8	691,4399		126,439,1980	no	coding	CACNA1B	NM_000718.3		490,802,2397	A1A1,A1R,RR		13.5756,47.6836,24.1529				1782,5596				SO:0001651	inframe_deletion	774	exon19			.	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.2976_2990delGGAGAAGGAGACCAC	9.37:g.140918171_140918185delGGAGAAGGAGACCAC	ENSP00000360423:p.Glu993_Thr997del	Somatic	108	.	.		WXS	Illumina HiSeq	Phase_I	41	27	0.659	NM_001243812	B1AQK5	In_Frame_Del	DEL	ENST00000371372.1	37	CCDS59522.1																																																																																			GGAGAAGGAGACCAC|0.621;-|0.379	0.379	strong		0.735	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
CMA1	1215	hgsc.bcm.edu	37	14	24976605	24976605	+	Frame_Shift_Del	DEL	T	T	-	rs542619483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24976605delT	ENST00000250378.3	-	2	195	c.166delA	c.(166-168)atafs	p.I56fs	RP11-80A15.1_ENST00000555109.1_Intron|CMA1_ENST00000206446.4_Intron	NM_001836.3	NP_001827.1	P23946	CMA1_HUMAN	chymase 1, mast cell	56	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|cellular response to glucose stimulus (GO:0071333)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|interleukin-1 beta biosynthetic process (GO:0050720)|midbrain development (GO:0030901)|peptide metabolic process (GO:0006518)|positive regulation of angiogenesis (GO:0045766)|regulation of inflammatory response (GO:0050727)	extracellular region (GO:0005576)|intracellular (GO:0005622)	peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			kidney(1)|lung(8)|pancreas(1)|prostate(1)	11				GBM - Glioblastoma multiforme(265;0.0271)		TTCCGTCTTATAAGGAAACCA	0.488													?|T|-|unsure	8	0.00159744	0.0061	0.0	5008	,	,		19307	0.0		0.0	False		,,,				2504	0.0				p.I56fs		Pindel,Atlas-Indel	.											.	CMA1	21	.	0			c.167delT						PASS	.			12,4252		0,12,2120	143.0	139.0	140.0			5.0	0.2	14		140	0,8254		0,0,4127	no	frameshift	CMA1	NM_001836.2		0,12,6247	A1A1,A1R,RR		0.0,0.2814,0.0959			24976605	12,12506	2203	4300	6503	SO:0001589	frameshift_variant	1215	exon2			.		CCDS9630.1	14q12	2012-08-30			ENSG00000092009	ENSG00000092009	3.4.21.39		2097	protein-coding gene	gene with protein product		118938				8468056	Standard	NM_001836		Approved		uc001wpp.1	P23946	OTTHUMG00000140181	ENST00000250378.3:c.166delA	14.37:g.24976605delT	ENSP00000250378:p.Ile56fs	Somatic	147	.	.		WXS	Illumina HiSeq	Phase_I	120	39	0.325	NM_001836	B5BUM8|Q16018|Q3SY36|Q3SY37|Q9UDH5	Frame_Shift_Del	DEL	ENST00000250378.3	37	CCDS9630.1																																																																																			.	.	none		0.488	CMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276535.2		
SSPO	23145	hgsc.bcm.edu	37	7	149516839	149516839	+	RNA	DEL	C	C	-	rs528618910|rs145311298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149516839delC	ENST00000378016.2	+	0	12041							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)			AGTCCCTGGTCCTGGTGTGAC	0.697													CC|CC|C|deletion	406	0.0810703	0.2837	0.0317	5008	,	,		15514	0.0		0.007	False		,,,				2504	0.002				p.S4014fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.12040delT						PASS	.			831,2461		172,487,987	9.0	15.0	13.0			4.0	1.0	7	dbSNP_134	14	84,7080		18,48,3516	no	frameshift	SSPO	NM_198455.2		190,535,4503	A1A1,A1R,RR		1.1725,25.243,8.751			149516839	915,9541	1593	3760	5353			23145	exon85			.	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.149516839delC		Somatic	61	.	.		WXS	Illumina HiSeq	Phase_I	50	34	0.680	NM_198455	Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	37																																																																																				C|0.933;-|0.067	0.067	strong		0.697	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
TMPRSS6	164656	hgsc.bcm.edu	37	22	37465386	37465390	+	Splice_Site	DEL	TGGGG	TGGGG	-	rs188283136|rs200434923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGGGG	TGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37465386_37465390delTGGGG	ENST00000346753.3	-	16	1985		c.e16-2		TMPRSS6_ENST00000406856.1_Splice_Site|TMPRSS6_ENST00000381792.2_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	84	.	.		WXS	Illumina HiSeq	Phase_I	75	16	0.213	.	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
RP1-274L7.1	0	hgsc.bcm.edu	37	X	129630968	129630969	+	lincRNA	DEL	GT	GT	-	rs372692629		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:129630968_129630969delGT	ENST00000458525.1	-	0	1015				FAM45B_ENST00000592932.1_RNA																							GAATATAAAAGTGTGTAGGACT	0.381																																					.		Pindel,Atlas-Indel	.											.	FAM45B	26	.	0			.						PASS	.																																					55855	.			.																													X.37:g.129630972_129630973delGT		Somatic	383	.	.		WXS	Illumina HiSeq	Phase_I	411	82	0.200	.		RNA	DEL	ENST00000458525.1	37																																																																																				.	.	weak		0.381	RP1-274L7.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000058271.1		
MTFP1	51537	hgsc.bcm.edu	37	22	30824659	30824660	+	3'UTR	INS	-	-	A	rs527818803|rs149958301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30824659_30824660insA	ENST00000266263.5	+	0	989_990				MTFP1_ENST00000407550.3_3'UTR|RP4-539M6.19_ENST00000439838.1_3'UTR|MTFP1_ENST00000355143.4_Stop_Codon_Ins	NM_016498.4	NP_057582.2	Q9UDX5	MTFP1_HUMAN	mitochondrial fission process 1						apoptotic process (GO:0006915)|mitochondrial fission (GO:0000266)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(1)|lung(2)	4						GACAGAAGCTTAGAGACAAAGG	0.559													A|A|AA|insertion	54	0.0107827	0.0393	0.0029	5008	,	,		20262	0.0		0.0	False		,,,				2504	0.0				p.X136delinsX		Pindel,Atlas-Indel	.											.	MTFP1	7	.	0			c.406_407insA						PASS	.		,	105,4159		0,105,2027					,	-0.6	0.0		dbSNP_134	38	1,8253		0,1,4126	yes	utr-3,frameshift	MTFP1	NM_016498.4,NM_001003704.2	,	0,106,6153	A1A1,A1R,RR		0.0121,2.4625,0.8468	,	,		106,12412				SO:0001624	3_prime_UTR_variant	51537	exon3			.	AF151076	CCDS33634.1, CCDS33635.1	22q	2010-09-02			ENSG00000242114	ENSG00000242114			26945	protein-coding gene	gene with protein product		610235				15155745, 15985469	Standard	NM_016498		Approved	MTP18, HSPC242		Q9UDX5	OTTHUMG00000151057	ENST00000266263.5:c.*139->A	22.37:g.30824660_30824660dupA		Somatic	72	.	.		WXS	Illumina HiSeq	Phase_I	75	27	0.360	NM_001003704	A6NFQ5|Q9H3K1|Q9P0N6	Frame_Shift_Ins	INS	ENST00000266263.5	37	CCDS33635.1																																																																																			-|0.993;A|0.007	0.007	strong		0.559	MTFP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321126.3	NM_016498	
SSPO	23145	hgsc.bcm.edu	37	7	149484830	149484830	+	RNA	DEL	G	G	-	rs137977793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149484830delG	ENST00000378016.2	+	0	3652							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)			ATTATGCCACGCGGAGGTCCC	0.667													G|G|-|deletion	82	0.0163738	0.0598	0.0029	5008	,	,		17852	0.0		0.001	False		,,,				2504	0.0				p.H1217fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.3651delC						PASS	.			183,3691		17,149,1771	8.0	12.0	11.0			-4.0	0.0	7	dbSNP_134	11	3,7937		1,1,3968	no	frameshift	SSPO	NM_198455.2		18,150,5739	A1A1,A1R,RR		0.0378,4.7238,1.5744			149484830	186,11628	2003	4151	6154			23145	exon25			.	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.149484830delG		Somatic	52	.	.		WXS	Illumina HiSeq	Phase_I	46	11	0.239	NM_198455	Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	37																																																																																				G|0.985;-|0.015	0.015	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
OR8B12	219858	hgsc.bcm.edu	37	11	124413049	124413051	+	In_Frame_Del	DEL	AGA	AGA	-	rs201026337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124413049_124413051delAGA	ENST00000306842.2	-	1	524_526	c.500_502delTCT	c.(499-504)ttctgt>tgt	p.F167del		NM_001005195.1	NP_001005195.1	Q8NGG6	OR8BC_HUMAN	olfactory receptor, family 8, subfamily B, member 12	167						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)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		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;0.0213)		TTGTCAGCACAGAAGGTCAGGTT	0.493														86	0.0171725	0.0628	0.0043	5008	,	,		23161	0.0		0.0	False		,,,				2504	0.0				p.167_168del		Pindel,Atlas-Indel	.											.	OR8B12	66	.	0			c.501_503del						PASS	.			187,4077		2,183,1947						3.9	1.0			135	4,8250		0,4,4123	no	coding	OR8B12	NM_001005195.1		2,187,6070	A1A1,A1R,RR		0.0485,4.3856,1.5258				191,12327				SO:0001651	inframe_deletion	219858	exon1			.		CCDS31711.1	11q24.2	2013-09-24			ENSG00000170953	ENSG00000170953		"""GPCR / Class A : Olfactory receptors"""	15307	protein-coding gene	gene with protein product							Standard	NM_001005195		Approved		uc010sam.2	Q8NGG6	OTTHUMG00000165922	ENST00000306842.2:c.500_502delTCT	11.37:g.124413049_124413051delAGA	ENSP00000307159:p.Phe167del	Somatic	125	.	.		WXS	Illumina HiSeq	Phase_I	108	45	0.417	NM_001005195	B2RNF6|Q6IEW8|Q96RC7	In_Frame_Del	DEL	ENST00000306842.2	37	CCDS31711.1																																																																																			AGA|0.983;-|0.017	0.017	strong		0.493	OR8B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387061.1		
SLC38A10	124565	hgsc.bcm.edu	37	17	79219501	79219503	+	In_Frame_Del	DEL	ATG	ATG	-	rs10569617|rs3833102|rs201518560	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	252	.	.		WXS	Illumina HiSeq	Phase_I	224	68	0.304	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	
WDR81	124997	hgsc.bcm.edu	37	17	1631341	1631343	+	In_Frame_Del	DEL	GAG	GAG	-	rs577690948|rs200758098|rs35048651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1631341_1631343delGAG	ENST00000409644.1	+	1	3088_3090	c.3088_3090delGAG	c.(3088-3090)gagdel	p.E1033del	WDR81_ENST00000545662.1_5'Flank|WDR81_ENST00000437219.2_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_5'UTR|WDR81_ENST00000419248.1_Intron|WDR81_ENST00000446363.1_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1033				Missing (in Ref. 1; BAB84937). {ECO:0000305}.	negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGGGGCTGCTGAGGAGGAGGAGA	0.695														1061	0.211861	0.115	0.196	5008	,	,		16982	0.1835		0.1948	False		,,,				2504	0.4008				p.1029_1030del		Pindel,Atlas-Indel	.											.	WDR81	180	.	0			c.3087_3089del						PASS	.		,,,	549,3367		98,353,1507					,,,	-11.3	0.0		dbSNP_130	17	1642,6232		262,1118,2557	no	utr-5,intron,coding,intron	WDR81	NM_152348.3,NM_001163811.1,NM_001163809.1,NM_001163673.1	,,,	360,1471,4064	A1A1,A1R,RR		20.8534,14.0194,18.5835	,,,	,,,		2191,9599				SO:0001651	inframe_deletion	124997	exon1			.	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.3088_3090delGAG	17.37:g.1631350_1631352delGAG	ENSP00000386609:p.Glu1033del	Somatic	54	.	.		WXS	Illumina HiSeq	Phase_I	65	13	0.200	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	In_Frame_Del	DEL	ENST00000409644.1	37	CCDS54062.1																																																																																			-|0.172;GAG|0.828	0.172	strong		0.695	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
KRTAP6-2	337967	hgsc.bcm.edu	37	21	31971075	31971076	+	Frame_Shift_Ins	INS	-	-	A	rs74773890|rs113467703|rs113674499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31971075_31971076insA	ENST00000334897.3	-	1	143_144	c.118_119insT	c.(118-120)tatfs	p.Y40fs	KRTAP22-1_ENST00000334680.2_5'Flank	NM_181604.1	NP_853635.1	Q3LI66	KRA62_HUMAN	keratin associated protein 6-2	40						intermediate filament (GO:0005882)				endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11						GCCATGACCATAGCCACAGCAG	0.564													A|A|AA|insertion	66	0.0131789	0.0484	0.0029	5008	,	,		15138	0.0		0.0	False		,,,				2504	0.0				p.Y40fs		Pindel,Atlas-Indel	.											.	KRTAP6-2	24	.	0			c.119_120insT						PASS	.			171,4093		4,163,1965						-6.6	0.0		dbSNP_132	106	1,8253		0,1,4126	no	frameshift	KRTAP6-2	NM_181604.1		4,164,6091	A1A1,A1R,RR		0.0121,4.0103,1.374				172,12346				SO:0001589	frameshift_variant	337967	exon1			.	AP001708	CCDS13600.1	21q22.1	2011-02-10			ENSG00000186930	ENSG00000186930		"""Keratin associated proteins"""	18932	protein-coding gene	gene with protein product						12359730	Standard	NM_181604		Approved	KAP6.2	uc011adc.2	Q3LI66	OTTHUMG00000057794	ENST00000334897.3:c.119dupT	21.37:g.31971076_31971076dupA	ENSP00000334560:p.Tyr40fs	Somatic	206	.	.		WXS	Illumina HiSeq	Phase_I	200	60	0.300	NM_181604		Frame_Shift_Ins	INS	ENST00000334897.3	37	CCDS13600.1																																																																																			-|0.990;A|0.010	0.010	strong		0.564	KRTAP6-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128246.3		
ZSCAN29	146050	hgsc.bcm.edu	37	15	43658416	43658418	+	In_Frame_Del	DEL	CCT	CCT	-	rs377169169|rs151154169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43658416_43658418delCCT	ENST00000396976.2	-	3	1246_1248	c.1112_1114delAGG	c.(1111-1116)gaggga>gga	p.E371del	ZSCAN29_ENST00000568898.1_Intron|ZSCAN29_ENST00000562072.1_In_Frame_Del_p.E370del|ZSCAN29_ENST00000396972.1_Intron	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	371					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)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		TCTTCTGCTCCCTCCTCATGCTG	0.601														118	0.0235623	0.0855	0.0058	5008	,	,		18099	0.0		0.001	False		,,,				2504	0.0				p.371_372del		Pindel,Atlas-Indel	.											.	ZSCAN29	57	.	0			c.1113_1115del						PASS	.			330,3934		28,274,1830						-9.0	0.0		dbSNP_119	68	3,8251		0,3,4124	no	coding	ZSCAN29	NM_152455.3		28,277,5954	A1A1,A1R,RR		0.0363,7.7392,2.6602				333,12185				SO:0001651	inframe_deletion	146050	exon3			.	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"""-"", ""Zinc fingers, C2H2-type"""	26673	protein-coding gene	gene with protein product			"""zinc finger protein 690"""	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.1112_1114delAGG	15.37:g.43658419_43658421delCCT	ENSP00000380174:p.Glu371del	Somatic	61	.	.		WXS	Illumina HiSeq	Phase_I	74	25	0.338	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	In_Frame_Del	DEL	ENST00000396976.2	37	CCDS10095.2																																																																																			CCT|0.977;-|0.023	0.023	strong		0.601	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455	
OR4C46	119749	hgsc.bcm.edu	37	11	51515413	51515441	+	Frame_Shift_Del	DEL	GGTCACCATCACTGCCAGCCCATCACTGG	GGTCACCATCACTGCCAGCCCATCACTGG	-	rs372979385|rs142892443|rs148928414|rs151059393|rs545486160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGTCACCATCACTGCCAGCCCATCACTGG	GGTCACCATCACTGCCAGCCCATCACTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:51515413_51515441delGGTCACCATCACTGCCAGCCCATCACTGG	ENST00000328188.1	+	1	132_160	c.132_160delGGTCACCATCACTGCCAGCCCATCACTGG	c.(130-162)gtggtcaccatcactgccagcccatcactggggfs	p.VTITASPSLG45fs		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	45						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P51Q(2)|p.V45fs*35(1)|p.G54W(1)		endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						TGCTCATTGTGGTCACCATCACTGCCAGCCCATCACTGGGGTCCCCCAT	0.445														96	0.0191693	0.0673	0.0101	5008	,	,		22740	0.0		0.0	False		,,,				2504	0.0				p.44_53del		Pindel,Atlas-Indel	.											OR4C46,colon,carcinoma,0,1	OR4C46	96	1	4	Substitution - Missense(3)|Deletion - Frameshift(1)	lung(4)	c.131_159del						PASS	.			322,3942		8,306,1818						1.5	0.0			233	9,8245		0,9,4118	no	frameshift	OR4C46	NM_001004703.1		8,315,5936	A1A1,A1R,RR		0.109,7.5516,2.6442				331,12187				SO:0001589	frameshift_variant	119749	exon1			.		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.132_160delGGTCACCATCACTGCCAGCCCATCACTGG	11.37:g.51515413_51515441delGGTCACCATCACTGCCAGCCCATCACTGG	ENSP00000329056:p.Val45fs	Somatic	212	.	.		WXS	Illumina HiSeq	Phase_I	117	74	0.632	NM_001004703		Frame_Shift_Del	DEL	ENST00000328188.1	37	CCDS31498.1																																																																																			.	.	none		0.445	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
UPP2	151531	hgsc.bcm.edu	37	2	158958551	158958552	+	De_novo_Start_InFrame	INS	-	-	A	rs74924675|rs11368509|rs67998287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:158958551_158958552insA	ENST00000005756.4	+	0	170_171				UPP2_ENST00000460456.1_3'UTR|UPP2_ENST00000409859.4_Splice_Site|UPP2_ENST00000605860.1_Splice_Site	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2						nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	ATCAATTTAAGGTGACTTTTCA	0.351													A|-|A|deletion	746	0.148962	0.3041	0.0447	5008	,	,		18031	0.1597		0.0388	False		,,,				2504	0.1155				.		Pindel,Atlas-Indel	.											.	UPP2	60	.	0			c.148-1->A						PASS	.		,	1082,3184		139,804,1190					,	-0.1	0.0		dbSNP_120	125	237,8017		6,225,3896	no	utr-5,frameshift-near-splice	UPP2	NM_173355.3,NM_001135098.1	,	145,1029,5086	A1A1,A1R,RR		2.8713,25.3633,10.5351	,	,		1319,11201						151531	exon3			.	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969		2.37:g.158958551_158958552insA		Somatic	92	.	.		WXS	Illumina HiSeq	Phase_I	101	36	0.356	NM_001135098	B3KV87	Splice_Site	INS	ENST00000005756.4	37	CCDS2207.1																																																																																			-|0.862;A|0.138	0.138	strong		0.351	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355	
TP53TG5	27296	hgsc.bcm.edu	37	20	44004156	44004158	+	In_Frame_Del	DEL	ATT	ATT	-	rs562359566|rs76663890|rs10546815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44004156_44004158delATT	ENST00000372726.3	-	4	445_447	c.289_291delAAT	c.(289-291)aatdel	p.N97del	TP53TG5_ENST00000537995.1_In_Frame_Del_p.N81del|SYS1_ENST00000426004.1_3'UTR|TP53TG5_ENST00000494455.1_5'UTR|SYS1-DBNDD2_ENST00000452133.1_Intron|SYS1-DBNDD2_ENST00000475242.1_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	59	.	.		WXS	Illumina HiSeq	Phase_I	56	39	0.696	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	
DCHS2	54798	hgsc.bcm.edu	37	4	155158259	155158260	+	In_Frame_Ins	INS	-	-	GTT	rs138652483|rs376550327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155158259_155158260insGTT	ENST00000357232.4	-	25	6178_6179	c.6179_6180insAAC	c.(6178-6180)act>acAACt	p.2060_2060T>TT		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2060	Cadherin 18. {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)		CAAGAAATTGAGTTGTTGATAT	0.376														103	0.0205671	0.0734	0.0058	5008	,	,		19389	0.0		0.002	False		,,,				2504	0.0				p.T2060delinsTT		Pindel,Atlas-Indel	.											.	DCHS2	594	.	0			c.6180_6181insAAC						PASS	.			254,4010		7,240,1885						3.4	0.1		dbSNP_134	82	6,8246		0,6,4120	no	coding	DCHS2	NM_017639.3		7,246,6005	A1A1,A1R,RR		0.0727,5.9568,2.0773				260,12256				SO:0001652	inframe_insertion	54798	exon25			.	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.6177_6179dupAAC	4.37:g.155158263_155158265dupGTT	ENSP00000349768:p.Thr2060dup	Somatic	140	.	.		WXS	Illumina HiSeq	Phase_I	126	40	0.317	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	In_Frame_Ins	INS	ENST00000357232.4	37	CCDS3785.1																																																																																			-|0.988;GTT|0.012	0.012	strong		0.376	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
LCNL1	401562	hgsc.bcm.edu	37	9	139879427	139879428	+	Frame_Shift_Ins	INS	-	-	GG			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139879427_139879428insGG	ENST00000408973.2	+	3	1053_1054	c.459_460insGG	c.(460-462)ctcfs	p.L154fs	LCNL1_ENST00000432827.1_Intron	NM_207510.3	NP_997393.3	Q6ZST4	LCNL1_HUMAN	lipocalin-like 1	154																	cctgcccctctctccctctctt	0.678																																					p.S153fs		Atlas-Indel	.											.	LCNL1	4	.	0			c.459_460insGG						PASS	.			103,3313		9,85,1614						-1.1	0.0			10	3,7317		0,3,3657	no	frameshift	LCNL1	NM_207510.3		9,88,5271	A1A1,A1R,RR		0.041,3.0152,0.9873				106,10630				SO:0001589	frameshift_variant	401562	exon3			.		CCDS43908.1	9q34.3	2014-01-22			ENSG00000214402	ENSG00000214402		"""Lipocalins"""	34436	protein-coding gene	gene with protein product							Standard	NM_207510		Approved	FLJ45224	uc004ckh.1	Q6ZST4	OTTHUMG00000159546	Exception_encountered	9.37:g.139879427_139879428insGG	ENSP00000386162:p.Leu154fs	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	217	14	0.0645161	NM_207510		Frame_Shift_Ins	INS	ENST00000408973.2	37	CCDS43908.1																																																																																			.	.	none		0.678	LCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356128.1	NM_207510	
ACIN1	22985	hgsc.bcm.edu	37	14	23548787	23548788	+	In_Frame_Ins	INS	-	-	GTGAAT	rs55838227|rs34870944|rs61741619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23548787_23548788insGTGAAT	ENST00000262710.1	-	6	2257_2258	c.1930_1931insATTCAC	c.(1930-1932)cgt>cATTCACgt	p.643_644insHS	ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000555053.1_In_Frame_Ins_p.643_644insHS|ACIN1_ENST00000605057.1_In_Frame_Ins_p.585_586insHS|ACIN1_ENST00000457657.1_In_Frame_Ins_p.603_604insHS	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	643	Ser-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S643_R644insHS(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		TGAACGAGAACGTGAACGTGAC	0.49																																					p.R644delinsHSR		Pindel,Atlas-Indel	.											.	ACIN1	147	.	1	Insertion - In frame(1)	upper_aerodigestive_tract(1)	c.1931_1932insATTCAC						PASS	.																																			SO:0001652	inframe_insertion	22985	exon6			.	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1930_1931insATTCAC	14.37:g.23548787_23548788insGTGAAT	ENSP00000262710:p.Ser643_Arg644insHisSer	Somatic	193	.	.		WXS	Illumina HiSeq	Phase_I	163	35	0.215	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	In_Frame_Ins	INS	ENST00000262710.1	37	CCDS9587.1																																																																																			-|0.604;GTGAAT|0.396	0.396	strong		0.490	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057775	46057804	+	In_Frame_Del	DEL	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	-	rs138406502|rs587625812|rs587722247|rs146378555|rs587701287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057775_46057804delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	ENST00000380095.1	+	1	503_532	c.441_470delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	c.(439-471)tgtgtgcctgtctgctctaagtccgtctgctat>tgt	p.VPVCSKSVCY148del	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	148	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						AGGCCTGCTGTGTGCCTGTCTGCTCTAAGTCCGTCTGCTATGTGCCTGTG	0.622																																					p.147_157del		Atlas-Indel	.											.	KRTAP10-10	37	.	0			c.440_469del						PASS	.		,	9,4255		1,7,2124					,	2.3	0.0			280	5,8249		2,1,4124	no	coding,intron	TSPEAR,KRTAP10-10	NM_181688.1,NM_144991.2	,	3,8,6248	A1A1,A1R,RR		0.0606,0.2111,0.1118	,	,		14,12504				SO:0001651	inframe_deletion	353333	exon1			.	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.441_470delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	21.37:g.46057775_46057804delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	ENSP00000369438:p.Val148_Tyr157del	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	167	45	0.269461	NM_181688		In_Frame_Del	DEL	ENST00000380095.1	37	CCDS33585.1																																																																																			.	.	none		0.622	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
MZT2A	653784	hgsc.bcm.edu	37	2	132248330	132248331	+	Intron	INS	-	-	GT	rs59442386|rs111311763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:132248330_132248331insGT	ENST00000309451.6	-	2	365				MIR4784_ENST00000579560.1_RNA|MZT2A_ENST00000410036.2_Intron|AC093838.4_ENST00000438378.2_RNA	NM_001085365.1	NP_001078834.1	Q6P582	MZT2A_HUMAN	mitotic spindle organizing protein 2A							centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				breast(1)|lung(1)	2						GAGGGAACCCGGGGGGCCTGGA	0.589														253	0.0505192	0.1815	0.0173	5008	,	,		18369	0.0		0.001	False		,,,				2504	0.0				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																			SO:0001627	intron_variant	100873780	.			.	BC018206	CCDS42758.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000173272	ENSG00000173272			33187	protein-coding gene	gene with protein product	"""mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A"""	613449	"""family with sequence similarity 128, member A"""	FAM128A		20360068	Standard	NM_001085365		Approved	MOZART2A	uc002tsw.4	Q6P582	OTTHUMG00000153606	ENST00000309451.6:c.319+1117->AC	2.37:g.132248330_132248331insGT		Somatic	266	.	.		WXS	Illumina HiSeq	Phase_I	271	63	0.232	.	Q3SWV8|Q8WVB2	RNA	INS	ENST00000309451.6	37	CCDS42758.1																																																																																			-|0.500;GC|0.500	.	alt		0.589	MZT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331811.2		
MN1	4330	hgsc.bcm.edu	37	22	28194912	28194913	+	In_Frame_Ins	INS	-	-	TGC			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:28194912_28194913insTGC	ENST00000302326.4	-	1	2573_2574	c.1619_1620insGCA	c.(1618-1620)caa>caGCAa	p.540_540Q>QQ		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	540	Poly-Gln.				intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						gctgttgctgttgctgctgctg	0.658			T	ETV6	"""AML, meningioma"""																																p.Q540delinsQQ		Atlas-Indel	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	MN1,NS,carcinoma,0,1	MN1	122	1	0			c.1620_1621insGCA						PASS	.																																			SO:0001652	inframe_insertion	4330	exon1			.	X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"""probable tumor suppressor protein MN1"""	156100	"""meningioma chromosome region"""	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.1617_1619dupGCA	22.37:g.28194919_28194921dupTGC	ENSP00000304956:p.Gln550dup	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_002430	A9Z1V9	In_Frame_Ins	INS	ENST00000302326.4	37	CCDS42998.1																																																																																			.	.	weak		0.658	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
CLCA4	22802	hgsc.bcm.edu	37	1	87045903	87045908	+	In_Frame_Del	DEL	CCTACT	CCTACT	-	rs56040873|rs77594462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCTACT	CCTACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87045903_87045908delCCTACT	ENST00000370563.3	+	14	2677_2682	c.2635_2640delCCTACT	c.(2635-2640)cctactdel	p.PT885del	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	885					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		TGAtcctacacctactcctactccta	0.345																																					p.878_880del		Pindel,Atlas-Indel	.											.	CLCA4	131	.	0			c.2634_2639del						PASS	.			2247,6,1315		606,4,1031,1,0,142						-0.9	0.0		dbSNP_108	97	5524,10,2288		1973,7,1571,1,1,358	no	codingComplex	CLCA4	NM_012128.3		2579,11,2602,2,1,500	A1A1,A1A2,A1R,A2A2,A2R,RR		29.3787,37.0235,31.7735				7771,16,3603				SO:0001651	inframe_deletion	22802	exon14			.	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2635_2640delCCTACT	1.37:g.87045909_87045914delCCTACT	ENSP00000359594:p.Pro885_Thr886del	Somatic	146	.	.		WXS	Illumina HiSeq	Phase_I	181	46	0.254	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	In_Frame_Del	DEL	ENST00000370563.3	37	CCDS41355.1																																																																																			.	.	weak		0.345	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
SEC63	11231	hgsc.bcm.edu	37	6	108214734	108214735	+	In_Frame_Ins	INS	-	-	GTA			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:108214734_108214735insGTA	ENST00000369002.4	-	16	1804_1805	c.1625_1626insTAC	c.(1624-1626)cca>ccTACa	p.542_543insT		NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	542					liver development (GO:0001889)|multicellular organismal aging (GO:0010259)|nitrogen compound metabolic process (GO:0006807)|posttranslational protein targeting to membrane (GO:0006620)|posttranslational protein targeting to membrane, translocation (GO:0031204)|protein targeting to membrane (GO:0006612)|renal system development (GO:0072001)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.P542Q(1)		endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		GCTTTGACTGTGGTAATAGCAC	0.322																																					p.P542delinsPT		Pindel,Atlas-Indel	.											.	SEC63	79	.	1	Substitution - Missense(1)	lung(1)	c.1626_1627insTAC						PASS	.			6,4258		0,6,2126						-3.9	0.9			138	0,8254		0,0,4127	no	coding	SEC63	NM_007214.4		0,6,6253	A1A1,A1R,RR		0.0,0.1407,0.0479				6,12512				SO:0001652	inframe_insertion	11231	exon16			.	BC048287	CCDS5061.1	6q21	2011-09-05	2006-09-12		ENSG00000025796	ENSG00000025796		"""Heat shock proteins / DNAJ (HSP40)"""	21082	protein-coding gene	gene with protein product		608648	"""SEC63-like (S. cerevisiae)"""			10219736, 10543453	Standard	NM_007214		Approved	SEC63L, PRO2507, ERdj2, DNAJC23	uc003psc.4	Q9UGP8	OTTHUMG00000015316	ENST00000369002.4:c.1625_1626insTAC	6.37:g.108214734_108214735insGTA	ENSP00000357998:p.Pro542_Gln543insThr	Somatic	104	.	.		WXS	Illumina HiSeq	Phase_I	110	39	0.355	NM_007214	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	In_Frame_Ins	INS	ENST00000369002.4	37	CCDS5061.1																																																																																			.	.	none		0.322	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214	
MICA	100507436	hgsc.bcm.edu	37	6	31380161	31380161	+	Frame_Shift_Del	DEL	G	G	-	rs41293539|rs547446871|rs138201170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31380161delG	ENST00000449934.2	+	5	1006	c.952delG	c.(952-954)ggcfs	p.G318fs	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				TGTTGCTGCTGGCTGCTGCTA	0.453													?|GG|G|unsure	1026	0.204872	0.0537	0.2824	5008	,	,		19280	0.3869		0.1272	False		,,,				2504	0.2464				p.A317fs		Atlas-Indel	.											.	MICA	21	.	0			c.951delT						PASS	.						218.0	178.0	190.0					6																	31380161		692	1576	2268	SO:0001589	frameshift_variant	100507436	exon5			.	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.952delG	6.37:g.31380161delG	ENSP00000413079:p.Gly318fs	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	91	17	0.186813	NM_001177519		Frame_Shift_Del	DEL	ENST00000449934.2	37	CCDS56412.1																																																																																			.	.	strong		0.453	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
ZCCHC6	79670	hgsc.bcm.edu	37	9	88937852	88937854	+	In_Frame_Del	DEL	TTT	TTT	-	rs58050565|rs77621374|rs200402481|rs397759922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	230	.	.		WXS	Illumina HiSeq	Phase_I	210	62	0.295	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	
MAGI1	9223	hgsc.bcm.edu	37	3	65425560	65425561	+	In_Frame_Ins	INS	-	-	CTG	rs113903140|rs35698502|rs142043619|rs377562449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:65425560_65425561insCTG	ENST00000497477.2	-	9	1262_1263	c.1263_1264insCAG	c.(1261-1266)cagaca>cagCAGaca	p.421_422insQ	MAGI1_ENST00000483466.1_In_Frame_Ins_p.421_422insQ|MAGI1_ENST00000402939.2_In_Frame_Ins_p.421_422insQ|MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000330909.8_In_Frame_Ins_p.421_422insQ			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	421	Poly-Gln.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		CAACCTTCTGTctgctgctgct	0.559											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T422delinsQT		Pindel,Atlas-Indel	.											.	MAGI1	481	.	0			c.1264_1265insCAG						PASS	.																																			SO:0001652	inframe_insertion	9223	exon9			.	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.1261_1263dupCAG	3.37:g.65425567_65425569dupCTG	ENSP00000424369:p.Gln421_Gln421dup	Somatic	52	.	.	1084	WXS	Illumina HiSeq	Phase_I	57	23	0.404	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	In_Frame_Ins	INS	ENST00000497477.2	37																																																																																				.	.	strong		0.559	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
RNF34	80196	hgsc.bcm.edu	37	12	121858078	121858080	+	In_Frame_Del	DEL	GAT	GAT	-	rs370767127|rs72059744|rs185279212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121858078_121858080delGAT	ENST00000392464.2	+	4	736_738	c.667_669delGAT	c.(667-669)gatdel	p.D229del	RNF34_ENST00000361234.5_In_Frame_Del_p.D229del|RNF34_ENST00000555076.1_Intron|RNF34_ENST00000392465.3_In_Frame_Del_p.D230del					ring finger protein 34, E3 ubiquitin protein ligase											breast(1)|large_intestine(1)	2	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)		AAACACAGAAgatgatgatgacg	0.404														186	0.0371406	0.1339	0.013	5008	,	,		22592	0.0		0.0	False		,,,				2504	0.0				p.223_224del		Pindel,Atlas-Indel	.											.	RNF34	54	.	0			c.669_671del						PASS	.		,	485,3779		29,427,1676					,	-2.2	0.9		dbSNP_130	70	6,8246		0,6,4120	no	coding,coding	RNF34	NM_194271.1,NM_025126.2	,	29,433,5796	A1A1,A1R,RR		0.0727,11.3743,3.923	,	,		491,12025				SO:0001651	inframe_deletion	80196	exon5			.	AF306709, AB084914	CCDS9221.1, CCDS31915.1, CCDS73538.1	12q24.31	2012-02-23	2012-02-23			ENSG00000170633		"""RING-type (C3HC4) zinc fingers"""	17297	protein-coding gene	gene with protein product		608299	"""ring finger protein 34"""			12118383	Standard	NM_025126		Approved	RIFF, FLJ21786, RIF	uc001ual.2	Q969K3		ENST00000392464.2:c.667_669delGAT	12.37:g.121858084_121858086delGAT	ENSP00000376257:p.Asp229del	Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	92	35	0.380	NM_194271		In_Frame_Del	DEL	ENST00000392464.2	37																																																																																				GAT|0.969;-|0.031	0.031	strong		0.404	RNF34-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000413892.1	NM_194271	
KLF17	128209	hgsc.bcm.edu	37	1	44596380	44596382	+	In_Frame_Del	DEL	CAA	CAA	-	rs200059598|rs34057178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44596380_44596382delCAA	ENST00000372299.3	+	3	1180_1182	c.1122_1124delCAA	c.(1120-1125)gccaac>gcc	p.N378del	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	378					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					ACCCACAGGCCAACAACAACAAT	0.493														1153	0.230232	0.0719	0.2723	5008	,	,		21631	0.2887		0.175	False		,,,				2504	0.411				p.374_375del		Pindel,Atlas-Indel	.											.	KLF17	92	.	0			c.1121_1123del						PASS	.			430,3836		27,376,1730						-0.7	0.0		dbSNP_126	87	1593,6661		149,1295,2683	no	coding	KLF17	NM_173484.3		176,1671,4413	A1A1,A1R,RR		19.2997,10.0797,16.1581				2023,10497				SO:0001651	inframe_deletion	128209	exon3			.	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.1122_1124delCAA	1.37:g.44596389_44596391delCAA	ENSP00000361373:p.Asn378del	Somatic	109	.	.		WXS	Illumina HiSeq	Phase_I	97	37	0.381	NM_173484	Q86VQ7|Q8N805	In_Frame_Del	DEL	ENST00000372299.3	37	CCDS508.1																																																																																			CAA|0.811;-|0.189	0.189	strong		0.493	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
TBC1D5	9779	hgsc.bcm.edu	37	3	17208285	17208286	+	Frame_Shift_Del	DEL	CG	CG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:17208285_17208286delCG	ENST00000253692.7	-	21	3731_3732	c.2067_2068delCG	c.(2065-2070)agcgttfs	p.V690fs	TBC1D5_ENST00000446818.2_Frame_Shift_Del_p.V712fs|TBC1D5_ENST00000414318.2_5'UTR|TBC1D5_ENST00000429383.4_Frame_Shift_Del_p.V690fs	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	690						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						GACATTTGAACGCTCTGGCCTT	0.51																																					p.712_712del		Pindel,Atlas-Indel	.											.	TBC1D5	69	.	0			c.2134_2135del						PASS	.																																			SO:0001589	frameshift_variant	9779	exon23			.	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.2067_2068delCG	3.37:g.17208285_17208286delCG	ENSP00000253692:p.Val690fs	Somatic	165	.	.		WXS	Illumina HiSeq	Phase_I	180	46	0.256	NM_001134381	A6NP25|C9JP52	Frame_Shift_Del	DEL	ENST00000253692.7	37	CCDS33714.1																																																																																			.	.	none		0.510	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744	
FOXD4L2	100036519	hgsc.bcm.edu	37	9	42719280	42719280	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:42719280delC	ENST00000377590.1	+	1	2047	c.1215delC	c.(1213-1215)tgcfs	p.C405fs		NM_001099279.1	NP_001092749.1	Q6VB85	FX4L2_HUMAN	forkhead box D4-like 2	405					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.W406fs*>11(1)		haematopoietic_and_lymphoid_tissue(1)	1				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		GGGCGCGGTGCTGGGCGGGCA	0.677																																					p.C405fs		Atlas-Indel	.											.	FOXD4L4	5	.	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.1214delG						PASS	.																																			SO:0001589	frameshift_variant	349334	exon1			.			9p12	2008-07-21			ENSG00000204828				24813	protein-coding gene	gene with protein product						12421752	Standard			Approved	OTTHUMG00000066752	uc004acn.3	Q6VB85	OTTHUMG00000066752	ENST00000377590.1:c.1215delC	9.37:g.42719280delC	ENSP00000366814:p.Cys405fs	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	338	49	0.14497	NM_199244		Frame_Shift_Del	DEL	ENST00000377590.1	37	CCDS43817.1																																																																																			.	.	weak		0.677	FOXD4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143077.1	NM_001099279	
SERPINB3	6317	hgsc.bcm.edu	37	18	61323014	61323014	+	Frame_Shift_Del	DEL	T	T	-	rs201374310|rs386804125|rs60286570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323014delT	ENST00000283752.5	-	8	1193	c.1050delA	c.(1048-1050)gtafs	p.V350fs	SERPINB3_ENST00000332821.8_Frame_Shift_Del_p.V298fs|SERPINB11_ENST00000489748.1_RNA	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	350					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						ATCCGAATCCTACTACAGCGG	0.493																																					p.G351fs		Atlas-Indel	.											.	SERPINB3	90	.	0			c.1051delG						PASS	.			402,3860		46,310,1775	115.0	125.0	122.0			-4.0	0.0	18	dbSNP_130	124	9,8245		0,9,4118	no	frameshift	SERPINB3	NM_006919.2		46,319,5893	A1A1,A1R,RR		0.109,9.4322,3.2838			61323014	411,12105	2202	4300	6502	SO:0001589	frameshift_variant	6317	exon8			.	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1050delA	18.37:g.61323014delT	ENSP00000283752:p.Val350fs	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	182	49	0.269231	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Frame_Shift_Del	DEL	ENST00000283752.5	37	CCDS11987.1																																																																																			T|0.960;-|0.040	0.040	strong		0.493	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
RTKN2	219790	hgsc.bcm.edu	37	10	63976913	63976918	+	In_Frame_Del	DEL	AGCTTC	AGCTTC	-	rs115357868|rs201442319|rs149331212|rs59044276|rs76810894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGCTTC	AGCTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:63976913_63976918delAGCTTC	ENST00000373789.3	-	9	1075_1080	c.979_984delGAAGCT	c.(979-984)gaagctdel	p.EA327del	RTKN2_ENST00000315289.2_In_Frame_Del_p.EA108del|RTKN2_ENST00000395265.1_In_Frame_Del_p.EA327del	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	327	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					GTTCCACTTTAGCTTCAATTTCCTCT	0.354														704	0.140575	0.295	0.1066	5008	,	,		17288	0.005		0.16	False		,,,				2504	0.0757				p.327_329del		Pindel,Atlas-Indel	.											.	RTKN2	68	.	0			c.980_985del						PASS	.			1087,3173		162,763,1205						6.0	1.0		dbSNP_129	131	1232,7022		103,1026,2998	no	coding	RTKN2	NM_145307.2		265,1789,4203	A1A1,A1R,RR		14.9261,25.5164,18.5312				2319,10195				SO:0001651	inframe_deletion	219790	exon9			.	BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"""Pleckstrin homology (PH) domain containing"""	19364	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family K member 1"""	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.979_984delGAAGCT	10.37:g.63976913_63976918delAGCTTC	ENSP00000362894:p.Glu327_Ala328del	Somatic	55	.	.		WXS	Illumina HiSeq	Phase_I	14	10	0.714	NM_145307	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	In_Frame_Del	DEL	ENST00000373789.3	37	CCDS7263.1																																																																																			AGCTTC|0.861;-|0.139	0.139	strong		0.354	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307	
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959341	45959343	+	In_Frame_Del	DEL	GGA	GGA	-	rs150327748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45959341_45959343delGGA	ENST00000400375.1	-	1	735_737	c.691_693delTCC	c.(691-693)tccdel	p.S231del	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	231	24 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(3)|prostate(4)|skin(1)	11						GGAGGGACACGGAGGAGGAGGGT	0.68														148	0.0295527	0.1029	0.0159	5008	,	,		16669	0.0		0.001	False		,,,				2504	0.0				p.231_232del		Pindel,Atlas-Indel	.											.	KRTAP10-1	34	.	0			c.692_694del						PASS	.		,	367,3897		17,333,1782					,	0.4	0.3		dbSNP_134	76	0,8254		0,0,4127	no	coding,intron	TSPEAR,KRTAP10-1	NM_198691.2,NM_144991.2	,	17,333,5909	A1A1,A1R,RR		0.0,8.6069,2.9318	,	,		367,12151				SO:0001651	inframe_deletion	386677	exon1			.	AJ566380	CCDS42954.1	21q22.3	2007-10-05			ENSG00000215455	ENSG00000215455		"""Keratin associated proteins"""	22966	protein-coding gene	gene with protein product				KRTAP18-1			Standard	NM_198691		Approved	KAP10.1, KAP18.1	uc002zfh.1	P60331	OTTHUMG00000057627	ENST00000400375.1:c.691_693delTCC	21.37:g.45959347_45959349delGGA	ENSP00000383226:p.Ser231del	Somatic	106	.	.		WXS	Illumina HiSeq	Phase_I	104	23	0.221	NM_198691	Q0VAR0|Q0VAR1	In_Frame_Del	DEL	ENST00000400375.1	37	CCDS42954.1																																																																																			GGA|0.975;-|0.025	0.025	strong		0.680	KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1		
NELFA	7469	hgsc.bcm.edu	37	4	1988188	1988189	+	Intron	INS	-	-	CT	rs35401110|rs3034718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1988188_1988189insCT	ENST00000411638.2	-	5	650				NELFA_ENST00000382882.3_Intron|MIR943_ENST00000401286.1_RNA|NELFA_ENST00000542778.1_Intron	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	155	.	.		WXS	Illumina HiSeq	Phase_I	205	52	0.254	.	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	
PABPC3	5042	hgsc.bcm.edu	37	13	25671097	25671098	+	Frame_Shift_Ins	INS	-	-	T	rs140090397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25671097_25671098insT	ENST00000281589.3	+	1	798_799	c.761_762insT	c.(760-765)aaggagfs	p.KE254fs		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	254	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		ATGAATGGAAAGGAGCTCAATG	0.401													-|-|T|insertion	483	0.0964457	0.1694	0.0576	5008	,	,		25438	0.0337		0.0358	False		,,,				2504	0.1524				p.K254fs		Atlas-Indel	.											.	PABPC3	129	.	0			c.761_762insT						PASS	.																																			SO:0001589	frameshift_variant	5042	exon1			.	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	Exception_encountered	13.37:g.25671097_25671098insT	ENSP00000281589:p.Lys254fs	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	177	14	0.079096	NM_030979	Q8NHV0|Q9H086	Frame_Shift_Ins	INS	ENST00000281589.3	37	CCDS9311.1																																																																																			.	.	strong		0.401	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
OR52D1	390066	hgsc.bcm.edu	37	11	5510540	5510541	+	Frame_Shift_Ins	INS	-	-	GGCT	rs146317894|rs576495879|rs190320444|rs36066208|rs377247106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5510540_5510541insGGCT	ENST00000322641.5	+	1	626_627	c.604_605insGGCT	c.(604-606)gggfs	p.-203fs	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_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	135	.	.		WXS	Illumina HiSeq	Phase_I	134	21	0.157	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	
ORM2	5005	hgsc.bcm.edu	37	9	117095395	117095397	+	In_Frame_Del	DEL	AGG	AGG	-	rs530796283|rs537714275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117095395_117095397delAGG	ENST00000431067.2	+	6	623_625	c.587_589delAGG	c.(586-591)caggag>cag	p.E198del		NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	198					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	GAGAGGAAACAGGAGGAGGGGGA	0.581														13	0.00259585	0.0083	0.0014	5008	,	,		22543	0.0		0.001	False		,,,				2504	0.0				p.196_196del	NSCLC(65;867 1308 1814 2391 12508)	Atlas-Indel	.											.	ORM2	13	.	0			c.586_588del						PASS	.			39,3131		1,37,1547						1.8	0.0			15	1,5925		0,1,2962	no	coding	ORM2	NM_000608.2		1,38,4509	A1A1,A1R,RR		0.0169,1.2303,0.4398				40,9056				SO:0001651	inframe_deletion	5005	exon6			.		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.587_589delAGG	9.37:g.117095401_117095403delAGG	ENSP00000394936:p.Glu198del	Somatic	871	0	0		WXS	Illumina HiSeq	Phase_I	888	290	0.326577	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	In_Frame_Del	DEL	ENST00000431067.2	37	CCDS6804.1																																																																																			.	.	none		0.581	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
MDP1	145553	hgsc.bcm.edu	37	14	24683267	24683267	+	Frame_Shift_Del	DEL	A	A	-	rs3215610|rs398102305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24683267delA	ENST00000288087.7	-	6	605	c.494delT	c.(493-495)ttgfs	p.L165fs	TM9SF1_ENST00000556387.1_5'Flank|TM9SF1_ENST00000530611.1_5'Flank|CHMP4A_ENST00000530996.1_5'Flank|NEDD8-MDP1_ENST00000604306.1_5'Flank|CHMP4A_ENST00000609024.1_5'Flank|AL136419.6_ENST00000565988.1_RNA|CHMP4A_ENST00000347519.6_5'Flank|MDP1_ENST00000532557.1_5'UTR|MDP1_ENST00000396833.2_Frame_Shift_Del_p.F118fs|CHMP4A_ENST00000542700.2_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	90	.	.		WXS	Illumina HiSeq	Phase_I	136	46	0.338	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	
CCDC66	285331	hgsc.bcm.edu	37	3	56650054	56650055	+	In_Frame_Ins	INS	-	-	CTC	rs112267342|rs111934125|rs74400129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	85	27	0.318	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	
SLC3A1	6519	hgsc.bcm.edu	37	2	44528268	44528268	+	Splice_Site	DEL	T	T	-	rs556841667|rs61179824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44528268delT	ENST00000260649.6	+	6	1212		c.e6+2		SLC3A1_ENST00000409380.1_Splice_Site|SLC3A1_ENST00000409740.3_5'Flank|SLC3A1_ENST00000409387.1_Splice_Site|SLC3A1_ENST00000410056.3_Frame_Shift_Del_p.L380fs|SLC3A1_ENST00000409741.1_Splice_Site|SLC3A1_ENST00000409229.3_Splice_Site|SLC3A1_ENST00000409294.1_Intron	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1						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)	CAGATACAGGTTGACCACGGC	0.507													T|TT|T|insertion	560	0.111821	0.2708	0.0821	5008	,	,		20412	0.001		0.1243	False		,,,				2504	0.0194				.		Pindel,Atlas-Indel	.											.	SLC3A1	62	.	0			c.1136+1T>-	GRCh37	CS013629	SLC3A1	S	rs146125507	PASS	.			1011,3255		126,759,1248	78.0	75.0	76.0			5.3	1.0	2	dbSNP_134	89	935,7319		49,837,3241	no	splice-5	SLC3A1	NM_000341.3		175,1596,4489	A1A1,A1R,RR		11.3278,23.699,15.5431			44528268	1946,10574	2170	4288	6458	SO:0001630	splice_region_variant	6519	exon6			.		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.1136+2T>-	2.37:g.44528268delT		Somatic	109	.	.		WXS	Illumina HiSeq	Phase_I	128	35	0.273	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Splice_Site	DEL	ENST00000260649.6	37	CCDS1819.1																																																																																			T|0.888;-|0.112	0.112	strong		0.507	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	Intron
FRG2C	100288801	hgsc.bcm.edu	37	3	75713659	75713660	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75713659_75713660delAG	ENST00000308062.3	+	1	179_180	c.129_130delAG	c.(127-132)aaaggcfs	p.G44fs	FRG2C_ENST00000464571.1_Frame_Shift_Del_p.G44fs	NM_001124759.1	NP_001118231.1	A6NGY1	FRG2C_HUMAN	FSHD region gene 2 family, member C	44						nucleus (GO:0005634)				breast(2)|ovary(1)	3						TCAAAGGAAAAGGCAAGACCGC	0.525																																					p.43_43del		Atlas-Indel	.											.	FRG2C	16	.	0			c.128_129del						PASS	.																																			SO:0001589	frameshift_variant	100288801	exon1			.		CCDS43108.1	3p12.3	2009-11-25			ENSG00000172969	ENSG00000172969			33626	protein-coding gene	gene with protein product							Standard	NM_001124759		Approved			A6NGY1	OTTHUMG00000158963	ENST00000308062.3:c.129_130delAG	3.37:g.75713659_75713660delAG	ENSP00000312299:p.Gly44fs	Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	427	50	0.117096	NM_001124759		Frame_Shift_Del	DEL	ENST00000308062.3	37	CCDS43108.1																																																																																			.	.	none		0.525	FRG2C-001	KNOWN	NAGNAG_splice_site|not_best_in_genome_evidence|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352694.1	NM_001124759.1	
SPATA21	374955	hgsc.bcm.edu	37	1	16727305	16727306	+	In_Frame_Ins	INS	-	-	CTT	rs373005990|rs139527123|rs80260069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	192	.	.		WXS	Illumina HiSeq	Phase_I	183	95	0.519	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	
TRIM16	10626	hgsc.bcm.edu	37	17	15546132	15546133	+	Splice_Site	INS	-	-	A	rs577610193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15546132_15546133insA	ENST00000578237.1	-	7	1375		c.e7-2		TRIM16_ENST00000336708.7_Splice_Site|RP11-385D13.1_ENST00000455584.2_Splice_Site|TRIM16_ENST00000579219.1_5'UTR|TRIM16_ENST00000581224.1_Splice_Site|TRIM16_ENST00000416464.2_Splice_Site|TRIM16_ENST00000577886.1_5'UTR			O95361	TRI16_HUMAN	tripartite motif containing 16						histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		GAGTTCAGCCTAAAAGTGGAAA	0.515													AAAAA|AAAA|AAAAA|deletion	377	0.0752796	0.2511	0.0173	5008	,	,		20717	0.0		0.0099	False		,,,				2504	0.0235				.		Atlas-Indel	.											.	TRIM16	45	.	0			c.520-2->T						PASS	.			457,1595		140,177,709						3.8	0.9			2	44,3468		15,14,1727	no	splice-3	TRIM16	NM_006470.3		155,191,2436	A1A1,A1R,RR		1.2528,22.271,9.0043				501,5063				SO:0001630	splice_region_variant	10626	exon6			.	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"""Tripartite motif containing / Tripartite motif containing"""	17241	protein-coding gene	gene with protein product	"""estrogen-responsive B box protein"""	609505	"""tripartite motif-containing 16"""			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.520-2->T	17.37:g.15546136_15546136dupA		Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	402	88	0.218905	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Splice_Site	INS	ENST00000578237.1	37	CCDS11171.1																																																																																			.	.	none		0.515	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	Intron
LTF	4057	hgsc.bcm.edu	37	3	46496843	46496843	+	Frame_Shift_Del	DEL	C	C	-	rs571988865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46496843delC	ENST00000231751.4	-	5	884	c.589delG	c.(589-591)gaafs	p.E197fs	LTF_ENST00000426532.2_Frame_Shift_Del_p.E153fs|LTF_ENST00000417439.1_Frame_Shift_Del_p.E197fs	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	197	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		CATTTGTTTTCCCCTGTCCCC	0.562													CCCC|CCCC|CCC|deletion	12	0.00239617	0.0091	0.0	5008	,	,		22260	0.0		0.0	False		,,,				2504	0.0				p.E197fs		Pindel,Atlas-Indel	.											.	LTF	98	.	0			c.590delA						PASS	.		,	55,4211		13,29,2091	144.0	122.0	129.0		,	-9.6	0.0	3		130	74,8180		37,0,4090	no	frameshift,frameshift	LTF	NM_002343.3,NM_001199149.1	,	50,29,6181	A1A1,A1R,RR		0.8965,1.2893,1.0304	,	,	46496843	129,12391	2203	4300	6503	SO:0001589	frameshift_variant	4057	exon5			.		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.589delG	3.37:g.46496843delC	ENSP00000231751:p.Glu197fs	Somatic	128	.	.		WXS	Illumina HiSeq	Phase_I	143	43	0.301	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Frame_Shift_Del	DEL	ENST00000231751.4	37	CCDS33747.1																																																																																			.	.	none		0.562	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
Unknown	0	hgsc.bcm.edu	37	2	98129757	98129758	+	IGR	INS	-	-	T	rs367988895|rs567331785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98129757_98129758insT								AC159540.1 (38708 upstream) : ANKRD36B (34269 downstream)																							TTATTCTTAACTTTTCCCTAAC	0.337																																					p.K897fs		Atlas-Indel	.											.	.	.	.	0			c.2691_2692insA						PASS	.																																			SO:0001628	intergenic_variant	57730	exon38			.																													2.37:g.98129761_98129761dupT		Somatic	1139	0	0		WXS	Illumina HiSeq	Phase_I	678	61	0.0899705	NM_025190		Frame_Shift_Ins	INS		37																																																																																				.	.	weak	0	0.337								
FAM157A	728262	hgsc.bcm.edu	37	3	197880131	197880139	+	lincRNA	DEL	GCAGCAGCA	GCAGCAGCA	-	rs56683636		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCAGCAGCA	GCAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:197880131_197880139delGCAGCAGCA	ENST00000437428.2	+	0	11_19							C9JC47	F157A_HUMAN	family with sequence similarity 157, member A											NS(1)|skin(1)	2						ACAAGAACTGgcagcagcagcagcagcag	0.536																																					p.70_73del		Atlas-Indel	.											.	FAM157A	4	.	0			c.209_217del						PASS	.																																					728262	exon2			.			3q29	2013-01-30			ENSG00000236438	ENSG00000236438			34079	other	unknown							Standard	NM_001145248		Approved		uc011bup.1	C9JC47			3.37:g.197880140_197880148delGCAGCAGCA		Somatic	344	0	0		WXS	Illumina HiSeq	Phase_I	209	74	0.354067	NM_001145248		In_Frame_Del	DEL	ENST00000437428.2	37																																																																																				.	.	alt		0.536	FAM157A-001	KNOWN	not_best_in_genome_evidence|mRNA_end_NF|basic	lincRNA	lincRNA	OTTHUMT00000340078.2	NM_001145248	
DPP7	29952	hgsc.bcm.edu	37	9	140005117	140005118	+	Frame_Shift_Ins	INS	-	-	C	rs11391519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140005117_140005118insC	ENST00000371579.2	-	13	1465_1466	c.1461_1462insG	c.(1459-1464)gggcccfs	p.P488fs		NM_013379.2	NP_037511.2	Q9UHL4	DPP2_HUMAN	dipeptidyl-peptidase 7	488						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)		CTGAGTCTGGGCCCCCCACGCA	0.644													CCCCCC|CCCCCC|CCCCCCC|insertion	168	0.0335463	0.1157	0.0043	5008	,	,		15960	0.005		0.0	False		,,,				2504	0.0072				p.P488fs		Pindel,Atlas-Indel	.											.	DPP7	22	.	0			c.1462_1463insG						PASS	.			406,3854		27,352,1751						2.0	0.0		dbSNP_120	43	8,8238		0,8,4115	no	frameshift	DPP7	NM_013379.2		27,360,5866	A1A1,A1R,RR		0.097,9.5305,3.3104				414,12092				SO:0001589	frameshift_variant	29952	exon13			.	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.1462dupG	9.37:g.140005123_140005123dupC	ENSP00000360635:p.Pro488fs	Somatic	42	.	.		WXS	Illumina HiSeq	Phase_I	43	18	0.419	NM_013379	A8K7U7|Q5VSF1|Q969X4	Frame_Shift_Ins	INS	ENST00000371579.2	37	CCDS7030.1																																																																																			-|0.973;C|0.027	0.027	strong		0.644	DPP7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055279.1	NM_013379	
CLDN16	10686	hgsc.bcm.edu	37	3	190106072	190106072	+	Frame_Shift_Del	DEL	G	G	-	rs386669518|rs201380153|rs56086318|rs368234054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:190106072delG	ENST00000264734.2	+	1	412	c.164delG	c.(163-165)aggfs	p.R55fs	CLDN16_ENST00000468220.1_Intron|CLDN16_ENST00000456423.1_Frame_Shift_Del_p.R55fs	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	55					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		AGTGGGGCCAGGGCTGGTGTC	0.512													GGG|GGG|GG|deletion	586	0.117013	0.0681	0.1455	5008	,	,		21539	0.0208		0.2336	False		,,,				2504	0.1421				p.R55fs		Atlas-Indel	.											.	CLDN16	59	.	0			c.163delA						PASS	.						145.0	107.0	120.0					3																	190106072		2203	4291	6494	SO:0001589	frameshift_variant	10686	exon1			.	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"""Claudins"""	2037	protein-coding gene	gene with protein product	"""paracellin-1"", ""hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"""	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.164delG	3.37:g.190106072delG	ENSP00000264734:p.Arg55fs	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	235	101	0.429787	NM_006580		Frame_Shift_Del	DEL	ENST00000264734.2	37	CCDS3296.1																																																																																			.	.	strong		0.512	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580	
OR6Q1	219952	hgsc.bcm.edu	37	11	57799109	57799109	+	Frame_Shift_Del	DEL	C	C	-	rs34846253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57799109delC	ENST00000302622.3	+	1	708	c.685delC	c.(685-687)ctgfs	p.L230fs	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	230						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)				CGTCTGGACACTGCTGCACAT	0.532													C|C|-|deletion	594	0.11861	0.1225	0.1153	5008	,	,		22097	0.0218		0.2048	False		,,,				2504	0.1268				p.T228fs		Pindel,Atlas-Indel	.											.	OR6Q1	58	.	0			c.684delA	GRCh37	CD035873	OR6Q1	D	rs34846253	PASS	.			656,3608		57,542,1533	155.0	121.0	133.0			-7.0	0.1	11	dbSNP_126	158	1588,6664		147,1294,2685	no	frameshift	OR6Q1	NM_001005186.2		204,1836,4218	A1A1,A1R,RR		19.2438,15.3846,17.9291			57799109	2244,10272	2161	4187	6348	SO:0001589	frameshift_variant	219952	exon1			.	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.685delC	11.37:g.57799109delC	ENSP00000307734:p.Leu230fs	Somatic	205	.	.		WXS	Illumina HiSeq	Phase_I	218	65	0.298	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Frame_Shift_Del	DEL	ENST00000302622.3	37	CCDS31541.1																																																																																			C|0.867;-|0.133	0.133	strong		0.532	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
CFAP74	85452	hgsc.bcm.edu	37	1	1887092	1887092	+	IGR	DEL	G	G	-	rs3838976|rs139735565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	102	0	0		WXS	Illumina HiSeq	Phase_I	104	36	0.346154	NM_001080484		Frame_Shift_Del	DEL		37																																																																																				G|0.777;-|0.223	0.223	strong	0	0.632								
PROL1	58503	hgsc.bcm.edu	37	4	71275631	71275632	+	Frame_Shift_Ins	INS	-	-	C	rs573505950|rs201259916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71275631_71275632insC	ENST00000399575.2	+	3	760_761	c.586_587insC	c.(586-588)accfs	p.T196fs		NM_021225.4	NP_067048.4	Q99935	PROL1_HUMAN	proline rich, lacrimal 1	196	Thr-rich.				negative regulation of endopeptidase activity (GO:0010951)|regulation of sensory perception of pain (GO:0051930)|retina homeostasis (GO:0001895)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)|peptidase inhibitor activity (GO:0030414)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	15		all_hematologic(202;0.196)				ATCAGCAGCAACCCCCGCAGCA	0.49													CCCCC|CCCCC|CCCCCC|insertion	10	0.00199681	0.0068	0.0014	5008	,	,		19421	0.0		0.0	False		,,,				2504	0.0				p.T196fs		Pindel,Atlas-Indel	.											.	PROL1	46	.	0			c.586_587insC						PASS	.			26,3928		2,22,1953						0.2	0.0			139	0,8034		0,0,4017	no	frameshift	PROL1	NM_021225.4		2,22,5970	A1A1,A1R,RR		0.0,0.6576,0.2169				26,11962				SO:0001589	frameshift_variant	58503	exon3			.	S83198	CCDS43235.1	4q13.3	2011-10-28	2005-02-07		ENSG00000171199	ENSG00000171199			17279	protein-coding gene	gene with protein product		608936	"""proline rich 1"""			8670737	Standard	NM_021225		Approved	BPLP, PRL1, opiorphin	uc003hfi.3	Q99935	OTTHUMG00000160845	ENST00000399575.2:c.591dupC	4.37:g.71275636_71275636dupC	ENSP00000382485:p.Thr196fs	Somatic	167	.	.		WXS	Illumina HiSeq	Phase_I	197	65	0.330	NM_021225	A8MZ07|P85047	Frame_Shift_Ins	INS	ENST00000399575.2	37	CCDS43235.1																																																																																			.	.	none		0.490	PROL1-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000362639.1	NM_021225	
TNS1	7145	hgsc.bcm.edu	37	2	218762663	218762665	+	In_Frame_Del	DEL	TCC	TCC	-	rs200962764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218762663_218762665delTCC	ENST00000171887.4	-	6	476_478	c.24_26delGGA	c.(22-27)gaggac>gac	p.E8del	TNS1_ENST00000419504.1_In_Frame_Del_p.E8del|TNS1_ENST00000430930.1_In_Frame_Del_p.E8del|TNS1_ENST00000310858.6_In_Frame_Del_p.E39del	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	8	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.E8delE(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CTCACAGCTGTCCTCCATGGTCC	0.586														67	0.0133786	0.0287	0.0144	5008	,	,		22678	0.002		0.0109	False		,,,				2504	0.0061				p.9_9del		Pindel,Atlas-Indel	.											.	TNS1	251	.	1	Deletion - In frame(1)	pancreas(1)	c.25_27del						PASS	.			105,4159		1,103,2028						5.4	1.0			108	101,8153		3,95,4029	no	coding	TNS1	NM_022648.4		4,198,6057	A1A1,A1R,RR		1.2236,2.4625,1.6456				206,12312				SO:0001651	inframe_deletion	7145	exon6			.	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.24_26delGGA	2.37:g.218762666_218762668delTCC	ENSP00000171887:p.Glu8del	Somatic	112	.	.		WXS	Illumina HiSeq	Phase_I	128	47	0.367	NM_022648	Q4ZG71|Q6IPI5	In_Frame_Del	DEL	ENST00000171887.4	37	CCDS2407.1																																																																																			TCC|0.989;-|0.011	0.011	strong		0.586	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786895	75786895	+	Frame_Shift_Del	DEL	T	T	-	rs144168413		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75786895delT	ENST00000478296.1	-	4	2005	c.1729delA	c.(1729-1731)accfs	p.T577fs	ZNF717_ENST00000422325.1_Frame_Shift_Del_p.T627fs|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Frame_Shift_Del_p.T620fs|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	620					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TGACGAAAGGTTTTTCCACAT	0.393																																					p.T627fs		Pindel,Atlas-Indel	.											.	ZNF717	160	.	0			c.1880delC						PASS	.			1099,1747		297,505,621	13.0	14.0	14.0			1.0	0.0	3	dbSNP_134	23	3008,3596		614,1780,908	no	frameshift	ZNF717	NM_001128223.1		911,2285,1529	A1A1,A1R,RR		45.5482,38.6156,43.4603			75786895	4107,5343	589	1486	2075	SO:0001589	frameshift_variant	100131827	exon5			.	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1729delA	3.37:g.75786895delT	ENSP00000419377:p.Thr577fs	Somatic	54	.	.		WXS	Illumina HiSeq	Phase_I	125	30	0.240	NM_001128223		Frame_Shift_Del	DEL	ENST00000478296.1	37																																																																																				.	.	weak		0.393	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
LINC00471	151477	hgsc.bcm.edu	37	2	232373857	232373860	+	RNA	DEL	TTCT	TTCT	-	rs374163700|rs150545131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTCT	TTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:232373857_232373860delTTCT	ENST00000313064.2	-	0	558_561					NR_024079.1		Q8N535	CB052_HUMAN	long intergenic non-protein coding RNA 471																		TACAGAAGGATTCTTTATCTTCCT	0.5														25	0.00499201	0.0182	0.0014	5008	,	,		18054	0.0		0.0	False		,,,				2504	0.0				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.			63,4203		3,57,2073						-2.7	0.0		dbSNP_131	199	2,8252		0,2,4125	no	intergenic				3,59,6198	A1A1,A1R,RR		0.0242,1.4768,0.5192				65,12455						151477	.			.	BC033054		2q37.1	2012-10-12	2011-08-31	2011-08-31	ENSG00000181798	ENSG00000181798		"""Long non-coding RNAs"""	28668	non-coding RNA	RNA, long non-coding			"""chromosome 2 open reading frame 52"""	C2orf52		12477932	Standard	NR_024079		Approved	MGC43122	uc002vrx.1	Q8N535	OTTHUMG00000133227		2.37:g.232373857_232373860delTTCT		Somatic	237	.	.		WXS	Illumina HiSeq	Phase_I	251	69	0.275	.		RNA	DEL	ENST00000313064.2	37																																																																																				TTCT|0.994;-|0.006	0.006	strong		0.500	LINC00471-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000256963.2	NM_173513	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249117	71249118	+	In_Frame_Ins	INS	-	-	CCG			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249117_71249118insCCG	ENST00000398534.3	+	1	47_48	c.16_17insCCG	c.(16-18)tgc>tCCGgc	p.6_6C>SG		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	6						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						CTGCTGTGGCTGCTCTGGAGGC	0.658																																					p.C6delinsSG		Atlas-Indel	.											.	KRTAP5-8	28	.	0			c.16_17insCCG						PASS	.																																			SO:0001652	inframe_insertion	57830	exon1			.	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	Exception_encountered	11.37:g.71249117_71249118insCCG	ENSP00000420723:p.Cys6delinsSerGly	Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	228	18	0.0789474	NM_021046	Q6L8G7|Q6UTX6	In_Frame_Ins	INS	ENST00000398534.3	37	CCDS41683.1																																																																																			.	.	none		0.658	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
HCLS1	3059	hgsc.bcm.edu	37	3	121351315	121351316	+	In_Frame_Ins	INS	-	-	GGCTCAGGCTCA	rs150627065|rs372720825|rs80289672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121351315_121351316insGGCTCAGGCTCA	ENST00000314583.3	-	12	1194_1195	c.1103_1104insTGAGCCTGAGCC	c.(1102-1104)ccc>ccTGAGCCTGAGCCc	p.368_368P>PEPEP	HCLS1_ENST00000428394.2_In_Frame_Ins_p.331_331P>PEPEP|HCLS1_ENST00000473883.1_5'UTR	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		Pindel,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	122	.	.		WXS	Illumina HiSeq	Phase_I	137	26	0.190	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	
SALL1	6299	hgsc.bcm.edu	37	16	51175655	51175656	+	In_Frame_Ins	INS	-	-	GCT	rs113614842|rs199760974|rs372299573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:51175655_51175656insGCT	ENST00000251020.4	-	2	510_511	c.477_478insAGC	c.(475-480)agcggc>agcAGCggc	p.159_160insS	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_In_Frame_Ins_p.62_63insS	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	159	Poly-Gly.|Poly-Ser.		S -> G (in dbSNP:rs13336129). {ECO:0000269|PubMed:9973281}.		adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			ccgccgccgccgctgctgctgc	0.629																																					p.G160delinsSG	GBM(103;1352 1446 1855 4775 8890)	Atlas-Indel	.											.	SALL1	301	.	0			c.478_479insAGC						PASS	.																																			SO:0001652	inframe_insertion	6299	exon2			.	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.475_477dupAGC	16.37:g.51175662_51175664dupGCT	ENSP00000251020:p.Ser159_Ser159dup	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	147	32	0.217687	NM_002968	Q99881|Q9NSC3|Q9P1R0	In_Frame_Ins	INS	ENST00000251020.4	37	CCDS10747.1																																																																																			-|0.500;GCC|0.250;GCT|0.250	0.250	strong		0.629	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
OR5L2	26338	hgsc.bcm.edu	37	11	55594980	55594980	+	Frame_Shift_Del	DEL	G	G	-	rs571342053|rs144106069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55594980delG	ENST00000378397.1	+	1	286	c.286delG	c.(286-288)gggfs	p.G96fs		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	96						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)				CTCCTTCCTAGGGTGCATGGT	0.473										HNSCC(27;0.073)			|||unknown(ALL_OTHER_Ns)	28	0.00559105	0.0189	0.0043	5008	,	,		23720	0.0		0.0	False		,,,				2504	0.0				p.L95fs		Pindel,Atlas-Indel	.											OR5L2,NS,carcinoma,+2,2	OR5L2	135	2	0			c.285delA						PASS	.			101,4161		1,99,2031	187.0	181.0	183.0			-0.1	0.0	11	dbSNP_134	184	4,8248		0,4,4122	no	frameshift	OR5L2	NM_001004739.1		1,103,6153	A1A1,A1R,RR		0.0485,2.3698,0.8391			55594980	105,12409	2200	4296	6496	SO:0001589	frameshift_variant	26338	exon1			.	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.286delG	11.37:g.55594980delG	ENSP00000367650:p.Gly96fs	Somatic	201	.	.		WXS	Illumina HiSeq	Phase_I	141	37	0.262	NM_001004739	Q6IF66|Q96RB2	Frame_Shift_Del	DEL	ENST00000378397.1	37	CCDS31511.1																																																																																			G|0.995;-|0.005	0.005	strong		0.473	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
CA9	768	hgsc.bcm.edu	37	9	35674191	35674208	+	In_Frame_Del	DEL	GGAGAGGAGGATCTACCT	GGAGAGGAGGATCTACCT	-	rs113042654|rs201260414|rs137897809|rs146966274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGAGAGGAGGATCTACCT	GGAGAGGAGGATCTACCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35674191_35674208delGGAGAGGAGGATCTACCT	ENST00000378357.4	+	1	339_356	c.235_252delGGAGAGGAGGATCTACCT	c.(235-252)ggagaggaggatctacctdel	p.GEEDLP91del	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	91	Proteoglycan-like (PG).				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.P84P(1)|p.G79_P84delGEEDLP(1)		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)	GGATCCACCCGGAGAGGAGGATCTACCTGGAGAGGAGG	0.55														354	0.0706869	0.0991	0.0202	5008	,	,		22837	0.127		0.0408	False		,,,				2504	0.0409				p.78_84del		Pindel,Atlas-Indel	.											.	CA9	48	.	2	Substitution - coding silent(1)|Deletion - In frame(1)	urinary_tract(1)|skin(1)	c.234_251del						PASS	.			326,3938		23,280,1829						-6.7	0.0			54	243,8011		14,215,3898	no	coding	CA9	NM_001216.2		37,495,5727	A1A1,A1R,RR		2.944,7.6454,4.5455				569,11949				SO:0001651	inframe_deletion	768	exon1			.	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.235_252delGGAGAGGAGGATCTACCT	9.37:g.35674191_35674208delGGAGAGGAGGATCTACCT	ENSP00000367608:p.Gly91_Pro96del	Somatic	103	.	.		WXS	Illumina HiSeq	Phase_I	119	18	0.151	NM_001216	Q5T4R1	In_Frame_Del	DEL	ENST00000378357.4	37	CCDS6585.1																																																																																			GGAGAGGAGGATCTACCT|0.933;-|0.067	0.067	strong		0.550	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55324675	55324675	+	Intron	DEL	A	A	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55324675delA	ENST00000538269.1	+	2	61				KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396293.1_Intron|KIR2DL4_ENST00000396284.2_Frame_Shift_Del_p.K268fs|KIR3DL1_ENST00000541392.1_Intron|KIR2DL4_ENST00000346587.4_Intron|KIR2DL4_ENST00000359085.4_Frame_Shift_Del_p.K270fs|KIR2DL4_ENST00000357494.4_Intron|KIR2DL4_ENST00000463062.1_3'UTR|KIR2DL4_ENST00000345540.5_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)	p.M271fs*>3(1)		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)		CTGGTGCTCCAAAAAAAAAGT	0.532																																					p.S267fs		Atlas-Indel	.											.	KIR2DL4	62	.	1	Deletion - Frameshift(1)	ovary(1)	c.801delC						PASS	.		,,	51,3917		3,45,1936	66.0	101.0	90.0		,,	-1.0	0.0	19	dbSNP_134	94	51,8005		2,47,3979	no	frameshift,frameshift,intron	KIR2DL4	NM_002255.5,NM_001080772.1,NM_001080770.1	,,	5,92,5915	A1A1,A1R,RR		0.6331,1.2853,0.8483	,,	,,	55324675	102,11922	2077	4226	6303	SO:0001627	intron_variant	3805	exon6			.	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.35-4314A>-	19.37:g.55324675delA		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	92	10	0.108696	NM_001080772	O43473|Q14946|Q16541	Frame_Shift_Del	DEL	ENST00000538269.1	37																																																																																				A|1.000;|0.000	.	weak		0.532	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289	
CEP85L	387119	hgsc.bcm.edu	37	6	118812811	118812813	+	Intron	DEL	TGT	TGT	-	rs71866282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118812811_118812813delTGT	ENST00000368491.3	-	6	2059				CEP85L_ENST00000360290.3_In_Frame_Del_p.Q389del|CEP85L_ENST00000392500.3_In_Frame_Del_p.Q494del|CEP85L_ENST00000419517.2_In_Frame_Del_p.Q491del|CEP85L_ENST00000368488.5_Intron	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like							centrosome (GO:0005813)|cytoplasm (GO:0005737)											GCTGAGGAAATGTTGTTGACCTA	0.32														166	0.033147	0.059	0.0173	5008	,	,		18299	0.0		0.0189	False		,,,				2504	0.0583				p.492_492del		Pindel,Atlas-Indel	.											.	CEP85L	26	.	0			c.1474_1476del						PASS	.		,,	241,4015		6,229,1893					,,	3.5	0.0		dbSNP_130	43	164,8084		2,160,3962	no	coding,intron,intron	C6orf204	NM_206921.2,NM_001178035.1,NM_001042475.2	,,	8,389,5855	A1A1,A1R,RR		1.9884,5.6626,3.239	,,	,,		405,12099				SO:0001627	intron_variant	387119	exon6			.	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.1437+35ACA>-	6.37:g.118812814_118812816delTGT		Somatic	77	.	.		WXS	Illumina HiSeq	Phase_I	70	30	0.429	NM_206921	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	In_Frame_Del	DEL	ENST00000368491.3	37	CCDS43498.1																																																																																			TGT|0.979;-|0.021	0.021	strong		0.320	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346446	140346451	+	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs148181752		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGCTGC	TGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140346446_140346451delTGCTGC	ENST00000289269.5	+	1	627_632	c.95_100delTGCTGC	c.(94-102)ttgctgctg>ttg	p.32_34LLL>L	PCDHA12_ENST00000398631.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHAC1_ENST00000253807.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	32					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ctgctgctgttgctgctgctgctACC	0.704																																					p.32_33del	Melanoma(190;638 2083 3390 11909 52360)	Pindel,Atlas-Indel	.											.	PCDHAC2	142	.	0			c.94_99del						PASS	.		,,,,,,,,,,,,,,,,,,	283,11,3622		45,0,193,0,11,1709					,,,,,,,,,,,,,,,,,,	0.2	0.7		dbSNP_134	8	13,29,7600		3,0,7,1,27,3783	no	codingComplex,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,codingComplex,intron	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_031883.2,NM_031860.1,NM_031857.1,NM_031849.1,NM_031411.1,NM_018911.2,NM_018910.2,NM_018909.2,NM_018908.2,NM_018907.2,NM_018906.2,NM_018905.2,NM_018904.2,NM_018903.2,NM_018902.3,NM_018901.2,NM_018900.2,NM_018899.5,NM_018898.3	,,,,,,,,,,,,,,,,,,	48,0,200,1,38,5492	A1A1,A1A2,A1R,A2A2,A2R,RR		0.5496,7.5077,2.9071	,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,		296,40,11222				SO:0001651	inframe_deletion	56134	exon1			.	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.95_100delTGCTGC	5.37:g.140346452_140346457delTGCTGC	ENSP00000289269:p.Leu34_Leu35del	Somatic	90	.	.		WXS	Illumina HiSeq	Phase_I	80	17	0.213	NM_031883	Q2M3V1|Q9Y5F4	In_Frame_Del	DEL	ENST00000289269.5	37	CCDS4242.1																																																																																			TGCTGC|0.974;-|0.026	0.026	strong		0.704	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
ZNF594	84622	hgsc.bcm.edu	37	17	5085878	5085879	+	Frame_Shift_Del	DEL	CT	CT	-	rs146837771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085878_5085879delCT	ENST00000399604.4	-	1	1813_1814	c.1673_1674delAG	c.(1672-1674)gagfs	p.E558fs	ZNF594_ENST00000575779.1_Frame_Shift_Del_p.E558fs			Q96JF6	ZN594_HUMAN	zinc finger protein 594	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)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GAATTTTCTGCTCTCCCCTAAG	0.47														55	0.0109824	0.0378	0.0029	5008	,	,		21001	0.0		0.003	False		,,,				2504	0.0				p.558_559del		Pindel,Atlas-Indel	.											.	ZNF594	89	.	0			c.1674_1675del						PASS	.			154,3700		12,130,1785						-0.1	0.0		dbSNP_134	128	1,8047		0,1,4023	no	frameshift	ZNF594	NM_032530.1		12,131,5808	A1A1,A1R,RR		0.0124,3.9958,1.3023				155,11747				SO:0001589	frameshift_variant	84622	exon2			.	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.1673_1674delAG	17.37:g.5085880_5085881delCT	ENSP00000382513:p.Glu558fs	Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	117	33	0.282	NM_032530	Q6RFS0	Frame_Shift_Del	DEL	ENST00000399604.4	37	CCDS42241.1																																																																																			CT|0.987;-|0.013	0.013	strong		0.470	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
CYP3A43	64816	hgsc.bcm.edu	37	7	99434078	99434078	+	Frame_Shift_Del	DEL	A	A	-	rs61469810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99434078delA	ENST00000354829.2	+	2	177	c.74delA	c.(73-75)tatfs	p.Y25fs	CYP3A43_ENST00000415413.1_Frame_Shift_Del_p.Y25fs|CYP3A43_ENST00000342499.4_Intron|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000417625.1_Frame_Shift_Del_p.Y25fs|CYP3A43_ENST00000421837.2_Frame_Shift_Del_p.Y25fs|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000222382.5_Frame_Shift_Del_p.Y25fs|CYP3A43_ENST00000312017.5_Frame_Shift_Del_p.Y25fs	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	25			YGTHSHKLFKKLGIPGPTPLPFLGTILFYLRGLWNFDRECN EKYGEMWGLYEGQQPMLVIMDPD -> LGPIHINFLRSWEF LGQPLCLFWELFCSTLGVFGILTENVMKNTEKCGGCMRGNS PCWSSWIPT (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)	TTTTATAGTTATGGGACCCAT	0.408													A|A|-|deletion	528	0.105431	0.3154	0.0447	5008	,	,		17588	0.001		0.0378	False		,,,				2504	0.0419				p.Y25fs		Pindel,Atlas-Indel	.											.	CYP3A43	52	.	0			c.73delT	GRCh37	CD040166	CYP3A43	D	rs61469810	PASS	.		,,	1069,3195		129,811,1192	58.0	71.0	67.0		,,	2.4	0.3	7	dbSNP_129	71	297,7957		9,279,3839	no	frameshift,frameshift,frameshift	CYP3A43	NM_057096.2,NM_057095.1,NM_022820.3	,,	138,1090,5031	A1A1,A1R,RR		3.5983,25.0704,10.9123	,,	,,	99434078	1366,11152	2088	4291	6379	SO:0001589	frameshift_variant	64816	exon2			.	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.74delA	7.37:g.99434078delA	ENSP00000346887:p.Tyr25fs	Somatic	109	.	.		WXS	Illumina HiSeq	Phase_I	98	32	0.327	NM_057095	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Frame_Shift_Del	DEL	ENST00000354829.2	37	CCDS5676.1																																																																																			A|0.903;-|0.097	0.097	strong		0.408	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1		
TNRC6A	27327	hgsc.bcm.edu	37	16	24788401	24788402	+	In_Frame_Ins	INS	-	-	GCA	rs112426081|rs575176088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24788401_24788402insGCA	ENST00000395799.3	+	5	440_441	c.311_312insGCA	c.(310-315)ccgcag>ccGCAgcag	p.108_109insQ	TNRC6A_ENST00000315183.7_In_Frame_Ins_p.108_109insQ	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	108	Gln-rich.|Interaction with argonaute family proteins.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		cagcagcagccgcagcagcagc	0.589														11	0.00219649	0.0083	0.0	5008	,	,		10840	0.0		0.0	False		,,,				2504	0.0				p.P104delinsPQ		Atlas-Indel	.											TNRC6A,NS,carcinoma,0,1	TNRC6A	171	1	0			c.311_312insGCA						PASS	.			43,3543		6,31,1756						-2.9	0.0		dbSNP_132	22	8,7216		1,6,3605	no	coding	TNRC6A	NM_014494.2		7,37,5361	A1A1,A1R,RR		0.1107,1.1991,0.4718				51,10759				SO:0001652	inframe_insertion	27327	exon5			.	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.321_323dupGCA	16.37:g.24788408_24788410dupGCA	ENSP00000379144:p.Gln111_Gln112dup	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	55	11	0.2	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	In_Frame_Ins	INS	ENST00000395799.3	37	CCDS10624.2																																																																																			-|0.500;GCA|0.500	0.500	weak		0.589	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
CBLC	23624	hgsc.bcm.edu	37	19	45296846	45296847	+	Frame_Shift_Ins	INS	-	-	C	rs66944506|rs77920506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45296846_45296847insC	ENST00000270279.3	+	8	1316_1317	c.1253_1254insC	c.(1252-1257)gaccagfs	p.Q419fs	CBLC_ENST00000341505.4_Frame_Shift_Ins_p.Q373fs	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	419	Interaction with RET.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				AACAGCAGTGACCAGGAAGGCA	0.629			M		AML								CC|CC|CCC|insertion	434	0.0866613	0.2148	0.0245	5008	,	,		17683	0.0962		0.002	False		,,,				2504	0.0348				p.D418fs		Pindel,Atlas-Indel	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.1253_1254insC						PASS	.		,	780,3484		76,628,1428					,	0.9	0.0		dbSNP_130	36	24,8230		1,22,4104	no	frameshift,frameshift	CBLC	NM_012116.3,NM_001130852.1	,	77,650,5532	A1A1,A1R,RR		0.2908,18.2927,6.4228	,	,		804,11714				SO:0001589	frameshift_variant	23624	exon8			.	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.1255dupC	19.37:g.45296848_45296848dupC	ENSP00000270279:p.Gln419fs	Somatic	52	.	.		WXS	Illumina HiSeq	Phase_I	65	28	0.431	NM_012116	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Frame_Shift_Ins	INS	ENST00000270279.3	37	CCDS12643.1																																																																																			-|0.926;C|0.074	0.074	strong		0.629	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140772899	140772899	+	Frame_Shift_Del	DEL	C	C	-	rs397780331|rs3214276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140772899delC	ENST00000398604.2	+	1	519	c.519delC	c.(517-519)agcfs	p.S173fs	PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	173	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)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCAGCTCAGCCCCAATCACC	0.572													|||unknown(NO_COVERAGE)	639	0.127596	0.1747	0.1513	5008	,	,		17007	0.1181		0.0586	False		,,,				2504	0.1278				p.S173fs		Pindel,Atlas-Indel	.											.	PCDHGA8	146	.	0			c.518delG						PASS	.		,,,,,,,,,,,,	743,3289		100,543,1373	50.0	60.0	56.0		,,,,,,,,,,,,	2.5	1.0	5	dbSNP_106	62	639,7495		39,561,3467	yes	frameshift,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,frameshift,intron	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_032088.1,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_014004.2,NM_003736.2	,,,,,,,,,,,,	139,1104,4840	A1A1,A1R,RR		7.8559,18.4276,11.3595	,,,,,,,,,,,,	,,,,,,,,,,,,	140772899	1382,10784	2064	4239	6303	SO:0001589	frameshift_variant	9708	exon1			.	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.519delC	5.37:g.140772899delC	ENSP00000381605:p.Ser173fs	Somatic	121	.	.		WXS	Illumina HiSeq	Phase_I	153	53	0.346	NM_014004	A7MCZ4|O15039	Frame_Shift_Del	DEL	ENST00000398604.2	37	CCDS47291.1																																																																																			C|0.882;-|0.118	0.118	strong		0.572	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
OR2W3	343171	hgsc.bcm.edu	37	1	248059779	248059780	+	Frame_Shift_Ins	INS	-	-	A	rs80255919|rs112696640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248059779_248059780insA	ENST00000360358.3	+	1	891_892	c.891_892insA	c.(892-894)aagfs	p.K298fs	OR2W3_ENST00000537741.1_Frame_Shift_Ins_p.K298fs	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A300fs*>16(1)		breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			ACAGAGAGGTGAAGGGGGCACT	0.54													AA|AA|AAA|insertion	673	0.134385	0.1339	0.1931	5008	,	,		18884	0.0317		0.1312	False		,,,				2504	0.2025				p.V297fs		Pindel,Atlas-Indel	.											.	OR2W3	113	.	1	Insertion - Frameshift(1)	upper_aerodigestive_tract(1)	c.891_892insA						PASS	.			569,3697		41,487,1605						4.3	1.0		dbSNP_132	41	1288,6960		99,1090,2935	no	frameshift	OR2W3	NM_001001957.2		140,1577,4540	A1A1,A1R,RR		15.6159,13.338,14.8394				1857,10657				SO:0001589	frameshift_variant	343171	exon1			.	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.893dupA	1.37:g.248059781_248059781dupA	ENSP00000353516:p.Lys298fs	Somatic	128	.	.		WXS	Illumina HiSeq	Phase_I	128	60	0.469	NM_001001957	Q6IF06|Q8NG86	Frame_Shift_Ins	INS	ENST00000360358.3	37	CCDS31099.1																																																																																			-|0.876;A|0.124	0.124	strong		0.540	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957	
ETFB	2109	hgsc.bcm.edu	37	19	51857874	51857875	+	Intron	INS	-	-	CCACAG	rs113835487|rs397825770|rs61361626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51857874_51857875insCCACAG	ENST00000309244.4	-	2	149				CTD-2616J11.9_ENST00000600974.1_RNA|ETFB_ENST00000354232.4_In_Frame_Ins_p.5_6insWL|CTD-2616J11.11_ENST00000600067.1_Intron	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		TTTATGGTAACCCACAGTGAGA	0.381														409	0.0816693	0.2595	0.0375	5008	,	,		22079	0.001		0.005	False		,,,				2504	0.0348				p.V7delinsLWV		Pindel,Atlas-Indel	.											.	ETFB	46	.	0			c.19_20insCTGTGG						PASS	.		,	1043,3221		124,795,1213					,	-0.7	0.0		dbSNP_130	53	41,8213		0,41,4086	no	intron,coding	ETFB	NM_001985.2,NM_001014763.1	,	124,836,5299	A1A1,A1R,RR		0.4967,24.4606,8.6595	,	,		1084,11434				SO:0001627	intron_variant	2109	exon1			.	X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379			3482	protein-coding gene	gene with protein product		130410					Standard	NM_001014763		Approved		uc002pwg.3	P38117		ENST00000309244.4:c.58-312->CTGTGG	19.37:g.51857875_51857880dupCCACAG		Somatic	79	.	.		WXS	Illumina HiSeq	Phase_I	90	20	0.222	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	In_Frame_Ins	INS	ENST00000309244.4	37	CCDS12828.1																																																																																			-|0.937;CCACAG|0.063	0.063	strong		0.381	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
SLC4A2	6522	hgsc.bcm.edu	37	7	150763616	150763621	+	In_Frame_Del	DEL	GGAGGC	GGAGGC	-	rs150330052|rs199537782|rs374531279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGAGGC	GGAGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150763616_150763621delGGAGGC	ENST00000485713.1	+	6	1631_1636	c.591_596delGGAGGC	c.(589-597)gaggaggcg>gag	p.EA202del	SLC4A2_ENST00000392826.2_In_Frame_Del_p.EA193del|SLC4A2_ENST00000413384.2_In_Frame_Del_p.EA202del|SLC4A2_ENST00000461735.1_In_Frame_Del_p.EA188del|SLC4A2_ENST00000310317.5_In_Frame_Del_p.EA120del	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	202	Pro-rich.		E -> V (in dbSNP:rs2229551). {ECO:0000269|Ref.2}.		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)		CCCAGGTGGAGGAGGCGGAGGCGGAG	0.733														191	0.038139	0.1316	0.0173	5008	,	,		15101	0.001		0.003	False		,,,				2504	0.001				p.197_199del		Pindel,Atlas-Indel	.											.	SLC4A2	98	.	0			c.590_595del						PASS	.		,,,	390,3074		94,202,1436					,,,	4.7	1.0		dbSNP_130	8	34,6758		8,18,3370	no	coding,coding,coding,coding	SLC4A2	NM_003040.3,NM_001199694.1,NM_001199693.1,NM_001199692.1	,,,	102,220,4806	A1A1,A1R,RR		0.5006,11.2587,4.1342	,,,	,,,		424,9832				SO:0001651	inframe_deletion	6522	exon6			.		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.591_596delGGAGGC	7.37:g.150763622_150763627delGGAGGC	ENSP00000419412:p.Glu202_Ala203del	Somatic	56	.	.		WXS	Illumina HiSeq	Phase_I	49	12	0.245	NM_001199692	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	In_Frame_Del	DEL	ENST00000485713.1	37	CCDS5917.1																																																																																			GGAGGC|0.962;-|0.038	0.038	strong		0.733	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
TICAM1	148022	hgsc.bcm.edu	37	19	4817288	4817289	+	In_Frame_Ins	INS	-	-	AGG	rs144100421|rs11466722|rs368322317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4817288_4817289insAGG	ENST00000248244.5	-	2	1330_1331	c.1101_1102insCCT	c.(1099-1104)ccttca>cctCCTtca	p.367_368insP		NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	367	Pro-rich.				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)		GGAGTAGATGAaggaggaggag	0.52														798	0.159345	0.2761	0.1311	5008	,	,		14915	0.0665		0.1491	False		,,,				2504	0.1278				p.S368delinsPS		Pindel,Atlas-Indel	.											.	TICAM1	69	.	0			c.1102_1103insCCT						PASS	.																																			SO:0001652	inframe_insertion	148022	exon2			.	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.1099_1101dupCCT	19.37:g.4817295_4817297dupAGG	ENSP00000248244:p.Pro367_Pro367dup	Somatic	248	.	.		WXS	Illumina HiSeq	Phase_I	231	48	0.208	NM_182919	B3Y691|O75532|Q86XP8|Q96GA0	In_Frame_Ins	INS	ENST00000248244.5	37	CCDS12136.1																																																																																			.	.	strong		0.520	TICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450435.1	NM_014261	
C8orf82	414919	hgsc.bcm.edu	37	8	145753431	145753431	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145753431delT	ENST00000524821.1	-	2	397	c.182delA	c.(181-183)aagfs	p.K61fs	C8orf82_ENST00000313465.5_Frame_Shift_Del_p.K61fs|LRRC24_ENST00000529415.2_5'Flank|LRRC24_ENST00000533758.1_5'Flank			Q6P1X6	CH082_HUMAN	chromosome 8 open reading frame 82	61										endometrium(1)|urinary_tract(1)	2						GATGAAATTCTTCATTTTGGA	0.582																																					p.K61fs		Pindel,Atlas-Indel	.											C8orf82,bladder,carcinoma,0,1	C8orf82	7	1	0			c.183delG						PASS	.			1,4263		0,1,2131	86.0	84.0	85.0			3.7	1.0	8		85	0,8254		0,0,4127	no	frameshift	C8orf82	NM_001001795.1		0,1,6258	A1A1,A1R,RR		0.0,0.0235,0.0080			145753431	1,12517	2203	4300	6503	SO:0001589	frameshift_variant	414919	exon2			.		CCDS34970.1	8q24	2012-04-18			ENSG00000213563	ENSG00000213563			33826	protein-coding gene	gene with protein product						12477932	Standard	NM_001001795		Approved	MGC70857	uc003zdp.1	Q6P1X6	OTTHUMG00000165181	ENST00000524821.1:c.182delA	8.37:g.145753431delT	ENSP00000436621:p.Lys61fs	Somatic	51	.	.		WXS	Illumina HiSeq	Phase_I	57	28	0.491	NM_001001795	Q6GMR2|Q6P2Q7	Frame_Shift_Del	DEL	ENST00000524821.1	37	CCDS34970.1																																																																																			.	.	none		0.582	C8orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382503.1	NM_001001795	
OR52D1	390066	hgsc.bcm.edu	37	11	5510498	5510499	+	Frame_Shift_Ins	INS	-	-	C	rs571241475|rs386750177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5510498_5510499insC	ENST00000322641.5	+	1	584_585	c.562_563insC	c.(562-564)gccfs	p.A188fs	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	188					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)		TATGGGCATTGCCCGACTGGCC	0.51													CCC|CCC|CCCC|insertion	9	0.00179712	0.0053	0.0029	5008	,	,		22033	0.0		0.0	False		,,,				2504	0.0				p.A188fs		Atlas-Indel	.											.	OR52D1	66	.	0			c.562_563insC						PASS	.																																			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.565dupC	11.37:g.5510501_5510501dupC	ENSP00000326232:p.Ala188fs	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	134	54	0.402985	NM_001005163	B9EGY9|Q6IFI6	Frame_Shift_Ins	INS	ENST00000322641.5	37	CCDS31384.1																																																																																			.	.	none		0.510	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163	
BDNF	627	hgsc.bcm.edu	37	11	27680797	27680806	+	5'UTR	DEL	GAAGACTTGC	GAAGACTTGC	-	rs57127302|rs113353767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAAGACTTGC	GAAGACTTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:27680797_27680806delGAAGACTTGC	ENST00000525528.1	-	0	399_408				BDNF_ENST00000438929.1_Intron|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000530861.1_Intron|BDNF-AS_ENST00000532965.1_RNA|BDNF_ENST00000395980.2_Intron|BDNF_ENST00000533246.1_Intron|BDNF-AS_ENST00000499008.3_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000395983.3_Intron|BDNF_ENST00000439476.2_5'UTR|BDNF_ENST00000584049.1_Intron|BDNF_ENST00000418212.1_Intron|BDNF_ENST00000533131.1_Intron|BDNF-AS_ENST00000500662.2_RNA|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000525950.1_Intron|BDNF_ENST00000395981.3_Intron|BDNF_ENST00000420794.1_Intron|BDNF_ENST00000395978.3_Intron|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000532997.1_Intron|BDNF_ENST00000395986.2_Intron|BDNF_ENST00000356660.4_Intron|BDNF_ENST00000314915.6_Intron	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor						axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						aaaggccatagaagacttgccttatgtcat	0.371														176	0.0351438	0.0908	0.0173	5008	,	,		20161	0.0308		0.008	False		,,,				2504	0.0051				.		Pindel,Atlas-Indel	.											.	BDNF	63	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	627	.			.	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"""Endogenous ligands"""	1033	protein-coding gene	gene with protein product	"""neurotrophin"""	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.-695GCAAGTCTTC>-	11.37:g.27680797_27680806delGAAGACTTGC		Somatic	158	.	.		WXS	Illumina HiSeq	Phase_I	108	33	0.306	.	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	RNA	DEL	ENST00000525528.1	37	CCDS7866.1																																																																																			GAAGACTTGC|0.962;-|0.038	0.038	strong		0.371	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735	
RBPJL	11317	hgsc.bcm.edu	37	20	43940531	43940542	+	In_Frame_Del	DEL	CAGCGCGTCCGG	CAGCGCGTCCGG	-	rs142744285|rs367731607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAGCGCGTCCGG	CAGCGCGTCCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43940531_43940542delCAGCGCGTCCGG	ENST00000343694.3	+	5	453_464	c.381_392delCAGCGCGTCCGG	c.(379-393)gacagcgcgtccggc>gac	p.SASG128del	RBPJL_ENST00000372743.1_In_Frame_Del_p.SASG128del|RBPJL_ENST00000372741.3_In_Frame_Del_p.SASG128del	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	128					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	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 (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				TGGGACTGGACAGCGCGTCCGGCAGCGCCACT	0.66											OREG0025979	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		73	0.0145767	0.0454	0.0072	5008	,	,		19337	0.0		0.004	False		,,,				2504	0.0041				p.127_131del		Pindel,Atlas-Indel	.											.	RBPJL	67	.	0			c.380_391del						PASS	.			129,3693		18,93,1800						4.2	1.0		dbSNP_134	9	24,7388		7,10,3689	no	coding	RBPJL	NM_014276.2		25,103,5489	A1A1,A1R,RR		0.3238,3.3752,1.3619				153,11081				SO:0001651	inframe_deletion	11317	exon5			.	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.381_392delCAGCGCGTCCGG	20.37:g.43940531_43940542delCAGCGCGTCCGG	ENSP00000341243:p.Ser128_Gly131del	Somatic	127	.	.	920	WXS	Illumina HiSeq	Phase_I	118	45	0.381	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	In_Frame_Del	DEL	ENST00000343694.3	37	CCDS13349.1																																																																																			CAGCGCGTCCGG|0.987;-|0.013	0.013	strong		0.660	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
RPGR	6103	hgsc.bcm.edu	37	X	38145916	38145918	+	Intron	DEL	TCC	TCC	-	rs201730068		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145916_38145918delTCC	ENST00000339363.3	-	14	2688				TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000378505.2_In_Frame_Del_p.778_779EE>E|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						ccccgctctttcctcctttttcc	0.542														37	0.00980132	0.0257	0.0043	3775	,	,		10718	0.0		0.0	False		,,,				2504	0.0				p.779_779del		Pindel,Atlas-Indel	.											.	RPGR	175	.	0			c.2335_2337del						PASS	.		,	118,3082		5,95,13,1328,331					,	-2.0	0.0			235	8,5495		2,0,4,2080,1335	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	7,95,17,3408,1666	A1A1,A1R,A1,RR,R		0.1454,3.6875,1.4478	,	,		126,8577				SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+428GGA>-	X.37:g.38145919_38145921delTCC		Somatic	462	.	.		WXS	Illumina HiSeq	Phase_I	486	107	0.220	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				TCC|0.991;-|0.009	0.009	strong		0.542	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
LGR6	59352	hgsc.bcm.edu	37	1	202183358	202183358	+	Intron	DEL	G	G	-	rs74355478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:202183358delG	ENST00000367278.3	+	2	301				LGR6_ENST00000255432.7_Intron|LGR6_ENST00000439764.2_Frame_Shift_Del_p.A26fs	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6						G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						ACGGCGCGGTGCGCCCAGGTA	0.711													G|G|-|deletion	446	0.0890575	0.1762	0.1455	5008	,	,		10051	0.0397		0.0547	False		,,,				2504	0.0174				p.G25fs		Pindel,Atlas-Indel	.											.	LGR6	102	.	0			c.75delT						PASS	.		,,	600,3594		55,490,1552	9.0	12.0	11.0		,,	-1.9	0.0	1	dbSNP_131	12	450,7766		25,400,3683	yes	intron,frameshift,intron	LGR6	NM_021636.2,NM_001017404.1,NM_001017403.1	,,	80,890,5235	A1A1,A1R,RR		5.4771,14.3062,8.4609	,,	,,	202183358	1050,11360	2123	4261	6384	SO:0001627	intron_variant	59352	exon1			.	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.213-11193G>-	1.37:g.202183358delG		Somatic	235	.	.		WXS	Illumina HiSeq	Phase_I	270	79	0.293	NM_001017404	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Frame_Shift_Del	DEL	ENST00000367278.3	37	CCDS30971.1																																																																																			G|0.905;-|0.095	0.095	strong		0.711	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
GFM2	84340	hgsc.bcm.edu	37	5	74021847	74021852	+	In_Frame_Del	DEL	ACTCAA	ACTCAA	-	rs5868753|rs76339998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ACTCAA	ACTCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:74021847_74021852delACTCAA	ENST00000296805.3	-	18	2283_2288	c.1826_1831delTTGAGT	c.(1825-1833)tttgagtat>tat	p.FE609del	GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000509430.1_In_Frame_Del_p.FE609del|GFM2_ENST00000345239.2_In_Frame_Del_p.FE562del|RNU6-658P_ENST00000384606.1_RNA	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2									p.F609Y(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(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;1.86e-56)		CTTTCAGCATACTCAAACTCAATCAC	0.413														1915	0.382388	0.7572	0.3372	5008	,	,		20860	0.1974		0.2425	False		,,,				2504	0.2423				p.609_611del		Pindel,Atlas-Indel	.											.	GFM2	38	.	1	Substitution - Missense(1)	lung(1)	c.1827_1832del						PASS	.																																			SO:0001651	inframe_deletion	84340	exon18			.	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1826_1831delTTGAGT	5.37:g.74021853_74021858delACTCAA	ENSP00000296805:p.Phe609_Glu610del	Somatic	122	.	.		WXS	Illumina HiSeq	Phase_I	118	34	0.288	NM_032380		In_Frame_Del	DEL	ENST00000296805.3	37	CCDS4023.1																																																																																			ACTCAA|0.643;-|0.357	0.357	strong		0.413	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
ATP2C2	9914	hgsc.bcm.edu	37	16	84497336	84497337	+	Stop_Codon_Ins	INS	-	-	AGTGGA	rs149491518|rs568403499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84497336_84497337insAGTGGA	ENST00000262429.4	+	0	2928_2929				ATP2C2_ENST00000420010.2_3'UTR|RP11-517C16.2_ENST00000565700.1_RNA|ATP2C2_ENST00000416219.2_Stop_Codon_Ins	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2						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						TGAAGATGTGTAGTGGACCGCA	0.54														67	0.0133786	0.0499	0.0014	5008	,	,		19122	0.0		0.0	False		,,,				2504	0.0				p.X947delinsX		Pindel,Atlas-Indel	.											.	ATP2C2	75	.	0			c.2839_2840insAGTGGA						PASS	.			151,3647		1,149,1749						3.1	0.0		dbSNP_134	118	1,7939		0,1,3969	no	coding	ATP2C2	NM_014861.2		1,150,5718	A1A1,A1R,RR		0.0126,3.9758,1.2949				152,11586				SO:0001567	stop_retained_variant	9914	exon27			.	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.2839_2844dupAGTGGA	16.37:g.84497337_84497342dupAGTGGA		Somatic	146	.	.		WXS	Illumina HiSeq	Phase_I	120	26	0.217	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	In_Frame_Ins	INS	ENST00000262429.4	37	CCDS42207.1																																																																																			-|0.987;AGTGGA|0.013	0.013	strong		0.540	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
LRRC46	90506	hgsc.bcm.edu	37	17	45914125	45914136	+	In_Frame_Del	DEL	AGGAGCTGGAGC	AGGAGCTGGAGC	-	rs142960476|rs377191761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGGAGCTGGAGC	AGGAGCTGGAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45914125_45914136delAGGAGCTGGAGC	ENST00000269025.4	+	8	968_979	c.605_616delAGGAGCTGGAGC	c.(604-618)aaggagctggagcag>aag	p.ELEQ203del		NM_033413.3	NP_219481.1	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	203										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	9						GGCTTCCTCAAGGAGCTGGAGCAGGAGCTGAG	0.684														156	0.0311502	0.1104	0.013	5008	,	,		19410	0.0		0.0	False		,,,				2504	0.001				p.202_205del		Pindel,Atlas-Indel	.											.	LRRC46	25	.	0			c.604_615del						PASS	.			383,3877		24,335,1771						-3.3	0.8		dbSNP_134	24	7,8231		1,5,4113	no	coding	LRRC46	NM_033413.3		25,340,5884	A1A1,A1R,RR		0.085,8.9906,3.1205				390,12108				SO:0001651	inframe_deletion	90506	exon8			.		CCDS11518.1	17q21.32	2005-08-09				ENSG00000141294			25047	protein-coding gene	gene with protein product						12477932	Standard	NM_033413		Approved	MGC16309	uc002ima.3	Q96FV0		ENST00000269025.4:c.605_616delAGGAGCTGGAGC	17.37:g.45914125_45914136delAGGAGCTGGAGC	ENSP00000269025:p.Glu203_Gln206del	Somatic	184	.	.		WXS	Illumina HiSeq	Phase_I	131	35	0.267	NM_033413	A8K9Q0	In_Frame_Del	DEL	ENST00000269025.4	37	CCDS11518.1																																																																																			AGGAGCTGGAGC|0.978;-|0.022	0.022	strong		0.684	LRRC46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441377.1	NM_033413	
UPK3BL	100134938	hgsc.bcm.edu	37	7	102281151	102281152	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:102281151_102281152insA	ENST00000340457.8	-	2	230_231	c.181_182insT	c.(181-183)tccfs	p.S61fs	POLR2J2_ENST00000591000.1_3'UTR|POLR2J2_ENST00000476151.1_3'UTR|POLR2J2_ENST00000333432.6_Frame_Shift_Ins_p.V99fs|RP11-514P8.6_ENST00000519541.1_Frame_Shift_Ins_p.S61fs	NM_001114403.2	NP_001107875.1	B0FP48	UPK3L_HUMAN	uroplakin 3B-like	61						integral component of membrane (GO:0016021)				kidney(2)|stomach(1)	3						CGTGAAGGTGGACAGGGTGAGC	0.609																																					p.S61fs		Atlas-Indel	.											.	UPK3BL	6	.	0			c.182_183insT						PASS	.																																			SO:0001589	frameshift_variant	100134938	exon2			.	EU341824	CCDS47675.1	7q22.1	2014-02-12	2010-03-03		ENSG00000267368	ENSG00000267368			37278	protein-coding gene	gene with protein product	"""uroplakin-like protein"""						Standard	NM_001114403		Approved	UPLP		B0FP48	OTTHUMG00000165036	ENST00000340457.8:c.182dupT	7.37:g.102281152_102281152dupA	ENSP00000342938:p.Ser61fs	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	78	27	0.346154	NM_001114403		Frame_Shift_Ins	INS	ENST00000340457.8	37	CCDS47675.1																																																																																			.	.	none		0.609	UPK3BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381510.1	NM_001114403	
MTERF4	130916	hgsc.bcm.edu	37	2	242035516	242035518	+	In_Frame_Del	DEL	TCA	TCA	-	rs142629642|rs10203977		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242035516_242035518delTCA	ENST00000391980.2	-	4	1099_1101	c.1041_1043delTGA	c.(1039-1044)gatgag>gag	p.D347del	MTERFD2_ENST00000406593.1_In_Frame_Del_p.D159del|MTERFD2_ENST00000495694.1_Intron|MTERFD2_ENST00000464344.2_Intron	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		347			D -> E (in dbSNP:rs10203977).		rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		attgtcctcctcatcatcgtcat	0.512																																					p.348_348del		Pindel,Atlas-Indel	.											.	MTERFD2	33	.	0			c.1042_1044del						PASS	.			252,4010		8,236,1887						0.5	0.0		dbSNP_130	242	5,8249		0,5,4122	no	coding	MTERFD2	NM_182501.3		8,241,6009	A1A1,A1R,RR		0.0606,5.9127,2.0534				257,12259				SO:0001651	inframe_deletion	130916	exon4			.																												ENST00000391980.2:c.1041_1043delTGA	2.37:g.242035519_242035521delTCA	ENSP00000375840:p.Asp347del	Somatic	219	.	.		WXS	Illumina HiSeq	Phase_I	224	44	0.196	NM_182501	A8K6K0|Q9P0E0	In_Frame_Del	DEL	ENST00000391980.2	37	CCDS2544.1																																																																																			.	.	strong		0.512	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4		
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609296	32609297	+	Frame_Shift_Ins	INS	-	-	G	rs9279910|rs9282026		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32609296_32609297insG	ENST00000343139.5	+	2	394_395	c.292_293insG	c.(292-294)atcfs	p.I98fs	HLA-DQA1_ENST00000374949.2_Frame_Shift_Ins_p.I98fs|HLA-DQA1_ENST00000395363.1_Frame_Shift_Ins_p.I98fs	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	97	Alpha-1.		L -> M (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).|L -> V (in allele DQA1*03:01, allele DQA1*03:02 and allele DQA1*03:03).		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						CAACTTGAACATCATGATTAAA	0.48																																					p.I98fs		Atlas-Indel	.											.	HLA-DQA1	52	.	0			c.292_293insG						PASS	.			427,3759		87,253,1753						-3.9	0.0		dbSNP_118	83	1014,6964		244,526,3219	no	frameshift	HLA-DQA1	NM_002122.3		331,779,4972	A1A1,A1R,RR		12.71,10.2007,11.8464				1441,10723				SO:0001589	frameshift_variant	3117	exon2			.		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	Exception_encountered	6.37:g.32609296_32609297insG	ENSP00000339398:p.Ile98fs	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	20	14	0.7	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	Frame_Shift_Ins	INS	ENST00000343139.5	37	CCDS4752.1																																																																																			-|0.857;G|0.143	0.143	strong		0.480	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
AMBN	258	hgsc.bcm.edu	37	4	71468346	71468348	+	In_Frame_Del	DEL	AGG	AGG	-	rs368655454|rs141384720|rs199556863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	285	.	.		WXS	Illumina HiSeq	Phase_I	220	55	0.250	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	
ADAM33	80332	hgsc.bcm.edu	37	20	3652979	3652983	+	Intron	DEL	GCGCA	GCGCA	-	rs56355127|rs143884879|rs374693928|rs186219489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCGCA	GCGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3652979_3652983delGCGCA	ENST00000356518.2	-	14	1643				ADAM33_ENST00000466620.1_Intron|ADAM33_ENST00000379861.4_Intron|ADAM33_ENST00000350009.2_Intron	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33						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						GGCTTCAGCTGCGCAGGTGACGGGT	0.673														252	0.0503195	0.1702	0.013	5008	,	,		18370	0.0		0.0139	False		,,,				2504	0.0041				.		Pindel,Atlas-Indel	.											.	ADAM33	76	.	0			.						PASS	.		,	535,3721		37,461,1630					,	4.6	0.9		dbSNP_129	39	78,8172		1,76,4048	no	intron,intron	ADAM33	NM_153202.1,NM_025220.2	,	38,537,5678	A1A1,A1R,RR		0.9455,12.5705,4.9016	,	,		613,11893				SO:0001627	intron_variant	80332	.			.	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.1402-3TGCGC>-	20.37:g.3652979_3652983delGCGCA		Somatic	86	.	.		WXS	Illumina HiSeq	Phase_I	71	26	0.366	.	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Splice_Site	DEL	ENST00000356518.2	37	CCDS13058.1																																																																																			GCGCA|0.958;-|0.042	0.042	strong		0.673	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220	
KGFLP1	387628	hgsc.bcm.edu	37	9	46687757	46687757	+	lincRNA	DEL	G	G	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:46687757delG	ENST00000429818.1	-	0	283				RP11-111F5.5_ENST00000377614.3_RNA																							ACCAGAGGCCGGGGAAGGCGC	0.627																																					.		Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																					0	.			.																													9.37:g.46687757delG		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	210	35	0.166667	.		RNA	DEL	ENST00000429818.1	37																																																																																				.	.	none		0.627	RP11-111F5.4-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037089.1		
ZNF107	51427	hgsc.bcm.edu	37	7	64169017	64169018	+	Frame_Shift_Ins	INS	-	-	A	rs376059343|rs375319415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:64169017_64169018insA	ENST00000395391.1	+	4	3710_3711	c.2335_2336insA	c.(2335-2337)gagfs	p.E779fs	ZNF107_ENST00000423627.1_Frame_Shift_Ins_p.E779fs|ZNF107_ENST00000344930.3_Frame_Shift_Ins_p.E779fs			Q9UII5	ZN107_HUMAN	zinc finger protein 107	779					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				CTACAAATGTGAGTATGGCAAA	0.351													?|A|AA|unsure	47	0.00938498	0.0348	0.0	5008	,	,		19143	0.001		0.0	False		,,,				2504	0.0				p.E779fs		Atlas-Indel	.											.	ZNF107	107	.	0			c.2335_2336insA						PASS	.																																			SO:0001589	frameshift_variant	51427	exon7			.	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"""Zinc fingers, C2H2-type"""	12887	protein-coding gene	gene with protein product		603989	"""zinc finger protein 588"", ""zinc finger protein 107 (Y8)"""	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.2336dupA	7.37:g.64169018_64169018dupA	ENSP00000378789:p.Glu779fs	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	44	15	0.340909	NM_016220		Frame_Shift_Ins	INS	ENST00000395391.1	37	CCDS5527.1																																																																																			.	.	weak		0.351	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220	
ARID1A	8289	hgsc.bcm.edu	37	1	27097616	27097618	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:27097616_27097618delAAG	ENST00000324856.7	+	12	3576_3578	c.3205_3207delAAG	c.(3205-3207)aagdel	p.K1069del	ARID1A_ENST00000457599.2_In_Frame_Del_p.K1069del|ARID1A_ENST00000374152.2_In_Frame_Del_p.K686del|ARID1A_ENST00000540690.1_5'Flank	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1069	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		ACAGGTCAACAAGAACAAAAAAT	0.483			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.1068_1069del		Pindel,Atlas-Indel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.3204_3206del						PASS	.																																			SO:0001651	inframe_deletion	8289	exon12			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3205_3207delAAG	1.37:g.27097616_27097618delAAG	ENSP00000320485:p.Lys1069del	Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	79	16	0.203	NM_139135	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	In_Frame_Del	DEL	ENST00000324856.7	37	CCDS285.1																																																																																			.	.	none		0.483	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
ROBO3	64221	hgsc.bcm.edu	37	11	124750448	124750453	+	In_Frame_Del	DEL	CGGAGT	CGGAGT	-	rs55725290|rs56085444|rs71859853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CGGAGT	CGGAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	90	.	.		WXS	Illumina HiSeq	Phase_I	95	31	0.326	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	
RSPH10B2	728194	hgsc.bcm.edu	37	7	6838173	6838176	+	Stop_Codon_Del	DEL	AGAG	AGAG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGAG	AGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6838173_6838176delAGAG	ENST00000403107.1	+	0	2999_3002				CCZ1B_ENST00000597208.1_5'Flank|CCZ1B_ENST00000316731.8_3'UTR|RSPH10B2_ENST00000433859.2_Stop_Codon_Del|RSPH10B2_ENST00000404077.1_Stop_Codon_Del|RSPH10B2_ENST00000297186.3_Stop_Codon_Del|RSPH10B2_ENST00000359718.3_3'UTR			B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B2 (Chlamydomonas)											breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|skin(2)	15						AAGAAAAAGTAGAGAGACACGAGG	0.49																																					p.871_871del		Atlas-Indel	.											.	RSPH10B	28	.	0			c.2611_2884del						PASS	.																																			SO:0001567	stop_retained_variant	222967	exon21			.		CCDS43552.1	7p22.1	2008-07-04			ENSG00000169402	ENSG00000169402			34385	protein-coding gene	gene with protein product							Standard	NM_001099697		Approved		uc003sqw.1	B2RC85	OTTHUMG00000151856	Exception_encountered	7.37:g.6838173_6838176delAGAG		Somatic	497	0	0		WXS	Illumina HiSeq	Phase_I	379	34	0.0897098	NM_173565	A6NMW7|B2RXI4|B2RXJ0|Q86ST9|Q8NE68	Frame_Shift_Del	DEL	ENST00000403107.1	37	CCDS43552.1																																																																																			.	.	none		0.490	RSPH10B2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324184.4	NM_001099697	
ANKRD40	91369	hgsc.bcm.edu	37	17	48777220	48777221	+	In_Frame_Ins	INS	-	-	TCA	rs377717183|rs138572332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48777220_48777221insTCA	ENST00000285243.6	-	3	586_587	c.317_318insTGA	c.(316-318)gac>gaTGAc	p.106_106D>DD		NM_052855.3	NP_443087.1	Q6AI12	ANR40_HUMAN	ankyrin repeat domain 40	106	Poly-Asp.									breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11			BRCA - Breast invasive adenocarcinoma(22;2.03e-09)			GGGGGAGGTTGtcatcatcatc	0.406														235	0.0469249	0.0908	0.0807	5008	,	,		16671	0.0337		0.004	False		,,,				2504	0.0215				p.D106delinsDD		Atlas-Indel	.											.	ANKRD40	35	.	0			c.318_319insTGA						PASS	.																																			SO:0001652	inframe_insertion	91369	exon3			.	BC012978	CCDS11572.1	17q21.33	2013-01-10			ENSG00000154945	ENSG00000154945		"""Ankyrin repeat domain containing"""	28233	protein-coding gene	gene with protein product						12477932	Standard	NM_052855		Approved	MGC15396	uc002iso.3	Q6AI12	OTTHUMG00000162255	ENST00000285243.6:c.315_317dupTGA	17.37:g.48777227_48777229dupTCA	ENSP00000285243:p.Asp106dup	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	51	15	0.294118	NM_052855	Q96E32	In_Frame_Ins	INS	ENST00000285243.6	37	CCDS11572.1																																																																																			-|0.957;TCA|0.043	0.043	strong		0.406	ANKRD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368201.2	NM_052855	
C11orf16	56673	hgsc.bcm.edu	37	11	8942889	8942890	+	Frame_Shift_Del	DEL	AT	AT	-	rs398102297|rs10583719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:8942889_8942890delAT	ENST00000326053.5	-	6	1483_1484	c.1377_1378delAT	c.(1375-1380)atatgtfs	p.IC459fs	C11orf16_ENST00000525780.1_Intron	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	459										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)		TTCCACTGACATATTGCAAGGC	0.54														164	0.0327476	0.1135	0.0173	5008	,	,		18882	0.0		0.002	False		,,,				2504	0.0				p.460_460del		Pindel,Atlas-Indel	.											.	C11orf16	43	.	0			c.1378_1379del						PASS	.			445,3819		22,401,1709						-1.1	0.0		dbSNP_119	130	6,8248		0,6,4121	no	frameshift	C11orf16	NM_020643.2		22,407,5830	A1A1,A1R,RR		0.0727,10.4362,3.6028				451,12067				SO:0001589	frameshift_variant	56673	exon6			.	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.1377_1378delAT	11.37:g.8942891_8942892delAT	ENSP00000318999:p.Ile459fs	Somatic	174	.	.		WXS	Illumina HiSeq	Phase_I	179	52	0.291	NM_020643	Q53FB2|Q8N6Y9	Frame_Shift_Del	DEL	ENST00000326053.5	37	CCDS7794.1																																																																																			AT|0.978;-|0.022	0.022	strong		0.540	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643	
ATXN1	6310	hgsc.bcm.edu	37	6	16327915	16327916	+	In_Frame_Ins	INS	-	-	TGC	rs11969612|rs369629396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:16327915_16327916insTGC	ENST00000244769.4	-	8	1562_1563	c.626_627insGCA	c.(625-627)cat>caGCAt	p.208_209insQ	ATXN1_ENST00000436367.1_In_Frame_Ins_p.208_209insQ	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	208	Poly-Gln.		H -> Q (in dbSNP:rs11969612).		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.H209delH(2)|p.H209_H211delHQH(1)		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)				gctgatgctgatgctgctgctg	0.668																																					p.H209delinsQH		Pindel,Atlas-Indel	.											ATXN1,colon,carcinoma,0,1	ATXN1	117	1	3	Deletion - In frame(3)	upper_aerodigestive_tract(1)|large_intestine(1)|prostate(1)	c.627_628insGCA						PASS	.																																			SO:0001652	inframe_insertion	6310	exon7			.	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.624_626dupGCA	6.37:g.16327922_16327924dupTGC	ENSP00000244769:p.Gln209_Gln210dup	Somatic	69	.	.		WXS	Illumina HiSeq	Phase_I	68	14	0.206	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	In_Frame_Ins	INS	ENST00000244769.4	37	CCDS34342.1																																																																																			.	.	weak		0.668	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
CHD1	1105	hgsc.bcm.edu	37	5	98192165	98192167	+	In_Frame_Del	DEL	AGG	AGG	-	rs398102328|rs79267787|rs138635992|rs61749618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:98192165_98192167delAGG	ENST00000284049.3	-	35	5199_5201	c.5050_5052delCCT	c.(5050-5052)cctdel	p.P1684del		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1684					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)	p.P1684delP(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TGGAGCCATAAGGAGATCTCTGA	0.453														1065	0.21266	0.3411	0.2262	5008	,	,		18993	0.0427		0.2763	False		,,,				2504	0.1391				p.1684_1685del		Pindel,Atlas-Indel	.											.	CHD1	137	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.5051_5053del						PASS	.			1429,2837		256,917,960						5.8	1.0		dbSNP_130	90	2258,5994		309,1640,2177	no	coding	CHD1	NM_001270.2		565,2557,3137	A1A1,A1R,RR		27.3631,33.4974,29.4536				3687,8831				SO:0001651	inframe_deletion	1105	exon35			.	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.5050_5052delCCT	5.37:g.98192165_98192167delAGG	ENSP00000284049:p.Pro1684del	Somatic	231	.	.		WXS	Illumina HiSeq	Phase_I	231	113	0.489	NM_001270	Q17RZ3	In_Frame_Del	DEL	ENST00000284049.3	37	CCDS34204.1																																																																																			AGG|0.775;-|0.225	0.225	strong		0.453	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
TLDC1	57707	hgsc.bcm.edu	37	16	84529358	84529360	+	In_Frame_Del	DEL	CTC	CTC	-	rs200260198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84529358_84529360delCTC	ENST00000343629.6	-	3	495_497	c.313_315delGAG	c.(313-315)gagdel	p.E105del	TLDC1_ENST00000561807.1_5'UTR|TLDC1_ENST00000535580.1_In_Frame_Del_p.E78del|RP11-517C16.4_ENST00000568771.1_RNA	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	105						lysosomal membrane (GO:0005765)											TGAGACTCTTCTCCTCGGAGTTT	0.542														32	0.00638978	0.0219	0.0029	5008	,	,		19194	0.0		0.001	False		,,,				2504	0.0				p.105_106del		Pindel,Atlas-Indel	.											.	KIAA1609	39	.	0			c.314_316del						PASS	.			120,4144		5,110,2017						4.2	0.9			119	32,8222		12,8,4107	no	coding	KIAA1609	NM_020947.3		17,118,6124	A1A1,A1R,RR		0.3877,2.8143,1.2143				152,12366				SO:0001651	inframe_deletion	57707	exon3			.	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"""TLD domain containing 1"""		"""KIAA1609"""	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.313_315delGAG	16.37:g.84529361_84529363delCTC	ENSP00000343635:p.Glu105del	Somatic	226	.	.		WXS	Illumina HiSeq	Phase_I	184	53	0.288	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	In_Frame_Del	DEL	ENST00000343629.6	37	CCDS32498.1																																																																																			CTC|0.994;-|0.006	0.006	strong		0.542	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947	
SLC39A14	23516	hgsc.bcm.edu	37	8	22262229	22262234	+	In_Frame_Del	DEL	GCTGCT	GCTGCT	-	rs145380823|rs111662782|rs3052256|rs150063686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCTGCT	GCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22262229_22262234delGCTGCT	ENST00000381237.1	+	2	125_130	c.6_11delGCTGCT	c.(4-12)aagctgctg>aag	p.LL5del	SLC39A14_ENST00000359741.5_In_Frame_Del_p.LL5del|SLC39A14_ENST00000289952.5_In_Frame_Del_p.LL5del|SLC39A14_ENST00000240095.6_In_Frame_Del_p.LL5del	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	5					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		TCACCATGAAGCTGCTGCTGCTGCAC	0.617														1591	0.317692	0.6929	0.1571	5008	,	,		16427	0.1806		0.2078	False		,,,				2504	0.1789				p.2_4del		Pindel,Atlas-Indel	.											.	SLC39A14	59	.	0			c.5_10del						PASS	.		,,,	2454,1772		745,964,404					,,,	3.4	1.0		dbSNP_132	80	1420,6814		142,1136,2839	no	coding,coding,coding,coding	SLC39A14	NM_015359.4,NM_001135154.1,NM_001135153.1,NM_001128431.2	,,,	887,2100,3243	A1A1,A1R,RR		17.2456,41.9309,31.0915	,,,	,,,		3874,8586				SO:0001651	inframe_deletion	23516	exon2			.	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"""Solute carriers"""	20858	protein-coding gene	gene with protein product		608736	"""solute carrier family 39 (metal ion transporter), member 14"""			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.6_11delGCTGCT	8.37:g.22262235_22262240delGCTGCT	ENSP00000370635:p.Leu5_Leu6del	Somatic	165	.	.		WXS	Illumina HiSeq	Phase_I	91	62	0.681	NM_001135154	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	In_Frame_Del	DEL	ENST00000381237.1	37	CCDS47823.1																																																																																			GCTGCT|0.701;-|0.299	0.299	strong		0.617	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677	
HCG9	10255	hgsc.bcm.edu	37	6	29943255	29943259	+	lincRNA	DEL	GGGCT	GGGCT	-	rs150979551|rs200099079|rs367615224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGGCT	GGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29943255_29943259delGGGCT	ENST00000376800.3	+	0	367_371									HLA complex group 9 (non-protein coding)																		GACTTCAGAAGGGCTGGTTTGTCCG	0.61														1167	0.233027	0.3396	0.2637	5008	,	,		18155	0.1478		0.164	False		,,,				2504	0.226				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																					10255	.			.	AB088085		6p21.3	2012-10-16	2011-04-11		ENSG00000204625	ENSG00000204625		"""Long non-coding RNAs"""	21243	non-coding RNA	RNA, long non-coding		615797	"""HLA complex group 9"""			10727083, 10557312	Standard	NR_028032		Approved	PERB11, HCGIX, HCGIX4, HCGIX-4	uc003rth.3		OTTHUMG00000031119		6.37:g.29943255_29943259delGGGCT		Somatic	175	.	.		WXS	Illumina HiSeq	Phase_I	125	26	0.208	.		RNA	DEL	ENST00000376800.3	37																																																																																				GGGCT|0.787;-|0.213	0.213	strong		0.610	HCG9-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000076199.4	NR_028032	
PACS2	23241	hgsc.bcm.edu	37	14	105848398	105848398	+	Intron	DEL	G	G	-	rs112632153		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105848398delG	ENST00000325438.8	+	13	1905				PACS2_ENST00000551743.1_5'Flank|PACS2_ENST00000547217.1_Intron|PACS2_ENST00000458164.2_Intron|PACS2_ENST00000430725.2_Intron|PACS2_ENST00000447393.1_Intron			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2						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)		AGCTGCAGGTGGGGGTGGAGG	0.692																																					.		Pindel,Atlas-Indel	.											.	PACS2	75	.	0			c.1413+2G>-						PASS	.		,	1305,2627		331,643,992	6.0	8.0	7.0		,	-6.9	0.0	14	dbSNP_132	8	9,7675		2,5,3835	no	intron,intron	PACS2	NM_015197.3,NM_001100913.2	,	333,648,4827	A1A1,A1R,RR		0.1171,33.1892,11.312	,	,	105848398	1314,10302	1897	4089	5986	SO:0001627	intron_variant	23241	exon13			.	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.1401+15G>-	14.37:g.105848398delG		Somatic	40	.	.		WXS	Illumina HiSeq	Phase_I	39	14	0.359	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Splice_Site	DEL	ENST00000325438.8	37	CCDS32168.1																																																																																			G|0.920;-|0.080	0.080	strong		0.692	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355	
OR6P1	128366	hgsc.bcm.edu	37	1	158533298	158533299	+	Frame_Shift_Ins	INS	-	-	A	rs201077183		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158533298_158533299insA	ENST00000334632.1	-	1	95_96	c.96_97insT	c.(94-99)tttgcafs	p.A33fs		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(4)|lung(1)	6						AGGTAAATTGCAAAAAAAAGGA	0.47																																					p.A33fs		Pindel,Atlas-Indel	.											.	OR6P1	47	.	0			c.97_98insT						PASS	.																																			SO:0001589	frameshift_variant	128366	exon1			.	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.97dupT	1.37:g.158533306_158533306dupA	ENSP00000334721:p.Ala33fs	Somatic	94	.	.		WXS	Illumina HiSeq	Phase_I	95	28	0.295	NM_001160325	Q6IFR9	Frame_Shift_Ins	INS	ENST00000334632.1	37	CCDS53391.1																																																																																			-|0.995;A|0.005	0.005	strong		0.470	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
BORA	79866	hgsc.bcm.edu	37	13	73317740	73317741	+	Splice_Site	INS	-	-	GTGA	rs71664409|rs10648315|rs370727431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:73317740_73317741insGTGA	ENST00000390667.5	+	6	551	c.454_454insGTGA	c.(454-456)gct>GTGAgct	p.A152fs	BORA_ENST00000464754.1_3'UTR|BORA_ENST00000377815.3_Splice_Site_p.A82fs	NM_024808.2	NP_079084.2	Q6PGQ7	BORA_HUMAN	bora, aurora kinase A activator	152					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of mitosis (GO:0007088)|regulation of mitotic spindle organization (GO:0060236)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)	protein kinase binding (GO:0019901)										GAAAAGCGATGGTGAGTATGAA	0.337														680	0.135783	0.4062	0.0418	5008	,	,		13893	0.0238		0.0109	False		,,,				2504	0.0808				p.A152fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.454_455insGTGA						PASS	.			1176,2370		209,758,806						5.7	1.0		dbSNP_119	62	77,7741		0,77,3832	no	frameshift-near-splice	BORA	NM_024808.2		209,835,4638	A1A1,A1R,RR		0.9849,33.1641,11.026				1253,10111				SO:0001630	splice_region_variant	79866	exon6			.	BC025367	CCDS9446.1, CCDS66560.1, CCDS9446.2, CCDS73583.1	13q22.1	2013-08-13	2011-08-09	2011-08-09	ENSG00000136122	ENSG00000136122			24724	protein-coding gene	gene with protein product		610510	"""chromosome 13 open reading frame 34"""	C13orf34		16890155, 18378770, 18566290, 19487276	Standard	NM_001286746		Approved	FLJ22624	uc001viv.1	Q6PGQ7	OTTHUMG00000017068	ENST00000390667.5:c.454+1->GTGA	13.37:g.73317741_73317744dupGTGA		Somatic	217	.	.		WXS	Illumina HiSeq	Phase_I	205	58	0.283	NM_024808	B4DQ30|Q5W0P3|Q5W0P4|Q86YC6|Q96IW9|Q9H640	Frame_Shift_Ins	INS	ENST00000390667.5	37	CCDS9446.1																																																																																			.	.	strong		0.337	BORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045245.3	NM_024808	Frame_Shift_Ins
FAM83G	644815	hgsc.bcm.edu	37	17	18874685	18874686	+	In_Frame_Ins	INS	-	-	GGT	rs3071666|rs75294421|rs538676818|rs36060906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18874685_18874686insGGT	ENST00000388995.6	-	6	2681_2682	c.2458_2459insACC	c.(2458-2460)cgc>cACCgc	p.819_820insH	SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000317977.6_Intron|FAM83G_ENST00000585154.2_In_Frame_Ins_p.819_820insH|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000345041.4_In_Frame_Ins_p.819_820insH			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	819					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						GGGGTCTTTGCGGTCCCGGGGG	0.634														3264	0.651757	0.674	0.6801	5008	,	,		17224	0.6349		0.5865	False		,,,				2504	0.6861				p.R820delinsHR		Pindel,Atlas-Indel	.											.	FAM83G	51	.	0			c.2459_2460insACC						PASS	.		,,	2729,1459		927,875,292					,,	-11.1	0.0		dbSNP_102	49	4619,3535		1344,1931,802	no	intron,intron,coding	SLC5A10,FAM83G	NM_152351.3,NM_001042450.1,NM_001039999.2	,,	2271,2806,1094	A1A1,A1R,RR		43.353,34.8376,40.4635	,,	,,		7348,4994				SO:0001652	inframe_insertion	644815	exon6			.	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.2456_2458dupACC	17.37:g.18874686_18874688dupGGT	ENSP00000373647:p.Asp819_Arg820insHis	Somatic	74	.	.		WXS	Illumina HiSeq	Phase_I	47	33	0.702	NM_001039999	Q3KQZ4|Q6ZW60	In_Frame_Ins	INS	ENST00000388995.6	37	CCDS42276.1																																																																																			-|0.250;GGT|0.750	0.750	strong		0.634	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
FOXD4L3	286380	hgsc.bcm.edu	37	9	70919085	70919085	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:70919085delC	ENST00000342833.2	+	1	1810	c.1218delC	c.(1216-1218)tgcfs	p.C406fs		NM_199135.4	NP_954586.4	Q6VB84	FX4L3_HUMAN	forkhead box D4-like 3	406						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			ovary(1)	1				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		GGGCGCGGTGCTGGGCGGGCA	0.677																																					p.C406fs		Atlas-Indel	.											.	FOXD4L3	7	.	0			c.1217delG						PASS	.						2.0	3.0	2.0					9																	70919085		917	2379	3296	SO:0001589	frameshift_variant	286380	exon1			.	AY344642	CCDS43833.1	9q13	2008-05-13				ENSG00000187559			18523	protein-coding gene	gene with protein product		611086				12421752	Standard	NM_199135		Approved	OTTHUMG00000019959, FOXD6	uc004agm.1	Q6VB84	OTTHUMG00000019959	ENST00000342833.2:c.1218delC	9.37:g.70919085delC	ENSP00000341961:p.Cys406fs	Somatic	668	0	0		WXS	Illumina HiSeq	Phase_I	931	76	0.0816327	NM_199135	Q5JTX9	Frame_Shift_Del	DEL	ENST00000342833.2	37	CCDS43833.1																																																																																			.	.	none		0.677	FOXD4L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052539.2	NM_199358	
KANK3	256949	hgsc.bcm.edu	37	19	8389893	8389895	+	In_Frame_Del	DEL	TCC	TCC	-	rs367746100|rs111905975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8389893_8389895delTCC	ENST00000593649.1	-	8	2087_2089	c.2022_2024delGGA	c.(2020-2025)gaggac>gac	p.E674del	KANK3_ENST00000330915.3_In_Frame_Del_p.E674del			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	674										breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						CACAGCCATGTCCTCCTCTTCCT	0.626														770	0.153754	0.2958	0.1383	5008	,	,		19550	0.0655		0.1223	False		,,,				2504	0.0961				p.675_675del		Pindel,Atlas-Indel	.											.	KANK3	35	.	0			c.2023_2025del						PASS	.			1092,3172		142,808,1182						3.3	1.0		dbSNP_132	62	1089,7165		100,889,3138	no	coding	KANK3	NM_198471.2		242,1697,4320	A1A1,A1R,RR		13.1936,25.6098,17.4229				2181,10337				SO:0001651	inframe_deletion	256949	exon8			.	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.2022_2024delGGA	19.37:g.8389896_8389898delTCC	ENSP00000470728:p.Glu674del	Somatic	85	.	.		WXS	Illumina HiSeq	Phase_I	88	30	0.341	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	In_Frame_Del	DEL	ENST00000593649.1	37																																																																																				TCC|0.852;-|0.148	0.148	strong		0.626	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471	
PODXL2	50512	hgsc.bcm.edu	37	3	127379364	127379369	+	In_Frame_Del	DEL	GAAGAG	GAAGAG	-	rs200281996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAAGAG	GAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127379364_127379369delGAAGAG	ENST00000342480.6	+	3	532_537	c.493_498delGAAGAG	c.(493-498)gaagagdel	p.EE171del		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	171	Glu-rich.				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						agaggaggaagaagaggaagaggaag	0.553														37	0.00738818	0.0212	0.0014	5008	,	,		22508	0.005		0.0	False		,,,				2504	0.0031				p.164_166del		Pindel,Atlas-Indel	.											.	PODXL2	53	.	0			c.492_497del						PASS	.			61,4203		1,59,2072						-4.8	0.4			53	3,8251		1,1,4125	no	coding	PODXL2	NM_015720.2		2,60,6197	A1A1,A1R,RR		0.0363,1.4306,0.5113				64,12454				SO:0001651	inframe_deletion	50512	exon3			.	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.493_498delGAAGAG	3.37:g.127379370_127379375delGAAGAG	ENSP00000345359:p.Glu171_Glu172del	Somatic	95	.	.		WXS	Illumina HiSeq	Phase_I	79	29	0.367	NM_015720	Q6UVY4|Q8WUV6	In_Frame_Del	DEL	ENST00000342480.6	37	CCDS3044.1																																																																																			GAAGAG|0.992;-|0.008	0.008	strong		0.553	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720	
HRC	3270	hgsc.bcm.edu	37	19	49657594	49657595	+	In_Frame_Ins	INS	-	-	TTCTTCTTT	rs372033596		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657594_49657595insTTCTTCTTT	ENST00000252825.4	-	1	1086_1087	c.900_901insAAAGAAGAA	c.(898-903)catgaa>catAAAGAAGAAgaa	p.300_301HE>HKEEE	HRC_ENST00000595625.1_In_Frame_Ins_p.300_301HE>HKEEE	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	300	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		TCATCTTCTTCATGGCTTCGGT	0.545																																					p.E301delinsKEEE	Melanoma(37;75 1097 24567 25669 30645)	Atlas-Indel	.											.	HRC	85	.	0			c.901_902insAAAGAAGAA						PASS	.																																			SO:0001652	inframe_insertion	3270	exon1			.		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.900_901insAAAGAAGAA	19.37:g.49657594_49657595insTTCTTCTTT	ENSP00000252825:p.His300_Glu301insLysGluGlu	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	213	28	0.131455	NM_002152	Q504Y6	In_Frame_Ins	INS	ENST00000252825.4	37	CCDS12759.1																																																																																			.	.	none		0.545	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
C14orf23	387978	hgsc.bcm.edu	37	14	29261307	29261308	+	Frame_Shift_Ins	INS	-	-	C	rs56363493|rs34203558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:29261307_29261308insC	ENST00000399387.4	+	3	448_449	c.344_345insC	c.(343-348)aaaaaafs	p.K115fs	C14orf23_ENST00000550266.1_Intron|C14orf23_ENST00000548213.1_Intron					chromosome 14 open reading frame 23											central_nervous_system(1)	1						TCAGCACTAAAAAAAACAAACA	0.381																																					.		Atlas-Indel	.											.	C14orf23	5	.	0			.						PASS	.																																			SO:0001589	frameshift_variant	387978	.			.			14q11.2	2013-01-15			ENSG00000186960	ENSG00000186960			19828	other	unknown							Standard	NR_026731		Approved		uc001wqf.3	Q86U37	OTTHUMG00000029410	Exception_encountered	14.37:g.29261307_29261308insC	ENSP00000382318:p.Lys115fs	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	93	32	0.344086	.		RNA	INS	ENST00000399387.4	37																																																																																				-|0.736;C|0.264	0.264	strong		0.381	C14orf23-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000134019.2	NR_026731	
OR2T27	403239	hgsc.bcm.edu	37	1	248813309	248813310	+	Frame_Shift_Ins	INS	-	-	A	rs141113411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813309_248813310insA	ENST00000344889.3	-	1	875_876	c.876_877insT	c.(874-879)cttaggfs	p.R293fs		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCTTGTTCCTAAGGCTGTAAA	0.485													AA|AA|AAA|insertion	231	0.0461262	0.1664	0.013	5008	,	,		19512	0.0		0.0	False		,,,				2504	0.002				p.R293_N294delinsX		Atlas-Indel	.											.	OR2T27	52	.	0			c.877_878insT						PASS	.			510,3700		101,308,1696						0.7	0.2		dbSNP_134	74	5,8185		0,5,4090	no	frameshift	OR2T27	NM_001001824.1		101,313,5786	A1A1,A1R,RR		0.0611,12.114,4.1532				515,11885				SO:0001589	frameshift_variant	403239	exon1			.		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.877dupT	1.37:g.248813311_248813311dupA	ENSP00000342008:p.Arg293fs	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	251	39	0.155378	NM_001001824		Frame_Shift_Ins	INS	ENST00000344889.3	37	CCDS31124.1																																																																																			-|0.960;A|0.040	0.040	strong		0.485	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
CIC	23152	hgsc.bcm.edu	37	19	42794829	42794831	+	In_Frame_Del	DEL	AAG	AAG	-	rs587778196		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42794829_42794831delAAG	ENST00000575354.2	+	10	1949_1951	c.1909_1911delAAG	c.(1909-1911)aagdel	p.K637del	CIC_ENST00000572681.2_In_Frame_Del_p.K1546del|CIC_ENST00000160740.3_In_Frame_Del_p.K637del	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	637	Pro-rich.				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)				GCCCCCAAACAAGGAGGAGCAAG	0.695			"""Mis, F, S"""		oligodendroglioma																																p.636_637del		Pindel,Atlas-Indel	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.1908_1910del						PASS	.																																			SO:0001651	inframe_deletion	23152	exon10			.	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.1909_1911delAAG	19.37:g.42794829_42794831delAAG	ENSP00000458663:p.Lys637del	Somatic	87	.	.		WXS	Illumina HiSeq	Phase_I	107	33	0.308	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	In_Frame_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																			.	.	none		0.695	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2		
SMPD2	6610	hgsc.bcm.edu	37	6	109764875	109764877	+	In_Frame_Del	DEL	GGA	GGA	-	rs142982624|rs370460899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:109764875_109764877delGGA	ENST00000258052.3	+	10	1398_1400	c.1039_1041delGGA	c.(1039-1041)ggadel	p.G349del	PPIL6_ENST00000440797.2_5'Flank|PPIL6_ENST00000521072.2_5'Flank|PPIL6_ENST00000424445.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	349					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)		CCTGGCGGCTGGAGGAGGGGCCG	0.635														223	0.0445288	0.1573	0.0159	5008	,	,		16679	0.0		0.004	False		,,,				2504	0.0				p.346_347del		Pindel,Atlas-Indel	.											.	SMPD2	25	.	0			c.1038_1040del						PASS	.			602,3662		46,510,1576						-8.7	0.0		dbSNP_134	49	14,8240		3,8,4116	no	coding	SMPD2	NM_003080.2		49,518,5692	A1A1,A1R,RR		0.1696,14.1182,4.9209				616,11902				SO:0001651	inframe_deletion	6610	exon10			.	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.1039_1041delGGA	6.37:g.109764878_109764880delGGA	ENSP00000258052:p.Gly349del	Somatic	123	.	.		WXS	Illumina HiSeq	Phase_I	102	34	0.333	NM_003080	Q5TED1|Q9BWR3	In_Frame_Del	DEL	ENST00000258052.3	37	CCDS5075.1																																																																																			GGA|0.957;-|0.043	0.043	strong		0.635	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1		
OR2A14	135941	hgsc.bcm.edu	37	7	143826730	143826732	+	In_Frame_Del	DEL	CTT	CTT	-	rs66549240|rs34602346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	353	.	.		WXS	Illumina HiSeq	Phase_I	313	61	0.195	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		
NCOA3	8202	hgsc.bcm.edu	37	20	46279864	46279866	+	In_Frame_Del	DEL	CAA	CAA	-	rs578139784|rs112826888|rs1132443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:46279864_46279866delCAA	ENST00000371998.3	+	20	3981_3983	c.3790_3792delCAA	c.(3790-3792)caadel	p.Q1276del	NCOA3_ENST00000372004.3_In_Frame_Del_p.Q1272del|NCOA3_ENST00000371997.3_In_Frame_Del_p.Q1267del|NCOA3_ENST00000341724.6_In_Frame_Del_p.Q1202del			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)			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						gcagcagcagcaacagcaacagc	0.567														844	0.16853	0.3699	0.098	5008	,	,		14322	0.0952		0.0795	False		,,,				2504	0.1135				p.1263_1264del		Pindel,Atlas-Indel	.											NCOA3,colon,carcinoma,0,1	NCOA3	156	1	0			c.3789_3791del						PASS	.																																			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.3790_3792delCAA	20.37:g.46279864_46279866delCAA	ENSP00000361066:p.Gln1276del	Somatic	97	.	.		WXS	Illumina HiSeq	Phase_I	106	16	0.151	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	In_Frame_Del	DEL	ENST00000371998.3	37	CCDS13407.1																																																																																			.	.	weak		0.567	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
MPRIP	23164	hgsc.bcm.edu	37	17	17075181	17075181	+	Splice_Site	DEL	T	T	-	rs3215213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17075181delT	ENST00000341712.4	+	16	2311		c.e16+2		RP11-45M22.3_ENST00000584203.1_RNA|MPRIP_ENST00000395804.3_Splice_Site|MPRIP_ENST00000444976.1_Splice_Site|MPRIP_ENST00000395811.5_Splice_Site|RNU6-767P_ENST00000384132.1_RNA			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CCATCTCAGGTTGGGGGGTGG	0.552													T|TT|T|insertion	1097	0.21905	0.3071	0.1542	5008	,	,		16246	0.2808		0.0626	False		,,,				2504	0.2434				.		Pindel,Atlas-Indel	.											.	MPRIP	87	.	0			c.2311+1T>-						PASS	.		,	1210,3054		169,872,1091	24.0	35.0	32.0		,	5.8	1.0	17	dbSNP_106	36	640,7614		35,570,3522	no	splice-5,splice-5	MPRIP	NM_201274.3,NM_015134.3	,	204,1442,4613	A1A1,A1R,RR		7.7538,28.3771,14.7787	,	,	17075181	1850,10668	2139	4282	6421	SO:0001630	splice_region_variant	23164	exon16			.	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"""Pleckstrin homology (PH) domain containing"""	30321	protein-coding gene	gene with protein product	"""Rho interacting protein 3"""	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.2311+2T>-	17.37:g.17075181delT		Somatic	79	.	.		WXS	Illumina HiSeq	Phase_I	89	36	0.404	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Splice_Site	DEL	ENST00000341712.4	37	CCDS32578.1																																																																																			T|0.807;-|0.193	0.193	strong		0.552	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	Intron
USP34	9736	hgsc.bcm.edu	37	2	61575022	61575023	+	In_Frame_Ins	INS	-	-	TGG			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61575022_61575023insTGG	ENST00000398571.2	-	15	2343_2344	c.2267_2268insCCA	c.(2266-2268)cat>caCCAt	p.756_756H>HH		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	756					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)			ggtggtggtgatggtggtggtg	0.386																																					p.H756delinsHH		Pindel,Atlas-Indel	.											.	USP34	334	.	0			c.2268_2269insCCA						PASS	.																																			SO:0001652	inframe_insertion	9736	exon15			.	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.2265_2267dupCCA	2.37:g.61575029_61575031dupTGG	ENSP00000381577:p.His760dup	Somatic	41	.	.		WXS	Illumina HiSeq	Phase_I	54	17	0.315	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	In_Frame_Ins	INS	ENST00000398571.2	37	CCDS42686.1																																																																																			.	.	none		0.386	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
DMXL1	1657	hgsc.bcm.edu	37	5	118529595	118529597	+	In_Frame_Del	DEL	AAT	AAT	-	rs200335120|rs374810198|rs146526208|rs150940354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118529595_118529597delAAT	ENST00000311085.8	+	30	7467_7469	c.7387_7389delAAT	c.(7387-7389)aatdel	p.N2463del	DMXL1_ENST00000539542.1_In_Frame_Del_p.N2463del	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2463	Poly-Asp.									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)		tgatgatgacaatgatgatgatg	0.315														32	0.00638978	0.0234	0.0014	5008	,	,		16171	0.0		0.0	False		,,,				2504	0.0				p.2462_2463del		Pindel,Atlas-Indel	.											.	DMXL1	268	.	0			c.7386_7388del						PASS	.			93,4171		1,91,2040						-10.3	0.2			98	1,8253		0,1,4126	no	coding	DMXL1	NM_005509.4		1,92,6166	A1A1,A1R,RR		0.0121,2.1811,0.7509				94,12424				SO:0001651	inframe_deletion	1657	exon30			.	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.7387_7389delAAT	5.37:g.118529595_118529597delAAT	ENSP00000309690:p.Asn2463del	Somatic	52	.	.		WXS	Illumina HiSeq	Phase_I	55	10	0.182	NM_005509		In_Frame_Del	DEL	ENST00000311085.8	37	CCDS4125.1																																																																																			.	.	weak		0.315	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
BMP15	9210	hgsc.bcm.edu	37	X	50659210	50659211	+	In_Frame_Ins	INS	-	-	TCT	rs531409392|rs371124071|rs111889793		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:50659210_50659211insTCT	ENST00000252677.3	+	2	782_783	c.782_783insTCT	c.(781-786)tctctt>tcTCTtctt	p.263_264insL		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	263			L -> LL (no or minor deleterious effect detected). {ECO:0000269|PubMed:16464940, ECO:0000269|PubMed:16508750, ECO:0000269|PubMed:16645022, ECO:0000269|PubMed:19263482}.		female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					GAAAGGGAATCTCTTCTCCGGA	0.465														696	0.184371	0.3918	0.0591	3775	,	,		13145	0.0605		0.003	False		,,,				2504	0.0746				p.S261delinsSL		Pindel,Atlas-Indel	.											.	BMP15	62	.	0			c.782_783insTCT						PASS	.			1671,2050		330,777,234,485,303						2.3	0.0		dbSNP_132	65	35,6448		0,30,5,2327,1764	no	coding	BMP15	NM_005448.2		330,807,239,2812,2067	A1A1,A1R,A1,RR,R		0.5399,44.9073,16.7189				1706,8498				SO:0001652	inframe_insertion	9210	exon2			.	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"""Bone morphogenetic proteins"""	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.786_788dupTCT	X.37:g.50659214_50659216dupTCT	ENSP00000252677:p.Leu263_Leu263dup	Somatic	221	.	.		WXS	Illumina HiSeq	Phase_I	247	83	0.336	NM_005448	Q17RM6|Q5JST1|Q9UMS1	In_Frame_Ins	INS	ENST00000252677.3	37	CCDS14334.1																																																																																			.	.	none		0.465	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448	
FOXD4L6	653404	hgsc.bcm.edu	37	9	69200395	69200395	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:69200395delG	ENST00000377473.1	-	1	1809	c.1218delC	c.(1216-1218)tgcfs	p.C406fs		NM_001085476.1	NP_001078945.1	Q3SYB3	FX4L6_HUMAN	forkhead box D4-like 6	406					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGCCCGCCCAGCACCGCGCCC	0.677																																					p.W407fs		Atlas-Indel	.											.	.	.	.	0			c.1219delT						PASS	.						1.0	2.0	2.0					9																	69200395		633	1796	2429	SO:0001589	frameshift_variant	653404	exon1			.		CCDS43826.1	9q12	2014-05-06			ENSG00000204793	ENSG00000273514			31986	protein-coding gene	gene with protein product							Standard	NM_001085476		Approved	OTTHUMG00000066822	uc004afi.2	Q3SYB3	OTTHUMG00000188618	ENST00000377473.1:c.1218delC	9.37:g.69200395delG	ENSP00000366693:p.Cys406fs	Somatic	643	0	0		WXS	Illumina HiSeq	Phase_I	1099	96	0.0873521	NM_001085476	B2RPC4|Q4V336	Frame_Shift_Del	DEL	ENST00000377473.1	37	CCDS43826.1																																																																																			.	.	none		0.677	FOXD4L6-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143174.1	NM_001085476	
ZNF107	51427	hgsc.bcm.edu	37	7	64169019	64169020	+	Frame_Shift_Ins	INS	-	-	AA	rs201020174|rs376059343|rs4717205|rs77413930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:64169019_64169020insAA	ENST00000395391.1	+	4	3712_3713	c.2337_2338insAA	c.(2338-2340)tatfs	p.Y780fs	ZNF107_ENST00000423627.1_Frame_Shift_Ins_p.Y780fs|ZNF107_ENST00000344930.3_Frame_Shift_Ins_p.Y780fs			Q9UII5	ZN107_HUMAN	zinc finger protein 107	780					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				ACAAATGTGAGTATGGCAAAAC	0.351																																					p.E779fs		Atlas-Indel	.											.	ZNF107	107	.	0			c.2337_2338insAA						PASS	.		,	1052,3200		165,722,1239					,	0.4	0.0			28	80,8168		0,80,4044	no	frameshift,frameshift	ZNF107	NM_016220.3,NM_001013746.1	,	165,802,5283	A1A1,A1R,RR		0.9699,24.7413,9.056	,	,		1132,11368				SO:0001589	frameshift_variant	51427	exon7			.	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"""Zinc fingers, C2H2-type"""	12887	protein-coding gene	gene with protein product		603989	"""zinc finger protein 588"", ""zinc finger protein 107 (Y8)"""	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		Exception_encountered	7.37:g.64169019_64169020insAA	ENSP00000378789:p.Tyr780fs	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	41	13	0.317073	NM_016220		Frame_Shift_Ins	INS	ENST00000395391.1	37	CCDS5527.1																																																																																			-|0.838;AA|0.162	0.162	strong		0.351	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220	
CFAP74	85452	hgsc.bcm.edu	37	1	1900106	1900107	+	IGR	INS	-	-	CTC	rs61233860|rs145742571|rs72634902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1900106_1900107insCTC								TMEM52 (49394 upstream) : C1orf222 (19455 downstream)																							ACTGTGGTCTTCTTGCAAAAGT	0.569														997	0.199081	0.1324	0.1945	5008	,	,		21168	0.3284		0.2376	False		,,,				2504	0.1196				p.K405delinsEK		Pindel,Atlas-Indel	.											.	KIAA1751	92	.	0			c.1213_1214insGAG						PASS	.			643,3311		79,485,1413						-3.9	0.0		dbSNP_129	188	1999,6033		265,1469,2282	no	coding	KIAA1751	NM_001080484.1		344,1954,3695	A1A1,A1R,RR		24.8879,16.262,22.0424				2642,9344				SO:0001628	intergenic_variant	85452	exon11			.																													1.37:g.1900106_1900107insCTC		Somatic	176	.	.		WXS	Illumina HiSeq	Phase_I	164	42	0.256	NM_001080484		In_Frame_Ins	INS		37																																																																																				.	.	strong	0	0.569								
HCG17	414778	hgsc.bcm.edu	37	6	30229034	30229035	+	lincRNA	INS	-	-	T	rs11393606|rs568184983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30229034_30229035insT	ENST00000453558.1	-	0	126				HLA-L_ENST00000463348.1_RNA					HLA complex group 17 (non-protein coding)																		TGAGGCCACCCTGAGGTGCTGG	0.599													T|T|TT|insertion	1991	0.397564	0.3003	0.4496	5008	,	,		19996	0.5308		0.2465	False		,,,				2504	0.5102				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.			1185,3073		160,865,1104						4.0	1.0		dbSNP_120	97	1988,6262		247,1494,2384	no	intergenic				407,2359,3488	A1A1,A1R,RR		24.097,27.83,25.3678				3173,9335						3139	.			.	AB023055		6p21	2012-11-02	2008-08-13		ENSG00000241701	ENSG00000270604		"""Long non-coding RNAs"""	31339	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 46"", ""long intergenic non-protein coding RNA 46"""						Standard	NR_052012		Approved	NCRNA00046, LINC00046	uc031snc.1		OTTHUMG00000031114		6.37:g.30229035_30229035dupT		Somatic	248	.	.		WXS	Illumina HiSeq	Phase_I	266	58	0.218	.		RNA	INS	ENST00000453558.1	37																																																																																				-|0.500;T|0.500	0.500	strong		0.599	HCG17-002	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000256054.1	NR_052012	
SLC22A25	387601	hgsc.bcm.edu	37	11	62996774	62996775	+	Frame_Shift_Ins	INS	-	-	A	rs112260121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62996774_62996775insA	ENST00000306494.6	-	1	349_350	c.350_351insT	c.(349-351)gtgfs	p.V117fs	SLC22A10_ENST00000535888.1_Intron|SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000525620.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						CCCAGCCATCCACACAGGGCTC	0.51													A|A|AA|insertion	42	0.00838658	0.0318	0.0	5008	,	,		19685	0.0		0.0	False		,,,				2504	0.0				p.V117fs		Pindel,Atlas-Indel	.											.	SLC22A25	87	.	0			c.351_352insT						PASS	.			104,4160		2,100,2030						1.9	1.0		dbSNP_132	130	4,8250		0,4,4123	yes	frameshift	SLC22A25	NM_199352.3		2,104,6153	A1A1,A1R,RR		0.0485,2.439,0.8628				108,12410				SO:0001589	frameshift_variant	387601	exon1			.	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.351dupT	11.37:g.62996775_62996775dupA	ENSP00000307443:p.Val117fs	Somatic	235	.	.		WXS	Illumina HiSeq	Phase_I	200	57	0.285	NM_199352		Frame_Shift_Ins	INS	ENST00000306494.6	37	CCDS31592.1																																																																																			-|0.990;A|0.010	0.010	strong		0.510	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
OR9K2	441639	hgsc.bcm.edu	37	12	55523587	55523587	+	Frame_Shift_Del	DEL	T	T	-	rs398102299|rs58036029|rs200050297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	131	.	.		WXS	Illumina HiSeq	Phase_I	104	40	0.385	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		
ADRM1	11047	hgsc.bcm.edu	37	20	60883770	60883778	+	In_Frame_Del	DEL	GACACGAAG	GACACGAAG	-	rs374034164		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GACACGAAG	GACACGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60883770_60883778delGACACGAAG	ENST00000253003.2	+	10	1223_1231	c.1177_1185delGACACGAAG	c.(1177-1185)gacacgaagdel	p.DTK393del	LAMA5_ENST00000492698.1_Intron|RP11-157P1.4_ENST00000414042.1_RNA	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	393	Interaction with UCHL5.				positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			GAAAGAGGGCGACACGAAGGACAAGAAGG	0.574																																					p.392_395del		Pindel,Atlas-Indel	.											.	ADRM1	28	.	0			c.1176_1184del						PASS	.		,	23,2,4215		0,0,23,0,2,2095					,	-0.2	0.8			134	185,0,8059		3,0,179,0,0,3940	no	codingComplex,codingComplex	ADRM1	NM_175573.1,NM_007002.2	,	3,0,202,0,2,6035	A1A1,A1A2,A1R,A2A2,A2R,RR		2.2441,0.5896,1.6822	,	,		208,2,12274				SO:0001651	inframe_deletion	11047	exon10			.	D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.1177_1185delGACACGAAG	20.37:g.60883770_60883778delGACACGAAG	ENSP00000253003:p.Asp393_Lys395del	Somatic	250	.	.		WXS	Illumina HiSeq	Phase_I	243	56	0.230	NM_007002	A0PKB1|Q96FJ7|Q9H1P2	In_Frame_Del	DEL	ENST00000253003.2	37	CCDS13496.1																																																																																			GACACGAAG|0.012;-|0.988	0.988	strong		0.574	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1		
KRTAP2-3	730755	hgsc.bcm.edu	37	17	39216302	39216303	+	Start_Codon_Ins	INS	-	-	G	rs201832186|rs369140188|rs369908545|rs370014641|rs113441706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39216302_39216303insG	ENST00000391418.2	-	0	41_42					NM_001165252.1	NP_001158724.1	P0C7H8	KRA23_HUMAN	keratin associated protein 2-3							keratin filament (GO:0045095)											GAGCCGGTCATGGTGGTGTCTG	0.634																																					p.M1fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1_2insC						PASS	.			720,2376		135,450,963						4.5	1.0		dbSNP_132	8	423,4813		81,261,2276	no	frameshift	LOC730755	NM_001165252.1		216,711,3239	A1A1,A1R,RR		8.0787,23.2558,13.7182				1143,7189				SO:0001582	initiator_codon_variant	730755	exon1			.	BC012486	CCDS54123.1	17q21.2	2012-08-03			ENSG00000212724	ENSG00000212724		"""Keratin associated proteins"""	18906	protein-coding gene	gene with protein product							Standard	NM_001165252		Approved	KAP2.3	uc002hvx.3	P0C7H8	OTTHUMG00000133655	ENST00000391418.2:c.2dupC	17.37:g.39216304_39216304dupG		Somatic	38	.	.		WXS	Illumina HiSeq	Phase_I	47	28	0.596	NM_001165252		Frame_Shift_Ins	INS	ENST00000391418.2	37	CCDS54123.1																																																																																			-|0.804;G|0.196	0.196	strong		0.634	KRTAP2-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257692.1	NM_001165252	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324139	39324140	+	In_Frame_Ins	INS	-	-	GCAGCAGGTGGTCTG	rs12603046		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324139_39324140insGCAGCAGGTGGTCTG	ENST00000391356.2	-	1	284_285	c.285_286insCAGACCACCTGCTGC	c.(283-288)tgcagg>tgcCAGACCACCTGCTGCagg	p.94_95insCQTTC		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	94	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				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	0.614																																					p.R96delinsQTTCCR		Atlas-Indel	.											.	KRTAP4-3	40	.	0			c.286_287insCAGACCACCTGCTGC						PASS	.			851,185,2620		113,2,623,8,167,915						-9.2	0.0			10	64,1597,6043		3,0,58,27,1543,2221	no	codingComplex	KRTAP4-3	NM_033187.1		116,2,681,35,1710,3136	A1A1,A1A2,A1R,A2A2,A2R,RR		21.5602,28.337,23.7412				915,1782,8663				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.285_286insCAGACCACCTGCTGC	17.37:g.39324139_39324140insGCAGCAGGTGGTCTG	ENSP00000375151:p.Cys94_Cys95insCysGlnThrThrCys	Somatic	427	0	0		WXS	Illumina HiSeq	Phase_I	287	159	0.554007	NM_033187		In_Frame_Ins	INS	ENST00000391356.2	37	CCDS42331.1																																																																																			.	.	none		0.614	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
HRC	3270	hgsc.bcm.edu	37	19	49657889	49657890	+	In_Frame_Ins	INS	-	-	TCCTCCTCC	rs369248456|rs57199624|rs147238387|rs551367394|rs542091249		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657889_49657890insTCCTCCTCC	ENST00000252825.4	-	1	791_792	c.605_606insGGAGGAGGA	c.(604-606)gaa>gaGGAGGAGGAa	p.202_202E>EEEE	HRC_ENST00000595625.1_In_Frame_Ins_p.202_202E>EEEE	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	202	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		AGGcctcctcttcctcctcctc	0.569																																					p.E202delinsEEEE	Melanoma(37;75 1097 24567 25669 30645)	Atlas-Indel	.											.	HRC	85	.	0			c.606_607insGGAGGAGGA						PASS	.																																			SO:0001652	inframe_insertion	3270	exon1			.		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.597_605dupGGAGGAGGA	19.37:g.49657890_49657898dupTCCTCCTCC	ENSP00000252825:p.GluGluGlu202dup	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	170	31	0.182353	NM_002152	Q504Y6	In_Frame_Ins	INS	ENST00000252825.4	37	CCDS12759.1																																																																																			.	.	alt		0.569	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
UGDH	7358	hgsc.bcm.edu	37	4	39515807	39515813	+	Intron	DEL	AAAAAGA	AAAAAGA	-	rs201039591|rs372782074|rs151116497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAAAAGA	AAAAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39515807_39515813delAAAAAGA	ENST00000316423.6	-	3	505				UGDH_ENST00000501493.2_Intron|UGDH_ENST00000506179.1_Intron|UGDH_ENST00000507089.1_Intron|UGDH_ENST00000515398.1_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	116	.	.		WXS	Illumina HiSeq	Phase_I	84	33	0.393	.	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	
ONECUT2	9480	hgsc.bcm.edu	37	18	55103476	55103477	+	In_Frame_Ins	INS	-	-	CAC			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:55103476_55103477insCAC	ENST00000491143.2	+	1	560_561	c.528_529insCAC	c.(529-531)cac>CACcac	p.177_177H>HH	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	177	Poly-His.				cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	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)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		accaccatccgcaccaccacca	0.658																																					p.P176delinsPH		Pindel,Atlas-Indel	.											.	ONECUT2	42	.	0			c.528_529insCAC						PASS	.																																			SO:0001652	inframe_insertion	9480	exon1			.	Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"""Homeoboxes / CUT class"""	8139	protein-coding gene	gene with protein product		604894	"""one cut domain, family member 2"""			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.550_552dupCAC	18.37:g.55103483_55103485dupCAC	ENSP00000419185:p.His184dup	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	66	11	0.167	NM_004852		In_Frame_Ins	INS	ENST00000491143.2	37	CCDS42440.1																																																																																			.	.	none		0.658	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3		
OSBPL1A	114876	hgsc.bcm.edu	37	18	21740032	21740033	+	IGR	DEL	TG	TG	-	rs149126027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:21740032_21740033delTG	ENST00000319481.3	-	0	4195				RP11-799B12.4_ENST00000583267.1_lincRNA|CABYR_ENST00000327201.6_3'UTR|CABYR_ENST00000581397.1_3'UTR|CABYR_ENST00000399496.3_3'UTR|CABYR_ENST00000399499.1_3'UTR|CABYR_ENST00000415309.2_3'UTR	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A						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)					AACTGAAAACTGGTAGGTACAC	0.406														131	0.0261581	0.0976	0.0029	5008	,	,		21848	0.0		0.0	False		,,,				2504	0.0				p.379_380del		Pindel,Atlas-Indel	.											.	CABYR	51	.	0			c.1137_1138del						PASS	.		,,,,,	310,3948		19,272,1838					,,,,,	2.1	1.0		dbSNP_134	57	0,8248		0,0,4124	no	frameshift-near-splice,frameshift-near-splice,utr-3,frameshift-near-splice,frameshift-near-splice,utr-3	CABYR	NM_153770.1,NM_153769.1,NM_153768.1,NM_138644.1,NM_138643.1,NM_012189.2	,,,,,	19,272,5962	A1A1,A1R,RR		0.0,7.2804,2.4788	,,,,,	,,,,,		310,12196				SO:0001628	intergenic_variant	26256	exon5			.	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		18.37:g.21740032_21740033delTG		Somatic	57	.	.		WXS	Illumina HiSeq	Phase_I	77	26	0.338	NM_153769	B7Z7D3|Q9BZF5|Q9NW87	Frame_Shift_Del	DEL	ENST00000319481.3	37	CCDS11884.1																																																																																			TG|0.978;-|0.022	0.022	strong		0.406	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597	
CFAP74	85452	hgsc.bcm.edu	37	1	1887112	1887112	+	IGR	DEL	C	C	-	rs3838975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	109	0	0		WXS	Illumina HiSeq	Phase_I	102	40	0.392157	NM_001080484		Frame_Shift_Del	DEL		37																																																																																				C|0.783;-|0.217	0.217	strong	0	0.667								
SERPINB3	6317	hgsc.bcm.edu	37	18	61323011	61323012	+	Frame_Shift_Ins	INS	-	-	GCCA	rs60533853|rs3180227|rs386804125|rs72132327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323011_61323012insGCCA	ENST00000283752.5	-	8	1195_1196	c.1052_1053insTGGC	c.(1051-1053)ggafs	p.G351fs	SERPINB3_ENST00000332821.8_Frame_Shift_Ins_p.G299fs|SERPINB11_ENST00000489748.1_RNA	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	351			G -> A (increased antiprotease activity and increased MAPK8 inhibition activity; dbSNP:rs3180227). {ECO:0000269|PubMed:12975381, ECO:0000269|PubMed:14970861, ECO:0000269|PubMed:21383048, ECO:0000269|Ref.6}.		negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						ATGATCCGAATCCTACTACAGC	0.49																																					p.G351fs		Atlas-Indel	.											.	SERPINB3	90	.	0			c.1053_1054insTGGC						PASS	.																																			SO:0001589	frameshift_variant	6317	exon8			.	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1052_1053insTGGC	18.37:g.61323011_61323012insGCCA	ENSP00000283752:p.Gly351fs	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	192	49	0.255208	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Frame_Shift_Ins	INS	ENST00000283752.5	37	CCDS11987.1																																																																																			.	.	alt		0.490	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
DUPD1	338599	hgsc.bcm.edu	37	10	76803600	76803602	+	In_Frame_Del	DEL	AGA	AGA	-	rs571550955|rs370448554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76803600_76803602delAGA	ENST00000338487.5	-	2	373_375	c.374_376delTCT	c.(373-378)ttctac>tac	p.F125del		NM_001003892.1	NP_001003892.1	Q68J44	DUPD1_HUMAN	dual specificity phosphatase and pro isomerase domain containing 1	125	Tyrosine-protein phosphatase.				protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(2)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					GCCGCCGGGTAGAAGAAGACACT	0.68														33	0.00658946	0.0219	0.0058	5008	,	,		9789	0.0		0.0	False		,,,				2504	0.0				p.125_126del		Pindel,Atlas-Indel	.											.	DUPD1	30	.	0			c.375_377del						PASS	.			103,4161		6,91,2035						2.5	0.2			84	42,8212		16,10,4101	no	coding	DUPD1	NM_001003892.1		22,101,6136	A1A1,A1R,RR		0.5088,2.4156,1.1583				145,12373				SO:0001651	inframe_deletion	338599	exon2			.		CCDS31223.1	10q22.3	2011-06-09			ENSG00000188716	ENSG00000188716		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	23481	protein-coding gene	gene with protein product							Standard	NM_001003892		Approved	DUSP27	uc001jwq.1	Q68J44	OTTHUMG00000018512	ENST00000338487.5:c.374_376delTCT	10.37:g.76803606_76803608delAGA	ENSP00000340609:p.Phe125del	Somatic	44	.	.		WXS	Illumina HiSeq	Phase_I	56	18	0.321	NM_001003892	B2RP93	In_Frame_Del	DEL	ENST00000338487.5	37	CCDS31223.1																																																																																			.	.	none		0.680	DUPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048777.2	XM_291741	
DEFB119	245932	hgsc.bcm.edu	37	20	29965208	29965211	+	Frame_Shift_Del	DEL	ACTG	ACTG	-	rs374993061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ACTG	ACTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:29965208_29965211delACTG	ENST00000376321.3	-	2	212_215	c.93_96delCAGT	c.(91-96)aacagtfs	p.NS31fs	DEFB119_ENST00000492344.1_5'UTR|DEFB119_ENST00000339144.3_3'UTR|SNORA40_ENST00000390832.1_RNA	NM_153289.3	NP_695021.2	Q8N690	DB119_HUMAN	defensin, beta 119	31					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				large_intestine(2)|lung(1)|prostate(1)	4	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			TACAAATTCCACTGTTACCCATGC	0.431														26	0.00519169	0.0182	0.0029	5008	,	,		21220	0.0		0.0	False		,,,				2504	0.0				p.32_33del		Pindel,Atlas-Indel	.											DEFB119_ENST00000376321,NS,malignant_melanoma,+1,2	DEFB119	37	2	0			c.94_97del						PASS	.		,	106,4154		3,100,2027					,	3.3	0.3			168	2,8248		0,2,4123	no	utr-3,frameshift	DEFB119	NM_173460.1,NM_153289.2	,	3,102,6150	A1A1,A1R,RR		0.0242,2.4883,0.8633	,	,		108,12402				SO:0001589	frameshift_variant	245932	exon2			.	AA939044	CCDS13178.1, CCDS33455.1	20q11.21	2007-02-19	2003-10-06		ENSG00000180483	ENSG00000180483		"""Defensins, beta"""	18099	protein-coding gene	gene with protein product			"""defensin, beta 120"""	DEFB120		11854508	Standard	NM_153289		Approved	DEFB-19, DEFB-20	uc002wvu.2	Q8N690	OTTHUMG00000032172	ENST00000376321.3:c.93_96delCAGT	20.37:g.29965208_29965211delACTG	ENSP00000365499:p.Asn31fs	Somatic	110	.	.		WXS	Illumina HiSeq	Phase_I	88	36	0.409	NM_153289	Q5GRG1|Q5JWP1|Q5TH42|Q8N689	Frame_Shift_Del	DEL	ENST00000376321.3	37	CCDS13178.1																																																																																			.	.	weak		0.431	DEFB119-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078514.1	NM_153289	
HABP2	3026	hgsc.bcm.edu	37	10	115348749	115348751	+	3'UTR	DEL	CTT	CTT	-	rs141729427|rs148467563|rs200486696|rs11575787|rs144589482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115348749_115348751delCTT	ENST00000351270.3	+	0	2400_2402				HABP2_ENST00000542051.1_3'UTR|NRAP_ENST00000369360.3_In_Frame_Del_p.K1699del|NRAP_ENST00000369358.4_In_Frame_Del_p.K1734del|NRAP_ENST00000359988.3_In_Frame_Del_p.K1726del|NRAP_ENST00000360478.3_In_Frame_Del_p.K1691del	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2						cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	ACAGCAGGGCCTTCTTCTTTTTG	0.537														34	0.00678914	0.025	0.0014	5008	,	,		16073	0.0		0.0	False		,,,				2504	0.0				p.1727_1728del		Pindel,Atlas-Indel	.											.	NRAP	208	.	0			c.5180_5182del						PASS	.		,,,	162,4102		7,148,1977					,,,	3.8	1.0		dbSNP_120	163	28,8226		11,6,4110	no	coding,coding,utr-3,utr-3	HABP2,NRAP	NM_198060.2,NM_006175.3,NM_004132.3,NM_001177660.1	,,,	18,154,6087	A1A1,A1R,RR		0.3392,3.7992,1.5178	,,,	,,,		190,12328				SO:0001624	3_prime_UTR_variant	4892	exon42			.		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	ENST00000351270.3:c.*623CTT>-	10.37:g.115348755_115348757delCTT		Somatic	144	.	.		WXS	Illumina HiSeq	Phase_I	187	61	0.326	NM_001261463	A8K467|B7Z8U5|F5H5M6|O00663	In_Frame_Del	DEL	ENST00000351270.3	37	CCDS7577.1																																																																																			CTT|0.992;-|0.008	0.008	strong		0.537	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
APOL1	8542	hgsc.bcm.edu	37	22	36662042	36662047	+	In_Frame_Del	DEL	ATAATT	ATAATT	-	rs143830837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ATAATT	ATAATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36662042_36662047delATAATT	ENST00000397278.3	+	6	1389_1394	c.1160_1165delATAATT	c.(1159-1167)aataattat>aat	p.NY388del	APOL1_ENST00000347595.7_In_Frame_Del_p.NY267del|APOL1_ENST00000319136.4_In_Frame_Del_p.NY404del|APOL1_ENST00000422706.1_In_Frame_Del_p.NY388del|APOL1_ENST00000426053.1_In_Frame_Del_p.NY370del|APOL1_ENST00000397279.4_In_Frame_Del_p.NY388del	NM_003661.3	NP_003652.2	O14791	APOL1_HUMAN	apolipoprotein L, 1	388					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cholesterol metabolic process (GO:0008203)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)|intrinsic component of membrane (GO:0031224)|very-low-density lipoprotein particle (GO:0034361)	chloride channel activity (GO:0005254)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	14						ATTCTCAACAATAATTATAAGATTCT	0.495														176	0.0351438	0.1286	0.0086	5008	,	,		20512	0.0		0.0	False		,,,				2504	0.0				p.403_404del		Pindel,Atlas-Indel	.											.	APOL1	35	.	0			c.1207_1212del						PASS	.		,,,	570,3688		45,480,1604				http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,,	-5.9	0.0		dbSNP_130	43	1,8249		0,1,4124	no	coding,coding,coding,coding	APOL1	NM_145343.2,NM_003661.3,NM_001136541.1,NM_001136540.1	,,,	45,481,5728	A1A1,A1R,RR		0.0121,13.3866,4.5651	,,,	,,,		571,11937				SO:0001651	inframe_deletion	8542	exon7			.	AF019225	CCDS13925.1, CCDS13926.1, CCDS46702.1	22q13.1	2014-09-17			ENSG00000100342	ENSG00000100342		"""Apolipoproteins"""	618	protein-coding gene	gene with protein product		603743		APOL		9325276, 11374903, 16020735	Standard	NM_003661		Approved		uc011amp.2	O14791	OTTHUMG00000030427	ENST00000397278.3:c.1160_1165delATAATT	22.37:g.36662042_36662047delATAATT	ENSP00000380448:p.Asn388_Tyr389del	Somatic	198	.	.		WXS	Illumina HiSeq	Phase_I	192	53	0.276	NM_145343	A5PLQ4|B4DU12|E9PF24|O60804|Q5R3P7|Q5R3P8|Q96AB8|Q96PM4|Q9BQ03	In_Frame_Del	DEL	ENST00000397278.3	37	CCDS13926.1																																																																																			ATAATT|0.979;-|0.021	0.021	strong		0.495	APOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319100.4	NM_145343	
HACE1	57531	hgsc.bcm.edu	37	6	105192108	105192110	+	Intron	DEL	AAC	AAC	-	rs72218235|rs374160571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:105192108_105192110delAAC	ENST00000262903.4	-	22	2719				HACE1_ENST00000517995.1_Intron|HACE1_ENST00000369125.2_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	122	.	.		WXS	Illumina HiSeq	Phase_I	121	34	0.281	.	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	
FMO2	2327	hgsc.bcm.edu	37	1	171162551	171162552	+	In_Frame_Ins	INS	-	-	GAC	rs2020868|rs397844260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171162551_171162552insGAC	ENST00000209929.7	+	3	368_369	c.210_211insGAC	c.(211-213)gac>GACgac	p.71_71D>DD	FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_In_Frame_Ins_p.71_71D>DD			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	71					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCTGTTTCAGTGACTTTCCAAT	0.342														516	0.103035	0.298	0.0476	5008	,	,		17166	0.002		0.0447	False		,,,				2504	0.0429				p.S70delinsSD		Pindel,Atlas-Indel	.											.	FMO2	66	.	0			c.210_211insGAC						PASS	.			1054,3212		148,758,1227						4.3	1.0		dbSNP_98	103	398,7856		12,374,3741	no	coding	FMO2	NM_001460.2		160,1132,4968	A1A1,A1R,RR		4.8219,24.707,11.5974				1452,11068				SO:0001652	inframe_insertion	2327	exon3			.	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.211_213dupGAC	1.37:g.171162552_171162554dupGAC	ENSP00000209929:p.Asp71dup	Somatic	76	.	.		WXS	Illumina HiSeq	Phase_I	58	19	0.328	NM_001460	Q53XR0	In_Frame_Ins	INS	ENST00000209929.7	37	CCDS1293.1																																																																																			-|0.904;GAC|0.096	0.096	strong		0.342	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
OR2A1	346528	hgsc.bcm.edu	37	7	144015524	144015527	+	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs559439902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGTT	TGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:144015524_144015527delTGTT	ENST00000408951.1	+	1	307_310	c.307_310delTGTT	c.(307-312)tgtttgfs	p.CL103fs	OR2A1-AS1_ENST00000475089.1_RNA|OR2A1-AS1_ENST00000486094.1_RNA|OR2A1-AS1_ENST00000478806.1_RNA|OR2A1-AS1_ENST00000467944.1_RNA|OR2A1-AS1_ENST00000478925.1_RNA|OR2A1-AS1_ENST00000493539.1_RNA|OR2A1-AS1_ENST00000463561.1_RNA|OR2A1-AS1_ENST00000487102.1_RNA|OR2A1-AS1_ENST00000476560.1_RNA|OR2A1-AS1_ENST00000488041.1_RNA|OR2A1-AS1_ENST00000496968.1_RNA|OR2A1-AS1_ENST00000461843.1_RNA|OR2A1-AS1_ENST00000489488.1_RNA	NM_001005287.1	NP_001005287.1	Q8NGT9	OR2A1_HUMAN	olfactory receptor, family 2, subfamily A, member 1	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|lung(3)|skin(2)	6	Melanoma(164;0.14)					GACCTTTCTCTGTTTGAGTTTTGG	0.569														126	0.0251597	0.0908	0.0086	5008	,	,		44510	0.0		0.0	False		,,,				2504	0.0				p.102_103del		Atlas-Indel	.											.	OR2A1	10	.	0			c.306_309del						PASS	.			296,3480		1,294,1593						-5.2	0.1			171	15,6777		4,7,3385	no	frameshift	OR2A1	NM_001005287.1		5,301,4978	A1A1,A1R,RR		0.2208,7.839,2.9428				311,10257				SO:0001589	frameshift_variant	346528	exon1			.		CCDS43673.1	7q35	2013-09-20			ENSG00000221970	ENSG00000221970		"""GPCR / Class A : Olfactory receptors"""	8229	protein-coding gene	gene with protein product							Standard	NM_001005287		Approved		uc011kub.2	Q8NGT9	OTTHUMG00000158005	ENST00000408951.1:c.307_310delTGTT	7.37:g.144015524_144015527delTGTT	ENSP00000386175:p.Cys103fs	Somatic	626	0	0		WXS	Illumina HiSeq	Phase_I	1136	133	0.117077	NM_001005287	Q6IF44|Q96R46	Frame_Shift_Del	DEL	ENST00000408951.1	37	CCDS43673.1																																																																																			.	.	none		0.569	OR2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349985.1		
QRICH2	84074	hgsc.bcm.edu	37	17	74288565	74288567	+	In_Frame_Del	DEL	TGA	TGA	-	rs35035566|rs79093440|rs34007000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74288565_74288567delTGA	ENST00000262765.5	-	4	1922_1924	c.1743_1745delTCA	c.(1741-1746)catcag>cag	p.H581del		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	581	Gln-rich.							p.H581Q(5)|p.Q582R(1)		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						CAAACCACGCTGATGATCTGCAC	0.537														2352	0.469649	0.7073	0.3098	5008	,	,		27303	0.5734		0.2753	False		,,,				2504	0.3548				p.582_582del		Pindel,Atlas-Indel	.											QRICH2,NS,carcinoma,-1,1	QRICH2	143	1	6	Substitution - Missense(6)	kidney(4)|lung(2)	c.1744_1746del						PASS	.			2830,1434		943,944,245						1.4	0.0		dbSNP_126	148	2377,5877		324,1729,2074	no	coding	QRICH2	NM_032134.1		1267,2673,2319	A1A1,A1R,RR		28.7982,33.6304,41.5961				5207,7311				SO:0001651	inframe_deletion	84074	exon4			.	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.1743_1745delTCA	17.37:g.74288568_74288570delTGA	ENSP00000262765:p.His581del	Somatic	155	.	.		WXS	Illumina HiSeq	Phase_I	145	27	0.186	NM_032134	A2RRE1|Q96LM3	In_Frame_Del	DEL	ENST00000262765.5	37	CCDS32741.1																																																																																			TGA|0.548;-|0.452	0.452	strong		0.537	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
LIPM	340654	hgsc.bcm.edu	37	10	90562801	90562802	+	Splice_Site	INS	-	-	T	rs535896941|rs554915830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90562801_90562802insT	ENST00000404743.4	+	1	314		c.e1+1		LIPM_ENST00000539337.1_Splice_Site	NM_001128215.1	NP_001121687.1	Q5VYY2	LIPM_HUMAN	lipase, family member M						lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)|skin(1)	7						CATGAATATTGTAAGTTGGGAT	0.347													T|T|TT|insertion	3	0.000599042	0.0023	0.0	5008	,	,		21071	0.0		0.0	False		,,,				2504	0.0				.		Pindel,Atlas-Indel	.											.	LIPM	17	.	0			c.147+1->T						PASS	.			4,2254		1,2,1126						4.9	1.0			127	0,4458		0,0,2229	no	splice-5	LIPM	NM_001128215.1		1,2,3355	A1A1,A1R,RR		0.0,0.1771,0.0596				4,6712				SO:0001630	splice_region_variant	340654	exon1			.		CCDS44457.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000173239	ENSG00000173239			23455	protein-coding gene	gene with protein product		613923	"""lipase-like, ab-hydrolase domain containing 3"""	LIPL3			Standard	NM_001128215		Approved	bA304I5.1	uc009xtm.1	Q5VYY2	OTTHUMG00000018698	ENST00000404743.4:c.147+1->T	10.37:g.90562802_90562802dupT		Somatic	129	.	.		WXS	Illumina HiSeq	Phase_I	104	35	0.337	NM_001128215	A6PVS3|B2RXK7|B5MCR3	Splice_Site	INS	ENST00000404743.4	37	CCDS44457.1																																																																																			.	.	none		0.347	LIPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049261.3	XM_291663	Intron
TRPM3	80036	hgsc.bcm.edu	37	9	73151130	73151133	+	Frame_Shift_Del	DEL	TCTC	TCTC	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:73151130_73151133delTCTC	ENST00000377110.3	-	25	5103_5106	c.4860_4863delGAGA	c.(4858-4863)gagagafs	p.ER1620fs	TRPM3_ENST00000377106.1_Frame_Shift_Del_p.ER1492fs|TRPM3_ENST00000358082.3_Frame_Shift_Del_p.ER1482fs|TRPM3_ENST00000357533.2_Frame_Shift_Del_p.ER1624fs|TRPM3_ENST00000396285.1_Frame_Shift_Del_p.ER1479fs|TRPM3_ENST00000360823.2_Frame_Shift_Del_p.ER1482fs|TRPM3_ENST00000408909.2_Frame_Shift_Del_p.ER1479fs|TRPM3_ENST00000396280.5_Frame_Shift_Del_p.ER1469fs|TRPM3_ENST00000377105.1_Frame_Shift_Del_p.ER1479fs|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396292.4_Frame_Shift_Del_p.ER1492fs|TRPM3_ENST00000423814.3_Frame_Shift_Del_p.ER1647fs			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1645					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						TGGACAGGGTTCTCTCTGAGTTAT	0.544																																					p.1621_1622del		Pindel,Atlas-Indel	.											.	TRPM3	700	.	0			c.4861_4864del						PASS	.		,,,,,,	5,4259		0,5,2127					,,,,,,	-3.5	0.6			363	0,8254		0,0,4127	no	frameshift,frameshift,frameshift,frameshift,frameshift,frameshift,frameshift	TRPM3	NM_206947.3,NM_206946.3,NM_206945.3,NM_206944.3,NM_024971.5,NM_020952.4,NM_001007471.2	,,,,,,	0,5,6254	A1A1,A1R,RR		0.0,0.1173,0.0399	,,,,,,	,,,,,,		5,12513				SO:0001589	frameshift_variant	80036	exon25			.	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.4860_4863delGAGA	9.37:g.73151130_73151133delTCTC	ENSP00000366314:p.Glu1620fs	Somatic	439	.	.		WXS	Illumina HiSeq	Phase_I	453	86	0.190	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Frame_Shift_Del	DEL	ENST00000377110.3	37	CCDS43835.1																																																																																			.	.	none		0.544	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945	
PLIN5	440503	hgsc.bcm.edu	37	19	4529255	4529257	+	In_Frame_Del	DEL	GAG	GAG	-	rs140507757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4529255_4529257delGAG	ENST00000381848.3	-	5	428_430	c.348_350delCTC	c.(346-351)acctca>aca	p.S117del	CTB-50L17.14_ENST00000586020.1_3'UTR	NM_001013706.2	NP_001013728.2	Q00G26	PLIN5_HUMAN	perilipin 5	117	Essential for lipid droplet targeting. {ECO:0000250}.				lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|mitochondrion localization (GO:0051646)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of lipase activity (GO:0060192)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of triglyceride catabolic process (GO:0010897)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of lipase activity (GO:0060193)|positive regulation of lipid storage (GO:0010884)|positive regulation of sequestering of triglyceride (GO:0010890)|positive regulation of triglyceride biosynthetic process (GO:0010867)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)				endometrium(4)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10						GTCCTTGGCTGAGGTCACCACCT	0.67														54	0.0107827	0.0401	0.0014	5008	,	,		14860	0.0		0.0	False		,,,				2504	0.0				p.117_117del		Pindel,Atlas-Indel	.											.	PLIN5	27	.	0			c.349_351del						PASS	.			141,3831		9,123,1854						-7.4	1.0		dbSNP_134	48	0,8030		0,0,4015	no	coding	PLIN5	NM_001013706.2		9,123,5869	A1A1,A1R,RR		0.0,3.5498,1.1748				141,11861				SO:0001651	inframe_deletion	440503	exon5			.	DQ839131	CCDS42473.1	19p13.3	2009-08-12			ENSG00000214456	ENSG00000214456		"""Perilipins"""	33196	protein-coding gene	gene with protein product	"""lipid storage droplet protein 5"""	613248				17234449, 19638644	Standard	NM_001013706		Approved	LSDP5, LSDA5, OXPAT, MLDP	uc002mas.3	Q00G26		ENST00000381848.3:c.348_350delCTC	19.37:g.4529255_4529257delGAG	ENSP00000371272:p.Ser117del	Somatic	143	.	.		WXS	Illumina HiSeq	Phase_I	118	36	0.305	NM_001013706	A2RRC1|Q6ZS68	In_Frame_Del	DEL	ENST00000381848.3	37	CCDS42473.1																																																																																			GAG|0.986;-|0.014	0.014	strong		0.670	PLIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458647.1	NM_001013706	
C2orf71	388939	hgsc.bcm.edu	37	2	29287926	29287927	+	In_Frame_Ins	INS	-	-	GCT	rs139768554|rs72122505|rs201781577|rs35753661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29287926_29287927insGCT	ENST00000331664.5	-	2	3674_3675	c.3675_3676insAGC	c.(3673-3678)agcgag>agcAGCgag	p.1225_1226insS	C2orf71_ENST00000602958.1_5'Flank	NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1225			S -> SS. {ECO:0000269|PubMed:21412943}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)		p.S1225_E1226insS(2)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GGGCTCTCCTCGCTGCTGCTGC	0.624														1871	0.373602	0.5257	0.2637	5008	,	,		17644	0.4931		0.2545	False		,,,				2504	0.2454				p.E1226delinsSE		Pindel,Atlas-Indel	.											.	C2orf71	146	.	2	Insertion - In frame(2)	ovary(1)|breast(1)	c.3676_3677insAGC						PASS	.			1580,1994		462,656,669						5.2	1.0		dbSNP_130	16	1923,5511		406,1111,2200	no	coding	C2orf71	NM_001029883.1		868,1767,2869	A1A1,A1R,RR		25.8676,44.2082,31.8223				3503,7505				SO:0001652	inframe_insertion	388939	exon2			.		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3673_3675dupAGC	2.37:g.29287933_29287935dupGCT	ENSP00000332809:p.Ser1225_Ser1225dup	Somatic	77	.	.		WXS	Illumina HiSeq	Phase_I	69	19	0.275	NM_001029883		In_Frame_Ins	INS	ENST00000331664.5	37	CCDS42669.1																																																																																			.	.	strong		0.624	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
TSPYL6	388951	hgsc.bcm.edu	37	2	54482704	54482709	+	In_Frame_Del	DEL	GGGCCC	GGGCCC	-	rs76397255|rs398060196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGGCCC	GGGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:54482704_54482709delGGGCCC	ENST00000317802.7	-	1	700_705	c.580_585delGGGCCC	c.(580-585)gggcccdel	p.GP194del	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	194					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						CCACGTTCAGGGGCCCGGGCCCGGGC	0.626														798	0.159345	0.1921	0.111	5008	,	,		19038	0.1865		0.1143	False		,,,				2504	0.1677				p.194_196del		Pindel,Atlas-Indel	.											.	TSPYL6	54	.	0			c.581_586del						PASS	.		,	65,738,2585		2,12,49,141,444,1046					,	0.3	0.0		dbSNP_134	31	3,1183,6334		0,1,2,162,858,2737	no	intron,codingComplex	ACYP2,TSPYL6	NM_138448.3,NM_001003937.2	,	2,13,51,303,1302,3783	A1A1,A1A2,A1R,A2A2,A2R,RR		15.7713,23.7013,18.2343	,	,		68,1921,8919				SO:0001651	inframe_deletion	388951	exon1			.	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.580_585delGGGCCC	2.37:g.54482710_54482715delGGGCCC	ENSP00000417919:p.Gly194_Pro195del	Somatic	68	.	.		WXS	Illumina HiSeq	Phase_I	76	28	0.368	NM_001003937	Q6NUJ3	In_Frame_Del	DEL	ENST00000317802.7	37	CCDS42682.1																																																																																			GGGCCC|0.831;-|0.169	0.169	strong		0.626	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609299	32609299	+	Frame_Shift_Del	DEL	A	A	-	rs199556640|rs371894400|rs1064944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32609299delA	ENST00000343139.5	+	2	397	c.295delA	c.(295-297)atgfs	p.M99fs	HLA-DQA1_ENST00000374949.2_Frame_Shift_Del_p.M99fs|HLA-DQA1_ENST00000395363.1_Frame_Shift_Del_p.M99fs	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	98	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						CTTGAACATCATGATTAAACG	0.478																																					p.I98fs		Atlas-Indel	.											.	HLA-DQA1	52	.	0			c.294delC						PASS	.			349,3769		119,111,1829	95.0	82.0	86.0			2.2	0.0	6	dbSNP_118	84	786,7010		289,208,3401	no	frameshift	HLA-DQA1	NM_002122.3		408,319,5230	A1A1,A1R,RR		10.0821,8.475,9.5266			32609299	1135,10779	2029	3748	5777	SO:0001589	frameshift_variant	3117	exon2			.		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.295delA	6.37:g.32609299delA	ENSP00000339398:p.Met99fs	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	14	14	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	Frame_Shift_Del	DEL	ENST00000343139.5	37	CCDS4752.1																																																																																			A|0.857;-|0.143	0.143	strong		0.478	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
ADAM28	10863	hgsc.bcm.edu	37	8	24184128	24184129	+	In_Frame_Ins	INS	-	-	ATC	rs111491080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24184128_24184129insATC	ENST00000265769.4	+	10	1062_1063	c.952_953insATC	c.(952-954)tat>tATCat	p.318_319insH	ADAM28_ENST00000518516.1_3'UTR|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000397649.3_In_Frame_Ins_p.65_66insH|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000540823.1_In_Frame_Ins_p.85_86insH|ADAM28_ENST00000437154.2_In_Frame_Ins_p.318_319insH	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	318	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		GTGTTCTCCTTATTCTGTTGGC	0.332														3	0.000599042	0.0023	0.0	5008	,	,		18291	0.0		0.0	False		,,,				2504	0.0				p.Y318delinsYH	NSCLC(193;488 2149 22258 34798 40734)	Pindel,Atlas-Indel	.											.	ADAM28	100	.	0			c.952_953insATC						PASS	.		,	20,4244		0,20,2112					,	4.3	1.0		dbSNP_132	294	0,8252		0,0,4126	no	coding,coding	ADAM28	NM_021777.3,NM_014265.4	,	0,20,6238	A1A1,A1R,RR		0.0,0.469,0.1598	,	,		20,12496				SO:0001652	inframe_insertion	10863	exon10			.	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	Exception_encountered	8.37:g.24184128_24184129insATC	ENSP00000265769:p.Tyr318_Ser319insHis	Somatic	269	.	.		WXS	Illumina HiSeq	Phase_I	282	83	0.294	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	In_Frame_Ins	INS	ENST00000265769.4	37	CCDS34865.1																																																																																			-|0.500;ATC|0.500	0.500	weak		0.332	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
ARID1B	57492	hgsc.bcm.edu	37	6	157099402	157099403	+	In_Frame_Ins	INS	-	-	CAGCAG			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:157099402_157099403insCAGCAG	ENST00000350026.5	+	1	340_341	c.339_340insCAGCAG	c.(340-342)cag>CAGCAGcag	p.114_114Q>QQQ	RP11-230C9.3_ENST00000604792.1_RNA|ARID1B_ENST00000367148.1_In_Frame_Ins_p.114_114Q>QQQ|MIR4466_ENST00000606121.1_RNA|ARID1B_ENST00000275248.4_In_Frame_Ins_p.56_56Q>QQQ|ARID1B_ENST00000346085.5_In_Frame_Ins_p.114_114Q>QQQ|RP11-230C9.2_ENST00000603191.1_lincRNA	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	114	Gln-rich.|Poly-Gln.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		TAAACCAGTTCcagcagcagca	0.639																																					p.F113delinsFQQ		Atlas-Indel	.											.	ARID1B	320	.	0			c.339_340insCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	57492	exon1			.	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.352_357dupCAGCAG	6.37:g.157099403_157099408dupCAGCAG	ENSP00000055163:p.GlnGln130dup	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	In_Frame_Ins	INS	ENST00000350026.5	37	CCDS5251.2																																																																																			.	.	none		0.639	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262109	39262138	+	In_Frame_Del	DEL	TCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	TCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	-	rs200757692|rs188946528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	TCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39262109_39262138delTCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	ENST00000391415.1	+	1	526_555	c.469_498delTCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	c.(469-498)tccagctgctgccgcccctcttgctgtgaadel	p.SSCCRPSCCE157del		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	157	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R149C(1)|p.R161C(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						ctgcagcatctccagctgctgccgcccctcttgctgtgaatccagctgct	0.657														480	0.0958466	0.1634	0.1153	5008	,	,		24433	0.1458		0.0169	False		,,,				2504	0.0204				p.156_166del		Atlas-Indel	.											.	KRTAP4-9	110	.	2	Substitution - Missense(2)	endometrium(2)	c.468_497del						PASS	.			281,3501		42,197,1652						-1.0	0.0			9	86,7288		12,62,3613	no	coding	KRTAP4-9	NM_001146041.1		54,259,5265	A1A1,A1R,RR		1.1663,7.4299,3.2897				367,10789				SO:0001651	inframe_deletion	100132386	exon1			.	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.469_498delTCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	17.37:g.39262109_39262138delTCCAGCTGCTGCCGCCCCTCTTGCTGTGAA	ENSP00000375234:p.Ser157_Glu166del	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	185	22	0.118919	NM_001146041		In_Frame_Del	DEL	ENST00000391415.1	37	CCDS54124.1																																																																																			.	.	none		0.657	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
ANO7	50636	hgsc.bcm.edu	37	2	242163366	242163367	+	Frame_Shift_Del	DEL	CA	CA	-	rs60985508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242163366_242163367delCA	ENST00000274979.8	+	24	2844_2845	c.2741_2742delCA	c.(2740-2742)tcafs	p.S914fs		NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	914					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						CCCGAGGGCTCAGAGGCAAGTC	0.629														474	0.0946486	0.3374	0.0259	5008	,	,		17263	0.0		0.002	False		,,,				2504	0.0082				p.914_914del		Pindel,Atlas-Indel	.											.	ANO7	136	.	0			c.2740_2741del						PASS	.			1308,2958		197,914,1022						0.8	0.0		dbSNP_129	69	22,8232		0,22,4105	no	frameshift	ANO7	NM_001001891.3		197,936,5127	A1A1,A1R,RR		0.2665,30.661,10.623				1330,11190				SO:0001589	frameshift_variant	50636	exon24			.	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.2741_2742delCA	2.37:g.242163366_242163367delCA	ENSP00000274979:p.Ser914fs	Somatic	92	.	.		WXS	Illumina HiSeq	Phase_I	87	16	0.184	NM_001001891	Q6IWH6	Frame_Shift_Del	DEL	ENST00000274979.8	37	CCDS33423.1																																																																																			CA|0.917;-|0.083	0.083	strong		0.629	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
HAVCR1	26762	hgsc.bcm.edu	37	5	156479568	156479569	+	In_Frame_Ins	INS	-	-	GTT	rs386693994|rs139041445|rs6149307|rs10068551|rs141023871|rs77147640|rs376729615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156479568_156479569insGTT	ENST00000339252.3	-	3	1008_1009	c.476_477insAAC	c.(475-477)acg>acAACg	p.159_159T>TT	HAVCR1_ENST00000425854.1_In_Frame_Ins_p.159_159T>TT|HAVCR1_ENST00000522693.1_In_Frame_Ins_p.159_159T>TT|HAVCR1_ENST00000544197.1_In_Frame_Ins_p.159_159T>TT|HAVCR1_ENST00000523175.1_In_Frame_Ins_p.159_159T>TT	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)	p.T160_V161insT(1)		endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTGGAACAGTCGTCATTGGAAC	0.49														1655	0.330471	0.6165	0.2363	5008	,	,		22483	0.2232		0.2097	False		,,,				2504	0.2454				p.T159delinsTT		Pindel,Atlas-Indel	.											.	HAVCR1	84	.	1	Insertion - In frame(1)	ovary(1)	c.477_478insAAC						PASS	.																																			SO:0001652	inframe_insertion	26762	exon4			.	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"""Immunoglobulin superfamily / V-set domain containing"""	17866	protein-coding gene	gene with protein product	"""T-cell immunoglobulin mucin family member 1"""	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.476_477insAAC	5.37:g.156479568_156479569insGTT	ENSP00000344844:p.Thr160dup	Somatic	424	.	.		WXS	Illumina HiSeq	Phase_I	517	78	0.151	NM_001099414	O43656	In_Frame_Ins	INS	ENST00000339252.3	37	CCDS43392.1																																																																																			.	.	strong		0.490	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
MUC20	200958	hgsc.bcm.edu	37	3	195447912	195447914	+	In_Frame_Del	DEL	TTC	TTC	-	rs201907823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195447912_195447914delTTC	ENST00000447234.2	+	1	160_162	c.34_36delTTC	c.(34-36)ttcdel	p.F14del	MUC20_ENST00000485430.1_3'UTR|MUC20_ENST00000436408.1_In_Frame_Del_p.F14del|MUC20_ENST00000320736.6_In_Frame_Del_p.F14del	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	14					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)		TCTGCCCCTTTTCTTCTTCTGCT	0.611														210	0.0419329	0.1104	0.0202	5008	,	,		38073	0.0		0.0149	False		,,,				2504	0.0358				p.11_12del		Atlas-Indel	.											.	MUC20	84	.	0			c.33_35del						PASS	.			386,3300		8,370,1465						1.6	0.2			59	120,7760		1,118,3821	no	coding	MUC20	NM_152673.2		9,488,5286	A1A1,A1R,RR		1.5228,10.4721,4.3749				506,11060				SO:0001651	inframe_deletion	200958	exon1			.	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.34_36delTTC	3.37:g.195447918_195447920delTTC	ENSP00000414350:p.Phe14del	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	368	62	0.168478	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	In_Frame_Del	DEL	ENST00000447234.2	37																																																																																				TTC|0.981;-|0.019	0.019	strong		0.611	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
FMO2	2327	hgsc.bcm.edu	37	1	171165803	171165803	+	Frame_Shift_Del	DEL	G	G	-	rs28369860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171165803delG	ENST00000209929.7	+	4	495	c.337delG	c.(337-339)gtgfs	p.V113fs	RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Frame_Shift_Del_p.V113fs|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	113					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGTCCTTAGTGTGAGAAAATG	0.453													G|G|-|deletion	515	0.102835	0.2973	0.0476	5008	,	,		22626	0.002		0.0447	False		,,,				2504	0.0429				p.S112fs		Pindel,Atlas-Indel	.											.	FMO2	66	.	0			c.336delT	GRCh37	CD033950	FMO2	D	rs28369860	PASS	.			1055,3211		149,757,1227	106.0	106.0	106.0			2.2	1.0	1	dbSNP_125	115	398,7856		12,374,3741	no	frameshift	FMO2	NM_001460.2		161,1131,4968	A1A1,A1R,RR		4.8219,24.7304,11.6054			171165803	1453,11067	2093	4290	6383	SO:0001589	frameshift_variant	2327	exon4			.	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.337delG	1.37:g.171165803delG	ENSP00000209929:p.Val113fs	Somatic	184	.	.		WXS	Illumina HiSeq	Phase_I	155	43	0.277	NM_001460	Q53XR0	Frame_Shift_Del	DEL	ENST00000209929.7	37	CCDS1293.1																																																																																			.	.	weak		0.453	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
KCNA7	3743	hgsc.bcm.edu	37	19	49573363	49573365	+	In_Frame_Del	DEL	GGA	GGA	-	rs10535426|rs12975537|rs375428032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49573363_49573365delGGA	ENST00000221444.1	-	2	1681_1683	c.1326_1328delTCC	c.(1324-1329)cctcca>cca	p.442_443PP>P		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	442					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	TGCCCAGAGTGGAGGTGGTAGCT	0.631														725	0.144768	0.2988	0.1398	5008	,	,		15138	0.0486		0.0875	False		,,,				2504	0.0982				p.443_443del	Colon(74;686 1235 3793 23366 48562)	Pindel,Atlas-Indel	.											.	KCNA7	30	.	0			c.1327_1329del						PASS	.			1096,3166		123,850,1158						-0.9	0.9		dbSNP_107	73	770,7484		38,694,3395	no	coding	KCNA7	NM_031886.2		161,1544,4553	A1A1,A1R,RR		9.3288,25.7156,14.9089				1866,10650				SO:0001651	inframe_deletion	3743	exon2			.	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.1326_1328delTCC	19.37:g.49573363_49573365delGGA	ENSP00000221444:p.Pro443del	Somatic	64	.	.		WXS	Illumina HiSeq	Phase_I	75	27	0.360	NM_031886	A1KYX7|Q9BYS4	In_Frame_Del	DEL	ENST00000221444.1	37	CCDS12755.1																																																																																			GGA|0.851;-|0.149	0.149	strong		0.631	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886	
OR4L1	122742	hgsc.bcm.edu	37	14	20528449	20528467	+	Frame_Shift_Del	DEL	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC	-	rs145273733|rs111945603|rs112516164|rs75613488|rs139767954|rs112425920|rs33965693|rs112192573|rs200018603|rs201521851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20528449_20528467delCATAGATTTGCTCACTGAC	ENST00000315683.1	+	1	246_264	c.246_264delCATAGATTTGCTCACTGAC	c.(244-264)atcatagatttgctcactgacfs	p.IIDLLTD82fs		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L85F(1)|p.I83fs*10(1)		central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		CCAAGATGATCATAGATTTGCTCACTGACCACAAGACCA	0.466														2665	0.532149	0.4849	0.5562	5008	,	,		20575	0.5734		0.3837	False		,,,				2504	0.6892				p.82_88del		Pindel,Atlas-Indel	.											.	OR4L1	98	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	upper_aerodigestive_tract(1)|lung(1)	c.245_263del						PASS	.																																			SO:0001589	frameshift_variant	122742	exon1			.		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.246_264delCATAGATTTGCTCACTGAC	14.37:g.20528449_20528467delCATAGATTTGCTCACTGAC	ENSP00000319217:p.Ile82fs	Somatic	243	.	.		WXS	Illumina HiSeq	Phase_I	192	59	0.307	NM_001004717	Q6IEZ5	Frame_Shift_Del	DEL	ENST00000315683.1	37	CCDS32029.1																																																																																			CATAGATTTGCTCACTGAC|0.504;-|0.496	0.496	strong		0.466	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
SSPO	23145	hgsc.bcm.edu	37	7	149519007	149519007	+	RNA	DEL	G	G	-	rs568158666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149519007delG	ENST00000378016.2	+	0	12811							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)			CTCCTGTGGAGGTGGAAACCA	0.682													GG|GG|G|deletion	26	0.00519169	0.0197	0.0	5008	,	,		16479	0.0		0.0	False		,,,				2504	0.0				p.G4270fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.12810delA						PASS	.			63,3869		2,59,1905	16.0	19.0	18.0			3.2	1.0	7		18	2,7986		1,0,3993	no	frameshift	SSPO	NM_198455.2		3,59,5898	A1A1,A1R,RR		0.025,1.6022,0.5453			149519007	65,11855	2040	4183	6223			23145	exon90			.	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.149519007delG		Somatic	181	.	.		WXS	Illumina HiSeq	Phase_I	198	54	0.273	NM_198455	Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	37																																																																																				.	.	none		0.682	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
YWHAE	7531	hgsc.bcm.edu	37	17	1265304	1265305	+	Splice_Site	INS	-	-	A	rs543499657|rs34985093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1265304_1265305insA	ENST00000264335.8	-	3	532		c.e3-2		YWHAE_ENST00000575977.1_Intron|YWHAE_ENST00000571732.1_Splice_Site|YWHAE_ENST00000573026.1_Intron	NM_006761.4	NP_006752.1	P62258	1433E_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cerebral cortex development (GO:0021987)|G2/M transition of mitotic cell cycle (GO:0000086)|hippo signaling (GO:0035329)|hippocampus development (GO:0021766)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|mitotic cell cycle (GO:0000278)|negative regulation of peptidyl-serine dephosphorylation (GO:1902309)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|substantia nigra development (GO:0021762)|viral process (GO:0016032)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|membrane (GO:0016020)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|ion channel binding (GO:0044325)|MHC class II protein complex binding (GO:0023026)|phosphoprotein binding (GO:0051219)|phosphoserine binding (GO:0050815)|poly(A) RNA binding (GO:0044822)|potassium channel regulator activity (GO:0015459)|protein heterodimerization activity (GO:0046982)			kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(18;0.203)	UCEC - Uterine corpus endometrioid carcinoma (25;0.0887)		AGTCTCAACCtaaaaaaaaaaa	0.322			T	"""FAM22a, FAM22B"""	edometrial stromal sarcoma		Miller-Dieker lissencephaly syndrome						|||unknown(HR)	578	0.115415	0.3669	0.0346	5008	,	,		19509	0.0188		0.0099	False		,,,				2504	0.0409				.		Atlas-Indel	.		Dom	yes		17	17p13.3	7531	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (14-3-3 epsilon)"""	yes	M	.	YWHAE	50	.	0			c.265-2->T						PASS	.																																			SO:0001630	splice_region_variant	7531	exon4			.	U54778	CCDS11001.1	17p13.3	2013-12-03	2013-12-03		ENSG00000108953	ENSG00000108953			12851	protein-coding gene	gene with protein product	"""14-3-3 epsilon"""	605066	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide"""			9371399	Standard	NM_006761		Approved	FLJ45465	uc002fsj.3	P62258	OTTHUMG00000134316	ENST00000264335.8:c.265-2->T	17.37:g.1265315_1265315dupA		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	68	15	0.220588	NM_006761	B3KY71|D3DTH5|P29360|P42655|Q4VJB6|Q53XZ5|Q63631|Q7M4R4	Splice_Site	INS	ENST00000264335.8	37	CCDS11001.1																																																																																			.	.	none		0.322	YWHAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259354.3	NM_006761	Intron
CDCP2	200008	hgsc.bcm.edu	37	1	54610404	54610405	+	Frame_Shift_Del	DEL	TG	TG	-	rs558673127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54610404_54610405delTG	ENST00000371330.1	-	2	1008_1009	c.161_162delCA	c.(160-162)acafs	p.T54fs	RP11-446E24.4_ENST00000311841.7_3'UTR|RP11-446E24.4_ENST00000525949.1_5'UTR	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	54	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						AGCTGCACTCTGTGTTGTAGGG	0.559														3	0.000599042	0.0015	0.0014	5008	,	,		20392	0.0		0.0	False		,,,				2504	0.0				p.54_55del		Pindel,Atlas-Indel	.											.	CDCP2	52	.	0			c.162_163del						PASS	.			66,4200		31,4,2098						4.5	1.0			74	145,8109		72,1,4054	no	frameshift	CDCP2	NM_201546.2		103,5,6152	A1A1,A1R,RR		1.7567,1.5471,1.6853				211,12309				SO:0001589	frameshift_variant	200008	exon2			.		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.161_162delCA	1.37:g.54610406_54610407delTG	ENSP00000360381:p.Thr54fs	Somatic	138	.	.		WXS	Illumina HiSeq	Phase_I	119	33	0.277	NM_201546	Q6ZWJ3	Frame_Shift_Del	DEL	ENST00000371330.1	37	CCDS588.2																																																																																			.	.	none		0.559	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	
APLP2	334	hgsc.bcm.edu	37	11	129991653	129991658	+	In_Frame_Del	DEL	GAAGAG	GAAGAG	-	rs3837393|rs545528084|rs71750553|rs565247278|rs76279939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAAGAG	GAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:129991653_129991658delGAAGAG	ENST00000263574.5	+	5	733_738	c.661_666delGAAGAG	c.(661-666)gaagagdel	p.EE225del	APLP2_ENST00000345598.5_Intron|APLP2_ENST00000528499.1_In_Frame_Del_p.EE225del|APLP2_ENST00000539648.1_In_Frame_Del_p.EE69del|APLP2_ENST00000338167.5_In_Frame_Del_p.EE225del|APLP2_ENST00000278756.7_In_Frame_Del_p.EE235del|APLP2_ENST00000543137.1_In_Frame_Del_p.EE132del	NM_001642.2	NP_001633.1	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2	225	Asp/Glu-rich (highly acidic).|Poly-Glu.				cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0197)|Lung(977;0.24)		agaggaagatgaagaggaagaggaag	0.427														458	0.0914537	0.1626	0.0764	5008	,	,		21044	0.0625		0.0964	False		,,,				2504	0.0307				p.230_232del		Pindel,Atlas-Indel	.											.	APLP2	71	.	0			c.690_695del						PASS	.		,,,	811,3453		85,641,1406					,,,	-9.0	0.0		dbSNP_130	90	825,7429		35,755,3337	no	coding,intron,coding,coding	APLP2	NM_001642.2,NM_001142278.1,NM_001142277.1,NM_001142276.1	,,,	120,1396,4743	A1A1,A1R,RR		9.9952,19.0197,13.0692	,,,	,,,		1636,10882				SO:0001651	inframe_deletion	334	exon5			.	L19597	CCDS8486.1, CCDS44773.1, CCDS44774.1, CCDS44775.1, CCDS58196.1	11q24	2008-02-05			ENSG00000084234	ENSG00000084234			598	protein-coding gene	gene with protein product		104776		APPL2		10702673	Standard	NM_001642		Approved	APPH	uc021qsg.1	Q06481	OTTHUMG00000165767	ENST00000263574.5:c.661_666delGAAGAG	11.37:g.129991659_129991664delGAAGAG	ENSP00000263574:p.Glu225_Glu226del	Somatic	115	.	.		WXS	Illumina HiSeq	Phase_I	98	19	0.194	NM_001243299	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	In_Frame_Del	DEL	ENST00000263574.5	37	CCDS8486.1																																																																																			GAAGAG|0.892;-|0.108	0.108	strong		0.427	APLP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386109.1	NM_001642	
SSPO	23145	hgsc.bcm.edu	37	7	149503917	149503920	+	RNA	DEL	GATA	GATA	-	rs72359812|rs66470151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GATA	GATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149503917_149503920delGATA	ENST00000378016.2	+	0	8745							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)			AGGGCCCCGGGATAGATAGAGTGT	0.652														1379	0.275359	0.4803	0.2334	5008	,	,		17754	0.1895		0.1581	False		,,,				2504	0.2372				p.2915_2915del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.8744_8745del						PASS	.			1437,2153		344,749,702						3.3	0.9		dbSNP_130	28	1265,6541		120,1025,2758	no	frameshift	SSPO	NM_198455.2		464,1774,3460	A1A1,A1R,RR		16.2055,40.0279,23.7101				2702,8694						23145	exon59			.	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.149503921_149503924delGATA		Somatic	136	.	.		WXS	Illumina HiSeq	Phase_I	124	75	0.605	NM_198455	Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	37																																																																																				GATA|0.750;-|0.250	0.250	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
NOTCH1	4851	hgsc.bcm.edu	37	9	139390649	139390650	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139390649_139390650delAG	ENST00000277541.6	-	34	7616_7617	c.7541_7542delCT	c.(7540-7542)cctfs	p.P2514fs		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2514					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P2515fs*4(145)|p.T2512fs*1(1)|p.E2515fs*3(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		CAGGGGACTCAGGGGACGGGGT	0.663			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																											p.2514_2515del		Pindel,Atlas-Indel	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	147	Complex - frameshift(145)|Deletion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(147)	c.7542_7543del						PASS	.																																			SO:0001589	frameshift_variant	4851	exon34			.	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.7541_7542delCT	9.37:g.139390649_139390650delAG	ENSP00000277541:p.Pro2514fs	Somatic	113	.	.		WXS	Illumina HiSeq	Phase_I	118	38	0.322	NM_017617	Q59ED8|Q5SXM3	Frame_Shift_Del	DEL	ENST00000277541.6	37	CCDS43905.1																																																																																			.	.	none		0.663	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
DHRS11	79154	hgsc.bcm.edu	37	17	34958760	34958761	+	IGR	INS	-	-	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34958760_34958761insG	ENST00000251312.5	+	0	1598				MRM1_ENST00000250156.7_Frame_Shift_Ins_p.I175fs|MRM1_ENST00000585770.1_Intron	NM_024308.3	NP_077284.2	Q6UWP2	DHR11_HUMAN	dehydrogenase/reductase (SDR family) member 11							extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(4)	5						GTGGATAAGGTCATCACCAGCC	0.594																																					p.V174fs		Pindel,Atlas-Indel	.											.	MRM1	19	.	0			c.521_522insG						PASS	.																																			SO:0001628	intergenic_variant	79922	exon1			.		CCDS11315.2	17q12	2014-05-06			ENSG00000108272	ENSG00000278535		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	28639	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 24C, member 1"""					12975309, 19027726	Standard	NM_024308		Approved	MGC4172, SDR24C1	uc002hnd.3	Q6UWP2	OTTHUMG00000188442		17.37:g.34958760_34958761insG		Somatic	29	.	.		WXS	Illumina HiSeq	Phase_I	33	12	0.364	NM_024864	B2RDZ3|Q9BUC7|Q9H674	Frame_Shift_Ins	INS	ENST00000251312.5	37	CCDS11315.2																																																																																			.	.	none		0.594	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308	
IFNE	338376	hgsc.bcm.edu	37	9	21482239	21482241	+	5'UTR	DEL	AAT	AAT	-	rs3028326|rs397894161|rs34533918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21482239_21482241delAAT	ENST00000448696.3	-	0	71_73				MIR31HG_ENST00000304425.3_RNA	NM_176891.4	NP_795372.1	Q86WN2	IFNE_HUMAN	interferon, epsilon						adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(2)|lung(1)|skin(1)	4						TGCTTGAGCAAATAATTaatttt	0.261														783	0.15635	0.1604	0.0937	5008	,	,		15774	0.2083		0.0577	False		,,,				2504	0.2434				.		Pindel,Atlas-Indel	.											.	IFNE	16	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	338376	.			.	AY190045	CCDS34997.1	9p21.1	2008-12-12			ENSG00000184995	ENSG00000184995			18163	protein-coding gene	gene with protein product		615223				15546383, 17287131	Standard	NM_176891		Approved	IFNE1	uc003zpg.3	Q86WN2	OTTHUMG00000019672	ENST00000448696.3:c.-548ATT>-	9.37:g.21482242_21482244delAAT		Somatic	37	.	.		WXS	Illumina HiSeq	Phase_I	42	11	0.262	.		RNA	DEL	ENST00000448696.3	37	CCDS34997.1																																																																																			AAT|0.882;-|0.118	0.118	strong		0.261	IFNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051901.2	NM_176891	
CACNA1F	778	hgsc.bcm.edu	37	X	49076224	49076225	+	In_Frame_Ins	INS	-	-	TCC	rs112450928|rs375862263|rs377271774		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49076224_49076225insTCC	ENST00000376265.2	-	20	2505_2506	c.2444_2445insGGA	c.(2443-2445)gaa>gaGGAa	p.815_815E>EE	CACNA1F_ENST00000323022.5_In_Frame_Ins_p.804_804E>EE|CACNA1F_ENST00000480889.1_5'Flank|CACNA1F_ENST00000376251.1_In_Frame_Ins_p.750_750E>EE	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	815	Poly-Glu.				axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	cttcctcttcttcctcctcctc	0.505														365	0.0966887	0.2466	0.0331	3775	,	,		13574	0.0		0.008	False		,,,				2504	0.0082				p.E815delinsEE		Pindel,Atlas-Indel	.											.	CACNA1F	218	.	0			c.2445_2446insGGA						PASS	.																																			SO:0001652	inframe_insertion	778	exon20			.	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.2442_2444dupGGA	X.37:g.49076231_49076233dupTCC	ENSP00000365441:p.Glu825dup	Somatic	84	.	.		WXS	Illumina HiSeq	Phase_I	112	24	0.214	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	In_Frame_Ins	INS	ENST00000376265.2	37	CCDS35253.1																																																																																			-|0.908;TCC|0.092	0.092	strong		0.505	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
TPSD1	23430	hgsc.bcm.edu	37	16	1306560	1306560	+	Frame_Shift_Del	DEL	G	G	-	rs3830782|rs397840555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1306560delG	ENST00000211076.3	+	2	274	c.126delG	c.(124-126)cagfs	p.Q42fs	TPSD1_ENST00000397534.2_Frame_Shift_Del_p.Q35fs|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	42	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TTGGGGGGCAGGAGGCCCCCA	0.697													|||unknown(ALL_OTHER_Ns)	1341	0.267772	0.4191	0.3401	5008	,	,		17418	0.1528		0.2217	False		,,,				2504	0.1779				p.Q42fs		Atlas-Indel	.											.	TPSD1	47	.	0			c.125delA						PASS	.			1594,2670		311,972,849	32.0	48.0	43.0			-2.8	0.0	16	dbSNP_114	55	1800,6452		185,1430,2511	no	frameshift	TPSD1	NM_012217.2		496,2402,3360	A1A1,A1R,RR		21.8129,37.3827,27.1173			1306560	3394,9122	2038	4218	6256	SO:0001589	frameshift_variant	23430	exon2			.	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.126delG	16.37:g.1306560delG	ENSP00000211076:p.Gln42fs	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	198	105	0.530303	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Frame_Shift_Del	DEL	ENST00000211076.3	37	CCDS10432.1																																																																																			G|0.731;-|0.269	0.269	strong		0.697	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
SSC5D	284297	hgsc.bcm.edu	37	19	56029616	56029617	+	In_Frame_Ins	INS	-	-	CCA	rs35104581|rs71181782|rs150781976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56029616_56029617insCCA	ENST00000389623.6	+	14	3996_3997	c.3973_3974insCCA	c.(3973-3975)ccc>cCCAcc	p.1327_1328insT		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1327	Pro-rich.|Thr-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						gacccctcaccccACAACTCCT	0.599														1953	0.389976	0.4486	0.4193	5008	,	,		12005	0.5466		0.3012	False		,,,				2504	0.2198				p.P1325delinsPT		Atlas-Indel	.											.	SSC5D	65	.	0			c.3973_3974insCCA						PASS	.			1160,1648		342,476,586						2.2	0.0		dbSNP_126	332	1299,3745		266,767,1489	no	coding	SSC5D	NM_001144950.1		608,1243,2075	A1A1,A1R,RR		25.7534,41.3105,31.3169				2459,5393				SO:0001652	inframe_insertion	284297	exon14			.		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.3974_3976dupCCA	19.37:g.56029617_56029619dupCCA	ENSP00000374274:p.Thr1327_Thr1327dup	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	151	50	0.331126	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	
CCDC34	91057	hgsc.bcm.edu	37	11	27384449	27384466	+	In_Frame_Del	DEL	TCATCCACGTCTTCCTCA	TCATCCACGTCTTCCTCA	-	rs368035683|rs138931796|rs377198931|rs3207371|rs558321598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCATCCACGTCTTCCTCA	TCATCCACGTCTTCCTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:27384449_27384466delTCATCCACGTCTTCCTCA	ENST00000328697.6	-	1	949_966	c.276_293delTGAGGAAGACGTGGATGA	c.(274-294)gatgaggaagacgtggatgaa>gaa	p.DEEDVD92del	CCDC34_ENST00000317945.6_In_Frame_Del_p.DEEDVD92del	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	92	Asp-rich.									endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						ATGGGCATCTTCATCCACGTCTTCCTCATCATCCACGT	0.592														162	0.0323482	0.1097	0.0144	5008	,	,		19380	0.001		0.004	False		,,,				2504	0.002				p.93_98del		Pindel,Atlas-Indel	.											.	CCDC34	48	.	0			c.277_294del						PASS	.		,	353,3911		23,307,1802					,	0.9	0.0		dbSNP_134	173	50,8204		11,28,4088	no	coding,coding	CCDC34	NM_080654.2,NM_030771.1	,	34,335,5890	A1A1,A1R,RR		0.6058,8.2786,3.2194	,	,		403,12115				SO:0001651	inframe_deletion	91057	exon1			.	AF382034	CCDS7863.1, CCDS31448.1	11p14.1	2010-03-30			ENSG00000109881	ENSG00000109881			25079	protein-coding gene	gene with protein product		612324				11173847	Standard	NM_080654		Approved	NY-REN-41, L15, RAMA3	uc001mrh.1	Q96HJ3	OTTHUMG00000166211	ENST00000328697.6:c.276_293delTGAGGAAGACGTGGATGA	11.37:g.27384449_27384466delTCATCCACGTCTTCCTCA	ENSP00000330240:p.Asp92_Asp97del	Somatic	294	.	.		WXS	Illumina HiSeq	Phase_I	215	39	0.181	NM_030771	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	In_Frame_Del	DEL	ENST00000328697.6	37	CCDS31448.1																																																																																			TCATCCACGTCTTCCTCA|0.966;-|0.034	0.034	strong		0.592	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771	
ZNF717	100131827	hgsc.bcm.edu	37	3	75790810	75790811	+	Frame_Shift_Ins	INS	-	-	T	rs199577560	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75790810_75790811insT	ENST00000477374.1	-	3	305_306	c.134_135insA	c.(133-135)accfs	p.T45fs	ZNF717_ENST00000422325.1_Frame_Shift_Ins_p.T45fs|ZNF717_ENST00000478296.1_5'UTR|ZNF717_ENST00000400845.3_Frame_Shift_Ins_p.T38fs|ZNF717_ENST00000491507.1_5'UTR			Q9BY31	ZN717_HUMAN	zinc finger protein 717	38	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						CCCTGTACAGGGTCCTCTGAGC	0.51																																					p.T45fs		Atlas-Indel	.											.	ZNF717	160	.	0			c.135_136insA						PASS	.																																			SO:0001589	frameshift_variant	100131827	exon3			.	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000477374.1:c.134_135insA	3.37:g.75790810_75790811insT	ENSP00000417902:p.Thr45fs	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	80	12	0.15	NM_001128223		Frame_Shift_Ins	INS	ENST00000477374.1	37																																																																																				.	.	none		0.510	ZNF717-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000352767.1	NM_001128223	
PEBP4	157310	hgsc.bcm.edu	37	8	22570908	22570908	+	Frame_Shift_Del	DEL	T	T	-	rs35121552|rs398102329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22570908delT	ENST00000256404.6	-	7	750	c.659delA	c.(658-660)aacfs	p.N220fs	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	220						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)		CTCCGCCTGGTTTTTGTGCTT	0.602													TTTT|TTTTT|TTTT|insertion	1434	0.286342	0.2413	0.4582	5008	,	,		16468	0.2996		0.3231	False		,,,				2504	0.1738				p.N220fs		Pindel,Atlas-Indel	.											.	PEBP4	23	.	0			c.660delC						PASS	.			1065,2683		185,695,994	54.0	57.0	56.0			-4.5	0.0	8	dbSNP_130	78	2573,5375		433,1707,1834	no	frameshift	PEBP4	NM_144962.2		618,2402,2828	A1A1,A1R,RR		32.3729,28.4152,31.1047			22570908	3638,8058	1899	4079	5978	SO:0001589	frameshift_variant	157310	exon7			.	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.659delA	8.37:g.22570908delT	ENSP00000256404:p.Asn220fs	Somatic	158	.	.		WXS	Illumina HiSeq	Phase_I	146	38	0.260	NM_144962	Q5EVA1|Q8WW74	Frame_Shift_Del	DEL	ENST00000256404.6	37	CCDS43724.1																																																																																			T|0.680;-|0.320	0.320	strong		0.602	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
ZFHX3	463	hgsc.bcm.edu	37	16	72831357	72831358	+	In_Frame_Ins	INS	-	-	TTG	rs568545014|rs34918837|rs552138038|rs372909378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:72831357_72831358insTTG	ENST00000268489.5	-	9	5895_5896	c.5223_5224insCAA	c.(5221-5226)caagca>caaCAAgca	p.1741_1742insQ	ZFHX3_ENST00000397992.5_In_Frame_Ins_p.827_828insQ	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1741	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)				AGCGTTTGTGCttgttgttgtt	0.53														242	0.0483227	0.1755	0.0115	5008	,	,		29749	0.002		0.0	False		,,,				2504	0.0				p.A1742delinsQA		Atlas-Indel	.											.	ZFHX3	404	.	0			c.5224_5225insCAA						PASS	.																																			SO:0001652	inframe_insertion	463	exon9			.	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.5221_5223dupCAA	16.37:g.72831364_72831366dupTTG	ENSP00000268489:p.Gln1742_Gln1743dup	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	184	51	0.277174	NM_006885	D3DWS8|O15101|Q13719	In_Frame_Ins	INS	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	weak		0.530	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
PDE6H	5149	hgsc.bcm.edu	37	12	15134337	15134337	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15134337delT	ENST00000266395.2	+	4	285	c.179delT	c.(178-180)atcfs	p.I60fs		NM_006205.2	NP_006196.1	Q13956	CNCG_HUMAN	phosphodiesterase 6H, cGMP-specific, cone, gamma	60					activation of MAPK activity (GO:0000187)|negative regulation of catalytic activity (GO:0043086)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|response to stimulus (GO:0050896)|visual perception (GO:0007601)		3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|lung(6)|ovary(1)|skin(2)	10					Sildenafil(DB00203)|Vardenafil(DB00862)	CTTGCAGATATCACAGTGATT	0.498																																					p.I60fs		Pindel,Atlas-Indel	.											.	PDE6H	13	.	0			c.178delA						PASS	.						180.0	154.0	163.0					12																	15134337		2203	4300	6503	SO:0001589	frameshift_variant	5149	exon4			.		CCDS8672.1	12p13	2008-03-18					3.1.4.17	"""Phosphodiesterases"""	8790	protein-coding gene	gene with protein product		601190				8786098	Standard	NM_006205		Approved		uc001rcr.3	Q13956		ENST00000266395.2:c.179delT	12.37:g.15134337delT	ENSP00000266395:p.Ile60fs	Somatic	110	.	.		WXS	Illumina HiSeq	Phase_I	106	33	0.311	NM_006205	Q52LY7	Frame_Shift_Del	DEL	ENST00000266395.2	37	CCDS8672.1																																																																																			.	.	none		0.498	PDE6H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400880.1		
ZNF474	133923	hgsc.bcm.edu	37	5	121488636	121488636	+	Frame_Shift_Del	DEL	T	T	-	rs3217313|rs398102325|rs75331699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:121488636delT	ENST00000296600.4	+	2	1334	c.951delT	c.(949-951)aatfs	p.N317fs	CTC-441N14.2_ENST00000504829.1_RNA|ZNF474_ENST00000514925.1_Intron|CTC-441N14.1_ENST00000505209.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	317							metal ion binding (GO:0046872)	p.L318fs*1(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		AATATCAGAATTTGAATTTAG	0.438													TTT|TTT|TT|deletion	933	0.186302	0.4168	0.062	5008	,	,		20196	0.1994		0.0497	False		,,,				2504	0.09				p.N317fs		Atlas-Indel	.											.	ZNF474	43	.	1	Deletion - Frameshift(1)	stomach(1)	c.950delA						PASS	.			1518,2746		264,990,878	44.0	62.0	56.0			4.0	0.0	5	dbSNP_106	66	362,7892		6,350,3771	yes	frameshift	ZNF474	NM_207317.1		270,1340,4649	A1A1,A1R,RR		4.3858,35.6004,15.0184			121488636	1880,10638	2181	4300	6481	SO:0001589	frameshift_variant	133923	exon2			.	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"""Zinc fingers, C2H2-type"""	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.951delT	5.37:g.121488636delT	ENSP00000296600:p.Asn317fs	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	38	12	0.315789	NM_207317	A8K4M0|Q96M07	Frame_Shift_Del	DEL	ENST00000296600.4	37	CCDS4130.1																																																																																			T|0.822;-|0.178	0.178	strong		0.438	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317	
CLECL1	160365	hgsc.bcm.edu	37	12	9885707	9885708	+	Frame_Shift_Ins	INS	-	-	TAAGT	rs71929655|rs113575400|rs113222621|rs71045297|rs398070028		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9885707_9885708insTAAGT	ENST00000327839.3	-	1	187_188	c.153_154insACTTA	c.(151-156)ttatcafs	p.S52fs		NM_172004.3	NP_742001.1	Q8IZS7	CLCL1_HUMAN	C-type lectin-like 1	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.S52fs*26(1)		breast(1)|kidney(1)|large_intestine(4)|lung(3)	9						GAAACTTCTGATAAGTAAATTG	0.401														2748	0.548722	0.7564	0.4597	5008	,	,		20040	0.38		0.496	False		,,,				2504	0.5593				p.S52fs		Pindel,Atlas-Indel	.											.	CLECL1	18	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.154_155insACTTA						PASS	.			2986,1278		1042,902,188						1.9	0.0		dbSNP_130	78	4130,4124		1066,1998,1063	no	frameshift	CLECL1	NM_172004.2		2108,2900,1251	A1A1,A1R,RR		49.9637,29.9719,43.1539				7116,5402				SO:0001589	frameshift_variant	160365	exon1			.	AF518873	CCDS8603.1, CCDS73441.1	12p13.31	2007-06-21				ENSG00000184293			24462	protein-coding gene	gene with protein product	"""dendritic cell associated lectin 1"""	607467				12421943	Standard	NM_172004		Approved	DCAL1	uc001qwi.3	Q8IZS7		ENST00000327839.3:c.149_153dupACTTA	12.37:g.9885708_9885712dupTAAGT	ENSP00000331766:p.Ser52fs	Somatic	110	.	.		WXS	Illumina HiSeq	Phase_I	117	44	0.376	NM_001267701		Frame_Shift_Ins	INS	ENST00000327839.3	37	CCDS8603.1																																																																																			-|0.485;TAAGT|0.515	0.515	strong		0.401	CLECL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399815.1	NM_172004	
ST6GALNAC5	81849	hgsc.bcm.edu	37	1	77334292	77334293	+	In_Frame_Ins	INS	-	-	CAGCAA	rs60179124|rs201548881|rs62637703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:77334292_77334293insCAGCAA	ENST00000477717.1	+	2	361_362	c.126_127insCAGCAA	c.(127-129)cag>CAGCAAcag	p.43_43Q>QQQ	ST6GALNAC5_ENST00000496845.1_3'UTR	NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	43	Poly-Gln.				glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						agcagcagcagcagcagcaaca	0.713														341	0.0680911	0.2216	0.0288	5008	,	,		11798	0.0		0.0258	False		,,,				2504	0.002				p.Q42delinsQQQ		Atlas-Indel	.											.	ST6GALNAC5	59	.	0			c.126_127insCAGCAA						PASS	.			818,37,3099		139,15,525,4,14,1280						2.2	1.0		dbSNP_129	13	373,14,7183		30,0,313,2,10,3430	no	codingComplex	ST6GALNAC5	NM_030965.1		169,15,838,6,24,4710	A1A1,A1A2,A1R,A2A2,A2R,RR		5.1123,21.6237,10.7775				1191,51,10282				SO:0001652	inframe_insertion	81849	exon2			.		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"""Sialyltransferases"""	19342	protein-coding gene	gene with protein product		610134	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"""	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	Exception_encountered	1.37:g.77334292_77334293insCAGCAA	ENSP00000417583:p.GlnGln49dup	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	136	63	0.463235	NM_030965	B1AK82	In_Frame_Ins	INS	ENST00000477717.1	37	CCDS673.1																																																																																			-|0.929;CAGCAA|0.071	0.071	strong		0.713	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965	
NUP155	9631	hgsc.bcm.edu	37	5	37309372	37309374	+	Intron	DEL	AGA	AGA	-	rs552603277|rs201100022|rs3835198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37309372_37309374delAGA	ENST00000231498.3	-	24	2832				NUP155_ENST00000513532.1_Intron|NUP155_ENST00000502533.1_Intron|NUP155_ENST00000381843.2_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	52	.	.		WXS	Illumina HiSeq	Phase_I	53	23	0.434	.	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	
PABPC1	26986	hgsc.bcm.edu	37	8	101721933	101721933	+	Frame_Shift_Del	DEL	T	T	-	rs112966887		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721933delT	ENST00000318607.5	-	8	2127	c.999delA	c.(997-999)aaafs	p.K333fs	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519004.1_Frame_Shift_Del_p.K288fs|PABPC1_ENST00000522387.1_Frame_Shift_Del_p.K301fs|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	333	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)			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)			AACCAAACCCTTTGCTGCGAC	0.383																																					p.G334fs		Atlas-Indel	.											.	PABPC1	76	.	0			c.1000delG						PASS	.						58.0	53.0	54.0					8																	101721933		2203	4300	6503	SO:0001589	frameshift_variant	26986	exon8			.	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.999delA	8.37:g.101721933delT	ENSP00000313007:p.Lys333fs	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	188	39	0.207447	NM_002568	Q15097|Q93004	Frame_Shift_Del	DEL	ENST00000318607.5	37	CCDS6289.1																																																																																			T|0.500;-|0.500	0.500	strong		0.383	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
FOXD4L3	286380	hgsc.bcm.edu	37	9	70918118	70918119	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:70918118_70918119delCA	ENST00000342833.2	+	1	843_844	c.251_252delCA	c.(250-252)tcafs	p.S84fs		NM_199135.4	NP_954586.4	Q6VB84	FX4L3_HUMAN	forkhead box D4-like 3	84						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			ovary(1)	1				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		AGCGACCCCTCAGAGTTTGGCA	0.698																																					p.84_84del		Atlas-Indel	.											.	FOXD4L3	7	.	0			c.250_251del						PASS	.																																			SO:0001589	frameshift_variant	286380	exon1			.	AY344642	CCDS43833.1	9q13	2008-05-13				ENSG00000187559			18523	protein-coding gene	gene with protein product		611086				12421752	Standard	NM_199135		Approved	OTTHUMG00000019959, FOXD6	uc004agm.1	Q6VB84	OTTHUMG00000019959	ENST00000342833.2:c.251_252delCA	9.37:g.70918118_70918119delCA	ENSP00000341961:p.Ser84fs	Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	469	74	0.157783	NM_199135	Q5JTX9	Frame_Shift_Del	DEL	ENST00000342833.2	37	CCDS43833.1																																																																																			.	.	none		0.698	FOXD4L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052539.2	NM_199358	
C10orf113	387638	hgsc.bcm.edu	37	10	21435341	21435344	+	Frame_Shift_Del	DEL	CACT	CACT	-	rs200339723|rs45546236|rs72102767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CACT	CACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:21435341_21435344delCACT	ENST00000534331.1	-	1	144_147	c.94_97delAGTG	c.(94-99)agtgttfs	p.SV32fs	C10orf113_ENST00000377118.4_Frame_Shift_Del_p.SV22fs|NEBL_ENST00000417816.2_Intron|C10orf113_ENST00000529198.1_Frame_Shift_Del_p.SV32fs	NM_001010896.2	NP_001010896.2	Q5VZT2	CJ113_HUMAN	chromosome 10 open reading frame 113	32										endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|pancreas(1)	7						AAAGCACAAACACTCTCTCTCATA	0.397														1260	0.251597	0.2315	0.1671	5008	,	,		20280	0.3571		0.1948	False		,,,				2504	0.2883				p.32_33del		Pindel,Atlas-Indel	.											.	C10orf113	32	.	0			c.95_98del						PASS	.		,,,	902,3362		95,712,1325					,,,	-1.1	0.0		dbSNP_130	149	1513,6741		144,1225,2758	no	intron,frameshift,intron,frameshift	NEBL,C10orf113	NM_213569.2,NM_001177483.1,NM_001173484.1,NM_001010896.2	,,,	239,1937,4083	A1A1,A1R,RR		18.3305,21.1538,19.2922	,,,	,,,		2415,10103				SO:0001589	frameshift_variant	387638	exon1			.		CCDS31162.1, CCDS31162.2, CCDS53496.1	10p12.31	2012-06-12			ENSG00000204683	ENSG00000204683			31447	protein-coding gene	gene with protein product							Standard	NM_001010896		Approved	bA165O3.1	uc001iqm.3	Q5VZT2	OTTHUMG00000017786	ENST00000534331.1:c.94_97delAGTG	10.37:g.21435341_21435344delCACT	ENSP00000433646:p.Ser32fs	Somatic	130	.	.		WXS	Illumina HiSeq	Phase_I	151	59	0.391	NM_001177483	B9EIM9|E9PRX7	Frame_Shift_Del	DEL	ENST00000534331.1	37	CCDS31162.2																																																																																			CACT|0.769;-|0.231	0.231	strong		0.397	C10orf113-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047108.3	NM_001010896	
DEFB126	81623	hgsc.bcm.edu	37	20	126311	126312	+	Frame_Shift_Del	DEL	CC	CC	-	rs376364807|rs11467417|rs386393058		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:126311_126312delCC	ENST00000382398.3	+	2	574_575	c.314_315delCC	c.(313-315)accfs	p.T105fs	DEFB126_ENST00000542572.1_3'UTR	NM_030931.3	NP_112193.1	Q9BYW3	DB126_HUMAN	defensin, beta 126	105					defense response to bacterium (GO:0042742)	cell surface (GO:0009986)|extracellular region (GO:0005576)|glycocalyx (GO:0030112)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			ATGGCTCCTACCCCCGTTTCTC	0.455																																					p.105_105del		Pindel,Atlas-Indel	.											.	DEFB126	52	.	0			c.313_314del						PASS	.			2386,1878		678,1030,424						-4.7	0.0		dbSNP_120	113	4702,3552		1341,2020,766	no	frameshift	DEFB126	NM_030931.2		2019,3050,1190	A1A1,A1R,RR		43.0337,44.0432,43.3775				7088,5430				SO:0001589	frameshift_variant	81623	exon2			.		CCDS12990.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125788	ENSG00000125788		"""Defensins, beta"""	15900	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 8"""	C20orf8		11854508	Standard	NM_030931		Approved	bA530N10.1, DEFB-26	uc002wcx.3	Q9BYW3	OTTHUMG00000031616	ENST00000382398.3:c.314_315delCC	20.37:g.126313_126314delCC	ENSP00000371835:p.Thr105fs	Somatic	34	.	.		WXS	Illumina HiSeq	Phase_I	24	12	0.500	NM_030931	Q562G3|Q9H1M5	Frame_Shift_Del	DEL	ENST00000382398.3	37	CCDS12990.1																																																																																			CC|0.459;-|0.541	0.541	strong		0.455	DEFB126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077428.2	NM_030931	
HSPBAP1	79663	hgsc.bcm.edu	37	3	122459290	122459291	+	In_Frame_Ins	INS	-	-	AGA	rs71270423|rs370465518|rs34964328|rs16338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122459290_122459291insAGA	ENST00000306103.2	-	8	1511_1512	c.1368_1369insTCT	c.(1366-1371)cctcaa>cctTCTcaa	p.456_457PQ>PSQ	HSPBAP1_ENST00000383659.1_3'UTR	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	456				P -> PS (in Ref. 3; AAH17763). {ECO:0000305}.		cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(114;0.0531)		ATGAATGTTTGAGGAGTCGTAG	0.386														759	0.151558	0.2277	0.1671	5008	,	,		16998	0.126		0.1382	False		,,,				2504	0.0777				p.Q457delinsSQ		Pindel,Atlas-Indel	.											HSPBAP1,NS,carcinoma,+1,1	HSPBAP1	32	1	0			c.1369_1370insTCT						PASS	.			830,3436		82,666,1385						1.2	0.0		dbSNP_54	189	1244,7010		94,1056,2977	no	coding	HSPBAP1	NM_024610.5		176,1722,4362	A1A1,A1R,RR		15.0715,19.4562,16.5655				2074,10446				SO:0001652	inframe_insertion	79663	exon8			.	AF400663	CCDS3017.1	3q21.1	2008-07-18	2002-08-29		ENSG00000169087	ENSG00000169087			16389	protein-coding gene	gene with protein product		608263	"""HSPB (heat shock 27kD) associated protein 1"""			11978969	Standard	NM_024610		Approved	FLJ22623, PASS1	uc003efu.2	Q96EW2	OTTHUMG00000159550	ENST00000306103.2:c.1368_1369insTCT	3.37:g.122459290_122459291insAGA	ENSP00000302562:p.Pro456_Gln457insSer	Somatic	296	.	.		WXS	Illumina HiSeq	Phase_I	296	71	0.240	NM_024610	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	In_Frame_Ins	INS	ENST00000306103.2	37	CCDS3017.1																																																																																			-|0.847;AGA|0.153	0.153	strong		0.386	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610	
ZNF717	100131827	hgsc.bcm.edu	37	3	75787812	75787813	+	Frame_Shift_Ins	INS	-	-	T	rs138918118|rs143242394		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75787812_75787813insT	ENST00000478296.1	-	4	1087_1088	c.811_812insA	c.(811-813)agcfs	p.S271fs	ZNF717_ENST00000422325.1_Frame_Shift_Ins_p.S321fs|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Frame_Shift_Ins_p.S314fs|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	314					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						GGACTTATAGCTGAACAATTTT	0.426																																					p.S321fs		Atlas-Indel	.											ZNF717,rectum,carcinoma,0,1	ZNF717	160	1	0			c.962_963insA						PASS	.			368,754		140,88,333						-3.2	0.0		dbSNP_130	5	819,1629		327,165,732	no	frameshift	ZNF717	NM_001128223.1		467,253,1065	A1A1,A1R,RR		33.4559,32.7986,33.2493				1187,2383				SO:0001589	frameshift_variant	100131827	exon5			.	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.812dupA	3.37:g.75787813_75787813dupT	ENSP00000419377:p.Ser271fs	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	70	10	0.142857	NM_001128223		Frame_Shift_Ins	INS	ENST00000478296.1	37																																																																																				.	.	weak		0.426	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
AXDND1	126859	hgsc.bcm.edu	37	1	179504026	179504028	+	In_Frame_Del	DEL	AAG	AAG	-	rs551573109|rs141228272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179504026_179504028delAAG	ENST00000367618.3	+	25	3347_3349	c.2960_2962delAAG	c.(2959-2964)aaagaa>aaa	p.E991del		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	991	Glu-rich.		E -> Q (in dbSNP:rs6425573).							NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agagaagtaaaagaagaagaaga	0.325																																					p.987_987del		Pindel,Atlas-Indel	.											.	AXDND1	142	.	0			c.2959_2961del						PASS	.																																			SO:0001651	inframe_deletion	126859	exon25			.	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2960_2962delAAG	1.37:g.179504035_179504037delAAG	ENSP00000356590:p.Glu991del	Somatic	219	.	.		WXS	Illumina HiSeq	Phase_I	203	53	0.261	NM_144696	Q6AWB2|Q96LJ3|Q96M01	In_Frame_Del	DEL	ENST00000367618.3	37	CCDS30948.1																																																																																			AAG|0.640;-|0.360	0.360	strong		0.325	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	
C14orf23	387978	hgsc.bcm.edu	37	14	29261309	29261310	+	In_Frame_Ins	INS	-	-	AAC	rs79677598|rs71101677|rs56025822|rs151028783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	111	.	.		WXS	Illumina HiSeq	Phase_I	92	29	0.315	.		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	
SUMF2	25870	hgsc.bcm.edu	37	7	56140760	56140761	+	Frame_Shift_Del	DEL	TT	TT	-	rs146946713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:56140760_56140761delTT	ENST00000413756.1	+	3	318_319	c.295_296delTT	c.(295-297)tttfs	p.F99fs	SUMF2_ENST00000395436.2_Frame_Shift_Del_p.F118fs|SUMF2_ENST00000437307.2_Frame_Shift_Del_p.F99fs|SUMF2_ENST00000275607.9_Frame_Shift_Del_p.F11fs|SUMF2_ENST00000342190.6_Frame_Shift_Del_p.F118fs|SUMF2_ENST00000434526.2_Frame_Shift_Del_p.F118fs|SUMF2_ENST00000395435.2_Frame_Shift_Del_p.F118fs			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	99					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CTTTGAGGACTTTGTCTCTGAT	0.48														49	0.00978435	0.034	0.0058	5008	,	,		19873	0.0		0.0	False		,,,				2504	0.0				p.117_118del		Pindel,Atlas-Indel	.											.	SUMF2	56	.	0			c.351_352del						PASS	.		,,,,	133,4131		2,129,2001					,,,,	0.9	0.9		dbSNP_134	120	0,8254		0,0,4127	yes	frameshift,frameshift,frameshift,frameshift,frameshift	SUMF2	NM_015411.2,NM_001146333.1,NM_001130069.2,NM_001042470.1,NM_001042469.1	,,,,	2,129,6128	A1A1,A1R,RR		0.0,3.1191,1.0625	,,,,	,,,,		133,12385				SO:0001589	frameshift_variant	25870	exon3			.	AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103			20415	protein-coding gene	gene with protein product		607940				12757706	Standard	NM_015411		Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.295_296delTT	7.37:g.56140760_56140761delTT	ENSP00000406445:p.Phe99fs	Somatic	105	.	.		WXS	Illumina HiSeq	Phase_I	101	43	0.426	NM_001130069	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Frame_Shift_Del	DEL	ENST00000413756.1	37																																																																																				TT|0.993;-|0.007	0.007	strong		0.480	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411	
ATG2B	55102	hgsc.bcm.edu	37	14	96790337	96790338	+	Splice_Site	INS	-	-	A	rs74857333|rs34296665|rs397948209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:96790337_96790338insA	ENST00000359933.4	-	16	3331		c.e16-2		snoU13_ENST00000458931.1_RNA	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B						autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		GGAACGATCCTAAAAAAAAAGA	0.386													AAAAAAAAAA|AAAAAAAAA|AAAAAAAAAA|deletion	1785	0.35643	0.4902	0.2291	5008	,	,		17409	0.3472		0.3002	False		,,,				2504	0.3333				.		Pindel	.											.	ATG2B	169	.	0			c.2438-2->T						PASS	.			1613,1945		375,863,541						5.3	1.0		dbSNP_126	66	2130,5696		281,1568,2064	no	splice-3	ATG2B	NM_018036.5		656,2431,2605	A1A1,A1R,RR		27.217,45.3345,32.8795				3743,7641				SO:0001630	splice_region_variant	55102	exon17			.	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.2438-2->T	14.37:g.96790346_96790346dupA		Somatic	24	.	.		WXS	Illumina HiSeq	Phase_I	28	17	0.607	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Splice_Site	INS	ENST00000359933.4	37	CCDS9944.2																																																																																			-|0.648;A|0.352	0.352	strong		0.386	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	Intron
RBM12B	389677	hgsc.bcm.edu	37	8	94747893	94747895	+	In_Frame_Del	DEL	CTC	CTC	-	rs533252158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:94747893_94747895delCTC	ENST00000399300.2	-	3	957_959	c.744_746delGAG	c.(742-747)aggaga>aga	p.248_249RR>R	RBM12B_ENST00000520961.1_Intron|RBM12B_ENST00000517700.1_In_Frame_Del_p.248_249RR>R|RP11-10N23.4_ENST00000517998.1_RNA	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	248							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TTCTTCAGATCTCCTAAGAACGT	0.399														7	0.00139776	0.0053	0.0	5008	,	,		20603	0.0		0.0	False		,,,				2504	0.0				p.249_249del		Pindel	.											.	RBM12B	78	.	0			c.745_747del						PASS	.			18,3614		1,16,1799						1.5	0.9			136	4,7904		2,0,3952	no	coding	RBM12B	NM_203390.2		3,16,5751	A1A1,A1R,RR		0.0506,0.4956,0.1906				22,11518				SO:0001651	inframe_deletion	389677	exon3			.		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.744_746delGAG	8.37:g.94747893_94747895delCTC	ENSP00000382239:p.Arg249del	Somatic	151	.	.		WXS	Illumina HiSeq	Phase_I	134	45	0.336	NM_203390	A8MYB5	In_Frame_Del	DEL	ENST00000399300.2	37	CCDS43755.1																																																																																			.	.	none		0.399	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390	
RPGR	6103	hgsc.bcm.edu	37	X	38145694	38145717	+	Intron	DEL	TCCTCCTCTTCCCCCTCCCCTTCC	TCCTCCTCTTCCCCCTCCCCTTCC	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCCTCCTCTTCCCCCTCCCCTTCC	TCCTCCTCTTCCCCCTCCCCTTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145694_38145717delTCCTCCTCTTCCCCCTCCCCTTCC	ENST00000339363.3	-	14	2688				TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000378505.2_In_Frame_Del_p.845_853EEGEGEEEE>E|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						cccttctccttcctcctcttccccctccccttcctcctcttccc	0.607																																					p.846_853del		Pindel	.											.	RPGR	175	.	0			c.2536_2559del	GRCh37	CD022920|CD077431|CI033306|CM004110|CM066945	orf15	D|I|M		PASS	.																																			SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+629GGAAGGGGAGGGGGAAGAGGAGGA>-	X.37:g.38145694_38145717delTCCTCCTCTTCCCCCTCCCCTTCC		Somatic	100	.	.		WXS	Illumina HiSeq	Phase_I	120	24	0.200	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				.	.	none		0.607	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
RELN	5649	hgsc.bcm.edu	37	7	103301976	103301977	+	Splice_Site	INS	-	-	A	rs146986040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103301976_103301977insA	ENST00000428762.1	-	12	1449		c.e12-2		RELN_ENST00000343529.5_Splice_Site|RELN_ENST00000424685.2_Splice_Site	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin						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)		ACATCCCATCTAAAAAAAAAGG	0.351													AAAAAAAAAA|AAAAAAAAA|AAAAAAAAAA|deletion	95	0.0189696	0.0666	0.0086	5008	,	,		18640	0.0		0.001	False		,,,				2504	0.0				.	NSCLC(146;835 1944 15585 22231 52158)	Pindel	.											.	RELN	593	.	0			c.1290-2->T						PASS	.																																			SO:0001630	splice_region_variant	5649	exon13			.		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.1290-2->T	7.37:g.103301985_103301985dupA		Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	68	14	0.206	NM_005045	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Splice_Site	INS	ENST00000428762.1	37	CCDS47680.1																																																																																			.	.	strong		0.351	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	Intron
NADK	65220	hgsc.bcm.edu	37	1	1684348	1684350	+	In_Frame_Del	DEL	CCT	CCT	-	rs139135464|rs558864951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1684348_1684350delCCT	ENST00000341426.5	-	12	1555_1557	c.1334_1336delAGG	c.(1333-1338)gagggc>ggc	p.E445del	NADK_ENST00000342348.5_In_Frame_Del_p.E413del|NADK_ENST00000344463.4_In_Frame_Del_p.E590del|NADK_ENST00000378625.1_In_Frame_Del_p.E590del|NADK_ENST00000341991.3_In_Frame_Del_p.E445del	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	445	Poly-Glu.			E -> EE (in Ref. 2; BAB14412). {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)		TTGACCTAGCcctcctcctcctc	0.631																																					p.590_591del		Pindel	.											.	NADK	79	.	0			c.1770_1772del						PASS	.																																			SO:0001651	inframe_deletion	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_1336delAGG	1.37:g.1684357_1684359delCCT	ENSP00000341679:p.Glu445del	Somatic	82	.	.		WXS	Illumina HiSeq	Phase_I	129	29	0.225	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	In_Frame_Del	DEL	ENST00000341426.5	37	CCDS30565.1																																																																																			.	.	strong		0.631	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018	
ZNF271	10778	hgsc.bcm.edu	37	18	32889822	32889823	+	RNA	INS	-	-	ATTGGTGTCCAAAACTGACACA	rs569387923|rs58173030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:32889822_32889823insATTGGTGTCCAAAACTGACACA	ENST00000399070.3	+	0	4216_4217					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						atggacatgagattggtgtcca	0.411														9	0.00179712	0.0061	0.0014	5008	,	,		19822	0.0		0.0	False		,,,				2504	0.0				.		Pindel	.											.	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.32889822_32889823insATTGGTGTCCAAAACTGACACA		Somatic	43	.	.		WXS	Illumina HiSeq	Phase_I	44	16	0.364	.	B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	RNA	INS	ENST00000399070.3	37																																																																																				.	.	none		0.411	ZNF271-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255767.2	NR_024565	
CFAP74	85452	hgsc.bcm.edu	37	1	1887092	1887112	+	IGR	DEL	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	-	rs3838976|rs199780644|rs3838975|rs562842260|rs139735565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	108	.	.		WXS	Illumina HiSeq	Phase_I	105	23	0.219	NM_001080484		In_Frame_Del	DEL		37																																																																																				-|0.223;G|0.777	0.223	alt	0	0.643								
DSPP	1834	hgsc.bcm.edu	37	4	88535832	88535833	+	In_Frame_Ins	INS	-	-	TAGCAGTGACAGCAGCAG	rs201553143|rs142316753		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88535832_88535833insTAGCAGTGACAGCAGCAG	ENST00000282478.7	+	4	2051_2052	c.2018_2019insTAGCAGTGACAGCAGCAG	c.(2017-2022)gatagc>gaTAGCAGTGACAGCAGCAGtagc	p.680_681insSDSSSS	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_In_Frame_Ins_p.680_681insSDSSSS			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	680	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gacagcagtgatagcagtgaca	0.485																																					p.D673delinsDSSDSSS		Pindel	.											.	DSPP	174	.	0			c.2018_2019insTAGCAGTGACAGCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2019_2036dupTAGCAGTGACAGCAGCAG	4.37:g.88535832_88535833insTAGCAGTGACAGCAGCAG	ENSP00000282478:p.Ser675_Ser680dup	Somatic	349	.	.		WXS	Illumina HiSeq	Phase_I	369	59	0.160	NM_014208	A8MUI0|O95815	In_Frame_Ins	INS	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	alt		0.485	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ZNF233	353355	hgsc.bcm.edu	37	19	44778796	44778799	+	Frame_Shift_Del	DEL	GTTG	GTTG	-	rs59660444|rs76295615|rs2884016|rs386809644|rs386809645|rs2884015|rs75921463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GTTG	GTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44778796_44778799delGTTG	ENST00000391958.2	+	5	2110_2113	c.1983_1986delGTTG	c.(1981-1986)tcgttgfs	p.SL661fs	ZNF235_ENST00000589799.1_Intron|ZNF233_ENST00000592581.1_3'UTR|ZNF233_ENST00000334152.1_Frame_Shift_Del_p.SL643fs	NM_181756.2	NP_861421.2	A6NK53	ZN233_HUMAN	zinc finger protein 233	661					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)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|skin(3)|urinary_tract(1)	20		Prostate(69;0.0435)|all_neural(266;0.226)				GTAAGAGTTCGTTGTCTTCAGATT	0.417																																					p.661_662del		Pindel	.											.	ZNF233	73	.	0			c.1982_1985del						PASS	.																																			SO:0001589	frameshift_variant	353355	exon5			.	AY166792	CCDS33047.1	19q13.31	2013-01-08				ENSG00000159915		"""Zinc fingers, C2H2-type"", ""-"""	30946	protein-coding gene	gene with protein product						12743021	Standard	NM_001207005		Approved	FLJ38032	uc021uvi.1	A6NK53		ENST00000391958.2:c.1983_1986delGTTG	19.37:g.44778796_44778799delGTTG	ENSP00000375820:p.Ser661fs	Somatic	55	.	.		WXS	Illumina HiSeq	Phase_I	58	36	0.621	NM_001207005	B2RN78|B2RN79|Q86WL8	Frame_Shift_Del	DEL	ENST00000391958.2	37	CCDS33047.1																																																																																			-|0.300;G|0.700	0.300	alt		0.417	ZNF233-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460737.1	NM_181756	
ODF1	4956	hgsc.bcm.edu	37	8	103573020	103573037	+	In_Frame_Del	DEL	TGCAGCCCCTGCAACCCG	TGCAGCCCCTGCAACCCG	-	rs143802899|rs111689913|rs568456031|rs372688769|rs369192995|rs377699584|rs62523272|rs62523273|rs386728348|rs58232162|rs150771034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGCAGCCCCTGCAACCCG	TGCAGCCCCTGCAACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103573020_103573037delTGCAGCCCCTGCAACCCG	ENST00000285402.3	+	2	817_834	c.661_678delTGCAGCCCCTGCAACCCG	c.(661-678)tgcagcccctgcaacccgdel	p.CSPCNP221del	ODF1_ENST00000518835.1_In_Frame_Del_p.CSPCNP14del	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	221	C-X-P repeat region.		Missing. {ECO:0000269|PubMed:8111388}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.C218_P226delCNPCSPCNP(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			ctgcaacccctgcagcccctgcaacccgtgcagcccAT	0.546																																					p.220_226del		Pindel	.											.	ODF1	55	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.660_677del						PASS	.																																			SO:0001651	inframe_deletion	4956	exon2			.	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"""Heat shock proteins / HSPB"""	8113	protein-coding gene	gene with protein product	"""cancer/testis antigen 133"""	182878	"""outer dense fibre of sperm tails 1"""			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.661_678delTGCAGCCCCTGCAACCCG	8.37:g.103573020_103573037delTGCAGCCCCTGCAACCCG	ENSP00000285402:p.Cys221_Pro226del	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	100	16	0.160	NM_024410	Q3SX72	In_Frame_Del	DEL	ENST00000285402.3	37	CCDS6293.1																																																																																			.	.	strong		0.546	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1		
KRT3	3850	hgsc.bcm.edu	37	12	53189414	53189431	+	In_Frame_Del	DEL	CCAAAGCCACCAGCCCCT	CCAAAGCCACCAGCCCCT	-	rs148531142|rs184322044|rs142692092		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCAAAGCCACCAGCCCCT	CCAAAGCCACCAGCCCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53189414_53189431delCCAAAGCCACCAGCCCCT	ENST00000417996.2	-	1	470_487	c.396_413delAGGGGCTGGTGGCTTTGG	c.(394-414)ggaggggctggtggctttggt>ggt	p.132_138GGAGGFG>G	KRT3_ENST00000309505.3_In_Frame_Del_p.132_138GGAGGFG>G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	132	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						accaggaccaccaaagccaccagcccctccaaagccac	0.633																																					p.133_138del		Pindel	.											.	KRT3	65	.	0			c.397_414del						PASS	.			595,3499		80,435,1532						-0.9	0.2			185	257,7693		40,177,3758	no	coding	KRT3	NM_057088.2		120,612,5290	A1A1,A1R,RR		3.2327,14.5335,7.0741				852,11192				SO:0001651	inframe_deletion	3850	exon1			.		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.396_413delAGGGGCTGGTGGCTTTGG	12.37:g.53189414_53189431delCCAAAGCCACCAGCCCCT	ENSP00000413479:p.Gly132_Phe137del	Somatic	162	.	.		WXS	Illumina HiSeq	Phase_I	167	35	0.210	NM_057088	A6NIS2|Q701L8	In_Frame_Del	DEL	ENST00000417996.2	37	CCDS44895.1																																																																																			.	.	none		0.633	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
TMEM87B	84910	hgsc.bcm.edu	37	2	112832536	112832538	+	Splice_Site	DEL	AAT	AAT	-	rs201146763|rs71385858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	.											.	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	263	.	.		WXS	Illumina HiSeq	Phase_I	231	53	0.229	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
TMEM255B	348013	hgsc.bcm.edu	37	13	114503876	114503916	+	Splice_Site	DEL	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	-	rs9577890|rs111667140|rs41284485|rs9577889|rs114746443|rs66696122|rs371072437|rs115620789|rs550352190|rs386775130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114503876_114503916delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	ENST00000375353.3	+	6	527_536	c.500_509delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	c.(499-510)gcctgcgggagg>gg	p.ACGR167fs		NM_182614.2	NP_872420.1	Q8WV15	T255B_HUMAN	transmembrane protein 255B	167						integral component of membrane (GO:0016021)											GACCTCTATGCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAG	0.643																																					p.167_170del		Pindel	.											.	.	.	.	0			c.499_509del						PASS	.																																			SO:0001630	splice_region_variant	348013	exon6			.	BC018995	CCDS45071.1	13q34	2012-11-30	2012-11-30	2012-11-30	ENSG00000184497	ENSG00000184497			28297	protein-coding gene	gene with protein product			"""family with sequence similarity 70, member B"""	FAM70B		12477932	Standard	NM_182614		Approved	MGC20579	uc001vuh.3	Q8WV15	OTTHUMG00000017398	ENST00000375353.3:c.509+1CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA>-	13.37:g.114503876_114503916delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA		Somatic	199	.	.		WXS	Illumina HiSeq	Phase_I	138	25	0.181	NM_182614		Frame_Shift_Del	DEL	ENST00000375353.3	37	CCDS45071.1																																																																																			.	.	none		0.643	TMEM255B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045953.4	NM_182614	Frame_Shift_Del
COX20	116228	hgsc.bcm.edu	37	1	245008378	245008380	+	IGR	DEL	TTG	TTG	-	rs147190115|rs376977668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:245008378_245008380delTTG	ENST00000411948.2	+	0	2631				HNRNPU-AS1_ENST00000475997.1_RNA|HNRNPU-AS1_ENST00000489705.1_RNA	NM_198076.4	NP_932342.1	Q5RI15	COX20_HUMAN	COX20 cytochrome C oxidase assembly factor							integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)											ctgtgtatttttgttgttgttct	0.31														559	0.111621	0.1475	0.0922	5008	,	,		17666	0.0109		0.162	False		,,,				2504	0.1288				.		Pindel	.											.	.	.	.	0			.						PASS	.																																			SO:0001628	intergenic_variant	284702	.			.	BC062419	CCDS31080.1	1q44	2013-05-24	2013-05-23	2012-02-24	ENSG00000203667	ENSG00000203667		"""Mitochondrial respiratory chain complex assembly factors"""	26970	protein-coding gene	gene with protein product		614698	"""family with sequence similarity 36, member A"", ""COX20 Cox2 chaperone homolog (S. cerevisiae)"""	FAM36A		22356826, 23125284	Standard	NM_198076		Approved	FLJ43269	uc001iar.3	Q5RI15	OTTHUMG00000040401		1.37:g.245008384_245008386delTTG		Somatic	25	.	.		WXS	Illumina HiSeq	Phase_I	31	10	0.323	.	Q8WV86	RNA	DEL	ENST00000411948.2	37	CCDS31080.1																																																																																			TTG|0.891;-|0.109	0.109	strong		0.310	COX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097174.1	NM_198076	
ZNF107	51427	hgsc.bcm.edu	37	7	64169019	64169019	+	Frame_Shift_Del	DEL	G	G	-	rs201020174|rs376059343|rs4717205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:64169019delG	ENST00000395391.1	+	4	3712	c.2337delG	c.(2335-2337)gagfs	p.E779fs	ZNF107_ENST00000423627.1_Frame_Shift_Del_p.E779fs|ZNF107_ENST00000344930.3_Frame_Shift_Del_p.E779fs			Q9UII5	ZN107_HUMAN	zinc finger protein 107	779					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				ACAAATGTGAGTATGGCAAAA	0.348																																					p.E779fs		Pindel	.											.	ZNF107	107	.	0			c.2336delA						PASS	.						24.0	29.0	28.0					7																	64169019		2199	4297	6496	SO:0001589	frameshift_variant	51427	exon7			.	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"""Zinc fingers, C2H2-type"""	12887	protein-coding gene	gene with protein product		603989	"""zinc finger protein 588"", ""zinc finger protein 107 (Y8)"""	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.2337delG	7.37:g.64169019delG	ENSP00000378789:p.Glu779fs	Somatic	43	.	.		WXS	Illumina HiSeq	Phase_I	42	13	0.310	NM_016220		Frame_Shift_Del	DEL	ENST00000395391.1	37	CCDS5527.1																																																																																			.	.	alt		0.348	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220	
SELPLG	6404	hgsc.bcm.edu	37	12	109017651	109017680	+	In_Frame_Del	DEL	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	-	rs200527674|rs540144714|rs368721402|rs63748999|rs372173288|rs201851784|rs377406736|rs200694582|rs200732108|rs199985195|rs558357966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109017651_109017680delGAGTGGTCTGTGCCTCCGTGGGCACTGGTT	ENST00000550948.1	-	2	628_657	c.404_433delAACCAGTGCCCACGGAGGCACAGACCACTC	c.(403-435)caaccagtgcccacggaggcacagaccactcca>cca	p.QPVPTEAQTT135del	SELPLG_ENST00000228463.6_In_Frame_Del_p.QPVPTEAQTT151del|SELPLG_ENST00000388962.3_Splice_Site_p.NQCPR131del			Q14242	SELPL_HUMAN	selectin P ligand	135	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.Q135P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GCTGCCAGTGGAGTGGTCTGTGCCTCCGTGGGCACTGGTTGAGTGGTCTG	0.617														558	0.111422	0.0817	0.0879	5008	,	,		27757	0.13		0.0835	False		,,,				2504	0.1779				p.151_161del		Pindel	.											.	SELPLG	138	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.453_482del						PASS	.		,	500,3762		33,434,1664					,	-2.0	0.0		dbSNP_129	146	1398,6854		132,1134,2860	no	coding,coding	SELPLG	NM_003006.4,NM_001206609.1	,	165,1568,4524	A1A1,A1R,RR		16.9413,11.7316,15.167	,	,		1898,10616				SO:0001651	inframe_deletion	6404	exon2			.		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.404_433delAACCAGTGCCCACGGAGGCACAGACCACTC	12.37:g.109017651_109017680delGAGTGGTCTGTGCCTCCGTGGGCACTGGTT	ENSP00000447752:p.Gln135_Thr144del	Somatic	305	.	.		WXS	Illumina HiSeq	Phase_I	279	48	0.172	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	In_Frame_Del	DEL	ENST00000550948.1	37	CCDS31895.2																																																																																			.	.	none		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
GPSM2	29899	hgsc.bcm.edu	37	1	109465166	109465168	+	In_Frame_Del	DEL	CTT	CTT	-	rs374875864|rs79761186|rs35029887|rs201481482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109465166_109465168delCTT	ENST00000406462.2	+	14	2341_2343	c.1568_1570delCTT	c.(1567-1572)acttct>act	p.S525del	AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_In_Frame_Del_p.S525del			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	525					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		TCAACAACAACTTCTTCCACTCC	0.374																																					p.523_523del		Pindel	.											.	GPSM2	56	.	0			c.1567_1569del						PASS	.			2409,1857		681,1047,405						-3.5	0.0		dbSNP_126	157	2331,5923		336,1659,2132	no	coding	GPSM2	NM_013296.4		1017,2706,2537	A1A1,A1R,RR		28.2409,43.5302,37.8594				4740,7780				SO:0001651	inframe_deletion	29899	exon13			.	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"""Tetratricopeptide (TTC) repeat domain containing"""	29501	protein-coding gene	gene with protein product		609245	"""G-protein signalling modulator 2 (AGS3-like, C. elegans)"", ""deafness, autosomal recessive 82"""	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.1568_1570delCTT	1.37:g.109465169_109465171delCTT	ENSP00000385510:p.Ser525del	Somatic	196	.	.		WXS	Illumina HiSeq	Phase_I	146	40	0.274	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	In_Frame_Del	DEL	ENST00000406462.2	37	CCDS792.2																																																																																			CTT|0.700;-|0.300	0.300	strong		0.374	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305775	39305776	+	In_Frame_Ins	INS	-	-	GGCAGCAGCTGGGGC	rs535144703|rs141265645|rs58117746|rs146438235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305775_39305776insGGCAGCAGCTGGGGC	ENST00000343246.4	-	1	278_279	c.244_245insGCCCCAGCTGCTGCC	c.(244-246)cag>cGCCCCAGCTGCTGCCag	p.81_82insRPSCC		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	81	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)			gcaggtggtctggcagcagcag	0.653														2119	0.423123	0.5401	0.4236	5008	,	,		17097	0.3065		0.3897	False		,,,				2504	0.4192				p.Q82delinsRPSCCQ		Pindel	.											KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	1	0			c.245_246insGCCCCAGCTGCTGCC						PASS	.																																			SO:0001652	inframe_insertion	85289	exon1			.	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.244_245insGCCCCAGCTGCTGCC	17.37:g.39305775_39305776insGGCAGCAGCTGGGGC	ENSP00000340546:p.Cys81_Gln82insArgProSerCysCys	Somatic	137	.	.		WXS	Illumina HiSeq	Phase_I	90	26	0.289	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	37	CCDS32650.1																																																																																			.	.	none		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
ABCF1	23	hgsc.bcm.edu	37	6	30545854	30545854	+	Splice_Site	DEL	A	A	-	rs555740367		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30545854delA	ENST00000326195.8	+	4	330	c.218delA	c.(217-219)caa>ca	p.Q73fs	ABCF1_ENST00000376545.3_Splice_Site_p.Q73fs|ABCF1_ENST00000396515.4_Splice_Site_p.Q73fs	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	73					inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						TCTCAGCAGCAAAAAAAAAAG	0.493																																					p.Q73fs		Pindel	.											.	ABCF1	61	.	0			c.217delC						PASS	.		,	66,405,3793		0,0,66,1,403,1662	64.0	70.0	68.0		,	5.5	1.0	6		71	105,634,7515		0,1,104,0,633,3389	no	codingComplex-near-splice,codingComplex-near-splice	ABCF1	NM_001090.2,NM_001025091.1	,	0,1,170,1,1036,5051	A1A1,A1A2,A1R,A2A2,A2R,RR		8.9532,11.046,9.6661	,	,	30545854	171,1039,11308	2203	4300	6503	SO:0001630	splice_region_variant	23	exon4			.	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"""ATP binding cassette transporters / subfamily F"""	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.217-1A>-	6.37:g.30545854delA		Somatic	65	.	.		WXS	Illumina HiSeq	Phase_I	62	10	0.161	NM_001090	A2BF75|O14897|Q69YP6	Frame_Shift_Del	DEL	ENST00000326195.8	37	CCDS34380.1																																																																																			.	.	none		0.493	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3		Frame_Shift_Del
PRKCSH	5589	hgsc.bcm.edu	37	19	11558341	11558343	+	In_Frame_Del	DEL	GAG	GAG	-	rs397840350|rs71166603|rs3217229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11558341_11558343delGAG	ENST00000589838.1	+	10	937_939	c.937_939delGAG	c.(937-939)gagdel	p.E325del	PRKCSH_ENST00000412601.1_In_Frame_Del_p.E325del|PRKCSH_ENST00000587327.1_In_Frame_Del_p.E325del|PRKCSH_ENST00000252455.2_In_Frame_Del_p.E325del|PRKCSH_ENST00000591462.1_In_Frame_Del_p.E325del|PRKCSH_ENST00000592741.1_In_Frame_Del_p.E325del			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	325	Glu-rich (acidic).			Missing (in Ref. 1; AAA52493, 2; AAA98668, 4; AAP88860 and 6; AAH13586). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						GTCGCCCACAgaggaggaggagg	0.65														2250	0.449281	0.559	0.4323	5008	,	,		15796	0.3661		0.4245	False		,,,				2504	0.4243				p.312_313del		Pindel	.											.	PRKCSH	55	.	0			c.936_938del						PASS	.																																			SO:0001651	inframe_deletion	5589	exon11			.		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"""EF-hand domain containing"""	9411	protein-coding gene	gene with protein product		177060	"""polycystic liver disease"""	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.937_939delGAG	19.37:g.11558350_11558352delGAG	ENSP00000465461:p.Glu325del	Somatic	150	.	.		WXS	Illumina HiSeq	Phase_I	175	55	0.314	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	In_Frame_Del	DEL	ENST00000589838.1	37	CCDS32911.1																																																																																			GAG|0.500;-|0.500	0.500	strong		0.650	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
CALHM3	119395	hgsc.bcm.edu	37	10	105233174	105233175	+	In_Frame_Ins	INS	-	-	GGGGGCTCAGGCACTGCG	rs143800079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105233174_105233175insGGGGGCTCAGGCACTGCG	ENST00000369783.4	-	3	1037_1038	c.830_831insCGCAGTGCCTGAGCCCCC	c.(829-831)cca>ccCGCAGTGCCTGAGCCCCCa	p.277_277P>PAVPEPP		NM_001129742.1	NP_001123214.1	Q86XJ0	CAHM3_HUMAN	calcium homeostasis modulator 3	283					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)	2						CCAGGCCTTCTGGGGGCTCAGG	0.673														657	0.13119	0.3495	0.0648	5008	,	,		17893	0.124		0.004	False		,,,				2504	0.0215				p.P277delinsPAVPEPP		Pindel	.											.	CALHM3	46	.	0			c.831_832insCGCAGTGCCTGAGCCCCC						PASS	.			510,1718		115,280,719						-7.8	0.0		dbSNP_134	19	9,4303		0,9,2147	no	coding	CALHM3	NM_001129742.1		115,289,2866	A1A1,A1R,RR		0.2087,22.8905,7.9358				519,6021				SO:0001652	inframe_insertion	119395	exon3			.	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.813_830dupCGCAGTGCCTGAGCCCCC	10.37:g.105233174_105233175insGGGGGCTCAGGCACTGCG	ENSP00000358798:p.AlaValProGluProPro277dup	Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	70	11	0.157	NM_001129742	Q5W090|Q8IXR2	In_Frame_Ins	INS	ENST00000369783.4	37	CCDS44476.1																																																																																			-|0.871;GGGGGCTCAGGCACTGCG|0.129	0.129	strong		0.673	CALHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050157.1	NM_182494	
ACIN1	22985	hgsc.bcm.edu	37	14	23549879	23549881	+	In_Frame_Del	DEL	TCC	TCC	-	rs3841035|rs57580458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23549879_23549881delTCC	ENST00000262710.1	-	6	1164_1166	c.837_839delGGA	c.(835-840)gaggaa>gaa	p.279_280EE>E	ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000555053.1_In_Frame_Del_p.279_280EE>E|ACIN1_ENST00000605057.1_In_Frame_Del_p.221_222EE>E|ACIN1_ENST00000457657.1_In_Frame_Del_p.239_240EE>E	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	279	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		atcatcttcttcctcctcctcct	0.458														537	0.107228	0.1475	0.0576	5008	,	,		22843	0.2073		0.0497	False		,,,				2504	0.044				p.280_280del		Pindel	.											.	ACIN1	147	.	0			c.838_840del						PASS	.																																			SO:0001651	inframe_deletion	22985	exon6			.	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.837_839delGGA	14.37:g.23549888_23549890delTCC	ENSP00000262710:p.Glu281del	Somatic	150	.	.		WXS	Illumina HiSeq	Phase_I	172	29	0.169	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	In_Frame_Del	DEL	ENST00000262710.1	37	CCDS9587.1																																																																																			.	.	strong		0.458	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
PCSK9	255738	hgsc.bcm.edu	37	1	55505552	55505553	+	In_Frame_Ins	INS	-	-	CTG	rs35574083|rs371488778|rs113330492|rs45454392|rs67610340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55505552_55505553insCTG	ENST00000302118.5	+	1	332_333	c.42_43insCTG	c.(43-45)ctg>CTGctg	p.15_15L>LL	PCSK9_ENST00000543384.1_5'Flank|PCSK9_ENST00000452118.2_In_Frame_Ins_p.15_15L>LL	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	15					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.P14_L15insL(2)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						Ggccgctgccactgctgctgct	0.703																																					p.P14delinsPL	Pancreas(137;1454 1827 5886 22361 42375)	Pindel	.											.	PCSK9	76	.	2	Insertion - In frame(2)	breast(1)|central_nervous_system(1)	c.42_43insCTG						PASS	.																																			SO:0001652	inframe_insertion	255738	exon1			.	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.61_63dupCTG	1.37:g.55505559_55505561dupCTG	ENSP00000303208:p.Leu23dup	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	78	13	0.167	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	In_Frame_Ins	INS	ENST00000302118.5	37	CCDS603.1																																																																																			.	.	none		0.703	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
C11orf40	143501	hgsc.bcm.edu	37	11	4592706	4592707	+	Frame_Shift_Ins	INS	-	-	AC	rs80310454|rs67702097|rs141600462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4592706_4592707insAC	ENST00000307616.1	-	4	599_600	c.600_601insGT	c.(598-603)tgtatgfs	p.M201fs		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	201										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)		acacgatccatacagtttttcc	0.426																																					p.M201fs		Pindel	.											.	C11orf40	37	.	0			c.601_602insGT						PASS	.			2670,1456		925,820,318						-0.7	0.0		dbSNP_130	78	4274,3706		1320,1634,1036	no	frameshift	C11orf40	NM_144663.1		2245,2454,1354	A1A1,A1R,RR		46.4411,35.2884,42.64				6944,5162				SO:0001589	frameshift_variant	143501	exon4			.		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.599_600dupGT	11.37:g.4592707_4592708dupAC	ENSP00000302918:p.Met201fs	Somatic	152	.	.		WXS	Illumina HiSeq	Phase_I	161	46	0.286	NM_144663		Frame_Shift_Ins	INS	ENST00000307616.1	37	CCDS31354.1																																																																																			-|0.377;AC|0.623	0.623	strong		0.426	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663	
ATR	545	hgsc.bcm.edu	37	3	142274740	142274740	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:142274740delT	ENST00000350721.4	-	10	2441	c.2320delA	c.(2320-2322)atafs	p.I774fs	ATR_ENST00000383101.3_Frame_Shift_Del_p.I710fs	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	774					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.I774fs*5(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GGACTAGGTATTTTTTTTTTC	0.328								Other conserved DNA damage response genes																													p.I774fs		Pindel	.											.	ATR	285	.	1	Deletion - Frameshift(1)	breast(1)	c.2321delT						PASS	.						72.0	79.0	77.0					3																	142274740		2203	4300	6503	SO:0001589	frameshift_variant	545	exon10			.	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.2320delA	3.37:g.142274740delT	ENSP00000343741:p.Ile774fs	Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	74	17	0.230	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Frame_Shift_Del	DEL	ENST00000350721.4	37	CCDS3124.1																																																																																			.	.	none		0.328	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
PA2G4	5036	hgsc.bcm.edu	37	12	56500502	56500503	+	Splice_Site	INS	-	-	A	rs71074902|rs34728522|rs398019698		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56500502_56500503insA	ENST00000303305.6	+	2	636		c.e2+2		PA2G4_ENST00000552766.1_Splice_Site|RP11-603J24.17_ENST00000548595.1_RNA|RP11-603J24.9_ENST00000548861.1_Splice_Site	NM_006191.2	NP_006182.2	Q9UQ80	PA2G4_HUMAN	proliferation-associated 2G4, 38kDa						cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of translation (GO:0006417)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)	p.?(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(18;0.0739)			TGAAGAAAGGTAAAAAAAAAAA	0.396																																					.		Pindel	.											.	PA2G4	24	.	1	Unknown(1)	ovary(1)	c.217+2->A						PASS	.																																			SO:0001630	splice_region_variant	5036	exon2			.	U59435, BC007561	CCDS8902.1	12q13.2	2008-09-05	2002-08-29		ENSG00000170515	ENSG00000170515			8550	protein-coding gene	gene with protein product		602145	"""proliferation-associated 2G4, 38kD"""			9345902	Standard	NM_006191		Approved		uc001sjm.3	Q9UQ80	OTTHUMG00000170173	ENST00000303305.6:c.217+2->A	12.37:g.56500513_56500513dupA		Somatic	32	.	.		WXS	Illumina HiSeq	Phase_I	35	12	0.343	NM_006191	O43846|Q9UM59	Splice_Site	INS	ENST00000303305.6	37	CCDS8902.1																																																																																			-|0.250;A|0.750	0.750	weak		0.396	PA2G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407767.1	NM_006191	Intron
CELA1	1990	hgsc.bcm.edu	37	12	51740388	51740416	+	Splice_Site	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-	rs150350903|rs573952082|rs532961697|rs141305161|rs117443541|rs377599213|rs143199509|rs61761206|rs3059200|rs148235680|rs370927847|rs907354|rs148270827|rs116944010|rs57614420|rs386762976|rs55827519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:51740388_51740416delCTGGACCATATCCACTTACCATAAAGGAC	ENST00000293636.1	-	1	47_57	c.7_17delGTCCTTTATGGTAAGTGGATATGGTCCAG	c.(7-18)gtcctttatggt>t	p.VLYG3fs		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	3					exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)|p.L4P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						AGGGTTGCGACTGGACCATATCCACTTACCATAAAGGACCAGCATGTTG	0.511																																					p.3_6del		Pindel	.											.	CELA1	39	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.8_16del						PASS	.																																			SO:0001630	splice_region_variant	1990	exon1			.		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.16+1GTCCTTTATGGTAAGTGGATATGGTCCAG>-	12.37:g.51740388_51740416delCTGGACCATATCCACTTACCATAAAGGAC		Somatic	161	.	.		WXS	Illumina HiSeq	Phase_I	123	19	0.154	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	In_Frame_Del	DEL	ENST00000293636.1	37	CCDS8812.1																																																																																			-|0.574;CACCAGGAAGCG|0.426	0.574	alt		0.511	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	Frame_Shift_Del
CRELD2	79174	hgsc.bcm.edu	37	22	50315936	50315973	+	Intron	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-	rs377640443|rs562885075|rs542695980|rs113299196|rs7410276|rs12160965|rs371945800|rs386822607|rs386822606|rs564615833|rs368043307|rs71805922|rs386822608|rs73891177|rs553609580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50315936_50315973delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	ENST00000328268.4	+	6	666				CRELD2_ENST00000403427.3_Intron|CRELD2_ENST00000404488.3_Splice_Site_p.PQQSGPASPI198fs|CRELD2_ENST00000444954.1_Intron|CRELD2_ENST00000407217.3_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)		TTCTTACGCCCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCGCCTTGCTGTC	0.622																																					p.198_207del		Pindel	.											.	CRELD2	57	.	0			c.593_620del						PASS	.		,	660,2750		176,308,1221					,	-1.2	0.0		dbSNP_130	26	366,6880		58,250,3315	no	intron,frameshift-near-splice	CRELD2	NM_024324.3,NM_001135101.1	,	234,558,4536	A1A1,A1R,RR		5.0511,19.3548,9.6284	,	,		1026,9630				SO:0001627	intron_variant	79174	exon6			.	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.593-287CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG>-	22.37:g.50315936_50315973delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG		Somatic	50	.	.		WXS	Illumina HiSeq	Phase_I	31	29	0.935	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Frame_Shift_Del	DEL	ENST00000328268.4	37	CCDS14082.1																																																																																			.	.	none		0.622	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
NFKB1	4790	hgsc.bcm.edu	37	4	103534740	103534741	+	Splice_Site	INS	-	-	A	rs386357216|rs148268461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:103534740_103534741insA	ENST00000505458.1	+	23	3023		c.e23+2		NFKB1_ENST00000226574.4_Splice_Site|NFKB1_ENST00000600343.1_Splice_Site|NFKB1_ENST00000394820.4_Splice_Site			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1						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)	AGCAAATAGGTAAAAAAAAAGA	0.5													?|AAAAAAAAA|AAAAAAAAAA|unsure	422	0.0842652	0.1641	0.0389	5008	,	,		18742	0.0605		0.0696	False		,,,				2504	0.0481				.		Pindel	.											.	NFKB1	78	.	0			c.2746+2->A						PASS	.		,	509,3757		21,467,1645					,	4.8	1.0		dbSNP_126	29	537,7717		10,517,3600	no	splice-5,splice-5	NFKB1	NM_003998.3,NM_001165412.1	,	31,984,5245	A1A1,A1R,RR		6.5059,11.9316,8.3546	,	,		1046,11474				SO:0001630	splice_region_variant	4790	exon23			.	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.2746+2->A	4.37:g.103534749_103534749dupA		Somatic	82	.	.		WXS	Illumina HiSeq	Phase_I	63	17	0.270	NM_001165412	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Splice_Site	INS	ENST00000505458.1	37	CCDS54783.1																																																																																			-|0.899;A|0.101	0.101	strong		0.500	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1		Intron
RPL14	9045	hgsc.bcm.edu	37	3	40503521	40503529	+	In_Frame_Del	DEL	CTGCTGCTG	CTGCTGCTG	-	rs147295890|rs201931132|rs370958149|rs201325213|rs111899316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTGCTGCTG	CTGCTGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:40503521_40503529delCTGCTGCTG	ENST00000396203.2	+	6	578_586	c.446_454delCTGCTGCTG	c.(445-456)actgctgctgct>act	p.AAA156del	RPL14_ENST00000416518.1_3'UTR|RPL14_ENST00000338970.6_In_Frame_Del_p.AAA156del	NM_001034996.2	NP_001030168.1	P50914	RL14_HUMAN	ribosomal protein L14	156					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)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)								KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		ACTAAGGGTActgctgctgctgctgctgc	0.483																																					p.149_151del		Pindel	.											.	RPL14	21	.	0			c.445_453del						PASS	.																																			SO:0001651	inframe_deletion	9045	exon6			.	D87735	CCDS33739.1, CCDS43070.1	3p22-p21.2	2008-07-18			ENSG00000188846	ENSG00000188846		"""L ribosomal proteins"""	10305	protein-coding gene	gene with protein product	"""CAG-ISL 7"", ""60S ribosomal protein L14"""					9480843	Standard	NM_003973		Approved	L14, hRL14, RL14, CTG-B33	uc003ckg.4	P50914	OTTHUMG00000156046	ENST00000396203.2:c.446_454delCTGCTGCTG	3.37:g.40503530_40503538delCTGCTGCTG	ENSP00000379506:p.Ala156_Ala158del	Somatic	58	.	.		WXS	Illumina HiSeq	Phase_I	81	27	0.333	NM_001034996	Q45RF0|Q53G20|Q8TBD5|Q8WUT0|Q92579|Q96GR0|Q9BSB8|Q9BW65|Q9BYF6	In_Frame_Del	DEL	ENST00000396203.2	37	CCDS43070.1																																																																																			.	.	strong		0.483	RPL14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342889.2	NM_003973	
SERPINB3	6317	hgsc.bcm.edu	37	18	61323012	61323014	+	In_Frame_Del	DEL	CCT	CCT	-	rs3180227|rs60286570|rs386804125|rs72132327|rs201374310	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323012_61323014delCCT	ENST00000283752.5	-	8	1193_1195	c.1050_1052delAGG	c.(1048-1053)gtagga>gta	p.G351del	SERPINB3_ENST00000332821.8_In_Frame_Del_p.G299del|SERPINB11_ENST00000489748.1_RNA	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	351			G -> A (increased antiprotease activity and increased MAPK8 inhibition activity; dbSNP:rs3180227). {ECO:0000269|PubMed:12975381, ECO:0000269|PubMed:14970861, ECO:0000269|PubMed:21383048, ECO:0000269|Ref.6}.		negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TGATCCGAATCCTACTACAGCGG	0.488																																					p.351_351del		Pindel	.											.	SERPINB3	90	.	0			c.1051_1053del						PASS	.																																			SO:0001651	inframe_deletion	6317	exon8			.	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1050_1052delAGG	18.37:g.61323012_61323014delCCT	ENSP00000283752:p.Gly351del	Somatic	211	.	.		WXS	Illumina HiSeq	Phase_I	190	42	0.221	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	In_Frame_Del	DEL	ENST00000283752.5	37	CCDS11987.1																																																																																			.	.	alt		0.488	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
NKAP	79576	hgsc.bcm.edu	37	X	119070328	119070330	+	In_Frame_Del	DEL	GAT	GAT	-	rs10577974		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:119070328_119070330delGAT	ENST00000371410.3	-	4	769_771	c.603_605delATC	c.(601-606)tcatcg>tcg	p.201_202SS>S	NKAP_ENST00000477789.1_5'UTR	NM_024528.3	NP_078804.2	Q8N5F7	NKAP_HUMAN	NFKB activating protein	201	Lys-rich.|Necessary for interaction with CIR1.				granulocyte differentiation (GO:0030851)|hematopoietic stem cell proliferation (GO:0071425)|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 alpha-beta T cell differentiation (GO:0046638)|stem cell maintenance (GO:0019827)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)	p.S202L(1)		breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)	20						TTTTCTTTTCGATGATTTTTTCT	0.34														357	0.0945695	0.1747	0.0476	3775	,	,		11854	0.001		0.0388	False		,,,				2504	0.0542				p.202_202del		Pindel	.											.	NKAP	53	.	1	Substitution - Missense(1)	large_intestine(1)	c.604_606del						PASS	.			823,2898		78,555,112,959,425						-0.6	1.0		dbSNP_119	144	341,6143		8,230,95,2119,1675	no	coding	NKAP	NM_024528.3		86,785,207,3078,2100	A1A1,A1R,A1,RR,R		5.2591,22.1177,11.4062				1164,9041				SO:0001651	inframe_deletion	79576	exon4			.	BC012770	CCDS14592.1	Xq24	2010-07-20			ENSG00000101882	ENSG00000101882			29873	protein-coding gene	gene with protein product	"""NF kappaB activating protein"""	300766				14550261	Standard	NM_024528		Approved	FLJ22626	uc004esh.3	Q8N5F7	OTTHUMG00000022284	ENST00000371410.3:c.603_605delATC	X.37:g.119070331_119070333delGAT	ENSP00000360464:p.Ser202del	Somatic	447	.	.		WXS	Illumina HiSeq	Phase_I	366	93	0.254	NM_024528	Q6IPW6|Q96BQ2|Q9H638	In_Frame_Del	DEL	ENST00000371410.3	37	CCDS14592.1																																																																																			.	.	weak		0.340	NKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058072.1	NM_024528	
RPGR	6103	hgsc.bcm.edu	37	X	38145199	38145201	+	Intron	DEL	TCC	TCC	-	rs200955614		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145199_38145201delTCC	ENST00000339363.3	-	14	2688				TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000378505.2_In_Frame_Del_p.1017_1018EE>E|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						cacttccccttcctcttcttcct	0.581														38	0.0100662	0.0265	0.0043	3775	,	,		8305	0.0		0.0	False		,,,				2504	0.0				p.1018_1018del		Pindel	.											.	RPGR	175	.	0			c.3052_3054del	GRCh37	CD004123	orf15	D		PASS	.		,	173,3490		4,136,29,1439,476					,	-0.5	0.0			35	175,6221		2,108,63,2240,1633	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	6,244,92,3679,2109	A1A1,A1R,A1,RR,R		2.7361,4.7229,3.4596	,	,		348,9711				SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+1145GGA>-	X.37:g.38145199_38145201delTCC		Somatic	29	.	.		WXS	Illumina HiSeq	Phase_I	55	10	0.182	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				TCC|0.992;-|0.008	0.008	strong		0.581	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
ZNF720	124411	hgsc.bcm.edu	37	16	31770696	31770697	+	Stop_Codon_Ins	INS	-	-	A	rs398119344|rs34487972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31770696_31770697insA	ENST00000316491.9	+	0	579_580				ZNF720_ENST00000539915.1_Stop_Codon_Ins|ZNF720_ENST00000534369.1_Intron|ZNF720_ENST00000531864.2_Intron	NM_001130913.1	NP_001124385.1	Q7Z2F6	ZN720_HUMAN	zinc finger protein 720						regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)|lung(1)|stomach(1)	4						atcctatggtgaaaaaaatcaa	0.332													AAAAAAA|AAAAAAA|AAAAAAAA|insertion	2393	0.477835	0.4864	0.4568	5008	,	,		14830	0.3185		0.6769	False		,,,				2504	0.4407				p.X127delinsX		Pindel	.											.	ZNF720	15	.	0			c.380_381insA						PASS	.			910,912		273,364,274						0.2	0.1		dbSNP_134	65	2657,1163		997,663,250	no	frameshift	ZNF720	NM_001130913.1		1270,1027,524	A1A1,A1R,RR		30.445,49.9451,36.7777				3567,2075				SO:0001567	stop_retained_variant	124411	exon5			.	AK128671	CCDS45473.1	16p11.2	2013-01-08				ENSG00000197302		"""Zinc fingers, C2H2-type"", ""-"""	26987	protein-coding gene	gene with protein product							Standard	NM_001130913		Approved		uc002ecq.3	Q7Z2F6		ENST00000316491.9:c.385dupA	16.37:g.31770703_31770703dupA		Somatic	232	.	.		WXS	Illumina HiSeq	Phase_I	201	64	0.318	NM_001130913	Q6ZQX1	Frame_Shift_Ins	INS	ENST00000316491.9	37	CCDS45473.1																																																																																			A|1.000;|0.000	1.000	strong		0.332	ZNF720-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394883.3	NM_001004300	
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1606121	1606150	+	In_Frame_Del	DEL	CCACAGCCACCCTTGGATCCCCCACAAGAG	CCACAGCCACCCTTGGATCCCCCACAAGAG	-	rs138363822|rs199501537|rs80025267|rs76191756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCACAGCCACCCTTGGATCCCCCACAAGAG	CCACAGCCACCCTTGGATCCCCCACAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1606121_1606150delCCACAGCCACCCTTGGATCCCCCACAAGAG	ENST00000382171.2	-	1	363_392	c.330_359delCTCTTGTGGGGGATCCAAGGGTGGCTGTGG	c.(328-360)ggctcttgtgggggatccaagggtggctgtggt>ggt	p.110_120GSCGGSKGGCG>G	KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	110	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACAGCCGGAACCACAGCCACCCTTGGATCCCCCACAAGAGCCACAGCCCC	0.661																																					p.111_120del		Pindel	.											.	KRTAP5-1	74	.	0			c.331_360del						PASS	.			2171,2035		609,953,541						-5.2	0.0			71	4129,4059		1127,1875,1092	no	coding	KRTAP5-1	NM_001005922.1		1736,2828,1633	A1A1,A1R,RR		49.5725,48.3833,49.169				6300,6094				SO:0001651	inframe_deletion	387264	exon1			.	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.330_359delCTCTTGTGGGGGATCCAAGGGTGGCTGTGG	11.37:g.1606121_1606150delCCACAGCCACCCTTGGATCCCCCACAAGAG	ENSP00000371606:p.Gly110_Cys119del	Somatic	277	.	.		WXS	Illumina HiSeq	Phase_I	153	45	0.294	NM_001005922		In_Frame_Del	DEL	ENST00000382171.2	37	CCDS31330.1																																																																																			.	.	none		0.661	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
CLDN16	10686	hgsc.bcm.edu	37	3	190106073	190106074	+	Frame_Shift_Del	DEL	GG	GG	-	rs386669518|rs3214506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:190106073_190106074delGG	ENST00000264734.2	+	1	413_414	c.165_166delGG	c.(163-168)agggctfs	p.RA55fs	CLDN16_ENST00000468220.1_Intron|CLDN16_ENST00000456423.1_Frame_Shift_Del_p.RA55fs	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	55					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		GTGGGGCCAGGGCTGGTGTCTG	0.505																																					p.55_55del		Pindel	.											.	CLDN16	59	.	0			c.164_165del	GRCh37	CX001601	CLDN16	X		PASS	.																																			SO:0001589	frameshift_variant	10686	exon1			.	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"""Claudins"""	2037	protein-coding gene	gene with protein product	"""paracellin-1"", ""hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"""	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.165_166delGG	3.37:g.190106073_190106074delGG	ENSP00000264734:p.Arg55fs	Somatic	205	.	.		WXS	Illumina HiSeq	Phase_I	238	38	0.160	NM_006580		Frame_Shift_Del	DEL	ENST00000264734.2	37	CCDS3296.1																																																																																			.	.	none		0.505	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580	
CYP2F1	1572	hgsc.bcm.edu	37	19	41622107	41622108	+	Frame_Shift_Ins	INS	-	-	C	rs79512346|rs79756737|rs3833221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41622107_41622108insC	ENST00000331105.2	+	2	86_87	c.14_15insC	c.(13-18)agcacafs	p.T6fs		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	6					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						GACAGCATAAGCACAGCCATCT	0.574													C|C|CC|insertion	1362	0.271965	0.4251	0.1873	5008	,	,		21760	0.251		0.1799	False		,,,				2504	0.2413				p.S5fs		Pindel	.											.	CYP2F1	60	.	0			c.14_15insC	GRCh37	CI071425	CYP2F1	I	rs3833221	PASS	.			1649,2615		313,1023,796						-0.3	0.0		dbSNP_107	110	1550,6704		137,1276,2714	yes	frameshift	CYP2F1	NM_000774.3		450,2299,3510	A1A1,A1R,RR		18.7788,38.6726,25.5552				3199,9319				SO:0001589	frameshift_variant	1572	exon2			.	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"""Cytochrome P450s"""	2632	protein-coding gene	gene with protein product		124070	"""cytochrome P450, subfamily IIF, polypeptide 1"""	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.15dupC	19.37:g.41622108_41622108dupC	ENSP00000333534:p.Thr6fs	Somatic	105	.	.		WXS	Illumina HiSeq	Phase_I	101	59	0.584	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Frame_Shift_Ins	INS	ENST00000331105.2	37	CCDS12572.1																																																																																			-|0.741;C|0.259	0.259	strong		0.574	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
DMKN	93099	hgsc.bcm.edu	37	19	36002371	36002394	+	In_Frame_Del	DEL	CCACTGCTGCCGCCACTGCTGCCG	CCACTGCTGCCGCCACTGCTGCCG	-	rs112672248|rs142519211|rs11667007|rs12981076|rs146822312|rs148799704|rs56743379|rs371511253|rs117522133|rs59309505|rs58579970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCACTGCTGCCGCCACTGCTGCCG	CCACTGCTGCCGCCACTGCTGCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002371_36002394delCCACTGCTGCCGCCACTGCTGCCG	ENST00000339686.3	-	5	1013_1036	c.837_860delCGGCAGCAGTGGCGGCAGCAGTGG	c.(835-861)ggcggcagcagtggcggcagcagtggt>ggt	p.279_287GGSSGGSSG>G	DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000451297.2_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000447113.2_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000424570.2_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000440396.1_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000418261.1_In_Frame_Del_p.279_287GGSSGGSSG>G	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	279	Gly-rich.		G -> S (in dbSNP:rs11667007). {ECO:0000269|PubMed:17380110}.	G -> GSSSG (in Ref. 4; AAQ88778). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			actgctgccaccactgctgccgccactgctgccgccactgctgc	0.638																																					p.280_287del		Pindel	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.838_861del						PASS	.																																			SO:0001651	inframe_deletion	93099	exon5			.	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.837_860delCGGCAGCAGTGGCGGCAGCAGTGG	19.37:g.36002371_36002394delCCACTGCTGCCGCCACTGCTGCCG	ENSP00000342012:p.Gly279_Ser286del	Somatic	91	.	.		WXS	Illumina HiSeq	Phase_I	90	25	0.278	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	In_Frame_Del	DEL	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	none		0.638	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197501	39197638	+	In_Frame_Del	DEL	CAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGA	CAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGA	-	rs201337527|rs28754643|rs138200823|rs202102709|rs200387980|rs563248221|rs141856614|rs145621540|rs140730427|rs541445273|rs184451637|rs368924344|rs371365111|rs188978965|rs200996142|rs530531259|rs367698389|rs146863522|rs375968978|rs369511015|rs150218495|rs201624038|rs112542604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGA	CAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39197501_39197638delCAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGA	ENST00000306271.4	-	1	75_212	c.12_149delTCAGACCAGCTTCTGTGGATTTCCCAGCTGCTCCACCAGTGGGACCTGCGGCTCCAGCTGCTGCCAGCCAAGCTGCTGTGAGACCAGCTCCTGCCAGCCACGCTGCTGTGAGACCAGCTGCTGCCAGCCAAGCTGCTG	c.(10-150)tgtcagaccagcttctgtggatttcccagctgctccaccagtgggacctgcggctccagctgctgccagccaagctgctgtgagaccagctcctgccagccacgctgctgtgagaccagctgctgccagccaagctgctgc>tgc	p.4_50CQTSFCGFPSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCC>C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	4			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)		p.S34C(6)|p.R38S(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GCTGGTCTGGCAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGACAGCAGGCCA	0.571																																					p.5_50del		Pindel	.											.	KRTAP1-1	23	.	7	Substitution - Missense(7)	kidney(4)|lung(1)|NS(1)|prostate(1)	c.13_150del						PASS	.																																			SO:0001651	inframe_deletion	81851	exon1			.	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.12_149delTCAGACCAGCTTCTGTGGATTTCCCAGCTGCTCCACCAGTGGGACCTGCGGCTCCAGCTGCTGCCAGCCAAGCTGCTGTGAGACCAGCTCCTGCCAGCCACGCTGCTGTGAGACCAGCTGCTGCCAGCCAAGCTGCTG	17.37:g.39197501_39197638delCAGCAGCTTGGCTGGCAGCAGCTGGTCTCACAGCAGCGTGGCTGGCAGGAGCTGGTCTCACAGCAGCTTGGCTGGCAGCAGCTGGAGCCGCAGGTCCCACTGGTGGAGCAGCTGGGAAATCCACAGAAGCTGGTCTGA	ENSP00000305975:p.Cys4_Cys49del	Somatic	224	.	.		WXS	Illumina HiSeq	Phase_I	229	43	0.188	NM_030967	A6NC32|Q96S60|Q96S67	In_Frame_Del	DEL	ENST00000306271.4	37	CCDS42324.1																																																																																			.	.	none		0.571	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
KAT6B	23522	hgsc.bcm.edu	37	10	76781906	76781908	+	In_Frame_Del	DEL	GAA	GAA	-	rs72074375|rs144154275|rs371512199|rs79644703|rs559824889|rs71929101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76781906_76781908delGAA	ENST00000287239.4	+	16	3778_3780	c.3289_3291delGAA	c.(3289-3291)gaadel	p.E1104del	KAT6B_ENST00000372725.1_In_Frame_Del_p.E812del|KAT6B_ENST00000372711.1_In_Frame_Del_p.E921del|RP11-77G23.2_ENST00000413431.1_RNA|KAT6B_ENST00000490365.1_3'UTR|RP11-77G23.5_ENST00000436608.1_RNA|KAT6B_ENST00000372714.1_In_Frame_Del_p.E812del|KAT6B_ENST00000372724.1_In_Frame_Del_p.E812del	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	162	.	.	1170	WXS	Illumina HiSeq	Phase_I	149	59	0.396	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	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121653375	121653377	+	In_Frame_Del	DEL	TGA	TGA	-	rs80103123|rs35947407|rs398111797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:121653375_121653377delTGA	ENST00000393386.2	+	12	4686_4688	c.4275_4277delTGA	c.(4273-4278)ggtgat>ggt	p.D1431del	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	1431					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)	p.G1425G(1)		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						atgatgatggtgatgatgatgat	0.424														2357	0.470647	0.559	0.464	5008	,	,		22105	0.3542		0.3708	False		,,,				2504	0.5787				p.1425_1426del		Pindel	.											PTPRZ1,leg,malignant_melanoma,-1,1	PTPRZ1	605	1	1	Substitution - coding silent(1)	skin(1)	c.4274_4276del						PASS	.																																			SO:0001651	inframe_deletion	5803	exon12			.	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.4275_4277delTGA	7.37:g.121653384_121653386delTGA	ENSP00000377047:p.Asp1431del	Somatic	124	.	.		WXS	Illumina HiSeq	Phase_I	141	39	0.277	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	In_Frame_Del	DEL	ENST00000393386.2	37	CCDS34740.1																																																																																			TGA|0.585;-|0.415	0.415	strong		0.424	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
C14orf23	387978	hgsc.bcm.edu	37	14	29261305	29261306	+	In_Frame_Ins	INS	-	-	AAC	rs202195469|rs200251419|rs565026588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:29261305_29261306insAAC	ENST00000399387.4	+	3	446_447	c.342_343insAAC	c.(343-345)aaa>AACaaa	p.114_115insN	C14orf23_ENST00000550266.1_Intron|C14orf23_ENST00000548213.1_Intron					chromosome 14 open reading frame 23											central_nervous_system(1)	1						CTTCAGCACTAAAAAAAACAAA	0.376																																					.		Pindel	.											.	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.29261305_29261306insAAC	ENSP00000382318:p.Leu114_Lys115insAsn	Somatic	112	.	.		WXS	Illumina HiSeq	Phase_I	92	29	0.315	.		RNA	INS	ENST00000399387.4	37																																																																																				-|0.668;AAC|0.332	0.332	strong		0.376	C14orf23-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000134019.2	NR_026731	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46012225	46012226	+	In_Frame_Ins	INS	-	-	CAGCAGCTGGGGGCA			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46012225_46012226insCAGCAGCTGGGGGCA	ENST00000400368.1	-	1	160_161	c.140_141insTGCCCCCAGCTGCTG	c.(139-141)tgc>tgTGCCCCCAGCTGCTGc	p.47_47C>CAPSCC	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	47	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						GGGCCGGGGCGCAGCAGGGGGG	0.683																																					p.C47delinsCAPSCC		Pindel	.											.	KRTAP10-6	57	.	0			c.141_142insTGCCCCCAGCTGCTG						PASS	.																																			SO:0001652	inframe_insertion	386674	exon1			.	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.140_141insTGCCCCCAGCTGCTG	21.37:g.46012225_46012226insCAGCAGCTGGGGGCA	Exception_encountered	Somatic	93	.	.		WXS	Illumina HiSeq	Phase_I	58	14	0.241	NM_198688		In_Frame_Ins	INS	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.683	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
ACTRT2	140625	hgsc.bcm.edu	37	1	2938408	2938410	+	In_Frame_Del	DEL	AGA	AGA	-	rs4013154|rs201580305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:2938408_2938410delAGA	ENST00000378404.2	+	1	363_365	c.158_160delAGA	c.(157-162)cagaag>cag	p.K55del		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	55				Missing (in Ref. 5; AAH29499). {ECO:0000305}.		cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		GAGGCCAACCAGAAGAAGTACTT	0.611														563	0.11242	0.0106	0.2176	5008	,	,		17049	0.1925		0.1581	False		,,,				2504	0.046				p.53_53del		Pindel	.											ACTRT2,NS,carcinoma,-1,1	ACTRT2	69	1	0			c.157_159del						PASS	.			152,4114		9,134,1990						4.1	0.8		dbSNP_108	43	1412,6842		109,1194,2824	no	coding	ACTRT2	NM_080431.4		118,1328,4814	A1A1,A1R,RR		17.1069,3.5631,12.492				1564,10956				SO:0001651	inframe_deletion	140625	exon1			.	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.158_160delAGA	1.37:g.2938411_2938413delAGA	ENSP00000367658:p.Lys55del	Somatic	103	.	.		WXS	Illumina HiSeq	Phase_I	122	33	0.270	NM_080431	B1AN52|Q8NHS6|Q8TDG1	In_Frame_Del	DEL	ENST00000378404.2	37	CCDS45.1																																																																																			AGA|0.848;-|0.152	0.152	strong		0.611	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431	
GPRASP2	114928	hgsc.bcm.edu	37	X	101970172	101970183	+	In_Frame_Del	DEL	GGCCCAGGCATG	GGCCCAGGCATG	-	rs61097741|rs538885190		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGCCCAGGCATG	GGCCCAGGCATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101970172_101970183delGGCCCAGGCATG	ENST00000535209.1	+	4	1206_1217	c.375_386delGGCCCAGGCATG	c.(373-387)gaggcccaggcatgg>gag	p.AQAW126del	GPRASP2_ENST00000543253.1_In_Frame_Del_p.AQAW126del|GPRASP2_ENST00000332262.5_In_Frame_Del_p.AQAW126del			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	126						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						CCAAGGATGAGGCCCAGGCATGGGCCCAGAGT	0.58														34	0.00900662	0.0257	0.0	3775	,	,		16957	0.0		0.0	False		,,,				2504	0.0				p.125_129del		Pindel	.											.	GPRASP2	89	.	0			c.374_385del						PASS	.		,,,,,	82,3637		5,65,7,1522,528					,,,,,	3.6	0.4		dbSNP_129	99	5,6479		1,2,1,2354,1769	no	coding,coding,coding,coding,coding,coding	GPRASP2,ARMCX5-GPRASP2	NM_138437.5,NM_001199818.1,NM_001184876.2,NM_001184875.2,NM_001184874.2,NM_001004051.3	,,,,,	6,67,8,3876,2297	A1A1,A1R,A1,RR,R		0.0771,2.2049,0.8527	,,,,,	,,,,,		87,10116				SO:0001651	inframe_deletion	114928	exon4			.	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"""Armadillo repeat containing"""	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.375_386delGGCCCAGGCATG	X.37:g.101970172_101970183delGGCCCAGGCATG	ENSP00000437394:p.Ala126_Trp129del	Somatic	90	.	.		WXS	Illumina HiSeq	Phase_I	82	38	0.463	NM_138437	D3DXA0|Q8NAB4	In_Frame_Del	DEL	ENST00000535209.1	37	CCDS14501.1																																																																																			.	.	none		0.580	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
TNRC6B	23112	hgsc.bcm.edu	37	22	40697177	40697179	+	In_Frame_Del	DEL	GCA	GCA	-	rs66700157|rs10617561|rs139908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:40697177_40697179delGCA	ENST00000454349.2	+	15	4171_4173	c.3960_3962delGCA	c.(3958-3963)ctgcag>ctg	p.Q1328del	TNRC6B_ENST00000402203.1_In_Frame_Del_p.Q524del|TNRC6B_ENST00000301923.9_In_Frame_Del_p.Q524del|TNRC6B_ENST00000335727.9_In_Frame_Del_p.Q1218del	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	1328	Silencing domain; interaction with CNOT1 and PAN3.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						TGAGTGCACTgcagcagcagcag	0.596														1289	0.257388	0.4622	0.1499	5008	,	,		20853	0.0179		0.2396	False		,,,				2504	0.3221				p.1320_1321del		Pindel	.											.	TNRC6B	195	.	0			c.3959_3961del						PASS	.																																			SO:0001651	inframe_deletion	23112	exon15			.	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"""Trinucleotide (CAG) repeat containing"""	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.3960_3962delGCA	22.37:g.40697186_40697188delGCA	ENSP00000401946:p.Gln1328del	Somatic	79	.	.		WXS	Illumina HiSeq	Phase_I	77	21	0.273	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	In_Frame_Del	DEL	ENST00000454349.2	37	CCDS54533.1																																																																																			GCA|0.779;-|0.221	0.221	strong		0.596	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding			
GPR39	2863	hgsc.bcm.edu	37	2	133403034	133403036	+	In_Frame_Del	DEL	AGA	AGA	-	rs557760477|rs113224054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:133403034_133403036delAGA	ENST00000329321.3	+	2	1686_1688	c.1217_1219delAGA	c.(1216-1221)gagaag>gag	p.K407del	GPR39_ENST00000470071.1_3'UTR|LYPD1_ENST00000397463.2_3'UTR	NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	407					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGGAGAACTGAGAAGATTTTCTT	0.601														13	0.00259585	0.0098	0.0	5008	,	,		18521	0.0		0.0	False		,,,				2504	0.0				p.406_406del		Pindel	.											.	GPR39	60	.	0			c.1216_1218del						PASS	.		,,	25,4241		2,21,2110					,,	-1.8	0.0		dbSNP_132	52	2,8252		1,0,4126	no	utr-3,coding,utr-3	GPR39,LYPD1	NM_144586.5,NM_001508.2,NM_001077427.2	,,	3,21,6236	A1A1,A1R,RR		0.0242,0.586,0.2157	,,	,,		27,12493				SO:0001651	inframe_deletion	2863	exon2			.	AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.1217_1219delAGA	2.37:g.133403037_133403039delAGA	ENSP00000327417:p.Lys407del	Somatic	26	.	.		WXS	Illumina HiSeq	Phase_I	23	10	0.435	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	In_Frame_Del	DEL	ENST00000329321.3	37	CCDS2170.1																																																																																			AGA|0.500;-|0.500	0.500	weak		0.601	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1		
TBC1D1	23216	hgsc.bcm.edu	37	4	37962609	37962610	+	Intron	DEL	AT	AT	-	rs199908908|rs200376306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:37962609_37962610delAT	ENST00000261439.4	+	3	772				TBC1D1_ENST00000508802.1_Intron|PTTG2_ENST00000504686.1_Frame_Shift_Del_p.H185fs	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						TCCTTCAAGCATTCTGTCGACC	0.441														72	0.014377	0.0129	0.0173	5008	,	,		19631	0.001		0.0189	False		,,,				2504	0.0235				p.185_185del		Pindel	.											.	PTTG2	15	.	0			c.553_554del						PASS	.		,	57,4209		0,57,2076					,	1.4	0.0			194	116,8138		1,114,4012	no	intron,frameshift	PTTG2,TBC1D1	NM_015173.2,NM_006607.2	,	1,171,6088	A1A1,A1R,RR		1.4054,1.3361,1.3818	,	,		173,12347				SO:0001627	intron_variant	10744	exon1			.	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.418-53520AT>-	4.37:g.37962609_37962610delAT		Somatic	113	.	.		WXS	Illumina HiSeq	Phase_I	106	43	0.406	NM_006607	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Frame_Shift_Del	DEL	ENST00000261439.4	37	CCDS33972.1																																																																																			AT|0.986;-|0.014	0.014	strong		0.441	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
RPF2	84154	hgsc.bcm.edu	37	6	111310252	111310252	+	Missense_Mutation	SNP	G	G	A	rs6909298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:111310252G>A	ENST00000441448.2	+	3	270	c.178G>A	c.(178-180)Ggt>Agt	p.G60S		NM_032194.1	NP_115570.1	Q9H7B2	RPF2_HUMAN	ribosome production factor 2 homolog (S. cerevisiae)	60	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.		G -> S (in dbSNP:rs6909298).			nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)	7						AAAACCATACGGTGTACTATA	0.254													G|||	113	0.0225639	0.0809	0.0086	5008	,	,		15215	0.0		0.0	False		,,,				2504	0.0				p.G60S		Atlas-SNP	.											.	RPF2	26	.	0			c.G178A						PASS	.	G	SER/GLY	308,4064	152.2+/-185.9	17,274,1895	41.0	44.0	43.0		178	3.1	0.9	6	dbSNP_116	43	0,8588		0,0,4294	yes	missense	RPF2	NM_032194.1	56	17,274,6189	AA,AG,GG		0.0,7.0448,2.3765	benign	60/307	111310252	308,12652	2186	4294	6480	SO:0001583	missense	84154	exon3			CCATACGGTGTAC	AK024740	CCDS5088.1	6q21	2009-09-25	2009-09-25	2009-09-25	ENSG00000197498	ENSG00000197498			20870	protein-coding gene	gene with protein product	"""ribosomal processing factor 2 homolog (S. cerevisiae)"""		"""brix domain containing 1"""	BXDC1		12048200	Standard	NM_032194		Approved	FLJ21087, bA397G5.4	uc003pun.3	Q9H7B2	OTTHUMG00000015368	ENST00000441448.2:c.178G>A	6.37:g.111310252G>A	ENSP00000402338:p.Gly60Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	133	66	0.496241	NM_032194	Q5VXN1|Q8N4A1	Missense_Mutation	SNP	ENST00000441448.2	37	CCDS5088.1	41	0.018772893772893772	41	0.08333333333333333	0	0.0	0	0.0	0	0.0	g	6.952	0.545509	0.13312	0.070448	0.0	ENSG00000197498	ENST00000441448;ENST00000368864;ENST00000425871	T;T;T	0.18960	2.18;2.18;2.18	4.92	3.11	0.35812	Brix domain (3);	0.105052	0.64402	D	0.000005	T	0.02380	0.0073	N	0.00765	-1.205	0.36277	D	0.855568	B	0.06786	0.001	B	0.10450	0.005	T	0.27297	-1.0078	10	0.33940	T	0.23	-35.436	11.9222	0.52797	0.1536:0.0:0.8463:0.0	rs6909298;rs52791590;rs6909298	60	Q9H7B2	RPF2_HUMAN	S	60;21;27	ENSP00000402338:G60S;ENSP00000357857:G21S;ENSP00000414026:G27S	ENSP00000357857:G21S	G	+	1	0	RPF2	111416945	1.000000	0.71417	0.914000	0.36105	0.019000	0.09904	4.189000	0.58358	1.209000	0.43321	-0.448000	0.05591	GGT	G|0.977;A|0.023	0.023	strong		0.254	RPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041813.2	NM_032194	
SEC16A	9919	hgsc.bcm.edu	37	9	139370829	139370829	+	Silent	SNP	G	G	A	rs114386206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139370829G>A	ENST00000371706.3	-	1	738	c.705C>T	c.(703-705)ccC>ccT	p.P235P	SEC16A_ENST00000431893.2_Silent_p.P235P|SEC16A_ENST00000290037.6_Silent_p.P235P|SEC16A_ENST00000313050.7_Silent_p.P413P			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	235					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)		GTGTAGGTGCGGGCGGACGGC	0.592													g|||	19	0.00379393	0.0136	0.0014	5008	,	,		16416	0.0		0.0	False		,,,				2504	0.0				p.P413P		Atlas-SNP	.											.	SEC16A	249	.	0			c.C1239T						PASS	.	C		42,3906		0,42,1932	21.0	24.0	23.0		1239	-7.4	0.0	9	dbSNP_132	23	9,8283		0,9,4137	no	coding-synonymous	SEC16A	NM_014866.1		0,51,6069	AA,AG,GG		0.1085,1.0638,0.4167		413/2358	139370829	51,12189	1974	4146	6120	SO:0001819	synonymous_variant	9919	exon3			AGGTGCGGGCGGA	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.705C>T	9.37:g.139370829G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	121	45	0.371901	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				G|0.996;A|0.004	0.004	strong		0.592	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
CTBS	1486	hgsc.bcm.edu	37	1	85039955	85039955	+	Silent	SNP	G	G	A	rs2303307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	94	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	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	
ZNF700	90592	hgsc.bcm.edu	37	19	12059467	12059467	+	Missense_Mutation	SNP	C	C	G	rs73509026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12059467C>G	ENST00000254321.5	+	4	771	c.628C>G	c.(628-630)Cga>Gga	p.R210G	ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000538752.1_Intron|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF700_ENST00000482090.1_Missense_Mutation_p.R192G|ZNF763_ENST00000590798.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	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)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						TTCAAGCATTCGAAGACACAT	0.383													c|||	318	0.0634984	0.1505	0.0288	5008	,	,		21685	0.0218		0.0378	False		,,,				2504	0.0399				p.R213G		Atlas-SNP	.											ZNF700,NS,carcinoma,-1,1	ZNF700	81	1	0			c.C637G						PASS	.	C	GLY/ARG	584,3822	254.0+/-259.7	38,508,1657	89.0	93.0	92.0		628	0.6	0.0	19	dbSNP_130	92	256,8344	99.7+/-161.2	2,252,4046	yes	missense	ZNF700	NM_144566.1	125	40,760,5703	GG,GC,CC		2.9767,13.2547,6.4586	probably-damaging	210/743	12059467	840,12166	2203	4300	6503	SO:0001583	missense	90592	exon4			AGCATTCGAAGAC	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"""Zinc fingers, C2H2-type"", ""-"""	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.628C>G	19.37:g.12059467C>G	ENSP00000254321:p.Arg210Gly	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	116	65	0.560345	NM_001271848	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	37	CCDS32915.1	123	0.05631868131868132	67	0.13617886178861788	13	0.03591160220994475	16	0.027972027972027972	27	0.03562005277044855	c	9.486	1.099434	0.20552	0.132547	0.029767	ENSG00000196757	ENST00000254321	T	0.07114	3.22	0.554	0.554	0.17241	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	M	0.63169	1.94	0.09310	N	1	P	0.51057	0.941	P	0.50708	0.648	T	0.31110	-0.9955	9	0.21540	T	0.41	.	3.5609	0.07882	0.4412:0.5587:1.0E-4:0.0	.	210	Q9H0M5	ZN700_HUMAN	G	210	ENSP00000254321:R210G	ENSP00000254321:R210G	R	+	1	2	ZNF700	11920467	0.000000	0.05858	0.032000	0.17829	0.334000	0.28698	-1.823000	0.01710	0.535000	0.28714	0.305000	0.20034	CGA	C|0.940;G|0.060	0.060	strong		0.383	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566	
EIF2A	83939	hgsc.bcm.edu	37	3	150285535	150285535	+	Silent	SNP	T	T	C	rs376872417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150285535T>C	ENST00000460851.1	+	7	640	c.531T>C	c.(529-531)ccT>ccC	p.P177P	SERP1_ENST00000490945.1_Intron|EIF2A_ENST00000383043.3_5'Flank|EIF2A_ENST00000406576.3_Silent_p.P116P|EIF2A_ENST00000487799.1_Silent_p.P152P|SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000273435.5_Silent_p.P172P			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	177					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)			TATTATCACCTGGACCCCAAC	0.279													T|||	3	0.000599042	0.0023	0.0	5008	,	,		19889	0.0		0.0	False		,,,				2504	0.0				p.P177P		Atlas-SNP	.											.	EIF2A	59	.	0			c.T531C						PASS	.	T		3,3595		0,3,1796	77.0	67.0	70.0		531	2.2	1.0	3		70	0,8122		0,0,4061	no	coding-synonymous	EIF2A	NM_032025.3		0,3,5857	CC,CT,TT		0.0,0.0834,0.0256		177/586	150285535	3,11717	1799	4061	5860	SO:0001819	synonymous_variant	83939	exon7			ATCACCTGGACCC	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.531T>C	3.37:g.150285535T>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	187	95	0.508021	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Silent	SNP	ENST00000460851.1	37	CCDS46935.1																																																																																			.	.	weak		0.279	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025	
TNPO2	30000	hgsc.bcm.edu	37	19	12813683	12813683	+	Silent	SNP	T	T	C	rs16978630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12813683T>C	ENST00000592287.1	-	20	2367	c.2259A>G	c.(2257-2259)gaA>gaG	p.E753E	TNPO2_ENST00000588216.1_Silent_p.E753E|TNPO2_ENST00000441499.1_Silent_p.E753E|TNPO2_ENST00000425528.1_Silent_p.E753E|TNPO2_ENST00000356861.5_Silent_p.E753E|TNPO2_ENST00000450764.2_Silent_p.E753E	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	753					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GGTTAATGATTTCCACCAGGT	0.632													C|||	747	0.149161	0.5333	0.0461	5008	,	,		16704	0.0		0.0099	False		,,,				2504	0.0				p.E753E		Atlas-SNP	.											.	TNPO2	108	.	0			c.A2259G						PASS	.	C	,,	1692,2404		359,974,715	244.0	265.0	258.0		2259,2259,2259	1.0	1.0	19	dbSNP_123	258	127,8261		1,125,4068	no	coding-synonymous,coding-synonymous,coding-synonymous	TNPO2	NM_001136195.1,NM_001136196.1,NM_013433.4	,,	360,1099,4783	CC,CT,TT		1.5141,41.3086,14.5707	,,	753/888,753/898,753/888	12813683	1819,10665	2048	4194	6242	SO:0001819	synonymous_variant	30000	exon20			AATGATTTCCACC	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"""Importins"""	19998	protein-coding gene	gene with protein product	"""importin 3"", ""karyopherin beta 2b"""	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.2259A>G	19.37:g.12813683T>C		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	314	141	0.449045	NM_013433	O14655|Q6IN77	Silent	SNP	ENST00000592287.1	37	CCDS45991.1																																																																																			T|0.866;C|0.134	0.134	strong		0.632	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433	
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39280053	39280053	+	Missense_Mutation	SNP	T	T	A	rs622950		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39280053T>A	ENST00000394014.1	-	1	366	c.322A>T	c.(322-324)Acc>Tcc	p.T108S		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	108	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].		Missing (in allele KAP4.12-v1). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCAGGTGGTCTGACAGCAG	0.677																																					p.T108S		Atlas-SNP	.											.	KRTAP4-12	32	.	0			c.A322T						PASS	.	T	SER/THR	1462,2916		98,1266,825	41.0	49.0	46.0		322	-0.6	0.0	17	dbSNP_83	46	137,8431		5,127,4152	no	missense	KRTAP4-12	NM_031854.2	58	103,1393,4977	AA,AT,TT		1.599,33.3942,12.3513	benign	108/202	39280053	1599,11347	2189	4284	6473	SO:0001583	missense	83755	exon1			AGGTGGTCTGACA	AJ406943	CCDS32649.1	17q21.2	2013-06-25			ENSG00000213416	ENSG00000213416		"""Keratin associated proteins"""	16776	protein-coding gene	gene with protein product						11279113	Standard	NM_031854		Approved	KAP4.12	uc002hwa.3	Q9BQ66	OTTHUMG00000133632	ENST00000394014.1:c.322A>T	17.37:g.39280053T>A	ENSP00000377582:p.Thr108Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	168	119	0.708333	NM_031854	A3KMC5|Q495I0	Missense_Mutation	SNP	ENST00000394014.1	37	CCDS32649.1	365	0.1671245421245421	202	0.4105691056910569	46	0.1270718232044199	100	0.17482517482517482	17	0.022427440633245383	.	6.963	0.547632	0.13312	0.333942	0.01599	ENSG00000213416	ENST00000394014	T	0.00557	6.62	4.52	-0.636	0.11508	.	.	.	.	.	T	0.00012	0.0000	N	0.17594	0.5	0.58432	P	9.99999999995449E-6	B	0.06786	0.001	B	0.12156	0.007	T	0.01428	-1.1357	8	0.09084	T	0.74	.	7.4144	0.27036	0.0853:0.0:0.4573:0.4575	rs622950	108	Q9BQ66	KR412_HUMAN	S	108	ENSP00000377582:T108S	ENSP00000377582:T108S	T	-	1	0	KRTAP4-12	36533579	0.000000	0.05858	0.014000	0.15608	0.547000	0.35210	-1.287000	0.02785	0.061000	0.16311	0.375000	0.23000	ACC	T|0.831;A|0.169	0.169	strong		0.677	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1		
PTPRA	5786	hgsc.bcm.edu	37	20	2945759	2945759	+	Missense_Mutation	SNP	C	C	T	rs1178027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2945759C>T	ENST00000216877.6	+	5	726	c.326C>T	c.(325-327)cCa>cTa	p.P109L	PTPRA_ENST00000425918.2_Missense_Mutation_p.P120L|PTPRA_ENST00000380393.3_Missense_Mutation_p.P109L|PTPRA_ENST00000399903.2_Missense_Mutation_p.P109L|PTPRA_ENST00000318266.5_Missense_Mutation_p.P109L|PTPRA_ENST00000356147.3_Missense_Mutation_p.P109L|PTPRA_ENST00000358719.4_5'UTR	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	109			P -> L (in dbSNP:rs1178027).		axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.P109L(1)		NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						ACGTGGCTTCCAGATAACCAG	0.473													C|||	1347	0.26897	0.6747	0.2017	5008	,	,		17844	0.1181		0.0885	False		,,,				2504	0.1094				p.P109L		Atlas-SNP	.											PTPRA,NS,carcinoma,0,1	PTPRA	75	1	1	Substitution - Missense(1)	stomach(1)	c.C326T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	2456,1950	615.3+/-392.5	676,1104,423	104.0	110.0	108.0		326,326,326	2.1	0.9	20	dbSNP_87	108	864,7736	195.2+/-240.5	42,780,3478	yes	missense,missense,missense	PTPRA	NM_002836.3,NM_080840.2,NM_080841.2	98,98,98	718,1884,3901	TT,TC,CC		10.0465,44.2578,25.5267	benign,benign,benign	109/803,109/794,109/794	2945759	3320,9686	2203	4300	6503	SO:0001583	missense	5786	exon9			GGCTTCCAGATAA		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.326C>T	20.37:g.2945759C>T	ENSP00000216877:p.Pro109Leu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Missense_Mutation	SNP	ENST00000216877.6	37	CCDS13039.1	527	0.2413003663003663	317	0.6443089430894309	63	0.17403314917127072	81	0.14160839160839161	66	0.0870712401055409	C	12.84	2.059033	0.36373	0.557422	0.100465	ENSG00000132670	ENST00000380393;ENST00000455631;ENST00000216877;ENST00000399903;ENST00000431048;ENST00000418580;ENST00000425918;ENST00000318266;ENST00000430705;ENST00000356147	T;T;T;T;T;T;T;T;T	0.49432	3.92;0.87;3.95;3.92;1.08;3.92;3.95;0.78;3.95	5.25	2.1	0.27182	.	0.899723	0.09220	U	0.831993	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.99999798651	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.43718	-0.9374	9	0.56958	D	0.05	.	6.3363	0.21298	0.0:0.6683:0.1548:0.1769	rs1178027;rs3746691;rs52796339;rs59628468;rs1178027	120;109	B7Z2A4;P18433-4	.;.	L	109;109;109;109;109;109;120;109;109;109	ENSP00000369756:P109L;ENSP00000414089:P109L;ENSP00000216877:P109L;ENSP00000382787:P109L;ENSP00000390775:P109L;ENSP00000393553:P120L;ENSP00000314568:P109L;ENSP00000394132:P109L;ENSP00000348468:P109L	ENSP00000216877:P109L	P	+	2	0	PTPRA	2893759	0.997000	0.39634	0.902000	0.35471	0.988000	0.76386	0.786000	0.26844	0.659000	0.30945	0.655000	0.94253	CCA	C|0.738;T|0.262	0.262	strong		0.473	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3		
MBTPS2	51360	hgsc.bcm.edu	37	X	21861434	21861434	+	Silent	SNP	A	A	G	rs3213451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:21861434A>G	ENST00000379484.5	+	2	321	c.222A>G	c.(220-222)caA>caG	p.Q74Q	MBTPS2_ENST00000365779.2_Silent_p.Q74Q|MBTPS2_ENST00000465888.1_3'UTR	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	154	0	0		WXS	Illumina HiSeq	Phase_I	166	71	0.427711	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		
LRP4	4038	hgsc.bcm.edu	37	11	46917868	46917868	+	Missense_Mutation	SNP	A	A	G	rs7926667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46917868A>G	ENST00000378623.1	-	9	1183	c.941T>C	c.(940-942)tTg>tCg	p.L314S		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	314	LDL-receptor class A 8. {ECO:0000255|PROSITE-ProRule:PRU00124}.		L -> S (in dbSNP:rs7926667).		dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GAACTGGTCCAAGGCACATTG	0.562													G|||	306	0.0611022	0.2216	0.0173	5008	,	,		20751	0.0		0.001	False		,,,				2504	0.0				p.L314S		Atlas-SNP	.											.	LRP4	160	.	0			c.T941C						PASS	.	G	SER/LEU	769,3633	752.8+/-412.3	67,635,1499	90.0	86.0	87.0		941	6.0	0.9	11	dbSNP_116	87	3,8595	818.6+/-406.8	0,3,4296	yes	missense	LRP4	NM_002334.3	145	67,638,5795	GG,GA,AA		0.0349,17.4693,5.9385	benign	314/1906	46917868	772,12228	2201	4299	6500	SO:0001583	missense	4038	exon9			TGGTCCAAGGCAC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.941T>C	11.37:g.46917868A>G	ENSP00000367888:p.Leu314Ser	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	22	7	0.318182	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	100	0.045787545787545784	92	0.18699186991869918	8	0.022099447513812154	0	0.0	0	0.0	G	4.491	0.091136	0.08632	0.174693	3.49E-4	ENSG00000134569	ENST00000378623	T	0.55234	0.53	5.96	5.96	0.96718	.	0.074366	0.56097	N	0.000024	T	0.00039	0.0001	N	0.02368	-0.58	0.42982	P	0.005531999999999981	B	0.02656	0.0	B	0.06405	0.002	T	0.08806	-1.0704	9	0.07482	T	0.82	.	10.2442	0.43330	0.0677:0.0:0.7975:0.1348	rs7926667;rs52792198;rs7926667	314	O75096	LRP4_HUMAN	S	314	ENSP00000367888:L314S	ENSP00000367888:L314S	L	-	2	0	LRP4	46874444	1.000000	0.71417	0.886000	0.34754	0.907000	0.53573	4.687000	0.61708	1.543000	0.49345	-0.119000	0.15052	TTG	A|0.948;G|0.052	0.052	strong		0.562	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
TRPM6	140803	hgsc.bcm.edu	37	9	77376633	77376633	+	Silent	SNP	A	A	G	rs2274925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:77376633A>G	ENST00000360774.1	-	27	5001	c.4764T>C	c.(4762-4764)aaT>aaC	p.N1588N	TRPM6_ENST00000376864.4_Silent_p.N1588N|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000361255.3_Silent_p.N1583N|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000451710.3_Silent_p.N1588N|TRPM6_ENST00000449912.2_Silent_p.N1583N	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1588					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						GTCCTTGAGTATTCTTCTTTT	0.418													A|||	845	0.16873	0.3457	0.0663	5008	,	,		18651	0.1597		0.0785	False		,,,				2504	0.1043				p.N1588N		Atlas-SNP	.											.	TRPM6	377	.	0			c.T4764C						PASS	.	A	,,	1392,3014	457.6+/-351.7	237,918,1048	186.0	163.0	171.0		4749,4749,4764	0.2	0.1	9	dbSNP_100	171	599,8001	157.9+/-211.5	19,561,3720	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	256,1479,4768	GG,GA,AA		6.9651,31.5933,15.3083	,,	1583/2018,1583/2018,1588/2023	77376633	1991,11015	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon27			TTGAGTATTCTTC	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.4764T>C	9.37:g.77376633A>G		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	214	138	0.64486	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																			A|0.851;G|0.149	0.149	strong		0.418	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
DTX4	23220	hgsc.bcm.edu	37	11	58949852	58949852	+	Silent	SNP	C	C	T	rs75403375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58949852C>T	ENST00000227451.3	+	2	956	c.852C>T	c.(850-852)acC>acT	p.T284T	DTX4_ENST00000532982.1_Silent_p.T178T	NM_015177.1	NP_055992.1	Q9Y2E6	DTX4_HUMAN	deltex 4, E3 ubiquitin ligase	284					innate immune response (GO:0045087)|Notch signaling pathway (GO:0007219)|positive regulation of type I interferon production (GO:0032481)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	20		all_epithelial(135;0.125)				ACAGCAAGACCGGAAGGGTGG	0.637													C|||	135	0.0269569	0.0983	0.0072	5008	,	,		19567	0.0		0.0	False		,,,				2504	0.0				p.T284T		Atlas-SNP	.											.	DTX4	84	.	0			c.C852T						PASS	.	C		245,3755		7,231,1762	30.0	40.0	37.0		852	-9.1	0.0	11	dbSNP_132	37	0,8320		0,0,4160	no	coding-synonymous	DTX4	NM_015177.1		7,231,5922	TT,TC,CC		0.0,6.125,1.9886		284/620	58949852	245,12075	2000	4160	6160	SO:0001819	synonymous_variant	23220	exon2			CAAGACCGGAAGG	AB023154	CCDS44612.1	11q12.2	2014-01-28	2014-01-28		ENSG00000110042	ENSG00000110042		"""RING-type (C3HC4) zinc fingers"""	29151	protein-coding gene	gene with protein product			"""deltex 4 homolog (Drosophila)"", ""deltex homolog 4 (Drosophila)"""			10231032, 22388039	Standard	NM_015177		Approved	KIAA0937, RNF155	uc001nns.2	Q9Y2E6	OTTHUMG00000167336	ENST00000227451.3:c.852C>T	11.37:g.58949852C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_015177	Q0VF38	Silent	SNP	ENST00000227451.3	37	CCDS44612.1																																																																																			C|0.975;T|0.025	0.025	strong		0.637	DTX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394228.1	XM_166213	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65347723	65347723	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65347723C>T	ENST00000309295.4	+	5	749	c.484C>T	c.(484-486)Cgt>Tgt	p.R162C		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	162						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						GCGGGAGGGCCGTGCCACGTG	0.617																																					p.R162C		Atlas-SNP	.											EHBP1L1,colon,carcinoma,-1,1	EHBP1L1	64	1	0			c.C484T						scavenged	.						82.0	90.0	87.0					11																	65347723		2197	4290	6487	SO:0001583	missense	254102	exon5			GAGGGCCGTGCCA	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.484C>T	11.37:g.65347723C>T	ENSP00000312671:p.Arg162Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	97	3	0.0309278	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	37	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.298806	0.81025	.	.	ENSG00000173442	ENST00000309295;ENST00000533237	T;T	0.44881	0.91;0.91	5.56	5.56	0.83823	.	0.093689	0.43579	D	0.000545	T	0.53206	0.1782	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.55617	-0.8113	10	0.87932	D	0	.	15.0194	0.71617	0.0:1.0:0.0:0.0	.	162	Q8N3D4	EH1L1_HUMAN	C	162	ENSP00000312671:R162C;ENSP00000431996:R162C	ENSP00000312671:R162C	R	+	1	0	EHBP1L1	65104299	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	3.759000	0.55227	2.619000	0.88677	0.555000	0.69702	CGT	.	.	none		0.617	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
MMP23B	8510	hgsc.bcm.edu	37	1	1571841	1571841	+	IGR	SNP	A	A	C	rs150949339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1571841A>C	ENST00000356026.5	+	0	1326				CDK11B_ENST00000341832.6_Missense_Mutation_p.D596E|CDK11B_ENST00000317673.7_Missense_Mutation_p.D641E|CDK11B_ENST00000340677.5_Missense_Mutation_p.D630E|CDK11B_ENST00000407249.3_Missense_Mutation_p.D643E			O75900	MMP23_HUMAN	matrix metallopeptidase 23B						proteolysis (GO:0006508)|reproduction (GO:0000003)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D643E(3)		large_intestine(1)	1	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)	Marimastat(DB00786)	GGGTCCCCAGATCCTGAAAGA	0.577																																					p.D638E		Atlas-SNP	.											CDK11A,rectum,carcinoma,0,5	CDK11B	37	5	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(1)|lung(1)|central_nervous_system(1)	c.T1914G						scavenged	.	A	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	663,3183		0,663,1260	41.0	40.0	40.0		1665,1152,1554,1563,1683,1656	2.6	1.0	1	dbSNP_134	40	156,8096		0,156,3970	no	missense,missense,missense,missense,missense,missense	CDK11B	NM_033486.1,NM_033487.1,NM_033488.1,NM_033489.1,NM_033492.1,NM_033493.1	45,45,45,45,45,45	0,819,5230	CC,CA,AA		1.8905,17.2387,6.7697	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	555/698,384/527,518/661,521/664,561/704,552/695	1571841	819,11279	1923	4126	6049	SO:0001628	intergenic_variant	984	exon18			CCCCAGATCCTGA		CCDS30559.1	1p36.3	2013-01-11	2005-08-08		ENSG00000189409	ENSG00000189409		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7171	protein-coding gene	gene with protein product	"""matrix metalloproteinase 22"", ""femalysin"", ""matrix metalloproteinase in the female reproductive tract"""	603321	"""matrix metalloproteinase 23B"""	MMP22		9740677, 9750192	Standard	XM_005244810		Approved	MIFR, MIFR-1	uc001agp.3	O75900	OTTHUMG00000074713		1.37:g.1571841A>C		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	221	47	0.21267	NM_033486	A2AGN0|A2AGN1|O75894|O75895|Q5QPQ8|Q76P96|Q7LDM6|Q7LDM7|Q9UBR9|Q9UJK8	Missense_Mutation	SNP	ENST00000356026.5	37	CCDS30559.1																																																																																			A|0.994;C|0.006	0.006	strong		0.577	MMP23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158492.2	NM_006983	
OTOF	9381	hgsc.bcm.edu	37	2	26699159	26699159	+	Silent	SNP	C	C	T	rs4997760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26699159C>T	ENST00000272371.2	-	23	2829	c.2703G>A	c.(2701-2703)tcG>tcA	p.S901S	OTOF_ENST00000339598.3_Silent_p.S154S|OTOF_ENST00000402415.3_Silent_p.S211S|OTOF_ENST00000338581.6_Silent_p.S154S|OTOF_ENST00000403946.3_Silent_p.S901S	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	901					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCAGCCTGCCGAGCCGAAGC	0.697													C|||	310	0.061901	0.0673	0.0375	5008	,	,		9343	0.125		0.0169	False		,,,				2504	0.0532				p.S901S	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.G2703A						PASS	.	C	,,,	306,3940		28,250,1845	26.0	26.0	26.0		462,2703,633,462	-9.8	0.0	2	dbSNP_113	26	107,8223		4,99,4062	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	32,349,5907	TT,TC,CC		1.2845,7.2068,3.284	,,,	154/1231,901/1998,211/1308,154/1231	26699159	413,12163	2123	4165	6288	SO:0001819	synonymous_variant	9381	exon23			GCCTGCCGAGCCG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2703G>A	2.37:g.26699159C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	78	51	0.653846	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			C|0.956;T|0.044	0.044	strong		0.697	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
ZNF804B	219578	hgsc.bcm.edu	37	7	88965040	88965040	+	Missense_Mutation	SNP	C	C	T	rs56948780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88965040C>T	ENST00000333190.4	+	4	3353	c.2744C>T	c.(2743-2745)aCt>aTt	p.T915I		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	915			T -> I (in dbSNP:rs56948780).				metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GAATCAAACACTGCAGAAGGA	0.433										HNSCC(36;0.09)			T|||	199	0.0397364	0.1445	0.0101	5008	,	,		18290	0.0		0.001	False		,,,				2504	0.0				p.T915I		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C2744T						PASS	.	T	ILE/THR	522,3884	769.0+/-413.6	33,456,1714	93.0	99.0	97.0		2744	2.7	0.0	7	dbSNP_129	97	7,8593	818.2+/-406.9	0,7,4293	yes	missense	ZNF804B	NM_181646.2	89	33,463,6007	TT,TC,CC		0.0814,11.8475,4.0674	benign	915/1350	88965040	529,12477	2203	4300	6503	SO:0001583	missense	219578	exon4			CAAACACTGCAGA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2744C>T	7.37:g.88965040C>T	ENSP00000329638:p.Thr915Ile	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	130	65	0.5	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	67	0.030677655677655676	63	0.12804878048780488	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	T	0.047	-1.263638	0.01445	0.118475	8.14E-4	ENSG00000182348	ENST00000333190	T	0.04406	3.63	5.02	2.67	0.31697	.	1.602880	0.03170	N	0.170660	T	0.00039	0.0001	N	0.01168	-0.975	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41875	-0.9484	10	0.02654	T	1	3.734	4.3373	0.11092	0.1723:0.2578:0.0:0.5699	rs56948780	915	A4D1E1	Z804B_HUMAN	I	915	ENSP00000329638:T915I	ENSP00000329638:T915I	T	+	2	0	ZNF804B	88802976	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	0.929000	0.28844	0.092000	0.17331	-0.254000	0.11334	ACT	C|0.964;T|0.036	0.036	strong		0.433	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
EP400	57634	hgsc.bcm.edu	37	12	132547162	132547162	+	Silent	SNP	G	G	A	rs55938102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132547162G>A	ENST00000333577.4	+	48	8467	c.8358G>A	c.(8356-8358)acG>acA	p.T2786T	EP400_ENST00000389561.2_Silent_p.T2750T|EP400_ENST00000389562.2_Silent_p.T2749T|EP400_ENST00000330386.6_Silent_p.T2669T|EP400_ENST00000332482.4_Silent_p.T2713T			Q96L91	EP400_HUMAN	E1A binding protein p400	2786	Interaction with ZNF42. {ECO:0000250}.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		aacagACGACGACGACCTCTC	0.607													G|||	639	0.127596	0.3321	0.036	5008	,	,		15276	0.0734		0.0447	False		,,,				2504	0.0573				p.T2750T		Atlas-SNP	.											.	EP400	370	.	0			c.G8250A						PASS	.	G		1278,3128	431.4+/-342.9	193,892,1118	79.0	62.0	68.0		8250	0.8	0.0	12	dbSNP_129	68	214,8386	89.2+/-151.4	4,206,4090	no	coding-synonymous	EP400	NM_015409.4		197,1098,5208	AA,AG,GG		2.4884,29.0059,11.4716		2750/3124	132547162	1492,11514	2203	4300	6503	SO:0001819	synonymous_variant	57634	exon47			GACGACGACGACC	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8358G>A	12.37:g.132547162G>A		Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	262	132	0.503817	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				G|0.890;A|0.110	0.110	strong		0.607	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
IFNA13	3447	hgsc.bcm.edu	37	9	21367519	21367519	+	Missense_Mutation	SNP	G	G	C	rs145283706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21367519G>C	ENST00000449498.1	-	1	556	c.491C>G	c.(490-492)gCc>gGc	p.A164G		NM_006900.3	NP_008831.3	P01562	IFNA1_HUMAN	interferon, alpha 13	163					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		AACCTCCCAGGCACAAGGGCT	0.443																																					p.A164G		Atlas-SNP	.											.	IFNA13	19	.	0			c.C491G						PASS	.						108.0	102.0	104.0					9																	21367519		2202	4280	6482	SO:0001583	missense	3447	exon1			TCCCAGGCACAAG		CCDS6505.2	9p22	2010-12-10			ENSG00000233816	ENSG00000233816		"""Interferons"""	5419	protein-coding gene	gene with protein product		147578				1385305	Standard	NM_006900		Approved		uc003zpa.2	P01562	OTTHUMG00000019675	ENST00000449498.1:c.491C>G	9.37:g.21367519G>C	ENSP00000394494:p.Ala164Gly	Somatic	569	1	0.00175747		WXS	Illumina HiSeq	Phase_I	592	229	0.386824	NM_006900	D4Q9M8|Q14605|Q2M1L8|Q52LB8|Q5VYQ2|Q7M4Q1|Q8WZ68|Q9UMJ3	Missense_Mutation	SNP	ENST00000449498.1	37	CCDS6505.2	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852515	0.71719	.	.	ENSG00000233816	ENST00000449498	T	0.18960	2.18	2.56	1.64	0.23874	.	0.126331	0.52532	D	0.000075	T	0.50446	0.1616	M	0.92317	3.295	0.27386	N	0.95527	P	0.39847	0.691	D	0.65140	0.932	T	0.42899	-0.9424	10	0.87932	D	0	.	6.7704	0.23591	0.1469:0.0:0.8531:0.0	.	164	E9PB07	.	G	164	ENSP00000394494:A164G	ENSP00000394494:A164G	A	-	2	0	IFNA13	21357519	1.000000	0.71417	0.994000	0.49952	0.928000	0.56348	2.320000	0.43797	0.402000	0.25451	0.313000	0.20887	GCC	G|0.832;C|0.168	0.168	strong		0.443	IFNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051904.2	NM_006900	
ARAP2	116984	hgsc.bcm.edu	37	4	36152584	36152584	+	Silent	SNP	G	G	T	rs13148785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	92	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	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	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921333	12921333	+	Missense_Mutation	SNP	G	G	A	rs56145411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12921333G>A	ENST00000240189.2	+	4	1211	c.1124G>A	c.(1123-1125)tGc>tAc	p.C375Y		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	375			C -> R (in dbSNP:rs17039307).		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)		GGCCTGAGCTGCTGCTCCCAG	0.562													.|||	1359	0.271366	0.3858	0.1844	5008	,	,		27344	0.2857		0.2157	False		,,,				2504	0.2209				p.C375Y		Atlas-SNP	.											PRAMEF2,NS,carcinoma,+1,1	PRAMEF2	85	1	0			c.G1124A						PASS	.						111.0	118.0	116.0					1																	12921333		2201	4294	6495	SO:0001583	missense	65122	exon4			TGAGCTGCTGCTC		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.1124G>A	1.37:g.12921333G>A	ENSP00000240189:p.Cys375Tyr	Somatic	383	0	0		WXS	Illumina HiSeq	Phase_I	497	391	0.78672	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	357	0.16346153846153846	115	0.23373983739837398	63	0.17403314917127072	80	0.13986013986013987	99	0.13060686015831136	g	3.142	-0.176022	0.06380	.	.	ENSG00000120952	ENST00000240189	T	0.09163	3.01	0.824	-0.682	0.11339	.	1.330770	0.04798	N	0.433017	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	1.999999999946489E-6	B	0.09022	0.002	B	0.29440	0.102	T	0.47114	-0.9142	9	0.72032	D	0.01	.	5.1225	0.14867	0.5904:0.0:0.4096:0.0	rs56145411	375	O60811	PRAM2_HUMAN	Y	375	ENSP00000240189:C375Y	ENSP00000240189:C375Y	C	+	2	0	PRAMEF2	12843920	0.000000	0.05858	0.596000	0.28811	0.002000	0.02628	-0.801000	0.04550	-2.179000	0.00767	-2.900000	0.00093	TGC	G|0.837;A|0.163	0.163	strong		0.562	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
ZNF492	57615	hgsc.bcm.edu	37	19	22846962	22846962	+	Missense_Mutation	SNP	G	G	C	rs138844698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22846962G>C	ENST00000456783.2	+	4	735	c.491G>C	c.(490-492)aGt>aCt	p.S164T	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	164					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)				AGAATTCATAGTGGAGAGAAA	0.338													N|||	246	0.0491214	0.1778	0.0115	5008	,	,		17962	0.0		0.003	False		,,,				2504	0.0				p.S164T		Atlas-SNP	.											.	ZNF492	129	.	0			c.G491C						PASS	.						14.0	20.0	18.0					19																	22846962		1994	4214	6208	SO:0001583	missense	57615	exon4			TTCATAGTGGAGA	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.491G>C	19.37:g.22846962G>C	ENSP00000413660:p.Ser164Thr	Somatic	281	2	0.00711744		WXS	Illumina HiSeq	Phase_I	160	119	0.74375	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	93	0.042582417582417584	87	0.17682926829268292	4	0.011049723756906077	0	0.0	2	0.002638522427440633	.	0.004	-2.252690	0.00268	.	.	ENSG00000229676	ENST00000456783	T	0.12879	2.64	1.3	1.3	0.21679	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00890	-1.11	0.52501	P	4.999999999999449E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.44452	-0.9327	8	0.02654	T	1	.	6.7224	0.23338	0.0:0.7004:0.2996:0.0	.	164	Q9P255	ZN492_HUMAN	T	164	ENSP00000413660:S164T	ENSP00000413660:S164T	S	+	2	0	ZNF492	22638802	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.346000	0.00503	-0.381000	0.07882	-1.146000	0.01853	AGT	G|0.957;C|0.043	0.043	strong		0.338	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49969501	49969501	+	Silent	SNP	G	G	A	rs61732839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49969501G>A	ENST00000293350.4	+	14	2062	c.1899G>A	c.(1897-1899)gcG>gcA	p.A633A	ALDH16A1_ENST00000433981.2_Silent_p.A468A|ALDH16A1_ENST00000540132.1_Silent_p.A470A|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000455361.2_Silent_p.A582A	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	633						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)		GACTTCGGGCGTGGGGGGCCC	0.716													G|||	188	0.0375399	0.1324	0.0159	5008	,	,		14127	0.001		0.001	False		,,,				2504	0.0				p.A633A		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1899A						PASS	.	G	,	360,3874		8,344,1765	9.0	11.0	11.0		1746,1899	-8.7	0.0	19	dbSNP_129	11	9,8349		0,9,4170	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	8,353,5935	AA,AG,GG		0.1077,8.5026,2.9304	,	582/752,633/803	49969501	369,12223	2117	4179	6296	SO:0001819	synonymous_variant	126133	exon14			TCGGGCGTGGGGG	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.1899G>A	19.37:g.49969501G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			G|0.975;A|0.025	0.025	strong		0.716	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
FAM214A	56204	hgsc.bcm.edu	37	15	52901109	52901109	+	Missense_Mutation	SNP	T	T	C	rs61731676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52901109T>C	ENST00000261844.7	-	6	2154	c.2002A>G	c.(2002-2004)Aaa>Gaa	p.K668E	FAM214A_ENST00000546305.2_Missense_Mutation_p.K675E	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	668																	CCAAAGAATTTTGGATTATAG	0.269													T|||	98	0.0195687	0.0726	0.0029	5008	,	,		17454	0.0		0.0	False		,,,				2504	0.0				p.K668E		Atlas-SNP	.											.	.	.	.	0			c.A2002G						PASS	.	T	GLU/LYS	195,3367		6,183,1592	51.0	47.0	48.0		2002	5.2	0.2	15	dbSNP_129	48	1,8081		0,1,4040	yes	missense	KIAA1370	NM_019600.2	56	6,184,5632	CC,CT,TT		0.0124,5.4745,1.6833	benign	668/1077	52901109	196,11448	1781	4041	5822	SO:0001583	missense	56204	exon6			AGAATTTTGGATT	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.2002A>G	15.37:g.52901109T>C	ENSP00000261844:p.Lys668Glu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	T	0	-2.662882	0.00107	0.054745	1.24E-4	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T;T	0.29397	1.65;1.57;1.65	6.16	5.24	0.73138	.	0.435251	0.24628	N	0.036918	T	0.00524	0.0017	N	0.00368	-1.59	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.21314	-1.0249	10	0.02654	T	1	.	11.867	0.52499	0.0:0.859:0.0:0.141	.	675;668	F5H8G0;Q32MH5	.;K1370_HUMAN	E	668;668;667;675	ENSP00000261844:K668E;ENSP00000382153:K668E;ENSP00000443598:K675E	ENSP00000261844:K668E	K	-	1	0	KIAA1370	50688401	0.012000	0.17670	0.195000	0.23364	0.037000	0.13140	1.798000	0.38814	1.598000	0.50083	-0.248000	0.11899	AAA	T|0.982;C|0.018	0.018	strong		0.269	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
SFI1	9814	hgsc.bcm.edu	37	22	31946282	31946282	+	Silent	SNP	T	T	C	rs16989753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31946282T>C	ENST00000400288.2	+	6	597	c.492T>C	c.(490-492)taT>taC	p.Y164Y	SFI1_ENST00000432498.1_Silent_p.Y164Y|SFI1_ENST00000443326.1_Silent_p.Y82Y|SFI1_ENST00000540643.1_Silent_p.Y140Y|SFI1_ENST00000414585.1_Intron|SFI1_ENST00000400289.1_Silent_p.Y82Y|SFI1_ENST00000443011.1_Intron	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	164					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GGAAGACCTATGTGCGTCAGC	0.463													C|||	138	0.0275559	0.0492	0.013	5008	,	,		21780	0.0089		0.0368	False		,,,				2504	0.0184				p.Y164Y		Atlas-SNP	.											.	SFI1	78	.	0			c.T492C						PASS	.	C	,	195,3737		9,177,1780	107.0	100.0	102.0		492,492	-5.4	0.0	22	dbSNP_123	102	417,7889		10,397,3746	no	coding-synonymous,coding-synonymous	SFI1	NM_001007467.1,NM_014775.2	,	19,574,5526	CC,CT,TT		5.0205,4.9593,5.0008	,	164/1243,164/1212	31946282	612,11626	1966	4153	6119	SO:0001819	synonymous_variant	9814	exon6			GACCTATGTGCGT	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.492T>C	22.37:g.31946282T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	140	65	0.464286	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Silent	SNP	ENST00000400288.2	37	CCDS43004.1																																																																																			T|0.966;C|0.034	0.034	strong		0.463	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	
CDHR3	222256	hgsc.bcm.edu	37	7	105658460	105658460	+	Missense_Mutation	SNP	C	C	G	rs73195662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:105658460C>G	ENST00000317716.9	+	12	1675	c.1595C>G	c.(1594-1596)aCc>aGc	p.T532S	CDHR3_ENST00000478080.1_Missense_Mutation_p.T444S|CDHR3_ENST00000542731.1_Missense_Mutation_p.T532S|CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000343407.5_Intron	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	532	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(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						TGTGAAACAACCCCCATCTAT	0.488													C|||	337	0.0672923	0.0431	0.0447	5008	,	,		18793	0.0387		0.0775	False		,,,				2504	0.135				p.T532S		Atlas-SNP	.											.	CDHR3	153	.	0			c.C1595G						PASS	.	C	SER/THR	183,3713		4,175,1769	65.0	64.0	64.0		1595	-1.2	0.0	7	dbSNP_130	64	545,7757		16,513,3622	yes	missense	CDHR3	NM_152750.4	58	20,688,5391	GG,GC,CC		6.5647,4.6971,5.9682	benign	532/886	105658460	728,11470	1948	4151	6099	SO:0001583	missense	222256	exon12			AAACAACCCCCAT	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1595C>G	7.37:g.105658460C>G	ENSP00000325954:p.Thr532Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	116	0.05311355311355311	18	0.036585365853658534	17	0.04696132596685083	23	0.04020979020979021	58	0.07651715039577836	C	7.175	0.588425	0.13812	0.046971	0.065647	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080	T;T;T	0.51325	0.71;0.71;0.71	5.66	-1.2	0.09554	Cadherin (5);Cadherin-like (1);	0.771574	0.12213	N	0.489099	T	0.01287	0.0042	N	0.26162	0.8	0.58432	P	1.0000000000287557E-6	B;B	0.22983	0.078;0.078	B;B	0.21360	0.023;0.034	T	0.09552	-1.0669	9	0.28530	T	0.3	-2.9536	1.3079	0.02092	0.2058:0.4159:0.1062:0.272	.	519;532	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	S	532;532;444	ENSP00000439766:T532S;ENSP00000325954:T532S;ENSP00000417771:T444S	ENSP00000325954:T532S	T	+	2	0	CDHR3	105445696	0.002000	0.14202	0.006000	0.13384	0.099000	0.18886	-0.044000	0.12023	0.068000	0.16574	0.655000	0.94253	ACC	C|0.945;G|0.055	0.055	strong		0.488	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
KIAA1211	57482	hgsc.bcm.edu	37	4	57181629	57181629	+	Missense_Mutation	SNP	C	C	T	rs61750793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57181629C>T	ENST00000504228.1	+	6	2066	c.1961C>T	c.(1960-1962)cCc>cTc	p.P654L	KIAA1211_ENST00000264229.6_Missense_Mutation_p.P654L|KIAA1211_ENST00000541073.1_Missense_Mutation_p.P647L			Q6ZU35	K1211_HUMAN	KIAA1211	654				P -> L (in Ref. 2; BAC86392). {ECO:0000305}.						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)					AAGGCTAAGCCCCGCCAGGAG	0.682													C|||	1008	0.201278	0.1415	0.196	5008	,	,		13963	0.254		0.2823	False		,,,				2504	0.1483				p.P654L		Atlas-SNP	.											.	KIAA1211	178	.	0			c.C1961T						PASS	.	C	LEU/PRO	5,3863		0,5,1929	18.0	22.0	21.0		1961	-0.8	0.0	4	dbSNP_129	21	45,8165		5,35,4065	no	missense	KIAA1211	NM_020722.1	98	5,40,5994	TT,TC,CC		0.5481,0.1293,0.414	benign	654/1234	57181629	50,12028	1934	4105	6039	SO:0001583	missense	57482	exon8			CTAAGCCCCGCCA	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.1961C>T	4.37:g.57181629C>T	ENSP00000423366:p.Pro654Leu	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	45	28	0.622222	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	496	0.2271062271062271	72	0.14634146341463414	76	0.20994475138121546	140	0.24475524475524477	208	0.27440633245382584	C	3.586	-0.084625	0.07097	0.001293	0.005481	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.01745	4.66;4.66;4.66	4.38	-0.764	0.11027	.	.	.	.	.	T	0.00012	0.0000	L	0.38531	1.155	0.50632	P	1.1600000000000499E-4	B;B	0.12013	0.005;0.005	B;B	0.08055	0.002;0.003	T	0.41070	-0.9529	8	0.11794	T	0.64	-4.4597	4.0737	0.09894	0.407:0.2333:0.0:0.3598	rs61750793	647;654	F5H1N7;Q6ZU35	.;K1211_HUMAN	L	654;654;647;564	ENSP00000264229:P654L;ENSP00000423366:P654L;ENSP00000444006:P647L	ENSP00000264229:P654L	P	+	2	0	KIAA1211	56876386	0.013000	0.17824	0.016000	0.15963	0.002000	0.02628	0.689000	0.25437	-0.084000	0.12595	-1.008000	0.02478	CCC	C|0.760;T|0.240	0.240	strong		0.682	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
DPH7	92715	hgsc.bcm.edu	37	9	140472034	140472034	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140472034G>C	ENST00000277540.2	-	2	332	c.175C>G	c.(175-177)Cct>Gct	p.P59A	DPH7_ENST00000479650.1_Intron	NM_138778.2	NP_620133.1	Q9BTV6	DPH7_HUMAN	diphthamide biosynthesis 7	59					peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)												CGGACCTGAGGCTCCTTAACT	0.458																																					p.P59A		Atlas-SNP	.											.	WDR85	20	.	0			c.C175G						PASS	.						110.0	98.0	102.0					9																	140472034		2203	4300	6503	SO:0001583	missense	92715	exon2			CCTGAGGCTCCTT	AK075115	CCDS7047.1	9q34.3	2013-06-20	2013-06-20	2013-06-20	ENSG00000148399	ENSG00000148399		"""WD repeat domain containing"""	25199	protein-coding gene	gene with protein product		613210	"""chromosome 9 open reading frame 112"", ""WD repeat domain 85"""	C9orf112, WDR85		23486472	Standard	NM_138778		Approved	FLJ90634, RRT2	uc004cnk.1	Q9BTV6	OTTHUMG00000020991	ENST00000277540.2:c.175C>G	9.37:g.140472034G>C	ENSP00000277540:p.Pro59Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	133	92	0.691729	NM_138778	Q96AB7	Missense_Mutation	SNP	ENST00000277540.2	37	CCDS7047.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471496	0.43942	.	.	ENSG00000148399	ENST00000277540	T	0.12569	2.67	5.11	4.2	0.49525	.	0.243332	0.33875	N	0.004464	T	0.09468	0.0233	L	0.32530	0.975	0.29436	N	0.859517	B	0.33549	0.417	B	0.30105	0.111	T	0.11690	-1.0577	10	0.21540	T	0.41	.	10.6122	0.45429	0.0936:0.0:0.9064:0.0	.	59	Q9BTV6	WDR85_HUMAN	A	59	ENSP00000277540:P59A	ENSP00000277540:P59A	P	-	1	0	WDR85	139591855	0.998000	0.40836	0.361000	0.25849	0.016000	0.09150	1.030000	0.30153	2.363000	0.80096	0.455000	0.32223	CCT	.	.	none		0.458	DPH7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055350.1	NM_138778	
TRIM5	85363	hgsc.bcm.edu	37	11	5688940	5688940	+	Splice_Site	SNP	C	C	T	rs11038628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5688940C>T	ENST00000380034.3	-	5	1002	c.746G>A	c.(745-747)gGt>gAt	p.G249D	TRIM5_ENST00000483835.1_5'UTR|TRIM5_ENST00000396853.4_Intron|TRIM5_ENST00000380027.1_Splice_Site_p.G249D|TRIM5_ENST00000396847.3_Splice_Site_p.G249D|TRIM5_ENST00000305836.5_Intron|TRIM5_ENST00000396855.3_Splice_Site_p.G249D	NM_033034.2|NM_033092.2	NP_149023.2|NP_149083.2	Q9C035	TRIM5_HUMAN	tripartite motif containing 5	249			G -> D (in dbSNP:rs11038628). {ECO:0000269|PubMed:16401428, ECO:0000269|Ref.9}.		activation of innate immune response (GO:0002218)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|signaling pattern recognition receptor activity (GO:0008329)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		GCCATCCACACCCTAGGAAGA	0.418													C|||	1228	0.245208	0.3124	0.2291	5008	,	,		16810	0.4256		0.0586	False		,,,				2504	0.1718				p.G249D		Atlas-SNP	.											.	TRIM5	111	.	0			c.G746A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY	1122,3280	401.5+/-332.0	146,830,1225	131.0	119.0	123.0		746,746,746	1.3	1.0	11	dbSNP_120	123	502,8092	144.3+/-200.2	20,462,3815	yes	missense-near-splice,missense-near-splice,missense-near-splice	TRIM5	NM_033034.2,NM_033092.2,NM_033093.2	94,94,94	166,1292,5040	TT,TC,CC		5.8413,25.4884,12.4962	possibly-damaging,possibly-damaging,possibly-damaging	249/494,249/348,249/327	5688940	1624,11372	2201	4297	6498	SO:0001630	splice_region_variant	85363	exon5			TCCACACCCTAGG	AF220025	CCDS31392.1, CCDS31393.1, CCDS31394.1	11p15	2014-06-03	2011-01-25		ENSG00000132256	ENSG00000132256		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16276	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM5"", ""tripartite motif protein TRIM"""	608487	"""tripartite motif-containing 5"""			11331580	Standard	NM_033034		Approved	RNF88, TRIM5alpha	uc001mbm.2	Q9C035	OTTHUMG00000066893	ENST00000380034.3:c.745-1G>A	11.37:g.5688940C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	71	45	0.633803	NM_033093	A6NGQ1|A8WFA8|D3DQS8|D3DQS9|G3GJY1|Q2MLV4|Q2MLV8|Q2MLV9|Q2MLW1|Q2MLW3|Q2MLW4|Q2MLW6|Q2MLW7|Q2MLX1|Q2MLX2|Q2MLX3|Q2MLX5|Q2MLY3|Q2MLY4|Q2V6Q6|Q6GX26|Q8WU46|Q96SR5|Q9C031|Q9C032|Q9C033|Q9C034	Missense_Mutation	SNP	ENST00000380034.3	37	CCDS31393.1	519|519	0.23763736263736263|0.23763736263736263	160|160	0.3252032520325203|0.3252032520325203	73|73	0.20165745856353592|0.20165745856353592	243|243	0.42482517482517484|0.42482517482517484	43|43	0.05672823218997362|0.05672823218997362	C|C	0.074|0.074	-1.197052|-1.197052	0.01594|0.01594	0.254884|0.254884	0.058413|0.058413	ENSG00000132256|ENSG00000132256	ENST00000396855;ENST00000380034;ENST00000380027;ENST00000396847|ENST00000438025	T;T;T;T|.	0.03920|.	3.76;3.76;3.76;3.76|.	3.6|3.6	1.31|1.31	0.21738|0.21738	.|.	118.454000|.	0.00166|.	N|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02842|0.02842	-0.48|-0.48	0.09310|0.09310	P|P	0.99999999276468|0.99999999276468	B;B;B|.	0.06786|.	0.001;0.0;0.0|.	B;B;B|.	0.08055|.	0.003;0.002;0.001|.	T|T	0.47761|0.47761	-0.9092|-0.9092	9|4	0.02654|.	T|.	1|.	.|.	4.6583|4.6583	0.12630|0.12630	0.0:0.3059:0.0:0.6941|0.0:0.3059:0.0:0.6941	rs11038628;rs52820439;rs61161783;rs11038628|rs11038628;rs52820439;rs61161783;rs11038628	249;249;249|.	Q9C035-3;Q9C035-4;Q9C035|.	.;.;TRIM5_HUMAN|.	D|M	249|126	ENSP00000380064:G249D;ENSP00000369373:G249D;ENSP00000369366:G249D;ENSP00000380058:G249D|.	ENSP00000369366:G249D|.	G|V	-|-	2|1	0|0	TRIM5|TRIM5	5645516|5645516	0.411000|0.411000	0.25384|0.25384	0.971000|0.971000	0.41717|0.41717	0.026000|0.026000	0.11368|0.11368	-0.094000|-0.094000	0.11094|0.11094	0.279000|0.279000	0.22186|0.22186	-0.378000|-0.378000	0.06908|0.06908	GGT|GTG	C|0.821;T|0.179	0.179	strong		0.418	TRIM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143360.3	NM_033034	Missense_Mutation
PCSK7	9159	hgsc.bcm.edu	37	11	117097931	117097931	+	Silent	SNP	C	C	T	rs45528535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117097931C>T	ENST00000320934.3	-	5	1341	c.711G>A	c.(709-711)gcG>gcA	p.A237A		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	237	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		TGGGCACAGCCGCGATCTCTC	0.607			T	IGH@	MLCLS						OREG0021371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	227	0.0453275	0.1415	0.0375	5008	,	,		18045	0.0		0.0119	False		,,,				2504	0.002				p.A237A		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	PCSK7,NS,carcinoma,-2,1	PCSK7	59	1	0			c.G711A						PASS	.	C		535,3867	243.1+/-252.9	28,479,1694	114.0	94.0	101.0		711	-11.2	0.0	11	dbSNP_127	101	31,8561	22.2+/-67.0	0,31,4265	no	coding-synonymous	PCSK7	NM_004716.2		28,510,5959	TT,TC,CC		0.3608,12.1536,4.3559		237/786	117097931	566,12428	2201	4296	6497	SO:0001819	synonymous_variant	9159	exon5			CACAGCCGCGATC	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.711G>A	11.37:g.117097931C>T		Somatic	78	0	0	1478	WXS	Illumina HiSeq	Phase_I	79	28	0.35443	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			C|0.956;T|0.044	0.044	strong		0.607	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
ADRB1	153	hgsc.bcm.edu	37	10	115805057	115805057	+	Missense_Mutation	SNP	G	G	T	rs17875445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115805057G>T	ENST00000369295.2	+	1	1252	c.1166G>T	c.(1165-1167)gGa>gTa	p.G389V		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	389			R -> G (reduced binding to G proteins; dbSNP:rs1801253). {ECO:0000269|PubMed:10212248, ECO:0000269|PubMed:10477438, ECO:0000269|PubMed:15164054, ECO:0000269|Ref.3}.|R -> L. {ECO:0000269|Ref.3}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	GCCTTCCAGGGACTGCTCTGC	0.721													G|||	27	0.00539137	0.0197	0.0014	5008	,	,		5822	0.0		0.0	False		,,,				2504	0.0				p.G389V		Atlas-SNP	.											.	ADRB1	16	.	0			c.G1166T						PASS	.	G	VAL/GLY	35,4029		0,35,1997	15.0	13.0	13.0		1166	1.7	1.0	10	dbSNP_124	13	0,7986		0,0,3993	no	missense	ADRB1	NM_000684.2	109	0,35,5990	TT,TG,GG		0.0,0.8612,0.2905		389/478	115805057	35,12015	2032	3993	6025	SO:0001583	missense	153	exon1			TCCAGGGACTGCT	J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"""GPCR / Class A : Adrenoceptors : beta"""	285	protein-coding gene	gene with protein product		109630	"""adrenergic, beta-1-, receptor"""	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.1166G>T	10.37:g.115805057G>T	ENSP00000358301:p.Gly389Val	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_000684	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Missense_Mutation	SNP	ENST00000369295.2	37	CCDS7586.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	G	8.144	0.785930	0.16189	0.008612	0.0	ENSG00000043591	ENST00000369295	T	0.37235	1.21	3.81	1.72	0.24424	.	0.000000	0.85682	U	0.000000	T	0.26484	0.0647	M	0.64404	1.975	0.36477	D	0.867582	.	.	.	.	.	.	T	0.37079	-0.9721	8	0.62326	D	0.03	.	7.2309	0.26043	0.3079:0.0:0.6921:0.0	rs17875445	.	.	.	V	389	ENSP00000358301:G389V	ENSP00000358301:G389V	G	+	2	0	ADRB1	115795047	1.000000	0.71417	0.998000	0.56505	0.291000	0.27294	3.494000	0.53273	0.129000	0.18514	0.484000	0.47621	GGA	G|0.994;T|0.006	0.006	strong		0.721	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1		
TMEM63A	9725	hgsc.bcm.edu	37	1	226050503	226050503	+	Silent	SNP	G	G	A	rs10915888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226050503G>A	ENST00000366835.3	-	11	1065	c.795C>T	c.(793-795)aaC>aaT	p.N265N	TMEM63A_ENST00000537914.1_De_novo_Start_OutOfFrame|TMEM63A_ENST00000474478.1_5'UTR	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	265					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)					GTTTGGCCACGTTGTAGCACA	0.572													G|||	199	0.0397364	0.1392	0.0202	5008	,	,		18776	0.0		0.0	False		,,,				2504	0.001				p.N265N		Atlas-SNP	.											.	TMEM63A	75	.	0			c.C795T						PASS	.	G		574,3832	255.8+/-260.9	35,504,1664	114.0	81.0	92.0		795	-1.0	0.8	1	dbSNP_120	92	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TMEM63A	NM_014698.2		35,506,5962	AA,AG,GG		0.0233,13.0277,4.4287		265/808	226050503	576,12430	2203	4300	6503	SO:0001819	synonymous_variant	9725	exon11			GGCCACGTTGTAG		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.795C>T	1.37:g.226050503G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	203	108	0.53202	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			G|0.956;A|0.044	0.044	strong		0.572	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
EEA1	8411	hgsc.bcm.edu	37	12	93202801	93202801	+	Silent	SNP	C	C	T	rs7970286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:93202801C>T	ENST00000322349.8	-	18	2595	c.2331G>A	c.(2329-2331)gaG>gaA	p.E777E		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	777					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						ACATTTCCTTCTCCATTTCAA	0.358													C|||	2346	0.46845	0.1679	0.5245	5008	,	,		13451	0.8681		0.3569	False		,,,				2504	0.5378				p.E777E		Atlas-SNP	.											.	EEA1	104	.	0			c.G2331A						PASS	.	C		921,3485	349.3+/-310.3	112,697,1394	125.0	110.0	115.0		2331	2.9	1.0	12	dbSNP_116	115	2984,5616	463.0+/-365.8	512,1960,1828	no	coding-synonymous	EEA1	NM_003566.3		624,2657,3222	TT,TC,CC		34.6977,20.9033,30.0246		777/1412	93202801	3905,9101	2203	4300	6503	SO:0001819	synonymous_variant	8411	exon18			TTCCTTCTCCATT	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.2331G>A	12.37:g.93202801C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	113	56	0.495575	NM_003566	Q14221	Silent	SNP	ENST00000322349.8	37	CCDS31874.1																																																																																			C|0.618;T|0.382	0.382	strong		0.358	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
ARNT2	9915	hgsc.bcm.edu	37	15	80873642	80873642	+	Silent	SNP	C	C	G	rs79914316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80873642C>G	ENST00000303329.4	+	17	1980	c.1815C>G	c.(1813-1815)acC>acG	p.T605T	ARNT2_ENST00000527771.1_Silent_p.T594T|RP11-379K22.3_ENST00000603875.1_RNA|hsa-mir-5572_ENST00000583188.1_RNA|ARNT2_ENST00000533983.1_Silent_p.T594T	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	605					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)	p.T605>?(1)		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)			CGAGCCACACCTACCCGGCAG	0.552													C|||	445	0.0888578	0.1415	0.0231	5008	,	,		19919	0.1131		0.0209	False		,,,				2504	0.1094				p.T605T		Atlas-SNP	.											.	ARNT2	88	.	1	Complex(1)	NS(1)	c.C1815G						PASS	.	C		531,3875	241.5+/-251.9	32,467,1704	99.0	85.0	90.0		1815	-0.6	0.8	15	dbSNP_131	90	32,8568	22.2+/-67.0	0,32,4268	no	coding-synonymous	ARNT2	NM_014862.3		32,499,5972	GG,GC,CC		0.3721,12.0517,4.3288		605/718	80873642	563,12443	2203	4300	6503	SO:0001819	synonymous_variant	9915	exon17			CCACACCTACCCG	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.1815C>G	15.37:g.80873642C>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	194	97	0.5	NM_014862	B4DIS7|O15024|Q8IYC2	Silent	SNP	ENST00000303329.4	37	CCDS32307.1																																																																																			C|0.947;G|0.053	0.053	strong		0.552	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2		
SVEP1	79987	hgsc.bcm.edu	37	9	113265448	113265448	+	Silent	SNP	A	A	G	rs10120982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113265448A>G	ENST00000401783.2	-	6	1689	c.1353T>C	c.(1351-1353)tgT>tgC	p.C451C	SVEP1_ENST00000374469.1_Silent_p.C428C|SVEP1_ENST00000374461.1_Silent_p.C428C|SVEP1_ENST00000302728.8_Silent_p.C451C|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	451	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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						CCCTTGTAGAACAGCTGATGT	0.393													A|||	56	0.0111821	0.0378	0.0072	5008	,	,		20793	0.0		0.001	False		,,,				2504	0.0				p.C451C		Atlas-SNP	.											SVEP1,NS,carcinoma,-1,2	SVEP1	326	2	0			c.T1353C						PASS	.	A		130,3830		4,122,1854	152.0	149.0	150.0		1353	0.9	1.0	9	dbSNP_119	150	2,8308		0,2,4153	no	coding-synonymous	SVEP1	NM_153366.3		4,124,6007	GG,GA,AA		0.0241,3.2828,1.0758		451/3572	113265448	132,12138	1980	4155	6135	SO:0001819	synonymous_variant	79987	exon6			TGTAGAACAGCTG	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.1353T>C	9.37:g.113265448A>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	202	59	0.292079	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			A|0.992;G|0.008	0.008	strong		0.393	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
HMCN1	83872	hgsc.bcm.edu	37	1	186026474	186026474	+	Missense_Mutation	SNP	T	T	C	rs12129650	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186026474T>C	ENST00000271588.4	+	46	7482	c.7253T>C	c.(7252-7254)aTa>aCa	p.I2418T	HMCN1_ENST00000367492.2_Missense_Mutation_p.I2418T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2418	Ig-like C2-type 22.		I -> T (in dbSNP:rs12129650). {ECO:0000269|PubMed:14570714, ECO:0000269|Ref.1}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTGCCTTCCATAACCTGGTTC	0.413													T|||	2654	0.529952	0.5393	0.6124	5008	,	,		15388	0.5675		0.496	False		,,,				2504	0.455				p.I2418T		Atlas-SNP	.											.	HMCN1	797	.	0			c.T7253C						PASS	.	T	THR/ILE	2446,1960	619.5+/-393.4	686,1074,443	115.0	115.0	115.0		7253	4.7	0.9	1	dbSNP_120	115	4387,4213	583.2+/-391.5	1138,2111,1051	yes	missense	HMCN1	NM_031935.2	89	1824,3185,1494	CC,CT,TT		48.9884,44.4848,47.4627	benign	2418/5636	186026474	6833,6173	2203	4300	6503	SO:0001583	missense	83872	exon46			CTTCCATAACCTG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7253T>C	1.37:g.186026474T>C	ENSP00000271588:p.Ile2418Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1198	0.5485347985347986	254	0.516260162601626	216	0.5966850828729282	341	0.5961538461538461	387	0.5105540897097626	T	18.19	3.569521	0.65765	0.555152	0.510116	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.72282	-0.64;-0.64	5.8	4.67	0.58626	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.183947	0.56097	N	0.000027	T	0.00012	0.0000	M	0.85542	2.76	0.20307	P	0.9999161177	P	0.48998	0.918	B	0.44315	0.446	T	0.47674	-0.9099	9	0.56958	D	0.05	.	11.7655	0.51928	0.0:0.0685:0.0:0.9315	rs12129650;rs52819931;rs57046032;rs12129650	2418	Q96RW7	HMCN1_HUMAN	T	2418	ENSP00000271588:I2418T;ENSP00000356462:I2418T	ENSP00000271588:I2418T	I	+	2	0	HMCN1	184293097	1.000000	0.71417	0.907000	0.35723	0.830000	0.47004	5.743000	0.68655	1.020000	0.39573	-0.263000	0.10527	ATA	C|0.538;N|0.000	0.538	strong		0.413	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
ADAMTS15	170689	hgsc.bcm.edu	37	11	130318935	130318935	+	Silent	SNP	C	C	A	rs146878786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:130318935C>A	ENST00000299164.2	+	1	67	c.67C>A	c.(67-69)Cgg>Agg	p.R23R		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15	23						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(8)|urinary_tract(1)	36	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		TGAGCCAGAGCGGGAGGTAGT	0.662													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		14248	0.0		0.0	False		,,,				2504	0.0				p.R23R		Atlas-SNP	.											.	ADAMTS15	103	.	0			c.C67A						PASS	.	C		46,4356	44.6+/-78.6	0,46,2155	29.0	30.0	30.0		67	2.4	0.4	11	dbSNP_134	30	0,8594		0,0,4297	no	coding-synonymous	ADAMTS15	NM_139055.2		0,46,6452	AA,AC,CC		0.0,1.045,0.354		23/951	130318935	46,12950	2201	4297	6498	SO:0001819	synonymous_variant	170689	exon1			CCAGAGCGGGAGG	AJ315733	CCDS8488.1	11q25	2008-02-01	2005-08-19		ENSG00000166106	ENSG00000166106		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	16305	protein-coding gene	gene with protein product		607509	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 15"""			11867212	Standard	NM_139055		Approved		uc010scd.2	Q8TE58	OTTHUMG00000165657	ENST00000299164.2:c.67C>A	11.37:g.130318935C>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_139055	Q32MI6	Silent	SNP	ENST00000299164.2	37	CCDS8488.1																																																																																			C|0.997;A|0.003	0.003	strong		0.662	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	NM_139055	
PRB1	5542	hgsc.bcm.edu	37	12	11506211	11506211	+	Missense_Mutation	SNP	A	A	C	rs76504934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11506211A>C	ENST00000500254.2	-	4	464	c.427T>G	c.(427-429)Tct>Gct	p.S143A	PRB1_ENST00000545626.1_Missense_Mutation_p.S123A|PRB1_ENST00000546254.1_Missense_Mutation_p.S143A	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1	0	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].		Missing (in allele M).|Missing (in allele S).|Missing (in clone CP-4).|Missing (in clone CP-5).			extracellular region (GO:0005576)		p.S143A(1)		NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			CCTGGAGGAGATCGGGCACTT	0.607													N|||	2280	0.455272	0.2746	0.5706	5008	,	,		18678	0.4355		0.668	False		,,,				2504	0.4192				p.S143A		Atlas-SNP	.											PRB1,NS,carcinoma,0,1	PRB1	33	1	1	Substitution - Missense(1)	prostate(1)	c.T427G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER	1480,2820		371,738,1041	166.0	194.0	184.0		367,427,826	-0.7	0.0	12	dbSNP_131	184	5684,2866		1915,1854,506	no	missense,missense,missense	PRB1	NM_199354.2,NM_199353.2,NM_005039.3	99,99,99	2286,2592,1547	CC,CA,AA		33.5205,34.4186,44.249	benign,benign,benign	123/179,143/199,276/332	11506211	7164,5686	2150	4275	6425	SO:0001583	missense	5542	exon4			GAGGAGATCGGGC		CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.427T>G	12.37:g.11506211A>C	ENSP00000420826:p.Ser143Ala	Somatic	425	0	0		WXS	Illumina HiSeq	Phase_I	1306	421	0.322358	NM_199353	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Missense_Mutation	SNP	ENST00000500254.2	37	CCDS8642.1	1122	0.5137362637362637	157	0.31910569105691056	208	0.574585635359116	253	0.4423076923076923	504	0.6649076517150396	.	0.016	-1.539278	0.00942	0.344186	0.664795	ENSG00000251655	ENST00000545626;ENST00000500254;ENST00000546254	T;T;T	0.04360	3.64;3.64;3.64	0.522	-0.658	0.11428	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.26363	0.147;0.147	B;B	0.17979	0.02;0.02	T	0.05084	-1.0907	8	0.27082	T	0.32	.	4.5503	0.12108	0.3073:0.0:0.6927:0.0	.	123;143	G3V1R1;G3V1M9	.;.	A	123;143;143	ENSP00000444249:S123A;ENSP00000420826:S143A;ENSP00000442127:S143A	ENSP00000420826:S143A	S	-	1	0	PRB1	11397478	.	.	0.001000	0.08648	0.038000	0.13279	.	.	-0.283000	0.09115	0.113000	0.15668	TCT	A|0.446;C|0.554	0.554	strong		0.607	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039	
ALX4	60529	hgsc.bcm.edu	37	11	44286722	44286722	+	Silent	SNP	C	C	T	rs145904583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44286722C>T	ENST00000329255.3	-	4	1021	c.918G>A	c.(916-918)ccG>ccA	p.P306P		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	306			P -> L. {ECO:0000269|PubMed:22829454}.		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)	p.P306P(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						CGAGCCAGGACGGGTTCTGAA	0.687													C|||	47	0.00938498	0.0325	0.0043	5008	,	,		16566	0.0		0.0	False		,,,				2504	0.001				p.P306P		Atlas-SNP	.											ALX4,NS,carcinoma,0,1	ALX4	58	1	1	Substitution - coding silent(1)	prostate(1)	c.G918A						PASS	.	C		100,4198		1,98,2050	17.0	16.0	16.0		918	-7.6	0.3	11	dbSNP_134	16	5,8425		0,5,4210	no	coding-synonymous	ALX4	NM_021926.3		1,103,6260	TT,TC,CC		0.0593,2.3267,0.825		306/412	44286722	105,12623	2149	4215	6364	SO:0001819	synonymous_variant	60529	exon4			CCAGGACGGGTTC	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.918G>A	11.37:g.44286722C>T		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	221	109	0.493213	NM_021926	Q96JN7|Q9H198|Q9HAY9	Silent	SNP	ENST00000329255.3	37	CCDS31468.1																																																																																			C|0.991;T|0.009	0.009	strong		0.687	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1		
ZNF729	100287226	hgsc.bcm.edu	37	19	22499853	22499853	+	Missense_Mutation	SNP	A	A	G	rs78300029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22499853A>G	ENST00000601693.1	+	4	3752	c.3634A>G	c.(3634-3636)Aga>Gga	p.R1212G	ZNF729_ENST00000357491.6_Intron			A6NN14	ZN729_HUMAN	zinc finger protein 729	1212					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						AATTCATACCAGAGAGAAACC	0.353													G|||	122	0.024361	0.0893	0.0058	5008	,	,		19855	0.0		0.0	False		,,,				2504	0.0				p.R1212G		Atlas-SNP	.											.	ZNF729	78	.	0			c.A3634G						PASS	.																																			SO:0001583	missense	100287226	exon4			CATACCAGAGAGA		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.3634A>G	19.37:g.22499853A>G	ENSP00000469582:p.Arg1212Gly	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	12	5	0.416667	NM_001242680	M0QY45	Missense_Mutation	SNP	ENST00000601693.1	37	CCDS59368.1																																																																																			A|0.971;G|0.029	0.029	strong		0.353	ZNF729-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464396.1	XM_496301	
PKP2	5318	hgsc.bcm.edu	37	12	33031023	33031023	+	Missense_Mutation	SNP	G	G	A	rs62001016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:33031023G>A	ENST00000070846.6	-	3	815	c.791C>T	c.(790-792)gCa>gTa	p.A264V	PKP2_ENST00000340811.4_Missense_Mutation_p.A264V	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	264					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					AGTGAGCCCTGCCGTCAGGTA	0.647													G|||	58	0.0115815	0.0408	0.0058	5008	,	,		18240	0.0		0.0	False		,,,				2504	0.0				p.A264V		Atlas-SNP	.											.	PKP2	110	.	0			c.C791T						PASS	.	G	VAL/ALA,VAL/ALA	137,4269	96.7+/-135.4	1,135,2067	52.0	48.0	49.0		791,791	3.8	0.0	12	dbSNP_129	49	0,8600		0,0,4300	yes	missense,missense	PKP2	NM_001005242.2,NM_004572.3	64,64	1,135,6367	AA,AG,GG		0.0,3.1094,1.0534	benign,benign	264/838,264/882	33031023	137,12869	2203	4300	6503	SO:0001583	missense	5318	exon3			AGCCCTGCCGTCA	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.791C>T	12.37:g.33031023G>A	ENSP00000070846:p.Ala264Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	G	1.719	-0.497156	0.04291	0.031094	0.0	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.81163	-1.46;-1.39	4.73	3.84	0.44239	.	5.091870	0.00357	N	0.000025	T	0.42944	0.1225	N	0.22421	0.69	0.09310	N	1	B;B;B	0.19200	0.034;0.02;0.006	B;B;B	0.21708	0.036;0.016;0.01	T	0.49862	-0.8894	10	0.21540	T	0.41	-14.3867	10.8315	0.46663	0.0896:0.0:0.9104:0.0	.	264;264;264	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	V	264	ENSP00000342800:A264V;ENSP00000070846:A264V	ENSP00000070846:A264V	A	-	2	0	PKP2	32922290	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	0.892000	0.28322	0.994000	0.38892	0.650000	0.86243	GCA	G|0.988;A|0.012	0.012	strong		0.647	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919928	12919928	+	Missense_Mutation	SNP	A	A	G	rs72472698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919928A>G	ENST00000240189.2	+	3	755	c.668A>G	c.(667-669)aAg>aGg	p.K223R		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	223					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)		CTGATAAGAAAGCTTTATTGT	0.388													.|||	550	0.109824	0.1271	0.0994	5008	,	,		22697	0.131		0.1083	False		,,,				2504	0.0736				p.K223R		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.A668G						PASS	.	A	ARG/LYS	621,3783	261.9+/-264.6	70,481,1651	101.0	106.0	104.0		668	-1.1	0.0	1	dbSNP_130	104	965,7619	205.1+/-247.6	81,803,3408	yes	missense	PRAMEF2	NM_023014.1	26	151,1284,5059	GG,GA,AA		11.2418,14.1008,12.2113	possibly-damaging	223/475	12919928	1586,11402	2202	4292	6494	SO:0001583	missense	65122	exon3			TAAGAAAGCTTTA		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.668A>G	1.37:g.12919928A>G	ENSP00000240189:p.Lys223Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	134	78	0.58209	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	233	0.10668498168498168	46	0.09349593495934959	36	0.09944751381215469	62	0.10839160839160839	89	0.11741424802110818	A	7.603	0.673163	0.14776	0.141008	0.112418	ENSG00000120952	ENST00000240189	T	0.16196	2.36	0.842	-1.06	0.10002	.	2.602770	0.01453	N	0.015575	T	0.00109	0.0003	L	0.39020	1.185	0.80722	P	0.0	P	0.50443	0.935	B	0.44108	0.441	T	0.13575	-1.0504	9	0.15066	T	0.55	.	2.8122	0.05445	0.5906:0.0:0.0:0.4094	.	223	O60811	PRAM2_HUMAN	R	223	ENSP00000240189:K223R	ENSP00000240189:K223R	K	+	2	0	PRAMEF2	12842515	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-3.831000	0.00355	-0.306000	0.08818	0.163000	0.16589	AAG	A|0.885;G|0.115	0.115	strong		0.388	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
NWD1	284434	hgsc.bcm.edu	37	19	16890243	16890243	+	Missense_Mutation	SNP	C	C	G	rs773930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16890243C>G	ENST00000552788.1	+	10	2698	c.2698C>G	c.(2698-2700)Cag>Gag	p.Q900E	NWD1_ENST00000379808.3_Missense_Mutation_p.Q900E|NWD1_ENST00000339803.6_Missense_Mutation_p.Q765E|NWD1_ENST00000549814.1_Missense_Mutation_p.Q900E|NWD1_ENST00000524140.2_Missense_Mutation_p.Q900E|NWD1_ENST00000523826.1_Missense_Mutation_p.Q694E			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	900			Q -> E (in dbSNP:rs773930).				ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CATGGAAGAGCAGCATGTGAT	0.552											OREG0025337	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	937	0.187101	0.5817	0.0778	5008	,	,		20337	0.0		0.0427	False		,,,				2504	0.0726				p.Q900E		Atlas-SNP	.											.	NWD1	303	.	0			c.C2698G						PASS	.	C	GLU/GLN	2061,2345		495,1071,637	208.0	164.0	179.0		2698	-4.1	0.0	19	dbSNP_86	179	391,8209		7,377,3916	yes	missense	NWD1	NM_001007525.3	29	502,1448,4553	GG,GC,CC		4.5465,46.7771,18.8528	possibly-damaging	900/1433	16890243	2452,10554	2203	4300	6503	SO:0001583	missense	284434	exon12			GAAGAGCAGCATG	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.2698C>G	19.37:g.16890243C>G	ENSP00000447224:p.Gln900Glu	Somatic	74	0	0	713	WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		330	0.1510989010989011	272	0.5528455284552846	25	0.06906077348066299	0	0.0	33	0.04353562005277045	-	0.023	-1.401628	0.01165	0.467771	0.045465	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.39406	1.6;1.08;1.6;3.57;3.57;3.57	5.08	-4.05	0.03998	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.156090	0.06265	N	0.694563	T	0.00012	0.0000	L	0.49350	1.555	0.80722	P	0.0	B;B;B	0.29301	0.039;0.241;0.039	B;B;B	0.25140	0.016;0.058;0.01	T	0.48375	-0.9041	9	0.20046	T	0.44	2.0E-4	2.7587	0.05300	0.3759:0.2799:0.2577:0.0865	rs773930;rs52816786;rs59224614;rs773930	900;900;765	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	E	765;900;900;900;694;900;765	ENSP00000428579:Q900E;ENSP00000447548:Q900E;ENSP00000369136:Q900E;ENSP00000428955:Q694E;ENSP00000447224:Q900E;ENSP00000340159:Q765E	ENSP00000340159:Q765E	Q	+	1	0	NWD1	16751243	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.426000	0.07008	-0.101000	0.12219	0.479000	0.44913	CAG	C|0.826;G|0.174	0.174	strong		0.552	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
TEX15	56154	hgsc.bcm.edu	37	8	30702602	30702602	+	Missense_Mutation	SNP	T	T	C	rs323345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:30702602T>C	ENST00000256246.2	-	1	4006	c.3932A>G	c.(3931-3933)aAc>aGc	p.N1311S		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1311			N -> S (in dbSNP:rs323345). {ECO:0000269|PubMed:11279525}.		fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TGTAATAATGTTTTGTTTGGG	0.358													C|||	1642	0.327875	0.8487	0.1599	5008	,	,		20157	0.0704		0.1272	False		,,,				2504	0.2147				p.N1311S		Atlas-SNP	.											.	TEX15	350	.	0			c.A3932G						PASS	.	C	SER/ASN	3195,1211	399.9+/-331.4	1171,853,179	107.0	115.0	113.0		3932	-7.4	0.0	8	dbSNP_79	113	1012,7584	765.7+/-407.6	66,880,3352	yes	missense	TEX15	NM_031271.3	46	1237,1733,3531	CC,CT,TT		11.7729,27.4852,32.3566	benign	1311/2790	30702602	4207,8795	2203	4298	6501	SO:0001583	missense	56154	exon1			ATAATGTTTTGTT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.3932A>G	8.37:g.30702602T>C	ENSP00000256246:p.Asn1311Ser	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	193	192	0.994819	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	605	0.27701465201465203	411	0.8353658536585366	62	0.1712707182320442	39	0.06818181818181818	93	0.12269129287598944	C	3.112	-0.182359	0.06340	0.725148	0.117729	ENSG00000133863	ENST00000256246	T	0.21031	2.03	6.07	-7.43	0.01383	.	0.922343	0.09316	N	0.818928	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.28554	-1.0040	9	0.87932	D	0	.	5.6396	0.17557	0.0937:0.1285:0.1853:0.5925	rs323345;rs52829503;rs60104740;rs323345	1311	Q9BXT5	TEX15_HUMAN	S	1311	ENSP00000256246:N1311S	ENSP00000256246:N1311S	N	-	2	0	TEX15	30822144	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.083000	0.03397	-2.295000	0.00662	-0.735000	0.03563	AAC	T|0.707;C|0.293	0.293	strong		0.358	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
ZNF30	90075	hgsc.bcm.edu	37	19	35434512	35434512	+	Silent	SNP	T	T	C	rs2651109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35434512T>C	ENST00000601142.1	+	5	879	c.642T>C	c.(640-642)agT>agC	p.S214S	ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000426813.2_Silent_p.S133S|ZNF30_ENST00000303586.7_Silent_p.S215S|ZNF30_ENST00000439785.1_Silent_p.S215S			P17039	ZNF30_HUMAN	zinc finger protein 30	214					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		AGACTATTAGTGGTAGCTATC	0.418													C|||	3272	0.653355	0.9402	0.4049	5008	,	,		22288	0.6052		0.5129	False		,,,				2504	0.636				p.S215S		Atlas-SNP	.											.	ZNF30	44	.	0			c.T645C						PASS	.	C	,,	3461,581		1492,477,52	41.0	45.0	44.0		645,645,642	-1.7	0.0	19	dbSNP_100	44	4040,4416		972,2096,1160	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	,,	2464,2573,1212	CC,CT,TT		47.7767,14.3741,39.9824	,,	215/625,215/625,214/624	35434512	7501,4997	2021	4228	6249	SO:0001819	synonymous_variant	90075	exon5			TATTAGTGGTAGC	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.642T>C	19.37:g.35434512T>C		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	110	108	0.981818	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Silent	SNP	ENST00000601142.1	37	CCDS46045.1																																																																																			T|0.345;C|0.655	0.655	strong		0.418	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
SSPO	23145	hgsc.bcm.edu	37	7	149488991	149488991	+	RNA	SNP	T	T	C	rs893601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149488991T>C	ENST00000378016.2	+	0	5332							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)			GCAGTGCCACTCACCCCAGAA	0.662													C|||	202	0.0403355	0.1029	0.0144	5008	,	,		16534	0.004		0.003	False		,,,				2504	0.0501				p.S1778P		Atlas-SNP	.											.	.	.	.	0			c.T5332C						PASS	.	C		297,3797		12,273,1762	19.0	23.0	22.0		5336	4.8	0.1	7	dbSNP_86	22	18,8330		0,18,4156	yes	coding-notMod3	SSPO	NM_198455.2		12,291,5918	CC,CT,TT		0.2156,7.2545,2.5317			149488991	315,12127	2047	4174	6221			23145	exon35			TGCCACTCACCCC	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.149488991T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.976;C|0.024	0.024	strong		0.662	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
ZNF286A	57335	hgsc.bcm.edu	37	17	15604508	15604508	+	Missense_Mutation	SNP	C	C	G	rs144115902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15604508C>G	ENST00000464847.2	+	2	633	c.80C>G	c.(79-81)aCa>aGa	p.T27R	ZNF286A_ENST00000421016.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000413242.2_Missense_Mutation_p.T27R|ZNF286A_ENST00000593105.1_Missense_Mutation_p.T17R|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000395894.2_Missense_Mutation_p.T27R|ZNF286A_ENST00000395893.2_Missense_Mutation_p.T27R|ZNF286A_ENST00000472486.1_Missense_Mutation_p.T17R|ZNF286A_ENST00000585194.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000581529.1_Missense_Mutation_p.T17R|ZNF286A_ENST00000583566.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000580259.1_Missense_Mutation_p.T27R			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	27					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(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		GAGAAGAGCACAGAAGAGGGA	0.478													C|||	121	0.0241613	0.0855	0.0115	5008	,	,		21616	0.0		0.0	False		,,,				2504	0.0				p.T27R		Atlas-SNP	.											.	ZNF286A	58	.	0			c.C80G						PASS	.	C	ARG/THR,ARG/THR	334,4072		6,322,1875	220.0	201.0	207.0		80,80	4.3	0.8	17	dbSNP_134	207	4,8592		0,4,4294	no	missense,missense	ZNF286A	NM_001130842.1,NM_020652.2	71,71	6,326,6169	GG,GC,CC		0.0465,7.5806,2.5996	benign,benign	27/522,27/522	15604508	338,12664	2203	4298	6501	SO:0001583	missense	57335	exon3			AGAGCACAGAAGA	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"""Zinc fingers, C2H2-type"", ""-"""	13501	protein-coding gene	gene with protein product			"""zinc finger protein 286"""	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.80C>G	17.37:g.15604508C>G	ENSP00000464218:p.Thr27Arg	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	222	110	0.495495	NM_020652	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	49	0.022435897435897436	41	0.08333333333333333	6	0.016574585635359115	0	0.0	2	0.002638522427440633	.	12.15	1.851494	0.32699	0.075806	4.65E-4	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894;ENST00000395893	T;T;T;T	0.07327	3.55;3.2;5.46;5.59	4.3	4.3	0.51218	.	1.408720	0.05359	N	0.533364	T	0.00384	0.0012	N	0.14661	0.345	0.26812	N	0.968979	B	0.19583	0.037	B	0.20955	0.032	T	0.25152	-1.0140	10	0.14252	T	0.57	-0.6478	12.9853	0.58588	0.0:1.0:0.0:0.0	.	27	Q9HBT8	Z286A_HUMAN	R	27;17;27;27	ENSP00000397163:T27R;ENSP00000408168:T17R;ENSP00000379231:T27R;ENSP00000379230:T27R	ENSP00000435872:T27R	T	+	2	0	ZNF286A	15545233	0.001000	0.12720	0.848000	0.33437	0.905000	0.53344	0.004000	0.13106	2.320000	0.78422	0.555000	0.69702	ACA	C|0.978;G|0.022	0.022	strong		0.478	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652	
TUBB8	347688	hgsc.bcm.edu	37	10	95167	95167	+	Silent	SNP	G	G	A	rs202227666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:95167G>A	ENST00000309812.4	-	1	74	c.12C>T	c.(10-12)atC>atT	p.I4I	TUBB8_ENST00000413237.3_Intron|TUBB8_ENST00000447903.2_Intron|TUBB8_ENST00000332708.5_Silent_p.I4I	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	4					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		GCGTGAGCACGATCTCCCTCA	0.667																																					p.I4I	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,colon,carcinoma,-2,2	TUBB8	62	2	0			c.C12T						scavenged	.						18.0	17.0	17.0					10																	95167		2197	4294	6491	SO:0001819	synonymous_variant	347688	exon1			GAGCACGATCTCC	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.12C>T	10.37:g.95167G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	148	8	0.0540541	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1																																																																																			G|0.980;A|0.019	0.019	strong		0.667	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
GUCA2B	2981	hgsc.bcm.edu	37	1	42619139	42619139	+	Silent	SNP	A	A	G	rs1047047	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:42619139A>G	ENST00000372581.1	+	1	48	c.18A>G	c.(16-18)gcA>gcG	p.A6A		NM_007102.2	NP_009033.1	Q16661	GUC2B_HUMAN	guanylate cyclase activator 2B (uroguanylin)	6					body fluid secretion (GO:0007589)|cGMP biosynthetic process (GO:0006182)|excretion (GO:0007588)|negative regulation of blood pressure (GO:0045776)|positive regulation of guanylate cyclase activity (GO:0031284)	extracellular vesicular exosome (GO:0070062)	calcium sensitive guanylate cyclase activator activity (GO:0008048)			breast(1)|large_intestine(2)	3	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCAGGGCTGCATCAGGGCTCC	0.637													G|||	1580	0.315495	0.4614	0.2896	5008	,	,		16480	0.4038		0.165	False		,,,				2504	0.2004				p.A6A		Atlas-SNP	.											.	GUCA2B	9	.	0			c.A18G						PASS	.	G		1701,2705	646.7+/-398.4	320,1061,822	67.0	56.0	60.0		18	2.3	0.0	1	dbSNP_86	60	1298,7302	754.4+/-407.5	81,1136,3083	no	coding-synonymous	GUCA2B	NM_007102.2		401,2197,3905	GG,GA,AA		15.093,38.6064,23.0586		6/113	42619139	2999,10007	2203	4300	6503	SO:0001819	synonymous_variant	2981	exon1			GGCTGCATCAGGG	BC069301	CCDS464.1	1p34-p33	2014-01-30			ENSG00000044012	ENSG00000044012		"""Endogenous ligands"""	4683	protein-coding gene	gene with protein product	"""prepro-uroguanylin"""	601271				8605041, 9268639	Standard	NM_007102		Approved		uc001chc.1	Q16661	OTTHUMG00000007024	ENST00000372581.1:c.18A>G	1.37:g.42619139A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_007102	Q52LV0	Silent	SNP	ENST00000372581.1	37	CCDS464.1																																																																																			A|0.756;G|0.244	0.244	strong		0.637	GUCA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018307.1	NM_007102	
SLC2A9	56606	hgsc.bcm.edu	37	4	10027542	10027542	+	Missense_Mutation	SNP	C	C	T	rs6820230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:10027542C>T	ENST00000506583.1	-	3	266	c.49G>A	c.(49-51)Gcg>Acg	p.A17T	SLC2A9_ENST00000309065.3_Missense_Mutation_p.A17T			Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	46					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	TTCTTTTTCGCTGAATCACTT	0.423													C|||	1345	0.26857	0.5507	0.2205	5008	,	,		20219	0.0972		0.2972	False		,,,				2504	0.0685				p.A17T		Atlas-SNP	.											SLC2A9,NS,carcinoma,+2,1	SLC2A9	158	1	0			c.G49A						PASS	.	C	THR/ALA	2173,2233	585.0+/-386.2	526,1121,556	130.0	131.0	131.0		49	0.9	0.0	4	dbSNP_116	131	2340,6260	390.9+/-343.5	333,1674,2293	yes	missense	SLC2A9	NM_001001290.1	58	859,2795,2849	TT,TC,CC		27.2093,49.3191,34.6994		17/512	10027542	4513,8493	2203	4300	6503	SO:0001583	missense	56606	exon2			TTTTCGCTGAATC	AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"""Solute carriers"""	13446	protein-coding gene	gene with protein product	"""urate voltage-driven efflux transporter 1"""	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000506583.1:c.49G>A	4.37:g.10027542C>T	ENSP00000422209:p.Ala17Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_001001290	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000506583.1	37	CCDS3406.1	617	0.2825091575091575	269	0.5467479674796748	85	0.23480662983425415	50	0.08741258741258741	213	0.28100263852242746	C	3.384	-0.125708	0.06795	0.493191	0.272093	ENSG00000109667	ENST00000506583;ENST00000309065;ENST00000513129	D;D;D	0.87334	-1.62;-1.62;-2.24	3.59	0.892	0.19230	.	.	.	.	.	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	0.40098	-0.9581	7	.	.	.	.	3.6186	0.08086	0.0:0.5531:0.2107:0.2362	rs6820230;rs52816748;rs56455102;rs56938107;rs6820230	17	Q9NRM0-2	.	T	17	ENSP00000422209:A17T;ENSP00000311383:A17T;ENSP00000426800:A17T	.	A	-	1	0	SLC2A9	9636640	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.100000	0.10990	0.155000	0.19261	0.561000	0.74099	GCG	C|0.682;T|0.318	0.318	strong		0.423	SLC2A9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207054.2		
PCDHB6	56130	hgsc.bcm.edu	37	5	140531426	140531426	+	Missense_Mutation	SNP	G	G	A	rs146552509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140531426G>A	ENST00000231136.1	+	1	1588	c.1588G>A	c.(1588-1590)Ggc>Agc	p.G530S	PCDHB6_ENST00000543635.1_Missense_Mutation_p.G394S	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	530	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.G530S(2)		cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTTCCGCGTGGGCGCCACAGA	0.662																																					p.G530S		Atlas-SNP	.											PCDHB6,trunk,malignant_melanoma,0,2	PCDHB6	161	2	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|skin(1)	c.G1588A						scavenged	.						65.0	71.0	69.0					5																	140531426		2203	4300	6503	SO:0001583	missense	56130	exon1			CGCGTGGGCGCCA	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1588G>A	5.37:g.140531426G>A	ENSP00000231136:p.Gly530Ser	Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	405	16	0.0395062	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.830005	0.32329	.	.	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.01647	4.71;4.71	4.19	-4.24	0.03777	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.01061	0.0035	N	0.02181	-0.65	0.09310	N	1	B	0.28933	0.228	B	0.36922	0.236	T	0.51301	-0.8723	9	0.59425	D	0.04	.	9.2605	0.37610	0.263:0.612:0.125:0.0	.	530	Q9Y5E3	PCDB6_HUMAN	S	394;530;315	ENSP00000438466:G394S;ENSP00000231136:G530S	ENSP00000231136:G530S	G	+	1	0	PCDHB6	140511610	0.000000	0.05858	0.930000	0.37139	0.993000	0.82548	-4.320000	0.00253	-0.705000	0.05035	0.556000	0.70494	GGC	G|0.994;A|0.006	0.006	strong		0.662	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261994	39261994	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39261994G>A	ENST00000391415.1	+	1	411	c.354G>A	c.(352-354)agG>agA	p.R118R		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	118	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						GCCACCCTAGGtgctgcatct	0.667																																					p.R118R		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	2	0			c.G354A						scavenged	.						26.0	30.0	29.0					17																	39261994		692	1591	2283	SO:0001819	synonymous_variant	100132386	exon1			CCCTAGGTGCTGC	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.354G>A	17.37:g.39261994G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	91	3	0.032967	NM_001146041		Silent	SNP	ENST00000391415.1	37	CCDS54124.1																																																																																			.	.	none		0.667	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
ADAM33	80332	hgsc.bcm.edu	37	20	3650205	3650205	+	Missense_Mutation	SNP	G	G	A	rs2280090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3650205G>A	ENST00000356518.2	-	20	2561	c.2320C>T	c.(2320-2322)Ccc>Tcc	p.P774S	ADAM33_ENST00000466620.1_5'UTR|ADAM33_ENST00000379861.4_Missense_Mutation_p.P774S|ADAM33_ENST00000350009.2_Missense_Mutation_p.P748S	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	774			P -> S (in dbSNP:rs2280090). {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						AGGGGCCAGGGCTGTCCAGTG	0.657													G|||	723	0.144369	0.1641	0.0836	5008	,	,		16017	0.129		0.1421	False		,,,				2504	0.1789				p.P774S		Atlas-SNP	.											.	ADAM33	76	.	0			c.C2320T						PASS	.	G	SER/PRO,SER/PRO	627,3773		44,539,1617	20.0	19.0	20.0		2320,2242	-0.2	0.0	20	dbSNP_100	20	1134,7454		83,968,3243	yes	missense,missense	ADAM33	NM_025220.2,NM_153202.1	74,74	127,1507,4860	AA,AG,GG		13.2045,14.25,13.5587	benign,benign	774/814,748/788	3650205	1761,11227	2200	4294	6494	SO:0001583	missense	80332	exon20			GCCAGGGCTGTCC	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.2320C>T	20.37:g.3650205G>A	ENSP00000348912:p.Pro774Ser	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Missense_Mutation	SNP	ENST00000356518.2	37	CCDS13058.1	318	0.14560439560439561	97	0.19715447154471544	37	0.10220994475138122	72	0.1258741258741259	112	0.14775725593667546	G	10.34	1.324213	0.24080	0.1425	0.132045	ENSG00000149451	ENST00000356518;ENST00000379861;ENST00000350009;ENST00000439201	T;T;T	0.01629	4.83;4.82;4.72	4.23	-0.229	0.13094	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;P	0.42692	0.061;0.036;0.036;0.787	B;B;B;B	0.33121	0.015;0.007;0.007;0.158	T	0.46624	-0.9178	8	0.17369	T	0.5	.	4.2557	0.10715	0.3043:0.1706:0.5251:0.0	rs2280090;rs17548858	748;774;774;654	Q9BZ11-2;Q9BZ11;A2A2L3;Q08AM2	.;ADA33_HUMAN;.;.	S	774;774;748;654	ENSP00000348912:P774S;ENSP00000369190:P774S;ENSP00000322550:P748S	ENSP00000322550:P748S	P	-	1	0	ADAM33	3598205	0.001000	0.12720	0.009000	0.14445	0.135000	0.20990	0.039000	0.13884	-0.099000	0.12263	0.561000	0.74099	CCC	G|0.871;A|0.129	0.129	strong		0.657	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220	
ITIH6	347365	hgsc.bcm.edu	37	X	54815065	54815065	+	Missense_Mutation	SNP	G	G	C	rs140757238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54815065G>C	ENST00000218436.6	-	5	663	c.634C>G	c.(634-636)Cca>Gca	p.P212A	ITIH6_ENST00000498398.1_5'Flank	NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	212					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CTGGTGGATGGGGGTGAATCC	0.587													G|||	52	0.0137748	0.0371	0.0043	3775	,	,		11601	0.0		0.0	False		,,,				2504	0.0				p.P212A		Atlas-SNP	.											.	.	.	.	0			c.C634G						PASS	.	G	ALA/PRO	212,3623		3,177,29,1452,542	65.0	44.0	51.0		634	1.7	0.0	X	dbSNP_134	51	3,6725		0,1,2,2427,1870	yes	missense	ITIH5L	NM_198510.2	27	3,178,31,3879,2412	CC,CG,C,GG,G		0.0446,5.528,2.0354	possibly-damaging	212/1314	54815065	215,10348	2203	4300	6503	SO:0001583	missense	347365	exon5			TGGATGGGGGTGA	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.634C>G	X.37:g.54815065G>C	ENSP00000218436:p.Pro212Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	24	0.014466546112115732	11	0.023404255319148935	0	0.0	0	0.0	0	0.0	G	1.845	-0.466354	0.04476	0.05528	4.46E-4	ENSG00000102313	ENST00000218436	T	0.02177	4.41	3.88	1.7	0.24286	.	0.424226	0.19726	U	0.107470	T	0.00271	0.0008	L	0.39898	1.24	0.42463	P	0.007206000000000046	B	0.14805	0.011	B	0.19148	0.024	T	0.37888	-0.9686	9	0.14656	T	0.56	.	6.3923	0.21593	0.1233:0.0:0.6815:0.1952	.	212	Q6UXX5	ITH5L_HUMAN	A	212	ENSP00000218436:P212A	ENSP00000218436:P212A	P	-	1	0	ITIH5L	54831790	1.000000	0.71417	0.042000	0.18584	0.218000	0.24690	1.253000	0.32886	0.488000	0.27723	0.171000	0.16805	CCA	G|0.976;C|0.024	0.024	strong		0.587	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
HELB	92797	hgsc.bcm.edu	37	12	66717910	66717910	+	Silent	SNP	G	G	T	rs34109029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:66717910G>T	ENST00000247815.4	+	10	2504	c.2445G>T	c.(2443-2445)acG>acT	p.T815T		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	815					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)		TTTCTGGTACGCTTCCTGATT	0.368													T|||	655	0.130791	0.2814	0.0375	5008	,	,		18364	0.1498		0.0199	False		,,,				2504	0.0879				p.T815T		Atlas-SNP	.											.	HELB	90	.	0			c.G2445T						PASS	.	T		1029,3377	726.9+/-409.8	126,777,1300	100.0	109.0	106.0		2445	0.1	0.0	12	dbSNP_126	106	101,8499	814.3+/-407.0	0,101,4199	no	coding-synonymous	HELB	NM_033647.2		126,878,5499	TT,TG,GG		1.1744,23.3545,8.6883		815/1088	66717910	1130,11876	2203	4300	6503	SO:0001819	synonymous_variant	92797	exon10			TGGTACGCTTCCT	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.2445G>T	12.37:g.66717910G>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Silent	SNP	ENST00000247815.4	37	CCDS8976.1																																																																																			G|0.913;T|0.087	0.087	strong		0.368	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
SNX20	124460	hgsc.bcm.edu	37	16	50709792	50709792	+	Silent	SNP	C	C	T	rs35435054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50709792C>T	ENST00000330943.4	-	3	342	c.171G>A	c.(169-171)acG>acA	p.T57T	SNX20_ENST00000423026.2_Silent_p.T57T|SNX20_ENST00000300590.3_Silent_p.T57T	NM_182854.2	NP_878274.1	Q7Z614	SNX20_HUMAN	sorting nexin 20	57					protein transport (GO:0015031)	endosome (GO:0005768)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)			kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(2)|stomach(1)	15						GAAGCTCCCGCGTGGTCATGC	0.552													C|||	70	0.0139776	0.0499	0.0043	5008	,	,		21120	0.0		0.001	False		,,,				2504	0.0				p.T57T		Atlas-SNP	.											SNX20_ENST00000300590,NS,carcinoma,-1,2	SNX20	50	2	0			c.G171A						PASS	.	C	,,	220,4176	132.1+/-168.6	5,210,1983	103.0	92.0	96.0		171,171,171	-11.3	0.1	16	dbSNP_126	96	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SNX20	NM_001144972.1,NM_153337.2,NM_182854.2	,,	5,211,6282	TT,TC,CC		0.0116,5.0045,1.7005	,,	57/103,57/130,57/317	50709792	221,12775	2198	4300	6498	SO:0001819	synonymous_variant	124460	exon3			CTCCCGCGTGGTC	AK055837	CCDS10745.1, CCDS10744.1, CCDS45481.1	16q12.1	2008-03-25	2008-03-25		ENSG00000167208	ENSG00000167208		"""Sorting nexins"""	30390	protein-coding gene	gene with protein product	"""selectin ligand interactor cytoplasmic 1"""	613281				18196517, 16782399	Standard	NM_182854		Approved	SLIC-1, SLIC1	uc002egk.2	Q7Z614	OTTHUMG00000133173	ENST00000330943.4:c.171G>A	16.37:g.50709792C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_001144972	A8K9D5|Q08E98|Q6P4H2|Q8IV59	Silent	SNP	ENST00000330943.4	37	CCDS10745.1																																																																																			C|0.981;T|0.019	0.019	strong		0.552	SNX20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256879.2	NM_153337	
OBSCN	84033	hgsc.bcm.edu	37	1	228547511	228547511	+	Intron	SNP	G	G	A	rs115442906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228547511G>A	ENST00000422127.1	+	80	18705				OBSCN_ENST00000284548.11_Silent_p.T6306T|OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366709.4_Silent_p.T3425T|OBSCN_ENST00000366707.4_Intron	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)				TGTATGTGACGGAGGCCGAGG	0.672													G|||	235	0.0469249	0.1573	0.0086	5008	,	,		16229	0.0149		0.002	False		,,,				2504	0.0041				p.T6306T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G18918A						PASS	.	G	,	472,3526		20,432,1547	14.0	17.0	16.0		,18918	-9.1	0.3	1	dbSNP_132	16	20,8282		0,20,4131	no	intron,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	20,452,5678	AA,AG,GG		0.2409,11.8059,4.0	,	,6306/6621	228547511	492,11808	1999	4151	6150	SO:0001627	intron_variant	84033	exon81			TGTGACGGAGGCC	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.18662-2766G>A	1.37:g.228547511G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	121	66	0.545455	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																																																																																			G|0.950;A|0.050	0.050	strong		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
LILRB2	10288	hgsc.bcm.edu	37	19	54782388	54782388	+	Silent	SNP	T	T	C	rs28405793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782388T>C	ENST00000391749.4	-	7	1255	c.984A>G	c.(982-984)tcA>tcG	p.S328S	LILRB2_ENST00000391746.1_Silent_p.S328S|LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000314446.5_Silent_p.S328S|LILRB2_ENST00000434421.1_Silent_p.S212S|LILRB2_ENST00000391748.1_Silent_p.S328S	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	328					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)		CTGGCTGCACTGAGATGAAGG	0.612													.|||	687	0.137181	0.4614	0.0447	5008	,	,		16587	0.0288		0.003	False		,,,				2504	0.0143				p.S328S		Atlas-SNP	.											LILRB2,NS,carcinoma,-1,1	LILRB2	94	1	0			c.A984G						scavenged	.						50.0	65.0	60.0					19																	54782388		2203	4300	6503	SO:0001819	synonymous_variant	10288	exon7			CTGCACTGAGATG	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.984A>G	19.37:g.54782388T>C		Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	211	83	0.393365	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Silent	SNP	ENST00000391749.4	37	CCDS12886.1																																																																																			T|0.954;C|0.046	0.046	strong		0.612	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
RFTN1	23180	hgsc.bcm.edu	37	3	16358584	16358584	+	Silent	SNP	T	T	C	rs690241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:16358584T>C	ENST00000334133.4	-	10	1760	c.1488A>G	c.(1486-1488)tcA>tcG	p.S496S	OXNAD1_ENST00000544043.1_Intron|RP11-415F23.2_ENST00000607464.1_RNA|OXNAD1_ENST00000435829.2_Intron|OXNAD1_ENST00000605932.1_Intron|RFTN1_ENST00000483671.1_5'UTR|OXNAD1_ENST00000606098.1_Intron|RFTN1_ENST00000432519.1_Silent_p.S460S	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	496					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						GCTGCTGTCCTGAAACACAGT	0.527													C|||	2878	0.574681	0.7375	0.5346	5008	,	,		19821	0.5099		0.5596	False		,,,				2504	0.4652				p.S496S		Atlas-SNP	.											.	RFTN1	79	.	0			c.A1488G						PASS	.	C		3038,1368	452.2+/-349.9	1058,922,223	131.0	121.0	124.0		1488	-9.7	0.0	3	dbSNP_83	124	4836,3764	535.6+/-382.8	1364,2108,828	no	coding-synonymous	RFTN1	NM_015150.1		2422,3030,1051	CC,CT,TT		43.7674,31.0486,39.4587		496/579	16358584	7874,5132	2203	4300	6503	SO:0001819	synonymous_variant	23180	exon10			CTGTCCTGAAACA	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.1488A>G	3.37:g.16358584T>C		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Silent	SNP	ENST00000334133.4	37	CCDS33712.1																																																																																			T|0.400;C|0.600	0.600	strong		0.527	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150	
IGSF22	283284	hgsc.bcm.edu	37	11	18743529	18743529	+	Missense_Mutation	SNP	T	T	C	rs115954314	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18743529T>C	ENST00000513874.1	-	3	308	c.169A>G	c.(169-171)Agc>Ggc	p.S57G	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	57										NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						ATGTTTGAGCTCCGGGTCACT	0.627											OREG0020822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	34	0.00678914	0.025	0.0014	5008	,	,		17155	0.0		0.0	False		,,,				2504	0.0				p.S57G		Atlas-SNP	.											.	IGSF22	211	.	0			c.A169G						PASS	.	T	GLY/SER	74,3986		0,74,1956	74.0	81.0	79.0		169	3.0	0.0	11	dbSNP_132	79	1,8327		0,1,4163	yes	missense	IGSF22	NM_173588.3	56	0,75,6119	CC,CT,TT		0.012,1.8227,0.6054	possibly-damaging	57/1327	18743529	75,12313	2030	4164	6194	SO:0001583	missense	283284	exon3			TTGAGCTCCGGGT	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.169A>G	11.37:g.18743529T>C	ENSP00000421191:p.Ser57Gly	Somatic	50	0	0	90	WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	T	13.41	2.229888	0.39399	0.018227	1.2E-4	ENSG00000179057	ENST00000513874	T	0.53640	0.61	4.23	3.05	0.35203	.	0.206612	0.23787	U	0.044561	T	0.09423	0.0232	N	0.14661	0.345	0.09310	N	1	B	0.20261	0.043	B	0.17433	0.018	T	0.08700	-1.0709	10	0.28530	T	0.3	.	5.4317	0.16456	0.1745:0.0:0.1813:0.6442	.	57	D6RGV7	.	G	57	ENSP00000421191:S57G	ENSP00000322422:S57G	S	-	1	0	IGSF22	18700105	0.780000	0.28664	0.001000	0.08648	0.989000	0.77384	2.349000	0.44054	0.471000	0.27319	0.533000	0.62120	AGC	T|0.992;C|0.008	0.008	strong		0.627	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
STAB2	55576	hgsc.bcm.edu	37	12	104086631	104086631	+	Silent	SNP	C	C	T	rs703651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	161	0	0		WXS	Illumina HiSeq	Phase_I	163	73	0.447853	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		
OR2T29	343563	hgsc.bcm.edu	37	1	248722777	248722777	+	Missense_Mutation	SNP	T	T	A	rs77589892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248722777T>A	ENST00000328570.3	-	1	20	c.16A>T	c.(16-18)Agg>Tgg	p.R6W	RP11-438F14.3_ENST00000438623.1_RNA	NM_001004694.2	NP_001004694.2	Q8NH02	O2T29_HUMAN	olfactory receptor, family 2, subfamily T, member 29	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|lung(4)	5	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)			TTGGCCATCCTGGTGATGTTG	0.463																																					p.R6W		Atlas-SNP	.											.	OR2T29	8	.	0			c.A16T						PASS	.	A	TRP/ARG	2570,1836		591,1388,224	78.0	65.0	69.0		16	-0.6	0.0	1	dbSNP_131	69	2027,6569		69,1889,2340	no	missense	OR2T29	NM_001004694.2	101	660,3277,2564	AA,AT,TT		23.5807,41.6704,35.3561		6/316	248722777	4597,8405	2203	4298	6501	SO:0001583	missense	343563	exon1			CCATCCTGGTGAT		CCDS55695.1	1q44	2012-08-09			ENSG00000182783	ENSG00000182783		"""GPCR / Class A : Olfactory receptors"""	31253	protein-coding gene	gene with protein product							Standard	NM_001004694		Approved		uc001ieo.2	Q8NH02	OTTHUMG00000040382	ENST00000328570.3:c.16A>T	1.37:g.248722777T>A	ENSP00000331774:p.Arg6Trp	Somatic	866	0	0		WXS	Illumina HiSeq	Phase_I	1192	558	0.468121	NM_001004694		Missense_Mutation	SNP	ENST00000328570.3	37	CCDS55695.1	.	.	.	.	.	.	.	.	.	.	N	7.770	0.707330	0.15239	0.583296	0.235807	ENSG00000182783	ENST00000328570	T	0.00466	7.23	2.34	-0.604	0.11626	.	0.645074	0.13113	N	0.412838	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	.	.	.	.	.	.	T	0.00006	-1.2513	7	0.20519	T	0.43	.	7.9651	0.30094	0.4093:0.0:0.0:0.5907	.	.	.	.	W	6	ENSP00000331774:R6W	ENSP00000331774:R6W	R	-	1	2	OR2T29	246789400	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.533000	0.06157	-0.193000	0.10415	-4.084000	0.00011	AGG	T|0.770;A|0.230	0.230	strong		0.463	OR2T29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097132.1	NM_001004694	
LRSAM1	90678	hgsc.bcm.edu	37	9	130263362	130263362	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130263362C>T	ENST00000323301.4	+	24	2590	c.1986C>T	c.(1984-1986)tcC>tcT	p.S662S	LRSAM1_ENST00000300417.6_Silent_p.S662S|LRSAM1_ENST00000483302.1_3'UTR|LRSAM1_ENST00000373322.1_Silent_p.S662S|LRSAM1_ENST00000373324.4_Silent_p.S635S	NM_138361.5	NP_612370.3	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif containing 1	662					cell death (GO:0008219)|negative regulation of endocytosis (GO:0045806)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent endocytosis (GO:0070086)|viral budding (GO:0046755)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(2)	16						TGAGGCCATCCGCTCCCCCTG	0.662																																					p.S662S		Atlas-SNP	.											.	LRSAM1	40	.	0			c.C1986T						PASS	.						57.0	55.0	56.0					9																	130263362		2203	4300	6503	SO:0001819	synonymous_variant	90678	exon25			GCCATCCGCTCCC	AK056203	CCDS6873.1, CCDS55347.1	9q34.13	2014-09-17			ENSG00000148356	ENSG00000148356		"""Sterile alpha motif (SAM) domain containing"""	25135	protein-coding gene	gene with protein product		610933				12975309	Standard	NM_001005373		Approved	FLJ31641	uc004brd.2	Q6UWE0	OTTHUMG00000020701	ENST00000323301.4:c.1986C>T	9.37:g.130263362C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	20	0.294118	NM_001005373	Q5VVV0|Q8NB40|Q96GT5|Q96MX5|Q96MZ7	Silent	SNP	ENST00000323301.4	37	CCDS6873.1																																																																																			.	.	none		0.662	LRSAM1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054164.1	NM_138361	
SLC37A1	54020	hgsc.bcm.edu	37	21	43974226	43974226	+	Silent	SNP	T	T	C	rs2839550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43974226T>C	ENST00000352133.2	+	10	1805	c.823T>C	c.(823-825)Ttg>Ctg	p.L275L	SLC37A1_ENST00000398341.3_Silent_p.L275L			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	275					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						GAAGCAAATCTTGAAGAGCGA	0.433													T|||	622	0.124201	0.3275	0.0893	5008	,	,		17220	0.001		0.1054	False		,,,				2504	0.0204				p.L275L		Atlas-SNP	.											.	SLC37A1	48	.	0			c.T823C						PASS	.	T		1207,3199	417.4+/-337.9	172,863,1168	61.0	57.0	58.0		823	-5.1	0.0	21	dbSNP_100	58	812,7788	188.1+/-235.2	33,746,3521	no	coding-synonymous	SLC37A1	NM_018964.3		205,1609,4689	CC,CT,TT		9.4419,27.3945,15.5236		275/534	43974226	2019,10987	2203	4300	6503	SO:0001819	synonymous_variant	54020	exon11			CAAATCTTGAAGA	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"""Solute carriers"""	11024	protein-coding gene	gene with protein product		608094	"""solute carrier family 37 (glycerol-3-phosphate transporter), member 1"""			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.823T>C	21.37:g.43974226T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	57	36	0.631579	NM_018964	D3DSJ7|Q9HAQ1	Silent	SNP	ENST00000352133.2	37	CCDS13689.1																																																																																			T|0.848;C|0.152	0.152	strong		0.433	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
ZBTB18	10472	hgsc.bcm.edu	37	1	244217662	244217662	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:244217662T>C	ENST00000358704.4	+	2	735	c.586T>C	c.(586-588)Ttg>Ctg	p.L196L		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	187				KLNILPSKRDLAAEPGNMWMRLPSDSAGIPQAGGEAEPHAT AAGKTVASPCSSTESLSQRSVTSVRDSADVDCVLDLSVKSS LSGVENLNSSYFSSQ -> IEHPAQQKGLGGRAWEHVDAIA LRLSRHPPGWRRGRATRHSSWKNSSQPLQLNRVFVPE (in Ref. 1; AAA81368). {ECO:0000305}.	cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GTGGATGCGATTGCCCTCAGA	0.567																																					p.L196L		Atlas-SNP	.											.	.	.	.	0			c.T586C						PASS	.						51.0	57.0	55.0					1																	244217662		2203	4300	6503	SO:0001819	synonymous_variant	10472	exon2			ATGCGATTGCCCT	U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13030	protein-coding gene	gene with protein product		608433	"""zinc finger protein 238"""	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.586T>C	1.37:g.244217662T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	167	91	0.54491	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Silent	SNP	ENST00000358704.4	37	CCDS1622.1																																																																																			.	.	none		0.567	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768	
ZP2	7783	hgsc.bcm.edu	37	16	21217061	21217061	+	Silent	SNP	G	G	A	rs16971234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:21217061G>A	ENST00000574002.1	-	7	1001	c.519C>T	c.(517-519)gaC>gaT	p.D173D	ZP2_ENST00000574091.1_Silent_p.D173D|ZP2_ENST00000219593.4_Silent_p.D173D|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	173		Cleavage. {ECO:0000250}.			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)		CCTTACTGTCGTCAGCCAAGC	0.358													G|||	1418	0.283147	0.3654	0.2378	5008	,	,		23231	0.4157		0.1074	False		,,,				2504	0.2485				p.D173D		Atlas-SNP	.											.	ZP2	92	.	0			c.C519T						PASS	.	G		1448,2950	467.6+/-354.9	239,970,990	92.0	97.0	95.0		519	-6.1	0.0	16	dbSNP_123	95	1020,7580	217.4+/-256.1	62,896,3342	no	coding-synonymous	ZP2	NM_003460.1		301,1866,4332	AA,AG,GG		11.8605,32.9241,18.9875		173/746	21217061	2468,10530	2199	4300	6499	SO:0001819	synonymous_variant	7783	exon6			ACTGTCGTCAGCC	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.519C>T	16.37:g.21217061G>A		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	118	116	0.983051	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Silent	SNP	ENST00000574002.1	37	CCDS10596.1																																																																																			G|0.763;A|0.237	0.237	strong		0.358	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
EHMT1	79813	hgsc.bcm.edu	37	9	140671147	140671147	+	Silent	SNP	C	C	T	rs7868455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140671147C>T	ENST00000460843.1	+	12	1896	c.1869C>T	c.(1867-1869)aaC>aaT	p.N623N	EHMT1_ENST00000462484.1_Silent_p.N623N|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000334856.6_Silent_p.N592N	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	623					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GAGTCAATAACGCCAGCTATT	0.527													C|||	315	0.0628994	0.2315	0.0115	5008	,	,		18209	0.0		0.001	False		,,,				2504	0.0				p.N623N		Atlas-SNP	.											.	EHMT1	196	.	0			c.C1869T						PASS	.	C	,	712,3694	297.3+/-284.7	63,586,1554	126.0	111.0	116.0		1869,1869	-6.8	0.8	9	dbSNP_116	116	11,8589	7.7+/-29.5	0,11,4289	no	coding-synonymous,coding-synonymous	EHMT1	NM_001145527.1,NM_024757.4	,	63,597,5843	TT,TC,CC		0.1279,16.1598,5.559	,	623/809,623/1299	140671147	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	79813	exon12			CAATAACGCCAGC	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.1869C>T	9.37:g.140671147C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			C|0.939;T|0.061	0.061	strong		0.527	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
RNF181	51255	hgsc.bcm.edu	37	2	85824251	85824251	+	Missense_Mutation	SNP	T	T	C	rs6643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85824251T>C	ENST00000306368.4	+	4	382	c.352T>C	c.(352-354)Tat>Cat	p.Y118H	RNF181_ENST00000441634.1_Missense_Mutation_p.Y118H	NM_016494.3	NP_057578.1	Q9P0P0	RN181_HUMAN	ring finger protein 181	118			Y -> H (in dbSNP:rs6643). {ECO:0000269|Ref.3}.		protein autoubiquitination (GO:0051865)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			lung(1)|stomach(1)	2						CTTGTGCCGCTATGAGCTGCC	0.512													C|||	1139	0.227436	0.5189	0.0807	5008	,	,		22018	0.2966		0.0358	False		,,,				2504	0.0634				p.Y118H		Atlas-SNP	.											.	RNF181	10	.	0			c.T352C						PASS	.	C	HIS/TYR	1927,2479	625.0+/-394.4	438,1051,714	154.0	154.0	154.0		352	4.3	1.0	2	dbSNP_52	154	233,8367	809.0+/-407.2	3,227,4070	yes	missense	RNF181	NM_016494.3	83	441,1278,4784	CC,CT,TT		2.7093,43.7358,16.6077	benign	118/154	85824251	2160,10846	2203	4300	6503	SO:0001583	missense	51255	exon4			TGCCGCTATGAGC	AF151072	CCDS1981.1	2p11.2	2013-01-09			ENSG00000168894	ENSG00000168894		"""RING-type (C3HC4) zinc fingers"""	28037	protein-coding gene	gene with protein product		612490				11042152	Standard	XM_005264359		Approved	HSPC238	uc002spv.1	Q9P0P0	OTTHUMG00000130182	ENST00000306368.4:c.352T>C	2.37:g.85824251T>C	ENSP00000306906:p.Tyr118His	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	192	85	0.442708	NM_016494	Q53H81	Missense_Mutation	SNP	ENST00000306368.4	37	CCDS1981.1	508	0.2326007326007326	268	0.5447154471544715	28	0.07734806629834254	185	0.32342657342657344	27	0.03562005277044855	C	5.720	0.317352	0.10845	0.437358	0.027093	ENSG00000168894	ENST00000441634;ENST00000306368;ENST00000456023	T;T	0.67523	-0.24;-0.27	5.39	4.31	0.51392	Zinc finger, RING/FYVE/PHD-type (1);	0.313852	0.33650	N	0.004686	T	0.00012	0.0000	N	0.10945	0.07	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.36335	-0.9752	9	0.06625	T	0.88	.	10.7512	0.46211	0.0:0.8159:0.0:0.1841	rs6643;rs1044643;rs2232749;rs3184444;rs11541121;rs17149265;rs60600233;rs6643	118	Q9P0P0	RN181_HUMAN	H	118;118;114	ENSP00000412025:Y118H;ENSP00000306906:Y118H	ENSP00000306906:Y118H	Y	+	1	0	RNF181	85677762	0.998000	0.40836	1.000000	0.80357	0.922000	0.55478	2.607000	0.46300	1.276000	0.44395	-0.215000	0.12644	TAT	T|0.797;C|0.203	0.203	strong		0.512	RNF181-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252500.1	NM_016494	
ITGA11	22801	hgsc.bcm.edu	37	15	68631920	68631920	+	Silent	SNP	C	C	T	rs9302249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68631920C>T	ENST00000315757.7	-	11	1280	c.1194G>A	c.(1192-1194)acG>acA	p.T398T	ITGA11_ENST00000423218.2_Silent_p.T398T	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	398					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)			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						TCCCGGCACTCGTCTCCTTTA	0.582													C|||	302	0.0603035	0.2201	0.013	5008	,	,		17677	0.0		0.001	False		,,,				2504	0.001				p.T398T		Atlas-SNP	.											ITGA11,colon,carcinoma,-1,1	ITGA11	110	1	0			c.G1194A						PASS	.	C		666,3374		51,564,1405	69.0	75.0	73.0		1194	-3.1	0.2	15	dbSNP_119	73	4,8346		0,4,4171	no	coding-synonymous	ITGA11	NM_001004439.1		51,568,5576	TT,TC,CC		0.0479,16.4851,5.4076		398/1189	68631920	670,11720	2020	4175	6195	SO:0001819	synonymous_variant	22801	exon11			GGCACTCGTCTCC	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.1194G>A	15.37:g.68631920C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	78	32	0.410256	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			C|0.956;T|0.044	0.044	strong		0.582	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
DOCK11	139818	hgsc.bcm.edu	37	X	117680019	117680019	+	Silent	SNP	G	G	C	rs61740837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:117680019G>C	ENST00000276202.7	+	6	561	c.498G>C	c.(496-498)gtG>gtC	p.V166V	DOCK11_ENST00000276204.6_Silent_p.V166V	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	166	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						AGGGTGGTGTGATAAAACAAG	0.338													G|||	33	0.00874172	0.0234	0.0014	3775	,	,		12505	0.0		0.001	False		,,,				2504	0.0				p.V166V		Atlas-SNP	.											.	DOCK11	185	.	0			c.G498C						PASS	.	G		75,3760		0,67,8,1565,563	143.0	120.0	128.0		498	2.2	1.0	X	dbSNP_129	128	0,6728		0,0,0,2428,1872	no	coding-synonymous	DOCK11	NM_144658.3		0,67,8,3993,2435	CC,CG,C,GG,G		0.0,1.9557,0.71		166/2074	117680019	75,10488	2203	4300	6503	SO:0001819	synonymous_variant	139818	exon6			TGGTGTGATAAAA	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"""Pleckstrin homology (PH) domain containing"""	23483	protein-coding gene	gene with protein product	"""zizimin2"""	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.498G>C	X.37:g.117680019G>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	201	77	0.383085	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																			G|0.993;C|0.007	0.007	strong		0.338	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
TNFRSF10B	8795	hgsc.bcm.edu	37	8	22926313	22926313	+	Missense_Mutation	SNP	G	G	A	rs1129424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22926313G>A	ENST00000276431.4	-	1	379	c.95C>T	c.(94-96)cCc>cTc	p.P32L	TNFRSF10B_ENST00000542226.1_5'UTR|RP11-875O11.3_ENST00000520840.1_RNA|TNFRSF10B_ENST00000347739.3_Missense_Mutation_p.P32L|RP11-875O11.2_ENST00000501897.1_RNA	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	12	0	0		WXS	Illumina HiSeq	Phase_I	27	27	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	
TSPYL5	85453	hgsc.bcm.edu	37	8	98289714	98289714	+	Missense_Mutation	SNP	G	G	C	rs2635164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:98289714G>C	ENST00000322128.3	-	1	462	c.359C>G	c.(358-360)aCt>aGt	p.T120S		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	120			T -> S (in dbSNP:rs2635164).		cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					CACGAAGACAGTGTCTGCGGC	0.721													G|||	1178	0.235224	0.5129	0.1787	5008	,	,		12121	0.0933		0.1372	False		,,,				2504	0.1472				p.T120S		Atlas-SNP	.											.	TSPYL5	48	.	0			c.C359G						PASS	.	G	SER/THR	1792,2522		386,1020,751	10.0	12.0	11.0		359	3.3	0.6	8	dbSNP_100	11	1062,7310		85,892,3209	yes	missense	TSPYL5	NM_033512.2	58	471,1912,3960	CC,CG,GG		12.6851,41.5392,22.4972	possibly-damaging	120/418	98289714	2854,9832	2157	4186	6343	SO:0001583	missense	85453	exon1			AAGACAGTGTCTG	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.359C>G	8.37:g.98289714G>C	ENSP00000322802:p.Thr120Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_033512	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	37	CCDS34927.1	445	0.20375457875457875	228	0.4634146341463415	66	0.18232044198895028	45	0.07867132867132867	106	0.13984168865435356	G	5.440	0.266334	0.10294	0.415392	0.126851	ENSG00000180543	ENST00000322128	T	0.12774	2.65	4.16	3.27	0.37495	.	0.252185	0.20796	N	0.085534	T	0.00012	0.0000	N	0.00926	-1.1	0.45194	P	0.001794999999999991	P	0.37061	0.58	B	0.35114	0.196	T	0.30650	-0.9971	9	0.02654	T	1	-2.746	8.3789	0.32459	0.1076:0.0:0.8924:0.0	rs2635164	120	Q86VY4	TSYL5_HUMAN	S	120	ENSP00000322802:T120S	ENSP00000322802:T120S	T	-	2	0	TSPYL5	98358890	0.973000	0.33851	0.646000	0.29493	0.871000	0.50021	1.939000	0.40213	1.298000	0.44778	0.650000	0.86243	ACT	G|0.810;C|0.190	0.190	strong		0.721	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512	
KCNK5	8645	hgsc.bcm.edu	37	6	39158773	39158773	+	Missense_Mutation	SNP	G	G	T	rs9462487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:39158773G>T	ENST00000359534.3	-	5	1731	c.1393C>A	c.(1393-1395)Ccc>Acc	p.P465T		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	465			P -> T (in dbSNP:rs9462487).		excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						GAGGAGGAGGGGAACTCGCCC	0.602													G|||	91	0.0181709	0.0666	0.0043	5008	,	,		18529	0.0		0.0	False		,,,				2504	0.0				p.P465T		Atlas-SNP	.											.	KCNK5	57	.	0			c.C1393A						PASS	.	G	THR/PRO	243,4163		9,225,1969	55.0	47.0	50.0		1393	5.9	1.0	6	dbSNP_119	50	2,8596		0,2,4297	yes	missense	KCNK5	NM_003740.3	38	9,227,6266	TT,TG,GG		0.0233,5.5152,1.884	benign	465/500	39158773	245,12759	2203	4299	6502	SO:0001583	missense	8645	exon5			AGGAGGGGAACTC	AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.1393C>A	6.37:g.39158773G>T	ENSP00000352527:p.Pro465Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_003740	B2RAQ6|B5TJL2|Q5VV76	Missense_Mutation	SNP	ENST00000359534.3	37	CCDS4841.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	G	10.53	1.376641	0.24857	0.055152	2.33E-4	ENSG00000164626	ENST00000359534	T	0.19669	2.13	5.94	5.94	0.96194	.	1.555240	0.03069	N	0.156855	T	0.08223	0.0205	N	0.17082	0.46	0.32749	N	0.506676	P	0.42456	0.78	B	0.40636	0.335	T	0.00433	-1.1742	10	0.44086	T	0.13	.	8.6716	0.34154	0.1137:0.1388:0.7475:0.0	rs9462487;rs9462487	465	O95279	KCNK5_HUMAN	T	465	ENSP00000352527:P465T	ENSP00000352527:P465T	P	-	1	0	KCNK5	39266751	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	1.915000	0.39976	2.826000	0.97356	0.561000	0.74099	CCC	G|0.980;T|0.020	0.020	strong		0.602	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740	
BOD1	91272	hgsc.bcm.edu	37	5	173036257	173036257	+	Silent	SNP	A	A	G	rs77014290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:173036257A>G	ENST00000311086.4	-	3	766	c.543T>C	c.(541-543)tcT>tcC	p.S181S	BOD1_ENST00000480951.1_Intron|BOD1_ENST00000471339.1_5'Flank|BOD1_ENST00000285908.5_Intron	NM_138369.2	NP_612378.1	Q96IK1	BOD1_HUMAN	biorientation of chromosomes in cell division 1	181					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|kinetochore (GO:0000776)		p.S181S(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(2)	7						AAGTGTCCTGAGATGGAGCTG	0.512																																					p.S181S		Atlas-SNP	.											BOD1,NS,carcinoma,0,1	BOD1	15	1	1	Substitution - coding silent(1)	lung(1)	c.T543C						PASS	.						92.0	91.0	91.0					5																	173036257		2203	4300	6503	SO:0001819	synonymous_variant	91272	exon3			GTCCTGAGATGGA	AY303777	CCDS4389.1, CCDS54951.1	5q35.2	2013-10-11	2009-03-04	2009-03-04	ENSG00000145919	ENSG00000145919			25114	protein-coding gene	gene with protein product	"""biorientation defective 1"""		"""family with sequence similarity 44, member B"""	FAM44B		17938248	Standard	NM_138369		Approved		uc003mcq.2	Q96IK1	OTTHUMG00000130540	ENST00000311086.4:c.543T>C	5.37:g.173036257A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	225	32	0.142222	NM_138369	B4DXH8|Q9BTW1	Silent	SNP	ENST00000311086.4	37	CCDS4389.1	.	.	.	.	.	.	.	.	.	.	A	10.16	1.274704	0.23307	.	.	ENSG00000145919	ENST00000477985	.	.	.	5.86	2.54	0.30619	.	0.220881	0.48767	D	0.000172	T	0.46580	0.1400	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40701	-0.9549	6	0.39692	T	0.17	-11.0788	1.6489	0.02767	0.2536:0.1527:0.4384:0.1553	.	.	.	.	P	114	.	ENSP00000420005:S114P	S	-	1	0	BOD1	172968863	0.999000	0.42202	0.962000	0.40283	0.898000	0.52572	0.891000	0.28309	0.806000	0.34183	-0.177000	0.13119	TCA	A|0.981;G|0.019	0.019	strong		0.512	BOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252963.1	NM_138369	
COL28A1	340267	hgsc.bcm.edu	37	7	7410391	7410391	+	Missense_Mutation	SNP	A	A	C	rs76240858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:7410391A>C	ENST00000399429.3	-	33	3171	c.3031T>G	c.(3031-3033)Tct>Gct	p.S1011A		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	1011					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TCTGGAGTAGATTCACTGAGT	0.373													A|||	17	0.00339457	0.0113	0.0	5008	,	,		16003	0.0		0.002	False		,,,				2504	0.0				p.S1011A		Atlas-SNP	.											.	COL28A1	113	.	0			c.T3031G						PASS	.	A	ALA/SER	37,3663		0,37,1813	127.0	116.0	120.0		3031	0.1	0.0	7	dbSNP_131	120	2,8168		0,2,4083	yes	missense	COL28A1	NM_001037763.2	99	0,39,5896	CC,CA,AA		0.0245,1.0,0.3286	possibly-damaging	1011/1126	7410391	39,11831	1850	4085	5935	SO:0001583	missense	340267	exon33			GAGTAGATTCACT	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.3031T>G	7.37:g.7410391A>C	ENSP00000382356:p.Ser1011Ala	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	32	0.329897	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	9	0.004120879120879121	8	0.016260162601626018	0	0.0	0	0.0	1	0.0013192612137203166	A	10.22	1.291183	0.23564	0.01	2.45E-4	ENSG00000215018	ENST00000399429	D	0.88509	-2.39	3.85	0.134	0.14771	.	1.902650	0.03097	U	0.160580	T	0.69415	0.3108	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60556	-0.7240	10	0.18710	T	0.47	0.0019	6.0507	0.19785	0.6632:0.0:0.3368:0.0	.	1011	Q2UY09	COSA1_HUMAN	A	1011	ENSP00000382356:S1011A	ENSP00000382356:S1011A	S	-	1	0	COL28A1	7376916	0.764000	0.28473	0.033000	0.17914	0.275000	0.26752	0.791000	0.26915	0.014000	0.14944	-0.290000	0.09829	TCT	A|0.997;C|0.003	0.003	strong		0.373	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
FLG	2312	hgsc.bcm.edu	37	1	152281523	152281523	+	Missense_Mutation	SNP	A	A	C	rs80059102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281523A>C	ENST00000368799.1	-	3	5874	c.5839T>G	c.(5839-5841)Tgg>Ggg	p.W1947G	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	425	2	0.00470588		WXS	Illumina HiSeq	Phase_I	859	325	0.378347	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	
CDHR3	222256	hgsc.bcm.edu	37	7	105671267	105671267	+	Silent	SNP	T	T	C	rs10270308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:105671267T>C	ENST00000317716.9	+	18	2414	c.2334T>C	c.(2332-2334)gaT>gaC	p.D778D	CDHR3_ENST00000478080.1_Silent_p.D690D|CDHR3_ENST00000542731.1_Silent_p.D778D|CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000343407.5_3'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	778					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						CTATCTTTGATGGAGAAGCCA	0.418													T|||	1065	0.21266	0.382	0.1729	5008	,	,		23524	0.3621		0.0129	False		,,,				2504	0.0634				p.D778D		Atlas-SNP	.											.	CDHR3	153	.	0			c.T2334C						PASS	.	T		1187,2657		184,819,919	122.0	118.0	120.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2334	1.5	1.0	7	dbSNP_119	120	44,8230		0,44,4093	yes	coding-synonymous	CDHR3	NM_152750.4		184,863,5012	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	0.5318,30.8793,10.1584		778/886	105671267	1231,10887	1922	4137	6059	SO:0001819	synonymous_variant	222256	exon18			CTTTGATGGAGAA	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.2334T>C	7.37:g.105671267T>C		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	180	85	0.472222	NM_152750	Q8TCI7	Silent	SNP	ENST00000317716.9	37	CCDS47684.1																																																																																			T|0.795;C|0.205	0.205	strong		0.418	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
MAGEC3	139081	hgsc.bcm.edu	37	X	140967195	140967195	+	Missense_Mutation	SNP	T	T	A	rs11095910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:140967195T>A	ENST00000298296.1	+	3	493	c.493T>A	c.(493-495)Ttg>Atg	p.L165M	MAGEC3_ENST00000448920.1_5'Flank|MAGEC3_ENST00000536088.1_5'Flank|MAGEC3_ENST00000443323.2_5'Flank	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	165			L -> M (in dbSNP:rs11095910).							NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					TGGAAAAAGGTTGTGGGGGGA	0.572													t|||	1395	0.369536	0.348	0.3314	3775	,	,		10454	0.3651		0.0676	False		,,,				2504	0.2751				p.L165M		Atlas-SNP	.											.	MAGEC3	228	.	0			c.T493A						PASS	.	T	MET/LEU	1596,2227		297,764,238,570,323	26.0	21.0	23.0		493	-0.4	0.0	X	dbSNP_120	23	569,6148		19,382,149,2027,1712	yes	missense	MAGEC3	NM_138702.1	15	316,1146,387,2597,2035	AA,AT,A,TT,T		8.471,41.7473,20.5408	benign	165/644	140967195	2165,8375	2192	4289	6481	SO:0001583	missense	139081	exon3			AAAAGGTTGTGGG	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.493T>A	X.37:g.140967195T>A	ENSP00000298296:p.Leu165Met	Somatic	332	2	0.0060241		WXS	Illumina HiSeq	Phase_I	367	238	0.648501	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	525	0.31645569620253167	121	0.3151041666666667	72	0.23529411764705882	136	0.3090909090909091	37	0.05096418732782369	A	0.001	-4.228477	0.00001	0.417473	0.08471	ENSG00000165509	ENST00000298296	T	0.07908	3.15	0.225	-0.451	0.12214	.	.	.	.	.	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	0.48340	-0.9044	7	0.42905	T	0.14	.	.	.	.	rs11095910;rs11095910	165	Q8TD91	MAGC3_HUMAN	M	165	ENSP00000298296:L165M	ENSP00000298296:L165M	L	+	1	2	MAGEC3	140794861	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.506000	0.00223	-2.698000	0.00400	-2.905000	0.00092	TTG	T|0.739;A|0.261	0.261	strong		0.572	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
NRAP	4892	hgsc.bcm.edu	37	10	115393929	115393929	+	Missense_Mutation	SNP	G	G	A	rs3189030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115393929G>A	ENST00000359988.3	-	15	1713	c.1469C>T	c.(1468-1470)tCg>tTg	p.S490L	NRAP_ENST00000369360.3_Missense_Mutation_p.S455L|NRAP_ENST00000369358.4_Missense_Mutation_p.S490L|NRAP_ENST00000360478.3_Missense_Mutation_p.S455L	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)		GTCAGTCACCGAGCTGTACTT	0.453													G|||	1456	0.290735	0.1203	0.2781	5008	,	,		19322	0.4266		0.328	False		,,,				2504	0.3517				p.S490L		Atlas-SNP	.											NRAP,NS,adenoma,0,1	NRAP	208	1	0			c.C1469T						PASS	.	G	LEU/SER,LEU/SER	614,3792	269.2+/-268.9	52,510,1641	210.0	181.0	191.0		1364,1469	3.3	0.7	10	dbSNP_105	191	2652,5948	426.9+/-355.4	387,1878,2035	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	145,145	439,2388,3676	AA,AG,GG		30.8372,13.9355,25.1115	benign,benign	455/1696,490/1731	115393929	3266,9740	2203	4300	6503	SO:0001583	missense	4892	exon15			GTCACCGAGCTGT		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.1469C>T	10.37:g.115393929G>A	ENSP00000353078:p.Ser490Leu	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	122	52	0.42623	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	654	0.29945054945054944	57	0.11585365853658537	113	0.31215469613259667	253	0.4423076923076923	231	0.30474934036939316	G	9.361	1.068063	0.20067	0.139355	0.308372	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350;ENST00000369343	T;T;T;T	0.17854	2.48;2.45;2.33;2.25	5.17	3.28	0.37604	.	0.399627	0.28296	N	0.015870	T	0.00012	0.0000	M	0.65498	2.005	0.34483	P	0.295894	B;B	0.23316	0.083;0.05	B;B	0.17433	0.018;0.008	T	0.44097	-0.9350	9	0.29301	T	0.29	.	10.6605	0.45700	0.072:0.1322:0.7957:0.0	rs3189030;rs56518502;rs59496803;rs3189030	455;490	Q86VF7-4;Q86VF7	.;NRAP_HUMAN	L	490;455;490;455;219;219	ENSP00000358365:S490L;ENSP00000358367:S455L;ENSP00000353078:S490L;ENSP00000353666:S455L	ENSP00000353078:S490L	S	-	2	0	NRAP	115383919	1.000000	0.71417	0.668000	0.29813	0.069000	0.16628	2.948000	0.49066	0.542000	0.28846	-0.444000	0.05651	TCG	G|0.727;A|0.273	0.273	strong		0.453	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
PLD3	23646	hgsc.bcm.edu	37	19	40882588	40882588	+	Silent	SNP	C	C	T	rs57187324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40882588C>T	ENST00000409587.1	+	11	1489	c.1092C>T	c.(1090-1092)atC>atT	p.I364I	PLD3_ENST00000409735.4_Silent_p.I364I|PLD3_ENST00000356508.5_Silent_p.I364I|PLD3_ENST00000409281.1_Silent_p.I364I|PLD3_ENST00000409419.1_Silent_p.I364I			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	364					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			GCCTGCTCATCAGCTGCTGGG	0.632													c|||	39	0.00778754	0.0295	0.0	5008	,	,		16027	0.0		0.0	False		,,,				2504	0.0				p.I364I		Atlas-SNP	.											.	PLD3	71	.	0			c.C1092T						PASS	.		,	124,4282	92.0+/-130.7	2,120,2081	79.0	72.0	74.0		1092,1092	3.2	1.0	19	dbSNP_129	74	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PLD3	NM_001031696.2,NM_012268.2	,	2,120,6381	TT,TC,CC		0.0,2.8143,0.9534	,	364/491,364/491	40882588	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	23646	exon11			GCTCATCAGCTGC	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"""phospholipase D3"""			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.1092C>T	19.37:g.40882588C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_012268	Q92853|Q9BW87	Silent	SNP	ENST00000409587.1	37	CCDS33027.1																																																																																			C|0.990;T|0.010	0.010	strong		0.632	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268	
LHX8	431707	hgsc.bcm.edu	37	1	75622616	75622616	+	Silent	SNP	C	C	T	rs941032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:75622616C>T	ENST00000294638.5	+	9	1513	c.849C>T	c.(847-849)caC>caT	p.H283H	LHX8_ENST00000356261.3_Silent_p.H273H	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8	283					female gonad development (GO:0008585)|forebrain neuron development (GO:0021884)|learning or memory (GO:0007611)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	female germ cell nucleus (GO:0001674)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(18)|ovary(3)|urinary_tract(1)	30						ACAAGAAACACGTCAGTCCTA	0.502													C|||	1973	0.39397	0.4758	0.3026	5008	,	,		17790	0.2063		0.3907	False		,,,				2504	0.545				p.H283H		Atlas-SNP	.											.	LHX8	73	.	0			c.C849T						PASS	.	C		2044,2362	566.8+/-382.0	484,1076,643	291.0	261.0	272.0		849	-3.0	0.8	1	dbSNP_86	272	3551,5049	517.5+/-379.0	748,2055,1497	yes	coding-synonymous	LHX8	NM_001001933.1		1232,3131,2140	TT,TC,CC		41.2907,46.3913,43.0186		283/357	75622616	5595,7411	2203	4300	6503	SO:0001819	synonymous_variant	431707	exon9			GAAACACGTCAGT	AB050476	CCDS30756.1, CCDS58008.1	1p31.1	2011-06-20			ENSG00000162624	ENSG00000162624		"""Homeoboxes / LIM class"""	28838	protein-coding gene	gene with protein product		604425				9598319	Standard	NM_001256114		Approved	Lhx7	uc031pmx.1	Q68G74	OTTHUMG00000009692	ENST00000294638.5:c.849C>T	1.37:g.75622616C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	187	187	1	NM_001001933	E9PGE3	Silent	SNP	ENST00000294638.5	37	CCDS30756.1																																																																																			C|0.598;N|0.000	.	strong		0.502	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	NM_001001933	
ADCY9	115	hgsc.bcm.edu	37	16	4043415	4043415	+	Missense_Mutation	SNP	T	T	C	rs113187435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4043415T>C	ENST00000294016.3	-	4	2519	c.1981A>G	c.(1981-1983)Agc>Ggc	p.S661G	ADCY9_ENST00000571889.1_5'UTR	NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	661					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						ACCTTGGTGCTGTTTTTATGC	0.532													T|||	37	0.00738818	0.0272	0.0014	5008	,	,		19275	0.0		0.0	False		,,,				2504	0.0				p.S661G		Atlas-SNP	.											.	ADCY9	151	.	0			c.A1981G						PASS	.	T	GLY/SER	111,4283	85.8+/-124.5	1,109,2087	235.0	202.0	213.0		1981	4.2	0.8	16	dbSNP_132	213	0,8600		0,0,4300	yes	missense	ADCY9	NM_001116.3	56	1,109,6387	CC,CT,TT		0.0,2.5262,0.8542	benign	661/1354	4043415	111,12883	2197	4300	6497	SO:0001583	missense	115	exon4			TGGTGCTGTTTTT	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.1981A>G	16.37:g.4043415T>C	ENSP00000294016:p.Ser661Gly	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	245	116	0.473469	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	T	11.87	1.769081	0.31320	0.025262	0.0	ENSG00000162104	ENST00000294016	D	0.84070	-1.8	5.36	4.24	0.50183	.	0.368925	0.31884	N	0.006919	T	0.43366	0.1244	N	0.14661	0.345	0.31169	N	0.703441	B	0.02656	0.0	B	0.01281	0.0	T	0.54977	-0.8212	10	0.28530	T	0.3	.	8.1862	0.31341	0.0:0.1581:0.0:0.8419	.	661	O60503	ADCY9_HUMAN	G	661	ENSP00000294016:S661G	ENSP00000294016:S661G	S	-	1	0	ADCY9	3983416	1.000000	0.71417	0.842000	0.33263	0.993000	0.82548	1.848000	0.39309	0.845000	0.35118	0.445000	0.29226	AGC	T|0.991;C|0.009	0.009	strong		0.532	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
OR52A5	390054	hgsc.bcm.edu	37	11	5153261	5153261	+	Silent	SNP	A	A	G	rs2472530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5153261A>G	ENST00000307388.1	-	1	611	c.612T>C	c.(610-612)ttT>ttC	p.F204F		NM_001005160.2	NP_001005160.1	Q9H2C5	O52A5_HUMAN	olfactory receptor, family 52, subfamily A, member 5	204					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(18)|skin(3)	35		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		CAAAGGCAACAAATAGGCCAT	0.423													A|||	995	0.198682	0.0144	0.232	5008	,	,		23011	0.3929		0.2028	False		,,,				2504	0.2198				p.F204F		Atlas-SNP	.											.	OR52A5	80	.	0			c.T612C						PASS	.	A		220,4182	131.0+/-167.6	7,206,1988	108.0	104.0	105.0		612	5.1	1.0	11	dbSNP_100	105	1823,6773	326.6+/-317.4	213,1397,2688	no	coding-synonymous	OR52A5	NM_001005160.2		220,1603,4676	GG,GA,AA		21.2075,4.9977,15.7178		204/317	5153261	2043,10955	2201	4298	6499	SO:0001819	synonymous_variant	390054	exon1			GGCAACAAATAGG	BK004433	CCDS31373.1	11p15.4	2012-08-09			ENSG00000171944	ENSG00000171944		"""GPCR / Class A : Olfactory receptors"""	19580	protein-coding gene	gene with protein product							Standard	NM_001005160		Approved		uc010qyx.2	Q9H2C5	OTTHUMG00000066616	ENST00000307388.1:c.612T>C	11.37:g.5153261A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_001005160		Silent	SNP	ENST00000307388.1	37	CCDS31373.1																																																																																			A|0.815;G|0.185	0.185	strong		0.423	OR52A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142823.1	NM_001005160	
DNAH9	1770	hgsc.bcm.edu	37	17	11622729	11622729	+	Silent	SNP	C	C	T	rs61739488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11622729C>T	ENST00000262442.4	+	27	5699	c.5631C>T	c.(5629-5631)acC>acT	p.T1877T	DNAH9_ENST00000454412.2_Silent_p.T1877T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1877	AAA 1. {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)		CAGGCAAGACCGAGACCACCA	0.607													c|||	256	0.0511182	0.1861	0.0115	5008	,	,		16870	0.0		0.001	False		,,,				2504	0.001				p.T1877T		Atlas-SNP	.											.	DNAH9	695	.	0			c.C5631T						PASS	.	G		706,3700	294.1+/-283.0	52,602,1549	92.0	79.0	83.0		5631	-10.4	0.0	17	dbSNP_129	83	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	DNAH9	NM_001372.3		52,609,5842	TT,TC,CC		0.0814,16.0236,5.4821		1877/4487	11622729	713,12293	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon27			CAAGACCGAGACC	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.5631C>T	17.37:g.11622729C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.950;T|0.050	0.050	strong		0.607	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
PI15	51050	hgsc.bcm.edu	37	8	75737636	75737636	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:75737636C>T	ENST00000260113.2	+	2	331	c.152C>T	c.(151-153)gCg>gTg	p.A51V	PI15_ENST00000523773.1_Missense_Mutation_p.A51V|RP11-758M4.4_ENST00000523860.1_RNA|RP11-758M4.4_ENST00000518128.1_RNA	NM_015886.3	NP_056970.1	O43692	PI15_HUMAN	peptidase inhibitor 15	51						extracellular vesicular exosome (GO:0070062)	peptidase inhibitor activity (GO:0030414)	p.A51V(2)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|skin(1)	30	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)			TTAGATTCAGCGGATATCCCC	0.468																																					p.A51V		Atlas-SNP	.											PI15,colon,carcinoma,0,2	PI15	73	2	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C152T						scavenged	.						101.0	93.0	95.0					8																	75737636		2203	4300	6503	SO:0001583	missense	51050	exon2			ATTCAGCGGATAT	D45027	CCDS6218.1	8q13.3	2005-08-17	2005-08-17		ENSG00000137558	ENSG00000137558			8946	protein-coding gene	gene with protein product		607076	"""protease inhibitor 15"""			8882727, 9473672	Standard	XM_005251255		Approved	P25TI	uc003yal.3	O43692	OTTHUMG00000164528	ENST00000260113.2:c.152C>T	8.37:g.75737636C>T	ENSP00000260113:p.Ala51Val	Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	99	2	0.020202	NM_015886	Q68CY1	Missense_Mutation	SNP	ENST00000260113.2	37	CCDS6218.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.678959	0.29783	.	.	ENSG00000137558	ENST00000260113;ENST00000523773	T;T	0.09723	2.95;2.95	5.35	3.54	0.40534	CAP domain (1);	0.493618	0.22667	N	0.057111	T	0.06690	0.0171	N	0.14661	0.345	0.47009	D	0.999284	B	0.09022	0.002	B	0.04013	0.001	T	0.30416	-0.9979	10	0.22706	T	0.39	.	12.2372	0.54522	0.0:0.8614:0.0:0.1386	.	51	O43692	PI15_HUMAN	V	51	ENSP00000260113:A51V;ENSP00000428567:A51V	ENSP00000260113:A51V	A	+	2	0	PI15	75900191	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	1.516000	0.35856	0.923000	0.37045	0.655000	0.94253	GCG	.	.	none		0.468	PI15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379115.1	NM_015886	
C19orf80	55908	hgsc.bcm.edu	37	19	11350340	11350340	+	Silent	SNP	C	C	G	rs892066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11350340C>G	ENST00000252453.8	+	1	46	c.27C>G	c.(25-27)ctC>ctG	p.L9L	C19orf80_ENST00000591200.1_Intron|DOCK6_ENST00000294618.7_Intron|DOCK6_ENST00000319867.7_5'Flank	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	9					cellular lipid metabolic process (GO:0044255)|glucose metabolic process (GO:0006006)|positive regulation of protein processing (GO:0010954)|regulation of lipoprotein metabolic process (GO:0050746)|triglyceride homeostasis (GO:0070328)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|breast(1)|endometrium(2)	4						TGTGCCTGCTCTGGGCCCTGG	0.622													G|||	1875	0.374401	0.8101	0.255	5008	,	,		18798	0.3115		0.1093	False		,,,				2504	0.2076				p.L9L		Atlas-SNP	.											.	C19orf80	8	.	0			c.C27G						PASS	.	G	,	2763,1365		932,899,233	34.0	35.0	35.0		27,	-3.2	0.2	19	dbSNP_86	35	1149,7247		92,965,3141	no	coding-synonymous,intron	C19orf80,DOCK6	NM_018687.6,NM_020812.2	,	1024,1864,3374	GG,GC,CC		13.6851,33.0669,31.236	,	9/199,	11350340	3912,8612	2064	4198	6262	SO:0001819	synonymous_variant	55908	exon1			CCTGCTCTGGGCC		CCDS54220.1	19p13.2	2014-02-13			ENSG00000130173	ENSG00000130173			24933	protein-coding gene	gene with protein product	"""lipasin"", ""betatrophin"""					22809513, 23150577, 24262987	Standard	NM_018687		Approved	TD26, RIFL, ANGPTL8	uc021upg.1	Q6UXH0		ENST00000252453.8:c.27C>G	19.37:g.11350340C>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	180	180	1	NM_018687	Q9NQZ1	Silent	SNP	ENST00000252453.8	37	CCDS54220.1																																																																																			C|0.688;G|0.312	0.312	strong		0.622	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921332	12921332	+	Missense_Mutation	SNP	T	T	C	rs17039307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12921332T>C	ENST00000240189.2	+	4	1210	c.1123T>C	c.(1123-1125)Tgc>Cgc	p.C375R		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	375			C -> R (in dbSNP:rs17039307).		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)		TGGCCTGAGCTGCTGCTCCCA	0.557													.|||	2053	0.409944	0.4728	0.3473	5008	,	,		27939	0.4385		0.3449	False		,,,				2504	0.407				p.C375R		Atlas-SNP	.											PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	0			c.T1123C						scavenged	.						111.0	118.0	115.0					1																	12921332		2201	4294	6495	SO:0001583	missense	65122	exon4			CTGAGCTGCTGCT		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.1123T>C	1.37:g.12921332T>C	ENSP00000240189:p.Cys375Arg	Somatic	386	24	0.0621762		WXS	Illumina HiSeq	Phase_I	504	502	0.996032	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.280337	0.00254	.	.	ENSG00000120952	ENST00000240189	T	0.08984	3.03	0.824	0.824	0.18818	.	1.330770	0.04798	N	0.433017	T	0.01940	0.0061	N	0.00583	-1.355	0.29017	N	0.886535	B	0.02656	0.0	B	0.04013	0.001	T	0.44298	-0.9337	10	0.02654	T	1	.	3.343	0.07126	0.0:0.6873:0.0:0.3127	rs17039307	375	O60811	PRAM2_HUMAN	R	375	ENSP00000240189:C375R	ENSP00000240189:C375R	C	+	1	0	PRAMEF2	12843919	0.000000	0.05858	0.645000	0.29479	0.002000	0.02628	-0.464000	0.06688	-0.055000	0.13244	-1.206000	0.01644	TGC	.	.	weak		0.557	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
LUZP1	7798	hgsc.bcm.edu	37	1	23415518	23415518	+	Missense_Mutation	SNP	C	C	T	rs12066671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23415518C>T	ENST00000302291.4	-	5	3902	c.3101G>A	c.(3100-3102)aGt>aAt	p.S1034N	RP1-184J9.2_ENST00000427154.1_RNA|LUZP1_ENST00000374623.3_Missense_Mutation_p.S1034N|LUZP1_ENST00000418342.1_Missense_Mutation_p.S1034N			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	1034			S -> N (in dbSNP:rs12066671).		artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		CCTGTAGACACTGAGTGTACA	0.552													C|||	381	0.0760783	0.2693	0.0331	5008	,	,		19540	0.0		0.002	False		,,,				2504	0.0				p.S1034N		Atlas-SNP	.											.	LUZP1	83	.	0			c.G3101A						PASS	.	C	ASN/SER,ASN/SER	921,3485	353.1+/-312.0	102,717,1384	117.0	109.0	112.0		3101,3101	2.3	0.0	1	dbSNP_120	112	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	46,46	102,725,5676	TT,TC,CC		0.093,20.9033,7.1429	benign,benign	1034/1077,1034/1077	23415518	929,12077	2203	4300	6503	SO:0001583	missense	7798	exon5			TAGACACTGAGTG	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.3101G>A	1.37:g.23415518C>T	ENSP00000303758:p.Ser1034Asn	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	328	166	0.506098	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	125	0.05723443223443223	115	0.23373983739837398	10	0.027624309392265192	0	0.0	0	0.0	C	7.770	0.707239	0.15239	0.209033	9.3E-4	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291	T;T;T	0.13420	2.59;2.59;2.59	5.53	2.34	0.29019	.	0.527164	0.17464	N	0.173327	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.30281	0.275	B	0.27076	0.076	T	0.44697	-0.9311	9	0.39692	T	0.17	.	9.0334	0.36273	0.1575:0.5558:0.2867:0.0	rs12066671;rs52805088;rs12066671	1034	Q86V48	LUZP1_HUMAN	N	1034	ENSP00000393460:S1034N;ENSP00000363752:S1034N;ENSP00000303758:S1034N	ENSP00000303758:S1034N	S	-	2	0	LUZP1	23288105	0.000000	0.05858	0.008000	0.14137	0.279000	0.26890	0.390000	0.20768	0.750000	0.32877	0.655000	0.94253	AGT	C|0.925;T|0.075	0.075	strong		0.552	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631	
DNAH14	127602	hgsc.bcm.edu	37	1	225528340	225528340	+	Missense_Mutation	SNP	C	C	T	rs12184324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225528340C>T	ENST00000445597.2	+	47	7927	c.7927C>T	c.(7927-7929)Ctt>Ttt	p.L2643F	DNAH14_ENST00000430092.1_Missense_Mutation_p.L3446F|DNAH14_ENST00000439375.2_Missense_Mutation_p.L3446F			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2643					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						GAGTATTTCCCTTGATGCCAT	0.358													C|||	437	0.0872604	0.2383	0.0591	5008	,	,		19059	0.0337		0.0338	False		,,,				2504	0.0133				p.L3446F		Atlas-SNP	.											.	DNAH14	300	.	0			c.C10336T						PASS	.	C	PHE/LEU	298,1086		34,230,428	130.0	109.0	115.0		10336	3.3	0.1	1	dbSNP_120	115	157,3025		5,147,1439	yes	missense	DNAH14	NM_001373.1	22	39,377,1867	TT,TC,CC		4.934,21.5318,9.965	probably-damaging	3446/4516	225528340	455,4111	692	1591	2283	SO:0001583	missense	127602	exon67			ATTTCCCTTGATG	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.7927C>T	1.37:g.225528340C>T	ENSP00000409472:p.Leu2643Phe	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	188	85	0.452128	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		167	0.07646520146520147	112	0.22764227642276422	15	0.04143646408839779	14	0.024475524475524476	26	0.03430079155672823	C	14.59	2.580954	0.46006	0.215318	0.04934	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.22134	1.97;1.97;1.97	5.35	3.3	0.37823	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999940378	D	0.59767	0.986	P	0.56865	0.808	T	0.17899	-1.0354	7	0.59425	D	0.04	.	3.8902	0.09116	0.1337:0.4897:0.2849:0.0917	rs12184324;rs61359963;rs12184324	3446	Q0VDD8-4	.	F	2643;3446;3446	ENSP00000409472:L2643F;ENSP00000414402:L3446F;ENSP00000392061:L3446F	ENSP00000414402:L3446F	L	+	1	0	DNAH14	223594963	0.992000	0.36948	0.116000	0.21606	0.406000	0.30931	1.856000	0.39389	1.382000	0.46385	0.603000	0.83216	CTT	C|0.907;T|0.093	0.093	strong		0.358	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713771	32713771	+	Missense_Mutation	SNP	T	T	C	rs148720159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32713771T>C	ENST00000374940.3	+	3	637	c.535T>C	c.(535-537)Ttc>Ctc	p.F179L		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	179	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)"""	TTACCTCACCTTCCTCCCTTC	0.512																																					p.F179L		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.T535C						PASS	.						197.0	208.0	204.0					6																	32713771		1511	2707	4218	SO:0001583	missense	3118	exon3			CTCACCTTCCTCC		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.535T>C	6.37:g.32713771T>C	ENSP00000364076:p.Phe179Leu	Somatic	587	1	0.00170358		WXS	Illumina HiSeq	Phase_I	627	129	0.205742	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	15.07	2.724544	0.48728	.	.	ENSG00000237541	ENST00000374940	T	0.02737	4.18	3.06	3.06	0.35304	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.85682	U	0.000000	T	0.02533	0.0077	M	0.68728	2.09	0.44862	D	0.997875	B	0.25563	0.129	B	0.36719	0.231	T	0.14643	-1.0465	10	0.66056	D	0.02	.	9.4676	0.38822	0.0:0.0:0.0:1.0	.	179	P01906	DQA2_HUMAN	L	179	ENSP00000364076:F179L	ENSP00000364076:F179L	F	+	1	0	HLA-DQA2	32821749	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	5.148000	0.64857	1.388000	0.46506	0.147000	0.16070	TTC	T|0.667;C|0.333	0.333	strong		0.512	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
PRODH2	58510	hgsc.bcm.edu	37	19	36302897	36302897	+	Silent	SNP	G	G	A	rs145376615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36302897G>A	ENST00000301175.3	-	5	809	c.792C>T	c.(790-792)ccC>ccT	p.P264P		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	264					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)			CCAGCCTCTCGGGGCTCAGCT	0.637													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		18798	0.0		0.0	False		,,,				2504	0.0				p.P264P		Atlas-SNP	.											.	PRODH2	68	.	0			c.C792T						PASS	.	G		87,4319	72.5+/-110.5	0,87,2116	51.0	47.0	48.0		792	-9.5	0.2	19	dbSNP_134	48	0,8600		0,0,4300	no	coding-synonymous	PRODH2	NM_021232.1		0,87,6416	AA,AG,GG		0.0,1.9746,0.6689		264/537	36302897	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	58510	exon5			CCTCTCGGGGCTC	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.792C>T	19.37:g.36302897G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_021232		Silent	SNP	ENST00000301175.3	37	CCDS12478.1																																																																																			A|0.006;G|0.994;T|0.000	0.006	strong		0.637	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	
MYL9	10398	hgsc.bcm.edu	37	20	35176541	35176541	+	Silent	SNP	G	G	A	rs11553089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:35176541G>A	ENST00000279022.2	+	3	395	c.291G>A	c.(289-291)acG>acA	p.T97T	MYL9_ENST00000346786.2_Intron|RP5-977B1.11_ENST00000561134.1_RNA|RP5-977B1.7_ENST00000425233.1_RNA|RP5-977B1.7_ENST00000439595.1_RNA	NM_006097.4	NP_006088.2	P24844	MYL9_HUMAN	myosin, light chain 9, regulatory	97					axon guidance (GO:0007411)|muscle contraction (GO:0006936)|platelet aggregation (GO:0070527)|regulation of muscle contraction (GO:0006937)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)			endometrium(2)|kidney(1)|large_intestine(3)|lung(2)	8	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				TGAACGGCACGGACCCCGAGG	0.607													G|||	112	0.0223642	0.0787	0.0101	5008	,	,		17578	0.0		0.0	False		,,,				2504	0.001				p.T97T		Atlas-SNP	.											.	MYL9	13	.	0			c.G291A						PASS	.	G	,	262,4144	151.0+/-185.0	10,242,1951	114.0	78.0	91.0		291,	-9.7	0.1	20	dbSNP_120	91	1,8599		0,1,4299	no	coding-synonymous,intron	MYL9	NM_006097.3,NM_181526.1	,	10,243,6250	AA,AG,GG		0.0116,5.9464,2.0221	,	97/173,	35176541	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	10398	exon3			CGGCACGGACCCC	J02854	CCDS13276.1, CCDS13277.1	20q11.23	2013-01-10	2006-09-29		ENSG00000101335	ENSG00000101335		"""Myosins / Light chain"", ""EF-hand domain containing"""	15754	protein-coding gene	gene with protein product	"""myosin regulatory light chain 2, smooth muscle isoform"", ""myosin regulatory light chain 1"""	609905	"""myosin, light polypeptide 9, regulatory"""			2526655	Standard	NM_006097		Approved	MYRL2, MLC2, LC20, MRLC1	uc002xfl.2	P24844	OTTHUMG00000032387	ENST00000279022.2:c.291G>A	20.37:g.35176541G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	101	60	0.594059	NM_006097	E1P5T6|Q9BQL9|Q9BUF9|Q9H136	Silent	SNP	ENST00000279022.2	37	CCDS13276.1																																																																																			G|0.975;A|0.025	0.025	strong		0.607	MYL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079015.2	NM_006097	
DPY19L2	283417	hgsc.bcm.edu	37	12	64062023	64062023	+	Missense_Mutation	SNP	A	A	C	rs10878073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:64062023A>C	ENST00000324472.4	-	1	334	c.151T>G	c.(151-153)Tcc>Gcc	p.S51A	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	51			S -> A (in dbSNP:rs10878073). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GACCTCCAGGAGCCCCTTGGC	0.642													a|||	1979	0.395168	0.4425	0.2565	5008	,	,		15241	0.5714		0.1978	False		,,,				2504	0.4509				p.S51A		Atlas-SNP	.											.	DPY19L2	97	.	0			c.T151G						PASS	.	A	ALA/SER	1708,2698		318,1072,813	43.0	53.0	49.0		151	-2.2	0.0	12	dbSNP_120	49	1715,6881		177,1361,2760	yes	missense	DPY19L2	NM_173812.4	99	495,2433,3573	CC,CA,AA		19.9511,38.7653,26.3267	benign	51/759	64062023	3423,9579	2203	4298	6501	SO:0001583	missense	283417	exon1			TCCAGGAGCCCCT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.151T>G	12.37:g.64062023A>C	ENSP00000315988:p.Ser51Ala	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	177	73	0.412429	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	748	0.3424908424908425	180	0.36585365853658536	98	0.27071823204419887	324	0.5664335664335665	146	0.19261213720316622	a	2.066	-0.414146	0.04766	0.387653	0.199511	ENSG00000177990	ENST00000324472;ENST00000542209	T;T	0.32753	1.44;2.38	1.61	-2.25	0.06888	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.43893	-0.9363	7	.	.	.	.	7.1276	0.25482	0.6882:0.3118:0.0:0.0	rs10878073;rs10878073	51	Q6NUT2	D19L2_HUMAN	A	51	ENSP00000315988:S51A;ENSP00000444932:S51A	.	S	-	1	0	DPY19L2	62348290	0.378000	0.25114	0.010000	0.14722	0.014000	0.08584	-0.429000	0.06982	-0.692000	0.05128	-1.193000	0.01689	TCC	A|0.717;C|0.283	0.283	strong		0.642	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
OR2T27	403239	hgsc.bcm.edu	37	1	248813352	248813352	+	Silent	SNP	G	G	A	rs147773385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813352G>A	ENST00000344889.3	-	1	833	c.834C>T	c.(832-834)taC>taT	p.Y278Y		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y278*(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TAAGGATGGTGTAGAAGGCAG	0.522													G|||	106	0.0211661	0.0772	0.0058	5008	,	,		16990	0.0		0.0	False		,,,				2504	0.0				p.Y278Y		Atlas-SNP	.											OR2T27,colon,carcinoma,0,1	OR2T27	52	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C834T						scavenged	.	G		158,4196		8,142,2027	78.0	73.0	74.0		834	0.4	1.0	1	dbSNP_134	74	0,8548		0,0,4274	no	coding-synonymous	OR2T27	NM_001001824.1		8,142,6301	AA,AG,GG		0.0,3.6288,1.2246		278/318	248813352	158,12744	2177	4274	6451	SO:0001819	synonymous_variant	403239	exon1			GATGGTGTAGAAG		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.834C>T	1.37:g.248813352G>A		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	166	26	0.156627	NM_001001824		Silent	SNP	ENST00000344889.3	37	CCDS31124.1																																																																																			G|0.986;A|0.014	0.014	strong		0.522	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
USP6NL	9712	hgsc.bcm.edu	37	10	11505175	11505175	+	Silent	SNP	A	A	G	rs3740204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	36	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	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	
FAM179A	165186	hgsc.bcm.edu	37	2	29225502	29225502	+	Silent	SNP	T	T	G	rs72786178|rs386644304|rs200686651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29225502T>G	ENST00000379558.4	+	5	879	c.528T>G	c.(526-528)ccT>ccG	p.P176P	FAM179A_ENST00000403861.2_Silent_p.P176P	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	176										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						GGCCGATGCCTCTCATCCAGA	0.657													T|||	946	0.188898	0.4372	0.1066	5008	,	,		17273	0.1617		0.0726	False		,,,				2504	0.0593				p.P176P		Atlas-SNP	.											.	FAM179A	106	.	0			c.T528G						PASS	.	T		1443,2525		270,903,811	28.0	35.0	33.0		528	-3.7	1.0	2	dbSNP_130	33	565,7761		15,535,3613	no	coding-synonymous	FAM179A	NM_199280.2		285,1438,4424	GG,GT,TT		6.786,36.3659,16.3332		176/1020	29225502	2008,10286	1984	4163	6147	SO:0001819	synonymous_variant	165186	exon5			GATGCCTCTCATC	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.528T>G	2.37:g.29225502T>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			T|0.833;G|0.167	0.167	strong		0.657	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
EGFLAM	133584	hgsc.bcm.edu	37	5	38425110	38425110	+	Missense_Mutation	SNP	C	C	A	rs6897179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38425110C>A	ENST00000354891.3	+	13	2072	c.1726C>A	c.(1726-1728)Cat>Aat	p.H576N	EGFLAM_ENST00000322350.5_Missense_Mutation_p.H576N|EGFLAM_ENST00000397202.2_De_novo_Start_OutOfFrame|EGFLAM-AS1_ENST00000508986.1_RNA|EGFLAM_ENST00000336740.6_Missense_Mutation_p.H342N	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	576	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.		H -> N (in dbSNP:rs6897179).		extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					CTCGTGCATCCATGGTGGCAC	0.498													A|||	659	0.131589	0.3699	0.0965	5008	,	,		17534	0.0536		0.0268	False		,,,				2504	0.0225				p.H576N	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C1726A						PASS	.	A	ASN/HIS,ASN/HIS,ASN/HIS	1305,3101	698.1+/-406.3	194,917,1092	169.0	156.0	161.0		1726,1726,1024	3.4	0.5	5	dbSNP_116	161	206,8394	810.1+/-407.1	1,204,4095	yes	missense,missense,missense	EGFLAM	NM_001205301.1,NM_152403.3,NM_182798.2	68,68,68	195,1121,5187	AA,AC,CC		2.3953,29.6187,11.6177	benign,benign,benign	576/1018,576/1010,342/776	38425110	1511,11495	2203	4300	6503	SO:0001583	missense	133584	exon13			TGCATCCATGGTG	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"""Fibronectin type III domain containing"""	26810	protein-coding gene	gene with protein product	"""pikachurin"", ""agrin-like"""					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.1726C>A	5.37:g.38425110C>A	ENSP00000346964:p.His576Asn	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	165	82	0.49697	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	255	0.11675824175824176	173	0.3516260162601626	28	0.07734806629834254	34	0.05944055944055944	20	0.026385224274406333	A	4.570	0.105940	0.08780	0.296187	0.023953	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000339580	D;D;D	0.90620	-2.7;-2.7;-2.7	5.91	3.44	0.39384	Concanavalin A-like lectin/glucanase, subgroup (1);EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.090430	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00514	-1.41	0.09310	P	1.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.19289	-1.0310	9	0.02654	T	1	-12.699	13.906	0.63836	0.6415:0.3585:0.0:0.0	rs6897179;rs52828439;rs58194950;rs6897179	342;576;576	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	N	576;576;342;342	ENSP00000346964:H576N;ENSP00000313084:H576N;ENSP00000337607:H342N	ENSP00000313084:H576N	H	+	1	0	EGFLAM	38460867	1.000000	0.71417	0.465000	0.27155	0.901000	0.52897	4.561000	0.60809	0.112000	0.17975	-0.256000	0.11100	CAT	C|0.880;A|0.120	0.120	strong		0.498	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	
LRTM1	57408	hgsc.bcm.edu	37	3	54958884	54958884	+	Silent	SNP	A	A	G	rs35757787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:54958884A>G	ENST00000273286.5	-	2	528	c.366T>C	c.(364-366)ccT>ccC	p.P122P	CACNA2D3_ENST00000474759.1_Intron|CACNA2D3_ENST00000490478.1_Intron|LRTM1_ENST00000493075.1_Silent_p.P46P|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000288197.5_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	122						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		CCCTCAGCTGAGGGAGGGAAT	0.478													A|||	154	0.0307508	0.1127	0.0058	5008	,	,		20302	0.0		0.001	False		,,,				2504	0.0				p.P122P		Atlas-SNP	.											.	LRTM1	52	.	0			c.T366C						PASS	.	A	,	420,3986	205.8+/-227.6	14,392,1797	76.0	75.0	75.0		,366	-11.5	0.0	3	dbSNP_126	75	2,8598	2.2+/-6.3	0,2,4298	no	intron,coding-synonymous	CACNA2D3,LRTM1	NM_018398.2,NM_020678.2	,	14,394,6095	GG,GA,AA		0.0233,9.5325,3.2447	,	,122/346	54958884	422,12584	2203	4300	6503	SO:0001819	synonymous_variant	57408	exon2			CAGCTGAGGGAGG	AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.366T>C	3.37:g.54958884A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_020678	Q8IUU2	Silent	SNP	ENST00000273286.5	37	CCDS2876.1																																																																																			A|0.971;G|0.029	0.029	strong		0.478	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678	
TUBB	203068	hgsc.bcm.edu	37	6	30695920	30695920	+	IGR	SNP	C	C	T	rs1136719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30695920C>T	ENST00000327892.8	+	0	2670				FLOT1_ENST00000456573.2_Silent_p.V371V|FLOT1_ENST00000376389.3_Silent_p.V419V	NM_178014.2	NP_821133.1	P07437	TBB5_HUMAN	tubulin, beta class I						cell division (GO:0051301)|cellular component movement (GO:0006928)|cellular process (GO:0009987)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cell body (GO:0044297)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|kidney(8)|large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	16					Colchicine(DB01394)|Podofilox(DB01179)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	GCTTGTGATTCACCTGGCAAA	0.532													C|||	474	0.0946486	0.1641	0.0476	5008	,	,		19883	0.0774		0.0388	False		,,,				2504	0.1094				p.V419V		Atlas-SNP	.											.	FLOT1	28	.	0			c.G1257A						PASS	.	C		454,2568		34,386,1091	154.0	131.0	139.0		1257	0.9	1.0	6	dbSNP_86	139	202,5216		5,192,2512	no	coding-synonymous	FLOT1	NM_005803.2		39,578,3603	TT,TC,CC		3.7283,15.0232,7.7725		419/428	30695920	656,7784	1511	2709	4220	SO:0001628	intergenic_variant	10211	exon13			GTGATTCACCTGG	AB062393	CCDS4687.1	6p21.33	2011-10-10	2011-10-10		ENSG00000196230	ENSG00000196230		"""Tubulins"""	20778	protein-coding gene	gene with protein product	"""class I beta-tubulin"", ""beta1-tubulin"""	191130	"""tubulin, beta polypeptide"", ""tubulin, beta"""			11504633, 8270253	Standard	NM_001293212		Approved	OK/SW-cl.56, MGC16435, M40, Tubb5	uc003nrl.3	P07437	OTTHUMG00000031059		6.37:g.30695920C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_005803	P05218|Q8WUC1|Q9CY33	Silent	SNP	ENST00000327892.8	37	CCDS4687.1																																																																																			T|0.057;G|0.183;C|0.746;A|0.014	0.057	strong		0.532	TUBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076074.2	NM_178014	
ST8SIA3	51046	hgsc.bcm.edu	37	18	55021725	55021725	+	Missense_Mutation	SNP	A	A	C	rs3745060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:55021725A>C	ENST00000324000.3	+	2	2306	c.272A>C	c.(271-273)aAa>aCa	p.K91T		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	91			K -> T (in dbSNP:rs3745060).		cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|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)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		TCTAAGTGGAAATTTAATCGG	0.403													C|||	1846	0.36861	0.5204	0.3199	5008	,	,		18792	0.495		0.159	False		,,,				2504	0.2832				p.K91T		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.A272C						PASS	.	C	THR/LYS	1999,2407	616.4+/-392.8	455,1089,659	110.0	109.0	109.0		272	2.0	1.0	18	dbSNP_107	109	1365,7235	755.4+/-407.5	100,1165,3035	yes	missense	ST8SIA3	NM_015879.2	78	555,2254,3694	CC,CA,AA		15.8721,45.37,25.865	benign	91/381	55021725	3364,9642	2203	4300	6503	SO:0001583	missense	51046	exon2			AGTGGAAATTTAA	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"""Sialyltransferases"""	14269	protein-coding gene	gene with protein product	"""ST8Sia III"""	609478	"""sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"""	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.272A>C	18.37:g.55021725A>C	ENSP00000320431:p.Lys91Thr	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_015879	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	37	CCDS32834.1	763	0.34935897435897434	240	0.4878048780487805	102	0.281767955801105	306	0.534965034965035	115	0.1517150395778364	C	2.834	-0.241904	0.05906	0.4537	0.158721	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.39997	1.05	4.88	2.02	0.26589	.	0.387780	0.31495	N	0.007546	T	0.00012	0.0000	N	0.14661	0.345	0.49798	P	1.7400000000000748E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.47302	-0.9128	9	0.08837	T	0.75	-6.3465	2.5347	0.04711	0.2854:0.336:0.2786:0.1	rs3745060;rs52812069;rs56693866;rs3745060	91	O43173	SIA8C_HUMAN	T	198;91	ENSP00000320431:K91T	ENSP00000320431:K91T	K	+	2	0	ST8SIA3	53172723	0.043000	0.20138	0.987000	0.45799	0.979000	0.70002	-0.004000	0.12878	-0.039000	0.13602	-0.352000	0.07741	AAA	A|0.692;C|0.308	0.308	strong		0.403	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879	
CAMK4	814	hgsc.bcm.edu	37	5	110820116	110820116	+	Silent	SNP	T	T	G	rs6886469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:110820116T>G	ENST00000282356.4	+	11	1772	c.1374T>G	c.(1372-1374)gcT>gcG	p.A458A	CAMK4_ENST00000512890.1_3'UTR|CAMK4_ENST00000512453.1_Silent_p.A458A	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	458					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		GAAGCTCTGCTGTGGGTTTTG	0.512													T|||	46	0.0091853	0.034	0.0014	5008	,	,		19121	0.0		0.0	False		,,,				2504	0.0				p.A458A		Atlas-SNP	.											.	CAMK4	77	.	0			c.T1374G						PASS	.	T		114,4290	87.3+/-125.9	3,108,2091	47.0	47.0	47.0		1374	-3.5	0.0	5	dbSNP_116	47	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CAMK4	NM_001744.4		3,110,6389	GG,GT,TT		0.0233,2.5886,0.892		458/474	110820116	116,12888	2202	4300	6502	SO:0001819	synonymous_variant	814	exon11			CTCTGCTGTGGGT	D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"""brain Ca++-calmodulin-dependent protein kinase type IV"", ""calcium/calmodulin-dependent protein kinase type IV catalytic chain"", ""CAM kinase IV"", ""CAM kinase- GR"""	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.1374T>G	5.37:g.110820116T>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	69	40	0.57971	NM_001744	D3DSZ7	Silent	SNP	ENST00000282356.4	37	CCDS4103.1																																																																																			T|0.991;G|0.009	0.009	strong		0.512	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744	
BSN	8927	hgsc.bcm.edu	37	3	49701983	49701983	+	Silent	SNP	G	G	A	rs9858542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49701983G>A	ENST00000296452.4	+	9	11850	c.11736G>A	c.(11734-11736)acG>acA	p.T3912T		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3912					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GCAAACTGACGGAAGGTATGC	0.637													G|||	978	0.195288	0.2171	0.17	5008	,	,		17930	0.0516		0.3241	False		,,,				2504	0.1994				p.T3912T		Atlas-SNP	.											BSN,NS,carcinoma,+1,1	BSN	272	1	0			c.G11736A						PASS	.	G		1044,3362	379.7+/-323.4	120,804,1279	48.0	54.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	11736	-10.1	0.6	3	dbSNP_119	52	2577,6023	416.5+/-352.1	402,1773,2125	yes	coding-synonymous	BSN	NM_003458.3		522,2577,3404	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	29.9651,23.695,27.841		3912/3927	49701983	3621,9385	2203	4300	6503	SO:0001819	synonymous_variant	8927	exon9			ACTGACGGAAGGT	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.11736G>A	3.37:g.49701983G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	41	14	0.341463	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			G|0.749;A|0.251	0.251	strong		0.637	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
TEX11	56159	hgsc.bcm.edu	37	X	69890301	69890301	+	Missense_Mutation	SNP	C	C	T	rs4844247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:69890301C>T	ENST00000395889.2	-	17	1506	c.1351G>A	c.(1351-1353)Gaa>Aaa	p.E451K	TEX11_ENST00000374333.2_Missense_Mutation_p.E436K|TEX11_ENST00000374320.2_Missense_Mutation_p.E126K|TEX11_ENST00000344304.3_Missense_Mutation_p.E451K	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	451			E -> K (in dbSNP:rs4844247). {ECO:0000269|PubMed:15489334}.		chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					AGATCCATTTCATCAGTTGAA	0.363													C|||	505	0.133775	0.0908	0.1859	3775	,	,		15241	0.125		0.0249	False		,,,				2504	0.1074				p.E451K		Atlas-SNP	.											.	TEX11	132	.	0			c.G1351A						PASS	.	C	LYS/GLU,LYS/GLU	409,3426		19,302,69,1311,502	115.0	96.0	102.0		1351,1306	-0.5	0.0	X	dbSNP_111	102	263,6465		4,176,79,2248,1793	yes	missense,missense	TEX11	NM_001003811.1,NM_031276.2	56,56	23,478,148,3559,2295	TT,TC,T,CC,C		3.909,10.6649,6.3618	benign,benign	451/941,436/926	69890301	672,9891	2203	4300	6503	SO:0001583	missense	56159	exon17			CCATTTCATCAGT	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"""testis expressed sequence 11"""			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.1351G>A	X.37:g.69890301C>T	ENSP00000379226:p.Glu451Lys	Somatic	350	0	0		WXS	Illumina HiSeq	Phase_I	319	139	0.435737	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	37	CCDS35323.1	210	0.12658227848101267	26	0.05803571428571429	42	0.13043478260869565	45	0.08964143426294821	14	0.01876675603217158	C	1.430	-0.570586	0.03910	0.106649	0.03909	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82	3.77	-0.491	0.12045	Tetratricopeptide-like helical (1);	0.364588	0.25698	N	0.028893	T	0.00552	0.0018	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.03095	-1.1073	8	.	.	.	1.2168	6.1459	0.20285	0.0:0.1736:0.3448:0.4816	rs4844247;rs17857083;rs52815445;rs4844247	436;451	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	K	436;451;126;451	ENSP00000363453:E436K;ENSP00000379226:E451K;ENSP00000363440:E126K;ENSP00000340995:E451K	.	E	-	1	0	TEX11	69807026	0.261000	0.24063	0.000000	0.03702	0.009000	0.06853	1.102000	0.31050	-0.527000	0.06374	-0.558000	0.04189	GAA	C|0.911;T|0.089	0.089	strong		0.363	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1		
UBP1	7342	hgsc.bcm.edu	37	3	33458266	33458266	+	Missense_Mutation	SNP	T	T	C	rs3736563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:33458266T>C	ENST00000283629.3	-	3	855	c.326A>G	c.(325-327)aAt>aGt	p.N109S	UBP1_ENST00000447368.2_Missense_Mutation_p.N109S|RNU7-110P_ENST00000516891.1_RNA|UBP1_ENST00000283628.5_Missense_Mutation_p.N109S	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	109			N -> S (in dbSNP:rs3736563). {ECO:0000269|PubMed:8114710}.		angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						TAATTTTCCATTGATCTCAGG	0.294													C|||	2399	0.479034	0.5333	0.5605	5008	,	,		18916	0.6091		0.3141	False		,,,				2504	0.3834				p.N109S		Atlas-SNP	.											.	UBP1	42	.	0			c.A326G						PASS	.	C	SER/ASN,SER/ASN,SER/ASN	2363,2043	566.7+/-382.0	610,1143,450	104.0	107.0	106.0		326,326,326	4.0	1.0	3	dbSNP_107	106	2423,6175	697.0+/-404.9	332,1759,2208	yes	missense,missense,missense	UBP1	NM_001128160.1,NM_001128161.1,NM_014517.4	46,46,46	942,2902,2658	CC,CT,TT		28.181,46.3686,36.8041	benign,benign,benign	109/505,109/541,109/541	33458266	4786,8218	2203	4299	6502	SO:0001583	missense	7342	exon3			TTTCCATTGATCT	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.326A>G	3.37:g.33458266T>C	ENSP00000283629:p.Asn109Ser	Somatic	355	0	0		WXS	Illumina HiSeq	Phase_I	371	176	0.474394	NM_001128160	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	37	CCDS2659.1	993	0.45467032967032966	253	0.5142276422764228	182	0.5027624309392266	309	0.5402097902097902	249	0.32849604221635886	C	2.681	-0.275386	0.05679	0.536314	0.28181	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628;ENST00000456378	T;T;T;T	0.16324	2.35;2.35;2.35;2.35	5.73	3.95	0.45737	CP2 transcription factor (1);	0.144057	0.64402	N	0.000005	T	0.00012	0.0000	N	0.03608	-0.345	0.44247	P	0.002905999999999964	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.44590	-0.9318	9	0.07325	T	0.83	-11.4831	2.3834	0.04360	0.113:0.4797:0.1756:0.2318	rs3736563;rs57275094;rs3736563	109;109	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	S	109	ENSP00000283629:N109S;ENSP00000395558:N109S;ENSP00000283628:N109S;ENSP00000401614:N109S	ENSP00000283628:N109S	N	-	2	0	UBP1	33433270	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	1.041000	0.30291	0.464000	0.27142	-0.119000	0.15052	AAT	T|0.585;C|0.415	0.415	strong		0.294	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517	
OR51B6	390058	hgsc.bcm.edu	37	11	5373646	5373646	+	Silent	SNP	T	T	C	rs5024041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5373646T>C	ENST00000380219.1	+	1	909	c.909T>C	c.(907-909)cgT>cgC	p.R303R	HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	303					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)		GCATACTTCGTTTATTCTCTC	0.413													C|||	3023	0.603634	0.5764	0.5692	5008	,	,		20475	0.5466		0.6054	False		,,,				2504	0.7219				p.R303R		Atlas-SNP	.											OR51B6,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	OR51B6	53	1	0			c.T909C						scavenged	.	C		2551,1849	483.7+/-359.8	736,1079,385	87.0	88.0	88.0		909	-1.1	0.0	11	dbSNP_113	88	5122,3468	490.7+/-372.9	1520,2082,693	no	coding-synonymous	OR51B6	NM_001004750.1		2256,3161,1078	CC,CT,TT		40.3725,42.0227,40.9315		303/313	5373646	7673,5317	2200	4295	6495	SO:0001819	synonymous_variant	390058	exon1			ACTTCGTTTATTC		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.909T>C	11.37:g.5373646T>C		Somatic	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001004750		Silent	SNP	ENST00000380219.1	37	CCDS31379.1																																																																																			T|0.407;C|0.593	0.593	strong		0.413	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
ODAM	54959	hgsc.bcm.edu	37	4	71068489	71068489	+	Missense_Mutation	SNP	T	T	C	rs3196714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	201	0	0		WXS	Illumina HiSeq	Phase_I	234	114	0.487179	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	
CA8	767	hgsc.bcm.edu	37	8	61178574	61178574	+	Silent	SNP	T	T	C	rs7464181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	65	0	0		WXS	Illumina HiSeq	Phase_I	84	32	0.380952	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		
TSSK3	81629	hgsc.bcm.edu	37	1	32829261	32829261	+	Missense_Mutation	SNP	A	A	G	rs35508255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:32829261A>G	ENST00000373534.3	+	2	716	c.211A>G	c.(211-213)Atc>Gtc	p.I71V	FAM229A_ENST00000432622.1_5'Flank|FAM229A_ENST00000415596.1_Intron	NM_052841.3	NP_443073.1	Q96PN8	TSSK3_HUMAN	testis-specific serine kinase 3	71	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		I -> V (in dbSNP:rs35508255).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|large_intestine(6)|lung(5)|skin(2)|stomach(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212)				CAAGAACATCATCCAGGTGTA	0.562													A|||	81	0.0161741	0.0582	0.0058	5008	,	,		19728	0.0		0.0	False		,,,				2504	0.0				p.I71V		Atlas-SNP	.											.	TSSK3	22	.	0			c.A211G						PASS	.	A	VAL/ILE	208,4198	128.2+/-165.1	5,198,2000	79.0	84.0	82.0		211	1.9	1.0	1	dbSNP_126	82	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TSSK3	NM_052841.3	29	5,201,6297	GG,GA,AA		0.0349,4.7208,1.6223	benign	71/269	32829261	211,12795	2203	4300	6503	SO:0001583	missense	81629	exon2			AACATCATCCAGG	AF296450	CCDS362.1	1p35-p34	2008-02-05	2005-03-10	2005-03-12	ENSG00000162526	ENSG00000162526			15473	protein-coding gene	gene with protein product		607660	"""serine/threonine kinase 22C (spermiogenesis associated)"""	STK22C		11597141	Standard	NM_052841		Approved	SPOGA3	uc001bvf.3	Q96PN8	OTTHUMG00000007585	ENST00000373534.3:c.211A>G	1.37:g.32829261A>G	ENSP00000362634:p.Ile71Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	147	82	0.557823	NM_052841	Q5TEE5	Missense_Mutation	SNP	ENST00000373534.3	37	CCDS362.1	39	0.017857142857142856	36	0.07317073170731707	3	0.008287292817679558	0	0.0	0	0.0	A	9.836	1.189629	0.21954	0.047208	3.49E-4	ENSG00000162526	ENST00000373534	T	0.15372	2.43	5.42	1.88	0.25563	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.086426	0.49916	N	0.000121	T	0.00496	0.0016	N	0.02379	-0.575	0.80722	D	1	P	0.45715	0.865	P	0.45232	0.474	T	0.45512	-0.9256	10	0.13470	T	0.59	.	8.5454	0.33417	0.7713:0.0:0.2287:0.0	rs35508255;rs61742632	71	Q96PN8	TSSK3_HUMAN	V	71	ENSP00000362634:I71V	ENSP00000362634:I71V	I	+	1	0	TSSK3	32601848	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.475000	0.35409	0.456000	0.26937	-0.274000	0.10170	ATC	A|0.981;G|0.019	0.019	strong		0.562	TSSK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020049.1		
ZNF841	284371	hgsc.bcm.edu	37	19	52570783	52570783	+	Silent	SNP	A	A	G	rs16983414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52570783A>G	ENST00000426391.2	-	5	555	c.4T>C	c.(4-6)Ttg>Ctg	p.L2L	ZNF841_ENST00000594295.1_Silent_p.L118L|ZNF841_ENST00000359973.2_Silent_p.L2L|ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000389534.4_Silent_p.L118L			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	2					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(4)|kidney(3)|lung(3)	11						TGTCCTTCCAACATCACTGCT	0.353													A|||	987	0.197085	0.2262	0.1988	5008	,	,		16023	0.121		0.0994	False		,,,				2504	0.3354				p.L118L		Atlas-SNP	.											.	ZNF841	183	.	0			c.T352C						PASS	.	A		308,1076		28,252,412	132.0	101.0	110.0		352	2.3	0.0	19	dbSNP_123	110	353,2829		20,313,1258	no	coding-synonymous	ZNF841	NM_001136499.1		48,565,1670	GG,GA,AA		11.0937,22.2543,14.4766		118/925	52570783	661,3905	692	1591	2283	SO:0001819	synonymous_variant	284371	exon7			CTTCCAACATCAC	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.4T>C	19.37:g.52570783A>G		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	214	91	0.425234	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Silent	SNP	ENST00000426391.2	37																																																																																				A|0.829;G|0.171	0.171	strong		0.353	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155	
ERBB2	2064	hgsc.bcm.edu	37	17	37872035	37872035	+	Missense_Mutation	SNP	G	G	T	rs4252633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37872035G>T	ENST00000269571.5	+	12	1515	c.1356G>T	c.(1354-1356)tgG>tgT	p.W452C	ERBB2_ENST00000578199.1_Missense_Mutation_p.W422C|ERBB2_ENST00000540147.1_Missense_Mutation_p.W422C|ERBB2_ENST00000406381.2_Missense_Mutation_p.W422C|ERBB2_ENST00000445658.2_Missense_Mutation_p.W176C|ERBB2_ENST00000540042.1_Missense_Mutation_p.W422C|ERBB2_ENST00000584601.1_Missense_Mutation_p.W422C|ERBB2_ENST00000541774.1_Missense_Mutation_p.W437C|ERBB2_ENST00000584450.1_Missense_Mutation_p.W452C			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	452			W -> C (in dbSNP:rs4252633). {ECO:0000269|Ref.3}.		axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GCATCAGCTGGCTGGGGCTGC	0.627		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)			G|||	90	0.0179712	0.0673	0.0014	5008	,	,		19038	0.0		0.0	False		,,,				2504	0.0				p.W452C		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	ERBB2	429	.	0			c.G1356T						PASS	.	G	CYS/TRP,CYS/TRP	210,4196	129.0+/-165.8	6,198,1999	98.0	81.0	86.0		1266,1356	2.8	1.0	17	dbSNP_111	86	0,8600		0,0,4300	yes	missense,missense	ERBB2	NM_001005862.1,NM_004448.2	215,215	6,198,6299	TT,TG,GG		0.0,4.7662,1.6146	possibly-damaging,possibly-damaging	422/1226,452/1256	37872035	210,12796	2203	4300	6503	SO:0001583	missense	2064	exon12			CAGCTGGCTGGGG	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1356G>T	17.37:g.37872035G>T	ENSP00000269571:p.Trp452Cys	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	G	8.363	0.833490	0.16820	0.047662	0.0	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147;ENST00000540042	T;T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25;-1.25	5.93	2.79	0.32731	EGF receptor, L domain (1);	.	.	.	.	T	0.16685	0.0401	L	0.34521	1.04	0.35496	D	0.799411	P;D;D;P	0.57257	0.951;0.979;0.965;0.903	P;P;P;P	0.62885	0.88;0.874;0.762;0.908	T	0.62680	-0.6803	9	0.72032	D	0.01	.	3.232	0.06751	0.1435:0.2503:0.4775:0.1287	rs4252633	176;422;437;452	B4DTR1;F5H1T4;P04626-4;P04626	.;.;.;ERBB2_HUMAN	C	422;437;176;452;422;422	ENSP00000385185:W422C;ENSP00000446466:W437C;ENSP00000404047:W176C;ENSP00000269571:W452C;ENSP00000443562:W422C;ENSP00000446382:W422C	ENSP00000269571:W452C	W	+	3	0	ERBB2	35125561	0.528000	0.26314	0.995000	0.50966	0.899000	0.52679	-0.034000	0.12225	0.381000	0.24851	-0.305000	0.09177	TGG	G|0.979;T|0.021	0.021	strong		0.627	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
PTGS1	5742	hgsc.bcm.edu	37	9	125143792	125143792	+	Silent	SNP	C	C	A	rs5788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125143792C>A	ENST00000362012.2	+	6	644	c.639C>A	c.(637-639)ggC>ggA	p.G213G	PTGS1_ENST00000540753.1_Silent_p.G188G|PTGS1_ENST00000373698.5_Silent_p.G104G|PTGS1_ENST00000223423.4_Silent_p.G213G	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						PASS	.	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	179	0	0		WXS	Illumina HiSeq	Phase_I	175	174	0.994286	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		
ACIN1	22985	hgsc.bcm.edu	37	14	23549948	23549948	+	Missense_Mutation	SNP	C	C	T	rs11555803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23549948C>T	ENST00000262710.1	-	6	1097	c.770G>A	c.(769-771)aGa>aAa	p.R257K	ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000555053.1_Missense_Mutation_p.R257K|ACIN1_ENST00000605057.1_Missense_Mutation_p.R199K|ACIN1_ENST00000457657.1_Missense_Mutation_p.R217K	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	257	Glu-rich.		R -> K (in dbSNP:rs11555803).		apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		CCTTAGGTTTCTGGAAGGTGT	0.473													C|||	114	0.0227636	0.0825	0.0072	5008	,	,		20266	0.0		0.0	False		,,,				2504	0.0				p.R257K		Atlas-SNP	.											.	ACIN1	147	.	0			c.G770A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG	356,4050	183.6+/-211.2	16,324,1863	175.0	179.0	178.0		770,650,770	5.5	1.0	14	dbSNP_120	178	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense,missense	ACIN1	NM_001164814.1,NM_001164815.1,NM_014977.3	26,26,26	16,332,6155	TT,TC,CC		0.093,8.0799,2.7987	probably-damaging,probably-damaging,probably-damaging	257/1329,217/1302,257/1342	23549948	364,12642	2203	4300	6503	SO:0001583	missense	22985	exon6			AGGTTTCTGGAAG	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.770G>A	14.37:g.23549948C>T	ENSP00000262710:p.Arg257Lys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	C	22.9	4.351242	0.82132	0.080799	9.3E-4	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.27890	2.05;1.64;2.04	5.47	5.47	0.80525	.	0.000000	0.43260	D	0.000591	T	0.03178	0.0093	L	0.43152	1.355	0.38624	D	0.951213	D;P	0.53312	0.959;0.932	D;P	0.65684	0.937;0.867	T	0.01039	-1.1472	10	0.17832	T	0.49	-10.3899	14.8326	0.70159	0.0:1.0:0.0:0.0	rs11555803;rs52803485;rs11555803	257;257	G3V3M7;Q9UKV3	.;ACINU_HUMAN	K	257;217;257	ENSP00000262710:R257K;ENSP00000405677:R217K;ENSP00000451328:R257K	ENSP00000262710:R257K	R	-	2	0	ACIN1	22619788	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	3.549000	0.53681	2.569000	0.86673	0.650000	0.86243	AGA	C|0.971;T|0.029	0.029	strong		0.473	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
SLC10A6	345274	hgsc.bcm.edu	37	4	87769929	87769929	+	Missense_Mutation	SNP	T	T	C	rs13106574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:87769929T>C	ENST00000273905.6	-	1	487	c.340A>G	c.(340-342)Att>Gtt	p.I114V	SLC10A6_ENST00000505535.1_5'UTR	NM_197965.2	NP_932069.1	Q3KNW5	SOAT_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 6	114			I -> V (in dbSNP:rs13106574). {ECO:0000269|PubMed:15489334}.		sodium-dependent organic anion transport (GO:0043251)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)|sodium-dependent organic anion transmembrane transporter activity (GO:0043250)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	9		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.00099)		AAGGTGAAAATGTTAGAGATG	0.488													T|||	495	0.0988419	0.118	0.1268	5008	,	,		17437	0.001		0.1769	False		,,,				2504	0.0736				p.I114V		Atlas-SNP	.											.	SLC10A6	40	.	0			c.A340G						PASS	.	T	VAL/ILE	518,3888	237.4+/-249.2	30,458,1715	78.0	84.0	82.0		340	2.6	1.0	4	dbSNP_121	82	1726,6874	315.7+/-312.4	178,1370,2752	yes	missense	SLC10A6	NM_197965.2	29	208,1828,4467	CC,CT,TT		20.0698,11.7567,17.2536	benign	114/378	87769929	2244,10762	2203	4300	6503	SO:0001583	missense	345274	exon1			TGAAAATGTTAGA	AJ583502	CCDS3614.1	4q22.1	2013-07-18	2013-07-18		ENSG00000145283	ENSG00000145283		"""Solute carriers"""	30603	protein-coding gene	gene with protein product		613366				15020217, 17491011	Standard	NM_197965		Approved	SOAT	uc003hqd.2	Q3KNW5	OTTHUMG00000130596	ENST00000273905.6:c.340A>G	4.37:g.87769929T>C	ENSP00000273905:p.Ile114Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	127	65	0.511811	NM_197965	Q70EX7	Missense_Mutation	SNP	ENST00000273905.6	37	CCDS3614.1	224	0.10256410256410256	54	0.10975609756097561	46	0.1270718232044199	0	0.0	124	0.16358839050131926	T	10.69	1.422271	0.25639	0.117567	0.200698	ENSG00000145283	ENST00000273905	T	0.08984	3.03	5.59	2.64	0.31445	.	0.077016	0.52532	N	0.000071	T	0.00012	0.0000	N	0.13272	0.32	0.41065	P	0.014599000000000029	B	0.25169	0.119	B	0.31812	0.136	T	0.47394	-0.9121	9	0.15066	T	0.55	-17.4279	5.4631	0.16627	0.0:0.1238:0.1603:0.7158	rs13106574;rs52789983;rs59733764;rs13106574	114	Q3KNW5	SOAT_HUMAN	V	114	ENSP00000273905:I114V	ENSP00000273905:I114V	I	-	1	0	SLC10A6	87988953	1.000000	0.71417	0.956000	0.39512	0.893000	0.52053	1.263000	0.33004	0.751000	0.32900	0.533000	0.62120	ATT	T|0.854;C|0.146	0.146	strong		0.488	SLC10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253043.2	NM_197965	
GGT5	2687	hgsc.bcm.edu	37	22	24628928	24628928	+	Silent	SNP	G	G	A	rs762276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24628928G>A	ENST00000327365.4	-	4	875	c.459C>T	c.(457-459)cgC>cgT	p.R153R	GGT5_ENST00000263112.7_Silent_p.R121R|GGT5_ENST00000418439.2_Missense_Mutation_p.P78S|GGT5_ENST00000398292.3_Silent_p.R153R	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	153					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						GGCGGCCATGGCGGCGGTGGG	0.701													G|||	639	0.127596	0.0197	0.1888	5008	,	,		13019	0.1746		0.1571	False		,,,				2504	0.1513				p.R153R		Atlas-SNP	.											.	GGT5	61	.	0			c.C459T						PASS	.	G	,,	213,4145		9,195,1975	18.0	21.0	20.0		459,363,459	2.4	1.0	22	dbSNP_86	20	1070,7426		54,962,3232	no	coding-synonymous,coding-synonymous,coding-synonymous	GGT5	NM_001099781.1,NM_001099782.1,NM_004121.2	,,	63,1157,5207	AA,AG,GG		12.5942,4.8876,9.9813	,,	153/588,121/555,153/587	24628928	1283,11571	2179	4248	6427	SO:0001819	synonymous_variant	2687	exon4			GCCATGGCGGCGG	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"""Gamma-glutamyltransferases"""	4260	protein-coding gene	gene with protein product		137168	"""gamma-glutamyltransferase-like activity 1"""	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.459C>T	22.37:g.24628928G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	43	26	0.604651	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Silent	SNP	ENST00000327365.4	37	CCDS13825.1	294	0.1346153846153846	12	0.024390243902439025	68	0.1878453038674033	103	0.18006993006993008	111	0.14643799472295516	G	15.59	2.879364	0.51801	0.048876	0.125942	ENSG00000099998	ENST00000418439	T	0.19938	2.11	4.51	2.36	0.29203	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.45806	P	0.0013119999999999798	B	0.14438	0.01	B	0.10450	0.005	T	0.24368	-1.0162	7	0.72032	D	0.01	-40.7365	3.3668	0.07206	0.0949:0.1713:0.557:0.1767	rs762276	78	E7EUG3	.	S	78	ENSP00000392146:P78S	ENSP00000392146:P78S	P	-	1	0	GGT5	22958928	0.009000	0.17119	1.000000	0.80357	0.947000	0.59692	-0.683000	0.05179	0.627000	0.30340	0.585000	0.79938	CCA	G|0.864;A|0.136	0.136	strong		0.701	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121	
CC2D1A	54862	hgsc.bcm.edu	37	19	14029627	14029627	+	Missense_Mutation	SNP	A	A	C	rs11883041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14029627A>C	ENST00000318003.7	+	9	1256	c.1015A>C	c.(1015-1017)Aca>Cca	p.T339P	CC2D1A_ENST00000589606.1_Missense_Mutation_p.T339P	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	339	Pro-rich.		T -> P (in dbSNP:rs11883041).		positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			GCCCTCCACAACAGGTAGGTT	0.667													C|||	325	0.0648962	0.2284	0.0159	5008	,	,		14367	0.0		0.002	False		,,,				2504	0.0102				p.T339P		Atlas-SNP	.											.	CC2D1A	67	.	0			c.A1015C						PASS	.	C	PRO/THR	682,3144		67,548,1298	28.0	33.0	31.0		1015	5.1	0.9	19	dbSNP_120	31	24,8200		0,24,4088	yes	missense	CC2D1A	NM_017721.4	38	67,572,5386	CC,CA,AA		0.2918,17.8254,5.8589	benign	339/952	14029627	706,11344	1913	4112	6025	SO:0001583	missense	54862	exon9			TCCACAACAGGTA	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.1015A>C	19.37:g.14029627A>C	ENSP00000313601:p.Thr339Pro	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	91	53	0.582418	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	111	0.050824175824175824	102	0.2073170731707317	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	C	0.076	-1.192871	0.01607	0.178254	0.002918	ENSG00000132024	ENST00000318003;ENST00000397486	T	0.39056	1.1	5.05	5.05	0.67936	.	0.269287	0.37623	N	0.002004	T	0.00012	0.0000	N	0.00788	-1.185	0.54753	P	2.0000000000020002E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.16958	-1.0385	9	0.02654	T	1	-5.773	10.9037	0.47067	0.1877:0.8123:0.0:0.0	rs11883041;rs11883041	339;339;93	Q6P1N0-2;Q6P1N0;C9J1T8	.;C2D1A_HUMAN;.	P	339;93	ENSP00000313601:T339P	ENSP00000313601:T339P	T	+	1	0	CC2D1A	13890627	0.965000	0.33210	0.874000	0.34290	0.095000	0.18619	2.306000	0.43673	1.370000	0.46153	-0.217000	0.12591	ACA	A|0.943;C|0.057	0.057	strong		0.667	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
SYCE1L	100130958	hgsc.bcm.edu	37	16	77246093	77246093	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:77246093G>A	ENST00000378644.4	+	8	545	c.490G>A	c.(490-492)Gag>Aag	p.E164K	RP11-538I12.2_ENST00000569032.1_RNA	NM_001129979.1	NP_001123451.1	A8MT33	SYC1L_HUMAN	synaptonemal complex central element protein 1-like	164					synaptonemal complex assembly (GO:0007130)	synaptonemal complex (GO:0000795)				breast(1)|prostate(1)	2						GCTGCTCTCGGAGAGTGAGCC	0.721																																					p.E164K		Atlas-SNP	.											.	SYCE1L	10	.	0			c.G490A						PASS	.						8.0	11.0	10.0					16																	77246093		690	1581	2271	SO:0001583	missense	100130958	exon8			CTCTCGGAGAGTG		CCDS45533.1	16q23.1	2009-10-06			ENSG00000205078	ENSG00000205078			37236	protein-coding gene	gene with protein product	"""meiosis-related protein"""					16328886	Standard	NM_001129979		Approved	MRP2	uc010vnh.1	A8MT33		ENST00000378644.4:c.490G>A	16.37:g.77246093G>A	ENSP00000367911:p.Glu164Lys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	123	67	0.544715	NM_001129979	A6NF23	Missense_Mutation	SNP	ENST00000378644.4	37	CCDS45533.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999402	0.74818	.	.	ENSG00000205078	ENST00000378644	T	0.38560	1.13	3.47	1.38	0.22167	.	0.000000	0.41396	U	0.000894	T	0.58004	0.2092	M	0.72118	2.19	0.20975	N	0.999814	D	0.76494	0.999	D	0.80764	0.994	T	0.48747	-0.9008	10	0.72032	D	0.01	.	9.4908	0.38958	0.0:0.4243:0.5757:0.0	.	164	A8MT33	SYC1L_HUMAN	K	164	ENSP00000367911:E164K	ENSP00000367911:E164K	E	+	1	0	SYCE1L	75803594	0.957000	0.32711	0.327000	0.25402	0.186000	0.23388	1.540000	0.36115	0.416000	0.25844	0.471000	0.43371	GAG	.	.	none		0.721	SYCE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433889.1	NM_001129979	
NOP16	51491	hgsc.bcm.edu	37	5	175811233	175811233	+	Silent	SNP	C	C	T	rs1065206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:175811233C>T	ENST00000389158.5	-	5	971	c.536G>A	c.(535-537)tGa>tAa	p.*179*	NOP16_ENST00000507413.1_Silent_p.V54V|NOP16_ENST00000510123.1_Missense_Mutation_p.D149N			Q9Y3C1	NOP16_HUMAN	NOP16 nucleolar protein	0						intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|lung(4)|ovary(1)	8						GTAAACCAGTCACTCCACCTC	0.537													C|||	316	0.063099	0.1513	0.0519	5008	,	,		18191	0.0		0.0636	False		,,,				2504	0.0164				p.D150N		Atlas-SNP	.											.	NOP16	26	.	0			c.G448A						PASS	.	C		540,3476		29,482,1497	122.0	122.0	122.0		536	4.5	1.0	5	dbSNP_86	122	583,7761		25,533,3614	yes	coding-synonymous	NOP16	NM_016391.4		54,1015,5111	TT,TC,CC		6.9871,13.4462,9.0858		179/179	175811233	1123,11237	2008	4172	6180	SO:0001819	synonymous_variant	51491	exon5			ACCAGTCACTCCA		CCDS43403.1, CCDS58991.1	5q35.2	2012-12-10	2012-12-10		ENSG00000048162	ENSG00000048162			26934	protein-coding gene	gene with protein product	"""hypothetical protein HSPC111"", ""HBV pre-S2 trans-regulated protein 3"""	612861	"""nucleolar protein 16 homolog (yeast)"", ""NOP16 nucleolar protein homolog (yeast)"""			10810093, 11042152	Standard	NM_001291308		Approved	HSPC111, HSPC185, LOC51491	uc003mee.4	Q9Y3C1	OTTHUMG00000163186	ENST00000389158.5:c.536G>A	5.37:g.175811233C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_001256539	B4DV13|D6RGD3|Q05D05|Q6IAI6|Q8IXL5	Missense_Mutation	SNP	ENST00000389158.5	37	CCDS43403.1	137	0.06272893772893773	65	0.13211382113821138	21	0.058011049723756904	0	0.0	51	0.06728232189973615	C	17.23	3.335836	0.60853	0.134462	0.069871	ENSG00000048162	ENST00000510123;ENST00000341213;ENST00000451293	.	.	.	5.35	4.47	0.54385	.	0.684833	0.15269	N	0.271348	T	0.00967	0.0032	.	.	.	0.09310	P	1.0	D;D	0.59767	0.986;0.986	P;P	0.49637	0.617;0.617	T	0.29212	-1.0019	7	0.87932	D	0	-10.2921	14.9771	0.71283	0.0:0.9285:0.0:0.0715	rs1065206;rs3172922;rs60934001;rs1065206	150;149	Q6PIM0;D6RGD3	.;.	N	149;154;150	.	ENSP00000340662:D154N	D	-	1	0	NOP16	175743839	1.000000	0.71417	0.975000	0.42487	0.029000	0.11900	1.731000	0.38135	2.941000	0.99782	0.655000	0.94253	GAC	C|0.924;T|0.076	0.076	strong		0.537	NOP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371963.1	NM_016391	
ALDH1B1	219	hgsc.bcm.edu	37	9	38395928	38395928	+	Silent	SNP	C	C	T	rs2073477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:38395928C>T	ENST00000377698.3	+	2	336	c.183C>T	c.(181-183)acC>acT	p.T61T		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	61					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)			NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		ACCCTACCACCGGGGAGGTCA	0.602													C|||	1341	0.267772	0.2292	0.2968	5008	,	,		19392	0.3899		0.1372	False		,,,				2504	0.3078				p.T61T		Atlas-SNP	.											ALDH1B1,NS,carcinoma,0,1	ALDH1B1	50	1	0			c.C183T						PASS	.	C		1057,3349	387.2+/-326.4	130,797,1276	90.0	85.0	87.0		183	-11.6	0.0	9	dbSNP_96	87	1092,7508	228.3+/-263.4	75,942,3283	no	coding-synonymous	ALDH1B1	NM_000692.4		205,1739,4559	TT,TC,CC		12.6977,23.99,16.5231		61/518	38395928	2149,10857	2203	4300	6503	SO:0001819	synonymous_variant	219	exon2			TACCACCGGGGAG	M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"""Aldehyde dehydrogenases"""	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.183C>T	9.37:g.38395928C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_000692	B2R8F0|Q8WX76|Q9BV45	Silent	SNP	ENST00000377698.3	37	CCDS6615.1																																																																																			C|0.796;T|0.204	0.204	strong		0.602	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1		
UGT3A2	167127	hgsc.bcm.edu	37	5	36049324	36049324	+	Silent	SNP	G	G	A	rs148290056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36049324G>A	ENST00000282507.3	-	4	611	c.510C>T	c.(508-510)ttC>ttT	p.F170F	UGT3A2_ENST00000545528.1_Intron|UGT3A2_ENST00000504954.1_Intron|UGT3A2_ENST00000513300.1_Silent_p.F136F	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	170					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CCAAAGAGCCGAATGAAGTGG	0.453																																					p.F170F		Atlas-SNP	.											.	UGT3A2	117	.	0			c.C510T						PASS	.	G	,	33,4373	39.2+/-71.8	0,33,2170	87.0	82.0	84.0		408,510	-2.3	0.0	5	dbSNP_134	84	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	UGT3A2	NM_001168316.1,NM_174914.3	,	0,33,6470	AA,AG,GG		0.0,0.749,0.2537	,	136/490,170/524	36049324	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	167127	exon4			AGAGCCGAATGAA		CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"""UDP glucuronosyltransferases"""	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.510C>T	5.37:g.36049324G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	112	46	0.410714	NM_174914	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Silent	SNP	ENST00000282507.3	37	CCDS3914.1																																																																																			G|0.996;A|0.004	0.004	strong		0.453	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914	
CHDH	55349	hgsc.bcm.edu	37	3	53857676	53857676	+	Silent	SNP	C	C	T	rs17053532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	13	0	0		WXS	Illumina HiSeq	Phase_I	14	11	0.785714	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	
GPR87	53836	hgsc.bcm.edu	37	3	151017855	151017855	+	Splice_Site	SNP	T	T	G	rs141290943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151017855T>G	ENST00000260843.4	-	2	498	c.34A>C	c.(34-36)Aat>Cat	p.N12H	MED12L_ENST00000491549.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	12					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)			GACGGCTTACTTGGTAATTTT	0.413													T|||	4	0.000798722	0.003	0.0	5008	,	,		18522	0.0		0.0	False		,,,				2504	0.0				p.N12H		Atlas-SNP	.											.	GPR87	52	.	0			c.A34C						PASS	.	T	HIS/ASN,	32,4374	37.6+/-69.7	0,32,2171	102.0	94.0	97.0		34,	1.4	1.0	3	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,intron	GPR87,MED12L	NM_023915.3,NM_053002.4	68,	0,33,6470	GG,GT,TT		0.0116,0.7263,0.2537	benign,	12/359,	151017855	33,12973	2203	4300	6503	SO:0001630	splice_region_variant	53836	exon2			GCTTACTTGGTAA	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.34+1A>C	3.37:g.151017855T>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	73	44	0.60274	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	37	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	T	9.296	1.051901	0.19827	0.007263	1.16E-4	ENSG00000138271	ENST00000260843	T	0.62232	0.04	4.49	1.38	0.22167	.	0.688041	0.13625	N	0.374112	T	0.28067	0.0692	N	0.08118	0	0.80722	D	1	B	0.17268	0.021	B	0.13407	0.009	T	0.04855	-1.0922	9	.	.	.	-0.5324	7.7237	0.28746	0.0:0.8001:0.0:0.1999	.	12	Q9BY21	GPR87_HUMAN	H	12	ENSP00000260843:N12H	.	N	-	1	0	GPR87	152500545	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	1.189000	0.32114	0.152000	0.19188	0.533000	0.62120	AAT	T|0.998;G|0.002	0.002	strong		0.413	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1		Missense_Mutation
ADCY2	108	hgsc.bcm.edu	37	5	7520881	7520881	+	Missense_Mutation	SNP	G	G	T	rs13166360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	190	0	0		WXS	Illumina HiSeq	Phase_I	172	89	0.517442	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	
SIRPA	140885	hgsc.bcm.edu	37	20	1895950	1895950	+	Missense_Mutation	SNP	C	C	G	rs138283486|rs386811661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1895950C>G	ENST00000358771.4	+	2	437	c.285C>G	c.(283-285)gaC>gaG	p.D95E	SIRPA_ENST00000400068.3_Missense_Mutation_p.D95E|SIRPA_ENST00000356025.3_Missense_Mutation_p.D95E	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	95	Ig-like V-type.		D -> E. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CTGTTTCAGACCTCACAAAGA	0.527													C|||	1881	0.375599	0.2368	0.402	5008	,	,		14766	0.5883		0.2942	False		,,,				2504	0.409				p.D95E	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											.	SIRPA	83	.	0			c.C285G						PASS	.						128.0	106.0	113.0					20																	1895950		2202	4287	6489	SO:0001583	missense	140885	exon3			TTCAGACCTCACA	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.285C>G	20.37:g.1895950C>G	ENSP00000351621:p.Asp95Glu	Somatic	533	0	0		WXS	Illumina HiSeq	Phase_I	339	21	0.0619469	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	C	11.32	1.604197	0.28534	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.64803	-0.12;-0.12;-0.12	4.78	-2.65	0.06095	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.307559	0.27012	N	0.021368	T	0.64114	0.2569	M	0.83483	2.645	0.09310	N	0.999993	B;B;P	0.43352	0.049;0.019;0.804	B;B;P	0.46049	0.211;0.01;0.502	T	0.62296	-0.6884	10	0.54805	T	0.06	.	9.4883	0.38944	0.0:0.3689:0.0:0.6311	.	75;95;95	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	E	95	ENSP00000382941:D95E;ENSP00000348307:D95E;ENSP00000351621:D95E	ENSP00000348307:D95E	D	+	3	2	SIRPA	1843950	0.000000	0.05858	0.007000	0.13788	0.002000	0.02628	-1.635000	0.02018	-0.560000	0.06102	-0.266000	0.10368	GAC	C|0.693;G|0.307	0.307	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
MAP10	54627	hgsc.bcm.edu	37	1	232943513	232943513	+	Missense_Mutation	SNP	A	A	T	rs61735509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232943513A>T	ENST00000418460.1	+	1	2871	c.2744A>T	c.(2743-2745)cAc>cTc	p.H915L		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	773					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										TCACCTGTACACTCATACAGA	0.388													A|||	96	0.0191693	0.0696	0.0058	5008	,	,		19105	0.0		0.0	False		,,,				2504	0.0				p.H915L		Atlas-SNP	.											.	.	.	.	0			c.A2744T						PASS	.	A	LEU/HIS	220,3454		5,210,1622	47.0	47.0	47.0		2744	-4.8	0.0	1	dbSNP_129	47	6,8134		0,6,4064	yes	missense	KIAA1383	NM_019090.2	99	5,216,5686	TT,TA,AA		0.0737,5.988,1.913	benign	915/1048	232943513	226,11588	1837	4070	5907	SO:0001583	missense	54627	exon1			CTGTACACTCATA	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.2744A>T	1.37:g.232943513A>T	ENSP00000403208:p.His915Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	26	0.011904761904761904	24	0.04878048780487805	2	0.0055248618784530384	0	0.0	0	0.0	A	0.104	-1.148237	0.01714	0.05988	7.37E-4	ENSG00000212916	ENST00000418460	.	.	.	5.94	-4.76	0.03229	.	1.184600	0.06521	N	0.739754	T	0.01489	0.0048	N	0.16307	0.4	0.09310	N	1	B	0.15141	0.012	B	0.14578	0.011	T	0.20207	-1.0282	9	0.11485	T	0.65	0.0447	0.8514	0.01173	0.2763:0.1074:0.2072:0.409	rs61735509	773	Q9P2G4	K1383_HUMAN	L	915	.	ENSP00000403208:H915L	H	+	2	0	KIAA1383	231010136	0.000000	0.05858	0.012000	0.15200	0.035000	0.12851	0.776000	0.26704	-0.904000	0.03876	0.482000	0.46254	CAC	A|0.989;T|0.011	0.011	strong		0.388	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
CLEC4F	165530	hgsc.bcm.edu	37	2	71043607	71043607	+	Silent	SNP	G	G	C	rs114209954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71043607G>C	ENST00000272367.2	-	4	982	c.906C>G	c.(904-906)acC>acG	p.T302T	CLEC4F_ENST00000426626.1_Silent_p.T302T	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	302					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						TAAAGGCCTGGGTCTGGGAGT	0.403													G|||	63	0.0125799	0.0461	0.0029	5008	,	,		19886	0.0		0.0	False		,,,				2504	0.0				p.T302T	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.C906G						PASS	.	G		214,4192	126.1+/-163.2	4,206,1993	89.0	95.0	93.0		906	-0.9	0.3	2	dbSNP_132	93	1,8599		0,1,4299	no	coding-synonymous	CLEC4F	NM_173535.2		4,207,6292	CC,CG,GG		0.0116,4.857,1.6531		302/590	71043607	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	165530	exon4			GGCCTGGGTCTGG	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.906C>G	2.37:g.71043607G>C		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	171	82	0.479532	NM_173535	A4QPA5	Silent	SNP	ENST00000272367.2	37	CCDS1910.1																																																																																			G|0.985;C|0.015	0.015	strong		0.403	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
FLG	2312	hgsc.bcm.edu	37	1	152276490	152276490	+	Silent	SNP	C	C	T	rs199933055		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276490C>T	ENST00000368799.1	-	3	10907	c.10872G>A	c.(10870-10872)gaG>gaA	p.E3624E	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3624	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)			ATCCATGTCTCTCTCCTGCAC	0.547									Ichthyosis				c|||	1	0.000199681	0.0	0.0	5008	,	,		24918	0.0		0.0	False		,,,				2504	0.001				p.E3624E		Atlas-SNP	.											FLG,NS,carcinoma,-2,1	FLG	900	1	0			c.G10872A						scavenged	.						273.0	219.0	237.0					1																	152276490		2201	4296	6497	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ATGTCTCTCTCCT	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.10872G>A	1.37:g.152276490C>T		Somatic	401	0	0		WXS	Illumina HiSeq	Phase_I	631	9	0.0142631	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			C|0.999;G|0.001	.	weak		0.547	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FRMD4B	23150	hgsc.bcm.edu	37	3	69246129	69246129	+	Silent	SNP	A	A	G	rs78327349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:69246129A>G	ENST00000398540.3	-	13	1097	c.1014T>C	c.(1012-1014)gcT>gcC	p.A338A	FRMD4B_ENST00000542259.1_Silent_p.A284A|FRMD4B_ENST00000478263.1_5'UTR	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	338	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		GAGAAGAGTTAGCATACCATG	0.398													A|||	161	0.0321486	0.0893	0.0144	5008	,	,		19072	0.0149		0.0089	False		,,,				2504	0.0092				p.A338A		Atlas-SNP	.											.	FRMD4B	90	.	0			c.T1014C						PASS	.	A		367,3437		20,327,1555	104.0	102.0	103.0		1014	-1.2	1.0	3	dbSNP_132	103	34,8204		0,34,4085	no	coding-synonymous	FRMD4B	NM_015123.1		20,361,5640	GG,GA,AA		0.4127,9.6477,3.33		338/1035	69246129	401,11641	1902	4119	6021	SO:0001819	synonymous_variant	23150	exon13			AGAGTTAGCATAC	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.1014T>C	3.37:g.69246129A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_015123	Q8TAI3	Silent	SNP	ENST00000398540.3	37	CCDS46863.1																																																																																			A|0.976;G|0.024	0.024	strong		0.398	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1		
FUT6	2528	hgsc.bcm.edu	37	19	5831840	5831840	+	Missense_Mutation	SNP	C	C	T	rs17855739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5831840C>T	ENST00000318336.4	-	3	1933	c.739G>A	c.(739-741)Gag>Aag	p.E247K	FUT6_ENST00000286955.5_Missense_Mutation_p.E247K|FUT6_ENST00000527106.1_Missense_Mutation_p.E247K|FUT6_ENST00000524754.1_Missense_Mutation_p.E247K|FUT6_ENST00000592563.1_Missense_Mutation_p.E247K	NM_000150.2	NP_000141.1	P51993	FUT6_HUMAN	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	247			E -> K (found in alpha(1,3)- fucosyltransferase-deficient individuals; complete enzyme inactivation; dbSNP:rs17855739). {ECO:0000269|PubMed:11102976, ECO:0000269|PubMed:8175676}.		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						AAGGAGTTCTCGAAGGCCAGA	0.627													C|||	805	0.160743	0.351	0.0461	5008	,	,		17359	0.1319		0.0417	False		,,,				2504	0.137				p.E247K		Atlas-SNP	.											FUT6,NS,carcinoma,+2,1	FUT6	30	1	0			c.G739A	GRCh37	CM940795	FUT6	M	rs17855739	PASS	.	C	LYS/GLU,LYS/GLU	1273,3133	433.5+/-343.6	156,961,1086	88.0	88.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	739,739	2.0	0.9	19	dbSNP_123	88	389,8207	124.1+/-182.9	12,365,3921	no	missense,missense	FUT6	NM_000150.2,NM_001040701.1	56,56	168,1326,5007	TT,TC,CC		4.5254,28.8924,12.7826	benign,benign	247/360,247/360	5831840	1662,11340	2203	4298	6501	SO:0001583	missense	2528	exon3			AGTTCTCGAAGGC		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.739G>A	19.37:g.5831840C>T	ENSP00000313398:p.Glu247Lys	Somatic	375	0	0		WXS	Illumina HiSeq	Phase_I	376	166	0.441489	NM_000150	A6NEX0|D6W637|Q9UND8	Missense_Mutation	SNP	ENST00000318336.4	37	CCDS12152.1	278	0.12728937728937728	190	0.3861788617886179	18	0.049723756906077346	35	0.06118881118881119	35	0.04617414248021108	C	16.35	3.099891	0.56183	0.288924	0.045254	ENSG00000156413	ENST00000524754;ENST00000527106;ENST00000318336;ENST00000286955;ENST00000341530	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	3.07	1.97	0.26223	.	0.000000	0.64402	D	0.000016	T	0.00012	0.0000	H	0.99261	4.49	0.27631	P	0.9480265999999999	P;P	0.52170	0.951;0.917	P;P	0.58077	0.832;0.832	T	0.02352	-1.1172	9	0.72032	D	0.01	.	10.1858	0.42998	0.0:0.7931:0.2069:0.0	rs17855739	247;247	C9J8A2;P51993	.;FUT6_HUMAN	K	247	ENSP00000431708:E247K;ENSP00000432954:E247K;ENSP00000313398:E247K;ENSP00000286955:E247K	ENSP00000286955:E247K	E	-	1	0	FUT6	5782840	0.963000	0.33076	0.857000	0.33713	0.070000	0.16714	2.244000	0.43124	0.548000	0.28955	0.430000	0.28490	GAG	C|0.878;T|0.122	0.122	strong		0.627	FUT6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394218.2	NM_000150	
TNFRSF18	8784	hgsc.bcm.edu	37	1	1141824	1141824	+	Missense_Mutation	SNP	G	G	C	rs11466676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1141824G>C	ENST00000379268.2	-	1	247	c.128C>G	c.(127-129)aCg>aGg	p.T43R	TNFRSF18_ENST00000486728.1_5'Flank|TNFRSF18_ENST00000328596.6_Missense_Mutation_p.T43R|TNFRSF18_ENST00000379265.5_Missense_Mutation_p.T43R	NM_004195.2|NM_148902.1	NP_004186.1|NP_683700.1	Q9Y5U5	TNR18_HUMAN	tumor necrosis factor receptor superfamily, member 18	43			T -> R (in dbSNP:rs11466676).		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			lung(1)	1	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;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GTCCGTTCCCGTCCCAAGCAG	0.716													g|||	238	0.047524	0.1702	0.0173	5008	,	,		12979	0.0		0.001	False		,,,				2504	0.0				p.T43R	GBM(157;472 1934 13810 14591 35952)	Atlas-SNP	.											.	TNFRSF18	13	.	0			c.C128G						PASS	.	G	ARG/THR,ARG/THR,ARG/THR	308,3220		10,288,1466	4.0	5.0	5.0		128,128,128	2.1	0.0	1	dbSNP_120	5	2,7088		0,2,3543	no	missense,missense,missense	TNFRSF18	NM_004195.2,NM_148901.1,NM_148902.1	71,71,71	10,290,5009	CC,CG,GG		0.0282,8.7302,2.9196	benign,benign,benign	43/242,43/256,43/235	1141824	310,10308	1764	3545	5309	SO:0001583	missense	8784	exon1			GTTCCCGTCCCAA	AF125304	CCDS9.1, CCDS10.1, CCDS30552.1	1p36.3	2011-08-11			ENSG00000186891	ENSG00000186891		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11914	protein-coding gene	gene with protein product		603905				9177197, 10037686	Standard	NM_004195		Approved	AITR, GITR, CD357	uc001add.3	Q9Y5U5	OTTHUMG00000001414	ENST00000379268.2:c.128C>G	1.37:g.1141824G>C	ENSP00000368570:p.Thr43Arg	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	22	9	0.409091	NM_148902	B1AME1|O95851|Q5U0I4|Q9NYJ9	Missense_Mutation	SNP	ENST00000379268.2	37	CCDS10.1	84	0.038461538461538464	75	0.1524390243902439	6	0.016574585635359115	2	0.0034965034965034965	1	0.0013192612137203166	G	12.07	1.828233	0.32329	0.087302	2.82E-4	ENSG00000186891	ENST00000328596;ENST00000379268;ENST00000379265	T;T;T	0.60171	1.64;0.31;0.21	3.1	2.14	0.27477	.	0.907582	0.08998	U	0.863377	T	0.00524	0.0017	L	0.50333	1.59	0.80722	P	0.0	D;D;D	0.57571	0.98;0.98;0.98	P;P;P	0.52309	0.695;0.673;0.582	T	0.11084	-1.0602	9	0.87932	D	0	-4.6596	8.7668	0.34708	0.0:0.233:0.767:0.0	rs11466676	43;43;43	Q9Y5U5-2;Q9Y5U5;B1AME3	.;TNR18_HUMAN;.	R	43	ENSP00000328207:T43R;ENSP00000368570:T43R;ENSP00000368567:T43R	ENSP00000328207:T43R	T	-	2	0	TNFRSF18	1131687	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.161000	0.10026	0.563000	0.29222	0.462000	0.41574	ACG	G|0.955;C|0.045	0.045	strong		0.716	TNFRSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004083.2	NM_004195	
IQGAP3	128239	hgsc.bcm.edu	37	1	156526387	156526387	+	Missense_Mutation	SNP	C	C	G	rs11264498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156526387C>G	ENST00000361170.2	-	12	1238	c.1228G>C	c.(1228-1230)Gtg>Ctg	p.V410L		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	410			V -> L (in dbSNP:rs11264498).		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)					ACAGGGTACACTGGAGGCAGC	0.602													C|||	1894	0.378195	0.1407	0.5519	5008	,	,		17223	0.4286		0.6272	False		,,,				2504	0.2679				p.V410L		Atlas-SNP	.											.	IQGAP3	146	.	0			c.G1228C						PASS	.	C	LEU/VAL	1045,3361	383.5+/-324.9	126,793,1284	55.0	46.0	49.0		1228	5.5	1.0	1	dbSNP_120	49	5490,3110	655.3+/-401.2	1773,1944,583	yes	missense	IQGAP3	NM_178229.4	32	1899,2737,1867	GG,GC,CC		36.1628,23.7177,49.754	probably-damaging	410/1632	156526387	6535,6471	2203	4300	6503	SO:0001583	missense	128239	exon12			GGTACACTGGAGG	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.1228G>C	1.37:g.156526387C>G	ENSP00000354451:p.Val410Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	1032	0.4725274725274725	82	0.16666666666666666	207	0.5718232044198895	262	0.458041958041958	481	0.6345646437994723	C	23.0	4.361937	0.82353	0.237177	0.638372	ENSG00000183856	ENST00000361170	T	0.13089	2.62	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000001	T	0.26991	0.0661	L	0.58354	1.805	0.09310	P	0.9999999329442	D	0.64830	0.994	D	0.70716	0.97	T	0.01004	-1.1484	9	0.72032	D	0.01	-21.1507	18.0563	0.89365	0.0:1.0:0.0:0.0	rs11264498;rs17391967;rs52823677;rs57058839;rs11264498	410	Q86VI3	IQGA3_HUMAN	L	410	ENSP00000354451:V410L	ENSP00000354451:V410L	V	-	1	0	IQGAP3	154793011	1.000000	0.71417	0.988000	0.46212	0.445000	0.32107	5.769000	0.68865	2.589000	0.87451	0.491000	0.48974	GTG	C|0.513;G|0.487	0.487	strong		0.602	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240611	39240611	+	Silent	SNP	G	G	A	rs529043715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39240611G>A	ENST00000391417.4	+	1	153	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	51	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						GCTGCTGCAGGCCCCAGTGCT	0.647													g|||	99	0.0197684	0.0726	0.0029	5008	,	,		18224	0.0		0.001	False		,,,				2504	0.0				p.R51R		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,+1,2	KRTAP4-7	49	2	0			c.G153A						PASS	.						15.0	24.0	21.0					17																	39240611		691	1591	2282	SO:0001819	synonymous_variant	100132476	exon1			CTGCAGGCCCCAG	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.153G>A	17.37:g.39240611G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	176	35	0.198864	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	37	CCDS45673.1																																																																																			.	.	none		0.647	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
OAS3	4940	hgsc.bcm.edu	37	12	113386779	113386779	+	Missense_Mutation	SNP	C	C	G	rs2285933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113386779C>G	ENST00000228928.7	+	6	1322	c.1143C>G	c.(1141-1143)agC>agG	p.S381R	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	381	Linker.		S -> R (in dbSNP:rs2285933). {ECO:0000269|PubMed:15489334}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						GAGCAGGGAGCAAACCTCCCT	0.607													C|||	1405	0.280551	0.4092	0.379	5008	,	,		19978	0.1577		0.2565	False		,,,				2504	0.1881				p.S381R		Atlas-SNP	.											OAS3,brain,glioma,0,1	OAS3	63	1	0			c.C1143G						PASS	.	C	ARG/SER	1450,2514		249,952,781	37.0	41.0	40.0		1143	0.0	0.0	12	dbSNP_100	40	2178,6156		291,1596,2280	yes	missense	OAS3	NM_006187.2	110	540,2548,3061	GG,GC,CC		26.1339,36.5792,29.5007	benign	381/1088	113386779	3628,8670	1982	4167	6149	SO:0001583	missense	4940	exon6			AGGGAGCAAACCT	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.1143C>G	12.37:g.113386779C>G	ENSP00000228928:p.Ser381Arg	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	175	71	0.405714	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	621	0.28434065934065933	194	0.3943089430894309	117	0.32320441988950277	105	0.18356643356643357	205	0.2704485488126649	C	2.291	-0.362396	0.05103	0.365792	0.261339	ENSG00000111331	ENST00000228928;ENST00000323881	T	0.06687	3.27	3.0	0.0313	0.14170	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.26002	0.139	B	0.12156	0.007	T	0.47623	-0.9103	8	0.51188	T	0.08	.	3.3881	0.07278	0.0:0.52:0.2178:0.2622	rs2285933;rs2285933	381	Q9Y6K5	OAS3_HUMAN	R	381	ENSP00000228928:S381R	ENSP00000228928:S381R	S	+	3	2	OAS3	111871162	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.993000	0.03720	-0.002000	0.14469	-0.145000	0.13849	AGC	C|0.724;G|0.276	0.276	strong		0.607	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
MUC4	4585	hgsc.bcm.edu	37	3	195507780	195507780	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507780G>A	ENST00000463781.3	-	2	11130	c.10671C>T	c.(10669-10671)gaC>gaT	p.D3557D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D3557D	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)		CCGAGGAAGCGTCGGTGACAG	0.592																																					p.D3557D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	0			c.C10671T						scavenged	.						25.0	21.0	23.0					3																	195507780		653	1573	2226	SO:0001819	synonymous_variant	4585	exon2			GGAAGCGTCGGTG	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.10671C>T	3.37:g.195507780G>A		Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	183	52	0.284153	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																																																																																			.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MFSD4	148808	hgsc.bcm.edu	37	1	205561372	205561372	+	Silent	SNP	C	C	T	rs7529077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:205561372C>T	ENST00000367147.4	+	7	1347	c.1254C>T	c.(1252-1254)ttC>ttT	p.F418F	MFSD4_ENST00000536357.1_Silent_p.F331F|RNU6-418P_ENST00000384035.1_RNA|MFSD4_ENST00000539267.1_Silent_p.F418F	NM_181644.4	NP_857595.3	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing 4	418					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			GCAGCACCTTCCCCAGCATGC	0.637											OREG0014160	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	671	0.133986	0.2171	0.1311	5008	,	,		12809	0.0149		0.2187	False		,,,				2504	0.0593				p.F418F		Atlas-SNP	.											.	MFSD4	46	.	0			c.C1254T						PASS	.	C		958,3448	352.8+/-311.9	105,748,1350	89.0	67.0	75.0		1254	2.7	1.0	1	dbSNP_116	75	1940,6660	333.2+/-320.4	218,1504,2578	no	coding-synonymous	MFSD4	NM_181644.4		323,2252,3928	TT,TC,CC		22.5581,21.7431,22.282		418/515	205561372	2898,10108	2203	4300	6503	SO:0001819	synonymous_variant	148808	exon7			CACCTTCCCCAGC	BC036549	CCDS1455.1	1q32.1	2008-02-05			ENSG00000174514	ENSG00000174514			25433	protein-coding gene	gene with protein product							Standard	NM_181644		Approved	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004	uc001hcv.4	Q8N468	OTTHUMG00000037197	ENST00000367147.4:c.1254C>T	1.37:g.205561372C>T		Somatic	166	1	0.0060241	2153	WXS	Illumina HiSeq	Phase_I	176	176	1	NM_181644	B7Z8X3|Q6UY25|Q8NAY0|Q8TCP4	Silent	SNP	ENST00000367147.4	37	CCDS1455.1																																																																																			C|0.812;T|0.188	0.188	strong		0.637	MFSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090391.1	NM_181644	
TMIGD2	126259	hgsc.bcm.edu	37	19	4292597	4292597	+	Silent	SNP	C	C	T	rs888932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000600114.1_Silent_p.*163*|TMIGD2_ENST00000595645.1_Silent_p.*279*	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	40	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	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	
TEX15	56154	hgsc.bcm.edu	37	8	30702785	30702785	+	Missense_Mutation	SNP	T	T	C	rs61736163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:30702785T>C	ENST00000256246.2	-	1	3823	c.3749A>G	c.(3748-3750)aAc>aGc	p.N1250S		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1250					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		ATCACAATCGTTGCCTGTACT	0.328													T|||	747	0.149161	0.298	0.0677	5008	,	,		20077	0.0575		0.0626	False		,,,				2504	0.1892				p.N1250S		Atlas-SNP	.											.	TEX15	350	.	0			c.A3749G						PASS	.	T	SER/ASN	1136,3270	404.4+/-333.1	138,860,1205	83.0	79.0	80.0		3749	1.2	0.0	8	dbSNP_129	80	445,8155	133.8+/-191.2	10,425,3865	yes	missense	TEX15	NM_031271.3	46	148,1285,5070	CC,CT,TT		5.1744,25.783,12.1559	benign	1250/2790	30702785	1581,11425	2203	4300	6503	SO:0001583	missense	56154	exon1			CAATCGTTGCCTG	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.3749A>G	8.37:g.30702785T>C	ENSP00000256246:p.Asn1250Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	244	0.11172161172161173	140	0.2845528455284553	23	0.06353591160220995	37	0.06468531468531469	44	0.05804749340369393	T	0.403	-0.917217	0.02415	0.25783	0.051744	ENSG00000133863	ENST00000256246	T	0.21734	1.99	5.03	1.25	0.21368	.	0.574533	0.17844	N	0.160095	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.21452	0.056	B	0.18871	0.023	T	0.40794	-0.9544	9	0.87932	D	0	.	4.4223	0.11486	0.0:0.177:0.1673:0.6556	rs61736163	1250	Q9BXT5	TEX15_HUMAN	S	1250	ENSP00000256246:N1250S	ENSP00000256246:N1250S	N	-	2	0	TEX15	30822327	0.962000	0.33011	0.001000	0.08648	0.074000	0.17049	0.433000	0.21477	0.124000	0.18369	0.533000	0.62120	AAC	T|0.886;C|0.114	0.114	strong		0.328	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
EIF4EBP2	1979	hgsc.bcm.edu	37	10	72179746	72179746	+	Silent	SNP	C	C	T	rs1043098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	122	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	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	
CDC5L	988	hgsc.bcm.edu	37	6	44371714	44371714	+	Silent	SNP	C	C	T	rs6934058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	50	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	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		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417732	105417732	+	Silent	SNP	G	G	A	rs190986194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417732G>A	ENST00000333244.5	-	7	4175	c.4056C>T	c.(4054-4056)gaC>gaT	p.D1352D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1352						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)			GTGCAGACAGGTCCACGGAGG	0.597													.|||	283	0.0565096	0.0113	0.1297	5008	,	,		13768	0.0129		0.1153	False		,,,				2504	0.0501				p.D1352D		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4056T						PASS	.						126.0	107.0	114.0					14																	105417732		1812	2877	4689	SO:0001819	synonymous_variant	113146	exon7			AGACAGGTCCACG	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.4056C>T	14.37:g.105417732G>A		Somatic	363	0	0		WXS	Illumina HiSeq	Phase_I	258	105	0.406977	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.914;A|0.086	0.086	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TRIM39	56658	hgsc.bcm.edu	37	6	30309508	30309508	+	Silent	SNP	T	T	C	rs2074474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30309508T>C	ENST00000396547.1	+	8	1189	c.1029T>C	c.(1027-1029)ccT>ccC	p.P343P	TRIM39-RPP21_ENST00000513556.1_Silent_p.P225P|TRIM39_ENST00000376659.5_Silent_p.P313P|TRIM39_ENST00000376656.4_Silent_p.P343P|TRIM39_ENST00000396551.3_Silent_p.P313P|TRIM39_ENST00000396548.1_Silent_p.P313P|TRIM39_ENST00000540416.1_Silent_p.P313P			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	343	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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						CCCTGGACCCTGAGACAGCTC	0.562													T|||	1887	0.376797	0.3109	0.451	5008	,	,		20955	0.5119		0.2435	False		,,,				2504	0.411				p.P343P		Atlas-SNP	.											TRIM39_ENST00000376656,NS,malignant_melanoma,+2,1	TRIM39	56	1	0			c.T1029C						PASS	.	T	,,	852,2170		114,624,773	59.0	44.0	49.0		939,1029,939	-7.9	1.0	6	dbSNP_96	49	1327,4089		157,1013,1538	yes	coding-synonymous,coding-synonymous,coding-synonymous	TRIM39,TRIM39-RPP21	NM_001199119.1,NM_021253.3,NM_172016.2	,,	271,1637,2311	CC,CT,TT		24.5015,28.1932,25.8237	,,	313/504,343/519,313/489	30309508	2179,6259	1511	2708	4219	SO:0001819	synonymous_variant	56658	exon9			GGACCCTGAGACA	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.1029T>C	6.37:g.30309508T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_021253	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Silent	SNP	ENST00000396547.1	37	CCDS34377.1																																																																																			T|0.701;C|0.299	0.299	strong		0.562	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	
ITGAD	3681	hgsc.bcm.edu	37	16	31422071	31422071	+	Missense_Mutation	SNP	C	C	G	rs142278416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31422071C>G	ENST00000389202.2	+	12	1277	c.1228C>G	c.(1228-1230)Cta>Gta	p.L410V		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	410					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CTCCACCGAGCTAGCCCTGTG	0.667													c|||	38	0.00758786	0.0265	0.0043	5008	,	,		7588	0.0		0.0	False		,,,				2504	0.0				p.L410V		Atlas-SNP	.											.	ITGAD	154	.	0			c.C1228G						PASS	.	C	VAL/LEU	110,4284		2,106,2089	28.0	30.0	29.0		1228	1.0	0.0	16	dbSNP_134	29	1,8597		0,1,4298	yes	missense	ITGAD	NM_005353.2	32	2,107,6387	GG,GC,CC		0.0116,2.5034,0.8544	benign	410/1162	31422071	111,12881	2197	4299	6496	SO:0001583	missense	3681	exon12			ACCGAGCTAGCCC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.1228C>G	16.37:g.31422071C>G	ENSP00000373854:p.Leu410Val	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	190	89	0.468421	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	c	0.001	-2.980833	0.00046	0.025034	1.16E-4	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.15139	2.45	4.4	1.04	0.20106	.	.	.	.	.	T	0.01387	0.0045	N	0.01446	-0.86	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.001	T	0.40232	-0.9574	9	0.02654	T	1	.	7.4596	0.27287	0.0:0.3542:0.5324:0.1134	.	426;410	Q59H14;Q13349	.;ITAD_HUMAN	V	426;410	ENSP00000373854:L410V	ENSP00000373854:L410V	L	+	1	2	ITGAD	31329572	0.949000	0.32298	0.037000	0.18230	0.014000	0.08584	-0.348000	0.07740	0.286000	0.22352	0.197000	0.17608	CTA	C|0.991;G|0.009	0.009	strong		0.667	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
NUDCD1	84955	hgsc.bcm.edu	37	8	110301998	110301998	+	Missense_Mutation	SNP	T	T	C	rs2980618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110301998T>C	ENST00000239690.4	-	5	1179	c.805A>G	c.(805-807)Ata>Gta	p.I269V	NUDCD1_ENST00000427660.2_Missense_Mutation_p.I240V	NM_032869.3	NP_116258.2			NudC domain containing 1											breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(2)|skin(1)	25	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)			TTCTCTGATATGTCTTCATCC	0.299													T|||	1901	0.379593	0.177	0.4914	5008	,	,		12649	0.4603		0.3569	False		,,,				2504	0.5143				p.I269V		Atlas-SNP	.											.	NUDCD1	58	.	0			c.A805G						PASS	.	T	VAL/ILE,VAL/ILE	1006,3400	368.3+/-318.6	131,744,1328	57.0	58.0	58.0		718,805	1.5	1.0	8	dbSNP_101	58	3396,5204	500.8+/-375.3	655,2086,1559	yes	missense,missense	NUDCD1	NM_001128211.1,NM_032869.3	29,29	786,2830,2887	CC,CT,TT		39.4884,22.8325,33.8459	benign,benign	240/555,269/584	110301998	4402,8604	2203	4300	6503	SO:0001583	missense	84955	exon5			CTGATATGTCTTC	AF283302	CCDS6312.1, CCDS47910.1	8q23	2005-02-07			ENSG00000120526	ENSG00000120526			24306	protein-coding gene	gene with protein product		606109				11416219	Standard	NM_032869		Approved	CML66, FLJ14991	uc003ynb.4	Q96RS6	OTTHUMG00000164931	ENST00000239690.4:c.805A>G	8.37:g.110301998T>C	ENSP00000239690:p.Ile269Val	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	256	98	0.382812	NM_032869		Missense_Mutation	SNP	ENST00000239690.4	37	CCDS6312.1	825	0.37774725274725274	89	0.18089430894308944	168	0.46408839779005523	280	0.48951048951048953	288	0.37994722955145116	T	2.496	-0.316379	0.05422	0.228325	0.394884	ENSG00000120526	ENST00000239690;ENST00000427660	T;T	0.16196	2.37;2.36	5.69	1.55	0.23275	HSP20-like chaperone (1);	0.308209	0.41194	D	0.000923	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.46133	-0.9213	9	0.30078	T	0.28	-0.2599	5.01	0.14308	0.1016:0.067:0.2299:0.6015	rs2980618;rs17365593;rs17846354;rs17859390;rs52832306;rs59034628;rs2980618	182;269;240	Q96RS6-3;Q96RS6;Q96RS6-2	.;NUDC1_HUMAN;.	V	269;240	ENSP00000239690:I269V;ENSP00000410707:I240V	ENSP00000239690:I269V	I	-	1	0	NUDCD1	110371174	0.164000	0.22935	0.979000	0.43373	0.958000	0.62258	0.454000	0.21827	0.388000	0.25054	0.533000	0.62120	ATA	T|0.657;C|0.343	0.343	strong		0.299	NUDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380996.1	NM_032869	
SLC9A4	389015	hgsc.bcm.edu	37	2	103095531	103095531	+	Silent	SNP	T	T	C	rs61731286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:103095531T>C	ENST00000295269.4	+	2	947	c.490T>C	c.(490-492)Ttg>Ctg	p.L164L		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	164					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GTGGGCAGTATTGGGGGCCCT	0.602													C|||	747	0.149161	0.2958	0.0648	5008	,	,		16740	0.1429		0.0865	False		,,,				2504	0.0818				p.L164L		Atlas-SNP	.											.	SLC9A4	115	.	0			c.T490C						PASS	.	C		987,3419	731.9+/-410.3	121,745,1337	50.0	49.0	49.0		490	2.7	0.2	2	dbSNP_129	49	577,8023	793.0+/-407.5	18,541,3741	no	coding-synonymous	SLC9A4	NM_001011552.3		139,1286,5078	CC,CT,TT		6.7093,22.4013,12.0252		164/799	103095531	1564,11442	2203	4300	6503	SO:0001819	synonymous_variant	389015	exon2			GCAGTATTGGGGG		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.490T>C	2.37:g.103095531T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_001011552	Q69YK0	Silent	SNP	ENST00000295269.4	37	CCDS33264.1																																																																																			T|0.874;C|0.126	0.126	strong		0.602	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416344	105416344	+	Missense_Mutation	SNP	T	T	G	rs368838079		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416344T>G	ENST00000333244.5	-	7	5563	c.5444A>C	c.(5443-5445)gAt>gCt	p.D1815A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1815						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)			GGCAGTCACATCCTTGTCGGC	0.612																																					p.D1815A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A5444C						PASS	.	T	ALA/ASP	15,3901		2,11,1945	157.0	191.0	180.0		5444	0.1	0.0	14		180	0,8254		0,0,4127	no	missense	AHNAK2	NM_138420.2	126	2,11,6072	GG,GT,TT		0.0,0.383,0.1233	benign	1815/5796	105416344	15,12155	1958	4127	6085	SO:0001583	missense	113146	exon7			GTCACATCCTTGT	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.5444A>C	14.37:g.105416344T>G	ENSP00000353114:p.Asp1815Ala	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	301	16	0.0531561	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	13.76	2.332517	0.41297	0.00383	0.0	ENSG00000185567	ENST00000333244	T	0.01947	4.54	4.3	0.0484	0.14285	.	.	.	.	.	T	0.04861	0.0131	M	0.92317	3.295	0.09310	N	1	B	0.33637	0.42	B	0.25506	0.061	T	0.18524	-1.0334	9	0.34782	T	0.22	-8.5499	7.3574	0.26727	0.0:0.0901:0.4093:0.5005	.	1815	Q8IVF2	AHNK2_HUMAN	A	1815	ENSP00000353114:D1815A	ENSP00000353114:D1815A	D	-	2	0	AHNAK2	104487389	0.291000	0.24352	0.004000	0.12327	0.019000	0.09904	2.523000	0.45580	0.079000	0.16929	0.374000	0.22700	GAT	.	.	weak		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ARAP3	64411	hgsc.bcm.edu	37	5	141036337	141036337	+	Silent	SNP	A	A	G	rs7703648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141036337A>G	ENST00000239440.4	-	26	3668	c.3603T>C	c.(3601-3603)gcT>gcC	p.A1201A	ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000513878.1_Silent_p.A863A|ARAP3_ENST00000508305.1_Silent_p.A1032A	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1201	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				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)	p.A1201A(1)		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						AGAGCAGGGAAGCTGAGCAGG	0.577													G|||	2411	0.48143	0.7065	0.4885	5008	,	,		18041	0.3889		0.4314	False		,,,				2504	0.319				p.A1201A		Atlas-SNP	.											ARAP3,NS,carcinoma,0,1	ARAP3	139	1	1	Substitution - coding silent(1)	stomach(1)	c.T3603C						PASS	.	G		2873,1533	476.8+/-357.7	935,1003,265	40.0	40.0	40.0		3603	-0.1	1.0	5	dbSNP_116	40	3475,5125	626.4+/-397.8	733,2009,1558	no	coding-synonymous	ARAP3	NM_022481.5		1668,3012,1823	GG,GA,AA		40.407,34.7935,48.8082		1201/1545	141036337	6348,6658	2203	4300	6503	SO:0001819	synonymous_variant	64411	exon26			CAGGGAAGCTGAG	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.3603T>C	5.37:g.141036337A>G		Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	37	CCDS4266.1																																																																																			A|0.497;G|0.503	0.503	strong		0.577	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
MCEE	84693	hgsc.bcm.edu	37	2	71351403	71351403	+	Missense_Mutation	SNP	C	C	A	rs6748672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71351403C>A	ENST00000244217.5	-	2	328	c.311G>T	c.(310-312)cGt>cTt	p.R104L	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	104			R -> L (in dbSNP:rs6748672). {ECO:0000269|PubMed:15489334}.		cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)			kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						TGGACTGTCACGTCCCAATGG	0.428													C|||	1009	0.201478	0.2277	0.1729	5008	,	,		17794	0.2282		0.1342	False		,,,				2504	0.228				p.R104L		Atlas-SNP	.											MCEE,NS,carcinoma,-1,1	MCEE	19	1	0			c.G311T						PASS	.	C	LEU/ARG	1003,3403	373.4+/-320.8	113,777,1313	80.0	76.0	77.0		311	-4.6	0.0	2	dbSNP_116	77	1449,7151	277.2+/-292.7	121,1207,2972	yes	missense	MCEE	NM_032601.3	102	234,1984,4285	AA,AC,CC		16.8488,22.7644,18.8528	benign	104/177	71351403	2452,10554	2203	4300	6503	SO:0001583	missense	84693	exon2			CTGTCACGTCCCA	AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"""glyoxalase domain containing 2"""	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.311G>T	2.37:g.71351403C>A	ENSP00000244217:p.Arg104Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	151	74	0.490066	NM_032601	Q53TP1|Q8WW63	Missense_Mutation	SNP	ENST00000244217.5	37	CCDS1915.1	377	0.17261904761904762	108	0.21951219512195122	61	0.1685082872928177	102	0.17832167832167833	106	0.13984168865435356	C	10.04	1.241494	0.22711	0.227644	0.168488	ENSG00000124370	ENST00000244217;ENST00000494660;ENST00000486135	T;T;T	0.64438	-0.1;-0.1;-0.1	5.38	-4.61	0.03380	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.710167	0.14406	N	0.321551	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B	0.14438	0.01	B	0.10450	0.005	T	0.06698	-1.0812	9	0.62326	D	0.03	-12.157	6.8041	0.23768	0.1109:0.3619:0.0:0.5272	rs6748672;rs17851835;rs52804383;rs58491237;rs6748672	104	Q96PE7	MCEE_HUMAN	L	104;9;9	ENSP00000244217:R104L;ENSP00000437361:R9L;ENSP00000441569:R9L	ENSP00000244217:R104L	R	-	2	0	MCEE	71204911	0.658000	0.27402	0.000000	0.03702	0.217000	0.24651	0.803000	0.27083	-1.053000	0.03218	-0.259000	0.10710	CGT	C|0.817;A|0.183	0.183	strong		0.428	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601	
TMCC3	57458	hgsc.bcm.edu	37	12	94972290	94972290	+	Silent	SNP	C	C	T	rs2270893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:94972290C>T	ENST00000261226.4	-	3	1142	c.1011G>A	c.(1009-1011)gaG>gaA	p.E337E	TMCC3_ENST00000551457.1_Silent_p.E306E	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	337						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						GCAGCTGGTCCTCCAGTCGCT	0.542													C|||	2604	0.519968	0.5234	0.5634	5008	,	,		16768	0.4653		0.5378	False		,,,				2504	0.5225				p.E337E		Atlas-SNP	.											TMCC3,NS,carcinoma,0,1	TMCC3	63	1	0			c.G1011A						PASS	.	C		2276,2130	598.6+/-389.1	590,1096,517	71.0	57.0	62.0		1011	-1.1	1.0	12	dbSNP_100	62	4626,3974	600.1+/-394.2	1263,2100,937	no	coding-synonymous	TMCC3	NM_020698.2		1853,3196,1454	TT,TC,CC		46.2093,48.3432,46.9322		337/478	94972290	6902,6104	2203	4300	6503	SO:0001819	synonymous_variant	57458	exon3			CTGGTCCTCCAGT	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"""Transmembrane and coiled-coil domain containing"""	29199	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 3"""			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.1011G>A	12.37:g.94972290C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_020698	Q8IWB2	Silent	SNP	ENST00000261226.4	37	CCDS31877.1																																																																																			C|0.474;T|0.526	0.526	strong		0.542	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110007834	110007834	+	Silent	SNP	T	T	C	rs78240010	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:110007834T>C	ENST00000278590.3	+	2	519	c.468T>C	c.(466-468)ccT>ccC	p.P156P	ZC3H12C_ENST00000528673.1_Silent_p.P157P|ZC3H12C_ENST00000453089.2_Silent_p.P125P	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	156							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		AGAAACCACCTGATGTGGTGC	0.413													N|||	66	0.0131789	0.0431	0.0043	5008	,	,		22894	0.003		0.0	False		,,,				2504	0.0031				p.P156P		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.T468C						PASS	.	C		127,3593		4,119,1737	71.0	66.0	67.0		468	-8.4	0.9	11	dbSNP_132	67	0,8192		0,0,4096	no	coding-synonymous	ZC3H12C	NM_033390.1		4,119,5833	CC,CT,TT		0.0,3.414,1.0662		156/884	110007834	127,11785	1860	4096	5956	SO:0001819	synonymous_variant	85463	exon2			ACCACCTGATGTG		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.468T>C	11.37:g.110007834T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	37	CCDS44727.1																																																																																			T|0.992;C|0.008	0.008	strong		0.413	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
PABPC3	5042	hgsc.bcm.edu	37	13	25671795	25671795	+	Missense_Mutation	SNP	C	C	T	rs113416318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25671795C>T	ENST00000281589.3	+	1	1496	c.1459C>T	c.(1459-1461)Cgt>Tgt	p.R487C		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	487					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AGTGGGTCCACGTCctgcagc	0.522													c|||	175	0.0349441	0.0537	0.0403	5008	,	,		21647	0.0119		0.0159	False		,,,				2504	0.0491				p.R487C		Atlas-SNP	.											PABPC3,rectum,carcinoma,0,1	PABPC3	129	1	0			c.C1459T						scavenged	.																																			SO:0001583	missense	5042	exon1			GGTCCACGTCCTG	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1459C>T	13.37:g.25671795C>T	ENSP00000281589:p.Arg487Cys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	5	0.0442478	NM_030979	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.862076	0.51482	.	.	ENSG00000151846	ENST00000281589	T	0.31247	1.5	0.875	0.875	0.19130	.	0.135300	0.32190	U	0.006459	T	0.29556	0.0737	L	0.59436	1.845	0.58432	D	0.999997	D	0.58970	0.984	P	0.45660	0.489	T	0.12630	-1.0540	10	0.72032	D	0.01	.	7.5489	0.27783	0.0:1.0:0.0:0.0	.	487	Q9H361	PABP3_HUMAN	C	487	ENSP00000281589:R487C	ENSP00000281589:R487C	R	+	1	0	PABPC3	24569795	1.000000	0.71417	0.944000	0.38274	0.640000	0.38277	4.773000	0.62331	0.759000	0.33084	0.313000	0.20887	CGT	C|0.988;T|0.012	0.012	strong		0.522	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
PTAFR	5724	hgsc.bcm.edu	37	1	28476520	28476520	+	Missense_Mutation	SNP	T	T	C	rs5939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:28476520T>C	ENST00000373857.3	-	2	1647	c.1013A>G	c.(1012-1014)aAt>aGt	p.N338S	PTAFR_ENST00000305392.3_Missense_Mutation_p.N338S|PTAFR_ENST00000539896.1_Missense_Mutation_p.N338S	NM_000952.4|NM_001164722.2|NM_001164723.2	NP_000943.1|NP_001158194.1|NP_001158195.1	P25105	PTAFR_HUMAN	platelet-activating factor receptor	338			N -> S (in dbSNP:rs5939). {ECO:0000269|PubMed:10391209}.		chemotaxis (GO:0006935)|cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|inositol trisphosphate biosynthetic process (GO:0032959)|interferon-gamma-mediated signaling pathway (GO:0060333)|phosphatidylinositol-mediated signaling (GO:0048015)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|phospholipid binding (GO:0005543)|platelet activating factor receptor activity (GO:0004992)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|stomach(1)	15		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)		TTTGAGGGAATTGCCAGGGAT	0.527													T|||	120	0.0239617	0.0862	0.0086	5008	,	,		21965	0.0		0.0	False		,,,				2504	0.0				p.N338S		Atlas-SNP	.											.	PTAFR	30	.	0			c.A1013G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN	324,4082	173.4+/-203.2	12,300,1891	100.0	107.0	105.0		1013,1013,1013,1013	-1.5	0.0	1	dbSNP_52	105	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense,missense	PTAFR	NM_000952.4,NM_001164721.1,NM_001164722.2,NM_001164723.2	46,46,46,46	12,307,6184	CC,CT,TT		0.0814,7.3536,2.545	benign,benign,benign,benign	338/343,338/343,338/343,338/343	28476520	331,12675	2203	4300	6503	SO:0001583	missense	5724	exon3			AGGGAATTGCCAG	BC063000	CCDS318.1	1p35-p34.3	2012-08-20			ENSG00000169403	ENSG00000169403		"""GPCR / Class A : Platelet-activating factor receptors"""	9582	protein-coding gene	gene with protein product		173393				1322356	Standard	NM_001164721		Approved		uc001bpl.3	P25105	OTTHUMG00000003953	ENST00000373857.3:c.1013A>G	1.37:g.28476520T>C	ENSP00000362965:p.Asn338Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	151	68	0.450331	NM_001164723	A3KMC8|A8K2H5	Missense_Mutation	SNP	ENST00000373857.3	37	CCDS318.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	T	3.748	-0.052169	0.07362	0.073536	8.14E-4	ENSG00000169403	ENST00000373857;ENST00000539896;ENST00000305392	T;T;T	0.70399	-0.48;-0.48;-0.48	5.38	-1.47	0.08772	.	1.433670	0.04726	N	0.420206	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04495	-1.0947	10	0.07813	T	0.8	.	1.6592	0.02787	0.1391:0.3175:0.1355:0.408	rs5939;rs5939	338	P25105	PTAFR_HUMAN	S	338	ENSP00000362965:N338S;ENSP00000442658:N338S;ENSP00000301974:N338S	ENSP00000301974:N338S	N	-	2	0	PTAFR	28349107	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.242000	0.08928	-0.555000	0.06142	-0.418000	0.06021	AAT	T|0.975;C|0.025	0.025	strong		0.527	PTAFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011258.1	NM_000952	
ATG16L1	55054	hgsc.bcm.edu	37	2	234183368	234183368	+	Missense_Mutation	SNP	A	A	G	rs2241880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234183368A>G	ENST00000392017.4	+	9	1155	c.898A>G	c.(898-900)Act>Gct	p.T300A	ATG16L1_ENST00000498620.1_3'UTR|SCARNA5_ENST00000516201.1_RNA|ATG16L1_ENST00000373525.5_Missense_Mutation_p.T156A|ATG16L1_ENST00000392020.4_Missense_Mutation_p.T281A|ATG16L1_ENST00000392018.1_Missense_Mutation_p.T317A|ATG16L1_ENST00000347464.5_Missense_Mutation_p.T137A	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	300			T -> A (associated with susceptibility to IBD10; has no effect on the stability of the protein; enhances the cleavage and the degradation mediated by activated CASP3; results in reduced autophagy and defective clearance of intestinal pathogens; dbSNP:rs2241880). {ECO:0000269|PubMed:15620219}.		autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		CAATGTGGATACTCATCCTGG	0.473													A|||	1983	0.395966	0.3101	0.3213	5008	,	,		21225	0.3224		0.5368	False		,,,				2504	0.4959				p.T300A		Atlas-SNP	.											.	ATG16L1	83	.	0			c.A898G	GRCh37	CM070026	ATG16L1	M	rs2241880	PASS	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	1428,2978	465.9+/-354.3	234,960,1009	181.0	149.0	160.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	646,550,841,898,409	-11.4	0.0	2	dbSNP_98	160	4506,4094	592.4+/-393.0	1198,2110,992	yes	missense,missense,missense,missense,missense	ATG16L1	NM_001190266.1,NM_001190267.1,NM_017974.3,NM_030803.6,NM_198890.2	58,58,58,58,58	1432,3070,2001	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	47.6047,32.4103,45.6251	benign,benign,benign,benign,benign	216/524,184/492,281/589,300/608,137/445	234183368	5934,7072	2203	4300	6503	SO:0001583	missense	55054	exon9			GTGGATACTCATC	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"""WD repeat domain containing"""	21498	protein-coding gene	gene with protein product		610767	"""APG16 autophagy 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like 1 (S. cerevisiae)"""	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.898A>G	2.37:g.234183368A>G	ENSP00000375872:p.Thr300Ala	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	198	106	0.535354	NM_030803	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Missense_Mutation	SNP	ENST00000392017.4	37	CCDS2503.2	851	0.38965201465201466	123	0.25	136	0.3756906077348066	190	0.3321678321678322	402	0.5303430079155673	A	10.98	1.504884	0.26949	0.324103	0.523953	ENSG00000085978	ENST00000392017;ENST00000347464;ENST00000444735;ENST00000373525;ENST00000419681;ENST00000392020;ENST00000392018	T;T;T;T;T;T;T	0.48522	0.88;0.92;1.09;0.99;1.71;0.81;0.91	5.71	-11.4	0.00090	WD40 repeat-like-containing domain (1);	1.946940	0.02287	N	0.069914	T	0.00012	0.0000	N	0.04203	-0.255	0.47341	P	6.049999999999667E-4	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.10450	0.0;0.001;0.005;0.0;0.001	T	0.27536	-1.0071	9	0.14252	T	0.57	.	12.6604	0.56811	0.1798:0.4806:0.3396:0.0	rs2241880;rs17607702;rs52836811;rs57853061;rs2241880	254;281;156;300;137	B7ZLM5;Q676U5-2;Q676U5-4;Q676U5;A3EXL0	.;.;.;A16L1_HUMAN;.	A	300;137;173;156;137;281;317	ENSP00000375872:T300A;ENSP00000318259:T137A;ENSP00000409215:T173A;ENSP00000362625:T156A;ENSP00000398773:T137A;ENSP00000375875:T281A;ENSP00000375873:T317A	ENSP00000318259:T137A	T	+	1	0	ATG16L1	233848107	0.000000	0.05858	0.001000	0.08648	0.985000	0.73830	-0.395000	0.07287	-1.999000	0.00967	0.528000	0.53228	ACT	G|0.422;N|0.000	0.422	strong		0.473	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974	
PREX2	80243	hgsc.bcm.edu	37	8	68968166	68968166	+	Silent	SNP	C	C	A	rs1434774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:68968166C>A	ENST00000288368.4	+	10	1472	c.1195C>A	c.(1195-1197)Cga>Aga	p.R399R	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	399	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						GATCAAAGACCGAAAGAGAAA	0.398													A|||	2813	0.561701	0.8865	0.4755	5008	,	,		18944	0.2688		0.5239	False		,,,				2504	0.5245				p.R399R		Atlas-SNP	.											PREX2_ENST00000354677,NS,malignant_melanoma,-1,2	PREX2	614	2	0			c.C1195A						PASS	.	A	,	3625,781	314.7+/-293.7	1503,619,81	117.0	128.0	124.0		1195,1195	3.2	1.0	8	dbSNP_88	124	4214,4386	583.1+/-391.5	1038,2138,1124	no	coding-synonymous,coding-synonymous	PREX2	NM_024870.2,NM_025170.4	,	2541,2757,1205	AA,AC,CC		49.0,17.7258,39.7278	,	399/1607,399/980	68968166	7839,5167	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon10			AAAGACCGAAAGA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1195C>A	8.37:g.68968166C>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	83	26	0.313253	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			C|0.420;A|0.580	0.580	strong		0.398	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
TRAPPC4	51399	hgsc.bcm.edu	37	11	118895686	118895686	+	IGR	SNP	C	C	T	rs8192696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118895686C>T	ENST00000533632.1	+	0	1759				SLC37A4_ENST00000525102.1_5'UTR|SLC37A4_ENST00000545985.1_Silent_p.T408T|SLC37A4_ENST00000330775.7_Silent_p.T429T|SLC37A4_ENST00000357590.5_Silent_p.T430T|SLC37A4_ENST00000538950.1_Silent_p.T335T|TRAPPC4_ENST00000533058.1_Missense_Mutation_p.P234L	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4						dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)				NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		AGAAGGCAGCCGTGCTGGCCG	0.592													T|||	1241	0.247804	0.3638	0.2161	5008	,	,		19263	0.0823		0.2157	False		,,,				2504	0.317				p.T430T		Atlas-SNP	.											.	SLC37A4	19	.	0			c.G1290A						PASS	.	T	,,,,	1363,2679		231,901,889	47.0	54.0	51.0		1225,1291,1006,1225,1225	-0.1	0.9	11	dbSNP_117	51	1809,6553		200,1409,2572	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC37A4	NM_001164277.1,NM_001164278.1,NM_001164279.1,NM_001164280.1,NM_001467.5	,,,,	431,2310,3461	TT,TC,CC		21.6336,33.7209,25.5724	,,,,	408/430,430/452,335/357,408/430,408/430	118895686	3172,9232	2021	4181	6202	SO:0001628	intergenic_variant	2542	exon12			GGCAGCCGTGCTG	AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"""Trafficking protein particle complex"""	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296			11.37:g.118895686C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	105	44	0.419048	NM_001164278	A8K3A5|B4DME1	Silent	SNP	ENST00000533632.1	37	CCDS8407.1	455	0.20833333333333334	179	0.3638211382113821	83	0.2292817679558011	36	0.06293706293706294	157	0.20712401055408972	T	10.78	1.446975	0.25987	0.337209	0.216336	ENSG00000196655	ENST00000533058	T	0.51071	0.72	5.27	-0.0512	0.13827	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.48185	P	3.9999999999995595E-4	.	.	.	.	.	.	T	0.35871	-0.9771	5	0.87932	D	0	-10.0	9.1911	0.37200	0.0:0.1376:0.3931:0.4693	rs8192696;rs17849572;rs17849775;rs57728725;rs8192696	.	.	.	L	234	ENSP00000432920:P234L	ENSP00000432920:P234L	P	+	2	0	TRAPPC4	118400896	0.000000	0.05858	0.928000	0.36995	0.888000	0.51559	-1.146000	0.03191	-0.115000	0.11915	-1.466000	0.01016	CCG	C|0.768;T|0.232	0.232	strong		0.592	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146	
ZNF835	90485	hgsc.bcm.edu	37	19	57176304	57176304	+	Missense_Mutation	SNP	T	T	G	rs12460400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	114	0	0		WXS	Illumina HiSeq	Phase_I	101	40	0.39604	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	
OR4D9	390199	hgsc.bcm.edu	37	11	59282651	59282651	+	Missense_Mutation	SNP	C	C	T	rs76276934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59282651C>T	ENST00000329328.3	+	1	266	c.266C>T	c.(265-267)aCa>aTa	p.T89I		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						CTATCAGAGACAAAAACCATC	0.483													c|||	108	0.0215655	0.0802	0.0029	5008	,	,		20793	0.0		0.0	False		,,,				2504	0.0				p.T89I		Atlas-SNP	.											.	OR4D9	47	.	0			c.C266T						PASS	.	C	ILE/THR	263,4139	149.5+/-183.7	9,245,1947	122.0	118.0	119.0		266	-6.1	0.0	11	dbSNP_131	119	1,8589		0,1,4294	yes	missense	OR4D9	NM_001004711.1	89	9,246,6241	TT,TC,CC		0.0116,5.9746,2.032	benign	89/315	59282651	264,12728	2201	4295	6496	SO:0001583	missense	390199	exon1			CAGAGACAAAAAC	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"""GPCR / Class A : Olfactory receptors"""	15178	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily D, member 9 pseudogene"""				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.266C>T	11.37:g.59282651C>T	ENSP00000328563:p.Thr89Ile	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	C	1.435	-0.569257	0.03910	0.059746	1.16E-4	ENSG00000172742	ENST00000329328	T	0.01397	4.94	4.02	-6.07	0.02158	GPCR, rhodopsin-like superfamily (1);	0.913714	0.08973	U	0.866909	T	0.00039	0.0001	L	0.39085	1.19	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46076	-0.9217	10	0.52906	T	0.07	.	2.2328	0.04001	0.3788:0.3173:0.1962:0.1076	.	89	Q8NGE8	OR4D9_HUMAN	I	89	ENSP00000328563:T89I	ENSP00000328563:T89I	T	+	2	0	OR4D9	59039227	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.882000	0.00714	-1.736000	0.01352	-1.265000	0.01443	ACA	C|0.979;T|0.021	0.021	strong		0.483	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711	
SPATC1L	84221	hgsc.bcm.edu	37	21	47588365	47588365	+	Missense_Mutation	SNP	G	G	A	rs73908565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47588365G>A	ENST00000291672.5	-	3	1462	c.401C>T	c.(400-402)tCc>tTc	p.S134F	SPATC1L_ENST00000330205.6_5'UTR	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	134																	CAGGAGCGGGGACAGCTTCCT	0.647													G|||	123	0.0245607	0.09	0.0058	5008	,	,		16558	0.0		0.0	False		,,,				2504	0.0				p.S134F		Atlas-SNP	.											.	.	.	.	0			c.C401T						PASS	.	G	PHE/SER,	106,1278		7,92,593	49.0	52.0	51.0		401,	3.2	0.7	21	dbSNP_130	51	1,3181		0,1,1590	yes	missense,utr-5	C21orf56	NM_001142854.1,NM_032261.4	155,	7,93,2183	AA,AG,GG		0.0314,7.659,2.3434	probably-damaging,	134/341,	47588365	107,4459	692	1591	2283	SO:0001583	missense	84221	exon3			AGCGGGGACAGCT	BC009497	CCDS13732.1, CCDS46653.1	21q22.3	2013-01-21	2012-11-12	2012-11-12	ENSG00000160284	ENSG00000160284			1298	protein-coding gene	gene with protein product	"""speriolin-like protein"""	612412	"""chromosome 21 open reading frame 56"""	C21orf56			Standard	NM_032261		Approved		uc011afu.2	Q9H0A9	OTTHUMG00000090487	ENST00000291672.5:c.401C>T	21.37:g.47588365G>A	ENSP00000291672:p.Ser134Phe	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	127	57	0.448819	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Missense_Mutation	SNP	ENST00000291672.5	37	CCDS46653.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	G	10.80	1.453781	0.26161	0.07659	3.14E-4	ENSG00000160284	ENST00000291672	T	0.55588	0.51	5.21	3.23	0.37069	.	0.477138	0.17215	N	0.182544	T	0.02193	0.0068	L	0.29908	0.895	0.09310	N	0.999992	P	0.44195	0.828	P	0.45138	0.471	T	0.00449	-1.1732	10	0.31617	T	0.26	-26.6257	12.7958	0.57558	0.0:0.3352:0.6648:0.0	.	134	Q9H0A9	CU056_HUMAN	F	134	ENSP00000291672:S134F	ENSP00000291672:S134F	S	-	2	0	C21orf56	46412793	0.073000	0.21202	0.739000	0.30968	0.521000	0.34408	0.543000	0.23237	1.164000	0.42652	0.467000	0.42956	TCC	G|0.978;A|0.022	0.022	strong		0.647	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
CHCHD3	54927	hgsc.bcm.edu	37	7	132470419	132470419	+	Silent	SNP	G	G	A	rs147050556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:132470419G>A	ENST00000262570.5	-	8	807	c.663C>T	c.(661-663)agC>agT	p.S221S	CHCHD3_ENST00000476546.1_5'UTR|CHCHD3_ENST00000448878.1_Silent_p.S226S	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	221					inner mitochondrial membrane organization (GO:0007007)|mitochondrial fusion (GO:0008053)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein complex scaffold (GO:0032947)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	7						TCTCAAGCATGCTCTGCAAGA	0.353													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19096	0.0		0.0	False		,,,				2504	0.0				p.S221S		Atlas-SNP	.											.	CHCHD3	21	.	0			c.C663T						PASS	.	G		18,4388	25.3+/-52.1	0,18,2185	100.0	95.0	97.0		663	5.8	1.0	7	dbSNP_134	97	0,8600		0,0,4300	no	coding-synonymous	CHCHD3	NM_017812.2		0,18,6485	AA,AG,GG		0.0,0.4085,0.1384		221/228	132470419	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	54927	exon8			AAGCATGCTCTGC	BC011596	CCDS5828.1	7q33	2012-10-02			ENSG00000106554	ENSG00000106554		"""Coiled-coil-helix-coiled-coil-helix domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21906	protein-coding gene	gene with protein product	"""mitochondrial inner membrane organizing system 3"", ""protein phosphatase 1, regulatory subunit 22"""	613748				22252321, 23019327, 21081504, 17624330	Standard	NM_017812		Approved	FLJ20420, MINOS3, PPP1R22	uc003vre.3	Q9NX63	OTTHUMG00000155231	ENST00000262570.5:c.663C>T	7.37:g.132470419G>A		Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	324	186	0.574074	NM_017812		Silent	SNP	ENST00000262570.5	37	CCDS5828.1																																																																																			G|0.998;A|0.002	0.002	strong		0.353	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812	
NOL10	79954	hgsc.bcm.edu	37	2	10729257	10729257	+	Missense_Mutation	SNP	T	T	C	rs34359340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10729257T>C	ENST00000381685.5	-	19	1861	c.1756A>G	c.(1756-1758)Aca>Gca	p.T586A	NOL10_ENST00000345985.3_Missense_Mutation_p.T536A|NOL10_ENST00000538384.1_Missense_Mutation_p.T560A|NOL10_ENST00000542668.1_Missense_Mutation_p.T536A|AC092687.5_ENST00000414538.1_RNA	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	586						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		TTTAGGACTGTCTGCTGGTCC	0.473													T|||	179	0.0357428	0.1301	0.0101	5008	,	,		18410	0.0		0.0	False		,,,				2504	0.0				p.T586A		Atlas-SNP	.											.	NOL10	22	.	0			c.A1756G						PASS	.	T	ALA/THR	471,3935	223.0+/-239.6	22,427,1754	167.0	172.0	170.0		1756	2.9	1.0	2	dbSNP_126	170	0,8600		0,0,4300	yes	missense	NOL10	NM_024894.2	58	22,427,6054	CC,CT,TT		0.0,10.69,3.6214	probably-damaging	586/689	10729257	471,12535	2203	4300	6503	SO:0001583	missense	79954	exon19			GGACTGTCTGCTG	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1756A>G	2.37:g.10729257T>C	ENSP00000371101:p.Thr586Ala	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	247	116	0.469636	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Missense_Mutation	SNP	ENST00000381685.5	37	CCDS1673.2	59	0.027014652014652016	57	0.11585365853658537	2	0.0055248618784530384	0	0.0	0	0.0	T	4.966	0.179358	0.09443	0.1069	0.0	ENSG00000115761	ENST00000345985;ENST00000381685;ENST00000542668;ENST00000538384	T;T;T;T	0.40756	1.02;2.21;1.61;2.21	5.35	2.93	0.34026	.	0.131457	0.64402	N	0.000001	T	0.00496	0.0016	M	0.65975	2.015	0.58432	D	0.999992	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.04737	-1.0930	10	0.07644	T	0.81	-16.2693	8.127	0.31005	0.0:0.0702:0.1358:0.794	rs34359340	560;586;536	B4DLV0;Q9BSC4;Q9BSC4-2	.;NOL10_HUMAN;.	A	536;586;536;560	ENSP00000263837:T536A;ENSP00000371101:T586A;ENSP00000437625:T536A;ENSP00000439663:T560A	ENSP00000263837:T536A	T	-	1	0	NOL10	10646708	1.000000	0.71417	0.966000	0.40874	0.758000	0.43043	2.567000	0.45956	0.415000	0.25817	-0.435000	0.05868	ACA	T|0.964;C|0.036	0.036	strong		0.473	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
NGEF	25791	hgsc.bcm.edu	37	2	233757679	233757679	+	Silent	SNP	G	G	A	rs748002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233757679G>A	ENST00000264051.3	-	7	1349	c.1071C>T	c.(1069-1071)gcC>gcT	p.A357A	NGEF_ENST00000539537.1_Silent_p.A80A|NGEF_ENST00000373552.4_Silent_p.A265A	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	357	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		AGAAGTGGTCGGCCGCATAAC	0.567													G|||	1504	0.300319	0.2791	0.3963	5008	,	,		20098	0.3492		0.326	False		,,,				2504	0.184				p.A357A		Atlas-SNP	.											NGEF_ENST00000264051,caecum,carcinoma,-1,4	NGEF	198	4	0			c.C1071T						PASS	.	G	,	1260,3146	430.6+/-342.6	172,916,1115	192.0	157.0	169.0		795,1071	3.5	1.0	2	dbSNP_86	169	2603,5997	420.7+/-353.5	398,1807,2095	no	coding-synonymous,coding-synonymous	NGEF	NM_001114090.1,NM_019850.2	,	570,2723,3210	AA,AG,GG		30.2674,28.5974,29.7017	,	265/619,357/711	233757679	3863,9143	2203	4300	6503	SO:0001819	synonymous_variant	25791	exon7			GTGGTCGGCCGCA	AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"""Rho guanine nucleotide exchange factors"""	7807	protein-coding gene	gene with protein product	"""ephexin"""	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.1071C>T	2.37:g.233757679G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	151	79	0.523179	NM_019850	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Silent	SNP	ENST00000264051.3	37	CCDS2500.1	740	0.33882783882783885	134	0.27235772357723576	134	0.3701657458563536	221	0.38636363636363635	251	0.3311345646437995	G	2.595	-0.294311	0.05568	0.285974	0.302674	ENSG00000066248	ENST00000420650	.	.	.	5.28	3.46	0.39613	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	4.000000000004E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	-33.2265	5.3969	0.16275	0.2597:0.1473:0.593:0.0	rs748002;rs16829683;rs17852957;rs748002	.	.	.	X	150	.	.	R	-	1	2	NGEF	233465923	0.000000	0.05858	0.987000	0.45799	0.327000	0.28475	-0.253000	0.08794	0.597000	0.29811	0.561000	0.74099	CGA	G|0.695;A|0.305	0.305	strong		0.567	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799	
RNF130	55819	hgsc.bcm.edu	37	5	179393867	179393867	+	Silent	SNP	T	T	C	rs10060093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179393867T>C	ENST00000261947.4	-	7	1487	c.1089A>G	c.(1087-1089)tcA>tcG	p.S363S	RNF130_ENST00000521389.1_Silent_p.S363S|CTC-563A5.2_ENST00000510240.1_RNA|RNF130_ENST00000522208.2_Silent_p.S363S	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)			GAGGAAGAGGTGAGATCCCCG	0.582													C|||	123	0.0245607	0.0893	0.0029	5008	,	,		17689	0.002		0.001	False		,,,				2504	0.0				p.S363S	GBM(24;432 554 38471 39699 51728)	Atlas-SNP	.											.	RNF130	49	.	0			c.A1089G						PASS	.	C		291,4115	799.7+/-415.5	9,273,1921	100.0	91.0	94.0		1089	-6.4	0.4	5	dbSNP_119	94	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous	RNF130	NM_018434.4		9,277,6217	CC,CT,TT		0.0465,6.6046,2.2682		363/420	179393867	295,12711	2203	4300	6503	SO:0001819	synonymous_variant	55819	exon7			AAGAGGTGAGATC	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.1089A>G	5.37:g.179393867T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	182	82	0.450549	NM_018434		Silent	SNP	ENST00000261947.4	37																																																																																				T|0.972;C|0.028	0.028	strong		0.582	RNF130-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374205.1	NM_018434	
RIMKLB	57494	hgsc.bcm.edu	37	12	8926015	8926015	+	Silent	SNP	C	C	T	rs386760122|rs2302488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:8926015C>T	ENST00000538135.1	+	6	1621	c.796C>T	c.(796-798)Ctg>Ttg	p.L266L	RIMKLB_ENST00000535829.1_Silent_p.L266L|RIMKLB_ENST00000357529.3_Silent_p.L266L|A2ML1-AS1_ENST00000537288.1_RNA|RIMKLB_ENST00000299673.5_3'UTR			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	266	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|citrate-L-glutamate ligase activity (GO:0072591)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						CATTGATCTGCTGATGAAAGA	0.473													T|||	384	0.0766773	0.2602	0.0259	5008	,	,		-128	0.0159		0.003	False		,,,				2504	0.0031				p.L266L		Atlas-SNP	.											.	RIMKLB	47	.	0			c.C796T						PASS	.	T		905,3245		101,703,1271	189.0	193.0	191.0		796	0.6	0.9	12	dbSNP_100	191	24,8424		0,24,4200	yes	coding-synonymous	RIMKLB	NM_020734.2		101,727,5471	TT,TC,CC		0.2841,21.8072,7.3742		266/387	8926015	929,11669	2075	4224	6299	SO:0001819	synonymous_variant	57494	exon7			GATCTGCTGATGA	AB033064	CCDS41748.1	12p13.31	2011-09-21	2008-10-13	2008-10-13	ENSG00000166532	ENSG00000166532	6.3.2.N6		29228	protein-coding gene	gene with protein product	"""N-acetylaspartyl-glutamate synthetase"""	614054	"""family with sequence similarity 80, member B"""	FAM80B		10574462, 20643647	Standard	XM_006719116		Approved	KIAA1238, NAAGS, NAAGS-I	uc001qux.2	Q9ULI2		ENST00000538135.1:c.796C>T	12.37:g.8926015C>T		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	267	116	0.434457	NM_020734	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Silent	SNP	ENST00000538135.1	37	CCDS41748.1																																																																																			C|0.911;T|0.089	0.089	strong		0.473	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1	NM_020734	
MUC16	94025	hgsc.bcm.edu	37	19	9060541	9060541	+	Missense_Mutation	SNP	C	C	T	rs11882256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	284	0	0		WXS	Illumina HiSeq	Phase_I	277	116	0.418773	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	
GRM1	2911	hgsc.bcm.edu	37	6	146755561	146755561	+	Missense_Mutation	SNP	C	C	G	rs146753539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:146755561C>G	ENST00000282753.1	+	8	3449	c.3214C>G	c.(3214-3216)Ccg>Gcg	p.P1072A	GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000361719.2_Missense_Mutation_p.P1072A|GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000507907.1_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1072	Gln/Pro-rich.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CCCGCCACCTCCGCAGCACCT	0.682													C|||	28	0.00559105	0.0174	0.0043	5008	,	,		14178	0.0		0.002	False		,,,				2504	0.0				p.P1072A		Atlas-SNP	.											GRM1,NS,carcinoma,-1,1	GRM1	419	1	0			c.C3214G						PASS	.	C	ALA/PRO,	67,4321		0,67,2127	29.0	33.0	32.0		3214,	2.9	0.5	6	dbSNP_134	32	12,8572		0,12,4280	yes	missense,utr-3	GRM1	NM_000838.3,NM_001114329.1	27,	0,79,6407	GG,GC,CC		0.1398,1.5269,0.609	benign,	1072/1195,	146755561	79,12893	2194	4292	6486	SO:0001583	missense	2911	exon9			CCACCTCCGCAGC	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3214C>G	6.37:g.146755561C>G	ENSP00000282753:p.Pro1072Ala	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	23	0.338235	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	13	0.005952380952380952	10	0.02032520325203252	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	9.887	1.203100	0.22121	0.015269	0.001398	ENSG00000152822	ENST00000361719;ENST00000282753	D;D	0.87809	-2.3;-2.3	5.71	2.87	0.33458	.	0.283949	0.40144	N	0.001180	T	0.65386	0.2686	L	0.29908	0.895	0.22142	N	0.999333	B	0.13594	0.008	B	0.16722	0.016	T	0.60383	-0.7274	10	0.51188	T	0.08	.	9.181	0.37141	0.0:0.7456:0.1201:0.1343	.	1072	Q13255	GRM1_HUMAN	A	1072	ENSP00000354896:P1072A;ENSP00000282753:P1072A	ENSP00000282753:P1072A	P	+	1	0	GRM1	146797254	0.024000	0.19004	0.468000	0.27192	0.601000	0.36947	0.978000	0.29488	0.730000	0.32425	0.462000	0.41574	CCG	C|0.993;G|0.007	0.007	strong		0.682	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
TRAPPC5	126003	hgsc.bcm.edu	37	19	7747445	7747445	+	Silent	SNP	G	G	A	rs1053363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7747445G>A	ENST00000317378.5	+	2	493	c.306G>A	c.(304-306)gcG>gcA	p.A102A	TRAPPC5_ENST00000426877.2_Silent_p.A102A|TRAPPC5_ENST00000595985.1_Silent_p.A35A|TRAPPC5_ENST00000596148.1_Silent_p.A102A|CTD-3214H19.16_ENST00000597959.1_3'UTR	NM_174894.2	NP_777554.1	Q8IUR0	TPPC5_HUMAN	trafficking protein particle complex 5	102					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|TRAPP complex (GO:0030008)				NS(1)|lung(2)	3						GCAAGGAGGCGGACAAGCTGG	0.632													G|||	1217	0.243011	0.4274	0.1326	5008	,	,		13972	0.127		0.174	False		,,,				2504	0.2628				p.A102A		Atlas-SNP	.											.	TRAPPC5	11	.	0			c.G306A						PASS	.	G	,,	1729,2653		355,1019,817	37.0	41.0	39.0		306,306,306	-8.2	0.6	19	dbSNP_86	39	1408,7148		106,1196,2976	no	coding-synonymous,coding-synonymous,coding-synonymous	TRAPPC5	NM_001042461.1,NM_001042462.1,NM_174894.1	,,	461,2215,3793	AA,AG,GG		16.4563,39.4569,24.2464	,,	102/189,102/189,102/189	7747445	3137,9801	2191	4278	6469	SO:0001819	synonymous_variant	126003	exon2			GGAGGCGGACAAG	BC042161	CCDS42490.1	19p13.3	2011-10-10				ENSG00000181029		"""Trafficking protein particle complex"""	23067	protein-coding gene	gene with protein product							Standard	NM_001042462		Approved	MGC52424, TRS31	uc002mhj.2	Q8IUR0		ENST00000317378.5:c.306G>A	19.37:g.7747445G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	65	41	0.630769	NM_001042461	A8K7I6	Silent	SNP	ENST00000317378.5	37	CCDS42490.1																																																																																			T|0.000;G|0.798;C|0.000;A|0.202	0.202	strong		0.632	TRAPPC5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461252.1	XM_058961	
PSG9	5678	hgsc.bcm.edu	37	19	43773572	43773572	+	Silent	SNP	G	G	A	rs8101210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43773572G>A	ENST00000270077.3	-	1	108	c.12C>T	c.(10-12)ctC>ctT	p.L4L	PSG9_ENST00000593948.1_Silent_p.L4L|PSG9_ENST00000596730.1_Silent_p.L4L|PSG9_ENST00000418820.2_Silent_p.L4L|PSG9_ENST00000291752.5_Silent_p.L4L|PSG9_ENST00000244293.7_Silent_p.L4L|PSG9_ENST00000443718.3_Silent_p.L4L	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	4				L -> F (in Ref. 5; AAA60203). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				AAGGGGCTGGGAGGGGCCCCA	0.617													G|||	952	0.190096	0.2141	0.147	5008	,	,		17084	0.381		0.0835	False		,,,				2504	0.1012				p.L4L		Atlas-SNP	.											PSG9,NS,carcinoma,-2,1	PSG9	77	1	0			c.C12T						PASS	.	G		884,3522	343.6+/-307.7	83,718,1402	110.0	104.0	106.0		12	-0.6	0.0	19	dbSNP_116	106	524,8076	147.1+/-202.6	23,478,3799	no	coding-synonymous	PSG9	NM_002784.3		106,1196,5201	AA,AG,GG		6.093,20.0635,10.8258		4/427	43773572	1408,11598	2203	4300	6503	SO:0001819	synonymous_variant	5678	exon1			GGCTGGGAGGGGC	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.12C>T	19.37:g.43773572G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Silent	SNP	ENST00000270077.3	37	CCDS12618.1																																																																																			G|0.863;A|0.137	0.137	strong		0.617	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
TSKS	60385	hgsc.bcm.edu	37	19	50251701	50251701	+	Missense_Mutation	SNP	C	C	T	rs199829146		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50251701C>T	ENST00000246801.3	-	3	507	c.425G>A	c.(424-426)cGc>cAc	p.R142H	TSKS_ENST00000358830.3_5'Flank	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	142					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		GTCTTTGGCGCGGACCAATCC	0.557																																					p.R142H		Atlas-SNP	.											TSKS,NS,carcinoma,+1,2	TSKS	97	2	0			c.G425A						PASS	.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	115.0	94.0	101.0		425	3.8	0.8	19		101	0,8600		0,0,4300	yes	missense	TSKS	NM_021733.1	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	142/593	50251701	1,13005	2203	4300	6503	SO:0001583	missense	60385	exon3			TTGGCGCGGACCA	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 161"""	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.425G>A	19.37:g.50251701C>T	ENSP00000246801:p.Arg142His	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	165	71	0.430303	NM_021733	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.621834	0.46840	2.27E-4	0.0	ENSG00000126467	ENST00000246801	T	0.48522	0.81	4.85	3.82	0.43975	.	0.122950	0.34628	N	0.003810	T	0.35098	0.0920	L	0.29908	0.895	0.80722	D	1	B	0.20459	0.045	B	0.16722	0.016	T	0.23440	-1.0188	10	0.72032	D	0.01	-9.0121	10.2244	0.43216	0.0:0.9063:0.0:0.0937	.	142	Q9UJT2	TSKS_HUMAN	H	142	ENSP00000246801:R142H	ENSP00000246801:R142H	R	-	2	0	TSKS	54943513	0.829000	0.29322	0.834000	0.33040	0.990000	0.78478	1.653000	0.37323	1.274000	0.44362	0.462000	0.41574	CGC	.	.	weak		0.557	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	
MUC4	4585	hgsc.bcm.edu	37	3	195511338	195511338	+	Silent	SNP	G	G	A	rs201931644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511338G>A	ENST00000463781.3	-	2	7572	c.7113C>T	c.(7111-7113)gtC>gtT	p.V2371V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V2371V	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)		AAGAGCTGGTGACAGGAAGAG	0.592													.|||	157	0.0313498	0.0711	0.0115	5008	,	,		16440	0.002		0.0209	False		,,,				2504	0.0327				p.V2371V		Atlas-SNP	.											.	MUC4	1505	.	0			c.C7113T						PASS	.						24.0	27.0	26.0					3																	195511338		681	1584	2265	SO:0001819	synonymous_variant	4585	exon2			GCTGGTGACAGGA	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.7113C>T	3.37:g.195511338G>A		Somatic	519	0	0		WXS	Illumina HiSeq	Phase_I	108	61	0.564815	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|0.995;A|0.005	0.005	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KRT83	3889	hgsc.bcm.edu	37	12	52712975	52712975	+	Silent	SNP	G	G	A	rs3741715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52712975G>A	ENST00000293670.3	-	2	620	c.558C>T	c.(556-558)aaC>aaT	p.N186N		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	186	Coil 1B.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CCTGCACGTGGTTGAGCTCTG	0.622													g|||	1816	0.36262	0.3654	0.3386	5008	,	,		16668	0.506		0.2823	False		,,,				2504	0.3108				p.N186N	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											.	KRT83	64	.	0			c.C558T						PASS	.	G		1606,2800	498.4+/-364.1	307,992,904	139.0	146.0	144.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	558	4.8	1.0	12	dbSNP_107	144	2547,6053	415.2+/-351.7	403,1741,2156	no	coding-synonymous	KRT83	NM_002282.3		710,2733,3060	AA,AG,GG		29.6163,36.4503,31.9314		186/494	52712975	4153,8853	2203	4300	6503	SO:0001819	synonymous_variant	3889	exon2			CACGTGGTTGAGC	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.558C>T	12.37:g.52712975G>A		Somatic	372	0	0		WXS	Illumina HiSeq	Phase_I	411	195	0.474453	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																			.	.	weak		0.622	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
DZANK1	55184	hgsc.bcm.edu	37	20	18395988	18395988	+	Missense_Mutation	SNP	C	C	T	rs6035037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:18395988C>T	ENST00000358866.6	-	10	1082	c.1060G>A	c.(1060-1062)Ggc>Agc	p.G354S	DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000357236.4_Missense_Mutation_p.G240S|DZANK1_ENST00000262547.5_Missense_Mutation_p.G354S|DZANK1_ENST00000329494.5_Missense_Mutation_p.G356S			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	354							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						CCACACCAGCCGCAGAAGGAC	0.562													C|||	1251	0.2498	0.1573	0.2983	5008	,	,		15727	0.1696		0.3151	False		,,,				2504	0.3558				p.G354S		Atlas-SNP	.											DZANK1,NS,carcinoma,0,2	DZANK1	65	2	0			c.G1060A						PASS	.	C	SER/GLY	643,3185		54,535,1325	77.0	87.0	84.0		1060	3.5	1.0	20	dbSNP_114	84	2529,5711		368,1793,1959	yes	missense	DZANK1	NM_001099407.1	56	422,2328,3284	TT,TC,CC		30.6917,16.7973,26.2844	benign	354/753	18395988	3172,8896	1914	4120	6034	SO:0001583	missense	55184	exon11			ACCAGCCGCAGAA	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"""Ankyrin repeat domain containing"""	15858	protein-coding gene	gene with protein product	"""ankyrin repeat domain 64"""		"""chromosome 20 open reading frame 12"""	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.1060G>A	20.37:g.18395988C>T	ENSP00000351734:p.Gly354Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Missense_Mutation	SNP	ENST00000358866.6	37	CCDS46582.1	515	0.2358058608058608	77	0.1565040650406504	98	0.27071823204419887	104	0.18181818181818182	236	0.3113456464379947	C	14.53	2.562631	0.45694	0.167973	0.306917	ENSG00000089091	ENST00000377630;ENST00000262547;ENST00000329494;ENST00000414623;ENST00000357236	T;T;T;T	0.61627	0.26;0.09;0.76;0.21	5.57	3.54	0.40534	.	0.634496	0.17261	N	0.180784	T	0.00012	0.0000	N	0.10972	0.075	0.50467	P	1.2199999999995548E-4	B;B;B	0.32031	0.267;0.352;0.063	B;B;B	0.24848	0.056;0.048;0.004	T	0.25467	-1.0131	9	0.46703	T	0.11	-6.1428	8.6331	0.33930	0.0:0.7597:0.1522:0.0881	rs6035037;rs17204022;rs52820643;rs61438457;rs6035037	373;240;354	B7Z631;Q9NVP4-4;Q9NVP4	.;.;DZAN1_HUMAN	S	181;354;356;180;240	ENSP00000366857:G181S;ENSP00000262547:G354S;ENSP00000328866:G356S;ENSP00000349774:G240S	ENSP00000262547:G354S	G	-	1	0	C20orf12	18343988	0.998000	0.40836	0.980000	0.43619	0.858000	0.48976	3.120000	0.50430	0.619000	0.30197	0.313000	0.20887	GGC	C|0.764;T|0.236	0.236	strong		0.562	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407	
SLC9C2	284525	hgsc.bcm.edu	37	1	173526520	173526520	+	Missense_Mutation	SNP	C	C	T	rs116588526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173526520C>T	ENST00000367714.3	-	10	1596	c.1174G>A	c.(1174-1176)Gtt>Att	p.V392I	SLC9C2_ENST00000536496.1_Missense_Mutation_p.V290I|RP3-436N22.3_ENST00000431459.1_RNA|SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	392					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										AGATTATAAACATCAGGAGCC	0.343													C|||	61	0.0121805	0.0454	0.0014	5008	,	,		17169	0.0		0.0	False		,,,				2504	0.0				p.V392I		Atlas-SNP	.											.	.	.	.	0			c.G1174A						PASS	.	C	ILE/VAL	125,4281	89.7+/-128.4	3,119,2081	112.0	124.0	120.0		1174	-9.1	0.1	1	dbSNP_132	120	0,8600		0,0,4300	yes	missense	SLC9A11	NM_178527.3	29	3,119,6381	TT,TC,CC		0.0,2.837,0.9611	benign	392/1125	173526520	125,12881	2203	4300	6503	SO:0001583	missense	284525	exon10			TATAAACATCAGG	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.1174G>A	1.37:g.173526520C>T	ENSP00000356687:p.Val392Ile	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	223	118	0.529148	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	C	0.013	-1.635886	0.00806	0.02837	0.0	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.22945	1.93;1.93	5.57	-9.13	0.00704	Cation/H+ exchanger (1);	1.176240	0.06215	N	0.685727	T	0.02342	0.0072	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39440	-0.9614	10	0.21014	T	0.42	-6.9326	11.2419	0.48974	0.1172:0.6529:0.0:0.2299	.	392	Q5TAH2	S9A11_HUMAN	I	392;290	ENSP00000356687:V392I;ENSP00000445437:V290I	ENSP00000356687:V392I	V	-	1	0	SLC9A11	171793143	0.001000	0.12720	0.050000	0.19076	0.051000	0.14879	-1.894000	0.01607	-1.269000	0.02436	-1.130000	0.01982	GTT	C|0.989;T|0.011	0.011	strong		0.343	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
GPATCH2	55105	hgsc.bcm.edu	37	1	217793718	217793718	+	Silent	SNP	A	A	G	rs34839777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:217793718A>G	ENST00000366935.3	-	2	290	c.180T>C	c.(178-180)ccT>ccC	p.P60P	GPATCH2_ENST00000366934.3_Silent_p.P60P	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	60					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		GGCGTTTCAGAGGGCAAGATA	0.498													A|||	38	0.00758786	0.0265	0.0043	5008	,	,		17711	0.0		0.0	False		,,,				2504	0.0				p.P60P		Atlas-SNP	.											.	GPATCH2	53	.	0			c.T180C						PASS	.	A		114,4292	85.3+/-124.0	3,108,2092	136.0	123.0	128.0		180	-4.0	1.0	1	dbSNP_126	128	0,8600		0,0,4300	no	coding-synonymous	GPATCH2	NM_018040.2		3,108,6392	GG,GA,AA		0.0,2.5874,0.8765		60/529	217793718	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	55105	exon2			TTTCAGAGGGCAA	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.180T>C	1.37:g.217793718A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Silent	SNP	ENST00000366935.3	37	CCDS1518.1																																																																																			A|0.990;G|0.010	0.010	strong		0.498	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040	
CYP4F12	66002	hgsc.bcm.edu	37	19	15793282	15793282	+	Silent	SNP	A	A	G	rs35352350		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15793282A>G	ENST00000550308.1	+	6	989	c.609A>G	c.(607-609)ctA>ctG	p.L203L	CYP4F12_ENST00000324632.10_Silent_p.L203L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	203					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	TGGACAGTCTACAGAAATGCA	0.527																																					p.L203L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A609G						PASS	.	G		62,4344		0,62,2141	115.0	108.0	111.0		609	1.3	1.0	19	dbSNP_126	111	0,8600		0,0,4300	no	coding-synonymous	CYP4F12	NM_023944.3		0,62,6441	GG,GA,AA		0.0,1.4072,0.4767		203/525	15793282	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	66002	exon6			CAGTCTACAGAAA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.609A>G	19.37:g.15793282A>G		Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	395	56	0.141772	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			A|0.991;G|0.009	0.009	strong		0.527	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
IFNA16	3449	hgsc.bcm.edu	37	9	21216910	21216910	+	Missense_Mutation	SNP	A	A	G	rs386733486|rs28368162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21216910A>G	ENST00000380216.1	-	1	400	c.395T>C	c.(394-396)aTt>aCt	p.I132T		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	132					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		CATCAGGGCAATCTCTTCCAC	0.473													G|||	130	0.0259585	0.0499	0.0216	5008	,	,		19296	0.0		0.0427	False		,,,				2504	0.0061				p.I132T		Atlas-SNP	.											.	IFNA16	27	.	0			c.T395C						PASS	.	G	THR/ILE	99,4307		4,91,2108	196.0	191.0	193.0		395	-0.9	0.0	9	dbSNP_125	193	184,8416		7,170,4123	no	missense	IFNA16	NM_002173.2	89	11,261,6231	GG,GA,AA		2.1395,2.2469,2.1759	benign	132/190	21216910	283,12723	2203	4300	6503	SO:0001583	missense	3449	exon1			AGGGCAATCTCTT		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"""Interferons"""	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.395T>C	9.37:g.21216910A>G	ENSP00000369564:p.Ile132Thr	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	296	123	0.415541	NM_002173	Q5VV12	Missense_Mutation	SNP	ENST00000380216.1	37	CCDS34996.1	41	0.018772893772893772	12	0.024390243902439025	6	0.016574585635359115	0	0.0	23	0.030343007915567283	-	0.004	-2.304892	0.00240	0.022469	0.021395	ENSG00000147885	ENST00000380216	T	0.03004	4.08	2.62	-0.859	0.10685	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.666310	0.02964	N	0.143572	T	0.00241	0.0007	N	0.00016	-2.855	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49560	-0.8927	10	0.02654	T	1	.	4.1205	0.10103	0.3484:0.1729:0.4786:0.0	rs28368162	132	P05015	IFN16_HUMAN	T	132	ENSP00000369564:I132T	ENSP00000369564:I132T	I	-	2	0	IFNA16	21206910	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.374000	0.07484	-0.779000	0.04560	-1.160000	0.01791	ATT	A|0.974;G|0.026	0.026	strong		0.473	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173	
DMKN	93099	hgsc.bcm.edu	37	19	36002381	36002381	+	Missense_Mutation	SNP	C	C	T	rs56743379|rs12981076|rs59309505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002381C>T	ENST00000339686.3	-	5	1026	c.850G>A	c.(850-852)Ggc>Agc	p.G284S	DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000451297.2_Missense_Mutation_p.G284S|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.G284S|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.G284S|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.G284S|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.G284S	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	284	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			ccactgctgccgccactgctg	0.622													-|||	1296	0.258786	0.4531	0.2133	5008	,	,		10950	0.2679		0.0924	False		,,,				2504	0.1902				p.G284S		Atlas-SNP	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.G850A						PASS	.						25.0	20.0	22.0					19																	36002381		2193	4268	6461	SO:0001583	missense	93099	exon5			TGCTGCCGCCACT	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.850G>A	19.37:g.36002381C>T	ENSP00000342012:p.Gly284Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	83	80	0.963855	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	678	0.31043956043956045	225	0.4573170731707317	90	0.24861878453038674	233	0.40734265734265734	130	0.17150395778364116	-	8.814	0.935828	0.18206	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	3.0	-3.4	0.04853	.	0.338457	0.21736	N	0.069899	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B;B	0.15141	0.0;0.001;0.001;0.001;0.012	B;B;B;B;B	0.08055	0.001;0.003;0.003;0.003;0.002	T	0.43925	-0.9361	9	0.11794	T	0.64	0.198	10.2806	0.43537	0.0:0.6239:0.0:0.3761	rs12981076;rs61179178	284;284;284;284;284	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	S	284	ENSP00000342012:G284S;ENSP00000394908:G284S;ENSP00000415277:G284S;ENSP00000414743:G284S;ENSP00000388404:G284S;ENSP00000409513:G284S	ENSP00000342012:G284S	G	-	1	0	DMKN	40694221	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.399000	0.00484	-1.308000	0.02318	-0.361000	0.07541	GGC	C|0.689;T|0.311	0.311	strong		0.622	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
GPR113	165082	hgsc.bcm.edu	37	2	26536299	26536299	+	Silent	SNP	C	C	G	rs11886746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26536299C>G	ENST00000311519.1	-	9	1418	c.1419G>C	c.(1417-1419)ccG>ccC	p.P473P	GPR113_ENST00000541401.1_Silent_p.P76P|GPR113_ENST00000333478.6_Silent_p.P274P|GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000421160.2_Silent_p.P404P	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	473					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)					TGCTGTGGACCGGCCCCCAGA	0.647													g|||	2002	0.39976	0.4856	0.3228	5008	,	,		18410	0.3353		0.328	False		,,,				2504	0.4785				p.P473P		Atlas-SNP	.											.	GPR113	134	.	0			c.G1419C						PASS	.	A	,,	2072,2334		494,1084,625	31.0	30.0	30.0		1419,1212,822	-0.3	0.0	2	dbSNP_120	30	2780,5820		446,1888,1966	no	coding-synonymous,coding-synonymous,coding-synonymous	GPR113	NM_001145168.1,NM_001145169.1,NM_153835.3	,,	940,2972,2591	GG,GC,CC		32.3256,47.0268,37.3059	,,	473/1080,404/998,274/874	26536299	4852,8154	2203	4300	6503	SO:0001819	synonymous_variant	165082	exon9			GTGGACCGGCCCC	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.1419G>C	2.37:g.26536299C>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Silent	SNP	ENST00000311519.1	37	CCDS46239.1																																																																																			C|0.631;G|0.369	0.369	strong		0.647	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
TTN	7273	hgsc.bcm.edu	37	2	179498303	179498303	+	Silent	SNP	T	T	C	rs16866425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000431752.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Silent_p.K5196K|TTN_ENST00000342992.6_Silent_p.K11693K|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Silent_p.K5321K|TTN_ENST00000342175.6_Silent_p.K5388K|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000418062.1_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	214	0	0		WXS	Illumina HiSeq	Phase_I	241	106	0.439834	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29910586	29910586	+	Silent	SNP	G	G	A	rs12721672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29910586G>A	ENST00000396634.1	+	4	467	c.126G>A	c.(124-126)ggG>ggA	p.G42G	HLA-A_ENST00000376809.5_Silent_p.G42G|HLA-A_ENST00000376802.2_Silent_p.G42G|HLA-A_ENST00000376806.5_Silent_p.G42G			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	42	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.R41fs*31(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						CCGGCCGCGGGGAGCCCCGCT	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)			g|||	682	0.136182	0.2405	0.134	5008	,	,		14806	0.131		0.0666	False		,,,				2504	0.0736				p.G42G		Atlas-SNP	.											.	HLA-A	89	.	1	Deletion - Frameshift(1)	ovary(1)	c.G126A						PASS	.						23.0	21.0	22.0					6																	29910586		2198	4294	6492	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCGCGGGGAGCCC	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.126G>A	6.37:g.29910586G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	111	23	0.207207	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			A|0.105;G|0.895	0.105	strong		0.711	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CUX2	23316	hgsc.bcm.edu	37	12	111785586	111785586	+	Silent	SNP	T	T	C	rs3803167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:111785586T>C	ENST00000261726.6	+	22	4072	c.3918T>C	c.(3916-3918)gaT>gaC	p.D1306D		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1306					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						TGGAGGAGGATGCTGAGGAAG	0.612													C|||	2644	0.527955	0.6195	0.451	5008	,	,		14602	0.7639		0.2435	False		,,,				2504	0.5082				p.D1306D		Atlas-SNP	.											.	CUX2	145	.	0			c.T3918C						PASS	.	C		2298,1986		614,1070,458	47.0	55.0	52.0		3918	-8.0	0.0	12	dbSNP_107	52	1843,6617		209,1425,2596	no	coding-synonymous	CUX2	NM_015267.3		823,2495,3054	CC,CT,TT		21.7849,46.3585,32.4937		1306/1487	111785586	4141,8603	2142	4230	6372	SO:0001819	synonymous_variant	23316	exon22			GGAGGATGCTGAG	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"""Homeoboxes / CUT class"""	19347	protein-coding gene	gene with protein product		610648	"""cut-like 2 (Drosophila)"""	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.3918T>C	12.37:g.111785586T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_015267	A7E2Y4	Silent	SNP	ENST00000261726.6	37	CCDS41837.1																																																																																			T|0.524;C|0.476	0.476	strong		0.612	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	
SNX27	81609	hgsc.bcm.edu	37	1	151638486	151638486	+	Splice_Site	SNP	T	T	C	rs150091333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151638486T>C	ENST00000458013.2	+	6	1104	c.984T>C	c.(982-984)ttT>ttC	p.F328F	SNX27_ENST00000368838.1_Splice_Site_p.F235F|SNX27_ENST00000368843.3_Splice_Site_p.F328F|SNX27_ENST00000482791.1_3'UTR			Q96L92	SNX27_HUMAN	sorting nexin family member 27	328	FERM-like region F1.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|establishment of natural killer cell polarity (GO:0001770)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to plasma membrane (GO:1990126)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(1)|large_intestine(2)|ovary(2)	5	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GTCACTCCTTTGGTAAGTACC	0.403													T|||	19	0.00379393	0.0144	0.0	5008	,	,		21524	0.0		0.0	False		,,,				2504	0.0				p.F328F	Colon(46;291 966 40145 41237 41888)	Atlas-SNP	.											.	SNX27	44	.	0			c.T984C						PASS	.	T		62,4344	58.1+/-94.6	0,62,2141	169.0	146.0	154.0		984	3.9	1.0	1	dbSNP_134	154	6,8594	5.0+/-18.6	0,6,4294	yes	coding-synonymous-near-splice	SNX27	NM_030918.5		0,68,6435	CC,CT,TT		0.0698,1.4072,0.5228		328/529	151638486	68,12938	2203	4300	6503	SO:0001630	splice_region_variant	81609	exon6			CTCCTTTGGTAAG	AB007957	CCDS1001.1	1q21.3	2008-03-11			ENSG00000143376	ENSG00000143376		"""Sorting nexins"""	20073	protein-coding gene	gene with protein product		611541				12461558	Standard	XM_005245509		Approved	MY014, KIAA0488, MGC20471	uc001eyn.1	Q96L92	OTTHUMG00000013052	ENST00000458013.2:c.985+1T>C	1.37:g.151638486T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_030918	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	Silent	SNP	ENST00000458013.2	37																																																																																				T|0.994;C|0.006	0.006	strong		0.403	SNX27-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000036624.3	NM_030918	Silent
GNA14	9630	hgsc.bcm.edu	37	9	80144099	80144099	+	Silent	SNP	G	G	A	rs12346870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:80144099G>A	ENST00000341700.6	-	2	708	c.195C>T	c.(193-195)gaC>gaT	p.D65D	RP11-466A17.1_ENST00000439145.1_RNA	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	65					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						TTCTGTCTTCGTCGCTGTAAC	0.448													G|||	114	0.0227636	0.0809	0.0086	5008	,	,		21370	0.0		0.001	False		,,,				2504	0.0				p.D65D		Atlas-SNP	.											.	GNA14	50	.	0			c.C195T						PASS	.	G		273,4133	154.0+/-187.5	12,249,1942	339.0	317.0	324.0		195	-0.6	1.0	9	dbSNP_120	324	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GNA14	NM_004297.3		12,251,6240	AA,AG,GG		0.0233,6.1961,2.1144		65/356	80144099	275,12731	2203	4300	6503	SO:0001819	synonymous_variant	9630	exon2			GTCTTCGTCGCTG	AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.195C>T	9.37:g.80144099G>A		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	324	213	0.657407	NM_004297	B1ALW3	Silent	SNP	ENST00000341700.6	37	CCDS6657.1																																																																																			G|0.976;A|0.024	0.024	strong		0.448	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1		
STRN4	29888	hgsc.bcm.edu	37	19	47226450	47226450	+	Silent	SNP	A	A	G	rs28684509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47226450A>G	ENST00000263280.6	-	13	1735	c.1686T>C	c.(1684-1686)tgT>tgC	p.C562C	STRN4_ENST00000594357.2_5'UTR|STRN4_ENST00000391910.3_Silent_p.C569C|STRN4_ENST00000539396.1_Silent_p.C443C	NM_001039877.1|NM_013403.2	NP_001034966.1|NP_037535.2	Q9NRL3	STRN4_HUMAN	striatin, calmodulin binding protein 4	562						cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		CATCAGCAGAACAGGAGGCCA	0.716													G|||	438	0.0874601	0.2829	0.0231	5008	,	,		16355	0.0337		0.007	False		,,,				2504	0.0072				p.C569C		Atlas-SNP	.											.	STRN4	33	.	0			c.T1707C						PASS	.	G	,	891,3399		78,735,1332	16.0	16.0	16.0		1707,1686	3.9	1.0	19	dbSNP_125	16	8,8456		0,8,4224	no	coding-synonymous,coding-synonymous	STRN4	NM_001039877.1,NM_013403.2	,	78,743,5556	GG,GA,AA		0.0945,20.7692,7.0488	,	569/761,562/754	47226450	899,11855	2145	4232	6377	SO:0001819	synonymous_variant	29888	exon13			AGCAGAACAGGAG	AF212940	CCDS12690.1, CCDS42581.1	19q13.32	2013-01-10			ENSG00000090372	ENSG00000090372		"""WD repeat domain containing"""	15721	protein-coding gene	gene with protein product		614767				10748158	Standard	XM_006723171		Approved	zinedin, ZIN	uc002pfm.3	Q9NRL3		ENST00000263280.6:c.1686T>C	19.37:g.47226450A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	157	61	0.388535	NM_001039877	A0A024R0V2|B4DQH7|F8VYA6|Q8NE53	Silent	SNP	ENST00000263280.6	37	CCDS12690.1																																																																																			A|0.904;G|0.096	0.096	strong		0.716	STRN4-001	KNOWN	NMD_exception|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466607.2		
AKR7A2	8574	hgsc.bcm.edu	37	1	19634964	19634964	+	Missense_Mutation	SNP	C	C	G	rs859208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19634964C>G	ENST00000235835.3	-	2	492	c.471G>C	c.(469-471)caG>caC	p.Q157H		NM_003689.3	NP_003680.2	O43488	ARK72_HUMAN	aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)	157			Q -> H (in dbSNP:rs859208). {ECO:0000269|PubMed:18752886}.		carbohydrate metabolic process (GO:0005975)|cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|phenanthrene-9,10-epoxide hydrolase activity (GO:0019119)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GGTGCAGCCGCTGGCAGGCAT	0.612													G|||	507	0.101238	0.2965	0.0216	5008	,	,		17828	0.0466		0.0	False		,,,				2504	0.0542				p.Q157H		Atlas-SNP	.											.	AKR7A2	19	.	0			c.G471C						PASS	.	G	HIS/GLN	1214,3192	702.5+/-406.9	159,896,1148	35.0	37.0	36.0		471	-1.6	1.0	1	dbSNP_86	36	11,8589	815.5+/-407.0	0,11,4289	no	missense	AKR7A2	NM_003689.2	24	159,907,5437	GG,GC,CC		0.1279,27.5533,9.4187	benign	157/360	19634964	1225,11781	2203	4300	6503	SO:0001583	missense	8574	exon2			CAGCCGCTGGCAG	AF026947	CCDS194.1	1p36.13	2010-09-30			ENSG00000053371	ENSG00000053371		"""Aldo-keto reductases"""	389	protein-coding gene	gene with protein product		603418				9576847	Standard	NM_003689		Approved	AFAR	uc001bbw.3	O43488	OTTHUMG00000002522	ENST00000235835.3:c.471G>C	1.37:g.19634964C>G	ENSP00000235835:p.Gln157His	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	192	99	0.515625	NM_003689	O75749|Q5TG63	Missense_Mutation	SNP	ENST00000235835.3	37	CCDS194.1	166|166	0.076007326007326|0.076007326007326	145|145	0.29471544715447157|0.29471544715447157	5|5	0.013812154696132596|0.013812154696132596	16|16	0.027972027972027972|0.027972027972027972	0|0	0.0|0.0	G|G	0.019|0.019	-1.457599|-1.457599	0.01071|0.01071	0.275533|0.275533	0.001279|0.001279	ENSG00000053371|ENSG00000053371	ENST00000235835;ENST00000330072|ENST00000489286	T;T|.	0.24723|.	1.84;1.84|.	4.09|4.09	-1.58|-1.58	0.08479|0.08479	NADP-dependent oxidoreductase domain (3);|.	0.533647|.	0.21446|.	N|.	0.074405|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02765|0.02765	-0.5|-0.5	0.46725|0.46725	P|P	8.240000000000469E-4|8.240000000000469E-4	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.10450|.	0.005;0.003;0.005|.	T|T	0.42430|0.42430	-0.9452|-0.9452	9|4	0.10636|.	T|.	0.68|.	.|.	0.6684|0.6684	0.00854|0.00854	0.1973:0.2501:0.1723:0.3803|0.1973:0.2501:0.1723:0.3803	rs859208;rs859208|rs859208;rs859208	128;128;157|.	C9JSL3;B4DZX4;O43488|.	.;.;ARK72_HUMAN|.	H|T	157;147|85	ENSP00000235835:Q157H;ENSP00000339084:Q147H|.	ENSP00000235835:Q157H|.	Q|S	-|-	3|2	2|0	AKR7A2|AKR7A2	19507551|19507551	0.613000|0.613000	0.27009|0.27009	0.987000|0.987000	0.45799|0.45799	0.344000|0.344000	0.29017|0.29017	-0.114000|-0.114000	0.10757|0.10757	-0.437000|-0.437000	0.07243|0.07243	-0.216000|-0.216000	0.12614|0.12614	CAG|AGC	C|0.915;G|0.085	0.085	strong		0.612	AKR7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007165.2	NM_003689	
IGSF22	283284	hgsc.bcm.edu	37	11	18735480	18735480	+	Missense_Mutation	SNP	G	G	A	rs111397851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18735480G>A	ENST00000513874.1	-	14	2153	c.2014C>T	c.(2014-2016)Cgt>Tgt	p.R672C	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	672	Ig-like 4.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CTGTCTTCACGCACACAGTTG	0.602													g|||	236	0.0471246	0.1415	0.0317	5008	,	,		23327	0.0		0.0258	False		,,,				2504	0.001				p.R672C		Atlas-SNP	.											.	IGSF22	211	.	0			c.C2014T						PASS	.		CYS/ARG	491,3899	207.2+/-228.6	24,443,1728	88.0	95.0	93.0		2014	1.0	0.0	11	dbSNP_132	93	219,8353	90.4+/-152.6	3,213,4070	yes	missense	IGSF22	NM_173588.3	180	27,656,5798	AA,AG,GG		2.5548,11.1845,5.4775	probably-damaging	672/1327	18735480	710,12252	2195	4286	6481	SO:0001583	missense	283284	exon14			CTTCACGCACACA	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.2014C>T	11.37:g.18735480G>A	ENSP00000421191:p.Arg672Cys	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	194	107	0.551546	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	94	0.04304029304029304	61	0.12398373983739837	15	0.04143646408839779	0	0.0	18	0.023746701846965697	G	11.60	1.686151	0.29962	0.111845	0.025548	ENSG00000179057	ENST00000513874	T	0.46063	0.88	3.98	0.959	0.19624	.	0.000000	0.33327	U	0.005033	T	0.02418	0.0074	H	0.97896	4.1	0.09310	N	1	D	0.89917	1.0	D	0.79784	0.993	T	0.16129	-1.0413	10	0.62326	D	0.03	.	3.8194	0.08828	0.1944:0.0:0.384:0.4215	.	672	D6RGV7	.	C	672	ENSP00000421191:R672C	ENSP00000322422:R672C	R	-	1	0	IGSF22	18692056	0.003000	0.15002	0.002000	0.10522	0.321000	0.28281	0.178000	0.16820	0.027000	0.15297	0.448000	0.29417	CGT	G|0.961;A|0.039	0.039	strong		0.602	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
RNF207	388591	hgsc.bcm.edu	37	1	6271125	6271125	+	Silent	SNP	A	A	G	rs1052598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6271125A>G	ENST00000377939.4	+	12	1183	c.1056A>G	c.(1054-1056)ccA>ccG	p.P352P	RNF207_ENST00000377948.2_Intron	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	352						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		GTCTGGAGCCACTGCTGCTGC	0.672													G|||	673	0.134385	0.3517	0.0648	5008	,	,		16225	0.0476		0.0408	False		,,,				2504	0.0757				p.P352P		Atlas-SNP	.											RNF207,NS,carcinoma,+1,1	RNF207	45	1	0			c.A1056G						PASS	.	G		1225,2955		185,855,1050	14.0	19.0	17.0		1056	0.1	1.0	1	dbSNP_86	17	333,8089		8,317,3886	no	coding-synonymous	RNF207	NM_207396.2		193,1172,4936	GG,GA,AA		3.9539,29.3062,12.3631		352/635	6271125	1558,11044	2090	4211	6301	SO:0001819	synonymous_variant	388591	exon12			GGAGCCACTGCTG	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1056A>G	1.37:g.6271125A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	162	99	0.611111	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Silent	SNP	ENST00000377939.4	37	CCDS59.2																																																																																			A|0.878;G|0.122	0.122	strong		0.672	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
RFX6	222546	hgsc.bcm.edu	37	6	117243260	117243260	+	Silent	SNP	T	T	C	rs7764347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117243260T>C	ENST00000332958.2	+	13	1399	c.1383T>C	c.(1381-1383)acT>acC	p.T461T		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	461					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AGAATGCCACTGTGGAGGCTT	0.338													C|||	1699	0.339257	0.2935	0.2939	5008	,	,		16993	0.4226		0.2217	False		,,,				2504	0.4683				p.T461T		Atlas-SNP	.											.	RFX6	141	.	0			c.T1383C						PASS	.	C		1237,3169	705.8+/-407.3	187,863,1153	102.0	106.0	105.0		1383	-6.9	0.9	6	dbSNP_116	105	1530,7070	746.7+/-407.3	144,1242,2914	no	coding-synonymous	RFX6	NM_173560.3		331,2105,4067	CC,CT,TT		17.7907,28.0754,21.2748		461/929	117243260	2767,10239	2203	4300	6503	SO:0001819	synonymous_variant	222546	exon13			TGCCACTGTGGAG	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1383T>C	6.37:g.117243260T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_173560	Q5T6B3	Silent	SNP	ENST00000332958.2	37	CCDS5113.1																																																																																			T|0.750;C|0.250	0.250	strong		0.338	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560	
QPCT	25797	hgsc.bcm.edu	37	2	37579937	37579937	+	Silent	SNP	C	C	T	rs2230299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37579937C>T	ENST00000338415.3	+	2	284	c.126C>T	c.(124-126)taC>taT	p.Y42Y	QPCT_ENST00000537448.1_Intron	NM_012413.3	NP_036545.1	Q16769	QPCT_HUMAN	glutaminyl-peptide cyclotransferase	42					cellular protein modification process (GO:0006464)|peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	extracellular vesicular exosome (GO:0070062)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)	p.Y42Y(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|stomach(2)	17		Ovarian(717;0.051)|all_hematologic(82;0.21)				CTCAGAATTACCACCAGCCAG	0.363													T|||	1469	0.293331	0.5401	0.3012	5008	,	,		19797	0.3383		0.0686	False		,,,				2504	0.1391				p.Y42Y		Atlas-SNP	.											QPCT,NS,carcinoma,0,1	QPCT	34	1	1	Substitution - coding silent(1)	stomach(1)	c.C126T						PASS	.	T		2116,2290	600.5+/-389.5	524,1068,611	86.0	93.0	91.0		126	-1.2	0.8	2	dbSNP_100	91	442,8158	799.7+/-407.4	19,404,3877	no	coding-synonymous	QPCT	NM_012413.3		543,1472,4488	TT,TC,CC		5.1395,48.0254,19.6678		42/362	37579937	2558,10448	2203	4300	6503	SO:0001819	synonymous_variant	25797	exon2			GAATTACCACCAG	X71125	CCDS1790.1	2p22	2008-07-31	2008-07-31		ENSG00000115828	ENSG00000115828	2.3.2.5		9753	protein-coding gene	gene with protein product	"""glutaminyl cyclase"""	607065				7999256	Standard	NM_012413		Approved	QC, GCT	uc002rqg.3	Q16769	OTTHUMG00000100963	ENST00000338415.3:c.126C>T	2.37:g.37579937C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	133	78	0.586466	NM_012413	Q16770|Q3KRG6|Q53TR4	Silent	SNP	ENST00000338415.3	37	CCDS1790.1																																																																																			C|0.765;T|0.235	0.235	strong		0.363	QPCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218572.2		
ABCA3	21	hgsc.bcm.edu	37	16	2373687	2373687	+	Silent	SNP	C	C	T	rs74002800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2373687C>T	ENST00000301732.5	-	7	1150	c.450G>A	c.(448-450)gtG>gtA	p.V150V	ABCA3_ENST00000382381.3_Silent_p.V150V|ABCA3_ENST00000567910.1_Silent_p.V150V	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	150					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	GGTGATATTTCACCTGTGGAA	0.517													C|||	172	0.034345	0.1218	0.0159	5008	,	,		18945	0.0		0.0	False		,,,				2504	0.0				p.V150V		Atlas-SNP	.											.	ABCA3	176	.	0			c.G450A						PASS	.	C		498,3898	228.8+/-243.5	29,440,1729	170.0	192.0	185.0		450	0.9	0.9	16	dbSNP_130	185	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	ABCA3	NM_001089.2		29,446,6023	TT,TC,CC		0.0698,11.3285,3.8781		150/1705	2373687	504,12492	2198	4300	6498	SO:0001819	synonymous_variant	21	exon7			ATATTTCACCTGT	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"""ATP binding cassette transporters / subfamily A"""	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.450G>A	16.37:g.2373687C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	46	0.365079	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			C|0.963;T|0.037	0.037	strong		0.517	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
NDRG4	65009	hgsc.bcm.edu	37	16	58540875	58540875	+	Silent	SNP	G	G	A	rs17821543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58540875G>A	ENST00000570248.1	+	8	682	c.576G>A	c.(574-576)gtG>gtA	p.V192V	NDRG4_ENST00000563799.1_Silent_p.V210V|NDRG4_ENST00000562999.1_Silent_p.V192V|NDRG4_ENST00000566192.1_Silent_p.V192V|NDRG4_ENST00000394282.4_Silent_p.V244V|NDRG4_ENST00000356752.4_Silent_p.V222V|NDRG4_ENST00000394279.2_Silent_p.V224V|NDRG4_ENST00000258187.5_Silent_p.V224V|NDRG4_ENST00000569923.1_Silent_p.V137V|NDRG4_ENST00000568640.1_Silent_p.V210V	NM_001242835.1	NP_001229764.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	192					cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						TTGGGAACGTGGTGAACCAGG	0.612													G|||	187	0.0373403	0.0038	0.0288	5008	,	,		17683	0.0		0.0865	False		,,,				2504	0.0767				p.V244V		Atlas-SNP	.											.	NDRG4	29	.	0			c.G732A						PASS	.	G	,,,,,,	79,4317	67.6+/-105.2	2,75,2121	108.0	86.0	94.0		732,666,630,576,576,672,672	3.2	1.0	16	dbSNP_123	94	612,7988	159.8+/-213.0	28,556,3716	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDRG4	NM_001130487.1,NM_001242833.1,NM_001242834.1,NM_001242835.1,NM_001242836.1,NM_020465.3,NM_022910.3	,,,,,,	30,631,5837	AA,AG,GG		7.1163,1.7971,5.317	,,,,,,	244/392,222/370,210/358,192/353,192/340,224/372,224/372	58540875	691,12305	2198	4300	6498	SO:0001819	synonymous_variant	65009	exon10			GAACGTGGTGAAC	AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034			14466	protein-coding gene	gene with protein product		614463				11352569, 16408304	Standard	NM_020465		Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000570248.1:c.576G>A	16.37:g.58540875G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_001130487	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	Silent	SNP	ENST00000570248.1	37	CCDS58466.1																																																																																			G|0.951;A|0.049	0.049	strong		0.612	NDRG4-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422671.2		
TUBB8	347688	hgsc.bcm.edu	37	10	93714	93714	+	Silent	SNP	A	A	C	rs41288743		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:93714A>C	ENST00000309812.4	-	4	680	c.618T>G	c.(616-618)gcT>gcG	p.A206A	TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000447903.2_Silent_p.A134A|TUBB8_ENST00000332708.5_3'UTR	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	206					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)		TGTCATACAGAGCTTCGTTAT	0.537																																					p.A206A	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,NS,carcinoma,0,1	TUBB8	62	1	0			c.T618G						scavenged	.						94.0	87.0	90.0					10																	93714		2203	4299	6502	SO:0001819	synonymous_variant	347688	exon4			ATACAGAGCTTCG	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.618T>G	10.37:g.93714A>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	84	14	0.166667	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1																																																																																			.	.	weak		0.537	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
CLSTN1	22883	hgsc.bcm.edu	37	1	9804693	9804693	+	Missense_Mutation	SNP	C	C	T	rs7550295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	44	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	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		
OAS1	4938	hgsc.bcm.edu	37	12	113348870	113348870	+	Missense_Mutation	SNP	G	G	A	rs1131454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113348870G>A	ENST00000202917.5	+	3	747	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Missense_Mutation_p.G162S|OAS1_ENST00000452357.2_Missense_Mutation_p.G162S|OAS1_ENST00000551241.1_Missense_Mutation_p.G162S	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	162			G -> S (in dbSNP:rs1131454). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1651324, ECO:0000269|PubMed:17024523, ECO:0000269|PubMed:2416561, ECO:0000269|PubMed:3753689, ECO:0000269|PubMed:3754863, ECO:0000269|Ref.10, ECO:0000269|Ref.9}.		cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						GTTGACTGGCGGCTATAAACC	0.507													G|||	2373	0.473842	0.149	0.6268	5008	,	,		20016	0.5913		0.5746	False		,,,				2504	0.5798				p.G162S		Atlas-SNP	.											.	OAS1	128	.	0			c.G484A	GRCh37	CM060397	OAS1	M	rs1131454	PASS	.	G	SER/GLY,SER/GLY,SER/GLY	1081,3325	391.9+/-328.3	151,779,1273	71.0	64.0	67.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	484,484,484	-5.9	0.0	12	dbSNP_86	67	4868,3732	617.7+/-396.7	1397,2074,829	yes	missense,missense,missense	OAS1	NM_001032409.1,NM_002534.2,NM_016816.2	56,56,56	1548,2853,2102	AA,AG,GG		43.3953,24.5347,45.7404	benign,benign,benign	162/415,162/365,162/401	113348870	5949,7057	2203	4300	6503	SO:0001583	missense	4938	exon3			ACTGGCGGCTATA	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"""2',5'-oligoadenylate synthetase 1 (40-46 kD)"""	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.484G>A	12.37:g.113348870G>A	ENSP00000202917:p.Gly162Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001032409	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	37	CCDS41838.1	1064	0.48717948717948717	77	0.1565040650406504	210	0.580110497237569	344	0.6013986013986014	433	0.5712401055408971	G	7.616	0.675789	0.14841	0.245347	0.566047	ENSG00000089127	ENST00000202917;ENST00000445409;ENST00000452357;ENST00000551241;ENST00000377508;ENST00000550689	T;T;T;T;T	0.08282	3.11;3.11;3.11;3.11;3.11	4.16	-5.92	0.02261	.	4.278070	0.00481	N	0.000139	T	0.00012	0.0000	L	0.35542	1.07	0.80722	P	0.0	B;B;B;B;B	0.12630	0.002;0.005;0.0;0.006;0.002	B;B;B;B;B	0.14023	0.003;0.004;0.004;0.01;0.004	T	0.41752	-0.9491	9	0.26408	T	0.33	0.0918	4.839	0.13478	0.5189:0.0:0.216:0.2651	rs1131454;rs2070164;rs3191365;rs3741981;rs11543293;rs17413811;rs17834195;rs52812159;rs56435707;rs57921148;rs3741981	162;162;162;162;162	E7EMI9;F8VXY3;P00973;P00973-3;P00973-2	.;.;OAS1_HUMAN;.;.	S	162;162;162;162;162;158	ENSP00000202917:G162S;ENSP00000388001:G162S;ENSP00000415721:G162S;ENSP00000448790:G162S;ENSP00000448348:G158S	ENSP00000202917:G162S	G	+	1	0	OAS1	111833253	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.338000	0.07842	-1.602000	0.01599	-0.254000	0.11334	GGC	A|0.381;C|0.108;G|0.441;T|0.070	0.381	strong		0.507	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2		
OTUD1	220213	hgsc.bcm.edu	37	10	23729362	23729362	+	Missense_Mutation	SNP	A	A	T	rs139969083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:23729362A>T	ENST00000376495.3	+	1	1165	c.976A>T	c.(976-978)Agc>Tgc	p.S326C		NM_001145373.2	NP_001138845.1	Q5VV17	OTUD1_HUMAN	OTU deubiquitinase 1	326	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				protein K63-linked deubiquitination (GO:0070536)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)	5						CCGAGCTGTCAGCAAGACGGT	0.572													A|||	37	0.00738818	0.0008	0.0216	5008	,	,		17948	0.0		0.0179	False		,,,				2504	0.0031				p.S326C		Atlas-SNP	.											.	OTUD1	9	.	0			c.A976T						PASS	.						44.0	48.0	47.0					10																	23729362		692	1591	2283	SO:0001583	missense	220213	exon1			GCTGTCAGCAAGA	AK096389	CCDS44366.1	10p12.31	2014-02-24	2014-02-24		ENSG00000165312	ENSG00000165312		"""OTU domain containing"""	27346	protein-coding gene	gene with protein product		612022	"""OTU domain containing 1"""	OTDC1		23827681	Standard	NM_001145373		Approved	DUBA7	uc001irr.2	Q5VV17	OTTHUMG00000017819	ENST00000376495.3:c.976A>T	10.37:g.23729362A>T	ENSP00000365678:p.Ser326Cys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_001145373		Missense_Mutation	SNP	ENST00000376495.3	37	CCDS44366.1	19	0.0086996336996337	0	0.0	8	0.022099447513812154	0	0.0	11	0.014511873350923483	A	12.88	2.069510	0.36470	.	.	ENSG00000165312	ENST00000376495	T	0.37915	1.17	4.54	4.54	0.55810	Ovarian tumour, otubain (2);	0.065026	0.64402	U	0.000010	T	0.11537	0.0281	N	0.25647	0.755	0.36643	D	0.876951	B	0.29232	0.238	B	0.24974	0.057	T	0.14254	-1.0479	10	0.31617	T	0.26	-6.0858	8.0773	0.30724	0.6739:0.0:0.0:0.3261	.	326	Q5VV17	OTUD1_HUMAN	C	326	ENSP00000365678:S326C	ENSP00000365678:S326C	S	+	1	0	OTUD1	23769368	1.000000	0.71417	0.997000	0.53966	0.984000	0.73092	4.170000	0.58229	1.666000	0.50821	0.533000	0.62120	AGC	A|0.989;T|0.011	0.011	strong		0.572	OTUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047215.1	XM_166659	
INSL6	11172	hgsc.bcm.edu	37	9	5185365	5185365	+	Missense_Mutation	SNP	A	A	G	rs2149554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5185365A>G	ENST00000381641.3	-	1	303	c.238T>C	c.(238-240)Ttc>Ctc	p.F80L		NM_007179.2	NP_009110.2	Q9Y581	INSL6_HUMAN	insulin-like 6	80			F -> L (in dbSNP:rs2149554).		fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(2)	15	all_hematologic(13;0.137)	Breast(48;0.147)|Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0128)|Lung(218;0.145)		GGGCTTTCGAACTGGTATGGG	0.537													A|||	503	0.100439	0.3646	0.0274	5008	,	,		16500	0.0		0.001	False		,,,				2504	0.001				p.F80L		Atlas-SNP	.											INSL6,NS,carcinoma,+2,1	INSL6	35	1	0			c.T238C						scavenged	.	A	LEU/PHE	1275,3131	436.4+/-344.6	176,923,1104	118.0	126.0	123.0		238	0.5	0.0	9	dbSNP_96	123	10,8590	6.4+/-24.3	0,10,4290	yes	missense	INSL6	NM_007179.2	22	176,933,5394	GG,GA,AA		0.1163,28.9378,9.8801	benign	80/214	5185365	1285,11721	2203	4300	6503	SO:0001583	missense	11172	exon1			TTTCGAACTGGTA	AF156094	CCDS6458.1	9p24	2008-07-21			ENSG00000120210	ENSG00000120210			6089	protein-coding gene	gene with protein product	"""relaxin/insulin-like factor 1"""	606414				10819760	Standard	NM_007179		Approved	RIF1	uc003zix.3	Q9Y581	OTTHUMG00000019489	ENST00000381641.3:c.238T>C	9.37:g.5185365A>G	ENSP00000371054:p.Phe80Leu	Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_007179	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000381641.3	37	CCDS6458.1	184	0.08424908424908426	174	0.35365853658536583	10	0.027624309392265192	0	0.0	0	0.0	A	5.443	0.266871	0.10294	0.289378	0.001163	ENSG00000120210	ENST00000381641	T	0.40476	1.03	4.39	0.455	0.16649	Insulin-like (3);	3.103370	0.00944	N	0.002876	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.29427	-1.0012	9	0.11485	T	0.65	-13.6373	3.4873	0.07625	0.5569:0.1995:0.2435:0.0	rs2149554;rs52816055;rs56640305;rs2149554	80	Q9Y581	INSL6_HUMAN	L	80	ENSP00000371054:F80L	ENSP00000371054:F80L	F	-	1	0	INSL6	5175365	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.553000	0.06012	0.067000	0.16545	0.533000	0.62120	TTC	A|0.897;G|0.103	0.103	strong		0.537	INSL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051608.3	NM_007179	
HHIPL2	79802	hgsc.bcm.edu	37	1	222721288	222721288	+	Silent	SNP	C	C	T	rs4846382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:222721288C>T	ENST00000343410.6	-	1	157	c.99G>A	c.(97-99)ttG>ttA	p.L33L		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	33					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)		CCACCTGGCCCAACAAGAATA	0.577													C|||	2914	0.581869	0.3124	0.7205	5008	,	,		16120	0.6379		0.6044	False		,,,				2504	0.7669				p.L33L		Atlas-SNP	.											.	HHIPL2	122	.	0			c.G99A						PASS	.	C		1464,2374		291,882,746	38.0	44.0	42.0		99	1.5	0.4	1	dbSNP_111	42	5085,3161		1574,1937,612	no	coding-synonymous	HHIPL2	NM_024746.3		1865,2819,1358	TT,TC,CC		38.3337,38.1449,45.8044		33/725	222721288	6549,5535	1919	4123	6042	SO:0001819	synonymous_variant	79802	exon1			CTGGCCCAACAAG	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.99G>A	1.37:g.222721288C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	154	77	0.5	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	37	CCDS1530.2																																																																																			C|0.444;T|0.556	0.556	strong		0.577	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
ICAM5	7087	hgsc.bcm.edu	37	19	10404588	10404588	+	Silent	SNP	T	T	C	rs116688659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10404588T>C	ENST00000221980.4	+	7	1743	c.1680T>C	c.(1678-1680)tcT>tcC	p.S560S		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	560	Ig-like C2-type 6.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CTCGGGGCTCTGCGGCCAAAA	0.662													T|||	24	0.00479233	0.0182	0.0	5008	,	,		17413	0.0		0.0	False		,,,				2504	0.0				p.S560S		Atlas-SNP	.											.	ICAM5	53	.	0			c.T1680C						PASS	.	T		55,4349	54.2+/-90.2	0,55,2147	42.0	49.0	47.0		1680	-9.2	0.0	19	dbSNP_132	47	0,8600		0,0,4300	no	coding-synonymous	ICAM5	NM_003259.3		0,55,6447	CC,CT,TT		0.0,1.2489,0.4229		560/925	10404588	55,12949	2202	4300	6502	SO:0001819	synonymous_variant	7087	exon7			GGGCTCTGCGGCC	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1680T>C	19.37:g.10404588T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_003259	Q9Y6F3	Silent	SNP	ENST00000221980.4	37	CCDS12233.1																																																																																			T|0.995;C|0.005	0.005	strong		0.662	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
PUS7L	83448	hgsc.bcm.edu	37	12	44148259	44148259	+	Missense_Mutation	SNP	T	T	C	rs1057190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:44148259T>C	ENST00000416848.2	-	2	1278	c.790A>G	c.(790-792)Aaa>Gaa	p.K264E	PUS7L_ENST00000344862.5_Missense_Mutation_p.K264E|PUS7L_ENST00000551923.1_Missense_Mutation_p.K264E|PUS7L_ENST00000553166.1_Missense_Mutation_p.K264E|PUS7L_ENST00000431332.3_Intron	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	264			K -> E (in dbSNP:rs1057190). {ECO:0000269|PubMed:17974005}.		pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		CAATTCATTTTAGAAAAAGAT	0.383													C|||	1341	0.267772	0.5908	0.1657	5008	,	,		16995	0.1905		0.1083	False		,,,				2504	0.1472				p.K264E		Atlas-SNP	.											.	PUS7L	73	.	0			c.A790G						PASS	.	C	GLU/LYS,GLU/LYS,GLU/LYS	2262,2144	579.2+/-384.9	572,1118,513	129.0	126.0	127.0		790,790,790	5.3	0.8	12	dbSNP_86	127	990,7610	772.6+/-407.7	48,894,3358	yes	missense,missense,missense	PUS7L	NM_001098614.1,NM_001098615.1,NM_031292.3	56,56,56	620,2012,3871	CC,CT,TT		11.5116,48.6609,25.0038	benign,benign,benign	264/702,264/702,264/702	44148259	3252,9754	2203	4300	6503	SO:0001583	missense	83448	exon2			TCATTTTAGAAAA	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.790A>G	12.37:g.44148259T>C	ENSP00000415899:p.Lys264Glu	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	285	283	0.992982	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Missense_Mutation	SNP	ENST00000416848.2	37	CCDS8743.1	502	0.22985347985347984	277	0.5630081300813008	56	0.15469613259668508	92	0.16083916083916083	77	0.10158311345646438	C	0.160	-1.082297	0.01888	0.513391	0.115116	ENSG00000129317	ENST00000416848;ENST00000344862;ENST00000551923;ENST00000553166	T;T;T;T	0.21361	2.02;2.02;2.02;2.01	5.35	5.35	0.76521	Pseudouridine synthase, catalytic domain (1);	0.255452	0.44097	N	0.000491	T	0.00012	0.0000	N	0.00347	-1.61	0.27947	P	0.9373084	B	0.02656	0.0	B	0.01281	0.0	T	0.41787	-0.9489	9	0.02654	T	1	-9.231	13.0403	0.58895	0.0:0.8633:0.0:0.1367	rs1057190;rs52792291;rs60869292;rs1057190	264	Q9H0K6	PUS7L_HUMAN	E	264	ENSP00000415899:K264E;ENSP00000343081:K264E;ENSP00000447706:K264E;ENSP00000446865:K264E	ENSP00000343081:K264E	K	-	1	0	PUS7L	42434526	0.025000	0.19082	0.771000	0.31576	0.065000	0.16274	2.632000	0.46511	1.604000	0.50143	-0.119000	0.15052	AAA	T|0.749;C|0.251	0.251	strong		0.383	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274360	39274360	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39274360A>T	ENST00000391413.2	-	1	246	c.208T>A	c.(208-210)Tgc>Agc	p.C70S		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	70	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CTGGAGATGCAGCATCTGGGG	0.667																																					p.C70S		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,1	KRTAP4-11	94	1	0			c.T208A						scavenged	.						7.0	12.0	11.0					17																	39274360		677	1580	2257	SO:0001583	missense	653240	exon1			AGATGCAGCATCT	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.208T>A	17.37:g.39274360A>T	ENSP00000375232:p.Cys70Ser	Somatic	189	2	0.010582		WXS	Illumina HiSeq	Phase_I	169	15	0.0887574	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	13.38	2.219303	0.39201	.	.	ENSG00000212721	ENST00000391413	T	0.02280	4.36	3.77	1.34	0.21922	.	0.000000	0.36972	U	0.002304	T	0.04770	0.0129	M	0.90252	3.1	0.23636	N	0.997233	B	0.17268	0.021	B	0.17722	0.019	T	0.23048	-1.0199	10	0.54805	T	0.06	.	4.9719	0.14119	0.7038:0.1861:0.1101:0.0	.	70	Q9BYQ6	KR411_HUMAN	S	70	ENSP00000375232:C70S	ENSP00000375232:C70S	C	-	1	0	KRTAP4-11	36527886	0.844000	0.29557	0.494000	0.27515	0.120000	0.20174	1.052000	0.30429	0.644000	0.30656	0.496000	0.49642	TGC	.	.	none		0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
LAD1	3898	hgsc.bcm.edu	37	1	201355669	201355669	+	Missense_Mutation	SNP	T	T	C	rs68021059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201355669T>C	ENST00000391967.2	-	3	1121	c.820A>G	c.(820-822)Act>Gct	p.T274A	LAD1_ENST00000367313.3_Missense_Mutation_p.T288A|LAD1_ENST00000488842.1_5'Flank	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	274						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						GCATCTGCAGTTGGGCTCTTC	0.637													T|||	365	0.0728834	0.1377	0.0778	5008	,	,		12772	0.0		0.0885	False		,,,				2504	0.0409				p.T274A		Atlas-SNP	.											.	LAD1	42	.	0			c.A820G						PASS	.	T	ALA/THR	536,3868	219.1+/-236.9	37,462,1703	63.0	72.0	69.0		820	-3.4	0.0	1	dbSNP_130	69	700,7900	164.6+/-216.9	30,640,3630	yes	missense	LAD1	NM_005558.3	58	67,1102,5333	CC,CT,TT		8.1395,12.1708,9.5048	benign	274/518	201355669	1236,11768	2202	4300	6502	SO:0001583	missense	3898	exon3			CTGCAGTTGGGCT	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.820A>G	1.37:g.201355669T>C	ENSP00000375829:p.Thr274Ala	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	170	170	1	NM_005558	O95614|Q96GD8	Missense_Mutation	SNP	ENST00000391967.2	37	CCDS1410.1	164	0.07509157509157509	65	0.13211382113821138	33	0.09116022099447514	0	0.0	66	0.0870712401055409	T	0.012	-1.653285	0.00779	0.121708	0.081395	ENSG00000159166	ENST00000391967;ENST00000367313	T;T	0.10288	2.89;2.91	3.16	-3.42	0.04825	.	1.877400	0.02959	N	0.142802	T	0.00039	0.0001	N	0.01576	-0.805	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.32322	-0.9911	9	0.07175	T	0.84	.	3.498	0.07662	0.1833:0.2964:0.0:0.5203	.	288;274	E9PDI4;O00515	.;LAD1_HUMAN	A	274;288	ENSP00000375829:T274A;ENSP00000356282:T288A	ENSP00000356282:T288A	T	-	1	0	LAD1	199622292	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.209000	0.09358	-0.983000	0.03511	-1.248000	0.01517	ACT	T|0.917;C|0.083	0.083	strong		0.637	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
KLHDC7B	113730	hgsc.bcm.edu	37	22	50988062	50988062	+	Silent	SNP	G	G	T	rs140519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50988062G>T	ENST00000395676.2	+	1	1601	c.1467G>T	c.(1465-1467)gtG>gtT	p.V489V	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	489										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)		GCGACATCGTGGCACTGGGGG	0.667													G|||	2029	0.405152	0.1936	0.4366	5008	,	,		13461	0.5784		0.495	False		,,,				2504	0.3978				p.V489V		Atlas-SNP	.											KLHDC7B,extremity,malignant_melanoma,+2,1	KLHDC7B	39	1	0			c.G1467T						PASS	.	G		1017,3389		119,779,1305	48.0	54.0	52.0		1467	3.2	1.0	22	dbSNP_78	52	4137,4459		1014,2109,1175	no	coding-synonymous	KLHDC7B	NM_138433.3		1133,2888,2480	TT,TG,GG		48.127,23.0822,39.6401		489/595	50988062	5154,7848	2203	4298	6501	SO:0001819	synonymous_variant	113730	exon1			CATCGTGGCACTG	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.1467G>T	22.37:g.50988062G>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_138433		Silent	SNP	ENST00000395676.2	37	CCDS14097.2																																																																																			G|0.594;T|0.406	0.406	strong		0.667	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433	
EXOC3L2	90332	hgsc.bcm.edu	37	19	45719426	45719426	+	Silent	SNP	G	G	A	rs34958174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45719426G>A	ENST00000252482.3	-	8	873	c.846C>T	c.(844-846)gcC>gcT	p.A282A	AC006126.3_ENST00000591569.1_Intron|EXOC3L2_ENST00000413988.1_Silent_p.A282A			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	282					exocytosis (GO:0006887)	exocyst (GO:0000145)				endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		GGGGCACCACGGCATCCAGCC	0.632													G|||	266	0.053115	0.1914	0.0187	5008	,	,		16902	0.0		0.0	False		,,,				2504	0.0				p.A282A		Atlas-SNP	.											.	EXOC3L2	30	.	0			c.C846T						PASS	.	G		636,3770	254.0+/-259.7	55,526,1622	51.0	40.0	44.0		846	-9.1	0.6	19	dbSNP_126	44	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	EXOC3L2	NM_138568.3		55,529,5919	AA,AG,GG		0.0349,14.4349,4.9131		282/410	45719426	639,12367	2203	4300	6503	SO:0001819	synonymous_variant	90332	exon9			CACCACGGCATCC	AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.846C>T	19.37:g.45719426G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_138568	Q8N9W2|Q96GV2	Silent	SNP	ENST00000252482.3	37	CCDS12657.1																																																																																			G|0.946;A|0.054	0.054	strong		0.632	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568	
DNAH14	127602	hgsc.bcm.edu	37	1	225355716	225355716	+	Missense_Mutation	SNP	T	T	C	rs78614986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225355716T>C	ENST00000445597.2	+	23	4240	c.4240T>C	c.(4240-4242)Tat>Cat	p.Y1414H	DNAH14_ENST00000430092.1_Missense_Mutation_p.Y1819H|DNAH14_ENST00000439375.2_Missense_Mutation_p.Y1819H			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1414					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TATACAGTTTTATAATCAACT	0.269													T|||	28	0.00559105	0.0204	0.0014	5008	,	,		16127	0.0		0.0	False		,,,				2504	0.0				p.Y1819H		Atlas-SNP	.											.	DNAH14	300	.	0			c.T5455C						PASS	.	T	HIS/TYR	41,1343		0,41,651	50.0	50.0	50.0		5455	-2.7	1.0	1	dbSNP_132	50	0,3156		0,0,1578	no	missense	DNAH14	NM_001373.1	83	0,41,2229	CC,CT,TT		0.0,2.9624,0.9031	probably-damaging	1819/4516	225355716	41,4499	692	1578	2270	SO:0001583	missense	127602	exon35			CAGTTTTATAATC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.4240T>C	1.37:g.225355716T>C	ENSP00000409472:p.Tyr1414His	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	279	131	0.469534	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	T	10.64	1.405909	0.25378	0.029624	0.0	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375;ENST00000328556	T;T;T;T	0.39997	2.15;1.05;1.05;1.42	5.24	-2.69	0.06022	.	.	.	.	.	T	0.13372	0.0324	L	0.43598	1.365	0.80722	D	1	B	0.12630	0.006	B	0.16722	0.016	T	0.08785	-1.0705	9	0.54805	T	0.06	.	12.5268	0.56091	0.0:0.5994:0.0:0.4006	.	1819	Q0VDD8-4	.	H	1414;1819;1819;913	ENSP00000409472:Y1414H;ENSP00000414402:Y1819H;ENSP00000392061:Y1819H;ENSP00000332424:Y913H	ENSP00000332424:Y913H	Y	+	1	0	DNAH14	223422339	0.356000	0.24930	0.977000	0.42913	0.834000	0.47266	-1.031000	0.03578	-0.549000	0.06191	-0.237000	0.12165	TAT	T|0.993;C|0.007	0.007	strong		0.269	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
SLC37A3	84255	hgsc.bcm.edu	37	7	140051116	140051116	+	Missense_Mutation	SNP	G	G	A	rs76089276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140051116G>A	ENST00000326232.9	-	9	1042	c.839C>T	c.(838-840)gCg>gTg	p.A280V	SLC37A3_ENST00000429996.2_3'UTR|SLC37A3_ENST00000447932.2_Missense_Mutation_p.A280V|SLC37A3_ENST00000340308.3_Missense_Mutation_p.A280V	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	280					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					GAAGCTTATCGCCTTGACTTG	0.468													G|||	167	0.0333466	0.1188	0.0115	5008	,	,		20455	0.0		0.002	False		,,,				2504	0.0				p.A280V	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.C839T						PASS	.	G	VAL/ALA,VAL/ALA	454,3952	216.4+/-235.1	19,416,1768	152.0	129.0	137.0		839,839	5.2	1.0	7	dbSNP_131	137	8,8592	5.0+/-18.6	0,8,4292	yes	missense,missense	SLC37A3	NM_032295.2,NM_207113.1	64,64	19,424,6060	AA,AG,GG		0.093,10.3041,3.5522	probably-damaging,probably-damaging	280/444,280/495	140051116	462,12544	2203	4300	6503	SO:0001583	missense	84255	exon9			CTTATCGCCTTGA	AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"""Solute carriers"""	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.839C>T	7.37:g.140051116G>A	ENSP00000321498:p.Ala280Val	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	187	83	0.44385	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	37	CCDS5859.1	71|71	0.03250915750915751|0.03250915750915751	66|66	0.13414634146341464|0.13414634146341464	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	20.6|20.6	4.022383|4.022383	0.75275|0.75275	0.103041|0.103041	9.3E-4|9.3E-4	ENSG00000157800|ENSG00000157800	ENST00000340308;ENST00000447932;ENST00000326232|ENST00000485734	T;T;T|.	0.58060|.	0.36;0.36;0.36|.	5.2|5.2	5.2|5.2	0.72013|0.72013	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.04407|.	0.0121|.	M|M	0.86097|0.86097	2.795|2.795	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.79108|.	0.981;0.992;0.979|.	T|.	0.49716|.	-0.8910|.	10|.	0.62326|.	D|.	0.03|.	-43.077|-43.077	18.7136|18.7136	0.91667|0.91667	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	280;280;280|.	Q8NCC5-2;Q8NCC5-3;Q8NCC5|.	.;.;SPX3_HUMAN|.	V|X	280|59	ENSP00000343358:A280V;ENSP00000397481:A280V;ENSP00000321498:A280V|.	ENSP00000321498:A280V|.	A|R	-|-	2|1	0|2	SLC37A3|SLC37A3	139697585|139697585	1.000000|1.000000	0.71417|0.71417	0.951000|0.951000	0.38953|0.38953	0.262000|0.262000	0.26303|0.26303	7.710000|7.710000	0.84655|0.84655	2.575000|2.575000	0.86900|0.86900	0.563000|0.563000	0.77884|0.77884	GCG|CGA	G|0.969;A|0.031	0.031	strong		0.468	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295	
MGAM	8972	hgsc.bcm.edu	37	7	141754625	141754625	+	Silent	SNP	C	C	T	rs115294234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141754625C>T	ENST00000549489.2	+	27	3326	c.3231C>T	c.(3229-3231)acC>acT	p.T1077T	MGAM_ENST00000475668.2_Silent_p.T1077T	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1077	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)	CATCCAGCACCCCTGAGGGTC	0.448													c|||	56	0.0111821	0.0401	0.0043	5008	,	,		19007	0.0		0.0	False		,,,				2504	0.0				p.T1077T		Atlas-SNP	.											.	MGAM	767	.	0			c.C3231T						PASS	.	C		137,3699		4,129,1785	142.0	135.0	137.0		3231	1.1	0.2	7	dbSNP_132	137	0,8226		0,0,4113	no	coding-synonymous	MGAM	NM_004668.2		4,129,5898	TT,TC,CC		0.0,3.5714,1.1358		1077/1858	141754625	137,11925	1918	4113	6031	SO:0001819	synonymous_variant	8972	exon27			CAGCACCCCTGAG	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.3231C>T	7.37:g.141754625C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	190	95	0.5	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			C|0.985;T|0.015	0.015	strong		0.448	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
RNF186	54546	hgsc.bcm.edu	37	1	20141528	20141528	+	Missense_Mutation	SNP	C	C	T	rs1541185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	276	150	0.543478	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	
CLDN22	53842	hgsc.bcm.edu	37	4	184240777	184240777	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:184240777A>G	ENST00000323319.5	-	1	1150	c.595T>C	c.(595-597)Tac>Cac	p.Y199H	WWC2_ENST00000403733.3_3'UTR	NM_001111319.1	NP_001104789.1	Q8N7P3	CLD22_HUMAN	claudin 22	199					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			cervix(1)|kidney(1)|lung(3)|prostate(1)|skin(1)	7		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.0172)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|Esophageal squamous(56;0.176)		all cancers(43;4.1e-26)|Epithelial(43;6.45e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|Colorectal(24;5.87e-06)|GBM - Glioblastoma multiforme(59;6.5e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		GCCACTGCGTAGTGGCCCGAA	0.542																																					p.Y199H		Atlas-SNP	.											CLDN22,NS,carcinoma,+2,1	CLDN22	20	1	0			c.T595C						scavenged	.						232.0	210.0	217.0					4																	184240777		1568	3582	5150	SO:0001583	missense	53842	exon1			CTGCGTAGTGGCC	AK098064	CCDS43286.1	4q35.1	2010-08-05			ENSG00000177300	ENSG00000177300		"""Claudins"""	2044	protein-coding gene	gene with protein product							Standard	NM_001111319		Approved	CLDN21	uc010isa.1	Q8N7P3	OTTHUMG00000160627	ENST00000323319.5:c.595T>C	4.37:g.184240777A>G	ENSP00000318113:p.Tyr199His	Somatic	243	2	0.00823045		WXS	Illumina HiSeq	Phase_I	300	153	0.51	NM_001111319		Missense_Mutation	SNP	ENST00000323319.5	37	CCDS43286.1	.	.	.	.	.	.	.	.	.	.	A	11.23	1.577764	0.28180	.	.	ENSG00000177300	ENST00000323319	D	0.85411	-1.98	6.07	2.4	0.29515	.	0.831349	0.11145	N	0.594777	T	0.80974	0.4727	M	0.63843	1.955	0.09310	N	1	B	0.29508	0.246	B	0.26094	0.066	T	0.69135	-0.5225	10	0.54805	T	0.06	.	6.5842	0.22612	0.7044:0.0:0.1875:0.108	.	199	Q8N7P3	CLD22_HUMAN	H	199	ENSP00000318113:Y199H	ENSP00000318113:Y199H	Y	-	1	0	CLDN22	184477771	0.029000	0.19370	0.651000	0.29564	0.026000	0.11368	0.963000	0.29293	0.176000	0.19873	-1.139000	0.01908	TAC	.	.	none		0.542	CLDN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361493.1		
NAA16	79612	hgsc.bcm.edu	37	13	41929296	41929296	+	Missense_Mutation	SNP	A	A	G	rs17062054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:41929296A>G	ENST00000379406.3	+	10	1355	c.1031A>G	c.(1030-1032)gAa>gGa	p.E344G	NAA16_ENST00000379367.3_Missense_Mutation_p.E344G|RNU6-57P_ENST00000411348.1_RNA|NAA16_ENST00000403412.3_Missense_Mutation_p.E344G	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	344			E -> G (in dbSNP:rs17062054).		N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						ATAATCCAGGAACTTGTTACT	0.254													A|||	379	0.0756789	0.2723	0.0259	5008	,	,		14616	0.0		0.001	False		,,,				2504	0.0				p.E344G		Atlas-SNP	.											.	NAA16	74	.	0			c.A1031G						PASS	.	A	GLY/GLU,,GLY/GLU	1062,3342	336.3+/-304.3	129,804,1269	92.0	103.0	99.0		1031,924,1031	5.2	1.0	13	dbSNP_123	99	17,8567	6.4+/-24.3	0,17,4275	yes	missense,coding-synonymous,missense	NAA16	NM_001110798.1,NM_018527.3,NM_024561.4	98,,98	129,821,5544	GG,GA,AA		0.198,24.1144,8.3077	possibly-damaging,,possibly-damaging	344/430,308/312,344/865	41929296	1079,11909	2202	4292	6494	SO:0001583	missense	79612	exon10			TCCAGGAACTTGT	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"""N(alpha)-acetyltransferase subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	26164	protein-coding gene	gene with protein product			"""NMDA receptor regulated 1-like"""	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.1031A>G	13.37:g.41929296A>G	ENSP00000368716:p.Glu344Gly	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	36	13	0.361111	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	37	CCDS9379.1	122	0.055860805860805864	111	0.22560975609756098	11	0.03038674033149171	0	0.0	0	0.0	A	20.6	4.024646	0.75390	0.241144	0.00198	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.50001	0.76;0.76;0.76	5.23	5.23	0.72850	.	0.074309	0.56097	D	0.000039	T	0.00039	0.0001	.	.	.	0.18873	P	0.9999871049	P;P	0.48640	0.866;0.913	P;P	0.57548	0.61;0.823	T	0.00814	-1.1555	8	0.72032	D	0.01	-14.8273	15.0951	0.72226	1.0:0.0:0.0:0.0	rs17062054;rs52827917;rs59013357;rs17062054	344;344	Q6N069;Q6N069-4	NAA16_HUMAN;.	G	344	ENSP00000368674:E344G;ENSP00000368716:E344G;ENSP00000386103:E344G	ENSP00000368674:E344G	E	+	2	0	NAA16	40827296	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.480000	0.81109	1.980000	0.57719	0.533000	0.62120	GAA	A|0.919;G|0.081	0.081	strong		0.254	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527	
ADAM12	8038	hgsc.bcm.edu	37	10	127737930	127737930	+	Silent	SNP	G	G	A	rs2292692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	141	0	0		WXS	Illumina HiSeq	Phase_I	136	60	0.441176	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		
GIMAP7	168537	hgsc.bcm.edu	37	7	150217248	150217248	+	Silent	SNP	A	A	G	rs3735081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150217248A>G	ENST00000313543.4	+	2	343	c.186A>G	c.(184-186)gtA>gtG	p.V62V		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	62	AIG1-type G.				GTP catabolic process (GO:0006184)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTCTTGTTGTAGACACTCCAG	0.522													G|||	3914	0.78155	0.9713	0.7277	5008	,	,		18549	0.7421		0.6302	False		,,,				2504	0.7597				p.V62V		Atlas-SNP	.											GIMAP7,NS,carcinoma,+2,1	GIMAP7	47	1	0			c.A186G						PASS	.	G		4031,375	191.2+/-216.9	1849,333,21	53.0	51.0	52.0		186	-7.2	0.2	7	dbSNP_107	52	5377,3223	486.1+/-371.8	1691,1995,614	no	coding-synonymous	GIMAP7	NM_153236.3		3540,2328,635	GG,GA,AA		37.4767,8.5111,27.6642		62/301	150217248	9408,3598	2203	4300	6503	SO:0001819	synonymous_variant	168537	exon2			TGTTGTAGACACT	BC027613	CCDS5903.1	7q36.1	2014-04-04			ENSG00000179144	ENSG00000179144		"""GTPases, IMAP"""	22404	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 7"""					15474311	Standard	NM_153236		Approved	MGC27027, IAN7	uc003whk.3	Q8NHV1	OTTHUMG00000157626	ENST00000313543.4:c.186A>G	7.37:g.150217248A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_153236		Silent	SNP	ENST00000313543.4	37	CCDS5903.1																																																																																			A|0.252;G|0.748	0.748	strong		0.522	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236	
PELP1	27043	hgsc.bcm.edu	37	17	4586220	4586220	+	Silent	SNP	G	G	A	rs35109567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4586220G>A	ENST00000574876.1	-	4	465	c.448C>T	c.(448-450)Ctg>Ttg	p.L150L	PELP1_ENST00000572293.1_Silent_p.L200L|PELP1_ENST00000570823.1_5'Flank|PELP1_ENST00000269230.7_Silent_p.L150L|PELP1_ENST00000436683.2_Silent_p.L3L|PELP1_ENST00000301396.4_Silent_p.L150L|AC091153.4_ENST00000441700.2_RNA			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	150					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						GCCACGGCCAGCTCCATTGTG	0.557													g|||	138	0.0275559	0.1014	0.0058	5008	,	,		16714	0.0		0.0	False		,,,				2504	0.0				p.L150L		Atlas-SNP	.											.	PELP1	102	.	0			c.C448T						PASS	.			338,3568		15,308,1630	24.0	28.0	27.0		448	-3.3	1.0	17	dbSNP_126	27	5,8279		0,5,4137	no	coding-synonymous	PELP1	NM_014389.2		15,313,5767	AA,AG,GG		0.0604,8.6534,2.8138		150/1131	4586220	343,11847	1953	4142	6095	SO:0001819	synonymous_variant	27043	exon4			CGGCCAGCTCCAT		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.448C>T	17.37:g.4586220G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	176	84	0.477273	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			G|0.974;A|0.026	0.026	strong		0.557	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
AHSG	197	hgsc.bcm.edu	37	3	186338634	186338634	+	Missense_Mutation	SNP	G	G	A	rs77385737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186338634G>A	ENST00000273784.5	+	7	1098	c.1022G>A	c.(1021-1023)cGc>cAc	p.R341H	AHSG_ENST00000411641.2_Missense_Mutation_p.R340H	NM_001622.2	NP_001613.2	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	340					acute-phase response (GO:0006953)|negative regulation of bone mineralization (GO:0030502)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|ossification (GO:0001503)|pinocytosis (GO:0006907)|positive regulation of phagocytosis (GO:0050766)|regulation of bone mineralization (GO:0030500)|regulation of inflammatory response (GO:0050727)|skeletal system development (GO:0001501)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|kinase inhibitor activity (GO:0019210)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(2)|stomach(1)	22	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		CGGAAAACACGCACAGTGGTG	0.602													.|||	17	0.00339457	0.0121	0.0	5008	,	,		21835	0.0		0.001	False		,,,				2504	0.0				p.R340H		Atlas-SNP	.											AHSG,NS,carcinoma,+1,1	AHSG	40	1	0			c.G1019A						scavenged	.	G	HIS/ARG	59,4347	58.1+/-94.6	1,57,2145	81.0	77.0	79.0		1019	1.7	0.0	3	dbSNP_132	79	2,8598	2.2+/-6.3	0,2,4298	yes	missense	AHSG	NM_001622.2	29	1,59,6443	AA,AG,GG		0.0233,1.3391,0.469	probably-damaging	340/368	186338634	61,12945	2203	4300	6503	SO:0001583	missense	197	exon7			AAACACGCACAGT	D67013, M16961	CCDS3278.1	3q27.3	2006-02-22			ENSG00000145192	ENSG00000145192			349	protein-coding gene	gene with protein product		138680				9322749, 7736783	Standard	NM_001622		Approved	FETUA, A2HS, HSGA	uc003fqk.4	P02765	OTTHUMG00000156605	ENST00000273784.5:c.1022G>A	3.37:g.186338634G>A	ENSP00000273784:p.Arg341His	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	169	86	0.508876	NM_001622	A8K9N6|B2R7G1|O14961|O14962|Q9P152	Missense_Mutation	SNP	ENST00000273784.5	37		5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	g	9.995	1.232001	0.22626	0.013391	2.33E-4	ENSG00000145192	ENST00000411641;ENST00000541510;ENST00000273784	T;T	0.05258	3.47;3.47	4.63	1.7	0.24286	.	0.972799	0.08447	N	0.944617	T	0.04634	0.0126	L	0.44542	1.39	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.001	B;B;B	0.06405	0.002;0.0;0.0	T	0.38436	-0.9661	10	0.44086	T	0.13	-0.6739	7.4138	0.27032	0.3211:0.508:0.1709:0.0	.	406;340;341	F5H0Q5;P02765;C9JV77	.;FETUA_HUMAN;.	H	340;406;341	ENSP00000393887:R340H;ENSP00000273784:R341H	ENSP00000273784:R341H	R	+	2	0	AHSG	187821328	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.305000	0.08188	0.216000	0.20781	-0.344000	0.07964	CGC	G|0.996;A|0.004	0.004	strong		0.602	AHSG-002	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000344762.1	NM_001622	
CBLN1	869	hgsc.bcm.edu	37	16	49314837	49314837	+	Silent	SNP	T	T	G	rs61735589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	130	0	0		WXS	Illumina HiSeq	Phase_I	162	71	0.438272	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	
METTL4	64863	hgsc.bcm.edu	37	18	2555002	2555002	+	Silent	SNP	C	C	T	rs12607882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2555002C>T	ENST00000574538.1	-	4	1270	c.495G>A	c.(493-495)ttG>ttA	p.L165L	snoU109_ENST00000459316.1_RNA|METTL4_ENST00000319888.6_Silent_p.L165L	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	165					nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						CTTCCTGGATCAACTGTAAAG	0.368													T|||	613	0.122404	0.264	0.0994	5008	,	,		19418	0.1329		0.0457	False		,,,				2504	0.0153				p.L165L		Atlas-SNP	.											.	METTL4	40	.	0			c.G495A						PASS	.	T		1003,3403	719.0+/-408.9	116,771,1316	113.0	132.0	125.0		495	3.4	1.0	18	dbSNP_120	125	375,8225	799.3+/-407.4	10,355,3935	yes	coding-synonymous	METTL4	NM_022840.3		126,1126,5251	TT,TC,CC		4.3605,22.7644,10.5951		165/473	2555002	1378,11628	2203	4300	6503	SO:0001819	synonymous_variant	64863	exon4			CTGGATCAACTGT		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.495G>A	18.37:g.2555002C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Silent	SNP	ENST00000574538.1	37	CCDS11826.1																																																																																			C|0.894;T|0.106	0.106	strong		0.368	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840	
LMF1	64788	hgsc.bcm.edu	37	16	929606	929606	+	Silent	SNP	C	C	T	rs61740409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:929606C>T	ENST00000262301.11	-	6	879	c.861G>A	c.(859-861)gcG>gcA	p.A287A	LMF1_ENST00000543238.1_Silent_p.A50A|LMF1_ENST00000568897.1_Silent_p.A70A|LMF1_ENST00000399843.2_Silent_p.A287A|LMF1_ENST00000568268.1_5'UTR	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	287					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)				GGATGATGCACGCCCGCCGGC	0.657													C|||	369	0.0736821	0.1868	0.0346	5008	,	,		15136	0.0179		0.002	False		,,,				2504	0.0798				p.A287A		Atlas-SNP	.											.	LMF1	42	.	0			c.G861A						PASS	.	C		608,3588		38,532,1528	48.0	59.0	56.0		861	3.0	0.0	16	dbSNP_129	56	5,8419		0,5,4207	no	coding-synonymous	LMF1	NM_022773.2		38,537,5735	TT,TC,CC		0.0594,14.49,4.8574		287/568	929606	613,12007	2098	4212	6310	SO:0001819	synonymous_variant	64788	exon6			GATGCACGCCCGC	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.861G>A	16.37:g.929606C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	162	160	0.987654	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			C|0.940;T|0.060	0.060	strong		0.657	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
C10orf12	26148	hgsc.bcm.edu	37	10	98742605	98742605	+	Silent	SNP	C	C	T	rs3814163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98742605C>T	ENST00000286067.2	+	1	1565	c.1458C>T	c.(1456-1458)ctC>ctT	p.L486L		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	486								p.L486L(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		TTGACTCACTCGAAGAGAATT	0.423													C|||	1034	0.20647	0.2821	0.1441	5008	,	,		20933	0.2808		0.0229	False		,,,				2504	0.2607				p.L486L		Atlas-SNP	.											C10orf12,NS,carcinoma,0,1	C10orf12	94	1	1	Substitution - coding silent(1)	stomach(1)	c.C1458T						scavenged	.	C		1057,3349	359.9+/-315.0	136,785,1282	75.0	81.0	79.0		1458	-6.4	0.3	10	dbSNP_107	79	207,8393	82.6+/-145.2	2,203,4095	no	coding-synonymous	C10orf12	NM_015652.2		138,988,5377	TT,TC,CC		2.407,23.99,9.7186		486/1248	98742605	1264,11742	2203	4300	6503	SO:0001819	synonymous_variant	26148	exon1			CTCACTCGAAGAG	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.1458C>T	10.37:g.98742605C>T		Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	56	34	0.607143	NM_015652	Q9H945|Q9Y457	Silent	SNP	ENST00000286067.2	37	CCDS7452.1																																																																																			C|0.862;T|0.138	0.138	strong		0.423	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
LMAN1L	79748	hgsc.bcm.edu	37	15	75113083	75113083	+	Silent	SNP	A	A	G	rs1531163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75113083A>G	ENST00000309664.5	+	8	1021	c.882A>G	c.(880-882)aaA>aaG	p.K294K	LMAN1L_ENST00000379709.3_Silent_p.K282K|RP11-414J4.2_ENST00000564823.1_RNA	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	294						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TAACTCCAAAATCAGACTCTG	0.617													G|||	1299	0.259385	0.4297	0.1239	5008	,	,		19876	0.1746		0.0517	False		,,,				2504	0.4264				p.K294K		Atlas-SNP	.											.	LMAN1L	43	.	0			c.A882G						PASS	.	G		1596,2798	663.2+/-401.2	315,966,916	76.0	76.0	76.0		882	-1.3	0.0	15	dbSNP_88	76	336,8256	804.1+/-407.3	5,326,3965	no	coding-synonymous	LMAN1L	NM_021819.2		320,1292,4881	GG,GA,AA		3.9106,36.3223,14.8776		294/527	75113083	1932,11054	2197	4296	6493	SO:0001819	synonymous_variant	79748	exon8			TCCAAAATCAGAC	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.882A>G	15.37:g.75113083A>G		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_021819	Q6UWN2	Silent	SNP	ENST00000309664.5	37	CCDS10270.1																																																																																			A|0.825;G|0.175	0.175	strong		0.617	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		
ZNF729	100287226	hgsc.bcm.edu	37	19	22496625	22496625	+	Missense_Mutation	SNP	A	A	G	rs75458675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22496625A>G	ENST00000601693.1	+	4	524	c.406A>G	c.(406-408)Aaa>Gaa	p.K136E	ZNF729_ENST00000357491.6_Missense_Mutation_p.K136E			A6NN14	ZN729_HUMAN	zinc finger protein 729	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)			breast(5)|central_nervous_system(1)|lung(32)|ovary(3)	41						TAAGATGCACAAAGAAGGTTA	0.313													G|||	219	0.04373	0.1573	0.0144	5008	,	,		17026	0.0		0.0	False		,,,				2504	0.001				p.K136E		Atlas-SNP	.											.	ZNF729	78	.	0			c.A406G						PASS	.																																			SO:0001583	missense	100287226	exon4			ATGCACAAAGAAG		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.406A>G	19.37:g.22496625A>G	ENSP00000469582:p.Lys136Glu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_001242680	M0QY45	Missense_Mutation	SNP	ENST00000601693.1	37	CCDS59368.1	86	0.039377289377289376	76	0.15447154471544716	6	0.016574585635359115	0	0.0	4	0.005277044854881266	.	0.010	-1.771585	0.00645	.	.	ENSG00000196350	ENST00000357491	T	0.06687	3.27	1.51	-3.02	0.05446	.	.	.	.	.	T	0.00039	0.0001	L	0.59436	1.845	.	.	.	.	.	.	.	.	.	T	0.41822	-0.9487	6	0.05351	T	0.99	.	7.3459	0.26664	0.4764:0.0:0.5236:0.0	.	.	.	.	E	136	ENSP00000350085:K136E	ENSP00000350085:K136E	K	+	1	0	ZNF729	22288465	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.201000	0.09464	-1.811000	0.01229	-1.811000	0.00612	AAA	A|0.960;G|0.040	0.040	strong		0.313	ZNF729-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464396.1	XM_496301	
TACR1	6869	hgsc.bcm.edu	37	2	75425728	75425728	+	Silent	SNP	A	A	G	rs6715729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:75425728A>G	ENST00000305249.5	-	1	1098	c.333T>C	c.(331-333)ttT>ttC	p.F111F	TACR1_ENST00000409848.3_Silent_p.F111F	NM_001058.3	NP_001049.1	P25103	NK1R_HUMAN	tachykinin receptor 1	111					acute inflammatory response (GO:0002526)|aggressive behavior (GO:0002118)|angiotensin-mediated drinking behavior (GO:0003051)|associative learning (GO:0008306)|behavioral response to pain (GO:0048266)|detection of abiotic stimulus (GO:0009582)|eating behavior (GO:0042755)|inflammatory response (GO:0006954)|long-term memory (GO:0007616)|operant conditioning (GO:0035106)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of action potential (GO:0045760)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of ossification (GO:0045778)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of saliva secretion (GO:0046878)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|positive regulation of vasoconstriction (GO:0045907)|regulation of smooth muscle cell migration (GO:0014910)|regulation of smooth muscle cell proliferation (GO:0048660)|response to auditory stimulus (GO:0010996)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to heat (GO:0009408)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to ozone (GO:0010193)|response to progesterone (GO:0032570)|smooth muscle contraction involved in micturition (GO:0060083)|sperm ejaculation (GO:0042713)|tachykinin receptor signaling pathway (GO:0007217)	cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance P receptor activity (GO:0016496)|tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(8)|ovary(1)|skin(1)	24					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)	CGGCGATGGGAAAGAAGTTGT	0.498													G|||	2830	0.565096	0.9085	0.4971	5008	,	,		21192	0.3869		0.4682	False		,,,				2504	0.4325				p.F111F	Pancreas(64;62 1268 3653 14826 43765)	Atlas-SNP	.											.	TACR1	62	.	0			c.T333C						PASS	.	G	,	3695,711	291.0+/-281.2	1551,593,59	161.0	143.0	149.0		333,333	5.4	1.0	2	dbSNP_116	149	4113,4487	586.5+/-392.1	1001,2111,1188	no	coding-synonymous,coding-synonymous	TACR1	NM_001058.3,NM_015727.2	,	2552,2704,1247	GG,GA,AA		47.8256,16.1371,39.9662	,	111/408,111/312	75425728	7808,5198	2203	4300	6503	SO:0001819	synonymous_variant	6869	exon1			GATGGGAAAGAAG	M76675	CCDS1958.1, CCDS46345.1	2p13.1-p12	2012-08-08			ENSG00000115353	ENSG00000115353		"""GPCR / Class A : Tachykinin receptors"""	11526	protein-coding gene	gene with protein product		162323		TAC1R		1657150	Standard	NM_001058		Approved	SPR, NK1R, NKIR	uc002sng.2	P25103	OTTHUMG00000129973	ENST00000305249.5:c.333T>C	2.37:g.75425728A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001058	A8K150	Silent	SNP	ENST00000305249.5	37	CCDS1958.1																																																																																			A|0.425;G|0.575	0.575	strong		0.498	TACR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252239.3	NM_001058	
GEMIN4	50628	hgsc.bcm.edu	37	17	649164	649164	+	Missense_Mutation	SNP	G	G	A	rs34519093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:649164G>A	ENST00000319004.5	-	2	2237	c.2119C>T	c.(2119-2121)Cgc>Tgc	p.R707C	GEMIN4_ENST00000576778.1_Missense_Mutation_p.R696C	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	707					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TTGCTGAAGCGGTCCAAGAGC	0.542													T|||	116	0.0231629	0.0832	0.0058	5008	,	,		19134	0.0		0.002	False		,,,				2504	0.0				p.R707C		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C2119T						PASS	.	T	CYS/ARG	263,3613		6,251,1681	28.0	29.0	29.0		2119	-6.4	0.0	17	dbSNP_126	29	4,8282		0,4,4139	yes	missense	GEMIN4	NM_015721.2	180	6,255,5820	AA,AG,GG		0.0483,6.7853,2.1954	benign	707/1059	649164	267,11895	1938	4143	6081	SO:0001583	missense	50628	exon2			TGAAGCGGTCCAA	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.2119C>T	17.37:g.649164G>A	ENSP00000321706:p.Arg707Cys	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	35	22	0.628571	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	50	0.022893772893772892	46	0.09349593495934959	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	T	8.559	0.877352	0.17395	0.067853	4.83E-4	ENSG00000179409	ENST00000319004	T	0.05855	3.38	5.56	-6.42	0.01932	.	0.696678	0.15313	N	0.268978	T	0.00109	0.0003	N	0.02011	-0.69	0.25173	N	0.990269	B	0.02656	0.0	B	0.01281	0.0	T	0.37454	-0.9705	10	0.48119	T	0.1	-0.0898	4.5907	0.12306	0.2625:0.4379:0.0738:0.2258	rs34519093	707	P57678	GEMI4_HUMAN	C	707	ENSP00000321706:R707C	ENSP00000321706:R707C	R	-	1	0	GEMIN4	595914	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.501000	0.02281	-2.443000	0.00548	-3.149000	0.00058	CGC	G|0.978;A|0.022	0.022	strong		0.542	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
INTS1	26173	hgsc.bcm.edu	37	7	1538174	1538174	+	Silent	SNP	C	C	T	rs143126716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1538174C>T	ENST00000404767.3	-	10	1384	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	INTS1_ENST00000389470.4_Silent_p.A561A|INTS1_ENST00000493531.1_5'Flank	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	433					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		TGTCCTTGTGCGCGCTCAGCA	0.652													C|||	63	0.0125799	0.0431	0.0086	5008	,	,		10067	0.0		0.0	False		,,,				2504	0.0				p.A433A		Atlas-SNP	.											INTS1,NS,carcinoma,-1,1	INTS1	145	1	0			c.G1299A						PASS	.			125,4145		4,117,2014	85.0	97.0	93.0		1299	-9.7	0.0	7	dbSNP_134	93	6,8488		0,6,4241	no	coding-synonymous	INTS1	NM_001080453.2		4,123,6255	TT,TC,CC		0.0706,2.9274,1.0263		433/2191	1538174	131,12633	2135	4247	6382	SO:0001819	synonymous_variant	26173	exon10			CTTGTGCGCGCTC	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.1299G>A	7.37:g.1538174C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	166	166	1	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																			C|0.988;T|0.012	0.012	strong		0.652	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
OR10H2	26538	hgsc.bcm.edu	37	19	15838972	15838972	+	Missense_Mutation	SNP	T	T	A	rs4569397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15838972T>A	ENST00000305899.3	+	1	139	c.119T>A	c.(118-120)cTg>cAg	p.L40Q		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	40			L -> Q (in dbSNP:rs4569397).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					TTCACGCTGCTGGGCAACCTG	0.582													T|||	1310	0.261581	0.4319	0.2752	5008	,	,		22562	0.0119		0.3131	False		,,,				2504	0.226				p.L40Q		Atlas-SNP	.											OR10H2,NS,carcinoma,-1,1	OR10H2	59	1	0			c.T119A						PASS	.	T	GLN/LEU	1798,2608		372,1054,777	228.0	189.0	202.0		119	2.9	1.0	19	dbSNP_111	202	2471,6125		379,1713,2206	no	missense	OR10H2	NM_013939.2	113	751,2767,2983	AA,AT,TT		28.7459,40.808,32.8334	probably-damaging	40/316	15838972	4269,8733	2203	4298	6501	SO:0001583	missense	26538	exon1			CGCTGCTGGGCAA	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.119T>A	19.37:g.15838972T>A	ENSP00000306095:p.Leu40Gln	Somatic	356	0	0		WXS	Illumina HiSeq	Phase_I	321	140	0.436137	NM_013939	Q6IFQ1|Q96R58	Missense_Mutation	SNP	ENST00000305899.3	37	CCDS12333.1	563	0.25778388278388276	198	0.4024390243902439	115	0.31767955801104975	11	0.019230769230769232	239	0.3153034300791557	.	16.52	3.146455	0.57044	0.40808	0.287459	ENSG00000171942	ENST00000305899	T	0.00625	6.14	2.88	2.88	0.33553	.	0.000000	0.38720	N	0.001598	T	0.00012	0.0000	M	0.93016	3.37	0.29061	P	0.88391	D	0.89917	1.0	D	0.91635	0.999	T	0.40646	-0.9552	9	0.40728	T	0.16	.	4.5583	0.12147	0.0:0.1544:0.0:0.8456	rs4569397	40	O60403	O10H2_HUMAN	Q	40	ENSP00000306095:L40Q	ENSP00000306095:L40Q	L	+	2	0	OR10H2	15699972	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	0.639000	0.24690	1.186000	0.42985	0.438000	0.28831	CTG	T|0.581;A|0.419	0.419	strong		0.582	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
SLC6A18	348932	hgsc.bcm.edu	37	5	1240757	1240757	+	Nonsense_Mutation	SNP	C	C	G	rs7447815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:1240757C>G	ENST00000324642.3	+	7	1080	c.957C>G	c.(955-957)taC>taG	p.Y319*	SLC6A18_ENST00000296821.4_Intron	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	319					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CTAATGACTACGAGCACTGCC	0.612													C|||	1746	0.348642	0.3638	0.3775	5008	,	,		19420	0.2351		0.3688	False		,,,				2504	0.4039				p.Y319X		Atlas-SNP	.											.	SLC6A18	84	.	0			c.C957G	GRCh37	CM086962	SLC6A18	M	rs7447815	PASS	.	C	stop/TYR	1534,2872	484.6+/-360.1	249,1036,918	142.0	107.0	119.0		957	-3.1	0.0	5	dbSNP_116	119	3206,5394	484.0+/-371.3	622,1962,1716	yes	stop-gained	SLC6A18	NM_182632.2		871,2998,2634	GG,GC,CC		37.2791,34.8162,36.4447		319/629	1240757	4740,8266	2203	4300	6503	SO:0001587	stop_gained	348932	exon7			TGACTACGAGCAC	AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"""Solute carriers"""	26441	protein-coding gene	gene with protein product		610300	"""solute carrier family 6 (neurotransmitter transporter), member 18"", ""solute carrier family 6, member 18"""			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.957C>G	5.37:g.1240757C>G	ENSP00000323549:p.Tyr319*	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_182632		Nonsense_Mutation	SNP	ENST00000324642.3	37	CCDS3860.1	743	0.3402014652014652	188	0.3821138211382114	135	0.3729281767955801	140	0.24475524475524477	280	0.36939313984168864	C	13.94	2.386926	0.42308	0.348162	0.372791	ENSG00000164363	ENST00000324642	.	.	.	4.51	-3.14	0.05250	.	0.627859	0.15102	N	0.280472	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.214	0.59844	0.0:0.2103:0.0:0.7897	rs7447815;rs7447815	.	.	.	X	319	.	ENSP00000323549:Y319X	Y	+	3	2	SLC6A18	1293757	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.005000	0.00650	-0.907000	0.03862	-1.743000	0.00684	TAC	C|0.649;G|0.351	0.351	strong		0.612	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632	
TEP1	7011	hgsc.bcm.edu	37	14	20864049	20864049	+	Silent	SNP	A	A	G	rs2228026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20864049A>G	ENST00000262715.5	-	11	1759	c.1719T>C	c.(1717-1719)atT>atC	p.I573I	TEP1_ENST00000556935.1_Silent_p.I465I	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	573	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)		CGAGGGCATCAATGGCATCAT	0.498													A|||	149	0.0297524	0.003	0.0274	5008	,	,		18256	0.0		0.0557	False		,,,				2504	0.0716				p.I573I		Atlas-SNP	.											.	TEP1	224	.	0			c.T1719C						PASS	.	A		46,4360	47.5+/-82.1	0,46,2157	131.0	127.0	128.0		1719	1.5	0.2	14	dbSNP_98	128	474,8126	139.8+/-196.4	19,436,3845	no	coding-synonymous	TEP1	NM_007110.4		19,482,6002	GG,GA,AA		5.5116,1.044,3.9982		573/2628	20864049	520,12486	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon11			GGCATCAATGGCA		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.1719T>C	14.37:g.20864049A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			A|0.963;G|0.037	0.037	strong		0.498	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
AWAT1	158833	hgsc.bcm.edu	37	X	69455671	69455671	+	Missense_Mutation	SNP	G	G	A	rs61995694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:69455671G>A	ENST00000374521.3	+	2	223	c.182G>A	c.(181-183)cGa>cAa	p.R61Q	AWAT1_ENST00000480702.1_3'UTR	NM_001013579.2	NP_001013597.1	Q58HT5	AWAT1_HUMAN	acyl-CoA wax alcohol acyltransferase 1	61					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(3)|ovary(4)|skin(1)	15						ACCCCAGAGCGAGGTAAGACT	0.512													g|||	113	0.0299338	0.0825	0.0058	3775	,	,		15173	0.0		0.0	False		,,,				2504	0.0				p.R61Q		Atlas-SNP	.											.	AWAT1	74	.	0			c.G182A						PASS	.		GLN/ARG	342,3493		13,270,46,1349,525	184.0	144.0	158.0		182	1.1	0.6	X	dbSNP_129	158	2,6726		0,2,0,2426,1872	yes	missense	AWAT1	NM_001013579.2	43	13,272,46,3775,2397	AA,AG,A,GG,G		0.0297,8.9179,3.2567	benign	61/329	69455671	344,10219	2203	4300	6503	SO:0001583	missense	158833	exon2			CAGAGCGAGGTAA	BC039181	CCDS35321.1	Xq13.1	2010-01-25	2009-02-23	2009-02-23	ENSG00000204195	ENSG00000204195			23252	protein-coding gene	gene with protein product		300924	"""diacylglycerol O-acyltransferase 2-like 3"""	DGAT2L3		14970677, 15671038	Standard	NM_001013579		Approved		uc004dxy.3	Q58HT5	OTTHUMG00000021773	ENST00000374521.3:c.182G>A	X.37:g.69455671G>A	ENSP00000363645:p.Arg61Gln	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	119	49	0.411765	NM_001013579	Q5JT21|Q6IEE4	Missense_Mutation	SNP	ENST00000374521.3	37	CCDS35321.1	46	0.027727546714888487	32	0.06808510638297872	3	0.008287292817679558	0	0.0	0	0.0	g	2.423	-0.332574	0.05314	0.089179	2.97E-4	ENSG00000204195	ENST00000374521	T	0.17528	2.27	5.03	1.06	0.20224	.	0.715401	0.13082	N	0.415230	T	0.00241	0.0007	N	0.04162	-0.26	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.09377	0.004	T	0.42749	-0.9433	9	0.02654	T	1	-0.016	7.6926	0.28577	0.6396:0.0:0.3604:0.0	rs61995694	61	Q58HT5	AWAT1_HUMAN	Q	61	ENSP00000363645:R61Q	ENSP00000363645:R61Q	R	+	2	0	AWAT1	69372396	0.002000	0.14202	0.579000	0.28588	0.849000	0.48306	0.034000	0.13776	-0.029000	0.13827	-0.372000	0.07161	CGA	G|0.967;A|0.033	0.033	strong		0.512	AWAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057066.3	NM_001013579	
SCAF11	9169	hgsc.bcm.edu	37	12	46339033	46339033	+	Splice_Site	SNP	A	A	G	rs11183245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:46339033A>G	ENST00000369367.3	-	6	695	c.462T>C	c.(460-462)caT>caC	p.H154H	SCAF11_ENST00000419565.2_Splice_Site_p.H154H	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	154					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						GTAACTTACTATGTATCCACT	0.318													A|||	66	0.0131789	0.0477	0.0029	5008	,	,		17740	0.0		0.001	False		,,,				2504	0.0				p.H154H		Atlas-SNP	.											.	SCAF11	145	.	0			c.T462C						PASS	.	A		167,3485		4,159,1663	111.0	105.0	107.0		462	-1.8	0.0	12	dbSNP_120	107	0,8134		0,0,4067	yes	coding-synonymous-near-splice	SCAF11	NM_004719.2		4,159,5730	GG,GA,AA		0.0,4.5728,1.4169		154/1464	46339033	167,11619	1826	4067	5893	SO:0001630	splice_region_variant	9169	exon6			CTTACTATGTATC	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.463+1T>C	12.37:g.46339033A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_004719	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	37	CCDS8748.2																																																																																			A|0.972;G|0.028	0.028	strong		0.318	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	Silent
SYNE2	23224	hgsc.bcm.edu	37	14	64450479	64450479	+	Missense_Mutation	SNP	A	A	G	rs78191145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64450479A>G	ENST00000344113.4	+	18	2238	c.2026A>G	c.(2026-2028)Aaa>Gaa	p.K676E	SYNE2_ENST00000554584.1_Missense_Mutation_p.K676E|SYNE2_ENST00000358025.3_Missense_Mutation_p.K676E|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	676					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)		ACTGATGATAAAAAAACAGGA	0.303													A|||	31	0.0061901	0.0234	0.0	5008	,	,		14554	0.0		0.0	False		,,,				2504	0.0				p.K676E		Atlas-SNP	.											.	SYNE2	577	.	0			c.A2026G						PASS	.	A	GLU/LYS,GLU/LYS	85,3501		3,79,1711	40.0	39.0	39.0		2026,2026	3.0	0.1	14	dbSNP_131	39	0,8130		0,0,4065	yes	missense,missense	SYNE2	NM_015180.4,NM_182914.2	56,56	3,79,5776	GG,GA,AA		0.0,2.3703,0.7255	probably-damaging,probably-damaging	676/6886,676/6908	64450479	85,11631	1793	4065	5858	SO:0001583	missense	23224	exon18			ATGATAAAAAAAC	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.2026A>G	14.37:g.64450479A>G	ENSP00000341781:p.Lys676Glu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	138	80	0.57971	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	A	10.57	1.387852	0.25031	0.023703	0.0	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.57436	0.76;0.76;0.4	5.56	3.05	0.35203	.	0.110909	0.38778	N	0.001580	T	0.24160	0.0585	L	0.44542	1.39	0.20196	N	0.999925	P;P	0.46064	0.798;0.872	B;P	0.45856	0.3;0.495	T	0.16100	-1.0414	10	0.52906	T	0.07	.	11.2166	0.48830	0.565:0.435:0.0:0.0	.	676;676	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	E	676	ENSP00000350719:K676E;ENSP00000341781:K676E;ENSP00000452570:K676E	ENSP00000261678:K676E	K	+	1	0	SYNE2	63520232	0.770000	0.28543	0.119000	0.21687	0.552000	0.35366	1.368000	0.34216	0.909000	0.36697	0.528000	0.53228	AAA	A|0.996;G|0.004	0.004	strong		0.303	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
SDC3	9672	hgsc.bcm.edu	37	1	31349795	31349795	+	Silent	SNP	G	G	A	rs142879690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:31349795G>A	ENST00000339394.6	-	3	648	c.474C>T	c.(472-474)acC>acT	p.T158T	SDC3_ENST00000336798.7_Silent_p.T100T|SDC3_ENST00000471567.1_5'UTR	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	158	Ser/Thr-rich (mucin-like).				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|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)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		TAGTGGAGACGGTGGTGGCTC	0.667													G|||	5	0.000998403	0.0038	0.0	5008	,	,		12182	0.0		0.0	False		,,,				2504	0.0				p.T158T		Atlas-SNP	.											.	SDC3	45	.	0			c.C474T						PASS	.	G		21,4385	25.3+/-52.1	0,21,2182	36.0	38.0	37.0		474	-1.0	0.3	1	dbSNP_134	37	0,8598		0,0,4299	no	coding-synonymous	SDC3	NM_014654.3		0,21,6481	AA,AG,GG		0.0,0.4766,0.1615		158/443	31349795	21,12983	2203	4299	6502	SO:0001819	synonymous_variant	9672	exon3			GGAGACGGTGGTG	AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"""Proteoglycans / Cell Surface : Syndecans"""	10660	protein-coding gene	gene with protein product	"""syndecan proteoglycan 3"""	186357	"""syndecan 3 (N-syndecan)"""			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.474C>T	1.37:g.31349795G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	37	CCDS30661.1																																																																																			G|0.998;A|0.002	0.002	strong		0.667	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
PHF21B	112885	hgsc.bcm.edu	37	22	45312244	45312244	+	Silent	SNP	G	G	A	rs6519902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45312244G>A	ENST00000313237.5	-	4	630	c.480C>T	c.(478-480)gcC>gcT	p.A160A	PHF21B_ENST00000447824.3_Silent_p.A148A|PHF21B_ENST00000403565.1_5'UTR|PHF21B_ENST00000396103.3_Silent_p.A160A|PHF21B_ENST00000404079.2_Silent_p.A148A	NM_138415.4	NP_612424.1	Q96EK2	PF21B_HUMAN	PHD finger protein 21B	160							zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(14)|ovary(2)|prostate(1)|skin(2)	25		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		CCATGGCGGCGGCATTGCTGG	0.687													G|||	747	0.149161	0.326	0.0908	5008	,	,		15178	0.0119		0.0974	False		,,,				2504	0.1462				p.A160A		Atlas-SNP	.											PHF21B,colon,carcinoma,0,1	PHF21B	61	1	0			c.C480T						PASS	.	G	,,	1199,3201		174,851,1175	21.0	27.0	25.0		480,444,480	-2.2	0.2	22	dbSNP_116	25	908,7684		57,794,3445	no	coding-synonymous,coding-synonymous,coding-synonymous	PHF21B	NM_001135862.2,NM_001242450.1,NM_138415.4	,,	231,1645,4620	AA,AG,GG		10.568,27.25,16.2177	,,	160/490,148/478,160/532	45312244	2107,10885	2200	4296	6496	SO:0001819	synonymous_variant	112885	exon4			GGCGGCGGCATTG	AK091480	CCDS14061.1, CCDS56234.1, CCDS63504.1	22q13.31	2013-01-28			ENSG00000056487	ENSG00000056487		"""Zinc fingers, PHD-type"""	25161	protein-coding gene	gene with protein product			"""PHD finger protein 4"""	PHF4		12477932	Standard	NM_138415		Approved	BHC80L, FLJ34161	uc011aql.2	Q96EK2	OTTHUMG00000151199	ENST00000313237.5:c.480C>T	22.37:g.45312244G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_138415	B0QYW3|B0QYW4|B3KRU4|B7Z4F8|Q5TFL2|Q6ICC0	Silent	SNP	ENST00000313237.5	37	CCDS14061.1																																																																																			G|0.850;A|0.150	0.150	strong		0.687	PHF21B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321731.2	NM_138415	
CUEDC1	404093	hgsc.bcm.edu	37	17	55950064	55950064	+	Silent	SNP	C	C	T	rs35704289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:55950064C>T	ENST00000577830.1	-	5	1157	c.744G>A	c.(742-744)gaG>gaA	p.E248E	CUEDC1_ENST00000407144.2_Silent_p.E248E|CUEDC1_ENST00000578357.1_5'Flank|CUEDC1_ENST00000360238.2_Silent_p.E248E|CUEDC1_ENST00000577840.1_Silent_p.E111E	NM_001271875.1	NP_001258804.1	Q9NWM3	CUED1_HUMAN	CUE domain containing 1	248										endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12						TCCGTTGCAGCTCCTTCATGA	0.622													C|||	1172	0.234026	0.2595	0.3285	5008	,	,		19550	0.0069		0.3221	False		,,,				2504	0.2761				p.E248E		Atlas-SNP	.											.	CUEDC1	37	.	0			c.G744A						PASS	.	C		1185,3221	415.7+/-337.3	173,839,1191	77.0	62.0	67.0		744	4.5	1.0	17	dbSNP_126	67	2914,5686	456.1+/-364.0	500,1914,1886	no	coding-synonymous	CUEDC1	NM_017949.1		673,2753,3077	TT,TC,CC		33.8837,26.8951,31.5162		248/387	55950064	4099,8907	2203	4300	6503	SO:0001819	synonymous_variant	404093	exon5			TTGCAGCTCCTTC	AK000746	CCDS11599.1	17q23.2	2004-03-16				ENSG00000180891			31350	protein-coding gene	gene with protein product							Standard	NM_001271875		Approved		uc002ive.2	Q9NWM3		ENST00000577830.1:c.744G>A	17.37:g.55950064C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_001271875	D3DTZ2|Q9NWD0	Silent	SNP	ENST00000577830.1	37	CCDS11599.1																																																																																			C|0.717;T|0.283	0.283	strong		0.622	CUEDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443305.1	NM_017949	
ELL	8178	hgsc.bcm.edu	37	19	18561420	18561420	+	Silent	SNP	C	C	T	rs34078075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18561420C>T	ENST00000262809.4	-	8	1403	c.1332G>A	c.(1330-1332)tcG>tcA	p.S444S	ELL_ENST00000596124.3_Silent_p.S311S	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	444					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)		GCTTGCTGCGCGAGGGGCTGC	0.687			T	MLL	AL								C|||	107	0.0213658	0.0681	0.0144	5008	,	,		14591	0.0		0.007	False		,,,				2504	0.0				p.S444S		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.G1332A						PASS	.	C		273,4131		5,263,1934	35.0	21.0	26.0		1332	-5.8	0.0	19	dbSNP_126	26	55,8539		0,55,4242	no	coding-synonymous	ELL	NM_006532.3		5,318,6176	TT,TC,CC		0.64,6.1989,2.5235		444/622	18561420	328,12670	2202	4297	6499	SO:0001819	synonymous_variant	8178	exon8			GCTGCGCGAGGGG	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.1332G>A	19.37:g.18561420C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	266	134	0.503759	NM_006532		Silent	SNP	ENST00000262809.4	37	CCDS12380.1																																																																																			C|0.976;T|0.024	0.024	strong		0.687	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532	
DNAH8	1769	hgsc.bcm.edu	37	6	38843426	38843426	+	Silent	SNP	C	C	T	rs6458080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:38843426C>T	ENST00000359357.3	+	51	7283	c.7029C>T	c.(7027-7029)gtC>gtT	p.V2343V	DNAH8_ENST00000441566.1_Silent_p.V2307V|DNAH8_ENST00000449981.2_Silent_p.V2560V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2343					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						TTTCCTGTGTCGAACATCTTC	0.363													C|||	2676	0.534345	0.3638	0.6138	5008	,	,		14846	0.8333		0.3767	False		,,,				2504	0.5624				p.V2560V		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,+1,2	DNAH8	1239	2	0			c.C7680T						PASS	.	C		1608,2798	496.4+/-363.5	304,1000,899	78.0	77.0	77.0		7680	-6.9	0.0	6	dbSNP_116	77	3682,4918	526.6+/-381.0	790,2102,1408	no	coding-synonymous	DNAH8	NM_001206927.1		1094,3102,2307	TT,TC,CC		42.814,36.4957,40.6735		2560/4708	38843426	5290,7716	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon53			CTGTGTCGAACAT	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.7029C>T	6.37:g.38843426C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				C|0.539;T|0.461	0.461	strong		0.363	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
RPGR	6103	hgsc.bcm.edu	37	X	38146029	38146029	+	Intron	SNP	C	C	T	rs147619484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38146029C>T	ENST00000339363.3	-	14	2688				TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000378505.2_Silent_p.E741E|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						tgtctccctcctcttcttctc	0.532													C|||	488	0.129272	0.1271	0.1427	3775	,	,		12242	0.0516		0.0527	False		,,,				2504	0.1186				p.E741E		Atlas-SNP	.											.	RPGR	175	.	0			c.G2223A						PASS	.		,	516,3144		35,379,67,1174,417	190.0	112.0	138.0		,2223	-2.1	0.0	X	dbSNP_134	138	301,6182		2,202,95,2179,1622	no	intron,coding-synonymous	RPGR	NM_000328.2,NM_001034853.1	,	37,581,162,3353,2039	TT,TC,T,CC,C		4.6429,14.0984,8.0548	,	,741/1153	38146029	817,9326	2072	4100	6172	SO:0001627	intron_variant	6103	exon15			TCCCTCCTCTTCT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+317G>A	X.37:g.38146029C>T		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	253	120	0.474308	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Silent	SNP	ENST00000339363.3	37																																																																																				C|0.900;T|0.100	0.100	strong		0.532	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
P2RY14	9934	hgsc.bcm.edu	37	3	150931385	150931385	+	Silent	SNP	A	A	G	rs12631155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150931385A>G	ENST00000309170.3	-	3	1032	c.720T>C	c.(718-720)ttT>ttC	p.F240F	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|P2RY14_ENST00000424796.2_Silent_p.F240F	NM_001081455.1|NM_014879.3	NP_001074924.1|NP_055694.3	Q15391	P2Y14_HUMAN	purinergic receptor P2Y, G-protein coupled, 14	240					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|UDP-activated nucleotide receptor activity (GO:0045029)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)	20			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CAAAAAACACAAACACGATGC	0.408													G|||	407	0.08127	0.2118	0.0187	5008	,	,		20043	0.0228		0.004	False		,,,				2504	0.089				p.F240F		Atlas-SNP	.											.	P2RY14	50	.	0			c.T720C						PASS	.	G	,,	821,3585	741.0+/-411.2	76,669,1458	90.0	93.0	92.0		720,720,	-9.7	0.0	3	dbSNP_120	92	11,8589	817.8+/-406.9	0,11,4289	no	coding-synonymous,coding-synonymous,intron	P2RY14,MED12L	NM_001081455.1,NM_014879.3,NM_053002.4	,,	76,680,5747	GG,GA,AA		0.1279,18.6337,6.397	,,	240/339,240/339,	150931385	832,12174	2203	4300	6503	SO:0001819	synonymous_variant	9934	exon3			AAACACAAACACG	D13626	CCDS3156.1	3q21-q25	2012-08-08	2004-07-12	2004-07-14	ENSG00000174944	ENSG00000174944		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	16442	protein-coding gene	gene with protein product		610116	"""G protein-coupled receptor 105"""	GPR105			Standard	NM_014879		Approved	KIAA0001	uc003eys.1	Q15391	OTTHUMG00000159859	ENST00000309170.3:c.720T>C	3.37:g.150931385A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	117	64	0.547009	NM_014879	Q8IYT7	Silent	SNP	ENST00000309170.3	37	CCDS3156.1																																																																																			A|0.934;G|0.066	0.066	strong		0.408	P2RY14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357789.1	NM_014879	
TAF2	6873	hgsc.bcm.edu	37	8	120744399	120744399	+	Missense_Mutation	SNP	C	C	T	rs956749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120744399C>T	ENST00000378164.2	-	26	3663	c.3365G>A	c.(3364-3366)aGt>aAt	p.S1122N		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	1122			S -> N (in dbSNP:rs956749).		G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TGGATGCATACTCATCTCCAA	0.453													C|||	418	0.0834665	0.23	0.0447	5008	,	,		18612	0.001		0.0557	False		,,,				2504	0.0266				p.S1122N		Atlas-SNP	.											.	TAF2	204	.	0			c.G3365A						PASS	.	C	ASN/SER	918,3488	351.8+/-311.4	94,730,1379	178.0	176.0	177.0		3365	3.2	0.5	8	dbSNP_86	177	541,8059	150.4+/-205.3	19,503,3778	yes	missense	TAF2	NM_003184.3	46	113,1233,5157	TT,TC,CC		6.2907,20.8352,11.2179	benign	1122/1200	120744399	1459,11547	2203	4300	6503	SO:0001583	missense	6873	exon26			TGCATACTCATCT	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.3365G>A	8.37:g.120744399C>T	ENSP00000367406:p.Ser1122Asn	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	37	CCDS34937.1	188	0.08608058608058608	132	0.2682926829268293	12	0.03314917127071823	0	0.0	44	0.05804749340369393	C	4.530	0.098338	0.08681	0.208352	0.062907	ENSG00000064313	ENST00000378164;ENST00000529653	T;T	0.30981	2.51;1.51	6.02	3.19	0.36642	.	0.492555	0.23459	N	0.047954	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	0.40683	-0.9550	9	0.15952	T	0.53	-25.9834	5.9026	0.18976	0.0:0.529:0.317:0.154	rs956749;rs52829498;rs61430226;rs956749	1122	Q6P1X5	TAF2_HUMAN	N	1122;298	ENSP00000367406:S1122N;ENSP00000436750:S298N	ENSP00000367406:S1122N	S	-	2	0	TAF2	120813580	0.138000	0.22547	0.508000	0.27688	0.068000	0.16541	0.868000	0.27982	1.507000	0.48752	0.650000	0.86243	AGT	C|0.895;T|0.105	0.105	strong		0.453	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
LFNG	3955	hgsc.bcm.edu	37	7	2566484	2566484	+	Silent	SNP	C	C	T	rs61743870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2566484C>T	ENST00000222725.5	+	7	1022	c.1002C>T	c.(1000-1002)taC>taT	p.Y334Y	LFNG_ENST00000359574.3_Silent_p.Y334Y|LFNG_ENST00000402045.1_Silent_p.Y205Y|LFNG_ENST00000402506.1_Silent_p.Y263Y|MIR4648_ENST00000580107.1_RNA|LFNG_ENST00000338732.3_Silent_p.Y205Y	NM_001040167.1	NP_001035257.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	334					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		CGCTGAGCTACGGTATGTTTG	0.672													C|||	402	0.0802716	0.0537	0.0634	5008	,	,		16295	0.1399		0.0239	False		,,,				2504	0.1247				p.Y334Y		Atlas-SNP	.											.	LFNG	57	.	0			c.C1002T						PASS	.	C	,,,	202,4204	116.7+/-154.6	3,196,2004	32.0	33.0	33.0		1002,1002,789,615	-7.6	0.9	7	dbSNP_129	33	174,8422	75.7+/-138.4	0,174,4124	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LFNG	NM_001040167.1,NM_001040168.1,NM_001166355.1,NM_002304.2	,,,	3,370,6128	TT,TC,CC		2.0242,4.5847,2.8919	,,,	334/380,334/362,263/309,205/251	2566484	376,12626	2203	4298	6501	SO:0001819	synonymous_variant	3955	exon7			GAGCTACGGTATG	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"""Beta 3-glycosyltransferases"""	6560	protein-coding gene	gene with protein product		602576	"""lunatic fringe (Drosophila) homolog"", ""lunatic fringe homolog (Drosophila)"""			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000222725.5:c.1002C>T	7.37:g.2566484C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_001040167	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Silent	SNP	ENST00000222725.5	37	CCDS34587.1																																																																																			C|0.965;T|0.035	0.035	strong		0.672	LFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325021.1	NM_002304	
DDX27	55661	hgsc.bcm.edu	37	20	47858695	47858695	+	Missense_Mutation	SNP	G	G	A	rs143843778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47858695G>A	ENST00000371764.4	+	18	2170	c.2161G>A	c.(2161-2163)Gcc>Acc	p.A721T	DDX27_ENST00000484427.1_3'UTR|ZNFX1_ENST00000469991.1_Intron|ZNFX1_ENST00000371754.4_Intron	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	721						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GAATCGCAGAGCCAAGCGGGC	0.567													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		17319	0.0		0.0	False		,,,				2504	0.0				p.A721T		Atlas-SNP	.											.	DDX27	74	.	0			c.G2161A						PASS	.	G	THR/ALA	54,4352	54.9+/-90.9	0,54,2149	48.0	45.0	46.0		2161	1.7	1.0	20	dbSNP_134	46	0,8600		0,0,4300	yes	missense	DDX27	NM_017895.7	58	0,54,6449	AA,AG,GG		0.0,1.2256,0.4152	benign	721/797	47858695	54,12952	2203	4300	6503	SO:0001583	missense	55661	exon18			CGCAGAGCCAAGC	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.2161G>A	20.37:g.47858695G>A	ENSP00000360828:p.Ala721Thr	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	133	56	0.421053	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	G	12.62	1.992729	0.35131	0.012256	0.0	ENSG00000124228	ENST00000371764	T	0.01438	4.89	5.83	1.74	0.24563	.	0.354569	0.32473	N	0.006059	T	0.00695	0.0023	N	0.22421	0.69	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.58222	-0.7674	10	0.17369	T	0.5	-2.8822	4.7211	0.12918	0.3373:0.1498:0.513:0.0	.	721	Q96GQ7	DDX27_HUMAN	T	721	ENSP00000360828:A721T	ENSP00000360828:A721T	A	+	1	0	DDX27	47292102	0.998000	0.40836	0.996000	0.52242	0.995000	0.86356	0.954000	0.29175	0.098000	0.17522	0.561000	0.74099	GCC	G|0.996;A|0.004	0.004	strong		0.567	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		
RERE	473	hgsc.bcm.edu	37	1	8421092	8421092	+	Silent	SNP	C	C	T	rs2784735	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:8421092C>T	ENST00000337907.3	-	19	3109	c.2475G>A	c.(2473-2475)ccG>ccA	p.P825P	RERE_ENST00000377464.1_Silent_p.P557P|RERE_ENST00000400907.2_Intron|RERE_ENST00000476556.1_Silent_p.P271P|RERE_ENST00000400908.2_Silent_p.P825P	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	825	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GAGGCTGCAGCGGgggatgtg	0.726													c|||	2293	0.457867	0.1899	0.5115	5008	,	,		12102	0.8353		0.4553	False		,,,				2504	0.3957				p.P825P		Atlas-SNP	.											RERE,NS,carcinoma,0,1	RERE	129	1	0			c.G2475A						PASS	.	C	,,	709,2809		128,453,1178	3.0	3.0	3.0		2475,813,2475	-10.4	0.0	1	dbSNP_100	3	2774,4342		656,1462,1440	no	coding-synonymous,coding-synonymous,coding-synonymous	RERE	NM_001042681.1,NM_001042682.1,NM_012102.3	,,	784,1915,2618	TT,TC,CC		38.9826,20.1535,32.7534	,,	825/1567,271/1013,825/1567	8421092	3483,7151	1759	3558	5317	SO:0001819	synonymous_variant	473	exon19			CTGCAGCGGGGGA	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2475G>A	1.37:g.8421092C>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	18	11	0.611111	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Silent	SNP	ENST00000337907.3	37	CCDS95.1																																																																																			C|0.486;T|0.514	0.514	strong		0.726	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
ZNF577	84765	hgsc.bcm.edu	37	19	52376434	52376434	+	Missense_Mutation	SNP	T	T	C	rs34295271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52376434T>C	ENST00000301399.5	-	7	1174	c.809A>G	c.(808-810)tAt>tGt	p.Y270C	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.Y211C|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000451628.2_Missense_Mutation_p.Y211C	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		ACTGCACCCATAGAGTTTCTC	0.483													T|||	546	0.109026	0.0764	0.1153	5008	,	,		20978	0.0427		0.0358	False		,,,				2504	0.2924				p.Y270C		Atlas-SNP	.											.	ZNF577	63	.	0			c.A809G						PASS	.	T	CYS/TYR,CYS/TYR	293,4113		12,269,1922	64.0	59.0	61.0		632,809	-0.6	0.0	19	dbSNP_126	61	160,8440		1,158,4141	yes	missense,missense	ZNF577	NM_001135590.1,NM_032679.2	194,194	13,427,6063	CC,CT,TT		1.8605,6.65,3.483	probably-damaging,probably-damaging	211/427,270/486	52376434	453,12553	2203	4300	6503	SO:0001583	missense	84765	exon7			CACCCATAGAGTT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.809A>G	19.37:g.52376434T>C	ENSP00000301399:p.Tyr270Cys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	30	0.352941	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	37	CCDS12842.2	117	0.05357142857142857	26	0.052845528455284556	39	0.10773480662983426	25	0.043706293706293704	27	0.03562005277044855	.	3.636	-0.074610	0.07184	0.0665	0.018605	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	3.1	-0.56	0.11789	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01189	0.0039	M	0.86097	2.795	0.09310	N	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.927;0.996	T	0.01557	-1.1325	9	0.87932	D	0	.	4.6071	0.12383	0.4289:0.0:0.296:0.275	rs34295271	270;211	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	C	270;211;211;270	ENSP00000301399:Y270C;ENSP00000413476:Y211C;ENSP00000389652:Y211C;ENSP00000404509:Y270C	ENSP00000301399:Y270C	Y	-	2	0	ZNF577	57068246	0.004000	0.15560	0.001000	0.08648	0.025000	0.11179	0.487000	0.22356	-0.383000	0.07858	-2.316000	0.00254	TAT	T|0.960;C|0.040	0.040	strong		0.483	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
SGCG	6445	hgsc.bcm.edu	37	13	23824783	23824783	+	Silent	SNP	T	T	G	rs1800351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23824783T>G	ENST00000218867.3	+	4	436	c.312T>G	c.(310-312)ctT>ctG	p.L104L	SGCG_ENST00000545013.1_Silent_p.L104L|SGCG_ENST00000537476.1_Silent_p.L104L	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	104					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		CATCTCTGCTTCTACAATCAA	0.368													T|||	2628	0.52476	0.7035	0.4236	5008	,	,		15922	0.7014		0.333	False		,,,				2504	0.3701				p.L104L		Atlas-SNP	.											.	SGCG	64	.	0			c.T312G						PASS	.	T		2958,1448	681.6+/-404.0	996,966,241	95.0	83.0	87.0		312	0.1	0.8	13	dbSNP_89	87	3170,5430	480.1+/-370.3	584,2002,1714	no	coding-synonymous	SGCG	NM_000231.2		1580,2968,1955	GG,GT,TT		36.8605,32.8643,47.1167		104/292	23824783	6128,6878	2203	4300	6503	SO:0001819	synonymous_variant	6445	exon4			TCTGCTTCTACAA	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"""Maghrebian myopathy (autosomal recessive)"", ""35kD dystrophin-associated glycoprotein"", ""limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)"", ""gamma sarcoglycan"""	608896	"""sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"""	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.312T>G	13.37:g.23824783T>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_000231	Q32M32|Q5T9J6	Silent	SNP	ENST00000218867.3	37	CCDS9299.1																																																																																			T|0.510;G|0.490	0.490	strong		0.368	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231	
OR8D2	283160	hgsc.bcm.edu	37	11	124190036	124190036	+	Missense_Mutation	SNP	G	G	A	rs61735123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124190036G>A	ENST00000357438.2	-	1	148	c.58C>T	c.(58-60)Cgc>Tgc	p.R20C		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	20						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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		AGTTCTGGGCGTTGTGTCAAG	0.438													A|||	134	0.0267572	0.093	0.013	5008	,	,		17109	0.001		0.0	False		,,,				2504	0.001				p.R20C		Atlas-SNP	.											.	OR8D2	65	.	0			c.C58T						PASS	.	A	CYS/ARG	378,4022	188.5+/-214.9	16,346,1838	67.0	67.0	67.0		58	-6.8	0.0	11	dbSNP_129	67	5,8593	4.3+/-15.6	0,5,4294	yes	missense	OR8D2	NM_001002918.1	180	16,351,6132	AA,AG,GG		0.0582,8.5909,2.9466	benign	20/312	124190036	383,12615	2200	4299	6499	SO:0001583	missense	283160	exon1			CTGGGCGTTGTGT	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"""GPCR / Class A : Olfactory receptors"""	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.58C>T	11.37:g.124190036G>A	ENSP00000350022:p.Arg20Cys	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	37	CCDS31707.1	33	0.01510989010989011	28	0.056910569105691054	5	0.013812154696132596	0	0.0	0	0.0	g	6.776	0.512072	0.12944	0.085909	5.82E-4	ENSG00000197263	ENST00000357438	T	0.00438	7.42	3.42	-6.85	0.01681	.	1.442220	0.04657	N	0.408191	T	0.00012	0.0000	N	0.25380	0.74	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35943	-0.9768	10	0.72032	D	0.01	.	6.2183	0.20667	0.4743:0.0:0.1929:0.3328	.	20	Q9GZM6	OR8D2_HUMAN	C	20	ENSP00000350022:R20C	ENSP00000350022:R20C	R	-	1	0	OR8D2	123695246	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-2.227000	0.01210	-3.085000	0.00249	-0.684000	0.03749	CGC	G|0.972;A|0.028	0.028	strong		0.438	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918	
TTN	7273	hgsc.bcm.edu	37	2	179400895	179400895	+	Missense_Mutation	SNP	C	C	T	rs2278196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179400895C>T	ENST00000591111.1	-	307	95880	c.95656G>A	c.(95656-95658)Gtc>Atc	p.V31886I	TTN_ENST00000589042.1_Missense_Mutation_p.V33527I|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V24462I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V30959I|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V24587I|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V24654I|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31886	Ig-like 141.		V -> I. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACCATTTGACGATAGGTTTT	0.403													C|||	328	0.0654952	0.0847	0.036	5008	,	,		21422	0.1488		0.0298	False		,,,				2504	0.0112				p.V33527I		Atlas-SNP	.											.	TTN	18412	.	0			c.G100579A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	247,3549		8,231,1659	122.0	107.0	112.0		73384,92875,73759,73960	5.8	1.0	2	dbSNP_100	112	143,8087		3,137,3975	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	11,368,5634	TT,TC,CC		1.7375,6.5068,3.243	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	24462/26927,30959/33424,24587/27052,24654/27119	179400895	390,11636	1898	4115	6013	SO:0001583	missense	7273	exon357			ATTTGACGATAGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.95656G>A	2.37:g.179400895C>T	ENSP00000465570:p.Val31886Ile	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	207	107	0.516908	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		155	0.07097069597069597	37	0.07520325203252033	13	0.03591160220994475	84	0.14685314685314685	21	0.027704485488126648	C	14.71	2.617959	0.46736	0.065068	0.017375	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	5.76	5.76	0.90799	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00384	0.0012	N	0.11789	0.175	0.22771	P	0.99875326	P;P;P;P	0.42248	0.774;0.774;0.774;0.774	B;B;B;B	0.27380	0.079;0.079;0.079;0.079	T	0.34700	-0.9818	8	0.87932	D	0	.	19.9595	0.97236	0.0:1.0:0.0:0.0	rs2278196;rs52810709;rs2278196	24462;24587;24654;31886	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	30959;24462;24654;24587;24459	ENSP00000343764:V30959I;ENSP00000434586:V24462I;ENSP00000340554:V24654I;ENSP00000352154:V24587I	ENSP00000340554:V24654I	V	-	1	0	TTN	179109141	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	4.881000	0.63114	2.706000	0.92434	0.563000	0.77884	GTC	C|0.930;T|0.070	0.070	strong		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
EPN3	55040	hgsc.bcm.edu	37	17	48619249	48619249	+	Missense_Mutation	SNP	C	C	A	rs4794159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48619249C>A	ENST00000268933.3	+	10	2209	c.1630C>A	c.(1630-1632)Ccg>Acg	p.P544T	EPN3_ENST00000541226.1_3'UTR|EPN3_ENST00000537145.1_Missense_Mutation_p.P572T	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	544	3 X 3 AA repeats of N-P-F.		P -> T (in dbSNP:rs4794159). {ECO:0000269|PubMed:14702039}.			clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			CGCGGGCGAGCCGGGCAGGCC	0.721													C|||	1854	0.370208	0.5227	0.4481	5008	,	,		11892	0.1091		0.4642	False		,,,				2504	0.2812				p.P544T		Atlas-SNP	.											EPN3,NS,carcinoma,0,1	EPN3	32	1	0			c.C1630A						PASS	.	C	THR/PRO	2124,2270		539,1046,612	17.0	21.0	19.0		1630	5.1	0.0	17	dbSNP_111	19	3968,4620		958,2052,1284	no	missense	EPN3	NM_017957.2	38	1497,3098,1896	AA,AC,CC		46.204,48.3386,46.9265	possibly-damaging	544/633	48619249	6092,6890	2197	4294	6491	SO:0001583	missense	55040	exon10			GGCGAGCCGGGCA	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.1630C>A	17.37:g.48619249C>A	ENSP00000268933:p.Pro544Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	37	CCDS11570.1	806	0.36904761904761907	236	0.4796747967479675	166	0.4585635359116022	62	0.10839160839160839	342	0.45118733509234826	C	17.75	3.467176	0.63625	0.483386	0.46204	ENSG00000049283	ENST00000268933;ENST00000537145	T;T	0.45276	0.9;0.9	5.13	5.13	0.70059	.	0.831291	0.10264	N	0.695608	T	0.00012	0.0000	M	0.62154	1.92	0.09310	P	1.0	P;P	0.43352	0.804;0.764	B;P	0.45428	0.36;0.48	T	0.48536	-0.9027	9	0.20519	T	0.43	-4.8223	18.1664	0.89729	0.0:1.0:0.0:0.0	rs4794159	572;544	F6QWW5;Q9H201	.;EPN3_HUMAN	T	544;572	ENSP00000268933:P544T;ENSP00000439512:P572T	ENSP00000268933:P544T	P	+	1	0	EPN3	45974248	0.998000	0.40836	0.016000	0.15963	0.172000	0.22775	5.548000	0.67255	2.406000	0.81754	0.491000	0.48974	CCG	C|0.565;A|0.435	0.435	strong		0.721	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
RNF111	54778	hgsc.bcm.edu	37	15	59368167	59368167	+	Silent	SNP	G	G	A	rs7178935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:59368167G>A	ENST00000557998.1	+	7	1988	c.1701G>A	c.(1699-1701)gtG>gtA	p.V567V	RNF111_ENST00000348370.4_Silent_p.V567V|RNF111_ENST00000559209.1_Silent_p.V567V|RNF111_ENST00000561186.1_Silent_p.V567V|RNF111_ENST00000434298.1_Silent_p.V567V	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	567					gene expression (GO:0010467)|pattern specification process (GO:0007389)|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 of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		CATTGCCAGTGGACCTGAGCA	0.393													A|||	2135	0.426318	0.6589	0.451	5008	,	,		16474	0.4563		0.2634	False		,,,				2504	0.2311				p.V567V	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.G1701A						PASS	.	A		2650,1734	518.8+/-369.8	824,1002,366	84.0	74.0	77.0		1701	-1.7	1.0	15	dbSNP_116	77	2367,6215	699.6+/-405.1	348,1671,2272	no	coding-synonymous	RNF111	NM_017610.6		1172,2673,2638	AA,AG,GG		27.581,39.5529,38.6935		567/987	59368167	5017,7949	2192	4291	6483	SO:0001819	synonymous_variant	54778	exon7			GCCAGTGGACCTG	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"""RING-type (C3HC4) zinc fingers"""	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1701G>A	15.37:g.59368167G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Silent	SNP	ENST00000557998.1	37	CCDS58366.1																																																																																			G|0.595;A|0.405	0.405	strong		0.393	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610	
TRIM49C	642612	hgsc.bcm.edu	37	11	89774448	89774448	+	Silent	SNP	G	G	A	rs77759231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:89774448G>A	ENST00000448984.1	+	8	1418	c.1089G>A	c.(1087-1089)aaG>aaA	p.K363K	TRIM49C_ENST00000432771.1_Intron	NM_001195234.1	NP_001182163.1	P0CI26	TR49C_HUMAN	tripartite motif containing 49C	363	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|lung(4)	8						TGTATCGGAAGGAGAAGAATC	0.453													N|||	2316	0.46246	0.5265	0.5058	5008	,	,		16455	0.4603		0.3519	False		,,,				2504	0.4611				p.K363K		Atlas-SNP	.											.	TRIM49C	48	.	0			c.G1089A						PASS	.																																			SO:0001819	synonymous_variant	642612	exon8			TCGGAAGGAGAAG	BC126470	CCDS53694.1	11q14.3	2014-02-17	2012-05-18	2012-05-18	ENSG00000204449	ENSG00000204449		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	38877	protein-coding gene	gene with protein product			"""tripartite motif containing 49-like 2"""	TRIM49L2			Standard	NM_001195234		Approved		uc010rua.2	P0CI26		ENST00000448984.1:c.1089G>A	11.37:g.89774448G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	218	130	0.59633	NM_001195234	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Silent	SNP	ENST00000448984.1	37	CCDS53694.1																																																																																			G|0.693;A|0.307	0.307	strong		0.453	TRIM49C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395455.1	NM_001195234	
CCHCR1	54535	hgsc.bcm.edu	37	6	31118304	31118304	+	Silent	SNP	C	C	T	rs139910767		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31118304C>T	ENST00000376266.5	-	7	995	c.873G>A	c.(871-873)gcG>gcA	p.A291A	CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000396268.3_Silent_p.A380A|CCHCR1_ENST00000396263.2_Silent_p.A291A|CCHCR1_ENST00000451521.2_Silent_p.A344A	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	291					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						GCAGCAGCTCCGCGGTGGCAT	0.657													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19191	0.0		0.0	False		,,,				2504	0.0				p.A380A		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G1140A						PASS	.	C	,,	3,3019		0,3,1508	48.0	34.0	39.0		1032,1140,873	-9.5	0.0	6	dbSNP_134	39	0,5414		0,0,2707	no	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	0,3,4215	TT,TC,CC		0.0,0.0993,0.0356	,,	344/836,380/872,291/783	31118304	3,8433	1511	2707	4218	SO:0001819	synonymous_variant	54535	exon7			CAGCTCCGCGGTG	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.873G>A	6.37:g.31118304C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			C|0.999;T|0.001	0.001	strong		0.657	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
LRP4	4038	hgsc.bcm.edu	37	11	46914526	46914526	+	Silent	SNP	C	C	T	rs61741501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46914526C>T	ENST00000378623.1	-	13	1937	c.1695G>A	c.(1693-1695)gaG>gaA	p.E565E		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	565					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		CAACTTACCCCTCCATGGGAT	0.567													C|||	306	0.0611022	0.2216	0.0173	5008	,	,		17231	0.0		0.001	False		,,,				2504	0.0				p.E565E		Atlas-SNP	.											.	LRP4	160	.	0			c.G1695A						PASS	.	C		763,3639	303.2+/-287.8	67,629,1505	43.0	41.0	42.0		1695	2.7	1.0	11	dbSNP_129	42	3,8595	2.2+/-6.3	0,3,4296	no	coding-synonymous	LRP4	NM_002334.3		67,632,5801	TT,TC,CC		0.0349,17.333,5.8923		565/1906	46914526	766,12234	2201	4299	6500	SO:0001819	synonymous_variant	4038	exon13			TTACCCCTCCATG	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.1695G>A	11.37:g.46914526C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	37	CCDS31478.1																																																																																			C|0.947;T|0.053	0.053	strong		0.567	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
MUC17	140453	hgsc.bcm.edu	37	7	100679296	100679296	+	Silent	SNP	C	C	T	rs73168392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100679296C>T	ENST00000306151.4	+	3	4663	c.4599C>T	c.(4597-4599)agC>agT	p.S1533S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1533	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)					AAATCAACAGCCTTTCAACAA	0.478																																					p.S1533S		Atlas-SNP	.											.	MUC17	804	.	0			c.C4599T						PASS	.						264.0	230.0	241.0					7																	100679296		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CAACAGCCTTTCA	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.4599C>T	7.37:g.100679296C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	178	44	0.247191	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			C|0.867;T|0.133	0.133	strong		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CATSPER3	347732	hgsc.bcm.edu	37	5	134347241	134347241	+	Silent	SNP	T	T	C	rs7719874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134347241T>C	ENST00000282611.6	+	8	1211	c.1125T>C	c.(1123-1125)caT>caC	p.H375H		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	375					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGATCGTGCATGTGCTGAGCC	0.562													T|||	293	0.0585064	0.2126	0.0144	5008	,	,		19649	0.0		0.002	False		,,,				2504	0.0				p.H375H		Atlas-SNP	.											.	CATSPER3	38	.	0			c.T1125C						PASS	.	T		785,3621	317.2+/-295.0	66,653,1484	88.0	76.0	80.0		1125	-5.6	0.1	5	dbSNP_116	80	7,8593	6.4+/-24.3	0,7,4293	no	coding-synonymous	CATSPER3	NM_178019.2		66,660,5777	CC,CT,TT		0.0814,17.8166,6.0895		375/399	134347241	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	347732	exon8			CGTGCATGTGCTG	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.1125T>C	5.37:g.134347241T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_178019	Q86XS6	Silent	SNP	ENST00000282611.6	37	CCDS4181.1																																																																																			T|0.929;C|0.071	0.071	strong		0.562	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
USP10	9100	hgsc.bcm.edu	37	16	84778690	84778690	+	Silent	SNP	C	C	T	rs1812062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	188	0	0		WXS	Illumina HiSeq	Phase_I	209	103	0.492823	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		
PARP4	143	hgsc.bcm.edu	37	13	25049676	25049676	+	Silent	SNP	G	G	A	rs73463182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25049676G>A	ENST00000381989.3	-	15	1953	c.1848C>T	c.(1846-1848)gcC>gcT	p.A616A		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	616	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				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)		AGTTCCCAGAGGCATCCTGGA	0.453													.|||	908	0.18131	0.2564	0.0937	5008	,	,		18770	0.2937		0.0835	False		,,,				2504	0.1268				p.A616A		Atlas-SNP	.											.	PARP4	142	.	0			c.C1848T						PASS	.	G		993,3413	370.3+/-319.5	121,751,1331	108.0	109.0	109.0		1848	-0.1	0.1	13	dbSNP_131	109	640,7960	164.1+/-216.5	30,580,3690	no	coding-synonymous	PARP4	NM_006437.3		151,1331,5021	AA,AG,GG		7.4419,22.5374,12.5557		616/1725	25049676	1633,11373	2203	4300	6503	SO:0001819	synonymous_variant	143	exon15			CCCAGAGGCATCC	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.1848C>T	13.37:g.25049676G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	177	89	0.502825	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			G|0.865;A|0.135	0.135	strong		0.453	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
ZNF417	147687	hgsc.bcm.edu	37	19	58420699	58420699	+	Missense_Mutation	SNP	C	C	A	rs3745133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58420699C>A	ENST00000312026.5	-	3	1111	c.947G>T	c.(946-948)cGt>cTt	p.R316L	CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000595559.1_Missense_Mutation_p.R315L|ZNF417_ENST00000536263.1_Missense_Mutation_p.R117L	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	316				R -> L (in Ref. 3; AAH25783). {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)	p.R316L(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		AGTGTGAACACGCTGATGGCT	0.458													C|||	1690	0.33746	0.4153	0.2911	5008	,	,		25205	0.2817		0.3499	False		,,,				2504	0.3098				p.R316L		Atlas-SNP	.											ZNF417,NS,carcinoma,0,1	ZNF417	44	1	1	Substitution - Missense(1)	stomach(1)	c.G947T						PASS	.						167.0	147.0	154.0					19																	58420699		2203	4300	6503	SO:0001583	missense	147687	exon3			TGAACACGCTGAT	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.947G>T	19.37:g.58420699C>A	ENSP00000311319:p.Arg316Leu	Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	353	52	0.147309	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	645	0.29532967032967034	167	0.3394308943089431	107	0.2955801104972376	118	0.2062937062937063	253	0.3337730870712401	.	8.577	0.881369	0.17467	.	.	ENSG00000173480	ENST00000312026;ENST00000536263	T;T	0.25085	1.82;1.82	2.15	-2.01	0.07410	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.60012	1.86	0.80722	P	0.0	P	0.38335	0.627	B	0.36922	0.236	T	0.32981	-0.9886	8	0.66056	D	0.02	.	7.8865	0.29653	0.0:0.6777:0.0:0.3223	rs3745133;rs17856732	316	Q8TAU3	ZN417_HUMAN	L	316;117	ENSP00000311319:R316L;ENSP00000442760:R117L	ENSP00000311319:R316L	R	-	2	0	ZNF417	63112511	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-2.414000	0.01037	-0.691000	0.05135	-1.050000	0.02344	CGT	C|0.500;A|0.500	0.500	weak		0.458	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
ASMTL	8623	hgsc.bcm.edu	37	X	1522330	1522330	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1522330C>T	ENST00000381317.3	-	13	1730	c.1698G>A	c.(1696-1698)gcG>gcA	p.A566A	ASMTL_ENST00000416733.2_Silent_p.A490A|ASMTL-AS1_ENST00000425740.2_RNA|ASMTL_ENST00000534940.1_Silent_p.A508A|ASMTL_ENST00000381333.4_Silent_p.A550A|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000443929.1_RNA|ASMTL-AS1_ENST00000602357.1_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	566	ASMT-like.					cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGGCGCGCTGCGCCACCCTCT	0.652													c|||	79	0.0157748	0.059	0.0014	5008	,	,		19966	0.0		0.0	False		,,,				2504	0.0				p.A566A		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1698A						PASS	.		,,	259,3999		9,241,1879	76.0	84.0	81.0		1524,1650,1698	0.3	0.0	X	dbSNP_134	81	2,8470		0,2,4234	no	coding-synonymous,coding-synonymous,coding-synonymous	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	,,	9,243,6113	TT,TC,CC		0.0236,6.0827,2.0503	,,	508/564,550/606,566/622	1522330	261,12469	2129	4236	6365	SO:0001819	synonymous_variant	8623	exon13			GCGCTGCGCCACC	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.1698G>A	X.37:g.1522330C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	189	98	0.518519	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Silent	SNP	ENST00000381317.3	37	CCDS43917.1																																																																																			C|0.982;T|0.018	0.018	strong		0.652	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
KL	9365	hgsc.bcm.edu	37	13	33628239	33628239	+	Silent	SNP	G	G	A	rs9527026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33628239G>A	ENST00000380099.3	+	2	1163	c.1155G>A	c.(1153-1155)aaG>aaA	p.K385K	KL_ENST00000426690.2_Silent_p.K78K|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	385	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		CTCACATGAAGTTCCGCCAAT	0.408													A|||	651	0.129992	0.2005	0.0821	5008	,	,		18159	0.0		0.1938	False		,,,				2504	0.137				p.K385K		Atlas-SNP	.											.	KL	106	.	0			c.G1155A						PASS	.	A		815,3591	748.9+/-412.0	74,667,1462	174.0	180.0	178.0		1155	3.2	1.0	13	dbSNP_119	178	1411,7189	752.1+/-407.4	116,1179,3005	no	coding-synonymous	KL	NM_004795.3		190,1846,4467	AA,AG,GG		16.407,18.4975,17.1152		385/1013	33628239	2226,10780	2203	4300	6503	SO:0001819	synonymous_variant	9365	exon2			CATGAAGTTCCGC	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1155G>A	13.37:g.33628239G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	37	CCDS9347.1																																																																																			G|0.844;A|0.156	0.156	strong		0.408	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
USH2A	7399	hgsc.bcm.edu	37	1	216424275	216424275	+	Missense_Mutation	SNP	C	C	G	rs696723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:216424275C>G	ENST00000307340.3	-	12	2523	c.2137G>C	c.(2137-2139)Ggc>Cgc	p.G713R	USH2A_ENST00000366943.2_Missense_Mutation_p.G713R|USH2A_ENST00000366942.3_Missense_Mutation_p.G713R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	713	Laminin EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00460}.		G -> R (in USH2A; abolishes interaction with collagen IV; unknown pathological significance; dbSNP:rs696723). {ECO:0000269|PubMed:10909849, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:15241801, ECO:0000269|PubMed:15325563, 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)		TTGCACTGGCCTGAATTTTGG	0.408										HNSCC(13;0.011)			C|||	299	0.0597045	0.1936	0.0144	5008	,	,		17962	0.0		0.0109	False		,,,				2504	0.0225				p.G713R		Atlas-SNP	.											.	USH2A	1168	.	0			c.G2137C	GRCh37	CM001809	USH2A	M	rs696723	PASS	.	C	ARG/GLY,ARG/GLY	768,3638	311.9+/-292.3	79,610,1514	146.0	133.0	137.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2137,2137	4.2	1.0	1	dbSNP_86	137	97,8503	53.1+/-113.8	0,97,4203	yes	missense,missense	USH2A	NM_007123.5,NM_206933.2	125,125	79,707,5717	GG,GC,CC		1.1279,17.4308,6.6508	probably-damaging,probably-damaging	713/1547,713/5203	216424275	865,12141	2203	4300	6503	SO:0001583	missense	7399	exon12			ACTGGCCTGAATT	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.2137G>C	1.37:g.216424275C>G	ENSP00000305941:p.Gly713Arg	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	207	95	0.458937	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	95	0.043498168498168496	84	0.17073170731707318	6	0.016574585635359115	0	0.0	5	0.006596306068601583	C	17.95	3.514960	0.64634	0.174308	0.011279	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.75821	-0.97;-0.97;-0.97	5.26	4.2	0.49525	EGF-like, laminin (3);	0.000000	0.44902	D	0.000419	T	0.01661	0.0053	M	0.94021	3.485	0.09310	P	0.999999192511	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	T	0.51880	-0.8649	9	0.72032	D	0.01	.	11.5314	0.50612	0.0:0.8931:0.0:0.1069	rs696723;rs9442163;rs17026444;rs52831353;rs696723	713;713	O75445-2;O75445	.;USH2A_HUMAN	R	713	ENSP00000305941:G713R;ENSP00000355910:G713R;ENSP00000355909:G713R	ENSP00000305941:G713R	G	-	1	0	USH2A	214490898	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.442000	0.66575	0.969000	0.38237	0.655000	0.94253	GGC	C|0.942;G|0.058	0.058	strong		0.408	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
CDH23	64072	hgsc.bcm.edu	37	10	73558886	73558886	+	Missense_Mutation	SNP	G	G	A	rs4747194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73558886G>A	ENST00000224721.6	+	50	7093	c.7088G>A	c.(7087-7089)cGg>cAg	p.R2363Q	CDH23_ENST00000398788.3_Missense_Mutation_p.R118Q|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2358	Cadherin 22. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.R2363Q(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ATTGCCAACCGGACAGTGGAC	0.572													G|||	1709	0.341254	0.267	0.3501	5008	,	,		19822	0.5298		0.2783	False		,,,				2504	0.3057				p.R2358Q		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - Missense(1)	stomach(1)	c.G7073A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	1060,2966		127,806,1080	85.0	95.0	92.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7073,353,353	2.7	1.0	10	dbSNP_111	92	2191,6191		309,1573,2309	yes	missense,missense,missense	CDH23	NM_022124.5,NM_001171934.1,NM_001171933.1	43,43,43	436,2379,3389	AA,AG,GG		26.1393,26.3289,26.2008	benign,benign,benign	2358/3355,118/1080,118/1115	73558886	3251,9157	2013	4191	6204	SO:0001583	missense	64072	exon49			CCAACCGGACAGT	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.7088G>A	10.37:g.73558886G>A	ENSP00000224721:p.Arg2363Gln	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		765	0.35027472527472525	144	0.2926829268292683	109	0.3011049723756906	300	0.5244755244755245	212	0.2796833773087071	G	14.24	2.477311	0.44044	0.263289	0.261393	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.01725	4.67	5.55	2.71	0.32032	Cadherin (4);Cadherin-like (1);	0.138749	0.45867	N	0.000323	T	0.00012	0.0000	L	0.53617	1.68	0.20764	P	0.999855664	B;B	0.18310	0.004;0.027	B;B	0.16289	0.01;0.015	T	0.22941	-1.0202	9	0.08179	T	0.78	.	10.5972	0.45345	0.2081:0.0:0.7919:0.0	rs4747194;rs52818762;rs57656556;rs4747194	2358;2358	E9PEX1;Q9H251	.;CAD23_HUMAN	Q	2363;2358;2361;118	ENSP00000381768:R118Q	ENSP00000224721:R2363Q	R	+	2	0	CDH23	73228892	1.000000	0.71417	0.958000	0.39756	0.856000	0.48823	0.823000	0.27366	0.314000	0.23086	-0.137000	0.14449	CGG	G|0.658;A|0.342	0.342	strong		0.572	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
ABCC1	4363	hgsc.bcm.edu	37	16	16184366	16184366	+	Silent	SNP	G	G	T	rs28364004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16184366G>T	ENST00000399410.3	+	19	2740	c.2565G>T	c.(2563-2565)ctG>ctT	p.L855L	ABCC1_ENST00000349029.5_Silent_p.L740L|ABCC1_ENST00000399408.2_Silent_p.L855L|ABCC1_ENST00000345148.5_Silent_p.L855L|ABCC1_ENST00000351154.5_Silent_p.L796L|ABCC1_ENST00000346370.5_Silent_p.L799L	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	855	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	ACCAGGAGCTGCTGGCTCGAG	0.607													G|||	24	0.00479233	0.0136	0.0072	5008	,	,		19519	0.0		0.001	False		,,,				2504	0.0				p.L855L		Atlas-SNP	.											.	ABCC1	156	.	0			c.G2565T						PASS	.	G	,,,,	40,4072		0,40,2016	34.0	36.0	36.0		2565,2388,2397,2220,2565	3.3	1.0	16	dbSNP_126	36	7,8397		0,7,4195	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	0,47,6211	TT,TG,GG		0.0833,0.9728,0.3755	,,,,	855/1532,796/1473,799/1476,740/1417,855/1467	16184366	47,12469	2056	4202	6258	SO:0001819	synonymous_variant	4363	exon19			GGAGCTGCTGGCT	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.2565G>T	16.37:g.16184366G>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			G|0.983;T|0.017	0.017	strong		0.607	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
ZBTB7B	51043	hgsc.bcm.edu	37	1	154988957	154988957	+	Silent	SNP	A	A	G	rs2242195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:154988957A>G	ENST00000368426.3	+	4	1553	c.1416A>G	c.(1414-1416)ccA>ccG	p.P472P	ZBTB7B_ENST00000417934.2_Silent_p.P506P|ZBTB7B_ENST00000535420.1_Silent_p.P472P|ZBTB7B_ENST00000292176.2_Silent_p.P472P	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	472					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CCCACTACCCACCACCCTCTA	0.657													G|||	3373	0.673522	0.4811	0.7478	5008	,	,		17839	0.9127		0.5785	False		,,,				2504	0.7321				p.P506P		Atlas-SNP	.											ZBTB7B,NS,carcinoma,+1,1	ZBTB7B	69	1	0			c.A1518G						PASS	.	G		2259,2147	576.8+/-384.3	574,1111,518	103.0	79.0	87.0		1416	-7.6	0.8	1	dbSNP_98	87	4787,3813	538.4+/-383.4	1330,2127,843	no	coding-synonymous	ZBTB7B	NM_015872.2		1904,3238,1361	GG,GA,AA		44.3372,48.729,45.825		472/540	154988957	7046,5960	2203	4300	6503	SO:0001819	synonymous_variant	51043	exon5			CTACCCACCACCC	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	18668	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 15"""	607646	"""zinc finger protein 67 homolog (mouse)"""	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.1416A>G	1.37:g.154988957A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Silent	SNP	ENST00000368426.3	37	CCDS1081.1																																																																																			A|0.422;G|0.578	0.578	strong		0.657	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872	
SPPL2C	162540	hgsc.bcm.edu	37	17	43922640	43922640	+	Missense_Mutation	SNP	G	G	A	rs17763658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43922640G>A	ENST00000329196.5	+	1	385	c.368G>A	c.(367-369)cGg>cAg	p.R123Q	MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	123	PA.		R -> Q (in dbSNP:rs17763658).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										ATCGTGAGCCGGGTCAGTGAC	0.637													G|||	454	0.090655	0.0734	0.0663	5008	,	,		17382	0.1181		0.0805	False		,,,				2504	0.1135				p.R123Q		Atlas-SNP	.											.	.	.	.	0			c.G368A						PASS	.	G	GLN/ARG	344,4062	178.0+/-206.8	15,314,1874	53.0	53.0	53.0		368	0.5	0.1	17	dbSNP_123	53	589,8011	155.8+/-209.8	23,543,3734	yes	missense	IMP5	NM_175882.2	43	38,857,5608	AA,AG,GG		6.8488,7.8075,7.1736	probably-damaging	123/685	43922640	933,12073	2203	4300	6503	SO:0001583	missense	162540	exon1			TGAGCCGGGTCAG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.368G>A	17.37:g.43922640G>A	ENSP00000332488:p.Arg123Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	191	0.08745421245421245	39	0.07926829268292683	29	0.08011049723756906	63	0.11013986013986014	60	0.079155672823219	G	8.681	0.905052	0.17760	0.078075	0.068488	ENSG00000185294	ENST00000329196	T	0.07688	3.17	4.64	0.472	0.16758	Protease-associated domain, PA (1);	0.368339	0.19781	N	0.106216	T	0.00241	0.0007	L	0.49350	1.555	0.26367	P	0.9769541	P	0.52842	0.956	P	0.51453	0.67	T	0.19943	-1.0290	9	0.37606	T	0.19	-3.1037	6.8244	0.23874	0.3859:0.0:0.6141:0.0	rs17763658;rs52794767;rs17763658	123	Q8IUH8	IMP5_HUMAN	Q	123	ENSP00000332488:R123Q	ENSP00000332488:R123Q	R	+	2	0	AC217771.1	41278420	1.000000	0.71417	0.141000	0.22245	0.005000	0.04900	1.345000	0.33953	-0.018000	0.14079	-0.808000	0.03180	CGG	G|0.922;A|0.078	0.078	strong		0.637	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
DNAH1	25981	hgsc.bcm.edu	37	3	52391735	52391735	+	Silent	SNP	A	A	C	rs11714402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52391735A>C	ENST00000420323.2	+	23	4225	c.3964A>C	c.(3964-3966)Agg>Cgg	p.R1322R		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1322	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGAGACCAAGAGGAGCGCCTT	0.632													C|||	807	0.161142	0.3101	0.1542	5008	,	,		17029	0.0238		0.165	False		,,,				2504	0.1022				p.R1322R		Atlas-SNP	.											DNAH1_ENST00000420323,NS,carcinoma,0,2	DNAH1	534	2	0			c.A3964C						scavenged	.	C		885,3197		102,681,1258	29.0	32.0	31.0		3964	-1.0	0.6	3	dbSNP_120	31	1421,6957		112,1197,2880	no	coding-synonymous	DNAH1	NM_015512.4		214,1878,4138	CC,CA,AA		16.9611,21.6805,18.5072		1322/4266	52391735	2306,10154	2041	4189	6230	SO:0001819	synonymous_variant	25981	exon23			ACCAAGAGGAGCG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.3964A>C	3.37:g.52391735A>C		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	136	70	0.514706	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	37	CCDS46842.1																																																																																			A|0.837;C|0.163	0.163	strong		0.632	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
DCST1	149095	hgsc.bcm.edu	37	1	155019710	155019710	+	Missense_Mutation	SNP	A	A	C	rs11264300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155019710A>C	ENST00000295542.1	+	14	1630	c.1534A>C	c.(1534-1536)Atg>Ctg	p.M512L	DCST1_ENST00000368419.2_Missense_Mutation_p.M512L|DCST1_ENST00000392480.1_Missense_Mutation_p.M512L|DCST1_ENST00000423025.2_Missense_Mutation_p.M487L|RP11-307C12.11_ENST00000452962.1_RNA	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	512			M -> L (in dbSNP:rs11264300). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			GGGAGACTCCATGCTAGCCCG	0.532													A|||	2777	0.554513	0.3858	0.5865	5008	,	,		18637	0.8849		0.3569	False		,,,				2504	0.6227				p.M512L		Atlas-SNP	.											DCST1,rectum,carcinoma,0,1	DCST1	69	1	0			c.A1534C						PASS	.	A	LEU/MET,LEU/MET	1798,2608	527.6+/-372.2	350,1098,755	88.0	86.0	87.0		1459,1534	3.7	1.0	1	dbSNP_120	87	2984,5616	462.0+/-365.6	524,1936,1840	yes	missense,missense	DCST1	NM_001143687.2,NM_152494.3	15,15	874,3034,2595	CC,CA,AA		34.6977,40.808,36.7676	benign,benign	487/682,512/707	155019710	4782,8224	2203	4300	6503	SO:0001583	missense	149095	exon14			GACTCCATGCTAG	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.1534A>C	1.37:g.155019710A>C	ENSP00000295542:p.Met512Leu	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	179	179	1	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	37	CCDS1083.1	1163	0.5325091575091575	179	0.3638211382113821	193	0.5331491712707183	517	0.9038461538461539	274	0.36147757255936674	A	11.83	1.756878	0.31137	0.40808	0.346977	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	4.88	3.73	0.42828	Dendritic cell-specific transmembrane protein-like (1);	0.190127	0.51477	N	0.000086	T	0.06416	0.0165	L	0.31420	0.93	0.36215	P	0.148416	B;B	0.16166	0.016;0.016	B;B	0.18561	0.022;0.022	T	0.24048	-1.0171	9	0.06494	T	0.89	-31.4022	8.753	0.34629	0.8085:0.1915:0.0:0.0	rs11264300;rs52800761;rs60521342;rs11264300	487;512	E9PHV3;Q5T197	.;DCST1_HUMAN	L	512;512;487;512	ENSP00000295542:M512L;ENSP00000376271:M512L;ENSP00000387369:M487L;ENSP00000357404:M512L	ENSP00000295542:M512L	M	+	1	0	DCST1	153286334	1.000000	0.71417	1.000000	0.80357	0.492000	0.33523	3.293000	0.51779	0.960000	0.38005	0.533000	0.62120	ATG	A|0.559;C|0.441	0.441	strong		0.532	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494	
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186196	39186196	+	Silent	SNP	A	A	G	rs386797029|rs150267202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39186196A>G	ENST00000377747.4	-	1	160	c.135T>C	c.(133-135)atT>atC	p.I45I	KRTAP1-5_ENST00000361883.5_5'Flank	NM_001257305.1	NP_001244234.1	P0C5Y4	KRA14_HUMAN	keratin associated protein 1-4	45						keratin filament (GO:0045095)				lung(1)	1						GGCCATAGCCAATGCCACCAC	0.647													a|||	535	0.106829	0.1891	0.1167	5008	,	,		18067	0.1627		0.0159	False		,,,				2504	0.0245				p.I45I		Atlas-SNP	.											.	KRTAP1-4	4	.	0			c.T135C						PASS	.																																			SO:0001819	synonymous_variant	728255	exon1			ATAGCCAATGCCA	AC007455	CCDS58548.1	17q21.2	2010-06-22			ENSG00000204887	ENSG00000204887		"""Keratin associated proteins"""	18904	protein-coding gene	gene with protein product		608821					Standard	NM_001257305		Approved	KAP1.4	uc031raf.1	P0C5Y4	OTTHUMG00000133631	ENST00000377747.4:c.135T>C	17.37:g.39186196A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_001257305	A6NJ92	Silent	SNP	ENST00000377747.4	37	CCDS58548.1																																																																																			A|0.898;G|0.102	0.102	strong		0.647	KRTAP1-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257776.3		
MAN2B1	4125	hgsc.bcm.edu	37	19	12766624	12766624	+	Missense_Mutation	SNP	C	C	A	rs377104016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12766624C>A	ENST00000456935.2	-	14	1754	c.1714G>T	c.(1714-1716)Gcc>Tcc	p.A572S	MAN2B1_ENST00000221363.4_Missense_Mutation_p.A571S|MAN2B1_ENST00000495617.1_5'Flank	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	572					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)	p.A572T(1)		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						AAGCCCAGGGCGGGCAGTGAG	0.612													C|||	2	0.000399361	0.0	0.0	5008	,	,		17585	0.0		0.0	False		,,,				2504	0.002				p.A572S		Atlas-SNP	.											MAN2B1,NS,carcinoma,0,1	MAN2B1	91	1	1	Substitution - Missense(1)	prostate(1)	c.G1714T						PASS	.	C	SER/ALA,SER/ALA	3,4403	8.1+/-20.4	0,3,2200	58.0	64.0	62.0		1714,1711	4.0	1.0	19		62	0,8600		0,0,4300	no	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	99,99	0,3,6500	AA,AC,CC		0.0,0.0681,0.0231	benign,benign	572/1012,571/1011	12766624	3,13003	2203	4300	6503	SO:0001583	missense	4125	exon14			CCAGGGCGGGCAG		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.1714G>T	19.37:g.12766624C>A	ENSP00000395473:p.Ala572Ser	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	37	21	0.567568	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.66|19.66	3.869012|3.869012	0.72065|0.72065	6.81E-4|6.81E-4	0.0|0.0	ENSG00000104774|ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363|ENST00000433513	T;T|.	0.81163|.	-1.46;-1.46|.	5.16|5.16	4.03|4.03	0.46877|0.46877	Glycosyl hydrolases 38, C-terminal (1);Glycosyl hydrolase, family 13, all-beta (1);Glycoside hydrolase-type carbohydrate-binding (1);|.	0.000000|.	0.33712|.	N|.	0.004633|.	T|T	0.76593|0.76593	0.4009|0.4009	M|M	0.85041|0.85041	2.73|2.73	0.39975|0.39975	D|D	0.974849|0.974849	P;D|.	0.58970|.	0.928;0.984|.	P;P|.	0.59288|.	0.774;0.855|.	T|T	0.80151|0.80151	-0.1502|-0.1502	10|5	0.54805|.	T|.	0.06|.	-16.9432|-16.9432	12.4629|12.4629	0.55741|0.55741	0.0:0.8153:0.1847:0.0|0.0:0.8153:0.1847:0.0	.|.	571;572|.	G5E928;O00754|.	.;MA2B1_HUMAN|.	S|L	572;511;571|107	ENSP00000395473:A572S;ENSP00000221363:A571S|.	ENSP00000221363:A571S|.	A|R	-|-	1|2	0|0	MAN2B1|MAN2B1	12627624|12627624	0.995000|0.995000	0.38212|0.38212	0.986000|0.986000	0.45419|0.45419	0.762000|0.762000	0.43233|0.43233	2.575000|2.575000	0.46025|0.46025	2.389000|2.389000	0.81357|0.81357	0.313000|0.313000	0.20887|0.20887	GCC|CGC	.	.	weak		0.612	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
CDK2	1017	hgsc.bcm.edu	37	12	56363357	56363357	+	Silent	SNP	G	G	A	rs2069406	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56363357G>A	ENST00000266970.4	+	5	825	c.585G>A	c.(583-585)gaG>gaA	p.E195E	RP11-973D8.4_ENST00000554022.1_RNA|PMEL_ENST00000548493.1_5'Flank|PMEL_ENST00000360714.4_5'Flank|CDK2_ENST00000553376.1_Silent_p.E195E|PMEL_ENST00000539511.1_5'Flank|PMEL_ENST00000536427.1_5'Flank|PMEL_ENST00000548689.1_5'Flank|PMEL_ENST00000548747.1_5'Flank|PMEL_ENST00000552882.1_5'Flank|CDK2_ENST00000354056.4_Intron|CDK2_ENST00000556656.1_3'UTR|CDK2_ENST00000440311.2_Intron	NM_001798.3	NP_001789.2	P24941	CDK2_HUMAN	cyclin-dependent kinase 2	195	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|blood coagulation (GO:0007596)|cellular response to nitric oxide (GO:0071732)|centrosome duplication (GO:0051298)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone phosphorylation (GO:0016572)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|mitotic nuclear division (GO:0007067)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transport (GO:0006813)|Ras protein signal transduction (GO:0007265)|regulation of gene silencing (GO:0060968)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	Cajal body (GO:0015030)|centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|condensed chromosome (GO:0000793)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|X chromosome (GO:0000805)|Y chromosome (GO:0000806)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	18			UCEC - Uterine corpus endometrioid carcinoma (6;0.123)|OV - Ovarian serous cystadenocarcinoma(18;0.235)		Bosutinib(DB06616)	TCTTTGCTGAGATGGTATGGA	0.562													G|||	213	0.0425319	0.1528	0.0159	5008	,	,		17480	0.0		0.0	False		,,,				2504	0.0				p.E195E		Atlas-SNP	.											.	CDK2	27	.	0			c.G585A						PASS	.	G	,	539,3867	244.0+/-253.5	33,473,1697	93.0	80.0	84.0		585,	4.5	1.0	12	dbSNP_96	84	9,8591	7.7+/-29.5	0,9,4291	no	coding-synonymous,intron	CDK2	NM_001798.3,NM_052827.2	,	33,482,5988	AA,AG,GG		0.1047,12.2333,4.2134	,	195/299,	56363357	548,12458	2203	4300	6503	SO:0001819	synonymous_variant	1017	exon5			TGCTGAGATGGTA	M68520	CCDS8898.1, CCDS8899.1	12q13	2011-11-08				ENSG00000123374		"""Cyclin-dependent kinases"""	1771	protein-coding gene	gene with protein product		116953				1717994, 8275715	Standard	NM_001798		Approved		uc001sit.4	P24941		ENST00000266970.4:c.585G>A	12.37:g.56363357G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	124	48	0.387097	NM_001798	A8K7C6|O75100	Silent	SNP	ENST00000266970.4	37	CCDS8898.1																																																																																			G|0.958;A|0.042	0.042	strong		0.562	CDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409650.1		
ACVR2B	93	hgsc.bcm.edu	37	3	38523754	38523754	+	Silent	SNP	C	C	T	rs149695736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38523754C>T	ENST00000352511.4	+	9	1612	c.1140C>T	c.(1138-1140)gcC>gcT	p.A380A		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	380	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		AGAGAGATGCCTTCCTGCGCA	0.572													C|||	8	0.00159744	0.0061	0.0	5008	,	,		21138	0.0		0.0	False		,,,				2504	0.0				p.A380A		Atlas-SNP	.											ACVR2B_ENST00000352511,caecum,carcinoma,0,2	ACVR2B	88	2	0			c.C1140T						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	128.0	96.0	107.0		1140	3.5	1.0	3	dbSNP_134	107	0,8600		0,0,4300	yes	coding-synonymous	ACVR2B	NM_001106.3		0,10,6493	TT,TC,CC		0.0,0.227,0.0769		380/513	38523754	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	93	exon9			AGATGCCTTCCTG	X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	ENST00000352511.4:c.1140C>T	3.37:g.38523754C>T		Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	277	141	0.509025	NM_001106	Q4VAV0	Silent	SNP	ENST00000352511.4	37	CCDS2679.1																																																																																			C|0.999;T|0.001	0.001	strong		0.572	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106	
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39155881	39155881	+	Silent	SNP	C	C	T	rs3813048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39155881C>T	ENST00000391587.1	-	1	257	c.225G>A	c.(223-225)ccG>ccA	p.P75P		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	75						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				TCTCCAGGCCCGGAGTTGGCT	0.622													T|||	1498	0.299121	0.6112	0.2061	5008	,	,		17181	0.2312		0.1223	False		,,,				2504	0.1953				p.P75P		Atlas-SNP	.											.	KRTAP3-2	11	.	0			c.G225A						PASS	.						61.0	79.0	73.0					17																	39155881		2201	4296	6497	SO:0001819	synonymous_variant	83897	exon1			CAGGCCCGGAGTT	AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"""Keratin associated proteins"""	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.225G>A	17.37:g.39155881C>T		Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	216	65	0.300926	NM_031959		Silent	SNP	ENST00000391587.1	37	CCDS32644.1																																																																																			C|0.778;T|0.222	0.222	strong		0.622	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257685.1		
BTBD11	121551	hgsc.bcm.edu	37	12	107937768	107937768	+	Missense_Mutation	SNP	G	G	A	rs1558781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:107937768G>A	ENST00000280758.5	+	3	1870	c.1342G>A	c.(1342-1344)Ggc>Agc	p.G448S	BTBD11_ENST00000490090.2_Missense_Mutation_p.G448S|BTBD11_ENST00000420571.2_Missense_Mutation_p.G448S	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	448			G -> S (in dbSNP:rs1558781).			integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CAAGCACCACGGCAATGGCAC	0.572													G|||	883	0.176318	0.1891	0.2637	5008	,	,		17911	0.2579		0.1014	False		,,,				2504	0.09				p.G448S		Atlas-SNP	.											BTBD11,NS,carcinoma,-1,2	BTBD11	122	2	0			c.G1342A						PASS	.	G	SER/GLY	897,3509	348.0+/-309.7	109,679,1415	49.0	44.0	46.0		1342	4.9	0.9	12	dbSNP_88	46	1012,7588	217.6+/-256.2	56,900,3344	yes	missense	BTBD11	NM_001018072.1	56	165,1579,4759	AA,AG,GG		11.7674,20.3586,14.6778	benign	448/1105	107937768	1909,11097	2203	4300	6503	SO:0001583	missense	121551	exon3			CACCACGGCAATG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.1342G>A	12.37:g.107937768G>A	ENSP00000280758:p.Gly448Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	396	0.1813186813186813	84	0.17073170731707318	79	0.21823204419889503	158	0.2762237762237762	75	0.09894459102902374	G	15.23	2.771922	0.49680	0.203586	0.117674	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000490090;ENST00000550706;ENST00000415943	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.76	4.87	0.63330	.	0.154372	0.64402	D	0.000017	T	0.00012	0.0000	N	0.16266	0.395	0.09310	P	0.9999999999999999	B;B;P	0.52316	0.179;0.064;0.952	B;B;B	0.39185	0.024;0.007;0.293	T	0.36720	-0.9736	9	0.25106	T	0.35	.	12.0181	0.53326	0.1384:0.0:0.8616:0.0	rs1558781;rs1558781	448;448;448	A6QL63-2;A6QL63;A6QL63-3	.;BTBDB_HUMAN;.	S	448;448;448;79;82	ENSP00000280758:G448S;ENSP00000413889:G448S;ENSP00000447319:G448S;ENSP00000447606:G79S;ENSP00000407416:G82S	ENSP00000280758:G448S	G	+	1	0	BTBD11	106461898	1.000000	0.71417	0.933000	0.37362	0.988000	0.76386	4.346000	0.59367	1.438000	0.47492	-0.137000	0.14449	GGC	G|0.845;A|0.155	0.155	strong		0.572	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
PROS1	5627	hgsc.bcm.edu	37	3	93624961	93624961	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:93624961G>A	ENST00000394236.3	-	5	689	c.373C>T	c.(373-375)Cca>Tca	p.P125S	PROS1_ENST00000407433.1_5'UTR	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	125	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)	TCATTGCATGGCAGAGGACTA	0.353																																					p.P125S		Atlas-SNP	.											PROS1,NS,carcinoma,0,1	PROS1	126	1	0			c.C373T						scavenged	.						113.0	116.0	115.0					3																	93624961		2203	4300	6503	SO:0001583	missense	5627	exon5			TGCATGGCAGAGG		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.373C>T	3.37:g.93624961G>A	ENSP00000377783:p.Pro125Ser	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	220	3	0.0136364	NM_000313	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Missense_Mutation	SNP	ENST00000394236.3	37	CCDS2923.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.313446	0.81358	.	.	ENSG00000184500	ENST00000394236;ENST00000348974	D;D	0.95035	-3.59;-3.14	4.44	4.44	0.53790	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.97495	0.9180	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98459	1.0595	10	0.87932	D	0	.	17.2572	0.87060	0.0:0.0:1.0:0.0	.	125	P07225	PROS_HUMAN	S	125;157	ENSP00000377783:P125S;ENSP00000330021:P157S	ENSP00000330021:P157S	P	-	1	0	PROS1	95107651	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	7.098000	0.76974	2.314000	0.78098	0.484000	0.47621	CCA	.	.	none		0.353	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313	
TMPRSS7	344805	hgsc.bcm.edu	37	3	111760812	111760812	+	Missense_Mutation	SNP	G	G	C	rs11914332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:111760812G>C	ENST00000452346.2	+	3	347	c.344G>C	c.(343-345)cGc>cCc	p.R115P	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.R3P			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	115	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GGGATGTTTCGCATCACCAAC	0.453													G|||	227	0.0453275	0.0719	0.0519	5008	,	,		19940	0.0159		0.0408	False		,,,				2504	0.0399				p.R3P		Atlas-SNP	.											TMPRSS7_ENST00000419127,colon,carcinoma,+1,2	TMPRSS7	126	2	0			c.G8C						scavenged	.						119.0	101.0	107.0					3																	111760812		692	1591	2283	SO:0001583	missense	344805	exon2			TGTTTCGCATCAC	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"""Serine peptidases / Transmembrane"""	30846	protein-coding gene	gene with protein product			"""type II transmembrane serine protease 7"""			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.344G>C	3.37:g.111760812G>C	ENSP00000398236:p.Arg115Pro	Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	142	73	0.514085	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	37		99	0.04532967032967033	37	0.07520325203252033	21	0.058011049723756904	11	0.019230769230769232	30	0.0395778364116095	G	24.0	4.480901	0.84747	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	T;T	0.49432	0.78;0.78	5.55	5.55	0.83447	.	.	.	.	.	T	0.05823	0.0152	L	0.29908	0.895	0.19300	P	0.9999771033	D	0.60575	0.988	P	0.62014	0.897	T	0.35450	-0.9788	8	0.87932	D	0	.	16.4227	0.83772	0.0:0.0:1.0:0.0	rs11914332;rs59564744;rs11914332	3	Q7RTY8-2	.	P	115;102;102;3	ENSP00000398236:R115P;ENSP00000411645:R3P	ENSP00000411645:R3P	R	+	2	0	TMPRSS7	113243502	1.000000	0.71417	0.998000	0.56505	0.920000	0.55202	8.189000	0.89712	2.622000	0.88805	0.557000	0.71058	CGC	G|0.957;C|0.043	0.043	strong		0.453	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599	
CEP85L	387119	hgsc.bcm.edu	37	6	118791804	118791804	+	Missense_Mutation	SNP	T	T	C	rs7743702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118791804T>C	ENST00000368491.3	-	11	2539	c.1918A>G	c.(1918-1920)Atg>Gtg	p.M640V	CEP85L_ENST00000368488.5_Missense_Mutation_p.M643V	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	640			M -> V (in dbSNP:rs7743702).			centrosome (GO:0005813)|cytoplasm (GO:0005737)											TTTCCTTGCATAGACTAGAAT	0.318													T|||	166	0.033147	0.059	0.0173	5008	,	,		15160	0.0		0.0189	False		,,,				2504	0.0583				p.M643V		Atlas-SNP	.											.	CEP85L	26	.	0			c.A1927G						PASS	.	T	VAL/MET,VAL/MET	199,3401		4,191,1605	74.0	70.0	72.0		1918,1927	1.6	1.0	6	dbSNP_116	72	166,7950		2,162,3894	yes	missense,missense	C6orf204	NM_001042475.2,NM_001178035.1	21,21	6,353,5499	CC,CT,TT		2.0453,5.5278,3.1154	benign,benign	640/806,643/809	118791804	365,11351	1800	4058	5858	SO:0001583	missense	387119	exon12			CTTGCATAGACTA	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.1918A>G	6.37:g.118791804T>C	ENSP00000357477:p.Met640Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	131	69	0.526718	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	46	0.021062271062271064	26	0.052845528455284556	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	12.46	1.943229	0.34283	0.055278	0.020453	ENSG00000111860	ENST00000368491;ENST00000368488	T;T	0.10960	2.82;2.82	5.69	1.6	0.23607	.	0.484848	0.22127	N	0.064253	T	0.02304	0.0071	L	0.36672	1.1	0.29229	N	0.873412	B	0.21225	0.053	B	0.18561	0.022	T	0.36601	-0.9741	10	0.49607	T	0.09	-6.4463	2.3369	0.04250	0.257:0.0736:0.133:0.5364	rs7743702;rs52838185;rs7743702	640	Q5SZL2	CF204_HUMAN	V	640;643	ENSP00000357477:M640V;ENSP00000357474:M643V	ENSP00000357474:M643V	M	-	1	0	C6orf204	118898497	0.926000	0.31397	1.000000	0.80357	0.939000	0.58152	0.058000	0.14301	0.932000	0.37266	0.533000	0.62120	ATG	T|0.975;C|0.025	0.025	strong		0.318	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
C3orf22	152065	hgsc.bcm.edu	37	3	126272160	126272160	+	Missense_Mutation	SNP	T	T	C	rs146981008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126272160T>C	ENST00000318225.2	-	2	452	c.74A>G	c.(73-75)aAg>aGg	p.K25R		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	25										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		CGGAAACTTCTTGGCAAAATT	0.562													T|||	5	0.000998403	0.0008	0.0058	5008	,	,		17166	0.0		0.0	False		,,,				2504	0.0				p.K25R		Atlas-SNP	.											.	C3orf22	17	.	0			c.A74G						PASS	.	T	ARG/LYS	5,4401	9.9+/-24.2	0,5,2198	242.0	246.0	245.0		74	1.9	0.5	3	dbSNP_134	245	0,8600		0,0,4300	yes	missense	C3orf22	NM_152533.1	26	0,5,6498	CC,CT,TT		0.0,0.1135,0.0384	possibly-damaging	25/142	126272160	5,13001	2203	4300	6503	SO:0001583	missense	152065	exon2			AACTTCTTGGCAA		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.74A>G	3.37:g.126272160T>C	ENSP00000316644:p.Lys25Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_152533	B3KUS9	Missense_Mutation	SNP	ENST00000318225.2	37	CCDS3040.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	T	9.445	1.088997	0.20390	0.001135	0.0	ENSG00000180697	ENST00000318225	.	.	.	2.96	1.87	0.25490	.	0.557035	0.13645	N	0.372704	T	0.11750	0.0286	N	0.12746	0.255	0.21604	N	0.999627	B	0.17667	0.023	B	0.17433	0.018	T	0.19877	-1.0292	9	0.22109	T	0.4	.	3.4088	0.07351	0.0:0.2278:0.0:0.7722	.	25	Q8N5N4	CC022_HUMAN	R	25	.	ENSP00000316644:K25R	K	-	2	0	C3orf22	127754850	0.013000	0.17824	0.465000	0.27155	0.240000	0.25518	0.519000	0.22862	0.602000	0.29896	0.402000	0.26972	AAG	T|0.999;C|0.001	0.001	strong		0.562	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533	
LILRA1	11024	hgsc.bcm.edu	37	19	55106317	55106317	+	Silent	SNP	A	A	G	rs10416917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55106317A>G	ENST00000251372.3	+	4	440	c.258A>G	c.(256-258)ccA>ccG	p.P86P	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Silent_p.P86P|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	86	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		TCCCCATCCCATCCATCACCT	0.562													N|||	1461	0.291733	0.5189	0.2709	5008	,	,		20479	0.2718		0.1034	False		,,,				2504	0.2137				p.P86P		Atlas-SNP	.											.	LILRA1	105	.	0			c.A258G						PASS	.	G		2091,2315	573.3+/-383.5	477,1137,589	159.0	149.0	152.0		258	-0.7	0.0	19	dbSNP_119	152	967,7633	210.5+/-251.4	57,853,3390	no	coding-synonymous	LILRA1	NM_006863.1		534,1990,3979	GG,GA,AA		11.2442,47.458,23.5122		86/490	55106317	3058,9948	2203	4300	6503	SO:0001819	synonymous_variant	11024	exon4			CATCCCATCCATC	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.258A>G	19.37:g.55106317A>G		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	303	302	0.9967	NM_006863	O75018|Q3MJA6	Silent	SNP	ENST00000251372.3	37	CCDS12901.1																																																																																			A|0.762;G|0.238	0.238	strong		0.562	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
CETP	1071	hgsc.bcm.edu	37	16	57015084	57015084	+	Silent	SNP	C	C	G	rs7192120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57015084C>G	ENST00000566128.1	+	12	1233	c.966C>G	c.(964-966)acC>acG	p.T322T	CETP_ENST00000379780.2_Silent_p.T327T|CETP_ENST00000200676.3_Silent_p.T387T					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						TCGTGACTACCGTCCAGGCCT	0.522													C|||	120	0.0239617	0.0847	0.0115	5008	,	,		17602	0.0		0.0	False		,,,				2504	0.0				p.T387T		Atlas-SNP	.											CETP,colon,carcinoma,+2,1	CETP	50	1	0			c.C1161G						PASS	.	C		261,4135	148.8+/-183.1	5,251,1942	86.0	91.0	90.0		1161	-5.8	0.0	16	dbSNP_116	90	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous	CETP	NM_000078.2		5,253,6240	GG,GC,CC		0.0233,5.9372,2.0237		387/494	57015084	263,12733	2198	4300	6498	SO:0001819	synonymous_variant	1071	exon12			GACTACCGTCCAG	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.966C>G	16.37:g.57015084C>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_000078		Silent	SNP	ENST00000566128.1	37																																																																																				C|0.979;G|0.021	0.021	strong		0.522	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
GYS2	2998	hgsc.bcm.edu	37	12	21692210	21692210	+	Silent	SNP	T	T	C	rs142883971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21692210T>C	ENST00000261195.2	-	15	2126	c.1872A>G	c.(1870-1872)gaA>gaG	p.E624E		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	624					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GTGATGTTAGTTCCACATGGA	0.303													T|||	17	0.00339457	0.0121	0.0014	5008	,	,		16759	0.0		0.0	False		,,,				2504	0.0				p.E624E	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											GYS2,NS,carcinoma,-2,1	GYS2	110	1	0			c.A1872G						PASS	.	T		72,4334	63.5+/-100.7	0,72,2131	166.0	173.0	171.0		1872	-3.7	0.0	12	dbSNP_134	171	0,8600		0,0,4300	no	coding-synonymous	GYS2	NM_021957.3		0,72,6431	CC,CT,TT		0.0,1.6341,0.5536		624/704	21692210	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	2998	exon15			TGTTAGTTCCACA		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1872A>G	12.37:g.21692210T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_021957	A0AVD8	Silent	SNP	ENST00000261195.2	37	CCDS8690.1																																																																																			T|0.995;C|0.005	0.005	strong		0.303	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957	
HEXDC	284004	hgsc.bcm.edu	37	17	80377690	80377690	+	Silent	SNP	T	T	G	rs1141463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80377690T>G	ENST00000327949.9	+	1	26	c.15T>G	c.(13-15)acT>acG	p.T5T	HEXDC_ENST00000577944.1_Silent_p.T5T|OGFOD3_ENST00000313056.5_5'Flank|OGFOD3_ENST00000329197.5_5'Flank|Y_RNA_ENST00000364369.1_RNA|HEXDC_ENST00000337014.6_Silent_p.T5T			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	252	0	0		WXS	Illumina HiSeq	Phase_I	275	124	0.450909	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	
PRR5	55615	hgsc.bcm.edu	37	22	45075738	45075738	+	Missense_Mutation	SNP	T	T	C	rs763213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	158	0	0		WXS	Illumina HiSeq	Phase_I	139	63	0.453237	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	
TEK	7010	hgsc.bcm.edu	37	9	27220066	27220066	+	Silent	SNP	G	G	A	rs2273719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:27220066G>A	ENST00000380036.4	+	21	3565	c.3123G>A	c.(3121-3123)ggG>ggA	p.G1041G	TEK_ENST00000519097.1_Silent_p.G893G|TEK_ENST00000406359.4_Silent_p.G998G	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	1041	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CCTACTGCGGGATGACTTGTG	0.527													G|||	1123	0.224241	0.3888	0.1614	5008	,	,		18605	0.1736		0.1332	False		,,,				2504	0.1922				p.G1041G		Atlas-SNP	.											.	TEK	250	.	0			c.G3123A						PASS	.	G		1559,2847	489.0+/-361.4	266,1027,910	139.0	135.0	136.0		3123	-0.5	1.0	9	dbSNP_100	136	1362,7238	265.7+/-286.3	99,1164,3037	no	coding-synonymous	TEK	NM_000459.3		365,2191,3947	AA,AG,GG		15.8372,35.3836,22.4589		1041/1125	27220066	2921,10085	2203	4300	6503	SO:0001819	synonymous_variant	7010	exon21			CTGCGGGATGACT	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.3123G>A	9.37:g.27220066G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	161	82	0.509317	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																			G|0.791;A|0.209	0.209	strong		0.527	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
VPS13A	23230	hgsc.bcm.edu	37	9	79959197	79959197	+	Splice_Site	SNP	G	G	A	rs73449933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79959197G>A	ENST00000360280.3	+	51	7415	c.7155G>A	c.(7153-7155)gaG>gaA	p.E2385E	VPS13A_ENST00000376634.4_Splice_Site_p.E2385E|VPS13A_ENST00000357409.5_Splice_Site_p.E2385E|VPS13A_ENST00000376636.3_Splice_Site_p.E2346E	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2385					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						TAGATAACGAGGTAAGTTTTT	0.289													G|||	71	0.0141773	0.053	0.0014	5008	,	,		13508	0.0		0.0	False		,,,				2504	0.0				p.E2385E		Atlas-SNP	.											.	VPS13A	735	.	0			c.G7155A						PASS	.	G	,,,	169,4237	101.2+/-139.8	3,163,2037	80.0	91.0	87.0		7038,7155,7155,7155	2.7	1.0	9	dbSNP_130	87	1,8585	1.2+/-3.3	0,1,4292	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	3,164,6329	AA,AG,GG		0.0116,3.8357,1.3085	,,,	2346/3136,2385/3070,2385/3096,2385/3175	79959197	170,12822	2203	4293	6496	SO:0001630	splice_region_variant	23230	exon51			TAACGAGGTAAGT	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.7155+1G>A	9.37:g.79959197G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	81	57	0.703704	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			G|0.986;A|0.014	0.014	strong		0.289	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	Silent
ADAM18	8749	hgsc.bcm.edu	37	8	39581417	39581417	+	Missense_Mutation	SNP	A	A	G	rs76378145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39581417A>G	ENST00000265707.5	+	19	2213	c.2168A>G	c.(2167-2169)gAg>gGg	p.E723G	ADAM18_ENST00000523755.1_3'UTR|ADAM18_ENST00000541111.1_Missense_Mutation_p.E137G|ADAM18_ENST00000379866.1_Missense_Mutation_p.E699G	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	723					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)			GAGAATGCAGAGTATAATCGG	0.274													A|||	127	0.0253594	0.0893	0.0101	5008	,	,		14686	0.0		0.002	False		,,,				2504	0.0				p.E723G		Atlas-SNP	.											.	ADAM18	169	.	0			c.A2168G						PASS	.		GLY/GLU	371,4033	172.3+/-202.3	20,331,1851	84.0	89.0	87.0		2168	3.6	0.0	8	dbSNP_132	87	2,8588	2.2+/-6.3	0,2,4293	yes	missense	ADAM18	NM_014237.2	98	20,333,6144	GG,GA,AA		0.0233,8.4242,2.8706	benign	723/740	39581417	373,12621	2202	4295	6497	SO:0001583	missense	8749	exon19			ATGCAGAGTATAA	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.2168A>G	8.37:g.39581417A>G	ENSP00000265707:p.Glu723Gly	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	51	0.023351648351648352	45	0.09146341463414634	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	a	9.078	0.998571	0.19121	0.084242	2.33E-4	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000541111	D;D;D	0.93953	-3.32;-3.32;-3.32	4.77	3.61	0.41365	.	0.638567	0.13741	N	0.365922	T	0.38241	0.1033	M	0.68593	2.085	0.09310	N	1	B;B	0.27910	0.193;0.046	B;B	0.27170	0.077;0.035	T	0.67333	-0.5697	10	0.52906	T	0.07	.	7.6055	0.28100	0.9001:0.0:0.0999:0.0	.	699;723	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	G	723;699;137	ENSP00000265707:E723G;ENSP00000369195:E699G;ENSP00000444729:E137G	ENSP00000265707:E723G	E	+	2	0	ADAM18	39700574	0.174000	0.23070	0.007000	0.13788	0.001000	0.01503	2.076000	0.41548	0.933000	0.37291	-0.393000	0.06486	GAG	A|0.972;G|0.028	0.028	strong		0.274	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
CAT	847	hgsc.bcm.edu	37	11	34482908	34482908	+	Silent	SNP	C	C	T	rs769217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34482908C>T	ENST00000241052.4	+	9	1256	c.1167C>T	c.(1165-1167)gaC>gaT	p.D389D		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	389					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	ACCAGCGTGACGGCCCGATGT	0.607													C|||	1316	0.26278	0.1422	0.2896	5008	,	,		18460	0.5		0.2147	False		,,,				2504	0.2117				p.D389D		Atlas-SNP	.											.	CAT	42	.	0			c.C1167T	GRCh37	CM025323	CAT	M	rs769217	PASS	.	C		739,3665	305.8+/-289.2	57,625,1520	113.0	106.0	108.0		1167	-2.6	1.0	11	dbSNP_92	108	2007,6589	351.1+/-328.1	209,1589,2500	no	coding-synonymous	CAT	NM_001752.3		266,2214,4020	TT,TC,CC		23.3481,16.7802,21.1231		389/528	34482908	2746,10254	2202	4298	6500	SO:0001819	synonymous_variant	847	exon9			GCGTGACGGCCCG	AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.1167C>T	11.37:g.34482908C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	123	68	0.552846	NM_001752	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Silent	SNP	ENST00000241052.4	37	CCDS7891.1																																																																																			C|0.745;T|0.255	0.255	strong		0.607	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752	
ST6GALNAC3	256435	hgsc.bcm.edu	37	1	76878097	76878097	+	Silent	SNP	G	G	A	rs17098940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:76878097G>A	ENST00000328299.3	+	3	766	c.618G>A	c.(616-618)aaG>aaA	p.K206K	ST6GALNAC3_ENST00000464140.1_3'UTR	NM_152996.2	NP_694541.2	Q8NDV1	SIA7C_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	206					glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sialyltransferase activity (GO:0008373)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|ovary(3)|prostate(1)|skin(2)	36						AAACTGGGAAGGACAGGTGAG	0.383													A|||	213	0.0425319	0.1558	0.0101	5008	,	,		18401	0.0		0.0	False		,,,				2504	0.0				p.K206K		Atlas-SNP	.											.	ST6GALNAC3	71	.	0			c.G618A						PASS	.	A	,	562,3844		36,490,1677	45.0	43.0	44.0		618,618	2.4	1.0	1	dbSNP_123	44	4,8590		0,4,4293	no	coding-synonymous,coding-synonymous	ST6GALNAC3	NM_001160011.1,NM_152996.2	,	36,494,5970	AA,AG,GG		0.0465,12.7553,4.3538	,	206/211,206/306	76878097	566,12434	2203	4297	6500	SO:0001819	synonymous_variant	256435	exon3			TGGGAAGGACAGG		CCDS672.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000184005	ENSG00000184005		"""Sialyltransferases"""	19343	protein-coding gene	gene with protein product	"""ST6GALNAC III"""	610133	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) C"""	SIAT7C			Standard	NM_152996		Approved		uc001dhh.2	Q8NDV1	OTTHUMG00000009615	ENST00000328299.3:c.618G>A	1.37:g.76878097G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_001160011	Q6PCE0|Q6UX29|Q8N259	Silent	SNP	ENST00000328299.3	37	CCDS672.1																																																																																			G|0.955;A|0.045	0.045	strong		0.383	ST6GALNAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026501.1	NM_152996	
OR2T6	254879	hgsc.bcm.edu	37	1	248551203	248551203	+	Silent	SNP	T	T	C	rs6700947|rs386642006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248551203T>C	ENST00000355728.2	+	1	294	c.294T>C	c.(292-294)acT>acC	p.T98T		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCGCCTGCACTGCTCAGTGCT	0.532													t|||	1850	0.369409	0.4962	0.3127	5008	,	,		19053	0.4365		0.1769	False		,,,				2504	0.3671				p.T98T		Atlas-SNP	.											.	OR2T6	101	.	0			c.T294C						PASS	.	C		1893,2513	538.7+/-375.1	423,1047,733	122.0	121.0	121.0		294	-7.1	0.1	1	dbSNP_116	121	1297,7303	256.5+/-280.9	92,1113,3095	no	coding-synonymous	OR2T6	NM_001005471.1		515,2160,3828	CC,CT,TT		15.0814,42.9641,24.5271		98/309	248551203	3190,9816	2203	4300	6503	SO:0001819	synonymous_variant	254879	exon1			CTGCACTGCTCAG	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"""GPCR / Class A : Olfactory receptors"""	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.294T>C	1.37:g.248551203T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	117	55	0.470085	NM_001005471	A6NE36	Silent	SNP	ENST00000355728.2	37	CCDS31114.1																																																																																			T|0.722;C|0.278	0.278	strong		0.532	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471	
ENTPD2	954	hgsc.bcm.edu	37	9	139945363	139945363	+	Silent	SNP	G	G	A	rs2292925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139945363G>A	ENST00000355097.2	-	5	812	c.765C>T	c.(763-765)agC>agT	p.S255S	RP11-229P13.15_ENST00000439076.1_RNA|ENTPD2_ENST00000460614.1_5'Flank|ENTPD2_ENST00000312665.5_Silent_p.S255S	NM_001246.3|NM_203468.2	NP_001237.1|NP_982293.1	Q9Y5L3	ENTP2_HUMAN	ectonucleoside triphosphate diphosphohydrolase 2	255					G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|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)|lung(5)|prostate(1)|skin(2)|urinary_tract(3)	12	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CCTGGAGGGCGCTGGCCAGCA	0.647													G|||	1097	0.21905	0.0507	0.317	5008	,	,		14884	0.3472		0.2247	False		,,,				2504	0.2393				p.S255S		Atlas-SNP	.											.	ENTPD2	30	.	0			c.C765T						PASS	.	G	,	386,4008	188.1+/-214.6	18,350,1829	47.0	39.0	42.0		765,765	-1.4	0.1	9	dbSNP_100	42	1938,6656	337.7+/-322.4	209,1520,2568	no	coding-synonymous,coding-synonymous	ENTPD2	NM_001246.2,NM_203468.1	,	227,1870,4397	AA,AG,GG		22.5506,8.7847,17.8934	,	255/473,255/496	139945363	2324,10664	2197	4297	6494	SO:0001819	synonymous_variant	954	exon5			GAGGGCGCTGGCC	U91510	CCDS7025.1, CCDS7026.1	9q34	2008-07-21			ENSG00000054179	ENSG00000054179			3364	protein-coding gene	gene with protein product	"""CD39-like-1"", ""ecto-ATPase"""	602012		CD39L1		9271669	Standard	NM_203468		Approved	NTPDase-2	uc004ckw.2	Q9Y5L3	OTTHUMG00000020953	ENST00000355097.2:c.765C>T	9.37:g.139945363G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	69	44	0.637681	NM_203468	O15464|Q5SPY6|Q5SPY7	Silent	SNP	ENST00000355097.2	37	CCDS7026.1																																																																																			G|0.806;A|0.194	0.194	strong		0.647	ENTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055169.1	NM_203468	
CMYA5	202333	hgsc.bcm.edu	37	5	79024779	79024779	+	Missense_Mutation	SNP	A	A	G	rs16877109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79024779A>G	ENST00000446378.2	+	2	222	c.191A>G	c.(190-192)tAt>tGt	p.Y64C		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	64			Y -> C (in dbSNP:rs16877109).		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)		AAGCAGGAGTATATCATATCT	0.353													G|||	1389	0.277356	0.5961	0.085	5008	,	,		14505	0.3621		0.0815	False		,,,				2504	0.0971				p.Y64C		Atlas-SNP	.											.	CMYA5	643	.	0			c.A191G						PASS	.	G	CYS/TYR	1907,1791		493,921,435	108.0	101.0	103.0		191	5.7	1.0	5	dbSNP_123	103	710,7492		39,632,3430	yes	missense	CMYA5	NM_153610.3	194	532,1553,3865	GG,GA,AA		8.6564,48.4316,21.9916	benign	64/4070	79024779	2617,9283	1849	4101	5950	SO:0001583	missense	202333	exon2			AGGAGTATATCAT	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.191A>G	5.37:g.79024779A>G	ENSP00000394770:p.Tyr64Cys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	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	628	0.2875457875457875	306	0.6219512195121951	31	0.0856353591160221	232	0.40559440559440557	59	0.07783641160949868	G	2.421	-0.333065	0.05278	0.515684	0.086564	ENSG00000164309	ENST00000446378	T	0.21361	2.01	5.7	5.7	0.88788	.	0.000000	0.53938	N	0.000054	T	0.00012	0.0000	N	0.00926	-1.1	0.42356	P	0.007600999999999969	B	0.02656	0.0	B	0.01281	0.0	T	0.39742	-0.9599	9	0.02654	T	1	.	10.3643	0.44015	0.1642:0.0:0.8358:0.0	rs16877109;rs16877109	64	Q8N3K9	CMYA5_HUMAN	C	64	ENSP00000394770:Y64C	ENSP00000394770:Y64C	Y	+	2	0	CMYA5	79060535	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.366000	0.66122	1.415000	0.47037	-0.119000	0.15052	TAT	A|0.702;G|0.298	0.298	strong		0.353	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
TRIM26	7726	hgsc.bcm.edu	37	6	30166266	30166266	+	Silent	SNP	C	C	T	rs2523721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30166266C>T	ENST00000454678.2	-	5	910	c.474G>A	c.(472-474)agG>agA	p.R158R	TRIM26_ENST00000437089.1_Silent_p.R158R|TRIM26_ENST00000453195.1_Silent_p.R158R|TRIM26_ENST00000487829.1_5'Flank	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	158					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						TGTCTCTGTCCCTCCTTAGGG	0.562													T|||	1153	0.230232	0.4017	0.1585	5008	,	,		20227	0.1081		0.1829	False		,,,				2504	0.2239				p.R158R		Atlas-SNP	.											.	TRIM26	74	.	0			c.G474A						PASS	.	T	,	1011,2011		166,679,666	133.0	141.0	138.0		474,474	2.2	1.0	6	dbSNP_100	138	1083,4335		116,851,1742	yes	coding-synonymous,coding-synonymous	TRIM26	NM_001242783.1,NM_003449.4	,	282,1530,2408	TT,TC,CC		19.9889,33.4547,24.8104	,	158/540,158/540	30166266	2094,6346	1511	2709	4220	SO:0001819	synonymous_variant	7726	exon4			TCTGTCCCTCCTT	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.474G>A	6.37:g.30166266C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_001242783	A6NG96|Q5SRL2	Silent	SNP	ENST00000454678.2	37	CCDS4678.1																																																																																			C|0.765;T|0.235	0.235	strong		0.562	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449	
TIMMDC1	51300	hgsc.bcm.edu	37	3	119222456	119222456	+	Silent	SNP	G	G	C	rs1131265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119222456G>C	ENST00000494664.1	+	3	640	c.438G>C	c.(436-438)gtG>gtC	p.V146V	TIMMDC1_ENST00000493694.1_Intron	NM_016589.3	NP_057673.2	Q9NPL8	TIDC1_HUMAN	translocase of inner mitochondrial membrane domain containing 1	146						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.V146V(1)		autonomic_ganglia(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	15						CAGTGTTTGTGACTATATTCA	0.408													G|||	1038	0.207268	0.1747	0.0994	5008	,	,		17210	0.3562		0.164	False		,,,				2504	0.2188				p.V146V		Atlas-SNP	.											TIMMDC1,NS,carcinoma,0,1	TIMMDC1	29	1	1	Substitution - coding silent(1)	stomach(1)	c.G438C						PASS	.	G		914,3492	343.1+/-307.5	100,714,1389	79.0	77.0	77.0		438	3.7	1.0	3	dbSNP_86	77	1590,7010	285.9+/-297.4	156,1278,2866	no	coding-synonymous	TIMMDC1	NM_016589.3		256,1992,4255	CC,CG,GG		18.4884,20.7444,19.2527		146/286	119222456	2504,10502	2203	4300	6503	SO:0001819	synonymous_variant	51300	exon3			GTTTGTGACTATA	AF210057	CCDS33831.1	3q13.33	2013-12-05	2011-07-05	2011-07-05	ENSG00000113845	ENSG00000113845			1321	protein-coding gene	gene with protein product		615534	"""chromosome 3 open reading frame 1"""	C3orf1		11092749	Standard	NM_016589		Approved	FLJ22597	uc003ecn.3	Q9NPL8	OTTHUMG00000159388	ENST00000494664.1:c.438G>C	3.37:g.119222456G>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_016589	D3DN81|Q6IAJ7|Q6UWU6|Q9NPR3|Q9NPS5|Q9P0Y6	Silent	SNP	ENST00000494664.1	37	CCDS33831.1																																																																																			G|0.795;C|0.205	0.205	strong		0.408	TIMMDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355077.3	NM_016589	
AZU1	566	hgsc.bcm.edu	37	19	830854	830854	+	Silent	SNP	T	T	C	rs595844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:830854T>C	ENST00000233997.2	+	4	528	c.507T>C	c.(505-507)ttT>ttC	p.F169F		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	169	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		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;0.000172)|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)		TTCCCAGGTTTGTCAACGTGA	0.662													t|||	3340	0.666933	0.941	0.6398	5008	,	,		14888	0.495		0.5497	False		,,,				2504	0.6135				p.F169F		Atlas-SNP	.											AZU1,NS,carcinoma,0,1	AZU1	31	1	0			c.T507C						PASS	.	T		3866,540	769.9+/-413.7	1698,470,35	41.0	40.0	40.0		507	-3.0	0.0	19	dbSNP_83	40	4598,4002	595.3+/-393.4	1242,2114,944	no	coding-synonymous	AZU1	NM_001700.3		2940,2584,979	CC,CT,TT		46.5349,12.256,34.9223		169/252	830854	8464,4542	2203	4300	6503	SO:0001819	synonymous_variant	566	exon4			CAGGTTTGTCAAC	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.507T>C	19.37:g.830854T>C		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Silent	SNP	ENST00000233997.2	37	CCDS12044.1																																																																																			T|0.360;C|0.640	0.640	strong		0.662	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
MROH6	642475	hgsc.bcm.edu	37	8	144652780	144652780	+	Silent	SNP	T	T	A	rs11990485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144652780T>A	ENST00000398882.3	-	5	1024	c.768A>T	c.(766-768)ggA>ggT	p.G256G	MROH6_ENST00000532704.1_5'Flank|MROH6_ENST00000534459.1_5'Flank|MROH6_ENST00000524906.1_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA|MROH6_ENST00000533679.1_5'Flank	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	256																	CCCTCGTGGCTCCCACGCAGC	0.662													T|||	70	0.0139776	0.0522	0.0014	5008	,	,		12771	0.0		0.0	False		,,,				2504	0.0				p.G256G		Atlas-SNP	.											.	.	.	.	0			c.A768T						PASS	.	T		171,3991		2,167,1912	30.0	35.0	34.0		768	-0.9	1.0	8	dbSNP_120	34	1,8441		0,1,4220	no	coding-synonymous	C8orf73	NM_001100878.1		2,168,6132	AA,AT,TT		0.0118,4.1086,1.3646		256/720	144652780	172,12432	2081	4221	6302	SO:0001819	synonymous_variant	642475	exon5			CGTGGCTCCCACG	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"""maestro heat-like repeat containing"""	27814	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 73"""	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.768A>T	8.37:g.144652780T>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_001100878	A8MWB1	Silent	SNP	ENST00000398882.3	37	CCDS47928.1																																																																																			T|0.989;A|0.011	0.011	strong		0.662	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878	
PARVG	64098	hgsc.bcm.edu	37	22	44586522	44586522	+	Silent	SNP	C	C	T	rs2272942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44586522C>T	ENST00000444313.3	+	7	964	c.480C>T	c.(478-480)gtC>gtT	p.V160V	PARVG_ENST00000422871.1_Silent_p.V160V|PARVG_ENST00000415224.1_Silent_p.V160V	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	160					actin cytoskeleton reorganization (GO:0031532)|cell-matrix adhesion (GO:0007160)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)	17		Ovarian(80;0.024)|all_neural(38;0.0299)				CAACCAACGTCCAGGTGGAGG	0.602													C|||	875	0.17472	0.0696	0.1758	5008	,	,		19312	0.12		0.3618	False		,,,				2504	0.18				p.V160V		Atlas-SNP	.											.	PARVG	41	.	0			c.C480T						PASS	.	C	,,	439,3967	212.8+/-232.6	24,391,1788	86.0	68.0	74.0		480,480,480	-0.3	0.4	22	dbSNP_100	74	2938,5662	457.4+/-364.3	501,1936,1863	no	coding-synonymous,coding-synonymous,coding-synonymous	PARVG	NM_001137605.1,NM_001137606.1,NM_022141.5	,,	525,2327,3651	TT,TC,CC		34.1628,9.9637,25.9649	,,	160/332,160/332,160/332	44586522	3377,9629	2203	4300	6503	SO:0001819	synonymous_variant	64098	exon7			CAACGTCCAGGTG	AF237772	CCDS14057.1	22q13.31	2013-01-24			ENSG00000138964	ENSG00000138964		"""Parvins"""	14654	protein-coding gene	gene with protein product		608122				11171322	Standard	NM_022141		Approved		uc003bep.4	Q9HBI0	OTTHUMG00000150473	ENST00000444313.3:c.480C>T	22.37:g.44586522C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	81	51	0.62963	NM_001137606	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Silent	SNP	ENST00000444313.3	37	CCDS14057.1																																																																																			C|0.747;T|0.253	0.253	strong		0.602	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141	
SLC4A11	83959	hgsc.bcm.edu	37	20	3214581	3214581	+	Silent	SNP	C	C	T	rs3803956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3214581C>T	ENST00000380056.3	-	5	686	c.639G>A	c.(637-639)tcG>tcA	p.S213S	SLC4A11_ENST00000539553.2_Silent_p.S197S|SLC4A11_ENST00000380059.3_Silent_p.S240S	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	213			S -> L (in CHED2). {ECO:0000269|PubMed:17679935}.|S -> P (in CDPD). {ECO:0000269|PubMed:17220209}.		bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						TGCAGAGCCACGACTGCTGGT	0.627													C|||	833	0.166334	0.2186	0.1254	5008	,	,		17524	0.128		0.1779	False		,,,				2504	0.1524				p.S240S	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.G720A						PASS	.	C	,,	933,3473	355.6+/-313.1	107,719,1377	123.0	114.0	117.0		591,720,639	-10.4	0.0	20	dbSNP_107	117	1489,7111	283.3+/-296.1	121,1247,2932	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	,,	228,1966,4309	TT,TC,CC		17.314,21.1757,18.6222	,,	197/876,240/919,213/892	3214581	2422,10584	2203	4300	6503	SO:0001819	synonymous_variant	83959	exon6			GAGCCACGACTGC	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.639G>A	20.37:g.3214581C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Silent	SNP	ENST00000380056.3	37	CCDS13052.1																																																																																			C|0.820;T|0.180	0.180	strong		0.627	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
KIF6	221458	hgsc.bcm.edu	37	6	39688551	39688551	+	Missense_Mutation	SNP	T	T	C	rs114269617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:39688551T>C	ENST00000287152.7	-	2	197	c.103A>G	c.(103-105)Agc>Ggc	p.S35G	KIF6_ENST00000373215.3_Missense_Mutation_p.S35G|KIF6_ENST00000373216.3_Missense_Mutation_p.S35G|KIF6_ENST00000538893.1_Missense_Mutation_p.S35G	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	35	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						ATTTCCAAGCTAGGTATTAAT	0.318													T|||	48	0.00958466	0.0325	0.0014	5008	,	,		18134	0.0		0.004	False		,,,				2504	0.0				p.S35G		Atlas-SNP	.											.	KIF6	233	.	0			c.A103G						PASS	.	T	GLY/SER	184,4222	117.5+/-155.4	2,180,2021	97.0	101.0	100.0		103	0.2	0.4	6	dbSNP_132	100	3,8597	1.2+/-3.3	0,3,4297	yes	missense	KIF6	NM_145027.4	56	2,183,6318	CC,CT,TT		0.0349,4.1761,1.4378	possibly-damaging	35/815	39688551	187,12819	2203	4300	6503	SO:0001583	missense	221458	exon2			CCAAGCTAGGTAT	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"""Kinesins"""	21202	protein-coding gene	gene with protein product		613919	"""chromosome 6 open reading frame 102"""	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.103A>G	6.37:g.39688551T>C	ENSP00000287152:p.Ser35Gly	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	27	0.012362637362637362	23	0.046747967479674794	0	0.0	0	0.0	4	0.005277044854881266	T	11.68	1.711929	0.30322	0.041761	3.49E-4	ENSG00000164627	ENST00000287152;ENST00000373216;ENST00000373215;ENST00000538893	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	6.06	0.196	0.15159	Kinesin, motor domain (3);	.	.	.	.	T	0.43590	0.1254	L	0.47190	1.495	0.09310	N	1	B;B;B	0.25390	0.021;0.005;0.125	B;B;B	0.34452	0.018;0.008;0.183	T	0.46992	-0.9151	9	0.42905	T	0.14	.	4.8731	0.13642	0.3772:0.0982:0.0:0.5246	.	35;35;35	E7EUN7;F6VGH2;Q6ZMV9	.;.;KIF6_HUMAN	G	35	ENSP00000287152:S35G;ENSP00000362312:S35G;ENSP00000362311:S35G;ENSP00000441435:S35G	ENSP00000287152:S35G	S	-	1	0	KIF6	39796529	0.318000	0.24598	0.387000	0.26183	0.989000	0.77384	0.951000	0.29135	0.492000	0.27815	0.533000	0.62120	AGC	T|0.984;C|0.016	0.016	strong		0.318	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	
CLDN15	24146	hgsc.bcm.edu	37	7	100875772	100875772	+	Silent	SNP	T	T	G	rs1047319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100875772T>G	ENST00000401528.1	-	6	1731	c.606A>C	c.(604-606)ccA>ccC	p.P202P	CLDN15_ENST00000308344.5_Silent_p.P202P|CLDN15_ENST00000433422.1_5'Flank	NM_001185080.1	NP_001172009.1	P56746	CLD15_HUMAN	claudin 15	202					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|ion transport (GO:0006811)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.P202P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	10	Lung NSC(181;0.168)|all_lung(186;0.215)					TCACGGACACTGGAGCCTGGT	0.716													T|||	1127	0.22504	0.1846	0.2061	5008	,	,		11952	0.1677		0.2435	False		,,,				2504	0.3333				p.P202P		Atlas-SNP	.											CLDN15,NS,lymphoid_neoplasm,0,1	CLDN15	20	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.A606C						PASS	.	T	,	837,3567		88,661,1453	38.0	35.0	36.0		606,606	-1.3	0.0	7	dbSNP_86	36	1950,6648		247,1456,2596	no	coding-synonymous,coding-synonymous	CLDN15	NM_001185080.1,NM_014343.2	,	335,2117,4049	GG,GT,TT		22.6797,19.0054,21.4352	,	202/229,202/229	100875772	2787,10215	2202	4299	6501	SO:0001819	synonymous_variant	24146	exon5			GGACACTGGAGCC	AJ245738	CCDS5717.1	7q22	2008-07-18			ENSG00000106404	ENSG00000106404		"""Claudins"""	2036	protein-coding gene	gene with protein product		615778					Standard	NM_014343		Approved		uc003uyg.2	P56746	OTTHUMG00000150512	ENST00000401528.1:c.606A>C	7.37:g.100875772T>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_014343	B3KPB5	Silent	SNP	ENST00000401528.1	37	CCDS5717.1																																																																																			T|0.787;G|0.213	0.213	strong		0.716	CLDN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318698.1	NM_014343	
OR1E2	8388	hgsc.bcm.edu	37	17	3336723	3336723	+	Missense_Mutation	SNP	A	A	G	rs73296096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3336723A>G	ENST00000248384.1	-	1	412	c.413T>C	c.(412-414)cTc>cCc	p.L138P		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	138					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						GTAGTGCAGGAGGAAGCAGAT	0.552													G|||	153	0.0305511	0.1112	0.0072	5008	,	,		19727	0.0		0.001	False		,,,				2504	0.0				p.L138P		Atlas-SNP	.											.	OR1E2	25	.	0			c.T413C						PASS	.	-	PRO/LEU	356,4050	793.7+/-415.2	24,308,1871	90.0	75.0	80.0		413		1.0	17	dbSNP_130	80	2,8598	819.2+/-406.8	0,2,4298	yes	missense	OR1E2	NM_003554.1	98	24,310,6169	GG,GA,AA		0.0233,8.0799,2.7526		138/324	3336723	358,12648	2203	4300	6503	SO:0001583	missense	8388	exon1			TGCAGGAGGAAGC	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"""GPCR / Class A : Olfactory receptors"""	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.413T>C	17.37:g.3336723A>G	ENSP00000248384:p.Leu138Pro	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	223	98	0.439462	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	37	CCDS11026.1	49	0.022435897435897436	49	0.09959349593495935	0	0.0	0	0.0	0	0.0	G	2.920	-0.223476	0.06061	0.080799	2.33E-4	ENSG00000127780	ENST00000248384	T	0.02890	4.12	.	.	.	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.25307	N	0.989232	.	.	.	.	.	.	T	0.50825	-0.8782	5	0.72032	D	0.01	.	.	.	.	.	138	P47887	OR1E2_HUMAN	P	138	ENSP00000248384:L138P	ENSP00000248384:L138P	L	-	2	0	OR1E2	3283473	.	.	0.977000	0.42913	0.222000	0.24845	.	.	0.000000	0.14550	0.000000	0.15137	CTC	A|0.975;G|0.025	0.025	strong		0.552	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1		
FGFRL1	53834	hgsc.bcm.edu	37	4	1019011	1019011	+	Missense_Mutation	SNP	C	C	T	rs4647932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1019011C>T	ENST00000398484.2	+	8	1971	c.1391C>T	c.(1390-1392)cCa>cTa	p.P464L	FGFRL1_ENST00000510644.1_Missense_Mutation_p.P464L|RP11-460I19.2_ENST00000503095.1_lincRNA|FGFRL1_ENST00000264748.6_Missense_Mutation_p.P464L|FGFRL1_ENST00000504138.1_Missense_Mutation_p.P464L			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	464			P -> L (in dbSNP:rs4647932).		diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCCCAGGCCCAGTTGCTGGC	0.622													C|||	146	0.0291534	0.0068	0.0504	5008	,	,		14211	0.0218		0.0567	False		,,,				2504	0.0235				p.P464L		Atlas-SNP	.											FGFRL1,NS,carcinoma,0,1	FGFRL1	77	1	0			c.C1391T	GRCh37	CM067667	FGFRL1	M	rs4647932	PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	76,4306		1,74,2116	15.0	17.0	16.0		1391,1391,1391	1.5	0.0	4	dbSNP_111	16	578,8016		25,528,3744	yes	missense,missense,missense	FGFRL1	NM_001004356.2,NM_001004358.1,NM_021923.3	98,98,98	26,602,5860	TT,TC,CC		6.7256,1.7344,5.0401	benign,benign,benign	464/505,464/505,464/505	1019011	654,12322	2191	4297	6488	SO:0001583	missense	53834	exon7			CAGGCCCAGTTGC		CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418		"""Immunoglobulin superfamily / I-set domain containing"""	3693	protein-coding gene	gene with protein product		605830					Standard	NM_021923		Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.1391C>T	4.37:g.1019011C>T	ENSP00000381498:p.Pro464Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	NM_001004356	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Missense_Mutation	SNP	ENST00000398484.2	37	CCDS3344.1	72	0.03296703296703297	6	0.012195121951219513	21	0.058011049723756904	11	0.019230769230769232	34	0.044854881266490766	C	8.467	0.856661	0.17106	0.017344	0.067256	ENSG00000127418	ENST00000398484;ENST00000510644;ENST00000504138;ENST00000264748	T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78	4.38	1.5	0.22942	.	0.581982	0.16507	N	0.211416	T	0.09291	0.0229	L	0.27053	0.805	0.46185	D	0.99891	B	0.02656	0.0	B	0.06405	0.002	T	0.24048	-1.0171	10	0.87932	D	0	-0.8596	5.6428	0.17572	0.156:0.6709:0.0:0.1731	rs4647932;rs61088669;rs4647932	464	Q8N441	FGRL1_HUMAN	L	464	ENSP00000381498:P464L;ENSP00000425025:P464L;ENSP00000423091:P464L;ENSP00000264748:P464L	ENSP00000264748:P464L	P	+	2	0	FGFRL1	1009011	0.001000	0.12720	0.001000	0.08648	0.085000	0.17905	0.468000	0.22051	0.327000	0.23409	-0.137000	0.14449	CCA	C|0.955;T|0.045	0.045	strong		0.622	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923	
TRGC1	6966	hgsc.bcm.edu	37	7	38305142	38305142	+	RNA	SNP	G	G	C	rs113809137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:38305142G>C	ENST00000443402.2	-	0	137					NM_001003799.1|NM_001003806.1	NP_001003799.1|NP_001003806.1	P0CF51	TRGC1_HUMAN	T cell receptor gamma constant 1							integral component of membrane (GO:0016021)											TTCTTTTCTTGCCAATGTATC	0.398													g|||	1036	0.206869	0.1596	0.1686	5008	,	,		17640	0.1944		0.2515	False		,,,				2504	0.2648				p.G42G		Atlas-SNP	.											.	.	.	.	0			c.C126G						PASS	.	G	,	601,3039		80,441,1299	167.0	173.0	171.0		126,	3.3	0.9	7	dbSNP_132	171	1903,6245		234,1435,2405	no	coding-synonymous,utr-5	TARP	NM_001003799.1,NM_001003806.1	,	314,1876,3704	CC,CG,GG		23.3554,16.511,21.2419	,	42/59,	38305142	2504,9284	1820	4074	5894			0	exon2			TTTCTTGCCAATG	M14996		7p14	2012-02-07			ENSG00000211689	ENSG00000211689		"""T cell receptors / TRG locus"""	12275	other	T cell receptor gene	"""T-cell receptor, gamma, constant region C1"""	186970		TCRGC1		2879283	Standard	NG_001336		Approved	C1		P0CF51	OTTHUMG00000155219		7.37:g.38305142G>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	182	83	0.456044	NM_001003799		Silent	SNP	ENST00000443402.2	37																																																																																				G|0.805;C|0.195	0.195	strong		0.398	TRGC1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	TR_C_gene	TR_C_gene	OTTHUMT00000338825.3	NG_001336	
C3orf33	285315	hgsc.bcm.edu	37	3	155493497	155493497	+	Silent	SNP	T	T	C	rs377018605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:155493497T>C	ENST00000340171.2	-	3	413	c.315A>G	c.(313-315)tcA>tcG	p.S105S	C3orf33_ENST00000534941.1_Silent_p.S62S			Q6P1S2	CC033_HUMAN	chromosome 3 open reading frame 33	105					negative regulation of ERK1 and ERK2 cascade (GO:0070373)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)			breast(1)|kidney(1)|large_intestine(3)|lung(3)	8			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TACTTCTCAATGAAGCTATAA	0.269													T|||	6	0.00119808	0.0038	0.0014	5008	,	,		15710	0.0		0.0	False		,,,				2504	0.0				p.S62S		Atlas-SNP	.											.	C3orf33	18	.	0			c.A186G						PASS	.	T		16,3586		0,16,1785	67.0	70.0	69.0		186	-4.1	0.7	3		69	1,8111		0,1,4055	no	coding-synonymous	C3orf33	NM_173657.1		0,17,5840	CC,CT,TT		0.0123,0.4442,0.1451		62/252	155493497	17,11697	1801	4056	5857	SO:0001819	synonymous_variant	285315	exon4			TCTCAATGAAGCT	AF115515	CCDS54659.1	3q25.31	2012-10-31			ENSG00000174928	ENSG00000174928			26434	protein-coding gene	gene with protein product						20680465	Standard	NM_173657		Approved	FLJ31139, AC3-33	uc003fal.1	Q6P1S2	OTTHUMG00000158496	ENST00000340171.2:c.315A>G	3.37:g.155493497T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	NM_173657	A8K1H5|Q86YE6|Q8IXA7|Q96NB5	Silent	SNP	ENST00000340171.2	37																																																																																				.	.	weak		0.269	C3orf33-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351167.1	NM_173657	
OR8G5	219865	hgsc.bcm.edu	37	11	124134743	124134743	+	Silent	SNP	G	G	A	rs2466637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124134743G>A	ENST00000524943.2	+	1	21	c.21G>A	c.(19-21)ggG>ggA	p.G7G	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	7						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		ATAAACAAGGGATCACTTTCC	0.323													g|||	2195	0.438299	0.292	0.5591	5008	,	,		17989	0.5823		0.5527	False		,,,				2504	0.2843				p.G7G	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.G21A						PASS	.	G		1236,2412		207,822,795	29.0	27.0	28.0		21	-6.8	0.0	11	dbSNP_100	28	4455,3701		1234,1987,857	no	coding-synonymous	OR8G5	NM_001005198.1		1441,2809,1652	AA,AG,GG		45.3776,33.8816,48.2125		7/347	124134743	5691,6113	1824	4078	5902	SO:0001819	synonymous_variant	219865	exon1			ACAAGGGATCACT	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.21G>A	11.37:g.124134743G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001005198	B2RND3|Q6IEU6	Silent	SNP	ENST00000524943.2	37																																																																																				G|0.522;A|0.478	0.478	strong		0.323	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
COL6A3	1293	hgsc.bcm.edu	37	2	238253332	238253332	+	Silent	SNP	G	G	A	rs10084221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238253332G>A	ENST00000295550.4	-	36	7781	c.7329C>T	c.(7327-7329)gcC>gcT	p.A2443A	COL6A3_ENST00000472056.1_Silent_p.A1836A|COL6A3_ENST00000409809.1_Silent_p.A2237A|COL6A3_ENST00000346358.4_Silent_p.A2243A|COL6A3_ENST00000347401.3_Silent_p.A2242A|COL6A3_ENST00000353578.4_Silent_p.A2237A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2443	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)		CAGCCACCCGGGCCCCCCGTG	0.557													G|||	355	0.0708866	0.2171	0.0375	5008	,	,		19167	0.005		0.0189	False		,,,				2504	0.0184				p.A2443A		Atlas-SNP	.											.	COL6A3	608	.	0			c.C7329T						PASS	.	G	,,	801,3605	296.7+/-284.4	54,693,1456	55.0	61.0	59.0		7329,5508,6711	3.4	1.0	2	dbSNP_119	59	177,8423	78.6+/-141.3	1,175,4124	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	55,868,5580	AA,AG,GG		2.0581,18.1798,7.5196	,,	2443/3178,1836/2571,2237/2972	238253332	978,12028	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon36			CACCCGGGCCCCC	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.7329C>T	2.37:g.238253332G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.935;A|0.065	0.065	strong		0.557	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
FAT3	120114	hgsc.bcm.edu	37	11	92568196	92568196	+	Silent	SNP	C	C	T	rs374591402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92568196C>T	ENST00000298047.6	+	14	10049	c.10032C>T	c.(10030-10032)gaC>gaT	p.D3344D	FAT3_ENST00000525166.1_Silent_p.D3194D|FAT3_ENST00000409404.2_Silent_p.D3344D			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3344	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)				TCAGCCAAGACGTCTACAGTG	0.527										TCGA Ovarian(4;0.039)			C|||	4	0.000798722	0.0023	0.0	5008	,	,		17326	0.0		0.0	False		,,,				2504	0.001				p.D3344D		Atlas-SNP	.											.	FAT3	1822	.	0			c.C10032T						PASS	.	C		7,3905		0,7,1949	55.0	55.0	55.0		10032	-1.9	1.0	11		55	0,8324		0,0,4162	no	coding-synonymous	FAT3	NM_001008781.2		0,7,6111	TT,TC,CC		0.0,0.1789,0.0572		3344/4558	92568196	7,12229	1956	4162	6118	SO:0001819	synonymous_variant	120114	exon14			CCAAGACGTCTAC	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.10032C>T	11.37:g.92568196C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	150	83	0.553333	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	weak		0.527	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
APEH	327	hgsc.bcm.edu	37	3	49714225	49714225	+	Silent	SNP	T	T	C	rs1131095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49714225T>C	ENST00000296456.5	+	9	1252	c.852T>C	c.(850-852)taT>taC	p.Y284Y	APEH_ENST00000438011.1_Silent_p.Y284Y	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	284					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.Y284Y(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCCTGTATTATGTGGACCTCA	0.587													T|||	1015	0.202676	0.2413	0.17	5008	,	,		22856	0.0565		0.3241	False		,,,				2504	0.1994				p.Y284Y		Atlas-SNP	.											APEH,NS,carcinoma,0,1	APEH	45	1	1	Substitution - coding silent(1)	stomach(1)	c.T852C						PASS	.	T		1101,3305	397.0+/-330.2	135,831,1237	171.0	152.0	158.0		852	-8.4	0.7	3	dbSNP_86	158	2578,6022	419.6+/-353.1	402,1774,2124	no	coding-synonymous	APEH	NM_001640.3		537,2605,3361	CC,CT,TT		29.9767,24.9887,28.2869		284/733	49714225	3679,9327	2203	4300	6503	SO:0001819	synonymous_variant	327	exon9			GTATTATGTGGAC	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.852T>C	3.37:g.49714225T>C		Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	301	166	0.551495	NM_001640	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	37	CCDS2801.1																																																																																			T|0.737;C|0.263	0.263	strong		0.587	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
URB2	9816	hgsc.bcm.edu	37	1	229783328	229783328	+	Silent	SNP	G	G	C	rs115914317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229783328G>C	ENST00000258243.2	+	7	4114	c.3978G>C	c.(3976-3978)ctG>ctC	p.L1326L		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1326						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						TAGATGTCCTGGCTGCACTGC	0.552													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17934	0.0		0.0	False		,,,				2504	0.0				p.L1326L		Atlas-SNP	.											.	URB2	152	.	0			c.G3978C						PASS	.	G		51,4355	53.6+/-89.4	0,51,2152	78.0	71.0	73.0		3978	4.7	1.0	1	dbSNP_132	73	0,8600		0,0,4300	no	coding-synonymous	URB2	NM_014777.2		0,51,6452	CC,CG,GG		0.0,1.1575,0.3921		1326/1525	229783328	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	9816	exon7			TGTCCTGGCTGCA	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.3978G>C	1.37:g.229783328G>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	147	76	0.517007	NM_014777	Q5VYC9	Silent	SNP	ENST00000258243.2	37	CCDS31052.1																																																																																			G|0.997;C|0.003	0.003	strong		0.552	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
LRRC37B	114659	hgsc.bcm.edu	37	17	30372739	30372739	+	Missense_Mutation	SNP	C	C	T	rs1638299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:30372739C>T	ENST00000341671.7	+	8	2149	c.2144C>T	c.(2143-2145)gCc>gTc	p.A715V	SH3GL1P1_ENST00000579186.1_RNA|LRRC37B_ENST00000327564.7_Missense_Mutation_p.A742V|LRRC37B_ENST00000394713.3_Missense_Mutation_p.A664V|LRRC37B_ENST00000543378.2_Missense_Mutation_p.A633V|LRRC37B_ENST00000584368.1_Missense_Mutation_p.A676V	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	715						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.A715V(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				AGCCATATGGCCTGCTGCCTC	0.433																																					p.A715V		Atlas-SNP	.											LRRC37B,NS,carcinoma,0,1	LRRC37B	67	1	1	Substitution - Missense(1)	stomach(1)	c.C2144T						scavenged	.						99.0	82.0	88.0					17																	30372739		2202	4297	6499	SO:0001583	missense	114659	exon8			ATATGGCCTGCTG	AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"""KIAA0563-related"""					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.2144C>T	17.37:g.30372739C>T	ENSP00000340519:p.Ala715Val	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	59	17	0.288136	NM_052888	Q17RC9|Q5YKG6	Missense_Mutation	SNP	ENST00000341671.7	37	CCDS32609.1	277	0.12683150183150182	150	0.3048780487804878	44	0.12154696132596685	46	0.08041958041958042	37	0.048812664907651716	N	15.46	2.840171	0.51057	.	.	ENSG00000185158	ENST00000543378;ENST00000327564;ENST00000394713;ENST00000341671	T;T;T;T	0.50813	0.73;0.73;0.87;0.73	1.9	-0.245	0.13027	.	.	.	.	.	T	0.00012	0.0000	M	0.74881	2.28	0.20403	N	0.999908	D;B	0.61697	0.99;0.106	P;B	0.56434	0.798;0.003	T	0.01283	-1.1396	9	0.54805	T	0.06	.	6.0128	0.19586	0.0:0.6886:0.0:0.3114	rs1638299;rs4091279;rs7208720	664;715	Q17RC9;Q96QE4	.;LR37B_HUMAN	V	633;742;664;715	ENSP00000443345:A633V;ENSP00000332536:A742V;ENSP00000378202:A664V;ENSP00000340519:A715V	ENSP00000332536:A742V	A	+	2	0	LRRC37B	27396852	0.015000	0.18098	0.648000	0.29521	0.279000	0.26890	0.127000	0.15790	-0.021000	0.14009	-0.431000	0.05894	GCC	C|0.910;T|0.090	0.090	strong		0.433	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	NM_052888	
TM2D3	80213	hgsc.bcm.edu	37	15	102192540	102192540	+	Silent	SNP	T	T	G	rs675436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:102192540T>G	ENST00000333202.3	-	1	30	c.25A>C	c.(25-27)Agg>Cgg	p.R9R	TM2D3_ENST00000559107.1_Silent_p.R9R|TM2D3_ENST00000428002.2_Silent_p.R9R|TM2D3_ENST00000561373.1_5'Flank|TM2D3_ENST00000347970.3_Silent_p.R9R|TARSL2_ENST00000559492.1_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	44	0	0		WXS	Illumina HiSeq	Phase_I	58	21	0.362069	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	
RANBP2	5903	hgsc.bcm.edu	37	2	109371659	109371659	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:109371659G>A	ENST00000283195.6	+	17	2536	c.2410G>A	c.(2410-2412)Gca>Aca	p.A804T		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	804					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						ACCTCGATGGGCAGAAGATCA	0.308																																					p.A804T		Atlas-SNP	.											RANBP2_ENST00000283195,NS,carcinoma,0,2	RANBP2	488	2	0			c.G2410A						scavenged	.						140.0	163.0	155.0					2																	109371659		2199	4297	6496	SO:0001583	missense	5903	exon17			CGATGGGCAGAAG	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2410G>A	2.37:g.109371659G>A	ENSP00000283195:p.Ala804Thr	Somatic	844	3	0.0035545		WXS	Illumina HiSeq	Phase_I	922	10	0.010846	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	g	28.4	4.919938	0.92249	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.19105	2.17	5.8	5.8	0.92144	.	.	.	.	.	T	0.34337	0.0894	L	0.34521	1.04	0.49130	D	0.999754	D	0.67145	0.996	P	0.58331	0.837	T	0.01532	-1.1331	9	0.54805	T	0.06	-13.8517	20.0609	0.97674	0.0:0.0:1.0:0.0	.	804	P49792	RBP2_HUMAN	T	804	ENSP00000283195:A804T	ENSP00000283195:A804T	A	+	1	0	RANBP2	108738091	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.714000	0.74692	2.737000	0.93849	0.542000	0.68232	GCA	.	.	none		0.308	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
MTERF4	130916	hgsc.bcm.edu	37	2	242035544	242035544	+	Missense_Mutation	SNP	G	G	C	rs2240539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242035544G>C	ENST00000391980.2	-	4	1073	c.1015C>G	c.(1015-1017)Ctg>Gtg	p.L339V	MTERFD2_ENST00000406593.1_Missense_Mutation_p.L151V|MTERFD2_ENST00000495694.1_Intron|MTERFD2_ENST00000464344.2_Intron	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		339			L -> V (in dbSNP:rs2240539).		rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		tcctcatcCAGACTTGCCCTT	0.498													G|||	523	0.104433	0.1762	0.0951	5008	,	,		21954	0.124		0.0626	False		,,,				2504	0.0368				p.L339V		Atlas-SNP	.											.	MTERFD2	33	.	0			c.C1015G						PASS	.	G	VAL/LEU	813,3593	325.9+/-299.3	83,647,1473	267.0	186.0	213.0		1015	-3.8	0.0	2	dbSNP_98	213	589,8011	156.9+/-210.6	21,547,3732	yes	missense	MTERFD2	NM_182501.3	32	104,1194,5205	CC,CG,GG		6.8488,18.4521,10.7796	benign	339/382	242035544	1402,11604	2203	4300	6503	SO:0001583	missense	130916	exon4			CATCCAGACTTGC																												ENST00000391980.2:c.1015C>G	2.37:g.242035544G>C	ENSP00000375840:p.Leu339Val	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	232	125	0.538793	NM_182501	A8K6K0|Q9P0E0	Missense_Mutation	SNP	ENST00000391980.2	37	CCDS2544.1	242	0.1108058608058608	90	0.18292682926829268	35	0.09668508287292818	70	0.12237762237762238	47	0.06200527704485488	G	11.69	1.714390	0.30413	0.184521	0.068488	ENSG00000122085	ENST00000391980;ENST00000406593	T;T	0.05649	3.41;3.41	3.71	-3.84	0.04256	.	2.125570	0.02588	N	0.099626	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.08055	0.003	T	0.43814	-0.9368	9	0.42905	T	0.14	-1.5584	1.5814	0.02635	0.1427:0.3269:0.1599:0.3705	rs2240539;rs52817647;rs2240539	339	Q7Z6M4	MTER2_HUMAN	V	339;151	ENSP00000375840:L339V;ENSP00000384998:L151V	ENSP00000241527:L339V	L	-	1	2	MTERFD2	241684217	0.557000	0.26546	0.000000	0.03702	0.075000	0.17131	-0.466000	0.06672	-0.827000	0.04278	0.460000	0.39030	CTG	G|0.889;C|0.111	0.111	strong		0.498	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4		
CYP4A11	1579	hgsc.bcm.edu	37	1	47398496	47398496	+	Missense_Mutation	SNP	A	A	G	rs1126742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47398496A>G	ENST00000310638.4	-	11	1332	c.1301T>C	c.(1300-1302)tTc>tCc	p.F434S	CYP4A11_ENST00000462347.1_Missense_Mutation_p.F336S|CYP4A11_ENST00000496519.1_5'Flank|CYP4A11_ENST00000371905.1_Missense_Mutation_p.F434S|CYP4A11_ENST00000371904.4_Missense_Mutation_p.F435S	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	434			F -> S (associated with hypertension; significantly reduced arachidonic acid and lauric acid metabolizing activity; dbSNP:rs1126742). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:15895287, ECO:0000269|PubMed:8274222, ECO:0000269|PubMed:8363569, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	TGCAAAACGGAAAGGGTCAAA	0.547													G|||	1209	0.241414	0.3336	0.1542	5008	,	,		20640	0.2579		0.1451	False		,,,				2504	0.2607				p.F434S		Atlas-SNP	.											.	CYP4A11	77	.	0			c.T1301C	GRCh37	CM050003	CYP4A11	M	rs1126742	PASS	.	G	SER/PHE	1273,3133		223,827,1153	289.0	307.0	301.0		1301	0.3	0.1	1	dbSNP_86	301	1115,7485		89,937,3274	no	missense	CYP4A11	NM_000778.3	155	312,1764,4427	GG,GA,AA		12.9651,28.8924,18.3608	benign	434/520	47398496	2388,10618	2203	4300	6503	SO:0001583	missense	1579	exon11			AAACGGAAAGGGT	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"""Cytochrome P450s"""	2642	protein-coding gene	gene with protein product		601310	"""cytochrome P450, subfamily IVA, polypeptide 11"""	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.1301T>C	1.37:g.47398496A>G	ENSP00000311095:p.Phe434Ser	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	245	101	0.412245	NM_000778	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	37	CCDS543.1	379	0.17353479853479853	114	0.23170731707317074	46	0.1270718232044199	116	0.20279720279720279	103	0.1358839050131926	N	2.872	-0.233838	0.05983	0.288924	0.129651	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905	T;T;T	0.66995	-0.24;-0.24;-0.24	5.11	0.315	0.15852	.	0.447956	0.24483	N	0.038125	T	0.00012	0.0000	N	0.01779	-0.725	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.06405	0.002	T	0.19224	-1.0312	9	0.11182	T	0.66	.	5.1371	0.14941	0.5073:0.0:0.2854:0.2073	rs1126742;rs3181965;rs4233507;rs17411649;rs56782585	434	Q02928	CP4AB_HUMAN	S	434;435;434	ENSP00000311095:F434S;ENSP00000360971:F435S;ENSP00000360972:F434S	ENSP00000311095:F434S	F	-	2	0	CYP4A11	47171083	0.000000	0.05858	0.053000	0.19242	0.662000	0.39071	-0.066000	0.11598	0.032000	0.15435	-0.128000	0.14901	TTC	A|0.500;G|0.500	0.500	weak		0.547	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778	
CPA5	93979	hgsc.bcm.edu	37	7	130008285	130008285	+	Silent	SNP	T	T	C	rs17164867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:130008285T>C	ENST00000485477.1	+	12	2287	c.1158T>C	c.(1156-1158)taT>taC	p.Y386Y	CPA5_ENST00000355388.3_Silent_p.Y386Y|CPA5_ENST00000461828.1_Silent_p.Y386Y|CPA5_ENST00000466363.2_Silent_p.Y386Y|CPA5_ENST00000393213.3_Silent_p.Y386Y|CPA5_ENST00000474905.1_Silent_p.Y386Y|CPA5_ENST00000431780.2_Missense_Mutation_p.M358T			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	386						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					ACTGGGCCTATGACAGTGGCA	0.557													C|||	765	0.152756	0.2602	0.0937	5008	,	,		17924	0.0268		0.1958	False		,,,				2504	0.135				p.M358T		Atlas-SNP	.											.	CPA5	61	.	0			c.T1073C						PASS	.	C	,THR/MET,	1076,3330	722.0+/-409.2	135,806,1262	145.0	129.0	134.0		1158,1073,1158	-7.8	0.6	7	dbSNP_123	134	1798,6802	733.0+/-406.9	189,1420,2691	yes	coding-synonymous,missense,coding-synonymous	CPA5	NM_001127441.1,NM_001127442.1,NM_080385.4	,81,	324,2226,3953	CC,CT,TT		20.907,24.4212,22.0975	,,	386/437,358/404,386/437	130008285	2874,10132	2203	4300	6503	SO:0001819	synonymous_variant	93979	exon11			GGCCTATGACAGT	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.1158T>C	7.37:g.130008285T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_001127442	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	37	CCDS5819.1	335	0.1533882783882784	128	0.2601626016260163	38	0.10497237569060773	13	0.022727272727272728	156	0.20580474934036938	C	7.244	0.601842	0.13939	0.244212	0.20907	ENSG00000158525	ENST00000431780;ENST00000479492	T	0.11930	2.73	5.81	-7.82	0.01205	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.33163	-0.9879	6	.	.	.	.	19.8416	0.96692	0.0:0.7195:0.0:0.2805	rs17164867;rs17854249;rs61027423	358	G3V0G8	.	T	358;35	ENSP00000393045:M358T	.	M	+	2	0	CPA5	129795521	0.000000	0.05858	0.630000	0.29268	0.009000	0.06853	-2.080000	0.01368	-1.647000	0.01511	-2.133000	0.00342	ATG	C|0.201;T|0.799	0.201	strong		0.557	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441	
SMR3A	26952	hgsc.bcm.edu	37	4	71232701	71232701	+	Missense_Mutation	SNP	C	C	T	rs6853742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71232701C>T	ENST00000226460.4	+	3	491	c.395C>T	c.(394-396)cCt>cTt	p.P132L		NM_012390.3	NP_036522.3	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3A	132	Pro-rich.		P -> L (in dbSNP:rs6853742). {ECO:0000269|PubMed:9354371}.			extracellular region (GO:0005576)		p.P132L(1)		endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)	15		all_hematologic(202;0.196)				CTCCCTACTCCTGCACCCTAA	0.488													C|||	3300	0.658946	0.7678	0.7017	5008	,	,		17875	0.5903		0.6909	False		,,,				2504	0.5194				p.P132L		Atlas-SNP	.											SMR3A,NS,carcinoma,0,1	SMR3A	35	1	1	Substitution - Missense(1)	prostate(1)	c.C395T						PASS	.	C	LEU/PRO	3394,1012	728.9+/-410.0	1297,800,106	78.0	76.0	76.0		395	1.6	0.0	4	dbSNP_116	76	5766,2834	675.5+/-403.2	1921,1924,455	yes	missense	SMR3A	NM_012390.3	98	3218,2724,561	TT,TC,CC		32.9535,22.9687,29.571	benign	132/135	71232701	9160,3846	2203	4300	6503	SO:0001583	missense	26952	exon3			CTACTCCTGCACC	D89501	CCDS34000.1	4q13.3	2009-04-17	2008-02-27	2005-02-07	ENSG00000109208	ENSG00000109208			19216	protein-coding gene	gene with protein product			"""proline rich 5 (salivary)"", ""submaxillary gland androgen regulated protein 3 homolog A (mouse)"""	PROL5		9354371, 17512016	Standard	NM_012390		Approved	PBI, PRL5	uc003hfg.1	Q99954	OTTHUMG00000160839	ENST00000226460.4:c.395C>T	4.37:g.71232701C>T	ENSP00000226460:p.Pro132Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	119	67	0.563025	NM_012390		Missense_Mutation	SNP	ENST00000226460.4	37	CCDS34000.1	1504	0.6886446886446886	384	0.7804878048780488	250	0.6906077348066298	349	0.6101398601398601	521	0.6873350923482849	C	4.553	0.102743	0.08731	0.770313	0.670465	ENSG00000109208	ENST00000226460	T	0.28069	1.63	3.34	1.6	0.23607	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.19073	0.033	B	0.15052	0.012	T	0.40021	-0.9585	8	0.02654	T	1	.	5.7651	0.18221	0.0:0.7476:0.0:0.2524	rs6853742;rs17717779;rs52813334;rs60016415;rs6853742	132	Q99954	SMR3A_HUMAN	L	132	ENSP00000226460:P132L	ENSP00000226460:P132L	P	+	2	0	SMR3A	71267290	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.013000	0.13310	0.420000	0.25954	-0.254000	0.11334	CCT	C|0.296;N|0.000	.	strong		0.488	SMR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362574.1	NM_012390	
OAS1	4938	hgsc.bcm.edu	37	12	113357237	113357237	+	Missense_Mutation	SNP	G	G	C	rs1051042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113357237G>C	ENST00000202917.5	+	6	1345	c.1082G>C	c.(1081-1083)aGg>aCg	p.R361T	RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Intron|OAS1_ENST00000551241.1_Intron	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	361			R -> T (in dbSNP:rs1051042). {ECO:0000269|PubMed:17024523, ECO:0000269|PubMed:2416561, ECO:0000269|Ref.7}.		cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						GATCCCAGGAGGTATCAGAAA	0.507													G|||	3942	0.787141	0.9728	0.7954	5008	,	,		24573	0.745		0.6521	False		,,,				2504	0.7127				p.R361T		Atlas-SNP	.											.	OAS1	128	.	0			c.G1082C						PASS	.	G	,THR/ARG	4067,339	795.3+/-415.3	1875,317,11	105.0	101.0	102.0		,1082	-4.5	0.0	12	dbSNP_86	102	5554,3046	662.1+/-401.9	1809,1936,555	yes	intron,missense	OAS1	NM_001032409.1,NM_016816.2	,71	3684,2253,566	CC,CG,GG		35.4186,7.6941,26.0264	,benign	,361/401	113357237	9621,3385	2203	4300	6503	SO:0001583	missense	4938	exon6			CCAGGAGGTATCA	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"""2',5'-oligoadenylate synthetase 1 (40-46 kD)"""	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.1082G>C	12.37:g.113357237G>C	ENSP00000202917:p.Arg361Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_016816	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	37	CCDS41838.1	1709	0.7825091575091575	483	0.9817073170731707	280	0.7734806629834254	447	0.7814685314685315	499	0.658311345646438	G	1.907	-0.451701	0.04572	0.923059	0.645814	ENSG00000089127	ENST00000202917	T	0.05382	3.45	2.35	-4.47	0.03525	.	.	.	.	.	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	0.12889	-1.0530	8	0.17832	T	0.49	20.7501	1.1302	0.01743	0.1578:0.2658:0.3485:0.2279	rs1051042;rs3168659;rs17237688;rs52806792;rs59618405;rs1051042	361	P00973	OAS1_HUMAN	T	361	ENSP00000202917:R361T	ENSP00000202917:R361T	R	+	2	0	OAS1	111841620	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.899000	0.01600	-1.192000	0.02691	-1.267000	0.01435	AGG	G|0.261;C|0.739	0.739	strong		0.507	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2		
ZNF676	163223	hgsc.bcm.edu	37	19	22363448	22363448	+	Silent	SNP	A	A	T	rs200452805		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22363448A>T	ENST00000397121.2	-	3	1388	c.1071T>A	c.(1069-1071)atT>atA	p.I357I		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	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)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				CAGTATGAATAATCTTATGTT	0.383																																					p.I357I		Atlas-SNP	.											ZNF676,rectum,carcinoma,0,2	ZNF676	146	2	0			c.T1071A						scavenged	.						68.0	74.0	72.0					19																	22363448		2162	4271	6433	SO:0001819	synonymous_variant	163223	exon3			ATGAATAATCTTA	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.1071T>A	19.37:g.22363448A>T		Somatic	34	2	0.0588235		WXS	Illumina HiSeq	Phase_I	58	10	0.172414	NM_001001411	A8MVX5	Silent	SNP	ENST00000397121.2	37	CCDS42539.1																																																																																			.	.	weak		0.383	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
ARHGAP40	343578	hgsc.bcm.edu	37	20	37257590	37257590	+	Silent	SNP	C	C	G	rs6070809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	209	0	0		WXS	Illumina HiSeq	Phase_I	221	99	0.447964	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418275	105418275	+	Silent	SNP	T	T	C	rs2819441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105418275T>C	ENST00000333244.5	-	7	3632	c.3513A>G	c.(3511-3513)ccA>ccG	p.P1171P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1171						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCCCGAACGATGGCATCTTGA	0.617													.|||	117	0.0233626	0.0408	0.0058	5008	,	,		18029	0.0516		0.004	False		,,,				2504	0.0031				p.P1171P		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A3513G						PASS	.	T		1112,2754		226,660,1047	188.0	191.0	190.0		3513	-8.8	0.0	14	dbSNP_100	190	1855,6381		286,1283,2549	no	coding-synonymous	AHNAK2	NM_138420.2		512,1943,3596	CC,CT,TT		22.5231,28.7636,24.5166		1171/5796	105418275	2967,9135	1933	4118	6051	SO:0001819	synonymous_variant	113146	exon7			GAACGATGGCATC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3513A>G	14.37:g.105418275T>C		Somatic	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	309	166	0.537217	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.267;T|0.733	0.267	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ERCC5	2073	hgsc.bcm.edu	37	13	103506690	103506690	+	Missense_Mutation	SNP	G	G	A	rs4987063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103506690G>A	ENST00000355739.4	+	4	1856	c.433G>A	c.(433-435)Gtt>Att	p.V145I	ERCC5_ENST00000535557.1_Missense_Mutation_p.V145I|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.C570Y	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	145			V -> I (in dbSNP:rs4987063).		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)					CGACCTCTATGTTTTGCCTCC	0.363			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	35	0.00698882	0.0257	0.0014	5008	,	,		19977	0.0		0.0	False		,,,				2504	0.0				p.V599I		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.G1795A						PASS	.	G	ILE/VAL,ILE/VAL	91,4315	74.7+/-112.8	2,87,2114	123.0	116.0	118.0		1795,433	2.4	0.2	13	dbSNP_111	118	0,8600		0,0,4300	yes	missense,missense	ERCC5,BIVM-ERCC5	NM_001204425.1,NM_000123.3	29,29	2,87,6414	AA,AG,GG		0.0,2.0654,0.6997	benign,benign	599/1641,145/1187	103506690	91,12915	2203	4300	6503	SO:0001583	missense	0	exon12	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CTCTATGTTTTGC	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.433G>A	13.37:g.103506690G>A	ENSP00000347978:p.Val145Ile	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	96	35	0.364583	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	G	4.272	0.049520	0.08243	0.020654	0.0	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000535557	T;T	0.23147	3.49;1.92	6.03	2.39	0.29439	.	0.420080	0.25570	N	0.029763	T	0.07413	0.0187	L	0.28556	0.865	0.26071	N	0.981225	B;B;B	0.22080	0.038;0.064;0.051	B;B;B	0.23275	0.045;0.014;0.01	T	0.18209	-1.0344	10	0.25751	T	0.34	-2.6138	5.2232	0.15379	0.2217:0.0:0.6337:0.1446	rs4987063	145;145;570	B4DSI5;P28715;Q59FZ7	.;ERCC5_HUMAN;.	I	570;145;145	ENSP00000347978:V145I;ENSP00000442117:V145I	ENSP00000347978:V145I	V	+	1	0	ERCC5	102304691	0.999000	0.42202	0.227000	0.23927	0.161000	0.22273	3.038000	0.49783	0.424000	0.26061	-0.136000	0.14681	GTT	G|0.993;A|0.007	0.007	strong		0.363	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
UVSSA	57654	hgsc.bcm.edu	37	4	1374769	1374769	+	Silent	SNP	G	G	A	rs115722661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1374769G>A	ENST00000389851.4	+	12	2301	c.1854G>A	c.(1852-1854)gaG>gaA	p.E618E	UVSSA_ENST00000511216.1_Silent_p.E618E|UVSSA_ENST00000512728.1_Silent_p.E169E|UVSSA_ENST00000511563.1_Silent_p.E169E|UVSSA_ENST00000507531.1_Silent_p.E618E	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	618					protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										AGAAGCAGGAGCGCCCGGGTA	0.667													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		15251	0.0		0.0	False		,,,				2504	0.0				p.E618E		Atlas-SNP	.											.	.	.	.	0			c.G1854A						PASS	.	G		67,4331	61.1+/-98.1	0,67,2132	30.0	34.0	33.0		1854	-3.4	0.0	4	dbSNP_133	33	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	KIAA1530	NM_020894.2		0,68,6430	AA,AG,GG		0.0116,1.5234,0.5232		618/710	1374769	68,12928	2199	4299	6498	SO:0001819	synonymous_variant	57654	exon12			GCAGGAGCGCCCG	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"""KIAA1530"""	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.1854G>A	4.37:g.1374769G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	202	97	0.480198	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	37	CCDS33938.1																																																																																			G|0.995;A|0.005	0.005	strong		0.667	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894	
OR10X1	128367	hgsc.bcm.edu	37	1	158549264	158549264	+	Silent	SNP	G	G	A	rs863360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	267	0	0		WXS	Illumina HiSeq	Phase_I	252	127	0.503968	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	
FBN3	84467	hgsc.bcm.edu	37	19	8137052	8137052	+	Silent	SNP	G	G	A	rs10420783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8137052G>A	ENST00000600128.1	-	63	8382	c.7968C>T	c.(7966-7968)ccC>ccT	p.P2656P	FBN3_ENST00000601739.1_Silent_p.P2656P|FBN3_ENST00000270509.2_Silent_p.P2656P			Q75N90	FBN3_HUMAN	fibrillin 3	2656						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						CCTGGGGTCCGGGGCTGAAGC	0.672													G|||	256	0.0511182	0.1846	0.0173	5008	,	,		19707	0.0		0.0	False		,,,				2504	0.0				p.P2656P		Atlas-SNP	.											.	FBN3	300	.	0			c.C7968T						PASS	.	G		653,3753	279.0+/-274.6	45,563,1595	99.0	107.0	104.0		7968	-7.2	0.0	19	dbSNP_119	104	12,8588	7.7+/-29.5	0,12,4288	no	coding-synonymous	FBN3	NM_032447.3		45,575,5883	AA,AG,GG		0.1395,14.8207,5.113		2656/2810	8137052	665,12341	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon62			GGGTCCGGGGCTG		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.7968C>T	19.37:g.8137052G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.949;A|0.051	0.051	strong		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
DNHD1	144132	hgsc.bcm.edu	37	11	6588553	6588553	+	Silent	SNP	C	C	T	rs56313830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6588553C>T	ENST00000527990.2	+	34	11814	c.11814C>T	c.(11812-11814)ggC>ggT	p.G3938G	DNHD1_ENST00000254579.6_Silent_p.G3938G			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3938					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)		GTGCATTGGGCGCTTTGGCTC	0.597													C|||	967	0.193091	0.531	0.1239	5008	,	,		21235	0.0149		0.0417	False		,,,				2504	0.1247				p.G3938G		Atlas-SNP	.											.	DNHD1	198	.	0			c.C11814T						PASS	.	C		1869,2321		424,1021,650	54.0	62.0	59.0		11814	0.7	1.0	11	dbSNP_129	59	384,8054		6,372,3841	no	coding-synonymous	DNHD1	NM_144666.2		430,1393,4491	TT,TC,CC		4.5508,44.6062,17.8413		3938/4754	6588553	2253,10375	2095	4219	6314	SO:0001819	synonymous_variant	144132	exon36			ATTGGGCGCTTTG	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.11814C>T	11.37:g.6588553C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	85	49	0.576471	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			C|0.870;T|0.130	0.130	strong		0.597	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
HCLS1	3059	hgsc.bcm.edu	37	3	121361787	121361787	+	Silent	SNP	G	G	A	rs2070178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121361787G>A	ENST00000314583.3	-	6	532	c.441C>T	c.(439-441)caC>caT	p.H147H	HCLS1_ENST00000428394.2_Silent_p.H147H|HCLS1_ENST00000473883.1_5'UTR	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	147					actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		TCTGAGATGTGTGCTTCTCCA	0.473													G|||	1157	0.23103	0.1838	0.1744	5008	,	,		19684	0.2768		0.2197	False		,,,				2504	0.2996				p.H147H		Atlas-SNP	.											.	HCLS1	78	.	0			c.C441T						PASS	.	G		924,3482	354.9+/-312.8	94,736,1373	198.0	197.0	198.0		441	1.7	0.2	3	dbSNP_96	198	1959,6641	345.6+/-325.8	234,1491,2575	no	coding-synonymous	HCLS1	NM_005335.4		328,2227,3948	AA,AG,GG		22.7791,20.9714,22.1667		147/487	121361787	2883,10123	2203	4300	6503	SO:0001819	synonymous_variant	3059	exon6			AGATGTGTGCTTC		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"""cortactin-like"""	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.441C>T	3.37:g.121361787G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Silent	SNP	ENST00000314583.3	37	CCDS3003.1																																																																																			G|0.772;A|0.228	0.228	strong		0.473	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335	
KRT6C	286887	hgsc.bcm.edu	37	12	52866060	52866060	+	Missense_Mutation	SNP	C	C	T	rs11608915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52866060C>T	ENST00000252250.6	-	2	592	c.545G>A	c.(544-546)cGg>cAg	p.R182Q		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	182	Coil 1A.|Rod.		R -> Q (in dbSNP:rs11608915). {ECO:0000269|PubMed:15489334}.		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)		CTCTAGGAACCGCACCTGGAA	0.547													C|||	2006	0.400559	0.1997	0.3271	5008	,	,		17211	0.506		0.4682	False		,,,				2504	0.546				p.R182Q		Atlas-SNP	.											.	KRT6C	55	.	0			c.G545A						PASS	.	C	GLN/ARG	1118,3284		196,726,1279	63.0	41.0	49.0		545	2.1	0.9	12	dbSNP_120	49	4107,4245		1573,961,1642	yes	missense	KRT6C	NM_173086.4	43	1769,1687,2921	TT,TC,CC		49.1739,25.3975,40.9675	probably-damaging	182/565	52866060	5225,7529	2201	4176	6377	SO:0001583	missense	286887	exon2			AGGAACCGCACCT	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.545G>A	12.37:g.52866060C>T	ENSP00000252250:p.Arg182Gln	Somatic	331	1	0.00302115		WXS	Illumina HiSeq	Phase_I	334	147	0.44012	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	37	CCDS8829.1	826	0.3782051282051282	111	0.22560975609756098	119	0.3287292817679558	242	0.4230769230769231	354	0.46701846965699206	C	17.53	3.412329	0.62511	0.253975	0.491739	ENSG00000170465	ENST00000252250;ENST00000411979	D	0.92099	-2.97	3.03	2.12	0.27331	Filament (1);	0.000000	0.56097	D	0.000035	T	0.00012	0.0000	M	0.88105	2.93	0.23227	P	0.99808916	D	0.71674	0.998	P	0.62184	0.899	T	0.00001	-1.2726	9	0.62326	D	0.03	.	11.1947	0.48707	0.0:0.9042:0.0:0.0958	rs11608915;rs11608915	182	P48668	K2C6C_HUMAN	Q	182;167	ENSP00000252250:R182Q	ENSP00000252250:R182Q	R	-	2	0	KRT6C	51152327	1.000000	0.71417	0.924000	0.36721	0.495000	0.33615	5.704000	0.68347	0.814000	0.34374	0.407000	0.27541	CGG	C|0.677;T|0.323	0.323	strong		0.547	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
NMU	10874	hgsc.bcm.edu	37	4	56475330	56475330	+	Missense_Mutation	SNP	T	T	C	rs35892915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:56475330T>C	ENST00000264218.3	-	4	341	c.236A>G	c.(235-237)gAg>gGg	p.E79G	NMU_ENST00000505262.1_Missense_Mutation_p.E79G|NMU_ENST00000507338.1_Missense_Mutation_p.E79G|NMU_ENST00000511469.1_Missense_Mutation_p.E63G|NMU_ENST00000515325.1_5'UTR	NM_006681.2	NP_006672.1	P48645	NMU_HUMAN	neuromedin U	79			E -> G (in dbSNP:rs35892915).		digestion (GO:0007586)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of hormone secretion (GO:0046887)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic transmission (GO:0050806)|regulation of smooth muscle contraction (GO:0006940)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|terminal bouton (GO:0043195)	receptor binding (GO:0005102)			lung(3)|ovary(1)|urinary_tract(1)	5	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)		GCAAAGCTCCTCCAGTGCGTT	0.363													T|||	114	0.0227636	0.0847	0.0029	5008	,	,		19593	0.0		0.0	False		,,,				2504	0.0				p.E79G		Atlas-SNP	.											.	NMU	17	.	0			c.A236G						PASS	.	T	GLY/GLU	312,4094	168.0+/-198.9	9,294,1900	111.0	111.0	111.0		236	1.7	0.9	4	dbSNP_126	111	5,8595	3.0+/-9.4	0,5,4295	yes	missense	NMU	NM_006681.2	98	9,299,6195	CC,CT,TT		0.0581,7.0813,2.4373	possibly-damaging	79/175	56475330	317,12689	2203	4300	6503	SO:0001583	missense	10874	exon4			AGCTCCTCCAGTG	X76029	CCDS3501.1, CCDS75125.1	4q12	2013-02-26			ENSG00000109255	ENSG00000109255		"""Endogenous ligands"""	7859	protein-coding gene	gene with protein product	"""prepro-NMU"""	605103				7619205	Standard	XM_005265713		Approved		uc003hbc.3	P48645	OTTHUMG00000102161	ENST00000264218.3:c.236A>G	4.37:g.56475330T>C	ENSP00000264218:p.Glu79Gly	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_006681		Missense_Mutation	SNP	ENST00000264218.3	37	CCDS3501.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	T	13.36	2.215110	0.39102	0.070813	5.81E-4	ENSG00000109255	ENST00000511469;ENST00000264218;ENST00000505262;ENST00000541393;ENST00000507338	T;T;T;T	0.51574	0.7;0.7;1.31;0.7	5.51	1.72	0.24424	.	0.342720	0.28778	N	0.014164	T	0.04363	0.0120	M	0.65498	2.005	0.34244	D	0.67794	P	0.38922	0.651	B	0.35859	0.212	T	0.26538	-1.0100	10	0.66056	D	0.02	-11.2	8.6898	0.34260	0.0:0.2134:0.0:0.7866	rs35892915	79	P48645	NMU_HUMAN	G	63;79;79;79;79	ENSP00000422399:E63G;ENSP00000264218:E79G;ENSP00000424246:E79G;ENSP00000422870:E79G	ENSP00000264218:E79G	E	-	2	0	NMU	56170087	1.000000	0.71417	0.873000	0.34254	0.350000	0.29205	2.040000	0.41203	0.073000	0.16731	0.533000	0.62120	GAG	T|0.978;C|0.022	0.022	strong		0.363	NMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220006.2		
FAM188B	84182	hgsc.bcm.edu	37	7	30831088	30831088	+	Missense_Mutation	SNP	G	G	A	rs35897481	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30831088G>A	ENST00000265299.6	+	5	1048	c.971G>A	c.(970-972)aGg>aAg	p.R324K	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	324			R -> K (in dbSNP:rs35897481).							endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GACACGGACAGGATGCCCTTG	0.642													G|||	815	0.16274	0.2224	0.0793	5008	,	,		19040	0.1409		0.0905	False		,,,				2504	0.2382				p.R324K		Atlas-SNP	.											.	FAM188B	62	.	0			c.G971A						PASS	.	G	LYS/ARG	719,3405		57,605,1400	50.0	63.0	58.0		971	0.8	0.0	7	dbSNP_126	58	691,7713		34,623,3545	yes	missense	FAM188B	NM_032222.2	26	91,1228,4945	AA,AG,GG		8.2223,17.4345,11.2548	benign	324/758	30831088	1410,11118	2062	4202	6264	SO:0001583	missense	84182	exon5			CGGACAGGATGCC	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.971G>A	7.37:g.30831088G>A	ENSP00000265299:p.Arg324Lys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_032222	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	37	CCDS43565.1	290	0.13278388278388278	104	0.21138211382113822	34	0.09392265193370165	80	0.13986013986013987	72	0.09498680738786279	G	1.495	-0.553703	0.03996	0.174345	0.082223	ENSG00000106125	ENST00000265299	T	0.03242	4.0	4.26	0.813	0.18749	.	0.928186	0.09238	N	0.829588	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41752	-0.9491	9	0.87932	D	0	-0.0755	4.5086	0.11899	0.2007:0.1914:0.6079:0.0	rs35897481	324	Q4G0A6	F188B_HUMAN	K	324	ENSP00000265299:R324K	ENSP00000265299:R324K	R	+	2	0	FAM188B	30797613	0.001000	0.12720	0.000000	0.03702	0.028000	0.11728	0.335000	0.19806	0.029000	0.15352	0.563000	0.77884	AGG	G|0.881;A|0.119	0.119	strong		0.642	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
TPST2	8459	hgsc.bcm.edu	37	22	26936766	26936766	+	Silent	SNP	G	G	A	rs58274935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26936766G>A	ENST00000338754.4	-	3	1101	c.831C>T	c.(829-831)gtC>gtT	p.V277V	TPST2_ENST00000403880.1_Silent_p.V277V|TPST2_ENST00000398110.2_Silent_p.V277V	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	277					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						TGGACAGGGAGACACCACCGG	0.597													G|||	341	0.0680911	0.0469	0.0476	5008	,	,		18035	0.0833		0.0736	False		,,,				2504	0.09				p.V277V		Atlas-SNP	.											.	TPST2	23	.	0			c.C831T						PASS	.	G	,	191,4215	118.8+/-156.5	7,177,2019	40.0	41.0	40.0		831,831	3.0	1.0	22	dbSNP_129	40	442,8158	132.3+/-190.0	15,412,3873	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	22,589,5892	AA,AG,GG		5.1395,4.335,4.867	,	277/378,277/378	26936766	633,12373	2203	4300	6503	SO:0001819	synonymous_variant	8459	exon3			CAGGGAGACACCA	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.831C>T	22.37:g.26936766G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_001008566	B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																			G|0.952;A|0.048	0.048	strong		0.597	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595	
TSPAN9	10867	hgsc.bcm.edu	37	12	3387697	3387697	+	Silent	SNP	T	T	C	rs16930370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:3387697T>C	ENST00000011898.5	+	4	335	c.174T>C	c.(172-174)atT>atC	p.I58I	TSPAN9_ENST00000492305.1_3'UTR|TSPAN9_ENST00000537971.1_Silent_p.I58I|TSPAN9_ENST00000407263.1_Silent_p.I58I	NM_006675.4	NP_006666.1	O75954	TSN9_HUMAN	tetraspanin 9	58						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)				endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			ACCTGGTCATTGCCATAGGCA	0.587													C|||	865	0.172724	0.2761	0.1571	5008	,	,		21227	0.1022		0.1839	False		,,,				2504	0.1053				p.I58I		Atlas-SNP	.											.	TSPAN9	20	.	0			c.T174C						PASS	.	C	,	1251,3155	704.2+/-407.1	178,895,1130	156.0	137.0	143.0		174,174	0.8	1.0	12	dbSNP_123	143	1522,7078	747.6+/-407.3	144,1234,2922	no	coding-synonymous,coding-synonymous	TSPAN9	NM_001168320.1,NM_006675.4	,	322,2129,4052	CC,CT,TT		17.6977,28.3931,21.3209	,	58/240,58/240	3387697	2773,10233	2203	4300	6503	SO:0001819	synonymous_variant	10867	exon4			GGTCATTGCCATA	AF089749	CCDS8520.1	12p13.33-p13.32	2013-02-14			ENSG00000011105	ENSG00000011105		"""Tetraspanins"""	21640	protein-coding gene	gene with protein product		613137				10719184, 11739647	Standard	NM_006675		Approved	NET-5	uc021qtd.1	O75954	OTTHUMG00000150333	ENST00000011898.5:c.174T>C	12.37:g.3387697T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	221	221	1	NM_006675	D3DUQ7|Q53FV2|Q6FGJ8	Silent	SNP	ENST00000011898.5	37	CCDS8520.1																																																																																			T|0.797;C|0.203	0.203	strong		0.587	TSPAN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317606.2	NM_006675	
ZNF98	148198	hgsc.bcm.edu	37	19	22575423	22575423	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22575423C>G	ENST00000357774.5	-	4	735	c.614G>C	c.(613-615)aGt>aCt	p.S205T		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	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)			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)				TTTCTCTCCACTATGAATTCT	0.348																																					p.S205T		Atlas-SNP	.											ZNF98_ENST00000357774,NS,carcinoma,+1,2	ZNF98	230	2	0			c.G614C						scavenged	.						9.0	9.0	9.0					19																	22575423		1852	4073	5925	SO:0001583	missense	148198	exon4			TCTCCACTATGAA		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.614G>C	19.37:g.22575423C>G	ENSP00000350418:p.Ser205Thr	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	276	6	0.0217391	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	0.005	-2.150128	0.00328	.	.	ENSG00000197360	ENST00000357774	T	0.12879	2.64	1.28	-2.56	0.06268	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02888	0.0086	N	0.01284	-0.91	0.22330	N	0.999198	B	0.02656	0.0	B	0.04013	0.001	T	0.37776	-0.9691	9	0.02654	T	1	.	4.6015	0.12356	0.1579:0.4487:0.3933:0.0	.	205	A6NK75	ZNF98_HUMAN	T	205	ENSP00000350418:S205T	ENSP00000350418:S205T	S	-	2	0	ZNF98	22367263	0.006000	0.16342	0.000000	0.03702	0.002000	0.02628	-0.375000	0.07475	-1.007000	0.03408	-0.731000	0.03576	AGT	.	.	none		0.348	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887149	9887149	+	Missense_Mutation	SNP	G	G	C	rs11662946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9887149G>C	ENST00000306084.6	+	2	872	c.673G>C	c.(673-675)Gcc>Ccc	p.A225P	TXNDC2_ENST00000536353.2_Intron|TXNDC2_ENST00000357775.5_Missense_Mutation_p.A158P	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	225	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.		A -> P (in dbSNP:rs11662946).		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						GGGCAATATTGCCAAGACCTC	0.572													g|||	327	0.0652955	0.0477	0.0591	5008	,	,		22613	0.0228		0.0716	False		,,,				2504	0.1309				p.A225P		Atlas-SNP	.											TXNDC2_ENST00000306084,colon,carcinoma,-1,2	TXNDC2	168	2	0			c.G673C						scavenged	.	G	PRO/ALA,PRO/ALA	218,4188	131.8+/-168.3	4,210,1989	130.0	132.0	131.0		673,472	-2.8	0.0	18	dbSNP_120	131	668,7932	167.1+/-218.9	29,610,3661	no	missense,missense	TXNDC2	NM_001098529.1,NM_032243.5	27,27	33,820,5650	CC,CG,GG		7.7674,4.9478,6.8122	benign,benign	225/554,158/487	9887149	886,12120	2203	4300	6503	SO:0001583	missense	84203	exon2			AATATTGCCAAGA	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.673G>C	18.37:g.9887149G>C	ENSP00000304908:p.Ala225Pro	Somatic	134	3	0.0223881		WXS	Illumina HiSeq	Phase_I	154	84	0.545455	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	105	0.04807692307692308	14	0.028455284552845527	20	0.055248618784530384	16	0.027972027972027972	55	0.07255936675461741	g	0.015	-1.566545	0.00903	0.049478	0.077674	ENSG00000168454	ENST00000357775;ENST00000306084;ENST00000426718	T;T	0.11604	2.76;2.76	3.14	-2.78	0.05859	.	2.212560	0.02264	N	0.067858	T	0.00144	0.0004	N	0.00377	-1.585	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35375	-0.9791	9	.	.	.	.	2.2647	0.04076	0.1466:0.2121:0.4354:0.2058	rs11662946;rs11662946	225	Q86VQ3	TXND2_HUMAN	P	158;225;225	ENSP00000350419:A158P;ENSP00000304908:A225P	.	A	+	1	0	TXNDC2	9877149	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.313000	0.08103	-0.458000	0.07023	-0.266000	0.10368	GCC	G|0.937;C|0.063	0.063	strong		0.572	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
SNED1	25992	hgsc.bcm.edu	37	2	241991875	241991875	+	Silent	SNP	G	G	A	rs57214830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241991875G>A	ENST00000310397.8	+	15	2073	c.2073G>A	c.(2071-2073)cgG>cgA	p.R691R	SNED1_ENST00000342631.6_Silent_p.R691R|SNED1_ENST00000401884.1_Silent_p.R691R|SNED1_ENST00000405547.3_Silent_p.R691R|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000469006.1_3'UTR	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	691	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		TGGGACGCCGGTGCCAGGCAG	0.637													G|||	1286	0.256789	0.2126	0.245	5008	,	,		17592	0.4067		0.1928	False		,,,				2504	0.2362				p.R691R		Atlas-SNP	.											.	SNED1	76	.	0			c.G2073A						PASS	.	G		800,3316		93,614,1351	43.0	49.0	47.0		2073	2.2	1.0	2	dbSNP_129	47	1433,6939		134,1165,2887	yes	coding-synonymous	SNED1	NM_001080437.1		227,1779,4238	AA,AG,GG		17.1166,19.4363,17.8812		691/1414	241991875	2233,10255	2058	4186	6244	SO:0001819	synonymous_variant	25992	exon15			ACGCCGGTGCCAG	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.2073G>A	2.37:g.241991875G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																			G|0.756;A|0.244	0.244	strong		0.637	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
OR10H4	126541	hgsc.bcm.edu	37	19	16060658	16060658	+	Missense_Mutation	SNP	A	A	G	rs11880184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16060658A>G	ENST00000322107.1	+	1	841	c.841A>G	c.(841-843)Act>Gct	p.T281A		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	281			T -> A (in dbSNP:rs11880184).			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(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						CACCACCTATACTGTCTTCAC	0.458													A|||	1211	0.241813	0.4622	0.1772	5008	,	,		21784	0.0546		0.2644	False		,,,				2504	0.1595				p.T281A		Atlas-SNP	.											.	OR10H4	48	.	0			c.A841G						PASS	.	A	ALA/THR	1849,2557	537.5+/-374.7	383,1083,737	151.0	133.0	139.0		841	1.0	1.0	19	dbSNP_120	139	2048,6552	357.0+/-330.6	235,1578,2487	yes	missense	OR10H4	NM_001004465.1	58	618,2661,3224	GG,GA,AA		23.814,41.9655,29.9631	benign	281/317	16060658	3897,9109	2203	4300	6503	SO:0001583	missense	126541	exon1			ACCTATACTGTCT	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"""GPCR / Class A : Olfactory receptors"""	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.841A>G	19.37:g.16060658A>G	ENSP00000318834:p.Thr281Ala	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_001004465	Q6IFJ2|Q96R57	Missense_Mutation	SNP	ENST00000322107.1	37	CCDS32941.1	549	0.25137362637362637	237	0.4817073170731707	82	0.2265193370165746	40	0.06993006993006994	190	0.25065963060686014	a	3.362	-0.130215	0.06753	0.419655	0.23814	ENSG00000176231	ENST00000322107	T	0.00235	8.48	0.988	0.988	0.19796	GPCR, rhodopsin-like superfamily (1);	0.168007	0.27710	U	0.018178	T	0.00012	0.0000	M	0.64404	1.975	0.80722	P	0.0	B	0.21071	0.051	B	0.27887	0.084	T	0.45190	-0.9278	9	0.54805	T	0.06	.	2.8548	0.05569	0.7132:0.0:0.2868:0.0	rs11880184;rs59076186	281	Q8NGA5	O10H4_HUMAN	A	281	ENSP00000318834:T281A	ENSP00000318834:T281A	T	+	1	0	OR10H4	15921658	0.005000	0.15991	0.972000	0.41901	0.349000	0.29174	0.803000	0.27083	0.700000	0.31782	0.397000	0.26171	ACT	A|0.722;G|0.278	0.278	strong		0.458	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1		
TRIM31	11074	hgsc.bcm.edu	37	6	30071330	30071330	+	Missense_Mutation	SNP	C	C	T	rs1116221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30071330C>T	ENST00000376734.3	-	9	1386	c.1261G>A	c.(1261-1263)Gag>Aag	p.E421K	TRIM31_ENST00000540829.1_Missense_Mutation_p.E421K|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000485864.1_5'Flank	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	421			E -> K (in dbSNP:rs1116221). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						GAAGGAACCTCACAAAACCAA	0.582													C|||	1312	0.261981	0.4115	0.2248	5008	,	,		17945	0.0992		0.2207	False		,,,				2504	0.2965				p.E421K		Atlas-SNP	.											.	TRIM31	40	.	0			c.G1261A						PASS	.	C	LYS/GLU	1136,1884		203,730,577	149.0	166.0	160.0		1261	1.0	0.0	6	dbSNP_86	160	1412,4004		173,1066,1469	yes	missense	TRIM31	NM_007028.3	56	376,1796,2046	TT,TC,CC		26.0709,37.6159,30.2039	possibly-damaging	421/426	30071330	2548,5888	1510	2708	4218	SO:0001583	missense	11074	exon9			GAACCTCACAAAA	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.1261G>A	6.37:g.30071330C>T	ENSP00000365924:p.Glu421Lys	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	54	32	0.592593	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Missense_Mutation	SNP	ENST00000376734.3	37	CCDS34374.1	544	0.2490842490842491	214	0.4349593495934959	90	0.24861878453038674	63	0.11013986013986014	177	0.23350923482849603	C	9.318	1.057418	0.19907	0.376159	0.260709	ENSG00000204616	ENST00000376734;ENST00000376728;ENST00000540829	T;T	0.70045	-0.45;-0.45	1.99	1.05	0.20165	.	.	.	.	.	T	0.13200	0.0320	N	0.08118	0	0.80722	P	0.0	P	0.41524	0.753	B	0.28991	0.097	T	0.06661	-1.0814	8	0.09084	T	0.74	.	5.5601	0.17140	0.3261:0.6739:0.0:0.0	rs1116221;rs4081515;rs17187903;rs17845513;rs17858403;rs59822889;rs1116221	421	Q9BZY9	TRI31_HUMAN	K	421	ENSP00000365924:E421K;ENSP00000444311:E421K	ENSP00000365918:E421K	E	-	1	0	TRIM31	30179309	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.968000	0.29357	0.371000	0.24564	0.573000	0.79308	GAG	C|0.710;T|0.290	0.290	strong		0.582	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
ASB18	401036	hgsc.bcm.edu	37	2	237103697	237103697	+	Missense_Mutation	SNP	G	G	T	rs10177957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:237103697G>T	ENST00000409749.3	-	6	1218	c.1219C>A	c.(1219-1221)Cac>Aac	p.H407N	AC079135.1_ENST00000483218.1_RNA|ASB18_ENST00000330842.6_Missense_Mutation_p.H378N|AC079135.1_ENST00000415226.1_RNA	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	407	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.		H -> N (in dbSNP:rs10177957).		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)		AACGGCTTGTGCATCTGGAAG	0.537													G|||	543	0.108427	0.1732	0.0735	5008	,	,		17656	0.002		0.1352	False		,,,				2504	0.1278				p.H407N		Atlas-SNP	.											.	ASB18	34	.	0			c.C1219A						PASS	.	G	ASN/HIS	660,3554		49,562,1496	54.0	66.0	62.0		1219	3.7	1.0	2	dbSNP_119	62	970,7516		61,848,3334	yes	missense	ASB18	NM_212556.2	68	110,1410,4830	TT,TG,GG		11.4306,15.6621,12.8346	possibly-damaging	407/467	237103697	1630,11070	2107	4243	6350	SO:0001583	missense	401036	exon6			GCTTGTGCATCTG	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.1219C>A	2.37:g.237103697G>T	ENSP00000386532:p.His407Asn	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_212556	B6ZDL7	Missense_Mutation	SNP	ENST00000409749.3	37	CCDS46548.1	206	0.09432234432234432	65	0.13211382113821138	33	0.09116022099447514	0	0.0	108	0.1424802110817942	G	18.15	3.561021	0.65538	0.156621	0.114306	ENSG00000182177	ENST00000330842;ENST00000409749	T;T	0.39056	1.1;1.15	4.64	3.73	0.42828	SOCS protein, C-terminal (1);	.	.	.	.	T	0.00328	0.0010	M	0.83223	2.63	0.20638	P	0.999874701	D	0.54047	0.964	P	0.52823	0.71	T	0.20174	-1.0283	8	0.62326	D	0.03	.	11.276	0.49168	0.088:0.0:0.912:0.0	rs10177957;rs58809580;rs10177957	407	Q6ZVZ8	ASB18_HUMAN	N	378;407	ENSP00000329970:H378N;ENSP00000386532:H407N	ENSP00000329970:H378N	H	-	1	0	ASB18	236768436	1.000000	0.71417	0.975000	0.42487	0.858000	0.48976	3.588000	0.53964	2.411000	0.81874	0.561000	0.74099	CAC	G|0.894;T|0.106	0.106	strong		0.537	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556	
OSER1	51526	hgsc.bcm.edu	37	20	42825929	42825929	+	Silent	SNP	C	C	T	rs8268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42825929C>T	ENST00000372970.2	-	6	822	c.642G>A	c.(640-642)gtG>gtA	p.V214V	OSER1_ENST00000255174.2_Silent_p.V214V			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	214					cellular response to hydrogen peroxide (GO:0070301)												AAAAGGAATACACTTCCATAT	0.498													C|||	1496	0.298722	0.41	0.1124	5008	,	,		23065	0.4147		0.1471	False		,,,				2504	0.317				p.V214V		Atlas-SNP	.											.	C20orf111	28	.	0			c.G642A						PASS	.	C		1506,2900	480.4+/-358.8	237,1032,934	144.0	123.0	130.0		642	-3.3	0.9	20	dbSNP_52	130	1152,7448	237.6+/-269.4	73,1006,3221	no	coding-synonymous	C20orf111	NM_016470.7		310,2038,4155	TT,TC,CC		13.3953,34.1807,20.4367		214/293	42825929	2658,10348	2203	4300	6503	SO:0001819	synonymous_variant	51526	exon4			GGAATACACTTCC	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"""peroxide-inducible transcript 1"", ""oxidative stress-responsive 1"""		"""chromosome 20 open reading frame 111"""	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.642G>A	20.37:g.42825929C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	142	76	0.535211	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Silent	SNP	ENST00000372970.2	37	CCDS13327.1																																																																																			C|0.766;T|0.234	0.234	strong		0.498	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470	
ATP1A4	480	hgsc.bcm.edu	37	1	160136350	160136350	+	Silent	SNP	G	G	A	rs7529215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160136350G>A	ENST00000368081.4	+	8	1551	c.1080G>A	c.(1078-1080)gcG>gcA	p.A360A		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	360					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGCGCATGGCGCGGAAGAACT	0.567													g|||	2345	0.468251	0.2806	0.5375	5008	,	,		19774	0.4851		0.5457	False		,,,				2504	0.5757				p.A360A		Atlas-SNP	.											.	ATP1A4	167	.	0			c.G1080A						PASS	.	A		1475,2931	473.1+/-356.6	267,941,995	88.0	79.0	82.0		1080	-8.6	0.0	1	dbSNP_116	82	4867,3733	618.0+/-396.7	1413,2041,846	no	coding-synonymous	ATP1A4	NM_144699.3		1680,2982,1841	AA,AG,GG		43.407,33.4771,48.7621		360/1030	160136350	6342,6664	2203	4300	6503	SO:0001819	synonymous_variant	480	exon8			CATGGCGCGGAAG	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"""ATPases / P-type"""	14073	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-4"", ""sodium pump subunit alpha-4"", ""sodium-potassium ATPase catalytic subunit alpha-4"""	607321	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 2"""	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1080G>A	1.37:g.160136350G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	198	108	0.545455	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	37	CCDS1197.1																																																																																			G|0.522;A|0.478	0.478	strong		0.567	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	
NCOA6	23054	hgsc.bcm.edu	37	20	33338099	33338099	+	Silent	SNP	G	G	A	rs61736335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33338099G>A	ENST00000374796.2	-	10	4469	c.1899C>T	c.(1897-1899)ggC>ggT	p.G633G	NCOA6_ENST00000359003.2_Silent_p.G633G			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	633	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						GGACCATCTGGCCCTGGGAGG	0.587													G|||	11	0.00219649	0.0083	0.0	5008	,	,		17579	0.0		0.0	False		,,,				2504	0.0				p.G633G		Atlas-SNP	.											.	NCOA6	219	.	0			c.C1899T						PASS	.	G	,	60,4346	58.1+/-94.6	0,60,2143	112.0	100.0	104.0		1899,1899	-0.8	1.0	20	dbSNP_129	104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NCOA6	NM_001242539.1,NM_014071.3	,	0,61,6442	AA,AG,GG		0.0116,1.3618,0.469	,	633/1071,633/2064	33338099	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	23054	exon9			CATCTGGCCCTGG	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.1899C>T	20.37:g.33338099G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	198	101	0.510101	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	CCDS13241.1																																																																																			G|0.996;A|0.004	0.004	strong		0.587	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
DNHD1	144132	hgsc.bcm.edu	37	11	6550309	6550309	+	Missense_Mutation	SNP	G	G	A	rs2344829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6550309G>A	ENST00000527990.2	+	10	2305	c.2305G>A	c.(2305-2307)Ggg>Agg	p.G769R	DNHD1_ENST00000254579.6_Missense_Mutation_p.G769R			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	769					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)		CACAAAAGGCGGGTTGCTGCT	0.527													A|||	3582	0.715256	0.6422	0.6527	5008	,	,		20739	0.874		0.6292	False		,,,				2504	0.7832				p.G769R		Atlas-SNP	.											.	DNHD1	198	.	0			c.G2305A						PASS	.	A	ARG/GLY	894,490		284,326,82	142.0	136.0	138.0		2305	3.0	1.0	11	dbSNP_100	138	2137,1045		722,693,176	yes	missense	DNHD1	NM_144666.2	125	1006,1019,258	AA,AG,GG		32.841,35.4046,33.618	benign	769/4754	6550309	3031,1535	692	1591	2283	SO:0001583	missense	144132	exon12			AAAGGCGGGTTGC	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.2305G>A	11.37:g.6550309G>A	ENSP00000436180:p.Gly769Arg	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	132	67	0.507576	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	1538	0.7042124542124543	330	0.6707317073170732	235	0.649171270718232	487	0.8513986013986014	486	0.6411609498680739	A	5.682	0.310322	0.10733	0.645954	0.67159	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210	T;T	0.25579	1.79;1.79	5.54	3.02	0.34903	.	.	.	.	.	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	0.16364	-1.0405	8	0.27082	T	0.32	.	6.0678	0.19873	0.6721:0.2398:0.0882:0.0	rs2344829;rs52815182;rs58903745;rs2344829	769	Q96M86	DNHD1_HUMAN	R	769;769;35	ENSP00000254579:G769R;ENSP00000436180:G769R	ENSP00000254579:G769R	G	+	1	0	DNHD1	6506885	0.799000	0.28903	0.992000	0.48379	0.938000	0.57974	1.170000	0.31883	0.928000	0.37168	-0.269000	0.10298	GGG	G|0.292;A|0.708	0.708	strong		0.527	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
LIPG	9388	hgsc.bcm.edu	37	18	47088741	47088741	+	Silent	SNP	C	C	T	rs874566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47088741C>T	ENST00000261292.4	+	1	341	c.63C>T	c.(61-63)agC>agT	p.S21S	LIPG_ENST00000427224.2_Silent_p.S21S|LIPG_ENST00000580036.1_Silent_p.S21S|LIPG_ENST00000577628.1_Intron	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial	21					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						CTGCGGGGAGCCCCGTACCTT	0.557													C|||	224	0.0447284	0.1551	0.0216	5008	,	,		14167	0.0		0.004	False		,,,				2504	0.0				p.S21S	Pancreas(126;280 1778 12814 26243 34948)	Atlas-SNP	.											.	LIPG	47	.	0			c.C63T						PASS	.	C		677,3729	285.7+/-278.4	57,563,1583	81.0	81.0	81.0		63	2.6	0.0	18	dbSNP_86	81	37,8563	25.1+/-72.6	0,37,4263	no	coding-synonymous	LIPG	NM_006033.2		57,600,5846	TT,TC,CC		0.4302,15.3654,5.4898		21/501	47088741	714,12292	2203	4300	6503	SO:0001819	synonymous_variant	9388	exon1			GGGGAGCCCCGTA	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.63C>T	18.37:g.47088741C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_006033	B0LPG6|Q6P9C8|Q6UW82	Silent	SNP	ENST00000261292.4	37	CCDS11938.1																																																																																			C|0.953;T|0.047	0.047	strong		0.557	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	NM_006033	
MFSD3	113655	hgsc.bcm.edu	37	8	145736101	145736101	+	Silent	SNP	G	G	A	rs34730139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145736101G>A	ENST00000301327.4	+	3	1211	c.951G>A	c.(949-951)ttG>ttA	p.L317L	CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000532237.1_5'Flank	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3	317	Leu-rich.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-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;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GCACAATCTTGAGAGGTGAGG	0.652													G|||	212	0.0423323	0.1543	0.0115	5008	,	,		18901	0.0		0.0	False		,,,				2504	0.0				p.L317L		Atlas-SNP	.											.	MFSD3	17	.	0			c.G951A						PASS	.	G		493,3913	222.0+/-238.9	32,429,1742	46.0	52.0	50.0		951	1.8	0.8	8	dbSNP_126	50	4,8592	2.2+/-6.3	0,4,4294	no	coding-synonymous	MFSD3	NM_138431.1		32,433,6036	AA,AG,GG		0.0465,11.1893,3.8225		317/413	145736101	497,12505	2203	4298	6501	SO:0001819	synonymous_variant	113655	exon3			AATCTTGAGAGGT		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177	ENST00000301327.4:c.951G>A	8.37:g.145736101G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_138431		Silent	SNP	ENST00000301327.4	37	CCDS6431.1																																																																																			G|0.966;A|0.034	0.034	strong		0.652	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431	
RMDN2	151393	hgsc.bcm.edu	37	2	38178406	38178406	+	Intron	SNP	A	A	G	rs4670799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:38178406A>G	ENST00000406384.1	+	2	646				RMDN2_ENST00000402091.3_Silent_p.R16R|RMDN2_ENST00000354545.2_Intron|RMDN2_ENST00000407257.1_Silent_p.R16R|RMDN2-AS1_ENST00000414365.2_RNA|RMDN2_ENST00000417700.2_Intron|RMDN2_ENST00000234195.3_Silent_p.R16R	NM_001170792.1	NP_001164263.1	Q96LZ7	RMD2_HUMAN	regulator of microtubule dynamics 2							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)											GCTTCCAACGATGTTCTCCAG	0.458													A|||	1644	0.328275	0.2247	0.3804	5008	,	,		19531	0.0883		0.4553	False		,,,				2504	0.5481				p.R16R		Atlas-SNP	.											.	.	.	.	0			c.A48G						PASS	.	A	,,,	1215,3191	422.8+/-339.9	167,881,1155	73.0	71.0	72.0		,,,48	0.3	0.0	2	dbSNP_111	72	4127,4471	562.5+/-388.0	991,2145,1163	no	intron,intron,intron,coding-synonymous	FAM82A1	NM_001170791.1,NM_001170792.1,NM_001170793.1,NM_144713.3	,,,	1158,3026,2318	GG,GA,AA		47.9995,27.576,41.0797	,,,	,,,16/574	38178406	5342,7662	2203	4299	6502	SO:0001627	intron_variant	151393	exon2			CCAACGATGTTCT	AK057516	CCDS1792.1, CCDS54351.1, CCDS54352.1	2p22.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000115841	ENSG00000115841			26567	protein-coding gene	gene with protein product		611872	"""family with sequence similarity 82, member A1"""	FAM82A, FAM82A1		12477932	Standard	XM_005264161		Approved	FLJ32954, RMD2	uc002rqn.2	Q96LZ7	OTTHUMG00000128487	ENST00000406384.1:c.452+21534A>G	2.37:g.38178406A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_144713	A9UMZ7|A9UN00|Q4ZG33|Q6UXN4|Q8N657|Q8N9A2|Q8NCV6|Q8NHM0	Silent	SNP	ENST00000406384.1	37	CCDS54351.1																																																																																			A|0.638;G|0.362	0.362	strong		0.458	RMDN2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325577.1	NM_144713	
OBSCN	84033	hgsc.bcm.edu	37	1	228468244	228468244	+	Silent	SNP	G	G	A	rs12061320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228468244G>A	ENST00000422127.1	+	30	7988	c.7944G>A	c.(7942-7944)gtG>gtA	p.V2648V	OBSCN_ENST00000359599.6_Silent_p.V1495V|OBSCN_ENST00000284548.11_Silent_p.V2648V|OBSCN_ENST00000570156.2_Silent_p.V3077V|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2648	Ig-like 26.				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)				AGCCGGTGGTGTTCCTGAAGG	0.642													g|||	569	0.113618	0.115	0.0173	5008	,	,		16189	0.3185		0.0268	False		,,,				2504	0.0583				p.V3077V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G9231A						PASS	.		,	452,3880		24,404,1738	46.0	54.0	51.0		7944,7944	2.2	1.0	1	dbSNP_120	51	156,8368		0,156,4106	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	24,560,5844	AA,AG,GG		1.8301,10.434,4.7293	,	2648/7969,2648/6621	228468244	608,12248	2166	4262	6428	SO:0001819	synonymous_variant	84033	exon35			GGTGGTGTTCCTG	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.7944G>A	1.37:g.228468244G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	93	54	0.580645	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																																																																																			G|0.865;A|0.135	0.135	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
NRXN1	9378	hgsc.bcm.edu	37	2	50280469	50280469	+	Silent	SNP	C	C	T	rs74714098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:50280469C>T	ENST00000406316.2	-	20	5454	c.3978G>A	c.(3976-3978)acG>acA	p.T1326T	NRXN1_ENST00000342183.5_Silent_p.T291T|NRXN1_ENST00000402717.3_Silent_p.T1348T|NRXN1_ENST00000406859.3_Silent_p.T1326T|NRXN1_ENST00000405472.3_Silent_p.T1348T|NRXN1_ENST00000401710.1_Silent_p.T344T|NRXN1_ENST00000404971.1_Silent_p.T1396T|NRXN1_ENST00000401669.2_Silent_p.T1356T	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1326	Poly-Thr.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TAGCCAGGGTCGTGGTAGTCT	0.473													C|||	82	0.0163738	0.0575	0.0043	5008	,	,		16560	0.0		0.001	False		,,,				2504	0.002				p.T1396T		Atlas-SNP	.											.	NRXN1	1118	.	0			c.G4188A						PASS	.	C	,,	186,4220	119.2+/-156.9	6,174,2023	135.0	131.0	132.0		4188,3978,873	-7.8	0.8	2	dbSNP_131	132	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	NRXN1	NM_001135659.1,NM_004801.4,NM_138735.2	,,	6,175,6322	TT,TC,CC		0.0116,4.2215,1.4378	,,	1396/1548,1326/1478,291/443	50280469	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	9378	exon22			CAGGGTCGTGGTA	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3978G>A	2.37:g.50280469C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	204	104	0.509804	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			C|0.983;T|0.017	0.017	strong		0.473	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
SELP	6403	hgsc.bcm.edu	37	1	169562904	169562904	+	Silent	SNP	C	C	T	rs6128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169562904C>T	ENST00000263686.6	-	14	2383	c.2346G>A	c.(2344-2346)acG>acA	p.T782T	SELP_ENST00000367788.2_Silent_p.T720T|SELP_ENST00000367786.2_Silent_p.T720T|SELP_ENST00000367794.2_Silent_p.T720T|SELP_ENST00000367792.2_Silent_p.T598T|SELP_ENST00000367791.2_Silent_p.T596T|SELP_ENST00000458599.2_Silent_p.T598T|SELP_ENST00000367793.2_Silent_p.T720T	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	86	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	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	
MUC4	4585	hgsc.bcm.edu	37	3	195513318	195513318	+	Silent	SNP	G	G	A	rs199718749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513318G>A	ENST00000463781.3	-	2	5592	c.5133C>T	c.(5131-5133)acC>acT	p.T1711T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T1711T	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)		CAGGAAGAGGGGTGGCCTGAC	0.602													.|||	179	0.0357428	0.0953	0.013	5008	,	,		25138	0.002		0.0169	False		,,,				2504	0.0256				p.T1711T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C5133T						PASS	.						26.0	27.0	27.0					3																	195513318		690	1583	2273	SO:0001819	synonymous_variant	4585	exon2			AAGAGGGGTGGCC	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.5133C>T	3.37:g.195513318G>A		Somatic	510	0	0		WXS	Illumina HiSeq	Phase_I	475	164	0.345263	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|0.993;A|0.007	0.007	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CCP110	9738	hgsc.bcm.edu	37	16	19547503	19547503	+	Missense_Mutation	SNP	C	C	T	rs3751821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19547503C>T	ENST00000381396.5	+	4	759	c.512C>T	c.(511-513)cCg>cTg	p.P171L	CCP110_ENST00000396208.2_Missense_Mutation_p.P171L|CCP110_ENST00000396212.2_Missense_Mutation_p.P171L	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	171	CEP97 binding.		P -> L (in dbSNP:rs3751821).		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)		p.P171L(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						TTTAATTCTCCGAAGCAATGT	0.378													C|||	1203	0.240216	0.3313	0.2579	5008	,	,		18797	0.3849		0.0755	False		,,,				2504	0.1247				p.P171L		Atlas-SNP	.											CCP110,NS,carcinoma,0,1	CCP110	57	1	1	Substitution - Missense(1)	stomach(1)	c.C512T						PASS	.	C	LEU/PRO,LEU/PRO	1269,3125	431.4+/-342.9	170,929,1098	97.0	105.0	102.0		512,512	-2.3	0.4	16	dbSNP_107	102	565,8035	152.5+/-207.1	15,535,3750	yes	missense,missense	CCP110	NM_001199022.1,NM_014711.4	98,98	185,1464,4848	TT,TC,CC		6.5698,28.8803,14.1142	benign,benign	171/1013,171/992	19547503	1834,11160	2197	4300	6497	SO:0001583	missense	9738	exon4			ATTCTCCGAAGCA	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.512C>T	16.37:g.19547503C>T	ENSP00000370803:p.Pro171Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	521	0.23855311355311357	175	0.3556910569105691	77	0.212707182320442	215	0.3758741258741259	54	0.0712401055408971	C	0.441	-0.898743	0.02472	0.288803	0.065698	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.13657	2.57;2.58;2.57	5.89	-2.28	0.06826	.	1.287990	0.05136	N	0.493485	T	0.00012	0.0000	N	0.00707	-1.245	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.46803	-0.9165	9	0.29301	T	0.29	-0.0337	7.3644	0.26764	0.1116:0.4194:0.0:0.4689	rs3751821;rs52803660;rs60078054;rs3751821	171;171	O43303;O43303-2	CP110_HUMAN;.	L	171	ENSP00000379515:P171L;ENSP00000370803:P171L;ENSP00000379511:P171L	ENSP00000370803:P171L	P	+	2	0	CCP110	19455004	0.000000	0.05858	0.357000	0.25798	0.964000	0.63967	-0.239000	0.08965	-0.069000	0.12931	-0.290000	0.09829	CCG	C|0.801;T|0.199	0.199	strong		0.378	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
NWD1	284434	hgsc.bcm.edu	37	19	16860602	16860602	+	Silent	SNP	T	T	C	rs61731252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860602T>C	ENST00000552788.1	+	4	1149	c.1149T>C	c.(1147-1149)cgT>cgC	p.R383R	NWD1_ENST00000379808.3_Silent_p.R383R|NWD1_ENST00000339803.6_Silent_p.R248R|NWD1_ENST00000549814.1_Silent_p.R383R|NWD1_ENST00000524140.2_Silent_p.R383R|NWD1_ENST00000523826.1_Silent_p.R177R			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	383	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CAGATGCCCGTGGCCTGCTGA	0.622													t|||	337	0.0672923	0.1838	0.0274	5008	,	,		17972	0.0079		0.0288	False		,,,				2504	0.0389				p.R383R		Atlas-SNP	.											.	NWD1	303	.	0			c.T1149C						PASS	.			733,3673		58,617,1528	32.0	34.0	33.0		1149	-4.7	0.0	19	dbSNP_129	33	320,8280		7,306,3987	no	coding-synonymous	NWD1	NM_001007525.3		65,923,5515	CC,CT,TT		3.7209,16.6364,8.0963		383/1433	16860602	1053,11953	2203	4300	6503	SO:0001819	synonymous_variant	284434	exon6			TGCCCGTGGCCTG	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1149T>C	19.37:g.16860602T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_001007525	C9J021|Q68CT3	Silent	SNP	ENST00000552788.1	37																																																																																				T|0.927;C|0.073	0.073	strong		0.622	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
IGSF5	150084	hgsc.bcm.edu	37	21	41143018	41143018	+	Missense_Mutation	SNP	T	T	A	rs74817033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:41143018T>A	ENST00000380588.4	+	4	697	c.594T>A	c.(592-594)agT>agA	p.S198R	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	198	Ig-like V-type 2.				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)				ACCTTCAAAGTGCAGTGAGCA	0.557													T|||	215	0.0429313	0.1551	0.0144	5008	,	,		15696	0.0		0.0	False		,,,				2504	0.0				p.S198R		Atlas-SNP	.											.	IGSF5	62	.	0			c.T594A						PASS	.	T	ARG/SER	560,3846	251.8+/-258.4	34,492,1677	76.0	72.0	73.0		594	-3.7	0.0	21	dbSNP_131	73	5,8595	3.7+/-12.6	0,5,4295	yes	missense	IGSF5	NM_001080444.1	110	34,497,5972	AA,AT,TT		0.0581,12.7099,4.3441	benign	198/408	41143018	565,12441	2203	4300	6503	SO:0001583	missense	150084	exon4			TCAAAGTGCAGTG		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.594T>A	21.37:g.41143018T>A	ENSP00000369962:p.Ser198Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_001080444		Missense_Mutation	SNP	ENST00000380588.4	37	CCDS33562.1	87	0.03983516483516483	78	0.15853658536585366	9	0.024861878453038673	0	0.0	0	0.0	T	17.24	3.339873	0.60963	0.127099	5.81E-4	ENSG00000183067	ENST00000380588	T	0.12147	2.71	5.11	-3.69	0.04450	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.194230	0.52532	N	0.000061	T	0.00039	0.0001	L	0.40543	1.245	0.80722	P	0.0	P	0.37708	0.606	B	0.37198	0.243	T	0.40175	-0.9577	9	0.14252	T	0.57	-6.954	5.6797	0.17769	0.0:0.2935:0.239:0.4676	.	198	Q9NSI5	IGSF5_HUMAN	R	198	ENSP00000369962:S198R	ENSP00000369962:S198R	S	+	3	2	IGSF5	40064888	0.001000	0.12720	0.000000	0.03702	0.931000	0.56810	-0.287000	0.08388	-0.719000	0.04942	0.528000	0.53228	AGT	T|0.959;A|0.041	0.041	strong		0.557	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		
FOCAD	54914	hgsc.bcm.edu	37	9	20820346	20820346	+	Silent	SNP	A	A	T	rs147147351		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:20820346A>T	ENST00000380249.1	+	15	1948	c.1584A>T	c.(1582-1584)cgA>cgT	p.R528R	FOCAD_ENST00000338382.6_Silent_p.R528R|FOCAD_ENST00000605086.1_5'UTR	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	528						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											AAATTCTACGAATAATACAAC	0.378													A|||	1	0.000199681	0.0008	0.0	5008	,	,		17668	0.0		0.0	False		,,,				2504	0.0				p.R528R		Atlas-SNP	.											KIAA1797,rectum,carcinoma,+1,1	.	.	1	0			c.A1584T						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	101.0	96.0	98.0		1584	1.8	1.0	9	dbSNP_134	98	0,8600		0,0,4300	no	coding-synonymous	KIAA1797	NM_017794.3		0,3,6500	TT,TA,AA		0.0,0.0681,0.0231		528/1802	20820346	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	54914	exon15			TCTACGAATAATA	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.1584A>T	9.37:g.20820346A>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Silent	SNP	ENST00000380249.1	37	CCDS34993.1																																																																																			A|1.000;T|0.000	0.000	strong		0.378	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
ZBTB38	253461	hgsc.bcm.edu	37	3	141162185	141162185	+	Missense_Mutation	SNP	T	T	G	rs16851435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141162185T>G	ENST00000514251.1	+	4	1234	c.955T>G	c.(955-957)Tcc>Gcc	p.S319A	ZBTB38_ENST00000441582.2_Missense_Mutation_p.S319A|ZBTB38_ENST00000321464.5_Missense_Mutation_p.S320A					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						TGTCCATTTTTCCAGGGAAGA	0.458													T|||	847	0.169129	0.087	0.2219	5008	,	,		20680	0.3095		0.1113	False		,,,				2504	0.1575				p.S319A		Atlas-SNP	.											.	ZBTB38	92	.	0			c.T955G						PASS	.	T	ALA/SER	372,3436		17,338,1549	69.0	68.0	68.0		955	-2.6	0.0	3	dbSNP_123	68	862,7360		40,782,3289	yes	missense	ZBTB38	NM_001080412.2	99	57,1120,4838	GG,GT,TT		10.4841,9.7689,10.2577	benign	319/1196	141162185	1234,10796	1904	4111	6015	SO:0001583	missense	253461	exon8			CATTTTTCCAGGG	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.955T>G	3.37:g.141162185T>G	ENSP00000426387:p.Ser319Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_001080412		Missense_Mutation	SNP	ENST00000514251.1	37	CCDS43157.1	385	0.1762820512820513	42	0.08536585365853659	71	0.19613259668508287	194	0.33916083916083917	78	0.10290237467018469	T	3.800	-0.041870	0.07452	0.097689	0.104841	ENSG00000177311	ENST00000509883;ENST00000514251;ENST00000441582;ENST00000321464	T;T;T;T	0.09350	3.39;2.99;2.99;3.0	5.28	-2.59	0.06209	.	0.690156	0.14567	N	0.311714	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.16603	0.018	B	0.16289	0.015	T	0.48410	-0.9038	8	.	.	.	-1.5088	11.4515	0.50156	0.0:0.5188:0.0:0.4812	rs16851435;rs52829558;rs16851435	319	Q8NAP3	ZBT38_HUMAN	A	319;319;319;320	ENSP00000424254:S319A;ENSP00000426387:S319A;ENSP00000406955:S319A;ENSP00000372635:S320A	.	S	+	1	0	ZBTB38	142644875	0.000000	0.05858	0.019000	0.16419	0.426000	0.31534	-0.438000	0.06905	-0.388000	0.07797	-0.353000	0.07706	TCC	G|0.170;N|0.000	0.170	strong		0.458	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
RGS13	6003	hgsc.bcm.edu	37	1	192613522	192613522	+	Missense_Mutation	SNP	C	C	T	rs146420296		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:192613522C>T	ENST00000391995.2	+	4	346	c.58C>T	c.(58-60)Cct>Tct	p.P20S	RGS13_ENST00000543215.1_Missense_Mutation_p.P20S	NM_002927.4	NP_002918.1	O14921	RGS13_HUMAN	regulator of G-protein signaling 13	20					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of GTPase activity (GO:0043547)|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)			endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|skin(1)	19						TAAGAGGCCCCCTTCAAAGTA	0.289																																					p.P20S		Atlas-SNP	.											.	RGS13	31	.	0			c.C58T						PASS	.	C	SER/PRO,SER/PRO	1,4405	2.1+/-5.4	0,1,2202	122.0	135.0	131.0		58,58	3.7	0.5	1	dbSNP_134	131	0,8598		0,0,4299	no	missense,missense	RGS13	NM_002927.4,NM_144766.2	74,74	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	20/160,20/160	192613522	1,13003	2203	4299	6502	SO:0001583	missense	6003	exon4			AGGCCCCCTTCAA	AF030107	CCDS1376.1	1q31.2	2008-02-05	2007-08-14		ENSG00000127074	ENSG00000127074		"""Regulators of G-protein signaling"""	9995	protein-coding gene	gene with protein product		607190	"""regulator of G-protein signalling 13"""			11875076	Standard	NM_144766		Approved		uc001gsk.3	O14921	OTTHUMG00000035601	ENST00000391995.2:c.58C>T	1.37:g.192613522C>T	ENSP00000375853:p.Pro20Ser	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	214	96	0.448598	NM_002927	Q6PGR2|Q8TD63|Q9BX45	Missense_Mutation	SNP	ENST00000391995.2	37	CCDS1376.1	.	.	.	.	.	.	.	.	.	.	C	4.758	0.140916	0.09083	2.27E-4	0.0	ENSG00000127074	ENST00000391995;ENST00000543215	T;T	0.29655	1.56;1.56	5.62	3.67	0.42095	.	0.906400	0.09503	N	0.793331	T	0.18130	0.0435	N	0.24115	0.695	0.23653	N	0.997194	B	0.06786	0.001	B	0.06405	0.002	T	0.28073	-1.0055	10	0.07175	T	0.84	.	8.174	0.31270	0.0:0.7495:0.1625:0.0881	.	20	O14921	RGS13_HUMAN	S	20	ENSP00000375853:P20S;ENSP00000442837:P20S	ENSP00000375853:P20S	P	+	1	0	RGS13	190880145	0.086000	0.21541	0.478000	0.27316	0.701000	0.40568	1.077000	0.30741	1.460000	0.47911	0.655000	0.94253	CCT	C|1.000;T|0.000	0.000	weak		0.289	RGS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086400.1	NM_002927	
CILP2	148113	hgsc.bcm.edu	37	19	19656615	19656615	+	Silent	SNP	C	C	T	rs61744761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19656615C>T	ENST00000291495.5	+	8	3346	c.3261C>T	c.(3259-3261)ggC>ggT	p.G1087G	CILP2_ENST00000586018.1_Silent_p.G1093G	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	1087						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCTCTGACGGCTTCTCCAGAG	0.622													C|||	582	0.116214	0.174	0.1167	5008	,	,		14302	0.0		0.166	False		,,,				2504	0.1063				p.G1087G		Atlas-SNP	.											.	CILP2	84	.	0			c.C3261T						PASS	.	C		761,3643	284.3+/-277.5	57,647,1498	31.0	24.0	26.0		3261	3.5	1.0	19	dbSNP_129	26	1411,7189	252.2+/-278.4	111,1189,3000	no	coding-synonymous	CILP2	NM_153221.2		168,1836,4498	TT,TC,CC		16.407,17.2797,16.7026		1087/1157	19656615	2172,10832	2202	4300	6502	SO:0001819	synonymous_variant	148113	exon8			TGACGGCTTCTCC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.3261C>T	19.37:g.19656615C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	214	94	0.439252	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			C|0.845;T|0.155	0.155	strong		0.622	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
TAS2R41	259287	hgsc.bcm.edu	37	7	143175345	143175345	+	Missense_Mutation	SNP	C	C	T	rs10278721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143175345C>T	ENST00000408916.1	+	1	380	c.380C>T	c.(379-381)cCa>cTa	p.P127L	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	127			P -> L (in dbSNP:rs10278721). {ECO:0000269|PubMed:12379855, ECO:0000269|PubMed:15496549}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					TGGAGGTTCCCAGGGTGGGTG	0.498													C|||	1058	0.211262	0.0227	0.2695	5008	,	,		15749	0.2956		0.2535	False		,,,				2504	0.2945				p.P127L		Atlas-SNP	.											.	TAS2R41	43	.	0			c.C380T						PASS	.	C	LEU/PRO	232,3666		9,214,1726	57.0	56.0	57.0		380	1.5	0.3	7	dbSNP_119	57	2266,6026		312,1642,2192	yes	missense	TAS2R41	NM_176883.2	98	321,1856,3918	TT,TC,CC		27.3275,5.9518,20.4922	benign	127/308	143175345	2498,9692	1949	4146	6095	SO:0001583	missense	259287	exon1			GGTTCCCAGGGTG	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.380C>T	7.37:g.143175345C>T	ENSP00000386201:p.Pro127Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_176883	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Missense_Mutation	SNP	ENST00000408916.1	37	CCDS43663.1	497	0.22756410256410256	19	0.03861788617886179	95	0.26243093922651933	193	0.3374125874125874	190	0.25065963060686014	C	15.91	2.973193	0.53614	0.059518	0.273275	ENSG00000221855	ENST00000408916	T	0.33654	1.4	5.7	1.47	0.22746	.	0.790114	0.10721	U	0.641758	T	0.00012	0.0000	L	0.35593	1.075	0.80722	P	0.0	B	0.33583	0.418	B	0.32393	0.145	T	0.42068	-0.9473	9	0.62326	D	0.03	.	1.6792	0.02828	0.1616:0.3844:0.2791:0.175	rs10278721;rs10278721	127	P59536	T2R41_HUMAN	L	127	ENSP00000386201:P127L	ENSP00000386201:P127L	P	+	2	0	TAS2R41	142885467	0.000000	0.05858	0.272000	0.24630	0.814000	0.46013	0.291000	0.18994	0.745000	0.32763	0.655000	0.94253	CCA	C|0.770;T|0.230	0.230	strong		0.498	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1		
FIG4	9896	hgsc.bcm.edu	37	6	110064928	110064928	+	Missense_Mutation	SNP	A	A	T	rs2295837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:110064928A>T	ENST00000230124.3	+	10	1214	c.1090A>T	c.(1090-1092)Atg>Ttg	p.M364L	FIG4_ENST00000441478.2_Missense_Mutation_p.M87L	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	364	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.		M -> L (in dbSNP:rs2295837).		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)		CTTTGACCAGATGTTCCAGAG	0.438													A|||	501	0.10004	0.0174	0.1153	5008	,	,		17593	0.1984		0.0408	False		,,,				2504	0.1605				p.M364L		Atlas-SNP	.											.	FIG4	77	.	0			c.A1090T						PASS	.	A	LEU/MET	95,4311	76.8+/-115.0	0,95,2108	141.0	129.0	133.0		1090	4.9	1.0	6	dbSNP_100	133	307,8293	111.0+/-171.3	6,295,3999	yes	missense	FIG4	NM_014845.5	15	6,390,6107	TT,TA,AA		3.5698,2.1562,3.0909	benign	364/908	110064928	402,12604	2203	4300	6503	SO:0001583	missense	9896	exon10			GACCAGATGTTCC	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.1090A>T	6.37:g.110064928A>T	ENSP00000230124:p.Met364Leu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_014845	Q53H49|Q5TCS6	Missense_Mutation	SNP	ENST00000230124.3	37	CCDS5078.1	216	0.0989010989010989	11	0.022357723577235773	30	0.08287292817679558	137	0.2395104895104895	38	0.05013192612137203	A	9.724	1.160495	0.21454	0.021562	0.035698	ENSG00000112367	ENST00000441478;ENST00000230124	T;T	0.40476	1.03;1.03	4.88	4.88	0.63580	Synaptojanin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.04092	0.0114	N	0.00385	-1.57	0.09310	P	0.99999639549	B;B	0.18610	0.0;0.029	B;B	0.16289	0.001;0.015	T	0.28299	-1.0048	9	0.02654	T	1	-12.8017	14.7843	0.69790	1.0:0.0:0.0:0.0	rs2295837;rs2295837	87;364	F5H8L9;Q92562	.;FIG4_HUMAN	L	87;364	ENSP00000399443:M87L;ENSP00000230124:M364L	ENSP00000230124:M364L	M	+	1	0	FIG4	110171621	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.970000	0.93415	1.957000	0.56846	0.528000	0.53228	ATG	A|0.937;T|0.063	0.063	strong		0.438	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845	
IQCK	124152	hgsc.bcm.edu	37	16	19800213	19800213	+	Missense_Mutation	SNP	T	T	C	rs7191155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19800213T>C	ENST00000320394.6	+	8	1358	c.659T>C	c.(658-660)cTc>cCc	p.L220P	IQCK_ENST00000541926.1_Intron|IQCK_ENST00000433597.2_Missense_Mutation_p.L132P|IQCK_ENST00000564186.1_Missense_Mutation_p.L220P|IQCK_ENST00000562762.1_3'UTR	NM_153208.1	NP_694940.1	Q8N0W5	IQCK_HUMAN	IQ motif containing K	220			L -> P (in dbSNP:rs7191155).							kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						GAAGCAGCCCTCTACATTCAA	0.488													T|||	895	0.178714	0.1014	0.111	5008	,	,		17116	0.2133		0.1571	False		,,,				2504	0.318				p.L220P		Atlas-SNP	.											.	IQCK	35	.	0			c.T659C						PASS	.	T	PRO/LEU	429,3965	207.5+/-228.8	29,371,1797	119.0	116.0	117.0		659	5.6	0.0	16	dbSNP_116	117	1508,7092	285.8+/-297.4	150,1208,2942	yes	missense	IQCK	NM_153208.1	98	179,1579,4739	CC,CT,TT		17.5349,9.7633,14.9069	possibly-damaging	220/288	19800213	1937,11057	2197	4300	6497	SO:0001583	missense	124152	exon8			CAGCCCTCTACAT	AF520569	CCDS10580.1	16p12.3	2008-02-05			ENSG00000174628	ENSG00000174628			28556	protein-coding gene	gene with protein product						10493829	Standard	NM_153208		Approved	MGC35048, FLJ36575	uc002dgr.3	Q8N0W5	OTTHUMG00000131453	ENST00000320394.6:c.659T>C	16.37:g.19800213T>C	ENSP00000324901:p.Leu220Pro	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_153208	B2RDU0|O43327|Q8NFF4	Missense_Mutation	SNP	ENST00000320394.6	37	CCDS10580.1	351	0.16071428571428573	75	0.1524390243902439	42	0.11602209944751381	121	0.21153846153846154	113	0.14907651715039577	T	12.64	1.999548	0.35320	0.097633	0.175349	ENSG00000174628	ENST00000320394;ENST00000433597	T;T	0.25579	1.79;1.79	5.61	5.61	0.85477	.	0.587224	0.15180	N	0.276170	T	0.00039	0.0001	L	0.59436	1.845	0.58432	P	4.000000000004E-6	D	0.63880	0.993	P	0.59487	0.858	T	0.11421	-1.0588	8	.	.	.	-7.9261	10.0302	0.42096	0.1502:0.0:0.0:0.8498	rs7191155;rs52798290;rs57181115;rs7191155	220	Q8N0W5	IQCK_HUMAN	P	220;132	ENSP00000324901:L220P;ENSP00000406013:L132P	.	L	+	2	0	IQCK	19707714	0.020000	0.18652	0.003000	0.11579	0.051000	0.14879	2.363000	0.44178	2.125000	0.65367	0.533000	0.62120	CTC	T|0.841;C|0.159	0.159	strong		0.488	IQCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254273.2	NM_153208	
ZSWIM6	57688	hgsc.bcm.edu	37	5	60628414	60628414	+	Silent	SNP	G	G	T	rs111274143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:60628414G>T	ENST00000252744.5	+	1	315	c.315G>T	c.(313-315)gtG>gtT	p.V105V		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	105	Gly-rich.				neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						CGGAGCCGGTGCAGCGCCGCA	0.711													G|||	509	0.101637	0.0794	0.1037	5008	,	,		2581	0.0724		0.1431	False		,,,				2504	0.1176				p.V105V		Atlas-SNP	.											.	ZSWIM6	51	.	0			c.G315T						PASS	.						6.0	11.0	9.0					5																	60628414		679	1570	2249	SO:0001819	synonymous_variant	57688	exon1			GCCGGTGCAGCGC	BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449		"""Zinc fingers, SWIM-type"""	29316	protein-coding gene	gene with protein product		615951				10997877, 16427614	Standard	NM_020928		Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.315G>T	5.37:g.60628414G>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_020928		Silent	SNP	ENST00000252744.5	37	CCDS47215.1																																																																																			G|0.894;T|0.106	0.106	strong		0.711	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368710.1	NM_020928	
PDGFRB	5159	hgsc.bcm.edu	37	5	149499672	149499672	+	Silent	SNP	T	T	C	rs246395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149499672T>C	ENST00000261799.4	-	19	3070	c.2601A>G	c.(2599-2601)ttA>ttG	p.L867L		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	867	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	p.L867L(1)		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)	CCATCCACTTTAAAGGCAAAA	0.572			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""								C|||	1184	0.236422	0.1528	0.2997	5008	,	,		21447	0.1538		0.2903	False		,,,				2504	0.3344				p.L867L		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	PDGFRB,NS,carcinoma,0,1	PDGFRB	142	1	1	Substitution - coding silent(1)	stomach(1)	c.A2601G						PASS	.	C		822,3584	748.8+/-412.0	78,666,1459	84.0	76.0	79.0		2601	2.7	1.0	5	dbSNP_79	79	2833,5767	673.2+/-403.0	457,1919,1924	no	coding-synonymous	PDGFRB	NM_002609.3		535,2585,3383	CC,CT,TT		32.9419,18.6564,28.1024		867/1107	149499672	3655,9351	2203	4300	6503	SO:0001819	synonymous_variant	5159	exon19			CCACTTTAAAGGC	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.2601A>G	5.37:g.149499672T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	54	37	0.685185	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																			T|0.745;C|0.255	0.255	strong		0.572	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
MBOAT7	79143	hgsc.bcm.edu	37	19	54682538	54682538	+	Silent	SNP	C	C	T	rs116423748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54682538C>T	ENST00000245615.1	-	7	1455	c.975G>A	c.(973-975)caG>caA	p.Q325Q	MBOAT7_ENST00000431666.2_Silent_p.Q252Q|MBOAT7_ENST00000338624.6_Silent_p.Q252Q|MBOAT7_ENST00000391754.1_Silent_p.Q325Q	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	325					glycerophospholipid biosynthetic process (GO:0046474)|layer formation in cerebral cortex (GO:0021819)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|ventricular system development (GO:0021591)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipid acyltransferase activity (GO:0071617)			endometrium(4)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	10	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CCAGCCACCACTGCACCGTCA	0.567													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		19150	0.0		0.0	False		,,,				2504	0.0				p.Q325Q	NSCLC(97;826 2151 10470 22540)	Atlas-SNP	.											.	MBOAT7	37	.	0			c.G975A						PASS	.	C	,,,	116,4290	86.3+/-125.0	2,112,2089	85.0	63.0	70.0		756,975,756,975	2.5	1.0	19	dbSNP_132	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MBOAT7	NM_001146056.1,NM_001146082.1,NM_001146083.1,NM_024298.3	,,,	2,113,6388	TT,TC,CC		0.0116,2.6328,0.8996	,,,	252/400,325/345,252/400,325/473	54682538	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	79143	exon7			CCACCACTGCACC	AF211969	CCDS12883.1, CCDS54315.1, CCDS54316.1	19q13.4	2008-12-15	2008-01-17	2008-01-17	ENSG00000125505	ENSG00000125505			15505	protein-coding gene	gene with protein product	"""lysophosphatidylinositol acyltransferase"""	606048	"""leukocyte receptor cluster (LRC) member 4"""	LENG4		10941842, 8702217, 18094042	Standard	NM_024298		Approved	BB1, hMBOA-7, LPIAT	uc002qdr.3	Q96N66	OTTHUMG00000066516	ENST00000245615.1:c.975G>A	19.37:g.54682538C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	121	61	0.504132	NM_001146082	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Silent	SNP	ENST00000245615.1	37	CCDS12883.1																																																																																			C|0.991;T|0.009	0.009	strong		0.567	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298	
NFAM1	150372	hgsc.bcm.edu	37	22	42805444	42805444	+	Missense_Mutation	SNP	G	G	C	rs17003048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42805444G>C	ENST00000329021.5	-	3	598	c.561C>G	c.(559-561)aaC>aaG	p.N187K		NM_145912.5	NP_666017.1	Q8NET5	NFAM1_HUMAN	NFAT activating protein with ITAM motif 1	187			N -> K (in dbSNP:rs17003048).		B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cytokine production (GO:0001819)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of B cell differentiation (GO:0045577)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(3)	4						CCCGTACCTTGTTCCAGAGCA	0.662													C|||	158	0.0315495	0.1157	0.0058	5008	,	,		16803	0.0		0.001	False		,,,				2504	0.0				p.N187K		Atlas-SNP	.											.	NFAM1	12	.	0			c.C561G						PASS	.	C	LYS/ASN	450,3956	785.4+/-414.7	22,406,1775	102.0	96.0	98.0		561	4.8	1.0	22	dbSNP_123	98	3,8597	818.9+/-406.8	0,3,4297	yes	missense	NFAM1	NM_145912.5	94	22,409,6072	CC,CG,GG		0.0349,10.2133,3.483	benign	187/271	42805444	453,12553	2203	4300	6503	SO:0001583	missense	150372	exon3			TACCTTGTTCCAG	BC038241	CCDS14034.1	22q13.2	2005-02-01			ENSG00000235568	ENSG00000235568			29872	protein-coding gene	gene with protein product		608740				12615919	Standard	NM_145912		Approved	CNAIP	uc003bcn.4	Q8NET5	OTTHUMG00000150923	ENST00000329021.5:c.561C>G	22.37:g.42805444G>C	ENSP00000333680:p.Asn187Lys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_145912	B0QYD0|Q20WL2|Q5JZ96|Q8IUY8|Q8TEM8	Missense_Mutation	SNP	ENST00000329021.5	37	CCDS14034.1	55	0.025183150183150184	53	0.10772357723577236	2	0.0055248618784530384	0	0.0	0	0.0	C	0.145	-1.097589	0.01843	0.102133	3.49E-4	ENSG00000235568	ENST00000329021	T	0.18174	2.23	4.8	4.8	0.61643	.	0.000000	0.46145	N	0.000311	T	0.00073	0.0002	N	0.00159	-1.955	0.19300	N	0.99998	B	0.02656	0.0	B	0.01281	0.0	T	0.39354	-0.9618	10	0.02654	T	1	-15.1863	11.2161	0.48827	0.0:0.8139:0.1861:0.0	rs17003048;rs17003048	187	Q8NET5	NFAM1_HUMAN	K	187	ENSP00000333680:N187K	ENSP00000333680:N187K	N	-	3	2	NFAM1	41135388	1.000000	0.71417	1.000000	0.80357	0.058000	0.15608	1.335000	0.33839	1.036000	0.39998	-0.322000	0.08575	AAC	G|0.962;C|0.038	0.038	strong		0.662	NFAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320541.1	NM_145912	
OR52E6	390078	hgsc.bcm.edu	37	11	5862532	5862532	+	Missense_Mutation	SNP	A	A	C	rs10742809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	121	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	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	
DNAH8	1769	hgsc.bcm.edu	37	6	38851669	38851669	+	Silent	SNP	C	C	T	rs4714192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:38851669C>T	ENST00000359357.3	+	54	7757	c.7503C>T	c.(7501-7503)taC>taT	p.Y2501Y	DNAH8_ENST00000441566.1_Silent_p.Y2465Y|DNAH8_ENST00000449981.2_Silent_p.Y2718Y			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2501	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.Y2501Y(1)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTGAAAGCTACGTGGATAAGC	0.363													C|||	1220	0.24361	0.1339	0.2262	5008	,	,		12180	0.3512		0.1978	False		,,,				2504	0.3405				p.Y2718Y		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	1	Substitution - coding silent(1)	stomach(1)	c.C8154T						PASS	.	C		651,3755	277.2+/-273.6	63,525,1615	107.0	108.0	107.0		8154	-1.3	1.0	6	dbSNP_111	107	2078,6522	359.5+/-331.6	244,1590,2466	no	coding-synonymous	DNAH8	NM_001206927.1		307,2115,4081	TT,TC,CC		24.1628,14.7753,20.9826		2718/4708	38851669	2729,10277	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon56			AAGCTACGTGGAT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.7503C>T	6.37:g.38851669C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				C|0.782;T|0.218	0.218	strong		0.363	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
TLR5	7100	hgsc.bcm.edu	37	1	223284528	223284528	+	Missense_Mutation	SNP	A	A	G	rs5744174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:223284528A>G	ENST00000540964.1	-	4	2307	c.1846T>C	c.(1846-1848)Ttc>Ctc	p.F616L	TLR5_ENST00000342210.6_Missense_Mutation_p.F616L			O60602	TLR5_HUMAN	toll-like receptor 5	616	LRRCT.		F -> L (in dbSNP:rs5744174). {ECO:0000269|PubMed:14623910, ECO:0000269|PubMed:16027372, ECO:0000269|PubMed:9596645}.|Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1). {ECO:0000269|PubMed:14623910}.		cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		ACCCCAGAGAACGAGTCAGGG	0.433													G|||	1454	0.290335	0.1089	0.3487	5008	,	,		20738	0.1984		0.4095	False		,,,				2504	0.4663				p.F616L		Atlas-SNP	.											.	TLR5	86	.	0			c.T1846C						PASS	.	G	LEU/PHE	742,3664	756.3+/-412.6	61,620,1522	89.0	91.0	90.0		1846	-11.2	0.0	1	dbSNP_114	90	3610,4990	625.1+/-397.7	738,2134,1428	yes	missense	TLR5	NM_003268.5	22	799,2754,2950	GG,GA,AA		41.9767,16.8407,33.4615	benign	616/859	223284528	4352,8654	2203	4300	6503	SO:0001583	missense	7100	exon6			CAGAGAACGAGTC		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"""Toll/interleukin-1 receptor-like protein 3"""	603031	"""systemic lupus erythematosus susceptibility 1"""	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.1846T>C	1.37:g.223284528A>G	ENSP00000440643:p.Phe616Leu	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	168	70	0.416667	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Missense_Mutation	SNP	ENST00000540964.1	37	CCDS31033.1	604	0.2765567765567766	69	0.1402439024390244	124	0.3425414364640884	104	0.18181818181818182	307	0.4050131926121372	G	0.008	-1.889258	0.00527	0.168407	0.419767	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	T;T;T	0.17213	2.29;2.29;2.29	5.59	-11.2	0.00127	Cysteine-rich flanking region, C-terminal (1);	0.464610	0.24633	N	0.036880	T	0.00012	0.0000	N	0.01003	-1.06	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.25187	-1.0139	9	0.02654	T	1	.	12.7011	0.57034	0.5768:0.2038:0.2194:0.0	rs5744174;rs17748224;rs5744174	616	O60602	TLR5_HUMAN	L	616	ENSP00000440643:F616L;ENSP00000355846:F616L;ENSP00000340089:F616L	ENSP00000340089:F616L	F	-	1	0	TLR5	221351151	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.885000	0.04161	-3.660000	0.00125	-1.702000	0.00720	TTC	A|0.691;G|0.309	0.309	strong		0.433	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268	
RP1L1	94137	hgsc.bcm.edu	37	8	10465942	10465942	+	Missense_Mutation	SNP	T	T	A	rs28446662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10465942T>A	ENST00000382483.3	-	4	5889	c.5666A>T	c.(5665-5667)gAt>gTt	p.D1889V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1969					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)		GGTCTCTACATCTTCTGACTC	0.602													t|||	1189	0.23742	0.1679	0.3386	5008	,	,		16217	0.3929		0.2147	False		,,,				2504	0.1227				p.D1889V		Atlas-SNP	.											.	RP1L1	453	.	0			c.A5666T						PASS	.	T	VAL/ASP	726,3178		68,590,1294	158.0	174.0	169.0		5666	-2.8	0.0	8	dbSNP_125	169	1669,6635		168,1333,2651	no	missense	RP1L1	NM_178857.5	152	236,1923,3945	AA,AT,TT		20.0987,18.5963,19.6183	benign	1889/2401	10465942	2395,9813	1952	4152	6104	SO:0001583	missense	94137	exon4			TCTACATCTTCTG	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.5666A>T	8.37:g.10465942T>A	ENSP00000371923:p.Asp1889Val	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	566	0.2591575091575092	62	0.12601626016260162	102	0.281767955801105	238	0.4160839160839161	164	0.21635883905013192	t	3.686	-0.064495	0.07273	0.185963	0.200987	ENSG00000183638	ENST00000382483	T	0.07688	3.17	1.4	-2.8	0.05823	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.46105	-0.9215	8	0.30078	T	0.28	.	4.5421	0.12064	0.0:0.1945:0.191:0.6145	rs28446662	1889	A6NKC6	.	V	1889	ENSP00000371923:D1889V	ENSP00000371923:D1889V	D	-	2	0	RP1L1	10503352	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.203000	0.03019	-0.837000	0.04223	-0.375000	0.07067	GAT	T|0.764;A|0.236	0.236	strong		0.602	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
GABRP	2568	hgsc.bcm.edu	37	5	170215670	170215670	+	Silent	SNP	G	G	A	rs7725726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:170215670G>A	ENST00000518525.1	+	3	515	c.51G>A	c.(49-51)gaG>gaA	p.E17E	GABRP_ENST00000519385.1_Silent_p.E17E|GABRP_ENST00000519598.1_Silent_p.E17E|GABRP_ENST00000265294.4_Silent_p.E17E|MIR4454_ENST00000518172.1_RNA			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	17					signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCTTCACTGAGAGGTGAGCTT	0.552													A|||	1230	0.245607	0.5159	0.1816	5008	,	,		17601	0.1647		0.0696	False		,,,				2504	0.1902				p.E17E		Atlas-SNP	.											.	GABRP	65	.	0			c.G51A						PASS	.	A		1984,2422	616.5+/-392.8	444,1096,663	176.0	160.0	165.0		51	-1.2	0.0	5	dbSNP_116	165	618,7982	791.8+/-407.5	22,574,3704	no	coding-synonymous	GABRP	NM_014211.2		466,1670,4367	AA,AG,GG		7.186,45.0295,20.0062		17/441	170215670	2602,10404	2203	4300	6503	SO:0001819	synonymous_variant	2568	exon2			CACTGAGAGGTGA	U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4089	protein-coding gene	gene with protein product	"""GABA(A) receptor, pi"""	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.51G>A	5.37:g.170215670G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_014211	A8KA36|D3DQL2|Q32MJ1	Silent	SNP	ENST00000518525.1	37	CCDS4375.1																																																																																			G|0.788;A|0.212	0.212	strong		0.552	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211	
PPP1R1C	151242	hgsc.bcm.edu	37	2	182981968	182981968	+	Silent	SNP	A	A	G	rs1882212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000409702.1_Silent_p.A92A|PPP1R1C_ENST00000280295.3_Silent_p.A99A|PPP1R1C_ENST00000475249.1_Intron	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	307	2	0.00651466		WXS	Illumina HiSeq	Phase_I	321	321	1	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	
TCEAL5	340543	hgsc.bcm.edu	37	X	102529190	102529190	+	Missense_Mutation	SNP	C	C	G	rs6621640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102529190C>G	ENST00000372680.1	-	3	596	c.302G>C	c.(301-303)cGg>cCg	p.R101P		NM_001012979.2	NP_001012997.1	Q5H9L2	TCAL5_HUMAN	transcription elongation factor A (SII)-like 5	101					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	11						TTCGGCGGCCCGCGGCTGGCT	0.597													C||||C|||	556|556	0.147285|0.147285	0.2867|0.2867	0.0504|0.0504	3775|3775	,|,	,|,		11271|11271	0.1091|0.1091		0.008|0.008	False|False		,,,|,,,				2504|2504	0.0245|0.0245				p.R101P		Atlas-SNP	.											.	TCEAL5	28	.	0			c.G302C						PASS	.	C	PRO/ARG	1306,2528		250,614,192,768,378	76.0	85.0	82.0		302	-1.1	0.0	X	dbSNP_116	82	81,6647		2,55,22,2371,1850	no	missense	TCEAL5	NM_001012979.2	103	252,669,214,3139,2228	GG,GC,G,CC,C		1.2039,34.0636,13.132	probably-damaging	101/207	102529190	1387,9175	2202	4300	6502	SO:0001583	missense	340543	exon3			GCGGCCCGCGGCT		CCDS35356.1	Xq22.2	2014-03-21			ENSG00000204065	ENSG00000204065			22282	protein-coding gene	gene with protein product						16221301	Standard	NM_001012979		Approved	WEX4	uc004ejz.2	Q5H9L2	OTTHUMG00000022092	ENST00000372680.1:c.302G>C	X.37:g.102529190C>G	ENSP00000361765:p.Arg101Pro	Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	349	205	0.587393	NM_001012979	A2RUJ4	Missense_Mutation	SNP	ENST00000372680.1	37	CCDS35356.1	223	0.13441832429174203	107	0.25970873786407767	14	0.040229885057471264	31	0.05762081784386617	5	0.006631299734748011	C	18.09	3.547358	0.65311	0.340636	0.012039	ENSG00000204065	ENST00000372680	T	0.26660	1.72	2.93	-1.09	0.09904	.	0.000000	0.33534	N	0.004804	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	D	0.89917	1.0	D	0.76071	0.987	T	0.21552	-1.0242	9	0.49607	T	0.09	.	2.6606	0.05026	0.2162:0.3639:0.0:0.4199	rs6621640	101	Q5H9L2	TCAL5_HUMAN	P	101	ENSP00000361765:R101P	ENSP00000361765:R101P	R	-	2	0	TCEAL5	102415846	0.000000	0.05858	0.000000	0.03702	0.886000	0.51366	-0.535000	0.06142	-0.424000	0.07382	0.292000	0.19580	CGG	C|0.861;G|0.139	0.139	strong		0.597	TCEAL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057696.1	XM_291334	
OR10S1	219873	hgsc.bcm.edu	37	11	123848212	123848212	+	Missense_Mutation	SNP	C	C	T	rs17759513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123848212C>T	ENST00000531945.1	-	1	276	c.187G>A	c.(187-189)Ggc>Agc	p.G63S		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	63			G -> S (in dbSNP:rs17759513).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		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)		GAGTCAGAGCCCACAGTTAGG	0.527													C|||	867	0.173123	0.1301	0.2147	5008	,	,		22925	0.1171		0.2903	False		,,,				2504	0.1391				p.G63S		Atlas-SNP	.											.	OR10S1	78	.	0			c.G187A						PASS	.	C	SER/GLY	660,3744	281.1+/-275.7	45,570,1587	71.0	63.0	66.0		187	1.9	1.0	11	dbSNP_123	66	2219,6379	374.8+/-337.5	296,1627,2376	yes	missense	OR10S1	NM_001004474.1	56	341,2197,3963	TT,TC,CC		25.8083,14.9864,22.1427	benign	63/332	123848212	2879,10123	2202	4299	6501	SO:0001583	missense	219873	exon1			CAGAGCCCACAGT	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"""GPCR / Class A : Olfactory receptors"""	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.187G>A	11.37:g.123848212C>T	ENSP00000431914:p.Gly63Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	63	23	0.365079	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	37	CCDS31701.1	433	0.19826007326007325	65	0.13211382113821138	87	0.24033149171270718	73	0.12762237762237763	208	0.27440633245382584	C	9.701	1.154552	0.21371	0.149864	0.258083	ENSG00000196248	ENST00000531945	T	0.01076	5.37	4.84	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	1.379400	0.05329	U	0.527956	T	0.00012	0.0000	N	0.03930	-0.32	0.52099	P	5.900000000003125E-5	B	0.14438	0.01	B	0.08055	0.003	T	0.41680	-0.9495	9	0.22109	T	0.4	-6.4442	4.5215	0.11960	0.1454:0.5349:0.0:0.3197	rs17759513;rs52797693;rs60266391;rs17759513	63	Q8NGN2	O10S1_HUMAN	S	63	ENSP00000431914:G63S	ENSP00000431914:G63S	G	-	1	0	OR10S1	123353422	0.000000	0.05858	0.998000	0.56505	0.996000	0.88848	-0.391000	0.07323	0.668000	0.31126	0.638000	0.83543	GGC	C|0.792;N|0.000	.	strong		0.527	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474	
CDT1	81620	hgsc.bcm.edu	37	16	88872229	88872229	+	Missense_Mutation	SNP	A	A	G	rs480727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88872229A>G	ENST00000301019.4	+	5	1403	c.784A>G	c.(784-786)Acc>Gcc	p.T262A		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)		CAAGGATGGCACCAGGAGGTC	0.597													G|||	2861	0.571286	0.7526	0.5043	5008	,	,		15961	0.7024		0.3897	False		,,,				2504	0.4254				p.T262A	Melanoma(159;511 3380 30971)	Atlas-SNP	.											.	CDT1	30	.	0			c.A784G						PASS	.	G	ALA/THR	3130,1260	420.8+/-339.2	1114,902,179	42.0	44.0	44.0		784	-1.3	0.0	16	dbSNP_83	44	3304,5292	638.8+/-399.4	620,2064,1614	yes	missense	CDT1	NM_030928.3	58	1734,2966,1793	GG,GA,AA		38.4365,28.7016,49.5457	benign	262/547	88872229	6434,6552	2195	4298	6493	SO:0001583	missense	81620	exon5			GATGGCACCAGGA	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.784A>G	16.37:g.88872229A>G	ENSP00000301019:p.Thr262Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_030928		Missense_Mutation	SNP	ENST00000301019.4	37	CCDS32510.1	1239	0.5673076923076923	362	0.7357723577235772	171	0.4723756906077348	416	0.7272727272727273	290	0.38258575197889183	G	0.050	-1.252044	0.01469	0.712984	0.384365	ENSG00000167513	ENST00000301019	T	0.24723	1.84	4.83	-1.33	0.09172	.	0.865536	0.10187	N	0.705131	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.12156	0.007	T	0.28490	-1.0042	9	0.16420	T	0.52	.	5.5378	0.17021	0.3888:0.0:0.4893:0.1219	rs480727;rs3169256;rs60443747;rs480727	262	Q9H211	CDT1_HUMAN	A	262	ENSP00000301019:T262A	ENSP00000301019:T262A	T	+	1	0	CDT1	87399730	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.763000	0.04740	-0.900000	0.03896	-0.355000	0.07637	ACC	A|0.452;G|0.548	0.548	strong		0.597	CDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423215.1	NM_030928	
HIPK1	204851	hgsc.bcm.edu	37	1	114505000	114505000	+	Silent	SNP	G	G	A	rs17852555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:114505000G>A	ENST00000369558.1	+	9	2275	c.2043G>A	c.(2041-2043)ccG>ccA	p.P681P	HIPK1_ENST00000369554.2_Silent_p.P681P|HIPK1_ENST00000369553.1_Silent_p.P287P|HIPK1_ENST00000426820.2_Silent_p.P681P|HIPK1_ENST00000406344.1_Silent_p.P287P|HIPK1_ENST00000369561.4_Silent_p.P647P|HIPK1_ENST00000369555.2_Silent_p.P681P|HIPK1_ENST00000340480.4_Silent_p.P307P|HIPK1_ENST00000369559.4_Silent_p.P681P			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	681					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)		ATGCTGTACCGATTGTACCCC	0.448													A|||	1189	0.23742	0.351	0.196	5008	,	,		18319	0.245		0.2286	False		,,,				2504	0.1145				p.P681P		Atlas-SNP	.											.	HIPK1	195	.	0			c.G2043A						PASS	.	A	,,,	1435,2971	683.7+/-404.3	233,969,1001	109.0	102.0	104.0		2043,861,2043,921	-0.7	1.0	1	dbSNP_123	104	2085,6515	718.0+/-406.2	251,1583,2466	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HIPK1	NM_152696.3,NM_181358.2,NM_198268.2,NM_198269.2	,,,	484,2552,3467	AA,AG,GG		24.2442,32.5692,27.0644	,,,	681/1076,287/817,681/1211,307/837	114505000	3520,9486	2203	4300	6503	SO:0001819	synonymous_variant	204851	exon9			TGTACCGATTGTA	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.2043G>A	1.37:g.114505000G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	143	67	0.468531	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Silent	SNP	ENST00000369558.1	37	CCDS867.1																																																																																			G|0.743;A|0.257	0.257	strong		0.448	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268	
FRZB	2487	hgsc.bcm.edu	37	2	183702691	183702691	+	Silent	SNP	G	G	A	rs1561367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:183702691G>A	ENST00000295113.4	-	5	1455	c.846C>T	c.(844-846)ctC>ctT	p.L282L		NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein	282	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			CTTTTTTACCGAGTCGATCCT	0.328													G|||	15	0.00299521	0.0113	0.0	5008	,	,		17089	0.0		0.0	False		,,,				2504	0.0				p.L282L		Atlas-SNP	.											.	FRZB	42	.	0			c.C846T						PASS	.	G		60,4346	57.4+/-93.9	0,60,2143	80.0	75.0	77.0		846	1.7	1.0	2	dbSNP_88	77	0,8600		0,0,4300	no	coding-synonymous	FRZB	NM_001463.3		0,60,6443	AA,AG,GG		0.0,1.3618,0.4613		282/326	183702691	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	2487	exon5			TTTACCGAGTCGA	U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"""Secreted frizzled-related proteins"""	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.846C>T	2.37:g.183702691G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_001463	O00181|Q99686	Silent	SNP	ENST00000295113.4	37	CCDS2286.1																																																																																			G|0.997;A|0.003	0.003	strong		0.328	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463	
UTP3	57050	hgsc.bcm.edu	37	4	71555656	71555656	+	Missense_Mutation	SNP	T	T	G	rs111975570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71555656T>G	ENST00000254803.2	+	1	1461	c.1262T>G	c.(1261-1263)cTt>cGt	p.L421R		NM_020368.2	NP_065101.1	Q9NQZ2	SAS10_HUMAN	UTP3, small subunit (SSU) processome component, homolog (S. cerevisiae)	421					brain development (GO:0007420)|chromatin modification (GO:0016568)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(4)	18			Lung(101;0.235)			AATAGGGGACTTACTCCTAGG	0.388													T|||	36	0.0071885	0.0272	0.0	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.L421R		Atlas-SNP	.											.	UTP3	40	.	0			c.T1262G						PASS	.	T	ARG/LEU	64,4342	61.1+/-98.1	0,64,2139	89.0	95.0	93.0		1262	5.5	1.0	4	dbSNP_132	93	0,8600		0,0,4300	yes	missense	UTP3	NM_020368.2	102	0,64,6439	GG,GT,TT		0.0,1.4526,0.4921	probably-damaging	421/480	71555656	64,12942	2203	4300	6503	SO:0001583	missense	57050	exon1			GGGGACTTACTCC	AL136590	CCDS3546.1	4q13.3	2008-02-05			ENSG00000132467	ENSG00000132467			24477	protein-coding gene	gene with protein product	"""disrupter of silencing 10"""	611614				12477932	Standard	NM_020368		Approved	FLJ23256, DKFZp761F222, SAS10, CRLZ1	uc003hfo.3	Q9NQZ2	OTTHUMG00000129911	ENST00000254803.2:c.1262T>G	4.37:g.71555656T>G	ENSP00000254803:p.Leu421Arg	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_020368	Q6FI82	Missense_Mutation	SNP	ENST00000254803.2	37	CCDS3546.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	T	20.6	4.011830	0.75046	0.014526	0.0	ENSG00000132467	ENST00000254803	T	0.62788	-0.0	5.46	5.46	0.80206	Something about silencing protein 10 (Sas10), C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70710	0.3255	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85360	0.1107	10	0.72032	D	0.01	-6.9132	15.8384	0.78818	0.0:0.0:0.0:1.0	.	421	Q9NQZ2	SAS10_HUMAN	R	421	ENSP00000254803:L421R	ENSP00000254803:L421R	L	+	2	0	UTP3	71774520	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.366000	0.79548	2.191000	0.70037	0.533000	0.62120	CTT	T|0.994;G|0.006	0.006	strong		0.388	UTP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252163.2	NM_020368	
ATOH1	474	hgsc.bcm.edu	37	4	94750227	94750227	+	Silent	SNP	G	G	A	rs138388359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:94750227G>A	ENST00000306011.3	+	1	186	c.150G>A	c.(148-150)ccG>ccA	p.P50P		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	50					auditory receptor cell fate determination (GO:0042668)|auditory receptor cell fate specification (GO:0042667)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|cerebral cortex development (GO:0021987)|inner ear morphogenesis (GO:0042472)|negative regulation of apoptotic process (GO:0043066)|neuron migration (GO:0001764)|positive regulation of auditory receptor cell differentiation (GO:0045609)|positive regulation of neuron differentiation (GO:0045666)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|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)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)		CCGTCTACCCGCCTGAGCTGT	0.672													G|||	8	0.00159744	0.0061	0.0	5008	,	,		13999	0.0		0.0	False		,,,				2504	0.0				p.P50P		Atlas-SNP	.											.	ATOH1	40	.	0			c.G150A						PASS	.	G		30,4376	32.6+/-62.9	0,30,2173	34.0	36.0	35.0		150	-6.8	0.4	4	dbSNP_134	35	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	ATOH1	NM_005172.1		0,31,6470	AA,AG,GG		0.0116,0.6809,0.2384		50/355	94750227	31,12971	2203	4298	6501	SO:0001819	synonymous_variant	474	exon1			CTACCCGCCTGAG	U61148	CCDS3638.1	4q22	2013-05-21			ENSG00000172238	ENSG00000172238		"""Basic helix-loop-helix proteins"""	797	protein-coding gene	gene with protein product		601461				8872459	Standard	NM_005172		Approved	HATH1, MATH-1, Math1, bHLHa14	uc003hta.1	Q92858	OTTHUMG00000130972	ENST00000306011.3:c.150G>A	4.37:g.94750227G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_005172	Q14CT9	Silent	SNP	ENST00000306011.3	37	CCDS3638.1																																																																																			A|0.001;G|0.999;T|0.000	0.001	strong		0.672	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172	
SRCIN1	80725	hgsc.bcm.edu	37	17	36708277	36708277	+	Missense_Mutation	SNP	C	C	T	rs7222929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36708277C>T	ENST00000264659.7	-	14	2796	c.2572G>A	c.(2572-2574)Gtg>Atg	p.V858M	SRCIN1_ENST00000578925.1_Missense_Mutation_p.V892M|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	730	Pro-rich.				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)	p.V858M(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						TCGAAGTCCACGCTCTTGTTG	0.622													C|||	237	0.0473243	0.1679	0.0144	5008	,	,		17220	0.0		0.0	False		,,,				2504	0.0051				p.V858M		Atlas-SNP	.											SRCIN1,rectum,carcinoma,0,1	SRCIN1	66	1	1	Substitution - Missense(1)	large_intestine(1)	c.G2572A						scavenged	.	C	MET/VAL	600,3358		49,502,1428	40.0	47.0	45.0		2572	-1.4	0.4	17	dbSNP_116	45	10,8258		0,10,4124	yes	missense	SRCIN1	NM_025248.2	21	49,512,5552	TT,TC,CC		0.1209,15.1592,4.9894	benign	858/1184	36708277	610,11616	1979	4134	6113	SO:0001583	missense	80725	exon14			AGTCCACGCTCTT		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.2572G>A	17.37:g.36708277C>T	ENSP00000264659:p.Val858Met	Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_025248	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	37	CCDS45660.1	90	0.04120879120879121	84	0.17073170731707318	6	0.016574585635359115	0	0.0	0	0.0	C	6.675	0.493112	0.12702	0.151592	0.001209	ENSG00000017373	ENST00000264659;ENST00000542707;ENST00000398579	T	0.43688	0.94	4.69	-1.42	0.08913	.	0.364146	0.27420	N	0.019451	T	0.00039	0.0001	L	0.29908	0.895	0.51233	P	8.900000000000574E-5	P;B;B;B	0.36110	0.537;0.216;0.216;0.015	B;B;B;B	0.13407	0.009;0.004;0.004;0.002	T	0.14671	-1.0464	9	0.44086	T	0.13	-10.5966	0.5426	0.00648	0.3992:0.1273:0.2332:0.2403	rs7222929;rs52804512;rs7222929	164;730;730;858	Q9C0H9-4;Q9C0H9-2;Q9C0H9;Q9C0H9-5	.;.;SRCN1_HUMAN;.	M	858;639;712	ENSP00000264659:V858M	ENSP00000264659:V858M	V	-	1	0	SRCIN1	33961803	0.447000	0.25673	0.424000	0.26647	0.293000	0.27360	-0.300000	0.08243	-0.160000	0.11002	-1.334000	0.01262	GTG	C|0.930;T|0.070	0.070	strong		0.622	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248	
MUC17	140453	hgsc.bcm.edu	37	7	100677556	100677556	+	Silent	SNP	A	A	C	rs4373459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677556A>C	ENST00000306151.4	+	3	2923	c.2859A>C	c.(2857-2859)acA>acC	p.T953T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	953	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)					ACACCAGCACACCTGTGACCA	0.498																																					p.T953T		Atlas-SNP	.											MUC17,colon,carcinoma,0,1	MUC17	804	1	0			c.A2859C						scavenged	.	A		426,3980	162.9+/-194.8	0,426,1777	317.0	293.0	301.0		2859	-0.2	0.0	7	dbSNP_111	301	518,8082	119.5+/-178.9	0,518,3782	no	coding-synonymous	MUC17	NM_001040105.1		0,944,5559	CC,CA,AA		6.0233,9.6686,7.2582		953/4494	100677556	944,12062	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CAGCACACCTGTG	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.2859A>C	7.37:g.100677556A>C		Somatic	153	3	0.0196078		WXS	Illumina HiSeq	Phase_I	245	62	0.253061	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			A|0.947;C|0.053	0.053	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PLD1	5337	hgsc.bcm.edu	37	3	171320907	171320907	+	Silent	SNP	C	C	T	rs6766336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:171320907C>T	ENST00000351298.4	-	27	3312	c.3186G>A	c.(3184-3186)ggG>ggA	p.G1062G	PLD1_ENST00000342215.6_3'UTR|PLD1_ENST00000356327.5_Silent_p.G1024G	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	1062					chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	CCTCTTTGGTCCCAACAGAAG	0.473													T|||	243	0.0485224	0.1657	0.0202	5008	,	,		19816	0.0		0.007	False		,,,				2504	0.0031				p.G1062G	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.G3186A						PASS	.	T	,	651,3755	765.8+/-413.4	44,563,1596	94.0	94.0	94.0		3072,3186	3.7	1.0	3	dbSNP_116	94	116,8484	814.2+/-407.0	1,114,4185	no	coding-synonymous,coding-synonymous	PLD1	NM_001130081.2,NM_002662.4	,	45,677,5781	TT,TC,CC		1.3488,14.7753,5.8973	,	1024/1037,1062/1075	171320907	767,12239	2203	4300	6503	SO:0001819	synonymous_variant	5337	exon27			TTTGGTCCCAACA	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.3186G>A	3.37:g.171320907C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_002662		Silent	SNP	ENST00000351298.4	37	CCDS3216.1																																																																																			C|0.942;T|0.058	0.058	strong		0.473	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
PRSS36	146547	hgsc.bcm.edu	37	16	31151622	31151622	+	Missense_Mutation	SNP	C	C	T	rs61729752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31151622C>T	ENST00000268281.4	-	14	2340	c.2282G>A	c.(2281-2283)aGg>aAg	p.R761K	PRSS36_ENST00000418068.2_Intron|PRSS36_ENST00000569305.1_Missense_Mutation_p.R756K	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	761	Peptidase S1 3. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						TACCTCACACCTGTTCTCCTG	0.537													c|||	78	0.0155751	0.0545	0.0086	5008	,	,		17560	0.0		0.0	False		,,,				2504	0.0				p.R761K		Atlas-SNP	.											.	PRSS36	50	.	0			c.G2282A						PASS	.		LYS/ARG	237,4157	139.6+/-175.2	8,221,1968	57.0	54.0	55.0		2282	2.9	1.0	16	dbSNP_129	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PRSS36	NM_173502.3	26	8,222,6267	TT,TC,CC		0.0116,5.3937,1.8316	benign	761/856	31151622	238,12756	2197	4300	6497	SO:0001583	missense	146547	exon14			TCACACCTGTTCT	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"""Serine peptidases / Serine peptidases"""	26906	protein-coding gene	gene with protein product	"""polyserase 2"""	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.2282G>A	16.37:g.31151622C>T	ENSP00000268281:p.Arg761Lys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_173502	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	37	CCDS32436.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	10.18	1.279325	0.23307	0.053937	1.16E-4	ENSG00000178226	ENST00000268281	T	0.58940	0.3	4.92	2.86	0.33363	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.07818	0.0196	L	0.40543	1.245	0.21740	N	0.99957	B;B	0.09022	0.002;0.002	B;B	0.12156	0.007;0.007	T	0.12967	-1.0527	9	0.59425	D	0.04	.	6.1003	0.20043	0.0:0.7536:0.0:0.2464	.	756;761	B7ZMK8;Q5K4E3	.;POLS2_HUMAN	K	761	ENSP00000268281:R761K	ENSP00000268281:R761K	R	-	2	0	PRSS36	31059123	0.001000	0.12720	1.000000	0.80357	0.981000	0.71138	-0.769000	0.04710	1.125000	0.41998	0.555000	0.69702	AGG	C|0.982;T|0.018	0.018	strong		0.537	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502	
CCDC168	643677	hgsc.bcm.edu	37	13	103387667	103387667	+	Missense_Mutation	SNP	G	G	A	rs79455872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103387667G>A	ENST00000322527.2	-	1	1492	c.1493C>T	c.(1492-1494)tCa>tTa	p.S498L		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	498																	TACATCACTTGAAAGTTCTCC	0.428													G|||	160	0.0319489	0.1172	0.0043	5008	,	,		21385	0.0		0.001	False		,,,				2504	0.001				p.S5127L		Atlas-SNP	.											.	.	.	.	0			c.C15380T						PASS	.	G	LEU/SER	166,1218		11,144,537	93.0	72.0	78.0		15380	0.7	0.0	13	dbSNP_132	78	6,3176		0,6,1585	yes	missense	CCDC168	NM_001146197.1	145	11,150,2122	AA,AG,GG		0.1886,11.9942,3.767	probably-damaging	5127/7082	103387667	172,4394	692	1591	2283	SO:0001583	missense	643677	exon4			TCACTTGAAAGTT		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.1493C>T	13.37:g.103387667G>A	ENSP00000320232:p.Ser498Leu	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	286	132	0.461538	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		57	0.0260989010989011	56	0.11382113821138211	1	0.0027624309392265192	0	0.0	0	0.0	G	13.70	2.316654	0.40996	0.119942	0.001886	ENSG00000175820	ENST00000322527	T	0.03580	3.88	3.59	0.657	0.17850	.	0.303088	0.18152	N	0.150052	T	0.00109	0.0003	L	0.54323	1.7	0.09310	N	1	D	0.61697	0.99	P	0.58077	0.832	T	0.40040	-0.9584	10	0.21014	T	0.42	.	6.3169	0.21196	0.0:0.3699:0.4233:0.2068	.	498	Q8NDH2	CC168_HUMAN	L	498	ENSP00000320232:S498L	ENSP00000320232:S498L	S	-	2	0	CCDC168	102185668	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	0.183000	0.16919	0.082000	0.17018	0.467000	0.42956	TCA	G|0.970;A|0.030	0.030	strong		0.428	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
SIRPB1	10326	hgsc.bcm.edu	37	20	1552457	1552457	+	Silent	SNP	G	G	A	rs16995332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1552457G>A	ENST00000381605.4	-	3	724	c.660C>T	c.(658-660)gaC>gaT	p.D220D	SIRPB1_ENST00000262929.5_Intron|SIRPB1_ENST00000381603.3_Intron|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	220	Ig-like C1-type 1.				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						GAGAGTGAACGTCCCCACGGG	0.587													.|||	341	0.0680911	0.0832	0.0576	5008	,	,		20250	0.002		0.1382	False		,,,				2504	0.0511				p.D220D		Atlas-SNP	.											.	SIRPB1	83	.	0			c.C660T						PASS	.	G	,	407,3999		16,375,1812	161.0	140.0	147.0		,660	-2.7	0.0	20	dbSNP_123	147	1134,7466		74,986,3240	no	intron,coding-synonymous	SIRPB1	NM_001083910.2,NM_006065.3	,	90,1361,5052	AA,AG,GG		13.186,9.2374,11.8484	,	,220/399	1552457	1541,11465	2203	4300	6503	SO:0001819	synonymous_variant	10326	exon3			GTGAACGTCCCCA	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.660C>T	20.37:g.1552457G>A		Somatic	672	0	0		WXS	Illumina HiSeq	Phase_I	688	344	0.5	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			G|0.896;A|0.104	0.104	strong		0.587	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
OVGP1	5016	hgsc.bcm.edu	37	1	111957693	111957693	+	Missense_Mutation	SNP	A	A	G	rs2485319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	292	0	0		WXS	Illumina HiSeq	Phase_I	288	134	0.465278	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	
CTC1	80169	hgsc.bcm.edu	37	17	8141779	8141779	+	Silent	SNP	T	T	C	rs73244859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8141779T>C	ENST00000315684.8	-	3	373	c.366A>G	c.(364-366)gcA>gcG	p.A122A	CTC1_ENST00000581671.1_5'UTR	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	122					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						GTTCCAAGTCTGCCGATAGGT	0.547													C|||	111	0.0221645	0.0787	0.0	5008	,	,		19305	0.003		0.001	False		,,,				2504	0.0031				p.A122A		Atlas-SNP	.											.	CTC1	75	.	0			c.A366G						PASS	.	C		248,3754		8,232,1761	125.0	125.0	125.0		366	1.5	0.0	17	dbSNP_130	125	0,8334		0,0,4167	no	coding-synonymous	CTC1	NM_025099.5		8,232,5928	CC,CT,TT		0.0,6.1969,2.0104		122/1218	8141779	248,12088	2001	4167	6168	SO:0001819	synonymous_variant	80169	exon3			CAAGTCTGCCGAT	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.366A>G	17.37:g.8141779T>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	201	102	0.507463	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	37	CCDS42259.1																																																																																			T|0.984;C|0.016	0.016	strong		0.547	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
TNXB	7148	hgsc.bcm.edu	37	6	32014190	32014190	+	Silent	SNP	G	G	A	rs116701346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32014190G>A	ENST00000375244.3	-	31	10569	c.10368C>T	c.(10366-10368)acC>acT	p.T3456T	TNXB_ENST00000375247.2_Silent_p.T3454T|TNXB_ENST00000451343.1_5'Flank			P22105	TENX_HUMAN	tenascin XB	3501	Fibronectin type-III 26. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCTCAGCCACGGTCAGTTCCC	0.632													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		18563	0.0		0.0	False		,,,				2504	0.0				p.T3454T		Atlas-SNP	.											.	TNXB	553	.	0			c.C10362T						PASS	.	G		13,2817		0,13,1402	27.0	32.0	30.0		10362	-4.5	0.2	6	dbSNP_132	30	2,5274		0,2,2636	no	coding-synonymous	TNXB	NM_019105.6		0,15,4038	AA,AG,GG		0.0379,0.4594,0.185		3454/4243	32014190	15,8091	1415	2638	4053	SO:0001819	synonymous_variant	7148	exon31			AGCCACGGTCAGT	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.10368C>T	6.37:g.32014190G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	47	0.594937	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				G|0.996;A|0.004	0.004	strong		0.632	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
ZNF429	353088	hgsc.bcm.edu	37	19	21719401	21719401	+	Silent	SNP	T	T	C	rs35782355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21719401T>C	ENST00000358491.4	+	4	754	c.546T>C	c.(544-546)ttT>ttC	p.F182F	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	182					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						GCAAATCATTTTGCATGCTTT	0.328													t|||	2793	0.557708	0.4781	0.5288	5008	,	,		20186	0.6389		0.5388	False		,,,				2504	0.6217				p.F182F		Atlas-SNP	.											.	ZNF429	338	.	0			c.T546C						PASS	.	T		2049,2339		493,1063,638	49.0	52.0	51.0		546	0.2	0.2	19	dbSNP_126	51	4797,3801		1380,2037,882	no	coding-synonymous	ZNF429	NM_001001415.2		1873,3100,1520	CC,CT,TT		44.208,46.6955,47.2817		182/675	21719401	6846,6140	2194	4299	6493	SO:0001819	synonymous_variant	353088	exon4			ATCATTTTGCATG	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"""Zinc fingers, C2H2-type"", ""-"""	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.546T>C	19.37:g.21719401T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_001001415	A6NLV7|Q9BZE6	Silent	SNP	ENST00000358491.4	37	CCDS42537.1																																																																																			T|0.444;C|0.556	0.556	strong		0.328	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415	
PLEKHN1	84069	hgsc.bcm.edu	37	1	902128	902128	+	Missense_Mutation	SNP	C	C	T	rs28499371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:902128C>T	ENST00000379409.2	+	2	158	c.128C>T	c.(127-129)gCt>gTt	p.A43V	PLEKHN1_ENST00000379410.3_Missense_Mutation_p.A43V|PLEKHN1_ENST00000379407.3_Missense_Mutation_p.A43V			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	43										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)		GGCCCCGAGGCTGCTCGAAGC	0.726													C|||	281	0.0561102	0.0295	0.0922	5008	,	,		12661	0.1409		0.003	False		,,,				2504	0.0337				p.A43V		Atlas-SNP	.											.	PLEKHN1	49	.	0			c.C128T						PASS	.	C	VAL/ALA,VAL/ALA	103,4037		1,101,1968	6.0	9.0	8.0		128,128	1.7	0.1	1	dbSNP_125	8	16,8166		0,16,4075	yes	missense,missense	PLEKHN1	NM_001160184.1,NM_032129.2	64,64	1,117,6043	TT,TC,CC		0.1956,2.4879,0.9658	possibly-damaging,possibly-damaging	43/577,43/612	902128	119,12203	2070	4091	6161	SO:0001583	missense	84069	exon2			CCGAGGCTGCTCG	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.128C>T	1.37:g.902128C>T	ENSP00000368719:p.Ala43Val	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	15	6	0.4	NM_001160184	Q494U2|Q5SV98|Q9H0M7	Missense_Mutation	SNP	ENST00000379409.2	37		135	0.061813186813186816	17	0.034552845528455285	28	0.07734806629834254	88	0.15384615384615385	2	0.002638522427440633	C	11.69	1.714499	0.30413	0.024879	0.001956	ENSG00000187583	ENST00000379410;ENST00000379407;ENST00000379409	T;T;T	0.52057	0.7;0.7;0.68	5.01	1.74	0.24563	.	0.656433	0.13318	N	0.396910	T	0.00210	0.0006	L	0.32530	0.975	0.80722	P	0.0	B;B;B	0.28350	0.033;0.208;0.11	B;B;B	0.26202	0.067;0.063;0.018	T	0.06954	-1.0798	9	0.62326	D	0.03	.	6.8953	0.24253	0.0:0.6193:0.1899:0.1909	rs28499371	43;43;43	Q494U1-3;Q494U1;Q494U1-2	.;PKHN1_HUMAN;.	V	43	ENSP00000368720:A43V;ENSP00000368717:A43V;ENSP00000368719:A43V	ENSP00000368717:A43V	A	+	2	0	PLEKHN1	891991	0.000000	0.05858	0.098000	0.21074	0.024000	0.10985	-0.081000	0.11321	0.510000	0.28216	0.558000	0.71614	GCT	C|0.935;T|0.065	0.065	strong		0.726	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129	
RPH3AL	9501	hgsc.bcm.edu	37	17	171098	171098	+	Silent	SNP	T	T	G	rs73971738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:171098T>G	ENST00000331302.7	-	4	493	c.186A>C	c.(184-186)gcA>gcC	p.A62A	RPH3AL_ENST00000576001.1_5'Flank|RP11-1260E13.1_ENST00000570501.1_RNA|RPH3AL_ENST00000323434.8_Silent_p.A62A|RPH3AL_ENST00000536489.2_Silent_p.A62A|RP11-1260E13.1_ENST00000572998.1_RNA	NM_001190411.1|NM_006987.3	NP_001177340.1|NP_008918.1	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	62	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of protein secretion (GO:0050714)|regulation of calcium ion-dependent exocytosis (GO:0017158)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|secretory granule membrane (GO:0030667)	cytoskeletal protein binding (GO:0008092)|metal ion binding (GO:0046872)			NS(2)|breast(1)|kidney(1)|large_intestine(1)|skin(1)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		CGAGCCGCTCTGCCCTCTGGA	0.682													G|||	700	0.139776	0.2708	0.0893	5008	,	,		13780	0.0536		0.1173	False		,,,				2504	0.1104				p.A62A		Atlas-SNP	.											.	RPH3AL	18	.	0			c.A186C						PASS	.	G	,,,	1093,3313	720.2+/-409.0	124,845,1234	85.0	85.0	85.0		186,186,186,186	-5.0	0.9	17	dbSNP_130	85	1079,7521	768.7+/-407.6	73,933,3294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RPH3AL	NM_001190411.1,NM_001190412.1,NM_001190413.1,NM_006987.3	,,,	197,1778,4528	GG,GT,TT		12.5465,24.8071,16.7	,,,	62/316,62/287,62/287,62/316	171098	2172,10834	2203	4300	6503	SO:0001819	synonymous_variant	9501	exon3			CCGCTCTGCCCTC		CCDS10994.1, CCDS54059.1	17p13.3	2014-07-02			ENSG00000181031	ENSG00000181031		"""Synaptotagmins"""	10296	protein-coding gene	gene with protein product		604881				10395805	Standard	NM_006987		Approved	Noc2	uc021tmx.1	Q9UNE2	OTTHUMG00000090273	ENST00000331302.7:c.186A>C	17.37:g.171098T>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_001190413	D3DTG7|Q9BSB3	Silent	SNP	ENST00000331302.7	37	CCDS10994.1																																																																																			T|0.845;G|0.155	0.155	strong		0.682	RPH3AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206597.2	NM_006987	
NETO1	81832	hgsc.bcm.edu	37	18	70417378	70417378	+	Missense_Mutation	SNP	G	G	C	rs17086286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:70417378G>C	ENST00000327305.6	-	9	2117	c.1460C>G	c.(1459-1461)gCa>gGa	p.A487G	NETO1_ENST00000583169.1_Missense_Mutation_p.A487G|NETO1_ENST00000299430.2_Missense_Mutation_p.A486G|RNA5SP460_ENST00000516789.1_RNA	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	487			A -> G (in dbSNP:rs17086286).		memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		ACAGGCATCTGCAGCATCTTG	0.488													G|||	94	0.01877	0.0688	0.0043	5008	,	,		18531	0.0		0.0	False		,,,				2504	0.0				p.A487G		Atlas-SNP	.											.	NETO1	178	.	0			c.C1460G						PASS	.	G	GLY/ALA,GLY/ALA	265,4141	149.9+/-184.0	4,257,1942	165.0	141.0	149.0		1460,1460	4.9	0.8	18	dbSNP_123	149	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	NETO1	NM_001201465.1,NM_138966.3	60,60	4,260,6239	CC,CG,GG		0.0349,6.0145,2.0606	possibly-damaging,possibly-damaging	487/534,487/534	70417378	268,12738	2203	4300	6503	SO:0001583	missense	81832	exon9			GCATCTGCAGCAT	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.1460C>G	18.37:g.70417378G>C	ENSP00000313088:p.Ala487Gly	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	212	93	0.438679	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	34	0.015567765567765568	34	0.06910569105691057	0	0.0	0	0.0	0	0.0	G	17.20	3.327871	0.60743	0.060145	3.49E-4	ENSG00000166342	ENST00000327305;ENST00000299430	T;T	0.26518	1.74;1.73	5.76	4.86	0.63082	.	0.000000	0.64402	D	0.000014	T	0.02012	0.0063	L	0.42245	1.32	0.80722	D	1	P;P	0.40731	0.728;0.608	B;B	0.41036	0.346;0.188	T	0.00389	-1.1770	10	0.41790	T	0.15	-3.6568	16.2419	0.82418	0.0:0.0:0.8668:0.1332	rs17086286;rs52790393;rs17086286	486;487	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	G	487;486	ENSP00000313088:A487G;ENSP00000299430:A486G	ENSP00000299430:A486G	A	-	2	0	NETO1	68568358	1.000000	0.71417	0.836000	0.33094	0.968000	0.65278	7.044000	0.76578	2.725000	0.93324	0.460000	0.39030	GCA	G|0.978;C|0.022	0.022	strong		0.488	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999	
PRR21	643905	hgsc.bcm.edu	37	2	240982009	240982009	+	Missense_Mutation	SNP	G	G	A	rs202192655		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240982009G>A	ENST00000408934.1	-	1	390	c.391C>T	c.(391-393)Ccc>Tcc	p.P131S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	131	Pro-rich.							p.P131S(2)		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						AGGGCCGTGGGTGAAGAGGCA	0.647																																					p.P131S		Atlas-SNP	.											PRR21,NS,malignant_melanoma,0,2	PRR21	53	2	2	Substitution - Missense(2)	NS(2)	c.C391T						scavenged	.						4.0	3.0	3.0					2																	240982009		1301	2740	4041	SO:0001583	missense	643905	exon1			CCGTGGGTGAAGA	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.391C>T	2.37:g.240982009G>A	ENSP00000386166:p.Pro131Ser	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	12	2	0.166667	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	-	0.018	-1.469388	0.01044	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13307	2.6;2.6	1.73	-3.03	0.05429	.	.	.	.	.	T	0.10766	0.0263	N	0.08118	0	0.09310	N	1	D	0.63880	0.993	P	0.61940	0.896	T	0.12993	-1.0526	9	0.10111	T	0.7	.	7.6745	0.28478	0.3709:0.0:0.6291:0.0	.	131	Q8WXC7	PRR21_HUMAN	S	131	ENSP00000386166:P131S;ENSP00000418240:P131S	ENSP00000386166:P131S	P	-	1	0	PRR21	240630682	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.053000	0.03500	-0.874000	0.04027	-0.481000	0.04817	CCC	.	.	weak		0.647	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
SPOCK2	9806	hgsc.bcm.edu	37	10	73826775	73826775	+	Silent	SNP	G	G	A	rs7079142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73826775G>A	ENST00000373109.2	-	8	1257	c.813C>T	c.(811-813)gcC>gcT	p.A271A	SPOCK2_ENST00000317376.4_Silent_p.A271A|SPOCK2_ENST00000536168.1_Silent_p.A271A|SPOCK2_ENST00000460053.1_5'UTR	NM_001244950.1	NP_001231879.1	Q92563	TICN2_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2	271					extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of cell differentiation (GO:0045595)|signal transduction (GO:0007165)|synapse assembly (GO:0007416)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)			endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						GGTTGATGGCGGCCAGCTCCG	0.582													G|||	46	0.0091853	0.034	0.0014	5008	,	,		18389	0.0		0.0	False		,,,				2504	0.0				p.A271A		Atlas-SNP	.											.	SPOCK2	32	.	0			c.C813T						PASS	.	G		112,4294	85.8+/-124.5	0,112,2091	121.0	106.0	111.0		813	-7.5	0.6	10	dbSNP_116	111	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	SPOCK2	NM_014767.2		0,115,6388	AA,AG,GG		0.0349,2.542,0.8842		271/425	73826775	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	9806	exon8			GATGGCGGCCAGC	AJ001453	CCDS7313.1, CCDS44431.1	10q22.1	2013-09-19			ENSG00000107742	ENSG00000107742			13564	protein-coding gene	gene with protein product		607988				10386950	Standard	NM_014767		Approved	KIAA0275, testican-2	uc001jso.2	Q92563	OTTHUMG00000018430	ENST00000373109.2:c.813C>T	10.37:g.73826775G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_001244950	C9J767|Q6UW87	Silent	SNP	ENST00000373109.2	37	CCDS7313.1																																																																																			G|0.990;A|0.010	0.010	strong		0.582	SPOCK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048560.2		
MICA	100507436	hgsc.bcm.edu	37	6	31380198	31380198	+	Missense_Mutation	SNP	C	C	T	rs61738275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31380198C>T	ENST00000449934.2	+	5	1043	c.989C>T	c.(988-990)cCg>cTg	p.P330L	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)				TTTCTATGTCCGTTGTTGTAA	0.483													c|||	1350	0.269569	0.385	0.3386	5008	,	,		18668	0.1786		0.1928	False		,,,				2504	0.2372				p.P330L		Atlas-SNP	.											.	MICA	21	.	0			c.C989T						PASS	.	C	LEU/PRO	460,924		102,256,334	148.0	139.0	142.0		989	-2.0	0.0	6	dbSNP_129	142	488,2694		47,394,1150	yes	missense	MICA	NM_001177519.1	98	149,650,1484	TT,TC,CC		15.3363,33.237,20.7622	benign	330/333	31380198	948,3618	692	1591	2283	SO:0001583	missense	100507436	exon5			TATGTCCGTTGTT	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.989C>T	6.37:g.31380198C>T	ENSP00000413079:p.Pro330Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	575	0.2632783882783883	181	0.3678861788617886	138	0.3812154696132597	95	0.1660839160839161	161	0.21240105540897097	-	8.649	0.897873	0.17686	0.33237	0.153363	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.01203	5.64;5.18	1.38	-2.03	0.07365	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	0.80722	P	0.0	B;B	0.27732	0.187;0.187	B;B	0.10450	0.005;0.005	T	0.41716	-0.9493	8	0.87932	D	0	.	2.723	0.05206	0.0:0.3727:0.2545:0.3728	rs61738275	192;330	Q5SS58;Q96QC4	.;.	L	192;330;287;330;221	ENSP00000413079:P330L;ENSP00000402410:P221L	ENSP00000365394:P330L	P	+	2	0	MICA	31488177	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.952000	0.00677	-0.645000	0.05458	0.378000	0.23410	CCG	C|0.748;T|0.252	0.252	strong		0.483	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587067	15587067	+	Silent	SNP	T	T	A	rs35927052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15587067T>A	ENST00000340880.4	-	2	894	c.414A>T	c.(412-414)atA>atT	p.I138I	PGLYRP2_ENST00000292609.4_Silent_p.I138I	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	138					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)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|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)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						AGGGCAAATTTATGACCCTGC	0.607													T|||	123	0.0245607	0.0477	0.0058	5008	,	,		18627	0.006		0.008	False		,,,				2504	0.0429				p.I138I		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.A414T						PASS	.	T		193,4213	121.7+/-159.2	3,187,2013	85.0	77.0	79.0		414	-9.2	0.0	19	dbSNP_126	79	75,8525	44.9+/-103.4	0,75,4225	no	coding-synonymous	PGLYRP2	NM_052890.3		3,262,6238	AA,AT,TT		0.8721,4.3804,2.0606		138/577	15587067	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	114770	exon2			CAAATTTATGACC	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.414A>T	19.37:g.15587067T>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	109	59	0.541284	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Silent	SNP	ENST00000340880.4	37	CCDS12330.2																																																																																			T|0.981;A|0.019	0.019	strong		0.607	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
OR2A25	392138	hgsc.bcm.edu	37	7	143771937	143771937	+	Missense_Mutation	SNP	G	G	C	rs2961135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	267	133	0.498127	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		
ANK1	286	hgsc.bcm.edu	37	8	41525914	41525914	+	Silent	SNP	C	C	T	rs750625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:41525914C>T	ENST00000347528.4	-	39	5348	c.5265G>A	c.(5263-5265)gtG>gtA	p.V1755V	ANK1_ENST00000379758.2_Silent_p.V1755V|ANK1_ENST00000265709.8_Silent_p.V1796V|RP11-930P14.1_ENST00000522388.1_RNA|ANK1_ENST00000352337.4_Silent_p.V1755V|ANK1_ENST00000289734.7_Silent_p.V1755V|ANK1_ENST00000396945.1_Silent_p.V1755V|ANK1_ENST00000396942.1_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	203	0	0		WXS	Illumina HiSeq	Phase_I	219	107	0.488584	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	
WDR87	83889	hgsc.bcm.edu	37	19	38377404	38377404	+	Missense_Mutation	SNP	C	C	T	rs201328117		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38377404C>T	ENST00000303868.5	-	6	7014	c.6790G>A	c.(6790-6792)Gag>Aag	p.E2264K	WDR87_ENST00000447313.2_Missense_Mutation_p.E2303K	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2264	Glu-rich.									NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						tcctcctcctcccttacctcc	0.488																																					p.E2264K		Atlas-SNP	.											.	WDR87	191	.	0			c.G6790A						PASS	.						66.0	49.0	54.0					19																	38377404		692	1591	2283	SO:0001583	missense	83889	exon6			CCTCCTCCCTTAC	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.6790G>A	19.37:g.38377404C>T	ENSP00000368025:p.Glu2264Lys	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	67	12	0.179104	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.286996	0.23478	.	.	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.41400	1.0;1.0	4.47	4.47	0.54385	.	.	.	.	.	T	0.39682	0.1087	L	0.29908	0.895	0.09310	N	1	D;D	0.69078	0.997;0.997	P;P	0.58577	0.841;0.841	T	0.13872	-1.0493	9	0.06099	T	0.92	.	9.1387	0.36890	0.0:0.8956:0.0:0.1044	.	2264;2303	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	K	2303;2264	ENSP00000405012:E2303K;ENSP00000368025:E2264K	ENSP00000368025:E2264K	E	-	1	0	WDR87	43069244	0.001000	0.12720	0.064000	0.19789	0.078000	0.17371	0.800000	0.27042	2.412000	0.81896	0.450000	0.29827	GAG	.	.	weak		0.488	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
MYRIP	25924	hgsc.bcm.edu	37	3	40251392	40251392	+	Silent	SNP	T	T	C	rs1799418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:40251392T>C	ENST00000302541.6	+	11	2055	c.1713T>C	c.(1711-1713)gaT>gaC	p.D571D	MYRIP_ENST00000539167.1_Silent_p.D384D|MYRIP_ENST00000425621.1_Silent_p.D571D|MYRIP_ENST00000444716.1_Silent_p.D571D|MYRIP_ENST00000396217.3_Silent_p.D482D|RN7SL411P_ENST00000585204.1_RNA|MYRIP_ENST00000459828.1_3'UTR	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	571	Actin-binding.			D -> E (in Ref. 1; AAM43954). {ECO:0000305}.	intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		AGGCTCGGGATCCCCAGACTC	0.483													C|||	1843	0.368011	0.2791	0.5216	5008	,	,		19456	0.2589		0.5517	False		,,,				2504	0.3027				p.D571D		Atlas-SNP	.											.	MYRIP	98	.	0			c.T1713C						PASS	.	C		1331,3075	695.1+/-405.9	198,935,1070	108.0	103.0	105.0		1713	1.0	0.0	3	dbSNP_89	105	4601,3999	554.4+/-386.5	1261,2079,960	no	coding-synonymous	MYRIP	NM_015460.2		1459,3014,2030	CC,CT,TT		46.5,30.2088,45.6097		571/860	40251392	5932,7074	2203	4300	6503	SO:0001819	synonymous_variant	25924	exon11			TCGGGATCCCCAG	AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"""A-kinase anchor proteins"""	19156	protein-coding gene	gene with protein product	"""synaptotagmin-like protein homologue lacking C2 domains-c"", ""rab effector MYRIP"", ""Slp homologue lacking C2 domains"""	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.1713T>C	3.37:g.40251392T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	178	175	0.983146	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Silent	SNP	ENST00000302541.6	37	CCDS2689.1																																																																																			C|0.439;N|0.001	0.439	strong		0.483	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
MAPRE1	22919	hgsc.bcm.edu	37	20	31427635	31427635	+	Silent	SNP	C	C	T	rs2070090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31427635C>T	ENST00000375571.5	+	5	709	c.570C>T	c.(568-570)gaC>gaT	p.D190D		NM_012325.2	NP_036457.1	Q15691	MARE1_HUMAN	microtubule-associated protein, RP/EB family, member 1	190	EB1 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00576}.|Interaction with CDK5RAP2.|Interaction with MTUS2/TIP150.				cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of microtubule plus-end binding (GO:1903033)|protein localization to microtubule (GO:0035372)	cell projection membrane (GO:0031253)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule plus-end (GO:0035371)	microtubule plus-end binding (GO:0051010)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8						GCAACGGAGACGACGAGGCAG	0.612													C|||	1557	0.310903	0.4372	0.2161	5008	,	,		17507	0.3651		0.1461	False		,,,				2504	0.3211				p.D190D		Atlas-SNP	.											.	MAPRE1	17	.	0			c.C570T						PASS	.	C		1686,2720	513.1+/-368.2	311,1064,828	128.0	133.0	131.0		570	1.6	1.0	20	dbSNP_96	131	1437,7163	276.1+/-292.1	120,1197,2983	no	coding-synonymous	MAPRE1	NM_012325.2		431,2261,3811	TT,TC,CC		16.7093,38.266,24.012		190/269	31427635	3123,9883	2203	4300	6503	SO:0001819	synonymous_variant	22919	exon5			CGGAGACGACGAG	U24166	CCDS13208.1	20q11.1-q11.3	2013-01-17			ENSG00000101367	ENSG00000101367			6890	protein-coding gene	gene with protein product	"""adenomatous polyposis coli-binding protein EB1"""	603108				7606712, 9724749, 11470413	Standard	NM_012325		Approved	EB1	uc002wyh.3	Q15691	OTTHUMG00000032228	ENST00000375571.5:c.570C>T	20.37:g.31427635C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_012325	B2R6I7|E1P5M8|Q3KQS8	Silent	SNP	ENST00000375571.5	37	CCDS13208.1																																																																																			C|0.738;T|0.261	0.261	strong		0.612	MAPRE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078647.2	NM_012325	
ZNF285	26974	hgsc.bcm.edu	37	19	44891748	44891748	+	Missense_Mutation	SNP	T	T	C	rs60800862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44891748T>C	ENST00000330997.4	-	4	723	c.659A>G	c.(658-660)gAa>gGa	p.E220G	ZNF285_ENST00000591679.1_Missense_Mutation_p.E227G|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Missense_Mutation_p.E220G	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	220					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						ATTACGTTTTTCAACCGTTGA	0.463													T|||	110	0.0219649	0.0809	0.0043	5008	,	,		19447	0.0		0.0	False		,,,				2504	0.0				p.E220G		Atlas-SNP	.											.	ZNF285	86	.	0			c.A659G						PASS	.	T	GLY/GLU	255,4151	145.4+/-180.2	6,243,1954	103.0	100.0	101.0		659	-0.2	0.0	19	dbSNP_129	101	1,8599		0,1,4299	yes	missense	ZNF285	NM_152354.3	98	6,244,6253	CC,CT,TT		0.0116,5.7876,1.9683		220/591	44891748	256,12750	2203	4300	6503	SO:0001583	missense	26974	exon4			CGTTTTTCAACCG	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.659A>G	19.37:g.44891748T>C	ENSP00000333595:p.Glu220Gly	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	6.112	0.388881	0.11581	0.057876	1.16E-4	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.28454	1.61	3.27	-0.157	0.13387	.	.	.	.	.	T	0.01905	0.0060	L	0.38175	1.15	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.21075	-1.0256	9	0.24483	T	0.36	.	3.8075	0.08783	0.1682:0.3505:0.0:0.4813	rs60800862	244;220	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	G	243;220	ENSP00000333595:E220G	ENSP00000333595:E220G	E	-	2	0	ZNF285	49583588	0.000000	0.05858	0.002000	0.10522	0.168000	0.22595	-0.057000	0.11768	0.046000	0.15833	0.373000	0.22412	GAA	T|0.983;C|0.017	0.017	strong		0.463	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
ITGA11	22801	hgsc.bcm.edu	37	15	68628049	68628049	+	Missense_Mutation	SNP	T	T	G	rs2306024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68628049T>G	ENST00000315757.7	-	12	1497	c.1411A>C	c.(1411-1413)Atg>Ctg	p.M471L	ITGA11_ENST00000423218.2_Missense_Mutation_p.M471L	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	471			M -> L (in dbSNP:rs2306024).		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)			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						TGGCCCCGCATAGCCTGGTGG	0.637													G|||	555	0.110823	0.236	0.049	5008	,	,		19262	0.0962		0.0606	False		,,,				2504	0.0521				p.M471L		Atlas-SNP	.											.	ITGA11	110	.	0			c.A1411C						PASS	.	G	LEU/MET	779,3287		76,627,1330	28.0	35.0	32.0		1411	5.8	1.0	15	dbSNP_100	32	415,7947		7,401,3773	yes	missense	ITGA11	NM_001004439.1	15	83,1028,5103	GG,GT,TT		4.9629,19.1589,9.6073	benign	471/1189	68628049	1194,11234	2033	4181	6214	SO:0001583	missense	22801	exon12			CCCGCATAGCCTG	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.1411A>C	15.37:g.68628049T>G	ENSP00000327290:p.Met471Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	223	0.1021062271062271	115	0.23373983739837398	22	0.06077348066298342	42	0.07342657342657342	44	0.05804749340369393	G	9.874	1.199726	0.22121	0.191589	0.049629	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491;ENST00000537153	T;T	0.09073	3.02;3.02	5.77	5.77	0.91146	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00114	-2.085	0.47009	P	7.139999999999924E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43686	-0.9376	9	0.02654	T	1	.	15.5168	0.75830	0.0:0.0:0.8606:0.1394	rs2306024;rs52790479;rs60175306;rs2306024	471;471	A8K8T0;Q9UKX5	.;ITA11_HUMAN	L	471;471;106;471	ENSP00000327290:M471L;ENSP00000403392:M471L	ENSP00000327290:M471L	M	-	1	0	ITGA11	66415103	1.000000	0.71417	0.999000	0.59377	0.937000	0.57800	5.486000	0.66856	1.456000	0.47831	-0.121000	0.15023	ATG	T|0.895;G|0.105	0.105	strong		0.637	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
MYOM1	8736	hgsc.bcm.edu	37	18	3176063	3176063	+	Silent	SNP	C	C	T	rs2230162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3176063C>T	ENST00000356443.4	-	6	1332	c.999G>A	c.(997-999)ggG>ggA	p.G333G	MYOM1_ENST00000261606.7_Silent_p.G333G|MYOM1_ENST00000400569.3_Silent_p.G333G	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	333	Ig-like C2-type 1.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			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						GAGTGTGCATCCCATATCGAC	0.423													T|||	1368	0.273163	0.2436	0.2161	5008	,	,		22191	0.2659		0.3062	False		,,,				2504	0.3272				p.G333G		Atlas-SNP	.											.	MYOM1	192	.	0			c.G999A						PASS	.	T	,	1005,2911		130,745,1083	106.0	104.0	104.0		999,999	4.7	1.0	18	dbSNP_98	104	2585,5711		409,1767,1972	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	539,2512,3055	TT,TC,CC		31.1596,25.6639,29.3973	,	333/1686,333/1590	3176063	3590,8622	1958	4148	6106	SO:0001819	synonymous_variant	8736	exon6			GTGCATCCCATAT	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.999G>A	18.37:g.3176063C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	109	62	0.568807	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			T|0.164;G|0.282	0.164	strong		0.423	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
MT-CO1	4512	hgsc.bcm.edu	37	M	6253	6253	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:6253T>C	ENST00000361624.2	+	1	350	c.350T>C	c.(349-351)aTa>aCa	p.I117T	MT-CO2_ENST00000361739.1_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TN_ENST00000387400.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TM_ENST00000387377.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TQ_ENST00000387372.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TW_ENST00000387382.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TK_ENST00000387421.1_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	117					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						CGCATCTGCTATAGTGGAGGC	0.537																																					p.M117T		Atlas-SNP	.											.	.	.	.	0			c.T350C						PASS	.																																			SO:0001583	missense	5742	exon1			CTGCTATAGTGGA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.350T>C	M.37:g.6253T>C	ENSP00000354499:p.Ile117Thr	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	ENST00000361624	Q34770	Missense_Mutation	SNP	ENST00000361624.2	37																																																																																				.	.	none		0.537	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028	
C4orf17	84103	hgsc.bcm.edu	37	4	100443853	100443853	+	Silent	SNP	A	A	G	rs17029090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100443853A>G	ENST00000326581.4	+	3	686	c.324A>G	c.(322-324)ccA>ccG	p.P108P	C4orf17_ENST00000514652.1_Silent_p.P108P|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	108										central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		AAGTGCCTCCACGGCCTCATT	0.507													A|||	599	0.119609	0.2504	0.062	5008	,	,		17252	0.1558		0.0119	False		,,,				2504	0.0573				p.P108P		Atlas-SNP	.											.	C4orf17	42	.	0			c.A324G						PASS	.	A		1020,3386	373.0+/-320.6	132,756,1315	54.0	54.0	54.0		324	-6.9	0.0	4	dbSNP_123	54	160,8440	75.4+/-138.0	3,154,4143	no	coding-synonymous	C4orf17	NM_032149.2		135,910,5458	GG,GA,AA		1.8605,23.1502,9.0727		108/360	100443853	1180,11826	2203	4300	6503	SO:0001819	synonymous_variant	84103	exon3			GCCTCCACGGCCT	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.324A>G	4.37:g.100443853A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Silent	SNP	ENST00000326581.4	37	CCDS3649.1																																																																																			A|0.895;G|0.105	0.105	strong		0.507	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
SLC27A3	11000	hgsc.bcm.edu	37	1	153748219	153748219	+	Silent	SNP	C	C	T	rs36064263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153748219C>T	ENST00000368661.3	+	1	452	c.387C>T	c.(385-387)acC>acT	p.T129T	SLC27A3_ENST00000484014.1_Intron|SLC27A3_ENST00000271857.2_Silent_p.T210T	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	129					fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCGCGCACACCTTTCTCATTC	0.721													C|||	599	0.119609	0.3048	0.062	5008	,	,		14222	0.0129		0.0716	False		,,,				2504	0.0695				p.T129T		Atlas-SNP	.											.	SLC27A3	42	.	0			c.C387T						PASS	.	C		702,3060		49,604,1228	11.0	13.0	12.0		387	3.6	1.0	1	dbSNP_126	12	424,7226		6,412,3407	no	coding-synonymous	SLC27A3	NM_024330.1		55,1016,4635	TT,TC,CC		5.5425,18.6603,9.8668		129/731	153748219	1126,10286	1881	3825	5706	SO:0001819	synonymous_variant	11000	exon1			GCACACCTTTCTC	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.387C>T	1.37:g.153748219C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Silent	SNP	ENST00000368661.3	37	CCDS1053.1																																																																																			C|0.897;T|0.103	0.103	strong		0.721	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330	
BDP1	55814	hgsc.bcm.edu	37	5	70845400	70845400	+	Missense_Mutation	SNP	A	A	G	rs59354595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70845400A>G	ENST00000358731.4	+	34	7225	c.6962A>G	c.(6961-6963)aAa>aGa	p.K2321R	BDP1_ENST00000380675.2_Intron	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2321					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)		ATATTGGTCAAATCAGTGAAT	0.418													A|||	204	0.0407348	0.146	0.013	5008	,	,		18672	0.0		0.002	False		,,,				2504	0.0				p.K2321R		Atlas-SNP	.											.	BDP1	204	.	0			c.A6962G						PASS	.	A	ARG/LYS	479,3309		28,423,1443	93.0	88.0	89.0		6962	2.3	0.8	5	dbSNP_129	89	3,8211		0,3,4104	yes	missense	BDP1	NM_018429.2	26	28,426,5547	GG,GA,AA		0.0365,12.6452,4.016	benign	2321/2625	70845400	482,11520	1894	4107	6001	SO:0001583	missense	55814	exon34			TGGTCAAATCAGT	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.6962A>G	5.37:g.70845400A>G	ENSP00000351575:p.Lys2321Arg	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	228	103	0.451754	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	79	0.036172161172161175	73	0.1483739837398374	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	A	12.53	1.964625	0.34659	0.126452	3.65E-4	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.04551	3.6	5.96	2.27	0.28462	.	0.277827	0.31577	N	0.007413	T	0.00012	0.0000	N	0.21448	0.665	0.80722	D	1	B	0.28178	0.202	B	0.26202	0.067	T	0.61033	-0.7144	10	0.12766	T	0.61	.	4.5339	0.12019	0.6602:0.1661:0.1737:0.0	rs59354595;rs61734266	2321	A6H8Y1	BDP1_HUMAN	R	2321;1869	ENSP00000351575:K2321R	ENSP00000351575:K2321R	K	+	2	0	BDP1	70881156	0.700000	0.27796	0.848000	0.33437	0.954000	0.61252	0.169000	0.16641	0.157000	0.19338	0.533000	0.62120	AAA	A|0.963;G|0.037	0.037	strong		0.418	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
MUC5B	727897	hgsc.bcm.edu	37	11	1272858	1272858	+	Silent	SNP	C	C	T	rs4963059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	113	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	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	
CLEC3A	10143	hgsc.bcm.edu	37	16	78064733	78064733	+	Missense_Mutation	SNP	C	C	A	rs2072663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:78064733C>A	ENST00000575655.1	+	3	670	c.589C>A	c.(589-591)Caa>Aaa	p.Q197K	CLEC3A_ENST00000565808.1_3'UTR|CLEC3A_ENST00000299642.4_Missense_Mutation_p.Q206K|RP11-281J9.2_ENST00000563114.1_RNA	NM_005752.4	NP_005743.4	O75596	CLC3A_HUMAN	C-type lectin domain family 3, member A	197			Q -> K (in dbSNP:rs2072663). {ECO:0000269|PubMed:12975309}.		skeletal system development (GO:0001501)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	18						CACCATCCCTCAATAGGTCTT	0.413													C|||	658	0.13139	0.0719	0.1441	5008	,	,		20795	0.245		0.1223	False		,,,				2504	0.0951				p.Q206K		Atlas-SNP	.											.	CLEC3A	39	.	0			c.C616A						PASS	.	C	LYS/GLN	363,4033	170.1+/-200.6	15,333,1850	67.0	69.0	69.0		589	3.8	0.3	16	dbSNP_96	69	1147,7451	227.5+/-262.8	82,983,3234	yes	missense	CLEC3A	NM_005752.4	53	97,1316,5084	AA,AC,CC		13.3403,8.2575,11.6207	benign	197/198	78064733	1510,11484	2198	4299	6497	SO:0001583	missense	10143	exon3			ATCCCTCAATAGG	AF077345	CCDS10927.1, CCDS10927.2	16q23	2008-02-05	2005-02-09	2005-02-11	ENSG00000166509	ENSG00000166509		"""C-type lectin domain containing"""	2052	protein-coding gene	gene with protein product		613588	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived)"""	CLECSF1		10524194	Standard	NM_001244755		Approved		uc002ffh.5	O75596	OTTHUMG00000137620	ENST00000575655.1:c.589C>A	16.37:g.78064733C>A	ENSP00000460682:p.Gln197Lys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_005752	B2R8C4|Q3SX91|Q6UXF5	Missense_Mutation	SNP	ENST00000575655.1	37		329	0.15064102564102563	49	0.09959349593495935	45	0.12430939226519337	143	0.25	92	0.12137203166226913	C	10.14	1.268501	0.23136	0.082575	0.133403	ENSG00000166509	ENST00000299642	.	.	.	6.07	3.85	0.44370	.	21.172100	0.01519	N	0.018298	T	0.00012	0.0000	N	0.08118	0	0.50813	P	1.020000000000465E-4	B	0.06786	0.001	B	0.01281	0.0	T	0.21109	-1.0255	8	0.21540	T	0.41	.	10.2292	0.43245	0.0:0.1348:0.0:0.8652	rs2072663;rs2234867;rs60748914;rs2072663	197	O75596	CLC3A_HUMAN	K	197	.	ENSP00000299642:Q197K	Q	+	1	0	CLEC3A	76622234	0.904000	0.30761	0.264000	0.24511	0.032000	0.12392	3.057000	0.49931	0.547000	0.28938	-0.238000	0.12139	CAA	C|0.867;A|0.133	0.133	strong		0.413	CLEC3A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005752	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518233	161518233	+	Silent	SNP	C	C	A	rs139622799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161518233C>A	ENST00000436743.1	-	4	451	c.297G>T	c.(295-297)ccG>ccT	p.P99P	FCGR3A_ENST00000443193.1_Silent_p.P134P|RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000540048.1_Silent_p.P99P|FCGR3A_ENST00000367969.3_Silent_p.P135P|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)	99	Ig-like C2-type 1.				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)	CTAGCTGCACCGGGTCACTGA	0.512																																					p.P135P		Atlas-SNP	.											FCGR3A,lower_third,carcinoma,-2,1	FCGR3A	38	1	0			c.G405T						scavenged	.	C	,,,,	144,4262	81.4+/-119.9	0,144,2059	114.0	112.0	113.0		405,402,297,297,294	-8.9	0.0	1	dbSNP_134	113	7,8587	5.0+/-18.6	0,7,4290	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCGR3A	NM_000569.6,NM_001127592.1,NM_001127593.1,NM_001127595.1,NM_001127596.1	,,,,	0,151,6349	AA,AC,CC		0.0815,3.2683,1.1615	,,,,	135/291,134/290,99/255,99/255,98/254	161518233	151,12849	2203	4297	6500	SO:0001819	synonymous_variant	2214	exon3			CTGCACCGGGTCA	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.297G>T	1.37:g.161518233C>A		Somatic	488	2	0.00409836		WXS	Illumina HiSeq	Phase_I	585	181	0.309402	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Silent	SNP	ENST00000436743.1	37	CCDS44266.1	32	0.014652014652014652	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	11.25	1.583746	0.28268	0.032683	8.15E-4	ENSG00000203747	ENST00000426740	.	.	.	4.43	-8.86	0.00795	.	.	.	.	.	T	0.26011	0.0634	.	.	.	0.38428	D	0.94635	.	.	.	.	.	.	T	0.47873	-0.9083	4	.	.	.	.	7.0855	0.25255	0.2513:0.1676:0.0:0.5811	.	.	.	.	L	116	.	.	R	-	2	0	FCGR3A	159784857	0.000000	0.05858	0.029000	0.17559	0.763000	0.43281	-5.433000	0.00123	-3.094000	0.00246	-0.218000	0.12543	CGG	C|0.985;A|0.015	0.015	strong		0.512	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
TLR3	7098	hgsc.bcm.edu	37	4	187004544	187004544	+	Silent	SNP	C	C	T	rs35111588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187004544C>T	ENST00000296795.3	+	4	1808	c.1704C>T	c.(1702-1704)aaC>aaT	p.N568N	TLR3_ENST00000504367.1_Silent_p.N291N	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	568					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|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)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		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;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		ACATCCTTAACTTGGAGTCCA	0.423													C|||	296	0.0591054	0.2156	0.013	5008	,	,		20763	0.0		0.002	False		,,,				2504	0.0				p.N568N		Atlas-SNP	.											.	TLR3	83	.	0			c.C1704T						PASS	.	C		714,3692	297.8+/-285.0	60,594,1549	92.0	90.0	91.0		1704	-2.8	0.9	4	dbSNP_126	91	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	TLR3	NM_003265.2		60,602,5841	TT,TC,CC		0.093,16.2052,5.5513		568/905	187004544	722,12284	2203	4300	6503	SO:0001819	synonymous_variant	7098	exon4			CCTTAACTTGGAG	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"""CD molecules"""	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.1704C>T	4.37:g.187004544C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Silent	SNP	ENST00000296795.3	37	CCDS3846.1																																																																																			C|0.949;T|0.051	0.051	strong		0.423	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4		
ORAOV1	220064	hgsc.bcm.edu	37	11	69490001	69490001	+	Missense_Mutation	SNP	C	C	T	rs56107468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:69490001C>T	ENST00000535657.1	-	1	88	c.7G>A	c.(7-9)Ggc>Agc	p.G3S	ORAOV1_ENST00000279147.4_Missense_Mutation_p.G3S|ORAOV1_ENST00000542341.1_Missense_Mutation_p.G3S|ORAOV1_ENST00000536870.1_Missense_Mutation_p.G3S|ORAOV1_ENST00000539414.1_Missense_Mutation_p.G3S			Q8WV07	ORAV1_HUMAN	oral cancer overexpressed 1	3			G -> S (in dbSNP:rs56107468).							NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;5.64e-57)|all cancers(3;5.98e-51)|BRCA - Breast invasive adenocarcinoma(2;5.49e-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)			TCCTGACTGCCAGCCATAGCG	0.677													C|||	111	0.0221645	0.0802	0.0072	5008	,	,		15446	0.0		0.0	False		,,,				2504	0.0				p.G3S		Atlas-SNP	.											.	ORAOV1	11	.	0			c.G7A						PASS	.	C	SER/GLY	279,4109		8,263,1923	28.0	26.0	26.0		7	1.8	0.1	11	dbSNP_129	26	3,8577		0,3,4287	yes	missense	ORAOV1	NM_153451.2	56	8,266,6210	TT,TC,CC		0.035,6.3582,2.1746	benign	3/138	69490001	282,12686	2194	4290	6484	SO:0001583	missense	220064	exon1			GACTGCCAGCCAT		CCDS8192.1	11q13.2	2010-11-23			ENSG00000149716	ENSG00000149716			17589	protein-coding gene	gene with protein product	"""oral cancer overexpressed protein 1-A"""	607224				12172009	Standard	NM_153451		Approved	TAOS1	uc001opc.3	Q8WV07		ENST00000535657.1:c.7G>A	11.37:g.69490001C>T	ENSP00000446129:p.Gly3Ser	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	218	101	0.463303	NM_153451	B2R4R2|Q8NFK0	Missense_Mutation	SNP	ENST00000535657.1	37	CCDS8192.1	46	0.021062271062271064	42	0.08536585365853659	4	0.011049723756906077	0	0.0	0	0.0	C	12.95	2.091045	0.36855	0.063582	3.5E-4	ENSG00000149716	ENST00000538554;ENST00000376587;ENST00000279147;ENST00000536870;ENST00000535657;ENST00000539414;ENST00000441922;ENST00000542341;ENST00000355486;ENST00000543023	T;T;T;T;T;T;T	0.44083	0.95;1.04;0.93;1.04;1.03;0.97;1.03	3.78	1.83	0.25207	.	0.922530	0.09022	N	0.859968	T	0.01029	0.0034	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.34015	0.435;0.034;0.004;0.041	B;B;B;B	0.35510	0.204;0.017;0.01;0.017	T	0.09662	-1.0664	10	0.09338	T	0.73	-25.5519	3.1767	0.06571	0.209:0.5597:0.0:0.2313	rs56107468	3;3;3;3	B4DFA5;F5H6T8;F5GWS9;Q8WV07	.;.;.;ORAV1_HUMAN	S	3	ENSP00000446428:G3S;ENSP00000279147:G3S;ENSP00000441984:G3S;ENSP00000446129:G3S;ENSP00000444112:G3S;ENSP00000409643:G3S;ENSP00000437367:G3S	ENSP00000279147:G3S	G	-	1	0	ORAOV1	69199182	0.000000	0.05858	0.060000	0.19600	0.298000	0.27526	0.050000	0.14120	0.878000	0.35920	0.561000	0.74099	GGC	C|0.978;T|0.022	0.022	strong		0.677	ORAOV1-009	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000396821.1	NM_153451	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786681	75786681	+	Missense_Mutation	SNP	G	G	A	rs111677009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75786681G>A	ENST00000478296.1	-	4	2219	c.1943C>T	c.(1942-1944)cCg>cTg	p.P648L	ZNF717_ENST00000422325.1_Missense_Mutation_p.P698L|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.P691L|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	688					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						GCTTTTCCCCGGTGTGAGTTC	0.408																																					p.P698L		Atlas-SNP	.											.	ZNF717	160	.	0			c.C2093T						PASS	.						4.0	4.0	4.0					3																	75786681		561	1392	1953	SO:0001583	missense	100131827	exon5			TTCCCCGGTGTGA	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1943C>T	3.37:g.75786681G>A	ENSP00000419377:p.Pro648Leu	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	52	11	0.211538	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		.	.	.	.	.	.	.	.	.	.	.	5.989	0.366403	0.11352	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.05580	3.42;3.55;3.54	1.27	-2.53	0.06326	.	.	.	.	.	T	0.01627	0.0052	N	0.00525	-1.395	0.34331	P	0.31233	B	0.02656	0.0	B	0.01281	0.0	T	0.45011	-0.9290	8	0.87932	D	0	.	3.1326	0.06429	0.3655:0.0:0.1987:0.4358	.	698	C9JSV9	.	L	648;698;691	ENSP00000419377:P648L;ENSP00000409514:P698L;ENSP00000383643:P691L	ENSP00000383643:P691L	P	-	2	0	ZNF717	75869371	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-7.316000	0.00039	-1.950000	0.01030	-3.190000	0.00055	CCG	G|0.083;A|0.917	0.917	weak		0.408	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
USP17L2	377630	hgsc.bcm.edu	37	8	11995276	11995276	+	Missense_Mutation	SNP	C	C	T	rs372605534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11995276C>T	ENST00000333796.3	-	1	1310	c.994G>A	c.(994-996)Gac>Aac	p.D332N	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	332	USP.			D -> N (in Ref. 1; AAR91701). {ECO:0000305}.	apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.D332N(1)		central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						TAATGTCCGTCGTGACAACTC	0.493													T|||	288	0.057508	0.1876	0.0288	5008	,	,		20795	0.005		0.003	False		,,,				2504	0.0123				p.D332N		Atlas-SNP	.											USP17L2,NS,carcinoma,0,1	USP17L2	47	1	1	Substitution - Missense(1)	ovary(1)	c.G994A						scavenged	.						21.0	24.0	23.0					8																	11995276		1690	3931	5621	SO:0001583	missense	377630	exon1			GTCCGTCGTGACA	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"""deubiquitinating enzyme 3"""	610186	"""ubiquitin specific peptidase 17-like 2"""				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.994G>A	8.37:g.11995276C>T	ENSP00000333329:p.Asp332Asn	Somatic	322	2	0.00621118		WXS	Illumina HiSeq	Phase_I	351	148	0.421652	NM_201402		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	.	.	.	.	.	.	.	.	.	.	T	4.883	0.164168	0.09287	.	.	ENSG00000223443	ENST00000333796	T	0.28895	1.59	0.935	-0.328	0.12690	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.717965	0.12292	N	0.481969	T	0.12817	0.0311	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42378	-0.9455	8	0.08381	T	0.77	.	6.32	0.21213	0.0:0.6535:0.0:0.3465	.	332	Q6R6M4	U17L2_HUMAN	N	332	ENSP00000333329:D332N	ENSP00000333329:D332N	D	-	1	0	USP17L2	12032685	1.000000	0.71417	0.001000	0.08648	0.007000	0.05969	2.426000	0.44731	-0.621000	0.05633	-0.849000	0.03036	GAC	.	.	weak		0.493	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402	
C8orf82	414919	hgsc.bcm.edu	37	8	145754187	145754187	+	Silent	SNP	C	C	G	rs115228909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145754187C>G	ENST00000524821.1	-	1	329	c.114G>C	c.(112-114)ccG>ccC	p.P38P	C8orf82_ENST00000313465.5_Silent_p.P38P|LRRC24_ENST00000529415.2_5'Flank|LRRC24_ENST00000533758.1_5'Flank			Q6P1X6	CH082_HUMAN	chromosome 8 open reading frame 82	38										endometrium(1)|urinary_tract(1)	2						CGCGGGTCCGCGGCTCCGGAC	0.746													c|||	780	0.155751	0.5635	0.0403	5008	,	,		6049	0.001		0.004	False		,,,				2504	0.002				p.P38P		Atlas-SNP	.											.	C8orf82	7	.	0			c.G114C						PASS	.	G		1591,2607		290,1011,798	5.0	6.0	6.0		114	-0.9	0.1	8	dbSNP_132	6	49,8371		2,45,4163	no	coding-synonymous	C8orf82	NM_001001795.1		292,1056,4961	GG,GC,CC		0.5819,37.899,12.9973		38/217	145754187	1640,10978	2099	4210	6309	SO:0001819	synonymous_variant	414919	exon1			GGTCCGCGGCTCC		CCDS34970.1	8q24	2012-04-18			ENSG00000213563	ENSG00000213563			33826	protein-coding gene	gene with protein product						12477932	Standard	NM_001001795		Approved	MGC70857	uc003zdp.1	Q6P1X6	OTTHUMG00000165181	ENST00000524821.1:c.114G>C	8.37:g.145754187C>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_001001795	Q6GMR2|Q6P2Q7	Silent	SNP	ENST00000524821.1	37	CCDS34970.1	294	0.1346153846153846	277	0.5630081300813008	15	0.04143646408839779	0	0.0	2	0.002638522427440633	c	7.737	0.700437	0.15106	0.37899	0.005819	ENSG00000213563	ENST00000527462	.	.	.	4.65	-0.859	0.10685	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999987	.	.	.	.	.	.	T	0.45512	-0.9256	3	.	.	.	-15.6032	3.0047	0.06025	0.1607:0.2923:0.4219:0.1251	.	.	.	.	P	87	.	.	R	-	2	0	C8orf82	145724995	0.038000	0.19896	0.066000	0.19879	0.001000	0.01503	-1.219000	0.02973	-0.475000	0.06852	-2.111000	0.00353	CGC	C|0.864;G|0.136	0.136	strong		0.746	C8orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382503.1	NM_001001795	
RACGAP1	29127	hgsc.bcm.edu	37	12	50384469	50384469	+	Silent	SNP	A	A	G	rs56699050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50384469A>G	ENST00000427314.2	-	18	2044	c.1821T>C	c.(1819-1821)ccT>ccC	p.P607P	RACGAP1_ENST00000548961.1_Intron|RACGAP1_ENST00000454520.2_Silent_p.P607P|RACGAP1_ENST00000312377.5_Silent_p.P607P|RACGAP1_ENST00000551016.1_Silent_p.P607P|RACGAP1_ENST00000547905.1_Silent_p.P607P|RACGAP1_ENST00000434422.1_Silent_p.P607P	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						CTGCATACCTAGGAGTGTTCT	0.403													G|||	407	0.08127	0.2988	0.0173	5008	,	,		18804	0.0		0.0	False		,,,				2504	0.0				p.P607P		Atlas-SNP	.											.	RACGAP1	36	.	0			c.T1821C						PASS	.	G	,,	1092,3314	721.2+/-409.1	136,820,1247	106.0	109.0	108.0		1821,1821,1821	2.9	1.0	12	dbSNP_129	108	5,8595	819.1+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	RACGAP1	NM_001126103.1,NM_001126104.1,NM_013277.3	,,	136,825,5542	GG,GA,AA		0.0581,24.7844,8.4346	,,	607/633,607/633,607/633	50384469	1097,11909	2203	4300	6503	SO:0001819	synonymous_variant	29127	exon18			ATACCTAGGAGTG		CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000427314.2:c.1821T>C	12.37:g.50384469A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_013277		Silent	SNP	ENST00000427314.2	37	CCDS8795.1																																																																																			A|0.918;G|0.082	0.082	strong		0.403	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277	
SLC27A6	28965	hgsc.bcm.edu	37	5	128362830	128362830	+	Silent	SNP	A	A	G	rs2304578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:128362830A>G	ENST00000262462.4	+	7	2270	c.1260A>G	c.(1258-1260)gaA>gaG	p.E420E	SLC27A6_ENST00000395266.1_Silent_p.E420E|SLC27A6_ENST00000506176.1_Silent_p.E420E			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	420					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)		TTGCAGGAGAACCTGGACTTC	0.378													A|||	352	0.0702875	0.2042	0.036	5008	,	,		19304	0.0188		0.0159	False		,,,				2504	0.0225				p.E420E		Atlas-SNP	.											.	SLC27A6	112	.	0			c.A1260G						PASS	.	A	,	735,3671	297.0+/-284.5	58,619,1526	77.0	80.0	79.0		1260,1260	2.1	1.0	5	dbSNP_100	79	147,8453	72.3+/-134.9	0,147,4153	no	coding-synonymous,coding-synonymous	SLC27A6	NM_001017372.1,NM_014031.3	,	58,766,5679	GG,GA,AA		1.7093,16.6818,6.7815	,	420/620,420/620	128362830	882,12124	2203	4300	6503	SO:0001819	synonymous_variant	28965	exon7			AGGAGAACCTGGA	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.1260A>G	5.37:g.128362830A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	161	87	0.540373	NM_001017372	Q6IAM5|Q7Z6E6|Q86YF6	Silent	SNP	ENST00000262462.4	37	CCDS4145.1																																																																																			A|0.935;G|0.065	0.065	strong		0.378	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031	
ZNF80	7634	hgsc.bcm.edu	37	3	113955726	113955726	+	Nonsense_Mutation	SNP	G	G	A	rs79892855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113955726G>A	ENST00000482457.2	-	1	699	c.196C>T	c.(196-198)Cga>Tga	p.R66*	RP11-553L6.2_ENST00000493033.1_RNA|RP11-553L6.2_ENST00000481773.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	66					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			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)				TGCTGATGTCGAACAAGGAGG	0.483													G|||	74	0.0147764	0.053	0.0043	5008	,	,		24200	0.0		0.0	False		,,,				2504	0.001				p.R66X	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.C196T						PASS	.	G	stop/ARG	188,4218	120.4+/-158.0	5,178,2020	105.0	90.0	95.0		196	-1.3	0.0	3	dbSNP_131	95	0,8600		0,0,4300	yes	stop-gained	ZNF80	NM_007136.3		5,178,6320	AA,AG,GG		0.0,4.2669,1.4455		66/274	113955726	188,12818	2203	4300	6503	SO:0001587	stop_gained	7634	exon1			GATGTCGAACAAG	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.196C>T	3.37:g.113955726G>A	ENSP00000417192:p.Arg66*	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_007136	Q6NSW4|Q6NT14	Nonsense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	28	0.01282051282051282	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	0	0.0	G	33	5.211008	0.95069	0.042669	0.0	ENSG00000174255	ENST00000482457	.	.	.	3.01	-1.33	0.09172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	0.2983	0.00269	0.2292:0.1648:0.2619:0.3441	.	.	.	.	X	66	.	ENSP00000309812:R66X	R	-	1	2	ZNF80	115438416	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.585000	0.00423	-0.318000	0.08665	-0.136000	0.14681	CGA	G|0.987;A|0.013	0.013	strong		0.483	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
LDB3	11155	hgsc.bcm.edu	37	10	88446985	88446985	+	Silent	SNP	T	T	C	rs76615432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:88446985T>C	ENST00000372066.3	+	5	583	c.504T>C	c.(502-504)gaT>gaC	p.D168D	LDB3_ENST00000352360.5_Intron|LDB3_ENST00000361373.4_Intron|LDB3_ENST00000429277.2_Silent_p.D283D|LDB3_ENST00000263066.6_Silent_p.D168D|LDB3_ENST00000458213.2_Silent_p.D168D|LDB3_ENST00000542786.1_3'UTR|LDB3_ENST00000372056.4_Silent_p.D283D|LDB3_ENST00000310944.6_Intron	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	149	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	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		
KRT75	9119	hgsc.bcm.edu	37	12	52822464	52822464	+	Missense_Mutation	SNP	T	T	C	rs2232402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52822464T>C	ENST00000252245.5	-	6	1319	c.1099A>G	c.(1099-1101)Atc>Gtc	p.I367V	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	367	Coil 2.|Rod.		I -> V (in dbSNP:rs2232402).		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)		ATTTCAGAGATCTCTTGTTTG	0.512													T|||	103	0.0205671	0.0764	0.0029	5008	,	,		21269	0.0		0.0	False		,,,				2504	0.0				p.I367V		Atlas-SNP	.											KRT75,NS,carcinoma,+2,3	KRT75	75	3	0			c.A1099G						PASS	.	T	VAL/ILE	373,4033	189.2+/-215.4	16,341,1846	193.0	158.0	170.0		1099	5.2	1.0	12	dbSNP_98	170	1,8599		0,1,4299	yes	missense	KRT75	NM_004693.2	29	16,342,6145	CC,CT,TT		0.0116,8.4657,2.8756	probably-damaging	367/552	52822464	374,12632	2203	4300	6503	SO:0001583	missense	9119	exon6			CAGAGATCTCTTG	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.1099A>G	12.37:g.52822464T>C	ENSP00000252245:p.Ile367Val	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	T	18.53	3.644098	0.67244	0.084657	1.16E-4	ENSG00000170454	ENST00000252245	D	0.89617	-2.54	5.18	5.18	0.71444	Prefoldin (1);Filament (1);	0.000000	0.51477	D	0.000081	T	0.59128	0.2171	M	0.81802	2.56	0.42420	D	0.992635	D	0.69078	0.997	D	0.70935	0.971	T	0.77680	-0.2497	10	0.66056	D	0.02	.	15.0403	0.71785	0.0:0.0:0.0:1.0	rs2232402;rs52796316;rs60556458;rs2232402	367	O95678	K2C75_HUMAN	V	367	ENSP00000252245:I367V	ENSP00000252245:I367V	I	-	1	0	KRT75	51108731	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	5.064000	0.64338	1.966000	0.57179	0.459000	0.35465	ATC	T|0.969;C|0.031	0.031	strong		0.512	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
TMEM47	83604	hgsc.bcm.edu	37	X	34674970	34674970	+	Silent	SNP	C	C	G	rs5928617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	124	0	0		WXS	Illumina HiSeq	Phase_I	166	85	0.512048	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	
MARCO	8685	hgsc.bcm.edu	37	2	119739063	119739063	+	Missense_Mutation	SNP	T	T	C	rs6761637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:119739063T>C	ENST00000327097.4	+	9	980	c.845T>C	c.(844-846)tTc>tCc	p.F282S	MARCO_ENST00000541757.1_Missense_Mutation_p.F204S	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	282	Collagen-like.		F -> S (in dbSNP:rs6761637).		apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						AAAGGTGACTTCGGGAGGCCA	0.532													C|||	844	0.16853	0.3548	0.0476	5008	,	,		16791	0.123		0.0358	False		,,,				2504	0.1861				p.F282S	GBM(8;18 374 7467 11269 32796)	Atlas-SNP	.											MARCO,brain,glioma,0,1	MARCO	120	1	0			c.T845C						PASS	.	C	SER/PHE	1300,3106	690.3+/-405.2	199,902,1102	32.0	35.0	34.0		845	4.4	0.0	2	dbSNP_116	34	448,8152	796.4+/-407.5	13,422,3865	yes	missense	MARCO	NM_006770.3	155	212,1324,4967	CC,CT,TT		5.2093,29.5052,13.44	benign	282/521	119739063	1748,11258	2203	4300	6503	SO:0001583	missense	8685	exon9			GTGACTTCGGGAG	AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"""scavenger receptor class A, member 2"""	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.845T>C	2.37:g.119739063T>C	ENSP00000318916:p.Phe282Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_006770	B4DW79|Q9Y5S3	Missense_Mutation	SNP	ENST00000327097.4	37	CCDS2124.1	269	0.12316849816849818	145	0.29471544715447157	20	0.055248618784530384	72	0.1258741258741259	32	0.04221635883905013	C	3.494	-0.103147	0.06967	0.295052	0.052093	ENSG00000019169	ENST00000327097;ENST00000410021;ENST00000541757	D;D	0.93247	-1.68;-3.19	5.33	4.45	0.53987	.	0.611500	0.15982	N	0.235279	T	0.00012	0.0000	N	0.02403	-0.565	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08207	-1.0733	8	.	.	.	.	7.9847	0.30205	0.0:0.819:0.0:0.181	rs6761637;rs52807463;rs59619363;rs6761637	282	Q9UEW3	MARCO_HUMAN	S	282;282;204	ENSP00000318916:F282S;ENSP00000441769:F204S	.	F	+	2	0	MARCO	119455533	0.001000	0.12720	0.022000	0.16811	0.051000	0.14879	0.546000	0.23284	0.834000	0.34852	-0.119000	0.15052	TTC	T|0.873;C|0.127	0.127	strong		0.532	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770	
PCDHGB6	56100	hgsc.bcm.edu	37	5	140789933	140789933	+	Missense_Mutation	SNP	G	G	A	rs3749767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140789933G>A	ENST00000520790.1	+	1	2164	c.2164G>A	c.(2164-2166)Gct>Act	p.A722T	PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_5'Flank|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	722			A -> T (in dbSNP:rs3749767).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			TCTCAGCCCTGCTACTTGGGA	0.542													.|||	1536	0.306709	0.5265	0.2594	5008	,	,		20334	0.1935		0.1918	False		,,,				2504	0.2781				p.A722T		Atlas-SNP	.											.	PCDHGB6	120	.	0			c.G2164A						PASS	.	A	,,,,,,,,,,,,,THR/ALA,,THR/ALA	1995,2125		483,1029,548	141.0	147.0	145.0		,,,,,,,,,,,,,2164,,2164	-10.2	0.0	5	dbSNP_107	145	1821,6585		192,1437,2574	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,missense	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032100.1	,,,,,,,,,,,,,58,,58	675,2466,3122	AA,AG,GG		21.6631,48.4223,30.4646	,,,,,,,,,,,,,,,	,,,,,,,,,,,,,722/931,,722/821	140789933	3816,8710	2060	4203	6263	SO:0001583	missense	56100	exon1			AGCCCTGCTACTT	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.2164G>A	5.37:g.140789933G>A	ENSP00000428603:p.Ala722Thr	Somatic	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	345	157	0.455072	NM_032100	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	37	CCDS54929.1	620	0.2838827838827839	250	0.508130081300813	94	0.2596685082872928	117	0.20454545454545456	159	0.20976253298153033	a	5.515	0.279981	0.10458	0.484223	0.216631	ENSG00000253305	ENST00000520790	T	0.14391	2.51	5.11	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.12837	0.003;0.008	T	0.37957	-0.9683	8	0.30854	T	0.27	.	14.1643	0.65466	0.1425:0.0:0.6368:0.2208	rs3749767;rs52817710;rs61103125;rs3749767	722;722	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	T	722	ENSP00000428603:A722T	ENSP00000428603:A722T	A	+	1	0	PCDHGB6	140770117	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.063000	0.01388	-3.157000	0.00229	-2.917000	0.00090	GCT	G|0.702;A|0.298	0.298	strong		0.542	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926	
ZBBX	79740	hgsc.bcm.edu	37	3	167000256	167000256	+	Missense_Mutation	SNP	G	G	C	rs12638625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:167000256G>C	ENST00000392766.2	-	19	2247	c.1907C>G	c.(1906-1908)gCa>gGa	p.A636G	ZBBX_ENST00000307529.5_Missense_Mutation_p.A675G|ZBBX_ENST00000455345.2_Missense_Mutation_p.A675G|ZBBX_ENST00000392764.1_Missense_Mutation_p.A607G|ZBBX_ENST00000392767.2_Missense_Mutation_p.A636G	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	636			A -> G (in dbSNP:rs12638625). {ECO:0000269|PubMed:14702039}.			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						TGGAAAATTTGCTGTTGAAGG	0.338																																					p.A675G		Atlas-SNP	.											.	ZBBX	299	.	0			c.C2024G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	982,2656		134,714,971	124.0	120.0	121.0		2024,1820,1907	1.5	0.8	3	dbSNP_120	121	2451,5685		353,1745,1970	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	60,60,60	487,2459,2941	CC,CG,GG		30.1254,26.9929,29.1575	benign,benign,benign	675/840,607/772,636/801	167000256	3433,8341	1819	4068	5887	SO:0001583	missense	79740	exon20			AAATTTGCTGTTG	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.1907C>G	3.37:g.167000256G>C	ENSP00000376519:p.Ala636Gly	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	171	75	0.438596	NM_001199201	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	861	0.3942307692307692	135	0.27439024390243905	136	0.3756906077348066	370	0.6468531468531469	220	0.29023746701846964	G	6.009	0.370125	0.11352	0.269929	0.301254	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.14391	2.68;2.68;2.53;2.53;2.51	5.28	1.47	0.22746	.	0.759635	0.12007	N	0.508267	T	0.00012	0.0000	L	0.53249	1.67	0.49130	P	2.4400000000002198E-4	B;B	0.28760	0.221;0.141	B;B	0.33295	0.161;0.077	T	0.21724	-1.0237	9	0.40728	T	0.16	-1.7821	4.4295	0.11520	0.2482:0.0:0.5988:0.153	rs12638625;rs52789532;rs12638625	675;636	A8MT70-2;A8MT70	.;ZBBX_HUMAN	G	636;636;675;675;607	ENSP00000376519:A636G;ENSP00000376520:A636G;ENSP00000390232:A675G;ENSP00000305065:A675G;ENSP00000376517:A607G	ENSP00000305065:A675G	A	-	2	0	ZBBX	168482950	0.997000	0.39634	0.831000	0.32960	0.003000	0.03518	0.491000	0.22419	-0.014000	0.14175	-0.911000	0.02809	GCA	G|0.622;C|0.378	0.378	strong		0.338	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
VWF	7450	hgsc.bcm.edu	37	12	6182828	6182828	+	Missense_Mutation	SNP	A	A	T	rs1800387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6182828A>T	ENST00000261405.5	-	8	1208	c.954T>A	c.(952-954)aaT>aaA	p.N318K		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	318	TIL 1.		N -> K (in dbSNP:rs1800387).		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GACACATTTCATTGATGTGCA	0.537													A|||	779	0.155551	0.4705	0.0735	5008	,	,		20376	0.001		0.0328	False		,,,				2504	0.0736				p.N318K		Atlas-SNP	.											.	VWF	338	.	0			c.T954A						PASS	.	A	LYS/ASN	1814,2592	532.8+/-373.5	380,1054,769	121.0	101.0	108.0		954	-3.5	0.0	12	dbSNP_89	108	222,8378	92.8+/-154.8	1,220,4079	yes	missense	VWF	NM_000552.3	94	381,1274,4848	TT,TA,AA		2.5814,41.1711,15.6543	benign	318/2814	6182828	2036,10970	2203	4300	6503	SO:0001583	missense	7450	exon8			CATTTCATTGATG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.954T>A	12.37:g.6182828A>T	ENSP00000261405:p.Asn318Lys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	28	0.318182	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	283	0.1295787545787546	235	0.47764227642276424	30	0.08287292817679558	0	0.0	18	0.023746701846965697	A	13.32	2.203429	0.38905	0.411711	0.025814	ENSG00000110799	ENST00000261405	D	0.90069	-2.61	5.07	-3.54	0.04653	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	1.028730	0.07777	N	0.952644	T	0.00012	0.0000	L	0.42632	1.34	0.09310	P	0.99999999821589	B;P	0.42161	0.005;0.772	B;B	0.40444	0.02;0.329	T	0.09357	-1.0678	9	0.32370	T	0.25	.	1.2239	0.01929	0.3764:0.2668:0.2306:0.1262	rs1800387;rs56444638;rs1800387	318;318	B4DNX0;P04275	.;VWF_HUMAN	K	318	ENSP00000261405:N318K	ENSP00000261405:N318K	N	-	3	2	VWF	6053089	0.916000	0.31088	0.012000	0.15200	0.881000	0.50899	0.118000	0.15605	-0.694000	0.05113	0.402000	0.26972	AAT	A|0.839;T|0.161	0.161	strong		0.537	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
LOXHD1	125336	hgsc.bcm.edu	37	18	44102193	44102193	+	Silent	SNP	G	G	A	rs187103862		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44102193G>A	ENST00000398722.4	-	25	4121	c.4122C>T	c.(4120-4122)atC>atT	p.I1374I	LOXHD1_ENST00000441551.2_Silent_p.I1446I|LOXHD1_ENST00000582408.1_Silent_p.I541I|LOXHD1_ENST00000536736.1_Silent_p.I1652I|LOXHD1_ENST00000300591.6_Silent_p.I541I|LOXHD1_ENST00000579038.1_Silent_p.I445I|LOXHD1_ENST00000441893.2_Silent_p.I585I			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	1374	PLAT 10. {ECO:0000255|PROSITE- ProRule:PRU00152}.				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)	p.I1374I(1)|p.I1652I(1)		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						CATCCTCCCCGATGAGAAAGA	0.572													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19237	0.0		0.0	False		,,,				2504	0.0				p.I1652I		Atlas-SNP	.											LOXHD1_ENST00000398722,NS,carcinoma,0,2	LOXHD1	367	2	2	Substitution - coding silent(2)	endometrium(2)	c.C4956T						PASS	.	G	,	1,1383		0,1,691	114.0	101.0	105.0		1623,4956	-5.2	0.4	18		105	0,3182		0,0,1591	no	coding-synonymous,coding-synonymous	LOXHD1	NM_001145472.2,NM_144612.6	,	0,1,2282	AA,AG,GG		0.0,0.0723,0.0219	,	541/1115,1652/2212	44102193	1,4565	692	1591	2283	SO:0001819	synonymous_variant	125336	exon32			CTCCCCGATGAGA	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.4122C>T	18.37:g.44102193G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Silent	SNP	ENST00000398722.4	37																																																																																				G|1.000;A|0.000	0.000	strong		0.572	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
NSMCE1	197370	hgsc.bcm.edu	37	16	27238110	27238110	+	Silent	SNP	C	C	T	rs1127228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27238110C>T	ENST00000361439.4	-	6	630	c.531G>A	c.(529-531)gaG>gaA	p.E177E	NSMCE1_ENST00000565384.1_5'UTR	NM_145080.3	NP_659547.2	Q8WV22	NSE1_HUMAN	non-SMC element 1 homolog (S. cerevisiae)	177					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|intracellular signal transduction (GO:0035556)|positive regulation of response to DNA damage stimulus (GO:2001022)|protein ubiquitination (GO:0016567)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)	7						GGATGTATTGCTCCATCTCCA	0.627													C|||	1582	0.315895	0.1747	0.2334	5008	,	,		20417	0.4653		0.3519	False		,,,				2504	0.3742				p.E177E		Atlas-SNP	.											.	NSMCE1	28	.	0			c.G531A						PASS	.	C		772,3422		63,646,1388	121.0	130.0	127.0		531	3.1	1.0	16	dbSNP_86	127	2871,5543		507,1857,1843	no	coding-synonymous	NSMCE1	NM_145080.3		570,2503,3231	TT,TC,CC		34.1217,18.4072,28.8944		177/267	27238110	3643,8965	2097	4207	6304	SO:0001819	synonymous_variant	197370	exon6			GTATTGCTCCATC	AF161451	CCDS10628.2	16p12.1	2010-03-23	2006-07-05		ENSG00000169189	ENSG00000169189			29897	protein-coding gene	gene with protein product						11927594	Standard	XM_005255163		Approved	NSE1	uc002doi.1	Q8WV22	OTTHUMG00000131674	ENST00000361439.4:c.531G>A	16.37:g.27238110C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_145080	D3DWF6|Q9P045|Q9P049	Silent	SNP	ENST00000361439.4	37	CCDS10628.2																																																																																			C|0.668;T|0.332	0.332	strong		0.627	NSMCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254577.3	NM_145080	
EP400	57634	hgsc.bcm.edu	37	12	132547090	132547090	+	Silent	SNP	A	A	G	rs7974276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132547090A>G	ENST00000333577.4	+	48	8395	c.8286A>G	c.(8284-8286)caA>caG	p.Q2762Q	EP400_ENST00000389561.2_Silent_p.Q2726Q|EP400_ENST00000389562.2_Silent_p.Q2725Q|EP400_ENST00000330386.6_Silent_p.Q2645Q|EP400_ENST00000332482.4_Silent_p.Q2689Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2762	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcaacaacagcagc	0.557													G|||	1450	0.289537	0.6316	0.1671	5008	,	,		15386	0.1865		0.1322	False		,,,				2504	0.182				p.Q2726Q		Atlas-SNP	.											EP400,colon,carcinoma,0,3	EP400	370	3	0			c.A8178G						scavenged	.						26.0	30.0	29.0					12																	132547090		2181	4250	6431	SO:0001819	synonymous_variant	57634	exon47			GCAGCAACAACAG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8286A>G	12.37:g.132547090A>G		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	112	75	0.669643	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				A|0.794;G|0.206	0.206	strong		0.557	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
TEX19	400629	hgsc.bcm.edu	37	17	80320303	80320303	+	Missense_Mutation	SNP	G	G	T	rs147220016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80320303G>T	ENST00000333437.4	+	2	587	c.277G>T	c.(277-279)Ggg>Tgg	p.G93W		NM_207459.3	NP_997342.1	Q8NA77	TEX19_HUMAN	testis expressed 19	93					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6						GCCTGTGCAGGGGGGCTCTGA	0.652													.|||	10	0.00199681	0.0008	0.0086	5008	,	,		18460	0.0		0.002	False		,,,				2504	0.001				p.G93W		Atlas-SNP	.											.	TEX19	17	.	0			c.G277T						PASS	.	G	TRP/GLY	2,4404	4.2+/-10.8	0,2,2201	39.0	42.0	41.0		277	1.9	0.0	17	dbSNP_134	41	32,8566	21.0+/-64.5	0,32,4267	yes	missense	TEX19	NM_207459.3	184	0,34,6468	TT,TG,GG		0.3722,0.0454,0.2615	probably-damaging	93/165	80320303	34,12970	2203	4299	6502	SO:0001583	missense	400629	exon2			GTGCAGGGGGGCT	BC016939	CCDS11809.1	17q25.3	2009-04-14			ENSG00000182459	ENSG00000182459			33802	protein-coding gene	gene with protein product		615647					Standard	NM_207459		Approved	FLJ35767	uc002keq.3	Q8NA77	OTTHUMG00000132857	ENST00000333437.4:c.277G>T	17.37:g.80320303G>T	ENSP00000331500:p.Gly93Trp	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	74	26	0.351351	NM_207459		Missense_Mutation	SNP	ENST00000333437.4	37	CCDS11809.1	5	0.0022893772893772895	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	13.50	2.255828	0.39896	4.54E-4	0.003722	ENSG00000182459	ENST00000333437	.	.	.	3.22	1.94	0.25998	.	.	.	.	.	T	0.39627	0.1085	L	0.29908	0.895	0.09310	N	1	D	0.69078	0.997	D	0.71870	0.975	T	0.20739	-1.0266	8	0.66056	D	0.02	-41.824	8.5403	0.33388	0.0:0.4168:0.5832:0.0	.	93	Q8NA77	TEX19_HUMAN	W	93	.	ENSP00000331500:G93W	G	+	1	0	TEX19	77913592	0.022000	0.18835	0.005000	0.12908	0.002000	0.02628	0.388000	0.20735	0.628000	0.30357	0.462000	0.41574	GGG	G|0.997;T|0.003	0.003	strong		0.652	TEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256331.1	NM_207459	
HTR6	3362	hgsc.bcm.edu	37	1	19992372	19992372	+	Silent	SNP	G	G	T	rs8192529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19992372G>T	ENST00000289753.1	+	1	593	c.126G>T	c.(124-126)gcG>gcT	p.A42A		NM_000871.1	NP_000862.1	P50406	5HT6R_HUMAN	5-hydroxytryptamine (serotonin) receptor 6, G protein-coupled	42					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)	TGACGGCGGCGGCCAACTCGC	0.711													G|||	142	0.0283546	0.0303	0.0259	5008	,	,		13132	0.001		0.0517	False		,,,				2504	0.0317				p.A42A	Esophageal Squamous(168;1879 2619 6848 21062)	Atlas-SNP	.											.	HTR6	38	.	0			c.G126T						PASS	.	G		74,4278		3,68,2105	11.0	11.0	11.0		126	0.2	1.0	1	dbSNP_117	11	223,8271		2,219,4026	no	coding-synonymous	HTR6	NM_000871.1		5,287,6131	TT,TG,GG		2.6254,1.7004,2.312		42/441	19992372	297,12549	2176	4247	6423	SO:0001819	synonymous_variant	3362	exon1			GGCGGCGGCCAAC	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.126G>T	1.37:g.19992372G>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	23	8	0.347826	NM_000871	Q13640|Q5TGZ1	Silent	SNP	ENST00000289753.1	37	CCDS197.1																																																																																			G|0.970;T|0.030	0.030	strong		0.711	HTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007704.1	NM_000871	
CNGB3	54714	hgsc.bcm.edu	37	8	87680282	87680282	+	Missense_Mutation	SNP	C	C	T	rs16916632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87680282C>T	ENST00000320005.5	-	5	655	c.608G>A	c.(607-609)cGa>cAa	p.R203Q		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	203			R -> Q (in ACHM3; unknown pathological significance; dbSNP:rs16916632). {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						AAGTTTAATTCGCTTTAAGTA	0.398													C|||	278	0.0555112	0.1952	0.0101	5008	,	,		14978	0.003		0.0	False		,,,				2504	0.0102				p.R203Q		Atlas-SNP	.											.	CNGB3	176	.	0			c.G608A						PASS	.	C	GLN/ARG	679,3727	286.0+/-278.5	46,587,1570	238.0	228.0	231.0		608	-6.8	0.0	8	dbSNP_123	231	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CNGB3	NM_019098.4	43	46,589,5868	TT,TC,CC		0.0233,15.4108,5.236	benign	203/810	87680282	681,12325	2203	4300	6503	SO:0001583	missense	54714	exon5			TTAATTCGCTTTA	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.608G>A	8.37:g.87680282C>T	ENSP00000316605:p.Arg203Gln	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	185	86	0.464865	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	73	0.033424908424908424	72	0.14634146341463414	1	0.0027624309392265192	0	0.0	0	0.0	C	12.18	1.862010	0.32884	0.154108	2.33E-4	ENSG00000170289	ENST00000320005	D	0.97016	-4.21	6.1	-6.81	0.01704	.	1.625600	0.03560	N	0.226891	T	0.07369	0.0186	L	0.40543	1.245	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.68375	-0.5425	9	0.23891	T	0.37	.	13.0899	0.59162	0.1009:0.116:0.0:0.7831	rs16916632;rs52789907;rs16916632	203;203	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	Q	203	ENSP00000316605:R203Q	ENSP00000316605:R203Q	R	-	2	0	CNGB3	87749398	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.590000	0.05760	-1.332000	0.02249	-0.143000	0.13931	CGA	C|0.951;T|0.049	0.049	strong		0.398	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098	
FOXN1	8456	hgsc.bcm.edu	37	17	26864302	26864302	+	Missense_Mutation	SNP	G	G	C	rs532648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26864302G>C	ENST00000226247.2	+	8	1824	c.1795G>C	c.(1795-1797)Gcc>Ccc	p.A599P	FOXN1_ENST00000579795.1_Missense_Mutation_p.A599P	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	599			A -> P (in dbSNP:rs532648).		defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					TGACTTGGCAGCCCCGGGCAG	0.677													C|||	1967	0.392772	0.6309	0.3862	5008	,	,		16861	0.2212		0.334	False		,,,				2504	0.3129				p.A599P		Atlas-SNP	.											.	FOXN1	51	.	0			c.G1795C						PASS	.	C	PRO/ALA	2506,1900	539.4+/-375.3	695,1116,392	39.0	40.0	39.0		1795	2.2	0.9	17	dbSNP_83	39	2419,6181	693.8+/-404.7	333,1753,2214	yes	missense	FOXN1	NM_003593.2	27	1028,2869,2606	CC,CG,GG		28.1279,43.123,37.8671	benign	599/649	26864302	4925,8081	2203	4300	6503	SO:0001583	missense	8456	exon8			TTGGCAGCCCCGG	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"""Forkhead boxes"""	12765	protein-coding gene	gene with protein product		600838	"""winged-helix nude"", ""Rowett nude"""	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.1795G>C	17.37:g.26864302G>C	ENSP00000226247:p.Ala599Pro	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_003593	B2R9Q7|O15352	Missense_Mutation	SNP	ENST00000226247.2	37	CCDS11232.1	829	0.37957875457875456	313	0.6361788617886179	137	0.3784530386740331	144	0.2517482517482518	235	0.3100263852242744	C	0.003	-2.391997	0.00200	0.56877	0.281279	ENSG00000109101	ENST00000226247	D	0.92348	-3.02	4.2	2.18	0.27775	.	0.393102	0.22159	N	0.063817	T	0.00012	0.0000	N	0.00335	-1.625	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41822	-0.9487	9	0.02654	T	1	.	5.1473	0.14991	0.1624:0.5975:0.0991:0.141	rs532648;rs3744636	599	O15353	FOXN1_HUMAN	P	599	ENSP00000226247:A599P	ENSP00000226247:A599P	A	+	1	0	FOXN1	23888429	0.000000	0.05858	0.918000	0.36340	0.306000	0.27790	0.598000	0.24074	-0.141000	0.11374	-2.896000	0.00094	GCC	G|0.618;C|0.382	0.382	strong		0.677	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1		
MRPS27	23107	hgsc.bcm.edu	37	5	71524163	71524163	+	Silent	SNP	A	A	T	rs10942927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71524163A>T	ENST00000261413.5	-	8	663	c.624T>A	c.(622-624)ctT>ctA	p.L208L	MRPS27_ENST00000515404.1_Silent_p.L152L|MRPS27_ENST00000457646.4_Silent_p.L152L|MRPS27_ENST00000513900.1_Silent_p.L222L|MRPS27_ENST00000522562.1_5'UTR	NM_015084.2	NP_055899.2	Q92552	RT27_HUMAN	mitochondrial ribosomal protein S27	208						mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)		CTGGAAGCAAAAGGGATGCAC	0.398													T|||	955	0.190695	0.1256	0.17	5008	,	,		18027	0.0218		0.3688	False		,,,				2504	0.2843				p.L208L		Atlas-SNP	.											.	MRPS27	23	.	0			c.T624A						PASS	.	T		680,3726	763.4+/-413.2	53,574,1576	156.0	152.0	153.0		624	-1.9	0.1	5	dbSNP_120	153	2944,5656	669.0+/-402.6	520,1904,1876	no	coding-synonymous	MRPS27	NM_015084.2		573,2478,3452	TT,TA,AA		34.2326,15.4335,27.8641		208/415	71524163	3624,9382	2203	4300	6503	SO:0001819	synonymous_variant	23107	exon8			AAGCAAAAGGGAT	D87453	CCDS4013.1, CCDS68890.1, CCDS75257.1	5q13.2	2012-09-13			ENSG00000113048	ENSG00000113048		"""Mitochondrial ribosomal proteins / small subunits"""	14512	protein-coding gene	gene with protein product		611989					Standard	NM_015084		Approved	KIAA0264	uc003kbz.4	Q92552	OTTHUMG00000100951	ENST00000261413.5:c.624T>A	5.37:g.71524163A>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_015084	B4DRT2|Q6P1S1	Silent	SNP	ENST00000261413.5	37	CCDS4013.1																																																																																			A|0.768;T|0.232	0.232	strong		0.398	MRPS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218560.2	NM_015084	
DLK1	8788	hgsc.bcm.edu	37	14	101201206	101201206	+	Silent	SNP	C	C	T	rs139584149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101201206C>T	ENST00000341267.4	+	5	1367	c.1125C>T	c.(1123-1125)agC>agT	p.S375S	DLK1_ENST00000331224.6_Silent_p.S302S|RP11-566J3.4_ENST00000608876.1_lincRNA	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	375					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)				CCACCTTCAGCAAGGAGGCCG	0.552													C|||	50	0.00998403	0.0371	0.0	5008	,	,		16616	0.0		0.001	False		,,,				2504	0.0				p.S375S		Atlas-SNP	.											.	DLK1	57	.	0			c.C1125T						PASS	.	C		105,4301	82.4+/-120.9	1,103,2099	92.0	92.0	92.0		1125	3.5	0.9	14	dbSNP_134	92	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	DLK1	NM_003836.5		1,107,6395	TT,TC,CC		0.0465,2.3831,0.8381		375/384	101201206	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	8788	exon5			CTTCAGCAAGGAG	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.1125C>T	14.37:g.101201206C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	26	16	0.615385	NM_003836	P15803|Q96DW5	Silent	SNP	ENST00000341267.4	37	CCDS9963.1																																																																																			C|0.991;T|0.009	0.009	strong		0.552	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
ZDHHC11	79844	hgsc.bcm.edu	37	5	825280	825280	+	Splice_Site	SNP	C	C	T	rs1809008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:825280C>T	ENST00000283441.8	-	8	1405	c.1022G>A	c.(1021-1023)cGg>cAg	p.R341Q	ZDHHC11_ENST00000424784.2_Splice_Site_p.R341Q|ZDHHC11_ENST00000503758.2_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	341			R -> Q (in dbSNP:rs1809008).			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			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)			GCAACTTACCCGTGCCGTCGA	0.537													c|||	1874	0.374201	0.6422	0.3386	5008	,	,		27210	0.4127		0.1541	False		,,,				2504	0.2239				p.R341Q		Atlas-SNP	.											.	ZDHHC11	97	.	0			c.G1022A						PASS	.	C	GLN/ARG	2381,2025		580,1221,402	159.0	115.0	130.0		1022	-0.3	0.0	5	dbSNP_92	130	854,7732		60,734,3499	yes	missense-near-splice	ZDHHC11	NM_024786.2	43	640,1955,3901	TT,TC,CC		9.9464,45.9601,24.8999	benign	341/413	825280	3235,9757	2203	4293	6496	SO:0001630	splice_region_variant	79844	exon8			CTTACCCGTGCCG	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.1023+1G>A	5.37:g.825280C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	208	208	1	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	688	0.315018315018315	298	0.6056910569105691	93	0.2569060773480663	234	0.4090909090909091	63	0.08311345646437995	N	1.075	-0.668841	0.03403	0.540399	0.099464	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.28069	1.63;1.63	0.131	-0.261	0.12963	.	.	.	.	.	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	0.43180	-0.9407	7	0.10902	T	0.67	.	.	.	.	rs1809008;rs61386472	341	Q9H8X9	ZDH11_HUMAN	Q	341	ENSP00000397719:R341Q;ENSP00000283441:R341Q	ENSP00000283441:R341Q	R	-	2	0	ZDHHC11	878280	0.003000	0.15002	0.002000	0.10522	0.002000	0.02628	-0.384000	0.07389	-1.204000	0.02648	-1.197000	0.01672	CGG	C|0.724;T|0.276	0.276	strong		0.537	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	Missense_Mutation
WBP4	11193	hgsc.bcm.edu	37	13	41639377	41639377	+	Silent	SNP	C	C	T	rs61740513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:41639377C>T	ENST00000379487.3	+	4	616	c.216C>T	c.(214-216)gcC>gcT	p.A72A	WBP4_ENST00000542082.1_Silent_p.A51A	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	72					mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		AGGCAGCTGCCCTGAAAGCAT	0.368													C|||	126	0.0251597	0.0908	0.0072	5008	,	,		14418	0.0		0.001	False		,,,				2504	0.0				p.A72A		Atlas-SNP	.											.	WBP4	40	.	0			c.C216T						PASS	.	C		411,3995	201.5+/-224.5	14,383,1806	64.0	69.0	67.0		216	2.8	1.0	13	dbSNP_129	67	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WBP4	NM_007187.3		14,385,6104	TT,TC,CC		0.0233,9.3282,3.1755		72/377	41639377	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	11193	exon4			AGCTGCCCTGAAA	AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"""formin binding protein 21"""	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.216C>T	13.37:g.41639377C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_007187	B7Z4M2|Q32P29	Silent	SNP	ENST00000379487.3	37	CCDS9375.1																																																																																			C|0.967;T|0.033	0.033	strong		0.368	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187	
SSRP1	6749	hgsc.bcm.edu	37	11	57101000	57101000	+	Silent	SNP	G	G	C	rs7932705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57101000G>C	ENST00000278412.2	-	4	521	c.255C>G	c.(253-255)ctC>ctG	p.L85L		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	85					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						AGAAATCAGAGAGTTTCTCAA	0.468													G|||	76	0.0151757	0.0537	0.0072	5008	,	,		19918	0.0		0.0	False		,,,				2504	0.0				p.L85L	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.C255G						PASS	.	G		189,4213	122.1+/-159.5	2,185,2014	90.0	87.0	88.0		255	-0.2	1.0	11	dbSNP_116	88	5,8587	3.7+/-12.6	0,5,4291	no	coding-synonymous	SSRP1	NM_003146.2		2,190,6305	CC,CG,GG		0.0582,4.2935,1.493		85/710	57101000	194,12800	2201	4296	6497	SO:0001819	synonymous_variant	6749	exon4			ATCAGAGAGTTTC	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.255C>G	11.37:g.57101000G>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	111	63	0.567568	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			G|0.986;C|0.014	0.014	strong		0.468	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146	
PALLD	23022	hgsc.bcm.edu	37	4	169432841	169432841	+	Silent	SNP	G	G	A	rs1806729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169432841G>A	ENST00000505667.1	+	2	359	c.186G>A	c.(184-186)aaG>aaA	p.K62K	PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000261509.6_Silent_p.K62K|PALLD_ENST00000333488.4_5'UTR			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	62					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)		ACTCGGAAAAGGAGATCTCGC	0.507									Pancreatic Cancer, Familial Clustering of				G|||	1182	0.236022	0.2231	0.1844	5008	,	,		18749	0.1925		0.329	False		,,,				2504	0.2393				p.K62K	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.G186A						PASS	.	G	,	1040,3366	361.4+/-315.7	139,762,1302	39.0	40.0	40.0		186,186	3.7	1.0	4	dbSNP_92	40	2789,5811	426.7+/-355.4	460,1869,1971	no	coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_016081.3	,	599,2631,3273	AA,AG,GG		32.4302,23.6042,29.4403	,	62/1124,62/1107	169432841	3829,9177	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	GGAAAAGGAGATC	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.186G>A	4.37:g.169432841G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			G|0.728;A|0.272	0.272	strong		0.507	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
CDH26	60437	hgsc.bcm.edu	37	20	58558015	58558015	+	Missense_Mutation	SNP	T	T	C	rs6015609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58558015T>C	ENST00000244047.5	+	5	742	c.431T>C	c.(430-432)aTt>aCt	p.I144T	CDH26_ENST00000348616.4_Missense_Mutation_p.I144T			Q8IXH8	CAD26_HUMAN	cadherin 26	144	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> T (in dbSNP:rs6015609).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			ACAGGAAAAATTGTGGATACA	0.383													T|||	272	0.0543131	0.1989	0.0101	5008	,	,		19452	0.0		0.002	False		,,,				2504	0.0				p.I144T		Atlas-SNP	.											CDH26_ENST00000244047,colon,carcinoma,0,2	CDH26	229	2	0			c.T431C						PASS	.	T	THR/ILE	677,3729	286.9+/-279.0	43,591,1569	163.0	164.0	163.0		431	1.2	0.0	20	dbSNP_114	163	7,8593	5.7+/-21.5	0,7,4293	yes	missense	CDH26	NM_177980.2	89	43,598,5862	CC,CT,TT		0.0814,15.3654,5.2591	possibly-damaging	144/833	58558015	684,12322	2203	4300	6503	SO:0001583	missense	60437	exon5			GAAAAATTGTGGA	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"""Cadherins / Major cadherins"""	15902	protein-coding gene	gene with protein product			"""cadherin-like 26"""				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.431T>C	20.37:g.58558015T>C	ENSP00000244047:p.Ile144Thr	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	219	107	0.488584	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	37		110	0.05036630036630037	107	0.21747967479674796	3	0.008287292817679558	0	0.0	0	0.0	T	9.677	1.148287	0.21288	0.153654	8.14E-4	ENSG00000124215	ENST00000244047;ENST00000348616	T;T	0.60548	0.18;0.18	4.91	1.24	0.21308	.	0.657454	0.14814	N	0.296857	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.14438	0.01	B	0.20577	0.03	T	0.13361	-1.0512	9	0.12766	T	0.61	.	4.1382	0.10181	0.1494:0.1729:0.0:0.6776	rs6015609;rs58633041;rs6015609	144	Q8IXH8-4	.	T	144	ENSP00000244047:I144T;ENSP00000339390:I144T	ENSP00000244047:I144T	I	+	2	0	CDH26	57991410	0.000000	0.05858	0.000000	0.03702	0.615000	0.37417	0.068000	0.14531	0.213000	0.20722	0.533000	0.62120	ATT	T|0.938;C|0.062	0.062	strong		0.383	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	
MICAL2	9645	hgsc.bcm.edu	37	11	12225946	12225946	+	Silent	SNP	T	T	G	rs3763823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:12225946T>G	ENST00000256194.4	+	4	702	c.414T>G	c.(412-414)cgT>cgG	p.R138R	MICAL2_ENST00000537344.1_Silent_p.R138R|MICAL2_ENST00000342902.5_Silent_p.R138R|MICAL2_ENST00000527546.1_Silent_p.R138R|MICAL2_ENST00000527195.1_3'UTR|MICAL2_ENST00000379612.3_Silent_p.R138R	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	138	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		ATGACCTTCGTGGCCTGGGAG	0.547													G|||	3511	0.701078	0.8911	0.7089	5008	,	,		20509	0.6508		0.5905	False		,,,				2504	0.6043				p.R138R		Atlas-SNP	.											MICAL2,colon,carcinoma,0,2	MICAL2	114	2	0			c.T414G						PASS	.	G		3683,719	295.9+/-283.9	1531,621,49	114.0	101.0	105.0		414	0.2	1.0	11	dbSNP_107	105	4804,3784	535.8+/-382.9	1333,2138,823	no	coding-synonymous	MICAL2	NM_014632.2		2864,2759,872	GG,GT,TT		44.0615,16.3335,34.6651		138/1125	12225946	8487,4503	2201	4294	6495	SO:0001819	synonymous_variant	9645	exon4			CCTTCGTGGCCTG	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.414T>G	11.37:g.12225946T>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																			T|0.332;G|0.668	0.668	strong		0.547	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
BACE2	25825	hgsc.bcm.edu	37	21	42551183	42551183	+	Intron	SNP	G	G	A	rs202000983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:42551183G>A	ENST00000330333.6	+	1	775				PLAC4_ENST00000430327.2_RNA|BACE2-IT1_ENST00000433378.1_RNA|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000536486.1_RNA|PLAC4_ENST00000414699.1_RNA|PLAC4_ENST00000440221.2_RNA|BACE2_ENST00000328735.6_Intron	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				gaggagtgagggagtccaggg	0.607													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		20303	0.0		0.0	False		,,,				2504	0.0				p.P125S		Atlas-SNP	.											.	.	.	.	0			c.C373T						PASS	.	G	,,,SER/PRO	16,4350		0,16,2167	126.0	106.0	113.0		,,,373	0.2	0.0	21		113	0,8470		0,0,4235	yes	intron,intron,intron,missense	BACE2,PLAC4	NM_012105.3,NM_138991.1,NM_138992.1,NM_182832.2	,,,74	0,16,6402	AA,AG,GG		0.0,0.3665,0.1246	,,,possibly-damaging	,,,125/151	42551183	16,12820	2183	4235	6418	SO:0001627	intron_variant	191585	exon1			AGTGAGGGAGTCC	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10681G>A	21.37:g.42551183G>A		Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	297	158	0.531987	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	37	CCDS13668.1																																																																																			.	.	weak		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1		
ERCC4	2072	hgsc.bcm.edu	37	16	14031695	14031695	+	Silent	SNP	A	A	G	rs2020958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:14031695A>G	ENST00000311895.7	+	9	1893	c.1884A>G	c.(1882-1884)gaA>gaG	p.E628E	CTD-2135D7.2_ENST00000575137.1_RNA|CTD-2135D7.2_ENST00000570663.1_RNA	NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	628					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						AAGAAAAGGAAGCTTTTGAAA	0.393			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				A|||	77	0.0153754	0.0582	0.0	5008	,	,		16132	0.0		0.0	False		,,,				2504	0.0				p.E628E		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.A1884G						PASS	.	A		170,4224	105.2+/-143.6	3,164,2030	76.0	75.0	75.0		1884	4.2	1.0	16	dbSNP_94	75	0,8600		0,0,4300	no	coding-synonymous	ERCC4	NM_005236.2		3,164,6330	GG,GA,AA		0.0,3.8689,1.3083		628/917	14031695	170,12824	2197	4300	6497	SO:0001819	synonymous_variant	2072	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AAAGGAAGCTTTT	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.1884A>G	16.37:g.14031695A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Silent	SNP	ENST00000311895.7	37	CCDS32390.1																																																																																			A|0.982;G|0.018	0.018	strong		0.393	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236	
LYPD4	147719	hgsc.bcm.edu	37	19	42342319	42342319	+	Silent	SNP	A	A	G	rs2290695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42342319A>G	ENST00000330743.3	-	4	1439	c.228T>C	c.(226-228)gtT>gtC	p.V76V	LYPD4_ENST00000343055.4_Silent_p.V41V|LYPD4_ENST00000601246.1_Silent_p.V41V|AC020956.3_ENST00000593354.1_lincRNA	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	76						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						TAAAGCCCACAACTCCCCTTG	0.577													-|||	3032	0.605431	0.91	0.5764	5008	,	,		17010	0.5208		0.4722	False		,,,				2504	0.4387				p.V76V		Atlas-SNP	.											.	LYPD4	30	.	0			c.T228C						PASS	.			3672,734	756.9+/-412.7	1543,586,74	56.0	55.0	55.0		228	-3.5	0.4	19	dbSNP_100	55	4144,4456	564.2+/-388.3	975,2194,1131	no	coding-synonymous	LYPD4	NM_173506.4		2518,2780,1205	GG,GA,AA		48.186,16.6591,39.9047		76/247	42342319	7816,5190	2203	4300	6503	SO:0001819	synonymous_variant	147719	exon4			GCCCACAACTCCC	AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.228T>C	19.37:g.42342319A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_173506	Q8IYW0	Silent	SNP	ENST00000330743.3	37	CCDS12587.1																																																																																			A|0.389;G|0.611	0.611	strong		0.577	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1	NM_173506	
B4GALNT2	124872	hgsc.bcm.edu	37	17	47246979	47246979	+	Silent	SNP	A	A	G	rs16946912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:47246979A>G	ENST00000300404.2	+	11	1649	c.1590A>G	c.(1588-1590)gaA>gaG	p.E530E	B4GALNT2_ENST00000393354.2_Silent_p.E470E|B4GALNT2_ENST00000504681.1_Silent_p.E444E|RP11-708H21.4_ENST00000575159.1_lincRNA	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	530					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			TGGACTCAGAACTGGCTGCCC	0.527													G|||	611	0.122005	0.1641	0.0749	5008	,	,		20337	0.0218		0.1193	False		,,,				2504	0.2045				p.E530E	GBM(124;244 1635 8663 18097 33175)	Atlas-SNP	.											.	B4GALNT2	67	.	0			c.A1590G						PASS	.	G	,,	597,3809	771.2+/-413.8	34,529,1640	97.0	89.0	92.0		1410,1332,1590	0.9	0.0	17	dbSNP_123	92	904,7696	778.2+/-407.7	49,806,3445	no	coding-synonymous,coding-synonymous,coding-synonymous	B4GALNT2	NM_001159387.1,NM_001159388.1,NM_153446.2	,,	83,1335,5085	GG,GA,AA		10.5116,13.5497,11.5408	,,	470/507,444/481,530/567	47246979	1501,11505	2203	4300	6503	SO:0001819	synonymous_variant	124872	exon11			CTCAGAACTGGCT	AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	24136	protein-coding gene	gene with protein product		111730	"""UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"""	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1590A>G	17.37:g.47246979A>G		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	26	8	0.307692	NM_153446	B4DZE4|Q14CP1|Q86Y40	Silent	SNP	ENST00000300404.2	37	CCDS11544.1																																																																																			A|0.888;G|0.112	0.112	strong		0.527	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446	
TRMT2B	79979	hgsc.bcm.edu	37	X	100278558	100278558	+	Silent	SNP	T	T	C	rs61745518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:100278558T>C	ENST00000372936.3	-	8	1429	c.657A>G	c.(655-657)gtA>gtG	p.V219V	TRMT2B_ENST00000338687.7_Silent_p.V174V|TRMT2B_ENST00000372939.1_Silent_p.V174V|TRMT2B_ENST00000478422.1_5'Flank|TRMT2B_ENST00000545398.1_Silent_p.V219V|TRMT2B_ENST00000372931.5_Silent_p.V219V|TRMT2B_ENST00000372935.1_Silent_p.V219V	NM_024917.5	NP_079193.2	Q96GJ1	TRM2_HUMAN	tRNA methyltransferase 2 homolog B (S. cerevisiae)	219						mitochondrion (GO:0005739)	S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity (GO:0030697)			breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	24						CTTCATGAAATACAAGGCAGG	0.458													T|||	74	0.0196026	0.0545	0.0029	3775	,	,		14763	0.0		0.0	False		,,,				2504	0.0				p.V219V		Atlas-SNP	.											.	TRMT2B	33	.	0			c.A657G						PASS	.	T	,,,	236,3599		8,187,33,1437,538	142.0	110.0	121.0		657,522,657,657	0.3	0.6	X	dbSNP_129	121	1,6727		0,1,0,2427,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRMT2B	NM_001167970.1,NM_001167971.1,NM_001167972.1,NM_024917.5	,,,	8,188,33,3864,2410	CC,CT,C,TT,T		0.0149,6.1538,2.2437	,,,	219/505,174/460,219/505,219/505	100278558	237,10326	2203	4300	6503	SO:0001819	synonymous_variant	79979	exon7			ATGAAATACAAGG	BC020116	CCDS14477.1, CCDS55464.1	Xq22.1	2012-06-12	2012-06-12	2008-09-17	ENSG00000188917	ENSG00000188917			25748	protein-coding gene	gene with protein product			"""chromosome X open reading frame 34"""	CXorf34		14702039	Standard	NM_024917		Approved	FLJ12687	uc004egq.3	Q96GJ1	OTTHUMG00000022017	ENST00000372936.3:c.657A>G	X.37:g.100278558T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	180	175	0.972222	NM_001167972	A6NDG5|A6NEI9|A6NMG6|Q5JPF0|Q5JVY6|Q96HU7|Q96IH9|Q9H9K2	Silent	SNP	ENST00000372936.3	37	CCDS14477.1																																																																																			T|0.979;C|0.021	0.021	strong		0.458	TRMT2B-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057512.1	NM_024917	
IRGM	345611	hgsc.bcm.edu	37	5	150227998	150227998	+	Silent	SNP	C	C	T	rs10065172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150227998C>T	ENST00000522154.1	+	2	1426	c.313C>T	c.(313-315)Ctg>Ttg	p.L105L		NM_001145805.1	NP_001139277.1	A1A4Y4	IRGM_HUMAN	immunity-related GTPase family, M	105	IRG-type G.				autophagy (GO:0006914)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)	cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)										GGAGAACTACCTGATGGAAAT	0.493													C|||	1521	0.303714	0.5023	0.1484	5008	,	,		23823	0.4335		0.1054	False		,,,				2504	0.2157				p.L105L		Atlas-SNP	.											.	IRGM	8	.	0			c.C313T	GRCh37	CM073146	IRGM	M	rs10065172	PASS	.	C		598,786		131,336,225	100.0	83.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	313	-0.9	0.0	5	dbSNP_119	88	292,2890		22,248,1321	no	coding-synonymous	IRGM	NM_001145805.1		153,584,1546	TT,TC,CC		9.1766,43.2081,19.4919		105/182	150227998	890,3676	692	1591	2283	SO:0001819	synonymous_variant	345611	exon2			AACTACCTGATGG	BC038539	CCDS47313.1	5q33.1	2012-02-21	2005-03-23	2005-03-23	ENSG00000237693	ENSG00000237693			29597	protein-coding gene	gene with protein product		608212	"""immunity-related GTPase family, M1"""	IRGM1		7561525, 14576437	Standard	NM_001145805		Approved	LRG47, LRG-47, IFI1	uc010jhk.3	A1A4Y4	OTTHUMG00000163647	ENST00000522154.1:c.313C>T	5.37:g.150227998C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	179	80	0.446927	NM_001145805	B3VEX0	Silent	SNP	ENST00000522154.1	37	CCDS47313.1																																																																																			C|0.714;T|0.286	0.286	strong		0.493	IRGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374648.1	NM_001145805	
OR2D3	120775	hgsc.bcm.edu	37	11	6942628	6942628	+	Silent	SNP	A	A	C	rs11605995	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6942628A>C	ENST00000317834.3	+	1	424	c.396A>C	c.(394-396)gcA>gcC	p.A132A		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|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)		CGCTGCTGGCAGTGATGTCCT	0.483													C|||	2040	0.407348	0.6241	0.3329	5008	,	,		19923	0.4464		0.1948	False		,,,				2504	0.3456				p.A132A		Atlas-SNP	.											.	OR2D3	51	.	0			c.A396C						PASS	.	C		2479,1923	547.5+/-377.3	692,1095,414	165.0	155.0	158.0		396	-10.1	0.0	11	dbSNP_120	158	1701,6891	738.4+/-407.1	172,1357,2767	no	coding-synonymous	OR2D3	NM_001004684.1		864,2452,3181	CC,CA,AA		19.7975,43.6847,32.1687		132/331	6942628	4180,8814	2201	4296	6497	SO:0001819	synonymous_variant	120775	exon1			GCTGGCAGTGATG	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.396A>C	11.37:g.6942628A>C		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	266	125	0.469925	NM_001004684	B2RP06|Q6IFG8|Q96R51	Silent	SNP	ENST00000317834.3	37	CCDS31417.1																																																																																			A|0.655;C|0.345	0.345	strong		0.483	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
SPHK1	8877	hgsc.bcm.edu	37	17	74383475	74383475	+	Silent	SNP	T	T	C	rs3744037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74383475T>C	ENST00000545180.1	+	8	1772	c.963T>C	c.(961-963)taT>taC	p.Y321Y	SPHK1_ENST00000392496.3_Silent_p.Y321Y|SPHK1_ENST00000323374.4_Silent_p.Y407Y|SPHK1_ENST00000590959.1_Silent_p.Y335Y|SPHK1_ENST00000592299.1_Silent_p.Y321Y			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	321					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	ACTTGGTATATGTGCCCGTGG	0.597													T|||	1073	0.214257	0.2057	0.1715	5008	,	,		20914	0.4028		0.1392	False		,,,				2504	0.1391				p.Y407Y	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.T1221C						PASS	.	T	,,,	932,3474	352.3+/-311.7	92,748,1363	88.0	80.0	83.0		963,963,1005,1221	-8.2	0.0	17	dbSNP_107	83	1416,7184	272.7+/-290.2	104,1208,2988	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK1	NM_001142601.1,NM_001142602.1,NM_021972.3,NM_182965.2	,,,	196,1956,4351	CC,CT,TT		16.4651,21.153,18.0532	,,,	321/385,321/385,335/399,407/471	74383475	2348,10658	2203	4300	6503	SO:0001819	synonymous_variant	8877	exon6			GGTATATGTGCCC	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.963T>C	17.37:g.74383475T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	102	62	0.607843	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Silent	SNP	ENST00000545180.1	37	CCDS45785.1																																																																																			T|0.796;C|0.204	0.204	strong		0.597	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972	
OR4K15	81127	hgsc.bcm.edu	37	14	20444012	20444012	+	Missense_Mutation	SNP	A	A	T	rs3861512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20444012A>T	ENST00000305051.5	+	1	410	c.335A>T	c.(334-336)gAg>gTg	p.E112V		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	112			E -> V (in dbSNP:rs3861512). {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)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTCTGGTTGAGCGCAAGACT	0.448													A|||	1093	0.218251	0.2141	0.1715	5008	,	,		22012	0.123		0.2227	False		,,,				2504	0.3507				p.E112V		Atlas-SNP	.											OR4K15,colon,carcinoma,0,2	OR4K15	82	2	0			c.A335T						PASS	.	A	VAL/GLU	1058,3348		122,814,1267	126.0	132.0	130.0		335	-0.3	0.0	14	dbSNP_108	130	2282,6312		290,1702,2305	yes	missense	OR4K15	NM_001005486.1	121	412,2516,3572	TT,TA,AA		26.5534,24.0127,25.6923	benign	112/349	20444012	3340,9660	2203	4297	6500	SO:0001583	missense	81127	exon1			TGGTTGAGCGCAA		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.335A>T	14.37:g.20444012A>T	ENSP00000304077:p.Glu112Val	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	198	196	0.989899	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	400	0.18315018315018314	95	0.19308943089430894	65	0.17955801104972377	66	0.11538461538461539	174	0.22955145118733508	.	6.499	0.460280	0.12342	0.240127	0.265534	ENSG00000169488	ENST00000305051	T	0.01572	4.76	3.6	-0.288	0.12855	GPCR, rhodopsin-like superfamily (1);	0.388604	0.21610	N	0.071810	T	0.00012	0.0000	M	0.71036	2.16	0.80722	P	0.0	P	0.37781	0.608	B	0.38428	0.273	T	0.48007	-0.9072	9	0.66056	D	0.02	.	7.2471	0.26127	0.5441:0.0:0.4559:0.0	rs3861512;rs17210948;rs52792471;rs61025663;rs3861512	112	Q8NH41	OR4KF_HUMAN	V	112	ENSP00000304077:E112V	ENSP00000304077:E112V	E	+	2	0	OR4K15	19513852	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	0.973000	0.29422	-0.252000	0.09528	-0.361000	0.07541	GAG	A|0.772;T|0.228	0.228	strong		0.448	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
PNPLA3	80339	hgsc.bcm.edu	37	22	44324727	44324727	+	Missense_Mutation	SNP	C	C	G	rs738409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44324727C>G	ENST00000216180.3	+	3	617	c.444C>G	c.(442-444)atC>atG	p.I148M	PNPLA3_ENST00000478713.1_3'UTR|PNPLA3_ENST00000423180.2_Missense_Mutation_p.I144M	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	148	Patatin.		I -> M (common polymorphism; fails to hydrolyze emulsified triglycerides; associated with increased hepatic fat content and serum aspartate aminotransferase concentrations; dbSNP:rs738409). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18728122, ECO:0000269|PubMed:18820647, ECO:0000269|PubMed:19224197, ECO:0000269|PubMed:19738004}.		acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)	p.I148M(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				CCTGCTTCATCCCCTTCTACA	0.507													C|||	1313	0.262181	0.118	0.4841	5008	,	,		20458	0.3502		0.2256	False		,,,				2504	0.2464				p.I148M		Atlas-SNP	.											PNPLA3,NS,carcinoma,0,1	PNPLA3	53	1	1	Substitution - Missense(1)	stomach(1)	c.C444G	GRCh37	CM086892	PNPLA3	M	rs738409	PASS	.	C	MET/ILE	639,3767	274.9+/-272.2	58,523,1622	311.0	260.0	277.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	444	-2.0	0.3	22	dbSNP_86	277	1901,6699	335.0+/-321.2	208,1485,2607	yes	missense	PNPLA3	NM_025225.2	10	266,2008,4229	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	22.1047,14.503,19.5294	probably-damaging	148/482	44324727	2540,10466	2203	4300	6503	SO:0001583	missense	80339	exon3			CTTCATCCCCTTC		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"""Patatin-like phospholipase domain containing"""	18590	protein-coding gene	gene with protein product		609567	"""chromosome 22 open reading frame 20"", ""adiponutrin"""	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.444C>G	22.37:g.44324727C>G	ENSP00000216180:p.Ile148Met	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	170	76	0.447059	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Missense_Mutation	SNP	ENST00000216180.3	37	CCDS14054.1	622	0.2847985347985348	59	0.11991869918699187	164	0.4530386740331492	235	0.41083916083916083	164	0.21635883905013192	C	12.12	1.841297	0.32513	0.14503	0.221047	ENSG00000100344	ENST00000216180;ENST00000423180	T;T	0.80738	-1.41;-1.41	5.7	-1.97	0.07503	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.316000	0.28156	N	0.016391	T	0.00012	0.0000	M	0.92026	3.265	0.21355	P	0.999710835	D	0.64830	0.994	D	0.66497	0.944	T	0.20107	-1.0285	9	0.62326	D	0.03	-21.2182	6.3831	0.21546	0.0:0.4064:0.2195:0.3741	rs738409;rs3747205;rs17855952;rs738409	148	Q9NST1	PLPL3_HUMAN	M	148;144	ENSP00000216180:I148M;ENSP00000397987:I144M	ENSP00000216180:I148M	I	+	3	3	PNPLA3	42656060	0.058000	0.20735	0.289000	0.24876	0.080000	0.17528	-0.914000	0.04038	-0.125000	0.11703	-0.136000	0.14681	ATC	C|0.774;G|0.226	0.226	strong		0.507	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225	
PRDM10	56980	hgsc.bcm.edu	37	11	129772309	129772309	+	Silent	SNP	G	G	A	rs12275633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:129772309G>A	ENST00000360871.3	-	21	3601	c.3370C>T	c.(3370-3372)Ctg>Ttg	p.L1124L	PRDM10_ENST00000358825.5_Silent_p.L1128L|PRDM10_ENST00000304538.6_Silent_p.L991L|PRDM10_ENST00000528746.1_Silent_p.L1085L|PRDM10_ENST00000423662.2_Silent_p.L1029L|PRDM10_ENST00000526082.1_Silent_p.L1042L	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	1115					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)		TGGGGGTCCAGGGAGTCACTG	0.512													A|||	401	0.0800719	0.2912	0.0216	5008	,	,		20324	0.0		0.001	False		,,,				2504	0.0				p.L1128L		Atlas-SNP	.											.	PRDM10	120	.	0			c.C3382T						PASS	.	A	,,,	1030,3372	726.5+/-409.7	128,774,1299	280.0	239.0	252.0		3382,3370,3085,2971	-2.2	0.7	11	dbSNP_120	252	6,8588	818.8+/-406.8	0,6,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRDM10	NM_020228.2,NM_199437.1,NM_199438.1,NM_199439.1	,,,	128,780,5590	AA,AG,GG		0.0698,23.3985,7.9717	,,,	1128/1161,1124/1157,1029/1062,991/1024	129772309	1036,11960	2201	4297	6498	SO:0001819	synonymous_variant	56980	exon22			GGTCCAGGGAGTC	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.3370C>T	11.37:g.129772309G>A		Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	279	146	0.523297	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																			G|0.921;A|0.079	0.079	strong		0.512	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
CELSR1	9620	hgsc.bcm.edu	37	22	46760086	46760086	+	Missense_Mutation	SNP	C	C	T	rs35364389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	50	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	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	
AKR7A3	22977	hgsc.bcm.edu	37	1	19611227	19611227	+	Silent	SNP	G	G	A	rs1065658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19611227G>A	ENST00000361640.4	-	5	1197	c.657C>T	c.(655-657)ccC>ccT	p.P219P		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	219					cellular aldehyde metabolic process (GO:0006081)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)	13		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGCGGCCCACGGGCTGTTTCC	0.587													G|||	735	0.146765	0.1293	0.1383	5008	,	,		16948	0.0258		0.1789	False		,,,				2504	0.2679				p.P219P		Atlas-SNP	.											.	AKR7A3	30	.	0			c.C657T						PASS	.	G		566,3832		49,468,1682	122.0	132.0	129.0		657	-6.0	0.2	1	dbSNP_86	129	1590,7010		158,1274,2868	no	coding-synonymous	AKR7A3	NM_012067.2		207,1742,4550	AA,AG,GG		18.4884,12.8695,16.5872		219/332	19611227	2156,10842	2199	4300	6499	SO:0001819	synonymous_variant	22977	exon5			GCCCACGGGCTGT	AF040639	CCDS193.1	1p36.13	2008-05-14			ENSG00000162482	ENSG00000162482		"""Aldo-keto reductases"""	390	protein-coding gene	gene with protein product		608477				10383892	Standard	NM_012067		Approved		uc001bbv.1	O95154	OTTHUMG00000002523	ENST00000361640.4:c.657C>T	1.37:g.19611227G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	229	96	0.419214	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Silent	SNP	ENST00000361640.4	37	CCDS193.1																																																																																			G|0.842;A|0.158	0.158	strong		0.587	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067	
ANKFN1	162282	hgsc.bcm.edu	37	17	54431364	54431364	+	Silent	SNP	T	T	C	rs9902114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:54431364T>C	ENST00000318698.2	+	5	602	c.567T>C	c.(565-567)atT>atC	p.I189I	ANKFN1_ENST00000566473.2_Silent_p.I189I	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	189										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						ATGTGCCCATTGCAAGGATTC	0.473													T|||	356	0.0710863	0.2564	0.0245	5008	,	,		20607	0.0		0.0	False		,,,				2504	0.0				p.I189I		Atlas-SNP	.											.	ANKFN1	115	.	0			c.T567C						PASS	.	T		906,3500	348.5+/-309.9	89,728,1386	132.0	103.0	113.0		567	1.8	1.0	17	dbSNP_119	113	21,8579	15.3+/-51.7	1,19,4280	no	coding-synonymous	ANKFN1	NM_153228.2		90,747,5666	CC,CT,TT		0.2442,20.5629,7.1275		189/764	54431364	927,12079	2203	4300	6503	SO:0001819	synonymous_variant	162282	exon5			GCCCATTGCAAGG	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.567T>C	17.37:g.54431364T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_153228		Silent	SNP	ENST00000318698.2	37	CCDS32686.1																																																																																			T|0.926;C|0.074	0.074	strong		0.473	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228	
CD300E	342510	hgsc.bcm.edu	37	17	72608834	72608834	+	Silent	SNP	G	G	A	rs579238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72608834G>A	ENST00000328630.3	-	4	616	c.576C>T	c.(574-576)gtC>gtT	p.V192V	CD300E_ENST00000426295.2_Silent_p.V233V|CD300E_ENST00000392619.1_Silent_p.V219V			Q496F6	CLM2_HUMAN	CD300e molecule	192					innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						TCACCCAGAAGACAGCACCCA	0.627													G|||	1319	0.263379	0.3525	0.2133	5008	,	,		16911	0.1042		0.3022	False		,,,				2504	0.3027				p.V192V		Atlas-SNP	.											.	CD300E	70	.	0			c.C576T						PASS	.	G		1474,2932	474.8+/-357.1	246,982,975	76.0	74.0	75.0		576	4.0	1.0	17	dbSNP_83	75	2492,6108	408.9+/-349.7	372,1748,2180	no	coding-synonymous	CD300E	NM_181449.2		618,2730,3155	AA,AG,GG		28.9767,33.4544,30.4936		192/206	72608834	3966,9040	2203	4300	6503	SO:0001819	synonymous_variant	342510	exon4			CCAGAAGACAGCA	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.576C>T	17.37:g.72608834G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_181449	B4DNS1|Q7Z7I3	Silent	SNP	ENST00000328630.3	37	CCDS11702.1																																																																																			G|0.713;A|0.287	0.287	strong		0.627	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449	
CAPN5	726	hgsc.bcm.edu	37	11	76796022	76796022	+	Silent	SNP	C	C	A	rs34236021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:76796022C>A	ENST00000278559.3	+	2	279	c.90C>A	c.(88-90)ccC>ccA	p.P30P	CAPN5_ENST00000531028.1_Silent_p.P30P|CAPN5_ENST00000529629.1_Silent_p.P30P|CAPN5_ENST00000456580.2_Silent_p.P30P	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	30	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						TCGAGGACCCCCTCTTCCCCG	0.637													c|||	176	0.0351438	0.1278	0.0072	5008	,	,		14704	0.0		0.002	False		,,,				2504	0.0				p.P30P		Atlas-SNP	.											.	CAPN5	67	.	0			c.C90A						PASS	.	C		424,3976	186.0+/-213.0	16,392,1792	33.0	37.0	36.0		90	0.5	1.0	11	dbSNP_126	36	9,8575	6.4+/-24.3	0,9,4283	no	coding-synonymous	CAPN5	NM_004055.4		16,401,6075	AA,AC,CC		0.1048,9.6364,3.3349		30/641	76796022	433,12551	2200	4292	6492	SO:0001819	synonymous_variant	726	exon2			GGACCCCCTCTTC		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"""vitreoretinopathy, neovascular inflammatory"""	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.90C>A	11.37:g.76796022C>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	73	24	0.328767	NM_004055	O00263	Silent	SNP	ENST00000278559.3	37	CCDS8248.1																																																																																			C|0.973;A|0.027	0.027	strong		0.637	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055	
SSR2	6746	hgsc.bcm.edu	37	1	155988108	155988108	+	Silent	SNP	A	A	G	rs34428308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155988108A>G	ENST00000295702.4	-	3	278	c.207T>C	c.(205-207)ttT>ttC	p.F69F	SSR2_ENST00000496742.1_Intron|SSR2_ENST00000480567.1_Silent_p.F69F|SSR2_ENST00000529008.1_Silent_p.F69F	NM_003145.3	NP_003136.1	P43308	SSRB_HUMAN	signal sequence receptor, beta (translocon-associated protein beta)	69					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|stomach(1)	10	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					ACACAATGCCAAAGTCTTCTG	0.468													A|||	43	0.00858626	0.0318	0.0014	5008	,	,		20208	0.0		0.0	False		,,,				2504	0.0				p.F69F		Atlas-SNP	.											.	SSR2	20	.	0			c.T207C						PASS	.	A		164,4242	108.2+/-146.6	4,156,2043	114.0	105.0	108.0		207	1.1	1.0	1	dbSNP_126	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SSR2	NM_003145.3		4,157,6342	GG,GA,AA		0.0116,3.7222,1.2686		69/184	155988108	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	6746	exon3			AATGCCAAAGTCT	BC000341	CCDS1126.1	1q21-q23	2008-02-05			ENSG00000163479	ENSG00000163479			11324	protein-coding gene	gene with protein product		600867				7789174	Standard	NM_003145		Approved	TLAP, TRAPB	uc001fmx.3	P43308	OTTHUMG00000017456	ENST00000295702.4:c.207T>C	1.37:g.155988108A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_003145	B2R9K9|D3DVA7|Q53HI0|Q5VY95|Q5VY96|Q6IB31|Q9BWE4	Silent	SNP	ENST00000295702.4	37	CCDS1126.1																																																																																			A|0.990;G|0.010	0.010	strong		0.468	SSR2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046172.2	NM_003145	
TRIM29	23650	hgsc.bcm.edu	37	11	119996490	119996490	+	Silent	SNP	G	G	A	rs61753082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119996490G>A	ENST00000341846.5	-	4	1663	c.1242C>T	c.(1240-1242)gaC>gaT	p.D414D	TRIM29_ENST00000524816.3_5'Flank|TRIM29_ENST00000528870.1_5'Flank|TRIM29_ENST00000541857.1_Silent_p.D147D|TRIM29_ENST00000529044.1_Silent_p.D153D	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	414					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		TGAGCAGGTCGTCCTTGAAGT	0.562													G|||	105	0.0209665	0.0719	0.0144	5008	,	,		11882	0.0		0.0	False		,,,				2504	0.0				p.D414D		Atlas-SNP	.											.	TRIM29	78	.	0			c.C1242T						PASS	.	G		298,4100	162.2+/-194.2	15,268,1916	101.0	87.0	92.0		1242	-8.7	0.6	11	dbSNP_129	92	0,8590		0,0,4295	no	coding-synonymous	TRIM29	NM_012101.3		15,268,6211	AA,AG,GG		0.0,6.7758,2.2944		414/589	119996490	298,12690	2199	4295	6494	SO:0001819	synonymous_variant	23650	exon4			CAGGTCGTCCTTG	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"""Tripartite motif containing / Tripartite motif containing"""	17274	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM29"", ""ataxia-telangiectasia group D-associated protein"""	610658	"""tripartite motif-containing 29"""			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.1242C>T	11.37:g.119996490G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	118	78	0.661017	NM_012101	Q96AA9|Q9BZY7	Silent	SNP	ENST00000341846.5	37	CCDS8428.1																																																																																			G|0.979;A|0.021	0.021	strong		0.562	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101	
PDIA5	10954	hgsc.bcm.edu	37	3	122864436	122864436	+	Silent	SNP	G	G	A	rs8739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122864436G>A	ENST00000316218.7	+	12	1073	c.978G>A	c.(976-978)gcG>gcA	p.A326A	PDIA5_ENST00000467157.1_3'UTR	NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	326	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		ATGGAGAAGCGGATGTAAGCT	0.502													G|||	3482	0.695288	0.7398	0.5778	5008	,	,		19059	0.8155		0.5775	False		,,,				2504	0.7157				p.A326A		Atlas-SNP	.											PDIA5,caecum,carcinoma,+1,2	PDIA5	66	2	0			c.G978A						PASS	.	G		3022,1384	689.1+/-405.1	1009,1004,190	113.0	107.0	109.0		978	-9.6	0.3	3	dbSNP_52	109	4697,3903	606.0+/-395.0	1263,2171,866	no	coding-synonymous	PDIA5	NM_006810.3		2272,3175,1056	AA,AG,GG		45.3837,31.4117,40.6505		326/520	122864436	7719,5287	2203	4300	6503	SO:0001819	synonymous_variant	10954	exon12			AGAAGCGGATGTA	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"""Protein disulfide isomerases"""	24811	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 5"""			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.978G>A	3.37:g.122864436G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_006810	D3DN95|Q9BV43	Silent	SNP	ENST00000316218.7	37	CCDS3020.1																																																																																			A|0.501;C|0.057;G|0.305;T|0.138	0.501	strong		0.502	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810	
CYP4F12	66002	hgsc.bcm.edu	37	19	15791212	15791212	+	Silent	SNP	A	A	C	rs386807228|rs142773675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791212A>C	ENST00000550308.1	+	5	788	c.408A>C	c.(406-408)atA>atC	p.I136I	CYP4F12_ENST00000324632.10_Silent_p.I136I	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	136					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GAGAAGGGATACTGCTGAGTG	0.567													.|||	100	0.0199681	0.0711	0.0072	5008	,	,		19609	0.0		0.001	False		,,,				2504	0.0				p.I136I		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A408C						PASS	.						30.0	35.0	33.0					19																	15791212		2202	4298	6500	SO:0001819	synonymous_variant	66002	exon5			AGGGATACTGCTG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.408A>C	19.37:g.15791212A>C		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	258	48	0.186047	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			A|0.969;C|0.031	0.031	strong		0.567	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
PABPC1	26986	hgsc.bcm.edu	37	8	101719138	101719138	+	Missense_Mutation	SNP	C	C	T	rs79940439		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101719138C>T	ENST00000318607.5	-	10	2552	c.1424G>A	c.(1423-1425)cGa>cAa	p.R475Q	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519004.1_Missense_Mutation_p.R430Q|PABPC1_ENST00000522387.1_Missense_Mutation_p.R443Q|PABPC1_ENST00000519596.1_Intron	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	475					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TGACATGACTCGTGGAACCTG	0.398																																					p.R475Q		Atlas-SNP	.											.	PABPC1	76	.	0			c.G1424A						PASS	.						79.0	75.0	76.0					8																	101719138		2203	4300	6503	SO:0001583	missense	26986	exon10			ATGACTCGTGGAA	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.1424G>A	8.37:g.101719138C>T	ENSP00000313007:p.Arg475Gln	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	90	22	0.244444	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.8|25.8	4.676811|4.676811	0.88445|0.88445	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000520868;ENST00000517403|ENST00000318607;ENST00000519004;ENST00000522387;ENST00000522658	.|T;T;T;T	.|0.45276	.|1.71;1.67;2.73;0.9	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	.|0.128720	.|0.35378	.|N	.|0.003252	T|T	0.33904|0.33904	0.0879|0.0879	L|L	0.28504|0.28504	0.86|0.86	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.18968	.|0.032;0.001;0.001	.|B;B;B	.|0.09377	.|0.004;0.001;0.0	T|T	0.10474|0.10474	-1.0628|-1.0628	5|10	.|0.15952	.|T	.|0.53	.|.	20.0338|20.0338	0.97549|0.97549	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|443;475;475	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	K|Q	8;128|475;430;443;22	.|ENSP00000313007:R475Q;ENSP00000429594:R430Q;ENSP00000429395:R443Q;ENSP00000428840:R22Q	.|ENSP00000313007:R475Q	E|R	-|-	1|2	0|0	PABPC1|PABPC1	101788314|101788314	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.212000|7.212000	0.77941|0.77941	2.816000|2.816000	0.96949|0.96949	0.650000|0.650000	0.86243|0.86243	GAG|CGA	.	.	weak		0.398	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
RETSAT	54884	hgsc.bcm.edu	37	2	85570849	85570849	+	Missense_Mutation	SNP	C	C	T	rs4832168	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85570849C>T	ENST00000295802.4	-	10	1718	c.1606G>A	c.(1606-1608)Ggg>Agg	p.G536R	RETSAT_ENST00000263854.6_Missense_Mutation_p.R480Q|RETSAT_ENST00000457495.2_Missense_Mutation_p.G475R|RETSAT_ENST00000475624.2_5'UTR	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	536			G -> R (in dbSNP:rs4832168).		oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	TGGTCAGCCCCGTAGCAGGCA	0.617																																					p.G536R		Atlas-SNP	.											.	RETSAT	56	.	0			c.G1606A						PASS	.						45.0	47.0	47.0					2																	85570849		2203	4300	6503	SO:0001583	missense	54884	exon10			CAGCCCCGTAGCA	AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	1.3.99.23		25991	protein-coding gene	gene with protein product						12975309, 15358783	Standard	NM_017750		Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.1606G>A	2.37:g.85570849C>T	ENSP00000295802:p.Gly536Arg	Somatic	542	0	0		WXS	Illumina HiSeq	Phase_I	418	38	0.0909091	NM_017750	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Missense_Mutation	SNP	ENST00000295802.4	37	CCDS1972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.42|19.42	3.824131|3.824131	0.71143|0.71143	.|.	.|.	ENSG00000042445|ENSG00000042445	ENST00000295802;ENST00000457495|ENST00000263854	T;T|.	0.57273|.	0.41;0.41|.	5.02|5.02	4.13|4.13	0.48395|0.48395	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.81322|0.81322	0.4798|0.4798	M|M	0.92604|0.92604	3.325|3.325	0.43467|0.43467	P|P	0.004322999999999966|0.004322999999999966	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.998|.	D|D	0.88450|0.88450	0.3048|0.3048	9|5	0.87932|0.87932	D|D	0|0	-20.6594|-20.6594	13.4883|13.4883	0.61379|0.61379	0.0:0.8417:0.1583:0.0|0.0:0.8417:0.1583:0.0	rs4832168;rs13011440;rs57883711|rs4832168;rs13011440;rs57883711	475;475;536|.	G5E9N3;B4DKE1;Q6NUM9|.	.;.;RETST_HUMAN|.	R|Q	536;475|480	ENSP00000295802:G536R;ENSP00000405040:G475R|.	ENSP00000295802:G536R|ENSP00000263854:R480Q	G|R	-|-	1|2	0|0	RETSAT|RETSAT	85424360|85424360	0.934000|0.934000	0.31675|0.31675	0.996000|0.996000	0.52242|0.52242	0.483000|0.483000	0.33249|0.33249	3.819000|3.819000	0.55686|0.55686	1.226000|1.226000	0.43582|0.43582	-0.305000|-0.305000	0.09177|0.09177	GGG|CGG	C|0.990;T|0.010	0.010	strong		0.617	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750	
ABCC12	94160	hgsc.bcm.edu	37	16	48145742	48145742	+	Missense_Mutation	SNP	T	T	A	rs34135219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48145742T>A	ENST00000311303.3	-	14	2414	c.2069A>T	c.(2068-2070)gAg>gTg	p.E690V	ABCC12_ENST00000448542.1_Missense_Mutation_p.E690V|ABCC12_ENST00000416054.1_3'UTR	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	690	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		E -> V (in dbSNP:rs34135219).			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)				CCCTCTCTCCTCCATTAACTC	0.458													T|||	249	0.0497204	0.1399	0.0159	5008	,	,		20912	0.0149		0.003	False		,,,				2504	0.0358				p.E690V		Atlas-SNP	.											.	ABCC12	190	.	0			c.A2069T						PASS	.	T	VAL/GLU	506,3896	237.7+/-249.4	28,450,1723	160.0	150.0	154.0		2069	3.1	1.0	16	dbSNP_126	154	33,8567	21.6+/-65.8	0,33,4267	yes	missense	ABCC12	NM_033226.2	121	28,483,5990	AA,AT,TT		0.3837,11.4948,4.1455	benign	690/1360	48145742	539,12463	2201	4300	6501	SO:0001583	missense	94160	exon14			CTCTCCTCCATTA	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.2069A>T	16.37:g.48145742T>A	ENSP00000311030:p.Glu690Val	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	235	118	0.502128	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	71	0.03250915750915751	62	0.12601626016260162	6	0.016574585635359115	3	0.005244755244755245	0	0.0	T	12.35	1.912301	0.33721	0.114948	0.003837	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939	T;T	0.68331	-0.32;-0.32	5.56	3.08	0.35506	ABC transporter-like (1);	0.429810	0.26623	N	0.023346	T	0.00936	0.0031	L	0.55213	1.73	0.58432	D	0.999997	B	0.19445	0.036	B	0.22880	0.042	T	0.03060	-1.1077	10	0.45353	T	0.12	.	7.8142	0.29249	0.1333:0.0777:0.0:0.789	rs34135219;rs58143374	690	Q96J65	MRP9_HUMAN	V	690;690;632	ENSP00000311030:E690V;ENSP00000401855:E690V	ENSP00000311030:E690V	E	-	2	0	ABCC12	46703243	0.815000	0.29118	1.000000	0.80357	0.501000	0.33797	1.779000	0.38624	0.951000	0.37770	0.459000	0.35465	GAG	T|0.963;A|0.037	0.037	strong		0.458	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53671754	53671754	+	Missense_Mutation	SNP	C	C	T	rs2111119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53671754C>T	ENST00000379925.3	-	21	3123	c.3073G>A	c.(3073-3075)Ggc>Agc	p.G1025S	RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.G991S|RPGRIP1L_ENST00000568009.1_5'UTR|RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.G1025S|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.G991S	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1025			G -> S (in dbSNP:rs2111119). {ECO:0000269|PubMed:19430481}.		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)	p.G1025S(1)		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)				TCTACACTGCCTTCTTGTGAA	0.358													T|||	832	0.166134	0.171	0.0778	5008	,	,		18350	0.3204		0.0855	False		,,,				2504	0.1462				p.G1025S		Atlas-SNP	.											RPGRIP1L,NS,carcinoma,0,1	RPGRIP1L	118	1	1	Substitution - Missense(1)	stomach(1)	c.G3073A						PASS	.	T	SER/GLY,SER/GLY	688,3708	758.8+/-412.8	46,596,1556	115.0	110.0	111.0		2971,3073	3.0	0.5	16	dbSNP_96	111	744,7856	784.1+/-407.6	27,690,3583	yes	missense,missense	RPGRIP1L	NM_001127897.1,NM_015272.2	56,56	73,1286,5139	TT,TC,CC		8.6512,15.6506,11.0188	benign,benign	991/1236,1025/1316	53671754	1432,11564	2198	4300	6498	SO:0001583	missense	23322	exon21			CACTGCCTTCTTG		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.3073G>A	16.37:g.53671754C>T	ENSP00000369257:p.Gly1025Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	109	37	0.33945	NM_015272	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	332	0.152014652014652	83	0.16869918699186992	24	0.06629834254143646	161	0.28146853146853146	64	0.08443271767810026	T	0.361	-0.939658	0.02322	0.156506	0.086512	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.74632	-0.64;-0.86	5.23	2.95	0.34219	.	0.323250	0.30781	N	0.008887	T	0.00012	0.0000	N	0.08118	0	0.22489	P	0.999050911	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08269	-1.0730	9	0.02654	T	1	-0.0432	8.5044	0.33179	0.0:0.289:0.0:0.711	rs2111119;rs52836388;rs57405487;rs2111119	1025;991	Q68CZ1;Q68CZ1-2	FTM_HUMAN;.	S	1025;991	ENSP00000369257:G1025S;ENSP00000262135:G991S	ENSP00000262135:G991S	G	-	1	0	RPGRIP1L	52229255	0.984000	0.35163	0.546000	0.28166	0.630000	0.37929	1.723000	0.38053	0.024000	0.15214	-0.361000	0.07541	GGC	C|0.869;T|0.131	0.131	strong		0.358	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
SALL4	57167	hgsc.bcm.edu	37	20	50406892	50406892	+	Silent	SNP	C	C	T	rs61737143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50406892C>T	ENST00000217086.4	-	2	2241	c.2130G>A	c.(2128-2130)acG>acA	p.T710T	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	710					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						TGGGAAGAGGCGTGGGGACCT	0.587													C|||	91	0.0181709	0.0643	0.0072	5008	,	,		18206	0.0		0.001	False		,,,				2504	0.0				p.T710T		Atlas-SNP	.											.	SALL4	168	.	0			c.G2130A						PASS	.	C		253,4153	143.5+/-178.5	11,231,1961	41.0	38.0	39.0		2130	-6.0	0.0	20	dbSNP_129	39	0,8600		0,0,4300	no	coding-synonymous	SALL4	NM_020436.3		11,231,6261	TT,TC,CC		0.0,5.7422,1.9453		710/1054	50406892	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			AAGAGGCGTGGGG	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.2130G>A	20.37:g.50406892C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	158	55	0.348101	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			C|0.982;T|0.018	0.018	strong		0.587	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
SSPO	23145	hgsc.bcm.edu	37	7	149515824	149515824	+	RNA	SNP	C	C	T	rs745044	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149515824C>T	ENST00000378016.2	+	0	11725							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)			CAGCCGCACCCGCCTCTGCCT	0.672													C|||	410	0.081869	0.2867	0.0317	5008	,	,		14119	0.0		0.007	False		,,,				2504	0.002				p.R3909C		Atlas-SNP	.											.	.	.	.	0			c.C11725T						PASS	.	C		942,3078		107,728,1175	17.0	20.0	19.0		11739	3.1	0.6	7	dbSNP_86	19	70,8268		0,70,4099	no	coding-notMod3	SSPO	NM_198455.2		107,798,5274	TT,TC,CC		0.8395,23.4328,8.189			149515824	1012,11346	2010	4169	6179			23145	exon83			CGCACCCGCCTCT	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.149515824C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.940;T|0.060	0.060	strong		0.672	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CD200R1	131450	hgsc.bcm.edu	37	3	112642568	112642568	+	Missense_Mutation	SNP	C	C	G	rs9865242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112642568C>G	ENST00000471858.1	-	7	1166	c.934G>C	c.(934-936)Gag>Cag	p.E312Q	CD200R1_ENST00000308611.3_Missense_Mutation_p.E335Q|CD200R1_ENST00000295863.4_3'UTR	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	312			E -> Q (in dbSNP:rs9865242). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039}.		regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TGTAATGCCTCAGATGCCTTC	0.378													G|||	3261	0.651158	0.7209	0.6066	5008	,	,		19251	0.7024		0.5328	False		,,,				2504	0.6575				p.E335Q		Atlas-SNP	.											.	CD200R1	91	.	0			c.G1003C						PASS	.	G	GLN/GLU,GLN/GLU	3013,1393	459.8+/-352.4	1023,967,213	192.0	173.0	180.0		1003,934	2.5	0.0	3	dbSNP_119	180	4582,4018	555.1+/-386.6	1225,2132,943	yes	missense,missense	CD200R1	NM_138806.3,NM_170780.2	29,29	2248,3099,1156	GG,GC,CC		46.7209,31.616,41.6039	benign,benign	335/349,312/326	112642568	7595,5411	2203	4300	6503	SO:0001583	missense	131450	exon8			ATGCCTCAGATGC	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.934G>C	3.37:g.112642568C>G	ENSP00000418928:p.Glu312Gln	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	207	206	0.995169	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	37	CCDS2970.1	1375	0.6295787545787546	342	0.6951219512195121	222	0.6132596685082873	398	0.6958041958041958	413	0.5448548812664907	G	0.342	-0.949804	0.02285	0.68384	0.532791	ENSG00000163606	ENST00000471858;ENST00000308611	T;T	0.13901	2.55;2.57	5.6	2.49	0.30216	.	1.507110	0.05097	N	0.486254	T	0.00012	0.0000	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	0.38178	-0.9673	9	0.02654	T	1	.	4.4375	0.11557	0.0811:0.1253:0.5105:0.2831	rs9865242;rs58650611;rs9865242	312;335	Q8TD46;Q8TD46-4	MO2R1_HUMAN;.	Q	312;335	ENSP00000418928:E312Q;ENSP00000311035:E335Q	ENSP00000311035:E335Q	E	-	1	0	CD200R1	114125258	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	0.073000	0.14640	0.321000	0.23259	-0.127000	0.14921	GAG	C|0.406;G|0.594	0.594	strong		0.378	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
KCNMB2	10242	hgsc.bcm.edu	37	3	178546026	178546026	+	Silent	SNP	T	T	C	rs9831934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:178546026T>C	ENST00000432997.1	+	4	640	c.288T>C	c.(286-288)aaT>aaC	p.N96N	KCNMB2_ENST00000358316.3_Silent_p.N96N|RP11-385J1.2_ENST00000451742.1_RNA|KCNMB2_ENST00000452583.1_Silent_p.N96N|RP11-385J1.2_ENST00000425330.1_RNA|RP11-385J1.2_ENST00000432385.1_RNA|RP11-385J1.2_ENST00000437488.1_RNA|KCNMB2_ENST00000420517.2_Silent_p.N96N	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	108					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(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	AAACATTTAATTGCTCCTTCA	0.522													T|||	2919	0.582867	0.9289	0.5245	5008	,	,		20296	0.2252		0.5825	False		,,,				2504	0.5256				p.N96N		Atlas-SNP	.											.	KCNMB2	35	.	0			c.T288C						PASS	.	T	,	3833,573	773.0+/-413.9	1669,495,39	140.0	117.0	125.0		288,288	-4.7	1.0	3	dbSNP_119	125	5039,3561	629.7+/-398.3	1511,2017,772	no	coding-synonymous,coding-synonymous	KCNMB2	NM_005832.3,NM_181361.1	,	3180,2512,811	CC,CT,TT		41.407,13.005,31.7853	,	96/236,96/236	178546026	8872,4134	2203	4300	6503	SO:0001819	synonymous_variant	10242	exon5			ATTTAATTGCTCC	AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584		"""Potassium channels"""	6286	protein-coding gene	gene with protein product		605214				10097176	Standard	NM_181361		Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.288T>C	3.37:g.178546026T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	161	161	1	NM_005832	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Silent	SNP	ENST00000432997.1	37	CCDS3223.1																																																																																			T|0.360;C|0.640	0.640	strong		0.522	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348251.1	NM_181361	
PCDHGA11	56105	hgsc.bcm.edu	37	5	140801298	140801298	+	Silent	SNP	C	C	A	rs73792198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140801298C>A	ENST00000398587.2	+	1	537	c.504C>A	c.(502-504)ctC>ctA	p.L168L	PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000518882.1_Silent_p.L168L|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	168	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAACTCCCTCCAGAGCTACC	0.537													c|||	641	0.127995	0.1762	0.1513	5008	,	,		18291	0.1181		0.0586	False		,,,				2504	0.1278				p.L168L		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.C504A						PASS	.	C	,,,,,,,,,,,,,,,,,,,	660,3218		58,544,1337	36.0	37.0	37.0		,,,504,,,,,,,,,,,,,,,504,504	-0.1	1.0	5	dbSNP_130	37	617,7691		25,567,3562	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032091.1,NM_032092.1	,,,,,,,,,,,,,,,,,,,	83,1111,4899	AA,AC,CC		7.4266,17.0191,10.4792	,,,,,,,,,,,,,,,,,,,	,,,168/936,,,,,,,,,,,,,,,168/838,168/751	140801298	1277,10909	1939	4154	6093	SO:0001819	synonymous_variant	56105	exon1			CTCCCTCCAGAGC	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"""Cadherins / Protocadherins : Clustered"""	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.504C>A	5.37:g.140801298C>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_032091	B7ZVY8|Q9Y5D8|Q9Y5D9	Silent	SNP	ENST00000398587.2	37	CCDS47294.1																																																																																			C|0.885;A|0.115	0.115	strong		0.537	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914	
CFAP46	54777	hgsc.bcm.edu	37	10	134682802	134682802	+	Missense_Mutation	SNP	C	C	T	rs7084629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134682802C>T	ENST00000368586.5	-	33	4686	c.4586G>A	c.(4585-4587)tGc>tAc	p.C1529Y		NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTCGCTGACGCACACCTGCCC	0.687													T|||	639	0.127596	0.3359	0.0432	5008	,	,		14721	0.0198		0.0249	False		,,,				2504	0.1227				p.C1529Y		Atlas-SNP	.											.	TTC40	100	.	0			c.G4586A						PASS	.																																			SO:0001583	missense	54777	exon33			CTGACGCACACCT																												ENST00000368586.5:c.4586G>A	10.37:g.134682802C>T	ENSP00000357575:p.Cys1529Tyr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	210	0.09615384615384616	168	0.34146341463414637	14	0.03867403314917127	12	0.02097902097902098	16	0.021108179419525065	T	9.396	1.076860	0.20227	.	.	ENSG00000171811	ENST00000368586	T	0.08458	3.09	4.81	4.81	0.61882	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.49130	P	2.4900000000005473E-4	.	.	.	.	.	.	T	0.42699	-0.9436	5	0.02654	T	1	.	8.3416	0.32247	0.0:0.093:0.0:0.907	rs7084629;rs57852866;rs7084629	.	.	.	Y	1529	ENSP00000357575:C1529Y	ENSP00000357575:C1529Y	C	-	2	0	C10orf93	134532792	0.327000	0.24678	0.001000	0.08648	0.000000	0.00434	1.473000	0.35387	0.690000	0.31570	-0.332000	0.08345	TGC	C|0.878;T|0.122	0.122	strong		0.687	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
RTP5	285093	hgsc.bcm.edu	37	2	242814604	242814604	+	Silent	SNP	G	G	C	rs78628254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242814604G>C	ENST00000343216.3	+	2	925	c.897G>C	c.(895-897)ccG>ccC	p.P299P		NM_173821.2	NP_776182.2																					TCTGCAGCCCGGTTGGCGTGG	0.667													G|||	228	0.0455272	0.1664	0.0086	5008	,	,		18709	0.0		0.002	False		,,,				2504	0.0				p.P299P		Atlas-SNP	.											.	.	.	.	0			c.G897C						PASS	.			556,3250		37,482,1384	36.0	41.0	39.0		897	-5.6	0.0	2	dbSNP_131	39	3,8227		0,3,4112	no	coding-synonymous	C2orf85	NM_173821.2		37,485,5496	CC,CG,GG		0.0365,14.6085,4.6444		299/573	242814604	559,11477	1903	4115	6018	SO:0001819	synonymous_variant	285093	exon2			CAGCCCGGTTGGC																												ENST00000343216.3:c.897G>C	2.37:g.242814604G>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_173821		Silent	SNP	ENST00000343216.3	37	CCDS42843.1																																																																																			G|0.967;C|0.033	0.033	strong		0.667	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
CILP2	148113	hgsc.bcm.edu	37	19	19654117	19654117	+	Silent	SNP	G	G	C	rs7252453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19654117G>C	ENST00000291495.5	+	7	1123	c.1038G>C	c.(1036-1038)ctG>ctC	p.L346L	CILP2_ENST00000586018.1_Silent_p.L352L	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	346	Ig-like C2-type.					extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						ACCTGGAGCTGCGGGGACTGC	0.652													C|||	1277	0.254992	0.4947	0.2248	5008	,	,		16755	0.0308		0.173	False		,,,				2504	0.2679				p.L346L		Atlas-SNP	.											.	CILP2	84	.	0			c.G1038C						PASS	.	C		1950,2456	604.8+/-390.4	430,1090,683	44.0	49.0	47.0		1038	-9.6	0.0	19	dbSNP_116	47	1516,7084	738.0+/-407.0	125,1266,2909	no	coding-synonymous	CILP2	NM_153221.2		555,2356,3592	CC,CG,GG		17.6279,44.2578,26.6492		346/1157	19654117	3466,9540	2203	4300	6503	SO:0001819	synonymous_variant	148113	exon7			GGAGCTGCGGGGA	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1038G>C	19.37:g.19654117G>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	167	166	0.994012	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			G|0.754;C|0.246	0.246	strong		0.652	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
SLX4	84464	hgsc.bcm.edu	37	16	3640274	3640274	+	Missense_Mutation	SNP	G	G	A	rs714181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3640274G>A	ENST00000294008.3	-	12	4005	c.3365C>T	c.(3364-3366)cCg>cTg	p.P1122L		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1122	Interaction with PLK1 and TERF2-TERF2IP.		P -> L (in dbSNP:rs714181). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GTCAATAGACGGAGATTTTTC	0.493								Direct reversal of damage					A|||	1200	0.239617	0.5484	0.147	5008	,	,		18117	0.0843		0.0865	False		,,,				2504	0.2055				p.P1122L		Atlas-SNP	.											.	SLX4	173	.	0			c.C3365T						PASS	.	A	LEU/PRO	2027,2367	610.6+/-391.6	463,1101,633	104.0	99.0	101.0		3365	-0.7	0.0	16	dbSNP_86	101	723,7877	786.7+/-407.6	23,677,3600	yes	missense	SLX4	NM_032444.2	98	486,1778,4233	AA,AG,GG		8.407,46.1311,21.1636	benign	1122/1835	3640274	2750,10244	2197	4300	6497	SO:0001583	missense	84464	exon12			ATAGACGGAGATT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.3365C>T	16.37:g.3640274G>A	ENSP00000294008:p.Pro1122Leu	Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	431	0.19734432234432234	272	0.5528455284552846	55	0.15193370165745856	48	0.08391608391608392	56	0.07387862796833773	A	2.635	-0.285532	0.05605	0.461311	0.08407	ENSG00000188827	ENST00000294008	T	0.16897	2.31	6.07	-0.664	0.11406	.	0.670897	0.14312	N	0.327602	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.41928	-0.9481	9	0.22706	T	0.39	.	6.0854	0.19964	0.3816:0.0:0.4976:0.1208	rs714181;rs17857104;rs52826780;rs60671054;rs714181	1122	Q8IY92	SLX4_HUMAN	L	1122	ENSP00000294008:P1122L	ENSP00000294008:P1122L	P	-	2	0	SLX4	3580275	0.001000	0.12720	0.000000	0.03702	0.605000	0.37080	0.088000	0.14979	-0.331000	0.08501	-0.254000	0.11334	CCG	G|0.785;N|0.000	.	strong		0.493	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
ITSN2	50618	hgsc.bcm.edu	37	2	24498674	24498674	+	Silent	SNP	C	C	T	rs77507357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:24498674C>T	ENST00000355123.4	-	18	2432	c.1989G>A	c.(1987-1989)caG>caA	p.Q663Q	ITSN2_ENST00000361999.3_Silent_p.Q636Q|SCARNA21_ENST00000515996.1_RNA|ITSN2_ENST00000406921.3_Silent_p.Q663Q	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	663					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTTATAAAGCTGTTCAAGGG	0.338													T|||	40	0.00798722	0.0303	0.0	5008	,	,		17795	0.0		0.0	False		,,,				2504	0.0				p.Q663Q		Atlas-SNP	.											.	ITSN2	224	.	0			c.G1989A						PASS	.	T	,,	143,4263	812.9+/-416.1	4,135,2064	147.0	140.0	142.0		1989,1908,1989	-4.5	0.9	2	dbSNP_132	142	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ITSN2	NM_006277.2,NM_019595.3,NM_147152.2	,,	4,135,6364	TT,TC,CC		0.0,3.2456,1.0995	,,	663/1698,636/1671,663/1250	24498674	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	50618	exon18			ATAAAGCTGTTCA	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.1989G>A	2.37:g.24498674C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	201	104	0.517413	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2																																																																																			C|0.989;T|0.011	0.011	strong		0.338	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
UBE2U	148581	hgsc.bcm.edu	37	1	64686577	64686577	+	Missense_Mutation	SNP	C	C	T	rs139887828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:64686577C>T	ENST00000371076.3	+	6	737	c.493C>T	c.(493-495)Cgt>Tgt	p.R165C	UBE2U_ENST00000464349.1_3'UTR	NM_152489.1	NP_689702.1	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)	165					protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			large_intestine(3)|lung(2)|skin(1)	6						TAAAGACCCACGTAAATGTAT	0.284													C|||	38	0.00758786	0.0272	0.0029	5008	,	,		13978	0.0		0.0	False		,,,				2504	0.0				p.R165C		Atlas-SNP	.											.	UBE2U	16	.	0			c.C493T						PASS	.	C	CYS/ARG	138,4268	98.5+/-137.1	0,138,2065	92.0	99.0	96.0		493	-5.5	0.0	1	dbSNP_134	96	1,8589	1.2+/-3.3	0,1,4294	yes	missense	UBE2U	NM_152489.1	180	0,139,6359	TT,TC,CC		0.0116,3.1321,1.0696	benign	165/227	64686577	139,12857	2203	4295	6498	SO:0001583	missense	148581	exon6			GACCCACGTAAAT	BC029895	CCDS627.1	1p31.3	2008-02-05			ENSG00000177414	ENSG00000177414		"""Ubiquitin-conjugating enzymes E2"""	28559	protein-coding gene	gene with protein product						12477932	Standard	NM_152489		Approved	MGC35130	uc001dbn.1	Q5VVX9	OTTHUMG00000009023	ENST00000371076.3:c.493C>T	1.37:g.64686577C>T	ENSP00000360116:p.Arg165Cys	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	159	78	0.490566	NM_152489	Q8N1D4	Missense_Mutation	SNP	ENST00000371076.3	37	CCDS627.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	C	7.130	0.579790	0.13686	0.031321	1.16E-4	ENSG00000177414	ENST00000371077;ENST00000371076	T;T	0.72942	-0.7;-0.69	4.12	-5.54	0.02544	Ubiquitin-conjugating enzyme/RWD-like (1);	2.859510	0.01357	N	0.012095	T	0.25419	0.0618	N	0.14661	0.345	0.09310	N	1	B	0.24043	0.096	B	0.09377	0.004	T	0.18366	-1.0339	10	0.87932	D	0	.	3.3218	0.07053	0.095:0.4157:0.2415:0.2478	.	165	Q5VVX9	UBE2U_HUMAN	C	165	ENSP00000360117:R165C;ENSP00000360116:R165C	ENSP00000360116:R165C	R	+	1	0	UBE2U	64459165	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.259000	0.08721	-1.248000	0.02503	-0.229000	0.12294	CGT	C|0.991;T|0.009	0.009	strong		0.284	UBE2U-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025005.1	NM_152489	
TNS4	84951	hgsc.bcm.edu	37	17	38645125	38645125	+	Missense_Mutation	SNP	A	A	G	rs3764424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	185	0	0		WXS	Illumina HiSeq	Phase_I	157	75	0.477707	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	
YEATS4	8089	hgsc.bcm.edu	37	12	69783937	69783937	+	Silent	SNP	T	T	C	rs315121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:69783937T>C	ENST00000247843.2	+	7	795	c.525T>C	c.(523-525)ctT>ctC	p.L175L	YEATS4_ENST00000548020.1_Silent_p.L121L	NM_006530.2	NP_006521.1	O95619	YETS4_HUMAN	YEATS domain containing 4	175	Interaction with MLLT10.|Interaction with TACC1.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding transcription factor activity (GO:0003700)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(1)	5	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			TTGCAGAGCTTGAAGTGAAAA	0.318													T|||	246	0.0491214	0.1225	0.036	5008	,	,		18245	0.0		0.0457	False		,,,				2504	0.0133				p.L175L		Atlas-SNP	.											.	YEATS4	15	.	0			c.T525C						PASS	.	T		523,3859		30,463,1698	24.0	26.0	25.0		525	0.1	1.0	12	dbSNP_79	25	375,8211		6,363,3924	no	coding-synonymous	YEATS4	NM_006530.2		36,826,5622	CC,CT,TT		4.3676,11.9352,6.9247		175/228	69783937	898,12070	2191	4293	6484	SO:0001819	synonymous_variant	8089	exon7			AGAGCTTGAAGTG	AJ245746	CCDS8990.1, CCDS73495.1	12q13-q15	2008-02-05				ENSG00000127337			24859	protein-coding gene	gene with protein product		602116				9302258, 11903063	Standard	XM_005269163		Approved	NuBI-1, GAS41, YAF9	uc001sux.3	O95619	OTTHUMG00000169358	ENST00000247843.2:c.525T>C	12.37:g.69783937T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	99	36	0.363636	NM_006530	Q9NQD0	Silent	SNP	ENST00000247843.2	37	CCDS8990.1																																																																																			T|0.931;G|0.001	.	strong		0.318	YEATS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403663.1	NM_006530	
LAMB4	22798	hgsc.bcm.edu	37	7	107706208	107706208	+	Splice_Site	SNP	C	C	T	rs73725316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107706208C>T	ENST00000388781.3	-	21	2918	c.2835G>A	c.(2833-2835)acG>acA	p.T945T	LAMB4_ENST00000388780.3_Splice_Site_p.T945T|LAMB4_ENST00000205386.4_Splice_Site_p.T945T	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	945	Laminin EGF-like 9. {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						ACTGCATACCCGTATAACCTT	0.373													C|||	42	0.00838658	0.0303	0.0029	5008	,	,		20016	0.0		0.0	False		,,,				2504	0.0				p.T945T		Atlas-SNP	.											.	LAMB4	253	.	0			c.G2835A						PASS	.	C		113,4293	85.3+/-124.0	2,109,2092	123.0	116.0	118.0		2835	2.2	0.6	7	dbSNP_130	118	0,8600		0,0,4300	yes	coding-synonymous-near-splice	LAMB4	NM_007356.2		2,109,6392	TT,TC,CC		0.0,2.5647,0.8688		945/1762	107706208	113,12893	2203	4300	6503	SO:0001630	splice_region_variant	22798	exon21			CATACCCGTATAA	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.2836+1G>A	7.37:g.107706208C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	108	51	0.472222	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			C|0.992;T|0.008	0.008	strong		0.373	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	Silent
PKD1	5310	hgsc.bcm.edu	37	16	2152850	2152850	+	Silent	SNP	A	A	G	rs9926309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2152850A>G	ENST00000262304.4	-	24	9121	c.8913T>C	c.(8911-8913)gcT>gcC	p.A2971A	PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Silent_p.A2971A	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2971					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						GCCGGTGGTCAGCACCCTGGA	0.642													g|||	190	0.0379393	0.1369	0.0115	5008	,	,		11693	0.001		0.0	False		,,,				2504	0.0				p.A2971A		Atlas-SNP	.											.	PKD1	184	.	0			c.T8913C						PASS	.	G	,	394,3996	767.2+/-413.5	22,350,1823	62.0	72.0	69.0		8913,8913	-9.1	0.0	16	dbSNP_119	69	5,8575	816.3+/-406.9	0,5,4285	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	22,355,6108	GG,GA,AA		0.0583,8.9749,3.0763	,	2971/4303,2971/4304	2152850	399,12571	2195	4290	6485	SO:0001819	synonymous_variant	5310	exon24			GTGGTCAGCACCC	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.8913T>C	16.37:g.2152850A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	68	24	0.352941	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1	49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	G	0.702	-0.790596	0.02884	0.089749	5.83E-4	ENSG00000008710	ENST00000382481	.	.	.	4.55	-9.1	0.00714	.	.	.	.	.	T	0.04137	0.0115	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	T	0.65701	-0.6104	5	0.87932	D	0	.	9.2021	0.37265	0.2909:0.5516:0.0851:0.0724	rs9926309	.	.	.	P	1209	.	ENSP00000371921:L1209P	L	-	2	0	PKD1	2092851	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-2.024000	0.01436	-1.933000	0.01052	-1.087000	0.02190	CTG	A|0.976;G|0.024	0.024	strong		0.642	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
AKAP12	9590	hgsc.bcm.edu	37	6	151672285	151672285	+	Missense_Mutation	SNP	A	A	G	rs13212161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:151672285A>G	ENST00000253332.1	+	3	2948	c.2759A>G	c.(2758-2760)gAa>gGa	p.E920G	AKAP12_ENST00000402676.2_Missense_Mutation_p.E920G|AKAP12_ENST00000359755.5_Missense_Mutation_p.E815G|AKAP12_ENST00000354675.6_Missense_Mutation_p.E822G			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	920			E -> G (in dbSNP:rs13212161). {ECO:0000269|PubMed:17974005}.		G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		TCAGTGACAGAACCTCTTGAA	0.478													A|||	484	0.0966454	0.1157	0.0778	5008	,	,		20022	0.0099		0.0895	False		,,,				2504	0.181				p.E920G	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.A2759G						PASS	.	A	GLY/GLU,GLY/GLU	443,3963	205.2+/-227.1	18,407,1778	59.0	64.0	62.0		2759,2465	-1.9	0.0	6	dbSNP_121	62	796,7804	184.2+/-232.2	31,734,3535	yes	missense,missense	AKAP12	NM_005100.3,NM_144497.2	98,98	49,1141,5313	GG,GA,AA		9.2558,10.0545,9.5264	probably-damaging,probably-damaging	920/1783,822/1685	151672285	1239,11767	2203	4300	6503	SO:0001583	missense	9590	exon4			TGACAGAACCTCT	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.2759A>G	6.37:g.151672285A>G	ENSP00000253332:p.Glu920Gly	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	159	0.07280219780219781	54	0.10975609756097561	29	0.08011049723756906	8	0.013986013986013986	68	0.08970976253298153	A	12.91	2.078920	0.36662	0.100545	0.092558	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.09817	2.94;2.94;2.95;2.95	5.27	-1.87	0.07737	.	0.697267	0.12510	N	0.462550	T	0.03178	0.0093	M	0.73598	2.24	0.58432	P	1.999999999946489E-6	B;B;B	0.21606	0.058;0.058;0.034	B;B;B	0.18561	0.022;0.022;0.01	T	0.37842	-0.9688	9	0.27785	T	0.31	.	1.9513	0.03367	0.4458:0.1278:0.3027:0.1237	rs13212161;rs52810987;rs59507175;rs13212161	815;822;920	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	G	920;920;822;815	ENSP00000384537:E920G;ENSP00000253332:E920G;ENSP00000346702:E822G;ENSP00000352794:E815G	ENSP00000253332:E920G	E	+	2	0	AKAP12	151713978	0.667000	0.27484	0.000000	0.03702	0.292000	0.27327	1.177000	0.31969	-0.215000	0.10063	0.379000	0.24179	GAA	A|0.908;G|0.092	0.092	strong		0.478	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
CETN1	1068	hgsc.bcm.edu	37	18	580623	580623	+	Missense_Mutation	SNP	T	T	C	rs61734344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:580623T>C	ENST00000327228.3	+	1	257	c.215T>C	c.(214-216)aTg>aCg	p.M72T		NM_004066.1	NP_004057.1	Q12798	CETN1_HUMAN	centrin, EF-hand protein, 1	72	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to heat (GO:0034605)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|photoreceptor connecting cilium (GO:0032391)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|calcium ion binding (GO:0005509)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(3)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(2)	25						ATGAAGAAAATGATCTCCGAG	0.552													T|||	900	0.179712	0.2322	0.1239	5008	,	,		17797	0.244		0.1292	False		,,,				2504	0.1339				p.M72T		Atlas-SNP	.											.	CETN1	48	.	0			c.T215C						PASS	.	T	THR/MET	910,3496	350.8+/-311.0	116,678,1409	75.0	60.0	65.0		215	5.2	1.0	18	dbSNP_129	65	1254,7346	251.8+/-278.1	100,1054,3146	yes	missense	CETN1	NM_004066.1	81	216,1732,4555	CC,CT,TT		14.5814,20.6537,16.6385	probably-damaging	72/173	580623	2164,10842	2203	4300	6503	SO:0001583	missense	1068	exon1			AGAAAATGATCTC	U03270	CCDS11820.1	18p11.32	2013-01-10			ENSG00000177143	ENSG00000177143		"""EF-hand domain containing"""	1866	protein-coding gene	gene with protein product		603187		CETN		8175926	Standard	NM_004066		Approved	CEN1	uc002kko.1	Q12798	OTTHUMG00000131471	ENST00000327228.3:c.215T>C	18.37:g.580623T>C	ENSP00000319052:p.Met72Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_004066	B2R536	Missense_Mutation	SNP	ENST00000327228.3	37	CCDS11820.1	373	0.1707875457875458	129	0.2621951219512195	45	0.12430939226519337	101	0.17657342657342656	98	0.12928759894459102	T	15.06	2.720817	0.48728	0.206537	0.145814	ENSG00000177143	ENST00000327228	T	0.39056	1.1	5.2	5.2	0.72013	EF-hand-like domain (1);	0.045696	0.85682	D	0.000000	T	0.00039	0.0001	M	0.80982	2.52	0.09310	P	0.99999999872817	D	0.55172	0.97	D	0.85130	0.997	T	0.02431	-1.1160	9	0.87932	D	0	.	13.3624	0.60663	0.0:0.0:0.0:1.0	rs61734344	72	Q12798	CETN1_HUMAN	T	72	ENSP00000319052:M72T	ENSP00000319052:M72T	M	+	2	0	CETN1	570623	1.000000	0.71417	0.995000	0.50966	0.042000	0.13812	7.846000	0.86887	2.324000	0.78689	0.533000	0.62120	ATG	T|0.833;C|0.167	0.167	strong		0.552	CETN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254314.2	NM_004066	
ZBTB38	253461	hgsc.bcm.edu	37	3	141163655	141163655	+	Missense_Mutation	SNP	G	G	A	rs3732867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141163655G>A	ENST00000514251.1	+	4	2704	c.2425G>A	c.(2425-2427)Gct>Act	p.A809T	ZBTB38_ENST00000441582.2_Missense_Mutation_p.A809T|ZBTB38_ENST00000321464.5_Missense_Mutation_p.A810T					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						CACAAATATTGCTGAAGAAAC	0.428													G|||	118	0.0235623	0.0461	0.0014	5008	,	,		21336	0.0298		0.002	False		,,,				2504	0.0245				p.A809T		Atlas-SNP	.											ZBTB38,NS,carcinoma,-1,1	ZBTB38	92	1	0			c.G2425A						PASS	.	G	THR/ALA	185,3525		8,169,1678	55.0	54.0	54.0		2425	-1.2	0.0	3	dbSNP_107	54	4,8194		0,4,4095	yes	missense	ZBTB38	NM_001080412.2	58	8,173,5773	AA,AG,GG		0.0488,4.9865,1.5872	benign	809/1196	141163655	189,11719	1855	4099	5954	SO:0001583	missense	253461	exon8			AATATTGCTGAAG	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.2425G>A	3.37:g.141163655G>A	ENSP00000426387:p.Ala809Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_001080412		Missense_Mutation	SNP	ENST00000514251.1	37	CCDS43157.1	32	0.014652014652014652	14	0.028455284552845527	1	0.0027624309392265192	16	0.027972027972027972	1	0.0013192612137203166	G	0.034	-1.318516	0.01320	0.049865	4.88E-4	ENSG00000177311	ENST00000514251;ENST00000441582;ENST00000321464	T;T;T	0.08896	3.04;3.04;3.04	5.02	-1.2	0.09554	.	2.632110	0.01787	N	0.032085	T	0.01287	0.0042	L	0.44542	1.39	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.38607	-0.9653	9	.	.	.	3.9658	9.4461	0.38699	0.326:0.0:0.5779:0.0961	rs3732867;rs52837576;rs3732867	810;809	B4DYR8;Q8NAP3	.;ZBT38_HUMAN	T	809;809;810	ENSP00000426387:A809T;ENSP00000406955:A809T;ENSP00000372635:A810T	.	A	+	1	0	ZBTB38	142646345	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.033000	0.12246	-0.419000	0.07439	-0.813000	0.03139	GCT	G|0.980;A|0.020	0.020	strong		0.428	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
IFNA16	3449	hgsc.bcm.edu	37	9	21216934	21216934	+	Missense_Mutation	SNP	G	G	A	rs28368161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21216934G>A	ENST00000380216.1	-	1	376	c.371C>T	c.(370-372)aCa>aTa	p.T124I		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	124					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		AACCTCCTGTGTCACACAGGC	0.458													A|||	130	0.0259585	0.0499	0.0216	5008	,	,		20091	0.0		0.0427	False		,,,				2504	0.0061				p.T124I		Atlas-SNP	.											.	IFNA16	27	.	0			c.C371T						PASS	.	A	ILE/THR	205,4201		5,195,2003	169.0	168.0	168.0		371	-5.2	0.0	9	dbSNP_125	168	394,8206		7,380,3913	no	missense	IFNA16	NM_002173.2	89	12,575,5916	AA,AG,GG		4.5814,4.6527,4.6056	benign	124/190	21216934	599,12407	2203	4300	6503	SO:0001583	missense	3449	exon1			TCCTGTGTCACAC		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"""Interferons"""	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.371C>T	9.37:g.21216934G>A	ENSP00000369564:p.Thr124Ile	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	344	150	0.436047	NM_002173	Q5VV12	Missense_Mutation	SNP	ENST00000380216.1	37	CCDS34996.1	58	0.026556776556776556	22	0.044715447154471545	4	0.011049723756906077	0	0.0	32	0.04221635883905013	-	0.015	-1.568968	0.00895	0.046527	0.045814	ENSG00000147885	ENST00000380216	T	0.03358	3.96	2.62	-5.24	0.02789	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	2.137070	0.01644	N	0.024229	T	0.00328	0.0010	N	0.05414	-0.055	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.43376	-0.9395	10	0.15952	T	0.53	.	2.5466	0.04738	0.2352:0.4841:0.121:0.1597	rs28368161	124	P05015	IFN16_HUMAN	I	124	ENSP00000369564:T124I	ENSP00000369564:T124I	T	-	2	0	IFNA16	21206934	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-3.047000	0.00630	-1.390000	0.02087	-1.451000	0.01035	ACA	G|0.966;A|0.034	0.034	strong		0.458	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173	
WDFY4	57705	hgsc.bcm.edu	37	10	50019740	50019740	+	Missense_Mutation	SNP	T	T	C	rs114590878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50019740T>C	ENST00000325239.5	+	29	5228	c.5201T>C	c.(5200-5202)aTg>aCg	p.M1734T	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1734						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						ACAGAGCTGATGGACGGGCCC	0.527													c|||	68	0.0135783	0.0446	0.0115	5008	,	,		21523	0.0		0.001	False		,,,				2504	0.0				p.M1734T		Atlas-SNP	.											.	WDFY4	205	.	0			c.T5201C						PASS	.		THR/MET	55,1329		1,53,638	127.0	116.0	120.0		5201	-9.3	0.0	10	dbSNP_132	120	2,3180		0,2,1589	yes	missense	WDFY4	NM_020945.1	81	1,55,2227	CC,CT,TT		0.0629,3.974,1.2484	benign	1734/3185	50019740	57,4509	692	1591	2283	SO:0001583	missense	57705	exon30			AGCTGATGGACGG	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.5201T>C	10.37:g.50019740T>C	ENSP00000320563:p.Met1734Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	123	69	0.560976	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	C	1.196	-0.633873	0.03584	0.03974	6.29E-4	ENSG00000128815	ENST00000426033;ENST00000325239	T	0.53857	0.6	5.62	-9.26	0.00662	.	0.878748	0.09893	N	0.742057	T	0.01940	0.0061	N	0.00170	-1.935	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17077	-1.0381	9	.	.	.	.	4.1195	0.10099	0.0879:0.2511:0.1727:0.4883	.	262;1734	F2Z372;Q6ZS81	.;WDFY4_HUMAN	T	1734	ENSP00000320563:M1734T	.	M	+	2	0	WDFY4	49689746	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-1.181000	0.03085	-3.275000	0.00198	-1.367000	0.01198	ATG	T|0.992;C|0.008	0.008	strong		0.527	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
NWD1	284434	hgsc.bcm.edu	37	19	16860084	16860084	+	Missense_Mutation	SNP	C	C	T	rs11668502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860084C>T	ENST00000552788.1	+	4	631	c.631C>T	c.(631-633)Ctc>Ttc	p.L211F	NWD1_ENST00000379808.3_Missense_Mutation_p.L211F|NWD1_ENST00000339803.6_Missense_Mutation_p.L76F|NWD1_ENST00000549814.1_Missense_Mutation_p.L211F|NWD1_ENST00000524140.2_Missense_Mutation_p.L211F|NWD1_ENST00000523826.1_Missense_Mutation_p.L5F			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	211			L -> F (in dbSNP:rs11668502).				ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GGTGGACCGGCTCGCGGATGG	0.587													C|||	330	0.0658946	0.1785	0.0274	5008	,	,		17649	0.0079		0.0288	False		,,,				2504	0.0389				p.L211F		Atlas-SNP	.											.	NWD1	303	.	0			c.C631T						PASS	.						86.0	69.0	75.0					19																	16860084		2203	4300	6503	SO:0001583	missense	284434	exon6			GACCGGCTCGCGG	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.631C>T	19.37:g.16860084C>T	ENSP00000447224:p.Leu211Phe	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		121	0.0554029304029304	87	0.17682926829268292	14	0.03867403314917127	1	0.0017482517482517483	19	0.025065963060686015	c	12.93	2.086336	0.36855	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.57595	1.92;1.92;1.92;0.4;1.92;0.39	4.52	4.52	0.55395	.	0.333272	0.25729	N	0.028692	T	0.00144	0.0004	N	0.24115	0.695	0.36708	P	0.11951900000000004	D;D;D	0.67145	0.996;0.995;0.996	P;P;P	0.61201	0.862;0.885;0.853	T	0.03728	-1.1009	9	0.29301	T	0.29	-22.6306	12.6977	0.57014	0.0:1.0:0.0:0.0	rs11668502;rs11668502	211;211;76	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	F	76;211;211;211;5;211;76	ENSP00000428579:L211F;ENSP00000447548:L211F;ENSP00000369136:L211F;ENSP00000428955:L5F;ENSP00000447224:L211F;ENSP00000340159:L76F	ENSP00000340159:L76F	L	+	1	0	NWD1	16721084	0.998000	0.40836	0.983000	0.44433	0.320000	0.28249	3.307000	0.51888	2.068000	0.61886	0.542000	0.68232	CTC	C|0.936;T|0.064	0.064	strong		0.587	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
CEP250	11190	hgsc.bcm.edu	37	20	34089679	34089679	+	Silent	SNP	C	C	T	rs224379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34089679C>T	ENST00000397527.1	+	29	4626	c.3906C>T	c.(3904-3906)tcC>tcT	p.S1302S	CEP250_ENST00000342580.4_Silent_p.S1246S	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1302	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)			AAGAGAAATCCAAGTGGGAAG	0.493													C|||	14	0.00279553	0.0106	0.0	5008	,	,		22493	0.0		0.0	False		,,,				2504	0.0				p.S1302S		Atlas-SNP	.											.	CEP250	141	.	0			c.C3906T						PASS	.	C		58,4346	56.2+/-92.4	0,58,2144	50.0	50.0	50.0		3906	1.9	1.0	20	dbSNP_79	50	0,8600		0,0,4300	no	coding-synonymous	CEP250	NM_007186.3		0,58,6444	TT,TC,CC		0.0,1.317,0.446		1302/2443	34089679	58,12946	2202	4300	6502	SO:0001819	synonymous_variant	11190	exon29			GAAATCCAAGTGG	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.3906C>T	20.37:g.34089679C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																			C|0.996;T|0.004	0.004	strong		0.493	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
TLR1	7096	hgsc.bcm.edu	37	4	38798648	38798648	+	Missense_Mutation	SNP	C	C	A	rs5743618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38798648C>A	ENST00000502213.2	-	3	2034	c.1805G>T	c.(1804-1806)aGc>aTc	p.S602I	TLR1_ENST00000308979.2_Missense_Mutation_p.S602I|TLR1_ENST00000510552.1_5'Flank			Q15399	TLR1_HUMAN	toll-like receptor 1	602			S -> I (severe impairment of activity; dbSNP:rs5743618). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19924287, ECO:0000269|PubMed:21618349, ECO:0000269|PubMed:9435236}.		cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						ATCCAAGTAGCTGCAGAGGGA	0.527													A|||	4009	0.800519	0.9644	0.7161	5008	,	,		17831	0.994		0.327	False		,,,				2504	0.9264				p.S602I	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.G1805T	GRCh37	CM073378	TLR1	M	rs5743618	PASS	.	A	ILE/SER	3744,660	269.8+/-269.2	1604,536,62	62.0	85.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1805	2.8	0.4	4	dbSNP_114	77	2480,6120	694.3+/-404.7	377,1726,2197	no	missense	TLR1	NM_003263.3	142	1981,2262,2259	AA,AC,CC		28.8372,14.9864,47.8622	benign	602/787	38798648	6224,6780	2202	4300	6502	SO:0001583	missense	7096	exon4			AAGTAGCTGCAGA	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1805G>T	4.37:g.38798648C>A	ENSP00000421259:p.Ser602Ile	Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Missense_Mutation	SNP	ENST00000502213.2	37	CCDS33973.1	1461	0.6689560439560439	468	0.9512195121951219	237	0.6546961325966851	564	0.986013986013986	192	0.2532981530343008	A	0.014	-1.580406	0.00879	0.850136	0.288372	ENSG00000174125	ENST00000308979;ENST00000502213	T;T	0.01767	4.65;4.65	5.43	2.76	0.32466	.	1.586730	0.03541	N	0.223979	T	0.00012	0.0000	N	0.00082	-2.215	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34800	-0.9814	9	0.02654	T	1	.	8.4818	0.33047	0.4839:0.3908:0.0:0.1253	rs5743618;rs6842300;rs59314548	602	Q15399	TLR1_HUMAN	I	602	ENSP00000354932:S602I;ENSP00000421259:S602I	ENSP00000354932:S602I	S	-	2	0	TLR1	38475043	0.000000	0.05858	0.429000	0.26710	0.653000	0.38743	0.626000	0.24492	0.431000	0.26258	-0.256000	0.11100	AGC	.	.	weak		0.527	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
SPATA20	64847	hgsc.bcm.edu	37	17	48628470	48628470	+	Missense_Mutation	SNP	T	T	A	rs9913430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48628470T>A	ENST00000356488.4	+	11	1530	c.1447T>A	c.(1447-1449)Tca>Aca	p.S483T	SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000393244.3_Missense_Mutation_p.S439T|SPATA20_ENST00000006658.6_Missense_Mutation_p.S499T	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	483			S -> T (in dbSNP:rs9913430). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CTTGCTCAATTCAGGGCTGGA	0.637											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1785	0.35643	0.7542	0.3617	5008	,	,		13551	0.0843		0.2773	False		,,,				2504	0.1769				p.S499T		Atlas-SNP	.											SPATA20,colon,carcinoma,0,1	SPATA20	59	1	0			c.T1495A						PASS	.	A	THR/SER	2995,1409	454.5+/-350.7	1020,955,227	35.0	33.0	34.0		1495	-6.5	0.0	17	dbSNP_119	34	2359,6241	696.9+/-404.9	312,1735,2253	yes	missense	SPATA20	NM_022827.2	58	1332,2690,2480	AA,AT,TT		27.4302,31.9936,41.1719	benign	499/803	48628470	5354,7650	2202	4300	6502	SO:0001583	missense	64847	exon12			CTCAATTCAGGGC		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1447T>A	17.37:g.48628470T>A	ENSP00000348878:p.Ser483Thr	Somatic	94	0	0	119	WXS	Illumina HiSeq	Phase_I	101	96	0.950495	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	736	0.336996336996337	345	0.7012195121951219	128	0.35359116022099446	54	0.0944055944055944	209	0.2757255936675462	A	0.808	-0.753198	0.03041	0.680064	0.274302	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.29142	1.58;1.58;1.58	5.95	-6.46	0.01908	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	1.194140	0.05720	N	0.597621	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	0.04013	0.0;0.001	T	0.31138	-0.9954	9	0.08599	T	0.76	-33.8639	6.734	0.23399	0.2286:0.0:0.3033:0.4681	rs9913430;rs17855970;rs58643872;rs9913430	483;499	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	T	499;483;439	ENSP00000006658:S499T;ENSP00000348878:S483T;ENSP00000376935:S439T	ENSP00000006658:S499T	S	+	1	0	SPATA20	45983469	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-0.109000	0.10840	-2.343000	0.00623	-1.068000	0.02270	TCA	T|0.605;A|0.395	0.395	strong		0.637	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
DNAJC15	29103	hgsc.bcm.edu	37	13	43597865	43597865	+	Missense_Mutation	SNP	A	A	G	rs12015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	81	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	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	
POLE	5426	hgsc.bcm.edu	37	12	133236000	133236000	+	Silent	SNP	C	C	T	rs5744857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133236000C>T	ENST00000320574.5	-	26	3199	c.3156G>A	c.(3154-3156)acG>acA	p.T1052T	POLE_ENST00000535270.1_Silent_p.T1025T	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1052					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)	TGCTGATGGACGTAGACTTCT	0.567								DNA polymerases (catalytic subunits)					T|||	3032	0.605431	0.7602	0.5317	5008	,	,		19097	0.6736		0.4314	False		,,,				2504	0.5573				p.T1052T		Atlas-SNP	.											POLE_ENST00000320574,caecum,carcinoma,-1,2	POLE	416	2	0			c.G3156A						PASS	.	T		3091,1315	441.8+/-346.5	1076,939,188	90.0	81.0	84.0		3156	-11.7	0.0	12	dbSNP_114	84	3704,4896	619.9+/-397.0	798,2108,1394	no	coding-synonymous	POLE	NM_006231.2		1874,3047,1582	TT,TC,CC		43.0698,29.8457,47.7549		1052/2287	133236000	6795,6211	2203	4300	6503	SO:0001819	synonymous_variant	5426	exon26			GATGGACGTAGAC		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.3156G>A	12.37:g.133236000C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	136	60	0.441176	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			C|0.443;T|0.557	0.557	strong		0.567	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
OR2L3	391192	hgsc.bcm.edu	37	1	248224578	248224578	+	Missense_Mutation	SNP	T	T	C	rs60743763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248224578T>C	ENST00000359959.3	+	1	595	c.595T>C	c.(595-597)Ttt>Ctt	p.F199L	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	199						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(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	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;0.0278)			GGGCACAGTGTTTTTGAGCAC	0.488													t|||	389	0.0776757	0.1324	0.0288	5008	,	,		24690	0.119		0.0626	False		,,,				2504	0.0112				p.F199L		Atlas-SNP	.											OR2L3,NS,carcinoma,-1,1	OR2L3	97	1	0			c.T595C						scavenged	.						179.0	198.0	191.0					1																	248224578		2189	4300	6489	SO:0001583	missense	391192	exon1			ACAGTGTTTTTGA	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"""GPCR / Class A : Olfactory receptors"""	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.595T>C	1.37:g.248224578T>C	ENSP00000353044:p.Phe199Leu	Somatic	532	1	0.0018797		WXS	Illumina HiSeq	Phase_I	334	23	0.0688623	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	145	0.06639194139194139	38	0.07723577235772358	9	0.024861878453038673	67	0.11713286713286714	31	0.040897097625329816	T	7.648	0.682293	0.14907	.	.	ENSG00000198128	ENST00000359959	T	0.00042	8.84	2.05	0.915	0.19366	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33732	U	0.004607	T	0.00012	0.0000	N	0.13043	0.29	0.09310	N	1	P	0.49447	0.924	P	0.56088	0.791	T	0.44667	-0.9313	10	0.51188	T	0.08	.	0.1554	0.00097	0.2252:0.2557:0.23:0.2891	rs60743763	199	Q8NG85	OR2L3_HUMAN	L	199	ENSP00000353044:F199L	ENSP00000353044:F199L	F	+	1	0	OR2L3	246291201	0.000000	0.05858	0.068000	0.19968	0.037000	0.13140	-2.920000	0.00694	0.928000	0.37168	0.379000	0.24179	TTT	T|0.933;C|0.067	0.067	strong		0.488	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
NLRP14	338323	hgsc.bcm.edu	37	11	7064271	7064271	+	Silent	SNP	T	T	C	rs116753166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7064271T>C	ENST00000299481.4	+	4	1360	c.1014T>C	c.(1012-1014)taT>taC	p.Y338Y		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	338	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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)		GAGAGGAGTATATTTACCAGT	0.398													T|||	87	0.0173722	0.0613	0.0072	5008	,	,		22160	0.0		0.001	False		,,,				2504	0.0				p.Y338Y		Atlas-SNP	.											.	NLRP14	187	.	0			c.T1014C						PASS	.	T		260,4142	146.9+/-181.5	14,232,1955	100.0	105.0	103.0		1014	2.2	0.4	11	dbSNP_132	103	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	NLRP14	NM_176822.3		14,233,6250	CC,CT,TT		0.0116,5.9064,2.0086		338/1094	7064271	261,12733	2201	4296	6497	SO:0001819	synonymous_variant	338323	exon4			GGAGTATATTTAC	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.1014T>C	11.37:g.7064271T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	166	82	0.493976	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	37	CCDS7776.1																																																																																			T|0.983;C|0.017	0.017	strong		0.398	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49965956	49965956	+	Missense_Mutation	SNP	G	G	A	rs10406757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49965956G>A	ENST00000293350.4	+	8	1205	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T	ALDH16A1_ENST00000433981.2_Missense_Mutation_p.A183T|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.A185T|CTD-3148I10.9_ENST00000599536.1_5'Flank|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.A297T	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	348						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)		CCGGGGGGCTGCCGCATGTGA	0.687													G|||	187	0.0373403	0.1324	0.0159	5008	,	,		12025	0.0		0.001	False		,,,				2504	0.0				p.A348T		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1042A						PASS	.	G	THR/ALA,THR/ALA	423,3981		21,381,1800	23.0	26.0	25.0		889,1042	2.8	0.5	19	dbSNP_119	25	4,8592		0,4,4294	yes	missense,missense	ALDH16A1	NM_001145396.1,NM_153329.3	58,58	21,385,6094	AA,AG,GG		0.0465,9.6049,3.2846	probably-damaging,probably-damaging	297/752,348/803	49965956	427,12573	2202	4298	6500	SO:0001583	missense	126133	exon8			GGGGCTGCCGCAT	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.1042G>A	19.37:g.49965956G>A	ENSP00000293350:p.Ala348Thr	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	323	171	0.529412	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	37	CCDS12766.1	52	0.023809523809523808	45	0.09146341463414634	7	0.019337016574585635	0	0.0	0	0.0	G	13.56	2.274535	0.40194	0.096049	4.65E-4	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.03	2.77	0.32553	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.412335	0.24688	N	0.036418	T	0.11410	0.0278	L	0.55834	1.745	0.09310	N	1	D;D;D	0.76494	0.999;0.998;0.997	D;D;D	0.69307	0.943;0.963;0.932	T	0.22906	-1.0203	10	0.32370	T	0.25	-22.8219	6.9006	0.24281	0.0956:0.0:0.7322:0.1723	rs10406757	185;297;348	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	T	348;297;185;183	ENSP00000293350:A348T;ENSP00000410142:A297T;ENSP00000445088:A185T;ENSP00000398675:A183T	ENSP00000293350:A348T	A	+	1	0	ALDH16A1	54657768	0.494000	0.26043	0.530000	0.27963	0.649000	0.38597	3.254000	0.51477	1.286000	0.44565	0.485000	0.47835	GCC	A|0.034;C|0.000;G|0.965	0.034	strong		0.687	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
FGF6	2251	hgsc.bcm.edu	37	12	4554549	4554549	+	Missense_Mutation	SNP	G	G	A	rs17183529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:4554549G>A	ENST00000228837.2	-	1	231	c.188C>T	c.(187-189)gCc>gTc	p.A63V		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	63			A -> V (in dbSNP:rs17183529). {ECO:0000269|Ref.2}.		angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|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)|insulin receptor signaling pathway (GO:0008286)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)	p.A63V(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			AGCTAGCCCGGCGCGAGACCT	0.642													G|||	21	0.00419329	0.0159	0.0	5008	,	,		17319	0.0		0.0	False		,,,				2504	0.0				p.A63V		Atlas-SNP	.											FGF6,colon,carcinoma,-1,2	FGF6	40	2	1	Substitution - Missense(1)	large_intestine(1)	c.C188T						PASS	.	G	VAL/ALA	57,4349	51.6+/-87.1	0,57,2146	88.0	83.0	85.0		188	4.1	0.0	12	dbSNP_123	85	0,8600		0,0,4300	no	missense	FGF6	NM_020996.1	64	0,57,6446	AA,AG,GG		0.0,1.2937,0.4383	benign	63/209	4554549	57,12949	2203	4300	6503	SO:0001583	missense	2251	exon1			AGCCCGGCGCGAG	X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"""Endogenous ligands"""	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.188C>T	12.37:g.4554549G>A	ENSP00000228837:p.Ala63Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_020996	Q0VAE1	Missense_Mutation	SNP	ENST00000228837.2	37	CCDS8527.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	10.67	1.415816	0.25552	0.012937	0.0	ENSG00000111241	ENST00000228837	T	0.26810	1.71	5.0	4.09	0.47781	.	0.553031	0.20578	N	0.089588	T	0.18257	0.0438	L	0.49126	1.545	0.09310	N	0.999998	B	0.30146	0.27	B	0.34991	0.193	T	0.12578	-1.0542	10	0.36615	T	0.2	.	9.216	0.37348	0.0768:0.1473:0.7759:0.0	rs17183529	63	P10767	FGF6_HUMAN	V	63	ENSP00000228837:A63V	ENSP00000228837:A63V	A	-	2	0	FGF6	4424810	0.756000	0.28383	0.004000	0.12327	0.229000	0.25112	3.566000	0.53805	1.215000	0.43411	0.561000	0.74099	GCC	G|0.996;A|0.004	0.004	strong		0.642	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996	
IL1A	3552	hgsc.bcm.edu	37	2	113539224	113539224	+	Silent	SNP	G	G	A	rs20540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113539224G>A	ENST00000263339.3	-	4	431	c.276C>T	c.(274-276)atC>atT	p.I92I		NM_000575.3	NP_000566.3	P01583	IL1A_HUMAN	interleukin 1, alpha	92					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|response to copper ion (GO:0046688)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	copper ion binding (GO:0005507)|cytokine activity (GO:0005125)			breast(2)|large_intestine(1)|lung(9)	12					Rilonacept(DB06372)	CATCATCAGTGATGGATTGGC	0.453													G|||	96	0.0191693	0.0719	0.0014	5008	,	,		23080	0.0		0.0	False		,,,				2504	0.0				p.I92I		Atlas-SNP	.											.	IL1A	19	.	0			c.C276T						PASS	.	G		263,4143	149.9+/-184.0	9,245,1949	218.0	203.0	208.0		276	0.0	0.0	2	dbSNP_67	208	0,8600		0,0,4300	no	coding-synonymous	IL1A	NM_000575.3		9,245,6249	AA,AG,GG		0.0,5.9691,2.0221		92/272	113539224	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	3552	exon4			ATCAGTGATGGAT	M28983	CCDS2101.1	2q14	2014-01-30			ENSG00000115008	ENSG00000115008		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5991	protein-coding gene	gene with protein product	"""preinterleukin 1 alpha"", ""hematopoietin-1"", ""pro-interleukin-1-alpha"""	147760		IL1		8188271, 2989698	Standard	NM_000575		Approved	IL1F1, IL-1A, IL1-ALPHA	uc002tig.3	P01583	OTTHUMG00000131315	ENST00000263339.3:c.276C>T	2.37:g.113539224G>A		Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	242	112	0.46281	NM_000575	Q53QF9|Q7RU02	Silent	SNP	ENST00000263339.3	37	CCDS2101.1																																																																																			G|0.980;A|0.020	0.020	strong		0.453	IL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254084.1	NM_000575	
IL4R	3566	hgsc.bcm.edu	37	16	27373966	27373966	+	Silent	SNP	C	C	T	rs2234899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27373966C>T	ENST00000395762.2	+	11	1552	c.1293C>T	c.(1291-1293)tgC>tgT	p.C431C	IL4R_ENST00000170630.2_Silent_p.C431C|IL4R_ENST00000543915.2_Silent_p.C431C|IL4R_ENST00000380922.3_Silent_p.C416C	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						GGGAGTCATGCCTTCTTCCAC	0.617													C|||	152	0.0303514	0.1044	0.0086	5008	,	,		19640	0.0		0.008	False		,,,				2504	0.0				p.C431C		Atlas-SNP	.											IL4R,lymph_node,lymphoid_neoplasm,+2,1	IL4R	70	1	0			c.C1293T						PASS	.	C		380,4014	189.9+/-215.9	8,364,1825	75.0	74.0	75.0		1293	-0.2	0.0	16	dbSNP_98	75	68,8532	40.3+/-97.0	2,64,4234	no	coding-synonymous	IL4R	NM_000418.2		10,428,6059	TT,TC,CC		0.7907,8.6482,3.4477		431/826	27373966	448,12546	2197	4300	6497	SO:0001819	synonymous_variant	3566	exon11			GTCATGCCTTCTT	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.1293C>T	16.37:g.27373966C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	97	30	0.309278	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Silent	SNP	ENST00000395762.2	37	CCDS10629.1																																																																																			C|0.966;T|0.034	0.034	strong		0.617	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
C10orf111	221060	hgsc.bcm.edu	37	10	15138615	15138615	+	Missense_Mutation	SNP	C	C	T	rs7896053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:15138615C>T	ENST00000378207.3	-	2	482	c.209G>A	c.(208-210)aGg>aAg	p.R70K	RPP38_ENST00000378197.4_5'Flank|RPP38_ENST00000378202.5_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	185	0	0		WXS	Illumina HiSeq	Phase_I	206	206	1	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	
SUPT7L	9913	hgsc.bcm.edu	37	2	27883958	27883958	+	Silent	SNP	C	C	T	rs6756254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27883958C>T	ENST00000337768.5	-	3	881	c.312G>A	c.(310-312)tcG>tcA	p.S104S	SUPT7L_ENST00000464789.2_Silent_p.S102S|SUPT7L_ENST00000406540.1_Silent_p.S102S|SUPT7L_ENST00000405491.1_Silent_p.S102S|SUPT7L_ENST00000404798.2_Intron|SLC4A1AP_ENST00000326019.6_5'Flank	NM_001282729.1|NM_014860.1	NP_001269658.1|NP_055675.1	O94864	ST65G_HUMAN	suppressor of Ty 7 (S. cerevisiae)-like	104					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|maintenance of protein location in nucleus (GO:0051457)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)					ACCCAGGGCACGAGGGAAGAG	0.527													C|||	333	0.0664936	0.2307	0.0187	5008	,	,		20175	0.0		0.0129	False		,,,				2504	0.002				p.S104S		Atlas-SNP	.											.	SUPT7L	36	.	0			c.G312A						PASS	.	C		690,3508		61,568,1470	117.0	123.0	121.0		312	-2.7	0.3	2	dbSNP_116	121	65,8345		0,65,4140	no	coding-synonymous	SUPT7L	NM_014860.1		61,633,5610	TT,TC,CC		0.7729,16.4364,5.9883		104/415	27883958	755,11853	2099	4205	6304	SO:0001819	synonymous_variant	9913	exon3			AGGGCACGAGGGA	AF197954	CCDS42667.1, CCDS62885.1, CCDS62886.1	2p23.3	2008-02-05			ENSG00000119760	ENSG00000119760			30632	protein-coding gene	gene with protein product		612762				9872452, 11564863	Standard	NM_001282732		Approved	STAF65, gamma, KIAA0764, SPT7L	uc002rli.1	O94864	OTTHUMG00000151947	ENST00000337768.5:c.312G>A	2.37:g.27883958C>T		Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	440	194	0.440909	NM_014860	B4E3W3|Q6IB21|Q9H2T6	Silent	SNP	ENST00000337768.5	37	CCDS42667.1																																																																																			C|0.940;T|0.060	0.060	strong		0.527	SUPT7L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324568.1	NM_014860	
PREX1	57580	hgsc.bcm.edu	37	20	47295906	47295906	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47295906C>T	ENST00000371941.3	-	13	1603	c.1581G>A	c.(1579-1581)ccG>ccA	p.P527P	PREX1_ENST00000396220.1_Silent_p.P527P	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	527	DEP 2. {ECO:0000255|PROSITE- ProRule:PRU00066}.				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)			ACTTGATCACCGGGGTGTAGA	0.512																																					p.P527P		Atlas-SNP	.											.	PREX1	441	.	0			c.G1581A						PASS	.						117.0	112.0	114.0					20																	47295906		2203	4300	6503	SO:0001819	synonymous_variant	57580	exon13			GATCACCGGGGTG	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.1581G>A	20.37:g.47295906C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			.	.	none		0.512	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254318	39254318	+	Missense_Mutation	SNP	C	C	T	rs138296121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39254318C>T	ENST00000333822.4	-	1	75	c.19G>A	c.(19-21)Ggc>Agc	p.G7S		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	7					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						CACACGGAGCCACAACAGGAG	0.557													C|||	453	0.0904553	0.1392	0.1138	5008	,	,		18412	0.1508		0.0159	False		,,,				2504	0.0225				p.G7S		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.G19A						PASS	.	C	SER/GLY	146,1238		7,132,553	29.0	29.0	29.0		19	3.1	1.0	17	dbSNP_134	29	48,3134		0,48,1543	no	missense	KRTAP4-8	NM_031960.2	56	7,180,2096	TT,TC,CC		1.5085,10.5491,4.2488	possibly-damaging	7/186	39254318	194,4372	692	1591	2283	SO:0001583	missense	728224	exon1			CGGAGCCACAACA	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.19G>A	17.37:g.39254318C>T	ENSP00000328444:p.Gly7Ser	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	277	122	0.440433	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	217	0.09935897435897435	69	0.1402439024390244	36	0.09944751381215469	99	0.17307692307692307	13	0.017150395778364115	.	3.927	-0.016893	0.07681	0.105491	0.015085	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01272	5.07	3.1	3.1	0.35709	.	0.137136	0.32935	U	0.005468	T	0.00012	0.0000	L	0.52905	1.665	0.35623	P	0.19040400000000002	P	0.43094	0.799	B	0.40702	0.338	T	0.38714	-0.9648	9	0.08599	T	0.76	.	7.6799	0.28507	0.2519:0.7481:0.0:0.0	.	7	Q9BYQ9	KRA48_HUMAN	S	7	ENSP00000328444:G7S	ENSP00000414561:G7S	G	-	1	0	KRTAP4-8	36507844	1.000000	0.71417	0.999000	0.59377	0.195000	0.23768	1.980000	0.40618	1.733000	0.51620	0.449000	0.29647	GGC	C|0.900;T|0.100	0.100	strong		0.557	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
TRIM36	55521	hgsc.bcm.edu	37	5	114480364	114480364	+	Silent	SNP	C	C	T	rs7716270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:114480364C>T	ENST00000282369.3	-	4	823	c.702G>A	c.(700-702)ctG>ctA	p.L234L	TRIM36_ENST00000513154.1_Silent_p.L222L|TRIM36_ENST00000514154.1_Silent_p.L79L|TRIM36_ENST00000515104.1_5'Flank	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	234					acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		CCAACTTACACAGATGGCAAA	0.378													T|||	1704	0.340256	0.5787	0.2896	5008	,	,		18668	0.4345		0.0785	False		,,,				2504	0.226				p.L234L		Atlas-SNP	.											.	TRIM36	126	.	0			c.G702A						PASS	.	T		2279,2125	577.0+/-384.4	608,1063,531	138.0	129.0	132.0		702	0.9	1.0	5	dbSNP_116	132	830,7770	781.4+/-407.6	42,746,3512	no	coding-synonymous	TRIM36	NM_018700.3		650,1809,4043	TT,TC,CC		9.6512,48.2516,23.908		234/729	114480364	3109,9895	2202	4300	6502	SO:0001819	synonymous_variant	55521	exon4			CTTACACAGATGG	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16280	protein-coding gene	gene with protein product	"""zinc-binding protein Rbcc728"", ""tripartite motif protein 36"", ""RING finger protein 98"""	609317	"""tripartite motif-containing 36"""			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.702G>A	5.37:g.114480364C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	144	69	0.479167	NM_018700	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Silent	SNP	ENST00000282369.3	37	CCDS4115.1																																																																																			C|0.732;T|0.268	0.268	strong		0.378	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700	
MRPL45	84311	hgsc.bcm.edu	37	17	36453208	36453208	+	Missense_Mutation	SNP	T	T	C	rs11559007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36453208T>C	ENST00000312513.5	+	1	220	c.59T>C	c.(58-60)tTt>tCt	p.F20S		NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	20						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GGCTGGTGGTTTCGGCAGGTG	0.572													C|||	1310	0.261581	0.7458	0.1585	5008	,	,		18189	0.0		0.1541	False		,,,				2504	0.0603				p.F20S		Atlas-SNP	.											MRPL45,NS,carcinoma,0,1	MRPL45	27	1	0			c.T59C						scavenged	.	C	SER/PHE	641,743		287,67,338	50.0	81.0	72.0		59	3.3	1.0	17	dbSNP_134	72	225,2957		27,171,1393	no	missense	MRPL45	NM_032351.4	155	314,238,1731	CC,CT,TT		7.071,46.315,18.9663	benign	20/307	36453208	866,3700	692	1591	2283	SO:0001583	missense	84311	exon1			GGTGGTTTCGGCA	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"""Mitochondrial ribosomal proteins / large subunits"""	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.59T>C	17.37:g.36453208T>C	ENSP00000308901:p.Phe20Ser	Somatic	99	4	0.040404		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_032351	A1L436|Q6ZMJ5	Missense_Mutation	SNP	ENST00000312513.5	37	CCDS11326.1	478	0.21886446886446886	267	0.5426829268292683	68	0.1878453038674033	35	0.06118881118881119	108	0.1424802110817942	C	2.695	-0.272197	0.05716	0.46315	0.07071	ENSG00000174100	ENST00000312513	T	0.25749	1.78	4.28	3.31	0.37934	.	.	.	.	.	T	0.00012	0.0000	N	0.00138	-2.015	0.48511	P	3.370000000000317E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.40664	-0.9551	8	0.29301	T	0.29	.	6.6711	0.23068	0.0:0.783:0.0:0.217	.	20	Q9BRJ2	RM45_HUMAN	S	20	ENSP00000308901:F20S	ENSP00000308901:F20S	F	+	2	0	MRPL45	.	0.996000	0.38824	0.988000	0.46212	0.947000	0.59692	0.684000	0.25364	0.565000	0.29255	-0.282000	0.10007	TTT	T|0.781;C|0.219	0.219	strong		0.572	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351	
CCDC88C	440193	hgsc.bcm.edu	37	14	91770308	91770308	+	Silent	SNP	C	C	T	rs112741231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91770308C>T	ENST00000389857.6	-	20	3458	c.3372G>A	c.(3370-3372)acG>acA	p.T1124T		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1124					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GGGAACTCAGCGTGGAGTTCT	0.662													c|||	111	0.0221645	0.0772	0.013	5008	,	,		16262	0.0		0.0	False		,,,				2504	0.0				p.T1124T		Atlas-SNP	.											CCDC88C_ENST00000389857,NS,carcinoma,0,2	CCDC88C	192	2	0			c.G3372A						PASS	.	C		250,3982		8,234,1874	43.0	49.0	47.0		3372	-11.0	0.2	14	dbSNP_132	47	9,8477		0,9,4234	no	coding-synonymous	CCDC88C	NM_001080414.3		8,243,6108	TT,TC,CC		0.1061,5.9074,2.0365		1124/2029	91770308	259,12459	2116	4243	6359	SO:0001819	synonymous_variant	440193	exon20			ACTCAGCGTGGAG		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.3372G>A	14.37:g.91770308C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			C|0.983;T|0.017	0.017	strong		0.662	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
KRT34	3885	hgsc.bcm.edu	37	17	39535388	39535388	+	Missense_Mutation	SNP	T	T	C	rs2071599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39535388T>C	ENST00000394001.1	-	6	1073	c.1043A>G	c.(1042-1044)cAc>cGc	p.H348R		NM_021013.3	NP_066293.2	O76011	KRT34_HUMAN	keratin 34	348	Coil 2.|Rod.		H -> R (in dbSNP:rs2071599).		epidermis development (GO:0008544)	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)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Breast(137;0.000496)				GGAGCTGTAGTGGGCCTCGCT	0.582													c|||	856	0.170927	0.4297	0.085	5008	,	,		22237	0.0774		0.1024	False		,,,				2504	0.0491				p.H348R		Atlas-SNP	.											.	KRT34	71	.	0			c.A1043G						PASS	.	C	ARG/HIS	1622,2784		237,1148,818	94.0	85.0	88.0		1043	4.9	1.0	17	dbSNP_96	88	932,7668		31,870,3399	no	missense	KRT34	NM_021013.3	29	268,2018,4217	CC,CT,TT		10.8372,36.8134,19.6371	benign	348/437	39535388	2554,10452	2203	4300	6503	SO:0001583	missense	3885	exon6			CTGTAGTGGGCCT	Y16790	CCDS11390.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131737	ENSG00000131737		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6452	protein-coding gene	gene with protein product	"""hard keratin type I 4"""	602763	"""keratin, hair, acidic, 4"""	KRTHA4		2431943, 9756910, 16831889	Standard	NM_021013		Approved	Ha-4	uc002hwm.3	O76011	OTTHUMG00000133436	ENST00000394001.1:c.1043A>G	17.37:g.39535388T>C	ENSP00000377570:p.His348Arg	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	207	203	0.980676	NM_021013	Q8IUT8|Q8N4W2	Missense_Mutation	SNP	ENST00000394001.1	37	CCDS11390.1	306	0.1401098901098901	168	0.34146341463414637	32	0.08839779005524862	37	0.06468531468531469	69	0.09102902374670185	c	4.348	0.064063	0.08388	0.368134	0.108372	ENSG00000131737	ENST00000394001;ENST00000251648	.	.	.	4.91	4.91	0.64330	Filament (1);	0.000000	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00015	-2.875	0.43698	P	0.003846000000000016	B	0.02656	0.0	B	0.01281	0.0	T	0.43343	-0.9397	8	0.02654	T	1	.	12.8943	0.58091	0.0:0.9204:0.0:0.0796	rs2071599	348	O76011	KRT34_HUMAN	R	306;348	.	ENSP00000251648:H348R	H	-	2	0	KRT34	36788914	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	3.975000	0.56859	1.218000	0.43458	-0.227000	0.12334	CAC	T|0.874;C|0.126	0.126	strong		0.582	KRT34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257304.3	NM_021013	
CUBN	8029	hgsc.bcm.edu	37	10	17146590	17146590	+	Silent	SNP	A	A	G	rs12571671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:17146590A>G	ENST00000377833.4	-	12	1310	c.1245T>C	c.(1243-1245)ggT>ggC	p.G415G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	415	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.G415G(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TACAAAAATAACCAGAGACAG	0.378													A|||	585	0.116813	0.0862	0.0937	5008	,	,		12733	0.25		0.0378	False		,,,				2504	0.1186				p.G415G		Atlas-SNP	.											CUBN,NS,carcinoma,0,1	CUBN	515	1	1	Substitution - coding silent(1)	stomach(1)	c.T1245C						PASS	.	A		403,4003	198.1+/-222.0	21,361,1821	71.0	57.0	62.0		1245	1.8	1.0	10	dbSNP_120	62	221,8379	90.6+/-152.8	5,211,4084	no	coding-synonymous	CUBN	NM_001081.3		26,572,5905	GG,GA,AA		2.5698,9.1466,4.7978		415/3624	17146590	624,12382	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon12			AAAATAACCAGAG	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.1245T>C	10.37:g.17146590A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	142	73	0.514085	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			A|0.935;G|0.065	0.065	strong		0.378	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
GNRHR	2798	hgsc.bcm.edu	37	4	68619601	68619601	+	Silent	SNP	G	G	A	rs4986942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:68619601G>A	ENST00000226413.4	-	1	477	c.453C>T	c.(451-453)agC>agT	p.S151S	UBA6-AS1_ENST00000502758.1_RNA|UBA6-AS1_ENST00000500538.2_RNA|GNRHR_ENST00000420975.2_Silent_p.S151S	NM_000406.2	NP_000397.1	P30968	GNRHR_HUMAN	gonadotropin-releasing hormone receptor	151					cellular response to gonadotropin-releasing hormone (GO:0097211)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gonadotropin-releasing hormone receptor activity (GO:0004968)			endometrium(2)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	13					Abarelix(DB00106)|Buserelin(DB06719)|Cetrorelix(DB00050)|Danazol(DB01406)|Degarelix(DB06699)|Gonadorelin(DB00644)|Goserelin(DB00014)|Leuprolide(DB00007)|Nafarelin(DB00666)	CTTTGCTGTTGCTTTTCAAAG	0.498													G|||	333	0.0664936	0.087	0.0908	5008	,	,		19267	0.0069		0.0815	False		,,,				2504	0.0675				p.S151S		Atlas-SNP	.											.	GNRHR	31	.	0			c.C453T						PASS	.	G	,	466,3940	221.7+/-238.7	27,412,1764	64.0	62.0	62.0		453,453	5.3	0.2	4	dbSNP_118	62	853,7747	194.4+/-239.8	40,773,3487	no	coding-synonymous,coding-synonymous	GNRHR	NM_000406.2,NM_001012763.1	,	67,1185,5251	AA,AG,GG		9.9186,10.5765,10.1415	,	151/329,151/250	68619601	1319,11687	2203	4300	6503	SO:0001819	synonymous_variant	2798	exon1			GCTGTTGCTTTTC		CCDS3517.1, CCDS47064.1	4q21.2	2012-08-08			ENSG00000109163	ENSG00000109163		"""GPCR / Class A : Gonadotropin-releasing hormone receptors"""	4421	protein-coding gene	gene with protein product		138850		GRHR		8386108	Standard	NM_000406		Approved	LHRHR	uc003hdn.3	P30968	OTTHUMG00000129302	ENST00000226413.4:c.453C>T	4.37:g.68619601G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	164	64	0.390244	NM_000406	O75793|Q14D13|Q92644	Silent	SNP	ENST00000226413.4	37	CCDS3517.1																																																																																			G|0.914;A|0.086	0.086	strong		0.498	GNRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251432.2		
ATP12A	479	hgsc.bcm.edu	37	13	25266932	25266932	+	Silent	SNP	C	C	A	rs963984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25266932C>A	ENST00000381946.3	+	10	1442	c.1275C>A	c.(1273-1275)gtC>gtA	p.V425V	ATP12A_ENST00000218548.6_Silent_p.V431V			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	425					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)		CAGACCAAGTCTTTGACCAAA	0.512													C|||	1165	0.232628	0.1263	0.2983	5008	,	,		21097	0.4593		0.0805	False		,,,				2504	0.2526				p.V431V	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C1293A						PASS	.	C	,	499,3907	232.6+/-246.1	32,435,1736	213.0	211.0	212.0		1293,1275	0.4	0.2	13	dbSNP_86	212	809,7791	188.6+/-235.5	47,715,3538	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	79,1150,5274	AA,AC,CC		9.407,11.3255,10.0569	,	431/1046,425/1040	25266932	1308,11698	2203	4300	6503	SO:0001819	synonymous_variant	479	exon10			CCAAGTCTTTGAC	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.1275C>A	13.37:g.25266932C>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.845;A|0.155	0.155	strong		0.512	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
MYO7A	4647	hgsc.bcm.edu	37	11	76922208	76922208	+	Silent	SNP	G	G	A	rs111033209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:76922208G>A	ENST00000409709.3	+	45	6335	c.6063G>A	c.(6061-6063)aaG>aaA	p.K2021K	MYO7A_ENST00000409619.2_Silent_p.K1972K|MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000458637.2_Silent_p.K1983K	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2021	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						AGTTGCCCAAGTATCTCCGAG	0.617													G|||	155	0.0309505	0.1142	0.0043	5008	,	,		19584	0.0		0.001	False		,,,				2504	0.0				p.K2021K		Atlas-SNP	.											.	MYO7A	164	.	0			c.G6063A						PASS	.	G	,	352,3800		22,308,1746	19.0	23.0	22.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6063,5949	1.4	1.0	11	dbSNP_132	22	6,8398		0,6,4196	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	22,314,5942	AA,AG,GG		0.0714,8.4778,2.8512	,	2021/2216,1983/2176	76922208	358,12198	2076	4202	6278	SO:0001819	synonymous_variant	4647	exon45			GCCCAAGTATCTC	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.6063G>A	11.37:g.76922208G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			G|0.966;A|0.034	0.034	strong		0.617	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
UPP2	151531	hgsc.bcm.edu	37	2	158958605	158958605	+	Missense_Mutation	SNP	G	G	T	rs6710480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:158958605G>T	ENST00000005756.4	+	1	224	c.30G>T	c.(28-30)agG>agT	p.R10S	UPP2_ENST00000460456.1_3'UTR|UPP2_ENST00000409859.4_Missense_Mutation_p.R67S|UPP2_ENST00000605860.1_Missense_Mutation_p.R67S	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	10			R -> S (in dbSNP:rs6710480).		nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	CCTCCAATAGGTCCATGAGAT	0.333													T|||	849	0.169529	0.3676	0.0576	5008	,	,		18023	0.1627		0.0408	False		,,,				2504	0.1207				p.R67S		Atlas-SNP	.											.	UPP2	60	.	0			c.G201T						PASS	.	T	SER/ARG,SER/ARG	1404,3002	685.7+/-404.6	239,926,1038	149.0	160.0	156.0		201,30	-1.0	0.0	2	dbSNP_116	156	252,8348	807.6+/-407.2	6,240,4054	yes	missense,missense	UPP2	NM_001135098.1,NM_173355.3	110,110	245,1166,5092	TT,TG,GG		2.9302,31.8656,12.7326	probably-damaging,probably-damaging	67/375,10/318	158958605	1656,11350	2203	4300	6503	SO:0001583	missense	151531	exon3			CAATAGGTCCATG	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.30G>T	2.37:g.158958605G>T	ENSP00000005756:p.Arg10Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	37	CCDS2207.1	340	0.15567765567765568	207	0.42073170731707316	25	0.06906077348066299	84	0.14685314685314685	24	0.0316622691292876	T	0.005	-2.125537	0.00342	0.318656	0.029302	ENSG00000007001	ENST00000409859;ENST00000005756	T;T	0.32272	1.46;1.56	5.67	-1.0	0.10196	.	0.631105	0.16810	N	0.198610	T	0.00012	0.0000	N	0.10874	0.06	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41270	-0.9518	9	0.06757	T	0.87	.	1.6005	0.02673	0.393:0.1422:0.3228:0.142	rs6710480;rs52815667;rs61084278;rs6710480	10	O95045	UPP2_HUMAN	S	67;10	ENSP00000387230:R67S;ENSP00000005756:R10S	ENSP00000005756:R10S	R	+	3	2	UPP2	158666851	0.138000	0.22547	0.000000	0.03702	0.004000	0.04260	0.306000	0.19279	-0.421000	0.07416	-2.990000	0.00078	AGG	G|0.846;T|0.154	0.154	strong		0.333	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355	
MSLN	10232	hgsc.bcm.edu	37	16	816973	816973	+	Missense_Mutation	SNP	A	A	G	rs35317722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:816973A>G	ENST00000382862.3	+	14	1581	c.1486A>G	c.(1486-1488)Aac>Gac	p.N496D	MSLN_ENST00000566549.1_Missense_Mutation_p.N488D|MSLN_ENST00000545450.2_Missense_Mutation_p.N488D|MSLN_ENST00000563941.1_Missense_Mutation_p.N488D	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	496					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)				CCAGAACATGAACGGGTCCGA	0.627													A|||	151	0.0301518	0.1104	0.0072	5008	,	,		18480	0.0		0.0	False		,,,				2504	0.0				p.N496D		Atlas-SNP	.											.	MSLN	109	.	0			c.A1486G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN	341,4039	175.5+/-204.9	19,303,1868	79.0	80.0	79.0		1462,1462,1486	-0.5	0.0	16	dbSNP_126	79	3,8581	3.0+/-9.4	0,3,4289	yes	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	23,23,23	19,306,6157	GG,GA,AA		0.0349,7.7854,2.6535	benign,benign,benign	488/623,488/623,496/631	816973	344,12620	2190	4292	6482	SO:0001583	missense	10232	exon14			AACATGAACGGGT	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.1486A>G	16.37:g.816973A>G	ENSP00000372313:p.Asn496Asp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_013404	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	66	0.03021978021978022	63	0.12804878048780488	3	0.008287292817679558	0	0.0	0	0.0	A	5.121	0.207947	0.09704	0.077854	3.49E-4	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.12039	2.72;2.72	5.13	-0.498	0.12019	.	0.811867	0.11375	N	0.570445	T	0.00073	0.0002	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.15719	0.004;0.009;0.014;0.004	B;B;B;B	0.13407	0.005;0.009;0.005;0.005	T	0.44620	-0.9316	10	0.11485	T	0.65	-15.2008	5.1406	0.14957	0.4492:0.2783:0.0:0.2724	rs35317722	487;496;488;488	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	D	496;488;488;496	ENSP00000442965:N488D;ENSP00000372313:N496D	ENSP00000372313:N496D	N	+	1	0	MSLN	756974	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.121000	0.15667	0.222000	0.20900	0.443000	0.29094	AAC	A|0.970;G|0.030	0.030	strong		0.627	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
IRF1	3659	hgsc.bcm.edu	37	5	131822055	131822055	+	Silent	SNP	T	T	C	rs9282762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:131822055T>C	ENST00000245414.4	-	7	813	c.555A>G	c.(553-555)ccA>ccG	p.P185P	IRF1_ENST00000463784.1_5'Flank|IRF1_ENST00000405885.2_Silent_p.P185P	NM_002198.2	NP_002189.1	P10914	IRF1_HUMAN	interferon regulatory factor 1	185					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell cycle arrest (GO:0007050)|cellular response to interferon-beta (GO:0035458)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000564)|regulation of cell cycle (GO:0051726)|regulation of innate immune response (GO:0045088)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.026)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	LUAD - Lung adenocarcinoma(142;0.247)		TGACAGCACATGGCGACAGTG	0.577													C|||	2036	0.40655	0.4758	0.3588	5008	,	,		19987	0.3829		0.3449	False		,,,				2504	0.4346				p.P185P		Atlas-SNP	.											.	IRF1	26	.	0			c.A555G						PASS	.	C	,	2158,2248	588.0+/-386.8	521,1116,566	72.0	70.0	71.0		,555	-7.7	0.0	5	dbSNP_118	71	2806,5794	672.0+/-402.9	460,1886,1954	no	utr-3,coding-synonymous	IRF1,C5orf56	NM_001207002.1,NM_002198.2	,	981,3002,2520	CC,CT,TT		32.6279,48.9787,38.167	,	,185/326	131822055	4964,8042	2203	4300	6503	SO:0001819	synonymous_variant	3659	exon7			AGCACATGGCGAC		CCDS4155.1	5q23-q31	2008-07-18			ENSG00000125347	ENSG00000125347			6116	protein-coding gene	gene with protein product	"""interferon regulatory factor-1"""	147575				2726461, 1680796	Standard	NM_002198		Approved	MAR	uc003kxa.2	P10914	OTTHUMG00000059497	ENST00000245414.4:c.555A>G	5.37:g.131822055T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	NM_002198	Q96GG7	Silent	SNP	ENST00000245414.4	37	CCDS4155.1																																																																																			T|0.623;C|0.377	0.377	strong		0.577	IRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132340.1	NM_002198	
MEGF8	1954	hgsc.bcm.edu	37	19	42873089	42873089	+	Silent	SNP	G	G	A	rs10425783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42873089G>A	ENST00000251268.6	+	37	6576	c.6576G>A	c.(6574-6576)acG>acA	p.T2192T	MEGF8_ENST00000378073.4_5'Flank|MEGF8_ENST00000334370.4_Silent_p.T2125T	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2192	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				GCAACGAGACGCAGAATTGCC	0.662													G|||	133	0.0265575	0.093	0.0115	5008	,	,		17876	0.0		0.002	False		,,,				2504	0.0				p.T2192T		Atlas-SNP	.											.	MEGF8	358	.	0			c.G6576A						PASS	.	G		335,4071	176.9+/-206.0	17,301,1885	82.0	84.0	83.0		6375	-9.5	0.0	19	dbSNP_119	83	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	MEGF8	NM_001410.2		17,311,6175	AA,AG,GG		0.1163,7.6033,2.6526		2125/2779	42873089	345,12661	2203	4300	6503	SO:0001819	synonymous_variant	1954	exon37			CGAGACGCAGAAT	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.6576G>A	19.37:g.42873089G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																				G|0.969;A|0.031	0.031	strong		0.662	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
SACS	26278	hgsc.bcm.edu	37	13	23914286	23914286	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23914286T>C	ENST00000382292.3	-	9	4002	c.3729A>G	c.(3727-3729)gaA>gaG	p.E1243E	SACS_ENST00000402364.1_Silent_p.E493E|SACS_ENST00000382298.3_Silent_p.E1243E			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1243					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GATAGTAGTCTTCATCACTAA	0.323																																					p.E1243E		Atlas-SNP	.											.	SACS	871	.	0			c.A3729G						PASS	.						44.0	43.0	43.0					13																	23914286		2202	4300	6502	SO:0001819	synonymous_variant	26278	exon10			GTAGTCTTCATCA	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.3729A>G	13.37:g.23914286T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	121	62	0.512397	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			.	.	none		0.323	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
CLEC16A	23274	hgsc.bcm.edu	37	16	11272227	11272227	+	Missense_Mutation	SNP	C	C	T	rs61744103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11272227C>T	ENST00000409790.1	+	24	3072	c.2842C>T	c.(2842-2844)Ctt>Ttt	p.L948F	CLEC16A_ENST00000381822.2_Missense_Mutation_p.L35F	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						TAAGCCTCACCTTCCTGACCA	0.592													C|||	90	0.0179712	0.0658	0.0043	5008	,	,		6774	0.0		0.0	False		,,,				2504	0.0				p.L948F		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2842T						PASS	.	C	PHE/LEU	177,4103		3,171,1966	100.0	111.0	107.0		2842	2.0	0.9	16	dbSNP_129	107	1,8491		0,1,4245	yes	missense	CLEC16A	NM_015226.2	22	3,172,6211	TT,TC,CC		0.0118,4.1355,1.3937	benign	948/1054	11272227	178,12594	2140	4246	6386	SO:0001583	missense	23274	exon23			CCTCACCTTCCTG	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.2842C>T	16.37:g.11272227C>T	ENSP00000387122:p.Leu948Phe	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	46	0.597403	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	C	10.65	1.409444	0.25378	0.041355	1.18E-4	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.50548	0.74	4.13	2.02	0.26589	.	1.046110	0.07487	N	0.904880	T	0.11879	0.0289	N	0.03608	-0.345	0.09310	N	1	D;B	0.69078	0.997;0.0	D;B	0.63283	0.913;0.0	T	0.21895	-1.0232	10	0.32370	T	0.25	-2.4515	5.4981	0.16813	0.3727:0.5235:0.0:0.1038	rs61744103	35;948	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	F	948;948;35	ENSP00000387122:L948F	ENSP00000371244:L35F	L	+	1	0	CLEC16A	11179728	0.120000	0.22244	0.917000	0.36280	0.855000	0.48748	0.314000	0.19432	0.815000	0.34398	0.563000	0.77884	CTT	C|0.991;T|0.009	0.009	strong		0.592	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
CCL18	6362	hgsc.bcm.edu	37	17	34391721	34391721	+	Missense_Mutation	SNP	G	G	A	rs73290772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34391721G>A	ENST00000004921.3	+	1	82	c.19G>A	c.(19-21)Gcc>Acc	p.A7T		NM_002988.2	NP_002979.1	P55774	CCL18_HUMAN	chemokine (C-C motif) ligand 18 (pulmonary and activation-regulated)	7					cell chemotaxis (GO:0060326)|cell communication (GO:0007154)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|response to biotic stimulus (GO:0009607)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CCTTGCAGCTGCCCTCCTTGT	0.587													G|||	32	0.00638978	0.0227	0.0014	5008	,	,		20323	0.0		0.001	False		,,,				2504	0.0				p.A7T		Atlas-SNP	.											.	CCL18	9	.	0			c.G19A						PASS	.	G	THR/ALA	83,4323	70.9+/-108.8	1,81,2121	175.0	144.0	154.0		19	-4.2	0.0	17	dbSNP_130	154	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CCL18	NM_002988.2	58	1,85,6417	AA,AG,GG		0.0465,1.8838,0.6689	possibly-damaging	7/90	34391721	87,12919	2203	4300	6503	SO:0001583	missense	6362	exon1			GCAGCTGCCCTCC	Y13710	CCDS11306.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000006074	ENSG00000275385		"""Chemokine ligands"""	10616	protein-coding gene	gene with protein product		603757	"""small inducible cytokine subfamily A (Cys-Cys), member 18, pulmonary and activation-regulated"""	SCYA18		9233607, 10049593	Standard	NM_002988		Approved	DC-CK1, PARC, AMAC-1, DCCK1, MIP-4, CKb7	uc002hku.3	P55774	OTTHUMG00000188410	ENST00000004921.3:c.19G>A	17.37:g.34391721G>A	ENSP00000004921:p.Ala7Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	150	74	0.493333	NM_002988	B5BUM2|Q53X71	Missense_Mutation	SNP	ENST00000004921.3	37	CCDS11306.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	15.95	2.982703	0.53827	0.018838	4.65E-4	ENSG00000006074	ENST00000004921	T	0.03468	3.92	4.63	-4.23	0.03789	.	0.749621	0.12687	N	0.447482	T	0.02418	0.0074	.	.	.	0.09310	N	1	D	0.65815	0.995	P	0.53954	0.738	T	0.10382	-1.0632	9	0.37606	T	0.19	.	5.6346	0.17530	0.3533:0.0:0.5254:0.1213	.	7	P55774	CCL18_HUMAN	T	7	ENSP00000004921:A7T	ENSP00000004921:A7T	A	+	1	0	CCL18	31415834	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.697000	0.05098	-0.814000	0.04352	-0.311000	0.09066	GCC	G|0.994;A|0.006	0.006	strong		0.587	CCL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256583.1	NM_002988	
FRMPD2	143162	hgsc.bcm.edu	37	10	49440168	49440168	+	Silent	SNP	C	C	T	rs11816450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:49440168C>T	ENST00000374201.3	-	10	1460	c.1158G>A	c.(1156-1158)gcG>gcA	p.A386A	FRMPD2_ENST00000305531.3_Silent_p.A362A|FRMPD2_ENST00000407470.4_Silent_p.A355A	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	386	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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)		TTTTCATATACGCCAAGCCAA	0.498													C|||	226	0.0451278	0.1188	0.0173	5008	,	,		20618	0.0258		0.0109	False		,,,				2504	0.0204				p.A386A		Atlas-SNP	.											.	FRMPD2	157	.	0			c.G1158A						PASS	.	C		431,3975	209.8+/-230.5	28,375,1800	127.0	118.0	121.0		1158	-3.0	0.3	10	dbSNP_120	121	57,8543	34.8+/-89.0	2,53,4245	no	coding-synonymous	FRMPD2	NM_001018071.3		30,428,6045	TT,TC,CC		0.6628,9.7821,3.7521		386/1310	49440168	488,12518	2203	4300	6503	SO:0001819	synonymous_variant	143162	exon10			CATATACGCCAAG	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.1158G>A	10.37:g.49440168C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	42	0.43299	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Silent	SNP	ENST00000374201.3	37	CCDS31195.1																																																																																			C|0.961;T|0.039	0.039	strong		0.498	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
DNAJB1	3337	hgsc.bcm.edu	37	19	14629150	14629150	+	Silent	SNP	G	G	A	rs3962158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14629150G>A	ENST00000254322.2	-	1	82	c.12C>T	c.(10-12)gaC>gaT	p.D4D	DNAJB1_ENST00000396969.4_Intron	NM_006145.1	NP_006136.1	P25685	DNJB1_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 1	4	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				chaperone cofactor-dependent protein refolding (GO:0070389)|chaperone mediated protein folding requiring cofactor (GO:0051085)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(1328;0.0476)		TCTGGTAGTAGTCTTTACCCA	0.706													G|||	1717	0.342851	0.4493	0.3343	5008	,	,		9161	0.1071		0.3211	False		,,,				2504	0.4703				p.D4D		Atlas-SNP	.											.	DNAJB1	38	.	0			c.C12T						PASS	.	G		1765,2629		361,1043,793	22.0	23.0	23.0		12	-4.9	1.0	19	dbSNP_108	23	2657,5935		462,1733,2101	no	coding-synonymous	DNAJB1	NM_006145.1		823,2776,2894	AA,AG,GG		30.9241,40.1684,34.0521		4/341	14629150	4422,8564	2197	4296	6493	SO:0001819	synonymous_variant	3337	exon1			GTAGTAGTCTTTA	D49547	CCDS12312.1, CCDS74295.1	19p13.12	2014-08-12			ENSG00000132002	ENSG00000132002		"""Heat shock proteins / DNAJ (HSP40)"""	5270	protein-coding gene	gene with protein product	"""radial spoke 16 homolog B (Chlamydomonas)"""	604572		HSPF1		8975727, 8250930	Standard	XM_006722733		Approved	Hsp40, Sis1, RSPH16B	uc002myz.1	P25685	OTTHUMG00000183289	ENST00000254322.2:c.12C>T	19.37:g.14629150G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_006145	B4DX52	Silent	SNP	ENST00000254322.2	37	CCDS12312.1																																																																																			G|0.685;A|0.315	0.315	strong		0.706	DNAJB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465987.1	NM_006145	
MUC17	140453	hgsc.bcm.edu	37	7	100677279	100677279	+	Missense_Mutation	SNP	G	G	C	rs76184171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	202	50	0.247525	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	
PHF21B	112885	hgsc.bcm.edu	37	22	45283897	45283897	+	Silent	SNP	C	C	T	rs6006901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45283897C>T	ENST00000313237.5	-	10	1293	c.1143G>A	c.(1141-1143)ccG>ccA	p.P381P	PHF21B_ENST00000403565.1_Silent_p.P177P|PHF21B_ENST00000396103.3_Silent_p.P339P|PHF21B_ENST00000404079.2_Silent_p.P327P	NM_138415.4	NP_612424.1	Q96EK2	PF21B_HUMAN	PHD finger protein 21B	381							zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(14)|ovary(2)|prostate(1)|skin(2)	25		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		TCTTGAGGGGCGGCTCCAGGC	0.687													C|||	905	0.180711	0.354	0.1225	5008	,	,		13675	0.0833		0.1004	False		,,,				2504	0.1708				p.P381P		Atlas-SNP	.											.	PHF21B	61	.	0			c.G1143A						PASS	.	C	,,	1265,3101		185,895,1103	12.0	12.0	12.0		1017,981,1143	-2.4	1.0	22	dbSNP_114	12	898,7656		62,774,3441	no	coding-synonymous,coding-synonymous,coding-synonymous	PHF21B	NM_001135862.2,NM_001242450.1,NM_138415.4	,,	247,1669,4544	TT,TC,CC		10.498,28.9739,16.7415	,,	339/490,327/478,381/532	45283897	2163,10757	2183	4277	6460	SO:0001819	synonymous_variant	112885	exon10			GAGGGGCGGCTCC	AK091480	CCDS14061.1, CCDS56234.1, CCDS63504.1	22q13.31	2013-01-28			ENSG00000056487	ENSG00000056487		"""Zinc fingers, PHD-type"""	25161	protein-coding gene	gene with protein product			"""PHD finger protein 4"""	PHF4		12477932	Standard	NM_138415		Approved	BHC80L, FLJ34161	uc011aql.2	Q96EK2	OTTHUMG00000151199	ENST00000313237.5:c.1143G>A	22.37:g.45283897C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_138415	B0QYW3|B0QYW4|B3KRU4|B7Z4F8|Q5TFL2|Q6ICC0	Silent	SNP	ENST00000313237.5	37	CCDS14061.1																																																																																			C|0.826;T|0.174	0.174	strong		0.687	PHF21B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321731.2	NM_138415	
MYH14	79784	hgsc.bcm.edu	37	19	50726570	50726570	+	Silent	SNP	G	G	A	rs4801822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50726570G>A	ENST00000596571.1	+	4	657	c.657G>A	c.(655-657)gcG>gcA	p.A219A	MYH14_ENST00000440075.2_Silent_p.A219A|MYH14_ENST00000262269.8_Silent_p.A219A|MYH14_ENST00000425460.1_Silent_p.A219A|MYH14_ENST00000376970.2_Silent_p.A219A|MYH14_ENST00000601313.1_Silent_p.A219A|MYH14_ENST00000598205.1_Silent_p.A219A			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	219	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)	p.A219A(2)		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)		CCCACGTGGCGTCGTCTCCAA	0.632													A|||	2368	0.472843	0.1573	0.4942	5008	,	,		17994	0.5804		0.6123	False		,,,				2504	0.6299				p.A219A		Atlas-SNP	.											MYH14_ENST00000262269,NS,carcinoma,0,2	MYH14	261	2	2	Substitution - coding silent(2)	prostate(2)	c.G657A						PASS	.	A	,,	987,3349		132,723,1313	44.0	51.0	49.0		657,657,657	-6.1	0.1	19	dbSNP_111	49	5380,3192		1712,1956,618	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	1844,2679,1931	AA,AG,GG		37.2375,22.7629,49.326	,,	219/2004,219/2037,219/1996	50726570	6367,6541	2168	4286	6454	SO:0001819	synonymous_variant	79784	exon5			CGTGGCGTCGTCT	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.657G>A	19.37:g.50726570G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	145	79	0.544828	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			G|0.507;A|0.494	0.494	strong		0.632	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
LMAN1L	79748	hgsc.bcm.edu	37	15	75111530	75111530	+	Missense_Mutation	SNP	G	G	A	rs62621375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75111530G>A	ENST00000309664.5	+	6	774	c.635G>A	c.(634-636)gGt>gAt	p.G212D	LMAN1L_ENST00000379709.3_Missense_Mutation_p.G212D|RP11-414J4.2_ENST00000564823.1_RNA	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	212	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGTGATCCAGGTGAGTTCTGT	0.612													A|||	374	0.0746805	0.2723	0.0144	5008	,	,		19129	0.001		0.003	False		,,,				2504	0.0				p.G212D		Atlas-SNP	.											.	LMAN1L	43	.	0			c.G635A						PASS	.	A	ASP/GLY	1009,3385	728.8+/-410.0	126,757,1314	207.0	185.0	193.0		635	5.7	0.0	15	dbSNP_129	193	6,8586	818.6+/-406.8	0,6,4290	yes	missense	LMAN1L	NM_021819.2	94	126,763,5604	AA,AG,GG		0.0698,22.9631,7.8161	benign	212/527	75111530	1015,11971	2197	4296	6493	SO:0001583	missense	79748	exon6			ATCCAGGTGAGTT	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.635G>A	15.37:g.75111530G>A	ENSP00000310431:p.Gly212Asp	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	225	224	0.995556	NM_021819	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	37	CCDS10270.1	151	0.06913919413919414	143	0.29065040650406504	5	0.013812154696132596	1	0.0017482517482517483	2	0.002638522427440633	A	4.989	0.183651	0.09495	0.229631	6.98E-4	ENSG00000140506	ENST00000309664;ENST00000456603;ENST00000379709	T;T	0.63255	-0.03;-0.03	5.67	5.67	0.87782	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.744014	0.12971	N	0.424120	T	0.00012	0.0000	N	0.00072	-2.265	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.20174	-1.0283	8	.	.	.	.	8.6109	0.33801	0.9131:0.0:0.0869:0.0	rs62621375	104;212;140;212	B4DGW5;Q9HAT1-3;B4DU67;Q9HAT1	.;.;.;LMA1L_HUMAN	D	212;104;212	ENSP00000310431:G212D;ENSP00000369031:G212D	.	G	+	2	0	LMAN1L	72898583	0.706000	0.27856	0.008000	0.14137	0.095000	0.18619	2.764000	0.47613	0.987000	0.38709	-0.332000	0.08345	GGT	G|0.924;A|0.076	0.076	strong		0.612	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		
DYSF	8291	hgsc.bcm.edu	37	2	71838597	71838597	+	Silent	SNP	C	C	A	rs2303606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71838597C>A	ENST00000258104.3	+	38	4285	c.4008C>A	c.(4006-4008)atC>atA	p.I1336I	DYSF_ENST00000409366.1_Silent_p.I1337I|DYSF_ENST00000429174.2_Silent_p.I1336I|DYSF_ENST00000410041.1_Silent_p.I1354I|DYSF_ENST00000394120.2_Silent_p.I1337I|DYSF_ENST00000409651.1_Silent_p.I1368I|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409744.1_Silent_p.I1323I|DYSF_ENST00000409762.1_Silent_p.I1353I|DYSF_ENST00000409582.3_Silent_p.I1353I|DYSF_ENST00000413539.2_Silent_p.I1367I|DYSF_ENST00000410020.3_Silent_p.I1354I	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1336	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GTGCTTAGATCCTGGCATGGG	0.647													C|||	2251	0.449481	0.3585	0.5331	5008	,	,		17324	0.4792		0.5378	False		,,,				2504	0.3916				p.I1368I		Atlas-SNP	.											.	DYSF	536	.	0			c.C4104A						PASS	.	C	,,,,,,,,,,,,,	1741,2665	514.2+/-368.6	338,1065,800	53.0	51.0	52.0		4011,3966,3966,4008,4101,4059,4059,4104,4011,3969,4062,3969,4062,4008	2.8	1.0	2	dbSNP_100	52	4392,4208	577.1+/-390.5	1120,2152,1028	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	1458,3217,1828	AA,AC,CC		48.9302,39.5143,47.1552	,,,,,,,,,,,,,	1337/2082,1322/2067,1322/2088,1336/2102,1367/2112,1353/2098,1353/2119,1368/2113,1337/2103,1323/2089,1354/2099,1323/2068,1354/2120,1336/2081	71838597	6133,6873	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon39			TTAGATCCTGGCA	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4008C>A	2.37:g.71838597C>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			C|0.529;A|0.471	0.471	strong		0.647	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
THBS2	7058	hgsc.bcm.edu	37	6	169648723	169648723	+	Missense_Mutation	SNP	G	G	C	rs36088849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:169648723G>C	ENST00000366787.3	-	4	647	c.398C>G	c.(397-399)aCc>aGc	p.T133S		NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	133	Heparin-binding. {ECO:0000255}.|Laminin G-like.		T -> S (in dbSNP:rs36088849).		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)		CACATGCCGGGTGCCGTCAAT	0.652													G|||	119	0.023762	0.0885	0.0029	5008	,	,		18772	0.0		0.0	False		,,,				2504	0.0				p.T133S	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.C398G						PASS	.	G	SER/THR	345,4061	168.7+/-199.5	15,315,1873	84.0	70.0	75.0		398	0.2	0.0	6	dbSNP_126	75	3,8597	3.0+/-9.4	0,3,4297	yes	missense	THBS2	NM_003247.2	58	15,318,6170	CC,CG,GG		0.0349,7.8302,2.6757	benign	133/1173	169648723	348,12658	2203	4300	6503	SO:0001583	missense	7058	exon4			TGCCGGGTGCCGT		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.398C>G	6.37:g.169648723G>C	ENSP00000355751:p.Thr133Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	NM_003247	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	G	1.088	-0.664792	0.03428	0.078302	3.49E-4	ENSG00000186340	ENST00000366787	T	0.01998	4.51	4.61	0.151	0.14888	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	1.763740	0.03486	U	0.215882	T	0.00384	0.0012	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46952	-0.9154	10	0.22706	T	0.39	-3.9265	3.3224	0.07054	0.1616:0.2494:0.4685:0.1205	rs36088849	133	P35442	TSP2_HUMAN	S	133	ENSP00000355751:T133S	ENSP00000355751:T133S	T	-	2	0	THBS2	169390648	0.018000	0.18449	0.000000	0.03702	0.012000	0.07955	1.512000	0.35812	0.080000	0.16959	0.563000	0.77884	ACC	G|0.977;C|0.023	0.023	strong		0.652	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
FGD3	89846	hgsc.bcm.edu	37	9	95768396	95768396	+	Silent	SNP	C	C	T	rs199786328		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95768396C>T	ENST00000375482.3	+	6	1267	c.771C>T	c.(769-771)gcC>gcT	p.A257A	FGD3_ENST00000416701.2_Silent_p.A257A|FGD3_ENST00000337352.6_Silent_p.A257A	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	257	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)|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)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						TTGACCGAGCCGTAGGGCTGG	0.587																																					p.A257A		Atlas-SNP	.											.	FGD3	116	.	0			c.C771T						PASS	.	C	,	1,4327		0,1,2163	64.0	71.0	69.0		771,771	-7.4	0.0	9		69	0,8568		0,0,4284	no	coding-synonymous,coding-synonymous	FGD3	NM_001083536.1,NM_033086.2	,	0,1,6447	TT,TC,CC		0.0,0.0231,0.0078	,	257/726,257/726	95768396	1,12895	2164	4284	6448	SO:0001819	synonymous_variant	89846	exon6			CCGAGCCGTAGGG	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16027	protein-coding gene	gene with protein product			"""FGD1 family, member 3"""			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.771C>T	9.37:g.95768396C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	85	56	0.658824	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Silent	SNP	ENST00000375482.3	37	CCDS43849.1																																																																																			C|1.000;T|0.000	0.000	strong		0.587	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086	
JAG1	182	hgsc.bcm.edu	37	20	10624502	10624502	+	Silent	SNP	G	G	A	rs56225585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:10624502G>A	ENST00000254958.5	-	20	2897	c.2382C>T	c.(2380-2382)agC>agT	p.S794S	JAG1_ENST00000423891.2_Silent_p.S635S|JAG1_ENST00000488480.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	794	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						CACAGGTGCCGCTGTTGTAAC	0.522									Alagille Syndrome				G|||	475	0.0948482	0.3396	0.0375	5008	,	,		16433	0.0		0.0	False		,,,				2504	0.0				p.S794S		Atlas-SNP	.											.	JAG1	213	.	0			c.C2382T						PASS	.	G		1227,3179	422.3+/-339.7	166,895,1142	72.0	60.0	64.0		2382	-5.8	0.8	20	dbSNP_129	64	22,8578	15.3+/-51.7	0,22,4278	no	coding-synonymous	JAG1	NM_000214.2		166,917,5420	AA,AG,GG		0.2558,27.8484,9.6033		794/1219	10624502	1249,11757	2203	4300	6503	SO:0001819	synonymous_variant	182	exon20	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GGTGCCGCTGTTG	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2382C>T	20.37:g.10624502G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			G|0.914;A|0.086	0.086	strong		0.522	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
TRAF3	7187	hgsc.bcm.edu	37	14	103336654	103336654	+	Missense_Mutation	SNP	A	A	G	rs147686384		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103336654A>G	ENST00000560371.1	+	2	333	c.116A>G	c.(115-117)tAc>tGc	p.Y39C	TRAF3_ENST00000392745.2_Missense_Mutation_p.Y39C|TRAF3_ENST00000351691.5_Missense_Mutation_p.Y39C|TRAF3_ENST00000539721.1_Missense_Mutation_p.Y39C|TRAF3_ENST00000347662.4_Missense_Mutation_p.Y39C	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	39					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|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)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Y39C(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		CAAGGAGGTTACAAGGAAAAG	0.567																																					p.Y39C		Atlas-SNP	.											TRAF3,NS,carcinoma,0,1	TRAF3	60	1	1	Substitution - Missense(1)	endometrium(1)	c.A116G						scavenged	.	A	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	0,4406		0,0,2203	98.0	87.0	91.0		116,116,116,116	5.4	1.0	14	dbSNP_134	91	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,missense	TRAF3	NM_001199427.1,NM_003300.3,NM_145725.2,NM_145726.2	194,194,194,194	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging	39/486,39/569,39/569,39/544	103336654	2,13004	2203	4300	6503	SO:0001583	missense	7187	exon3			GAGGTTACAAGGA	U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.116A>G	14.37:g.103336654A>G	ENSP00000454207:p.Tyr39Cys	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	111	4	0.036036	NM_145726	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Missense_Mutation	SNP	ENST00000560371.1	37	CCDS9975.1	.	.	.	.	.	.	.	.	.	.	A	17.28	3.349702	0.61183	0.0	2.33E-4	ENSG00000131323	ENST00000392745;ENST00000347662;ENST00000351691;ENST00000539721	T;T;T;T	0.52057	2.09;2.02;2.02;0.68	5.44	5.44	0.79542	.	0.051260	0.85682	D	0.000000	T	0.65228	0.2671	M	0.62209	1.925	0.49130	D	0.999751	D;D;D	0.69078	0.997;0.993;0.997	D;P;P	0.67382	0.951;0.848;0.808	T	0.68633	-0.5357	10	0.72032	D	0.01	-38.5373	15.5035	0.75719	1.0:0.0:0.0:0.0	.	39;39;39	Q13114-2;A6NHG8;Q13114	.;.;TRAF3_HUMAN	C	39	ENSP00000376500:Y39C;ENSP00000328003:Y39C;ENSP00000332468:Y39C;ENSP00000445998:Y39C	ENSP00000328003:Y39C	Y	+	2	0	TRAF3	102406407	1.000000	0.71417	0.998000	0.56505	0.476000	0.33039	6.147000	0.71783	2.062000	0.61559	0.533000	0.62120	TAC	A|1.000;G|0.000	0.000	weak		0.567	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	
NEFM	4741	hgsc.bcm.edu	37	8	24771318	24771318	+	Silent	SNP	G	G	A	rs61735462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24771318G>A	ENST00000221166.5	+	1	794	c.12G>A	c.(10-12)acG>acA	p.T4T	NEFM_ENST00000518131.1_Silent_p.T4T|NEFM_ENST00000433454.2_5'Flank|GS1-72M22.1_ENST00000607058.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|NEFM_ENST00000437366.2_Silent_p.T4T|NEFM_ENST00000521540.1_3'UTR			P07197	NFM_HUMAN	neurofilament, medium polypeptide	4	Head.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)	p.?(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		TGAGCTACACGTTGGACTCGC	0.697													g|||	42	0.00838658	0.031	0.0	5008	,	,		13480	0.0		0.001	False		,,,				2504	0.0				p.T4T		Atlas-SNP	.											.	NEFM	115	.	1	Unknown(1)	breast(1)	c.G12A						PASS	.			92,4278		0,92,2093	13.0	16.0	15.0		12	-0.2	0.9	8	dbSNP_129	15	3,8561		0,3,4279	no	coding-synonymous	NEFM	NM_005382.2		0,95,6372	AA,AG,GG		0.035,2.1053,0.7345		4/917	24771318	95,12839	2185	4282	6467	SO:0001819	synonymous_variant	4741	exon1			CTACACGTTGGAC	BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"""Intermediate filaments type IV"""	7734	protein-coding gene	gene with protein product		162250	"""neurofilament, medium polypeptide 150kDa"""	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.12G>A	8.37:g.24771318G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_005382	B4DGN2|E9PBF7|Q4QRK6	Silent	SNP	ENST00000221166.5	37	CCDS6046.1																																																																																			G|0.992;A|0.008	0.008	strong		0.697	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382	
PRRG4	79056	hgsc.bcm.edu	37	11	32852172	32852172	+	Missense_Mutation	SNP	G	G	A	rs33962176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:32852172G>A	ENST00000257836.3	+	2	350	c.97G>A	c.(97-99)Gaa>Aaa	p.E33K		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	33			E -> K (in dbSNP:rs33962176).			extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.E33K(1)		large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	7	Breast(20;0.206)					GCATGCGGGAGAAGAAGGTAA	0.488													G|||	364	0.0726837	0.0688	0.0504	5008	,	,		14880	0.0		0.1193	False		,,,				2504	0.1207				p.E33K		Atlas-SNP	.											PRRG4,NS,carcinoma,0,1	PRRG4	15	1	1	Substitution - Missense(1)	prostate(1)	c.G97A						PASS	.	G	LYS/GLU	329,4075	173.7+/-203.5	11,307,1884	90.0	80.0	84.0		97	2.8	0.6	11	dbSNP_126	84	1049,7549	220.9+/-258.5	48,953,3298	yes	missense	PRRG4	NM_024081.5	56	59,1260,5182	AA,AG,GG		12.2005,7.4705,10.5984	benign	33/227	32852172	1378,11624	2202	4299	6501	SO:0001583	missense	79056	exon2			GCGGGAGAAGAAG	AF326351	CCDS7881.1	11p13	2008-02-05			ENSG00000135378	ENSG00000135378			30799	protein-coding gene	gene with protein product		611690				11171957	Standard	NM_024081		Approved	TMG4	uc001mtx.3	Q9BZD6	OTTHUMG00000166219	ENST00000257836.3:c.97G>A	11.37:g.32852172G>A	ENSP00000257836:p.Glu33Lys	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_024081		Missense_Mutation	SNP	ENST00000257836.3	37	CCDS7881.1	154	0.07051282051282051	31	0.06300813008130081	18	0.049723756906077346	0	0.0	105	0.13852242744063326	G	6.368	0.436089	0.12104	0.074705	0.122005	ENSG00000135378	ENST00000257836	D	0.97731	-4.51	4.99	2.84	0.33178	Gamma-carboxyglutamic acid-rich (GLA) domain (1);	0.376451	0.29172	N	0.012929	T	0.07234	0.0183	N	0.12746	0.255	0.42859	P	0.005898999999999988	B	0.06786	0.001	B	0.08055	0.003	T	0.66388	-0.5936	9	0.07175	T	0.84	-10.946	4.509	0.11901	0.3813:0.0:0.6187:0.0	rs33962176	33	Q9BZD6	TMG4_HUMAN	K	33	ENSP00000257836:E33K	ENSP00000257836:E33K	E	+	1	0	PRRG4	32808748	0.617000	0.27043	0.589000	0.28718	0.051000	0.14879	0.807000	0.27140	1.086000	0.41228	-0.192000	0.12808	GAA	G|0.902;A|0.098	0.098	strong		0.488	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081	
SEC31B	25956	hgsc.bcm.edu	37	10	102262227	102262227	+	Silent	SNP	C	C	G	rs143541316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102262227C>G	ENST00000370345.3	-	11	1291	c.1194G>C	c.(1192-1194)ctG>ctC	p.L398L	SEC31B_ENST00000494350.1_5'Flank|SEC31B_ENST00000451524.1_Silent_p.L398L	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	398					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)		CAAAAGTAACCAGCTTCCCTC	0.483													c|||	34	0.00678914	0.0219	0.0043	5008	,	,		19175	0.0		0.002	False		,,,				2504	0.0				p.L398L		Atlas-SNP	.											.	SEC31B	84	.	0			c.G1194C						PASS	.			126,4280	92.5+/-131.2	3,120,2080	40.0	42.0	41.0		1194	4.5	1.0	10	dbSNP_134	41	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	SEC31B	NM_015490.3		3,126,6374	GG,GC,CC		0.0698,2.8597,1.0149		398/1180	102262227	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	25956	exon11			AGTAACCAGCTTC	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.1194G>C	10.37:g.102262227C>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	ENST00000370345.3	37	CCDS7495.1																																																																																			C|0.990;G|0.010	0.010	strong		0.483	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
GAS2L3	283431	hgsc.bcm.edu	37	12	101018161	101018161	+	Silent	SNP	C	C	T	rs1045603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101018161C>T	ENST00000539410.1	+	9	1964	c.1578C>T	c.(1576-1578)tcC>tcT	p.S526S	GAS2L3_ENST00000266754.5_Silent_p.S526S|GAS2L3_ENST00000547754.1_Silent_p.S526S|GAS2L3_ENST00000537247.1_Silent_p.S422S			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	526					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						AAACCAGTTCCAAAACCATAG	0.448													C|||	504	0.100639	0.093	0.1427	5008	,	,		18489	0.0962		0.1123	False		,,,				2504	0.0736				p.S526S		Atlas-SNP	.											.	GAS2L3	76	.	0			c.C1578T						PASS	.	C		350,4056	181.2+/-209.3	12,326,1865	55.0	56.0	56.0		1578	-2.7	0.4	12	dbSNP_86	56	881,7719	199.0+/-243.2	49,783,3468	no	coding-synonymous	GAS2L3	NM_174942.1		61,1109,5333	TT,TC,CC		10.2442,7.9437,9.4649		526/695	101018161	1231,11775	2203	4300	6503	SO:0001819	synonymous_variant	283431	exon10			CAGTTCCAAAACC	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.1578C>T	12.37:g.101018161C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_174942	B2RCN2	Silent	SNP	ENST00000539410.1	37	CCDS9079.1																																																																																			C|0.901;T|0.099	0.099	strong		0.448	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	
LGR4	55366	hgsc.bcm.edu	37	11	27402475	27402475	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:27402475C>T	ENST00000379214.4	-	8	1240	c.797G>A	c.(796-798)gGa>gAa	p.G266E	LGR4_ENST00000389858.4_Missense_Mutation_p.G242E	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	266					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.G266V(1)		NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						ATCAAATGCTCCATCAGGGAT	0.318																																					p.G266E		Atlas-SNP	.											LGR4,NS,NS,0,1	LGR4	87	1	1	Substitution - Missense(1)	NS(1)	c.G797A						scavenged	.						43.0	46.0	45.0					11																	27402475		2202	4292	6494	SO:0001583	missense	55366	exon8			AATGCTCCATCAG	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"""GPCR / Class A : Orphans"""	13299	protein-coding gene	gene with protein product		606666	"""G protein-coupled receptor 48"", ""leucine-rich repeat-containing G protein-coupled receptor 4"""	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.797G>A	11.37:g.27402475C>T	ENSP00000368516:p.Gly266Glu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	177	2	0.0112994	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Missense_Mutation	SNP	ENST00000379214.4	37	CCDS31449.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.159291	0.57368	.	.	ENSG00000205213	ENST00000379214;ENST00000389858	T;T	0.02345	4.34;4.33	5.55	4.64	0.57946	.	0.060171	0.64402	D	0.000002	T	0.08980	0.0222	L	0.41356	1.27	0.80722	D	1	B;D	0.71674	0.044;0.998	B;D	0.66716	0.067;0.946	T	0.21415	-1.0246	10	0.41790	T	0.15	.	14.4971	0.67698	0.0:0.929:0.0:0.071	.	242;266	G5E9B3;Q9BXB1	.;LGR4_HUMAN	E	266;242	ENSP00000368516:G266E;ENSP00000374508:G242E	ENSP00000368516:G266E	G	-	2	0	LGR4	27359051	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	5.792000	0.69052	1.336000	0.45506	0.460000	0.39030	GGA	.	.	none		0.318	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490	
RAB3IL1	5866	hgsc.bcm.edu	37	11	61675644	61675644	+	Missense_Mutation	SNP	T	T	C	rs174477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61675644T>C	ENST00000394836.2	-	2	303	c.146A>G	c.(145-147)cAa>cGa	p.Q49R	RAB3IL1_ENST00000301773.5_Missense_Mutation_p.Q96R	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	49			Q -> R (in dbSNP:rs174477).		positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						CTCCTGGCCTTGGGCCTCCTC	0.682													T|||	369	0.0736821	0.0998	0.0807	5008	,	,		15756	0.0		0.1451	False		,,,				2504	0.0358				p.Q96R		Atlas-SNP	.											RAB3IL1,NS,carcinoma,0,1	RAB3IL1	39	1	0			c.A287G						PASS	.	T	ARG/GLN	439,3883		20,399,1742	8.0	9.0	9.0		146	-1.3	0.1	11	dbSNP_79	9	1141,7311		89,963,3174	no	missense	RAB3IL1	NM_013401.2	43	109,1362,4916	CC,CT,TT		13.4998,10.1573,12.3689	benign	49/383	61675644	1580,11194	2161	4226	6387	SO:0001583	missense	5866	exon2			TGGCCTTGGGCCT	AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.146A>G	11.37:g.61675644T>C	ENSP00000378313:p.Gln49Arg	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	92	36	0.391304	NM_001271686	Q86V32|Q9P1Q8	Missense_Mutation	SNP	ENST00000394836.2	37	CCDS8014.1	193	0.08836996336996338	53	0.10772357723577236	34	0.09392265193370165	0	0.0	106	0.13984168865435356	T	6.248	0.413969	0.11870	0.101573	0.134998	ENSG00000167994	ENST00000394836;ENST00000301773;ENST00000531922	T;T;T	0.44881	0.91;0.91;0.91	4.73	-1.31	0.09230	.	0.527456	0.16430	N	0.214781	T	0.00144	0.0004	L	0.44542	1.39	0.80722	P	0.0	P;B	0.41265	0.744;0.089	B;B	0.31495	0.131;0.021	T	0.07385	-1.0775	9	0.41790	T	0.15	1.193	0.4651	0.00523	0.1991:0.3048:0.203:0.2931	rs174477	96;49	Q8TBN0-2;Q8TBN0	.;R3GEF_HUMAN	R	49;96;96	ENSP00000378313:Q49R;ENSP00000301773:Q96R;ENSP00000435444:Q96R	ENSP00000301773:Q96R	Q	-	2	0	RAB3IL1	61432220	0.013000	0.17824	0.103000	0.21229	0.109000	0.19521	-0.071000	0.11505	-0.066000	0.12998	0.459000	0.35465	CAA	T|0.917;C|0.083	0.083	strong		0.682	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401	
PDLIM4	8572	hgsc.bcm.edu	37	5	131607721	131607721	+	Silent	SNP	C	C	T	rs10479001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:131607721C>T	ENST00000253754.3	+	7	856	c.792C>T	c.(790-792)ggC>ggT	p.G264G	P4HA2_ENST00000471826.1_Intron|PDLIM4_ENST00000379018.3_Missense_Mutation_p.A225V	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	264	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.						zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|urinary_tract(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCATCAGGGGCACCATCGTCA	0.622													C|||	350	0.0698882	0.1702	0.0764	5008	,	,		17367	0.0		0.0507	False		,,,				2504	0.0215				p.A225V		Atlas-SNP	.											PDLIM4,NS,carcinoma,0,1	PDLIM4	22	1	0			c.C674T						PASS	.	C	VAL/ALA,	538,3868	245.0+/-254.1	34,470,1699	119.0	86.0	97.0		674,792	0.8	1.0	5	dbSNP_119	97	409,8191	129.2+/-187.3	11,387,3902	yes	missense,coding-synonymous	PDLIM4	NM_001131027.1,NM_003687.3	64,	45,857,5601	TT,TC,CC		4.7558,12.2106,7.2813	,	225/247,264/331	131607721	947,12059	2203	4300	6503	SO:0001819	synonymous_variant	8572	exon6			CAGGGGCACCATC	AF153882	CCDS4152.1, CCDS47261.1	5q31.1	2008-02-05			ENSG00000131435	ENSG00000131435			16501	protein-coding gene	gene with protein product		603422				9573374	Standard	NM_001131027		Approved	RIL	uc003kwn.3	P50479	OTTHUMG00000059645	ENST00000253754.3:c.792C>T	5.37:g.131607721C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_001131027	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Missense_Mutation	SNP	ENST00000253754.3	37	CCDS4152.1	160	0.07326007326007326	87	0.17682926829268292	35	0.09668508287292818	0	0.0	38	0.05013192612137203	C	16.22	3.062134	0.55432	0.122106	0.047558	ENSG00000131435	ENST00000379018	T	0.19806	2.12	5.05	0.828	0.18841	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.50813	P	1.100000000000545E-4	B	0.12630	0.006	B	0.13407	0.009	T	0.26950	-1.0088	7	0.54805	T	0.06	-13.028	3.9412	0.09328	0.118:0.5178:0.2255:0.1387	rs10479001;rs10479001	225	P50479-2	.	V	225	ENSP00000368303:A225V	ENSP00000368303:A225V	A	+	2	0	PDLIM4	131635620	0.198000	0.23374	0.998000	0.56505	0.949000	0.60115	-0.353000	0.07691	0.123000	0.18342	0.655000	0.94253	GCA	C|0.913;T|0.087	0.087	strong		0.622	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687	
PLIN4	729359	hgsc.bcm.edu	37	19	4512676	4512676	+	Silent	SNP	T	T	G	rs59593546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512676T>G	ENST00000301286.3	-	3	1253	c.1254A>C	c.(1252-1254)acA>acC	p.T418T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	418	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						CGGTGTCCTTTGTACCTGTTG	0.552													G|||	667	0.133187	0.4138	0.0331	5008	,	,		18918	0.001		0.0149	False		,,,				2504	0.0828				p.T418T		Atlas-SNP	.											.	PLIN4	191	.	0			c.A1254C						PASS	.	T		904,2990		362,180,1405	85.0	127.0	114.0		1254	-8.2	0.0	19	dbSNP_129	114	78,8286		20,38,4124	no	coding-synonymous	PLIN4	NM_001080400.1		382,218,5529	GG,GT,TT		0.9326,23.2152,8.0111		418/1358	4512676	982,11276	1947	4182	6129	SO:0001819	synonymous_variant	729359	exon3			GTCCTTTGTACCT	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.1254A>C	19.37:g.4512676T>G		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	148	12	0.0810811	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			T|0.939;G|0.061	0.061	strong		0.552	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
SPATA31A3	727830	hgsc.bcm.edu	37	9	40702846	40702846	+	Missense_Mutation	SNP	C	C	T	rs200010477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:40702846C>T	ENST00000356699.5	+	4	532	c.503C>T	c.(502-504)aCc>aTc	p.T168I	SPATA31A3_ENST00000463536.1_3'UTR|RP11-395E19.5_ENST00000432614.1_lincRNA	NM_001083124.1	NP_001076593.1	Q5VYP0	S31A3_HUMAN	SPATA31 subfamily A, member 3	168	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTGGCCTCCACCCCATCACCA	0.592																																					p.T168I		Atlas-SNP	.											FAM75A3_ENST00000356699,NS,carcinoma,-1,6	.	.	6	0			c.C503T						scavenged	.						29.0	32.0	32.0					9																	40702846		1192	2948	4140	SO:0001583	missense	727830	exon4			CCTCCACCCCATC			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000147926				32003	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A3"""	FAM75A3		20850414	Standard	NM_001083124		Approved	OTTHUMG00000013164, DKFZp434B204	uc010mmj.3	Q5VYP0	OTTHUMG00000013164	ENST00000356699.5:c.503C>T	9.37:g.40702846C>T	ENSP00000349132:p.Thr168Ile	Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	321	80	0.249221	NM_001083124		Missense_Mutation	SNP	ENST00000356699.5	37	CCDS47969.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.507524	0.27036	.	.	ENSG00000147926	ENST00000356699	T	0.05580	3.42	2.04	-3.77	0.04346	.	2.363890	0.02457	N	0.086169	T	0.05044	0.0135	L	0.41415	1.275	0.80722	P	0.0	P	0.37101	0.582	B	0.33339	0.162	T	0.22695	-1.0209	9	0.51188	T	0.08	1.2989	0.8573	0.01185	0.376:0.2856:0.1919:0.1465	.	168	Q5VYP0	F75A3_HUMAN	I	168	ENSP00000349132:T168I	ENSP00000349132:T168I	T	+	2	0	FAM75A3	40692846	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.670000	0.05256	-0.955000	0.03636	-0.714000	0.03626	ACC	.	.	weak		0.592	SPATA31A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036919.1	NM_001083124	
PIK3C3	5289	hgsc.bcm.edu	37	18	39576682	39576682	+	Silent	SNP	G	G	A	rs140083392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:39576682G>A	ENST00000262039.4	+	9	1058	c.972G>A	c.(970-972)acG>acA	p.T324T	PIK3C3_ENST00000398870.3_Silent_p.T261T	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	324	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						ATTATCTTACGAATCAAGAAA	0.279										TSP Lung(28;0.18)			G|||	5	0.000998403	0.0038	0.0	5008	,	,		15613	0.0		0.0	False		,,,				2504	0.0				p.T324T	NSCLC(37;552 1060 2683 16430 37914)	Atlas-SNP	.											PIK3C3,NS,carcinoma,+1,1	PIK3C3	138	1	0			c.G972A						scavenged	.	G		4,4392	8.1+/-20.4	0,4,2194	66.0	70.0	68.0		972	-5.3	1.0	18	dbSNP_134	68	0,8550		0,0,4275	no	coding-synonymous	PIK3C3	NM_002647.2		0,4,6469	AA,AG,GG		0.0,0.091,0.0309		324/888	39576682	4,12942	2198	4275	6473	SO:0001819	synonymous_variant	5289	exon9			TCTTACGAATCAA	Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"""phosphoinositide-3-kinase, class 3"""			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.972G>A	18.37:g.39576682G>A		Somatic	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	163	65	0.398773	NM_002647	Q15134	Silent	SNP	ENST00000262039.4	37	CCDS11920.1																																																																																			G|0.999;A|0.001	0.001	strong		0.279	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647	
RHPN2	85415	hgsc.bcm.edu	37	19	33486992	33486992	+	Missense_Mutation	SNP	A	A	C	rs75351369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33486992A>C	ENST00000254260.3	-	11	1395	c.1360T>G	c.(1360-1362)Tac>Gac	p.Y454D	RHPN2_ENST00000400226.4_Missense_Mutation_p.Y303D	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	454	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)					TGCTGGGCGTACGTGAGCCGG	0.627													A|||	129	0.0257588	0.0915	0.0115	5008	,	,		18136	0.0		0.0	False		,,,				2504	0.0				p.Y454D		Atlas-SNP	.											.	RHPN2	107	.	0			c.T1360G						PASS	.	A	ASP/TYR	312,4094	167.6+/-198.6	8,296,1899	82.0	66.0	72.0		1360	3.8	0.8	19	dbSNP_131	72	5,8595	5.0+/-18.6	0,5,4295	no	missense	RHPN2	NM_033103.4	160	8,301,6194	CC,CA,AA		0.0581,7.0813,2.4373	probably-damaging	454/687	33486992	317,12689	2203	4300	6503	SO:0001583	missense	85415	exon11			GGGCGTACGTGAG	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.1360T>G	19.37:g.33486992A>C	ENSP00000254260:p.Tyr454Asp	Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	290	143	0.493103	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	50	0.022893772893772892	47	0.09552845528455285	3	0.008287292817679558	0	0.0	0	0.0	A	15.96	2.987827	0.53934	0.070813	5.81E-4	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.18502	2.21;2.21	4.86	3.82	0.43975	BRO1 domain (3);	0.230044	0.46758	D	0.000279	T	0.01387	0.0045	M	0.89287	3.02	0.41757	D	0.989692	D	0.56968	0.978	D	0.65233	0.933	T	0.00111	-1.2045	10	0.87932	D	0	0.6788	9.3929	0.38383	0.9165:0.0:0.0835:0.0	.	454	Q8IUC4	RHPN2_HUMAN	D	454;184;303	ENSP00000254260:Y454D;ENSP00000402244:Y303D	ENSP00000254260:Y454D	Y	-	1	0	RHPN2	38178832	0.997000	0.39634	0.822000	0.32727	0.459000	0.32528	2.550000	0.45811	0.669000	0.31146	0.477000	0.44152	TAC	A|0.973;C|0.027	0.027	strong		0.627	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
MZF1	7593	hgsc.bcm.edu	37	19	59074653	59074653	+	Missense_Mutation	SNP	T	T	C	rs4756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:59074653T>C	ENST00000215057.2	-	6	1551	c.991A>G	c.(991-993)Atc>Gtc	p.I331V	AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000600534.1_RNA|MZF1_ENST00000599369.1_Missense_Mutation_p.I331V|MZF1_ENST00000594234.1_Intron	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	331			I -> V (in dbSNP:rs4756).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		CGGGTGGTGATCAGAGCAGGG	0.701													.|||	1870	0.373403	0.6649	0.3646	5008	,	,		15453	0.1677		0.2634	False		,,,				2504	0.3108				p.I331V		Atlas-SNP	.											.	MZF1	37	.	0			c.A991G						PASS	.	C	VAL/ILE,VAL/ILE	2678,1710		866,946,382	12.0	14.0	13.0		991,991	2.5	0.0	19	dbSNP_52	13	1841,6751		208,1425,2663	yes	missense,missense	MZF1	NM_003422.2,NM_198055.1	29,29	1074,2371,3045	CC,CT,TT		21.4269,38.9699,34.8151	benign,benign	331/735,331/735	59074653	4519,8461	2194	4296	6490	SO:0001583	missense	7593	exon6			TGGTGATCAGAGC	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"""-"", ""Zinc fingers, C2H2-type"""	13108	protein-coding gene	gene with protein product		194550	"""zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"""	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.991A>G	19.37:g.59074653T>C	ENSP00000215057:p.Ile331Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	51	49	0.960784	NM_198055	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	37	CCDS12988.1	733	0.3356227106227106	337	0.6849593495934959	114	0.3149171270718232	90	0.15734265734265734	192	0.2532981530343008	.	0.815	-0.750491	0.03041	0.610301	0.214269	ENSG00000099326	ENST00000215057	T	0.05855	3.38	3.56	2.52	0.30459	.	1.488780	0.04858	N	0.443602	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	0.30794	-0.9966	9	0.28530	T	0.3	-0.5135	3.3254	0.07064	0.203:0.5745:0.0:0.2225	rs4756;rs3167718;rs3764524;rs4756	331	P28698	MZF1_HUMAN	V	331	ENSP00000215057:I331V	ENSP00000215057:I331V	I	-	1	0	MZF1	63766465	0.000000	0.05858	0.005000	0.12908	0.271000	0.26615	0.024000	0.13555	0.498000	0.27948	-0.349000	0.07799	ATC	T|0.658;C|0.342	0.342	strong		0.701	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055	
UNC45B	146862	hgsc.bcm.edu	37	17	33475426	33475426	+	Silent	SNP	C	C	T	rs16970656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33475426C>T	ENST00000268876.5	+	2	241	c.144C>T	c.(142-144)aaC>aaT	p.N48N	UNC45B_ENST00000378449.1_Silent_p.N48N|UNC45B_ENST00000433649.1_Silent_p.N48N|UNC45B_ENST00000394570.2_Silent_p.N48N|UNC45B_ENST00000591048.1_Silent_p.N48N	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	48					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)				TTTATCGGAACCGGGCAGCCT	0.637													C|||	90	0.0179712	0.0658	0.0043	5008	,	,		18215	0.0		0.0	False		,,,				2504	0.0				p.N48N		Atlas-SNP	.											.	UNC45B	133	.	0			c.C144T						PASS	.	C	,	259,4147	144.2+/-179.2	2,255,1946	54.0	51.0	52.0		144,144	1.8	1.0	17	dbSNP_123	52	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	UNC45B	NM_001033576.1,NM_173167.2	,	2,257,6244	TT,TC,CC		0.0233,5.8783,2.0068	,	48/930,48/932	33475426	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	146862	exon2			TCGGAACCGGGCA	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.144C>T	17.37:g.33475426C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001267052	Q495Q8|Q495Q9	Silent	SNP	ENST00000268876.5	37	CCDS11292.1																																																																																			C|0.975;T|0.025	0.025	strong		0.637	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	
ATP13A4	84239	hgsc.bcm.edu	37	3	193209178	193209178	+	Missense_Mutation	SNP	T	T	C	rs6788448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:193209178T>C	ENST00000342695.4	-	6	865	c.543A>G	c.(541-543)atA>atG	p.I181M	ATP13A4_ENST00000295548.3_Missense_Mutation_p.I181M|ATP13A4_ENST00000392443.3_Missense_Mutation_p.I181M	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	181			I -> M (in dbSNP:rs6788448). {ECO:0000269|PubMed:15925480}.			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		TAGGCCCACATATTAACCTCC	0.358													T|||	2361	0.471446	0.5318	0.4928	5008	,	,		18519	0.4673		0.3946	False		,,,				2504	0.4581				p.I181M		Atlas-SNP	.											.	ATP13A4	154	.	0			c.A543G						PASS	.	T	MET/ILE	2270,2136	597.1+/-388.8	571,1128,504	101.0	100.0	101.0		543	4.6	1.0	3	dbSNP_116	101	3476,5124	508.3+/-377.0	727,2022,1551	yes	missense	ATP13A4	NM_032279.2	10	1298,3150,2055	CC,CT,TT		40.4186,48.4793,44.1796	probably-damaging	181/1197	193209178	5746,7260	2203	4300	6503	SO:0001583	missense	84239	exon6			CCCACATATTAAC	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.543A>G	3.37:g.193209178T>C	ENSP00000339182:p.Ile181Met	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	37	CCDS3304.2	989	0.45283882783882784	260	0.5284552845528455	179	0.494475138121547	257	0.4493006993006993	293	0.3865435356200528	T	17.12	3.308038	0.60305	0.515207	0.404186	ENSG00000127249	ENST00000392443;ENST00000342695;ENST00000295548	T;T;T	0.78707	-1.2;-1.2;-1.2	5.81	4.63	0.57726	ATPase, P-type cation-transporter, N-terminal (2);	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	M	0.79123	2.44	0.28947	P	0.890639	D;D	0.76494	0.998;0.999	D;D	0.77004	0.981;0.989	T	0.44065	-0.9352	9	0.48119	T	0.1	-19.2398	9.3177	0.37943	0.287:0.0:0.0:0.713	rs6788448;rs56481856;rs60242198;rs6788448	181;181	Q4VNC1-2;Q4VNC1	.;AT134_HUMAN	M	181	ENSP00000376238:I181M;ENSP00000339182:I181M;ENSP00000295548:I181M	ENSP00000295548:I181M	I	-	3	3	ATP13A4	194691872	0.701000	0.27806	1.000000	0.80357	0.947000	0.59692	-0.447000	0.06828	0.992000	0.38840	0.482000	0.46254	ATA	T|0.559;C|0.441	0.441	strong		0.358	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
FES	2242	hgsc.bcm.edu	37	15	91434277	91434277	+	Silent	SNP	C	C	T	rs2229074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91434277C>T	ENST00000328850.3	+	11	1528	c.1386C>T	c.(1384-1386)caC>caT	p.H462H	FES_ENST00000394300.3_Silent_p.H404H|FES_ENST00000450438.2_Intron|FES_ENST00000414248.2_Intron|FES_ENST00000394302.1_Intron|FES_ENST00000444422.2_Intron	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	462	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)			lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			TGTGGTACCACGGGGCCATCC	0.647													C|||	297	0.0593051	0.2126	0.0202	5008	,	,		18427	0.0		0.002	False		,,,				2504	0.0				p.H462H		Atlas-SNP	.											.	FES	102	.	0			c.C1386T						PASS	.	C	,,,	799,3595		75,649,1473	58.0	49.0	52.0		1212,,,1386	-8.0	0.8	15	dbSNP_98	52	9,8581		0,9,4286	no	coding-synonymous,intron,intron,coding-synonymous	FES	NM_001143783.1,NM_001143784.1,NM_001143785.1,NM_002005.3	,,,	75,658,5759	TT,TC,CC		0.1048,18.1839,6.223	,,,	404/765,,,462/823	91434277	808,12176	2197	4295	6492	SO:0001819	synonymous_variant	2242	exon11			GTACCACGGGGCC	X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"""SH2 domain containing"""	3657	protein-coding gene	gene with protein product	"""Oncogene FES, feline sarcoma virus"", ""c-fes/fps protein"""	190030	"""feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog"", ""feline sarcoma oncogene"""			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.1386C>T	15.37:g.91434277C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	100	98	0.98	NM_002005	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Silent	SNP	ENST00000328850.3	37	CCDS10365.1																																																																																			C|0.935;T|0.065	0.065	strong		0.647	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005	
PTGER3	5733	hgsc.bcm.edu	37	1	71512643	71512643	+	Silent	SNP	C	C	A	rs5671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:71512643C>A	ENST00000306666.5	-	1	828	c.618G>T	c.(616-618)acG>acT	p.T206T	PTGER3_ENST00000351052.5_Silent_p.T206T|PTGER3_ENST00000370924.4_Silent_p.T206T|PTGER3_ENST00000354608.5_Silent_p.T206T|PTGER3_ENST00000370931.3_Silent_p.T206T|ZRANB2-AS1_ENST00000450461.1_RNA|PTGER3_ENST00000414819.1_Silent_p.T206T|PTGER3_ENST00000370932.2_Silent_p.T206T|PTGER3_ENST00000460330.1_Silent_p.T206T|PTGER3_ENST00000356595.4_Silent_p.T206T	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	206					cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	TGAAGCACCACGTCCCGGGCC	0.677													C|||	355	0.0708866	0.1589	0.0706	5008	,	,		15416	0.0		0.0845	False		,,,				2504	0.0112				p.T206T		Atlas-SNP	.											PTGER3_ENST00000460330,NS,carcinoma,0,5	PTGER3	246	5	0			c.G618T						PASS	.	C	,,,,,,	692,3712	279.9+/-275.1	44,604,1554	55.0	57.0	57.0		618,618,618,618,618,618,618	-1.9	1.0	1	dbSNP_52	57	731,7869	174.5+/-224.7	37,657,3606	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTGER3	NM_001126044.1,NM_198714.1,NM_198715.2,NM_198716.1,NM_198717.1,NM_198718.1,NM_198719.1	,,,,,,	81,1261,5160	AA,AC,CC		8.5,15.713,10.9428	,,,,,,	206/391,206/391,206/389,206/375,206/366,206/419,206/391	71512643	1423,11581	2202	4300	6502	SO:0001819	synonymous_variant	5733	exon1			GCACCACGTCCCG	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"""GPCR / Class A : Prostanoid receptors"""	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.618G>T	1.37:g.71512643C>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	96	56	0.583333	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Silent	SNP	ENST00000306666.5	37	CCDS657.1																																																																																			C|0.893;A|0.107	0.107	strong		0.677	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957	
CPXM2	119587	hgsc.bcm.edu	37	10	125651150	125651150	+	Missense_Mutation	SNP	G	G	A	rs112027854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:125651150G>A	ENST00000241305.3	-	1	180	c.26C>T	c.(25-27)cCa>cTa	p.P9L	CPXM2_ENST00000368854.3_Intron	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	9					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)		GGCCAGCGCTGGGGTAGCGGT	0.751													g|||	131	0.0261581	0.0938	0.0101	5008	,	,		8004	0.0		0.0	False		,,,				2504	0.0				p.P9L		Atlas-SNP	.											CPXM2,rectum,carcinoma,0,1	CPXM2	120	1	0			c.C26T						PASS	.		LEU/PRO	153,2681		2,149,1266	4.0	6.0	5.0		26	-2.5	0.0	10	dbSNP_132	5	3,5397		0,3,2697	no	missense	CPXM2	NM_198148.2	98	2,152,3963	AA,AG,GG		0.0556,5.3987,1.8946	benign	9/757	125651150	156,8078	1417	2700	4117	SO:0001583	missense	119587	exon1			AGCGCTGGGGTAG	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.26C>T	10.37:g.125651150G>A	ENSP00000241305:p.Pro9Leu	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	18	7	0.388889	NM_198148	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	g	12.37	1.916952	0.33815	0.053987	5.56E-4	ENSG00000121898	ENST00000241305;ENST00000418782	D	0.96716	-4.1	3.45	-2.48	0.06423	.	3.521810	0.01155	N	0.006503	T	0.66406	0.2786	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.78841	-0.2045	10	0.30078	T	0.28	0.0228	7.7622	0.28959	0.6768:0.0:0.3232:0.0	.	9	Q8N436	CPXM2_HUMAN	L	9	ENSP00000241305:P9L	ENSP00000241305:P9L	P	-	2	0	CPXM2	125641140	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.090000	0.11163	-0.418000	0.07450	-0.701000	0.03672	CCA	G|0.500;A|0.500	0.500	weak		0.751	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148	
MMS22L	253714	hgsc.bcm.edu	37	6	97613299	97613299	+	Missense_Mutation	SNP	G	G	A	rs10484830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:97613299G>A	ENST00000275053.4	-	21	3309	c.3044C>T	c.(3043-3045)cCg>cTg	p.P1015L	MMS22L_ENST00000369251.2_Missense_Mutation_p.P975L	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1015			P -> L (in dbSNP:rs10484830).		double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						ATAGGCATTCGGATTTTGAGA	0.353													G|||	486	0.0970447	0.2935	0.0317	5008	,	,		17448	0.001		0.0298	False		,,,				2504	0.046				p.P1015L		Atlas-SNP	.											.	MMS22L	102	.	0			c.C3044T						PASS	.	G	LEU/PRO	1079,3327	389.3+/-327.3	136,807,1260	86.0	78.0	81.0		3044	4.7	1.0	6	dbSNP_119	81	346,8254	117.7+/-177.3	3,340,3957	yes	missense	MMS22L	NM_198468.2	98	139,1147,5217	AA,AG,GG		4.0233,24.4893,10.9565	benign	1015/1244	97613299	1425,11581	2203	4300	6503	SO:0001583	missense	253714	exon21			GCATTCGGATTTT		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"""chromosome 6 open reading frame 167"""	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3044C>T	6.37:g.97613299G>A	ENSP00000275053:p.Pro1015Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	37	CCDS5039.1	181	0.08287545787545787	138	0.2804878048780488	14	0.03867403314917127	1	0.0017482517482517483	28	0.036939313984168866	G	14.46	2.541625	0.45280	0.244893	0.040233	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.28255	1.62;1.62	5.65	4.7	0.59300	.	0.288860	0.38720	N	0.001593	T	0.10723	0.0262	L	0.40543	1.245	0.31635	P	0.648543	B;B	0.31680	0.335;0.335	B;B	0.25614	0.062;0.038	T	0.08764	-1.0706	9	0.41790	T	0.15	-3.6329	8.0473	0.30557	0.0:0.1139:0.4797:0.4064	rs10484830;rs52811524;rs10484830	975;1015	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	L	1015;975	ENSP00000275053:P1015L;ENSP00000358254:P975L	ENSP00000275053:P1015L	P	-	2	0	MMS22L	97720020	0.999000	0.42202	0.999000	0.59377	0.913000	0.54294	2.661000	0.46758	2.647000	0.89833	0.655000	0.94253	CCG	G|0.898;A|0.102	0.102	strong		0.353	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468	
KRT6C	286887	hgsc.bcm.edu	37	12	52865924	52865924	+	Silent	SNP	G	G	A	rs77218649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52865924G>A	ENST00000252250.6	-	2	728	c.681C>T	c.(679-681)agC>agT	p.S227S		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	227	Coil 1B.|Rod.		S -> N (in dbSNP:rs17099602). {ECO:0000269|PubMed:7543104}.		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)		CCCCGACGATGCTGTCCAGCT	0.592													G|||	128	0.0255591	0.0961	0.0014	5008	,	,		17326	0.0		0.0	False		,,,				2504	0.0				p.S227S		Atlas-SNP	.											.	KRT6C	55	.	0			c.C681T						PASS	.	G		354,4050		39,276,1887	135.0	87.0	103.0		681	-2.5	0.0	12	dbSNP_131	103	4,8524		1,2,4261	no	coding-synonymous	KRT6C	NM_173086.4		40,278,6148	AA,AG,GG		0.0469,8.0381,2.7683		227/565	52865924	358,12574	2202	4264	6466	SO:0001819	synonymous_variant	286887	exon2			GACGATGCTGTCC	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.681C>T	12.37:g.52865924G>A		Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	398	189	0.474874	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Silent	SNP	ENST00000252250.6	37	CCDS8829.1																																																																																			G|0.976;A|0.024	0.024	strong		0.592	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
DSP	1832	hgsc.bcm.edu	37	6	7565596	7565596	+	Missense_Mutation	SNP	C	C	T	rs139509870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7565596C>T	ENST00000379802.3	+	7	1123	c.782C>T	c.(781-783)gCg>gTg	p.A261V	DSP_ENST00000418664.2_Missense_Mutation_p.A261V	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	261	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				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)		GTGCAGAAAGCGTCCTTTGAG	0.473													C|||	2	0.000399361	0.0	0.0029	5008	,	,		19062	0.0		0.0	False		,,,				2504	0.0				p.A261V		Atlas-SNP	.											.	DSP	306	.	0			c.C782T						PASS	.	C	VAL/ALA,VAL/ALA	5,4401	9.9+/-24.2	0,5,2198	106.0	95.0	98.0		782,782	4.6	0.7	6	dbSNP_134	98	0,8600		0,0,4300	no	missense,missense	DSP	NM_001008844.1,NM_004415.2	64,64	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	benign,benign	261/2273,261/2872	7565596	5,13001	2203	4300	6503	SO:0001583	missense	1832	exon7			AGAAAGCGTCCTT	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.782C>T	6.37:g.7565596C>T	ENSP00000369129:p.Ala261Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	14.58	2.579212	0.46006	0.001135	0.0	ENSG00000096696	ENST00000379802;ENST00000418664;ENST00000397483	D;D	0.92752	-3.1;-3.1	5.42	4.55	0.56014	.	0.366306	0.23134	N	0.051542	T	0.74854	0.3771	L	0.29908	0.895	0.25172	N	0.990271	B;B	0.26483	0.15;0.15	B;B	0.14578	0.006;0.011	T	0.66484	-0.5912	10	0.45353	T	0.12	.	7.1237	0.25458	0.1483:0.7018:0.0:0.1499	.	308;261	Q4LE79;P15924	.;DESP_HUMAN	V	261;261;66	ENSP00000369129:A261V;ENSP00000396591:A261V	ENSP00000369129:A261V	A	+	2	0	DSP	7510595	0.687000	0.27671	0.682000	0.30024	0.913000	0.54294	1.332000	0.33805	1.284000	0.44531	0.563000	0.77884	GCG	C|1.000;T|0.000	0.000	strong		0.473	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
ABCC6	368	hgsc.bcm.edu	37	16	16276292	16276292	+	Missense_Mutation	SNP	T	T	C	rs59593133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16276292T>C	ENST00000205557.7	-	17	2253	c.2224A>G	c.(2224-2226)Atc>Gtc	p.I742V	ABCC6_ENST00000574094.1_Intron	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	742	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		I -> V (in dbSNP:rs59593133). {ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:19339160}.		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)	GAAGTGTGGATTCCCTCAGGG	0.567													C|||	115	0.0229633	0.0552	0.0101	5008	,	,		18398	0.0		0.0129	False		,,,				2504	0.0225				p.I742V		Atlas-SNP	.											.	ABCC6	110	.	0			c.A2224G						PASS	.	C	VAL/ILE	227,4167	804.8+/-415.8	4,219,1974	92.0	91.0	91.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2224	-0.3	0.0	16	dbSNP_129	91	112,8488	814.3+/-407.0	0,112,4188	yes	missense	ABCC6	NM_001171.5	29	4,331,6162	CC,CT,TT		1.3023,5.1661,2.6089	benign	742/1504	16276292	339,12655	2197	4300	6497	SO:0001583	missense	368	exon17			TGTGGATTCCCTC	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.2224A>G	16.37:g.16276292T>C	ENSP00000205557:p.Ile742Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	43	0.019688644688644688	30	0.06097560975609756	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	3.153	-0.173855	0.06421	0.051661	0.013023	ENSG00000091262	ENST00000205557;ENST00000456970	D;D	0.90261	-2.64;-2.64	4.62	-0.32	0.12721	ATPase, AAA+ type, core (1);ABC transporter-like (2);	1.278710	0.05798	N	0.611594	T	0.39572	0.1083	N	0.16790	0.44	0.22629	N	0.998919	B	0.02656	0.0	B	0.04013	0.001	T	0.56486	-0.7971	10	0.38643	T	0.18	.	6.5361	0.22355	0.0:0.4662:0.1283:0.4055	rs59593133;rs61731976	742	O95255	MRP6_HUMAN	V	742	ENSP00000205557:I742V;ENSP00000405002:I742V	ENSP00000205557:I742V	I	-	1	0	ABCC6	16183793	0.044000	0.20184	0.037000	0.18230	0.002000	0.02628	0.428000	0.21395	-0.160000	0.11002	-0.320000	0.08662	ATC	T|0.975;C|0.025	0.025	strong		0.567	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
PABPC1	26986	hgsc.bcm.edu	37	8	101724606	101724606	+	Missense_Mutation	SNP	G	G	A	rs202060459		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101724606G>A	ENST00000318607.5	-	7	2084	c.956C>T	c.(955-957)aCa>aTa	p.T319I	PABPC1_ENST00000519004.1_Missense_Mutation_p.T274I|PABPC1_ENST00000522387.1_Missense_Mutation_p.T287I|PABPC1_ENST00000519596.1_5'UTR	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	241	0	0		WXS	Illumina HiSeq	Phase_I	269	3	0.0111524	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	
ABCA8	10351	hgsc.bcm.edu	37	17	66928470	66928470	+	Silent	SNP	C	C	T	rs28385895|rs386798698|rs202032826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66928470C>T	ENST00000269080.2	-	6	893	c.756G>A	c.(754-756)aaG>aaA	p.K252K	ABCA8_ENST00000430352.2_Silent_p.K252K|ABCA8_ENST00000586539.1_Silent_p.K252K	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	252					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)					TCATCAAGGCCTTCATCCTTT	0.393													C|||	383	0.0764776	0.2738	0.0231	5008	,	,		20456	0.0		0.005	False		,,,				2504	0.0				p.K252K		Atlas-SNP	.											.	ABCA8	213	.	0			c.G756A						PASS	.																																			SO:0001819	synonymous_variant	10351	exon6			CAAGGCCTTCATC	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.756G>A	17.37:g.66928470C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	37	CCDS11680.1																																																																																			C|0.959;T|0.041	0.041	strong		0.393	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
KDM4C	23081	hgsc.bcm.edu	37	9	6986589	6986589	+	Missense_Mutation	SNP	A	A	C	rs111451391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:6986589A>C	ENST00000381309.3	+	11	2165	c.1600A>C	c.(1600-1602)Agc>Cgc	p.S534R	KDM4C_ENST00000428870.2_Missense_Mutation_p.S221R|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000535193.1_Missense_Mutation_p.S556R|KDM4C_ENST00000543771.1_Missense_Mutation_p.S534R|KDM4C_ENST00000381306.3_Missense_Mutation_p.S534R|KDM4C_ENST00000536108.1_Missense_Mutation_p.S353R	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	534					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						TGATGTGGAGAGCCATGGGAA	0.498													A|||	63	0.0125799	0.0023	0.0865	5008	,	,		19983	0.0		0.0	False		,,,				2504	0.0				p.S556R		Atlas-SNP	.											KDM4C,NS,carcinoma,-2,1	KDM4C	186	1	0			c.A1666C						scavenged	.	A	ARG/SER,ARG/SER,ARG/SER,ARG/SER	5,4401	9.9+/-24.2	0,5,2198	101.0	90.0	94.0		1600,1600,1666,1600	4.2	1.0	9	dbSNP_132	94	1,8599		0,1,4299	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	110,110,110,110	0,6,6497	CC,CA,AA		0.0116,0.1135,0.0461	benign,benign,benign,benign	534/1048,534/814,556/836,534/1057	6986589	6,13000	2203	4300	6503	SO:0001583	missense	23081	exon11			GTGGAGAGCCATG	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.1600A>C	9.37:g.6986589A>C	ENSP00000370710:p.Ser534Arg	Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	31	0.014194139194139194	1	0.0020325203252032522	30	0.08287292817679558	0	0.0	0	0.0	A	13.15	2.149919	0.37923	0.001135	1.16E-4	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000536108;ENST00000428870	T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6	5.3	4.17	0.49024	.	2.061340	0.01784	N	0.031882	T	0.04952	0.0133	M	0.66939	2.045	0.29043	N	0.884963	P;P;B;P	0.42203	0.773;0.603;0.112;0.603	B;B;B;B	0.38616	0.277;0.202;0.064;0.246	T	0.14671	-1.0464	10	0.13470	T	0.59	-1.3627	8.4932	0.33112	0.8984:0.0:0.1016:0.0	.	534;556;534;534	F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;KDM4C_HUMAN;.	R	556;534;534;534;353;221	ENSP00000442382:S556R;ENSP00000445427:S534R;ENSP00000370710:S534R;ENSP00000370707:S534R;ENSP00000440656:S353R;ENSP00000405739:S221R	ENSP00000370707:S534R	S	+	1	0	KDM4C	6976589	1.000000	0.71417	0.979000	0.43373	0.845000	0.48019	4.096000	0.57734	1.040000	0.40099	0.533000	0.62120	AGC	A|0.995;C|0.004;T|0.000	0.004	strong		0.498	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
MICALL2	79778	hgsc.bcm.edu	37	7	1481983	1481983	+	Missense_Mutation	SNP	G	G	A	rs4075307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1481983G>A	ENST00000297508.7	-	7	1731	c.1556C>T	c.(1555-1557)cCg>cTg	p.P519L	MICALL2_ENST00000405088.4_Missense_Mutation_p.P307L	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	519	Mediates targeting to the cell plasma membrane. {ECO:0000250}.		P -> L (in dbSNP:rs4075307).		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)		CGTGCTCAGCGGGGCTGGCGG	0.647													G|||	174	0.0347444	0.1241	0.013	5008	,	,		14709	0.0		0.001	False		,,,				2504	0.0				p.P519L		Atlas-SNP	.											.	MICALL2	63	.	0			c.C1556T						PASS	.		LEU/PRO	437,3969	208.8+/-229.8	24,389,1790	121.0	118.0	119.0		1556	1.3	0.0	7	dbSNP_108	119	5,8595	3.7+/-12.6	0,5,4295	yes	missense	MICALL2	NM_182924.3	98	24,394,6085	AA,AG,GG		0.0581,9.9183,3.3984	possibly-damaging	519/905	1481983	442,12564	2203	4300	6503	SO:0001583	missense	79778	exon7			CTCAGCGGGGCTG	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.1556C>T	7.37:g.1481983G>A	ENSP00000297508:p.Pro519Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	37	CCDS5324.1	55	0.025183150183150184	50	0.1016260162601626	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	13.70	2.314588	0.40996	0.099183	5.81E-4	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.69806	2.37;-0.43	3.76	1.29	0.21616	.	0.235349	0.21901	N	0.067446	T	0.01156	0.0038	L	0.32530	0.975	0.09310	N	0.999999	B;D	0.53312	0.136;0.959	B;B	0.33690	0.006;0.168	T	0.04140	-1.0974	10	0.17832	T	0.49	.	3.0549	0.06181	0.2049:0.2804:0.5147:0.0	rs4075307;rs16870427;rs4075307	519;307	Q8IY33;D3YTD2	MILK2_HUMAN;.	L	307;519	ENSP00000385928:P307L;ENSP00000297508:P519L	ENSP00000297508:P519L	P	-	2	0	MICALL2	1448509	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	0.665000	0.25083	0.674000	0.31244	0.561000	0.74099	CCG	G|0.965;A|0.035	0.035	strong		0.647	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
E4F1	1877	hgsc.bcm.edu	37	16	2273676	2273676	+	Missense_Mutation	SNP	C	C	A	rs200831818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2273676C>A	ENST00000301727.4	+	1	110	c.62C>A	c.(61-63)gCc>gAc	p.A21D	E4F1_ENST00000565090.1_Missense_Mutation_p.A21D|E4F1_ENST00000564139.1_Missense_Mutation_p.A21D	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1	21					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|mitotic cell cycle arrest (GO:0071850)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell cycle process (GO:0010564)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle, embryonic (GO:0009794)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			ovary(1)	1						CAGGCCGAAGCCGGGCGGGAA	0.711													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		11713	0.0		0.0	False		,,,				2504	0.0				p.A21D		Atlas-SNP	.											.	E4F1	53	.	0			c.C62A						PASS	.	C	ASP/ALA	26,4326		0,26,2150	12.0	16.0	15.0		62	4.7	1.0	16		15	0,8536		0,0,4268	yes	missense	E4F1	NM_004424.3	126	0,26,6418	AA,AC,CC		0.0,0.5974,0.2017	probably-damaging	21/785	2273676	26,12862	2176	4268	6444	SO:0001583	missense	1877	exon1			CCGAAGCCGGGCG	U87269	CCDS32370.1, CCDS73809.1, CCDS73810.1	16p13.3	2013-01-08				ENSG00000167967		"""Zinc fingers, C2H2-type"""	3121	protein-coding gene	gene with protein product		603022				9763670, 8828041	Standard	XM_005255155		Approved	E4F	uc002cpm.3	Q66K89		ENST00000301727.4:c.62C>A	16.37:g.2273676C>A	ENSP00000301727:p.Ala21Asp	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_004424	A8K2R4|O00146	Missense_Mutation	SNP	ENST00000301727.4	37	CCDS32370.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.476414	0.26511	0.005974	0.0	ENSG00000167967	ENST00000301727	T	0.09723	2.95	4.68	4.68	0.58851	.	0.718111	0.13054	N	0.417418	T	0.11537	0.0281	N	0.14661	0.345	0.44523	D	0.997474	D;D;D	0.64830	0.985;0.994;0.985	P;P;P	0.57911	0.767;0.829;0.767	T	0.18241	-1.0343	10	0.59425	D	0.04	-23.6911	16.3289	0.83001	0.0:1.0:0.0:0.0	.	17;21;21	E9PFZ8;E7EMF7;Q66K89	.;.;E4F1_HUMAN	D	21	ENSP00000301727:A21D	ENSP00000301727:A21D	A	+	2	0	E4F1	2213677	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	1.236000	0.32683	2.425000	0.82216	0.655000	0.94253	GCC	.	.	weak		0.711	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424	
ANKLE1	126549	hgsc.bcm.edu	37	19	17394124	17394124	+	Missense_Mutation	SNP	T	T	G	rs2363956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17394124T>G	ENST00000394458.3	+	5	827	c.551T>G	c.(550-552)tTg>tGg	p.L184W	ANKLE1_ENST00000433424.2_Missense_Mutation_p.L238W|ANKLE1_ENST00000594072.1_Missense_Mutation_p.L173W|ANKLE1_ENST00000598347.1_Missense_Mutation_p.L184W|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	91	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	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	
OR8J1	219477	hgsc.bcm.edu	37	11	56128226	56128226	+	Silent	SNP	T	T	C	rs11823483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56128226T>C	ENST00000303039.3	+	1	536	c.504T>C	c.(502-504)taT>taC	p.Y168Y		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	168						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)					CTGTGTCTTATTGCTCTTCTA	0.388													T|||	240	0.0479233	0.1687	0.0231	5008	,	,		18982	0.0		0.001	False		,,,				2504	0.0				p.Y168Y		Atlas-SNP	.											.	OR8J1	87	.	0			c.T504C						PASS	.	T		628,3774	272.5+/-270.8	48,532,1621	120.0	108.0	112.0		504	-2.3	1.0	11	dbSNP_120	112	9,8583	4.3+/-15.6	0,9,4287	no	coding-synonymous	OR8J1	NM_001005205.2		48,541,5908	CC,CT,TT		0.1047,14.2662,4.9023		168/317	56128226	637,12357	2201	4296	6497	SO:0001819	synonymous_variant	219477	exon1			GTCTTATTGCTCT	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.504T>C	11.37:g.56128226T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	161	73	0.453416	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Silent	SNP	ENST00000303039.3	37	CCDS31529.1																																																																																			T|0.955;C|0.045	0.045	strong		0.388	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
ZNF286A	57335	hgsc.bcm.edu	37	17	15611495	15611495	+	Missense_Mutation	SNP	T	T	C	rs3760299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15611495T>C	ENST00000464847.2	+	4	821	c.268T>C	c.(268-270)Tac>Cac	p.Y90H	ZNF286A_ENST00000421016.1_Missense_Mutation_p.Y90H|ZNF286A_ENST00000413242.2_Missense_Mutation_p.Y90H|ZNF286A_ENST00000593105.1_Missense_Mutation_p.Y80H|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000395894.2_Missense_Mutation_p.Y90H|ZNF286A_ENST00000395893.2_Missense_Mutation_p.Y90H|ZNF286A_ENST00000472486.1_Missense_Mutation_p.Y80H|ZNF286A_ENST00000585194.1_Missense_Mutation_p.Y90H|ZNF286A_ENST00000581529.1_Silent_p.A41A|ZNF286A_ENST00000583566.1_Missense_Mutation_p.Y90H|ZNF286A_ENST00000580259.1_Silent_p.A51A			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	90	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		Y -> H (in dbSNP:rs3760299). {ECO:0000269|PubMed:11347906}.		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(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		ACCTGAGAGCTACAACTTGGA	0.378													T|||	2545	0.508187	0.5703	0.4207	5008	,	,		11126	0.626		0.3708	False		,,,				2504	0.5061				p.Y90H		Atlas-SNP	.											ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	0			c.T268C						PASS	.	T	HIS/TYR,HIS/TYR	2462,1944	615.4+/-392.6	698,1066,439	55.0	56.0	55.0		268,268	3.9	0.3	17	dbSNP_107	55	3159,5441	476.7+/-369.5	575,2009,1716	yes	missense,missense	ZNF286A	NM_001130842.1,NM_020652.2	83,83	1273,3075,2155	CC,CT,TT		36.7326,44.1217,43.2185	benign,benign	90/522,90/522	15611495	5621,7385	2203	4300	6503	SO:0001583	missense	57335	exon5			GAGAGCTACAACT	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"""Zinc fingers, C2H2-type"", ""-"""	13501	protein-coding gene	gene with protein product			"""zinc finger protein 286"""	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.268T>C	17.37:g.15611495T>C	ENSP00000464218:p.Tyr90His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	58	0.557692	NM_020652	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	1057	0.483974358974359	287	0.5833333333333334	140	0.3867403314917127	344	0.6013986013986014	286	0.37730870712401055	t	9.566	1.119785	0.20877	0.558783	0.367326	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894;ENST00000395893	T;T;T;T	0.00801	5.68;5.68;5.68;5.68	4.97	3.9	0.45041	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	N	0.04880	-0.145	0.47065	P	6.930000000000547E-4	B	0.06786	0.001	B	0.04013	0.001	T	0.10730	-1.0617	8	0.62326	D	0.03	-3.2436	7.5099	0.27566	0.0:0.0964:0.0:0.9036	rs3760299;rs52804179;rs59667491;rs3760299	90	Q9HBT8	Z286A_HUMAN	H	90;80;90;90	ENSP00000397163:Y90H;ENSP00000408168:Y80H;ENSP00000379231:Y90H;ENSP00000379230:Y90H	ENSP00000435872:Y90H	Y	+	1	0	ZNF286A	15552220	0.129000	0.22400	0.340000	0.25575	0.402000	0.30811	1.340000	0.33896	1.029000	0.39812	0.533000	0.62120	TAC	T|0.541;C|0.459	0.459	strong		0.378	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652	
OR6C68	403284	hgsc.bcm.edu	37	12	55887054	55887054	+	Missense_Mutation	SNP	C	C	G	rs56760228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55887054C>G	ENST00000548615.1	+	1	893	c.893C>G	c.(892-894)gCc>gGc	p.A298G	RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|OR6C68_ENST00000379662.1_Missense_Mutation_p.A303G	NM_001005519.2	NP_001005519.2	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C, member 68	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(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15						GTTAAACAAGCCTTTCATGAC	0.289													C|||	306	0.0611022	0.2163	0.0288	5008	,	,		17663	0.0		0.0	False		,,,				2504	0.0				p.A298G		Atlas-SNP	.											.	OR6C68	36	.	0			c.C893G						PASS	.	G	GLY/ALA	793,3609		73,647,1481	32.0	36.0	35.0		893	3.2	0.2	12	dbSNP_129	35	9,8583		0,9,4287	yes	missense	OR6C68	NM_001005519.2	60	73,656,5768	GG,GC,CC		0.1047,18.0145,6.1721	benign	298/313	55887054	802,12192	2201	4296	6497	SO:0001583	missense	403284	exon1			AACAAGCCTTTCA		CCDS31826.1, CCDS31826.2	12q13.2	2013-09-23			ENSG00000205327	ENSG00000205327		"""GPCR / Class A : Olfactory receptors"""	31297	protein-coding gene	gene with protein product							Standard	NM_001005519		Approved		uc031qhq.1	A6NDL8	OTTHUMG00000169958	ENST00000548615.1:c.893C>G	12.37:g.55887054C>G	ENSP00000448811:p.Ala298Gly	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	23	0.370968	NM_001005519		Missense_Mutation	SNP	ENST00000548615.1	37	CCDS31826.2	104	0.047619047619047616	93	0.18902439024390244	11	0.03038674033149171	0	0.0	0	0.0	c	4.988	0.183559	0.09495	0.180145	0.001047	ENSG00000205327	ENST00000379662;ENST00000548615	T;T	0.45276	0.9;0.9	5.03	3.19	0.36642	.	0.288458	0.24461	N	0.038338	T	0.00073	0.0002	M	0.61703	1.905	0.80722	P	0.0	B	0.30914	0.3	B	0.38296	0.27	T	0.09185	-1.0686	9	0.72032	D	0.01	.	7.1754	0.25742	0.1288:0.6768:0.1243:0.0702	rs56760228	298	A6NDL8	O6C68_HUMAN	G	303;298	ENSP00000368983:A303G;ENSP00000448811:A298G	ENSP00000368983:A303G	A	+	2	0	OR6C68	54173321	0.000000	0.05858	0.226000	0.23910	0.035000	0.12851	0.005000	0.13129	0.628000	0.30357	-3.065000	0.00067	GCC	C|0.953;G|0.047	0.047	strong		0.289	OR6C68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406677.1		
DGKI	9162	hgsc.bcm.edu	37	7	137128830	137128830	+	Silent	SNP	T	T	C	rs1918837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:137128830T>C	ENST00000288490.5	-	29	2778	c.2778A>G	c.(2776-2778)gaA>gaG	p.E926E	DGKI_ENST00000494390.1_5'UTR|DGKI_ENST00000446122.1_Silent_p.E908E|DGKI_ENST00000453654.2_Silent_p.E595E|DGKI_ENST00000424189.2_Silent_p.E939E	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	926					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						TACCATGATCTTCTGAAGAGA	0.299													T|||	2228	0.444888	0.2057	0.5274	5008	,	,		16450	0.6627		0.3598	False		,,,				2504	0.5726				p.E926E		Atlas-SNP	.											.	DGKI	335	.	0			c.A2778G						PASS	.	T		1016,3384	366.4+/-317.8	112,792,1296	58.0	56.0	57.0		2778	5.5	1.0	7	dbSNP_92	57	3044,5556	455.4+/-363.8	548,1948,1804	no	coding-synonymous	DGKI	NM_004717.2		660,2740,3100	CC,CT,TT		35.3953,23.0909,31.2308		926/1066	137128830	4060,8940	2200	4300	6500	SO:0001819	synonymous_variant	9162	exon29			ATGATCTTCTGAA	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2778A>G	7.37:g.137128830T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	37	CCDS5845.1																																																																																			T|0.641;C|0.359	0.359	strong		0.299	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79068649	79068649	+	Silent	SNP	G	G	A	rs59275951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:79068649G>A	ENST00000388820.4	-	11	1797	c.1587C>T	c.(1585-1587)ccC>ccT	p.P529P	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	529	Disintegrin.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GGAAGCCCACGGGTACGCACT	0.637													g|||	387	0.0772764	0.174	0.0187	5008	,	,		17624	0.121		0.005	False		,,,				2504	0.0174				p.P529P		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C1587T						PASS	.	A		705,3687	745.8+/-411.7	47,611,1538	73.0	87.0	82.0		1587	-9.2	0.2	15	dbSNP_129	82	19,8567	813.9+/-407.0	1,17,4275	no	coding-synonymous	ADAMTS7	NM_014272.3		48,628,5813	AA,AG,GG		0.2213,16.0519,5.5787		529/1687	79068649	724,12254	2196	4293	6489	SO:0001819	synonymous_variant	11173	exon11			GCCCACGGGTACG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.1587C>T	15.37:g.79068649G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			G|0.940;A|0.060	0.060	strong		0.637	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
DNAH10	196385	hgsc.bcm.edu	37	12	124281322	124281322	+	Silent	SNP	T	T	C	rs76791219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124281322T>C	ENST00000409039.3	+	12	1777	c.1752T>C	c.(1750-1752)caT>caC	p.H584H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	584	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)		GGATTAAGCATACCATCCTCC	0.428													C|||	902	0.180112	0.4463	0.1196	5008	,	,		18752	0.0476		0.1093	False		,,,				2504	0.0726				p.H584H		Atlas-SNP	.											.	DNAH10	888	.	0			c.T1752C						PASS	.	C		1809,2597	639.6+/-397.1	382,1045,776	147.0	130.0	136.0		1752	2.5	1.0	12	dbSNP_131	136	934,7666	776.9+/-407.7	55,824,3421	no	coding-synonymous	DNAH10	NM_207437.3		437,1869,4197	CC,CT,TT		10.8605,41.0576,21.0903		584/4472	124281322	2743,10263	2203	4300	6503	SO:0001819	synonymous_variant	196385	exon12			TAAGCATACCATC	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.1752T>C	12.37:g.124281322T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	166	166	1	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			T|0.812;C|0.188	0.188	strong		0.428	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
MAVS	57506	hgsc.bcm.edu	37	20	3846397	3846397	+	Missense_Mutation	SNP	C	C	T	rs7269320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3846397C>T	ENST00000428216.2	+	7	1354	c.1226C>T	c.(1225-1227)tCt>tTt	p.S409F	MAVS_ENST00000416600.2_Missense_Mutation_p.S268F|MAVS_ENST00000358134.6_3'UTR	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	409			S -> F (in dbSNP:rs7269320). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16125763, ECO:0000269|PubMed:16177806}.		activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						GACAGCAGCTCTGAGAATAGG	0.622													C|||	1062	0.212061	0.4123	0.1268	5008	,	,		16817	0.0883		0.159	False		,,,				2504	0.184				p.S409F		Atlas-SNP	.											.	MAVS	34	.	0			c.C1226T						PASS	.	C	PHE/SER,PHE/SER	1581,2825	463.0+/-353.4	263,1055,885	27.0	27.0	27.0		803,1226	0.2	0.0	20	dbSNP_116	27	1393,7207	255.4+/-280.3	106,1181,3013	yes	missense,missense	MAVS	NM_001206491.1,NM_020746.4	155,155	369,2236,3898	TT,TC,CC		16.1977,35.8829,22.8664	probably-damaging,probably-damaging	268/400,409/541	3846397	2974,10032	2203	4300	6503	SO:0001583	missense	57506	exon7			GCAGCTCTGAGAA	DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"""virus-induced signaling adaptor"", ""IFN-B promoter stimulator 1"", ""CARD adaptor inducing IFN-beta"""	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.1226C>T	20.37:g.3846397C>T	ENSP00000401980:p.Ser409Phe	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Missense_Mutation	SNP	ENST00000428216.2	37	CCDS33437.1	415	0.190018315018315	195	0.39634146341463417	56	0.15469613259668508	59	0.10314685314685315	105	0.13852242744063326	C	12.98	2.101712	0.37048	0.358829	0.161977	ENSG00000088888	ENST00000416600;ENST00000428216	T;T	0.36699	1.24;2.25	3.35	0.169	0.15017	.	4.947810	0.00166	N	0.000001	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	D	0.61697	0.99	D	0.64410	0.925	T	0.16897	-1.0387	9	0.44086	T	0.13	0.2835	3.8256	0.08853	0.0:0.5595:0.2022:0.2383	rs7269320;rs17857294;rs56601673;rs58912255;rs7269320	409	Q7Z434	MAVS_HUMAN	F	268;409	ENSP00000413749:S268F;ENSP00000401980:S409F	ENSP00000413749:S268F	S	+	2	0	MAVS	3794397	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.229000	0.09098	0.073000	0.16731	0.655000	0.94253	TCT	C|0.786;T|0.214	0.214	strong		0.622	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746	
CAMK1	8536	hgsc.bcm.edu	37	3	9804658	9804658	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9804658G>A	ENST00000256460.3	-	5	546	c.369C>T	c.(367-369)ttC>ttT	p.F123F	OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Intron|OGG1_ENST00000349503.5_Intron|OGG1_ENST00000449570.2_Intron|OGG1_ENST00000302008.8_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	123	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|nucleocytoplasmic transport (GO:0006913)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of synapse structural plasticity (GO:0051835)|protein phosphorylation (GO:0006468)|regulation of muscle cell differentiation (GO:0051147)|regulation of protein binding (GO:0043393)|regulation of protein localization (GO:0032880)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	12	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		CCAGCACCTGGAAGATGAGGC	0.597																																					p.F123F		Atlas-SNP	.											.	CAMK1	32	.	0			c.C369T						PASS	.						71.0	63.0	66.0					3																	9804658		2203	4300	6503	SO:0001819	synonymous_variant	8536	exon5			CACCTGGAAGATG	L41816	CCDS2582.1	3p25.3	2004-02-27			ENSG00000134072	ENSG00000134072			1459	protein-coding gene	gene with protein product		604998				7641687	Standard	NM_003656		Approved	CaMKI	uc003bst.3	Q14012	OTTHUMG00000128419	ENST00000256460.3:c.369C>T	3.37:g.9804658G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	121	70	0.578512	NM_003656	Q3KPF6	Silent	SNP	ENST00000256460.3	37	CCDS2582.1																																																																																			.	.	none		0.597	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656	
PSG8	440533	hgsc.bcm.edu	37	19	43269705	43269705	+	Missense_Mutation	SNP	G	G	A	rs71337226|rs34129574|rs7245423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43269705G>A	ENST00000306511.4	-	1	126	c.29C>T	c.(28-30)aCa>aTa	p.T10I	PSG8_ENST00000406636.3_Missense_Mutation_p.T10I|PSG8_ENST00000401467.2_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.T10I	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	10				TQR -> MQH (in Ref. 2; CAH18672). {ECO:0000305}.		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)				GATGCGCTGTGTGCAGGGAGG	0.592													.|||	1787	0.356829	0.7315	0.2709	5008	,	,		17015	0.0913		0.3091	False		,,,				2504	0.2342				p.T10I		Atlas-SNP	.											.	PSG8	101	.	0			c.C29T						PASS	.	A	ILE/THR,ILE/THR,ILE/THR	1734,1288		659,416,436	121.0	121.0	121.0		29,29,29	-2.7	0.0	19	dbSNP_116	121	1261,4157		251,759,1699	no	missense,missense,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	89,89,89	910,1175,2135	AA,AG,GG		23.2743,42.6208,35.4858	probably-damaging,probably-damaging,probably-damaging	10/420,10/298,10/427	43269705	2995,5445	1511	2709	4220	SO:0001583	missense	440533	exon1			CGCTGTGTGCAGG	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.29C>T	19.37:g.43269705G>A	ENSP00000305005:p.Thr10Ile	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_001130168	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	599	0.2742673992673993	269	0.5467479674796748	100	0.27624309392265195	40	0.06993006993006994	190	0.25065963060686014	g	5.454	0.268926	0.10349	0.573792	0.232743	ENSG00000124467	ENST00000404209;ENST00000406636;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T;T	0.25749	2.18;1.78;3.3;2.19	1.35	-2.7	0.06004	.	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	D;P;P	0.60160	0.987;0.848;0.918	P;P;P	0.56960	0.81;0.521;0.558	T	0.46512	-0.9186	8	0.56958	D	0.05	.	1.4681	0.02410	0.1869:0.268:0.387:0.1581	rs7245423;rs57041720	10;10;10	Q9UQ74-2;Q9UQ74;A5PKV3	.;PSG8_HUMAN;.	I	10	ENSP00000385869:T10I;ENSP00000385081:T10I;ENSP00000386090:T10I;ENSP00000305005:T10I	ENSP00000305005:T10I	T	-	2	0	PSG8	47961545	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.768000	0.04715	-2.180000	0.00766	-1.139000	0.01908	ACA	G|0.635;A|0.365	0.365	strong		0.592	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
DSC3	1825	hgsc.bcm.edu	37	18	28611061	28611061	+	Missense_Mutation	SNP	A	A	T	rs276937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28611061A>T	ENST00000360428.4	-	3	312	c.232T>A	c.(232-234)Tca>Aca	p.S78T	DSC3_ENST00000434452.1_Missense_Mutation_p.S78T	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	78			S -> T (in dbSNP:rs276937).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			GTGTACACTGACCCATCATTT	0.413													A|||	2178	0.434904	0.3132	0.3401	5008	,	,		13475	0.6835		0.3549	False		,,,				2504	0.4928				p.S78T		Atlas-SNP	.											.	DSC3	225	.	0			c.T232A						PASS	.	A	THR/SER,THR/SER	1465,2941	469.0+/-355.3	240,985,978	73.0	65.0	67.0		232,232	2.8	0.0	18	dbSNP_79	67	2764,5836	439.1+/-359.1	443,1878,1979	yes	missense,missense	DSC3	NM_001941.3,NM_024423.2	58,58	683,2863,2957	TT,TA,AA		32.1395,33.2501,32.5158	possibly-damaging,possibly-damaging	78/897,78/840	28611061	4229,8777	2203	4300	6503	SO:0001583	missense	1825	exon3			ACACTGACCCATC	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.232T>A	18.37:g.28611061A>T	ENSP00000353608:p.Ser78Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_024423	A6NN35|Q14200|Q9HAZ9	Missense_Mutation	SNP	ENST00000360428.4	37	CCDS32810.1	942	0.43131868131868134	158	0.32113821138211385	127	0.35082872928176795	397	0.6940559440559441	260	0.34300791556728233	A	8.716	0.913305	0.17907	0.332501	0.321395	ENSG00000134762	ENST00000360428;ENST00000434452	T;T	0.38560	1.13;1.13	5.26	2.83	0.33086	Cadherin prodomain-like (1);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	M	0.62266	1.93	0.58432	P	5.000000000032756E-6	B;P	0.38335	0.267;0.627	B;B	0.40940	0.344;0.329	T	0.36696	-0.9737	8	0.26408	T	0.33	.	7.2036	0.25895	0.7754:0.147:0.0776:0.0	rs276937;rs1098249;rs1303278;rs1602889;rs17799213;rs52793945;rs59695561;rs276937	78;78	Q14574;Q14574-2	DSC3_HUMAN;.	T	78	ENSP00000353608:S78T;ENSP00000392068:S78T	ENSP00000353608:S78T	S	-	1	0	DSC3	26865059	0.998000	0.40836	0.005000	0.12908	0.004000	0.04260	3.054000	0.49908	0.442000	0.26555	-0.256000	0.11100	TCA	A|0.626;T|0.374	0.374	strong		0.413	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
RBAK	57786	hgsc.bcm.edu	37	7	5103773	5103773	+	Missense_Mutation	SNP	G	G	A	rs35352738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5103773G>A	ENST00000353796.3	+	6	1010	c.686G>A	c.(685-687)gGg>gAg	p.G229E	RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK_ENST00000396912.1_Missense_Mutation_p.G229E|RBAK-RBAKDN_ENST00000407184.1_Intron	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	229	Required for interaction with RB1.		G -> E (in dbSNP:rs35352738).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		GCTTACATAGGGGAGAAGCCC	0.368													G|||	207	0.0413339	0.1498	0.0115	5008	,	,		20379	0.0		0.001	False		,,,				2504	0.0				p.G229E		Atlas-SNP	.											.	RBAK	82	.	0			c.G686A						PASS	.	G	GLU/GLY,,GLU/GLY	576,3830	243.7+/-253.3	45,486,1672	44.0	46.0	45.0		686,,686	0.7	0.0	7	dbSNP_126	45	7,8593	3.7+/-12.6	0,7,4293	yes	missense,intron,missense	RBAK,RBAK-LOC389458	NM_001204456.1,NM_001204513.1,NM_021163.3	98,,98	45,493,5965	AA,AG,GG		0.0814,13.0731,4.4825	benign,,benign	229/715,,229/715	5103773	583,12423	2203	4300	6503	SO:0001583	missense	57786	exon6			ACATAGGGGAGAA	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"""Zinc fingers, C2H2-type"", ""-"""	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.686G>A	7.37:g.5103773G>A	ENSP00000275423:p.Gly229Glu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_001204456	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Missense_Mutation	SNP	ENST00000353796.3	37	CCDS5337.1	82	0.037545787545787544	76	0.15447154471544716	2	0.0055248618784530384	1	0.0017482517482517483	3	0.00395778364116095	G	2.134	-0.398395	0.04865	0.130731	8.14E-4	ENSG00000146587	ENST00000353796;ENST00000396912	T;T	0.02050	4.48;4.48	3.67	0.7	0.18099	.	0.303658	0.23977	N	0.042715	T	0.00012	0.0000	M	0.71206	2.165	0.41778	D	0.989802	P	0.34522	0.455	B	0.30029	0.11	T	0.41963	-0.9479	8	.	.	.	.	4.7743	0.13171	0.1895:0.0:0.6347:0.1758	rs35352738;rs61753113	229	Q9NYW8	RBAK_HUMAN	E	229	ENSP00000275423:G229E;ENSP00000380120:G229E	.	G	+	2	0	RBAK	5070299	0.954000	0.32549	0.005000	0.12908	0.290000	0.27261	2.745000	0.47459	0.135000	0.18707	0.484000	0.47621	GGG	G|0.959;A|0.041	0.041	strong		0.368	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
PKD1	5310	hgsc.bcm.edu	37	16	2159341	2159341	+	Missense_Mutation	SNP	C	C	T	rs137978188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2159341C>T	ENST00000262304.4	-	15	6035	c.5827G>A	c.(5827-5829)Gtc>Atc	p.V1943I	PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Missense_Mutation_p.V1943I|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1943	PKD 15. {ECO:0000255|PROSITE- ProRule:PRU00151}.		V -> I (in dbSNP:rs137978188). {ECO:0000269|PubMed:11967008}.		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						TGGTCTCCGACGCGGGGGAAG	0.711													c|||	232	0.0463259	0.1687	0.013	5008	,	,		15215	0.0		0.0	False		,,,				2504	0.0				p.V1943I		Atlas-SNP	.											.	PKD1	184	.	0			c.G5827A						PASS	.	C	ILE/VAL,ILE/VAL	416,3736		14,388,1674	11.0	14.0	13.0		5827,5827	3.3	0.0	16	dbSNP_134	13	7,8223		0,7,4108	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	29,29	14,395,5782	TT,TC,CC		0.0851,10.0193,3.4162	possibly-damaging,possibly-damaging	1943/4303,1943/4304	2159341	423,11959	2076	4115	6191	SO:0001583	missense	5310	exon15			CTCCGACGCGGGG	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.5827G>A	16.37:g.2159341C>T	ENSP00000262304:p.Val1943Ile	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	20	7	0.35	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	92	0.04212454212454213	87	0.17682926829268292	5	0.013812154696132596	0	0.0	0	0.0	c	6.976	0.550123	0.13374	0.100193	8.51E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000382481	T;T	0.61158	0.13;0.13	5.33	3.35	0.38373	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (2);	0.353980	0.28618	N	0.014707	T	0.00144	0.0004	M	0.64567	1.98	0.80722	P	0.0	P;P	0.45957	0.702;0.869	B;P	0.46208	0.139;0.507	T	0.08106	-1.0738	9	0.33141	T	0.24	.	3.5344	0.07789	0.1467:0.5701:0.1424:0.1408	.	1943;1943	P98161-3;P98161	.;PKD1_HUMAN	I	1943;1943;222	ENSP00000262304:V1943I;ENSP00000399501:V1943I	ENSP00000262304:V1943I	V	-	1	0	PKD1	2099342	0.029000	0.19370	0.001000	0.08648	0.000000	0.00434	2.253000	0.43205	0.627000	0.30340	-0.340000	0.08031	GTC	C|0.958;T|0.042	0.042	strong		0.711	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
KIAA1107	23285	hgsc.bcm.edu	37	1	92646431	92646431	+	Missense_Mutation	SNP	A	A	G	rs7523466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:92646431A>G	ENST00000370378.4	+	8	1975	c.1877A>G	c.(1876-1878)gAt>gGt	p.D626G	KIAA1107_ENST00000409154.4_Missense_Mutation_p.D681G	NM_015237.2	NP_056052.2	Q9UPP5	K1107_HUMAN	KIAA1107	681										breast(4)|central_nervous_system(1)|endometrium(3)|kidney(2)|prostate(1)|skin(3)	14						GAAACAGATGATTGCGATGCA	0.318													A|||	20	0.00399361	0.0144	0.0014	5008	,	,		21343	0.0		0.0	False		,,,				2504	0.0				p.D626G		Atlas-SNP	.											.	KIAA1107	60	.	0			c.A1877G						PASS	.	A	GLY/ASP	16,1368		0,16,676	46.0	40.0	42.0		1877	3.3	0.0	1	dbSNP_116	42	0,3182		0,0,1591	yes	missense	KIAA1107	NM_015237.2	94	0,16,2267	GG,GA,AA		0.0,1.1561,0.3504	benign	626/1355	92646431	16,4550	692	1591	2283	SO:0001583	missense	23285	exon8			CAGATGATTGCGA	AB029030	CCDS44172.1	1p22.1	2008-02-05			ENSG00000069712	ENSG00000069712			29192	protein-coding gene	gene with protein product						10470851	Standard	NM_015237		Approved		uc010otd.2	Q9UPP5	OTTHUMG00000010292	ENST00000370378.4:c.1877A>G	1.37:g.92646431A>G	ENSP00000359404:p.Asp626Gly	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_015237	O14767|Q8N3X7	Missense_Mutation	SNP	ENST00000370378.4	37	CCDS44172.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	A	0.013	-1.646340	0.00792	0.011561	0.0	ENSG00000069712	ENST00000409154;ENST00000370378	T;T	0.05382	3.45;3.49	5.62	3.32	0.38043	.	1.054050	0.07354	N	0.882889	T	0.01523	0.0049	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.12837	0.008	T	0.48681	-0.9014	10	0.27785	T	0.31	.	9.7427	0.40429	0.8607:0.0:0.1393:0.0	rs7523466;rs52806057;rs7523466	626	E9PEZ5	.	G	681;626	ENSP00000386957:D681G;ENSP00000359404:D626G	ENSP00000359404:D626G	D	+	2	0	KIAA1107	92419019	0.014000	0.17966	0.001000	0.08648	0.062000	0.15995	1.181000	0.32017	0.436000	0.26393	-0.256000	0.11100	GAT	A|0.994;G|0.006	0.006	strong		0.318	KIAA1107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028375.3	XM_034086	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415899	105415899	+	Silent	SNP	A	A	G	rs11850869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105415899A>G	ENST00000333244.5	-	7	6008	c.5889T>C	c.(5887-5889)gcT>gcC	p.A1963A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1963						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)			CATCCAGCTTAGCCTTCTGGG	0.597													.|||	339	0.0676917	0.2315	0.013	5008	,	,		18512	0.0218		0.001	False		,,,				2504	0.001				p.A1963A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T5889C						PASS	.	G		716,3310		132,452,1429	142.0	155.0	151.0		5889	-2.9	0.0	14	dbSNP_120	151	7,8261		1,5,4128	no	coding-synonymous	AHNAK2	NM_138420.2		133,457,5557	GG,GA,AA		0.0847,17.7844,5.8809		1963/5796	105415899	723,11571	2013	4134	6147	SO:0001819	synonymous_variant	113146	exon7			CAGCTTAGCCTTC	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.5889T>C	14.37:g.105415899A>G		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	296	294	0.993243	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.965;G|0.035	0.035	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ARRDC2	27106	hgsc.bcm.edu	37	19	18121154	18121154	+	Silent	SNP	G	G	A	rs17852059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18121154G>A	ENST00000222250.4	+	6	1142	c.999G>A	c.(997-999)ccG>ccA	p.P333P	ARRDC2_ENST00000379656.3_Silent_p.P328P	NM_015683.1	NP_056498.1	Q8TBH0	ARRD2_HUMAN	arrestin domain containing 2	333					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)	12						GGGCCTTGCCGGAGCGGCCTG	0.652													G|||	269	0.0537141	0.1157	0.0288	5008	,	,		18135	0.002		0.0467	False		,,,				2504	0.0481				p.P333P		Atlas-SNP	.											.	ARRDC2	60	.	0			c.G999A						PASS	.	G	,	493,3913	210.2+/-230.7	25,443,1735	28.0	31.0	30.0		984,999	-9.6	0.0	19	dbSNP_123	30	430,8166	128.8+/-187.0	14,402,3882	no	coding-synonymous,coding-synonymous	ARRDC2	NM_001025604.1,NM_015683.1	,	39,845,5617	AA,AG,GG		5.0023,11.1893,7.0989	,	328/403,333/408	18121154	923,12079	2203	4298	6501	SO:0001819	synonymous_variant	27106	exon6			CTTGCCGGAGCGG		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.999G>A	19.37:g.18121154G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_015683	B2RBG9|O95895|Q6ZRV9|Q8WYG6	Silent	SNP	ENST00000222250.4	37	CCDS12370.1																																																																																			G|0.939;A|0.061	0.061	strong		0.652	ARRDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466845.1	NM_015683	
GSE1	23199	hgsc.bcm.edu	37	16	85695298	85695298	+	Silent	SNP	C	C	T	rs61737039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:85695298C>T	ENST00000253458.7	+	9	2363	c.2187C>T	c.(2185-2187)ttC>ttT	p.F729F	GSE1_ENST00000393243.1_Silent_p.F656F|GSE1_ENST00000405402.2_Silent_p.F625F|RN7SL381P_ENST00000577658.1_RNA	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	729																	ATGATGAGTTCCTGCAGCAGC	0.716													C|||	66	0.0131789	0.0469	0.0043	5008	,	,		14613	0.0		0.001	False		,,,				2504	0.0				p.F729F		Atlas-SNP	.											.	.	.	.	0			c.C2187T						PASS	.	C	,	139,4221		2,135,2043	11.0	14.0	13.0		1875,2187	-1.5	1.0	16	dbSNP_129	13	3,8533		0,3,4265	no	coding-synonymous,coding-synonymous	KIAA0182	NM_001134473.1,NM_014615.2	,	2,138,6308	TT,TC,CC		0.0351,3.1881,1.1011	,	625/1114,729/1218	85695298	142,12754	2180	4268	6448	SO:0001819	synonymous_variant	23199	exon9			TGAGTTCCTGCAG	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"""genetic suppressor element 1"""		"""KIAA0182"", ""Gse1 coiled-coil protein homolog (mouse)"""	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.2187C>T	16.37:g.85695298C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Silent	SNP	ENST00000253458.7	37	CCDS10952.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	C	5.452	0.268528	0.10349	0.031881	3.51E-4	ENSG00000131149	ENST00000412692	.	.	.	4.88	-1.45	0.08828	.	.	.	.	.	T	0.17238	0.0414	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31052	-0.9957	4	.	.	.	-10.3922	10.1383	0.42719	0.0:0.4732:0.0:0.5268	rs61737039	.	.	.	F	536	.	.	S	+	2	0	KIAA0182	84252799	0.988000	0.35896	0.990000	0.47175	0.473000	0.32948	0.303000	0.19210	-0.171000	0.10797	-0.291000	0.09656	TCC	C|0.988;T|0.012	0.012	strong		0.716	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615	
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743086	22743086	+	Missense_Mutation	SNP	C	C	T	rs201721928		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:22743086C>T	ENST00000560659.2	+	8	1321	c.1321C>T	c.(1321-1323)Cgg>Tgg	p.R441W	GOLGA6L1_ENST00000316397.3_Missense_Mutation_p.R491W			Q8N7Z2	GG6L1_HUMAN	golgin A6 family-like 1	485										NS(1)|breast(2)|endometrium(5)|large_intestine(1)|lung(1)|skin(1)	11						ggagaagatacggaagcagga	0.562																																					p.R491W		Atlas-SNP	.											.	GOLGA6L1	20	.	0			c.C1471T						PASS	.						4.0	3.0	4.0					15																	22743086		1053	1506	2559	SO:0001583	missense	283767	exon8			AAGATACGGAAGC	AK097517	CCDS73699.1	15q11.2	2012-10-05	2010-02-12		ENSG00000197414	ENSG00000277865			37444	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 1"""				Standard	NM_001001413		Approved		uc010tzx.1	Q8N7Z2	OTTHUMG00000171883	ENST00000560659.2:c.1321C>T	15.37:g.22743086C>T	ENSP00000452626:p.Arg441Trp	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	348	72	0.206897	NM_001001413		Missense_Mutation	SNP	ENST00000560659.2	37		.	.	.	.	.	.	.	.	.	.	.	2.598	-0.293699	0.05568	.	.	ENSG00000197414	ENST00000316397;ENST00000355145	T	0.11385	2.78	.	.	.	.	.	.	.	.	T	0.13500	0.0327	L	0.52573	1.65	0.09310	N	1	.	.	.	.	.	.	T	0.25257	-1.0137	5	0.62326	D	0.03	.	.	.	.	.	.	.	.	W	491	ENSP00000320207:R491W	ENSP00000320207:R491W	R	+	1	2	GOLGA6L1	20294450	0.006000	0.16342	0.011000	0.14972	0.011000	0.07611	-0.992000	0.03724	0.149000	0.19098	0.152000	0.16155	CGG	.	.	weak		0.562	GOLGA6L1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000415616.2	NM_001001413	
TSPYL5	85453	hgsc.bcm.edu	37	8	98289986	98289986	+	Silent	SNP	C	C	T	rs28669903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:98289986C>T	ENST00000322128.3	-	1	190	c.87G>A	c.(85-87)ccG>ccA	p.P29P		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	29					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					GGGCGTCGTCCGGAGCAGGGC	0.721													C|||	2924	0.583866	0.385	0.6599	5008	,	,		12258	0.6339		0.6312	False		,,,				2504	0.6984				p.P29P		Atlas-SNP	.											TSPYL5,NS,carcinoma,-2,1	TSPYL5	48	1	0			c.G87A						PASS	.	C		1848,2418		440,968,725	9.0	10.0	9.0		87	-7.6	0.0	8	dbSNP_125	9	5578,2722		1923,1732,495	no	coding-synonymous	TSPYL5	NM_033512.2		2363,2700,1220	TT,TC,CC		32.7952,43.3193,40.904		29/418	98289986	7426,5140	2133	4150	6283	SO:0001819	synonymous_variant	85453	exon1			GTCGTCCGGAGCA	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.87G>A	8.37:g.98289986C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_033512	B3KRF0|Q9C0B3	Silent	SNP	ENST00000322128.3	37	CCDS34927.1																																																																																			C|0.406;T|0.594	0.594	strong		0.721	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512	
C2orf16	84226	hgsc.bcm.edu	37	2	27803810	27803810	+	Silent	SNP	C	C	T	rs13408423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27803810C>T	ENST00000408964.2	+	1	4422	c.4371C>T	c.(4369-4371)ccC>ccT	p.P1457P	ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000355467.4_5'Flank|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000413371.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|RP11-158I13.2_ENST00000505973.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1457						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TGCCCAAGCCCACAGATTCCC	0.493													C|||	55	0.0109824	0.0378	0.0043	5008	,	,		18436	0.0		0.002	False		,,,				2504	0.0				p.P1457P		Atlas-SNP	.											.	C2orf16	357	.	0			c.C4371T						PASS	.	C		118,3726		3,112,1807	97.0	100.0	99.0		4371	2.5	0.0	2	dbSNP_121	99	2,8260		0,2,4129	no	coding-synonymous	C2orf16	NM_032266.3		3,114,5936	TT,TC,CC		0.0242,3.0697,0.9912		1457/1985	27803810	120,11986	1922	4131	6053	SO:0001819	synonymous_variant	84226	exon1			CAAGCCCACAGAT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4371C>T	2.37:g.27803810C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	42	0.617647	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			C|0.986;T|0.014	0.014	strong		0.493	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
PDZD2	23037	hgsc.bcm.edu	37	5	32087828	32087828	+	Missense_Mutation	SNP	C	C	T	rs36097367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32087828C>T	ENST00000438447.1	+	20	4662	c.4274C>T	c.(4273-4275)aCg>aTg	p.T1425M	PDZD2_ENST00000282493.3_Missense_Mutation_p.T1425M			O15018	PDZD2_HUMAN	PDZ domain containing 2	1425			T -> M (in dbSNP:rs36097367).		cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						AGCCCTGTGACGGACATTGAC	0.607													C|||	183	0.0365415	0.1346	0.0058	5008	,	,		18447	0.0		0.001	False		,,,				2504	0.0				p.T1425M		Atlas-SNP	.											PDZD2,NS,carcinoma,-1,1	PDZD2	306	1	0			c.C4274T						PASS	.	C	MET/THR	527,3879	232.0+/-245.7	27,473,1703	40.0	41.0	41.0		4274	4.7	0.8	5	dbSNP_126	41	5,8595	4.3+/-15.6	0,5,4295	yes	missense	PDZD2	NM_178140.2	81	27,478,5998	TT,TC,CC		0.0581,11.961,4.0904	probably-damaging	1425/2840	32087828	532,12474	2203	4300	6503	SO:0001583	missense	23037	exon19			CTGTGACGGACAT	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.4274C>T	5.37:g.32087828C>T	ENSP00000402033:p.Thr1425Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	149	89	0.597315	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	50	0.022893772893772892	48	0.0975609756097561	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	17.75	3.467294	0.63625	0.11961	5.81E-4	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.09723	2.95;2.95	5.55	4.67	0.58626	.	0.000000	0.45867	D	0.000323	T	0.00384	0.0012	L	0.59436	1.845	0.38283	D	0.942477	D	0.89917	1.0	D	0.71656	0.974	T	0.00203	-1.1924	10	0.87932	D	0	.	13.494	0.61414	0.1575:0.8425:0.0:0.0	rs36097367	1425	O15018	PDZD2_HUMAN	M	1425;1226;1425	ENSP00000402033:T1425M;ENSP00000282493:T1425M	ENSP00000282493:T1425M	T	+	2	0	PDZD2	32123585	0.993000	0.37304	0.800000	0.32199	0.624000	0.37722	3.702000	0.54800	1.331000	0.45412	0.655000	0.94253	ACG	C|0.961;T|0.039	0.039	strong		0.607	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
WNT16	51384	hgsc.bcm.edu	37	7	120969769	120969769	+	Missense_Mutation	SNP	G	G	A	rs2908004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	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	
KIAA0319	9856	hgsc.bcm.edu	37	6	24596433	24596433	+	Missense_Mutation	SNP	A	A	C	rs73727343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24596433A>C	ENST00000378214.3	-	3	993	c.469T>G	c.(469-471)Tca>Gca	p.S157A	KIAA0319_ENST00000430948.2_Missense_Mutation_p.S112A|KIAA0319_ENST00000537886.1_Missense_Mutation_p.S157A|KIAA0319_ENST00000543707.1_Missense_Mutation_p.S157A|KIAA0319_ENST00000535378.1_Missense_Mutation_p.S148A	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	157				S -> A (in Ref. 1; BAA20777 and 5; AAI52461). {ECO:0000305}.	negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						TAGTCATCTGAGTACTCAGAC	0.597													A|||	134	0.0267572	0.0961	0.0072	5008	,	,		17776	0.0		0.002	False		,,,				2504	0.0				p.S157A		Atlas-SNP	.											.	KIAA0319	117	.	0			c.T469G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER	322,4084	170.5+/-200.9	9,304,1890	75.0	79.0	78.0		442,469,334,469,469	-3.2	0.1	6	dbSNP_130	78	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense	KIAA0319	NM_001168374.1,NM_001168375.1,NM_001168376.1,NM_001168377.1,NM_014809.3	99,99,99,99,99	9,307,6187	CC,CA,AA		0.0349,7.3082,2.4988	benign,benign,benign,benign,benign	148/1064,157/1073,112/1028,157/1012,157/1073	24596433	325,12681	2203	4300	6503	SO:0001583	missense	9856	exon3			CATCTGAGTACTC	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.469T>G	6.37:g.24596433A>C	ENSP00000367459:p.Ser157Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	65	0.02976190476190476	58	0.11788617886178862	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	4.600	0.111504	0.08831	0.073082	3.49E-4	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.06371	3.31;3.32;3.32;3.31;3.31	4.43	-3.24	0.05094	.	1.418230	0.04637	N	0.404692	T	0.01156	0.0038	L	0.29908	0.895	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.10450	0.005;0.003;0.001	T	0.48375	-0.9041	10	0.29301	T	0.29	-0.0017	0.6264	0.00786	0.3156:0.2275:0.2714:0.1855	.	157;148;157	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	A	157;148;112;157;157	ENSP00000439700:S157A;ENSP00000442403:S148A;ENSP00000401086:S112A;ENSP00000367459:S157A;ENSP00000437656:S157A	ENSP00000367459:S157A	S	-	1	0	KIAA0319	24704412	0.000000	0.05858	0.057000	0.19452	0.884000	0.51177	-1.251000	0.02882	-0.187000	0.10516	0.421000	0.28195	TCA	A|0.970;C|0.030	0.030	strong		0.597	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
AHNAK	79026	hgsc.bcm.edu	37	11	62291912	62291912	+	Missense_Mutation	SNP	C	C	T	rs115362908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62291912C>T	ENST00000378024.4	-	5	10251	c.9977G>A	c.(9976-9978)aGt>aAt	p.S3326N	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3326					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TATATCCAAACTGGGAGCTTT	0.413													C|||	16	0.00319489	0.0098	0.0043	5008	,	,		19033	0.0		0.0	False		,,,				2504	0.0				p.S3326N		Atlas-SNP	.											.	AHNAK	532	.	0			c.G9977A						PASS	.	C	ASN/SER,	53,4351	52.3+/-87.9	3,47,2152	58.0	53.0	55.0		9977,	1.6	0.1	11	dbSNP_132	55	1,8597	1.2+/-3.3	0,1,4298	yes	missense,intron	AHNAK	NM_001620.1,NM_024060.2	46,	3,48,6450	TT,TC,CC		0.0116,1.2035,0.4153	benign,	3326/5891,	62291912	54,12948	2202	4299	6501	SO:0001583	missense	79026	exon5			TCCAAACTGGGAG	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.9977G>A	11.37:g.62291912C>T	ENSP00000367263:p.Ser3326Asn	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	45	0.592105	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	C	1.856	-0.463832	0.04476	0.012035	1.16E-4	ENSG00000124942	ENST00000378024	T	0.00672	5.89	4.07	1.61	0.23674	.	.	.	.	.	T	0.00608	0.0020	L	0.28556	0.865	0.09310	N	1	B	0.25719	0.132	B	0.35278	0.199	T	0.48747	-0.9008	9	0.20519	T	0.43	.	6.9065	0.24311	0.0:0.2034:0.0:0.7966	.	3326	Q09666	AHNK_HUMAN	N	3326	ENSP00000367263:S3326N	ENSP00000367263:S3326N	S	-	2	0	AHNAK	62048488	0.000000	0.05858	0.067000	0.19924	0.419000	0.31324	0.794000	0.26958	0.089000	0.17243	0.305000	0.20034	AGT	C|0.996;T|0.004	0.004	strong		0.413	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
MX2	4600	hgsc.bcm.edu	37	21	42749081	42749081	+	Splice_Site	SNP	T	T	C	rs56680307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:42749081T>C	ENST00000330714.3	+	2	432	c.248T>C	c.(247-249)aTg>aCg	p.M83T	MX2_ENST00000543692.1_Splice_Site_p.M83T	NM_002463.1	NP_002454.1	P20592	MX2_HUMAN	MX dynamin-like GTPase 2	83					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|GTP catabolic process (GO:0006184)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of nucleocytoplasmic transport (GO:0046822)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	34		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				CCAAGGGCAATGGTAAGCCCG	0.552													A|||	357	0.0712859	0.1891	0.0288	5008	,	,		17946	0.0546		0.002	False		,,,				2504	0.0307				p.M83T		Atlas-SNP	.											.	MX2	84	.	0			c.T248C						PASS	.	A	THR/MET	755,3651		64,627,1512	106.0	119.0	115.0		248	2.5	0.2	21	dbSNP_129	115	17,8583		0,17,4283	yes	missense-near-splice	MX2	NM_002463.1	81	64,644,5795	CC,CT,TT		0.1977,17.1357,5.9357	benign	83/716	42749081	772,12234	2203	4300	6503	SO:0001630	splice_region_variant	4600	exon2			GGGCAATGGTAAG		CCDS13672.1	21q22.3	2014-07-15	2014-07-15		ENSG00000183486	ENSG00000183486			7533	protein-coding gene	gene with protein product	"""interferon-regulated resistance GTP-binding protein MXB"", ""second interferon-induced protein p78"""	147890	"""myxovirus (influenza) resistance 2, homolog of murine"", ""myxovirus (influenza virus) resistance 2 (mouse)"""			2481229, 8798556	Standard	NM_002463		Approved	MXB	uc002yzf.1	P20592	OTTHUMG00000086753	ENST00000330714.3:c.249+1T>C	21.37:g.42749081T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_002463	B7Z5D3|D3DSI7	Missense_Mutation	SNP	ENST00000330714.3	37	CCDS13672.1	131	0.059981684981684984	100	0.2032520325203252	13	0.03591160220994475	18	0.03146853146853147	0	0.0	A	12.34	1.908362	0.33721	0.171357	0.001977	ENSG00000183486	ENST00000330714;ENST00000436410;ENST00000435611;ENST00000543692;ENST00000418103	D;D	0.91180	-2.41;-2.8	2.47	2.47	0.30058	.	1.146510	0.06303	N	0.701305	T	0.00271	0.0008	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.04752	-1.0929	10	0.22109	T	0.4	.	4.8404	0.13487	0.7257:0.0:0.0:0.2743	rs56680307;rs61730272	83	P20592	MX2_HUMAN	T	83	ENSP00000333657:M83T;ENSP00000446017:M83T	ENSP00000333657:M83T	M	+	2	0	MX2	41670951	0.911000	0.30947	0.166000	0.22797	0.020000	0.10135	0.996000	0.29719	0.385000	0.24970	-0.364000	0.07487	ATG	T|0.941;C|0.059	0.059	strong		0.552	MX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195147.1	NM_002463	Missense_Mutation
NOL10	79954	hgsc.bcm.edu	37	2	10797952	10797952	+	Silent	SNP	G	G	A	rs61737663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10797952G>A	ENST00000381685.5	-	11	927	c.822C>T	c.(820-822)ccC>ccT	p.P274P	NOL10_ENST00000345985.3_Intron|NOL10_ENST00000538384.1_Silent_p.P248P|NOL10_ENST00000542668.1_Silent_p.P224P	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	274						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		CGGACTTAATGGGCAGCCCAT	0.348													G|||	83	0.0165735	0.0582	0.0086	5008	,	,		18192	0.0		0.0	False		,,,				2504	0.0				p.P274P		Atlas-SNP	.											.	NOL10	22	.	0			c.C822T						PASS	.	G		67,1317		0,67,625	131.0	122.0	124.0		822	3.5	1.0	2	dbSNP_129	124	0,3182		0,0,1591	no	coding-synonymous	NOL10	NM_024894.2		0,67,2216	AA,AG,GG		0.0,4.841,1.4674		274/689	10797952	67,4499	692	1591	2283	SO:0001819	synonymous_variant	79954	exon11			CTTAATGGGCAGC	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.822C>T	2.37:g.10797952G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	192	92	0.479167	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Silent	SNP	ENST00000381685.5	37	CCDS1673.2																																																																																			G|0.988;A|0.012	0.012	strong		0.348	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
DCHS2	54798	hgsc.bcm.edu	37	4	155158104	155158104	+	Missense_Mutation	SNP	G	G	A	rs17031279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155158104G>A	ENST00000357232.4	-	25	6334	c.6335C>T	c.(6334-6336)aCg>aTg	p.T2112M		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2112	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.		T -> M (in dbSNP:rs17031279).		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)		TGTAACAAGCGTGCTTCCAAC	0.383													G|||	106	0.0211661	0.0749	0.0058	5008	,	,		22095	0.0		0.002	False		,,,				2504	0.001				p.T2112M		Atlas-SNP	.											.	DCHS2	594	.	0			c.C6335T						PASS	.	G	MET/THR	258,4148	149.2+/-183.4	6,246,1951	158.0	152.0	154.0		6335	4.1	0.1	4	dbSNP_123	154	5,8595	4.3+/-15.6	0,5,4295	yes	missense	DCHS2	NM_017639.3	81	6,251,6246	AA,AG,GG		0.0581,5.8557,2.0221	probably-damaging	2112/2917	155158104	263,12743	2203	4300	6503	SO:0001583	missense	54798	exon25			ACAAGCGTGCTTC	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.6335C>T	4.37:g.155158104G>A	ENSP00000349768:p.Thr2112Met	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	178	90	0.505618	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	G	10.93	1.488688	0.26686	0.058557	5.81E-4	ENSG00000197410	ENST00000357232	T	0.52754	0.65	5.82	4.09	0.47781	Cadherin (3);Cadherin-like (1);	0.347781	0.26669	N	0.023120	T	0.14614	0.0353	M	0.76002	2.32	0.30495	N	0.770966	D	0.89917	1.0	D	0.66847	0.947	T	0.47995	-0.9073	10	0.42905	T	0.14	.	4.1039	0.10028	0.147:0.1359:0.5918:0.1253	rs17031279;rs52827899;rs17031279	2112	Q6V1P9	PCD23_HUMAN	M	2112	ENSP00000349768:T2112M	ENSP00000349768:T2112M	T	-	2	0	DCHS2	155377554	0.994000	0.37717	0.138000	0.22173	0.167000	0.22549	2.937000	0.48979	1.459000	0.47892	0.557000	0.71058	ACG	G|0.979;A|0.021	0.021	strong		0.383	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
USP2	9099	hgsc.bcm.edu	37	11	119243612	119243612	+	Silent	SNP	T	T	C	rs4938649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119243612T>C	ENST00000260187.2	-	2	873	c.579A>G	c.(577-579)gaA>gaG	p.E193E	RP11-334E6.3_ENST00000530918.2_RNA|USP2_ENST00000455332.2_Intron	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	193	Necessary for interaction with MDM4.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		CGACCAGGTATTCAGGGCAGC	0.637													C|||	239	0.0477236	0.1195	0.0274	5008	,	,		17377	0.0407		0.002	False		,,,				2504	0.0194				p.E193E		Atlas-SNP	.											.	USP2	71	.	0			c.A579G						PASS	.	C		503,3895	779.2+/-414.3	28,447,1724	66.0	69.0	68.0		579	1.2	0.9	11	dbSNP_111	68	8,8582	818.2+/-406.9	0,8,4287	no	coding-synonymous	USP2	NM_004205.4		28,455,6011	CC,CT,TT		0.0931,11.437,3.9344		193/606	119243612	511,12477	2199	4295	6494	SO:0001819	synonymous_variant	9099	exon2			CAGGTATTCAGGG	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.579A>G	11.37:g.119243612T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	46	29	0.630435	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	37	CCDS8422.1																																																																																			T|0.959;C|0.041	0.041	strong		0.637	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997	
CNST	163882	hgsc.bcm.edu	37	1	246755204	246755204	+	Missense_Mutation	SNP	C	C	T	rs116182112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:246755204C>T	ENST00000366513.4	+	2	609	c.340C>T	c.(340-342)Cca>Tca	p.P114S	CNST_ENST00000483271.1_3'UTR|CNST_ENST00000366512.3_Missense_Mutation_p.P114S	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	114					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						AAAAAGAAGTCCAAGAAGCAA	0.393													C|||	10	0.00199681	0.0076	0.0	5008	,	,		20543	0.0		0.0	False		,,,				2504	0.0				p.P114S		Atlas-SNP	.											.	CNST	73	.	0			c.C340T						PASS	.	C	SER/PRO,SER/PRO	22,4376		0,22,2177	30.0	31.0	31.0		340,340	-12.3	0.0	1	dbSNP_132	31	1,8591		0,1,4295	yes	missense,missense	CNST	NM_001139459.1,NM_152609.2	74,74	0,23,6472	TT,TC,CC		0.0116,0.5002,0.1771	benign,benign	114/617,114/726	246755204	23,12967	2199	4296	6495	SO:0001583	missense	163882	exon2			AGAAGTCCAAGAA	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26486	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 64"""	613439	"""chromosome 1 open reading frame 71"""	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.340C>T	1.37:g.246755204C>T	ENSP00000355470:p.Pro114Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	37	CCDS1628.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	0.124	-1.122387	0.01785	0.005002	1.16E-4	ENSG00000162852	ENST00000366513;ENST00000366512;ENST00000366511	T;T;T	0.21734	1.99;1.99;1.99	6.17	-12.3	0.00002	.	1.657020	0.02939	N	0.140268	T	0.08268	0.0206	L	0.39633	1.23	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.14559	-1.0468	10	0.25751	T	0.34	-0.1849	3.0934	0.06301	0.2575:0.3466:0.279:0.1169	.	114;114	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	S	114	ENSP00000355470:P114S;ENSP00000355469:P114S;ENSP00000355468:P114S	ENSP00000355468:P114S	P	+	1	0	CNST	244821827	0.031000	0.19500	0.002000	0.10522	0.852000	0.48524	-1.106000	0.03319	-4.388000	0.00052	-1.094000	0.02160	CCA	C|0.998;T|0.002	0.002	strong		0.393	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609	
MUC4	4585	hgsc.bcm.edu	37	3	195513598	195513598	+	Missense_Mutation	SNP	G	G	A	rs57748294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513598G>A	ENST00000463781.3	-	2	5312	c.4853C>T	c.(4852-4854)cCt>cTt	p.P1618L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1618L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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	0.562																																					p.P1618L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C4853T						PASS	.						11.0	16.0	15.0					3																	195513598		661	1535	2196	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.4853C>T	3.37:g.195513598G>A	ENSP00000417498:p.Pro1618Leu	Somatic	537	0	0		WXS	Illumina HiSeq	Phase_I	455	286	0.628571	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	.	.	.	.	.	.	.	.	.	.	-	5.217	0.225606	0.09916	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.5;1.5	.	.	.	.	.	.	.	.	T	0.30039	0.0752	N	0.19112	0.55	0.80722	P	0.0	P	0.52170	0.951	P	0.62560	0.904	T	0.36016	-0.9765	6	.	.	.	.	5.8679	0.18786	8.0E-4:0.0:0.9992:0.0	rs57748294	1618	E7ESK3	.	L	1618	ENSP00000417498:P1618L;ENSP00000420243:P1618L	.	P	-	2	0	MUC4	196997993	0.001000	0.12720	0.025000	0.17156	0.025000	0.11179	0.563000	0.23547	0.088000	0.17205	0.089000	0.15464	CCT	A|0.075;G|0.923;T|0.002	0.075	strong		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
AACS	65985	hgsc.bcm.edu	37	12	125626685	125626685	+	Silent	SNP	C	C	T	rs3751180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125626685C>T	ENST00000316519.6	+	18	2135	c.1929C>T	c.(1927-1929)atC>atT	p.I643I	AACS_ENST00000543665.1_Silent_p.I75I|AACS_ENST00000545511.1_Silent_p.I155I|AACS_ENST00000261686.6_Missense_Mutation_p.R576C|AACS_ENST00000316543.10_Silent_p.I241I	NM_023928.3	NP_076417.2	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	643					adipose tissue development (GO:0060612)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cellular response to testosterone stimulus (GO:0071394)|fatty acid metabolic process (GO:0006631)|liver development (GO:0001889)|positive regulation of insulin secretion (GO:0032024)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to purine-containing compound (GO:0014074)|response to starvation (GO:0042594)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)	acetoacetate-CoA ligase activity (GO:0030729)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)	p.I643I(1)		breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|liver(1)|lung(16)|ovary(1)|stomach(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		AACAGATCATCGCTGGAAAAG	0.522													C|||	475	0.0948482	0.1278	0.0403	5008	,	,		21262	0.1994		0.0139	False		,,,				2504	0.0644				p.I643I		Atlas-SNP	.											AACS,NS,carcinoma,0,1	AACS	59	1	1	Substitution - coding silent(1)	stomach(1)	c.C1929T						PASS	.	C		480,3926	226.5+/-242.0	15,450,1738	115.0	106.0	109.0		1929	-9.3	0.0	12	dbSNP_107	109	125,8475	64.2+/-126.4	0,125,4175	no	coding-synonymous	AACS	NM_023928.3		15,575,5913	TT,TC,CC		1.4535,10.8942,4.6517		643/673	125626685	605,12401	2203	4300	6503	SO:0001819	synonymous_variant	65985	exon18			GATCATCGCTGGA	AK022451	CCDS9263.1	12q24.31	2010-09-29			ENSG00000081760	ENSG00000081760	6.2.1.16	"""Acyl-CoA synthetase family"""	21298	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 1"""	614364				12623130, 17762044	Standard	NM_023928		Approved	FLJ12389, SUR-5, ACSF1	uc001uhc.3	Q86V21	OTTHUMG00000168550	ENST00000316519.6:c.1929C>T	12.37:g.125626685C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_023928	Q49AB9|Q49AC3|Q658Q8|Q8IWD2|Q8NEW5|Q9BSJ9|Q9H829|Q9HA19	Silent	SNP	ENST00000316519.6	37	CCDS9263.1	191	0.08745421245421245	53	0.10772357723577236	16	0.04419889502762431	115	0.20104895104895104	7	0.009234828496042216	C	12.82	2.052375	0.36181	0.108942	0.014535	ENSG00000081760	ENST00000261686	T	0.10099	2.91	4.63	-9.26	0.00662	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.38575	P	0.04996100000000003	B	0.06786	0.001	B	0.01281	0.0	T	0.40156	-0.9578	7	0.66056	D	0.02	.	3.6244	0.08108	0.0757:0.1654:0.1934:0.5654	rs3751180;rs3751180	576	Q86V21-2	.	C	576	ENSP00000261686:R576C	ENSP00000261686:R576C	R	+	1	0	AACS	124192638	0.645000	0.27286	0.000000	0.03702	0.005000	0.04900	-0.309000	0.08145	-2.789000	0.00357	-0.275000	0.10095	CGC	C|0.931;T|0.069	0.069	strong		0.522	AACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400202.1	NM_023928	
PISD	23761	hgsc.bcm.edu	37	22	32015766	32015766	+	Silent	SNP	G	G	A	rs41282571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32015766G>A	ENST00000439502.2	-	8	1285	c.1062C>T	c.(1060-1062)ttC>ttT	p.F354F	PISD_ENST00000336566.4_Silent_p.F353F|PISD_ENST00000397500.1_3'UTR|PISD_ENST00000478893.1_5'Flank|PISD_ENST00000382151.2_Silent_p.F320F|PISD_ENST00000266095.5_Silent_p.F320F			Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase	354					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylserine decarboxylase activity (GO:0004609)			central_nervous_system(3)|endometrium(2)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12					Phosphatidylserine(DB00144)	TGTGCGTCACGAAGCTGAAGT	0.612													G|||	181	0.0361422	0.0234	0.0187	5008	,	,		20115	0.0069		0.0368	False		,,,				2504	0.0951				p.F320F		Atlas-SNP	.											.	PISD	53	.	0			c.C960T						PASS	.	G		90,4316	76.2+/-114.5	0,90,2113	163.0	125.0	138.0		960	-1.6	1.0	22	dbSNP_127	138	245,8355	97.2+/-158.9	3,239,4058	no	coding-synonymous	PISD	NM_014338.3		3,329,6171	AA,AG,GG		2.8488,2.0427,2.5757		320/376	32015766	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	23761	exon9			CGTCACGAAGCTG		CCDS13899.1	22q12.2	2011-01-25			ENSG00000241878	ENSG00000241878	4.1.1.65		8999	protein-coding gene	gene with protein product		612770				10591208	Standard	NM_014338		Approved	dJ858B16.2, PSDC	uc003alk.2	Q9UG56	OTTHUMG00000030252	ENST00000439502.2:c.1062C>T	22.37:g.32015766G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	232	110	0.474138	NM_014338	B1AKM7|O43207|O95535|Q6IC28|Q96GQ2|Q9UGA9	Silent	SNP	ENST00000439502.2	37		58	0.026556776556776556	15	0.03048780487804878	10	0.027624309392265192	3	0.005244755244755245	30	0.0395778364116095	G	4.359	0.066221	0.08388	0.020427	0.028488	ENSG00000241878	ENST00000435900	.	.	.	4.88	-1.64	0.08318	.	.	.	.	.	T	0.22704	0.0548	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29274	-1.0017	4	.	.	.	-24.3787	9.3904	0.38370	0.5267:0.0:0.4733:0.0	rs41282571;rs61747366	.	.	.	L	307	.	.	S	-	2	0	PISD	30345766	1.000000	0.71417	0.970000	0.41538	0.458000	0.32498	0.891000	0.28309	-0.578000	0.05959	-0.216000	0.12614	TCG	A|0.028;C|0.000;G|0.972	0.028	strong		0.612	PISD-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000075106.4		
MRPL23	6150	hgsc.bcm.edu	37	11	1972229	1972229	+	Missense_Mutation	SNP	G	G	A	rs377324983		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1972229G>A	ENST00000397298.3	+	2	203	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	MRPL23_ENST00000381519.1_Missense_Mutation_p.V40M|MRPL23_ENST00000397294.3_Missense_Mutation_p.V40M|MRPL23_ENST00000397297.3_Missense_Mutation_p.V40M|MRPL23_ENST00000486931.1_3'UTR|MRPL23_ENST00000381514.3_Missense_Mutation_p.V40M	NM_021134.3	NP_066957.3	Q16540	RM23_HUMAN	mitochondrial ribosomal protein L23	40					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(1)|ovary(1)	4		all_epithelial(84;6.24e-05)|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;0.0026)|Lung(200;0.0171)|LUSC - Lung squamous cell carcinoma(625;0.0842)		CGAGGACACCGTGCAGTTCCG	0.657													G|||	1	0.000199681	0.0	0.0	5008	,	,		15615	0.001		0.0	False		,,,				2504	0.0				p.V40M		Atlas-SNP	.											.	MRPL23	14	.	0			c.G118A						PASS	.						38.0	31.0	33.0					11																	1972229		2198	4297	6495	SO:0001583	missense	6150	exon2			GACACCGTGCAGT	AB051340	CCDS31336.1	11p15.5	2012-09-13			ENSG00000214026	ENSG00000214026		"""Mitochondrial ribosomal proteins / large subunits"""	10322	protein-coding gene	gene with protein product		600789		RPL23L		8541832	Standard	NM_021134		Approved	L23MRP	uc001lux.3	Q16540	OTTHUMG00000012476	ENST00000397298.3:c.118G>A	11.37:g.1972229G>A	ENSP00000380466:p.Val40Met	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_021134	A8MT29|Q96Q71	Missense_Mutation	SNP	ENST00000397298.3	37	CCDS31336.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.663671	0.88251	.	.	ENSG00000214026	ENST00000397298;ENST00000381519;ENST00000397297;ENST00000381514;ENST00000397294	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	4.46	4.46	0.54185	Ribosomal protein L23/L15e (1);Nucleotide-binding, alpha-beta plait (1);	0.159427	0.41097	U	0.000941	T	0.71921	0.3397	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.80522	-0.1345	10	0.72032	D	0.01	.	17.4877	0.87693	0.0:0.0:1.0:0.0	.	40	Q16540	RM23_HUMAN	M	40	ENSP00000380466:V40M;ENSP00000370930:V40M;ENSP00000380465:V40M;ENSP00000370925:V40M;ENSP00000380462:V40M	ENSP00000370925:V40M	V	+	1	0	MRPL23	1928805	1.000000	0.71417	0.996000	0.52242	0.876000	0.50452	5.989000	0.70587	2.199000	0.70637	0.491000	0.48974	GTG	.	.	weak		0.657	MRPL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034765.2	NM_021134	
ULK4	54986	hgsc.bcm.edu	37	3	41756965	41756965	+	Missense_Mutation	SNP	C	C	T	rs61744388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:41756965C>T	ENST00000301831.4	-	24	3013	c.2551G>A	c.(2551-2553)Gta>Ata	p.V851I		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	851					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TGAAGCACTACAGGCATCAGG	0.428													T|||	1330	0.265575	0.5348	0.1628	5008	,	,		17563	0.1478		0.1839	False		,,,				2504	0.18				p.V851I		Atlas-SNP	.											.	ULK4	150	.	0			c.G2551A						PASS	.	T	ILE/VAL	1816,2052		436,944,554	103.0	104.0	104.0		2551	-10.1	0.0	3	dbSNP_129	104	1420,6868		128,1164,2852	yes	missense	ULK4	NM_017886.2	29	564,2108,3406	TT,TC,CC		17.1332,46.9493,26.6206	benign	851/1276	41756965	3236,8920	1934	4144	6078	SO:0001583	missense	54986	exon24			GCACTACAGGCAT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2551G>A	3.37:g.41756965C>T	ENSP00000301831:p.Val851Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	550	0.2518315018315018	262	0.532520325203252	57	0.1574585635359116	86	0.15034965034965034	145	0.19129287598944592	T	8.060	0.767962	0.15983	0.469493	0.171332	ENSG00000168038	ENST00000301831	T	0.62941	-0.01	5.72	-10.1	0.00402	Armadillo-type fold (1);	0.423778	0.22435	N	0.060092	T	0.00012	0.0000	N	0.24115	0.695	0.49915	P	1.6599999999999948E-4	B	0.09022	0.002	B	0.10450	0.005	T	0.36768	-0.9734	9	0.25106	T	0.35	.	25.2475	0.99993	0.0:0.8218:0.0:0.1782	.	851	Q96C45	ULK4_HUMAN	I	851	ENSP00000301831:V851I	ENSP00000301831:V851I	V	-	1	0	ULK4	41731969	0.000000	0.05858	0.000000	0.03702	0.404000	0.30871	-0.947000	0.03901	-2.451000	0.00543	-1.977000	0.00459	GTA	C|0.772;T|0.228	0.228	strong		0.428	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
ANGPT4	51378	hgsc.bcm.edu	37	20	860426	860426	+	Silent	SNP	G	G	A	rs61737018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:860426G>A	ENST00000381922.3	-	6	1119	c.1017C>T	c.(1015-1017)acC>acT	p.T339T	ANGPT4_ENST00000546022.1_Silent_p.T339T	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	339	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						GAAAATTCACGGTGCCATTCT	0.612													G|||	745	0.148762	0.2632	0.0663	5008	,	,		14818	0.1062		0.0746	False		,,,				2504	0.1728				p.T339T	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											.	ANGPT4	77	.	0			c.C1017T						PASS	.	G		951,3455	359.4+/-314.8	98,755,1350	83.0	75.0	78.0		1017	-8.3	0.0	20	dbSNP_129	78	672,7928	169.4+/-220.8	20,632,3648	no	coding-synonymous	ANGPT4	NM_015985.2		118,1387,4998	AA,AG,GG		7.814,21.5842,12.4789		339/504	860426	1623,11383	2203	4300	6503	SO:0001819	synonymous_variant	51378	exon6			ATTCACGGTGCCA	AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"""Fibrinogen C domain containing"""	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.1017C>T	20.37:g.860426G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																			G|0.879;A|0.121	0.121	strong		0.612	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985	
FCER2	2208	hgsc.bcm.edu	37	19	7754101	7754101	+	Missense_Mutation	SNP	G	G	A	rs34694289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7754101G>A	ENST00000346664.5	-	11	1156	c.944C>T	c.(943-945)cCc>cTc	p.P315L	FCER2_ENST00000597921.1_Missense_Mutation_p.P315L|FCER2_ENST00000360067.4_Missense_Mutation_p.P314L	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)	315					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						AGGGGCAGAGGGGGTGGGCAG	0.637													G|||	51	0.0101837	0.0386	0.0	5008	,	,		14053	0.0		0.0	False		,,,				2504	0.0				p.P315L		Atlas-SNP	.											.	FCER2	19	.	0			c.C944T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	130,4276	87.3+/-125.9	4,122,2077	33.0	32.0	32.0		941,944,944	-0.9	0.0	19	dbSNP_126	32	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	FCER2	NM_001207019.2,NM_001220500.1,NM_002002.4	98,98,98	4,123,6376	AA,AG,GG		0.0116,2.9505,1.0072	probably-damaging,probably-damaging,probably-damaging	314/321,315/322,315/322	7754101	131,12875	2203	4300	6503	SO:0001583	missense	2208	exon11			GCAGAGGGGGTGG	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.944C>T	19.37:g.7754101G>A	ENSP00000264072:p.Pro315Leu	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	235	138	0.587234	NM_002002		Missense_Mutation	SNP	ENST00000346664.5	37	CCDS12184.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	12.45	1.942513	0.34283	0.029505	1.16E-4	ENSG00000104921	ENST00000346664;ENST00000360067	T;T	0.04156	3.69;3.71	2.72	-0.925	0.10458	.	.	.	.	.	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.12156	0.007	T	0.44544	-0.9321	9	0.87932	D	0	.	4.2641	0.10754	0.1588:0.4449:0.3963:0.0	rs34694289	315	P06734	FCER2_HUMAN	L	315;314	ENSP00000264072:P315L;ENSP00000353178:P314L	ENSP00000264072:P315L	P	-	2	0	FCER2	7660101	0.000000	0.05858	0.000000	0.03702	0.306000	0.27790	-0.171000	0.09883	0.008000	0.14787	0.298000	0.19748	CCC	G|0.990;A|0.010	0.010	strong		0.637	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002	
FAM118A	55007	hgsc.bcm.edu	37	22	45723842	45723842	+	Silent	SNP	G	G	A	rs17851057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45723842G>A	ENST00000216214.3	+	5	1254	c.420G>A	c.(418-420)agG>agA	p.R140R	FAM118A_ENST00000441876.2_Silent_p.R140R|FAM118A_ENST00000405673.1_Silent_p.R140R|FAM118A_ENST00000405548.3_5'Flank	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	140						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TGATGGACAGGGGCGCCATGG	0.597													G|||	2686	0.536342	0.851	0.4006	5008	,	,		18320	0.5268		0.2932	False		,,,				2504	0.4673				p.R140R		Atlas-SNP	.											.	FAM118A	32	.	0			c.G420A						PASS	.	G	,	3316,1090	717.8+/-408.8	1258,800,145	58.0	48.0	52.0		420,420	-0.2	0.9	22	dbSNP_123	52	2444,6156	402.6+/-347.5	354,1736,2210	no	coding-synonymous,coding-synonymous	FAM118A	NM_001104595.1,NM_017911.2	,	1612,2536,2355	AA,AG,GG		28.4186,24.739,44.2873	,	140/358,140/358	45723842	5760,7246	2203	4300	6503	SO:0001819	synonymous_variant	55007	exon4			GGACAGGGGCGCC	BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 8"""	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.420G>A	22.37:g.45723842G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	149	81	0.543624	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Silent	SNP	ENST00000216214.3	37	CCDS14065.1																																																																																			G|0.539;A|0.461	0.461	strong		0.597	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
PCSK7	9159	hgsc.bcm.edu	37	11	117089801	117089801	+	Missense_Mutation	SNP	T	T	C	rs61729982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117089801T>C	ENST00000320934.3	-	11	2033	c.1403A>G	c.(1402-1404)aAc>aGc	p.N468S	PCSK7_ENST00000540028.1_Missense_Mutation_p.N109S	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	468	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CCTCCAGGCGTTGAGGAGGCC	0.607			T	IGH@	MLCLS								T|||	20	0.00399361	0.0151	0.0	5008	,	,		21331	0.0		0.0	False		,,,				2504	0.0				p.N468S		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.A1403G						PASS	.	T	SER/ASN	48,4354	49.6+/-84.7	0,48,2153	67.0	53.0	57.0		1403	5.2	0.9	11	dbSNP_129	57	0,8592		0,0,4296	yes	missense	PCSK7	NM_004716.2	46	0,48,6449	CC,CT,TT		0.0,1.0904,0.3694	benign	468/786	117089801	48,12946	2201	4296	6497	SO:0001583	missense	9159	exon11			CAGGCGTTGAGGA	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.1403A>G	11.37:g.117089801T>C	ENSP00000325917:p.Asn468Ser	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	41	29	0.707317	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	37	CCDS8382.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	13.08	2.129420	0.37630	0.010904	0.0	ENSG00000160613	ENST00000320934;ENST00000540028;ENST00000543900	D;D	0.83163	-1.69;-1.69	5.2	5.2	0.72013	Peptidase S8/S53, subtilisin/kexin/sedolisin (2);	0.050433	0.85682	D	0.000000	T	0.65688	0.2715	L	0.43923	1.385	0.52501	D	0.999951	B	0.18013	0.025	B	0.17722	0.019	T	0.71583	-0.4549	10	0.59425	D	0.04	-22.611	13.9011	0.63804	0.0:0.0:0.0:1.0	.	468	Q16549	PCSK7_HUMAN	S	468;109;468	ENSP00000325917:N468S;ENSP00000441944:N109S	ENSP00000325917:N468S	N	-	2	0	PCSK7	116595011	0.999000	0.42202	0.924000	0.36721	0.523000	0.34469	3.028000	0.49705	1.977000	0.57605	0.482000	0.46254	AAC	T|0.996;C|0.004	0.004	strong		0.607	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
CMTR2	55783	hgsc.bcm.edu	37	16	71317567	71317567	+	Missense_Mutation	SNP	A	A	G	rs16970857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71317567A>G	ENST00000338099.5	-	3	2593	c.2257T>C	c.(2257-2259)Ttc>Ctc	p.F753L	CMTR2_ENST00000434935.2_Missense_Mutation_p.F753L			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	753			F -> L (in dbSNP:rs16970857).		7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										TGAATAATGAAATGCAAATGC	0.368													A|||	159	0.0317492	0.1165	0.0072	5008	,	,		19301	0.0		0.0	False		,,,				2504	0.0				p.F753L		Atlas-SNP	.											.	FTSJD1	70	.	0			c.T2257C						PASS	.	A	LEU/PHE,LEU/PHE	481,3915	216.8+/-235.3	32,417,1749	41.0	44.0	43.0		2257,2257	3.6	1.0	16	dbSNP_123	43	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	FTSJD1	NM_001099642.1,NM_018348.5	22,22	32,420,6046	GG,GA,AA		0.0349,10.9418,3.7242	benign,benign	753/771,753/771	71317567	484,12512	2198	4300	6498	SO:0001583	missense	55783	exon3			TAATGAAATGCAA	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.2257T>C	16.37:g.71317567A>G	ENSP00000337512:p.Phe753Leu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	180	88	0.488889	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	A	4.716	0.133141	0.09032	0.109418	3.49E-4	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.09445	2.98;2.98	5.8	3.58	0.41010	.	0.463445	0.21366	N	0.075705	T	0.00073	0.0002	N	0.01168	-0.975	0.21499	N	0.99967	B	0.02656	0.0	B	0.01281	0.0	T	0.45600	-0.9250	10	0.02654	T	1	-21.5732	6.5334	0.22339	0.7212:0.147:0.1318:0.0	rs16970857;rs52837568;rs16970857	753	Q8IYT2	FTSJ1_HUMAN	L	753	ENSP00000337512:F753L;ENSP00000411148:F753L	ENSP00000337512:F753L	F	-	1	0	FTSJD1	69875068	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	0.876000	0.28092	1.020000	0.39573	0.477000	0.44152	TTC	A|0.964;G|0.036	0.036	strong		0.368	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
KIF20A	10112	hgsc.bcm.edu	37	5	137520025	137520025	+	Missense_Mutation	SNP	G	G	A	rs142495138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:137520025G>A	ENST00000394894.3	+	12	1676	c.1450G>A	c.(1450-1452)Gtg>Atg	p.V484M	KIF20A_ENST00000508792.1_Missense_Mutation_p.V466M	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	484	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule bundle formation (GO:0001578)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|liver(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(1)	27			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GATTGTCAATGTGAATCCCTG	0.512																																					p.V484M		Atlas-SNP	.											.	KIF20A	53	.	0			c.G1450A						PASS	.	G	MET/VAL	4,4402	8.1+/-20.4	0,4,2199	170.0	163.0	165.0		1450	3.7	1.0	5	dbSNP_134	165	0,8600		0,0,4300	no	missense	KIF20A	NM_005733.2	21	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	probably-damaging	484/891	137520025	4,13002	2203	4300	6503	SO:0001583	missense	10112	exon12			GTCAATGTGAATC	AF070672	CCDS4199.1	5q31	2008-02-05	2003-01-13	2003-01-17	ENSG00000112984	ENSG00000112984		"""Kinesins"""	9787	protein-coding gene	gene with protein product		605664	"""RAB6 interacting, kinesin-like (rabkinesin6)"""	RAB6KIFL		11416179, 10806357	Standard	NM_005733		Approved		uc003lcj.3	O95235	OTTHUMG00000129195	ENST00000394894.3:c.1450G>A	5.37:g.137520025G>A	ENSP00000378356:p.Val484Met	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	208	107	0.514423	NM_005733	B4DL79|D3DQB6	Missense_Mutation	SNP	ENST00000394894.3	37	CCDS4199.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.921838	0.33908	9.08E-4	0.0	ENSG00000112984	ENST00000394894;ENST00000508792	T;T	0.55930	0.49;0.49	5.49	3.72	0.42706	Kinesin, motor domain (3);	0.175916	0.27164	N	0.020639	T	0.46268	0.1384	L	0.50919	1.6	0.40300	D	0.978593	B;B	0.25272	0.122;0.036	B;B	0.32149	0.141;0.051	T	0.47341	-0.9125	10	0.72032	D	0.01	-5.3957	6.3677	0.21463	0.3825:0.0:0.6175:0.0	.	466;484	B4DL79;O95235	.;KI20A_HUMAN	M	484;466	ENSP00000378356:V484M;ENSP00000420880:V466M	ENSP00000378356:V484M	V	+	1	0	KIF20A	137547924	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	3.399000	0.52586	0.874000	0.35823	0.643000	0.83706	GTG	G|1.000;A|0.000	0.000	strong		0.512	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733	
SLC2A2	6514	hgsc.bcm.edu	37	3	170724955	170724955	+	Silent	SNP	C	C	T	rs5404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:170724955C>T	ENST00000314251.3	-	5	673	c.594G>A	c.(592-594)acG>acA	p.T198T	SLC2A2_ENST00000382808.4_Silent_p.T79T	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	198					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TAAGAATGCCCGTGACGATGG	0.488													C|||	759	0.151558	0.3086	0.1254	5008	,	,		19830	0.0159		0.1103	False		,,,				2504	0.1401				p.T198T		Atlas-SNP	.											.	SLC2A2	71	.	0			c.G594A	GRCh37	CM052367	SLC2A2	M	rs5404	PASS	.	C		1242,3164	426.6+/-341.2	174,894,1135	104.0	93.0	97.0		594	-11.5	0.0	3	dbSNP_52	97	874,7726	196.8+/-241.6	42,790,3468	no	coding-synonymous	SLC2A2	NM_000340.1		216,1684,4603	TT,TC,CC		10.1628,28.1888,16.2694		198/525	170724955	2116,10890	2203	4300	6503	SO:0001819	synonymous_variant	6514	exon5			AATGCCCGTGACG	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.594G>A	3.37:g.170724955C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	132	55	0.416667	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	37	CCDS3215.1																																																																																			C|0.847;T|0.153	0.153	strong		0.488	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
OR8U1	219417	hgsc.bcm.edu	37	11	56143952	56143952	+	Silent	SNP	T	T	C	rs78408319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56143952T>C	ENST00000302270.1	+	1	853	c.853T>C	c.(853-855)Ttg>Ctg	p.L285L		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	285						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)					CATTCCCATGTTGAATCCCTT	0.388													T|||	237	0.0473243	0.1664	0.0231	5008	,	,		18826	0.0		0.001	False		,,,				2504	0.0				p.L285L		Atlas-SNP	.											.	OR8U1	59	.	0			c.T853C						PASS	.	T		535,3441		39,457,1492	139.0	144.0	142.0		853	-11.4	0.2	11	dbSNP_132	142	8,8396		0,8,4194	no	coding-synonymous	OR8U1	NM_001005204.1		39,465,5686	CC,CT,TT		0.0952,13.4557,4.3861		285/310	56143952	543,11837	1988	4202	6190	SO:0001819	synonymous_variant	219417	exon1			CCCATGTTGAATC	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.853T>C	11.37:g.56143952T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_001005204		Silent	SNP	ENST00000302270.1	37	CCDS41647.1																																																																																			T|0.973;C|0.027	0.027	strong		0.388	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
OR7C1	26664	hgsc.bcm.edu	37	19	14910900	14910900	+	Missense_Mutation	SNP	A	A	T	rs149561973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14910900A>T	ENST00000248073.2	-	1	123	c.49T>A	c.(49-51)Ttt>Att	p.F17I	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	17					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						GTTGCTGAAAATCCCAGGAGG	0.438													.|||	27	0.00539137	0.0204	0.0	5008	,	,		18932	0.0		0.0	False		,,,				2504	0.0				p.F17I		Atlas-SNP	.											.	OR7C1	58	.	0			c.T49A						PASS	.	A	ILE/PHE	29,4371		0,29,2171	94.0	90.0	91.0		49	2.6	0.9	19	dbSNP_134	91	0,8592		0,0,4296	yes	missense	OR7C1	NM_198944.1	21	0,29,6467	TT,TA,AA		0.0,0.6591,0.2232	possibly-damaging	17/321	14910900	29,12963	2200	4296	6496	SO:0001583	missense	26664	exon1			CTGAAAATCCCAG	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.49T>A	19.37:g.14910900A>T	ENSP00000248073:p.Phe17Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_198944	Q15621|Q6IFP2|Q96R94	Missense_Mutation	SNP	ENST00000248073.2	37	CCDS12317.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	a	13.45	2.240147	0.39598	0.006591	0.0	ENSG00000127530	ENST00000248073	T	0.06608	3.28	3.67	2.6	0.31112	.	0.214512	0.23239	U	0.050361	T	0.01870	0.0059	L	0.50919	1.6	0.24836	N	0.992496	P	0.41748	0.761	B	0.37267	0.245	T	0.28170	-1.0052	10	0.54805	T	0.06	.	7.5523	0.27804	0.8084:0.0:0.0:0.1915	.	17	O76099	OR7C1_HUMAN	I	17	ENSP00000248073:F17I	ENSP00000248073:F17I	F	-	1	0	OR7C1	14771900	0.001000	0.12720	0.913000	0.36048	0.090000	0.18270	-0.216000	0.09266	0.552000	0.29026	0.433000	0.28618	TTT	A|0.994;T|0.006	0.006	strong		0.438	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1		
ZMYM6	9204	hgsc.bcm.edu	37	1	35454115	35454115	+	Silent	SNP	A	A	G	rs61745582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35454115A>G	ENST00000357182.4	-	16	2795	c.2568T>C	c.(2566-2568)taT>taC	p.Y856Y	ZMYM6_ENST00000487874.1_Intron|ZMYM6_ENST00000373340.2_Intron|ZMYM6_ENST00000493328.1_5'UTR	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	856					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				tttctactaaatatggtttaa	0.338													A|||	214	0.0427316	0.1513	0.0187	5008	,	,		17989	0.0		0.001	False		,,,				2504	0.0				p.Y856Y		Atlas-SNP	.											.	ZMYM6	110	.	0			c.T2568C						PASS	.	A		249,2077		15,219,929	17.0	16.0	16.0		2568	2.4	1.0	1	dbSNP_129	16	5,5061		0,5,2528	no	coding-synonymous	ZMYM6	NM_007167.3		15,224,3457	GG,GA,AA		0.0987,10.7051,3.4361		856/1326	35454115	254,7138	1163	2533	3696	SO:0001819	synonymous_variant	9204	exon16			TACTAAATATGGT	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"""Zinc fingers, MYM type"", ""Zinc fingers, BED-type"""	13050	protein-coding gene	gene with protein product	"""zinc finger, BED-type containing 7"""	613567	"""zinc finger protein 258"", ""zinc finger, MYM-type containing 6"""	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.2568T>C	1.37:g.35454115A>G		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	229	112	0.489083	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Silent	SNP	ENST00000357182.4	37	CCDS387.2																																																																																			A|0.962;G|0.038	0.038	strong		0.338	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167	
LPA	4018	hgsc.bcm.edu	37	6	161007538	161007538	+	Missense_Mutation	SNP	G	G	C	rs7765803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:161007538G>C	ENST00000316300.5	-	25	4116	c.4072C>G	c.(4072-4074)Ctc>Gtc	p.L1358V	LPA_ENST00000447678.1_Missense_Mutation_p.L1358V			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3866	Kringle 12. {ECO:0000255|PROSITE- ProRule:PRU00121}.				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)	GTTGTGAGGAGAGTTGATTCC	0.517													C|||	2049	0.409145	0.5772	0.268	5008	,	,		19647	0.4107		0.3648	False		,,,				2504	0.3262				p.L1358V		Atlas-SNP	.											.	LPA	237	.	0			c.C4072G						PASS	.	C	VAL/LEU	2242,1964		617,1008,478	137.0	137.0	137.0		4072	-2.6	0.0	6	dbSNP_116	137	2935,5587		530,1875,1856	yes	missense	LPA	NM_005577.2	32	1147,2883,2334	CC,CG,GG		34.4403,46.6952,40.6741	benign	1358/2041	161007538	5177,7551	2103	4261	6364	SO:0001583	missense	4018	exon26			TGAGGAGAGTTGA	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.4072C>G	6.37:g.161007538G>C	ENSP00000321334:p.Leu1358Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	174	96	0.551724	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	931	0.42628205128205127	303	0.6158536585365854	99	0.27348066298342544	240	0.4195804195804196	289	0.3812664907651715	c	0.004	-2.377643	0.00207	0.533048	0.344403	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.61980	0.06;0.06	2.04	-2.6	0.06190	Kringle (1);Kringle-like fold (1);	.	.	.	.	T	0.04092	0.0114	N	0.00138	-2.015	0.80722	P	0.0	B	0.26483	0.15	B	0.17722	0.019	T	0.17684	-1.0361	8	0.02654	T	1	.	6.4809	0.22063	0.1895:0.2458:0.5647:0.0	rs7765803;rs7765803	3866	P08519	APOA_HUMAN	V	1358	ENSP00000321334:L1358V;ENSP00000395608:L1358V	ENSP00000321334:L1358V	L	-	1	0	LPA	160927528	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.546000	0.02188	-0.794000	0.04468	-0.980000	0.02579	CTC	G|0.569;C|0.431	0.431	strong		0.517	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
MC3R	4159	hgsc.bcm.edu	37	20	54824029	54824029	+	Missense_Mutation	SNP	G	G	A	rs3827103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	81	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	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		
DENND2A	27147	hgsc.bcm.edu	37	7	140227293	140227293	+	Missense_Mutation	SNP	A	A	G	rs6464833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140227293A>G	ENST00000275884.6	-	14	2747	c.2330T>C	c.(2329-2331)aTc>aCc	p.I777T	DENND2A_ENST00000496613.1_Missense_Mutation_p.I777T|DENND2A_ENST00000537639.1_Missense_Mutation_p.I777T			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	777	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.		I -> T (in dbSNP:rs6464833).		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)					CTTGGACAGGATGCTGCAGCC	0.647													G|||	849	0.169529	0.4682	0.0778	5008	,	,		15675	0.0069		0.0785	False		,,,				2504	0.092				p.I777T		Atlas-SNP	.											.	DENND2A	132	.	0			c.T2330C						PASS	.	G	THR/ILE	1537,2653		298,941,856	13.0	19.0	17.0		2330	4.8	1.0	7	dbSNP_116	17	698,7764		36,626,3569	yes	missense	DENND2A	NM_015689.3	89	334,1567,4425	GG,GA,AA		8.2486,36.6826,17.6652	benign	777/1010	140227293	2235,10417	2095	4231	6326	SO:0001583	missense	27147	exon13			GACAGGATGCTGC	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.2330T>C	7.37:g.140227293A>G	ENSP00000275884:p.Ile777Thr	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Missense_Mutation	SNP	ENST00000275884.6	37	CCDS43659.1	317	0.14514652014652016	226	0.45934959349593496	29	0.08011049723756906	2	0.0034965034965034965	60	0.079155672823219	G	8.282	0.815778	0.16607	0.366826	0.082486	ENSG00000146966	ENST00000275884;ENST00000537639;ENST00000496613	T;T;T	0.10860	2.83;2.83;2.83	4.83	4.83	0.62350	DENN (3);	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00368	-1.59	0.39604	P	0.030217999999999967	B	0.02656	0.0	B	0.01281	0.0	T	0.46076	-0.9217	9	0.02654	T	1	-13.0039	13.2808	0.60212	0.0769:0.0:0.9231:0.0	rs6464833;rs10355571;rs56455864;rs60863036;rs6464833	777	Q9ULE3	DEN2A_HUMAN	T	777	ENSP00000275884:I777T;ENSP00000442245:I777T;ENSP00000419654:I777T	ENSP00000275884:I777T	I	-	2	0	DENND2A	139873762	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.300000	0.78841	1.035000	0.39972	-0.215000	0.12644	ATC	A|0.830;G|0.170	0.170	strong		0.647	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
CCDC107	203260	hgsc.bcm.edu	37	9	35661057	35661057	+	Missense_Mutation	SNP	C	C	G	rs10441685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35661057C>G	ENST00000426546.2	+	5	791	c.725C>G	c.(724-726)tCc>tGc	p.S242C	CCDC107_ENST00000378406.1_3'UTR|CCDC107_ENST00000421582.2_3'UTR|ARHGEF39_ENST00000490970.1_5'Flank|ARHGEF39_ENST00000378387.3_3'UTR|CCDC107_ENST00000378407.3_3'UTR|ARHGEF39_ENST00000378395.2_3'UTR|ARHGEF39_ENST00000343259.3_3'UTR|CCDC107_ENST00000378409.3_Missense_Mutation_p.S215C|CCDC107_ENST00000327351.2_3'UTR	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	242			S -> C (in dbSNP:rs10441685).			integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CTAGCTACTTCCTGGGAGGTG	0.597													C|||	358	0.0714856	0.1982	0.0216	5008	,	,		19531	0.0139		0.0338	False		,,,				2504	0.0337				p.S242C		Atlas-SNP	.											.	CCDC107	12	.	0			c.C725G						PASS	.	C	CYS/SER,,,,CYS/SER	698,3708	290.4+/-280.9	47,604,1552	72.0	71.0	71.0		644,,,,725	4.4	0.0	9	dbSNP_119	71	229,8371	93.1+/-155.1	2,225,4073	no	missense,utr-3,utr-3,utr-3,missense	C9orf100,CCDC107	NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2,NM_174923.2	112,,,,112	49,829,5625	GG,GC,CC		2.6628,15.842,7.1275	possibly-damaging,,,,possibly-damaging	215/257,,,,242/284	35661057	927,12079	2203	4300	6503	SO:0001583	missense	203260	exon5			CTACTTCCTGGGA	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.725C>G	9.37:g.35661057C>G	ENSP00000414964:p.Ser242Cys	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Missense_Mutation	SNP	ENST00000426546.2	37	CCDS6583.1	145	0.06639194139194139	99	0.20121951219512196	10	0.027624309392265192	9	0.015734265734265736	27	0.03562005277044855	C	10.84	1.464832	0.26335	0.15842	0.026628	ENSG00000159884	ENST00000426546;ENST00000378409	T;T	0.39592	1.48;1.07	5.34	4.44	0.53790	.	0.688813	0.13667	N	0.371165	T	0.00039	0.0001	L	0.34521	1.04	0.40203	P	0.022464999999999957	D;D	0.61697	0.99;0.99	P;P	0.53549	0.729;0.729	T	0.06058	-1.0848	9	0.48119	T	0.1	-0.1448	9.9115	0.41408	0.0:0.9082:0.0:0.0918	rs10441685	215;242	F8W8S5;Q8WV48	.;CC107_HUMAN	C	242;215	ENSP00000414964:S242C;ENSP00000367665:S215C	ENSP00000367665:S215C	S	+	2	0	CCDC107	35651057	0.014000	0.17966	0.007000	0.13788	0.048000	0.14542	1.958000	0.40402	1.487000	0.48415	0.655000	0.94253	TCC	C|0.929;G|0.071	0.071	strong		0.597	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923	
E2F4	1874	hgsc.bcm.edu	37	16	67235672	67235672	+	IGR	SNP	C	C	T	rs33948247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67235672C>T	ENST00000379378.3	+	0	2096				ELMO3_ENST00000477898.1_Missense_Mutation_p.R203C|ELMO3_ENST00000360833.1_Missense_Mutation_p.R352C|ELMO3_ENST00000393997.2_Missense_Mutation_p.R369C|MIR328_ENST00000385213.1_RNA	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding						blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		GCAGGTCCTACGCCAGGCTGC	0.637													C|||	104	0.0207668	0.0106	0.0288	5008	,	,		15790	0.0		0.0616	False		,,,				2504	0.0082				p.R369C		Atlas-SNP	.											.	ELMO3	41	.	0			c.C1105T						PASS	.	C	CYS/ARG	71,4085		0,71,2007	33.0	41.0	39.0		1105	5.6	1.0	16	dbSNP_126	39	472,7948		13,446,3751	yes	missense	ELMO3	NM_024712.3	180	13,517,5758	TT,TC,CC		5.6057,1.7084,4.3177	probably-damaging	369/774	67235672	543,12033	2078	4210	6288	SO:0001628	intergenic_variant	79767	exon11			GTCCTACGCCAGG	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975		16.37:g.67235672C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_024712	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	37	CCDS32464.1	69	0.03159340659340659	3	0.006097560975609756	16	0.04419889502762431	0	0.0	50	0.06596306068601583	C	33	5.223713	0.95139	0.017084	0.056057	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.30981	1.51;1.51	5.55	5.55	0.83447	Engulfment/cell motility, ELMO (2);	0.000000	0.85682	D	0.000000	T	0.10035	0.0246	M	0.79123	2.44	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.30001	-0.9993	10	0.87932	D	0	-19.9951	18.0933	0.89480	0.0:1.0:0.0:0.0	rs33948247	316;352;369	Q96BJ8;F8W9E7;Q96BJ8-3	ELMO3_HUMAN;.;.	C	352;369	ENSP00000354077:R352C;ENSP00000377566:R369C	ENSP00000354077:R352C	R	+	1	0	ELMO3	65793173	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	5.768000	0.68858	2.630000	0.89119	0.561000	0.74099	CGC	C|0.960;T|0.040	0.040	strong		0.637	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
CEP131	22994	hgsc.bcm.edu	37	17	79182778	79182778	+	Silent	SNP	T	T	C	rs62075318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79182778T>C	ENST00000269392.4	-	3	469	c.222A>G	c.(220-222)agA>agG	p.R74R	AZI1_ENST00000450824.2_Silent_p.R74R|AZI1_ENST00000575907.1_Silent_p.R74R|AZI1_ENST00000374782.3_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	134	0	0		WXS	Illumina HiSeq	Phase_I	145	83	0.572414	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		
SQSTM1	8878	hgsc.bcm.edu	37	5	179260661	179260661	+	Silent	SNP	G	G	A	rs10058037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179260661G>A	ENST00000389805.4	+	7	1222	c.1044G>A	c.(1042-1044)ccG>ccA	p.P348P	SQSTM1_ENST00000376929.3_Silent_p.P264P|SQSTM1_ENST00000360718.5_Silent_p.P264P|SQSTM1_ENST00000402874.3_Silent_p.P264P|SQSTM1_ENST00000510187.1_Intron	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	348	Interaction with NTRK1. {ECO:0000250}.				apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cell differentiation (GO:0030154)|endosomal transport (GO:0016197)|immune system process (GO:0002376)|intracellular signal transduction (GO:0035556)|macroautophagy (GO:0016236)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein heterooligomerization (GO:0051291)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of Ras protein signal transduction (GO:0046578)|response to stress (GO:0006950)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|lysosome (GO:0005764)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)		SQSTM1/ALK(2)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(5)|ovary(1)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGTGGACCCGTCTACAGGTG	0.542													G|||	165	0.0329473	0.118	0.0086	5008	,	,		19610	0.001		0.001	False		,,,				2504	0.001				p.P348P		Atlas-SNP	.											SQSTM1,NS,carcinoma,+1,1	SQSTM1	30	1	0			c.G1044A						PASS	.	G	,,	415,3991	205.8+/-227.6	17,381,1805	93.0	87.0	89.0		792,792,1044	-10.5	0.0	5	dbSNP_119	89	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	SQSTM1	NM_001142298.1,NM_001142299.1,NM_003900.4	,,	17,383,6103	AA,AG,GG		0.0233,9.419,3.2062	,,	264/357,264/357,348/441	179260661	417,12589	2203	4300	6503	SO:0001819	synonymous_variant	8878	exon7			GGACCCGTCTACA	U46751	CCDS34317.1, CCDS47355.1	5q35	2008-02-05	2004-04-15		ENSG00000161011	ENSG00000161011			11280	protein-coding gene	gene with protein product		601530	"""Paget disease of bone 3"", ""oxidative stress induced like"""	PDB3, OSIL		8650207, 8551575	Standard	NM_003900		Approved	p62, p60, p62B, A170	uc003mkw.4	Q13501	OTTHUMG00000150643	ENST00000389805.4:c.1044G>A	5.37:g.179260661G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_003900	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	Silent	SNP	ENST00000389805.4	37	CCDS34317.1																																																																																			G|0.960;A|0.040	0.040	strong		0.542	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1		
CRYBA1	1411	hgsc.bcm.edu	37	17	27580756	27580756	+	Silent	SNP	C	C	T	rs1047790	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27580756C>T	ENST00000225387.3	+	5	457	c.456C>T	c.(454-456)ggC>ggT	p.G152G		NM_005208.4	NP_005199.2	P05813	CRBA1_HUMAN	crystallin, beta A1	152	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|large_intestine(2)|lung(1)|prostate(1)	5			BRCA - Breast invasive adenocarcinoma(11;3.3e-05)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			AAGCCATGGGCTGGTTCAACA	0.453													T|||	1456	0.290735	0.3578	0.1916	5008	,	,		17909	0.3244		0.173	False		,,,				2504	0.3569				p.G152G		Atlas-SNP	.											.	CRYBA1	15	.	0			c.C456T						PASS	.	T		1462,2944	680.2+/-403.8	236,990,977	83.0	82.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	456	-4.9	0.8	17	dbSNP_86	82	1403,7197	753.3+/-407.4	104,1195,3001	no	coding-synonymous	CRYBA1	NM_005208.4		340,2185,3978	TT,TC,CC		16.314,33.182,22.0283		152/216	27580756	2865,10141	2203	4300	6503	SO:0001819	synonymous_variant	1411	exon5			CATGGGCTGGTTC		CCDS11249.1	17q11.2-q12	2008-07-18			ENSG00000108255	ENSG00000108255			2394	protein-coding gene	gene with protein product	"""eye lens structural protein"""	123610		CRYB1		3745196, 3770741	Standard	NM_005208		Approved		uc002hdw.3	P05813	OTTHUMG00000132729	ENST00000225387.3:c.456C>T	17.37:g.27580756C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_005208	Q13633|Q14CM9	Silent	SNP	ENST00000225387.3	37	CCDS11249.1																																																																																			C|0.756;T|0.244	0.244	strong		0.453	CRYBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256071.2	NM_005208	
YARS2	51067	hgsc.bcm.edu	37	12	32908237	32908237	+	Missense_Mutation	SNP	C	C	A	rs11539445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:32908237C>A	ENST00000324868.8	-	1	599	c.572G>T	c.(571-573)gGt>gTt	p.G191V		NM_001040436.2	NP_001035526.1	Q9Y2Z4	SYYM_HUMAN	tyrosyl-tRNA synthetase 2, mitochondrial	191			G -> V (in dbSNP:rs11539445). {ECO:0000269|PubMed:10810093}.		gene expression (GO:0010467)|mitochondrial tyrosyl-tRNA aminoacylation (GO:0070184)|translation (GO:0006412)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)|tyrosine binding (GO:0072545)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	16	Lung NSC(5;2.43e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)				L-Tyrosine(DB00135)	GCGGAAGTGACCCCCCACTGC	0.637											OREG0021729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	634	0.126597	0.177	0.0937	5008	,	,		16266	0.0833		0.162	False		,,,				2504	0.09				p.G191V		Atlas-SNP	.											.	YARS2	33	.	0			c.G572T						PASS	.	C	VAL/GLY	714,3692	279.9+/-275.1	54,606,1543	51.0	56.0	55.0		572	4.2	1.0	12	dbSNP_120	55	1231,7369	238.8+/-270.1	104,1023,3173	yes	missense	YARS2	NM_001040436.2	109	158,1629,4716	AA,AC,CC		14.314,16.2052,14.9546	probably-damaging	191/478	32908237	1945,11061	2203	4300	6503	SO:0001583	missense	51067	exon1			AAGTGACCCCCCA	AF132939	CCDS31770.1	12p11.21	2014-03-19	2007-02-23		ENSG00000139131	ENSG00000139131	6.1.1.1	"""Aminoacyl tRNA synthetases / Class I"""	24249	protein-coding gene	gene with protein product	"""tyrosine tRNA ligase 2, mitochondrial"""	610957				15779907, 15840810	Standard	NM_001040436		Approved	FLJ13995, CGI-04, mt-TyrRS	uc001rli.3	Q9Y2Z4	OTTHUMG00000169454	ENST00000324868.8:c.572G>T	12.37:g.32908237C>A	ENSP00000320658:p.Gly191Val	Somatic	82	0	0	836	WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_001040436	D3DUW8|Q9H817	Missense_Mutation	SNP	ENST00000324868.8	37	CCDS31770.1	279	0.12774725274725274	86	0.17479674796747968	33	0.09116022099447514	41	0.07167832167832168	119	0.15699208443271767	C	15.93	2.978490	0.53720	0.162052	0.14314	ENSG00000139131	ENST00000324868	T	0.51071	0.72	5.09	4.2	0.49525	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.058780	0.64402	D	0.000001	T	0.00073	0.0002	N	0.04203	-0.255	0.09310	P	0.9999999854493	P	0.38078	0.617	B	0.34722	0.188	T	0.09422	-1.0675	9	0.72032	D	0.01	-16.2261	11.5881	0.50931	0.1398:0.7255:0.1347:0.0	rs11539445;rs60431927	191	Q9Y2Z4	SYYM_HUMAN	V	191	ENSP00000320658:G191V	ENSP00000320658:G191V	G	-	2	0	YARS2	32799504	0.221000	0.23642	0.999000	0.59377	0.947000	0.59692	4.211000	0.58507	1.384000	0.46424	0.644000	0.83932	GGT	C|0.856;A|0.144	0.144	strong		0.637	YARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404153.1	NM_015936	
PABPC1	26986	hgsc.bcm.edu	37	8	101721817	101721817	+	Missense_Mutation	SNP	T	T	C	rs201076736		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721817T>C	ENST00000318607.5	-	8	2243	c.1115A>G	c.(1114-1116)gAa>gGa	p.E372G	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519004.1_Missense_Mutation_p.E327G|PABPC1_ENST00000522387.1_Missense_Mutation_p.E340G|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	372					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			CTGGCGCTCTTCTTTGCGCTG	0.493																																					p.E372G		Atlas-SNP	.											.	PABPC1	76	.	0			c.A1115G						PASS	.						138.0	118.0	125.0					8																	101721817		2203	4300	6503	SO:0001583	missense	26986	exon8			CGCTCTTCTTTGC	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.1115A>G	8.37:g.101721817T>C	ENSP00000313007:p.Glu372Gly	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	345	126	0.365217	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.6|27.6	4.844761|4.844761	0.91197|0.91197	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387|ENST00000519100	T;T;T|.	0.06068|.	3.35;3.35;3.35|.	5.05|5.05	5.05|5.05	0.67936|0.67936	Nucleotide-binding, alpha-beta plait (1);|.	0.000000|.	0.64402|.	D|.	0.000005|.	T|T	0.80380|0.80380	0.4612|0.4612	M|M	0.88450|0.88450	2.955|2.955	0.80722|0.80722	D|D	1|1	D;D;D|.	0.76494|.	0.998;0.977;0.999|.	D;P;D|.	0.79784|.	0.963;0.822;0.993|.	D|D	0.84036|0.84036	0.0362|0.0362	10|5	0.87932|.	D|.	0|.	.|.	15.0956|15.0956	0.72232|0.72232	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	340;372;372|.	E7ERJ7;B3KT93;P11940|.	.;.;PABP1_HUMAN|.	G|E	372;372;327;340|241	ENSP00000313007:E372G;ENSP00000429594:E327G;ENSP00000429395:E340G|.	ENSP00000313007:E372G|.	E|K	-|-	2|1	0|0	PABPC1|PABPC1	101790993|101790993	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.968000|7.968000	0.87980|0.87980	2.028000|2.028000	0.59812|0.59812	0.459000|0.459000	0.35465|0.35465	GAA|AAG	.	.	weak		0.493	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
Unknown	0	hgsc.bcm.edu	37	11	124095916	124095916	+	IGR	SNP	C	C	T	rs11825213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124095916C>T								OR10D3 (38964 upstream) : OR8G1 (24506 downstream)																							CAATTCACACCGGCTTTATGT	0.453													c|||	364	0.0726837	0.1921	0.062	5008	,	,		22953	0.0377		0.002	False		,,,				2504	0.0276				p.T173T		Atlas-SNP	.											.	.	.	.	0			c.C519T						PASS	.	C		693,3405		52,589,1408	284.0	294.0	291.0		519	-5.5	0.0	11	dbSNP_120	291	8,8480		0,8,4236	no	coding-synonymous	OR8G2	NM_001007249.1		52,597,5644	TT,TC,CC		0.0943,16.9107,5.5697		173/305	124095916	701,11885	2049	4244	6293	SO:0001628	intergenic_variant	26492	exon1			TCACACCGGCTTT																													11.37:g.124095916C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	167	66	0.39521	NM_001007249		Silent	SNP		37																																																																																				C|0.927;T|0.073	0.073	strong	0	0.453								
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186052	39186052	+	Silent	SNP	G	G	A	rs150955506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39186052G>A	ENST00000377747.4	-	1	304	c.279C>T	c.(277-279)gcC>gcT	p.A93A	KRTAP1-5_ENST00000361883.5_5'Flank	NM_001257305.1	NP_001244234.1	P0C5Y4	KRA14_HUMAN	keratin associated protein 1-4	93						keratin filament (GO:0045095)				lung(1)	1						AGGAGGCCTCGGCGTGGTGCA	0.667													g|||	535	0.106829	0.1891	0.1167	5008	,	,		18492	0.1627		0.0159	False		,,,				2504	0.0245				p.A93A		Atlas-SNP	.											.	KRTAP1-4	4	.	0			c.C279T						PASS	.																																			SO:0001819	synonymous_variant	728255	exon1			GGCCTCGGCGTGG	AC007455	CCDS58548.1	17q21.2	2010-06-22			ENSG00000204887	ENSG00000204887		"""Keratin associated proteins"""	18904	protein-coding gene	gene with protein product		608821					Standard	NM_001257305		Approved	KAP1.4	uc031raf.1	P0C5Y4	OTTHUMG00000133631	ENST00000377747.4:c.279C>T	17.37:g.39186052G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	163	85	0.521472	NM_001257305	A6NJ92	Silent	SNP	ENST00000377747.4	37	CCDS58548.1																																																																																			G|0.888;A|0.112	0.112	strong		0.667	KRTAP1-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257776.3		
TMEM132C	92293	hgsc.bcm.edu	37	12	129189850	129189850	+	Silent	SNP	C	C	T	rs7959567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:129189850C>T	ENST00000435159.2	+	9	2337	c.2337C>T	c.(2335-2337)tgC>tgT	p.C779C	TMEM132C_ENST00000315208.8_Silent_p.C395C|TMEM132C_ENST00000537538.1_Silent_p.C164C	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	779						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						CCGAGGCCTGCCAGAAATCTA	0.647													C|||	362	0.0722843	0.1853	0.0749	5008	,	,		18772	0.0		0.0497	False		,,,				2504	0.0153				p.C779C		Atlas-SNP	.											.	TMEM132C	142	.	0			c.C2337T						PASS	.	C		228,1156		19,190,483	20.0	26.0	24.0		2337	3.2	1.0	12	dbSNP_116	24	163,3019		2,159,1430	no	coding-synonymous	TMEM132C	NM_001136103.2		21,349,1913	TT,TC,CC		5.1226,16.474,8.5633		779/1109	129189850	391,4175	692	1591	2283	SO:0001819	synonymous_variant	92293	exon9			GGCCTGCCAGAAA	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.2337C>T	12.37:g.129189850C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_001136103	Q69YX8	Silent	SNP	ENST00000435159.2	37																																																																																				C|0.910;T|0.090	0.090	strong		0.647	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
APOBR	55911	hgsc.bcm.edu	37	16	28508447	28508447	+	Silent	SNP	A	A	G	rs40831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:28508447A>G	ENST00000431282.1	+	3	2068	c.2058A>G	c.(2056-2058)gcA>gcG	p.A686A	APOBR_ENST00000328423.5_Silent_p.A686A|CLN3_ENST00000569430.1_5'Flank|APOBR_ENST00000564831.1_Silent_p.A695A|CLN3_ENST00000567160.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	686	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						AGGGAGAGGCATCTGTCTCAG	0.612													G|||	2463	0.491813	0.5605	0.5317	5008	,	,		16515	0.373		0.3678	False		,,,				2504	0.6207				p.A695A		Atlas-SNP	.											.	APOBR	89	.	0			c.A2085G						PASS	.	G		2138,2056		584,970,543	22.0	28.0	26.0		2058	0.4	0.0	16	dbSNP_76	26	3458,4958		747,1964,1497	no	coding-synonymous	APOBR	NM_018690.3		1331,2934,2040	GG,GA,AA		41.0884,49.0224,44.3775		686/1089	28508447	5596,7014	2097	4208	6305	SO:0001819	synonymous_variant	55911	exon2			AGAGGCATCTGTC	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.2058A>G	16.37:g.28508447A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	37																																																																																				A|0.584;G|0.416	0.416	strong		0.612	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
TLN1	7094	hgsc.bcm.edu	37	9	35714269	35714269	+	Silent	SNP	G	G	A	rs35844106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35714269G>A	ENST00000314888.9	-	24	3440	c.3087C>T	c.(3085-3087)acC>acT	p.T1029T	TLN1_ENST00000540444.1_Silent_p.T1029T	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1029					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)			CAGCCAGCGCGGTGCCCAGGT	0.582													G|||	22	0.00439297	0.0166	0.0	5008	,	,		21795	0.0		0.0	False		,,,				2504	0.0				p.T1029T		Atlas-SNP	.											.	TLN1	185	.	0			c.C3087T						PASS	.	G		63,4343	58.1+/-94.6	0,63,2140	58.0	55.0	56.0		3087	-11.8	0.0	9	dbSNP_126	56	0,8600		0,0,4300	yes	coding-synonymous	TLN1	NM_006289.3		0,63,6440	AA,AG,GG		0.0,1.4299,0.4844		1029/2542	35714269	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	7094	exon24			CAGCGCGGTGCCC	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.3087C>T	9.37:g.35714269G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																			G|0.995;A|0.005	0.005	strong		0.582	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
MUC4	4585	hgsc.bcm.edu	37	3	195508190	195508190	+	Missense_Mutation	SNP	G	G	C	rs201771865		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508190G>C	ENST00000463781.3	-	2	10720	c.10261C>G	c.(10261-10263)Cac>Gac	p.H3421D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3421D	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)		GGGGTGGCGTGACCTGTGGAT	0.582																																					p.H3421D		Atlas-SNP	.											MUC4_ENST00000463781,NS,haematopoietic_neoplasm,+2,3	MUC4	1505	3	0			c.C10261G						scavenged	.						27.0	21.0	23.0					3																	195508190		689	1579	2268	SO:0001583	missense	4585	exon2			TGGCGTGACCTGT	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.10261C>G	3.37:g.195508190G>C	ENSP00000417498:p.His3421Asp	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	265	11	0.0415094	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	4.507	0.094038	0.08632	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.56;1.56	0.894	0.894	0.19242	.	.	.	.	.	T	0.14270	0.0345	N	0.19112	0.55	0.09310	N	1	B	0.30727	0.292	B	0.19391	0.025	T	0.20140	-1.0284	8	.	.	.	.	4.1118	0.10062	0.0:0.0:0.5985:0.4015	.	3293	E7ESK3	.	D	3421	ENSP00000417498:H3421D;ENSP00000420243:H3421D	.	H	-	1	0	MUC4	196992969	0.000000	0.05858	0.014000	0.15608	0.010000	0.07245	-0.114000	0.10757	0.420000	0.25954	0.089000	0.15464	CAC	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SNRPA	6626	hgsc.bcm.edu	37	19	41263403	41263403	+	Silent	SNP	A	A	G	rs2230694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41263403A>G	ENST00000243563.3	+	2	790	c.240A>G	c.(238-240)aaA>aaG	p.K80K	SNRPA_ENST00000599570.1_3'UTR	NM_004596.4	NP_004587.1	P09012	SNRPA_HUMAN	small nuclear ribonucleoprotein polypeptide A	80	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snRNA binding (GO:0017069)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TCTATGACAAACCTATGGTGA	0.547													G|||	930	0.185703	0.4077	0.0778	5008	,	,		19227	0.2073		0.0726	False		,,,				2504	0.0562				p.K80K		Atlas-SNP	.											.	SNRPA	20	.	0			c.A240G						PASS	.	G		1443,2963	682.0+/-404.1	237,969,997	85.0	84.0	84.0		240	2.8	1.0	19	dbSNP_98	84	587,8013	792.9+/-407.5	13,561,3726	no	coding-synonymous	SNRPA	NM_004596.4		250,1530,4723	GG,GA,AA		6.8256,32.7508,15.6082		80/283	41263403	2030,10976	2203	4300	6503	SO:0001819	synonymous_variant	6626	exon2			TGACAAACCTATG	X06347	CCDS12565.1	19q13.1	2013-02-12				ENSG00000077312		"""RNA binding motif (RRM) containing"""	11151	protein-coding gene	gene with protein product		182285				1701111	Standard	NM_004596		Approved	U1A, U1-A, Mud1	uc002ooz.3	P09012		ENST00000243563.3:c.240A>G	19.37:g.41263403A>G		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	168	167	0.994048	NM_004596		Silent	SNP	ENST00000243563.3	37	CCDS12565.1																																																																																			A|0.811;C|0.000;G|0.189;T|0.000	0.189	strong		0.547	SNRPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463118.2	NM_004596	
ARID4B	51742	hgsc.bcm.edu	37	1	235357460	235357460	+	Silent	SNP	A	A	G	rs62000435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235357460A>G	ENST00000264183.3	-	19	2490	c.1993T>C	c.(1993-1995)Ttg>Ctg	p.L665L	ARID4B_ENST00000366603.2_Silent_p.L665L|ARID4B_ENST00000349213.3_Silent_p.L579L	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	665					histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			GGTTTGGACAAGCGCCGAAGT	0.343													A|||	25	0.00499201	0.0174	0.0029	5008	,	,		16650	0.0		0.0	False		,,,				2504	0.0				p.L665L		Atlas-SNP	.											.	ARID4B	142	.	0			c.T1993C						PASS	.	A	,,	112,4294	82.4+/-120.9	1,110,2092	144.0	135.0	138.0		1993,1993,1735	3.9	1.0	1	dbSNP_129	138	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ARID4B	NM_001206794.1,NM_016374.5,NM_031371.3	,,	1,112,6390	GG,GA,AA		0.0233,2.542,0.8765	,,	665/1313,665/1313,579/1227	235357460	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	51742	exon19			TGGACAAGCGCCG	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.1993T>C	1.37:g.235357460A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	191	100	0.52356	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Silent	SNP	ENST00000264183.3	37	CCDS31061.1																																																																																			A|0.992;G|0.008	0.008	strong		0.343	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	
CFLAR	8837	hgsc.bcm.edu	37	2	202025375	202025375	+	Silent	SNP	G	G	A	rs33914895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:202025375G>A	ENST00000309955.3	+	9	1529	c.1014G>A	c.(1012-1014)agG>agA	p.R338R	CFLAR_ENST00000340870.5_Silent_p.R338R|CFLAR_ENST00000457277.1_Silent_p.R338R|CFLAR_ENST00000479953.2_Silent_p.R242R|CFLAR_ENST00000423241.2_Silent_p.R338R|CFLAR_ENST00000341582.6_Silent_p.R303R|CFLAR-AS1_ENST00000415011.2_RNA|CFLAR_ENST00000355558.4_Intron|CFLAR_ENST00000443227.1_Silent_p.R242R	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	338	Caspase.|Interaction with TRAF1 and TRAF2.|Interaction with caspase-3.|Interaction with caspase-8 subunits p18 and p10.|Not proteolytically processed and involved in apoptosis inhibition.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						ACATCAGGAGGATGTTCATGG	0.532													G|||	35	0.00698882	0.0008	0.013	5008	,	,		21739	0.001		0.0229	False		,,,				2504	0.001				p.R338R	Pancreas(16;548 657 22190 32864 42338)	Atlas-SNP	.											.	CFLAR	37	.	0			c.G1014A						PASS	.	G	,,,,,,	25,4381	32.6+/-62.9	1,23,2179	107.0	94.0	98.0		1014,279,909,726,726,726,1014	2.8	1.0	2	dbSNP_126	98	209,8391	88.9+/-151.2	4,201,4095	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CFLAR	NM_001127183.2,NM_001202515.1,NM_001202516.1,NM_001202517.1,NM_001202518.1,NM_001202519.1,NM_003879.5	,,,,,,	5,224,6274	AA,AG,GG		2.4302,0.5674,1.7992	,,,,,,	338/481,93/236,303/446,242/385,242/367,242/367,338/481	202025375	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	8837	exon9			CAGGAGGATGTTC	AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402		"""Endogenous ligands"""	1876	protein-coding gene	gene with protein product		603599		CASP8AP1		9208847, 9217161	Standard	NM_003879		Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000309955.3:c.1014G>A	2.37:g.202025375G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_003879	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	Silent	SNP	ENST00000309955.3	37	CCDS2337.1																																																																																			G|0.985;A|0.015	0.015	strong		0.532	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3	NM_003879	
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138417642	138417642	+	Missense_Mutation	SNP	C	C	T	rs73730479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:138417642C>T	ENST00000310018.2	-	17	2170	c.1888G>A	c.(1888-1890)Gca>Aca	p.A630T	ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.A630T|ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.A630T	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	630					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|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 part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|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)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						TAGAGGGGTGCGTTGGAAGAG	0.373													C|||	210	0.0419329	0.121	0.0245	5008	,	,		16608	0.0268		0.002	False		,,,				2504	0.0041				p.A630T		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.G1888A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	470,3936	220.0+/-237.6	22,426,1755	99.0	96.0	97.0		1888,1888,1888	1.5	0.0	7	dbSNP_130	97	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	58,58,58	22,432,6049	TT,TC,CC		0.0698,10.6673,3.6598	benign,benign,benign	630/841,630/841,630/841	138417642	476,12530	2203	4300	6503	SO:0001583	missense	50617	exon16			GGGGTGCGTTGGA	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"""ATPases / V-type"""	866	protein-coding gene	gene with protein product		605239	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 4"", ""ATPase, H+ transporting, lysosomal V0 subunit A4"""	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1888G>A	7.37:g.138417642C>T	ENSP00000308122:p.Ala630Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_130841	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	37	CCDS5849.1	92	0.04212454212454213	61	0.12398373983739837	9	0.024861878453038673	20	0.03496503496503497	2	0.002638522427440633	C	9.110	1.006311	0.19199	0.106673	6.98E-4	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.85702	-2.02;-2.02;-2.02	5.88	1.49	0.22878	.	0.899723	0.09437	N	0.802370	T	0.02807	0.0084	L	0.37750	1.13	0.09310	N	1	P	0.47350	0.894	B	0.34452	0.183	T	0.01639	-1.1306	10	0.17369	T	0.5	-0.0025	8.1138	0.30930	0.0:0.5837:0.215:0.2013	.	630	Q9HBG4	VPP4_HUMAN	T	630	ENSP00000308122:A630T;ENSP00000376774:A630T;ENSP00000253856:A630T	ENSP00000308122:A630T	A	-	1	0	ATP6V0A4	138068182	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	0.199000	0.17237	0.383000	0.24910	0.655000	0.94253	GCA	C|0.963;T|0.037	0.037	strong		0.373	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632	
MDN1	23195	hgsc.bcm.edu	37	6	90424458	90424458	+	Silent	SNP	C	C	T	rs114422841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90424458C>T	ENST00000369393.3	-	46	6988	c.6873G>A	c.(6871-6873)tcG>tcA	p.S2291S	MDN1_ENST00000428876.1_Silent_p.S2291S			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2291					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CAGGATCCATCGAGAGGAAAA	0.433													C|||	13	0.00259585	0.0083	0.0	5008	,	,		20221	0.0		0.001	False		,,,				2504	0.001				p.S2291S		Atlas-SNP	.											.	MDN1	478	.	0			c.G6873A						PASS	.	C		54,4352	52.3+/-87.9	0,54,2149	67.0	64.0	65.0		6873	-4.0	1.0	6	dbSNP_132	65	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MDN1	NM_014611.1		0,56,6447	TT,TC,CC		0.0233,1.2256,0.4306		2291/5597	90424458	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon46			ATCCATCGAGAGG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.6873G>A	6.37:g.90424458C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			C|0.996;T|0.004	0.004	strong		0.433	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
PCDH15	65217	hgsc.bcm.edu	37	10	55955485	55955485	+	Silent	SNP	A	A	G	rs7921598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:55955485A>G	ENST00000320301.6	-	11	1657	c.1263T>C	c.(1261-1263)acT>acC	p.T421T	PCDH15_ENST00000395438.1_Silent_p.T421T|PCDH15_ENST00000395430.1_Silent_p.T421T|PCDH15_ENST00000414778.1_Silent_p.T426T|PCDH15_ENST00000361849.3_Silent_p.T421T|PCDH15_ENST00000395432.2_Silent_p.T384T|PCDH15_ENST00000373957.3_Silent_p.T399T|PCDH15_ENST00000395446.1_Silent_p.T421T|PCDH15_ENST00000437009.1_Silent_p.T421T|PCDH15_ENST00000395445.1_Silent_p.T421T|PCDH15_ENST00000409834.1_Silent_p.T25T|PCDH15_ENST00000395440.1_Silent_p.T421T|PCDH15_ENST00000373965.2_Silent_p.T421T|PCDH15_ENST00000373955.1_Silent_p.T421T|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Silent_p.T399T	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	421	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TTAAAGGTGAAGTCAAATTGA	0.358										HNSCC(58;0.16)			G|||	1282	0.25599	0.5348	0.2118	5008	,	,		17037	0.0863		0.1382	False		,,,				2504	0.2065				p.T426T		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T1278C						PASS	.	G	,,,,,,,,,,,	2108,2298	601.9+/-389.8	506,1096,601	124.0	116.0	119.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1278,1263,1263,1263,1152,1197,1278,1263,1278,1263,1197,1263	4.1	0.9	10	dbSNP_116	119	1102,7498	768.6+/-407.6	65,972,3263	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	,,,,,,,,,,,	571,2068,3864	GG,GA,AA		12.814,47.8438,24.6809	,,,,,,,,,,,	426/1963,421/1958,421/1887,421/1953,384/1916,399/1936,426/1791,421/1540,426/1683,421/1678,399/1933,421/1956	55955485	3210,9796	2203	4300	6503	SO:0001819	synonymous_variant	65217	exon12			AGGTGAAGTCAAA	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.1263T>C	10.37:g.55955485A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			A|0.756;G|0.244	0.244	strong		0.358	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
FCRL5	83416	hgsc.bcm.edu	37	1	157514685	157514685	+	Silent	SNP	G	G	A	rs11803066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157514685G>A	ENST00000361835.3	-	4	652	c.495C>T	c.(493-495)cgC>cgT	p.R165R	FCRL5_ENST00000368191.3_Silent_p.R80R|FCRL5_ENST00000368189.3_Silent_p.R165R|FCRL5_ENST00000368190.3_Silent_p.R165R|FCRL5_ENST00000356953.4_Silent_p.R165R	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	165					negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				ATCCAGTACAGCGATATGCAC	0.368													G|||	72	0.014377	0.053	0.0029	5008	,	,		21706	0.0		0.0	False		,,,				2504	0.0				p.R165R		Atlas-SNP	.											.	FCRL5	177	.	0			c.C495T						PASS	.	G	,	233,4173	138.8+/-174.5	5,223,1975	153.0	142.0	146.0		495,495	-3.5	0.0	1	dbSNP_120	146	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FCRL5	NM_001195388.1,NM_031281.2	,	5,223,6275	AA,AG,GG		0.0,5.2882,1.7915	,	165/999,165/978	157514685	233,12773	2203	4300	6503	SO:0001819	synonymous_variant	83416	exon4			AGTACAGCGATAT	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.495C>T	1.37:g.157514685G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	190	103	0.542105	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Silent	SNP	ENST00000361835.3	37	CCDS1165.1																																																																																			G|0.982;A|0.018	0.018	strong		0.368	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
CRAT	1384	hgsc.bcm.edu	37	9	131866523	131866523	+	Silent	SNP	C	C	G	rs2228304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131866523C>G	ENST00000318080.2	-	3	648	c.354G>C	c.(352-354)tcG>tcC	p.S118S	AL158151.2_ENST00000408594.1_RNA|CRAT_ENST00000464290.1_Intron	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	118					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	CGCCTGGGCTCGAGTAGATGA	0.647													C|||	717	0.143171	0.3691	0.0519	5008	,	,		15850	0.123		0.006	False		,,,				2504	0.0644				p.S118S		Atlas-SNP	.											.	CRAT	43	.	0			c.G354C						PASS	.	C		1401,3001	448.3+/-348.6	229,943,1029	51.0	38.0	42.0		354	2.0	1.0	9	dbSNP_98	42	52,8548	27.9+/-77.7	0,52,4248	no	coding-synonymous	CRAT	NM_000755.3		229,995,5277	GG,GC,CC		0.6047,31.8264,11.1752		118/627	131866523	1453,11549	2201	4300	6501	SO:0001819	synonymous_variant	1384	exon3			TGGGCTCGAGTAG	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"""carnitine acetyltransferase"""			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.354G>C	9.37:g.131866523C>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	122	81	0.663934	NM_000755	Q5T952|Q9BW16	Silent	SNP	ENST00000318080.2	37	CCDS6919.1																																																																																			C|0.852;G|0.148	0.148	strong		0.647	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1		
AFF2	2334	hgsc.bcm.edu	37	X	148035200	148035200	+	Silent	SNP	G	G	A	rs12011040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:148035200G>A	ENST00000370460.2	+	10	1967	c.1488G>A	c.(1486-1488)tcG>tcA	p.S496S	AFF2_ENST00000370457.5_Silent_p.S463S|AFF2_ENST00000342251.3_Silent_p.S463S|AFF2_ENST00000286437.5_Silent_p.S137S	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	496					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GCTCTGAGTCGGATTCAGACA	0.587													A|||	536	0.141987	0.3381	0.0476	3775	,	,		11768	0.003		0.0388	False		,,,				2504	0.0143				p.S496S		Atlas-SNP	.											.	AFF2	679	.	0			c.G1488A						PASS	.	A	,,,,,	1531,2304		268,774,221,590,350	126.0	118.0	121.0		1389,1458,1383,1371,411,1488	-10.0	0.0	X	dbSNP_120	121	287,6441		3,196,85,2229,1787	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AFF2	NM_001169122.1,NM_001169123.1,NM_001169124.1,NM_001169125.1,NM_001170628.1,NM_002025.3	,,,,,	271,970,306,2819,2137	AA,AG,A,GG,G		4.2658,39.9218,17.211	,,,,,	463/1277,486/1302,461/1277,457/1273,137/953,496/1312	148035200	1818,8745	2203	4300	6503	SO:0001819	synonymous_variant	2334	exon10			TGAGTCGGATTCA	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1488G>A	X.37:g.148035200G>A		Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	415	140	0.337349	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	37	CCDS14684.1																																																																																			0|0.003;A|0.180	0.180	strong		0.587	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
KIF19	124602	hgsc.bcm.edu	37	17	72349040	72349040	+	Silent	SNP	C	C	T	rs9897137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	87	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	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	
RAPGEF2	9693	hgsc.bcm.edu	37	4	160273927	160273927	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:160273927C>T	ENST00000264431.4	+	21	3892	c.3473C>T	c.(3472-3474)tCg>tTg	p.S1158L		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1158	Ser-rich.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.S1146L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		GTTAGCAATTCGTCTTTTGAC	0.478																																					p.S1158L		Atlas-SNP	.											RAPGEF2,NS,carcinoma,0,2	RAPGEF2	171	2	1	Substitution - Missense(1)	large_intestine(1)	c.C3473T						scavenged	.						123.0	117.0	119.0					4																	160273927		1935	4134	6069	SO:0001583	missense	9693	exon21			GCAATTCGTCTTT	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.3473C>T	4.37:g.160273927C>T	ENSP00000264431:p.Ser1158Leu	Somatic	211	2	0.00947867		WXS	Illumina HiSeq	Phase_I	211	3	0.014218	NM_014247	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.7|21.7	4.191721|4.191721	0.78902|0.78902	.|.	.|.	ENSG00000109756|ENSG00000109756	ENST00000510253|ENST00000264431	.|T	.|0.43294	.|0.95	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.40619|0.40619	0.1124|0.1124	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|B	.|0.31290	.|0.318	.|B	.|0.26969	.|0.075	T|T	0.21245|0.21245	-1.0251|-1.0251	5|10	.|0.48119	.|T	.|0.1	.|.	19.9832|19.9832	0.97338|0.97338	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1158	.|Q9Y4G8	.|RPGF2_HUMAN	C|L	215|1158	.|ENSP00000264431:S1158L	.|ENSP00000264431:S1158L	R|S	+|+	1|2	0|0	RAPGEF2|RAPGEF2	160493377|160493377	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.993000|0.993000	0.82548|0.82548	5.675000|5.675000	0.68123|0.68123	2.722000|2.722000	0.93159|0.93159	0.655000|0.655000	0.94253|0.94253	CGT|TCG	.	.	none		0.478	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	
NCOR2	9612	hgsc.bcm.edu	37	12	124821705	124821705	+	Silent	SNP	G	G	A	rs3741512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124821705G>A	ENST00000405201.1	-	38	5709	c.5709C>T	c.(5707-5709)ccC>ccT	p.P1903P	NCOR2_ENST00000429285.2_Silent_p.P1893P|NCOR2_ENST00000356219.3_Silent_p.P1910P|NCOR2_ENST00000397355.1_Silent_p.P1894P|NCOR2_ENST00000404621.1_Silent_p.P1893P|NCOR2_ENST00000404121.2_Silent_p.P1464P			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1914					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)		CCGGGCGAACGGGTGAGGAGG	0.667													g|||	120	0.0239617	0.0862	0.0086	5008	,	,		14245	0.0		0.0	False		,,,				2504	0.0				p.P1903P		Atlas-SNP	.											.	NCOR2	475	.	0			c.C5709T						PASS	.		,,	227,3647		6,215,1716	12.0	17.0	15.0		5679,5679,5709	-6.6	0.7	12	dbSNP_107	15	2,7984		0,2,3991	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	6,217,5707	AA,AG,GG		0.025,5.8596,1.9309	,,	1893/2459,1893/2505,1903/2515	124821705	229,11631	1937	3993	5930	SO:0001819	synonymous_variant	9612	exon40			GCGAACGGGTGAG	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.5709C>T	12.37:g.124821705G>A		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	269	131	0.486989	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2	70	0.03205128205128205	67	0.13617886178861788	3	0.008287292817679558	0	0.0	0	0.0	g	6.208	0.406498	0.11754	0.058596	2.5E-4	ENSG00000196498	ENST00000440187	.	.	.	4.36	-6.64	0.01801	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.99999815647	.	.	.	.	.	.	T	0.31613	-0.9937	3	.	.	.	-11.6142	1.0444	0.01566	0.3119:0.1788:0.3193:0.1901	rs3741512	.	.	.	C	138	.	.	R	-	1	0	NCOR2	123387658	0.000000	0.05858	0.747000	0.31113	0.653000	0.38743	-2.100000	0.01345	-0.547000	0.06207	-2.034000	0.00421	CGT	G|0.966;A|0.034	0.034	strong		0.667	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
ADCK2	90956	hgsc.bcm.edu	37	7	140374049	140374049	+	Missense_Mutation	SNP	T	T	C	rs1140034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140374049T>C	ENST00000072869.4	+	1	1097	c.919T>C	c.(919-921)Tcc>Ccc	p.S307P	ADCK2_ENST00000476491.1_Missense_Mutation_p.S307P	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	307	Protein kinase.		S -> P (in dbSNP:rs1140034). {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)					CAACCTCATCTCCGTGGCAGT	0.557													C|||	1580	0.315495	0.7163	0.2118	5008	,	,		17427	0.1071		0.1123	False		,,,				2504	0.271				p.S307P		Atlas-SNP	.											.	ADCK2	37	.	0			c.T919C						PASS	.	C	PRO/SER	2749,1657	481.4+/-359.1	869,1011,323	44.0	47.0	46.0		919	4.1	0.8	7	dbSNP_86	46	894,7706	751.4+/-407.4	58,778,3464	yes	missense	ADCK2	NM_052853.3	74	927,1789,3787	CC,CT,TT		10.3953,37.6078,28.0101	benign	307/627	140374049	3643,9363	2203	4300	6503	SO:0001583	missense	90956	exon1			CTCATCTCCGTGG	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.919T>C	7.37:g.140374049T>C	ENSP00000072869:p.Ser307Pro	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	36	35	0.972222	NM_052853	Q96CN6|Q9Y6T5	Missense_Mutation	SNP	ENST00000072869.4	37	CCDS5861.1	546|546	0.25|0.25	341|341	0.693089430894309|0.693089430894309	64|64	0.17679558011049723|0.17679558011049723	57|57	0.09965034965034965|0.09965034965034965	84|84	0.11081794195250659|0.11081794195250659	C|C	4.131|4.131	0.022505|0.022505	0.08006|0.08006	0.623922|0.623922	0.103953|0.103953	ENSG00000133597|ENSG00000133597	ENST00000483369|ENST00000072869;ENST00000476491	.|T;T	.|0.55760	.|0.5;0.5	4.06|4.06	4.06|4.06	0.47325|0.47325	.|ABC-1 (1);	.|0.222345	.|0.38326	.|N	.|0.001726	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00677|0.00677	-1.265|-1.265	0.53688|0.53688	P|P	2.1000000000048757E-5|2.1000000000048757E-5	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.44452|0.44452	-0.9327|-0.9327	4|9	.|0.02654	.|T	.|1	-10.3382|-10.3382	11.9728|11.9728	0.53073|0.53073	0.0:0.9153:0.0:0.0847|0.0:0.9153:0.0:0.0847	rs1140034;rs2968557;rs3204120;rs11540282;rs17400305;rs60137398;rs1140034|rs1140034;rs2968557;rs3204120;rs11540282;rs17400305;rs60137398;rs1140034	.|307;307	.|C9JE15;Q7Z695	.|.;ADCK2_HUMAN	P|P	144|307	.|ENSP00000072869:S307P;ENSP00000420512:S307P	.|ENSP00000072869:S307P	L|S	+|+	2|1	0|0	ADCK2|ADCK2	140020518|140020518	0.994000|0.994000	0.37717|0.37717	0.754000|0.754000	0.31244|0.31244	0.549000|0.549000	0.35272|0.35272	2.580000|2.580000	0.46068|0.46068	0.953000|0.953000	0.37825|0.37825	-0.215000|-0.215000	0.12644|0.12644	CTC|TCC	T|0.719;C|0.281	0.281	strong		0.557	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853	
PPP1R26	9858	hgsc.bcm.edu	37	9	138377853	138377853	+	Silent	SNP	A	A	G	rs2004074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138377853A>G	ENST00000356818.2	+	4	2046	c.1497A>G	c.(1495-1497)gtA>gtG	p.V499V	PPP1R26_ENST00000605660.1_Silent_p.V499V|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000401470.3_Silent_p.V499V|PPP1R26_ENST00000605286.1_Silent_p.V499V|PPP1R26_ENST00000604351.1_Silent_p.V499V	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	499					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CGGCCCCTGTAGAGGGCAGTG	0.612													G|||	2141	0.427516	0.3275	0.4971	5008	,	,		18876	0.6577		0.2107	False		,,,				2504	0.499				p.V499V		Atlas-SNP	.											KIAA0649,colon,carcinoma,0,1	.	.	1	0			c.A1497G						PASS	.	G		1266,3140	686.0+/-404.6	174,918,1111	48.0	48.0	48.0		1497	2.8	0.0	9	dbSNP_92	48	1799,6801	719.5+/-406.3	193,1413,2694	no	coding-synonymous	KIAA0649	NM_014811.3		367,2331,3805	GG,GA,AA		20.9186,28.7335,23.566		499/1210	138377853	3065,9941	2203	4300	6503	SO:0001819	synonymous_variant	9858	exon4			CCCTGTAGAGGGC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.1497A>G	9.37:g.138377853A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																			A|0.691;G|0.309	0.309	strong		0.612	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
KLRG1	10219	hgsc.bcm.edu	37	12	9142297	9142297	+	Silent	SNP	T	T	C	rs1805723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9142297T>C	ENST00000266551.4	+	1	81	c.66T>C	c.(64-66)taT>taC	p.Y22Y	KLRG1_ENST00000538029.1_Intron|RP11-259O18.4_ENST00000545706.1_RNA|KLRG1_ENST00000356986.3_Silent_p.Y22Y	NM_005810.3	NP_005801.3	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G, member 1	22					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8						AGAATGACTATGGACCACAGC	0.428													t|||	1731	0.345647	0.1377	0.3775	5008	,	,		-128	0.3998		0.4334	False		,,,				2504	0.4581				p.Y22Y		Atlas-SNP	.											.	KLRG1	16	.	0			c.T66C						PASS	.	C		761,3645	310.5+/-291.6	63,635,1505	92.0	88.0	89.0		66	-0.1	0.0	12	dbSNP_92	89	3836,4764	541.4+/-384.0	852,2132,1316	no	coding-synonymous	KLRG1	NM_005810.3		915,2767,2821	CC,CT,TT		44.6047,17.2719,35.3452		22/190	9142297	4597,8409	2203	4300	6503	SO:0001819	synonymous_variant	10219	exon1			TGACTATGGACCA	AF097358	CCDS8599.1	12p13.31	2011-08-30			ENSG00000139187	ENSG00000139187		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	6380	protein-coding gene	gene with protein product	"""C-type lectin domain family 15, member A"""	604874				9862378, 9842918, 16461340, 16140789	Standard	NM_005810		Approved	MAFA, 2F1, MAFA-L, CLEC15A	uc001qvg.3	Q96E93		ENST00000266551.4:c.66T>C	12.37:g.9142297T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_005810	B7ZAM2|O43198|O75613	Silent	SNP	ENST00000266551.4	37																																																																																				T|0.639;C|0.361	0.361	strong		0.428	KLRG1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399145.1	NM_005810	
MSH5	4439	hgsc.bcm.edu	37	6	31729925	31729925	+	Missense_Mutation	SNP	C	C	T	rs1802127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31729925C>T	ENST00000375755.3	+	24	2642	c.2356C>T	c.(2356-2358)Cct>Tct	p.P786S	SAPCD1_ENST00000425424.1_5'Flank|MSH5-SAPCD1_ENST00000491552.1_3'UTR|SAPCD1-AS1_ENST00000419679.1_RNA|SAPCD1_ENST00000415669.2_5'Flank|MSH5_ENST00000431848.2_Missense_Mutation_p.P485S|MSH5_ENST00000534153.4_Missense_Mutation_p.P803S|MSH5_ENST00000375750.3_Missense_Mutation_p.P786S|MSH5_ENST00000395853.1_Missense_Mutation_p.P460S|MSH5-SAPCD1_ENST00000493662.2_Missense_Mutation_p.P803S|MSH5_ENST00000375742.3_Missense_Mutation_p.P803S|MSH5_ENST00000375740.3_Missense_Mutation_p.P774S|MSH5_ENST00000375703.3_Missense_Mutation_p.P787S	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	786			P -> S (in dbSNP:rs1802127). {ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						ACCCATCAAGCCTGTCAAGGA	0.493								Direct reversal of damage;Mismatch excision repair (MMR)					C|||	237	0.0473243	0.1278	0.0677	5008	,	,		20593	0.0		0.0199	False		,,,				2504	0.001				p.P787S		Atlas-SNP	.											.	MSH5	108	.	0			c.C2359T	GRCh37	CM062879	MSH5	M	rs1802127	PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	510,3896	236.8+/-248.8	25,460,1718	91.0	90.0	90.0		2356,2320,2359,2356	4.8	1.0	6	dbSNP_89	90	187,8413	83.7+/-146.2	4,179,4117	yes	missense,missense,missense,missense	MSH5	NM_002441.4,NM_025259.5,NM_172165.3,NM_172166.3	74,74,74,74	29,639,5835	TT,TC,CC		2.1744,11.5751,5.3591	benign,benign,benign,benign	786/835,774/823,787/836,786/835	31729925	697,12309	2203	4300	6503	SO:0001583	missense	4439	exon24			ATCAAGCCTGTCA	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.2356C>T	6.37:g.31729925C>T	ENSP00000364908:p.Pro786Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	159	73	0.459119	NM_172165	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Missense_Mutation	SNP	ENST00000375755.3	37	CCDS4720.1	109	0.04990842490842491	68	0.13821138211382114	26	0.0718232044198895	0	0.0	15	0.01978891820580475	C	12.68	2.009778	0.35415	0.115751	0.021744	ENSG00000204410;ENSG00000204410;ENSG00000204410;ENSG00000204410;ENSG00000204410;ENSG00000204410;ENSG00000204410;ENSG00000204410;ENSG00000204410;ENSG00000255152	ENST00000375755;ENST00000375742;ENST00000375750;ENST00000534153;ENST00000375703;ENST00000375740;ENST00000431848;ENST00000395853;ENST00000429846;ENST00000491552	D;D;D;D;D;D;D;D;T	0.86432	-1.87;-1.87;-1.87;-1.87;-1.87;-2.12;-1.71;-1.7;1.01	5.63	4.76	0.60689	.	0.190852	0.46145	D	0.000318	T	0.59500	0.2198	N	0.24115	0.695	0.24721	P	0.993149	B;B;B;B;B	0.32753	0.049;0.383;0.306;0.035;0.253	B;B;B;B;B	0.30029	0.024;0.107;0.11;0.039;0.108	T	0.53662	-0.8407	9	0.13108	T	0.6	-16.5078	8.2023	0.31432	0.0:0.7575:0.1591:0.0834	rs1802127;rs16900023;rs28399984;rs52814864;rs1802127	441;774;786;787;803	Q59EC5;O43196-4;O43196;O43196-2;O43196-3	.;.;MSH5_HUMAN;.;.	S	786;803;786;803;787;774;485;460;108;142	ENSP00000364908:P786S;ENSP00000364894:P803S;ENSP00000364903:P786S;ENSP00000431693:P803S;ENSP00000364855:P787S;ENSP00000364892:P774S;ENSP00000416784:P485S;ENSP00000379194:P460S;ENSP00000406849:P108S	ENSP00000364855:P787S	P	+	1	0	MSH5;MSH5-C6orf26	31837904	0.717000	0.27966	0.970000	0.41538	0.926000	0.56050	2.164000	0.42387	1.360000	0.45960	0.655000	0.94253	CCT	C|0.942;T|0.058	0.058	strong		0.493	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4		
LGI4	163175	hgsc.bcm.edu	37	19	35617270	35617270	+	Silent	SNP	T	T	C	rs1319969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35617270T>C	ENST00000310123.3	-	8	1722	c.1203A>G	c.(1201-1203)acA>acG	p.T401T	LGI4_ENST00000392225.3_Missense_Mutation_p.Q427R|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	401					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CGGGGATGTCTGTGCGTCTCT	0.667													T|||	1835	0.366414	0.3359	0.2493	5008	,	,		13875	0.2669		0.3708	False		,,,				2504	0.589				p.T401T		Atlas-SNP	.											LGI4,NS,carcinoma,0,1	LGI4	32	1	0			c.A1203G						PASS	.	T		1566,2840	452.0+/-349.9	280,1006,917	29.0	28.0	28.0		1203	-9.0	0.3	19	dbSNP_88	28	3066,5534	438.8+/-359.0	529,2008,1763	no	coding-synonymous	LGI4	NM_139284.2		809,3014,2680	CC,CT,TT		35.6512,35.5424,35.6143		401/538	35617270	4632,8374	2203	4300	6503	SO:0001819	synonymous_variant	163175	exon8			GATGTCTGTGCGT	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.1203A>G	19.37:g.35617270T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_139284	B2RN53|B9EGS7|Q5M8T1	Silent	SNP	ENST00000310123.3	37	CCDS12444.1	694	0.31776556776556775	183	0.3719512195121951	85	0.23480662983425415	136	0.23776223776223776	290	0.38258575197889183	T	8.894	0.954608	0.18431	0.355424	0.356512	ENSG00000153902	ENST00000392225	T	0.65732	-0.17	4.51	-9.02	0.00741	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999394594	.	.	.	.	.	.	T	0.39292	-0.9621	5	0.87932	D	0	.	10.368	0.44035	0.0:0.126:0.3738:0.5002	rs1319969;rs3810442;rs17656168;rs61511650	.	.	.	R	427	ENSP00000376059:Q427R	ENSP00000376059:Q427R	Q	-	2	0	LGI4	40309110	0.000000	0.05858	0.336000	0.25522	0.936000	0.57629	-4.585000	0.00212	-2.941000	0.00297	-1.540000	0.00911	CAG	T|0.660;C|0.340	0.340	strong		0.667	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1		
SLC22A25	387601	hgsc.bcm.edu	37	11	62931547	62931547	+	Splice_Site	SNP	T	T	C	rs114205803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62931547T>C	ENST00000306494.6	-	9	1394		c.e9-2		SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000525620.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						GCTCTTCCCCTTGGAGTAAAA	0.403													T|||	18	0.00359425	0.0136	0.0	5008	,	,		20838	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	SLC22A25	87	.	0			c.1395-2A>G						PASS	.	T		48,4354	35.2+/-66.4	1,46,2154	102.0	113.0	110.0			3.9	0.7	11	dbSNP_132	110	0,8596		0,0,4298	yes	splice-3	SLC22A25	NM_199352.3		1,46,6452	CC,CT,TT		0.0,1.0904,0.3693			62931547	48,12950	2201	4298	6499	SO:0001630	splice_region_variant	387601	exon10			TTCCCCTTGGAGT	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.1395-2A>G	11.37:g.62931547T>C		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	230	91	0.395652	NM_199352		Splice_Site	SNP	ENST00000306494.6	37	CCDS31592.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	T	10.76	1.441510	0.25900	0.010904	0.0	ENSG00000196600	ENST00000306494	.	.	.	3.88	3.88	0.44766	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2959	0.37815	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC22A25	62688123	0.077000	0.21312	0.693000	0.30195	0.010000	0.07245	1.743000	0.38258	1.768000	0.52137	0.477000	0.44152	.	T|0.996;C|0.004	0.004	strong		0.403	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	Intron
GPR112	139378	hgsc.bcm.edu	37	X	135426693	135426693	+	Missense_Mutation	SNP	A	A	G	rs4829829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:135426693A>G	ENST00000394143.1	+	6	1119	c.828A>G	c.(826-828)atA>atG	p.I276M	GPR112_ENST00000412101.1_Missense_Mutation_p.I71M|GPR112_ENST00000370652.1_Missense_Mutation_p.I276M|GPR112_ENST00000287534.4_Missense_Mutation_p.I213M|GPR112_ENST00000394141.1_Missense_Mutation_p.I71M	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	276			I -> M (in dbSNP:rs4829829). {ECO:0000269|Ref.2}.		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GCATACCTATATTTGCAACTG	0.363													a|||	1702	0.450861	0.4228	0.3545	3775	,	,		15401	0.2024		0.3738	False		,,,				2504	0.3241				p.I276M		Atlas-SNP	.											.	GPR112	459	.	0			c.A828G						PASS	.		MET/ILE	2087,1748		484,812,307,336,264	199.0	154.0	169.0		828	-8.6	0.0	X	dbSNP_111	169	3203,3525		555,1185,908,688,964	yes	missense	GPR112	NM_153834.3	10	1039,1997,1215,1024,1228	GG,GA,G,AA,A		47.607,45.5802,49.9195	benign	276/3081	135426693	5290,5273	2203	4300	6503	SO:0001583	missense	139378	exon6			ACCTATATTTGCA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.828A>G	X.37:g.135426693A>G	ENSP00000377699:p.Ile276Met	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	229	164	0.716157	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	710	0.4279686558167571	138	0.372972972972973	80	0.27972027972027974	76	0.15702479338842976	187	0.3191126279863481	a	2.435	-0.329891	0.05314	0.544198	0.47607	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.30448	1.55;1.55;1.53;1.66;1.53	4.27	-8.55	0.00908	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.11235	0.004;0.002;0.001	B;B;B	0.09377	0.004;0.004;0.002	T	0.43228	-0.9404	8	0.37606	T	0.19	.	0.3544	0.00354	0.2435:0.2422:0.2647:0.2496	rs4829829;rs59872615;rs4829829	213;71;276	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	M	276;276;71;213;71	ENSP00000377699:I276M;ENSP00000359686:I276M;ENSP00000416526:I71M;ENSP00000287534:I213M;ENSP00000377697:I71M	ENSP00000287534:I213M	I	+	3	3	GPR112	135254359	0.001000	0.12720	0.000000	0.03702	0.050000	0.14768	-0.872000	0.04219	-2.190000	0.00757	-0.485000	0.04761	ATA	A|0.517;0|0.025	.	strong		0.363	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
GRM3	2913	hgsc.bcm.edu	37	7	86479694	86479694	+	Silent	SNP	G	G	A	rs76035289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:86479694G>A	ENST00000361669.2	+	5	3499	c.2400G>A	c.(2398-2400)acG>acA	p.T800T	GRM3_ENST00000439827.1_Missense_Mutation_p.D445N|GRM3_ENST00000546348.1_Silent_p.T392T|GRM3_ENST00000536043.1_Silent_p.T672T|GRM3_ENST00000394720.2_Missense_Mutation_p.D443N	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	800					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					AGGTGCAGACGACAACCATGT	0.458													G|||	68	0.0135783	0.0469	0.0058	5008	,	,		21770	0.001		0.001	False		,,,				2504	0.0				p.T800T	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.G2400A						PASS	.	G		178,4228	115.0+/-153.0	2,174,2027	218.0	151.0	173.0		2400	-11.9	0.1	7	dbSNP_131	173	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	GRM3	NM_000840.2		2,181,6320	AA,AG,GG		0.0814,4.0399,1.4224		800/880	86479694	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	2913	exon5			GCAGACGACAACC		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.2400G>A	7.37:g.86479694G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	156	82	0.525641	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Silent	SNP	ENST00000361669.2	37	CCDS5600.1	30	0.013736263736263736	29	0.05894308943089431	0	0.0	0	0.0	1	0.0013192612137203166	G	9.085	1.000326	0.19121	0.040399	8.14E-4	ENSG00000198822	ENST00000439827;ENST00000394720	D;D	0.85773	-2.03;-2.03	5.97	-11.9	0.00025	.	.	.	.	.	T	0.21841	0.0526	.	.	.	0.09310	N	0.999991	B	0.02656	0.0	B	0.01281	0.0	T	0.49799	-0.8901	8	0.66056	D	0.02	.	2.9374	0.05819	0.4424:0.2623:0.1692:0.1262	.	445	G5E9K2	.	N	445;443	ENSP00000398767:D445N;ENSP00000378209:D443N	ENSP00000378209:D443N	D	+	1	0	GRM3	86317630	0.000000	0.05858	0.132000	0.22025	0.766000	0.43426	-1.862000	0.01653	-2.006000	0.00958	-1.779000	0.00650	GAC	G|0.985;A|0.015	0.015	strong		0.458	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
CD1E	913	hgsc.bcm.edu	37	1	158325765	158325765	+	Silent	SNP	C	C	T	rs61734677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158325765C>T	ENST00000368167.3	+	4	1013	c.774C>T	c.(772-774)gaC>gaT	p.D258D	CD1E_ENST00000368163.3_Intron|CD1E_ENST00000368165.3_Silent_p.D168D|CD1E_ENST00000368164.3_Silent_p.D69D|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368161.3_Silent_p.D258D|CD1E_ENST00000368156.1_Silent_p.D168D|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368166.3_Silent_p.D69D|CD1E_ENST00000434258.1_Silent_p.D256D|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000452291.2_Silent_p.D69D|CD1E_ENST00000368160.3_Silent_p.D258D|CD1E_ENST00000444681.2_Silent_p.D159D	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	258	Ig-like.				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)					AGCGAGGGGACGTCCTGCCTA	0.617													C|||	198	0.0395367	0.1483	0.0029	5008	,	,		15430	0.0		0.0	False		,,,				2504	0.0				p.D258D		Atlas-SNP	.											.	CD1E	129	.	0			c.C774T						PASS	.	C	,,,,,,,,,,,,	609,3797	265.9+/-266.9	48,513,1642	115.0	111.0	112.0		774,774,,207,207,504,,,207,,477,504,774	-5.1	0.0	1	dbSNP_129	112	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	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	,,,,,,,,,,,,	48,519,5936	TT,TC,CC		0.0698,13.8221,4.7286	,,,,,,,,,,,,	258/377,258/291,,69/188,69/102,168/299,,,69/200,,159/290,168/287,258/389	158325765	615,12391	2203	4300	6503	SO:0001819	synonymous_variant	913	exon4			AGGGGACGTCCTG	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.774C>T	1.37:g.158325765C>T		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	313	162	0.517572	NM_001042584	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	Silent	SNP	ENST00000368167.3	37	CCDS41417.1	66	0.03021978021978022	65	0.13211382113821138	1	0.0027624309392265192	0	0.0	0	0.0	C	0.065	-1.215843	0.01542	0.138221	6.98E-4	ENSG00000158488	ENST00000368162	.	.	.	4.6	-5.12	0.02893	.	.	.	.	.	T	0.10551	0.0258	.	.	.	0.20074	N	0.999933	.	.	.	.	.	.	T	0.29701	-1.0003	4	.	.	.	-27.8278	6.6347	0.22877	0.1308:0.2718:0.0:0.5974	rs61734677	.	.	.	C	28	.	.	R	+	1	0	CD1E	156592389	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-4.235000	0.00269	-1.234000	0.02548	-1.008000	0.02478	CGT	C|0.978;T|0.022	0.022	strong		0.617	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893	
FAM179A	165186	hgsc.bcm.edu	37	2	29225504	29225504	+	Missense_Mutation	SNP	T	T	C	rs72786179|rs386644304|rs200686651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29225504T>C	ENST00000379558.4	+	5	881	c.530T>C	c.(529-531)cTc>cCc	p.L177P	FAM179A_ENST00000403861.2_Missense_Mutation_p.L177P	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	177										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						CCGATGCCTCTCATCCAGAGC	0.652													C|||	946	0.188898	0.4372	0.1066	5008	,	,		17380	0.1617		0.0726	False		,,,				2504	0.0593				p.L177P		Atlas-SNP	.											.	FAM179A	106	.	0			c.T530C						PASS	.	C	PRO/LEU	1441,2533		271,899,817	28.0	35.0	33.0		530	5.2	1.0	2	dbSNP_130	33	564,7764		16,532,3616	yes	missense	FAM179A	NM_199280.2	98	287,1431,4433	CC,CT,TT		6.7723,36.2607,16.2982	benign	177/1020	29225504	2005,10297	1987	4164	6151	SO:0001583	missense	165186	exon5			TGCCTCTCATCCA	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.530T>C	2.37:g.29225504T>C	ENSP00000368876:p.Leu177Pro	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	424	0.19413919413919414	226	0.45934959349593496	37	0.10220994475138122	105	0.18356643356643357	56	0.07387862796833773	C	1.584	-0.530884	0.04112	0.362607	0.067723	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.03889	3.77;3.98	5.18	5.18	0.71444	.	.	.	.	.	T	0.00012	0.0000	N	0.01168	-0.975	0.28820	P	0.897713	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39563	-0.9608	8	0.02654	T	1	.	9.9709	0.41754	0.0:0.9061:0.0:0.0939	.	177;177	F8W8E4;Q6ZUX3	.;F179A_HUMAN	P	177	ENSP00000368876:L177P;ENSP00000384699:L177P	ENSP00000368876:L177P	L	+	2	0	FAM179A	29079008	1.000000	0.71417	1.000000	0.80357	0.542000	0.35054	2.670000	0.46833	1.192000	0.43071	-0.227000	0.12334	CTC	T|0.832;C|0.168	0.168	strong		0.652	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
MPDZ	8777	hgsc.bcm.edu	37	9	13150531	13150531	+	Silent	SNP	T	T	C	rs10756457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:13150531T>C	ENST00000319217.7	-	25	3856	c.3609A>G	c.(3607-3609)aaA>aaG	p.K1203K	MPDZ_ENST00000381015.4_Silent_p.K1203K|MPDZ_ENST00000541718.1_Silent_p.K1203K|MPDZ_ENST00000536827.1_Silent_p.K1203K|MPDZ_ENST00000447879.1_Silent_p.K1203K|MPDZ_ENST00000381022.2_Silent_p.K1203K|MPDZ_ENST00000538841.1_Silent_p.K95K|MPDZ_ENST00000546205.1_Silent_p.K1217K	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	120	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	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	
BCL2A1	597	hgsc.bcm.edu	37	15	80263111	80263111	+	Missense_Mutation	SNP	C	C	A	rs34080999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80263111C>A	ENST00000267953.3	-	1	677	c.351G>T	c.(349-351)gaG>gaT	p.E117D	BCL2A1_ENST00000335661.6_Missense_Mutation_p.E117D	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	117			E -> D (in dbSNP:rs34080999).		extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						AATATGAAATCTCCTTATAGG	0.383													C|||	191	0.038139	0.1384	0.0086	5008	,	,		17180	0.0		0.002	False		,,,				2504	0.0				p.E117D		Atlas-SNP	.											.	BCL2A1	28	.	0			c.G351T						PASS	.	C	ASP/GLU,ASP/GLU	472,3934	219.1+/-236.9	26,420,1757	118.0	125.0	123.0		351,351	-5.0	0.0	15	dbSNP_126	123	7,8593	6.4+/-24.3	0,7,4293	yes	missense,missense	BCL2A1	NM_001114735.1,NM_004049.3	45,45	26,427,6050	AA,AC,CC		0.0814,10.7127,3.6829	benign,benign	117/164,117/176	80263111	479,12527	2203	4300	6503	SO:0001583	missense	597	exon1			TGAAATCTCCTTA		CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.351G>T	15.37:g.80263111C>A	ENSP00000267953:p.Glu117Asp	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	224	105	0.46875	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	55	0.025183150183150184	50	0.1016260162601626	5	0.013812154696132596	0	0.0	0	0.0	C	11.44	1.639200	0.29157	0.107127	8.14E-4	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.11604	2.76;2.76	4.98	-5.04	0.02964	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);	1.167600	0.06235	N	0.689282	T	0.00144	0.0004	N	0.21448	0.665	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44742	-0.9308	10	0.15499	T	0.54	-25.672	8.3287	0.32173	0.0:0.3478:0.4258:0.2264	rs34080999	117;117	Q86W13;Q16548	.;B2LA1_HUMAN	D	117	ENSP00000267953:E117D;ENSP00000335250:E117D	ENSP00000267953:E117D	E	-	3	2	BCL2A1	78050166	0.457000	0.25752	0.000000	0.03702	0.018000	0.09664	-0.218000	0.09240	-0.861000	0.04094	0.655000	0.94253	GAG	C|0.968;A|0.032	0.032	strong		0.383	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049	
STARD13	90627	hgsc.bcm.edu	37	13	33704346	33704346	+	Silent	SNP	C	C	T	rs114088950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33704346C>T	ENST00000336934.5	-	5	584	c.468G>A	c.(466-468)gtG>gtA	p.V156V	STARD13_ENST00000399365.3_Silent_p.V38V|STARD13_ENST00000255486.4_Silent_p.V148V	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	156					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)		AGAGGTCGTCCACACGAGACC	0.557													C|||	86	0.0171725	0.0492	0.0014	5008	,	,		21153	0.0		0.0	False		,,,				2504	0.0204				p.V156V		Atlas-SNP	.											.	STARD13	100	.	0			c.G468A						PASS	.	C	,,	147,4259	103.8+/-142.4	3,141,2059	82.0	62.0	69.0		114,468,444	5.4	1.0	13	dbSNP_132	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	3,142,6358	TT,TC,CC		0.0116,3.3364,1.1379	,,	38/996,156/1114,148/1106	33704346	148,12858	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon5			GTCGTCCACACGA	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.468G>A	13.37:g.33704346C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			C|0.986;T|0.014	0.014	strong		0.557	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
SH2D3A	10045	hgsc.bcm.edu	37	19	6763718	6763718	+	Silent	SNP	A	A	G	rs2305805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6763718A>G	ENST00000245908.6	-	2	311	c.42T>C	c.(40-42)ccT>ccC	p.P14P	SH2D3A_ENST00000599563.1_5'Flank|SH2D3A_ENST00000437152.3_Missense_Mutation_p.L9P	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	14					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						CGTGGTACCAAGGTTGGCCAG	0.617													G|||	1303	0.260184	0.4682	0.1571	5008	,	,		14692	0.0565		0.2247	False		,,,				2504	0.2986				p.P14P		Atlas-SNP	.											.	SH2D3A	53	.	0			c.T42C						PASS	.	G		1863,2543	628.9+/-395.2	393,1077,733	90.0	72.0	78.0		42	2.0	1.0	19	dbSNP_100	78	1866,6734	725.7+/-406.6	208,1450,2642	no	coding-synonymous	SH2D3A	NM_005490.2		601,2527,3375	GG,GA,AA		21.6977,42.2833,28.6714		14/577	6763718	3729,9277	2203	4300	6503	SO:0001819	synonymous_variant	10045	exon2			GTACCAAGGTTGG	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"""SH2 domain containing"""	16885	protein-coding gene	gene with protein product		604721	"""SH2 domain-containing 3A"""			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.42T>C	19.37:g.6763718A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	78	32	0.410256	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Silent	SNP	ENST00000245908.6	37	CCDS12173.1	480	0.21978021978021978	204	0.4146341463414634	64	0.17679558011049723	37	0.06468531468531469	175	0.23087071240105542	G	8.380	0.837313	0.16891	0.422833	0.216977	ENSG00000125731	ENST00000437152	T	0.32272	1.46	4.21	2.03	0.26663	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.26469	P	0.9753131	B	0.02656	0.0	B	0.01281	0.0	T	0.48151	-0.9060	6	.	.	.	-7.4148	4.1083	0.10047	0.2892:0.1735:0.5373:0.0	rs2305805;rs58578745;rs2305805	9	B4DRS7	.	P	9	ENSP00000393303:L9P	.	L	-	2	0	SH2D3A	6714718	1.000000	0.71417	0.998000	0.56505	0.453000	0.32348	0.586000	0.23894	0.175000	0.19841	-0.119000	0.15052	CTT	A|0.742;G|0.258	0.258	strong		0.617	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490	
MYOM3	127294	hgsc.bcm.edu	37	1	24421950	24421950	+	Missense_Mutation	SNP	C	C	G	rs4319261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24421950C>G	ENST00000374434.3	-	8	934	c.772G>C	c.(772-774)Gat>Cat	p.D258H	MYOM3_ENST00000330966.7_Missense_Mutation_p.D259H|MYOM3_ENST00000475306.1_5'UTR|MYOM3_ENST00000329601.7_Missense_Mutation_p.D258H	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	258			D -> H (in dbSNP:rs4319261). {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)		ATCTCTGAATCGAAGCCAGCA	0.507													C|||	2056	0.410543	0.5416	0.3386	5008	,	,		18793	0.377		0.497	False		,,,				2504	0.2301				p.D258H		Atlas-SNP	.											.	MYOM3	131	.	0			c.G772C						PASS	.	C	HIS/ASP	1877,1889		489,899,495	110.0	113.0	112.0		772	5.8	1.0	1	dbSNP_111	112	3907,4327		929,2049,1139	yes	missense	MYOM3	NM_152372.3	81	1418,2948,1634	GG,GC,CC		47.4496,49.8407,48.2	benign	258/1438	24421950	5784,6216	1883	4117	6000	SO:0001583	missense	127294	exon8			CTGAATCGAAGCC	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.772G>C	1.37:g.24421950C>G	ENSP00000363557:p.Asp258His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	1004	0.4597069597069597	275	0.5589430894308943	136	0.3756906077348066	200	0.34965034965034963	393	0.5184696569920845	C	8.135	0.783923	0.16189	0.498407	0.474496	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.58358	0.38;0.39;0.34	5.81	5.81	0.92471	.	0.367568	0.32918	N	0.005498	T	0.00012	0.0000	N	0.20530	0.585	0.24931	P	0.99191579	B;D	0.76494	0.235;0.999	B;P	0.60117	0.097;0.869	T	0.48547	-0.9026	9	0.24483	T	0.36	.	17.0405	0.86488	0.0:1.0:0.0:0.0	rs4319261;rs4319261	258;258	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	H	258;259;258	ENSP00000363557:D258H;ENSP00000332670:D259H;ENSP00000328415:D258H	ENSP00000328415:D258H	D	-	1	0	MYOM3	24294537	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	4.329000	0.59260	2.764000	0.94973	0.558000	0.71614	GAT	C|0.542;G|0.458	0.458	strong		0.507	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
APOBEC4	403314	hgsc.bcm.edu	37	1	183616926	183616926	+	Missense_Mutation	SNP	T	T	C	rs1174657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	167	0	0		WXS	Illumina HiSeq	Phase_I	235	116	0.493617	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	
SLC38A6	145389	hgsc.bcm.edu	37	14	61445981	61445981	+	5'Flank	SNP	C	C	T	rs114005374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:61445981C>T	ENST00000267488.4	+	0	0				SLC38A6_ENST00000354886.2_5'Flank|TRMT5_ENST00000261249.6_Missense_Mutation_p.R212Q|RP11-193F5.1_ENST00000553946.1_RNA|SLC38A6_ENST00000456840.2_5'Flank	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6						amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)		p.R212Q(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		CTGATGATCTCGAAGGTTTAG	0.353													C|||	11	0.00219649	0.0083	0.0	5008	,	,		21341	0.0		0.0	False		,,,				2504	0.0				p.R212Q		Atlas-SNP	.											TRMT5,caecum,carcinoma,0,1	TRMT5	44	1	1	Substitution - Missense(1)	large_intestine(1)	c.G635A						PASS	.	C	GLN/ARG	11,4395	17.9+/-39.9	0,11,2192	99.0	93.0	95.0		635	4.8	1.0	14	dbSNP_132	95	0,8600		0,0,4300	yes	missense	TRMT5	NM_020810.2	43	0,11,6492	TT,TC,CC		0.0,0.2497,0.0846	probably-damaging	212/510	61445981	11,12995	2203	4300	6503	SO:0001631	upstream_gene_variant	57570	exon2			TGATCTCGAAGGT	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335		14.37:g.61445981C>T	Exception_encountered	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	NM_020810	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000267488.4	37	CCDS9751.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	35	5.439965	0.96168	0.002497	0.0	ENSG00000126814	ENST00000261249	T	0.23754	1.89	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.51856	0.1699	M	0.91920	3.255	0.58432	D	0.999998	D	0.76494	0.999	D	0.73708	0.981	T	0.65709	-0.6102	10	0.46703	T	0.11	-9.0897	18.1347	0.89614	0.0:1.0:0.0:0.0	.	212	Q32P41	TRM5_HUMAN	Q	212	ENSP00000261249:R212Q	ENSP00000261249:R212Q	R	-	2	0	TRMT5	60515734	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.317000	0.79018	2.489000	0.83994	0.655000	0.94253	CGA	C|0.999;T|0.001	0.001	strong		0.353	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1		
FMN2	56776	hgsc.bcm.edu	37	1	240371034	240371034	+	Silent	SNP	A	A	C	rs150102515		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:240371034A>C	ENST00000319653.9	+	5	3152	c.2922A>C	c.(2920-2922)ggA>ggC	p.G974G		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	974	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)			CCGGAGCAGGAATACCTCCTC	0.706																																					p.G974G		Atlas-SNP	.											FMN2,NS,carcinoma,0,1	FMN2	451	1	0			c.A2922C						scavenged	.						22.0	23.0	23.0					1																	240371034		2200	4296	6496	SO:0001819	synonymous_variant	56776	exon5			AGCAGGAATACCT	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.2922A>C	1.37:g.240371034A>C		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	201	7	0.0348259	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			A|0.999;C|0.001	0.001	weak		0.706	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
DOCK4	9732	hgsc.bcm.edu	37	7	111462465	111462465	+	Silent	SNP	C	C	T	rs17158877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:111462465C>T	ENST00000437633.1	-	27	3139	c.2883G>A	c.(2881-2883)ccG>ccA	p.P961P	DOCK4_ENST00000428084.1_Silent_p.P961P|DOCK4-AS1_ENST00000452714.1_RNA	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	961					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)	p.P949P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				GAAACATCTCCGGGCGTATCA	0.378													T|||	610	0.121805	0.3956	0.0202	5008	,	,		19490	0.0228		0.003	False		,,,				2504	0.0481				p.P961P		Atlas-SNP	.											DOCK4,NS,carcinoma,0,1	DOCK4	365	1	1	Substitution - coding silent(1)	stomach(1)	c.G2883A						PASS	.	T		1214,2484		212,790,847	84.0	76.0	79.0		2883	-8.8	0.8	7	dbSNP_123	79	32,8146		0,32,4057	no	coding-synonymous	DOCK4	NM_014705.3		212,822,4904	TT,TC,CC		0.3913,32.8286,10.4917		961/1967	111462465	1246,10630	1849	4089	5938	SO:0001819	synonymous_variant	9732	exon27			CATCTCCGGGCGT		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.2883G>A	7.37:g.111462465C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_014705	O14584|O94824|Q8NB45	Silent	SNP	ENST00000437633.1	37	CCDS47688.1	224	0.10256410256410256	201	0.40853658536585363	9	0.024861878453038673	12	0.02097902097902098	2	0.002638522427440633	T	10.46	1.356288	0.24598	0.328286	0.003913	ENSG00000128512	ENST00000423057;ENST00000445943	.	.	.	5.57	-8.83	0.00806	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999986311	.	.	.	.	.	.	T	0.38929	-0.9638	3	.	.	.	.	4.4577	0.11650	0.1383:0.4592:0.1551:0.2474	rs17158877;rs17158877	.	.	.	Q	413;985	.	.	R	-	2	0	DOCK4	111249701	0.008000	0.16893	0.758000	0.31321	0.996000	0.88848	-1.339000	0.02652	-1.590000	0.01623	-0.269000	0.10298	CGG	C|0.884;T|0.116	0.116	strong		0.378	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
CENPJ	55835	hgsc.bcm.edu	37	13	25480616	25480616	+	Silent	SNP	T	T	A	rs17081368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25480616T>A	ENST00000381884.4	-	7	1745	c.1560A>T	c.(1558-1560)acA>acT	p.T520T	CENPJ_ENST00000545981.1_Silent_p.T520T	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	520					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		CTTTACCTTGTGTCTTATTCC	0.448													T|||	248	0.0495208	0.1785	0.0159	5008	,	,		17190	0.0		0.001	False		,,,				2504	0.0				p.T520T		Atlas-SNP	.											.	CENPJ	116	.	0			c.A1560T						PASS	.	T		656,3750	274.3+/-271.8	47,562,1594	73.0	77.0	76.0		1560	0.4	0.0	13	dbSNP_123	76	12,8586	8.4+/-32.0	0,12,4287	no	coding-synonymous	CENPJ	NM_018451.3		47,574,5881	AA,AT,TT		0.1396,14.8888,5.1369		520/1339	25480616	668,12336	2203	4299	6502	SO:0001819	synonymous_variant	55835	exon7			ACCTTGTGTCTTA	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"""centrosomal P4.1-associated protein"""	609279	"""microcephaly, primary autosomal recessive 6"""	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.1560A>T	13.37:g.25480616T>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Silent	SNP	ENST00000381884.4	37	CCDS9310.1																																																																																			T|0.950;A|0.050	0.050	strong		0.448	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451	
TRPM3	80036	hgsc.bcm.edu	37	9	73461337	73461337	+	Silent	SNP	T	T	A	rs7862440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:73461337T>A	ENST00000377111.2	-	4	876	c.633A>T	c.(631-633)gcA>gcT	p.A211A	TRPM3_ENST00000377106.1_Silent_p.A58A|TRPM3_ENST00000358082.3_Silent_p.A58A|TRPM3_ENST00000357533.2_Silent_p.A213A|TRPM3_ENST00000396285.1_Silent_p.A58A|TRPM3_ENST00000360823.2_Silent_p.A58A|TRPM3_ENST00000408909.2_Silent_p.A58A|TRPM3_ENST00000396280.5_Silent_p.A58A|TRPM3_ENST00000361823.5_Silent_p.A58A|TRPM3_ENST00000377110.3_Silent_p.A211A|TRPM3_ENST00000377105.1_Silent_p.A58A|TRPM3_ENST00000396283.1_Silent_p.A58A|TRPM3_ENST00000396292.4_Silent_p.A58A|TRPM3_ENST00000423814.3_Silent_p.A213A|TRPM3_ENST00000377097.3_Silent_p.A58A|TRPM3_ENST00000377101.1_Silent_p.A58A	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	211					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						CAGTTGTCATTGCTGCTTTGA	0.483													A|||	2607	0.520567	0.5885	0.5591	5008	,	,		17392	0.2728		0.5835	False		,,,				2504	0.592				p.A211A		Atlas-SNP	.											.	TRPM3	700	.	0			c.A633T						PASS	.	A	,,,,,,,,	2473,1933	550.0+/-377.9	707,1059,437	221.0	213.0	215.0		174,633,174,174,174,174,174,174,174	2.6	1.0	9	dbSNP_116	215	5069,3531	515.0+/-378.5	1482,2105,713	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPM3	NM_001007470.1,NM_001007471.2,NM_020952.4,NM_024971.5,NM_206944.3,NM_206945.3,NM_206946.3,NM_206947.3,NM_206948.2	,,,,,,,,	2189,3164,1150	AA,AT,TT		41.0581,43.872,42.0114	,,,,,,,,	58/256,211/1708,58/1555,58/1567,58/1545,58/1557,58/1580,58/1570,58/231	73461337	7542,5464	2203	4300	6503	SO:0001819	synonymous_variant	80036	exon4			TGTCATTGCTGCT	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.633A>T	9.37:g.73461337T>A		Somatic	479	1	0.00208768		WXS	Illumina HiSeq	Phase_I	461	461	1	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377111.2	37		1074|1074	0.49175824175824173|0.49175824175824173	280|280	0.5691056910569106|0.5691056910569106	214|214	0.5911602209944752|0.5911602209944752	139|139	0.243006993006993|0.243006993006993	441|441	0.5817941952506597|0.5817941952506597	A|A	10.70|10.70	1.423613|1.423613	0.25639|0.25639	0.56128|0.56128	0.589419|0.589419	ENSG00000083067|ENSG00000083067	ENST00000396280|ENST00000377097	.|.	.|.	.|.	5.54|5.54	2.61|2.61	0.31194|0.31194	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43589|0.43589	-0.9382|-0.9382	3|3	.|.	.|.	.|.	-20.3858|-20.3858	2.883|2.883	0.05653|0.05653	0.1967:0.2206:0.4692:0.1136|0.1967:0.2206:0.4692:0.1136	rs7862440;rs17845693;rs17858635;rs7862440|rs7862440;rs17845693;rs17858635;rs7862440	.|.	.|.	.|.	Y|L	58|101	.|.	.|.	N|Q	-|-	1|2	0|0	TRPM3|TRPM3	72651157|72651157	0.994000|0.994000	0.37717|0.37717	0.998000|0.998000	0.56505|0.56505	0.974000|0.974000	0.67602|0.67602	0.268000|0.268000	0.18571|0.18571	0.020000|0.020000	0.15106|0.15106	-1.003000|-1.003000	0.02500|0.02500	AAT|CAA	T|0.455;A|0.545	0.545	strong		0.483	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945	
SLC1A6	6511	hgsc.bcm.edu	37	19	15063757	15063757	+	Silent	SNP	A	A	G	rs2229896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15063757A>G	ENST00000221742.3	-	8	1489	c.1482T>C	c.(1480-1482)atT>atC	p.I494I	SLC1A6_ENST00000430939.2_Silent_p.I430I|SLC1A6_ENST00000600144.1_Silent_p.I416I	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	494					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						AGTCCACGGCAATGATGAGCG	0.597													N|||	1265	0.252596	0.4236	0.2118	5008	,	,		14440	0.3244		0.1421	False		,,,				2504	0.09				p.I494I		Atlas-SNP	.											.	SLC1A6	111	.	0			c.T1482C						PASS	.	G		1658,2748		331,996,876	196.0	148.0	164.0		1482	-2.1	1.0	19	dbSNP_98	164	1024,7576		66,892,3342	no	coding-synonymous	SLC1A6	NM_005071.1		397,1888,4218	GG,GA,AA		11.907,37.6305,20.6213		494/565	15063757	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	6511	exon8			CACGGCAATGATG		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1482T>C	19.37:g.15063757A>G		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	292	143	0.489726	NM_005071	Q8N753	Silent	SNP	ENST00000221742.3	37	CCDS12321.1																																																																																			T|0.131;G|0.183;C|0.054;A|0.632	0.183	strong		0.597	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
TF	7018	hgsc.bcm.edu	37	3	133476629	133476629	+	Missense_Mutation	SNP	A	A	G	rs8177238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133476629A>G	ENST00000402696.3	+	8	1372	c.887A>G	c.(886-888)gAc>gGc	p.D296G	TF_ENST00000264998.3_Missense_Mutation_p.D169G	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	296	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.		D -> G (in allele TF*D1; dbSNP:rs8177238). {ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	TTTGGCAAAGACAAATCAAAA	0.433													A|||	70	0.0139776	0.0492	0.0043	5008	,	,		21606	0.002		0.0	False		,,,				2504	0.0				p.D296G		Atlas-SNP	.											TF,NS,carcinoma,+1,1	TF	116	1	0			c.A887G	GRCh37	CM840005	TF	M	rs8177238	PASS	.	A	GLY/ASP	174,4232	114.2+/-152.2	3,168,2032	79.0	80.0	80.0		887	-2.0	0.0	3	dbSNP_117	80	0,8600		0,0,4300	yes	missense	TF	NM_001063.3	94	3,168,6332	GG,GA,AA		0.0,3.9492,1.3378	benign	296/699	133476629	174,12832	2203	4300	6503	SO:0001583	missense	7018	exon8			GCAAAGACAAATC		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.887A>G	3.37:g.133476629A>G	ENSP00000385834:p.Asp296Gly	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Missense_Mutation	SNP	ENST00000402696.3	37	CCDS3080.1	28	0.01282051282051282	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	0	0.0	A	11.96	1.794981	0.31777	0.039492	0.0	ENSG00000091513	ENST00000402696;ENST00000264998	T;T	0.36878	1.23;1.23	4.91	-1.97	0.07503	.	0.691902	0.14583	N	0.310751	T	0.03305	0.0096	N	0.26130	0.795	0.09310	N	1	B	0.02656	0.0	B	0.12837	0.008	T	0.18524	-1.0334	10	0.19147	T	0.46	-12.1952	10.8343	0.46677	0.5329:0.0:0.4671:0.0	rs8177238;rs8177238	296	P02787	TRFE_HUMAN	G	296;169	ENSP00000385834:D296G;ENSP00000264998:D169G	ENSP00000264998:D169G	D	+	2	0	TF	134959319	0.021000	0.18746	0.001000	0.08648	0.826000	0.46750	0.020000	0.13466	-0.189000	0.10482	0.459000	0.35465	GAC	A|0.984;G|0.016	0.016	strong		0.433	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
S100A3	6274	hgsc.bcm.edu	37	1	153520954	153520954	+	Missense_Mutation	SNP	C	C	T	rs36022742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153520954C>T	ENST00000368713.3	-	2	204	c.8G>A	c.(7-9)aGg>aAg	p.R3K	S100A3_ENST00000368712.1_Missense_Mutation_p.R3K|S100A4_ENST00000368714.1_Intron|S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000368716.4_5'Flank	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	3			R -> K (in dbSNP:rs36022742).			cytoplasm (GO:0005737)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|liver(1)|lung(1)	3	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)			CTCCAGAGGCCTGGCCATCCT	0.602													C|||	713	0.142372	0.3896	0.0994	5008	,	,		17421	0.0149		0.0517	False		,,,				2504	0.0634				p.R3K		Atlas-SNP	.											.	S100A3	7	.	0			c.G8A						PASS	.	C	LYS/ARG	1514,2892	471.8+/-356.2	272,970,961	105.0	105.0	105.0		8	0.8	0.0	1	dbSNP_126	105	465,8135	135.4+/-192.6	16,433,3851	yes	missense	S100A3	NM_002960.1	26	288,1403,4812	TT,TC,CC		5.407,34.3622,15.2161	benign	3/102	153520954	1979,11027	2203	4300	6503	SO:0001583	missense	6274	exon2			AGAGGCCTGGCCA	BC012893	CCDS1043.1	1q21	2008-02-05	2001-11-28		ENSG00000188015	ENSG00000188015		"""S100 calcium binding proteins"""	10493	protein-coding gene	gene with protein product		176992	"""S100 calcium-binding protein A3"""	S100E		8341667	Standard	NM_002960		Approved		uc001fca.1	P33764	OTTHUMG00000013550	ENST00000368713.3:c.8G>A	1.37:g.153520954C>T	ENSP00000357702:p.Arg3Lys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_002960	D3DV51|Q6FGE4	Missense_Mutation	SNP	ENST00000368713.3	37	CCDS1043.1	255	0.11675824175824176	180	0.36585365853658536	33	0.09116022099447514	9	0.015734265734265736	33	0.04353562005277045	C	7.322	0.617075	0.14129	0.343622	0.05407	ENSG00000188015	ENST00000368713;ENST00000368712	T;T	0.13538	2.58;2.58	5.05	0.817	0.18773	EF-hand-like domain (1);	0.427486	0.25430	N	0.030730	T	0.02418	0.0074	N	0.14661	0.345	0.80722	P	0.0	B	0.22276	0.067	B	0.15052	0.012	T	0.40739	-0.9547	9	0.56958	D	0.05	.	8.5814	0.33630	0.0:0.4703:0.4447:0.085	rs36022742;rs59565142;rs61732314	3	P33764	S10A3_HUMAN	K	3	ENSP00000357702:R3K;ENSP00000357701:R3K	ENSP00000357701:R3K	R	-	2	0	S100A3	151787578	0.000000	0.05858	0.002000	0.10522	0.038000	0.13279	-0.160000	0.10041	-0.025000	0.13918	-0.163000	0.13421	AGG	C|0.861;T|0.139	0.139	strong		0.602	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960	
C2CD5	9847	hgsc.bcm.edu	37	12	22680809	22680809	+	Silent	SNP	T	T	C	rs12322490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:22680809T>C	ENST00000333957.4	-	4	450	c.195A>G	c.(193-195)ttA>ttG	p.L65L	C2CD5_ENST00000542676.1_Silent_p.L65L|C2CD5_ENST00000396028.2_Silent_p.L65L|C2CD5_ENST00000536386.1_Silent_p.L65L|C2CD5_ENST00000544930.1_5'UTR|C2CD5_ENST00000545552.1_Silent_p.L65L|C2CD5_ENST00000540703.1_5'Flank|C2CD5_ENST00000446597.1_Silent_p.L65L	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	65	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										GTTCATCTTGTAAGTCTTCAT	0.303													T|||	229	0.0457268	0.1649	0.0159	5008	,	,		16020	0.0		0.0	False		,,,				2504	0.0				p.L65L		Atlas-SNP	.											.	.	.	.	0			c.A195G						PASS	.	T		560,3846	250.0+/-257.2	37,486,1680	142.0	130.0	134.0		195	0.2	1.0	12	dbSNP_120	134	7,8593	5.0+/-18.6	0,7,4293	yes	coding-synonymous	KIAA0528	NM_014802.1		37,493,5973	CC,CT,TT		0.0814,12.7099,4.3595		65/1001	22680809	567,12439	2203	4300	6503	SO:0001819	synonymous_variant	9847	exon4			ATCTTGTAAGTCT	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"""138 kDa C2 domain-containing phosphoprotein"""		"""KIAA0528"""	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.195A>G	12.37:g.22680809T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	135	93	0.688889	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	37	CCDS31758.1																																																																																			T|0.950;C|0.050	0.050	strong		0.303	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	
OR1A1	8383	hgsc.bcm.edu	37	17	3119767	3119767	+	Missense_Mutation	SNP	C	C	T	rs769427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	89	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	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	
TMEM116	89894	hgsc.bcm.edu	37	12	112375990	112375990	+	Missense_Mutation	SNP	A	A	C	rs3752630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:112375990A>C	ENST00000550831.3	-	5	432	c.64T>G	c.(64-66)Tgt>Ggt	p.C22G	TMEM116_ENST00000549537.2_5'UTR|TMEM116_ENST00000355445.3_Missense_Mutation_p.C79G|TMEM116_ENST00000437003.2_Missense_Mutation_p.C22G|TMEM116_ENST00000552374.2_Missense_Mutation_p.C114G|TMEM116_ENST00000354825.3_Missense_Mutation_p.C22G	NM_138341.2	NP_612350.1	Q8NCL8	TM116_HUMAN	transmembrane protein 116	22			C -> G (in dbSNP:rs3752630).			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)	8						GCCATTTGACAAACTCGACAA	0.328													C|||	1126	0.22484	0.3116	0.1383	5008	,	,		17904	0.2728		0.165	False		,,,				2504	0.181				p.C114G		Atlas-SNP	.											.	TMEM116	17	.	0			c.T340G						PASS	.	C	GLY/CYS,GLY/CYS,GLY/CYS	1224,3182		160,904,1139	74.0	77.0	76.0		235,340,64	3.8	0.8	12	dbSNP_107	76	1419,7181		124,1171,3005	yes	missense,missense,missense	TMEM116	NM_001193453.1,NM_001193531.1,NM_138341.2	159,159,159	284,2075,4144	CC,CA,AA		16.5,27.7803,20.3214	benign,benign,benign	79/303,114/338,22/246	112375990	2643,10363	2203	4300	6503	SO:0001583	missense	89894	exon6			TTTGACAAACTCG	AK074648	CCDS9157.1, CCDS55886.1, CCDS55887.1	12q24.13	2012-03-02			ENSG00000198270	ENSG00000198270			25084	protein-coding gene	gene with protein product						12477932	Standard	NM_001193453		Approved	FLJ90167	uc001ttd.2	Q8NCL8	OTTHUMG00000169606	ENST00000550831.3:c.64T>G	12.37:g.112375990A>C	ENSP00000450377:p.Cys22Gly	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	176	95	0.539773	NM_001193531	G3V1W7|G5E985|Q6NSH5|Q8IZ66	Missense_Mutation	SNP	ENST00000550831.3	37	CCDS9157.1	490	0.22435897435897437	155	0.3150406504065041	57	0.1574585635359116	157	0.2744755244755245	121	0.15963060686015831	N	9.079	0.998886	0.19121	0.277803	0.165	ENSG00000198270	ENST00000355445;ENST00000354825;ENST00000550831;ENST00000437003;ENST00000552374;ENST00000550037	T;T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13;1.13	5.65	3.84	0.44239	.	0.212377	0.39985	N	0.001208	T	0.00012	0.0000	N	0.00268	-1.735	0.58432	P	1.999999999946489E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.39800	-0.9596	9	0.02654	T	1	-1.49	5.6836	0.17790	0.1556:0.6817:0.0:0.1627	rs3752630;rs57885084;rs3752630	114;79;114;22	F8VNZ8;G5E985;G3V1W7;Q8NCL8	.;.;.;TM116_HUMAN	G	79;22;22;22;114;114	ENSP00000347620:C79G;ENSP00000346883:C22G;ENSP00000450377:C22G;ENSP00000395861:C22G;ENSP00000447731:C114G;ENSP00000446516:C114G	ENSP00000346883:C22G	C	-	1	0	TMEM116	110860373	0.997000	0.39634	0.823000	0.32752	0.743000	0.42351	0.422000	0.21296	0.363000	0.24346	-1.207000	0.01640	TGT	A|0.783;C|0.217	0.217	strong		0.328	TMEM116-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405026.3	NM_138341	
IQCG	84223	hgsc.bcm.edu	37	3	197659160	197659160	+	Missense_Mutation	SNP	C	C	G	rs67877771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:197659160C>G	ENST00000265239.6	-	6	953	c.529G>C	c.(529-531)Gat>Cat	p.D177H	IQCG_ENST00000455191.1_Missense_Mutation_p.D177H|IQCG_ENST00000453254.1_Missense_Mutation_p.D177H	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	177				D -> H (in Ref. 4; AAH04816). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		GCAATCACATCGCTGAAAAAC	0.428													C|||	1411	0.281749	0.5227	0.1715	5008	,	,		16755	0.2262		0.166	False		,,,				2504	0.2106				p.D177H		Atlas-SNP	.											IQCG,rectum,carcinoma,0,1	IQCG	44	1	0			c.G529C						PASS	.	C	HIS/ASP,HIS/ASP	1970,2436	556.1+/-379.4	417,1136,650	107.0	101.0	103.0		529,529	2.9	1.0	3	dbSNP_130	103	1429,7171	275.3+/-291.7	117,1195,2988	yes	missense,missense	IQCG	NM_001134435.1,NM_032263.3	81,81	534,2331,3638	GG,GC,CC		16.6163,44.7118,26.1341	probably-damaging,probably-damaging	177/444,177/444	197659160	3399,9607	2203	4300	6503	SO:0001583	missense	84223	exon6			TCACATCGCTGAA	AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 9"""	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.529G>C	3.37:g.197659160C>G	ENSP00000265239:p.Asp177His	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_032263	Q9BST2|Q9HAG8	Missense_Mutation	SNP	ENST00000265239.6	37	CCDS3331.1	554	0.25366300366300365	256	0.5203252032520326	51	0.1408839779005525	120	0.2097902097902098	127	0.16754617414248021	C	12.96	2.093755	0.36952	0.447118	0.166163	ENSG00000114473	ENST00000265239;ENST00000455191;ENST00000453254;ENST00000416896	T;T;T;T	0.55930	0.74;0.74;0.77;0.49	4.81	2.88	0.33553	.	0.205977	0.38837	N	0.001547	T	0.00012	0.0000	M	0.75264	2.295	0.27204	P	0.9600887	D;D	0.89917	1.0;0.999	D;D	0.70935	0.971;0.948	T	0.47381	-0.9122	9	0.59425	D	0.04	-14.1493	7.1513	0.25612	0.0:0.7581:0.0:0.2419	.	177;177	C9JKX8;Q9H095	.;IQCG_HUMAN	H	177;177;177;158	ENSP00000265239:D177H;ENSP00000407736:D177H;ENSP00000389897:D177H;ENSP00000406411:D158H	ENSP00000265239:D177H	D	-	1	0	IQCG	199143557	0.961000	0.32948	0.987000	0.45799	0.493000	0.33554	1.099000	0.31013	1.073000	0.40885	0.460000	0.39030	GAT	C|0.746;G|0.254	0.254	strong		0.428	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263	
GREB1	9687	hgsc.bcm.edu	37	2	11736305	11736305	+	Missense_Mutation	SNP	G	G	A	rs36030386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11736305G>A	ENST00000381486.2	+	13	2194	c.1894G>A	c.(1894-1896)Gct>Act	p.A632T	GREB1_ENST00000234142.5_Missense_Mutation_p.A632T	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	632			A -> T (in dbSNP:rs36030386).			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)		TTCCTCACTCGCTGCCTCTTC	0.478													A|||	1079	0.215455	0.5696	0.1182	5008	,	,		15567	0.0317		0.1362	False		,,,				2504	0.0767				p.A632T	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.G1894A						PASS	.	A	THR/ALA	1771,2279		397,977,651	118.0	111.0	113.0		1894	1.4	0.1	2	dbSNP_126	113	1194,7216		93,1008,3104	yes	missense	GREB1	NM_014668.3	58	490,1985,3755	AA,AG,GG		14.1974,43.7284,23.7961	benign	632/1950	11736305	2965,9495	2025	4205	6230	SO:0001583	missense	9687	exon13			TCACTCGCTGCCT		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.1894G>A	2.37:g.11736305G>A	ENSP00000370896:p.Ala632Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	422	0.19322344322344323	253	0.5142276422764228	44	0.12154696132596685	20	0.03496503496503497	105	0.13852242744063326	A	1.886	-0.456552	0.04540	0.437284	0.141974	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000432985	T;T;T	0.43294	3.29;3.29;0.95	4.63	1.38	0.22167	.	1.029010	0.07715	N	0.942640	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	0.45906	-0.9229	9	0.08599	T	0.76	-34.9125	0.7537	0.00995	0.458:0.129:0.2244:0.1886	rs36030386	266;632	C9JIG0;Q4ZG55	.;GREB1_HUMAN	T	632;632;266	ENSP00000370896:A632T;ENSP00000234142:A632T;ENSP00000403886:A266T	ENSP00000234142:A632T	A	+	1	0	GREB1	11653756	0.010000	0.17322	0.058000	0.19502	0.940000	0.58332	-0.047000	0.11963	-0.071000	0.12886	-1.189000	0.01698	GCT	G|0.826;A|0.174	0.174	strong		0.478	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
CEP85	64793	hgsc.bcm.edu	37	1	26581981	26581981	+	Silent	SNP	G	G	A	rs34867486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26581981G>A	ENST00000252992.4	+	4	659	c.528G>A	c.(526-528)gcG>gcA	p.A176A	CEP85_ENST00000451429.2_Silent_p.A125A	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	176						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						AAGAAGAGGCGAGGAAGTTTG	0.473													G|||	105	0.0209665	0.0749	0.0086	5008	,	,		21433	0.0		0.0	False		,,,				2504	0.0				p.A176A		Atlas-SNP	.											CEP85,NS,carcinoma,+2,1	CEP85	61	1	0			c.G528A						PASS	.	G		236,4170	141.1+/-176.5	3,230,1970	87.0	85.0	86.0		528	3.6	0.7	1	dbSNP_126	86	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous	CEP85	NM_022778.2		3,233,6267	AA,AG,GG		0.0349,5.3563,1.8376		176/763	26581981	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	64793	exon4			AGAGGCGAGGAAG	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"""coiled-coil domain containing 21"""	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.528G>A	1.37:g.26581981G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Silent	SNP	ENST00000252992.4	37	CCDS277.1																																																																																			G|0.979;A|0.021	0.021	strong		0.473	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778	
HECTD2	143279	hgsc.bcm.edu	37	10	93260363	93260363	+	Silent	SNP	C	C	T	rs34553731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:93260363C>T	ENST00000298068.5	+	19	2149	c.2055C>T	c.(2053-2055)gaC>gaT	p.D685D	HECTD2_ENST00000446394.1_Silent_p.D689D|HECTD2_ENST00000536715.1_Silent_p.D274D|HECTD2_ENST00000371667.1_Silent_p.D335D	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	685	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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)			breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						CAAAAACGGACTTAACTATAA	0.418													C|||	61	0.0121805	0.0439	0.0029	5008	,	,		16343	0.0		0.001	False		,,,				2504	0.0				p.D685D	NSCLC(12;376 469 1699 39910 41417)	Atlas-SNP	.											.	HECTD2	60	.	0			c.C2055T						PASS	.	C		205,4201	127.0+/-164.0	5,195,2003	103.0	95.0	98.0		2055	3.9	0.6	10	dbSNP_126	98	6,8594	3.0+/-9.4	0,6,4294	no	coding-synonymous	HECTD2	NM_182765.3		5,201,6297	TT,TC,CC		0.0698,4.6527,1.6223		685/777	93260363	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	143279	exon19			AACGGACTTAACT	AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"""HECT domain containing 2"""			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.2055C>T	10.37:g.93260363C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_182765	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Silent	SNP	ENST00000298068.5	37	CCDS7414.1																																																																																			C|0.985;T|0.015	0.015	strong		0.418	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1		
SHROOM1	134549	hgsc.bcm.edu	37	5	132159393	132159393	+	Silent	SNP	G	G	A	rs33935150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132159393G>A	ENST00000378679.3	-	8	2679	c.1875C>T	c.(1873-1875)aaC>aaT	p.N625N	SHROOM1_ENST00000319854.3_Silent_p.N625N|SHROOM1_ENST00000488072.1_5'UTR|SHROOM1_ENST00000378676.1_Silent_p.N556N	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	625	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGGTGGCAGGGTTTTCAAGCC	0.597													G|||	379	0.0756789	0.1664	0.0144	5008	,	,		17766	0.1349		0.0119	False		,,,				2504	0.001				p.N625N		Atlas-SNP	.											.	SHROOM1	35	.	0			c.C1875T						PASS	.	G	,	690,3716	281.4+/-275.9	51,588,1564	52.0	53.0	52.0		1875,1875	-0.4	0.0	5	dbSNP_126	52	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,coding-synonymous	SHROOM1	NM_001172700.1,NM_133456.2	,	51,609,5843	AA,AG,GG		0.2442,15.6605,5.4667	,	625/853,625/848	132159393	711,12295	2203	4300	6503	SO:0001819	synonymous_variant	134549	exon5			GGCAGGGTTTTCA	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.1875C>T	5.37:g.132159393G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Silent	SNP	ENST00000378679.3	37	CCDS54902.1																																																																																			G|0.939;A|0.061	0.061	strong		0.597	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456	
ACSM5	54988	hgsc.bcm.edu	37	16	20432605	20432605	+	Missense_Mutation	SNP	A	A	G	rs59025904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20432605A>G	ENST00000331849.4	+	5	796	c.649A>G	c.(649-651)Atg>Gtg	p.M217V		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	217			M -> V (in dbSNP:rs59025904).		fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						GCACAACTGCATGAGGACAAA	0.517													G|||	684	0.136581	0.3079	0.0605	5008	,	,		14543	0.0615		0.0487	False		,,,				2504	0.1268				p.M217V		Atlas-SNP	.											.	ACSM5	101	.	0			c.A649G						PASS	.	G	VAL/MET	1224,3182	706.7+/-407.4	172,880,1151	61.0	60.0	60.0		649	1.2	0.0	16	dbSNP_129	60	496,8104	797.0+/-407.5	13,470,3817	yes	missense	ACSM5	NM_017888.2	21	185,1350,4968	GG,GA,AA		5.7674,27.7803,13.2247	benign	217/580	20432605	1720,11286	2203	4300	6503	SO:0001583	missense	54988	exon5			AACTGCATGAGGA		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.649A>G	16.37:g.20432605A>G	ENSP00000327916:p.Met217Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	250	0.11446886446886446	145	0.29471544715447157	27	0.07458563535911603	37	0.06468531468531469	41	0.05408970976253298	G	0.001	-3.144640	0.00029	0.277803	0.057674	ENSG00000183549	ENST00000331849	T	0.42513	0.97	4.43	1.23	0.21249	AMP-dependent synthetase/ligase (1);	0.373188	0.22389	N	0.060709	T	0.00012	0.0000	N	0.00113	-2.09	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41052	-0.9530	9	0.02654	T	1	-3.0733	9.1067	0.36703	0.1418:0.3348:0.5234:0.0	rs59025904	217	Q6NUN0	ACSM5_HUMAN	V	217	ENSP00000327916:M217V	ENSP00000327916:M217V	M	+	1	0	ACSM5	20340106	0.004000	0.15560	0.023000	0.16930	0.055000	0.15305	-0.147000	0.10234	-0.295000	0.08960	-2.208000	0.00301	ATG	A|0.875;G|0.125	0.125	strong		0.517	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
LILRA6	79168	hgsc.bcm.edu	37	19	54744182	54744182	+	Missense_Mutation	SNP	A	A	T	rs3193485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54744182A>T	ENST00000396365.2	-	6	1265	c.1226T>A	c.(1225-1227)tTc>tAc	p.F409Y	LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.F409Y|LILRA6_ENST00000245621.5_Missense_Mutation_p.F409Y	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	409					immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.F409Y(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CTCACTGGGGAAAGACAGCAG	0.622																																					p.F409Y		Atlas-SNP	.											LILRA6,nipple,malignant_melanoma,0,1	LILRA6	75	1	1	Substitution - Missense(1)	skin(1)	c.T1226A						scavenged	.						97.0	135.0	122.0					19																	54744182		2197	4300	6497	SO:0001583	missense	79168	exon6			CTGGGGAAAGACA	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.1226T>A	19.37:g.54744182A>T	ENSP00000379651:p.Phe409Tyr	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	285	63	0.221053	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.262301	0.00021	.	.	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.00717	5.79;5.79;5.79	2.71	-5.43	0.02632	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	12.755800	0.00166	N	0.000006	T	0.00845	0.0028	L	0.56199	1.76	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.002	B;B;B	0.06405	0.0;0.0;0.002	T	0.53641	-0.8410	10	0.09338	T	0.73	.	2.0397	0.03547	0.4944:0.1022:0.2479:0.1555	rs3193485	409;409;409	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	Y	409	ENSP00000411227:F409Y;ENSP00000379651:F409Y;ENSP00000245621:F409Y	ENSP00000245621:F409Y	F	-	2	0	LILRA6	59435994	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.946000	0.00167	-4.280000	0.00059	-3.764000	0.00021	TTC	.	.	alt		0.622	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
RFTN1	23180	hgsc.bcm.edu	37	3	16364919	16364919	+	Silent	SNP	A	A	C	rs690216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:16364919A>C	ENST00000334133.4	-	9	1568	c.1296T>G	c.(1294-1296)ccT>ccG	p.P432P	OXNAD1_ENST00000544043.1_Intron|OXNAD1_ENST00000435829.2_Intron|OXNAD1_ENST00000605932.1_Intron|RFTN1_ENST00000483671.1_5'UTR|OXNAD1_ENST00000606098.1_Intron|RFTN1_ENST00000432519.1_Silent_p.P396P	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	79	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	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	
ZNF860	344787	hgsc.bcm.edu	37	3	32031962	32031962	+	Missense_Mutation	SNP	A	A	G	rs1808125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:32031962A>G	ENST00000360311.4	+	2	1940	c.1391A>G	c.(1390-1392)cAt>cGt	p.H464R		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	464					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						AAGACCTTCCATCACAATTCA	0.418													a|||	3114	0.621805	0.9054	0.4813	5008	,	,		19471	0.7599		0.2773	False		,,,				2504	0.5501				p.H464R		Atlas-SNP	.											ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	0			c.A1391G						PASS	.						22.0	58.0	48.0					3																	32031962		627	1568	2195	SO:0001583	missense	344787	exon2			CCTTCCATCACAA	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1391A>G	3.37:g.32031962A>G	ENSP00000373274:p.His464Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	99	53	0.535354	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	991	0.45375457875457875	324	0.6585365853658537	145	0.4005524861878453	368	0.6433566433566433	154	0.20316622691292877	a	0.169	-1.073378	0.01918	.	.	ENSG00000197385	ENST00000360311	T	0.17370	2.28	0.3	-0.599	0.11645	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00399	-1.545	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.42032	-0.9475	7	.	.	.	.	4.0852	0.09943	0.2146:0.4157:0.3696:0.0	rs1808125;rs60384157	464	A6NHJ4	ZN860_HUMAN	R	464	ENSP00000373274:H464R	.	H	+	2	0	ZNF860	32006966	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.083000	0.03397	-3.961000	0.00087	-3.988000	0.00014	CAT	A|0.545;G|0.455	0.455	strong		0.418	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
KIAA1377	57562	hgsc.bcm.edu	37	11	101829070	101829070	+	Silent	SNP	C	C	T	rs61742070	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:101829070C>T	ENST00000263468.8	+	5	948	c.678C>T	c.(676-678)ctC>ctT	p.L226L	KIAA1377_ENST00000537689.1_Silent_p.L27L	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	226										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AGAAACTCCTCGAAGATCAAC	0.343													C|||	49	0.00978435	0.0371	0.0	5008	,	,		18452	0.0		0.0	False		,,,				2504	0.0				p.L226L		Atlas-SNP	.											.	KIAA1377	111	.	0			c.C678T						PASS	.	C		129,4277	90.2+/-128.9	0,129,2074	105.0	113.0	110.0		678	0.7	1.0	11	dbSNP_129	110	0,8598		0,0,4299	no	coding-synonymous	KIAA1377	NM_020802.2		0,129,6373	TT,TC,CC		0.0,2.9278,0.992		226/1118	101829070	129,12875	2203	4299	6502	SO:0001819	synonymous_variant	57562	exon5			ACTCCTCGAAGAT	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.678C>T	11.37:g.101829070C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_020802	Q4G0U6	Silent	SNP	ENST00000263468.8	37	CCDS31658.1																																																																																			C|0.989;T|0.011	0.011	strong		0.343	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
HLA-A	3105	hgsc.bcm.edu	37	6	29912315	29912315	+	Missense_Mutation	SNP	A	A	C	rs41554316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29912315A>C	ENST00000396634.1	+	7	1275	c.934A>C	c.(934-936)Att>Ctt	p.I312L	HLA-A_ENST00000376809.5_Missense_Mutation_p.I312L|HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376806.5_Missense_Mutation_p.I312L			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	312					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						CGTGGGCATCATTGCTGGCCT	0.607									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.I312L		Atlas-SNP	.											.	HLA-A	89	.	0			c.A934C						PASS	.						106.0	100.0	102.0					6																	29912315		1510	2709	4219	SO:0001583	missense	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGCATCATTGCTG	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.934A>C	6.37:g.29912315A>C	ENSP00000379873:p.Ile312Leu	Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	530	173	0.326415	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	278	0.12728937728937728	107	0.21747967479674796	53	0.1464088397790055	87	0.1520979020979021	31	0.040897097625329816	.	6.803	0.517242	0.13005	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809	T;T;T	0.00695	5.86;5.83;5.86	3.69	-7.38	0.01407	.	0.936076	0.08704	U	0.905960	T	0.00440	0.0014	M	0.78049	2.395	0.09310	N	1	B;B;B;B;B	0.18461	0.028;0.0;0.018;0.0;0.0	B;B;B;B;B	0.22753	0.004;0.003;0.041;0.003;0.002	T	0.34079	-0.9843	10	0.87932	D	0	.	7.9928	0.30250	0.3199:0.1368:0.5432:0.0	rs41554316	191;312;312;312;312	B4DVB9;P16188;Q5SRN5;P30455;P04439	.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	L	312	ENSP00000379873:I312L;ENSP00000366002:I312L;ENSP00000366005:I312L	ENSP00000366002:I312L	I	+	1	0	HLA-A	30020294	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.381000	0.00491	-1.707000	0.01402	-1.766000	0.00665	ATT	A|0.889;C|0.111	0.111	strong		0.607	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CAPN12	147968	hgsc.bcm.edu	37	19	39234674	39234674	+	Silent	SNP	G	G	A	rs111831826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39234674G>A	ENST00000328867.4	-	1	440	c.132C>T	c.(130-132)atC>atT	p.I44I	CAPN12_ENST00000601953.1_Intron	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	44					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			CGCGGAACAGGATCCCCGAAT	0.637													g|||	11	0.00219649	0.0083	0.0	5008	,	,		16631	0.0		0.0	False		,,,				2504	0.0				p.I44I		Atlas-SNP	.											.	CAPN12	43	.	0			c.C132T						PASS	.	G		27,4379	32.6+/-62.9	0,27,2176	82.0	67.0	72.0		132	2.6	1.0	19	dbSNP_132	72	0,8600		0,0,4300	no	coding-synonymous	CAPN12	NM_144691.3		0,27,6476	AA,AG,GG		0.0,0.6128,0.2076		44/720	39234674	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	147968	exon1			GAACAGGATCCCC	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.132C>T	19.37:g.39234674G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			G|0.998;A|0.002	0.002	strong		0.637	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
ZNF469	84627	hgsc.bcm.edu	37	16	88504850	88504850	+	Missense_Mutation	SNP	G	G	C	rs1105066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88504850G>C	ENST00000437464.1	+	2	10888	c.10888G>C	c.(10888-10890)Gag>Cag	p.E3630Q	ZNF469_ENST00000565624.1_Missense_Mutation_p.E3658Q	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	3630			E -> Q (in dbSNP:rs1105066). {ECO:0000269|PubMed:11347906}.		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						CATGGTGTCTGAGGGGGGGCC	0.642													G|||	1958	0.390974	0.531	0.3818	5008	,	,		13825	0.38		0.3926	False		,,,				2504	0.2178				p.E3630Q		Atlas-SNP	.											.	ZNF469	121	.	0			c.G10888C						PASS	.	G	GLN/GLU	729,639		200,329,155	7.0	11.0	10.0		10888	1.3	0.1	16	dbSNP_86	10	1311,1845		287,737,554	yes	missense	ZNF469	NM_001127464.1	29	487,1066,709	CC,CG,GG		41.5399,46.7105,45.0928	benign	3630/3926	88504850	2040,2484	684	1578	2262	SO:0001583	missense	84627	exon2			GTGTCTGAGGGGG	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.10888G>C	16.37:g.88504850G>C	ENSP00000402343:p.Glu3630Gln	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	886	0.4056776556776557	265	0.5386178861788617	133	0.3674033149171271	195	0.3409090909090909	293	0.3865435356200528	G	9.407	1.079583	0.20309	0.532895	0.415399	ENSG00000225614	ENST00000437464	T	0.09911	2.93	4.65	1.33	0.21861	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P	0.34724	0.465	B	0.30572	0.117	T	0.38972	-0.9636	8	0.49607	T	0.09	-3.6085	6.1191	0.20144	0.1901:0.1577:0.6522:0.0	rs1105066;rs3812952;rs57863012;rs1105066	3630	Q96JG9	ZN469_HUMAN	Q	3630	ENSP00000402343:E3630Q	ENSP00000402343:E3630Q	E	+	1	0	ZNF469	87032351	0.000000	0.05858	0.122000	0.21767	0.019000	0.09904	-0.519000	0.06260	0.950000	0.37743	0.561000	0.74099	GAG	G|0.601;C|0.399	0.399	strong		0.642	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
ADAMTS10	81794	hgsc.bcm.edu	37	19	8669931	8669931	+	Missense_Mutation	SNP	G	G	C	rs7255721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8669931G>C	ENST00000597188.1	-	4	671	c.401C>G	c.(400-402)aCc>aGc	p.T134S	ADAMTS10_ENST00000596709.1_5'UTR|ADAMTS10_ENST00000270328.4_Missense_Mutation_p.T134S	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	134			T -> S (in dbSNP:rs7255721). {ECO:0000269|PubMed:15355968}.			extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						CACATGGGAGGTGCTGGCCTG	0.622													C|||	4477	0.89397	0.9766	0.8516	5008	,	,		15683	0.9702		0.7048	False		,,,				2504	0.9284				p.T134S		Atlas-SNP	.											.	ADAMTS10	132	.	0			c.C401G						PASS	.	C	SER/THR	4069,273		1906,257,8	8.0	10.0	9.0		401	5.2	1.0	19	dbSNP_116	9	5979,2533		2139,1701,416	yes	missense	ADAMTS10	NM_030957.2	58	4045,1958,424	CC,CG,GG		29.758,6.2874,21.8298	benign	134/1104	8669931	10048,2806	2171	4256	6427	SO:0001583	missense	81794	exon4			TGGGAGGTGCTGG	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13201	protein-coding gene	gene with protein product		608990	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"""				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.401C>G	19.37:g.8669931G>C	ENSP00000471851:p.Thr134Ser	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_030957	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	37	CCDS12206.1	1862	0.8525641025641025	478	0.9715447154471545	297	0.8204419889502762	552	0.965034965034965	535	0.7058047493403694	C	3.922	-0.017841	0.07681	0.937126	0.70242	ENSG00000142303	ENST00000270328	T	0.58060	0.36	5.24	5.24	0.73138	Peptidase M12B, propeptide (1);	0.190363	0.46758	N	0.000276	T	0.00012	0.0000	N	0.00471	-1.455	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.41179	-0.9523	9	0.02654	T	1	.	10.455	0.44546	0.0:0.789:0.1357:0.0753	rs7255721;rs7255721	134	Q9H324	ATS10_HUMAN	S	134	ENSP00000270328:T134S	ENSP00000270328:T134S	T	-	2	0	ADAMTS10	8575931	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	0.951000	0.29135	1.228000	0.43614	-0.322000	0.08575	ACC	G|0.152;C|0.848	0.848	strong		0.622	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957	
CMYA5	202333	hgsc.bcm.edu	37	5	79025634	79025634	+	Missense_Mutation	SNP	G	G	A	rs1366271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79025634G>A	ENST00000446378.2	+	2	1077	c.1046G>A	c.(1045-1047)gGc>gAc	p.G349D		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	349			G -> D (in dbSNP:rs1366271).		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)		TCAAGTAGTGGCAGAGCAGAA	0.433													A|||	1175	0.234625	0.441	0.072	5008	,	,		21209	0.3621		0.0815	False		,,,				2504	0.0971				p.G349D		Atlas-SNP	.											.	CMYA5	643	.	0			c.G1046A						PASS	.	A	ASP/GLY	1546,2600		300,946,827	70.0	67.0	68.0		1046	2.8	0.2	5	dbSNP_88	68	725,7709		40,645,3532	yes	missense	CMYA5	NM_153610.3	94	340,1591,4359	AA,AG,GG		8.5962,37.289,18.0525	benign	349/4070	79025634	2271,10309	2073	4217	6290	SO:0001583	missense	202333	exon2			GTAGTGGCAGAGC	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.1046G>A	5.37:g.79025634G>A	ENSP00000394770:p.Gly349Asp	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	215	215	1	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	535	0.24496336996336995	218	0.44308943089430897	26	0.0718232044198895	232	0.40559440559440557	59	0.07783641160949868	A	1.948	-0.442042	0.04604	0.37289	0.085962	ENSG00000164309	ENST00000446378	T	0.29397	1.57	5.34	2.82	0.32997	.	1.606740	0.03686	N	0.246341	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	0.42068	-0.9473	9	0.02654	T	1	.	5.9887	0.19448	0.5997:0.3163:0.084:0.0	rs1366271;rs60907015;rs1366271	349	Q8N3K9	CMYA5_HUMAN	D	349	ENSP00000394770:G349D	ENSP00000394770:G349D	G	+	2	0	CMYA5	79061390	0.000000	0.05858	0.156000	0.22583	0.307000	0.27823	0.303000	0.19210	0.060000	0.16281	-0.269000	0.10298	GGC	G|0.742;A|0.258	0.258	strong		0.433	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
MICA	100507436	hgsc.bcm.edu	37	6	31378358	31378358	+	Missense_Mutation	SNP	T	T	G	rs1063630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31378358T>G	ENST00000449934.2	+	2	163	c.109T>G	c.(109-111)Tgg>Ggg	p.W37G	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				GGTGCTGTCCTGGGATGGATC	0.512													c|||	1343	0.268171	0.3797	0.3386	5008	,	,		20004	0.1786		0.1928	False		,,,				2504	0.2372				p.W37G		Atlas-SNP	.											.	MICA	21	.	0			c.T109G						PASS	.	C	GLY/TRP	476,908		97,282,313	9.0	10.0	10.0		109	-2.2	0.0	6	dbSNP_86	10	534,2640		46,442,1099	no	missense	MICA	NM_001177519.1	184	143,724,1412	GG,GT,TT		16.8242,34.3931,22.1588	benign	37/333	31378358	1010,3548	692	1587	2279	SO:0001583	missense	100507436	exon2			CTGTCCTGGGATG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.109T>G	6.37:g.31378358T>G	ENSP00000413079:p.Trp37Gly	Somatic	326	2	0.00613497		WXS	Illumina HiSeq	Phase_I	285	285	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	575	0.2632783882783883	179	0.3638211382113821	140	0.3867403314917127	95	0.1660839160839161	161	0.21240105540897097	N	6.451	0.451312	0.12223	0.343931	0.168242	ENSG00000204520	ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.00682	5.86;5.86	2.89	-2.15	0.07102	.	2.042530	0.02822	N	0.125645	T	0.00271	0.0008	N	0.16903	0.455	0.80722	P	0.0	B	0.32071	0.355	B	0.36845	0.234	T	0.41805	-0.9488	9	0.56958	D	0.05	.	4.6738	0.12701	0.1467:0.4801:0.0:0.3732	rs1063630;rs17206511;rs17882548;rs59366444	37	Q96QC4	.	G	37;37;37;24	ENSP00000413079:W37G;ENSP00000402410:W24G	ENSP00000365394:W37G	W	+	1	0	MICA	31486337	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.968000	0.03817	-0.789000	0.04498	-3.462000	0.00035	TGG	C|0.003;G|0.250;T|0.747	0.250	strong		0.512	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
PDPR	55066	hgsc.bcm.edu	37	16	70180088	70180088	+	Missense_Mutation	SNP	A	A	T	rs2287978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70180088A>T	ENST00000288050.4	+	16	2876	c.1919A>T	c.(1918-1920)tAt>tTt	p.Y640F	PDPR_ENST00000567046.1_De_novo_Start_OutOfFrame|PDPR_ENST00000398122.3_Missense_Mutation_p.Y540F|PDPR_ENST00000568530.1_Missense_Mutation_p.Y640F|PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000542659.1_De_novo_Start_InFrame	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	640					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		GAGTTGTCCTATGCCCCTATG	0.468													.|||	559	0.111621	0.0091	0.0893	5008	,	,		24813	0.1865		0.1173	False		,,,				2504	0.183				p.Y640F		Atlas-SNP	.											.	PDPR	66	.	0			c.A1919T						PASS	.	A	PHE/TYR	106,3632		4,98,1767	115.0	116.0	115.0		1919	5.0	1.0	16	dbSNP_134	115	956,7278		43,870,3204	no	missense	PDPR	NM_017990.3	22	47,968,4971	TT,TA,AA		11.6104,2.8357,8.8707	possibly-damaging	640/880	70180088	1062,10910	1869	4117	5986	SO:0001583	missense	55066	exon16			TGTCCTATGCCCC		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1919A>T	16.37:g.70180088A>T	ENSP00000288050:p.Tyr640Phe	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	181	91	0.502762	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.851062	0.71719	0.028357	0.116104	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055	D;D	0.83163	-1.69;-1.69	5.02	5.02	0.67125	Glycine cleavage T-protein, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.06096	0.0158	N	0.14661	0.345	0.09310	P	1.0	D;D	0.64830	0.994;0.965	D;P	0.63033	0.91;0.845	T	0.64097	-0.6487	9	0.59425	D	0.04	.	13.9208	0.63930	1.0:0.0:0.0:0.0	.	368;640	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	F	640;540;368	ENSP00000288050:Y640F;ENSP00000381190:Y540F	ENSP00000205055:Y368F	Y	+	2	0	PDPR	68737589	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.097000	0.94193	1.898000	0.54952	0.379000	0.24179	TAT	A|0.750;T|0.250	0.250	weak		0.468	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119894	38119894	+	Missense_Mutation	SNP	G	G	A	rs35105846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38119894G>A	ENST00000406386.3	+	7	1586	c.1331G>A	c.(1330-1332)aGt>aAt	p.S444N		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	444					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.S444N(1)		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)					TCCTCTCCCAGTAGAGCTACA	0.587																																					p.S444N		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	1	Substitution - Missense(1)	prostate(1)	c.G1331A						scavenged	.						70.0	74.0	73.0					22																	38119894		1882	4104	5986	SO:0001583	missense	11078	exon7			CTCCCAGTAGAGC	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.1331G>A	22.37:g.38119894G>A	ENSP00000384312:p.Ser444Asn	Somatic	297	1	0.003367		WXS	Illumina HiSeq	Phase_I	361	16	0.0443213	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	3.506	-0.100772	0.06967	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19938	2.11	3.02	-0.653	0.11447	.	.	.	.	.	T	0.04003	0.0112	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33266	-0.9875	9	0.15952	T	0.53	.	0.3565	0.00358	0.3833:0.1916:0.2386:0.1864	rs35105846	444	Q9H2D6	TARA_HUMAN	N	444	ENSP00000384312:S444N	ENSP00000384312:S444N	S	+	2	0	TRIOBP	36449840	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.155000	0.03163	-0.991000	0.03476	-3.651000	0.00026	AGT	G|0.500;A|0.500	0.500	strong		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
RFTN1	23180	hgsc.bcm.edu	37	3	16364954	16364954	+	Missense_Mutation	SNP	C	C	T	rs11554130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:16364954C>T	ENST00000334133.4	-	9	1533	c.1261G>A	c.(1261-1263)Gta>Ata	p.V421I	OXNAD1_ENST00000544043.1_Intron|OXNAD1_ENST00000435829.2_Intron|OXNAD1_ENST00000605932.1_Intron|RFTN1_ENST00000483671.1_5'UTR|OXNAD1_ENST00000606098.1_Intron|RFTN1_ENST00000432519.1_Missense_Mutation_p.V385I	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	421			V -> I (in dbSNP:rs11554130). {ECO:0000269|Ref.1}.		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						TTGGTGGATACACTCCCCTCG	0.448													C|||	992	0.198083	0.5204	0.1124	5008	,	,		20261	0.0258		0.1551	False		,,,				2504	0.045				p.V421I		Atlas-SNP	.											.	RFTN1	79	.	0			c.G1261A						PASS	.	C	ILE/VAL	1971,2435	555.4+/-379.2	439,1093,671	103.0	92.0	96.0		1261	0.1	0.0	3	dbSNP_120	96	1230,7370	246.2+/-274.8	93,1044,3163	yes	missense	RFTN1	NM_015150.1	29	532,2137,3834	TT,TC,CC		14.3023,44.7345,24.6117	possibly-damaging	421/579	16364954	3201,9805	2203	4300	6503	SO:0001583	missense	23180	exon9			TGGATACACTCCC	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.1261G>A	3.37:g.16364954C>T	ENSP00000334153:p.Val421Ile	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	63	38	0.603175	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Missense_Mutation	SNP	ENST00000334133.4	37	CCDS33712.1	418	0.19139194139194138	246	0.5	44	0.12154696132596685	14	0.024475524475524476	114	0.1503957783641161	C	13.16	2.154612	0.38021	0.447345	0.143023	ENSG00000131378	ENST00000432519;ENST00000334133	T;T	0.32023	1.47;1.47	5.35	0.123	0.14709	.	0.306284	0.32503	N	0.006011	T	0.00012	0.0000	M	0.62723	1.935	0.32857	P	0.492536	B;B	0.23249	0.082;0.082	B;B	0.26202	0.067;0.039	T	0.41502	-0.9505	9	0.51188	T	0.08	-10.3163	3.686	0.08328	0.2251:0.4273:0.0:0.3476	rs11554130;rs59839635	385;421	G3XAJ6;Q14699	.;RFTN1_HUMAN	I	385;421	ENSP00000403926:V385I;ENSP00000334153:V421I	ENSP00000334153:V421I	V	-	1	0	RFTN1	16339958	0.020000	0.18652	0.002000	0.10522	0.954000	0.61252	0.214000	0.17541	0.264000	0.21851	0.555000	0.69702	GTA	C|0.775;T|0.225	0.225	strong		0.448	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150	
PREX2	80243	hgsc.bcm.edu	37	8	69104701	69104701	+	Silent	SNP	G	G	A	rs116570374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:69104701G>A	ENST00000288368.4	+	37	4822	c.4545G>A	c.(4543-4545)tcG>tcA	p.S1515S		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1515					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CAGTTTCCTCGGAGCTGTGCA	0.557													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		12376	0.0		0.0	False		,,,				2504	0.0				p.S1515S		Atlas-SNP	.											.	PREX2	614	.	0			c.G4545A						PASS	.	G		93,4313	75.7+/-113.9	1,91,2111	57.0	47.0	50.0		4545	-3.1	1.0	8	dbSNP_132	50	2,8598		0,2,4298	no	coding-synonymous	PREX2	NM_024870.2		1,93,6409	AA,AG,GG		0.0233,2.1108,0.7304		1515/1607	69104701	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon37			TTCCTCGGAGCTG	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4545G>A	8.37:g.69104701G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			G|0.993;A|0.007	0.007	strong		0.557	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
HTR4	3360	hgsc.bcm.edu	37	5	147845463	147845463	+	Missense_Mutation	SNP	G	G	A	rs73266449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147845463G>A	ENST00000314512.6	-	7	1265	c.1102C>T	c.(1102-1104)Ctc>Ttc	p.L368F	HTR4_ENST00000521735.1_Missense_Mutation_p.L368F|HTR4_ENST00000521530.1_Intron|HTR4_ENST00000354217.2_Intron	NM_199453.3	NP_955525.1	Q13639	5HT4R_HUMAN	5-hydroxytryptamine (serotonin) receptor 4, G protein-coupled	0					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|regulation of appetite (GO:0032098)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cinitapride(DB08810)|Cisapride(DB00604)|Ergoloid mesylate(DB01049)|Metoclopramide(DB01233)|Ondansetron(DB00904)	AAGAGCAGGAGGAAGCTGGAG	0.433													G|||	200	0.0399361	0.1437	0.0144	5008	,	,		17221	0.0		0.0	False		,,,				2504	0.0				p.L368F	GBM(120;370 1604 14007 17804 41573)	Atlas-SNP	.											.	HTR4	161	.	0			c.C1102T						PASS	.	G	,PHE/LEU	459,3947	219.4+/-237.2	28,403,1772	150.0	163.0	158.0		,1102	-7.4	0.3	5	dbSNP_130	158	3,8597	3.0+/-9.4	0,3,4297	yes	intron,missense	HTR4	NM_001040169.2,NM_199453.3	,22	28,406,6069	AA,AG,GG		0.0349,10.4176,3.5522	,	,368/379	147845463	462,12544	2203	4300	6503	SO:0001583	missense	3360	exon6			GCAGGAGGAAGCT	Y08756	CCDS4291.1, CCDS34270.1, CCDS34271.1, CCDS34272.1, CCDS34273.1, CCDS34273.2, CCDS75353.1	5q31-q33	2012-08-08	2012-02-03		ENSG00000164270	ENSG00000164270		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5299	protein-coding gene	gene with protein product		602164	"""5-hydroxytryptamine (serotonin) receptor 4"""			9371406, 9276448	Standard	NM_199453		Approved	5-HT4	uc021yfj.1	Q13639	OTTHUMG00000129931	ENST00000314512.6:c.1102C>T	5.37:g.147845463G>A	ENSP00000314906:p.Leu368Phe	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	255	118	0.462745	NM_199453	C4WYH4|Q546Q1|Q684M0|Q712M9|Q96KH9|Q96KI0|Q9H199|Q9NY73|Q9UBM6|Q9UBT4|Q9UE22|Q9UE23|Q9UQR6	Missense_Mutation	SNP	ENST00000314512.6	37	CCDS34271.1	77	0.035256410256410256	72	0.14634146341463414	5	0.013812154696132596	0	0.0	0	0.0	G	9.178	1.022933	0.19433	0.104176	3.49E-4	ENSG00000164270	ENST00000314512;ENST00000521735	T;T	0.71817	-0.6;-0.6	5.06	-7.41	0.01392	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.31926	P	0.612866	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	7	0.09843	T	0.71	.	16.3003	0.82806	0.6695:0.0:0.3305:0.0	.	368	Q684M0	.	F	368	ENSP00000314906:L368F;ENSP00000430979:L368F	ENSP00000314906:L368F	L	-	1	0	HTR4	147825656	0.873000	0.30073	0.266000	0.24541	0.912000	0.54170	-0.283000	0.08433	-2.141000	0.00805	-2.010000	0.00438	CTC	G|0.967;A|0.033	0.033	strong		0.433	HTR4-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374235.1	NM_000870	
GABRG2	2566	hgsc.bcm.edu	37	5	161528280	161528280	+	Silent	SNP	C	C	T	rs211037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:161528280C>T	ENST00000361925.4	+	5	808	c.588C>T	c.(586-588)aaC>aaT	p.N196N	GABRG2_ENST00000356592.3_Silent_p.N196N|GABRG2_ENST00000414552.2_Silent_p.N196N|GABRG2_ENST00000393933.4_Silent_p.N101N			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	196					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.N196N(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AATTGCACAACTTTCCAATGG	0.358													C|||	1861	0.371605	0.4682	0.2507	5008	,	,		17256	0.6012		0.2435	False		,,,				2504	0.2219				p.N196N		Atlas-SNP	.											GABRG2,NS,carcinoma,0,1	GABRG2	142	1	1	Substitution - coding silent(1)	stomach(1)	c.C588T						PASS	.	C	,,	1906,2500	545.1+/-376.7	413,1080,710	112.0	104.0	106.0		588,588,588	3.5	1.0	5	dbSNP_79	106	2088,6512	358.8+/-331.3	269,1550,2481	no	coding-synonymous,coding-synonymous,coding-synonymous	GABRG2	NM_000816.3,NM_198903.2,NM_198904.2	,,	682,2630,3191	TT,TC,CC		24.2791,43.2592,30.7089	,,	196/468,196/516,196/476	161528280	3994,9012	2203	4300	6503	SO:0001819	synonymous_variant	2566	exon5			GCACAACTTTCCA		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4087	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma 2"""	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.588C>T	5.37:g.161528280C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_198904	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Silent	SNP	ENST00000361925.4	37	CCDS4358.1																																																																																			C|0.648;T|0.352	0.352	strong		0.358	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1		
FCRL1	115350	hgsc.bcm.edu	37	1	157771979	157771979	+	Silent	SNP	C	C	T	rs12035302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157771979C>T	ENST00000368176.3	-	5	679	c.612G>A	c.(610-612)ccG>ccA	p.P204P	FCRL1_ENST00000491942.1_Silent_p.P204P|FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000358292.3_Silent_p.P204P	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	204						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)			GGCGAGACACCGGGACTGAGG	0.582													C|||	122	0.024361	0.0832	0.0058	5008	,	,		19850	0.006		0.001	False		,,,				2504	0.001				p.P204P	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.G612A						PASS	.	C	,,	291,4115	141.5+/-176.9	15,261,1927	34.0	36.0	35.0		612,612,612	1.2	1.0	1	dbSNP_120	35	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	FCRL1	NM_001159397.1,NM_001159398.1,NM_052938.4	,,	15,266,6222	TT,TC,CC		0.0581,6.6046,2.2759	,,	204/367,204/429,204/430	157771979	296,12710	2203	4300	6503	SO:0001819	synonymous_variant	115350	exon5			AGACACCGGGACT	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.612G>A	1.37:g.157771979C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	136	65	0.477941	NM_001159397	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Silent	SNP	ENST00000368176.3	37	CCDS1170.1																																																																																			C|0.978;T|0.022	0.022	strong		0.582	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938	
PDHX	8050	hgsc.bcm.edu	37	11	34969150	34969150	+	Silent	SNP	C	C	T	rs34582941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34969150C>T	ENST00000227868.4	+	3	423	c.339C>T	c.(337-339)atC>atT	p.I113I	PDHX_ENST00000448838.3_Silent_p.I98I|PDHX_ENST00000430469.2_Silent_p.I113I			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	113	Lipoyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.				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)			TGGCCAAAATCGTGGTAAGTT	0.353													C|||	272	0.0543131	0.1974	0.0159	5008	,	,		15319	0.0		0.0	False		,,,				2504	0.0				p.I113I		Atlas-SNP	.											.	PDHX	40	.	0			c.C339T						PASS	.	C	,,	720,3684	299.3+/-285.7	67,586,1549	163.0	154.0	157.0		294,339,339	-2.9	1.0	11	dbSNP_126	157	10,8586	5.7+/-21.5	0,10,4288	no	coding-synonymous,coding-synonymous,coding-synonymous	PDHX	NM_001135024.1,NM_001166158.1,NM_003477.2	,,	67,596,5837	TT,TC,CC		0.1163,16.3488,5.6154	,,	98/487,113/275,113/502	34969150	730,12270	2202	4298	6500	SO:0001819	synonymous_variant	8050	exon3			CAAAATCGTGGTA	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.339C>T	11.37:g.34969150C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Silent	SNP	ENST00000227868.4	37	CCDS7896.1																																																																																			C|0.951;T|0.049	0.049	strong		0.353	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
CARD11	84433	hgsc.bcm.edu	37	7	2969689	2969689	+	Missense_Mutation	SNP	T	T	G	rs41515445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2969689T>G	ENST00000396946.4	-	12	1993	c.1590A>C	c.(1588-1590)gaA>gaC	p.E530D		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	530					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)		CGTCCGTGCCTTCTTCCTCGT	0.622			Mis		DLBCL								T|||	141	0.028155	0.1036	0.0058	5008	,	,		16650	0.0		0.0	False		,,,				2504	0.0				p.E530D		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.A1590C						PASS	.	T	ASP/GLU	398,4008	195.3+/-220.0	17,364,1822	115.0	78.0	91.0		1590	-5.4	0.0	7	dbSNP_127	91	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CARD11	NM_032415.4	45	17,366,6120	GG,GT,TT		0.0233,9.0331,3.0755	benign	530/1155	2969689	400,12606	2203	4300	6503	SO:0001583	missense	84433	exon12			CGTGCCTTCTTCC	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.1590A>C	7.37:g.2969689T>G	ENSP00000380150:p.Glu530Asp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	50	0.022893772893772892	46	0.09349593495934959	4	0.011049723756906077	0	0.0	0	0.0	T	4.090	0.014638	0.07959	0.090331	2.33E-4	ENSG00000198286	ENST00000396946;ENST00000355508	T;T	0.30981	1.51;2.48	3.85	-5.41	0.02648	.	1.090360	0.06781	N	0.785380	T	0.00384	0.0012	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23868	-1.0176	10	0.02654	T	1	-2.0525	5.5885	0.17287	0.3319:0.0:0.5015:0.1665	rs41515445;rs58644294	530	Q9BXL7	CAR11_HUMAN	D	530;2	ENSP00000380150:E530D;ENSP00000347695:E2D	ENSP00000347695:E2D	E	-	3	2	CARD11	2936215	0.001000	0.12720	0.000000	0.03702	0.021000	0.10359	-0.891000	0.04135	-0.959000	0.03618	0.459000	0.35465	GAA	T|0.972;G|0.028	0.028	strong		0.622	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
TTC21A	199223	hgsc.bcm.edu	37	3	39180263	39180263	+	Missense_Mutation	SNP	G	G	A	rs704959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39180263G>A	ENST00000431162.2	+	29	4081	c.3947G>A	c.(3946-3948)aGg>aAg	p.R1316K	TTC21A_ENST00000301819.6_Missense_Mutation_p.R1317K|TTC21A_ENST00000440121.1_Missense_Mutation_p.R1268K|TTC21A_ENST00000493856.1_3'UTR			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	1316			R -> K (in dbSNP:rs704959). {ECO:0000269|PubMed:12543795}.							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)		AAGGCCCGAAGGTCCCTGAGG	0.562													G|||	2735	0.546126	0.1573	0.6571	5008	,	,		17827	0.7252		0.666	False		,,,				2504	0.6851				p.R1316K		Atlas-SNP	.											.	TTC21A	96	.	0			c.G3947A						PASS	.	G	LYS/ARG,LYS/ARG	984,2752		119,746,1003	53.0	52.0	52.0		3803,3947	4.4	1.0	3	dbSNP_86	52	5400,2794		1789,1822,486	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	26,26	1908,2568,1489	AA,AG,GG		34.0981,26.3383,46.4878	benign,benign	1268/1273,1316/1321	39180263	6384,5546	1868	4097	5965	SO:0001583	missense	199223	exon29			CCCGAAGGTCCCT	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.3947G>A	3.37:g.39180263G>A	ENSP00000398211:p.Arg1316Lys	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	155	155	1	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	1227	0.5618131868131868	82	0.16666666666666666	229	0.6325966850828729	408	0.7132867132867133	508	0.6701846965699209	G	10.82	1.459146	0.26248	0.263383	0.659019	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.60299	0.2;0.2;0.32	5.28	4.41	0.53225	.	0.269330	0.31772	N	0.007087	T	0.00012	0.0000	N	0.22421	0.69	0.45899	P	0.0012579999999999814	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.45789	-0.9237	9	0.05525	T	0.97	-9.0211	4.3881	0.11327	0.0852:0.1533:0.6034:0.1581	rs704959;rs3172272;rs61259562;rs704959	1268;1317;1316	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	K	1317;1299;1316;1268	ENSP00000301819:R1317K;ENSP00000398211:R1316K;ENSP00000410882:R1268K	ENSP00000301819:R1317K	R	+	2	0	TTC21A	39155267	0.929000	0.31497	0.987000	0.45799	0.936000	0.57629	0.882000	0.28186	1.226000	0.43582	0.561000	0.74099	AGG	G|0.450;A|0.550	0.550	strong		0.562	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
MUC17	140453	hgsc.bcm.edu	37	7	100684573	100684573	+	Silent	SNP	G	G	A	rs144023476	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100684573G>A	ENST00000306151.4	+	3	9940	c.9876G>A	c.(9874-9876)acG>acA	p.T3292T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3292	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)					GCACCACAACGGTGGCCAGTT	0.512													G|||	172	0.034345	0.0688	0.0072	5008	,	,		27204	0.0298		0.0149	False		,,,				2504	0.0317				p.T3292T		Atlas-SNP	.											MUC17,NS,haematopoietic_neoplasm,0,1	MUC17	804	1	0			c.G9876A						scavenged	.	G		35,4371	28.1+/-56.4	2,31,2170	331.0	330.0	330.0		9876	-2.6	0.0	7	dbSNP_134	330	5,8595	2.2+/-6.3	0,5,4295	no	coding-synonymous	MUC17	NM_001040105.1		2,36,6465	AA,AG,GG		0.0581,0.7944,0.3076		3292/4494	100684573	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CACAACGGTGGCC	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.9876G>A	7.37:g.100684573G>A		Somatic	141	2	0.0141844		WXS	Illumina HiSeq	Phase_I	158	13	0.0822785	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.984;A|0.016	0.016	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
HK2	3099	hgsc.bcm.edu	37	2	75107671	75107671	+	Silent	SNP	C	C	T	rs28363033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:75107671C>T	ENST00000290573.2	+	10	2145	c.1545C>T	c.(1543-1545)taC>taT	p.Y515Y	HK2_ENST00000409174.1_Silent_p.Y487Y	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	515	Catalytic.|Hexokinase type-1 2.				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						TGCCCACCTACGTGTGTGCTA	0.597													C|||	56	0.0111821	0.0393	0.0043	5008	,	,		19072	0.0		0.001	False		,,,				2504	0.0				p.Y515Y		Atlas-SNP	.											.	HK2	85	.	0			c.C1545T						PASS	.	C		155,4251	107.3+/-145.7	4,147,2052	64.0	63.0	63.0		1545	-4.0	0.9	2	dbSNP_125	63	0,8600		0,0,4300	no	coding-synonymous	HK2	NM_000189.4		4,147,6352	TT,TC,CC		0.0,3.5179,1.1918		515/918	75107671	155,12851	2203	4300	6503	SO:0001819	synonymous_variant	3099	exon10			CACCTACGTGTGT		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.1545C>T	2.37:g.75107671C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	163	62	0.380368	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	37	CCDS1956.1																																																																																			C|0.988;T|0.012	0.012	strong		0.597	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
ZNF592	9640	hgsc.bcm.edu	37	15	85326315	85326315	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85326315A>C	ENST00000560079.2	+	4	697	c.409A>C	c.(409-411)Acc>Ccc	p.T137P	ZNF592_ENST00000299927.3_Missense_Mutation_p.T137P	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	137					cell death (GO:0008219)|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(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GCCATTACCCACCTTCAACCA	0.478																																					p.T137P		Atlas-SNP	.											.	ZNF592	95	.	0			c.A409C						PASS	.						99.0	105.0	103.0					15																	85326315		2203	4299	6502	SO:0001583	missense	9640	exon4			TTACCCACCTTCA	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.409A>C	15.37:g.85326315A>C	ENSP00000452877:p.Thr137Pro	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.196504	0.58126	.	.	ENSG00000166716	ENST00000299927	T	0.00640	6.03	6.06	6.06	0.98353	.	0.249606	0.46145	D	0.000302	T	0.02156	0.0067	L	0.48642	1.525	0.43852	D	0.99644	D	0.65815	0.995	D	0.63381	0.914	T	0.64580	-0.6374	10	0.72032	D	0.01	-20.196	14.5614	0.68140	1.0:0.0:0.0:0.0	.	137	Q92610	ZN592_HUMAN	P	137	ENSP00000299927:T137P	ENSP00000299927:T137P	T	+	1	0	ZNF592	83127319	0.986000	0.35501	0.998000	0.56505	0.999000	0.98932	3.000000	0.49481	2.324000	0.78689	0.533000	0.62120	ACC	.	.	none		0.478	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
RAB3IL1	5866	hgsc.bcm.edu	37	11	61672235	61672235	+	Silent	SNP	T	T	C	rs174473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61672235T>C	ENST00000394836.2	-	6	934	c.777A>G	c.(775-777)acA>acG	p.T259T	RAB3IL1_ENST00000301773.5_Silent_p.T233T	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	259					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						CCTCCTGCATTGTGAAGTCCA	0.682													C|||	1755	0.350439	0.3601	0.2161	5008	,	,		15452	0.378		0.2336	False		,,,				2504	0.5245				p.T259T		Atlas-SNP	.											.	RAB3IL1	39	.	0			c.A777G						PASS	.	C		1565,2829		282,1001,914	22.0	22.0	22.0		777	-4.3	0.0	11	dbSNP_79	22	1877,6717		220,1437,2640	no	coding-synonymous	RAB3IL1	NM_013401.2		502,2438,3554	CC,CT,TT		21.8408,35.6168,26.5014		259/383	61672235	3442,9546	2197	4297	6494	SO:0001819	synonymous_variant	5866	exon6			CTGCATTGTGAAG	AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.777A>G	11.37:g.61672235T>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	230	87	0.378261	NM_013401	Q86V32|Q9P1Q8	Silent	SNP	ENST00000394836.2	37	CCDS8014.1																																																																																			T|0.713;C|0.287	0.287	strong		0.682	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401	
CAPN6	827	hgsc.bcm.edu	37	X	110494841	110494841	+	Missense_Mutation	SNP	C	C	G	rs12013711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:110494841C>G	ENST00000324068.1	-	6	996	c.829G>C	c.(829-831)Gtg>Ctg	p.V277L	CAPN6_ENST00000541758.1_Missense_Mutation_p.V22L	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	277	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		V -> L (in dbSNP:rs12013711). {ECO:0000269|Ref.4}.		microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						ACCATATACACCTTCTCAGCA	0.478													G|||	740	0.196026	0.5083	0.0605	3775	,	,		14134	0.002		0.0239	False		,,,				2504	0.0				p.V277L		Atlas-SNP	.											.	CAPN6	120	.	0			c.G829C						PASS	.	G	LEU/VAL	2345,1490		605,789,346,238,225	253.0	254.0	254.0		829	5.3	1.0	X	dbSNP_120	254	211,6517		4,155,48,2269,1824	yes	missense	CAPN6	NM_014289.3	32	609,944,394,2507,2049	GG,GC,G,CC,C		3.1361,38.8527,24.1977	benign	277/642	110494841	2556,8007	2203	4300	6503	SO:0001583	missense	827	exon6			TATACACCTTCTC	AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.829G>C	X.37:g.110494841C>G	ENSP00000317214:p.Val277Leu	Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	345	344	0.997101	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Missense_Mutation	SNP	ENST00000324068.1	37	CCDS14555.1	288	0.1735985533453888	171	0.5181818181818182	16	0.04519774011299435	0	0.0	12	0.016	G	4.454	0.084028	0.08583	0.611473	0.031361	ENSG00000077274	ENST00000324068;ENST00000541758	T;T	0.41758	0.99;2.39	6.17	5.31	0.75309	Peptidase C2, calpain, catalytic domain (3);	0.137951	0.49916	N	0.000139	T	0.00012	0.0000	N	0.04768	-0.165	0.58432	P	9.000000000036756E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.43376	-0.9395	9	0.02654	T	1	.	11.5044	0.50456	0.0682:0.1227:0.8091:0.0	rs12013711;rs17880204;rs52812550;rs56633453;rs60491464;rs12013711	277	Q9Y6Q1	CAN6_HUMAN	L	277;22	ENSP00000317214:V277L;ENSP00000441736:V22L	ENSP00000317214:V277L	V	-	1	0	CAPN6	110381497	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	2.455000	0.44988	0.729000	0.32403	-0.170000	0.13304	GTG	C|0.722;0|0.021	.	strong		0.478	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1		
ABHD11	83451	hgsc.bcm.edu	37	7	73151643	73151643	+	Missense_Mutation	SNP	C	C	T	rs61745525|rs386714666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73151643C>T	ENST00000222800.3	-	4	610	c.541G>A	c.(541-543)Gtg>Atg	p.V181M	ABHD11_ENST00000437775.2_Missense_Mutation_p.V174M|ABHD11_ENST00000458339.1_Intron|ABHD11_ENST00000395147.4_Intron|LINC00035_ENST00000427153.1_RNA|ABHD11_ENST00000468998.1_5'Flank	NM_148912.2	NP_683710.1	Q8NFV4	ABHDB_HUMAN	abhydrolase domain containing 11	181						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Lung NSC(55;0.0908)|all_lung(88;0.198)				ATGGCTGCCACATAGGTTGCA	0.557													C|||	228	0.0455272	0.1649	0.0144	5008	,	,		21333	0.0		0.0	False		,,,				2504	0.0				p.V181M		Atlas-SNP	.											.	ABHD11	11	.	0			c.G541A						PASS	.	C	,MET/VAL,MET/VAL	436,3970		29,378,1796	89.0	73.0	79.0		,541,520	-9.2	0.0	7	dbSNP_129	79	3,8597		0,3,4297	yes	intron,missense,missense	ABHD11	NM_001145364.1,NM_148912.2,NM_148913.2	,21,21	29,381,6093	TT,TC,CC		0.0349,9.8956,3.3754	,benign,benign	,181/316,174/309	73151643	439,12567	2203	4300	6503	SO:0001583	missense	83451	exon4			CTGCCACATAGGT	AF217971	CCDS5558.1, CCDS47607.1, CCDS47608.1, CCDS75615.1	7q11.23	2010-08-05	2005-01-24	2005-01-27	ENSG00000106077	ENSG00000106077		"""Abhydrolase domain containing"""	16407	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 21"""	WBSCR21		12073013	Standard	NR_026910		Approved	PP1226	uc003tzb.3	Q8NFV4	OTTHUMG00000130029	ENST00000222800.3:c.541G>A	7.37:g.73151643C>T	ENSP00000222800:p.Val181Met	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_148912	H7BYM8|Q6PJU0|Q8N722|Q8N723|Q8NFV2|Q8NFV3|Q9HBS8	Missense_Mutation	SNP	ENST00000222800.3	37	CCDS5558.1	73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	C	6.139	0.393893	0.11638	0.098956	3.49E-4	ENSG00000106077	ENST00000437775;ENST00000222800	T;T	0.68479	-0.33;-0.33	4.62	-9.25	0.00666	.	0.399068	0.28388	N	0.015523	T	0.00328	0.0010	L	0.31578	0.945	0.09310	P	0.99999999628235	B;B	0.18310	0.027;0.017	B;B	0.19666	0.015;0.026	T	0.01456	-1.1350	9	0.36615	T	0.2	-0.2939	3.1353	0.06437	0.2531:0.453:0.1175:0.1763	.	174;181	Q8NFV4-4;Q8NFV4	.;ABHDB_HUMAN	M	174;181	ENSP00000416970:V174M;ENSP00000222800:V181M	ENSP00000222800:V181M	V	-	1	0	ABHD11	72789579	0.406000	0.25344	0.004000	0.12327	0.014000	0.08584	-0.283000	0.08433	-1.427000	0.01992	-0.367000	0.07326	GTG	C|0.963;T|0.037	0.037	strong		0.557	ABHD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252306.1		
ZNF420	147923	hgsc.bcm.edu	37	19	37618157	37618157	+	Silent	SNP	T	T	C	rs78427535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37618157T>C	ENST00000337995.3	+	5	479	c.264T>C	c.(262-264)gaT>gaC	p.D88D	ZNF585A_ENST00000588723.1_Intron|ZNF420_ENST00000304239.7_Silent_p.D88D|CTC-454I21.4_ENST00000587645.1_RNA	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	88					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATTCCAGGGATTATTTGGAAG	0.373													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		18952	0.0		0.0	False		,,,				2504	0.0				p.D88D		Atlas-SNP	.											.	ZNF420	71	.	0			c.T264C						PASS	.	T		250,4156	145.0+/-179.8	7,236,1960	83.0	83.0	83.0		264	-4.2	0.0	19	dbSNP_131	83	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	ZNF420	NM_144689.3		7,243,6253	CC,CT,TT		0.0814,5.6741,1.976		88/689	37618157	257,12749	2203	4300	6503	SO:0001819	synonymous_variant	147923	exon5			CAGGGATTATTTG	AK056695	CCDS12498.1	19q13.12	2013-01-08			ENSG00000197050	ENSG00000197050		"""Zinc fingers, C2H2-type"", ""-"""	20649	protein-coding gene	gene with protein product							Standard	NM_144689		Approved	FLJ32191	uc002ofl.3	Q8TAQ5	OTTHUMG00000048168	ENST00000337995.3:c.264T>C	19.37:g.37618157T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	148	72	0.486486	NM_144689	B2RDY6|Q96ML5	Silent	SNP	ENST00000337995.3	37	CCDS12498.1																																																																																			T|0.984;C|0.016	0.016	strong		0.373	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109587.3	NM_144689	
BDNF	627	hgsc.bcm.edu	37	11	27679976	27679976	+	Missense_Mutation	SNP	C	C	T	rs146354977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:27679976C>T	ENST00000525528.1	-	1	1229	c.136G>A	c.(136-138)Gtg>Atg	p.V46M	BDNF_ENST00000438929.1_Missense_Mutation_p.V128M|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000530861.1_Missense_Mutation_p.V46M|BDNF-AS_ENST00000532965.1_RNA|BDNF_ENST00000395980.2_Missense_Mutation_p.V46M|BDNF_ENST00000533246.1_Missense_Mutation_p.V46M|BDNF-AS_ENST00000499008.3_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000395983.3_Missense_Mutation_p.V46M|BDNF_ENST00000439476.2_Missense_Mutation_p.V46M|BDNF_ENST00000584049.1_5'UTR|BDNF_ENST00000418212.1_Missense_Mutation_p.V46M|BDNF_ENST00000533131.1_Missense_Mutation_p.V46M|BDNF-AS_ENST00000500662.2_RNA|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000525950.1_Missense_Mutation_p.V46M|BDNF_ENST00000395981.3_Missense_Mutation_p.V46M|BDNF_ENST00000420794.1_Missense_Mutation_p.V46M|BDNF_ENST00000395978.3_Missense_Mutation_p.V46M|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000532997.1_Missense_Mutation_p.V46M|BDNF_ENST00000395986.2_Missense_Mutation_p.V61M|BDNF_ENST00000356660.4_Missense_Mutation_p.V46M|BDNF_ENST00000314915.6_Missense_Mutation_p.V54M	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor	46					axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						GGCCCATTCACGCTCTCCAGA	0.547													C|||	3	0.000599042	0.0023	0.0	5008	,	,		18690	0.0		0.0	False		,,,				2504	0.0				p.V128M		Atlas-SNP	.											.	BDNF	63	.	0			c.G382A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1,4403	2.1+/-5.4	0,1,2201	149.0	149.0	149.0		136,136,136,136,223,382,136,136,136,136,136,136,160,136,136,181,136	-1.7	1.0	11	dbSNP_134	149	0,8598		0,0,4299	no	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	BDNF	NM_001143805.1,NM_001143806.1,NM_001143807.1,NM_001143808.1,NM_001143809.1,NM_001143810.1,NM_001143811.1,NM_001143812.1,NM_001143813.1,NM_001143814.1,NM_001143816.1,NM_001709.4,NM_170731.4,NM_170732.4,NM_170733.3,NM_170734.3,NM_170735.5	21,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	46/248,46/248,46/248,46/248,75/277,128/330,46/248,46/248,46/248,46/248,46/248,46/248,54/256,46/248,46/248,61/263,46/248	27679976	1,13001	2202	4299	6501	SO:0001583	missense	627	exon3			CATTCACGCTCTC	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"""Endogenous ligands"""	1033	protein-coding gene	gene with protein product	"""neurotrophin"""	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.136G>A	11.37:g.27679976C>T	ENSP00000437138:p.Val46Met	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_001143810	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Missense_Mutation	SNP	ENST00000525528.1	37	CCDS7866.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	6.658	0.489860	0.12702	2.27E-4	0.0	ENSG00000176697	ENST00000439476;ENST00000525528;ENST00000395986;ENST00000533131;ENST00000356660;ENST00000418212;ENST00000533246;ENST00000530861;ENST00000395983;ENST00000438929;ENST00000395980;ENST00000532997;ENST00000395981;ENST00000395978;ENST00000525950;ENST00000314915;ENST00000420794;ENST00000528035	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62	6.16	-1.67	0.08238	.	0.752012	0.13050	N	0.417798	T	0.20495	0.0493	N	0.14661	0.345	0.26003	N	0.98209	B;B;B;B;B	0.19445	0.012;0.013;0.014;0.002;0.036	B;B;B;B;B	0.16722	0.016;0.002;0.01;0.003;0.01	T	0.20306	-1.0279	10	0.87932	D	0	-29.8815	9.1961	0.37228	0.0:0.2875:0.1522:0.5603	.	75;128;54;46;61	P23560-5;P23560-4;P23560-2;P23560;P23560-3	.;.;.;BDNF_HUMAN;.	M	46;46;61;46;46;46;46;46;46;128;46;46;46;46;46;54;46;46	ENSP00000389345:V46M;ENSP00000437138:V46M;ENSP00000379309:V61M;ENSP00000432727:V46M;ENSP00000349084:V46M;ENSP00000400502:V46M;ENSP00000432376:V46M;ENSP00000435564:V46M;ENSP00000379307:V46M;ENSP00000414303:V128M;ENSP00000379304:V46M;ENSP00000435805:V46M;ENSP00000379305:V46M;ENSP00000379302:V46M;ENSP00000432035:V46M;ENSP00000320002:V54M;ENSP00000389564:V46M	ENSP00000320002:V54M	V	-	1	0	BDNF	27636552	0.977000	0.34250	0.957000	0.39632	0.991000	0.79684	0.156000	0.16382	-0.215000	0.10063	-0.142000	0.14014	GTG	C|0.999;T|0.001	0.001	strong		0.547	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735	
SLC9A3	6550	hgsc.bcm.edu	37	5	491906	491906	+	Silent	SNP	G	G	A	rs6870920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:491906G>A	ENST00000264938.3	-	2	501	c.492C>T	c.(490-492)ggC>ggT	p.G164G	SLC9A3_ENST00000514375.1_Silent_p.G164G	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	164					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			TGAGGAAGACGCCGTAGAGGG	0.672													G|||	181	0.0361422	0.1301	0.0101	5008	,	,		11795	0.0		0.002	False		,,,				2504	0.0				p.G164G		Atlas-SNP	.											SLC9A3,head_neck,malignant_melanoma,-1,1	SLC9A3	89	1	0			c.C492T						PASS	.	G		407,3969		28,351,1809	27.0	20.0	22.0		492	-8.3	0.5	5	dbSNP_116	22	11,8555		0,11,4272	no	coding-synonymous	SLC9A3	NM_004174.2		28,362,6081	AA,AG,GG		0.1284,9.3007,3.2298		164/835	491906	418,12524	2188	4283	6471	SO:0001819	synonymous_variant	6550	exon2			GAAGACGCCGTAG		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"""Solute carriers"""	11073	protein-coding gene	gene with protein product		182307	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3"""	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.492C>T	5.37:g.491906G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																			G|0.958;A|0.042	0.042	strong		0.672	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	
PITPNM1	9600	hgsc.bcm.edu	37	11	67267636	67267636	+	Silent	SNP	G	G	A	rs59249357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67267636G>A	ENST00000534749.1	-	5	1085	c.897C>T	c.(895-897)gcC>gcT	p.A299A	PITPNM1_ENST00000436757.2_Silent_p.A299A|PITPNM1_ENST00000356404.3_Silent_p.A299A			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	299					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						CATCGGGGGAGGCATCTGGGC	0.687													G|||	68	0.0135783	0.0492	0.0043	5008	,	,		14719	0.0		0.0	False		,,,				2504	0.0				p.A299A	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.C897T						PASS	.						26.0	32.0	30.0					11																	67267636		2172	4257	6429	SO:0001819	synonymous_variant	9600	exon6			GGGGGAGGCATCT	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"""PYK2 N-terminal domain-interacting receptor 2"", ""retinal degeneration B alpha 1"""	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.897C>T	11.37:g.67267636G>A		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_001130848	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Silent	SNP	ENST00000534749.1	37	CCDS31620.1																																																																																			A|0.006;C|0.005;G|0.988	0.006	strong		0.687	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910	
HS3ST2	9956	hgsc.bcm.edu	37	16	22826321	22826321	+	Silent	SNP	G	G	A	rs111703383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:22826321G>A	ENST00000261374.3	+	1	824	c.390G>A	c.(388-390)gtG>gtA	p.V130V		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	130					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|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 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)			breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		CCCGGGCCGTGCTGGAGTTTA	0.637													G|||	271	0.0541134	0.1959	0.0173	5008	,	,		13590	0.0		0.0	False		,,,				2504	0.0				p.V130V		Atlas-SNP	.											.	HS3ST2	59	.	0			c.G390A						PASS	.	G		724,3626		47,630,1498	15.0	19.0	17.0		390	4.1	1.0	16	dbSNP_132	17	4,8560		0,4,4278	no	coding-synonymous	HS3ST2	NM_006043.1		47,634,5776	AA,AG,GG		0.0467,16.6437,5.6373		130/368	22826321	728,12186	2175	4282	6457	SO:0001819	synonymous_variant	9956	exon1			GGCCGTGCTGGAG	AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.390G>A	16.37:g.22826321G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_006043	Q52LZ1	Silent	SNP	ENST00000261374.3	37	CCDS10606.1																																																																																			G|0.949;A|0.051	0.051	strong		0.637	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043	
URB1	9875	hgsc.bcm.edu	37	21	33688865	33688865	+	Silent	SNP	A	A	G	rs7279896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33688865A>G	ENST00000382751.3	-	38	6661	c.6546T>C	c.(6544-6546)gcT>gcC	p.A2182A		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	2182						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						GGCCCTGGGCAGCCACCAGCT	0.627													G|||	1252	0.25	0.5779	0.1052	5008	,	,		17415	0.1369		0.1233	False		,,,				2504	0.1564				p.A2182A		Atlas-SNP	.											.	URB1	176	.	0			c.T6546C						PASS	.	G		727,657		198,331,163	21.0	27.0	25.0		6546	-1.8	0.4	21	dbSNP_116	25	408,2774		29,350,1212	no	coding-synonymous	URB1	NM_014825.2		227,681,1375	GG,GA,AA		12.8221,47.4711,24.8576		2182/2272	33688865	1135,3431	692	1591	2283	SO:0001819	synonymous_variant	9875	exon38			CTGGGCAGCCACC	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.6546T>C	21.37:g.33688865A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																			A|0.758;G|0.242	0.242	strong		0.627	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
IGFALS	3483	hgsc.bcm.edu	37	16	1840777	1840777	+	Missense_Mutation	SNP	G	G	A	rs9282731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1840777G>A	ENST00000215539.3	-	2	1752	c.1642C>T	c.(1642-1644)Cgg>Tgg	p.R548W	IGFALS_ENST00000415638.3_Missense_Mutation_p.R586W			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit	548	LRRCT.		R -> W (in dbSNP:rs9282731).		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						GCGAAGTCCCGCAGCGCCTTG	0.667													G|||	458	0.0914537	0.2837	0.0159	5008	,	,		13459	0.003		0.004	False		,,,				2504	0.0665				p.R586W		Atlas-SNP	.											.	IGFALS	29	.	0			c.C1756T						PASS	.	G	TRP/ARG,TRP/ARG	1035,3305		125,785,1260	21.0	18.0	19.0		1756,1642	-2.2	0.0	16	dbSNP_118	19	14,8548		0,14,4267	yes	missense,missense	IGFALS	NM_001146006.1,NM_004970.2	101,101	125,799,5527	AA,AG,GG		0.1635,23.8479,8.1305	probably-damaging,probably-damaging	586/644,548/606	1840777	1049,11853	2170	4281	6451	SO:0001583	missense	3483	exon2			AGTCCCGCAGCGC	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.1642C>T	16.37:g.1840777G>A	ENSP00000215539:p.Arg548Trp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	109	61	0.559633	NM_001146006	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	124	0.056776556776556776	117	0.23780487804878048	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	G	12.57	1.976387	0.34848	0.238479	0.001635	ENSG00000099769	ENST00000215539;ENST00000415638	T;T	0.25749	1.78;1.78	4.54	-2.24	0.06909	Cysteine-rich flanking region, C-terminal (1);	0.186351	0.45361	N	0.000368	T	0.00012	0.0000	L	0.53780	1.695	0.09310	P	0.9999999850705	B;B	0.33135	0.399;0.399	B;B	0.23275	0.045;0.045	T	0.27571	-1.0070	9	0.40728	T	0.16	.	6.0748	0.19909	0.1844:0.0:0.5355:0.2801	rs9282731;rs9282731	586;548	E9PGU3;P35858	.;ALS_HUMAN	W	548;586	ENSP00000215539:R548W;ENSP00000416683:R586W	ENSP00000215539:R548W	R	-	1	2	IGFALS	1780778	0.001000	0.12720	0.006000	0.13384	0.033000	0.12548	-0.195000	0.09546	-0.354000	0.08212	-0.219000	0.12488	CGG	G|0.909;A|0.091	0.091	strong		0.667	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
PHC1	1911	hgsc.bcm.edu	37	12	9070366	9070366	+	Silent	SNP	T	T	A	rs4883198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9070366T>A	ENST00000543824.1	+	3	425	c.93T>A	c.(91-93)ctT>ctA	p.L31L	PHC1_ENST00000433847.2_3'UTR|PHC1_ENST00000544916.1_Silent_p.L31L|PHC1_ENST00000536844.1_5'UTR|PHC1_ENST00000433083.2_Silent_p.L31L			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	31					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						AAATGTCACTTTATGAACGAC	0.517													A|||	3444	0.6877	0.5469	0.5908	5008	,	,		-128	0.749		0.7167	False		,,,				2504	0.8538				p.L31L		Atlas-SNP	.											.	PHC1	67	.	0			c.T93A						PASS	.	A		2632,1774	521.7+/-370.6	772,1088,343	40.0	37.0	38.0		93	2.0	1.0	12	dbSNP_111	38	6238,2362	391.8+/-343.8	2240,1758,302	no	coding-synonymous	PHC1	NM_004426.2		3012,2846,645	AA,AT,TT		27.4651,40.2633,31.8007		31/1005	9070366	8870,4136	2203	4300	6503	SO:0001819	synonymous_variant	1911	exon2			GTCACTTTATGAA	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.93T>A	12.37:g.9070366T>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	280	145	0.517857	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Silent	SNP	ENST00000543824.1	37	CCDS8597.1																																																																																			T|0.310;A|0.690	0.690	strong		0.517	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	
SCAMP5	192683	hgsc.bcm.edu	37	15	75305058	75305058	+	Silent	SNP	G	G	T	rs60910940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75305058G>T	ENST00000361900.6	+	4	255	c.48G>T	c.(46-48)ccG>ccT	p.P16P	SCAMP5_ENST00000565923.1_3'UTR|SCAMP5_ENST00000425597.3_Silent_p.P16P|SCAMP5_ENST00000545456.1_5'UTR|SCAMP5_ENST00000562212.1_Silent_p.P16P	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	16					exocytosis (GO:0006887)|negative regulation of endocytosis (GO:0045806)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of cytokine secretion (GO:0050715)|protein transport (GO:0015031)|response to endoplasmic reticulum stress (GO:0034976)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)|trans-Golgi network membrane (GO:0032588)				large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	5						AATTCATCCCGCTGAAGCCAT	0.507													G|||	168	0.0335463	0.1241	0.0043	5008	,	,		19935	0.0		0.001	False		,,,				2504	0.0				p.P16P		Atlas-SNP	.											.	SCAMP5	34	.	0			c.G48T						PASS	.	G	,,	388,3722		14,360,1681	97.0	102.0	101.0		48,48,48	-10.7	0.4	15	dbSNP_129	101	3,8399		0,3,4198	no	coding-synonymous,coding-synonymous,coding-synonymous	SCAMP5	NM_001178111.1,NM_001178112.1,NM_138967.3	,,	14,363,5879	TT,TG,GG		0.0357,9.4404,3.125	,,	16/236,16/236,16/236	75305058	391,12121	2055	4201	6256	SO:0001819	synonymous_variant	192683	exon4			CATCCCGCTGAAG	AL833230	CCDS45306.1	15q24.2	2014-05-20			ENSG00000198794	ENSG00000198794		"""Secretory carrier membrane proteins"""	30386	protein-coding gene	gene with protein product		613766				12477932	Standard	NM_001178111		Approved	MGC24969	uc002azk.2	Q8TAC9	OTTHUMG00000172704	ENST00000361900.6:c.48G>T	15.37:g.75305058G>T		Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	167	167	1	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Silent	SNP	ENST00000361900.6	37	CCDS45306.1																																																																																			G|0.966;T|0.034	0.034	strong		0.507	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967	
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049939	69049939	+	Missense_Mutation	SNP	G	G	T	rs4241344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69049939G>T	ENST00000295381.3	+	10	2084	c.1665G>T	c.(1663-1665)agG>agT	p.R555S	ARHGAP25_ENST00000409202.3_Missense_Mutation_p.R556S|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.R549S|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.R249S|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.R516S|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.R548S	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	555			R -> S (in dbSNP:rs4241344). {ECO:0000269|PubMed:14702039}.		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CTTTGCAGAGGATGGTCCAAG	0.448													G|||	1332	0.265974	0.1725	0.3156	5008	,	,		20655	0.4435		0.1869	False		,,,				2504	0.2556				p.R556S		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.G1668T						PASS	.	G	SER/ARG,SER/ARG,SER/ARG,SER/ARG	758,3646	286.0+/-278.5	53,652,1497	70.0	78.0	75.0		1668,1647,1548,1644	3.5	0.7	2	dbSNP_111	75	1644,6956	282.4+/-295.5	170,1304,2826	yes	missense,missense,missense,missense	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	110,110,110,110	223,1956,4323	TT,TG,GG		19.1163,17.2116,18.4712	benign,benign,benign,benign	556/647,549/640,516/607,548/639	69049939	2402,10602	2202	4300	6502	SO:0001583	missense	9938	exon10			GCAGAGGATGGTC	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1665G>T	2.37:g.69049939G>T	ENSP00000295381:p.Arg555Ser	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		554|554	0.25366300366300365|0.25366300366300365	78|78	0.15853658536585366|0.15853658536585366	109|109	0.3011049723756906|0.3011049723756906	224|224	0.3916083916083916|0.3916083916083916	143|143	0.18865435356200527|0.18865435356200527	G|G	2.826|2.826	-0.243736|-0.243736	0.05906|0.05906	0.172116|0.172116	0.191163|0.191163	ENSG00000163219|ENSG00000163219	ENST00000497259|ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000543533;ENST00000479844	.|T;T;T;T;T;T	.|0.38560	.|3.05;3.05;2.8;1.13;1.13;1.13	5.42|5.42	3.55|3.55	0.40652|0.40652	.|.	.|0.731496	.|0.14039	.|N	.|0.345562	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.26403|0.26403	P|P	0.976394|0.976394	.|B;B;B;B;B	.|0.06786	.|0.001;0.0;0.0;0.0;0.0	.|B;B;B;B;B	.|0.04013	.|0.001;0.0;0.0;0.0;0.0	T|T	0.43925|0.43925	-0.9361|-0.9361	4|9	.|0.07030	.|T	.|0.85	.|.	1.9238|1.9238	0.03313|0.03313	0.1885:0.154:0.4993:0.1582|0.1885:0.154:0.4993:0.1582	rs4241344;rs52800040;rs60408659;rs4241344|rs4241344;rs52800040;rs60408659;rs4241344	.|516;556;549;548;555	.|E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331	.|.;.;.;.;RHG25_HUMAN	V|S	415|555;556;516;548;549;549;540;249	.|ENSP00000295381:R555S;ENSP00000386911:R556S;ENSP00000420583:R516S;ENSP00000386863:R548S;ENSP00000386241:R549S;ENSP00000417467:R249S	.|ENSP00000295381:R555S	G|R	+|+	2|3	0|2	ARHGAP25|ARHGAP25	68903443|68903443	0.001000|0.001000	0.12720|0.12720	0.746000|0.746000	0.31095|0.31095	0.615000|0.615000	0.37417|0.37417	0.193000|0.193000	0.17116|0.17116	0.698000|0.698000	0.31739|0.31739	0.557000|0.557000	0.71058|0.71058	GGA|AGG	G|0.789;T|0.211	0.211	strong		0.448	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
FAT3	120114	hgsc.bcm.edu	37	11	92088177	92088177	+	Silent	SNP	C	C	T	rs7479732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92088177C>T	ENST00000298047.6	+	1	2916	c.2899C>T	c.(2899-2901)Ctg>Ttg	p.L967L	FAT3_ENST00000525166.1_Silent_p.L817L|FAT3_ENST00000541502.1_Silent_p.L967L|FAT3_ENST00000409404.2_Silent_p.L967L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	967	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)				AGATCTTGGACTGGGGGGTCA	0.458										TCGA Ovarian(4;0.039)			T|||	1758	0.351038	0.8079	0.1801	5008	,	,		19090	0.1746		0.2038	False		,,,				2504	0.1881				p.L967L		Atlas-SNP	.											FAT3_ENST00000409404,colon,carcinoma,0,2	FAT3	1822	2	0			c.C2899T						PASS	.	T		2521,1247		857,807,220	71.0	70.0	70.0		2899	2.5	1.0	11	dbSNP_116	70	1774,6460		199,1376,2542	no	coding-synonymous	FAT3	NM_001008781.2		1056,2183,2762	TT,TC,CC		21.5448,33.0945,35.7857		967/4558	92088177	4295,7707	1884	4117	6001	SO:0001819	synonymous_variant	120114	exon1			CTTGGACTGGGGG	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.2899C>T	11.37:g.92088177C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.697;T|0.303	0.303	strong		0.458	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
GANC	2595	hgsc.bcm.edu	37	15	42643529	42643529	+	Missense_Mutation	SNP	T	T	C	rs7181742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42643529T>C	ENST00000318010.8	+	23	2774	c.2534T>C	c.(2533-2535)tTt>tCt	p.F845S	CAPN3_ENST00000356316.3_5'UTR|RP11-164J13.1_ENST00000495723.1_RNA	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	845			F -> S (in dbSNP:rs7181742). {ECO:0000269|PubMed:12370436}.		carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	TATTCCAGTTTTGCTGACCAG	0.488													C|||	1895	0.378395	0.7405	0.3847	5008	,	,		17663	0.1577		0.1332	False		,,,				2504	0.364				p.F845S		Atlas-SNP	.											.	GANC	57	.	0			c.T2534C						PASS	.	C	SER/PHE	2763,1643	503.7+/-365.6	905,953,345	118.0	107.0	111.0		2534	3.5	1.0	15	dbSNP_116	111	1195,7403	763.2+/-407.6	97,1001,3201	yes	missense	GANC	NM_198141.2	155	1002,1954,3546	CC,CT,TT		13.8986,37.2901,30.4368	benign	845/915	42643529	3958,9046	2203	4299	6502	SO:0001583	missense	2595	exon23			CCAGTTTTGCTGA	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.2534T>C	15.37:g.42643529T>C	ENSP00000326227:p.Phe845Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Missense_Mutation	SNP	ENST00000318010.8	37	CCDS10084.1	616	0.28205128205128205	334	0.6788617886178862	119	0.3287292817679558	73	0.12762237762237763	90	0.11873350923482849	C	10.48	1.362931	0.24684	0.627099	0.138986	ENSG00000214013	ENST00000318010	D	0.85773	-2.03	5.38	3.48	0.39840	.	0.456476	0.26045	N	0.026670	T	0.00012	0.0000	N	0.00377	-1.585	0.09310	P	0.9999999897697	B	0.02656	0.0	B	0.01281	0.0	T	0.45629	-0.9248	9	0.02654	T	1	-7.2067	4.1575	0.10268	0.0915:0.1781:0.5876:0.1428	rs7181742;rs52820484;rs58917918;rs7181742	845	Q8TET4	GANC_HUMAN	S	845	ENSP00000326227:F845S	ENSP00000447925:F77S	F	+	2	0	GANC	40430821	1.000000	0.71417	1.000000	0.80357	0.562000	0.35680	2.048000	0.41278	0.677000	0.31305	-0.128000	0.14901	TTT	T|0.702;C|0.298	0.298	strong		0.488	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
SFXN3	81855	hgsc.bcm.edu	37	10	102795819	102795819	+	Missense_Mutation	SNP	A	A	T	rs35361377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102795819A>T	ENST00000224807.5	+	5	860	c.404A>T	c.(403-405)aAc>aTc	p.N135I	SFXN3_ENST00000393459.1_Missense_Mutation_p.N131I	NM_030971.3	NP_112233.2	Q9BWM7	SFXN3_HUMAN	sideroflexin 3	135					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(252;0.234)		Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		GCCATTGTTAACTACTCCAAC	0.572													A|||	59	0.0117812	0.0431	0.0029	5008	,	,		18920	0.0		0.0	False		,,,				2504	0.0				p.N135I		Atlas-SNP	.											.	SFXN3	19	.	0			c.A404T						PASS	.	A	ILE/ASN	161,4245	109.1+/-147.4	3,155,2045	173.0	153.0	159.0		404	5.4	1.0	10	dbSNP_126	159	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SFXN3	NM_030971.3	149	3,156,6344	TT,TA,AA		0.0116,3.6541,1.2456	probably-damaging	135/326	102795819	162,12844	2203	4300	6503	SO:0001583	missense	81855	exon5			TTGTTAACTACTC	AK074707	CCDS7508.2	10q24.32	2008-09-04			ENSG00000107819	ENSG00000107819		"""Sideroflexins"""	16087	protein-coding gene	gene with protein product		615571					Standard	NM_030971		Approved	SFX3	uc001ksp.3	Q9BWM7	OTTHUMG00000018921	ENST00000224807.5:c.404A>T	10.37:g.102795819A>T	ENSP00000224807:p.Asn135Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	67	0.577586	NM_030971	Q8NCJ0|Q9NTP4	Missense_Mutation	SNP	ENST00000224807.5	37	CCDS7508.2	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	A	29.2	4.982999	0.93044	0.036541	1.16E-4	ENSG00000107819	ENST00000393459;ENST00000224807	T;T	0.54279	0.58;0.58	5.36	5.36	0.76844	.	0.041188	0.85682	D	0.000000	T	0.54886	0.1886	H	0.96111	3.77	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.996	T	0.80699	-0.1266	10	0.87932	D	0	-24.293	15.3508	0.74384	1.0:0.0:0.0:0.0	rs35361377	139;135;135	B4DRS6;A6NCZ6;Q9BWM7	.;.;SFXN3_HUMAN	I	131;135	ENSP00000377103:N131I;ENSP00000224807:N135I	ENSP00000224807:N135I	N	+	2	0	SFXN3	102785809	1.000000	0.71417	0.991000	0.47740	0.988000	0.76386	9.329000	0.96413	2.024000	0.59613	0.379000	0.24179	AAC	A|0.986;T|0.014	0.014	strong		0.572	SFXN3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_030971	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52131119	52131119	+	Missense_Mutation	SNP	A	A	G	rs2278831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52131119A>G	ENST00000534261.2	-	6	1364	c.965T>C	c.(964-966)tTc>tCc	p.F322S	SIGLEC5_ENST00000222107.4_Missense_Mutation_p.F322S|SIGLEC5_ENST00000429354.3_Missense_Mutation_p.F322S|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.F322S|SIGLEC5_ENST00000570106.2_Missense_Mutation_p.F322S			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	322	Ig-like C2-type 2.		F -> S (in dbSNP:rs2278831).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		AATTTGCAGGAAGCCCAGCGG	0.547													A|||	478	0.0954473	0.0983	0.0692	5008	,	,		17551	0.1419		0.0676	False		,,,				2504	0.091				p.F322S		Atlas-SNP	.											.	SIGLEC5	67	.	0			c.T965C						PASS	.	A	SER/PHE	393,4013		13,367,1823	30.0	35.0	33.0		965	2.8	0.8	19	dbSNP_100	33	646,7954		28,590,3682	yes	missense	SIGLEC5	NM_003830.2	155	41,957,5505	GG,GA,AA		7.5116,8.9197,7.9886	benign	322/552	52131119	1039,11967	2203	4300	6503	SO:0001583	missense	8778	exon5			TGCAGGAAGCCCA	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.965T>C	19.37:g.52131119A>G	ENSP00000473238:p.Phe322Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	NM_003830		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	233	0.10668498168498168	57	0.11585365853658537	41	0.1132596685082873	85	0.1486013986013986	50	0.06596306068601583	A	0.363	-0.938499	0.02340	0.089197	0.075116	ENSG00000105501	ENST00000222107;ENST00000429354	T;T	0.12879	2.64;2.64	3.88	2.84	0.33178	Immunoglobulin-like (1);	0.737030	0.11702	N	0.537799	T	0.00012	0.0000	N	0.00060	-2.34	0.45791	P	0.0013300000000000534	B	0.06786	0.001	B	0.01281	0.0	T	0.38222	-0.9671	9	0.02654	T	1	.	7.8326	0.29351	0.1179:0.0:0.8821:0.0	rs2278831;rs59229972;rs2278831	322	O15389	SIGL5_HUMAN	S	322	ENSP00000222107:F322S;ENSP00000415200:F322S	ENSP00000222107:F322S	F	-	2	0	SIGLEC5	56822931	0.891000	0.30450	0.836000	0.33094	0.029000	0.11900	0.734000	0.26101	0.968000	0.38212	-0.251000	0.11542	TTC	A|0.913;G|0.087	0.087	strong		0.547	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
ZRANB1	54764	hgsc.bcm.edu	37	10	126631482	126631482	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:126631482C>T	ENST00000359653.4	+	1	791	c.420C>T	c.(418-420)taC>taT	p.Y140Y	RP11-298J20.4_ENST00000508096.1_RNA|RP11-298J20.3_ENST00000449984.1_RNA	NM_017580.2	NP_060050.2	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1	140					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|positive regulation of Wnt signaling pathway (GO:0030177)|protein deubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0071947)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell morphogenesis (GO:0022604)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	23		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)		GTGAGGAATACAATGATAGAA	0.443																																					p.Y140Y		Atlas-SNP	.											ZRANB1,NS,carcinoma,+1,1	ZRANB1	60	1	0			c.C420T						scavenged	.						104.0	100.0	101.0					10																	126631482		2203	4300	6503	SO:0001819	synonymous_variant	54764	exon1			GGAATACAATGAT	AJ252060	CCDS7642.1	10q26.12	2014-02-24			ENSG00000019995	ENSG00000019995		"""Zinc fingers, RAN-binding domain containing"", ""OTU domain containing"""	18224	protein-coding gene	gene with protein product		611749				11463333	Standard	NM_017580		Approved	TRABID	uc001lic.3	Q9UGI0	OTTHUMG00000019223	ENST00000359653.4:c.420C>T	10.37:g.126631482C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	110	2	0.0181818	NM_017580	B4DZ98|D3DRF4|Q5SQP6|Q69YK3	Silent	SNP	ENST00000359653.4	37	CCDS7642.1																																																																																			.	.	none		0.443	ZRANB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050898.1	NM_017580	
PI16	221476	hgsc.bcm.edu	37	6	36922684	36922684	+	Missense_Mutation	SNP	A	A	C	rs1405069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36922684A>C	ENST00000373674.3	+	1	476	c.148A>C	c.(148-150)Acg>Ccg	p.T50P		NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	50	SCP.		T -> P (in dbSNP:rs1405069). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743}.		negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GGTATCCCCGACGGCCTCAGA	0.622													C|||	2725	0.544129	0.7542	0.5692	5008	,	,		16200	0.4841		0.4513	False		,,,				2504	0.3998				p.T50P		Atlas-SNP	.											.	PI16	50	.	0			c.A148C						PASS	.	C	PRO/THR,PRO/THR	3052,1354	445.9+/-347.8	1054,944,205	45.0	45.0	45.0	http://www.ncbi.nlm.nih.gov/pubmed?term	148,148	3.7	0.0	6	dbSNP_88	45	3833,4767	608.6+/-395.4	841,2151,1308	yes	missense,missense	PI16	NM_001199159.1,NM_153370.2	38,38	1895,3095,1513	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	44.5698,30.7308,47.0629	benign,benign	50/464,50/464	36922684	6885,6121	2203	4300	6503	SO:0001583	missense	221476	exon2			TCCCCGACGGCCT		CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"""microseminoprotein, beta-binding protein"""		"""protease inhibitor 16"""				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.148A>C	6.37:g.36922684A>C	ENSP00000362778:p.Thr50Pro	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	93	57	0.612903	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	37	CCDS34440.1	1235	0.5654761904761905	382	0.7764227642276422	197	0.5441988950276243	307	0.5367132867132867	349	0.4604221635883905	C	0.006	-2.053793	0.00390	0.692692	0.445698	ENSG00000164530	ENST00000536757;ENST00000373674	T	0.06068	3.35	5.51	3.71	0.42584	CAP domain (3);	0.422460	0.23327	N	0.049395	T	0.00384	0.0012	N	0.00392	-1.555	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45366	-0.9266	9	0.02654	T	1	.	5.8977	0.18949	0.2752:0.5838:0.0:0.141	rs1405069;rs1724101;rs11550708;rs17524663;rs17846145;rs17859153;rs61063989;rs1405069	50;50	Q6UXB8;Q6UXB8-2	PI16_HUMAN;.	P	50	ENSP00000362778:T50P	ENSP00000362778:T50P	T	+	1	0	PI16	37030662	0.001000	0.12720	0.003000	0.11579	0.089000	0.18198	0.522000	0.22909	0.291000	0.22468	-0.323000	0.08544	ACG	A|0.456;C|0.544	0.544	strong		0.622	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370	
FLG	2312	hgsc.bcm.edu	37	1	152278689	152278689	+	Silent	SNP	C	C	A	rs57672167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152278689C>A	ENST00000368799.1	-	3	8708	c.8673G>T	c.(8671-8673)gtG>gtT	p.V2891V	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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						scavenged	.	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	705	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	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	
KIAA1211	57482	hgsc.bcm.edu	37	4	57182758	57182758	+	Silent	SNP	C	C	T	rs28559894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57182758C>T	ENST00000504228.1	+	6	3195	c.3090C>T	c.(3088-3090)gaC>gaT	p.D1030D	KIAA1211_ENST00000264229.6_Silent_p.D1030D|KIAA1211_ENST00000541073.1_Silent_p.D1023D			Q6ZU35	K1211_HUMAN	KIAA1211	1030										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)					AGAAGAGGGACGAGGAGGAAG	0.627													C|||	1128	0.22524	0.1407	0.2233	5008	,	,		12589	0.254		0.341	False		,,,				2504	0.1922				p.D1030D		Atlas-SNP	.											KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	0			c.C3090T						PASS	.	C		672,3328		52,568,1380	18.0	21.0	20.0		3090	-6.2	0.0	4	dbSNP_125	20	2858,5480		498,1862,1809	no	coding-synonymous	KIAA1211	NM_020722.1		550,2430,3189	TT,TC,CC		34.2768,16.8,28.6108		1030/1234	57182758	3530,8808	2000	4169	6169	SO:0001819	synonymous_variant	57482	exon8			GAGGGACGAGGAG	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.3090C>T	4.37:g.57182758C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																			C|0.728;T|0.272	0.272	strong		0.627	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
ANKRD24	170961	hgsc.bcm.edu	37	19	4216931	4216931	+	Missense_Mutation	SNP	A	A	G	rs61741405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4216931A>G	ENST00000600132.1	+	18	2050	c.1774A>G	c.(1774-1776)Aca>Gca	p.T592A	ANKRD24_ENST00000262970.5_Missense_Mutation_p.T682A|ANKRD24_ENST00000318934.4_Missense_Mutation_p.T592A	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	592										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		AGCTGAGGCCACAGGAGCCAA	0.562													A|||	46	0.0091853	0.0325	0.0043	5008	,	,		19640	0.0		0.0	False		,,,				2504	0.0				p.T592A		Atlas-SNP	.											.	ANKRD24	180	.	0			c.A1774G						PASS	.	A	ALA/THR	159,3919		5,149,1885	31.0	36.0	35.0		1774	-6.7	0.0	19	dbSNP_129	35	1,8381		0,1,4190	yes	missense	ANKRD24	NM_133475.1	58	5,150,6075	GG,GA,AA		0.0119,3.899,1.2841	benign	592/1147	4216931	160,12300	2039	4191	6230	SO:0001583	missense	170961	exon18			GAGGCCACAGGAG	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1774A>G	19.37:g.4216931A>G	ENSP00000471252:p.Thr592Ala	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	a	2.619	-0.288978	0.05605	0.03899	1.19E-4	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.33216	1.47;1.42	3.39	-6.68	0.01778	.	2.468300	0.02265	N	0.067899	T	0.02455	0.0075	N	0.24115	0.695	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.10086	-1.0645	10	0.21540	T	0.41	3.2671	5.3297	0.15926	0.5536:0.0:0.1925:0.2539	rs61741405	592;682	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	A	592;682	ENSP00000321731:T592A;ENSP00000262970:T682A	ENSP00000262970:T682A	T	+	1	0	ANKRD24	4167931	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.277000	0.08502	-0.988000	0.03489	0.172000	0.16884	ACA	A|0.987;G|0.013	0.013	strong		0.562	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
OPN4	94233	hgsc.bcm.edu	37	10	88421041	88421041	+	Silent	SNP	C	C	T	rs7478092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:88421041C>T	ENST00000241891.5	+	7	1136	c.969C>T	c.(967-969)taC>taT	p.Y323Y	OPN4_ENST00000372071.2_Silent_p.Y334Y	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	323					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						GTCCTAGGTACGCACACGTCC	0.587													C|||	375	0.0748802	0.1762	0.0259	5008	,	,		18007	0.0357		0.0169	False		,,,				2504	0.0726				p.Y334Y		Atlas-SNP	.											.	OPN4	61	.	0			c.C1002T						PASS	.	C	,	681,3725	286.0+/-278.5	50,581,1572	219.0	153.0	175.0		1002,969	-3.2	0.1	10	dbSNP_116	175	146,8454	71.0+/-133.6	1,144,4155	no	coding-synonymous,coding-synonymous	OPN4	NM_001030015.2,NM_033282.3	,	51,725,5727	TT,TC,CC		1.6977,15.4562,6.3586	,	334/490,323/479	88421041	827,12179	2203	4300	6503	SO:0001819	synonymous_variant	94233	exon8			TAGGTACGCACAC	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.969C>T	10.37:g.88421041C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Silent	SNP	ENST00000241891.5	37	CCDS7376.1																																																																																			C|0.934;T|0.066	0.066	strong		0.587	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
CYP4B1	1580	hgsc.bcm.edu	37	1	47280859	47280859	+	Missense_Mutation	SNP	G	G	A	rs2297810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47280859G>A	ENST00000271153.4	+	8	1029	c.993G>A	c.(991-993)atG>atA	p.M331I	CYP4B1_ENST00000452782.2_Missense_Mutation_p.M169I|CYP4B1_ENST00000371923.4_Missense_Mutation_p.M332I|CYP4B1_ENST00000371919.4_Missense_Mutation_p.M317I			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	331			M -> I (in allele CYP4B1*2, allele CYP4B1*7 and allele CYP4B1*5; dbSNP:rs2297810). {ECO:0000269|PubMed:12142726, ECO:0000269|Ref.5}.		biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	TCTACTGCATGGCCCTGTACC	0.562													g|||	1356	0.270767	0.4614	0.2334	5008	,	,		20608	0.2808		0.1312	False		,,,				2504	0.1728				p.M332I		Atlas-SNP	.											.	CYP4B1	81	.	0			c.G996A						PASS	.	G	ILE/MET,ILE/MET	1819,2587	533.4+/-373.7	380,1059,764	126.0	100.0	109.0		993,996	4.0	1.0	1	dbSNP_100	109	1265,7335	253.3+/-279.0	98,1069,3133	yes	missense,missense	CYP4B1	NM_000779.3,NM_001099772.1	10,10	478,2128,3897	AA,AG,GG		14.7093,41.2846,23.7121	benign,benign	331/512,332/513	47280859	3084,9922	2203	4300	6503	SO:0001583	missense	1580	exon8			CTGCATGGCCCTG	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"""Cytochrome P450s"""	2644	protein-coding gene	gene with protein product		124075	"""cytochrome P450, subfamily IVB, polypeptide 1"""				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.993G>A	1.37:g.47280859G>A	ENSP00000271153:p.Met331Ile	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	155	77	0.496774	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Missense_Mutation	SNP	ENST00000271153.4	37	CCDS542.1	626	0.2866300366300366	246	0.5	79	0.21823204419889503	194	0.33916083916083917	107	0.14116094986807387	g	34	5.379942	0.95945	0.412846	0.147093	ENSG00000142973	ENST00000371923;ENST00000271153;ENST00000371919;ENST00000452782;ENST00000468637	T;T;T;T;T	0.79033	-1.23;-1.23;-0.26;-1.23;-1.23	5.85	3.95	0.45737	.	0.099034	0.64402	D	0.000001	T	0.00012	0.0000	N	0.12920	0.275	0.22389	P	0.999143936	B;B;B	0.26577	0.153;0.032;0.018	B;B;B	0.27262	0.078;0.03;0.05	T	0.43294	-0.9400	9	0.54805	T	0.06	.	12.1686	0.54144	0.0655:0.1195:0.815:0.0	rs2297810;rs12724127;rs17102584;rs56573458;rs58421583;rs2297810	317;332;331	Q8IZB0;P13584-2;P13584	.;.;CP4B1_HUMAN	I	332;331;317;169;168	ENSP00000360991:M332I;ENSP00000271153:M331I;ENSP00000360987:M317I;ENSP00000400413:M169I;ENSP00000437670:M168I	ENSP00000271153:M331I	M	+	3	0	CYP4B1	47053446	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	7.945000	0.87732	1.475000	0.48197	0.643000	0.83706	ATG	G|0.736;A|0.264	0.264	strong		0.562	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779	
COPA	1314	hgsc.bcm.edu	37	1	160302298	160302298	+	Missense_Mutation	SNP	T	T	C	rs57425682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160302298T>C	ENST00000241704.7	-	6	665	c.436A>G	c.(436-438)Aca>Gca	p.T146A	COPA_ENST00000368069.3_Missense_Mutation_p.T146A	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	146					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AAGTCTTCTGTGGGGTGGAAC	0.473													C|||	275	0.0549121	0.177	0.0202	5008	,	,		16356	0.0238		0.0	False		,,,				2504	0.0031				p.T146A		Atlas-SNP	.											.	COPA	181	.	0			c.A436G						PASS	.	C	ALA/THR,ALA/THR	633,3773	767.1+/-413.5	60,513,1630	132.0	118.0	123.0		436,436	3.9	1.0	1	dbSNP_129	123	8,8592	818.9+/-406.8	0,8,4292	yes	missense,missense	COPA	NM_001098398.1,NM_004371.3	58,58	60,521,5922	CC,CT,TT		0.093,14.3668,4.9285	benign,benign	146/1234,146/1225	160302298	641,12365	2203	4300	6503	SO:0001583	missense	1314	exon6			CTTCTGTGGGGTG	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"""WD repeat domain containing"", ""Endogenous ligands"""	2230	protein-coding gene	gene with protein product	"""proxenin"", ""xenin"""	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.436A>G	1.37:g.160302298T>C	ENSP00000241704:p.Thr146Ala	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_001098398	Q5T201|Q8IXZ9	Missense_Mutation	SNP	ENST00000241704.7	37	CCDS1202.1	95	0.043498168498168496	66	0.13414634146341464	9	0.024861878453038673	20	0.03496503496503497	0	0.0	C	13.43	2.233892	0.39498	0.143668	9.3E-4	ENSG00000122218	ENST00000368069;ENST00000241704	T;T	0.59906	0.23;0.23	5.05	3.92	0.45320	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.119729	0.64402	N	0.000017	T	0.26340	0.0643	L	0.39020	1.185	0.42906	P	0.005758999999999959	B;B	0.06786	0.001;0.001	B;B	0.16289	0.012;0.015	T	0.05517	-1.0880	9	0.54805	T	0.06	-2.4504	7.7922	0.29127	0.7177:0.1453:0.0:0.137	rs57425682;rs61739741	146;146	P53621;P53621-2	COPA_HUMAN;.	A	146	ENSP00000357048:T146A;ENSP00000241704:T146A	ENSP00000241704:T146A	T	-	1	0	COPA	158568922	1.000000	0.71417	0.999000	0.59377	0.678000	0.39670	4.802000	0.62539	0.403000	0.25479	-1.641000	0.00772	ACA	T|0.956;C|0.044	0.044	strong		0.473	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371	
CST4	1472	hgsc.bcm.edu	37	20	23666606	23666606	+	Silent	SNP	C	C	T	rs112139500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23666606C>T	ENST00000217423.3	-	3	421	c.351G>A	c.(349-351)ttG>ttA	p.L117L		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	117					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CGAAAGAGCACAACTGTTTCT	0.537													c|||	541	0.108027	0.1929	0.0663	5008	,	,		17992	0.0208		0.1252	False		,,,				2504	0.0951				p.L117L		Atlas-SNP	.											.	CST4	37	.	0			c.G351A						PASS	.	C		787,3619	317.2+/-295.0	71,645,1487	92.0	86.0	89.0		351	-0.4	0.0	20	dbSNP_132	89	1018,7582	217.3+/-256.0	57,904,3339	no	coding-synonymous	CST4	NM_001899.2		128,1549,4826	TT,TC,CC		11.8372,17.862,13.8782		117/142	23666606	1805,11201	2203	4300	6503	SO:0001819	synonymous_variant	1472	exon3			AGAGCACAACTGT		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.351G>A	20.37:g.23666606C>T		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	208	93	0.447115	NM_001899	Q9UBI5|Q9UCS9	Silent	SNP	ENST00000217423.3	37	CCDS13159.1																																																																																			C|0.873;T|0.127	0.127	strong		0.537	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899	
CAPN3	825	hgsc.bcm.edu	37	15	42681199	42681199	+	Missense_Mutation	SNP	G	G	A	rs1801449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42681199G>A	ENST00000397163.3	+	5	925	c.706G>A	c.(706-708)Gca>Aca	p.A236T	CAPN3_ENST00000356316.3_Missense_Mutation_p.A149T|CAPN3_ENST00000349748.3_Missense_Mutation_p.A236T|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000357568.3_Missense_Mutation_p.A236T|CAPN3_ENST00000318023.7_Missense_Mutation_p.A236T	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	236	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		A -> T (in dbSNP:rs1801449). {ECO:0000269|Ref.5}.		apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AGGAGGGGTGGCAGAGTTTTT	0.502													A|||	1353	0.270168	0.7458	0.0922	5008	,	,		18256	0.1121		0.0477	False		,,,				2504	0.1452				p.A236T		Atlas-SNP	.											.	CAPN3	172	.	0			c.G706A						PASS	.	A	THR/ALA,THR/ALA,THR/ALA	2737,1669	509.4+/-367.2	875,987,341	119.0	114.0	116.0		706,706,706	5.4	1.0	15	dbSNP_89	116	427,8171	800.2+/-407.4	11,405,3883	yes	missense,missense,missense	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1	58,58,58	886,1392,4224	AA,AG,GG		4.9663,37.8802,24.331	benign,benign,benign	236/822,236/816,236/730	42681199	3164,9840	2203	4299	6502	SO:0001583	missense	825	exon5			GGGGTGGCAGAGT	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"""EF-hand domain containing"""	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.706G>A	15.37:g.42681199G>A	ENSP00000380349:p.Ala236Thr	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	229	107	0.467249	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Missense_Mutation	SNP	ENST00000397163.3	37	CCDS45245.1	483	0.22115384615384615	352	0.7154471544715447	44	0.12154696132596685	51	0.08916083916083917	36	0.047493403693931395	A	14.44	2.535870	0.45176	0.621198	0.049663	ENSG00000092529	ENST00000356316;ENST00000397163;ENST00000357568;ENST00000349748;ENST00000318023	D;D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35;-2.35	5.41	5.41	0.78517	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.04805	-0.155	0.39232	P	0.036297000000000024	B;B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0;0.001	B;B;B;B;B;B	0.10450	0.0;0.001;0.001;0.001;0.001;0.005	T	0.38972	-0.9636	9	0.02654	T	1	.	11.4886	0.50369	0.9302:0.0:0.0698:0.0	rs1801449;rs58405398;rs1801449	149;149;236;236;236;149	C6EVS4;C6EVS3;P20807-2;P20807-3;P20807;Q762C8	.;.;.;.;CAN3_HUMAN;.	T	149;236;236;236;236	ENSP00000348667:A149T;ENSP00000380349:A236T;ENSP00000350181:A236T;ENSP00000183936:A236T;ENSP00000326281:A236T	ENSP00000326281:A236T	A	+	1	0	CAPN3	40468491	1.000000	0.71417	0.990000	0.47175	0.874000	0.50279	7.222000	0.78025	1.082000	0.41137	-0.361000	0.07541	GCA	G|0.759;A|0.241	0.241	strong		0.502	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		
ELMOD1	55531	hgsc.bcm.edu	37	11	107501428	107501428	+	Missense_Mutation	SNP	A	A	T	rs201717101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:107501428A>T	ENST00000265840.7	+	4	431	c.166A>T	c.(166-168)Aca>Tca	p.T56S	ELMOD1_ENST00000443271.2_Missense_Mutation_p.T56S|ELMOD1_ENST00000531234.1_Missense_Mutation_p.T50S	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	56					phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)	cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)			endometrium(2)|large_intestine(5)|liver(2)|lung(7)|pancreas(2)|prostate(1)	19		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		TTTCACAGAAACATCACTGAG	0.313													A|||	6	0.00119808	0.0045	0.0	5008	,	,		19465	0.0		0.0	False		,,,				2504	0.0				p.T56S		Atlas-SNP	.											.	ELMOD1	40	.	0			c.A166T						PASS	.	A	SER/THR,SER/THR	8,3684		0,8,1838	93.0	89.0	90.0		166,166	3.2	1.0	11		90	0,8158		0,0,4079	yes	missense,missense	ELMOD1	NM_001130037.1,NM_018712.3	58,58	0,8,5917	TT,TA,AA		0.0,0.2167,0.0675	benign,benign	56/327,56/335	107501428	8,11842	1846	4079	5925	SO:0001583	missense	55531	exon4			ACAGAAACATCAC	AL359601	CCDS44723.1, CCDS44724.1	11q23.1	2012-10-15	2006-01-20		ENSG00000110675	ENSG00000110675			25334	protein-coding gene	gene with protein product		615456	"""ELMO domain containing 1"""			12477932	Standard	NM_018712		Approved	DKFZp547C176	uc010rvs.2	Q8N336	OTTHUMG00000166361	ENST00000265840.7:c.166A>T	11.37:g.107501428A>T	ENSP00000265840:p.Thr56Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	152	58	0.381579	NM_018712	B4E167|G5E9S5|Q9NPW3	Missense_Mutation	SNP	ENST00000265840.7	37	CCDS44723.1	.	.	.	.	.	.	.	.	.	.	A	10.08	1.251659	0.22880	0.002167	0.0	ENSG00000110675	ENST00000531234;ENST00000265840;ENST00000443271	.	.	.	5.62	3.19	0.36642	.	0.250304	0.42294	D	0.000737	T	0.09686	0.0238	N	0.01277	-0.915	0.30939	N	0.726031	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.20538	-1.0272	9	0.08381	T	0.77	.	4.3202	0.11013	0.5821:0.0:0.178:0.2399	.	56;56	Q8N336;G5E9S5	ELMD1_HUMAN;.	S	50;56;56	.	ENSP00000265840:T56S	T	+	1	0	ELMOD1	107006638	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.228000	0.32588	0.957000	0.37930	0.533000	0.62120	ACA	.	.	weak		0.313	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389406.1	NM_018712	
ATP2A3	489	hgsc.bcm.edu	37	17	3844787	3844787	+	Silent	SNP	C	C	G	rs1800912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3844787C>G	ENST00000352011.3	-	13	1761	c.1707G>C	c.(1705-1707)gcG>gcC	p.A569A	ATP2A3_ENST00000397041.3_Silent_p.A569A|ATP2A3_ENST00000397043.3_Silent_p.A569A|ATP2A3_ENST00000309890.7_Silent_p.A569A|ATP2A3_ENST00000397035.3_Silent_p.A569A|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000359983.3_Silent_p.A569A			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	569					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		TCCTTGGGGGCGCGTCCCGGG	0.652													c|||	741	0.147963	0.1589	0.2637	5008	,	,		17537	0.004		0.2515	False		,,,				2504	0.093				p.A569A	GBM(32;29 774 15719 37967)	Atlas-SNP	.											ATP2A3,NS,carcinoma,-2,1	ATP2A3	148	1	0			c.G1707C						PASS	.		,,,,,,	776,3630	305.8+/-289.2	74,628,1501	86.0	85.0	85.0		1707,1707,1707,1707,1707,1707,1707	-7.3	0.0	17	dbSNP_89	85	2122,6478	357.5+/-330.8	286,1550,2464	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	360,2178,3965	GG,GC,CC		24.6744,17.6123,22.282	,,,,,,	569/1000,569/1053,569/1045,569/1044,569/1030,569/999,569/1030	3844787	2898,10108	2203	4300	6503	SO:0001819	synonymous_variant	489	exon13			TGGGGGCGCGTCC		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1707G>C	17.37:g.3844787C>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	125	65	0.52	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			C|0.787;G|0.213	0.213	strong		0.652	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
SLC37A2	219855	hgsc.bcm.edu	37	11	124949044	124949044	+	Silent	SNP	C	C	T	rs33932952|rs373958961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124949044C>T	ENST00000403796.2	+	5	652	c.351C>T	c.(349-351)taC>taT	p.Y117Y	SLC37A2_ENST00000298280.5_Silent_p.Y117Y|SLC37A2_ENST00000407458.1_Silent_p.Y117Y|SLC37A2_ENST00000308074.4_Silent_p.Y117Y	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	117					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.Y117Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		TCCGTTACTACCTCTCAGCTG	0.542													C|||	664	0.132588	0.18	0.1023	5008	,	,		20435	0.0605		0.1918	False		,,,				2504	0.1033				p.Y117Y	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											SLC37A2,NS,carcinoma,0,1	SLC37A2	105	1	1	Substitution - coding silent(1)	stomach(1)	c.C351T						PASS	.	C	,	887,3515	344.1+/-307.9	92,703,1406	153.0	147.0	149.0		351,351	4.6	1.0	11	dbSNP_126	149	1719,6879	314.6+/-311.9	172,1375,2752	no	coding-synonymous,coding-synonymous	SLC37A2	NM_001145290.1,NM_198277.2	,	264,2078,4158	TT,TC,CC		19.993,20.1499,20.0462	,	117/502,117/506	124949044	2606,10394	2201	4299	6500	SO:0001819	synonymous_variant	219855	exon5			TTACTACCTCTCA	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.351C>T	11.37:g.124949044C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	139	77	0.553957	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Silent	SNP	ENST00000403796.2	37	CCDS44757.1																																																																																			C|0.814;T|0.186	0.186	strong		0.542	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
USP6	9098	hgsc.bcm.edu	37	17	5072333	5072333	+	Missense_Mutation	SNP	T	T	G	rs3816913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5072333T>G	ENST00000574788.1	+	35	5730	c.3500T>G	c.(3499-3501)aTc>aGc	p.I1167S	USP6_ENST00000304328.5_Missense_Mutation_p.I850S|USP6_ENST00000250066.6_Missense_Mutation_p.I1167S|USP6_ENST00000332776.4_3'UTR			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	1167	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						AGCGCTAACATCAGCAGCAGC	0.507			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								t|||	513	0.102436	0.1974	0.0418	5008	,	,		19709	0.0794		0.1163	False		,,,				2504	0.0266				p.I1167S		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.T3500G						PASS	.	G	SER/ILE	703,3703	278.4+/-274.2	61,581,1561	34.0	34.0	34.0		3500	1.2	0.0	17	dbSNP_107	34	945,7651	196.9+/-241.7	53,839,3406	no	missense	USP6	NM_004505.2	142	114,1420,4967	GG,GT,TT		10.9935,15.9555,12.675	benign	1167/1407	5072333	1648,11354	2203	4298	6501	SO:0001583	missense	9098	exon27			CTAACATCAGCAG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.3500T>G	17.37:g.5072333T>G	ENSP00000460380:p.Ile1167Ser	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	294	121	0.411565	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	246	0.11263736263736264	94	0.1910569105691057	16	0.04419889502762431	52	0.09090909090909091	84	0.11081794195250659	t	0.036	-1.305728	0.01353	0.159555	0.109935	ENSG00000129204	ENST00000250066;ENST00000304328	T;T	0.13778	2.98;2.56	2.35	1.22	0.21188	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.756886	0.13090	N	0.414589	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.24092	0.029;0.097	B;B	0.28011	0.03;0.085	T	0.43605	-0.9381	9	0.07813	T	0.8	.	5.438	0.16492	0.0:0.0:0.2935:0.7065	rs3816913	850;1167	P35125-2;P35125	.;UBP6_HUMAN	S	1167;850	ENSP00000250066:I1167S;ENSP00000305473:I850S	ENSP00000250066:I1167S	I	+	2	0	USP6	5013057	0.058000	0.20735	0.003000	0.11579	0.116000	0.19942	1.968000	0.40500	0.160000	0.19432	-1.396000	0.01147	ATC	T|0.884;G|0.116	0.116	strong		0.507	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
DCC	1630	hgsc.bcm.edu	37	18	50705370	50705370	+	Missense_Mutation	SNP	A	A	T	rs116498325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:50705370A>T	ENST00000442544.2	+	9	2073	c.1457A>T	c.(1456-1458)cAg>cTg	p.Q486L	DCC_ENST00000581580.1_Missense_Mutation_p.Q141L|DCC_ENST00000412726.1_Missense_Mutation_p.Q334L	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	486	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		GGGTCCCTTCAGCTCACTGTG	0.463													A|||	15	0.00299521	0.0106	0.0014	5008	,	,		16535	0.0		0.0	False		,,,				2504	0.0				p.Q486L		Atlas-SNP	.											.	DCC	360	.	0			c.A1457T						PASS	.	A	LEU/GLN	43,4363	46.0+/-80.4	1,41,2161	100.0	90.0	94.0		1457	5.6	1.0	18	dbSNP_132	94	0,8600		0,0,4300	yes	missense	DCC	NM_005215.3	113	1,41,6461	TT,TA,AA		0.0,0.9759,0.3306	possibly-damaging	486/1448	50705370	43,12963	2203	4300	6503	SO:0001583	missense	1630	exon9			CCCTTCAGCTCAC	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.1457A>T	18.37:g.50705370A>T	ENSP00000389140:p.Gln486Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	164	78	0.47561	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	A	15.68	2.903669	0.52333	0.009759	0.0	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.57752	0.38;0.38	5.62	5.62	0.85841	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.076791	0.52532	D	0.000063	T	0.63534	0.2519	M	0.72894	2.215	0.53688	D	0.999971	P;P;D	0.58970	0.769;0.769;0.984	P;P;D	0.65874	0.593;0.593;0.939	T	0.71533	-0.4564	10	0.87932	D	0	.	15.0981	0.72250	1.0:0.0:0.0:0.0	.	334;334;486	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	L	486;419;334	ENSP00000389140:Q486L;ENSP00000397322:Q334L	ENSP00000304146:Q419L	Q	+	2	0	DCC	48959368	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.534000	0.90620	2.266000	0.75297	0.533000	0.62120	CAG	A|0.996;T|0.004	0.004	strong		0.463	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
KCNJ4	3761	hgsc.bcm.edu	37	22	38823895	38823895	+	Silent	SNP	G	G	A	rs105154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38823895G>A	ENST00000303592.3	-	2	501	c.243C>T	c.(241-243)gcC>gcT	p.A81A	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	81					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					CGTGGAAGAAGGCGATACACC	0.692													G|||	310	0.061901	0.1861	0.0187	5008	,	,		15064	0.0		0.0159	False		,,,				2504	0.0358				p.A81A		Atlas-SNP	.											.	KCNJ4	74	.	0			c.C243T						PASS	.	G	,	748,3658	294.7+/-283.3	60,628,1515	71.0	45.0	54.0		243,243	3.8	1.0	22	dbSNP_79	54	174,8426	78.4+/-141.0	2,170,4128	no	coding-synonymous,coding-synonymous	KCNJ4	NM_004981.1,NM_152868.1	,	62,798,5643	AA,AG,GG		2.0233,16.9768,7.089	,	81/446,81/446	38823895	922,12084	2203	4300	6503	SO:0001819	synonymous_variant	3761	exon2			GAAGAAGGCGATA	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.243C>T	22.37:g.38823895G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_004981	Q14D44	Silent	SNP	ENST00000303592.3	37	CCDS13971.1																																																																																			G|0.921;A|0.079	0.079	strong		0.692	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981	
ETAA1	54465	hgsc.bcm.edu	37	2	67624739	67624739	+	Silent	SNP	C	C	A	rs182131786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:67624739C>A	ENST00000272342.5	+	1	289	c.159C>A	c.(157-159)ccC>ccA	p.P53P		NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	53						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						AGGGGCCTCCCGGGCCAGTGC	0.721													C|||	5	0.000998403	0.0038	0.0	5008	,	,		11612	0.0		0.0	False		,,,				2504	0.0				p.P53P		Atlas-SNP	.											ETAA1,colon,carcinoma,+2,1	ETAA1	88	1	0			c.C159A						PASS	.	C		10,4090		0,10,2040	5.0	7.0	6.0		159	-0.4	0.0	2		6	1,8047		0,1,4023	no	coding-synonymous	ETAA1	NM_019002.3		0,11,6063	AA,AC,CC		0.0124,0.2439,0.0905		53/927	67624739	11,12137	2050	4024	6074	SO:0001819	synonymous_variant	54465	exon1			GCCTCCCGGGCCA	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.159C>A	2.37:g.67624739C>A		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	33	23	0.69697	NM_019002	Q05BT7|Q53SC4	Silent	SNP	ENST00000272342.5	37	CCDS1882.1																																																																																			C|0.999;A|0.001	0.001	strong		0.721	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002	
FAT2	2196	hgsc.bcm.edu	37	5	150946444	150946444	+	Silent	SNP	G	G	A	rs142348925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150946444G>A	ENST00000261800.5	-	1	2061	c.2049C>T	c.(2047-2049)atC>atT	p.I683I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	683					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)			TAAAGTGGAGGATAGTCTTTG	0.408													G|||	2	0.000399361	0.0015	0.0	5008	,	,		22771	0.0		0.0	False		,,,				2504	0.0				p.I683I		Atlas-SNP	.											.	FAT2	465	.	0			c.C2049T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	117.0	110.0	112.0		2049	2.8	1.0	5	dbSNP_134	112	0,8600		0,0,4300	no	coding-synonymous	FAT2	NM_001447.2		0,6,6497	AA,AG,GG		0.0,0.1362,0.0461		683/4350	150946444	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			GTGGAGGATAGTC	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.2049C>T	5.37:g.150946444G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	220	98	0.445455	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.999;A|0.001	0.001	strong		0.408	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
COX7B	1349	hgsc.bcm.edu	37	X	77158147	77158147	+	Missense_Mutation	SNP	C	C	A	rs61752458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:77158147C>A	ENST00000481445.1	+	2	164	c.48C>A	c.(46-48)agC>agA	p.S16R	COX7B_ENST00000475465.1_3'UTR	NM_001866.2	NP_001857.1	P24311	COX7B_HUMAN	cytochrome c oxidase subunit VIIb	16					cellular metabolic process (GO:0044237)|central nervous system development (GO:0007417)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)	cytochrome-c oxidase activity (GO:0004129)			endometrium(2)	2						AAGTTCGAAGCATTCAGCAAA	0.388													C|||	49	0.0129801	0.0356	0.0029	3775	,	,		15718	0.0		0.0	False		,,,				2504	0.0				p.S16R		Atlas-SNP	.											.	COX7B	8	.	0			c.C48A						PASS	.	C	ARG/SER	101,3734		1,83,16,1548,555	138.0	107.0	118.0		48	3.1	1.0	X	dbSNP_129	118	0,6728		0,0,0,2428,1872	yes	missense	COX7B	NM_001866.2	110	1,83,16,3976,2427	AA,AC,A,CC,C		0.0,2.6336,0.9562	benign	16/81	77158147	101,10462	2203	4300	6503	SO:0001583	missense	1349	exon2			TCGAAGCATTCAG	Z14244	CCDS14437.1	Xq21.1	2011-07-04			ENSG00000131174	ENSG00000131174		"""Mitochondrial respiratory chain complex / Complex IV"""	2291	protein-coding gene	gene with protein product		300885				8382530	Standard	NM_001866		Approved		uc004ecu.1	P24311	OTTHUMG00000022718	ENST00000481445.1:c.48C>A	X.37:g.77158147C>A	ENSP00000417656:p.Ser16Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_001866	B2R4M3|Q6ICR1	Missense_Mutation	SNP	ENST00000481445.1	37	CCDS14437.1	11	0.006630500301386378	4	0.008298755186721992	1	0.002777777777777778	0	0.0	0	0.0	C	17.45	3.392912	0.62066	0.026336	0.0	ENSG00000131174	ENST00000481445	T	0.48836	0.8	4.92	3.13	0.36017	.	0.349121	0.32401	N	0.006153	T	0.29288	0.0729	.	.	.	0.40351	P	0.02086100000000002	P	0.43542	0.81	P	0.53062	0.717	T	0.56619	-0.7949	8	0.52906	T	0.07	-0.0019	6.4067	0.21668	0.1816:0.7202:0.0:0.0982	rs61752458	16	P24311	COX7B_HUMAN	R	16	ENSP00000417656:S16R	ENSP00000417656:S16R	S	+	3	2	COX7B	77044803	1.000000	0.71417	0.997000	0.53966	0.814000	0.46013	0.699000	0.25586	0.330000	0.23485	0.523000	0.50628	AGC	C|0.991;A|0.009	0.009	strong		0.388	COX7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058970.1	NM_001866	
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19126492	19126492	+	Missense_Mutation	SNP	T	T	A	rs8051801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19126492T>A	ENST00000381440.3	+	1	1239	c.709T>A	c.(709-711)Tgc>Agc	p.C237S	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	237			C -> S (in dbSNP:rs8051801).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TGATGCCTTCTGCGTGGATGT	0.657											OREG0023657	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	43	0.00858626	0.0325	0.0	5008	,	,		17049	0.0		0.0	False		,,,				2504	0.0				p.C237S		Atlas-SNP	.											.	ITPRIPL2	40	.	0			c.T709A						PASS	.	T	SER/CYS	146,4248	100.7+/-139.4	3,140,2054	74.0	78.0	77.0		709	4.7	1.0	16	dbSNP_116	77	0,8600		0,0,4300	yes	missense	ITPRIPL2	NM_001034841.3	112	3,140,6354	AA,AT,TT		0.0,3.3227,1.1236	probably-damaging	237/536	19126492	146,12848	2197	4300	6497	SO:0001583	missense	162073	exon1			GCCTTCTGCGTGG		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"""inositol 1,4,5-triphosphate receptor interacting protein-like 2"""				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.709T>A	16.37:g.19126492T>A	ENSP00000370849:p.Cys237Ser	Somatic	86	0	0	730	WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_001034841		Missense_Mutation	SNP	ENST00000381440.3	37	CCDS32395.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	T	22.2	4.253591	0.80135	0.033227	0.0	ENSG00000205730	ENST00000381440	T	0.16597	2.33	4.71	4.71	0.59529	.	0.382932	0.21183	U	0.078791	T	0.10895	0.0266	L	0.27053	0.805	0.46521	D	0.999086	D	0.71674	0.998	D	0.78314	0.991	T	0.01452	-1.1351	10	0.72032	D	0.01	-13.7638	13.3495	0.60593	0.0:0.0:0.0:1.0	rs8051801;rs8051801	237	Q3MIP1	IPIL2_HUMAN	S	237	ENSP00000370849:C237S	ENSP00000370849:C237S	C	+	1	0	ITPRIPL2	19033993	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.264000	0.58859	1.743000	0.51761	0.533000	0.62120	TGC	T|0.989;A|0.011	0.011	strong		0.657	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	NM_001034841	
C20orf144	128864	hgsc.bcm.edu	37	20	32251396	32251396	+	Missense_Mutation	SNP	A	A	G	rs7260921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:32251396A>G	ENST00000375222.3	+	2	247	c.185A>G	c.(184-186)cAa>cGa	p.Q62R	NECAB3_ENST00000246190.6_Intron|NECAB3_ENST00000375238.4_Intron|ACTL10_ENST00000330271.4_5'Flank|NECAB3_ENST00000606525.1_5'Flank	NM_080825.3	NP_543015.1	Q9BQM9	CT144_HUMAN	chromosome 20 open reading frame 144	62			Q -> R (in dbSNP:rs7260921).							lung(1)	1						AACGCTGGGCAACGGATTGAC	0.706													G|||	772	0.154153	0.4198	0.2147	5008	,	,		13324	0.0377		0.0	False		,,,				2504	0.0307				p.Q62R		Atlas-SNP	.											.	C20orf144	4	.	0			c.A185G						PASS	.	G	,,ARG/GLN	1056,2632		125,806,913	14.0	16.0	16.0		,,185	1.9	0.2	20	dbSNP_116	16	14,7620		0,14,3803	yes	intron,intron,missense	NECAB3,C20orf144	NM_031231.3,NM_031232.3,NM_080825.3	,,43	125,820,4716	GG,GA,AA		0.1834,28.6334,9.4506	,,benign	,,62/154	32251396	1070,10252	1844	3817	5661	SO:0001583	missense	128864	exon2			CTGGGCAACGGAT	AL121906	CCDS13223.1	20q11.22	2012-07-17			ENSG00000149609	ENSG00000149609			16137	protein-coding gene	gene with protein product	"""bcl-2-like protein from testis"""					11780052	Standard	NM_080825		Approved	dJ63M2.6, bclt	uc002wzs.2	Q9BQM9	OTTHUMG00000032263	ENST00000375222.3:c.185A>G	20.37:g.32251396A>G	ENSP00000364370:p.Gln62Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_080825	Q1AHR2	Missense_Mutation	SNP	ENST00000375222.3	37	CCDS13223.1	288	0.13186813186813187	191	0.3882113821138211	69	0.19060773480662985	28	0.04895104895104895	0	0.0	G	3.709	-0.059895	0.07317	0.286334	0.001834	ENSG00000149609	ENST00000375222	T	0.39056	1.1	4.08	1.94	0.25998	.	0.154572	0.29730	N	0.011360	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	0.42999	-0.9418	9	0.07030	T	0.85	-13.4911	3.3533	0.07160	0.2205:0.0:0.5775:0.202	rs7260921;rs59444064;rs7260921	62	Q9BQM9	CT144_HUMAN	R	62	ENSP00000364370:Q62R	ENSP00000364370:Q62R	Q	+	2	0	C20orf144	31715057	0.000000	0.05858	0.171000	0.22900	0.071000	0.16799	-0.477000	0.06583	0.498000	0.27948	-0.355000	0.07637	CAA	A|0.881;G|0.119	0.119	strong		0.706	C20orf144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078714.2	NM_080825	
GPR20	2843	hgsc.bcm.edu	37	8	142367559	142367559	+	Silent	SNP	G	G	A	rs11785629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:142367559G>A	ENST00000377741.3	-	2	555	c.465C>T	c.(463-465)ccC>ccT	p.P155P	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	155					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(3)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	15	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			GGGAGCCTTCGGGCCGCACGA	0.687													G|||	3011	0.601238	0.4539	0.7277	5008	,	,		15148	0.5099		0.7237	False		,,,				2504	0.6789				p.P155P		Atlas-SNP	.											.	GPR20	43	.	0			c.C465T						PASS	.	G		2254,2148		597,1060,544	17.0	20.0	19.0		465	-9.7	0.0	8	dbSNP_120	19	5923,2675		2065,1793,441	no	coding-synonymous	GPR20	NM_005293.2		2662,2853,985	AA,AG,GG		31.1119,48.796,37.1		155/359	142367559	8177,4823	2201	4299	6500	SO:0001819	synonymous_variant	2843	exon2			GCCTTCGGGCCGC	U66579	CCDS34949.1	8q24.3	2012-08-21				ENSG00000204882		"""GPCR / Class A : Orphans"""	4475	protein-coding gene	gene with protein product		601908				18347022	Standard	NM_005293		Approved		uc003ywf.3	Q99678		ENST00000377741.3:c.465C>T	8.37:g.142367559G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	30	20	0.666667	NM_005293	Q17R96	Silent	SNP	ENST00000377741.3	37	CCDS34949.1																																																																																			G|0.364;A|0.636	0.636	strong		0.687	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293	
NOL8	55035	hgsc.bcm.edu	37	9	95077498	95077498	+	Missense_Mutation	SNP	C	C	T	rs58545014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95077498C>T	ENST00000535387.1	-	6	1408	c.1409G>A	c.(1408-1410)gGa>gAa	p.G470E	NOL8_ENST00000358855.4_Missense_Mutation_p.G402E|NOL8_ENST00000442668.2_Missense_Mutation_p.G470E|NOL8_ENST00000545558.1_Missense_Mutation_p.G470E|NOL8_ENST00000542053.1_Missense_Mutation_p.G402E					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						CTCCTCACCTCCTTCAGAGTC	0.433													C|||	166	0.033147	0.1172	0.0159	5008	,	,		20446	0.0		0.0	False		,,,				2504	0.0				p.G470E		Atlas-SNP	.											.	NOL8	118	.	0			c.G1409A						PASS	.	C	GLU/GLY	379,3445		15,349,1548	67.0	62.0	63.0		1409	-2.3	0.0	9	dbSNP_129	63	9,8283		0,9,4137	yes	missense	NOL8	NM_017948.5	98	15,358,5685	TT,TC,CC		0.1085,9.9111,3.2024	benign	470/1168	95077498	388,11728	1912	4146	6058	SO:0001583	missense	55035	exon7			TCACCTCCTTCAG	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.1409G>A	9.37:g.95077498C>T	ENSP00000441300:p.Gly470Glu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	161	118	0.732919	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	C	2.889	-0.230150	0.05983	0.099111	0.001085	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.15256	2.71;2.7;2.71;2.93;2.7;2.44	5.69	-2.34	0.06704	.	1.014810	0.07869	N	0.967526	T	0.00039	0.0001	N	0.16656	0.425	0.80722	P	0.0	B	0.15141	0.012	B	0.11329	0.006	T	0.41124	-0.9526	9	0.10377	T	0.69	-5.5238	1.3463	0.02164	0.171:0.3053:0.1593:0.3644	rs58545014;rs61740235	470	Q76FK4	NOL8_HUMAN	E	470;472;402;470;470;402;470	ENSP00000401177:G470E;ENSP00000351723:G402E;ENSP00000441140:G470E;ENSP00000441300:G470E;ENSP00000440709:G402E;ENSP00000414112:G470E	ENSP00000351723:G402E	G	-	2	0	NOL8	94117319	0.000000	0.05858	0.000000	0.03702	0.182000	0.23217	-1.648000	0.01995	-0.302000	0.08869	-0.345000	0.07892	GGA	C|0.972;T|0.028	0.028	strong		0.433	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
RPGR	6103	hgsc.bcm.edu	37	X	38145715	38145715	+	Intron	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145715T>C	ENST00000339363.3	-	14	2688				TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000378505.2_Missense_Mutation_p.E846G|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						cccctccccttcctcctcttc	0.602																																					p.E846G		Atlas-SNP	.											.	RPGR	175	.	0			c.A2537G						PASS	.						39.0	26.0	31.0					X																	38145715		1741	3341	5082	SO:0001627	intron_variant	6103	exon15			TCCCCTTCCTCCT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+631A>G	X.37:g.38145715T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	115	8	0.0695652	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		.	.	.	.	.	.	.	.	.	.	t	5.065	0.197625	0.09652	.	.	ENSG00000156313	ENST00000378505	T	0.02525	4.26	1.54	1.54	0.23209	.	1.854680	0.04946	U	0.459387	T	0.04137	0.0115	L	0.50333	1.59	0.45676	D	0.998598	B	0.13594	0.008	B	0.06405	0.002	T	0.32745	-0.9895	10	0.66056	D	0.02	.	4.6898	0.12776	0.0:0.1904:0.0:0.8096	.	846	E9PE28	.	G	846	ENSP00000367766:E846G	ENSP00000367766:E846G	E	-	2	0	RPGR	38030659	0.004000	0.15560	0.004000	0.12327	0.000000	0.00434	0.336000	0.19823	0.671000	0.31185	0.000000	0.15137	GAA	.	.	none		0.602	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
SLC5A6	8884	hgsc.bcm.edu	37	2	27430237	27430237	+	Silent	SNP	T	T	C	rs56970590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27430237T>C	ENST00000310574.3	-	3	755	c.282A>G	c.(280-282)cgA>cgG	p.R94R	SLC5A6_ENST00000408041.1_Silent_p.R94R	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	94					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	GGGTCCCAAATCGGTAGATCT	0.587													T|||	245	0.0489217	0.0832	0.0375	5008	,	,		21395	0.001		0.0497	False		,,,				2504	0.0593				p.R94R		Atlas-SNP	.											.	SLC5A6	63	.	0			c.A282G						PASS	.	T		347,4059	180.1+/-208.5	13,321,1869	62.0	58.0	59.0		282	-5.2	0.1	2	dbSNP_129	59	413,8187	128.8+/-187.0	14,385,3901	no	coding-synonymous	SLC5A6	NM_021095.2		27,706,5770	CC,CT,TT		4.8023,7.8756,5.8435		94/636	27430237	760,12246	2203	4300	6503	SO:0001819	synonymous_variant	8884	exon3			CCCAAATCGGTAG	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"""Solute carriers"""	11041	protein-coding gene	gene with protein product		604024	"""solute carrier family 5 (sodium-dependent vitamin transporter), member 6"""			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.282A>G	2.37:g.27430237T>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	214	123	0.574766	NM_021095	B2RB85|D6W549|Q969Y5	Silent	SNP	ENST00000310574.3	37	CCDS1740.1																																																																																			T|0.952;C|0.048	0.048	strong		0.587	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095	
BAIAP3	8938	hgsc.bcm.edu	37	16	1391362	1391362	+	Silent	SNP	A	A	G	rs75271587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1391362A>G	ENST00000324385.5	+	8	866	c.708A>G	c.(706-708)gcA>gcG	p.A236A	BAIAP3_ENST00000421665.2_Silent_p.A201A|BAIAP3_ENST00000562208.1_Silent_p.A178A|BAIAP3_ENST00000397489.1_Silent_p.A218A|BAIAP3_ENST00000397488.2_Silent_p.A218A|BAIAP3_ENST00000568887.1_Silent_p.A173A|BAIAP3_ENST00000426824.3_Silent_p.A201A	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	236	C2 1. {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)				AGCCCCGTGCACAGAAGGAGC	0.682													G|||	52	0.0103834	0.0386	0.0014	5008	,	,		17448	0.0		0.0	False		,,,				2504	0.0				p.A236A		Atlas-SNP	.											.	BAIAP3	88	.	0			c.A708G						PASS	.	G	,,,,	126,4260		1,124,2068	37.0	36.0	36.0		603,603,534,519,708	-5.2	0.0	16	dbSNP_131	36	0,8590		0,0,4295	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	,,,,	1,124,6363	GG,GA,AA		0.0,2.8728,0.971	,,,,	201/1117,201/1153,178/1130,173/1125,236/1188	1391362	126,12850	2193	4295	6488	SO:0001819	synonymous_variant	8938	exon8			CCGTGCACAGAAG	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.708A>G	16.37:g.1391362A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	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																																																																																			A|0.988;G|0.012	0.012	strong		0.682	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
SLC7A14	57709	hgsc.bcm.edu	37	3	170198898	170198898	+	Silent	SNP	C	C	T	rs3732449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:170198898C>T	ENST00000231706.5	-	7	1488	c.1173G>A	c.(1171-1173)tcG>tcA	p.S391S	CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000486975.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	391			S -> L (in RP68; uncertain pathological significance). {ECO:0000269|PubMed:24670872}.		negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			CCAGGAACCCCGACACGATGC	0.587													c|||	1690	0.33746	0.5212	0.2608	5008	,	,		18123	0.3849		0.1968	False		,,,				2504	0.2393				p.S391S		Atlas-SNP	.											.	SLC7A14	110	.	0			c.G1173A						PASS	.	T		2131,2275	578.2+/-384.6	503,1125,575	54.0	47.0	50.0		1173	-10.6	0.1	3	dbSNP_107	50	1557,7043	293.4+/-301.3	134,1289,2877	no	coding-synonymous	SLC7A14	NM_020949.2		637,2414,3452	TT,TC,CC		18.1047,48.3659,28.3561		391/772	170198898	3688,9318	2203	4300	6503	SO:0001819	synonymous_variant	57709	exon7			GAACCCCGACACG	BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"""Solute carriers"""	29326	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 142"""	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.1173G>A	3.37:g.170198898C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_020949	B3KV33|Q9HCF9	Silent	SNP	ENST00000231706.5	37	CCDS33892.1																																																																																			C|0.688;T|0.312	0.312	strong		0.587	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949	
KDR	3791	hgsc.bcm.edu	37	4	55956183	55956183	+	Silent	SNP	G	G	T	rs145298133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:55956183G>T	ENST00000263923.4	-	23	3427	c.3132C>A	c.(3130-3132)atC>atA	p.I1044I	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	1044	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAAAGTCACAGATTTTAACCA	0.428			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			G|||	3	0.000599042	0.0023	0.0	5008	,	,		18361	0.0		0.0	False		,,,				2504	0.0				p.I1044I		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.C3132A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	94.0	93.0	94.0		3132	5.7	1.0	4	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	KDR	NM_002253.2		0,10,6493	TT,TG,GG		0.0,0.227,0.0769		1044/1357	55956183	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	3791	exon23			GTCACAGATTTTA	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.3132C>A	4.37:g.55956183G>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	80	28	0.35	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	37	CCDS3497.1																																																																																			G|0.999;T|0.001	0.001	strong		0.428	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
GH2	2689	hgsc.bcm.edu	37	17	61957610	61957610	+	3'UTR	SNP	G	G	T	rs58696130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61957610G>T	ENST00000423893.2	-	0	786				GH2_ENST00000449787.2_3'UTR|GH2_ENST00000332800.7_3'UTR|GH2_ENST00000456543.2_Missense_Mutation_p.P241T			P01242	SOM2_HUMAN	growth hormone 2						JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	24						AAGGCTGGTGGGCACTGGAGT	0.552													G|||	144	0.028754	0.1044	0.0072	5008	,	,		19214	0.0		0.001	False		,,,				2504	0.0				p.P241T		Atlas-SNP	.											.	GH2	73	.	0			c.C721A						PASS	.	G	,,,THR/PRO	304,2350		17,270,1040	36.0	38.0	37.0		,,,721	0.8	0.0	17	dbSNP_129	37	1,4617		0,1,2308	yes	utr-3,utr-3,utr-3,missense	GH2	NM_002059.3,NM_022556.2,NM_022557.2,NM_022558.2	,,,38	17,271,3348	TT,TG,GG		0.0217,11.4544,4.1942	,,,	,,,241/246	61957610	305,6967	1327	2309	3636	SO:0001624	3_prime_UTR_variant	2689	exon5			CTGGTGGGCACTG	J03756	CCDS11647.1, CCDS11648.1, CCDS45757.1, CCDS45758.1	17q22-q24	2014-01-30						"""Endogenous ligands"""	4262	protein-coding gene	gene with protein product	"""placental-specific growth hormone"", ""placenta-specific growth hormone"""	139240				6306568	Standard	NM_002059		Approved	GH-V, GHV, GHL, hGH-V	uc002jcl.2	P01242		ENST00000423893.2:c.*71C>A	17.37:g.61957610G>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	132	71	0.537879	NM_022558	B1A4H5|B1A4H7|O14643|O14644|P09587	Missense_Mutation	SNP	ENST00000423893.2	37	CCDS11647.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	g	10.77	1.444668	0.25987	0.114544	2.17E-4	ENSG00000136487	ENST00000456543	D	0.89552	-2.53	1.79	0.797	0.18654	.	.	.	.	.	T	0.06735	0.0172	N	0.24115	0.695	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.45279	-0.9272	9	0.87932	D	0	.	4.4826	0.11774	0.2024:0.0:0.7976:0.0	rs58696130;rs61764021	241	O14644	.	T	241	ENSP00000394122:P241T	ENSP00000394122:P241T	P	-	1	0	GH2	59311342	0.006000	0.16342	0.002000	0.10522	0.048000	0.14542	0.969000	0.29370	0.321000	0.23259	-0.699000	0.03677	CCA	G|0.983;T|0.017	0.017	strong		0.552	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1	NM_002059	
C11orf40	143501	hgsc.bcm.edu	37	11	4593411	4593411	+	Missense_Mutation	SNP	G	G	A	rs34097396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4593411G>A	ENST00000307616.1	-	3	421	c.422C>T	c.(421-423)aCg>aTg	p.T141M		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	141										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)		GAAAGAAAGCGTGATAAGATC	0.428													G|||	462	0.0922524	0.2103	0.072	5008	,	,		21422	0.0397		0.0716	False		,,,				2504	0.0225				p.T141M		Atlas-SNP	.											.	C11orf40	37	.	0			c.C422T						PASS	.	G	MET/THR	934,3468	356.4+/-313.5	113,708,1380	146.0	131.0	136.0		422	-1.7	0.0	11	dbSNP_126	136	593,8003	156.9+/-210.6	30,533,3735	yes	missense	C11orf40	NM_144663.1	81	143,1241,5115	AA,AG,GG		6.8986,21.2176,11.748	benign	141/218	4593411	1527,11471	2201	4298	6499	SO:0001583	missense	143501	exon3			GAAAGCGTGATAA		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.422C>T	11.37:g.4593411G>A	ENSP00000302918:p.Thr141Met	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	153	78	0.509804	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	37	CCDS31354.1	199	0.09111721611721611	100	0.2032520325203252	27	0.07458563535911603	24	0.04195804195804196	48	0.0633245382585752	G	0.060	-1.226114	0.01518	0.212176	0.068986	ENSG00000171987	ENST00000307616	T	0.54071	0.59	0.835	-1.67	0.08238	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.17465	0.022	B	0.04013	0.001	T	0.11084	-1.0602	8	0.87932	D	0	.	4.4149	0.11452	0.4476:0.0:0.5524:0.0	rs34097396	141	Q8WZ69	CK040_HUMAN	M	141	ENSP00000302918:T141M	ENSP00000302918:T141M	T	-	2	0	C11orf40	4549987	0.001000	0.12720	0.006000	0.13384	0.016000	0.09150	0.055000	0.14229	-0.765000	0.04645	-0.684000	0.03749	ACG	G|0.888;A|0.112	0.112	strong		0.428	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663	
GPC3	2719	hgsc.bcm.edu	37	X	132670269	132670269	+	Silent	SNP	T	T	C	rs61754631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:132670269T>C	ENST00000370818.3	-	8	2071	c.1626A>G	c.(1624-1626)gcA>gcG	p.A542A	GPC3_ENST00000543339.1_Silent_p.A488A|GPC3_ENST00000394299.2_Silent_p.A565A	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	542					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|body morphogenesis (GO:0010171)|bone mineralization (GO:0030282)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cell proliferation involved in metanephros development (GO:0072203)|chondroitin sulfate metabolic process (GO:0030204)|coronary vasculature development (GO:0060976)|embryonic hindlimb morphogenesis (GO:0035116)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lung development (GO:0030324)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesonephric duct morphogenesis (GO:0072180)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of growth (GO:0045926)|negative regulation of smoothened signaling pathway (GO:0045879)|osteoclast differentiation (GO:0030316)|phototransduction, visible light (GO:0007603)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endocytosis (GO:0045807)|positive regulation of glucose import (GO:0046326)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	peptidyl-dipeptidase inhibitor activity (GO:0060422)			breast(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|prostate(1)|skin(2)	36	Acute lymphoblastic leukemia(192;0.000127)					CCTTCGGAGTTGCCTGCTGAC	0.502			"""T, D, Mis, N, F, S"""			Wilms tumour			Simpson-Golabi-Behmel syndrome				C|||	203	0.0537748	0.1505	0.0058	3775	,	,		12135	0.0		0.0	False		,,,				2504	0.0				p.A565A		Atlas-SNP	.	yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	.	GPC3	88	.	0			c.A1695G						PASS	.	C	,,,	741,3094		68,494,111,1070,460	274.0	217.0	236.0		1695,1578,1464,1626	2.1	0.0	X	dbSNP_129	236	5,6723		0,2,3,2426,1869	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPC3	NM_001164617.1,NM_001164618.1,NM_001164619.1,NM_004484.3	,,,	68,496,114,3496,2329	CC,CT,C,TT,T		0.0743,19.322,7.0624	,,,	565/604,526/565,488/527,542/581	132670269	746,9817	2203	4300	6503	SO:0001819	synonymous_variant	2719	exon9	Familial Cancer Database	SGBS	CGGAGTTGCCTGC	L47125	CCDS14638.1, CCDS55496.1	Xq26	2014-09-17			ENSG00000147257	ENSG00000147257		"""Proteoglycans / Cell Surface : Glypicans"""	4451	protein-coding gene	gene with protein product	"""glypican proteoglycan 3"""	300037		SDYS		8589713, 9787072	Standard	NM_004484		Approved	OCI-5, SGBS, SGBS1, SGB, DGSX	uc010nrn.2	P51654	OTTHUMG00000022448	ENST00000370818.3:c.1626A>G	X.37:g.132670269T>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	193	119	0.61658	NM_001164617	C9JLE3|G3V1R0|Q2L880|Q2L882	Silent	SNP	ENST00000370818.3	37	CCDS14638.1																																																																																			T|0.927;C|0.073	0.073	strong		0.502	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484	
LCN10	414332	hgsc.bcm.edu	37	9	139634495	139634495	+	Nonsense_Mutation	SNP	G	G	A	rs9886752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139634495G>A	ENST00000474369.1	-	4	441	c.442C>T	c.(442-444)Cag>Tag	p.Q148*	LCN10_ENST00000497771.1_Nonsense_Mutation_p.Q161*|LCN6_ENST00000480584.1_5'Flank|LCN6_ENST00000435202.1_3'UTR|LCN10_ENST00000527229.1_Nonsense_Mutation_p.Q125*			Q6JVE6	LCN10_HUMAN	lipocalin 10	148					transport (GO:0006810)	extracellular region (GO:0005576)				breast(2)|cervix(1)|large_intestine(1)	4	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)		GAAACATTCTGCCTATCTGAG	0.542													g|||	998	0.199281	0.1808	0.2421	5008	,	,		19016	0.2698		0.1491	False		,,,				2504	0.1728				p.Q161X		Atlas-SNP	.											.	LCN10	21	.	0			c.C481T						PASS	.		stop/GLN	795,3607		82,631,1488	71.0	57.0	62.0		481	1.7	0.1	9	dbSNP_119	62	1317,7273		105,1107,3083	yes	stop-gained	LCN10	NM_001001712.2		187,1738,4571	AA,AG,GG		15.3318,18.06,16.2562		161/201	139634495	2112,10880	2201	4295	6496	SO:0001587	stop_gained	414332	exon5			CATTCTGCCTATC	AY301271	CCDS35182.2	9q34.3	2011-10-24			ENSG00000187922	ENSG00000187922		"""Lipocalins"""	20892	protein-coding gene	gene with protein product		612904				15363845	Standard	NM_001001712		Approved		uc004civ.3	Q6JVE6	OTTHUMG00000150428	ENST00000474369.1:c.442C>T	9.37:g.139634495G>A	ENSP00000420564:p.Gln148*	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	117	79	0.675214	NM_001001712	A2RUU3|B0QZ79	Nonsense_Mutation	SNP	ENST00000474369.1	37	CCDS35182.2	438	0.20054945054945056	99	0.20121951219512196	77	0.212707182320442	151	0.263986013986014	111	0.14643799472295516	g	11.56	1.674100	0.29693	0.1806	0.153318	ENSG00000187922	ENST00000527229;ENST00000497771;ENST00000474369	.	.	.	2.66	1.7	0.24286	.	0.672061	0.12237	N	0.486894	.	.	.	.	.	.	0.09310	P	0.999999999541476	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	7.2424	0.26104	0.0:0.2777:0.7222:0.0	rs9886752;rs61671998;rs9886752	.	.	.	X	125;161;148	.	ENSP00000420564:Q148X	Q	-	1	0	LCN10	138754316	0.004000	0.15560	0.055000	0.19348	0.030000	0.12068	1.072000	0.30678	0.657000	0.30906	0.539000	0.68188	CAG	G|0.818;A|0.182	0.182	strong		0.542	LCN10-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318062.2	NM_001001712	
DPY19L2	283417	hgsc.bcm.edu	37	12	64057543	64057543	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:64057543C>T	ENST00000324472.4	-	3	628	c.445G>A	c.(445-447)Gaa>Aaa	p.E149K	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	149					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)	p.E149*(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		CTAACCATTTCAGTGCGAAAA	0.333																																					p.E149K		Atlas-SNP	.											DPY19L2,caecum,carcinoma,0,1	DPY19L2	97	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.G445A						scavenged	.						58.0	55.0	56.0					12																	64057543		2203	4299	6502	SO:0001583	missense	283417	exon3			CCATTTCAGTGCG		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.445G>A	12.37:g.64057543C>T	ENSP00000315988:p.Glu149Lys	Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	344	21	0.0610465	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.990830	0.54041	.	.	ENSG00000177990	ENST00000324472;ENST00000538147	T;T	0.68331	-0.32;-0.32	2.5	2.5	0.30297	.	0.000000	0.85682	U	0.000000	T	0.81230	0.4779	M	0.86740	2.835	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.83031	-0.0162	9	.	.	.	.	10.7323	0.46104	0.0:1.0:0.0:0.0	.	149	Q6NUT2	D19L2_HUMAN	K	149;6	ENSP00000315988:E149K;ENSP00000439567:E6K	.	E	-	1	0	DPY19L2	62343810	1.000000	0.71417	0.999000	0.59377	0.753000	0.42808	6.967000	0.76079	1.389000	0.46526	0.184000	0.17185	GAA	.	.	none		0.333	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
MTUS1	57509	hgsc.bcm.edu	37	8	17612064	17612064	+	Missense_Mutation	SNP	A	A	C	rs75253845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17612064A>C	ENST00000262102.6	-	2	1477	c.1253T>G	c.(1252-1254)aTg>aGg	p.M418R	MTUS1_ENST00000381862.3_Missense_Mutation_p.M418R|MTUS1_ENST00000519263.1_Missense_Mutation_p.M418R|MTUS1_ENST00000381869.3_Missense_Mutation_p.M418R	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	418					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)		GCTAATGACCATATCATTTGC	0.443													A|||	134	0.0267572	0.0991	0.0043	5008	,	,		19985	0.0		0.0	False		,,,				2504	0.0				p.M418R		Atlas-SNP	.											.	MTUS1	144	.	0			c.T1253G						PASS	.	A	ARG/MET,ARG/MET	262,3548		9,244,1652	97.0	92.0	93.0		1253,1253	-3.9	0.0	8	dbSNP_131	93	0,8240		0,0,4120	yes	missense,missense	MTUS1	NM_001001924.2,NM_001001925.2	91,91	9,244,5772	CC,CA,AA		0.0,6.8766,2.1743	benign,benign	418/1271,418/1217	17612064	262,11788	1905	4120	6025	SO:0001583	missense	57509	exon2			ATGACCATATCAT	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.1253T>G	8.37:g.17612064A>C	ENSP00000262102:p.Met418Arg	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	134	68	0.507463	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	A	0.005	-2.138056	0.00335	0.068766	0.0	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.17854	3.24;3.27;3.24;2.25	5.0	-3.89	0.04193	.	1.334190	0.04473	N	0.376484	T	0.00356	0.0011	N	0.24115	0.695	0.09310	N	1	B;B;B	0.30824	0.296;0.296;0.296	B;B;B	0.27380	0.079;0.037;0.053	T	0.23048	-1.0199	10	0.66056	D	0.02	1.3614	1.2801	0.02039	0.384:0.2677:0.2254:0.1229	.	418;418;418	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	R	418	ENSP00000371293:M418R;ENSP00000262102:M418R;ENSP00000430167:M418R;ENSP00000371286:M418R	ENSP00000262102:M418R	M	-	2	0	MTUS1	17656344	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.074000	0.14662	-0.755000	0.04709	-0.336000	0.08194	ATG	A|0.978;C|0.022	0.022	strong		0.443	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
OBSCN	84033	hgsc.bcm.edu	37	1	228461655	228461655	+	Silent	SNP	C	C	T	rs138055037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228461655C>T	ENST00000422127.1	+	18	5366	c.5322C>T	c.(5320-5322)caC>caT	p.H1774H	OBSCN_ENST00000359599.6_Silent_p.H621H|OBSCN_ENST00000284548.11_Silent_p.H1774H|RP5-1139B12.2_ENST00000602517.1_RNA|RP5-1139B12.3_ENST00000602947.1_RNA|RP5-1139B12.3_ENST00000602529.1_RNA|OBSCN_ENST00000570156.2_Silent_p.H2149H|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1774	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)				GGGACACCCACACCCTGACCG	0.662													C|||	35	0.00698882	0.0265	0.0	5008	,	,		17285	0.0		0.0	False		,,,				2504	0.0				p.H2149H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C6447T						PASS	.	C	,	115,4115		1,113,2001	19.0	23.0	22.0		5322,5322	1.3	1.0	1	dbSNP_134	22	0,8446		0,0,4223	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1,113,6224	TT,TC,CC		0.0,2.7187,0.9072	,	1774/7969,1774/6621	228461655	115,12561	2115	4223	6338	SO:0001819	synonymous_variant	84033	exon22			CACCCACACCCTG	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.5322C>T	1.37:g.228461655C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	184	103	0.559783	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|0.996;T|0.004	0.004	strong		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CLGN	1047	hgsc.bcm.edu	37	4	141317068	141317068	+	Missense_Mutation	SNP	G	G	A	rs12513290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:141317068G>A	ENST00000325617.5	-	10	1494	c.1054C>T	c.(1054-1056)Cgg>Tgg	p.R352W	CLGN_ENST00000537281.1_Missense_Mutation_p.R352W|CLGN_ENST00000414773.1_Missense_Mutation_p.R352W	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	352			R -> W (in dbSNP:rs12513290).		binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					CACCCAATCCGACATGCTGGA	0.433													G|||	575	0.114816	0.031	0.1066	5008	,	,		16562	0.2054		0.0905	False		,,,				2504	0.1656				p.R352W		Atlas-SNP	.											.	CLGN	76	.	0			c.C1054T						PASS	.	G	TRP/ARG,TRP/ARG	178,4228	115.4+/-153.4	2,174,2027	95.0	89.0	91.0		1054,1054	2.9	0.5	4	dbSNP_120	91	696,7904	172.2+/-222.9	20,656,3624	yes	missense,missense	CLGN	NM_001130675.1,NM_004362.2	101,101	22,830,5651	AA,AG,GG		8.093,4.0399,6.72	probably-damaging,probably-damaging	352/611,352/611	141317068	874,12132	2203	4300	6503	SO:0001583	missense	1047	exon11			CAATCCGACATGC	D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.1054C>T	4.37:g.141317068G>A	ENSP00000326699:p.Arg352Trp	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	186	82	0.44086	NM_001130675	B3KS90|B4DXV8|D3DNY8	Missense_Mutation	SNP	ENST00000325617.5	37	CCDS3751.1	237	0.10851648351648352	9	0.018292682926829267	40	0.11049723756906077	117	0.20454545454545456	71	0.09366754617414248	G	18.84	3.708290	0.68615	0.040399	0.08093	ENSG00000153132	ENST00000325617;ENST00000414773;ENST00000537281;ENST00000545667	T;T;T	0.51071	0.72;0.72;0.72	5.84	2.91	0.33838	Calreticulin/calnexin, P (2);	0.910390	0.09524	N	0.790437	T	0.00039	0.0001	N	0.03983	-0.305	0.42398	P	0.007441000000000031	D	0.61080	0.989	P	0.55303	0.773	T	0.09015	-1.0694	9	0.62326	D	0.03	0.2054	8.164	0.31215	0.0:0.3769:0.4022:0.2209	rs12513290;rs57052004;rs12513290	352	O14967	CLGN_HUMAN	W	352;352;352;269	ENSP00000326699:R352W;ENSP00000392782:R352W;ENSP00000439381:R352W	ENSP00000326699:R352W	R	-	1	2	CLGN	141536518	0.997000	0.39634	0.452000	0.26994	0.561000	0.35649	3.127000	0.50484	1.466000	0.48025	-0.320000	0.08662	CGG	G|0.909;A|0.091	0.091	strong		0.433	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362	
GPR116	221395	hgsc.bcm.edu	37	6	46856100	46856100	+	Silent	SNP	G	G	A	rs678312	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46856100G>A	ENST00000283296.7	-	4	588	c.300C>T	c.(298-300)acC>acT	p.T100T	GPR116_ENST00000456426.2_Silent_p.T100T|GPR116_ENST00000265417.7_Silent_p.T100T|GPR116_ENST00000478711.1_5'UTR|GPR116_ENST00000362015.4_Silent_p.T100T	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	100					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)			TCAAAATGTCGGTAATTTGGT	0.403													G|||	4312	0.861022	0.9387	0.8602	5008	,	,		21901	0.8413		0.8618	False		,,,				2504	0.7761				p.T100T	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.C300T						PASS	.	G	,	4096,310	797.8+/-415.4	1904,288,11	136.0	129.0	131.0		300,300	-10.9	0.0	6	dbSNP_83	131	7530,1070	769.5+/-407.6	3296,938,66	no	coding-synonymous,coding-synonymous	GPR116	NM_001098518.1,NM_015234.4	,	5200,1226,77	AA,AG,GG		12.4419,7.0359,10.6105	,	100/1347,100/1347	46856100	11626,1380	2203	4300	6503	SO:0001819	synonymous_variant	221395	exon4			AATGTCGGTAATT	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.300C>T	6.37:g.46856100G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	241	241	1	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	37	CCDS4919.1																																																																																			G|0.108;A|0.892	0.892	strong		0.403	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
SBF1	6305	hgsc.bcm.edu	37	22	50899103	50899103	+	Silent	SNP	G	G	A	rs77064034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50899103G>A	ENST00000390679.3	-	24	3190	c.3006C>T	c.(3004-3006)gaC>gaT	p.D1002D	SBF1_ENST00000380817.3_Silent_p.D1002D|SBF1_ENST00000348911.6_Silent_p.D1003D			O95248	MTMR5_HUMAN	SET binding factor 1	1002					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)		GCTCGGCGCTGTCAGACCCCA	0.627													G|||	99	0.0197684	0.0711	0.0072	5008	,	,		16560	0.0		0.0	False		,,,				2504	0.0				p.D1002D		Atlas-SNP	.											.	SBF1	211	.	0			c.C3006T						PASS	.	G		270,3750		8,254,1748	87.0	92.0	90.0		3006	-3.9	1.0	22	dbSNP_131	90	1,8301		0,1,4150	no	coding-synonymous	SBF1	NM_002972.2		8,255,5898	AA,AG,GG		0.012,6.7164,2.1993		1002/1894	50899103	271,12051	2010	4151	6161	SO:0001819	synonymous_variant	6305	exon24			GGCGCTGTCAGAC	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.3006C>T	22.37:g.50899103G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																				G|0.990;A|0.010	0.010	strong		0.627	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
CETP	1071	hgsc.bcm.edu	37	16	57003846	57003846	+	Missense_Mutation	SNP	C	C	T	rs34716057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57003846C>T	ENST00000566128.1	+	5	532	c.265C>T	c.(265-267)Cgg>Tgg	p.R89W	CETP_ENST00000379780.2_Missense_Mutation_p.R154W|CETP_ENST00000200676.3_Missense_Mutation_p.R154W|CETP_ENST00000569082.1_3'UTR					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						TGGTAGAGTGCGGACCGATGC	0.597													C|||	41	0.0081869	0.0295	0.0029	5008	,	,		19510	0.0		0.0	False		,,,				2504	0.0				p.R154W		Atlas-SNP	.											.	CETP	50	.	0			c.C460T						PASS	.	C	TRP/ARG	116,4280	88.7+/-127.4	3,110,2085	133.0	80.0	98.0		460	-2.7	0.0	16	dbSNP_126	98	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CETP	NM_000078.2	101	3,112,6383	TT,TC,CC		0.0233,2.6388,0.908	probably-damaging	154/494	57003846	118,12878	2198	4300	6498	SO:0001583	missense	1071	exon5			AGAGTGCGGACCG	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.265C>T	16.37:g.57003846C>T	ENSP00000456276:p.Arg89Trp	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	C	9.523	1.108810	0.20714	0.026388	2.33E-4	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.06768	3.26;3.26	4.05	-2.74	0.05932	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.824610	0.10339	U	0.686590	T	0.01730	0.0055	N	0.12182	0.205	0.09310	N	1	D;B	0.71674	0.998;0.066	P;B	0.50754	0.649;0.021	T	0.18935	-1.0321	10	0.66056	D	0.02	-16.4666	2.4134	0.04430	0.1231:0.3542:0.3268:0.1959	rs34716057;rs35242580;rs59039225	154;154	P11597-2;P11597	.;CETP_HUMAN	W	154	ENSP00000200676:R154W;ENSP00000369106:R154W	ENSP00000200676:R154W	R	+	1	2	CETP	55561347	0.074000	0.21230	0.000000	0.03702	0.001000	0.01503	0.020000	0.13466	-0.956000	0.03631	-1.961000	0.00478	CGG	C|0.992;T|0.008	0.008	strong		0.597	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
NLRP6	171389	hgsc.bcm.edu	37	11	285256	285256	+	Silent	SNP	G	G	A	rs144727560	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:285256G>A	ENST00000312165.5	+	8	2631	c.2631G>A	c.(2629-2631)gcG>gcA	p.A877A	RP11-326C3.2_ENST00000525217.1_RNA|RP11-326C3.2_ENST00000534742.1_RNA|NLRP6_ENST00000534750.1_Silent_p.A876A|RP11-326C3.2_ENST00000533924.1_RNA	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	877					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	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;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		CACACCCAGCGCTGGACGGCC	0.597													G|||	19	0.00379393	0.0106	0.0029	5008	,	,		15333	0.0		0.0	False		,,,				2504	0.0031				p.A877A		Atlas-SNP	.											.	NLRP6	4	.	0			c.G2631A						PASS	.	G		49,4357	45.3+/-79.5	0,49,2154	84.0	69.0	74.0		2631	-4.3	0.0	11	dbSNP_134	74	0,8600		0,0,4300	no	coding-synonymous	NLRP6	NM_138329.1		0,49,6454	AA,AG,GG		0.0,1.1121,0.3767		877/893	285256	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	171389	exon8			CCCAGCGCTGGAC	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.2631G>A	11.37:g.285256G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	37	CCDS7693.1																																																																																			G|0.995;A|0.005	0.005	strong		0.597	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
PDLIM5	10611	hgsc.bcm.edu	37	4	95539204	95539204	+	Missense_Mutation	SNP	C	C	T	rs141653509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:95539204C>T	ENST00000317968.4	+	8	1106	c.970C>T	c.(970-972)Cgg>Tgg	p.R324W	PDLIM5_ENST00000437932.1_Missense_Mutation_p.R215W|PDLIM5_ENST00000514743.1_Missense_Mutation_p.R353W|PDLIM5_ENST00000542407.1_Missense_Mutation_p.R202W|PDLIM5_ENST00000380176.3_3'UTR	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	324					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)		AGCTTCCACACGGAGCATGCC	0.547													C|||	7	0.00139776	0.0045	0.0	5008	,	,		15988	0.001		0.0	False		,,,				2504	0.0				p.R353W		Atlas-SNP	.											PDLIM5,NS,carcinoma,-1,1	PDLIM5	76	1	0			c.C1057T						PASS	.	C	TRP/ARG,TRP/ARG	25,4381	30.8+/-60.4	0,25,2178	48.0	48.0	48.0		643,970	0.8	0.0	4	dbSNP_134	48	0,8600		0,0,4300	yes	missense,missense	PDLIM5	NM_001011513.2,NM_006457.3	101,101	0,25,6478	TT,TC,CC		0.0,0.5674,0.1922	probably-damaging,probably-damaging	215/488,324/597	95539204	25,12981	2203	4300	6503	SO:0001583	missense	10611	exon12			TCCACACGGAGCA	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.970C>T	4.37:g.95539204C>T	ENSP00000321746:p.Arg324Trp	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	115	64	0.556522	NM_001256426	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.95	1.494439	0.26774	0.005674	0.0	ENSG00000163110	ENST00000437932;ENST00000317968;ENST00000503974;ENST00000542407;ENST00000514743	T;T;T;T;T	0.59364	0.48;0.67;0.48;0.27;0.46	5.14	0.821	0.18799	.	0.458336	0.23654	N	0.045883	T	0.33323	0.0859	L	0.47716	1.5	0.09310	N	1	B;B;B;B	0.23490	0.009;0.086;0.005;0.006	B;B;B;B	0.10450	0.002;0.004;0.003;0.005	T	0.29671	-1.0004	10	0.59425	D	0.04	.	2.7512	0.05281	0.4316:0.3432:0.1293:0.0959	.	221;353;324;215	E9PBF5;D6RB78;Q96HC4;Q96HC4-4	.;.;PDLI5_HUMAN;.	W	215;324;221;202;353	ENSP00000398469:R215W;ENSP00000321746:R324W;ENSP00000424297:R221W;ENSP00000442187:R202W;ENSP00000424360:R353W	ENSP00000321746:R324W	R	+	1	2	PDLIM5	95758227	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.059000	0.11731	0.187000	0.20147	0.585000	0.79938	CGG	C|0.999;T|0.001	0.001	strong		0.547	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		
NR5A2	2494	hgsc.bcm.edu	37	1	200143281	200143281	+	Silent	SNP	C	C	T	rs1060060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200143281C>T	ENST00000367362.3	+	8	1815	c.1569C>T	c.(1567-1569)aaC>aaT	p.N523N	NR5A2_ENST00000236914.3_Silent_p.N477N|NR5A2_ENST00000544748.1_Silent_p.N451N	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	523					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|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)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					AGCACCTGAACGGGGATGTGC	0.448													C|||	1775	0.354433	0.3669	0.3213	5008	,	,		17133	0.5179		0.2913	False		,,,				2504	0.2577				p.C523C	Melanoma(179;1138 2773 15678 26136)	Atlas-SNP	.											NR5A2,NS,carcinoma,+1,1	NR5A2	83	1	0			c.C1569T						PASS	.	C	,	1499,2907	478.1+/-358.1	267,965,971	60.0	55.0	56.0		1431,1569	-0.3	1.0	1	dbSNP_86	56	2522,6078	413.5+/-351.2	386,1750,2164	no	coding-synonymous,coding-synonymous	NR5A2	NM_003822.3,NM_205860.1	,	653,2715,3135	TT,TC,CC		29.3256,34.0218,30.9165	,	477/496,523/542	200143281	4021,8985	2203	4300	6503	SO:0001819	synonymous_variant	2494	exon8			CCTGAACGGGGAT	U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"""Nuclear hormone receptors"""	7984	protein-coding gene	gene with protein product	"""liver receptor homolog-1"""	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.1569C>T	1.37:g.200143281C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_205860	B4E2P3|O95642|Q147U3	Silent	SNP	ENST00000367362.3	37	CCDS1401.1																																																																																			T|0.348;G|0.007	0.348	strong		0.448	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2		
PI16	221476	hgsc.bcm.edu	37	6	36927136	36927136	+	Silent	SNP	C	C	T	rs74853487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36927136C>T	ENST00000373674.3	+	2	715	c.387C>T	c.(385-387)taC>taT	p.Y129Y		NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	129	SCP.				negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCGGCCACTACACGCAGGTGT	0.736													C|||	209	0.0417332	0.1505	0.0115	5008	,	,		12458	0.0		0.002	False		,,,				2504	0.0				p.Y129Y		Atlas-SNP	.											.	PI16	50	.	0			c.C387T						PASS	.	C	,	454,3804		20,414,1695	11.0	9.0	9.0		387,387	4.5	1.0	6	dbSNP_131	9	20,8338		0,20,4159	no	coding-synonymous,coding-synonymous	PI16	NM_001199159.1,NM_153370.2	,	20,434,5854	TT,TC,CC		0.2393,10.6623,3.7571	,	129/464,129/464	36927136	474,12142	2129	4179	6308	SO:0001819	synonymous_variant	221476	exon3			CCACTACACGCAG		CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"""microseminoprotein, beta-binding protein"""		"""protease inhibitor 16"""				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.387C>T	6.37:g.36927136C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Silent	SNP	ENST00000373674.3	37	CCDS34440.1																																																																																			C|0.966;T|0.034	0.034	strong		0.736	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370	
FLG	2312	hgsc.bcm.edu	37	1	152284823	152284823	+	Missense_Mutation	SNP	A	A	G	rs74129459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284823A>G	ENST00000368799.1	-	3	2574	c.2539T>C	c.(2539-2541)Tca>Cca	p.S847P	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	847	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)			CTTCTGCTTGACCCCGGGTGT	0.582									Ichthyosis																												p.S847P		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.T2539C						PASS	.						322.0	322.0	322.0					1																	152284823		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGCTTGACCCCGG	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.2539T>C	1.37:g.152284823A>G	ENSP00000357789:p.Ser847Pro	Somatic	410	0	0		WXS	Illumina HiSeq	Phase_I	477	23	0.048218	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	7.279	0.608792	0.14066	.	.	ENSG00000143631	ENST00000368799	T	0.03772	3.81	3.63	2.44	0.29823	.	.	.	.	.	T	0.05731	0.0150	L	0.58428	1.81	0.09310	N	1	D	0.76494	0.999	D	0.68765	0.96	T	0.31530	-0.9940	9	0.34782	T	0.22	.	6.6957	0.23197	0.7566:0.2434:0.0:0.0	.	847	P20930	FILA_HUMAN	P	847	ENSP00000357789:S847P	ENSP00000357789:S847P	S	-	1	0	FLG	150551447	0.001000	0.12720	0.003000	0.11579	0.020000	0.10135	0.252000	0.18278	0.443000	0.26582	0.392000	0.25879	TCA	A|0.984;T|0.016	.	alt		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PRR32	100130613	hgsc.bcm.edu	37	X	125954900	125954900	+	Silent	SNP	C	C	T	rs41309536		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:125954900C>T	ENST00000371125.3	+	2	359	c.279C>T	c.(277-279)taC>taT	p.Y93Y		NM_001122716.1	NP_001116188.1	B1ATL7	PRR32_HUMAN		93																	GACACCCCTACGGGCCACCAC	0.527													C|||	461	0.122119	0.025	0.1499	3775	,	,		13119	0.247		0.0169	False		,,,				2504	0.0593				p.Y93Y		Atlas-SNP	.											.	.	.	.	0			c.C279T						PASS	.						62.0	48.0	52.0					X																	125954900		692	1591	2283	SO:0001819	synonymous_variant	100130613	exon2			CCCCTACGGGCCA																												ENST00000371125.3:c.279C>T	X.37:g.125954900C>T		Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	203	118	0.581281	NM_001122716		Silent	SNP	ENST00000371125.3	37	CCDS48163.1																																																																																			C|0.878;T|0.122	0.122	strong		0.527	CXorf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058188.1		
ZNF112	7771	hgsc.bcm.edu	37	19	44831989	44831989	+	Missense_Mutation	SNP	T	T	G	rs2609881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44831989T>G	ENST00000337401.4	-	5	2427	c.2339A>C	c.(2338-2340)gAg>gCg	p.E780A	ZNF112_ENST00000354340.4_Missense_Mutation_p.E774A|ZNF112_ENST00000536500.1_Missense_Mutation_p.E797A	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	780			E -> A (in dbSNP:rs2609881).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TGTACACACCTCACATTTGTA	0.478													T|||	1279	0.255391	0.4781	0.3256	5008	,	,		22728	0.1855		0.1292	False		,,,				2504	0.1063				p.E780A		Atlas-SNP	.											.	ZFP112	219	.	0			c.A2339C						PASS	.	T	ALA/GLU,ALA/GLU	1877,2529	541.4+/-375.8	395,1087,721	224.0	211.0	215.0		2339,2321	1.7	0.2	19	dbSNP_100	215	1078,7522	225.7+/-261.6	70,938,3292	yes	missense,missense	ZFP112	NM_001083335.1,NM_013380.3	107,107	465,2025,4013	GG,GT,TT		12.5349,42.601,22.7203	benign,benign	780/914,774/908	44831989	2955,10051	2203	4300	6503	SO:0001583	missense	7771	exon5			CACACCTCACATT	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.2339A>C	19.37:g.44831989T>G	ENSP00000337081:p.Glu780Ala	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	278	277	0.996403	NM_001083335	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	37	CCDS54276.1	513	0.2348901098901099	210	0.4268292682926829	113	0.31215469613259667	97	0.16958041958041958	93	0.12269129287598944	T	9.365	1.069027	0.20147	0.42601	0.125349	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.07444	3.19;3.19;3.19	5.18	1.71	0.24356	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.240848	0.21440	N	0.074510	T	0.00012	0.0000	L	0.57130	1.785	0.80722	P	0.0	B;B;B	0.12630	0.006;0.004;0.003	B;B;B	0.12156	0.007;0.004;0.007	T	0.45556	-0.9253	9	0.16420	T	0.52	-4.5387	9.0429	0.36329	0.1285:0.0:0.5287:0.3428	rs2609881;rs52828382;rs60369874;rs2609881	779;797;780	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	A	780;780;774;797;779	ENSP00000337081:E780A;ENSP00000346305:E774A;ENSP00000441990:E797A	ENSP00000253426:E779A	E	-	2	0	ZNF285	49523829	0.000000	0.05858	0.181000	0.23098	0.976000	0.68499	-1.254000	0.02874	0.019000	0.15079	0.460000	0.39030	GAG	T|0.766;G|0.234	0.234	strong		0.478	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380	
SIRPA	140885	hgsc.bcm.edu	37	20	1896060	1896060	+	Missense_Mutation	SNP	T	T	C	rs114499682|rs386811663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1896060T>C	ENST00000358771.4	+	2	547	c.395T>C	c.(394-396)gTg>gCg	p.V132A	SIRPA_ENST00000400068.3_Missense_Mutation_p.V132A|SIRPA_ENST00000356025.3_Missense_Mutation_p.V132A	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	132	Ig-like V-type.		V -> T (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CCCGATGACGTGGAGTTTAAG	0.527													T|||	2050	0.409345	0.2761	0.4222	5008	,	,		15517	0.625		0.3171	False		,,,				2504	0.453				p.V132A	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,caecum,carcinoma,+1,2	SIRPA	83	2	0			c.T395C						PASS	.						110.0	94.0	99.0					20																	1896060		2199	4290	6489	SO:0001583	missense	140885	exon3			ATGACGTGGAGTT	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.395T>C	20.37:g.1896060T>C	ENSP00000351621:p.Val132Ala	Somatic	455	0	0		WXS	Illumina HiSeq	Phase_I	275	46	0.167273	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.858225	0.32791	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.63913	-0.07;-0.07;-0.07	5.11	-4.1	0.03940	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	2.497550	0.01234	N	0.008420	T	0.55257	0.1909	L	0.47190	1.495	0.09310	N	1	B;B;B	0.18741	0.028;0.011;0.03	B;B;B	0.33295	0.113;0.125;0.161	T	0.39165	-0.9627	10	0.33141	T	0.24	.	4.5618	0.12163	0.5656:0.1906:0.0:0.2438	.	112;132;132	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	A	132	ENSP00000382941:V132A;ENSP00000348307:V132A;ENSP00000351621:V132A	ENSP00000348307:V132A	V	+	2	0	SIRPA	1844060	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-1.908000	0.01587	-0.575000	0.05982	-0.530000	0.04314	GTG	T|0.684;C|0.317	0.317	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
CPA3	1359	hgsc.bcm.edu	37	3	148601596	148601596	+	Silent	SNP	G	G	A	rs140411214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148601596G>A	ENST00000296046.3	+	9	1027	c.975G>A	c.(973-975)gaG>gaA	p.E325E	RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)	325					angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			CTAACCATGAGGACTTGGTAC	0.398													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		20428	0.0		0.0	False		,,,				2504	0.0				p.E325E		Atlas-SNP	.											.	CPA3	75	.	0			c.G975A						PASS	.	G		66,4340	62.3+/-99.4	0,66,2137	96.0	80.0	86.0		975	0.8	0.1	3	dbSNP_134	86	0,8600		0,0,4300	no	coding-synonymous	CPA3	NM_001870.2		0,66,6437	AA,AG,GG		0.0,1.498,0.5075		325/418	148601596	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	1359	exon9			CCATGAGGACTTG		CCDS3138.1	3q24	2012-02-10			ENSG00000163751	ENSG00000163751	3.4.17.1		2298	protein-coding gene	gene with protein product	"""mast cell carboxypeptidase A"", ""tissue carboxypeptidase A"""	114851					Standard	NM_001870		Approved		uc003ewm.3	P15088	OTTHUMG00000159526	ENST00000296046.3:c.975G>A	3.37:g.148601596G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	143	67	0.468531	NM_001870	Q96E94	Silent	SNP	ENST00000296046.3	37	CCDS3138.1																																																																																			G|0.995;A|0.005	0.005	strong		0.398	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	NM_001870	
MYO19	80179	hgsc.bcm.edu	37	17	34858985	34858985	+	Missense_Mutation	SNP	A	A	G	rs61743158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34858985A>G	ENST00000431794.3	-	21	2554	c.2032T>C	c.(2032-2034)Tgc>Cgc	p.C678R	MYO19_ENST00000268852.9_Missense_Mutation_p.C478R	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	678	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GAGGATGTGCAAGGATGAAGC	0.493													G|||	24	0.00479233	0.0174	0.0014	5008	,	,		18666	0.0		0.0	False		,,,				2504	0.0				p.C678R		Atlas-SNP	.											.	MYO19	130	.	0			c.T2032C						PASS	.	G	ARG/CYS,ARG/CYS	77,3859		3,71,1894	191.0	202.0	198.0		2032,1432	4.3	0.6	17	dbSNP_129	198	0,8298		0,0,4149	yes	missense,missense	MYO19	NM_001163735.1,NM_025109.5	180,180	3,71,6043	GG,GA,AA		0.0,1.9563,0.6294	benign,benign	678/971,478/771	34858985	77,12157	1968	4149	6117	SO:0001583	missense	80179	exon22			ATGTGCAAGGATG	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.2032T>C	17.37:g.34858985A>G	ENSP00000409936:p.Cys678Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	154	65	0.422078	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	4.905	0.168151	0.09339	0.019563	0.0	ENSG00000141140	ENST00000431794;ENST00000268852	D;D	0.94966	-3.57;-3.57	5.25	4.27	0.50696	Myosin head, motor domain (1);	.	.	.	.	T	0.70141	0.3190	N	0.00926	-1.1	0.23515	N	0.997514	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.67360	-0.5690	9	0.23302	T	0.38	.	7.8717	0.29569	0.0883:0.1733:0.7385:0.0	.	678;478	Q96H55;Q96H55-4	MYO19_HUMAN;.	R	678;478	ENSP00000409936:C678R;ENSP00000268852:C478R	ENSP00000268852:C478R	C	-	1	0	MYO19	31933098	0.261000	0.24063	0.559000	0.28332	0.034000	0.12701	1.018000	0.30002	0.706000	0.31912	-0.213000	0.12676	TGC	A|0.995;G|0.005	0.005	strong		0.493	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
TPM4	7171	hgsc.bcm.edu	37	19	16186865	16186865	+	5'Flank	SNP	G	G	A	rs114042568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16186865G>A	ENST00000300933.4	+	0	0				TPM4_ENST00000344824.6_Silent_p.E41E|TPM4_ENST00000538887.1_Silent_p.E41E	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4						cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)		TPM4/ALK(12)	breast(1)|large_intestine(3)	4						AGGTGGAGGAGGAGCTGACGC	0.617			T	ALK	ALCL								G|||	90	0.0179712	0.062	0.0115	5008	,	,		14293	0.0		0.0	False		,,,				2504	0.0				p.E41E		Atlas-SNP	.		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	.	TPM4	28	.	0			c.G123A						PASS	.	G		143,2989		7,129,1430	30.0	31.0	31.0		123	1.8	1.0	19	dbSNP_132	31	1,7153		0,1,3576	no	coding-synonymous	TPM4	NM_001145160.1		7,130,5006	AA,AG,GG		0.014,4.5658,1.4		41/285	16186865	144,10142	1566	3577	5143	SO:0001631	upstream_gene_variant	7171	exon2			GGAGGAGGAGCTG		CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"""Tropomyosins"""	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134		19.37:g.16186865G>A	Exception_encountered	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_001145160	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Silent	SNP	ENST00000300933.4	37	CCDS12338.1																																																																																			G|0.989;A|0.011	0.011	strong		0.617	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290	
FCGRT	2217	hgsc.bcm.edu	37	19	50017191	50017191	+	Silent	SNP	G	G	T	rs11551281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50017191G>T	ENST00000221466.5	+	3	612	c.126G>T	c.(124-126)ccG>ccT	p.P42P	FCGRT_ENST00000594823.1_3'UTR|FCGRT_ENST00000599988.1_Intron|FCGRT_ENST00000426395.3_Silent_p.P42P|FCGRT_ENST00000596975.1_Silent_p.P42P	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	42	Alpha-1.				antigen processing and presentation (GO:0019882)|IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor (GO:0002416)|immune response (GO:0006955)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG binding (GO:0019864)			endometrium(3)|kidney(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	9		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;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		CGCCTGCCCCGGGGACTCCTG	0.652													G|||	98	0.0195687	0.0363	0.0029	5008	,	,		13393	0.0456		0.0	False		,,,				2504	0.002				p.P42P		Atlas-SNP	.											.	FCGRT	23	.	0			c.G126T						PASS	.	G	,	151,4255	103.0+/-141.5	3,145,2055	108.0	109.0	109.0		126,126	-5.5	0.0	19	dbSNP_120	109	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	FCGRT	NM_001136019.2,NM_004107.4	,	3,148,6352	TT,TG,GG		0.0349,3.4271,1.1841	,	42/366,42/366	50017191	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	2217	exon3			TGCCCCGGGGACT	U12255	CCDS12770.1	19q13.3	2013-01-11				ENSG00000104870		"""Immunoglobulin superfamily / C1-set domain containing"""	3621	protein-coding gene	gene with protein product		601437				7964511, 8646894	Standard	NM_001136019		Approved	FCRN, alpha-chain	uc002pog.2	P55899		ENST00000221466.5:c.126G>T	19.37:g.50017191G>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	162	88	0.54321	NM_001136019	Q5HYM5|Q9HBV7|Q9NZ19	Silent	SNP	ENST00000221466.5	37	CCDS12770.1																																																																																			G|0.984;T|0.016	0.016	strong		0.652	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1		
MYO5B	4645	hgsc.bcm.edu	37	18	47462657	47462657	+	Silent	SNP	G	G	A	rs1627232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47462657G>A	ENST00000285039.7	-	16	2267	c.1968C>T	c.(1966-1968)cgC>cgT	p.R656R		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	656	Actin-binding. {ECO:0000255}.|Myosin motor.		R -> C (in DIAR2). {ECO:0000269|PubMed:18724368}.		endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		GCTTGATGCAGCGGACATAGT	0.537													g|||	167	0.0333466	0.0923	0.0043	5008	,	,		19813	0.0268		0.0109	False		,,,				2504	0.0041				p.R656R		Atlas-SNP	.											.	MYO5B	178	.	0			c.C1968T						PASS	.	A		271,3913		12,247,1833	96.0	99.0	98.0		1968	1.7	1.0	18	dbSNP_89	98	15,8451		0,15,4218	no	coding-synonymous	MYO5B	NM_001080467.2		12,262,6051	AA,AG,GG		0.1772,6.4771,2.2609		656/1849	47462657	286,12364	2092	4233	6325	SO:0001819	synonymous_variant	4645	exon16			GATGCAGCGGACA	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.1968C>T	18.37:g.47462657G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	143	63	0.440559	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			G|0.961;A|0.039	0.039	strong		0.537	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
HLA-DMA	3108	hgsc.bcm.edu	37	6	32917126	32917126	+	Missense_Mutation	SNP	C	C	T	rs9469319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32917126C>T	ENST00000374843.4	-	4	788	c.703G>A	c.(703-705)Gtg>Atg	p.V235M	HLA-DMA_ENST00000395305.3_Missense_Mutation_p.V140M|XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000395303.3_Missense_Mutation_p.V201M|HLA-DMA_ENST00000464392.1_5'UTR	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	235			V -> M (in dbSNP:rs9469319).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						CCAAAGGCCACGCCACACAGC	0.592													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		19854	0.0		0.0	False		,,,				2504	0.0				p.V235M		Atlas-SNP	.											.	HLA-DMA	20	.	0			c.G703A						PASS	.	C	MET/VAL	21,4385	28.1+/-56.4	0,21,2182	91.0	85.0	87.0		703	-2.8	0.0	6	dbSNP_119	87	1,8599	1.2+/-3.3	0,1,4299	yes	missense	HLA-DMA	NM_006120.3	21	0,22,6481	TT,TC,CC		0.0116,0.4766,0.1692	possibly-damaging	235/262	32917126	22,12984	2203	4300	6503	SO:0001583	missense	3108	exon4			AGGCCACGCCACA		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.703G>A	6.37:g.32917126C>T	ENSP00000363976:p.Val235Met	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_006120	Q29639|Q29640	Missense_Mutation	SNP	ENST00000374843.4	37	CCDS4761.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	11.77	1.739075	0.30774	0.004766	1.16E-4	ENSG00000204257	ENST00000395305;ENST00000395303;ENST00000374843;ENST00000456800	T;T;T;T	0.01821	5.12;4.62;5.63;5.55	5.0	-2.84	0.05751	.	0.963671	0.08623	N	0.918117	T	0.00724	0.0024	M	0.71581	2.175	0.09310	N	1	P	0.52316	0.952	B	0.37780	0.258	T	0.41840	-0.9486	10	0.87932	D	0	.	1.2422	0.01965	0.127:0.2689:0.2786:0.3255	rs9469319;rs9469319	235	Q31604	.	M	140;201;235;265	ENSP00000378716:V140M;ENSP00000378714:V201M;ENSP00000363976:V235M;ENSP00000409668:V265M	ENSP00000363976:V235M	V	-	1	0	HLA-DMA	33025104	0.000000	0.05858	0.006000	0.13384	0.598000	0.36846	-1.977000	0.01495	-0.428000	0.07339	0.551000	0.68910	GTG	C|0.997;T|0.003	0.003	strong		0.592	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	NM_006120	
HTR3A	3359	hgsc.bcm.edu	37	11	113857661	113857661	+	Missense_Mutation	SNP	G	G	A	rs35815285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:113857661G>A	ENST00000504030.2	+	8	1476	c.1031G>A	c.(1030-1032)cGt>cAt	p.R344H	HTR3A_ENST00000535865.1_Missense_Mutation_p.R88H|HTR3A_ENST00000355556.2_Missense_Mutation_p.R382H|HTR3A_ENST00000299961.5_Missense_Mutation_p.R329H|HTR3A_ENST00000375498.2_Missense_Mutation_p.R350H|HTR3A_ENST00000506841.2_Missense_Mutation_p.R376H			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	344			R -> H (in dbSNP:rs35815285). {ECO:0000269|PubMed:16487942}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	GCTTGGCTGCGTCACCTGGTT	0.592													G|||	172	0.034345	0.121	0.0144	5008	,	,		17839	0.0		0.002	False		,,,				2504	0.0				p.R382H		Atlas-SNP	.											HTR3A,NS,carcinoma,+1,1	HTR3A	93	1	0			c.G1145A	GRCh37	CM011786	HTR3A	M	rs35815285	scavenged	.	G	HIS/ARG,HIS/ARG,HIS/ARG	419,3983	205.2+/-227.1	17,385,1799	55.0	50.0	52.0		1049,986,1145	3.5	0.6	11	dbSNP_126	52	6,8586	5.0+/-18.6	0,6,4290	yes	missense,missense,missense	HTR3A	NM_000869.5,NM_001161772.2,NM_213621.3	29,29,29	17,391,6089	AA,AG,GG		0.0698,9.5184,3.2707	possibly-damaging,possibly-damaging,possibly-damaging	350/485,329/464,382/517	113857661	425,12569	2201	4296	6497	SO:0001583	missense	3359	exon7			GGCTGCGTCACCT	D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5297	protein-coding gene	gene with protein product		182139	"""5-hydroxytryptamine (serotonin) receptor 3A"""	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.1031G>A	11.37:g.113857661G>A	ENSP00000424189:p.Arg344His	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	119	69	0.579832	NM_213621	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		59	0.027014652014652016	52	0.10569105691056911	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	G	18.10	3.548612	0.65311	0.095184	6.98E-4	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000535865;ENST00000299961	D;T;D;T;D;D	0.87966	-2.32;-0.77;-2.32;-0.77;-2.32;-2.32	5.37	3.51	0.40186	.	0.166108	0.48767	D	0.000170	T	0.12603	0.0306	L	0.45581	1.43	0.44104	D	0.996877	P;D;D	0.58970	0.944;0.98;0.984	P;P;P	0.52957	0.602;0.681;0.714	T	0.55405	-0.8146	10	0.59425	D	0.04	-19.81	6.9616	0.24599	0.3829:0.0:0.6171:0.0	rs35815285	329;382;350	B4DSY6;G5E986;Q7KZM7	.;.;.	H	344;382;350;376;88;329	ENSP00000424189:R344H;ENSP00000347754:R382H;ENSP00000364648:R350H;ENSP00000424776:R376H;ENSP00000437776:R88H;ENSP00000299961:R329H	ENSP00000299961:R329H	R	+	2	0	HTR3A	113362871	1.000000	0.71417	0.646000	0.29493	0.545000	0.35147	4.552000	0.60747	0.765000	0.33221	0.561000	0.74099	CGT	G|0.965;A|0.035	0.035	strong		0.592	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869	
UNC79	57578	hgsc.bcm.edu	37	14	94173098	94173098	+	Missense_Mutation	SNP	G	G	A	rs76642035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94173098G>A	ENST00000393151.2	+	50	7756	c.7756G>A	c.(7756-7758)Gtg>Atg	p.V2586M	UNC79_ENST00000555664.1_Missense_Mutation_p.V2547M|UNC79_ENST00000256339.4_Missense_Mutation_p.V2409M|UNC79_ENST00000553484.1_Missense_Mutation_p.V2608M			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2586					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TCAGAACCACGTGAACCACCA	0.557													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		17791	0.0		0.0	False		,,,				2504	0.0				p.V2409M		Atlas-SNP	.											.	UNC79	366	.	0			c.G7225A						PASS	.	G	MET/VAL	61,4345	57.4+/-93.9	1,59,2143	69.0	74.0	73.0		7225	5.8	1.0	14	dbSNP_131	73	0,8600		0,0,4300	yes	missense	UNC79	NM_020818.3	21	1,59,6443	AA,AG,GG		0.0,1.3845,0.469	probably-damaging	2409/2459	94173098	61,12945	2203	4300	6503	SO:0001583	missense	57578	exon50			AACCACGTGAACC	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7756G>A	14.37:g.94173098G>A	ENSP00000376858:p.Val2586Met	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	23.0	4.363881	0.82353	0.013845	0.0	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.19806	2.12;2.14;2.12;2.12	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.36110	0.0955	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.05037	-1.0910	10	0.52906	T	0.07	-21.9581	20.0407	0.97588	0.0:0.0:1.0:0.0	.	2608	C9JQL1	.	M	2409;2547;2608;2586;2608	ENSP00000256339:V2409M;ENSP00000450868:V2547M;ENSP00000451360:V2608M;ENSP00000376858:V2586M	ENSP00000256339:V2409M	V	+	1	0	KIAA1409	93242851	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.869000	0.99810	2.746000	0.94184	0.561000	0.74099	GTG	G|0.996;A|0.004	0.004	strong		0.557	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
SOX30	11063	hgsc.bcm.edu	37	5	157078475	157078475	+	Silent	SNP	C	C	G	rs3749797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:157078475C>G	ENST00000265007.6	-	1	953	c.612G>C	c.(610-612)ccG>ccC	p.P204P	SOX30_ENST00000311371.5_Silent_p.P204P|SOX30_ENST00000519442.1_Intron	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	204					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGATGGCTGCCGGGCTTTTGC	0.657													.|||	830	0.165735	0.2912	0.1326	5008	,	,		15560	0.0724		0.1571	False		,,,				2504	0.1247				p.P204P	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											SOX30,NS,carcinoma,0,1	SOX30	67	1	0			c.G612C						PASS	.	C	,	1112,3290		124,864,1213	64.0	74.0	71.0		612,612	1.9	0.0	5	dbSNP_107	71	1095,7499		75,945,3277	no	coding-synonymous,coding-synonymous	SOX30	NM_007017.2,NM_178424.1	,	199,1809,4490	GG,GC,CC		12.7414,25.2612,16.9821	,	204/502,204/754	157078475	2207,10789	2201	4297	6498	SO:0001819	synonymous_variant	11063	exon1			GGCTGCCGGGCTT	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.612G>C	5.37:g.157078475C>G		Somatic	281	1	0.00355872		WXS	Illumina HiSeq	Phase_I	198	196	0.989899	NM_178424	O94995|Q8IYX6	Silent	SNP	ENST00000265007.6	37	CCDS4339.1																																																																																			C|0.825;G|0.175	0.175	strong		0.657	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
BPIFB4	149954	hgsc.bcm.edu	37	20	31680334	31680334	+	Missense_Mutation	SNP	C	C	T	rs17122711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31680334C>T	ENST00000375483.3	+	9	1214	c.1214C>T	c.(1213-1215)cCg>cTg	p.P405L		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	405						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCTCCCAAGCCGATGCCAGAG	0.597													C|||	161	0.0321486	0.0961	0.0216	5008	,	,		21163	0.0		0.0189	False		,,,				2504	0.0				p.P405L		Atlas-SNP	.											.	.	.	.	0			c.C1214T						PASS	.	C	LEU/PRO	349,4057	181.9+/-209.8	11,327,1865	71.0	64.0	67.0		1214	-1.9	0.0	20	dbSNP_123	67	162,8438	75.4+/-138.0	2,158,4140	yes	missense	BPIFB4	NM_182519.2	98	13,485,6005	TT,TC,CC		1.8837,7.921,3.929	benign	405/615	31680334	511,12495	2203	4300	6503	SO:0001583	missense	149954	exon9			CCAAGCCGATGCC	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.1214C>T	20.37:g.31680334C>T	ENSP00000364632:p.Pro405Leu	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	73	0.033424908424908424	54	0.10975609756097561	5	0.013812154696132596	0	0.0	14	0.018469656992084433	C	7.618	0.676280	0.14841	0.07921	0.018837	ENSG00000186191	ENST00000375483	T	0.06608	3.28	5.25	-1.89	0.07689	.	1.301950	0.05005	N	0.469943	T	0.00178	0.0005	L	0.57536	1.79	0.20703	N	0.999864	B	0.16603	0.018	B	0.14023	0.01	T	0.45145	-0.9281	9	.	.	.	-0.1506	13.7686	0.63010	0.4693:0.5307:0.0:0.0	rs17122711;rs52819586;rs17122711	405	P59827	BPIB4_HUMAN	L	405	ENSP00000364632:P405L	.	P	+	2	0	BPIFB4	31143995	0.000000	0.05858	0.003000	0.11579	0.029000	0.11900	-0.355000	0.07671	-0.070000	0.12908	-0.346000	0.07831	CCG	C|0.960;T|0.040	0.040	strong		0.597	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
NWD1	284434	hgsc.bcm.edu	37	19	16860558	16860558	+	Missense_Mutation	SNP	G	G	A	rs61733271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860558G>A	ENST00000552788.1	+	4	1105	c.1105G>A	c.(1105-1107)Gtc>Atc	p.V369I	NWD1_ENST00000379808.3_Missense_Mutation_p.V369I|NWD1_ENST00000339803.6_Missense_Mutation_p.V234I|NWD1_ENST00000549814.1_Missense_Mutation_p.V369I|NWD1_ENST00000524140.2_Missense_Mutation_p.V369I|NWD1_ENST00000523826.1_Missense_Mutation_p.V163I			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	369	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GACAGTGACCGTCCTGCGGCT	0.622													g|||	330	0.0658946	0.1785	0.0274	5008	,	,		18889	0.0079		0.0288	False		,,,				2504	0.0389				p.V369I		Atlas-SNP	.											.	NWD1	303	.	0			c.G1105A						PASS	.		ILE/VAL	715,3691		56,603,1544	32.0	33.0	32.0		1105	1.0	0.2	19	dbSNP_129	32	322,8276		8,306,3985	yes	missense	NWD1	NM_001007525.3	29	64,909,5529	AA,AG,GG		3.7451,16.2279,7.9745	benign	369/1433	16860558	1037,11967	2203	4299	6502	SO:0001583	missense	284434	exon6			GTGACCGTCCTGC	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1105G>A	19.37:g.16860558G>A	ENSP00000447224:p.Val369Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		121	0.0554029304029304	87	0.17682926829268292	14	0.03867403314917127	1	0.0017482517482517483	19	0.025065963060686015	N	3.273	-0.148788	0.06627	0.162279	0.037451	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05;-1.05	4.42	1.02	0.19986	.	0.069867	0.56097	N	0.000032	T	0.00210	0.0006	L	0.28115	0.83	0.33929	P	0.358212	B;B;B	0.27166	0.17;0.066;0.081	B;B;B	0.32624	0.149;0.017;0.029	T	0.04103	-1.0977	9	0.12103	T	0.63	-23.6771	8.4041	0.32603	0.2739:0.0:0.7261:0.0	rs61733271	369;369;234	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	I	234;369;369;369;163;369;234	ENSP00000428579:V369I;ENSP00000447548:V369I;ENSP00000369136:V369I;ENSP00000428955:V163I;ENSP00000447224:V369I;ENSP00000340159:V234I	ENSP00000340159:V234I	V	+	1	0	NWD1	16721558	0.407000	0.25352	0.207000	0.23584	0.656000	0.38851	0.720000	0.25896	0.094000	0.17404	-0.155000	0.13514	GTC	G|0.927;A|0.073	0.073	strong		0.622	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
VWA8	23078	hgsc.bcm.edu	37	13	42404710	42404710	+	Missense_Mutation	SNP	C	C	T	rs41288297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:42404710C>T	ENST00000379310.3	-	14	1723	c.1655G>A	c.(1654-1656)cGt>cAt	p.R552H	VWA8_ENST00000281496.6_Missense_Mutation_p.R552H	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	552						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										CTCCTTTAAACGCATATACCT	0.378													C|||	227	0.0453275	0.087	0.0389	5008	,	,		16008	0.0		0.0417	False		,,,				2504	0.044				p.R552H		Atlas-SNP	.											.	.	.	.	0			c.G1655A						PASS	.	C	HIS/ARG,HIS/ARG	396,4010	197.4+/-221.5	28,340,1835	115.0	111.0	112.0		1655,1655	2.3	0.0	13	dbSNP_127	112	438,8162	133.6+/-191.1	13,412,3875	yes	missense,missense	KIAA0564	NM_001009814.1,NM_015058.1	29,29	41,752,5710	TT,TC,CC		5.093,8.9877,6.4124	benign,benign	552/1040,552/1906	42404710	834,12172	2203	4300	6503	SO:0001583	missense	23078	exon14			TTTAAACGCATAT	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"""KIAA0564"""	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.1655G>A	13.37:g.42404710C>T	ENSP00000368612:p.Arg552His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	72	0.03296703296703297	32	0.06504065040650407	11	0.03038674033149171	0	0.0	29	0.03825857519788918	C	12.11	1.840629	0.32513	0.089877	0.05093	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	T;T	0.12039	2.92;2.72	6.06	2.3	0.28687	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.620900	0.17234	N	0.181819	T	0.00241	0.0007	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.13407	0.009	T	0.38090	-0.9677	10	0.39692	T	0.17	.	4.2991	0.10916	0.1533:0.4749:0.0:0.3718	rs41288297;rs57164625;rs61743604	552	A3KMH1	K0564_HUMAN	H	456;552;552	ENSP00000368612:R552H;ENSP00000281496:R552H	ENSP00000251030:R456H	R	-	2	0	KIAA0564	41302710	0.001000	0.12720	0.002000	0.10522	0.947000	0.59692	0.837000	0.27558	0.904000	0.36572	-0.133000	0.14855	CGT	C|0.947;T|0.053	0.053	strong		0.378	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
FAM149A	25854	hgsc.bcm.edu	37	4	187078819	187078819	+	Silent	SNP	C	C	G	rs2276923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187078819C>G	ENST00000356371.5	+	8	1548	c.1548C>G	c.(1546-1548)tcC>tcG	p.S516S	FAM149A_ENST00000503432.1_Silent_p.S225S|FAM149A_ENST00000502970.1_Silent_p.S225S|FAM149A_ENST00000227065.4_Silent_p.S225S|FAM149A_ENST00000514153.1_Silent_p.S225S|FAM149A_ENST00000514829.1_3'UTR|FAM149A_ENST00000389354.5_Silent_p.S225S			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	516										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)		GCCCCCCGTCCGGACACGCCG	0.587													C|||	917	0.183107	0.1929	0.2421	5008	,	,		17100	0.2024		0.1501	False		,,,				2504	0.1421				p.S225S		Atlas-SNP	.											.	FAM149A	52	.	0			c.C675G						PASS	.	C	,	835,3571	328.5+/-300.6	70,695,1438	63.0	68.0	66.0		675,675	0.9	0.7	4	dbSNP_100	66	1231,7369	244.9+/-273.9	91,1049,3160	no	coding-synonymous,coding-synonymous	FAM149A	NM_001006655.2,NM_015398.2	,	161,1744,4598	GG,GC,CC		14.314,18.9514,15.885	,	225/483,225/483	187078819	2066,10940	2203	4300	6503	SO:0001819	synonymous_variant	25854	exon7			CCCGTCCGGACAC	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.1548C>G	4.37:g.187078819C>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Silent	SNP	ENST00000356371.5	37																																																																																				C|0.839;G|0.161	0.161	strong		0.587	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
IGDCC4	57722	hgsc.bcm.edu	37	15	65681648	65681648	+	Missense_Mutation	SNP	A	A	G	rs144676391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65681648A>G	ENST00000352385.2	-	14	2719	c.2510T>C	c.(2509-2511)gTg>gCg	p.V837A		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	837	Fibronectin type-III 4. {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						GCGCTCCACCACAGAGCCGAA	0.572													A|||	21	0.00419329	0.0159	0.0	5008	,	,		16119	0.0		0.0	False		,,,				2504	0.0				p.V837A		Atlas-SNP	.											.	IGDCC4	95	.	0			c.T2510C						PASS	.	A	ALA/VAL	46,4356	48.2+/-83.0	0,46,2155	82.0	63.0	69.0		2510	4.3	1.0	15	dbSNP_134	69	0,8598		0,0,4299	yes	missense	IGDCC4	NM_020962.1	64	0,46,6454	GG,GA,AA		0.0,1.045,0.3538	benign	837/1251	65681648	46,12954	2201	4299	6500	SO:0001583	missense	57722	exon14			TCCACCACAGAGC		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.2510T>C	15.37:g.65681648A>G	ENSP00000319623:p.Val837Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	50	18	0.36	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	A	13.90	2.373757	0.42105	0.01045	0.0	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.54279	0.58	5.37	4.26	0.50523	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.256570	0.38058	N	0.001833	T	0.18676	0.0448	N	0.13098	0.295	0.30508	N	0.76971	B	0.23377	0.084	B	0.17722	0.019	T	0.15925	-1.0420	10	0.35671	T	0.21	-20.1912	10.6197	0.45472	0.9248:0.0:0.0752:0.0	.	837	Q8TDY8	IGDC4_HUMAN	A	837;566	ENSP00000319623:V837A	ENSP00000319623:V837A	V	-	2	0	IGDCC4	63468701	1.000000	0.71417	0.996000	0.52242	0.975000	0.68041	5.865000	0.69583	2.043000	0.60533	0.454000	0.30748	GTG	A|0.995;G|0.005	0.005	strong		0.572	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
DNASE1	1773	hgsc.bcm.edu	37	16	3707262	3707262	+	Silent	SNP	G	G	A	rs8176920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3707262G>A	ENST00000246949.5	+	7	3833	c.624G>A	c.(622-624)ctG>ctA	p.L208L	DNASE1_ENST00000407479.1_Silent_p.L208L|DNASE1_ENST00000414110.2_Silent_p.L91L	NM_005223.3	NP_005214.2	P24855	DNAS1_HUMAN	deoxyribonuclease I	208					apoptotic process (GO:0006915)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	deoxyribonuclease I activity (GO:0004530)			lung(1)	1		Ovarian(90;0.0261)		Kidney(780;0.0556)		CCATCCGCCTGTGGACAAGCC	0.617													G|||	160	0.0319489	0.1195	0.0029	5008	,	,		18167	0.0		0.0	False		,,,				2504	0.0				p.L208L		Atlas-SNP	.											.	DNASE1	16	.	0			c.G624A						PASS	.	G		370,4024	189.9+/-215.9	14,342,1841	86.0	69.0	75.0		624	1.8	1.0	16	dbSNP_117	75	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	DNASE1	NM_005223.3		14,345,6138	AA,AG,GG		0.0349,8.4206,2.8706		208/283	3707262	373,12621	2197	4300	6497	SO:0001819	synonymous_variant	1773	exon7			CCGCCTGTGGACA		CCDS10507.1	16p13.3	2008-02-05			ENSG00000213918	ENSG00000213918	3.1.21.1		2956	protein-coding gene	gene with protein product		125505		DNL1		2349940	Standard	XM_005255148		Approved		uc002cvr.3	P24855	OTTHUMG00000129426	ENST00000246949.5:c.624G>A	16.37:g.3707262G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_005223	B4DV35|Q14UU9|Q14UV0	Silent	SNP	ENST00000246949.5	37	CCDS10507.1																																																																																			G|0.970;A|0.030	0.030	strong		0.617	DNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251585.2		
TFDP3	51270	hgsc.bcm.edu	37	X	132352230	132352230	+	Missense_Mutation	SNP	C	C	G	rs28455963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:132352230C>G	ENST00000310125.4	-	1	146	c.58G>C	c.(58-60)Gag>Cag	p.E20Q		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	20					cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					GTCTGGTTCTCGTCCATTAAG	0.483													G|||	383	0.101457	0.2247	0.0389	3775	,	,		13274	0.002		0.0288	False		,,,				2504	0.0286				p.E20Q		Atlas-SNP	.											.	TFDP3	92	.	0			c.G58C						PASS	.	G	GLN/GLU	304,905		40,182,42,295,133	63.0	47.0	52.0		58	0.2	0.0	X	dbSNP_125	52	85,2306		3,62,17,735,774	yes	missense	TFDP3	NM_016521.2	29	43,244,59,1030,907	GG,GC,G,CC,C		3.555,25.1447,10.8056	benign	20/406	132352230	389,3211	692	1591	2283	SO:0001583	missense	51270	exon1			GGTTCTCGTCCAT	AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"""E2F-like protein"", ""cancer/testis antigen 30"""	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.58G>C	X.37:g.132352230C>G	ENSP00000385461:p.Glu20Gln	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	170	116	0.682353	NM_016521	Q6DK49|Q9NZ54	Missense_Mutation	SNP	ENST00000310125.4	37	CCDS14636.2	154	0.09282700421940929	74	0.17703349282296652	13	0.03651685393258427	2	0.0034965034965034965	14	0.01907356948228883	G	0.008	-1.897626	0.00517	0.251447	0.03555	ENSG00000183434	ENST00000310125	T	0.19806	2.12	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	N	0.00260	-1.75	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34378	-0.9831	7	0.02654	T	1	.	.	.	.	rs28455963	20	Q5H9I0	TFDP3_HUMAN	Q	20	ENSP00000385461:E20Q	ENSP00000385461:E20Q	E	-	1	0	TFDP3	132179896	0.988000	0.35896	0.016000	0.15963	0.016000	0.09150	0.556000	0.23438	-0.705000	0.05035	-0.699000	0.03677	GAG	C|0.877;G|0.123	0.123	strong		0.483	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521	
C6orf52	347744	hgsc.bcm.edu	37	6	10687325	10687325	+	Silent	SNP	C	C	T	rs144052767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10687325C>T	ENST00000426700.2	-	2	143	c.144G>A	c.(142-144)gcG>gcA	p.A48A	C6orf52_ENST00000379586.1_Intron|C6orf52_ENST00000460742.2_5'UTR|C6orf52_ENST00000467832.2_Intron|C6orf52_ENST00000259983.3_Silent_p.A48A|C6orf52_ENST00000503680.1_5'UTR			Q5T4I8	CF052_HUMAN	chromosome 6 open reading frame 52	48										endometrium(1)|prostate(1)	2						CGTGCTGTCGCGCATACCAGT	0.507													C|||	61	0.0121805	0.0431	0.0043	5008	,	,		20327	0.0		0.001	False		,,,				2504	0.0				p.A48A		Atlas-SNP	.											C6orf52,caecum,carcinoma,0,1	C6orf52	9	1	0			c.G144A						scavenged	.	C		74,1310		1,72,619	105.0	93.0	97.0		144	1.1	0.0	6	dbSNP_134	97	2,3180		0,2,1589	no	coding-synonymous	C6orf52	NM_001145020.1		1,74,2208	TT,TC,CC		0.0629,5.3468,1.6645		48/153	10687325	76,4490	692	1591	2283	SO:0001819	synonymous_variant	347744	exon3			CTGTCGCGCATAC	BC016820	CCDS47371.1	6p24.2	2009-09-22	2007-06-07	2007-06-07	ENSG00000137434	ENSG00000137434			20881	protein-coding gene	gene with protein product						12477932	Standard	NM_001145020		Approved		uc011dij.2	Q5T4I8	OTTHUMG00000014240	ENST00000426700.2:c.144G>A	6.37:g.10687325C>T		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_001145020	Q5T4I7|Q96AS6	Silent	SNP	ENST00000426700.2	37	CCDS47371.1																																																																																			C|0.990;T|0.010	0.010	strong		0.507	C6orf52-002	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039825.2	NM_001145020	
HDAC7	51564	hgsc.bcm.edu	37	12	48185449	48185449	+	Missense_Mutation	SNP	G	G	A	rs73291234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48185449G>A	ENST00000427332.2	-	15	1892	c.1736C>T	c.(1735-1737)tCg>tTg	p.S579L	HDAC7_ENST00000354334.3_Missense_Mutation_p.S581L|HDAC7_ENST00000488927.1_5'UTR|HDAC7_ENST00000552960.1_Missense_Mutation_p.S601L|HDAC7_ENST00000380610.4_Missense_Mutation_p.S635L|HDAC7_ENST00000080059.7_Missense_Mutation_p.S618L			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	579	Histone deacetylase.				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)		AGAGTGGACCGACTGCAGCTC	0.632													G|||	51	0.0101837	0.0356	0.0058	5008	,	,		13311	0.0		0.0	False		,,,				2504	0.0				p.S618L		Atlas-SNP	.											.	HDAC7	71	.	0			c.C1853T						PASS	.	G	LEU/SER,LEU/SER	134,4272	96.2+/-134.9	4,126,2073	41.0	43.0	42.0		1742,1853	3.5	0.8	12	dbSNP_130	42	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	HDAC7	NM_001098416.2,NM_015401.3	145,145	4,127,6372	AA,AG,GG		0.0116,3.0413,1.038	possibly-damaging,possibly-damaging	581/955,618/992	48185449	135,12871	2203	4300	6503	SO:0001583	missense	51564	exon15			TGGACCGACTGCA	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.1736C>T	12.37:g.48185449G>A	ENSP00000404394:p.Ser579Leu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	172	79	0.459302	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	37		17|17	0.007783882783882784|0.007783882783882784	15|15	0.03048780487804878|0.03048780487804878	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.73|16.73	3.204615|3.204615	0.58234|0.58234	0.030413|0.030413	1.16E-4|1.16E-4	ENSG00000061273|ENSG00000061273	ENST00000548080|ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332	.|T;T;T;T;T	.|0.68903	.|-0.36;-0.36;-0.36;-0.36;-0.36	5.3|5.3	3.48|3.48	0.39840|0.39840	.|.	.|0.194140	.|0.45606	.|N	.|0.000346	T|T	0.19127|0.19127	0.0459|0.0459	N|N	0.02539|0.02539	-0.55|-0.55	0.45295|0.45295	D|D	0.998291|0.998291	.|D;D;D	.|0.59767	.|0.963;0.986;0.978	.|B;P;B	.|0.48627	.|0.209;0.584;0.398	T|T	0.07654|0.07654	-1.0761|-1.0761	5|10	.|0.21540	.|T	.|0.41	.|.	7.5367|7.5367	0.27714|0.27714	0.1551:0.1369:0.708:0.0|0.1551:0.1369:0.708:0.0	.|.	.|618;601;581	.|Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.|.;.;.	W|L	59|618;581;601;635;579	.|ENSP00000080059:S618L;ENSP00000351326:S581L;ENSP00000448532:S601L;ENSP00000369984:S635L;ENSP00000404394:S579L	.|ENSP00000080059:S618L	R|S	-|-	1|2	2|0	HDAC7|HDAC7	46471716|46471716	1.000000|1.000000	0.71417|0.71417	0.765000|0.765000	0.31456|0.31456	0.970000|0.970000	0.65996|0.65996	5.572000|5.572000	0.67411|0.67411	0.759000|0.759000	0.33084|0.33084	-0.261000|-0.261000	0.10672|0.10672	CGG|TCG	G|0.989;A|0.011	0.011	strong		0.632	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2		
SKIV2L	6499	hgsc.bcm.edu	37	6	31928039	31928039	+	Silent	SNP	C	C	G	rs11541400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31928039C>G	ENST00000375394.2	+	4	392	c.279C>G	c.(277-279)gtC>gtG	p.V93V	SKIV2L_ENST00000544581.1_Intron|NELFE_ENST00000375425.5_5'Flank|NELFE_ENST00000444811.2_5'Flank|NELFE_ENST00000375429.3_5'Flank|SKIV2L_ENST00000488648.1_3'UTR	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	93					ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						TTTTGGCTGTCCTGGGAGCCC	0.517													C|||	22	0.00439297	0.0121	0.0058	5008	,	,		19192	0.0		0.002	False		,,,				2504	0.0				p.V93V		Atlas-SNP	.											.	SKIV2L	97	.	0			c.C279G						PASS	.	C		28,2994		0,28,1483	140.0	173.0	161.0		279	0.1	0.0	6	dbSNP_120	161	33,5385		0,33,2676	no	coding-synonymous	SKIV2L	NM_006929.4		0,61,4159	GG,GC,CC		0.6091,0.9265,0.7227		93/1247	31928039	61,8379	1511	2709	4220	SO:0001819	synonymous_variant	6499	exon4			GGCTGTCCTGGGA		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"""superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"""	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.279C>G	6.37:g.31928039C>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_006929	O15005|Q12902|Q15476|Q5ST66	Silent	SNP	ENST00000375394.2	37	CCDS4731.1																																																																																			C|0.993;G|0.007	0.007	strong		0.517	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3		
RPL37	6167	hgsc.bcm.edu	37	5	40834595	40834595	+	Silent	SNP	G	G	A	rs6495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:40834595G>A	ENST00000274242.5	-	2	266	c.117C>T	c.(115-117)taC>taT	p.Y39Y	RPL37_ENST00000508493.1_Silent_p.Y39Y|RPL37_ENST00000509877.1_Silent_p.Y39Y|SNORD72_ENST00000390994.1_RNA|RPL37_ENST00000504562.1_5'UTR	NM_000997.4	NP_000988.1	P61927	RL37_HUMAN	ribosomal protein L37	39					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)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			lung(3)|ovary(1)	4		Breast(839;0.238)				GCTTGGCAGGGTAGCCACATT	0.483													G|||	19	0.00379393	0.0136	0.0014	5008	,	,		19990	0.0		0.0	False		,,,				2504	0.0				p.Y39Y	Colon(188;1411 2035 4978 19588 31462)	Atlas-SNP	.											.	RPL37	7	.	0			c.C117T						PASS	.	G		41,4365	44.6+/-78.6	0,41,2162	58.0	53.0	55.0		117	2.9	1.0	5	dbSNP_52	55	0,8600		0,0,4300	no	coding-synonymous	RPL37	NM_000997.4		0,41,6462	AA,AG,GG		0.0,0.9305,0.3152		39/98	40834595	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	6167	exon2			GGCAGGGTAGCCA	L11567	CCDS3934.1	5p13.1	2013-09-23			ENSG00000145592	ENSG00000145592		"""L ribosomal proteins"""	10347	protein-coding gene	gene with protein product	"""60S ribosomal protein L37a"""	604181				7545944, 9582194	Standard	NM_000997		Approved	L37	uc003jme.1	P61927	OTTHUMG00000094774	ENST00000274242.5:c.117C>T	5.37:g.40834595G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_000997	B2R4H2|P02403|Q6IBB4|Q99883	Silent	SNP	ENST00000274242.5	37	CCDS3934.1																																																																																			G|0.996;A|0.004	0.004	strong		0.483	RPL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000211583.2	NM_000997	
SORBS1	10580	hgsc.bcm.edu	37	10	97174352	97174352	+	Missense_Mutation	SNP	T	T	C	rs2281939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:97174352T>C	ENST00000361941.3	-	7	735	c.709A>G	c.(709-711)Acg>Gcg	p.T237A	SORBS1_ENST00000371245.3_Missense_Mutation_p.T168A|SORBS1_ENST00000371227.4_Missense_Mutation_p.T237A|SORBS1_ENST00000371246.2_Missense_Mutation_p.T237A|SORBS1_ENST00000354106.3_Missense_Mutation_p.T228A|SORBS1_ENST00000371247.2_Missense_Mutation_p.T237A|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000277982.5_Missense_Mutation_p.T237A|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000393949.1_Missense_Mutation_p.T228A|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000371249.2_Missense_Mutation_p.T205A|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000353505.5_Missense_Mutation_p.T168A	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		GATGGTGGCGTCTGGCTAATG	0.637													T|||	802	0.160144	0.3434	0.062	5008	,	,		17833	0.1171		0.0586	False		,,,				2504	0.1309				p.T237A		Atlas-SNP	.											SORBS1_ENST00000371247,NS,carcinoma,+2,2	SORBS1	185	2	0			c.A709G	GRCh37	CM012804	SORBS1	M	rs2281939	PASS	.	T	ALA/THR,ALA/THR,ALA/THR,,,ALA/THR,	1344,3062	420.2+/-338.9	210,924,1069	31.0	32.0	31.0		709,709,502,,,613,	1.8	1.0	10	dbSNP_100	31	444,8154	130.0+/-188.0	13,418,3868	yes	missense,missense,missense,intron,intron,missense,intron	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	58,58,58,,,58,	223,1342,4937	CC,CT,TT		5.164,30.5039,13.7496	possibly-damaging,possibly-damaging,possibly-damaging,,,possibly-damaging,	237/1293,237/1152,168/906,,,205/817,	97174352	1788,11216	2203	4299	6502	SO:0001583	missense	10580	exon7			GTGGCGTCTGGCT	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.709A>G	10.37:g.97174352T>C	ENSP00000355136:p.Thr237Ala	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	160	72	0.45	NM_001034955		Missense_Mutation	SNP	ENST00000361941.3	37	CCDS31255.1	300	0.13736263736263737	168	0.34146341463414637	21	0.058011049723756904	68	0.11888111888111888	43	0.05672823218997362	T	6.644	0.487361	0.12641	0.305039	0.05164	ENSG00000095637	ENST00000371245;ENST00000371249;ENST00000371247;ENST00000371227;ENST00000371246;ENST00000393949;ENST00000353505;ENST00000361941;ENST00000277982;ENST00000354106	T;T;T;T;T;T;T;T;T;T	0.39056	1.59;1.57;1.1;1.57;1.1;1.1;1.59;1.1;1.1;1.1	5.54	1.8	0.24995	.	0.341205	0.21497	N	0.073592	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	0.999999999036363	P;P;P;B;P;B;P	0.43788	0.817;0.739;0.787;0.038;0.571;0.329;0.514	B;B;B;B;B;B;B	0.39840	0.164;0.225;0.311;0.054;0.121;0.077;0.17	T	0.38112	-0.9676	9	0.34782	T	0.22	-1.483	6.5738	0.22553	0.0:0.138:0.1308:0.7313	rs2281939;rs17849165;rs61182067;rs2281939	435;205;237;205;168;237;237	B7Z9B7;F2Z2S3;Q9BX66-11;Q9BX66-10;Q9BX66-3;Q9BX66;Q9BX66-2	.;.;.;.;.;SRBS1_HUMAN;.	A	168;205;237;237;237;228;168;237;237;228	ENSP00000360291:T168A;ENSP00000360295:T205A;ENSP00000360293:T237A;ENSP00000360271:T237A;ENSP00000360292:T237A;ENSP00000377521:T228A;ENSP00000343998:T168A;ENSP00000355136:T237A;ENSP00000277982:T237A;ENSP00000277984:T228A	ENSP00000277982:T237A	T	-	1	0	SORBS1	97164342	1.000000	0.71417	0.960000	0.40013	0.967000	0.64934	1.022000	0.30052	0.053000	0.16036	0.454000	0.30748	ACG	T|0.860;C|0.140	0.140	strong		0.637	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
MCM2	4171	hgsc.bcm.edu	37	3	127323830	127323830	+	Silent	SNP	C	C	T	rs893293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127323830C>T	ENST00000265056.7	+	4	748	c.504C>T	c.(502-504)atC>atT	p.I168I		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	168	Interaction with KAT7. {ECO:0000250}.				cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						AGGAGATGATCGAGAGCATCG	0.667													C|||	2985	0.596046	0.4849	0.6124	5008	,	,		16738	0.626		0.7783	False		,,,				2504	0.5164				p.I168I		Atlas-SNP	.											.	MCM2	79	.	0			c.C504T						PASS	.	C		2321,2085	603.5+/-390.1	599,1123,481	66.0	62.0	63.0		504	-5.8	0.9	3	dbSNP_92	63	6484,2116	715.2+/-406.0	2427,1630,243	no	coding-synonymous	MCM2	NM_004526.2		3026,2753,724	TT,TC,CC		24.6047,47.3218,32.3005		168/905	127323830	8805,4201	2203	4300	6503	SO:0001819	synonymous_variant	4171	exon4			GATGATCGAGAGC	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"""mitotin"""	116945	"""minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)"", ""MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"""	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.504C>T	3.37:g.127323830C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	164	85	0.518293	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Silent	SNP	ENST00000265056.7	37	CCDS3043.1	1426	0.6529304029304029	244	0.4959349593495935	222	0.6132596685082873	368	0.6433566433566433	592	0.7810026385224275	C	11.66	1.705740	0.30232	0.526782	0.753953	ENSG00000073111	ENST00000491422	.	.	.	5.29	-5.75	0.02384	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.23833	-1.0177	3	.	.	.	-28.0212	7.8484	0.29440	0.202:0.2493:0.0:0.5488	rs893293;rs1627583;rs17538467;rs17850234;rs17851129;rs17851499;rs59954953;rs893293	.	.	.	L	31	.	.	S	+	2	0	MCM2	128806520	0.006000	0.16342	0.922000	0.36590	0.986000	0.74619	-1.096000	0.03353	-0.956000	0.03631	-0.469000	0.05056	TCG	C|0.348;T|0.652	0.652	strong		0.667	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1		
NKD2	85409	hgsc.bcm.edu	37	5	1036482	1036482	+	Missense_Mutation	SNP	C	C	A	rs35679233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:1036482C>A	ENST00000296849.5	+	9	999	c.770C>A	c.(769-771)aCg>aAg	p.T257K	NKD2_ENST00000537972.1_Missense_Mutation_p.T257K|NKD2_ENST00000382730.2_5'Flank|NKD2_ENST00000274150.4_Missense_Mutation_p.T257K	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	257			T -> K (in dbSNP:rs35679233).		exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			GAGAACTACACGTCCAGATTC	0.647													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		10087	0.0		0.0	False		,,,				2504	0.0				p.T257K		Atlas-SNP	.											.	NKD2	39	.	0			c.C770A						PASS	.	C	LYS/THR	64,4342	58.7+/-95.3	0,64,2139	100.0	78.0	85.0		770	2.7	0.2	5	dbSNP_126	85	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NKD2	NM_033120.2	78	0,65,6438	AA,AC,CC		0.0116,1.4526,0.4998	probably-damaging	257/452	1036482	65,12941	2203	4300	6503	SO:0001583	missense	85409	exon9			ACTACACGTCCAG	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"""EF-hand domain containing"""	17046	protein-coding gene	gene with protein product	"""naked cuticle-2"", ""Dvl-binding protein NKD2"""	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.770C>A	5.37:g.1036482C>A	ENSP00000296849:p.Thr257Lys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_001271082	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	37	CCDS3859.1	11	0.005036630036630037	8	0.016260162601626018	3	0.008287292817679558	0	0.0	0	0.0	C	14.85	2.658436	0.47467	0.014526	1.16E-4	ENSG00000145506	ENST00000296849;ENST00000274150;ENST00000537972	T;T;T	0.75589	0.25;-0.95;-0.95	4.5	2.69	0.31865	.	0.066054	0.64402	D	0.000014	T	0.71056	0.3295	M	0.76170	2.325	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.68039	0.938;0.955	T	0.76066	-0.3095	10	0.87932	D	0	-4.1939	7.4699	0.27342	0.0:0.7924:0.0:0.2076	rs35679233	257;257	Q969F2-2;Q969F2	.;NKD2_HUMAN	K	257	ENSP00000296849:T257K;ENSP00000274150:T257K;ENSP00000440925:T257K	ENSP00000274150:T257K	T	+	2	0	NKD2	1089482	0.977000	0.34250	0.199000	0.23439	0.223000	0.24884	2.475000	0.45162	0.339000	0.23719	0.491000	0.48974	ACG	C|0.994;A|0.006	0.006	strong		0.647	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120	
RGR	5995	hgsc.bcm.edu	37	10	86012713	86012713	+	Silent	SNP	C	C	T	rs1042454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:86012713C>T	ENST00000359452.4	+	4	509	c.471C>T	c.(469-471)taC>taT	p.Y157Y	RGR_ENST00000358110.5_Silent_p.Y153Y	NM_001012720.1|NM_002921.3	NP_001012738.1|NP_002912.2	P47804	RGR_HUMAN	retinal G protein coupled receptor	153					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.Y157Y(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	17						GGGGTCACTACGACTATGAGC	0.602													T|||	2520	0.503195	0.8548	0.4841	5008	,	,		16744	0.3313		0.3588	False		,,,				2504	0.3671				p.Y157Y	NSCLC(15;204 545 5889 6385 32445)	Atlas-SNP	.											RGR,NS,adenoma,0,2	RGR	42	2	1	Substitution - coding silent(1)	stomach(1)	c.C471T						PASS	.	T	,,	3437,969	364.1+/-316.8	1366,705,132	92.0	71.0	78.0		459,459,471	2.6	1.0	10	dbSNP_86	78	3133,5467	656.7+/-401.4	552,2029,1719	no	coding-synonymous,coding-synonymous,coding-synonymous	RGR	NM_001012720.1,NM_001012722.1,NM_002921.3	,,	1918,2734,1851	TT,TC,CC		36.4302,21.9927,49.4849	,,	153/292,153/254,157/296	86012713	6570,6436	2203	4300	6503	SO:0001819	synonymous_variant	5995	exon4			TCACTACGACTAT	BC011349	CCDS7374.1, CCDS41543.1	10q23	2013-02-14			ENSG00000148604	ENSG00000148604		"""GPCR / Class A : Opsin receptors"""	9990	protein-coding gene	gene with protein product	"""RGR-opsin"""	600342				8641686	Standard	NM_002921		Approved	RP44	uc001kdd.1	P47804	OTTHUMG00000018636	ENST00000359452.4:c.471C>T	10.37:g.86012713C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_002921	A6NKK7|Q96FC5	Silent	SNP	ENST00000359452.4	37	CCDS7374.1																																																																																			C|0.502;T|0.498	0.498	strong		0.602	RGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049116.1	NM_002921	
NOD1	10392	hgsc.bcm.edu	37	7	30491311	30491311	+	Silent	SNP	C	C	T	rs2075821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30491311C>T	ENST00000222823.4	-	6	2247	c.1722G>A	c.(1720-1722)gcG>gcA	p.A574A		NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	574					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|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)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|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 cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|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 tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|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)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						GGTCTTCCCGCGCCGGACCAC	0.602													C|||	1589	0.317292	0.3321	0.1643	5008	,	,		18471	0.3849		0.2366	False		,,,				2504	0.4192				p.A574A		Atlas-SNP	.											.	NOD1	79	.	0			c.G1722A						PASS	.	C		1429,2977	459.6+/-352.3	242,945,1016	54.0	60.0	58.0		1722	-10.6	0.0	7	dbSNP_96	58	2227,6373	377.2+/-338.5	318,1591,2391	no	coding-synonymous	NOD1	NM_006092.2		560,2536,3407	TT,TC,CC		25.8953,32.433,28.1101		574/954	30491311	3656,9350	2203	4300	6503	SO:0001819	synonymous_variant	10392	exon6			TTCCCGCGCCGGA	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.1722G>A	7.37:g.30491311C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_006092	B4DTU3|Q549U4|Q8IWF5	Silent	SNP	ENST00000222823.4	37	CCDS5427.1																																																																																			C|0.707;T|0.293	0.293	strong		0.602	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
TRPM2	7226	hgsc.bcm.edu	37	21	45799018	45799018	+	Missense_Mutation	SNP	G	G	A	rs45485992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45799018G>A	ENST00000397928.1	+	8	1598	c.1153G>A	c.(1153-1155)Gtg>Atg	p.V385M	TRPM2_ENST00000300482.5_Missense_Mutation_p.V385M|TRPM2_ENST00000397932.2_Missense_Mutation_p.V385M|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000300481.9_Missense_Mutation_p.V385M	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	385			V -> M (in dbSNP:rs45485992). {ECO:0000269|Ref.6}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GAAACTGAGCGTGTTCTTCCA	0.587													G|||	14	0.00279553	0.0106	0.0	5008	,	,		22548	0.0		0.0	False		,,,				2504	0.0				p.V385M		Atlas-SNP	.											.	TRPM2	196	.	0			c.G1153A						PASS	.	G	MET/VAL	53,4353	54.2+/-90.2	2,49,2152	127.0	92.0	104.0		1153	-7.7	0.0	21	dbSNP_127	104	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TRPM2	NM_003307.3	21	2,50,6451	AA,AG,GG		0.0116,1.2029,0.4152	benign	385/1504	45799018	54,12952	2203	4300	6503	SO:0001583	missense	7226	exon8			CTGAGCGTGTTCT	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.1153G>A	21.37:g.45799018G>A	ENSP00000381023:p.Val385Met	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	3.161	-0.172171	0.06421	0.012029	1.16E-4	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	3.84	-7.69	0.01263	.	1.065880	0.07211	N	0.859284	T	0.10380	0.0254	L	0.36672	1.1	0.09310	N	1	B;B	0.25743	0.133;0.133	B;B	0.13407	0.009;0.003	T	0.09037	-1.0693	10	0.45353	T	0.12	-4.1705	3.8491	0.08948	0.4825:0.2381:0.193:0.0864	rs45485992;rs61737083	385;385	E9PGK7;O94759	.;TRPM2_HUMAN	M	385	ENSP00000300482:V385M;ENSP00000381023:V385M;ENSP00000300481:V385M;ENSP00000381026:V385M	ENSP00000300481:V385M	V	+	1	0	TRPM2	44623446	0.000000	0.05858	0.002000	0.10522	0.332000	0.28634	-0.968000	0.03817	-2.737000	0.00381	-1.087000	0.02190	GTG	G|0.994;A|0.006	0.006	strong		0.587	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
MYO15A	51168	hgsc.bcm.edu	37	17	18022385	18022385	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18022385C>A	ENST00000205890.5	+	2	609	c.271C>A	c.(271-273)Cgc>Agc	p.R91S		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	91					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)					GACGCAGATGCGCATGGGCAA	0.662																																					p.R91S		Atlas-SNP	.											.	MYO15A	268	.	0			c.C271A						PASS	.						12.0	15.0	14.0					17																	18022385		1990	4132	6122	SO:0001583	missense	51168	exon2			CAGATGCGCATGG	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.271C>A	17.37:g.18022385C>A	ENSP00000205890:p.Arg91Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	84	48	0.571429	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957666	0.53400	.	.	ENSG00000091536	ENST00000205890	D	0.91407	-2.84	5.05	2.82	0.32997	.	.	.	.	.	D	0.85961	0.5819	L	0.29908	0.895	0.80722	D	1	D	0.54207	0.965	P	0.46479	0.518	D	0.86392	0.1736	9	0.72032	D	0.01	.	10.2951	0.43618	0.2213:0.6572:0.1215:0.0	.	91	Q9UKN7	MYO15_HUMAN	S	91	ENSP00000205890:R91S	ENSP00000205890:R91S	R	+	1	0	MYO15A	17963110	0.968000	0.33430	0.999000	0.59377	0.455000	0.32408	0.304000	0.19228	2.333000	0.79357	0.561000	0.74099	CGC	.	.	none		0.662	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305911	39305911	+	Missense_Mutation	SNP	G	G	A	rs557154279|rs141058010	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305911G>A	ENST00000343246.4	-	1	143	c.109C>T	c.(109-111)Cgc>Tgc	p.R37C		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	37	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)			CAGCTGGGGCGGCAGCAGGTG	0.657																																					p.R37C		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	1	0			c.C109T						scavenged	.						25.0	29.0	27.0					17																	39305911		2176	4272	6448	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.109C>T	17.37:g.39305911G>A	ENSP00000340546:p.Arg37Cys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	193	5	0.0259067	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	12.13	1.844454	0.32606	.	.	ENSG00000198271	ENST00000343246	T	0.01455	4.87	3.22	-1.8	0.07907	.	2.080600	0.03668	U	0.243553	T	0.02767	0.0083	L	0.57536	1.79	0.18873	N	0.999989	B	0.18461	0.028	B	0.12837	0.008	T	0.47045	-0.9147	10	0.56958	D	0.05	.	5.7249	0.18008	0.1011:0.0:0.4232:0.4757	.	37	Q9BYR2	KRA45_HUMAN	C	37	ENSP00000340546:R37C	ENSP00000340546:R37C	R	-	1	0	KRTAP4-5	36559437	0.000000	0.05858	0.674000	0.29902	0.928000	0.56348	-0.202000	0.09451	-0.272000	0.09259	0.556000	0.70494	CGC	.	.	weak		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
STAG1	10274	hgsc.bcm.edu	37	3	136062724	136062724	+	Missense_Mutation	SNP	C	C	G	rs34149860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:136062724C>G	ENST00000383202.2	-	30	3652	c.3396G>C	c.(3394-3396)caG>caC	p.Q1132H	STAG1_ENST00000434713.2_Missense_Mutation_p.Q872H|STAG1_ENST00000236698.5_Missense_Mutation_p.Q1132H|STAG1_ENST00000536929.1_Missense_Mutation_p.Q716H	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1132			Q -> H (in dbSNP:rs34149860).		chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						GTTCTTGAATCTGGTCTCCCA	0.448													C|||	436	0.0870607	0.3124	0.0303	5008	,	,		20341	0.0		0.002	False		,,,				2504	0.0				p.Q1132H		Atlas-SNP	.											.	STAG1	135	.	0			c.G3396C						PASS	.	C	HIS/GLN	1218,3188	421.7+/-339.5	170,878,1155	100.0	99.0	99.0		3396	3.5	1.0	3	dbSNP_126	99	12,8588	8.4+/-32.0	0,12,4288	yes	missense	STAG1	NM_005862.2	24	170,890,5443	GG,GC,CC		0.1395,27.6441,9.4572	benign	1132/1259	136062724	1230,11776	2203	4300	6503	SO:0001583	missense	10274	exon30			TTGAATCTGGTCT	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.3396G>C	3.37:g.136062724C>G	ENSP00000372689:p.Gln1132His	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	160	87	0.54375	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	157	0.07188644688644688	145	0.29471544715447157	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	C	8.880	0.951348	0.18431	0.276441	0.001395	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.32272	1.87;1.9;1.85;1.46	5.48	3.45	0.39498	.	0.196262	0.47455	D	0.000221	T	0.00012	0.0000	N	0.11201	0.11	0.26204	P	0.9793941	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.002	T	0.34725	-0.9817	9	0.41790	T	0.15	.	9.8937	0.41304	0.0:0.7454:0.0:0.2546	rs34149860	1132;1132	Q6P275;Q8WVM7	.;STAG1_HUMAN	H	1132;1132;872;716	ENSP00000372689:Q1132H;ENSP00000236698:Q1132H;ENSP00000404396:Q872H;ENSP00000445787:Q716H	ENSP00000236698:Q1132H	Q	-	3	2	STAG1	137545414	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.602000	0.36783	1.316000	0.45131	-0.137000	0.14449	CAG	C|0.914;G|0.086	0.086	strong		0.448	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862	
SLC2A4RG	56731	hgsc.bcm.edu	37	20	62374096	62374096	+	Silent	SNP	C	C	T	rs7996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62374096C>T	ENST00000266077.2	+	7	1057	c.1005C>T	c.(1003-1005)gtC>gtT	p.V335V	RP4-583P15.10_ENST00000433905.2_RNA|SLC2A4RG_ENST00000493772.1_3'UTR|RP4-583P15.10_ENST00000447343.2_RNA	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	335					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)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					CCACGGAGGTCGGAGCCTGCC	0.716													C|||	197	0.0393371	0.1407	0.0115	5008	,	,		9403	0.001		0.002	False		,,,				2504	0.0				p.V335V		Atlas-SNP	.											.	SLC2A4RG	20	.	0			c.C1005T						PASS	.	C		498,3864		21,456,1704	11.0	13.0	12.0		1005	2.4	0.0	20	dbSNP_52	12	5,8553		0,5,4274	no	coding-synonymous	SLC2A4RG	NM_020062.3		21,461,5978	TT,TC,CC		0.0584,11.4168,3.8932		335/388	62374096	503,12417	2181	4279	6460	SO:0001819	synonymous_variant	56731	exon7			GGAGGTCGGAGCC	AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"""GLUT4 enhancer factor"", ""Huntington's disease gene regulatory region-binding protein 1"""	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.1005C>T	20.37:g.62374096C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_020062	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Silent	SNP	ENST00000266077.2	37	CCDS13537.1																																																																																			C|0.956;T|0.044	0.044	strong		0.716	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1	NM_020062	
PRDM10	56980	hgsc.bcm.edu	37	11	129785615	129785615	+	Silent	SNP	C	C	T	rs3734071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:129785615C>T	ENST00000360871.3	-	16	2697	c.2466G>A	c.(2464-2466)acG>acA	p.T822T	PRDM10_ENST00000358825.5_Silent_p.T826T|PRDM10_ENST00000304538.6_Silent_p.T736T|PRDM10_ENST00000528746.1_Silent_p.T796T|PRDM10_ENST00000423662.2_Silent_p.T740T|PRDM10_ENST00000526082.1_Silent_p.T740T	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	826					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)		CGATGGTGCCCGTCAGCTGGG	0.617													C|||	1173	0.234225	0.4236	0.1931	5008	,	,		15763	0.4077		0.0258	False		,,,				2504	0.0429				p.T826T		Atlas-SNP	.											.	PRDM10	120	.	0			c.G2478A						PASS	.	C	,,,	1644,2758	503.9+/-365.7	309,1026,866	124.0	117.0	120.0		2478,2466,2220,2208	-12.3	0.1	11	dbSNP_107	120	203,8391	87.1+/-149.5	2,199,4096	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRDM10	NM_020228.2,NM_199437.1,NM_199438.1,NM_199439.1	,,,	311,1225,4962	TT,TC,CC		2.3621,37.3467,14.2121	,,,	826/1161,822/1157,740/1062,736/1024	129785615	1847,11149	2201	4297	6498	SO:0001819	synonymous_variant	56980	exon17			GGTGCCCGTCAGC	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.2466G>A	11.37:g.129785615C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																			C|0.823;T|0.177	0.177	strong		0.617	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
RXFP3	51289	hgsc.bcm.edu	37	5	33937215	33937215	+	Silent	SNP	C	C	T	rs78710898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:33937215C>T	ENST00000330120.3	+	1	725	c.370C>T	c.(370-372)Ctg>Ttg	p.L124L		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	124					G-protein coupled receptor signaling pathway (GO:0007186)|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)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)			endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						CGTCACCAACCTGGCGCTGAC	0.582													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		19766	0.0		0.0	False		,,,				2504	0.0				p.L124L		Atlas-SNP	.											.	RXFP3	114	.	0			c.C370T						PASS	.	C		146,4260	101.2+/-139.8	5,136,2062	137.0	126.0	129.0		370	4.8	1.0	5	dbSNP_132	129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RXFP3	NM_016568.3		5,137,6361	TT,TC,CC		0.0116,3.3137,1.1302		124/470	33937215	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	51289	exon1			ACCAACCTGGCGC	D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"""GPCR / Class A : Relaxin family peptide receptors"""	24883	protein-coding gene	gene with protein product		609445	"""relaxin 3 receptor 1"", ""relaxin family peptide receptor 3"""	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.370C>T	5.37:g.33937215C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	139	76	0.546763	NM_016568	Q14DA5	Silent	SNP	ENST00000330120.3	37	CCDS3900.1																																																																																			C|0.989;T|0.011	0.011	strong		0.582	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568	
GAD2	2572	hgsc.bcm.edu	37	10	26559610	26559610	+	Silent	SNP	C	C	T	rs1805397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:26559610C>T	ENST00000376261.3	+	10	1520	c.1017C>T	c.(1015-1017)acC>acT	p.T339T	GAD2_ENST00000259271.3_Silent_p.T339T	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	339					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)	p.T339T(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CTGGAACCACCGTGTACGGAG	0.478													C|||	24	0.00479233	0.0008	0.0058	5008	,	,		20405	0.0		0.0189	False		,,,				2504	0.0				p.T339T		Atlas-SNP	.											.	GAD2	116	.	1	Substitution - coding silent(1)	lung(1)	c.C1017T						PASS	.	C	,	20,4386	27.2+/-55.0	0,20,2183	170.0	162.0	165.0		1017,1017	-11.5	0.4	10	dbSNP_92	165	165,8435	77.2+/-139.8	2,161,4137	no	coding-synonymous,coding-synonymous	GAD2	NM_000818.2,NM_001134366.1	,	2,181,6320	TT,TC,CC		1.9186,0.4539,1.4224	,	339/586,339/586	26559610	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	2572	exon10			AACCACCGTGTAC	AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"""glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"""			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.1017C>T	10.37:g.26559610C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	157	80	0.509554	NM_000818	Q9UD87	Silent	SNP	ENST00000376261.3	37	CCDS7149.1																																																																																			C|0.988;T|0.012	0.012	strong		0.478	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818	
CTC-497E21.3	0	hgsc.bcm.edu	37	11	13031846	13031846	+	lincRNA	SNP	G	G	A	rs12793946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:13031846G>A	ENST00000533002.1	-	0	0																											CAATTCGCCAGCAGGTGCAGC	0.657													G|||	254	0.0507188	0.0144	0.0692	5008	,	,		15594	0.001		0.1312	False		,,,				2504	0.0552				p.Q241Q		Atlas-SNP	.											.	.	.	.	0			c.G723A						PASS	.	G		118,4064		0,118,1973	12.0	13.0	13.0		723	3.5	1.0	11	dbSNP_121	13	928,7216		42,844,3186	no	coding-synonymous	RASSF10	NM_001080521.2		42,962,5159	AA,AG,GG		11.3949,2.8216,8.4861		241/508	13031846	1046,11280	2091	4072	6163			644943	exon1			TCGCCAGCAGGTG																													11.37:g.13031846G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	188	92	0.489362	NM_001080521		Silent	SNP	ENST00000533002.1	37																																																																																				G|0.931;A|0.069	0.069	strong		0.657	CTC-497E21.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000387000.1		
LYRM4	57128	hgsc.bcm.edu	37	6	5260936	5260936	+	Missense_Mutation	SNP	A	A	C	rs2224391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:5260936A>C	ENST00000330636.4	-	1	236	c.31T>G	c.(31-33)Tct>Gct	p.S11A	LYRM4_ENST00000500576.2_Missense_Mutation_p.S11A|LYRM4_ENST00000468929.1_Missense_Mutation_p.S11A|LYRM4_ENST00000480566.1_Missense_Mutation_p.S11A|LYRM4_ENST00000464010.1_Missense_Mutation_p.S11A|FARS2_ENST00000274680.4_5'Flank|FARS2_ENST00000324331.6_5'Flank	NM_020408.4	NP_065141.3	Q9HD34	LYRM4_HUMAN	LYR motif containing 4	11			S -> A (in dbSNP:rs2224391). {ECO:0000269|PubMed:15489334}.		small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)				endometrium(1)	1	Ovarian(93;0.11)	all_hematologic(90;0.0901)				CGGTACAGAGATAACACTTGT	0.597													C|||	2018	0.402955	0.8396	0.3256	5008	,	,		8154	0.256		0.2525	False		,,,				2504	0.1738				p.S11A	NSCLC(130;1006 2426 17608 36797)	Atlas-SNP	.											.	LYRM4	5	.	0			c.T31G						PASS	.	C	ALA/SER,ALA/SER,ALA/SER	3199,1133		1226,747,193	21.0	21.0	21.0	http://www.ncbi.nlm.nih.gov/pubmed?term	31,31,31	4.2	1.0	6	dbSNP_96	21	2111,6375		305,1501,2437	yes	missense,missense,missense	LYRM4	NM_001164840.1,NM_001164841.1,NM_020408.4	99,99,99	1531,2248,2630	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	24.8763,26.1542,41.4261	benign,benign,benign	11/131,11/97,11/92	5260936	5310,7508	2166	4243	6409	SO:0001583	missense	57128	exon1			ACAGAGATAACAC	AF258559	CCDS4493.1, CCDS54961.1	6p25.1	2008-02-05	2006-09-19	2006-09-19	ENSG00000214113	ENSG00000214113		"""LYR motif containing"""	21365	protein-coding gene	gene with protein product		613311	"""chromosome 6 open reading frame 149"""	C6orf149			Standard	XM_005249239		Approved	CGI-203, ISD11	uc021ykw.1	Q9HD34	OTTHUMG00000014173	ENST00000330636.4:c.31T>G	6.37:g.5260936A>C	ENSP00000418787:p.Ser11Ala	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	25	14	0.56	NM_020408	A8K543|Q5XKP1	Missense_Mutation	SNP	ENST00000330636.4	37	CCDS4493.1	857	0.3923992673992674	406	0.8252032520325203	125	0.3453038674033149	141	0.2465034965034965	185	0.24406332453825857	C	14.64	2.596201	0.46318	0.738458	0.248763	ENSG00000214113	ENST00000468929;ENST00000330636;ENST00000464010;ENST00000480566;ENST00000500576	T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55	5.04	4.18	0.49190	.	0.885835	0.09315	N	0.819095	T	0.20047	0.0482	L	0.29908	0.895	0.58432	P	2.9999999999752447E-6	B;B	0.21147	0.012;0.052	B;B	0.27715	0.011;0.082	T	0.14868	-1.0457	9	0.25106	T	0.35	3.934	6.484	0.22079	0.1795:0.7276:0.0:0.0929	rs2224391;rs59639417;rs2224391	11;11	C9JRX8;Q9HD34	.;LYRM4_HUMAN	A	11	ENSP00000418321:S11A;ENSP00000418787:S11A;ENSP00000420026:S11A;ENSP00000419928:S11A;ENSP00000443900:S11A	ENSP00000418787:S11A	S	-	1	0	LYRM4	5205935	1.000000	0.71417	0.990000	0.47175	0.848000	0.48234	1.219000	0.32479	0.551000	0.29008	-0.729000	0.03580	TCT	A|0.556;C|0.444	0.444	strong		0.597	LYRM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353461.3	NM_020408	
DBH	1621	hgsc.bcm.edu	37	9	136507473	136507473	+	Missense_Mutation	SNP	G	G	A	rs5320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136507473G>A	ENST00000393056.2	+	3	643	c.631G>A	c.(631-633)Gcg>Acg	p.A211T		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	211			A -> T (in dbSNP:rs5320). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:3443096}.		behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	GCCCTCAGACGCGTGCACCAT	0.607													G|||	510	0.101837	0.171	0.0447	5008	,	,		19685	0.1121		0.0616	False		,,,				2504	0.0798				p.A211T		Atlas-SNP	.											.	DBH	86	.	0			c.G631A						PASS	.	G	THR/ALA	635,3771	272.2+/-270.6	35,565,1603	69.0	64.0	66.0		631	-4.7	0.0	9	dbSNP_52	66	482,8118	140.1+/-196.7	18,446,3836	yes	missense	DBH	NM_000787.3	58	53,1011,5439	AA,AG,GG		5.6047,14.4122,8.5883	benign	211/618	136507473	1117,11889	2203	4300	6503	SO:0001583	missense	1621	exon3			TCAGACGCGTGCA	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.631G>A	9.37:g.136507473G>A	ENSP00000376776:p.Ala211Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	106	27	0.254717	NM_000787	Q5T381|Q96AG2	Missense_Mutation	SNP	ENST00000393056.2	37	CCDS6977.2	231	0.10576923076923077	87	0.17682926829268292	19	0.052486187845303865	76	0.13286713286713286	49	0.06464379947229551	G	0.079	-1.187984	0.01607	0.144122	0.056047	ENSG00000123454	ENST00000393056;ENST00000371880;ENST00000263611	T;T	0.34072	1.38;1.38	4.67	-4.71	0.03279	Copper type II, ascorbate-dependent monooxygenase, N-terminal (1);PHM/PNGase F domain (1);	1.057760	0.07311	N	0.875897	T	0.00039	0.0001	N	0.01242	-0.935	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.29671	-1.0004	9	0.22109	T	0.4	-12.7818	5.3345	0.15949	0.3613:0.1174:0.4357:0.0856	rs5320;rs61440943;rs5320	211	P09172	DOPO_HUMAN	T	211;148;148	ENSP00000376776:A211T;ENSP00000263611:A148T	ENSP00000263611:A148T	A	+	1	0	DBH	135497294	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.137000	0.10389	-0.677000	0.05231	-0.573000	0.04149	GCG	G|0.905;A|0.095	0.095	strong		0.607	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
MED24	9862	hgsc.bcm.edu	37	17	38189659	38189659	+	Missense_Mutation	SNP	C	C	T	rs34585432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38189659C>T	ENST00000394128.2	-	7	691	c.610G>A	c.(610-612)Gcc>Acc	p.A204T	MED24_ENST00000501516.3_Missense_Mutation_p.A223T|MED24_ENST00000356271.3_Missense_Mutation_p.A191T|MED24_ENST00000394127.2_Missense_Mutation_p.A191T|MED24_ENST00000394126.1_Missense_Mutation_p.A229T|MED24_ENST00000479829.1_5'Flank	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	204			A -> T (in dbSNP:rs34585432). {ECO:0000269|PubMed:8590280}.		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)					CTGAGATTGGCCAGGATCTCT	0.567													C|||	29	0.00579073	0.0204	0.0029	5008	,	,		19434	0.0		0.0	False		,,,				2504	0.0				p.A204T		Atlas-SNP	.											.	MED24	89	.	0			c.G610A						PASS	.	C	THR/ALA,THR/ALA	92,4314	70.9+/-108.8	1,90,2112	43.0	38.0	40.0		571,610	3.7	1.0	17	dbSNP_126	40	0,8600		0,0,4300	yes	missense,missense	MED24	NM_001079518.1,NM_014815.3	58,58	1,90,6412	TT,TC,CC		0.0,2.0881,0.7074	benign,benign	191/977,204/990	38189659	92,12914	2203	4300	6503	SO:0001583	missense	9862	exon7			GATTGGCCAGGAT	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.610G>A	17.37:g.38189659C>T	ENSP00000377686:p.Ala204Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	13.03	2.115269	0.37339	0.020881	0.0	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000543759;ENST00000535508;ENST00000431269;ENST00000428757	T;T;T	0.42131	0.98;0.98;0.98	5.67	3.69	0.42338	Mediator complex, subunit Med24, N-terminal (1);	0.307388	0.34314	N	0.004079	T	0.23054	0.0557	N	0.08118	0	0.25781	N	0.984725	B;B;B;B;B;B;B;B;D	0.71674	0.367;0.166;0.166;0.357;0.034;0.017;0.034;0.042;0.998	B;B;B;B;B;B;B;B;D	0.78314	0.253;0.096;0.096;0.257;0.04;0.005;0.025;0.042;0.991	T	0.07233	-1.0783	10	0.33141	T	0.24	-14.6106	8.965	0.35872	0.0:0.7801:0.0:0.2199	rs34585432	178;191;154;133;154;114;191;204;146	B9TX63;B9TX65;B4DV99;B4DDR8;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;.;.;.;MED24_HUMAN;.	T	204;204;204;154;191;146;178;178;114;223	ENSP00000377686:A204T;ENSP00000443344:A154T;ENSP00000377685:A191T	ENSP00000348610:A204T	A	-	1	0	MED24	35443185	0.924000	0.31332	1.000000	0.80357	0.613000	0.37349	0.946000	0.29069	1.402000	0.46780	0.655000	0.94253	GCC	C|0.993;T|0.007	0.007	strong		0.567	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
PLXNA4	91584	hgsc.bcm.edu	37	7	131864657	131864657	+	Silent	SNP	G	G	A	rs374317794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:131864657G>A	ENST00000359827.3	-	20	4625	c.3663C>T	c.(3661-3663)taC>taT	p.Y1221Y	PLXNA4_ENST00000321063.4_Silent_p.Y1221Y			Q9HCM2	PLXA4_HUMAN	plexin A4	1221	IPT/TIG 4.				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						TCCCCGGGGAGTACTCCATGC	0.637													G|||	6	0.00119808	0.0045	0.0	5008	,	,		16981	0.0		0.0	False		,,,				2504	0.0				p.Y1221Y		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C3663T						PASS	.	G		9,4255		0,9,2123	15.0	17.0	17.0		3663	4.0	1.0	7		17	0,8480		0,0,4240	no	coding-synonymous	PLXNA4	NM_020911.1		0,9,6363	AA,AG,GG		0.0,0.2111,0.0706		1221/1895	131864657	9,12735	2132	4240	6372	SO:0001819	synonymous_variant	91584	exon20			CGGGGAGTACTCC	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.3663C>T	7.37:g.131864657G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			.	.	weak		0.637	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
WDR90	197335	hgsc.bcm.edu	37	16	711712	711712	+	Silent	SNP	C	C	T	rs3177415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	124	0	0		WXS	Illumina HiSeq	Phase_I	119	50	0.420168	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	
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39411711	39411711	+	Missense_Mutation	SNP	C	C	G	rs150962386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39411711C>G	ENST00000394008.1	+	1	76	c.74C>G	c.(73-75)aCc>aGc	p.T25S		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	30	14 X 5 AA repeats of C-C-[RQVGE]- [SPSTNQ]-[TASL].					keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			ACCACTGTGACCACCTGCAGC	0.627													.|||	219	0.04373	0.1566	0.0159	5008	,	,		17225	0.0		0.001	False		,,,				2504	0.0				p.T25S		Atlas-SNP	.											.	KRTAP9-9	24	.	0			c.C74G						PASS	.																																			SO:0001583	missense	81870	exon1			CTGTGACCACCTG	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"""Keratin associated proteins"""	16773	protein-coding gene	gene with protein product			"""keratin associated protein 9-5"""	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.74C>G	17.37:g.39411711C>G	ENSP00000377576:p.Thr25Ser	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	37	CCDS54127.1	82	0.037545787545787544	72	0.14634146341463414	10	0.027624309392265192	0	0.0	0	0.0	.	6.971	0.549071	0.13312	.	.	ENSG00000198083	ENST00000394008	T	0.00724	5.78	2.19	1.14	0.20703	.	.	.	.	.	T	0.00012	0.0000	N	0.13168	0.305	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.40997	-0.9533	9	0.08381	T	0.77	.	7.4223	0.27079	0.0:0.8514:0.0:0.1486	.	30	Q9BYP9	KRA99_HUMAN	S	25	ENSP00000377576:T25S	ENSP00000377576:T25S	T	+	2	0	KRTAP9-9	36665237	0.931000	0.31567	0.005000	0.12908	0.354000	0.29330	2.718000	0.47236	0.474000	0.27392	0.456000	0.33151	ACC	C|0.962;G|0.038	0.038	strong		0.627	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975	
KRT72	140807	hgsc.bcm.edu	37	12	52994955	52994955	+	Silent	SNP	G	G	A	rs61747192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52994955G>A	ENST00000537672.2	-	1	292	c.282C>T	c.(280-282)ccC>ccT	p.P94P	KRT72_ENST00000354310.4_Silent_p.P94P|KRT72_ENST00000398066.3_5'UTR|KRT72_ENST00000293745.2_Silent_p.P94P|RP11-641A6.2_ENST00000551089.1_RNA	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	94	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		GGATGCCCCCGGGTGGGCACA	0.746													G|||	876	0.17492	0.0862	0.0879	5008	,	,		14031	0.4444		0.1223	False		,,,				2504	0.1329				p.P94P		Atlas-SNP	.											.	KRT72	70	.	0			c.C282T						PASS	.	G	,,	506,3900	229.8+/-244.2	34,438,1731	35.0	36.0	36.0		282,282,282	-8.3	0.1	12	dbSNP_131	36	1080,7520	223.3+/-260.1	68,944,3288	no	coding-synonymous,coding-synonymous,coding-synonymous	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	,,	102,1382,5019	AA,AG,GG		12.5581,11.4843,12.1944	,,	94/512,94/470,94/512	52994955	1586,11420	2203	4300	6503	SO:0001819	synonymous_variant	140807	exon1			GCCCCCGGGTGGG	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.282C>T	12.37:g.52994955G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Silent	SNP	ENST00000537672.2	37	CCDS8833.1	424	0.19413919413919414	42	0.08536585365853659	33	0.09116022099447514	254	0.44405594405594406	95	0.12532981530343007	G	13.71	2.316979	0.40996	0.114843	0.125581	ENSG00000170486	ENST00000549979	.	.	.	4.49	-8.29	0.01009	.	0.000000	0.52532	D	0.000075	T	0.00012	0.0000	.	.	.	0.22446	P	0.999095179	.	.	.	.	.	.	T	0.28038	-1.0056	4	.	.	.	.	3.2959	0.06966	0.2814:0.4304:0.1238:0.1645	.	.	.	.	L	80	.	.	P	-	2	0	KRT72	51281222	0.000000	0.05858	0.051000	0.19133	0.895000	0.52256	-7.169000	0.00042	-1.814000	0.01224	-0.311000	0.09066	CCG	G|0.856;A|0.144	0.144	strong		0.746	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
OR5B3	441608	hgsc.bcm.edu	37	11	58170469	58170469	+	Silent	SNP	C	C	A	rs11229412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58170469C>A	ENST00000309403.2	-	1	413	c.414G>T	c.(412-414)gtG>gtT	p.V138V		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V138V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GACGAGCACACACAGTTGTTG	0.493													c|||	1453	0.290136	0.3525	0.2695	5008	,	,		20988	0.1448		0.3638	False		,,,				2504	0.2945				p.V138V		Atlas-SNP	.											OR5B3,NS,carcinoma,0,1	OR5B3	65	1	1	Substitution - coding silent(1)	stomach(1)	c.G414T						scavenged	.	C		1442,2960	467.9+/-355.0	229,984,988	121.0	109.0	113.0		414	-0.8	0.3	11	dbSNP_120	113	3094,5496	473.5+/-368.6	550,1994,1751	no	coding-synonymous	OR5B3	NM_001005469.1		779,2978,2739	AA,AC,CC		36.0186,32.7578,34.9138		138/315	58170469	4536,8456	2201	4295	6496	SO:0001819	synonymous_variant	441608	exon1			AGCACACACAGTT	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.414G>T	11.37:g.58170469C>A		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	124	69	0.556452	NM_001005469	Q6IEV6	Silent	SNP	ENST00000309403.2	37	CCDS31549.1																																																																																			C|0.672;A|0.328	0.328	strong		0.493	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
PAPLN	89932	hgsc.bcm.edu	37	14	73731012	73731012	+	Silent	SNP	C	C	T	rs151179834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:73731012C>T	ENST00000554301.1	+	20	3118	c.2955C>T	c.(2953-2955)cgC>cgT	p.R985R	PAPLN_ENST00000427855.1_Silent_p.R985R|PAPLN_ENST00000555445.1_Silent_p.R969R|PAPLN_ENST00000340738.5_Silent_p.R958R|PAPLN_ENST00000381166.3_Silent_p.R985R|PAPLN_ENST00000554314.1_3'UTR			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	985	Ig-like C2-type 1.					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)		GGCCAGGCCGCGACTCCCAGA	0.652													C|||	64	0.0127796	0.0015	0.0303	5008	,	,		15789	0.001		0.0258	False		,,,				2504	0.0143				p.R958R		Atlas-SNP	.											.	PAPLN	180	.	0			c.C2874T						PASS	.	C		18,4388	24.3+/-50.5	1,16,2186	61.0	65.0	64.0		2874	-8.2	0.0	14	dbSNP_134	64	175,8425	80.1+/-142.7	0,175,4125	no	coding-synonymous	PAPLN	NM_173462.3		1,191,6311	TT,TC,CC		2.0349,0.4085,1.4839		958/1252	73731012	193,12813	2203	4300	6503	SO:0001819	synonymous_variant	89932	exon20			AGGCCGCGACTCC	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.2955C>T	14.37:g.73731012C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	106	58	0.54717	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	37																																																																																				C|0.984;T|0.016	0.016	strong		0.652	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
PHYHD1	254295	hgsc.bcm.edu	37	9	131689361	131689361	+	Silent	SNP	G	G	A	rs751340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131689361G>A	ENST00000372592.3	+	4	1011	c.78G>A	c.(76-78)gcG>gcA	p.A26A	PHYHD1_ENST00000308941.5_Silent_p.A26A|PHYHD1_ENST00000421063.2_Silent_p.A26A|PHYHD1_ENST00000353176.5_Silent_p.A26A	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	26							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.A26A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						TCTTGTCTGCGGAAGAGTGTG	0.542													A|||	1852	0.369808	0.4228	0.4294	5008	,	,		20654	0.2371		0.4105	False		,,,				2504	0.3507				p.A26A		Atlas-SNP	.											PHYHD1,caecum,carcinoma,+1,2	PHYHD1	29	2	1	Substitution - coding silent(1)	stomach(1)	c.G78A						PASS	.	A	,,	1846,2560	634.6+/-396.2	366,1114,723	212.0	175.0	187.0		78,78,78	-9.8	0.0	9	dbSNP_86	187	3252,5348	649.9+/-400.7	632,1988,1680	no	coding-synonymous,coding-synonymous,coding-synonymous	PHYHD1	NM_001100876.1,NM_001100877.1,NM_174933.3	,,	998,3102,2403	AA,AG,GG		37.814,41.8974,39.1973	,,	26/292,26/271,26/298	131689361	5098,7908	2203	4300	6503	SO:0001819	synonymous_variant	254295	exon2			GTCTGCGGAAGAG	BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.78G>A	9.37:g.131689361G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	204	204	1	NM_001100877	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Silent	SNP	ENST00000372592.3	37	CCDS43885.1																																																																																			G|0.615;A|0.385	0.385	strong		0.542	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933	
RHNO1	83695	hgsc.bcm.edu	37	12	2994562	2994562	+	Silent	SNP	T	T	C	rs371402573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:2994562T>C	ENST00000489288.2	+	2	182	c.30T>C	c.(28-30)ccT>ccC	p.P10P	RHNO1_ENST00000461997.2_Silent_p.P10P|RHNO1_ENST00000464682.2_Intron	NM_001252499.2|NM_001257097.1|NM_001257098.1	NP_001239428.1|NP_001244026.1|NP_001244027.1	Q9BSD3	RHNO1_HUMAN	RAD9-HUS1-RAD1 interacting nuclear orphan 1	10					cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|positive regulation of G0 to G1 transition (GO:0070318)|recombinational repair (GO:0000725)	chromosome (GO:0005694)|nucleus (GO:0005634)											GCCGCCAGCCTTCCCAGAAAG	0.552													T|||	3	0.000599042	0.0015	0.0014	5008	,	,		13532	0.0		0.0	False		,,,				2504	0.0				p.P10P		Atlas-SNP	.											.	.	.	.	0			c.T30C						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	68.0	67.0	67.0			-10.7	0.0	12		67	0,8600		0,0,4300	no	intergenic				0,1,6502	CC,CT,TT		0.0,0.0227,0.0077			2994562	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	83695	exon2			CCAGCCTTCCCAG	AK021945	CCDS8518.1, CCDS58199.1	12p13.33	2012-08-23	2012-08-23	2012-08-23	ENSG00000171792	ENSG00000171792			28206	protein-coding gene	gene with protein product	"""Rad9, Rad1, Hus1 interacting nuclear orphan"""	614085	"""chromosome 12 open reading frame 32"""	C12orf32		20811708, 21659603	Standard	NM_001252499		Approved	HKMT1188, MGC13204, RHINO	uc031qfq.1	Q9BSD3	OTTHUMG00000158557	ENST00000489288.2:c.30T>C	12.37:g.2994562T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	162	94	0.580247	NM_001257098	B7Z989	Silent	SNP	ENST00000489288.2	37	CCDS8518.1																																																																																			.	.	weak		0.552	RHNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351286.2	NM_031465	
IFNA14	3448	hgsc.bcm.edu	37	9	21239589	21239589	+	Missense_Mutation	SNP	T	T	G	rs551644142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21239589T>G	ENST00000380222.2	-	1	389	c.346A>C	c.(346-348)Atg>Ctg	p.M116L		NM_002172.2	NP_002163.2	P01570	IFN14_HUMAN	interferon, alpha 14	116					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)	11				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		AGGTCATTCATTTGCTGGAAA	0.463													T|||	19	0.00379393	0.0061	0.0014	5008	,	,		18999	0.0		0.0089	False		,,,				2504	0.001				p.M116L		Atlas-SNP	.											IFNA14,NS,haematopoietic_neoplasm,+2,3	IFNA14	29	3	0			c.A346C						scavenged	.						137.0	143.0	141.0					9																	21239589		2203	4300	6503	SO:0001583	missense	3448	exon1			CATTCATTTGCTG		CCDS6501.1	9p22	2010-08-24			ENSG00000228083	ENSG00000228083		"""Interferons"""	5420	protein-coding gene	gene with protein product		147579				1385305	Standard	NM_002172		Approved	LEIF2H, IFN-alphaH	uc010mis.3	P01570	OTTHUMG00000019665	ENST00000380222.2:c.346A>C	9.37:g.21239589T>G	ENSP00000369571:p.Met116Leu	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	404	35	0.0866337	NM_002172	Q5VZ56|Q7M4S1	Missense_Mutation	SNP	ENST00000380222.2	37	CCDS6501.1	.	.	.	.	.	.	.	.	.	.	-	0.010	-1.777501	0.00640	.	.	ENSG00000228083	ENST00000380222	T	0.02216	4.39	3.38	2.46	0.29980	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.649130	0.15209	N	0.274576	T	0.00496	0.0016	N	0.00057	-2.36	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43925	-0.9361	10	0.02654	T	1	.	8.3389	0.32232	0.0:0.0:0.5688:0.4312	.	116	P01570	IFN14_HUMAN	L	116	ENSP00000369571:M116L	ENSP00000369571:M116L	M	-	1	0	IFNA14	21229589	0.001000	0.12720	0.066000	0.19879	0.025000	0.11179	0.128000	0.15810	0.748000	0.32831	-0.829000	0.03081	ATG	.	.	none		0.463	IFNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051894.1	NM_002172	
GPR112	139378	hgsc.bcm.edu	37	X	135431236	135431236	+	Missense_Mutation	SNP	T	T	C	rs5930932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:135431236T>C	ENST00000394143.1	+	6	5662	c.5371T>C	c.(5371-5373)Ttt>Ctt	p.F1791L	GPR112_ENST00000412101.1_Missense_Mutation_p.F1586L|GPR112_ENST00000370652.1_Missense_Mutation_p.F1791L|GPR112_ENST00000287534.4_Missense_Mutation_p.F1728L|GPR112_ENST00000394141.1_Missense_Mutation_p.F1586L	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1791			F -> L (in dbSNP:rs5930932).		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)	p.F1791L(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CACCAATTGCTTTTCTTCTAA	0.383													c|||	1834	0.485828	0.4569	0.3617	3775	,	,		15609	0.2778		0.3797	False		,,,				2504	0.3241				p.F1791L		Atlas-SNP	.											.	GPR112	459	.	1	Substitution - Missense(1)	prostate(1)	c.T5371C						PASS	.		LEU/PHE	2257,1576		567,784,339,280,232	133.0	133.0	133.0		5371	-1.8	0.0	X	dbSNP_114	133	3229,3499		567,1181,914,680,958	yes	missense	GPR112	NM_153834.3	22	1134,1965,1253,960,1190	CC,CT,C,TT,T		47.9935,41.1166,48.0542	benign	1791/3081	135431236	5486,5075	2202	4300	6502	SO:0001583	missense	139378	exon6			AATTGCTTTTCTT	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5371T>C	X.37:g.135431236T>C	ENSP00000377699:p.Phe1791Leu	Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	313	170	0.543131	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	786	0.47377938517179025	152	0.4175824175824176	84	0.29577464788732394	112	0.24669603524229075	190	0.3242320819112628	c	0.020	-1.432654	0.01108	0.588834	0.479935	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.20463	2.11;2.11;2.07;2.25;2.07	3.63	-1.78	0.07957	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.37291	-0.9712	8	0.21014	T	0.42	.	5.3382	0.15969	0.0:0.2802:0.1606:0.5593	rs5930932;rs6635265;rs52832481;rs60264923;rs5930932	1728;1586;1791	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	L	1791;1791;1586;1728;1586	ENSP00000377699:F1791L;ENSP00000359686:F1791L;ENSP00000416526:F1586L;ENSP00000287534:F1728L;ENSP00000377697:F1586L	ENSP00000287534:F1728L	F	+	1	0	GPR112	135258902	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.934000	0.03955	-1.013000	0.03383	-1.690000	0.00728	TTT	0|0.015;C|0.499	0.499	strong		0.383	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
FAT3	120114	hgsc.bcm.edu	37	11	92534968	92534968	+	Missense_Mutation	SNP	G	G	A	rs370539148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92534968G>A	ENST00000298047.6	+	9	8806	c.8789G>A	c.(8788-8790)cGa>cAa	p.R2930Q	FAT3_ENST00000525166.1_Missense_Mutation_p.R2780Q|FAT3_ENST00000409404.2_Missense_Mutation_p.R2930Q			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2930	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)				GAAGTGTACCGAGGGAATGTG	0.552										TCGA Ovarian(4;0.039)			G|||	4	0.000798722	0.003	0.0	5008	,	,		21033	0.0		0.0	False		,,,				2504	0.0				p.R2930Q		Atlas-SNP	.											.	FAT3	1822	.	0			c.G8789A						PASS	.	G	GLN/ARG	7,4033		0,7,2013	94.0	93.0	93.0		8789	5.1	1.0	11		93	0,8374		0,0,4187	no	missense	FAT3	NM_001008781.2	43	0,7,6200	AA,AG,GG		0.0,0.1733,0.0564	possibly-damaging	2930/4558	92534968	7,12407	2020	4187	6207	SO:0001583	missense	120114	exon9			TGTACCGAGGGAA	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.8789G>A	11.37:g.92534968G>A	ENSP00000298047:p.Arg2930Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	16.93	3.257586	0.59321	0.001733	0.0	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.01725	4.67;4.67;4.67	6.04	5.08	0.68730	.	.	.	.	.	T	0.02455	0.0075	N	0.20766	0.605	0.80722	D	1	D	0.59357	0.985	P	0.52267	0.694	T	0.71206	-0.4661	9	0.24483	T	0.36	.	10.4452	0.44490	0.157:0.0:0.843:0.0	.	2930	Q8TDW7-3	.	Q	2930;2930;2780	ENSP00000298047:R2930Q;ENSP00000387040:R2930Q;ENSP00000432586:R2780Q	ENSP00000298047:R2930Q	R	+	2	0	FAT3	92174616	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	1.983000	0.40648	1.433000	0.47394	0.563000	0.77884	CGA	.	.	weak		0.552	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
MYH13	8735	hgsc.bcm.edu	37	17	10223697	10223697	+	Missense_Mutation	SNP	G	G	T	rs2074876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10223697G>T	ENST00000418404.3	-	24	3391	c.3228C>A	c.(3226-3228)gaC>gaA	p.D1076E	MYH13_ENST00000252172.4_Missense_Mutation_p.D1076E|RP11-401O9.3_ENST00000577743.1_RNA|RP11-401O9.4_ENST00000609088.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1076			D -> E (in dbSNP:rs2074876). {ECO:0000269|PubMed:10388558}.		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						TTTGCTGCTTGTCATTTTCTA	0.443													G|||	1214	0.242412	0.1694	0.1614	5008	,	,		14696	0.4067		0.1044	False		,,,				2504	0.3712				p.D1076E		Atlas-SNP	.											MYH13_ENST00000252172,colon,carcinoma,-1,2	MYH13	533	2	0			c.C3228A						PASS	.	G	GLU/ASP	524,3194		40,444,1375	77.0	75.0	75.0		3228	3.7	1.0	17	dbSNP_96	75	821,7363		39,743,3310	yes	missense	MYH13	NM_003802.2	45	79,1187,4685	TT,TG,GG		10.0318,14.0936,11.3006	benign	1076/1939	10223697	1345,10557	1859	4092	5951	SO:0001583	missense	8735	exon25			CTGCTTGTCATTT	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.3228C>A	17.37:g.10223697G>T	ENSP00000404570:p.Asp1076Glu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	460	0.21062271062271062	85	0.17276422764227642	50	0.13812154696132597	246	0.43006993006993005	79	0.10422163588390501	G	14.79	2.640617	0.47153	0.140936	0.100318	ENSG00000006788	ENST00000252172	T	0.80566	-1.39	3.68	3.68	0.42216	Myosin tail (1);	.	.	.	.	T	0.00012	0.0000	L	0.61218	1.895	0.32109	P	0.589576	B	0.06786	0.001	B	0.26864	0.074	T	0.25984	-1.0116	8	0.49607	T	0.09	.	10.2665	0.43457	0.1097:0.0:0.8903:0.0	rs2074876;rs61443677;rs2074876	1076	Q9UKX3	MYH13_HUMAN	E	1076	ENSP00000252172:D1076E	ENSP00000252172:D1076E	D	-	3	2	MYH13	10164422	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.879000	0.28146	2.044000	0.60594	0.655000	0.94253	GAC	G|0.786;T|0.214	0.214	strong		0.443	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	
KIAA1462	57608	hgsc.bcm.edu	37	10	30316872	30316872	+	Silent	SNP	T	T	C	rs3739996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:30316872T>C	ENST00000375377.1	-	3	2306	c.2205A>G	c.(2203-2205)gcA>gcG	p.A735A		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	735					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						CGGTAGGGAATGCTGTGTGCG	0.577													T|||	1058	0.211262	0.1127	0.2406	5008	,	,		20585	0.2242		0.3897	False		,,,				2504	0.1268				p.A735A		Atlas-SNP	.											.	KIAA1462	162	.	0			c.A2205G						PASS	.	T		556,3696		45,466,1615	54.0	57.0	56.0		2205	-11.2	0.0	10	dbSNP_107	56	3196,5302		593,2010,1646	no	coding-synonymous	KIAA1462	NM_020848.2		638,2476,3261	CC,CT,TT		37.6088,13.0762,29.4275		735/1360	30316872	3752,8998	2126	4249	6375	SO:0001819	synonymous_variant	57608	exon3			AGGGAATGCTGTG	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.2205A>G	10.37:g.30316872T>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	183	82	0.448087	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																			T|0.732;C|0.268	0.268	strong		0.577	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
TACC1	6867	hgsc.bcm.edu	37	8	38677242	38677242	+	Silent	SNP	G	G	A	rs16887780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:38677242G>A	ENST00000317827.4	+	3	859	c.480G>A	c.(478-480)acG>acA	p.T160T	TACC1_ENST00000520973.1_5'UTR|TACC1_ENST00000520611.1_5'Flank|TACC1_ENST00000348567.4_Intron|TACC1_ENST00000443286.2_Silent_p.T176T|TACC1_ENST00000276520.8_Intron|TACC1_ENST00000520615.1_5'UTR|TACC1_ENST00000520340.1_Silent_p.T124T|TACC1_ENST00000379931.3_Silent_p.T160T|TACC1_ENST00000518415.1_Silent_p.T115T|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000519416.1_5'UTR|TACC1_ENST00000330691.6_Intron	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	160	Interaction with TDRD7.				cell cycle (GO:0007049)|cell division (GO:0051301)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				breast(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(3)	17		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			AGGATTCCACGGATATCTCGG	0.493													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		20225	0.0		0.0	False		,,,				2504	0.0				p.T160T		Atlas-SNP	.											.	TACC1	98	.	0			c.G480A						PASS	.	G	,,	120,4286	89.7+/-128.4	1,118,2084	101.0	101.0	101.0		,,480	-1.6	0.0	8	dbSNP_123	101	1,8599	1.2+/-3.3	0,1,4299	yes	intron,utr-5,coding-synonymous	TACC1	NM_001122824.1,NM_001146216.2,NM_006283.2	,,	1,119,6383	AA,AG,GG		0.0116,2.7236,0.9303	,,	,,160/806	38677242	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	6867	exon3			TTCCACGGATATC	AF049910	CCDS6109.1, CCDS47845.1, CCDS55224.1	8p11	2012-12-20			ENSG00000147526	ENSG00000147526			11522	protein-coding gene	gene with protein product		605301					Standard	NM_006283		Approved		uc010lwp.3	O75410	OTTHUMG00000164018	ENST00000317827.4:c.480G>A	8.37:g.38677242G>A		Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	230	117	0.508696	NM_006283	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Silent	SNP	ENST00000317827.4	37	CCDS6109.1																																																																																			G|0.991;A|0.009	0.009	strong		0.493	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376768.1	NM_006283	
ZNF492	57615	hgsc.bcm.edu	37	19	22846623	22846623	+	Missense_Mutation	SNP	G	G	A	rs71355986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.						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	81	0	0		WXS	Illumina HiSeq	Phase_I	23	22	0.956522	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	
ZNF285	26974	hgsc.bcm.edu	37	19	44892266	44892266	+	Splice_Site	SNP	T	T	C	rs200167944		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44892266T>C	ENST00000330997.4	-	4	207		c.e4-2		ZNF285_ENST00000591679.1_Splice_Site|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_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	122	3	0.0245902		WXS	Illumina HiSeq	Phase_I	132	7	0.0530303	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
RERE	473	hgsc.bcm.edu	37	1	8420966	8420966	+	Silent	SNP	G	G	A	rs77608355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:8420966G>A	ENST00000337907.3	-	19	3235	c.2601C>T	c.(2599-2601)ggC>ggT	p.G867G	RERE_ENST00000377464.1_Silent_p.G599G|RERE_ENST00000400907.2_Intron|RERE_ENST00000476556.1_Silent_p.G313G|RERE_ENST00000400908.2_Silent_p.G867G	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	867	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GCTGTGGGGGGCCTGGGTGCT	0.726													G|||	162	0.0323482	0.1165	0.0115	5008	,	,		10147	0.0		0.0	False		,,,				2504	0.0				p.G867G		Atlas-SNP	.											.	RERE	129	.	0			c.C2601T						PASS	.	G	,,	201,3379		0,201,1589	3.0	3.0	3.0		2601,939,2601	-10.4	0.5	1	dbSNP_131	3	2,7358		0,2,3678	no	coding-synonymous,coding-synonymous,coding-synonymous	RERE	NM_001042681.1,NM_001042682.1,NM_012102.3	,,	0,203,5267	AA,AG,GG		0.0272,5.6145,1.8556	,,	867/1567,313/1013,867/1567	8420966	203,10737	1790	3680	5470	SO:0001819	synonymous_variant	473	exon19			TGGGGGGCCTGGG	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2601C>T	1.37:g.8420966G>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	11	9	0.818182	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Silent	SNP	ENST00000337907.3	37	CCDS95.1																																																																																			G|0.972;A|0.028	0.028	strong		0.726	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
THRAP3	9967	hgsc.bcm.edu	37	1	36752687	36752687	+	Missense_Mutation	SNP	A	A	G	rs58840555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36752687A>G	ENST00000354618.5	+	4	1080	c.856A>G	c.(856-858)Act>Gct	p.T286A	THRAP3_ENST00000469141.2_Missense_Mutation_p.T286A	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	286	Ser-rich.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GATGGGCTCAACTCTGCCGAG	0.597			T	USP6	aneurysmal bone cysts								A|||	283	0.0565096	0.1997	0.0274	5008	,	,		19531	0.0		0.0	False		,,,				2504	0.0				p.T286A	Pancreas(129;785 1795 20938 23278 32581)	Atlas-SNP	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	THRAP3	93	.	0			c.A856G						PASS	.	A	ALA/THR	773,3633	311.1+/-291.9	88,597,1518	75.0	77.0	76.0		856	-10.2	0.1	1	dbSNP_129	76	9,8591	7.1+/-27.0	0,9,4291	no	missense	THRAP3	NM_005119.3	58	88,606,5809	GG,GA,AA		0.1047,17.5443,6.0126	benign	286/956	36752687	782,12224	2203	4300	6503	SO:0001583	missense	9967	exon4			GGCTCAACTCTGC	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.856A>G	1.37:g.36752687A>G	ENSP00000346634:p.Thr286Ala	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	121	49	0.404959	NM_005119	D3DPS5|Q5VTK6	Missense_Mutation	SNP	ENST00000354618.5	37	CCDS405.1	101	0.04624542124542125	89	0.18089430894308944	12	0.03314917127071823	0	0.0	0	0.0	A	0.128	-1.116496	0.01799	0.175443	0.001047	ENSG00000054118	ENST00000354618;ENST00000469141	T;T	0.12774	2.65;2.65	5.85	-10.2	0.00374	.	0.656822	0.15045	N	0.283624	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	0.12967	-1.0527	9	0.06365	T	0.9	0.3741	7.9158	0.29816	0.1879:0.0:0.445:0.3671	rs58840555;rs61732681	286	Q9Y2W1	TR150_HUMAN	A	286	ENSP00000346634:T286A;ENSP00000433825:T286A	ENSP00000346634:T286A	T	+	1	0	THRAP3	36525274	0.000000	0.05858	0.133000	0.22050	0.263000	0.26337	-0.599000	0.05700	-2.368000	0.00604	-2.215000	0.00298	ACT	A|0.946;G|0.054	0.054	strong		0.597	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119	
AXIN1	8312	hgsc.bcm.edu	37	16	348222	348222	+	Silent	SNP	C	C	T	rs214250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:348222C>T	ENST00000262320.3	-	6	1655	c.1284G>A	c.(1282-1284)tcG>tcA	p.S428S	AXIN1_ENST00000481769.1_5'UTR|AXIN1_ENST00000354866.3_Silent_p.S428S	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	428	Interaction with GSK3B. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)	p.S428S(1)		biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GGGGCCCTGACGATGGATCGC	0.647											OREG0003699	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	1053	0.210264	0.4304	0.1671	5008	,	,		15375	0.0556		0.2227	False		,,,				2504	0.09				p.S428S		Atlas-SNP	.											AXIN1,cerebellum,primitive_neuroectodermal_tumour-medulloblastoma,0,1	AXIN1	290	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G1284A						PASS	.	G	,	1441,2729		260,921,904	14.0	6.0	9.0		1284,1284	-1.9	0.0	16	dbSNP_79	9	1635,6563		205,1225,2669	no	coding-synonymous,coding-synonymous	AXIN1	NM_003502.3,NM_181050.2	,	465,2146,3573	TT,TC,CC		19.9439,34.5564,24.8706	,	428/863,428/827	348222	3076,9292	2085	4099	6184	SO:0001819	synonymous_variant	8312	exon6			CCCTGACGATGGA	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	903	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 49"""	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1284G>A	16.37:g.348222C>T		Somatic	48	0	0	587	WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Silent	SNP	ENST00000262320.3	37	CCDS10405.1																																																																																			C|0.770;T|0.230	0.230	strong		0.647	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		
CYP3A43	64816	hgsc.bcm.edu	37	7	99457605	99457605	+	Missense_Mutation	SNP	C	C	G	rs680055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99457605C>G	ENST00000354829.2	+	10	1121	c.1018C>G	c.(1018-1020)Ccc>Gcc	p.P340A	CYP3A43_ENST00000415413.1_Missense_Mutation_p.P129A|CYP3A43_ENST00000342499.4_Missense_Mutation_p.P200A|CYP3A43_ENST00000444905.1_Missense_Mutation_p.P87A|CYP3A43_ENST00000417625.1_Missense_Mutation_p.P230A|CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000222382.5_Missense_Mutation_p.P340A|CYP3A43_ENST00000312017.5_Missense_Mutation_p.P340A	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	340			Missing (in allele CYP3A43*2).|P -> A (in allele CYP3A43*3; dbSNP:rs680055). {ECO:0000269|PubMed:14695544}.		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)	CGCAGTTTTACCCAATAAGGT	0.493													C|||	624	0.124601	0.3782	0.0519	5008	,	,		19594	0.002		0.0557	False		,,,				2504	0.0307				p.P340A		Atlas-SNP	.											.	CYP3A43	52	.	0			c.C1018G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	1338,3068	447.9+/-348.5	190,958,1055	94.0	90.0	91.0		1018,1018,1018	1.6	0.7	7	dbSNP_83	91	420,8180	130.5+/-188.4	15,390,3895	yes	missense,missense,missense	CYP3A43	NM_022820.3,NM_057095.1,NM_057096.2	27,27,27	205,1348,4950	GG,GC,CC		4.8837,30.3677,13.5168	benign,benign,benign	340/505,340/504,340/421	99457605	1758,11248	2203	4300	6503	SO:0001583	missense	64816	exon10			GTTTTACCCAATA	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.1018C>G	7.37:g.99457605C>G	ENSP00000346887:p.Pro340Ala	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	127	54	0.425197	NM_057096	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	37	CCDS5676.1	263	0.12042124542124542	201	0.40853658536585363	22	0.06077348066298342	1	0.0017482517482517483	39	0.051451187335092345	C	9.485	1.099179	0.20552	0.303677	0.048837	ENSG00000021461	ENST00000354829;ENST00000417625;ENST00000342499;ENST00000444905;ENST00000415413;ENST00000312017;ENST00000222382	T;T;T;T;T;T;T	0.79247	-0.31;-0.31;-0.31;-0.31;-1.25;-0.31;-0.31	2.49	1.58	0.23477	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	0.9999999999379743	P;D;P;B;B	0.54207	0.899;0.965;0.946;0.015;0.015	P;P;P;B;B	0.57371	0.47;0.819;0.696;0.009;0.009	T	0.15607	-1.0431	9	0.59425	D	0.04	.	7.3043	0.26438	0.0:0.8526:0.0:0.1474	rs680055;rs60416653;rs680055	230;200;340;340;340	Q495Y1;F8W6L8;Q9HB55-3;Q75MK2;Q9HB55	.;.;.;.;CP343_HUMAN	A	340;230;200;87;129;340;340	ENSP00000346887:P340A;ENSP00000416581:P230A;ENSP00000345351:P200A;ENSP00000405557:P87A;ENSP00000401521:P129A;ENSP00000312110:P340A;ENSP00000222382:P340A	ENSP00000222382:P340A	P	+	1	0	CYP3A43	99295541	0.981000	0.34729	0.667000	0.29798	0.365000	0.29674	4.142000	0.58044	0.586000	0.29626	0.205000	0.17691	CCC	C|0.863;G|0.137	0.137	strong		0.493	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1		
PIGP	51227	hgsc.bcm.edu	37	21	38444881	38444881	+	Missense_Mutation	SNP	G	G	A	rs73200245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38444881G>A	ENST00000464265.1	-	1	230	c.7C>T	c.(7-9)Cca>Tca	p.P3S	TTC3_ENST00000540756.1_5'Flank|TTC3_ENST00000399010.1_5'Flank|PIGP_ENST00000399098.1_Intron|PIGP_ENST00000329667.3_5'Flank|TTC3_ENST00000355666.1_5'Flank|PIGP_ENST00000360525.4_Intron|PIGP_ENST00000399103.1_Intron|PIGP_ENST00000399102.1_Intron	NM_153681.2	NP_710148.1	P57054	PIGP_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class P	3				P -> S (in Ref. 1; BAA96872). {ECO:0000305}.	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)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			kidney(1)|urinary_tract(1)	2		Myeloproliferative disorder(46;0.0412)				GTGCTCCGTGGCACCATTGAT	0.632													G|||	1046	0.208866	0.3775	0.3573	5008	,	,		14000	0.0823		0.1521	False		,,,				2504	0.0644				p.P3S		Atlas-SNP	.											.	PIGP	9	.	0			c.C7T						PASS	.	G	SER/PRO,	1489,2917	475.5+/-357.3	242,1005,956	127.0	127.0	127.0		7,	-4.1	0.0	21	dbSNP_130	127	1380,7220	266.9+/-287.0	115,1150,3035	yes	missense,intron	PIGP	NM_153681.2,NM_153682.2	74,	357,2155,3991	AA,AG,GG		16.0465,33.7948,22.059	benign,	3/159,	38444881	2869,10137	2203	4300	6503	SO:0001583	missense	51227	exon1			TCCGTGGCACCAT	AB037162	CCDS13649.1, CCDS13650.1	21q22.2	2013-02-26	2006-06-28	2005-11-10	ENSG00000185808	ENSG00000185808	2.4.1.198	"""Phosphatidylinositol glycan anchor biosynthesis"""	3046	protein-coding gene	gene with protein product	"""phosphatidylinositol-n-acetylglucosaminyltranferase subunit"""	605938	"""Down syndrome critical region gene 5"", ""phosphatidylinositol glycan, class P"""	DSCR5		10814524, 15221505	Standard	NR_028352		Approved	DCRC, DSRC	uc002yvw.1	P57054	OTTHUMG00000086653	ENST00000464265.1:c.7C>T	21.37:g.38444881G>A	ENSP00000420037:p.Pro3Ser	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_153681	B2RB18|B2RE99|B5BU92|D3DSG7|J3KR75|Q53Y28|Q96KI1|Q9NZA6	Missense_Mutation	SNP	ENST00000464265.1	37	CCDS13649.1	484	0.2216117216117216	184	0.37398373983739835	124	0.3425414364640884	56	0.0979020979020979	120	0.158311345646438	G	11.31	1.601930	0.28534	0.337948	0.160465	ENSG00000185808	ENST00000464265	T	0.23348	1.91	4.39	-4.09	0.03951	.	6.970870	0.00357	N	0.000039	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	9.99999999995449E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.43147	-0.9409	9	0.30854	T	0.27	12.7861	2.1501	0.03797	0.1513:0.4097:0.1697:0.2693	.	3	P57054	PIGP_HUMAN	S	3	ENSP00000420037:P3S	ENSP00000420037:P3S	P	-	1	0	PIGP	37366751	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.903000	0.04084	-0.353000	0.08224	-0.457000	0.05445	CCA	G|0.789;A|0.211	0.211	strong		0.632	PIGP-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194769.2	NM_153681	
EGFLAM	133584	hgsc.bcm.edu	37	5	38412674	38412674	+	Missense_Mutation	SNP	C	C	T	rs16903965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38412674C>T	ENST00000354891.3	+	11	1764	c.1418C>T	c.(1417-1419)aCg>aTg	p.T473M	EGFLAM_ENST00000322350.5_Missense_Mutation_p.T473M|EGFLAM_ENST00000397202.2_5'UTR|EGFLAM_ENST00000336740.6_Missense_Mutation_p.T239M	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	473	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.		T -> M (in dbSNP:rs16903965). {ECO:0000269|PubMed:15489334}.		extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					GGTTGGCACACGGTTATGCTC	0.512													C|||	617	0.123203	0.1059	0.0476	5008	,	,		17477	0.2381		0.1392	False		,,,				2504	0.0654				p.T473M	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C1418T						PASS	.	C	MET/THR,MET/THR,MET/THR	372,4034	189.9+/-215.9	20,332,1851	97.0	94.0	95.0		1418,1418,716	5.2	0.8	5	dbSNP_123	95	848,7752	193.8+/-239.4	44,760,3496	yes	missense,missense,missense	EGFLAM	NM_001205301.1,NM_152403.3,NM_182798.2	81,81,81	64,1092,5347	TT,TC,CC		9.8605,8.443,9.3803	possibly-damaging,possibly-damaging,possibly-damaging	473/1018,473/1010,239/776	38412674	1220,11786	2203	4300	6503	SO:0001583	missense	133584	exon11			GGCACACGGTTAT	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"""Fibronectin type III domain containing"""	26810	protein-coding gene	gene with protein product	"""pikachurin"", ""agrin-like"""					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.1418C>T	5.37:g.38412674C>T	ENSP00000346964:p.Thr473Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	300	0.13736263736263737	35	0.07113821138211382	19	0.052486187845303865	131	0.229020979020979	115	0.1517150395778364	C	13.76	2.333393	0.41297	0.08443	0.098605	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000339580	T;T;T	0.76448	-1.02;-1.02;-1.02	6.07	5.16	0.70880	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.357840	0.33401	N	0.004955	T	0.00178	0.0005	M	0.84511	2.7	0.09310	P	0.9999999999999996	D;D;D	0.71674	0.995;0.997;0.998	P;D;P	0.63793	0.839;0.918;0.896	T	0.37842	-0.9688	9	0.66056	D	0.02	-0.4212	6.8131	0.23814	0.0:0.6476:0.1859:0.1665	rs16903965;rs17855880;rs52789261;rs57587907;rs16903965	239;473;473	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	M	473;473;239;239	ENSP00000346964:T473M;ENSP00000313084:T473M;ENSP00000337607:T239M	ENSP00000313084:T473M	T	+	2	0	EGFLAM	38448431	0.832000	0.29368	0.812000	0.32479	0.131000	0.20780	1.374000	0.34283	1.489000	0.48450	-0.355000	0.07637	ACG	C|0.891;T|0.109	0.109	strong		0.512	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43678796	43678796	+	Missense_Mutation	SNP	C	C	T	rs2435381	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:43678796C>T	ENST00000374466.3	+	8	1770	c.1435C>T	c.(1435-1437)Cct>Tct	p.P479S		NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	479			P -> S (in dbSNP:rs2435381). {ECO:0000269|PubMed:17974005}.		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)			endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GACTCCGGTTCCTGGTCTTTT	0.493													C|||	794	0.158546	0.0204	0.1945	5008	,	,		18543	0.1974		0.2644	False		,,,				2504	0.1708				p.P479S		Atlas-SNP	.											.	CSGALNACT2	67	.	0			c.C1435T						PASS	.	C	SER/PRO	306,4100	166.2+/-197.5	12,282,1909	140.0	138.0	138.0		1435	5.9	1.0	10	dbSNP_100	138	2293,6307	387.6+/-342.3	316,1661,2323	no	missense	CSGALNACT2	NM_018590.3	74	328,1943,4232	TT,TC,CC		26.6628,6.9451,19.9831	benign	479/543	43678796	2599,10407	2203	4300	6503	SO:0001583	missense	55454	exon8			CCGGTTCCTGGTC	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"""Beta 4-glycosyltransferases"""	24292	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"""					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.1435C>T	10.37:g.43678796C>T	ENSP00000363590:p.Pro479Ser	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	232	103	0.443966	NM_018590	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Missense_Mutation	SNP	ENST00000374466.3	37	CCDS7201.1	402	0.18406593406593408	16	0.032520325203252036	79	0.21823204419889503	115	0.20104895104895104	192	0.2532981530343008	C	13.73	2.324034	0.41096	0.069451	0.266628	ENSG00000169826	ENST00000374466	T	0.28069	1.63	5.87	5.87	0.94306	.	0.145736	0.64402	N	0.000004	T	0.00012	0.0000	L	0.39566	1.225	0.09310	P	1.0	B	0.25521	0.128	B	0.27887	0.084	T	0.23440	-1.0188	9	0.40728	T	0.16	-13.0868	20.5827	0.99408	0.0:1.0:0.0:0.0	rs2435381;rs3758518;rs17435753;rs2435381	479	Q8N6G5	CGAT2_HUMAN	S	479	ENSP00000363590:P479S	ENSP00000363590:P479S	P	+	1	0	CSGALNACT2	42998802	0.941000	0.31946	1.000000	0.80357	0.989000	0.77384	2.883000	0.48554	2.941000	0.99782	0.655000	0.94253	CCT	C|0.815;T|0.185	0.185	strong		0.493	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590	
ACOX1	51	hgsc.bcm.edu	37	17	73944496	73944496	+	Missense_Mutation	SNP	G	G	A	rs35629489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73944496G>A	ENST00000301608.4	-	13	1831	c.1771C>T	c.(1771-1773)Cgt>Tgt	p.R591C	ACOX1_ENST00000537812.1_Missense_Mutation_p.R553C|ACOX1_ENST00000293217.5_Missense_Mutation_p.R591C	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	591					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	TCCTTTACACGCTGGTTTACT	0.388													G|||	69	0.013778	0.0461	0.0043	5008	,	,		18689	0.0		0.002	False		,,,				2504	0.0031				p.R591C		Atlas-SNP	.											ACOX1_ENST00000301608,caecum,carcinoma,0,2	ACOX1	85	2	0			c.C1771T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	111,4295	85.8+/-124.5	1,109,2093	152.0	132.0	139.0		1657,1771,1771	5.2	0.1	17	dbSNP_126	139	12,8588	9.1+/-34.3	0,12,4288	yes	missense,missense,missense	ACOX1	NM_001185039.1,NM_004035.6,NM_007292.5	180,180,180	1,121,6381	AA,AG,GG		0.1395,2.5193,0.9457	probably-damaging,probably-damaging,probably-damaging	553/623,591/661,591/661	73944496	123,12883	2203	4300	6503	SO:0001583	missense	51	exon13			TTACACGCTGGTT	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"""acyl-Coenzyme A oxidase 1, palmitoyl"""			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.1771C>T	17.37:g.73944496G>A	ENSP00000301608:p.Arg591Cys	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	39	12	0.307692	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	37	CCDS11735.1	25	0.011446886446886446	23	0.046747967479674794	0	0.0	0	0.0	2	0.002638522427440633	G	15.54	2.864717	0.51482	0.025193	0.001395	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.47177	0.85;0.85;0.85	5.25	5.25	0.73442	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.099482	0.64402	D	0.000003	T	0.31575	0.0801	M	0.86178	2.8	0.38755	D	0.954204	D;D;P;B	0.76494	0.999;0.998;0.47;0.268	P;P;B;B	0.60117	0.869;0.869;0.106;0.045	T	0.65796	-0.6081	10	0.72032	D	0.01	-11.4201	19.7385	0.96217	0.0:0.0:1.0:0.0	rs35629489	523;553;591;591	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	C	591;591;553;591;523	ENSP00000301608:R591C;ENSP00000293217:R591C;ENSP00000441257:R553C	ENSP00000293217:R591C	R	-	1	0	ACOX1	71456091	1.000000	0.71417	0.099000	0.21106	0.405000	0.30901	5.538000	0.67193	2.838000	0.97847	0.655000	0.94253	CGT	G|0.989;A|0.011	0.011	strong		0.388	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1		
BIN1	274	hgsc.bcm.edu	37	2	127827598	127827598	+	Silent	SNP	C	C	T	rs61748158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:127827598C>T	ENST00000316724.5	-	5	795	c.384G>A	c.(382-384)acG>acA	p.T128T	BIN1_ENST00000259238.4_Silent_p.T128T|BIN1_ENST00000393041.3_Silent_p.T128T|BIN1_ENST00000357970.3_Silent_p.T128T|BIN1_ENST00000351659.3_Silent_p.T128T|BIN1_ENST00000376113.2_Silent_p.T128T|BIN1_ENST00000393040.3_Silent_p.T128T|BIN1_ENST00000346226.3_Silent_p.T128T|BIN1_ENST00000348750.4_Silent_p.T128T|BIN1_ENST00000409400.1_Silent_p.T128T|BIN1_ENST00000352848.3_Silent_p.T128T	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	128	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				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)		GGCCCAGGTACGTGTCCATGG	0.597													C|||	18	0.00359425	0.0106	0.0014	5008	,	,		19793	0.003		0.0	False		,,,				2504	0.0				p.T128T		Atlas-SNP	.											.	BIN1	85	.	0			c.G384A						PASS	.	C	,,,,,,,,,	24,4382		0,24,2179	138.0	108.0	118.0		384,384,384,384,384,384,384,384,384,384	-9.6	0.6	2	dbSNP_129	118	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	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	,,,,,,,,,	0,24,6479	TT,TC,CC		0.0,0.5447,0.1845	,,,,,,,,,	128/455,128/594,128/551,128/507,128/498,128/519,128/483,128/476,128/440,128/410	127827598	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	274	exon5			CAGGTACGTGTCC	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.384G>A	2.37:g.127827598C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_139346	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			C|0.998;T|0.002	0.002	strong		0.597	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
TGIF1	7050	hgsc.bcm.edu	37	18	3452262	3452262	+	Silent	SNP	C	C	T	rs8098291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3452262C>T	ENST00000330513.5	+	1	588	c.285C>T	c.(283-285)tcC>tcT	p.S95S	TGIF1_ENST00000577543.1_Intron|TGIF1_ENST00000405385.3_Intron|TGIF1_ENST00000551402.1_Intron|TGIF1_ENST00000407501.2_Intron|TGIF1_ENST00000548489.2_Intron|TGIF1_ENST00000343820.5_Intron|TGIF1_ENST00000345133.5_Intron|TGIF1_ENST00000551541.1_Intron|TGIF1_ENST00000400167.2_5'Flank|TGIF1_ENST00000401449.1_Intron	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	95					determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	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 negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				GTGCCCTCTCCCCGGAGCTGG	0.771													C|||	265	0.0529153	0.1861	0.0245	5008	,	,		9736	0.0		0.002	False		,,,				2504	0.0				p.S95S		Atlas-SNP	.											.	TGIF1	41	.	0			c.C285T						PASS	.	C	,,,,,,	598,3670		33,532,1569	8.0	9.0	9.0		,285,,,,,	3.5	0.0	18	dbSNP_116	9	17,8359		0,17,4171	no	intron,coding-synonymous,intron,intron,intron,intron,intron	TGIF1	NM_003244.2,NM_170695.2,NM_173207.1,NM_173208.1,NM_173209.1,NM_173210.1,NM_174886.1	,,,,,,	33,549,5740	TT,TC,CC		0.203,14.0112,4.864	,,,,,,	,95/402,,,,,	3452262	615,12029	2134	4188	6322	SO:0001819	synonymous_variant	7050	exon1			CCTCTCCCCGGAG	X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"""Homeoboxes / TALE class"""	11776	protein-coding gene	gene with protein product		602630	"""TGFB-induced factor (TALE family homeobox)"""	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.285C>T	18.37:g.3452262C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	22	14	0.636364	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Silent	SNP	ENST00000330513.5	37	CCDS11834.1																																																																																			C|0.953;T|0.047	0.047	strong		0.771	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
PIEZO1	9780	hgsc.bcm.edu	37	16	88800122	88800122	+	Silent	SNP	C	C	G	rs9928479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88800122C>G	ENST00000301015.9	-	18	2607	c.2361G>C	c.(2359-2361)cgG>cgC	p.R787R	RP5-1142A6.2_ENST00000440406.2_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	787					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						GCTCCAGCAGCCGCTCAGCCA	0.662													c|||	303	0.0605032	0.2194	0.0187	5008	,	,		15726	0.0		0.0	False		,,,				2504	0.0				p.R787R		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G2361C						PASS	.						4.0	9.0	8.0					16																	88800122		636	1499	2135	SO:0001819	synonymous_variant	9780	exon18			CAGCAGCCGCTCA	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.2361G>C	16.37:g.88800122C>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	64	21	0.328125	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	93	0.042582417582417584	85	0.17276422764227642	6	0.016574585635359115	0	0.0	2	0.002638522427440633	C	11.51	1.659600	0.29515	.	.	ENSG00000103335	ENST00000451779	.	.	.	4.7	0.207	0.15214	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.9999999999997674	.	.	.	.	.	.	T	0.13683	-1.0500	3	.	.	.	-48.0889	6.7645	0.23558	0.1152:0.2818:0.5236:0.0793	rs9928479;rs61498906	.	.	.	P	733	.	.	A	-	1	0	FAM38A	87327623	1.000000	0.71417	0.996000	0.52242	0.970000	0.65996	1.524000	0.35942	-0.107000	0.12088	0.556000	0.70494	GCT	C|0.955;G|0.045	0.045	strong		0.662	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
MGP	4256	hgsc.bcm.edu	37	12	15038703	15038703	+	Missense_Mutation	SNP	G	G	A	rs142330429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15038703G>A	ENST00000539261.1	-	1	157	c.23C>T	c.(22-24)gCc>gTc	p.A8V	C12orf60_ENST00000527783.1_Intron|MGP_ENST00000228938.5_Missense_Mutation_p.A8V	NM_000900.3	NP_000891.2	P08493	MGP_HUMAN	matrix Gla protein	8					cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|ossification (GO:0001503)|regulation of bone mineralization (GO:0030500)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|structural constituent of bone (GO:0008147)			large_intestine(1)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	7						GGCCAGGATGGCAAGAAGGAT	0.488													G|||	77	0.0153754	0.0	0.0	5008	,	,		18540	0.0308		0.004	False		,,,				2504	0.0429				p.A8V		Atlas-SNP	.											.	MGP	16	.	0			c.C23T						PASS	.	G	VAL/ALA,VAL/ALA	3,4403	6.2+/-15.9	0,3,2200	145.0	117.0	126.0		23,23	5.2	0.3	12	dbSNP_134	126	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	MGP	NM_000900.3,NM_001190839.1	64,64	0,5,6498	AA,AG,GG		0.0233,0.0681,0.0384	benign,benign	8/104,8/129	15038703	5,13001	2203	4300	6503	SO:0001583	missense	4256	exon1			AGGATGGCAAGAA	M58549	CCDS8669.1, CCDS53752.1	12p12.3	2006-12-15			ENSG00000111341	ENSG00000111341			7060	protein-coding gene	gene with protein product		154870				2394711	Standard	NM_000900		Approved		uc021qvr.1	P08493	OTTHUMG00000168740	ENST00000539261.1:c.23C>T	12.37:g.15038703G>A	ENSP00000445907:p.Ala8Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_000900	A0M8W5|B2R519|J3KMX7|Q2TU41|Q567P9|Q6ICN5	Missense_Mutation	SNP	ENST00000539261.1	37	CCDS8669.1	19	0.0086996336996337	0	0.0	0	0.0	16	0.027972027972027972	3	0.00395778364116095	G	0.375	-0.932067	0.02359	6.81E-4	2.33E-4	ENSG00000111341	ENST00000539261;ENST00000228938	T;T	0.36340	1.63;1.26	5.22	5.22	0.72569	.	0.572076	0.17597	N	0.168558	T	0.08492	0.0211	N	0.10874	0.06	0.09310	N	1	B	0.16603	0.018	B	0.16722	0.016	T	0.10894	-1.0610	10	0.66056	D	0.02	0.4235	14.1517	0.65389	0.0:0.0:1.0:0.0	.	8	P08493	MGP_HUMAN	V	8	ENSP00000445907:A8V;ENSP00000228938:A8V	ENSP00000228938:A8V	A	-	2	0	MGP	14929970	0.421000	0.25465	0.332000	0.25469	0.140000	0.21249	3.653000	0.54446	2.721000	0.93114	0.655000	0.94253	GCC	G|0.994;A|0.006	0.006	strong		0.488	MGP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400864.1	NM_000900	
ZNF30	90075	hgsc.bcm.edu	37	19	35434238	35434238	+	Missense_Mutation	SNP	A	A	G	rs386808878|rs1811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35434238A>G	ENST00000601142.1	+	5	605	c.368A>G	c.(367-369)cAg>cGg	p.Q123R	ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000595818.1_3'UTR|ZNF30_ENST00000426813.2_Missense_Mutation_p.Q42R|ZNF30_ENST00000303586.7_Missense_Mutation_p.Q124R|ZNF30_ENST00000439785.1_Missense_Mutation_p.Q124R			P17039	ZNF30_HUMAN	zinc finger protein 30	123			Q -> R (in dbSNP:rs1811). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15057824, ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		CGTGAATGTCAGGAATATGGA	0.388													G|||	2935	0.586062	0.6997	0.3761	5008	,	,		16378	0.6032		0.5119	False		,,,				2504	0.6401				p.Q124R		Atlas-SNP	.											.	ZNF30	44	.	0			c.A371G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN	2464,1286		816,832,227	91.0	87.0	88.0		371,371,368	-0.5	0.1	19	dbSNP_36	88	3901,4325		938,2025,1150	yes	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	43,43,43	1754,2857,1377	GG,GA,AA		47.4228,34.2933,46.852	benign,benign,benign	124/625,124/625,123/624	35434238	6365,5611	1875	4113	5988	SO:0001583	missense	90075	exon5			AATGTCAGGAATA	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.368A>G	19.37:g.35434238A>G	ENSP00000469954:p.Gln123Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	1240	0.5677655677655677	341	0.693089430894309	159	0.43922651933701656	357	0.6241258741258742	383	0.5052770448548812	G	5.442	0.266597	0.10294	0.657067	0.474228	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813	T;T	0.27890	1.64;1.64	1.91	-0.504	0.11997	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.15870	0.014;0.003	T	0.29761	-1.0001	8	0.41790	T	0.15	.	6.151	0.20313	0.8252:0.0:0.1748:0.0	rs1811;rs3193069;rs52822507;rs58128455;rs1811	124;123	P17039-2;P17039	.;ZNF30_HUMAN	R	124;123;42	ENSP00000403441:Q124R;ENSP00000416457:Q42R	ENSP00000303889:Q123R	Q	+	2	0	ZNF30	40126078	0.000000	0.05858	0.103000	0.21229	0.005000	0.04900	-3.046000	0.00630	-0.594000	0.05836	-2.522000	0.00184	CAG	A|0.410;G|0.590	0.590	strong		0.388	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
FCGBP	8857	hgsc.bcm.edu	37	19	40405999	40405999	+	Missense_Mutation	SNP	C	C	A	rs7248839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40405999C>A	ENST00000221347.6	-	10	4854	c.4847G>T	c.(4846-4848)gGc>gTc	p.G1616V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1616	Cys-rich.		G -> V (in dbSNP:rs7248839).			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)			GCACACCATGCCTTTACCCGC	0.642													C|||	659	0.131589	0.1324	0.1916	5008	,	,		19537	0.0357		0.172	False		,,,				2504	0.1452				p.G1616V		Atlas-SNP	.											FCGBP,mouth,carcinoma,+1,1	FCGBP	416	1	0			c.G4847T						scavenged	.						80.0	60.0	67.0					19																	40405999		2201	4292	6493	SO:0001583	missense	8857	exon10			ACCATGCCTTTAC	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.4847G>T	19.37:g.40405999C>A	ENSP00000221347:p.Gly1616Val	Somatic	818	8	0.00977995		WXS	Illumina HiSeq	Phase_I	542	86	0.158672	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	227	0.10393772893772894	60	0.12195121951219512	41	0.1132596685082873	18	0.03146853146853147	108	0.1424802110817942	C	9.121	1.008963	0.19199	.	.	ENSG00000090920	ENST00000221347	T	0.04454	3.62	3.4	1.07	0.20283	von Willebrand factor, type C (1);	.	.	.	.	T	0.00039	0.0001	L	0.61387	1.9	0.80722	P	0.0	B	0.24963	0.115	B	0.24269	0.052	T	0.32079	-0.9920	8	0.22706	T	0.39	.	7.7598	0.28946	0.4526:0.5474:0.0:0.0	rs7248839	1616	Q9Y6R7	FCGBP_HUMAN	V	1616	ENSP00000221347:G1616V	ENSP00000221347:G1616V	G	-	2	0	FCGBP	45097839	0.003000	0.15002	0.001000	0.08648	0.014000	0.08584	0.661000	0.25023	0.128000	0.18479	0.306000	0.20318	GGC	C|0.897;A|0.103	0.103	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
LGI3	203190	hgsc.bcm.edu	37	8	22009053	22009053	+	Silent	SNP	G	G	A	rs35142808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22009053G>A	ENST00000306317.2	-	7	1067	c.778C>T	c.(778-780)Ctg>Ttg	p.L260L	LGI3_ENST00000424267.2_Silent_p.L236L	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	260					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		TCCCACTTCAGGATGGTGCAG	0.602													G|||	174	0.0347444	0.1203	0.0043	5008	,	,		19819	0.0		0.003	False		,,,				2504	0.0092				p.L260L		Atlas-SNP	.											.	LGI3	44	.	0			c.C778T						PASS	.	G		467,3939	219.4+/-237.2	32,403,1768	87.0	89.0	89.0		778	4.2	0.8	8	dbSNP_126	89	25,8575	17.9+/-57.8	1,23,4276	no	coding-synonymous	LGI3	NM_139278.2		33,426,6044	AA,AG,GG		0.2907,10.5992,3.7829		260/549	22009053	492,12514	2203	4300	6503	SO:0001819	synonymous_variant	203190	exon7			ACTTCAGGATGGT	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.778C>T	8.37:g.22009053G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_139278	A5PLP2|Q86TL4|Q8N296	Silent	SNP	ENST00000306317.2	37	CCDS6025.1																																																																																			G|0.968;A|0.032	0.032	strong		0.602	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1		
EPHB6	2051	hgsc.bcm.edu	37	7	142563253	142563253	+	Missense_Mutation	SNP	T	T	G	rs8177146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142563253T>G	ENST00000392957.2	+	8	1757	c.970T>G	c.(970-972)Tct>Gct	p.S324A	EPHB6_ENST00000442129.1_Missense_Mutation_p.S324A|EPHB6_ENST00000411471.2_Missense_Mutation_p.S47A	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	324	Cys-rich.		S -> A (in dbSNP:rs8177146). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.2}.			extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GCTCTATAAGTCTTCTGCTGG	0.662													G|||	342	0.0682907	0.1301	0.0375	5008	,	,		14216	0.0099		0.0288	False		,,,				2504	0.1074				p.S324A		Atlas-SNP	.											.	EPHB6	168	.	0			c.T970G						PASS	.	G	ALA/SER	492,3914	779.6+/-414.4	37,418,1748	49.0	47.0	48.0		970	4.5	1.0	7	dbSNP_117	48	123,8477	813.3+/-407.0	2,119,4179	yes	missense	EPHB6	NM_004445.3	99	39,537,5927	GG,GT,TT		1.4302,11.1666,4.7286	benign	324/1022	142563253	615,12391	2203	4300	6503	SO:0001583	missense	2051	exon8			TATAAGTCTTCTG	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.970T>G	7.37:g.142563253T>G	ENSP00000376684:p.Ser324Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	117	0.05357142857142857	75	0.1524390243902439	14	0.03867403314917127	7	0.012237762237762238	21	0.027704485488126648	G	0.100	-1.152918	0.01700	0.111666	0.014302	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.15603	2.41;2.41;2.41	5.43	4.54	0.55810	Tyrosine-protein kinase ephrin type A/B receptor-like (1);	0.000000	0.46442	N	0.000283	T	0.00039	0.0001	N	0.00746	-1.225	0.54753	P	1.399999999995849E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.35425	-0.9789	9	0.02654	T	1	.	12.7255	0.57168	0.0:0.0:0.5683:0.4317	rs8177146;rs58284647;rs8177146	324	O15197	EPHB6_HUMAN	A	324;324;47	ENSP00000376684:S324A;ENSP00000410789:S324A;ENSP00000409061:S47A	ENSP00000376684:S324A	S	+	1	0	EPHB6	142273375	0.074000	0.21230	0.971000	0.41717	0.271000	0.26615	-0.105000	0.10907	0.663000	0.31027	-0.217000	0.12591	TCT	T|0.947;G|0.053	0.053	strong		0.662	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13754394	13754394	+	Silent	SNP	C	C	T	rs2401809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13754394C>T	ENST00000265104.4	-	62	10577	c.10473G>A	c.(10471-10473)acG>acA	p.T3491T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3491					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)					CACTGATGAGCGTGGAAGCTG	0.398									Kartagener syndrome				C|||	1644	0.328275	0.3298	0.2911	5008	,	,		18118	0.122		0.3847	False		,,,				2504	0.5072				p.T3491T		Atlas-SNP	.											.	DNAH5	868	.	0			c.G10473A						PASS	.	C		1493,2913	475.5+/-357.3	240,1013,950	127.0	121.0	123.0		10473	-7.5	0.1	5	dbSNP_100	123	3128,5472	475.8+/-369.2	559,2010,1731	no	coding-synonymous	DNAH5	NM_001369.2		799,3023,2681	TT,TC,CC		36.3721,33.8856,35.5298		3491/4625	13754394	4621,8385	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon62	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GATGAGCGTGGAA	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.10473G>A	5.37:g.13754394C>T		Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	255	251	0.984314	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			C|0.669;T|0.331	0.331	strong		0.398	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
TUBA3E	112714	hgsc.bcm.edu	37	2	130951488	130951488	+	Silent	SNP	A	A	G	rs2443644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:130951488A>G	ENST00000312988.7	-	4	1027	c.927T>C	c.(925-927)caT>caC	p.H309H		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	309					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					TGTACTTGCCATGGCGAGGGT	0.577																																					p.H309H		Atlas-SNP	.											TUBA3E,right_upper_lobe,carcinoma,-1,1	TUBA3E	73	1	0			c.T927C						scavenged	.						155.0	139.0	145.0					2																	130951488		2203	4300	6503	SO:0001819	synonymous_variant	112714	exon4			CTTGCCATGGCGA	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.927T>C	2.37:g.130951488A>G		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	282	63	0.223404	NM_207312		Silent	SNP	ENST00000312988.7	37	CCDS2158.1																																																																																			A|0.985;G|0.015	0.015	strong		0.577	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
NAV3	89795	hgsc.bcm.edu	37	12	78598891	78598891	+	Silent	SNP	G	G	A	rs9971904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	69	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	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	
FNDC1	84624	hgsc.bcm.edu	37	6	159650978	159650978	+	Missense_Mutation	SNP	A	A	G	rs509648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	117	0	0		WXS	Illumina HiSeq	Phase_I	140	74	0.528571	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	
PQLC2	54896	hgsc.bcm.edu	37	1	19652063	19652063	+	Silent	SNP	G	G	A	rs11558390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19652063G>A	ENST00000375153.3	+	4	1009	c.369G>A	c.(367-369)acG>acA	p.T123T	PQLC2_ENST00000375155.3_Silent_p.T123T|PQLC2_ENST00000400548.2_Silent_p.T58T	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	89	0	0		WXS	Illumina HiSeq	Phase_I	82	80	0.97561	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	
DCHS2	54798	hgsc.bcm.edu	37	4	155407595	155407595	+	Nonstop_Mutation	SNP	C	C	A	rs140554741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155407595C>A	ENST00000456341.2	-	2	2108	c.2109G>T	c.(2107-2109)taG>taT	p.*703Y	DCHS2_ENST00000339452.1_Intron|DCHS2_ENST00000443500.1_Nonstop_Mutation_p.*710Y			Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	0	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)	p.*710Y(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)		TACAGGAAATCTAGGCAAGAT	0.353													C|||	93	0.0185703	0.0008	0.0086	5008	,	,		21542	0.001		0.0298	False		,,,				2504	0.0562				p.X710Y		Atlas-SNP	.											DCHS2_ENST00000443500,NS,carcinoma,0,1	DCHS2	594	1	1	Nonstop extension(1)	kidney(1)	c.G2130T						PASS	.						268.0	215.0	231.0					4																	155407595		692	1591	2283	SO:0001578	stop_lost	54798	exon2			GGAAATCTAGGCA	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		ENST00000456341.2:c.2109G>T	4.37:g.155407595C>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	97	36	0.371134	NM_001142553	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000456341.2	37		24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	C	13.13	2.144810	0.37825	.	.	ENSG00000197410	ENST00000456341;ENST00000443500	.	.	.	2.87	-2.53	0.06326	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.6935	0.05127	0.3797:0.2807:0.0:0.3396	.	.	.	.	Y	703;710	.	.	X	-	3	2	DCHS2	155627045	0.000000	0.05858	0.000000	0.03702	0.592000	0.36648	-0.749000	0.04813	-0.726000	0.04895	0.561000	0.74099	TAG	C|0.989;A|0.011	0.011	strong		0.353	DCHS2-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000365285.1	NM_001142552	
TECTA	7007	hgsc.bcm.edu	37	11	121016424	121016424	+	Missense_Mutation	SNP	A	A	G	rs200852252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:121016424A>G	ENST00000392793.1	+	12	3975	c.3704A>G	c.(3703-3705)aAc>aGc	p.N1235S	TECTA_ENST00000478058.1_3'UTR|TECTA_ENST00000264037.2_Missense_Mutation_p.N1235S			O75443	TECTA_HUMAN	tectorin alpha	1235	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)		AGCATGCAGAACAGCACCTAT	0.532													A|||	4	0.000798722	0.0015	0.0029	5008	,	,		22478	0.0		0.0	False		,,,				2504	0.0				p.N1235S		Atlas-SNP	.											.	TECTA	329	.	0			c.A3704G						PASS	.	A	SER/ASN	2,4404	4.2+/-10.8	0,2,2201	157.0	126.0	136.0		3704	4.6	1.0	11		136	0,8598		0,0,4299	no	missense	TECTA	NM_005422.2	46	0,2,6500	GG,GA,AA		0.0,0.0454,0.0154	probably-damaging	1235/2156	121016424	2,13002	2203	4299	6502	SO:0001583	missense	7007	exon11			TGCAGAACAGCAC	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.3704A>G	11.37:g.121016424A>G	ENSP00000376543:p.Asn1235Ser	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	150	71	0.473333	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	17.08	3.298372	0.60195	4.54E-4	0.0	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.62788	-0.0;-0.0	5.76	4.57	0.56435	von Willebrand factor, type D domain (3);	0.000000	0.85682	D	0.000000	T	0.72463	0.3463	L	0.55213	1.73	0.40504	D	0.980674	D	0.76494	0.999	D	0.83275	0.996	T	0.70927	-0.4739	10	0.31617	T	0.26	.	12.6018	0.56501	0.8617:0.1383:0.0:0.0	.	1235	O75443	TECTA_HUMAN	S	1235	ENSP00000376543:N1235S;ENSP00000264037:N1235S	ENSP00000264037:N1235S	N	+	2	0	TECTA	120521634	1.000000	0.71417	0.970000	0.41538	0.986000	0.74619	5.257000	0.65473	2.196000	0.70406	0.482000	0.46254	AAC	A|1.000;G|0.000	0.000	strong		0.532	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
CYP4A22	284541	hgsc.bcm.edu	37	1	47607281	47607281	+	Missense_Mutation	SNP	C	C	T	rs12564525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47607281C>T	ENST00000371891.3	+	3	407	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000371890.3_Missense_Mutation_p.R126W|CYP4A22_ENST00000294337.3_Missense_Mutation_p.R126W|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	126			R -> W (in allele CYP4A22*8, allele CYP4A22*9, allele CYP4A22*11, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs12564525). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCTGGCTCCACGGATTGGTAT	0.453													c|||	1859	0.371206	0.2254	0.2867	5008	,	,		23221	0.6141		0.2058	False		,,,				2504	0.5481				p.R126W	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.C376T						PASS	.	T	TRP/ARG	1099,3307	720.2+/-409.0	129,841,1233	132.0	122.0	125.0		376	1.7	0.7	1	dbSNP_120	125	1802,6798	732.5+/-406.8	197,1408,2695	yes	missense	CYP4A22	NM_001010969.2	101	326,2249,3928	TT,TC,CC		20.9535,24.9433,22.3051	benign	126/520	47607281	2901,10105	2203	4300	6503	SO:0001583	missense	284541	exon3			GCTCCACGGATTG		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.376C>T	1.37:g.47607281C>T	ENSP00000360958:p.Arg126Trp	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	164	85	0.518293	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	682	0.31227106227106227	103	0.20934959349593496	90	0.24861878453038674	342	0.5979020979020979	147	0.19393139841688653	t	0.721	-0.783423	0.02907	0.249433	0.209535	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.67865	-0.27;-0.29;-0.29	1.66	1.66	0.24008	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00003	-3.465	0.51482	P	7.900000000005125E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48514	-0.9029	9	0.02654	T	1	.	6.8608	0.24066	0.0:0.126:0.0:0.874	rs12564525;rs57365220	126;126	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	W	126	ENSP00000360957:R126W;ENSP00000360958:R126W;ENSP00000294337:R126W	ENSP00000294337:R126W	R	+	1	2	CYP4A22	47379868	1.000000	0.71417	0.697000	0.30258	0.155000	0.21991	2.836000	0.48183	0.117000	0.18138	-0.665000	0.03846	CGG	C|0.715;T|0.285	0.285	strong		0.453	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
OR6C74	254783	hgsc.bcm.edu	37	12	55641295	55641295	+	Missense_Mutation	SNP	A	A	G	rs4388990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	243	0	0		WXS	Illumina HiSeq	Phase_I	204	74	0.362745	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		
TMEM63A	9725	hgsc.bcm.edu	37	1	226055595	226055595	+	Silent	SNP	G	G	A	rs2292564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226055595G>A	ENST00000366835.3	-	7	777	c.507C>T	c.(505-507)gaC>gaT	p.D169D	TMEM63A_ENST00000537914.1_5'Flank|TMEM63A_ENST00000474478.1_5'Flank	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	169					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)	p.D169D(1)		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)					TACCCAGCAAGTCCCCTGAGA	0.547													G|||	2154	0.430112	0.5189	0.3127	5008	,	,		19546	0.5188		0.2624	False		,,,				2504	0.4744				p.D169D		Atlas-SNP	.											TMEM63A,NS,carcinoma,0,1	TMEM63A	75	1	1	Substitution - coding silent(1)	stomach(1)	c.C507T						PASS	.	G		1936,2470	549.9+/-377.9	427,1082,694	136.0	106.0	116.0		507	4.8	0.6	1	dbSNP_100	116	2486,6114	408.4+/-349.5	375,1736,2189	no	coding-synonymous	TMEM63A	NM_014698.2		802,2818,2883	AA,AG,GG		28.907,43.9401,33.9997		169/808	226055595	4422,8584	2203	4300	6503	SO:0001819	synonymous_variant	9725	exon7			CAGCAAGTCCCCT		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.507C>T	1.37:g.226055595G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			G|0.640;A|0.360	0.360	strong		0.547	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
MFSD5	84975	hgsc.bcm.edu	37	12	53647373	53647373	+	Silent	SNP	T	T	C	rs10876422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53647373T>C	ENST00000329548.4	+	2	945	c.754T>C	c.(754-756)Ttg>Ctg	p.L252L	MFSD5_ENST00000534842.1_Silent_p.L359L	NM_032889.4	NP_116278.3	Q6N075	MFSD5_HUMAN	major facilitator superfamily domain containing 5	252					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(3)|urinary_tract(1)	16						CGTGCTGCTGTTGGGCACCAT	0.587													T|||	2320	0.463259	0.2625	0.4135	5008	,	,		21472	0.5972		0.4632	False		,,,				2504	0.6319				p.L359L		Atlas-SNP	.											.	MFSD5	40	.	0			c.T1075C						PASS	.	T	,	1332,3074	444.9+/-347.5	198,936,1069	103.0	101.0	101.0		1075,754	2.0	1.0	12	dbSNP_120	101	4039,4561	556.5+/-386.9	956,2127,1217	no	coding-synonymous,coding-synonymous	MFSD5	NM_001170790.1,NM_032889.4	,	1154,3063,2286	CC,CT,TT		46.9651,30.2315,41.2963	,	359/558,252/451	53647373	5371,7635	2203	4300	6503	SO:0001819	synonymous_variant	84975	exon2			CTGCTGTTGGGCA	AK097576	CCDS8851.1, CCDS53796.1	12q13.13	2012-03-09			ENSG00000182544	ENSG00000182544			28156	protein-coding gene	gene with protein product							Standard	NM_032889		Approved	MGC11308	uc001sch.2	Q6N075	OTTHUMG00000170028	ENST00000329548.4:c.754T>C	12.37:g.53647373T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_001170790	G3V1N7|Q6NW04|Q8N7W8|Q8NCK0|Q96IA5	Silent	SNP	ENST00000329548.4	37	CCDS8851.1																																																																																			T|0.569;C|0.431	0.431	strong		0.587	MFSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406896.1	NM_032889	
DNAH10	196385	hgsc.bcm.edu	37	12	124401172	124401172	+	Missense_Mutation	SNP	G	G	A	rs61740383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124401172G>A	ENST00000409039.3	+	62	10562	c.10537G>A	c.(10537-10539)Gac>Aac	p.D3513N		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3513	AAA 5. {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)		TATCCTGGGAGACAAGGAAGT	0.433													G|||	327	0.0652955	0.2322	0.0231	5008	,	,		21713	0.0		0.003	False		,,,				2504	0.001				p.D3513N		Atlas-SNP	.											.	DNAH10	888	.	0			c.G10537A						PASS	.	G	ASN/ASP	688,3042		58,572,1235	71.0	72.0	72.0		10537	4.7	1.0	12	dbSNP_129	72	38,8150		1,36,4057	yes	missense	DNAH10	NM_207437.3	23	59,608,5292	AA,AG,GG		0.4641,18.445,6.0916	probably-damaging	3513/4472	124401172	726,11192	1865	4094	5959	SO:0001583	missense	196385	exon62			CTGGGAGACAAGG	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.10537G>A	12.37:g.124401172G>A	ENSP00000386770:p.Asp3513Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	113	0.051739926739926737	100	0.2032520325203252	11	0.03038674033149171	0	0.0	2	0.002638522427440633	G	32	5.137071	0.94517	0.18445	0.004641	ENSG00000197653	ENST00000409039	T	0.33654	1.4	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.00144	0.0004	M	0.90425	3.115	0.09310	P	0.999999878792	D	0.89917	1.0	D	0.87578	0.998	T	0.02471	-1.1154	9	0.87932	D	0	.	17.7267	0.88367	0.0:0.0:1.0:0.0	rs61740383	3513	Q8IVF4	DYH10_HUMAN	N	3513	ENSP00000386770:D3513N	ENSP00000386770:D3513N	D	+	1	0	DNAH10	122967125	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.869000	0.99810	2.177000	0.69029	0.561000	0.74099	GAC	G|0.957;A|0.043	0.043	strong		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
C1orf94	84970	hgsc.bcm.edu	37	1	34663411	34663411	+	Missense_Mutation	SNP	C	C	G	rs1414474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:34663411C>G	ENST00000488417.1	+	2	1026	c.906C>G	c.(904-906)gaC>gaG	p.D302E	C1orf94_ENST00000373374.3_Missense_Mutation_p.D112E	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	302			D -> E (in dbSNP:rs1414474). {ECO:0000269|PubMed:15489334}.							central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				CACGTCCTGACAAGCTCCCTG	0.607													C|||	836	0.166933	0.1369	0.2233	5008	,	,		19091	0.0863		0.2048	False		,,,				2504	0.2117				p.D302E		Atlas-SNP	.											.	C1orf94	156	.	0			c.C906G						PASS	.	C	GLU/ASP,GLU/ASP	742,3664	306.3+/-289.4	59,624,1520	56.0	51.0	53.0		906,336	1.3	0.7	1	dbSNP_88	53	2029,6571	352.5+/-328.7	240,1549,2511	yes	missense,missense	C1orf94	NM_001134734.1,NM_032884.3	45,45	299,2173,4031	GG,GC,CC		23.593,16.8407,21.3056	benign,benign	302/599,112/409	34663411	2771,10235	2203	4300	6503	SO:0001583	missense	84970	exon2			TCCTGACAAGCTC	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.906C>G	1.37:g.34663411C>G	ENSP00000435634:p.Asp302Glu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	37	CCDS44108.1	343	0.15705128205128205	75	0.1524390243902439	78	0.2154696132596685	43	0.07517482517482517	147	0.19393139841688653	C	8.449	0.852550	0.17106	0.168407	0.23593	ENSG00000142698	ENST00000373374;ENST00000488417	T;T	0.26223	1.75;1.75	4.46	1.31	0.21738	.	0.913614	0.09296	N	0.821662	T	0.00012	0.0000	L	0.40543	1.245	0.45777	P	0.0013370000000000326	B	0.13594	0.008	B	0.12156	0.007	T	0.31336	-0.9947	9	0.37606	T	0.19	-13.8187	6.5487	0.22420	0.0:0.5515:0.3483:0.1002	rs1414474;rs17484993;rs17845124;rs17857924;rs1414474	302	Q6P1W5	CA094_HUMAN	E	112;302	ENSP00000362472:D112E;ENSP00000435634:D302E	ENSP00000362472:D112E	D	+	3	2	C1orf94	34435998	0.958000	0.32768	0.721000	0.30653	0.408000	0.30992	-0.116000	0.10724	0.486000	0.27676	0.557000	0.71058	GAC	C|0.796;G|0.204	0.204	strong		0.607	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
OR2T2	401992	hgsc.bcm.edu	37	1	248616401	248616401	+	Silent	SNP	G	G	A	rs77680148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248616401G>A	ENST00000342927.3	+	1	325	c.303G>A	c.(301-303)caG>caA	p.Q101Q		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	101						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTGCAGTTCAGATCTTCCTCT	0.532																																					p.Q101Q		Atlas-SNP	.											.	OR2T2	73	.	0			c.G303A						PASS	.						303.0	339.0	327.0					1																	248616401		2203	4300	6503	SO:0001819	synonymous_variant	401992	exon1			AGTTCAGATCTTC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.303G>A	1.37:g.248616401G>A		Somatic	1147	0	0		WXS	Illumina HiSeq	Phase_I	1155	256	0.221645	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			G|0.913;A|0.087	0.087	strong		0.532	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592215	1592215	+	Intron	SNP	C	C	G	rs41289057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1592215C>G	ENST00000381605.4	-	1	141				SIRPB1_ENST00000568365.1_Missense_Mutation_p.G74A|SIRPB1_ENST00000279477.7_Missense_Mutation_p.G74A|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000381596.1_5'UTR|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						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						TAATTCCCGGCCTGGTCCAGC	0.522													c|||	3213	0.641573	0.7254	0.5029	5008	,	,		7138	0.7351		0.4781	False		,,,				2504	0.6984				p.G74A		Atlas-SNP	.											.	SIRPB1	83	.	0			c.G221C						PASS	.						66.0	79.0	75.0					20																	1592215		452	1342	1794	SO:0001627	intron_variant	10326	exon2			TCCCGGCCTGGTC	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.76+8299G>C	20.37:g.1592215C>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	301	41	0.136213	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	821	0.3759157509157509	204	0.4146341463414634	117	0.32320441988950277	293	0.5122377622377622	207	0.27308707124010556	.	5.490	0.275498	0.10403	.	.	ENSG00000101307	ENST00000279477;ENST00000381596	T	0.66995	-0.24	2.75	-5.49	0.02584	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.52905	1.665	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.35151	-0.9800	8	0.36615	T	0.2	.	9.7994	0.40755	0.0:0.6565:0.0:0.3435	rs41289057	74	Q5TFQ8	SIRBL_HUMAN	A	74	ENSP00000279477:G74A	ENSP00000279477:G74A	G	-	2	0	SIRPB1	1540215	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.679000	0.01940	-1.538000	0.01734	-0.474000	0.04947	GGC	C|0.624;G|0.376	0.376	strong		0.522	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
UBA6	55236	hgsc.bcm.edu	37	4	68534392	68534392	+	Splice_Site	SNP	C	C	T	rs10010188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:68534392C>T	ENST00000322244.5	-	9	729	c.670G>A	c.(670-672)Gca>Aca	p.A224T	UBA6_ENST00000420827.2_Splice_Site_p.A224T	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	224			A -> T (in dbSNP:rs10010188). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17597759, ECO:0000269|PubMed:17974005}.		protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						CCAGGATTTGCCTAAAAATAA	0.299													C|||	776	0.154952	0.1536	0.1167	5008	,	,		17296	0.1052		0.165	False		,,,				2504	0.2249				p.A224T		Atlas-SNP	.											UBA6,colon,carcinoma,+1,1	UBA6	98	1	0			c.G670A						PASS	.	C	THR/ALA	736,3670	296.7+/-284.4	70,596,1537	80.0	77.0	78.0		670	4.7	1.0	4	dbSNP_119	78	1203,7395	240.4+/-271.1	79,1045,3175	yes	missense-near-splice	UBA6	NM_018227.5	58	149,1641,4712	TT,TC,CC		13.9916,16.7045,14.9108	benign	224/1053	68534392	1939,11065	2203	4299	6502	SO:0001630	splice_region_variant	55236	exon9			GATTTGCCTAAAA	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"""Ubiquitin-like modifier activating enzymes"""	25581	protein-coding gene	gene with protein product	"""UBA6, ubiquitin-activating enzyme E1"""	611361	"""ubiquitin-activating enzyme E1-like 2"""	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.670-1G>A	4.37:g.68534392C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Missense_Mutation	SNP	ENST00000322244.5	37	CCDS3516.1	341	0.15613553113553114	83	0.16869918699186992	49	0.13535911602209943	76	0.13286713286713286	133	0.17546174142480211	C	14.72	2.619904	0.46736	0.167045	0.139916	ENSG00000033178	ENST00000322244;ENST00000420827	T;T	0.29397	1.57;1.57	5.54	4.69	0.59074	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.408988	0.27298	N	0.020013	T	0.00073	0.0002	L	0.46614	1.455	0.29936	P	0.821452	P;P;P	0.40602	0.723;0.723;0.536	B;B;B	0.37144	0.242;0.16;0.079	T	0.09487	-1.0672	9	0.54805	T	0.06	-9.4738	12.6904	0.56972	0.443:0.557:0.0:0.0	rs10010188;rs17571482;rs61257058;rs10010188	224;224;224	A0AVT1-4;A0AVT1-3;A0AVT1	.;.;UBA6_HUMAN	T	224	ENSP00000313454:A224T;ENSP00000399234:A224T	ENSP00000313454:A224T	A	-	1	0	UBA6	68216987	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	2.201000	0.42734	1.328000	0.45358	0.655000	0.94253	GCA	C|0.849;T|0.151	0.151	strong		0.299	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	Missense_Mutation
ERO1LB	56605	hgsc.bcm.edu	37	1	236381825	236381825	+	Missense_Mutation	SNP	G	G	C	rs1055851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:236381825G>C	ENST00000354619.5	-	16	1596	c.1395C>G	c.(1393-1395)caC>caG	p.H465Q	GPR137B_ENST00000477559.1_Intron	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	465			H -> Q (in dbSNP:rs1055851). {ECO:0000269|PubMed:10818100}.		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)	ATTACCTACTGTGTTGTAATA	0.323													G|||	2851	0.569289	0.4803	0.5821	5008	,	,		15123	0.8839		0.4006	False		,,,				2504	0.5297				p.H465Q		Atlas-SNP	.											.	ERO1LB	48	.	0			c.C1395G						PASS	.	G	GLN/HIS	2147,2251	560.0+/-380.4	511,1125,563	57.0	63.0	61.0		1395	4.6	1.0	1	dbSNP_86	61	3443,5119	496.6+/-374.3	679,2085,1517	yes	missense	ERO1LB	NM_019891.3	24	1190,3210,2080	CC,CG,GG		40.2126,48.8176,43.1327	benign	465/468	236381825	5590,7370	2199	4281	6480	SO:0001583	missense	56605	exon16			CCTACTGTGTTGT	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.1395C>G	1.37:g.236381825G>C	ENSP00000346635:p.His465Gln	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	227	101	0.444934	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	37	CCDS31064.1	1234	0.565018315018315	229	0.4654471544715447	209	0.5773480662983426	509	0.8898601398601399	287	0.3786279683377309	G	9.953	1.220760	0.22457	0.488176	0.402126	ENSG00000086619	ENST00000354619	T	0.29397	1.57	5.54	4.62	0.57501	.	0.301526	0.36932	N	0.002322	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.9999999999999994	B	0.06786	0.001	B	0.04013	0.001	T	0.37731	-0.9693	9	0.21014	T	0.42	-19.4628	10.5749	0.45221	0.0766:0.169:0.7544:0.0	rs1055851;rs1749597;rs3196339;rs10317930;rs12735870;rs52808904;rs1055851	465	Q86YB8	ERO1B_HUMAN	Q	465	ENSP00000346635:H465Q	ENSP00000346635:H465Q	H	-	3	2	ERO1LB	234448448	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.371000	0.20450	2.600000	0.87896	0.650000	0.86243	CAC	G|0.530;C|0.470	0.470	strong		0.323	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891	
DNPEP	23549	hgsc.bcm.edu	37	2	220250769	220250769	+	Missense_Mutation	SNP	T	T	C	rs6742404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220250769T>C	ENST00000273075.4	-	6	731	c.511A>G	c.(511-513)Att>Gtt	p.I171V	DNPEP_ENST00000523282.1_Missense_Mutation_p.I179V|AC053503.4_ENST00000420563.1_RNA|DNPEP_ENST00000373972.1_Missense_Mutation_p.I96V	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	161					peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATGCGAAGAATGGGCCGCTCC	0.627													T|||	134	0.0267572	0.0961	0.0101	5008	,	,		19551	0.0		0.0	False		,,,				2504	0.0				p.I171V		Atlas-SNP	.											.	DNPEP	40	.	0			c.A511G						PASS	.	T	VAL/ILE	385,3907		26,333,1787	83.0	94.0	90.0		511	3.7	1.0	2	dbSNP_116	90	1,8519		0,1,4259	yes	missense	DNPEP	NM_012100.2	29	26,334,6046	CC,CT,TT		0.0117,8.9702,3.0128	benign	171/486	220250769	386,12426	2146	4260	6406	SO:0001583	missense	23549	exon6			GAAGAATGGGCCG		CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.511A>G	2.37:g.220250769T>C	ENSP00000273075:p.Ile171Val	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	210	111	0.528571	NM_012100	Q9BW44|Q9NUV5	Missense_Mutation	SNP	ENST00000273075.4	37	CCDS42823.1	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	T	12.99	2.104829	0.37145	0.089702	1.17E-4	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000373972;ENST00000523282;ENST00000535056;ENST00000457935;ENST00000429013;ENST00000521459;ENST00000322176;ENST00000434339;ENST00000430206	.	.	.	4.87	3.71	0.42584	Peptidase M18, domain 2 (1);	0.138463	0.51477	D	0.000095	T	0.03477	0.0100	L	0.46614	1.455	0.49798	D	0.999821	B;B;B;B;B	0.21606	0.005;0.058;0.033;0.005;0.002	B;B;B;B;B	0.24269	0.033;0.052;0.052;0.015;0.02	T	0.04017	-1.0984	9	0.49607	T	0.09	-6.0541	10.134	0.42695	0.0:0.0791:0.0:0.9209	rs6742404	179;171;179;161;171	E7ETB3;B7Z822;B7Z7F0;Q9ULA0;Q53SB6	.;.;.;DNPEP_HUMAN;.	V	171;171;96;179;64;179;157;171;171;96;96	.	ENSP00000273075:I171V	I	-	1	0	DNPEP	219959013	0.580000	0.26733	0.998000	0.56505	0.850000	0.48378	0.182000	0.16900	0.718000	0.32166	0.459000	0.35465	ATT	T|0.962;C|0.038	0.038	strong		0.627	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100	
KAT7	11143	hgsc.bcm.edu	37	17	47895271	47895271	+	Silent	SNP	T	T	C	rs17853073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:47895271T>C	ENST00000259021.4	+	9	1333	c.1053T>C	c.(1051-1053)taT>taC	p.Y351Y	KAT7_ENST00000435742.2_Silent_p.Y165Y|KAT7_ENST00000503935.2_Silent_p.Y195Y|KAT7_ENST00000513980.1_Intron|KAT7_ENST00000454930.2_Silent_p.Y212Y|KAT7_ENST00000509773.1_Silent_p.Y241Y|KAT7_ENST00000510819.1_Silent_p.Y182Y|KAT7_ENST00000424009.2_Silent_p.Y321Y	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	351	MYST-type HAT.				chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										ATACCTGGTATCATTCTCCAT	0.433													C|||	211	0.0421326	0.1528	0.0086	5008	,	,		22669	0.0		0.002	False		,,,				2504	0.001				p.Y351Y		Atlas-SNP	.											.	.	.	.	0			c.T1053C						PASS	.	C	,,,,	522,3884	778.0+/-414.3	31,460,1712	92.0	87.0	88.0		963,636,723,546,1053	2.9	1.0	17	dbSNP_123	88	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KAT7	NM_001199155.1,NM_001199156.1,NM_001199157.1,NM_001199158.1,NM_007067.4	,,,,	31,462,6010	CC,CT,TT		0.0233,11.8475,4.0289	,,,,	321/582,212/473,241/502,182/443,351/612	47895271	524,12482	2203	4300	6503	SO:0001819	synonymous_variant	11143	exon9			CTGGTATCATTCT	AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"""	17016	protein-coding gene	gene with protein product	"""histone acetyltransferase binding to ORC1"""	609880	"""MYST histone acetyltransferase 2"""	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.1053T>C	17.37:g.47895271T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	174	91	0.522988	NM_007067	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Silent	SNP	ENST00000259021.4	37	CCDS11554.1																																																																																			T|0.965;C|0.035	0.035	strong		0.433	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067	
TAS2R50	259296	hgsc.bcm.edu	37	12	11139305	11139305	+	Missense_Mutation	SNP	G	G	A	rs142843602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11139305G>A	ENST00000506868.1	-	1	206	c.155C>T	c.(154-156)gCg>gTg	p.A52V	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	52					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						TCTGGAGACCGCCAGAGCAGT	0.378													G|||	27	0.00539137	0.0	0.0	5008	,	,		17272	0.0258		0.0	False		,,,				2504	0.001				p.A52V		Atlas-SNP	.											.	TAS2R50	37	.	0			c.C155T						PASS	.	G	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	76.0	85.0	82.0		155	1.2	0.0	12	dbSNP_134	82	0,8600		0,0,4300	yes	missense	TAS2R50	NM_176890.2	64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	52/300	11139305	1,13005	2203	4300	6503	SO:0001583	missense	259296	exon1			GAGACCGCCAGAG	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.155C>T	12.37:g.11139305G>A	ENSP00000424040:p.Ala52Val	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	199	93	0.467337	NM_176890	P59545|Q2M255|Q645Y0	Missense_Mutation	SNP	ENST00000506868.1	37	CCDS8638.1	15	0.006868131868131868	0	0.0	0	0.0	15	0.026223776223776224	0	0.0	G	12.99	2.104800	0.37145	2.27E-4	0.0	ENSG00000212126	ENST00000506868	T	0.56275	0.47	2.19	1.24	0.21308	.	0.218955	0.26646	U	0.023231	T	0.27063	0.0663	L	0.58510	1.815	0.09310	N	1	D	0.58620	0.983	P	0.51742	0.678	T	0.22730	-1.0208	10	0.49607	T	0.09	.	4.5161	0.11935	0.0:0.2513:0.4926:0.2561	.	52	P59544	T2R50_HUMAN	V	52	ENSP00000424040:A52V	ENSP00000424040:A52V	A	-	2	0	TAS2R50	11030572	0.000000	0.05858	0.002000	0.10522	0.139000	0.21198	-0.343000	0.07791	0.232000	0.21100	0.313000	0.20887	GCG	G|0.993;A|0.007	0.007	strong		0.378	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890	
FLG	2312	hgsc.bcm.edu	37	1	152275559	152275559	+	Missense_Mutation	SNP	A	A	G	rs3126065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152275559A>G	ENST00000368799.1	-	3	11838	c.11803T>C	c.(11803-11805)Tca>Cca	p.S3935P	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3935	Ser-rich.		S -> P (in dbSNP:rs3126065).		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)			GAATCTTGTGAAAGACTACTA	0.468									Ichthyosis				A|||	548	0.109425	0.3979	0.0303	5008	,	,		22781	0.0		0.001	False		,,,				2504	0.0				p.S3935P		Atlas-SNP	.											.	FLG	900	.	0			c.T11803C						PASS	.	A	PRO/SER	1446,2960	468.3+/-355.1	228,990,985	138.0	133.0	135.0		11803	-0.9	0.0	1	dbSNP_103	135	14,8586	9.8+/-36.6	0,14,4286	yes	missense	FLG	NM_002016.1	74	228,1004,5271	GG,GA,AA		0.1628,32.8189,11.2256	probably-damaging	3935/4062	152275559	1460,11546	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTTGTGAAAGACT	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.11803T>C	1.37:g.152275559A>G	ENSP00000357789:p.Ser3935Pro	Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	185	0.08470695970695971	174	0.35365853658536583	11	0.03038674033149171	0	0.0	0	0.0	A	4.914	0.169897	0.09339	0.328189	0.001628	ENSG00000143631	ENST00000368799	T	0.03772	3.81	2.35	-0.929	0.10444	.	.	.	.	.	T	0.01661	0.0053	L	0.52573	1.65	0.80722	P	0.0	D	0.53885	0.963	B	0.44108	0.441	T	0.39461	-0.9613	8	0.46703	T	0.11	.	1.6209	0.02713	0.4417:0.0:0.2748:0.2835	rs3126065;rs3126065	3935	P20930	FILA_HUMAN	P	3935	ENSP00000357789:S3935P	ENSP00000357789:S3935P	S	-	1	0	FLG	150542183	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.627000	0.05521	-0.321000	0.08627	0.533000	0.62120	TCA	A|0.871;G|0.129	0.129	strong		0.468	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
C19orf10	56005	hgsc.bcm.edu	37	19	4658047	4658047	+	Silent	SNP	A	A	G	rs12683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4658047A>G	ENST00000262947.3	-	6	527	c.492T>C	c.(490-492)atT>atC	p.I164I	AC005339.2_ENST00000598070.1_RNA	NM_019107.3	NP_061980.1	Q969H8	CS010_HUMAN	chromosome 19 open reading frame 10	164					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)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)		p.I164I(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.015)		CCTTGGCCACAATCACCAGCT	0.562													A|||	830	0.165735	0.4357	0.0375	5008	,	,		17774	0.1369		0.0318	False		,,,				2504	0.0593				p.I164I		Atlas-SNP	.											C19orf10,NS,lymphoid_neoplasm,0,1	C19orf10	9	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.T492C						PASS	.	A		1660,2746	481.9+/-359.3	305,1050,848	54.0	48.0	50.0		492	-7.4	1.0	19	dbSNP_52	50	194,8406	82.3+/-144.9	2,190,4108	no	coding-synonymous	C19orf10	NM_019107.3		307,1240,4956	GG,GA,AA		2.2558,37.6759,14.255		164/174	4658047	1854,11152	2203	4300	6503	SO:0001819	synonymous_variant	56005	exon6			GGCCACAATCACC	AF282264	CCDS12133.1	19p13.3	2013-11-27	2003-06-25	2003-06-27	ENSG00000074842	ENSG00000074842			16948	protein-coding gene	gene with protein product		606746	"""interleukin 27 working designation"""	IL27, IL27w		17362502, 21128247	Standard	NM_019107		Approved	R33729_1, IL25, SF20, IL-25, IL-27	uc002may.3	Q969H8		ENST00000262947.3:c.492T>C	19.37:g.4658047A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_019107	D6W628|O75256|O75272|Q9BTK7|Q9NP69	Silent	SNP	ENST00000262947.3	37	CCDS12133.1																																																																																			T|0.000;G|0.142;N|0.001;A|0.857	0.142	strong		0.562	C19orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458937.1	NM_019107	
ZNF577	84765	hgsc.bcm.edu	37	19	52376119	52376119	+	Missense_Mutation	SNP	G	G	A	rs10407911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52376119G>A	ENST00000301399.5	-	7	1489	c.1124C>T	c.(1123-1125)aCt>aTt	p.T375I	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.T316I|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000451628.2_Missense_Mutation_p.T316I	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	375			T -> I (in dbSNP:rs10407911).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TCTTATGTGAGTTTTCTCATG	0.438													G|||	781	0.15595	0.2436	0.1354	5008	,	,		19775	0.0427		0.0358	False		,,,				2504	0.2924				p.T375I		Atlas-SNP	.											.	ZNF577	63	.	0			c.C1124T						PASS	.	G	ILE/THR,ILE/THR	899,3507		97,705,1401	91.0	97.0	95.0		947,1124	-1.5	0.0	19	dbSNP_119	95	162,8438		1,160,4139	yes	missense,missense	ZNF577	NM_001135590.1,NM_032679.2	89,89	98,865,5540	AA,AG,GG		1.8837,20.404,8.1578	benign,benign	316/427,375/486	52376119	1061,11945	2203	4300	6503	SO:0001583	missense	84765	exon7			ATGTGAGTTTTCT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1124C>T	19.37:g.52376119G>A	ENSP00000301399:p.Thr375Ile	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	117	47	0.401709	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	37	CCDS12842.2	202	0.0924908424908425	103	0.20934959349593496	47	0.1298342541436464	25	0.043706293706293704	27	0.03562005277044855	.	0.003	-2.529336	0.00147	0.20404	0.018837	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.06142	3.34;3.34;3.34;3.34	3.06	-1.48	0.08745	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.25647	0.755	0.47341	P	6.009999999999627E-4	B;B	0.16166	0.016;0.005	B;B	0.10450	0.003;0.005	T	0.45789	-0.9237	8	0.02654	T	1	.	8.2631	0.31797	0.4153:0.0:0.5847:0.0	rs10407911;rs10407911	375;316	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	I	375;316;316;375	ENSP00000301399:T375I;ENSP00000413476:T316I;ENSP00000389652:T316I;ENSP00000404509:T375I	ENSP00000301399:T375I	T	-	2	0	ZNF577	57067931	0.000000	0.05858	0.002000	0.10522	0.272000	0.26649	-0.348000	0.07740	-0.115000	0.11915	-0.742000	0.03525	ACT	G|0.909;A|0.091	0.091	strong		0.438	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
LILRB4	11006	hgsc.bcm.edu	37	19	55178162	55178162	+	Missense_Mutation	SNP	A	A	G	rs11574576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55178162A>G	ENST00000391736.1	+	12	1318	c.1003A>G	c.(1003-1005)Aac>Gac	p.N335D	LILRB4_ENST00000270452.2_Missense_Mutation_p.N335D|LILRB4_ENST00000391733.3_Missense_Mutation_p.N336D|LILRB4_ENST00000391734.3_Missense_Mutation_p.N335D|LILRB4_ENST00000430952.2_Missense_Mutation_p.N335D	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	335			N -> D (in dbSNP:rs11574576).		immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		TGCCGTGAAGAACACACAGCC	0.612													A|||	2247	0.448682	0.4395	0.3429	5008	,	,		17280	0.5615		0.2903	False		,,,				2504	0.5828				p.N335D		Atlas-SNP	.											.	LILRB4	86	.	0			c.A1003G						PASS	.	A	ASP/ASN,ASP/ASN	1749,2657	521.1+/-370.4	367,1015,821	125.0	113.0	117.0		1003,1003	-3.5	0.0	19	dbSNP_120	117	2451,6149	405.5+/-348.5	339,1773,2188	yes	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	23,23	706,2788,3009	GG,GA,AA		28.5,39.6959,32.2928	benign,benign	335/448,335/449	55178162	4200,8806	2203	4300	6503	SO:0001583	missense	11006	exon10			GTGAAGAACACAC	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1003A>G	19.37:g.55178162A>G	ENSP00000375616:p.Asn335Asp	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	233	111	0.476395	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	895	0.4097985347985348	215	0.4369918699186992	111	0.30662983425414364	337	0.5891608391608392	232	0.30606860158311344	A	0.007	-2.003554	0.00431	0.396959	0.285	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00454	7.33;7.33;7.34;7.32;7.35;7.36	1.9	-3.45	0.04781	.	.	.	.	.	T	0.00012	0.0000	N	0.00332	-1.63	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.001;0.0	T	0.24476	-1.0159	8	0.02654	T	1	.	6.5292	0.22318	0.6493:0.0:0.3507:0.0	rs11574576;rs13343440;rs52815740;rs59068627;rs11574576	335;334;336;335;335	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;.;LIRB4_HUMAN	D	335;335;335;335;336;334	ENSP00000375616:N335D;ENSP00000270452:N335D;ENSP00000408995:N335D;ENSP00000375614:N335D;ENSP00000375613:N336D;ENSP00000401962:N334D	ENSP00000270452:N335D	N	+	1	0	LILRB4	59869974	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	0.001000	0.13038	-0.842000	0.04195	-0.330000	0.08379	AAC	A|0.646;C|0.000;G|0.354	0.354	strong		0.612	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24256389	24256389	+	Silent	SNP	A	A	T	rs7001097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24256389A>T	ENST00000256412.4	+	9	985	c.765A>T	c.(763-765)atA>atT	p.I255I	ADAMDEC1_ENST00000538205.1_Silent_p.I176I|ADAMDEC1_ENST00000522298.1_Silent_p.I176I|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	255	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TTCCACAGATATATAACACCA	0.413													T|||	88	0.0175719	0.0635	0.0058	5008	,	,		20707	0.0		0.0	False		,,,				2504	0.0				p.I255I	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.A765T						PASS	.	T	,,	261,4145	803.2+/-415.7	11,239,1953	92.0	91.0	91.0		528,528,765	0.2	0.9	8	dbSNP_116	91	2,8598	818.9+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	11,241,6251	TT,TA,AA		0.0233,5.9237,2.0221	,,	176/392,176/392,255/471	24256389	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon9			ACAGATATATAAC	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.765A>T	8.37:g.24256389A>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	113	51	0.451327	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			A|0.977;T|0.023	0.023	strong		0.413	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
SIRPA	140885	hgsc.bcm.edu	37	20	1896100	1896100	+	Splice_Site	SNP	C	C	T	rs6136375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1896100C>T	ENST00000358771.4	+	2	587	c.435C>T	c.(433-435)cgC>cgT	p.R145R	SIRPA_ENST00000400068.3_Splice_Site_p.R145R|SIRPA_ENST00000356025.3_Splice_Site_p.R145R	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	145					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		TGTCTGTGCGCGGTGAGTACA	0.542																																					p.R145R	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											.	SIRPA	83	.	0			c.C435T						PASS	.	T	,,	1297,3109	432.2+/-343.2	196,905,1102	101.0	90.0	93.0		435,435,435	-8.5	0.0	20	dbSNP_114	93	3231,5365	470.8+/-367.9	618,1995,1685	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SIRPA	NM_001040022.1,NM_001040023.1,NM_080792.2	,,	814,2900,2787	TT,TC,CC		37.5872,29.4371,34.8254	,,	145/505,145/505,145/505	1896100	4528,8474	2203	4298	6501	SO:0001630	splice_region_variant	140885	exon3			TGTGCGCGGTGAG	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.436+1C>T	20.37:g.1896100C>T		Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	209	48	0.229665	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Silent	SNP	ENST00000358771.4	37	CCDS13022.1																																																																																			C|0.633;T|0.367	0.367	strong		0.542	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	Silent
MFSD12	126321	hgsc.bcm.edu	37	19	3546340	3546340	+	Silent	SNP	G	G	A	rs11555328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3546340G>A	ENST00000355415.2	-	7	1276	c.1107C>T	c.(1105-1107)taC>taT	p.Y369Y	MFSD12_ENST00000591878.1_5'Flank|MFSD12_ENST00000398558.4_Silent_p.Y369Y|AC005786.7_ENST00000589360.1_RNA|MFSD12_ENST00000389395.3_Silent_p.Y369Y	NM_174983.3	NP_778148.2	Q6NUT3	MFS12_HUMAN	major facilitator superfamily domain containing 12	369					transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				cervix(1)|endometrium(2)|lung(4)|urinary_tract(2)	9						CAGCCGCTGCGTACACGGCCA	0.677													G|||	924	0.184505	0.3737	0.1326	5008	,	,		14365	0.0129		0.1491	False		,,,				2504	0.1789				p.Y369Y		Atlas-SNP	.											.	MFSD12	22	.	0			c.C1107T						PASS	.	G	,,	1320,3020		213,894,1063	22.0	30.0	28.0		1107,1107,1107	-5.5	0.0	19	dbSNP_120	28	1381,7147		115,1151,2998	no	coding-synonymous,coding-synonymous,coding-synonymous	C19orf28	NM_001042680.1,NM_021731.2,NM_174983.3	,,	328,2045,4061	AA,AG,GG		16.1937,30.4147,20.9901	,,	369/474,369/539,369/481	3546340	2701,10167	2170	4264	6434	SO:0001819	synonymous_variant	126321	exon7			CGCTGCGTACACG	AF218008	CCDS42465.1, CCDS74256.1	19p13.3	2012-03-09	2011-11-24	2011-11-24	ENSG00000161091	ENSG00000161091			28299	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 28"""	C19orf28		12477932	Standard	NM_174983		Approved	MGC20700, PP3501	uc002lxw.3	Q6NUT3		ENST00000355415.2:c.1107C>T	19.37:g.3546340G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	172	69	0.401163	NM_001042680	A8MXP7|D6W615|E9PAJ8|Q8N459	Silent	SNP	ENST00000355415.2	37	CCDS42465.1																																																																																			G|0.834;A|0.166	0.166	strong		0.677	MFSD12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452949.2	NM_174983	
DLG5	9231	hgsc.bcm.edu	37	10	79556305	79556305	+	Missense_Mutation	SNP	C	C	T	rs74140334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79556305C>T	ENST00000372391.2	-	28	5217	c.5212G>A	c.(5212-5214)Gct>Act	p.A1738T	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Missense_Mutation_p.A1398T	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1738	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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)			GGCCTCAGAGCGGTGCAGTCC	0.597													C|||	70	0.0139776	0.0514	0.0014	5008	,	,		19795	0.0		0.001	False		,,,				2504	0.0				p.A1738T		Atlas-SNP	.											.	DLG5	154	.	0			c.G5212A						PASS	.	C	THR/ALA	164,4242	110.4+/-148.6	2,160,2041	100.0	85.0	90.0		5212	2.4	0.1	10	dbSNP_130	90	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DLG5	NM_004747.3	58	2,162,6339	TT,TC,CC		0.0233,3.7222,1.2763	benign	1738/1920	79556305	166,12840	2203	4300	6503	SO:0001583	missense	9231	exon28			TCAGAGCGGTGCA	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.5212G>A	10.37:g.79556305C>T	ENSP00000361467:p.Ala1738Thr	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	210	96	0.457143	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	37	CCDS7353.2	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	6.638	0.486271	0.12641	0.037222	2.33E-4	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.16457	2.34;2.34;2.34	5.97	2.38	0.29361	Guanylate kinase/L-type calcium channel (1);	0.200014	0.25233	N	0.032160	T	0.00552	0.0018	N	0.03608	-0.345	0.29378	N	0.863515	B;B	0.27882	0.0;0.192	B;B	0.21360	0.0;0.034	T	0.39333	-0.9619	10	0.02654	T	1	.	8.5372	0.33371	0.6271:0.2508:0.0:0.1221	.	1738;1398	Q8TDM6;Q8TDM6-2	DLG5_HUMAN;.	T	1738;699;1398	ENSP00000361467:A1738T;ENSP00000394797:A699T;ENSP00000361464:A1398T	ENSP00000361464:A1398T	A	-	1	0	DLG5	79226311	0.996000	0.38824	0.059000	0.19551	0.082000	0.17680	3.446000	0.52928	0.153000	0.19213	-0.262000	0.10625	GCT	C|0.988;T|0.012	0.012	strong		0.597	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
PIWIL4	143689	hgsc.bcm.edu	37	11	94320300	94320300	+	Silent	SNP	C	C	T	rs145516372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94320300C>T	ENST00000299001.6	+	7	1012	c.801C>T	c.(799-801)gtC>gtT	p.V267V	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	267					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GTTACAAAGTCCTCCGGAATG	0.433													C|||	51	0.0101837	0.0371	0.0029	5008	,	,		18230	0.0		0.0	False		,,,				2504	0.0				p.V267V		Atlas-SNP	.											.	PIWIL4	70	.	0			c.C801T						PASS	.	C		116,4286	88.7+/-127.4	2,112,2087	188.0	191.0	190.0		801	1.8	0.9	11	dbSNP_134	190	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	PIWIL4	NM_152431.2		2,113,6384	TT,TC,CC		0.0116,2.6352,0.9001		267/853	94320300	117,12881	2201	4298	6499	SO:0001819	synonymous_variant	143689	exon7			CAAAGTCCTCCGG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.801C>T	11.37:g.94320300C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	124	47	0.379032	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			C|0.992;T|0.008	0.008	strong		0.433	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
ALDH1A1	216	hgsc.bcm.edu	37	9	75545882	75545882	+	Silent	SNP	G	G	A	rs13959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:75545882G>A	ENST00000297785.3	-	3	279	c.225C>T	c.(223-225)tcC>tcT	p.S75S	ALDH1A1_ENST00000482210.1_5'UTR|ALDH1A1_ENST00000376939.1_Silent_p.S75S	NM_000689.4	NP_000680.2	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1 family, member A1	75					cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|positive regulation of Ras GTPase activity (GO:0032320)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|androgen binding (GO:0005497)|Ras GTPase activator activity (GO:0005099)|retinal dehydrogenase activity (GO:0001758)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)	17					Tretinoin(DB00755)|Vitamin A(DB00162)	TACGCCACGGGGATCCAATCT	0.468													A|||	2050	0.409345	0.1664	0.4885	5008	,	,		18441	0.4554		0.503	False		,,,				2504	0.5378				p.S75S		Atlas-SNP	.											.	ALDH1A1	98	.	0			c.C225T						PASS	.	A		1101,3305	720.0+/-409.0	128,845,1230	84.0	87.0	86.0		225	-1.8	1.0	9	dbSNP_52	86	4295,4305	578.0+/-390.7	1051,2193,1056	no	coding-synonymous	ALDH1A1	NM_000689.4		1179,3038,2286	AA,AG,GG		49.9419,24.9887,41.4885		75/502	75545882	5396,7610	2203	4300	6503	SO:0001819	synonymous_variant	216	exon3			CCACGGGGATCCA	K03000	CCDS6644.1	9q21.13	2010-08-05			ENSG00000165092	ENSG00000165092	1.2.1.36, 1.2.1.3	"""Aldehyde dehydrogenases"""	402	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 1"""	100640		PUMB1, ALDH1		1709013	Standard	NM_000689		Approved	RALDH1	uc004ajd.3	P00352	OTTHUMG00000020019	ENST00000297785.3:c.225C>T	9.37:g.75545882G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	106	38	0.358491	NM_000689	O00768|Q5SYR1	Silent	SNP	ENST00000297785.3	37	CCDS6644.1																																																																																			G|0.598;A|0.402	0.402	strong		0.468	ALDH1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052679.1		
BPIFA3	128861	hgsc.bcm.edu	37	20	31812949	31812949	+	Silent	SNP	C	C	T	rs147632261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31812949C>T	ENST00000375454.3	+	4	642	c.432C>T	c.(430-432)atC>atT	p.I144I	BPIFA3_ENST00000490499.1_3'UTR|BPIFA3_ENST00000375452.3_Silent_p.I108I	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	144						extracellular region (GO:0005576)	lipid binding (GO:0008289)										ATATGAGCATCGTTGTGGAGT	0.522													C|||	24	0.00479233	0.0136	0.0029	5008	,	,		22489	0.0		0.004	False		,,,				2504	0.0				p.I144I		Atlas-SNP	.											.	.	.	.	0			c.C432T						PASS	.	C	,	54,4352	52.9+/-88.7	0,54,2149	205.0	196.0	199.0		324,432	2.5	0.1	20	dbSNP_134	199	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous,coding-synonymous	BPIFA3	NM_001042439.1,NM_178466.3	,	0,64,6439	TT,TC,CC		0.1163,1.2256,0.4921	,	108/219,144/255	31812949	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	128861	exon4			GAGCATCGTTGTG		CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"""BPI fold containing"""	16204	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 71"""	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.432C>T	20.37:g.31812949C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	162	84	0.518519	NM_178466	Q5JWG8|Q6NZ38	Silent	SNP	ENST00000375454.3	37	CCDS13216.2																																																																																			C|0.995;T|0.005	0.005	strong		0.522	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466	
MDC1	9656	hgsc.bcm.edu	37	6	30673489	30673489	+	Silent	SNP	G	G	C	rs9295905	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30673489G>C	ENST00000376406.3	-	10	4118	c.3471C>G	c.(3469-3471)acC>acG	p.T1157T	MDC1_ENST00000376405.2_Silent_p.T893T|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1157	Interaction with the PRKDC complex.|Pro-rich.			Missing (in Ref. 2; CAH18685). {ECO:0000305}.	DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						CTGGTTCAGGGGTCTTGACAG	0.602								Other conserved DNA damage response genes					G|||	316	0.063099	0.1324	0.0504	5008	,	,		18792	0.0635		0.0189	False		,,,				2504	0.0235				p.T1157T		Atlas-SNP	.											.	MDC1	218	.	0			c.C3471G						PASS	.	G		495,3911	232.3+/-245.9	36,423,1744	167.0	181.0	176.0		3471	-1.2	0.0	6	dbSNP_119	176	140,8460	69.0+/-131.5	2,136,4162	no	coding-synonymous	MDC1	NM_014641.2		38,559,5906	CC,CG,GG		1.6279,11.2347,4.8824		1157/2090	30673489	635,12371	2203	4300	6503	SO:0001819	synonymous_variant	9656	exon10			TTCAGGGGTCTTG	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.3471C>G	6.37:g.30673489G>C		Somatic	359	0	0		WXS	Illumina HiSeq	Phase_I	401	211	0.526185	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	37	CCDS34384.1	142	0.06501831501831502	63	0.12804878048780488	19	0.052486187845303865	49	0.08566433566433566	11	0.014511873350923483	G	6.445	0.450240	0.12223	0.112347	0.016279	ENSG00000137337	ENST00000417033	.	.	.	4.01	-1.23	0.09465	.	.	.	.	.	T	0.11196	0.0273	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.26155	-1.0111	3	.	.	.	-1.07	3.6257	0.08112	0.4055:0.0:0.4247:0.1698	rs9295905	.	.	.	A	218	.	.	P	-	1	0	MDC1	30781468	0.000000	0.05858	0.000000	0.03702	0.370000	0.29829	-0.722000	0.04958	-0.385000	0.07833	0.478000	0.44815	CCC	G|0.944;C|0.056	0.056	strong		0.602	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
SPANXN3	139067	hgsc.bcm.edu	37	X	142596941	142596941	+	Missense_Mutation	SNP	C	C	G	rs6654212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:142596941C>G	ENST00000370503.2	-	2	212	c.129G>C	c.(127-129)aaG>aaC	p.K43N	GS1-256O22.5_ENST00000431432.1_RNA	NM_001009609.2	NP_001009609.1	Q5MJ09	SPXN3_HUMAN	SPANX family, member N3	43			K -> N (in dbSNP:rs6654212). {ECO:0000269|PubMed:16251457}.							endometrium(1)|large_intestine(1)|lung(9)|ovary(2)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;6.56e-05)					ATGTTTTTGTCTTCTTCAAAC	0.378													c|||	544	0.144106	0.1831	0.0591	3775	,	,		15102	0.0476		0.0895	False		,,,				2504	0.1258				p.K43N		Atlas-SNP	.											.	SPANXN3	49	.	0			c.G129C						PASS	.	C	ASN/LYS	792,3043		71,529,121,1032,450	105.0	95.0	98.0		129	-5.3	0.0	X	dbSNP_116	98	731,5997		31,468,201,1929,1671	yes	missense	SPANXN3	NM_001009609.2	94	102,997,322,2961,2121	GG,GC,G,CC,C		10.865,20.6519,14.4183	possibly-damaging	43/142	142596941	1523,9040	2203	4300	6503	SO:0001583	missense	139067	exon2			TTTTGTCTTCTTC		CCDS35418.1	Xq27.3	2012-06-12			ENSG00000189252	ENSG00000189252			33176	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 8"""	300666				14973187, 17012309	Standard	NM_001009609		Approved	SPANX-N3, CT11.8	uc004fbw.3	Q5MJ09	OTTHUMG00000022582	ENST00000370503.2:c.129G>C	X.37:g.142596941C>G	ENSP00000359534:p.Lys43Asn	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_001009609	Q0ZNK4	Missense_Mutation	SNP	ENST00000370503.2	37	CCDS35418.1	207	0.12477396021699819	71	0.16435185185185186	14	0.040229885057471264	12	0.022058823529411766	45	0.06164383561643835	c	7.133	0.580348	0.13686	0.206519	0.10865	ENSG00000189252	ENST00000370503	T	0.15372	2.43	3.04	-5.31	0.02730	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B	0.18863	0.031	B	0.19666	0.026	T	0.37888	-0.9686	8	0.56958	D	0.05	.	4.8777	0.13664	0.157:0.4963:0.0:0.3467	rs6654212;rs52789445;rs6654212	43	Q5MJ09	SPXN3_HUMAN	N	43	ENSP00000359534:K43N	ENSP00000359534:K43N	K	-	3	2	SPANXN3	142424607	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.570000	0.05895	-1.453000	0.01928	-0.207000	0.12724	AAG	C|0.847;0|0.012	.	strong		0.378	SPANXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058620.2	NM_001009609	
MUC4	4585	hgsc.bcm.edu	37	3	195511486	195511486	+	Missense_Mutation	SNP	G	G	T	rs71180962|rs202186297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511486G>T	ENST00000463781.3	-	2	7424	c.6965C>A	c.(6964-6966)cCt>cAt	p.P2322H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2322H	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	0.592																																					p.P2322H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C6965A						scavenged	.						6.0	6.0	6.0					3																	195511486		588	1429	2017	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.6965C>A	3.37:g.195511486G>T	ENSP00000417498:p.Pro2322His	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	113	26	0.230089	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	5.604	0.296160	0.10622	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33654	1.4;1.41	.	.	.	.	0.000000	0.25881	U	0.027698	T	0.14527	0.0351	N	0.08118	0	0.20489	N	0.999896	B	0.22909	0.077	B	0.11329	0.006	T	0.21518	-1.0243	8	.	.	.	.	6.7067	0.23254	2.0E-4:0.0:0.9998:0.0	.	2322	E7ESK3	.	H	2322	ENSP00000417498:P2322H;ENSP00000420243:P2322H	.	P	-	2	0	MUC4	196995881	0.000000	0.05858	0.002000	0.10522	0.095000	0.18619	-2.721000	0.00811	0.488000	0.27723	0.064000	0.15345	CCT	G|0.996;T|0.005	0.005	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF419	79744	hgsc.bcm.edu	37	19	58002859	58002859	+	Silent	SNP	T	T	C	rs62126198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58002859T>C	ENST00000221735.7	+	3	279	c.93T>C	c.(91-93)gaT>gaC	p.D31D	ZNF419_ENST00000442920.2_Silent_p.D18D|ZNF419_ENST00000520540.1_Silent_p.D19D|ZNF419_ENST00000354197.4_Silent_p.D19D|ZNF419_ENST00000518999.1_Silent_p.D32D|ZNF419_ENST00000426954.2_Silent_p.D19D|AC003005.4_ENST00000601674.1_Silent_p.D18D|ZNF419_ENST00000424930.2_Silent_p.D32D|ZNF419_ENST00000415379.2_Silent_p.D18D|ZNF419_ENST00000347466.6_Silent_p.D32D			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	31	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D32D(1)|p.D11D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		CCTTTGAGGATGTGGCTGTCT	0.498																																					p.D32D		Atlas-SNP	.											ZNF419_ENST00000284020,colon,carcinoma,0,2	ZNF419	134	2	2	Substitution - coding silent(2)	large_intestine(2)	c.T96C						scavenged	.						174.0	165.0	168.0					19																	58002859		2203	4300	6503	SO:0001819	synonymous_variant	79744	exon3			TGAGGATGTGGCT	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.93T>C	19.37:g.58002859T>C		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	312	23	0.073718	NM_001098494	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	37	CCDS54326.1																																																																																			T|0.996;C|0.004	0.004	strong		0.498	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	
OTOGL	283310	hgsc.bcm.edu	37	12	80747209	80747209	+	Missense_Mutation	SNP	C	C	G	rs7312569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:80747209C>G	ENST00000547103.1	+	45	5455	c.5449C>G	c.(5449-5451)Cta>Gta	p.L1817V	OTOGL_ENST00000458043.2_Missense_Mutation_p.L1829V|OTOGL_ENST00000546620.1_5'Flank			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1817					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						CTGTTTGAATCTAAGAGAAGA	0.458													C|||	868	0.173323	0.1846	0.2075	5008	,	,		16401	0.0575		0.1819	False		,,,				2504	0.2444				p.L1829V		Atlas-SNP	.											.	OTOGL	235	.	0			c.C5485G						PASS	.	C	VAL/LEU	688,3198		61,566,1316	72.0	69.0	70.0		5485	0.4	0.1	12	dbSNP_116	70	1621,6675		159,1303,2686	yes	missense	OTOGL	NM_173591.3	32	220,1869,4002	GG,GC,CC		19.5395,17.7046,18.9542		1829/2345	80747209	2309,9873	1943	4148	6091	SO:0001583	missense	283310	exon45			TTGAATCTAAGAG	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5449C>G	12.37:g.80747209C>G	ENSP00000447211:p.Leu1817Val	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	42	0.385321	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		327|327	0.14972527472527472|0.14972527472527472	86|86	0.17479674796747968|0.17479674796747968	75|75	0.20718232044198895|0.20718232044198895	30|30	0.05244755244755245|0.05244755244755245	136|136	0.17941952506596306|0.17941952506596306	C|C	5.903|5.903	0.350723|0.350723	0.11182|0.11182	0.177046|0.177046	0.195395|0.195395	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043	.|T;T	.|0.55052	.|0.54;0.54	5.74|5.74	0.452|0.452	0.16634|0.16634	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.45285|0.45285	1.41|1.41	0.54753|0.54753	P|P	1.799999999996249E-5|1.799999999996249E-5	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.10847|0.10847	-1.0612|-1.0612	4|6	.|0.31617	.|T	.|0.26	.|.	3.0832|3.0832	0.06269|0.06269	0.1146:0.1279:0.1196:0.6379|0.1146:0.1279:0.1196:0.6379	rs7312569;rs17249560;rs7312569|rs7312569;rs17249560;rs7312569	.|.	.|.	.|.	M|V	271|1817;1829	.|ENSP00000447211:L1817V;ENSP00000400895:L1829V	.|ENSP00000400895:L1829V	I|L	+|+	3|1	3|2	OTOGL|OTOGL	79271340|79271340	0.049000|0.049000	0.20398|0.20398	0.071000|0.071000	0.20095|0.20095	0.298000|0.298000	0.27526|0.27526	0.246000|0.246000	0.18160|0.18160	-0.156000|-0.156000	0.11079|0.11079	-0.294000|-0.294000	0.09567|0.09567	ATC|CTA	C|0.844;G|0.156	0.156	strong		0.458	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
OR8H3	390152	hgsc.bcm.edu	37	11	55889918	55889918	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55889918G>A	ENST00000313472.3	+	1	70	c.70G>A	c.(70-72)Gtc>Atc	p.V24I		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	24						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)					CTCTGAAGAGGTCCAGATGGC	0.453																																					p.V24I		Atlas-SNP	.											.	OR8H3	92	.	0			c.G70A						PASS	.						204.0	194.0	198.0					11																	55889918		2201	4296	6497	SO:0001583	missense	390152	exon1			GAAGAGGTCCAGA	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.70G>A	11.37:g.55889918G>A	ENSP00000323928:p.Val24Ile	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	231	18	0.0779221	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	G	1.503	-0.551434	0.03996	.	.	ENSG00000181761	ENST00000313472	T	0.01359	4.98	3.43	-6.36	0.01969	.	1.100610	0.06932	N	0.811320	T	0.00552	0.0018	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49504	-0.8933	10	0.54805	T	0.06	.	2.0752	0.03623	0.3689:0.211:0.3126:0.1075	.	24	Q8N146	OR8H3_HUMAN	I	24	ENSP00000323928:V24I	ENSP00000323928:V24I	V	+	1	0	OR8H3	55646494	0.000000	0.05858	0.104000	0.21259	0.032000	0.12392	-5.175000	0.00144	-0.849000	0.04158	-1.252000	0.01501	GTC	.	.	none		0.453	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45221404	45221404	+	Missense_Mutation	SNP	C	C	T	rs74393756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45221404C>T	ENST00000389774.2	+	8	761	c.620C>T	c.(619-621)cCg>cTg	p.P207L	ARHGAP8_ENST00000336963.4_Missense_Mutation_p.P176L|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.P386L|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.P386L|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.P176L|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.P307L|ARHGAP8_ENST00000389773.5_Missense_Mutation_p.P298L	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	207					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		GGCCGGACGCCGCCTCCCACC	0.647													c|||	92	0.0183706	0.0666	0.0043	5008	,	,		12937	0.0		0.0	False		,,,				2504	0.001				p.P298L		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C893T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	258,4146	146.1+/-180.8	6,246,1950	35.0	37.0	36.0		620,527,893,527	1.2	0.0	22	dbSNP_131	36	4,8594	3.7+/-12.6	0,4,4295	yes	missense,missense,missense,missense	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	98,98,98,98	6,250,6245	TT,TC,CC		0.0465,5.8583,2.0151	benign,benign,benign,benign	207/465,176/306,298/556,176/434	45221404	262,12740	2202	4299	6501	SO:0001583	missense	553158	exon10			GGACGCCGCCTCC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.620C>T	22.37:g.45221404C>T	ENSP00000374424:p.Pro207Leu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	185	83	0.448649	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	32|32	0.014652014652014652|0.014652014652014652	30|30	0.06097560975609756|0.06097560975609756	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	c|c	11.26|11.26	1.586905|1.586905	0.28268|0.28268	0.058583|0.058583	4.65E-4|4.65E-4	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484|ENSG00000248405	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000336963;ENST00000356099|ENST00000515632	T;T;T;T;T;T;T|.	0.60548|.	2.27;2.25;2.25;2.27;2.2;0.18;2.21|.	4.6|4.6	1.18|1.18	0.20946|0.20946	.|.	1.887620|.	0.03242|.	N|.	0.180497|.	T|T	0.07863|0.07863	0.0197|0.0197	M|M	0.67953|0.67953	2.075|2.075	0.09310|0.09310	N|N	0.999994|0.999994	B;B;P;B;B;B;B|.	0.48640|.	0.214;0.007;0.913;0.318;0.049;0.002;0.328|.	B;B;B;B;B;B;B|.	0.28553|.	0.018;0.002;0.091;0.018;0.004;0.001;0.011|.	T|T	0.07597|0.07597	-1.0764|-1.0764	10|5	0.52906|.	T|.	0.07|.	.|.	7.5251|7.5251	0.27650|0.27650	0.0:0.7049:0.0:0.2951|0.0:0.7049:0.0:0.2951	.|.	212;176;212;207;217;386;307|.	B7ZMA4;A6ZJ79;A2RU51;P85298;Q6PCC7;B1AHC4;B1AHC3|.	.;.;.;RHG08_HUMAN;.;.;.|.	L|C	307;386;386;298;207;176;176|230	ENSP00000354732:P307L;ENSP00000262731:P386L;ENSP00000429240:P386L;ENSP00000374423:P298L;ENSP00000374424:P207L;ENSP00000337287:P176L;ENSP00000348407:P176L|.	ENSP00000337287:P176L|.	P|R	+|+	2|1	0|0	PRR5-ARHGAP8;ARHGAP8|PRR5-ARHGAP8	43600068|43600068	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.734000|0.734000	0.26101|0.26101	0.120000|0.120000	0.18254|0.18254	-0.130000|-0.130000	0.14895|0.14895	CCG|CGC	C|0.978;T|0.022	0.022	strong		0.647	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
TAF2	6873	hgsc.bcm.edu	37	8	120793296	120793296	+	Silent	SNP	C	C	T	rs7002501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120793296C>T	ENST00000378164.2	-	17	2548	c.2250G>A	c.(2248-2250)caG>caA	p.Q750Q		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	750					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			ACTGTACCTTCTGTAGAAAAT	0.318													C|||	1318	0.263179	0.5106	0.1715	5008	,	,		16484	0.0407		0.2058	False		,,,				2504	0.2822				p.Q750Q		Atlas-SNP	.											.	TAF2	204	.	0			c.G2250A						PASS	.	C		2063,2343	561.5+/-380.7	476,1111,616	59.0	65.0	63.0		2250	1.3	1.0	8	dbSNP_116	63	2085,6515	357.5+/-330.8	229,1627,2444	no	coding-synonymous	TAF2	NM_003184.3		705,2738,3060	TT,TC,CC		24.2442,46.8225,31.893		750/1200	120793296	4148,8858	2203	4300	6503	SO:0001819	synonymous_variant	6873	exon17			TACCTTCTGTAGA	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2250G>A	8.37:g.120793296C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Silent	SNP	ENST00000378164.2	37	CCDS34937.1																																																																																			C|0.713;T|0.287	0.287	strong		0.318	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
PTX4	390667	hgsc.bcm.edu	37	16	1537706	1537706	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1537706C>T	ENST00000447419.2	-	2	432	c.407G>A	c.(406-408)cGg>cAg	p.R136Q	PTX4_ENST00000293922.1_Missense_Mutation_p.R131Q|PTX4_ENST00000440447.2_Intron			Q96A99	PTX4_HUMAN	pentraxin 4, long	136						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						TTCCCGGGCCCGCTGCTGGCT	0.701																																					p.R131Q		Atlas-SNP	.											.	PTX4	46	.	0			c.G392A						PASS	.						25.0	30.0	29.0					16																	1537706		2196	4288	6484	SO:0001583	missense	390667	exon2			CGGGCCCGCTGCT		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.407G>A	16.37:g.1537706C>T	ENSP00000445277:p.Arg136Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		.	.	.	.	.	.	.	.	.	.	C	7.483	0.649068	0.14516	.	.	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.04809	3.7;3.55	4.93	-9.57	0.00562	.	4.517250	0.00481	N	0.000132	T	0.02047	0.0064	N	0.04018	-0.295	0.09310	N	1	B	0.15719	0.014	B	0.04013	0.001	T	0.36817	-0.9732	10	0.21014	T	0.42	.	6.6714	0.23070	0.1895:0.3178:0.0:0.4926	.	131	Q96A99-2	.	Q	136;131	ENSP00000445277:R136Q;ENSP00000293922:R131Q	ENSP00000293922:R131Q	R	-	2	0	PTX4	1477707	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.508000	0.02266	-2.491000	0.00516	-1.170000	0.01741	CGG	.	.	none		0.701	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
OR2A7	401427	hgsc.bcm.edu	37	7	143956461	143956461	+	Silent	SNP	T	T	C	rs199974780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143956461T>C	ENST00000493325.1	-	1	354	c.261A>G	c.(259-261)ccA>ccG	p.P87P	RP4-545C24.1_ENST00000460955.1_RNA|OR2A1-AS1_ENST00000478806.1_RNA|ARHGEF35_ENST00000543357.1_Intron|OR2A1-AS1_ENST00000463561.1_RNA|OR2A1-AS1_ENST00000487102.1_RNA|OR2A1-AS1_ENST00000476560.1_RNA|OR2A1-AS1_ENST00000461843.1_RNA|OR2A1-AS1_ENST00000489488.1_RNA	NM_001005328.1	NP_001005328.1	Q96R45	OR2A7_HUMAN	olfactory receptor, family 2, subfamily A, member 7	87						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(1)|lung(3)|ovary(1)	6	Melanoma(164;0.14)					TGGGCTTGGCTGGATGCAGGA	0.572																																					p.P87P		Atlas-SNP	.											OR2A7_ENST00000493325,NS,carcinoma,0,2	OR2A7	33	2	0			c.A261G						scavenged	.						5.0	6.0	5.0					7																	143956461		1342	3122	4464	SO:0001819	synonymous_variant	401427	exon1			CTTGGCTGGATGC		CCDS55177.1	7q35	2013-09-20			ENSG00000243896	ENSG00000243896		"""GPCR / Class A : Olfactory receptors"""	8234	protein-coding gene	gene with protein product							Standard	NM_001005328		Approved	HSDJ0798C17	uc011kuc.2	Q96R45	OTTHUMG00000158002	ENST00000493325.1:c.261A>G	7.37:g.143956461T>C		Somatic	347	1	0.00288184		WXS	Illumina HiSeq	Phase_I	575	75	0.130435	NM_001005328	B2RN57|Q6IFP4	Silent	SNP	ENST00000493325.1	37	CCDS55177.1																																																																																			T|0.500;C|0.500	0.500	weak		0.572	OR2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349979.1		
SIMC1	375484	hgsc.bcm.edu	37	5	175722243	175722243	+	Missense_Mutation	SNP	A	A	G	rs7736723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:175722243A>G	ENST00000443967.1	+	5	1992	c.1585A>G	c.(1585-1587)Atg>Gtg	p.M529V	SIMC1_ENST00000341199.6_Missense_Mutation_p.M114V|SIMC1_ENST00000429602.2_Missense_Mutation_p.M548V|SIMC1_ENST00000430704.2_Missense_Mutation_p.M114V			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	529							SUMO polymer binding (GO:0032184)										GGAGGCCTACATGCTTCTCAT	0.483													A|||	81	0.0161741	0.059	0.0043	5008	,	,		16361	0.0		0.0	False		,,,				2504	0.0				p.M114V		Atlas-SNP	.											.	.	.	.	0			c.A340G						PASS	.	A	VAL/MET	276,4128	150.7+/-184.7	3,270,1929	39.0	32.0	34.0		340	4.2	1.0	5	dbSNP_129	34	1,8595	1.2+/-3.3	0,1,4297	no	missense	C5orf25	NM_198567.4	21	3,271,6226	GG,GA,AA		0.0116,6.267,2.1308	possibly-damaging	114/458	175722243	277,12723	2202	4298	6500	SO:0001583	missense	375484	exon2			GCCTACATGCTTC	BC037298	CCDS4398.2	5q35.2	2013-08-14	2012-11-14	2012-11-14	ENSG00000170085	ENSG00000170085			24779	protein-coding gene	gene with protein product	"""oocyte maturation associated 1"", ""platform element for inhibition of autolytic degradation"""		"""chromosome 5 open reading frame 25"""	C5orf25		23086935, 23707407	Standard	NM_198567		Approved	FLJ44216, OOMA1, PLEIAD	uc003mds.4	Q8NDZ2	OTTHUMG00000130663	ENST00000443967.1:c.1585A>G	5.37:g.175722243A>G	ENSP00000406571:p.Met529Val	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	323	134	0.414861	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Missense_Mutation	SNP	ENST00000443967.1	37		32	0.014652014652014652	32	0.06504065040650407	0	0.0	0	0.0	0	0.0	A	16.45	3.127921	0.56721	0.06267	1.16E-4	ENSG00000170085	ENST00000341199;ENST00000430704;ENST00000443967;ENST00000429602	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.24	4.24	0.50183	.	0.174470	0.43747	D	0.000531	T	0.05686	0.0149	L	0.48642	1.525	0.25231	N	0.989824	P;P;D	0.57257	0.865;0.782;0.979	B;B;P	0.53401	0.391;0.327;0.725	T	0.01238	-1.1409	10	0.51188	T	0.08	-16.7421	12.4812	0.55844	1.0:0.0:0.0:0.0	rs55844480	548;114;529	B4DRM7;Q8NDZ2-3;Q8NDZ2	.;.;CE025_HUMAN	V	114;114;529;548	ENSP00000342075:M114V;ENSP00000409287:M114V;ENSP00000406571:M529V;ENSP00000410552:M548V	ENSP00000342075:M114V	M	+	1	0	C5orf25	175654849	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.371000	0.59523	1.775000	0.52247	0.496000	0.49642	ATG	A|1.000;|0.000	.	weak		0.483	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567	
COL5A1	1289	hgsc.bcm.edu	37	9	137630361	137630361	+	Splice_Site	SNP	G	G	A	rs61729545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:137630361G>A	ENST00000371817.3	+	10	1845	c.1431G>A	c.(1429-1431)gcG>gcA	p.A477A		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	477	Interrupted collagenous region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AAGGCCCCGCGGTGAGTATCC	0.637													G|||	351	0.0700879	0.2549	0.0202	5008	,	,		15920	0.0		0.0	False		,,,				2504	0.0				p.A477A		Atlas-SNP	.											COL5A1,NS,carcinoma,+1,1	COL5A1	323	1	0			c.G1431A						PASS	.	G		894,3512	343.1+/-307.5	90,714,1399	42.0	46.0	44.0		1431	-5.2	0.9	9	dbSNP_129	44	13,8587	7.1+/-27.0	0,13,4287	yes	coding-synonymous-near-splice	COL5A1	NM_000093.3		90,727,5686	AA,AG,GG		0.1512,20.2905,6.9737		477/1839	137630361	907,12099	2203	4300	6503	SO:0001630	splice_region_variant	1289	exon10			CCCCGCGGTGAGT	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1431+1G>A	9.37:g.137630361G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	160	100	0.625	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			G|0.937;A|0.063	0.063	strong		0.637	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Silent
ARHGEF28	64283	hgsc.bcm.edu	37	5	73148481	73148481	+	Missense_Mutation	SNP	G	G	A	rs2973566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:73148481G>A	ENST00000426542.2	+	13	1774	c.1754G>A	c.(1753-1755)aGa>aAa	p.R585K	ARHGEF28_ENST00000287898.5_Missense_Mutation_p.R585K|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.R585K|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.R585K|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.R585K|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.R272K|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.R585K			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	585			R -> K (in dbSNP:rs2973566).		central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GTAGAGCAAAGAGCTTACAGC	0.378													G|||	821	0.163938	0.0877	0.2464	5008	,	,		21296	0.0754		0.2654	False		,,,				2504	0.1953				p.R585K		Atlas-SNP	.											.	.	.	.	0			c.G1754A						PASS	.	G	LYS/ARG,LYS/ARG	477,3293		35,407,1443	165.0	156.0	159.0		1754,1754	6.2	1.0	5	dbSNP_101	159	2289,5937		330,1629,2154	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	26,26	365,2036,3597	AA,AG,GG		27.8264,12.6525,23.0577	probably-damaging,probably-damaging	585/1732,585/1706	73148481	2766,9230	1885	4113	5998	SO:0001583	missense	64283	exon14			AGCAAAGAGCTTA		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.1754G>A	5.37:g.73148481G>A	ENSP00000412175:p.Arg585Lys	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	171	85	0.497076	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	374	0.17124542124542125	43	0.08739837398373984	88	0.2430939226519337	39	0.06818181818181818	204	0.2691292875989446	G	32	5.116278	0.94339	0.126525	0.278264	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.13778	2.77;2.74;2.75;2.56;2.74;2.75;2.57	6.17	6.17	0.99709	.	.	.	.	.	T	0.00012	0.0000	M	0.66939	2.045	0.31753	P	0.634368	D;D;D;D	0.63046	0.986;0.986;0.986;0.992	P;P;P;P	0.60117	0.744;0.744;0.744;0.869	T	0.22277	-1.0221	8	0.41790	T	0.15	.	14.6223	0.68594	0.0696:0.0:0.9304:0.0	rs2973566;rs52806455;rs57829934;rs2973566	272;585;585;585	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	K	585;585;585;585;585;585;272	ENSP00000296794:R585K;ENSP00000441913:R585K;ENSP00000441436:R585K;ENSP00000287898:R585K;ENSP00000411459:R585K;ENSP00000412175:R585K;ENSP00000296799:R272K	ENSP00000287898:R585K	R	+	2	0	RP11-428C6.1	73184237	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.093000	0.71422	2.941000	0.99782	0.655000	0.94253	AGA	G|0.830;A|0.170	0.170	strong		0.378	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1268304	1268304	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1268304A>G	ENST00000529681.1	+	31	10252	c.10194A>G	c.(10192-10194)acA>acG	p.T3398T	MUC5B_ENST00000447027.1_Silent_p.T3401T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3398	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)		ctacgatcacagccaccggct	0.622																																					p.T3398T		Atlas-SNP	.											MUC5B,NS,lymphoid_neoplasm,0,2	MUC5B	473	2	0			c.A10194G						scavenged	.						122.0	165.0	151.0					11																	1268304		2001	3979	5980	SO:0001819	synonymous_variant	727897	exon31			GATCACAGCCACC	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.10194A>G	11.37:g.1268304A>G		Somatic	741	1	0.00134953		WXS	Illumina HiSeq	Phase_I	857	33	0.0385064	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|1.000;|0.000	1.000	weak		0.622	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ARSI	340075	hgsc.bcm.edu	37	5	149677818	149677818	+	Silent	SNP	G	G	A	rs77943970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149677818G>A	ENST00000328668.7	-	2	1248	c.669C>T	c.(667-669)caC>caT	p.H223H		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	223					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)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCTGAGGGCTGTGGCTGGCCA	0.627													G|||	122	0.024361	0.0257	0.0375	5008	,	,		19157	0.0		0.0577	False		,,,				2504	0.0041				p.H223H		Atlas-SNP	.											.	ARSI	65	.	0			c.C669T						PASS	.	G		117,4289	90.2+/-128.9	0,117,2086	52.0	54.0	53.0		669	1.5	1.0	5	dbSNP_132	53	362,8238	120.1+/-179.3	11,340,3949	no	coding-synonymous	ARSI	NM_001012301.2		11,457,6035	AA,AG,GG		4.2093,2.6555,3.6829		223/570	149677818	479,12527	2203	4300	6503	SO:0001819	synonymous_variant	340075	exon2			AGGGCTGTGGCTG	AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"""Arylsulfatase family"""	32521	protein-coding gene	gene with protein product		610009	"""arylsulfatase I"""			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.669C>T	5.37:g.149677818G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_001012301	A1L3B0|B3KV22|B7XD03	Silent	SNP	ENST00000328668.7	37	CCDS34275.1																																																																																			G|0.967;A|0.033	0.033	strong		0.627	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301	
ATP2B3	492	hgsc.bcm.edu	37	X	152830495	152830495	+	Silent	SNP	T	T	C	rs5986910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:152830495T>C	ENST00000349466.2	+	20	3602	c.3276T>C	c.(3274-3276)caT>caC	p.H1092H	ATP2B3_ENST00000370186.1_Silent_p.H1078H|ATP2B3_ENST00000393842.1_Silent_p.H1078H|ATP2B3_ENST00000359149.3_Silent_p.H1092H|ATP2B3_ENST00000370181.2_Silent_p.H1078H|ATP2B3_ENST00000263519.4_Silent_p.H1092H			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	1092					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGATCGACCATGCCGAGCGGG	0.672													C|||	206	0.0545695	0.1467	0.0144	3775	,	,		12860	0.0		0.002	False		,,,				2504	0.0				p.H1092H		Atlas-SNP	.											.	ATP2B3	552	.	0			c.T3276C						PASS	.		,	667,3161		51,473,92,1107,474	24.0	23.0	23.0		3276,3276	0.6	1.0	X	dbSNP_114	23	13,6711		0,8,5,2420,1863	no	coding-synonymous,coding-synonymous	ATP2B3	NM_001001344.2,NM_021949.3	,	51,481,97,3527,2337	CC,CT,C,TT,T		0.1933,17.4242,6.4443	,	1092/1221,1092/1174	152830495	680,9872	2197	4296	6493	SO:0001819	synonymous_variant	492	exon19			CGACCATGCCGAG	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"""ATPases / P-type"""	816	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 3"", ""cilia and flagella associated protein 39"""	300014	"""spinocerebellar ataxia, X-linked 1"", ""cerebellar ataxia 2 (X-linked)"""	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.3276T>C	X.37:g.152830495T>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	194	64	0.329897	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	37	CCDS35440.1																																																																																			T|0.920;C|0.080	0.080	strong		0.672	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262121	39262121	+	Missense_Mutation	SNP	C	C	T	rs200757692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39262121C>T	ENST00000391415.1	+	1	538	c.481C>T	c.(481-483)Cgc>Tgc	p.R161C		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	161	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R149C(1)|p.R161C(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						cagctgctgccgcccctcttg	0.657																																					p.R161C		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	2	2	Substitution - Missense(2)	endometrium(2)	c.C481T						scavenged	.						7.0	11.0	10.0					17																	39262121		682	1570	2252	SO:0001583	missense	100132386	exon1			TGCTGCCGCCCCT	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.481C>T	17.37:g.39262121C>T	ENSP00000375234:p.Arg161Cys	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	151	17	0.112583	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	11.80	1.746361	0.30955	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00605	6.27	2.98	0.469	0.16741	.	0.000000	0.40640	U	0.001042	T	0.00552	0.0018	M	0.70275	2.135	0.09310	N	1	P	0.34587	0.458	B	0.19391	0.025	T	0.50857	-0.8778	10	0.52906	T	0.07	.	1.9066	0.03278	0.202:0.4678:0.1985:0.1317	.	161	Q9BYQ8	KRA49_HUMAN	C	149;161;152	ENSP00000375234:R161C	ENSP00000334461:R152C	R	+	1	0	KRTAP4-9	36515647	0.000000	0.05858	0.321000	0.25320	0.226000	0.24999	-1.001000	0.03690	0.325000	0.23359	0.197000	0.17608	CGC	.	.	none		0.657	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
PTPRJ	5795	hgsc.bcm.edu	37	11	48166642	48166642	+	Silent	SNP	C	C	T	rs34300475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48166642C>T	ENST00000418331.2	+	14	3229	c.2877C>T	c.(2875-2877)cgC>cgT	p.R959R		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	959					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)			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						CCTTCAGTCGCTACTCAGATG	0.532													C|||	350	0.0698882	0.2564	0.013	5008	,	,		22420	0.0		0.002	False		,,,				2504	0.0				p.R959R		Atlas-SNP	.											.	PTPRJ	225	.	0			c.C2877T						PASS	.	C		789,3613	319.1+/-295.9	68,653,1480	164.0	145.0	151.0		2877	2.3	0.0	11	dbSNP_126	151	5,8591	3.0+/-9.4	0,5,4293	no	coding-synonymous	PTPRJ	NM_002843.3		68,658,5773	TT,TC,CC		0.0582,17.9237,6.1086		959/1338	48166642	794,12204	2201	4298	6499	SO:0001819	synonymous_variant	5795	exon14			CAGTCGCTACTCA	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.2877C>T	11.37:g.48166642C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	198	100	0.50505	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Silent	SNP	ENST00000418331.2	37	CCDS7945.1																																																																																			C|0.944;T|0.056	0.056	strong		0.532	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
ZNF570	148268	hgsc.bcm.edu	37	19	37975400	37975400	+	Silent	SNP	T	T	C	rs78317808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37975400T>C	ENST00000330173.1	+	5	1405	c.876T>C	c.(874-876)caT>caC	p.H292H	ZNF570_ENST00000586475.1_Silent_p.H348H|ZNF570_ENST00000388801.3_Silent_p.H89H	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	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)			endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAGTTCAACATCTGCGAGTTC	0.423													T|||	91	0.0181709	0.0651	0.0072	5008	,	,		21985	0.0		0.0	False		,,,				2504	0.0				p.H292H		Atlas-SNP	.											.	ZNF570	58	.	0			c.T876C						PASS	.	T		263,4143	148.0+/-182.4	8,247,1948	77.0	73.0	74.0		876	2.2	1.0	19	dbSNP_131	74	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	ZNF570	NM_144694.1		8,253,6242	CC,CT,TT		0.0698,5.9691,2.0683		292/537	37975400	269,12737	2203	4300	6503	SO:0001819	synonymous_variant	148268	exon5			TCAACATCTGCGA	AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"""Zinc fingers, C2H2-type"", ""-"""	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.876T>C	19.37:g.37975400T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	36	0.590164	NM_144694	A1L472|B4DMP1	Silent	SNP	ENST00000330173.1	37	CCDS12504.1																																																																																			T|0.983;C|0.017	0.017	strong		0.423	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694	
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67242087	67242087	+	Splice_Site	SNP	G	G	A	rs3816989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:67242087G>A	ENST00000282670.2	+	4	464		c.e4+1			NM_152665.2	NP_689878.2	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1											large_intestine(2)|lung(10)|skin(1)	13						CATTTCTGAGGTACGTGTGTG	0.368													G|||	654	0.130591	0.0794	0.1009	5008	,	,		17193	0.1488		0.1511	False		,,,				2504	0.181				.		Atlas-SNP	.											.	TCTEX1D1	27	.	0			c.336+1G>A						PASS	.	G		366,4040	185.7+/-212.7	18,330,1855	94.0	93.0	94.0			5.9	1.0	1	dbSNP_107	94	1187,7413	241.5+/-271.8	84,1019,3197	yes	splice-5	TCTEX1D1	NM_152665.2		102,1349,5052	AA,AG,GG		13.8023,8.3069,11.9406			67242087	1553,11453	2203	4300	6503	SO:0001630	splice_region_variant	200132	exon4			TCTGAGGTACGTG	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.336+1G>A	1.37:g.67242087G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	194	97	0.5	NM_152665	Q06YR9|Q5VYE1	Splice_Site	SNP	ENST00000282670.2	37	CCDS633.1	264	0.12087912087912088	35	0.07113821138211382	42	0.11602209944751381	82	0.14335664335664336	105	0.13852242744063326	G	18.01	3.528188	0.64860	0.083069	0.138023	ENSG00000152760	ENST00000282670	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0921	0.93231	0.0:0.0:1.0:0.0	rs3816989;rs12748193;rs3816989	.	.	.	.	-1	.	.	.	+	.	.	TCTEX1D1	67014675	1.000000	0.71417	0.999000	0.59377	0.672000	0.39443	8.439000	0.90308	2.809000	0.96659	0.655000	0.94253	.	G|0.879;A|0.121	0.121	strong		0.368	TCTEX1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025399.2	NM_152665	Intron
EFHD1	80303	hgsc.bcm.edu	37	2	233498669	233498669	+	Silent	SNP	G	G	T	rs2276557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233498669G>T	ENST00000264059.3	+	1	732	c.255G>T	c.(253-255)ccG>ccT	p.P85P	EFHD1_ENST00000409613.1_Intron	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	85					neuron projection development (GO:0031175)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|large_intestine(2)|lung(3)	7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		CGGAGTTCCCGGAGTTCAGCC	0.701													G|||	1213	0.242212	0.1286	0.1571	5008	,	,		9824	0.6329		0.1899	False		,,,				2504	0.1074				p.P85P		Atlas-SNP	.											.	EFHD1	28	.	0			c.G255T						PASS	.	G		572,3778		37,498,1640	16.0	19.0	18.0		255	-3.3	0.9	2	dbSNP_100	18	1649,6885		159,1331,2777	no	coding-synonymous	EFHD1	NM_025202.3		196,1829,4417	TT,TG,GG		19.3227,13.1494,17.2384		85/240	233498669	2221,10663	2175	4267	6442	SO:0001819	synonymous_variant	80303	exon1			GTTCCCGGAGTTC		CCDS2497.1, CCDS58755.1	2q37.1	2014-07-01	2005-01-25		ENSG00000115468	ENSG00000115468		"""EF-hand domain containing"""	29556	protein-coding gene	gene with protein product	"""swiprosin-2"""	611617	"""EF hand domain containing 1"""			21244694	Standard	NM_025202		Approved	FLJ13612	uc002vtc.3	Q9BUP0	OTTHUMG00000133263	ENST00000264059.3:c.255G>T	2.37:g.233498669G>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	9	5	0.555556	NM_025202	B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	Silent	SNP	ENST00000264059.3	37	CCDS2497.1																																																																																			G|0.726;T|0.274	0.274	strong		0.701	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202	
VPS8	23355	hgsc.bcm.edu	37	3	184573603	184573603	+	Silent	SNP	A	A	G	rs16859356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184573603A>G	ENST00000437079.3	+	14	1311	c.1140A>G	c.(1138-1140)ctA>ctG	p.L380L	VPS8_ENST00000436792.2_Silent_p.L378L|VPS8_ENST00000287546.4_Silent_p.L380L|VPS8_ENST00000446204.2_Silent_p.L378L	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	380							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)			TTCATTTTCTATTGGTAAGTC	0.378													A|||	145	0.0289537	0.1051	0.0086	5008	,	,		18410	0.0		0.0	False		,,,				2504	0.0				p.L380L		Atlas-SNP	.											.	VPS8	109	.	0			c.A1140G						PASS	.	A	,	311,3443		12,287,1578	178.0	169.0	172.0		1140,1134	-6.0	0.5	3	dbSNP_123	172	6,8222		0,6,4108	no	coding-synonymous,coding-synonymous	VPS8	NM_001009921.2,NM_015303.3	,	12,293,5686	GG,GA,AA		0.0729,8.2845,2.6456	,	380/1429,378/1427	184573603	317,11665	1877	4114	5991	SO:0001819	synonymous_variant	23355	exon13			TTTTCTATTGGTA	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.1140A>G	3.37:g.184573603A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	120	69	0.575	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Silent	SNP	ENST00000437079.3	37	CCDS46971.1																																																																																			A|0.971;G|0.029	0.029	strong		0.378	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	
MOAP1	64112	hgsc.bcm.edu	37	14	93649552	93649552	+	Silent	SNP	A	A	G	rs114256363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:93649552A>G	ENST00000556883.1	-	2	1520	c.1036T>C	c.(1036-1038)Ttg>Ctg	p.L346L	MOAP1_ENST00000298894.4_Silent_p.L346L|TMEM251_ENST00000283534.4_5'Flank|RP11-371E8.4_ENST00000557574.1_5'Flank|TMEM251_ENST00000415050.2_5'Flank			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	346					apoptotic signaling pathway (GO:0097190)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	13		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		TTACCTTCCAATATTGCCTGG	0.473													A|||	96	0.0191693	0.0696	0.0058	5008	,	,		21495	0.0		0.0	False		,,,				2504	0.0				p.L346L		Atlas-SNP	.											.	MOAP1	32	.	0			c.T1036C						PASS	.	A		233,4173	139.2+/-174.8	8,217,1978	99.0	90.0	93.0		1036	-4.4	0.0	14	dbSNP_132	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MOAP1	NM_022151.4		8,218,6277	GG,GA,AA		0.0116,5.2882,1.7992		346/352	93649552	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	64112	exon3			CTTCCAATATTGC	BC015044	CCDS9908.1	14q32.12	2012-02-09			ENSG00000165943	ENSG00000165943		"""Paraneoplastic Ma antigens"""	16658	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 4"""	609485				11060313	Standard	NM_022151		Approved	MAP-1, PNMA4	uc001ybj.3	Q96BY2	OTTHUMG00000169184	ENST00000556883.1:c.1036T>C	14.37:g.93649552A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_022151	B2RDF6|Q9H833|Q9HAS1	Silent	SNP	ENST00000556883.1	37	CCDS9908.1																																																																																			A|0.982;G|0.018	0.018	strong		0.473	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1		
WDR87	83889	hgsc.bcm.edu	37	19	38383386	38383386	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38383386C>T	ENST00000303868.5	-	4	3064	c.2840G>A	c.(2839-2841)cGt>cAt	p.R947H	WDR87_ENST00000447313.2_Missense_Mutation_p.R986H	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	947										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						CATTCCTAGACGCTTCAGCCC	0.512																																					p.R947H		Atlas-SNP	.											WDR87,colon,carcinoma,0,1	WDR87	191	1	0			c.G2840A						PASS	.						191.0	153.0	164.0					19																	38383386		692	1591	2283	SO:0001583	missense	83889	exon4			CCTAGACGCTTCA	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.2840G>A	19.37:g.38383386C>T	ENSP00000368025:p.Arg947His	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	248	133	0.53629	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.806795	0.50421	.	.	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.64618	-0.11;-0.11	5.27	1.93	0.25924	.	0.124727	0.33457	N	0.004882	T	0.54919	0.1888	M	0.66939	2.045	0.25293	N	0.989346	B;B	0.25486	0.127;0.127	B;B	0.18263	0.021;0.021	T	0.54503	-0.8284	10	0.87932	D	0	-5.9939	8.0083	0.30338	0.0:0.7327:0.0:0.2673	.	947;986	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	H	986;947	ENSP00000405012:R986H;ENSP00000368025:R947H	ENSP00000368025:R947H	R	-	2	0	WDR87	43075226	0.501000	0.26099	0.982000	0.44146	0.996000	0.88848	0.382000	0.20635	0.611000	0.30052	0.549000	0.68633	CGT	.	.	none		0.512	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
PCDHGA1	56114	hgsc.bcm.edu	37	5	140712299	140712299	+	Missense_Mutation	SNP	A	A	T	rs62378404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140712299A>T	ENST00000517417.1	+	1	2048	c.2048A>T	c.(2047-2049)aAa>aTa	p.K683I	PCDHGA1_ENST00000378105.3_Missense_Mutation_p.K683I	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	683					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCTCCGCCAAACCCAACGAT	0.692																																					p.K683I		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.A2048T						PASS	.						67.0	80.0	76.0					5																	140712299		2203	4296	6499	SO:0001583	missense	56114	exon1			CCGCCAAACCCAA	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.2048A>T	5.37:g.140712299A>T	ENSP00000431083:p.Lys683Ile	Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	326	159	0.48773	NM_018912	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	113	0.051739926739926737	45	0.09146341463414634	18	0.049723756906077346	14	0.024475524475524476	36	0.047493403693931395	A	13.01	2.110756	0.37242	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.51817	0.73;0.69	3.87	-0.312	0.12758	.	3.140790	0.01069	N	0.004795	T	0.01661	0.0053	L	0.38175	1.15	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.15870	0.014;0.002	T	0.15723	-1.0427	10	0.59425	D	0.04	.	4.888	0.13713	0.6559:0.1574:0.1867:0.0	rs62378404	683;683	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	I	683	ENSP00000431083:K683I;ENSP00000367345:K683I	ENSP00000367345:K683I	K	+	2	0	PCDHGA1	140692483	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	1.355000	0.34068	0.173000	0.19788	0.477000	0.44152	AAA	A|0.958;T|0.042	0.042	strong		0.692	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912	
LANCL2	55915	hgsc.bcm.edu	37	7	55433880	55433880	+	Silent	SNP	G	G	C	rs2272262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:55433880G>C	ENST00000254770.2	+	1	740	c.162G>C	c.(160-162)gcG>gcC	p.A54A		NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	54					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			GTCCCCCGGCGACCACGGATG	0.726													C|||	1451	0.289736	0.4357	0.1988	5008	,	,		12860	0.1558		0.331	False		,,,				2504	0.2526				p.A54A		Atlas-SNP	.											.	LANCL2	54	.	0			c.G162C						PASS	.	C		1722,2634		395,932,851	8.0	11.0	10.0		162	1.4	0.0	7	dbSNP_100	10	2782,5752		515,1752,2000	no	coding-synonymous	LANCL2	NM_018697.3		910,2684,2851	CC,CG,GG		32.599,39.5317,34.9418		54/451	55433880	4504,8386	2178	4267	6445	SO:0001819	synonymous_variant	55915	exon1			CCCGGCGACCACG	AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434			6509	protein-coding gene	gene with protein product	"""testis-specific adriamycin sensitivity protein"", ""G protein-coupled receptor 69B"""	612919	"""LanC (bacterial lantibiotic synthetase component C)-like 2"""	GPR69B		11762191	Standard	NM_018697		Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.162G>C	7.37:g.55433880G>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	39	38	0.974359	NM_018697	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Silent	SNP	ENST00000254770.2	37	CCDS5517.1																																																																																			G|0.685;C|0.315	0.315	strong		0.726	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697	
ACTRT2	140625	hgsc.bcm.edu	37	1	2938265	2938265	+	Silent	SNP	C	C	T	rs4576609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:2938265C>T	ENST00000378404.2	+	1	220	c.15C>T	c.(13-15)caC>caT	p.H5H		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	5						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		TTAATCCGCACGCTTTAGACT	0.567													C|||	1010	0.201677	0.1324	0.2406	5008	,	,		17517	0.3978		0.161	False		,,,				2504	0.1074				p.H5H		Atlas-SNP	.											.	ACTRT2	69	.	0			c.C15T						PASS	.	C		624,3782	251.8+/-258.4	49,526,1628	56.0	62.0	60.0		15	-4.0	0.0	1	dbSNP_111	60	1537,7063	286.6+/-297.8	124,1289,2887	no	coding-synonymous	ACTRT2	NM_080431.4		173,1815,4515	TT,TC,CC		17.8721,14.1625,16.6154		5/378	2938265	2161,10845	2203	4300	6503	SO:0001819	synonymous_variant	140625	exon1			TCCGCACGCTTTA	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.15C>T	1.37:g.2938265C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_080431	B1AN52|Q8NHS6|Q8TDG1	Silent	SNP	ENST00000378404.2	37	CCDS45.1																																																																																			C|0.804;T|0.196	0.196	strong		0.567	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431	
ZDHHC23	254887	hgsc.bcm.edu	37	3	113673098	113673098	+	Missense_Mutation	SNP	C	C	T	rs149202494		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113673098C>T	ENST00000330212.3	+	3	1012	c.713C>T	c.(712-714)aCa>aTa	p.T238I	ZDHHC23_ENST00000498275.1_Missense_Mutation_p.T232I	NM_173570.3	NP_775841.2	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC-type containing 23	238					protein localization to plasma membrane (GO:0072659)|protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|urinary_tract(2)	16						AATCGCACAACAAAGGATGAC	0.597													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18066	0.0		0.0	False		,,,				2504	0.0				p.T238I		Atlas-SNP	.											.	ZDHHC23	38	.	0			c.C713T						PASS	.	C	ILE/THR	2,4404	4.2+/-10.8	0,2,2201	81.0	79.0	80.0		713	-1.8	0.0	3	dbSNP_134	80	0,8600		0,0,4300	no	missense	ZDHHC23	NM_173570.3	89	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	238/410	113673098	2,13004	2203	4300	6503	SO:0001583	missense	254887	exon3			GCACAACAAAGGA	AK127025	CCDS33827.1	3q13.31	2008-05-02			ENSG00000184307	ENSG00000184307		"""Zinc fingers, DHHC-type"""	28654	protein-coding gene	gene with protein product						12477932	Standard	NM_173570		Approved	MGC42530	uc003eau.3	Q8IYP9	OTTHUMG00000159335	ENST00000330212.3:c.713C>T	3.37:g.113673098C>T	ENSP00000330485:p.Thr238Ile	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	168	84	0.5	NM_173570	D3DN76	Missense_Mutation	SNP	ENST00000330212.3	37	CCDS33827.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.022	-1.410585	0.01145	4.54E-4	0.0	ENSG00000184307	ENST00000330212;ENST00000498275	T;T	0.24723	1.84;1.84	5.11	-1.77	0.07982	.	1.393810	0.04616	N	0.401098	T	0.09555	0.0235	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25363	-1.0134	10	0.20519	T	0.43	-12.359	5.4023	0.16303	0.0:0.3117:0.1628:0.5255	.	238	Q8IYP9	ZDH23_HUMAN	I	238;232	ENSP00000330485:T238I;ENSP00000417840:T232I	ENSP00000330485:T238I	T	+	2	0	ZDHHC23	115155788	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.478000	0.06575	-0.376000	0.07943	-0.459000	0.05422	ACA	C|1.000;T|0.000	0.000	strong		0.597	ZDHHC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354702.1	NM_173570	
PTPRJ	5795	hgsc.bcm.edu	37	11	48166267	48166267	+	Missense_Mutation	SNP	G	G	C	rs4752904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48166267G>C	ENST00000418331.2	+	13	2968	c.2616G>C	c.(2614-2616)gaG>gaC	p.E872D		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	872	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> D (in dbSNP:rs4752904). {ECO:0000269|PubMed:12089527, ECO:0000269|PubMed:15378013, ECO:0000269|PubMed:7937872, ECO:0000269|PubMed:7994032}.		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)			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						ACACGTATGAGGATTTCAAAA	0.403													G|||	1839	0.367212	0.056	0.5908	5008	,	,		23017	0.3839		0.5835	False		,,,				2504	0.3896				p.E872D		Atlas-SNP	.											.	PTPRJ	225	.	0			c.G2616C	GRCh37	CM043073	PTPRJ	M	rs4752904	PASS	.	G	ASP/GLU	654,3748	277.5+/-273.7	49,556,1596	99.0	94.0	96.0		2616	-10.9	0.0	11	dbSNP_111	96	4952,3644	625.0+/-397.7	1407,2138,753	yes	missense	PTPRJ	NM_002843.3	45	1456,2694,2349	CC,CG,GG		42.3918,14.8569,43.1297	possibly-damaging	872/1338	48166267	5606,7392	2201	4298	6499	SO:0001583	missense	5795	exon13			GTATGAGGATTTC	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.2616G>C	11.37:g.48166267G>C	ENSP00000400010:p.Glu872Asp	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	117	60	0.512821	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	955	0.43727106227106227	39	0.07926829268292683	214	0.5911602209944752	252	0.4405594405594406	450	0.5936675461741425	G	4.648	0.120524	0.08881	0.148569	0.576082	ENSG00000149177	ENST00000418331	T	0.13657	2.57	5.45	-10.9	0.00192	Fibronectin, type III (2);	.	.	.	.	T	0.00012	0.0000	N	0.17082	0.46	0.21184	P	0.999766262	B	0.13145	0.007	B	0.11329	0.006	T	0.47535	-0.9110	8	0.02654	T	1	.	1.7439	0.02958	0.2538:0.0802:0.3284:0.3375	rs4752904;rs17789721;rs52831595;rs56898824;rs4752904	872	Q12913	PTPRJ_HUMAN	D	872	ENSP00000400010:E872D	ENSP00000400010:E872D	E	+	3	2	PTPRJ	48122843	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-4.356000	0.00247	-2.555000	0.00477	-0.911000	0.02809	GAG	G|0.569;C|0.431	0.431	strong		0.403	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057949	46057949	+	Silent	SNP	C	C	T	rs78352751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057949C>T	ENST00000380095.1	+	1	677	c.615C>T	c.(613-615)ccC>ccT	p.P205P	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	205	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						GCTGCGTGCCCGTCCCCTCCT	0.701													C|||	103	0.0205671	0.0756	0.0043	5008	,	,		20099	0.0		0.0	False		,,,				2504	0.0				p.P205P		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C615T						PASS	.						95.0	98.0	97.0					21																	46057949		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CGTGCCCGTCCCC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.615C>T	21.37:g.46057949C>T		Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	471	121	0.2569	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.982;T|0.018	0.018	strong		0.701	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85432040	85432040	+	Missense_Mutation	SNP	T	T	A	rs7312075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:85432040T>A	ENST00000393217.2	+	2	147	c.86T>A	c.(85-87)aTt>aAt	p.I29N	TSPAN19_ENST00000547403.2_5'Flank|TSPAN19_ENST00000532498.2_5'Flank	NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	29			I -> N (in dbSNP:rs7312075). {ECO:0000269|PubMed:14702039}.					p.I29N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		AAAGAAGACATTGAGAGTGAT	0.368													T|||	596	0.11901	0.0129	0.1916	5008	,	,		11658	0.2202		0.0934	False		,,,				2504	0.1329				p.I29N		Atlas-SNP	.											LRRIQ1,NS,carcinoma,0,1	LRRIQ1	512	1	1	Substitution - Missense(1)	stomach(1)	c.T86A						PASS	.	T	ASN/ILE	114,4292	85.8+/-124.5	1,112,2090	119.0	116.0	117.0		86	-1.4	0.1	12	dbSNP_116	117	757,7843	180.5+/-229.4	30,697,3573	yes	missense	LRRIQ1	NM_001079910.1	149	31,809,5663	AA,AT,TT		8.8023,2.5874,6.6969	possibly-damaging	29/1723	85432040	871,12135	2203	4300	6503	SO:0001583	missense	84125	exon2			AAGACATTGAGAG	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.86T>A	12.37:g.85432040T>A	ENSP00000376910:p.Ile29Asn	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	115	41	0.356522	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	270	0.12362637362637363	9	0.018292682926829267	61	0.1685082872928177	127	0.22202797202797203	73	0.09630606860158311	T	3.997	-0.003389	0.07773	0.025874	0.088023	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393212;ENST00000393217	T;T	0.53640	0.93;0.61	4.27	-1.37	0.09056	.	0.827624	0.10075	N	0.719238	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	2.9999999999752447E-6	B;B	0.31519	0.244;0.327	B;B	0.26969	0.075;0.05	T	0.18023	-1.0350	9	0.72032	D	0.01	.	0.8095	0.01091	0.1699:0.3022:0.1754:0.3525	rs7312075;rs52803324;rs7312075	29;29	Q96JM4;C9JI57	LRIQ1_HUMAN;.	N	29	ENSP00000376906:I29N;ENSP00000376910:I29N	ENSP00000256007:I29N	I	+	2	0	LRRIQ1	83956171	0.001000	0.12720	0.121000	0.21740	0.065000	0.16274	-0.599000	0.05700	-0.029000	0.13827	-0.256000	0.11100	ATT	T|0.916;A|0.084	0.084	strong		0.368	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
CLEC16A	23274	hgsc.bcm.edu	37	16	11133642	11133642	+	Silent	SNP	G	G	A	rs61740101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11133642G>A	ENST00000409790.1	+	14	1799	c.1569G>A	c.(1567-1569)caG>caA	p.Q523Q	CLEC16A_ENST00000409552.3_Silent_p.Q505Q|CLEC16A_ENST00000465491.1_3'UTR	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						AGCGAATCCAGCTCCCCGTGC	0.547													G|||	64	0.0127796	0.0477	0.0014	5008	,	,		18325	0.0		0.0	False		,,,				2504	0.0				p.Q523Q		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1569A						PASS	.	G		137,3891		6,125,1883	51.0	55.0	54.0		1569	3.3	1.0	16	dbSNP_129	54	0,8358		0,0,4179	no	coding-synonymous	CLEC16A	NM_015226.2		6,125,6062	AA,AG,GG		0.0,3.4012,1.1061		523/1054	11133642	137,12249	2014	4179	6193	SO:0001819	synonymous_variant	23274	exon13			AATCCAGCTCCCC	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.1569G>A	16.37:g.11133642G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			G|0.989;A|0.011	0.011	strong		0.547	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
COX18	285521	hgsc.bcm.edu	37	4	73930552	73930552	+	Silent	SNP	G	G	A	rs3762883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:73930552G>A	ENST00000295890.4	-	4	754	c.663C>T	c.(661-663)ccC>ccT	p.P221P	COX18_ENST00000507544.2_Silent_p.P222P	NM_173827.2	NP_776188.1	Q8N8Q8	COX18_HUMAN	COX18 cytochrome C oxidase assembly factor	221					protein insertion into mitochondrial membrane (GO:0051204)|protein transport (GO:0015031)|respiratory chain complex IV assembly (GO:0008535)	integral component of mitochondrial inner membrane (GO:0031305)	protein transporter activity (GO:0008565)			large_intestine(4)|lung(2)	6	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAGTGGAGTCGGGTGCAGTGA	0.383													c|||	1710	0.341454	0.1891	0.2983	5008	,	,		17295	0.3879		0.4563	False		,,,				2504	0.4121				p.P221P		Atlas-SNP	.											.	COX18	20	.	0			c.C663T						PASS	.	T		1055,3351		146,763,1294	77.0	76.0	77.0		663	0.5	0.3	4	dbSNP_107	77	3677,4923		774,2129,1397	no	coding-synonymous	COX18	NM_173827.2		920,2892,2691	AA,AG,GG		42.7558,23.9446,36.3832		221/334	73930552	4732,8274	2203	4300	6503	SO:0001819	synonymous_variant	285521	exon4			GGAGTCGGGTGCA	AY957564	CCDS3554.1, CCDS75139.1	4q13.3	2013-06-12	2013-06-12		ENSG00000163626	ENSG00000163626		"""Mitochondrial respiratory chain complex assembly factors"""	26801	protein-coding gene	gene with protein product		610428	"""COX18 cytochrome c oxidase assembly homolog (S. cerevisiae)"", ""cytochrome c oxidase assembly homolog 18 (yeast)"""			16212937, 16911509	Standard	XM_005265679		Approved	FLJ38991	uc003hgm.1	Q8N8Q8	OTTHUMG00000129917	ENST00000295890.4:c.663C>T	4.37:g.73930552G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	232	117	0.50431	NM_173827	Q2PB66|Q2PB67|Q2PB68|Q49B97|Q6IPP9	Silent	SNP	ENST00000295890.4	37	CCDS3554.1																																																																																			G|0.650;C|0.000;A|0.350	0.350	strong		0.383	COX18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252169.2	NM_173827	
GALNT10	55568	hgsc.bcm.edu	37	5	153783753	153783753	+	Silent	SNP	C	C	T	rs6580076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:153783753C>T	ENST00000297107.6	+	8	1283	c.1146C>T	c.(1144-1146)gcC>gcT	p.A382A	GALNT10_ENST00000519544.1_3'UTR|GALNT10_ENST00000377657.3_Silent_p.A53A|GALNT10_ENST00000377661.2_Silent_p.A320A|SAP30L-AS1_ENST00000519727.1_RNA|SAP30L-AS1_ENST00000524264.1_RNA	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	382	Flexible loop.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.A382A(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			AGGTCCCGGCCGGAGTCAGCC	0.632													C|||	1429	0.285343	0.5083	0.1585	5008	,	,		19763	0.1637		0.1571	False		,,,				2504	0.3313				p.A382A		Atlas-SNP	.											GALNT10,NS,carcinoma,0,1	GALNT10	70	1	1	Substitution - coding silent(1)	stomach(1)	c.C1146T						PASS	.	C		1935,2471	545.4+/-376.8	432,1071,700	63.0	56.0	59.0		1146	-10.8	0.7	5	dbSNP_116	59	1471,7129	279.3+/-293.9	110,1251,2939	no	coding-synonymous	GALNT10	NM_198321.3		542,2322,3639	TT,TC,CC		17.1047,43.9174,26.1879		382/604	153783753	3406,9600	2203	4300	6503	SO:0001819	synonymous_variant	55568	exon8			CCCGGCCGGAGTC	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19873	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 10"""	608043	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"""			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.1146C>T	5.37:g.153783753C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	167	67	0.401198	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Silent	SNP	ENST00000297107.6	37	CCDS4325.1																																																																																			C|0.733;T|0.267	0.267	strong		0.632	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321	
KCNS1	3787	hgsc.bcm.edu	37	20	43727155	43727155	+	Silent	SNP	C	C	T	rs13043825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43727155C>T	ENST00000306117.1	-	4	654	c.258G>A	c.(256-258)gaG>gaA	p.E86E	KCNS1_ENST00000537075.1_Silent_p.E86E	NM_002251.3	NP_002242.2	Q96KK3	KCNS1_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1	86					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(1)|lung(3)|ovary(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				GCCGCGCCTGCTCCTCCGACG	0.741													C|||	658	0.13139	0.0113	0.1729	5008	,	,		8507	0.131		0.2893	False		,,,				2504	0.1022				p.E86E		Atlas-SNP	.											.	KCNS1	30	.	0			c.G258A						PASS	.	C		198,3818		14,170,1824	8.0	10.0	9.0		258	3.8	1.0	20	dbSNP_121	9	1830,5974		196,1438,2268	no	coding-synonymous	KCNS1	NM_002251.3		210,1608,4092	TT,TC,CC		23.4495,4.9303,17.1574		86/527	43727155	2028,9792	2008	3902	5910	SO:0001819	synonymous_variant	3787	exon4			CGCCTGCTCCTCC	AF043473	CCDS13342.1	20q12	2011-07-05			ENSG00000124134	ENSG00000124134		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6300	protein-coding gene	gene with protein product		602905				9305895, 16382104	Standard	NM_002251		Approved	Kv9.1	uc002xnc.3	Q96KK3	OTTHUMG00000033079	ENST00000306117.1:c.258G>A	20.37:g.43727155C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	11	8	0.727273	NM_002251	A2RUL9|B7ZM31|O43652|Q6DJU6	Silent	SNP	ENST00000306117.1	37	CCDS13342.1																																																																																			C|0.838;T|0.162	0.162	strong		0.741	KCNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080507.3	NM_002251	
TMCO3	55002	hgsc.bcm.edu	37	13	114156093	114156093	+	Silent	SNP	C	C	T	rs2260080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114156093C>T	ENST00000434316.2	+	5	1202	c.843C>T	c.(841-843)tcC>tcT	p.S281S	TMCO3_ENST00000375391.1_Silent_p.S281S|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	281						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.S281S(1)		NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			GAATGCTGTCCTTGCCTTGTG	0.408													.|||	1207	0.241014	0.4107	0.147	5008	,	,		22189	0.2708		0.1581	False		,,,				2504	0.1329				p.S281S		Atlas-SNP	.											TMCO3,NS,carcinoma,0,1	TMCO3	77	1	1	Substitution - coding silent(1)	stomach(1)	c.C843T						PASS	.	C		1535,2871	486.2+/-360.5	264,1007,932	167.0	164.0	165.0		843	-3.1	0.1	13	dbSNP_100	165	1275,7325	252.3+/-278.5	90,1095,3115	no	coding-synonymous	TMCO3	NM_017905.4		354,2102,4047	TT,TC,CC		14.8256,34.8389,21.6054		281/678	114156093	2810,10196	2203	4300	6503	SO:0001819	synonymous_variant	55002	exon5			GCTGTCCTTGCCT	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.843C>T	13.37:g.114156093C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																			C|0.772;T|0.228	0.228	strong		0.408	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
NCOR1	9611	hgsc.bcm.edu	37	17	16001756	16001756	+	Silent	SNP	G	G	A	rs79413281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16001756G>A	ENST00000268712.3	-	21	3002	c.2745C>T	c.(2743-2745)ctC>ctT	p.L915L	NCOR1_ENST00000395848.1_Silent_p.L822L|NCOR1_ENST00000395851.1_Silent_p.L931L|RNU6-314P_ENST00000516574.1_RNA	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	915					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GAGATGAGACGAGTATAGATC	0.378													a|||	109	0.0217652	0.0764	0.0115	5008	,	,		17847	0.0		0.0	False		,,,				2504	0.0				p.L931L		Atlas-SNP	.											.	NCOR1	240	.	0			c.C2793T						PASS	.	A	,,	262,4144	802.4+/-415.7	7,248,1948	87.0	87.0	87.0		2466,2793,2745	-5.2	0.8	17	dbSNP_132	87	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR1	NM_001190438.1,NM_001190440.1,NM_006311.3	,,	7,252,6244	AA,AG,GG		0.0465,5.9464,2.0452	,,	822/915,931/2338,915/2441	16001756	266,12740	2203	4300	6503	SO:0001819	synonymous_variant	9611	exon20			TGAGACGAGTATA	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.2745C>T	17.37:g.16001756G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	119	51	0.428571	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	37	CCDS11175.1																																																																																			G|0.981;A|0.019	0.019	strong		0.378	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
ALDH3A2	224	hgsc.bcm.edu	37	17	19578873	19578873	+	Silent	SNP	A	A	T	rs7216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19578873A>T	ENST00000176643.6	+	10	1892	c.1446A>T	c.(1444-1446)gcA>gcT	p.A482A	ALDH3A2_ENST00000571163.1_Nonsense_Mutation_p.R77*|ALDH3A2_ENST00000395575.2_Silent_p.A482A|SLC47A2_ENST00000463318.1_5'Flank|ALDH3A2_ENST00000581518.1_Splice_Site|ALDH3A2_ENST00000574597.1_3'UTR|ALDH3A2_ENST00000339618.4_3'UTR|ALDH3A2_ENST00000579855.1_Silent_p.A482A			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	482					cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1)	13	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)					CTCTCCAGGCAGAATATTACT	0.398													T|||	3398	0.678514	0.5045	0.6715	5008	,	,		19666	0.9861		0.5616	False		,,,				2504	0.7219				p.A482A		Atlas-SNP	.											.	ALDH3A2	41	.	0			c.A1446T						PASS	.	T	,	2348,2058	569.2+/-382.6	618,1112,473	199.0	191.0	194.0		1446,	1.6	0.2	17	dbSNP_52	194	4814,3786	535.3+/-382.8	1329,2156,815	no	coding-synonymous,utr-3	ALDH3A2	NM_000382.2,NM_001031806.1	,	1947,3268,1288	TT,TA,AA		44.0233,46.709,44.9331	,	482/486,	19578873	7162,5844	2203	4300	6503	SO:0001819	synonymous_variant	224	exon10			CCAGGCAGAATAT	L47162	CCDS11210.1, CCDS32589.1	17p11.2	2010-05-07			ENSG00000072210	ENSG00000072210	1.2.1.3	"""Aldehyde dehydrogenases"""	403	protein-coding gene	gene with protein product	"""fatty aldehyde dehydrogenase"""	609523		SLS, ALDH10		7894487	Standard	NM_000382		Approved	FALDH	uc002gwa.1	P51648	OTTHUMG00000059471	ENST00000176643.6:c.1446A>T	17.37:g.19578873A>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	137	62	0.452555	NM_000382	Q6I9T3|Q93011|Q96J37	Silent	SNP	ENST00000176643.6	37	CCDS11210.1																																																																																			A|0.406;T|0.594	0.594	strong		0.398	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1		
RICTOR	253260	hgsc.bcm.edu	37	5	38950761	38950761	+	Silent	SNP	A	A	G	rs150422546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38950761A>G	ENST00000357387.3	-	31	3219	c.3189T>C	c.(3187-3189)gaT>gaC	p.D1063D	RICTOR_ENST00000296782.5_Silent_p.D1063D	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)					CTTCATTGATATCAAGGAAAA	0.348													A|||	6	0.00119808	0.0045	0.0	5008	,	,		17156	0.0		0.0	False		,,,				2504	0.0				p.D1063D		Atlas-SNP	.											.	RICTOR	182	.	0			c.T3189C						PASS	.	A		9,4395	15.5+/-35.6	0,9,2193	98.0	106.0	103.0		3189	-0.0	1.0	5	dbSNP_134	103	0,8592		0,0,4296	yes	coding-synonymous	RICTOR	NM_152756.3		0,9,6489	GG,GA,AA		0.0,0.2044,0.0693		1063/1709	38950761	9,12987	2202	4296	6498	SO:0001819	synonymous_variant	253260	exon31			ATTGATATCAAGG		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.3189T>C	5.37:g.38950761A>G		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	210	111	0.528571	NM_152756		Silent	SNP	ENST00000357387.3	37	CCDS34148.1																																																																																			A|0.999;G|0.001	0.001	strong		0.348	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
LILRA1	11024	hgsc.bcm.edu	37	19	55107313	55107313	+	Missense_Mutation	SNP	T	T	C	rs36029771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55107313T>C	ENST00000251372.3	+	6	1053	c.871T>C	c.(871-873)Tac>Cac	p.Y291H	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	291	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		GAGCCGCTCCTACGGGGGCCA	0.657													t|||	1458	0.291134	0.5189	0.2666	5008	,	,		15549	0.2758		0.0974	False		,,,				2504	0.2157				p.Y291H		Atlas-SNP	.											.	LILRA1	105	.	0			c.T871C						PASS	.						39.0	56.0	50.0					19																	55107313		2202	4300	6502	SO:0001583	missense	11024	exon6			CGCTCCTACGGGG	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.871T>C	19.37:g.55107313T>C	ENSP00000251372:p.Tyr291His	Somatic	310	1	0.00322581		WXS	Illumina HiSeq	Phase_I	212	201	0.948113	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	470	0.21520146520146521	193	0.39227642276422764	79	0.21823204419889503	142	0.24825174825174826	56	0.07387862796833773	t	0.004	-2.309842	0.00237	.	.	ENSG00000104974	ENST00000251372	T	0.00659	5.94	1.73	-1.24	0.09435	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.842666	0.10069	N	0.719984	T	0.00012	0.0000	N	0.00134	-2.025	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.32640	-0.9899	9	0.02654	T	1	.	4.5295	0.11997	0.0:0.4043:0.0:0.5957	rs36029771;rs61739254	291	O75019	LIRA1_HUMAN	H	291	ENSP00000251372:Y291H	ENSP00000251372:Y291H	Y	+	1	0	LILRA1	59799125	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.361000	0.07612	-0.269000	0.09298	-1.366000	0.01203	TAC	T|0.849;C|0.151	0.151	strong		0.657	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
ERI1	90459	hgsc.bcm.edu	37	8	8869129	8869129	+	Missense_Mutation	SNP	T	T	G	rs112570397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8869129T>G	ENST00000523898.1	+	4	1044	c.365T>G	c.(364-366)tTt>tGt	p.F122C	ERI1_ENST00000519292.1_Missense_Mutation_p.F122C|ERI1_ENST00000250263.7_Missense_Mutation_p.F122C			Q8IV48	ERI1_HUMAN	exoribonuclease 1	122					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						GAGAGCAATTTTGCTGACAGT	0.348													G|||	41	0.0081869	0.0303	0.0014	5008	,	,		17758	0.0		0.0	False		,,,				2504	0.0				p.F122C		Atlas-SNP	.											.	ERI1	20	.	0			c.T365G						PASS	.	G	CYS/PHE	121,4285	813.8+/-416.2	1,119,2083	82.0	82.0	82.0		365	1.7	0.0	8	dbSNP_132	82	0,8600		0,0,4300	yes	missense	ERI1	NM_153332.3	205	1,119,6383	GG,GT,TT		0.0,2.7463,0.9303	benign	122/350	8869129	121,12885	2203	4300	6503	SO:0001583	missense	90459	exon3			GCAATTTTGCTGA	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.365T>G	8.37:g.8869129T>G	ENSP00000429615:p.Phe122Cys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_153332	A8K4U7|Q9NSX3	Missense_Mutation	SNP	ENST00000523898.1	37	CCDS5972.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	G	10.23	1.293512	0.23564	0.027463	0.0	ENSG00000104626	ENST00000523898;ENST00000250263;ENST00000519292	T;T;T	0.43688	0.94;0.94;0.94	5.79	1.69	0.24217	.	1.091090	0.06714	N	0.773725	T	0.09992	0.0245	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18272	-1.0342	10	0.46703	T	0.11	-26.669	3.9327	0.09293	0.1405:0.3665:0.3736:0.1193	.	122	Q8IV48	ERI1_HUMAN	C	122	ENSP00000429615:F122C;ENSP00000250263:F122C;ENSP00000430190:F122C	ENSP00000250263:F122C	F	+	2	0	ERI1	8906539	0.000000	0.05858	0.000000	0.03702	0.943000	0.58893	-0.253000	0.08794	0.078000	0.16900	-0.231000	0.12243	TTT	T|0.991;G|0.009	0.009	strong		0.348	ERI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251471.2	NM_153332	
DSG1	1828	hgsc.bcm.edu	37	18	28919911	28919911	+	Missense_Mutation	SNP	A	A	G	rs61730306|rs386802123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28919911A>G	ENST00000257192.4	+	11	1822	c.1610A>G	c.(1609-1611)aAa>aGa	p.K537R		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	537					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)			AACGGAGCCAAAGATTTGTTA	0.418													a|||	745	0.148762	0.2428	0.0994	5008	,	,		16748	0.0645		0.0845	False		,,,				2504	0.2096				p.K537R		Atlas-SNP	.											.	DSG1	176	.	0			c.A1610G						PASS	.	G	ARG/LYS	12,4394		2,8,2193	97.0	97.0	97.0		1610	-2.2	0.0	18	dbSNP_129	97	2,8598		1,0,4299	yes	missense	DSG1	NM_001942.2	26	3,8,6492	GG,GA,AA		0.0233,0.2724,0.1076	benign	537/1050	28919911	14,12992	2203	4300	6503	SO:0001583	missense	1828	exon11			GAGCCAAAGATTT	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.1610A>G	18.37:g.28919911A>G	ENSP00000257192:p.Lys537Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	109	43	0.394495	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	250	0.11446886446886446	119	0.241869918699187	40	0.11049723756906077	33	0.057692307692307696	58	0.07651715039577836	a	0.011	-1.713122	0.00706	0.002724	2.33E-4	ENSG00000134760	ENST00000257192	T	0.56275	0.47	1.12	-2.24	0.06909	.	1.652450	0.04589	N	0.396400	T	0.00012	0.0000	N	0.12182	0.205	0.47547	P	5.460000000000464E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.07271	-1.0781	9	0.11794	T	0.64	.	4.5681	0.12196	0.5075:0.0:0.4925:0.0	rs61730306	537	Q02413	DSG1_HUMAN	R	537	ENSP00000257192:K537R	ENSP00000257192:K537R	K	+	2	0	DSG1	27173909	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.976000	0.03786	-1.292000	0.02366	-1.322000	0.01289	AAA	A|0.893;G|0.107	0.107	strong		0.418	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
PCNT	5116	hgsc.bcm.edu	37	21	47754541	47754541	+	Silent	SNP	A	A	G	rs61735824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47754541A>G	ENST00000359568.5	+	3	605	c.498A>G	c.(496-498)ccA>ccG	p.P166P	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	166					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)					ACCACCCACCAGAACAGCGTG	0.547													a|||	127	0.0253594	0.0295	0.0403	5008	,	,		21418	0.0		0.0408	False		,,,				2504	0.0194				p.P166P		Atlas-SNP	.											.	PCNT	283	.	0			c.A498G						PASS	.	A		153,4253	104.7+/-143.2	0,153,2050	199.0	128.0	152.0		498	-0.5	0.0	21	dbSNP_129	152	477,8123	140.0+/-196.6	15,447,3838	yes	coding-synonymous	PCNT	NM_006031.5		15,600,5888	GG,GA,AA		5.5465,3.4725,4.8439		166/3337	47754541	630,12376	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon3			CCCACCAGAACAG	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.498A>G	21.37:g.47754541A>G		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	334	111	0.332335	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			A|0.956;G|0.044	0.044	strong		0.547	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
TCTE1	202500	hgsc.bcm.edu	37	6	44249939	44249939	+	Silent	SNP	G	G	A	rs34405945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44249939G>A	ENST00000371505.4	-	4	1326	c.1204C>T	c.(1204-1206)Ctg>Ttg	p.L402L	TCTE1_ENST00000371503.3_Intron|RP11-444E17.6_ENST00000505802.1_Intron|TCTE1_ENST00000371504.1_Intron|TMEM151B_ENST00000438774.2_Intron	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	402										breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GGCTCAGACAGCTCATTGCCA	0.602													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		18613	0.0		0.0	False		,,,				2504	0.0				p.L402L		Atlas-SNP	.											.	TCTE1	77	.	0			c.C1204T						PASS	.	G		113,4293	85.8+/-124.5	0,113,2090	159.0	127.0	138.0		1204	2.4	1.0	6	dbSNP_126	138	1,8599		0,1,4299	yes	coding-synonymous	TCTE1	NM_182539.3		0,114,6389	AA,AG,GG		0.0116,2.5647,0.8765		402/502	44249939	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	202500	exon4			CAGACAGCTCATT	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.1204C>T	6.37:g.44249939G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	183	98	0.535519	NM_182539	B4DX59|Q8IYS6	Silent	SNP	ENST00000371505.4	37	CCDS4910.1																																																																																			G|0.988;A|0.012	0.012	strong		0.602	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539	
BOC	91653	hgsc.bcm.edu	37	3	112993412	112993412	+	Silent	SNP	C	C	T	rs7615578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112993412C>T	ENST00000495514.1	+	9	2129	c.1425C>T	c.(1423-1425)ccC>ccT	p.P475P	BOC_ENST00000273395.4_Silent_p.P475P|BOC_ENST00000355385.3_Silent_p.P475P|BOC_ENST00000497495.1_3'UTR			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	475	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			CCGAGGCTCCCATCATCCTCA	0.672													C|||	55	0.0109824	0.0401	0.0029	5008	,	,		17614	0.0		0.0	False		,,,				2504	0.0				p.P475P		Atlas-SNP	.											.	BOC	139	.	0			c.C1425T						PASS	.	C		178,4226		3,172,2027	29.0	34.0	32.0		1425	-2.2	0.3	3	dbSNP_116	32	2,8596		0,2,4297	no	coding-synonymous	BOC	NM_033254.2		3,174,6324	TT,TC,CC		0.0233,4.0418,1.3844		475/1115	112993412	180,12822	2202	4299	6501	SO:0001819	synonymous_variant	91653	exon9			GGCTCCCATCATC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1425C>T	3.37:g.112993412C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	215	104	0.483721	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.985;T|0.015	0.015	strong		0.672	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
PDIA2	64714	hgsc.bcm.edu	37	16	336396	336396	+	Missense_Mutation	SNP	G	G	A	rs400037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:336396G>A	ENST00000219406.6	+	8	1181	c.1163G>A	c.(1162-1164)cGg>cAg	p.R388Q	PDIA2_ENST00000404312.1_Missense_Mutation_p.R385Q	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	388	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.		R -> Q (in dbSNP:rs400037).		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)				TGGGATCAGCGGCCAGTTAAG	0.562													g|||	844	0.16853	0.3457	0.1455	5008	,	,		12070	0.0377		0.1899	False		,,,				2504	0.0583				p.R388Q		Atlas-SNP	.											.	PDIA2	51	.	0			c.G1163A						PASS	.		GLN/ARG	1142,2676		163,816,930	58.0	64.0	62.0		1163	-2.3	1.0	16	dbSNP_80	62	1679,6571		183,1313,2629	yes	missense	PDIA2	NM_006849.2	43	346,2129,3559	AA,AG,GG		20.3515,29.9109,23.3759	benign	388/526	336396	2821,9247	1909	4125	6034	SO:0001583	missense	64714	exon8			ATCAGCGGCCAGT	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.1163G>A	16.37:g.336396G>A	ENSP00000219406:p.Arg388Gln	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	207	102	0.492754	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	394	0.1804029304029304	177	0.3597560975609756	51	0.1408839779005525	27	0.0472027972027972	139	0.18337730870712401	g	0.021	-1.423957	0.01126	0.299109	0.203515	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312;ENST00000435833	T;T;T	0.16897	2.31;2.31;3.97	4.04	-2.31	0.06765	Thioredoxin-like fold (3);	1.119980	0.06633	N	0.759534	T	0.00012	0.0000	N	0.01188	-0.97	0.80722	P	0.0	B	0.12013	0.005	B	0.10450	0.005	T	0.46442	-0.9191	9	0.02654	T	1	.	9.7883	0.40690	0.6167:0.0:0.3833:0.0	rs400037;rs58645006;rs400037	388	Q13087	PDIA2_HUMAN	Q	388;357;385;17	ENSP00000219406:R388Q;ENSP00000384410:R385Q;ENSP00000405081:R17Q	ENSP00000219406:R388Q	R	+	2	0	PDIA2	276397	0.000000	0.05858	0.958000	0.39756	0.812000	0.45895	-0.094000	0.11094	-0.251000	0.09542	0.479000	0.44913	CGG	G|0.810;A|0.190	0.190	strong		0.562	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
CNDP2	55748	hgsc.bcm.edu	37	18	72168608	72168608	+	Silent	SNP	G	G	A	rs2303463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:72168608G>A	ENST00000324262.4	+	3	421	c.105G>A	c.(103-105)ccG>ccA	p.P35P	CNDP2_ENST00000579847.1_Silent_p.P35P|CNDP2_ENST00000324301.8_Silent_p.P35P	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	35					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.P35P(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		CTGCGTGGCCGGAGAAGAGAG	0.507													G|||	1233	0.246206	0.2231	0.3127	5008	,	,		19326	0.2956		0.164	False		,,,				2504	0.2638				p.P35P		Atlas-SNP	.											CNDP2,caecum,carcinoma,0,2	CNDP2	55	2	1	Substitution - coding silent(1)	stomach(1)	c.G105A						PASS	.	G	,	937,3469	358.4+/-314.3	119,699,1385	173.0	152.0	159.0		105,105	-11.6	0.3	18	dbSNP_100	159	1623,6977	301.7+/-305.6	134,1355,2811	no	coding-synonymous,coding-synonymous	CNDP2	NM_001168499.1,NM_018235.2	,	253,2054,4196	AA,AG,GG		18.8721,21.2665,19.6832	,	35/392,35/476	72168608	2560,10446	2203	4300	6503	SO:0001819	synonymous_variant	55748	exon2			GTGGCCGGAGAAG	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.105G>A	18.37:g.72168608G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	207	91	0.439614	NM_001168499	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Silent	SNP	ENST00000324262.4	37	CCDS12006.1																																																																																			G|0.791;A|0.209	0.209	strong		0.507	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
CSMD1	64478	hgsc.bcm.edu	37	8	2800096	2800096	+	Missense_Mutation	SNP	C	C	T	rs11984691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2800096C>T	ENST00000520002.1	-	70	10991	c.10436G>A	c.(10435-10437)aGt>aAt	p.S3479N	CSMD1_ENST00000542608.1_Missense_Mutation_p.S3301N|CSMD1_ENST00000602557.1_Missense_Mutation_p.S3479N|CSMD1_ENST00000602723.1_Missense_Mutation_p.S3302N|CSMD1_ENST00000537824.1_Missense_Mutation_p.S3478N|CSMD1_ENST00000400186.3_Missense_Mutation_p.S3302N			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3479			S -> N (in dbSNP:rs11984691).			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)		GTGGTAATGACTGGAAGAGTC	0.378													c|||	303	0.0605032	0.177	0.0346	5008	,	,		16155	0.0069		0.0119	False		,,,				2504	0.0266				p.S3478N		Atlas-SNP	.											.	CSMD1	1469	.	0			c.G10433A						PASS	.	T	ASN/SER	559,3139		50,459,1340	47.0	50.0	49.0		10433	0.6	0.0	8	dbSNP_120	49	146,8032		3,140,3946	yes	missense	CSMD1	NM_033225.5	46	53,599,5286	TT,TC,CC		1.7853,15.1163,5.9363	benign	3478/3565	2800096	705,11171	1849	4089	5938	SO:0001583	missense	64478	exon69			TAATGACTGGAAG			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.10436G>A	8.37:g.2800096C>T	ENSP00000430733:p.Ser3479Asn	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	71	42	0.591549	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		133	0.060897435897435896	106	0.21544715447154472	17	0.04696132596685083	4	0.006993006993006993	6	0.0079155672823219	c	0.274	-0.990665	0.02162	0.151163	0.017853	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T;T;T;T	0.22539	1.95;2.03;2.05;1.95	5.67	0.558	0.17266	.	0.121454	0.53938	N	0.000060	T	0.00012	0.0000	N	0.01505	-0.83	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	0.45411	-0.9263	9	0.02654	T	1	.	11.0611	0.47948	0.0:0.2633:0.0:0.7367	rs11984691;rs52793013;rs59724479;rs11984691	3479;3479;3301	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	N	3302;3479;3340;3478;3301	ENSP00000383047:S3302N;ENSP00000430733:S3479N;ENSP00000441462:S3478N;ENSP00000446243:S3301N	ENSP00000320445:S3340N	S	-	2	0	CSMD1	2787503	0.957000	0.32711	0.000000	0.03702	0.003000	0.03518	1.593000	0.36686	-0.388000	0.07797	-2.082000	0.00379	AGT	C|0.939;T|0.061	0.061	strong		0.378	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
ZNF202	7753	hgsc.bcm.edu	37	11	123600475	123600475	+	Missense_Mutation	SNP	A	A	G	rs1144507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123600475A>G	ENST00000529691.1	-	3	680	c.461T>C	c.(460-462)gTg>gCg	p.V154A	ZNF202_ENST00000530393.1_Missense_Mutation_p.V154A|ZNF202_ENST00000336139.4_Missense_Mutation_p.V154A			O95125	ZN202_HUMAN	zinc finger protein 202	154			V -> A (in dbSNP:rs1144507). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9790754, ECO:0000269|Ref.2, ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		CTCAGGCTCCACTCCTAAATG	0.567													G|||	3332	0.665335	0.767	0.6744	5008	,	,		17779	0.4812		0.7038	False		,,,				2504	0.6718				p.V154A		Atlas-SNP	.											.	ZNF202	72	.	0			c.T461C						PASS	.	G	ALA/VAL	3349,1055	385.4+/-325.7	1283,783,136	80.0	73.0	75.0		461	2.2	0.1	11	dbSNP_87	75	5952,2646	428.2+/-355.8	2060,1832,407	yes	missense	ZNF202	NM_003455.2	64	3343,2615,543	GG,GA,AA		30.7746,23.9555,28.4649	benign	154/649	123600475	9301,3701	2202	4299	6501	SO:0001583	missense	7753	exon5			GGCTCCACTCCTA	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.461T>C	11.37:g.123600475A>G	ENSP00000433881:p.Val154Ala	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	37	CCDS8443.1	1449	0.6634615384615384	370	0.7520325203252033	263	0.7265193370165746	294	0.513986013986014	522	0.6886543535620053	G	0.954	-0.705563	0.03255	0.760445	0.692254	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691	T;T;T	0.05199	3.48;3.48;3.48	5.32	2.24	0.28232	Transcription regulator SCAN (1);	0.889113	0.09433	N	0.802821	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18366	-1.0339	9	0.07482	T	0.82	0.0046	3.4437	0.07473	0.291:0.0:0.5312:0.1778	rs1144507;rs1676625;rs17127630;rs17845378;rs17858233;rs52822077;rs61168479;rs1144507	154	O95125	ZN202_HUMAN	A	154	ENSP00000337724:V154A;ENSP00000432504:V154A;ENSP00000433881:V154A	ENSP00000337724:V154A	V	-	2	0	ZNF202	123105685	0.015000	0.18098	0.097000	0.21041	0.608000	0.37181	0.449000	0.21744	0.242000	0.21303	-0.226000	0.12346	GTG	A|0.307;G|0.693	0.693	strong		0.567	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
LRP12	29967	hgsc.bcm.edu	37	8	105503401	105503401	+	Missense_Mutation	SNP	T	T	C	rs16871494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:105503401T>C	ENST00000276654.5	-	7	2188	c.2080A>G	c.(2080-2082)Agt>Ggt	p.S694G	LRP12_ENST00000518375.1_5'UTR|LRP12_ENST00000424843.2_Missense_Mutation_p.S675G	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	694			S -> G (in dbSNP:rs16871494).		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(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			GTTGAGGAACTTGCACATGCT	0.532													T|||	177	0.0353435	0.1286	0.0072	5008	,	,		19333	0.0		0.002	False		,,,				2504	0.0				p.S694G		Atlas-SNP	.											.	LRP12	124	.	0			c.A2080G						PASS	.	T	GLY/SER,GLY/SER	469,3937	220.4+/-237.8	15,439,1749	99.0	84.0	90.0		2023,2080	3.1	0.8	8	dbSNP_123	90	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	LRP12	NM_001135703.2,NM_013437.4	56,56	15,444,6044	CC,CT,TT		0.0581,10.6446,3.6445	benign,benign	675/841,694/860	105503401	474,12532	2203	4300	6503	SO:0001583	missense	29967	exon7			AGGAACTTGCACA	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.2080A>G	8.37:g.105503401T>C	ENSP00000276654:p.Ser694Gly	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	189	93	0.492063	NM_013437	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000276654.5	37	CCDS6303.1	80	0.03663003663003663	78	0.15853658536585366	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	8.256	0.809999	0.16537	0.106446	5.81E-4	ENSG00000147650	ENST00000424843;ENST00000276654;ENST00000520873	D;D	0.85484	-1.99;-1.94	5.49	3.13	0.36017	.	0.595743	0.20652	N	0.088183	T	0.00608	0.0020	N	0.14661	0.345	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.00857	-1.1538	10	0.38643	T	0.18	-5.7539	8.0472	0.30555	0.0:0.2201:0.0:0.7799	rs16871494;rs52835469;rs16871494	675;694	Q9Y561-2;Q9Y561	.;LRP12_HUMAN	G	675;694;59	ENSP00000399148:S675G;ENSP00000276654:S694G	ENSP00000276654:S694G	S	-	1	0	LRP12	105572577	0.961000	0.32948	0.772000	0.31596	0.845000	0.48019	1.626000	0.37039	0.482000	0.27582	0.528000	0.53228	AGT	T|0.957;C|0.043	0.043	strong		0.532	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437	
ITGA2B	3674	hgsc.bcm.edu	37	17	42455126	42455126	+	Silent	SNP	C	C	T	rs114232872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42455126C>T	ENST00000262407.5	-	21	2158	c.2127G>A	c.(2125-2127)aaG>aaA	p.K709K	ITGA2B_ENST00000353281.4_Silent_p.K709K	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	709					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	TCTCATTCTCCTTCTTCTGAT	0.502													C|||	24	0.00479233	0.0159	0.0043	5008	,	,		14353	0.0		0.0	False		,,,				2504	0.0				p.K709K		Atlas-SNP	.											.	ITGA2B	88	.	0			c.G2127A						PASS	.	C		57,4349	54.9+/-90.9	0,57,2146	86.0	75.0	79.0		2127	-0.0	1.0	17	dbSNP_132	79	0,8600		0,0,4300	no	coding-synonymous	ITGA2B	NM_000419.3		0,57,6446	TT,TC,CC		0.0,1.2937,0.4383		709/1040	42455126	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	3674	exon21			ATTCTCCTTCTTC		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.2127G>A	17.37:g.42455126C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	37	CCDS32665.1																																																																																			C|0.995;T|0.005	0.005	strong		0.502	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		
XPO6	23214	hgsc.bcm.edu	37	16	28123226	28123226	+	Silent	SNP	G	G	A	rs205384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:28123226G>A	ENST00000304658.5	-	17	2753	c.2253C>T	c.(2251-2253)caC>caT	p.H751H	XPO6_ENST00000565698.1_Silent_p.H737H	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	751					protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						TGAGGCTGGCGTGGTTGATGG	0.587													G|||	833	0.166334	0.1339	0.2363	5008	,	,		16977	0.1032		0.2773	False		,,,				2504	0.1115				p.H751H		Atlas-SNP	.											.	XPO6	177	.	0			c.C2253T						PASS	.	G		622,3610		54,514,1548	72.0	79.0	77.0		2253	-6.3	0.3	16	dbSNP_79	77	2468,5998		368,1732,2133	no	coding-synonymous	XPO6	NM_015171.2		422,2246,3681	AA,AG,GG		29.1519,14.6975,24.3345		751/1126	28123226	3090,9608	2116	4233	6349	SO:0001819	synonymous_variant	23214	exon17			GCTGGCGTGGTTG	AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"""Exportins"""	19733	protein-coding gene	gene with protein product		608411	"""RAN binding protein 20"""	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.2253C>T	16.37:g.28123226G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	174	82	0.471264	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Silent	SNP	ENST00000304658.5	37	CCDS42135.1																																																																																			A|0.220;C|0.000;G|0.780	0.220	strong		0.587	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195	
ANKIB1	54467	hgsc.bcm.edu	37	7	92027537	92027537	+	Silent	SNP	C	C	G	rs1861635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:92027537C>G	ENST00000265742.3	+	20	2920	c.2544C>G	c.(2542-2544)tcC>tcG	p.S848S		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	848							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CTCTGAGTTCCTTGGATGAAG	0.398													C|||	775	0.154752	0.0643	0.1167	5008	,	,		16849	0.3413		0.0845	False		,,,				2504	0.184				p.S848S		Atlas-SNP	.											.	ANKIB1	92	.	0			c.C2544G						PASS	.	C		219,3475		1,217,1629	66.0	60.0	61.0		2544	5.0	1.0	7	dbSNP_92	61	788,7438		46,696,3371	no	coding-synonymous	ANKIB1	NM_019004.1		47,913,5000	GG,GC,CC		9.5794,5.9285,8.448		848/1090	92027537	1007,10913	1847	4113	5960	SO:0001819	synonymous_variant	54467	exon20			GAGTTCCTTGGAT	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.2544C>G	7.37:g.92027537C>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	120	63	0.525	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Silent	SNP	ENST00000265742.3	37	CCDS47639.1																																																																																			C|0.845;G|0.155	0.155	strong		0.398	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1		
GPR112	139378	hgsc.bcm.edu	37	X	135430483	135430483	+	Missense_Mutation	SNP	T	T	C	rs912002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:135430483T>C	ENST00000394143.1	+	6	4909	c.4618T>C	c.(4618-4620)Tct>Cct	p.S1540P	GPR112_ENST00000412101.1_Missense_Mutation_p.S1335P|GPR112_ENST00000370652.1_Missense_Mutation_p.S1540P|GPR112_ENST00000287534.4_Missense_Mutation_p.S1477P|GPR112_ENST00000394141.1_Missense_Mutation_p.S1335P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1540			S -> P (in dbSNP:rs912002).		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					AACTAAATCTTCTAAAACAAT	0.418													t|||	1764	0.467285	0.4251	0.3573	3775	,	,		14599	0.255		0.3797	False		,,,				2504	0.3221				p.S1540P		Atlas-SNP	.											.	GPR112	459	.	0			c.T4618C						PASS	.		PRO/SER	2110,1725		493,813,311,326,260	96.0	94.0	95.0		4618	1.7	0.1	X	dbSNP_86	95	3223,3505		567,1177,912,684,960	yes	missense	GPR112	NM_153834.3	74	1060,1990,1223,1010,1220	CC,CT,C,TT,T		47.9043,44.9804,49.5124	probably-damaging	1540/3081	135430483	5333,5230	2203	4300	6503	SO:0001583	missense	139378	exon6			AAATCTTCTAAAA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4618T>C	X.37:g.135430483T>C	ENSP00000377699:p.Ser1540Pro	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	163	111	0.680982	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	754	0.45449065702230257	137	0.37027027027027026	83	0.2902097902097902	103	0.22391304347826088	190	0.3242320819112628	t	14.52	2.560180	0.45590	0.550196	0.479043	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.40756	1.06;1.06;1.02;1.13;1.02	3.02	1.66	0.24008	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	D;D;D	0.76494	0.997;0.999;0.998	D;D;D	0.80764	0.986;0.994;0.987	T	0.44483	-0.9325	8	0.87932	D	0	.	4.2365	0.10628	0.3093:0.0:0.0:0.6907	rs912002;rs52799687;rs61339577;rs912002	1477;1335;1540	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	P	1540;1540;1335;1477;1335	ENSP00000377699:S1540P;ENSP00000359686:S1540P;ENSP00000416526:S1335P;ENSP00000287534:S1477P;ENSP00000377697:S1335P	ENSP00000287534:S1477P	S	+	1	0	GPR112	135258149	0.316000	0.24580	0.086000	0.20670	0.250000	0.25880	0.927000	0.28818	1.195000	0.43115	0.378000	0.23410	TCT	0|0.015;C|0.478	0.478	strong		0.418	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
EVA1C	59271	hgsc.bcm.edu	37	21	33867447	33867447	+	Missense_Mutation	SNP	G	G	A	rs61744983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33867447G>A	ENST00000300255.2	+	5	1218	c.745G>A	c.(745-747)Gtg>Atg	p.V249M	EVA1C_ENST00000382699.3_Missense_Mutation_p.V249M|EVA1C_ENST00000401402.3_Intron|EVA1C_ENST00000485488.1_3'UTR	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	249	SUEL-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00260}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										TTTGCCAGGCGTGAAAAAATA	0.507													G|||	16	0.00319489	0.0121	0.0	5008	,	,		18504	0.0		0.0	False		,,,				2504	0.0				p.V249M		Atlas-SNP	.											.	.	.	.	0			c.G745A						PASS	.	G	MET/VAL	36,4370	40.0+/-72.8	0,36,2167	133.0	106.0	115.0		745	5.6	1.0	21	dbSNP_129	115	0,8600		0,0,4300	yes	missense	C21orf63	NM_058187.3	21	0,36,6467	AA,AG,GG		0.0,0.8171,0.2768	possibly-damaging	249/442	33867447	36,12970	2203	4300	6503	SO:0001583	missense	59271	exon5			CCAGGCGTGAAAA	AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 64"", ""chromosome 21 open reading frame 63"", ""family with sequence similarity 176, member C"""	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.745G>A	21.37:g.33867447G>A	ENSP00000300255:p.Val249Met	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	159	88	0.553459	NM_058187	A6ND58|Q8IXZ0	Missense_Mutation	SNP	ENST00000300255.2	37	CCDS13614.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	24.5	4.540898	0.85917	0.008171	0.0	ENSG00000166979	ENST00000300255;ENST00000382699	T;T	0.19250	2.16;2.16	5.62	5.62	0.85841	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.245509	0.41605	D	0.000854	T	0.41766	0.1173	M	0.75884	2.315	0.46564	D	0.999108	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.987	T	0.40664	-0.9551	10	0.56958	D	0.05	0.1652	19.264	0.93979	0.0:0.0:1.0:0.0	rs61744983	249;249	A6ND58;P58658	.;CU063_HUMAN	M	249	ENSP00000300255:V249M;ENSP00000372146:V249M	ENSP00000300255:V249M	V	+	1	0	C21orf63	32789318	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.445000	0.73456	2.631000	0.89168	0.655000	0.94253	GTG	G|0.997;A|0.003	0.003	strong		0.507	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187	
ZBP1	81030	hgsc.bcm.edu	37	20	56189985	56189985	+	Missense_Mutation	SNP	C	C	G	rs16981187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:56189985C>G	ENST00000371173.3	-	4	637	c.460G>C	c.(460-462)Gac>Cac	p.D154H	ZBP1_ENST00000343535.4_Missense_Mutation_p.D154H|ZBP1_ENST00000541799.1_Missense_Mutation_p.D154H|ZBP1_ENST00000538947.1_5'Flank|ZBP1_ENST00000395822.3_Missense_Mutation_p.D79H|ZBP1_ENST00000340462.4_Missense_Mutation_p.D131H	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	154			D -> H (in dbSNP:rs16981187).		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)			TCATCCATGTCCAGAAGGTGC	0.572													C|||	268	0.0535144	0.0719	0.0432	5008	,	,		21012	0.0079		0.0487	False		,,,				2504	0.0879				p.D154H		Atlas-SNP	.											.	ZBP1	65	.	0			c.G460C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	317,4089	169.4+/-200.1	15,287,1901	222.0	174.0	191.0		460,235,460,460	-5.4	0.0	20	dbSNP_123	191	408,8192	128.7+/-186.9	13,382,3905	yes	missense,missense,missense,missense	ZBP1	NM_001160417.1,NM_001160418.1,NM_001160419.1,NM_030776.2	81,81,81,81	28,669,5806	GG,GC,CC		4.7442,7.1947,5.5744	probably-damaging,probably-damaging,probably-damaging,probably-damaging	154/429,79/355,154/249,154/430	56189985	725,12281	2203	4300	6503	SO:0001583	missense	81030	exon4			CCATGTCCAGAAG	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.460G>C	20.37:g.56189985C>G	ENSP00000360215:p.Asp154His	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	249	127	0.51004	NM_001160419	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Missense_Mutation	SNP	ENST00000371173.3	37	CCDS13461.1	95	0.043498168498168496	38	0.07723577235772358	18	0.049723756906077346	1	0.0017482517482517483	38	0.05013192612137203	C	9.503	1.103680	0.20632	0.071947	0.047442	ENSG00000124256	ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535;ENST00000541799	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	3.39	-5.43	0.02632	Winged helix-turn-helix transcription repressor DNA-binding (1);	1.755500	0.02862	N	0.130409	T	0.00875	0.0029	N	0.17082	0.46	0.09310	N	1	B;B;B;B	0.32543	0.324;0.375;0.375;0.375	B;B;B;B	0.34301	0.077;0.126;0.179;0.126	T	0.08493	-1.0719	10	0.42905	T	0.14	-2.5151	5.7903	0.18357	0.0:0.1813:0.4126:0.406	rs16981187;rs16981187	154;154;79;154	F5GYT1;A2RRL9;A2A2F7;Q9H171	.;.;.;ZBP1_HUMAN	H	154;79;131;154;154;154	ENSP00000360215:D154H;ENSP00000379167:D79H;ENSP00000344954:D131H;ENSP00000340584:D154H;ENSP00000440552:D154H	ENSP00000344954:D131H	D	-	1	0	ZBP1	55623391	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.232000	0.02936	-1.257000	0.02475	-0.175000	0.13238	GAC	C|0.946;G|0.054	0.054	strong		0.572	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776	
MAK	4117	hgsc.bcm.edu	37	6	10792040	10792040	+	Missense_Mutation	SNP	C	C	A	rs62000445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10792040C>A	ENST00000313243.2	-	10	1566	c.1184G>T	c.(1183-1185)cGt>cTt	p.R395L	SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000536370.1_3'UTR|MAK_ENST00000474039.1_Missense_Mutation_p.R395L|RP11-637O19.3_ENST00000480294.1_Intron|MAK_ENST00000538030.1_Missense_Mutation_p.R395L|MAK_ENST00000354489.2_Missense_Mutation_p.R395L			P20794	MAK_HUMAN	male germ cell-associated kinase	395					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				CTGACCCCAACGCCTCCTACC	0.448													C|||	48	0.00958466	0.0348	0.0029	5008	,	,		17957	0.0		0.0	False		,,,				2504	0.0				p.R395L		Atlas-SNP	.											MAK,NS,carcinoma,-1,1	MAK	47	1	0			c.G1184T						PASS	.	C	LEU/ARG,LEU/ARG	125,4281	93.4+/-132.2	3,119,2081	114.0	104.0	107.0		1184,1184	5.0	0.9	6	dbSNP_129	107	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	MAK	NM_001242385.1,NM_005906.4	102,102	3,120,6380	AA,AC,CC		0.0116,2.837,0.9688	probably-damaging,probably-damaging	395/584,395/624	10792040	126,12880	2203	4300	6503	SO:0001583	missense	4117	exon10			CCCCAACGCCTCC		CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1184G>T	6.37:g.10792040C>A	ENSP00000313021:p.Arg395Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	C	22.3	4.265065	0.80358	0.02837	1.16E-4	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030	T;T;T	0.77877	-1.13;-1.13;-0.92	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.86230	0.5883	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.87928	0.2708	10	0.87932	D	0	.	16.8762	0.86052	0.0:1.0:0.0:0.0	.	395	P20794	MAK_HUMAN	L	395	ENSP00000313021:R395L;ENSP00000346484:R395L;ENSP00000442250:R395L	ENSP00000313021:R395L	R	-	2	0	MAK	10900026	0.999000	0.42202	0.902000	0.35471	0.522000	0.34438	5.363000	0.66104	2.487000	0.83934	0.655000	0.94253	CGT	C|0.991;A|0.009	0.009	strong		0.448	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906	
ACAP2	23527	hgsc.bcm.edu	37	3	195027339	195027339	+	Silent	SNP	G	G	A	rs12491026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195027339G>A	ENST00000326793.6	-	13	1247	c.1017C>T	c.(1015-1017)tgC>tgT	p.C339C		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	339	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						CCTGGAGCATGCAACTTCTAA	0.383													g|||	339	0.0676917	0.0507	0.0836	5008	,	,		15108	0.128		0.0119	False		,,,				2504	0.0746				p.C339C		Atlas-SNP	.											.	ACAP2	72	.	0			c.C1017T						PASS	.	A		204,4202	128.6+/-165.4	3,198,2002	110.0	110.0	110.0		1017	-1.1	1.0	3	dbSNP_120	110	157,8443	74.8+/-137.4	1,155,4144	no	coding-synonymous	ACAP2	NM_012287.5		4,353,6146	AA,AG,GG		1.8256,4.63,2.7756		339/779	195027339	361,12645	2203	4300	6503	SO:0001819	synonymous_variant	23527	exon13			GAGCATGCAACTT		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16469	protein-coding gene	gene with protein product		607766	"""centaurin, beta 2"""	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.1017C>T	3.37:g.195027339G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Silent	SNP	ENST00000326793.6	37	CCDS33924.1	120	0.054945054945054944	24	0.04878048780487805	30	0.08287292817679558	55	0.09615384615384616	11	0.014511873350923483	g	6.170	0.399485	0.11696	0.0463	0.018256	ENSG00000114331	ENST00000439758	.	.	.	5.68	-1.11	0.09840	.	.	.	.	.	T	0.02929	0.0087	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.07693	-1.0759	4	.	.	.	.	11.9371	0.52880	0.3522:0.0:0.6478:0.0	rs12491026;rs12491026	.	.	.	Y	214	.	.	H	-	1	0	ACAP2	196508628	1.000000	0.71417	0.987000	0.45799	0.712000	0.41017	1.237000	0.32695	-0.420000	0.07427	-1.249000	0.01516	CAT	G|0.957;A|0.043	0.043	strong		0.383	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287	
PPP1R11	6992	hgsc.bcm.edu	37	6	30036471	30036471	+	Silent	SNP	C	C	A	rs2074482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30036471C>A	ENST00000376772.3	+	2	497	c.174C>A	c.(172-174)tcC>tcA	p.S58S	PPP1R11_ENST00000376769.2_Silent_p.S6S|PPP1R11_ENST00000376763.1_Silent_p.S6S|PPP1R11_ENST00000376773.1_Silent_p.S6S|PPP1R11_ENST00000376758.1_Silent_p.S6S|PPP1R11_ENST00000376765.2_Silent_p.S6S	NM_021959.2	NP_068778.1	O60927	PP1RB_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 11	58						cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)			lung(2)|ovary(1)|prostate(1)|skin(2)	6						GCCGCTCATCCAAATGTGAGT	0.507													A|||	958	0.191294	0.2988	0.1744	5008	,	,		18885	0.1905		0.0954	False		,,,				2504	0.1575				p.S58S	Pancreas(185;1767 3918 43793)	Atlas-SNP	.											.	PPP1R11	10	.	0			c.C174A						PASS	.	A		772,2250		93,586,832	78.0	72.0	74.0		174	-0.3	1.0	6	dbSNP_96	74	650,4768		48,554,2107	no	coding-synonymous	PPP1R11	NM_021959.2		141,1140,2939	AA,AC,CC		11.997,25.546,16.8483		58/127	30036471	1422,7018	1511	2709	4220	SO:0001819	synonymous_variant	6992	exon2			CTCATCCAAATGT	X81003	CCDS4671.1	6p21.3	2012-04-17			ENSG00000204619	ENSG00000204619		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9285	protein-coding gene	gene with protein product		606670		TCTE5		9843442, 8781118	Standard	NM_021959		Approved	HCGV, Tctex5, HCG-V	uc003npb.3	O60927	OTTHUMG00000031260	ENST00000376772.3:c.174C>A	6.37:g.30036471C>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_021959		Silent	SNP	ENST00000376772.3	37	CCDS4671.1																																																																																			C|0.809;A|0.191	0.191	strong		0.507	PPP1R11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076557.3	NM_021959	
HLA-DOA	3111	hgsc.bcm.edu	37	6	32975896	32975896	+	Silent	SNP	A	A	G	rs364950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32975896A>G	ENST00000229829.5	-	2	300	c.225T>C	c.(223-225)ggT>ggC	p.G75G	HLA-DOA_ENST00000495532.1_5'UTR|HLA-DOA_ENST00000450833.2_Silent_p.G45G	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	75	Alpha-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)|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						GGGCAAAGTCACCAAACTCAG	0.612													G|||	401	0.0800719	0.233	0.0749	5008	,	,		16847	0.0		0.0408	False		,,,				2504	0.0				p.G75G		Atlas-SNP	.											.	HLA-DOA	22	.	0			c.T225C						PASS	.	G		616,2406		51,514,946	58.0	52.0	54.0		225	1.6	0.1	6	dbSNP_80	54	141,5277		1,139,2569	no	coding-synonymous	HLA-DOA	NM_002119.3		52,653,3515	GG,GA,AA		2.6024,20.3839,8.9692		75/251	32975896	757,7683	1511	2709	4220	SO:0001819	synonymous_variant	3111	exon2			AAAGTCACCAAAC	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.225T>C	6.37:g.32975896A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_002119	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Silent	SNP	ENST00000229829.5	37	CCDS4763.1																																																																																			A|0.906;G|0.094	0.094	strong		0.612	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119	
XIRP2	129446	hgsc.bcm.edu	37	2	168041152	168041152	+	Splice_Site	SNP	T	T	C	rs16853169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:168041152T>C	ENST00000409728.1	+	4	750		c.e4+2		XIRP2_ENST00000420519.1_Splice_Site|XIRP2_ENST00000409605.1_5'Flank|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409195.1_Intron|XIRP2_ENST00000295237.9_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_5'Flank	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	165	0	0		WXS	Illumina HiSeq	Phase_I	172	89	0.517442	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
KIF1C	10749	hgsc.bcm.edu	37	17	4904564	4904564	+	Silent	SNP	T	T	C	rs17707385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4904564T>C	ENST00000320785.5	+	5	588	c.231T>C	c.(229-231)atT>atC	p.I77I		NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	77	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						ATCGGGACATTGGAGAAGAGA	0.532													T|||	236	0.0471246	0.0076	0.0591	5008	,	,		21465	0.0466		0.1133	False		,,,				2504	0.0245				p.I77I	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											.	KIF1C	70	.	0			c.T231C						PASS	.	T		84,4322	70.9+/-108.8	1,82,2120	107.0	97.0	101.0		231	-2.8	1.0	17	dbSNP_123	101	924,7676	204.2+/-247.0	42,840,3418	no	coding-synonymous	KIF1C	NM_006612.5		43,922,5538	CC,CT,TT		10.7442,1.9065,7.7503		77/1104	4904564	1008,11998	2203	4300	6503	SO:0001819	synonymous_variant	10749	exon5			GGACATTGGAGAA	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.231T>C	17.37:g.4904564T>C		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	210	106	0.504762	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																			C|0.070;N|0.000	0.070	strong		0.532	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
ADGB	79747	hgsc.bcm.edu	37	6	147049868	147049868	+	Silent	SNP	G	G	A	rs3747756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:147049868G>A	ENST00000397944.3	+	20	2587	c.2511G>A	c.(2509-2511)caG>caA	p.Q837Q	ADGB_ENST00000367493.3_Silent_p.Q256Q	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	837					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						TAACTGCACAGCACTTCAGGG	0.413													G|||	1492	0.297923	0.3669	0.2651	5008	,	,		18092	0.4325		0.161	False		,,,				2504	0.2301				p.Q837Q		Atlas-SNP	.											.	ADGB	93	.	0			c.G2511A						PASS	.	G		494,890		96,302,294	104.0	90.0	94.0		2511	-1.8	1.0	6	dbSNP_107	94	581,2601		55,471,1065	no	coding-synonymous	C6orf103	NM_024694.3		151,773,1359	AA,AG,GG		18.259,35.6936,23.5436		837/1668	147049868	1075,3491	692	1591	2283	SO:0001819	synonymous_variant	79747	exon20			TGCACAGCACTTC	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.2511G>A	6.37:g.147049868G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	37																																																																																				G|0.716;A|0.284	0.284	strong		0.413	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
NIN	51199	hgsc.bcm.edu	37	14	51227000	51227000	+	Silent	SNP	A	A	G	rs4901055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:51227000A>G	ENST00000382041.3	-	17	2164	c.1974T>C	c.(1972-1974)caT>caC	p.H658H	NIN_ENST00000453196.1_Silent_p.H658H|NIN_ENST00000389868.3_Silent_p.H658H|NIN_ENST00000324330.9_Silent_p.H658H|NIN_ENST00000245441.5_Silent_p.H658H|NIN_ENST00000382043.4_Silent_p.H658H|NIN_ENST00000530997.2_Silent_p.H658H	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	658					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)					TTTCGTTCTCATGCCTTTGCT	0.478			T	PDGFRB	MPD								A|||	743	0.148363	0.3775	0.1138	5008	,	,		21891	0.004		0.1243	False		,,,				2504	0.0368				p.H658H		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.T1974C						PASS	.	A	,,,	1517,2889	444.3+/-347.3	258,1001,944	73.0	79.0	77.0		1974,1974,1974,1974	-0.7	0.6	14	dbSNP_111	77	1259,7341	243.5+/-273.1	111,1037,3152	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	,,,	369,2038,4096	GG,GA,AA		14.6395,34.4303,21.344	,,,	658/1378,658/2134,658/2047,658/2091	51227000	2776,10230	2203	4300	6503	SO:0001819	synonymous_variant	51199	exon17			GTTCTCATGCCTT	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.1974T>C	14.37:g.51227000A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	37	CCDS32079.1	341	0.15613553113553114	195	0.39634146341463417	48	0.13259668508287292	3	0.005244755244755245	95	0.12532981530343007	A	0.227	-1.023764	0.02061	0.344303	0.146395	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	5.93	-0.694	0.11294	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999822304	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.5257	13.3399	0.60538	0.6236:0.0:0.3764:0.0	rs4901055;rs59513340;rs4901055	.	.	.	R	149	.	.	X	-	1	0	NIN	50296750	0.002000	0.14202	0.582000	0.28627	0.047000	0.14425	-0.071000	0.11505	-0.332000	0.08489	-1.431000	0.01090	TGA	A|0.812;G|0.188	0.188	strong		0.478	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163205	163205	+	Silent	SNP	G	G	C	rs3810870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:163205G>C	ENST00000283426.6	+	11	2000	c.1950G>C	c.(1948-1950)gcG>gcC	p.A650A		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	650							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A650A(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GGGAACCTGCGCAACCACTGT	0.677																																					p.A650A		Atlas-SNP	.											PLEKHG4B_ENST00000283426,NS,carcinoma,0,1	PLEKHG4B	167	1	1	Substitution - coding silent(1)	prostate(1)	c.G1950C						PASS	.	C		3210,1132		1209,792,170	11.0	11.0	11.0		1950	-0.2	0.0	5	dbSNP_107	11	5916,2618		2093,1730,444	no	coding-synonymous	PLEKHG4B	NM_052909.3		3302,2522,614	CC,CG,GG		30.6773,26.0709,29.124		650/1272	163205	9126,3750	2171	4267	6438	SO:0001819	synonymous_variant	153478	exon11			ACCTGCGCAACCA	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1950G>C	5.37:g.163205G>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_052909		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																			G|0.419;C|0.581	0.581	strong		0.677	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
PRDM6	93166	hgsc.bcm.edu	37	5	122425832	122425832	+	Silent	SNP	G	G	T	rs13182369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:122425832G>T	ENST00000407847.4	+	2	537	c.123G>T	c.(121-123)gcG>gcT	p.A41A	AC106786.1_ENST00000458103.2_RNA|AC106786.1_ENST00000442777.2_RNA	NM_001136239.1	NP_001129711.1	Q9NQX0	PRDM6_HUMAN	PR domain containing 6	41					negative regulation of smooth muscle cell differentiation (GO:0051151)|negative regulation of transcription, DNA-templated (GO:0045892)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.A41A(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	7						GCGGCGCCGCGGGTCTCCTGA	0.761													G|||	1111	0.221845	0.2753	0.2622	5008	,	,		8018	0.0337		0.3966	False		,,,				2504	0.135				p.A41A		Atlas-SNP	.											PRDM6,NS,NS,0,1	PRDM6	26	1	1	Substitution - coding silent(1)	NS(1)	c.G123T						PASS	.						1.0	2.0	2.0					5																	122425832		394	1099	1493	SO:0001819	synonymous_variant	93166	exon2			CGCCGCGGGTCTC	AF272898	CCDS47259.1	5q21-q23	2013-01-08			ENSG00000061455	ENSG00000061455		"""Zinc fingers, C2H2-type"""	9350	protein-coding gene	gene with protein product							Standard	NM_001136239		Approved		uc003kti.3	Q9NQX0	OTTHUMG00000150469	ENST00000407847.4:c.123G>T	5.37:g.122425832G>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	30	17	0.566667	NM_001136239	B5MCJ4|Q9NQW9	Silent	SNP	ENST00000407847.4	37	CCDS47259.1																																																																																			G|0.741;T|0.259	0.259	strong		0.761	PRDM6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318226.2	XM_049619	
MUC4	4585	hgsc.bcm.edu	37	3	195511447	195511447	+	Missense_Mutation	SNP	G	G	A	rs577730605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511447G>A	ENST00000463781.3	-	2	7463	c.7004C>T	c.(7003-7005)aCg>aTg	p.T2335M	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2335M	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.T2335M(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)		AGGAAGAGGCGTGGTGTCACC	0.597													.|||	23	0.00459265	0.0159	0.0	5008	,	,		17550	0.0		0.001	False		,,,				2504	0.001				p.T2335M		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	1	Substitution - Missense(1)	endometrium(1)	c.C7004T						scavenged	.						5.0	6.0	6.0					3																	195511447		581	1479	2060	SO:0001583	missense	4585	exon2			AGAGGCGTGGTGT	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.7004C>T	3.37:g.195511447G>A	ENSP00000417498:p.Thr2335Met	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	119	7	0.0588235	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	3.781	-0.045698	0.07452	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36699	1.24;1.28	.	.	.	.	1.329500	0.07018	U	0.826373	T	0.30978	0.0782	N	0.19112	0.55	0.09310	N	1	D	0.64830	0.994	P	0.52909	0.713	T	0.26677	-1.0096	8	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	2335	E7ESK3	.	M	2335	ENSP00000417498:T2335M;ENSP00000420243:T2335M	.	T	-	2	0	MUC4	196995842	0.000000	0.05858	0.018000	0.16275	0.025000	0.11179	-0.545000	0.06069	0.064000	0.16427	0.064000	0.15345	ACG	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CTTN	2017	hgsc.bcm.edu	37	11	70279759	70279759	+	Missense_Mutation	SNP	G	G	A	rs56162978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:70279759G>A	ENST00000301843.8	+	17	1657	c.1451G>A	c.(1450-1452)aGc>aAc	p.S484N	CTTN_ENST00000376561.3_Missense_Mutation_p.S447N|CTTN_ENST00000538675.1_Missense_Mutation_p.S168N|CTTN_ENST00000346329.3_Missense_Mutation_p.S447N	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	484					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)		TTAGAGGACAGCACCTACGAT	0.517													G|||	261	0.0521166	0.1884	0.0173	5008	,	,		16431	0.0		0.0	False		,,,				2504	0.0				p.S484N		Atlas-SNP	.											.	CTTN	162	.	0			c.G1451A						PASS	.		ASN/SER,ASN/SER,ASN/SER	788,3612	319.1+/-295.9	55,678,1467	159.0	153.0	155.0		1340,1451,1340	-0.8	0.0	11	dbSNP_129	155	5,8583	3.7+/-12.6	0,5,4289	yes	missense,missense,missense	CTTN	NM_001184740.1,NM_005231.3,NM_138565.2	46,46,46	55,683,5756	AA,AG,GG		0.0582,17.9091,6.1056	benign,benign,benign	447/635,484/551,447/514	70279759	793,12195	2200	4294	6494	SO:0001583	missense	2017	exon17			AGGACAGCACCTA	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.1451G>A	11.37:g.70279759G>A	ENSP00000301843:p.Ser484Asn	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_005231	Q8N707|Q96H99	Missense_Mutation	SNP	ENST00000301843.8	37	CCDS41680.1	85	0.03891941391941392	81	0.16463414634146342	4	0.011049723756906077	0	0.0	0	0.0	G	1.497	-0.553053	0.03996	0.179091	5.82E-4	ENSG00000085733	ENST00000346329;ENST00000301843;ENST00000376561;ENST00000538675;ENST00000529736	T;T;T;T;T	0.32753	1.44;1.45;1.48;1.88;1.86	4.86	-0.816	0.10839	Src homology-3 domain (1);	0.722113	0.13537	N	0.380525	T	0.00039	0.0001	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.10450	0.005;0.0;0.0;0.001	T	0.21143	-1.0254	10	0.05525	T	0.97	-27.692	5.4208	0.16400	0.6072:0.1347:0.258:0.0	rs56162978;rs58344286	168;447;484;447	B4E358;Q96H99;Q14247;Q8N707	.;.;SRC8_HUMAN;.	N	447;484;447;168;141	ENSP00000317189:S447N;ENSP00000301843:S484N;ENSP00000365745:S447N;ENSP00000439762:S168N;ENSP00000431421:S141N	ENSP00000301843:S484N	S	+	2	0	CTTN	69957407	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.316000	0.19469	-0.462000	0.06984	-0.891000	0.02926	AGC	G|0.941;A|0.059	0.059	strong		0.517	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565	
RMND1	55005	hgsc.bcm.edu	37	6	151766822	151766822	+	Missense_Mutation	SNP	C	C	A	rs11550103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:151766822C>A	ENST00000367303.4	-	2	247	c.125G>T	c.(124-126)aGc>aTc	p.S42I	RMND1_ENST00000336451.3_5'Flank|RMND1_ENST00000491268.1_5'UTR	NM_017909.2	NP_060379.2	Q9NWS8	RMND1_HUMAN	required for meiotic nuclear division 1 homolog (S. cerevisiae)	42			S -> I (in dbSNP:rs11550103).		translation (GO:0006412)	mitochondrion (GO:0005739)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.146)	OV - Ovarian serous cystadenocarcinoma(155;6.8e-11)		TGTCAGTGTGCTGCATGTTGT	0.373													C|||	362	0.0722843	0.0454	0.0764	5008	,	,		17906	0.0159		0.1193	False		,,,				2504	0.1155				p.S42I		Atlas-SNP	.											RMND1,lymph_node,lymphoid_neoplasm,0,1	RMND1	32	1	0			c.G125T						PASS	.	C	ILE/SER	254,4152	146.1+/-180.8	7,240,1956	118.0	108.0	112.0		125	-3.4	0.0	6	dbSNP_120	112	1083,7517	227.2+/-262.7	62,959,3279	no	missense	RMND1	NM_017909.2	142	69,1199,5235	AA,AC,CC		12.593,5.7649,10.2799	benign	42/450	151766822	1337,11669	2203	4300	6503	SO:0001583	missense	55005	exon2			AGTGTGCTGCATG	AK000634	CCDS5232.1, CCDS75539.1	6q25.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000155906	ENSG00000155906			21176	protein-coding gene	gene with protein product		614917	"""chromosome 6 open reading frame 96"""	C6orf96			Standard	NM_001271937		Approved	bA351K16.3, FLJ20627, RMD1	uc003qoi.3	Q9NWS8	OTTHUMG00000015837	ENST00000367303.4:c.125G>T	6.37:g.151766822C>A	ENSP00000356272:p.Ser42Ile	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_017909	A8K8H4|Q0VDG6|Q5SZ48|Q5SZ83|Q6NSC5|Q96EN7	Missense_Mutation	SNP	ENST00000367303.4	37	CCDS5232.1	167	0.07646520146520147	28	0.056910569105691054	34	0.09392265193370165	10	0.017482517482517484	95	0.12532981530343007	C	10.21	1.288088	0.23478	0.057649	0.12593	ENSG00000155906	ENST00000367303	T	0.44881	0.91	5.46	-3.36	0.04913	.	1.251530	0.05252	N	0.514092	T	0.06416	0.0165	N	0.08118	0	0.80722	P	0.0	B;B	0.16396	0.017;0.0	B;B	0.16289	0.015;0.001	T	0.22906	-1.0203	9	0.34782	T	0.22	1.0502	2.8012	0.05415	0.1159:0.2957:0.1144:0.474	rs11550103;rs52812057;rs11550103	42;42	Q9NWS8-3;Q9NWS8	.;RMND1_HUMAN	I	42	ENSP00000356272:S42I	ENSP00000356272:S42I	S	-	2	0	RMND1	151808515	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-0.509000	0.06336	-0.325000	0.08577	0.563000	0.77884	AGC	C|0.912;A|0.088	0.088	strong		0.373	RMND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042718.2	NM_017909	
MUC5B	727897	hgsc.bcm.edu	37	11	1268064	1268064	+	Silent	SNP	C	C	T	rs200948102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	306	0	0		WXS	Illumina HiSeq	Phase_I	365	171	0.468493	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	
CCDC173	129881	hgsc.bcm.edu	37	2	170502509	170502509	+	Missense_Mutation	SNP	G	G	A	rs112720712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170502509G>A	ENST00000447353.1	-	9	1606	c.1501C>T	c.(1501-1503)Cct>Tct	p.P501S		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	501																	CCACCTCCAGGTCCTTCCTGT	0.433													G|||	49	0.00978435	0.034	0.0043	5008	,	,		17210	0.0		0.001	False		,,,				2504	0.0				p.P501S		Atlas-SNP	.											.	.	.	.	0			c.C1501T						PASS	.	G	SER/PRO	119,3659		2,115,1772	169.0	173.0	171.0		1501	2.0	1.0	2	dbSNP_132	171	0,8212		0,0,4106	yes	missense	C2orf77	NM_001085447.1	74	2,115,5878	AA,AG,GG		0.0,3.1498,0.9925	benign	501/553	170502509	119,11871	1889	4106	5995	SO:0001583	missense	129881	exon9			CTCCAGGTCCTTC	BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"""hypothetical LOC129881"""		"""chromosome 2 open reading frame 77"""	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.1501C>T	2.37:g.170502509G>A	ENSP00000391504:p.Pro501Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_001085447	Q6PJF6	Missense_Mutation	SNP	ENST00000447353.1	37	CCDS46445.1	20	0.009157509157509158	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.71	2.319074	0.41096	0.031498	0.0	ENSG00000154479	ENST00000447353	.	.	.	5.87	2.01	0.26516	.	0.916393	0.09355	N	0.813572	T	0.06462	0.0166	L	0.40543	1.245	0.20074	N	0.999938	B	0.09022	0.002	B	0.08055	0.003	T	0.24657	-1.0154	9	0.07482	T	0.82	.	1.5507	0.02574	0.229:0.2733:0.3648:0.1329	.	501	Q0VFZ6	CB077_HUMAN	S	501	.	ENSP00000391504:P501S	P	-	1	0	C2orf77	170210755	0.219000	0.23619	0.992000	0.48379	0.992000	0.81027	0.199000	0.17237	0.467000	0.27218	0.655000	0.94253	CCT	G|0.990;A|0.010	0.010	strong		0.433	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447	
GLRX	2745	hgsc.bcm.edu	37	5	95152313	95152313	+	Silent	SNP	A	A	G	rs4561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:95152313A>G	ENST00000379979.4	-	2	276	c.225T>C	c.(223-225)atT>atC	p.I75I	GLRX_ENST00000512469.2_Silent_p.I75I|GLRX_ENST00000505427.1_Silent_p.I75I|GLRX_ENST00000508780.1_Silent_p.I75I|GLRX_ENST00000237858.6_Silent_p.I75I|GLRX_ENST00000507605.1_5'UTR	NM_002064.2	NP_002055.1	P35754	GLRX1_HUMAN	glutaredoxin (thioltransferase)	75	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell redox homeostasis (GO:0045454)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of membrane potential (GO:0045838)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein deglutathionylation (GO:0080058)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|glutathione disulfide oxidoreductase activity (GO:0015038)|glutathione oxidoreductase activity (GO:0097573)|protein N-terminus binding (GO:0047485)			endometrium(3)|large_intestine(1)|lung(1)	5		all_cancers(142;3.38e-06)|all_epithelial(76;5.66e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;2.62e-16)	Glutathione(DB00143)	AATCTTTACCAATAAAGACTC	0.443													G|||	1509	0.301318	0.3169	0.2752	5008	,	,		19925	0.1716		0.4135	False		,,,				2504	0.317				p.I75I		Atlas-SNP	.											GLRX,NS,carcinoma,-1,1	GLRX	11	1	0			c.T225C						PASS	.	G	,	1469,2937	680.1+/-403.8	248,973,982	71.0	67.0	68.0		225,225	-6.0	0.0	5	dbSNP_52	68	3697,4903	620.4+/-397.1	811,2075,1414	no	coding-synonymous,coding-synonymous	GLRX	NM_001118890.1,NM_002064.2	,	1059,3048,2396	GG,GA,AA		42.9884,33.3409,39.7201	,	75/107,75/107	95152313	5166,7840	2203	4300	6503	SO:0001819	synonymous_variant	2745	exon2			TTTACCAATAAAG		CCDS4078.1	5q14	2008-02-05			ENSG00000173221	ENSG00000173221			4330	protein-coding gene	gene with protein product		600443				8838810	Standard	NM_002064		Approved	GRX, GRX1	uc021ybo.1	P35754	OTTHUMG00000121167	ENST00000379979.4:c.225T>C	5.37:g.95152313A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	185	98	0.52973	NM_001243659	B2R4L2|Q3KQS1|Q6ICT1	Silent	SNP	ENST00000379979.4	37	CCDS4078.1																																																																																			T|0.018;G|0.347	0.347	strong		0.443	GLRX-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370267.1	NM_002064	
URB1	9875	hgsc.bcm.edu	37	21	33719400	33719400	+	Silent	SNP	A	A	G	rs9981151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33719400A>G	ENST00000382751.3	-	22	3848	c.3733T>C	c.(3733-3735)Ttg>Ctg	p.L1245L		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	1245						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						AACCACAGCAAGTGGGTGCAG	0.672													G|||	1118	0.223243	0.4796	0.1023	5008	,	,		17504	0.1379		0.1223	False		,,,				2504	0.1544				p.L1245L		Atlas-SNP	.											.	URB1	176	.	0			c.T3733C						PASS	.	G		587,797		132,323,237	18.0	23.0	22.0		3733	2.9	1.0	21	dbSNP_119	22	408,2774		30,348,1213	no	coding-synonymous	URB1	NM_014825.2		162,671,1450	GG,GA,AA		12.8221,42.4133,21.7915		1245/2272	33719400	995,3571	692	1591	2283	SO:0001819	synonymous_variant	9875	exon22			ACAGCAAGTGGGT	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.3733T>C	21.37:g.33719400A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																			A|0.788;G|0.212	0.212	strong		0.672	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
GPR114	221188	hgsc.bcm.edu	37	16	57601792	57601792	+	Silent	SNP	C	C	T	rs9937918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57601792C>T	ENST00000340339.4	+	9	1369	c.846C>T	c.(844-846)cgC>cgT	p.R282R	GPR114_ENST00000349457.3_Silent_p.R282R|GPR114_ENST00000394361.4_3'UTR	NM_153837.1	NP_722579.1	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	282					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(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(5)|ovary(2)|stomach(1)|urinary_tract(1)	23						CCTTAACACGCATCCACATGA	0.597													c|||	2275	0.454273	0.3759	0.5029	5008	,	,		23261	0.7123		0.2783	False		,,,				2504	0.4407				p.R282R		Atlas-SNP	.											.	GPR114	52	.	0			c.C846T						PASS	.			1618,2778	499.8+/-364.5	299,1020,879	94.0	76.0	82.0		846	-4.1	0.1	16	dbSNP_119	82	2432,6168	398.2+/-346.0	342,1748,2210	no	coding-synonymous	GPR114	NM_153837.1		641,2768,3089	TT,TC,CC		28.2791,36.8062,31.1634		282/529	57601792	4050,8946	2198	4300	6498	SO:0001819	synonymous_variant	221188	exon9			AACACGCATCCAC	AY140956	CCDS10785.1	16q13	2014-08-08			ENSG00000159618	ENSG00000159618		"""-"", ""GPCR / Class B : Orphans"""	19010	protein-coding gene	gene with protein product						12435584	Standard	NM_153837		Approved	PGR27	uc002ely.3	Q8IZF4	OTTHUMG00000133461	ENST00000340339.4:c.846C>T	16.37:g.57601792C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_153837	B3KXZ5|Q6ZMH7|Q6ZML4|Q86SL8|Q8IZ14	Silent	SNP	ENST00000340339.4	37	CCDS10785.1																																																																																			C|0.625;T|0.375	0.375	strong		0.597	GPR114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257336.3	NM_153837	
SAMM50	25813	hgsc.bcm.edu	37	22	44368122	44368122	+	Missense_Mutation	SNP	A	A	G	rs3761472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44368122A>G	ENST00000350028.4	+	5	486	c.329A>G	c.(328-330)gAc>gGc	p.D110G	SAMM50_ENST00000493161.1_3'UTR|SAMM50_ENST00000396202.3_Intron	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	110			D -> G (in dbSNP:rs3761472). {ECO:0000269|PubMed:14702039}.		cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)		p.D110G(1)		endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				TTAGGTGATGACGCACTTCCA	0.363													A|||	1223	0.244209	0.171	0.2968	5008	,	,		17374	0.371		0.1879	False		,,,				2504	0.2331				p.D110G		Atlas-SNP	.											SAMM50,NS,carcinoma,0,1	SAMM50	30	1	1	Substitution - Missense(1)	stomach(1)	c.A329G						PASS	.	A	GLY/ASP	786,3620	318.5+/-295.7	88,610,1505	123.0	113.0	116.0		329	4.8	0.9	22	dbSNP_107	116	1339,7261	263.0+/-284.7	107,1125,3068	yes	missense	SAMM50	NM_015380.4	94	195,1735,4573	GG,GA,AA		15.5698,17.8393,16.3386	benign	110/470	44368122	2125,10881	2203	4300	6503	SO:0001583	missense	25813	exon5			GTGATGACGCACT	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"""sorting and assembly machinery component 50 homolog (S. cerevisiae)"""			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.329A>G	22.37:g.44368122A>G	ENSP00000345445:p.Asp110Gly	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Missense_Mutation	SNP	ENST00000350028.4	37	CCDS14055.1	554	0.25366300366300365	86	0.17479674796747968	96	0.26519337016574585	232	0.40559440559440557	140	0.18469656992084432	A	14.99	2.701189	0.48307	0.178393	0.155698	ENSG00000100347	ENST00000350028	T	0.54279	0.58	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.53249	1.67	0.09310	P	1.0	B	0.14438	0.01	B	0.17722	0.019	T	0.33574	-0.9863	9	0.48119	T	0.1	-28.447	13.7811	0.63084	1.0:0.0:0.0:0.0	rs3761472;rs11547246;rs52828379;rs57886466;rs3761472	110	Q9Y512	SAM50_HUMAN	G	110	ENSP00000345445:D110G	ENSP00000345445:D110G	D	+	2	0	SAMM50	42699455	0.998000	0.40836	0.898000	0.35279	0.991000	0.79684	3.639000	0.54339	1.916000	0.55485	0.533000	0.62120	GAC	A|0.790;G|0.210	0.210	strong		0.363	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
MARK3	4140	hgsc.bcm.edu	37	14	103941392	103941392	+	Missense_Mutation	SNP	A	A	G	rs56305318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103941392A>G	ENST00000429436.2	+	13	1837	c.1327A>G	c.(1327-1329)Agt>Ggt	p.S443G	MARK3_ENST00000216288.7_Missense_Mutation_p.S427G|MARK3_ENST00000553942.1_Missense_Mutation_p.S443G|MARK3_ENST00000303622.9_Missense_Mutation_p.S443G|MARK3_ENST00000335102.5_Missense_Mutation_p.S466G|MARK3_ENST00000561071.1_Intron|MARK3_ENST00000416682.2_Missense_Mutation_p.S466G|MARK3_ENST00000440884.3_Missense_Mutation_p.S364G	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	443			S -> G (in dbSNP:rs56305318). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9543386, ECO:0000269|Ref.2}.			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)			CACTGCAGATAGTGACCTCAA	0.448													A|||	242	0.0483227	0.1793	0.0072	5008	,	,		20680	0.0		0.0	False		,,,				2504	0.0				p.S443G		Atlas-SNP	.											.	MARK3	86	.	0			c.A1327G						PASS	.	A	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	577,3417		51,475,1471	59.0	61.0	60.0		1327,1327,1279,1090,1327	2.0	0.8	14	dbSNP_129	60	1,8343		0,1,4171	yes	missense,missense,missense,missense,missense	MARK3	NM_001128918.1,NM_001128919.1,NM_001128920.1,NM_001128921.1,NM_002376.5	56,56,56,56,56	51,476,5642	GG,GA,AA		0.012,14.4467,4.6847	benign,benign,benign,benign,benign	443/754,443/745,427/714,364/660,443/730	103941392	578,11760	1997	4172	6169	SO:0001583	missense	4140	exon13			GCAGATAGTGACC	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.1327A>G	14.37:g.103941392A>G	ENSP00000411397:p.Ser443Gly	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	48	0.564706	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	CCDS45165.1	87|87	0.03983516483516483|0.03983516483516483	83|83	0.16869918699186992|0.16869918699186992	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	A|A	12.87|12.87	2.068525|2.068525	0.36470|0.36470	0.144467|0.144467	1.2E-4|1.2E-4	ENSG00000075413|ENSG00000075413	ENST00000554627|ENST00000335102;ENST00000411530;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942	.|T;T;T;T;T;T;T	.|0.55234	.|0.53;0.53;0.53;0.53;0.53;0.53;0.53	5.78|5.78	2.0|2.0	0.26442|0.26442	.|.	.|0.269900	.|0.46758	.|N	.|0.000264	T|T	0.00144|0.00144	0.0004|0.0004	L|L	0.40543|0.40543	1.245|1.245	0.27271|0.27271	P|P	0.9583608|0.9583608	.|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	.|0.10450	.|0.001;0.004;0.001;0.001;0.0;0.005;0.001	T|T	0.07868|0.07868	-1.0750|-1.0750	4|9	.|0.29301	.|T	.|0.29	.|.	9.2811|9.2811	0.37729|0.37729	0.781:0.0:0.219:0.0|0.781:0.0:0.219:0.0	rs56305318;rs61730317|rs56305318;rs61730317	.|450;466;427;443;364;443;443	.|P27448-7;P27448-2;P27448-6;P27448;Q86TT8;P27448-4;P27448-3	.|.;.;.;MARK3_HUMAN;.;.;.	M|G	194|466;92;364;466;443;443;427;443	.|ENSP00000335347:S466G;ENSP00000402104:S364G;ENSP00000408092:S466G;ENSP00000411397:S443G;ENSP00000303698:S443G;ENSP00000216288:S427G;ENSP00000450772:S443G	.|ENSP00000216288:S443G	I|S	+|+	3|1	3|0	MARK3|MARK3	103011145|103011145	0.979000|0.979000	0.34478|0.34478	0.769000|0.769000	0.31535|0.31535	0.720000|0.720000	0.41350|0.41350	1.621000|1.621000	0.36986|0.36986	0.090000|0.090000	0.17273|0.17273	0.533000|0.533000	0.62120|0.62120	ATA|AGT	A|0.958;G|0.042	0.042	strong		0.448	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918	
GREB1	9687	hgsc.bcm.edu	37	2	11774324	11774324	+	Missense_Mutation	SNP	G	G	A	rs2304402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11774324G>A	ENST00000381486.2	+	29	5359	c.5059G>A	c.(5059-5061)Gac>Aac	p.D1687N	GREB1_ENST00000396123.1_Missense_Mutation_p.D685N|GREB1_ENST00000234142.5_Missense_Mutation_p.D1687N	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1687			D -> N (in dbSNP:rs2304402). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.			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)		GGCGGCCCCCGACATCATGCA	0.617													A|||	2028	0.404952	0.4213	0.3573	5008	,	,		19371	0.2996		0.4771	False		,,,				2504	0.4509				p.D1687N	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.G5059A						PASS	.	A	ASN/ASP	1815,2467		399,1017,725	88.0	96.0	94.0		5059	1.2	0.9	2	dbSNP_100	94	4301,4199		1117,2067,1066	yes	missense	GREB1	NM_014668.3	23	1516,3084,1791	AA,AG,GG		49.4,42.3867,47.8485	benign	1687/1950	11774324	6116,6666	2141	4250	6391	SO:0001583	missense	9687	exon29			GCCCCCGACATCA		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.5059G>A	2.37:g.11774324G>A	ENSP00000370896:p.Asp1687Asn	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	235	234	0.995745	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	893	0.4088827838827839	223	0.4532520325203252	141	0.38950276243093923	176	0.3076923076923077	353	0.4656992084432718	A	2.656	-0.280878	0.05642	0.423867	0.506	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.40756	1.02;1.02;1.02	5.01	1.17	0.20885	.	0.250963	0.42053	N	0.000763	T	0.00012	0.0000	N	0.02960	-0.455	0.53688	P	2.199999999996649E-5	B	0.06786	0.001	B	0.06405	0.002	T	0.47341	-0.9125	9	0.05351	T	0.99	-24.3036	9.4069	0.38466	0.6384:0.0:0.3616:0.0	rs2304402;rs17602548;rs58433267;rs2304402	1687	Q4ZG55	GREB1_HUMAN	N	1687;1687;685	ENSP00000370896:D1687N;ENSP00000234142:D1687N;ENSP00000379429:D685N	ENSP00000234142:D1687N	D	+	1	0	GREB1	11691775	0.523000	0.26274	0.861000	0.33841	0.137000	0.21094	1.219000	0.32479	-0.305000	0.08831	-0.521000	0.04368	GAC	G|0.556;A|0.444	0.444	strong		0.617	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
SPTA1	6708	hgsc.bcm.edu	37	1	158647522	158647522	+	Silent	SNP	A	A	G	rs703121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158647522A>G	ENST00000368147.4	-	7	1095	c.915T>C	c.(913-915)agT>agC	p.S305S		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	305					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)					GTCCCTTGTGACTGTGAAACA	0.463													A|||	2273	0.453874	0.2262	0.5058	5008	,	,		19106	0.5833		0.6153	False		,,,				2504	0.4254				p.S305S		Atlas-SNP	.											.	SPTA1	720	.	0			c.T915C						PASS	.	A		1077,2837		152,773,1032	98.0	91.0	93.0		915	2.3	1.0	1	dbSNP_86	93	4759,3543		1358,2043,750	no	coding-synonymous	SPTA1	NM_003126.2		1510,2816,1782	GG,GA,AA		42.6765,27.5166,47.7734		305/2420	158647522	5836,6380	1957	4151	6108	SO:0001819	synonymous_variant	6708	exon7			CTTGTGACTGTGA	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.915T>C	1.37:g.158647522A>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	213	96	0.450704	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			A|0.498;G|0.502	0.502	strong		0.463	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
STARD13	90627	hgsc.bcm.edu	37	13	33741716	33741716	+	Silent	SNP	C	C	T	rs17078661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33741716C>T	ENST00000336934.5	-	2	329	c.213G>A	c.(211-213)ggG>ggA	p.G71G	STARD13_ENST00000399365.3_5'UTR|STARD13_ENST00000255486.4_Silent_p.G63G|STARD13_ENST00000487412.1_5'UTR	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	71	SAM.				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)		ATTGCGGGAACCCGGCAGCAC	0.483													C|||	178	0.0355431	0.1301	0.0086	5008	,	,		18769	0.0		0.0	False		,,,				2504	0.0				p.G71G		Atlas-SNP	.											STARD13,NS,carcinoma,-1,1	STARD13	100	1	0			c.G213A						PASS	.	C	,,	558,3848	250.9+/-257.8	30,498,1675	96.0	93.0	94.0		,213,189	-3.2	1.0	13	dbSNP_123	94	7,8593	5.7+/-21.5	0,7,4293	no	utr-5,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	30,505,5968	TT,TC,CC		0.0814,12.6645,4.3441	,,	,71/1114,63/1106	33741716	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon2			CGGGAACCCGGCA	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.213G>A	13.37:g.33741716C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			C|0.960;T|0.040	0.040	strong		0.483	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
ZNF506	440515	hgsc.bcm.edu	37	19	19906131	19906131	+	Missense_Mutation	SNP	T	T	G	rs16996376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19906131T>G	ENST00000540806.2	-	4	653	c.565A>C	c.(565-567)Act>Cct	p.T189P	ZNF506_ENST00000450683.2_Missense_Mutation_p.T157P|ZNF506_ENST00000443905.2_Missense_Mutation_p.T189P|CTC-559E9.6_ENST00000591884.1_RNA|ZNF506_ENST00000587461.1_Intron|CTC-559E9.6_ENST00000589657.1_RNA|CTC-559E9.4_ENST00000590274.1_lincRNA			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	189			T -> P (in dbSNP:rs16996376).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						TTATATGTAGTACGGGTTGAA	0.303													t|||	327	0.0652955	0.2262	0.0288	5008	,	,		19010	0.0		0.007	False		,,,				2504	0.001				p.T189P		Atlas-SNP	.											.	ZNF506	36	.	0			c.A565C						PASS	.	T	PRO/THR,PRO/THR	787,3387		71,645,1371	51.0	53.0	52.0		565,469	1.0	0.1	19	dbSNP_123	52	66,8426		1,64,4181	yes	missense,missense	ZNF506	NM_001099269.2,NM_001145404.1	38,38	72,709,5552	GG,GT,TT		0.7772,18.8548,6.7346	possibly-damaging,possibly-damaging	189/445,157/413	19906131	853,11813	2087	4246	6333	SO:0001583	missense	440515	exon4			ATGTAGTACGGGT	AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"""Zinc fingers, C2H2-type"", ""-"""	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.565A>C	19.37:g.19906131T>G	ENSP00000440625:p.Thr189Pro	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_001099269	B3KTH6	Missense_Mutation	SNP	ENST00000540806.2	37	CCDS42531.1	131	0.059981684981684984	115	0.23373983739837398	13	0.03591160220994475	0	0.0	3	0.00395778364116095	t	13.27	2.185989	0.38609	0.188548	0.007772	ENSG00000081665	ENST00000443905;ENST00000540806;ENST00000450683	T;T;T	0.01172	5.23;5.23;5.23	0.974	0.974	0.19715	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.85373	2.75	0.80722	P	0.0	D;D	0.67145	0.996;0.967	D;P	0.65874	0.939;0.75	T	0.41980	-0.9478	8	0.87932	D	0	.	4.0711	0.09882	0.0:0.0:0.0:1.0	rs16996376;rs60499475;rs16996376	189;157	Q5JVG8;Q5JVG8-2	ZN506_HUMAN;.	P	189;189;157	ENSP00000393835:T189P;ENSP00000440625:T189P;ENSP00000408892:T157P	ENSP00000393835:T189P	T	-	1	0	ZNF506	19767131	0.000000	0.05858	0.061000	0.19648	0.058000	0.15608	-0.102000	0.10956	0.358000	0.24211	0.347000	0.21830	ACT	T|0.935;G|0.065	0.065	strong		0.303	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218	
SELPLG	6404	hgsc.bcm.edu	37	12	109017680	109017680	+	Missense_Mutation	SNP	T	T	G	rs63748999|rs200527674|rs372173288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109017680T>G	ENST00000550948.1	-	2	628	c.404A>C	c.(403-405)cAa>cCa	p.Q135P	SELPLG_ENST00000228463.6_Missense_Mutation_p.Q151P|SELPLG_ENST00000388962.3_Intron			Q14242	SELPL_HUMAN	selectin P ligand	135	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.Q135P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GGGCACTGGTTGAGTGGTCTG	0.617																																					p.Q151P		Atlas-SNP	.											SELPLG_ENST00000550948,NS,haematopoietic_neoplasm,0,1	SELPLG	138	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A452C						PASS	.						165.0	129.0	141.0					12																	109017680		2201	4282	6483	SO:0001583	missense	6404	exon2			ACTGGTTGAGTGG		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.404A>C	12.37:g.109017680T>G	ENSP00000447752:p.Gln135Pro	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	258	43	0.166667	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	N	7.318	0.616396	0.14129	.	.	ENSG00000110876	ENST00000550948;ENST00000228463	T;T	0.28666	1.6;1.6	3.51	-7.02	0.01589	.	3.684700	0.01036	N	0.004222	T	0.23727	0.0574	L	0.54323	1.7	0.09310	N	1	P;P	0.47604	0.898;0.898	B;B	0.40165	0.321;0.321	T	0.41088	-0.9528	10	0.29301	T	0.29	1.368	4.4646	0.11682	0.2642:0.4833:0.0955:0.157	.	151;135	B7Z5C7;Q14242	.;SELPL_HUMAN	P	135;151	ENSP00000447752:Q135P;ENSP00000228463:Q151P	ENSP00000228463:Q151P	Q	-	2	0	SELPLG	107541809	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.658000	0.05329	-1.703000	0.01409	-0.441000	0.05720	CAA	T|0.986;G|0.014	0.014	strong		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
WNT8B	7479	hgsc.bcm.edu	37	10	102242030	102242030	+	Silent	SNP	G	G	A	rs9420786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102242030G>A	ENST00000343737.5	+	6	641	c.513G>A	c.(511-513)gcG>gcA	p.A171A		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	171					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)		CTCCCCAGGCGGTGAAGGGCA	0.622											OREG0020440	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	90	0.0179712	0.0514	0.0029	5008	,	,		16675	0.002		0.001	False		,,,				2504	0.0174				p.A171A		Atlas-SNP	.											.	WNT8B	31	.	0			c.G513A						PASS	.	G		247,4131		4,239,1946	15.0	16.0	16.0		513	-3.3	0.9	10	dbSNP_119	16	2,8544		0,2,4271	no	coding-synonymous	WNT8B	NM_003393.3		4,241,6217	AA,AG,GG		0.0234,5.6418,1.9266		171/352	102242030	249,12675	2189	4273	6462	SO:0001819	synonymous_variant	7479	exon6			CCAGGCGGTGAAG	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.513G>A	10.37:g.102242030G>A		Somatic	17	0	0	1365	WXS	Illumina HiSeq	Phase_I	29	12	0.413793	NM_003393	O00771|Q5VX55|Q8WYK9	Silent	SNP	ENST00000343737.5	37	CCDS7494.1																																																																																			G|0.978;A|0.022	0.022	strong		0.622	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393	
LILRA1	11024	hgsc.bcm.edu	37	19	55106865	55106865	+	Missense_Mutation	SNP	T	T	C	rs373854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55106865T>C	ENST00000251372.3	+	5	841	c.659T>C	c.(658-660)cTa>cCa	p.L220P	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Missense_Mutation_p.L220P|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	220	Ig-like C2-type 2.		L -> P (in dbSNP:rs373854). {ECO:0000269|PubMed:9548455}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CTCCTGGTCCTAGGTGAGAAA	0.587													N|||	1496	0.298722	0.5212	0.268	5008	,	,		18238	0.2798		0.0994	False		,,,				2504	0.2444				p.L220P		Atlas-SNP	.											.	LILRA1	105	.	0			c.T659C						PASS	.	C	PRO/LEU	2057,2349		480,1097,626	103.0	114.0	110.0		659	1.2	0.2	19	dbSNP_80	110	728,7872		52,624,3624	no	missense	LILRA1	NM_006863.1	98	532,1721,4250	CC,CT,TT		8.4651,46.6863,21.4132	benign	220/490	55106865	2785,10221	2203	4300	6503	SO:0001583	missense	11024	exon5			TGGTCCTAGGTGA	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.659T>C	19.37:g.55106865T>C	ENSP00000251372:p.Leu220Pro	Somatic	323	1	0.00309598		WXS	Illumina HiSeq	Phase_I	336	335	0.997024	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	494	0.2261904761904762	209	0.4247967479674797	86	0.23756906077348067	147	0.256993006993007	52	0.06860158311345646	C	4.534	0.099125	0.08681	0.466863	0.084651	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.00737	5.76;5.76	2.24	1.17	0.20885	Immunoglobulin-like fold (1);	1.323100	0.05398	N	0.540098	T	0.00012	0.0000	N	0.00453	-1.485	0.36214	P	0.14844599999999997	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.15607	-1.0431	9	0.19147	T	0.46	.	4.0558	0.09816	0.0:0.6082:0.0:0.3918	rs373854	220;220	O75019-2;O75019	.;LIRA1_HUMAN	P	220	ENSP00000251372:L220P;ENSP00000413715:L220P	ENSP00000251372:L220P	L	+	2	0	LILRA1	59798677	0.701000	0.27806	0.157000	0.22605	0.249000	0.25844	0.348000	0.20031	0.247000	0.21414	-1.033000	0.02402	CTA	T|0.782;C|0.218	0.218	strong		0.587	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
IL20RA	53832	hgsc.bcm.edu	37	6	137323213	137323213	+	Missense_Mutation	SNP	G	G	A	rs1342642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:137323213G>A	ENST00000316649.5	-	7	1379	c.1144C>T	c.(1144-1146)Ctc>Ttc	p.L382F	IL20RA_ENST00000367748.1_Missense_Mutation_p.L271F|RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000541547.1_Missense_Mutation_p.L333F|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	155	0	0		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	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	
ABCC11	85320	hgsc.bcm.edu	37	16	48256602	48256602	+	Silent	SNP	T	T	C	rs16945974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48256602T>C	ENST00000394747.1	-	5	1033	c.684A>G	c.(682-684)caA>caG	p.Q228Q	ABCC11_ENST00000537808.1_Silent_p.Q228Q|ABCC11_ENST00000356608.2_Silent_p.Q228Q|ABCC11_ENST00000353782.5_Silent_p.Q228Q|ABCC11_ENST00000394748.1_Silent_p.Q228Q	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	228	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|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)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	TGGCTGTGCGTTGGTTGATGA	0.478													C|||	672	0.134185	0.3132	0.098	5008	,	,		21621	0.0437		0.1024	False		,,,				2504	0.044				p.Q228Q		Atlas-SNP	.											.	ABCC11	177	.	0			c.A684G						PASS	.	C	,,	1156,3244	712.0+/-408.1	152,852,1196	122.0	112.0	115.0		684,684,684	-0.8	0.4	16	dbSNP_123	115	755,7845	785.4+/-407.6	29,697,3574	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	181,1549,4770	CC,CT,TT		8.7791,26.2727,14.7	,,	228/1383,228/1383,228/1345	48256602	1911,11089	2200	4300	6500	SO:0001819	synonymous_variant	85320	exon5			TGTGCGTTGGTTG	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.684A>G	16.37:g.48256602T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	193	193	1	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			T|0.854;C|0.146	0.146	strong		0.478	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
CDC6	990	hgsc.bcm.edu	37	17	38447569	38447569	+	Silent	SNP	T	T	C	rs1130199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38447569T>C	ENST00000209728.4	+	3	909	c.438T>C	c.(436-438)tgT>tgC	p.C146C		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	146					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						AATCTGCATGTGTGAGACTAT	0.403													T|||	557	0.111222	0.3994	0.0375	5008	,	,		24231	0.0		0.003	False		,,,				2504	0.0				p.C146C		Atlas-SNP	.											.	CDC6	53	.	0			c.T438C						PASS	.	T		1438,2968	453.6+/-350.4	230,978,995	87.0	90.0	89.0		438	0.9	0.0	17	dbSNP_86	89	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous	CDC6	NM_001254.3		230,988,5285	CC,CT,TT		0.1163,32.6373,11.1333		146/561	38447569	1448,11558	2203	4300	6503	SO:0001819	synonymous_variant	990	exon3			TGCATGTGTGAGA	U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"""CDC6 (cell division cycle 6, S. cerevisiae) homolog"", ""CDC6 cell division cycle 6 homolog (S. cerevisiae)"", ""cell division cycle 6 homolog (S. cerevisiae)"""	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.438T>C	17.37:g.38447569T>C		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_001254	Q8TB30	Silent	SNP	ENST00000209728.4	37	CCDS11365.1																																																																																			T|0.886;C|0.114	0.114	strong		0.403	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1		
DNAJB9	4189	hgsc.bcm.edu	37	7	108213545	108213545	+	Silent	SNP	T	T	C	rs376971670		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:108213545T>C	ENST00000249356.3	+	3	966	c.420T>C	c.(418-420)caT>caC	p.H140H	DNAJB9_ENST00000465725.1_Intron	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	140					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)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	misfolded protein binding (GO:0051787)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13						TTGAAAATCATTTCCAGACAC	0.363																																					p.H140H		Atlas-SNP	.											DNAJB9,NS,carcinoma,+1,1	DNAJB9	25	1	0			c.T420C						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	110.0	109.0	109.0		420	0.7	1.0	7		109	0,8600		0,0,4300	no	coding-synonymous	DNAJB9	NM_012328.2		0,2,6501	CC,CT,TT		0.0,0.0454,0.0154		140/224	108213545	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	4189	exon3			AAATCATTTCCAG	AB026908	CCDS5752.1	7q31	2011-09-02			ENSG00000128590	ENSG00000128590		"""Heat shock proteins / DNAJ (HSP40)"""	6968	protein-coding gene	gene with protein product		602634		MDG1		9533036, 11147971	Standard	NM_012328		Approved		uc003vfn.3	Q9UBS3	OTTHUMG00000154866	ENST00000249356.3:c.420T>C	7.37:g.108213545T>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	176	83	0.471591	NM_012328		Silent	SNP	ENST00000249356.3	37	CCDS5752.1																																																																																			.	.	weak		0.363	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1		
SELE	6401	hgsc.bcm.edu	37	1	169697218	169697218	+	Silent	SNP	G	G	A	rs5365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169697218G>A	ENST00000333360.7	-	8	1399	c.1260C>T	c.(1258-1260)aaC>aaT	p.N420N	SELE_ENST00000367777.1_Silent_p.N420N|SELE_ENST00000367780.4_Intron|SELE_ENST00000367781.4_Intron|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367775.1_Intron|SELE_ENST00000367774.1_Intron|SELE_ENST00000367779.4_Intron|SELE_ENST00000367776.1_Intron|SELE_ENST00000367782.4_Silent_p.N420N	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	420	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)	TGGGCTTCTCGTTGTCCCACT	0.448													G|||	101	0.0201677	0.0756	0.0014	5008	,	,		19018	0.0		0.0	False		,,,				2504	0.0				p.N420N		Atlas-SNP	.											.	SELE	84	.	0			c.C1260T						PASS	.	G		284,4122	157.0+/-190.0	5,274,1924	96.0	109.0	104.0		1260	-10.5	0.0	1	dbSNP_52	104	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SELE	NM_000450.2		5,276,6222	AA,AG,GG		0.0233,6.4458,2.199		420/611	169697218	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	6401	exon8			CTTCTCGTTGTCC	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.1260C>T	1.37:g.169697218G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_000450	A2RRD6|P16111	Silent	SNP	ENST00000333360.7	37	CCDS1283.1																																																																																			G|0.982;A|0.018	0.018	strong		0.448	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450	
TMEM14B	81853	hgsc.bcm.edu	37	6	10751379	10751379	+	Silent	SNP	C	C	T	rs1046427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10751379C>T	ENST00000379542.5	+	4	281	c.114C>T	c.(112-114)tcC>tcT	p.S38S	TMEM14B_ENST00000475942.1_Silent_p.S38S|TMEM14B_ENST00000379530.3_Intron|SYCP2L_ENST00000543878.1_Intron|RP11-637O19.3_ENST00000480294.1_Intron|TMEM14B_ENST00000473276.1_Intron|RNA5SP203_ENST00000410451.1_RNA|TMEM14B_ENST00000461342.1_Intron|TMEM14B_ENST00000481240.1_Intron|TMEM14B_ENST00000491103.1_3'UTR|TMEM14B_ENST00000467317.1_Silent_p.S38S	NM_030969.3	NP_112231.3	Q9NUH8	TM14B_HUMAN	transmembrane protein 14B	38						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(2)|skin(2)	11	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)				GCGTGCCGTCCCTGGCTGCAG	0.542													C|||	117	0.0233626	0.0779	0.0115	5008	,	,		20713	0.0		0.004	False		,,,				2504	0.002				p.S38S		Atlas-SNP	.											.	TMEM14B	19	.	0			c.C114T						PASS	.	C	,	262,4142	148.4+/-182.8	15,232,1955	129.0	112.0	118.0		,114	3.1	0.9	6	dbSNP_86	118	28,8572	18.5+/-59.3	0,28,4272	no	intron,coding-synonymous	TMEM14B	NM_001127711.1,NM_030969.3	,	15,260,6227	TT,TC,CC		0.3256,5.9491,2.2301	,	,38/115	10751379	290,12714	2202	4300	6502	SO:0001819	synonymous_variant	81853	exon4			GCCGTCCCTGGCT	AL024498	CCDS4515.1, CCDS47372.1, CCDS75395.1, CCDS75396.1, CCDS75397.1	6p25.1-p23	2008-08-12			ENSG00000137210	ENSG00000137210			21384	protein-coding gene	gene with protein product							Standard	NM_030969		Approved	MGC1223	uc003mzk.4	Q9NUH8	OTTHUMG00000014246	ENST00000379542.5:c.114C>T	6.37:g.10751379C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_030969	Q5THN7|Q5THN8|Q96IX7|Q9BVN8	Silent	SNP	ENST00000379542.5	37	CCDS4515.1																																																																																			C|0.979;T|0.021	0.021	strong		0.542	TMEM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039836.1	NM_030969	
ZNF560	147741	hgsc.bcm.edu	37	19	9578459	9578459	+	Silent	SNP	C	C	T	rs16980696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9578459C>T	ENST00000301480.4	-	10	1377	c.1164G>A	c.(1162-1164)ccG>ccA	p.P388P		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	388					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						GAAAGCCTGACGGCACAGTGA	0.428													C|||	257	0.0513179	0.1672	0.0101	5008	,	,		21477	0.006		0.0229	False		,,,				2504	0.0				p.P388P		Atlas-SNP	.											.	ZNF560	162	.	0			c.G1164A						PASS	.	C		598,3808	260.1+/-263.5	42,514,1647	130.0	131.0	131.0		1164	-3.7	0.0	19	dbSNP_123	131	131,8469	67.0+/-129.4	0,131,4169	no	coding-synonymous	ZNF560	NM_152476.2		42,645,5816	TT,TC,CC		1.5233,13.5724,5.6051		388/791	9578459	729,12277	2203	4300	6503	SO:0001819	synonymous_variant	147741	exon10			GCCTGACGGCACA	AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"""Zinc fingers, C2H2-type"", ""-"""	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.1164G>A	19.37:g.9578459C>T		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	198	197	0.99495	NM_152476	Q495S9|Q495T1	Silent	SNP	ENST00000301480.4	37	CCDS12214.1																																																																																			C|0.951;T|0.049	0.049	strong		0.428	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476	
PCDHB6	56130	hgsc.bcm.edu	37	5	140531408	140531408	+	Missense_Mutation	SNP	T	T	G	rs148897759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140531408T>G	ENST00000231136.1	+	1	1570	c.1570T>G	c.(1570-1572)Tct>Gct	p.S524A	PCDHB6_ENST00000543635.1_Missense_Mutation_p.S388A	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	524	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S524A(1)		cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCCCTGCAGTCTTTCGAGTT	0.682													G|||	48	0.00958466	0.0204	0.0144	5008	,	,		16495	0.003		0.007	False		,,,				2504	0.001				p.S524A		Atlas-SNP	.											PCDHB6,trunk,malignant_melanoma,0,1	PCDHB6	161	1	1	Substitution - Missense(1)	skin(1)	c.T1570G						scavenged	.						79.0	85.0	83.0					5																	140531408		2203	4300	6503	SO:0001583	missense	56130	exon1			CTGCAGTCTTTCG	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1570T>G	5.37:g.140531408T>G	ENSP00000231136:p.Ser524Ala	Somatic	318	2	0.00628931		WXS	Illumina HiSeq	Phase_I	404	16	0.039604	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.556962	0.00910	.	.	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.01133	5.29;5.29	4.19	4.19	0.49359	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00845	0.0028	N	0.16066	0.365	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44574	-0.9319	9	0.02654	T	1	.	10.8888	0.46984	0.0:0.1407:0.7132:0.1461	.	524	Q9Y5E3	PCDB6_HUMAN	A	388;524;309	ENSP00000438466:S388A;ENSP00000231136:S524A	ENSP00000231136:S524A	S	+	1	0	PCDHB6	140511592	0.000000	0.05858	0.001000	0.08648	0.619000	0.37552	0.528000	0.23002	0.896000	0.36366	-0.224000	0.12420	TCT	T|0.997;G|0.003	0.003	strong		0.682	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
SPARC	6678	hgsc.bcm.edu	37	5	151054227	151054227	+	Silent	SNP	T	T	C	rs2304052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:151054227T>C	ENST00000231061.4	-	3	379	c.66A>G	c.(64-66)gaA>gaG	p.E22E	CTB-113P19.1_ENST00000518905.1_RNA|CTB-113P19.1_ENST00000510576.2_RNA	NM_003118.3	NP_003109.1	P09486	SPRC_HUMAN	secreted protein, acidic, cysteine-rich (osteonectin)	22	Asp/Glu-rich (acidic; binds calcium).				blood coagulation (GO:0007596)|bone development (GO:0060348)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|inner ear development (GO:0048839)|lung development (GO:0030324)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|regulation of cell morphogenesis (GO:0022604)|response to cadmium ion (GO:0046686)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to gravity (GO:0009629)|response to L-ascorbic acid (GO:0033591)|response to lead ion (GO:0010288)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nuclear matrix (GO:0016363)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|platelet alpha granule membrane (GO:0031092)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)			central_nervous_system(3)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(196;0.109)|all_hematologic(541;0.122)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;0.00118)		CAGGCAGGGCTTCTTGCTGCT	0.557													T|||	990	0.197684	0.4743	0.1153	5008	,	,		20294	0.0675		0.0855	False		,,,				2504	0.1319				p.E22E		Atlas-SNP	.											.	SPARC	38	.	0			c.A66G						PASS	.	T		1855,2551	538.8+/-375.1	370,1115,718	186.0	165.0	173.0		66	1.1	1.0	5	dbSNP_100	173	628,7972	162.6+/-215.3	20,588,3692	no	coding-synonymous	SPARC	NM_003118.2		390,1703,4410	CC,CT,TT		7.3023,42.1017,19.0912		22/304	151054227	2483,10523	2203	4300	6503	SO:0001819	synonymous_variant	6678	exon3			CAGGGCTTCTTGC		CCDS4318.1	5q31-q33	2012-10-02			ENSG00000113140	ENSG00000113140			11219	protein-coding gene	gene with protein product	"""cysteine-rich protein"", ""osteonectin"""	182120		ON		2838412, 3410046	Standard	NM_003118		Approved		uc003lui.4	P09486	OTTHUMG00000130122	ENST00000231061.4:c.66A>G	5.37:g.151054227T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_003118	D3DQH9|Q6IBK4	Silent	SNP	ENST00000231061.4	37	CCDS4318.1																																																																																			T|0.807;C|0.193	0.193	strong		0.557	SPARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252430.1	NM_003118	
DRC7	84229	hgsc.bcm.edu	37	16	57762401	57762401	+	Missense_Mutation	SNP	T	T	C	rs2923147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57762401T>C	ENST00000360716.3	+	17	2517	c.2296T>C	c.(2296-2298)Tgc>Cgc	p.C766R	CCDC135_ENST00000394337.4_Missense_Mutation_p.C766R|CCDC135_ENST00000336825.8_Missense_Mutation_p.C701R			Q8IY82	CC135_HUMAN		766			C -> R (in dbSNP:rs2923147). {ECO:0000269|PubMed:11230166}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						GAAACTAACATGCTGGCAGGC	0.622													c|||	1976	0.394569	0.7133	0.2954	5008	,	,		16930	0.3839		0.2256	False		,,,				2504	0.2188				p.C766R		Atlas-SNP	.											CCDC135,NS,carcinoma,0,1	CCDC135	97	1	0			c.T2296C						scavenged	.	C	ARG/CYS	2798,1594	487.6+/-361.0	900,998,298	46.0	51.0	49.0		2296	4.2	0.8	16	dbSNP_101	49	1710,6882	732.0+/-406.8	169,1372,2755	yes	missense	CCDC135	NM_032269.5	180	1069,2370,3053	CC,CT,TT		19.9022,36.2933,34.7197	benign	766/875	57762401	4508,8476	2196	4296	6492	SO:0001583	missense	84229	exon16			CTAACATGCTGGC																												ENST00000360716.3:c.2296T>C	16.37:g.57762401T>C	ENSP00000353942:p.Cys766Arg	Somatic	239	2	0.0083682		WXS	Illumina HiSeq	Phase_I	227	109	0.480176	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	843	0.385989010989011	344	0.6991869918699187	109	0.3011049723756906	218	0.3811188811188811	172	0.22691292875989447	c	0.059	-1.228281	0.01518	0.637067	0.199022	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.35973	1.28;1.28;1.28	5.15	4.16	0.48862	.	0.215200	0.37304	N	0.002154	T	0.00012	0.0000	N	0.00067	-2.295	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43180	-0.9407	9	0.02654	T	1	-14.2278	8.0328	0.30476	0.2595:0.6617:0.0:0.0788	rs2923147;rs3803595;rs57995451;rs2923147	701;766	Q8IY82-2;Q8IY82	.;CC135_HUMAN	R	766;701;766	ENSP00000377869:C766R;ENSP00000338938:C701R;ENSP00000353942:C766R	ENSP00000338938:C701R	C	+	1	0	CCDC135	56319902	0.054000	0.20591	0.822000	0.32727	0.661000	0.39034	1.019000	0.30014	1.184000	0.42957	-0.320000	0.08662	TGC	T|0.627;C|0.373	0.373	strong		0.622	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
ANKRD33	341405	hgsc.bcm.edu	37	12	52282865	52282865	+	Silent	SNP	C	C	T	rs35851809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52282865C>T	ENST00000340970.4	+	3	377	c.6C>T	c.(4-6)gtC>gtT	p.V2V	ANKRD33_ENST00000301190.6_Silent_p.V137V|ANKRD33_ENST00000538991.1_Intron|ANKRD33_ENST00000547119.1_3'UTR			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	2					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)		GCCTCATGGTCGCATGCTACC	0.607													c|||	7	0.00139776	0.0053	0.0	5008	,	,		18277	0.0		0.0	False		,,,				2504	0.0				p.V137V		Atlas-SNP	.											.	ANKRD33	33	.	0			c.C411T						PASS	.	T	,	29,4377	35.2+/-66.4	1,27,2175	91.0	96.0	95.0		6,411	-1.1	0.7	12	dbSNP_126	95	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ANKRD33	NM_001130015.1,NM_182608.3	,	1,27,6475	TT,TC,CC		0.0,0.6582,0.223	,	2/273,137/453	52282865	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	341405	exon3			CATGGTCGCATGC		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.6C>T	12.37:g.52282865C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Silent	SNP	ENST00000340970.4	37	CCDS44892.1																																																																																			C|0.998;T|0.002	0.002	strong		0.607	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
MS4A7	58475	hgsc.bcm.edu	37	11	60161273	60161273	+	Missense_Mutation	SNP	C	C	T	rs372900689		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60161273C>T	ENST00000300184.3	+	7	858	c.662C>T	c.(661-663)tCg>tTg	p.S221L	MS4A7_ENST00000534016.1_Missense_Mutation_p.S176L|MS4A14_ENST00000531787.1_Intron|MS4A14_ENST00000395001.1_5'Flank|MS4A7_ENST00000530234.2_Intron|MS4A7_ENST00000358246.1_Missense_Mutation_p.S176L|MS4A14_ENST00000395005.2_5'Flank|MS4A14_ENST00000300187.6_5'Flank|MS4A14_ENST00000531783.1_5'Flank	NM_021201.4|NM_206939.1	NP_067024.1|NP_996822.1	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member 7	221						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(8)|ovary(1)|skin(1)	20						TCATTTTCCTCGACCCAGTCA	0.348																																					p.S221L		Atlas-SNP	.											.	MS4A7	38	.	0			c.C662T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	103.0	105.0	104.0		527,662,527,662	-0.0	0.0	11		104	0,8600		0,0,4300	no	missense,missense,missense,missense	MS4A7	NM_206940.1,NM_206939.1,NM_206938.1,NM_021201.4	145,145,145,145	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign	176/196,221/241,176/196,221/241	60161273	1,13005	2203	4300	6503	SO:0001583	missense	58475	exon7			TTTCCTCGACCCA	AB026043	CCDS7985.1, CCDS7986.1	11q12	2008-03-25				ENSG00000166927			13378	protein-coding gene	gene with protein product		606502				11245982, 11401424	Standard	NM_021201		Approved	CD20L4, CFFM4, MS4A8	uc001npf.3	Q9GZW8		ENST00000300184.3:c.662C>T	11.37:g.60161273C>T	ENSP00000300184:p.Ser221Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	70	41	0.585714	NM_021201	A6NP53|Q6IAG8	Missense_Mutation	SNP	ENST00000300184.3	37	CCDS7985.1	.	.	.	.	.	.	.	.	.	.	c	0.019	-1.453245	0.01071	2.27E-4	0.0	ENSG00000166927	ENST00000300184;ENST00000358246;ENST00000534016;ENST00000530027	T;T;T;T	0.12984	3.36;2.63;2.63;2.9	3.79	-0.0112	0.13993	.	2.053890	0.03732	N	0.253570	T	0.05640	0.0148	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	0.27434	-1.0074	10	0.02654	T	1	-35.547	3.542	0.07815	0.0:0.2192:0.1969:0.5839	.	176;221	Q9GZW8-2;Q9GZW8	.;MS4A7_HUMAN	L	221;176;176;157	ENSP00000300184:S221L;ENSP00000350983:S176L;ENSP00000434637:S176L;ENSP00000434819:S157L	ENSP00000300184:S221L	S	+	2	0	MS4A7	59917849	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.094000	0.11094	-0.015000	0.14150	-0.592000	0.04112	TCG	.	.	weak		0.348	MS4A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394299.1		
TMEM259	91304	hgsc.bcm.edu	37	19	1014454	1014454	+	Missense_Mutation	SNP	C	C	T	rs141314760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1014454C>T	ENST00000356663.3	-	2	365	c.244G>A	c.(244-246)Gtc>Atc	p.V82I	TMEM259_ENST00000333175.5_Missense_Mutation_p.V82I	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	82						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											TAGGCCAGGACGAAGAGCACA	0.657													g|||	3	0.000599042	0.0023	0.0	5008	,	,		14663	0.0		0.0	False		,,,				2504	0.0				p.V82I		Atlas-SNP	.											.	.	.	.	0			c.G244A						PASS	.	G	ILE/VAL,ILE/VAL	16,4386		0,16,2185	27.0	26.0	26.0		244,244	1.9	1.0	19	dbSNP_134	26	0,8592		0,0,4296	yes	missense,missense	C19orf6	NM_001033026.1,NM_033420.3	29,29	0,16,6481	TT,TC,CC		0.0,0.3635,0.1231	benign,benign	82/621,82/409	1014454	16,12978	2201	4296	6497	SO:0001583	missense	91304	exon2			CCAGGACGAAGAG	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.244G>A	19.37:g.1014454C>T	ENSP00000349087:p.Val82Ile	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_033420	O60392|Q8NF79|Q96H30	Missense_Mutation	SNP	ENST00000356663.3	37	CCDS32862.1	.	.	.	.	.	.	.	.	.	.	c	1.363	-0.588083	0.03799	0.003635	0.0	ENSG00000182087	ENST00000356663;ENST00000333175	.	.	.	4.17	1.89	0.25635	.	0.121554	0.53938	D	0.000048	T	0.10078	0.0247	N	0.02202	-0.64	0.30205	N	0.798305	B;B	0.25904	0.003;0.137	B;B	0.17722	0.004;0.019	T	0.13255	-1.0516	9	0.12766	T	0.61	-12.4541	2.6922	0.05124	0.0:0.4533:0.2917:0.2549	.	82;82	Q4ZIN3-2;Q4ZIN3	.;MBRL_HUMAN	I	82	.	ENSP00000331423:V82I	V	-	1	0	C19orf6	965454	1.000000	0.71417	0.993000	0.49108	0.370000	0.29829	3.588000	0.53964	0.994000	0.38892	-0.233000	0.12211	GTC	C|0.999;T|0.001	0.001	strong		0.657	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420	
TYW1	55253	hgsc.bcm.edu	37	7	66648157	66648157	+	Silent	SNP	C	C	T	rs4145350	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:66648157C>T	ENST00000359626.5	+	14	1907	c.1743C>T	c.(1741-1743)aaC>aaT	p.N581N		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	581					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				AAGCATGGAACGTGGACGAGC	0.527																																					p.N581N		Atlas-SNP	.											.	TYW1	71	.	0			c.C1743T						PASS	.	C		1517,2889		140,1237,826	93.0	69.0	77.0		1743	-4.6	1.0	7	dbSNP_110	77	2010,6590		167,1676,2457	no	coding-synonymous	TYW1	NM_018264.2		307,2913,3283	TT,TC,CC		23.3721,34.4303,27.1183		581/733	66648157	3527,9479	2203	4300	6503	SO:0001819	synonymous_variant	55253	exon14			ATGGAACGTGGAC	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1743C>T	7.37:g.66648157C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	133	40	0.300752	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	37	CCDS5538.1																																																																																			C|0.778;T|0.222	0.222	strong		0.527	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
E2F4	1874	hgsc.bcm.edu	37	16	67234134	67234134	+	IGR	SNP	A	A	G	rs8058861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67234134A>G	ENST00000379378.3	+	0	2096				ELMO3_ENST00000477898.1_5'UTR|ELMO3_ENST00000360833.1_Missense_Mutation_p.N131D|ELMO3_ENST00000393997.2_Missense_Mutation_p.N148D|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000571638.1_3'UTR	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding						blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		GCTGCAGAGTAACAGTCCTGA	0.622													G|||	1010	0.201677	0.5182	0.0735	5008	,	,		13259	0.0238		0.0696	False		,,,				2504	0.184				p.N148D		Atlas-SNP	.											.	ELMO3	41	.	0			c.A442G						PASS	.	G	ASP/ASN	1657,2387		342,973,707	36.0	38.0	37.0		442	0.7	0.0	16	dbSNP_116	37	583,7741		29,525,3608	yes	missense	ELMO3	NM_024712.3	23	371,1498,4315	GG,GA,AA		7.0038,40.9743,18.1113	benign	148/774	67234134	2240,10128	2022	4162	6184	SO:0001628	intergenic_variant	79767	exon5			CAGAGTAACAGTC	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975		16.37:g.67234134A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_024712	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	37	CCDS32464.1	333	0.15247252747252749	239	0.48577235772357724	33	0.09116022099447514	12	0.02097902097902098	49	0.06464379947229551	G	10.23	1.291660	0.23564	0.409743	0.070038	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.46819	0.86;0.86	5.16	0.709	0.18150	.	1.206870	0.05741	N	0.601429	T	0.00012	0.0000	N	0.12182	0.205	0.36902	P	0.109541	B;B	0.18166	0.011;0.026	B;B	0.17722	0.019;0.019	T	0.45160	-0.9280	9	0.25106	T	0.35	-1.8862	1.3437	0.02159	0.2925:0.242:0.3415:0.124	rs8058861;rs8058861	131;148	F8W9E7;Q96BJ8-3	.;.	D	131;148	ENSP00000354077:N131D;ENSP00000377566:N148D	ENSP00000354077:N131D	N	+	1	0	ELMO3	65791635	0.001000	0.12720	0.035000	0.18076	0.556000	0.35491	-0.293000	0.08320	-0.315000	0.08703	-0.366000	0.07423	AAC	A|0.847;G|0.153	0.153	strong		0.622	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
HSPB3	8988	hgsc.bcm.edu	37	5	53751818	53751818	+	Missense_Mutation	SNP	G	G	A	rs35258119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:53751818G>A	ENST00000302005.1	+	1	374	c.199G>A	c.(199-201)Ggc>Agc	p.G67S		NM_006308.2	NP_006299.1	Q12988	HSPB3_HUMAN	heat shock 27kDa protein 3	67			G -> S (in dbSNP:rs35258119).		cell death (GO:0008219)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|large_intestine(4)|prostate(3)	8		Lung NSC(810;0.00104)				ACCCCGAGAAGGCAAATCCCA	0.552													G|||	41	0.0081869	0.028	0.0058	5008	,	,		19929	0.0		0.0	False		,,,				2504	0.0				p.G67S		Atlas-SNP	.											.	HSPB3	17	.	0			c.G199A						PASS	.	G	SER/GLY	90,4316	75.7+/-113.9	0,90,2113	84.0	76.0	79.0		199	2.1	0.0	5	dbSNP_126	79	0,8600		0,0,4300	yes	missense	HSPB3	NM_006308.2	56	0,90,6413	AA,AG,GG		0.0,2.0427,0.692	benign	67/151	53751818	90,12916	2203	4300	6503	SO:0001583	missense	8988	exon1			CGAGAAGGCAAAT	Y17782	CCDS3961.1	5q11.2	2011-09-02	2002-08-29		ENSG00000169271	ENSG00000169271		"""Heat shock proteins / HSPB"""	5248	protein-coding gene	gene with protein product		604624	"""heat shock 27kD protein 3"""			8972725, 9858786	Standard	NM_006308		Approved	HSPL27	uc003jph.2	Q12988	OTTHUMG00000096995	ENST00000302005.1:c.199G>A	5.37:g.53751818G>A	ENSP00000303394:p.Gly67Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	146	144	0.986301	NM_006308		Missense_Mutation	SNP	ENST00000302005.1	37	CCDS3961.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	9.517	1.107277	0.20714	0.020427	0.0	ENSG00000169271	ENST00000302005	D	0.91124	-2.79	5.89	2.12	0.27331	Heat shock protein Hsp20 (2);HSP20-like chaperone (1);	0.364101	0.27415	N	0.019475	T	0.69628	0.3132	N	0.16708	0.43	0.09310	N	1	B	0.19445	0.036	B	0.17722	0.019	T	0.65742	-0.6094	10	0.36615	T	0.2	-30.5173	10.6026	0.45375	0.2571:0.0:0.7429:0.0	rs35258119	67	Q12988	HSPB3_HUMAN	S	67	ENSP00000303394:G67S	ENSP00000303394:G67S	G	+	1	0	HSPB3	53787575	0.686000	0.27661	0.045000	0.18777	0.039000	0.13416	0.902000	0.28459	0.813000	0.34350	0.655000	0.94253	GGC	G|0.992;A|0.008	0.008	strong		0.552	HSPB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214074.2		
C2orf16	84226	hgsc.bcm.edu	37	2	27804690	27804690	+	Missense_Mutation	SNP	C	C	T	rs555322236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27804690C>T	ENST00000408964.2	+	1	5302	c.5251C>T	c.(5251-5253)Cac>Tac	p.H1751Y	ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000355467.4_5'Flank|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000413371.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|RP11-158I13.2_ENST00000505973.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1751	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GAGAAGACATCACAGTCCCTC	0.557													C|||	6	0.00119808	0.0038	0.0	5008	,	,		20958	0.001		0.0	False		,,,				2504	0.0				p.H1751Y		Atlas-SNP	.											.	C2orf16	357	.	0			c.C5251T						PASS	.						192.0	196.0	195.0					2																	27804690		1920	4145	6065	SO:0001583	missense	84226	exon1			AGACATCACAGTC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.5251C>T	2.37:g.27804690C>T	ENSP00000386190:p.His1751Tyr	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	158	13	0.0822785	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.428580	0.43122	.	.	ENSG00000221843	ENST00000408964	T	0.05199	3.48	3.97	2.1	0.27182	.	.	.	.	.	T	0.04770	0.0129	L	0.34521	1.04	0.09310	N	1	P	0.47604	0.898	B	0.37550	0.253	T	0.41520	-0.9504	9	0.30078	T	0.28	.	8.7197	0.34434	0.1703:0.6649:0.1648:0.0	.	1751	Q68DN1	CB016_HUMAN	Y	1751	ENSP00000386190:H1751Y	ENSP00000386190:H1751Y	H	+	1	0	C2orf16	27658194	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.020000	0.13466	0.607000	0.29982	0.456000	0.33151	CAC	.	.	none		0.557	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
ARSA	410	hgsc.bcm.edu	37	22	51064039	51064039	+	Missense_Mutation	SNP	G	G	C	rs743616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:51064039G>C	ENST00000547307.1	-	7	1577	c.1172C>G	c.(1171-1173)aCt>aGt	p.T391S	ARSA_ENST00000216124.5_Missense_Mutation_p.T393S|ARSA_ENST00000356098.5_Missense_Mutation_p.T393S|ARSA_ENST00000453344.2_Missense_Mutation_p.T307S|ARSA_ENST00000547805.1_Missense_Mutation_p.T391S|ARSA_ENST00000395619.3_Missense_Mutation_p.T393S|ARSA_ENST00000395621.3_Missense_Mutation_p.T393S|ARSA_ENST00000610191.1_5'Flank			P15289	ARSA_HUMAN	arylsulfatase A	391			T -> S (in dbSNP:rs743616). {ECO:0000269|PubMed:10477432, ECO:0000269|PubMed:11061266, ECO:0000269|PubMed:11456299, ECO:0000269|PubMed:11941485, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15326627, ECO:0000269|PubMed:15489334, 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)	GTACTTTCCAGTCCGCACAGC	0.652													C|||	2031	0.405551	0.3578	0.4697	5008	,	,		14864	0.3214		0.5288	False		,,,				2504	0.3845				p.T393S		Atlas-SNP	.											.	ARSA	19	.	0			c.C1178G	GRCh37	CM910052	ARSA	M	rs743616	PASS	.	C	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	1736,2670	646.8+/-398.4	352,1032,819	69.0	82.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1178,1178,1178,1178,920	-0.0	0.9	22	dbSNP_86	78	4560,4040	555.3+/-386.7	1220,2120,960	yes	missense,missense,missense,missense,missense	ARSA	NM_000487.5,NM_001085425.2,NM_001085426.2,NM_001085427.2,NM_001085428.2	58,58,58,58,58	1572,3152,1779	CC,CG,GG		46.9767,39.4008,48.4084	benign,benign,benign,benign,benign	393/510,393/510,393/510,393/510,307/424	51064039	6296,6710	2203	4300	6503	SO:0001583	missense	410	exon8			TTTCCAGTCCGCA	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.1172C>G	22.37:g.51064039G>C	ENSP00000448440:p.Thr391Ser	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	178	70	0.393258	NM_001085426	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Missense_Mutation	SNP	ENST00000547307.1	37		930	0.4258241758241758	181	0.3678861788617886	176	0.4861878453038674	185	0.32342657342657344	388	0.5118733509234829	C	8.274	0.813939	0.16537	0.394008	0.530233	ENSG00000100299	ENST00000356098;ENST00000216124;ENST00000547307;ENST00000547805;ENST00000395621;ENST00000453344;ENST00000395619	D;D;D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52	5.59	-0.0288	0.13920	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	1.175200	0.06015	N	0.650226	T	0.00012	0.0000	N	0.03071	-0.42	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24012	-1.0172	9	0.21014	T	0.42	.	1.5892	0.02650	0.1364:0.3411:0.1333:0.3891	rs743616;rs1051552;rs3171785;rs17184315;rs17856452;rs60738949;rs743616	391	P15289	ARSA_HUMAN	S	393;393;391;391;393;307;393	ENSP00000348406:T393S;ENSP00000216124:T393S;ENSP00000448440:T391S;ENSP00000448932:T391S;ENSP00000378983:T393S;ENSP00000412542:T307S;ENSP00000378981:T393S	ENSP00000216124:T393S	T	-	2	0	ARSA	49410905	0.000000	0.05858	0.862000	0.33874	0.935000	0.57460	0.103000	0.15292	0.053000	0.16036	-0.934000	0.02701	ACT	G|0.545;C|0.455	0.455	strong		0.652	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487	
RHPN2	85415	hgsc.bcm.edu	37	19	33493188	33493188	+	Missense_Mutation	SNP	T	T	A	rs193179333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33493188T>A	ENST00000254260.3	-	9	1105	c.1070A>T	c.(1069-1071)cAc>cTc	p.H357L	RHPN2_ENST00000400226.4_Missense_Mutation_p.H206L	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	357	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.H357L(2)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					AGTGAAGTAGTGGGCCAGGGC	0.647																																					p.H357L		Atlas-SNP	.											RHPN2,colon,carcinoma,0,9	RHPN2	107	9	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	c.A1070T						scavenged	.						45.0	42.0	43.0					19																	33493188		2203	4300	6503	SO:0001583	missense	85415	exon9			AAGTAGTGGGCCA	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.1070A>T	19.37:g.33493188T>A	ENSP00000254260:p.His357Leu	Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	201	5	0.0248756	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.323917	0.81580	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.20598	2.06;2.06	4.61	4.61	0.57282	BRO1 domain (3);	0.045255	0.85682	D	0.000000	T	0.46619	0.1402	M	0.87269	2.87	0.80722	D	1	D	0.61080	0.989	P	0.58077	0.832	T	0.57934	-0.7725	10	0.87932	D	0	-27.93	14.3018	0.66357	0.0:0.0:0.0:1.0	.	357	Q8IUC4	RHPN2_HUMAN	L	357;87;206	ENSP00000254260:H357L;ENSP00000402244:H206L	ENSP00000254260:H357L	H	-	2	0	RHPN2	38185028	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	7.570000	0.82390	1.829000	0.53265	0.374000	0.22700	CAC	T|0.902;A|0.097	0.097	strong		0.647	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
LMO7	4008	hgsc.bcm.edu	37	13	76195833	76195833	+	Missense_Mutation	SNP	A	A	G	rs143470231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:76195833A>G	ENST00000341547.4	+	1	1264	c.4A>G	c.(4-6)Aag>Gag	p.K2E	LMO7_ENST00000357063.3_Missense_Mutation_p.K2E|RP11-29G8.3_ENST00000563635.1_RNA|RP11-173B14.5_ENST00000568735.1_RNA|RP11-173B14.5_ENST00000568302.1_RNA|LMO7_ENST00000377534.3_Missense_Mutation_p.K2E	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	2					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)			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)		AACTGCTATGAAGAAAATTAG	0.363													A|||	57	0.0113818	0.0378	0.0101	5008	,	,		17645	0.0		0.0	False		,,,				2504	0.0				p.K2E		Atlas-SNP	.											LMO7_ENST00000357063,colon,carcinoma,-2,2	LMO7	334	2	0			c.A4G						PASS	.	A	GLU/LYS	168,4238	101.6+/-140.2	4,160,2039	40.0	38.0	39.0		4	1.0	0.2	13	dbSNP_134	39	0,8600		0,0,4300	yes	missense	LMO7	NM_005358.5	56	4,160,6339	GG,GA,AA		0.0,3.813,1.2917		2/1350	76195833	168,12838	2203	4300	6503	SO:0001583	missense	4008	exon1			GCTATGAAGAAAA	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000341547.4:c.4A>G	13.37:g.76195833A>G	ENSP00000342112:p.Lys2Glu	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000341547.4	37	CCDS9454.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	A	15.96	2.985987	0.53934	0.03813	0.0	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534	T;T;T	0.35048	1.33;1.39;1.44	5.23	1.02	0.19986	.	.	.	.	.	T	0.11707	0.0285	.	.	.	0.09310	N	1	D	0.57257	0.979	P	0.53266	0.722	T	0.11891	-1.0569	8	0.87932	D	0	.	1.7898	0.03049	0.5679:0.1723:0.0937:0.166	.	2	Q8WWI1-3	.	E	2	ENSP00000342112:K2E;ENSP00000349571:K2E;ENSP00000366757:K2E	ENSP00000342112:K2E	K	+	1	0	LMO7	75093834	0.987000	0.35691	0.226000	0.23910	0.335000	0.28730	2.364000	0.44187	0.796000	0.33947	0.460000	0.39030	AAG	A|0.987;G|0.013	0.013	strong		0.363	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358	
OR51I2	390064	hgsc.bcm.edu	37	11	5474894	5474894	+	Missense_Mutation	SNP	T	T	C	rs74049540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5474894T>C	ENST00000341449.2	+	1	257	c.176T>C	c.(175-177)aTg>aCg	p.M59T	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	59					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATGAGCCCATGTACTACTTC	0.572													T|||	291	0.058107	0.2118	0.0144	5008	,	,		21590	0.0		0.001	False		,,,				2504	0.0				p.M59T		Atlas-SNP	.											.	OR51I2	76	.	0			c.T176C						PASS	.	T	THR/MET	709,3693	295.6+/-283.7	60,589,1552	109.0	98.0	102.0		176	5.6	1.0	11	dbSNP_130	102	9,8585	5.0+/-18.6	0,9,4288	yes	missense	OR51I2	NM_001004754.2	81	60,598,5840	CC,CT,TT		0.1047,16.1063,5.5248	possibly-damaging	59/313	5474894	718,12278	2201	4297	6498	SO:0001583	missense	390064	exon1			AGCCCATGTACTA	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"""GPCR / Class A : Olfactory receptors"""	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.176T>C	11.37:g.5474894T>C	ENSP00000341987:p.Met59Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	128	0.05860805860805861	123	0.25	5	0.013812154696132596	0	0.0	0	0.0	T	13.85	2.359159	0.41801	0.161063	0.001047	ENSG00000187918	ENST00000341449	T	0.09817	2.94	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.94771	3.58	0.25314	P	0.9891777	D	0.55800	0.973	P	0.61201	0.885	T	0.04621	-1.0938	9	0.72032	D	0.01	.	14.7065	0.69194	0.0:0.0:0.0:1.0	.	59	Q9H344	O51I2_HUMAN	T	59	ENSP00000341987:M59T	ENSP00000341987:M59T	M	+	2	0	OR51I2	5431470	1.000000	0.71417	1.000000	0.80357	0.364000	0.29643	4.672000	0.61597	2.340000	0.79590	0.528000	0.53228	ATG	T|0.937;C|0.063	0.063	strong		0.572	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754	
RP1L1	94137	hgsc.bcm.edu	37	8	10470794	10470794	+	Missense_Mutation	SNP	G	G	C	rs77833234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10470794G>C	ENST00000382483.3	-	4	1037	c.814C>G	c.(814-816)Cca>Gca	p.P272A		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	272					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)		GGCAGCCGTGGCGTGCTGCCT	0.647													G|||	19	0.00379393	0.0144	0.0	5008	,	,		15506	0.0		0.0	False		,,,				2504	0.0				p.P272A		Atlas-SNP	.											.	RP1L1	453	.	0			c.C814G						PASS	.	G	ALA/PRO	38,3946		0,38,1954	53.0	59.0	57.0		814	0.2	0.0	8	dbSNP_131	57	2,8342		0,2,4170	no	missense	RP1L1	NM_178857.5	27	0,40,6124	CC,CG,GG		0.024,0.9538,0.3245	probably-damaging	272/2401	10470794	40,12288	1992	4172	6164	SO:0001583	missense	94137	exon4			GCCGTGGCGTGCT	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.814C>G	8.37:g.10470794G>C	ENSP00000371923:p.Pro272Ala	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	21	9	0.428571	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	20	0.009157509157509158	13	0.026422764227642278	2	0.0055248618784530384	2	0.0034965034965034965	3	0.00395778364116095	G	1.225	-0.625730	0.03610	0.009538	2.4E-4	ENSG00000183638	ENST00000382483	T	0.04194	3.68	5.33	0.147	0.14838	.	1.942830	0.03465	N	0.212853	T	0.01287	0.0042	L	0.38175	1.15	0.09310	N	1	B	0.22683	0.073	B	0.20767	0.031	T	0.43048	-0.9415	10	0.21014	T	0.42	-0.1152	0.8756	0.01223	0.251:0.3733:0.1891:0.1866	.	272	A6NKC6	.	A	272	ENSP00000371923:P272A	ENSP00000371923:P272A	P	-	1	0	RP1L1	10508204	0.087000	0.21565	0.000000	0.03702	0.005000	0.04900	1.861000	0.39438	0.162000	0.19483	-0.293000	0.09583	CCA	G|0.993;C|0.007	0.007	strong		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
CPO	130749	hgsc.bcm.edu	37	2	207833983	207833983	+	Silent	SNP	A	A	G	rs7582305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:207833983A>G	ENST00000272852.3	+	9	994	c.948A>G	c.(946-948)acA>acG	p.T316T		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	316						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)		ACAGTGGAACATATGGGTTTG	0.512													A|||	1443	0.288139	0.3714	0.2003	5008	,	,		19868	0.2589		0.3032	False		,,,				2504	0.2526				p.T316T		Atlas-SNP	.											CPO,NS,carcinoma,+2,1	CPO	42	1	0			c.A948G						scavenged	.	A		1560,2846	489.4+/-361.5	292,976,935	143.0	127.0	132.0		948	-10.3	0.0	2	dbSNP_116	132	2629,5971	424.1+/-354.6	404,1821,2075	no	coding-synonymous	CPO	NM_173077.2		696,2797,3010	GG,GA,AA		30.5698,35.4063,32.2082		316/375	207833983	4189,8817	2203	4300	6503	SO:0001819	synonymous_variant	130749	exon9			TGGAACATATGGG		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.948A>G	2.37:g.207833983A>G		Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	196	103	0.52551	NM_173077	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	37	CCDS2372.1																																																																																			A|0.685;G|0.315	0.315	strong		0.512	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
CHSY3	337876	hgsc.bcm.edu	37	5	129520679	129520679	+	Missense_Mutation	SNP	G	G	A	rs10068403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:129520679G>A	ENST00000305031.4	+	3	2202	c.1844G>A	c.(1843-1845)gGg>gAg	p.G615E		NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	615			G -> E (in dbSNP:rs10068403).		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)	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)	p.G615E(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		GAAATGGGAGGGCACAATGAA	0.358													G|||	854	0.170527	0.2965	0.1643	5008	,	,		21395	0.2579		0.006	False		,,,				2504	0.0838				p.G615E		Atlas-SNP	.											CHSY3,right_upper_lobe,carcinoma,+1,2	CHSY3	92	2	1	Substitution - Missense(1)	stomach(1)	c.G1844A						PASS	.	G	GLU/GLY	970,3436	357.1+/-313.8	103,764,1336	56.0	57.0	57.0		1844	0.3	0.0	5	dbSNP_119	57	60,8540	35.9+/-90.5	0,60,4240	yes	missense	CHSY3	NM_175856.4	98	103,824,5576	AA,AG,GG		0.6977,22.0154,7.9194	benign	615/883	129520679	1030,11976	2203	4300	6503	SO:0001583	missense	337876	exon3			TGGGAGGGCACAA	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.1844G>A	5.37:g.129520679G>A	ENSP00000302629:p.Gly615Glu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	27	0.380282	NM_175856	B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	37	CCDS34223.1	376	0.17216117216117216	171	0.3475609756097561	48	0.13259668508287292	151	0.263986013986014	6	0.0079155672823219	G	0.003	-2.405052	0.00195	0.220154	0.006977	ENSG00000198108	ENST00000305031	T	0.34472	1.36	4.12	0.333	0.15943	.	0.342006	0.24727	N	0.036100	T	0.00012	0.0000	N	0.01003	-1.06	0.34603	P	0.28325900000000004	B	0.11235	0.004	B	0.17098	0.017	T	0.43410	-0.9393	8	.	.	.	-1.8064	2.315	0.04196	0.2187:0.1294:0.5187:0.1331	rs10068403;rs17769784;rs10068403	615	Q70JA7	CHSS3_HUMAN	E	615	ENSP00000302629:G615E	.	G	+	2	0	CHSY3	129548578	0.995000	0.38212	0.008000	0.14137	0.710000	0.40934	2.503000	0.45407	0.028000	0.15324	-0.157000	0.13467	GGG	G|0.878;A|0.122	0.122	strong		0.358	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856	
SAP130	79595	hgsc.bcm.edu	37	2	128775464	128775464	+	Silent	SNP	A	A	G	rs6430968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128775464A>G	ENST00000259235.3	-	3	345	c.216T>C	c.(214-216)tcT>tcC	p.S72S	SAP130_ENST00000357702.5_Silent_p.S72S|SAP130_ENST00000259234.6_Silent_p.S46S	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	72					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		CACTGACTTCAGAATCTCGAC	0.502													A|||	184	0.0367412	0.1293	0.0159	5008	,	,		21218	0.0		0.002	False		,,,				2504	0.0				p.S72S		Atlas-SNP	.											.	SAP130	169	.	0			c.T216C						PASS	.	A	,	551,3855	247.5+/-255.7	37,477,1689	78.0	70.0	72.0		216,216	-1.2	1.0	2	dbSNP_116	72	20,8580	13.3+/-46.6	0,20,4280	yes	coding-synonymous,coding-synonymous	SAP130	NM_001145928.1,NM_024545.3	,	37,497,5969	GG,GA,AA		0.2326,12.5057,4.3903	,	72/1084,72/1049	128775464	571,12435	2203	4300	6503	SO:0001819	synonymous_variant	79595	exon3			GACTTCAGAATCT	BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"""sin3A-associated protein, 130kDa"""			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.216T>C	2.37:g.128775464A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Silent	SNP	ENST00000259235.3	37	CCDS2153.1																																																																																			A|0.965;G|0.035	0.035	strong		0.502	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350751	50350751	+	Missense_Mutation	SNP	G	G	C	rs201290098		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:50350751G>C	ENST00000289292.7	-	6	3674	c.3391C>G	c.(3391-3393)Cag>Gag	p.Q1131E	SHROOM4_ENST00000460112.3_Missense_Mutation_p.Q1015E|SHROOM4_ENST00000376020.2_Missense_Mutation_p.Q1131E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1131	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	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)					tcctcctcctgttgcttctgc	0.582																																					p.Q1131E		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C3391G						PASS	.						15.0	14.0	15.0					X																	50350751		2199	4294	6493	SO:0001583	missense	57477	exon6			CCTCCTGTTGCTT	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.3391C>G	X.37:g.50350751G>C	ENSP00000289292:p.Gln1131Glu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	70	6	0.0857143	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.554911	0.00918	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.06449	3.3;3.3;3.3	4.89	-0.0454	0.13851	.	1.383290	0.04423	N	0.367895	T	0.03827	0.0108	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36456	-0.9747	10	0.02654	T	1	.	4.0399	0.09746	0.093:0.4322:0.3193:0.1556	.	1131	Q9ULL8	SHRM4_HUMAN	E	1131;1131;1015	ENSP00000289292:Q1131E;ENSP00000365188:Q1131E;ENSP00000421450:Q1015E	ENSP00000289292:Q1131E	Q	-	1	0	SHROOM4	50367491	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.374000	0.20501	-0.047000	0.13423	-0.434000	0.05882	CAG	.	.	weak		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
EMR3	84658	hgsc.bcm.edu	37	19	14740942	14740942	+	Missense_Mutation	SNP	G	G	A	rs78700925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14740942G>A	ENST00000253673.5	-	14	1821	c.1721C>T	c.(1720-1722)cCa>cTa	p.P574L	EMR3_ENST00000599900.1_Missense_Mutation_p.P359L|EMR3_ENST00000443157.2_Missense_Mutation_p.P448L|EMR3_ENST00000344373.4_Missense_Mutation_p.P522L	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	574					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						CTGGGCAGCTGGACCCACCTG	0.542													G|||	94	0.01877	0.0688	0.0043	5008	,	,		14251	0.0		0.0	False		,,,				2504	0.0				p.P574L		Atlas-SNP	.											.	EMR3	99	.	0			c.C1721T						PASS	.	G	LEU/PRO	203,4203	126.6+/-163.6	4,195,2004	109.0	92.0	98.0		1721	2.7	0.0	19	dbSNP_131	98	1,8599	1.2+/-3.3	0,1,4299	yes	missense	EMR3	NM_032571.3	98	4,196,6303	AA,AG,GG		0.0116,4.6074,1.5685	possibly-damaging	574/653	14740942	204,12802	2203	4300	6503	SO:0001583	missense	84658	exon14			GCAGCTGGACCCA	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"""-"", ""GPCR / Class B : Orphans"""	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.1721C>T	19.37:g.14740942G>A	ENSP00000253673:p.Pro574Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_032571		Missense_Mutation	SNP	ENST00000253673.5	37	CCDS12315.1	29	0.013278388278388278	29	0.05894308943089431	0	0.0	0	0.0	0	0.0	G	10.10	1.256668	0.22965	0.046074	1.16E-4	ENSG00000131355	ENST00000443157;ENST00000253673;ENST00000344373	T;T;T	0.41065	1.03;1.01;1.01	3.76	2.72	0.32119	GPCR, family 2-like (1);	.	.	.	.	T	0.19805	0.0476	M	0.88570	2.965	0.20489	N	0.999896	D;D;D	0.89917	1.0;1.0;0.992	D;D;D	0.87578	0.996;0.998;0.968	T	0.17319	-1.0373	9	0.87932	D	0	.	9.204	0.37278	0.1094:0.0:0.8906:0.0	.	448;522;574	E7EW83;Q9BY15-2;Q9BY15	.;.;EMR3_HUMAN	L	448;574;522	ENSP00000396208:P448L;ENSP00000253673:P574L;ENSP00000340758:P522L	ENSP00000253673:P574L	P	-	2	0	EMR3	14601942	0.037000	0.19845	0.031000	0.17742	0.029000	0.11900	2.165000	0.42396	0.923000	0.37045	-0.136000	0.14681	CCA	G|0.984;A|0.016	0.016	strong		0.542	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571	
MUC4	4585	hgsc.bcm.edu	37	3	195512686	195512686	+	Missense_Mutation	SNP	G	G	T	rs79043683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512686G>T	ENST00000463781.3	-	2	6224	c.5765C>A	c.(5764-5766)cCt>cAt	p.P1922H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1922H	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)		GCTGGTGACAGGAAGAGAGGT	0.572																																					p.P1922H		Atlas-SNP	.											.	MUC4	1505	.	0			c.C5765A						PASS	.						51.0	43.0	46.0					3																	195512686		690	1590	2280	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.5765C>A	3.37:g.195512686G>T	ENSP00000417498:p.Pro1922His	Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	288	96	0.333333	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	.	.	.	.	.	.	.	.	.	.	-	3.439	-0.114521	0.06881	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.53	.	.	.	.	.	.	.	.	T	0.25865	0.0630	N	0.19112	0.55	0.09310	N	1	D	0.54964	0.969	P	0.52710	0.707	T	0.12319	-1.0552	7	.	.	.	.	6.7067	0.23254	2.0E-4:0.0:0.9998:0.0	.	1922	E7ESK3	.	H	1922	ENSP00000417498:P1922H;ENSP00000420243:P1922H	.	P	-	2	0	MUC4	196997081	0.012000	0.17670	0.002000	0.10522	0.020000	0.10135	0.556000	0.23438	0.488000	0.27723	0.064000	0.15345	CCT	G|0.992;T|0.008	0.008	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TBC1D9B	23061	hgsc.bcm.edu	37	5	179297352	179297352	+	Silent	SNP	A	A	G	rs384668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179297352A>G	ENST00000356834.3	-	16	2665	c.2628T>C	c.(2626-2628)tgT>tgC	p.C876C	TBC1D9B_ENST00000444477.2_Silent_p.C34C|TBC1D9B_ENST00000355235.3_Silent_p.C876C|TBC1D9B_ENST00000519746.1_Silent_p.C52C	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	876						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGTGGGAGCCACAGGCCCAGG	0.617													G|||	623	0.124401	0.444	0.0432	5008	,	,		19003	0.001		0.005	False		,,,				2504	0.0				p.C876C		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.T2628C						PASS	.	G	,	1543,2863	671.2+/-402.4	287,969,947	99.0	102.0	101.0		2628,2628	-7.3	0.3	5	dbSNP_80	101	15,8585	818.3+/-406.9	0,15,4285	no	coding-synonymous,coding-synonymous	TBC1D9B	NM_015043.3,NM_198868.2	,	287,984,5232	GG,GA,AA		0.1744,35.0204,11.9791	,	876/1234,876/1251	179297352	1558,11448	2203	4300	6503	SO:0001819	synonymous_variant	23061	exon16			GGAGCCACAGGCC	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"""EF-hand domain containing"""	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.2628T>C	5.37:g.179297352A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	37	CCDS43408.1																																																																																			A|0.890;G|0.110	0.110	strong		0.617	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043	
SPTBN1	6711	hgsc.bcm.edu	37	2	54895682	54895682	+	Silent	SNP	C	C	T	rs2229505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:54895682C>T	ENST00000356805.4	+	36	7352	c.7071C>T	c.(7069-7071)ttC>ttT	p.F2357F		NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	2357					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			AGAAGCGGTTCAGCCTTTTTG	0.522													C|||	178	0.0355431	0.1165	0.0245	5008	,	,		17151	0.001		0.005	False		,,,				2504	0.001				p.F2357F		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C7071T						PASS	.	C		429,3977		18,393,1792	25.0	23.0	24.0		7071	3.7	1.0	2	dbSNP_98	24	14,8584		0,14,4285	no	coding-synonymous	SPTBN1	NM_003128.2		18,407,6077	TT,TC,CC		0.1628,9.7367,3.4066		2357/2365	54895682	443,12561	2203	4299	6502	SO:0001819	synonymous_variant	6711	exon36			GCGGTTCAGCCTT		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.7071C>T	2.37:g.54895682C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			C|0.962;T|0.038	0.038	strong		0.522	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
PTPRF	5792	hgsc.bcm.edu	37	1	44019305	44019305	+	Silent	SNP	C	C	T	rs6684279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44019305C>T	ENST00000359947.4	+	4	574	c.234C>T	c.(232-234)ttC>ttT	p.F78F	PTPRF_ENST00000438120.1_Silent_p.F78F|PTPRF_ENST00000372414.3_Silent_p.F78F|PTPRF_ENST00000372413.3_Silent_p.F78F	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	78	Ig-like C2-type 1.				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)				CCCAGCGCTTCGAGGTGCGTC	0.597													C|||	165	0.0329473	0.118	0.0072	5008	,	,		21711	0.0		0.004	False		,,,				2504	0.0				p.F78F		Atlas-SNP	.											.	PTPRF	172	.	0			c.C234T						PASS	.	C	,	440,3966	210.2+/-230.7	23,394,1786	126.0	121.0	122.0		234,234	-9.8	0.6	1	dbSNP_116	122	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	23,395,6085	TT,TC,CC		0.0116,9.9864,3.3907	,	78/1908,78/1899	44019305	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon4			GCGCTTCGAGGTG	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.234C>T	1.37:g.44019305C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2																																																																																			C|0.964;T|0.036	0.036	strong		0.597	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
GPR55	9290	hgsc.bcm.edu	37	2	231775371	231775371	+	Missense_Mutation	SNP	C	C	T	rs80290067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231775371C>T	ENST00000392040.1	-	2	499	c.307G>A	c.(307-309)Gtc>Atc	p.V103I	GPR55_ENST00000392039.2_Missense_Mutation_p.V103I|AC012507.4_ENST00000454890.1_RNA	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	103					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)		TACATGCTGACGAAGTAAAGG	0.597													c|||	144	0.028754	0.1051	0.0072	5008	,	,		21034	0.0		0.0	False		,,,				2504	0.0				p.V103I		Atlas-SNP	.											.	GPR55	46	.	0			c.G307A						PASS	.	C	ILE/VAL	423,3983	197.1+/-221.3	26,371,1806	66.0	44.0	52.0		307	-5.3	0.7	2	dbSNP_131	52	5,8595	4.3+/-15.6	0,5,4295	yes	missense	GPR55	NM_005683.3	29	26,376,6101	TT,TC,CC		0.0581,9.6005,3.2908	benign	103/320	231775371	428,12578	2203	4300	6503	SO:0001583	missense	9290	exon2			TGCTGACGAAGTA	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.307G>A	2.37:g.231775371C>T	ENSP00000375894:p.Val103Ile	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_005683	Q8N580	Missense_Mutation	SNP	ENST00000392040.1	37	CCDS2480.1	53	0.024267399267399268	49	0.09959349593495935	4	0.011049723756906077	0	0.0	0	0.0	c	0.687	-0.795929	0.02862	0.096005	5.81E-4	ENSG00000135898	ENST00000392040;ENST00000392039;ENST00000438398	T;T;T	0.72835	-0.69;-0.69;-0.69	5.38	-5.31	0.02730	GPCR, rhodopsin-like superfamily (1);	0.408961	0.25774	N	0.028383	T	0.01254	0.0041	N	0.12569	0.235	0.24899	N	0.992118	B	0.17465	0.022	B	0.15870	0.014	T	0.13442	-1.0509	10	0.02654	T	1	-33.6109	12.2542	0.54615	0.0:0.5177:0.0:0.4823	.	103	Q9Y2T6	GPR55_HUMAN	I	103	ENSP00000375894:V103I;ENSP00000375893:V103I;ENSP00000412768:V103I	ENSP00000375893:V103I	V	-	1	0	GPR55	231483615	0.000000	0.05858	0.728000	0.30774	0.241000	0.25554	-0.686000	0.05161	-0.943000	0.03691	-1.598000	0.00824	GTC	C|0.971;T|0.029	0.029	strong		0.597	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683	
PLEKHG7	440107	hgsc.bcm.edu	37	12	93147901	93147901	+	Silent	SNP	C	C	T	rs74784157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:93147901C>T	ENST00000344636.3	+	6	535	c.351C>T	c.(349-351)caC>caT	p.H117H		NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	117	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						GACGGCTCCACGTGCCAGAGC	0.512													C|||	274	0.0547125	0.0787	0.0836	5008	,	,		20165	0.0139		0.0586	False		,,,				2504	0.0399				p.H117H		Atlas-SNP	.											.	PLEKHG7	38	.	0			c.C351T						PASS	.	C		275,4131	155.5+/-188.7	11,253,1939	104.0	93.0	96.0		351	3.2	1.0	12	dbSNP_131	96	475,8125	140.0+/-196.6	9,457,3834	no	coding-synonymous	PLEKHG7	NM_001004330.2		20,710,5773	TT,TC,CC		5.5233,6.2415,5.7666		117/380	93147901	750,12256	2203	4300	6503	SO:0001819	synonymous_variant	440107	exon6			GCTCCACGTGCCA	AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"""Pleckstrin homology (PH) domain containing"""	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.351C>T	12.37:g.93147901C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_001004330	B2RNR7	Silent	SNP	ENST00000344636.3	37	CCDS31873.1																																																																																			C|0.947;T|0.053	0.053	strong		0.512	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330	
LILRA6	79168	hgsc.bcm.edu	37	19	54744772	54744772	+	Missense_Mutation	SNP	T	T	G	rs77717986		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54744772T>G	ENST00000396365.2	-	5	929	c.890A>C	c.(889-891)tAt>tCt	p.Y297S	LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Missense_Mutation_p.Y297S|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.Y297S|LILRA6_ENST00000245621.5_Missense_Mutation_p.Y297S	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	297	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTGTGCACCATAGCACCTGTA	0.682																																					p.Y297S		Atlas-SNP	.											.	LILRA6	75	.	0			c.A890C						PASS	.						57.0	71.0	67.0					19																	54744772		2203	4300	6503	SO:0001583	missense	79168	exon5			GCACCATAGCACC	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.890A>C	19.37:g.54744772T>G	ENSP00000379651:p.Tyr297Ser	Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	475	64	0.134737	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	T	3.313	-0.140376	0.06669	.	.	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	2.1	2.1	0.27182	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.228496	0.22643	N	0.057421	T	0.24509	0.0594	M	0.68728	2.09	0.58432	D	0.999998	P;D;P;P	0.89917	0.674;1.0;0.63;0.674	P;D;P;B	0.91635	0.651;0.999;0.495;0.344	T	0.01266	-1.1401	10	0.48119	T	0.1	.	6.2058	0.20602	0.0:0.0:0.0:1.0	.	297;297;297;297	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	S	297	ENSP00000390120:Y297S;ENSP00000411227:Y297S;ENSP00000379651:Y297S;ENSP00000245621:Y297S	ENSP00000245621:Y297S	Y	-	2	0	LILRA6	59436584	0.024000	0.19004	0.735000	0.30896	0.045000	0.14185	0.527000	0.22987	1.233000	0.43693	0.136000	0.15936	TAT	.	.	weak		0.682	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
KIAA0556	23247	hgsc.bcm.edu	37	16	27709812	27709812	+	Silent	SNP	C	C	T	rs61740294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27709812C>T	ENST00000261588.4	+	9	1123	c.1104C>T	c.(1102-1104)agC>agT	p.S368S	CTD-2049O4.1_ENST00000564893.1_RNA|KIAA0556_ENST00000567894.1_3'UTR	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	368						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						AGCCAGCCAGCCCACTGCAGG	0.637													C|||	81	0.0161741	0.0575	0.0072	5008	,	,		17048	0.0		0.0	False		,,,				2504	0.0				p.S368S		Atlas-SNP	.											.	KIAA0556	348	.	0			c.C1104T						PASS	.	C		254,4140		7,240,1950	20.0	21.0	21.0		1104	1.3	0.2	16	dbSNP_129	21	0,8600		0,0,4300	no	coding-synonymous	KIAA0556	NM_015202.2		7,240,6250	TT,TC,CC		0.0,5.7806,1.9547		368/1619	27709812	254,12740	2197	4300	6497	SO:0001819	synonymous_variant	23247	exon9			AGCCAGCCCACTG	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.1104C>T	16.37:g.27709812C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_015202	A7E2C2	Silent	SNP	ENST00000261588.4	37	CCDS32415.1																																																																																			C|0.978;T|0.022	0.022	strong		0.637	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
CDC42BPB	9578	hgsc.bcm.edu	37	14	103434985	103434985	+	Silent	SNP	G	G	A	rs55659700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103434985G>A	ENST00000361246.2	-	15	2352	c.2064C>T	c.(2062-2064)tcC>tcT	p.S688S		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		TCTCCAGCTCGGATTTGATTT	0.453													G|||	45	0.00898562	0.0257	0.0159	5008	,	,		19256	0.0		0.0	False		,,,				2504	0.0				p.S688S		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.C2064T						PASS	.	G		111,4295	85.8+/-124.5	2,107,2094	83.0	90.0	88.0		2064	-9.2	0.2	14	dbSNP_129	88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CDC42BPB	NM_006035.3		2,108,6393	AA,AG,GG		0.0116,2.5193,0.8611		688/1712	103434985	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	9578	exon15			CAGCTCGGATTTG	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.2064C>T	14.37:g.103434985G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_006035		Silent	SNP	ENST00000361246.2	37	CCDS9978.1																																																																																			G|0.992;A|0.008	0.008	strong		0.453	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035	
PRAMEF12	390999	hgsc.bcm.edu	37	1	12837634	12837634	+	Silent	SNP	T	T	A	rs848578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12837634T>A	ENST00000357726.4	+	3	1371	c.1344T>A	c.(1342-1344)atT>atA	p.I448I		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	448					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)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	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;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGCCCAAGATTATTGTGTTCA	0.547													t|||	3322	0.663339	0.3729	0.8055	5008	,	,		20221	0.7192		0.8012	False		,,,				2504	0.7556				p.I448I		Atlas-SNP	.											.	PRAMEF12	69	.	0			c.T1344A						PASS	.	T		1892,2514		414,1064,725	127.0	126.0	126.0		1344	-5.5	0.0	1	dbSNP_86	126	6981,1619		2811,1359,130	yes	coding-synonymous	PRAMEF12	NM_001080830.1		3225,2423,855	AA,AT,TT		18.8256,42.9414,31.7776		448/484	12837634	8873,4133	2203	4300	6503	SO:0001819	synonymous_variant	390999	exon3			CAAGATTATTGTG		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"""-"""	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.1344T>A	1.37:g.12837634T>A		Somatic	533	0	0		WXS	Illumina HiSeq	Phase_I	572	571	0.998252	NM_001080830		Silent	SNP	ENST00000357726.4	37	CCDS41254.1																																																																																			T|0.287;C|0.001;A|0.713	0.713	strong		0.547	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760	
SEMG1	6406	hgsc.bcm.edu	37	20	43837053	43837053	+	Missense_Mutation	SNP	G	G	T	rs2233887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43837053G>T	ENST00000372781.3	+	2	1172	c.1115G>T	c.(1114-1116)cGc>cTc	p.R372L	SEMG1_ENST00000244069.6_Missense_Mutation_p.R312L	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	372	2 X 60 AA tandem repeats, type 1.|Repeat-rich region. {ECO:0000250}.		R -> L (in dbSNP:rs2233887). {ECO:0000269|PubMed:14629036}.		insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				GTATCCCAACGCAGTATTTAT	0.413													G|||	63	0.0125799	0.0371	0.0086	5008	,	,		22334	0.0		0.004	False		,,,				2504	0.0041				p.R372L		Atlas-SNP	.											SEMG1,bladder,carcinoma,+1,3	SEMG1	71	3	0			c.G1115T						PASS	.	G	LEU/ARG	143,4263	100.3+/-138.9	1,141,2061	75.0	70.0	72.0		1115	-0.4	0.0	20	dbSNP_98	72	18,8582	12.6+/-44.7	0,18,4282	yes	missense	SEMG1	NM_003007.3	102	1,159,6343	TT,TG,GG		0.2093,3.2456,1.2379		372/463	43837053	161,12845	2203	4300	6503	SO:0001583	missense	6406	exon2			CCCAACGCAGTAT		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"""semen coagulating protein"", ""cancer/testis antigen 103"""	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.1115G>T	20.37:g.43837053G>T	ENSP00000361867:p.Arg372Leu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	166	85	0.512048	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	23	0.010531135531135532	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	6.094	0.385541	0.11524	0.032456	0.002093	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.06218	3.33;3.33	0.951	-0.436	0.12275	.	.	.	.	.	T	0.00967	0.0032	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.42849	-0.9427	9	0.72032	D	0.01	.	3.6742	0.08286	0.0:0.0:0.5676:0.4324	rs2233887;rs52805273;rs2233887	312;372	P04279-2;P04279	.;SEMG1_HUMAN	L	312;372	ENSP00000244069:R312L;ENSP00000361867:R372L	ENSP00000244069:R312L	R	+	2	0	SEMG1	43270467	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.312000	0.08113	-0.121000	0.11787	0.404000	0.27445	CGC	G|0.984;T|0.016	0.016	strong		0.413	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
MUC5B	727897	hgsc.bcm.edu	37	11	1268528	1268528	+	Missense_Mutation	SNP	C	C	T	rs202008769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1268528C>T	ENST00000529681.1	+	31	10476	c.10418C>T	c.(10417-10419)tCg>tTg	p.S3473L	MUC5B_ENST00000447027.1_Missense_Mutation_p.S3476L|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3473	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)		GCCTGGACTTCGGCCACCTCG	0.672													-|||	12	0.00239617	0.0083	0.0014	5008	,	,		18693	0.0		0.0	False		,,,				2504	0.0				p.S3473L		Atlas-SNP	.											MUC5B,colon,carcinoma,0,4	MUC5B	473	4	0			c.C10418T						PASS	.	C	LEU/SER	11,4213		0,11,2101	60.0	85.0	77.0		10418	0.0	0.0	11		77	2,8406		0,2,4202	no	missense	MUC5B	NM_002458.2	145	0,13,6303	TT,TC,CC		0.0238,0.2604,0.1029	benign	3473/5763	1268528	13,12619	2112	4204	6316	SO:0001583	missense	727897	exon31			GGACTTCGGCCAC	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.10418C>T	11.37:g.1268528C>T	ENSP00000436812:p.Ser3473Leu	Somatic	462	0	0		WXS	Illumina HiSeq	Phase_I	657	250	0.380518	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	4.864	0.160630	0.09287	0.002604	2.38E-4	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.20598	2.06;2.24	2.0	0.00491	0.14060	.	.	.	.	.	T	0.16811	0.0404	L	0.50333	1.59	0.09310	N	1	B;B	0.33494	0.414;0.001	B;B	0.29716	0.106;0.0	T	0.18745	-1.0327	9	0.87932	D	0	.	5.899	0.18955	0.0:0.6851:0.0:0.3149	.	4001;3476	A7Y9J9;E9PBJ0	.;.	L	3473;3476;3445;3378	ENSP00000436812:S3473L;ENSP00000415793:S3476L	ENSP00000343037:S3445L	S	+	2	0	MUC5B	1225104	0.000000	0.05858	0.002000	0.10522	0.028000	0.11728	-1.189000	0.03061	0.007000	0.14760	-0.712000	0.03635	TCG	.	.	weak		0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
IGDCC4	57722	hgsc.bcm.edu	37	15	65676726	65676726	+	Missense_Mutation	SNP	C	C	T	rs33918653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65676726C>T	ENST00000352385.2	-	20	3583	c.3374G>A	c.(3373-3375)tGc>tAc	p.C1125Y	IGDCC4_ENST00000558048.1_5'UTR	NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	1125			C -> Y (in dbSNP:rs33918653).			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						CTGGTTCCTGCAGGCTGGGGG	0.522													C|||	1172	0.234026	0.1475	0.2579	5008	,	,		21304	0.4444		0.1869	False		,,,				2504	0.1656				p.C1125Y		Atlas-SNP	.											.	IGDCC4	95	.	0			c.G3374A						PASS	.	C	TYR/CYS	616,3786	268.6+/-268.5	44,528,1629	105.0	104.0	104.0		3374	4.3	1.0	15	dbSNP_126	104	1679,6919	310.8+/-310.0	163,1353,2783	yes	missense	IGDCC4	NM_020962.1	194	207,1881,4412	TT,TC,CC		19.5278,13.9936,17.6538	probably-damaging	1125/1251	65676726	2295,10705	2201	4299	6500	SO:0001583	missense	57722	exon20			TTCCTGCAGGCTG		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.3374G>A	15.37:g.65676726C>T	ENSP00000319623:p.Cys1125Tyr	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	24	17	0.708333	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	560	0.2564102564102564	69	0.1402439024390244	80	0.22099447513812154	264	0.46153846153846156	147	0.19393139841688653	C	18.83	3.707798	0.68615	0.139936	0.195278	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.60040	0.22	5.19	4.27	0.50696	.	0.126462	0.36778	N	0.002418	T	0.00012	0.0000	L	0.47716	1.5	0.29015	P	0.886638	D	0.57899	0.981	P	0.48840	0.592	T	0.46803	-0.9165	9	0.56958	D	0.05	-9.9263	10.5505	0.45085	0.0:0.9093:0.0:0.0907	rs33918653	1125	Q8TDY8	IGDC4_HUMAN	Y	1125;854	ENSP00000319623:C1125Y	ENSP00000319623:C1125Y	C	-	2	0	IGDCC4	63463779	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.349000	0.44054	1.187000	0.43000	0.561000	0.74099	TGC	C|0.807;T|0.193	0.193	strong		0.522	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
ARID5B	84159	hgsc.bcm.edu	37	10	63829539	63829539	+	Silent	SNP	C	C	T	rs76296217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:63829539C>T	ENST00000279873.7	+	8	1592	c.1182C>T	c.(1180-1182)acC>acT	p.T394T	ARID5B_ENST00000309334.5_Silent_p.T151T	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	394	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					CCACTTGTACCCGCAGACATT	0.428													C|||	107	0.0213658	0.003	0.0389	5008	,	,		19689	0.0		0.0716	False		,,,				2504	0.0041				p.T394T		Atlas-SNP	.											.	ARID5B	125	.	0			c.C1182T						PASS	.	C		83,4323	70.9+/-108.8	1,81,2121	50.0	51.0	51.0		1182	-2.3	1.0	10	dbSNP_131	51	652,7948	166.7+/-218.6	28,596,3676	no	coding-synonymous	ARID5B	NM_032199.2		29,677,5797	TT,TC,CC		7.5814,1.8838,5.6512		394/1189	63829539	735,12271	2203	4300	6503	SO:0001819	synonymous_variant	84159	exon8			TTGTACCCGCAGA	M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"""-"""	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.1182C>T	10.37:g.63829539C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Silent	SNP	ENST00000279873.7	37	CCDS31208.1																																																																																			C|0.954;T|0.046	0.046	strong		0.428	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4448940	4448940	+	Missense_Mutation	SNP	G	G	A	rs899440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4448940G>A	ENST00000254718.4	-	15	2344	c.2038C>T	c.(2038-2040)Cac>Tac	p.H680Y	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.H680Y			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	680			H -> Y (in dbSNP:rs899440).		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						GGGGTCAGGTGGGAGCAGATG	0.642													g|||	352	0.0702875	0.2519	0.0202	5008	,	,		16357	0.0		0.005	False		,,,				2504	0.0				p.H680Y		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C2038T						PASS	.	G	TYR/HIS,TYR/HIS	952,3454	352.8+/-311.9	98,756,1349	49.0	47.0	47.0		2038,2038	5.2	1.0	17	dbSNP_86	47	12,8588	7.7+/-29.5	0,12,4288	yes	missense,missense	MYBBP1A	NM_001105538.1,NM_014520.3	83,83	98,768,5637	AA,AG,GG		0.1395,21.6069,7.412	benign,benign	680/1333,680/1329	4448940	964,12042	2203	4300	6503	SO:0001583	missense	10514	exon15			TCAGGTGGGAGCA	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.2038C>T	17.37:g.4448940G>A	ENSP00000254718:p.His680Tyr	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	187	75	0.40107	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	127	0.05815018315018315	114	0.23170731707317074	7	0.019337016574585635	0	0.0	6	0.0079155672823219	g	15.08	2.726715	0.48833	0.216069	0.001395	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.52057	0.68;0.68	5.22	5.22	0.72569	Armadillo-type fold (1);	0.271812	0.41294	D	0.000905	T	0.00039	0.0001	L	0.49126	1.545	0.26790	P	0.969415	B;B	0.18968	0.032;0.026	B;B	0.29663	0.105;0.063	T	0.10613	-1.0622	9	0.17832	T	0.49	-30.6606	11.7659	0.51930	0.0:0.0:0.8245:0.1755	rs899440;rs899440	680;680	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	Y	680	ENSP00000370968:H680Y;ENSP00000254718:H680Y	ENSP00000254718:H680Y	H	-	1	0	MYBBP1A	4395689	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	2.767000	0.47637	2.606000	0.88127	0.542000	0.68232	CAC	G|0.935;A|0.065	0.065	strong		0.642	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
FOXRED2	80020	hgsc.bcm.edu	37	22	36902259	36902259	+	Missense_Mutation	SNP	G	G	A	rs56767103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36902259G>A	ENST00000397224.4	-	2	304	c.211C>T	c.(211-213)Cgc>Tgc	p.R71C	FOXRED2_ENST00000216187.6_Missense_Mutation_p.R71C|FOXRED2_ENST00000397223.4_Missense_Mutation_p.R71C	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	71			R -> C (in dbSNP:rs56767103).		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						CGCGGGTAGCGTGTGAAGAAG	0.667													G|||	144	0.028754	0.1059	0.0043	5008	,	,		16027	0.0		0.001	False		,,,				2504	0.0				p.R71C		Atlas-SNP	.											.	FOXRED2	48	.	0			c.C211T						PASS	.	G	CYS/ARG,CYS/ARG	385,4021	193.3+/-218.5	22,341,1840	70.0	52.0	59.0		211,211	5.0	1.0	22	dbSNP_129	59	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	FOXRED2	NM_001102371.1,NM_024955.5	180,180	22,344,6137	AA,AG,GG		0.0349,8.7381,2.9832	possibly-damaging,possibly-damaging	71/685,71/685	36902259	388,12618	2203	4300	6503	SO:0001583	missense	80020	exon2			GGTAGCGTGTGAA	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.211C>T	22.37:g.36902259G>A	ENSP00000380401:p.Arg71Cys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Missense_Mutation	SNP	ENST00000397224.4	37	CCDS13929.1	46	0.021062271062271064	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	22.6	4.317138	0.81469	0.087381	3.49E-4	ENSG00000100350	ENST00000397224;ENST00000216187;ENST00000397223;ENST00000423980	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	5.04	5.04	0.67666	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.201070	0.44097	D	0.000489	T	0.02083	0.0065	M	0.79123	2.44	0.40354	D	0.979162	D	0.65815	0.995	P	0.59703	0.862	T	0.00936	-1.1508	10	0.48119	T	0.1	-31.9668	7.8809	0.29621	0.0837:0.0:0.7553:0.161	rs56767103	71	Q8IWF2	FXRD2_HUMAN	C	71	ENSP00000380401:R71C;ENSP00000216187:R71C;ENSP00000380400:R71C;ENSP00000409692:R71C	ENSP00000216187:R71C	R	-	1	0	FOXRED2	35232205	1.000000	0.71417	0.977000	0.42913	0.953000	0.61014	4.550000	0.60733	2.337000	0.79520	0.561000	0.74099	CGC	G|0.974;A|0.026	0.026	strong		0.667	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	
SCNN1D	6339	hgsc.bcm.edu	37	1	1226063	1226063	+	Missense_Mutation	SNP	G	G	A	rs13306651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1226063G>A	ENST00000338555.2	+	12	2558	c.1414G>A	c.(1414-1416)Gcc>Acc	p.A472T	SCNN1D_ENST00000400928.3_Missense_Mutation_p.A472T|SCNN1D_ENST00000325425.8_Missense_Mutation_p.A538T|SCNN1D_ENST00000379116.5_Missense_Mutation_p.A636T			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	472			A -> T (in dbSNP:rs13306651).		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)	GTGGCCTTCCGCCAAGTCAGC	0.642													G|||	92	0.0183706	0.0174	0.0115	5008	,	,		15249	0.0099		0.0159	False		,,,				2504	0.0358				p.A636T		Atlas-SNP	.											.	SCNN1D	60	.	0			c.G1906A						PASS	.		THR/ALA	70,4308	64.1+/-101.4	0,70,2119	46.0	46.0	46.0		1906	-0.5	0.8	1	dbSNP_121	46	131,8441	66.3+/-128.7	2,127,4157	yes	missense	SCNN1D	NM_001130413.3	58	2,197,6276	AA,AG,GG		1.5282,1.5989,1.5521	benign	636/803	1226063	201,12749	2189	4286	6475	SO:0001583	missense	6339	exon15			CCTTCCGCCAAGT	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.1414G>A	1.37:g.1226063G>A	ENSP00000339504:p.Ala472Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Missense_Mutation	SNP	ENST00000338555.2	37		33|33	0.01510989010989011|0.01510989010989011	9|9	0.018292682926829267|0.018292682926829267	5|5	0.013812154696132596|0.013812154696132596	7|7	0.012237762237762238|0.012237762237762238	12|12	0.0158311345646438|0.0158311345646438	g|g	7.229|7.229	0.598909|0.598909	0.13939|0.13939	0.015989|0.015989	0.015282|0.015282	ENSG00000162572|ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928|ENST00000379099	T;T;T;T|.	0.63417|.	-0.04;-0.04;-0.04;-0.04|.	3.35|3.35	-0.489|-0.489	0.12052|0.12052	.|.	3.341150|.	0.01821|.	U|.	0.034076|.	T|T	0.12433|0.12433	0.0302|0.0302	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	P;P;D|.	0.58970|.	0.784;0.642;0.984|.	B;B;B|.	0.38458|.	0.274;0.169;0.173|.	T|T	0.21008|0.21008	-1.0258|-1.0258	10|5	0.18276|.	T|.	0.48|.	.|.	3.3384|3.3384	0.07110|0.07110	0.1217:0.1151:0.5221:0.2411|0.1217:0.1151:0.5221:0.2411	rs13306651;rs13306651|rs13306651;rs13306651	294;472;636|.	B1AMF2;P51172;A6NNF7|.	.;SCNND_HUMAN;.|.	T|H	503;636;472;538;472|288	ENSP00000368411:A636T;ENSP00000339504:A472T;ENSP00000321594:A538T;ENSP00000383717:A472T|.	ENSP00000321594:A538T|.	A|R	+|+	1|2	0|0	SCNN1D|SCNN1D	1215926|1215926	0.000000|0.000000	0.05858|0.05858	0.828000|0.828000	0.32881|0.32881	0.711000|0.711000	0.40976|0.40976	-0.651000|-0.651000	0.05372|0.05372	0.069000|0.069000	0.16605|0.16605	0.299000|0.299000	0.19835|0.19835	GCC|CGC	G|0.984;A|0.016	0.016	strong		0.642	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978	
KIAA1328	57536	hgsc.bcm.edu	37	18	34647323	34647323	+	Silent	SNP	T	T	A	rs3747896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:34647323T>A	ENST00000280020.5	+	7	1069	c.1047T>A	c.(1045-1047)ggT>ggA	p.G349G	KIAA1328_ENST00000586501.1_Silent_p.G65G|KIAA1328_ENST00000591619.1_Silent_p.G345G|KIAA1328_ENST00000543923.1_Silent_p.G241G|KIAA1328_ENST00000435985.2_Silent_p.G65G|KIAA1328_ENST00000586135.1_Silent_p.G65G	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	349										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		TGCATGGTGGTGGGGCACTGC	0.448													A|||	1299	0.259385	0.6445	0.1311	5008	,	,		19160	0.1101		0.1292	False		,,,				2504	0.1176				p.G349G		Atlas-SNP	.											.	KIAA1328	39	.	0			c.T1047A						PASS	.	A		2353,1669		730,893,388	72.0	69.0	70.0		1047	-0.9	0.0	18	dbSNP_107	70	1345,7043		269,807,3118	no	coding-synonymous	KIAA1328	NM_020776.1		999,1700,3506	AA,AT,TT		16.0348,41.4968,29.7985		349/578	34647323	3698,8712	2011	4194	6205	SO:0001819	synonymous_variant	57536	exon7			TGGTGGTGGGGCA	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.1047T>A	18.37:g.34647323T>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	192	190	0.989583	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Silent	SNP	ENST00000280020.5	37	CCDS45855.1																																																																																			A|0.237;G|0.031;T|0.732	0.237	strong		0.448	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776	
C9orf171	389799	hgsc.bcm.edu	37	9	135285802	135285802	+	Silent	SNP	G	G	A	rs111465967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135285802G>A	ENST00000343036.2	+	1	192	c.144G>A	c.(142-144)gaG>gaA	p.E48E	C9orf171_ENST00000393216.2_Silent_p.E48E|C9orf171_ENST00000393215.3_Silent_p.E48E	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	48										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						TGGAGAACGAGCGGCTGGGGG	0.706													G|||	178	0.0355431	0.0552	0.0144	5008	,	,		12105	0.0208		0.0239	False		,,,				2504	0.0511				p.E48E		Atlas-SNP	.											.	C9orf171	53	.	0			c.G144A						PASS	.	G		209,4079		4,201,1939	20.0	17.0	18.0		144	4.0	1.0	9	dbSNP_132	18	326,8108		6,314,3897	no	coding-synonymous	C9orf171	NM_207417.1		10,515,5836	AA,AG,GG		3.8653,4.8741,4.2053		48/321	135285802	535,12187	2144	4217	6361	SO:0001819	synonymous_variant	389799	exon1			GAACGAGCGGCTG	AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.144G>A	9.37:g.135285802G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	84	60	0.714286	NM_207417	Q147X1	Silent	SNP	ENST00000343036.2	37	CCDS6949.1																																																																																			G|0.959;A|0.041	0.041	strong		0.706	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417	
MRTO4	51154	hgsc.bcm.edu	37	1	19583636	19583636	+	Silent	SNP	C	C	T	rs1126682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19583636C>T	ENST00000330263.4	+	4	567	c.270C>T	c.(268-270)caC>caT	p.H90H		NM_016183.3	NP_057267.2	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog (S. cerevisiae)	90					ribosome biogenesis (GO:0042254)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|liver(2)|ovary(1)|pancreas(1)|stomach(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ACAACCTGCACCAGGTAAGTC	0.557													C|||	681	0.135982	0.1293	0.1311	5008	,	,		20981	0.0238		0.2008	False		,,,				2504	0.1973				p.H90H	GBM(192;2418 3032 7540 48714)	Atlas-SNP	.											MRTO4,NS,carcinoma,0,1	MRTO4	17	1	0			c.C270T						PASS	.	C		595,3811	261.0+/-264.0	43,509,1651	184.0	174.0	178.0		270	0.2	1.0	1	dbSNP_86	178	1553,7047	292.8+/-301.0	141,1271,2888	no	coding-synonymous	MRTO4	NM_016183.3		184,1780,4539	TT,TC,CC		18.0581,13.5043,16.5155		90/240	19583636	2148,10858	2203	4300	6503	SO:0001819	synonymous_variant	51154	exon4			CCTGCACCAGGTA	AK027569	CCDS191.1	1p36.13	2008-02-05	2006-12-21	2007-01-05	ENSG00000053372	ENSG00000053372			18477	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 33"", ""MRT4, mRNA turnover 4, homolog (S. cerevisiae)"""	C1orf33			Standard	NM_016183		Approved	dJ657E11.4, MRT4	uc001bbs.3	Q9UKD2	OTTHUMG00000002496	ENST00000330263.4:c.270C>T	1.37:g.19583636C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	157	60	0.382166	NM_016183	B3KNB3|Q5TG55|Q96SS6|Q9BPV9	Silent	SNP	ENST00000330263.4	37	CCDS191.1																																																																																			C|0.842;T|0.158	0.158	strong		0.557	MRTO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007075.2	NM_016183	
MAP3K5	4217	hgsc.bcm.edu	37	6	136904783	136904783	+	Silent	SNP	G	G	A	rs78692210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:136904783G>A	ENST00000359015.4	-	24	3681	c.3321C>T	c.(3319-3321)gcC>gcT	p.A1107A	MAP3K5_ENST00000463140.1_5'UTR|MAP3K5_ENST00000355845.4_Silent_p.A354A	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	1107					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		ACAGTGTGGTGGCTATGATTT	0.468													G|||	86	0.0171725	0.0356	0.0058	5008	,	,		13965	0.0268		0.0	False		,,,				2504	0.0082				p.A1107A		Atlas-SNP	.											.	MAP3K5	136	.	0			c.C3321T						PASS	.	G		99,4307	79.3+/-117.8	2,95,2106	157.0	137.0	143.0		3321	5.1	1.0	6	dbSNP_131	143	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	MAP3K5	NM_005923.3		2,110,6391	AA,AG,GG		0.1744,2.2469,0.8765		1107/1375	136904783	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	4217	exon24			TGTGGTGGCTATG	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.3321C>T	6.37:g.136904783G>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	249	113	0.453815	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	37	CCDS5179.1																																																																																			G|0.988;A|0.012	0.012	strong		0.468	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
CSTA	1475	hgsc.bcm.edu	37	3	122060390	122060390	+	Missense_Mutation	SNP	G	G	T	rs34021626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122060390G>T	ENST00000264474.3	+	3	322	c.273G>T	c.(271-273)aaG>aaT	p.K91N		NM_005213.3	NP_005204.1	P01040	CYTA_HUMAN	cystatin A (stefin A)	91					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)		ACAAAAACAAGGATGACGAGC	0.408													G|||	96	0.0191693	0.0688	0.0072	5008	,	,		18439	0.0		0.0	False		,,,				2504	0.0				p.K91N	Pancreas(26;157 1503 12440)	Atlas-SNP	.											.	CSTA	11	.	0			c.G273T						PASS	.	G	ASN/LYS	255,4151	147.6+/-182.1	8,239,1956	122.0	120.0	120.0		273	3.6	0.0	3	dbSNP_126	120	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CSTA	NM_005213.3	94	8,240,6255	TT,TG,GG		0.0116,5.7876,1.9683	benign	91/99	122060390	256,12750	2203	4300	6503	SO:0001583	missense	1475	exon3			AAACAAGGATGAC		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.273G>T	3.37:g.122060390G>T	ENSP00000264474:p.Lys91Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	48	0.55814	NM_005213	Q6IB90	Missense_Mutation	SNP	ENST00000264474.3	37	CCDS3011.1	33	0.01510989010989011	29	0.05894308943089431	4	0.011049723756906077	0	0.0	0	0.0	G	16.40	3.111876	0.56398	0.057876	1.16E-4	ENSG00000121552	ENST00000264474	T	0.77098	-1.07	5.34	3.56	0.40772	Proteinase inhibitor I25, cystatin (2);	0.284783	0.37053	N	0.002270	T	0.37945	0.1022	.	.	.	0.18873	N	0.999989	P	0.52577	0.954	P	0.57057	0.812	T	0.55541	-0.8125	9	0.49607	T	0.09	-9.3656	7.8305	0.29340	0.1844:0.0:0.8156:0.0	rs34021626	91	P01040	CYTA_HUMAN	N	91	ENSP00000264474:K91N	ENSP00000264474:K91N	K	+	3	2	CSTA	123543080	0.006000	0.16342	0.013000	0.15412	0.046000	0.14306	0.259000	0.18405	0.824000	0.34613	0.655000	0.94253	AAG	G|0.984;T|0.016	0.016	strong		0.408	CSTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355751.1	NM_005213	
PHC1	1911	hgsc.bcm.edu	37	12	9074259	9074259	+	Silent	SNP	C	C	T	rs1805741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9074259C>T	ENST00000543824.1	+	6	701	c.369C>T	c.(367-369)ccC>ccT	p.P123P	PHC1_ENST00000433847.2_3'UTR|PHC1_ENST00000544916.1_Silent_p.P123P|PHC1_ENST00000536844.1_5'UTR|PHC1_ENST00000433083.2_Silent_p.P86P			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	123					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						TGAGCTCTCCCAGTGCTACCA	0.562													C|||	3172	0.633387	0.3782	0.5764	5008	,	,		-128	0.7202		0.7078	False		,,,				2504	0.8528				p.P123P		Atlas-SNP	.											.	PHC1	67	.	0			c.C369T						PASS	.						93.0	81.0	85.0					12																	9074259		2203	4297	6500	SO:0001819	synonymous_variant	1911	exon5			CTCTCCCAGTGCT	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.369C>T	12.37:g.9074259C>T		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	303	128	0.422442	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Silent	SNP	ENST00000543824.1	37	CCDS8597.1																																																																																			.	.	weak		0.562	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	
NXPE1	120400	hgsc.bcm.edu	37	11	114393757	114393757	+	Missense_Mutation	SNP	C	C	T	rs79538449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:114393757C>T	ENST00000424269.1	-	4	951	c.952G>A	c.(952-954)Ggt>Agt	p.G318S	NXPE1_ENST00000251921.2_Missense_Mutation_p.G176S|NXPE1_ENST00000536271.1_Missense_Mutation_p.G34S			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	318						extracellular region (GO:0005576)											AAAGTATAACCACCAGGGACA	0.363													C|||	16	0.00319489	0.0121	0.0	5008	,	,		19211	0.0		0.0	False		,,,				2504	0.0				p.G176S		Atlas-SNP	.											.	NXPE1	8	.	0			c.G526A						PASS	.	C	SER/GLY	56,4346	56.2+/-92.4	0,56,2145	101.0	91.0	95.0		526	4.4	0.2	11	dbSNP_131	95	1,8591	1.2+/-3.3	0,1,4295	yes	missense	FAM55A	NM_152315.2	56	0,57,6440	TT,TC,CC		0.0116,1.2721,0.4387	probably-damaging	176/406	114393757	57,12937	2201	4296	6497	SO:0001583	missense	120400	exon5			TATAACCACCAGG	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member A"""	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.952G>A	11.37:g.114393757C>T	ENSP00000411690:p.Gly318Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	166	99	0.596386	NM_152315	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	33	5.276316	0.95459	0.012721	1.16E-4	ENSG00000095110	ENST00000536271;ENST00000251921;ENST00000424269	T;T;T	0.60797	0.55;0.29;0.16	4.4	4.4	0.53042	.	0.000000	0.64402	D	0.000003	T	0.72011	0.3408	M	0.84585	2.705	0.42372	D	0.992458	D	0.89917	1.0	D	0.97110	1.0	T	0.80777	-0.1231	10	0.87932	D	0	.	15.2699	0.73693	0.0:1.0:0.0:0.0	.	318	Q8N323	FA55A_HUMAN	S	34;176;318	ENSP00000445200:G34S;ENSP00000251921:G176S;ENSP00000411690:G318S	ENSP00000251921:G176S	G	-	1	0	FAM55A	113898967	0.425000	0.25498	0.152000	0.22495	0.689000	0.40095	2.280000	0.43443	2.372000	0.80975	0.650000	0.86243	GGT	C|0.997;T|0.003	0.003	strong		0.363	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315	
SLC36A3	285641	hgsc.bcm.edu	37	5	150667016	150667016	+	Missense_Mutation	SNP	T	T	C	rs978012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	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	
ZNF653	115950	hgsc.bcm.edu	37	19	11598483	11598483	+	Silent	SNP	T	T	C	rs311805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11598483T>C	ENST00000293771.5	-	4	931	c.795A>G	c.(793-795)ccA>ccG	p.P265P	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						CATTGCCTGCTGGGTTGGAGC	0.662													C|||	1540	0.307508	0.7632	0.2089	5008	,	,		14453	0.1181		0.1153	False		,,,				2504	0.1544				p.P265P	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											ZNF653,NS,carcinoma,0,2	ZNF653	48	2	0			c.A795G						PASS	.	C		2938,1468	448.3+/-348.6	988,962,253	43.0	46.0	45.0		795	-9.0	0.0	19	dbSNP_79	45	847,7751	757.7+/-407.5	45,757,3497	no	coding-synonymous	ZNF653	NM_138783.3		1033,1719,3750	CC,CT,TT		9.8511,33.3182,29.1064		265/616	11598483	3785,9219	2203	4299	6502	SO:0001819	synonymous_variant	115950	exon4			GCCTGCTGGGTTG	AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.795A>G	19.37:g.11598483T>C		Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	211	208	0.985782	NM_138783	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			T|0.731;C|0.269	0.269	strong		0.662	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
RNF43	54894	hgsc.bcm.edu	37	17	56435080	56435080	+	Missense_Mutation	SNP	G	G	C	rs9652855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56435080G>C	ENST00000584437.1	-	8	4012	c.2057C>G	c.(2056-2058)cCc>cGc	p.P686R	BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000500597.2_Missense_Mutation_p.P645R|RNF43_ENST00000581868.1_Missense_Mutation_p.P559R|RNF43_ENST00000583753.1_Missense_Mutation_p.P645R|RNF43_ENST00000577716.1_Missense_Mutation_p.P686R|RNF43_ENST00000407977.2_Missense_Mutation_p.P686R|RNF43_ENST00000577625.1_Missense_Mutation_p.P559R			Q68DV7	RNF43_HUMAN	ring finger protein 43	686	Pro-rich.		P -> R (in dbSNP:rs9652855). {ECO:0000269|PubMed:17974005}.		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)					TGCCACACTGGGGGTGTAATG	0.622													G|||	392	0.0782748	0.1377	0.0548	5008	,	,		17838	0.0		0.1223	False		,,,				2504	0.0501				p.P686R		Atlas-SNP	.											RNF43,lower_third,carcinoma,+1,1	RNF43	157	1	0			c.C2057G						scavenged	.	G	ARG/PRO	521,3885	229.4+/-244.0	28,465,1710	90.0	103.0	98.0		2057	3.1	0.0	17	dbSNP_119	98	1082,7518	221.9+/-259.1	77,928,3295	yes	missense	RNF43	NM_017763.4	103	105,1393,5005	CC,CG,GG		12.5814,11.8248,12.3251	possibly-damaging	686/784	56435080	1603,11403	2203	4300	6503	SO:0001583	missense	54894	exon9			ACACTGGGGGTGT		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.2057C>G	17.37:g.56435080G>C	ENSP00000463069:p.Pro686Arg	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	174	0.07967032967032966	61	0.12398373983739837	25	0.06906077348066299	0	0.0	88	0.11609498680738786	G	9.516	1.107052	0.20714	0.118248	0.125814	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.08807	3.19;3.05	5.18	3.1	0.35709	.	0.559581	0.16403	N	0.215931	T	0.00073	0.0002	L	0.32530	0.975	0.80722	P	0.0	B;B;B	0.12630	0.001;0.006;0.001	B;B;B	0.12156	0.002;0.007;0.001	T	0.15665	-1.0429	9	0.87932	D	0	-10.8686	8.1407	0.31082	0.0:0.1739:0.6457:0.1804	rs9652855;rs52806304;rs9652855	645;686;686	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	R	686;645	ENSP00000385328:P686R;ENSP00000441969:P645R	ENSP00000385328:P686R	P	-	2	0	RNF43	53790079	0.034000	0.19679	0.016000	0.15963	0.738000	0.42128	2.033000	0.41136	0.699000	0.31761	0.511000	0.50034	CCC	G|0.886;C|0.114	0.114	strong		0.622	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
SFI1	9814	hgsc.bcm.edu	37	22	31998612	31998612	+	Missense_Mutation	SNP	G	G	A	rs2006771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31998612G>A	ENST00000400288.2	+	17	1751	c.1646G>A	c.(1645-1647)cGa>cAa	p.R549Q	SFI1_ENST00000432498.1_Missense_Mutation_p.R518Q|SFI1_ENST00000443326.1_Missense_Mutation_p.R467Q|SFI1_ENST00000414585.1_Missense_Mutation_p.R396Q|SFI1_ENST00000540643.1_Missense_Mutation_p.R494Q|SFI1_ENST00000400289.1_Missense_Mutation_p.R467Q|SFI1_ENST00000443011.1_Missense_Mutation_p.R396Q	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	549			R -> Q (in dbSNP:rs2006771). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						CACGCAGAGCGACAGCTTCTG	0.557													G|||	1762	0.351837	0.4138	0.3847	5008	,	,		21320	0.12		0.4612	False		,,,				2504	0.3712				p.R549Q		Atlas-SNP	.											.	SFI1	78	.	0			c.G1646A						PASS	.	G	GLN/ARG,GLN/ARG	1797,2479		413,971,754	85.0	93.0	91.0		1646,1553	-3.7	0.4	22	dbSNP_92	91	3934,4548		920,2094,1227	yes	missense,missense	SFI1	NM_001007467.1,NM_014775.2	43,43	1333,3065,1981	AA,AG,GG		46.3806,42.0253,44.9208	benign,benign	549/1243,518/1212	31998612	5731,7027	2138	4241	6379	SO:0001583	missense	9814	exon17			CAGAGCGACAGCT	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.1646G>A	22.37:g.31998612G>A	ENSP00000383145:p.Arg549Gln	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	215	121	0.562791	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	37	CCDS43004.1	764	0.3498168498168498	200	0.4065040650406504	153	0.42265193370165743	70	0.12237762237762238	341	0.449868073878628	G	10.70	1.424511	0.25639	0.420253	0.463806	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000443326;ENST00000421060;ENST00000414585;ENST00000443011;ENST00000400289;ENST00000400288;ENST00000417682	T;T;T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;1.59;1.59;1.59	5.82	-3.74	0.04385	.	0.885835	0.10024	N	0.725566	T	0.00012	0.0000	N	0.08118	0	0.51482	P	7.199999999996098E-5	B;B;B;B;B;P	0.40931	0.023;0.115;0.41;0.138;0.236;0.733	B;B;B;B;B;B	0.30572	0.011;0.031;0.053;0.011;0.047;0.117	T	0.41179	-0.9523	9	0.11485	T	0.65	.	11.6767	0.51434	0.7757:0.0:0.2243:0.0	rs2006771;rs52793824;rs61276509;rs2006771	494;467;467;518;549;525	A8K8P3-9;A8K8P3-10;A8K8P3-3;A8K8P3-2;A8K8P3;A8K8P3-5	.;.;.;.;SFI1_HUMAN;.	Q	518;494;467;525;396;396;467;549;164	ENSP00000402679:R518Q;ENSP00000443025:R494Q;ENSP00000416469:R467Q;ENSP00000397148:R396Q;ENSP00000401199:R396Q;ENSP00000383146:R467Q;ENSP00000383145:R549Q;ENSP00000398871:R164Q	ENSP00000383145:R549Q	R	+	2	0	SFI1	30328612	0.018000	0.18449	0.428000	0.26697	0.574000	0.36063	-0.421000	0.07053	-0.393000	0.07739	0.561000	0.74099	CGA	G|0.614;A|0.386	0.386	strong		0.557	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	
MUC17	140453	hgsc.bcm.edu	37	7	100677519	100677519	+	Missense_Mutation	SNP	C	C	T	rs148817224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677519C>T	ENST00000306151.4	+	3	2886	c.2822C>T	c.(2821-2823)gCt>gTt	p.A941V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	941	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)					AGTTCTGAGGCTAGAACACTT	0.507													C|||	330	0.0658946	0.0756	0.0043	5008	,	,		32604	0.1042		0.003	False		,,,				2504	0.1217				p.A941V		Atlas-SNP	.											.	MUC17	804	.	0			c.C2822T						PASS	.						352.0	314.0	327.0					7																	100677519		2203	4300	6503	SO:0001583	missense	140453	exon3			CTGAGGCTAGAAC	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.2822C>T	7.37:g.100677519C>T	ENSP00000302716:p.Ala941Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	224	36	0.160714	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	4.096	0.015797	0.07959	.	.	ENSG00000169876	ENST00000306151	T	0.02656	4.21	1.19	-1.29	0.09288	.	.	.	.	.	T	0.01523	0.0049	N	0.11560	0.145	0.09310	N	1	B	0.20671	0.047	B	0.09377	0.004	T	0.46303	-0.9201	9	0.39692	T	0.17	.	3.6812	0.08310	0.0:0.5433:0.258:0.1987	.	941	Q685J3	MUC17_HUMAN	V	941	ENSP00000302716:A941V	ENSP00000302716:A941V	A	+	2	0	MUC17	100464239	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.131000	0.10482	-0.380000	0.07894	0.134000	0.15878	GCT	C|0.993;T|0.007	0.007	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PSG3	5671	hgsc.bcm.edu	37	19	43243218	43243218	+	Silent	SNP	A	A	G	rs34721205|rs12185497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43243218A>G	ENST00000327495.5	-	2	272	c.88T>C	c.(88-90)Ttg>Ctg	p.L30L	PSG3_ENST00000595140.1_Silent_p.L30L|PSG3_ENST00000490592.1_5'UTR	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	30			L -> P (in dbSNP:rs12185496). {ECO:0000269|PubMed:2302228, ECO:0000269|PubMed:2341148, ECO:0000269|PubMed:2350345, ECO:0000269|PubMed:3265688}.|L -> S (in dbSNP:rs12185496).		defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.L30L(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				GTGGTAGGCAAGTTCCAGAAG	0.483													.|||	3288	0.65655	0.8911	0.6571	5008	,	,		18356	0.4762		0.5507	False		,,,				2504	0.6339				p.L30L		Atlas-SNP	.											PSG3,NS,carcinoma,0,1	PSG3	82	1	1	Substitution - coding silent(1)	stomach(1)	c.T88C						PASS	.	G		3417,987		1553,311,338	106.0	140.0	128.0		88	1.4	0.0	19	dbSNP_120	128	3635,4965		1246,1143,1911	no	coding-synonymous	PSG3	NM_021016.3		2799,1454,2249	GG,GA,AA		42.2674,22.4114,45.7705		30/429	43243218	7052,5952	2202	4300	6502	SO:0001819	synonymous_variant	5671	exon2			TAGGCAAGTTCCA		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.88T>C	19.37:g.43243218A>G		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	213	210	0.985915	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Silent	SNP	ENST00000327495.5	37	CCDS12611.1																																																																																			A|0.407;G|0.593	0.593	strong		0.483	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016	
ANAPC15	25906	hgsc.bcm.edu	37	11	71821236	71821236	+	Silent	SNP	A	A	G	rs17161980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71821236A>G	ENST00000227618.4	-	5	441	c.216T>C	c.(214-216)gaT>gaC	p.D72D	ANAPC15_ENST00000535503.1_Silent_p.D72D|ANAPC15_ENST00000543587.1_Silent_p.D72D|ANAPC15_ENST00000545944.1_Silent_p.D72D|LRTOMT_ENST00000419228.1_3'UTR|ANAPC15_ENST00000542531.1_Silent_p.D72D|ANAPC15_ENST00000538919.1_Silent_p.D72D|ANAPC15_ENST00000535234.1_Silent_p.D72D|ANAPC15_ENST00000545680.1_Silent_p.D72D|LRTOMT_ENST00000307198.7_3'UTR|ANAPC15_ENST00000502597.2_5'UTR|ANAPC15_ENST00000538393.1_Silent_p.D72D|ANAPC15_ENST00000543015.1_5'UTR|LRTOMT_ENST00000435085.1_3'UTR|ANAPC15_ENST00000543050.1_Silent_p.D72D	NM_001278487.1|NM_001278491.1|NM_014042.2	NP_001265416.1|NP_001265420.1|NP_054761.1	P60006	APC15_HUMAN	anaphase promoting complex subunit 15	72	Asp-rich.				mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	anaphase-promoting complex (GO:0005680)|intracellular (GO:0005622)											tatcctcatcatcttcatcat	0.498													g|||	873	0.174321	0.208	0.1974	5008	,	,		23194	0.2242		0.0596	False		,,,				2504	0.1789				p.D72D		Atlas-SNP	.											.	.	.	.	0			c.T216C						PASS	.	G	,	819,3581	749.0+/-412.0	71,677,1452	329.0	281.0	297.0		,216	-5.3	0.5	11	dbSNP_123	297	451,8135	798.5+/-407.4	13,425,3855	no	utr-3,coding-synonymous	C11orf51,LRTOMT	NM_001145308.2,NM_014042.2	,	84,1102,5307	GG,GA,AA		5.2527,18.6136,9.7798	,	,72/122	71821236	1270,11716	2200	4293	6493	SO:0001819	synonymous_variant	25906	exon5			CTCATCATCTTCA	AL080071	CCDS8210.1, CCDS60880.1	11q13.4	2012-10-17	2012-05-31	2012-05-31	ENSG00000110200	ENSG00000110200		"""Anaphase promoting complex subunits"""	24531	protein-coding gene	gene with protein product		614717	"""chromosome 11 open reading frame 51"""	C11orf51		21926987	Standard	NM_014042		Approved	HSPC020, DKFZP564M082, APC15	uc001orw.3	P60006	OTTHUMG00000167865	ENST00000227618.4:c.216T>C	11.37:g.71821236A>G		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	190	96	0.505263	NM_014042	G3V1Q3|Q9CXK2|Q9Y269	Silent	SNP	ENST00000227618.4	37	CCDS8210.1																																																																																			A|0.864;G|0.136	0.136	strong		0.498	ANAPC15-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396695.1	NM_014042	
FAM73B	84895	hgsc.bcm.edu	37	9	131804785	131804785	+	Missense_Mutation	SNP	T	T	C	rs11544968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131804785T>C	ENST00000358369.4	+	3	525	c.299T>C	c.(298-300)gTg>gCg	p.V100A	FAM73B_ENST00000406926.2_Missense_Mutation_p.V100A|FAM73B_ENST00000277475.5_Missense_Mutation_p.V100A|FAM73B_ENST00000474534.1_3'UTR	NM_032809.2	NP_116198.2	Q7L4E1	FA73B_HUMAN	family with sequence similarity 73, member B	100			V -> A (in dbSNP:rs16930845).		bone development (GO:0060348)	integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)	13						GTCCCTTCAGTGAAGAAaggt	0.602													T|||	1068	0.213259	0.4183	0.1686	5008	,	,		22200	0.1944		0.0567	False		,,,				2504	0.1483				p.V100A		Atlas-SNP	.											.	FAM73B	37	.	0			c.T299C						PASS	.	T	ALA/VAL	1652,2736		298,1056,840	55.0	35.0	42.0		299	4.5	1.0	9	dbSNP_123	42	400,8172		9,382,3895	yes	missense	FAM73B	NM_032809.2	64	307,1438,4735	CC,CT,TT		4.6664,37.6481,15.8333	benign	100/594	131804785	2052,10908	2194	4286	6480	SO:0001583	missense	84895	exon3			CTTCAGTGAAGAA	AK074127	CCDS6917.1	9q34.13	2008-02-05	2005-08-11	2005-08-11	ENSG00000148343	ENSG00000148343			23621	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 54"""	C9orf54			Standard	NM_032809		Approved	FLJ14596, FLJ00199	uc004bxa.3	Q7L4E1	OTTHUMG00000020770	ENST00000358369.4:c.299T>C	9.37:g.131804785T>C	ENSP00000351138:p.Val100Ala	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_032809	Q8NBM3|Q8TEJ6|Q969E6	Missense_Mutation	SNP	ENST00000358369.4	37	CCDS6917.1	416	0.19047619047619047	216	0.43902439024390244	57	0.1574585635359116	108	0.1888111888111888	35	0.04617414248021108	T	12.26	1.884006	0.33255	0.376481	0.046664	ENSG00000148343	ENST00000358369;ENST00000406926;ENST00000277475	T;T;T	0.20200	2.09;2.09;2.09	5.67	4.51	0.55191	.	0.540568	0.19798	N	0.105805	T	0.00012	0.0000	N	0.22421	0.69	0.26401	P	0.9764219	B;B	0.17465	0.022;0.005	B;B	0.17433	0.018;0.007	T	0.44620	-0.9316	9	0.02654	T	1	-16.7083	6.9735	0.24662	0.0:0.0749:0.1509:0.7742	rs16930845;rs17452589;rs17485814;rs52826972;rs58723091;rs16930845	164;100	B4DZP8;Q7L4E1	.;FA73B_HUMAN	A	100	ENSP00000351138:V100A;ENSP00000384662:V100A;ENSP00000277475:V100A	ENSP00000277475:V100A	V	+	2	0	FAM73B	130844606	1.000000	0.71417	0.963000	0.40424	0.980000	0.70556	4.102000	0.57776	0.945000	0.37605	0.459000	0.35465	GTG	T|0.791;C|0.209	0.209	strong		0.602	FAM73B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054542.7	NM_032809	
EVX2	344191	hgsc.bcm.edu	37	2	176948445	176948445	+	Silent	SNP	C	C	G	rs61731351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:176948445C>G	ENST00000308618.4	-	1	196	c.60G>C	c.(58-60)acG>acC	p.T20T		NM_001080458.1	NP_001073927.1	Q03828	EVX2_HUMAN	even-skipped homeobox 2	20					limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(3)	16			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	READ - Rectum adenocarcinoma(9;0.0678)|Colorectal(32;0.115)		TCTTGCCCGCCGTAGGGCTGT	0.547													C|||	188	0.0375399	0.1369	0.0086	5008	,	,		16189	0.0		0.001	False		,,,				2504	0.0				p.T20T		Atlas-SNP	.											EVX2,NS,carcinoma,0,1	EVX2	51	1	0			c.G60C						PASS	.	C		572,3834	242.8+/-252.7	42,488,1673	68.0	79.0	75.0		60	0.0	1.0	2	dbSNP_129	75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EVX2	NM_001080458.1		42,489,5972	GG,GC,CC		0.0116,12.9823,4.4057		20/477	176948445	573,12433	2203	4300	6503	SO:0001819	synonymous_variant	344191	exon1			GCCCGCCGTAGGG		CCDS33333.1	2q31.1	2012-03-09	2007-02-15		ENSG00000174279	ENSG00000174279		"""Homeoboxes / ANTP class : HOXL subclass"""	3507	protein-coding gene	gene with protein product		142991	"""eve, even-skipped homeobox homolog 2 (Drosophila)"""			1675198	Standard	NM_001080458		Approved		uc010zeu.2	Q03828	OTTHUMG00000154173	ENST00000308618.4:c.60G>C	2.37:g.176948445C>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_001080458		Silent	SNP	ENST00000308618.4	37	CCDS33333.1																																																																																			C|0.930;G|0.070	0.070	strong		0.547	EVX2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359252.1		
NCOA3	8202	hgsc.bcm.edu	37	20	46268493	46268493	+	Silent	SNP	A	A	G	rs2076546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:46268493A>G	ENST00000371998.3	+	15	3071	c.2880A>G	c.(2878-2880)acA>acG	p.T960T	NCOA3_ENST00000372004.3_Silent_p.T960T|NCOA3_ENST00000371997.3_Silent_p.T955T|NCOA3_ENST00000341724.6_Silent_p.T890T			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	960					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						CTATTCCCACATTGCCTCTTC	0.488													G|||	673	0.134385	0.2549	0.0879	5008	,	,		20124	0.0933		0.0845	False		,,,				2504	0.0982				p.T960T		Atlas-SNP	.											.	NCOA3	156	.	0			c.A2880G						PASS	.	G	,,,	1039,3367	722.1+/-409.2	123,793,1287	91.0	93.0	92.0		2880,2865,2880,2880	-0.8	0.0	20	dbSNP_96	92	752,7848	784.0+/-407.6	43,666,3591	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	166,1459,4878	GG,GA,AA		8.7442,23.5815,13.7706	,,,	960/1424,955/1416,960/1421,960/1425	46268493	1791,11215	2203	4300	6503	SO:0001819	synonymous_variant	8202	exon15			TCCCACATTGCCT	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.2880A>G	20.37:g.46268493A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	52	0.619048	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			A|0.863;G|0.137	0.137	strong		0.488	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
ZNF7	7553	hgsc.bcm.edu	37	8	146067054	146067054	+	Missense_Mutation	SNP	G	G	A	rs1735169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:146067054G>A	ENST00000528372.1	+	5	802	c.562G>A	c.(562-564)Gga>Aga	p.G188R	ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000325241.6_Missense_Mutation_p.G188R|ZNF7_ENST00000529819.1_Intron|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000532393.1_3'UTR|ZNF7_ENST00000446747.2_Missense_Mutation_p.G199R|ZNF7_ENST00000544249.1_Missense_Mutation_p.G92R			P17097	ZNF7_HUMAN	zinc finger protein 7	188			G -> R (in dbSNP:rs1735169). {ECO:0000269|Ref.4}.		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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		TGAAAGTCAGGGAGAGAGTGC	0.537													A|||	2660	0.53115	0.6906	0.4294	5008	,	,		20626	0.5833		0.3579	False		,,,				2504	0.5123				p.G188R		Atlas-SNP	.											.	ZNF7	62	.	0			c.G562A						PASS	.	A	ARG/GLY	2939,1467	473.1+/-356.6	985,969,249	63.0	64.0	64.0		562	3.6	0.0	8	dbSNP_89	64	3291,5309	647.1+/-400.3	594,2103,1603	yes	missense	ZNF7	NM_003416.2	125	1579,3072,1852	AA,AG,GG		38.2674,33.2955,47.901	benign	188/687	146067054	6230,6776	2203	4300	6503	SO:0001583	missense	7553	exon5			AGTCAGGGAGAGA	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"""Zinc fingers, C2H2-type"", ""-"""	13139	protein-coding gene	gene with protein product		194531	"""zinc finger protein 7 (KOX 4, clone HF.16)"""			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.562G>A	8.37:g.146067054G>A	ENSP00000432724:p.Gly188Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Missense_Mutation	SNP	ENST00000528372.1	37	CCDS6435.1	1084	0.49633699633699635	340	0.6910569105691057	161	0.4447513812154696	309	0.5402097902097902	274	0.36147757255936674	A	0.293	-0.979022	0.02197	0.667045	0.382674	ENSG00000147789	ENST00000532777;ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	T;T;T;T;T	0.05855	7.32;3.48;3.49;3.38;3.48	4.67	3.6	0.41247	.	0.677726	0.12547	N	0.459388	T	0.00012	0.0000	N	0.01535	-0.81	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10109	-1.0644	9	0.35671	T	0.21	-1.9115	5.0258	0.14383	0.6855:0.0:0.3145:0.0	rs1735169;rs4083376;rs52811554;rs59813519;rs1735169	199;188	B4DT08;P17097	.;ZNF7_HUMAN	R	188;188;199;92;188	ENSP00000432641:G188R;ENSP00000320627:G188R;ENSP00000393260:G199R;ENSP00000439424:G92R;ENSP00000432724:G188R	ENSP00000320627:G188R	G	+	1	0	ZNF7	146037858	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.088000	0.11198	0.401000	0.25424	-0.521000	0.04368	GGA	G|0.515;A|0.485	0.485	strong		0.537	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416	
TNFRSF17	608	hgsc.bcm.edu	37	16	12061626	12061626	+	Silent	SNP	G	G	A	rs2017662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:12061626G>A	ENST00000053243.1	+	3	695	c.477G>A	c.(475-477)acG>acA	p.T159T	TNFRSF17_ENST00000396495.3_Silent_p.T110T|RP11-166B2.1_ENST00000532936.1_Intron	NM_001192.2	NP_001183.2	Q02223	TNR17_HUMAN	tumor necrosis factor receptor superfamily, member 17	159					cell proliferation (GO:0008283)|immune system process (GO:0002376)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			large_intestine(3)|lung(3)	6						TTGTCACCACGAAAACGAATG	0.483			T	IL2	intestinal T-cell lymphoma								G|||	700	0.139776	0.2224	0.2161	5008	,	,		20246	0.1677		0.0616	False		,,,				2504	0.0256				p.T159T		Atlas-SNP	.		Dom	yes		16	16p13.1	608	"""tumor necrosis factor receptor superfamily, member 17"""		L	TNFRSF17,colon,carcinoma,+1,1	TNFRSF17	16	1	0			c.G477A						PASS	.	G		940,3454	357.9+/-314.1	107,726,1364	127.0	108.0	115.0		477	-10.3	0.4	16	dbSNP_92	115	447,8153	133.9+/-191.4	14,419,3867	no	coding-synonymous	TNFRSF17	NM_001192.2		121,1145,5231	AA,AG,GG		5.1977,21.3928,10.6742		159/185	12061626	1387,11607	2197	4300	6497	SO:0001819	synonymous_variant	608	exon3			CACCACGAAAACG	Z29574	CCDS10552.1	16p13.1	2013-05-22			ENSG00000048462	ENSG00000048462		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11913	protein-coding gene	gene with protein product		109545		BCMA		1396583, 8165126	Standard	NM_001192		Approved	BCM, CD269, TNFRSF13A	uc002dbv.3	Q02223	OTTHUMG00000129826	ENST00000053243.1:c.477G>A	16.37:g.12061626G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_001192	Q2TQ40	Silent	SNP	ENST00000053243.1	37	CCDS10552.1																																																																																			G|0.872;A|0.128	0.128	strong		0.483	TNFRSF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252062.1		
WFS1	7466	hgsc.bcm.edu	37	4	6304087	6304087	+	Silent	SNP	A	A	G	rs1046316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6304087A>G	ENST00000226760.1	+	8	2735	c.2565A>G	c.(2563-2565)tcA>tcG	p.S855S	WFS1_ENST00000503569.1_Silent_p.S855S	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	855					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)		CCCAGCTCTCACCCACCAGGC	0.612													G|||	3906	0.779952	0.7806	0.7478	5008	,	,		20044	0.9038		0.6859	False		,,,				2504	0.771				p.S855S		Atlas-SNP	.											WFS1,NS,carcinoma,0,2	WFS1	71	2	0			c.A2565G	GRCh37	CM021366	WFS1	M	rs1046316	scavenged	.	G	,	3349,1057	374.6+/-321.3	1264,821,118	47.0	45.0	46.0		2565,2565	-6.1	0.0	4	dbSNP_86	46	5908,2692	420.7+/-353.5	2028,1852,420	no	coding-synonymous,coding-synonymous	WFS1	NM_001145853.1,NM_006005.3	,	3292,2673,538	GG,GA,AA		31.3023,23.99,28.8252	,	855/891,855/891	6304087	9257,3749	2203	4300	6503	SO:0001819	synonymous_variant	7466	exon8			GCTCTCACCCACC	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.2565A>G	4.37:g.6304087A>G		Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	37	CCDS3386.1																																																																																			A|0.271;G|0.729	0.729	strong		0.612	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
TNRC18	84629	hgsc.bcm.edu	37	7	5427652	5427652	+	Silent	SNP	G	G	A	rs4720623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	62	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	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			
GAD1	2571	hgsc.bcm.edu	37	2	171715387	171715387	+	Missense_Mutation	SNP	G	G	A	rs769402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:171715387G>A	ENST00000358196.3	+	16	2145	c.1595G>A	c.(1594-1596)cGg>cAg	p.R532Q		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	532			R -> Q (in dbSNP:rs769402). {ECO:0000269|Ref.9}.		gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CCTCAACGACGGGAAAAGCTA	0.453													G|||	305	0.0609026	0.2216	0.0159	5008	,	,		20178	0.0		0.001	False		,,,				2504	0.0				p.R532Q		Atlas-SNP	.											.	GAD1	79	.	0			c.G1595A						PASS	.	G	GLN/ARG	807,3599	321.3+/-297.0	68,671,1464	82.0	83.0	83.0		1595	3.8	1.0	2	dbSNP_98	83	13,8587	9.1+/-34.3	0,13,4287	yes	missense	GAD1	NM_000817.2	43	68,684,5751	AA,AG,GG		0.1512,18.3159,6.3048	benign	532/595	171715387	820,12186	2203	4300	6503	SO:0001583	missense	2571	exon16			AACGACGGGAAAA		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1595G>A	2.37:g.171715387G>A	ENSP00000350928:p.Arg532Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	105	0.04807692307692308	96	0.1951219512195122	9	0.024861878453038673	0	0.0	0	0.0	G	13.06	2.125053	0.37533	0.183159	0.001512	ENSG00000128683	ENST00000358196	T	0.16597	2.33	5.63	3.84	0.44239	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.174131	0.50627	N	0.000104	T	0.00012	0.0000	L	0.31526	0.94	0.09310	P	1.0	B	0.14012	0.009	B	0.04013	0.001	T	0.39440	-0.9614	9	0.12430	T	0.62	-7.3586	9.081	0.36552	0.2195:0.0:0.7805:0.0	rs769402;rs2229844;rs2266645;rs10209273;rs52821361;rs769402	532	Q99259	DCE1_HUMAN	Q	532	ENSP00000350928:R532Q	ENSP00000350928:R532Q	R	+	2	0	GAD1	171423633	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.305000	0.59110	0.736000	0.32559	0.655000	0.94253	CGG	G|0.935;A|0.065	0.065	strong		0.453	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
COL4A6	1288	hgsc.bcm.edu	37	X	107417730	107417730	+	Silent	SNP	G	G	A	rs5973851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:107417730G>A	ENST00000372216.4	-	31	3181	c.3081C>T	c.(3079-3081)ggC>ggT	p.G1027G	COL4A6_ENST00000545689.1_Silent_p.G1026G|COL4A6_ENST00000334504.7_Silent_p.G1026G|COL4A6_ENST00000394872.2_Silent_p.G1027G|COL4A6_ENST00000538570.1_Silent_p.G1026G	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	1027	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						GGCCAGGTAAGCCCCGGATTC	0.557									Alport syndrome with Diffuse Leiomyomatosis				G|||	1533	0.406093	0.2231	0.3934	3775	,	,		12961	0.4812		0.175	False		,,,				2504	0.3108				p.G1027G	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.C3081T						PASS	.	G	,	1065,2770		113,675,164,844,407	53.0	53.0	53.0		3081,3078	-2.2	0.6	X	dbSNP_114	53	1392,5336		114,772,392,1542,1480	no	coding-synonymous,coding-synonymous	COL4A6	NM_001847.2,NM_033641.2	,	227,1447,556,2386,1887	AA,AG,A,GG,G		20.6897,27.7705,23.2604	,	1027/1692,1026/1691	107417730	2457,8106	2203	4300	6503	SO:0001819	synonymous_variant	1288	exon31	Familial Cancer Database		AGGTAAGCCCCGG	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"""Collagens"""	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.3081C>T	X.37:g.107417730G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	151	58	0.384106	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Silent	SNP	ENST00000372216.4	37	CCDS14541.1																																																																																			G|0.712;A|0.288	0.288	strong		0.557	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2		
IL18BP	10068	hgsc.bcm.edu	37	11	71711438	71711438	+	Missense_Mutation	SNP	G	G	A	rs376290357		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71711438G>A	ENST00000393703.4	+	3	607	c.70G>A	c.(70-72)Gtc>Atc	p.V24I	IL18BP_ENST00000393707.4_Missense_Mutation_p.V24I|IL18BP_ENST00000531053.1_Missense_Mutation_p.V24I|IL18BP_ENST00000260049.5_Missense_Mutation_p.V24I|IL18BP_ENST00000393705.4_Missense_Mutation_p.V24I|IL18BP_ENST00000337131.5_Missense_Mutation_p.V24I|IL18BP_ENST00000404792.1_Missense_Mutation_p.V24I|IL18BP_ENST00000497194.2_Missense_Mutation_p.V24I	NM_001039660.1	NP_001034749.1	O95998	I18BP_HUMAN	interleukin 18 binding protein	24					cellular response to hydrogen peroxide (GO:0070301)|cellular response to tumor necrosis factor (GO:0071356)|extracellular negative regulation of signal transduction (GO:1900116)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	interleukin-18 binding (GO:0042007)|receptor antagonist activity (GO:0048019)			endometrium(2)|kidney(1)|large_intestine(3)|lung(1)	7						TGCCCACGTCGTCACTCTCCT	0.617																																					p.V24I		Atlas-SNP	.											.	IL18BP	15	.	0			c.G70A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	3,4255		0,3,2126	98.0	107.0	104.0		70,70,70,70,70,70,70	-8.2	0.0	11		104	0,8508		0,0,4254	no	missense,missense,missense,missense,missense,missense,missense	IL18BP	NM_001039659.1,NM_001039660.1,NM_001145055.1,NM_001145057.1,NM_005699.3,NM_173042.2,NM_173044.2	29,29,29,29,29,29,29	0,3,6380	AA,AG,GG		0.0,0.0705,0.0235	benign,benign,benign,benign,benign,benign,benign	24/195,24/195,24/116,24/195,24/200,24/195,24/164	71711438	3,12763	2129	4254	6383	SO:0001583	missense	10068	exon3			CACGTCGTCACTC	AF110798	CCDS8206.2, CCDS44666.1	11q13	2013-01-11			ENSG00000137496	ENSG00000137496		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5987	protein-coding gene	gene with protein product	"""MC51L-53L-54L homolog gene product"""	604113				10023777	Standard	NM_001145055		Approved	IL18BPa	uc001orf.1	O95998	OTTHUMG00000133713	ENST00000393703.4:c.70G>A	11.37:g.71711438G>A	ENSP00000377306:p.Val24Ile	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_001145057	B3KUZ0|B7WPK4|O95993|O96027|Q9NZA9|Q9UBR7	Missense_Mutation	SNP	ENST00000393703.4	37	CCDS8206.2	.	.	.	.	.	.	.	.	.	.	G	0	-2.676183	0.00102	7.05E-4	0.0	ENSG00000137496	ENST00000393703;ENST00000497194;ENST00000393705;ENST00000337131;ENST00000531053;ENST00000404792;ENST00000260049;ENST00000393707	T;T;T;T;T;T;T	0.35236	1.35;1.32;1.35;1.35;1.32;1.35;1.35	4.08	-8.16	0.01061	.	1.862160	0.02902	N	0.135517	T	0.13329	0.0323	N	0.04043	-0.29	0.09310	N	1	B;B;B	0.12013	0.001;0.005;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.20273	-1.0280	10	0.06099	T	0.92	-2.0645	7.9891	0.30229	0.1145:0.1776:0.6198:0.0881	.	24;24;24	O95998-3;G3V1C5;O95998	.;.;I18BP_HUMAN	I	24	ENSP00000377306:V24I;ENSP00000434717:V24I;ENSP00000377308:V24I;ENSP00000338723:V24I;ENSP00000434835:V24I;ENSP00000384212:V24I;ENSP00000260049:V24I	ENSP00000260049:V24I	V	+	1	0	IL18BP	71389086	0.000000	0.05858	0.000000	0.03702	0.070000	0.16714	-2.169000	0.01269	-3.683000	0.00121	-0.340000	0.08031	GTC	.	.	weak		0.617	IL18BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258012.2	NM_173042	
THBS1	7057	hgsc.bcm.edu	37	15	39880822	39880822	+	Missense_Mutation	SNP	A	A	G	rs2292305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39880822A>G	ENST00000260356.5	+	10	1732	c.1567A>G	c.(1567-1569)Aca>Gca	p.T523A		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	523	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.		T -> A (in dbSNP:rs2292305). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2918029}.		activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.T523A(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CAACAACCCCACACCCCAGTT	0.542													A|||	1375	0.274561	0.4644	0.1412	5008	,	,		20016	0.3056		0.1312	False		,,,				2504	0.228				p.T523A		Atlas-SNP	.											THBS1,NS,carcinoma,0,1	THBS1	106	1	1	Substitution - Missense(1)	stomach(1)	c.A1567G						scavenged	.	A	ALA/THR	1785,2615	527.1+/-372.1	368,1049,783	91.0	87.0	89.0		1567	-2.5	0.6	15	dbSNP_100	89	1134,7460	232.9+/-266.4	64,1006,3227	yes	missense	THBS1	NM_003246.2	58	432,2055,4010	GG,GA,AA		13.1953,40.5682,22.4642	benign	523/1171	39880822	2919,10075	2200	4297	6497	SO:0001583	missense	7057	exon10			AACCCCACACCCC		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1567A>G	15.37:g.39880822A>G	ENSP00000260356:p.Thr523Ala	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	553	0.2532051282051282	216	0.43902439024390244	54	0.14917127071823205	190	0.3321678321678322	93	0.12269129287598944	A	8.764	0.924339	0.18056	0.405682	0.131953	ENSG00000137801	ENST00000260356	T	0.60040	0.22	5.87	-2.47	0.06442	.	0.716432	0.11505	N	0.557327	T	0.00012	0.0000	N	0.00436	-1.5	0.43953	P	0.0033800000000000496	B	0.02656	0.0	B	0.01281	0.0	T	0.32428	-0.9907	9	0.06365	T	0.9	4.0151	7.117	0.25423	0.3584:0.2348:0.4067:0.0	rs2292305;rs58566849;rs2292305	523	P07996	TSP1_HUMAN	A	523	ENSP00000260356:T523A	ENSP00000260356:T523A	T	+	1	0	THBS1	37668114	0.000000	0.05858	0.617000	0.29091	0.985000	0.73830	0.374000	0.20501	-0.734000	0.04843	-0.993000	0.02533	ACA	A|0.756;G|0.244	0.244	strong		0.542	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
RRS1	23212	hgsc.bcm.edu	37	8	67342077	67342077	+	Silent	SNP	G	G	A	rs3739337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:67342077G>A	ENST00000320270.2	+	1	815	c.711G>A	c.(709-711)gaG>gaA	p.E237E	ADHFE1_ENST00000415254.1_5'Flank|ADHFE1_ENST00000379385.4_5'Flank|RP11-346I3.4_ENST00000499642.1_lincRNA|ADHFE1_ENST00000396623.3_5'Flank	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	35	0	0		WXS	Illumina HiSeq	Phase_I	33	14	0.424242	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	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110376861	110376861	+	Silent	SNP	G	G	A	rs7008687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110376861G>A	ENST00000378402.5	+	2	263	c.159G>A	c.(157-159)ggG>ggA	p.G53G		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	53	IPT/TIG 1.				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)			CTATAAGAGGGGAAGGTATCG	0.328										HNSCC(38;0.096)			G|||	1156	0.230831	0.4251	0.1542	5008	,	,		14556	0.002		0.2008	False		,,,				2504	0.2894				p.G53G		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G159A						PASS	.						46.0	42.0	43.0					8																	110376861		1807	4068	5875	SO:0001819	synonymous_variant	93035	exon2			AAGAGGGGAAGGT	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.159G>A	8.37:g.110376861G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			G|0.774;A|0.226	0.226	strong		0.328	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
MYO15A	51168	hgsc.bcm.edu	37	17	18025527	18025527	+	Missense_Mutation	SNP	A	A	G	rs76468019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18025527A>G	ENST00000205890.5	+	2	3751	c.3413A>G	c.(3412-3414)cAa>cGa	p.Q1138R		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1138					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)					CTGAAGCCTCAAGTCCAGCCC	0.617													G|||	193	0.0385383	0.0575	0.0043	5008	,	,		17100	0.1042		0.001	False		,,,				2504	0.0082				p.Q1138R		Atlas-SNP	.											MYO15A,NS,carcinoma,+1,1	MYO15A	268	1	0			c.A3413G						PASS	.	G	ARG/GLN	173,3893		4,165,1864	48.0	56.0	53.0		3413	-3.5	0.0	17	dbSNP_131	53	8,8344		0,8,4168	yes	missense	MYO15A	NM_016239.3	43	4,173,6032	GG,GA,AA		0.0958,4.2548,1.4576	benign	1138/3531	18025527	181,12237	2033	4176	6209	SO:0001583	missense	51168	exon2			AGCCTCAAGTCCA	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.3413A>G	17.37:g.18025527A>G	ENSP00000205890:p.Gln1138Arg	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	92	0.04212454212454213	20	0.04065040650406504	2	0.0055248618784530384	69	0.12062937062937062	1	0.0013192612137203166	N	0.922	-0.715649	0.03206	0.042548	9.58E-4	ENSG00000091536	ENST00000205890	D	0.87729	-2.29	5.08	-3.48	0.04739	.	.	.	.	.	T	0.01765	0.0056	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.21724	-1.0237	9	0.11485	T	0.65	.	0.5234	0.00616	0.1797:0.19:0.2801:0.3502	.	1138	Q9UKN7	MYO15_HUMAN	R	1138	ENSP00000205890:Q1138R	ENSP00000205890:Q1138R	Q	+	2	0	MYO15A	17966252	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.278000	0.08490	-1.082000	0.03101	-5.891000	0.00000	CAA	A|0.957;G|0.043	0.043	strong		0.617	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
SNED1	25992	hgsc.bcm.edu	37	2	242003487	242003487	+	Silent	SNP	C	C	T	rs17852471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242003487C>T	ENST00000310397.8	+	19	2544	c.2544C>T	c.(2542-2544)ggC>ggT	p.G848G	SNED1_ENST00000342631.6_Silent_p.G848G|SNED1_ENST00000401884.1_Silent_p.G848G|SNED1_ENST00000405547.3_Silent_p.G848G|AC005237.4_ENST00000458377.1_RNA	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	848	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		AGAGCGGCGGCGGGGCCTACC	0.697													C|||	1282	0.25599	0.2179	0.2478	5008	,	,		9290	0.4048		0.1829	False		,,,				2504	0.2352				p.G848G		Atlas-SNP	.											.	SNED1	76	.	0			c.C2544T						PASS	.	C		642,3114		71,500,1307	8.0	12.0	11.0		2544	-4.5	0.7	2	dbSNP_123	11	1180,6876		101,978,2949	no	coding-synonymous	SNED1	NM_001080437.1		172,1478,4256	TT,TC,CC		14.6475,17.0927,15.425		848/1414	242003487	1822,9990	1878	4028	5906	SO:0001819	synonymous_variant	25992	exon19			CGGCGGCGGGGCC	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.2544C>T	2.37:g.242003487C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	162	78	0.481481	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																			C|0.733;T|0.267	0.267	strong		0.697	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
UTP20	27340	hgsc.bcm.edu	37	12	101683929	101683929	+	Silent	SNP	C	C	T	rs703715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101683929C>T	ENST00000261637.4	+	7	786	c.612C>T	c.(610-612)aaC>aaT	p.N204N		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	204					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						CTGATAAAAACGCACTTTTCA	0.284													T|||	3339	0.666733	0.8533	0.5836	5008	,	,		18306	0.5982		0.6074	False		,,,				2504	0.6053				p.N204N		Atlas-SNP	.											UTP20,NS,malignant_melanoma,+1,1	UTP20	222	1	0			c.C612T						PASS	.	T		3631,773	304.9+/-288.7	1494,643,65	44.0	50.0	48.0		612	0.2	0.6	12	dbSNP_86	48	5152,3448	501.0+/-375.3	1582,1988,730	no	coding-synonymous	UTP20	NM_014503.2		3076,2631,795	TT,TC,CC		40.093,17.5522,32.4592		204/2786	101683929	8783,4221	2202	4300	6502	SO:0001819	synonymous_variant	27340	exon7			TAAAAACGCACTT	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.612C>T	12.37:g.101683929C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			C|0.346;T|0.654	0.654	strong		0.284	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
PTPRT	11122	hgsc.bcm.edu	37	20	41408886	41408886	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:41408886G>A	ENST00000373187.1	-	4	539	c.540C>T	c.(538-540)gaC>gaT	p.D180D	PTPRT_ENST00000373184.1_Silent_p.D180D|PTPRT_ENST00000373190.1_Silent_p.D180D|PTPRT_ENST00000373198.4_Silent_p.D180D|PTPRT_ENST00000356100.2_Silent_p.D180D|PTPRT_ENST00000373201.1_Silent_p.D180D|PTPRT_ENST00000373193.3_Silent_p.D180D			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	180	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				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)				CCCGGACCTCGTCCACGGCGA	0.532																																					p.D180D		Atlas-SNP	.											PTPRT,NS,carcinoma,0,2	PTPRT	372	2	0			c.C540T						scavenged	.						131.0	131.0	131.0					20																	41408886		2076	4217	6293	SO:0001819	synonymous_variant	11122	exon4			GACCTCGTCCACG	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.540C>T	20.37:g.41408886G>A		Somatic	52	1	0.0192308		WXS	Illumina HiSeq	Phase_I	65	20	0.307692	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																			.	.	none		0.532	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
GINS2	51659	hgsc.bcm.edu	37	16	85722496	85722496	+	Silent	SNP	A	A	C	rs80063963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:85722496A>C	ENST00000253462.3	-	1	109	c.9T>G	c.(7-9)gcT>gcG	p.A3A	C16orf74_ENST00000602758.1_5'Flank	NM_016095.2	NP_057179.1	Q9Y248	PSF2_HUMAN	GINS complex subunit 2 (Psf2 homolog)	3					DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)	nucleoplasm (GO:0005654)				endometrium(2)|large_intestine(2)|lung(2)	6						CGACCTCGGCAGCGTCCATGG	0.677													C|||	648	0.129393	0.444	0.0389	5008	,	,		8688	0.0317		0.001	False		,,,				2504	0.001				p.A3A		Atlas-SNP	.											.	GINS2	15	.	0			c.T9G						PASS	.	C		1403,2863		218,967,948	22.0	18.0	19.0		9	-7.3	0.0	16	dbSNP_131	19	14,8328		0,14,4157	no	coding-synonymous	GINS2	NM_016095.2		218,981,5105	CC,CA,AA		0.1678,32.888,11.2389		3/186	85722496	1417,11191	2133	4171	6304	SO:0001819	synonymous_variant	51659	exon1			CTCGGCAGCGTCC	BC003186	CCDS10953.1	16q24.1	2008-02-05			ENSG00000131153	ENSG00000131153			24575	protein-coding gene	gene with protein product		610609				11042152, 10810093	Standard	NM_016095		Approved	PSF2, Pfs2	uc002fja.3	Q9Y248	OTTHUMG00000137646	ENST00000253462.3:c.9T>G	16.37:g.85722496A>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_016095	D3DUM5|Q6IAG9	Silent	SNP	ENST00000253462.3	37	CCDS10953.1																																																																																			A|0.865;C|0.135	0.135	strong		0.677	GINS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269098.1	NM_016095	
MADD	8567	hgsc.bcm.edu	37	11	47306585	47306585	+	Missense_Mutation	SNP	G	G	A	rs1051006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:47306585G>A	ENST00000311027.5	+	13	2416	c.2251G>A	c.(2251-2253)Gtg>Atg	p.V751M	MADD_ENST00000407859.3_Missense_Mutation_p.V751M|MADD_ENST00000406482.1_Missense_Mutation_p.V751M|MADD_ENST00000349238.3_Missense_Mutation_p.V751M|MADD_ENST00000402192.2_Missense_Mutation_p.V751M|MADD_ENST00000395344.3_Missense_Mutation_p.V751M|MADD_ENST00000342922.4_Missense_Mutation_p.V751M|MADD_ENST00000402799.1_Missense_Mutation_p.V751M|MADD_ENST00000395336.3_Missense_Mutation_p.V751M	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)		CAAATCGAACGTGGACAGACG	0.552													G|||	1678	0.335064	0.3873	0.2608	5008	,	,		19647	0.622		0.162	False		,,,				2504	0.1994				p.V751M		Atlas-SNP	.											.	MADD	172	.	0			c.G2251A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1517,2885	481.4+/-359.1	266,985,950	91.0	88.0	89.0		2251,2251,2251,2251,2251,2251,2251,2251,2251,2251	-5.5	0.0	11	dbSNP_86	89	1414,7182	271.7+/-289.7	118,1178,3002	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	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	21,21,21,21,21,21,21,21,21,21	384,2163,3952	AA,AG,GG		16.4495,34.4616,22.5496	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	751/1545,751/1542,751/1648,751/1589,751/1566,751/1546,751/1609,751/1480,751/1582,751/1588	47306585	2931,10067	2201	4298	6499	SO:0001583	missense	8567	exon13			TCGAACGTGGACA	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.2251G>A	11.37:g.47306585G>A	ENSP00000310933:p.Val751Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	42	0.591549	NM_130474		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	711	0.32554945054945056	153	0.31097560975609756	100	0.27624309392265195	331	0.5786713286713286	127	0.16754617414248021	G	11.28	1.593369	0.28357	0.344616	0.164495	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T	0.06068	3.42;3.35;3.35;3.41;3.4;3.36;3.36;3.4;3.42	5.88	-5.48	0.02592	.	0.643077	0.16526	N	0.210600	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	1.999999999946489E-6	B;B;B;B;B;B;B;B;B;B	0.27932	0.122;0.008;0.006;0.013;0.062;0.194;0.002;0.006;0.003;0.003	B;B;B;B;B;B;B;B;B;B	0.20577	0.014;0.001;0.005;0.004;0.012;0.03;0.002;0.004;0.002;0.005	T	0.37549	-0.9701	9	0.35671	T	0.21	0.0134	4.5741	0.12225	0.5719:0.1332:0.1482:0.1467	rs1051006;rs3736103;rs17702266;rs58641924;rs1051006	751;751;751;751;751;751;751;751;751;751	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	M	751	ENSP00000343902:V751M;ENSP00000385585:V751M;ENSP00000384435:V751M;ENSP00000304505:V751M;ENSP00000310933:V751M;ENSP00000384204:V751M;ENSP00000378753:V751M;ENSP00000378745:V751M;ENSP00000384287:V751M	ENSP00000310933:V751M	V	+	1	0	MADD	47263161	0.000000	0.05858	0.000000	0.03702	0.994000	0.84299	-0.823000	0.04443	-0.592000	0.05851	0.655000	0.94253	GTG	G|0.733;A|0.267	0.267	strong		0.552	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
UBXN11	91544	hgsc.bcm.edu	37	1	26620761	26620761	+	Missense_Mutation	SNP	T	T	C	rs6695966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26620761T>C	ENST00000374222.1	-	9	958	c.494A>G	c.(493-495)gAg>gGg	p.E165G	UBXN11_ENST00000357089.4_Missense_Mutation_p.E132G|UBXN11_ENST00000436301.2_Missense_Mutation_p.E90G|UBXN11_ENST00000374217.2_Missense_Mutation_p.E132G|UBXN11_ENST00000535108.1_Missense_Mutation_p.E7G|UBXN11_ENST00000374221.3_Missense_Mutation_p.E165G|UBXN11_ENST00000314675.7_Intron|UBXN11_ENST00000374223.1_Intron			Q5T124	UBX11_HUMAN	UBX domain protein 11	165			E -> G (in dbSNP:rs6695966).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						TGTCTTGCTCTCTGAGTCCTC	0.607													T|||	98	0.0195687	0.0696	0.0086	5008	,	,		18835	0.0		0.0	False		,,,				2504	0.0				p.E165G		Atlas-SNP	.											.	UBXN11	54	.	0			c.A494G						PASS	.	T	,GLY/GLU,GLY/GLU	200,3930		2,196,1867	99.0	98.0	98.0		,395,494	4.5	0.1	1	dbSNP_116	98	3,8407		0,3,4202	yes	intron,missense,missense	UBXN11	NM_001077262.1,NM_145345.2,NM_183008.2	,98,98	2,199,6069	CC,CT,TT		0.0357,4.8426,1.6188	,possibly-damaging,possibly-damaging	,132/488,165/521	26620761	203,12337	2065	4205	6270	SO:0001583	missense	91544	exon9			TTGCTCTCTGAGT	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.494A>G	1.37:g.26620761T>C	ENSP00000363339:p.Glu165Gly	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	77	36	0.467532	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	T	20.1	3.936518	0.73442	0.048426	3.57E-4	ENSG00000158062	ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217;ENST00000389235;ENST00000535108;ENST00000436301;ENST00000374215;ENST00000452980;ENST00000442942;ENST00000450041;ENST00000423664	T;T;T;T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	4.47	4.47	0.54385	.	0.322809	0.32655	N	0.005820	T	0.11965	0.0291	M	0.61703	1.905	0.18873	N	0.999983	P;P;P;P;P	0.44139	0.734;0.799;0.827;0.827;0.799	B;B;P;P;B	0.46758	0.398;0.272;0.526;0.526;0.214	T	0.22277	-1.0221	10	0.72032	D	0.01	-25.9901	10.3196	0.43758	0.0:0.0:0.0:1.0	rs6695966;rs52794001;rs6695966	7;90;132;127;165	B7Z1T8;B7Z3N8;Q5T124-2;Q5T124-4;Q5T124	.;.;.;.;UBX11_HUMAN	G	132;165;165;132;132;7;90;127;132;132;90;127	ENSP00000349601:E132G;ENSP00000363338:E165G;ENSP00000363339:E165G;ENSP00000363334:E132G;ENSP00000446034:E7G;ENSP00000393858:E90G;ENSP00000363332:E127G;ENSP00000410357:E132G;ENSP00000404956:E132G;ENSP00000413448:E90G;ENSP00000394036:E127G	ENSP00000349601:E132G	E	-	2	0	UBXN11	26493348	0.829000	0.29322	0.059000	0.19551	0.483000	0.33249	2.735000	0.47377	2.013000	0.59113	0.459000	0.35465	GAG	T|0.974;C|0.026	0.026	strong		0.607	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
HERC6	55008	hgsc.bcm.edu	37	4	89319296	89319296	+	Missense_Mutation	SNP	T	T	C	rs17014118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:89319296T>C	ENST00000264346.7	+	8	1086	c.1027T>C	c.(1027-1029)Ttc>Ctc	p.F343L	HERC6_ENST00000380265.5_Missense_Mutation_p.F343L	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	343			F -> L (in dbSNP:rs17014118).		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)		TCTTTTAGACTTCGTGGATGT	0.294													C|||	2780	0.555112	0.826	0.4438	5008	,	,		16215	0.6944		0.173	False		,,,				2504	0.5174				p.F343L		Atlas-SNP	.											.	HERC6	104	.	0			c.T1027C						PASS	.	C	LEU/PHE,LEU/PHE	2599,1033		957,685,174	72.0	69.0	70.0		1027,1027	2.7	0.5	4	dbSNP_123	70	1194,6942		81,1032,2955	yes	missense,missense	HERC6	NM_001165136.1,NM_017912.3	22,22	1038,1717,3129	CC,CT,TT		14.6755,28.4416,32.2315	benign,benign	343/987,343/1023	89319296	3793,7975	1816	4068	5884	SO:0001583	missense	55008	exon8			TTAGACTTCGTGG	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.1027T>C	4.37:g.89319296T>C	ENSP00000264346:p.Phe343Leu	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	157	75	0.477707	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Missense_Mutation	SNP	ENST00000264346.7	37	CCDS47098.1	1083|1083	0.4958791208791209|0.4958791208791209	400|400	0.8130081300813008|0.8130081300813008	148|148	0.4088397790055249|0.4088397790055249	414|414	0.7237762237762237|0.7237762237762237	121|121	0.15963060686015831|0.15963060686015831	C|C	0.927|0.927	-0.714008|-0.714008	0.03206|0.03206	0.715584|0.715584	0.146755|0.146755	ENSG00000138642|ENSG00000138642	ENST00000380265;ENST00000511939;ENST00000264346|ENST00000438983	T;T|.	0.76448|.	-1.02;-1.02|.	4.57|4.57	2.65|2.65	0.31530|0.31530	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (1);|.	0.476065|.	0.18440|.	N|.	0.141160|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00289|0.00289	-1.7|-1.7	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.15407|0.15407	-1.0438|-1.0438	9|5	0.05959|0.38643	T|T	0.93|0.18	.|.	5.404|5.404	0.16310|0.16310	0.0:0.5673:0.0:0.4327|0.0:0.5673:0.0:0.4327	rs17014118;rs60402487;rs17014118|rs17014118;rs60402487;rs17014118	343;343|.	Q8IVU3-2;Q8IVU3|.	.;HERC6_HUMAN|.	L|P	343|297	ENSP00000369617:F343L;ENSP00000264346:F343L|.	ENSP00000264346:F343L|ENSP00000415718:L297P	F|L	+|+	1|2	0|0	HERC6|HERC6	89538319|89538319	0.034000|0.034000	0.19679|0.19679	0.480000|0.480000	0.27341|0.27341	0.658000|0.658000	0.38924|0.38924	0.319000|0.319000	0.19522|0.19522	0.560000|0.560000	0.29169|0.29169	-0.695000|-0.695000	0.03696|0.03696	TTC|CTT	T|0.490;C|0.510	0.510	strong		0.294	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2		
YTHDC2	64848	hgsc.bcm.edu	37	5	112889374	112889374	+	Missense_Mutation	SNP	G	G	A	rs10071816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	94	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	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	
SYNPO	11346	hgsc.bcm.edu	37	5	149998128	149998128	+	Missense_Mutation	SNP	G	G	A	rs6579797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149998128G>A	ENST00000394243.1	+	2	573	c.199G>A	c.(199-201)Gac>Aac	p.D67N	SYNPO_ENST00000522122.1_Missense_Mutation_p.D67N	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	67					positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)			NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGTGGGGACGACTCTGCCTG	0.667													A|||	861	0.171925	0.2648	0.0461	5008	,	,		18209	0.2738		0.0149	False		,,,				2504	0.1922				p.D67N		Atlas-SNP	.											SYNPO_ENST00000394243,colon,carcinoma,0,1	SYNPO	147	1	0			c.G199A						PASS	.	A	ASN/ASP,ASN/ASP	325,1059		33,259,400	50.0	64.0	60.0		199,199	3.6	0.1	5	dbSNP_116	60	41,3141		0,41,1550	yes	missense,missense	SYNPO	NM_001166208.1,NM_001166209.1	23,23	33,300,1950	AA,AG,GG		1.2885,23.4827,8.0158	,	67/930,67/930	149998128	366,4200	692	1591	2283	SO:0001583	missense	11346	exon2			GGGGACGACTCTG	AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.199G>A	5.37:g.149998128G>A	ENSP00000377789:p.Asp67Asn	Somatic	202	2	0.00990099		WXS	Illumina HiSeq	Phase_I	236	235	0.995763	NM_001166209	A5PKZ8|D3DQG8|O15271|Q9UPX1	Missense_Mutation	SNP	ENST00000394243.1	37	CCDS54937.1	312	0.14285714285714285	130	0.26422764227642276	14	0.03867403314917127	157	0.2744755244755245	11	0.014511873350923483	A	0.175	-1.067557	0.01934	0.234827	0.012885	ENSG00000171992	ENST00000394243;ENST00000522122	T;T	0.22134	1.97;1.97	3.56	3.56	0.40772	.	1.605810	0.04156	N	0.322269	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	0.39840	-0.9594	9	0.02654	T	1	-0.7622	5.5763	0.17225	0.8694:0.0:0.1306:0.0	rs6579797;rs6579797	67	Q8N3V7	SYNPO_HUMAN	N	67	ENSP00000377789:D67N;ENSP00000428378:D67N	ENSP00000377789:D67N	D	+	1	0	SYNPO	149978321	0.124000	0.22315	0.069000	0.20011	0.651000	0.38670	1.109000	0.31135	0.442000	0.26555	-0.521000	0.04368	GAC	G|0.850;A|0.150	0.150	strong		0.667	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286	
GAS8	2622	hgsc.bcm.edu	37	16	90095573	90095573	+	Intron	SNP	C	C	T	rs77382359		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:90095573C>T	ENST00000268699.4	+	2	212				C16orf3_ENST00000408886.2_Missense_Mutation_p.V60I|GAS8_ENST00000536122.1_Intron|GAS8_ENST00000540721.1_Intron	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		gggcaggctacggggcagctt	0.672																																					p.V60I		Atlas-SNP	.											C16orf3,rectum,carcinoma,0,1	C16orf3	14	1	0			c.G178A						PASS	.						22.0	20.0	21.0					16																	90095573		2194	4299	6493	SO:0001627	intron_variant	750	exon1			AGGCTACGGGGCA	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1443C>T	16.37:g.90095573C>T		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	241	22	0.0912863	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	c	0.708	-0.788068	0.02884	.	.	ENSG00000221819	ENST00000408886	T	0.47177	0.85	.	.	.	.	.	.	.	.	T	0.22244	0.0536	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.22208	-1.0223	4	.	.	.	.	.	.	.	.	68	O95177	CP003_HUMAN	I	60	ENSP00000386218:V60I	.	V	-	1	0	C16orf3	88623074	0.031000	0.19500	0.015000	0.15790	0.017000	0.09413	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GTA	C|0.500;T|0.500	0.500	weak		0.672	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
ITIH5	80760	hgsc.bcm.edu	37	10	7628027	7628027	+	Silent	SNP	C	C	T	rs11255206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:7628027C>T	ENST00000256861.6	-	8	1023	c.945G>A	c.(943-945)aaG>aaA	p.K315K	ITIH5_ENST00000298441.6_Silent_p.K101K|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397146.2_Silent_p.K315K|ITIH5_ENST00000446830.2_Silent_p.K97K|ITIH5_ENST00000397145.2_Silent_p.K315K	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	315	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						AGAGGGCATCCTTGGTCTAGG	0.493													C|||	98	0.0195687	0.0643	0.0043	5008	,	,		17370	0.0069		0.002	False		,,,				2504	0.001				p.K315K		Atlas-SNP	.											.	ITIH5	343	.	0			c.G945A						PASS	.	C	,,	215,4191	126.6+/-163.6	5,205,1993	94.0	84.0	87.0		945,945,303	-0.6	1.0	10	dbSNP_120	87	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	ITIH5	NM_001001851.2,NM_030569.6,NM_032817.5	,,	5,209,6289	TT,TC,CC		0.0465,4.8797,1.6838	,,	315/703,315/943,101/729	7628027	219,12787	2203	4300	6503	SO:0001819	synonymous_variant	80760	exon8			GGCATCCTTGGTC			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.945G>A	10.37:g.7628027C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																				C|0.983;T|0.017	0.017	strong		0.493	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
RBPJL	11317	hgsc.bcm.edu	37	20	43945487	43945487	+	Missense_Mutation	SNP	T	T	C	rs34078698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43945487T>C	ENST00000343694.3	+	12	1514	c.1442T>C	c.(1441-1443)gTg>gCg	p.V481A	RBPJL_ENST00000372743.1_Missense_Mutation_p.V480A|RBPJL_ENST00000464504.1_3'UTR|RBPJL_ENST00000372741.3_3'UTR	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	481	IPT/TIG.				positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	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 (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				GAATACAGCGTGCGGCCGGGT	0.667													C|||	84	0.0167732	0.0484	0.0086	5008	,	,		13248	0.0		0.004	False		,,,				2504	0.0102				p.V481A		Atlas-SNP	.											RBPJL,colon,carcinoma,+1,1	RBPJL	67	1	0			c.T1442C						PASS	.	C	ALA/VAL	200,4206	790.0+/-415.0	4,192,2007	41.0	50.0	47.0		1442	-1.1	0.3	20	dbSNP_126	47	17,8583	809.0+/-407.2	0,17,4283	yes	missense	RBPJL	NM_014276.2	64	4,209,6290	CC,CT,TT		0.1977,4.5393,1.6685	benign	481/518	43945487	217,12789	2203	4300	6503	SO:0001583	missense	11317	exon12			ACAGCGTGCGGCC	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.1442T>C	20.37:g.43945487T>C	ENSP00000341243:p.Val481Ala	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	33	0.01510989010989011	25	0.0508130081300813	4	0.011049723756906077	0	0.0	4	0.005277044854881266	C	1.885	-0.456982	0.04540	0.045393	0.001977	ENSG00000124232	ENST00000372743;ENST00000343694	T;T	0.35789	1.29;1.29	5.06	-1.14	0.09741	.	1.055390	0.07430	N	0.895594	T	0.01156	0.0038	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20405	-1.0276	10	0.18710	T	0.47	-0.9329	2.3328	0.04239	0.1025:0.2059:0.3513:0.3403	rs34078698;rs60037526	481	Q9UBG7	RBPJL_HUMAN	A	480;481	ENSP00000361828:V480A;ENSP00000341243:V481A	ENSP00000341243:V481A	V	+	2	0	RBPJL	43378901	0.000000	0.05858	0.271000	0.24616	0.392000	0.30506	-0.499000	0.06413	-0.341000	0.08376	-0.386000	0.06593	GTG	T|0.986;C|0.014	0.014	strong		0.667	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
WIPF3	644150	hgsc.bcm.edu	37	7	29924002	29924002	+	Missense_Mutation	SNP	C	C	A	rs371924598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:29924002C>A	ENST00000409290.1	+	4	892	c.892C>A	c.(892-894)Cct>Act	p.P298T	WIPF3_ENST00000409123.1_Missense_Mutation_p.P298T|WIPF3_ENST00000242140.5_Missense_Mutation_p.P298T	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	298	Poly-Pro.				cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						CCCGCTCCCCCCTTATGCTTC	0.672													C|||	18	0.00359425	0.0129	0.0	5008	,	,		5386	0.001		0.0	False		,,,				2504	0.0				p.P298T		Atlas-SNP	.											.	WIPF3	46	.	0			c.C892A						PASS	.	C	THR/PRO	24,3134		0,24,1555	4.0	4.0	4.0		892	1.0	0.0	7		4	2,7334		0,2,3666	no	missense	WIPF3	NM_001080529.2	38	0,26,5221	AA,AC,CC		0.0273,0.76,0.2478	benign	298/484	29924002	26,10468	1579	3668	5247	SO:0001583	missense	644150	exon5			CTCCCCCCTTATG	AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.892C>A	7.37:g.29924002C>A	ENSP00000386878:p.Pro298Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	140	69	0.492857	NM_001080529	B8ZZV2	Missense_Mutation	SNP	ENST00000409290.1	37	CCDS56472.1	.	.	.	.	.	.	.	.	.	.	C	6.789	0.514559	0.12944	0.0076	2.73E-4	ENSG00000122574	ENST00000409123;ENST00000409290;ENST00000242140	T;T;T	0.43688	0.94;0.94;0.94	4.02	0.979	0.19745	.	0.460073	0.18939	N	0.126985	T	0.16300	0.0392	N	0.12746	0.255	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15350	-1.0440	10	0.21014	T	0.42	.	11.6236	0.51132	0.4549:0.5451:0.0:0.0	.	298	A6NGB9	WIPF3_HUMAN	T	298	ENSP00000386790:P298T;ENSP00000386878:P298T;ENSP00000242140:P298T	ENSP00000242140:P298T	P	+	1	0	WIPF3	29890527	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.063000	0.11655	-0.325000	0.08577	-1.624000	0.00789	CCT	.	.	weak		0.672	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1		
NWD1	284434	hgsc.bcm.edu	37	19	16899852	16899852	+	Missense_Mutation	SNP	G	G	T	rs140602425		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16899852G>T	ENST00000552788.1	+	11	2791	c.2791G>T	c.(2791-2793)Gat>Tat	p.D931Y	NWD1_ENST00000379808.3_Missense_Mutation_p.D931Y|NWD1_ENST00000339803.6_Missense_Mutation_p.D796Y|NWD1_ENST00000549814.1_Missense_Mutation_p.D931Y|NWD1_ENST00000524140.2_Missense_Mutation_p.D931Y|NWD1_ENST00000523826.1_Missense_Mutation_p.D725Y			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	931							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TGCTTCAAAGGATTACACGCT	0.498																																					p.D931Y		Atlas-SNP	.											.	NWD1	303	.	0			c.G2791T						PASS	.	G	TYR/ASP	2,4404	4.2+/-10.8	0,2,2201	116.0	112.0	113.0		2791	5.7	0.3	19	dbSNP_134	113	0,8600		0,0,4300	no	missense	NWD1	NM_001007525.3	160	0,2,6501	TT,TG,GG		0.0,0.0454,0.0154	probably-damaging	931/1433	16899852	2,13004	2203	4300	6503	SO:0001583	missense	284434	exon13			TCAAAGGATTACA	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.2791G>T	19.37:g.16899852G>T	ENSP00000447224:p.Asp931Tyr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		.	.	.	.	.	.	.	.	.	.	G	13.13	2.144107	0.37825	4.54E-4	0.0	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	D;D;D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51;-2.51	5.65	5.65	0.86999	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.96914	0.8992	H	0.98701	4.305	0.32370	N	0.55603	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.98435	1.0584	10	0.87932	D	0	-35.093	15.2049	0.73173	0.0:0.0:1.0:0.0	.	931;931;796	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	Y	796;931;931;931;725;931;796	ENSP00000428579:D931Y;ENSP00000447548:D931Y;ENSP00000369136:D931Y;ENSP00000428955:D725Y;ENSP00000447224:D931Y;ENSP00000340159:D796Y	ENSP00000340159:D796Y	D	+	1	0	NWD1	16760852	1.000000	0.71417	0.252000	0.24328	0.003000	0.03518	5.303000	0.65738	2.661000	0.90470	0.591000	0.81541	GAT	G|1.000;T|0.000	0.000	weak		0.498	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
ARSG	22901	hgsc.bcm.edu	37	17	66364749	66364749	+	Silent	SNP	T	T	C	rs1558877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66364749T>C	ENST00000448504.2	+	7	1561	c.765T>C	c.(763-765)ccT>ccC	p.P255P	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Silent_p.P91P	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	255					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)			TGCCCTTACCTGTGACTCAGC	0.597													C|||	2561	0.511382	0.6581	0.6167	5008	,	,		18488	0.2708		0.506	False		,,,				2504	0.4918				p.P255P		Atlas-SNP	.											.	ARSG	55	.	0			c.T765C						PASS	.	C		2810,1596	494.5+/-363.0	918,974,311	92.0	90.0	91.0		765	0.5	0.0	17	dbSNP_88	91	4478,4122	563.6+/-388.2	1176,2126,998	no	coding-synonymous	ARSG	NM_014960.3		2094,3100,1309	CC,CT,TT		47.9302,36.2233,43.9643		255/526	66364749	7288,5718	2203	4300	6503	SO:0001819	synonymous_variant	22901	exon7			CTTACCTGTGACT	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.765T>C	17.37:g.66364749T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	37	CCDS11676.1																																																																																			T|0.481;C|0.519	0.519	strong		0.597	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
FUS	2521	hgsc.bcm.edu	37	16	31193948	31193948	+	Silent	SNP	C	C	T	rs61733962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31193948C>T	ENST00000254108.7	+	3	258	c.153C>T	c.(151-153)ggC>ggT	p.G51G	FUS_ENST00000568685.1_Silent_p.G51G|FUS_ENST00000380244.3_Silent_p.G51G|RP11-388M20.6_ENST00000564743.1_RNA	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	51	Gln/Gly/Ser/Tyr-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		CAGGCTATGGCCAGAGCAGCT	0.522			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""								C|||	169	0.033746	0.1097	0.0187	5008	,	,		19819	0.0		0.005	False		,,,				2504	0.0061				p.G51G		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	.	FUS	52	.	0			c.C153T						PASS	.	C	,,	427,3967	210.8+/-231.2	24,379,1794	100.0	95.0	97.0		153,153,153	1.4	1.0	16	dbSNP_129	97	30,8570	20.4+/-63.3	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	FUS	NM_001170634.1,NM_001170937.1,NM_004960.3	,,	24,409,6064	TT,TC,CC		0.3488,9.7178,3.517	,,	51/526,51/523,51/527	31193948	457,12537	2197	4300	6497	SO:0001819	synonymous_variant	2521	exon3			CTATGGCCAGAGC	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.153C>T	16.37:g.31193948C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	183	94	0.513661	NM_001170634	Q9H4A8	Silent	SNP	ENST00000254108.7	37	CCDS10707.1																																																																																			C|0.965;T|0.035	0.035	strong		0.522	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
OR4C16	219428	hgsc.bcm.edu	37	11	55339652	55339652	+	Nonsense_Mutation	SNP	C	C	T	rs1459101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55339652C>T	ENST00000314634.3	+	1	49	c.49C>T	c.(49-51)Cag>Tag	p.Q17*		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				TGGATTGACACAGGATCCTTT	0.388													c|||	1265	0.252596	0.1014	0.3242	5008	,	,		18829	0.3909		0.2843	False		,,,				2504	0.2311				p.Q17X		Atlas-SNP	.											OR4C16,NS,carcinoma,-2,1	OR4C16	104	1	0			c.C49T						scavenged	.	C	stop/GLN	561,3841	252.1+/-258.6	27,507,1667	132.0	122.0	125.0		49	0.8	0.0	11	dbSNP_88	125	2290,6302	386.3+/-341.8	329,1632,2335	yes	stop-gained	OR4C16	NM_001004701.2		356,2139,4002	TT,TC,CC		26.6527,12.7442,21.9409		17/311	55339652	2851,10143	2201	4296	6497	SO:0001587	stop_gained	219428	exon1			TTGACACAGGATC	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.49C>T	11.37:g.55339652C>T	ENSP00000324913:p.Gln17*	Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	164	79	0.481707	NM_001004701	Q6IEV8	Nonsense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	605	0.27701465201465203	47	0.09552845528455285	126	0.34806629834254144	214	0.3741258741258741	218	0.287598944591029	C	15.62	2.886232	0.51908	0.127442	0.266527	ENSG00000181935	ENST00000314634	.	.	.	4.98	0.756	0.18421	.	0.325431	0.26677	N	0.023065	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	5.4911	0.16777	0.0:0.5122:0.3092:0.1786	rs1459101;rs52825307;rs60632881;rs1459101	.	.	.	X	17	.	ENSP00000324913:Q17X	Q	+	1	0	OR4C16	55096228	0.000000	0.05858	0.017000	0.16124	0.810000	0.45777	-1.242000	0.02908	0.253000	0.21552	0.549000	0.68633	CAG	C|0.759;T|0.241	0.241	strong		0.388	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
OR6C4	341418	hgsc.bcm.edu	37	12	55945258	55945258	+	Missense_Mutation	SNP	T	T	C	rs11835716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55945258T>C	ENST00000394256.2	+	1	276	c.248T>C	c.(247-249)aTg>aCg	p.M83T	RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	83			M -> T (in dbSNP:rs11835716).			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(3)|lung(5)|skin(1)	11						CTGACCAGCATGACAACAGGA	0.433													T|||	594	0.11861	0.3623	0.0231	5008	,	,		20670	0.0913		0.002	False		,,,				2504	0.0051				p.M83T		Atlas-SNP	.											.	OR6C4	34	.	0			c.T248C						PASS	.	T	THR/MET	1311,3095	423.2+/-340.0	196,919,1088	88.0	94.0	92.0		248	4.8	1.0	12	dbSNP_120	92	23,8575	14.6+/-50.1	0,23,4276	yes	missense	OR6C4	NM_001005494.1	81	196,942,5364	CC,CT,TT		0.2675,29.7549,10.2584	benign	83/310	55945258	1334,11670	2203	4299	6502	SO:0001583	missense	341418	exon1			CCAGCATGACAAC	BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"""GPCR / Class A : Olfactory receptors"""	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.248T>C	12.37:g.55945258T>C	ENSP00000377799:p.Met83Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_001005494	A8MZG7|B2RNN2|Q6IFK1	Missense_Mutation	SNP	ENST00000394256.2	37	CCDS31827.1	246	0.11263736263736264	177	0.3597560975609756	8	0.022099447513812154	59	0.10314685314685315	2	0.002638522427440633	T	12.52	1.961912	0.34659	0.297549	0.002675	ENSG00000179626	ENST00000394256	T	0.00327	8.09	4.78	4.78	0.61160	GPCR, rhodopsin-like superfamily (1);	0.360722	0.23656	N	0.045877	T	0.00012	0.0000	N	0.10733	0.035	0.42975	P	0.005552000000000001	B	0.16166	0.016	B	0.17098	0.017	T	0.25187	-1.0139	9	0.72032	D	0.01	.	10.0791	0.42379	0.0:0.0818:0.0:0.9182	rs11835716;rs11835716	83	Q8NGE1	OR6C4_HUMAN	T	83	ENSP00000377799:M83T	ENSP00000377799:M83T	M	+	2	0	OR6C4	54231525	0.109000	0.22037	0.998000	0.56505	0.993000	0.82548	2.943000	0.49026	2.135000	0.66039	0.529000	0.55759	ATG	T|0.905;C|0.095	0.095	strong		0.433	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1		
C22orf23	84645	hgsc.bcm.edu	37	22	38341124	38341124	+	Missense_Mutation	SNP	T	T	G	rs35562630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38341124T>G	ENST00000249079.2	-	5	662	c.406A>C	c.(406-408)Atg>Ctg	p.M136L	C22orf23_ENST00000403305.1_Missense_Mutation_p.M136L|C22orf23_ENST00000403026.1_Missense_Mutation_p.M136L			Q9BZE7	EVG1_HUMAN	chromosome 22 open reading frame 23	136			M -> L (in dbSNP:rs35562630).							endometrium(3)|kidney(2)|large_intestine(7)	12	Melanoma(58;0.045)					CGTTCCTCCATGTCCTTCCCT	0.512													G|||	204	0.0407348	0.1513	0.0043	5008	,	,		16932	0.0		0.001	False		,,,				2504	0.0				p.M136L		Atlas-SNP	.											.	C22orf23	21	.	0			c.A406C						PASS	.	G	LEU/MET,LEU/MET	504,3902	779.8+/-414.4	23,458,1722	162.0	158.0	159.0		343,406	-8.1	0.0	22	dbSNP_126	159	7,8593	819.0+/-406.8	0,7,4293	yes	missense,missense	C22orf23	NM_001207062.1,NM_032561.4	15,15	23,465,6015	GG,GT,TT		0.0814,11.4389,3.929	benign,benign	115/197,136/218	38341124	511,12495	2203	4300	6503	SO:0001583	missense	84645	exon5			CCTCCATGTCCTT	AF324466	CCDS13962.1, CCDS74860.1	22q13.1	2013-10-11			ENSG00000128346	ENSG00000128346			18589	protein-coding gene	gene with protein product						11237012	Standard	NM_032561		Approved	FLJ32787, EVG1, LOC84645	uc003auj.2	Q9BZE7	OTTHUMG00000150672	ENST00000249079.2:c.406A>C	22.37:g.38341124T>G	ENSP00000249079:p.Met136Leu	Somatic	348	0	0		WXS	Illumina HiSeq	Phase_I	368	163	0.442935	NM_032561	Q5JYU9|Q96M68	Missense_Mutation	SNP	ENST00000249079.2	37	CCDS13962.1	74	0.03388278388278388	72	0.14634146341463414	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.88	2.367954	0.42003	0.114389	8.14E-4	ENSG00000128346	ENST00000403305;ENST00000249079;ENST00000403026;ENST00000418863	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.27	-8.07	0.01098	.	2.120180	0.02082	N	0.052461	T	0.00073	0.0002	N	0.02202	-0.64	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05599	-1.0875	9	0.25751	T	0.34	8.7692	3.5531	0.07854	0.1443:0.121:0.2065:0.5283	rs35562630	136	Q9BZE7	EVG1_HUMAN	L	136	ENSP00000384667:M136L;ENSP00000249079:M136L;ENSP00000384618:M136L;ENSP00000395077:M136L	ENSP00000249079:M136L	M	-	1	0	C22orf23	36671070	0.000000	0.05858	0.000000	0.03702	0.465000	0.32709	-0.628000	0.05515	-1.268000	0.02439	-0.121000	0.15023	ATG	T|0.946;G|0.054	0.054	strong		0.512	C22orf23-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319564.1	NM_032561	
NTRK1	4914	hgsc.bcm.edu	37	1	156838432	156838432	+	Missense_Mutation	SNP	C	C	T	rs55909005	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156838432C>T	ENST00000524377.1	+	6	751	c.710C>T	c.(709-711)aCg>aTg	p.T237M	NTRK1_ENST00000358660.3_Missense_Mutation_p.T237M|NTRK1_ENST00000368196.3_Missense_Mutation_p.T237M|NTRK1_ENST00000392302.2_Missense_Mutation_p.T207M	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	237	Ig-like C2-type 1.		T -> M (in dbSNP:rs55909005). {ECO:0000269|PubMed:17344846}.		activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	CAGTCAGCCACGGTGATGGTG	0.637			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)			C|||	87	0.0173722	0.0598	0.0115	5008	,	,		15696	0.0		0.0	False		,,,				2504	0.0				p.T237M		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	.	NTRK1	287	.	0			c.C710T						PASS	.	C	MET/THR,MET/THR,MET/THR	196,3896		4,188,1854	14.0	14.0	14.0		620,710,710	2.5	0.5	1	dbSNP_129	14	5,8021		0,5,4008	yes	missense,missense,missense	NTRK1	NM_001007792.1,NM_001012331.1,NM_002529.3	81,81,81	4,193,5862	TT,TC,CC		0.0623,4.7898,1.6587	probably-damaging,probably-damaging,probably-damaging	207/761,237/791,237/797	156838432	201,11917	2046	4013	6059	SO:0001583	missense	4914	exon6			CAGCCACGGTGAT	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8031	protein-coding gene	gene with protein product	"""high affinity nerve growth factor receptor"""	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.710C>T	1.37:g.156838432C>T	ENSP00000431418:p.Thr237Met	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_001012331	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	37	CCDS1161.1	27	0.012362637362637362	22	0.044715447154471545	5	0.013812154696132596	0	0.0	0	0.0	C	13.13	2.144047	0.37825	0.047898	6.23E-4	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	T;T;T;T	0.16073	2.37;2.37;2.37;2.37	4.38	2.47	0.30058	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.432209	0.19724	N	0.107503	T	0.16514	0.0397	L	0.52573	1.65	0.32458	N	0.544507	P;D;D;D	0.89917	0.791;1.0;1.0;0.998	B;P;D;P	0.85130	0.248;0.806;0.997;0.886	T	0.03354	-1.1045	10	0.35671	T	0.21	.	6.7504	0.23483	0.0:0.782:0.0:0.218	rs55909005	237;237;237;207	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	M	207;237;237;237	ENSP00000376120:T207M;ENSP00000357179:T237M;ENSP00000431418:T237M;ENSP00000351486:T237M	ENSP00000351486:T237M	T	+	2	0	NTRK1	155105056	0.172000	0.23043	0.531000	0.27976	0.749000	0.42624	0.489000	0.22387	0.577000	0.29470	0.462000	0.41574	ACG	C|0.987;T|0.013	0.013	strong		0.637	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	
SCGB1D1	10648	hgsc.bcm.edu	37	11	61959636	61959636	+	Missense_Mutation	SNP	C	C	T	rs116188604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61959636C>T	ENST00000306238.3	+	2	233	c.164C>T	c.(163-165)gCt>gTt	p.A55V		NM_006552.1	NP_006543.1	O95968	SG1D1_HUMAN	secretoglobin, family 1D, member 1	55						extracellular space (GO:0005615)	protein heterodimerization activity (GO:0046982)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|stomach(1)	9						CCTCTGGAAGCTGTTGCAGCC	0.423													C|||	69	0.013778	0.0484	0.0058	5008	,	,		21854	0.0		0.001	False		,,,				2504	0.0				p.A55V		Atlas-SNP	.											SCGB1D1,NS,carcinoma,0,1	SCGB1D1	18	1	0			c.C164T						PASS	.	C	VAL/ALA	192,4212	122.1+/-159.5	6,180,2016	132.0	126.0	128.0		164	-4.4	0.0	11	dbSNP_132	128	4,8594	3.7+/-12.6	0,4,4295	yes	missense	SCGB1D1	NM_006552.1	64	6,184,6311	TT,TC,CC		0.0465,4.3597,1.5075	probably-damaging	55/91	61959636	196,12806	2202	4299	6501	SO:0001583	missense	10648	exon2			TGGAAGCTGTTGC	AJ224171	CCDS8015.1	11q13	2011-12-14			ENSG00000168515	ENSG00000168515		"""Secretoglobins"""	18395	protein-coding gene	gene with protein product	"""prostatein-like lipophilin A"", ""lipophilin A (uteroglobin family member)"""	615060				9720917, 10066439, 22155607	Standard	NM_006552		Approved	LPHA, LIPA, MGC71958	uc001nsz.1	O95968	OTTHUMG00000167505	ENST00000306238.3:c.164C>T	11.37:g.61959636C>T	ENSP00000303070:p.Ala55Val	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	165	88	0.533333	NM_006552		Missense_Mutation	SNP	ENST00000306238.3	37	CCDS8015.1	36	0.016483516483516484	30	0.06097560975609756	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	13.33	2.203741	0.38905	0.043597	4.65E-4	ENSG00000168515	ENST00000306238	T	0.15372	2.43	3.88	-4.42	0.03579	.	1.484950	0.04929	N	0.456544	T	0.01029	0.0034	.	.	.	0.09310	N	1	P	0.42735	0.788	B	0.37144	0.242	T	0.14309	-1.0477	9	0.51188	T	0.08	.	3.9086	0.09193	0.269:0.2885:0.0:0.4425	.	55	O95968	SG1D1_HUMAN	V	55	ENSP00000303070:A55V	ENSP00000303070:A55V	A	+	2	0	SCGB1D1	61716212	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.404000	0.02494	-1.026000	0.03330	-0.857000	0.03018	GCT	C|0.982;T|0.018	0.018	strong		0.423	SCGB1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394856.1	NM_006552	
SIGLEC8	27181	hgsc.bcm.edu	37	19	51960940	51960940	+	Missense_Mutation	SNP	A	A	G	rs10409962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51960940A>G	ENST00000321424.3	-	2	574	c.508T>C	c.(508-510)Tcc>Ccc	p.S170P	SIGLEC8_ENST00000340550.5_Intron|SIGLEC8_ENST00000430817.1_Intron|SIGLEC8_ENST00000597352.1_5'UTR	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	170	Ig-like C2-type 1.		S -> P (in dbSNP:rs10409962). {ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.S170P(1)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		AGGTTCCTGGAGTGGCCAGAC	0.617													G|||	1148	0.229233	0.5855	0.1527	5008	,	,		17793	0.1022		0.0795	False		,,,				2504	0.0869				p.S170P		Atlas-SNP	.											SIGLEC8,colon,carcinoma,+1,2	SIGLEC8	130	2	1	Substitution - Missense(1)	stomach(1)	c.T508C						PASS	.	G	PRO/SER	2183,2223		536,1111,556	78.0	86.0	83.0		508	0.3	0.0	19	dbSNP_119	83	614,7986		24,566,3710	yes	missense	SIGLEC8	NM_014442.2	74	560,1677,4266	GG,GA,AA		7.1395,49.5461,21.5055	benign	170/500	51960940	2797,10209	2203	4300	6503	SO:0001583	missense	27181	exon2			TCCTGGAGTGGCC	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.508T>C	19.37:g.51960940A>G	ENSP00000321077:p.Ser170Pro	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_014442	Q7Z728	Missense_Mutation	SNP	ENST00000321424.3	37	CCDS33086.1	452	0.20695970695970695	274	0.556910569105691	57	0.1574585635359116	54	0.0944055944055944	67	0.08839050131926121	.	0.010	-1.781355	0.00634	0.495461	0.071395	ENSG00000105366	ENST00000321424	T	0.26810	1.71	2.69	0.336	0.15958	Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.596060	0.14002	N	0.348073	T	0.00012	0.0000	N	0.00298	-1.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41980	-0.9478	9	0.02654	T	1	.	2.171	0.03849	0.3096:0.0:0.4397:0.2507	rs10409962;rs17846502;rs17859571;rs10409962	170	Q9NYZ4	SIGL8_HUMAN	P	170	ENSP00000321077:S170P	ENSP00000321077:S170P	S	-	1	0	SIGLEC8	56652752	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.512000	0.06313	0.008000	0.14787	-0.304000	0.09214	TCC	A|0.783;G|0.217	0.217	strong		0.617	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442	
SULT1C4	27233	hgsc.bcm.edu	37	2	108994808	108994808	+	Missense_Mutation	SNP	C	C	G	rs1402467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	122	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	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	
TRPM3	80036	hgsc.bcm.edu	37	9	73240431	73240431	+	Silent	SNP	T	T	G	rs73451725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:73240431T>G	ENST00000357533.2	-	13	1640	c.1641A>C	c.(1639-1641)cgA>cgC	p.R547R	TRPM3_ENST00000377106.1_Intron|TRPM3_ENST00000358082.3_Intron|TRPM3_ENST00000396285.1_Intron|TRPM3_ENST00000360823.2_Intron|TRPM3_ENST00000408909.2_Silent_p.R392R|TRPM3_ENST00000396280.5_Silent_p.R392R|TRPM3_ENST00000377110.3_Intron|TRPM3_ENST00000377105.1_Silent_p.R392R|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396292.4_Intron|TRPM3_ENST00000423814.3_Intron			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	569					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						CTGGATACTCTCGCTTGGAAA	0.294													T|||	701	0.139976	0.1498	0.1167	5008	,	,		19826	0.2302		0.0885	False		,,,				2504	0.1033				p.R392R		Atlas-SNP	.											.	TRPM3	700	.	0			c.A1176C						PASS	.	T	,,,,,,	713,3693	291.3+/-281.4	60,593,1550	61.0	66.0	65.0		,,1176,,1176,,	6.0	1.0	9	dbSNP_130	65	846,7754	193.7+/-239.3	43,760,3497	no	intron,intron,coding-synonymous,intron,coding-synonymous,intron,intron	TRPM3	NM_001007471.2,NM_020952.4,NM_024971.5,NM_206944.3,NM_206945.3,NM_206946.3,NM_206947.3	,,,,,,	103,1353,5047	GG,GT,TT		9.8372,16.1825,11.9868	,,,,,,	,,392/1567,,392/1557,,	73240431	1559,11447	2203	4300	6503	SO:0001819	synonymous_variant	80036	exon13			ATACTCTCGCTTG	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000357533.2:c.1641A>C	9.37:g.73240431T>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	145	88	0.606897	NM_206945	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000357533.2	37																																																																																				T|0.873;G|0.127	0.127	strong		0.294	TRPM3-014	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000214163.1	NM_206945	
ILDR1	286676	hgsc.bcm.edu	37	3	121712098	121712098	+	Missense_Mutation	SNP	G	G	A	rs34284625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121712098G>A	ENST00000344209.5	-	7	1624	c.1498C>T	c.(1498-1500)Cac>Tac	p.H500Y	ILDR1_ENST00000462014.1_Missense_Mutation_p.H468Y|ILDR1_ENST00000273691.3_Missense_Mutation_p.H456Y|ILDR1_ENST00000393631.1_Missense_Mutation_p.H411Y|ILDR1_ENST00000460554.1_5'UTR	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	500					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		TGTGGGGAGTGCGAGCCGCGG	0.632													G|||	201	0.0401358	0.1445	0.0144	5008	,	,		15335	0.0		0.0	False		,,,				2504	0.0				p.H500Y		Atlas-SNP	.											.	ILDR1	120	.	0			c.C1498T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	520,3882		26,468,1707	23.0	24.0	24.0		1498,1231,1366	4.0	0.0	3	dbSNP_126	24	8,8590		0,8,4291	yes	missense,missense,missense	ILDR1	NM_001199799.1,NM_001199800.1,NM_175924.3	83,83,83	26,476,5998	AA,AG,GG		0.093,11.8128,4.0615	benign,benign,benign	500/547,411/458,456/503	121712098	528,12472	2201	4299	6500	SO:0001583	missense	286676	exon7			GGGAGTGCGAGCC	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"""deafness, autosomal recessive 42"""	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.1498C>T	3.37:g.121712098G>A	ENSP00000345667:p.His500Tyr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	173	81	0.468208	NM_001199799	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	37	CCDS56271.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	G	11.04	1.522102	0.27211	0.118128	9.3E-4	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000393631;ENST00000462014	T;T;T;T	0.76709	-0.44;-0.44;-1.04;-0.04	5.76	3.99	0.46301	.	1.592350	0.03082	N	0.158662	T	0.00784	0.0026	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B	0.32620	0.378;0.165;0.378;0.378	B;B;B;B	0.28849	0.095;0.044;0.095;0.095	T	0.22661	-1.0210	9	0.56958	D	0.05	-1.8466	11.555	0.50741	0.1185:0.0:0.8815:0.0	rs34284625	411;500;456;468	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	Y	456;500;411;468	ENSP00000273691:H456Y;ENSP00000345667:H500Y;ENSP00000377251:H411Y;ENSP00000419414:H468Y	ENSP00000273691:H456Y	H	-	1	0	ILDR1	123194788	0.109000	0.22037	0.001000	0.08648	0.252000	0.25951	2.180000	0.42537	0.802000	0.34089	0.563000	0.77884	CAC	G|0.956;A|0.044	0.044	strong		0.632	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924	
LMNTD1	160492	hgsc.bcm.edu	37	12	25672880	25672880	+	Missense_Mutation	SNP	T	T	C	rs34732786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672880T>C	ENST00000282881.6	-	6	1014	c.865A>G	c.(865-867)Aca>Gca	p.T289A	IFLTD1_ENST00000413632.2_Missense_Mutation_p.T270A|IFLTD1_ENST00000445693.1_Missense_Mutation_p.T226A|IFLTD1_ENST00000539744.1_Missense_Mutation_p.T192A|IFLTD1_ENST00000458174.2_Missense_Mutation_p.T310A	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		289			T -> A (in dbSNP:rs34732786).		cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					ATTGTAGCTGTAGATGCTGTC	0.378													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13206	0.0		0.0	False		,,,				2504	0.0				p.T310A		Atlas-SNP	.											.	IFLTD1	121	.	0			c.A928G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR	251,4155	146.5+/-181.1	5,241,1957	211.0	187.0	195.0		676,928,808,865	-7.0	0.0	12	dbSNP_126	195	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	58,58,58,58	5,242,6256	CC,CT,TT		0.0116,5.6968,1.9376	benign,benign,benign,benign	226/326,310/410,270/370,289/389	25672880	252,12754	2203	4300	6503	SO:0001583	missense	160492	exon7			TAGCTGTAGATGC																												ENST00000282881.6:c.865A>G	12.37:g.25672880T>C	ENSP00000282881:p.Thr289Ala	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	121	51	0.421488	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	8.850|8.850	0.944302|0.944302	0.18356|0.18356	0.056968|0.056968	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000539523;ENST00000545543|ENST00000543629	T;T;T;T;T;T;T|.	0.22945|.	2.72;2.75;2.72;2.72;2.54;1.93;2.5|.	4.84|4.84	-7.02|-7.02	0.01589|0.01589	.|.	.|.	.|.	.|.	.|.	T|T	0.02267|0.02267	0.0070|0.0070	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.17667|.	0.023;0.023;0.023;0.013|.	B;B;B;B|.	0.11329|.	0.003;0.006;0.006;0.002|.	T|T	0.21861|0.21861	-1.0233|-1.0233	9|5	0.62326|.	D|.	0.03|.	-0.6199|-0.6199	9.436|9.436	0.38639|0.38639	0.0:0.5472:0.2462:0.2065|0.0:0.5472:0.2462:0.2065	rs34732786|rs34732786	226;310;270;289|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	A|C	289;192;310;226;270;6;119|63	ENSP00000282881:T289A;ENSP00000443132:T192A;ENSP00000407353:T310A;ENSP00000407043:T226A;ENSP00000393150:T270A;ENSP00000438160:T6A;ENSP00000443596:T119A|.	ENSP00000282881:T289A|.	T|Y	-|-	1|2	0|0	IFLTD1|IFLTD1	25564147|25564147	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.013000|0.013000	0.08279|0.08279	-2.565000|-2.565000	0.00918|0.00918	-1.326000|-1.326000	0.02266|0.02266	0.477000|0.477000	0.44152|0.44152	ACA|TAC	T|0.980;C|0.020	0.020	strong		0.378	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
C6orf118	168090	hgsc.bcm.edu	37	6	165715673	165715673	+	Silent	SNP	A	A	G	rs9459356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:165715673A>G	ENST00000230301.8	-	2	158	c.138T>C	c.(136-138)aaT>aaC	p.N46N	C6orf118_ENST00000543069.1_5'UTR	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	46										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)		TCTGAAGCCGATTCAGAAGTT	0.542													G|||	806	0.160942	0.3548	0.1037	5008	,	,		17965	0.0129		0.1551	False		,,,				2504	0.0982				p.N46N		Atlas-SNP	.											.	C6orf118	116	.	0			c.T138C						PASS	.	G		1472,2934	679.0+/-403.6	256,960,987	82.0	91.0	88.0		138	-0.8	0.0	6	dbSNP_119	88	1227,7373	762.6+/-407.6	87,1053,3160	no	coding-synonymous	C6orf118	NM_144980.3		343,2013,4147	GG,GA,AA		14.2674,33.409,20.752		46/470	165715673	2699,10307	2203	4300	6503	SO:0001819	synonymous_variant	168090	exon2			AAGCCGATTCAGA		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.138T>C	6.37:g.165715673A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	191	83	0.434555	NM_144980	Q8TC11	Silent	SNP	ENST00000230301.8	37	CCDS5288.1																																																																																			A|0.802;G|0.198	0.198	strong		0.542	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
DIP2A	23181	hgsc.bcm.edu	37	21	47910523	47910523	+	Silent	SNP	A	A	G	rs7279002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47910523A>G	ENST00000417564.2	+	3	195	c.174A>G	c.(172-174)ccA>ccG	p.P58P	DIP2A_ENST00000400274.1_Silent_p.P58P|DIP2A_ENST00000466639.1_Silent_p.P58P|DIP2A_ENST00000435722.3_Silent_p.P58P|DIP2A_ENST00000457905.3_Silent_p.P58P|DIP2A_ENST00000427143.2_Intron|DIP2A_ENST00000318711.7_Silent_p.P58P			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	58	DMAP-interaction.				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)		GAATAGACCCATCTCTGCAAG	0.463													A|||	1797	0.358826	0.5053	0.1988	5008	,	,		19194	0.4067		0.2545	False		,,,				2504	0.3323				p.P58P		Atlas-SNP	.											.	DIP2A	332	.	0			c.A174G						PASS	.	A	,,,,,,	1640,2134		358,924,605	37.0	39.0	38.0		,174,174,174,174,174,174	-10.3	0.0	21	dbSNP_116	38	1911,6281		243,1425,2428	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIP2A	NM_001146114.1,NM_001146115.1,NM_001146116.1,NM_015151.3,NM_206889.2,NM_206890.2,NM_206891.2	,,,,,,	601,2349,3033	GG,GA,AA		23.3276,43.4552,29.6757	,,,,,,	,58/799,58/1568,58/1572,58/890,58/842,58/813	47910523	3551,8415	1887	4096	5983	SO:0001819	synonymous_variant	23181	exon3			AGACCCATCTCTG	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.174A>G	21.37:g.47910523A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	161	75	0.465839	NM_206891	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																			A|0.634;G|0.366	0.366	strong		0.463	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
CCDC40	55036	hgsc.bcm.edu	37	17	78014024	78014024	+	Silent	SNP	G	G	A	rs2885349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78014024G>A	ENST00000397545.4	+	3	534	c.507G>A	c.(505-507)tcG>tcA	p.S169S	CCDC40_ENST00000269318.5_Silent_p.S169S|CCDC40_ENST00000374876.4_Silent_p.S169S|CCDC40_ENST00000374877.3_Silent_p.S169S	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	169					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TAGGCCCGTCGGAGCAAATGG	0.612													G|||	316	0.063099	0.1884	0.0173	5008	,	,		14983	0.001		0.004	False		,,,				2504	0.0511				p.S169S		Atlas-SNP	.											CCDC40_ENST00000374877,rectum,carcinoma,+1,2	CCDC40	198	2	0			c.G507A						PASS	.	G		614,3338		46,522,1408	30.0	34.0	33.0		507	-1.7	0.0	17	dbSNP_101	33	14,8316		0,14,4151	no	coding-synonymous	CCDC40	NM_017950.3		46,536,5559	AA,AG,GG		0.1681,15.5364,5.1132		169/1143	78014024	628,11654	1976	4165	6141	SO:0001819	synonymous_variant	55036	exon3			CCCGTCGGAGCAA	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.507G>A	17.37:g.78014024G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																			G|0.968;A|0.032	0.032	strong		0.612	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082	
FMNL2	114793	hgsc.bcm.edu	37	2	153475556	153475556	+	Missense_Mutation	SNP	T	T	C	rs11897929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:153475556T>C	ENST00000288670.9	+	14	1878	c.1511T>C	c.(1510-1512)aTg>aCg	p.M504T	FMNL2_ENST00000475377.2_5'Flank	NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	504			M -> T (in dbSNP:rs11897929).		cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						ACATTGTCCATGGGGTCAGAA	0.537													T|||	386	0.0770767	0.2769	0.0259	5008	,	,		16892	0.0		0.002	False		,,,				2504	0.0				p.M504T		Atlas-SNP	.											.	FMNL2	75	.	0			c.T1511C						PASS	.	T	THR/MET	828,3056		87,654,1201	67.0	70.0	69.0		1511	-2.1	0.0	2	dbSNP_120	69	3,8279		0,3,4138	yes	missense	FMNL2	NM_052905.3	81	87,657,5339	CC,CT,TT		0.0362,21.3182,6.8305	benign	504/1093	153475556	831,11335	1942	4141	6083	SO:0001583	missense	114793	exon14			TGTCCATGGGGTC	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1511T>C	2.37:g.153475556T>C	ENSP00000288670:p.Met504Thr	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	172	93	0.540698	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	37	CCDS46429.1	136	0.06227106227106227	128	0.2601626016260163	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	T	0.957	-0.704556	0.03255	0.213182	3.62E-4	ENSG00000157827	ENST00000288670;ENST00000421344	D	0.90004	-2.6	5.57	-2.14	0.07123	.	0.947878	0.08957	N	0.869194	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.01520	-1.1334	9	0.13108	T	0.6	.	11.4827	0.50335	0.0:0.5749:0.0:0.4251	rs11897929;rs11897929	504	Q96PY5-3	.	T	504;1	ENSP00000288670:M504T	ENSP00000288670:M504T	M	+	2	0	FMNL2	153183802	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-0.531000	0.06171	-0.792000	0.04480	-0.973000	0.02599	ATG	T|0.920;C|0.080	0.080	strong		0.537	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
FARP2	9855	hgsc.bcm.edu	37	2	242352768	242352768	+	Missense_Mutation	SNP	A	A	C	rs16843643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242352768A>C	ENST00000264042.3	+	7	725	c.555A>C	c.(553-555)aaA>aaC	p.K185N	FARP2_ENST00000373287.4_Missense_Mutation_p.K185N|FARP2_ENST00000545004.1_Missense_Mutation_p.K185N	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	185	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		K -> N (in dbSNP:rs16843643).		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)		AGCACCTCAAAGTGAACGAGT	0.403													A|||	203	0.0405351	0.146	0.013	5008	,	,		20493	0.001		0.0	False		,,,				2504	0.0				p.K185N		Atlas-SNP	.											.	FARP2	92	.	0			c.A555C						PASS	.	A	ASN/LYS	514,3892	231.7+/-245.5	32,450,1721	104.0	82.0	90.0		555	-5.4	0.0	2	dbSNP_123	90	10,8590	7.7+/-29.5	0,10,4290	yes	missense	FARP2	NM_014808.2	94	32,460,6011	CC,CA,AA		0.1163,11.6659,4.0289	probably-damaging	185/1055	242352768	524,12482	2203	4300	6503	SO:0001583	missense	9855	exon7			CCTCAAAGTGAAC	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.555A>C	2.37:g.242352768A>C	ENSP00000264042:p.Lys185Asn	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	A	8.513	0.866895	0.17250	0.116659	0.001163	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287	T;T;T	0.30714	1.52;1.52;1.52	5.34	-5.39	0.02664	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.312765	0.32533	N	0.005966	T	0.00241	0.0007	L	0.41124	1.26	0.09310	N	1	D;B;P	0.54772	0.968;0.116;0.947	P;B;P	0.50791	0.598;0.078;0.65	T	0.03034	-1.1080	10	0.59425	D	0.04	.	3.6724	0.08279	0.3864:0.1157:0.3863:0.1116	rs16843643;rs52827477;rs59890453;rs16843643	185;185;185	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	N	185	ENSP00000264042:K185N;ENSP00000443876:K185N;ENSP00000362384:K185N	ENSP00000264042:K185N	K	+	3	2	FARP2	242001441	0.001000	0.12720	0.000000	0.03702	0.336000	0.28762	0.092000	0.15066	-1.367000	0.02152	0.528000	0.53228	AAA	A|0.960;C|0.040	0.040	strong		0.403	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
ZNF385C	201181	hgsc.bcm.edu	37	17	40183707	40183707	+	Silent	SNP	G	G	C	rs75049227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40183707G>C	ENST00000436535.3	-	4	606	c.606C>G	c.(604-606)gcC>gcG	p.A202A	ZNF385C_ENST00000461831.1_5'Flank			Q66K41	Z385C_HUMAN	zinc finger protein 385C	121						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	3		all_cancers(22;0.00127)|Breast(137;0.00104)|all_epithelial(22;0.0126)				CCCCATCCTGGGCCTGGGTGT	0.587													G|||	55	0.0109824	0.0416	0.0	5008	,	,		19297	0.0		0.0	False		,,,				2504	0.0				p.A123A		Atlas-SNP	.											.	ZNF385C	7	.	0			c.C369G						PASS	.																																			SO:0001819	synonymous_variant	201181	exon4			ATCCTGGGCCTGG	BC067901	CCDS74065.1	17q21.2	2012-10-05			ENSG00000187595	ENSG00000187595			33722	protein-coding gene	gene with protein product							Standard	NM_001242704		Approved		uc021txr.1	Q66K41	OTTHUMG00000132073	ENST00000436535.3:c.606C>G	17.37:g.40183707G>C		Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	358	172	0.480447	NM_001242704	Q4G0J1	Silent	SNP	ENST00000436535.3	37																																																																																				G|0.994;C|0.006	0.006	strong		0.587	ZNF385C-001	NOVEL	not_organism_supported|mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000347740.3	NM_001013624	
NECAB2	54550	hgsc.bcm.edu	37	16	84027966	84027966	+	Missense_Mutation	SNP	C	C	T	rs79514285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84027966C>T	ENST00000305202.4	+	7	673	c.656C>T	c.(655-657)cCc>cTc	p.P219L	NECAB2_ENST00000565691.1_Missense_Mutation_p.P136L|NECAB2_ENST00000567703.1_3'UTR	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	219						cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						AGCCCCACTCCCGCCTCTGCC	0.617													C|||	12	0.00239617	0.0083	0.0014	5008	,	,		16456	0.0		0.0	False		,,,				2504	0.0				p.P219L		Atlas-SNP	.											.	NECAB2	36	.	0			c.C656T						PASS	.	C	LEU/PRO	49,4351	50.2+/-85.5	0,49,2151	56.0	55.0	55.0		656	2.6	0.0	16	dbSNP_131	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NECAB2	NM_019065.2	98	0,50,6450	TT,TC,CC		0.0116,1.1136,0.3846	possibly-damaging	219/387	84027966	50,12950	2200	4300	6500	SO:0001583	missense	54550	exon7			CCACTCCCGCCTC	AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	23746	protein-coding gene	gene with protein product			"""EF-hand calcium binding protein 2"""	EFCBP2		12044471	Standard	NM_019065		Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.656C>T	16.37:g.84027966C>T	ENSP00000307449:p.Pro219Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_019065	A2RRG3|O75547|Q6ZSK0	Missense_Mutation	SNP	ENST00000305202.4	37	CCDS10940.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	6.435	0.448444	0.12223	0.011136	1.16E-4	ENSG00000103154	ENST00000305202	T	0.18338	2.22	4.58	2.62	0.31277	.	0.326488	0.32868	N	0.005554	T	0.09598	0.0236	L	0.44542	1.39	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.27773	-1.0064	10	0.21540	T	0.41	-9.3808	10.4175	0.44331	0.0:0.7817:0.1375:0.0809	.	219	Q7Z6G3	NECA2_HUMAN	L	219	ENSP00000307449:P219L	ENSP00000307449:P219L	P	+	2	0	NECAB2	82585467	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	1.654000	0.37334	0.128000	0.18479	-1.872000	0.00552	CCC	C|0.996;T|0.004	0.004	strong		0.617	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269077.2	NM_019065	
RRM2	6241	hgsc.bcm.edu	37	2	10263874	10263874	+	Silent	SNP	C	C	G	rs5030743	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10263874C>G	ENST00000304567.5	+	4	399	c.330C>G	c.(328-330)tcC>tcG	p.S110S	RP11-254F7.4_ENST00000607140.1_lincRNA|RRM2_ENST00000360566.2_Silent_p.S170S	NM_001034.3	NP_001025.1	P31350	RIR2_HUMAN	ribonucleotide reductase M2	110					deoxyribonucleoside diphosphate metabolic process (GO:0009186)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|skin(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.188)|OV - Ovarian serous cystadenocarcinoma(76;0.221)	Cladribine(DB00242)|Gallium nitrate(DB05260)	TGGACCTCTCCAAGGACATTC	0.438													C|||	135	0.0269569	0.0991	0.0058	5008	,	,		19414	0.0		0.0	False		,,,				2504	0.0				p.S170S		Atlas-SNP	.											.	RRM2	63	.	0			c.C510G						PASS	.	C	,	390,4016	196.4+/-220.7	16,358,1829	82.0	88.0	86.0		330,510	0.8	1.0	2	dbSNP_113	86	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	RRM2	NM_001034.3,NM_001165931.1	,	16,358,6129	GG,GC,CC		0.0,8.8516,2.9986	,	110/390,170/450	10263874	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	6241	exon4			CCTCTCCAAGGAC		CCDS1669.1, CCDS54334.1	2p25-p24	2012-10-02	2009-07-10		ENSG00000171848	ENSG00000171848	1.17.4.1		10452	protein-coding gene	gene with protein product		180390	"""ribonucleotide reductase M2 polypeptide"""				Standard	NM_001034		Approved		uc021vdr.1	P31350	OTTHUMG00000090449	ENST00000304567.5:c.330C>G	2.37:g.10263874C>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_001165931	B2R9B5|J3KP43|Q5WRU7	Silent	SNP	ENST00000304567.5	37	CCDS1669.1																																																																																			C|0.969;G|0.031	0.031	strong		0.438	RRM2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364902.2		
LRRC8E	80131	hgsc.bcm.edu	37	19	7963948	7963948	+	Missense_Mutation	SNP	G	G	A	rs3745379|rs386806520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7963948G>A	ENST00000306708.6	+	3	642	c.541G>A	c.(541-543)Gaa>Aaa	p.E181K	AC010336.1_ENST00000539278.1_3'UTR	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	181			E -> G (in dbSNP:rs2042919).		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						AGCAGCCACCGAACGGGCTGC	0.637													G|||	229	0.0457268	0.1029	0.0086	5008	,	,		17200	0.0833		0.0	False		,,,				2504	0.0031				p.E181K		Atlas-SNP	.											.	LRRC8E	67	.	0			c.G541A						PASS	.																																			SO:0001583	missense	80131	exon4			GCCACCGAACGGG		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.541G>A	19.37:g.7963948G>A	ENSP00000306524:p.Glu181Lys	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Missense_Mutation	SNP	ENST00000306708.6	37	CCDS12189.1	109	0.04990842490842491	54	0.10975609756097561	5	0.013812154696132596	50	0.08741258741258741	0	0.0	G	0.005	-2.195360	0.00299	.	.	ENSG00000171017	ENST00000306708	T	0.26223	1.75	5.19	3.03	0.35002	.	0.468333	0.23620	N	0.046258	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	B	0.22146	0.065	B	0.06405	0.002	T	0.28618	-1.0038	9	0.05525	T	0.97	.	5.1411	0.14959	0.1786:0.1724:0.649:0.0	rs3745379	181	Q6NSJ5	LRC8E_HUMAN	K	181	ENSP00000306524:E181K	ENSP00000306524:E181K	E	+	1	0	LRRC8E	7869948	0.000000	0.05858	0.006000	0.13384	0.002000	0.02628	0.333000	0.19768	0.751000	0.32900	0.655000	0.94253	GAA	G|0.950;A|0.050	0.050	strong		0.637	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
FRMD4B	23150	hgsc.bcm.edu	37	3	69271032	69271032	+	Silent	SNP	G	G	A	rs62254461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:69271032G>A	ENST00000398540.3	-	9	791	c.708C>T	c.(706-708)ctC>ctT	p.L236L	FRMD4B_ENST00000542259.1_Silent_p.L182L	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	236	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		GACCTCGAGTGAGACCTTTGA	0.358													G|||	198	0.0395367	0.0068	0.0663	5008	,	,		18997	0.001		0.1183	False		,,,				2504	0.0235				p.L236L		Atlas-SNP	.											.	FRMD4B	90	.	0			c.C708T						PASS	.	G		74,3708		0,74,1817	82.0	77.0	79.0		708	2.5	1.0	3	dbSNP_129	79	967,7249		63,841,3204	no	coding-synonymous	FRMD4B	NM_015123.1		63,915,5021	AA,AG,GG		11.7697,1.9566,8.6764		236/1035	69271032	1041,10957	1891	4108	5999	SO:0001819	synonymous_variant	23150	exon9			TCGAGTGAGACCT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.708C>T	3.37:g.69271032G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_015123	Q8TAI3	Silent	SNP	ENST00000398540.3	37	CCDS46863.1																																																																																			G|0.928;A|0.072	0.072	strong		0.358	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1		
DDX11	1663	hgsc.bcm.edu	37	12	31256546	31256546	+	Missense_Mutation	SNP	G	G	A	rs1046457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:31256546G>A	ENST00000407793.2	+	26	2818	c.2567G>A	c.(2566-2568)cGt>cAt	p.R856H	DDX11_ENST00000350437.4_Missense_Mutation_p.V808I|DDX11_ENST00000228264.6_Missense_Mutation_p.V832I|DDX11_ENST00000545668.1_Missense_Mutation_p.R856H|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Missense_Mutation_p.V858I	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	856			R -> H (in dbSNP:rs1046457).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					TTTTGCCAGCGTAGTGCTCCT	0.647										Multiple Myeloma(12;0.14)			A|||	3176	0.634185	0.708	0.611	5008	,	,		14475	0.8075		0.4384	False		,,,				2504	0.5736				p.V858I		Atlas-SNP	.											.	DDX11	188	.	0			c.G2572A						PASS	.	A	HIS/ARG,ILE/VAL,ILE/VAL	2845,1557		1010,825,366	26.0	39.0	34.0		2567,2572,2422	3.1	1.0	12	dbSNP_86	34	3631,4965		886,1859,1553	no	missense,missense,missense	DDX11	NM_152438.1,NM_030653.3,NM_004399.2	29,29,29	1896,2684,1919	AA,AG,GG		42.2406,35.3703,49.823	benign,benign,benign	856/971,858/907,808/857	31256546	6476,6522	2201	4298	6499	SO:0001583	missense	1663	exon26			GCCAGCGTAGTGC	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.2567G>A	12.37:g.31256546G>A	ENSP00000384703:p.Arg856His	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	164	85	0.518293	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	1165|1165	0.5334249084249084|0.5334249084249084	293|293	0.5955284552845529|0.5955284552845529	193|193	0.5331491712707183|0.5331491712707183	423|423	0.7395104895104895|0.7395104895104895	256|256	0.33773087071240104|0.33773087071240104	A|A	0.021|0.021	-1.427665|-1.427665	0.01117|0.01117	0.646297|0.646297	0.422406|0.422406	ENSG00000013573|ENSG00000013573	ENST00000407793;ENST00000545668|ENST00000542838;ENST00000228264;ENST00000350437	T;T|D;D;D	0.74106|0.90955	-0.81;-0.81|-2.76;-2.76;-2.76	3.14|3.14	3.14|3.14	0.36123|0.36123	Helicase, ATP-dependent, c2 type (1);|.	.|0.646978	.|0.15103	.|N	.|0.280427	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999996408|0.9999999999996408	B|B;B;B	0.02656|0.06786	0.0|0.0;0.001;0.0	B|B;B;B	0.01281|0.01281	0.0|0.0;0.0;0.0	T|T	0.43032|0.43032	-0.9416|-0.9416	7|8	0.46703|0.02654	T|T	0.11|1	.|.	6.4922|6.4922	0.22121|0.22121	0.8746:0.0:0.1254:0.0|0.8746:0.0:0.1254:0.0	rs1046457;rs3177434;rs3186439;rs17415422;rs58379983|rs1046457;rs3177434;rs3186439;rs17415422;rs58379983	856|832;808;858	Q96FC9|Q96FC9-3;Q96FC9-4;Q96FC9-2	DDX11_HUMAN|.;.;.	H|I	856|858;832;808	ENSP00000384703:R856H;ENSP00000440402:R856H|ENSP00000443426:V858I;ENSP00000228264:V832I;ENSP00000309965:V808I	ENSP00000384703:R856H|ENSP00000228264:V832I	R|V	+|+	2|1	0|0	DDX11|DDX11	31147813|31147813	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.179000|0.179000	0.23085|0.23085	2.796000|2.796000	0.47869|0.47869	0.313000|0.313000	0.23062|0.23062	-0.707000|-0.707000	0.03653|0.03653	CGT|GTA	G|0.494;A|0.506	0.506	strong		0.647	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036999	33036999	+	Missense_Mutation	SNP	T	T	C	rs1042190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33036999T>C	ENST00000419277.1	-	4	554	c.425A>G	c.(424-426)aAg>aGg	p.K142R	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.K142R	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	142	Alpha-2.|Ig-like C1-type.		K -> R (in allele DPA1*02:01 and allele DPA1*02:02; dbSNP:rs1042190).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						TGGGAAGAACTTGTCAATGTG	0.592													.|||	2158	0.430911	0.5772	0.2824	5008	,	,		19467	0.6508		0.1889	False		,,,				2504	0.3609				p.K142R		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.A425G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	1386,1632		317,752,440	115.0	137.0	129.0		425,425,425	0.8	0.9	6	dbSNP_86	129	954,4460		70,814,1823	yes	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	26,26,26	387,1566,2263	CC,CT,TT		17.621,45.9245,27.7514	benign,benign,benign	142/261,142/261,142/261	33036999	2340,6092	1509	2707	4216	SO:0001583	missense	3113	exon3			AAGAACTTGTCAA	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.425A>G	6.37:g.33036999T>C	ENSP00000393566:p.Lys142Arg	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	847	0.38782051282051283	272	0.5528455284552846	89	0.24585635359116023	356	0.6223776223776224	130	0.17150395778364116	T	13.63	2.295035	0.40594	0.459245	0.17621	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.08546	6.24;6.24;3.08	3.4	0.821	0.18799	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.154150	0.43919	U	0.000507	T	0.03263	0.0095	L	0.56280	1.765	0.40470	P	0.01966800000000002	B	0.21821	0.061	B	0.29440	0.102	T	0.23297	-1.0192	9	0.66056	D	0.02	.	6.4481	0.21887	0.0:0.2451:0.0:0.7549	rs1042190;rs2308926;rs45518435;rs52798036;rs1042190	142	P20036	DPA1_HUMAN	R	142;142;109;142	ENSP00000393566:K142R;ENSP00000402872:K142R;ENSP00000390929:K142R	ENSP00000393566:K142R	K	-	2	0	HLA-DPA1	33144977	0.919000	0.31177	0.935000	0.37517	0.984000	0.73092	0.797000	0.26999	0.038000	0.15604	0.523000	0.50628	AAG	.	.	weak		0.592	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
HAUS6	54801	hgsc.bcm.edu	37	9	19087154	19087154	+	Splice_Site	SNP	T	T	C	rs7875404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:19087154T>C	ENST00000380502.3	-	6	1052	c.585A>G	c.(583-585)caA>caG	p.Q195Q	HAUS6_ENST00000380496.1_Splice_Site_p.Q59Q|Y_RNA_ENST00000364248.1_RNA	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	195					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						TAACTGATAATCTGCAAGAAA	0.338													T|||	668	0.133387	0.2769	0.0634	5008	,	,		19522	0.0308		0.1282	False		,,,				2504	0.1002				p.Q195Q		Atlas-SNP	.											.	HAUS6	66	.	0			c.A585G						PASS	.	T		1233,3171	424.7+/-340.5	180,873,1149	129.0	127.0	128.0		585	1.2	0.5	9	dbSNP_116	128	970,7630	211.1+/-251.8	48,874,3378	yes	coding-synonymous-near-splice	HAUS6	NM_017645.3		228,1747,4527	CC,CT,TT		11.2791,27.9973,16.9409		195/956	19087154	2203,10801	2202	4300	6502	SO:0001630	splice_region_variant	54801	exon6			TGATAATCTGCAA	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.585-1A>G	9.37:g.19087154T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	135	59	0.437037	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																			T|0.849;C|0.151	0.151	strong		0.338	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	Silent
MTMR10	54893	hgsc.bcm.edu	37	15	31234064	31234064	+	Missense_Mutation	SNP	C	C	T	rs6493352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31234064C>T	ENST00000435680.1	-	16	2040	c.1943G>A	c.(1942-1944)cGt>cAt	p.R648H	MTMR10_ENST00000314404.8_Intron|MTMR10_ENST00000425768.1_3'UTR|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	190	0	0		WXS	Illumina HiSeq	Phase_I	212	113	0.533019	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	
RBM33	155435	hgsc.bcm.edu	37	7	155534653	155534653	+	Silent	SNP	C	C	G	rs73167165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:155534653C>G	ENST00000401878.3	+	13	2388	c.2190C>G	c.(2188-2190)ccC>ccG	p.P730P		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	730							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)		CTGCCACGCCCTCAGCACAAG	0.577													C|||	329	0.0656949	0.1566	0.0591	5008	,	,		16824	0.0198		0.0388	False		,,,				2504	0.0225				p.P730P		Atlas-SNP	.											.	RBM33	157	.	0			c.C2190G						PASS	.	C		634,3772	274.0+/-271.7	36,562,1605	93.0	91.0	92.0		2190	-5.4	0.0	7	dbSNP_130	92	309,8291	111.0+/-171.3	4,301,3995	no	coding-synonymous	RBM33	NM_053043.2		40,863,5600	GG,GC,CC		3.593,14.3895,7.2505		730/1171	155534653	943,12063	2203	4300	6503	SO:0001819	synonymous_variant	155435	exon13			CACGCCCTCAGCA	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.2190C>G	7.37:g.155534653C>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	130	54	0.415385	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Silent	SNP	ENST00000401878.3	37	CCDS5941.2	136	0.06227106227106227	71	0.1443089430894309	18	0.049723756906077346	13	0.022727272727272728	34	0.044854881266490766	C	2.751	-0.260061	0.05791	0.143895	0.03593	ENSG00000184863	ENST00000392761	T	0.28255	1.62	5.66	-5.38	0.02673	.	0.182576	0.39274	N	0.001411	T	0.00178	0.0005	.	.	.	0.09310	P	0.999999999673283	.	.	.	.	.	.	T	0.07616	-1.0763	6	0.59425	D	0.04	.	3.1545	0.06499	0.1798:0.3819:0.092:0.3462	.	.	.	.	R	502	ENSP00000376514:P502R	ENSP00000376514:P502R	P	+	2	0	RBM33	155227414	0.104000	0.21937	0.000000	0.03702	0.262000	0.26303	-1.069000	0.03444	-1.364000	0.02161	-0.229000	0.12294	CCT	C|0.931;G|0.069	0.069	strong		0.577	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408	
MMP20	9313	hgsc.bcm.edu	37	11	102487643	102487643	+	Missense_Mutation	SNP	T	T	C	rs61730848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:102487643T>C	ENST00000260228.2	-	2	286	c.274A>G	c.(274-276)Atg>Gtg	p.M92V	RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	82					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	ATCACGTTCATTGTGGTCTGG	0.458													T|||	12	0.00239617	0.0083	0.0014	5008	,	,		20171	0.0		0.0	False		,,,				2504	0.0				p.M92V		Atlas-SNP	.											.	MMP20	52	.	0			c.A274G						PASS	.	T	VAL/MET	31,4375	36.8+/-68.6	0,31,2172	174.0	149.0	158.0		274	4.0	0.4	11	dbSNP_129	158	0,8598		0,0,4299	yes	missense	MMP20	NM_004771.3	21	0,31,6471	CC,CT,TT		0.0,0.7036,0.2384	benign	92/484	102487643	31,12973	2203	4299	6502	SO:0001583	missense	9313	exon2			CGTTCATTGTGGT	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.274A>G	11.37:g.102487643T>C	ENSP00000260228:p.Met92Val	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	223	91	0.408072	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	T	8.312	0.822400	0.16678	0.007036	0.0	ENSG00000137674	ENST00000260228	T	0.34072	1.38	5.09	3.95	0.45737	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.248296	0.48286	D	0.000186	T	0.22126	0.0533	L	0.48174	1.505	0.31775	N	0.631573	B	0.10296	0.003	B	0.12837	0.008	T	0.24368	-1.0162	10	0.54805	T	0.06	.	7.274	0.26273	0.1337:0.0:0.2769:0.5894	.	92	O60882	MMP20_HUMAN	V	92	ENSP00000260228:M92V	ENSP00000260228:M92V	M	-	1	0	MMP20	101992853	0.016000	0.18221	0.382000	0.26119	0.387000	0.30353	0.103000	0.15292	1.044000	0.40200	0.533000	0.62120	ATG	T|0.998;C|0.002	0.002	strong		0.458	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
DNAJA4	55466	hgsc.bcm.edu	37	15	78567853	78567853	+	Silent	SNP	G	G	T	rs967821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:78567853G>T	ENST00000394852.3	+	5	850	c.660G>T	c.(658-660)ggG>ggT	p.G220G	DNAJA4_ENST00000446172.2_Silent_p.G193G|DNAJA4_ENST00000343789.3_Silent_p.G220G|DNAJA4_ENST00000394855.3_Silent_p.G249G	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	220					negative regulation of inclusion body assembly (GO:0090084)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	8						TGAAAGATGGGCAAAAGATAC	0.408													G|||	1024	0.204473	0.292	0.3429	5008	,	,		22376	0.1052		0.1909	False		,,,				2504	0.1043				p.G249G		Atlas-SNP	.											.	DNAJA4	63	.	0			c.G747T						PASS	.	G	,,	1123,3269	401.0+/-331.8	135,853,1208	93.0	84.0	87.0		660,579,747	2.3	1.0	15	dbSNP_86	87	1503,7083	285.7+/-297.3	147,1209,2937	no	coding-synonymous,coding-synonymous,coding-synonymous	DNAJA4	NM_001130182.1,NM_001130183.1,NM_018602.3	,,	282,2062,4145	TT,TG,GG		17.5052,25.5692,20.2342	,,	220/398,193/371,249/427	78567853	2626,10352	2196	4293	6489	SO:0001819	synonymous_variant	55466	exon6			AGATGGGCAAAAG	AF116663	CCDS10299.2, CCDS45316.1, CCDS45317.1	15q24.1	2011-09-02			ENSG00000140403	ENSG00000140403		"""Heat shock proteins / DNAJ (HSP40)"""	14885	protein-coding gene	gene with protein product						11147971	Standard	NM_018602		Approved	PRO1472	uc002bdi.3	Q8WW22	OTTHUMG00000143733	ENST00000394852.3:c.660G>T	15.37:g.78567853G>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_018602	E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Silent	SNP	ENST00000394852.3	37	CCDS45316.1																																																																																			G|0.788;T|0.212	0.212	strong		0.408	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	NM_018602	
AKAP13	11214	hgsc.bcm.edu	37	15	86182670	86182670	+	Silent	SNP	G	G	A	rs16942564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:86182670G>A	ENST00000394518.2	+	9	4322	c.4227G>A	c.(4225-4227)aaG>aaA	p.K1409K	AKAP13_ENST00000560579.1_3'UTR|RP11-815J21.4_ENST00000558980.1_RNA|AKAP13_ENST00000361243.2_Silent_p.K1409K	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1409					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						TGGCTTCCAAGCAGAGCCCAG	0.448													G|||	304	0.0607029	0.0681	0.1888	5008	,	,		19245	0.0377		0.0388	False		,,,				2504	0.0061				p.K1409K	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G4227A						PASS	.	G	,	313,4091	166.9+/-198.0	12,289,1901	106.0	97.0	100.0		4227,4227	-1.5	0.7	15	dbSNP_123	100	353,8245	119.4+/-178.7	2,349,3948	no	coding-synonymous,coding-synonymous	AKAP13	NM_006738.4,NM_007200.3	,	14,638,5849	AA,AG,GG		4.1056,7.1072,5.1223	,	1409/2818,1409/2814	86182670	666,12336	2202	4299	6501	SO:0001819	synonymous_variant	11214	exon9			TTCCAAGCAGAGC	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.4227G>A	15.37:g.86182670G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	73	41	0.561644	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	37	CCDS32319.1																																																																																			G|0.944;A|0.056	0.056	strong		0.448	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
PPP1R12C	54776	hgsc.bcm.edu	37	19	55623871	55623871	+	Missense_Mutation	SNP	T	T	G	rs116840455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55623871T>G	ENST00000263433.3	-	3	550	c.535A>C	c.(535-537)Atg>Ctg	p.M179L	PPP1R12C_ENST00000435544.2_Missense_Mutation_p.M105L|PPP1R12C_ENST00000376393.2_Missense_Mutation_p.M179L	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)		AGCCCCTCCATGGCGTCCGAC	0.701													T|||	47	0.00938498	0.0356	0.0	5008	,	,		12736	0.0		0.0	False		,,,				2504	0.0				p.M179L		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.A535C						PASS	.	T	LEU/MET	136,4270		0,136,2067	22.0	28.0	26.0		535	2.0	1.0	19	dbSNP_132	26	0,8596		0,0,4298	yes	missense	PPP1R12C	NM_017607.2	15	0,136,6365	GG,GT,TT		0.0,3.0867,1.046	possibly-damaging	179/783	55623871	136,12866	2203	4298	6501	SO:0001583	missense	54776	exon3			CCTCCATGGCGTC	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.535A>C	19.37:g.55623871T>G	ENSP00000263433:p.Met179Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	93	38	0.408602	NM_017607		Missense_Mutation	SNP	ENST00000263433.3	37	CCDS12916.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	T	17.05	3.291102	0.59976	0.030867	0.0	ENSG00000125503	ENST00000263433;ENST00000376393;ENST00000435544	T;T;T	0.51574	0.7;0.7;0.7	5.24	2.02	0.26589	Ankyrin repeat-containing domain (3);	0.106312	0.64402	D	0.000009	T	0.12263	0.0298	L	0.31578	0.945	0.41995	D	0.990866	B;B;B	0.25441	0.126;0.122;0.075	B;B;B	0.23150	0.02;0.044;0.02	T	0.03875	-1.0996	10	0.44086	T	0.13	.	7.5728	0.27918	0.0:0.2535:0.0:0.7465	.	105;179;179	B4DME2;Q9BZL4-3;Q9BZL4	.;.;PP12C_HUMAN	L	179;179;105	ENSP00000263433:M179L;ENSP00000365573:M179L;ENSP00000387833:M105L	ENSP00000263433:M179L	M	-	1	0	PPP1R12C	60315683	1.000000	0.71417	0.994000	0.49952	0.926000	0.56050	2.280000	0.43443	0.421000	0.25980	0.459000	0.35465	ATG	T|0.990;G|0.010	0.010	strong		0.701	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
PRPSAP1	5635	hgsc.bcm.edu	37	17	74307737	74307737	+	Silent	SNP	T	T	C	rs10459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74307737T>C	ENST00000446526.3	-	10	1489	c.1044A>G	c.(1042-1044)caA>caG	p.Q348Q	PRPSAP1_ENST00000324684.4_Silent_p.Q245Q|PRPSAP1_ENST00000588364.1_5'UTR	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	319					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						TCTTGGGACATTGCAGCTTCT	0.453													C|||	1284	0.25639	0.3154	0.17	5008	,	,		22164	0.4444		0.1471	False		,,,				2504	0.1564				p.Q348Q		Atlas-SNP	.											.	PRPSAP1	32	.	0			c.A1044G						PASS	.	C		1373,3033	689.2+/-405.1	200,973,1030	147.0	116.0	127.0		1044	4.9	1.0	17	dbSNP_52	127	1316,7284	758.1+/-407.5	115,1086,3099	no	coding-synonymous	PRPSAP1	NM_002766.2		315,2059,4129	CC,CT,TT		15.3023,31.1621,20.6751		348/386	74307737	2689,10317	2203	4300	6503	SO:0001819	synonymous_variant	5635	exon10			GGGACATTGCAGC	D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.1044A>G	17.37:g.74307737T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	152	80	0.526316	NM_002766	B2R6M4|Q96H06	Silent	SNP	ENST00000446526.3	37	CCDS11743.2																																																																																			T|0.766;C|0.234	0.234	strong		0.453	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786833	75786833	+	Silent	SNP	G	G	A	rs139448820		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75786833G>A	ENST00000478296.1	-	4	2067	c.1791C>T	c.(1789-1791)taC>taT	p.Y597Y	ZNF717_ENST00000422325.1_Silent_p.Y647Y|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Silent_p.Y640Y|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	640					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						CATTACATACGTAAGGTTTCT	0.433																																					p.Y647Y		Atlas-SNP	.											.	ZNF717	160	.	0			c.C1941T						PASS	.						40.0	44.0	43.0					3																	75786833		633	1557	2190	SO:0001819	synonymous_variant	100131827	exon5			ACATACGTAAGGT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1791C>T	3.37:g.75786833G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_001128223		Silent	SNP	ENST00000478296.1	37																																																																																				.	.	weak		0.433	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
SLITRK4	139065	hgsc.bcm.edu	37	X	142717383	142717383	+	Silent	SNP	A	A	G	rs73577386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:142717383A>G	ENST00000381779.4	-	2	1767	c.1542T>C	c.(1540-1542)agT>agC	p.S514S	SLITRK4_ENST00000338017.4_Silent_p.S514S|SLITRK4_ENST00000356928.1_Silent_p.S514S	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	514						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					CAAGGACCCCACTGACAGGCA	0.473													A|||	528	0.139868	0.3812	0.0317	3775	,	,		13652	0.0		0.002	False		,,,				2504	0.0				p.S514S		Atlas-SNP	.											.	SLITRK4	162	.	0			c.T1542C						PASS	.	A	,,	1667,2168		315,787,250,530,321	133.0	136.0	135.0		1542,1542,1542	-3.0	1.0	X	dbSNP_130	135	17,6711		0,11,6,2417,1866	no	coding-synonymous,coding-synonymous,coding-synonymous	SLITRK4	NM_001184749.1,NM_001184750.1,NM_173078.3	,,	315,798,256,2947,2187	GG,GA,G,AA,A		0.2527,43.4681,15.9424	,,	514/838,514/838,514/838	142717383	1684,8879	2203	4300	6503	SO:0001819	synonymous_variant	139065	exon2			GACCCCACTGACA	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.1542T>C	X.37:g.142717383A>G		Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Silent	SNP	ENST00000381779.4	37	CCDS14679.1																																																																																			A|0.836;G|0.164	0.164	strong		0.473	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078	
RPS6KA2	6196	hgsc.bcm.edu	37	6	166912062	166912062	+	Silent	SNP	C	C	T	rs2230732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:166912062C>T	ENST00000265678.4	-	8	904	c.681G>A	c.(679-681)gcG>gcA	p.A227A	RPS6KA2_ENST00000405189.3_Silent_p.A138A|RPS6KA2_ENST00000366863.2_Silent_p.A73A|RPS6KA2_ENST00000503859.1_Silent_p.A235A|RPS6KA2_ENST00000510118.1_Silent_p.A252A|RPS6KA2_ENST00000481261.2_Silent_p.A138A	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	93	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	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	
LILRA6	79168	hgsc.bcm.edu	37	19	54744209	54744209	+	Missense_Mutation	SNP	T	T	A	rs8105096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54744209T>A	ENST00000396365.2	-	6	1238	c.1199A>T	c.(1198-1200)tAc>tTc	p.Y400F	LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.Y400F|LILRA6_ENST00000245621.5_Missense_Mutation_p.Y400F	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	400	Ig-like C2-type 2.		Y -> H (in dbSNP:rs8104206).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTTGGAGCTGTATGAGCCGTA	0.587													.|||	254	0.0507188	0.1853	0.0115	5008	,	,		25300	0.0		0.001	False		,,,				2504	0.0				p.Y400F		Atlas-SNP	.											.	LILRA6	75	.	0			c.A1199T						PASS	.						83.0	115.0	104.0					19																	54744209		2196	4300	6496	SO:0001583	missense	79168	exon6			GAGCTGTATGAGC	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.1199A>T	19.37:g.54744209T>A	ENSP00000379651:p.Tyr400Phe	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	304	113	0.371711	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.514172	0.00151	.	.	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.00724	5.78;5.78;5.78	2.39	-4.78	0.03209	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	6.834670	0.00465	N	0.000119	T	0.00524	0.0017	N	0.11284	0.12	0.09310	N	1	B;B;B	0.22480	0.003;0.07;0.001	B;B;B	0.19666	0.008;0.01;0.026	T	0.46219	-0.9207	10	0.11182	T	0.66	.	4.2854	0.10853	0.4618:0.0:0.2971:0.2411	rs8105096;rs16985495;rs16989282	400;400;400	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	F	400	ENSP00000411227:Y400F;ENSP00000379651:Y400F;ENSP00000245621:Y400F	ENSP00000245621:Y400F	Y	-	2	0	LILRA6	59436021	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-3.402000	0.00483	-4.296000	0.00058	-3.711000	0.00023	TAC	C|0.155;T|0.845	.	strong		0.587	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
GPR68	8111	hgsc.bcm.edu	37	14	91700319	91700319	+	Missense_Mutation	SNP	A	A	G	rs151219229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91700319A>G	ENST00000531499.2	-	2	1415	c.1076T>C	c.(1075-1077)tTc>tCc	p.F359S	GPR68_ENST00000238699.3_Missense_Mutation_p.F369S|GPR68_ENST00000529300.1_5'Flank|GPR68_ENST00000535815.1_Missense_Mutation_p.F359S			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	359					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		GCCCGTGGGGAACCCGCCCGA	0.711													G|||	53	0.0105831	0.0393	0.0014	5008	,	,		13610	0.0		0.0	False		,,,				2504	0.0				p.F359S		Atlas-SNP	.											.	GPR68	32	.	0			c.T1076C						PASS	.	G	SER/PHE,SER/PHE	50,3832		0,50,1891	10.0	13.0	12.0		1076,1076	1.6	0.0	14	dbSNP_134	12	0,7436		0,0,3718	no	missense,missense	GPR68	NM_003485.3,NM_001177676.1	155,155	0,50,5609	GG,GA,AA		0.0,1.288,0.4418	benign,benign	359/366,359/366	91700319	50,11268	1941	3718	5659	SO:0001583	missense	8111	exon2			GTGGGGAACCCGC	U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"""GPCR / Class A : Orphans"""	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.1076T>C	14.37:g.91700319A>G	ENSP00000434045:p.Phe359Ser	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	42	11	0.261905	NM_001177676	Q13334|Q4VBB4|Q6IX34	Missense_Mutation	SNP	ENST00000531499.2	37	CCDS9894.2	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	4.035	0.004003	0.07866	0.01288	0.0	ENSG00000119714	ENST00000531499;ENST00000238699;ENST00000535815	T;T;T	0.61040	0.14;0.15;0.14	4.46	1.59	0.23543	.	0.406139	0.19168	N	0.121014	T	0.11324	0.0276	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16719	-1.0393	10	0.07175	T	0.84	.	4.0511	0.09796	0.2953:0.1741:0.5306:0.0	.	359;359	Q6NWR5;Q15743	.;OGR1_HUMAN	S	359;369;359	ENSP00000434045:F359S;ENSP00000238699:F369S;ENSP00000440797:F359S	ENSP00000238699:F369S	F	-	2	0	GPR68	90770072	.	.	0.005000	0.12908	0.002000	0.02628	.	.	-0.069000	0.12931	-0.227000	0.12334	TTC	A|0.995;G|0.005	0.005	strong		0.711	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2		
MTMR7	9108	hgsc.bcm.edu	37	8	17206588	17206588	+	Silent	SNP	G	G	A	rs2285291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17206588G>A	ENST00000180173.5	-	5	505	c.471C>T	c.(469-471)gtC>gtT	p.V157V	MTMR7_ENST00000523571.1_5'UTR|MTMR7_ENST00000521857.1_Silent_p.V157V	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	157	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)		AAGAGTCACAGACCTGTCACC	0.488													G|||	570	0.113818	0.0272	0.2046	5008	,	,		18749	0.2966		0.0686	False		,,,				2504	0.0245				p.V157V		Atlas-SNP	.											.	MTMR7	75	.	0			c.C471T						PASS	.	G		158,4248	106.9+/-145.3	0,158,2045	99.0	96.0	97.0		471	-5.0	0.9	8	dbSNP_100	97	360,8240	120.2+/-179.5	11,338,3951	no	coding-synonymous	MTMR7	NM_004686.4		11,496,5996	AA,AG,GG		4.186,3.586,3.9828		157/661	17206588	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	9108	exon5			GTCACAGACCTGT	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.471C>T	8.37:g.17206588G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_004686	A1L4K9|B4DG87|Q68DX4	Silent	SNP	ENST00000180173.5	37	CCDS34851.1																																																																																			G|0.923;A|0.077	0.077	strong		0.488	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
PXDNL	137902	hgsc.bcm.edu	37	8	52320786	52320786	+	Missense_Mutation	SNP	G	G	A	rs74731075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:52320786G>A	ENST00000356297.4	-	17	3498	c.3398C>T	c.(3397-3399)gCg>gTg	p.A1133V	PXDNL_ENST00000543296.1_Missense_Mutation_p.A1133V	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1133					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				ATCCACGGCCGCAGAATAAGC	0.547													G|||	131	0.0261581	0.0946	0.0072	5008	,	,		14026	0.0		0.001	False		,,,				2504	0.0				p.A1133V		Atlas-SNP	.											.	PXDNL	414	.	0			c.C3398T						PASS	.	G	VAL/ALA	264,3518		11,242,1638	73.0	79.0	77.0		3398	1.3	0.0	8	dbSNP_131	77	5,8231		0,5,4113	yes	missense	PXDNL	NM_144651.4	64	11,247,5751	AA,AG,GG		0.0607,6.9804,2.2383	benign	1133/1464	52320786	269,11749	1891	4118	6009	SO:0001583	missense	137902	exon17			ACGGCCGCAGAAT		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.3398C>T	8.37:g.52320786G>A	ENSP00000348645:p.Ala1133Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	51|51	0.023351648351648352|0.023351648351648352	48|48	0.0975609756097561|0.0975609756097561	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	0.006|0.006	-2.030686|-2.030686	0.00410|0.00410	0.069804|0.069804	6.07E-4|6.07E-4	ENSG00000147485|ENSG00000147485	ENST00000356297;ENST00000543296|ENST00000522933	T;T|.	0.69040|.	-0.37;-0.37|.	3.82|3.82	1.31|1.31	0.21738|0.21738	.|.	0.495534|.	0.16394|.	N|.	0.216355|.	T|T	0.00109|0.00109	0.0003|0.0003	N|N	0.00055|0.00055	-2.37|-2.37	0.25903|0.25903	N|N	0.983334|0.983334	B|.	0.11235|.	0.004|.	B|.	0.01281|.	0.0|.	T|T	0.35425|0.35425	-0.9789|-0.9789	10|5	0.02654|.	T|.	1|.	.|.	3.9194|3.9194	0.09237|0.09237	0.6521:0.2101:0.1378:0.0|0.6521:0.2101:0.1378:0.0	.|.	1133|.	A1KZ92|.	PXDNL_HUMAN|.	V|W	1133|252	ENSP00000348645:A1133V;ENSP00000444865:A1133V|.	ENSP00000348645:A1133V|.	A|R	-|-	2|1	0|2	PXDNL|PXDNL	52483339|52483339	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	6.058000|6.058000	0.71126|0.71126	-0.039000|-0.039000	0.13602|0.13602	-0.175000|-0.175000	0.13238|0.13238	GCG|CGG	G|0.973;A|0.027	0.027	strong		0.547	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
PAG1	55824	hgsc.bcm.edu	37	8	81897200	81897200	+	Silent	SNP	C	C	T	rs7006101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:81897200C>T	ENST00000220597.4	-	7	1397	c.687G>A	c.(685-687)tcG>tcA	p.S229S		NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	229					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			TTCTGTCCACCGAGGCATATT	0.488													C|||	704	0.140575	0.2852	0.0865	5008	,	,		20851	0.001		0.1083	False		,,,				2504	0.1605				p.S229S		Atlas-SNP	.											.	PAG1	39	.	0			c.G687A						PASS	.	C		1092,3314	394.2+/-329.2	141,810,1252	121.0	119.0	120.0		687	-11.1	0.0	8	dbSNP_116	120	849,7751	193.2+/-239.0	40,769,3491	no	coding-synonymous	PAG1	NM_018440.3		181,1579,4743	TT,TC,CC		9.8721,24.7844,14.9239		229/433	81897200	1941,11065	2203	4300	6503	SO:0001819	synonymous_variant	55824	exon7			GTCCACCGAGGCA	AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"""Csk-binding protein"", ""transmembrane adaptor protein PAG"""	605767	"""phosphoprotein associated with glycosphingolipid microdomains 1"""			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.687G>A	8.37:g.81897200C>T		Somatic	384	0	0		WXS	Illumina HiSeq	Phase_I	371	183	0.493261	NM_018440	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Silent	SNP	ENST00000220597.4	37	CCDS6227.1																																																																																			C|0.853;T|0.147	0.147	strong		0.488	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440	
MAPK7	5598	hgsc.bcm.edu	37	17	19285392	19285392	+	Silent	SNP	G	G	A	rs2233079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19285392G>A	ENST00000308406.5	+	5	2162	c.1776G>A	c.(1774-1776)gcG>gcA	p.A592A	MAPK7_ENST00000571657.1_Intron|MAPK7_ENST00000395602.4_Silent_p.A592A|MAPK7_ENST00000299612.7_Silent_p.A453A|MAPK7_ENST00000395604.3_Silent_p.A592A|MFAP4_ENST00000574313.2_5'Flank	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	592	May not be required for kinase activity; required to stimulate MEF2C activity. {ECO:0000250}.|Pro-rich.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|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 cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)			autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					ctgccccagcgccaacgccaa	0.657													G|||	165	0.0329473	0.118	0.013	5008	,	,		9722	0.0		0.0	False		,,,				2504	0.0				p.A592A		Atlas-SNP	.											.	MAPK7	72	.	0			c.G1776A						PASS	.	G	,,,	433,3955		29,375,1790	14.0	13.0	13.0		1776,1359,1776,1776	-8.4	0.0	17	dbSNP_98	13	9,8573		0,9,4282	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPK7	NM_002749.3,NM_139032.2,NM_139033.2,NM_139034.2	,,,	29,384,6072	AA,AG,GG		0.1049,9.8678,3.4079	,,,	592/817,453/678,592/817,592/817	19285392	442,12528	2194	4291	6485	SO:0001819	synonymous_variant	5598	exon5			CCCAGCGCCAACG	U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"""Mitogen-activated protein kinase cascade / Kinases"""	6880	protein-coding gene	gene with protein product	"""BMK1 kinase"", ""extracellular-signal-regulated kinase 5"""	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.1776G>A	17.37:g.19285392G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	200	114	0.57	NM_002749	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Silent	SNP	ENST00000308406.5	37	CCDS11206.1																																																																																			G|0.959;A|0.041	0.041	strong		0.657	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033	
OR8J3	81168	hgsc.bcm.edu	37	11	55904422	55904422	+	Missense_Mutation	SNP	A	A	G	rs114758947	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55904422A>G	ENST00000301529.1	-	1	772	c.773T>C	c.(772-774)aTg>aCg	p.M258T		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	258						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					CTGCAAATACATAAATAGCAT	0.428													A|||	88	0.0175719	0.0628	0.0058	5008	,	,		18131	0.0		0.001	False		,,,				2504	0.0				p.M258T		Atlas-SNP	.											.	OR8J3	112	.	0			c.T773C						PASS	.	A	THR/MET	235,4167	139.2+/-174.8	7,221,1973	138.0	133.0	135.0		773	2.1	0.5	11	dbSNP_132	135	2,8590	2.2+/-6.3	0,2,4294	yes	missense	OR8J3	NM_001004064.1	81	7,223,6267	GG,GA,AA		0.0233,5.3385,1.8239	probably-damaging	258/316	55904422	237,12757	2201	4296	6497	SO:0001583	missense	81168	exon1			AAATACATAAATA		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.773T>C	11.37:g.55904422A>G	ENSP00000301529:p.Met258Thr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	236	127	0.538136	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	37	CCDS31520.1	41	0.018772893772893772	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	7.537	0.659897	0.14645	0.053385	2.33E-4	ENSG00000167822	ENST00000301529	T	0.00164	8.64	3.27	2.11	0.27256	GPCR, rhodopsin-like superfamily (1);	0.136411	0.52532	D	0.000070	T	0.00039	0.0001	L	0.53561	1.675	0.09310	N	1	D	0.53619	0.961	P	0.62298	0.9	T	0.47169	-0.9138	10	0.72032	D	0.01	.	5.506	0.16854	0.6758:0.0:0.3242:0.0	.	258	Q8NGG0	OR8J3_HUMAN	T	258	ENSP00000301529:M258T	ENSP00000301529:M258T	M	-	2	0	OR8J3	55660998	0.000000	0.05858	0.453000	0.27007	0.065000	0.16274	-0.305000	0.08188	1.272000	0.44329	0.247000	0.18012	ATG	A|0.983;G|0.017	0.017	strong		0.428	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
GPR124	25960	hgsc.bcm.edu	37	8	37690615	37690615	+	Silent	SNP	G	G	A	rs61738775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:37690615G>A	ENST00000412232.2	+	9	1198	c.1185G>A	c.(1183-1185)ccG>ccA	p.P395P	GPR124_ENST00000315215.7_Silent_p.P395P	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	395					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			GGGGTGCCCCGGGCACCCGAG	0.682													G|||	321	0.0640974	0.2284	0.0159	5008	,	,		11914	0.005		0.002	False		,,,				2504	0.001				p.P395P		Atlas-SNP	.											.	GPR124	85	.	0			c.G1185A						PASS	.	G		846,3560	318.5+/-295.7	69,708,1426	41.0	47.0	45.0		1185	-10.2	0.3	8	dbSNP_129	45	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	GPR124	NM_032777.9		69,716,5718	AA,AG,GG		0.093,19.2011,6.5662		395/1339	37690615	854,12152	2203	4300	6503	SO:0001819	synonymous_variant	25960	exon9			TGCCCCGGGCACC	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17849	protein-coding gene	gene with protein product	"""tumor endothelial marker 5"""	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.1185G>A	8.37:g.37690615G>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	17	15	0.882353	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Silent	SNP	ENST00000412232.2	37	CCDS6097.2																																																																																			G|0.934;A|0.066	0.066	strong		0.682	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2		
RRP1	8568	hgsc.bcm.edu	37	21	45220483	45220483	+	Missense_Mutation	SNP	A	A	G	rs915770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45220483A>G	ENST00000497547.1	+	10	1094	c.977A>G	c.(976-978)aAa>aGa	p.K326R	RRP1_ENST00000471909.1_3'UTR	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)	p.K326R(1)		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)		CGTCTCTACAAAGTGATCCGG	0.537													A|||	1310	0.261581	0.3366	0.3012	5008	,	,		19266	0.2292		0.1581	False		,,,				2504	0.272				p.K326R		Atlas-SNP	.											RRP1,NS,carcinoma,0,1	RRP1	23	1	1	Substitution - Missense(1)	stomach(1)	c.A977G						PASS	.	A	ARG/LYS	1270,2840		202,866,987	53.0	56.0	55.0		977	5.2	1.0	21	dbSNP_86	55	1478,6904		139,1200,2852	yes	missense	RRP1	NM_003683.5	26	341,2066,3839	GG,GA,AA		17.633,30.9002,21.9981	possibly-damaging	326/462	45220483	2748,9744	2055	4191	6246	SO:0001583	missense	8568	exon10			TCTACAAAGTGAT	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.977A>G	21.37:g.45220483A>G	ENSP00000417464:p.Lys326Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_003683	A6NIB2	Missense_Mutation	SNP	ENST00000497547.1	37	CCDS42951.1	500	0.22893772893772893	163	0.3313008130081301	86	0.23756906077348067	134	0.23426573426573427	117	0.15435356200527706	A	17.93	3.509174	0.64410	0.309002	0.17633	ENSG00000160214	ENST00000497547;ENST00000400387	T	0.01215	5.16	5.2	5.2	0.72013	.	0.469084	0.25256	N	0.031994	T	0.00012	0.0000	L	0.52823	1.66	0.23906	P	0.99650116	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.994	T	0.56751	-0.7927	9	0.87932	D	0	.	11.4934	0.50394	1.0:0.0:0.0:0.0	rs915770;rs58923119;rs915770	326;326	B4DZM3;P56182	.;RRP1_HUMAN	R	326	ENSP00000417464:K326R	ENSP00000383237:K326R	K	+	2	0	RRP1	44044911	0.998000	0.40836	1.000000	0.80357	0.979000	0.70002	1.606000	0.36826	1.964000	0.57103	0.533000	0.62120	AAA	A|0.767;G|0.233	0.233	strong		0.537	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683	
USP50	373509	hgsc.bcm.edu	37	15	50836846	50836846	+	Silent	SNP	G	G	C	rs114737323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:50836846G>C	ENST00000532404.1	-	2	359	c.186C>G	c.(184-186)ctC>ctG	p.L62L	USP50_ENST00000530218.1_Intron	NM_203494.4	NP_987090.2	Q70EL3	UBP50_HUMAN	ubiquitin specific peptidase 50	62	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(5)	13				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)		AGATGCTGCAGAGACACTGTG	0.537													G|||	166	0.033147	0.121	0.0086	5008	,	,		16271	0.0		0.0	False		,,,				2504	0.0				p.L62L		Atlas-SNP	.											.	USP50	24	.	0			c.C186G						PASS	.	G		364,3704		20,324,1690	55.0	58.0	57.0		186	1.7	1.0	15	dbSNP_132	57	2,8376		0,2,4187	no	coding-synonymous	USP50	NM_203494.4		20,326,5877	CC,CG,GG		0.0239,8.9479,2.9407		62/335	50836846	366,12080	2034	4189	6223	SO:0001819	synonymous_variant	373509	exon2			GCTGCAGAGACAC	AI990110	CCDS53944.1	15q21.1	2008-02-05	2005-08-08			ENSG00000170236		"""Ubiquitin-specific peptidases"""	20079	protein-coding gene	gene with protein product			"""ubiquitin specific protease 50"""			12838346	Standard	NM_203494		Approved		uc021sky.1	Q70EL3		ENST00000532404.1:c.186C>G	15.37:g.50836846G>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_203494	E9PP86	Silent	SNP	ENST00000532404.1	37	CCDS53944.1																																																																																			G|0.957;C|0.043	0.043	strong		0.537	USP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395249.1		
PJA1	64219	hgsc.bcm.edu	37	X	68381912	68381912	+	Silent	SNP	G	G	A	rs3761646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:68381912G>A	ENST00000361478.1	-	2	1547	c.1170C>T	c.(1168-1170)ggC>ggT	p.G390G	PJA1_ENST00000374584.3_Silent_p.G202G|PJA1_ENST00000374571.4_Silent_p.G335G|PJA1_ENST00000374583.1_Silent_p.G390G|PJA1_ENST00000477231.1_5'Flank	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	390					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						CCCAGCTTTCGCCACTGGAGG	0.577													g|||	516	0.136689	0.053	0.2205	3775	,	,		12786	0.0774		0.1173	False		,,,				2504	0.0992				p.G390G		Atlas-SNP	.											.	PJA1	106	.	0			c.C1170T						PASS	.		,,	405,3430		20,295,70,1317,501	34.0	34.0	34.0		1005,606,1170	-6.7	0.0	X	dbSNP_107	34	1134,5593		78,681,297,1669,1574	no	coding-synonymous,coding-synonymous,coding-synonymous	PJA1	NM_001032396.2,NM_022368.4,NM_145119.3	,,	98,976,367,2986,2075	AA,AG,A,GG,G		16.8574,10.5606,14.5711	,,	335/589,202/456,390/644	68381912	1539,9023	2203	4299	6502	SO:0001819	synonymous_variant	64219	exon2			GCTTTCGCCACTG	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"""RING-type (C3HC4) zinc fingers"""	16648	protein-coding gene	gene with protein product		300420	"""praja 1"", ""praja ring finger 1"""			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.1170C>T	X.37:g.68381912G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Silent	SNP	ENST00000361478.1	37	CCDS14393.1																																																																																			G|0.863;0|0.003	.	strong		0.577	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119	
ZNF638	27332	hgsc.bcm.edu	37	2	71658541	71658541	+	Missense_Mutation	SNP	C	C	T	rs11542286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71658541C>T	ENST00000409544.1	+	26	6365	c.5735C>T	c.(5734-5736)gCg>gTg	p.A1912V	ZNF638_ENST00000264447.4_Missense_Mutation_p.A1912V|ZNF638_ENST00000409407.1_Missense_Mutation_p.A852V|ZNF638_ENST00000355812.3_3'UTR	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	208	0	0		WXS	Illumina HiSeq	Phase_I	199	199	1	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	
ADAM19	8728	hgsc.bcm.edu	37	5	156936364	156936364	+	Missense_Mutation	SNP	T	T	C	rs1422795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156936364T>C	ENST00000517905.1	-	9	894	c.850A>G	c.(850-852)Agt>Ggt	p.S284G	ADAM19_ENST00000257527.4_Missense_Mutation_p.S284G|ADAM19_ENST00000430702.2_Missense_Mutation_p.S17G|ADAM19_ENST00000394020.1_Missense_Mutation_p.S286G			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	284	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CGCCTCCAACTGAGAAAGGAC	0.483													T|||	2076	0.414537	0.6392	0.4438	5008	,	,		18036	0.126		0.3569	False		,,,				2504	0.4468				p.S284G		Atlas-SNP	.											.	ADAM19	216	.	0			c.A850G						PASS	.	T	GLY/SER	2552,1854	633.0+/-395.9	739,1074,390	101.0	96.0	98.0		850	1.3	0.5	5	dbSNP_88	98	3024,5576	465.5+/-366.5	521,1982,1797	yes	missense	ADAM19	NM_033274.3	56	1260,3056,2187	CC,CT,TT		35.1628,42.079,42.8725	possibly-damaging	284/919	156936364	5576,7430	2203	4300	6503	SO:0001583	missense	8728	exon9			TCCAACTGAGAAA	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"""ADAM metallopeptidase domain containing"""	197	protein-coding gene	gene with protein product	"""meltrin beta"""	603640	"""a disintegrin and metalloproteinase domain 19 (meltrin beta)"""			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.850A>G	5.37:g.156936364T>C	ENSP00000428654:p.Ser284Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	112	48	0.428571	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		826	0.3782051282051282	315	0.6402439024390244	158	0.43646408839779005	82	0.14335664335664336	271	0.3575197889182058	T	13.02	2.112287	0.37242	0.57921	0.351628	ENSG00000135074	ENST00000430702;ENST00000257527;ENST00000394020;ENST00000517905	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.39	1.33	0.21861	.	0.504141	0.21542	N	0.072867	T	0.00012	0.0000	L	0.42581	1.335	0.33665	P	0.38981600000000005	P;P	0.47545	0.897;0.682	B;B	0.39217	0.294;0.079	T	0.47018	-0.9149	9	0.33141	T	0.24	.	0.4223	0.00458	0.3419:0.1668:0.1317:0.3596	rs1422795;rs60215604;rs1422795	284;17	Q9H013-2;E9PD32	.;.	G	17;284;286;284	ENSP00000414088:S17G;ENSP00000257527:S284G;ENSP00000377588:S286G;ENSP00000428654:S284G	ENSP00000257527:S284G	S	-	1	0	ADAM19	156868942	0.000000	0.05858	0.470000	0.27216	0.961000	0.63080	0.027000	0.13621	0.411000	0.25702	0.533000	0.62120	AGT	T|0.592;C|0.408	0.408	strong		0.483	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274	
SERPINF2	5345	hgsc.bcm.edu	37	17	1657653	1657653	+	Missense_Mutation	SNP	G	G	A	rs1057335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1657653G>A	ENST00000324015.3	+	10	1378	c.1301G>A	c.(1300-1302)aGg>aAg	p.R434K	SERPINF2_ENST00000450523.2_Missense_Mutation_p.R370K|SERPINF2_ENST00000382061.4_Missense_Mutation_p.R434K	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	155	0	0		WXS	Illumina HiSeq	Phase_I	157	79	0.503185	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	
SLC36A2	153201	hgsc.bcm.edu	37	5	150696540	150696540	+	Silent	SNP	C	C	T	rs431240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150696540C>T	ENST00000335244.4	-	10	1419	c.1290G>A	c.(1288-1290)acG>acA	p.T430T	SLC36A2_ENST00000450886.1_Silent_p.T154T	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	430					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)	CTGAGTAGAACGTGGTGACCT	0.647													C|||	3373	0.673522	0.5862	0.683	5008	,	,		15210	0.8482		0.5348	False		,,,				2504	0.7474				p.T430T		Atlas-SNP	.											.	SLC36A2	71	.	0			c.G1290A						PASS	.	C		2614,1792	641.9+/-397.6	771,1072,360	72.0	62.0	65.0		1290	2.1	1.0	5	dbSNP_80	65	4539,4061	593.9+/-393.2	1187,2165,948	no	coding-synonymous	SLC36A2	NM_181776.2		1958,3237,1308	TT,TC,CC		47.2209,40.6718,45.0023		430/484	150696540	7153,5853	2203	4300	6503	SO:0001819	synonymous_variant	153201	exon10			GTAGAACGTGGTG	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.1290G>A	5.37:g.150696540C>T		Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	167	167	1	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Silent	SNP	ENST00000335244.4	37	CCDS4315.1																																																																																			C|0.410;T|0.590	0.590	strong		0.647	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1		
PPFIBP1	8496	hgsc.bcm.edu	37	12	27829369	27829369	+	Silent	SNP	T	T	C	rs35150305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27829369T>C	ENST00000318304.8	+	18	1753	c.1470T>C	c.(1468-1470)gcT>gcC	p.A490A	PPFIBP1_ENST00000542629.1_Silent_p.A459A|PPFIBP1_ENST00000228425.6_Silent_p.A473A|PPFIBP1_ENST00000537927.1_Silent_p.A337A	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	490					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)					AGGACAGAGCTCCGGCAGAAA	0.547													T|||	123	0.0245607	0.0915	0.0029	5008	,	,		17752	0.0		0.0	False		,,,				2504	0.0				p.A490A		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.T1470C						PASS	.	T	,,,	340,4066	176.2+/-205.4	9,322,1872	61.0	63.0	62.0		1011,1377,1419,1470	-2.5	0.0	12	dbSNP_126	62	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPFIBP1	NM_001198915.1,NM_001198916.1,NM_003622.3,NM_177444.2	,,,	9,325,6169	CC,CT,TT		0.0349,7.7167,2.6372	,,,	337/859,459/981,473/1006,490/1012	27829369	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	8496	exon18			CAGAGCTCCGGCA	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.1470T>C	12.37:g.27829369T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	130	71	0.546154	NM_177444	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	37	CCDS55812.1																																																																																			T|0.978;C|0.022	0.022	strong		0.547	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
DRD3	1814	hgsc.bcm.edu	37	3	113890789	113890789	+	Silent	SNP	T	T	C	rs3732783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113890789T>C	ENST00000460779.1	-	3	340	c.51A>G	c.(49-51)gcA>gcG	p.A17A	DRD3_ENST00000295881.7_Silent_p.A17A|DRD3_ENST00000467632.1_Silent_p.A17A|DRD3_ENST00000383673.2_Silent_p.A17A	NM_001282563.1	NP_001269492.1	P35462	DRD3_HUMAN	dopamine receptor D3	17					acid secretion (GO:0046717)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|arachidonic acid secretion (GO:0050482)|behavioral response to cocaine (GO:0048148)|cellular calcium ion homeostasis (GO:0006874)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric emptying (GO:0035483)|learning (GO:0007612)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of sodium:proton antiporter activity (GO:0032416)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of mitosis (GO:0045840)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of cAMP metabolic process (GO:0030814)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|regulation of dopamine secretion (GO:0014059)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of lipid metabolic process (GO:0019216)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of multicellular organism growth (GO:0040014)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to morphine (GO:0043278)|social behavior (GO:0035176)|synaptic transmission, dopaminergic (GO:0001963)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)	36					Amisulpride(DB06288)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Domperidone(DB01184)|Dopamine(DB00988)|Haloperidol(DB00502)|Iloperidone(DB04946)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pimozide(DB01100)|Pramipexole(DB00413)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sulpiride(DB00391)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TGGAGTTCTCTGCCCCACAGG	0.617													C|||	490	0.0978435	0.1377	0.098	5008	,	,		14701	0.0149		0.0805	False		,,,				2504	0.1472				p.A17A		Atlas-SNP	.											.	DRD3	76	.	0			c.A51G						PASS	.	C	,	496,3910		32,432,1739	31.0	28.0	29.0		51,51	-3.7	0.0	3	dbSNP_107	29	461,8139		13,435,3852	no	coding-synonymous,coding-synonymous	DRD3	NM_000796.3,NM_033663.3	,	45,867,5591	CC,CT,TT		5.3605,11.2574,7.3581	,	17/401,17/368	113890789	957,12049	2203	4300	6503	SO:0001819	synonymous_variant	1814	exon2			GTTCTCTGCCCCA		CCDS2978.1, CCDS33829.1	3q13.3	2012-08-08			ENSG00000151577	ENSG00000151577		"""GPCR / Class A : Dopamine receptors"""	3024	protein-coding gene	gene with protein product		126451				1916765	Standard	XM_005247171		Approved		uc003ebc.1	P35462	OTTHUMG00000159334	ENST00000460779.1:c.51A>G	3.37:g.113890789T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_033663	A1A4V5|Q4VBM8	Silent	SNP	ENST00000460779.1	37	CCDS2978.1																																																																																			T|0.920;C|0.080	0.080	strong		0.617	DRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354699.1	NM_000796.3	
OAS1	4938	hgsc.bcm.edu	37	12	113357209	113357209	+	Missense_Mutation	SNP	G	G	A	rs1131476	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113357209G>A	ENST00000202917.5	+	6	1317	c.1054G>A	c.(1054-1056)Gca>Aca	p.A352T	RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Intron|OAS1_ENST00000551241.1_Intron	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	352			A -> T (in dbSNP:rs1131476). {ECO:0000269|PubMed:17024523, ECO:0000269|PubMed:2416561, ECO:0000269|Ref.7}.		cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						AAGCAACAGTGCAGACGATGA	0.488													G|||	3945	0.78774	0.9728	0.7954	5008	,	,		25230	0.745		0.6551	False		,,,				2504	0.7127				p.A352T		Atlas-SNP	.											.	OAS1	128	.	0			c.G1054A						PASS	.	G	,THR/ALA	4067,339	795.3+/-415.3	1875,317,11	85.0	84.0	84.0		,1054	-1.4	0.0	12	dbSNP_86	84	5555,3045	662.1+/-401.9	1809,1937,554	yes	intron,missense	OAS1	NM_001032409.1,NM_016816.2	,58	3684,2254,565	AA,AG,GG		35.407,7.6941,26.0188	,benign	,352/401	113357209	9622,3384	2203	4300	6503	SO:0001583	missense	4938	exon6			AACAGTGCAGACG	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"""2',5'-oligoadenylate synthetase 1 (40-46 kD)"""	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.1054G>A	12.37:g.113357209G>A	ENSP00000202917:p.Ala352Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_016816	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	37	CCDS41838.1	1710	0.782967032967033	483	0.9817073170731707	280	0.7734806629834254	447	0.7814685314685315	500	0.6596306068601583	G	8.157	0.788731	0.16258	0.923059	0.64593	ENSG00000089127	ENST00000202917	T	0.05025	3.51	2.92	-1.38	0.09027	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.14615	-1.0466	8	0.18710	T	0.47	.	0.5426	0.00648	0.2483:0.1931:0.3612:0.1975	rs1131476;rs3177979;rs3191419;rs17237660;rs17413825;rs52792411;rs57784701;rs3177979	352	P00973	OAS1_HUMAN	T	352	ENSP00000202917:A352T	ENSP00000202917:A352T	A	+	1	0	OAS1	111841592	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.503000	0.00965	-0.316000	0.08690	0.557000	0.71058	GCA	A|0.746;C|0.000;G|0.253;N|0.000;T|0.000	0.746	strong		0.488	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2		
KIAA0895L	653319	hgsc.bcm.edu	37	16	67210855	67210855	+	Missense_Mutation	SNP	G	G	C	rs61733789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67210855G>C	ENST00000290881.7	-	8	2201	c.1275C>G	c.(1273-1275)caC>caG	p.H425Q	KIAA0895L_ENST00000563831.2_5'UTR|KIAA0895L_ENST00000561621.1_3'UTR|KIAA0895L_ENST00000563902.1_Missense_Mutation_p.H425Q			Q68EN5	K895L_HUMAN	KIAA0895-like	425										breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1)	17						GGGGCCGCAGGTGGTCCACAT	0.627													G|||	334	0.0666933	0.1929	0.0086	5008	,	,		17791	0.003		0.003	False		,,,				2504	0.0685				p.H425Q		Atlas-SNP	.											.	KIAA0895L	32	.	0			c.C1275G						PASS	.	G	GLN/HIS	589,3435		38,513,1461	61.0	66.0	64.0		1275	-3.4	1.0	16	dbSNP_129	64	8,8370		0,8,4181	yes	missense	KIAA0895L	NM_001040715.1	24	38,521,5642	CC,CG,GG		0.0955,14.6372,4.8137	benign	425/472	67210855	597,11805	2012	4189	6201	SO:0001583	missense	653319	exon7			CCGCAGGTGGTCC	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.1275C>G	16.37:g.67210855G>C	ENSP00000290881:p.His425Gln	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_001040715	A2VCS8|Q8N3H9|Q8NAQ5|Q96IE5	Missense_Mutation	SNP	ENST00000290881.7	37	CCDS42177.1	101	0.04624542124542125	95	0.19308943089430894	4	0.011049723756906077	2	0.0034965034965034965	0	0.0	G	11.37	1.618724	0.28801	0.146372	9.55E-4	ENSG00000196123	ENST00000290881	.	.	.	4.59	-3.36	0.04913	.	0.520084	0.22311	N	0.061738	T	0.00012	0.0000	N	0.11560	0.145	0.43271	P	0.004773000000000027	B;B	0.10296	0.001;0.003	B;B	0.11329	0.006;0.005	T	0.23868	-1.0176	8	0.17369	T	0.5	-13.5417	1.6114	0.02694	0.2829:0.364:0.2227:0.1304	rs61733789	425;270	Q68EN5;Q68EN5-3	K895L_HUMAN;.	Q	425	.	ENSP00000290881:H425Q	H	-	3	2	KIAA0895L	65768356	0.060000	0.20803	0.971000	0.41717	0.993000	0.82548	-0.536000	0.06135	-0.345000	0.08325	0.555000	0.69702	CAC	G|0.923;C|0.077	0.077	strong		0.627	KIAA0895L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421193.4	NM_001040715	
THNSL1	79896	hgsc.bcm.edu	37	10	25312689	25312689	+	Silent	SNP	A	A	G	rs4748997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:25312689A>G	ENST00000524413.1	+	3	884	c.537A>G	c.(535-537)ggA>ggG	p.G179G	THNSL1_ENST00000376356.4_Silent_p.G179G			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	179						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	AGAATTCTGGAACATCTATGA	0.358													A|||	1542	0.307907	0.0749	0.4308	5008	,	,		19714	0.4851		0.2714	False		,,,				2504	0.3906				p.G179G		Atlas-SNP	.											.	THNSL1	70	.	0			c.A537G						PASS	.	A		410,3996	190.2+/-216.2	26,358,1819	58.0	61.0	60.0		537	0.7	0.6	10	dbSNP_111	60	2451,6149	396.6+/-345.4	334,1783,2183	no	coding-synonymous	THNSL1	NM_024838.4		360,2141,4002	GG,GA,AA		28.5,9.3055,21.9975		179/744	25312689	2861,10145	2203	4300	6503	SO:0001819	synonymous_variant	79896	exon3			TTCTGGAACATCT	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"""threonine synthase-like 1 (bacterial)"""			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.537A>G	10.37:g.25312689A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_024838	B3KWL1|D3DRV3|Q5VV21	Silent	SNP	ENST00000524413.1	37	CCDS7147.1																																																																																			A|0.746;G|0.254	0.254	strong		0.358	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
OAS2	4939	hgsc.bcm.edu	37	12	113424893	113424893	+	Silent	SNP	C	C	G	rs2072138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113424893C>G	ENST00000342315.4	+	2	442	c.228C>G	c.(226-228)acC>acG	p.T76T	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Silent_p.T76T|OAS2_ENST00000449768.2_Silent_p.T76T	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	76	OAS domain 1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CCGATGGTACCCTTGTCCTCT	0.463													C|||	1097	0.21905	0.2141	0.3401	5008	,	,		19158	0.0863		0.2753	False		,,,				2504	0.2188				p.T76T	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											OAS2_ENST00000449768,NS,carcinoma,+1,1	OAS2	86	1	0			c.C228G						PASS	.	C	,,	1037,3369	379.7+/-323.4	117,803,1283	111.0	104.0	106.0		228,228,228	1.2	0.0	12	dbSNP_96	106	2475,6125	406.4+/-348.8	353,1769,2178	no	coding-synonymous,coding-synonymous,coding-synonymous	OAS2	NM_001032731.1,NM_002535.2,NM_016817.2	,,	470,2572,3461	GG,GC,CC		28.7791,23.5361,27.0029	,,	76/173,76/688,76/720	113424893	3512,9494	2203	4300	6503	SO:0001819	synonymous_variant	4939	exon2			TGGTACCCTTGTC	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.228C>G	12.37:g.113424893C>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	175	91	0.52	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Silent	SNP	ENST00000342315.4	37	CCDS31906.1																																																																																			C|0.753;G|0.247	0.247	strong		0.463	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1		
BANK1	55024	hgsc.bcm.edu	37	4	102965016	102965016	+	Missense_Mutation	SNP	A	A	G	rs140337324		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:102965016A>G	ENST00000322953.4	+	11	2195	c.1921A>G	c.(1921-1923)Aga>Gga	p.R641G	BANK1_ENST00000508653.1_Missense_Mutation_p.R508G|BANK1_ENST00000444316.2_Missense_Mutation_p.R611G|BANK1_ENST00000428908.1_Missense_Mutation_p.R508G|BANK1_ENST00000504592.1_Missense_Mutation_p.R626G	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	641					B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		AAAGACAGCCAGAAGACAATC	0.333													A|||	1	0.000199681	0.0008	0.0	5008	,	,		16410	0.0		0.0	False		,,,				2504	0.0				p.R641G		Atlas-SNP	.											.	BANK1	95	.	0			c.A1921G						PASS	.	A	GLY/ARG,GLY/ARG,GLY/ARG	7,4399	12.9+/-30.5	0,7,2196	130.0	137.0	135.0		1831,1522,1921	2.8	1.0	4	dbSNP_134	135	0,8598		0,0,4299	yes	missense,missense,missense	BANK1	NM_001083907.2,NM_001127507.2,NM_017935.4	125,125,125	0,7,6495	GG,GA,AA		0.0,0.1589,0.0538	probably-damaging,probably-damaging,probably-damaging	611/756,508/653,641/786	102965016	7,12997	2203	4299	6502	SO:0001583	missense	55024	exon11			ACAGCCAGAAGAC	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"""Ankyrin repeat domain containing"""	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.1921A>G	4.37:g.102965016A>G	ENSP00000320509:p.Arg641Gly	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	15.88	2.962531	0.53400	0.001589	0.0	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48	5.4	2.84	0.33178	.	0.152125	0.42172	D	0.000760	T	0.61739	0.2371	L	0.47716	1.5	0.27143	N	0.961604	P;D;D	0.89917	0.951;1.0;1.0	P;D;D	0.87578	0.631;0.998;0.998	T	0.53865	-0.8378	10	0.44086	T	0.13	.	9.7001	0.40180	0.6632:0.3368:0.0:0.0	.	508;641;626	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	G	626;641;508;508;611	ENSP00000421443:R626G;ENSP00000320509:R641G;ENSP00000412748:R508G;ENSP00000422314:R508G;ENSP00000388817:R611G	ENSP00000320509:R641G	R	+	1	2	BANK1	103184039	0.998000	0.40836	0.999000	0.59377	0.930000	0.56654	0.952000	0.29149	0.311000	0.23014	0.402000	0.26972	AGA	A|0.999;G|0.001	0.001	strong		0.333	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	
NIM1K	167359	hgsc.bcm.edu	37	5	43277283	43277283	+	Silent	SNP	G	G	A	rs61734291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:43277283G>A	ENST00000512796.1	+	3	1916	c.417G>A	c.(415-417)gtG>gtA	p.V139V	NIM1_ENST00000326035.2_Silent_p.V139V			Q8IY84	NIM1_HUMAN		139	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)										TTTACGAAGTGGTGGAGACCC	0.507													A|||	201	0.0401358	0.1437	0.0159	5008	,	,		20135	0.0		0.0	False		,,,				2504	0.0				p.V139V		Atlas-SNP	.											.	.	.	.	0			c.G417A						PASS	.	A		468,3938	783.5+/-414.6	26,416,1761	103.0	98.0	100.0		417	-8.7	0.5	5	dbSNP_129	100	4,8596	819.2+/-406.8	0,4,4296	no	coding-synonymous	NIM1	NM_153361.2		26,420,6057	AA,AG,GG		0.0465,10.6219,3.6291		139/437	43277283	472,12534	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			CGAAGTGGTGGAG																												ENST00000512796.1:c.417G>A	5.37:g.43277283G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_153361	B3KVM1	Silent	SNP	ENST00000512796.1	37	CCDS3943.1																																																																																			G|0.965;A|0.035	0.035	strong		0.507	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1		
PSRC1	84722	hgsc.bcm.edu	37	1	109824361	109824361	+	Silent	SNP	A	A	C	rs11800211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109824361A>C	ENST00000438534.2	-	4	537	c.399T>G	c.(397-399)tcT>tcG	p.S133S	PSRC1_ENST00000369907.3_Silent_p.S133S|PSRC1_ENST00000409138.2_Silent_p.S133S|PSRC1_ENST00000369909.2_Silent_p.S133S|PSRC1_ENST00000369904.3_Silent_p.S133S|PSRC1_ENST00000409267.1_Silent_p.S133S|PSRC1_ENST00000369903.2_Silent_p.S133S	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	133	4 X 4 AA repeats of P-X-X-P.				microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		TCCGCGTCAAAGAGTTCACAG	0.627													A|||	250	0.0499201	0.1831	0.0101	5008	,	,		18059	0.0		0.001	False		,,,				2504	0.0				p.S133S		Atlas-SNP	.											.	PSRC1	12	.	0			c.T399G						PASS	.	A	,,	768,3638	311.9+/-292.3	61,646,1496	59.0	62.0	61.0		399,399,399	0.7	0.9	1	dbSNP_120	61	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	PSRC1	NM_001005290.3,NM_001032291.2,NM_032636.7	,,	61,654,5788	CC,CA,AA		0.093,17.4308,5.9665	,,	133/311,133/334,133/334	109824361	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	84722	exon4			CGTCAAAGAGTTC		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"""differential display and activated by p53"""	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.399T>G	1.37:g.109824361A>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	146	83	0.568493	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Silent	SNP	ENST00000438534.2	37																																																																																				A|0.938;C|0.062	0.062	strong		0.627	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636	
KLHL26	55295	hgsc.bcm.edu	37	19	18778879	18778879	+	Silent	SNP	C	C	T	rs79044993	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18778879C>T	ENST00000300976.4	+	3	762	c.672C>T	c.(670-672)atC>atT	p.I224I	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	224	BACK.									breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						GTGCCGAGATCGACCTGTTCC	0.677													C|||	49	0.00978435	0.034	0.0043	5008	,	,		14950	0.0		0.001	False		,,,				2504	0.0				p.I224I		Atlas-SNP	.											.	KLHL26	43	.	0			c.C672T						PASS	.	C		121,4285	89.2+/-127.9	1,119,2083	38.0	38.0	38.0		672	-8.3	0.9	19	dbSNP_131	38	4,8592	3.7+/-12.6	0,4,4294	no	coding-synonymous	KLHL26	NM_018316.1		1,123,6377	TT,TC,CC		0.0465,2.7463,0.9614		224/616	18778879	125,12877	2203	4298	6501	SO:0001819	synonymous_variant	55295	exon3			CGAGATCGACCTG		CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"""Kelch-like"", ""BTB/POZ domain containing"""	25623	protein-coding gene	gene with protein product			"""kelch-like 26 (Drosophila)"""				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.672C>T	19.37:g.18778879C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.988;T|0.012	0.012	strong		0.677	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316	
AHRR	57491	hgsc.bcm.edu	37	5	433056	433056	+	Missense_Mutation	SNP	G	G	T	rs2303738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:433056G>T	ENST00000505113.1	+	10	1162	c.1118G>T	c.(1117-1119)gGc>gTc	p.G373V	AHRR_ENST00000506456.1_Missense_Mutation_p.G229V|AHRR_ENST00000512529.1_Missense_Mutation_p.G219V|AHRR_ENST00000316418.5_Missense_Mutation_p.G391V	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	373			G -> V (in dbSNP:rs2303738).		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)			CCCAAGGGGGGCTCAGGGTAA	0.647													G|||	173	0.0345447	0.053	0.0692	5008	,	,		16409	0.0208		0.0119	False		,,,				2504	0.0225				p.G391V		Atlas-SNP	.											.	AHRR	67	.	0			c.G1172T						PASS	.	G	VAL/GLY,VAL/GLY	146,3678		4,138,1770	13.0	14.0	14.0		1118,1172	-0.8	0.0	5	dbSNP_100	14	105,8089		0,105,3992	yes	missense,missense	AHRR	NM_001242412.1,NM_020731.4	109,109	4,243,5762	TT,TG,GG		1.2814,3.818,2.0885	benign,benign	373/702,391/720	433056	251,11767	1912	4097	6009	SO:0001583	missense	57491	exon11			AGGGGGGCTCAGG	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.1118G>T	5.37:g.433056G>T	ENSP00000424601:p.Gly373Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_020731	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	74	0.03388278388278388	27	0.054878048780487805	22	0.06077348066298342	15	0.026223776223776224	10	0.013192612137203167	G	5.002	0.186029	0.09495	0.03818	0.012814	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000506456	T;T;T;T	0.21031	2.35;2.35;2.04;2.03	4.46	-0.839	0.10759	.	1.832210	0.02893	N	0.134457	T	0.00998	0.0033	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.24083	-1.0170	10	0.44086	T	0.13	.	4.6987	0.12816	0.0:0.4127:0.3069:0.2804	rs2303738;rs2303738	229;373;391	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	V	373;391;219;229	ENSP00000424601:G373V;ENSP00000323816:G391V;ENSP00000424880:G219V;ENSP00000426932:G229V	ENSP00000323816:G391V	G	+	2	0	AHRR	486056	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.073000	0.14640	-0.284000	0.09102	-0.281000	0.10026	GGC	G|0.971;T|0.029	0.029	strong		0.647	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914000	31914000	+	Silent	SNP	T	T	A	rs1023364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31914000T>A	ENST00000334046.5	-	1	183	c.153A>T	c.(151-153)ggA>ggT	p.G51G		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	51						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						AGAATCCATATCCTTCACGGC	0.483													t|||	3745	0.747804	0.8033	0.7277	5008	,	,		16063	0.7024		0.7117	False		,,,				2504	0.771				p.G51G		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.A153T						PASS	.	T		3448,958	729.0+/-410.0	1350,748,105	109.0	120.0	116.0		153	-1.5	0.0	21	dbSNP_86	116	6103,2497	688.9+/-404.3	2167,1769,364	no	coding-synonymous	KRTAP19-6	NM_181612.2		3517,2517,469	AA,AT,TT		29.0349,21.7431,26.5647		51/59	31914000	9551,3455	2203	4300	6503	SO:0001819	synonymous_variant	337973	exon1			TCCATATCCTTCA	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"""Keratin associated proteins"""	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.153A>T	21.37:g.31914000T>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_181612	Q3LI71	Silent	SNP	ENST00000334046.5	37	CCDS13598.1																																																																																			T|0.271;A|0.729	0.729	strong		0.483	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4		
ALPPL2	251	hgsc.bcm.edu	37	2	233271852	233271852	+	Silent	SNP	C	C	T	rs61730280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233271852C>T	ENST00000295453.3	+	2	205	c.153C>T	c.(151-153)gcC>gcT	p.A51A		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	51					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		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)	Amifostine(DB01143)	CACAGACAGCCGCCAAGAACC	0.672													c|||	45	0.00898562	0.034	0.0	5008	,	,		15470	0.0		0.0	False		,,,				2504	0.0				p.A51A		Atlas-SNP	.											.	ALPPL2	36	.	0			c.C153T						PASS	.	C		143,4263	100.7+/-139.4	0,143,2060	67.0	81.0	76.0		153	-2.5	0.2	2	dbSNP_129	76	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ALPPL2	NM_031313.2		0,145,6358	TT,TC,CC		0.0233,3.2456,1.1149		51/533	233271852	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	251	exon2			GACAGCCGCCAAG	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.153C>T	2.37:g.233271852C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Silent	SNP	ENST00000295453.3	37	CCDS2491.1																																																																																			C|0.990;T|0.010	0.010	strong		0.672	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313	
OR2T6	254879	hgsc.bcm.edu	37	1	248551560	248551560	+	Silent	SNP	C	C	T	rs954474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248551560C>T	ENST00000355728.2	+	1	651	c.651C>T	c.(649-651)tcC>tcT	p.S217S		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGACTGCATCCTACACCAGGA	0.522													c|||	1471	0.29373	0.2247	0.2867	5008	,	,		22601	0.4365		0.175	False		,,,				2504	0.3671				p.S217S		Atlas-SNP	.											OR2T6,rectum,carcinoma,+1,2	OR2T6	101	2	0			c.C651T						PASS	.	C		988,3418	369.1+/-318.9	120,748,1335	295.0	225.0	249.0		651	3.2	0.7	1	dbSNP_86	249	1286,7314	255.4+/-280.3	90,1106,3104	no	coding-synonymous	OR2T6	NM_001005471.1		210,1854,4439	TT,TC,CC		14.9535,22.424,17.4842		217/309	248551560	2274,10732	2203	4300	6503	SO:0001819	synonymous_variant	254879	exon1			TGCATCCTACACC	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"""GPCR / Class A : Olfactory receptors"""	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.651C>T	1.37:g.248551560C>T		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	291	141	0.484536	NM_001005471	A6NE36	Silent	SNP	ENST00000355728.2	37	CCDS31114.1																																																																																			C|0.780;T|0.220	0.220	strong		0.522	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471	
ZNF175	7728	hgsc.bcm.edu	37	19	52090671	52090671	+	Missense_Mutation	SNP	T	T	A	rs60097262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52090671T>A	ENST00000262259.2	+	5	1445	c.1087T>A	c.(1087-1089)Tat>Aat	p.Y363N	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	363			Y -> N (in dbSNP:rs60097262).		defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		AAAGAAGCCCTATAAATGCCA	0.398													T|||	100	0.0199681	0.0711	0.0086	5008	,	,		22349	0.0		0.0	False		,,,				2504	0.0				p.Y363N		Atlas-SNP	.											.	ZNF175	65	.	0			c.T1087A						PASS	.	T	ASN/TYR	232,4174	138.4+/-174.2	5,222,1976	105.0	109.0	108.0		1087	0.1	1.0	19	dbSNP_129	108	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF175	NM_007147.2	143	5,223,6275	AA,AT,TT		0.0116,5.2655,1.7915	benign	363/712	52090671	233,12773	2203	4300	6503	SO:0001583	missense	7728	exon5			AAGCCCTATAAAT	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"""Zinc fingers, C2H2-type"", ""-"""	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.1087T>A	19.37:g.52090671T>A	ENSP00000262259:p.Tyr363Asn	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	130	56	0.430769	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	37	CCDS12837.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	T	10.98	1.503898	0.26949	0.052655	1.16E-4	ENSG00000105497	ENST00000262259	T	0.25749	1.78	2.3	0.113	0.14631	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03520	0.0101	M	0.89030	3	0.80722	D	1	P	0.41041	0.736	B	0.37304	0.246	T	0.02437	-1.1159	9	0.87932	D	0	.	4.9985	0.14253	0.0:0.4369:0.0:0.5631	rs60097262;rs61736481	363	Q9Y473	ZN175_HUMAN	N	363	ENSP00000262259:Y363N	ENSP00000262259:Y363N	Y	+	1	0	ZNF175	56782483	0.001000	0.12720	0.972000	0.41901	0.872000	0.50106	1.063000	0.30567	0.020000	0.15106	0.460000	0.39030	TAT	T|0.983;A|0.017	0.017	strong		0.398	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147	
MIS18BP1	55320	hgsc.bcm.edu	37	14	45711594	45711594	+	Silent	SNP	T	T	C	rs1266209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45711594T>C	ENST00000310806.4	-	4	1244	c.786A>G	c.(784-786)aaA>aaG	p.K262K	MIS18BP1_ENST00000492652.1_5'Flank	NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	262					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)			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						CCTTTTTGGATTTAGTGGTTG	0.343													C|||	1444	0.288339	0.6528	0.1916	5008	,	,		17981	0.1389		0.1243	False		,,,				2504	0.1871				p.K262K		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.A786G						PASS	.	C		2327,2077	571.1+/-383.0	627,1073,502	83.0	89.0	87.0		786	-2.0	0.0	14	dbSNP_87	87	941,7659	774.5+/-407.7	50,841,3409	no	coding-synonymous	MIS18BP1	NM_018353.4		677,1914,3911	CC,CT,TT		10.9419,47.1617,25.1307		262/1133	45711594	3268,9736	2202	4300	6502	SO:0001819	synonymous_variant	55320	exon4			TTTGGATTTAGTG	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.786A>G	14.37:g.45711594T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	133	54	0.406015	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Silent	SNP	ENST00000310806.4	37	CCDS9684.1																																																																																			T|0.738;C|0.262	0.262	strong		0.343	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2		
CCDC15	80071	hgsc.bcm.edu	37	11	124863136	124863136	+	Silent	SNP	C	C	A	rs7951202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124863136C>A	ENST00000344762.5	+	11	2470	c.2211C>A	c.(2209-2211)ccC>ccA	p.P737P	CCDC15_ENST00000529051.1_Silent_p.P737P	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	737						centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		CTGGAGTGCCCTTGGTATGTT	0.358													A|||	1437	0.286941	0.4705	0.1801	5008	,	,		21131	0.1935		0.1958	False		,,,				2504	0.3047				p.P737P		Atlas-SNP	.											.	CCDC15	134	.	0			c.C2211A						PASS	.	A		1594,2086		362,870,608	69.0	64.0	65.0		2211	-7.2	0.0	11	dbSNP_116	65	1643,6523		170,1303,2610	no	coding-synonymous	CCDC15	NM_025004.2		532,2173,3218	AA,AC,CC		20.12,43.3152,27.3257		737/952	124863136	3237,8609	1840	4083	5923	SO:0001819	synonymous_variant	80071	exon11			AGTGCCCTTGGTA	BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.2211C>A	11.37:g.124863136C>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	NM_025004	Q9H8U7	Silent	SNP	ENST00000344762.5	37	CCDS44756.1																																																																																			C|0.719;A|0.281	0.281	strong		0.358	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
OR2B2	81697	hgsc.bcm.edu	37	6	27879093	27879093	+	Silent	SNP	G	G	A	rs73392698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27879093G>A	ENST00000303324.2	-	1	1081	c.1005C>T	c.(1003-1005)tcC>tcT	p.S335S		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	335						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						GACAACTTGCGGAGAAGTTAG	0.318													G|||	86	0.0171725	0.0582	0.0101	5008	,	,		18973	0.0		0.002	False		,,,				2504	0.0				p.S335S		Atlas-SNP	.											.	OR2B2	54	.	0			c.C1005T						PASS	.	G		226,4180	133.3+/-169.7	3,220,1980	81.0	84.0	83.0		1005	-2.2	0.0	6	dbSNP_130	83	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	OR2B2	NM_033057.2		3,225,6275	AA,AG,GG		0.0581,5.1294,1.7761		335/358	27879093	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	81697	exon1			ACTTGCGGAGAAG	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.1005C>T	6.37:g.27879093G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Silent	SNP	ENST00000303324.2	37	CCDS4641.1																																																																																			G|0.984;A|0.016	0.016	strong		0.318	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1		
PGLYRP2	114770	hgsc.bcm.edu	37	19	15580694	15580694	+	Missense_Mutation	SNP	G	G	A	rs61734899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15580694G>A	ENST00000340880.4	-	4	1870	c.1390C>T	c.(1390-1392)Cac>Tac	p.H464Y	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.H464Y	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	464					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)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|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)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						CCCACCCAGTGCCAGCCGCGT	0.716													G|||	124	0.0247604	0.0484	0.0058	5008	,	,		13687	0.006		0.008	False		,,,				2504	0.0429				p.H464Y		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.C1390T						PASS	.	G	TYR/HIS	161,4189		2,157,2016	11.0	15.0	14.0		1390	2.9	1.0	19	dbSNP_129	14	65,8451		0,65,4193	yes	missense	PGLYRP2	NM_052890.3	83	2,222,6209	AA,AG,GG		0.7633,3.7011,1.7566	benign	464/577	15580694	226,12640	2175	4258	6433	SO:0001583	missense	114770	exon4			CCCAGTGCCAGCC	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.1390C>T	19.37:g.15580694G>A	ENSP00000345968:p.His464Tyr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	61	24	0.393443	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	34	0.015567765567765568	21	0.042682926829268296	3	0.008287292817679558	2	0.0034965034965034965	8	0.010554089709762533	G	12.80	2.046263	0.36085	0.037011	0.007633	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.17213	2.29;2.29	5.04	2.91	0.33838	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.380248	0.27554	N	0.018848	T	0.03564	0.0102	M	0.66378	2.025	0.35512	D	0.80071	B;B	0.09022	0.001;0.002	B;B	0.13407	0.008;0.009	T	0.08249	-1.0731	10	0.35671	T	0.21	-13.9263	4.8686	0.13620	0.1811:0.0:0.6507:0.1682	.	464;464	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	Y	464	ENSP00000345968:H464Y;ENSP00000292609:H464Y	ENSP00000292609:H464Y	H	-	1	0	PGLYRP2	15441694	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.700000	0.25601	0.540000	0.28808	-0.448000	0.05591	CAC	G|0.983;A|0.017	0.017	strong		0.716	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
SLC4A11	83959	hgsc.bcm.edu	37	20	3209254	3209254	+	Silent	SNP	G	G	A	rs139086376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3209254G>A	ENST00000380056.3	-	17	2387	c.2340C>T	c.(2338-2340)ccC>ccT	p.P780P	SLC4A11_ENST00000539553.2_Silent_p.P764P|SLC4A11_ENST00000380059.3_Silent_p.P807P|SLC4A11_ENST00000488544.1_5'Flank	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	780	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)			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						GCACGGGCTTGGGGATCCACT	0.652													G|||	31	0.0061901	0.0219	0.0029	5008	,	,		17235	0.0		0.0	False		,,,				2504	0.0				p.P807P	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.C2421T						PASS	.	G	,,	78,4328	65.8+/-103.3	0,78,2125	75.0	69.0	71.0		2292,2421,2340	4.0	1.0	20	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	,,	0,79,6424	AA,AG,GG		0.0116,1.7703,0.6074	,,	764/876,807/919,780/892	3209254	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	83959	exon18			GGGCTTGGGGATC	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.2340C>T	20.37:g.3209254G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Silent	SNP	ENST00000380056.3	37	CCDS13052.1																																																																																			G|0.994;A|0.006	0.006	strong		0.652	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
PDE3B	5140	hgsc.bcm.edu	37	11	14810762	14810762	+	Silent	SNP	A	A	G	rs4757268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:14810762A>G	ENST00000282096.4	+	4	1742	c.1389A>G	c.(1387-1389)agA>agG	p.R463R	PDE3B_ENST00000455098.2_Silent_p.R412R	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	463					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)	p.R463R(1)		NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	ATGGCAAAAGACCTCACCAAG	0.393													G|||	3362	0.671326	0.708	0.7017	5008	,	,		17342	0.6806		0.6173	False		,,,				2504	0.6462				p.R463R		Atlas-SNP	.											PDE3B,NS,carcinoma,0,1	PDE3B	98	1	1	Substitution - coding silent(1)	stomach(1)	c.A1389G						PASS	.	G		2979,1421	462.1+/-353.1	1012,955,233	74.0	74.0	74.0		1389	0.3	0.5	11	dbSNP_111	74	5213,3375	498.6+/-374.8	1581,2051,662	no	coding-synonymous	PDE3B	NM_000922.3		2593,3006,895	GG,GA,AA		39.299,32.2955,36.9264		463/1113	14810762	8192,4796	2200	4294	6494	SO:0001819	synonymous_variant	5140	exon4			CAAAAGACCTCAC	U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"""Phosphodiesterases"""	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.1389A>G	11.37:g.14810762A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	71	28	0.394366	NM_000922	B7ZM37|O00639|Q14408|Q6SEI4	Silent	SNP	ENST00000282096.4	37	CCDS7817.1																																																																																			A|0.362;G|0.638	0.638	strong		0.393	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922	
PRMT9	90826	hgsc.bcm.edu	37	4	148575601	148575601	+	Missense_Mutation	SNP	T	T	C	rs17023638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:148575601T>C	ENST00000322396.6	-	9	1689	c.1447A>G	c.(1447-1449)Agt>Ggt	p.S483G	TMEM184C_ENST00000508208.1_Intron|PRMT10_ENST00000541232.1_Missense_Mutation_p.S370G	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		483			S -> G (in dbSNP:rs17023638).			cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						TGGGTAAAACTTTTTGCAACA	0.403													T|||	127	0.0253594	0.0938	0.0043	5008	,	,		19860	0.0		0.0	False		,,,				2504	0.0				p.S483G		Atlas-SNP	.											.	PRMT10	68	.	0			c.A1447G						PASS	.	T	GLY/SER	301,4105	161.8+/-193.9	10,281,1912	108.0	108.0	108.0		1447	0.4	0.4	4	dbSNP_123	108	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PRMT10	NM_138364.2	56	10,282,6211	CC,CT,TT		0.0116,6.8316,2.322	benign	483/846	148575601	302,12704	2203	4300	6503	SO:0001583	missense	90826	exon9			TAAAACTTTTTGC																												ENST00000322396.6:c.1447A>G	4.37:g.148575601T>C	ENSP00000314396:p.Ser483Gly	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	102	43	0.421569	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	64	0.029304029304029304	64	0.13008130081300814	0	0.0	0	0.0	0	0.0	T	10.31	1.315040	0.23908	0.068316	1.16E-4	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.45668	0.89;0.89	6.04	0.437	0.16555	.	0.391208	0.33792	N	0.004547	T	0.00241	0.0007	L	0.31294	0.92	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.15150	-1.0447	9	0.13853	T	0.58	-20.9041	5.4198	0.16394	0.1195:0.2119:0.0:0.6686	rs17023638;rs17023638	483	Q6P2P2	ANM10_HUMAN	G	483;370	ENSP00000314396:S483G;ENSP00000439508:S370G	ENSP00000314396:S483G	S	-	1	0	PRMT10	148795051	0.002000	0.14202	0.389000	0.26208	0.971000	0.66376	0.093000	0.15086	0.116000	0.18110	0.459000	0.35465	AGT	T|0.963;C|0.037	0.037	strong		0.403	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
CCDC14	64770	hgsc.bcm.edu	37	3	123633665	123633665	+	Silent	SNP	T	T	C	rs13319634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:123633665T>C	ENST00000488653.2	-	13	2913	c.2823A>G	c.(2821-2823)agA>agG	p.R941R	CCDC14_ENST00000485727.1_Silent_p.R741R|CCDC14_ENST00000310351.4_Silent_p.R781R|CCDC14_ENST00000483247.1_5'UTR|CCDC14_ENST00000489746.1_Silent_p.R741R|CCDC14_ENST00000433542.2_Silent_p.R900R			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	941					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)		ACTTCTGGAGTCTAGCTATGT	0.403													T|||	124	0.0247604	0.09	0.0072	5008	,	,		477	0.0		0.0	False		,,,				2504	0.0				p.R900R		Atlas-SNP	.											.	CCDC14	97	.	0			c.A2700G						PASS	.	T		317,4089		15,287,1901	20.0	20.0	20.0		2700	-3.3	0.8	3	dbSNP_121	20	7,8589		0,7,4291	no	coding-synonymous	CCDC14	NM_022757.4		15,294,6192	CC,CT,TT		0.0814,7.1947,2.4919		900/913	123633665	324,12678	2203	4298	6501	SO:0001819	synonymous_variant	64770	exon12			CTGGAGTCTAGCT	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.2823A>G	3.37:g.123633665T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	197	82	0.416244	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Silent	SNP	ENST00000488653.2	37																																																																																				T|0.970;C|0.030	0.030	strong		0.403	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757	
OR5L1	219437	hgsc.bcm.edu	37	11	55579419	55579419	+	Silent	SNP	T	T	C	rs34948392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55579419T>C	ENST00000333973.2	+	1	566	c.477T>C	c.(475-477)caT>caC	p.H159H		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H159H(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				CTCTGATTCATTTGTGCTTAG	0.443													N|||	525	0.104832	0.1884	0.0461	5008	,	,		22589	0.0813		0.0924	False		,,,				2504	0.0706				p.H159H		Atlas-SNP	.											OR5L1,NS,carcinoma,+2,3	OR5L1	145	3	1	Substitution - coding silent(1)	stomach(1)	c.T477C						PASS	.	C		670,3730		63,544,1593	217.0	191.0	200.0		477	-4.7	0.0	11	dbSNP_126	200	725,7867		32,661,3603	no	coding-synonymous	OR5L1	NM_001004738.1		95,1205,5196	CC,CT,TT		8.4381,15.2273,10.7374		159/312	55579419	1395,11597	2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			GATTCATTTGTGC	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.477T>C	11.37:g.55579419T>C		Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	489	236	0.482618	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			T|0.896;C|0.104	0.104	strong		0.443	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
OR10H5	284433	hgsc.bcm.edu	37	19	15904914	15904914	+	Missense_Mutation	SNP	C	C	T	rs150835909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15904914C>T	ENST00000308940.8	+	1	154	c.56C>T	c.(55-57)gCc>gTc	p.A19V		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						GGCTTCTCTGCCTTCCCCCAC	0.582													.|||	34	0.00678914	0.025	0.0014	5008	,	,		19279	0.0		0.0	False		,,,				2504	0.0				p.A19V		Atlas-SNP	.											.	OR10H5	49	.	0			c.C56T						PASS	.	C	VAL/ALA	159,4247		6,147,2050	252.0	210.0	225.0		56	-1.8	0.2	19	dbSNP_134	225	2,8598		0,2,4298	no	missense	OR10H5	NM_001004466.1	64	6,149,6348	TT,TC,CC		0.0233,3.6087,1.2379	benign	19/316	15904914	161,12845	2203	4300	6503	SO:0001583	missense	284433	exon1			TCTCTGCCTTCCC	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.56C>T	19.37:g.15904914C>T	ENSP00000310704:p.Ala19Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	179	86	0.480447	NM_001004466	Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	.	4.228	0.041170	0.08196	0.036087	2.33E-4	ENSG00000172519	ENST00000308940	T	0.00330	8.08	3.45	-1.79	0.07932	.	0.432269	0.19564	N	0.111245	T	0.00039	0.0001	N	0.05199	-0.095	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27673	-1.0067	10	0.41790	T	0.15	.	6.7765	0.23622	0.4443:0.2643:0.2914:0.0	.	19	Q8NGA6	O10H5_HUMAN	V	19	ENSP00000310704:A19V	ENSP00000310704:A19V	A	+	2	0	OR10H5	15765914	0.000000	0.05858	0.153000	0.22517	0.262000	0.26303	-1.472000	0.02341	-0.540000	0.06265	0.573000	0.79308	GCC	C|0.990;T|0.010	0.010	strong		0.582	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
ISOC2	79763	hgsc.bcm.edu	37	19	55967848	55967848	+	Silent	SNP	C	C	T	rs11555784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55967848C>T	ENST00000425675.2	-	2	66	c.6G>A	c.(4-6)gcG>gcA	p.A2A	ISOC2_ENST00000438389.2_Silent_p.A2A|ISOC2_ENST00000085068.3_Silent_p.A2A			Q96AB3	ISOC2_HUMAN	isochorismatase domain containing 2	2					protein destabilization (GO:0031648)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			endometrium(1)|lung(4)|ovary(1)|stomach(1)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0535)		GCCTGGCAGCCGCCATTTTCT	0.642													.|||	227	0.0453275	0.1316	0.0331	5008	,	,		15010	0.0		0.0268	False		,,,				2504	0.0031				p.A2A		Atlas-SNP	.											.	ISOC2	16	.	0			c.G6A						PASS	.	C	,,	528,3878	229.1+/-243.8	32,464,1707	44.0	44.0	44.0		6,6,6	-2.1	0.1	19	dbSNP_126	44	295,8303	103.6+/-164.7	7,281,4011	no	coding-synonymous,coding-synonymous,coding-synonymous	ISOC2	NM_001136201.1,NM_001136202.1,NM_024710.2	,,	39,745,5718	TT,TC,CC		3.431,11.9837,6.3288	,,	2/206,2/136,2/222	55967848	823,12181	2203	4299	6502	SO:0001819	synonymous_variant	79763	exon2			GGCAGCCGCCATT	AK027122	CCDS12925.1, CCDS46194.1, CCDS46195.1	19q13.42	2011-07-14			ENSG00000063241	ENSG00000063241			26278	protein-coding gene	gene with protein product		612928				17658461	Standard	NM_024710		Approved	FLJ23469	uc002qla.3	Q96AB3		ENST00000425675.2:c.6G>A	19.37:g.55967848C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_001136202	Q6ZN91|Q9H5G0	Silent	SNP	ENST00000425675.2	37	CCDS46195.1																																																																																			C|0.939;T|0.061	0.061	strong		0.642	ISOC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453179.1	NM_024710	
NOC2L	26155	hgsc.bcm.edu	37	1	889421	889421	+	Missense_Mutation	SNP	C	C	T	rs3828050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:889421C>T	ENST00000327044.6	-	7	789	c.740G>A	c.(739-741)cGt>cAt	p.R247H	NOC2L_ENST00000487214.1_5'Flank	NM_015658.3	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog (S. cerevisiae)	247					apoptotic process (GO:0006915)|cellular response to UV (GO:0034644)|chromatin assembly (GO:0031497)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of histone acetylation (GO:0035067)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleolus to nucleoplasm transport (GO:0032066)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosome binding (GO:0031491)|poly(A) RNA binding (GO:0044822)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)	p.R247L(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	16	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		GATGTCCACACGAAGCTTCCC	0.647													C|||	2	0.000399361	0.0	0.0	5008	,	,		16641	0.002		0.0	False		,,,				2504	0.0				p.R247H		Atlas-SNP	.											NOC2L,NS,carcinoma,0,1	NOC2L	42	1	1	Substitution - Missense(1)	lung(1)	c.G740A						PASS	.						87.0	84.0	85.0					1																	889421		2203	4300	6503	SO:0001583	missense	26155	exon7			TCCACACGAAGCT	AL050019	CCDS3.1	1p36.33	2014-06-12			ENSG00000188976	ENSG00000188976			24517	protein-coding gene	gene with protein product	"""novel INHAT repressor"", ""protein phosphatase 1, regulatory subunit 12"""	610770					Standard	NM_015658		Approved	DKFZP564C186, NET7, NET15, NIR, PPP1R112	uc001abz.4	Q9Y3T9	OTTHUMG00000040720	ENST00000327044.6:c.740G>A	1.37:g.889421C>T	ENSP00000317992:p.Arg247His	Somatic	288	1	0.00347222		WXS	Illumina HiSeq	Phase_I	275	143	0.52	NM_015658	Q5SVA3|Q9BTN6	Missense_Mutation	SNP	ENST00000327044.6	37	CCDS3.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	11.92	1.783028	0.31593	.	.	ENSG00000188976	ENST00000327044	T	0.67698	-0.28	4.11	4.11	0.48088	Armadillo-type fold (1);	0.152310	0.44688	D	0.000440	T	0.62732	0.2452	L	0.53249	1.67	0.51767	D	0.99993	B;B;B	0.22146	0.065;0.065;0.031	B;B;B	0.18561	0.022;0.022;0.01	T	0.65730	-0.6097	10	0.66056	D	0.02	-17.7817	15.5423	0.76062	0.0:1.0:0.0:0.0	rs3828050	247;247;14	B3KNC3;Q9Y3T9;Q9H9J5	.;NOC2L_HUMAN;.	H	247	ENSP00000317992:R247H	ENSP00000317992:R247H	R	-	2	0	NOC2L	879284	0.999000	0.42202	0.993000	0.49108	0.561000	0.35649	4.286000	0.58995	2.135000	0.66039	0.306000	0.20318	CGT	C|0.999;T|0.001	0.001	strong		0.647	NOC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097869.1	NM_015658	
AGBL4	84871	hgsc.bcm.edu	37	1	49005351	49005351	+	Missense_Mutation	SNP	C	C	T	rs60977321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:49005351C>T	ENST00000371839.1	-	12	1443	c.1327G>A	c.(1327-1329)Gtg>Atg	p.V443M	AGBL4_ENST00000334103.7_Missense_Mutation_p.V176M	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	443			V -> M (in dbSNP:rs60977321).		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)			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)		TTTTCAACCACGGGGTTCAGC	0.512													C|||	322	0.0642971	0.233	0.0144	5008	,	,		17535	0.0		0.004	False		,,,				2504	0.0				p.V443M		Atlas-SNP	.											.	AGBL4	54	.	0			c.G1327A						PASS	.	C	MET/VAL	287,1097		31,225,436	134.0	111.0	118.0		1327	-2.2	1.0	1	dbSNP_129	118	4,3178		0,4,1587	yes	missense	AGBL4	NM_032785.3	21	31,229,2023	TT,TC,CC		0.1257,20.737,6.3732	benign	443/504	49005351	291,4275	692	1591	2283	SO:0001583	missense	84871	exon12			CAACCACGGGGTT	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.1327G>A	1.37:g.49005351C>T	ENSP00000360905:p.Val443Met	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	129	57	0.44186	NM_032785	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	37	CCDS44137.1	103	0.04716117216117216	100	0.2032520325203252	3	0.008287292817679558	0	0.0	0	0.0	C	4.542	0.100554	0.08731	0.20737	0.001257	ENSG00000186094	ENST00000371839;ENST00000411952;ENST00000334103	T;T	0.44881	2.53;0.91	4.65	-2.18	0.07037	.	2.280690	0.01719	N	0.028181	T	0.00012	0.0000	N	0.08118	0	0.52099	P	5.3999999999998494E-5	B;B;B	0.19583	0.0;0.002;0.037	B;B;B	0.08055	0.0;0.001;0.003	T	0.12863	-1.0531	9	0.25751	T	0.34	-0.0068	1.605	0.02682	0.2303:0.0994:0.4078:0.2624	rs60977321	455;176;443	Q5VU57-2;B4DGK1;Q5VU57	.;.;CBPC6_HUMAN	M	443;437;176	ENSP00000360905:V443M;ENSP00000335516:V176M	ENSP00000335516:V176M	V	-	1	0	AGBL4	48777938	0.020000	0.18652	0.992000	0.48379	0.242000	0.25591	-1.494000	0.02296	-0.194000	0.10399	-1.708000	0.00717	GTG	C|0.961;T|0.039	0.039	strong		0.512	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785	
AMPD3	272	hgsc.bcm.edu	37	11	10503756	10503756	+	Silent	SNP	G	G	A	rs16907852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:10503756G>A	ENST00000396554.3	+	4	941	c.600G>A	c.(598-600)ccG>ccA	p.P200P	AMPD3_ENST00000444303.2_Silent_p.P32P	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	191					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		CTGCACCTCCGGAAGAGGGCC	0.607													G|||	657	0.13119	0.3253	0.0879	5008	,	,		17518	0.003		0.0994	False		,,,				2504	0.0644				p.P200P		Atlas-SNP	.											.	AMPD3	68	.	0			c.G600A						PASS	.	G	,,,,	1210,3188		160,890,1149	37.0	42.0	40.0		600,573,594,573,96	-4.3	0.0	11	dbSNP_123	40	796,7790		30,736,3527	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMPD3	NM_000480.2,NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1	,,,,	190,1626,4676	AA,AG,GG		9.2709,27.5125,15.4498	,,,,	200/777,191/768,198/775,191/768,32/609	10503756	2006,10978	2199	4293	6492	SO:0001819	synonymous_variant	272	exon4			ACCTCCGGAAGAG	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.600G>A	11.37:g.10503756G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	37	CCDS7802.1																																																																																			G|0.846;A|0.154	0.154	strong		0.607	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
C5orf42	65250	hgsc.bcm.edu	37	5	37115116	37115116	+	Missense_Mutation	SNP	C	C	T	rs7702892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37115116C>T	ENST00000508244.1	-	49	9277	c.9184G>A	c.(9184-9186)Gga>Aga	p.G3062R	C5orf42_ENST00000274258.7_Missense_Mutation_p.G1960R|C5orf42_ENST00000425232.2_Missense_Mutation_p.G3062R			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	3062			G -> R (in dbSNP:rs7702892).			integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GCTTTGGCTCCACCAGCTTTT	0.363													C|||	124	0.0247604	0.0908	0.0058	5008	,	,		18889	0.0		0.0	False		,,,				2504	0.0				p.G3062R		Atlas-SNP	.											C5orf42_ENST00000425232,bladder,carcinoma,+1,2	C5orf42	422	2	0			c.G9184A						PASS	.	C	ARG/GLY	340,4066	175.5+/-204.9	13,314,1876	101.0	90.0	93.0		9184	2.0	0.0	5	dbSNP_116	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C5orf42	NM_023073.3	125	13,316,6174	TT,TC,CC		0.0233,7.7167,2.6296	benign	3062/3198	37115116	342,12664	2203	4300	6503	SO:0001583	missense	65250	exon50			TGGCTCCACCAGC		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.9184G>A	5.37:g.37115116C>T	ENSP00000421690:p.Gly3062Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	45	0.020604395604395604	43	0.08739837398373984	2	0.0055248618784530384	0	0.0	0	0.0	C	13.98	2.398422	0.42512	0.077167	2.33E-4	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429	T;T;T;T	0.22945	1.94;1.94;1.93;1.93	3.78	1.97	0.26223	.	1.267940	0.05991	U	0.646004	T	0.00608	0.0020	N	0.22421	0.69	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.15052	0.012;0.01	T	0.26224	-1.0109	10	0.25751	T	0.34	.	6.7291	0.23373	0.0:0.7655:0.0:0.2345	rs7702892;rs52808859;rs7702892	3062;1960	E9PH94;Q9H799	.;CE042_HUMAN	R	3062;3062;1960;2128	ENSP00000421690:G3062R;ENSP00000389014:G3062R;ENSP00000274258:G1960R;ENSP00000424223:G2128R	ENSP00000274258:G1960R	G	-	1	0	C5orf42	37150873	0.000000	0.05858	0.013000	0.15412	0.825000	0.46686	0.020000	0.13466	0.353000	0.24079	-0.137000	0.14449	GGA	C|0.970;T|0.030	0.030	strong		0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
IFT43	112752	hgsc.bcm.edu	37	14	76543004	76543004	+	Intron	SNP	G	G	A	rs17783366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:76543004G>A	ENST00000314067.6	+	6	329				IFT43_ENST00000238628.6_Missense_Mutation_p.D94N	NM_001102564.1	NP_001096034.1	Q96FT9	IFT43_HUMAN	intraflagellar transport 43						cilium morphogenesis (GO:0060271)|intraciliary retrograde transport (GO:0035721)	cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)				endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						GCATCACAGAGATTTGGGGCT	0.468													G|||	846	0.16893	0.0794	0.2046	5008	,	,		20530	0.119		0.3111	False		,,,				2504	0.1697				p.D94N		Atlas-SNP	.											.	IFT43	63	.	0			c.G280A						PASS	.	G	,ASN/ASP	506,3900	231.4+/-245.2	32,442,1729	119.0	103.0	109.0		,280	-0.3	0.0	14	dbSNP_123	109	2739,5861	436.1+/-358.2	422,1895,1983	yes	intron,missense	IFT43	NM_001102564.1,NM_052873.2	,23	454,2337,3712	AA,AG,GG		31.8488,11.4843,24.95	,	,94/214	76543004	3245,9761	2203	4300	6503	SO:0001627	intron_variant	112752	exon4			CACAGAGATTTGG	BC010436	CCDS9847.1, CCDS41973.1, CCDS58330.1	14q24.3	2014-07-03	2014-07-03	2011-06-09				"""Intraflagellar transport homologs"""	29669	protein-coding gene	gene with protein product		614068	"""chromosome 14 open reading frame 179"", ""intraflagellar transport 43 homolog (Chlamydomonas)"""	C14orf179		21378380	Standard	NM_052873		Approved	FLJ32173, MGC16028	uc010asm.1	Q96FT9		ENST00000314067.6:c.296-5634G>A	14.37:g.76543004G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	93	34	0.365591	NM_052873	B3KPT6|B4DZI9|G3V385|O95418|Q9ULA9	Missense_Mutation	SNP	ENST00000314067.6	37	CCDS41973.1	440	0.20146520146520147	56	0.11382113821138211	73	0.20165745856353592	81	0.14160839160839161	230	0.3034300791556728	G	13.47	2.247480	0.39697	0.114843	0.318488	ENSG00000119650	ENST00000238628	T	0.42513	0.97	3.98	-0.277	0.12898	.	1.421900	0.03796	N	0.263712	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.31724	-0.9933	8	0.15066	T	0.55	-15.6523	1.0305	0.01537	0.2168:0.186:0.4208:0.1764	rs17783366;rs17850656;rs52814736;rs61208018;rs17783366	94	Q96FT9-2	.	N	94	ENSP00000238628:D94N	ENSP00000238628:D94N	D	+	1	0	IFT43	75612757	0.000000	0.05858	0.000000	0.03702	0.954000	0.61252	-0.309000	0.08145	-0.160000	0.11002	0.561000	0.74099	GAT	G|0.774;A|0.226	0.226	strong		0.468	IFT43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052873	
WFS1	7466	hgsc.bcm.edu	37	4	6303022	6303022	+	Silent	SNP	C	C	T	rs1801214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6303022C>T	ENST00000226760.1	+	8	1670	c.1500C>T	c.(1498-1500)aaC>aaT	p.N500N	WFS1_ENST00000503569.1_Silent_p.N500N	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	500					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)		TCGTCCTCAACGTCAGCGTCC	0.577													c|||	3653	0.729433	0.6921	0.7046	5008	,	,		22288	0.9077		0.6352	False		,,,				2504	0.7106				p.N500N		Atlas-SNP	.											.	WFS1	71	.	0			c.C1500T						PASS	.		,	2980,1426	464.7+/-354.0	991,998,214	126.0	88.0	101.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1500,1500	-0.7	0.7	4	dbSNP_89	101	5244,3356	498.6+/-374.8	1575,2094,631	yes	coding-synonymous,coding-synonymous	WFS1	NM_001145853.1,NM_006005.3	,	2566,3092,845	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	39.0233,32.365,36.7676	,	500/891,500/891	6303022	8224,4782	2203	4300	6503	SO:0001819	synonymous_variant	7466	exon8			CCTCAACGTCAGC	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.1500C>T	4.37:g.6303022C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	37	CCDS3386.1																																																																																			A|0.000;C|0.334;G|0.000;T|0.666	0.666	strong		0.577	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
OR10V1	390201	hgsc.bcm.edu	37	11	59480952	59480952	+	Nonsense_Mutation	SNP	G	G	A	rs386754016|rs499037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59480952G>A	ENST00000307552.2	-	1	385	c.367C>T	c.(367-369)Cag>Tag	p.Q123*	STX3_ENST00000300150.7_5'UTR	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, member 1	123			Q -> R (in dbSNP:rs499033). {ECO:0000269|PubMed:12213199, 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)	p.Q123K(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(10)|skin(1)	16						GCTATAAACTGGTCATAAGCC	0.517													G|||	319	0.0636981	0.1127	0.1427	5008	,	,		20626	0.0377		0.0089	False		,,,				2504	0.0245				p.Q123X		Atlas-SNP	.											.	OR10V1	40	.	1	Substitution - Missense(1)	lung(1)	c.C367T						PASS	.	G	stop/GLN	389,4013	184.0+/-211.4	17,355,1829	73.0	61.0	65.0		367	4.4	1.0	11	dbSNP_83	65	108,8482	57.2+/-118.5	3,102,4190	yes	stop-gained	OR10V1	NM_001005324.1		20,457,6019	AA,AG,GG		1.2573,8.8369,3.8254		123/310	59480952	497,12495	2201	4295	6496	SO:0001587	stop_gained	390201	exon1			TAAACTGGTCATA	AB065807	CCDS31565.1	11q12.1	2012-08-09			ENSG00000172289	ENSG00000172289		"""GPCR / Class A : Olfactory receptors"""	15136	protein-coding gene	gene with protein product							Standard	NM_001005324		Approved		uc001nof.1	Q8NGI7	OTTHUMG00000167406	ENST00000307552.2:c.367C>T	11.37:g.59480952G>A	ENSP00000302199:p.Gln123*	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	69	26	0.376812	NM_001005324	Q6IFD9|Q96R50	Nonsense_Mutation	SNP	ENST00000307552.2	37	CCDS31565.1	108	0.04945054945054945	49	0.09959349593495935	37	0.10220994475138122	17	0.02972027972027972	5	0.006596306068601583	G	19.75	3.886451	0.72410	0.088369	0.012573	ENSG00000172289	ENST00000307552	.	.	.	4.36	4.36	0.52297	.	0.140023	0.32852	N	0.005569	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	10.0805	0.42386	0.0:0.0:0.7996:0.2004	rs499037;rs499037	.	.	.	X	123	.	ENSP00000302199:Q123X	Q	-	1	0	OR10V1	59237528	0.999000	0.42202	1.000000	0.80357	0.723000	0.41478	2.450000	0.44943	2.453000	0.82957	0.543000	0.68304	CAG	G|0.953;A|0.047	0.047	strong		0.517	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324	
KLHL33	123103	hgsc.bcm.edu	37	14	20897064	20897064	+	Missense_Mutation	SNP	C	C	T	rs7145318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20897064C>T	ENST00000344581.4	-	4	1768	c.1546G>A	c.(1546-1548)Gct>Act	p.A516T		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	516			A -> T (in dbSNP:rs7145318).									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)		TGCTGCACAGCGGGCAGTGTC	0.587													T|||	3232	0.645367	0.7542	0.4957	5008	,	,		19958	0.5972		0.6203	False		,,,				2504	0.68				p.A516T		Atlas-SNP	.											.	KLHL33	37	.	0			c.G1546A						PASS	.	T	THR/ALA	989,395		351,287,54	74.0	71.0	72.0		1546	-1.8	0.0	14	dbSNP_116	72	1835,1347		519,797,275	yes	missense	KLHL33	NM_001109997.2	58	870,1084,329	TT,TC,CC		42.3319,28.5405,38.1516	benign	516/534	20897064	2824,1742	692	1591	2283	SO:0001583	missense	123103	exon4			GCACAGCGGGCAG		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.1546G>A	14.37:g.20897064C>T	ENSP00000341549:p.Ala516Thr	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	216	213	0.986111	NM_001109997		Missense_Mutation	SNP	ENST00000344581.4	37	CCDS53882.1	1363	0.6240842490842491	369	0.75	200	0.5524861878453039	333	0.5821678321678322	461	0.6081794195250659	T	0.067	-1.210039	0.01555	0.714595	0.576681	ENSG00000185271	ENST00000344581	T	0.72394	-0.65	4.98	-1.81	0.07882	.	0.469168	0.19354	N	0.116322	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.39722	-0.9600	9	0.02654	T	1	.	7.0501	0.25069	0.0:0.4489:0.1929:0.3582	rs7145318;rs17211411;rs52824240;rs57617834;rs7145318	516	A6NCF5	KLH33_HUMAN	T	516	ENSP00000341549:A516T	ENSP00000341549:A516T	A	-	1	0	KLHL33	19966904	.	.	0.001000	0.08648	0.763000	0.43281	.	.	-0.418000	0.07450	-0.254000	0.11334	GCT	C|0.365;N|0.001	.	strong		0.587	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
TRIM33	51592	hgsc.bcm.edu	37	1	114948309	114948309	+	Silent	SNP	A	A	G	rs56056367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:114948309A>G	ENST00000358465.2	-	15	2574	c.2491T>C	c.(2491-2493)Ttg>Ctg	p.L831L	TRIM33_ENST00000369543.2_Silent_p.L831L|TRIM33_ENST00000476908.1_5'UTR|TRIM33_ENST00000450349.2_Silent_p.L463L	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	831					gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGCTTGCCAATGCATCCAAT	0.433			T	RET	papillary thyroid								A|||	122	0.024361	0.0552	0.0043	5008	,	,		19263	0.0149		0.001	False		,,,				2504	0.0307				p.L831L		Atlas-SNP	.		Dom	yes		1	1p13	51592	""" tripartite motif-containing 33 (PTC7,TIF1G)"""		E	.	TRIM33	115	.	0			c.T2491C						PASS	.	A	,	199,4207	124.1+/-161.4	4,191,2008	123.0	123.0	123.0		2491,2491	4.2	1.0	1	dbSNP_129	123	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	TRIM33	NM_015906.3,NM_033020.2	,	4,195,6304	GG,GA,AA		0.0465,4.5166,1.5608	,	831/1128,831/1111	114948309	203,12803	2203	4300	6503	SO:0001819	synonymous_variant	51592	exon15			TTGCCAATGCATC	AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"", ""RING-type (C3HC4) zinc fingers"""	16290	protein-coding gene	gene with protein product	"""transcriptional intermediary factor 1 gamma"", ""ret-fused gene 7"""	605769	"""tripartite motif-containing 33"""			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.2491T>C	1.37:g.114948309A>G		Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	283	145	0.512367	NM_033020	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Silent	SNP	ENST00000358465.2	37	CCDS872.1																																																																																			A|0.985;G|0.015	0.015	strong		0.433	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906	
NIPBL	25836	hgsc.bcm.edu	37	5	36985751	36985751	+	Silent	SNP	A	A	G	rs293756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36985751A>G	ENST00000282516.8	+	10	2968	c.2469A>G	c.(2467-2469)aaA>aaG	p.K823K	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Silent_p.K823K	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	823					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)			ATAAACAAAAATCAGATGACA	0.443													A|||	183	0.0365415	0.1354	0.0058	5008	,	,		19980	0.0		0.0	False		,,,				2504	0.0				p.K823K		Atlas-SNP	.											.	NIPBL	513	.	0			c.A2469G						PASS	.	A	,	506,3900	231.0+/-245.0	27,452,1724	68.0	67.0	67.0		2469,2469	-0.5	1.0	5	dbSNP_79	67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NIPBL	NM_015384.4,NM_133433.3	,	27,453,6023	GG,GA,AA		0.0116,11.4843,3.8982	,	823/2698,823/2805	36985751	507,12499	2203	4300	6503	SO:0001819	synonymous_variant	25836	exon10			ACAAAAATCAGAT	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.2469A>G	5.37:g.36985751A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	185	101	0.545946	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																			A|0.961;G|0.039	0.039	strong		0.443	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
DPH6	89978	hgsc.bcm.edu	37	15	35830665	35830665	+	Missense_Mutation	SNP	C	C	T	rs34907758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:35830665C>T	ENST00000256538.4	-	3	148	c.122G>A	c.(121-123)gGg>gAg	p.G41E	DPH6_ENST00000440392.2_Missense_Mutation_p.G41E	NM_080650.3	NP_542381.1	Q7L8W6	DPH6_HUMAN	diphthamine biosynthesis 6	41			G -> E (in dbSNP:rs34907758).		peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		ATP binding (GO:0005524)|diphthine-ammonia ligase activity (GO:0017178)										TTCATCAGACCCCACTGCAAC	0.433													C|||	152	0.0303514	0.1097	0.0101	5008	,	,		17189	0.0		0.0	False		,,,				2504	0.0				p.G41E		Atlas-SNP	.											.	ATPBD4	30	.	0			c.G122A						PASS	.	C	GLU/GLY,GLU/GLY	311,4091	161.4+/-193.6	13,285,1903	73.0	62.0	66.0		122,122	2.9	1.0	15	dbSNP_126	66	5,8589	3.7+/-12.6	0,5,4292	no	missense,missense	ATPBD4	NM_001141972.1,NM_080650.3	98,98	13,290,6195	TT,TC,CC		0.0582,7.065,2.4315	benign,benign	41/166,41/268	35830665	316,12680	2201	4297	6498	SO:0001583	missense	89978	exon3			TCAGACCCCACTG		CCDS10043.1, CCDS45213.1	15q14	2013-06-19	2013-06-19	2013-05-02	ENSG00000134146	ENSG00000134146	6.3.1.14		30543	protein-coding gene	gene with protein product	"""diphthine--ammonia ligase"""		"""ATP binding domain 4"", ""DPH6 homolog (S. cerevisiae)"""	ATPBD4		23169644, 23468660	Standard	NM_080650		Approved	MGC14798		Q7L8W6	OTTHUMG00000129759	ENST00000256538.4:c.122G>A	15.37:g.35830665C>T	ENSP00000256538:p.Gly41Glu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_001141972	B3KWG1|Q96HJ6	Missense_Mutation	SNP	ENST00000256538.4	37	CCDS10043.1	50	0.022893772893772892	44	0.08943089430894309	6	0.016574585635359115	0	0.0	0	0.0	C	8.198	0.797575	0.16327	0.07065	5.82E-4	ENSG00000134146	ENST00000256538;ENST00000440392	T;T	0.42900	1.54;0.96	5.8	2.88	0.33553	Domain of unknown function DUF71, ATP-binding domain (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.676327	0.14999	N	0.286217	T	0.00524	0.0017	N	0.02708	-0.52	0.22851	N	0.998659	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.20638	-1.0269	10	0.02654	T	1	-0.1968	7.3765	0.26831	0.0:0.5948:0.0:0.4052	rs34907758	41;41	B3KWG1;Q7L8W6	.;ATBD4_HUMAN	E	41	ENSP00000256538:G41E;ENSP00000406976:G41E	ENSP00000256538:G41E	G	-	2	0	ATPBD4	33617957	0.000000	0.05858	0.998000	0.56505	0.692000	0.40212	-0.022000	0.12480	0.362000	0.24319	-0.142000	0.14014	GGG	C|0.972;T|0.028	0.028	strong		0.433	DPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251973.1	NM_080650	
AGBL1	123624	hgsc.bcm.edu	37	15	86838497	86838497	+	Silent	SNP	C	C	T	rs9630451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:86838497C>T	ENST00000441037.2	+	16	2189	c.2094C>T	c.(2092-2094)gaC>gaT	p.D698D	AGBL1-AS1_ENST00000564487.1_RNA|AGBL1_ENST00000389298.3_Silent_p.D429D|AGBL1_ENST00000421325.2_Silent_p.D698D|AGBL1-AS1_ENST00000566878.1_RNA	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	698					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						CTCATCTTGACATCCTGGAAA	0.423													C|||	894	0.178514	0.4546	0.0519	5008	,	,		20602	0.1567		0.0447	False		,,,				2504	0.0552				p.D698D		Atlas-SNP	.											.	AGBL1	151	.	0			c.C2094T						PASS	.	C		1501,2289		306,889,700	52.0	53.0	53.0		2094	-1.9	0.0	15	dbSNP_119	53	313,7919		5,303,3808	no	coding-synonymous	AGBL1	NM_152336.2		311,1192,4508	TT,TC,CC		3.8022,39.6042,15.089		698/1067	86838497	1814,10208	1895	4116	6011	SO:0001819	synonymous_variant	123624	exon16			TCTTGACATCCTG	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2094C>T	15.37:g.86838497C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			C|0.819;T|0.181	0.181	strong		0.423	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
KCNH3	23416	hgsc.bcm.edu	37	12	49937813	49937813	+	Silent	SNP	A	A	G	rs1150057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49937813A>G	ENST00000257981.6	+	6	1199	c.939A>G	c.(937-939)gcA>gcG	p.A313A		NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	313					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						ATGTCATCGCAGCGCTGCCCT	0.617													G|||	1323	0.264177	0.59	0.1571	5008	,	,		15693	0.1002		0.1799	False		,,,				2504	0.1554				p.A313A		Atlas-SNP	.											.	KCNH3	88	.	0			c.A939G						PASS	.	G		2242,2164	582.8+/-385.7	566,1110,527	195.0	157.0	170.0		939	-10.4	0.0	12	dbSNP_87	170	1450,7150	751.3+/-407.4	127,1196,2977	no	coding-synonymous	KCNH3	NM_012284.1		693,2306,3504	GG,GA,AA		16.8605,49.1148,28.3869		313/1084	49937813	3692,9314	2203	4300	6503	SO:0001819	synonymous_variant	23416	exon6			CATCGCAGCGCTG	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.939A>G	12.37:g.49937813A>G		Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_012284	Q9UQ06	Silent	SNP	ENST00000257981.6	37	CCDS8786.1																																																																																			A|0.729;G|0.271	0.271	strong		0.617	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
CAND2	23066	hgsc.bcm.edu	37	3	12856856	12856856	+	Missense_Mutation	SNP	A	A	G	rs2305398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:12856856A>G	ENST00000456430.2	+	8	1264	c.1223A>G	c.(1222-1224)cAg>cGg	p.Q408R	CAND2_ENST00000295989.5_Missense_Mutation_p.Q315R	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	408			Q -> R (in dbSNP:rs2305398). {ECO:0000269|PubMed:9734811}.		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CGGCAAACACAGCCCCCGAAG	0.617													G|||	2887	0.576478	0.972	0.4986	5008	,	,		20497	0.2907		0.6551	False		,,,				2504	0.3108				p.Q408R	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.A1223G						PASS	.	G	ARG/GLN,ARG/GLN	3844,376		1752,340,18	46.0	54.0	51.0		1223,944	3.8	1.0	3	dbSNP_100	51	5225,3213		1621,1983,615	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	43,43	3373,2323,633	GG,GA,AA		38.0777,8.91,28.3536	benign,benign	408/1237,315/1120	12856856	9069,3589	2110	4219	6329	SO:0001583	missense	23066	exon8			AAACACAGCCCCC		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1223A>G	3.37:g.12856856A>G	ENSP00000387641:p.Gln408Arg	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	264	264	1	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1283	0.5874542124542125	469	0.9532520325203252	180	0.4972375690607735	150	0.26223776223776224	484	0.6385224274406333	G	0.066	-1.213618	0.01555	0.9109	0.619223	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.64991	-0.13;-0.13	4.86	3.85	0.44370	Armadillo-like helical (1);Armadillo-type fold (1);	0.296572	0.26016	N	0.026849	T	0.00012	0.0000	N	0.00399	-1.545	0.09310	P	0.999996978	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36504	-0.9745	9	0.07482	T	0.82	-22.8675	7.173	0.25728	0.2702:0.0:0.7298:0.0	rs2305398;rs17824975;rs59611646;rs2305398	408;315	O75155;O75155-2	CAND2_HUMAN;.	R	315;408	ENSP00000295989:Q315R;ENSP00000387641:Q408R	ENSP00000295989:Q315R	Q	+	2	0	CAND2	12831856	0.994000	0.37717	0.955000	0.39395	0.098000	0.18820	0.601000	0.24119	1.046000	0.40249	-0.215000	0.12644	CAG	G|0.597;N|0.001	0.597	strong		0.617	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
OR7D2	162998	hgsc.bcm.edu	37	19	9297196	9297196	+	Missense_Mutation	SNP	G	G	A	rs61739064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9297196G>A	ENST00000344248.2	+	1	918	c.739G>A	c.(739-741)Gtc>Atc	p.V247I		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	247					regulation of transcription, DNA-templated (GO:0006355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						TCACCTCTCCGTCGTTTCTTT	0.468													G|||	64	0.0127796	0.0484	0.0	5008	,	,		17847	0.0		0.0	False		,,,				2504	0.0				p.V247I		Atlas-SNP	.											.	OR7D2	55	.	0			c.G739A						PASS	.	G	ILE/VAL	210,4196	127.8+/-164.7	2,206,1995	91.0	76.0	81.0		739	2.2	0.0	19	dbSNP_129	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR7D2	NM_175883.2	29	2,207,6294	AA,AG,GG		0.0116,4.7662,1.6223	benign	247/313	9297196	211,12795	2203	4300	6503	SO:0001583	missense	162998	exon1			CTCTCCGTCGTTT	AK095468	CCDS32900.1	19p13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.739G>A	19.37:g.9297196G>A	ENSP00000345563:p.Val247Ile	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_175883	Q6IFJ7|Q8N133	Missense_Mutation	SNP	ENST00000344248.2	37	CCDS32900.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	G	9.760	1.169781	0.21621	0.047662	1.16E-4	ENSG00000188000	ENST00000344248	T	0.00253	8.43	2.2	2.2	0.27929	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35970	U	0.002872	T	0.00039	0.0001	M	0.78801	2.425	0.09310	N	1	P	0.40197	0.706	B	0.38378	0.272	T	0.38693	-0.9649	10	0.59425	D	0.04	.	11.9676	0.53044	0.0:0.0:1.0:0.0	rs61739064	247	Q96RA2	OR7D2_HUMAN	I	247	ENSP00000345563:V247I	ENSP00000345563:V247I	V	+	1	0	OR7D2	9158196	0.163000	0.22920	0.047000	0.18901	0.020000	0.10135	2.174000	0.42482	1.578000	0.49821	0.505000	0.49811	GTC	G|0.983;A|0.017	0.017	strong		0.468	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1		
UPP2	151531	hgsc.bcm.edu	37	2	158977928	158977928	+	Silent	SNP	A	A	C	rs10186677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:158977928A>C	ENST00000005756.4	+	5	656	c.462A>C	c.(460-462)gcA>gcC	p.A154A	UPP2_ENST00000460456.1_Intron|UPP2_ENST00000409859.4_Silent_p.A211A|UPP2_ENST00000605860.1_Silent_p.A211A	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	154					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	CAGGGATTGCACCAGGGACTG	0.383													A|||	84	0.0167732	0.0605	0.0058	5008	,	,		18783	0.0		0.0	False		,,,				2504	0.0				p.A211A		Atlas-SNP	.											.	UPP2	60	.	0			c.A633C						PASS	.	A	,	210,4196	129.0+/-165.8	5,200,1998	201.0	207.0	205.0		633,462	-4.8	0.0	2	dbSNP_119	205	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous,coding-synonymous	UPP2	NM_001135098.1,NM_173355.3	,	5,204,6293	CC,CA,AA		0.0465,4.7662,1.6456	,	211/375,154/318	158977928	214,12790	2203	4299	6502	SO:0001819	synonymous_variant	151531	exon7			GATTGCACCAGGG	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.462A>C	2.37:g.158977928A>C		Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	303	185	0.610561	NM_001135098	B3KV87	Silent	SNP	ENST00000005756.4	37	CCDS2207.1																																																																																			A|0.980;C|0.020	0.020	strong		0.383	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355	
IGSF5	150084	hgsc.bcm.edu	37	21	41142958	41142958	+	Silent	SNP	C	C	T	rs61737685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:41142958C>T	ENST00000380588.4	+	4	637	c.534C>T	c.(532-534)ctC>ctT	p.L178L	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	178	Ig-like V-type 2.				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)				CCTGGGAGCTCGGTCTCCTGG	0.517													C|||	230	0.0459265	0.1664	0.0144	5008	,	,		15063	0.0		0.0	False		,,,				2504	0.0				p.L178L		Atlas-SNP	.											.	IGSF5	62	.	0			c.C534T						PASS	.	C		580,3826	258.3+/-262.4	35,510,1658	68.0	66.0	66.0		534	-2.5	0.0	21	dbSNP_129	66	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	IGSF5	NM_001080444.1		35,516,5952	TT,TC,CC		0.0698,13.1639,4.5056		178/408	41142958	586,12420	2203	4300	6503	SO:0001819	synonymous_variant	150084	exon4			GGAGCTCGGTCTC		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.534C>T	21.37:g.41142958C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_001080444		Silent	SNP	ENST00000380588.4	37	CCDS33562.1																																																																																			C|0.957;T|0.043	0.043	strong		0.517	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		
INMT	11185	hgsc.bcm.edu	37	7	30795419	30795419	+	Silent	SNP	C	C	T	rs35221354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30795419C>T	ENST00000013222.5	+	3	760	c.744C>T	c.(742-744)gcC>gcT	p.A248A	INMT-FAM188B_ENST00000458257.1_Intron|INMT_ENST00000409539.1_Silent_p.A247A|INMT_ENST00000484180.1_3'UTR	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	248					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						CCAATGCTGCCAACAATGGGG	0.592													C|||	272	0.0543131	0.1921	0.0259	5008	,	,		20160	0.0		0.0	False		,,,				2504	0.0				p.A248A		Atlas-SNP	.											INMT,NS,carcinoma,+1,1	INMT	38	1	0			c.C744T						PASS	.	C	,	710,3696	297.3+/-284.7	54,602,1547	99.0	96.0	97.0		741,744	3.4	0.1	7	dbSNP_126	97	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	INMT	NM_001199219.1,NM_006774.4	,	54,609,5840	TT,TC,CC		0.0814,16.1144,5.5128	,	247/263,248/264	30795419	717,12289	2203	4300	6503	SO:0001819	synonymous_variant	11185	exon3			TGCTGCCAACAAT		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.744C>T	7.37:g.30795419C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Silent	SNP	ENST00000013222.5	37	CCDS5430.1																																																																																			C|0.947;T|0.053	0.053	strong		0.592	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
PCDHA10	56139	hgsc.bcm.edu	37	5	140237094	140237094	+	Silent	SNP	C	C	G	rs60872775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140237094C>G	ENST00000307360.5	+	1	1461	c.1461C>G	c.(1459-1461)gcC>gcG	p.A487A	PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Silent_p.A487A|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	487	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)			AGGAGAACGCCCTGGTGTCCT	0.662													.|||	56	0.0111821	0.0416	0.0014	5008	,	,		16717	0.0		0.0	False		,,,				2504	0.0				p.A487A		Atlas-SNP	.											.	PCDHA10	358	.	0			c.C1461G						PASS	.	C	,,,,,,,,,,,,,	141,4251	805.5+/-415.8	11,119,2066	76.0	78.0	78.0		,1461,,,,,,,,,,,1461,1461	1.8	1.0	5	dbSNP_129	78	0,8546		0,0,4273	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,coding-synonymous	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	,,,,,,,,,,,,,	11,119,6339	GG,GC,CC		0.0,3.2104,1.0898	,,,,,,,,,,,,,	,487/949,,,,,,,,,,,487/845,487/686	140237094	141,12797	2196	4273	6469	SO:0001819	synonymous_variant	56139	exon1			GAACGCCCTGGTG	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.1461C>G	5.37:g.140237094C>G		Somatic	365	0	0		WXS	Illumina HiSeq	Phase_I	309	157	0.508091	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	37	CCDS54921.1																																																																																			C|0.989;G|0.011	0.011	strong		0.662	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
ZNF714	148206	hgsc.bcm.edu	37	19	21300964	21300964	+	Silent	SNP	T	T	C	rs111456417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21300964T>C	ENST00000596143.1	+	5	1819	c.1494T>C	c.(1492-1494)caT>caC	p.H498H	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	498					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						TTACTAAACATAGGAAAATTC	0.423													.|||	232	0.0463259	0.0348	0.0389	5008	,	,		19554	0.001		0.1133	False		,,,				2504	0.045				p.H498H		Atlas-SNP	.											.	ZNF714	121	.	0			c.T1494C						PASS	.	T		156,4250		5,146,2052	74.0	82.0	80.0		1494	-0.3	0.0	19	dbSNP_132	80	703,7897		26,651,3623	no	coding-synonymous	ZNF714	NM_182515.3		31,797,5675	CC,CT,TT		8.1744,3.5406,6.6046		498/555	21300964	859,12147	2203	4300	6503	SO:0001819	synonymous_variant	148206	exon5			TAAACATAGGAAA	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.1494T>C	19.37:g.21300964T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_182515	Q49AI1|Q86W65|Q8ND40	Silent	SNP	ENST00000596143.1	37	CCDS54239.1																																																																																			T|0.935;C|0.065	0.065	strong		0.423	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
FAM205A	259308	hgsc.bcm.edu	37	9	34725116	34725116	+	Silent	SNP	G	G	A	rs62547038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:34725116G>A	ENST00000378788.3	-	4	2160	c.2121C>T	c.(2119-2121)gtC>gtT	p.V707V		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	707						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						CCACTGCCAGGACCCCAGAAA	0.547																																					p.V707V		Atlas-SNP	.											.	FAM205A	45	.	0			c.C2121T						PASS	.						17.0	13.0	14.0					9																	34725116		692	1590	2282	SO:0001819	synonymous_variant	259308	exon4			TGCCAGGACCCCA		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.2121C>T	9.37:g.34725116G>A		Somatic	447	0	0		WXS	Illumina HiSeq	Phase_I	492	138	0.280488	NM_001141917	A8MVW7	Silent	SNP	ENST00000378788.3	37	CCDS55305.1																																																																																			G|0.858;A|0.142	0.142	strong		0.547	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
SYCP2	10388	hgsc.bcm.edu	37	20	58496438	58496438	+	Missense_Mutation	SNP	A	A	G	rs61730337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58496438A>G	ENST00000357552.3	-	4	320	c.95T>C	c.(94-96)aTt>aCt	p.I32T	SYCP2_ENST00000476314.1_5'UTR|SYCP2_ENST00000371001.2_Missense_Mutation_p.I32T			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	32					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ACAAATATCAATTTGCAAAAG	0.308													A|||	98	0.0195687	0.0711	0.0043	5008	,	,		15338	0.0		0.001	False		,,,				2504	0.0				p.I32T		Atlas-SNP	.											.	SYCP2	204	.	0			c.T95C						PASS	.	A	THR/ILE	248,4154	140.0+/-175.5	7,234,1960	55.0	52.0	53.0		95	1.3	1.0	20	dbSNP_129	53	2,8578	2.2+/-6.3	0,2,4288	yes	missense	SYCP2	NM_014258.2	89	7,236,6248	GG,GA,AA		0.0233,5.6338,1.9257	possibly-damaging	32/1531	58496438	250,12732	2201	4290	6491	SO:0001583	missense	10388	exon3			ATATCAATTTGCA	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.95T>C	20.37:g.58496438A>G	ENSP00000350162:p.Ile32Thr	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	193	101	0.523316	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	37	CCDS13482.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	A	0.025	-1.384165	0.01194	0.056338	2.33E-4	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834;ENST00000425931	T;T;T;T	0.39997	2.62;2.62;2.37;1.05	5.04	1.3	0.21679	.	0.654897	0.15121	N	0.279380	T	0.01421	0.0046	N	0.22421	0.69	0.21553	N	0.999649	B	0.20052	0.041	B	0.14578	0.011	T	0.10706	-1.0618	10	0.12766	T	0.61	-9.6108	1.5416	0.02557	0.3441:0.1539:0.3533:0.1487	.	32	Q9BX26	SYCP2_HUMAN	T	32;32;32;31	ENSP00000360040:I32T;ENSP00000350162:I32T;ENSP00000402456:I32T;ENSP00000399300:I31T	ENSP00000350162:I32T	I	-	2	0	SYCP2	57929833	0.892000	0.30473	0.999000	0.59377	0.442000	0.32017	0.388000	0.20735	0.357000	0.24183	-0.538000	0.04264	ATT	A|0.979;G|0.021	0.021	strong		0.308	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	
UBTF	7343	hgsc.bcm.edu	37	17	42284951	42284951	+	Silent	SNP	A	A	G	rs113823176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42284951A>G	ENST00000302904.4	-	20	2532	c.2040T>C	c.(2038-2040)gaT>gaC	p.D680D	UBTF_ENST00000527034.1_Missense_Mutation_p.M642T|UBTF_ENST00000436088.1_Silent_p.D680D|UBTF_ENST00000529383.1_Silent_p.D680D|UBTF_ENST00000343638.5_Silent_p.D643D|UBTF_ENST00000393606.3_Silent_p.D643D|UBTF_ENST00000526094.1_Silent_p.D643D|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000533177.1_Silent_p.D643D			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	680	Asp/Glu/Ser-rich (acidic).				chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|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)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		cctcttcatcatcctcctcGG	0.587													A|||	59	0.0117812	0.0431	0.0029	5008	,	,		17778	0.0		0.0	False		,,,				2504	0.0				p.D680D		Atlas-SNP	.											.	UBTF	65	.	0			c.T2040C						PASS	.	A	,,	105,4301	82.4+/-120.9	1,103,2099	156.0	104.0	122.0		1929,1929,2040	-5.1	0.5	17	dbSNP_132	122	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	UBTF	NM_001076683.1,NM_001076684.2,NM_014233.3	,,	1,103,6399	GG,GA,AA		0.0,2.3831,0.8073	,,	643/728,643/728,680/765	42284951	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	7343	exon20			TTCATCATCCTCC	BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.2040T>C	17.37:g.42284951A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	223	118	0.529148	NM_014233	A8K6R8	Silent	SNP	ENST00000302904.4	37	CCDS11480.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	10.81	1.455714	0.26161	0.023831	0.0	ENSG00000108312	ENST00000527034	D	0.98280	-4.84	5.05	-5.13	0.02884	.	.	.	.	.	D	0.84840	0.5561	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.84157	0.0426	6	0.33940	T	0.23	-7.4078	5.2771	0.15655	0.2064:0.218:0.469:0.1066	.	.	.	.	T	642	ENSP00000431539:M642T	ENSP00000431539:M642T	M	-	2	0	UBTF	39640477	0.000000	0.05858	0.464000	0.27143	0.990000	0.78478	-2.032000	0.01426	-1.382000	0.02109	0.402000	0.26972	ATG	A|0.990;G|0.010	0.010	strong		0.587	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233	
OTOF	9381	hgsc.bcm.edu	37	2	26687761	26687761	+	Missense_Mutation	SNP	G	G	A	rs17005371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26687761G>A	ENST00000272371.2	-	39	5062	c.4936C>T	c.(4936-4938)Ccc>Tcc	p.P1646S	OTOF_ENST00000339598.3_Missense_Mutation_p.P879S|OTOF_ENST00000402415.3_Missense_Mutation_p.P956S|OTOF_ENST00000338581.6_Missense_Mutation_p.P879S|OTOF_ENST00000403946.3_Missense_Mutation_p.P1646S	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1646			P -> S (in dbSNP:rs17005371). {ECO:0000269|PubMed:16371502}.		membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATCTCAGAGGGCCCAGTGAAG	0.647													G|||	800	0.159744	0.5386	0.0764	5008	,	,		17381	0.0		0.0149	False		,,,				2504	0.0204				p.P1646S	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C4936T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	1949,2457	543.7+/-376.3	441,1067,695	50.0	58.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2635,4936,2866,2635	4.9	1.0	2	dbSNP_123	56	110,8490	57.9+/-119.4	0,110,4190	yes	missense,missense,missense,missense	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	74,74,74,74	441,1177,4885	AA,AG,GG		1.2791,44.2351,15.8312	benign,benign,benign,benign	879/1231,1646/1998,956/1308,879/1231	26687761	2059,10947	2203	4300	6503	SO:0001583	missense	9381	exon39			CAGAGGGCCCAGT	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.4936C>T	2.37:g.26687761G>A	ENSP00000272371:p.Pro1646Ser	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	224	109	0.486607	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	288	0.13186813186813187	255	0.5182926829268293	26	0.0718232044198895	0	0.0	7	0.009234828496042216	G	12.47	1.949107	0.34377	0.442351	0.012791	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.58506	0.33;0.33;0.33;0.33;0.33	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.38649	1.16	0.09310	P	0.99999858138	B;B;B;B	0.24368	0.102;0.041;0.035;0.01	B;B;B;B	0.24394	0.03;0.053;0.027;0.022	T	0.35375	-0.9791	9	0.08599	T	0.76	-25.2998	17.7125	0.88326	0.0:0.0:1.0:0.0	rs17005371;rs60119788;rs17005371	1646;879;956;879	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	S	879;879;956;1646;1646	ENSP00000345137:P879S;ENSP00000344521:P879S;ENSP00000383906:P956S;ENSP00000272371:P1646S;ENSP00000385255:P1646S	ENSP00000272371:P1646S	P	-	1	0	OTOF	26541265	1.000000	0.71417	0.995000	0.50966	0.500000	0.33767	6.504000	0.73704	2.260000	0.74910	0.561000	0.74099	CCC	G|0.841;A|0.159	0.159	strong		0.647	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
SPIDR	23514	hgsc.bcm.edu	37	8	48511729	48511729	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:48511729C>T	ENST00000297423.4	+	10	1899	c.1515C>T	c.(1513-1515)agC>agT	p.S505S	SPIDR_ENST00000518074.1_Silent_p.S445S|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Silent_p.S435S	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	505					cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											AGGGGGCCAGCTCAGGACACA	0.592																																					p.S505S		Atlas-SNP	.											.	KIAA0146	64	.	0			c.C1515T						PASS	.						29.0	36.0	33.0					8																	48511729		2051	4183	6234	SO:0001819	synonymous_variant	23514	exon10			GGCCAGCTCAGGA	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"""KIAA0146"""	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.1515C>T	8.37:g.48511729C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Silent	SNP	ENST00000297423.4	37	CCDS43737.1	.	.	.	.	.	.	.	.	.	.	C	3.747	-0.052466	0.07362	.	.	ENSG00000164808	ENST00000519401	.	.	.	4.68	0.555	0.17247	.	.	.	.	.	T	0.23846	0.0577	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24764	-1.0151	4	.	.	.	.	3.972	0.09457	0.1661:0.488:0.0:0.3459	.	.	.	.	V	187	.	.	A	+	2	0	KIAA0146	48674282	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.473000	0.06615	0.134000	0.18681	0.585000	0.79938	GCT	.	.	none		0.592	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394	
PNMAL1	55228	hgsc.bcm.edu	37	19	46973981	46973981	+	Silent	SNP	G	G	A	rs4803960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46973981G>A	ENST00000313683.10	-	2	617	c.312C>T	c.(310-312)gcC>gcT	p.A104A	PNMAL1_ENST00000438932.2_Silent_p.A104A|PNMAL1_ENST00000602246.1_Intron	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	104										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)		ttaaaaactcggcatcctggg	0.562													A|||	1183	0.236222	0.3313	0.2089	5008	,	,		18155	0.1796		0.2485	False		,,,				2504	0.1728				p.A104A		Atlas-SNP	.											.	PNMAL1	87	.	0			c.C312T						PASS	.	A	,	1536,2870	670.9+/-402.4	268,1000,935	43.0	44.0	43.0		312,312	-6.2	0.3	19	dbSNP_111	43	2106,6494	713.3+/-405.9	283,1540,2477	no	coding-synonymous,coding-synonymous	PNMAL1	NM_001103149.1,NM_018215.3	,	551,2540,3412	AA,AG,GG		24.4884,34.8616,28.0025	,	104/379,104/440	46973981	3642,9364	2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			AAACTCGGCATCC	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.312C>T	19.37:g.46973981G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1																																																																																			G|0.732;A|0.268	0.268	strong		0.562	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
MUC4	4585	hgsc.bcm.edu	37	3	195506460	195506460	+	Missense_Mutation	SNP	G	G	C	rs113130007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195506460G>C	ENST00000463781.3	-	2	12450	c.11991C>G	c.(11989-11991)caC>caG	p.H3997Q	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3997Q	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.H3997Q(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)		GAGGGGTGGCGTGACCTGTGG	0.602													.|||	3	0.000599042	0.0015	0.0	5008	,	,		9092	0.0		0.0	False		,,,				2504	0.001				p.H3997Q		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	c.C11991G						scavenged	.						13.0	10.0	11.0					3																	195506460		669	1476	2145	SO:0001583	missense	4585	exon2			GGTGGCGTGACCT	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.11991C>G	3.37:g.195506460G>C	ENSP00000417498:p.His3997Gln	Somatic	116	2	0.0172414		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	.	.	.	.	.	.	.	.	.	.	g	4.646	0.120143	0.08881	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.42;1.51	0.764	-0.332	0.12675	.	0.000000	0.25267	U	0.031920	T	0.16642	0.0400	N	0.19112	0.55	0.09310	N	1	B	0.29988	0.264	B	0.35899	0.213	T	0.21552	-1.0242	9	.	.	.	.	5.1972	0.15245	0.2456:0.0:0.7544:0.0	.	3869	E7ESK3	.	Q	3997	ENSP00000417498:H3997Q;ENSP00000420243:H3997Q	.	H	-	3	2	MUC4	196991239	0.000000	0.05858	0.001000	0.08648	0.185000	0.23345	-0.425000	0.07017	-0.110000	0.12022	0.064000	0.15345	CAC	C|0.994;G|0.006	0.994	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZSCAN25	221785	hgsc.bcm.edu	37	7	99226981	99226981	+	Missense_Mutation	SNP	C	C	G	rs10239632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99226981C>G	ENST00000394152.2	+	8	1300	c.973C>G	c.(973-975)Cct>Gct	p.P325A	ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.P325A|ZSCAN25_ENST00000262941.6_Missense_Mutation_p.P253A	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	325			P -> A (in dbSNP:rs10239632).		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)										GCCTGGGCTTCCTCCTCCCCA	0.627													C|||	185	0.0369409	0.1263	0.0216	5008	,	,		17584	0.0		0.003	False		,,,				2504	0.0				p.P325A		Atlas-SNP	.											.	.	.	.	0			c.C973G						PASS	.	C	ALA/PRO	449,3957	211.8+/-231.9	28,393,1782	59.0	54.0	56.0		973	2.7	0.0	7	dbSNP_119	56	7,8593	3.7+/-12.6	0,7,4293	yes	missense	ZNF498	NM_145115.2	27	28,400,6075	GG,GC,CC		0.0814,10.1906,3.5061	benign	325/545	99226981	456,12550	2203	4300	6503	SO:0001583	missense	221785	exon8			GGGCTTCCTCCTC	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"""-"", ""Zinc fingers, C2H2-type"""	21961	protein-coding gene	gene with protein product			"""zinc finger protein 498"""	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.973C>G	7.37:g.99226981C>G	ENSP00000377708:p.Pro325Ala	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	82	0.037545787545787544	71	0.1443089430894309	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	C	0.010	-1.757120	0.00657	0.101906	8.14E-4	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.08807	3.06;3.06;3.05	4.82	2.66	0.31614	.	0.503847	0.16909	N	0.194576	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.42616	-0.9441	9	0.09590	T	0.72	-0.7741	2.5036	0.04639	0.2459:0.4907:0.1618:0.1016	rs10239632;rs10239632	253;325	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	A	325;325;253	ENSP00000377708:P325A;ENSP00000334800:P325A;ENSP00000262941:P253A	ENSP00000262941:P253A	P	+	1	0	ZNF498	99064917	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	0.695000	0.25527	1.140000	0.42260	-0.502000	0.04539	CCT	C|0.966;G|0.034	0.034	strong		0.627	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115	
MUC17	140453	hgsc.bcm.edu	37	7	100677714	100677714	+	Missense_Mutation	SNP	C	C	T	rs79432420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677714C>T	ENST00000306151.4	+	3	3081	c.3017C>T	c.(3016-3018)aCt>aTt	p.T1006I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1006	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)					CTTTCAACAACTCCTGTTGAC	0.512																																					p.T1006I		Atlas-SNP	.											.	MUC17	804	.	0			c.C3017T						PASS	.	C	ILE/THR	815,3591		0,815,1388	393.0	332.0	353.0		3017	0.7	0.0	7	dbSNP_131	353	728,7872		0,728,3572	no	missense	MUC17	NM_001040105.1	89	0,1543,4960	TT,TC,CC		8.4651,18.4975,11.8638	probably-damaging	1006/4494	100677714	1543,11463	2203	4300	6503	SO:0001583	missense	140453	exon3			CAACAACTCCTGT	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.3017C>T	7.37:g.100677714C>T	ENSP00000302716:p.Thr1006Ile	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	289	61	0.211073	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	3.251	-0.153209	0.06585	0.184975	0.084651	ENSG00000169876	ENST00000306151	T	0.02421	4.3	0.74	0.74	0.18330	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.09310	N	1	D	0.69078	0.997	D	0.65684	0.937	T	0.58025	-0.7709	9	0.30854	T	0.27	.	7.4353	0.27152	0.0:1.0:0.0:0.0	.	1006	Q685J3	MUC17_HUMAN	I	1006	ENSP00000302716:T1006I	ENSP00000302716:T1006I	T	+	2	0	MUC17	100464434	0.000000	0.05858	0.010000	0.14722	0.012000	0.07955	-0.005000	0.12855	0.720000	0.32209	0.134000	0.15878	ACT	C|0.989;T|0.011	0.011	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
BMX	660	hgsc.bcm.edu	37	X	15555339	15555339	+	Silent	SNP	G	G	A	rs376617024		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:15555339G>A	ENST00000357607.2	+	14	1493	c.1305G>A	c.(1303-1305)aaG>aaA	p.K435K	BMX_ENST00000348343.6_Silent_p.K435K|BMX_ENST00000342014.6_Silent_p.K435K			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	435	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					AGCTGGGCAAGTGGAAGGGGC	0.473													g|||	2	0.000529801	0.0	0.0	3775	,	,		13134	0.002		0.0	False		,,,				2504	0.0				p.K435K		Atlas-SNP	.											.	BMX	73	.	0			c.G1305A						PASS	.	G	,	1,3834		0,1,1631,571	187.0	167.0	174.0		1305,1305	3.5	1.0	X		174	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous	BMX	NM_001721.6,NM_203281.2	,	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	,	435/676,435/676	15555339	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	660	exon14			GGGCAAGTGGAAG	AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	1079	protein-coding gene	gene with protein product	"""BTK-like on X chromosome"""	300101				7970727	Standard	NM_203281		Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.1305G>A	X.37:g.15555339G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	217	100	0.460829	NM_001721	A6NIH9|O60564|Q12871	Silent	SNP	ENST00000357607.2	37	CCDS14168.1																																																																																			.	.	weak		0.473	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	NM_001721	
MEGF11	84465	hgsc.bcm.edu	37	15	66411441	66411441	+	Missense_Mutation	SNP	C	C	T	rs16949528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:66411441C>T	ENST00000409699.2	-	4	456	c.284G>A	c.(283-285)aGc>aAc	p.S95N	MEGF11_ENST00000288745.3_Intron|MEGF11_ENST00000395625.2_Intron|MEGF11_ENST00000395614.1_5'UTR|MEGF11_ENST00000422354.1_Missense_Mutation_p.S95N|MEGF11_ENST00000360698.4_Missense_Mutation_p.S95N			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	95	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.|EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.		S -> N (in dbSNP:rs16949528). {ECO:0000269|PubMed:15489334}.		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						GAAGTCTCCGCTCTCATAGTA	0.607													T|||	2141	0.427516	0.5545	0.2867	5008	,	,		15476	0.4762		0.2555	False		,,,				2504	0.4826				p.S95N		Atlas-SNP	.											.	MEGF11	70	.	0			c.G284A						PASS	.	T	ASN/SER	732,648		187,358,145	68.0	70.0	70.0		284	1.7	0.3	15	dbSNP_123	70	889,2291		135,619,836	yes	missense	MEGF11	NM_032445.2	46	322,977,981	TT,TC,CC		27.956,46.9565,35.5482	benign	95/1045	66411441	1621,2939	690	1590	2280	SO:0001583	missense	84465	exon4			TCTCCGCTCTCAT	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.284G>A	15.37:g.66411441C>T	ENSP00000386908:p.Ser95Asn	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	30	0.652174	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	37	CCDS10213.2	834	0.38186813186813184	278	0.5650406504065041	95	0.26243093922651933	268	0.46853146853146854	193	0.2546174142480211	T	11.20	1.569365	0.28003	0.530435	0.27956	ENSG00000157890	ENST00000409699;ENST00000422354;ENST00000360698	D;D;D	0.87029	-2.2;-2.2;-2.13	5.29	1.74	0.24563	EMI domain (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	M	0.65498	2.005	0.44798	P	0.0021970000000000045	B	0.02656	0.0	B	0.08055	0.003	T	0.45600	-0.9250	8	0.20046	T	0.44	.	9.9341	0.41541	0.0:0.4872:0.0:0.5128	rs16949528;rs56708944	95	A6BM72	MEG11_HUMAN	N	95	ENSP00000386908:S95N;ENSP00000414475:S95N;ENSP00000353919:S95N	ENSP00000353919:S95N	S	-	2	0	MEGF11	64198495	0.920000	0.31207	0.279000	0.24732	0.913000	0.54294	1.643000	0.37217	-0.184000	0.10567	-0.269000	0.10298	AGC	C|0.642;T|0.358	0.358	strong		0.607	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445	
ZNF175	7728	hgsc.bcm.edu	37	19	52089982	52089982	+	Missense_Mutation	SNP	C	C	G	rs61736479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52089982C>G	ENST00000262259.2	+	5	756	c.398C>G	c.(397-399)tCc>tGc	p.S133C	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	133					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		TCATGGTGTTCCATTTTAGAA	0.403													C|||	740	0.147764	0.3752	0.1138	5008	,	,		20622	0.121		0.0129	False		,,,				2504	0.0307				p.S133C		Atlas-SNP	.											.	ZNF175	65	.	0			c.C398G						PASS	.	C	CYS/SER	1471,2935	472.6+/-356.4	251,969,983	80.0	79.0	79.0		398	0.1	0.0	19	dbSNP_129	79	60,8538	34.3+/-88.2	0,60,4239	yes	missense	ZNF175	NM_007147.2	112	251,1029,5222	GG,GC,CC		0.6978,33.3863,11.7733	probably-damaging	133/712	52089982	1531,11473	2203	4299	6502	SO:0001583	missense	7728	exon5			GGTGTTCCATTTT	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"""Zinc fingers, C2H2-type"", ""-"""	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.398C>G	19.37:g.52089982C>G	ENSP00000262259:p.Ser133Cys	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	164	82	0.5	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	37	CCDS12837.1	290	0.13278388278388278	171	0.3475609756097561	41	0.1132596685082873	69	0.12062937062937062	9	0.011873350923482849	C	10.21	1.286900	0.23478	0.333863	0.006978	ENSG00000105497	ENST00000262259	T	0.10099	2.91	2.35	0.133	0.14766	.	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	0.53005	P	3.2000000000032E-5	B	0.18013	0.025	B	0.14023	0.01	T	0.47623	-0.9103	8	0.40728	T	0.16	.	1.2576	0.01995	0.2257:0.4137:0.2212:0.1394	rs61736479	133	Q9Y473	ZN175_HUMAN	C	133	ENSP00000262259:S133C	ENSP00000262259:S133C	S	+	2	0	ZNF175	56781794	0.000000	0.05858	0.012000	0.15200	0.421000	0.31385	-0.493000	0.06459	0.112000	0.17975	0.655000	0.94253	TCC	C|0.885;G|0.115	0.115	strong		0.403	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147	
GPR110	266977	hgsc.bcm.edu	37	6	46977894	46977894	+	Missense_Mutation	SNP	C	C	T	rs115292676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46977894C>T	ENST00000371253.2	-	11	1492	c.1277G>A	c.(1276-1278)cGg>cAg	p.R426Q	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.R229Q	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	426					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						AATGAATTTCCGAGAAAAATT	0.428													C|||	59	0.0117812	0.0431	0.0014	5008	,	,		19836	0.0		0.0	False		,,,				2504	0.001				p.R426Q		Atlas-SNP	.											GPR110,colon,carcinoma,-1,2	GPR110	102	2	0			c.G1277A						PASS	.	C	GLN/ARG	135,4271	97.1+/-135.8	4,127,2072	80.0	77.0	78.0		1277	1.6	0.1	6	dbSNP_132	78	7,8593	5.7+/-21.5	0,7,4293	yes	missense	GPR110	NM_153840.2	43	4,134,6365	TT,TC,CC		0.0814,3.064,1.0918	possibly-damaging	426/911	46977894	142,12864	2203	4300	6503	SO:0001583	missense	266977	exon11			AATTTCCGAGAAA	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.1277G>A	6.37:g.46977894C>T	ENSP00000360299:p.Arg426Gln	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	178	100	0.561798	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	37	CCDS34471.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	C	8.645	0.896884	0.17686	0.03064	8.14E-4	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000283297	T;T	0.32515	1.45;1.45	5.35	1.57	0.23409	.	0.603370	0.14993	N	0.286596	T	0.08935	0.0221	M	0.67953	2.075	0.09310	N	1	B	0.22604	0.072	B	0.09377	0.004	T	0.38200	-0.9672	10	0.09843	T	0.71	-0.0889	5.8064	0.18442	0.0:0.5882:0.1282:0.2836	.	426	Q5T601	GP110_HUMAN	Q	426;426;229	ENSP00000360299:R426Q;ENSP00000283297:R229Q	ENSP00000283297:R229Q	R	-	2	0	GPR110	47085853	0.000000	0.05858	0.104000	0.21259	0.823000	0.46562	-0.323000	0.07997	0.340000	0.23745	0.555000	0.69702	CGG	C|0.989;T|0.011	0.011	strong		0.428	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
RELN	5649	hgsc.bcm.edu	37	7	103124207	103124207	+	Silent	SNP	T	T	C	rs1062831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103124207T>C	ENST00000428762.1	-	62	10233	c.10074A>G	c.(10072-10074)gcA>gcG	p.A3358A	RELN_ENST00000343529.5_Silent_p.A3358A|RELN_ENST00000473945.1_5'UTR|RN7SKP86_ENST00000410454.1_RNA|CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000424685.2_Silent_p.A3358A	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	3358					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)		GCAGCAGCACTGCCTTGTCCA	0.517													t|||	1160	0.231629	0.3828	0.147	5008	,	,		18742	0.2659		0.0954	False		,,,				2504	0.1922				p.A3358A	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A10074G						PASS	.	T	,	1490,2916	476.1+/-357.5	256,978,969	193.0	166.0	175.0		10074,10074	-11.5	0.0	7	dbSNP_86	175	783,7817	185.0+/-232.9	39,705,3556	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	295,1683,4525	CC,CT,TT		9.1047,33.8175,17.4765	,	3358/3461,3358/3459	103124207	2273,10733	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon62			CAGCACTGCCTTG		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.10074A>G	7.37:g.103124207T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	134	59	0.440298	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			T|0.807;C|0.193	0.193	strong		0.517	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
SLC26A11	284129	hgsc.bcm.edu	37	17	78201686	78201686	+	Silent	SNP	C	C	T	rs61011315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78201686C>T	ENST00000361193.3	+	7	943	c.663C>T	c.(661-663)caC>caT	p.H221H	SLC26A11_ENST00000572725.1_Silent_p.H221H|SLC26A11_ENST00000411502.3_Silent_p.H221H|SLC26A11_ENST00000546047.2_Silent_p.H221H	NM_001166347.1|NM_173626.3	NP_001159819.1|NP_775897.3			solute carrier family 26 (anion exchanger), member 11											central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	28	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TGCGGGACCACGTGCCTCCCG	0.667													C|||	260	0.0519169	0.1808	0.0115	5008	,	,		13801	0.0		0.0109	False		,,,				2504	0.002				p.H221H		Atlas-SNP	.											.	SLC26A11	60	.	0			c.C663T						PASS	.	C	,,,	718,3688	297.6+/-284.8	61,596,1546	84.0	67.0	72.0		663,663,663,663	-0.2	0.1	17	dbSNP_129	72	113,8487	60.2+/-122.0	2,109,4189	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC26A11	NM_001166347.1,NM_001166348.1,NM_001166349.1,NM_173626.3	,,,	63,705,5735	TT,TC,CC		1.314,16.296,6.3894	,,,	221/607,221/607,221/607,221/607	78201686	831,12175	2203	4300	6503	SO:0001819	synonymous_variant	284129	exon7			GGACCACGTGCCT		CCDS11771.2	17q25	2013-07-18	2013-07-18		ENSG00000181045	ENSG00000181045		"""Solute carriers"""	14471	protein-coding gene	gene with protein product		610117	"""solute carrier family 26, member 11"""				Standard	NM_001166347		Approved		uc010dhv.2	Q86WA9	OTTHUMG00000133419	ENST00000361193.3:c.663C>T	17.37:g.78201686C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_173626		Silent	SNP	ENST00000361193.3	37	CCDS11771.2																																																																																			C|0.944;T|0.056	0.056	strong		0.667	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1		
RACGAP1	29127	hgsc.bcm.edu	37	12	50384542	50384542	+	Missense_Mutation	SNP	T	T	C	rs140590023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50384542T>C	ENST00000427314.2	-	18	1971	c.1748A>G	c.(1747-1749)cAt>cGt	p.H583R	RACGAP1_ENST00000548961.1_Intron|RACGAP1_ENST00000454520.2_Missense_Mutation_p.H583R|RACGAP1_ENST00000312377.5_Missense_Mutation_p.H583R|RACGAP1_ENST00000551016.1_Missense_Mutation_p.H583R|RACGAP1_ENST00000547905.1_Missense_Mutation_p.H583R|RACGAP1_ENST00000434422.1_Missense_Mutation_p.H583R	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						GAGAAGCTGATGTTCAGGAGT	0.448													T|||	7	0.00139776	0.0053	0.0	5008	,	,		18657	0.0		0.0	False		,,,				2504	0.0				p.H583R		Atlas-SNP	.											.	RACGAP1	36	.	0			c.A1748G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS	24,4382	30.8+/-60.4	0,24,2179	99.0	100.0	100.0		1748,1748,1748	4.3	1.0	12	dbSNP_134	100	0,8600		0,0,4300	yes	missense,missense,missense	RACGAP1	NM_001126103.1,NM_001126104.1,NM_013277.3	29,29,29	0,24,6479	CC,CT,TT		0.0,0.5447,0.1845	benign,benign,benign	583/633,583/633,583/633	50384542	24,12982	2203	4300	6503	SO:0001583	missense	29127	exon18			AGCTGATGTTCAG		CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000427314.2:c.1748A>G	12.37:g.50384542T>C	ENSP00000404190:p.His583Arg	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	167	67	0.401198	NM_013277		Missense_Mutation	SNP	ENST00000427314.2	37	CCDS8795.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	10.23	1.292278	0.23564	0.005447	0.0	ENSG00000161800	ENST00000427314;ENST00000312377;ENST00000434422;ENST00000454520;ENST00000551016;ENST00000547905	T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81	5.44	4.26	0.50523	.	0.261377	0.45606	D	0.000346	T	0.12347	0.0300	L	0.40543	1.245	0.32252	N	0.571354	B	0.02656	0.0	B	0.04013	0.001	T	0.21042	-1.0257	10	0.12103	T	0.63	-5.0933	7.5935	0.28035	0.1299:0.0708:0.0:0.7993	.	583	Q9H0H5	RGAP1_HUMAN	R	583	ENSP00000404190:H583R;ENSP00000309871:H583R;ENSP00000413241:H583R;ENSP00000404808:H583R;ENSP00000449374:H583R;ENSP00000449370:H583R	ENSP00000309871:H583R	H	-	2	0	RACGAP1	48670809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.825000	0.62708	0.955000	0.37878	0.533000	0.62120	CAT	T|0.998;C|0.002	0.002	strong		0.448	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277	
TSPAN2	10100	hgsc.bcm.edu	37	1	115601528	115601528	+	Silent	SNP	C	C	G	rs3738702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:115601528C>G	ENST00000369516.2	-	5	451	c.420G>C	c.(418-420)ggG>ggC	p.G140G	TSPAN2_ENST00000491992.1_5'Flank|TSPAN2_ENST00000369515.2_Silent_p.G115G|TSPAN2_ENST00000369514.2_Silent_p.G140G	NM_005725.4	NP_005716.2	O60636	TSN2_HUMAN	tetraspanin 2	140					astrocyte development (GO:0014002)|axon development (GO:0061564)|brain development (GO:0007420)|inflammatory response (GO:0006954)|microglia development (GO:0014005)|myelination (GO:0042552)|oligodendrocyte differentiation (GO:0048709)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)				central_nervous_system(1)|large_intestine(4)|lung(3)|pancreas(1)|prostate(1)	10	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		TGATGAGTGTCCCATTGCCTT	0.413													C|||	474	0.0946486	0.1974	0.0865	5008	,	,		20595	0.0169		0.0746	False		,,,				2504	0.0624				p.G140G		Atlas-SNP	.											TSPAN2,NS,malignant_melanoma,-1,1	TSPAN2	37	1	0			c.G420C						PASS	.	C		746,3660	305.2+/-288.9	71,604,1528	273.0	248.0	257.0		420	-2.5	0.9	1	dbSNP_107	257	624,7976	162.0+/-214.8	15,594,3691	no	coding-synonymous	TSPAN2	NM_005725.4		86,1198,5219	GG,GC,CC		7.2558,16.9315,10.5336		140/222	115601528	1370,11636	2203	4300	6503	SO:0001819	synonymous_variant	10100	exon5			GAGTGTCCCATTG	AF054839	CCDS881.1	1p13.1	2013-02-14			ENSG00000134198	ENSG00000134198		"""Tetraspanins"""	20659	protein-coding gene	gene with protein product		613133				9714763, 11739647	Standard	NM_005725		Approved	TSPAN-2, TSN2, FLJ12082	uc001eft.3	O60636	OTTHUMG00000011878	ENST00000369516.2:c.420G>C	1.37:g.115601528C>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	141	68	0.482269	NM_005725	D6PTH4|Q5TET2|Q8WU05	Silent	SNP	ENST00000369516.2	37	CCDS881.1																																																																																			C|0.901;G|0.099	0.099	strong		0.413	TSPAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032828.1	NM_005725	
KRT78	196374	hgsc.bcm.edu	37	12	53240584	53240584	+	Silent	SNP	A	A	G	rs2682342	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53240584A>G	ENST00000304620.4	-	3	687	c.624T>C	c.(622-624)cgT>cgC	p.R208R	KRT78_ENST00000359499.4_Silent_p.R98R	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	208	Coil 1B.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						CAAGTGTGGCACGCCTGTGGG	0.567													G|||	1564	0.3123	0.6331	0.2421	5008	,	,		19681	0.3393		0.0934	False		,,,				2504	0.1258				p.R208R		Atlas-SNP	.											KRT78,caecum,carcinoma,-1,1	KRT78	41	1	0			c.T624C						PASS	.	G		2377,2029	562.8+/-381.0	642,1093,468	88.0	64.0	72.0		624	-4.8	0.0	12	dbSNP_100	72	850,7750	779.8+/-407.7	39,772,3489	no	coding-synonymous	KRT78	NM_173352.2		681,1865,3957	GG,GA,AA		9.8837,46.0508,24.8116		208/521	53240584	3227,9779	2203	4300	6503	SO:0001819	synonymous_variant	196374	exon3			TGTGGCACGCCTG	AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.624T>C	12.37:g.53240584A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Silent	SNP	ENST00000304620.4	37	CCDS8840.1																																																																																			A|0.737;G|0.263	0.263	strong		0.567	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352	
OR2A2	442361	hgsc.bcm.edu	37	7	143807304	143807304	+	Missense_Mutation	SNP	T	T	C	rs10252253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143807304T>C	ENST00000408979.2	+	1	698	c.629T>C	c.(628-630)cTt>cCt	p.L210P		NM_001005480.2	NP_001005480.2	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A, member 2	210			L -> P (in dbSNP:rs10252253).			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)					GTCGGGCCTCTTTCCTTGATT	0.522													.|||	802	0.160144	0.4039	0.1311	5008	,	,		20164	0.0		0.166	False		,,,				2504	0.0102				p.L210P		Atlas-SNP	.											OR2A2,colon,carcinoma,0,1	OR2A2	48	1	0			c.T629C						PASS	.	T	PRO/LEU	1470,2502		249,972,765	129.0	134.0	132.0		629	3.5	0.0	7	dbSNP_119	132	1680,6688		159,1362,2663	yes	missense	OR2A2	NM_001005480.2	98	408,2334,3428	CC,CT,TT		20.0765,37.0091,25.5267	benign	210/319	143807304	3150,9190	1986	4184	6170	SO:0001583	missense	442361	exon1			GGCCTCTTTCCTT		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.629T>C	7.37:g.143807304T>C	ENSP00000386209:p.Leu210Pro	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	116	65	0.560345	NM_001005480	B2RN85|Q8NGT6	Missense_Mutation	SNP	ENST00000408979.2	37	CCDS43671.1	372	0.17032967032967034	200	0.4065040650406504	52	0.143646408839779	0	0.0	120	0.158311345646438	T	9.379	1.072517	0.20147	0.370091	0.200765	ENSG00000221989	ENST00000408979	T	0.49432	0.78	3.47	3.47	0.39725	GPCR, rhodopsin-like superfamily (1);	0.293273	0.18405	U	0.142236	T	0.00012	0.0000	M	0.87900	2.915	0.38232	P	0.05894100000000002	B	0.31383	0.321	B	0.43728	0.429	T	0.40496	-0.9560	9	0.59425	D	0.04	-12.3573	10.1929	0.43037	0.0:0.0:0.0:1.0	rs10252253;rs59481350;rs10252253	210	Q6IF42	OR2A2_HUMAN	P	210	ENSP00000386209:L210P	ENSP00000386209:L210P	L	+	2	0	OR2A2	143438237	0.001000	0.12720	0.044000	0.18714	0.012000	0.07955	1.019000	0.30014	1.576000	0.49790	0.418000	0.28097	CTT	T|0.806;C|0.194	0.194	strong		0.522	OR2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349978.1		
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011406	46011406	+	Silent	SNP	G	G	T	rs374116165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011406G>T	ENST00000400368.1	-	1	980	c.960C>A	c.(958-960)gtC>gtA	p.V320V	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	320	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CACAGGAGGGGACGGGCACGC	0.701													.|||	155	0.0309505	0.1127	0.0086	5008	,	,		19947	0.0		0.0	False		,,,				2504	0.0				p.V320V		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C960A						PASS	.						68.0	83.0	78.0					21																	46011406		2201	4300	6501	SO:0001819	synonymous_variant	386674	exon1			GGAGGGGACGGGC	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.960C>A	21.37:g.46011406G>T		Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	258	46	0.178295	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	weak		0.701	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
AKIRIN2	55122	hgsc.bcm.edu	37	6	88385579	88385579	+	Splice_Site	SNP	G	G	A	rs63749091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88385579G>A	ENST00000257787.5	-	4	1124	c.600C>T	c.(598-600)agC>agT	p.S200S		NM_018064.3	NP_060534.1	Q53H80	AKIR2_HUMAN	akirin 2	200					embryo development (GO:0009790)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to lipopolysaccharide (GO:0032496)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)			large_intestine(4)	4						AATACTTACAGCTAGCAGGCT	0.303													A|||	164	0.0327476	0.1165	0.0144	5008	,	,		19800	0.0		0.0	False		,,,				2504	0.0				p.S200S		Atlas-SNP	.											.	AKIRIN2	13	.	0			c.C600T						PASS	.	A		466,3938	782.5+/-414.6	26,414,1762	71.0	69.0	70.0		600	4.6	1.0	6	dbSNP_129	70	1,8599	818.3+/-406.9	0,1,4299	yes	coding-synonymous-near-splice	AKIRIN2	NM_018064.3		26,415,6061	AA,AG,GG		0.0116,10.5813,3.5912		200/204	88385579	467,12537	2202	4300	6502	SO:0001630	splice_region_variant	55122	exon4			CTTACAGCTAGCA	BC000764	CCDS5013.1	6q15	2009-04-17	2008-06-23	2008-06-23	ENSG00000135334	ENSG00000135334			21407	protein-coding gene	gene with protein product		615165	"""chromosome 6 open reading frame 166"""	C6orf166			Standard	NM_018064		Approved	FLJ10342, dJ486L4.2	uc003pmk.3	Q53H80	OTTHUMG00000015180	ENST00000257787.5:c.601+1C>T	6.37:g.88385579G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_018064	Q9BQB1	Silent	SNP	ENST00000257787.5	37	CCDS5013.1																																																																																			G|0.968;A|0.032	0.032	strong		0.303	AKIRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041455.1	NM_018064	Silent
TOX	9760	hgsc.bcm.edu	37	8	59727966	59727966	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:59727966C>T	ENST00000361421.1	-	7	1543	c.1323G>A	c.(1321-1323)atG>atA	p.M441I	RNU4-50P_ENST00000364361.1_RNA	NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	441						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				GGGGCTGCTGCATGGTGAGCG	0.577																																					p.M441I	Pancreas(161;610 1969 17913 21374 22725)	Atlas-SNP	.											.	TOX	83	.	0			c.G1323A						PASS	.						69.0	73.0	72.0					8																	59727966		2203	4300	6503	SO:0001583	missense	9760	exon7			CTGCTGCATGGTG		CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.1323G>A	8.37:g.59727966C>T	ENSP00000354842:p.Met441Ile	Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	334	166	0.497006	NM_014729	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	37	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447063	0.63178	.	.	ENSG00000198846	ENST00000361421;ENST00000456290	T	0.12255	2.7	5.98	5.98	0.97165	.	0.196250	0.56097	D	0.000022	T	0.32675	0.0837	L	0.55213	1.73	0.80722	D	1	P	0.45126	0.851	P	0.58391	0.838	T	0.00031	-1.2282	9	.	.	.	.	20.4366	0.99092	0.0:1.0:0.0:0.0	.	441	O94900	TOX_HUMAN	I	441;191	ENSP00000354842:M441I	.	M	-	3	0	TOX	59890520	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.711000	0.74675	2.837000	0.97791	0.591000	0.81541	ATG	.	.	none		0.577	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729	
SSPO	23145	hgsc.bcm.edu	37	7	149489048	149489048	+	RNA	SNP	C	C	T	rs893602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149489048C>T	ENST00000378016.2	+	0	5389							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)			GCACAGCACCCGCCAGACCAG	0.652													C|||	131	0.0261581	0.0946	0.0086	5008	,	,		18478	0.0		0.0	False		,,,				2504	0.0				p.R1797C		Atlas-SNP	.											.	.	.	.	0			c.C5389T						PASS	.	C		257,3869		9,239,1815	28.0	32.0	31.0		5393	3.0	0.0	7	dbSNP_86	31	4,8368		0,4,4182	yes	coding-notMod3	SSPO	NM_198455.2		9,243,5997	TT,TC,CC		0.0478,6.2288,2.0883			149489048	261,12237	2063	4186	6249			23145	exon35			AGCACCCGCCAGA	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.149489048C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.979;T|0.021	0.021	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
ZNF645	158506	hgsc.bcm.edu	37	X	22291732	22291732	+	Silent	SNP	C	C	T	rs6629461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:22291732C>T	ENST00000323684.1	+	1	668	c.624C>T	c.(622-624)atC>atT	p.I208I		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	208					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						ATAAGGATATCCAGGCTCCTC	0.438													T|||	1014	0.268609	0.202	0.2608	3775	,	,		15996	0.3403		0.0885	False		,,,				2504	0.137				p.I208I		Atlas-SNP	.											.	ZNF645	67	.	0			c.C624T						PASS	.	T		937,2898		103,585,146,944,425	141.0	97.0	112.0		624	-2.1	0.0	X	dbSNP_116	112	795,5933		44,493,214,1891,1658	no	coding-synonymous	ZNF645	NM_152577.3		147,1078,360,2835,2083	TT,TC,T,CC,C		11.8163,24.4329,16.3969		208/426	22291732	1732,8831	2203	4300	6503	SO:0001819	synonymous_variant	158506	exon1			GGATATCCAGGCT	AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.624C>T	X.37:g.22291732C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_152577	A0AV29|A0AV31|E3SBK4|Q6DJY9	Silent	SNP	ENST00000323684.1	37	CCDS14205.1																																																																																			C|0.774;T|0.226	0.226	strong		0.438	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577	
CNTROB	116840	hgsc.bcm.edu	37	17	7847955	7847955	+	Splice_Site	SNP	C	C	A	rs11650083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7847955C>A	ENST00000563694.1	+	12	2658	c.1733C>A	c.(1732-1734)cCa>cAa	p.P578Q	CNTROB_ENST00000380262.3_Splice_Site_p.P578Q|CNTROB_ENST00000565740.1_Splice_Site_p.P578Q|CNTROB_ENST00000380255.3_Intron	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	578	Pro-rich.|Required for centrosome localization.		P -> Q (in dbSNP:rs11650083). {ECO:0000269|PubMed:11984006, ECO:0000269|PubMed:14702039}.		centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				CCCAACCCTCCAGTACGCCTT	0.557													C|||	3028	0.604633	0.447	0.6614	5008	,	,		4301	0.8016		0.4493	False		,,,				2504	0.7342				p.P578Q		Atlas-SNP	.											CNTROB,colon,carcinoma,0,1	CNTROB	61	1	0			c.C1733A						PASS	.	C	GLN/PRO,GLN/PRO	2082,2324	571.4+/-383.1	501,1080,622	99.0	91.0	94.0		1733,1733	-2.4	0.0	17	dbSNP_120	94	3952,4648	547.5+/-385.2	914,2124,1262	yes	missense-near-splice,missense-near-splice	CNTROB	NM_001037144.5,NM_053051.3	76,76	1415,3204,1884	AA,AC,CC		45.9535,47.2537,46.394	benign,benign	578/926,578/904	7847955	6034,6972	2203	4300	6503	SO:0001630	splice_region_variant	116840	exon12			ACCCTCCAGTACG	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.1734+1C>A	17.37:g.7847955C>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	117	55	0.470085	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Missense_Mutation	SNP	ENST00000563694.1	37	CCDS11126.1	1225	0.5608974358974359	234	0.47560975609756095	220	0.6077348066298343	424	0.7412587412587412	347	0.4577836411609499	C	8.908	0.957899	0.18507	0.472537	0.459535	ENSG00000170037	ENST00000380262	T	0.38077	1.16	4.56	-2.37	0.06643	.	1.024840	0.07770	N	0.951533	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B;B	0.12013	0.001;0.001;0.005	B;B;B	0.12156	0.001;0.001;0.007	T	0.40757	-0.9546	9	0.10902	T	0.67	-1.0583	4.5619	0.12165	0.5422:0.2684:0.0:0.1895	rs11650083;rs52795073;rs57150255;rs11650083	578;578;578	Q8N137-3;Q8N137;Q8N137-2	.;CNTRB_HUMAN;.	Q	578	ENSP00000369614:P578Q	ENSP00000369614:P578Q	P	+	2	0	CNTROB	7788680	0.021000	0.18746	0.002000	0.10522	0.010000	0.07245	-0.104000	0.10923	-0.113000	0.11958	0.561000	0.74099	CCA	C|0.491;A|0.509	0.509	strong		0.557	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	Missense_Mutation
FBLN2	2199	hgsc.bcm.edu	37	3	13649665	13649665	+	Silent	SNP	C	C	T	rs13327200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:13649665C>T	ENST00000295760.7	+	3	1479	c.1410C>T	c.(1408-1410)aaC>aaT	p.N470N	FBLN2_ENST00000535798.1_Silent_p.N496N|FBLN2_ENST00000492059.1_Silent_p.N470N|FBLN2_ENST00000404922.3_Silent_p.N470N	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	470	Anaphylatoxin-like 1. {ECO:0000255|PROSITE-ProRule:PRU00022}.				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)			CTGAGGACAACGTCTGCAGGT	0.632													C|||	454	0.090655	0.3222	0.0389	5008	,	,		20343	0.0		0.001	False		,,,				2504	0.0				p.N470N		Atlas-SNP	.											.	FBLN2	137	.	0			c.C1410T						PASS	.	C	,,	979,3341		108,763,1289	56.0	61.0	59.0		1410,1410,1410	-1.4	0.0	3	dbSNP_121	59	11,8503		0,11,4246	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLN2	NM_001004019.1,NM_001165035.1,NM_001998.2	,,	108,774,5535	TT,TC,CC		0.1292,22.662,7.7139	,,	470/1232,470/1232,470/1185	13649665	990,11844	2160	4257	6417	SO:0001819	synonymous_variant	2199	exon3			GGACAACGTCTGC	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.1410C>T	3.37:g.13649665C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	NM_001998	B7Z9C5|Q8IUI0|Q8IUI1	Silent	SNP	ENST00000295760.7	37	CCDS46762.1																																																																																			C|0.911;T|0.089	0.089	strong		0.632	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019	
VWDE	221806	hgsc.bcm.edu	37	7	12409327	12409327	+	Missense_Mutation	SNP	C	C	T	rs17165910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12409327C>T	ENST00000275358.3	-	12	2793	c.2605G>A	c.(2605-2607)Gag>Aag	p.E869K		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	869						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TATTTCCCCTCCTCCACAATC	0.418													C|||	785	0.156749	0.1755	0.0836	5008	,	,		18835	0.2024		0.1034	False		,,,				2504	0.1912				p.E869K		Atlas-SNP	.											.	VWDE	123	.	0			c.G2605A						PASS	.	C	LYS/GLU	240,1144		21,198,473	165.0	130.0	140.0		2605	4.8	1.0	7	dbSNP_123	140	366,2816		20,326,1245	yes	missense	VWDE	NM_001135924.1	56	41,524,1718	TT,TC,CC		11.5022,17.341,13.272	possibly-damaging	869/1591	12409327	606,3960	692	1591	2283	SO:0001583	missense	221806	exon12			TCCCCTCCTCCAC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.2605G>A	7.37:g.12409327C>T	ENSP00000275358:p.Glu869Lys	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	277	103	0.371841	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	340	0.15567765567765568	84	0.17073170731707318	31	0.0856353591160221	138	0.24125874125874125	87	0.11477572559366754	C	15.55	2.866174	0.51588	0.17341	0.115022	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.82081	-1.57	4.83	4.83	0.62350	.	0.183925	0.45867	D	0.000329	T	0.00109	0.0003	L	0.60455	1.87	0.43652	P	0.003940000000000055	D	0.57257	0.979	P	0.47528	0.549	T	0.01027	-1.1476	9	0.56958	D	0.05	.	13.1144	0.59292	0.1602:0.8398:0.0:0.0	rs17165910;rs52834764;rs17165910	869	Q8N2E2	VWDE_HUMAN	K	869;323	ENSP00000275358:E869K	ENSP00000275358:E869K	E	-	1	0	VWDE	12375852	1.000000	0.71417	1.000000	0.80357	0.239000	0.25481	2.771000	0.47670	2.512000	0.84698	0.655000	0.94253	GAG	C|0.841;T|0.159	0.159	strong		0.418	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
NRIP1	8204	hgsc.bcm.edu	37	21	16337448	16337448	+	Silent	SNP	C	C	A	rs28707654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:16337448C>A	ENST00000400202.1	-	3	3778	c.3066G>T	c.(3064-3066)ggG>ggT	p.G1022G	NRIP1_ENST00000400199.1_Silent_p.G1022G|AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Silent_p.G1022G			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	1022	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)		CTGGTCTAGACCCTGCACAGC	0.478													C|||	112	0.0223642	0.0787	0.0115	5008	,	,		19106	0.0		0.0	False		,,,				2504	0.0				p.G1022G		Atlas-SNP	.											.	NRIP1	103	.	0			c.G3066T						PASS	.	C		332,4072	171.6+/-201.8	15,302,1885	51.0	49.0	50.0		3066	-4.7	0.0	21	dbSNP_125	50	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	NRIP1	NM_003489.3		15,303,6183	AA,AC,CC		0.0116,7.5386,2.5611		1022/1159	16337448	333,12669	2202	4299	6501	SO:0001819	synonymous_variant	8204	exon4			TCTAGACCCTGCA	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.3066G>T	21.37:g.16337448C>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	37	CCDS13568.1																																																																																			C|0.978;A|0.022	0.022	strong		0.478	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
PCNXL4	64430	hgsc.bcm.edu	37	14	60585282	60585282	+	Missense_Mutation	SNP	G	G	A	rs144345462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:60585282G>A	ENST00000406854.1	+	7	2368	c.1814G>A	c.(1813-1815)cGa>cAa	p.R605Q	PCNXL4_ENST00000535349.1_5'UTR|PCNXL4_ENST00000404681.2_Missense_Mutation_p.R605Q|PCNXL4_ENST00000317623.4_Missense_Mutation_p.R371Q|PCNXL4_ENST00000406949.1_Missense_Mutation_p.R371Q			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	605						integral component of membrane (GO:0016021)											GGGTTTCCCCGACCTATTCAG	0.493													G|||	32	0.00638978	0.0242	0.0	5008	,	,		16639	0.0		0.0	False		,,,				2504	0.0				p.R371Q		Atlas-SNP	.											.	.	.	.	0			c.G1112A						PASS	.	G	GLN/ARG	39,4367	42.3+/-75.8	0,39,2164	70.0	63.0	65.0		1112	6.1	1.0	14	dbSNP_134	65	0,8600		0,0,4300	yes	missense	C14orf135	NM_022495.5	43	0,39,6464	AA,AG,GG		0.0,0.8852,0.2999	probably-damaging	371/939	60585282	39,12967	2203	4300	6503	SO:0001583	missense	64430	exon6			TTCCCCGACCTAT	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.1814G>A	14.37:g.60585282G>A	ENSP00000384801:p.Arg605Gln	Somatic	294	1	0.00340136		WXS	Illumina HiSeq	Phase_I	323	148	0.458204	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	G	36	5.921833	0.97105	0.008852	0.0	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681	T;T;T;T	0.57436	0.4;0.43;0.65;0.43	6.07	6.07	0.98685	.	.	.	.	.	T	0.46521	0.1397	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.67304	-0.5704	9	0.87932	D	0	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	605;371	Q63HM2;B5MC47	CN135_HUMAN;.	Q	371;605;371;605	ENSP00000317396:R371Q;ENSP00000384801:R605Q;ENSP00000385201:R371Q;ENSP00000385713:R605Q	ENSP00000317396:R371Q	R	+	2	0	C14orf135	59655035	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.126000	0.94411	2.890000	0.99128	0.650000	0.86243	CGA	G|0.991;A|0.009	0.009	strong		0.493	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
SLC23A2	9962	hgsc.bcm.edu	37	20	4843470	4843470	+	Silent	SNP	C	C	A	rs34073337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:4843470C>A	ENST00000379333.1	-	14	1832	c.1440G>T	c.(1438-1440)gcG>gcT	p.A480A	SLC23A2_ENST00000424750.2_Silent_p.A366A|SLC23A2_ENST00000338244.1_Silent_p.A480A	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	480					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						CCGGAAGGGACGCAAAGAGGG	0.562													C|||	314	0.0626997	0.1233	0.0533	5008	,	,		16336	0.0		0.0666	False		,,,				2504	0.0481				p.A480A		Atlas-SNP	.											SLC23A2,caecum,carcinoma,0,2	SLC23A2	62	2	0			c.G1440T						PASS	.	C	,	490,3916	228.1+/-243.1	25,440,1738	68.0	67.0	67.0		1440,1440	-6.8	0.9	20	dbSNP_126	67	508,8092	144.0+/-200.0	16,476,3808	no	coding-synonymous,coding-synonymous	SLC23A2	NM_005116.5,NM_203327.1	,	41,916,5546	AA,AC,CC		5.907,11.1212,7.6734	,	480/651,480/651	4843470	998,12008	2203	4300	6503	SO:0001819	synonymous_variant	9962	exon14			AAGGGACGCAAAG	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.1440G>T	20.37:g.4843470C>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	37	14	0.378378	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	37	CCDS13085.1	120	0.054945054945054944	45	0.09146341463414634	22	0.06077348066298342	1	0.0017482517482517483	52	0.06860158311345646	C	1.669	-0.509488	0.04231	0.111212	0.05907	ENSG00000089057	ENST00000423430	.	.	.	5.61	-6.79	0.01715	.	.	.	.	.	T	0.00328	0.0010	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.20706	-1.0267	3	.	.	.	-21.3707	2.9919	0.05986	0.1501:0.1241:0.4221:0.3037	rs34073337	.	.	.	F	237	.	.	V	-	1	0	SLC23A2	4791470	0.097000	0.21791	0.892000	0.35008	0.041000	0.13682	-0.896000	0.04114	-1.003000	0.03425	-0.972000	0.02603	GTC	C|0.930;A|0.070	0.070	strong		0.562	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1		
DSP	1832	hgsc.bcm.edu	37	6	7580958	7580958	+	Missense_Mutation	SNP	A	A	G	rs2076299|rs397516939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7580958A>G	ENST00000379802.3	+	23	4876	c.4535A>G	c.(4534-4536)tAt>tGt	p.Y1512C	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1512	Central fibrous rod domain.		Y -> C (in dbSNP:rs2076299). {ECO:0000269|PubMed:19863551, ECO:0000269|PubMed:20031617}.		adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AGGGTCCAGTATGACCTGCAG	0.428													A|||	1018	0.203275	0.3139	0.1772	5008	,	,		21936	0.2867		0.0358	False		,,,				2504	0.1585				p.Y1512C		Atlas-SNP	.											.	DSP	306	.	0			c.A4535G						PASS	.	A	,CYS/TYR	1193,3213	414.6+/-336.9	177,839,1187	121.0	117.0	118.0		,4535	1.8	0.4	6	dbSNP_96	118	380,8220	123.9+/-182.7	5,370,3925	yes	intron,missense	DSP	NM_001008844.1,NM_004415.2	,194	182,1209,5112	GG,GA,AA		4.4186,27.0767,12.0944	,benign	,1512/2872	7580958	1573,11433	2203	4300	6503	SO:0001583	missense	1832	exon23			TCCAGTATGACCT	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.4535A>G	6.37:g.7580958A>G	ENSP00000369129:p.Tyr1512Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	399	0.18269230769230768	132	0.2682926829268293	52	0.143646408839779	180	0.3146853146853147	35	0.04617414248021108	A	7.581	0.668762	0.14776	0.270767	0.044186	ENSG00000096696	ENST00000379802	T	0.70164	-0.46	5.74	1.8	0.24995	.	0.497515	0.18746	N	0.132315	T	0.28001	0.0690	N	0.14661	0.345	0.09310	P	0.9999999999893495	P	0.34462	0.454	B	0.36959	0.237	T	0.05273	-1.0895	9	0.52906	T	0.07	.	5.5709	0.17196	0.4336:0.0:0.0811:0.4854	rs2076299;rs52792530;rs57440467;rs2076299	1512	P15924	DESP_HUMAN	C	1512	ENSP00000369129:Y1512C	ENSP00000369129:Y1512C	Y	+	2	0	DSP	7525957	0.062000	0.20869	0.380000	0.26093	0.546000	0.35178	0.826000	0.27407	0.431000	0.26258	0.533000	0.62120	TAT	A|0.840;C|0.001	.	strong		0.428	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
KCNK17	89822	hgsc.bcm.edu	37	6	39267315	39267315	+	Missense_Mutation	SNP	C	C	T	rs2758910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:39267315C>T	ENST00000373231.4	-	5	1119	c.887G>A	c.(886-888)cGg>cAg	p.R296Q	KCNK17_ENST00000453413.2_3'UTR	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	296			R -> Q (in dbSNP:rs2758910).		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						CTCTGGCTCCCGGTCAGGTCC	0.587													c|||	39	0.00778754	0.0287	0.0014	5008	,	,		20167	0.0		0.0	False		,,,				2504	0.0				p.R296Q		Atlas-SNP	.											KCNK17,NS,carcinoma,-1,1	KCNK17	61	1	0			c.G887A						PASS	.	T	,GLN/ARG	142,4264	101.2+/-139.8	1,140,2062	90.0	79.0	83.0		,887	-2.5	0.0	6	dbSNP_100	83	0,8600		0,0,4300	yes	utr-3,missense	KCNK17	NM_001135111.1,NM_031460.3	,43	1,140,6362	TT,TC,CC		0.0,3.2229,1.0918	,benign	,296/333	39267315	142,12864	2203	4300	6503	SO:0001583	missense	89822	exon5			GGCTCCCGGTCAG	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.887G>A	6.37:g.39267315C>T	ENSP00000362328:p.Arg296Gln	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	165	80	0.484848	NM_031460	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Missense_Mutation	SNP	ENST00000373231.4	37	CCDS4842.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	c	10.09	1.254922	0.22965	0.032229	0.0	ENSG00000124780	ENST00000373231	T	0.15603	2.41	4.25	-2.45	0.06481	.	.	.	.	.	T	0.01765	0.0056	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.47262	-0.9131	9	0.11182	T	0.66	.	5.3132	0.15841	0.0:0.4054:0.1426:0.452	rs2758910;rs52820365;rs2758910	296	Q96T54	KCNKH_HUMAN	Q	296	ENSP00000362328:R296Q	ENSP00000362328:R296Q	R	-	2	0	KCNK17	39375293	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.463000	0.06696	-0.926000	0.03770	-0.119000	0.15052	CGG	C|0.989;T|0.011	0.011	strong		0.587	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460	
FAM161A	84140	hgsc.bcm.edu	37	2	62069358	62069358	+	Missense_Mutation	SNP	T	T	C	rs11125895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:62069358T>C	ENST00000405894.3	-	2	422	c.321A>G	c.(319-321)atA>atG	p.I107M	FAM161A_ENST00000404929.1_Missense_Mutation_p.I107M	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	107			I -> M (in dbSNP:rs11125895). {ECO:0000269|PubMed:17974005}.		cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CCATAGTTTCTATGTGGGCAG	0.388													T|||	802	0.160144	0.1104	0.1787	5008	,	,		19735	0.1508		0.173	False		,,,				2504	0.2106				p.I107M		Atlas-SNP	.											.	FAM161A	200	.	0			c.A321G						PASS	.	T	MET/ILE,MET/ILE	466,3200		23,420,1390	93.0	85.0	88.0		321,321	1.7	0.3	2	dbSNP_120	88	1522,6640		153,1216,2712	yes	missense,missense	FAM161A	NM_001201543.1,NM_032180.2	10,10	176,1636,4102	CC,CT,TT		18.6474,12.7114,16.8076	benign,benign	107/717,107/661	62069358	1988,9840	1833	4081	5914	SO:0001583	missense	84140	exon2			AGTTTCTATGTGG		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.321A>G	2.37:g.62069358T>C	ENSP00000385893:p.Ile107Met	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	145	63	0.434483	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	332	0.152014652014652	44	0.08943089430894309	78	0.2154696132596685	85	0.1486013986013986	125	0.16490765171503957	T	10.85	1.468017	0.26335	0.127114	0.186474	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.66099	-0.19;-0.19	5.95	1.73	0.24493	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.53688	P	2.199999999996649E-5	B;B	0.16396	0.008;0.017	B;B	0.10450	0.002;0.005	T	0.10268	-1.0637	8	0.30854	T	0.27	-6.3985	7.8459	0.29424	0.0:0.5917:0.0:0.4083	rs11125895;rs17573015;rs52802415;rs59431884;rs11125895	107;107	Q3B820;Q3B820-3	F161A_HUMAN;.	M	107	ENSP00000385158:I107M;ENSP00000385893:I107M	ENSP00000385158:I107M	I	-	3	3	FAM161A	61922862	0.996000	0.38824	0.261000	0.24466	0.960000	0.62799	1.338000	0.33873	0.020000	0.15106	0.533000	0.62120	ATA	T|0.833;C|0.167	0.167	strong		0.388	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
CYP11B1	1584	hgsc.bcm.edu	37	8	143961102	143961102	+	Missense_Mutation	SNP	C	C	T	rs4534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143961102C>T	ENST00000292427.4	-	1	160	c.128G>A	c.(127-129)cGg>cAg	p.R43Q	CYP11B1_ENST00000377675.3_Missense_Mutation_p.R43Q|CYP11B1_ENST00000517471.1_Missense_Mutation_p.R43Q	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	43			R -> Q (in dbSNP:rs4534). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:2401360}.		aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	GCCTGGACGCCGGGGCATGGC	0.642									Familial Hyperaldosteronism type I				.|||	737	0.147165	0.0182	0.0965	5008	,	,		19736	0.4425		0.0179	False		,,,				2504	0.1861				p.R43Q		Atlas-SNP	.											.	CYP11B1	128	.	0			c.G128A	GRCh37	HM972174	CYP11B1	M	rs4534	PASS	.	C	GLN/ARG,GLN/ARG	102,4304	81.9+/-120.4	0,102,2101	66.0	62.0	63.0		128,128	-4.5	0.0	8	dbSNP_52	63	169,8431	77.5+/-140.1	5,159,4136	no	missense,missense	CYP11B1	NM_000497.3,NM_001026213.1	43,43	5,261,6237	TT,TC,CC		1.9651,2.315,2.0837	benign,benign	43/504,43/438	143961102	271,12735	2203	4300	6503	SO:0001583	missense	1584	exon1	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	GGACGCCGGGGCA	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"""Cytochrome P450s"""	2591	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	610613	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"""	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.128G>A	8.37:g.143961102C>T	ENSP00000292427:p.Arg43Gln	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	166	84	0.506024	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	ENST00000292427.4	37	CCDS6392.1	298	0.13644688644688643	11	0.022357723577235773	31	0.0856353591160221	247	0.4318181818181818	9	0.011873350923482849	C	0.009	-1.852652	0.00563	0.02315	0.019651	ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675	T;T;T	0.73258	-0.32;-0.32;-0.73	2.96	-4.5	0.03493	.	1.282380	0.06023	N	0.651646	T	0.00012	0.0000	N	0.01742	-0.745	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	0.19811	-1.0294	9	0.25751	T	0.34	.	6.461	0.21956	0.0:0.3986:0.0:0.6014	rs4534;rs16914260;rs52795252;rs4534	43;43;43	Q4VAR0;Q4VAQ9;P15538	.;.;C11B1_HUMAN	Q	43	ENSP00000292427:R43Q;ENSP00000428043:R43Q;ENSP00000366903:R43Q	ENSP00000292427:R43Q	R	-	2	0	CYP11B1	143958104	0.001000	0.12720	0.001000	0.08648	0.081000	0.17604	-0.029000	0.12329	-0.469000	0.06911	-1.358000	0.01219	CGG	C|0.920;T|0.080	0.080	strong		0.642	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		
CORO2B	10391	hgsc.bcm.edu	37	15	69006909	69006909	+	Silent	SNP	C	C	T	rs17852399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:69006909C>T	ENST00000566799.1	+	7	806	c.777C>T	c.(775-777)tcC>tcT	p.S259S	CORO2B_ENST00000543950.1_Silent_p.S254S|CORO2B_ENST00000540068.1_Silent_p.S254S|CORO2B_ENST00000261861.5_Silent_p.S254S			Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B	259					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			kidney(3)|large_intestine(13)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						AGGACCTCTCCATGCCCCTGA	0.562													C|||	180	0.0359425	0.1225	0.0072	5008	,	,		18090	0.0		0.0109	False		,,,				2504	0.002				p.S259S		Atlas-SNP	.											.	CORO2B	68	.	0			c.C777T						PASS	.	C	,,	509,3891	235.2+/-247.8	28,453,1719	140.0	129.0	133.0		762,762,777	4.2	1.0	15	dbSNP_123	133	82,8514	46.7+/-105.8	0,82,4216	no	coding-synonymous,coding-synonymous,coding-synonymous	CORO2B	NM_001190456.1,NM_001190457.1,NM_006091.4	,,	28,535,5935	TT,TC,CC		0.9539,11.5682,4.5476	,,	254/476,254/476,259/481	69006909	591,12405	2200	4298	6498	SO:0001819	synonymous_variant	10391	exon7			CCTCTCCATGCCC	AB010098	CCDS53952.1, CCDS10229.2	15q22.31	2013-01-10	2001-11-28		ENSG00000103647	ENSG00000103647		"""Coronins"", ""WD repeat domain containing"""	2256	protein-coding gene	gene with protein product	"""clipin C"", ""coronin, actin-binding, 2B"""	605002	"""coronin, actin-binding protein, 2B"""			10224093, 10231032	Standard	NM_001190456		Approved	ClipinC, KIAA0925	uc021spj.1	Q9UQ03	OTTHUMG00000133288	ENST00000566799.1:c.777C>T	15.37:g.69006909C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	163	84	0.515337	NM_006091	A8K0W3|O94767|Q8TAN1	Silent	SNP	ENST00000566799.1	37	CCDS10229.2																																																																																			C|0.955;T|0.045	0.045	strong		0.562	CORO2B-203	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006091	
CEACAM4	1089	hgsc.bcm.edu	37	19	42132193	42132193	+	Missense_Mutation	SNP	T	T	C	rs3848568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42132193T>C	ENST00000221954.2	-	2	316	c.206A>G	c.(205-207)aAg>aGg	p.K69R	CEACAM4_ENST00000600925.1_Missense_Mutation_p.K69R	NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	69	Ig-like V-type.		K -> R (in dbSNP:rs3848568).			integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						CGTTTTCCCCTTGTGCCAATA	0.473													T|||	559	0.111621	0.3366	0.1009	5008	,	,		18434	0.0		0.0099	False		,,,				2504	0.0348				p.K69R		Atlas-SNP	.											.	CEACAM4	42	.	0			c.A206G						PASS	.	T	ARG/LYS	1274,3132	433.1+/-343.5	191,892,1120	123.0	121.0	122.0		206	-1.5	0.0	19	dbSNP_108	122	171,8429	79.5+/-142.1	4,163,4133	yes	missense	CEACAM4	NM_001817.2	26	195,1055,5253	CC,CT,TT		1.9884,28.9151,11.1103	benign	69/245	42132193	1445,11561	2203	4300	6503	SO:0001583	missense	1089	exon2			TTCCCCTTGTGCC	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"""Immunoglobulin superfamily / V-set domain containing"""	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.206A>G	19.37:g.42132193T>C	ENSP00000221954:p.Lys69Arg	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	237	132	0.556962	NM_001817	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	37	CCDS33033.1	232	0.10622710622710622	181	0.3678861788617886	44	0.12154696132596685	0	0.0	7	0.009234828496042216	T	12.11	1.839959	0.32513	0.289151	0.019884	ENSG00000105352	ENST00000221954	T	0.66638	-0.22	1.76	-1.49	0.08718	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.39085	1.19	0.80722	P	0.0	P;D	0.69078	0.711;0.997	P;D	0.79108	0.531;0.992	T	0.16482	-1.0401	8	0.30854	T	0.27	.	5.1146	0.14827	0.0:0.5172:0.0:0.4828	rs3848568;rs3848568	69;69	E7EMX3;O75871	.;CEAM4_HUMAN	R	69	ENSP00000221954:K69R	ENSP00000221954:K69R	K	-	2	0	CEACAM4	46824033	0.003000	0.15002	0.019000	0.16419	0.737000	0.42083	0.135000	0.15952	-0.458000	0.07023	0.172000	0.16884	AAG	T|0.883;C|0.117	0.117	strong		0.473	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817	
DACT2	168002	hgsc.bcm.edu	37	6	168709385	168709385	+	Missense_Mutation	SNP	T	T	C	rs374278981|rs6925614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:168709385T>C	ENST00000366795.3	-	4	1140	c.1052A>G	c.(1051-1053)gAg>gGg	p.E351G	DACT2_ENST00000610183.1_Missense_Mutation_p.E181G|DACT2_ENST00000366796.3_Intron|DACT2_ENST00000607983.1_Splice_Site	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	351			E -> G (in dbSNP:rs6925614).		epithelial cell morphogenesis (GO:0003382)|hematopoietic progenitor cell differentiation (GO:0002244)|inner medullary collecting duct development (GO:0072061)|negative regulation of cell adhesion (GO:0007162)|negative regulation of nodal signaling pathway (GO:1900108)|skin development (GO:0043588)	mitochondrion (GO:0005739)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)|transcription factor binding (GO:0008134)			endometrium(1)	1		Breast(66;1.46e-05)|Ovarian(120;0.0728)		OV - Ovarian serous cystadenocarcinoma(33;5.33e-21)|BRCA - Breast invasive adenocarcinoma(81;1.18e-06)|GBM - Glioblastoma multiforme(31;0.000957)		CTGTTCTCCCTCGCTACCCTT	0.652													C|||	1879	0.3752	0.4592	0.3804	5008	,	,		17919	0.246		0.3678	False		,,,				2504	0.3988				p.E351G		Atlas-SNP	.											DACT2_ENST00000366795,NS,carcinoma,-1,1	DACT2	46	1	0			c.A1052G						PASS	.	C	GLY/GLU	663,721		169,325,198	40.0	38.0	38.0		1052	-8.5	0.0	6	dbSNP_116	38	1132,2050		206,720,665	yes	missense	DACT2	NM_214462.3	98	375,1045,863	CC,CT,TT		35.5751,47.9046,39.3123	benign	351/775	168709385	1795,2771	692	1591	2283	SO:0001583	missense	168002	exon4			TCTCCCTCGCTAC	AF318336	CCDS47519.1, CCDS69241.1, CCDS75554.1	6q27	2013-05-15	2013-05-15	2003-09-17	ENSG00000164488	ENSG00000164488			21231	protein-coding gene	gene with protein product		608966	"""chromosome 6 open reading frame 116"", ""dapper homolog 2, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 2 (Xenopus laevis)"""	C6orf116			Standard	NM_001286351		Approved	bA503C24.7, DAPPER2	uc003qwq.3	Q5SW24	OTTHUMG00000016046	ENST00000366795.3:c.1052A>G	6.37:g.168709385T>C	ENSP00000355760:p.Glu351Gly	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Missense_Mutation	SNP	ENST00000366795.3	37	CCDS47519.1	772	0.3534798534798535	200	0.4065040650406504	138	0.3812154696132597	165	0.28846153846153844	269	0.3548812664907652	C	5.583	0.292297	0.10567	0.479046	0.355751	ENSG00000164488	ENST00000366795	T	0.39787	1.06	4.24	-8.48	0.00935	.	0.728918	0.12437	N	0.469055	T	0.04272	0.0118	N	0.03115	-0.41	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.27673	-1.0067	9	0.46703	T	0.11	-3.1909	4.4404	0.11572	0.1424:0.5155:0.1504:0.1917	rs6925614;rs61543421;rs6925614	351	Q5SW24	DACT2_HUMAN	G	351	ENSP00000355760:E351G	ENSP00000355760:E351G	E	-	2	0	DACT2	168452234	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.232000	0.09055	-1.890000	0.01111	-2.330000	0.00249	GAG	T|0.628;C|0.372	0.372	strong		0.652	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
DNAH1	25981	hgsc.bcm.edu	37	3	52365223	52365223	+	Missense_Mutation	SNP	G	G	A	rs55931436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52365223G>A	ENST00000420323.2	+	7	1192	c.931G>A	c.(931-933)Gac>Aac	p.D311N		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	311	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCTGGACTACGACGAGGAGAA	0.567													G|||	89	0.0177716	0.0643	0.0058	5008	,	,		20717	0.0		0.0	False		,,,				2504	0.0				p.D311N		Atlas-SNP	.											.	DNAH1	534	.	0			c.G931A						PASS	.	G	ASN/ASP	167,3917		5,157,1880	56.0	59.0	58.0		931	3.6	0.0	3	dbSNP_129	58	1,8383		0,1,4191	yes	missense	DNAH1	NM_015512.4	23	5,158,6071	AA,AG,GG		0.0119,4.0891,1.3474	benign	311/4266	52365223	168,12300	2042	4192	6234	SO:0001583	missense	25981	exon7			GACTACGACGAGG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.931G>A	3.37:g.52365223G>A	ENSP00000401514:p.Asp311Asn	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	194	91	0.469072	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	10.94	1.491737	0.26774	0.040891	1.19E-4	ENSG00000114841	ENST00000420323	T	0.23348	1.91	5.38	3.58	0.41010	.	0.000000	0.53938	D	0.000051	T	0.01627	0.0052	L	0.46885	1.475	0.26172	N	0.979848	B;P	0.39326	0.07;0.668	B;B	0.36186	0.022;0.219	T	0.01452	-1.1351	10	0.52906	T	0.07	.	11.8483	0.52397	0.1429:0.0:0.8571:0.0	rs55931436;rs61734655	311;311	C9JXH6;Q9P2D7-3	.;.	N	311	ENSP00000401514:D311N	ENSP00000401514:D311N	D	+	1	0	DNAH1	52340263	0.986000	0.35501	0.008000	0.14137	0.151000	0.21798	2.173000	0.42472	0.643000	0.30638	0.462000	0.41574	GAC	G|0.984;A|0.016	0.016	strong		0.567	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
MUC4	4585	hgsc.bcm.edu	37	3	195512565	195512565	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512565G>A	ENST00000463781.3	-	2	6345	c.5886C>T	c.(5884-5886)ccC>ccT	p.P1962P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.P1962P	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.P1952_T1967delPLPVTDASSVPTGHAT(4)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CGTGACCTGTGGGTACTGAGG	0.602																																					p.P1962P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	4	Deletion - In frame(4)	stomach(4)	c.C5886T						scavenged	.						53.0	41.0	45.0					3																	195512565		692	1591	2283	SO:0001819	synonymous_variant	4585	exon2			ACCTGTGGGTACT	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.5886C>T	3.37:g.195512565G>A		Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	269	3	0.0111524	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																																																																																			.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SVEP1	79987	hgsc.bcm.edu	37	9	113259152	113259152	+	Missense_Mutation	SNP	T	T	G	rs10817033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113259152T>G	ENST00000401783.2	-	8	2079	c.1743A>C	c.(1741-1743)caA>caC	p.Q581H	SVEP1_ENST00000374469.1_Missense_Mutation_p.Q558H|SVEP1_ENST00000374461.1_Missense_Mutation_p.Q558H|SVEP1_ENST00000302728.8_Missense_Mutation_p.Q581H|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	581	HYR 1. {ECO:0000255|PROSITE- ProRule:PRU00113}.		Q -> H (in dbSNP:rs10817033).		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						TGGCAGAATCTTGCTGTTCCA	0.398													T|||	464	0.0926518	0.1861	0.0836	5008	,	,		21855	0.001		0.1233	False		,,,				2504	0.0358				p.Q581H		Atlas-SNP	.											.	SVEP1	326	.	0			c.A1743C						PASS	.	T	HIS/GLN	687,3101		70,547,1277	98.0	91.0	93.0		1743	1.0	1.0	9	dbSNP_120	93	951,7239		63,825,3207	yes	missense	SVEP1	NM_153366.3	24	133,1372,4484	GG,GT,TT		11.6117,18.1362,13.6751	probably-damaging	581/3572	113259152	1638,10340	1894	4095	5989	SO:0001583	missense	79987	exon8			AGAATCTTGCTGT	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.1743A>C	9.37:g.113259152T>G	ENSP00000384917:p.Gln581His	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	187	117	0.625668	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	228	0.1043956043956044	99	0.20121951219512196	38	0.10497237569060773	0	0.0	91	0.12005277044854881	T	19.63	3.864224	0.71949	0.181362	0.116117	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.22945	1.93;1.93;1.93;1.93	5.8	0.969	0.19686	Hyalin (2);	0.055337	0.64402	D	0.000001	T	0.00039	0.0001	M	0.72118	2.19	0.36870	P	0.11113300000000004	D;D;B	0.76494	0.998;0.999;0.028	D;D;B	0.83275	0.996;0.983;0.011	T	0.02269	-1.1185	9	0.51188	T	0.08	.	5.2267	0.15399	0.0:0.2637:0.1483:0.588	rs10817033;rs52813620;rs10817033	581;581;581	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	H	581;558;581;558	ENSP00000384917:Q581H;ENSP00000363593:Q558H;ENSP00000304118:Q581H;ENSP00000363585:Q558H	ENSP00000304118:Q581H	Q	-	3	2	SVEP1	112298973	0.963000	0.33076	1.000000	0.80357	0.997000	0.91878	-0.153000	0.10144	0.462000	0.27095	0.528000	0.53228	CAA	T|0.887;G|0.113	0.113	strong		0.398	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TTBK1	84630	hgsc.bcm.edu	37	6	43252029	43252029	+	Missense_Mutation	SNP	T	T	C	rs3800298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43252029T>C	ENST00000259750.4	+	14	3634	c.3551T>C	c.(3550-3552)tTg>tCg	p.L1184S		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1184			L -> S (in dbSNP:rs3800298). {ECO:0000269|PubMed:17344846}.		substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			GCCCCAGCATTGGACACAGCC	0.682													C|||	1827	0.364816	0.5628	0.2378	5008	,	,		16925	0.3849		0.2515	False		,,,				2504	0.2832				p.L1184S		Atlas-SNP	.											TTBK1,NS,carcinoma,0,1	TTBK1	124	1	0			c.T3551C						PASS	.	C	SER/LEU	1274,1956		249,776,590	12.0	14.0	13.0		3551	4.8	0.2	6	dbSNP_107	13	1385,5175		125,1135,2020	yes	missense	TTBK1	NM_032538.1	145	374,1911,2610	CC,CT,TT		21.1128,39.4427,27.1604	benign	1184/1322	43252029	2659,7131	1615	3280	4895	SO:0001583	missense	84630	exon14			CAGCATTGGACAC	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.3551T>C	6.37:g.43252029T>C	ENSP00000259750:p.Leu1184Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	773	0.35393772893772896	282	0.573170731707317	94	0.2596685082872928	207	0.3618881118881119	190	0.25065963060686014	C	0.003	-2.531159	0.00145	0.394427	0.211128	ENSG00000146216	ENST00000259750	T	0.51574	0.7	4.77	4.77	0.60923	.	0.586807	0.15128	N	0.278991	T	0.04724	0.0128	N	0.00621	-1.32	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.34976	-0.9807	9	0.08381	T	0.77	.	7.4137	0.27032	0.0:0.808:0.0:0.192	rs3800298;rs58957853;rs3800298	1184	Q5TCY1	TTBK1_HUMAN	S	1184	ENSP00000259750:L1184S	ENSP00000259750:L1184S	L	+	2	0	TTBK1	43360007	0.001000	0.12720	0.242000	0.24170	0.258000	0.26162	1.185000	0.32065	1.258000	0.44101	-0.215000	0.12644	TTG	T|0.667;C|0.333	0.333	strong		0.682	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
MBL2	4153	hgsc.bcm.edu	37	10	54528236	54528236	+	Silent	SNP	G	G	A	rs35805975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:54528236G>A	ENST00000373968.3	-	4	472	c.408C>T	c.(406-408)aaC>aaT	p.N136N		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	136	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						GGAAGAACTTGTTCCCAACTT	0.463													G|||	56	0.0111821	0.0	0.0173	5008	,	,		18022	0.0		0.0358	False		,,,				2504	0.0082				p.N136N		Atlas-SNP	.											.	MBL2	55	.	0			c.C408T						PASS	.	G		22,4382	29.0+/-57.7	0,22,2180	91.0	97.0	95.0		408	-6.3	0.0	10	dbSNP_126	95	211,8389	90.4+/-152.6	2,207,4091	no	coding-synonymous	MBL2	NM_000242.2		2,229,6271	AA,AG,GG		2.4535,0.4995,1.7918		136/249	54528236	233,12771	2202	4300	6502	SO:0001819	synonymous_variant	4153	exon4			GAACTTGTTCCCA	AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"""Collectins"""	6922	protein-coding gene	gene with protein product		154545	"""mannose-binding lectin (protein C) 2, soluble (opsonic defect)"""	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.408C>T	10.37:g.54528236G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_000242	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Silent	SNP	ENST00000373968.3	37	CCDS7247.1																																																																																			G|0.981;A|0.019	0.019	strong		0.463	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242	
OGFOD1	55239	hgsc.bcm.edu	37	16	56496469	56496469	+	Missense_Mutation	SNP	G	G	A	rs147797412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:56496469G>A	ENST00000566157.1	+	4	494	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	OGFOD1_ENST00000565209.1_3'UTR|OGFOD1_ENST00000568397.1_Missense_Mutation_p.R124Q	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	124					cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	GAAGATTTCCGGTCCTGGCTT	0.393													G|||	5	0.000998403	0.0008	0.0029	5008	,	,		19961	0.0		0.0	False		,,,				2504	0.002				p.R124Q		Atlas-SNP	.											.	OGFOD1	31	.	0			c.G371A						PASS	.	G	GLN/ARG	4,4392	8.1+/-20.4	0,4,2194	80.0	77.0	78.0		371	5.6	1.0	16	dbSNP_134	78	0,8600		0,0,4300	yes	missense	OGFOD1	NM_018233.3	43	0,4,6494	AA,AG,GG		0.0,0.091,0.0308	possibly-damaging	124/543	56496469	4,12992	2198	4300	6498	SO:0001583	missense	55239	exon4			ATTTCCGGTCCTG	BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263			25585	protein-coding gene	gene with protein product	"""TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)"""	615857				10997877	Standard	NM_018233		Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	ENST00000566157.1:c.371G>A	16.37:g.56496469G>A	ENSP00000457258:p.Arg124Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_018233	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Missense_Mutation	SNP	ENST00000566157.1	37	CCDS10761.2	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474261	0.84640	9.1E-4	0.0	ENSG00000087263	ENST00000336111	.	.	.	5.61	5.61	0.85477	Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	T	0.59582	0.2204	M	0.79258	2.445	0.80722	D	1	D	0.58268	0.982	B	0.41510	0.359	T	0.67616	-0.5625	9	0.59425	D	0.04	-17.5224	13.8776	0.63662	0.0748:0.0:0.9252:0.0	.	124	Q8N543	OGFD1_HUMAN	Q	124	.	ENSP00000337196:R124Q	R	+	2	0	OGFOD1	55053970	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	6.847000	0.75404	2.658000	0.90341	0.585000	0.79938	CGG	G|1.000;A|0.000	0.000	weak		0.393	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	NM_018233	
MUC5B	727897	hgsc.bcm.edu	37	11	1272246	1272246	+	Silent	SNP	G	G	A	rs115045504	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1272246G>A	ENST00000529681.1	+	31	14194	c.14136G>A	c.(14134-14136)acG>acA	p.T4712T	MUC5B_ENST00000447027.1_Silent_p.T4715T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4712	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.		T -> M (in dbSNP:rs2943511). {ECO:0000269|PubMed:9013550}.		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)		tgaccagcacggccaccacac	0.617													g|||	69	0.013778	0.0477	0.0086	5008	,	,		18297	0.0		0.0	False		,,,				2504	0.0				p.T4712T		Atlas-SNP	.											MUC5B,colon,carcinoma,+1,2	MUC5B	473	2	0			c.G14136A						PASS	.	G		97,4189		3,91,2049	108.0	139.0	128.0		14136	-3.3	0.0	11	dbSNP_132	128	0,8456		0,0,4228	no	coding-synonymous	MUC5B	NM_002458.2		3,91,6277	AA,AG,GG		0.0,2.2632,0.7613		4712/5763	1272246	97,12645	2143	4228	6371	SO:0001819	synonymous_variant	727897	exon31			CAGCACGGCCACC	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.14136G>A	11.37:g.1272246G>A		Somatic	551	2	0.00362976		WXS	Illumina HiSeq	Phase_I	520	253	0.486538	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.988;A|0.012	0.012	strong		0.617	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ZNF799	90576	hgsc.bcm.edu	37	19	12502155	12502155	+	Missense_Mutation	SNP	T	T	G	rs201335235		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12502155T>G	ENST00000430385.3	-	4	1257	c.1057A>C	c.(1057-1059)Aaa>Caa	p.K353Q	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Missense_Mutation_p.K321Q	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	353					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)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						TCATGACTTTTCAGTGAACTA	0.413																																					p.K353Q		Atlas-SNP	.											.	ZNF799	111	.	0			c.A1057C						PASS	.						160.0	156.0	157.0					19																	12502155		2203	4300	6503	SO:0001583	missense	90576	exon4			GACTTTTCAGTGA	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"""Zinc fingers, C2H2-type"", ""-"""	28071	protein-coding gene	gene with protein product			"""zinc finger protein 842"""	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1057A>C	19.37:g.12502155T>G	ENSP00000411084:p.Lys353Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	111	8	0.0720721	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	37	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.323810	0.01309	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.04406	3.63;3.63	1.31	-1.61	0.08399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.12527	0.23	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49041	-0.8980	9	0.14252	T	0.57	.	6.8386	0.23951	0.0:0.0:0.2963:0.7037	.	353	Q96GE5	ZN799_HUMAN	Q	321;353	ENSP00000415278:K321Q;ENSP00000411084:K353Q	ENSP00000415278:K321Q	K	-	1	0	ZNF799	12363155	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.687000	0.05156	-0.936000	0.03723	-1.919000	0.00516	AAA	.	.	weak		0.413	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821	
FAM221B	392307	hgsc.bcm.edu	37	9	35826038	35826038	+	Missense_Mutation	SNP	T	T	C	rs13294245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	118	0	0	858	WXS	Illumina HiSeq	Phase_I	102	40	0.392157	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	
HRC	3270	hgsc.bcm.edu	37	19	49657583	49657583	+	Silent	SNP	G	G	A	rs144793394|rs386810104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657583G>A	ENST00000252825.4	-	1	1098	c.912C>T	c.(910-912)gaC>gaT	p.D304D	HRC_ENST00000595625.1_Silent_p.D304D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	304	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		CATCATCATTGTCATCTTCTT	0.537													A|||	248	0.0495208	0.1657	0.0187	5008	,	,		25781	0.0		0.0099	False		,,,				2504	0.0061				p.D304D	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.C912T						PASS	.						185.0	144.0	158.0					19																	49657583		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			ATCATTGTCATCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.912C>T	19.37:g.49657583G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	230	65	0.282609	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			G|0.999;A|0.001	0.001	weak		0.537	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
RPGR	6103	hgsc.bcm.edu	37	X	38147170	38147170	+	Missense_Mutation	SNP	C	C	T	rs1801688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38147170C>T	ENST00000339363.3	-	14	1864	c.1697G>A	c.(1696-1698)gGg>gAg	p.G566E	TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Missense_Mutation_p.G566E|RPGR_ENST00000378505.2_Missense_Mutation_p.G566E|RPGR_ENST00000318842.7_Missense_Mutation_p.G566E|RPGR_ENST00000309513.3_Missense_Mutation_p.G504E|RPGR_ENST00000338898.3_3'UTR			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	566	Glu-rich.		G -> E (in dbSNP:rs1801688). {ECO:0000269|PubMed:10480356, ECO:0000269|PubMed:10937588, ECO:0000269|PubMed:10980543, ECO:0000269|PubMed:9399904}.		cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						CATGAAAATCCCTTGTGACAC	0.438													C|||	489	0.129536	0.1278	0.1427	3775	,	,		15353	0.0516		0.0527	False		,,,				2504	0.1186				p.G566E		Atlas-SNP	.											.	RPGR	175	.	0			c.G1697A						PASS	.	C	GLU/GLY,GLU/GLY	614,3219		49,433,83,1149,488	320.0	228.0	259.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1697,1697	0.8	0.0	X	dbSNP_89	259	342,6386		4,229,105,2195,1767	yes	missense,missense	RPGR	NM_000328.2,NM_001034853.1	98,98	53,662,188,3344,2255	TT,TC,T,CC,C		5.0832,16.0188,9.0522	probably-damaging,probably-damaging	566/816,566/1153	38147170	956,9605	2202	4300	6502	SO:0001583	missense	6103	exon14			AAAATCCCTTGTG	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.1697G>A	X.37:g.38147170C>T	ENSP00000343671:p.Gly566Glu	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	269	140	0.520446	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		174	0.10488245931283906	34	0.0752212389380531	37	0.10818713450292397	23	0.04107142857142857	31	0.04234972677595628	C	9.487	1.099677	0.20552	0.160188	0.050832	ENSG00000156313	ENST00000339363;ENST00000309513;ENST00000318842;ENST00000342811;ENST00000378505	T;T;T;T;T	0.34072	2.4;2.67;2.67;1.46;1.38	5.25	0.8	0.18672	.	0.515186	0.19446	U	0.114080	T	0.00178	0.0005	L	0.32530	0.975	0.42524	P	0.006985000000000019	P;D	0.89917	0.911;1.0	B;D	0.79784	0.311;0.993	T	0.06127	-1.0844	9	0.33940	T	0.23	.	3.3108	0.07016	0.0:0.3733:0.2062:0.4204	rs1801688;rs1801688	566;566	E9PE28;Q92834-2	.;.	E	566;504;566;566;566	ENSP00000343671:G566E;ENSP00000308783:G504E;ENSP00000322219:G566E;ENSP00000339531:G566E;ENSP00000367766:G566E	ENSP00000308783:G504E	G	-	2	0	RPGR	38032114	0.011000	0.17503	0.003000	0.11579	0.001000	0.01503	0.224000	0.17738	0.100000	0.17581	-1.187000	0.01702	GGG	0|0.003;T|0.102	0.102	strong		0.438	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
UQCC1	55245	hgsc.bcm.edu	37	20	33971876	33971876	+	Missense_Mutation	SNP	T	T	C	rs114745625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33971876T>C	ENST00000374385.5	-	3	367	c.190A>G	c.(190-192)Ata>Gta	p.I64V	UQCC1_ENST00000374377.5_Intron|UQCC1_ENST00000374384.2_Missense_Mutation_p.I64V|UQCC1_ENST00000397554.1_Missense_Mutation_p.I64V|UQCC1_ENST00000397556.3_Intron|UQCC1_ENST00000349714.5_Missense_Mutation_p.I64V|UQCC1_ENST00000407996.2_Missense_Mutation_p.I64V|UQCC1_ENST00000491125.1_5'UTR|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000542501.1_Missense_Mutation_p.I64V|UQCC1_ENST00000359226.2_Missense_Mutation_p.I64V|UQCC1_ENST00000374380.2_Intron	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	64						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											TTCAGCTGTATGTCTATTCCA	0.438													T|||	13	0.00259585	0.0098	0.0	5008	,	,		21480	0.0		0.0	False		,,,				2504	0.0				p.I64V		Atlas-SNP	.											.	UQCC	41	.	0			c.A190G						PASS	.	T	,VAL/ILE,VAL/ILE	57,4349	56.2+/-92.4	1,55,2147	184.0	149.0	161.0		,190,190	-1.4	0.0	20	dbSNP_132	161	0,8600		0,0,4300	yes	intron,missense,missense	UQCC	NM_001184977.1,NM_018244.4,NM_199487.2	,29,29	1,55,6447	CC,CT,TT		0.0,1.2937,0.4383	,benign,benign	,64/300,64/274	33971876	57,12949	2203	4300	6503	SO:0001583	missense	55245	exon3			GCTGTATGTCTAT	AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"""Mitochondrial respiratory chain complex assembly factors"""	15891	protein-coding gene	gene with protein product	"""Basic FGF-repressed Zic-binding protein"", ""cytochrome B protein synthesis 3 homolog (S. cerevisiae)"""	611797	"""chromosome 20 open reading frame 44"", ""ubiquinol-cytochrome c reductase complex chaperone"""	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.190A>G	20.37:g.33971876T>C	ENSP00000363506:p.Ile64Val	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	218	104	0.477064	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Missense_Mutation	SNP	ENST00000374385.5	37	CCDS13252.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	T	0.042	-1.280171	0.01398	0.012937	0.0	ENSG00000101019	ENST00000349714;ENST00000359226;ENST00000374384;ENST00000374385;ENST00000407996;ENST00000542501;ENST00000438533;ENST00000397554	T;T;T;T;T;T;T;T	0.42900	1.55;1.57;1.66;1.66;0.96;1.54;1.62;1.62	5.02	-1.38	0.09027	.	0.874131	0.10138	N	0.711165	T	0.13500	0.0327	N	0.12961	0.28	0.09310	N	1	B;B;B;B;B	0.14012	0.009;0.0;0.002;0.0;0.0	B;B;B;B;B	0.13407	0.009;0.0;0.001;0.0;0.0	T	0.18777	-1.0326	10	0.27785	T	0.31	-3.4421	0.9374	0.01347	0.1611:0.3029:0.1662:0.3698	.	64;64;64;64;64	B7Z7J8;B7ZBG3;B1AKV2;B7ZBG4;Q9NVA1	.;.;.;.;UQCC_HUMAN	V	64;64;64;64;64;64;78;64	ENSP00000335364:I64V;ENSP00000352161:I64V;ENSP00000363505:I64V;ENSP00000363506:I64V;ENSP00000386064:I64V;ENSP00000445059:I64V;ENSP00000398531:I78V;ENSP00000380686:I64V	ENSP00000335364:I64V	I	-	1	0	UQCC	33435290	0.000000	0.05858	0.004000	0.12327	0.135000	0.20990	-0.025000	0.12413	0.080000	0.16959	0.533000	0.62120	ATA	T|0.997;C|0.003	0.003	strong		0.438	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244	
SNX7	51375	hgsc.bcm.edu	37	1	99164434	99164434	+	Silent	SNP	G	G	A	rs6577322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:99164434G>A	ENST00000306121.3	+	6	1020	c.1011G>A	c.(1009-1011)gaG>gaA	p.E337E	SNX7_ENST00000370189.5_Silent_p.E273E|SNX7_ENST00000529992.1_Silent_p.E282E	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	273					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		TTGTACATGAGTACGTGCTTT	0.418													G|||	1090	0.217652	0.2088	0.2781	5008	,	,		16727	0.0595		0.2654	False		,,,				2504	0.3006				p.E337E		Atlas-SNP	.											.	SNX7	76	.	0			c.G1011A						PASS	.	G	,	964,3442	361.9+/-315.9	100,764,1339	108.0	95.0	99.0		1011,846	1.0	1.0	1	dbSNP_116	99	2519,6081	411.3+/-350.5	362,1795,2143	no	coding-synonymous,coding-synonymous	SNX7	NM_015976.4,NM_152238.3	,	462,2559,3482	AA,AG,GG		29.2907,21.8793,26.7799	,	337/452,282/397	99164434	3483,9523	2203	4300	6503	SO:0001819	synonymous_variant	51375	exon6			ACATGAGTACGTG	AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"""Sorting nexins"""	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.1011G>A	1.37:g.99164434G>A		Somatic	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	194	110	0.56701	NM_015976	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Silent	SNP	ENST00000306121.3	37	CCDS755.2																																																																																			G|0.762;A|0.238	0.238	strong		0.418	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2		
LOXHD1	125336	hgsc.bcm.edu	37	18	44157797	44157797	+	Silent	SNP	G	G	T	rs112463030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44157797G>T	ENST00000398722.4	-	7	1008	c.1009C>A	c.(1009-1011)Cgg>Agg	p.R337R	LOXHD1_ENST00000441551.2_Silent_p.R615R|LOXHD1_ENST00000536736.1_Silent_p.R615R			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	337	PLAT 3. {ECO:0000255|PROSITE- ProRule:PRU00152}.				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						CTCACATTCCGCATGGTGACA	0.592													G|||	24	0.00479233	0.0166	0.0014	5008	,	,		20177	0.0		0.001	False		,,,				2504	0.0				p.R615R		Atlas-SNP	.											.	LOXHD1	367	.	0			c.C1843A						PASS	.	G		34,1350		1,32,659	62.0	64.0	63.0		1843	-2.2	1.0	18	dbSNP_132	63	0,3182		0,0,1591	no	coding-synonymous	LOXHD1	NM_144612.6		1,32,2250	TT,TG,GG		0.0,2.4566,0.7446		615/2212	44157797	34,4532	692	1591	2283	SO:0001819	synonymous_variant	125336	exon14			CATTCCGCATGGT	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.1009C>A	18.37:g.44157797G>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Silent	SNP	ENST00000398722.4	37		13	0.005952380952380952	12	0.024390243902439025	0	0.0	0	0.0	1	0.0013192612137203166	G	1.684	-0.505763	0.04261	0.024566	0.0	ENSG00000167210	ENST00000441551	.	.	.	5.66	-2.15	0.07102	.	.	.	.	.	T	0.54447	0.1859	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68205	-0.5470	4	.	.	.	.	18.5598	0.91096	0.0:0.0:0.2663:0.7337	.	.	.	.	E	595	.	.	A	-	2	0	LOXHD1	42411795	1.000000	0.71417	0.994000	0.49952	0.066000	0.16364	0.835000	0.27531	-0.232000	0.09811	-0.314000	0.08810	GCG	G|0.994;T|0.006	0.006	strong		0.592	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
GHRHR	2692	hgsc.bcm.edu	37	7	31009576	31009576	+	Missense_Mutation	SNP	G	G	T	rs4988498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:31009576G>T	ENST00000326139.2	+	4	409	c.363G>T	c.(361-363)gaG>gaT	p.E121D	GHRHR_ENST00000409904.3_Missense_Mutation_p.E57D|GHRHR_ENST00000409316.1_5'UTR	NM_000823.3	NP_000814.2	Q02643	GHRHR_HUMAN	growth hormone releasing hormone receptor	121			E -> D (in dbSNP:rs4988498).		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP-mediated signaling (GO:0019933)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|determination of adult lifespan (GO:0008340)|growth hormone secretion (GO:0030252)|hormone metabolic process (GO:0042445)|lactation (GO:0007595)|multicellular organismal reproductive process (GO:0048609)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of intracellular steroid hormone receptor signaling pathway (GO:0033143)|regulation of protein metabolic process (GO:0051246)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|somatotropin secreting cell development (GO:0060133)|water homeostasis (GO:0030104)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nuclear matrix (GO:0016363)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	G-protein coupled receptor activity (GO:0004930)|growth factor binding (GO:0019838)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35					Sermorelin(DB00010)|Tesamorelin(DB08869)	TGCTGGCTGAGGAGGTAAGAG	0.567													G|||	321	0.0640974	0.1641	0.0303	5008	,	,		18180	0.002		0.0577	False		,,,				2504	0.0235				p.E121D		Atlas-SNP	.											.	GHRHR	55	.	0			c.G363T						PASS	.	G	ASP/GLU	622,3784	270.1+/-269.4	45,532,1626	112.0	94.0	100.0		363	2.3	1.0	7	dbSNP_113	100	464,8136	138.4+/-195.2	11,442,3847	yes	missense	GHRHR	NM_000823.3	45	56,974,5473	TT,TG,GG		5.3953,14.1171,8.35	benign	121/424	31009576	1086,11920	2203	4300	6503	SO:0001583	missense	2692	exon4			GGCTGAGGAGGTA		CCDS5432.1	7p14	2012-08-10			ENSG00000106128	ENSG00000106128		"""GPCR / Class B : Glucagon receptors"""	4266	protein-coding gene	gene with protein product		139191				7680413, 7514564	Standard	NM_000823		Approved		uc003tbx.3	Q02643	OTTHUMG00000152801	ENST00000326139.2:c.363G>T	7.37:g.31009576G>T	ENSP00000320180:p.Glu121Asp	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	101	61	0.60396	NM_000823	Q99863	Missense_Mutation	SNP	ENST00000326139.2	37	CCDS5432.1	150	0.06868131868131869	90	0.18292682926829268	12	0.03314917127071823	2	0.0034965034965034965	46	0.06068601583113457	G	5.662	0.306778	0.10733	0.141171	0.053953	ENSG00000106128	ENST00000326139;ENST00000409904;ENST00000409233;ENST00000337750	T;T;T	0.68624	0.68;0.87;-0.34	4.17	2.34	0.29019	GPCR, family 2, extracellular hormone receptor domain (1);	.	.	.	.	T	0.00109	0.0003	N	0.25426	0.745	0.34334	P	0.311999	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.11329	0.006;0.004;0.002	T	0.05649	-1.0872	8	0.10636	T	0.68	.	6.876	0.24147	0.2158:0.0:0.7842:0.0	rs4988498;rs10278650;rs57488850;rs4988498	57;121;57	Q9HB45;Q02643;Q9HB44	.;GHRHR_HUMAN;.	D	121;57;57;57	ENSP00000320180:E121D;ENSP00000387113:E57D;ENSP00000338184:E57D	ENSP00000320180:E121D	E	+	3	2	GHRHR	30976101	0.973000	0.33851	0.957000	0.39632	0.642000	0.38348	-0.130000	0.10498	0.521000	0.28445	0.462000	0.41574	GAG	G|0.919;T|0.081	0.081	strong		0.567	GHRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327967.2		
MICALCL	84953	hgsc.bcm.edu	37	11	12315848	12315848	+	Silent	SNP	C	C	T	rs1493952	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	31	0	0		WXS	Illumina HiSeq	Phase_I	26	16	0.615385	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	
TTN	7273	hgsc.bcm.edu	37	2	179430224	179430224	+	Missense_Mutation	SNP	G	G	T	rs79926414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179430224G>T	ENST00000591111.1	-	276	75936	c.75712C>A	c.(75712-75714)Cag>Aag	p.Q25238K	TTN_ENST00000589042.1_Missense_Mutation_p.Q26879K|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Q17814K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Q24311K|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Q17939K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Q18006K|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25238					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)			AAACTAGGCTGTATAGTCAAG	0.388													G|||	79	0.0157748	0.0567	0.0058	5008	,	,		22772	0.0		0.0	False		,,,				2504	0.0				p.Q26879K		Atlas-SNP	.											.	TTN	18412	.	0			c.C80635A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN	176,3544		5,166,1689	130.0	127.0	128.0		54016,53815,72931,53440	5.5	1.0	2	dbSNP_131	128	1,8199		0,1,4099	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	53,53,53,53	5,167,5788	TT,TG,GG		0.0122,4.7312,1.4849	benign,benign,benign,benign	18006/27119,17939/27052,24311/33424,17814/26927	179430224	177,11743	1860	4100	5960	SO:0001583	missense	7273	exon326			TAGGCTGTATAGT	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.75712C>A	2.37:g.179430224G>T	ENSP00000465570:p.Gln25238Lys	Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	151	90	0.596026	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		42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	G	9.263	1.043608	0.19748	0.047312	1.22E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.61980	0.06;0.33;0.3;0.3	5.49	5.49	0.81192	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01835	0.0058	N	0.00465	-1.465	0.26115	N	0.980629	B;B;B;B	0.09022	0.001;0.002;0.002;0.001	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.07028	-1.0794	9	0.87932	D	0	.	14.8449	0.70254	0.0:0.2548:0.7452:0.0	.	17814;17939;18006;25238	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	24311;17814;18006;17939;17812	ENSP00000343764:Q24311K;ENSP00000434586:Q17814K;ENSP00000340554:Q18006K;ENSP00000352154:Q17939K	ENSP00000340554:Q18006K	Q	-	1	0	TTN	179138470	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.169000	0.50809	2.595000	0.87683	0.484000	0.47621	CAG	G|0.976;T|0.024	0.024	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FOXRED2	80020	hgsc.bcm.edu	37	22	36886178	36886178	+	Silent	SNP	A	A	G	rs73409777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36886178A>G	ENST00000397224.4	-	9	2025	c.1932T>C	c.(1930-1932)taT>taC	p.Y644Y	FOXRED2_ENST00000216187.6_Silent_p.Y644Y|FOXRED2_ENST00000366463.3_Silent_p.Y196Y|FOXRED2_ENST00000397223.4_Silent_p.Y644Y	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	644					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						CTGTGGGGGCATAGTCCCGCA	0.652													A|||	142	0.0283546	0.1044	0.0043	5008	,	,		16850	0.0		0.001	False		,,,				2504	0.0				p.Y644Y		Atlas-SNP	.											.	FOXRED2	48	.	0			c.T1932C						PASS	.	A	,	385,4021	187.8+/-214.3	21,343,1839	47.0	51.0	50.0		1932,1932	-3.8	0.0	22	dbSNP_130	50	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	FOXRED2	NM_001102371.1,NM_024955.5	,	21,346,6136	GG,GA,AA		0.0349,8.7381,2.9832	,	644/685,644/685	36886178	388,12618	2203	4300	6503	SO:0001819	synonymous_variant	80020	exon9			GGGGGCATAGTCC	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.1932T>C	22.37:g.36886178A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	37	CCDS13929.1																																																																																			A|0.975;G|0.025	0.025	strong		0.652	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144863320	144863320	+	Missense_Mutation	SNP	T	T	C	rs139822181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144863320T>C	ENST00000369354.3	-	37	6272	c.6083A>G	c.(6082-6084)aAa>aGa	p.K2028R	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.K2113R|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.K2164R|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.K2028R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.K1922R			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2028					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)		ACACATACCTTTCAGCCCCTT	0.488			T	PDGFRB	MPD																																p.K2028R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6083G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	158,4248	83.9+/-122.4	1,156,2046	153.0	151.0	152.0		5765,6083,6083	0.8	1.0	1	dbSNP_134	152	92,8506	30.7+/-82.3	0,92,4207	no	missense,missense,missense	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	26,26,26	1,248,6253	CC,CT,TT		1.07,3.586,1.9225	possibly-damaging,possibly-damaging,possibly-damaging	1922/2241,2028/2363,2028/2347	144863320	250,12754	2203	4299	6502	SO:0001583	missense	9659	exon37			ATACCTTTCAGCC	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.6083A>G	1.37:g.144863320T>C	ENSP00000358360:p.Lys2028Arg	Somatic	463	0	0		WXS	Illumina HiSeq	Phase_I	419	132	0.315036	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	103|103	0.04716117216117216|0.04716117216117216	36|36	0.07317073170731707|0.07317073170731707	6|6	0.016574585635359115|0.016574585635359115	47|47	0.08216783216783216|0.08216783216783216	14|14	0.018469656992084433|0.018469656992084433	T|T	15.03|15.03	2.712690|2.712690	0.48517|0.48517	0.03586|0.03586	0.0107|0.0107	ENSG00000178104|ENSG00000178104	ENST00000530130|ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T|T;T;T;T;T	0.43688|0.01933	0.94|4.55;4.63;4.63;4.66;4.64	4.83|4.83	0.789|0.789	0.18607|0.18607	.|.	.|.	.|.	.|.	.|.	T|T	0.03434|0.03434	0.0099|0.0099	L|L	0.57536|0.57536	1.79|1.79	0.58432|0.58432	D|D	0.999999|0.999999	.|B;D	.|0.71674	.|0.001;0.998	.|B;D	.|0.75484	.|0.003;0.986	T|T	0.48647|0.48647	-0.9017|-0.9017	7|9	0.02654|0.66056	T|D	1|0.02	.|.	6.37|6.37	0.21475|0.21475	0.0:0.0924:0.4573:0.4503|0.0:0.0924:0.4573:0.4503	.|.	.|1922;2028	.|Q5VU43-3;Q5VU43	.|.;MYOME_HUMAN	E|R	185|1922;2028;2028;2113;2164	ENSP00000432498:K185E|ENSP00000327209:K1922R;ENSP00000358360:K2028R;ENSP00000358363:K2028R;ENSP00000435654:K2113R;ENSP00000358366:K2164R	ENSP00000432498:K185E|ENSP00000327209:K1922R	K|K	-|-	1|2	0|0	PDE4DIP|PDE4DIP	143574677|143574677	0.972000|0.972000	0.33761|0.33761	0.982000|0.982000	0.44146|0.44146	0.844000|0.844000	0.47949|0.47949	1.578000|1.578000	0.36525|0.36525	0.276000|0.276000	0.22118|0.22118	-0.636000|-0.636000	0.03981|0.03981	AAG|AAA	T|0.967;C|0.033	0.033	strong		0.488	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
FYCO1	79443	hgsc.bcm.edu	37	3	46009491	46009491	+	Silent	SNP	C	C	T	rs3796376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46009491C>T	ENST00000296137.2	-	8	1540	c.1335G>A	c.(1333-1335)ctG>ctA	p.L445L	FYCO1_ENST00000535325.1_Silent_p.L445L	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	445					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CCAGGCGCTCCAGGCTGGCCC	0.627													C|||	808	0.161342	0.0333	0.1542	5008	,	,		17595	0.2927		0.2078	False		,,,				2504	0.1564				p.L445L		Atlas-SNP	.											.	FYCO1	115	.	0			c.G1335A						PASS	.	C		293,4113	161.1+/-193.3	6,281,1916	138.0	151.0	147.0		1335	2.3	0.9	3	dbSNP_107	147	1686,6914	309.2+/-309.3	161,1364,2775	no	coding-synonymous	FYCO1	NM_024513.2		167,1645,4691	TT,TC,CC		19.6047,6.65,15.2161		445/1479	46009491	1979,11027	2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			GCGCTCCAGGCTG	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.1335G>A	3.37:g.46009491C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	155	79	0.509677	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																			C|0.825;T|0.175	0.175	strong		0.627	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
IPO13	9670	hgsc.bcm.edu	37	1	44422367	44422367	+	Silent	SNP	A	A	G	rs36061711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44422367A>G	ENST00000372343.3	+	4	1760	c.1098A>G	c.(1096-1098)acA>acG	p.T366T	IPO13_ENST00000492152.1_3'UTR	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	366					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)				TCTGGTACACACTGCAGGTGT	0.532													A|||	196	0.0391374	0.1415	0.013	5008	,	,		20746	0.0		0.0	False		,,,				2504	0.0				p.T366T		Atlas-SNP	.											.	IPO13	86	.	0			c.A1098G						PASS	.	A		497,3909	231.4+/-245.2	31,435,1737	125.0	116.0	119.0		1098	-11.5	0.2	1	dbSNP_126	119	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	IPO13	NM_014652.3		31,437,6035	GG,GA,AA		0.0233,11.2801,3.8367		366/964	44422367	499,12507	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon4			GTACACACTGCAG	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.1098A>G	1.37:g.44422367A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	164	83	0.506098	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			A|0.964;G|0.036	0.036	strong		0.532	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652	
NPR2	4882	hgsc.bcm.edu	37	9	35811749	35811749	+	IGR	SNP	C	C	T	rs79261709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35811749C>T	ENST00000342694.2	+	0	3686				SPAG8_ENST00000484764.1_Silent_p.A96A|TMEM8B_ENST00000377996.1_5'Flank|SPAG8_ENST00000396638.2_Silent_p.A98A|SPAG8_ENST00000479751.1_5'Flank|AL133410.1_ENST00000582432.1_RNA|HINT2_ENST00000474908.1_5'Flank|SPAG8_ENST00000340291.2_Silent_p.A98A	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)			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)	AGCCGGGTCCCGCACAGGGCT	0.547													c|||	68	0.0135783	0.0492	0.0043	5008	,	,		17978	0.0		0.0	False		,,,				2504	0.0				p.A98A		Atlas-SNP	.											.	SPAG8	67	.	0			c.G294A						PASS	.	C	,	184,4222	115.0+/-153.0	2,180,2021	56.0	68.0	64.0		294,294	-2.2	0.0	9	dbSNP_131	64	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SPAG8	NM_001039592.1,NM_172312.1	,	2,180,6321	TT,TC,CC		0.0,4.1761,1.4147	,	98/486,98/502	35811749	184,12822	2203	4300	6503	SO:0001628	intergenic_variant	26206	exon2			GGGTCCCGCACAG	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.35811749C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_001039592	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	c	5.786	0.329334	0.10956	0.041761	0.0	ENSG00000137098	ENST00000497810	.	.	.	5.3	-2.21	0.06973	.	.	.	.	.	T	0.04003	0.0112	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.20538	-1.0272	4	.	.	.	3.7726	0.3647	0.00370	0.3138:0.2293:0.2557:0.2013	.	.	.	.	Q	96	.	.	R	-	2	0	SPAG8	35801749	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.424000	0.07025	-0.264000	0.09365	-0.710000	0.03640	CGG	C|0.988;T|0.012	0.012	strong		0.547	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036950	33036950	+	Silent	SNP	C	C	T	rs386699855|rs2308931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33036950C>T	ENST00000419277.1	-	4	603	c.474G>A	c.(472-474)ctG>ctA	p.L158L	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Silent_p.L158L	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	138	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	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	
FLG	2312	hgsc.bcm.edu	37	1	152276583	152276583	+	Missense_Mutation	SNP	C	C	G	rs12083389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276583C>G	ENST00000368799.1	-	3	10814	c.10779G>C	c.(10777-10779)gaG>gaC	p.E3593D	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3593	Ser-rich.		E -> D (in dbSNP:rs12083389).		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	0.552									Ichthyosis				G|||	1810	0.361422	0.4796	0.3213	5008	,	,		16486	0.4732		0.1233	False		,,,				2504	0.3599				p.E3593D		Atlas-SNP	.											.	FLG	900	.	0			c.G10779C						PASS	.	G	ASP/GLU	1672,2734		368,936,899	179.0	217.0	204.0		10779	2.5	0.0	1	dbSNP_120	204	274,8322		19,236,4043	no	missense	FLG	NM_002016.1	45	387,1172,4942	GG,GC,CC		3.1875,37.9483,14.9669	benign	3593/4062	152276583	1946,11056	2203	4298	6501	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.10779G>C	1.37:g.152276583C>G	ENSP00000357789:p.Glu3593Asp	Somatic	633	0	0		WXS	Illumina HiSeq	Phase_I	643	596	0.926905	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	620	0.2838827838827839	203	0.41260162601626016	84	0.23204419889502761	251	0.4388111888111888	82	0.10817941952506596	G	6.112	0.388950	0.11581	0.379483	0.031875	ENSG00000143631	ENST00000368799	T	0.00760	5.73	3.48	2.54	0.30619	.	.	.	.	.	T	0.00144	0.0004	N	0.02539	-0.55	0.80722	P	0.0	B	0.15719	0.014	B	0.15870	0.014	T	0.10474	-1.0628	8	0.05721	T	0.95	.	9.8829	0.41245	0.0:0.4036:0.5964:0.0	rs12083389	3593	P20930	FILA_HUMAN	D	3593	ENSP00000357789:E3593D	ENSP00000357789:E3593D	E	-	3	2	FLG	150543207	0.002000	0.14202	0.020000	0.16555	0.021000	0.10359	0.308000	0.19314	0.254000	0.21573	-0.301000	0.09380	GAG	C|0.820;G|0.180	0.180	strong		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MUC17	140453	hgsc.bcm.edu	37	7	100677378	100677378	+	Missense_Mutation	SNP	C	C	A	rs143956720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677378C>A	ENST00000306151.4	+	3	2745	c.2681C>A	c.(2680-2682)aCa>aAa	p.T894K		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	894	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)					GACACCAGCACACCTGTGACC	0.498																																					p.T894K		Atlas-SNP	.											MUC17,NS,lymphoid_neoplasm,0,1	MUC17	804	1	0			c.C2681A						PASS	.	C	LYS/THR	350,4056	140.4+/-175.9	0,350,1853	297.0	290.0	292.0		2681	0.3	0.0	7	dbSNP_134	292	167,8433	48.9+/-108.6	0,167,4133	no	missense	MUC17	NM_001040105.1	78	0,517,5986	AA,AC,CC		1.9419,7.9437,3.9751	probably-damaging	894/4494	100677378	517,12489	2203	4300	6503	SO:0001583	missense	140453	exon3			CCAGCACACCTGT	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.2681C>A	7.37:g.100677378C>A	ENSP00000302716:p.Thr894Lys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	165	35	0.212121	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	3.749	-0.052049	0.07362	0.079437	0.019419	ENSG00000169876	ENST00000306151	T	0.02421	4.3	1.25	0.305	0.15801	.	.	.	.	.	T	0.00178	0.0005	N	0.14661	0.345	0.09310	N	1	D	0.69078	0.997	P	0.52267	0.694	T	0.52609	-0.8553	9	0.27082	T	0.32	.	5.4285	0.16440	0.0:0.7817:0.0:0.2183	.	894	Q685J3	MUC17_HUMAN	K	894	ENSP00000302716:T894K	ENSP00000302716:T894K	T	+	2	0	MUC17	100464098	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.259000	0.18405	0.099000	0.17552	0.196000	0.17591	ACA	C|0.958;A|0.042	0.042	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CPPED1	55313	hgsc.bcm.edu	37	16	12798724	12798724	+	Missense_Mutation	SNP	C	C	T	rs145004672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:12798724C>T	ENST00000381774.4	-	3	712	c.472G>A	c.(472-474)Gtc>Atc	p.V158I	CPPED1_ENST00000433677.2_Intron|CPPED1_ENST00000261660.4_Intron	NM_018340.2	NP_060810.2	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain containing 1	158	Catalytic.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.V158I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|urinary_tract(1)	18						AGGAACAGGACGCCCCCGACC	0.612													C|||	42	0.00838658	0.0272	0.0029	5008	,	,		17716	0.003		0.0	False		,,,				2504	0.001				p.V158I		Atlas-SNP	.											CPPED1,rectum,carcinoma,0,1	CPPED1	41	1	1	Substitution - Missense(1)	large_intestine(1)	c.G472A						scavenged	.	C	,ILE/VAL	69,3929		1,67,1931	57.0	62.0	60.0		,472	4.4	0.8	16	dbSNP_134	60	1,8319		0,1,4159	yes	intron,missense	CPPED1	NM_001099455.1,NM_018340.2	,29	1,68,6090	TT,TC,CC		0.012,1.7259,0.5683	,possibly-damaging	,158/315	12798724	70,12248	1999	4160	6159	SO:0001583	missense	55313	exon3			ACAGGACGCCCCC	AK022710	CCDS42119.1, CCDS42120.1	16p13.12	2014-02-12	2009-03-13		ENSG00000103381	ENSG00000103381			25632	protein-coding gene	gene with protein product	"""complete S transactivated protein 1"""	615603				12477932	Standard	NM_018340		Approved	CSTP1, FLJ11151	uc002dca.4	Q9BRF8	OTTHUMG00000167711	ENST00000381774.4:c.472G>A	16.37:g.12798724C>T	ENSP00000371193:p.Val158Ile	Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_018340	B4DQ68|Q6MZY9|Q9H9M9|Q9NUT6	Missense_Mutation	SNP	ENST00000381774.4	37	CCDS42120.1	27	0.012362637362637362	23	0.046747967479674794	1	0.0027624309392265192	3	0.005244755244755245	0	0.0	C	16.61	3.171078	0.57584	0.017259	1.2E-4	ENSG00000103381	ENST00000381774	T	0.72505	-0.66	5.32	4.37	0.52481	Metallophosphoesterase domain (1);	0.053983	0.64402	D	0.000001	T	0.29882	0.0747	M	0.67397	2.05	0.80722	D	1	P	0.47191	0.891	B	0.43194	0.411	T	0.56165	-0.8024	10	0.46703	T	0.11	-31.751	12.0777	0.53653	0.0:0.9163:0.0:0.0837	.	158	Q9BRF8	CPPED_HUMAN	I	158	ENSP00000371193:V158I	ENSP00000371193:V158I	V	-	1	0	CPPED1	12706225	0.998000	0.40836	0.840000	0.33206	0.315000	0.28087	3.848000	0.55903	1.256000	0.44068	-0.128000	0.14901	GTC	C|0.988;T|0.012	0.012	strong		0.612	CPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395795.2	NM_018340	
ZNF326	284695	hgsc.bcm.edu	37	1	90486412	90486412	+	Silent	SNP	T	T	G	rs2816881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:90486412T>G	ENST00000340281.4	+	10	1379	c.1236T>G	c.(1234-1236)gtT>gtG	p.V412V	ZNF326_ENST00000455342.2_Silent_p.V206V|ZNF326_ENST00000370447.3_Silent_p.V323V	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	412					mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		CTTGCAGTGTTTATATCCCTG	0.348													G|||	3471	0.693091	0.6626	0.7205	5008	,	,		18601	0.8909		0.5736	False		,,,				2504	0.6339				p.V412V		Atlas-SNP	.											.	ZNF326	60	.	0			c.T1236G						PASS	.	G		2887,1519	480.8+/-358.9	946,995,262	142.0	140.0	141.0		1236	-1.4	1.0	1	dbSNP_100	141	4828,3772	534.7+/-382.7	1338,2152,810	no	coding-synonymous	ZNF326	NM_182976.2		2284,3147,1072	GG,GT,TT		43.8605,34.4757,40.6812		412/583	90486412	7715,5291	2203	4300	6503	SO:0001819	synonymous_variant	284695	exon10			CAGTGTTTATATC	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"""Zinc fingers, C2H2-type"""	14104	protein-coding gene	gene with protein product	"""ZNF-protein interacting with nuclear mRNPs and DBC1"""	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1236T>G	1.37:g.90486412T>G		Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	275	137	0.498182	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Silent	SNP	ENST00000340281.4	37	CCDS727.1																																																																																			T|0.355;G|0.645	0.645	strong		0.348	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781	
CASS4	57091	hgsc.bcm.edu	37	20	55033420	55033420	+	Missense_Mutation	SNP	C	C	T	rs35031530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:55033420C>T	ENST00000360314.3	+	7	2203	c.1978C>T	c.(1978-1980)Cct>Tct	p.P660S	CASS4_ENST00000371336.3_Missense_Mutation_p.P660S|AL121914.1_ENST00000390795.2_RNA|CASS4_ENST00000434344.1_Missense_Mutation_p.P223S	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	660			P -> S (in dbSNP:rs35031530). {ECO:0000269|PubMed:14702039}.		cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						TATACCTCAGCCTTCGAGTCA	0.507													C|||	735	0.146765	0.3086	0.0403	5008	,	,		13987	0.2381		0.004	False		,,,				2504	0.0562				p.P660S		Atlas-SNP	.											CASS4,NS,carcinoma,-1,1	CASS4	121	1	0			c.C1978T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	1094,3312	372.0+/-320.2	134,826,1243	51.0	57.0	55.0		1816,667,1978,1978	-2.6	0.0	20	dbSNP_126	55	33,8567	22.2+/-67.0	0,33,4267	yes	missense,missense,missense,missense	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	74,74,74,74	134,859,5510	TT,TC,CC		0.3837,24.8298,8.6652	benign,benign,benign,benign	606/733,223/350,660/787,660/787	55033420	1127,11879	2203	4300	6503	SO:0001583	missense	57091	exon6			CCTCAGCCTTCGA	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.1978C>T	20.37:g.55033420C>T	ENSP00000353462:p.Pro660Ser	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	102	101	0.990196	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	37	CCDS33492.1	297	0.13598901098901098	135	0.27439024390243905	12	0.03314917127071823	148	0.25874125874125875	2	0.002638522427440633	C	8.848	0.943837	0.18281	0.248298	0.003837	ENSG00000087589	ENST00000360314;ENST00000371336;ENST00000434344	T;T;T	0.20738	2.05;2.05;2.05	5.65	-2.58	0.06228	CAS family, DUF3513 (1);	1.567350	0.02946	N	0.141079	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.12837	0.003;0.004;0.008	T	0.41052	-0.9530	9	0.18276	T	0.48	-1.3722	0.1155	0.00060	0.2771:0.2108:0.1786:0.3335	rs35031530;rs57004305	606;223;660	B4DII4;Q9NQ75-3;Q9NQ75	.;.;CASS4_HUMAN	S	660;660;223	ENSP00000353462:P660S;ENSP00000360387:P660S;ENSP00000410027:P223S	ENSP00000353462:P660S	P	+	1	0	CASS4	54466827	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-0.416000	0.07097	-0.141000	0.11374	-0.878000	0.02970	CCT	C|0.905;T|0.095	0.095	strong		0.507	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
OR5B3	441608	hgsc.bcm.edu	37	11	58170291	58170291	+	Missense_Mutation	SNP	T	T	C	rs11229410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58170291T>C	ENST00000309403.2	-	1	591	c.592A>G	c.(592-594)Att>Gtt	p.I198V		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	198			I -> V (in dbSNP:rs11229410).			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(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ACAACATAAATAAGAACAAGC	0.373													C|||	1453	0.290136	0.3533	0.2695	5008	,	,		23834	0.1448		0.3628	False		,,,				2504	0.2945				p.I198V		Atlas-SNP	.											.	OR5B3	65	.	0			c.A592G						PASS	.	C	VAL/ILE	1442,2960	681.0+/-403.9	229,984,988	74.0	71.0	72.0		592	-8.1	0.0	11	dbSNP_120	72	3095,5495	658.3+/-401.6	550,1995,1750	yes	missense	OR5B3	NM_001005469.1	29	779,2979,2738	CC,CT,TT		36.0303,32.7578,34.9215	benign	198/315	58170291	4537,8455	2201	4295	6496	SO:0001583	missense	441608	exon1			CATAAATAAGAAC	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.592A>G	11.37:g.58170291T>C	ENSP00000308270:p.Ile198Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	655	0.2999084249084249	195	0.39634146341463417	89	0.24585635359116023	95	0.1660839160839161	276	0.3641160949868074	c	0.009	-1.829691	0.00584	0.327578	0.360303	ENSG00000172769	ENST00000309403	T	0.00091	8.74	4.05	-8.1	0.01086	GPCR, rhodopsin-like superfamily (1);	1.011050	0.07957	N	0.981760	T	0.00012	0.0000	N	0.03071	-0.42	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.06881	-1.0802	9	0.29301	T	0.29	-3.0942	9.5789	0.39475	0.0:0.1083:0.2724:0.6193	rs11229410;rs58700205;rs11229410	198	Q8NH48	OR5B3_HUMAN	V	198	ENSP00000308270:I198V	ENSP00000308270:I198V	I	-	1	0	OR5B3	57926867	0.524000	0.26282	0.001000	0.08648	0.011000	0.07611	0.903000	0.28475	-1.857000	0.01159	-0.147000	0.13772	ATT	C|0.321;T|0.679	0.321	strong		0.373	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
PRKD3	23683	hgsc.bcm.edu	37	2	37543544	37543544	+	Missense_Mutation	SNP	T	T	C	rs11896614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37543544T>C	ENST00000379066.1	-	2	886	c.124A>G	c.(124-126)Aat>Gat	p.N42D	PRKD3_ENST00000234179.2_Missense_Mutation_p.N42D|PRKD3_ENST00000477132.1_5'Flank			O94806	KPCD3_HUMAN	protein kinase D3	42			N -> D (in dbSNP:rs11896614).		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)				AAGCTTCCATTAGAGAGTCGG	0.502													T|||	171	0.0341454	0.0484	0.0259	5008	,	,		17335	0.002		0.0547	False		,,,				2504	0.0327				p.N42D	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.A124G						PASS	.	T	ASP/ASN	218,4188	132.5+/-169.0	4,210,1989	89.0	85.0	87.0		124	5.7	1.0	2	dbSNP_120	87	402,8198	128.2+/-186.4	14,374,3912	yes	missense	PRKD3	NM_005813.3	23	18,584,5901	CC,CT,TT		4.6744,4.9478,4.767	possibly-damaging	42/891	37543544	620,12386	2203	4300	6503	SO:0001583	missense	23683	exon1			TTCCATTAGAGAG	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.124A>G	2.37:g.37543544T>C	ENSP00000368356:p.Asn42Asp	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	143	65	0.454545	NM_005813	D6W587|Q53TR7|Q8NEL8	Missense_Mutation	SNP	ENST00000379066.1	37	CCDS1789.1	70	0.03205128205128205	13	0.026422764227642278	12	0.03314917127071823	1	0.0017482517482517483	44	0.05804749340369393	T	17.38	3.375423	0.61735	0.049478	0.046744	ENSG00000115825	ENST00000379066;ENST00000234179	T;T	0.65916	-0.18;-0.18	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.12987	0.0315	L	0.47716	1.5	0.54753	D	0.999986	B;B	0.16166	0.016;0.003	B;B	0.14578	0.011;0.002	T	0.29119	-1.0022	10	0.62326	D	0.03	-29.3475	14.4843	0.67606	0.0:0.0:0.0:1.0	rs11896614;rs17481958;rs52813548;rs56921154;rs11896614	42;42	O94806-2;O94806	.;KPCD3_HUMAN	D	42	ENSP00000368356:N42D;ENSP00000234179:N42D	ENSP00000234179:N42D	N	-	1	0	PRKD3	37397048	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.264000	0.78432	2.154000	0.67381	0.482000	0.46254	AAT	T|0.960;C|0.040	0.040	strong		0.502	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	
AMPH	273	hgsc.bcm.edu	37	7	38431511	38431511	+	Silent	SNP	C	C	T	rs2229922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:38431511C>T	ENST00000356264.2	-	19	1931	c.1716G>A	c.(1714-1716)gcG>gcA	p.A572A	AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000428293.2_Silent_p.A530A|AMPH_ENST00000325590.5_Silent_p.A530A	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	572					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						CCGGAGGAGCCGCGTCCTCGG	0.607													C|||	368	0.0734824	0.0401	0.0893	5008	,	,		15646	0.004		0.1064	False		,,,				2504	0.1452				p.A572A		Atlas-SNP	.											AMPH,NS,carcinoma,-1,1	AMPH	157	1	0			c.G1716A						PASS	.	C	,	166,4240	110.4+/-148.6	4,158,2041	59.0	56.0	57.0		1716,1590	-9.5	0.0	7	dbSNP_98	57	974,7626	212.0+/-252.4	45,884,3371	no	coding-synonymous,coding-synonymous	AMPH	NM_001635.3,NM_139316.2	,	49,1042,5412	TT,TC,CC		11.3256,3.7676,8.7652	,	572/696,530/654	38431511	1140,11866	2203	4300	6503	SO:0001819	synonymous_variant	273	exon19			AGGAGCCGCGTCC		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.1716G>A	7.37:g.38431511C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	113	68	0.60177	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Silent	SNP	ENST00000356264.2	37	CCDS5456.1	137	0.06272893772893773	26	0.052845528455284556	30	0.08287292817679558	0	0.0	81	0.10686015831134564	C	7.174	0.588285	0.13812	0.037676	0.113256	ENSG00000078053	ENST00000441628	.	.	.	5.75	-9.5	0.00584	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.17018	-1.0383	3	.	.	.	-0.0635	0.0536	0.00013	0.3054:0.1844:0.2262:0.2839	rs2229922;rs2229922	.	.	.	S	455	.	.	G	-	1	0	AMPH	38398036	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.378000	0.01068	-1.937000	0.01047	-0.229000	0.12294	GGC	C|0.919;T|0.081	0.081	strong		0.607	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
ABCB8	11194	hgsc.bcm.edu	37	7	150730712	150730712	+	Missense_Mutation	SNP	G	G	A	rs6975981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150730712G>A	ENST00000297504.6	+	3	233	c.167G>A	c.(166-168)aGc>aAc	p.S56N	ABCB8_ENST00000477719.1_Missense_Mutation_p.S39N|ABCB8_ENST00000477092.1_Missense_Mutation_p.S39N|ABCB8_ENST00000542328.1_Intron|ABCB8_ENST00000498578.1_Missense_Mutation_p.S39N|ABCB8_ENST00000493338.1_3'UTR|ABCB8_ENST00000358849.4_Missense_Mutation_p.S39N|ABCB8_ENST00000356058.4_Missense_Mutation_p.S76N			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	56					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)	GGCTACCGCAGCTCCTCCCTC	0.677													G|||	161	0.0321486	0.1157	0.0115	5008	,	,		16274	0.0		0.0	False		,,,				2504	0.0				p.S39N		Atlas-SNP	.											.	ABCB8	65	.	0			c.G116A						PASS	.	G	ASN/SER	340,4066	168.7+/-199.5	13,314,1876	41.0	45.0	44.0		116	2.2	0.0	7	dbSNP_116	44	10,8590	7.7+/-29.5	0,10,4290	yes	missense	ABCB8	NM_007188.3	46	13,324,6166	AA,AG,GG		0.1163,7.7167,2.6911	benign	39/719	150730712	350,12656	2203	4300	6503	SO:0001583	missense	11194	exon2			ACCGCAGCTCCTC	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.167G>A	7.37:g.150730712G>A	ENSP00000297504:p.Ser56Asn	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		65	0.02976190476190476	61	0.12398373983739837	4	0.011049723756906077	0	0.0	0	0.0	G	10.99	1.505996	0.26949	0.077167	0.001163	ENSG00000197150	ENST00000461373;ENST00000358849;ENST00000360651;ENST00000297504;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092	D;D;D;D;D;D	0.91011	-2.65;-2.66;-2.77;-2.01;-2.07;-2.1	4.07	2.23	0.28157	.	0.502250	0.22050	N	0.065324	T	0.05410	0.0143	N	0.24115	0.695	0.09310	N	1	B;B;B;B;P	0.40000	0.079;0.361;0.277;0.361;0.698	B;B;B;B;B	0.38562	0.035;0.051;0.109;0.081;0.276	T	0.29212	-1.0019	10	0.38643	T	0.18	0.0796	5.7097	0.17929	0.1091:0.1985:0.6924:0.0	rs6975981;rs60484309	39;56;39;39;76	A5D8W3;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8	.;ABCB8_HUMAN;.;.;.	N	76;39;39;56;39;76;39;39	ENSP00000351717:S39N;ENSP00000297504:S56N;ENSP00000418271:S39N;ENSP00000348353:S76N;ENSP00000419891:S39N;ENSP00000419558:S39N	ENSP00000297504:S56N	S	+	2	0	ABCB8	150361645	0.849000	0.29639	0.002000	0.10522	0.015000	0.08874	1.842000	0.39250	0.474000	0.27392	0.561000	0.74099	AGC	G|0.973;A|0.027	0.027	strong		0.677	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
SYNE2	23224	hgsc.bcm.edu	37	14	64461914	64461914	+	Silent	SNP	A	A	G	rs34001379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64461914A>G	ENST00000344113.4	+	23	3146	c.2934A>G	c.(2932-2934)gaA>gaG	p.E978E	SYNE2_ENST00000554584.1_Silent_p.E978E|SYNE2_ENST00000358025.3_Silent_p.E978E|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	978					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)		TCATCAAAGAACATGAGGTAC	0.318													A|||	32	0.00638978	0.0242	0.0	5008	,	,		18525	0.0		0.0	False		,,,				2504	0.0				p.E978E		Atlas-SNP	.											SYNE2,rectum,carcinoma,+2,1	SYNE2	577	1	0			c.A2934G						PASS	.	A	,	93,3593		3,87,1753	47.0	46.0	46.0		2934,2934	-0.1	1.0	14	dbSNP_126	46	0,8152		0,0,4076	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	3,87,5829	GG,GA,AA		0.0,2.5231,0.7856	,	978/6886,978/6908	64461914	93,11745	1843	4076	5919	SO:0001819	synonymous_variant	23224	exon23			CAAAGAACATGAG	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.2934A>G	14.37:g.64461914A>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	158	78	0.493671	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			A|0.995;G|0.005	0.005	strong		0.318	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
CLEC1A	51267	hgsc.bcm.edu	37	12	10251445	10251445	+	Missense_Mutation	SNP	C	C	G	rs2306894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:10251445C>G	ENST00000315330.4	-	1	139	c.77G>C	c.(76-78)gGc>gCc	p.G26A	CLEC1A_ENST00000457018.2_Missense_Mutation_p.G26A|CLEC1A_ENST00000420265.2_Missense_Mutation_p.G26A	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	26			G -> A (in dbSNP:rs2306894). {ECO:0000269|PubMed:10671229, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.G26A(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						TGTGGCAGAGCCTTGAGAATG	0.547													G|||	3358	0.670527	0.8918	0.6009	5008	,	,		17752	0.3502		0.8728	False		,,,				2504	0.5429				p.G26A		Atlas-SNP	.											CLEC1A,colon,carcinoma,0,2	CLEC1A	48	2	1	Substitution - Missense(1)	stomach(1)	c.G77C						PASS	.	G	ALA/GLY	3961,445	207.5+/-228.8	1786,389,28	102.0	83.0	89.0		77	4.7	0.0	12	dbSNP_100	89	7560,1040	214.3+/-254.0	3342,876,82	yes	missense	CLEC1A	NM_016511.2	60	5128,1265,110	GG,GC,CC		12.093,10.0999,11.4178	benign	26/281	10251445	11521,1485	2203	4300	6503	SO:0001583	missense	51267	exon1			GCAGAGCCTTGAG	AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"""C-type lectin domain containing"""	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.77G>C	12.37:g.10251445C>G	ENSP00000326407:p.Gly26Ala	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	172	172	1	NM_016511	Q8IUW7|Q9NZH3	Missense_Mutation	SNP	ENST00000315330.4	37	CCDS8612.1	1521	0.6964285714285714	428	0.8699186991869918	239	0.6602209944751382	190	0.3321678321678322	664	0.8759894459102903	G	1.549	-0.539636	0.04053	0.899001	0.87907	ENSG00000150048	ENST00000315330;ENST00000457018;ENST00000420265;ENST00000414501	T;T;T;T	0.38887	5.12;5.49;5.02;1.11	5.55	4.66	0.58398	.	0.349225	0.24869	N	0.034957	T	0.00012	0.0000	N	0.00742	-1.23	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	0.34925	-0.9809	9	0.07325	T	0.83	.	7.8886	0.29665	0.0861:0.1619:0.7521:0.0	rs2306894;rs17205927;rs52792342;rs61030141;rs2306894	26;26;26	E7ESV9;E9PFB4;Q8NC01	.;.;CLC1A_HUMAN	A	26	ENSP00000326407:G26A;ENSP00000415048:G26A;ENSP00000417010:G26A;ENSP00000396272:G26A	ENSP00000326407:G26A	G	-	2	0	CLEC1A	10142712	0.265000	0.24102	0.001000	0.08648	0.144000	0.21451	0.958000	0.29227	0.715000	0.32103	-0.127000	0.14921	GGC	C|0.179;G|0.819	0.819	strong		0.547	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511	
MICAL2	9645	hgsc.bcm.edu	37	11	12229655	12229655	+	Silent	SNP	T	T	G	rs2279390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:12229655T>G	ENST00000256194.4	+	5	846	c.558T>G	c.(556-558)gtT>gtG	p.V186V	MICAL2_ENST00000537344.1_Silent_p.V186V|MICAL2_ENST00000342902.5_Silent_p.V186V|MICAL2_ENST00000527546.1_Silent_p.V186V|MICAL2_ENST00000527195.1_3'UTR|MICAL2_ENST00000379612.3_Silent_p.V186V	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	186	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		TCGTGAAGGTTCTAGAGCCTC	0.423													T|||	2012	0.401757	0.4856	0.245	5008	,	,		20845	0.501		0.2584	False		,,,				2504	0.4448				p.V186V		Atlas-SNP	.											.	MICAL2	114	.	0			c.T558G						PASS	.	T		2029,2373	564.5+/-381.5	461,1107,633	185.0	169.0	174.0		558	-0.9	0.7	11	dbSNP_100	174	2028,6560	354.2+/-329.4	230,1568,2496	no	coding-synonymous	MICAL2	NM_014632.2		691,2675,3129	GG,GT,TT		23.6143,46.0927,31.2317		186/1125	12229655	4057,8933	2201	4294	6495	SO:0001819	synonymous_variant	9645	exon5			GAAGGTTCTAGAG	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.558T>G	11.37:g.12229655T>G		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	162	160	0.987654	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																			G|0.341;N|0.000	0.341	strong		0.423	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
SPATA4	132851	hgsc.bcm.edu	37	4	177113836	177113836	+	Silent	SNP	C	C	T	rs6832177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:177113836C>T	ENST00000280191.2	-	4	738	c.630G>A	c.(628-630)gcG>gcA	p.A210A	SPATA4_ENST00000515234.1_Silent_p.A37A	NM_144644.2	NP_653245.2	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	210						cytoplasm (GO:0005737)				NS(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)	22		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)		TGAGGAACTCCGCTTTAAGTT	0.373													c|||	1416	0.282748	0.2239	0.3646	5008	,	,		17787	0.255		0.3708	False		,,,				2504	0.2423				p.A210A		Atlas-SNP	.											SPATA4,NS,carcinoma,-1,1	SPATA4	44	1	0			c.G630A						PASS	.	C		1120,3286	398.3+/-330.8	147,826,1230	88.0	91.0	90.0		630	-3.7	0.0	4	dbSNP_116	90	3042,5558	466.9+/-366.9	551,1940,1809	no	coding-synonymous	SPATA4	NM_144644.2		698,2766,3039	TT,TC,CC		35.3721,25.4199,32.0006		210/306	177113836	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	132851	exon4			GAACTCCGCTTTA	AY040204	CCDS3826.1	4q34.2	2008-02-05			ENSG00000150628	ENSG00000150628			17333	protein-coding gene	gene with protein product		609879					Standard	NM_144644		Approved	TSARG2, SPEF1B	uc003iuo.1	Q8NEY3	OTTHUMG00000160788	ENST00000280191.2:c.630G>A	4.37:g.177113836C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	214	94	0.439252	NM_144644	Q8NCS5|Q8WW15	Silent	SNP	ENST00000280191.2	37	CCDS3826.1																																																																																			C|0.701;T|0.299	0.299	strong		0.373	SPATA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362326.1	NM_144644	
ERO1L	30001	hgsc.bcm.edu	37	14	53133134	53133134	+	Silent	SNP	A	A	G	rs34388088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:53133134A>G	ENST00000395686.3	-	7	811	c.588T>C	c.(586-588)gcT>gcC	p.A196A		NM_014584.1	NP_055399.1	Q96HE7	ERO1A_HUMAN	ERO1-like (S. cerevisiae)	196					4-hydroxyproline metabolic process (GO:0019471)|brown fat cell differentiation (GO:0050873)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum unfolded protein response (GO:0030968)|extracellular matrix organization (GO:0030198)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to temperature stimulus (GO:0009266)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular membrane-bounded organelle (GO:0043231)|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)		ERO1L/FERMT2(2)	breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12	Breast(41;0.226)					ATATTTTCCAAGCATCTGGTC	0.333													A|||	76	0.0151757	0.0537	0.0072	5008	,	,		17663	0.0		0.0	False		,,,				2504	0.0				p.A196A		Atlas-SNP	.											.	ERO1L	35	.	0			c.T588C						PASS	.	A		219,4187	129.4+/-166.1	8,203,1992	79.0	79.0	79.0		588	0.9	1.0	14	dbSNP_126	79	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ERO1L	NM_014584.1		8,208,6287	GG,GA,AA		0.0581,4.9705,1.7223		196/469	53133134	224,12782	2203	4300	6503	SO:0001819	synonymous_variant	30001	exon7			TTTCCAAGCATCT	AF081886	CCDS9709.1	14q22.1	2010-10-06	2001-11-28		ENSG00000197930	ENSG00000197930			13280	protein-coding gene	gene with protein product		615435	"""ERO1 (S. cerevisiae)-like"""			10671517	Standard	NM_014584		Approved	ERO1A, ERO1-alpha	uc001wzv.3	Q96HE7	OTTHUMG00000140301	ENST00000395686.3:c.588T>C	14.37:g.53133134A>G		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	199	84	0.422111	NM_014584	A8K9X4|A8MYW1|Q7LD45|Q9P1Q9|Q9UKV6	Silent	SNP	ENST00000395686.3	37	CCDS9709.1																																																																																			A|0.985;G|0.015	0.015	strong		0.333	ERO1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276892.1	NM_014584	
KLC3	147700	hgsc.bcm.edu	37	19	45848946	45848946	+	Silent	SNP	G	G	A	rs114640964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45848946G>A	ENST00000391946.2	+	2	249	c.147G>A	c.(145-147)gcG>gcA	p.A49A	KLC3_ENST00000470402.1_Silent_p.A63A|KLC3_ENST00000585434.1_Silent_p.A49A	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	49					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		GGCACCTGGCGGAGGCCCTGG	0.716													g|||	75	0.014976	0.0552	0.0029	5008	,	,		13066	0.0		0.0	False		,,,				2504	0.0				p.A49A		Atlas-SNP	.											.	KLC3	37	.	0			c.G147A						PASS	.	A		150,3632		0,150,1741	5.0	8.0	7.0		147	-4.1	0.9	19	dbSNP_132	7	2,7914		0,2,3956	no	coding-synonymous	KLC3	NM_177417.2		0,152,5697	AA,AG,GG		0.0253,3.9662,1.2994		49/505	45848946	152,11546	1891	3958	5849	SO:0001819	synonymous_variant	147700	exon2			CCTGGCGGAGGCC	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"""Tetratricopeptide (TTC) repeat domain containing"""	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.147G>A	19.37:g.45848946G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Silent	SNP	ENST00000391946.2	37	CCDS12660.2																																																																																			G|0.990;A|0.010	0.010	strong		0.716	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275	
OR5W2	390148	hgsc.bcm.edu	37	11	55681130	55681130	+	Missense_Mutation	SNP	A	A	T	rs34573569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55681130A>T	ENST00000344514.1	-	1	928	c.929T>A	c.(928-930)tTt>tAt	p.F310Y		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	310			F -> Y (in dbSNP:rs34573569).			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						ATTTCCttaaaataaaatttt	0.299													A|||	454	0.090655	0.1278	0.0403	5008	,	,		13909	0.0903		0.0944	False		,,,				2504	0.0726				p.F310Y	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.T929A						PASS	.	A	TYR/PHE	402,3740		23,356,1692	12.0	13.0	13.0		929	-0.4	0.0	11	dbSNP_126	13	624,7858		22,580,3639	yes	missense	OR5W2	NM_001001960.1	22	45,936,5331	TT,TA,AA		7.3568,9.7055,8.1274	probably-damaging	310/311	55681130	1026,11598	2071	4241	6312	SO:0001583	missense	390148	exon1			CCTTAAAATAAAA	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.929T>A	11.37:g.55681130A>T	ENSP00000342448:p.Phe310Tyr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	205	0.09386446886446886	74	0.15040650406504066	18	0.049723756906077346	46	0.08041958041958042	67	0.08839050131926121	.	13.26	2.183817	0.38609	0.097055	0.073568	ENSG00000187612	ENST00000344514	T	0.02280	4.36	4.0	-0.387	0.12463	.	0.579014	0.13070	N	0.416199	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.20164	0.042	B	0.21917	0.037	T	0.45716	-0.9242	9	0.59425	D	0.04	.	4.1446	0.10210	0.6166:0.0:0.2232:0.1602	rs34573569	310	Q8NH69	OR5W2_HUMAN	Y	310	ENSP00000342448:F310Y	ENSP00000342448:F310Y	F	-	2	0	OR5W2	55437706	.	.	0.027000	0.17364	0.423000	0.31445	.	.	0.003000	0.14656	0.448000	0.29417	TTT	A|0.877;T|0.123	0.123	strong		0.299	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
C17orf64	124773	hgsc.bcm.edu	37	17	58508618	58508618	+	Silent	SNP	T	T	C	rs3760332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:58508618T>C	ENST00000269127.4	+	6	786	c.702T>C	c.(700-702)acT>acC	p.T234T	RPL12P38_ENST00000588627.1_RNA	NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	234										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			CTCCAGAGACTGAACCGTAAG	0.458													C|||	1541	0.307708	0.8608	0.1023	5008	,	,		17422	0.1716		0.0765	False		,,,				2504	0.0838				p.T234T		Atlas-SNP	.											.	C17orf64	19	.	0			c.T702C						PASS	.	C		3104,1302		1120,864,219	43.0	55.0	51.0		702	-1.2	0.0	17	dbSNP_107	51	774,7826		30,714,3556	no	coding-synonymous	C17orf64	NM_181707.2		1150,1578,3775	CC,CT,TT		9.0,29.5506,29.817		234/237	58508618	3878,9128	2203	4300	6503	SO:0001819	synonymous_variant	124773	exon6			AGAGACTGAACCG	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.702T>C	17.37:g.58508618T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_181707	Q8IY87	Silent	SNP	ENST00000269127.4	37	CCDS32698.2																																																																																			T|0.702;C|0.298	0.298	strong		0.458	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707	
KALRN	8997	hgsc.bcm.edu	37	3	124374487	124374487	+	Silent	SNP	T	T	C	rs55750661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124374487T>C	ENST00000291478.5	+	6	904	c.741T>C	c.(739-741)taT>taC	p.Y247Y	KALRN_ENST00000428018.2_Silent_p.Y215Y|KALRN_ENST00000459915.1_Silent_p.Y36Y|KALRN_ENST00000360013.3_Silent_p.Y1944Y|KALRN_ENST00000393496.1_Silent_p.Y285Y	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1943					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						AGAAAGACTATGTCAAGGATC	0.493													t|||	8	0.00159744	0.0038	0.0029	5008	,	,		20398	0.0		0.001	False		,,,				2504	0.0				p.Y1944Y		Atlas-SNP	.											.	KALRN	556	.	0			c.T5832C						PASS	.	C	,	22,4384	29.0+/-57.7	0,22,2181	203.0	186.0	191.0		5832,741	-2.5	1.0	3	dbSNP_129	191	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_007064.3	,	0,24,6479	CC,CT,TT		0.0233,0.4993,0.1845	,	1944/2987,247/1290	124374487	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon39			AGACTATGTCAAG	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	ENST00000291478.5:c.741T>C	3.37:g.124374487T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	140	67	0.478571	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	37	CCDS3028.1	3	0.0013736263736263737	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	0	0.0	t	10.36	1.329889	0.24167	0.004993	2.33E-4	ENSG00000160145	ENST00000354186	.	.	.	5.42	-2.53	0.06326	.	.	.	.	.	T	0.55465	0.1922	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59112	-0.7515	4	.	.	.	.	13.5294	0.61613	0.0:0.5623:0.0:0.4377	rs55750661	.	.	.	T	1913	.	.	M	+	2	0	KALRN	125857177	0.434000	0.25570	0.977000	0.42913	0.995000	0.86356	-0.455000	0.06762	-0.595000	0.05828	-0.253000	0.11424	ATG	T|0.998;C|0.002	0.002	strong		0.493	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947	
FAM207A	85395	hgsc.bcm.edu	37	21	46396659	46396659	+	Missense_Mutation	SNP	G	G	C	rs3737075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46396659G>C	ENST00000291634.6	+	6	682	c.634G>C	c.(634-636)Gtg>Ctg	p.V212L	FAM207A_ENST00000397826.3_Missense_Mutation_p.V197L|FAM207A_ENST00000479127.1_3'UTR	NM_058190.2	NP_478070.1	Q9NSI2	F207A_HUMAN	family with sequence similarity 207, member A	212			V -> L (in dbSNP:rs3737075).														CAGCCCCCTGGTGGCCATCGG	0.632													G|||	762	0.152157	0.2042	0.2522	5008	,	,		15848	0.1091		0.165	False		,,,				2504	0.0419				p.V212L		Atlas-SNP	.											.	.	.	.	0			c.G634C						PASS	.	G	LEU/VAL	905,3417		109,687,1365	11.0	12.0	12.0		634	0.0	1.0	21	dbSNP_107	12	1335,7185		112,1111,3037	no	missense	FAM207A	NM_058190.2	32	221,1798,4402	CC,CG,GG		15.669,20.9394,17.4428	benign	212/231	46396659	2240,10602	2161	4260	6421	SO:0001583	missense	85395	exon6			CCCCTGGTGGCCA		CCDS13718.1	21q22.3	2011-08-15	2011-08-15	2011-08-15	ENSG00000160256	ENSG00000160256			15811	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 70"""	C21orf70			Standard	NM_058190		Approved	PRED56	uc002zgl.3	Q9NSI2	OTTHUMG00000090293	ENST00000291634.6:c.634G>C	21.37:g.46396659G>C	ENSP00000291634:p.Val212Leu	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_058190		Missense_Mutation	SNP	ENST00000291634.6	37	CCDS13718.1	364	0.16666666666666666	104	0.21138211382113822	67	0.1850828729281768	66	0.11538461538461539	127	0.16754617414248021	G	0.367	-0.935981	0.02340	0.209394	0.15669	ENSG00000160256	ENST00000291634;ENST00000397826	T;T	0.41065	1.01;1.01	4.35	0.0344	0.14183	.	0.627114	0.15229	N	0.273539	T	0.00012	0.0000	N	0.01352	-0.895	0.46478	P	9.320000000000439E-4	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.27331	-1.0077	9	0.02654	T	1	-6.2649	2.8182	0.05464	0.1701:0.3614:0.364:0.1045	rs3737075;rs4819002;rs60509357	197;212	Q9NSI2-2;Q9NSI2	.;F207A_HUMAN	L	212;197	ENSP00000291634:V212L;ENSP00000380926:V197L	ENSP00000291634:V212L	V	+	1	0	C21orf70	45221087	0.000000	0.05858	0.967000	0.41034	0.040000	0.13550	-0.231000	0.09069	0.181000	0.19994	-0.321000	0.08615	GTG	G|0.835;C|0.165	0.165	strong		0.632	FAM207A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206639.1	NM_058190	
KIAA0226L	80183	hgsc.bcm.edu	37	13	46919719	46919719	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:46919719C>T	ENST00000429979.1	-	13	2252	c.1648G>A	c.(1648-1650)Gag>Aag	p.E550K	KIAA0226L_ENST00000409879.2_Missense_Mutation_p.E393K|KIAA0226L_ENST00000378797.2_Intron|KIAA0226L_ENST00000378787.3_Intron|KIAA0226L_ENST00000534925.1_Missense_Mutation_p.E415K|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.E550K|KIAA0226L_ENST00000378781.3_3'UTR|KIAA0226L_ENST00000378784.4_Missense_Mutation_p.E483K|KIAA0226L_ENST00000322896.6_Missense_Mutation_p.E393K	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	550										NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						GGCACCTGCTCGAACTCCTTT	0.527																																					p.E550K		Atlas-SNP	.											.	KIAA0226L	63	.	0			c.G1648A						PASS	.						43.0	42.0	42.0					13																	46919719		1942	4138	6080	SO:0001583	missense	80183	exon13			CCTGCTCGAACTC	AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 18"""	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.1648G>A	13.37:g.46919719C>T	ENSP00000396935:p.Glu550Lys	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_025113	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Missense_Mutation	SNP	ENST00000429979.1	37	CCDS31970.2	.	.	.	.	.	.	.	.	.	.	C	18.22	3.574834	0.65878	.	.	ENSG00000102445	ENST00000429979;ENST00000378784;ENST00000389908;ENST00000409879;ENST00000322896;ENST00000534925	T;T;T;T	0.46819	0.86;0.87;0.86;0.89	5.35	4.51	0.55191	.	.	.	.	.	T	0.41396	0.1157	M	0.77616	2.38	0.80722	D	1	B;B;P;B;B	0.38677	0.231;0.231;0.642;0.251;0.434	B;B;B;B;B	0.33521	0.064;0.064;0.163;0.041;0.165	T	0.35599	-0.9782	9	0.08179	T	0.78	-17.8147	9.4511	0.38727	0.0:0.8394:0.0:0.1606	.	393;393;550;415;483	B7ZBN5;B7Z6E4;Q9H714;A8KAG9;Q9H714-3	.;.;K226L_HUMAN;.;.	K	550;483;550;393;393;415	ENSP00000396935:E550K;ENSP00000368061:E483K;ENSP00000374558:E550K;ENSP00000437501:E415K	ENSP00000315633:E393K	E	-	1	0	KIAA0226L	45817720	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.410000	0.52664	1.251000	0.43983	0.655000	0.94253	GAG	.	.	none		0.527	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113	
FREM1	158326	hgsc.bcm.edu	37	9	14816829	14816829	+	Missense_Mutation	SNP	G	G	C	rs7041710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14816829G>C	ENST00000380880.3	-	15	3370	c.2587C>G	c.(2587-2589)Ctc>Gtc	p.L863V	FREM1_ENST00000380881.4_Missense_Mutation_p.L864V|FREM1_ENST00000422223.2_Missense_Mutation_p.L863V			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	25	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	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	
TREM1	54210	hgsc.bcm.edu	37	6	41243926	41243926	+	Missense_Mutation	SNP	G	G	C	rs2234245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41243926G>C	ENST00000244709.4	-	4	705	c.642C>G	c.(640-642)ttC>ttG	p.F214L	TREM1_ENST00000589614.1_Intron|TREM1_ENST00000334475.6_Missense_Mutation_p.S150C	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	214			F -> L (in dbSNP:rs2234245).		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)					TCTTACTCAGGAATCCACCAG	0.547													G|||	140	0.0279553	0.1006	0.0101	5008	,	,		19431	0.0		0.0	False		,,,				2504	0.0				p.F214L		Atlas-SNP	.											.	TREM1	38	.	0			c.C642G						PASS	.	G	CYS/SER,LEU/PHE	299,4107	162.5+/-194.5	11,277,1915	174.0	143.0	154.0		449,642	1.0	0.1	6	dbSNP_98	154	7,8593	5.0+/-18.6	0,7,4293	yes	missense,missense	TREM1	NM_001242590.1,NM_018643.3	112,22	11,284,6208	CC,CG,GG		0.0814,6.7862,2.3528	possibly-damaging,possibly-damaging	150/151,214/235	41243926	306,12700	2203	4300	6503	SO:0001583	missense	54210	exon4			ACTCAGGAATCCA	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.642C>G	6.37:g.41243926G>C	ENSP00000244709:p.Phe214Leu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_018643	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Missense_Mutation	SNP	ENST00000244709.4	37	CCDS4854.1	46|46	0.021062271062271064|0.021062271062271064	41|41	0.08333333333333333|0.08333333333333333	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	18.63|18.63	3.665281|3.665281	0.67700|0.67700	0.067862|0.067862	8.14E-4|8.14E-4	ENSG00000124731|ENSG00000124731	ENST00000244709|ENST00000334475	T|T	0.04194|0.14144	3.68|2.53	4.86|4.86	1.0|1.0	0.19881|0.19881	.|.	0.883988|.	0.09394|.	N|.	0.808190|.	T|T	0.04543|0.04543	0.0124|0.0124	.|.	.|.	.|.	0.20196|0.20196	N|N	0.999924|0.999924	B|P	0.02656|0.41546	0.0|0.754	B|B	0.01281|0.41299	0.0|0.353	T|T	0.30650|0.30650	-0.9971|-0.9971	9|8	0.02654|0.87932	T|D	1|0	-4.1779|-4.1779	4.7266|4.7266	0.12943|0.12943	0.2677:0.1574:0.5749:0.0|0.2677:0.1574:0.5749:0.0	rs2234245|rs2234245	214|150	Q9NP99|Q9NP99-2	TREM1_HUMAN|.	L|C	214|150	ENSP00000244709:F214L|ENSP00000334284:S150C	ENSP00000244709:F214L|ENSP00000334284:S150C	F|S	-|-	3|2	2|0	TREM1|TREM1	41351904|41351904	0.593000|0.593000	0.26840|0.26840	0.056000|0.056000	0.19401|0.19401	0.730000|0.730000	0.41778|0.41778	0.268000|0.268000	0.18571|0.18571	0.059000|0.059000	0.16252|0.16252	0.655000|0.655000	0.94253|0.94253	TTC|TCC	G|0.979;C|0.021	0.021	strong		0.547	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040505.2	NM_018643	
DDX27	55661	hgsc.bcm.edu	37	20	47841660	47841660	+	Missense_Mutation	SNP	G	G	T	rs11553387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47841660G>T	ENST00000371764.4	+	6	626	c.617G>T	c.(616-618)gGa>gTa	p.G206V	DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	206						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GAAGCAGGAGGATTTTTTGAA	0.423													G|||	695	0.138778	0.1959	0.1729	5008	,	,		21632	0.0427		0.2008	False		,,,				2504	0.0726				p.G206V		Atlas-SNP	.											.	DDX27	74	.	0			c.G617T						PASS	.	G	VAL/GLY	826,3580	328.5+/-300.6	78,670,1455	116.0	118.0	117.0		617	5.2	1.0	20	dbSNP_120	117	1918,6682	340.3+/-323.5	200,1518,2582	yes	missense	DDX27	NM_017895.7	109	278,2188,4037	TT,TG,GG		22.3023,18.7472,21.098	benign	206/797	47841660	2744,10262	2203	4300	6503	SO:0001583	missense	55661	exon6			CAGGAGGATTTTT	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.617G>T	20.37:g.47841660G>T	ENSP00000360828:p.Gly206Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	210	94	0.447619	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	341	0.15613553113553114	95	0.19308943089430894	66	0.18232044198895028	28	0.04895104895104895	152	0.20052770448548812	G	11.72	1.721409	0.30503	0.187472	0.223023	ENSG00000124228	ENST00000371764	T	0.01484	4.84	5.2	5.2	0.72013	.	0.222295	0.44097	D	0.000490	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.9999999000127	B	0.20780	0.048	B	0.15052	0.012	T	0.61946	-0.6958	9	0.33141	T	0.24	-18.4289	17.0527	0.86524	0.0:0.0:1.0:0.0	rs11553387;rs11908296;rs52798552;rs56813891;rs11908296	206	Q96GQ7	DDX27_HUMAN	V	206	ENSP00000360828:G206V	ENSP00000360828:G206V	G	+	2	0	DDX27	47275067	1.000000	0.71417	1.000000	0.80357	0.261000	0.26267	3.430000	0.52807	2.814000	0.96858	0.655000	0.94253	GGA	A|0.001;C|0.006;G|0.814;T|0.179	0.179	strong		0.423	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		
FLG	2312	hgsc.bcm.edu	37	1	152276660	152276660	+	Missense_Mutation	SNP	G	G	C	rs7540123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276660G>C	ENST00000368799.1	-	3	10737	c.10702C>G	c.(10702-10704)Cag>Gag	p.Q3568E	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	501	1	0.00199601		WXS	Illumina HiSeq	Phase_I	501	101	0.201597	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	
PTX4	390667	hgsc.bcm.edu	37	16	1536117	1536117	+	Silent	SNP	G	G	A	rs58192896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536117G>A	ENST00000447419.2	-	3	1285	c.1260C>T	c.(1258-1260)ttC>ttT	p.F420F	PTX4_ENST00000293922.1_Silent_p.F415F|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	420	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						TGCTCCCCACGAAGGCCTCGG	0.647													G|||	277	0.0553115	0.1974	0.0231	5008	,	,		17589	0.0		0.0	False		,,,				2504	0.0				p.F415F		Atlas-SNP	.											.	PTX4	46	.	0			c.C1245T						PASS	.	G		831,3567	324.8+/-298.8	76,679,1444	65.0	62.0	63.0		1245	-10.4	0.5	16	dbSNP_129	63	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	PTX4	NM_001013658.1		76,682,5741	AA,AG,GG		0.0349,18.895,6.4164		415/474	1536117	834,12164	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			CCCCACGAAGGCC		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.1260C>T	16.37:g.1536117G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				G|0.941;A|0.059	0.059	strong		0.647	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
LILRB4	11006	hgsc.bcm.edu	37	19	55179377	55179377	+	Missense_Mutation	SNP	T	T	G	rs149600113		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55179377T>G	ENST00000391736.1	+	14	1569	c.1254T>G	c.(1252-1254)ttT>ttG	p.F418L	LILRB4_ENST00000270452.2_Missense_Mutation_p.F418L|LILRB4_ENST00000391733.3_Missense_Mutation_p.F419L|LILRB4_ENST00000391734.3_Missense_Mutation_p.F365L|LILRB4_ENST00000430952.2_Missense_Mutation_p.F417L	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	352	2	0.00568182		WXS	Illumina HiSeq	Phase_I	389	9	0.0231362	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		
OR52J3	119679	hgsc.bcm.edu	37	11	5067984	5067984	+	Missense_Mutation	SNP	A	A	G	rs2500016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5067984A>G	ENST00000380370.1	+	1	229	c.229A>G	c.(229-231)Aca>Gca	p.T77A		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	77			T -> A (in dbSNP:rs2500016). {ECO:0000269|PubMed:14983052, ECO:0000269|Ref.1, ECO:0000269|Ref.3}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGCCCTTTCTACAACCTCTGT	0.488													A|||	2442	0.48762	0.5915	0.4971	5008	,	,		19708	0.2619		0.508	False		,,,				2504	0.5521				p.T77A		Atlas-SNP	.											.	OR52J3	77	.	0			c.A229G						PASS	.	A	ALA/THR	2443,1959	621.2+/-393.7	687,1069,445	129.0	110.0	117.0		229	4.2	1.0	11	dbSNP_100	117	4304,4292	577.8+/-390.6	1067,2170,1061	no	missense	OR52J3	NM_001001916.2	58	1754,3239,1506	GG,GA,AA		49.9302,44.5025,48.092	probably-damaging	77/312	5067984	6747,6251	2201	4298	6499	SO:0001583	missense	119679	exon1			CTTTCTACAACCT	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.229A>G	11.37:g.5067984A>G	ENSP00000369728:p.Thr77Ala	Somatic	265	1	0.00377358		WXS	Illumina HiSeq	Phase_I	291	145	0.498282	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	995	0.4555860805860806	290	0.5894308943089431	170	0.4696132596685083	149	0.26048951048951047	386	0.5092348284960422	A	15.11	2.736934	0.49045	0.554975	0.500698	ENSG00000205495	ENST00000380370	T	0.04603	3.59	4.19	4.19	0.49359	GPCR, rhodopsin-like superfamily (1);	0.293409	0.24016	N	0.042331	T	0.00012	0.0000	M	0.74881	2.28	0.80722	P	0.0	P	0.47350	0.894	P	0.49301	0.606	T	0.24693	-1.0153	9	0.87932	D	0	.	12.2358	0.54514	1.0:0.0:0.0:0.0	rs2500016	77	Q8NH60	O52J3_HUMAN	A	77	ENSP00000369728:T77A	ENSP00000369728:T77A	T	+	1	0	OR52J3	5024560	0.001000	0.12720	0.986000	0.45419	0.937000	0.57800	0.843000	0.27640	1.742000	0.51746	0.533000	0.62120	ACA	A|0.493;G|0.507	0.507	strong		0.488	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
NLRP14	338323	hgsc.bcm.edu	37	11	7060092	7060092	+	Missense_Mutation	SNP	A	A	G	rs16921697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7060092A>G	ENST00000299481.4	+	2	621	c.275A>G	c.(274-276)aAa>aGa	p.K92R		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	92	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.		K -> R (in dbSNP:rs16921697). {ECO:0000269|PubMed:16931801}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)	p.K92R(1)|p.K92E(1)		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)		GAGAGAGCGAAAGAAGAGATC	0.463													A|||	408	0.0814696	0.0038	0.0533	5008	,	,		19978	0.2133		0.0258	False		,,,				2504	0.1278				p.K92R		Atlas-SNP	.											NLRP14_ENST00000299481,NS,carcinoma,0,2	NLRP14	187	2	2	Substitution - Missense(2)	stomach(2)	c.A275G						PASS	.	A	ARG/LYS	37,4365	39.2+/-71.8	0,37,2164	56.0	60.0	59.0		275	1.7	0.9	11	dbSNP_123	59	283,8309	101.6+/-162.9	2,279,4015	yes	missense	NLRP14	NM_176822.3	26	2,316,6179	GG,GA,AA		3.2938,0.8405,2.4627	possibly-damaging	92/1094	7060092	320,12674	2201	4296	6497	SO:0001583	missense	338323	exon2			GAGCGAAAGAAGA	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.275A>G	11.37:g.7060092A>G	ENSP00000299481:p.Lys92Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	176	0.08058608058608059	2	0.0040650406504065045	19	0.052486187845303865	133	0.23251748251748253	22	0.029023746701846966	A	6.877	0.531182	0.13127	0.008405	0.032938	ENSG00000158077	ENST00000299481	T	0.47177	0.85	4.08	1.71	0.24356	Pyrin (2);DEATH-like (2);	0.368276	0.23644	N	0.045991	T	0.00012	0.0000	L	0.37750	1.13	0.43377	P	0.004530000000000034	B	0.26672	0.156	B	0.30105	0.111	T	0.16689	-1.0394	9	0.06891	T	0.86	.	4.1081	0.10047	0.6793:0.2112:0.1095:0.0	rs16921697;rs52822095;rs16921697	92	Q86W24	NAL14_HUMAN	R	92	ENSP00000299481:K92R	ENSP00000299481:K92R	K	+	2	0	NLRP14	7016668	0.388000	0.25197	0.937000	0.37676	0.737000	0.42083	-0.064000	0.11636	0.358000	0.24211	0.533000	0.62120	AAA	A|0.957;G|0.043	0.043	strong		0.463	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
AGRP	181	hgsc.bcm.edu	37	16	67517179	67517179	+	Silent	SNP	C	C	T	rs34123523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67517179C>T	ENST00000290953.2	-	2	422	c.123G>A	c.(121-123)gaG>gaA	p.E41E	RP11-297D21.4_ENST00000602596.1_RNA|ATP6V0D1_ENST00000540149.1_5'Flank|ATP6V0D1_ENST00000290949.3_5'Flank	NM_001138.1	NP_001129.1	O00253	AGRP_HUMAN	agouti related neuropeptide	41					adult feeding behavior (GO:0008343)|eating behavior (GO:0042755)|feeding behavior (GO:0007631)|hormone-mediated signaling pathway (GO:0009755)|maternal process involved in female pregnancy (GO:0060135)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of feeding behavior (GO:2000253)|regulation of feeding behavior (GO:0060259)|response to insulin (GO:0032868)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)	neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			endometrium(1)	1		Acute lymphoblastic leukemia(13;0.00263)|all_hematologic(13;0.0274)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0717)|Epithelial(162;0.16)		GACCTGGGAGCTCTGGGAGCA	0.642													C|||	550	0.109824	0.2927	0.0591	5008	,	,		15113	0.003		0.0378	False		,,,				2504	0.0828				p.E41E		Atlas-SNP	.											.	AGRP	8	.	0			c.G123A						PASS	.	C		1036,3354		118,800,1277	15.0	16.0	16.0		123	1.3	0.6	16	dbSNP_126	16	358,8236		9,340,3948	no	coding-synonymous	AGRP	NM_001138.1		127,1140,5225	TT,TC,CC		4.1657,23.5991,10.7363		41/133	67517179	1394,11590	2195	4297	6492	SO:0001819	synonymous_variant	181	exon2			TGGGAGCTCTGGG	U88063	CCDS10839.1	16q22	2014-07-15	2014-07-15		ENSG00000159723	ENSG00000159723		"""Endogenous ligands"""	330	protein-coding gene	gene with protein product		602311	"""agouti (mouse) related protein"", ""agouti related protein homolog (mouse)"""			9119224, 9311920	Standard	NM_001138		Approved	Agrt, ART, ASIP2	uc002etg.1	O00253	OTTHUMG00000137509	ENST00000290953.2:c.123G>A	16.37:g.67517179C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	94	54	0.574468	NM_001138	O15459|Q2TBD9	Silent	SNP	ENST00000290953.2	37	CCDS10839.1																																																																																			C|0.877;T|0.123	0.123	strong		0.642	AGRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268828.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26168333	26168333	+	Silent	SNP	C	C	T	rs185388626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26168333C>T	ENST00000407587.2	+	7	1894	c.1725C>T	c.(1723-1725)gaC>gaT	p.D575D	MYO18B_ENST00000335473.7_Silent_p.D575D|MYO18B_ENST00000536101.1_Silent_p.D575D			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	575	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AGGTCGAGGACCTGGCCTCTC	0.607													C|||	18	0.00359425	0.0136	0.0	5008	,	,		11926	0.0		0.0	False		,,,				2504	0.0				p.D575D		Atlas-SNP	.											.	MYO18B	322	.	0			c.C1725T						PASS	.	C		70,3950		0,70,1940	108.0	107.0	107.0		1725	2.0	1.0	22		107	0,8346		0,0,4173	no	coding-synonymous	MYO18B	NM_032608.5		0,70,6113	TT,TC,CC		0.0,1.7413,0.5661		575/2568	26168333	70,12296	2010	4173	6183	SO:0001819	synonymous_variant	84700	exon7			CGAGGACCTGGCC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.1725C>T	22.37:g.26168333C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	94	53	0.56383	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				C|0.998;T|0.002	0.002	strong		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
LTF	4057	hgsc.bcm.edu	37	3	46501308	46501308	+	Splice_Site	SNP	T	T	C	rs61740461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46501308T>C	ENST00000231751.4	-	2	340	c.45A>G	c.(43-45)ggA>ggG	p.G15G	LTF_ENST00000426532.2_5'UTR|LTF_ENST00000417439.1_Splice_Site_p.G15G	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	15					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)		CCAGACACAGTCCTGGGAGAG	0.562													T|||	351	0.0700879	0.2549	0.0202	5008	,	,		17512	0.0		0.0	False		,,,				2504	0.0				p.G15G		Atlas-SNP	.											.	LTF	98	.	0			c.A45G						PASS	.	T	,	855,3551	318.8+/-295.8	83,689,1431	58.0	50.0	52.0		,45	0.4	1.0	3	dbSNP_129	52	6,8594	3.7+/-12.6	0,6,4294	yes	utr-5,coding-synonymous-near-splice	LTF	NM_001199149.1,NM_002343.3	,	83,695,5725	CC,CT,TT		0.0698,19.4054,6.62	,	,15/711	46501308	861,12145	2203	4300	6503	SO:0001630	splice_region_variant	4057	exon2			ACACAGTCCTGGG		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.44-1A>G	3.37:g.46501308T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	120	65	0.541667	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			T|0.931;C|0.069	0.069	strong		0.562	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	Silent
GPR148	344561	hgsc.bcm.edu	37	2	131486765	131486765	+	Missense_Mutation	SNP	C	C	G	rs80008074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131486765C>G	ENST00000309926.4	+	1	123	c.41C>G	c.(40-42)gCt>gGt	p.A14G		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					GGCACTACAGCTTGGCCGGCC	0.617													.|||	344	0.0686901	0.202	0.0375	5008	,	,		19856	0.0		0.0308	False		,,,				2504	0.0204				p.A14G		Atlas-SNP	.											.	GPR148	54	.	0			c.C41G						PASS	.	C	GLY/ALA	756,3650		81,594,1528	99.0	100.0	100.0		41	0.6	0.0	2	dbSNP_131	100	234,8366		3,228,4069	yes	missense	GPR148	NM_207364.2	60	84,822,5597	GG,GC,CC		2.7209,17.1584,7.6119	benign	14/348	131486765	990,12016	2203	4300	6503	SO:0001583	missense	344561	exon1			CTACAGCTTGGCC	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"""GPCR / Class A : Orphans"""	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.41C>G	2.37:g.131486765C>G	ENSP00000308908:p.Ala14Gly	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	218	106	0.486239	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	37	CCDS2163.1	144	0.06593406593406594	108	0.21951219512195122	15	0.04143646408839779	0	0.0	21	0.027704485488126648	.	7.664	0.685580	0.14973	0.171584	0.027209	ENSG00000173302	ENST00000309926	T	0.09163	3.01	2.41	0.555	0.17247	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.26635	0.155	B	0.28305	0.088	T	0.46345	-0.9198	8	0.51188	T	0.08	-0.8278	4.6863	0.12758	0.0:0.6753:0.0:0.3247	.	14	Q8TDV2	GP148_HUMAN	G	14	ENSP00000308908:A14G	ENSP00000308908:A14G	A	+	2	0	GPR148	131203235	0.003000	0.15002	0.003000	0.11579	0.025000	0.11179	0.139000	0.16036	0.127000	0.18452	-0.448000	0.05591	GCT	C|0.932;G|0.068	0.068	strong		0.617	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092	
TTN	7273	hgsc.bcm.edu	37	2	179666982	179666982	+	Missense_Mutation	SNP	C	C	A	rs35683768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179666982C>A	ENST00000591111.1	-	3	402	c.178G>T	c.(178-180)Gat>Tat	p.D60Y	TTN_ENST00000589042.1_Missense_Mutation_p.D60Y|TTN_ENST00000460472.2_Missense_Mutation_p.D60Y|TTN_ENST00000342992.6_Missense_Mutation_p.D60Y|TTN_ENST00000360870.5_Missense_Mutation_p.D60Y|TTN_ENST00000359218.5_Missense_Mutation_p.D60Y|TTN_ENST00000342175.6_Missense_Mutation_p.D60Y			Q8WZ42	TITIN_HUMAN	titin	32671	Ig-like 1.		D -> Y (in dbSNP:rs35683768). {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)			GCGCGGCCATCGCTAAAGGAG	0.537													C|||	145	0.0289537	0.0719	0.0202	5008	,	,		8936	0.0159		0.0089	False		,,,				2504	0.0112				p.D60Y		Atlas-SNP	.											.	TTN	18412	.	0			c.G178T						PASS	.	C	TYR/ASP,TYR/ASP,TYR/ASP,TYR/ASP,TYR/ASP	285,4121	157.0+/-190.0	8,269,1926	113.0	100.0	104.0		178,178,178,178,178	5.7	1.0	2	dbSNP_126	104	51,8549	32.8+/-85.7	0,51,4249	yes	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	160,160,160,160,160	8,320,6175	AA,AC,CC		0.593,6.4685,2.5834	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	60/26927,60/33424,60/5605,60/27052,60/27119	179666982	336,12670	2203	4300	6503	SO:0001583	missense	7273	exon3			GGCCATCGCTAAA	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.178G>T	2.37:g.179666982C>A	ENSP00000465570:p.Asp60Tyr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	124	72	0.580645	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		58	0.026556776556776556	38	0.07723577235772358	12	0.03314917127071823	4	0.006993006993006993	4	0.005277044854881266	C	15.72	2.915454	0.52546	0.064685	0.00593	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.74	5.74	0.90152	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.09512	0.0234	M	0.71036	2.16	0.38200	D	0.940151	D;D;D;D;D	0.76494	0.987;0.992;0.992;0.992;0.999	P;P;P;P;D	0.69654	0.8;0.8;0.886;0.886;0.965	T	0.47686	-0.9098	9	0.87932	D	0	.	19.919	0.97077	0.0:1.0:0.0:0.0	rs35683768	60;60;60;60;60	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	Y	60	ENSP00000343764:D60Y;ENSP00000434586:D60Y;ENSP00000340554:D60Y;ENSP00000352154:D60Y;ENSP00000354117:D60Y	ENSP00000340554:D60Y	D	-	1	0	TTN	179375227	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.089000	0.71384	2.707000	0.92482	0.655000	0.94253	GAT	C|0.975;A|0.025	0.025	strong		0.537	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RNASE11	122651	hgsc.bcm.edu	37	14	21052259	21052259	+	Silent	SNP	T	T	C	rs1429539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21052259T>C	ENST00000610205.1	-	3	558	c.375A>G	c.(373-375)acA>acG	p.T125T	RNASE11_ENST00000553849.1_Silent_p.T125T|RNASE11_ENST00000398008.2_Silent_p.T125T|RNASE11_ENST00000432835.2_Silent_p.T125T|RNASE11_ENST00000398009.2_Silent_p.T125T|RNASE11_ENST00000555841.1_Silent_p.T125T	NM_145250.3	NP_660293.1	Q8TAA1	RNS11_HUMAN	ribonuclease, RNase A family, 11 (non-active)	125						extracellular region (GO:0005576)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(6)|lung(7)|ovary(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	21	all_cancers(95;0.00238)	all_lung(585;0.235)	Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.0139)		GCATCACTTCTGTGGAGCTGC	0.493													C|||	1842	0.367812	0.5484	0.2723	5008	,	,		21015	0.1905		0.3539	False		,,,				2504	0.3885				p.T125T		Atlas-SNP	.											.	RNASE11	44	.	0			c.A375G						PASS	.	C		2223,2183	585.8+/-386.3	575,1073,555	86.0	74.0	78.0		375	-1.9	0.0	14	dbSNP_88	78	3189,5411	653.4+/-401.0	604,1981,1715	no	coding-synonymous	RNASE11	NM_145250.3		1179,3054,2270	CC,CT,TT		37.0814,49.5461,41.6116		125/200	21052259	5412,7594	2203	4300	6503	SO:0001819	synonymous_variant	122651	exon3			CACTTCTGTGGAG	BC025410	CCDS9553.1	14q11.1	2013-08-05	2004-11-18	2004-11-18	ENSG00000173464	ENSG00000173464		"""Ribonucleases, RNase A"""	19269	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 6"""	C14orf6			Standard	NM_145250		Approved		uc001vxs.3	Q8TAA1	OTTHUMG00000170990	ENST00000610205.1:c.375A>G	14.37:g.21052259T>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	230	228	0.991304	NM_145250		Silent	SNP	ENST00000610205.1	37	CCDS9553.1																																																																																			T|0.613;C|0.387	0.387	strong		0.493	RNASE11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073662.3	NM_145250	
ULK1	8408	hgsc.bcm.edu	37	12	132404110	132404110	+	Silent	SNP	C	C	T	rs113954208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132404110C>T	ENST00000321867.4	+	25	3129	c.2778C>T	c.(2776-2778)ctC>ctT	p.L926L	ULK1_ENST00000540647.1_Silent_p.L171L	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	926					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		CCGGCAAGCTCTGCCTGTCGT	0.657													C|||	16	0.00319489	0.0121	0.0	5008	,	,		16514	0.0		0.0	False		,,,				2504	0.0				p.L926L		Atlas-SNP	.											.	ULK1	92	.	0			c.C2778T						PASS	.	C		72,4334	63.5+/-100.7	1,70,2132	63.0	68.0	66.0		2778	1.7	1.0	12	dbSNP_132	66	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ULK1	NM_003565.2		1,71,6430	TT,TC,CC		0.0116,1.6341,0.5614		926/1051	132404110	73,12931	2203	4299	6502	SO:0001819	synonymous_variant	8408	exon25			CAAGCTCTGCCTG	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"""ATG1 autophagy related 1 homolog (S. cerevisiae)"""	603168	"""unc-51 (C. elegans)-like kinase 1"", ""unc-51-like kinase 1 (C. elegans)"""			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.2778C>T	12.37:g.132404110C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	69	41	0.594203	NM_003565	Q9UQ28	Silent	SNP	ENST00000321867.4	37	CCDS9274.1																																																																																			C|0.994;T|0.006	0.006	strong		0.657	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3		
MUC16	94025	hgsc.bcm.edu	37	19	8996460	8996460	+	Missense_Mutation	SNP	A	A	C	rs115933306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8996460A>C	ENST00000397910.4	-	61	41315	c.41112T>G	c.(41110-41112)gaT>gaG	p.D13704E	MUC16_ENST00000380951.5_Missense_Mutation_p.D345E	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13706	SEA 11. {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						TGCAGATGGCATCCACTCCAG	0.547													-|||	174	0.0347444	0.1271	0.0086	5008	,	,		19097	0.0		0.0	False		,,,				2504	0.0				p.D13704E		Atlas-SNP	.											.	MUC16	4315	.	0			c.T41112G						PASS	.	A	GLU/ASP	326,3522		18,290,1616	71.0	66.0	68.0		41112	-4.6	0.0	19	dbSNP_132	68	4,8262		0,4,4129	yes	missense	MUC16	NM_024690.2	45	18,294,5745	CC,CA,AA		0.0484,8.4719,2.7241	probably-damaging	13704/14508	8996460	330,11784	1924	4133	6057	SO:0001583	missense	94025	exon61			GATGGCATCCACT	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.41112T>G	19.37:g.8996460A>C	ENSP00000381008:p.Asp13704Glu	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	170	170	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	43|43	0.019688644688644688|0.019688644688644688	39|39	0.07926829268292683|0.07926829268292683	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	.|.	13.79|13.79	2.342264|2.342264	0.41498|0.41498	0.084719|0.084719	4.84E-4|4.84E-4	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T;T|.	0.35048|.	1.33;1.33|.	3.36|3.36	-4.56|-4.56	0.03431|0.03431	SEA (1);|.	0.216241|.	0.23120|.	U|.	0.051715|.	T|T	0.09468|0.09468	0.0233|0.0233	M|M	0.90082|0.90082	3.085|3.085	.|.	.|.	.|.	D;D|.	0.65815|.	0.995;0.959|.	P;D|.	0.67103|.	0.901;0.949|.	T|T	0.61197|0.61197	-0.7111|-0.7111	9|4	0.72032|.	D|.	0.01|.	-11.1203|-11.1203	8.9526|8.9526	0.35799|0.35799	0.6401:0.0:0.3599:0.0|0.6401:0.0:0.3599:0.0	.|.	21349;13704|.	Q8WXI7;B5ME49|.	MUC16_HUMAN;.|.	E|R	13704;345|544	ENSP00000381008:D13704E;ENSP00000370338:D345E|.	ENSP00000370338:D345E|.	D|M	-|-	3|2	2|0	MUC16|MUC16	8857460|8857460	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.010000|0.010000	0.07245|0.07245	-1.743000|-1.743000	0.01834|0.01834	-0.764000|-0.764000	0.04651|0.04651	-0.415000|-0.415000	0.06103|0.06103	GAT|ATG	A|0.974;C|0.026	0.026	strong		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CXCR2	3579	hgsc.bcm.edu	37	2	218999798	218999798	+	Silent	SNP	T	T	C	rs142747099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218999798T>C	ENST00000318507.2	+	3	701	c.274T>C	c.(274-276)Ttg>Ctg	p.L92L		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	92					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						GAACCTAGCCTTGGCCGACCT	0.567																																					p.L92L		Atlas-SNP	.											.	CXCR2	54	.	0			c.T274C						PASS	.	T	,	6,4400	11.4+/-27.6	0,6,2197	144.0	136.0	138.0		274,274	-0.1	0.8	2	dbSNP_134	138	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CXCR2	NM_001168298.1,NM_001557.3	,	0,6,6497	CC,CT,TT		0.0,0.1362,0.0461	,	92/361,92/361	218999798	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	3579	exon4			CTAGCCTTGGCCG	U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"", ""Interleukins and interleukin receptors"""	6027	protein-coding gene	gene with protein product		146928	"""interleukin 8 receptor, beta"""	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.274T>C	2.37:g.218999798T>C		Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	238	109	0.457983	NM_001168298	Q8IUZ1|Q9P2T6|Q9P2T7	Silent	SNP	ENST00000318507.2	37	CCDS2408.1																																																																																			T|0.999;C|0.001	0.001	strong		0.567	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2	NM_001557	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21952884	21952884	+	5'UTR	SNP	G	G	A	rs1130564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21952884G>A	ENST00000374765.4	-	0	95				RAP1GAP_ENST00000374757.3_5'UTR|RAP1GAP_ENST00000542643.2_5'UTR|RAP1GAP_ENST00000290101.4_Silent_p.S29S	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein						GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		TCTGCCCATCGCTCCTCCTGG	0.552													A|||	158	0.0315495	0.0507	0.0331	5008	,	,		17417	0.0		0.0517	False		,,,				2504	0.0164				p.S29S		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.C87T						PASS	.	A	,,	125,3011		1,123,1444	111.0	108.0	109.0		,87,	4.9	1.0	1	dbSNP_130	109	386,6778		9,368,3205	no	utr-5,coding-synonymous,utr-5	RAP1GAP	NM_001145657.1,NM_001145658.1,NM_002885.2	,,	10,491,4649	AA,AG,GG		5.3881,3.986,4.9612	,,	,29/728,	21952884	511,9789	1568	3582	5150	SO:0001623	5_prime_UTR_variant	5909	exon3			CCCATCGCTCCTC	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.-106C>T	1.37:g.21952884G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			G|0.955;A|0.045	0.045	strong		0.552	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
ATXN3	4287	hgsc.bcm.edu	37	14	92548785	92548785	+	Missense_Mutation	SNP	C	C	T	rs1048755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:92548785C>T	ENST00000532032.1	-	8	643	c.634G>A	c.(634-636)Gtg>Atg	p.V212M	ATXN3_ENST00000545170.1_Missense_Mutation_p.V212M|ATXN3_ENST00000502250.1_Missense_Mutation_p.V33M|ATXN3_ENST00000393287.5_Missense_Mutation_p.V212M|ATXN3_ENST00000429774.2_Missense_Mutation_p.V197M|ATXN3_ENST00000340660.6_Missense_Mutation_p.V157M|ATXN3_ENST00000503767.1_Missense_Mutation_p.V197M|ATXN3_ENST00000554491.1_5'UTR			P54252	ATX3_HUMAN	ataxin 3	212			V -> M (in dbSNP:rs1048755). {ECO:0000269|PubMed:7874163, ECO:0000269|PubMed:9274833, ECO:0000269|Ref.4}.		actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		GCTTCTAACACTCGTTCCAGG	0.398													C|||	1628	0.32508	0.3767	0.1455	5008	,	,		17313	0.4405		0.2237	False		,,,				2504	0.3681				p.V212M	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											.	ATXN3	46	.	0			c.G634A						PASS	.	C	MET/VAL,MET/VAL,,,,,MET/VAL,MET/VAL,MET/VAL,,MET/VAL,MET/VAL	1462,2944	472.2+/-356.3	252,958,993	132.0	118.0	123.0		589,481,,,,,271,97,424,,634,469	3.3	1.0	14	dbSNP_86	123	2087,6513	361.6+/-332.4	291,1505,2504	yes	missense,missense,intron,intron,intron,intron,missense,missense,missense,intron,missense,missense	ATXN3	NM_001127696.1,NM_001127697.2,NM_001164774.1,NM_001164776.1,NM_001164777.1,NM_001164778.1,NM_001164779.1,NM_001164780.1,NM_001164781.1,NM_001164782.1,NM_004993.5,NM_030660.4	21,21,,,,,21,21,21,,21,21	543,2463,3497	TT,TC,CC		24.2674,33.182,27.2874	benign,benign,,,,,benign,benign,benign,,benign,benign	197/347,161/311,,,,,91/241,33/183,142/292,,212/362,157/307	92548785	3549,9457	2203	4300	6503	SO:0001583	missense	4287	exon8			CTAACACTCGTTC	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"""Ataxins"""	7106	protein-coding gene	gene with protein product		607047	"""Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"""	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.634G>A	14.37:g.92548785C>T	ENSP00000437157:p.Val212Met	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	189	84	0.444444	NM_004993	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	37		671	0.30723443223443225	196	0.3983739837398374	49	0.13535911602209943	252	0.4405594405594406	174	0.22955145118733508	C	13.32	2.203207	0.38905	0.33182	0.242674	ENSG00000066427	ENST00000545278;ENST00000539555;ENST00000537884;ENST00000545170;ENST00000447800;ENST00000359819;ENST00000393289;ENST00000429774;ENST00000539454;ENST00000393287;ENST00000502250;ENST00000503767;ENST00000340660;ENST00000532032;ENST00000555381;ENST00000557311;ENST00000554592;ENST00000554672;ENST00000553491;ENST00000556220;ENST00000506466	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.33865	2.16;2.16;2.17;1.82;2.18;1.84;1.82;1.44;1.39;1.86;1.42;1.43;1.41;1.45	5.29	3.26	0.37387	.	0.533463	0.20675	N	0.087770	T	0.00012	0.0000	L	0.29908	0.895	0.46678	P	8.420000000000094E-4	B;B;B;B;B	0.25390	0.028;0.011;0.112;0.125;0.019	B;B;B;B;B	0.28232	0.043;0.01;0.087;0.087;0.036	T	0.47222	-0.9134	9	0.38643	T	0.18	.	11.6072	0.51039	0.1327:0.7949:0.0:0.0724	rs1048755;rs3188793;rs17807768;rs52836282;rs57139965;rs1048755	212;197;212;157;212	P54252;E9PB63;F5H096;P54252-3;P54252-2	ATX3_HUMAN;.;.;.;.	M	212;212;212;212;212;212;212;197;211;212;33;197;157;212;142;33;211;114;161;106;146	ENSP00000445618:V212M;ENSP00000389376:V197M;ENSP00000376965:V212M;ENSP00000425322:V33M;ENSP00000426697:V197M;ENSP00000339110:V157M;ENSP00000437157:V212M;ENSP00000451001:V142M;ENSP00000450642:V33M;ENSP00000451385:V211M;ENSP00000451417:V114M;ENSP00000451996:V161M;ENSP00000450641:V106M;ENSP00000435571:V146M	ENSP00000339110:V157M	V	-	1	0	ATXN3	91618538	0.993000	0.37304	0.995000	0.50966	0.984000	0.73092	2.237000	0.43061	1.243000	0.43853	0.485000	0.47835	GTG	C|0.699;T|0.301	0.301	strong		0.398	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	
FSCN1	6624	hgsc.bcm.edu	37	7	5643145	5643145	+	Silent	SNP	T	T	C	rs1640233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	128	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	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	
GPR108	56927	hgsc.bcm.edu	37	19	6737516	6737516	+	Silent	SNP	C	C	T	rs11539591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6737516C>T	ENST00000264080.7	-	1	98	c.72G>A	c.(70-72)gtG>gtA	p.V24V	TRIP10_ENST00000313244.9_5'Flank|TRIP10_ENST00000600428.1_5'Flank|TRIP10_ENST00000596758.1_5'Flank|TRIP10_ENST00000313285.8_5'Flank|GPR108_ENST00000430424.4_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	12	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	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		
PPP1R3F	89801	hgsc.bcm.edu	37	X	49142987	49142987	+	Missense_Mutation	SNP	C	C	T	rs372361395		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49142987C>T	ENST00000055335.6	+	4	1851	c.1835C>T	c.(1834-1836)aCg>aTg	p.T612M	PPP1R3F_ENST00000466508.1_Missense_Mutation_p.T266M|PPP1R3F_ENST00000495799.1_Missense_Mutation_p.T266M|PPP1R3F_ENST00000376188.1_Missense_Mutation_p.T266M|PPP1R3F_ENST00000438316.1_Missense_Mutation_p.T283M	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	612					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					GTGGTAGCCACGATGGGAGAT	0.612													C|||	1	0.000264901	0.0	0.0	3775	,	,		12213	0.001		0.0	False		,,,				2504	0.0				p.T612M		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.C1835T						PASS	.		MET/THR,MET/THR	1,3833		0,1,1631,570	36.0	26.0	29.0		797,1835	3.8	0.9	X		29	0,6728		0,0,2428,1872	no	missense,missense	PPP1R3F	NM_001184745.1,NM_033215.4	81,81	0,1,4059,2442	TT,TC,CC,C		0.0,0.0261,0.0095	probably-damaging,probably-damaging	266/454,612/800	49142987	1,10561	2202	4300	6502	SO:0001583	missense	89801	exon4			TAGCCACGATGGG		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14944	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3F"""			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.1835C>T	X.37:g.49142987C>T	ENSP00000055335:p.Thr612Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	110	54	0.490909	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	37	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.331209	0.41297	2.61E-4	0.0	ENSG00000049769	ENST00000466508;ENST00000438316;ENST00000055335;ENST00000495799;ENST00000376188	T;T;T;T;T	0.59224	0.7;0.71;0.28;0.7;0.7	4.71	3.82	0.43975	.	0.521490	0.17939	N	0.156901	T	0.60625	0.2283	L	0.27053	0.805	0.26861	N	0.967952	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.65987	0.917;0.917;0.94	T	0.53408	-0.8443	10	0.87932	D	0	-0.2653	10.192	0.43032	0.0:0.8014:0.1986:0.0	.	283;297;612	F5H262;A2VDJ8;Q6ZSY5	.;.;PPR3F_HUMAN	M	266;283;612;266;266	ENSP00000420687:T266M;ENSP00000415548:T283M;ENSP00000055335:T612M;ENSP00000417535:T266M;ENSP00000365359:T266M	ENSP00000055335:T612M	T	+	2	0	PPP1R3F	49029931	0.942000	0.31987	0.876000	0.34364	0.775000	0.43874	0.261000	0.18442	1.027000	0.39758	0.509000	0.49947	ACG	.	.	weak		0.612	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
MUC17	140453	hgsc.bcm.edu	37	7	100677516	100677516	+	Missense_Mutation	SNP	A	A	G	rs58478927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677516A>G	ENST00000306151.4	+	3	2883	c.2819A>G	c.(2818-2820)gAg>gGg	p.E940G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	940	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)					GTCAGTTCTGAGGCTAGAACA	0.502													A|||	330	0.0658946	0.0756	0.0043	5008	,	,		36868	0.1042		0.003	False		,,,				2504	0.1217				p.E940G		Atlas-SNP	.											.	MUC17	804	.	0			c.A2819G						PASS	.						356.0	316.0	329.0					7																	100677516		2203	4300	6503	SO:0001583	missense	140453	exon3			GTTCTGAGGCTAG	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.2819A>G	7.37:g.100677516A>G	ENSP00000302716:p.Glu940Gly	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	226	38	0.168142	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	2.952	-0.216452	0.06101	.	.	ENSG00000169876	ENST00000306151	T	0.02737	4.18	1.19	-2.38	0.06622	.	.	.	.	.	T	0.01765	0.0056	N	0.24115	0.695	0.09310	N	1	B	0.31931	0.347	B	0.23018	0.043	T	0.47923	-0.9079	9	0.22706	T	0.39	.	7.5159	0.27600	0.3362:0.6638:0.0:0.0	rs58478927	940	Q685J3	MUC17_HUMAN	G	940	ENSP00000302716:E940G	ENSP00000302716:E940G	E	+	2	0	MUC17	100464236	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-1.870000	0.01641	-0.830000	0.04262	0.113000	0.15668	GAG	A|0.995;G|0.005	0.005	strong		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ADAMTS1	9510	hgsc.bcm.edu	37	21	28214238	28214238	+	Silent	SNP	T	T	C	rs77718820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:28214238T>C	ENST00000284984.3	-	3	1603	c.1149A>G	c.(1147-1149)agA>agG	p.R383R		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	383	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		CGGAGCAGCTTCTGCTCGGAT	0.433													T|||	59	0.0117812	0.0439	0.0014	5008	,	,		17992	0.0		0.0	False		,,,				2504	0.0				p.R383R		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.A1149G						PASS	.	T		150,4256	103.4+/-141.9	3,144,2056	119.0	102.0	108.0		1149	0.5	1.0	21	dbSNP_131	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADAMTS1	NM_006988.3		3,145,6355	CC,CT,TT		0.0116,3.4044,1.161		383/968	28214238	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	9510	exon3			GCAGCTTCTGCTC	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	217	protein-coding gene	gene with protein product		605174	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"""			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.1149A>G	21.37:g.28214238T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	131	67	0.51145	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Silent	SNP	ENST00000284984.3	37	CCDS33524.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	11.14	1.552302	0.27739	0.034044	1.16E-4	ENSG00000154734	ENST00000451462	.	.	.	5.55	0.507	0.16967	.	.	.	.	.	T	0.14743	0.0356	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06862	-1.0803	4	.	.	.	.	6.0716	0.19893	0.0:0.3189:0.3426:0.3385	.	.	.	.	G	165	.	.	E	-	2	0	ADAMTS1	27136109	0.985000	0.35326	0.995000	0.50966	0.974000	0.67602	0.136000	0.15974	-0.047000	0.13423	0.533000	0.62120	GAA	T|0.990;C|0.010	0.010	strong		0.433	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2		
NWD1	284434	hgsc.bcm.edu	37	19	16860001	16860001	+	Missense_Mutation	SNP	A	A	T	rs76739123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860001A>T	ENST00000552788.1	+	4	548	c.548A>T	c.(547-549)cAg>cTg	p.Q183L	NWD1_ENST00000379808.3_Missense_Mutation_p.Q183L|NWD1_ENST00000339803.6_Missense_Mutation_p.Q48L|NWD1_ENST00000549814.1_Missense_Mutation_p.Q183L|NWD1_ENST00000524140.2_Missense_Mutation_p.Q183L|NWD1_ENST00000523826.1_De_novo_Start_OutOfFrame			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	183							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GACCGGGAACAGGGAGCCACC	0.572													A|||	120	0.0239617	0.0825	0.0101	5008	,	,		17868	0.0		0.001	False		,,,				2504	0.0031				p.Q183L		Atlas-SNP	.											.	NWD1	303	.	0			c.A548T						PASS	.	A	LEU/GLN	279,4127	157.0+/-190.0	5,269,1929	72.0	57.0	62.0		548	-7.3	0.0	19	dbSNP_131	62	10,8590	6.4+/-24.3	0,10,4290	yes	missense	NWD1	NM_001007525.3	113	5,279,6219	TT,TA,AA		0.1163,6.3323,2.2221	benign	183/1433	16860001	289,12717	2203	4300	6503	SO:0001583	missense	284434	exon6			GGGAACAGGGAGC	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.548A>T	19.37:g.16860001A>T	ENSP00000447224:p.Gln183Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	143	79	0.552448	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		49	0.022435897435897436	42	0.08536585365853659	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	a	2.726	-0.265505	0.05754	0.063323	0.001163	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000552788;ENST00000339803	T;T;T;T;T	0.56444	2.07;2.07;2.07;2.07;0.46	4.45	-7.35	0.01422	.	1.747030	0.02870	N	0.131458	T	0.01523	0.0049	L	0.39397	1.21	0.18873	N	0.999986	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10474	-1.0628	10	0.54805	T	0.06	-3.4934	2.1523	0.03803	0.2044:0.3718:0.2881:0.1356	.	183;48	Q149M9-3;C9J2Y8	.;.	L	48;183;183;183;183;48	ENSP00000428579:Q183L;ENSP00000447548:Q183L;ENSP00000369136:Q183L;ENSP00000447224:Q183L;ENSP00000340159:Q48L	ENSP00000340159:Q48L	Q	+	2	0	NWD1	16721001	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.401000	0.07232	-1.070000	0.03149	-0.499000	0.04595	CAG	A|0.975;T|0.025	0.025	strong		0.572	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
ZNF286B	729288	hgsc.bcm.edu	37	17	18566386	18566386	+	Missense_Mutation	SNP	G	G	A	rs143643706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18566386G>A	ENST00000545289.1	-	5	683	c.433C>T	c.(433-435)Cgg>Tgg	p.R145W	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	145					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						ACACTATTCCGTGTCAGTCTG	0.408													.|||	424	0.0846645	0.3071	0.0202	5008	,	,		22256	0.0		0.002	False		,,,				2504	0.002				p.R145W		Atlas-SNP	.											.	ZNF286B	75	.	0			c.C433T						PASS	.	G	TRP/ARG	315,1069		31,253,408	111.0	99.0	102.0		433	-3.4	0.0	17	dbSNP_134	102	11,3169		0,11,1579	no	missense	ZNF286B	NM_001145045.1	101	31,264,1987	AA,AG,GG		0.3459,22.7601,7.1429	probably-damaging	145/523	18566386	326,4238	692	1590	2282	SO:0001583	missense	729288	exon5			TATTCCGTGTCAG		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.433C>T	17.37:g.18566386G>A	ENSP00000461413:p.Arg145Trp	Somatic	390	0	0		WXS	Illumina HiSeq	Phase_I	353	137	0.388102	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.945;A|0.055	0.055	strong		0.408	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709935	31709935	+	Missense_Mutation	SNP	G	G	A	rs149814034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31709935G>A	ENST00000382835.2	-	1	77	c.52C>T	c.(52-54)Ctc>Ttc	p.L18F		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	18						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						ATGGCAGAGAGTGGTGGGGCA	0.453													G|||	9	0.00179712	0.0061	0.0014	5008	,	,		19096	0.0		0.0	False		,,,				2504	0.0				p.L18F		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.C52T						PASS	.	G	PHE/LEU	23,4383	30.8+/-60.4	0,23,2180	103.0	98.0	100.0		52	4.3	1.0	21	dbSNP_134	100	0,8600		0,0,4300	yes	missense	KRTAP27-1	NM_001077711.1	22	0,23,6480	AA,AG,GG		0.0,0.522,0.1768	probably-damaging	18/208	31709935	23,12983	2203	4300	6503	SO:0001583	missense	643812	exon1			CAGAGAGTGGTGG	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"""Keratin associated proteins"""	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.52C>T	21.37:g.31709935G>A	ENSP00000372286:p.Leu18Phe	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	211	94	0.445498	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	37	CCDS33532.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	14.33	2.502796	0.44558	0.00522	0.0	ENSG00000206107	ENST00000382835	T	0.03330	3.97	4.29	4.29	0.51040	.	0.619122	0.14168	U	0.336909	T	0.10594	0.0259	M	0.63428	1.95	0.36763	D	0.88338	D	0.89917	1.0	D	0.91635	0.999	T	0.00862	-1.1536	10	0.59425	D	0.04	-6.9941	12.5116	0.56009	0.0:0.0:1.0:0.0	.	18	Q3LI81	KR271_HUMAN	F	18	ENSP00000372286:L18F	ENSP00000372286:L18F	L	-	1	0	KRTAP27-1	30631806	0.995000	0.38212	0.952000	0.39060	0.168000	0.22595	3.701000	0.54793	2.665000	0.90641	0.579000	0.79373	CTC	G|0.997;A|0.003	0.003	strong		0.453	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711	
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914019	31914019	+	Missense_Mutation	SNP	C	C	T	rs77807247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31914019C>T	ENST00000334046.5	-	1	164	c.134G>A	c.(133-135)cGc>cAc	p.R45H		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	45						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						GCATGATGGGCGGCAGCAGCC	0.498													c|||	161	0.0321486	0.1135	0.0115	5008	,	,		14661	0.0		0.001	False		,,,				2504	0.002				p.R45H		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.G134A						PASS	.	C	HIS/ARG	371,4035	188.5+/-214.9	13,345,1845	110.0	120.0	116.0		134	-6.1	0.0	21	dbSNP_131	116	12,8588	9.8+/-36.6	0,12,4288	yes	missense	KRTAP19-6	NM_181612.2	29	13,357,6133	TT,TC,CC		0.1395,8.4203,2.9448	benign	45/59	31914019	383,12623	2203	4300	6503	SO:0001583	missense	337973	exon1			GATGGGCGGCAGC	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"""Keratin associated proteins"""	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.134G>A	21.37:g.31914019C>T	ENSP00000375107:p.Arg45His	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	NM_181612	Q3LI71	Missense_Mutation	SNP	ENST00000334046.5	37	CCDS13598.1	64	0.029304029304029304	58	0.11788617886178862	6	0.016574585635359115	0	0.0	0	0.0	c	6.926	0.540492	0.13250	0.084203	0.001395	ENSG00000186925	ENST00000334046;ENST00000437381	T	0.11169	2.8	4.39	-6.09	0.02145	.	0.598882	0.13443	N	0.387478	T	0.00109	0.0003	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.32587	-0.9901	9	0.87932	D	0	-1.818	7.3473	0.26670	0.1168:0.3112:0.0:0.5719	.	45	Q3LI70	KR196_HUMAN	H	45	ENSP00000375107:R45H	ENSP00000375107:R45H	R	-	2	0	KRTAP19-6	30835890	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.929000	0.03976	-1.347000	0.02208	-1.903000	0.00527	CGC	C|0.969;T|0.031	0.031	strong		0.498	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4		
MYO9B	4650	hgsc.bcm.edu	37	19	17317955	17317955	+	Silent	SNP	A	A	G	rs8110964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17317955A>G	ENST00000594824.1	+	35	5673	c.5526A>G	c.(5524-5526)tcA>tcG	p.S1842S	CTD-3032J10.3_ENST00000601929.1_RNA|MYO9B_ENST00000595618.1_Silent_p.S1842S|MYO9B_ENST00000397274.2_Silent_p.S1842S			Q13459	MYO9B_HUMAN	myosin IXB	1842	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.|Tail.				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						ACCGCATGTCACCTGGGGCGC	0.637													G|||	3162	0.63139	0.7073	0.6772	5008	,	,		14431	0.746		0.3926	False		,,,				2504	0.6237				p.S1842S		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	0			c.A5526G						scavenged	.	G	,	2827,1549		936,955,297	33.0	38.0	37.0		5526,5526	-8.3	0.1	19	dbSNP_116	37	3377,5189		705,1967,1611	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	1641,2922,1908	GG,GA,AA		39.4233,35.3976,47.9369	,	1842/2023,1842/2158	17317955	6204,6738	2188	4283	6471	SO:0001819	synonymous_variant	4650	exon35			CATGTCACCTGGG		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.5526A>G	19.37:g.17317955A>G		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	224	107	0.477679	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				A|0.384;G|0.616	0.616	strong		0.637	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
PCSK5	5125	hgsc.bcm.edu	37	9	78506181	78506181	+	Silent	SNP	C	C	A	rs34813806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:78506181C>A	ENST00000545128.1	+	1	622	c.84C>A	c.(82-84)ccC>ccA	p.P28P	PCSK5_ENST00000376767.3_Silent_p.P28P|PCSK5_ENST00000376752.4_Silent_p.P28P	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	28					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						GCCTGCTCCCCGTGTGTCGGA	0.677													C|||	55	0.0109824	0.0386	0.0058	5008	,	,		12564	0.0		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											.	PCSK5	329	.	0			c.C84A						PASS	.	C	,	116,4290	76.8+/-115.0	3,110,2090	42.0	51.0	48.0		84,84	-4.0	1.0	9	dbSNP_126	48	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	PCSK5	NM_001190482.1,NM_006200.3	,	3,116,6384	AA,AC,CC		0.0698,2.6328,0.938	,	28/1861,28/914	78506181	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	5125	exon1			GCTCCCCGTGTGT		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.84C>A	9.37:g.78506181C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	104	77	0.740385	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			C|0.990;A|0.010	0.010	strong		0.677	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
GMPR	2766	hgsc.bcm.edu	37	6	16279097	16279097	+	Silent	SNP	T	T	C	rs739473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:16279097T>C	ENST00000259727.4	+	6	744	c.630T>C	c.(628-630)caT>caC	p.H210H		NM_006877.3	NP_006868.3	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	210					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to cold (GO:0009409)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	20	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				ACTCTGCCCATGGCCTGAAGG	0.617													T|||	447	0.0892572	0.2171	0.0245	5008	,	,		20534	0.0685		0.0219	False		,,,				2504	0.0532				p.H210H		Atlas-SNP	.											.	GMPR	44	.	0			c.T630C						PASS	.	T		757,3649	311.6+/-292.2	65,627,1511	81.0	74.0	76.0		630	-8.1	0.6	6	dbSNP_86	76	154,8446	73.5+/-136.2	1,152,4147	no	coding-synonymous	GMPR	NM_006877.3		66,779,5658	CC,CT,TT		1.7907,17.1811,7.0045		210/346	16279097	911,12095	2203	4300	6503	SO:0001819	synonymous_variant	2766	exon6			TGCCCATGGCCTG		CCDS4537.1	6p23	2009-07-10			ENSG00000137198	ENSG00000137198	1.7.1.7		4376	protein-coding gene	gene with protein product		139265				2194676	Standard	NM_006877		Approved		uc003nbs.3	P36959	OTTHUMG00000014302	ENST00000259727.4:c.630T>C	6.37:g.16279097T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_006877	Q96HQ6	Silent	SNP	ENST00000259727.4	37	CCDS4537.1																																																																																			T|0.909;C|0.091	0.091	strong		0.617	GMPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039942.2		
VNN1	8876	hgsc.bcm.edu	37	6	133013576	133013576	+	Missense_Mutation	SNP	G	G	T	rs34535050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133013576G>T	ENST00000367928.4	-	5	987	c.974C>A	c.(973-975)gCg>gAg	p.A325E		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	325	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		A -> E (in dbSNP:rs34535050). {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)		TGATGAGAGCGCTTCTATACT	0.448													G|||	124	0.0247604	0.09	0.0058	5008	,	,		18388	0.0		0.001	False		,,,				2504	0.0				p.A325E		Atlas-SNP	.											.	VNN1	69	.	0			c.C974A						PASS	.	G	GLU/ALA	329,4077	173.7+/-203.5	15,299,1889	76.0	74.0	75.0		974	4.1	0.0	6	dbSNP_126	75	3,8597	2.2+/-6.3	0,3,4297	yes	missense	VNN1	NM_004666.2	107	15,302,6186	TT,TG,GG		0.0349,7.4671,2.5527	benign	325/514	133013576	332,12674	2203	4300	6503	SO:0001583	missense	8876	exon5			GAGAGCGCTTCTA	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.974C>A	6.37:g.133013576G>T	ENSP00000356905:p.Ala325Glu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	39	0.017857142857142856	36	0.07317073170731707	3	0.008287292817679558	0	0.0	0	0.0	G	0.747	-0.774241	0.02951	0.074671	3.49E-4	ENSG00000112299	ENST00000367928	D	0.87256	-2.23	5.85	4.05	0.47172	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (1);	1.202920	0.05711	N	0.595981	T	0.67316	0.2880	L	0.46157	1.445	0.09310	N	1	B	0.15141	0.012	B	0.20767	0.031	T	0.55082	-0.8196	10	0.15952	T	0.53	-14.8515	5.0557	0.14531	0.067:0.23:0.4724:0.2306	rs34535050	325	O95497	VNN1_HUMAN	E	325	ENSP00000356905:A325E	ENSP00000356905:A325E	A	-	2	0	VNN1	133055269	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.013000	0.13310	0.796000	0.33947	0.563000	0.77884	GCG	G|0.975;T|0.025	0.025	strong		0.448	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
DPCD	25911	hgsc.bcm.edu	37	10	103368654	103368654	+	Missense_Mutation	SNP	T	T	C	rs7006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:103368654T>C	ENST00000370151.4	+	5	516	c.467T>C	c.(466-468)tTg>tCg	p.L156S	DPCD_ENST00000370147.1_Missense_Mutation_p.C170R|DPCD_ENST00000370148.2_Missense_Mutation_p.C170R|FBXW4_ENST00000470093.1_5'Flank	NM_015448.1	NP_056263.1	Q9BVM2	DPCD_HUMAN	deleted in primary ciliary dyskinesia homolog (mouse)	156			L -> S (in dbSNP:rs7006). {ECO:0000269|PubMed:14630615, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|lateral ventricle development (GO:0021670)|left/right pattern formation (GO:0060972)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)	nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5						GATGACGCCTTGCTGAGCTTT	0.537													T|||	1138	0.227236	0.2882	0.2233	5008	,	,		21971	0.1637		0.3111	False		,,,				2504	0.1268				p.L156S		Atlas-SNP	.											.	DPCD	15	.	0			c.T467C						PASS	.	T	SER/LEU	1354,3052	450.8+/-349.5	195,964,1044	211.0	189.0	196.0		467	-0.6	0.1	10	dbSNP_52	196	2639,5961	426.7+/-355.4	422,1795,2083	yes	missense	DPCD	NM_015448.1	145	617,2759,3127	CC,CT,TT		30.686,30.7308,30.7012	benign	156/204	103368654	3993,9013	2203	4300	6503	SO:0001583	missense	25911	exon5			ACGCCTTGCTGAG		CCDS7514.1	10q24.32	2012-05-03			ENSG00000166171	ENSG00000166171			24542	protein-coding gene	gene with protein product						14630615	Standard	NM_015448		Approved	DKFZP566F084, RP11-529I10.4	uc001ktn.3	Q9BVM2	OTTHUMG00000018934	ENST00000370151.4:c.467T>C	10.37:g.103368654T>C	ENSP00000359170:p.Leu156Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	36	0.387097	NM_015448	A8K289|Q6QNL3|Q8N5R1|Q9UFY6	Missense_Mutation	SNP	ENST00000370151.4	37	CCDS7514.1	551|551	0.2522893772893773|0.2522893772893773	157|157	0.31910569105691056|0.31910569105691056	84|84	0.23204419889502761|0.23204419889502761	79|79	0.1381118881118881|0.1381118881118881	231|231	0.30474934036939316|0.30474934036939316	T|T	16.00|16.00	2.997571|2.997571	0.54147|0.54147	0.307308|0.307308	0.30686|0.30686	ENSG00000166171|ENSG00000166171	ENST00000370147;ENST00000370148|ENST00000370151	T;T|T	0.47869|0.28069	0.83;0.83|1.63	5.93|5.93	-0.552|-0.552	0.11818|0.11818	.|.	.|0.444204	.|0.25241	.|N	.|0.032083	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.12182|0.12182	0.205|0.205	0.22693|0.22693	P|P	0.99884019|0.99884019	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.44406|0.44406	-0.9330|-0.9330	6|9	0.87932|0.07990	D|T	0|0.79	-14.2862|-14.2862	10.3322|10.3322	0.43829|0.43829	0.0:0.5911:0.0:0.4089|0.0:0.5911:0.0:0.4089	rs7006;rs1047015;rs3187013;rs52814802;rs56505439;rs60202911;rs7006|rs7006;rs1047015;rs3187013;rs52814802;rs56505439;rs60202911;rs7006	.|156	.|Q9BVM2	.|DPCD_HUMAN	R|S	170|156	ENSP00000359166:C170R;ENSP00000359167:C170R|ENSP00000359170:L156S	ENSP00000359166:C170R|ENSP00000359170:L156S	C|L	+|+	1|2	0|0	DPCD|DPCD	103358644|103358644	0.055000|0.055000	0.20627|0.20627	0.079000|0.079000	0.20413|0.20413	0.768000|0.768000	0.43524|0.43524	0.568000|0.568000	0.23623|0.23623	-0.384000|-0.384000	0.07845|0.07845	-0.366000|-0.366000	0.07423|0.07423	TGC|TTG	T|0.720;C|0.280	0.280	strong		0.537	DPCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049958.2		
ZDHHC4	55146	hgsc.bcm.edu	37	7	6621277	6621277	+	Missense_Mutation	SNP	G	G	A	rs11559146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6621277G>A	ENST00000396706.2	+	4	600	c.157G>A	c.(157-159)Gtg>Atg	p.V53M	AC079742.4_ENST00000434951.1_RNA|ZDHHC4_ENST00000396707.2_Missense_Mutation_p.V53M|ZDHHC4_ENST00000396713.2_Missense_Mutation_p.V53M|ZDHHC4_ENST00000335965.6_Missense_Mutation_p.V53M|ZDHHC4_ENST00000396709.1_Missense_Mutation_p.V53M|ZDHHC4_ENST00000405731.3_Missense_Mutation_p.V53M			Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	53			V -> M (in dbSNP:rs11559146). {ECO:0000269|Ref.6}.			Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)		TCAGAGAGCCGTGCATGGATT	0.353													G|||	1633	0.326078	0.4418	0.3732	5008	,	,		20902	0.2351		0.2813	False		,,,				2504	0.2761				p.V53M		Atlas-SNP	.											.	ZDHHC4	36	.	0			c.G157A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL	1711,2695	515.0+/-368.8	328,1055,820	149.0	143.0	145.0		157,157,157,157	-8.1	0.0	7	dbSNP_120	145	2355,6245	394.1+/-344.6	327,1701,2272	yes	missense,missense,missense,missense	ZDHHC4	NM_001134387.1,NM_001134388.1,NM_001134389.1,NM_018106.3	21,21,21,21	655,2756,3092	AA,AG,GG		27.3837,38.8334,31.2625	benign,benign,benign,benign	53/345,53/345,53/345,53/345	6621277	4066,8940	2203	4300	6503	SO:0001583	missense	55146	exon4			AGAGCCGTGCATG	AF201931	CCDS5352.1	7p22.1	2011-01-11			ENSG00000136247	ENSG00000136247		"""Zinc fingers, DHHC-type"""	18471	protein-coding gene	gene with protein product							Standard	NM_018106		Approved	FLJ10479, ZNF374	uc003sqj.3	Q9NPG8	OTTHUMG00000023579	ENST00000396706.2:c.157G>A	7.37:g.6621277G>A	ENSP00000379934:p.Val53Met	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	197	100	0.507614	NM_018106	A4D2N9|Q53EV7|Q6FIB5|Q9H0R9	Missense_Mutation	SNP	ENST00000396706.2	37	CCDS5352.1	678	0.31043956043956045	216	0.43902439024390244	131	0.36187845303867405	112	0.1958041958041958	219	0.28891820580474936	g	6.178	0.400937	0.11696	0.388334	0.273837	ENSG00000136247	ENST00000405731;ENST00000396713;ENST00000396707;ENST00000335965;ENST00000396709;ENST00000483589;ENST00000396706	T;T;T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27;1.41;1.27	4.61	-8.12	0.01078	.	1.440670	0.03927	N	0.284580	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B;B	0.12013	0.003;0.005	B;B	0.08055	0.002;0.003	T	0.34502	-0.9826	9	0.30078	T	0.28	-34.9452	14.5694	0.68202	0.1382:0.1161:0.7457:0.0	rs11559146;rs28642371;rs59223464	53;53	Q9NPG8;C9J5I9	ZDHC4_HUMAN;.	M	53	ENSP00000385027:V53M;ENSP00000379941:V53M;ENSP00000379935:V53M;ENSP00000337475:V53M;ENSP00000379937:V53M;ENSP00000418496:V53M;ENSP00000379934:V53M	ENSP00000337475:V53M	V	+	1	0	ZDHHC4	6587802	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.776000	0.04674	-1.758000	0.01315	-1.155000	0.01812	GTG	G|0.691;A|0.309	0.309	strong		0.353	ZDHHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207477.3	NM_018106	
PDE4C	5143	hgsc.bcm.edu	37	19	18330144	18330144	+	Missense_Mutation	SNP	C	C	T	rs34503849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18330144C>T	ENST00000355502.3	-	12	1737	c.866G>A	c.(865-867)cGg>cAg	p.R289Q	PDE4C_ENST00000447275.3_Missense_Mutation_p.R183Q|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000539010.1_Missense_Mutation_p.R58Q|PDE4C_ENST00000594617.3_Missense_Mutation_p.R289Q|PDE4C_ENST00000262805.12_Missense_Mutation_p.R257Q|PDE4C_ENST00000597297.1_Missense_Mutation_p.R59Q|PDE4C_ENST00000594465.3_Missense_Mutation_p.R289Q|PDE4C_ENST00000598111.2_Missense_Mutation_p.R59Q			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	289			R -> Q (in dbSNP:rs34503849).		cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	GCCACTGATCCGGGACATGGG	0.642													C|||	87	0.0173722	0.0613	0.0058	5008	,	,		16374	0.001		0.001	False		,,,				2504	0.0				p.R289Q		Atlas-SNP	.											.	PDE4C	80	.	0			c.G866A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	201,4205	125.7+/-162.9	4,193,2006	52.0	50.0	51.0		866,770,548	3.7	1.0	19	dbSNP_126	51	0,8600		0,0,4300	yes	missense,missense,missense	PDE4C	NM_000923.4,NM_001098818.2,NM_001098819.2	43,43,43	4,193,6306	TT,TC,CC		0.0,4.562,1.5454	benign,benign,benign	289/713,257/681,183/607	18330144	201,12805	2203	4300	6503	SO:0001583	missense	5143	exon9			CTGATCCGGGACA		CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"""Phosphodiesterases"""	8782	protein-coding gene	gene with protein product	"""phosphodiesterase E1 dunce homolog (Drosophila)"""	600128	"""phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"""	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.866G>A	19.37:g.18330144C>T	ENSP00000347689:p.Arg289Gln	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	94	55	0.585106	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	37	CCDS12373.1	37	0.01694139194139194	33	0.06707317073170732	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	C	0.914	-0.718231	0.03182	0.04562	0.0	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000447275;ENST00000545961;ENST00000336173;ENST00000539010;ENST00000543547	T;T;T;T	0.68479	-0.31;-0.33;-0.32;-0.02	4.75	3.65	0.41850	.	1.896290	0.02956	N	0.142375	T	0.01730	0.0055	N	0.00038	-2.52	0.28550	N	0.911646	B;B;B;B	0.11235	0.0;0.004;0.001;0.0	B;B;B;B	0.06405	0.001;0.002;0.002;0.001	T	0.48570	-0.9024	10	0.02654	T	1	.	8.4709	0.32984	0.0:0.0967:0.0:0.9033	rs34503849	289;257;95;59	Q08493;Q08493-3;O43850;O76104	PDE4C_HUMAN;.;.;.	Q	368;289;277;257;183;95;58;58;398	ENSP00000347689:R289Q;ENSP00000262805:R257Q;ENSP00000402091:R183Q;ENSP00000439470:R58Q	ENSP00000262805:R257Q	R	-	2	0	PDE4C	18191144	1.000000	0.71417	0.991000	0.47740	0.118000	0.20060	4.475000	0.60210	0.657000	0.30906	-0.657000	0.03884	CGG	C|0.982;T|0.018	0.018	strong		0.642	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1		
PAN3	255967	hgsc.bcm.edu	37	13	28750683	28750683	+	Silent	SNP	A	A	G	rs142608239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:28750683A>G	ENST00000380958.3	+	3	758	c.606A>G	c.(604-606)ccA>ccG	p.P202P	PAN3_ENST00000399613.1_Silent_p.P56P	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit											endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		GTGCCAAGCCATATTCAGCCC	0.338													A|||	17	0.00339457	0.0121	0.0014	5008	,	,		18080	0.0		0.0	False		,,,				2504	0.0				p.P202P		Atlas-SNP	.											.	PAN3	123	.	0			c.A606G						PASS	.	A		60,4346	58.7+/-95.3	1,58,2144	125.0	122.0	123.0		606	4.4	1.0	13	dbSNP_134	123	0,8600		0,0,4300	no	coding-synonymous	PAN3	NM_175854.7		1,58,6444	GG,GA,AA		0.0,1.3618,0.4613		202/888	28750683	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	255967	exon3			CAAGCCATATTCA	AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"""PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.606A>G	13.37:g.28750683A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	123	72	0.585366	NM_175854		Silent	SNP	ENST00000380958.3	37	CCDS9329.2																																																																																			A|0.995;G|0.005	0.005	strong		0.338	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854	
KMT2C	58508	hgsc.bcm.edu	37	7	151945215	151945215	+	Silent	SNP	T	T	C	rs594178		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151945215T>C	ENST00000262189.6	-	14	2522	c.2304A>G	c.(2302-2304)tcA>tcG	p.S768S	KMT2C_ENST00000355193.2_Silent_p.S768S	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	768					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)										ATGAAAATGATGACTCTGTCT	0.418																																					p.S768S		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,2	MLL3	1564	2	0			c.A2304G						scavenged	.						154.0	136.0	142.0					7																	151945215		2203	4300	6503	SO:0001819	synonymous_variant	58508	exon14			AAATGATGACTCT	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.2304A>G	7.37:g.151945215T>C		Somatic	440	0	0		WXS	Illumina HiSeq	Phase_I	484	24	0.0495868	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																			T|0.750;C|0.250	0.250	strong		0.418	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
WFS1	7466	hgsc.bcm.edu	37	4	6293696	6293696	+	Silent	SNP	C	C	G	rs1801213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6293696C>G	ENST00000226760.1	+	6	854	c.684C>G	c.(682-684)cgC>cgG	p.R228R	WFS1_ENST00000503569.1_Silent_p.R228R	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	228					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)		AGCAGAGGCGCATGCTGGAGC	0.642													G|||	3788	0.75639	0.6959	0.7378	5008	,	,		16959	0.9038		0.6849	False		,,,				2504	0.773				p.R228R		Atlas-SNP	.											WFS1,NS,carcinoma,0,1	WFS1	71	1	0			c.C684G						PASS	.	G	,	2938,1454		985,968,243	47.0	40.0	42.0		684,684	1.5	1.0	4	dbSNP_89	42	5870,2728		1999,1872,428	no	coding-synonymous,coding-synonymous	WFS1	NM_001145853.1,NM_006005.3	,	2984,2840,671	GG,GC,CC		31.7283,33.1056,32.194	,	228/891,228/891	6293696	8808,4182	2196	4299	6495	SO:0001819	synonymous_variant	7466	exon6			GAGGCGCATGCTG	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.684C>G	4.37:g.6293696C>G		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	255	254	0.996078	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	37	CCDS3386.1	1662	0.760989010989011	345	0.7012195121951219	266	0.7348066298342542	536	0.9370629370629371	515	0.679419525065963	G	10.35	1.324588	0.24080	0.668944	0.682717	ENSG00000109501	ENST00000506362	.	.	.	4.37	1.53	0.23141	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999124776	.	.	.	.	.	.	T	0.18335	-1.0340	3	.	.	.	-44.9845	6.9398	0.24486	0.2177:0.2494:0.5329:0.0	rs1801213;rs2230718;rs7672995	.	.	.	G	94	.	.	A	+	2	0	WFS1	6344597	0.811000	0.29063	0.994000	0.49952	0.974000	0.67602	-0.097000	0.11042	0.069000	0.16605	-0.216000	0.12614	GCA	C|0.294;G|0.706	0.706	strong		0.642	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
ECHDC3	79746	hgsc.bcm.edu	37	10	11797484	11797484	+	Silent	SNP	A	A	G	rs34878615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:11797484A>G	ENST00000379215.4	+	4	679	c.468A>G	c.(466-468)caA>caG	p.Q156Q	ECHDC3_ENST00000496136.1_3'UTR	NM_024693.4	NP_078969	Q96DC8	ECHD3_HUMAN	enoyl CoA hydratase domain containing 3	156						mitochondrion (GO:0005739)	catalytic activity (GO:0003824)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)	4						CCGGCTGTCAACTGGTTGCCA	0.607													A|||	94	0.01877	0.0681	0.0043	5008	,	,		13971	0.0		0.001	False		,,,				2504	0.0				p.Q156Q		Atlas-SNP	.											.	ECHDC3	12	.	0			c.A468G						PASS	.	A		251,4155	144.6+/-179.5	10,231,1962	51.0	42.0	45.0		468	3.4	1.0	10	dbSNP_126	45	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ECHDC3	NM_024693.4		10,235,6258	GG,GA,AA		0.0465,5.6968,1.9606		156/304	11797484	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	79746	exon4			CTGTCAACTGGTT	AF275677	CCDS7084.1	10p14	2010-04-30	2010-04-30		ENSG00000134463	ENSG00000134463			23489	protein-coding gene	gene with protein product			"""enoyl Coenzyme A hydratase domain containing 3"""			12477932	Standard	NM_024693		Approved	FLJ20909	uc001ikw.4	Q96DC8	OTTHUMG00000017675	ENST00000379215.4:c.468A>G	10.37:g.11797484A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_024693	Q53HR9|Q5W0J7|Q8WYY8|Q9BVL8|Q9H7G4	Silent	SNP	ENST00000379215.4	37	CCDS7084.1																																																																																			A|0.981;G|0.019	0.019	strong		0.607	ECHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046771.1	NM_024693	
GPD2	2820	hgsc.bcm.edu	37	2	157425931	157425931	+	Missense_Mutation	SNP	A	A	C	rs35096779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:157425931A>C	ENST00000310454.6	+	11	1729	c.1357A>C	c.(1357-1359)Aaa>Caa	p.K453Q	GPD2_ENST00000409674.1_Missense_Mutation_p.K453Q|GPD2_ENST00000438166.2_Missense_Mutation_p.K453Q|GPD2_ENST00000409125.4_Missense_Mutation_p.K226Q|GPD2_ENST00000540309.1_Intron	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	453			K -> Q (in dbSNP:rs35096779).		camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						TGCTGCTGTCAAAACTCATAA	0.423													A|||	166	0.033147	0.1165	0.0159	5008	,	,		17986	0.0		0.001	False		,,,				2504	0.0				p.K453Q		Atlas-SNP	.											.	GPD2	59	.	0			c.A1357C						PASS	.	A	GLN/LYS,GLN/LYS	527,3879	239.6+/-250.7	30,467,1706	79.0	78.0	78.0		1357,1357	3.3	0.8	2	dbSNP_126	78	6,8594	3.7+/-12.6	0,6,4294	yes	missense,missense	GPD2	NM_000408.4,NM_001083112.2	53,53	30,473,6000	CC,CA,AA		0.0698,11.961,4.0981	benign,benign	453/728,453/728	157425931	533,12473	2203	4300	6503	SO:0001583	missense	2820	exon11			GCTGTCAAAACTC		CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"""EF-hand domain containing"""	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.1357A>C	2.37:g.157425931A>C	ENSP00000308610:p.Lys453Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Missense_Mutation	SNP	ENST00000310454.6	37	CCDS2202.1	63	0.028846153846153848	56	0.11382113821138211	7	0.019337016574585635	0	0.0	0	0.0	A	14.01	2.408743	0.42715	0.11961	6.98E-4	ENSG00000115159	ENST00000310454;ENST00000409125;ENST00000438166;ENST00000409674	T;T;T;T	0.60171	0.21;0.42;0.21;0.21	5.78	3.34	0.38264	.	0.179590	0.56097	N	0.000021	T	0.00967	0.0032	L	0.48877	1.53	0.39253	D	0.96407	B	0.06786	0.001	B	0.13407	0.009	T	0.02288	-1.1182	10	0.52906	T	0.07	.	13.5438	0.61690	0.6092:0.3908:0.0:0.0	rs35096779	453	P43304	GPDM_HUMAN	Q	453;226;453;453	ENSP00000308610:K453Q;ENSP00000386484:K226Q;ENSP00000409708:K453Q;ENSP00000386425:K453Q	ENSP00000308610:K453Q	K	+	1	0	GPD2	157134177	0.997000	0.39634	0.775000	0.31657	0.987000	0.75469	2.271000	0.43364	0.427000	0.26145	0.528000	0.53228	AAA	A|0.963;C|0.037	0.037	strong		0.423	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3		
HEPACAM	220296	hgsc.bcm.edu	37	11	124794763	124794763	+	Silent	SNP	T	T	G	rs36089266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124794763T>G	ENST00000298251.4	-	2	693	c.288A>C	c.(286-288)cgA>cgC	p.R96R		NM_152722.4	NP_689935.2			hepatic and glial cell adhesion molecule											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		GGATACGGTCTCGATAGTCAG	0.587													T|||	27	0.00539137	0.0204	0.0	5008	,	,		21438	0.0		0.0	False		,,,				2504	0.0				p.R96R		Atlas-SNP	.											HEPACAM,NS,carcinoma,-1,4	HEPACAM	64	4	0			c.A288C						PASS	.	T		52,4350	53.6+/-89.4	1,50,2150	142.0	125.0	131.0		288	1.8	1.0	11	dbSNP_126	131	0,8598		0,0,4299	no	coding-synonymous	HEPACAM	NM_152722.4		1,50,6449	GG,GT,TT		0.0,1.1813,0.4		96/417	124794763	52,12948	2201	4299	6500	SO:0001819	synonymous_variant	220296	exon2			ACGGTCTCGATAG	AK098396	CCDS8456.1	11q24.2	2013-01-29	2011-02-11		ENSG00000165478	ENSG00000165478		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26361	protein-coding gene	gene with protein product	"""glial cell adhesion molecule"""	611642	"""hepatocyte cell adhesion molecule"""			15885354, 15917256	Standard	NM_152722		Approved	FLJ25530, hepaCAM, GLIALCAM	uc001qbk.3	Q14CZ8	OTTHUMG00000165938	ENST00000298251.4:c.288A>C	11.37:g.124794763T>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_152722		Silent	SNP	ENST00000298251.4	37	CCDS8456.1																																																																																			T|0.994;G|0.006	0.006	strong		0.587	HEPACAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387125.1	NM_152722	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110489620	110489620	+	Silent	SNP	A	A	T	rs1783148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	62	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	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	
BCAT1	586	hgsc.bcm.edu	37	12	25031515	25031515	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25031515T>C	ENST00000261192.7	-	5	985	c.459A>G	c.(457-459)ccA>ccG	p.P153P	BCAT1_ENST00000544418.1_5'UTR|BCAT1_ENST00000538118.1_Silent_p.P152P|BCAT1_ENST00000342945.5_Silent_p.P92P|BCAT1_ENST00000539780.1_Silent_p.P116P|BCAT1_ENST00000539282.1_Silent_p.P165P	NM_001178091.1|NM_005504.6	NP_001171562.1|NP_005495.2	P54687	BCAT1_HUMAN	branched chain amino-acid transaminase 1, cytosolic	153					branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cell proliferation (GO:0008283)|cellular nitrogen compound metabolic process (GO:0034641)|G1/S transition of mitotic cell cycle (GO:0000082)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)			breast(1)|large_intestine(1)|lung(3)|prostate(2)	7	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)	ATGTTGAATATGGGACCCATT	0.363																																					p.P165P		Atlas-SNP	.											.	BCAT1	44	.	0			c.A495G						PASS	.						94.0	91.0	92.0					12																	25031515		1894	4128	6022	SO:0001819	synonymous_variant	586	exon5			TGAATATGGGACC		CCDS44845.1, CCDS53760.1, CCDS53761.1, CCDS53762.1, CCDS53763.1	12p12.1	2012-10-02	2010-05-07		ENSG00000060982	ENSG00000060982	2.6.1.42		976	protein-coding gene	gene with protein product		113520	"""branched chain aminotransferase 1, cytosolic"""	BCT1		9165094	Standard	NM_005504		Approved		uc010six.2	P54687	OTTHUMG00000169053	ENST00000261192.7:c.459A>G	12.37:g.25031515T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	106	9	0.0849057	NM_001178093	B3KY27|B7Z2M5|B7Z5L0|F5H5E4|Q68DQ7|Q96MY9	Silent	SNP	ENST00000261192.7	37	CCDS44845.1																																																																																			.	.	none		0.363	BCAT1-001	KNOWN	upstream_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402080.1	NM_005504	
TMEM18	129787	hgsc.bcm.edu	37	2	677295	677295	+	Silent	SNP	C	C	T	rs3210390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:677295C>T	ENST00000281017.3	-	1	144	c.51G>A	c.(49-51)gtG>gtA	p.V17V	AC092159.2_ENST00000435573.1_RNA|TMEM18_ENST00000355654.2_5'Flank|TMEM18_ENST00000405941.3_5'Flank|AC092159.2_ENST00000445418.1_RNA	NM_152834.2	NP_690047.2	Q96B42	TMM18_HUMAN	transmembrane protein 18	17					cell migration (GO:0016477)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(1)|lung(7)|ovary(1)	10	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;5.27e-05)|all_epithelial(98;2.11e-06)|Ovarian(717;0.0253)		all cancers(51;1.95e-21)|Epithelial(75;9.47e-21)|OV - Ovarian serous cystadenocarcinoma(76;8.15e-18)|GBM - Glioblastoma multiforme(21;0.0285)		TTACCGTGAGCACGGCTGGGA	0.677													C|||	603	0.120407	0.2458	0.0865	5008	,	,		11272	0.0129		0.1004	False		,,,				2504	0.1063				p.V17V		Atlas-SNP	.											.	TMEM18	22	.	0			c.G51A						PASS	.	C		958,3448		105,748,1350	40.0	32.0	35.0		51	-2.6	0.1	2	dbSNP_105	35	949,7649		53,843,3403	no	coding-synonymous	TMEM18	NM_152834.2		158,1591,4753	TT,TC,CC		11.0375,21.7431,14.6647		17/141	677295	1907,11097	2203	4299	6502	SO:0001819	synonymous_variant	129787	exon1			CGTGAGCACGGCT	AL137269	CCDS33141.1	2p25.3	2008-02-05			ENSG00000151353	ENSG00000151353			25257	protein-coding gene	gene with protein product		613220				12477932	Standard	NM_152834		Approved	DKFZp434C1714	uc002qwl.3	Q96B42	OTTHUMG00000151381	ENST00000281017.3:c.51G>A	2.37:g.677295C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_152834	D6W4X9|Q8N5H2|Q9NTH3	Silent	SNP	ENST00000281017.3	37	CCDS33141.1																																																																																			C|0.864;T|0.136	0.136	strong		0.677	TMEM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322427.1	NM_152834	
TRPM1	4308	hgsc.bcm.edu	37	15	31362352	31362352	+	Missense_Mutation	SNP	C	C	T	rs386782635|rs2241493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31362352C>T	ENST00000256552.6	-	4	308	c.161G>A	c.(160-162)aGc>aAc	p.S54N	TRPM1_ENST00000559179.1_Missense_Mutation_p.S32N|TRPM1_ENST00000542188.1_Missense_Mutation_p.S71N|TRPM1_ENST00000397795.2_Missense_Mutation_p.S32N	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)		CACCTGTTTGCTTTCCTCTTC	0.517													T|||	3961	0.790935	0.7405	0.8905	5008	,	,		20185	0.9296		0.8082	False		,,,				2504	0.6278				p.S71N		Atlas-SNP	.											.	TRPM1	183	.	0			c.G212A						PASS	.	T	ASN/SER	2992,974		1139,714,130	320.0	303.0	309.0		95	-1.7	0.0	15	dbSNP_98	309	6759,1577		2740,1279,149	yes	missense	TRPM1	NM_002420.4	46	3879,1993,279	TT,TC,CC		18.9179,24.5587,20.7365	benign	32/1604	31362352	9751,2551	1983	4168	6151	SO:0001583	missense	4308	exon3			TGTTTGCTTTCCT	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.161G>A	15.37:g.31362352C>T	ENSP00000256552:p.Ser54Asn	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	139	60	0.431655	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	1815	0.8310439560439561	362	0.7357723577235772	312	0.861878453038674	527	0.9213286713286714	614	0.8100263852242744	T	6.876	0.530991	0.13127	0.754413	0.810821	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.61274	0.12;0.12;0.12	6.03	-1.73	0.08081	.	1.191320	0.06210	N	0.684789	T	0.00012	0.0000	N	0.00841	-1.15	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.30995	-0.9959	9	0.16896	T	0.51	-10.5549	9.9581	0.41680	0.0:0.4609:0.2676:0.2715	rs2241493;rs52793730;rs57170646;rs2241493	32	Q7Z4N2	TRPM1_HUMAN	N	32;71;54;32	ENSP00000380897:S32N;ENSP00000437849:S71N;ENSP00000256552:S54N	ENSP00000256552:S54N	S	-	2	0	TRPM1	29149644	0.000000	0.05858	0.000000	0.03702	0.743000	0.42351	-0.595000	0.05727	-0.929000	0.03757	-0.982000	0.02568	AGC	C|0.189;T|0.811	0.811	strong		0.517	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
CST4	1472	hgsc.bcm.edu	37	20	23669488	23669488	+	Missense_Mutation	SNP	T	T	C	rs73902130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23669488T>C	ENST00000217423.3	-	1	189	c.119A>G	c.(118-120)aAt>aGt	p.N40S		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	40					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CCACTCATCATTGAGGTCTGC	0.577													.|||	170	0.0339457	0.1225	0.0115	5008	,	,		18118	0.0		0.0	False		,,,				2504	0.0				p.N40S		Atlas-SNP	.											CST4,colon,carcinoma,-1,1	CST4	37	1	0			c.A119G						PASS	.	T	SER/ASN	409,3997	201.1+/-224.2	18,373,1812	145.0	124.0	131.0		119	1.0	0.0	20	dbSNP_130	131	3,8597	2.2+/-6.3	0,3,4297	yes	missense	CST4	NM_001899.2	46	18,376,6109	CC,CT,TT		0.0349,9.2828,3.1678	benign	40/142	23669488	412,12594	2203	4300	6503	SO:0001583	missense	1472	exon1			TCATCATTGAGGT		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.119A>G	20.37:g.23669488T>C	ENSP00000217423:p.Asn40Ser	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	274	144	0.525547	NM_001899	Q9UBI5|Q9UCS9	Missense_Mutation	SNP	ENST00000217423.3	37	CCDS13159.1	58	0.026556776556776556	51	0.10365853658536585	7	0.019337016574585635	0	0.0	0	0.0	T	5.380	0.255435	0.10185	0.092828	3.49E-4	ENSG00000101441	ENST00000217423	T	0.15256	2.44	2.19	1.01	0.19927	Proteinase inhibitor I25, cystatin (2);	0.362807	0.27236	N	0.020294	T	0.00241	0.0007	N	0.26042	0.785	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.36286	-0.9754	10	0.20519	T	0.43	.	4.081	0.09925	0.0:0.1933:0.0:0.8067	.	40	P01036	CYTS_HUMAN	S	40	ENSP00000217423:N40S	ENSP00000217423:N40S	N	-	2	0	CST4	23617488	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.251000	0.18257	0.094000	0.17404	0.358000	0.22013	AAT	T|0.964;C|0.036	0.036	strong		0.577	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899	
ENPP2	5168	hgsc.bcm.edu	37	8	120575112	120575112	+	Silent	SNP	G	G	A	rs61740048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120575112G>A	ENST00000075322.6	-	24	2464	c.2406C>T	c.(2404-2406)aaC>aaT	p.N802N	ENPP2_ENST00000522167.1_Silent_p.N437N|ENPP2_ENST00000522826.1_Silent_p.N827N|ENPP2_ENST00000427067.2_Silent_p.N823N|ENPP2_ENST00000259486.6_Silent_p.N854N	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	802					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.N854N(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			AGCTCTCCTCGTTGTCAGGCC	0.478													G|||	21	0.00419329	0.0159	0.0	5008	,	,		19836	0.0		0.0	False		,,,				2504	0.0				p.N854N	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											ENPP2_ENST00000522826,colon,carcinoma,0,7	ENPP2	254	7	1	Substitution - coding silent(1)	kidney(1)	c.C2562T						PASS	.	G	,,	48,4358	48.2+/-83.0	0,48,2155	109.0	97.0	101.0		2406,2481,2562	-6.0	0.2	8	dbSNP_129	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	,,	0,49,6454	AA,AG,GG		0.0116,1.0894,0.3767	,,	802/864,827/889,854/916	120575112	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	5168	exon25			CTCCTCGTTGTCA	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2406C>T	8.37:g.120575112G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	121	61	0.504132	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			G|0.997;A|0.003	0.003	strong		0.478	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
ALK	238	hgsc.bcm.edu	37	2	29445425	29445425	+	Silent	SNP	G	G	A	rs56146053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29445425G>A	ENST00000389048.3	-	21	4314	c.3408C>T	c.(3406-3408)tcC>tcT	p.S1136S	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1136	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	TGGGCATTCCGGACACCTGGC	0.572			"""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				G|||	167	0.0333466	0.1225	0.0072	5008	,	,		16613	0.0		0.0	False		,,,				2504	0.0				p.S1136S		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,colon,carcinoma,0,1	ALK	533	1	0			c.C3408T						PASS	.	G		379,4027	193.0+/-218.2	13,353,1837	57.0	55.0	56.0		3408	-5.2	0.9	2	dbSNP_129	56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ALK	NM_004304.4		13,354,6136	AA,AG,GG		0.0116,8.6019,2.9217		1136/1621	29445425	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	238	exon21	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CATTCCGGACACC	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.3408C>T	2.37:g.29445425G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	138	57	0.413043	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.970;A|0.030	0.030	strong		0.572	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
TMEM132B	114795	hgsc.bcm.edu	37	12	125900104	125900104	+	Silent	SNP	A	A	T	rs143188464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125900104A>T	ENST00000299308.3	+	3	980	c.972A>T	c.(970-972)atA>atT	p.I324I		NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	324						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)		GTGTGAAGATAACGGCAGTGA	0.468													A|||	30	0.00599042	0.0219	0.0014	5008	,	,		18015	0.0		0.0	False		,,,				2504	0.0				p.I324I		Atlas-SNP	.											.	TMEM132B	207	.	0			c.A972T						PASS	.	A		118,4212		0,118,2047	77.0	92.0	87.0		972	-11.3	0.0	12	dbSNP_134	87	1,8527		0,1,4263	no	coding-synonymous	TMEM132B	NM_052907.2		0,119,6310	TT,TA,AA		0.0117,2.7252,0.9255		324/1079	125900104	119,12739	2165	4264	6429	SO:0001819	synonymous_variant	114795	exon3			GAAGATAACGGCA	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.972A>T	12.37:g.125900104A>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	156	81	0.519231	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																			A|0.994;T|0.006	0.006	strong		0.468	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
AGFG1	3267	hgsc.bcm.edu	37	2	228398422	228398422	+	Silent	SNP	A	A	G	rs13015491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228398422A>G	ENST00000310078.8	+	7	1232	c.972A>G	c.(970-972)gcA>gcG	p.A324A	AGFG1_ENST00000409171.1_Silent_p.A324A|AGFG1_ENST00000409979.2_Silent_p.A348A|AGFG1_ENST00000373671.3_Silent_p.A284A|AGFG1_ENST00000409315.1_Silent_p.A324A	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	324					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.A324A(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						TACAGACTGCAGACAAATATG	0.393													A|||	348	0.0694888	0.0023	0.1455	5008	,	,		19964	0.1042		0.0964	False		,,,				2504	0.0429				p.A348A		Atlas-SNP	.											AGFG1,NS,carcinoma,0,1	AGFG1	80	1	1	Substitution - coding silent(1)	stomach(1)	c.A1044G						PASS	.	A	,,,	93,4313	77.3+/-115.6	0,93,2110	82.0	79.0	80.0		1044,972,852,972	1.1	1.0	2	dbSNP_121	80	708,7892	173.9+/-224.3	25,658,3617	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AGFG1	NM_001135187.1,NM_001135188.1,NM_001135189.1,NM_004504.4	,,,	25,751,5727	GG,GA,AA		8.2326,2.1108,6.1587	,,,	348/585,324/561,284/523,324/563	228398422	801,12205	2203	4300	6503	SO:0001819	synonymous_variant	3267	exon8			GACTGCAGACAAA		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"""ADP-ribosylation factor GTPase activating proteins"""	5175	protein-coding gene	gene with protein product		600862	"""HIV-1 Rev binding protein"""	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.972A>G	2.37:g.228398422A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	148	83	0.560811	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Silent	SNP	ENST00000310078.8	37	CCDS2467.1																																																																																			A|0.931;G|0.069	0.069	strong		0.393	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504	
KIF4A	24137	hgsc.bcm.edu	37	X	69550080	69550080	+	Silent	SNP	A	A	G	rs5936873	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:69550080A>G	ENST00000374403.3	+	9	1051	c.969A>G	c.(967-969)acA>acG	p.T323T	KIF4A_ENST00000374388.3_Silent_p.T323T	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	323	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|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)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.T323T(1)		breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						TAGAGGAAACATTAAATACCC	0.373													A|||	321	0.0850331	0.0439	0.0086	3775	,	,		13400	0.2024		0.007	False		,,,				2504	0.047				p.T323T		Atlas-SNP	.											.	KIF4A	118	.	1	Substitution - coding silent(1)	stomach(1)	c.A969G						PASS	.	A		185,3650		4,156,21,1472,550	132.0	127.0	129.0		969	-3.2	0.9	X	dbSNP_114	129	78,6650		0,54,24,2374,1848	no	coding-synonymous	KIF4A	NM_012310.4		4,210,45,3846,2398	GG,GA,G,AA,A		1.1593,4.824,2.4898		323/1233	69550080	263,10300	2203	4300	6503	SO:0001819	synonymous_variant	24137	exon9			GGAAACATTAAAT	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"""Kinesins"""	13339	protein-coding gene	gene with protein product	"""chromokinesin"""	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.969A>G	X.37:g.69550080A>G		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	265	134	0.50566	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Silent	SNP	ENST00000374403.3	37	CCDS14401.1																																																																																			A|0.938;0|0.003	.	strong		0.373	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	
CYFIP2	26999	hgsc.bcm.edu	37	5	156742033	156742033	+	Silent	SNP	C	C	T	rs17054446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156742033C>T	ENST00000521420.1	+	12	1300	c.1209C>T	c.(1207-1209)ggC>ggT	p.G403G	CYFIP2_ENST00000435847.2_Silent_p.G103G|CYFIP2_ENST00000522463.1_Silent_p.G233G|CYFIP2_ENST00000377576.3_Silent_p.G429G|CYFIP2_ENST00000318218.6_Silent_p.G429G|CYFIP2_ENST00000347377.6_Silent_p.G429G|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000541131.1_Silent_p.G354G					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ACTGTCCTGGCACCGCGGAGG	0.512													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		19474	0.0		0.0	False		,,,				2504	0.0				p.G429G		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C1287T						PASS	.	C	,,	65,4037		0,65,1986	64.0	64.0	64.0		1287,1287,1287	4.6	1.0	5	dbSNP_123	64	0,8400		0,0,4200	no	coding-synonymous,coding-synonymous,coding-synonymous	CYFIP2	NM_001037332.2,NM_001037333.1,NM_014376.2	,,	0,65,6186	TT,TC,CC		0.0,1.5846,0.5199	,,	429/1254,429/1254,429/1254	156742033	65,12437	2051	4200	6251	SO:0001819	synonymous_variant	26999	exon13			TCCTGGCACCGCG	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.1209C>T	5.37:g.156742033C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_001037332		Silent	SNP	ENST00000521420.1	37																																																																																				C|0.993;T|0.007	0.007	strong		0.512	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
BTK	695	hgsc.bcm.edu	37	X	100617218	100617218	+	Silent	SNP	A	A	G	rs148358153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:100617218A>G	ENST00000308731.7	-	7	694	c.531T>C	c.(529-531)ccT>ccC	p.P177P	BTK_ENST00000372880.1_Silent_p.P177P	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	177					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						GAGAACTCCCAGGTTTTAAGC	0.498									Agammaglobulinemia, X-linked				A|||	26	0.00688742	0.0182	0.0029	3775	,	,		13779	0.0		0.0	False		,,,				2504	0.0				p.P177P		Atlas-SNP	.											.	BTK	87	.	0			c.T531C						PASS	.	A		73,3762		0,67,6,1565,565	111.0	95.0	100.0		531	2.7	1.0	X	dbSNP_134	100	0,6728		0,0,0,2428,1872	no	coding-synonymous	BTK	NM_000061.2		0,67,6,3993,2437	GG,GA,G,AA,A		0.0,1.9035,0.6911		177/660	100617218	73,10490	2203	4300	6503	SO:0001819	synonymous_variant	695	exon7	Familial Cancer Database	Bruton Type Agammaglobulinemia	ACTCCCAGGTTTT	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.531T>C	X.37:g.100617218A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_000061	B2RAW1|Q32ML5	Silent	SNP	ENST00000308731.7	37	CCDS14482.1																																																																																			A|0.993;G|0.007	0.007	strong		0.498	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061	
GPD1L	23171	hgsc.bcm.edu	37	3	32181761	32181761	+	Silent	SNP	C	C	T	rs9835387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:32181761C>T	ENST00000282541.5	+	4	609	c.408C>T	c.(406-408)gaC>gaT	p.D136D		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	136					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						TCATTTCTGACATCATCCGTG	0.512													C|||	750	0.14976	0.2965	0.1182	5008	,	,		19949	0.002		0.1362	False		,,,				2504	0.1401				p.D136D		Atlas-SNP	.											.	GPD1L	25	.	0			c.C408T						PASS	.	C		1282,3124	437.6+/-345.0	178,926,1099	178.0	178.0	178.0		408	5.5	1.0	3	dbSNP_119	178	1193,7407	241.8+/-272.0	95,1003,3202	no	coding-synonymous	GPD1L	NM_015141.3		273,1929,4301	TT,TC,CC		13.8721,29.0967,19.0297		136/352	32181761	2475,10531	2203	4300	6503	SO:0001819	synonymous_variant	23171	exon4			TTCTGACATCATC	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.408C>T	3.37:g.32181761C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_015141	A8K9U3|Q14702|Q9BRM5	Silent	SNP	ENST00000282541.5	37	CCDS33729.1																																																																																			C|0.828;T|0.172	0.172	strong		0.512	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141	
MUC4	4585	hgsc.bcm.edu	37	3	195513425	195513425	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513425C>G	ENST00000463781.3	-	2	5485	c.5026G>C	c.(5026-5028)Ggt>Cgt	p.G1676R	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G1676R	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)		GTGGCGTGACCGGTGGATGCT	0.607																																					p.G1676R		Atlas-SNP	.											MUC4_ENST00000463781,rectum,carcinoma,0,1	MUC4	1505	1	0			c.G5026C						scavenged	.						36.0	34.0	34.0					3																	195513425		689	1583	2272	SO:0001583	missense	4585	exon2			CGTGACCGGTGGA	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.5026G>C	3.37:g.195513425C>G	ENSP00000417498:p.Gly1676Arg	Somatic	523	0	0		WXS	Illumina HiSeq	Phase_I	468	61	0.130342	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	.	.	.	.	.	.	.	.	.	.	-	2.575	-0.298681	0.05532	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.49;1.45	0.423	-0.846	0.10734	.	.	.	.	.	T	0.22936	0.0554	N	0.08118	0	0.09310	N	1	D	0.64830	0.994	P	0.59546	0.859	T	0.12993	-1.0526	8	.	.	.	.	4.1233	0.10116	0.651:0.3489:1.0E-4:0.0	.	1676	E7ESK3	.	R	1676	ENSP00000417498:G1676R;ENSP00000420243:G1676R	.	G	-	1	0	MUC4	196997820	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	-0.235000	0.09016	-0.784000	0.04528	0.089000	0.15464	GGT	.	.	none		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF492	57615	hgsc.bcm.edu	37	19	22847084	22847084	+	Missense_Mutation	SNP	G	G	T	rs139985933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	526	2	0.00380228		WXS	Illumina HiSeq	Phase_I	465	330	0.709677	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	
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117746	46117746	+	Silent	SNP	C	C	T	rs112431728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46117746C>T	ENST00000400365.3	+	1	660	c.630C>T	c.(628-630)ccC>ccT	p.P210P	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	210	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						GCCGCGTGCCCGTCCCCTCCT	0.721													a|||	33	0.00658946	0.0242	0.0014	5008	,	,		14658	0.0		0.0	False		,,,				2504	0.0				p.P210P		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.C630T						PASS	.	A	,	115,4287		1,113,2087	53.0	68.0	63.0		,630	0.8	0.4	21	dbSNP_132	63	1,8581		0,1,4290	no	intron,coding-synonymous	TSPEAR,KRTAP10-12	NM_144991.2,NM_198699.1	,	1,114,6377	TT,TC,CC		0.0117,2.6124,0.8934	,	,210/246	46117746	116,12868	2201	4291	6492	SO:0001819	synonymous_variant	386685	exon1			CGTGCCCGTCCCC	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"""Keratin associated proteins"""	20533	protein-coding gene	gene with protein product			"""keratin associated protein 18-12"""	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.630C>T	21.37:g.46117746C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_198699	B2RPA3	Silent	SNP	ENST00000400365.3	37	CCDS42967.1																																																																																			C|0.994;T|0.006	0.006	strong		0.721	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699	
CR1	1378	hgsc.bcm.edu	37	1	207790088	207790088	+	Missense_Mutation	SNP	C	C	G	rs3811381	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207790088C>G	ENST00000367049.4	+	41	6830	c.6830C>G	c.(6829-6831)cCt>cGt	p.P2277R	CR1_ENST00000367051.1_Missense_Mutation_p.P1827R|CR1_ENST00000367052.1_Missense_Mutation_p.P1827R|CR1_ENST00000367053.1_Missense_Mutation_p.P1827R|CR1_ENST00000400960.2_Missense_Mutation_p.P1827R	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1827					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						ACAAGTGACCCTCAAGGGAAT	0.517													C|||	1316	0.26278	0.1172	0.2608	5008	,	,		19452	0.3224		0.1809	False		,,,				2504	0.4836				p.P2277R		Atlas-SNP	.											.	CR1	354	.	0			c.C6830G	GRCh37	CM025385	CR1	M	rs3811381	PASS	.	C	ARG/PRO,ARG/PRO	498,3414		34,430,1492	146.0	147.0	147.0		5480,6830	-5.6	0.0	1	dbSNP_107	147	1508,6762		125,1258,2752	no	missense,missense	CR1	NM_000573.3,NM_000651.4	103,103	159,1688,4244	GG,GC,CC		18.2346,12.7301,16.4669	benign,benign	1827/2040,2277/2490	207790088	2006,10176	1956	4135	6091	SO:0001583	missense	1378	exon41			GTGACCCTCAAGG	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.6830C>G	1.37:g.207790088C>G	ENSP00000356016:p.Pro2277Arg	Somatic	431	0	0		WXS	Illumina HiSeq	Phase_I	406	192	0.472906	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	429|429	0.19642857142857142|0.19642857142857142	64|64	0.13008130081300814|0.13008130081300814	102|102	0.281767955801105|0.281767955801105	131|131	0.229020979020979|0.229020979020979	132|132	0.1741424802110818|0.1741424802110818	C|C	0.010|0.010	-1.745772|-1.745772	0.00669|0.00669	0.127301|0.127301	0.182346|0.182346	ENSG00000203710|ENSG00000203710	ENST00000529814|ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	.|T;T;T;T;T	.|0.21543	.|2.0;2.0;2.0;2.0;2.0	4.15|4.15	-5.58|-5.58	0.02512|0.02512	.|Complement control module (2);Sushi/SCR/CCP (3);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.05078|0.05078	-0.115|-0.115	0.80722|0.80722	P|P	0.0|0.0	.|B;P	.|0.38711	.|0.005;0.643	.|B;B	.|0.32211	.|0.032;0.142	T|T	0.39643|0.39643	-0.9604|-0.9604	4|8	.|0.11794	.|T	.|0.64	.|.	3.1972|3.1972	0.06637|0.06637	0.5482:0.1261:0.1987:0.127|0.5482:0.1261:0.1987:0.127	rs3811381;rs56791502|rs3811381;rs56791502	.|1827;2277	.|P17927;E9PDY4	.|CR1_HUMAN;.	V|R	450|1827;1827;1827;1827;2277	.|ENSP00000356019:P1827R;ENSP00000356018:P1827R;ENSP00000356020:P1827R;ENSP00000383744:P1827R;ENSP00000356016:P2277R	.|ENSP00000356016:P2277R	L|P	+|+	1|2	0|0	CR1|CR1	205856711|205856711	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.021000|0.021000	0.10359|0.10359	-0.775000|-0.775000	0.04679|0.04679	-1.266000|-1.266000	0.02446|0.02446	-2.118000|-2.118000	0.00350|0.00350	CTC|CCT	C|0.800;G|0.200	0.200	strong		0.517	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
AHNAK2	113146	hgsc.bcm.edu	37	14	105413223	105413223	+	Silent	SNP	A	A	G	rs55797226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105413223A>G	ENST00000333244.5	-	7	8684	c.8565T>C	c.(8563-8565)gaT>gaC	p.D2855D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2855						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)			TGGTCTTAAGATCCCCTTGCA	0.632													.|||	2640	0.527157	0.5272	0.5086	5008	,	,		17242	0.4296		0.5318	False		,,,				2504	0.636				p.D2855D		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,0,1	AHNAK2	719	1	0			c.T8565C						scavenged	.	G		2295,1633		719,857,388	128.0	147.0	141.0		8565	-3.2	0.0	14	dbSNP_129	141	4487,3821		1227,2033,894	no	coding-synonymous	AHNAK2	NM_138420.2		1946,2890,1282	GG,GA,AA		45.9918,41.5733,44.5734		2855/5796	105413223	6782,5454	1964	4154	6118	SO:0001819	synonymous_variant	113146	exon7			CTTAAGATCCCCT	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.8565T>C	14.37:g.105413223A>G		Somatic	262	3	0.0114504		WXS	Illumina HiSeq	Phase_I	285	282	0.989474	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.492;G|0.508	0.508	strong		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SEC14L3	266629	hgsc.bcm.edu	37	22	30857448	30857448	+	Silent	SNP	A	A	G	rs5749104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30857448A>G	ENST00000215812.4	-	11	1020	c.930T>C	c.(928-930)gaT>gaC	p.D310D	SEC14L3_ENST00000401751.1_Silent_p.D251D|SEC14L3_ENST00000415957.2_Silent_p.D251D|SEC14L3_ENST00000539629.1_Silent_p.D251D|SEC14L3_ENST00000402286.1_Silent_p.D233D|SEC14L3_ENST00000403066.1_Silent_p.D251D|SEC14L3_ENST00000540910.1_Silent_p.D233D	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	310	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					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)	TGTCCGCACCATCAGATGAGA	0.597													G|||	3866	0.771965	0.9138	0.5648	5008	,	,		18876	0.8601		0.5785	False		,,,				2504	0.8354				p.D310D	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.T930C						PASS	.	G		3772,634	273.1+/-271.2	1604,564,35	54.0	50.0	51.0		930	-4.8	0.0	22	dbSNP_114	51	5018,3582	519.2+/-379.4	1454,2110,736	no	coding-synonymous	SEC14L3	NM_174975.4		3058,2674,771	GG,GA,AA		41.6512,14.3895,32.4158		310/401	30857448	8790,4216	2203	4300	6503	SO:0001819	synonymous_variant	266629	exon11			CGCACCATCAGAT	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.930T>C	22.37:g.30857448A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	141	61	0.432624	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Silent	SNP	ENST00000215812.4	37	CCDS13877.1																																																																																			A|0.276;G|0.724	0.724	strong		0.597	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
R3HDM1	23518	hgsc.bcm.edu	37	2	136393658	136393658	+	Splice_Site	SNP	A	A	G	rs961360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:136393658A>G	ENST00000264160.4	+	11	1178	c.808A>G	c.(808-810)Atg>Gtg	p.M270V	R3HDM1_ENST00000329971.3_Splice_Site_p.M226V|R3HDM1_ENST00000410054.1_Splice_Site_p.M214V|R3HDM1_ENST00000409478.1_Splice_Site_p.M226V|R3HDM1_ENST00000409606.1_Splice_Site_p.M270V	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	270	SUZ. {ECO:0000255|PROSITE- ProRule:PRU01009}.		M -> V (in dbSNP:rs961360). {ECO:0000269|PubMed:15489334}.				poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		TTTTCTGTAGATGAGAATACG	0.358													A|||	1549	0.309305	0.2511	0.2666	5008	,	,		17785	0.4702		0.2336	False		,,,				2504	0.3303				p.M270V		Atlas-SNP	.											R3HDM1,NS,carcinoma,-2,1	R3HDM1	84	1	0			c.A808G						PASS	.	A	VAL/MET	877,3529	341.0+/-306.5	75,727,1401	114.0	125.0	121.0		808	5.6	1.0	2	dbSNP_86	121	1508,7092	284.0+/-296.4	173,1162,2965	yes	missense-near-splice	R3HDM1	NM_015361.2	21	248,1889,4366	GG,GA,AA		17.5349,19.9047,18.3377	benign	270/1100	136393658	2385,10621	2203	4300	6503	SO:0001630	splice_region_variant	23518	exon11			CTGTAGATGAGAA	D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing"""	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.808-1A>G	2.37:g.136393658A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	90	36	0.4	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	37	CCDS2177.1	687	0.31456043956043955	137	0.2784552845528455	103	0.2845303867403315	274	0.479020979020979	173	0.22823218997361477	A	10.09	1.255536	0.22965	0.199047	0.175349	ENSG00000048991	ENST00000422577;ENST00000409478;ENST00000264160;ENST00000329971;ENST00000410054;ENST00000409606	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.58	5.58	0.84498	SUZ domain (1);	0.263218	0.49305	D	0.000150	T	0.00012	0.0000	N	0.14661	0.345	0.39165	P	0.03751199999999999	B;B;P;P	0.50156	0.006;0.216;0.895;0.932	B;B;P;D	0.67103	0.022;0.069;0.654;0.949	T	0.49447	-0.8939	8	.	.	.	-3.2018	16.0334	0.80603	1.0:0.0:0.0:0.0	rs961360;rs52817718;rs56663948;rs961360	226;270;214;270	G5E9G8;E9PBB4;E9PG42;Q15032	.;.;.;R3HD1_HUMAN	V	226;226;270;226;214;270	ENSP00000386457:M226V;ENSP00000264160:M270V;ENSP00000331396:M226V;ENSP00000386877:M214V;ENSP00000387010:M270V	.	M	+	1	0	R3HDM1	136110128	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	6.932000	0.75869	2.243000	0.73865	0.533000	0.62120	ATG	A|0.689;G|0.311	0.311	strong		0.358	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361	Missense_Mutation
NIPBL	25836	hgsc.bcm.edu	37	5	36986297	36986297	+	Silent	SNP	A	A	G	rs1669445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36986297A>G	ENST00000282516.8	+	10	3514	c.3015A>G	c.(3013-3015)ctA>ctG	p.L1005L	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Silent_p.L1005L	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1005					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)			TAGTTGTGCTACAAAAACTGT	0.333													A|||	184	0.0367412	0.1362	0.0058	5008	,	,		17335	0.0		0.0	False		,,,				2504	0.0				p.L1005L		Atlas-SNP	.											.	NIPBL	513	.	0			c.A3015G						PASS	.	A	,	504,3902	228.1+/-243.1	27,450,1726	130.0	147.0	141.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3015,3015	1.7	1.0	5	dbSNP_89	141	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NIPBL	NM_015384.4,NM_133433.3	,	27,451,6025	GG,GA,AA		0.0116,11.4389,3.8828	,	1005/2698,1005/2805	36986297	505,12501	2203	4300	6503	SO:0001819	synonymous_variant	25836	exon10			TGTGCTACAAAAA	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.3015A>G	5.37:g.36986297A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																			A|0.961;G|0.039	0.039	strong		0.333	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
KPRP	448834	hgsc.bcm.edu	37	1	152732998	152732998	+	Missense_Mutation	SNP	C	C	T	rs140912923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152732998C>T	ENST00000606109.1	+	1	962	c.934C>T	c.(934-936)Cgc>Tgc	p.R312C	KPRP_ENST00000368773.1_Missense_Mutation_p.R312C			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	312	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGTCCTCGCCGCCCCATTTC	0.597													C|||	24	0.00479233	0.0174	0.0014	5008	,	,		16798	0.0		0.0	False		,,,				2504	0.0				p.R312C		Atlas-SNP	.											KPRP,NS,carcinoma,0,3	KPRP	152	3	0			c.C934T						PASS	.	C	CYS/ARG	69,4337	62.9+/-100.1	2,65,2136	48.0	47.0	48.0		934	-8.3	0.0	1	dbSNP_134	48	0,8600		0,0,4300	no	missense	KPRP	NM_001025231.1	180	2,65,6436	TT,TC,CC		0.0,1.566,0.5305	possibly-damaging	312/580	152732998	69,12937	2203	4300	6503	SO:0001583	missense	448834	exon2			CCTCGCCGCCCCA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.934C>T	1.37:g.152732998C>T	ENSP00000475216:p.Arg312Cys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	C	9.290	1.050327	0.19827	0.01566	0.0	ENSG00000203786	ENST00000368773	T	0.16196	2.36	5.3	-8.26	0.01021	.	1.822830	0.02592	N	0.100084	T	0.03305	0.0096	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.43909	-0.9362	10	0.72032	D	0.01	-0.013	9.3493	0.38129	0.1476:0.6376:0.1235:0.0913	.	312	Q5T749	KPRP_HUMAN	C	312	ENSP00000357762:R312C	ENSP00000357762:R312C	R	+	1	0	KPRP	150999622	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.771000	0.04699	-1.006000	0.03412	-0.502000	0.04539	CGC	C|0.994;T|0.006	0.006	strong		0.597	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
KCTD19	146212	hgsc.bcm.edu	37	16	67324827	67324827	+	Silent	SNP	A	A	G	rs8053912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67324827A>G	ENST00000304372.5	-	15	2683	c.2628T>C	c.(2626-2628)gaT>gaC	p.D876D		NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	876					protein homooligomerization (GO:0051260)					endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		TGTGCCGGTCATCCTTGAAGC	0.612													G|||	1249	0.249401	0.7118	0.1037	5008	,	,		20282	0.003		0.0716	False		,,,				2504	0.1646				p.D876D		Atlas-SNP	.											.	KCTD19	82	.	0			c.T2628C						PASS	.	G		2198,1806		601,996,405	53.0	60.0	58.0		2628	0.9	1.0	16	dbSNP_116	58	619,7735		22,575,3580	no	coding-synonymous	KCTD19	NM_001100915.1		623,1571,3985	GG,GA,AA		7.4096,45.1049,22.795		876/927	67324827	2817,9541	2002	4177	6179	SO:0001819	synonymous_variant	146212	exon15			CCGGTCATCCTTG	AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 19"""				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.2628T>C	16.37:g.67324827A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_001100915	B4DZ49|Q8N804	Silent	SNP	ENST00000304372.5	37	CCDS42179.1																																																																																			A|0.834;G|0.166	0.166	strong		0.612	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367	
ZNF839	55778	hgsc.bcm.edu	37	14	102808273	102808273	+	Missense_Mutation	SNP	C	C	A	rs1053019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102808273C>A	ENST00000558850.1	+	8	2543	c.2193C>A	c.(2191-2193)ttC>ttA	p.F731L	ZNF839_ENST00000262236.5_Missense_Mutation_p.F733L|ZNF839_ENST00000559185.1_Missense_Mutation_p.F731L|ZNF839_ENST00000442396.2_Missense_Mutation_p.F847L|ZNF839_ENST00000420933.2_3'UTR|AL137229.1_ENST00000577622.1_RNA	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	731			F -> L (in dbSNP:rs1053019).				metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TGAACCGGTTCCCCTGTGGGA	0.572													C|||	358	0.0714856	0.1838	0.0375	5008	,	,		18344	0.001		0.0636	False		,,,				2504	0.0245				p.F847L		Atlas-SNP	.											.	ZNF839	41	.	0			c.C2541A						PASS	.	C	LEU/PHE	626,3306		51,524,1391	56.0	59.0	58.0		2541	-0.9	0.0	14	dbSNP_86	58	471,7829		16,439,3695	yes	missense	ZNF839	NM_018335.3	22	67,963,5086	AA,AC,CC		5.6747,15.9207,8.9683	benign	847/928	102808273	1097,11135	1966	4150	6116	SO:0001583	missense	55778	exon8			CCGGTTCCCCTGT	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.2193C>A	14.37:g.102808273C>A	ENSP00000453363:p.Phe731Leu	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Missense_Mutation	SNP	ENST00000558850.1	37	CCDS58336.1	143	0.06547619047619048	83	0.16869918699186992	17	0.04696132596685083	0	0.0	43	0.05672823218997362	C	8.347	0.830116	0.16749	0.159207	0.056747	ENSG00000022976	ENST00000442396;ENST00000262236;ENST00000398436;ENST00000420933	T;T	0.17528	2.27;2.27	4.37	-0.902	0.10537	.	1.215490	0.05661	N	0.586973	T	0.00039	0.0001	L	0.38838	1.175	0.80722	P	0.0	B;B;B	0.19817	0.039;0.005;0.005	B;B;B	0.18871	0.023;0.019;0.019	T	0.39272	-0.9622	9	0.25751	T	0.34	.	4.1834	0.10387	0.0:0.3135:0.3266:0.36	rs1053019;rs3193504;rs52808269;rs59353203;rs1053019	847;733;731	A8K0R7-5;A8K0R7-2;A8K0R7	.;.;ZN839_HUMAN	L	847;733;399;265	ENSP00000399863:F847L;ENSP00000262236:F733L	ENSP00000262236:F733L	F	+	3	2	ZNF839	101878026	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.095000	0.11077	-0.152000	0.11156	-0.346000	0.07831	TTC	C|0.920;A|0.080	0.080	strong		0.572	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
COL6A5	256076	hgsc.bcm.edu	37	3	130095598	130095598	+	Missense_Mutation	SNP	A	A	G	rs115250607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130095598A>G	ENST00000432398.2	+	3	1080	c.586A>G	c.(586-588)Agc>Ggc	p.S196G	COL6A5_ENST00000265379.6_Missense_Mutation_p.S196G	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	196	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						CAGAGACCTCAGCACATTTTC	0.463													A|||	97	0.019369	0.0703	0.0058	5008	,	,		20670	0.0		0.0	False		,,,				2504	0.0				p.S196G		Atlas-SNP	.											.	COL6A5	205	.	0			c.A586G						PASS	.	A	GLY/SER	75,1309		0,75,617	92.0	79.0	83.0		586	0.6	0.9	3	dbSNP_132	83	0,3182		0,0,1591	yes	missense	COL6A5	NM_153264.5	56	0,75,2208	GG,GA,AA		0.0,5.4191,1.6426	benign	196/2527	130095598	75,4491	692	1591	2283	SO:0001583	missense	256076	exon3			GACCTCAGCACAT	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.586A>G	3.37:g.130095598A>G	ENSP00000390895:p.Ser196Gly	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	175	73	0.417143	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	A	7.887	0.731439	0.15507	0.054191	0.0	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.77877	-1.13;-1.13	4.91	0.623	0.17654	.	.	.	.	.	T	0.12689	0.0308	N	0.11313	0.125	0.09310	N	0.999998	B	0.13145	0.007	B	0.19666	0.026	T	0.07731	-1.0757	9	0.20046	T	0.44	.	8.6998	0.34318	0.6916:0.0:0.3084:0.0	.	196	A8TX70-2	.	G	196	ENSP00000390895:S196G;ENSP00000265379:S196G	ENSP00000265379:S196G	S	+	1	0	COL6A5	131578288	0.000000	0.05858	0.929000	0.37066	0.781000	0.44180	-0.161000	0.10026	0.278000	0.22164	0.374000	0.22700	AGC	A|0.983;G|0.017	0.017	strong		0.463	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
GPKOW	27238	hgsc.bcm.edu	37	X	48970655	48970655	+	Silent	SNP	C	C	T	rs34057359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48970655C>T	ENST00000156109.5	-	11	1413	c.1335G>A	c.(1333-1335)cgG>cgA	p.R445R		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	445						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						GCACCAAAGCCCGGCTCCGTG	0.562													C|||	409	0.108344	0.289	0.0375	3775	,	,		16222	0.0		0.001	False		,,,				2504	0.0				p.R445R		Atlas-SNP	.											.	GPKOW	38	.	0			c.G1335A						PASS	.	C		1294,2541		185,734,190,713,381	148.0	110.0	123.0		1335	0.5	0.4	X	dbSNP_126	123	8,6720		0,8,0,2420,1872	no	coding-synonymous	GPKOW	NM_015698.4		185,742,190,3133,2253	TT,TC,T,CC,C		0.1189,33.7419,12.326		445/477	48970655	1302,9261	2203	4300	6503	SO:0001819	synonymous_variant	27238	exon11			CAAAGCCCGGCTC	U66359	CCDS35251.1	Xp11.23	2013-01-28			ENSG00000068394	ENSG00000068394		"""G patch domain containing"""	30677	protein-coding gene	gene with protein product	"""G patch domain containing 5"""					21880142, 22365833	Standard	NM_015698		Approved	T54, GPATC5, GPATCH5, Spp2	uc004dmr.3	Q92917	OTTHUMG00000021511	ENST00000156109.5:c.1335G>A	X.37:g.48970655C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	207	102	0.492754	NM_015698	Q59EK5|Q9BQA8	Silent	SNP	ENST00000156109.5	37	CCDS35251.1																																																																																			C|0.873;T|0.127	0.127	strong		0.562	GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698	
CCDC180	100499483	hgsc.bcm.edu	37	9	100105782	100105782	+	Missense_Mutation	SNP	C	C	G	rs2061634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100105782C>G	ENST00000357054.1	+	33	3919	c.2984C>G	c.(2983-2985)tCc>tGc	p.S995C	CCDC180_ENST00000529487.1_Missense_Mutation_p.S856C|CCDC180_ENST00000375202.2_Missense_Mutation_p.S856C|CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000411667.2_Missense_Mutation_p.S853C|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000460482.2_3'UTR			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	97	0	0		WXS	Illumina HiSeq	Phase_I	92	52	0.565217	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	
POC5	134359	hgsc.bcm.edu	37	5	75001590	75001590	+	Missense_Mutation	SNP	T	T	A	rs77025299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:75001590T>A	ENST00000428202.2	-	4	435	c.246A>T	c.(244-246)gaA>gaT	p.E82D	POC5_ENST00000504862.1_5'UTR|POC5_ENST00000380475.2_5'UTR|POC5_ENST00000510798.1_5'UTR|POC5_ENST00000446329.2_Missense_Mutation_p.E57D|POC5_ENST00000514838.2_Intron	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	82					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						CTATTGCAGTTTCTCTTACTT	0.284													T|||	295	0.0589058	0.211	0.0202	5008	,	,		16251	0.0		0.002	False		,,,				2504	0.0				p.E82D		Atlas-SNP	.											.	POC5	82	.	0			c.A246T						PASS	.	T	ASP/GLU,ASP/GLU	586,2982		47,492,1245	79.0	71.0	74.0		246,171	2.4	0.4	5	dbSNP_131	74	4,8068		0,4,4032	yes	missense,missense	POC5	NM_001099271.1,NM_152408.2	45,45	47,496,5277	AA,AT,TT		0.0496,16.4238,5.0687	benign,benign	82/576,57/551	75001590	590,11050	1784	4036	5820	SO:0001583	missense	134359	exon4			TGCAGTTTCTCTT	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.246A>T	5.37:g.75001590T>A	ENSP00000410216:p.Glu82Asp	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	55	19	0.345455	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	37	CCDS47236.1	96	0.04395604395604396	88	0.17886178861788618	8	0.022099447513812154	0	0.0	0	0.0	T	7.456	0.643625	0.14451	0.164238	4.96E-4	ENSG00000152359	ENST00000428202;ENST00000446329	T;T	0.25414	1.81;1.8	4.91	2.36	0.29203	.	0.396419	0.27609	N	0.018614	T	0.00039	0.0001	L	0.43701	1.375	0.09310	P	0.9999988642	B;B	0.12630	0.006;0.006	B;B	0.13407	0.009;0.006	T	0.16571	-1.0398	9	0.34782	T	0.22	-13.4474	9.2644	0.37632	0.0:0.0:0.3522:0.6478	.	82;57	Q8NA72;Q8NA72-3	POC5_HUMAN;.	D	82;57	ENSP00000410216:E82D;ENSP00000399481:E57D	ENSP00000410216:E82D	E	-	3	2	POC5	75037346	0.911000	0.30947	0.398000	0.26321	0.137000	0.21094	1.191000	0.32138	0.392000	0.25172	0.528000	0.53228	GAA	T|0.965;A|0.035	0.035	strong		0.284	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
PTGIR	5739	hgsc.bcm.edu	37	19	47124742	47124742	+	Missense_Mutation	SNP	G	G	C	rs28590598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47124742G>C	ENST00000291294.2	-	3	1089	c.956C>G	c.(955-957)tCg>tGg	p.S319W	PTGIR_ENST00000597185.1_Missense_Mutation_p.S48W|PTGIR_ENST00000598865.1_Missense_Mutation_p.S107W|PTGIR_ENST00000594275.1_Missense_Mutation_p.S76W	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	319			S -> W (in dbSNP:rs28590598).		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	GGGTGTCTGCGAGTCTCCGTG	0.647													G|||	136	0.0271565	0.0968	0.0101	5008	,	,		18475	0.0		0.001	False		,,,				2504	0.0				p.S319W		Atlas-SNP	.											.	PTGIR	31	.	0			c.C956G						PASS	.	G	TRP/SER	405,4001	184.3+/-211.7	22,361,1820	42.0	48.0	46.0		956	0.2	0.0	19	dbSNP_125	46	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PTGIR	NM_000960.3	177	22,363,6118	CC,CG,GG		0.0233,9.192,3.1293	probably-damaging	319/387	47124742	407,12599	2203	4300	6503	SO:0001583	missense	5739	exon3			GTCTGCGAGTCTC		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"""GPCR / Class A : Prostanoid receptors"""	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.956C>G	19.37:g.47124742G>C	ENSP00000291294:p.Ser319Trp	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_000960		Missense_Mutation	SNP	ENST00000291294.2	37	CCDS12686.1	52	0.023809523809523808	49	0.09959349593495935	3	0.008287292817679558	0	0.0	0	0.0	G	13.66	2.304672	0.40795	0.09192	2.33E-4	ENSG00000160013	ENST00000291294	T	0.41065	1.01	4.39	0.217	0.15264	.	0.792252	0.10334	N	0.687165	T	0.00998	0.0033	N	0.24115	0.695	0.09310	N	1	D	0.63046	0.992	P	0.51866	0.682	T	0.03202	-1.1061	10	0.66056	D	0.02	-8.4268	6.0489	0.19775	0.5271:0.0:0.4729:0.0	rs28590598	319	P43119	PI2R_HUMAN	W	319	ENSP00000291294:S319W	ENSP00000291294:S319W	S	-	2	0	PTGIR	51816582	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.177000	0.16801	-0.057000	0.13199	-0.258000	0.10820	TCG	G|0.973;C|0.027	0.027	strong		0.647	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1		
METAP2	10988	hgsc.bcm.edu	37	12	95879734	95879734	+	Silent	SNP	C	C	T	rs2305293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:95879734C>T	ENST00000323666.5	+	4	634	c.405C>T	c.(403-405)tgC>tgT	p.C135C	METAP2_ENST00000551840.1_Silent_p.C134C|METAP2_ENST00000550777.1_Silent_p.C99C|METAP2_ENST00000546753.1_Silent_p.C112C|METAP2_ENST00000261220.9_Silent_p.C112C	NM_006838.3	NP_006829.1			methionyl aminopeptidase 2											endometrium(3)|large_intestine(2)|lung(7)|prostate(1)	13						GACAAGAATGCGAATACCCAC	0.388													C|||	184	0.0367412	0.0038	0.0317	5008	,	,		17962	0.0238		0.0716	False		,,,				2504	0.0624				p.C135C		Atlas-SNP	.											.	METAP2	28	.	0			c.C405T						PASS	.	C		66,4340	61.1+/-98.1	0,66,2137	165.0	153.0	157.0		405	1.8	1.0	12	dbSNP_100	157	584,8016	155.8+/-209.8	13,558,3729	no	coding-synonymous	METAP2	NM_006838.3		13,624,5866	TT,TC,CC		6.7907,1.498,4.9977		135/479	95879734	650,12356	2203	4300	6503	SO:0001819	synonymous_variant	10988	exon4			AGAATGCGAATAC	U13261	CCDS9052.1	12q22	2014-09-04			ENSG00000111142		3.4.11.18		16672	protein-coding gene	gene with protein product	"""Peptidase M"""	601870				7644482, 8858118	Standard	NM_006838		Approved	MNPEP, p67, MAP2	uc001tec.3	P50579	OTTHUMG00000170280	ENST00000323666.5:c.405C>T	12.37:g.95879734C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_006838		Silent	SNP	ENST00000323666.5	37	CCDS9052.1																																																																																			C|0.954;T|0.046	0.046	strong		0.388	METAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408296.1	NM_006838	
UPK2	7379	hgsc.bcm.edu	37	11	118827655	118827655	+	Missense_Mutation	SNP	G	G	T	rs3886020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118827655G>T	ENST00000264031.2	+	2	174	c.139G>T	c.(139-141)Gcc>Tcc	p.A47S	UPK2_ENST00000534788.1_3'UTR	NM_006760.3	NP_006751.1	O00526	UPK2_HUMAN	uroplakin 2	47			A -> S (in dbSNP:rs3886020).		epithelial cell differentiation (GO:0030855)|membrane organization (GO:0061024)|multicellular organismal development (GO:0007275)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)				kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.122)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.47e-05)		CCTGCTGGTTGCCTTGCCCCC	0.597											OREG0021391	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	215	0.0429313	0.1581	0.0072	5008	,	,		19091	0.0		0.001	False		,,,				2504	0.0				p.A47S		Atlas-SNP	.											.	UPK2	12	.	0			c.G139T						PASS	.	G	SER/ALA	507,3893	234.9+/-247.6	33,441,1726	103.0	88.0	93.0		139	4.6	1.0	11	dbSNP_108	93	7,8583	4.3+/-15.6	0,7,4288	yes	missense	UPK2	NM_006760.3	99	33,448,6014	TT,TG,GG		0.0815,11.5227,3.9569	probably-damaging	47/185	118827655	514,12476	2200	4295	6495	SO:0001583	missense	7379	exon2			CTGGTTGCCTTGC	Y13645	CCDS8404.1	11q23	2008-07-21				ENSG00000110375			12579	protein-coding gene	gene with protein product	"""uroplakin II"", ""uroplakin-2"""	611558				9515818, 9846985	Standard	NM_006760		Approved	UP2, UPII, MGC138598	uc001puh.3	O00526		ENST00000264031.2:c.139G>T	11.37:g.118827655G>T	ENSP00000264031:p.Ala47Ser	Somatic	82	0	0	1491	WXS	Illumina HiSeq	Phase_I	95	57	0.6	NM_006760	B0YJ92|O00457|Q53YV0	Missense_Mutation	SNP	ENST00000264031.2	37	CCDS8404.1	81	0.03708791208791209	79	0.16056910569105692	2	0.0055248618784530384	0	0.0	0	0.0	G	19.30	3.800203	0.70567	0.115227	8.15E-4	ENSG00000110375	ENST00000264031	T	0.38887	1.11	5.5	4.56	0.56223	.	0.129460	0.35235	N	0.003349	T	0.00241	0.0007	L	0.53249	1.67	0.29043	N	0.884952	P	0.51240	0.943	P	0.52066	0.689	T	0.00071	-1.2131	10	0.36615	T	0.2	-9.9761	12.1032	0.53796	0.0:0.1729:0.8271:0.0	rs3886020	47	O00526	UPK2_HUMAN	S	47	ENSP00000264031:A47S	ENSP00000264031:A47S	A	+	1	0	UPK2	118332865	1.000000	0.71417	0.987000	0.45799	0.986000	0.74619	3.281000	0.51685	1.258000	0.44101	0.655000	0.94253	GCC	A|0.000;C|0.008	.	strong		0.597	UPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389311.1	NM_006760	
IFNA10	3446	hgsc.bcm.edu	37	9	21206919	21206919	+	Missense_Mutation	SNP	G	G	C	rs28368144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21206919G>C	ENST00000357374.2	-	1	223	c.178C>G	c.(178-180)Cga>Gga	p.R60G		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	60					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)	p.R60*(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		TGGGGGATTCGGAAATCATGT	0.522													c|||	200	0.0399361	0.1021	0.0231	5008	,	,		19534	0.0		0.0427	False		,,,				2504	0.0061				p.R60G		Atlas-SNP	.											IFNA10,NS,carcinoma,0,1	IFNA10	29	1	1	Substitution - Nonsense(1)	prostate(1)	c.C178G						PASS	.	C	GLY/ARG	61,4325		9,43,2141	112.0	119.0	116.0		178	-2.3	0.0	9	dbSNP_125	116	61,8533		4,53,4240	no	missense	IFNA10	NM_002171.1	125	13,96,6381	CC,CG,GG		0.7098,1.3908,0.9399	benign	60/190	21206919	122,12858	2193	4297	6490	SO:0001583	missense	3446	exon1			GGATTCGGAAATC		CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"""Interferons"""	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.178C>G	9.37:g.21206919G>C	ENSP00000369566:p.Arg60Gly	Somatic	340	1	0.00294118		WXS	Illumina HiSeq	Phase_I	326	324	0.993865	NM_002171	Q5VV13	Missense_Mutation	SNP	ENST00000357374.2	37	CCDS6499.1	55	0.025183150183150184	27	0.054878048780487805	6	0.016574585635359115	0	0.0	22	0.029023746701846966	-	0.009	-1.832426	0.00579	0.013908	0.007098	ENSG00000186803	ENST00000357374	T	0.03272	3.99	3.65	-2.28	0.06826	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.940550	0.02074	N	0.051796	T	0.00210	0.0006	N	0.00599	-1.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43491	-0.9388	10	0.02654	T	1	.	4.9576	0.14050	0.0:0.2273:0.3:0.4727	rs28368144	60	P01566	IFN10_HUMAN	G	60	ENSP00000369566:R60G	ENSP00000369566:R60G	R	-	1	2	IFNA10	21196919	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.481000	0.02323	-0.404000	0.07610	-1.257000	0.01473	CGA	G|0.959;C|0.041	0.041	strong		0.522	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171	
TMPRSS12	283471	hgsc.bcm.edu	37	12	51236802	51236802	+	Missense_Mutation	SNP	T	T	C	rs10876100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:51236802T>C	ENST00000398458.3	+	1	87	c.55T>C	c.(55-57)Tac>Cac	p.Y19H	TMPRSS12_ENST00000551456.1_Missense_Mutation_p.Y19H|RN7SL519P_ENST00000497925.2_RNA	NM_182559.2	NP_872365	Q86WS5	TMPSC_HUMAN	transmembrane (C-terminal) protease, serine 12	19			Y -> H (in dbSNP:rs10876100).			integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	18						CTCTCACTTATACTCAGACCA	0.652													T|||	1497	0.298922	0.3328	0.2709	5008	,	,		14242	0.4038		0.2207	False		,,,				2504	0.2454				p.Y19H		Atlas-SNP	.											.	TMPRSS12	33	.	0			c.T55C						PASS	.	T	HIS/TYR	1296,2708		208,880,914	29.0	30.0	30.0		55	1.1	0.0	12	dbSNP_120	30	1798,6492		209,1380,2556	yes	missense	TMPRSS12	NM_182559.2	83	417,2260,3470	CC,CT,TT		21.6888,32.3676,25.1667	benign	19/349	51236802	3094,9200	2002	4145	6147	SO:0001583	missense	283471	exon1			CACTTATACTCAG	BC048112	CCDS44881.1	12q13.12	2014-08-12	2010-04-21		ENSG00000186452	ENSG00000186452		"""Serine peptidases / Transmembrane"""	28779	protein-coding gene	gene with protein product			"""transmembrane protease, serine 12"""				Standard	NM_182559		Approved	MGC57341, CT151	uc001rwx.4	Q86WS5	OTTHUMG00000169483	ENST00000398458.3:c.55T>C	12.37:g.51236802T>C	ENSP00000381476:p.Tyr19His	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_182559	B9ZVX2	Missense_Mutation	SNP	ENST00000398458.3	37	CCDS44881.1	625	0.28617216117216115	163	0.3313008130081301	100	0.27624309392265195	212	0.3706293706293706	150	0.19788918205804748	T	4.132	0.022751	0.08006	0.323676	0.216888	ENSG00000186452	ENST00000551456;ENST00000398458	D;D	0.90133	-2.62;-2.53	3.44	1.08	0.20341	.	1.518320	0.04643	N	0.405589	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	0.04128	-1.0975	9	0.16896	T	0.51	0.5913	6.9674	0.24631	0.0:0.2249:0.0:0.7751	rs10876100;rs52803962;rs10876100	19;19	F8WBX2;Q86WS5	.;TMPSC_HUMAN	H	19	ENSP00000447259:Y19H;ENSP00000381476:Y19H	ENSP00000381476:Y19H	Y	+	1	0	TMPRSS12	49523069	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.077000	0.11394	-0.057000	0.13199	-1.777000	0.00654	TAC	T|0.715;C|0.285	0.285	strong		0.652	TMPRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404289.1	NM_182559	
ZNF224	7767	hgsc.bcm.edu	37	19	44611957	44611957	+	Silent	SNP	T	T	C	rs3746322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	127	72	0.566929	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	
SOWAHC	65124	hgsc.bcm.edu	37	2	110372688	110372688	+	Missense_Mutation	SNP	C	C	G	rs72938294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:110372688C>G	ENST00000356454.3	+	1	778	c.622C>G	c.(622-624)Ctg>Gtg	p.L208V	SEPT10_ENST00000356688.4_5'Flank|SEPT10_ENST00000545389.1_5'Flank|SEPT10_ENST00000397712.2_5'Flank|SEPT10_ENST00000397714.2_5'Flank|SEPT10_ENST00000334001.6_5'Flank|SEPT10_ENST00000415095.1_5'Flank|SEPT10_ENST00000437928.1_5'Flank	NM_023016.3	NP_075392.2	Q53LP3	SWAHC_HUMAN	sosondowah ankyrin repeat domain family member C	208																	CCTCCGTGACCTGGTGATGGG	0.736													C|||	95	0.0189696	0.0688	0.0058	5008	,	,		11693	0.0		0.0	False		,,,				2504	0.0				p.L208V		Atlas-SNP	.											.	.	.	.	0			c.C622G						PASS	.	C	VAL/LEU	168,3274		1,166,1554	8.0	9.0	9.0		622	1.7	0.0	2	dbSNP_130	9	3,6469		0,3,3233	yes	missense	ANKRD57	NM_023016.3	32	1,169,4787	GG,GC,CC		0.0464,4.8809,1.7248	possibly-damaging	208/526	110372688	171,9743	1721	3236	4957	SO:0001583	missense	65124	exon1			CGTGACCTGGTGA	AK023346	CCDS33270.1	2q13	2013-01-10	2012-01-12	2012-01-12	ENSG00000198142	ENSG00000198142		"""Ankyrin repeat domain containing"""	26149	protein-coding gene	gene with protein product			"""ankyrin repeat domain 57"""	C2orf26, ANKRD57		22234889	Standard	NM_023016		Approved	FLJ21870	uc002tfb.3	Q53LP3	OTTHUMG00000153219	ENST00000356454.3:c.622C>G	2.37:g.110372688C>G	ENSP00000365830:p.Leu208Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_023016	Q8NE15|Q9H6U1	Missense_Mutation	SNP	ENST00000356454.3	37	CCDS33270.1	36	0.016483516483516484	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	0.725	-0.782051	0.02907	0.048809	4.64E-4	ENSG00000198142	ENST00000356454	T	0.26373	1.74	3.58	1.66	0.24008	.	1.034310	0.07796	N	0.955796	T	0.01661	0.0053	N	0.22421	0.69	0.09310	N	1	B	0.22003	0.063	B	0.22386	0.039	T	0.27971	-1.0058	10	0.38643	T	0.18	-1.0053	4.8489	0.13528	0.1515:0.615:0.147:0.0865	.	208	Q53LP3	ANR57_HUMAN	V	208	ENSP00000365830:L208V	ENSP00000365830:L208V	L	+	1	2	ANKRD57	109729977	0.000000	0.05858	0.037000	0.18230	0.225000	0.24961	0.616000	0.24344	0.273000	0.22049	0.462000	0.41574	CTG	C|0.983;G|0.017	0.017	strong		0.736	SOWAHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330168.1	NM_023016	
UCP3	7352	hgsc.bcm.edu	37	11	73717263	73717263	+	Silent	SNP	G	G	A	rs2229706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73717263G>A	ENST00000314032.4	-	3	840	c.288C>T	c.(286-288)atC>atT	p.I96I	UCP3_ENST00000348534.4_Silent_p.I96I|UCP3_ENST00000426995.2_Silent_p.I96I	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	96					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)					CATAGAGGCCGATGCGGATGG	0.627													G|||	34	0.00678914	0.0242	0.0029	5008	,	,		18530	0.0		0.0	False		,,,				2504	0.0				p.I96I		Atlas-SNP	.											.	UCP3	31	.	0			c.C288T						PASS	.	G	,	102,4298	80.9+/-119.3	1,100,2099	44.0	43.0	43.0		288,288	-4.0	1.0	11	dbSNP_98	43	1,8585	1.2+/-3.3	0,1,4292	no	coding-synonymous,coding-synonymous	UCP3	NM_003356.3,NM_022803.2	,	1,101,6391	AA,AG,GG		0.0116,2.3182,0.7932	,	96/313,96/276	73717263	103,12883	2200	4293	6493	SO:0001819	synonymous_variant	7352	exon3			GAGGCCGATGCGG	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.288C>T	11.37:g.73717263G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_003356	O60475|Q96HL3	Silent	SNP	ENST00000314032.4	37	CCDS8229.1																																																																																			G|0.991;A|0.009	0.009	strong		0.627	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356	
KIAA0226L	80183	hgsc.bcm.edu	37	13	46946157	46946157	+	Missense_Mutation	SNP	C	C	T	rs1408184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:46946157C>T	ENST00000429979.1	-	3	1058	c.454G>A	c.(454-456)Ggg>Agg	p.G152R	KIAA0226L_ENST00000409879.2_Intron|KIAA0226L_ENST00000378797.2_Missense_Mutation_p.G152R|KIAA0226L_ENST00000378787.3_Missense_Mutation_p.G152R|KIAA0226L_ENST00000534925.1_Missense_Mutation_p.G17R|KIAA0226L_ENST00000480935.1_5'Flank|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.G152R|KIAA0226L_ENST00000378781.3_Missense_Mutation_p.G152R|KIAA0226L_ENST00000378784.4_Missense_Mutation_p.G85R|RNU2-6P_ENST00000411404.1_RNA|KIAA0226L_ENST00000322896.6_Intron	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	152			G -> R (in dbSNP:rs1408184). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						GCCAAAATCCCAGGGCTTGTG	0.512													T|||	2261	0.451478	0.5295	0.4121	5008	,	,		20853	0.5923		0.3469	False		,,,				2504	0.3364				p.G152R		Atlas-SNP	.											.	KIAA0226L	63	.	0			c.G454A						PASS	.	T	ARG/GLY	2128,2278	599.7+/-389.3	523,1082,598	69.0	68.0	68.0		454	1.0	0.0	13	dbSNP_88	68	2817,5783	675.5+/-403.2	456,1905,1939	yes	missense	KIAA0226L	NM_025113.2	125	979,2987,2537	TT,TC,CC		32.7558,48.2978,38.0209	benign	152/663	46946157	4945,8061	2203	4300	6503	SO:0001583	missense	80183	exon3			AAATCCCAGGGCT	AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 18"""	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.454G>A	13.37:g.46946157C>T	ENSP00000396935:p.Gly152Arg	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	172	88	0.511628	NM_025113	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Missense_Mutation	SNP	ENST00000429979.1	37	CCDS31970.2	1031	0.47206959706959706	280	0.5691056910569106	152	0.4198895027624309	341	0.5961538461538461	258	0.3403693931398417	T	7.723	0.697533	0.15106	0.482978	0.327558	ENSG00000102445	ENST00000378781;ENST00000429979;ENST00000378797;ENST00000378784;ENST00000389908;ENST00000378787;ENST00000534925;ENST00000417405;ENST00000439642	T;T;T;T;T;T;T;T;T	0.41758	0.99;1.02;0.99;1.01;1.02;0.99;1.03;1.0;0.99	5.83	0.984	0.19773	.	0.718736	0.13469	N	0.385568	T	0.00012	0.0000	N	0.00926	-1.1	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	0.44636	-0.9315	9	0.08837	T	0.75	-2.1112	8.5131	0.33229	0.0:0.404:0.0:0.596	rs1408184;rs3742267;rs17857288;rs52811841;rs57945176;rs1408184	152;152;152;85;152	E7EMA2;Q9H714-1;Q9H714;Q9H714-3;Q9H714-4	.;.;K226L_HUMAN;.;.	R	152;152;152;85;152;152;17;17;152	ENSP00000368057:G152R;ENSP00000396935:G152R;ENSP00000368074:G152R;ENSP00000368061:G85R;ENSP00000374558:G152R;ENSP00000368064:G152R;ENSP00000437501:G17R;ENSP00000402357:G17R;ENSP00000414579:G152R	ENSP00000368057:G152R	G	-	1	0	KIAA0226L	45844158	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	-0.213000	0.09305	0.153000	0.19213	-0.254000	0.11334	GGG	T|0.432;G|0.002	0.432	strong		0.512	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113	
DPY19L4	286148	hgsc.bcm.edu	37	8	95746883	95746883	+	Silent	SNP	G	G	A	rs113391412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:95746883G>A	ENST00000414645.2	+	3	252	c.153G>A	c.(151-153)aaG>aaA	p.K51K		NM_181787.2	NP_861452.2	Q7Z388	D19L4_HUMAN	dpy-19-like 4 (C. elegans)	51						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	21	Breast(36;3.85e-06)					GCTTTGCAAAGATTTTCATTG	0.348													G|||	49	0.00978435	0.0363	0.0014	5008	,	,		19614	0.0		0.0	False		,,,				2504	0.0				p.K51K		Atlas-SNP	.											.	DPY19L4	60	.	0			c.G153A						PASS	.	G		136,4270	93.9+/-132.6	1,134,2068	89.0	84.0	85.0		153	4.2	1.0	8	dbSNP_132	85	0,8600		0,0,4300	no	coding-synonymous	DPY19L4	NM_181787.2		1,134,6368	AA,AG,GG		0.0,3.0867,1.0457		51/724	95746883	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	286148	exon3			TGCAAAGATTTTC		CCDS34924.1	8q22.1	2006-11-24			ENSG00000156162	ENSG00000156162			27829	protein-coding gene	gene with protein product		613895					Standard	NM_181787		Approved		uc003ygx.2	Q7Z388	OTTHUMG00000164589	ENST00000414645.2:c.153G>A	8.37:g.95746883G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	114	67	0.587719	NM_181787	Q6ZW32|Q6ZW42|Q7Z329	Silent	SNP	ENST00000414645.2	37	CCDS34924.1																																																																																			G|0.988;A|0.012	0.012	strong		0.348	DPY19L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379339.1	NM_181787	
LRRC73	221424	hgsc.bcm.edu	37	6	43475195	43475195	+	Splice_Site	SNP	G	G	A	rs61746927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43475195G>A	ENST00000372441.1	-	5	1779	c.879C>T	c.(877-879)agC>agT	p.S293S		NM_001012974.1	NP_001012992.1	Q5JTD7	LRC73_HUMAN	leucine rich repeat containing 73	293																	GGTTCTTACCGCTGGGGCACA	0.632													G|||	74	0.0147764	0.0469	0.0144	5008	,	,		18063	0.0		0.002	False		,,,				2504	0.0				p.S293S		Atlas-SNP	.											.	.	.	.	0			c.C879T						PASS	.	G		237,4169	134.9+/-171.1	9,219,1975	33.0	38.0	36.0		879	-1.7	0.9	6	dbSNP_129	36	4,8596	3.7+/-12.6	0,4,4296	yes	coding-synonymous-near-splice	C6orf154	NM_001012974.1		9,223,6271	AA,AG,GG		0.0465,5.379,1.853		293/317	43475195	241,12765	2203	4300	6503	SO:0001630	splice_region_variant	221424	exon5			CTTACCGCTGGGG		CCDS34456.1	6p21.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000204052	ENSG00000204052			21375	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 154"""	C6orf154			Standard	NM_001012974		Approved	dJ337H4.2	uc003ovk.2	Q5JTD7	OTTHUMG00000014737	ENST00000372441.1:c.880+1C>T	6.37:g.43475195G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_001012974		Silent	SNP	ENST00000372441.1	37	CCDS34456.1																																																																																			G|0.980;A|0.020	0.020	strong		0.632	LRRC73-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040635.1	NM_001012974	Silent
PER3	8863	hgsc.bcm.edu	37	1	7880585	7880585	+	Silent	SNP	A	A	T	rs17031601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:7880585A>T	ENST00000361923.2	+	15	1993	c.1818A>T	c.(1816-1818)atA>atT	p.I606I	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Silent_p.I614I	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	606	CSNK1E binding domain. {ECO:0000250}.				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)		GACGGTCCATAGACACAGGAG	0.507													A|||	67	0.0133786	0.0477	0.0058	5008	,	,		18040	0.0		0.0	False		,,,				2504	0.0				p.I606I		Atlas-SNP	.											.	PER3	95	.	0			c.A1818T						PASS	.	A		174,4232	115.4+/-153.4	3,168,2032	79.0	65.0	70.0		1818	-0.2	0.0	1	dbSNP_123	70	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PER3	NM_016831.1		3,171,6329	TT,TA,AA		0.0349,3.9492,1.3609		606/1202	7880585	177,12829	2203	4300	6503	SO:0001819	synonymous_variant	8863	exon15			GTCCATAGACACA	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.1818A>T	1.37:g.7880585A>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	213	113	0.530516	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			A|0.985;T|0.015	0.015	strong		0.507	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
MARVELD2	153562	hgsc.bcm.edu	37	5	68715576	68715576	+	Missense_Mutation	SNP	G	G	A	rs140764671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68715576G>A	ENST00000325631.5	+	2	438	c.364G>A	c.(364-366)Gca>Aca	p.A122T	MARVELD2_ENST00000413223.2_Missense_Mutation_p.A122T	NM_001038603.2|NM_001244734.1	NP_001033692.2|NP_001231663.1	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	122					cell-cell junction organization (GO:0045216)|establishment of endothelial barrier (GO:0061028)|sensory perception of sound (GO:0007605)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(4)|skin(1)|urinary_tract(1)	15		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		AGCCTCTCCAGCAAGACCAAA	0.532													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		18849	0.0		0.0	False		,,,				2504	0.0				p.A122T		Atlas-SNP	.											.	MARVELD2	49	.	0			c.G364A						PASS	.	G	THR/ALA	75,4331	65.3+/-102.7	1,73,2129	53.0	54.0	54.0		364	-0.0	0.0	5	dbSNP_134	54	0,8600		0,0,4300	yes	missense	MARVELD2	NM_001038603.2	58	1,73,6429	AA,AG,GG		0.0,1.7022,0.5767	benign	122/559	68715576	75,12931	2203	4300	6503	SO:0001583	missense	153562	exon2			TCTCCAGCAAGAC	AK055094	CCDS34175.1, CCDS58956.1	5q13.1	2007-05-01	2004-07-12	2004-07-14	ENSG00000152939	ENSG00000152939			26401	protein-coding gene	gene with protein product	"""tricellulin"""	610572	"""MARVEL (membrane-associating) domain containing 2"", ""deafness, autosomal recessive 49"""	MRVLDC2, DFNB49		17186462	Standard	NM_001038603		Approved	FLJ30532, TRIC	uc003jwq.3	Q8N4S9	OTTHUMG00000162512	ENST00000325631.5:c.364G>A	5.37:g.68715576G>A	ENSP00000323264:p.Ala122Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_001244734	A1BQX0|A1BQX1|A8KA97|Q96NM9	Missense_Mutation	SNP	ENST00000325631.5	37	CCDS34175.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	2.825	-0.243931	0.05906	0.017022	0.0	ENSG00000152939	ENST00000325631;ENST00000282886;ENST00000454295;ENST00000515844;ENST00000512803;ENST00000436532;ENST00000413223	T;T;T;T;T;T	0.47869	1.48;0.9;0.83;1.48;1.45;1.45	5.07	-0.0336	0.13900	.	0.712658	0.14187	N	0.335596	T	0.12305	0.0299	N	0.12746	0.255	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.11329	0.004;0.006;0.002	T	0.10337	-1.0634	10	0.33940	T	0.23	-24.4939	4.5252	0.11978	0.4245:0.0:0.4294:0.1461	.	122;122;122	Q8N4S9-3;Q8N4S9-2;Q8N4S9	.;.;MALD2_HUMAN	T	122	ENSP00000323264:A122T;ENSP00000396244:A122T;ENSP00000421902:A122T;ENSP00000423490:A122T;ENSP00000414776:A122T;ENSP00000398922:A122T	ENSP00000282886:A122T	A	+	1	0	MARVELD2	68751332	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	-0.332000	0.07904	-0.087000	0.12528	-0.140000	0.14226	GCA	G|0.995;A|0.005	0.005	strong		0.532	MARVELD2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369583.1	NM_144724	
APP	351	hgsc.bcm.edu	37	21	27326977	27326977	+	Silent	SNP	A	A	G	rs45537238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:27326977A>G	ENST00000346798.3	-	13	1647	c.1614T>C	c.(1612-1614)taT>taC	p.Y538Y	APP_ENST00000359726.3_Silent_p.Y482Y|APP_ENST00000357903.3_Silent_p.Y519Y|APP_ENST00000440126.3_Silent_p.Y514Y|APP_ENST00000439274.2_Silent_p.Y482Y|APP_ENST00000348990.5_Silent_p.Y463Y|APP_ENST00000358918.3_Silent_p.Y538Y|APP_ENST00000448388.2_Silent_p.Y428Y|APP_ENST00000354192.3_Silent_p.Y407Y	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	538	Collagen-binding.				adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				TCATGCGCTCATAAATCACAC	0.458													G|||	124	0.0247604	0.0893	0.0072	5008	,	,		20225	0.0		0.001	False		,,,				2504	0.0				p.Y538Y		Atlas-SNP	.											.	APP	90	.	0			c.T1614C						PASS	.	G	,,,,,,,,,	332,4074	796.0+/-415.3	16,300,1887	104.0	81.0	89.0		1614,1542,1221,1446,1284,1614,1557,1389,1557,1389	-9.4	0.7	21	dbSNP_127	89	5,8595	818.8+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	APP	NM_000484.3,NM_001136016.3,NM_001136129.2,NM_001136130.2,NM_001136131.2,NM_001204301.1,NM_001204302.1,NM_001204303.1,NM_201413.2,NM_201414.2	,,,,,,,,,	16,305,6182	GG,GA,AA		0.0581,7.5352,2.5911	,,,,,,,,,	538/771,514/747,407/640,482/715,428/661,538/753,519/734,463/678,519/752,463/696	27326977	337,12669	2203	4300	6503	SO:0001819	synonymous_variant	351	exon13			GCGCTCATAAATC	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"""Endogenous ligands"""	620	protein-coding gene	gene with protein product	"""peptidase nexin-II"""	104760	"""Alzheimer disease"""	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1614T>C	21.37:g.27326977A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	153	81	0.529412	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Silent	SNP	ENST00000346798.3	37	CCDS13576.1	40	0.018315018315018316	36	0.07317073170731707	4	0.011049723756906077	0	0.0	0	0.0	G	8.620	0.891207	0.17613	0.075352	5.81E-4	ENSG00000142192	ENST00000448850	.	.	.	5.52	-9.36	0.00629	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.8727	19.7142	0.96108	0.2996:0.0:0.7004:0.0	rs45537238;rs60681122	.	.	.	R	441	.	.	X	-	1	0	APP	26248848	0.000000	0.05858	0.669000	0.29828	0.984000	0.73092	-1.770000	0.01791	-2.333000	0.00631	-1.115000	0.02055	TGA	A|0.977;G|0.023	0.023	strong		0.458	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057943	46057943	+	Silent	SNP	C	C	T	rs77446663		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057943C>T	ENST00000380095.1	+	1	671	c.609C>T	c.(607-609)tgC>tgT	p.C203C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	203	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CCACCTGCTGCGTGCCCGTCC	0.692																																					p.C203C		Atlas-SNP	.											KRTAP10-10,NS,carcinoma,+2,1	KRTAP10-10	37	1	0			c.C609T						PASS	.						97.0	100.0	99.0					21																	46057943		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CTGCTGCGTGCCC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.609C>T	21.37:g.46057943C>T		Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	456	117	0.256579	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.982;T|0.018	0.018	strong		0.692	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
PCDHA5	56143	hgsc.bcm.edu	37	5	140202418	140202418	+	Missense_Mutation	SNP	C	C	A	rs61735511	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140202418C>A	ENST00000529859.1	+	1	1058	c.1058C>A	c.(1057-1059)aCc>aAc	p.T353N	PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.T353N|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.T353N|PCDHA1_ENST00000504120.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	353	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|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)			GCCATAACCACCCTTTTCCTG	0.502													.|||	317	0.0632987	0.2322	0.013	5008	,	,		19770	0.0		0.001	False		,,,				2504	0.0				p.T353N		Atlas-SNP	.											PCDHA5_ENST00000529859,NS,carcinoma,-1,2	PCDHA5	361	2	0			c.C1058A						PASS	.	C	,,,,ASN/THR,,ASN/THR	861,3545	337.0+/-304.7	78,705,1420	87.0	80.0	83.0		,,,,1058,,1058	4.0	0.2	5	dbSNP_129	83	2,8598	2.2+/-6.3	0,2,4298	yes	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,65,,65	78,707,5718	AA,AC,CC		0.0233,19.5415,6.6354	,,,,,,	,,,,353/937,,353/817	140202418	863,12143	2203	4300	6503	SO:0001583	missense	56143	exon1			TAACCACCCTTTT	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.1058C>A	5.37:g.140202418C>A	ENSP00000436557:p.Thr353Asn	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	168	86	0.511905	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	96	0.04395604395604396	90	0.18292682926829268	6	0.016574585635359115	0	0.0	0	0.0	C	12.70	2.018078	0.35606	0.195415	2.33E-4	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.61510	0.1;0.1;0.24	3.97	3.97	0.46021	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.00073	0.0002	L	0.28400	0.85	0.35989	P	0.16346499999999997	B;B;B	0.25743	0.024;0.133;0.063	B;B;B	0.28709	0.093;0.043;0.042	T	0.16928	-1.0386	8	0.87932	D	0	.	16.4	0.83637	0.0:1.0:0.0:0.0	rs61735511	353;353;353	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	N	353	ENSP00000433416:T353N;ENSP00000436557:T353N;ENSP00000367366:T353N	ENSP00000367366:T353N	T	+	2	0	PCDHA5	140182602	1.000000	0.71417	0.240000	0.24138	0.827000	0.46813	7.800000	0.85949	1.900000	0.55004	0.655000	0.94253	ACC	C|0.940;A|0.060	0.060	strong		0.502	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
PCDH15	65217	hgsc.bcm.edu	37	10	56423968	56423968	+	Missense_Mutation	SNP	A	A	C	rs11004439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:56423968A>C	ENST00000320301.6	-	2	449	c.55T>G	c.(55-57)Tct>Gct	p.S19A	PCDH15_ENST00000395438.1_Missense_Mutation_p.S19A|PCDH15_ENST00000395430.1_Missense_Mutation_p.S19A|PCDH15_ENST00000414778.1_Missense_Mutation_p.S19A|PCDH15_ENST00000361849.3_Missense_Mutation_p.S19A|PCDH15_ENST00000395432.2_Missense_Mutation_p.S19A|PCDH15_ENST00000373957.3_Missense_Mutation_p.S19A|PCDH15_ENST00000395446.1_Missense_Mutation_p.S19A|PCDH15_ENST00000437009.1_Missense_Mutation_p.S19A|PCDH15_ENST00000395445.1_Missense_Mutation_p.S19A|PCDH15_ENST00000409834.1_5'UTR|PCDH15_ENST00000395440.1_Missense_Mutation_p.S19A|PCDH15_ENST00000373965.2_Missense_Mutation_p.S19A|PCDH15_ENST00000373955.1_Missense_Mutation_p.S19A|PCDH15_ENST00000395442.1_Missense_Mutation_p.S19A|PCDH15_ENST00000395433.1_Missense_Mutation_p.S19A	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	19			S -> A (in dbSNP:rs11004439). {ECO:0000269|PubMed:16369489, ECO:0000269|PubMed:22815625}.		equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TCAAAGAGAGAGCCCAGGATG	0.383										HNSCC(58;0.16)			A|||	866	0.172923	0.1248	0.268	5008	,	,		17077	0.1409		0.2485	False		,,,				2504	0.1258				p.S19A		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T55G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER	662,3744	279.6+/-274.9	38,586,1579	82.0	74.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	55,55,55,55,55,55,55,55,55,55,55,55	0.6	0.0	10	dbSNP_120	77	2148,6452	363.6+/-333.2	290,1568,2442	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	99,99,99,99,99,99,99,99,99,99,99,99	328,2154,4021	CC,CA,AA		24.9767,15.025,21.6054	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	19/1963,19/1958,19/1887,19/1953,19/1916,19/1936,19/1791,19/1540,19/1683,19/1678,19/1933,19/1956	56423968	2810,10196	2203	4300	6503	SO:0001583	missense	65217	exon2			AGAGAGAGCCCAG	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.55T>G	10.37:g.56423968A>C	ENSP00000322604:p.Ser19Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	455	0.20833333333333334	70	0.14227642276422764	105	0.2900552486187845	86	0.15034965034965034	194	0.2559366754617414	A	6.536	0.467173	0.12402	0.15025	0.249767	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955;ENST00000458638	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.63096	0.54;0.58;0.5;0.49;0.49;0.73;0.63;0.48;0.47;-0.02;0.11;0.48;0.48;0.51;0.61;0.93	5.8	0.635	0.17723	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.27229	0.033;0.033;0.033;0.033;0.112;0.033;0.033;0.059;0.105;0.048;0.172;0.0;0.023;0.0;0.033	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.26416	0.035;0.066;0.066;0.066;0.014;0.066;0.035;0.023;0.034;0.034;0.034;0.002;0.069;0.001;0.066	T	0.14671	-1.0464	8	0.49607	T	0.09	.	5.8385	0.18621	0.337:0.3921:0.0:0.271	rs11004439;rs17500214;rs52833921;rs61191357;rs11004439	19;19;19;19;19;19;19;19;19;19;19;19;19;19;19	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	A	19	ENSP00000363076:S19A;ENSP00000410304:S19A;ENSP00000378826:S19A;ENSP00000378832:S19A;ENSP00000378833:S19A;ENSP00000378829:S19A;ENSP00000378827:S19A;ENSP00000378820:S19A;ENSP00000354950:S19A;ENSP00000378821:S19A;ENSP00000363068:S19A;ENSP00000322604:S19A;ENSP00000378818:S19A;ENSP00000412628:S19A;ENSP00000363066:S19A;ENSP00000394465:S19A	ENSP00000322604:S19A	S	-	1	0	PCDH15	56093974	0.000000	0.05858	0.004000	0.12327	0.036000	0.12997	-0.338000	0.07842	0.451000	0.26802	-0.723000	0.03601	TCT	A|0.797;C|0.203	0.203	strong		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
GGN	199720	hgsc.bcm.edu	37	19	38876944	38876944	+	Missense_Mutation	SNP	C	C	T	rs151268424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38876944C>T	ENST00000334928.6	-	3	1090	c.958G>A	c.(958-960)Gaa>Aaa	p.E320K	GGN_ENST00000591809.1_Intron|AC005789.9_ENST00000585411.1_RNA|SPRED3_ENST00000587013.1_5'Flank	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	320	Interaction with GGNBP1. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GAGCACCCTTCGCCGTCTCCA	0.682													C|||	14	0.00279553	0.0106	0.0	5008	,	,		13386	0.0		0.0	False		,,,				2504	0.0				p.E320K		Atlas-SNP	.											.	GGN	50	.	0			c.G958A						PASS	.	C	LYS/GLU	53,4345		0,53,2146	24.0	28.0	27.0		958	3.3	1.0	19	dbSNP_134	27	0,8600		0,0,4300	yes	missense	GGN	NM_152657.3	56	0,53,6446	TT,TC,CC		0.0,1.2051,0.4078	possibly-damaging	320/653	38876944	53,12945	2199	4300	6499	SO:0001583	missense	199720	exon3			ACCCTTCGCCGTC	AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.958G>A	19.37:g.38876944C>T	ENSP00000334940:p.Glu320Lys	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	10	0.3125	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Missense_Mutation	SNP	ENST00000334928.6	37	CCDS12516.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	15.63	2.891749	0.52014	0.012051	0.0	ENSG00000179168	ENST00000334928	.	.	.	3.33	3.33	0.38152	.	0.000000	0.38005	N	0.001858	T	0.37183	0.0994	L	0.29908	0.895	0.30484	N	0.77204	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	T	0.28235	-1.0050	9	0.17369	T	0.5	-7.3092	10.004	0.41946	0.0:1.0:0.0:0.0	.	237;320	Q86UU5-2;Q86UU5	.;GGN_HUMAN	K	320	.	ENSP00000334940:E320K	E	-	1	0	GGN	43568784	0.987000	0.35691	1.000000	0.80357	0.788000	0.44548	1.158000	0.31737	1.679000	0.50963	0.462000	0.41574	GAA	C|0.996;T|0.004	0.004	strong		0.682	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657	
FAM45A	404636	hgsc.bcm.edu	37	10	120883045	120883045	+	Missense_Mutation	SNP	A	A	G	rs74157632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:120883045A>G	ENST00000361432.2	+	6	684	c.658A>G	c.(658-660)Aac>Gac	p.N220D	FAM45A_ENST00000489988.1_3'UTR|FAM45A_ENST00000535029.1_Silent_p.S182S|FAM45A_ENST00000544016.1_Missense_Mutation_p.N69D	NM_207009.2	NP_996892.1	Q8TCE6	FA45A_HUMAN	family with sequence similarity 45, member A	220										breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	14		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		CGTGCACCTCAACGCCGATGA	0.522													A|||	412	0.0822684	0.2345	0.0591	5008	,	,		17423	0.0466		0.007	False		,,,				2504	0.0072				p.N220D		Atlas-SNP	.											.	FAM45A	30	.	0			c.A658G						PASS	.	A	ASP/ASN	791,3615	316.9+/-294.8	65,661,1477	87.0	70.0	76.0		658	-6.0	0.0	10	dbSNP_130	76	56,8544	36.4+/-91.3	1,54,4245	yes	missense	FAM45A	NM_207009.2	23	66,715,5722	GG,GA,AA		0.6512,17.9528,6.5124	benign	220/358	120883045	847,12159	2203	4300	6503	SO:0001583	missense	404636	exon6			CACCTCAACGCCG	AF168713	CCDS7609.1	10q25	2008-09-04			ENSG00000119979	ENSG00000119979			31793	protein-coding gene	gene with protein product							Standard	NM_207009		Approved			Q8TCE6	OTTHUMG00000019143	ENST00000361432.2:c.658A>G	10.37:g.120883045A>G	ENSP00000354688:p.Asn220Asp	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_207009	B1AMV6|B4DDC3|D3DRC8|Q9NXW4	Missense_Mutation	SNP	ENST00000361432.2	37	CCDS7609.1	161|161	0.07371794871794872|0.07371794871794872	102|102	0.2073170731707317|0.2073170731707317	22|22	0.06077348066298342|0.06077348066298342	33|33	0.057692307692307696|0.057692307692307696	4|4	0.005277044854881266|0.005277044854881266	A|A	1.353|1.353	-0.590889|-0.590889	0.03799|0.03799	0.179528|0.179528	0.006512|0.006512	ENSG00000119979|ENSG00000119979	ENST00000361432;ENST00000544016|ENST00000546291	.|.	.|.	.|.	5.41|5.41	-5.98|-5.98	0.02220|0.02220	.|.	1.163350|.	0.05862|.	N|.	0.623246|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.001;0.001;0.001|.	T|T	0.31724|0.31724	-0.9933|-0.9933	8|5	0.11485|0.87932	T|D	0.65|0	.|.	6.6451|6.6451	0.22931|0.22931	0.2901:0.387:0.3228:0.0|0.2901:0.387:0.3228:0.0	.|.	147;69;212;220|.	B4DNL9;B4DMU4;Q8TCE6-2;Q8TCE6|.	.;.;.;FA45A_HUMAN|.	D|R	220;69|219	.|.	ENSP00000354688:N220D|ENSP00000442471:Q219R	N|Q	+|+	1|2	0|0	FAM45A|FAM45A	120873035|120873035	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.075000|0.075000	0.17131|0.17131	-0.489000|-0.489000	0.06490|0.06490	-0.952000|-0.952000	0.03649|0.03649	0.443000|0.443000	0.29094|0.29094	AAC|CAA	A|0.934;G|0.066	0.066	strong		0.522	FAM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050623.1	NM_207009	
DBH	1621	hgsc.bcm.edu	37	9	136521749	136521749	+	Silent	SNP	G	G	A	rs78516399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136521749G>A	ENST00000393056.2	+	10	1551	c.1539G>A	c.(1537-1539)caG>caA	p.Q513Q	DBH-AS1_ENST00000425189.1_RNA	NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	513					behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	GCTTCCTGCAGAAGTACTTCC	0.622													G|||	33	0.00658946	0.025	0.0	5008	,	,		17798	0.0		0.0	False		,,,				2504	0.0				p.Q513Q		Atlas-SNP	.											.	DBH	86	.	0			c.G1539A						PASS	.	G		77,4329	68.7+/-106.4	0,77,2126	47.0	44.0	45.0		1539	1.7	1.0	9	dbSNP_131	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DBH	NM_000787.3		0,78,6425	AA,AG,GG		0.0116,1.7476,0.5997		513/618	136521749	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	1621	exon10			CCTGCAGAAGTAC	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.1539G>A	9.37:g.136521749G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_000787	Q5T381|Q96AG2	Silent	SNP	ENST00000393056.2	37	CCDS6977.2																																																																																			G|0.993;A|0.007	0.007	strong		0.622	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
PROK2	60675	hgsc.bcm.edu	37	3	71821933	71821933	+	Missense_Mutation	SNP	G	G	T	rs60239864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:71821933G>T	ENST00000295619.3	-	4	340	c.332C>A	c.(331-333)cCa>cAa	p.P111Q	PROK2_ENST00000353065.3_Missense_Mutation_p.P90Q	NM_001126128.1	NP_001119600.1	Q9HC23	PROK2_HUMAN	prokineticin 2	111					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of apoptotic process (GO:0043066)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of smooth muscle contraction (GO:0045987)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	G-protein coupled receptor binding (GO:0001664)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6		Prostate(10;0.00899)		BRCA - Breast invasive adenocarcinoma(55;1.89e-05)|Epithelial(33;0.000173)|LUSC - Lung squamous cell carcinoma(21;0.00168)|Lung(16;0.00306)		GGCCAAGCCTGGCAGACATGG	0.408													G|||	33	0.00658946	0.0242	0.0014	5008	,	,		16471	0.0		0.0	False		,,,				2504	0.0				p.P111Q		Atlas-SNP	.											.	PROK2	13	.	0			c.C332A						PASS	.	G	GLN/PRO,GLN/PRO	86,4320	73.1+/-111.1	1,84,2118	79.0	85.0	83.0		332,269	5.8	1.0	3	dbSNP_129	83	0,8600		0,0,4300	yes	missense,missense	PROK2	NM_001126128.1,NM_021935.3	76,76	1,84,6418	TT,TG,GG		0.0,1.9519,0.6612	probably-damaging,probably-damaging	111/130,90/109	71821933	86,12920	2203	4300	6503	SO:0001583	missense	60675	exon4			AAGCCTGGCAGAC	AF333025	CCDS2916.1, CCDS46868.1	3p21.1	2013-02-28			ENSG00000163421	ENSG00000163421		"""Endogenous ligands"""	18455	protein-coding gene	gene with protein product	"""protein Bv8 homolog"""	607002				11054548, 11259612	Standard	NM_021935		Approved	PK2, BV8, MIT1, KAL4	uc003dpa.4	Q9HC23	OTTHUMG00000158809	ENST00000295619.3:c.332C>A	3.37:g.71821933G>T	ENSP00000295619:p.Pro111Gln	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	152	94	0.618421	NM_001126128	Q53Z79|Q6ISR0	Missense_Mutation	SNP	ENST00000295619.3	37	CCDS46868.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	27.9	4.873120	0.91664	0.019519	0.0	ENSG00000163421	ENST00000353065;ENST00000295619	T;T	0.72725	-0.68;-0.68	5.85	5.85	0.93711	Prokineticin domain (2);	0.000000	0.85682	D	0.000000	T	0.72020	0.3409	L	0.59436	1.845	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.974	T	0.77600	-0.2527	10	0.51188	T	0.08	-11.9075	18.9291	0.92558	0.0:0.0:1.0:0.0	rs60239864	111;90	Q9HC23;Q6ISR0	PROK2_HUMAN;.	Q	90;111	ENSP00000295618:P90Q;ENSP00000295619:P111Q	ENSP00000295619:P111Q	P	-	2	0	PROK2	71904623	1.000000	0.71417	0.980000	0.43619	0.999000	0.98932	8.067000	0.89488	2.773000	0.95371	0.650000	0.86243	CCA	G|0.994;T|0.006	0.006	strong		0.408	PROK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352302.1	NM_001126128	
OTOL1	131149	hgsc.bcm.edu	37	3	161221262	161221262	+	Silent	SNP	T	T	A	rs113998122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:161221262T>A	ENST00000327928.4	+	4	966	c.966T>A	c.(964-966)acT>acA	p.T322T		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	322	Collagen-like 3.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						GAGGCCCCACTGGGAAGAAGG	0.572													T|||	50	0.00998403	0.0378	0.0	5008	,	,		13649	0.0		0.0	False		,,,				2504	0.0				p.T322T		Atlas-SNP	.											.	OTOL1	63	.	0			c.T966A						PASS	.	T		116,3608		0,116,1746	30.0	30.0	30.0		966	-7.4	0.0	3	dbSNP_132	30	2,8184		0,2,4091	no	coding-synonymous	OTOL1	NM_001080440.1		0,118,5837	AA,AT,TT		0.0244,3.1149,0.9908		322/478	161221262	118,11792	1862	4093	5955	SO:0001819	synonymous_variant	131149	exon4			CCCCACTGGGAAG		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 15"""		"""otolin 1 homolog (zebrafish)"""			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.966T>A	3.37:g.161221262T>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	60	0.560748	NM_001080440		Silent	SNP	ENST00000327928.4	37	CCDS46948.1																																																																																			T|0.990;A|0.010	0.010	strong		0.572	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440	
ZNF425	155054	hgsc.bcm.edu	37	7	148801337	148801337	+	Silent	SNP	T	T	C	rs12704061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:148801337T>C	ENST00000378061.2	-	4	1758	c.1626A>G	c.(1624-1626)acA>acG	p.T542T		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	542					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			TCGTGTGCTCTGTGAGATGCG	0.637													T|||	1067	0.213059	0.3843	0.17	5008	,	,		18185	0.0923		0.2197	False		,,,				2504	0.1299				p.T542T		Atlas-SNP	.											.	ZNF425	99	.	0			c.A1626G						PASS	.	T		1543,2863	451.0+/-349.5	275,993,935	36.0	35.0	35.0		1626	-6.3	0.0	7	dbSNP_121	35	1673,6925	284.6+/-296.7	175,1323,2801	no	coding-synonymous	ZNF425	NM_001001661.2		450,2316,3736	CC,CT,TT		19.458,35.0204,24.7309		542/753	148801337	3216,9788	2203	4299	6502	SO:0001819	synonymous_variant	155054	exon4			GTGCTCTGTGAGA	AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"""Zinc fingers, C2H2-type"", ""-"""	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.1626A>G	7.37:g.148801337T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	NM_001001661	B3KPM1|Q08AG3	Silent	SNP	ENST00000378061.2	37	CCDS34773.1																																																																																			T|0.773;C|0.227	0.227	strong		0.637	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140	
CCDC168	643677	hgsc.bcm.edu	37	13	103386496	103386496	+	Silent	SNP	T	T	G	rs7988702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103386496T>G	ENST00000322527.2	-	1	2663	c.2664A>C	c.(2662-2664)ccA>ccC	p.P888P		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	888																	TATGTGACATTGGTGAAATCC	0.368													T|||	134	0.0267572	0.0976	0.0058	5008	,	,		24575	0.0		0.001	False		,,,				2504	0.0				p.P5517P		Atlas-SNP	.											.	.	.	.	0			c.A16551C						PASS	.	T		137,1247		10,117,565	160.0	130.0	139.0		16551	-0.0	0.1	13	dbSNP_116	139	4,3178		0,4,1587	no	coding-synonymous	CCDC168	NM_001146197.1		10,121,2152	GG,GT,TT		0.1257,9.8988,3.088		5517/7082	103386496	141,4425	692	1591	2283	SO:0001819	synonymous_variant	643677	exon4			TGACATTGGTGAA		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.2664A>C	13.37:g.103386496T>G		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	263	129	0.490494	NM_001146197	Q8N800	Silent	SNP	ENST00000322527.2	37																																																																																				T|0.974;G|0.026	0.026	strong		0.368	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
SYNE1	23345	hgsc.bcm.edu	37	6	152660451	152660451	+	Silent	SNP	G	G	A	rs71575926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:152660451G>A	ENST00000367255.5	-	75	12877	c.12276C>T	c.(12274-12276)ctC>ctT	p.L4092L	SYNE1_ENST00000341594.5_Silent_p.L3957L|SYNE1_ENST00000448038.1_Silent_p.L4021L|SYNE1_ENST00000423061.1_Silent_p.L4021L|SYNE1_ENST00000265368.4_Silent_p.L4092L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4092					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)		TGGAGCAAAGGAGATCTAGGT	0.413										HNSCC(10;0.0054)			G|||	367	0.0732827	0.0817	0.072	5008	,	,		19444	0.0258		0.1471	False		,,,				2504	0.0358				p.L4092L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C12276T						PASS	.	G	,	380,4026	192.6+/-218.0	22,336,1845	154.0	140.0	145.0		12063,12276	-2.6	1.0	6	dbSNP_130	145	1131,7469	233.3+/-266.6	77,977,3246	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	99,1313,5091	AA,AG,GG		13.1512,8.6246,11.6177	,	4021/8750,4092/8798	152660451	1511,11495	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon75			GCAAAGGAGATCT	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.12276C>T	6.37:g.152660451G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	41	0.650794	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																																																																																			G|0.895;A|0.105	0.105	strong		0.413	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
KANK1	23189	hgsc.bcm.edu	37	9	711396	711396	+	Missense_Mutation	SNP	C	C	G	rs28374506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:711396C>G	ENST00000382303.1	+	7	1282	c.630C>G	c.(628-630)caC>caG	p.H210Q	KANK1_ENST00000382293.3_Missense_Mutation_p.H52Q|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.H210Q	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	210			H -> Q (in dbSNP:rs28374506).		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)		CTGCCAAGCACCAGCTTCAGA	0.572													C|||	568	0.113419	0.3404	0.0432	5008	,	,		19957	0.0079		0.0159	False		,,,				2504	0.0654				p.H210Q		Atlas-SNP	.											.	KANK1	231	.	0			c.C630G						PASS	.	C	GLN/HIS,GLN/HIS	1282,3124	437.0+/-344.8	194,894,1115	67.0	64.0	65.0		630,156	0.9	0.8	9	dbSNP_125	65	59,8541	35.9+/-90.5	0,59,4241	yes	missense,missense	KANK1	NM_015158.2,NM_153186.3	24,24	194,953,5356	GG,GC,CC		0.686,29.0967,10.3106	benign,benign	210/1353,52/1195	711396	1341,11665	2203	4300	6503	SO:0001583	missense	23189	exon7			CAAGCACCAGCTT	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.630C>G	9.37:g.711396C>G	ENSP00000371740:p.His210Gln	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	146	73	0.5	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	206	0.09432234432234432	177	0.3597560975609756	18	0.049723756906077346	5	0.008741258741258742	6	0.0079155672823219	C	0.539	-0.854632	0.02630	0.290967	0.00686	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.00816	5.66;5.66;5.66	5.38	0.908	0.19326	.	0.316701	0.27223	N	0.020351	T	0.00012	0.0000	N	0.12471	0.22	0.09310	P	1.0	B;B	0.10296	0.003;0.002	B;B	0.14578	0.011;0.003	T	0.35919	-0.9769	9	0.06891	T	0.86	.	1.0739	0.01628	0.1389:0.2267:0.3055:0.3289	rs28374506;rs60319419	210;210	Q5W0W1;Q14678	.;KANK1_HUMAN	Q	210;210;210;52	ENSP00000371740:H210Q;ENSP00000371734:H210Q;ENSP00000371730:H52Q	ENSP00000346479:H210Q	H	+	3	2	KANK1	701396	0.564000	0.26602	0.797000	0.32132	0.552000	0.35366	-0.212000	0.09319	0.270000	0.21984	-0.137000	0.14449	CAC	C|0.902;G|0.098	0.098	strong		0.572	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
KIF26A	26153	hgsc.bcm.edu	37	14	104641612	104641612	+	Silent	SNP	T	T	C	rs4906422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:104641612T>C	ENST00000423312.2	+	12	2487	c.2487T>C	c.(2485-2487)ggT>ggC	p.G829G	KIF26A_ENST00000315264.7_Silent_p.G690G	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	829					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)		CCTCCAAGGGTCCCCGAGACG	0.682													C|||	1475	0.294529	0.1127	0.3545	5008	,	,		14159	0.3998		0.3022	False		,,,				2504	0.3814				p.G829G		Atlas-SNP	.											KIF26A,NS,carcinoma,0,1	KIF26A	84	1	0			c.T2487C						PASS	.	C		495,3585		34,427,1579	15.0	18.0	17.0		2487	-2.1	0.0	14	dbSNP_111	17	2411,5939		389,1633,2153	no	coding-synonymous	KIF26A	NM_015656.1		423,2060,3732	CC,CT,TT		28.8743,12.1324,23.3789		829/1883	104641612	2906,9524	2040	4175	6215	SO:0001819	synonymous_variant	26153	exon12			CAAGGGTCCCCGA	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.2487T>C	14.37:g.104641612T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			T|0.708;C|0.292	0.292	strong		0.682	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
SLC22A5	6584	hgsc.bcm.edu	37	5	131729935	131729935	+	Missense_Mutation	SNP	C	C	T	rs11568525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:131729935C>T	ENST00000245407.3	+	10	1866	c.1645C>T	c.(1645-1647)Ccc>Tcc	p.P549S	SLC22A5_ENST00000435065.2_Missense_Mutation_p.P573S	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	549			P -> S (associated with CDSP; unclassified missense variant; dbSNP:rs11568525). {ECO:0000269|PubMed:16931768, ECO:0000269|PubMed:20574985}.		carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	TCAAGAAAGGCCCACAATCCT	0.388													C|||	110	0.0219649	0.0809	0.0043	5008	,	,		21710	0.0		0.0	False		,,,				2504	0.0				p.P549S		Atlas-SNP	.											.	SLC22A5	34	.	0			c.C1645T						PASS	.	C	SER/PRO	307,4099	166.9+/-198.0	5,297,1901	124.0	117.0	119.0		1645	4.4	1.0	5	dbSNP_126	119	0,8600		0,0,4300	yes	missense	SLC22A5	NM_003060.3	74	5,297,6201	TT,TC,CC		0.0,6.9678,2.3604	benign	549/558	131729935	307,12699	2203	4300	6503	SO:0001583	missense	6584	exon10			GAAAGGCCCACAA	AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"""Solute carriers"""	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.1645C>T	5.37:g.131729935C>T	ENSP00000245407:p.Pro549Ser	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	139	55	0.395683	NM_003060	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Missense_Mutation	SNP	ENST00000245407.3	37	CCDS4154.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	C	10.62	1.402298	0.25291	0.069678	0.0	ENSG00000197375	ENST00000245407;ENST00000435065	T;T	0.72725	-0.64;-0.68	5.28	4.38	0.52667	.	0.594079	0.17842	N	0.160148	T	0.04815	0.0130	N	0.24115	0.695	0.29262	N	0.871235	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.002	T	0.04178	-1.0971	10	0.09084	T	0.74	.	10.2464	0.43343	0.0:0.9041:0.0:0.0959	rs11568525;rs45558436;rs52826155;rs57292152;rs11568525	573;549	A2Q0V1;O76082	.;S22A5_HUMAN	S	549;573	ENSP00000245407:P549S;ENSP00000402760:P573S	ENSP00000245407:P549S	P	+	1	0	SLC22A5	131757834	0.935000	0.31712	0.985000	0.45067	0.319000	0.28217	1.735000	0.38176	1.392000	0.46585	0.655000	0.94253	CCC	C|0.972;T|0.028	0.028	strong		0.388	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060	
OBSCN	84033	hgsc.bcm.edu	37	1	228473959	228473959	+	Missense_Mutation	SNP	T	T	G	rs202022683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228473959T>G	ENST00000422127.1	+	34	9229	c.9185T>G	c.(9184-9186)gTg>gGg	p.V3062G	OBSCN_ENST00000359599.6_Missense_Mutation_p.V1909G|OBSCN_ENST00000284548.11_Missense_Mutation_p.V3062G|OBSCN_ENST00000570156.2_Missense_Mutation_p.V3491G|OBSCN_ENST00000366709.4_Missense_Mutation_p.V181G|OBSCN_ENST00000366707.4_Missense_Mutation_p.V181G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3062	Ig-like 30.				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)				GGCTACCACGTGCTGACCCTG	0.662													T|||	36	0.0071885	0.0272	0.0	5008	,	,		17519	0.0		0.0	False		,,,				2504	0.0				p.V3491G		Atlas-SNP	.											OBSCN_ENST00000570156,NS,haematopoietic_neoplasm,0,4	OBSCN	2142	4	0			c.T10472G						scavenged	.	T	GLY/VAL,GLY/VAL	98,4070		1,96,1987	26.0	33.0	31.0		9185,9185	4.5	1.0	1	dbSNP_134	31	0,8434		0,0,4217	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	109,109	1,96,6204	GG,GT,TT		0.0,2.3512,0.7777	possibly-damaging,possibly-damaging	3062/7969,3062/6621	228473959	98,12504	2084	4217	6301	SO:0001583	missense	84033	exon39			ACCACGTGCTGAC	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.9185T>G	1.37:g.228473959T>G	ENSP00000409493:p.Val3062Gly	Somatic	192	2	0.0104167		WXS	Illumina HiSeq	Phase_I	204	101	0.495098	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	21.0	4.084154	0.76642	0.023512	0.0	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23	5.67	4.49	0.54785	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.638941	0.14451	N	0.318802	T	0.59555	0.2202	M	0.66939	2.045	0.39455	D	0.967471	P;D	0.54207	0.877;0.965	P;P	0.62435	0.818;0.902	T	0.66208	-0.5981	10	0.23891	T	0.37	.	6.0668	0.19868	0.1444:0.0756:0.0:0.7801	.	3062;3062	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	3062;3062;181;181;1909	ENSP00000284548:V3062G;ENSP00000409493:V3062G;ENSP00000355668:V181G;ENSP00000355670:V181G;ENSP00000352613:V1909G	ENSP00000284548:V3062G	V	+	2	0	OBSCN	226540582	0.533000	0.26354	0.959000	0.39883	0.795000	0.44927	1.070000	0.30653	2.155000	0.67459	0.459000	0.35465	GTG	.	.	weak		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
INMT	11185	hgsc.bcm.edu	37	7	30795412	30795412	+	Missense_Mutation	SNP	A	A	G	rs6970210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30795412A>G	ENST00000013222.5	+	3	753	c.737A>G	c.(736-738)aAt>aGt	p.N246S	INMT-FAM188B_ENST00000458257.1_Intron|INMT_ENST00000409539.1_Missense_Mutation_p.N245S|INMT_ENST00000484180.1_3'UTR	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	246			N -> S (in dbSNP:rs6970210).		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						TCTGTCACCAATGCTGCCAAC	0.597													A|||	207	0.0413339	0.1483	0.0159	5008	,	,		20207	0.0		0.0	False		,,,				2504	0.0				p.N246S		Atlas-SNP	.											.	INMT	38	.	0			c.A737G						PASS	.	A	SER/ASN,SER/ASN	581,3825	260.1+/-263.5	41,499,1663	105.0	101.0	102.0		734,737	-6.8	0.0	7	dbSNP_116	102	5,8595	3.7+/-12.6	0,5,4295	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	46,46	41,504,5958	GG,GA,AA		0.0581,13.1866,4.5056	benign,benign	245/263,246/264	30795412	586,12420	2203	4300	6503	SO:0001583	missense	11185	exon3			TCACCAATGCTGC		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.737A>G	7.37:g.30795412A>G	ENSP00000013222:p.Asn246Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	77	45	0.584416	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	73	0.033424908424908424	69	0.1402439024390244	4	0.011049723756906077	0	0.0	0	0.0	A	0.146	-1.096522	0.01843	0.131866	5.81E-4	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.03152	4.03;4.03	3.41	-6.82	0.01698	.	4.107550	0.00659	N	0.000590	T	0.00039	0.0001	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	0.37572	-0.9700	10	0.22109	T	0.4	-17.7793	1.9244	0.03314	0.1854:0.2999:0.3321:0.1826	rs6970210;rs52804035;rs6970210	245;246	B8ZZ69;O95050	.;INMT_HUMAN	S	246;245	ENSP00000013222:N246S;ENSP00000386961:N245S	ENSP00000013222:N246S	N	+	2	0	INMT	30761937	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.506000	0.00448	-4.223000	0.00063	-1.145000	0.01858	AAT	A|0.954;G|0.046	0.046	strong		0.597	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
FBP2	8789	hgsc.bcm.edu	37	9	97349591	97349591	+	Silent	SNP	G	G	T	rs2280301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:97349591G>T	ENST00000375337.3	-	2	397	c.331C>A	c.(331-333)Cgg>Agg	p.R111R		NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	111					carbohydrate metabolic process (GO:0005975)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(3)|lung(5)	9		Acute lymphoblastic leukemia(62;0.136)				TGACGCACCCGCTTCTCCTTG	0.522													T|||	554	0.110623	0.2579	0.049	5008	,	,		17195	0.0685		0.0437	False		,,,				2504	0.0675				p.R111R		Atlas-SNP	.											.	FBP2	26	.	0			c.C331A						PASS	.	T		1000,3406	730.0+/-410.1	108,784,1311	80.0	72.0	75.0		331	2.0	0.2	9	dbSNP_100	75	360,8240	803.3+/-407.3	8,344,3948	no	coding-synonymous	FBP2	NM_003837.2		116,1128,5259	TT,TG,GG		4.186,22.6963,10.4567		111/340	97349591	1360,11646	2203	4300	6503	SO:0001819	synonymous_variant	8789	exon2			GCACCCGCTTCTC	Y10812	CCDS6711.1	9q22.3	2012-08-13			ENSG00000130957	ENSG00000130957	3.1.3.11		3607	protein-coding gene	gene with protein product		603027				9678974	Standard	NM_003837		Approved		uc004auv.3	O00757	OTTHUMG00000020269	ENST00000375337.3:c.331C>A	9.37:g.97349591G>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	90	55	0.611111	NM_003837	Q17R39|Q6FI53	Silent	SNP	ENST00000375337.3	37	CCDS6711.1																																																																																			G|0.890;T|0.110	0.110	strong		0.522	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837	
TBC1D10A	83874	hgsc.bcm.edu	37	22	30700607	30700607	+	Silent	SNP	T	T	G	rs4823089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30700607T>G	ENST00000215790.7	-	2	386	c.222A>C	c.(220-222)gtA>gtC	p.V74V	TBC1D10A_ENST00000403362.1_5'UTR|TBC1D10A_ENST00000490449.1_5'UTR|TBC1D10A_ENST00000403477.3_Silent_p.V81V	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	74					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						CCTCCAGGGGTACTTCCTCCA	0.607													G|||	792	0.158147	0.1384	0.1571	5008	,	,		21842	0.1448		0.2535	False		,,,				2504	0.1012				p.V81V		Atlas-SNP	.											.	TBC1D10A	49	.	0			c.A243C						PASS	.	G	,	682,3724	762.1+/-413.1	57,568,1578	78.0	60.0	66.0		243,222	-1.9	1.0	22	dbSNP_111	66	2208,6392	709.0+/-405.7	288,1632,2380	no	coding-synonymous,coding-synonymous	TBC1D10A	NM_001204240.1,NM_031937.2	,	345,2200,3958	GG,GT,TT		25.6744,15.4789,22.2205	,	81/516,74/509	30700607	2890,10116	2203	4300	6503	SO:0001819	synonymous_variant	83874	exon2			CAGGGGTACTTCC	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.222A>C	22.37:g.30700607T>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_001204240	B3KXT8|O76053|Q20WK7|Q543A2	Silent	SNP	ENST00000215790.7	37	CCDS13874.1																																																																																			T|0.801;G|0.199	0.199	strong		0.607	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937	
NIPAL4	348938	hgsc.bcm.edu	37	5	156899925	156899925	+	Missense_Mutation	SNP	C	C	T	rs61743233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156899925C>T	ENST00000311946.7	+	6	1474	c.1358C>T	c.(1357-1359)tCa>tTa	p.S453L	ADAM19_ENST00000430702.2_Intron|NIPAL4_ENST00000435489.2_Missense_Mutation_p.S434L	NM_001099287.1	NP_001092757.1	Q0D2K0	NIPA4_HUMAN	NIPA-like domain containing 4	453						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(3)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|skin(1)	22						GCCAGCACCTCATCACCAGAA	0.478													C|||	470	0.0938498	0.1936	0.0576	5008	,	,		18624	0.003		0.0557	False		,,,				2504	0.1176				p.S453L		Atlas-SNP	.											.	NIPAL4	48	.	0			c.C1358T						PASS	.	C	LEU/SER,LEU/SER	638,3160		61,516,1322	49.0	48.0	48.0		1358,1301	5.5	0.5	5	dbSNP_129	48	445,7829		11,423,3703	yes	missense,missense	NIPAL4	NM_001099287.1,NM_001172292.1	145,145	72,939,5025	TT,TC,CC		5.3783,16.7983,8.9712	benign,benign	453/467,434/448	156899925	1083,10989	1899	4137	6036	SO:0001583	missense	348938	exon6			GCACCTCATCACC	AK026158	CCDS47328.1, CCDS54944.1	5q33.3	2009-03-24	2009-03-24		ENSG00000172548	ENSG00000172548			28018	protein-coding gene	gene with protein product	"""ichthyin"""	609383	"""NIPA-like 4"""			8619474, 9110174, 15317751	Standard	NM_001099287		Approved	ICHYN	uc003lwx.4	Q0D2K0	OTTHUMG00000163497	ENST00000311946.7:c.1358C>T	5.37:g.156899925C>T	ENSP00000311687:p.Ser453Leu	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_001099287	A8S6F1|A8S6F5|A8S6F8|B4DLF3|Q0D2J8|Q0D2J9	Missense_Mutation	SNP	ENST00000311946.7	37	CCDS47328.1	177	0.08104395604395605	111	0.22560975609756098	25	0.06906077348066299	0	0.0	41	0.05408970976253298	C	10.45	1.353625	0.24512	0.167983	0.053783	ENSG00000172548	ENST00000435489;ENST00000311946	D;D	0.90732	-2.7;-2.72	5.48	5.48	0.80851	.	0.452549	0.27231	N	0.020319	T	0.00109	0.0003	N	0.08118	0	0.51482	P	7.199999999996098E-5	B;B	0.09022	0.0;0.002	B;B	0.09377	0.0;0.004	T	0.25572	-1.0128	9	0.11485	T	0.65	-7.6764	17.1975	0.86897	0.0:1.0:0.0:0.0	rs61743233	434;453	Q0D2K0-2;Q0D2K0	.;NIPA4_HUMAN	L	434;453	ENSP00000406456:S434L;ENSP00000311687:S453L	ENSP00000311687:S453L	S	+	2	0	NIPAL4	156832503	0.001000	0.12720	0.456000	0.27044	0.041000	0.13682	1.200000	0.32247	2.739000	0.93911	0.561000	0.74099	TCA	C|0.922;T|0.078	0.078	strong		0.478	NIPAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373789.1	NM_001099287	
ZNF577	84765	hgsc.bcm.edu	37	19	52376207	52376207	+	Missense_Mutation	SNP	G	G	A	rs9807842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52376207G>A	ENST00000301399.5	-	7	1401	c.1036C>T	c.(1036-1038)Cgt>Tgt	p.R346C	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.R287C|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000451628.2_Missense_Mutation_p.R287C	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	346			R -> C (in dbSNP:rs9807842).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GTGTGAGTACGCTGATGCTGA	0.438													G|||	854	0.170527	0.2943	0.1427	5008	,	,		21986	0.0437		0.0358	False		,,,				2504	0.2924				p.R346C		Atlas-SNP	.											ZNF577,NS,lymphoid_neoplasm,+1,1	ZNF577	63	1	0			c.C1036T						PASS	.	G	CYS/ARG,CYS/ARG	1178,3228		167,844,1192	70.0	67.0	68.0		859,1036	-3.2	0.2	19	dbSNP_119	68	165,8435		1,163,4136	yes	missense,missense	ZNF577	NM_001135590.1,NM_032679.2	180,180	168,1007,5328	AA,AG,GG		1.9186,26.7363,10.326	probably-damaging,probably-damaging	287/427,346/486	52376207	1343,11663	2203	4300	6503	SO:0001583	missense	84765	exon7			GAGTACGCTGATG	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1036C>T	19.37:g.52376207G>A	ENSP00000301399:p.Arg346Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	37	CCDS12842.2	219	0.10027472527472528	117	0.23780487804878048	50	0.13812154696132597	25	0.043706293706293704	27	0.03562005277044855	.	12.93	2.085599	0.36758	0.267363	0.019186	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	2.95	-3.24	0.05094	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.92169	3.28	0.51233	P	8.500000000000174E-5	D;D	0.76494	0.999;0.999	P;P	0.57960	0.83;0.797	T	0.05818	-1.0862	8	0.87932	D	0	.	6.6383	0.22895	0.0:0.4074:0.194:0.3987	rs9807842;rs52803741;rs58621483;rs9807842	346;287	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	C	346;287;287;346	ENSP00000301399:R346C;ENSP00000413476:R287C;ENSP00000389652:R287C;ENSP00000404509:R346C	ENSP00000301399:R346C	R	-	1	0	ZNF577	57068019	0.000000	0.05858	0.161000	0.22692	0.337000	0.28794	-1.030000	0.03581	-0.269000	0.09298	-0.175000	0.13238	CGT	G|0.891;A|0.109	0.109	strong		0.438	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
PLK4	10733	hgsc.bcm.edu	37	4	128808620	128808620	+	Silent	SNP	A	A	T	rs112831813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:128808620A>T	ENST00000270861.5	+	6	1702	c.1428A>T	c.(1426-1428)gtA>gtT	p.V476V	PLK4_ENST00000515069.1_Silent_p.V476V|PLK4_ENST00000507249.1_Silent_p.V442V|PLK4_ENST00000514379.1_Silent_p.V435V|PLK4_ENST00000513090.1_Silent_p.V444V	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	476					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						CTGAAACCGTACAACAGTGGT	0.363													A|||	26	0.00519169	0.0182	0.0029	5008	,	,		16496	0.0		0.0	False		,,,				2504	0.0				p.V476V	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.A1428T						PASS	.	A	,,	76,4330	65.8+/-103.3	0,76,2127	65.0	66.0	65.0		1332,1305,1428	-5.6	0.9	4	dbSNP_132	65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	PLK4	NM_001190799.1,NM_001190801.1,NM_014264.4	,,	0,77,6426	TT,TA,AA		0.0116,1.7249,0.592	,,	444/939,435/930,476/971	128808620	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	10733	exon6			AACCGTACAACAG	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"""serine/threonine kinase 18"", ""polo-like kinase 4 (Drosophila)"""	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.1428A>T	4.37:g.128808620A>T		Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	482	238	0.493776	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Silent	SNP	ENST00000270861.5	37	CCDS3735.1																																																																																			A|0.993;T|0.007	0.007	strong		0.363	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3		
MN1	4330	hgsc.bcm.edu	37	22	28193097	28193097	+	Silent	SNP	C	C	T	rs45471598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:28193097C>T	ENST00000302326.4	-	1	4389	c.3435G>A	c.(3433-3435)ccG>ccA	p.P1145P		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	1145					intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						CGTCGGGTGGCGGGGCGCCGC	0.711			T	ETV6	"""AML, meningioma"""								C|||	265	0.0529153	0.1936	0.013	5008	,	,		13060	0.0		0.0	False		,,,				2504	0.0				p.P1145P		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	MN1,colon,carcinoma,0,1	MN1	122	1	0			c.G3435A						PASS	.	C		505,3385		19,467,1459	6.0	7.0	7.0		3435	-3.9	0.0	22	dbSNP_127	7	8,8188		0,8,4090	no	coding-synonymous	MN1	NM_002430.2		19,475,5549	TT,TC,CC		0.0976,12.982,4.2446		1145/1321	28193097	513,11573	1945	4098	6043	SO:0001819	synonymous_variant	4330	exon1			GGGTGGCGGGGCG	X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"""probable tumor suppressor protein MN1"""	156100	"""meningioma chromosome region"""	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.3435G>A	22.37:g.28193097C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	37	CCDS42998.1																																																																																			C|0.962;T|0.038	0.038	strong		0.711	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
N4BP2L2	10443	hgsc.bcm.edu	37	13	33016660	33016660	+	Missense_Mutation	SNP	C	C	T	rs17077568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33016660C>T	ENST00000504114.1	-	6	2060	c.1969G>A	c.(1969-1971)Gaa>Aaa	p.E657K	N4BP2L2_ENST00000399396.3_Missense_Mutation_p.E672K|N4BP2L2_ENST00000357505.6_Missense_Mutation_p.E657K|N4BP2L2_ENST00000380121.3_5'UTR|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.E575K			Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	0					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TTAGGTTCTTCCCATCTTTTC	0.393													C|||	295	0.0589058	0.1921	0.0159	5008	,	,		19009	0.0		0.0219	False		,,,				2504	0.0082				p.E672K		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.G2014A						PASS	.	C	LYS/GLU	519,3227		31,457,1385	57.0	58.0	58.0		2014	3.4	0.0	13	dbSNP_123	58	195,8053		3,189,3932	yes	missense	N4BP2L2	NM_033111.3	56	34,646,5317	TT,TC,CC		2.3642,13.8548,5.953	probably-damaging	672/753	33016660	714,11280	1873	4124	5997	SO:0001583	missense	10443	exon7			GTTCTTCCCATCT	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"""phosphonoformate immuno-associated protein 5"""	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000504114.1:c.1969G>A	13.37:g.33016660C>T	ENSP00000427477:p.Glu657Lys	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	104	45	0.432692	NM_033111	A3KME8	Missense_Mutation	SNP	ENST00000504114.1	37		117	0.05357142857142857	99	0.20121951219512196	6	0.016574585635359115	0	0.0	12	0.0158311345646438	C	15.94	2.981485	0.53827	0.138548	0.023642	ENSG00000139617;ENSG00000139617;ENSG00000244754;ENSG00000244754;ENSG00000244754;ENSG00000244754	ENST00000380121;ENST00000503296;ENST00000504114;ENST00000357505;ENST00000399396;ENST00000446957	D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14	5.4	3.41	0.39046	.	1.298430	0.04893	N	0.449986	T	0.00356	0.0011	L	0.60455	1.87	0.80722	P	0.0	B;B;P;B;P	0.37122	0.379;0.379;0.583;0.017;0.583	B;B;B;B;B	0.28553	0.091;0.091;0.091;0.012;0.091	T	0.38520	-0.9657	9	0.62326	D	0.03	-3.9312	5.4574	0.16598	0.0:0.6064:0.1691:0.2245	rs17077568;rs52816853;rs17077568	657;672;555;575;555	B4DPY1;Q92802-3;Q96KV2;Q92802-2;Q9Y3H6	.;.;.;.;.	K	555;584;657;657;672;575	ENSP00000427477:E657K;ENSP00000350104:E657K;ENSP00000382328:E672K;ENSP00000394239:E575K	ENSP00000350104:E657K	E	-	1	0	N4BP2L2;RP11-298P3.4	31914660	0.059000	0.20769	0.007000	0.13788	0.163000	0.22366	0.591000	0.23969	1.281000	0.44480	-0.266000	0.10368	GAA	C|0.928;T|0.072	0.072	strong		0.393	N4BP2L2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000361380.1	NM_014887	
CASP10	843	hgsc.bcm.edu	37	2	202074098	202074098	+	Missense_Mutation	SNP	G	G	A	rs13010627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:202074098G>A	ENST00000272879.5	+	9	1412	c.1228G>A	c.(1228-1230)Gta>Ata	p.V410I	CASP10_ENST00000286186.6_Missense_Mutation_p.V410I|CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000492363.1_3'UTR|CASP10_ENST00000346817.5_Missense_Mutation_p.V367I|CASP10_ENST00000448480.1_Missense_Mutation_p.V367I|CASP10_ENST00000313728.7_Missense_Mutation_p.V343I	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	410			V -> I (does not interfere with apoptosis in a dominant negative manner; dbSNP:rs13010627). {ECO:0000269|PubMed:10187817, ECO:0000269|PubMed:10412980, ECO:0000269|PubMed:16446975}.		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						ACAGCCTTCCGTATCCATCGA	0.532													G|||	96	0.0191693	0.0023	0.0389	5008	,	,		17299	0.001		0.0616	False		,,,				2504	0.0031				p.V410I		Atlas-SNP	.											.	CASP10	95	.	0			c.G1228A	GRCh37	CM990325	CASP10	M	rs13010627	PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,,ILE/VAL	70,4336	64.1+/-101.4	3,64,2136	85.0	77.0	80.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1027,1099,1099,1228,,1228	2.2	0.0	2	dbSNP_121	80	567,8033	154.0+/-208.3	20,527,3753	yes	missense,missense,missense,missense,utr-3,missense	CASP10	NM_001206524.1,NM_001206542.1,NM_001230.4,NM_032974.4,NM_032976.3,NM_032977.3	29,29,29,29,,29	23,591,5889	AA,AG,GG		6.593,1.5887,4.8977	benign,benign,benign,benign,,benign	343/456,367/479,367/480,410/522,,410/523	202074098	637,12369	2203	4300	6503	SO:0001583	missense	843	exon9			CCTTCCGTATCCA	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.1228G>A	2.37:g.202074098G>A	ENSP00000272879:p.Val410Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	141	79	0.560284	NM_032977	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Missense_Mutation	SNP	ENST00000272879.5	37	CCDS2338.1	62	0.028388278388278388	0	0.0	19	0.052486187845303865	0	0.0	43	0.05672823218997362	G	12.00	1.805808	0.31961	0.015887	0.06593	ENSG00000003400	ENST00000286186;ENST00000272879;ENST00000346817;ENST00000313728;ENST00000448480	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	5.05	2.23	0.28157	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);	1.359770	0.04834	N	0.439300	T	0.02418	0.0074	L	0.47016	1.485	0.18873	A	1.96587e-05	P;D;D;D;D	0.61080	0.868;0.98;0.977;0.967;0.989	P;P;P;P;P	0.54140	0.527;0.45;0.651;0.563;0.743	T	0.07908	-1.0748	9	0.25106	T	0.35	.	7.8129	0.29241	0.2042:0.0:0.6801:0.1157	rs13010627;rs17860404;rs52822381;rs13010627	343;367;410;367;410	Q92851-6;Q92851-5;Q92851;Q92851-2;Q92851-4	.;.;CASPA_HUMAN;.;.	I	410;410;367;343;367	ENSP00000286186:V410I;ENSP00000272879:V410I;ENSP00000237865:V367I;ENSP00000314599:V343I;ENSP00000396835:V367I	ENSP00000272879:V410I	V	+	1	0	CASP10	201782343	0.122000	0.22280	0.000000	0.03702	0.000000	0.00434	1.441000	0.35035	0.195000	0.20347	-0.813000	0.03139	GTA	G|0.963;A|0.037	0.037	strong		0.532	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977	
INMT	11185	hgsc.bcm.edu	37	7	30795448	30795448	+	Missense_Mutation	SNP	G	G	A	rs6970605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30795448G>A	ENST00000013222.5	+	3	789	c.773G>A	c.(772-774)cGc>cAc	p.R258H	INMT-FAM188B_ENST00000458257.1_Intron|INMT_ENST00000409539.1_Missense_Mutation_p.R257H|INMT_ENST00000484180.1_3'UTR	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	258			R -> H (in dbSNP:rs6970605).		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						ATTGTGGCTCGCAAGAAGCCT	0.572													G|||	223	0.0445288	0.146	0.0173	5008	,	,		19539	0.0		0.0099	False		,,,				2504	0.0082				p.R258H		Atlas-SNP	.											.	INMT	38	.	0			c.G773A						PASS	.	G	HIS/ARG,HIS/ARG	577,3829	258.3+/-262.4	40,497,1666	66.0	65.0	65.0		770,773	2.5	1.0	7	dbSNP_116	65	81,8519	46.7+/-105.8	0,81,4219	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	29,29	40,578,5885	AA,AG,GG		0.9419,13.0958,5.0592	possibly-damaging,possibly-damaging	257/263,258/264	30795448	658,12348	2203	4300	6503	SO:0001583	missense	11185	exon3			TGGCTCGCAAGAA		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.773G>A	7.37:g.30795448G>A	ENSP00000013222:p.Arg258His	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	82	0.037545787545787544	68	0.13821138211382114	4	0.011049723756906077	0	0.0	10	0.013192612137203167	G	16.07	3.018941	0.54576	0.130958	0.009419	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.03860	3.78;3.78	3.41	2.51	0.30379	.	0.519428	0.18005	N	0.154767	T	0.00109	0.0003	M	0.83774	2.66	0.25613	N	0.986477	D;D	0.61080	0.989;0.989	P;P	0.52386	0.697;0.697	T	0.07868	-1.0750	10	0.72032	D	0.01	.	8.7137	0.34399	0.0:0.2336:0.7664:0.0	rs6970605;rs6970605	257;258	B8ZZ69;O95050	.;INMT_HUMAN	H	258;257	ENSP00000013222:R258H;ENSP00000386961:R257H	ENSP00000013222:R258H	R	+	2	0	INMT	30761973	0.949000	0.32298	0.952000	0.39060	0.013000	0.08279	1.069000	0.30641	0.952000	0.37798	-0.305000	0.09177	CGC	G|0.956;A|0.044	0.044	strong		0.572	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
PTPLAD1	51495	hgsc.bcm.edu	37	15	65856653	65856653	+	Silent	SNP	G	G	A	rs11539008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65856653G>A	ENST00000261875.5	+	7	799	c.633G>A	c.(631-633)acG>acA	p.T211T	PTPLAD1_ENST00000565299.1_Silent_p.T249T|PTPLAD1_ENST00000568793.1_Silent_p.T186T|PTPLAD1_ENST00000562901.1_Silent_p.T94T|PTPLAD1_ENST00000566074.1_Silent_p.T94T|PTPLAD1_ENST00000566511.1_Silent_p.T94T|PTPLAD1_ENST00000442729.2_Silent_p.T156T|PTPLAD1_ENST00000569894.1_Silent_p.T94T	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	146	0	0		WXS	Illumina HiSeq	Phase_I	163	82	0.503067	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	
KANK1	23189	hgsc.bcm.edu	37	9	712066	712066	+	Silent	SNP	A	A	C	rs34680571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:712066A>C	ENST00000382303.1	+	7	1952	c.1300A>C	c.(1300-1302)Aga>Cga	p.R434R	KANK1_ENST00000382293.3_Silent_p.R276R|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Silent_p.R434R	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	434	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)		TGTTGAGATGAGAAATTGTGG	0.512													A|||	413	0.0824681	0.2352	0.0346	5008	,	,		21248	0.0		0.0139	False		,,,				2504	0.0654				p.R434R		Atlas-SNP	.											.	KANK1	231	.	0			c.A1300C						PASS	.	A	,	893,3513	347.2+/-309.4	94,705,1404	113.0	100.0	104.0		1300,826	4.5	0.1	9	dbSNP_126	104	56,8544	34.3+/-88.2	0,56,4244	no	coding-synonymous,coding-synonymous	KANK1	NM_015158.2,NM_153186.3	,	94,761,5648	CC,CA,AA		0.6512,20.2678,7.2966	,	434/1353,276/1195	712066	949,12057	2203	4300	6503	SO:0001819	synonymous_variant	23189	exon7			GAGATGAGAAATT	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.1300A>C	9.37:g.712066A>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	128	50	0.390625	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	37	CCDS34976.1																																																																																			T|0.000;C|0.069;A|0.931	0.069	strong		0.512	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
CHD7	55636	hgsc.bcm.edu	37	8	61765560	61765560	+	Silent	SNP	G	G	A	rs2068096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:61765560G>A	ENST00000423902.2	+	31	6755	c.6276G>A	c.(6274-6276)gaG>gaA	p.E2092E	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2092					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AGTGGTGGGAGTGTGGACGGC	0.567													G|||	622	0.124201	0.357	0.0749	5008	,	,		19016	0.0149		0.0378	False		,,,				2504	0.046				p.E2092E		Atlas-SNP	.											.	CHD7	534	.	0			c.G6276A						PASS	.	G		1157,3003		160,837,1083	84.0	97.0	93.0		6276	-0.4	0.8	8	dbSNP_96	93	351,8065		12,327,3869	no	coding-synonymous	CHD7	NM_017780.3		172,1164,4952	AA,AG,GG		4.1706,27.8125,11.9911		2092/2998	61765560	1508,11068	2080	4208	6288	SO:0001819	synonymous_variant	55636	exon31			GTGGGAGTGTGGA	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.6276G>A	8.37:g.61765560G>A		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	261	132	0.505747	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	CCDS47865.1																																																																																			G|0.886;A|0.114	0.114	strong		0.567	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
ADAT3	113179	hgsc.bcm.edu	37	19	1912934	1912934	+	Silent	SNP	T	T	C	rs12984675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1912934T>C	ENST00000602400.1	+	2	1068	c.840T>C	c.(838-840)acT>acC	p.T280T	ADAT3_ENST00000329478.2_Silent_p.T296T|SCAMP4_ENST00000414057.2_Intron|SCAMP4_ENST00000316097.8_Intron|SCAMP4_ENST00000409472.1_Intron			Q96EY9	ADAT3_HUMAN	adenosine deaminase, tRNA-specific 3	280					tRNA processing (GO:0008033)		hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|pancreas(1)|skin(2)	7		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)		ACCTGTGCACTGGCTACGACC	0.726													C|||	1819	0.363219	0.4803	0.4193	5008	,	,		11860	0.4038		0.2048	False		,,,				2504	0.2863				p.T296T		Atlas-SNP	.											.	ADAT3	15	.	0			c.T888C						PASS	.	C	,	1904,2498	591.8+/-387.6	426,1052,723	57.0	52.0	54.0		,840	-6.8	0.5	19	dbSNP_121	54	1294,7292	728.8+/-406.7	102,1090,3101	no	intron,coding-synonymous	SCAMP4,ADAT3	NM_079834.2,NM_138422.1	,	528,2142,3824	CC,CT,TT		15.071,43.2531,24.6227	,	,280/352	1912934	3198,9790	2201	4293	6494	SO:0001819	synonymous_variant	113179	exon2			GTGCACTGGCTAC	BC011824	CCDS12076.1, CCDS12076.2	19p13.3	2011-05-19	2011-05-19		ENSG00000213638	ENSG00000213638			25151	protein-coding gene	gene with protein product	"""tRNA-specific adenosine deaminase 3 homolog (S. cerevisiae)"""	615302	"""adenosine deaminase, tRNA-specific 3, TAD3 homolog (S. cerevisiae)"""			12457566	Standard	NM_138422		Approved	TAD3	uc002luh.4	Q96EY9	OTTHUMG00000154591	ENST00000602400.1:c.840T>C	19.37:g.1912934T>C		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_138422		Silent	SNP	ENST00000602400.1	37																																																																																				T|0.727;C|0.273	0.273	strong		0.726	ADAT3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_138422	
DPF2	5977	hgsc.bcm.edu	37	11	65113459	65113459	+	Silent	SNP	G	G	T	rs61736579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65113459G>T	ENST00000528416.1	+	8	967	c.834G>T	c.(832-834)ggG>ggT	p.G278G	DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000415073.2_Intron|DPF2_ENST00000252268.4_Silent_p.G292G	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	278					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						TCTGCCTGGGGGACTCAAAGA	0.537													G|||	57	0.0113818	0.0295	0.0029	5008	,	,		18964	0.0149		0.001	False		,,,				2504	0.0				p.G278G		Atlas-SNP	.											.	DPF2	54	.	0			c.G834T						PASS	.	G		96,4306	78.3+/-116.7	0,96,2105	118.0	123.0	121.0		834	-7.1	0.6	11	dbSNP_129	121	2,8592	1.2+/-3.3	0,2,4295	no	coding-synonymous	DPF2	NM_006268.4		0,98,6400	TT,TG,GG		0.0233,2.1808,0.7541		278/392	65113459	98,12898	2201	4297	6498	SO:0001819	synonymous_variant	5977	exon8			CCTGGGGGACTCA	U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"""Zinc fingers, PHD-type"""	9964	protein-coding gene	gene with protein product		601671	"""requiem, apoptosis response zinc finger gene"""	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.834G>T	11.37:g.65113459G>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_006268	A8K7C9|B4DT58	Silent	SNP	ENST00000528416.1	37	CCDS8100.1	26	0.011904761904761904	19	0.03861788617886179	0	0.0	7	0.012237762237762238	0	0.0	G	12.47	1.947810	0.34377	0.021808	2.33E-4	ENSG00000133884	ENST00000531989	D	0.90504	-2.68	5.92	-7.09	0.01553	.	0.000000	0.38005	N	0.001851	T	0.61515	0.2353	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69187	-0.5211	7	0.24483	T	0.36	-20.6054	6.2509	0.20845	0.5834:0.0898:0.2361:0.0906	rs61736579	.	.	.	V	41	ENSP00000435887:G41V	ENSP00000435887:G41V	G	+	2	0	DPF2	64870035	0.000000	0.05858	0.648000	0.29521	0.864000	0.49448	-1.570000	0.02140	-1.394000	0.02077	-2.076000	0.00381	GGG	G|0.989;T|0.011	0.011	strong		0.537	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268	
CAPN14	440854	hgsc.bcm.edu	37	2	31414851	31414851	+	Missense_Mutation	SNP	T	T	C	rs7587515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31414851T>C	ENST00000403897.3	-	11	1369	c.1228A>G	c.(1228-1230)Agg>Ggg	p.R410G	CAPN14_ENST00000444918.2_Missense_Mutation_p.R410G	NM_001145122.1	NP_001138594.1	A8MX76	CAN14_HUMAN	calpain 14	410	Domain III.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|endometrium(2)|prostate(1)|skin(1)|stomach(2)	7						TTGCGGCACCTGTGCCTGGGC	0.642													T|||	546	0.109026	0.3442	0.0519	5008	,	,		17912	0.0069		0.0378	False		,,,				2504	0.0102				p.R410G		Atlas-SNP	.											.	CAPN14	36	.	0			c.A1228G						PASS	.	T	GLY/ARG	435,949		79,277,336	30.0	38.0	35.0		1228	-3.1	0.0	2	dbSNP_116	35	95,3087		3,89,1499	yes	missense	CAPN14	NM_001145122.1	125	82,366,1835	CC,CT,TT		2.9855,31.4306,11.6075	possibly-damaging	410/685	31414851	530,4036	692	1591	2283	SO:0001583	missense	440854	exon11			GGCACCTGTGCCT	AC015980	CCDS46254.1	2p23.1-p21	2013-01-10			ENSG00000214711	ENSG00000214711		"""EF-hand domain containing"""	16664	protein-coding gene	gene with protein product		610229				11675017	Standard	NM_001145122		Approved		uc010yms.2	A8MX76	OTTHUMG00000152039	ENST00000403897.3:c.1228A>G	2.37:g.31414851T>C	ENSP00000385247:p.Arg410Gly	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	136	59	0.433824	NM_001145122	B3KRU9	Missense_Mutation	SNP	ENST00000403897.3	37	CCDS46254.1	205	0.09386446886446886	147	0.29878048780487804	24	0.06629834254143646	6	0.01048951048951049	28	0.036939313984168866	T	7.816	0.716792	0.15306	0.314306	0.029855	ENSG00000214711	ENST00000444918;ENST00000403897	D;D	0.87809	-2.3;-2.3	3.7	-3.09	0.05331	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.137517	0.44285	U	0.000474	T	0.00012	0.0000	M	0.80422	2.495	0.80722	P	0.0	P;P	0.49185	0.92;0.804	B;B	0.39217	0.294;0.194	T	0.08249	-1.0731	9	0.52906	T	0.07	.	7.4929	0.27473	0.0:0.0798:0.4016:0.5186	rs7587515;rs57833255;rs7587515	410;234	A8MX76;A8MX76-2	CAN14_HUMAN;.	G	410	ENSP00000398670:R410G;ENSP00000385247:R410G	ENSP00000385247:R410G	R	-	1	2	CAPN14	31268355	0.185000	0.23213	0.006000	0.13384	0.021000	0.10359	0.511000	0.22739	-0.314000	0.08716	-0.250000	0.11733	AGG	T|0.900;C|0.100	0.100	strong		0.642	CAPN14-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325010.1	NM_001145122	
SMAD6	4091	hgsc.bcm.edu	37	15	67073549	67073549	+	Silent	SNP	C	C	T	rs12591946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:67073549C>T	ENST00000288840.5	+	4	2198	c.1167C>T	c.(1165-1167)ttC>ttT	p.F389F	SMAD6_ENST00000338426.4_Silent_p.F128F	NM_005585.4	NP_005576.3	O43541	SMAD6_HUMAN	SMAD family member 6	389	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				BMP signaling pathway (GO:0030509)|cell-substrate adhesion (GO:0031589)|fat cell differentiation (GO:0045444)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|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)|response to estrogen (GO:0043627)|response to laminar fluid shear stress (GO:0034616)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity (GO:0030617)|type I activin receptor binding (GO:0070698)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			lung(1)|skin(1)	2						AGATCGGCTTCGGCATCCTGC	0.687													C|||	207	0.0413339	0.0015	0.0	5008	,	,		13948	0.1766		0.0	False		,,,				2504	0.0276				p.F389F	Esophageal Squamous(179;72 2004 22333 39628 47290)	Atlas-SNP	.											.	SMAD6	14	.	0			c.C1167T						PASS	.	C	,	15,4385		0,15,2185	29.0	28.0	29.0		384,1167	2.7	1.0	15	dbSNP_120	29	2,8594		0,2,4296	no	coding-synonymous,coding-synonymous	SMAD6	NM_001142861.2,NM_005585.4	,	0,17,6481	TT,TC,CC		0.0233,0.3409,0.1308	,	128/236,389/497	67073549	17,12979	2200	4298	6498	SO:0001819	synonymous_variant	4091	exon4			CGGCTTCGGCATC	BC012986	CCDS10221.1	15q22.31	2014-09-11	2006-11-06	2004-05-26	ENSG00000137834	ENSG00000137834		"""SMADs"""	6772	protein-coding gene	gene with protein product		602931	"""MAD, mothers against decapentaplegic homolog 6 (Drosophila)"", ""SMAD, mothers against DPP homolog 6 (Drosophila)"""	MADH7, MADH6		9256479	Standard	NR_027654		Approved	HsT17432	uc002aqf.3	O43541	OTTHUMG00000133218	ENST00000288840.5:c.1167C>T	15.37:g.67073549C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_005585	A9J6M5|O43654|Q15799|Q7Z7L4|Q96E31|Q9UKZ3	Silent	SNP	ENST00000288840.5	37	CCDS10221.1																																																																																			C|0.982;T|0.018	0.018	strong		0.687	SMAD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256953.2	NM_005585	
MUC4	4585	hgsc.bcm.edu	37	3	195508367	195508367	+	Missense_Mutation	SNP	G	G	A	rs55917029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508367G>A	ENST00000463781.3	-	2	10543	c.10084C>T	c.(10084-10086)Cct>Tct	p.P3362S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P3362S	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)		CCGGTGACAGGAAGAGGGGTG	0.592													.|||	191	0.038139	0.0998	0.0101	5008	,	,		17073	0.002		0.0179	False		,,,				2504	0.0327				p.P3362S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C10084T						PASS	.						38.0	30.0	33.0					3																	195508367		690	1586	2276	SO:0001583	missense	4585	exon2			TGACAGGAAGAGG	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.10084C>T	3.37:g.195508367G>A	ENSP00000417498:p.Pro3362Ser	Somatic	453	0	0		WXS	Illumina HiSeq	Phase_I	387	85	0.219638	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	8.179	0.793377	0.16327	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.49;1.41	1.03	1.03	0.20045	.	.	.	.	.	T	0.20901	0.0503	N	0.19112	0.55	0.09310	N	1	P	0.51933	0.949	P	0.45998	0.5	T	0.11743	-1.0575	8	.	.	.	.	7.5882	0.28006	0.0:0.0:1.0:0.0	.	3234	E7ESK3	.	S	3362	ENSP00000417498:P3362S;ENSP00000420243:P3362S	.	P	-	1	0	MUC4	196993146	0.105000	0.21958	0.003000	0.11579	0.015000	0.08874	0.368000	0.20399	0.494000	0.27859	0.089000	0.15464	CCT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF98	148198	hgsc.bcm.edu	37	19	22575504	22575504	+	Missense_Mutation	SNP	C	C	G	rs116270361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22575504C>G	ENST00000357774.5	-	4	654	c.533G>C	c.(532-534)gGa>gCa	p.G178A		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	178					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)				AGATTTCTTTCCAGTATGTCC	0.303													c|||	102	0.0203674	0.0741	0.0058	5008	,	,		17746	0.0		0.0	False		,,,				2504	0.0				p.G178A		Atlas-SNP	.											.	ZNF98	230	.	0			c.G533C						PASS	.	C	ALA/GLY	286,3752		6,274,1739	26.0	27.0	27.0		533	-1.8	0.0	19	dbSNP_132	27	2,8428		0,2,4213	no	missense	ZNF98	NM_001098626.1	60	6,276,5952	GG,GC,CC		0.0237,7.0827,2.3099	possibly-damaging	178/573	22575504	288,12180	2019	4215	6234	SO:0001583	missense	148198	exon4			TTCTTTCCAGTAT		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.533G>C	19.37:g.22575504C>G	ENSP00000350418:p.Gly178Ala	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	287	152	0.529617	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	42	0.019230769230769232	40	0.08130081300813008	2	0.0055248618784530384	0	0.0	0	0.0	.	12.41	1.928642	0.34002	0.070827	2.37E-4	ENSG00000197360	ENST00000357774	T	0.35236	1.32	1.28	-1.83	0.07833	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02767	0.0083	L	0.52905	1.665	0.30794	N	0.740644	P	0.45827	0.867	P	0.55713	0.782	T	0.22103	-1.0226	9	0.66056	D	0.02	.	4.2412	0.10648	0.2247:0.6036:0.0:0.1717	.	178	A6NK75	ZNF98_HUMAN	A	178	ENSP00000350418:G178A	ENSP00000350418:G178A	G	-	2	0	ZNF98	22367344	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.168000	0.16622	-0.223000	0.09943	0.305000	0.20034	GGA	C|0.976;G|0.024	0.024	strong		0.303	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
KALRN	8997	hgsc.bcm.edu	37	3	124174062	124174062	+	Silent	SNP	C	C	T	rs61747979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124174062C>T	ENST00000240874.3	+	22	3742	c.3585C>T	c.(3583-3585)gcC>gcT	p.A1195A	KALRN_ENST00000460856.1_Silent_p.A1186A|KALRN_ENST00000360013.3_Silent_p.A1195A	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1195					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.A1195A(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						TTCAGCTGGCCGATAGCTTTG	0.483													C|||	160	0.0319489	0.1172	0.0072	5008	,	,		21547	0.0		0.0	False		,,,				2504	0.0				p.A1195A		Atlas-SNP	.											.	KALRN	556	.	2	Substitution - coding silent(2)	lung(2)	c.C3585T						PASS	.	C	,	413,3993	203.5+/-225.9	25,363,1815	118.0	109.0	112.0		3585,3585	-9.4	0.0	3	dbSNP_129	112	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	25,366,6112	TT,TC,CC		0.0349,9.3736,3.1985	,	1195/2987,1195/1664	124174062	416,12590	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon22			GCTGGCCGATAGC	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.3585C>T	3.37:g.124174062C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	68	0.031135531135531136	66	0.13414634146341464	2	0.0055248618784530384	0	0.0	0	0.0	C	6.766	0.510205	0.12883	0.093736	3.49E-4	ENSG00000160145	ENST00000354186	.	.	.	4.71	-9.42	0.00610	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.9999999999999124	.	.	.	.	.	.	T	0.01925	-1.1246	3	.	.	.	.	3.8289	0.08865	0.2842:0.1245:0.0655:0.5257	rs61747979	.	.	.	L	1164	.	.	P	+	2	0	KALRN	125656752	0.000000	0.05858	0.027000	0.17364	0.936000	0.57629	-4.076000	0.00300	-4.614000	0.00039	-1.741000	0.00685	CCG	C|0.969;T|0.031	0.031	strong		0.483	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
ADARB2	105	hgsc.bcm.edu	37	10	1405835	1405835	+	Silent	SNP	G	G	A	rs35398040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:1405835G>A	ENST00000381312.1	-	3	790	c.465C>T	c.(463-465)gtC>gtT	p.V155V	RP11-398B16.2_ENST00000432987.1_RNA	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	155	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CTACCGCGAAGACCGGGGCAT	0.692													g|||	72	0.014377	0.0522	0.0043	5008	,	,		9729	0.0		0.0	False		,,,				2504	0.0				p.V155V		Atlas-SNP	.											.	ADARB2	95	.	0			c.C465T						PASS	.			185,4221	107.8+/-146.2	5,175,2023	35.0	30.0	32.0		465	1.2	1.0	10	dbSNP_126	32	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADARB2	NM_018702.3		5,176,6322	AA,AG,GG		0.0116,4.1988,1.4301		155/740	1405835	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	105	exon3			CGCGAAGACCGGG	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"""RED2 homolog (rat)"""	602065	"""adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)"", ""adenosine deaminase, RNA-specific, B2"""			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.465C>T	10.37:g.1405835G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Silent	SNP	ENST00000381312.1	37	CCDS7058.1																																																																																			G|0.981;A|0.019	0.019	strong		0.692	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702	
AMHR2	269	hgsc.bcm.edu	37	12	53823307	53823307	+	Silent	SNP	G	G	A	rs784890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53823307G>A	ENST00000257863.4	+	8	1118	c.1038G>A	c.(1036-1038)tcG>tcA	p.S346S	AMHR2_ENST00000550311.1_Silent_p.S346S|AMHR2_ENST00000379791.3_Silent_p.S346S	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	346	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	AAGATGGATCGTGTGCCATTG	0.572													G|||	760	0.151757	0.5514	0.0389	5008	,	,		16169	0.0		0.004	False		,,,				2504	0.0				p.S346S		Atlas-SNP	.											.	AMHR2	61	.	0			c.G1038A						PASS	.	G	,,	2068,2338	570.7+/-382.9	514,1040,649	109.0	98.0	102.0		1038,1038,1038	-10.0	0.9	12	dbSNP_86	102	27,8573	16.6+/-54.9	0,27,4273	no	coding-synonymous,coding-synonymous,coding-synonymous	AMHR2	NM_001164690.1,NM_001164691.1,NM_020547.2	,,	514,1067,4922	AA,AG,GG		0.314,46.936,16.108	,,	346/479,346/479,346/574	53823307	2095,10911	2203	4300	6503	SO:0001819	synonymous_variant	269	exon8			TGGATCGTGTGCC	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"""Muellerian inhibiting substance type II receptor"""	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.1038G>A	12.37:g.53823307G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_020547	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Silent	SNP	ENST00000257863.4	37	CCDS8858.1																																																																																			G|0.856;A|0.144	0.144	strong		0.572	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547	
MUC4	4585	hgsc.bcm.edu	37	3	195505774	195505774	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	238	2	0.00840336		WXS	Illumina HiSeq	Phase_I	209	10	0.0478469	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	
PSG8	440533	hgsc.bcm.edu	37	19	43269699	43269699	+	Missense_Mutation	SNP	C	C	T	rs71337226|rs7260508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43269699C>T	ENST00000306511.4	-	1	132	c.35G>A	c.(34-36)cGc>cAc	p.R12H	PSG8_ENST00000406636.3_Missense_Mutation_p.R12H|PSG8_ENST00000401467.2_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.R12H	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	12				TQR -> MQH (in Ref. 2; CAH18672). {ECO:0000305}.		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)				CCAGGTGATGCGCTGTGTGCA	0.592													.|||	1786	0.356629	0.7315	0.2709	5008	,	,		17382	0.0903		0.3091	False		,,,				2504	0.2342				p.R12H		Atlas-SNP	.											PSG8_ENST00000404209,NS,carcinoma,-1,2	PSG8	101	2	0			c.G35A						PASS	.	T	HIS/ARG,HIS/ARG,HIS/ARG	1977,1045		665,647,199	117.0	118.0	118.0		35,35,35	-2.7	0.0	19	dbSNP_116	118	1619,3799		254,1111,1344	no	missense,missense,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	29,29,29	919,1758,1543	TT,TC,CC		29.8819,34.5797,42.6066	benign,benign,benign	12/420,12/298,12/427	43269699	3596,4844	1511	2709	4220	SO:0001583	missense	440533	exon1			GTGATGCGCTGTG	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.35G>A	19.37:g.43269699C>T	ENSP00000305005:p.Arg12His	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001130168	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	706	0.3232600732600733	323	0.6565040650406504	109	0.3011049723756906	45	0.07867132867132867	229	0.3021108179419525	c	2.839	-0.240996	0.05906	0.654203	0.298819	ENSG00000124467	ENST00000404209;ENST00000406636;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.23348	2.18;1.91;2.19	1.35	-2.7	0.06004	.	.	.	.	.	T	0.00012	0.0000	N	0.01297	-0.9	0.80722	P	0.0	B;B;B	0.10296	0.002;0.003;0.001	B;B;B	0.08055	0.001;0.003;0.001	T	0.34925	-0.9809	8	0.18710	T	0.47	.	7.3607	0.26745	0.0:0.5348:0.0:0.4652	rs7260508;rs60422632	12;12;12	Q9UQ74-2;Q9UQ74;A5PKV3	.;PSG8_HUMAN;.	H	12	ENSP00000385869:R12H;ENSP00000385081:R12H;ENSP00000305005:R12H	ENSP00000305005:R12H	R	-	2	0	PSG8	47961539	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.718000	0.00813	-1.864000	0.01148	-2.741000	0.00127	CGC	C|0.620;T|0.380	0.380	strong		0.592	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
SYNGR3	9143	hgsc.bcm.edu	37	16	2042086	2042086	+	Missense_Mutation	SNP	G	G	A	rs199784173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2042086G>A	ENST00000248121.2	+	2	369	c.211G>A	c.(211-213)Ggc>Agc	p.G71S	SYNGR3_ENST00000562045.1_5'UTR	NM_004209.5	NP_004200.2	O43761	SNG3_HUMAN	synaptogyrin 3	71	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				positive regulation of transporter activity (GO:0032411)|substantia nigra development (GO:0021762)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|synaptic vesicle (GO:0008021)				endometrium(1)|lung(2)	3						CTGCCGCTTCGGCGTCGCGCT	0.716													G|||	18	0.00359425	0.0113	0.0043	5008	,	,		8658	0.0		0.0	False		,,,				2504	0.0				p.G71S		Atlas-SNP	.											.	SYNGR3	10	.	0			c.G211A						PASS	.	G	SER/GLY	21,3953		0,21,1966	6.0	6.0	6.0		211	4.2	1.0	16		6	0,8028		0,0,4014	no	missense	SYNGR3	NM_004209.5	56	0,21,5980	AA,AG,GG		0.0,0.5284,0.175	probably-damaging	71/230	2042086	21,11981	1987	4014	6001	SO:0001583	missense	9143	exon2			CGCTTCGGCGTCG	AJ002309	CCDS10456.1	16p13.3	2008-05-19			ENSG00000127561	ENSG00000127561			11501	protein-coding gene	gene with protein product		603927				9760194	Standard	NM_004209		Approved		uc002cod.3	O43761	OTTHUMG00000128711	ENST00000248121.2:c.211G>A	16.37:g.2042086G>A	ENSP00000248121:p.Gly71Ser	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	11	10	0.909091	NM_004209	B2R9S0	Missense_Mutation	SNP	ENST00000248121.2	37	CCDS10456.1	13	0.005952380952380952	11	0.022357723577235773	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	g	23.6	4.432249	0.83776	0.005284	0.0	ENSG00000127561	ENST00000248121;ENST00000320633	T	0.24908	1.83	4.2	4.2	0.49525	Marvel (1);MARVEL-like domain (1);	0.056575	0.64402	D	0.000001	T	0.31575	0.0801	M	0.66378	2.025	0.80722	D	1	D	0.89917	1.0	D	0.68621	0.959	T	0.40590	-0.9555	10	0.62326	D	0.03	.	15.6377	0.76966	0.0:0.0:1.0:0.0	.	71	O43761	SNG3_HUMAN	S	71	ENSP00000248121:G71S	ENSP00000248121:G71S	G	+	1	0	SYNGR3	1982087	1.000000	0.71417	1.000000	0.80357	0.135000	0.20990	9.184000	0.94893	2.340000	0.79590	0.561000	0.74099	GGC	G|0.994;A|0.006	0.006	strong		0.716	SYNGR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250616.1		
PKD1	5310	hgsc.bcm.edu	37	16	2162887	2162887	+	Silent	SNP	A	A	G	rs2369068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2162887A>G	ENST00000262304.4	-	13	3271	c.3063T>C	c.(3061-3063)ggT>ggC	p.G1021G	PKD1_ENST00000423118.1_Silent_p.G1021G|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1021					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						AGACCTGCAGACCCTGCATCC	0.642													g|||	916	0.182907	0.5356	0.1427	5008	,	,		11079	0.0		0.0944	False		,,,				2504	0.0143				p.G1021G		Atlas-SNP	.											.	PKD1	184	.	0			c.T3063C						PASS	.	G	,	2023,2373	604.7+/-390.4	468,1087,643	128.0	123.0	125.0		3063,3063	1.6	0.4	16	dbSNP_100	125	911,7689	775.7+/-407.7	55,801,3444	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	523,1888,4087	GG,GA,AA		10.593,46.0191,22.5762	,	1021/4303,1021/4304	2162887	2934,10062	2198	4300	6498	SO:0001819	synonymous_variant	5310	exon13			CTGCAGACCCTGC	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.3063T>C	16.37:g.2162887A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			A|0.796;G|0.204	0.204	strong		0.642	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
PER2	8864	hgsc.bcm.edu	37	2	239162182	239162182	+	Missense_Mutation	SNP	C	C	T	rs55704277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239162182C>T	ENST00000254657.3	-	19	2761	c.2482G>A	c.(2482-2484)Gcc>Acc	p.A828T	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	828					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		CAGGCTGTGGCGTTCAAGCCC	0.642													C|||	170	0.0339457	0.1203	0.0144	5008	,	,		13041	0.0		0.001	False		,,,				2504	0.0				p.A828T		Atlas-SNP	.											.	PER2	85	.	0			c.G2482A						PASS	.	C	THR/ALA	439,3963		25,389,1787	17.0	17.0	17.0		2482	-5.8	0.0	2	dbSNP_129	17	11,8585		0,11,4287	yes	missense	PER2	NM_022817.2	58	25,400,6074	TT,TC,CC		0.128,9.9727,3.4621	benign	828/1256	239162182	450,12548	2201	4298	6499	SO:0001583	missense	8864	exon19			CTGTGGCGTTCAA	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"""period (Drosophila) homolog 2"", ""period homolog 2 (Drosophila)"""			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2482G>A	2.37:g.239162182C>T	ENSP00000254657:p.Ala828Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	57	0.59375	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	37	CCDS2528.1	58	0.026556776556776556	51	0.10365853658536585	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	0.015	-1.561098	0.00910	0.099727	0.00128	ENSG00000132326	ENST00000254657	T	0.10763	2.84	4.21	-5.83	0.02325	.	0.461183	0.24407	N	0.038781	T	0.00109	0.0003	N	0.12443	0.215	0.09310	N	0.999999	B;B	0.12630	0.006;0.002	B;B	0.06405	0.002;0.002	T	0.30446	-0.9978	10	0.05721	T	0.95	-14.6187	5.5214	0.16936	0.2369:0.2108:0.0:0.5523	rs55704277;rs59829497	828;828	B4DH14;O15055	.;PER2_HUMAN	T	828	ENSP00000254657:A828T	ENSP00000254657:A828T	A	-	1	0	PER2	238826921	0.001000	0.12720	0.011000	0.14972	0.011000	0.07611	-0.224000	0.09164	-0.932000	0.03742	-2.664000	0.00146	GCC	C|0.962;T|0.038	0.038	strong		0.642	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817	
C17orf64	124773	hgsc.bcm.edu	37	17	58506785	58506785	+	Silent	SNP	G	G	T	rs9913666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:58506785G>T	ENST00000269127.4	+	5	576	c.492G>T	c.(490-492)ctG>ctT	p.L164L		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	164										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			AAGACAGTCTGCCCAAGCTCT	0.622													G|||	541	0.108027	0.3858	0.0418	5008	,	,		17929	0.0		0.002	False		,,,				2504	0.0				p.L164L		Atlas-SNP	.											.	C17orf64	19	.	0			c.G492T						PASS	.	G		1342,3064	443.9+/-347.2	217,908,1078	47.0	47.0	47.0		492	1.7	1.0	17	dbSNP_119	47	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	C17orf64	NM_181707.2		217,922,5364	TT,TG,GG		0.1628,30.4585,10.426		164/237	58506785	1356,11650	2203	4300	6503	SO:0001819	synonymous_variant	124773	exon5			CAGTCTGCCCAAG	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.492G>T	17.37:g.58506785G>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_181707	Q8IY87	Silent	SNP	ENST00000269127.4	37	CCDS32698.2																																																																																			G|0.912;T|0.088	0.088	strong		0.622	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707	
SPTB	6710	hgsc.bcm.edu	37	14	65249052	65249052	+	Missense_Mutation	SNP	C	C	G	rs17245552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:65249052C>G	ENST00000389721.5	-	19	4254	c.4222G>C	c.(4222-4224)Ggc>Cgc	p.G1408R	SPTB_ENST00000542895.1_Missense_Mutation_p.G1408R|SPTB_ENST00000556626.1_Missense_Mutation_p.G1408R|SPTB_ENST00000389722.3_Missense_Mutation_p.G1408R|SPTB_ENST00000389720.3_Missense_Mutation_p.G1408R	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1408			G -> R (in dbSNP:rs17245552).		actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		AGGTCCTTGCCCGGGTCGTCT	0.582													C|||	509	0.101637	0.0938	0.0187	5008	,	,		20009	0.2262		0.0427	False		,,,				2504	0.1033				p.G1408R		Atlas-SNP	.											.	SPTB	378	.	0			c.G4222C						PASS	.	C	ARG/GLY,ARG/GLY	316,4090	169.8+/-200.3	11,294,1898	109.0	98.0	101.0		4222,4222	5.4	1.0	14	dbSNP_123	101	489,8111	140.5+/-197.0	12,465,3823	yes	missense,missense	SPTB	NM_000347.5,NM_001024858.2	125,125	23,759,5721	GG,GC,CC		5.686,7.172,6.1895	probably-damaging,probably-damaging	1408/2138,1408/2329	65249052	805,12201	2203	4300	6503	SO:0001583	missense	6710	exon19			CCTTGCCCGGGTC		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4222G>C	14.37:g.65249052C>G	ENSP00000374371:p.Gly1408Arg	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	189	84	0.444444	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	212	0.09706959706959707	53	0.10772357723577236	8	0.022099447513812154	117	0.20454545454545456	34	0.044854881266490766	C	29.1	4.980937	0.92982	0.07172	0.05686	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000553938;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T;T	0.56941	0.43;0.99;0.43;0.99;0.99;0.43	5.36	5.36	0.76844	.	0.166644	0.53938	D	0.000059	T	0.00241	0.0007	M	0.84219	2.685	0.09310	P	0.99999815977	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.85130	0.995;0.997;0.989	T	0.00926	-1.1512	9	0.72032	D	0.01	.	18.2137	0.89878	0.0:1.0:0.0:0.0	rs17245552;rs52835393;rs17245552	192;1408;1412	E7EV95;P11277;Q59FP5	.;SPTB1_HUMAN;.	R	1412;1408;192;73;1408;1408;1408;1408	ENSP00000374372:G1408R;ENSP00000451324:G73R;ENSP00000451752:G1408R;ENSP00000374371:G1408R;ENSP00000443882:G1408R;ENSP00000374370:G1408R	ENSP00000334218:G192R	G	-	1	0	SPTB	64318805	0.994000	0.37717	1.000000	0.80357	0.985000	0.73830	6.066000	0.71185	2.681000	0.91329	0.462000	0.41574	GGC	C|0.925;G|0.075	0.075	strong		0.582	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
PRLR	5618	hgsc.bcm.edu	37	5	35072712	35072712	+	Missense_Mutation	SNP	T	T	G	rs72478580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:35072712T>G	ENST00000382002.5	-	6	934	c.508A>C	c.(508-510)Att>Ctt	p.I170L	PRLR_ENST00000397391.3_Missense_Mutation_p.I99L|PRLR_ENST00000231423.3_Missense_Mutation_p.I170L|PRLR_ENST00000310101.5_Missense_Mutation_p.I170L|PRLR_ENST00000348262.3_Missense_Mutation_p.I170L|PRLR_ENST00000511486.1_Missense_Mutation_p.I69L|PRLR_ENST00000509934.1_5'UTR|PRLR_ENST00000513753.1_Missense_Mutation_p.I170L|PRLR_ENST00000342362.5_Missense_Mutation_p.I69L|PRLR_ENST00000542609.1_Missense_Mutation_p.I170L	NM_000949.5	NP_000940.1	P16471	PRLR_HUMAN	prolactin receptor	170	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> L (in MFAB; confers constitutive activity). {ECO:0000269|PubMed:18779591}.		activation of JAK2 kinase activity (GO:0042977)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell surface receptor signaling pathway (GO:0007166)|embryo implantation (GO:0007566)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|prolactin signaling pathway (GO:0038161)|steroid biosynthetic process (GO:0006694)|T cell activation (GO:0042110)	cell surface (GO:0009986)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|ornithine decarboxylase activator activity (GO:0042978)|peptide hormone binding (GO:0017046)|prolactin receptor activity (GO:0004925)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Fluoxymesterone(DB01185)|Somatropin recombinant(DB00052)	TTTAATCGAATTTCATACAGG	0.443													T|||	63	0.0125799	0.0061	0.0288	5008	,	,		19623	0.0		0.0318	False		,,,				2504	0.0031				p.I170L		Atlas-SNP	.											.	PRLR	90	.	0			c.A508C	GRCh37	CM085654	PRLR	M	rs72478580	PASS	.	T	LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE	33,4373	39.2+/-71.8	0,33,2170	142.0	138.0	139.0		508,205,508,508,508,508	-1.0	1.0	5	dbSNP_130	139	206,8394	88.6+/-150.9	4,198,4098	yes	missense,missense,missense,missense,missense,missense	PRLR	NM_000949.5,NM_001204314.1,NM_001204315.1,NM_001204316.1,NM_001204317.1,NM_001204318.1	5,5,5,5,5,5	4,231,6268	GG,GT,TT		2.3953,0.749,1.8376	benign,benign,benign,benign,benign,benign	170/623,69/522,170/350,170/377,170/289,170/269	35072712	239,12767	2203	4300	6503	SO:0001583	missense	5618	exon6			ATCGAATTTCATA		CCDS3909.1, CCDS56358.1, CCDS56359.1, CCDS56360.1, CCDS56361.1, CCDS56362.1	5p14-p13	2013-02-27			ENSG00000113494	ENSG00000113494			9446	protein-coding gene	gene with protein product		176761					Standard	NM_001204315		Approved		uc003jjm.3	P16471	OTTHUMG00000090789	ENST00000382002.5:c.508A>C	5.37:g.35072712T>G	ENSP00000371432:p.Ile170Leu	Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	273	142	0.520147	NM_000949	B2R882|D1MDP1|Q16354|Q8TD75|Q8TD78|Q96P35|Q96P36|Q9BX87|Q9UHJ5	Missense_Mutation	SNP	ENST00000382002.5	37	CCDS3909.1	40	0.018315018315018316	4	0.008130081300813009	13	0.03591160220994475	0	0.0	23	0.030343007915567283	T	1.860	-0.462984	0.04476	0.00749	0.023953	ENSG00000113494	ENST00000231423;ENST00000513753;ENST00000348262;ENST00000397391;ENST00000542609;ENST00000342362;ENST00000382002;ENST00000511486;ENST00000310101	T;T;T;T;T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07	5.68	-1.03	0.10102	Fibronectin, type III (3);Long hematopoietin receptor, single chain, conserved site (1);Immunoglobulin-like fold (1);	0.468375	0.24592	N	0.037209	T	0.02571	0.0078	N	0.05199	-0.095	0.33895	D	0.637774	B;B;B;B;B;B;B	0.09022	0.0;0.001;0.002;0.001;0.001;0.0;0.0	B;B;B;B;B;B;B	0.18263	0.002;0.009;0.021;0.004;0.01;0.003;0.003	T	0.23154	-1.0196	10	0.02654	T	1	-4.5229	0.872	0.01216	0.2079:0.3206:0.208:0.2636	.	170;170;69;99;170;170;170	P16471-3;P16471;P16471-2;Q8TD76;P16471-7;P16471-6;P16471-4	.;PRLR_HUMAN;.;.;.;.;.	L	170;170;170;99;170;69;170;69;170	ENSP00000231423:I170L;ENSP00000424841:I170L;ENSP00000311613:I170L;ENSP00000380546:I99L;ENSP00000441813:I170L;ENSP00000339213:I69L;ENSP00000371432:I170L;ENSP00000422556:I69L;ENSP00000309008:I170L	ENSP00000231423:I170L	I	-	1	0	PRLR	35108469	0.986000	0.35501	0.999000	0.59377	0.603000	0.37013	0.115000	0.15540	0.120000	0.18254	-0.256000	0.11100	ATT	T|0.981;G|0.019	0.019	strong		0.443	PRLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207575.2		
ENTPD4	9583	hgsc.bcm.edu	37	8	23299225	23299225	+	Missense_Mutation	SNP	C	C	T	rs34849865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:23299225C>T	ENST00000358689.4	-	8	974	c.739G>A	c.(739-741)Gtt>Att	p.V247I	ENTPD4_ENST00000356206.6_Missense_Mutation_p.V247I|ENTPD4_ENST00000417069.2_Missense_Mutation_p.V247I	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	247					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)		ACTTCCACAACGGCCTCATCA	0.473													C|||	26	0.00519169	0.0197	0.0	5008	,	,		21884	0.0		0.0	False		,,,				2504	0.0				p.V247I		Atlas-SNP	.											.	ENTPD4	56	.	0			c.G739A						PASS	.	C	ILE/VAL,ILE/VAL	101,4305	81.9+/-120.4	1,99,2103	65.0	56.0	59.0		739,739	3.1	0.4	8	dbSNP_126	59	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ENTPD4	NM_001128930.2,NM_004901.4	29,29	1,101,6401	TT,TC,CC		0.0233,2.2923,0.7919	benign,benign	247/609,247/617	23299225	103,12903	2203	4300	6503	SO:0001583	missense	9583	exon8			CCACAACGGCCTC	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.739G>A	8.37:g.23299225C>T	ENSP00000351520:p.Val247Ile	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	39	0.661017	NM_004901	D3DSS3|O15092	Missense_Mutation	SNP	ENST00000358689.4	37	CCDS6041.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	C	12.07	1.826131	0.32237	0.022923	2.33E-4	ENSG00000197217	ENST00000356206;ENST00000358689;ENST00000417069	T;T;T	0.14144	2.57;2.53;2.58	5.87	3.1	0.35709	.	0.431567	0.26307	N	0.025140	T	0.05686	0.0149	L	0.49126	1.545	0.31429	N	0.673388	B;B;B	0.13594	0.008;0.003;0.003	B;B;B	0.15870	0.014;0.003;0.005	T	0.12192	-1.0557	10	0.25751	T	0.34	-13.4993	8.0326	0.30474	0.0:0.7229:0.1325:0.1446	rs34849865	247;247;247	Q8NE73;Q9Y227-2;Q9Y227	.;.;ENTP4_HUMAN	I	247	ENSP00000348536:V247I;ENSP00000351520:V247I;ENSP00000408573:V247I	ENSP00000348536:V247I	V	-	1	0	ENTPD4	23355170	0.005000	0.15991	0.412000	0.26496	0.832000	0.47134	0.266000	0.18534	0.385000	0.24970	0.655000	0.94253	GTT	C|0.993;T|0.007	0.007	strong		0.473	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901	
SERPINB10	5273	hgsc.bcm.edu	37	18	61587053	61587053	+	Missense_Mutation	SNP	G	G	A	rs17072146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61587053G>A	ENST00000238508.3	+	5	463	c.404G>A	c.(403-405)gGt>gAt	p.G135D		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	135			G -> D (in dbSNP:rs17072146).		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)				ACATATTTTGGTGCAGAACCT	0.353													G|||	858	0.171326	0.357	0.0836	5008	,	,		18431	0.2123		0.0258	False		,,,				2504	0.09				p.G135D		Atlas-SNP	.											.	SERPINB10	53	.	0			c.G404A						PASS	.	G	ASP/GLY	1268,3138	425.3+/-340.8	198,872,1133	71.0	85.0	80.0		404	3.4	0.9	18	dbSNP_123	80	133,8465	67.3+/-129.8	3,127,4169	yes	missense	SERPINB10	NM_005024.1	94	201,999,5302	AA,AG,GG		1.5469,28.7789,10.7736		135/398	61587053	1401,11603	2203	4299	6502	SO:0001583	missense	5273	exon4			ATTTTGGTGCAGA	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.404G>A	18.37:g.61587053G>A	ENSP00000238508:p.Gly135Asp	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	56	19	0.339286	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	344	0.1575091575091575	170	0.34552845528455284	28	0.07734806629834254	126	0.2202797202797203	20	0.026385224274406333	G	8.459	0.854792	0.17106	0.287789	0.015469	ENSG00000242550	ENST00000238508	D	0.83075	-1.68	5.33	3.43	0.39272	Serpin domain (3);	0.679950	0.15625	N	0.252701	T	0.00012	0.0000	L	0.48218	1.51	0.44966	P	0.0020120000000000138	B	0.29162	0.235	B	0.32465	0.146	T	0.10337	-1.0634	9	0.18276	T	0.48	.	6.6626	0.23022	0.0955:0.1799:0.7246:0.0	rs17072146;rs17072146	135	P48595	SPB10_HUMAN	D	135	ENSP00000238508:G135D	ENSP00000238508:G135D	G	+	2	0	SERPINB10	59738033	0.991000	0.36638	0.908000	0.35775	0.989000	0.77384	1.363000	0.34159	1.257000	0.44085	0.655000	0.94253	GGT	G|0.856;A|0.144	0.144	strong		0.353	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
IPO13	9670	hgsc.bcm.edu	37	1	44424525	44424525	+	Silent	SNP	G	G	A	rs74073335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44424525G>A	ENST00000372343.3	+	11	2654	c.1992G>A	c.(1990-1992)gaG>gaA	p.E664E		NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	664					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)				AAGGCCCTGAGCTTCGGAAGC	0.562													G|||	38	0.00758786	0.0287	0.0	5008	,	,		20073	0.0		0.0	False		,,,				2504	0.0				p.E664E		Atlas-SNP	.											.	IPO13	86	.	0			c.G1992A						PASS	.	G		124,4282	90.6+/-129.3	1,122,2080	84.0	78.0	80.0		1992	3.8	1.0	1	dbSNP_130	80	0,8600		0,0,4300	no	coding-synonymous	IPO13	NM_014652.3		1,122,6380	AA,AG,GG		0.0,2.8143,0.9534		664/964	44424525	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon11			CCCTGAGCTTCGG	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.1992G>A	1.37:g.44424525G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	166	96	0.578313	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			G|0.991;A|0.009	0.009	strong		0.562	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652	
HDHD1	8226	hgsc.bcm.edu	37	X	7023678	7023678	+	Missense_Mutation	SNP	G	G	A	rs1131197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:7023678G>A	ENST00000381077.5	-	2	339	c.263C>T	c.(262-264)aCg>aTg	p.T88M	HDHD1_ENST00000540122.1_Missense_Mutation_p.T88M|HDHD1_ENST00000498474.2_5'UTR|HDHD1_ENST00000424830.2_Missense_Mutation_p.T111M|HDHD1_ENST00000412827.2_Intron	NM_001178136.1|NM_012080.4	NP_001171607.1|NP_036212.3	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain containing 1	88			T -> M (in dbSNP:rs1131197). {ECO:0000269|PubMed:1284467, ECO:0000269|PubMed:14702039}.		nucleotide metabolic process (GO:0009117)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)			breast(2)|large_intestine(1)|lung(3)	6						GAGCGCAGCCGTGGGGAACAC	0.478													g|||	960	0.254305	0.0537	0.3372	3775	,	,		12780	0.2153		0.1779	False		,,,				2504	0.2648				p.T111M		Atlas-SNP	.											.	HDHD1	21	.	0			c.C332T						PASS	.	G	MET/THR,MET/THR,,MET/THR	347,3065		15,249,68,1157,502	59.0	61.0	60.0		332,263,,263	3.2	0.9	X	dbSNP_86	60	1564,4948		153,840,418,1362,1384	yes	missense,missense,intron,missense	HDHD1	NM_001135565.1,NM_001178135.1,NM_001178136.1,NM_012080.4	81,81,,81	168,1089,486,2519,1886	AA,AG,A,GG,G		24.0172,10.17,19.2563	benign,benign,,benign	111/252,88/209,,88/229	7023678	1911,8013	1991	4157	6148	SO:0001583	missense	8226	exon3			GCAGCCGTGGGGA	M86934	CCDS48075.1, CCDS48076.1, CCDS55366.1, CCDS55367.1	Xp22.32	2010-07-21	2010-07-21	2010-07-21	ENSG00000130021	ENSG00000130021			16818	protein-coding gene	gene with protein product		306480	"""family with sequence similarity 16, member A, X-linked"", ""haloacid dehalogenase-like hydrolase domain containing 1A"""	FAM16AX, HDHD1A		1734713, 1284467	Standard	NM_012080		Approved	DXF68S1E, GS1	uc011mhm.1	Q08623	OTTHUMG00000021101	ENST00000381077.5:c.263C>T	X.37:g.7023678G>A	ENSP00000370467:p.Thr88Met	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	262	121	0.461832	NM_001135565	B2R7X6|B4DV93|B7Z6Q3|E9PAV8|F5GWZ2|Q53F84|Q96EB8	Missense_Mutation	SNP	ENST00000381077.5	37	CCDS48075.1	410	0.24713682941531043	19	0.04008438818565401	73	0.24172185430463577	87	0.18669527896995708	97	0.14391691394658754	g	14.51	2.555468	0.45487	0.1017	0.240172	ENSG00000130021	ENST00000381077;ENST00000544385;ENST00000424830;ENST00000540122;ENST00000486446	T;T;T;T	0.06068	3.35;3.35;3.35;3.35	4.01	3.15	0.36227	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.051445	0.85682	D	0.000000	T	0.00012	0.0000	M	0.81179	2.53	0.19575	P	0.9999665773	D;D;D;D	0.89917	1.0;0.998;1.0;0.998	D;D;D;P	0.73708	0.978;0.941;0.981;0.88	T	0.12142	-1.0559	9	0.44086	T	0.13	-26.0628	10.1361	0.42708	0.1038:0.0:0.8962:0.0	rs1131197;rs12689910;rs60405234;rs12689910	88;111;88;88	Q08623-3;E9PAV8;E7EVH9;Q08623	.;.;.;HDHD1_HUMAN	M	88;104;111;88;88	ENSP00000370467:T88M;ENSP00000396452:T111M;ENSP00000441208:T88M;ENSP00000430995:T88M	ENSP00000370467:T88M	T	-	2	0	HDHD1	7033678	0.987000	0.35691	0.919000	0.36401	0.633000	0.38033	1.846000	0.39289	0.550000	0.28991	-0.195000	0.12781	ACG	0|0.023;T|0.097	.	strong		0.478	HDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055683.2	NM_012080	
PF4V1	5197	hgsc.bcm.edu	37	4	74719624	74719624	+	Silent	SNP	C	C	G	rs34446485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:74719624C>G	ENST00000226524.3	+	2	399	c.225C>G	c.(223-225)ctC>ctG	p.L75L		NM_002620.2	NP_002611.1	P10720	PF4V_HUMAN	platelet factor 4 variant 1	75					cell chemotaxis (GO:0060326)|immune response (GO:0006955)	extracellular space (GO:0005615)	heparin binding (GO:0008201)			endometrium(1)|liver(2)	3	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			CTGCCCAACTCATGTGAGTCC	0.602																																					p.L75L		Atlas-SNP	.											PF4V1,NS,carcinoma,0,1	PF4V1	8	1	0			c.C225G						scavenged	.	C		81,4307	17.9+/-39.9	7,67,2120	66.0	74.0	71.0		225	-2.3	0.1	4	dbSNP_126	71	31,8565	1.2+/-3.3	3,25,4270	no	coding-synonymous	PF4V1	NM_002620.2		10,92,6390	GG,GC,CC		0.3606,1.8459,0.8626		75/105	74719624	112,12872	2194	4298	6492	SO:0001819	synonymous_variant	5197	exon2			CCAACTCATGTGA	M26167	CCDS3561.1	4q12-q21	2008-08-15			ENSG00000109272	ENSG00000109272			8862	protein-coding gene	gene with protein product		173461				2725510	Standard	NM_002620		Approved	SCYB4V1, CXCL4V1, CXCL4L1	uc003hhg.1	P10720	OTTHUMG00000130177	ENST00000226524.3:c.225C>G	4.37:g.74719624C>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	150	40	0.266667	NM_002620	A1L4S0	Silent	SNP	ENST00000226524.3	37	CCDS3561.1																																																																																			C|0.981;G|0.019	0.019	strong		0.602	PF4V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252495.1		
BAALC	79870	hgsc.bcm.edu	37	8	104240275	104240275	+	Missense_Mutation	SNP	G	G	C	rs34542607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104240275G>C	ENST00000297574.6	+	4	630	c.491G>C	c.(490-492)aGc>aCc	p.S164T	RP11-318M2.2_ENST00000523614.2_RNA|RP11-318M2.3_ENST00000523775.1_RNA|BAALC_ENST00000523754.1_3'UTR|BAALC_ENST00000438105.2_3'UTR|RP11-318M2.2_ENST00000499522.2_RNA|BAALC_ENST00000309982.5_Missense_Mutation_p.S129T			Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic	164			S -> T (in dbSNP:rs34542607).			cytoplasm (GO:0005737)|membrane (GO:0016020)				kidney(1)|large_intestine(3)|lung(3)	7			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)			GTAACAGATAGCATCCAACAG	0.408													G|||	124	0.0247604	0.0908	0.0058	5008	,	,		24074	0.0		0.0	False		,,,				2504	0.0				p.S129T		Atlas-SNP	.											.	BAALC	15	.	0			c.G386C						PASS	.	G	,THR/SER	395,4011	198.1+/-222.0	21,353,1829	127.0	109.0	115.0		,386	3.9	0.9	8	dbSNP_126	115	1,8599	1.2+/-3.3	0,1,4299	yes	utr-3,missense	BAALC	NM_001024372.1,NM_024812.2	,58	21,354,6128	CC,CG,GG		0.0116,8.965,3.0447	,benign	,129/146	104240275	396,12610	2203	4300	6503	SO:0001583	missense	79870	exon3			CAGATAGCATCCA	AF363578	CCDS6297.1, CCDS47906.1	8q22.3	2008-07-29			ENSG00000164929	ENSG00000164929			14333	protein-coding gene	gene with protein product		606602				11707601	Standard	NM_024812		Approved		uc003yld.3	Q8WXS3	OTTHUMG00000164782	ENST00000297574.6:c.491G>C	8.37:g.104240275G>C	ENSP00000297574:p.Ser164Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_024812	Q8WTP6|Q8WXS0|Q8WXS1|Q8WXS2|Q9HA93	Missense_Mutation	SNP	ENST00000297574.6	37		56	0.02564102564102564	55	0.11178861788617886	1	0.0027624309392265192	0	0.0	0	0.0	G	12.02	1.813455	0.32053	0.08965	1.16E-4	ENSG00000164929	ENST00000309982;ENST00000297574	T;T	0.50813	0.73;0.73	4.8	3.9	0.45041	.	0.129605	0.48286	D	0.000192	T	0.00524	0.0017	.	.	.	0.80722	D	1	P;B	0.40970	0.734;0.447	B;B	0.32342	0.14;0.144	T	0.01894	-1.1252	9	0.22109	T	0.4	-12.8881	8.4904	0.33098	0.1123:0.0:0.8877:0.0	rs34542607	164;129	Q8WXS3;Q8WXS3-2	BAALC_HUMAN;.	T	129;164	ENSP00000312457:S129T;ENSP00000297574:S164T	ENSP00000297574:S164T	S	+	2	0	BAALC	104309451	1.000000	0.71417	0.886000	0.34754	0.987000	0.75469	2.175000	0.42491	1.113000	0.41760	0.591000	0.81541	AGC	G|0.971;C|0.029	0.029	strong		0.408	BAALC-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000380257.1		
SCML4	256380	hgsc.bcm.edu	37	6	108029091	108029091	+	Silent	SNP	G	G	A	rs3734753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:108029091G>A	ENST00000369020.3	-	7	1343	c.1098C>T	c.(1096-1098)caC>caT	p.H366H	SCML4_ENST00000369022.2_Silent_p.H308H|SCML4_ENST00000369025.2_Silent_p.H124H	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		AGAGCTCCACGTGAGGCCCCA	0.637													G|||	270	0.0539137	0.053	0.0144	5008	,	,		18839	0.1677		0.0169	False		,,,				2504	0.0041				p.H366H		Atlas-SNP	.											.	SCML4	65	.	0			c.C1098T						PASS	.	G		85,1299		1,83,608	44.0	52.0	49.0		1098	-0.3	1.0	6	dbSNP_107	49	64,3118		4,56,1531	no	coding-synonymous	SCML4	NM_198081.3		5,139,2139	AA,AG,GG		2.0113,6.1416,3.2633		366/415	108029091	149,4417	692	1591	2283	SO:0001819	synonymous_variant	256380	exon7			CTCCACGTGAGGC		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.1098C>T	6.37:g.108029091G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	148	65	0.439189	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Silent	SNP	ENST00000369020.3	37	CCDS5060.2																																																																																			G|0.941;A|0.059	0.059	strong		0.637	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
NOD1	10392	hgsc.bcm.edu	37	7	30492237	30492237	+	Missense_Mutation	SNP	C	C	T	rs2075820|rs398087981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30492237C>T	ENST00000222823.4	-	6	1321	c.796G>A	c.(796-798)Gag>Aag	p.E266K	NOD1_ENST00000423334.2_Silent_p.P220P	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	266	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		E -> K (in dbSNP:rs2075820).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|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)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|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 cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|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 tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|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)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						AACACCTCCTCGGGGTCCCGC	0.617													C|||	1690	0.33746	0.4032	0.1758	5008	,	,		18812	0.3869		0.2326	False		,,,				2504	0.4202				p.E266K		Atlas-SNP	.											.	NOD1	79	.	0			c.G796A	GRCh37	CM076359	NOD1	M	rs2075820	PASS	.	C	LYS/GLU	1670,2736	488.3+/-361.2	321,1028,854	69.0	67.0	68.0		796	5.5	0.8	7	dbSNP_96	68	2110,6490	351.5+/-328.3	282,1546,2472	yes	missense	NOD1	NM_006092.2	56	603,2574,3326	TT,TC,CC		24.5349,37.9029,29.0635	benign	266/954	30492237	3780,9226	2203	4300	6503	SO:0001583	missense	10392	exon6			CCTCCTCGGGGTC	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.796G>A	7.37:g.30492237C>T	ENSP00000222823:p.Glu266Lys	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_006092	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	37	CCDS5427.1	649	0.29716117216117216	195	0.39634146341463417	76	0.20994475138121546	209	0.36538461538461536	169	0.22295514511873352	C	16.00	2.999294	0.54147	0.379029	0.245349	ENSG00000106100	ENST00000222823	T	0.79033	-1.23	5.54	5.54	0.83059	NACHT nucleoside triphosphatase (1);	0.640387	0.17056	N	0.188744	T	0.00012	0.0000	L	0.54323	1.7	0.09310	P	0.9999999847827	P	0.47545	0.897	B	0.38156	0.266	T	0.36237	-0.9756	9	0.26408	T	0.33	.	11.8004	0.52124	0.0:0.9113:0.0:0.0887	rs2075820;rs60510801;rs2075820	266	Q9Y239	NOD1_HUMAN	K	266	ENSP00000222823:E266K	ENSP00000222823:E266K	E	-	1	0	NOD1	30458762	0.667000	0.27484	0.795000	0.32087	0.978000	0.69477	2.119000	0.41958	2.602000	0.87976	0.563000	0.77884	GAG	T|0.303;G|0.002	0.303	strong		0.617	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
BHLHB9	80823	hgsc.bcm.edu	37	X	102004046	102004046	+	Silent	SNP	G	G	A	rs17003869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102004046G>A	ENST00000372735.1	+	4	708	c.123G>A	c.(121-123)agG>agA	p.R41R	BHLHB9_ENST00000361229.4_Silent_p.R41R|BHLHB9_ENST00000457056.1_Silent_p.R41R|BHLHB9_ENST00000447531.1_Silent_p.R41R|BHLHB9_ENST00000448867.1_Silent_p.R41R			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	41					learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCAAGACCAGGGCCAAAGCAA	0.502													G|||	50	0.013245	0.0371	0.0014	3775	,	,		15788	0.0		0.0	False		,,,				2504	0.0				p.R41R		Atlas-SNP	.											.	BHLHB9	60	.	0			c.G123A						PASS	.	G	,,,,,,,	149,3686		2,117,28,1513,543	120.0	102.0	108.0		123,123,123,123,123,123,123,123	-3.2	0.0	X	dbSNP_123	108	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BHLHB9	NM_001142524.1,NM_001142525.1,NM_001142526.1,NM_001142527.1,NM_001142528.1,NM_001142529.1,NM_001142530.1,NM_030639.2	,,,,,,,	2,117,28,3941,2415	AA,AG,A,GG,G		0.0,3.8853,1.4106	,,,,,,,	41/548,41/548,41/548,41/548,41/548,41/548,41/548,41/548	102004046	149,10414	2203	4300	6503	SO:0001819	synonymous_variant	80823	exon2			GACCAGGGCCAAA	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"""Basic helix-loop-helix proteins"", ""Armadillo repeat containing"""	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.123G>A	X.37:g.102004046G>A		Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	412	145	0.351942	NM_001142530	Q9C0G2	Silent	SNP	ENST00000372735.1	37	CCDS14502.1																																																																																			0|0.003;A|0.015	0.015	strong		0.502	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639	
PABPC3	5042	hgsc.bcm.edu	37	13	25670873	25670873	+	Silent	SNP	A	A	G	rs77142265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25670873A>G	ENST00000281589.3	+	1	574	c.537A>G	c.(535-537)cgA>cgG	p.R179R		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	179					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		GTAAAGAACGAGAAGCTGAAC	0.408													a|||	274	0.0547125	0.0779	0.0591	5008	,	,		22193	0.0347		0.0318	False		,,,				2504	0.0644				p.R179R		Atlas-SNP	.											PABPC3,colon,carcinoma,+2,1	PABPC3	129	1	0			c.A537G						scavenged	.						103.0	96.0	98.0					13																	25670873		2203	4300	6503	SO:0001819	synonymous_variant	5042	exon1			AGAACGAGAAGCT	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.537A>G	13.37:g.25670873A>G		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	205	9	0.0439024	NM_030979	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	37	CCDS9311.1																																																																																			A|0.500;G|0.500	0.500	weak		0.408	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
ZBTB40	9923	hgsc.bcm.edu	37	1	22816687	22816687	+	Silent	SNP	A	A	G	rs115103344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:22816687A>G	ENST00000375647.4	+	2	453	c.246A>G	c.(244-246)aaA>aaG	p.K82K	ZBTB40_ENST00000374651.4_Silent_p.K82K|ZBTB40_ENST00000404138.1_Silent_p.K82K	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	82	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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)		ACACGGGCAAACTACCTGTGG	0.473													A|||	31	0.0061901	0.0204	0.0043	5008	,	,		21552	0.0		0.001	False		,,,				2504	0.0				p.K82K		Atlas-SNP	.											.	ZBTB40	87	.	0			c.A246G						PASS	.	A	,	74,4332	65.3+/-102.7	0,74,2129	90.0	85.0	87.0		246,246	-3.0	0.6	1	dbSNP_132	87	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ZBTB40	NM_001083621.1,NM_014870.3	,	0,75,6428	GG,GA,AA		0.0116,1.6795,0.5767	,	82/1240,82/1240	22816687	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	9923	exon3			GGGCAAACTACCT	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.246A>G	1.37:g.22816687A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	122	62	0.508197	NM_001083621	O75066|Q5TFU5|Q8N1R1	Silent	SNP	ENST00000375647.4	37	CCDS224.1																																																																																			A|0.993;G|0.007	0.007	strong		0.473	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870	
RGCC	28984	hgsc.bcm.edu	37	13	42032572	42032572	+	Silent	SNP	T	T	C	rs7136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:42032572T>C	ENST00000379359.3	+	2	350	c.201T>C	c.(199-201)agT>agC	p.S67S		NM_014059.2	NP_054778.2	Q9H4X1	RGCC_HUMAN	regulator of cell cycle	67	Ser/Thr-rich.				cellular response to hypoxia (GO:0071456)|complement activation (GO:0006956)|fibroblast activation (GO:0072537)|mitotic cell cycle arrest (GO:0071850)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of exit from mitosis (GO:0001100)|negative regulation of fibroblast growth factor production (GO:0090272)|negative regulation of mitotic cell cycle phase transition (GO:1901991)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of mitosis (GO:0045840)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stress fiber assembly (GO:0051496)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)										GCAGCGCCAGTGTCAGCGACA	0.682													.|||	2788	0.556709	0.7829	0.5447	5008	,	,		14651	0.6766		0.3946	False		,,,				2504	0.3027				p.S67S		Atlas-SNP	.											.	.	.	.	0			c.T201C						PASS	.	C		2432,1322		809,814,254	8.0	9.0	9.0		201	3.6	1.0	13	dbSNP_52	9	3009,5139		592,1825,1657	no	coding-synonymous	C13orf15	NM_014059.2		1401,2639,1911	CC,CT,TT		36.9293,35.2158,45.715		67/138	42032572	5441,6461	1877	4074	5951	SO:0001819	synonymous_variant	28984	exon2			CGCCAGTGTCAGC	AF036549	CCDS41880.1	13q14.11	2012-02-20	2012-02-20	2012-02-20	ENSG00000102760	ENSG00000102760			20369	protein-coding gene	gene with protein product	"""response gene to complement 32"""	610077	"""chromosome 13 open reading frame 15"""	C13orf15		17146433, 19158077, 19652095	Standard	NM_014059		Approved	bA157L14.2, RGC-32, RGC32	uc001uyi.2	Q9H4X1	OTTHUMG00000016796	ENST00000379359.3:c.201T>C	13.37:g.42032572T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_014059	Q6NZ48|Q9UL69	Silent	SNP	ENST00000379359.3	37	CCDS41880.1																																																																																			T|0.426;C|0.574	0.574	strong		0.682	RGCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044684.1	NM_014059	
SLC43A2	124935	hgsc.bcm.edu	37	17	1494567	1494567	+	Silent	SNP	G	G	A	rs12953268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1494567G>A	ENST00000301335.5	-	8	1015	c.927C>T	c.(925-927)gcC>gcT	p.A309A	SLC43A2_ENST00000574274.1_5'UTR|SLC43A2_ENST00000412517.3_Silent_p.A172A|SLC43A2_ENST00000571650.1_Silent_p.A309A|SLC43A2_ENST00000382147.4_Silent_p.A309A	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	309					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		GGGTACCTGCGGCATCCGGCT	0.682													G|||	1399	0.279353	0.0832	0.3127	5008	,	,		11580	0.1508		0.5388	False		,,,				2504	0.3865				p.A309A		Atlas-SNP	.											SLC43A2,NS,carcinoma,0,1	SLC43A2	37	1	0			c.C927T						scavenged	.	G		726,3680	287.2+/-279.2	55,616,1532	42.0	43.0	43.0		927	-5.5	0.1	17	dbSNP_121	43	4715,3885	595.2+/-393.4	1297,2121,882	no	coding-synonymous	SLC43A2	NM_152346.1		1352,2737,2414	AA,AG,GG		45.1744,16.4775,41.8345		309/570	1494567	5441,7565	2203	4300	6503	SO:0001819	synonymous_variant	124935	exon8			ACCTGCGGCATCC	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.927C>T	17.37:g.1494567G>A		Somatic	37	1	0.027027		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																			A|0.422;C|0.000;G|0.578	0.422	strong		0.682	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346	
FAM124A	220108	hgsc.bcm.edu	37	13	51855114	51855114	+	Missense_Mutation	SNP	G	G	T	rs74087446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:51855114G>T	ENST00000322475.8	+	4	1498	c.1363G>T	c.(1363-1365)Gca>Tca	p.A455S	FAM124A_ENST00000280057.6_Missense_Mutation_p.A491S	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	455										breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		CAGCCACTGGGCAGCTCACAA	0.587													G|||	93	0.0185703	0.0696	0.0014	5008	,	,		18065	0.0		0.0	False		,,,				2504	0.0				p.A491S		Atlas-SNP	.											.	FAM124A	61	.	0			c.G1471T						PASS	.	G	SER/ALA,SER/ALA	315,4091	168.3+/-199.2	15,285,1903	55.0	54.0	54.0		1363,1471	-8.6	0.0	13	dbSNP_130	54	0,8600		0,0,4300	yes	missense,missense	FAM124A	NM_001242312.1,NM_145019.3	99,99	15,285,6203	TT,TG,GG		0.0,7.1493,2.422	benign,benign	455/547,491/583	51855114	315,12691	2203	4300	6503	SO:0001583	missense	220108	exon5			CACTGGGCAGCTC	AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.1363G>T	13.37:g.51855114G>T	ENSP00000324625:p.Ala455Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	37	CCDS55900.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	G	6.025	0.373042	0.11409	0.071493	0.0	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.39406	1.13;1.08	5.07	-8.56	0.00904	.	2.466230	0.01371	N	0.012590	T	0.00440	0.0014	N	0.00368	-1.59	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.13818	-1.0495	10	0.05620	T	0.96	-11.5191	5.727	0.18018	0.0847:0.4204:0.3398:0.1551	.	455;491	Q86V42;Q86V42-2	F124A_HUMAN;.	S	455;491	ENSP00000324625:A455S;ENSP00000280057:A491S	ENSP00000280057:A491S	A	+	1	0	FAM124A	50753115	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.686000	0.05161	-1.642000	0.01521	-0.284000	0.09977	GCA	G|0.975;T|0.026	0.026	strong		0.587	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019	
TTN	7273	hgsc.bcm.edu	37	2	179560847	179560847	+	Missense_Mutation	SNP	C	C	T	rs73038324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179560847C>T	ENST00000591111.1	-	112	30225	c.30001G>A	c.(30001-30003)Gaa>Aaa	p.E10001K	TTN_ENST00000589042.1_Missense_Mutation_p.E10318K|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.E9074K|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAAGGTTCTTCGAAAGATTCA	0.383													C|||	194	0.038738	0.1377	0.0159	5008	,	,		19287	0.0		0.001	False		,,,				2504	0.0				p.E10318K		Atlas-SNP	.											.	TTN	18412	.	0			c.G30952A						PASS	.	C	,,,LYS/GLU	347,3211		17,313,1449	126.0	105.0	111.0		,,,27220	5.8	0.9	2	dbSNP_130	111	9,7899		0,9,3945	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,56	17,322,5394	TT,TC,CC		0.1138,9.7527,3.1048	,,,benign	,,,9074/33424	179560847	356,11110	1779	3954	5733	SO:0001583	missense	7273	exon114			GTTCTTCGAAAGA	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.30001G>A	2.37:g.179560847C>T	ENSP00000465570:p.Glu10001Lys	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	234	119	0.508547	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		84	0.038461538461538464	77	0.1565040650406504	7	0.019337016574585635	0	0.0	0	0.0	C	18.27	3.586510	0.66105	0.097527	0.001138	ENSG00000155657	ENST00000342992;ENST00000414766	T	0.64260	-0.09	5.78	5.78	0.91487	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.00356	0.0011	M	0.66939	2.045	0.09310	P	1.0	B;P	0.50710	0.327;0.938	B;B	0.36845	0.026;0.234	T	0.36915	-0.9728	8	0.87932	D	0	.	15.5205	0.75862	0.0:1.0:0.0:0.0	.	10001;10001	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	K	9074;196	ENSP00000343764:E9074K	ENSP00000343764:E9074K	E	-	1	0	TTN	179269092	0.966000	0.33281	0.949000	0.38748	0.899000	0.52679	2.415000	0.44635	2.729000	0.93468	0.650000	0.86243	GAA	C|0.968;T|0.032	0.032	strong		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
UACA	55075	hgsc.bcm.edu	37	15	70968850	70968850	+	Silent	SNP	A	A	G	rs61741196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70968850A>G	ENST00000322954.6	-	13	1298	c.1113T>C	c.(1111-1113)aaT>aaC	p.N371N	UACA_ENST00000560441.1_Silent_p.N358N|UACA_ENST00000539319.1_Silent_p.N262N|UACA_ENST00000379983.2_Silent_p.N358N	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	371					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						ATTTAAATCTATTTTTCAGAG	0.318													A|||	49	0.00978435	0.0356	0.0029	5008	,	,		16930	0.0		0.0	False		,,,				2504	0.0				p.N371N		Atlas-SNP	.											.	UACA	235	.	0			c.T1113C						PASS	.	A	,	142,4254	98.0+/-136.7	1,140,2057	61.0	63.0	62.0		1074,1113	-5.5	0.7	15	dbSNP_129	62	0,8584		0,0,4292	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	1,140,6349	GG,GA,AA		0.0,3.2302,1.094	,	358/1404,371/1417	70968850	142,12838	2198	4292	6490	SO:0001819	synonymous_variant	55075	exon13			AAATCTATTTTTC	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.1113T>C	15.37:g.70968850A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			A|0.989;G|0.011	0.011	strong		0.318	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
DDX60L	91351	hgsc.bcm.edu	37	4	169342926	169342926	+	Silent	SNP	G	G	A	rs73863330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169342926G>A	ENST00000511577.1	-	17	2626	c.2379C>T	c.(2377-2379)taC>taT	p.Y793Y	DDX60L_ENST00000505890.1_Silent_p.Y793Y|DDX60L_ENST00000260184.7_Silent_p.Y793Y			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	793	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)		CGGGTGCAACGTACACAACCA	0.468													g|||	24	0.00479233	0.0182	0.0	5008	,	,		23719	0.0		0.0	False		,,,				2504	0.0				p.Y793Y		Atlas-SNP	.											DDX60L,NS,carcinoma,-1,1	DDX60L	116	1	0			c.C2379T						PASS	.	A		61,4345	57.4+/-93.9	0,61,2142	225.0	226.0	226.0		2379	1.4	0.0	4	dbSNP_130	226	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	DDX60L	NM_001012967.1		0,72,6431	AA,AG,GG		0.1279,1.3845,0.5536		793/1707	169342926	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	91351	exon17			TGCAACGTACACA	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.2379C>T	4.37:g.169342926G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	106	62	0.584906	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				G|0.994;A|0.006	0.006	strong		0.468	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
CCDC105	126402	hgsc.bcm.edu	37	19	15133787	15133787	+	Silent	SNP	C	C	A	rs10424547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15133787C>A	ENST00000292574.3	+	7	1438	c.1356C>A	c.(1354-1356)atC>atA	p.I452I		NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	452						extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						GCAAGAACATCGGGCATGAGG	0.637													c|||	1610	0.321486	0.1203	0.4323	5008	,	,		15747	0.5208		0.2346	False		,,,				2504	0.3988				p.I452I		Atlas-SNP	.											.	CCDC105	53	.	0			c.C1356A						PASS	.			739,3667	291.5+/-281.6	62,615,1526	55.0	40.0	45.0		1356	-6.5	0.0	19	dbSNP_119	45	2035,6563	339.6+/-323.3	227,1581,2491	no	coding-synonymous	CCDC105	NM_173482.2		289,2196,4017	AA,AC,CC		23.6683,16.7726,21.3319		452/500	15133787	2774,10230	2203	4299	6502	SO:0001819	synonymous_variant	126402	exon7			GAACATCGGGCAT	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.1356C>A	19.37:g.15133787C>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	167	70	0.419162	NM_173482	Q8N7T5|Q8NDL5	Silent	SNP	ENST00000292574.3	37	CCDS12322.1																																																																																			C|0.749;A|0.251	0.251	strong		0.637	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482	
SNX31	169166	hgsc.bcm.edu	37	8	101608919	101608919	+	Missense_Mutation	SNP	T	T	C	rs2248609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101608919T>C	ENST00000311812.2	-	10	1076	c.926A>G	c.(925-927)cAg>cGg	p.Q309R	SNX31_ENST00000428383.2_Missense_Mutation_p.Q210R|SNX31_ENST00000519521.1_5'UTR	NM_152628.3	NP_689841.3	Q8N9S9	SNX31_HUMAN	sorting nexin 31	309			Q -> R (in dbSNP:rs2248609).		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)			AACGATGTCCTGGGTCTGGCT	0.498													T|||	1922	0.383786	0.5416	0.4611	5008	,	,		21650	0.1835		0.3539	False		,,,				2504	0.3528				p.Q309R		Atlas-SNP	.											.	SNX31	66	.	0			c.A926G						PASS	.	T	ARG/GLN	2351,2055	608.4+/-391.2	599,1153,451	117.0	115.0	116.0		926	0.9	0.6	8	dbSNP_100	116	2944,5656	457.9+/-364.5	524,1896,1880	yes	missense	SNX31	NM_152628.3	43	1123,3049,2331	CC,CT,TT		34.2326,46.6409,40.712	benign	309/441	101608919	5295,7711	2203	4300	6503	SO:0001583	missense	169166	exon10			ATGTCCTGGGTCT		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.926A>G	8.37:g.101608919T>C	ENSP00000312368:p.Gln309Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_152628	C9J6L9|Q8N0U9	Missense_Mutation	SNP	ENST00000311812.2	37	CCDS6288.1	797	0.3649267399267399	263	0.5345528455284553	162	0.44751381215469616	106	0.1853146853146853	266	0.35092348284960423	T	0.748	-0.773849	0.02951	0.533591	0.342326	ENSG00000174226	ENST00000311812;ENST00000428383	T;T	0.24723	2.19;1.84	4.55	0.908	0.19326	.	0.440276	0.20934	N	0.083042	T	0.00012	0.0000	L	0.45581	1.43	0.37480	P	0.08402500000000002	B;B	0.17667	0.023;0.003	B;B	0.16289	0.015;0.002	T	0.46610	-0.9179	9	0.15066	T	0.55	-3.2851	7.7599	0.28946	0.0:0.2575:0.0:0.7425	rs2248609;rs52819632;rs61025809;rs2248609	210;309	Q8N9S9-2;Q8N9S9	.;SNX31_HUMAN	R	309;210	ENSP00000312368:Q309R;ENSP00000405024:Q210R	ENSP00000312368:Q309R	Q	-	2	0	SNX31	101678095	0.991000	0.36638	0.572000	0.28498	0.048000	0.14542	0.177000	0.16801	0.005000	0.14708	0.460000	0.39030	CAG	T|0.613;C|0.387	0.387	strong		0.498	SNX31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379910.1	NM_152628	
FAT3	120114	hgsc.bcm.edu	37	11	92590448	92590448	+	Missense_Mutation	SNP	A	A	G	rs4753069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92590448A>G	ENST00000298047.6	+	19	11451	c.11434A>G	c.(11434-11436)Agt>Ggt	p.S3812G	FAT3_ENST00000525166.1_Missense_Mutation_p.S3662G|FAT3_ENST00000409404.2_Missense_Mutation_p.S3812G|FAT3_ENST00000533797.1_Missense_Mutation_p.S147G			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3812	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.		S -> G (in dbSNP:rs4753069). {ECO:0000269|PubMed:11811999}.		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)				GCAGTGTGTCAGTTATGAAGC	0.537										TCGA Ovarian(4;0.039)			G|||	4149	0.828474	0.9191	0.7968	5008	,	,		19078	0.6706		0.8121	False		,,,				2504	0.908				p.S3812G		Atlas-SNP	.											.	FAT3	1822	.	0			c.A11434G						PASS	.	G	GLY/SER	3706,356		1694,318,19	116.0	123.0	121.0		11434	4.1	0.4	11	dbSNP_111	121	6781,1615		2754,1273,171	yes	missense	FAT3	NM_001008781.2	56	4448,1591,190	GG,GA,AA		19.2354,8.7642,15.8212	benign	3812/4558	92590448	10487,1971	2031	4198	6229	SO:0001583	missense	120114	exon19			TGTGTCAGTTATG	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.11434A>G	11.37:g.92590448A>G	ENSP00000298047:p.Ser3812Gly	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		1749	0.8008241758241759	458	0.9308943089430894	288	0.7955801104972375	394	0.6888111888111889	609	0.8034300791556728	G	4.059	0.008696	0.07912	0.912358	0.807646	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;T	0.27890	1.64;1.64;1.64;1.64	5.95	4.1	0.47936	Concanavalin A-like lectin/glucanase, subgroup (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	N	0.02315	-0.6	0.09310	P	0.9999999999902903	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27297	-1.0078	8	0.14252	T	0.57	.	11.5604	0.50774	0.1905:0.0:0.8095:0.0	rs4753069;rs52805125;rs56954308;rs4753069	3812;3812	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	G	3812;3812;3662;147	ENSP00000298047:S3812G;ENSP00000387040:S3812G;ENSP00000432586:S3662G;ENSP00000436399:S147G	ENSP00000298047:S3812G	S	+	1	0	FAT3	92230096	0.995000	0.38212	0.419000	0.26584	0.944000	0.59088	2.301000	0.43628	0.446000	0.26666	-1.551000	0.00897	AGT	A|0.184;G|0.816	0.816	strong		0.537	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
HIVEP1	3096	hgsc.bcm.edu	37	6	12124587	12124587	+	Missense_Mutation	SNP	C	C	G	rs2228212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:12124587C>G	ENST00000379388.2	+	4	4891	c.4559C>G	c.(4558-4560)gCa>gGa	p.A1520G	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1520			A -> G (in dbSNP:rs2228212). {ECO:0000269|PubMed:15489334}.		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)				CAAATCCATGCACCGCCTAGC	0.438													C|||	1242	0.248003	0.1982	0.3141	5008	,	,		20407	0.1796		0.3439	False		,,,				2504	0.2403				p.A1520G		Atlas-SNP	.											.	HIVEP1	242	.	0			c.C4559G						PASS	.	C	GLY/ALA	815,3079		93,629,1225	71.0	68.0	69.0		4559	-3.8	0.0	6	dbSNP_98	69	2947,5359		515,1917,1721	yes	missense	HIVEP1	NM_002114.2	60	608,2546,2946	GG,GC,CC		35.4804,20.9296,30.8361	benign	1520/2719	12124587	3762,8438	1947	4153	6100	SO:0001583	missense	3096	exon4			TCCATGCACCGCC	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.4559C>G	6.37:g.12124587C>G	ENSP00000368698:p.Ala1520Gly	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	584	0.2673992673992674	102	0.2073170731707317	117	0.32320441988950277	92	0.16083916083916083	273	0.36015831134564646	C	8.046	0.764953	0.15914	0.209296	0.354804	ENSG00000095951	ENST00000379388	T	0.08984	3.03	5.93	-3.84	0.04256	.	2.326850	0.02143	N	0.057348	T	0.01558	0.0050	N	0.22421	0.69	0.80722	P	0.0	B	0.23806	0.091	B	0.16722	0.016	T	0.43940	-0.9360	8	.	.	.	3.6801	7.1783	0.25757	0.1612:0.3873:0.0:0.4515	rs2228212;rs17677180;rs52809676;rs2228212	1520	P15822	ZEP1_HUMAN	G	1520	ENSP00000368698:A1520G	.	A	+	2	0	HIVEP1	12232573	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.720000	0.04969	-0.373000	0.07979	-0.218000	0.12543	GCA	C|0.714;G|0.286	0.286	strong		0.438	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
DAW1	164781	hgsc.bcm.edu	37	2	228750106	228750106	+	Missense_Mutation	SNP	C	C	T	rs11894733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228750106C>T	ENST00000309931.2	+	2	163	c.80C>T	c.(79-81)aCt>aTt	p.T27I	SNORA25_ENST00000607153.1_RNA|DAW1_ENST00000545118.1_Missense_Mutation_p.T12I|DAW1_ENST00000373666.2_Missense_Mutation_p.T27I	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	27			T -> I (in dbSNP:rs11894733).			cilium (GO:0005929)											GAATTAAAGACTAAGTCCATA	0.343													C|||	299	0.0597045	0.2179	0.0159	5008	,	,		14283	0.0		0.0	False		,,,				2504	0.0				p.T27I		Atlas-SNP	.											.	.	.	.	0			c.C80T						PASS	.	C	ILE/THR	760,3646	307.2+/-289.9	67,626,1510	113.0	118.0	116.0		80	4.6	1.0	2	dbSNP_120	116	9,8591	7.1+/-27.0	0,9,4291	yes	missense	WDR69	NM_178821.1	89	67,635,5801	TT,TC,CC		0.1047,17.2492,5.9127	possibly-damaging	27/416	228750106	769,12237	2203	4300	6503	SO:0001583	missense	164781	exon2			TAAAGACTAAGTC		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.80C>T	2.37:g.228750106C>T	ENSP00000311899:p.Thr27Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_178821	Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	109	0.04990842490842491	102	0.2073170731707317	7	0.019337016574585635	0	0.0	0	0.0	C	12.91	2.079117	0.36662	0.172492	0.001047	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000440997;ENST00000545118	T;T;T;T	0.53423	0.69;0.64;0.71;0.62	5.52	4.61	0.57282	.	0.172732	0.50627	D	0.000108	T	0.00073	0.0002	M	0.81341	2.54	0.19575	P	0.9999648258	P	0.52170	0.951	P	0.44394	0.448	T	0.08638	-1.0712	9	0.41790	T	0.15	.	10.7579	0.46247	0.0:0.9014:0.0:0.0986	rs11894733;rs52813204;rs56552186;rs58221385;rs11894733	27	Q8N136	WDR69_HUMAN	I	27;27;12;12	ENSP00000362770:T27I;ENSP00000311899:T27I;ENSP00000394853:T12I;ENSP00000437887:T12I	ENSP00000311899:T27I	T	+	2	0	WDR69	228458350	1.000000	0.71417	0.995000	0.50966	0.330000	0.28571	4.893000	0.63199	1.234000	0.43709	0.655000	0.94253	ACT	C|0.939;T|0.061	0.061	strong		0.343	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821	
MEI1	150365	hgsc.bcm.edu	37	22	42191540	42191540	+	Silent	SNP	C	C	T	rs6002488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42191540C>T	ENST00000401548.3	+	29	3700	c.3660C>T	c.(3658-3660)ttC>ttT	p.F1220F	MEI1_ENST00000300398.4_Intron|MEI1_ENST00000476893.1_3'UTR|MEI1_ENST00000400107.1_Silent_p.F553F	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						ATGGCTTCTTCCAGCAGGTGG	0.572													c|||	943	0.188299	0.5681	0.1196	5008	,	,		19801	0.0278		0.0219	False		,,,				2504	0.0603				p.F1220F		Atlas-SNP	.											.	MEI1	87	.	0			c.C3660T						PASS	.	C		1859,2241		425,1009,616	77.0	79.0	79.0		3660	0.7	1.0	22	dbSNP_114	79	218,8166		4,210,3978	no	coding-synonymous	MEI1	NM_152513.3		429,1219,4594	TT,TC,CC		2.6002,45.3415,16.6373		1220/1275	42191540	2077,10407	2050	4192	6242	SO:0001819	synonymous_variant	150365	exon29			CTTCTTCCAGCAG	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"""spermatogenesis associated 38"""	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.3660C>T	22.37:g.42191540C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_152513		Silent	SNP	ENST00000401548.3	37	CCDS46718.1																																																																																			C|0.830;T|0.170	0.170	strong		0.572	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513	
CCDC15	80071	hgsc.bcm.edu	37	11	124862514	124862514	+	Silent	SNP	A	A	G	rs6590113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124862514A>G	ENST00000344762.5	+	10	2329	c.2070A>G	c.(2068-2070)gaA>gaG	p.E690E	CCDC15_ENST00000529051.1_Silent_p.E690E	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	690						centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		GAGTGAGAGAAGAATTGCCTC	0.363													G|||	1437	0.286941	0.4705	0.1801	5008	,	,		9619	0.1935		0.1958	False		,,,				2504	0.3047				p.E690E		Atlas-SNP	.											.	CCDC15	134	.	0			c.A2070G						PASS	.	G		1575,2085		356,863,611	66.0	60.0	62.0		2070	-2.2	0.0	11	dbSNP_116	62	1630,6548		170,1290,2629	no	coding-synonymous	CCDC15	NM_025004.2		526,2153,3240	GG,GA,AA		19.9315,43.0328,27.0738		690/952	124862514	3205,8633	1830	4089	5919	SO:0001819	synonymous_variant	80071	exon10			GAGAGAAGAATTG	BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.2070A>G	11.37:g.124862514A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_025004	Q9H8U7	Silent	SNP	ENST00000344762.5	37	CCDS44756.1																																																																																			A|0.728;G|0.272	0.272	strong		0.363	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
TG	7038	hgsc.bcm.edu	37	8	133900495	133900495	+	Missense_Mutation	SNP	G	G	A	rs16904774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133900495G>A	ENST00000220616.4	+	10	2483	c.2443G>A	c.(2443-2445)Gga>Aga	p.G815R	TG_ENST00000377869.1_Missense_Mutation_p.G815R	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	815	Thyroglobulin type-1 7. {ECO:0000255|PROSITE-ProRule:PRU00500}.		G -> R (in dbSNP:rs16904774).		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)		AGCAGCTTCCGGAAACTTCAG	0.512													G|||	258	0.0515176	0.1029	0.013	5008	,	,		19104	0.0883		0.0119	False		,,,				2504	0.0123				p.G815R		Atlas-SNP	.											.	TG	416	.	0			c.G2443A						PASS	.	G	ARG/GLY	400,4006	197.7+/-221.8	24,352,1827	74.0	71.0	72.0		2443	-1.2	0.0	8	dbSNP_123	72	16,8584	11.2+/-40.8	0,16,4284	yes	missense	TG	NM_003235.4	125	24,368,6111	AA,AG,GG		0.186,9.0785,3.1985	benign	815/2769	133900495	416,12590	2203	4300	6503	SO:0001583	missense	7038	exon10			GCTTCCGGAAACT	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.2443G>A	8.37:g.133900495G>A	ENSP00000220616:p.Gly815Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	138	60	0.434783	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	112	0.05128205128205128	51	0.10365853658536585	4	0.011049723756906077	45	0.07867132867132867	12	0.0158311345646438	G	0.299	-0.975229	0.02215	0.090785	0.00186	ENSG00000042832	ENST00000377869;ENST00000220616	T;T	0.62232	0.04;0.04	5.8	-1.19	0.09585	Thyroglobulin type-1 (2);	1.905200	0.02188	N	0.061091	T	0.01254	0.0041	N	0.13043	0.29	0.80722	P	0.0	B	0.15719	0.014	B	0.06405	0.002	T	0.14035	-1.0487	9	0.05721	T	0.95	.	8.1648	0.31220	0.5175:0.1056:0.3769:0.0	rs16904774;rs52835748;rs16904774	815	P01266	THYG_HUMAN	R	815	ENSP00000367100:G815R;ENSP00000220616:G815R	ENSP00000220616:G815R	G	+	1	0	TG	133969677	0.000000	0.05858	0.011000	0.14972	0.589000	0.36550	-0.692000	0.05127	-0.596000	0.05821	0.650000	0.86243	GGA	G|0.957;A|0.043	0.043	strong		0.512	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
USH2A	7399	hgsc.bcm.edu	37	1	215960167	215960167	+	Missense_Mutation	SNP	T	T	G	rs10864198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:215960167T>G	ENST00000307340.3	-	52	10618	c.10232A>C	c.(10231-10233)gAa>gCa	p.E3411A	USH2A_ENST00000366943.2_Missense_Mutation_p.E3411A	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3411	Fibronectin type-III 19. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> A (in dbSNP:rs10864198). {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)			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)		GCCACAATGTTCTGTGGCTTC	0.458										HNSCC(13;0.011)			G|||	2948	0.588658	0.7057	0.4899	5008	,	,		17203	0.6518		0.5358	False		,,,				2504	0.4898				p.E3411A		Atlas-SNP	.											.	USH2A	1168	.	0			c.A10232C						PASS	.	G	ALA/GLU	2959,1447	468.1+/-355.0	1004,951,248	64.0	60.0	61.0		10232	4.9	0.2	1	dbSNP_120	61	4462,4138	563.2+/-388.1	1153,2156,991	yes	missense	USH2A	NM_206933.2	107	2157,3107,1239	GG,GT,TT		48.1163,32.8416,42.9417	benign	3411/5203	215960167	7421,5585	2203	4300	6503	SO:0001583	missense	7399	exon52			CAATGTTCTGTGG	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.10232A>C	1.37:g.215960167T>G	ENSP00000305941:p.Glu3411Ala	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	1313	0.6011904761904762	346	0.7032520325203252	182	0.5027624309392266	383	0.6695804195804196	402	0.5303430079155673	G	0.015	-1.570097	0.00895	0.671584	0.518837	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.07327	3.21;3.2	4.88	4.88	0.63580	Fibronectin, type III (3);	0.000000	0.44688	N	0.000427	T	0.00012	0.0000	N	0.00077	-2.24	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.37572	-0.9700	9	0.02654	T	1	.	13.0708	0.59059	0.0:0.0:0.8389:0.1611	rs10864198;rs52802661;rs59777001;rs10864198	3411	O75445	USH2A_HUMAN	A	3411	ENSP00000305941:E3411A;ENSP00000355910:E3411A	ENSP00000305941:E3411A	E	-	2	0	USH2A	214026790	0.996000	0.38824	0.163000	0.22734	0.037000	0.13140	2.598000	0.46223	1.040000	0.40099	-0.121000	0.15023	GAA	T|0.409;G|0.591	0.591	strong		0.458	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
ZBTB11	27107	hgsc.bcm.edu	37	3	101370091	101370091	+	Silent	SNP	C	C	T	rs34525894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101370091C>T	ENST00000312938.4	-	11	3661	c.3081G>A	c.(3079-3081)caG>caA	p.Q1027Q		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	1027					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(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TCTGTCCTTGCTGTTGTGCTA	0.378													C|||	258	0.0515176	0.1891	0.0115	5008	,	,		24052	0.0		0.0	False		,,,				2504	0.0				p.Q1027Q		Atlas-SNP	.											.	ZBTB11	77	.	0			c.G3081A						PASS	.	C		757,3649	309.7+/-291.2	72,613,1518	132.0	129.0	130.0		3081	5.4	1.0	3	dbSNP_126	130	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZBTB11	NM_014415.3		72,615,5816	TT,TC,CC		0.0233,17.1811,5.8358		1027/1054	101370091	759,12247	2203	4300	6503	SO:0001819	synonymous_variant	27107	exon11			TCCTTGCTGTTGT	U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.3081G>A	3.37:g.101370091C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	221	95	0.429864	NM_014415	Q2NKP9	Silent	SNP	ENST00000312938.4	37	CCDS2943.1																																																																																			C|0.948;T|0.052	0.052	strong		0.378	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415	
MCF2L	23263	hgsc.bcm.edu	37	13	113729414	113729414	+	Missense_Mutation	SNP	C	C	T	rs74926660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113729414C>T	ENST00000375608.3	+	12	1367	c.1309C>T	c.(1309-1311)Cgg>Tgg	p.R437W	MCF2L_ENST00000423482.2_Missense_Mutation_p.R405W|MCF2L_ENST00000375604.2_Missense_Mutation_p.R464W|MCF2L_ENST00000442652.2_Missense_Mutation_p.R437W|MCF2L_ENST00000397030.1_Missense_Mutation_p.R440W|MCF2L_ENST00000375601.3_Missense_Mutation_p.R411W|MCF2L_ENST00000535094.2_Missense_Mutation_p.R407W|MCF2L_ENST00000434480.2_Missense_Mutation_p.R413W|MCF2L_ENST00000375597.4_Missense_Mutation_p.R405W|MCF2L_ENST00000421756.1_Missense_Mutation_p.R411W			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	437					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)				CCAGGAGCTCCGGCACCTCTG	0.667													C|||	67	0.0133786	0.0204	0.0231	5008	,	,		14912	0.0208		0.0	False		,,,				2504	0.0031				p.R407W		Atlas-SNP	.											.	MCF2L	182	.	0			c.C1219T						PASS	.	C	TRP/ARG,TRP/ARG	89,4317	75.2+/-113.4	0,89,2114	60.0	68.0	65.0		1219,1213	4.9	0.9	13	dbSNP_131	65	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	MCF2L	NM_001112732.2,NM_024979.4	101,101	0,91,6412	TT,TC,CC		0.0233,2.02,0.6997	probably-damaging,probably-damaging	407/1126,405/1124	113729414	91,12915	2203	4300	6503	SO:0001583	missense	23263	exon11			GAGCTCCGGCACC	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.1309C>T	13.37:g.113729414C>T	ENSP00000364758:p.Arg437Trp	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	37		32|32	0.014652014652014652|0.014652014652014652	14|14	0.028455284552845527|0.028455284552845527	4|4	0.011049723756906077|0.011049723756906077	12|12	0.02097902097902098|0.02097902097902098	2|2	0.002638522427440633|0.002638522427440633	C|C	14.59|14.59	2.580228|2.580228	0.46006|0.46006	0.0202|0.0202	2.33E-4|2.33E-4	ENSG00000126217|ENSG00000126217	ENST00000397017|ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000440749	.|T;T;T;T;T;T;T;T;T;T	.|0.18016	.|2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	.|0.622889	.|0.16873	.|N	.|0.196041	T|T	0.19565|0.19565	0.0470|0.0470	M|M	0.77616|0.77616	2.38|2.38	0.09310|0.09310	N|N	0.999999|0.999999	.|D;D;D;D;D;D	.|0.89917	.|0.999;0.996;0.999;1.0;0.985;0.999	.|P;P;P;D;P;D	.|0.70016	.|0.88;0.88;0.888;0.967;0.828;0.954	T|T	0.06180|0.06180	-1.0841|-1.0841	5|10	.|0.87932	.|D	.|0	.|.	13.7445|13.7445	0.62868|0.62868	0.0:0.8458:0.1542:0.0|0.0:0.8458:0.1542:0.0	.|.	.|405;407;464;369;405;437	.|E9PDN8;O15068-9;G5E9A1;E2QRA2;O15068-4;O15068	.|.;.;.;.;.;MCF2L_HUMAN	L|W	67|437;437;464;440;407;411;411;413;405;405;248	.|ENSP00000364758:R437W;ENSP00000401422:R437W;ENSP00000364754:R464W;ENSP00000380225:R440W;ENSP00000440374:R407W;ENSP00000397285:R411W;ENSP00000364751:R411W;ENSP00000407722:R413W;ENSP00000405639:R405W;ENSP00000364747:R405W	.|ENSP00000364747:R405W	P|R	+|+	2|1	0|2	MCF2L|MCF2L	112777415|112777415	0.609000|0.609000	0.26975|0.26975	0.886000|0.886000	0.34754|0.34754	0.181000|0.181000	0.23173|0.23173	1.666000|1.666000	0.37460|0.37460	2.239000|2.239000	0.73571|0.73571	0.561000|0.561000	0.74099|0.74099	CCG|CGG	C|0.990;T|0.010	0.010	strong		0.667	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
KRT8	3856	hgsc.bcm.edu	37	12	53298675	53298675	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53298675A>C	ENST00000552551.1	-	2	523	c.91T>G	c.(91-93)Tcc>Gcc	p.S31A	KRT8_ENST00000546897.1_Missense_Mutation_p.S31A|KRT8_ENST00000552150.1_Missense_Mutation_p.S59A|KRT8_ENST00000293308.6_Missense_Mutation_p.S31A			P05787	K2C8_HUMAN	keratin 8	31	Head.|Ser-rich.				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)	p.S31A(4)		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)	CTGATGCGGGAACCGGGCCCA	0.662																																					p.S59A		Atlas-SNP	.											KRT8,NS,carcinoma,0,5	KRT8	41	5	4	Substitution - Missense(4)	endometrium(2)|prostate(1)|liver(1)	c.T175G						scavenged	.						12.0	14.0	13.0					12																	53298675		2120	4158	6278	SO:0001583	missense	3856	exon2			TGCGGGAACCGGG	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.91T>G	12.37:g.53298675A>C	ENSP00000447566:p.Ser31Ala	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	129	4	0.0310078	NM_001256282	A8K4H3|B0AZN5|F8VXB4|Q14099|Q14716|Q14717|Q53GJ0|Q6DHW5|Q6GMY0|Q6P4C7|Q96J60	Missense_Mutation	SNP	ENST00000552551.1	37	CCDS8841.1	.	.	.	.	.	.	.	.	.	.	-	0.012	-1.651707	0.00785	.	.	ENSG00000170421	ENST00000552551;ENST00000293308;ENST00000547916;ENST00000546897;ENST00000552150;ENST00000546826;ENST00000548998;ENST00000547413;ENST00000546542	T;T;T;T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37	4.05	-8.11	0.01082	.	0.706613	0.13676	N	0.370518	T	0.40619	0.1124	N	0.01197	-0.965	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	0.43589	-0.9382	10	0.05351	T	0.99	.	6.5956	0.22672	0.4212:0.312:0.0:0.2668	.	59;31;31	F8VXB4;F8VU64;P05787	.;.;K2C8_HUMAN	A	31;31;31;31;59;31;71;31;109	ENSP00000447566:S31A;ENSP00000293308:S31A;ENSP00000447402:S31A;ENSP00000449404:S59A;ENSP00000447881:S31A;ENSP00000447040:S71A;ENSP00000448681:S31A;ENSP00000450228:S109A	ENSP00000293308:S31A	S	-	1	0	KRT8	51584942	0.005000	0.15991	0.000000	0.03702	0.065000	0.16274	-0.018000	0.12568	-3.264000	0.00201	-0.290000	0.09829	TCC	.	.	none		0.662	KRT8-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406385.1	NM_002273	
SPHK2	56848	hgsc.bcm.edu	37	19	49132646	49132646	+	Silent	SNP	G	G	A	rs75629654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49132646G>A	ENST00000245222.4	+	7	1947	c.1581G>A	c.(1579-1581)ctG>ctA	p.L527L	SPHK2_ENST00000600537.1_Silent_p.L468L|SPHK2_ENST00000443164.1_Silent_p.L589L|SPHK2_ENST00000340932.3_Silent_p.L489L|SPHK2_ENST00000599029.1_Silent_p.L491L|SPHK2_ENST00000599748.1_Silent_p.L491L|SPHK2_ENST00000598088.1_Silent_p.L527L	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	527					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)		GCACCCCGCTGCCCCCAGACT	0.711													G|||	273	0.0545128	0.1944	0.0216	5008	,	,		12771	0.001		0.0	False		,,,				2504	0.0				p.L527L		Atlas-SNP	.											.	SPHK2	62	.	0			c.G1581A						PASS	.	G	,,,	717,3679		52,613,1533	19.0	21.0	20.0		1404,1581,1473,1581	0.3	0.9	19	dbSNP_131	20	4,8590		0,4,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK2	NM_001204158.2,NM_001204159.2,NM_001204160.2,NM_020126.4	,,,	52,617,5826	AA,AG,GG		0.0465,16.3103,5.5504	,,,	468/596,527/655,491/619,527/655	49132646	721,12269	2198	4297	6495	SO:0001819	synonymous_variant	56848	exon7			CCCGCTGCCCCCA	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.1581G>A	19.37:g.49132646G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Silent	SNP	ENST00000245222.4	37	CCDS12727.1																																																																																			G|0.940;A|0.060	0.060	strong		0.711	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
GHR	2690	hgsc.bcm.edu	37	5	42719239	42719239	+	Missense_Mutation	SNP	A	A	C	rs6180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:42719239A>C	ENST00000230882.4	+	10	1820	c.1630A>C	c.(1630-1632)Atc>Ctc	p.I544L	GHR_ENST00000357703.3_Missense_Mutation_p.I522L|GHR_ENST00000537449.1_Missense_Mutation_p.I357L	NM_000163.4|NM_001242399.2|NM_001242400.2|NM_001242401.3|NM_001242402.2|NM_001242403.2|NM_001242404.2|NM_001242405.2|NM_001242406.2	NP_000154.1|NP_001229328.1|NP_001229329.1|NP_001229330.1|NP_001229331.1|NP_001229332.1|NP_001229333.1|NP_001229334.1|NP_001229335.1	P10912	GHR_HUMAN	growth hormone receptor	544			I -> L (polymorphism with a modifier effect on plasma HDL cholesterol levels in familial hypercholesterolemia patients; dbSNP:rs6180). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:12910492, ECO:0000269|PubMed:2813379}.		2-oxoglutarate metabolic process (GO:0006103)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPK activity (GO:0000187)|allantoin metabolic process (GO:0000255)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|endocytosis (GO:0006897)|fatty acid metabolic process (GO:0006631)|growth hormone receptor signaling pathway (GO:0060396)|insulin-like growth factor receptor signaling pathway (GO:0048009)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|multicellular organismal metabolic process (GO:0044236)|oxaloacetate metabolic process (GO:0006107)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|receptor internalization (GO:0031623)|regulation of multicellular organism growth (GO:0040014)|response to cycloheximide (GO:0046898)|response to estradiol (GO:0032355)|succinate metabolic process (GO:0006105)|taurine metabolic process (GO:0019530)|valine metabolic process (GO:0006573)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|growth hormone receptor complex (GO:0070195)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine receptor activity (GO:0004896)|growth factor binding (GO:0019838)|peptide hormone binding (GO:0017046)|proline-rich region binding (GO:0070064)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			NS(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	CAAAAAGTGCATCCCTGTGGC	0.478													A|||	2226	0.444489	0.379	0.4006	5008	,	,		24092	0.5694		0.4185	False		,,,				2504	0.4622				p.I551L		Atlas-SNP	.											.	GHR	94	.	0			c.A1651C	GRCh37	CM032246	GHR	M	rs6180	PASS	.	A	LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,,	1714,2692	515.9+/-369.0	327,1060,816	103.0	87.0	92.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1630,1651,1630,1630,1630,1630,1630,1630,1630,1564,,	3.4	1.0	5	dbSNP_52	92	3961,4639	550.4+/-385.7	903,2155,1242	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,utr-3,utr-3	GHR	NM_000163.4,NM_001242399.2,NM_001242400.2,NM_001242401.3,NM_001242402.2,NM_001242403.2,NM_001242404.2,NM_001242405.2,NM_001242406.2,NM_001242460.1,NM_001242461.1,NM_001242462.1	5,5,5,5,5,5,5,5,5,5,,	1230,3215,2058	CC,CA,AA		46.0581,38.9015,43.6337	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,	544/639,551/646,544/639,544/639,544/639,544/639,544/639,544/639,544/639,522/617,,	42719239	5675,7331	2203	4300	6503	SO:0001583	missense	2690	exon10			AAGTGCATCCCTG		CCDS3940.1, CCDS56364.1, CCDS75239.1, CCDS75240.1	5p14-p12	2013-03-25			ENSG00000112964	ENSG00000112964		"""Fibronectin type III domain containing"""	4263	protein-coding gene	gene with protein product	"""growth hormone binding protein"""	600946					Standard	NM_001242460		Approved	GHBP	uc003jmt.3	P10912	OTTHUMG00000094791	ENST00000230882.4:c.1630A>C	5.37:g.42719239A>C	ENSP00000230882:p.Ile544Leu	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	258	109	0.422481	NM_001242399	Q9HCX2	Missense_Mutation	SNP	ENST00000230882.4	37	CCDS3940.1	966	0.4423076923076923	180	0.36585365853658536	147	0.40607734806629836	334	0.583916083916084	305	0.4023746701846966	A	14.26	2.482225	0.44147	0.389015	0.460581	ENSG00000112964	ENST00000230882;ENST00000357703;ENST00000537449	T;T;T	0.35605	1.3;1.3;1.3	6.08	3.43	0.39272	.	0.537042	0.21498	N	0.073576	T	0.00012	0.0000	H	0.94808	3.585	0.49483	P	2.0600000000003948E-4	P	0.50272	0.933	P	0.62014	0.897	T	0.47861	-0.9084	9	0.51188	T	0.08	-7.1042	5.4155	0.16372	0.6692:0.0:0.2016:0.1292	rs6180;rs17231187;rs52796340;rs61155939;rs6180	544	P10912	GHR_HUMAN	L	544;522;357	ENSP00000230882:I544L;ENSP00000350335:I522L;ENSP00000442206:I357L	ENSP00000230882:I544L	I	+	1	0	GHR	42754996	0.991000	0.36638	0.951000	0.38953	0.529000	0.34654	1.574000	0.36482	1.135000	0.42183	0.482000	0.46254	ATC	A|0.548;C|0.448	0.448	strong		0.478	GHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211605.2	NM_000163	
GRIK5	2901	hgsc.bcm.edu	37	19	42560893	42560893	+	Missense_Mutation	SNP	G	G	A	rs139340543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42560893G>A	ENST00000262895.3	-	7	823	c.824C>T	c.(823-825)cCc>cTc	p.P275L	GRIK5_ENST00000593562.1_Missense_Mutation_p.P275L|GRIK5_ENST00000301218.4_Missense_Mutation_p.P275L	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	275					cellular response to glucose stimulus (GO:0071333)|establishment of localization in cell (GO:0051649)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|positive regulation of neuron apoptotic process (GO:0043525)|protein retention in ER lumen (GO:0006621)|receptor clustering (GO:0043113)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	35		Prostate(69;0.059)				AGGGTAGAAGGGGTGGGACGT	0.577													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20492	0.0		0.0	False		,,,				2504	0.0				p.P275L		Atlas-SNP	.											.	GRIK5	220	.	0			c.C824T						PASS	.	G	LEU/PRO	7,4399	12.9+/-30.5	0,7,2196	135.0	120.0	125.0		824	4.9	1.0	19	dbSNP_134	125	0,8600		0,0,4300	yes	missense	GRIK5	NM_002088.3	98	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	possibly-damaging	275/981	42560893	7,12999	2203	4300	6503	SO:0001583	missense	2901	exon7			TAGAAGGGGTGGG		CCDS12595.1	19q13.2	2012-08-29			ENSG00000105737	ENSG00000105737		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4583	protein-coding gene	gene with protein product		600283		GRIK2		7527545	Standard	NM_002088		Approved	GluK5, KA2	uc002osj.2	Q16478	OTTHUMG00000044573	ENST00000262895.3:c.824C>T	19.37:g.42560893G>A	ENSP00000262895:p.Pro275Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	122	54	0.442623	NM_002088	Q8WWG8	Missense_Mutation	SNP	ENST00000262895.3	37	CCDS12595.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	21.6	4.178464	0.78564	0.001589	0.0	ENSG00000105737	ENST00000262895;ENST00000301218	D;D	0.84873	-1.91;-1.91	4.93	4.93	0.64822	Extracellular ligand-binding receptor (1);	0.073753	0.53938	D	0.000048	D	0.88209	0.6375	M	0.64170	1.965	0.80722	D	1	B	0.33637	0.42	P	0.45138	0.471	D	0.88944	0.3382	10	0.72032	D	0.01	.	17.2807	0.87127	0.0:0.0:1.0:0.0	.	275	Q16478	GRIK5_HUMAN	L	275	ENSP00000262895:P275L;ENSP00000301218:P275L	ENSP00000262895:P275L	P	-	2	0	GRIK5	47252733	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.555000	0.82223	2.442000	0.82660	0.467000	0.42956	CCC	G|0.999;A|0.001	0.001	strong		0.577	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1		
BAG6	7917	hgsc.bcm.edu	37	6	31611746	31611746	+	Silent	SNP	G	G	A	rs7770976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31611746G>A	ENST00000375964.6	-	13	1900	c.1587C>T	c.(1585-1587)gcC>gcT	p.A529A	BAG6_ENST00000375976.4_Silent_p.A523A|BAG6_ENST00000211379.5_Silent_p.A523A|BAG6_ENST00000404765.2_Silent_p.A559A|BAG6_ENST00000362049.6_Silent_p.A523A|BAG6_ENST00000439687.2_Silent_p.A522A|BAG6_ENST00000470875.1_5'UTR	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	529	4 X 29 AA approximate repeats.|Pro-rich.				brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						TACCCAGACCGGCGCCCTGCT	0.572													g|||	249	0.0497204	0.1089	0.0706	5008	,	,		16839	0.0179		0.0229	False		,,,				2504	0.0153				p.A529A		Atlas-SNP	.											.	BAG6	73	.	0			c.C1587T						PASS	.		,,,,,	270,2752		11,248,1252	56.0	49.0	52.0		1569,1566,1569,1587,1569,1569	-9.5	0.0	6	dbSNP_116	52	150,5268		1,148,2560	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAG6	NM_001098534.1,NM_001199697.1,NM_001199698.1,NM_004639.3,NM_080702.2,NM_080703.2	,,,,,	12,396,3812	AA,AG,GG		2.7685,8.9345,4.9763	,,,,,	523/1127,522/904,523/1078,529/1133,523/1127,523/1127	31611746	420,8020	1511	2709	4220	SO:0001819	synonymous_variant	7917	exon13			CAGACCGGCGCCC	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"""HLA-B associated transcript 3"""	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.1587C>T	6.37:g.31611746G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Silent	SNP	ENST00000375964.6	37	CCDS47403.1	120	0.054945054945054944	62	0.12601626016260162	26	0.0718232044198895	16	0.027972027972027972	16	0.021108179419525065	g	10.06	1.247589	0.22880	0.089345	0.027685	ENSG00000204463	ENST00000453833	.	.	.	5.71	-9.46	0.00597	.	.	.	.	.	T	0.10121	0.0248	.	.	.	0.58432	P	5.000000000032756E-6	.	.	.	.	.	.	T	0.25606	-1.0127	3	.	.	.	.	7.8245	0.29307	0.1575:0.0958:0.5816:0.1651	rs7770976;rs11548859;rs7770976	.	.	.	W	158	.	.	R	-	1	2	BAG6	31719725	0.005000	0.15991	0.011000	0.14972	0.374000	0.29953	-0.801000	0.04550	-1.067000	0.03160	-0.311000	0.09066	CGG	G|0.940;A|0.060	0.060	strong		0.572	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703	
TRIO	7204	hgsc.bcm.edu	37	5	14397238	14397238	+	Silent	SNP	T	T	C	rs30774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	133	0	0		WXS	Illumina HiSeq	Phase_I	145	144	0.993103	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	
CUL9	23113	hgsc.bcm.edu	37	6	43188940	43188940	+	Silent	SNP	C	C	T	rs6917902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43188940C>T	ENST00000252050.4	+	34	6717	c.6633C>T	c.(6631-6633)gaC>gaT	p.D2211D	RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000354495.3_Silent_p.D2101D|CUL9_ENST00000372647.2_Silent_p.D2183D	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2211					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						AGTGGGTCGACGACGGTGGCT	0.617													T|||	1038	0.207268	0.4947	0.1686	5008	,	,		19497	0.0179		0.1342	False		,,,				2504	0.1166				p.D2211D		Atlas-SNP	.											.	CUL9	248	.	0			c.C6633T						PASS	.	T		2014,2392	613.0+/-392.1	464,1086,653	110.0	76.0	87.0		6633	-7.4	0.0	6	dbSNP_116	87	1463,7137	750.1+/-407.4	108,1247,2945	no	coding-synonymous	CUL9	NM_015089.2		572,2333,3598	TT,TC,CC		17.0116,45.7104,26.7338		2211/2518	43188940	3477,9529	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon34			GGTCGACGACGGT	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.6633C>T	6.37:g.43188940C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	142	69	0.485915	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.767;T|0.233	0.233	strong		0.617	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
C1orf177	163747	hgsc.bcm.edu	37	1	55307501	55307501	+	Silent	SNP	A	A	G	rs41297871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55307501A>G	ENST00000371273.3	+	10	1227	c.1212A>G	c.(1210-1212)ggA>ggG	p.G404G	C1orf177_ENST00000358193.3_3'UTR	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	404										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						ttactaagggaaagtgccctc	0.468													G|||	1154	0.230431	0.1498	0.281	5008	,	,		21304	0.4405		0.2316	False		,,,				2504	0.0859				p.G404G		Atlas-SNP	.											.	C1orf177	36	.	0			c.A1212G						PASS	.	G	,	237,1147		17,203,472	101.0	81.0	87.0		1212,	-3.0	0.3	1	dbSNP_127	87	653,2529		66,521,1004	no	coding-synonymous,utr-3	C1orf177	NM_001110533.1,NM_152607.2	,	83,724,1476	GG,GA,AA		20.5217,17.1243,19.4919	,	404/419,	55307501	890,3676	692	1591	2283	SO:0001819	synonymous_variant	163747	exon10			TAAGGGAAAGTGC	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.1212A>G	1.37:g.55307501A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_001110533	B7WPL2|Q8N7Y9	Silent	SNP	ENST00000371273.3	37	CCDS44153.1																																																																																			A|0.737;G|0.263	0.263	strong		0.468	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
C20orf196	149840	hgsc.bcm.edu	37	20	5843812	5843812	+	Silent	SNP	T	T	C	rs1699233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5843812T>C	ENST00000303142.6	+	3	408	c.321T>C	c.(319-321)ggT>ggC	p.G107G		NM_152504.2	NP_689717.2	Q8IYI0	CT196_HUMAN	chromosome 20 open reading frame 196	107										endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	9						AAATGTTTGGTCATCCACAGC	0.488													C|||	2169	0.433107	0.652	0.4121	5008	,	,		18382	0.3214		0.4294	False		,,,				2504	0.271				p.G107G		Atlas-SNP	.											.	C20orf196	17	.	0			c.T321C						PASS	.	C		2638,1768	522.8+/-370.9	787,1064,352	74.0	75.0	75.0		321	3.4	0.0	20	dbSNP_89	75	3698,4902	620.8+/-397.1	798,2102,1400	no	coding-synonymous	C20orf196	NM_152504.2		1585,3166,1752	CC,CT,TT		43.0,40.1271,48.716		107/206	5843812	6336,6670	2203	4300	6503	SO:0001819	synonymous_variant	149840	exon3			GTTTGGTCATCCA	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.321T>C	20.37:g.5843812T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	105	103	0.980952	NM_152504	A8K9J3|Q5TGA9|Q96LU1	Silent	SNP	ENST00000303142.6	37	CCDS13091.1																																																																																			T|0.525;C|0.475	0.475	strong		0.488	C20orf196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077882.2	NM_152504	
OR1E1	8387	hgsc.bcm.edu	37	17	3301293	3301293	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3301293G>A	ENST00000322608.2	-	1	411	c.412C>T	c.(412-414)Ccc>Tcc	p.P138S		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	138					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(2)|lung(5)	10						CAGAGCATGGGGCTCATGATG	0.562																																					p.P138S		Atlas-SNP	.											OR1E1,caecum,carcinoma,+1,1	OR1E1	37	1	0			c.C412T						scavenged	.						96.0	75.0	82.0					17																	3301293		2203	4300	6503	SO:0001583	missense	8387	exon1			GCATGGGGCTCAT	U04642	CCDS11024.1	17p13.3	2012-08-09			ENSG00000180016	ENSG00000180016		"""GPCR / Class A : Olfactory receptors"""	8189	protein-coding gene	gene with protein product				OR1E9P, OR1E5, OR1E6		8004088, 1370859	Standard	NM_003553		Approved	OR17-2, HGM071, OR17-32, OR13-66	uc002fvj.1	P30953	OTTHUMG00000090643	ENST00000322608.2:c.412C>T	17.37:g.3301293G>A	ENSP00000313384:p.Pro138Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	233	5	0.0214592	NM_003553	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Missense_Mutation	SNP	ENST00000322608.2	37	CCDS11024.1	.	.	.	.	.	.	.	.	.	.	G	9.718	1.158881	0.21454	.	.	ENSG00000180016	ENST00000322608	T	0.00584	6.4	4.69	3.7	0.42460	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000008	T	0.00608	0.0020	L	0.41415	1.275	0.26256	N	0.97866	B	0.23937	0.094	B	0.23419	0.046	T	0.45760	-0.9239	10	0.59425	D	0.04	.	7.9649	0.30094	0.0887:0.0:0.7519:0.1594	.	138	P30953	OR1E1_HUMAN	S	138	ENSP00000313384:P138S	ENSP00000313384:P138S	P	-	1	0	OR1E1	3248043	0.000000	0.05858	1.000000	0.80357	0.506000	0.33950	-0.760000	0.04756	2.449000	0.82847	0.591000	0.81541	CCC	.	.	none		0.562	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1	NM_003553	
C10orf25	220979	hgsc.bcm.edu	37	10	45496126	45496126	+	Missense_Mutation	SNP	G	G	A	rs41301609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:45496126G>A	ENST00000298298.1	-	1	210	c.182C>T	c.(181-183)cCa>cTa	p.P61L	ZNF22_ENST00000298299.3_5'UTR|CEP164P1_ENST00000456938.2_RNA	NM_001039380.2	NP_001034469.2	Q5T742	CJ025_HUMAN	chromosome 10 open reading frame 25	61			P -> L (in dbSNP:rs41301609).			extracellular region (GO:0005576)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6						CAAAATTTGTGGAAAGTATGC	0.458													A|||	276	0.0551118	0.0749	0.013	5008	,	,		17077	0.0972		0.0427	False		,,,				2504	0.0276				p.P61L		Atlas-SNP	.											.	C10orf25	11	.	0			c.C182T						PASS	.	A	LEU/PRO	243,4163	802.0+/-415.6	7,229,1967	72.0	74.0	73.0		182	-5.2	0.0	10	dbSNP_127	73	404,8196	800.0+/-407.4	6,392,3902	yes	missense	C10orf25	NM_001039380.2	98	13,621,5869	AA,AG,GG		4.6977,5.5152,4.9746	benign	61/123	45496126	647,12359	2203	4300	6503	SO:0001583	missense	220979	exon1			ATTTGTGGAAAGT	AK055129	CCDS31187.1	10q11.21	2003-11-21			ENSG00000165511	ENSG00000165511			23509	protein-coding gene	gene with protein product							Standard	NM_001039380		Approved	FLJ30567	uc001jbv.2	Q5T742	OTTHUMG00000018066	ENST00000298298.1:c.182C>T	10.37:g.45496126G>A	ENSP00000298298:p.Pro61Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_001039380	A1L424|Q96NM5	Missense_Mutation	SNP	ENST00000298298.1	37	CCDS31187.1	146	0.06684981684981685	41	0.08333333333333333	6	0.016574585635359115	66	0.11538461538461539	33	0.04353562005277045	A	6.705	0.498748	0.12762	0.055152	0.046977	ENSG00000165511	ENST00000298298	T	0.39997	1.05	2.81	-5.15	0.02866	.	.	.	.	.	T	0.00271	0.0008	N	0.08118	0	0.54753	P	1.3000000000040757E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.12734	-1.0536	8	0.87932	D	0	.	9.3936	0.38388	0.1834:0.1546:0.662:0.0	rs41301609	61	Q5T742	CJ025_HUMAN	L	61	ENSP00000298298:P61L	ENSP00000298298:P61L	P	-	2	0	C10orf25	44816132	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.507000	0.06352	-1.884000	0.01119	-0.360000	0.07572	CCA	G|0.948;A|0.052	0.052	strong		0.458	C10orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047763.1	NM_145022	
MST1L	11223	hgsc.bcm.edu	37	1	17087509	17087509	+	RNA	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17087509C>T	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										CCACATCCTCCTGCCAAGGCC	0.632																																					p.Q52Q		Atlas-SNP	.											.	.	.	.	0			c.G156A						PASS	.																																					11223	exon2			ATCCTCCTGCCAA	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.17087509C>T		Somatic	713	0	0		WXS	Illumina HiSeq	Phase_I	896	71	0.0792411	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				.	.	none		0.632	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
NACA	4666	hgsc.bcm.edu	37	12	57114869	57114869	+	Missense_Mutation	SNP	T	T	C	rs17118953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57114869T>C	ENST00000454682.1	-	3	726	c.445A>G	c.(445-447)Aag>Gag	p.K149E	NACA_ENST00000393891.4_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.K149E|NACA_ENST00000548563.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	149	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GCAGAACTCTTCTGAACTGAG	0.527			T	BCL6	NHL								T|||	455	0.0908546	0.2625	0.036	5008	,	,		19359	0.005		0.0268	False		,,,				2504	0.0521				p.K149E		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.A445G						PASS	.	T	GLU/LYS,,,	667,2469		77,513,978	53.0	51.0	52.0		445,,,	3.4	0.9	12	dbSNP_123	52	198,6966		3,192,3387	yes	missense,intron,intron,intron	NACA	NM_001113203.2,NM_001113201.1,NM_001113202.1,NM_005594.4	56,,,	80,705,4365	CC,CT,TT		2.7638,21.2691,8.3981	probably-damaging,,,	149/926,,,	57114869	865,9435	1568	3582	5150	SO:0001583	missense	4666	exon3			AACTCTTCTGAAC	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.445A>G	12.37:g.57114869T>C	ENSP00000403817:p.Lys149Glu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	37		142	0.06501831501831502	102	0.2073170731707317	16	0.04419889502762431	3	0.005244755244755245	21	0.027704485488126648	T	13.17	2.158250	0.38119	0.212691	0.027638	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.28895	1.59;1.59	3.38	3.38	0.38709	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.51767	P	6.60000000000105E-5	D;D	0.76494	0.999;0.996	D;D	0.75484	0.986;0.986	T	0.11743	-1.0575	8	0.87932	D	0	.	8.4227	0.32710	0.0:0.0:0.0:1.0	rs17118953;rs17118953	149;149	E9PAV3;F8VU71	.;.	E	149	ENSP00000403817:K149E;ENSP00000448035:K149E	ENSP00000403817:K149E	K	-	1	0	NACA	55401136	0.994000	0.37717	0.940000	0.37924	0.607000	0.37147	1.402000	0.34600	1.564000	0.49628	0.241000	0.17934	AAG	T|0.920;C|0.080	0.080	strong		0.527	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
F2RL3	9002	hgsc.bcm.edu	37	19	17001240	17001240	+	Silent	SNP	C	C	T	rs2227347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17001240C>T	ENST00000248076.3	+	2	1296	c.966C>T	c.(964-966)taC>taT	p.Y322Y		NM_003950.2	NP_003941.2	Q96RI0	PAR4_HUMAN	coagulation factor II (thrombin) receptor-like 3	322					blood coagulation (GO:0007596)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			cervix(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						ATGGTGCCTACGTGCCCAGCC	0.647													C|||	107	0.0213658	0.0779	0.0058	5008	,	,		17504	0.0		0.0	False		,,,				2504	0.0				p.Y322Y		Atlas-SNP	.											.	F2RL3	20	.	0			c.C966T						PASS	.	C		322,4082	164.4+/-196.0	5,312,1885	29.0	27.0	28.0		966	-1.0	0.8	19	dbSNP_98	28	2,8596	1.2+/-3.3	0,2,4297	no	coding-synonymous	F2RL3	NM_003950.2		5,314,6182	TT,TC,CC		0.0233,7.3115,2.4919		322/386	17001240	324,12678	2202	4299	6501	SO:0001819	synonymous_variant	9002	exon2			TGCCTACGTGCCC	AF055917	CCDS12350.1	19p12	2012-08-08						"""GPCR / Class A : Protease activated receptors"""	3540	protein-coding gene	gene with protein product	"""proteinase-activated receptor-4"""	602779				9618465	Standard	XM_005260139		Approved	PAR4	uc002nfa.3	Q96RI0		ENST00000248076.3:c.966C>T	19.37:g.17001240C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_003950	O76067|Q6DK42	Silent	SNP	ENST00000248076.3	37	CCDS12350.1																																																																																			C|0.971;A|0.000	.	strong		0.647	F2RL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462875.1		
JAG1	182	hgsc.bcm.edu	37	20	10639222	10639222	+	Silent	SNP	G	G	A	rs1801138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:10639222G>A	ENST00000254958.5	-	4	1103	c.588C>T	c.(586-588)tgC>tgT	p.C196C	JAG1_ENST00000423891.2_Silent_p.C37C	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	196	DSL. {ECO:0000255|PROSITE- ProRule:PRU00377}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						AGAACTTATTGCAGCCAAAGC	0.537									Alagille Syndrome				G|||	911	0.181909	0.2542	0.1311	5008	,	,		19308	0.2192		0.0408	False		,,,				2504	0.227				p.C196C		Atlas-SNP	.											.	JAG1	213	.	0			c.C588T	GRCh37	CM061817	JAG1	M	rs1801138	PASS	.	G		961,3445	364.6+/-317.1	104,753,1346	153.0	133.0	140.0		588	1.5	1.0	20	dbSNP_89	140	391,8209	126.0+/-184.5	10,371,3919	no	coding-synonymous	JAG1	NM_000214.2		114,1124,5265	AA,AG,GG		4.5465,21.8112,10.3952		196/1219	10639222	1352,11654	2203	4300	6503	SO:0001819	synonymous_variant	182	exon4	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CTTATTGCAGCCA	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.588C>T	20.37:g.10639222G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	149	76	0.510067	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			G|0.841;A|0.159	0.159	strong		0.537	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
TAF1	6872	hgsc.bcm.edu	37	X	70627477	70627477	+	Silent	SNP	G	G	A	rs7050748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70627477G>A	ENST00000373790.4	+	27	4209	c.4158G>A	c.(4156-4158)tcG>tcA	p.S1386S	TAF1_ENST00000276072.3_Silent_p.S1407S|TAF1_ENST00000423759.1_Silent_p.S1407S|TAF1_ENST00000449580.1_Silent_p.S1386S	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	1386	Interaction with ASF1A and ASF1B.				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)				TGACGCTGTCGTCCATCTTGG	0.438													A|||	293	0.0776159	0.2012	0.0274	3775	,	,		15657	0.0		0.005	False		,,,				2504	0.0031				p.S1407S		Atlas-SNP	.											.	TAF1	439	.	0			c.G4221A						PASS	.	A	,	921,2914		89,609,134,934,437	129.0	111.0	117.0		4221,4158	0.9	1.0	X	dbSNP_116	117	39,6689		0,29,10,2399,1862	no	coding-synonymous,coding-synonymous	TAF1	NM_004606.3,NM_138923.2	,	89,638,144,3333,2299	AA,AG,A,GG,G		0.5797,24.0156,9.0883	,	1407/1894,1386/1873	70627477	960,9603	2203	4300	6503	SO:0001819	synonymous_variant	6872	exon27			GCTGTCGTCCATC		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.4158G>A	X.37:g.70627477G>A		Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	316	136	0.43038	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	37	CCDS35325.1	117	0.0705244122965642	71	0.1658878504672897	6	0.01694915254237288	0	0.0	3	0.003968253968253968	.	8.199	0.797814	0.16327	0.240156	0.005797	ENSG00000147133	ENST00000463163;ENST00000437147	.	.	.	4.95	0.941	0.19519	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999938	.	.	.	.	.	.	T	0.28396	-1.0045	3	.	.	.	.	1.3732	0.02215	0.2938:0.111:0.1437:0.4515	rs7050748	.	.	.	H	52;41	.	.	R	+	2	0	TAF1	70544202	0.020000	0.18652	0.992000	0.48379	0.891000	0.51852	-0.742000	0.04850	-0.381000	0.07882	-0.574000	0.04147	CGT	0|0.003;A|0.098	0.098	strong		0.438	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
NCLN	56926	hgsc.bcm.edu	37	19	3207646	3207646	+	Missense_Mutation	SNP	A	A	G	rs2288949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3207646A>G	ENST00000246117.4	+	15	2083	c.1652A>G	c.(1651-1653)aAg>aGg	p.K551R	NCLN_ENST00000591062.1_3'UTR|NCLN_ENST00000590671.1_Missense_Mutation_p.K477R	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	551			K -> R (in dbSNP:rs2288949). {ECO:0000269|PubMed:11230166, ECO:0000269|Ref.6}.		regulation of signal transduction (GO:0009966)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				kidney(1)|lung(3)|skin(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.83e-113)|Epithelial(107;1.65e-111)|all cancers(105;1.53e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00139)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCCTCTACAAGACCGTCCAG	0.672													A|||	1029	0.205471	0.1301	0.1614	5008	,	,		13460	0.4087		0.0646	False		,,,				2504	0.274				p.K551R		Atlas-SNP	.											.	NCLN	27	.	0			c.A1652G						PASS	.	A	ARG/LYS	591,3815	251.2+/-258.0	38,515,1650	44.0	38.0	40.0		1652	2.6	1.0	19	dbSNP_100	40	398,8202	123.8+/-182.6	10,378,3912	yes	missense	NCLN	NM_020170.3	26	48,893,5562	GG,GA,AA		4.6279,13.4135,7.6042	benign	551/564	3207646	989,12017	2203	4300	6503	SO:0001583	missense	56926	exon15			TCTACAAGACCGT	BC025926	CCDS32869.1	19p13.3	2010-08-13	2010-08-13			ENSG00000125912			26923	protein-coding gene	gene with protein product	"""nicastrin-like protein"""	609156	"""nicalin homolog (zebrafish)"""			11230166	Standard	NM_020170		Approved	NICALIN, NET59	uc002lxi.3	Q969V3		ENST00000246117.4:c.1652A>G	19.37:g.3207646A>G	ENSP00000246117:p.Lys551Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	162	76	0.469136	NM_020170	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Missense_Mutation	SNP	ENST00000246117.4	37	CCDS32869.1	418	0.19139194139194138	66	0.13414634146341464	57	0.1574585635359116	244	0.42657342657342656	51	0.06728232189973615	A	12.46	1.945716	0.34377	0.134135	0.046279	ENSG00000125912	ENST00000246117	T	0.30448	1.53	3.61	2.58	0.30949	.	0.862061	0.10469	N	0.670979	T	0.00012	0.0000	N	0.12182	0.205	0.38347	P	0.05578000000000005	B;B	0.15930	0.015;0.009	B;B	0.16289	0.015;0.006	T	0.49072	-0.8977	9	0.20046	T	0.44	-8.9712	6.4848	0.22083	0.8827:0.0:0.1173:0.0	rs2288949;rs11551091;rs17696536;rs57678984;rs2288949	550;551	Q969V3-2;Q969V3	.;NCLN_HUMAN	R	551	ENSP00000246117:K551R	ENSP00000246117:K551R	K	+	2	0	NCLN	3158646	0.972000	0.33761	0.972000	0.41901	0.843000	0.47879	1.070000	0.30653	0.461000	0.27071	0.459000	0.35465	AAG	A|0.876;G|0.124	0.124	strong		0.672	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1	NM_020170	
CD6	923	hgsc.bcm.edu	37	11	60776307	60776307	+	Silent	SNP	G	G	C	rs79848107|rs386754116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000545105.1_Intron|CD6_ENST00000452451.2_Silent_p.A257A|CD6_ENST00000352009.5_Silent_p.A257A|CD6_ENST00000346437.4_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	76	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	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	
TTC23L	153657	hgsc.bcm.edu	37	5	34840841	34840841	+	Missense_Mutation	SNP	A	A	G	rs6451173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34840841A>G	ENST00000505624.1	+	2	168	c.65A>G	c.(64-66)cAt>cGt	p.H22R	CTD-2517O10.6_ENST00000606401.1_RNA|TTC23L_ENST00000514080.1_3'UTR	NM_144725.3	NP_653326.3	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like	22			H -> R (in dbSNP:rs6451173). {ECO:0000269|PubMed:14702039}.							breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(9)|prostate(2)|stomach(1)|urinary_tract(1)	22						TTCTGCTTCCATATGTAAGTA	0.478													G|||	2693	0.53774	0.8986	0.4121	5008	,	,		17940	0.256		0.5457	False		,,,				2504	0.4213				p.H22R		Atlas-SNP	.											.	TTC23L	47	.	0			c.A65G						PASS	.	G	ARG/HIS	3405,559		1472,461,49	198.0	193.0	195.0		65	-1.2	0.0	5	dbSNP_116	195	4521,3857		1196,2129,864	yes	missense	TTC23L	NM_144725.3	29	2668,2590,913	GG,GA,AA		46.0372,14.1019,35.7803	benign	22/362	34840841	7926,4416	1982	4189	6171	SO:0001583	missense	153657	exon2			GCTTCCATATGTA		CCDS54840.1	5p13.2	2008-07-14			ENSG00000205838	ENSG00000205838			26355	protein-coding gene	gene with protein product						12477932	Standard	NM_144725		Approved	FLJ25439	uc003jiu.3	Q6PF05	OTTHUMG00000162020	ENST00000505624.1:c.65A>G	5.37:g.34840841A>G	ENSP00000422188:p.His22Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	178	84	0.47191	NM_144725	Q6RGS4|Q8N7R3|Q96LJ2	Missense_Mutation	SNP	ENST00000505624.1	37	CCDS54840.1	1163	0.5325091575091575	430	0.8739837398373984	163	0.45027624309392267	146	0.25524475524475526	424	0.5593667546174143	G	0.541	-0.853436	0.02630	0.858981	0.539628	ENSG00000205838	ENST00000505624;ENST00000535797	T	0.12361	2.69	5.34	-1.25	0.09405	.	0.904334	0.09368	N	0.811725	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.47381	-0.9122	9	0.05721	T	0.95	-9.946	5.6206	0.17455	0.557:0.0:0.3192:0.1237	rs6451173;rs17523522;rs17857470;rs52815487;rs58670304;rs6451173	22	Q6PF05	TT23L_HUMAN	R	22	ENSP00000422188:H22R	ENSP00000425242:H22R	H	+	2	0	TTC23L	34876598	0.013000	0.17824	0.046000	0.18839	0.162000	0.22319	0.234000	0.17930	-0.345000	0.08325	-1.110000	0.02074	CAT	A|0.457;G|0.543	0.543	strong		0.478	TTC23L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366819.1	NM_144725	
KIT	3815	hgsc.bcm.edu	37	4	55602765	55602765	+	Silent	SNP	G	G	C	rs3733542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:55602765G>C	ENST00000288135.5	+	18	2683	c.2586G>C	c.(2584-2586)ctG>ctC	p.L862L		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	862	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|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 pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L862L(6)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTTGGGAGCTGTTCTCTTTAG	0.418		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors				G|||	822	0.164137	0.3759	0.0793	5008	,	,		19674	0.0565		0.0954	False		,,,				2504	0.1196				p.L862L		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	KIT,colon,carcinoma,0,10	KIT	7396	10	6	Substitution - coding silent(6)	haematopoietic_and_lymphoid_tissue(3)|bone(2)|stomach(1)	c.G2586C						PASS	.	G	,	1433,2973	466.2+/-354.4	229,975,999	142.0	144.0	143.0		2586,2574	-2.3	1.0	4	dbSNP_107	143	1078,7522	226.8+/-262.4	74,930,3296	no	coding-synonymous,coding-synonymous	KIT	NM_000222.2,NM_001093772.1	,	303,1905,4295	CC,CG,GG		12.5349,32.5238,19.3065	,	862/977,858/973	55602765	2511,10495	2203	4300	6503	SO:0001819	synonymous_variant	3815	exon18	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	GGAGCTGTTCTCT	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2586G>C	4.37:g.55602765G>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	95	31	0.326316	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																			G|0.828;C|0.172	0.172	strong		0.418	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
RAC2	5880	hgsc.bcm.edu	37	22	37622815	37622815	+	Silent	SNP	A	A	G	rs1064498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37622815A>G	ENST00000249071.6	-	6	598	c.477T>C	c.(475-477)gcT>gcC	p.A159A	RAC2_ENST00000406508.1_Silent_p.A115A|RAC2_ENST00000405484.1_Silent_p.A152A	NM_002872.3	NP_002863.1	P15153	RAC2_HUMAN	ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)	159					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|cell projection assembly (GO:0030031)|G-protein coupled receptor signaling pathway (GO:0007186)|lymphocyte aggregation (GO:0071593)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neutrophil chemotaxis (GO:0090023)|regulation of cell-substrate adhesion (GO:0010810)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of neutrophil migration (GO:1902622)|regulation of respiratory burst (GO:0060263)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)	12					Dextromethorphan(DB00514)	TCTGGGTGAGAGCTGAGCACT	0.632													g|||	1239	0.247404	0.4508	0.1023	5008	,	,		15446	0.3105		0.1501	False		,,,				2504	0.1104				p.A159A		Atlas-SNP	.											.	RAC2	22	.	0			c.T477C						PASS	.			1718,2688	650.4+/-399.0	342,1034,827	57.0	65.0	62.0		477	-0.1	0.9	22	dbSNP_86	62	1212,7386	761.9+/-407.6	81,1050,3168	no	coding-synonymous	RAC2	NM_002872.3		423,2084,3995	GG,GA,AA		14.0963,38.9923,22.5315		159/193	37622815	2930,10074	2203	4299	6502	SO:0001819	synonymous_variant	5880	exon6			GGTGAGAGCTGAG	M64595	CCDS13945.1	22q13.1	2014-09-17			ENSG00000128340	ENSG00000128340		"""Endogenous ligands"""	9802	protein-coding gene	gene with protein product		602049				2674130	Standard	NM_002872		Approved	EN-7	uc003arc.3	P15153	OTTHUMG00000150540	ENST00000249071.6:c.477T>C	22.37:g.37622815A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_002872	Q9UDJ4	Silent	SNP	ENST00000249071.6	37	CCDS13945.1																																																																																			T|0.000;G|0.229;A|0.771	0.229	strong		0.632	RAC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318812.1		
SBNO2	22904	hgsc.bcm.edu	37	19	1119019	1119019	+	Silent	SNP	C	C	T	rs2074920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1119019C>T	ENST00000361757.3	-	14	1755	c.1518G>A	c.(1516-1518)gcG>gcA	p.A506A	SBNO2_ENST00000438103.2_Silent_p.A449A|SBNO2_ENST00000587024.1_Silent_p.A506A	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	25	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	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	
PDIA2	64714	hgsc.bcm.edu	37	16	334890	334890	+	Missense_Mutation	SNP	G	G	A	rs419949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:334890G>A	ENST00000219406.6	+	4	571	c.553G>A	c.(553-555)Gag>Aag	p.E185K	PDIA2_ENST00000462950.1_3'UTR|PDIA2_ENST00000404312.1_Missense_Mutation_p.E182K	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	185			E -> K (in dbSNP:rs419949).		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)				CCTGCAGGACGAGGACGTGGC	0.677													g|||	511	0.102037	0.1641	0.1023	5008	,	,		16673	0.001		0.1839	False		,,,				2504	0.0378				p.E185K		Atlas-SNP	.											.	PDIA2	51	.	0			c.G553A						PASS	.	G	LYS/GLU	607,3523		36,535,1494	39.0	47.0	45.0		553	0.3	0.1	16	dbSNP_80	45	1658,6698		175,1308,2695	yes	missense	PDIA2	NM_006849.2	56	211,1843,4189	AA,AG,GG		19.842,14.6973,18.1403	benign	185/526	334890	2265,10221	2065	4178	6243	SO:0001583	missense	64714	exon4			CAGGACGAGGACG	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.553G>A	16.37:g.334890G>A	ENSP00000219406:p.Glu185Lys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	271	0.12408424908424909	93	0.18902439024390244	41	0.1132596685082873	0	0.0	137	0.18073878627968337	g	6.194	0.403887	0.11754	0.146973	0.19842	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312	T;T	0.23147	1.92;1.92	3.66	0.305	0.15801	Thioredoxin-like fold (2);	0.433699	0.23706	N	0.045370	T	0.00039	0.0001	M	0.67700	2.07	0.33439	P	0.41782600000000003	B	0.17852	0.024	B	0.24269	0.052	T	0.12400	-1.0549	9	0.36615	T	0.2	.	5.0832	0.14668	0.3036:0.1519:0.5445:0.0	rs419949;rs59217529;rs419949	185	Q13087	PDIA2_HUMAN	K	185;154;182	ENSP00000219406:E185K;ENSP00000384410:E182K	ENSP00000219406:E185K	E	+	1	0	PDIA2	274891	0.006000	0.16342	0.118000	0.21660	0.118000	0.20060	0.523000	0.22925	-0.003000	0.14444	-0.389000	0.06534	GAG	G|0.849;A|0.151	0.151	strong		0.677	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
DNAH2	146754	hgsc.bcm.edu	37	17	7673922	7673922	+	Silent	SNP	A	A	T	rs9910089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7673922A>T	ENST00000572933.1	+	26	5606	c.4146A>T	c.(4144-4146)atA>atT	p.I1382I	DNAH2_ENST00000389173.2_Silent_p.I1382I			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1382	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)				AGCTCGACATAGTACCCTACA	0.542													A|||	265	0.0529153	0.1301	0.0259	5008	,	,		21225	0.0		0.0368	False		,,,				2504	0.0389				p.I1382I		Atlas-SNP	.											.	DNAH2	498	.	0			c.A4146T						PASS	.	A		439,3967	212.2+/-232.1	29,381,1793	87.0	84.0	85.0		4146	1.8	1.0	17	dbSNP_119	85	248,8352	97.5+/-159.1	4,240,4056	no	coding-synonymous	DNAH2	NM_020877.2		33,621,5849	TT,TA,AA		2.8837,9.9637,5.2822		1382/4428	7673922	687,12319	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon25			CGACATAGTACCC	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.4146A>T	17.37:g.7673922A>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			A|0.949;T|0.051	0.051	strong		0.542	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489707	32489707	+	Silent	SNP	A	A	C	rs41559714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32489707A>C	ENST00000374975.3	-	2	407	c.345T>G	c.(343-345)ggT>ggG	p.G115G		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						TGAAGCTCTCACCAACCCCGT	0.622													A|||	1201	0.239816	0.2247	0.2911	5008	,	,		5491	0.2242		0.2416	False		,,,				2504	0.2382				p.G115G		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.T345G						PASS	.						39.0	32.0	34.0					6																	32489707		2154	4218	6372	SO:0001819	synonymous_variant	3127	exon2			GCTCTCACCAACC		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.345T>G	6.37:g.32489707A>C		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			.	.	weak		0.622	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
ZNF74	7625	hgsc.bcm.edu	37	22	20760106	20760106	+	Silent	SNP	C	C	T	rs2229316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:20760106C>T	ENST00000400451.2	+	5	1297	c.783C>T	c.(781-783)tcC>tcT	p.S261S	ZNF74_ENST00000403682.3_3'UTR|ZNF74_ENST00000357502.5_3'UTR|ZNF74_ENST00000356671.5_Silent_p.S261S|ZNF74_ENST00000405993.1_Silent_p.S229S	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	261					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GCCAGAGCTCCTCCCTCACGC	0.687													C|||	95	0.0189696	0.0696	0.0043	5008	,	,		15500	0.0		0.0	False		,,,				2504	0.0				p.S261S		Atlas-SNP	.											.	ZNF74	54	.	0			c.C783T						PASS	.	C		188,4216		6,176,2020	21.0	25.0	23.0		783	-7.0	0.0	22	dbSNP_98	23	3,8593		0,3,4295	no	coding-synonymous	ZNF74	NM_003426.2		6,179,6315	TT,TC,CC		0.0349,4.2688,1.4692		261/645	20760106	191,12809	2202	4298	6500	SO:0001819	synonymous_variant	7625	exon5			GAGCTCCTCCCTC	X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"""Zinc fingers, C2H2-type"", ""-"""	13144	protein-coding gene	gene with protein product		194548	"""zinc finger protein 74 (Cos52)"""			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.783C>T	22.37:g.20760106C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_003426	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Silent	SNP	ENST00000400451.2	37	CCDS42982.1																																																																																			C|0.982;T|0.018	0.018	strong		0.687	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426	
PLEKHA5	54477	hgsc.bcm.edu	37	12	19440471	19440471	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:19440471A>G	ENST00000299275.6	+	12	1832	c.1826A>G	c.(1825-1827)cAg>cGg	p.Q609R	PLEKHA5_ENST00000309364.4_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.Q367R|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.Q501R|PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.Q615R|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.Q501R|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.Q609R	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	609					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					GTTAGTCCCCAGAGCCTCCAA	0.403																																					p.Q615R	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A1844G						PASS	.						105.0	104.0	105.0					12																	19440471		2203	4300	6503	SO:0001583	missense	54477	exon13			GTCCCCAGAGCCT	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.1826A>G	12.37:g.19440471A>G	ENSP00000299275:p.Gln609Arg	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	160	83	0.51875	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	37	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	18.64	3.668063	0.67814	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000309364;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T;T	0.35048	2.5;1.33;2.5;2.5;1.33;2.5;2.5;1.33;1.57;1.57;2.5	5.86	4.73	0.59995	.	0.115083	0.64402	D	0.000011	T	0.52757	0.1754	M	0.70595	2.14	0.39754	D	0.971935	D;D;D;P;D;D;D	0.76494	0.988;0.999;0.998;0.584;0.995;0.986;0.999	P;D;D;B;D;P;D	0.85130	0.883;0.997;0.993;0.445;0.978;0.835;0.997	T	0.52571	-0.8558	10	0.10111	T	0.7	-14.8584	11.3548	0.49609	0.9297:0.0:0.0703:0.0	.	609;501;501;615;615;609;609	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;PKHA5_HUMAN;.	R	609;609;609;616;609;615;609;367;609;501;501;501	ENSP00000325155:Q609R;ENSP00000347560:Q609R;ENSP00000352104:Q609R;ENSP00000311239:Q609R;ENSP00000404296:Q615R;ENSP00000299275:Q609R;ENSP00000440611:Q367R;ENSP00000439673:Q609R;ENSP00000400411:Q501R;ENSP00000439837:Q501R;ENSP00000440371:Q501R	ENSP00000299275:Q609R	Q	+	2	0	PLEKHA5	19331738	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.067000	0.71193	2.241000	0.73720	0.482000	0.46254	CAG	.	.	none		0.403	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	
SMCO1	255798	hgsc.bcm.edu	37	3	196234777	196234777	+	Missense_Mutation	SNP	A	A	G	rs187809363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196234777A>G	ENST00000397537.2	-	3	782	c.626T>C	c.(625-627)aTa>aCa	p.I209T		NM_001077657.1	NP_001071125.1	Q147U7	SMCO1_HUMAN	single-pass membrane protein with coiled-coil domains 1	209						integral component of membrane (GO:0016021)											gacagatggtatcaaCTCTTC	0.428													A|||	7	0.00139776	0.0053	0.0	5008	,	,		17582	0.0		0.0	False		,,,				2504	0.0				p.I209T		Atlas-SNP	.											C3orf43,NS,malignant_melanoma,+1,1	C3orf43	25	1	0			c.T626C						PASS	.	A	THR/ILE	15,3743		0,15,1864	111.0	102.0	105.0		626	4.0	0.0	3		105	0,8236		0,0,4118	yes	missense	C3orf43	NM_001077657.1	89	0,15,5982	GG,GA,AA		0.0,0.3991,0.1251	benign	209/215	196234777	15,11979	1879	4118	5997	SO:0001583	missense	255798	exon3			GATGGTATCAACT	AK123917	CCDS43192.1	3q29	2013-03-08	2013-03-08	2013-03-08	ENSG00000214097	ENSG00000214097			27407	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 43"""	C3orf43			Standard	NM_001077657		Approved	FLJ41923, DKFZp313B0440		Q147U7	OTTHUMG00000155581	ENST00000397537.2:c.626T>C	3.37:g.196234777A>G	ENSP00000380671:p.Ile209Thr	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	208	97	0.466346	NM_001077657	B3KW20	Missense_Mutation	SNP	ENST00000397537.2	37	CCDS43192.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	11.14	1.550303	0.27739	0.003991	0.0	ENSG00000214097	ENST00000397537	T	0.36340	1.26	5.39	4.03	0.46877	.	.	.	.	.	T	0.28067	0.0692	L	0.29908	0.895	0.09310	N	1	B;B	0.26195	0.144;0.144	B;B	0.27715	0.051;0.082	T	0.18999	-1.0319	9	0.72032	D	0.01	-4.7237	9.3415	0.38082	0.9032:0.0:0.0968:0.0	.	209;201	Q147U7;E9PGG7	CC043_HUMAN;.	T	209	ENSP00000380671:I209T	ENSP00000380671:I209T	I	-	2	0	C3orf43	197719174	0.957000	0.32711	0.010000	0.14722	0.013000	0.08279	2.479000	0.45197	2.054000	0.61138	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	strong		0.428	SMCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340776.1	NM_001006109	
SRPK3	26576	hgsc.bcm.edu	37	X	153049535	153049535	+	Silent	SNP	A	A	G	rs4898444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153049535A>G	ENST00000370101.3	+	10	1060	c.1014A>G	c.(1012-1014)ccA>ccG	p.P338P	SRPK3_ENST00000370108.3_Intron|SRPK3_ENST00000370100.1_Intron|SRPK3_ENST00000370104.1_Silent_p.P337P|SRPK3_ENST00000393786.3_Intron|SRPK3_ENST00000489426.1_Silent_p.P405P	NM_001170760.1|NM_014370.3	NP_001164231.1|NP_055185.2	Q9UPE1	SRPK3_HUMAN	SRSF protein kinase 3	338	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|muscle tissue development (GO:0060537)|skeletal muscle tissue development (GO:0007519)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(2)|pancreas(2)|urinary_tract(1)	13	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCCCGCCCCAGGGGGCGGCC	0.692													G|||	2278	0.603444	0.3964	0.4539	3775	,	,		10079	0.631		0.2664	False		,,,				2504	0.547				p.P338P	Esophageal Squamous(167;766 3400 32156)	Atlas-SNP	.											.	SRPK3	63	.	0			c.A1014G						PASS	.	G	,,	1774,2049		401,698,274,530,291	20.0	24.0	23.0		1011,,1014	-9.0	0.0	X	dbSNP_111	23	2344,4361		315,1065,649,1041,1214	no	coding-synonymous,intron,coding-synonymous	SRPK3	NM_001170760.1,NM_001170761.1,NM_014370.3	,,	716,1763,923,1571,1505	GG,GA,G,AA,A		34.959,46.4033,39.1147	,,	337/567,,338/568	153049535	4118,6410	2194	4284	6478	SO:0001819	synonymous_variant	26576	exon10			CGCCCCAGGGGGC	AF027406	CCDS35441.1, CCDS55537.1, CCDS55538.1	Xq28	2010-06-23	2010-06-23	2006-08-17	ENSG00000184343	ENSG00000184343			11402	protein-coding gene	gene with protein product			"""serine/threonine kinase 23"", ""SFRS protein kinase 3"""	STK23		16140986	Standard	NM_014370		Approved	MSSK1	uc004fil.3	Q9UPE1	OTTHUMG00000024207	ENST00000370101.3:c.1014A>G	X.37:g.153049535A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	NM_014370	Q13583|Q4F970|Q562F5|Q9UM62	Silent	SNP	ENST00000370101.3	37	CCDS35441.1																																																																																			A|0.477;G|0.523	0.523	strong		0.692	SRPK3-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354501.1	NM_014370	
SDR42E1	93517	hgsc.bcm.edu	37	16	82033612	82033612	+	Missense_Mutation	SNP	T	T	C	rs16956174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	148	0	0		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	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	
RABEPK	10244	hgsc.bcm.edu	37	9	127975654	127975654	+	Missense_Mutation	SNP	C	C	T	rs1128362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127975654C>T	ENST00000373538.3	+	4	527	c.217C>T	c.(217-219)Cac>Tac	p.H73Y	RABEPK_ENST00000394124.4_Missense_Mutation_p.H73Y|RABEPK_ENST00000394125.4_Missense_Mutation_p.H73Y|RABEPK_ENST00000373544.1_Missense_Mutation_p.H73Y|RABEPK_ENST00000259460.8_Intron	NM_005833.3	NP_005824.2	Q7Z6M1	RABEK_HUMAN	Rab9 effector protein with kelch motifs	73			H -> Y (in dbSNP:rs16927965). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		receptor-mediated endocytosis (GO:0006898)|vesicle docking involved in exocytosis (GO:0006904)	endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15						TCCAGGAAAACACCAGTGGGA	0.493													C|||	483	0.0964457	0.118	0.0879	5008	,	,		18384	0.005		0.1362	False		,,,				2504	0.1268				p.H73Y		Atlas-SNP	.											.	RABEPK	46	.	0			c.C217T						PASS	.	C	TYR/HIS,,TYR/HIS	593,3813	259.5+/-263.1	41,511,1651	116.0	110.0	112.0		217,,217	3.6	1.0	9	dbSNP_123	112	1219,7381	246.7+/-275.0	94,1031,3175	yes	missense,intron,missense	RABEPK	NM_001174152.1,NM_001174153.1,NM_005833.3	83,,83	135,1542,4826	TT,TC,CC		14.1744,13.4589,13.932	probably-damaging,,probably-damaging	73/373,,73/373	127975654	1812,11194	2203	4300	6503	SO:0001583	missense	10244	exon4			GGAAAACACCAGT	BC000503	CCDS6862.1, CCDS55341.1	9q33.1-q33.3	2010-04-19			ENSG00000136933	ENSG00000136933			16896	protein-coding gene	gene with protein product		605962				9230071	Standard	NM_005833		Approved	RAB9P40, bA65N13.1	uc004bpi.3	Q7Z6M1	OTTHUMG00000020674	ENST00000373538.3:c.217C>T	9.37:g.127975654C>T	ENSP00000362639:p.His73Tyr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	77	21	0.272727	NM_005833	A8K403|O00568|Q69YR2|Q6FHA4|Q6IBG7|Q6P092|Q86Y76|Q9BWB1	Missense_Mutation	SNP	ENST00000373538.3	37	CCDS6862.1	200	0.09157509157509157	58	0.11788617886178862	40	0.11049723756906077	0	0.0	102	0.1345646437994723	C	11.28	1.592552	0.28357	0.134589	0.141744	ENSG00000136933	ENST00000394125;ENST00000373544;ENST00000394124;ENST00000373538;ENST00000416065	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	5.47	3.63	0.41609	Galactose oxidase, beta-propeller (1);	0.099119	0.64402	D	0.000002	T	0.00178	0.0005	L	0.47716	1.5	0.23425	P	0.99770432	B;P	0.50369	0.014;0.934	B;P	0.50708	0.017;0.648	T	0.07712	-1.0758	9	0.09590	T	0.72	-13.4768	9.2746	0.37692	0.0:0.8267:0.0:0.1733	rs16927965;rs17252930;rs17849327;rs52838209;rs16927965	73;73	Q7Z6M1;Q5T1S4	RABEK_HUMAN;.	Y	73;73;73;73;156	ENSP00000377683:H73Y;ENSP00000362645:H73Y;ENSP00000377682:H73Y;ENSP00000362639:H73Y;ENSP00000402234:H156Y	ENSP00000362639:H73Y	H	+	1	0	RABEPK	127015475	0.968000	0.33430	1.000000	0.80357	0.890000	0.51754	2.254000	0.43214	1.330000	0.45394	-0.218000	0.12543	CAC	C|0.880;T|0.120	0.120	strong		0.493	RABEPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054064.1	NM_005833	
DNA2	1763	hgsc.bcm.edu	37	10	70218890	70218890	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70218890C>T	ENST00000358410.3	-	5	740	c.690G>A	c.(688-690)tcG>tcA	p.S230S	RNA5SP319_ENST00000362768.1_RNA|DNA2_ENST00000399179.2_Silent_p.S230S|DNA2_ENST00000399180.2_Silent_p.S316S	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	230	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						GGAAGTCAGTCGAAGTGTTTT	0.358																																					p.S230S		Atlas-SNP	.											DNA2L,NS,carcinoma,-1,4	DNA2	76	4	0			c.G690A						PASS	.						88.0	78.0	81.0					10																	70218890		1845	4099	5944	SO:0001819	synonymous_variant	1763	exon5			GTCAGTCGAAGTG	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.690G>A	10.37:g.70218890C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	5	0.0485437	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				.	.	none		0.358	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
C5orf42	65250	hgsc.bcm.edu	37	5	37173977	37173977	+	Silent	SNP	A	A	G	rs61746147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37173977A>G	ENST00000508244.1	-	31	6144	c.6051T>C	c.(6049-6051)gcT>gcC	p.A2017A	C5orf42_ENST00000274258.7_Silent_p.A897A|C5orf42_ENST00000425232.2_Silent_p.A2017A			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2017						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GTGGTTGTGAAGCAACATTGA	0.418													A|||	122	0.024361	0.09	0.0043	5008	,	,		16616	0.0		0.0	False		,,,				2504	0.0				p.A2017A		Atlas-SNP	.											.	C5orf42	422	.	0			c.T6051C						PASS	.	A		341,4065	178.0+/-206.8	13,315,1875	140.0	133.0	135.0		6051	1.9	0.9	5	dbSNP_129	135	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous	C5orf42	NM_023073.3		13,317,6173	GG,GA,AA		0.0233,7.7394,2.6372		2017/3198	37173977	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	65250	exon32			TTGTGAAGCAACA		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.6051T>C	5.37:g.37173977A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			A|0.974;G|0.026	0.026	strong		0.418	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
GSN	2934	hgsc.bcm.edu	37	9	124091256	124091256	+	Missense_Mutation	SNP	G	G	T	rs9696578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124091256G>T	ENST00000373818.4	+	14	2072	c.2003G>T	c.(2002-2004)cGc>cTc	p.R668L	GSN_ENST00000449733.1_Missense_Mutation_p.R617L|GSN_ENST00000373808.2_Missense_Mutation_p.R617L|GSN_ENST00000373807.1_Missense_Mutation_p.R399L|GSN_ENST00000373806.1_Missense_Mutation_p.R93L|GSN_ENST00000412819.1_Missense_Mutation_p.R617L|GSN_ENST00000373823.3_Missense_Mutation_p.R617L|GSN_ENST00000341272.2_Missense_Mutation_p.R617L|GSN_ENST00000436847.1_Missense_Mutation_p.R628L|GSN_ENST00000545652.1_Missense_Mutation_p.R625L|GSN_ENST00000394353.2_Missense_Mutation_p.R628L	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	668	Actin-binding, Ca-sensitive. {ECO:0000255}.		R -> L (in dbSNP:rs9696578).		actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						CATCCTCCTCGCCTCTTTGCC	0.622													G|||	18	0.00359425	0.0129	0.0	5008	,	,		21562	0.0		0.001	False		,,,				2504	0.0				p.R668L		Atlas-SNP	.											.	GSN	81	.	0			c.G2003T						PASS	.	G	LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG	46,4360	49.6+/-84.7	0,46,2157	89.0	74.0	79.0		2003,1850,1850,1850,1850,1883,1883,1850	4.7	1.0	9	dbSNP_119	79	1,8599	2.2+/-6.3	0,1,4299	yes	missense,missense,missense,missense,missense,missense,missense,missense	GSN	NM_000177.4,NM_001127662.1,NM_001127663.1,NM_001127664.1,NM_001127665.1,NM_001127666.1,NM_001127667.1,NM_198252.2	102,102,102,102,102,102,102,102	0,47,6456	TT,TG,GG		0.0116,1.044,0.3614	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	668/783,617/732,617/732,617/732,617/732,628/743,628/743,617/732	124091256	47,12959	2203	4300	6503	SO:0001583	missense	2934	exon14			CTCCTCGCCTCTT	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"""amyloidosis, Finnish type"""	137350	"""gelsolin (amyloidosis, Finnish type)"""			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.2003G>T	9.37:g.124091256G>T	ENSP00000362924:p.Arg668Leu	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_000177	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Missense_Mutation	SNP	ENST00000373818.4	37	CCDS6828.1	7	0.003205128205128205	6	0.012195121951219513	0	0.0	0	0.0	1	0.0013192612137203166	G	27.6	4.842728	0.91197	0.01044	1.16E-4	ENSG00000148180	ENST00000373823;ENST00000436847;ENST00000394353;ENST00000449733;ENST00000412819;ENST00000341272;ENST00000373808;ENST00000394352;ENST00000456109;ENST00000545652;ENST00000373818;ENST00000373807;ENST00000373806;ENST00000373805	T;T;T;T;T;T;T;T;T;T;T	0.57595	1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;2.41;0.39	5.56	4.66	0.58398	.	0.110224	0.64402	D	0.000005	T	0.74527	0.3728	H	0.94964	3.605	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	0.91635	0.994;0.999;0.999;0.992;0.999	D	0.84690	0.0722	10	0.87932	D	0	-20.0116	15.541	0.76048	0.0:0.1383:0.8617:0.0	rs9696578;rs9696578	641;625;628;399;668	B7Z9A0;F5H1A8;B7Z373;Q5T0H9;P06396	.;.;.;.;GELS_HUMAN	L	617;628;628;617;617;617;617;601;591;625;668;399;93;93	ENSP00000362929:R617L;ENSP00000411293:R628L;ENSP00000377882:R628L;ENSP00000409358:R617L;ENSP00000416586:R617L;ENSP00000340888:R617L;ENSP00000362914:R617L;ENSP00000445823:R625L;ENSP00000362924:R668L;ENSP00000362913:R399L;ENSP00000362912:R93L	ENSP00000340888:R617L	R	+	2	0	GSN	123131077	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	9.362000	0.97126	1.322000	0.45245	0.655000	0.94253	CGC	G|0.993;T|0.007	0.007	strong		0.622	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177	
POLR2A	5430	hgsc.bcm.edu	37	17	7400815	7400815	+	Silent	SNP	T	T	C	rs2228128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7400815T>C	ENST00000322644.6	+	6	1359	c.960T>C	c.(958-960)aaT>aaC	p.N320N	POLR2A_ENST00000572844.1_Silent_p.N320N	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	320					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				TGGTGGACAATGAGCTGCCTG	0.597													T|||	589	0.117612	0.0598	0.1354	5008	,	,		18391	0.0536		0.2664	False		,,,				2504	0.0961				p.N320N		Atlas-SNP	.											.	POLR2A	157	.	0			c.T960C						PASS	.	T		393,4013	196.0+/-220.5	18,357,1828	75.0	63.0	67.0		960	-6.9	0.9	17	dbSNP_98	67	2415,6185	399.4+/-346.4	347,1721,2232	no	coding-synonymous	POLR2A	NM_000937.4		365,2078,4060	CC,CT,TT		28.0814,8.9197,21.59		320/1971	7400815	2808,10198	2203	4300	6503	SO:0001819	synonymous_variant	5430	exon6			GGACAATGAGCTG			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.960T>C	17.37:g.7400815T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	137	57	0.416058	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			T|0.818;C|0.182	0.182	strong		0.597	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
KRT73	319101	hgsc.bcm.edu	37	12	53005004	53005004	+	Missense_Mutation	SNP	T	T	C	rs607426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53005004T>C	ENST00000305748.3	-	6	1128	c.1094A>G	c.(1093-1095)gAg>gGg	p.E365G	RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000551089.1_RNA|RP11-641A6.2_ENST00000549180.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	365	Coil 2.|Rod.		E -> G (in dbSNP:rs607426).			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)		CTTCACACTCTCAATCTCCGA	0.567													T|||	104	0.0207668	0.0764	0.0043	5008	,	,		20476	0.0		0.0	False		,,,				2504	0.0				p.E365G		Atlas-SNP	.											.	KRT73	101	.	0			c.A1094G						PASS	.	T	GLY/GLU	214,4192	129.8+/-166.5	5,204,1994	144.0	125.0	131.0		1094	5.6	1.0	12	dbSNP_83	131	1,8599		0,1,4299	yes	missense	KRT73	NM_175068.2	98	5,205,6293	CC,CT,TT		0.0116,4.857,1.6531	benign	365/541	53005004	215,12791	2203	4300	6503	SO:0001583	missense	319101	exon6			ACACTCTCAATCT	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.1094A>G	12.37:g.53005004T>C	ENSP00000307014:p.Glu365Gly	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	211	97	0.459716	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	29	0.013278388278388278	27	0.054878048780487805	2	0.0055248618784530384	0	0.0	0	0.0	T	12.93	2.086766	0.36855	0.04857	1.16E-4	ENSG00000186049	ENST00000305748;ENST00000552855	D;D	0.89746	-2.56;-2.56	5.61	5.61	0.85477	Filament (1);	0.000000	0.53938	D	0.000057	T	0.63896	0.2550	M	0.83603	2.65	0.37997	D	0.934108	B	0.06786	0.001	B	0.13407	0.009	T	0.79019	-0.1974	10	0.44086	T	0.13	.	11.2067	0.48773	0.0:0.0715:0.0:0.9285	rs607426;rs1352442;rs1707745	365	Q86Y46	K2C73_HUMAN	G	365;110	ENSP00000307014:E365G;ENSP00000449081:E110G	ENSP00000307014:E365G	E	-	2	0	KRT73	51291271	0.995000	0.38212	0.995000	0.50966	0.919000	0.55068	3.762000	0.55250	2.276000	0.75962	0.454000	0.30748	GAG	T|0.980;C|0.020	0.020	strong		0.567	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
TGM6	343641	hgsc.bcm.edu	37	20	2380323	2380323	+	Silent	SNP	G	G	A	rs6114033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2380323G>A	ENST00000202625.2	+	6	850	c.789G>A	c.(787-789)aaG>aaA	p.K263K	TGM6_ENST00000477505.1_3'UTR|TGM6_ENST00000381423.1_Silent_p.K263K	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	263					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	AGTGGCTCAAGGGCAGGTACA	0.662													G|||	912	0.182109	0.1982	0.1974	5008	,	,		12837	0.1498		0.1153	False		,,,				2504	0.2515				p.K263K		Atlas-SNP	.											TGM6,NS,carcinoma,0,1	TGM6	126	1	0			c.G789A						scavenged	.	G		845,3561	315.2+/-294.0	72,701,1430	42.0	45.0	44.0		789	5.0	1.0	20	dbSNP_114	44	815,7785	179.2+/-228.4	45,725,3530	no	coding-synonymous	TGM6	NM_198994.2		117,1426,4960	AA,AG,GG		9.4767,19.1784,12.7633		263/707	2380323	1660,11346	2203	4300	6503	SO:0001819	synonymous_variant	343641	exon6			GCTCAAGGGCAGG	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.789G>A	20.37:g.2380323G>A		Somatic	239	2	0.0083682		WXS	Illumina HiSeq	Phase_I	303	157	0.518152	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	37	CCDS13025.1																																																																																			G|0.857;A|0.143	0.143	strong		0.662	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
TM7SF3	51768	hgsc.bcm.edu	37	12	27148324	27148324	+	Missense_Mutation	SNP	G	G	C	rs34735713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27148324G>C	ENST00000343028.4	-	5	761	c.536C>G	c.(535-537)cCa>cGa	p.P179R	TM7SF3_ENST00000542667.1_5'UTR	NM_016551.2	NP_057635.1	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3	179			P -> R (in dbSNP:rs34735713).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	18	Colorectal(261;0.0847)					AGCGTCACATGGTGGGGGATC	0.468													G|||	109	0.0217652	0.0779	0.0086	5008	,	,		21417	0.0		0.0	False		,,,				2504	0.0				p.P179R		Atlas-SNP	.											.	TM7SF3	41	.	0			c.C536G						PASS	.	G	ARG/PRO	360,4046	183.3+/-210.9	16,328,1859	68.0	56.0	60.0		536	2.5	0.0	12	dbSNP_126	60	5,8595	3.7+/-12.6	0,5,4295	yes	missense	TM7SF3	NM_016551.2	103	16,333,6154	CC,CG,GG		0.0581,8.1707,2.8064	possibly-damaging	179/571	27148324	365,12641	2203	4300	6503	SO:0001583	missense	51768	exon5			TCACATGGTGGGG	AB032470	CCDS8710.1	12q11-q12	2012-08-10			ENSG00000064115	ENSG00000064115			23049	protein-coding gene	gene with protein product		605181				10828615	Standard	NM_016551		Approved		uc010sjl.2	Q9NS93	OTTHUMG00000169243	ENST00000343028.4:c.536C>G	12.37:g.27148324G>C	ENSP00000342322:p.Pro179Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_016551	B3KMZ3|Q9NUS4	Missense_Mutation	SNP	ENST00000343028.4	37	CCDS8710.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	G	13.61	2.289340	0.40494	0.081707	5.81E-4	ENSG00000064115	ENST00000343028;ENST00000543803;ENST00000539741;ENST00000543088	T;T;T;T	0.44881	1.5;0.92;0.91;0.93	4.27	2.45	0.29901	.	0.491723	0.22200	N	0.063241	T	0.01870	0.0059	L	0.60455	1.87	0.09310	N	1	P	0.42409	0.779	B	0.33690	0.168	T	0.02184	-1.1199	10	0.66056	D	0.02	-0.8778	8.9426	0.35740	0.2425:0.0:0.7575:0.0	rs34735713	179	Q9NS93	TM7S3_HUMAN	R	179;77;57;57	ENSP00000342322:P179R;ENSP00000442617:P77R;ENSP00000441027:P57R;ENSP00000444632:P57R	ENSP00000342322:P179R	P	-	2	0	TM7SF3	27039591	0.546000	0.26457	0.001000	0.08648	0.002000	0.02628	3.800000	0.55537	0.574000	0.29417	-0.157000	0.13467	CCA	G|0.971;C|0.029	0.029	strong		0.468	TM7SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403033.1	NM_016551	
SPATC1L	84221	hgsc.bcm.edu	37	21	47581508	47581508	+	Missense_Mutation	SNP	C	C	A	rs74518516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47581508C>A	ENST00000291672.5	-	5	1869	c.808G>T	c.(808-810)Gtg>Ttg	p.V270L	SPATC1L_ENST00000330205.6_Missense_Mutation_p.V116L	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	270																	GCCGGGTGCACGTCGCGGCTG	0.692													C|||	122	0.024361	0.0877	0.0086	5008	,	,		12794	0.0		0.0	False		,,,				2504	0.0				p.V270L		Atlas-SNP	.											.	.	.	.	0			c.G808T						PASS	.	C	LEU/VAL,LEU/VAL	406,3986		22,362,1812	23.0	25.0	24.0		808,346	4.3	1.0	21	dbSNP_131	24	4,8584		0,4,4290	yes	missense,missense	C21orf56	NM_001142854.1,NM_032261.4	32,32	22,366,6102	AA,AC,CC		0.0466,9.2441,3.1587	benign,benign	270/341,116/187	47581508	410,12570	2196	4294	6490	SO:0001583	missense	84221	exon5			GGTGCACGTCGCG	BC009497	CCDS13732.1, CCDS46653.1	21q22.3	2013-01-21	2012-11-12	2012-11-12	ENSG00000160284	ENSG00000160284			1298	protein-coding gene	gene with protein product	"""speriolin-like protein"""	612412	"""chromosome 21 open reading frame 56"""	C21orf56			Standard	NM_032261		Approved		uc011afu.2	Q9H0A9	OTTHUMG00000090487	ENST00000291672.5:c.808G>T	21.37:g.47581508C>A	ENSP00000291672:p.Val270Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	99	57	0.575758	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Missense_Mutation	SNP	ENST00000291672.5	37	CCDS46653.1	57	0.0260989010989011	52	0.10569105691056911	5	0.013812154696132596	0	0.0	0	0.0	C	13.27	2.188243	0.38609	0.092441	4.66E-4	ENSG00000160284	ENST00000330205;ENST00000291672	T;T	0.50001	0.76;0.76	4.27	4.27	0.50696	.	0.098443	0.41938	D	0.000800	T	0.00637	0.0021	L	0.38838	1.175	0.27740	N	0.944518	B	0.32968	0.392	B	0.27380	0.079	T	0.02411	-1.1163	10	0.51188	T	0.08	-27.6288	8.1902	0.31363	0.0:0.8871:0.0:0.1129	.	270	Q9H0A9	CU056_HUMAN	L	116;270	ENSP00000333869:V116L;ENSP00000291672:V270L	ENSP00000291672:V270L	V	-	1	0	C21orf56	46405936	0.803000	0.28956	0.979000	0.43373	0.918000	0.54935	1.358000	0.34102	1.929000	0.55896	0.591000	0.81541	GTG	C|0.971;A|0.029	0.029	strong		0.692	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
POM121L2	94026	hgsc.bcm.edu	37	6	27278020	27278020	+	Missense_Mutation	SNP	C	C	A	rs16897515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27278020C>A	ENST00000444565.1	-	1	1929	c.1930G>T	c.(1930-1932)Ggt>Tgt	p.G644C	POM121L2_ENST00000377451.2_Missense_Mutation_p.G580C	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	644										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						TTCACTACACCAAAATCCAAA	0.517													C|||	723	0.144369	0.2443	0.147	5008	,	,		21112	0.0288		0.168	False		,,,				2504	0.1022				p.G644C		Atlas-SNP	.											.	POM121L2	61	.	0			c.G1930T						PASS	.	C	CYS/GLY	346,1038		41,264,387	54.0	51.0	52.0		1930	0.8	0.0	6	dbSNP_123	52	577,2605		45,487,1059	yes	missense	POM121L2	NM_033482.3	159	86,751,1446	AA,AC,CC		18.1332,25.0,20.2146	probably-damaging	644/1036	27278020	923,3643	692	1591	2283	SO:0001583	missense	94026	exon1			CTACACCAAAATC	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.1930G>T	6.37:g.27278020C>A	ENSP00000392726:p.Gly644Cys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	320	0.14652014652014653	128	0.2601626016260163	59	0.16298342541436464	10	0.017482517482517484	123	0.16226912928759896	C	15.86	2.958304	0.53400	0.25	0.181332	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.17054	2.3;2.31	3.96	0.825	0.18824	.	0.890845	0.09283	N	0.823423	T	0.15478	0.0373	L	0.42245	1.32	0.80722	P	0.0	D	0.89917	1.0	D	0.74023	0.982	T	0.08146	-1.0736	9	0.72032	D	0.01	.	5.5069	0.16858	0.0:0.5474:0.0:0.4526	rs16897515;rs16897515	644	C9J1I7	.	C	580;644	ENSP00000366671:G580C;ENSP00000392726:G644C	ENSP00000366671:G580C	G	-	1	0	POM121L2	27385999	0.002000	0.14202	0.000000	0.03702	0.640000	0.38277	1.292000	0.33342	0.148000	0.19059	-0.350000	0.07774	GGT	C|0.850;A|0.150	0.150	strong		0.517	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
GKN1	56287	hgsc.bcm.edu	37	2	69204629	69204629	+	Silent	SNP	T	T	C	rs35624281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69204629T>C	ENST00000377938.2	+	2	120	c.57T>C	c.(55-57)atT>atC	p.I19I		NM_019617.3	NP_062563.3	Q9NS71	GKN1_HUMAN	gastrokine 1	19					digestion (GO:0007586)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|secretory granule (GO:0030141)				breast(2)|large_intestine(4)|lung(5)	11						GATTTCAGATTGTCTTTGCTG	0.373													T|||	674	0.134585	0.0711	0.1268	5008	,	,		19283	0.2708		0.0437	False		,,,				2504	0.1789				p.I19I		Atlas-SNP	.											.	GKN1	24	.	0			c.T57C						PASS	.	T		324,4082	170.9+/-201.2	9,306,1888	215.0	182.0	193.0		57	-2.9	0.0	2	dbSNP_126	193	323,8277	114.0+/-174.0	11,301,3988	no	coding-synonymous	GKN1	NM_019617.3		20,607,5876	CC,CT,TT		3.7558,7.3536,4.9746		19/200	69204629	647,12359	2203	4300	6503	SO:0001819	synonymous_variant	56287	exon2			TCAGATTGTCTTT	AY139182	CCDS1891.2	2p13.3	2012-10-10			ENSG00000169605	ENSG00000169605		"""BRICHOS domain containing"""	23217	protein-coding gene	gene with protein product	"""BRICHOS domain containing 1"""	606402				12851218, 11562744	Standard	NM_019617		Approved	AMP18, CA11, BRICD1	uc002sfc.3	Q9NS71	OTTHUMG00000129574	ENST00000377938.2:c.57T>C	2.37:g.69204629T>C		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	183	97	0.530055	NM_019617	Q8IUA9	Silent	SNP	ENST00000377938.2	37	CCDS1891.2																																																																																			T|0.933;C|0.067	0.067	strong		0.373	GKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251769.2	NM_019617	
PABPC3	5042	hgsc.bcm.edu	37	13	25670868	25670868	+	Missense_Mutation	SNP	G	G	A	rs200859889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25670868G>A	ENST00000281589.3	+	1	569	c.532G>A	c.(532-534)Gaa>Aaa	p.E178K		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	178					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		GTCTCGTAAAGAACGAGAAGC	0.403													g|||	262	0.0523163	0.0756	0.0591	5008	,	,		22159	0.0298		0.0308	False		,,,				2504	0.0613				p.E178K		Atlas-SNP	.											PABPC3,NS,carcinoma,0,1	PABPC3	129	1	0			c.G532A						scavenged	.						104.0	98.0	100.0					13																	25670868		2203	4300	6503	SO:0001583	missense	5042	exon1			CGTAAAGAACGAG	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.532G>A	13.37:g.25670868G>A	ENSP00000281589:p.Glu178Lys	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	203	9	0.044335	NM_030979	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.906877	0.52333	.	.	ENSG00000151846	ENST00000281589	D	0.85861	-2.04	0.828	0.828	0.18841	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.47455	U	0.000224	T	0.76076	0.3937	L	0.60455	1.87	0.50632	D	0.999885	P	0.38455	0.632	B	0.28784	0.094	T	0.73858	-0.3850	10	0.66056	D	0.02	.	7.4633	0.27308	1.0E-4:0.0:0.9999:0.0	.	178	Q9H361	PABP3_HUMAN	K	178	ENSP00000281589:E178K	ENSP00000281589:E178K	E	+	1	0	PABPC3	24568868	1.000000	0.71417	0.959000	0.39883	0.390000	0.30446	6.438000	0.73426	0.748000	0.32831	0.305000	0.20034	GAA	.	.	weak		0.403	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
SSBP3	23648	hgsc.bcm.edu	37	1	54747176	54747176	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54747176C>T	ENST00000371320.3	-	5	711	c.301G>A	c.(301-303)Gtg>Atg	p.V101M	SSBP3_ENST00000417664.2_De_novo_Start_InFrame|SSBP3_ENST00000371319.3_Missense_Mutation_p.V101M|SSBP3_ENST00000357475.4_Missense_Mutation_p.V101M|SSBP3_ENST00000326956.7_5'UTR	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	101	Pro-rich.				head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						TTGCCAAGCACGGGGCTCGGG	0.617																																					p.V101M		Atlas-SNP	.											.	SSBP3	65	.	0			c.G301A						PASS	.						16.0	15.0	15.0					1																	54747176		2194	4286	6480	SO:0001583	missense	23648	exon5			CAAGCACGGGGCT		CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"""single-stranded DNA-binding protein 3"""			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.301G>A	1.37:g.54747176C>T	ENSP00000360371:p.Val101Met	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	105	35	0.333333	NM_145716	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Missense_Mutation	SNP	ENST00000371320.3	37	CCDS591.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.555184	0.86231	.	.	ENSG00000157216	ENST00000371320;ENST00000371319;ENST00000357475	.	.	.	4.83	4.83	0.62350	.	0.000000	0.64402	U	0.000001	T	0.77818	0.4187	M	0.68317	2.08	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.80764	0.994;0.981;0.973	T	0.78311	-0.2253	9	0.46703	T	0.11	-0.63	18.3318	0.90271	0.0:1.0:0.0:0.0	.	101;101;101	Q9BWW4-2;Q9BWW4-3;Q9BWW4	.;.;SSBP3_HUMAN	M	101	.	ENSP00000350067:V101M	V	-	1	0	SSBP3	54519764	1.000000	0.71417	0.977000	0.42913	0.991000	0.79684	7.369000	0.79578	2.409000	0.81822	0.563000	0.77884	GTG	.	.	none		0.617	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070	
AKNA	80709	hgsc.bcm.edu	37	9	117129921	117129921	+	Missense_Mutation	SNP	G	G	C	rs62640865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117129921G>C	ENST00000307564.4	-	6	1791	c.1630C>G	c.(1630-1632)Ctg>Gtg	p.L544V	AKNA_ENST00000223791.3_Missense_Mutation_p.L4V|AKNA_ENST00000374075.5_Missense_Mutation_p.L463V|AKNA_ENST00000374088.3_Missense_Mutation_p.L544V|AKNA_ENST00000312033.3_Missense_Mutation_p.L544V	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	544					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						AGCCACCCCAGGGTGGGCATG	0.607													G|||	180	0.0359425	0.1324	0.0072	5008	,	,		20087	0.0		0.0	False		,,,				2504	0.0				p.L544V		Atlas-SNP	.											.	AKNA	119	.	0			c.C1630G						PASS	.	G	VAL/LEU	445,3961	213.8+/-233.3	20,405,1778	50.0	50.0	50.0		1630	3.2	0.0	9	dbSNP_129	50	3,8597	2.2+/-6.3	0,3,4297	yes	missense	AKNA	NM_030767.4	32	20,408,6075	CC,CG,GG		0.0349,10.0999,3.4446	benign	544/1440	117129921	448,12558	2203	4300	6503	SO:0001583	missense	80709	exon6			ACCCCAGGGTGGG	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.1630C>G	9.37:g.117129921G>C	ENSP00000303769:p.Leu544Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	71	0.03250915750915751	68	0.13821138211382114	3	0.008287292817679558	0	0.0	0	0.0	G	8.010	0.757277	0.15846	0.100999	3.49E-4	ENSG00000106948	ENST00000307564;ENST00000394582;ENST00000374088;ENST00000223791;ENST00000374075;ENST00000312033	T;T;T;T;T	0.30714	2.72;2.72;2.46;2.72;1.52	5.05	3.17	0.36434	.	0.310451	0.23710	N	0.045338	T	0.00109	0.0003	N	0.14661	0.345	0.09310	N	0.999998	B;B	0.17268	0.005;0.021	B;B	0.15484	0.004;0.013	T	0.21042	-1.0257	10	0.30078	T	0.28	-0.342	6.9494	0.24536	0.0931:0.1751:0.7318:0.0	rs62640865	544;463	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	V	544;385;544;4;463;544	ENSP00000303769:L544V;ENSP00000363201:L544V;ENSP00000223791:L4V;ENSP00000363188:L463V;ENSP00000309222:L544V	ENSP00000223791:L4V	L	-	1	2	AKNA	116169742	0.004000	0.15560	0.002000	0.10522	0.008000	0.06430	1.056000	0.30480	0.802000	0.34089	0.655000	0.94253	CTG	G|0.957;C|0.043	0.043	strong		0.607	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
BCDIN3D	144233	hgsc.bcm.edu	37	12	50232169	50232169	+	Missense_Mutation	SNP	A	A	T	rs11169172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50232169A>T	ENST00000333924.4	-	2	905	c.864T>A	c.(862-864)agT>agA	p.S288R	BCDIN3D-AS1_ENST00000548872.1_RNA|BCDIN3D-AS1_ENST00000549124.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	288			S -> R (in dbSNP:rs11169172).		miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)	p.S288R(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						GCTTCTGGAAACTTAATCTGT	0.388													.|||	1423	0.284145	0.2549	0.3934	5008	,	,		22331	0.5337		0.0616	False		,,,				2504	0.2178				p.S288R		Atlas-SNP	.											BCDIN3D,NS,carcinoma,0,1	BCDIN3D	20	1	1	Substitution - Missense(1)	stomach(1)	c.T864A						scavenged	.	A	ARG/SER	961,3445	361.1+/-315.5	97,767,1339	138.0	136.0	136.0		864	3.6	0.9	12	dbSNP_120	136	529,8071	147.7+/-203.1	13,503,3784	yes	missense	BCDIN3D	NM_181708.2	110	110,1270,5123	TT,TA,AA		6.1512,21.8112,11.4563	benign	288/293	50232169	1490,11516	2203	4300	6503	SO:0001583	missense	144233	exon2			CTGGAAACTTAAT		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.864T>A	12.37:g.50232169A>T	ENSP00000335201:p.Ser288Arg	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	15	5	0.333333	NM_181708	A8K829	Missense_Mutation	SNP	ENST00000333924.4	37	CCDS8790.1	598	0.27380952380952384	118	0.23983739837398374	129	0.356353591160221	305	0.5332167832167832	46	0.06068601583113457	A	0.008	-1.866897	0.00547	0.218112	0.061512	ENSG00000186666	ENST00000333924	T	0.40225	1.04	4.79	3.64	0.41730	.	0.130149	0.35495	N	0.003162	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.99999999398211	B	0.02656	0.0	B	0.01281	0.0	T	0.45862	-0.9232	9	0.02654	T	1	.	7.8705	0.29563	0.1859:0.0:0.0:0.814	rs11169172;rs11169172	288	Q7Z5W3	BN3D2_HUMAN	R	288	ENSP00000335201:S288R	ENSP00000335201:S288R	S	-	3	2	BCDIN3D	48518436	0.005000	0.15991	0.861000	0.33841	0.031000	0.12232	0.191000	0.17076	0.964000	0.38108	-0.536000	0.04276	AGT	A|0.811;T|0.189	0.189	strong		0.388	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708	
INPP4A	3631	hgsc.bcm.edu	37	2	99193496	99193496	+	Silent	SNP	C	C	T	rs2230388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99193496C>T	ENST00000523221.1	+	23	2691	c.2691C>T	c.(2689-2691)agC>agT	p.S897S	INPP4A_ENST00000409851.3_Silent_p.S892S|INPP4A_ENST00000074304.5_Silent_p.S897S|INPP4A_ENST00000409463.1_Silent_p.S226S|INPP4A_ENST00000409016.4_Silent_p.S858S|INPP4A_ENST00000545415.1_Silent_p.S858S|INPP4A_ENST00000409540.3_Silent_p.S858S			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	897					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						GCTGCAAGAGCGCTAAGGACC	0.612													C|||	1284	0.25639	0.1589	0.2968	5008	,	,		17232	0.2937		0.2714	False		,,,				2504	0.3057				p.S897S		Atlas-SNP	.											.	INPP4A	205	.	0			c.C2691T						PASS	.	C	,,,	704,3520		63,578,1471	62.0	66.0	65.0		2691,2676,2574,2574	-3.1	1.0	2	dbSNP_98	65	2195,6257		291,1613,2322	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	354,2191,3793	TT,TC,CC		25.9702,16.6667,22.87	,,,	897/978,892/973,858/955,858/939	99193496	2899,9777	2112	4226	6338	SO:0001819	synonymous_variant	3631	exon25			CAAGAGCGCTAAG	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.2691C>T	2.37:g.99193496C>T		Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	251	118	0.47012	NM_001134224	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																			C|0.753;T|0.247	0.247	strong		0.612	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
DNAJC25	548645	hgsc.bcm.edu	37	9	114411945	114411945	+	Silent	SNP	G	G	T	rs7019332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114411945G>T	ENST00000313525.3	+	3	758	c.702G>T	c.(700-702)ggG>ggT	p.G234G	DNAJC25-GNG10_ENST00000374294.3_Intron|DNAJC25_ENST00000556107.1_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	234						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						ATATAAAGGGGGGCTATCAGA	0.353													G|||	1563	0.312101	0.3517	0.4251	5008	,	,		18464	0.4127		0.2306	False		,,,				2504	0.1585				p.G234G		Atlas-SNP	.											.	DNAJC25	20	.	0			c.G702T						PASS	.	G	,	1147,2465		194,759,853	41.0	42.0	42.0		702,	-0.3	1.0	9	dbSNP_116	42	1718,6410		175,1368,2521	no	coding-synonymous,intron	DNAJC25,DNAJC25-GNG10	NM_001015882.2,NM_004125.3	,	369,2127,3374	TT,TG,GG		21.1368,31.7553,24.4037	,	234/361,	114411945	2865,8875	1806	4064	5870	SO:0001819	synonymous_variant	548645	exon3			AAAGGGGGGCTAT		CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"""Heat shock proteins / DNAJ (HSP40)"""	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.702G>T	9.37:g.114411945G>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	67	25	0.373134	NM_001015882	Q5QTD8|Q96BN9	Silent	SNP	ENST00000313525.3	37	CCDS43862.1																																																																																			G|0.691;T|0.309	0.309	strong		0.353	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882	
TSSK1B	83942	hgsc.bcm.edu	37	5	112770054	112770054	+	Silent	SNP	G	G	A	rs111560230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112770054G>A	ENST00000390666.3	-	1	674	c.483C>T	c.(481-483)tgC>tgT	p.C161C	CTD-2201G3.1_ENST00000416046.2_RNA|CTD-2201G3.1_ENST00000383058.4_RNA|CTD-2201G3.1_ENST00000510381.2_RNA|MCC_ENST00000408903.3_Intron	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	161	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		CATCCCGCAGGCAGCGCTTGG	0.577													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21131	0.0		0.0	False		,,,				2504	0.0				p.C161C		Atlas-SNP	.											.	TSSK1B	89	.	0			c.C483T						PASS	.	G	,	2,4402	4.2+/-10.8	0,2,2200	81.0	77.0	78.0		,483	1.2	1.0	5	dbSNP_132	78	0,8600		0,0,4300	no	intron,coding-synonymous	MCC,TSSK1B	NM_001085377.1,NM_032028.3	,	0,2,6500	AA,AG,GG		0.0,0.0454,0.0154	,	,161/368	112770054	2,13002	2202	4300	6502	SO:0001819	synonymous_variant	83942	exon1			CCGCAGGCAGCGC	AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"""serine/threonine kinase 22D (spermiogenesis associated)"", ""testis-specific serine kinase 1"""	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.483C>T	5.37:g.112770054G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_032028	B2R8D9	Silent	SNP	ENST00000390666.3	37	CCDS4112.1																																																																																			G|0.500;A|0.500	0.500	strong		0.577	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028	
HRC	3270	hgsc.bcm.edu	37	19	49657713	49657713	+	Missense_Mutation	SNP	T	T	A	rs547456261|rs61355957|rs61198077|rs66501117|rs531655952|rs534731199|rs569932130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657713T>A	ENST00000252825.4	-	1	968	c.782A>T	c.(781-783)gAt>gTt	p.D261V	HRC_ENST00000595625.1_Missense_Mutation_p.D261V	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	261	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Asp-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		AATGGAGAcatcatcatcatc	0.498																																					p.D261V	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											HRC,NS,carcinoma,0,1	HRC	85	1	0			c.A782T						scavenged	.						143.0	105.0	118.0					19																	49657713		2203	4300	6503	SO:0001583	missense	3270	exon1			GAGACATCATCAT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.782A>T	19.37:g.49657713T>A	ENSP00000252825:p.Asp261Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	88	3	0.0340909	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	37	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	T	12.96	2.093755	0.36952	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.33438	1.41	3.29	1.02	0.19986	.	.	.	.	.	T	0.26738	0.0654	M	0.69823	2.125	0.09310	N	0.999995	B	0.24618	0.107	B	0.19666	0.026	T	0.29671	-1.0004	9	0.36615	T	0.2	2.7396	2.2712	0.04091	0.249:0.1435:0.0:0.6075	.	261	P23327	SRCH_HUMAN	V	261;231	ENSP00000252825:D261V	ENSP00000252825:D261V	D	-	2	0	HRC	54349525	0.000000	0.05858	0.174000	0.22961	0.528000	0.34623	-1.362000	0.02595	0.283000	0.22279	0.374000	0.22700	GAT	.	.	none		0.498	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
FBXW10	10517	hgsc.bcm.edu	37	17	18681913	18681913	+	Missense_Mutation	SNP	G	G	A	rs77288131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18681913G>A	ENST00000395665.4	+	14	2682	c.2461G>A	c.(2461-2463)Gcc>Acc	p.A821T	FBXW10_ENST00000308799.4_Missense_Mutation_p.A830T|FBXW10_ENST00000395667.1_Missense_Mutation_p.A820T|TVP23B_ENST00000476139.1_5'Flank|FBXW10_ENST00000301938.4_Missense_Mutation_p.A768T|TVP23B_ENST00000307767.8_5'Flank|TVP23B_ENST00000574226.1_5'Flank			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	821			A -> T (in dbSNP:rs1026259). {ECO:0000269|PubMed:11230166}.							NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GACTGTTAGCGCCCTGCAGCA	0.478													N|||	437	0.0872604	0.1263	0.0648	5008	,	,		16718	0.0635		0.0805	False		,,,				2504	0.0818				p.A821T		Atlas-SNP	.											.	FBXW10	82	.	0			c.G2461A						PASS	.	G	THR/ALA	480,3924	218.4+/-236.5	20,440,1742	43.0	45.0	44.0		2458	2.8	0.6	17	dbSNP_131	44	639,7957	162.2+/-214.9	20,599,3679	no	missense	FBXW10	NM_031456.3	58	40,1039,5421	AA,AG,GG		7.4337,10.8992,8.6077	benign	820/1052	18681913	1119,11881	2202	4298	6500	SO:0001583	missense	10517	exon14			GTTAGCGCCCTGC	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.2461G>A	17.37:g.18681913G>A	ENSP00000379025:p.Ala821Thr	Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	308	157	0.50974	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	197	0.0902014652014652	72	0.14634146341463414	28	0.07734806629834254	37	0.06468531468531469	60	0.079155672823219	G	3.176	-0.168987	0.06461	0.108992	0.074337	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.62105	0.05;0.29;0.09;0.16	3.88	2.81	0.32909	.	0.000000	0.35378	U	0.003241	T	0.00328	0.0010	L	0.38175	1.15	0.39205	P	0.03678199999999998	B;B;B;B	0.21821	0.025;0.056;0.008;0.061	B;B;B;B	0.17433	0.007;0.018;0.002;0.007	T	0.09773	-1.0659	9	0.33940	T	0.23	.	10.2526	0.43377	0.0:0.0:0.789:0.2109	.	768;830;821;820	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	T	820;830;768;821	ENSP00000379026:A820T;ENSP00000310382:A830T;ENSP00000306937:A768T;ENSP00000379025:A821T	ENSP00000306937:A768T	A	+	1	0	FBXW10	18622638	0.007000	0.16637	0.617000	0.29091	0.211000	0.24417	0.897000	0.28390	1.963000	0.57068	0.404000	0.27445	GCC	G|0.912;A|0.088	0.088	strong		0.478	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
SMPD2	6610	hgsc.bcm.edu	37	6	109762332	109762332	+	Missense_Mutation	SNP	C	C	T	rs1048197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:109762332C>T	ENST00000258052.3	+	1	367	c.8C>T	c.(7-9)cCc>cTc	p.P3L	PPIL6_ENST00000440797.2_5'UTR|PPIL6_ENST00000521072.2_5'UTR|PPIL6_ENST00000424445.2_5'UTR	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	3			P -> L (in dbSNP:rs1048197). {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)		ACCATGAAGCCCAACTTCTCC	0.692													C|||	551	0.110024	0.0567	0.1196	5008	,	,		13807	0.1885		0.0408	False		,,,				2504	0.1656				p.P3L		Atlas-SNP	.											.	SMPD2	25	.	0			c.C8T						PASS	.	C	,LEU/PRO,	240,4166	140.0+/-175.5	9,222,1972	114.0	102.0	106.0		,8,	4.3	1.0	6	dbSNP_86	106	310,8290	111.4+/-171.7	6,298,3996	yes	utr-5,missense,utr-5	SMPD2,PPIL6	NM_001111298.2,NM_003080.2,NM_173672.4	,98,	15,520,5968	TT,TC,CC		3.6047,5.4471,4.2288	,benign,	,3/424,	109762332	550,12456	2203	4300	6503	SO:0001583	missense	6610	exon1			TGAAGCCCAACTT	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.8C>T	6.37:g.109762332C>T	ENSP00000258052:p.Pro3Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	99	34	0.343434	NM_003080	Q5TED1|Q9BWR3	Missense_Mutation	SNP	ENST00000258052.3	37	CCDS5075.1	226	0.10347985347985347	30	0.06097560975609756	33	0.09116022099447514	124	0.21678321678321677	39	0.051451187335092345	C	17.86	3.491942	0.64074	0.054471	0.036047	ENSG00000135587	ENST00000258052	T	0.21932	1.98	6.07	4.29	0.51040	.	0.541238	0.20354	N	0.093981	T	0.04048	0.0113	N	0.12182	0.205	0.31916	P	0.614042	B	0.14805	0.011	B	0.09377	0.004	T	0.26395	-1.0104	9	0.44086	T	0.13	-13.1166	7.7329	0.28797	0.1621:0.7564:0.0:0.0815	rs1048197;rs3173166;rs60798697;rs1048197	3	O60906	NSMA_HUMAN	L	3	ENSP00000258052:P3L	ENSP00000258052:P3L	P	+	2	0	SMPD2	109869025	0.000000	0.05858	0.999000	0.59377	0.964000	0.63967	0.030000	0.13688	0.883000	0.36040	0.655000	0.94253	CCC	C|0.925;T|0.075	0.075	strong		0.692	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1		
ARHGAP8	23779	hgsc.bcm.edu	37	22	45244930	45244930	+	Silent	SNP	C	C	T	rs2269543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45244930C>T	ENST00000389774.2	+	11	1101	c.960C>T	c.(958-960)ctC>ctT	p.L320L	ARHGAP8_ENST00000336963.4_Silent_p.L289L|ARHGAP8_ENST00000517296.3_Silent_p.L499L|PRR5-ARHGAP8_ENST00000352766.7_Silent_p.L499L|ARHGAP8_ENST00000356099.6_Silent_p.L289L|PRR5-ARHGAP8_ENST00000361473.5_Silent_p.L420L|ARHGAP8_ENST00000389773.5_Silent_p.L411L	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	320	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		AGCAGATTCTCGGGATCACCT	0.647													C|||	1839	0.367212	0.5915	0.2594	5008	,	,		18232	0.3105		0.2495	False		,,,				2504	0.32				p.L411L		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C1233T						PASS	.	C	,,,	2352,2054	608.2+/-391.1	619,1114,470	137.0	134.0	135.0		960,867,1233,867	-7.6	0.0	22	dbSNP_100	135	2331,6269	391.0+/-343.5	304,1723,2273	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	,,,	923,2837,2743	TT,TC,CC		27.1047,46.6182,36.0065	,,,	320/465,289/306,411/556,289/434	45244930	4683,8323	2203	4300	6503	SO:0001819	synonymous_variant	553158	exon13			GATTCTCGGGATC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.960C>T	22.37:g.45244930C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000389774.2	37	CCDS33664.1	734	0.3360805860805861	259	0.5264227642276422	101	0.27900552486187846	189	0.3304195804195804	185	0.24406332453825857	C	2.230	-0.376321	0.05000	0.533818	0.271047	ENSG00000248405	ENST00000515632	.	.	.	3.82	-7.64	0.01286	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999630717	.	.	.	.	.	.	T	0.26849	-1.0091	3	.	.	.	.	9.5126	0.39087	0.0:0.1381:0.5818:0.2802	rs2269543;rs5766098;rs17845265;rs17858094;rs17859480;rs59025261;rs2269543	.	.	.	L	343	.	.	S	+	2	0	PRR5-ARHGAP8	43623594	0.000000	0.05858	0.002000	0.10522	0.505000	0.33919	-2.997000	0.00654	-1.448000	0.01941	-0.244000	0.11960	TCG	C|0.642;N|0.001	.	strong		0.647	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
KCNK13	56659	hgsc.bcm.edu	37	14	90528797	90528797	+	Missense_Mutation	SNP	G	G	A	rs7157583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:90528797G>A	ENST00000282146.4	+	1	689	c.248G>A	c.(247-249)cGg>cAg	p.R83Q		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	83					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)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				GAGGCCACTCGGGCCGGCATC	0.682													G|||	508	0.101438	0.3222	0.0389	5008	,	,		12807	0.0		0.007	False		,,,				2504	0.0491				p.R83Q		Atlas-SNP	.											.	KCNK13	76	.	0			c.G248A						PASS	.	G	GLN/ARG	961,3219		99,763,1228	6.0	7.0	7.0		248	-3.8	0.4	14	dbSNP_116	7	51,8133		0,51,4041	no	missense	KCNK13	NM_022054.2	43	99,814,5269	AA,AG,GG		0.6232,22.9904,8.1851	benign	83/409	90528797	1012,11352	2090	4092	6182	SO:0001583	missense	56659	exon1			CCACTCGGGCCGG	AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.248G>A	14.37:g.90528797G>A	ENSP00000282146:p.Arg83Gln	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_022054	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	37	CCDS9889.1	184	0.08424908424908426	165	0.3353658536585366	15	0.04143646408839779	0	0.0	4	0.005277044854881266	G	12.29	1.894020	0.33442	0.229904	0.006232	ENSG00000152315	ENST00000282146	T	0.11821	2.74	4.41	-3.75	0.04372	.	.	.	.	.	T	0.00012	0.0000	N	0.11064	0.09	0.80722	P	0.0	B	0.21381	0.055	B	0.29862	0.108	T	0.49652	-0.8917	8	0.14252	T	0.57	.	1.5031	0.02480	0.2056:0.3789:0.1937:0.2219	rs7157583	83	Q9HB14	KCNKD_HUMAN	Q	83	ENSP00000282146:R83Q	ENSP00000282146:R83Q	R	+	2	0	KCNK13	89598550	0.069000	0.21087	0.375000	0.26029	0.940000	0.58332	0.345000	0.19979	-0.339000	0.08401	0.313000	0.20887	CGG	G|0.915;A|0.085	0.085	strong		0.682	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054	
MBOAT4	619373	hgsc.bcm.edu	37	8	29990075	29990075	+	Missense_Mutation	SNP	C	C	T	rs16876563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:29990075C>T	ENST00000320542.3	-	3	776	c.692G>A	c.(691-693)gGa>gAa	p.G231E	LEPROTL1_ENST00000442880.2_Intron|LEPROTL1_ENST00000523116.1_Intron	NM_001100916.1	NP_001094386.1	Q96T53	MBOA4_HUMAN	membrane bound O-acyltransferase domain containing 4	231			G -> E (in dbSNP:rs16876563).		cellular protein metabolic process (GO:0044267)|peptidyl-serine octanoylation (GO:0018191)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	serine O-acyltransferase activity (GO:0016412)			endometrium(1)	1						ATCAGTCAGTCCCGCTCCTGC	0.557													C|||	227	0.0453275	0.1649	0.0115	5008	,	,		20664	0.0		0.001	False		,,,				2504	0.0				p.G231E		Atlas-SNP	.											MBOAT4_ENST00000320542,NS,carcinoma,+1,1	MBOAT4	31	1	0			c.G692A						PASS	.	C	GLU/GLY,	202,1182		14,174,504	142.0	133.0	135.0		692,	2.0	0.0	8	dbSNP_123	135	1,3181		0,1,1590	yes	missense,intron	LEPROTL1,MBOAT4	NM_001100916.1,NM_001128208.1	98,	14,175,2094	TT,TC,CC		0.0314,14.5954,4.4459	benign,	231/436,	29990075	203,4363	692	1591	2283	SO:0001583	missense	619373	exon3			GTCAGTCCCGCTC	AF359269	CCDS47835.1	8p12	2008-08-04	2006-06-29	2006-06-29	ENSG00000177669	ENSG00000177669			32311	protein-coding gene	gene with protein product	"""ghrelin O-acyltransferase"""	611940	"""O-acyltransferase (membrane bound) domain containing 4"""	OACT4		18443287	Standard	NM_001100916		Approved	FKSG89, GOAT	uc010lvg.3	Q96T53	OTTHUMG00000163824	ENST00000320542.3:c.692G>A	8.37:g.29990075C>T	ENSP00000314196:p.Gly231Glu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_001100916	B1Q003	Missense_Mutation	SNP	ENST00000320542.3	37	CCDS47835.1	78	0.03571428571428571	76	0.15447154471544716	2	0.0055248618784530384	0	0.0	0	0.0	C	3.261	-0.151211	0.06585	0.145954	3.14E-4	ENSG00000177669	ENST00000320542	T	0.73363	-0.74	4.87	1.96	0.26148	.	0.744599	0.12002	N	0.508753	T	0.00695	0.0023	M	0.63428	1.95	0.80722	P	0.0	B	0.26602	0.154	B	0.31101	0.124	T	0.24404	-1.0161	8	.	.	.	.	4.3137	0.10982	0.0:0.6049:0.1904:0.2047	rs16876563;rs52827595;rs16876563	231	Q96T53	MBOA4_HUMAN	E	231	ENSP00000314196:G231E	.	G	-	2	0	MBOAT4	30109617	0.000000	0.05858	0.041000	0.18516	0.046000	0.14306	0.566000	0.23593	1.277000	0.44412	0.563000	0.77884	GGA	C|0.952;T|0.048	0.048	strong		0.557	MBOAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375795.1		
MACC1	346389	hgsc.bcm.edu	37	7	20199835	20199835	+	Missense_Mutation	SNP	G	G	A	rs17142503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20199835G>A	ENST00000400331.5	-	5	457	c.149C>T	c.(148-150)cCg>cTg	p.P50L	MACC1_ENST00000332878.4_Missense_Mutation_p.P50L|MACC1_ENST00000589011.1_Missense_Mutation_p.P50L	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	50			P -> L (in dbSNP:rs17142503).		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						GAAAGCATCCGGCCAATTGTG	0.398													G|||	117	0.0233626	0.0802	0.0043	5008	,	,		16736	0.001		0.001	False		,,,				2504	0.0061				p.P50L		Atlas-SNP	.											MACC1,colon,carcinoma,-1,1	MACC1	99	1	0			c.C149T						PASS	.	G	LEU/PRO	269,4137	140.0+/-175.5	6,257,1940	75.0	76.0	76.0		149	4.9	0.1	7	dbSNP_123	76	6,8594	5.0+/-18.6	0,6,4294	yes	missense	MACC1	NM_182762.3	98	6,263,6234	AA,AG,GG		0.0698,6.1053,2.1144	benign	50/853	20199835	275,12731	2203	4300	6503	SO:0001583	missense	346389	exon5			GCATCCGGCCAAT		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.149C>T	7.37:g.20199835G>A	ENSP00000383185:p.Pro50Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	23	0.010531135531135532	20	0.04065040650406504	2	0.0055248618784530384	1	0.0017482517482517483	0	0.0	G	10.20	1.284308	0.23392	0.061053	6.98E-4	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.09538	2.97;2.97	5.82	4.95	0.65309	.	0.520649	0.21203	N	0.078429	T	0.01029	0.0034	L	0.40543	1.245	0.44469	D	0.997404	P	0.52692	0.955	B	0.42087	0.375	T	0.12192	-1.0557	10	0.54805	T	0.06	-2.2911	10.037	0.42135	0.0689:0.0:0.795:0.1362	rs17142503;rs17142503	50	Q6ZN28	MACC1_HUMAN	L	50	ENSP00000383185:P50L;ENSP00000328410:P50L	ENSP00000328410:P50L	P	-	2	0	MACC1	20166360	0.878000	0.30173	0.135000	0.22099	0.025000	0.11179	3.709000	0.54853	1.484000	0.48361	-0.198000	0.12761	CCG	G|0.982;A|0.018	0.018	strong		0.398	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762	
TRPM3	80036	hgsc.bcm.edu	37	9	73477930	73477930	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:73477930T>C	ENST00000377111.2	-	3	599	c.356A>G	c.(355-357)gAc>gGc	p.D119G	TRPM3_ENST00000377106.1_5'UTR|TRPM3_ENST00000358082.3_5'Flank|TRPM3_ENST00000357533.2_Missense_Mutation_p.D121G|TRPM3_ENST00000437699.3_5'UTR|TRPM3_ENST00000396285.1_5'Flank|TRPM3_ENST00000360823.2_5'UTR|TRPM3_ENST00000408909.2_5'Flank|TRPM3_ENST00000396280.5_5'Flank|TRPM3_ENST00000361823.5_5'UTR|TRPM3_ENST00000377110.3_Missense_Mutation_p.D119G|TRPM3_ENST00000377105.1_5'UTR|TRPM3_ENST00000396283.1_5'UTR|TRPM3_ENST00000396292.4_5'Flank|TRPM3_ENST00000423814.3_Missense_Mutation_p.D121G|TRPM3_ENST00000377097.3_5'UTR|TRPM3_ENST00000377101.1_5'UTR	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	119					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						AGACTGGATGTCATTTCGGGA	0.507																																					p.D119G		Atlas-SNP	.											TRPM3_ENST00000423814,right_upper_lobe,carcinoma,0,2	TRPM3	700	2	0			c.A356G						scavenged	.						171.0	177.0	175.0					9																	73477930		2203	4300	6503	SO:0001583	missense	80036	exon3			TGGATGTCATTTC	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.356A>G	9.37:g.73477930T>C	ENSP00000366315:p.Asp119Gly	Somatic	285	1	0.00350877		WXS	Illumina HiSeq	Phase_I	272	4	0.0147059	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.84|15.84	2.952557|2.952557	0.53293|0.53293	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000377111;ENST00000377110;ENST00000357533;ENST00000423814|ENST00000377097	T;T;T;T|.	0.71579|.	-0.58;-0.58;-0.58;-0.58|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.55226|0.55226	0.1907|0.1907	N|N	0.26042|0.26042	0.785|0.785	0.80722|0.80722	D|D	1|1	B;P;B;B|.	0.43024|.	0.049;0.798;0.024;0.0|.	B;P;B;B|.	0.46299|.	0.027;0.511;0.023;0.003|.	T|T	0.51560|0.51560	-0.8690|-0.8690	10|5	0.14656|.	T|.	0.56|.	-5.597|-5.597	16.4159|16.4159	0.83738|0.83738	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	119;121;119;119|.	Q9HCF6;Q4VXD2;Q9HCF6-2;Q9HCF6-10|.	TRPM3_HUMAN;.;.;.|.	G|A	119;119;121;121|9	ENSP00000366315:D119G;ENSP00000366314:D119G;ENSP00000350140:D121G;ENSP00000389542:D121G|.	ENSP00000350140:D121G|.	D|T	-|-	2|1	0|0	TRPM3|TRPM3	72667750|72667750	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.915000|5.915000	0.69973|0.69973	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.	none		0.507	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945	
FLG	2312	hgsc.bcm.edu	37	1	152281228	152281228	+	Missense_Mutation	SNP	C	C	G	rs7546186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281228C>G	ENST00000368799.1	-	3	6169	c.6134G>C	c.(6133-6135)aGt>aCt	p.S2045T	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	288	0	0		WXS	Illumina HiSeq	Phase_I	537	270	0.502793	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	
COBL	23242	hgsc.bcm.edu	37	7	51096992	51096992	+	Missense_Mutation	SNP	G	G	A	rs61737866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:51096992G>A	ENST00000265136.7	-	10	1966	c.1801C>T	c.(1801-1803)Cac>Tac	p.H601Y	COBL_ENST00000395542.2_Missense_Mutation_p.H683Y	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	601				H -> Y (in Ref. 5; AAH45771). {ECO:0000305}.	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)					GAAGCGGGGTGCAGGGCAGGT	0.562													G|||	130	0.0259585	0.0976	0.0	5008	,	,		20023	0.0		0.001	False		,,,				2504	0.0				p.H601Y	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C1801T						PASS	.	G	TYR/HIS	393,4013	196.4+/-220.7	22,349,1832	79.0	70.0	73.0		1801	-7.0	0.0	7	dbSNP_129	73	4,8596	3.0+/-9.4	0,4,4296	yes	missense	COBL	NM_015198.3	83	22,353,6128	AA,AG,GG		0.0465,8.9197,3.0524	benign	601/1262	51096992	397,12609	2203	4300	6503	SO:0001583	missense	23242	exon10			CGGGGTGCAGGGC	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.1801C>T	7.37:g.51096992G>A	ENSP00000265136:p.His601Tyr	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	249	112	0.449799	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	40|40	0.018315018315018316|0.018315018315018316	39|39	0.07926829268292683|0.07926829268292683	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	0.509|0.509	-0.867489|-0.867489	0.02590|0.02590	0.089197|0.089197	4.65E-4|4.65E-4	ENSG00000106078|ENSG00000106078	ENST00000452534|ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542;ENST00000457306	.|T;T;T;T	.|0.21734	.|1.99;1.99;1.99;1.99	5.59|5.59	-6.98|-6.98	0.01611|0.01611	.|.	.|2.903440	.|0.00947	.|N	.|0.002915	T|T	0.00271|0.00271	0.0008|0.0008	N|N	0.02539|0.02539	-0.55|-0.55	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B	.|0.04013	.|0.0;0.0;0.0;0.0;0.001	T|T	0.36866|0.36866	-0.9730|-0.9730	5|10	.|0.02654	.|T	.|1	.|.	11.0652|11.0652	0.47972|0.47972	0.6443:0.0913:0.2644:0.0|0.6443:0.0913:0.2644:0.0	.|.	.|601;658;601;683;143	.|O75128-3;O75128-7;O75128;O75128-2;O75128-6	.|.;.;COBL_HUMAN;.;.	V|Y	576|601;493;486;683;99	.|ENSP00000265136:H601Y;ENSP00000401204:H493Y;ENSP00000413498:H486Y;ENSP00000378912:H683Y	.|ENSP00000265136:H601Y	A|H	-|-	2|1	0|0	COBL|COBL	51064486|51064486	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.066000|0.066000	0.14489|0.14489	-1.290000|-1.290000	0.02372|0.02372	-0.145000|-0.145000	0.13849|0.13849	GCA|CAC	G|0.974;A|0.026	0.026	strong		0.562	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
MUC16	94025	hgsc.bcm.edu	37	19	9075737	9075737	+	Silent	SNP	T	T	C	rs2547071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	159	0	0		WXS	Illumina HiSeq	Phase_I	202	105	0.519802	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	
TTLL10	254173	hgsc.bcm.edu	37	1	1118275	1118275	+	Silent	SNP	C	C	T	rs61733845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1118275C>T	ENST00000379290.1	+	11	1109	c.936C>T	c.(934-936)tgC>tgT	p.C312C	TTLL10_ENST00000379289.1_Silent_p.C312C|TTLL10_ENST00000379288.3_Silent_p.C239C			Q6ZVT0	TTL10_HUMAN	tubulin tyrosine ligase-like family, member 10	312	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)					haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(2)|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;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;4.75e-36)|OV - Ovarian serous cystadenocarcinoma(86;5.82e-22)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|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;0.199)		TATGGATCTGCAAGCCCACAG	0.672													c|||	930	0.185703	0.4123	0.121	5008	,	,		13615	0.0407		0.0447	False		,,,				2504	0.2198				p.C312C		Atlas-SNP	.											.	TTLL10	66	.	0			c.C936T						PASS	.		,	1688,2698		321,1046,826	29.0	22.0	24.0		936,717	2.6	1.0	1	dbSNP_129	24	418,8166		10,398,3884	no	coding-synonymous,coding-synonymous	TTLL10	NM_001130045.1,NM_153254.2	,	331,1444,4710	TT,TC,CC		4.8695,38.4861,16.2375	,	312/674,239/405	1118275	2106,10864	2193	4292	6485	SO:0001819	synonymous_variant	254173	exon11			GATCTGCAAGCCC	AK093438	CCDS8.1, CCDS44036.1	1p36.33	2014-01-28	2005-07-29	2005-07-29	ENSG00000162571	ENSG00000162571		"""Tubulin tyrosine ligase-like family"""	26693	protein-coding gene	gene with protein product			"""tubulin tyrosine ligase-like family, member 5"""	TTLL5		15890843	Standard	NM_153254		Approved	FLJ36119	uc001acy.2	Q6ZVT0	OTTHUMG00000000851	ENST00000379290.1:c.936C>T	1.37:g.1118275C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	153	78	0.509804	NM_001130045	B1AMF6|Q5T2W4|Q5T2W5|Q8N9X2	Silent	SNP	ENST00000379290.1	37	CCDS44036.1																																																																																			C|0.845;T|0.155	0.155	strong		0.672	TTLL10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002421.3	NM_153254	
C1orf177	163747	hgsc.bcm.edu	37	1	55272743	55272743	+	Missense_Mutation	SNP	A	A	G	rs115158797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55272743A>G	ENST00000371273.3	+	2	194	c.179A>G	c.(178-180)tAt>tGt	p.Y60C	C1orf177_ENST00000358193.3_Missense_Mutation_p.Y60C	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	60										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						TCCACGCGTTATTCTACCCAA	0.572													A|||	49	0.00978435	0.0363	0.0014	5008	,	,		16140	0.0		0.0	False		,,,				2504	0.0				p.Y60C		Atlas-SNP	.											.	C1orf177	36	.	0			c.A179G						PASS	.	A	CYS/TYR,CYS/TYR	127,4279	93.9+/-132.6	2,123,2078	205.0	186.0	192.0		179,179	1.3	0.0	1	dbSNP_132	192	0,8600		0,0,4300	yes	missense,missense	C1orf177	NM_001110533.1,NM_152607.2	194,194	2,123,6378	GG,GA,AA		0.0,2.8824,0.9765	possibly-damaging,possibly-damaging	60/419,60/415	55272743	127,12879	2203	4300	6503	SO:0001583	missense	163747	exon2			CGCGTTATTCTAC	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.179A>G	1.37:g.55272743A>G	ENSP00000360320:p.Tyr60Cys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	159	78	0.490566	NM_001110533	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	CCDS44153.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	A	10.43	1.348922	0.24426	0.028824	0.0	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.26518	1.73;1.73	3.72	1.32	0.21799	.	1.288330	0.05479	N	0.554456	T	0.06462	0.0166	N	0.25647	0.755	0.09310	N	1	D;D	0.57257	0.979;0.979	P;P	0.53313	0.723;0.723	T	0.08249	-1.0731	10	0.39692	T	0.17	.	3.1969	0.06636	0.498:0.0:0.108:0.394	.	60;60	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	C	60	ENSP00000350924:Y60C;ENSP00000360320:Y60C	ENSP00000350924:Y60C	Y	+	2	0	C1orf177	55045331	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	1.170000	0.31883	0.264000	0.21851	0.379000	0.24179	TAT	A|0.989;G|0.011	0.011	strong		0.572	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
TBC1D17	79735	hgsc.bcm.edu	37	19	50386253	50386253	+	Silent	SNP	C	C	T	rs61741174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50386253C>T	ENST00000221543.5	+	9	1250	c.951C>T	c.(949-951)cgC>cgT	p.R317R	TBC1D17_ENST00000535102.2_Silent_p.R284R	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	317	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		GCCTGCGGCGCGAGGCCTGGA	0.637													C|||	49	0.00978435	0.0348	0.0043	5008	,	,		19944	0.0		0.0	False		,,,				2504	0.0				p.R317R		Atlas-SNP	.											.	TBC1D17	39	.	0			c.C951T						PASS	.	C	,	146,4258		5,136,2061	31.0	32.0	32.0		852,951	-10.1	0.0	19	dbSNP_129	32	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous	TBC1D17	NM_001168222.1,NM_024682.2	,	5,136,6357	TT,TC,CC		0.0,3.3152,1.1234	,	284/616,317/649	50386253	146,12850	2202	4296	6498	SO:0001819	synonymous_variant	79735	exon9			GCGGCGCGAGGCC	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.951C>T	19.37:g.50386253C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	113	62	0.548673	NM_024682	B4DT12|B9A6L8|F5H1W7	Silent	SNP	ENST00000221543.5	37	CCDS12785.1																																																																																			C|0.989;T|0.011	0.011	strong		0.637	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
FLG	2312	hgsc.bcm.edu	37	1	152280782	152280782	+	Missense_Mutation	SNP	A	A	G	rs2184953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152280782A>G	ENST00000368799.1	-	3	6615	c.6580T>C	c.(6580-6582)Tat>Cat	p.Y2194H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	423	0	0		WXS	Illumina HiSeq	Phase_I	767	767	1	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	
DNAH8	1769	hgsc.bcm.edu	37	6	38781866	38781866	+	Silent	SNP	C	C	G	rs1678690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:38781866C>G	ENST00000359357.3	+	23	2897	c.2643C>G	c.(2641-2643)tcC>tcG	p.S881S	DNAH8_ENST00000441566.1_Silent_p.S881S|DNAH8_ENST00000449981.2_Silent_p.S1098S			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	881					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.S881S(1)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ATATTATTTCCTTTATAAAAA	0.313													C|||	2510	0.501198	0.3124	0.5908	5008	,	,		18086	0.7946		0.3748	False		,,,				2504	0.5204				p.S1098S		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	1	Substitution - coding silent(1)	prostate(1)	c.C3294G						PASS	.	C		1493,2913	473.1+/-356.6	252,989,962	115.0	127.0	123.0		3294	2.1	1.0	6	dbSNP_89	123	3726,4874	529.8+/-381.7	823,2080,1397	no	coding-synonymous	DNAH8	NM_001206927.1		1075,3069,2359	GG,GC,CC		43.3256,33.8856,40.1276		1098/4708	38781866	5219,7787	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon25			TATTTCCTTTATA	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.2643C>G	6.37:g.38781866C>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	165	88	0.533333	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				C|0.558;G|0.442	0.442	strong		0.313	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
SRRT	51593	hgsc.bcm.edu	37	7	100482026	100482026	+	Silent	SNP	T	T	C	rs15624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100482026T>C	ENST00000347433.4	+	7	953	c.795T>C	c.(793-795)ctT>ctC	p.L265L	SRRT_ENST00000432932.1_Silent_p.L265L|SRRT_ENST00000457580.2_Silent_p.L265L|SRRT_ENST00000388793.4_Silent_p.L265L			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	265	Glu-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						AGAATGATCTTCGCATCCTGG	0.602													C|||	2889	0.576877	0.4107	0.6513	5008	,	,		13874	0.8095		0.5159	False		,,,				2504	0.5716				p.L265L		Atlas-SNP	.											.	SRRT	108	.	0			c.T795C						PASS	.	C	,,,	1949,2457	613.6+/-392.2	409,1131,663	39.0	36.0	37.0		795,795,795,795	-8.1	0.5	7	dbSNP_52	37	4503,4097	552.3+/-386.1	1218,2067,1015	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SRRT	NM_001128852.1,NM_001128853.1,NM_001128854.1,NM_015908.5	,,,	1627,3198,1678	CC,CT,TT		47.6395,44.2351,49.6079	,,,	265/876,265/873,265/872,265/877	100482026	6452,6554	2203	4300	6503	SO:0001819	synonymous_variant	51593	exon7			TGATCTTCGCATC		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"""arsenite resistance protein"""	614469	"""serrate RNA effector molecule homolog (Arabidopsis)"""			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.795T>C	7.37:g.100482026T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_001128853	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Silent	SNP	ENST00000347433.4	37	CCDS34709.1																																																																																			T|0.462;C|0.538	0.538	strong		0.602	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908	
ROBO4	54538	hgsc.bcm.edu	37	11	124767067	124767067	+	Missense_Mutation	SNP	T	T	C	rs59648931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124767067T>C	ENST00000306534.3	-	2	646	c.161A>G	c.(160-162)cAa>cGa	p.Q54R	ROBO4_ENST00000533054.1_Intron|ROBO4_ENST00000526899.1_5'UTR	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	54	Ig-like C2-type 1.		Q -> R (in dbSNP:rs59648931).		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GCCTGAGGCTTGGCAGCTCAT	0.677													C|||	1926	0.384585	0.646	0.2176	5008	,	,		16532	0.378		0.2555	False		,,,				2504	0.2894				p.Q54R		Atlas-SNP	.											.	ROBO4	130	.	0			c.A161G						PASS	.	C	ARG/GLN	2473,1929		709,1055,437	26.0	24.0	24.0		161	0.1	0.4	11	dbSNP_129	24	1992,6604		262,1468,2568	yes	missense	ROBO4	NM_019055.5	43	971,2523,3005	CC,CT,TT		23.1736,43.821,34.3514	benign	54/1008	124767067	4465,8533	2201	4298	6499	SO:0001583	missense	54538	exon2			GAGGCTTGGCAGC	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.161A>G	11.37:g.124767067T>C	ENSP00000304945:p.Gln54Arg	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	143	59	0.412587	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	
WNK4	65266	hgsc.bcm.edu	37	17	40939460	40939460	+	Silent	SNP	C	C	T	rs9916754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40939460C>T	ENST00000246914.5	+	7	1662	c.1641C>T	c.(1639-1641)gcC>gcT	p.A547A	WNK4_ENST00000587705.1_3'UTR	NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	547					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		TGCCCATGGCCCCCGGTCCCC	0.617													T|||	515	0.102835	0.2557	0.0231	5008	,	,		16975	0.0387		0.004	False		,,,				2504	0.1207				p.A547A	Esophageal Squamous(6;201 374 4964 23855 42828)	Atlas-SNP	.											.	WNK4	182	.	0			c.C1641T						PASS	.	T		1002,3404	730.1+/-410.1	116,770,1317	108.0	106.0	106.0		1641	2.5	0.1	17	dbSNP_119	106	11,8589	818.8+/-406.8	0,11,4289	no	coding-synonymous	WNK4	NM_032387.4		116,781,5606	TT,TC,CC		0.1279,22.7417,7.7887		547/1244	40939460	1013,11993	2203	4300	6503	SO:0001819	synonymous_variant	65266	exon7			CATGGCCCCCGGT	AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.1641C>T	17.37:g.40939460C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Silent	SNP	ENST00000246914.5	37	CCDS11439.1																																																																																			C|0.919;T|0.081	0.081	strong		0.617	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
ITPR1	3708	hgsc.bcm.edu	37	3	4716811	4716811	+	Silent	SNP	A	A	C	rs2306877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:4716811A>C	ENST00000443694.2	+	20	2613	c.2613A>C	c.(2611-2613)ctA>ctC	p.L871L	ITPR1_ENST00000456211.2_Silent_p.L871L|ITPR1_ENST00000423119.2_Silent_p.L886L|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Silent_p.L886L|ITPR1_ENST00000302640.8_Silent_p.L871L|ITPR1_ENST00000357086.4_Silent_p.L886L			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	886					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)	CTGACCTTCTACGATTAACTA	0.348													A|||	1667	0.332867	0.3911	0.3184	5008	,	,		21702	0.2897		0.1958	False		,,,				2504	0.4499				p.L886L		Atlas-SNP	.											.	ITPR1	659	.	0			c.A2658C						PASS	.	A	,,	1350,2396		263,824,786	131.0	119.0	123.0		2658,2613,2613	-10.1	0.1	3	dbSNP_100	123	1438,6746		124,1190,2778	no	coding-synonymous,coding-synonymous,coding-synonymous	ITPR1	NM_001099952.2,NM_001168272.1,NM_002222.5	,,	387,2014,3564	CC,CA,AA		17.5709,36.0384,23.3697	,,	886/2711,871/2744,871/2696	4716811	2788,9142	1873	4092	5965	SO:0001819	synonymous_variant	3708	exon23			CCTTCTACGATTA	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.2613A>C	3.37:g.4716811A>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	160	66	0.4125	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Silent	SNP	ENST00000443694.2	37	CCDS54551.1																																																																																			A|0.703;C|0.297	0.297	strong		0.348	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
TUBB2A	7280	hgsc.bcm.edu	37	6	3154882	3154882	+	Missense_Mutation	SNP	C	C	T	rs76334433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:3154882C>T	ENST00000333628.3	-	4	615	c.553G>A	c.(553-555)Gcc>Acc	p.A185T	RP1-40E16.11_ENST00000447644.1_RNA|TUBB2A_ENST00000489942.1_5'UTR	NM_001069.2	NP_001060.1	Q13885	TBB2A_HUMAN	tubulin, beta 2A class IIa	185					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|large_intestine(4)|lung(2)|skin(1)	9	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				GAGAGGGTGGCGTTGTAGGGC	0.552																																					p.A185T		Atlas-SNP	.											TUBB2A,NS,carcinoma,0,1	TUBB2A	23	1	0			c.G553A						scavenged	.						169.0	84.0	112.0					6																	3154882		2203	4299	6502	SO:0001583	missense	7280	exon4			GGGTGGCGTTGTA	AY159127	CCDS4484.1	6p25.2	2012-10-02	2011-10-10	2005-11-03	ENSG00000137267	ENSG00000137267		"""Tubulins"""	12412	protein-coding gene	gene with protein product	"""class IIa beta-tubulin"""	615101	"""tubulin, beta polypeptide"", ""tubulin, beta 2"", ""tubulin, beta 2A"""	TUBB, TUBB2		14574404	Standard	NM_001069		Approved	dJ40E16.7	uc003mvc.3	Q13885	OTTHUMG00000014135	ENST00000333628.3:c.553G>A	6.37:g.3154882C>T	ENSP00000369703:p.Ala185Thr	Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	499	69	0.138277	NM_001069	Q6FGZ8|Q8IWR2	Missense_Mutation	SNP	ENST00000333628.3	37	CCDS4484.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.543071	0.45280	.	.	ENSG00000137267	ENST00000333628;ENST00000392362	T	0.74526	-0.85	5.01	5.01	0.66863	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.53938	U	0.000054	T	0.62780	0.2456	L	0.52206	1.635	0.80722	D	1	P;B;B	0.36086	0.536;0.153;0.026	B;B;B	0.34242	0.178;0.118;0.118	T	0.71377	-0.4611	10	0.87932	D	0	.	18.6816	0.91548	0.0:1.0:0.0:0.0	.	185;185;185	B2R6L0;Q13885;Q8N6N5	.;TBB2A_HUMAN;.	T	185;95	ENSP00000369703:A185T	ENSP00000369703:A185T	A	-	1	0	TUBB2A	3099881	1.000000	0.71417	0.998000	0.56505	0.822000	0.46500	7.629000	0.83207	2.491000	0.84063	0.650000	0.86243	GCC	C|0.998;T|0.002	0.002	strong		0.552	TUBB2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039662.1	NM_001069	
CDK6	1021	hgsc.bcm.edu	37	7	92462572	92462572	+	Silent	SNP	G	G	A	rs189208543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:92462572G>A	ENST00000265734.4	-	2	477	c.66C>T	c.(64-66)ggC>ggT	p.G22G	CDK6_ENST00000491250.1_5'Flank|CDK6_ENST00000424848.2_Silent_p.G22G	NM_001259.6	NP_001250.1	Q00534	CDK6_HUMAN	cyclin-dependent kinase 6	22	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				astrocyte development (GO:0014002)|cell cycle arrest (GO:0007050)|cell dedifferentiation (GO:0043697)|cell division (GO:0051301)|dentate gyrus development (GO:0021542)|G1/S transition of mitotic cell cycle (GO:0000082)|generation of neurons (GO:0048699)|gliogenesis (GO:0042063)|hematopoietic stem cell differentiation (GO:0060218)|lateral ventricle development (GO:0021670)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular senescence (GO:2000773)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of osteoblast differentiation (GO:0045668)|Notch signaling pathway (GO:0007219)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of erythrocyte differentiation (GO:0045646)|regulation of gene expression (GO:0010468)|response to virus (GO:0009615)|T cell differentiation in thymus (GO:0033077)|type B pancreatic cell development (GO:0003323)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	11	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TCCCATAGGCGCCCTCCCCGA	0.706			T	MLLT10	ALL								G|||	7	0.00139776	0.0053	0.0	5008	,	,		13163	0.0		0.0	False		,,,				2504	0.0				p.G22G		Atlas-SNP	.		Dom	yes		7	7q21-q22	1021	cyclin-dependent kinase 6		L	.	CDK6	30	.	0			c.C66T						PASS	.	G	,	1,4401		0,1,2200	26.0	19.0	21.0		66,66	2.5	1.0	7		21	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	CDK6	NM_001145306.1,NM_001259.6	,	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	,	22/327,22/327	92462572	1,12995	2201	4297	6498	SO:0001819	synonymous_variant	1021	exon2			ATAGGCGCCCTCC		CCDS5628.1	7q21-q22	2011-11-08			ENSG00000105810	ENSG00000105810		"""Cyclin-dependent kinases"""	1777	protein-coding gene	gene with protein product		603368				1639063	Standard	NM_001259		Approved	PLSTIRE	uc010lez.3	Q00534	OTTHUMG00000131697	ENST00000265734.4:c.66C>T	7.37:g.92462572G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_001259	A4D1G0	Silent	SNP	ENST00000265734.4	37	CCDS5628.1																																																																																			G|0.998;A|0.002	0.002	strong		0.706	CDK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254605.2		
SLC2A2	6514	hgsc.bcm.edu	37	3	170715830	170715830	+	Silent	SNP	G	G	A	rs5398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:170715830G>A	ENST00000314251.3	-	11	1516	c.1437C>T	c.(1435-1437)ttC>ttT	p.F479F	SLC2A2_ENST00000382808.4_Silent_p.F360F	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	479					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TAAAAAATGTGAACAGGGTAA	0.438													A|||	1866	0.372604	0.6354	0.3084	5008	,	,		17963	0.2411		0.2903	False		,,,				2504	0.2832				p.F479F		Atlas-SNP	.											.	SLC2A2	71	.	0			c.C1437T						PASS	.	A		2589,1817	496.7+/-363.6	767,1055,381	43.0	47.0	46.0		1437	-3.7	0.1	3	dbSNP_52	46	2567,6033	674.3+/-403.1	354,1859,2087	no	coding-synonymous	SLC2A2	NM_000340.1		1121,2914,2468	AA,AG,GG		29.8488,41.2392,39.6432		479/525	170715830	5156,7850	2203	4300	6503	SO:0001819	synonymous_variant	6514	exon11			AAATGTGAACAGG	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.1437C>T	3.37:g.170715830G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	139	70	0.503597	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	37	CCDS3215.1																																																																																			G|0.622;A|0.378	0.378	strong		0.438	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
OR8H2	390151	hgsc.bcm.edu	37	11	55873401	55873401	+	Missense_Mutation	SNP	A	A	G	rs115405120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55873401A>G	ENST00000313503.1	+	1	883	c.883A>G	c.(883-885)Aaa>Gaa	p.K295E		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					TCTTAGAAACAAAGAGGTGAA	0.368										HNSCC(53;0.14)			a|||	35	0.00698882	0.0219	0.0086	5008	,	,		17201	0.0		0.0	False		,,,				2504	0.0				p.K295E		Atlas-SNP	.											.	OR8H2	117	.	0			c.A883G						PASS	.	A	GLU/LYS	102,4298	78.8+/-117.2	1,100,2099	81.0	89.0	87.0		883	3.3	1.0	11	dbSNP_132	87	2,8586	3.0+/-9.4	0,2,4292	yes	missense	OR8H2	NM_001005200.1	56	1,102,6391	GG,GA,AA		0.0233,2.3182,0.8007	possibly-damaging	295/313	55873401	104,12884	2200	4294	6494	SO:0001583	missense	390151	exon1			AGAAACAAAGAGG	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.883A>G	11.37:g.55873401A>G	ENSP00000323982:p.Lys295Glu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	19	0.0086996336996337	16	0.032520325203252036	3	0.008287292817679558	0	0.0	0	0.0	a	8.777	0.927390	0.18056	0.023182	2.33E-4	ENSG00000181767	ENST00000313503	T	0.44083	0.93	3.35	3.35	0.38373	.	0.000000	0.56097	D	0.000025	T	0.18341	0.0440	M	0.76170	2.325	0.25971	N	0.982491	B	0.28378	0.209	B	0.27380	0.079	T	0.35301	-0.9794	10	0.87932	D	0	.	8.3251	0.32151	0.9009:0.0:0.0991:0.0	.	295	Q8N162	OR8H2_HUMAN	E	295	ENSP00000323982:K295E	ENSP00000323982:K295E	K	+	1	0	OR8H2	55629977	0.009000	0.17119	0.992000	0.48379	0.067000	0.16453	2.182000	0.42556	1.497000	0.48584	0.362000	0.22060	AAA	A|0.991;G|0.009	0.009	strong		0.368	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
TMEM253	643382	hgsc.bcm.edu	37	14	21570614	21570614	+	Silent	SNP	A	A	C	rs4982408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21570614A>C	ENST00000556585.2	+	5	445	c.327A>C	c.(325-327)atA>atC	p.I109I	TMEM253_ENST00000418511.2_Silent_p.I109I|ZNF219_ENST00000451119.2_Intron			P0C7T8	TM253_HUMAN	transmembrane protein 253	109						integral component of membrane (GO:0016021)											TGGGTTTCATAGTGGTGGTGG	0.567													C|||	4009	0.800519	0.938	0.9135	5008	,	,		19579	0.6012		0.834	False		,,,				2504	0.7055				p.I109I		Atlas-SNP	.											.	.	.	.	0			c.A327C						PASS	.	C	,	1282,102		594,94,4	111.0	108.0	109.0		,327	-10.8	0.0	14	dbSNP_111	109	2660,522		1115,430,46	no	intron,coding-synonymous	ZNF219,C14orf176	NM_001102454.1,NM_001146683.1	,	1709,524,50	CC,CA,AA		16.4048,7.3699,13.6662	,	,109/218	21570614	3942,624	692	1591	2283	SO:0001819	synonymous_variant	643382	exon6			TTTCATAGTGGTG		CCDS53884.1	14q11.2	2012-10-24	2012-10-24	2012-10-24	ENSG00000232070	ENSG00000232070			32545	protein-coding gene	gene with protein product			"""non-protein coding RNA 220"", ""chromosome 14 open reading frame 95"", ""chromosome 14 open reading frame 176"""	NCRNA00220, C14orf95, C14orf176			Standard	NM_001146683		Approved		uc010tlo.2	P0C7T8	OTTHUMG00000171361	ENST00000556585.2:c.327A>C	14.37:g.21570614A>C		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	271	271	1	NM_001146683		Silent	SNP	ENST00000556585.2	37	CCDS53884.1																																																																																			A|0.198;C|0.802	0.802	strong		0.567	TMEM253-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413146.2	XM_926711	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412561	105412561	+	Missense_Mutation	SNP	C	C	T	rs3000771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105412561C>T	ENST00000333244.5	-	7	9346	c.9227G>A	c.(9226-9228)cGc>cAc	p.R3076H	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3076						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)			GGGTCCCTTGCGATCTACTTT	0.622																																					p.R3076H		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G9227A						PASS	.						73.0	82.0	79.0					14																	105412561		1827	4068	5895	SO:0001583	missense	113146	exon7			CCCTTGCGATCTA	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.9227G>A	14.37:g.105412561C>T	ENSP00000353114:p.Arg3076His	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	123	120	0.97561	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	798	0.36538461538461536	220	0.44715447154471544	153	0.42265193370165743	161	0.28146853146853146	264	0.3482849604221636	N	0.180	-1.063333	0.01950	.	.	ENSG00000185567	ENST00000333244	T	0.00724	5.78	3.02	1.83	0.25207	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P	0.42908	0.793	B	0.21151	0.033	T	0.01262	-1.1402	8	0.23302	T	0.38	.	4.7936	0.13261	0.5273:0.3595:0.1132:0.0	.	3076	Q8IVF2	AHNK2_HUMAN	H	3076	ENSP00000353114:R3076H	ENSP00000353114:R3076H	R	-	2	0	AHNAK2	104483606	.	.	0.002000	0.10522	0.000000	0.00434	.	.	-0.058000	0.13177	-2.897000	0.00093	CGC	C|0.635;T|0.365	0.365	strong		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
NUP88	4927	hgsc.bcm.edu	37	17	5294976	5294976	+	Silent	SNP	T	T	A	rs14231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5294976T>A	ENST00000573584.1	-	10	1898	c.1389A>T	c.(1387-1389)ccA>ccT	p.P463P		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	463					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA 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)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						GAATTGGAGCTGGCTGCCTGG	0.478													T|||	2766	0.552316	0.3971	0.4236	5008	,	,		23299	0.8254		0.4404	False		,,,				2504	0.6871				p.P463P		Atlas-SNP	.											.	NUP88	47	.	0			c.A1389T						PASS	.	T		1846,2560	537.0+/-374.6	407,1032,764	106.0	93.0	97.0		1389	-3.3	0.9	17	dbSNP_52	97	3390,5210	501.8+/-375.5	665,2060,1575	no	coding-synonymous	NUP88	NM_002532.4		1072,3092,2339	AA,AT,TT		39.4186,41.8974,40.2583		463/742	5294976	5236,7770	2203	4300	6503	SO:0001819	synonymous_variant	4927	exon10			TGGAGCTGGCTGC	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1389A>T	17.37:g.5294976T>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			T|0.571;A|0.429	0.429	strong		0.478	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
C8orf48	157773	hgsc.bcm.edu	37	8	13424767	13424767	+	Missense_Mutation	SNP	C	C	G	rs10096353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:13424767C>G	ENST00000297324.4	+	1	416	c.267C>G	c.(265-267)aaC>aaG	p.N89K	RP11-145O15.3_ENST00000529018.1_RNA	NM_001007090.2	NP_001007091	Q96LL4	CH048_HUMAN	chromosome 8 open reading frame 48	89										NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	5						AATGGATCAACTACCTCAAGC	0.408													C|||	67	0.0133786	0.0477	0.0043	5008	,	,		18906	0.0		0.001	False		,,,				2504	0.0				p.N89K		Atlas-SNP	.											.	C8orf48	18	.	0			c.C267G						PASS	.	C	LYS/ASN	49,1335		1,47,644	74.0	73.0	73.0		267	1.3	0.0	8	dbSNP_119	73	1,3181		0,1,1590	yes	missense	C8orf48	NM_001007090.2	94	1,48,2234	GG,GC,CC		0.0314,3.5405,1.0951	benign	89/320	13424767	50,4516	692	1591	2283	SO:0001583	missense	157773	exon1			GATCAACTACCTC	AK058131	CCDS47809.1	8p22	2012-04-13			ENSG00000164743	ENSG00000164743			26345	protein-coding gene	gene with protein product						12477932	Standard	NM_001007090		Approved	FLJ25402	uc003wwp.3	Q96LL4	OTTHUMG00000165482	ENST00000297324.4:c.267C>G	8.37:g.13424767C>G	ENSP00000297324:p.Asn89Lys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_001007090	Q96LJ9	Missense_Mutation	SNP	ENST00000297324.4	37	CCDS47809.1	22	0.010073260073260074	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	10.36	1.328375	0.24080	0.035405	3.14E-4	ENSG00000164743	ENST00000297324	T	0.37915	1.17	5.22	1.27	0.21489	.	0.960161	0.08527	N	0.932664	T	0.08537	0.0212	L	0.55481	1.735	0.09310	N	1	B	0.34241	0.444	B	0.35278	0.199	T	0.19418	-1.0306	10	0.44086	T	0.13	-4.0542	3.735	0.08507	0.1702:0.5609:0.0:0.2689	rs10096353;rs52814908;rs10096353	89	Q96LL4	CH048_HUMAN	K	89	ENSP00000297324:N89K	ENSP00000297324:N89K	N	+	3	2	C8orf48	13469138	0.000000	0.05858	0.001000	0.08648	0.533000	0.34776	-1.035000	0.03564	0.478000	0.27488	-0.140000	0.14226	AAC	C|0.990;G|0.010	0.010	strong		0.408	C8orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384400.1	NM_001007090	
ROBO4	54538	hgsc.bcm.edu	37	11	124756406	124756406	+	Silent	SNP	G	G	A	rs7104934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124756406G>A	ENST00000306534.3	-	16	3233	c.2748C>T	c.(2746-2748)agC>agT	p.S916S	ROBO4_ENST00000533054.1_Silent_p.S771S|RP11-664I21.5_ENST00000524453.1_RNA	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	916					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		CGAAACCAAAGCTATCCACAG	0.582													G|||	1173	0.234225	0.4811	0.121	5008	,	,		17633	0.0883		0.163	False		,,,				2504	0.2045				p.S916S		Atlas-SNP	.											.	ROBO4	130	.	0			c.C2748T						PASS	.	G		1775,2627	507.9+/-366.8	350,1075,776	46.0	51.0	49.0		2748	3.8	1.0	11	dbSNP_116	49	1179,7419	230.4+/-264.8	78,1023,3198	no	coding-synonymous	ROBO4	NM_019055.5		428,2098,3974	AA,AG,GG		13.7125,40.3226,22.7231		916/1008	124756406	2954,10046	2201	4299	6500	SO:0001819	synonymous_variant	54538	exon16			ACCAAAGCTATCC	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.2748C>T	11.37:g.124756406G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	121	71	0.586777	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			G|0.783;A|0.217	0.217	strong		0.582	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487172	32487172	+	Silent	SNP	C	C	T	rs72508430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32487172C>T	ENST00000374975.3	-	3	689	c.627G>A	c.(625-627)gtG>gtA	p.V209V		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						GAGGGCTCGTCACGCTTGGGT	0.488													C|||	1669	0.333267	0.4554	0.281	5008	,	,		12303	0.2966		0.2982	False		,,,				2504	0.2791				p.V209V		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,-2,1	HLA-DRB5	31	1	0			c.G627A						scavenged	.						73.0	83.0	80.0					6																	32487172		1892	3753	5645	SO:0001819	synonymous_variant	3127	exon3			GCTCGTCACGCTT		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.627G>A	6.37:g.32487172C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	75	64	0.853333	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			C|0.764;T|0.235	0.235	strong		0.488	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037560	33037560	+	Silent	SNP	G	G	A	rs1042176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33037560G>A	ENST00000419277.1	-	3	333	c.204C>T	c.(202-204)gaC>gaT	p.D68D	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Silent_p.D68D	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	68	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						TCTCCTTCTTGTCCAGATCCA	0.463													.|||	1301	0.259784	0.3971	0.2507	5008	,	,		19428	0.12		0.163	False		,,,				2504	0.3241				p.D68D		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C204T						PASS	.	G	,,	908,2114		141,626,744	67.0	90.0	82.0		204,204,204	2.1	0.9	6	dbSNP_86	82	808,4610		50,708,1951	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	191,1334,2695	AA,AG,GG		14.9133,30.0463,20.3318	,,	68/261,68/261,68/261	33037560	1716,6724	1511	2709	4220	SO:0001819	synonymous_variant	3113	exon2			CTTCTTGTCCAGA	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.204C>T	6.37:g.33037560G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	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	
TXLNB	167838	hgsc.bcm.edu	37	6	139581461	139581461	+	Silent	SNP	C	C	T	rs6904970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139581461C>T	ENST00000358430.3	-	6	1228	c.996G>A	c.(994-996)aaG>aaA	p.K332K		NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	332						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)		ATACATATTCCTTTTCTCGTT	0.388													C|||	399	0.0796725	0.2141	0.0476	5008	,	,		18813	0.001		0.0517	False		,,,				2504	0.0307				p.K332K		Atlas-SNP	.											.	TXLNB	96	.	0			c.G996A						PASS	.	C		759,3647	304.4+/-288.4	78,603,1522	103.0	89.0	94.0		996	5.6	1.0	6	dbSNP_116	94	446,8154	132.3+/-190.0	14,418,3868	no	coding-synonymous	TXLNB	NM_153235.3		92,1021,5390	TT,TC,CC		5.186,17.2265,9.265		332/685	139581461	1205,11801	2203	4300	6503	SO:0001819	synonymous_variant	167838	exon6			ATATTCCTTTTCT		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.996G>A	6.37:g.139581461C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Silent	SNP	ENST00000358430.3	37	CCDS34545.1	146	0.06684981684981685	91	0.18495934959349594	14	0.03867403314917127	1	0.0017482517482517483	40	0.052770448548812667	C	8.483	0.860121	0.17178	0.172265	0.05186	ENSG00000164440	ENST00000367652	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	T	0.53045	0.1772	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.55121	-0.8190	3	.	.	.	-22.4848	12.9619	0.58464	0.0:0.9261:0.0:0.0739	rs6904970	.	.	.	R	45	.	.	G	-	1	0	TXLNB	139623154	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	1.579000	0.36536	2.676000	0.91093	0.591000	0.81541	GGA	C|0.915;T|0.085	0.085	strong		0.388	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235	
GLYCTK	132158	hgsc.bcm.edu	37	3	52325039	52325039	+	Silent	SNP	G	G	A	rs35976326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52325039G>A	ENST00000436784.2	+	3	501	c.441G>A	c.(439-441)ccG>ccA	p.P147P	GLYCTK_ENST00000305690.8_Silent_p.P147P|GLYCTK_ENST00000461183.1_Silent_p.P63P|GLYCTK_ENST00000471180.1_Silent_p.P20P|GLYCTK-AS1_ENST00000493616.1_RNA|GLYCTK_ENST00000473032.1_Silent_p.P147P|GLYCTK_ENST00000477382.1_Silent_p.P147P|GLYCTK_ENST00000354773.4_Silent_p.P147P			Q8IVS8	GLCTK_HUMAN	glycerate kinase	147					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glycerate kinase activity (GO:0008887)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(193;3.56e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)|OV - Ovarian serous cystadenocarcinoma(275;0.235)		ACAACCTCCCGGACCGCGATG	0.622													G|||	756	0.150958	0.4032	0.0994	5008	,	,		21728	0.0		0.1014	False		,,,				2504	0.0532				p.P147P		Atlas-SNP	.											.	GLYCTK	30	.	0			c.G441A						PASS	.	G	,	1289,3117	436.6+/-344.7	190,909,1104	100.0	80.0	86.0		441,441	-10.8	0.2	3	dbSNP_126	86	1017,7583	216.3+/-255.4	58,901,3341	no	coding-synonymous,coding-synonymous	GLYCTK	NM_001144951.1,NM_145262.3	,	248,1810,4445	AA,AG,GG		11.8256,29.2556,17.7303	,	147/235,147/524	52325039	2306,10700	2203	4300	6503	SO:0001819	synonymous_variant	132158	exon3			CCTCCCGGACCGC		CCDS2852.1, CCDS46841.1	3p21.1	2008-01-22			ENSG00000168237	ENSG00000168237	2.7.1.31		24247	protein-coding gene	gene with protein product		610516				16753811	Standard	NM_145262		Approved	HBEBP4, HBEBP2	uc003ddo.3	Q8IVS8	OTTHUMG00000158380	ENST00000436784.2:c.441G>A	3.37:g.52325039G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_001144951	Q0P630|Q2EZ43|Q6Y2K6|Q7Z6G5|Q86YR8|Q8TED2|Q8WTY2	Silent	SNP	ENST00000436784.2	37	CCDS2852.1																																																																																			G|0.845;A|0.155	0.155	strong		0.622	GLYCTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350835.1	NM_145262	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414252	105414252	+	Silent	SNP	C	C	T	rs60106058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105414252C>T	ENST00000333244.5	-	7	7655	c.7536G>A	c.(7534-7536)aaG>aaA	p.K2512K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2512						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)			CGGCCTCCACCTTCGGCGCAG	0.622													.|||	2278	0.454872	0.4917	0.3746	5008	,	,		17291	0.3125		0.5089	False		,,,				2504	0.5532				p.K2512K		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	0			c.G7536A						PASS	.	C		2055,1805		596,863,471	129.0	149.0	143.0		7536	1.5	0.0	14	dbSNP_129	143	4338,3900		1149,2040,930	no	coding-synonymous	AHNAK2	NM_138420.2		1745,2903,1401	TT,TC,CC		47.3416,46.7617,47.1566		2512/5796	105414252	6393,5705	1930	4119	6049	SO:0001819	synonymous_variant	113146	exon7			CTCCACCTTCGGC	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.7536G>A	14.37:g.105414252C>T		Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	273	271	0.992674	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.601;T|0.399	0.399	strong		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CTRB1	1504	hgsc.bcm.edu	37	16	75258617	75258617	+	Silent	SNP	C	C	T	rs2287990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75258617C>T	ENST00000361017.4	+	7	653	c.645C>T	c.(643-645)ggC>ggT	p.G215G	RP11-331F4.4_ENST00000489723.1_RNA	NM_001906.4	NP_001897.4	P17538	CTRB1_HUMAN	chymotrypsinogen B1	215	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|lung(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.166)	Aprotinin(DB06692)	ACTCTGGCGGCCCCCTGGTCT	0.662													C|||	663	0.132388	0.1422	0.0735	5008	,	,		16125	0.245		0.1024	False		,,,				2504	0.0757				p.G215G		Atlas-SNP	.											.	CTRB1	8	.	0			c.C645T						PASS	.	C		581,3815	258.0+/-262.2	39,503,1656	45.0	46.0	45.0		645	1.4	0.9	16	dbSNP_100	45	841,7759	192.8+/-238.7	37,767,3496	yes	coding-synonymous	CTRB1	NM_001906.4		76,1270,5152	TT,TC,CC		9.7791,13.2166,10.9418		215/264	75258617	1422,11574	2198	4300	6498	SO:0001819	synonymous_variant	1504	exon7			TGGCGGCCCCCTG		CCDS32490.1	16q23.1	2008-02-05			ENSG00000168925	ENSG00000168925	3.4.21.1		2521	protein-coding gene	gene with protein product		118890		CTRB		2917002, 8186414	Standard	NM_001906		Approved		uc002fds.3	P17538	OTTHUMG00000159272	ENST00000361017.4:c.645C>T	16.37:g.75258617C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	97	58	0.597938	NM_001906		Silent	SNP	ENST00000361017.4	37	CCDS32490.1																																																																																			C|0.884;T|0.116	0.116	strong		0.662	CTRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354300.2	NM_001906	
RGS14	10636	hgsc.bcm.edu	37	5	176798996	176798996	+	Missense_Mutation	SNP	G	G	A	rs149981884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176798996G>A	ENST00000408923.3	+	15	1809	c.1621G>A	c.(1621-1623)Gag>Aag	p.E541K	RGS14_ENST00000506944.1_3'UTR	NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	541					cell division (GO:0051301)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitotic nuclear division (GO:0007067)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of synaptic plasticity (GO:0031914)|nucleocytoplasmic transport (GO:0006913)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neurogenesis (GO:0050769)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to oxidative stress (GO:0006979)|spindle organization (GO:0007051)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual learning (GO:0008542)|zygote asymmetric cell division (GO:0010070)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|microtubule (GO:0005874)|nuclear body (GO:0016604)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|spindle (GO:0005819)|spindle pole (GO:0000922)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|microtubule binding (GO:0008017)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(3)|upper_aerodigestive_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)			GCCCAGCTCCGAGGAGACCCC	0.632													C|||	36	0.0071885	0.0265	0.0	5008	,	,		15334	0.0		0.001	False		,,,				2504	0.0				p.E541K	NSCLC(47;353 1896 28036)	Atlas-SNP	.											.	RGS14	34	.	0			c.G1621A						PASS	.	C	LYS/GLU	74,3978		0,74,1952	109.0	131.0	124.0		1621	2.9	0.0	5	dbSNP_134	124	3,8353		0,3,4175	yes	missense	RGS14	NM_006480.4	56	0,77,6127	AA,AG,GG		0.0359,1.8263,0.6206	benign	541/567	176798996	77,12331	2026	4178	6204	SO:0001583	missense	10636	exon15			AGCTCCGAGGAGA	AF037195	CCDS43405.1	5q35.3	2008-02-05	2007-08-14		ENSG00000169220	ENSG00000169220		"""Regulators of G-protein signaling"""	9996	protein-coding gene	gene with protein product		602513	"""regulator of G-protein signalling 14"""				Standard	NM_006480		Approved		uc003mgf.3	O43566	OTTHUMG00000163324	ENST00000408923.3:c.1621G>A	5.37:g.176798996G>A	ENSP00000386229:p.Glu541Lys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	44	0.55	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Missense_Mutation	SNP	ENST00000408923.3	37	CCDS43405.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	5.842	0.339577	0.11069	0.018263	3.59E-4	ENSG00000169220	ENST00000408923;ENST00000336477	T	0.37584	1.19	4.84	2.9	0.33743	.	1.710450	0.02865	N	0.130773	T	0.09818	0.0241	N	0.14661	0.345	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.21827	-1.0234	10	0.06625	T	0.88	-0.2211	2.9504	0.05860	0.0:0.4578:0.2389:0.3033	.	312;389;541	B3KUX0;O43566-5;O43566	.;.;RGS14_HUMAN	K	541;322	ENSP00000386229:E541K	ENSP00000336864:E322K	E	+	1	0	RGS14	176731602	0.001000	0.12720	0.009000	0.14445	0.018000	0.09664	1.463000	0.35277	0.678000	0.31325	-0.756000	0.03474	GAG	G|0.995;A|0.005	0.005	strong		0.632	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480	
MCM2	4171	hgsc.bcm.edu	37	3	127323592	127323592	+	Silent	SNP	G	G	A	rs2257836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127323592G>A	ENST00000265056.7	+	3	622	c.378G>A	c.(376-378)cgG>cgA	p.R126R		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	126	Interaction with KAT7. {ECO:0000250}.				cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						AGGCTGGCCGGGGCCTGGGCC	0.672													G|||	309	0.0617013	0.0219	0.0014	5008	,	,		15255	0.2599		0.006	False		,,,				2504	0.0112				p.R126R		Atlas-SNP	.											.	MCM2	79	.	0			c.G378A						PASS	.	G		70,4326		1,68,2129	14.0	17.0	16.0		378	-2.4	1.0	3	dbSNP_100	16	12,8570		0,12,4279	no	coding-synonymous	MCM2	NM_004526.2		1,80,6408	AA,AG,GG		0.1398,1.5924,0.6318		126/905	127323592	82,12896	2198	4291	6489	SO:0001819	synonymous_variant	4171	exon3			TGGCCGGGGCCTG	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"""mitotin"""	116945	"""minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)"", ""MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"""	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.378G>A	3.37:g.127323592G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Silent	SNP	ENST00000265056.7	37	CCDS3043.1	189	0.08653846153846154	16	0.032520325203252036	0	0.0	166	0.2902097902097902	7	0.009234828496042216	G	11.20	1.568710	0.28003	0.015924	0.001398	ENSG00000073111	ENST00000539922	.	.	.	5.29	-2.37	0.06643	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999999733741	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.7759	0.01032	0.266:0.1952:0.3286:0.2103	rs2257836;rs17496916	.	.	.	.	-1	.	.	.	+	.	.	MCM2	128806282	0.310000	0.24527	0.972000	0.41901	0.963000	0.63663	-0.451000	0.06795	-0.314000	0.08716	0.591000	0.81541	.	G|0.902;A|0.098	0.098	strong		0.672	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1		
RRP1	8568	hgsc.bcm.edu	37	21	45219524	45219524	+	Silent	SNP	T	T	C	rs4566449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45219524T>C	ENST00000497547.1	+	9	1002	c.885T>C	c.(883-885)gtT>gtC	p.V295V	RRP1_ENST00000471909.1_3'UTR	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)		GCGGCCCCGTTCTCCAGGTGG	0.642													C|||	1747	0.348842	0.4213	0.3415	5008	,	,		14283	0.3175		0.2078	False		,,,				2504	0.4335				p.V295V		Atlas-SNP	.											.	RRP1	23	.	0			c.T885C						PASS	.	C		1553,2591		300,953,819	48.0	65.0	59.0		885	-3.6	0.0	21	dbSNP_111	59	1989,6443		252,1485,2479	no	coding-synonymous	RRP1	NM_003683.5		552,2438,3298	CC,CT,TT		23.5887,37.4759,28.1648		295/462	45219524	3542,9034	2072	4216	6288	SO:0001819	synonymous_variant	8568	exon9			CCCCGTTCTCCAG	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.885T>C	21.37:g.45219524T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	152	82	0.539474	NM_003683	A6NIB2	Silent	SNP	ENST00000497547.1	37	CCDS42951.1																																																																																			T|0.688;C|0.312	0.312	strong		0.642	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683	
MUC17	140453	hgsc.bcm.edu	37	7	100677974	100677974	+	Missense_Mutation	SNP	A	A	G	rs113876641	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677974A>G	ENST00000306151.4	+	3	3341	c.3277A>G	c.(3277-3279)Acc>Gcc	p.T1093A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1093	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)					CAGCATGCCAACCTCAACTTA	0.507																																					p.T1093A		Atlas-SNP	.											.	MUC17	804	.	0			c.A3277G						PASS	.						479.0	385.0	417.0					7																	100677974		2203	4300	6503	SO:0001583	missense	140453	exon3			ATGCCAACCTCAA	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.3277A>G	7.37:g.100677974A>G	ENSP00000302716:p.Thr1093Ala	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	398	57	0.143216	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	1.073	-0.669248	0.03403	.	.	ENSG00000169876	ENST00000306151	T	0.02258	4.37	0.693	-0.692	0.11301	.	.	.	.	.	T	0.00998	0.0033	N	0.14661	0.345	0.09310	N	1	P	0.37985	0.613	B	0.25140	0.058	T	0.46638	-0.9177	9	0.10902	T	0.67	.	4.0642	0.09852	0.7272:0.0:0.2728:0.0	.	1093	Q685J3	MUC17_HUMAN	A	1093	ENSP00000302716:T1093A	ENSP00000302716:T1093A	T	+	1	0	MUC17	100464694	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.411000	0.07142	-0.284000	0.09102	0.165000	0.16767	ACC	A|0.998;G|0.002	0.002	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SDCCAG8	10806	hgsc.bcm.edu	37	1	243493907	243493907	+	Missense_Mutation	SNP	A	A	T	rs2275155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:243493907A>T	ENST00000366541.3	+	10	1252	c.1134A>T	c.(1132-1134)gaA>gaT	p.E378D	SDCCAG8_ENST00000343783.6_Missense_Mutation_p.E233D|SDCCAG8_ENST00000355875.4_Missense_Mutation_p.E335D	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	378	Sufficient for homodimerization. {ECO:0000250}.		E -> D (in dbSNP:rs2275155).		establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		TTGAAAAAGAACTTGCATCTC	0.448													A|||	1359	0.271366	0.1702	0.2147	5008	,	,		11478	0.1935		0.3231	False		,,,				2504	0.4755				p.E378D		Atlas-SNP	.											SDCCAG8,NS,carcinoma,+2,1	SDCCAG8	73	1	0			c.A1134T						PASS	.	A	ASP/GLU	843,3563	330.4+/-301.5	94,655,1454	81.0	76.0	77.0		1134	0.2	0.7	1	dbSNP_100	77	2645,5955	419.4+/-353.1	395,1855,2050	yes	missense	SDCCAG8	NM_006642.3	45	489,2510,3504	TT,TA,AA		30.7558,19.133,26.8184	benign	378/714	243493907	3488,9518	2203	4300	6503	SO:0001583	missense	10806	exon10			AAAAGAACTTGCA	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.1134A>T	1.37:g.243493907A>T	ENSP00000355499:p.Glu378Asp	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	213	102	0.478873	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	37	CCDS31075.1	507	0.23214285714285715	78	0.15853658536585366	79	0.21823204419889503	103	0.18006993006993008	247	0.3258575197889182	A	17.68	3.450269	0.63290	0.19133	0.307558	ENSG00000054282	ENST00000355875;ENST00000366541;ENST00000343783;ENST00000435549	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.78	0.25	0.15535	.	0.100084	0.64402	D	0.000002	T	0.00012	0.0000	M	0.71581	2.175	0.34934	P	0.25036899999999995	P;B	0.50819	0.939;0.119	P;B	0.47075	0.536;0.084	T	0.24154	-1.0168	9	0.33141	T	0.24	-6.6197	8.5699	0.33563	0.6552:0.0:0.3448:0.0	rs2275155;rs52836454;rs2275155	335;378	E9PFS7;Q86SQ7	.;SDCG8_HUMAN	D	335;378;233;158	ENSP00000348137:E335D;ENSP00000355499:E378D;ENSP00000341260:E233D;ENSP00000410200:E158D	ENSP00000341260:E233D	E	+	3	2	SDCCAG8	241560530	0.996000	0.38824	0.707000	0.30419	0.873000	0.50193	0.375000	0.20518	-0.190000	0.10465	0.533000	0.62120	GAA	A|0.746;T|0.254	0.254	strong		0.448	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642	
POTEG	404785	hgsc.bcm.edu	37	14	19553494	19553494	+	Missense_Mutation	SNP	G	G	C	rs200256710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:19553494G>C	ENST00000409832.3	+	1	130	c.78G>C	c.(76-78)aaG>aaC	p.K26N		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	26										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						AGATGGGCAAGTGGTGCCGCC	0.582																																					p.K26N		Atlas-SNP	.											POTEG,NS,carcinoma,0,1	POTEG	118	1	0			c.G78C						scavenged	.						4.0	7.0	6.0					14																	19553494		1219	2779	3998	SO:0001583	missense	404785	exon1			GGGCAAGTGGTGC		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.78G>C	14.37:g.19553494G>C	ENSP00000386971:p.Lys26Asn	Somatic	1363	1	0.000733676		WXS	Illumina HiSeq	Phase_I	2158	285	0.132067	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	37	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	g	9.693	1.152413	0.21371	.	.	ENSG00000222036	ENST00000409832	T	0.46819	0.86	.	.	.	.	.	.	.	.	T	0.52025	0.1709	L	0.29908	0.895	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.37934	-0.9684	7	0.87932	D	0	.	.	.	.	.	26	Q6S5H5	POTEG_HUMAN	N	26	ENSP00000386971:K26N	ENSP00000386971:K26N	K	+	3	2	POTEG	18623494	0.003000	0.15002	0.038000	0.18304	0.017000	0.09413	-0.275000	0.08525	0.459000	0.27016	0.152000	0.16155	AAG	G|0.996;A|0.004	.	alt		0.582	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
PRR12	57479	hgsc.bcm.edu	37	19	50098423	50098423	+	Silent	SNP	G	G	A	rs12462756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	56	0	0		WXS	Illumina HiSeq	Phase_I	93	91	0.978495	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	
C1orf158	93190	hgsc.bcm.edu	37	1	12820870	12820870	+	Missense_Mutation	SNP	T	T	C	rs1132185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12820870T>C	ENST00000288048.5	+	4	787	c.571T>C	c.(571-573)Ttc>Ctc	p.F191L	C1orf158_ENST00000376210.3_Missense_Mutation_p.F153L	NM_152290.2	NP_689503.2	Q8N1D5	CA158_HUMAN	chromosome 1 open reading frame 158	191			F -> L (in dbSNP:rs1132185). {ECO:0000269|PubMed:15489334}.							central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|ovary(1)|skin(2)|urinary_tract(3)	10	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;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CCTGCATCCTTTCCCACACTT	0.572													C|||	4124	0.823482	0.9153	0.8545	5008	,	,		18125	0.7808		0.7873	False		,,,				2504	0.7587				p.F191L		Atlas-SNP	.											.	C1orf158	28	.	0			c.T571C						PASS	.	C	LEU/PHE	3936,470		1756,424,23	73.0	66.0	68.0		571	-8.7	0.0	1	dbSNP_86	68	6789,1811		2681,1427,192	yes	missense	C1orf158	NM_152290.2	22	4437,1851,215	CC,CT,TT		21.0581,10.6673,17.5381	benign	191/195	12820870	10725,2281	2203	4300	6503	SO:0001583	missense	93190	exon4			CATCCTTTCCCAC	BX647383	CCDS147.1	1p36.21	2008-02-05			ENSG00000157330	ENSG00000157330			28567	protein-coding gene	gene with protein product						12477932	Standard	NM_152290		Approved	MGC35194	uc001auh.3	Q8N1D5	OTTHUMG00000001888	ENST00000288048.5:c.571T>C	1.37:g.12820870T>C	ENSP00000288048:p.Phe191Leu	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_152290	Q5VUY4	Missense_Mutation	SNP	ENST00000288048.5	37	CCDS147.1	1812	0.8296703296703297	449	0.9126016260162602	302	0.8342541436464088	457	0.798951048951049	604	0.7968337730870713	.	5.655	0.305549	0.10678	0.893327	0.789419	ENSG00000157330	ENST00000288048;ENST00000376210	T;T	0.38077	1.17;1.16	4.34	-8.68	0.00859	.	2.467460	0.01330	N	0.011232	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	0.31888	-0.9927	9	0.13853	T	0.58	0.0239	1.1769	0.01837	0.2301:0.3027:0.1124:0.3547	rs1132185;rs3192730;rs9430817;rs17038529;rs17038532;rs17845913;rs17858888;rs60888644;rs1132185	191	Q8N1D5	CA158_HUMAN	L	191;153	ENSP00000288048:F191L;ENSP00000365383:F153L	ENSP00000288048:F191L	F	+	1	0	C1orf158	12743457	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.774000	0.04684	-1.940000	0.01043	-2.508000	0.00189	TTC	T|0.173;C|0.827	0.827	strong		0.572	C1orf158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005325.1	NM_152290	
GABRP	2568	hgsc.bcm.edu	37	5	170239112	170239112	+	Missense_Mutation	SNP	C	C	A	rs1063310	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:170239112C>A	ENST00000518525.1	+	11	1637	c.1173C>A	c.(1171-1173)ttC>ttA	p.F391L	GABRP_ENST00000519385.1_3'UTR|GABRP_ENST00000265294.4_Missense_Mutation_p.F391L			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	391			F -> L (in dbSNP:rs1063310). {ECO:0000269|PubMed:15489334}.		signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCGACAAGTTCAAGTTTGTCT	0.403													C|||	1121	0.223842	0.2821	0.1398	5008	,	,		20252	0.2589		0.2565	False		,,,				2504	0.135				p.F391L		Atlas-SNP	.											.	GABRP	65	.	0			c.C1173A						PASS	.	C	LEU/PHE	1338,3068	447.5+/-348.4	207,924,1072	118.0	111.0	113.0		1173	2.9	1.0	5	dbSNP_86	113	2099,6501	362.7+/-332.9	282,1535,2483	yes	missense	GABRP	NM_014211.2	22	489,2459,3555	AA,AC,CC		24.407,30.3677,26.4263	benign	391/441	170239112	3437,9569	2203	4300	6503	SO:0001583	missense	2568	exon10			CAAGTTCAAGTTT	U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4089	protein-coding gene	gene with protein product	"""GABA(A) receptor, pi"""	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.1173C>A	5.37:g.170239112C>A	ENSP00000430100:p.Phe391Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_014211	A8KA36|D3DQL2|Q32MJ1	Missense_Mutation	SNP	ENST00000518525.1	37	CCDS4375.1	563	0.25778388278388276	148	0.3008130081300813	55	0.15193370165745856	165	0.28846153846153844	195	0.25725593667546176	C	7.948	0.744234	0.15710	0.303677	0.24407	ENSG00000094755	ENST00000518525;ENST00000265294	T;T	0.80033	-1.33;-1.33	5.74	2.88	0.33553	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.439494	0.27595	N	0.018672	T	0.00012	0.0000	N	0.14661	0.345	0.33623	P	0.39497499999999997	B	0.20164	0.042	B	0.11329	0.006	T	0.07424	-1.0773	9	0.24483	T	0.36	.	6.0236	0.19642	0.0:0.6203:0.1353:0.2443	rs1063310;rs3173007;rs3805457;rs17565897;rs52815531;rs1063310	391	O00591	GBRP_HUMAN	L	391	ENSP00000430100:F391L;ENSP00000265294:F391L	ENSP00000265294:F391L	F	+	3	2	GABRP	170171690	0.998000	0.40836	1.000000	0.80357	0.984000	0.73092	0.331000	0.19733	0.295000	0.22570	0.655000	0.94253	TTC	C|0.739;A|0.261	0.261	strong		0.403	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211	
NUP85	79902	hgsc.bcm.edu	37	17	73230796	73230796	+	Silent	SNP	T	T	C	rs35857535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73230796T>C	ENST00000245544.4	+	17	1751	c.1680T>C	c.(1678-1680)ctT>ctC	p.L560L	NUP85_ENST00000579298.1_Silent_p.L515L|NUP85_ENST00000447371.2_Silent_p.L392L|NUP85_ENST00000541827.1_Silent_p.L514L|NUP85_ENST00000579324.1_Silent_p.L448L|NUP85_ENST00000540768.1_Silent_p.L163L	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	560					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)			CTTCTCTCCTTCTGTCCTTGA	0.522													T|||	530	0.105831	0.2209	0.0692	5008	,	,		20568	0.1002		0.002	False		,,,				2504	0.089				p.L560L		Atlas-SNP	.											.	NUP85	44	.	0			c.T1680C						PASS	.	T		747,3659	306.9+/-289.7	73,601,1529	223.0	189.0	200.0		1680	-4.2	0.5	17	dbSNP_126	200	20,8580	13.3+/-46.6	0,20,4280	no	coding-synonymous	NUP85	NM_024844.3		73,621,5809	CC,CT,TT		0.2326,16.9542,5.8973		560/657	73230796	767,12239	2203	4300	6503	SO:0001819	synonymous_variant	79902	exon17			TCTCCTTCTGTCC	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.1680T>C	17.37:g.73230796T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	83	29	0.349398	NM_024844	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Silent	SNP	ENST00000245544.4	37	CCDS32730.1																																																																																			T|0.935;C|0.065	0.065	strong		0.522	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844	
CLU	1191	hgsc.bcm.edu	37	8	27457507	27457507	+	Silent	SNP	G	G	C	rs9331937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27457507G>C	ENST00000316403.10	-	7	1359	c.954C>G	c.(952-954)ccC>ccG	p.P318P	CLU_ENST00000546343.1_Silent_p.P329P|CLU_ENST00000405140.3_Silent_p.P318P|CLU_ENST00000560366.1_Silent_p.P370P|CLU_ENST00000523500.1_Silent_p.P318P			P10909	CLUS_HUMAN	clusterin	318					blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		TAGCCTGGGAGGGGTTGTTGG	0.522													G|||	144	0.028754	0.1059	0.0058	5008	,	,		20885	0.0		0.0	False		,,,				2504	0.0				p.P318P		Atlas-SNP	.											.	CLU	54	.	0			c.C954G						PASS	.	G		375,4031	191.2+/-216.9	12,351,1840	57.0	54.0	55.0		954	-8.3	0.0	8	dbSNP_119	55	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CLU	NM_203339.2		12,353,6138	CC,CG,GG		0.0233,8.5111,2.8987		318/450	27457507	377,12629	2203	4300	6503	SO:0001819	synonymous_variant	1191	exon7			CTGGGAGGGGTTG	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"""complement lysis inhibitor"", ""sulfated glycoprotein 2"", ""testosterone-repressed prostate message 2"", ""apolipoprotein J"""	185430	"""clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"""	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.954C>G	8.37:g.27457507G>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Silent	SNP	ENST00000316403.10	37	CCDS47832.1	54|54	0.024725274725274724|0.024725274725274724	51|51	0.10365853658536585|0.10365853658536585	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	5.885|5.885	0.347360|0.347360	0.11126|0.11126	0.085111|0.085111	2.33E-4|2.33E-4	ENSG00000120885|ENSG00000120885	ENST00000522098|ENST00000521770	.|T	.|0.38401	.|1.14	5.62|5.62	-8.32|-8.32	0.00996|0.00996	.|.	.|0.050523	.|0.85682	.|D	.|0.000000	T|T	0.00724|0.00724	0.0024|0.0024	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.38134|0.38134	-0.9675|-0.9675	4|7	.|0.87932	.|D	.|0	-28.8002|-28.8002	0.2978|0.2978	0.00268|0.00268	0.2607:0.255:0.2311:0.2532|0.2607:0.255:0.2311:0.2532	rs9331937;rs9331937|rs9331937;rs9331937	.|.	.|.	.|.	V|R	181|9	.|ENSP00000428033:P9R	.|ENSP00000428033:P9R	L|P	-|-	1|2	0|0	CLU|CLU	27513424|27513424	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-3.122000|-3.122000	0.00594|0.00594	-1.333000|-1.333000	0.02247|0.02247	0.655000|0.655000	0.94253|0.94253	CTC|CCT	G|0.973;C|0.027	0.027	strong		0.522	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831	
BRPF1	7862	hgsc.bcm.edu	37	3	9780737	9780737	+	Silent	SNP	C	C	T	rs17050537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9780737C>T	ENST00000457855.1	+	2	665	c.654C>T	c.(652-654)gaC>gaT	p.D218D	BRPF1_ENST00000302054.3_Silent_p.D218D|BRPF1_ENST00000433861.2_Silent_p.D218D|BRPF1_ENST00000383829.2_Silent_p.D218D|BRPF1_ENST00000424362.1_Silent_p.D218D			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	218	Interaction with KAT6A and KAT6B.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					ATGACATGGACGAGGAGGACT	0.507													C|||	54	0.0107827	0.0408	0.0	5008	,	,		23526	0.0		0.0	False		,,,				2504	0.0				p.D218D		Atlas-SNP	.											.	BRPF1	104	.	0			c.C654T						PASS	.	C	,	87,4319	73.6+/-111.7	3,81,2119	125.0	117.0	120.0		654,654	-5.0	0.9	3	dbSNP_123	120	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	BRPF1	NM_001003694.1,NM_004634.2	,	3,81,6419	TT,TC,CC		0.0,1.9746,0.6689	,	218/1221,218/1215	9780737	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	7862	exon3			CATGGACGAGGAG	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"""peregrin"", ""bromodomain-containing protein, 140kD"""	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.654C>T	3.37:g.9780737C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	170	97	0.570588	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Silent	SNP	ENST00000457855.1	37	CCDS2575.1																																																																																			C|0.989;T|0.011	0.011	strong		0.507	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694	
ZBTB42	100128927	hgsc.bcm.edu	37	14	105268701	105268701	+	Silent	SNP	G	G	A	rs61734768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105268701G>A	ENST00000342537.7	+	1	1452	c.1167G>A	c.(1165-1167)ccG>ccA	p.P389P	ZBTB42_ENST00000555360.1_Silent_p.P389P	NM_001137601.1	NP_001131073.1	B2RXF5	ZBT42_HUMAN	zinc finger and BTB domain containing 42	389					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)										GAGAGAAGCCGCATGCCTGCC	0.592													G|||	269	0.0537141	0.1377	0.0274	5008	,	,		18458	0.005		0.0139	False		,,,				2504	0.0501				p.P389P		Atlas-SNP	.											.	ZBTB42	10	.	0			c.G1167A						PASS	.	G		148,1234		7,134,550	39.0	50.0	46.0		1167	-8.3	0.7	14	dbSNP_129	46	34,3138		1,32,1553	no	coding-synonymous	ZBTB42	NM_001137601.1		8,166,2103	AA,AG,GG		1.0719,10.7091,3.9965		389/423	105268701	182,4372	691	1586	2277	SO:0001819	synonymous_variant	100128927	exon2			GAAGCCGCATGCC	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.1167G>A	14.37:g.105268701G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_001137601	B7ZW21	Silent	SNP	ENST00000342537.7	37	CCDS45174.1																																																																																			G|0.959;A|0.041	0.041	strong		0.592	ZBTB42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410372.1		
ZNF689	115509	hgsc.bcm.edu	37	16	30616488	30616488	+	Silent	SNP	G	G	A	rs9937653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30616488G>A	ENST00000287461.3	-	3	937	c.600C>T	c.(598-600)tcC>tcT	p.S200S	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	200					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			GGCACTCGCCGGAGTGTGCCC	0.577													G|||	155	0.0309505	0.1135	0.0072	5008	,	,		14868	0.0		0.0	False		,,,				2504	0.0				p.S200S		Atlas-SNP	.											.	ZNF689	48	.	0			c.C600T						PASS	.	G		371,4023	190.2+/-216.2	14,343,1840	65.0	65.0	65.0		600	-9.9	0.1	16	dbSNP_119	65	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	ZNF689	NM_138447.1		14,347,6136	AA,AG,GG		0.0465,8.4433,2.8859		200/501	30616488	375,12619	2197	4300	6497	SO:0001819	synonymous_variant	115509	exon3			CTCGCCGGAGTGT	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"""Zinc fingers, C2H2-type"", ""-"""	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.600C>T	16.37:g.30616488G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	120	51	0.425	NM_138447	Q658J5	Silent	SNP	ENST00000287461.3	37	CCDS10686.1																																																																																			G|0.972;A|0.028	0.028	strong		0.577	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447	
KRT71	112802	hgsc.bcm.edu	37	12	52946543	52946543	+	Missense_Mutation	SNP	C	C	T	rs665522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	175	0	0		WXS	Illumina HiSeq	Phase_I	171	93	0.54386	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	
PIEZO1	9780	hgsc.bcm.edu	37	16	88800913	88800913	+	Silent	SNP	C	C	T	rs34908386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88800913C>T	ENST00000301015.9	-	16	2277	c.2031G>A	c.(2029-2031)gtG>gtA	p.V677V	RP5-1142A6.2_ENST00000567968.1_RNA|RP5-1142A6.2_ENST00000440406.2_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	677					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						AGAGCTCGGACACGCTGAACT	0.677													C|||	528	0.105431	0.2731	0.0504	5008	,	,		15584	0.0		0.1203	False		,,,				2504	0.0112				p.V677V		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G2031A						PASS	.						69.0	87.0	81.0					16																	88800913		692	1589	2281	SO:0001819	synonymous_variant	9780	exon16			CTCGGACACGCTG	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.2031G>A	16.37:g.88800913C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	95	55	0.578947	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	234	0.10714285714285714	113	0.22967479674796748	15	0.04143646408839779	0	0.0	106	0.13984168865435356	C	10.87	1.473128	0.26423	.	.	ENSG00000103335	ENST00000451779	.	.	.	4.76	3.72	0.42706	.	0.273257	0.29522	N	0.011908	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.03000	-1.1084	5	0.28530	T	0.3	-34.1835	14.0764	0.64893	0.0:0.7567:0.2433:0.0	rs34908386	.	.	.	I	623	.	ENSP00000408244:V623I	V	-	1	0	FAM38A	87328414	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	0.711000	0.25764	2.371000	0.80710	0.313000	0.20887	GTC	C|0.891;T|0.109	0.109	strong		0.677	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
EXOC8	149371	hgsc.bcm.edu	37	1	231472916	231472916	+	Silent	SNP	G	G	A	rs73116365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:231472916G>A	ENST00000360394.2	-	1	662	c.576C>T	c.(574-576)taC>taT	p.Y192Y	EXOC8_ENST00000366645.1_Silent_p.Y188Y|SPRTN_ENST00000008440.9_5'Flank|SPRTN_ENST00000295050.7_5'Flank|SPRTN_ENST00000391858.4_5'UTR	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	192	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular protein localization (GO:0034613)|cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(2)|endometrium(1)|large_intestine(2)|liver(1)|lung(5)|prostate(1)|skin(1)|stomach(1)	14	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				GGTCCGCATCGTATTCCACTA	0.587													G|||	77	0.0153754	0.0537	0.0072	5008	,	,		17457	0.0		0.001	False		,,,				2504	0.0				p.Y192Y		Atlas-SNP	.											.	EXOC8	42	.	0			c.C576T						PASS	.	G		215,4191	130.2+/-166.9	7,201,1995	77.0	66.0	70.0		576	1.2	1.0	1	dbSNP_130	70	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	EXOC8	NM_175876.3		7,203,6293	AA,AG,GG		0.0233,4.8797,1.6685		192/726	231472916	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	149371	exon1			CGCATCGTATTCC	AL117352	CCDS1593.1	1q42.2	2013-01-22			ENSG00000116903	ENSG00000116903			24659	protein-coding gene	gene with protein product		615283				12477932	Standard	NM_175876		Approved	SEC84, EXO84, Exo84p	uc001huq.3	Q8IYI6	OTTHUMG00000038025	ENST00000360394.2:c.576C>T	1.37:g.231472916G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_175876	B3KU33|Q5TE82	Silent	SNP	ENST00000360394.2	37	CCDS1593.1																																																																																			G|0.983;A|0.017	0.017	strong		0.587	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876	
MMP13	4322	hgsc.bcm.edu	37	11	102818662	102818662	+	Missense_Mutation	SNP	T	T	C	rs17860568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:102818662T>C	ENST00000260302.3	-	8	1197	c.1169A>G	c.(1168-1170)gAt>gGt	p.D390G	MMP13_ENST00000340273.4_Missense_Mutation_p.D390G	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	390	Interaction with collagen.		D -> G (in dbSNP:rs17860568). {ECO:0000269|Ref.4}.		bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	CTTGCCTGTATCCTCAAAGTG	0.438													T|||	41	0.0081869	0.0287	0.0014	5008	,	,		16765	0.0		0.002	False		,,,				2504	0.0				p.D390G		Atlas-SNP	.											.	MMP13	75	.	0			c.A1169G						PASS	.	T	GLY/ASP	75,4329	67.0+/-104.6	2,71,2129	135.0	113.0	120.0		1169	2.0	0.2	11	dbSNP_123	120	1,8597		0,1,4298	yes	missense	MMP13	NM_002427.3	94	2,72,6427	CC,CT,TT		0.0116,1.703,0.5845	benign	390/472	102818662	76,12926	2202	4299	6501	SO:0001583	missense	4322	exon8			CCTGTATCCTCAA	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"""Endogenous ligands"""	7159	protein-coding gene	gene with protein product	"""collagenase 3"""	600108	"""matrix metalloproteinase 13 (collagenase 3)"""			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.1169A>G	11.37:g.102818662T>C	ENSP00000260302:p.Asp390Gly	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	89	32	0.359551	NM_002427	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	37	CCDS8324.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	T	12.68	2.009730	0.35415	0.01703	1.16E-4	ENSG00000137745	ENST00000260302;ENST00000340273	T;T	0.02863	4.13;4.13	5.82	1.98	0.26296	Hemopexin/matrixin (2);	0.232869	0.49916	D	0.000139	T	0.01061	0.0035	L	0.39566	1.225	0.35073	D	0.762662	B	0.18741	0.03	B	0.30716	0.119	T	0.37407	-0.9707	10	0.44086	T	0.13	.	7.3488	0.26678	0.0:0.1373:0.2092:0.6535	rs17860568	390	P45452	MMP13_HUMAN	G	390	ENSP00000260302:D390G;ENSP00000339672:D390G	ENSP00000260302:D390G	D	-	2	0	MMP13	102323872	0.008000	0.16893	0.234000	0.24042	0.991000	0.79684	1.812000	0.38952	0.479000	0.27511	0.533000	0.62120	GAT	T|0.991;C|0.009	0.009	strong		0.438	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427	
BZRAP1	9256	hgsc.bcm.edu	37	17	56386358	56386358	+	Silent	SNP	T	T	A	rs2526360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	64	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	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	
LRIT2	340745	hgsc.bcm.edu	37	10	85982075	85982075	+	Silent	SNP	A	A	G	rs7901410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85982075A>G	ENST00000372113.4	-	3	1259	c.1254T>C	c.(1252-1254)taT>taC	p.Y418Y	LRIT2_ENST00000538192.1_Silent_p.Y428Y	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	418	Fibronectin type-III.					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						CATCCACAGCATAAGTATTGA	0.537													A|||	227	0.0453275	0.1672	0.0086	5008	,	,		21319	0.0		0.0	False		,,,				2504	0.0				p.Y418Y		Atlas-SNP	.											.	LRIT2	81	.	0			c.T1254C						PASS	.	A		602,3804	265.9+/-266.9	50,502,1651	121.0	114.0	116.0		1254	-10.1	0.0	10	dbSNP_116	116	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous	LRIT2	NM_001017924.2		50,520,5933	GG,GA,AA		0.2093,13.6632,4.767		418/551	85982075	620,12386	2203	4300	6503	SO:0001819	synonymous_variant	340745	exon3			CACAGCATAAGTA		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.1254T>C	10.37:g.85982075A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_001017924	B7ZME6	Silent	SNP	ENST00000372113.4	37	CCDS31234.1																																																																																			A|0.945;G|0.055	0.055	strong		0.537	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
C4orf45	152940	hgsc.bcm.edu	37	4	159894277	159894277	+	Missense_Mutation	SNP	T	T	C	rs17037858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:159894277T>C	ENST00000434826.2	-	2	335	c.251A>G	c.(250-252)tAt>tGt	p.Y84C	C4orf45_ENST00000508011.1_5'UTR	NM_152543.2	NP_689756.2	Q96LM5	CD045_HUMAN	chromosome 4 open reading frame 45	84			Y -> C (in dbSNP:rs17037858).							large_intestine(2)|lung(3)	5						GATAAAATTATACTGTGGTAT	0.353													T|||	414	0.0826677	0.0825	0.0274	5008	,	,		17528	0.2202		0.0338	False		,,,				2504	0.0307				p.Y84C		Atlas-SNP	.											.	C4orf45	8	.	0			c.A251G						PASS	.	T	CYS/TYR	219,3417		8,203,1607	87.0	75.0	78.0		251	1.6	0.1	4	dbSNP_123	78	256,7904		2,252,3826	yes	missense	C4orf45	NM_152543.2	194	10,455,5433	CC,CT,TT		3.1373,6.0231,4.0268	probably-damaging	84/187	159894277	475,11321	1818	4080	5898	SO:0001583	missense	152940	exon2			AAATTATACTGTG		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.251A>G	4.37:g.159894277T>C	ENSP00000412215:p.Tyr84Cys	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	124	59	0.475806	NM_152543	A8MPU3|C9J0T8	Missense_Mutation	SNP	ENST00000434826.2	37	CCDS47156.1	219	0.10027472527472528	57	0.11585365853658537	13	0.03591160220994475	127	0.22202797202797203	22	0.029023746701846966	T	8.180	0.793630	0.16327	0.060231	0.031373	ENSG00000164123	ENST00000434826	T	0.17370	2.28	5.69	1.65	0.23941	.	0.404294	0.21670	N	0.070893	T	0.00012	0.0000	M	0.73962	2.25	0.80722	P	0.0	B	0.16802	0.019	B	0.16289	0.015	T	0.20240	-1.0281	8	.	.	.	-8.8034	3.2754	0.06897	0.2095:0.191:0.0:0.5994	rs17037858;rs17037858	84	Q96LM5	CD045_HUMAN	C	84	ENSP00000412215:Y84C	.	Y	-	2	0	C4orf45	160113727	0.000000	0.05858	0.127000	0.21898	0.731000	0.41821	-0.406000	0.07187	0.431000	0.26258	0.533000	0.62120	TAT	T|0.903;C|0.097	0.097	strong		0.353	C4orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366636.1	NM_152543	
MBTPS1	8720	hgsc.bcm.edu	37	16	84097021	84097021	+	Missense_Mutation	SNP	C	C	G	rs35417190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84097021C>G	ENST00000343411.3	-	19	2956	c.2461G>C	c.(2461-2463)Gtt>Ctt	p.V821L		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	821					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)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TTTTCAACAACTGCTGTTTCC	0.438											OREG0023981	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	15	0.00299521	0.0091	0.0043	5008	,	,		17016	0.0		0.0	False		,,,				2504	0.0				p.V821L		Atlas-SNP	.											.	MBTPS1	85	.	0			c.G2461C						PASS	.	C	LEU/VAL	40,4360	43.8+/-77.6	0,40,2160	78.0	75.0	76.0		2461	2.4	0.1	16	dbSNP_126	76	0,8600		0,0,4300	yes	missense	MBTPS1	NM_003791.2	32	0,40,6460	GG,GC,CC		0.0,0.9091,0.3077	benign	821/1053	84097021	40,12960	2200	4300	6500	SO:0001583	missense	8720	exon19			CAACAACTGCTGT	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"""membrane-bound transcription factor protease, site 1"""			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.2461G>C	16.37:g.84097021C>G	ENSP00000344223:p.Val821Leu	Somatic	123	0	0	1226	WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	37	CCDS10941.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	C	10.63	1.403350	0.25291	0.009091	0.0	ENSG00000140943	ENST00000343411;ENST00000347334	T	0.30182	1.54	5.44	2.36	0.29203	.	0.294067	0.37261	N	0.002176	T	0.10465	0.0256	N	0.16656	0.425	0.40773	D	0.983105	B	0.02656	0.0	B	0.04013	0.001	T	0.10730	-1.0617	10	0.25106	T	0.35	-6.6213	4.5503	0.12108	0.2657:0.5222:0.0:0.2121	rs35417190	821	Q14703	MBTP1_HUMAN	L	821;266	ENSP00000344223:V821L	ENSP00000344223:V821L	V	-	1	0	MBTPS1	82654522	0.002000	0.14202	0.082000	0.20525	0.989000	0.77384	0.019000	0.13444	0.335000	0.23614	0.491000	0.48974	GTT	C|0.997;G|0.003	0.003	strong		0.438	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592535	167592535	+	Missense_Mutation	SNP	G	G	C	rs145355467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:167592535G>C	ENST00000366832.2	+	6	825	c.694G>C	c.(694-696)Ggt>Cgt	p.G232R		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	232										endometrium(1)|kidney(2)|lung(3)	6						GCAAAACTCCGGTGGCAGAAA	0.602													A|||	95	0.0189696	0.0325	0.0173	5008	,	,		13331	0.0		0.0199	False		,,,				2504	0.0204				p.G232R		Atlas-SNP	.											.	TCP10L2	41	.	0			c.G694C						PASS	.	A	ARG/GLY	49,1335		1,47,644	25.0	28.0	27.0		694	0.6	0.0	6	dbSNP_134	27	83,3099		3,77,1511	no	missense	TCP10L2	NM_001145121.1	125	4,124,2155	CC,CG,GG		2.6084,3.5405,2.8909	benign	232/354	167592535	132,4434	692	1591	2283	SO:0001583	missense	401285	exon6			AACTCCGGTGGCA		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.694G>C	6.37:g.167592535G>C	ENSP00000355797:p.Gly232Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	44	0.020146520146520148	22	0.044715447154471545	5	0.013812154696132596	0	0.0	17	0.022427440633245383	a	2.630	-0.286478	0.05605	0.035405	0.026084	ENSG00000166984	ENST00000366832	T	0.15603	2.41	1.87	0.56	0.17279	.	.	.	.	.	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47573	-0.9107	9	0.23302	T	0.38	.	1.791	0.03051	0.5132:0.0:0.1895:0.2973	.	232	B9ZVM9	TCP2L_HUMAN	R	232	ENSP00000355797:G232R	ENSP00000283507:G232R	G	+	1	0	TCP10L2	167512525	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-0.082000	0.11304	-0.235000	0.09767	-1.867000	0.00556	GGT	G|0.979;C|0.021	0.021	strong		0.602	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
MYO10	4651	hgsc.bcm.edu	37	5	16754991	16754991	+	Silent	SNP	C	C	T	rs61736777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16754991C>T	ENST00000513610.1	-	19	2329	c.1875G>A	c.(1873-1875)acG>acA	p.T625T		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	625	Myosin motor.				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						AGGAGCTTAGCGTTGCCATTA	0.398													C|||	153	0.0305511	0.1112	0.0072	5008	,	,		15693	0.0		0.001	False		,,,				2504	0.0				p.T625T		Atlas-SNP	.											.	MYO10	198	.	0			c.G1875A						PASS	.	C		322,3610		11,300,1655	69.0	66.0	67.0		1875	-11.5	0.0	5	dbSNP_129	67	4,8360		0,4,4178	no	coding-synonymous	MYO10	NM_012334.2		11,304,5833	TT,TC,CC		0.0478,8.1892,2.6513		625/2059	16754991	326,11970	1966	4182	6148	SO:0001819	synonymous_variant	4651	exon19			GCTTAGCGTTGCC	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.1875G>A	5.37:g.16754991C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			C|0.973;T|0.027	0.027	strong		0.398	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
CCKBR	887	hgsc.bcm.edu	37	11	6291120	6291120	+	Missense_Mutation	SNP	G	G	A	rs1805002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6291120G>A	ENST00000334619.2	+	2	566	c.373G>A	c.(373-375)Gtc>Atc	p.V125I	CCKBR_ENST00000532715.1_Intron|CCKBR_ENST00000525462.1_Missense_Mutation_p.V125I|CCKBR_ENST00000525014.1_Missense_Mutation_p.V125I	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	125			V -> I (in dbSNP:rs1805002).		cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	CTTTGGCACCGTCATCTGCAA	0.592													G|||	226	0.0451278	0.062	0.0346	5008	,	,		18733	0.0198		0.0636	False		,,,				2504	0.0368				p.V125I		Atlas-SNP	.											.	CCKBR	232	.	0			c.G373A	GRCh37	CM024094	CCKBR	M	rs1805002	PASS	.	G	ILE/VAL	250,4152	145.0+/-179.8	7,236,1958	83.0	69.0	74.0		373	3.9	1.0	11	dbSNP_89	74	458,8134	136.2+/-193.3	16,426,3854	yes	missense	CCKBR	NM_176875.2	29	23,662,5812	AA,AG,GG		5.3305,5.6792,5.4487	benign	125/448	6291120	708,12286	2201	4296	6497	SO:0001583	missense	887	exon2			GGCACCGTCATCT	D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"""GPCR / Class A : Cholecystokinin receptors"""	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.373G>A	11.37:g.6291120G>A	ENSP00000335544:p.Val125Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	37	CCDS7761.1	100	0.045787545787545784	30	0.06097560975609756	14	0.03867403314917127	13	0.022727272727272728	43	0.05672823218997362	G	16.88	3.245072	0.59103	0.056792	0.053305	ENSG00000110148	ENST00000334619;ENST00000525014;ENST00000525462	T;T;T	0.72051	-0.62;-0.62;-0.62	4.83	3.9	0.45041	GPCR, rhodopsin-like superfamily (1);	0.234868	0.35615	N	0.003083	T	0.12860	0.0312	L	0.41632	1.29	0.27696	N	0.945969	P;B;P	0.43231	0.801;0.334;0.462	B;B;B	0.33750	0.081;0.038;0.169	T	0.12218	-1.0556	10	0.34782	T	0.22	.	13.1706	0.59595	0.0:0.0:0.8388:0.1612	rs1805002;rs17239904;rs17846997;rs52798899;rs60198583;rs1805002	125;59;125	P32239-2;P32239-3;P32239	.;.;GASR_HUMAN	I	125	ENSP00000335544:V125I;ENSP00000437001:V125I;ENSP00000435534:V125I	ENSP00000335544:V125I	V	+	1	0	CCKBR	6247696	0.997000	0.39634	0.996000	0.52242	0.910000	0.53928	4.442000	0.59988	1.233000	0.43693	0.563000	0.77884	GTC	G|0.949;A|0.051	0.051	strong		0.592	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875	
DPYSL2	1808	hgsc.bcm.edu	37	8	26441477	26441477	+	Silent	SNP	G	G	A	rs11786691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:26441477G>A	ENST00000311151.5	+	3	703	c.291G>A	c.(289-291)ctG>ctA	p.L97L	DPYSL2_ENST00000523027.1_Silent_p.L61L|DPYSL2_ENST00000521913.1_Silent_p.L61L	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	97					axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)			breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		AGGCGGCCCTGGCTGGGGGAA	0.463													G|||	352	0.0702875	0.0696	0.0908	5008	,	,		19439	0.002		0.1312	False		,,,				2504	0.0644				p.L202L		Atlas-SNP	.											.	DPYSL2	49	.	0			c.G606A						PASS	.	G	,	357,4049	182.2+/-210.1	6,345,1852	101.0	103.0	102.0		606,291	3.6	1.0	8	dbSNP_120	102	1045,7555	222.7+/-259.7	58,929,3313	no	coding-synonymous,coding-synonymous	DPYSL2	NM_001197293.2,NM_001386.5	,	64,1274,5165	AA,AG,GG		12.1512,8.1026,10.7796	,	202/678,97/573	26441477	1402,11604	2203	4300	6503	SO:0001819	synonymous_variant	1808	exon3			GGCCCTGGCTGGG	D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964			3014	protein-coding gene	gene with protein product		602463				8973361	Standard	NM_001197293		Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000311151.5:c.291G>A	8.37:g.26441477G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_001197293	A8K5H2|B4DR31|D3DSS7|O00424	Silent	SNP	ENST00000311151.5	37	CCDS6051.1																																																																																			G|0.903;A|0.097	0.097	strong		0.463	DPYSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216904.3	NM_001386	
ZNF460	10794	hgsc.bcm.edu	37	19	57802824	57802824	+	Silent	SNP	G	G	A	rs2041110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57802824G>A	ENST00000360338.3	+	3	1237	c.915G>A	c.(913-915)aaG>aaA	p.K305K	ZNF460_ENST00000537645.1_Silent_p.K264K	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	305					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ACAATGAGAAGAAACCCTTCG	0.463													a|||	933	0.186302	0.0983	0.3084	5008	,	,		23078	0.1657		0.2515	False		,,,				2504	0.1728				p.K305K		Atlas-SNP	.											.	ZNF460	59	.	0			c.G915A						PASS	.	A		534,3872	776.9+/-414.2	29,476,1698	100.0	89.0	93.0		915	-3.0	0.0	19	dbSNP_94	93	2197,6403	711.0+/-405.8	294,1609,2397	no	coding-synonymous	ZNF460	NM_006635.3		323,2085,4095	AA,AG,GG		25.5465,12.1198,20.998		305/563	57802824	2731,10275	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			TGAGAAGAAACCC	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.915G>A	19.37:g.57802824G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			G|0.806;A|0.194	0.194	strong		0.463	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
PRF1	5551	hgsc.bcm.edu	37	10	72358407	72358407	+	Missense_Mutation	SNP	C	C	T	rs140787739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72358407C>T	ENST00000441259.1	-	3	1230	c.1070G>A	c.(1069-1071)cGg>cAg	p.R357Q	PRF1_ENST00000373209.2_Missense_Mutation_p.R357Q	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	357	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CAGTGCCTCCCGCCGCGGGTC	0.697			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				C|||	2	0.000399361	0.0008	0.0	5008	,	,		16023	0.0		0.0	False		,,,				2504	0.001				p.R357Q		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	PRF1,caecum,carcinoma,-1,1	PRF1	64	1	0			c.G1070A						PASS	.	C	GLN/ARG,GLN/ARG	5,4399		0,5,2197	19.0	23.0	22.0		1070,1070	4.9	1.0	10	dbSNP_134	22	2,8588		0,2,4293	yes	missense,missense	PRF1	NM_001083116.1,NM_005041.4	43,43	0,7,6490	TT,TC,CC		0.0233,0.1135,0.0539	probably-damaging,probably-damaging	357/556,357/556	72358407	7,12987	2202	4295	6497	SO:0001583	missense	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCCTCCCGCCGCG	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.1070G>A	10.37:g.72358407C>T	ENSP00000398568:p.Arg357Gln	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	37	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	C	18.09	3.547379	0.65311	0.001135	2.33E-4	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.85013	-1.93;-1.93	5.83	4.92	0.64577	Membrane attack complex component/perforin (MACPF) domain (3);	0.263415	0.37669	N	0.001991	D	0.88463	0.6443	M	0.66378	2.025	0.41451	D	0.987985	D	0.76494	0.999	P	0.61940	0.896	D	0.87239	0.2265	10	0.44086	T	0.13	-49.1524	7.9431	0.29969	0.0:0.8314:0.0:0.1686	.	357	P14222	PERF_HUMAN	Q	357	ENSP00000362305:R357Q;ENSP00000398568:R357Q	ENSP00000316746:R357Q	R	-	2	0	PRF1	72028413	0.050000	0.20438	0.966000	0.40874	0.070000	0.16714	0.384000	0.20668	2.741000	0.93983	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.697	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
LRRC56	115399	hgsc.bcm.edu	37	11	549949	549949	+	Missense_Mutation	SNP	G	G	A	rs371135949		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:549949G>A	ENST00000270115.7	+	7	874	c.374G>A	c.(373-375)cGc>cAc	p.R125H		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	125										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGCTGGCTCGCTGTGGCCTC	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		18623	0.001		0.0	False		,,,				2504	0.0				p.R125H		Atlas-SNP	.											.	LRRC56	23	.	0			c.G374A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	64.0	56.0	59.0		374	3.8	1.0	11		59	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRRC56	NM_198075.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	125/543	549949	1,13005	2203	4300	6503	SO:0001583	missense	115399	exon7			TGGCTCGCTGTGG		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.374G>A	11.37:g.549949G>A	ENSP00000270115:p.Arg125His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	75	27	0.36	NM_198075	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	37	CCDS7700.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.809742	0.70797	0.0	1.16E-4	ENSG00000161328	ENST00000270115	T	0.09538	2.97	4.71	3.8	0.43715	.	0.119263	0.64402	D	0.000014	T	0.21921	0.0528	L	0.46819	1.47	0.40148	D	0.976912	D	0.89917	1.0	D	0.81914	0.995	T	0.01256	-1.1404	10	0.72032	D	0.01	-17.8379	7.3187	0.26515	0.1956:0.0:0.8044:0.0	.	125	Q8IYG6	LRC56_HUMAN	H	125	ENSP00000270115:R125H	ENSP00000270115:R125H	R	+	2	0	LRRC56	539949	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	3.731000	0.55013	1.219000	0.43474	-0.186000	0.12905	CGC	.	.	weak		0.667	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075	
MAPT	4137	hgsc.bcm.edu	37	17	44061123	44061123	+	Missense_Mutation	SNP	C	C	T	rs73314997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:44061123C>T	ENST00000571987.1	+	5	953	c.953C>T	c.(952-954)tCg>tTg	p.S318L	MAPT_ENST00000351559.5_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.S318L|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.S318L|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.S318L|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000334239.8_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	318					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)	CAGGCGCACTCGGAGGAGCAT	0.637													C|||	277	0.0553115	0.2005	0.0144	5008	,	,		15384	0.0		0.002	False		,,,				2504	0.0				p.S318L		Atlas-SNP	.											MAPT,NS,carcinoma,-1,1	MAPT	135	1	0			c.C953T						PASS	.	C	LEU/SER,,,,,,LEU/SER,	759,3647	278.4+/-274.2	71,617,1515	35.0	41.0	39.0		953,,,,,,953,	4.4	0.0	17	dbSNP_130	39	13,8587	9.8+/-36.6	0,13,4287	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	145,,,,,,145,	71,630,5802	TT,TC,CC		0.1512,17.2265,5.9357	benign,,,,,,benign,	318/777,,,,,,318/759,	44061123	772,12234	2203	4300	6503	SO:0001583	missense	4137	exon6			CGCACTCGGAGGA	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.953C>T	17.37:g.44061123C>T	ENSP00000458742:p.Ser318Leu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	106	0.048534798534798536	97	0.19715447154471544	7	0.019337016574585635	0	0.0	2	0.002638522427440633	C	14.68	2.608431	0.46527	0.172265	0.001512	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.13657	2.6;2.57;2.6	4.38	4.38	0.52667	.	0.538008	0.14116	N	0.340390	T	0.00012	0.0000	L	0.47716	1.5	0.21355	P	0.999712994	B;B	0.29766	0.229;0.256	B;B	0.26202	0.052;0.067	T	0.24693	-1.0153	9	0.37606	T	0.19	0.1936	12.6117	0.56554	0.0:1.0:0.0:0.0	.	318;318	P10636-9;P10636	.;TAU_HUMAN	L	318	ENSP00000340820:S318L;ENSP00000262410:S318L;ENSP00000410838:S318L	ENSP00000262410:S318L	S	+	2	0	MAPT	41416960	0.001000	0.12720	0.004000	0.12327	0.004000	0.04260	1.349000	0.33998	2.440000	0.82611	0.561000	0.74099	TCG	C|0.655;A|0.015	.	strong		0.637	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
DIO1	1733	hgsc.bcm.edu	37	1	54359922	54359922	+	Silent	SNP	C	C	T	rs2294510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54359922C>T	ENST00000361921.3	+	1	63	c.39C>T	c.(37-39)ctC>ctT	p.L13L	DIO1_ENST00000322679.6_Silent_p.L13L|DIO1_ENST00000525202.1_Silent_p.L13L|DIO1_ENST00000534069.1_Intron|DIO1_ENST00000532493.1_Silent_p.L13L|DIO1_ENST00000524406.1_5'UTR|DIO1_ENST00000388876.3_Silent_p.L13L	NM_000792.5|NM_213593.3	NP_000783.2|NP_998758.1	P49895	IOD1_HUMAN	deiodinase, iodothyronine, type I	13					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)			cervix(1)|endometrium(2)|large_intestine(3)|lung(2)|skin(1)	9						TGAAGAGGCTCTGGGTGCTCT	0.577													C|||	510	0.101837	0.236	0.0548	5008	,	,		18471	0.1071		0.0408	False		,,,				2504	0.0112				p.L13L		Atlas-SNP	.											.	DIO1	66	.	0			c.C39T						PASS	.	C	,,,	933,3473	355.6+/-313.1	95,743,1365	89.0	79.0	82.0		39,39,39,39	-0.2	0.9	1	dbSNP_100	82	367,8233	121.8+/-180.9	12,343,3945	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIO1	NM_000792.5,NM_001039715.1,NM_001039716.1,NM_213593.3	,,,	107,1086,5310	TT,TC,CC		4.2674,21.1757,9.9954	,,,	13/250,13/202,13/162,13/186	54359922	1300,11706	2203	4300	6503	SO:0001819	synonymous_variant	1733	exon1			GAGGCTCTGGGTG		CCDS30722.1, CCDS41339.1, CCDS41340.1, CCDS53320.1	1p33-p32	2012-03-01			ENSG00000211452	ENSG00000211452	1.97.1.10		2883	protein-coding gene	gene with protein product		147892		TXDI1		8964838	Standard	NM_000792		Approved		uc001cwb.3	P49895	OTTHUMG00000008435	ENST00000361921.3:c.39C>T	1.37:g.54359922C>T		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	241	117	0.485477	NM_001039715	Q1RN02|Q3KNP8|Q6Q4C1|Q6Q4C2|Q6Q4C3|Q6Q4C4|Q6Q4C5|Q6Q4C6|Q6Q4C7|Q6Q4C9|Q8WWC6	Silent	SNP	ENST00000361921.3	37	CCDS41339.1																																																																																			C|0.898;T|0.102	0.102	strong		0.577	DIO1-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000023247.3		
MAGI3	260425	hgsc.bcm.edu	37	1	113933814	113933814	+	Silent	SNP	C	C	T	rs182574963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113933814C>T	ENST00000307546.9	+	1	234	c.159C>T	c.(157-159)ggC>ggT	p.G53G	MAGI3_ENST00000369617.4_Silent_p.G53G|MAGI3_ENST00000369611.4_Silent_p.G53G|MAGI3_ENST00000369615.1_Silent_p.G53G|MAGI3_ENST00000486456.1_3'UTR	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	53	Interaction with ADRB1 and TGFA. {ECO:0000250}.|PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGAGCCCGGCGGGGGCACCT	0.746													C|||	31	0.0061901	0.0204	0.0058	5008	,	,		9388	0.0		0.0	False		,,,				2504	0.0				p.G53G		Atlas-SNP	.											.	MAGI3	181	.	0			c.C159T						PASS	.	C	,	45,4037		0,45,1996	5.0	7.0	6.0		159,159	2.9	1.0	1		6	2,8118		0,2,4058	no	coding-synonymous,coding-synonymous	MAGI3	NM_001142782.1,NM_152900.2	,	0,47,6054	TT,TC,CC		0.0246,1.1024,0.3852	,	53/1482,53/1126	113933814	47,12155	2041	4060	6101	SO:0001819	synonymous_variant	260425	exon1			GCCCGGCGGGGGC	AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.159C>T	1.37:g.113933814C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	35	26	0.742857	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Silent	SNP	ENST00000307546.9	37	CCDS44196.1																																																																																			C|0.994;T|0.006	0.006	strong		0.746	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900	
POTEF	728378	hgsc.bcm.edu	37	2	130872871	130872871	+	Silent	SNP	C	C	T	rs199770435		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000357462.5_Silent_p.G184G|POTEF_ENST00000360967.5_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	724	1	0.00138122		WXS	Illumina HiSeq	Phase_I	720	25	0.0347222	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	
OR8H3	390152	hgsc.bcm.edu	37	11	55889987	55889987	+	Missense_Mutation	SNP	C	C	A	rs7107077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	301	0	0		WXS	Illumina HiSeq	Phase_I	349	98	0.280802	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	
RBMXL1	494115	hgsc.bcm.edu	37	1	89449168	89449168	+	Silent	SNP	T	T	A	rs59048247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89449168T>A	ENST00000321792.5	-	2	769	c.342A>T	c.(340-342)ggA>ggT	p.G114G	CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000399794.2_Silent_p.G114G|CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000413769.1_5'UTR	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	114					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										CTCCACTTCCTCCTCTTCCAG	0.512													.|||	318	0.0634984	0.2292	0.0187	5008	,	,		19592	0.0		0.002	False		,,,				2504	0.0				p.G114G		Atlas-SNP	.											.	.	.	.	0			c.A342T						PASS	.	T	,,,	876,3530	339.1+/-305.6	83,710,1410	90.0	98.0	96.0		,,342,342	-0.4	0.5	1	dbSNP_129	96	10,8590	7.1+/-27.0	0,10,4290	no	intron,intron,coding-synonymous,coding-synonymous	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	,,,	83,720,5700	AA,AT,TT		0.1163,19.882,6.8122	,,,	,,114/391,114/391	89449168	886,12120	2203	4300	6503	SO:0001819	synonymous_variant	494115	exon3			ACTTCCTCCTCTT	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.342A>T	1.37:g.89449168T>A		Somatic	394	0	0		WXS	Illumina HiSeq	Phase_I	338	150	0.443787	NM_001162536		Silent	SNP	ENST00000321792.5	37	CCDS716.1																																																																																			T|0.940;A|0.060	0.060	strong		0.512	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
DNAH14	127602	hgsc.bcm.edu	37	1	225539363	225539363	+	Missense_Mutation	SNP	G	G	A	rs12408617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225539363G>A	ENST00000445597.2	+	50	8623	c.8623G>A	c.(8623-8625)Ggt>Agt	p.G2875S	DNAH14_ENST00000430092.1_Missense_Mutation_p.G3678S|DNAH14_ENST00000439375.2_Missense_Mutation_p.G3678S			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2875					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						ATTTGAAATAGGTGAAAGTCA	0.378													G|||	435	0.086861	0.2368	0.0591	5008	,	,		15648	0.0337		0.0338	False		,,,				2504	0.0133				p.G3678S		Atlas-SNP	.											.	DNAH14	300	.	0			c.G11032A						PASS	.	G	SER/GLY	294,1090		34,226,432	87.0	76.0	80.0		11032	-8.0	0.0	1	dbSNP_120	80	157,3025		5,147,1439	yes	missense	DNAH14	NM_001373.1	56	39,373,1871	AA,AG,GG		4.934,21.2428,9.8774	benign	3678/4516	225539363	451,4115	692	1591	2283	SO:0001583	missense	127602	exon70			GAAATAGGTGAAA	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.8623G>A	1.37:g.225539363G>A	ENSP00000409472:p.Gly2875Ser	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		164	0.07509157509157509	109	0.22154471544715448	15	0.04143646408839779	14	0.024475524475524476	26	0.03430079155672823	G	2.400	-0.337782	0.05278	0.212428	0.04934	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.39997	1.05;1.05;1.05	5.18	-8.02	0.01118	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24835	-1.0149	7	0.09338	T	0.73	.	0.648	0.00821	0.186:0.2451:0.2699:0.2989	rs12408617;rs52793546;rs61441315;rs12408617	3678	Q0VDD8-4	.	S	2875;3678;3678	ENSP00000409472:G2875S;ENSP00000414402:G3678S;ENSP00000392061:G3678S	ENSP00000414402:G3678S	G	+	1	0	DNAH14	223605986	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.596000	0.05720	-1.072000	0.03141	-0.232000	0.12228	GGT	G|0.910;A|0.090	0.090	strong		0.378	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
CLEC18A	348174	hgsc.bcm.edu	37	16	69996928	69996928	+	Missense_Mutation	SNP	G	G	A	rs201545424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69996928G>A	ENST00000288040.6	+	11	1448	c.1261G>A	c.(1261-1263)Gac>Aac	p.D421N	CLEC18A_ENST00000568461.1_Missense_Mutation_p.D421N|CLEC18A_ENST00000393701.2_Missense_Mutation_p.D421N|CLEC18A_ENST00000449317.2_Missense_Mutation_p.D430N	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	421	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.			D -> N (in Ref. 4; AAH78143). {ECO:0000305}.		extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						CAACTGGAACGACCAGCGCTG	0.597																																					p.D421N		Atlas-SNP	.											CLEC18A,NS,carcinoma,0,1	CLEC18A	9	1	0			c.G1261A						scavenged	.						50.0	33.0	39.0					16																	69996928		2178	3959	6137	SO:0001583	missense	348174	exon12			TGGAACGACCAGC	AF428259	CCDS10886.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157322		"""C-type lectin domain containing"""	30388	protein-coding gene	gene with protein product	"""mannose receptor-like"""					12975309	Standard	NM_001136214		Approved	MRCL	uc010vlo.3	A5D8T8		ENST00000288040.6:c.1261G>A	16.37:g.69996928G>A	ENSP00000288040:p.Asp421Asn	Somatic	502	0	0		WXS	Illumina HiSeq	Phase_I	489	21	0.0429448	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Missense_Mutation	SNP	ENST00000288040.6	37	CCDS10886.1	.	.	.	.	.	.	.	.	.	.	.	15.17	2.752501	0.49362	.	.	ENSG00000157322	ENST00000393701;ENST00000449317;ENST00000288040	T;T;T	0.59906	0.23;0.23;0.23	1.77	1.77	0.24775	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	0.063063	0.64402	D	0.000011	T	0.64249	0.2581	L	0.52364	1.645	0.33125	D	0.542299	D	0.76494	0.999	D	0.83275	0.996	T	0.68454	-0.5404	9	.	.	.	.	7.0966	0.25313	0.0:0.0:1.0:0.0	.	421	A5D8T8	CL18A_HUMAN	N	421;430;421	ENSP00000377304:D421N;ENSP00000413990:D430N;ENSP00000288040:D421N	.	D	+	1	0	CLEC18A	68554429	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	3.563000	0.53784	1.309000	0.44985	0.175000	0.17021	GAC	G|0.500;A|0.500	0.500	weak		0.597	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619	
IFNA4	3441	hgsc.bcm.edu	37	9	21187146	21187146	+	Missense_Mutation	SNP	C	C	T	rs201186279		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21187146C>T	ENST00000421715.1	-	1	452	c.385G>A	c.(385-387)Gtg>Atg	p.V129M		NM_021068.2	NP_066546.1	P05014	IFNA4_HUMAN	interferon, alpha 4	129					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)	p.V129M(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17				GBM - Glioblastoma multiforme(5;2.69e-202)|Lung(24;2.26e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		GTCTCTTCCACCCCAACCTCC	0.458													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19919	0.0		0.0	False		,,,				2504	0.0				p.V129M	NSCLC(154;890 1986 23660 27800 51138)	Atlas-SNP	.											IFNA4,NS,carcinoma,0,1	IFNA4	34	1	1	Substitution - Missense(1)	endometrium(1)	c.G385A						scavenged	.						35.0	38.0	37.0					9																	21187146		2182	4253	6435	SO:0001583	missense	3441	exon1			CTTCCACCCCAAC		CCDS6498.1	9p22	2010-08-24			ENSG00000236637	ENSG00000236637		"""Interferons"""	5425	protein-coding gene	gene with protein product		147564				1385305	Standard	NM_021068		Approved	MGC142200, IFN-alpha4a	uc003zon.2	P05014	OTTHUMG00000019660	ENST00000421715.1:c.385G>A	9.37:g.21187146C>T	ENSP00000412897:p.Val129Met	Somatic	513	2	0.00389864		WXS	Illumina HiSeq	Phase_I	736	68	0.0923913	NM_021068	P13358|Q14CS4|Q5VV15	Missense_Mutation	SNP	ENST00000421715.1	37	CCDS6498.1	.	.	.	.	.	.	.	.	.	.	-	4.271	0.049496	0.08243	.	.	ENSG00000236637	ENST00000421715	T	0.03441	3.93	2.96	-5.93	0.02254	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.507550	0.03550	N	0.225260	T	0.05593	0.0147	M	0.73319	2.225	0.09310	N	1	B	0.18741	0.03	B	0.28305	0.088	T	0.38351	-0.9665	10	0.52906	T	0.07	.	1.8132	0.03095	0.1267:0.2025:0.3717:0.2991	.	129	P05014	IFNA4_HUMAN	M	129	ENSP00000412897:V129M	ENSP00000412897:V129M	V	-	1	0	IFNA4	21177146	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.851000	0.01669	-1.988000	0.00980	-1.417000	0.01113	GTG	.	.	weak		0.458	IFNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051889.1	NM_021068	
ESR2	2100	hgsc.bcm.edu	37	14	64724051	64724051	+	Silent	SNP	C	C	T	rs1256049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64724051C>T	ENST00000341099.4	-	6	1401	c.984G>A	c.(982-984)gtG>gtA	p.V328V	ESR2_ENST00000555278.1_Silent_p.V328V|ESR2_ENST00000353772.3_Silent_p.V328V|ESR2_ENST00000554572.1_Silent_p.V328V|ESR2_ENST00000542956.1_Silent_p.V328V|ESR2_ENST00000555483.1_5'UTR|ESR2_ENST00000557772.1_Silent_p.V328V|ESR2_ENST00000267525.6_Intron|ESR2_ENST00000358599.5_Silent_p.V328V|ESR2_ENST00000553796.1_Silent_p.V328V|ESR2_ENST00000357782.2_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	117	0	0		WXS	Illumina HiSeq	Phase_I	152	74	0.486842	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		
NSUN4	387338	hgsc.bcm.edu	37	1	46810530	46810530	+	Missense_Mutation	SNP	A	A	G	rs3737744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46810530A>G	ENST00000474844.1	+	2	801	c.151A>G	c.(151-153)Act>Gct	p.T51A	NSUN4_ENST00000536062.1_Missense_Mutation_p.T2A|NSUN4_ENST00000537428.1_Missense_Mutation_p.T2A|NSUN4_ENST00000498008.1_3'UTR	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	51			T -> A (in dbSNP:rs3737744). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)			endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					TTTTGACATGACTTACAGTGT	0.483													A|||	1525	0.304513	0.1415	0.3559	5008	,	,		23393	0.5169		0.3419	False		,,,				2504	0.2311				p.T51A		Atlas-SNP	.											.	NSUN4	26	.	0			c.A151G						PASS	.	A	ALA/THR	801,3605	321.5+/-297.2	77,647,1479	177.0	173.0	175.0		151	5.4	1.0	1	dbSNP_107	175	2849,5751	449.1+/-362.0	466,1917,1917	yes	missense	NSUN4	NM_199044.2	58	543,2564,3396	GG,GA,AA		33.1279,18.1798,28.064	benign	51/385	46810530	3650,9356	2203	4300	6503	SO:0001583	missense	387338	exon2			GACATGACTTACA	AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"""NOP2/Sun domain containing"""	31802	protein-coding gene	gene with protein product	"""sperm head and tail associated protein"""	615394	"""NOL1/NOP2/Sun domain family 4"", ""NOL1/NOP2/Sun domain family, member 4"""				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	ENST00000474844.1:c.151A>G	1.37:g.46810530A>G	ENSP00000419740:p.Thr51Ala	Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	227	107	0.471366	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Missense_Mutation	SNP	ENST00000474844.1	37	CCDS534.1	775	0.35485347985347987	81	0.16463414634146342	143	0.39502762430939226	282	0.493006993006993	269	0.3548812664907652	A	16.01	3.001459	0.54254	0.181798	0.331279	ENSG00000117481	ENST00000474844;ENST00000536062;ENST00000537428	T;T;T	0.14516	2.54;2.5;2.5	5.45	5.45	0.79879	.	0.207467	0.49916	D	0.000140	T	0.00012	0.0000	L	0.46157	1.445	0.24446	P	0.99450097	B	0.11235	0.004	B	0.10450	0.005	T	0.47381	-0.9122	9	0.17369	T	0.5	-15.6344	15.1862	0.73002	1.0:0.0:0.0:0.0	rs3737744;rs3895370;rs17845416;rs17858282;rs52835213;rs61120032;rs3737744	51	Q96CB9	NSUN4_HUMAN	A	51;2;2	ENSP00000419740:T51A;ENSP00000438912:T2A;ENSP00000437758:T2A	ENSP00000419740:T51A	T	+	1	0	NSUN4	46583117	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.480000	0.66820	2.080000	0.62538	0.460000	0.39030	ACT	G|0.311;N|0.000	0.311	strong		0.483	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	
YTHDC2	64848	hgsc.bcm.edu	37	5	112871458	112871458	+	Silent	SNP	C	C	G	rs77052070	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112871458C>G	ENST00000161863.4	+	7	1278	c.1065C>G	c.(1063-1065)ctC>ctG	p.L355L	YTHDC2_ENST00000515883.1_Silent_p.L355L	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	355	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)		ATGTAAATCTCTTTATAAGAT	0.279													C|||	63	0.0125799	0.0477	0.0	5008	,	,		17937	0.0		0.0	False		,,,				2504	0.0				p.L355L		Atlas-SNP	.											.	YTHDC2	118	.	0			c.C1065G						PASS	.	C		214,4190	128.6+/-165.4	2,210,1990	49.0	54.0	52.0		1065	-5.6	0.5	5	dbSNP_131	52	0,8594		0,0,4297	no	coding-synonymous	YTHDC2	NM_022828.3		2,210,6287	GG,GC,CC		0.0,4.8592,1.6464		355/1431	112871458	214,12784	2202	4297	6499	SO:0001819	synonymous_variant	64848	exon7			AAATCTCTTTATA	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.1065C>G	5.37:g.112871458C>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	109	41	0.376147	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																			C|0.984;G|0.016	0.016	strong		0.279	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
NOL8	55035	hgsc.bcm.edu	37	9	95076833	95076833	+	Missense_Mutation	SNP	C	C	G	rs373764183		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95076833C>G	ENST00000535387.1	-	6	2073	c.2074G>C	c.(2074-2076)Ggc>Cgc	p.G692R	NOL8_ENST00000358855.4_Missense_Mutation_p.G624R|NOL8_ENST00000442668.2_Missense_Mutation_p.G692R|NOL8_ENST00000545558.1_Missense_Mutation_p.G692R|NOL8_ENST00000542053.1_Missense_Mutation_p.G624R					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TTGTCAAAGCCTATGTTGTGA	0.433																																					p.G692R		Atlas-SNP	.											.	NOL8	118	.	0			c.G2074C						PASS	.	C	ARG/GLY	1,3761		0,1,1880	37.0	33.0	35.0		2074	1.5	0.0	9		35	0,8226		0,0,4113	no	missense	NOL8	NM_017948.5	125	0,1,5993	GG,GC,CC		0.0,0.0266,0.0083	probably-damaging	692/1168	95076833	1,11987	1881	4113	5994	SO:0001583	missense	55035	exon7			CAAAGCCTATGTT	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.2074G>C	9.37:g.95076833C>G	ENSP00000441300:p.Gly692Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	97	65	0.670103	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.582405	0.28180	2.66E-4	0.0	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77	5.48	1.52	0.23074	.	1.217900	0.05599	N	0.576075	T	0.33556	0.0867	L	0.29908	0.895	0.09310	N	1	P	0.41265	0.744	B	0.39068	0.289	T	0.21793	-1.0235	10	0.52906	T	0.07	0.5806	1.5277	0.02529	0.1481:0.4632:0.1439:0.2448	.	692	Q76FK4	NOL8_HUMAN	R	692;694;624;692;692;624;692	ENSP00000401177:G692R;ENSP00000351723:G624R;ENSP00000441140:G692R;ENSP00000441300:G692R;ENSP00000440709:G624R;ENSP00000414112:G692R	ENSP00000351723:G624R	G	-	1	0	NOL8	94116654	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	0.191000	0.17076	0.018000	0.15052	0.561000	0.74099	GGC	.	.	weak		0.433	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
MSH5	4439	hgsc.bcm.edu	37	6	31709045	31709045	+	Missense_Mutation	SNP	C	C	T	rs28381349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31709045C>T	ENST00000375755.3	+	3	539	c.253C>T	c.(253-255)Ctc>Ttc	p.L85F	MSH5_ENST00000482280.1_3'UTR|MSH5_ENST00000534153.4_Missense_Mutation_p.L85F|MSH5_ENST00000375750.3_Missense_Mutation_p.L85F|MSH5-SAPCD1_ENST00000493662.2_Missense_Mutation_p.L85F|MSH5_ENST00000375742.3_Missense_Mutation_p.L85F|MSH5_ENST00000375740.3_Missense_Mutation_p.L85F|CLIC1_ENST00000395892.1_5'Flank|MSH5_ENST00000375703.3_Missense_Mutation_p.L85F	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	85			L -> F (in dbSNP:rs28381349). {ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						CCACGAGAGCCTCAAGCTTCT	0.502								Direct reversal of damage;Mismatch excision repair (MMR)					C|||	163	0.0325479	0.0772	0.062	5008	,	,		17256	0.0		0.0169	False		,,,				2504	0.001				p.L85F		Atlas-SNP	.											.	MSH5	108	.	0			c.C253T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	207,2815		6,195,1310	237.0	213.0	222.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	253,253,253,253	5.0	1.0	6	dbSNP_125	222	115,5303		1,113,2595	yes	missense,missense,missense,missense	MSH5	NM_002441.4,NM_025259.5,NM_172165.3,NM_172166.3	22,22,22,22	7,308,3905	TT,TC,CC		2.1226,6.8498,3.8152	benign,benign,benign,benign	85/835,85/823,85/836,85/835	31709045	322,8118	1511	2709	4220	SO:0001583	missense	4439	exon3			GAGAGCCTCAAGC	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.253C>T	6.37:g.31709045C>T	ENSP00000364908:p.Leu85Phe	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	120	54	0.45	NM_172165	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Missense_Mutation	SNP	ENST00000375755.3	37	CCDS4720.1	82	0.037545787545787544	46	0.09349593495934959	22	0.06077348066298342	0	0.0	14	0.018469656992084433	C	9.092	1.002008	0.19121	0.068498	0.021226	ENSG00000204410	ENST00000375755;ENST00000375742;ENST00000375750;ENST00000425703;ENST00000534153;ENST00000375703;ENST00000375740	T;T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53;0.53	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000004	T	0.20007	0.0481	L	0.31420	0.93	0.41340	P	0.012704999999999966	B;B;B;B	0.32717	0.127;0.013;0.007;0.381	B;B;B;B	0.32533	0.049;0.013;0.025;0.147	T	0.06991	-1.0796	9	0.14656	T	0.56	-22.2256	9.4858	0.38928	0.0:0.9033:0.0:0.0967	rs28381349;rs28381349	85;85;85;85	O43196-4;O43196;O43196-2;O43196-3	.;MSH5_HUMAN;.;.	F	85	ENSP00000364908:L85F;ENSP00000364894:L85F;ENSP00000364903:L85F;ENSP00000402842:L85F;ENSP00000431693:L85F;ENSP00000364855:L85F;ENSP00000364892:L85F	ENSP00000364855:L85F	L	+	1	0	MSH5	31817024	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.032000	0.57274	2.348000	0.79779	0.650000	0.86243	CTC	C|0.957;T|0.043	0.043	strong		0.502	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4		
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39412125	39412125	+	Missense_Mutation	SNP	G	G	C	rs144403228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39412125G>C	ENST00000394008.1	+	1	490	c.488G>C	c.(487-489)tGc>tCc	p.C163S		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	148						keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GTGTCCAGCTGCTGCCAGCCT	0.557													.|||	77	0.0153754	0.056	0.0043	5008	,	,		22420	0.0		0.0	False		,,,				2504	0.0				p.C163S		Atlas-SNP	.											.	KRTAP9-9	24	.	0			c.G488C						PASS	.	G	SER/CYS	216,4190		6,204,1993	163.0	170.0	167.0		488	3.7	1.0	17	dbSNP_134	167	2,8598		0,2,4298	yes	missense	KRTAP9-9	NM_030975.2	112	6,206,6291	CC,CG,GG		0.0233,4.9024,1.6761	possibly-damaging	163/170	39412125	218,12788	2203	4300	6503	SO:0001583	missense	81870	exon1			CCAGCTGCTGCCA	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"""Keratin associated proteins"""	16773	protein-coding gene	gene with protein product			"""keratin associated protein 9-5"""	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.488G>C	17.37:g.39412125G>C	ENSP00000377576:p.Cys163Ser	Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	263	129	0.490494	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	37	CCDS54127.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	.	23.2	4.383020	0.82792	0.049024	2.33E-4	ENSG00000198083	ENST00000431129;ENST00000394008	T	0.02323	4.34	3.68	3.68	0.42216	.	.	.	.	.	T	0.01976	0.0062	M	0.81497	2.545	0.30835	N	0.736277	D	0.89917	1.0	D	0.72982	0.979	T	0.00388	-1.1771	9	0.46703	T	0.11	.	11.5975	0.50981	0.0:0.0:1.0:0.0	.	148	Q9BYP9	KRA99_HUMAN	S	169;163	ENSP00000377576:C163S	ENSP00000377576:C163S	C	+	2	0	KRTAP9-9	36665651	0.998000	0.40836	0.998000	0.56505	0.904000	0.53231	1.282000	0.33226	1.971000	0.57363	0.462000	0.41574	TGC	G|0.987;C|0.013	0.013	strong		0.557	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975	
RIMKLA	284716	hgsc.bcm.edu	37	1	42880516	42880516	+	Silent	SNP	T	T	C	rs1055055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:42880516T>C	ENST00000431473.3	+	5	1176	c.1047T>C	c.(1045-1047)agT>agC	p.S349S		NM_173642.3	NP_775913.2	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family member A	349					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)	p.S308S(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						CTACCTCTAGTGAAAGTGAGC	0.552													C|||	2451	0.489417	0.5197	0.5173	5008	,	,		20089	0.3433		0.6441	False		,,,				2504	0.4202				p.S349S		Atlas-SNP	.											RIMKLA,NS,carcinoma,0,1	RIMKLA	32	1	1	Substitution - coding silent(1)	stomach(1)	c.T1047C						scavenged	.	C		2364,2042	566.4+/-381.9	644,1076,483	73.0	72.0	73.0		1047	-3.2	0.9	1	dbSNP_86	73	5474,3126	476.6+/-369.4	1759,1956,585	yes	coding-synonymous	RIMKLA	NM_173642.3		2403,3032,1068	CC,CT,TT		36.3488,46.3459,39.7355		349/392	42880516	7838,5168	2203	4300	6503	SO:0001819	synonymous_variant	284716	exon5			CTCTAGTGAAAGT	BC039737	CCDS466.2	1p34.2	2011-09-21	2008-10-13	2008-10-13	ENSG00000177181	ENSG00000177181	6.3.2.N6		28725	protein-coding gene	gene with protein product	"""N-acetylaspartylglutamate synthetase II"""		"""family with sequence similarity 80, member A"""	FAM80A		20657015, 21454531	Standard	NM_173642		Approved	MGC47816, RP11-157D18.1, NAAGS-II	uc001chi.2	Q8IXN7	OTTHUMG00000007335	ENST00000431473.3:c.1047T>C	1.37:g.42880516T>C		Somatic	86	3	0.0348837		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_173642	Q5VUS5	Silent	SNP	ENST00000431473.3	37	CCDS466.2																																																																																			T|0.444;C|0.556	0.556	strong		0.552	RIMKLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019174.3	NM_173642	
NEU4	129807	hgsc.bcm.edu	37	2	242757820	242757820	+	Missense_Mutation	SNP	G	G	A	rs11545301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242757820G>A	ENST00000391969.2	+	5	1612	c.901G>A	c.(901-903)Ggg>Agg	p.G301R	NEU4_ENST00000404257.1_Missense_Mutation_p.G313R|NEU4_ENST00000405370.1_Missense_Mutation_p.G301R|NEU4_ENST00000407683.1_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	93	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	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	
EXOSC8	11340	hgsc.bcm.edu	37	13	37580139	37580139	+	Silent	SNP	G	G	A	rs1127446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:37580139G>A	ENST00000389704.3	+	6	586	c.321G>A	c.(319-321)caG>caA	p.Q107Q	EXOSC8_ENST00000489088.1_3'UTR	NM_181503.2	NP_852480.1	Q96B26	EXOS8_HUMAN	exosome component 8	107					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)			biliary_tract(1)|breast(1)|kidney(2)|pancreas(1)|prostate(1)|skin(1)	7		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)		TGGCTAGCCAGTTCATTGCAG	0.413													G|||	2071	0.413538	0.0817	0.4236	5008	,	,		14507	0.7232		0.3797	False		,,,				2504	0.5706				p.Q107Q		Atlas-SNP	.											.	EXOSC8	16	.	0			c.G321A						PASS	.	G		624,3782	268.6+/-268.5	47,530,1626	92.0	87.0	89.0		321	4.2	1.0	13	dbSNP_86	89	3428,5172	505.0+/-376.3	692,2044,1564	no	coding-synonymous	EXOSC8	NM_181503.2		739,2574,3190	AA,AG,GG		39.8605,14.1625,31.1549		107/277	37580139	4052,8954	2203	4300	6503	SO:0001819	synonymous_variant	11340	exon6			TAGCCAGTTCATT	AF025438	CCDS31958.1	13q13.1	2010-05-07			ENSG00000120699	ENSG00000120699	3.1.13.-		17035	protein-coding gene	gene with protein product	"""CBP-interacting protein 3"", ""Opa interacting protein 2"""	606019				9466265, 11929972	Standard	NM_181503		Approved	OIP2, RRP43, bA421P11.3, Rrp43p, EAP2, p9, CIP3	uc001uwa.3	Q96B26	OTTHUMG00000016742	ENST00000389704.3:c.321G>A	13.37:g.37580139G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_181503	O43480|Q5TBA5	Silent	SNP	ENST00000389704.3	37	CCDS31958.1																																																																																			G|0.659;A|0.341	0.341	strong		0.413	EXOSC8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044535.2	NM_181503	
PSMB10	5699	hgsc.bcm.edu	37	16	67969930	67969930	+	Silent	SNP	A	A	G	rs20549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67969930A>G	ENST00000358514.4	-	4	656	c.319T>C	c.(319-321)Tta>Cta	p.L107L	CTC-479C5.12_ENST00000573493.1_5'Flank	NM_002801.3	NP_002792.1	P40306	PSB10_HUMAN	proteasome (prosome, macropain) subunit, beta type, 10	107					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)|cell morphogenesis (GO:0000902)|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)|humoral immune response (GO:0006959)|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)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			NS(2)|endometrium(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)	Carfilzomib(DB08889)	CCCGTAGATAACGCGTGTAGC	0.672													G|||	1594	0.318291	0.6861	0.2406	5008	,	,		14862	0.0972		0.1839	False		,,,				2504	0.2423				p.L107L		Atlas-SNP	.											.	PSMB10	19	.	0			c.T319C						PASS	.	G		2610,1786		782,1046,370	29.0	34.0	32.0		319	2.0	1.0	16	dbSNP_67	32	1502,7088		162,1178,2955	no	coding-synonymous	PSMB10	NM_002801.3		944,2224,3325	GG,GA,AA		17.4854,40.6278,31.6649		107/274	67969930	4112,8874	2198	4295	6493	SO:0001819	synonymous_variant	5699	exon4			TAGATAACGCGTG	Y13640	CCDS10853.1	16q22.1	2008-02-05			ENSG00000205220	ENSG00000205220		"""Proteasome (prosome, macropain) subunits"""	9538	protein-coding gene	gene with protein product		176847		MECL1		8268911	Standard	NM_002801		Approved	LMP10, MGC1665, beta2i	uc002eux.2	P40306	OTTHUMG00000137553	ENST00000358514.4:c.319T>C	16.37:g.67969930A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_002801	B2R5J4|Q5U098	Silent	SNP	ENST00000358514.4	37	CCDS10853.1																																																																																			T|0.000;G|0.310;A|0.690	0.310	strong		0.672	PSMB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268887.1	NM_002801	
LILRA1	11024	hgsc.bcm.edu	37	19	55107308	55107308	+	Missense_Mutation	SNP	G	G	C	rs35534776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55107308G>C	ENST00000251372.3	+	6	1048	c.866G>C	c.(865-867)cGc>cCc	p.R289P	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	289	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CCTGTGAGCCGCTCCTACGGG	0.647													g|||	1458	0.291134	0.5182	0.268	5008	,	,		14929	0.2758		0.0974	False		,,,				2504	0.2157				p.R289P		Atlas-SNP	.											LILRA1,NS,carcinoma,0,1	LILRA1	105	1	0			c.G866C						PASS	.						43.0	58.0	53.0					19																	55107308		2203	4300	6503	SO:0001583	missense	11024	exon6			TGAGCCGCTCCTA	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.866G>C	19.37:g.55107308G>C	ENSP00000251372:p.Arg289Pro	Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	210	200	0.952381	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	460	0.21062271062271062	193	0.39227642276422764	76	0.20994475138121546	141	0.2465034965034965	50	0.06596306068601583	G	0.637	-0.814876	0.02776	.	.	ENSG00000104974	ENST00000251372	T	0.11277	2.79	1.58	-3.16	0.05217	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.535700	0.01092	N	0.005193	T	0.00012	0.0000	N	0.11892	0.195	0.80722	P	0.0	B	0.06786	0.001	B	0.12156	0.007	T	0.47195	-0.9136	9	0.23302	T	0.38	.	1.3079	0.02092	0.1666:0.3949:0.2401:0.1984	rs35534776;rs61739252	289	O75019	LIRA1_HUMAN	P	289	ENSP00000251372:R289P	ENSP00000251372:R289P	R	+	2	0	LILRA1	59799120	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-1.648000	0.01995	-1.418000	0.02014	-1.052000	0.02337	CGC	G|0.851;C|0.149	0.149	strong		0.647	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
MEI1	150365	hgsc.bcm.edu	37	22	42177816	42177816	+	Silent	SNP	C	C	A	rs6002481	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42177816C>A	ENST00000401548.3	+	24	3094	c.3054C>A	c.(3052-3054)tcC>tcA	p.S1018S	MEI1_ENST00000300398.4_Silent_p.S26S|MEI1_ENST00000476893.1_3'UTR|MEI1_ENST00000540880.1_3'UTR|MEI1_ENST00000400107.1_Silent_p.S351S	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						TCACTGCCTCCTTCTCTGCCC	0.562													C|||	935	0.186701	0.5643	0.1153	5008	,	,		21119	0.0288		0.0209	False		,,,				2504	0.0603				p.S1018S		Atlas-SNP	.											.	MEI1	87	.	0			c.C3054A						PASS	.	C		1837,2289		415,1007,641	44.0	44.0	44.0		3054	-1.4	0.4	22	dbSNP_114	44	224,8252		4,216,4018	no	coding-synonymous	MEI1	NM_152513.3		419,1223,4659	AA,AC,CC		2.6428,44.5225,16.3545		1018/1275	42177816	2061,10541	2063	4238	6301	SO:0001819	synonymous_variant	150365	exon24			TGCCTCCTTCTCT	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"""spermatogenesis associated 38"""	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.3054C>A	22.37:g.42177816C>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	179	85	0.47486	NM_152513		Silent	SNP	ENST00000401548.3	37	CCDS46718.1																																																																																			C|0.832;A|0.168	0.168	strong		0.562	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513	
SLC37A2	219855	hgsc.bcm.edu	37	11	124955032	124955032	+	Silent	SNP	T	T	C	rs948268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124955032T>C	ENST00000403796.2	+	14	1546	c.1245T>C	c.(1243-1245)gaT>gaC	p.D415D	SLC37A2_ENST00000298280.5_3'UTR|SLC37A2_ENST00000407458.1_Silent_p.D415D|SLC37A2_ENST00000308074.4_Silent_p.D415D|SLC37A2_ENST00000525837.1_3'UTR	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	415					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		TCTCTGCTGATCTGGTGAGTG	0.617													C|||	3331	0.665136	0.9478	0.513	5008	,	,		17342	0.4643		0.6213	False		,,,				2504	0.6431				p.D415D	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.T1245C						PASS	.	C	,	3915,487	227.2+/-242.5	1747,421,33	60.0	61.0	61.0		1245,1245	3.0	1.0	11	dbSNP_86	61	5300,3298	492.6+/-373.4	1666,1968,665	no	coding-synonymous,coding-synonymous	SLC37A2	NM_001145290.1,NM_198277.2	,	3413,2389,698	CC,CT,TT		38.3578,11.0632,29.1154	,	415/502,415/506	124955032	9215,3785	2201	4299	6500	SO:0001819	synonymous_variant	219855	exon14			TGCTGATCTGGTG	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.1245T>C	11.37:g.124955032T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Silent	SNP	ENST00000403796.2	37	CCDS44757.1																																																																																			T|0.312;C|0.688	0.688	strong		0.617	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
IKBKE	9641	hgsc.bcm.edu	37	1	206666601	206666601	+	Silent	SNP	C	C	A	rs144382861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206666601C>A	ENST00000367120.3	+	20	2308	c.1935C>A	c.(1933-1935)ctC>ctA	p.L645L	C1orf147_ENST00000367119.1_Intron|IKBKE_ENST00000537984.1_Silent_p.L560L	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	645	Interaction with DDX3X.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					CCCTGCAGCTCCTGGAAGAGC	0.587													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17760	0.0		0.0	False		,,,				2504	0.0				p.L645L		Atlas-SNP	.											.	IKBKE	77	.	0			c.C1935A						PASS	.	C	,,	21,4385	28.1+/-56.4	0,21,2182	61.0	68.0	65.0		1680,,1935	2.0	1.0	1	dbSNP_134	65	0,8600		0,0,4300	no	coding-synonymous,intron,coding-synonymous	IKBKE	NM_001193321.1,NM_001193322.1,NM_014002.3	,,	0,21,6482	AA,AC,CC		0.0,0.4766,0.1615	,,	560/632,,645/717	206666601	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	9641	exon20			GCAGCTCCTGGAA	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.1935C>A	1.37:g.206666601C>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_014002	D3DT78|Q3B754|Q3KR43|Q5JTS6	Silent	SNP	ENST00000367120.3	37	CCDS30996.1																																																																																			C|0.999;A|0.001	0.001	strong		0.587	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
FCGBP	8857	hgsc.bcm.edu	37	19	40368330	40368330	+	Missense_Mutation	SNP	C	C	T	rs74540349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40368330C>T	ENST00000221347.6	-	28	13025	c.13018G>A	c.(13018-13020)Gaa>Aaa	p.E4340K		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4340						extracellular vesicular exosome (GO:0070062)		p.E4340K(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)			CGCCAGTCTTCGATGACAACC	0.642																																					p.E4340K		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	stomach(1)	c.G13018A						PASS	.						130.0	140.0	136.0					19																	40368330		2203	4300	6503	SO:0001583	missense	8857	exon28			AGTCTTCGATGAC	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.13018G>A	19.37:g.40368330C>T	ENSP00000221347:p.Glu4340Lys	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	140	40	0.285714	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	478	0.21886446886446886	101	0.20528455284552846	56	0.15469613259668508	196	0.34265734265734266	125	0.16490765171503957	C	6.598	0.478746	0.12521	.	.	ENSG00000090920	ENST00000221347	D	0.85955	-2.05	4.08	-8.16	0.01061	Uncharacterised domain, cysteine-rich (2);	1.549620	0.03830	N	0.268942	T	0.00012	0.0000	N	0.03084	-0.415	0.80722	P	0.0	B	0.12013	0.005	B	0.04013	0.001	T	0.03259	-1.1055	9	0.12766	T	0.61	.	2.0488	0.03566	0.1461:0.4649:0.1867:0.2022	.	4340	Q9Y6R7	FCGBP_HUMAN	K	4340	ENSP00000221347:E4340K	ENSP00000221347:E4340K	E	-	1	0	FCGBP	45060170	0.000000	0.05858	0.001000	0.08648	0.220000	0.24768	-7.283000	0.00040	-1.584000	0.01636	0.305000	0.20034	GAA	C|0.827;T|0.173	0.173	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
MYO7B	4648	hgsc.bcm.edu	37	2	128367433	128367433	+	Missense_Mutation	SNP	G	G	A	rs61741454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128367433G>A	ENST00000409816.2	+	23	3066	c.3034G>A	c.(3034-3036)Gtc>Atc	p.V1012I	MYO7B_ENST00000389524.4_Missense_Mutation_p.V1012I|MYO7B_ENST00000428314.1_Missense_Mutation_p.V1012I			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1012	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GGCCGCCCTGGTCATATGGAA	0.592													G|||	36	0.0071885	0.0234	0.0072	5008	,	,		18749	0.0		0.0	False		,,,				2504	0.0				p.V1012I		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3034A						PASS	.	G	ILE/VAL	91,4015		2,87,1964	48.0	52.0	51.0		3034	2.6	0.0	2	dbSNP_129	51	2,8426		0,2,4212	yes	missense	MYO7B	NM_001080527.1	29	2,89,6176	AA,AG,GG		0.0237,2.2163,0.742	benign	1012/2117	128367433	93,12441	2053	4214	6267	SO:0001583	missense	4648	exon24			GCCCTGGTCATAT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3034G>A	2.37:g.128367433G>A	ENSP00000386461:p.Val1012Ile	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	203	105	0.517241	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	12	0.005494505494505495	9	0.018292682926829267	3	0.008287292817679558	0	0.0	0	0.0	G	8.417	0.845525	0.16963	0.022163	2.37E-4	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.87103	-2.21;-2.21;-2.21	5.47	2.57	0.30868	MyTH4 domain (2);	0.485163	0.20625	N	0.088698	T	0.62122	0.2402	N	0.17474	0.49	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.63328	-0.6662	10	0.72032	D	0.01	.	8.5581	0.33494	0.1397:0.1265:0.7338:0.0	rs61741454	1012	Q6PIF6	MYO7B_HUMAN	I	1012	ENSP00000374175:V1012I;ENSP00000415090:V1012I;ENSP00000386461:V1012I	ENSP00000374175:V1012I	V	+	1	0	MYO7B	128083903	0.888000	0.30383	0.039000	0.18376	0.011000	0.07611	2.293000	0.43558	0.678000	0.31325	0.655000	0.94253	GTC	G|0.993;A|0.007	0.007	strong		0.592	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
GIF	2694	hgsc.bcm.edu	37	11	59612859	59612859	+	Missense_Mutation	SNP	T	T	C	rs35211634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59612859T>C	ENST00000257248.2	-	1	115	c.68A>G	c.(67-69)cAg>cGg	p.Q23R	GIF_ENST00000541311.1_5'UTR	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	23			Q -> R (in dbSNP:rs35211634). {ECO:0000269|PubMed:14695536, ECO:0000269|PubMed:15738392}.		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)	GCATGAACTCTGGGTCTGGGT	0.537													C|||	514	0.102636	0.2716	0.0331	5008	,	,		17712	0.0417		0.0567	False		,,,				2504	0.0337				p.Q23R	NSCLC(53;1139 1245 16872 38474 42853)	Atlas-SNP	.											.	GIF	43	.	0			c.A68G						PASS	.	C	ARG/GLN	866,3536	744.2+/-411.5	90,686,1425	152.0	149.0	150.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	68	-4.4	0.0	11	dbSNP_126	150	413,8177	800.6+/-407.4	18,377,3900	yes	missense	GIF	NM_005142.2	43	108,1063,5325	CC,CT,TT		4.8079,19.6729,9.8445	benign	23/418	59612859	1279,11713	2201	4295	6496	SO:0001583	missense	2694	exon1			GAACTCTGGGTCT	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.68A>G	11.37:g.59612859T>C	ENSP00000257248:p.Gln23Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_005142	B2RAN8|B4DVZ1	Missense_Mutation	SNP	ENST00000257248.2	37	CCDS7977.1	185	0.08470695970695971	117	0.23780487804878048	10	0.027624309392265192	13	0.022727272727272728	45	0.059366754617414245	C	2.352	-0.348630	0.05208	0.196729	0.048079	ENSG00000134812	ENST00000257248	T	0.34667	1.35	5.46	-4.43	0.03568	.	0.905508	0.09152	N	0.841440	T	0.00012	0.0000	N	0.01267	-0.92	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44528	-0.9322	9	0.11794	T	0.64	2.9968	14.5605	0.68133	0.0:0.2199:0.0:0.7801	rs35211634;rs35211634	23;23	B4DVY6;P27352	.;IF_HUMAN	R	23	ENSP00000257248:Q23R	ENSP00000257248:Q23R	Q	-	2	0	GIF	59369435	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-2.402000	0.01047	-1.452000	0.01931	-0.215000	0.12644	CAG	T|0.902;C|0.098	0.098	strong		0.537	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142	
ZNHIT2	741	hgsc.bcm.edu	37	11	64884599	64884599	+	Missense_Mutation	SNP	G	G	A	rs35983251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64884599G>A	ENST00000310597.4	-	1	571	c.527C>T	c.(526-528)gCc>gTc	p.A176V	AP003068.12_ENST00000527789.1_RNA	NM_014205.2	NP_055020.1	Q9UHR6	ZNHI2_HUMAN	zinc finger, HIT-type containing 2	176			A -> V (in dbSNP:rs35983251).				metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6						CCGCTCGGCGGCCGCGGGCTC	0.721													G|||	118	0.0235623	0.0832	0.0086	5008	,	,		12576	0.0		0.002	False		,,,				2504	0.0				p.A176V		Atlas-SNP	.											.	ZNHIT2	12	.	0			c.C527T						PASS	.	G	VAL/ALA	263,3933		7,249,1842	6.0	9.0	8.0		527	1.0	0.0	11	dbSNP_126	8	2,8288		0,2,4143	no	missense	ZNHIT2	NM_014205.2	64	7,251,5985	AA,AG,GG		0.0241,6.2679,2.1224	possibly-damaging	176/404	64884599	265,12221	2098	4145	6243	SO:0001583	missense	741	exon1			TCGGCGGCCGCGG		CCDS8094.1	11q13	2012-08-08	2010-09-15	2004-07-14	ENSG00000174276	ENSG00000174276		"""Zinc fingers, HIT-type"""	1177	protein-coding gene	gene with protein product		604575	"""chromosome 11 open reading frame 5"", ""zinc finger, HIT domain containing 2"""	C11orf5			Standard	NM_014205		Approved	FON	uc001ocw.3	Q9UHR6	OTTHUMG00000165604	ENST00000310597.4:c.527C>T	11.37:g.64884599G>A	ENSP00000308548:p.Ala176Val	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	9	5	0.555556	NM_014205	Q3SY14|Q8IUV0	Missense_Mutation	SNP	ENST00000310597.4	37	CCDS8094.1	42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	G	2.847	-0.239276	0.05944	0.062679	2.41E-4	ENSG00000174276	ENST00000310597	T	0.32272	1.46	0.973	0.973	0.19710	.	1.340080	0.05310	U	0.524668	T	0.01320	0.0043	L	0.56769	1.78	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.27673	-1.0067	10	0.02654	T	1	-0.1191	7.7809	0.29064	0.0:0.0:1.0:0.0	rs35983251	176	Q9UHR6	ZNHI2_HUMAN	V	176	ENSP00000308548:A176V	ENSP00000308548:A176V	A	-	2	0	ZNHIT2	64641175	0.000000	0.05858	0.008000	0.14137	0.004000	0.04260	-0.476000	0.06591	0.821000	0.34540	0.561000	0.74099	GCC	G|0.980;A|0.020	0.020	strong		0.721	ZNHIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385260.1	NM_014205	
C2orf49	79074	hgsc.bcm.edu	37	2	105959592	105959592	+	Missense_Mutation	SNP	G	G	A	rs28930676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	82	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	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	
EMP2	2013	hgsc.bcm.edu	37	16	10631912	10631912	+	Silent	SNP	C	C	T	rs2279868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	74	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	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	
OR2L3	391192	hgsc.bcm.edu	37	1	248224587	248224587	+	Missense_Mutation	SNP	A	A	G	rs61525219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248224587A>G	ENST00000359959.3	+	1	604	c.604A>G	c.(604-606)Acc>Gcc	p.T202A	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	202						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(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	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;0.0278)			GTTTTTGAGCACCACCATCTT	0.493													a|||	288	0.057508	0.1218	0.0216	5008	,	,		24287	0.0704		0.0298	False		,,,				2504	0.0112				p.T202A		Atlas-SNP	.											OR2L3,NS,carcinoma,-1,1	OR2L3	97	1	0			c.A604G						scavenged	.						194.0	212.0	206.0					1																	248224587		2187	4300	6487	SO:0001583	missense	391192	exon1			TTGAGCACCACCA	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"""GPCR / Class A : Olfactory receptors"""	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.604A>G	1.37:g.248224587A>G	ENSP00000353044:p.Thr202Ala	Somatic	514	1	0.00194553		WXS	Illumina HiSeq	Phase_I	338	25	0.0739645	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	A	0.713	-0.786430	0.02907	.	.	ENSG00000198128	ENST00000359959	T	0.36157	1.27	2.05	-0.724	0.11177	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34002	U	0.004342	T	0.19967	0.0480	N	0.11756	0.17	0.09310	N	1	B	0.18013	0.025	B	0.30646	0.118	T	0.21109	-1.0255	10	0.56958	D	0.05	.	7.7621	0.28959	0.3671:0.0:0.6329:0.0	rs61525219	202	Q8NG85	OR2L3_HUMAN	A	202	ENSP00000353044:T202A	ENSP00000353044:T202A	T	+	1	0	OR2L3	246291210	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.037000	0.01420	-0.358000	0.08162	-1.678000	0.00738	ACC	.	.	weak		0.493	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
CLU	1191	hgsc.bcm.edu	37	8	27468005	27468005	+	Silent	SNP	G	G	A	rs9331892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27468005G>A	ENST00000316403.10	-	2	489	c.84C>T	c.(82-84)gaC>gaT	p.D28D	CLU_ENST00000546343.1_Silent_p.D39D|CLU_ENST00000405140.3_Silent_p.D28D|CLU_ENST00000560366.1_Silent_p.D80D|CLU_ENST00000523500.1_Silent_p.D28D			P10909	CLUS_HUMAN	clusterin	28				D -> S (in Ref. 9; AA sequence and 13; AA sequence). {ECO:0000305}.	blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		GGAGCTCATTGTCTGAGACCG	0.562													G|||	286	0.0571086	0.2095	0.013	5008	,	,		20395	0.0		0.0	False		,,,				2504	0.0				p.D28D		Atlas-SNP	.											.	CLU	54	.	0			c.C84T						PASS	.	G		775,3631	313.3+/-293.0	65,645,1493	114.0	103.0	107.0		84	2.2	0.0	8	dbSNP_119	107	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	CLU	NM_203339.2		65,653,5785	AA,AG,GG		0.093,17.5897,6.0203		28/450	27468005	783,12223	2203	4300	6503	SO:0001819	synonymous_variant	1191	exon2			CTCATTGTCTGAG	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"""complement lysis inhibitor"", ""sulfated glycoprotein 2"", ""testosterone-repressed prostate message 2"", ""apolipoprotein J"""	185430	"""clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"""	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.84C>T	8.37:g.27468005G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	138	53	0.384058	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Silent	SNP	ENST00000316403.10	37	CCDS47832.1																																																																																			G|0.944;A|0.056	0.056	strong		0.562	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831	
INF2	64423	hgsc.bcm.edu	37	14	105180977	105180977	+	Missense_Mutation	SNP	G	G	A	rs9672065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105180977G>A	ENST00000392634.4	+	21	3590	c.3478G>A	c.(3478-3480)Ggt>Agt	p.G1160S	INF2_ENST00000330634.7_Missense_Mutation_p.G1160S	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	1160					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CCACAGCCGTGGTGCCAGACC	0.652													G|||	110	0.0219649	0.0734	0.0144	5008	,	,		16731	0.0		0.003	False		,,,				2504	0.0				p.G1160S		Atlas-SNP	.											.	INF2	148	.	0			c.G3478A						PASS	.	G	SER/GLY,SER/GLY	221,3991		2,217,1887	38.0	46.0	43.0		3478,3478	-8.5	0.0	14	dbSNP_119	43	6,8424		0,6,4209	yes	missense,missense	INF2	NM_022489.3,NM_001031714.3	56,56	2,223,6096	AA,AG,GG		0.0712,5.2469,1.7956	benign,benign	1160/1250,1160/1241	105180977	227,12415	2106	4215	6321	SO:0001583	missense	64423	exon21			AGCCGTGGTGCCA	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.3478G>A	14.37:g.105180977G>A	ENSP00000376410:p.Gly1160Ser	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	39	26	0.666667	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	37	CCDS9989.2	48	0.02197802197802198	44	0.08943089430894309	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	2.964	-0.214005	0.06101	0.052469	7.12E-4	ENSG00000203485	ENST00000330634;ENST00000392634	T;T	0.79940	-1.3;-1.32	4.24	-8.47	0.00939	.	1.401710	0.05279	N	0.519086	T	0.02807	0.0084	N	0.02539	-0.55	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.38929	-0.9638	10	0.02654	T	1	.	10.5338	0.44992	0.7803:0.1044:0.1153:0.0	rs9672065	1160;1160	Q27J81-2;Q27J81	.;INF2_HUMAN	S	1160	ENSP00000376406:G1160S;ENSP00000376410:G1160S	ENSP00000252527:G628S	G	+	1	0	INF2	104252022	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.762000	0.01803	-2.735000	0.00382	-0.948000	0.02665	GGT	G|0.978;A|0.022	0.022	strong		0.652	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
SPATA31C1	441452	hgsc.bcm.edu	37	9	90534206	90534206	+	RNA	SNP	T	T	C	rs2481989		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:90534206T>C	ENST00000602681.1	+	0	952							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TGTCTCCCAGTGTCCAACAGG	0.582																																					p.C76R		Atlas-SNP	.											.	.	.	.	0			c.T226C						PASS	.						153.0	124.0	133.0					9																	90534206		692	1591	2283			441452	exon2			TCCCAGTGTCCAA	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"""family with sequence similarity 75, member C1"""	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		9.37:g.90534206T>C		Somatic	861	2	0.00232288		WXS	Illumina HiSeq	Phase_I	658	157	0.238602	NM_001145124		Missense_Mutation	SNP	ENST00000602681.1	37																																																																																				.	.	weak		0.582	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124	
BBS4	585	hgsc.bcm.edu	37	15	73027478	73027478	+	Missense_Mutation	SNP	T	T	C	rs2277598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:73027478T>C	ENST00000268057.4	+	13	1102	c.1061T>C	c.(1060-1062)aTa>aCa	p.I354T	BBS4_ENST00000542334.1_Missense_Mutation_p.I182T|BBS4_ENST00000395205.2_Missense_Mutation_p.I362T|BBS4_ENST00000539603.1_Missense_Mutation_p.I342T	NM_033028.4	NP_149017.2	Q96RK4	BBS4_HUMAN	Bardet-Biedl syndrome 4	354	Required for localization to centrosomes.		I -> T (in dbSNP:rs2277598). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15666242, ECO:0000269|PubMed:15770229}.		adult behavior (GO:0030534)|brain morphogenesis (GO:0048854)|centrosome organization (GO:0051297)|cerebral cortex development (GO:0021987)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|dendrite development (GO:0016358)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|maintenance of protein location in nucleus (GO:0051457)|melanosome transport (GO:0032402)|metabolic process (GO:0008152)|microtubule anchoring at centrosome (GO:0034454)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of systemic arterial blood pressure (GO:0003085)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of cilium assembly (GO:0045724)|positive regulation of multicellular organism growth (GO:0040018)|protein localization to centrosome (GO:0071539)|protein localization to organelle (GO:0033365)|protein transport (GO:0015031)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|regulation of cytokinesis (GO:0032465)|regulation of lipid metabolic process (GO:0019216)|retina homeostasis (GO:0001895)|retinal rod cell development (GO:0046548)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)|spermatid development (GO:0007286)|striatum development (GO:0021756)|visual perception (GO:0007601)	BBSome (GO:0034464)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary membrane (GO:0060170)|cilium (GO:0005929)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|pericentriolar material (GO:0000242)	alpha-tubulin binding (GO:0043014)|beta-tubulin binding (GO:0048487)|dynactin binding (GO:0034452)|microtubule motor activity (GO:0003777)|RNA polymerase II repressing transcription factor binding (GO:0001103)			autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(1)	19						CTGGAAGATATAGAAAATGCC	0.473									Bardet-Biedl syndrome				T|||	2148	0.428914	0.2413	0.4841	5008	,	,		21567	0.256		0.6561	False		,,,				2504	0.5879				p.I354T		Atlas-SNP	.											.	BBS4	34	.	0			c.T1061C						PASS	.	T	THR/ILE	1416,2980	463.0+/-353.4	232,952,1014	74.0	69.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1061	-4.4	0.0	15	dbSNP_100	71	5504,3090	660.1+/-401.7	1783,1938,576	yes	missense	BBS4	NM_033028.3	89	2015,2890,1590	CC,CT,TT		35.9553,32.2111,46.7283	benign	354/520	73027478	6920,6070	2198	4297	6495	SO:0001583	missense	585	exon13	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AAGATATAGAAAA	AF090947	CCDS10246.1, CCDS58377.1	15q22.3-q23	2013-01-10			ENSG00000140463	ENSG00000140463		"""Tetratricopeptide (TTC) repeat domain containing"""	969	protein-coding gene	gene with protein product		600374				7711739, 11381270	Standard	NM_033028		Approved		uc002avb.3	Q96RK4	OTTHUMG00000133510	ENST00000268057.4:c.1061T>C	15.37:g.73027478T>C	ENSP00000268057:p.Ile354Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_033028	B4E178|Q53DZ5|Q8NHU9|Q96H45	Missense_Mutation	SNP	ENST00000268057.4	37	CCDS10246.1	985	0.451007326007326	137	0.2784552845528455	209	0.5773480662983426	144	0.2517482517482518	495	0.6530343007915568	T	7.460	0.644540	0.14451	0.322111	0.640447	ENSG00000140463	ENST00000542334;ENST00000268057;ENST00000539603;ENST00000395205	T;T;T;T	0.78003	0.7;-1.14;-1.14;-1.14	5.06	-4.41	0.03590	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	1.024970	0.07731	N	0.945276	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.41106	-0.9527	9	0.28530	T	0.3	6.1291	9.4164	0.38523	0.0:0.4506:0.1014:0.448	rs2277598;rs17754163;rs17852451;rs52833624;rs57144099;rs2277598	342;354;362;354	F5H7I8;B2RB60;Q96RK4-2;Q96RK4	.;.;.;BBS4_HUMAN	T	182;354;342;362	ENSP00000445964:I182T;ENSP00000268057:I354T;ENSP00000442492:I342T;ENSP00000378631:I362T	ENSP00000268057:I354T	I	+	2	0	BBS4	70814531	0.000000	0.05858	0.000000	0.03702	0.778000	0.44026	-0.246000	0.08878	-0.575000	0.05982	-0.304000	0.09214	ATA	T|0.511;C|0.489	0.489	strong		0.473	BBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257473.2	NM_033028	
TTC4	7268	hgsc.bcm.edu	37	1	55197320	55197320	+	Silent	SNP	G	G	A	rs1062700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55197320G>A	ENST00000371281.3	+	7	930	c.843G>A	c.(841-843)ctG>ctA	p.L281L	MROH7-TTC4_ENST00000414150.2_3'UTR|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	281										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						TGCTCTTTCTGTACCCAGAGT	0.557													G|||	248	0.0495208	0.0651	0.0216	5008	,	,		18066	0.004		0.0606	False		,,,				2504	0.0838				p.L281L		Atlas-SNP	.											.	TTC4	21	.	0			c.G843A						PASS	.	G		311,4095	166.5+/-197.7	16,279,1908	79.0	69.0	72.0		843	0.9	1.0	1	dbSNP_86	72	399,8201	126.8+/-185.2	7,385,3908	no	coding-synonymous	TTC4	NM_004623.4		23,664,5816	AA,AG,GG		4.6395,7.0586,5.459		281/388	55197320	710,12296	2203	4300	6503	SO:0001819	synonymous_variant	7268	exon7			CTTTCTGTACCCA		CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"""Tetratricopeptide (TTC) repeat domain containing"""	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.843G>A	1.37:g.55197320G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	76	29	0.381579	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Silent	SNP	ENST00000371281.3	37	CCDS596.1																																																																																			G|0.946;A|0.054	0.054	strong		0.557	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623	
KIAA0556	23247	hgsc.bcm.edu	37	16	27689137	27689137	+	Missense_Mutation	SNP	G	G	T	rs147094899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27689137G>T	ENST00000261588.4	+	7	647	c.628G>T	c.(628-630)Gac>Tac	p.D210Y	CTD-2049O4.1_ENST00000564893.1_RNA|KIAA0556_ENST00000567894.1_3'UTR	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	210						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						TATTGAGGAAGACATACTCTC	0.507													G|||	40	0.00798722	0.028	0.0014	5008	,	,		16870	0.001		0.001	False		,,,				2504	0.0				p.D210Y		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G628T						PASS	.	G	TYR/ASP	81,4313	71.4+/-109.4	0,81,2116	65.0	59.0	61.0		628	4.5	1.0	16	dbSNP_134	61	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KIAA0556	NM_015202.2	160	0,82,6415	TT,TG,GG		0.0116,1.8434,0.6311	benign	210/1619	27689137	82,12912	2197	4300	6497	SO:0001583	missense	23247	exon7			GAGGAAGACATAC	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.628G>T	16.37:g.27689137G>T	ENSP00000261588:p.Asp210Tyr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	124	54	0.435484	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	12	0.005494505494505495	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.62	2.290322	0.40494	0.018434	1.16E-4	ENSG00000047578	ENST00000261588;ENST00000327217	T	0.49432	0.78	5.48	4.53	0.55603	.	0.296062	0.32175	N	0.006462	T	0.43612	0.1255	L	0.54323	1.7	0.36190	D	0.850035	D;D	0.76494	0.999;0.979	D;P	0.66497	0.944;0.81	T	0.65014	-0.6271	10	0.87932	D	0	-4.2839	10.458	0.44561	0.09:0.0:0.91:0.0	.	118;210	Q8N803;O60303	.;K0556_HUMAN	Y	210;117	ENSP00000261588:D210Y	ENSP00000261588:D210Y	D	+	1	0	KIAA0556	27596638	1.000000	0.71417	0.973000	0.42090	0.021000	0.10359	3.790000	0.55461	1.320000	0.45209	-0.137000	0.14449	GAC	G|0.993;T|0.007	0.007	strong		0.507	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
FLG	2312	hgsc.bcm.edu	37	1	152276871	152276871	+	Silent	SNP	A	A	G	rs3126066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276871A>G	ENST00000368799.1	-	3	10526	c.10491T>C	c.(10489-10491)gaT>gaC	p.D3497D	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3497	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)			GCCTGGAGCCATCTCCTGATT	0.582									Ichthyosis				G|||	2239	0.447085	0.5204	0.4395	5008	,	,		19200	0.6448		0.1471	False		,,,				2504	0.4581				p.D3497D		Atlas-SNP	.											.	FLG	900	.	0			c.T10491C						PASS	.	G		2040,2366	609.3+/-391.3	470,1100,633	267.0	264.0	265.0		10491	-4.6	0.0	1	dbSNP_103	265	1276,7318	759.6+/-407.6	123,1030,3144	no	coding-synonymous	FLG	NM_002016.1		593,2130,3777	GG,GA,AA		14.8476,46.3005,25.5077		3497/4062	152276871	3316,9684	2203	4297	6500	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GGAGCCATCTCCT	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.10491T>C	1.37:g.152276871A>G		Somatic	421	0	0		WXS	Illumina HiSeq	Phase_I	421	421	1	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.703;G|0.297	0.297	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
KIT	3815	hgsc.bcm.edu	37	4	55561862	55561862	+	Silent	SNP	G	G	T	rs56411694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:55561862G>T	ENST00000288135.5	+	2	349	c.252G>T	c.(250-252)acG>acT	p.T84T		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	84	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|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 pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AATGGATCACGGAAAAGGCAG	0.443		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors				G|||	99	0.0197684	0.0696	0.0101	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.T84T		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	.	KIT	7396	.	0			c.G252T						PASS	.	G	,	273,4133	155.5+/-188.7	9,255,1939	96.0	89.0	92.0		252,252	-10.4	0.0	4	dbSNP_129	92	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	KIT	NM_000222.2,NM_001093772.1	,	9,260,6234	TT,TG,GG		0.0581,6.1961,2.1375	,	84/977,84/973	55561862	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	3815	exon2	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	GATCACGGAAAAG	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.252G>T	4.37:g.55561862G>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																			G|0.981;T|0.019	0.019	strong		0.443	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
DDX20	11218	hgsc.bcm.edu	37	1	112298582	112298582	+	Silent	SNP	A	A	G	rs197392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:112298582A>G	ENST00000369702.4	+	1	656	c.36A>G	c.(34-36)gcA>gcG	p.A12A	FAM212B_ENST00000412270.1_5'Flank|FAM212B_ENST00000444059.2_5'Flank|DDX20_ENST00000536167.1_Silent_p.A12A	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	12					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAGCCTTAGCAGCAGTGGCGA	0.662													g|||	1214	0.242412	0.5666	0.147	5008	,	,		11743	0.0367		0.1978	False		,,,				2504	0.1299				p.A12A		Atlas-SNP	.											DDX20,NS,carcinoma,0,1	DDX20	50	1	0			c.A36G						PASS	.			1915,2403		428,1059,672	12.0	13.0	13.0		36	-5.7	0.0	1	dbSNP_79	13	1610,6958		184,1242,2858	no	coding-synonymous	DDX20	NM_007204.4		612,2301,3530	GG,GA,AA		18.7908,44.3492,27.3553		12/825	112298582	3525,9361	2159	4284	6443	SO:0001819	synonymous_variant	11218	exon1			CTTAGCAGCAGTG	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.36A>G	1.37:g.112298582A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	182	180	0.989011	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Silent	SNP	ENST00000369702.4	37	CCDS842.1																																																																																			A|0.755;G|0.245	0.245	strong		0.662	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
MR1	3140	hgsc.bcm.edu	37	1	181019202	181019202	+	Silent	SNP	C	C	T	rs61731104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:181019202C>T	ENST00000367580.5	+	3	389	c.384C>T	c.(382-384)acC>acT	p.T128T	MR1_ENST00000367579.3_Intron|MR1_ENST00000438435.2_3'UTR|MR1_ENST00000434571.2_Silent_p.T128T|MR1_ENST00000282990.6_Silent_p.T128T	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	128	Alpha-2.|Ligand-binding.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	ATGGAAGCACCACAGGATTTC	0.512													C|||	197	0.0393371	0.1218	0.0159	5008	,	,		20515	0.0228		0.0	False		,,,				2504	0.002				p.T128T	Colon(174;1412 1962 45296 46549 47110)	Atlas-SNP	.											.	MR1	46	.	0			c.C384T						PASS	.	C	,,,	437,3969	211.5+/-231.7	27,383,1793	113.0	103.0	107.0		,384,384,384	4.4	0.6	1	dbSNP_129	107	6,8594	4.3+/-15.6	0,6,4294	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	MR1	NM_001194999.1,NM_001195000.1,NM_001195035.1,NM_001531.2	,,,	27,389,6087	TT,TC,CC		0.0698,9.9183,3.4061	,,,	,128/250,128/215,128/342	181019202	443,12563	2203	4300	6503	SO:0001819	synonymous_variant	3140	exon4			AAGCACCACAGGA	AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"""Immunoglobulin superfamily / C1-set domain containing"""	4975	protein-coding gene	gene with protein product		600764	"""major histocompatibility complex, class I-like sequence"""	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.384C>T	1.37:g.181019202C>T		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	270	138	0.511111	NM_001195035	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Silent	SNP	ENST00000367580.5	37	CCDS1342.1																																																																																			C|0.967;T|0.033	0.033	strong		0.512	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531	
TAS2R20	259295	hgsc.bcm.edu	37	12	11149720	11149720	+	Missense_Mutation	SNP	A	A	G	rs10845280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11149720A>G	ENST00000538986.1	-	1	754	c.755T>C	c.(754-756)tTt>tCt	p.F252S	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	252			F -> S (in dbSNP:rs10845280). {ECO:0000269|PubMed:15496549}.		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)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						TCGCATCTTAAAATTCCAAAA	0.388													G|||	2118	0.422923	0.0651	0.3847	5008	,	,		19131	0.755		0.3817	False		,,,				2504	0.6339				p.F252S		Atlas-SNP	.											.	TAS2R20	17	.	0			c.T755C						PASS	.	G	SER/PHE	442,3964	211.5+/-231.7	19,404,1780	112.0	111.0	112.0		755	-2.3	0.0	12	dbSNP_120	112	3016,5584	464.9+/-366.4	544,1928,1828	yes	missense	TAS2R20	NM_176889.2	155	563,2332,3608	GG,GA,AA		35.0698,10.0318,26.5877	benign	252/310	11149720	3458,9548	2203	4300	6503	SO:0001583	missense	259295	exon1			ATCTTAAAATTCC	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.755T>C	12.37:g.11149720A>G	ENSP00000441624:p.Phe252Ser	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	172	72	0.418605	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	898	0.41117216117216115	33	0.06707317073170732	155	0.4281767955801105	426	0.7447552447552448	284	0.37467018469656993	a	0.490	-0.875796	0.02550	0.100318	0.350698	ENSG00000255837	ENST00000538986	T	0.35421	1.31	2.49	-2.3	0.06785	.	1.140010	0.06894	N	0.804836	T	0.00012	0.0000	N	0.04203	-0.255	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.36601	-0.9741	9	0.21540	T	0.41	.	5.6602	0.17664	0.4396:0.0:0.4277:0.1326	rs10845280;rs17743814;rs52818991;rs10845280	252	P59543	T2R20_HUMAN	S	252	ENSP00000441624:F252S	ENSP00000441624:F252S	F	-	2	0	TAS2R20	11040987	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.736000	0.01845	-1.545000	0.01719	-3.103000	0.00063	TTT	A|0.670;G|0.329	0.329	strong		0.388	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
SAMD11	148398	hgsc.bcm.edu	37	1	865694	865694	+	Missense_Mutation	SNP	C	C	T	rs9988179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:865694C>T	ENST00000342066.3	+	3	315	c.232C>T	c.(232-234)Cac>Tac	p.H78Y	AL645608.1_ENST00000598827.1_Missense_Mutation_p.C18Y	NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	78					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		GGATGGTCCGCACATCCGTAT	0.622													c|||	263	0.052516	0.0227	0.0965	5008	,	,		17146	0.1389		0.002	False		,,,				2504	0.0245				p.H78Y		Atlas-SNP	.											.	SAMD11	34	.	0			c.C232T						PASS	.	C	TYR/HIS	81,4307		2,77,2115	45.0	45.0	45.0		232	4.7	0.0	1	dbSNP_119	45	14,8580		0,14,4283	yes	missense	SAMD11	NM_152486.2	83	2,91,6398	TT,TC,CC		0.1629,1.8459,0.7318	probably-damaging	78/682	865694	95,12887	2194	4297	6491	SO:0001583	missense	148398	exon3			GGTCCGCACATCC	BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"""Sterile alpha motif (SAM) domain containing"""	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.232C>T	1.37:g.865694C>T	ENSP00000342313:p.His78Tyr	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	242	112	0.46281	NM_152486	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	Missense_Mutation	SNP	ENST00000342066.3	37	CCDS2.2	136	0.06227106227106227	14	0.028455284552845527	29	0.08011049723756906	91	0.1590909090909091	2	0.002638522427440633	c	14.40	2.525243	0.44969	0.018459	0.001629	ENSG00000187634	ENST00000420190;ENST00000437963;ENST00000342066	.	.	.	4.72	4.72	0.59763	.	0.195015	0.32372	N	0.006184	T	0.00271	0.0008	L	0.29908	0.895	0.33508	P	0.409276	D	0.61080	0.989	P	0.50314	0.637	T	0.06197	-1.0840	8	0.87932	D	0	-7.4627	17.0604	0.86546	0.0:1.0:0.0:0.0	rs9988179	78	Q96NU1	SAM11_HUMAN	Y	78	.	ENSP00000342313:H78Y	H	+	1	0	SAMD11	855557	0.077000	0.21312	0.008000	0.14137	0.268000	0.26511	3.430000	0.52807	2.369000	0.80426	0.556000	0.70494	CAC	C|0.974;T|0.026	0.026	strong		0.622	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276866.2	NM_152486	
RNF39	80352	hgsc.bcm.edu	37	6	30041009	30041009	+	Missense_Mutation	SNP	A	A	G	rs2074479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30041009A>G	ENST00000244360.6	-	3	704	c.607T>C	c.(607-609)Tcc>Ccc	p.S203P	RNF39_ENST00000376751.3_Missense_Mutation_p.S203P	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	203			S -> P (in dbSNP:rs2074479). {ECO:0000269|PubMed:14574404}.			cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										GATGACTTGGATGTTGGGACT	0.468													g|||	958	0.191294	0.2988	0.1744	5008	,	,		20885	0.1905		0.0954	False		,,,				2504	0.1575				p.S203P	NSCLC(8;188 360 1520 20207 31481)	Atlas-SNP	.											RNF39_ENST00000244360,NS,carcinoma,+1,1	RNF39	27	1	0			c.T607C						PASS	.		PRO/SER,PRO/SER	772,2250		93,586,832	131.0	128.0	129.0		607,607	4.0	0.7	6	dbSNP_96	129	650,4768		48,554,2107	yes	missense,missense	RNF39	NM_025236.3,NM_170769.2	74,74	141,1140,2939	GG,GA,AA		11.997,25.546,16.8483	benign,benign	203/421,203/355	30041009	1422,7018	1511	2709	4220	SO:0001583	missense	80352	exon3			ACTTGGATGTTGG	AF238315	CCDS4673.1, CCDS4674.1	6p21.3	2013-01-09			ENSG00000204618	ENSG00000204618		"""RING-type (C3HC4) zinc fingers"""	18064	protein-coding gene	gene with protein product		607524				11130983, 11716498	Standard	NM_170769		Approved	HZFw1, LIRF	uc003npe.3	Q9H2S5	OTTHUMG00000031288	ENST00000244360.6:c.607T>C	6.37:g.30041009A>G	ENSP00000244360:p.Ser203Pro	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Missense_Mutation	SNP	ENST00000244360.6	37	CCDS4673.1	404	0.184981684981685	146	0.2967479674796748	72	0.19889502762430938	115	0.20104895104895104	71	0.09366754617414248	g	0.008	-1.893380	0.00522	0.25546	0.11997	ENSG00000204618	ENST00000376751;ENST00000244360	T;T	0.70399	0.04;-0.48	3.99	3.99	0.46301	.	0.546488	0.13684	N	0.370007	T	0.19167	0.0460	N	0.01874	-0.695	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07139	-1.0788	9	0.13470	T	0.59	-19.0329	7.844	0.29414	0.1163:0.0:0.8837:0.0	rs2074479;rs52821835;rs60743069;rs2074479	203;203	Q9H2S5;Q9H2S5-2	RNF39_HUMAN;.	P	203	ENSP00000365942:S203P;ENSP00000244360:S203P	ENSP00000244360:S203P	S	-	1	0	RNF39	30148988	0.782000	0.28689	0.659000	0.29680	0.025000	0.11179	0.836000	0.27545	1.050000	0.40346	-0.372000	0.07161	TCC	A|0.808;G|0.192	0.192	strong		0.468	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769	
SSH3	54961	hgsc.bcm.edu	37	11	67075131	67075131	+	Silent	SNP	C	C	T	rs57238619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67075131C>T	ENST00000308127.4	+	7	892	c.714C>T	c.(712-714)tcC>tcT	p.S238S	SSH3_ENST00000532181.1_Intron|SSH3_ENST00000376757.5_Silent_p.S238S|SSH3_ENST00000308298.7_Silent_p.S238S	NM_017857.3	NP_060327.3	Q8TE77	SSH3_HUMAN	slingshot protein phosphatase 3	238					protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|DNA binding (GO:0003677)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			GACTGAACTCCGAACAGAGCT	0.642													C|||	508	0.101438	0.2231	0.0634	5008	,	,		19319	0.1101		0.0338	False		,,,				2504	0.0245				p.S238S		Atlas-SNP	.											.	SSH3	54	.	0			c.C714T						PASS	.	C		823,3577	317.4+/-295.1	74,675,1451	41.0	45.0	44.0		714	-2.2	1.0	11	dbSNP_129	44	216,8374	88.1+/-150.5	2,212,4081	no	coding-synonymous	SSH3	NM_017857.3		76,887,5532	TT,TC,CC		2.5146,18.7045,7.9985		238/660	67075131	1039,11951	2200	4295	6495	SO:0001819	synonymous_variant	54961	exon7			GAACTCCGAACAG	AF085851	CCDS8157.1	11q13	2013-03-05	2013-03-05		ENSG00000172830	ENSG00000172830		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30581	protein-coding gene	gene with protein product		606780	"""slingshot homolog 3 (Drosophila)"""			11832213	Standard	NM_017857		Approved	FLJ20515, FLJ10928	uc001okj.3	Q8TE77	OTTHUMG00000167105	ENST00000308127.4:c.714C>T	11.37:g.67075131C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	189	89	0.470899	NM_017857	Q6PK42|Q76I75|Q8N9L8|Q8WYL0|Q9NV45|Q9NWZ7	Silent	SNP	ENST00000308127.4	37	CCDS8157.1																																																																																			C|0.916;T|0.084	0.084	strong		0.642	SSH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393167.1	NM_018276	
PIWIL4	143689	hgsc.bcm.edu	37	11	94337220	94337220	+	Silent	SNP	C	C	T	rs593690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94337220C>T	ENST00000299001.6	+	13	1847	c.1636C>T	c.(1636-1638)Ctg>Ttg	p.L546L	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	546	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TGATGTTCAGCTGGTAAGTAC	0.318													T|||	2933	0.585663	0.9085	0.4524	5008	,	,		14671	0.502		0.4145	False		,,,				2504	0.5061				p.L546L		Atlas-SNP	.											.	PIWIL4	70	.	0			c.C1636T						PASS	.	T		3586,810	313.0+/-292.9	1473,640,85	89.0	90.0	90.0		1636	-0.6	1.0	11	dbSNP_83	90	3446,5146	623.1+/-397.4	706,2034,1556	no	coding-synonymous	PIWIL4	NM_152431.2		2179,2674,1641	TT,TC,CC		40.1071,18.4258,45.8577		546/853	94337220	7032,5956	2198	4296	6494	SO:0001819	synonymous_variant	143689	exon13			GTTCAGCTGGTAA	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1636C>T	11.37:g.94337220C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	69	23	0.333333	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			C|0.455;T|0.545	0.545	strong		0.318	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
RAPGEF1	2889	hgsc.bcm.edu	37	9	134473655	134473655	+	Silent	SNP	C	C	T	rs11243446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:134473655C>T	ENST00000372189.3	-	13	2109	c.1986G>A	c.(1984-1986)gaG>gaA	p.E662E	RAPGEF1_ENST00000372190.3_Silent_p.E680E|RAPGEF1_ENST00000372195.1_Silent_p.E679E	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	662					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)		CCACTTCCTCCTCCGACTGAG	0.587													C|||	468	0.0934505	0.1861	0.0418	5008	,	,		19644	0.0913		0.0229	False		,,,				2504	0.0798				p.E680E		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G2040A						PASS	.	C	,	622,3374		52,518,1428	57.0	60.0	59.0		1986,2040	1.1	1.0	9	dbSNP_120	59	172,8176		5,162,4007	no	coding-synonymous,coding-synonymous	RAPGEF1	NM_005312.2,NM_198679.1	,	57,680,5435	TT,TC,CC		2.0604,15.5656,6.4323	,	662/1078,680/1096	134473655	794,11550	1998	4174	6172	SO:0001819	synonymous_variant	2889	exon13			TTCCTCCTCCGAC	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.1986G>A	9.37:g.134473655C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	80	48	0.6	NM_198679	Q5JUE4|Q8IV73	Silent	SNP	ENST00000372189.3	37	CCDS48047.1	190	0.08699633699633699	89	0.18089430894308944	20	0.055248618784530384	63	0.11013986013986014	18	0.023746701846965697	C	7.173	0.587989	0.13812	0.155656	0.020604	ENSG00000107263	ENST00000414781	.	.	.	4.69	1.11	0.20524	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16335	-1.0406	3	.	.	.	.	4.7838	0.13215	0.0:0.5459:0.149:0.3051	rs11243446;rs11243446	.	.	.	R	90	.	.	G	-	1	0	RAPGEF1	133463476	0.512000	0.26186	0.980000	0.43619	0.729000	0.41735	-0.244000	0.08903	-0.007000	0.14345	-0.448000	0.05591	GGA	C|0.912;T|0.088	0.088	strong		0.587	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	
ZBED5	58486	hgsc.bcm.edu	37	11	10875200	10875200	+	Silent	SNP	C	C	T	rs2232925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:10875200C>T	ENST00000432999.2	-	3	1791	c.1293G>A	c.(1291-1293)gaG>gaA	p.E431E	ZBED5_ENST00000525350.1_Intron|ZBED5_ENST00000413761.2_Silent_p.E431E	NM_001143667.1|NM_021211.3	NP_001137139.1|NP_067034.2	Q49AG3	ZBED5_HUMAN	zinc finger, BED-type containing 5	431							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)	4						gccacctcacctctgtattta	0.373													C|||	417	0.0832668	0.2935	0.0346	5008	,	,		18511	0.0		0.005	False		,,,				2504	0.0				p.E431E		Atlas-SNP	.											.	ZBED5	50	.	0			c.G1293A						PASS	.	C	,	363,1021		52,259,381	76.0	66.0	69.0		1293,1293	1.1	1.0	11	dbSNP_98	69	9,3173		0,9,1582	no	coding-synonymous,coding-synonymous	ZBED5	NM_001143667.1,NM_021211.3	,	52,268,1963	TT,TC,CC		0.2828,26.2283,8.1472	,	431/694,431/694	10875200	372,4194	692	1591	2283	SO:0001819	synonymous_variant	58486	exon3			CCTCACCTCTGTA	AF205601		11p15.3	2013-05-03			ENSG00000236287	ENSG00000236287		"""Zinc fingers, BED-type"""	30803	protein-coding gene	gene with protein product		615251				10607616, 23533661	Standard	NM_021211		Approved	Buster1	uc009ygh.3	Q49AG3	OTTHUMG00000150341	ENST00000432999.2:c.1293G>A	11.37:g.10875200C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	78	28	0.358974	NM_021211	B2RCC1|Q05D82|Q86WW3|Q9NT24|Q9UBJ4	Silent	SNP	ENST00000432999.2	37																																																																																				C|0.888;T|0.112	0.112	strong		0.373	ZBED5-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000317691.1	NM_021211	
PSMD2	5708	hgsc.bcm.edu	37	3	184023918	184023918	+	Silent	SNP	A	A	G	rs34477849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184023918A>G	ENST00000310118.4	+	14	2337	c.1779A>G	c.(1777-1779)acA>acG	p.T593T	EIF2B5_ENST00000444495.1_Intron|PSMD2_ENST00000439383.1_Silent_p.T463T|PSMD2_ENST00000435761.1_Silent_p.T434T	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	593					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)	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)	enzyme regulator activity (GO:0030234)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|liver(1)|lung(12)|prostate(3)|upper_aerodigestive_tract(2)	27	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	TTGCCAACACACTGGTGGATG	0.507											OREG0015947	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	103	0.0205671	0.0741	0.0072	5008	,	,		22790	0.0		0.0	False		,,,				2504	0.0				p.T593T	Colon(24;313 636 6917 9932 15554)	Atlas-SNP	.											.	PSMD2	56	.	0			c.A1779G						PASS	.	A		261,4145	150.3+/-184.3	8,245,1950	150.0	112.0	125.0		1779	-12.0	0.0	3	dbSNP_126	125	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PSMD2	NM_002808.3		8,247,6248	GG,GA,AA		0.0233,5.9237,2.0221		593/909	184023918	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	5708	exon14			CAACACACTGGTG	AK095245	CCDS3258.1, CCDS63853.1, CCDS63854.1	3q27.3	2008-05-22			ENSG00000175166	ENSG00000175166		"""Proteasome (prosome, macropain) subunits"""	9559	protein-coding gene	gene with protein product		606223				8774743	Standard	NM_002808		Approved	S2, P97, TRAP2, MGC14274, Rpn1	uc003fnn.1	Q13200	OTTHUMG00000156796	ENST00000310118.4:c.1779A>G	3.37:g.184023918A>G		Somatic	284	1	0.00352113	1988	WXS	Illumina HiSeq	Phase_I	362	189	0.522099	NM_002808	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Silent	SNP	ENST00000310118.4	37	CCDS3258.1	35	0.016025641025641024	33	0.06707317073170732	2	0.0055248618784530384	0	0.0	0	0.0	A	9.215	1.031899	0.19590	0.059237	2.33E-4	ENSG00000175166	ENST00000432855	.	.	.	6.0	-12.0	0.00017	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54077	-0.8347	4	.	.	.	-13.3765	7.9576	0.30051	0.2487:0.1375:0.4867:0.1271	rs34477849;rs34477849	.	.	.	R	54	.	.	H	+	2	0	PSMD2	185506612	0.000000	0.05858	0.009000	0.14445	0.973000	0.67179	-2.546000	0.00932	-2.989000	0.00280	-1.179000	0.01719	CAC	A|0.976;G|0.024	0.024	strong		0.507	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808	
SLC19A2	10560	hgsc.bcm.edu	37	1	169446639	169446639	+	Silent	SNP	C	C	A	rs150548640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169446639C>A	ENST00000236137.5	-	2	797	c.561G>T	c.(559-561)ctG>ctT	p.L187L	SLC19A2_ENST00000367804.4_Intron	NM_006996.2	NP_008927.1	O60779	S19A2_HUMAN	solute carrier family 19 (thiamine transporter), member 2	187					folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|thiamine transport (GO:0015888)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid transporter activity (GO:0008517)|thiamine transmembrane transporter activity (GO:0015234)|thiamine uptake transmembrane transporter activity (GO:0015403)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	11	all_hematologic(923;0.208)				Thiamine(DB00152)	TCAGGCTGAACAGCGACCAGC	0.498													C|||	17	0.00339457	0.0106	0.0043	5008	,	,		19254	0.0		0.0	False		,,,				2504	0.0				p.L187L		Atlas-SNP	.											.	SLC19A2	35	.	0			c.G561T						PASS	.	C		48,4358	49.6+/-84.7	1,46,2156	57.0	59.0	58.0		561	-1.5	1.0	1	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous	SLC19A2	NM_006996.2		1,46,6456	AA,AC,CC		0.0,1.0894,0.3691		187/498	169446639	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	10560	exon2			GCTGAACAGCGAC	AF135488	CCDS1280.1	1q23.3	2013-05-22			ENSG00000117479	ENSG00000117479		"""Solute carriers"""	10938	protein-coding gene	gene with protein product		603941		TRMA		9399900, 10391221	Standard	NM_006996		Approved	THTR1	uc001gge.4	O60779	OTTHUMG00000035452	ENST00000236137.5:c.561G>T	1.37:g.169446639C>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	50	0.609756	NM_006996	B2R9H0|B4E1X4|Q8WV87|Q9UBL7|Q9UKJ2|Q9UN31|Q9UN43	Silent	SNP	ENST00000236137.5	37	CCDS1280.1																																																																																			C|0.996;A|0.004	0.004	strong		0.498	SLC19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086106.1	NM_006996	
UBAP2	55833	hgsc.bcm.edu	37	9	33927880	33927880	+	Nonstop_Mutation	SNP	C	C	G	rs16935295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:33927880C>G	ENST00000418786.2	-	17	2152	c.2060G>C	c.(2059-2061)tGa>tCa	p.*687S	UBAP2_ENST00000379238.1_Missense_Mutation_p.M762I|UBAP2_ENST00000539807.1_Missense_Mutation_p.M517I|UBAP2_ENST00000379235.1_Start_Codon_SNP_p.M1I|UBAP2_ENST00000360802.1_Missense_Mutation_p.M762I|UBAP2_ENST00000449054.1_Missense_Mutation_p.M762I|UBAP2_ENST00000379239.4_Missense_Mutation_p.M495I					ubiquitin associated protein 2											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)		TCGCGGTGTTCATGCTACTGG	0.637													C|||	151	0.0301518	0.1104	0.0058	5008	,	,		19308	0.0		0.001	False		,,,				2504	0.0				p.M762I		Atlas-SNP	.											.	UBAP2	82	.	0			c.G2286C						PASS	.	C	ILE/MET	448,3958	214.8+/-234.0	24,400,1779	90.0	87.0	88.0		2286	4.8	0.7	9	dbSNP_123	88	6,8594	5.0+/-18.6	0,6,4294	yes	missense	UBAP2	NM_018449.2	10	24,406,6073	GG,GC,CC		0.0698,10.168,3.4907	benign	762/1120	33927880	454,12552	2203	4300	6503	SO:0001578	stop_lost	55833	exon20			GGTGTTCATGCTA	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	ENST00000418786.2:c.2060G>C	9.37:g.33927880C>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	142	88	0.619718	NM_018449		Missense_Mutation	SNP	ENST00000418786.2	37		43|43	0.019688644688644688|0.019688644688644688	40|40	0.08130081300813008|0.08130081300813008	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	11.68|11.68	1.711377|1.711377	0.30322|0.30322	0.10168|0.10168	6.98E-4|6.98E-4	ENSG00000137073|ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379235;ENST00000379239;ENST00000539807;ENST00000351580|ENST00000418786	T;T;T;T;T;T|.	0.33216|.	1.66;1.66;1.66;1.42;1.66;1.66|.	5.77|5.77	4.85|4.85	0.62838|0.62838	.|.	0.315392|.	0.42682|.	D|.	0.000678|.	T|.	0.02267|.	0.0070|.	L|L	0.50919|0.50919	1.6|1.6	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.12013|.	0.005;0.002;0.002;0.002;0.003|.	B;B;B;B;B|.	0.09377|.	0.004;0.004;0.004;0.004;0.002|.	T|.	0.00761|.	-1.1577|.	10|.	0.23891|.	T|.	0.37|.	-1.1258|-1.1258	16.2411|16.2411	0.82409|0.82409	0.0:0.8668:0.1332:0.0|0.0:0.8668:0.1332:0.0	rs16935295;rs52823002;rs16935295|rs16935295;rs52823002;rs16935295	687;517;495;671;762|.	F5H4D5;F5H2U4;A6NCA8;F5H2C8;Q5T6F2|.	.;.;.;.;UBAP2_HUMAN|.	I|S	762;762;762;671;1;495;517;198|687	ENSP00000368540:M762I;ENSP00000416932:M762I;ENSP00000354039:M762I;ENSP00000368537:M1I;ENSP00000368541:M495I;ENSP00000439329:M517I|.	ENSP00000259602:M198I|.	M|X	-|-	3|2	0|2	UBAP2|UBAP2	33917880|33917880	1.000000|1.000000	0.71417|0.71417	0.710000|0.710000	0.30468|0.30468	0.061000|0.061000	0.15899|0.15899	1.399000|1.399000	0.34566|0.34566	1.383000|1.383000	0.46405|0.46405	0.655000|0.655000	0.94253|0.94253	ATG|TGA	C|0.965;G|0.035	0.035	strong		0.637	UBAP2-203	KNOWN	basic	protein_coding	protein_coding		NM_018449	
WDR27	253769	hgsc.bcm.edu	37	6	170036466	170036466	+	Splice_Site	SNP	C	C	A	rs111656694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170036466C>A	ENST00000448612.1	-	19	2113		c.e19+1		WDR27_ENST00000333572.6_Splice_Site|WDR27_ENST00000423258.1_Splice_Site|WDR27_ENST00000546525.1_Intron	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27							nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		GGGGTGCCTACCTCTTAATCT	0.373													C|||	139	0.0277556	0.0825	0.0245	5008	,	,		17163	0.004		0.005	False		,,,				2504	0.0041				.		Atlas-SNP	.											.	WDR27	129	.	0			c.2003+1G>T						PASS	.	C	,	310,3396		14,282,1557	56.0	60.0	59.0		,	5.0	0.1	6	dbSNP_132	59	36,8150		0,36,4057	yes	splice-5,splice-5	WDR27	NM_001202550.1,NM_182552.4	,	14,318,5614	AA,AC,CC		0.4398,8.3648,2.9095	,	,	170036466	346,11546	1853	4093	5946	SO:0001630	splice_region_variant	253769	exon20			TGCCTACCTCTTA	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"""WD repeat domain containing"""	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.2003+1G>T	6.37:g.170036466C>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_182552	A5PLM8|C9JGV0|Q5T066	Splice_Site	SNP	ENST00000448612.1	37	CCDS47520.2	53	0.024267399267399268	40	0.08130081300813008	10	0.027624309392265192	0	0.0	3	0.00395778364116095	C	13.36	2.212956	0.39102	0.083648	0.004398	ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000423258	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0154	0.86418	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR27	169778391	1.000000	0.71417	0.075000	0.20258	0.015000	0.08874	4.771000	0.62318	2.316000	0.78162	0.573000	0.79308	.	C|0.980;A|0.020	0.020	strong		0.373	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552	Intron
UBXN11	91544	hgsc.bcm.edu	37	1	26608877	26608877	+	Silent	SNP	G	G	A	rs1134582|rs140364749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26608877G>A	ENST00000374222.1	-	16	1940	c.1476C>T	c.(1474-1476)ggC>ggT	p.G492G	UBXN11_ENST00000357089.4_Silent_p.G459G|UBXN11_ENST00000374217.2_Silent_p.G459G|UBXN11_ENST00000374221.3_Silent_p.G492G|UBXN11_ENST00000314675.7_Silent_p.G372G|UBXN11_ENST00000374223.1_Silent_p.G249G			Q5T124	UBX11_HUMAN	UBX domain protein 11	492	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						cgggactggggccgggaccgg	0.721																																					p.G492G		Atlas-SNP	.											UBXN11,NS,carcinoma,0,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.C1476T						scavenged	.						33.0	40.0	38.0					1																	26608877		1787	4040	5827	SO:0001819	synonymous_variant	91544	exon16			ACTGGGGCCGGGA	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1476C>T	1.37:g.26608877G>A		Somatic	50	5	0.1		WXS	Illumina HiSeq	Phase_I	43	15	0.348837	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			G|0.870;A|0.130	0.130	strong		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
ICAM5	7087	hgsc.bcm.edu	37	19	10407169	10407169	+	Silent	SNP	G	G	C	rs710845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10407169G>C	ENST00000221980.4	+	11	2715	c.2652G>C	c.(2650-2652)ctG>ctC	p.L884L		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	884					phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CCGTGTGTCTGAACGGAgcgg	0.771													C|||	2557	0.510583	0.5681	0.6455	5008	,	,		6247	0.3313		0.5895	False		,,,				2504	0.4407				p.L884L		Atlas-SNP	.											.	ICAM5	53	.	0			c.G2652C						PASS	.	C		1682,962		566,550,206	4.0	3.0	3.0		2652	0.5	1.0	19	dbSNP_86	3	2905,1749		979,947,401	no	coding-synonymous	ICAM5	NM_003259.3		1545,1497,607	CC,CG,GG		37.5806,36.3843,37.1472		884/925	10407169	4587,2711	1322	2327	3649	SO:0001819	synonymous_variant	7087	exon11			GTGTCTGAACGGA	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.2652G>C	19.37:g.10407169G>C		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_003259	Q9Y6F3	Silent	SNP	ENST00000221980.4	37	CCDS12233.1																																																																																			G|0.499;C|0.501	0.501	strong		0.771	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
CD33	945	hgsc.bcm.edu	37	19	51738465	51738465	+	Missense_Mutation	SNP	G	G	A	rs58981829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51738465G>A	ENST00000262262.4	+	5	820	c.799G>A	c.(799-801)Gtt>Att	p.V267I	CD33_ENST00000421133.2_Missense_Mutation_p.V140I|CD33_ENST00000391796.3_Missense_Mutation_p.V267I|CD33_ENST00000436584.2_Missense_Mutation_p.V140I	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	267			V -> I (in dbSNP:rs58981829).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	AGGAGCTGGTGTTACAGCCCT	0.502													g|||	203	0.0405351	0.1399	0.0245	5008	,	,		19411	0.0		0.001	False		,,,				2504	0.0				p.V267I		Atlas-SNP	.											CD33,NS,carcinoma,0,1	CD33	55	1	0			c.G799A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	521,3885		29,463,1711	151.0	123.0	133.0		418,799,799	1.9	0.0	19	dbSNP_129	133	5,8595		0,5,4295	yes	missense,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	29,29,29	29,468,6006	AA,AG,GG		0.0581,11.8248,4.0443	benign,benign,benign	140/238,267/311,267/365	51738465	526,12480	2203	4300	6503	SO:0001583	missense	945	exon5			GCTGGTGTTACAG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.799G>A	19.37:g.51738465G>A	ENSP00000262262:p.Val267Ile	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	224	121	0.540179	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	67	0.030677655677655676	54	0.10975609756097561	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	.	6.151	0.396010	0.11638	0.118248	5.81E-4	ENSG00000105383	ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796	T;T;T;T	0.39997	1.05;2.69;2.69;2.16	4.13	1.93	0.25924	.	1.922710	0.03611	N	0.234840	T	0.00524	0.0017	L	0.35644	1.08	0.80722	P	0.0	B;B;B	0.10296	0.0;0.003;0.001	B;B;B	0.12156	0.002;0.007;0.002	T	0.10405	-1.0631	9	0.26408	T	0.33	.	9.5522	0.39317	0.195:0.0:0.805:0.0	rs58981829;rs61736474	140;267;267	C9JEN7;F8WAL2;P20138	.;.;CD33_HUMAN	I	140;267;140;267	ENSP00000403331:V140I;ENSP00000262262:V267I;ENSP00000410126:V140I;ENSP00000375673:V267I	ENSP00000262262:V267I	V	+	1	0	CD33	56430277	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.249000	0.18216	0.169000	0.19679	-0.939000	0.02691	GTT	G|0.955;A|0.045	0.045	strong		0.502	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
DLK1	8788	hgsc.bcm.edu	37	14	101200780	101200780	+	Silent	SNP	T	T	C	rs2295660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101200780T>C	ENST00000341267.4	+	5	941	c.699T>C	c.(697-699)tgT>tgC	p.C233C	DLK1_ENST00000331224.6_Intron	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	233	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)				GCTACGAGTGTCTGTGCAAGC	0.662													T|||	107	0.0213658	0.0371	0.0058	5008	,	,		15534	0.0506		0.003	False		,,,				2504	0.0				p.C233C		Atlas-SNP	.											.	DLK1	57	.	0			c.T699C						PASS	.	T		104,4300		1,102,2099	38.0	44.0	42.0		699	3.1	1.0	14	dbSNP_100	42	8,8590		0,8,4291	no	coding-synonymous	DLK1	NM_003836.5		1,110,6390	CC,CT,TT		0.093,2.3615,0.8614		233/384	101200780	112,12890	2202	4299	6501	SO:0001819	synonymous_variant	8788	exon5			CGAGTGTCTGTGC	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.699T>C	14.37:g.101200780T>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	46	15	0.326087	NM_003836	P15803|Q96DW5	Silent	SNP	ENST00000341267.4	37	CCDS9963.1																																																																																			T|0.981;C|0.019	0.019	strong		0.662	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
BAIAP2	10458	hgsc.bcm.edu	37	17	79089590	79089590	+	Missense_Mutation	SNP	A	A	G	rs4969391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79089590A>G	ENST00000321300.6	+	14	1649	c.1556A>G	c.(1555-1557)cAg>cGg	p.Q519R	BAIAP2_ENST00000428708.2_Missense_Mutation_p.Q519R|BAIAP2_ENST00000392411.3_Missense_Mutation_p.Q441R|BAIAP2_ENST00000435091.3_3'UTR|BAIAP2_ENST00000575245.1_3'UTR	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	519			Q -> R (in dbSNP:rs4969391).		actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GCCCACGTCCAGCTGAAGCCG	0.582													A|||	863	0.172324	0.1059	0.3631	5008	,	,		17328	0.1478		0.1561	False		,,,				2504	0.1687				p.Q519R		Atlas-SNP	.											BAIAP2_ENST00000321300,colon,carcinoma,0,1	BAIAP2	74	1	0			c.A1556G						PASS	.	A	ARG/GLN,,ARG/GLN	516,3890	234.6+/-247.4	35,446,1722	90.0	91.0	91.0		1556,,1556	5.0	1.0	17	dbSNP_111	91	1330,7270	259.8+/-282.9	98,1134,3068	yes	missense,utr-3,missense	BAIAP2	NM_001144888.1,NM_006340.2,NM_017451.2	43,,43	133,1580,4790	GG,GA,AA		15.4651,11.7113,14.1934	benign,,benign	519/535,,519/553	79089590	1846,11160	2203	4300	6503	SO:0001583	missense	10458	exon14			ACGTCCAGCTGAA	AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.1556A>G	17.37:g.79089590A>G	ENSP00000316338:p.Gln519Arg	Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Missense_Mutation	SNP	ENST00000321300.6	37	CCDS11775.1	410	0.18772893772893773	84	0.17073170731707318	112	0.30939226519337015	92	0.16083916083916083	122	0.16094986807387862	A	13.79	2.343165	0.41498	0.117113	0.154651	ENSG00000175866	ENST00000321300;ENST00000428708;ENST00000392411	T;T;T	0.38560	1.13;1.13;1.13	4.96	4.96	0.65561	.	1.320840	0.04637	N	0.404645	T	0.00012	0.0000	N	0.04508	-0.205	0.43761	P	0.0037289999999999823	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.18935	-1.0321	9	0.30854	T	0.27	-1.4439	8.529	0.33321	0.9135:0.0:0.0865:0.0	rs4969391;rs52805958;rs56955834;rs4969391	441;519;519	F8W878;Q9UQB8;Q9UQB8-2	.;BAIP2_HUMAN;.	R	519;519;441	ENSP00000316338:Q519R;ENSP00000401022:Q519R;ENSP00000376211:Q441R	ENSP00000316338:Q519R	Q	+	2	0	BAIAP2	76704185	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	4.516000	0.60496	1.862000	0.54008	0.379000	0.24179	CAG	A|0.843;G|0.157	0.157	strong		0.582	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		
MUC6	4588	hgsc.bcm.edu	37	11	1017483	1017483	+	Missense_Mutation	SNP	T	T	G	rs79986665		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017483T>G	ENST00000421673.2	-	31	5368	c.5318A>C	c.(5317-5319)cAc>cCc	p.H1773P		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1773	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			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)		TGTACTGGTGTGGTTGGGGGT	0.577																																					p.H1773P		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	0			c.A5318C						scavenged	.						544.0	541.0	542.0					11																	1017483		2199	4294	6493	SO:0001583	missense	4588	exon31			CTGGTGTGGTTGG	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.5318A>C	11.37:g.1017483T>G	ENSP00000406861:p.His1773Pro	Somatic	901	170	0.188679		WXS	Illumina HiSeq	Phase_I	1213	220	0.181369	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	T	4.174	0.030796	0.08101	.	.	ENSG00000184956	ENST00000421673	T	0.17528	2.27	2.91	0.844	0.18943	.	.	.	.	.	T	0.04907	0.0132	N	0.01109	-1.01	0.09310	N	1	B	0.15930	0.015	B	0.14023	0.01	T	0.43065	-0.9414	9	0.22706	T	0.39	.	6.6218	0.22808	0.0:0.1732:0.4682:0.3586	.	1773	Q6W4X9	MUC6_HUMAN	P	1773	ENSP00000406861:H1773P	ENSP00000406861:H1773P	H	-	2	0	MUC6	1007483	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.094000	0.11094	0.066000	0.16515	-0.743000	0.03520	CAC	T|0.500;G|0.500	0.500	weak		0.577	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
KIAA0196	9897	hgsc.bcm.edu	37	8	126079867	126079867	+	Silent	SNP	T	T	C	rs10429323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:126079867T>C	ENST00000318410.7	-	10	1594	c.1245A>G	c.(1243-1245)ttA>ttG	p.L415L	KIAA0196_ENST00000517845.1_Silent_p.L267L	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	415					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)			GTGCAGTATCTAACAGCAGCT	0.358													C|||	160	0.0319489	0.1157	0.0101	5008	,	,		15835	0.0		0.0	False		,,,				2504	0.0				p.L415L		Atlas-SNP	.											.	KIAA0196	90	.	0			c.A1245G						PASS	.	C		358,4048	793.9+/-415.2	17,324,1862	166.0	155.0	158.0		1245	4.7	1.0	8	dbSNP_119	158	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	KIAA0196	NM_014846.3		17,325,6161	CC,CT,TT		0.0116,8.1253,2.7603		415/1160	126079867	359,12647	2203	4300	6503	SO:0001819	synonymous_variant	9897	exon10			AGTATCTAACAGC		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.1245A>G	8.37:g.126079867T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1	51	0.023351648351648352	45	0.09146341463414634	6	0.016574585635359115	0	0.0	0	0.0	C	8.635	0.894613	0.17613	0.081253	1.16E-4	ENSG00000164961	ENST00000523273	.	.	.	5.61	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.6356	10.9586	0.47372	0.1293:0.8033:0.0:0.0675	rs10429323;rs10429323	.	.	.	W	32	.	.	X	-	2	0	KIAA0196	126149049	0.998000	0.40836	0.996000	0.52242	0.751000	0.42716	0.645000	0.24782	1.393000	0.46605	-0.320000	0.08662	TAG	T|0.971;C|0.029	0.029	strong		0.358	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
DMD	1756	hgsc.bcm.edu	37	X	32716110	32716110	+	Silent	SNP	C	C	T	rs1800265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:32716110C>T	ENST00000357033.4	-	9	1043	c.837G>A	c.(835-837)acG>acA	p.T279T	DMD_ENST00000288447.4_Silent_p.T271T|DMD_ENST00000378677.2_Silent_p.T275T	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	279			T -> A (in CMD3B). {ECO:0000269|PubMed:9170407}.		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)				CTAGACTGACCGTGATCTGCA	0.488													T|||	570	0.150993	0.3805	0.0865	3775	,	,		11752	0.002		0.002	False		,,,				2504	0.0031				p.T279T		Atlas-SNP	.											.	DMD	2127	.	0			c.G837A						PASS	.	T	,,,,	1838,1995		386,779,287,466,284	105.0	73.0	84.0		813,837,468,825,468	-1.6	1.0	X	dbSNP_89	84	21,6701		0,17,4,2410,1864	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	386,796,291,2876,2148	TT,TC,T,CC,C		0.3124,47.952,17.6125	,,,,	271/3678,279/3686,156/3563,275/3682,156/3563	32716110	1859,8696	2202	4295	6497	SO:0001819	synonymous_variant	1756	exon9			ACTGACCGTGATC	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.837G>A	X.37:g.32716110C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	150	77	0.513333	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																			C|0.852;T|0.148	0.148	strong		0.488	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047354	46047354	+	Missense_Mutation	SNP	A	A	G	rs62220927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46047354A>G	ENST00000397911.3	+	1	315	c.266A>G	c.(265-267)tAc>tGc	p.Y89C	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	89	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CAGCCGGCTTACTGCACCTCC	0.677													G|||	757	0.151158	0.382	0.0735	5008	,	,		18600	0.0109		0.0606	False		,,,				2504	0.1319				p.Y89C		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.A266G						PASS	.	G	,CYS/TYR	1527,2865	619.7+/-393.4	276,975,945	65.0	84.0	77.0		,266	3.3	0.6	21	dbSNP_129	77	440,8148	777.4+/-407.7	10,420,3864	no	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,194	286,1395,4809	GG,GA,AA		5.1234,34.7678,15.1541	,benign	,89/293	46047354	1967,11013	2196	4294	6490	SO:0001583	missense	386676	exon1			CGGCTTACTGCAC	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.266A>G	21.37:g.46047354A>G	ENSP00000381009:p.Tyr89Cys	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	172	68	0.395349	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	251	0.11492673992673992	173	0.3516260162601626	32	0.08839779005524862	7	0.012237762237762238	39	0.051451187335092345	g	0.006	-2.039182	0.00402	0.347678	0.051234	ENSG00000221837	ENST00000397911	T	0.00609	6.24	3.34	3.34	0.38264	.	.	.	.	.	T	0.00012	0.0000	N	0.00001	-3.815	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	7	.	.	.	.	5.2668	0.15603	0.1222:0.2084:0.6693:0.0	rs62220927	89	P60411	KR109_HUMAN	C	89	ENSP00000381009:Y89C	.	Y	+	2	0	KRTAP10-9	44871782	0.004000	0.15560	0.579000	0.28588	0.422000	0.31414	-0.003000	0.12901	0.518000	0.28383	-0.124000	0.14976	TAC	A|0.896;G|0.104	0.104	strong		0.677	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
AJAP1	55966	hgsc.bcm.edu	37	1	4772053	4772053	+	Silent	SNP	T	T	C	rs1061968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	86	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	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	
SLC30A5	64924	hgsc.bcm.edu	37	5	68419054	68419054	+	Silent	SNP	A	A	T	rs164572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68419054A>T	ENST00000396591.3	+	14	2410	c.1800A>T	c.(1798-1800)acA>acT	p.T600T	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	600					cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TGGCAGATACACTTGGCAGCA	0.318													A|||	2015	0.402356	0.2519	0.4107	5008	,	,		18363	0.5397		0.4225	False		,,,				2504	0.4376				p.T600T		Atlas-SNP	.											.	SLC30A5	54	.	0			c.A1800T						PASS	.	A		1157,3249	410.2+/-335.3	142,873,1188	129.0	114.0	119.0		1800	-1.5	1.0	5	dbSNP_79	119	3721,4879	533.2+/-382.4	829,2063,1408	no	coding-synonymous	SLC30A5	NM_022902.3		971,2936,2596	TT,TA,AA		43.2674,26.2596,37.5058		600/766	68419054	4878,8128	2203	4300	6503	SO:0001819	synonymous_variant	64924	exon14			AGATACACTTGGC	AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"""Solute carriers"""	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.1800A>T	5.37:g.68419054A>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	41	23	0.560976	NM_022902	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Silent	SNP	ENST00000396591.3	37	CCDS3996.1																																																																																			A|0.607;T|0.393	0.393	strong		0.318	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2		
TTN	7273	hgsc.bcm.edu	37	2	179479245	179479245	+	Silent	SNP	C	C	T	rs72677244	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179479245C>T	ENST00000591111.1	-	211	44297	c.44073G>A	c.(44071-44073)gaG>gaA	p.E14691E	TTN_ENST00000589042.1_Silent_p.E16332E|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Silent_p.E7267E|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Silent_p.E13764E|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN_ENST00000359218.5_Silent_p.E7392E|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342175.6_Silent_p.E7459E|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14691	Ig-like 96.				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)			CATTCACAGCCTCAATGATAT	0.418													C|||	363	0.072484	0.0847	0.0231	5008	,	,		18504	0.1567		0.0209	False		,,,				2504	0.0573				p.E16332E		Atlas-SNP	.											.	TTN	18412	.	0			c.G48996A						PASS	.	C	,,,	251,3699		7,237,1731	96.0	92.0	94.0		21801,41292,22176,22377	2.9	1.0	2	dbSNP_130	94	105,8175		1,103,4036	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	8,340,5767	TT,TC,CC		1.2681,6.3544,2.9109	,,,	7267/26927,13764/33424,7392/27052,7459/27119	179479245	356,11874	1975	4140	6115	SO:0001819	synonymous_variant	7273	exon261			CACAGCCTCAATG	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.44073G>A	2.37:g.179479245C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	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|0.941;T|0.059	0.059	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CXorf38	159013	hgsc.bcm.edu	37	X	40496354	40496354	+	Missense_Mutation	SNP	T	T	C	rs17145855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40496354T>C	ENST00000327877.5	-	4	552	c.526A>G	c.(526-528)Acg>Gcg	p.T176A	CXorf38_ENST00000378421.1_Missense_Mutation_p.T57A|CXorf38_ENST00000378426.1_Missense_Mutation_p.T57A|CXorf38_ENST00000440784.2_Missense_Mutation_p.T91A	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	176			T -> A (in dbSNP:rs17145855).							NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						CGAAGCCACGTAGAAGATACT	0.358													T|||	57	0.0150993	0.0424	0.0014	3775	,	,		14154	0.0		0.0	False		,,,				2504	0.0				p.T176A		Atlas-SNP	.											.	CXorf38	29	.	0			c.A526G						PASS	.	T	ALA/THR	179,3656		2,151,24,1479,547	56.0	51.0	53.0		526	-7.7	0.0	X	dbSNP_123	53	0,6728		0,0,0,2428,1872	yes	missense	CXorf38	NM_144970.2	58	2,151,24,3907,2419	CC,CT,C,TT,T		0.0,4.6675,1.6946	benign	176/320	40496354	179,10384	2203	4300	6503	SO:0001583	missense	159013	exon4			GCCACGTAGAAGA	AL832829	CCDS14253.1	Xp11	2008-02-05			ENSG00000185753	ENSG00000185753			28589	protein-coding gene	gene with protein product							Standard	NM_144970		Approved	MGC39350	uc004dew.3	Q8TB03	OTTHUMG00000024104	ENST00000327877.5:c.526A>G	X.37:g.40496354T>C	ENSP00000330488:p.Thr176Ala	Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	323	155	0.479876	NM_144970	B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	37	CCDS14253.1	16	0.009644364074743821	9	0.01882845188284519	0	0.0	0	0.0	0	0.0	T	0.117	-1.130194	0.01756	0.046675	0.0	ENSG00000185753	ENST00000378426;ENST00000327877;ENST00000378421;ENST00000440784	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	4.95	-7.7	0.01259	.	1.658950	0.02974	N	0.144773	T	0.02610	0.0079	N	0.14661	0.345	0.34371	P	0.30793899999999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10776	-1.0615	9	0.08837	T	0.75	0.4805	2.9505	0.05860	0.1431:0.3119:0.0909:0.4542	rs17145855;rs52818878;rs17145855	91;176	E7EN46;Q8TB03	.;CX038_HUMAN	A	57;176;57;91	ENSP00000367683:T57A;ENSP00000330488:T176A;ENSP00000367677:T57A;ENSP00000400019:T91A	ENSP00000330488:T176A	T	-	1	0	CXorf38	40381298	0.000000	0.05858	0.003000	0.11579	0.414000	0.31173	-1.312000	0.02720	-1.183000	0.02723	-0.537000	0.04273	ACG	0|0.003;C|0.018	0.018	strong		0.358	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3	NM_144970	
GLRA4	441509	hgsc.bcm.edu	37	X	102962343	102962343	+	Missense_Mutation	SNP	T	T	C	rs61744012		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102962343T>C	ENST00000372617.4	-	9	1603	c.1183A>G	c.(1183-1185)Att>Gtt	p.I395V		NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	395						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						GGACTATAAATGCCAGAACCT	0.527													T|||	48	0.0127152	0.0348	0.0029	3775	,	,		14232	0.0		0.0	False		,,,				2504	0.0				p.I395V		Atlas-SNP	.											.	GLRA4	86	.	0			c.A1183G						PASS	.	T	VAL/ILE	94,3180		0,77,17,1275,553	105.0	100.0	102.0		1183	5.0	1.0	X	dbSNP_129	102	1,6426		0,1,0,2321,1783	yes	missense	GLRA4	NM_001024452.2	29	0,78,17,3596,2336	CC,CT,C,TT,T		0.0156,2.8711,0.9793	benign	395/418	102962343	95,9606	1922	4105	6027	SO:0001583	missense	441509	exon9			TATAAATGCCAGA	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.1183A>G	X.37:g.102962343T>C	ENSP00000361700:p.Ile395Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	136	84	0.617647	NM_001024452		Missense_Mutation	SNP	ENST00000372617.4	37	CCDS43980.2	16	0.009644364074743821	12	0.024691358024691357	1	0.0027624309392265192	0	0.0	0	0.0	t	2.377	-0.343098	0.05243	0.028711	1.56E-4	ENSG00000188828	ENST00000372617	T	0.77877	-1.13	4.99	4.99	0.66335	.	1.027970	0.07653	N	0.932363	T	0.31263	0.0791	N	0.02539	-0.55	0.27370	N	0.955726	B	0.02656	0.0	B	0.01281	0.0	T	0.31223	-0.9951	10	0.25106	T	0.35	.	9.8284	0.40925	0.0:0.0:0.0:1.0	.	395	Q5JXX5	GLRA4_HUMAN	V	395	ENSP00000361700:I395V	ENSP00000361700:I395V	I	-	1	0	GLRA4	102848999	0.380000	0.25131	0.999000	0.59377	0.987000	0.75469	0.625000	0.24477	1.844000	0.53588	0.441000	0.28932	ATT	T|0.990;C|0.010	0.010	strong		0.527	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452	
ZNF814	730051	hgsc.bcm.edu	37	19	58385987	58385987	+	Missense_Mutation	SNP	C	C	G	rs111291730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58385987C>G	ENST00000435989.2	-	3	1005	c.771G>C	c.(769-771)ttG>ttC	p.L257F	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	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)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						GATGATTACTCAAGCTAGCAT	0.398													.|||	16	0.00319489	0.0121	0.0	5008	,	,		23651	0.0		0.0	False		,,,				2504	0.0				p.L257F		Atlas-SNP	.											.	ZNF814	93	.	0			c.G771C						PASS	.						120.0	91.0	100.0					19																	58385987		692	1591	2283	SO:0001583	missense	730051	exon3			ATTACTCAAGCTA		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.771G>C	19.37:g.58385987C>G	ENSP00000410545:p.Leu257Phe	Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	257	126	0.490272	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	.	6.736	0.504632	0.12822	.	.	ENSG00000204514	ENST00000435989	T	0.52057	0.68	2.23	-1.06	0.10002	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32010	0.0815	M	0.62723	1.935	0.09310	N	1	B	0.14805	0.011	B	0.12156	0.007	T	0.30208	-0.9986	9	0.49607	T	0.09	.	5.757	0.18178	0.2141:0.4859:0.3:0.0	.	257	B7Z6K7	ZN814_HUMAN	F	257	ENSP00000410545:L257F	ENSP00000410545:L257F	L	-	3	2	ZNF814	63077799	0.005000	0.15991	0.000000	0.03702	0.011000	0.07611	0.213000	0.17521	-0.743000	0.04784	-2.575000	0.00170	TTG	C|0.998;G|0.002	0.002	strong		0.398	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
CNGA4	1262	hgsc.bcm.edu	37	11	6262715	6262715	+	Silent	SNP	G	G	A	rs7129498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6262715G>A	ENST00000379936.2	+	5	1087	c.972G>A	c.(970-972)caG>caA	p.Q324Q	CNGA4_ENST00000533426.1_Silent_p.Q93Q	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	324					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 cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCATCTTACAGCACTTGCCTG	0.552													G|||	1062	0.212061	0.4546	0.1599	5008	,	,		21775	0.0407		0.163	False		,,,				2504	0.1483				p.Q324Q		Atlas-SNP	.											.	CNGA4	96	.	0			c.G972A						PASS	.	G		1736,2666	518.6+/-369.8	334,1068,799	99.0	93.0	95.0		972	1.2	1.0	11	dbSNP_116	95	1513,7079	287.0+/-298.0	125,1263,2908	no	coding-synonymous	CNGA4	NM_001037329.3		459,2331,3707	AA,AG,GG		17.6094,39.4366,25.0038		324/576	6262715	3249,9745	2201	4296	6497	SO:0001819	synonymous_variant	1262	exon5			CTTACAGCACTTG	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2152	protein-coding gene	gene with protein product		609472	"""cyclic nucleotide gated channel beta 2"""	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.972G>A	11.37:g.6262715G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_001037329		Silent	SNP	ENST00000379936.2	37	CCDS31408.1																																																																																			G|0.774;A|0.226	0.226	strong		0.552	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329	
PRCP	5547	hgsc.bcm.edu	37	11	82550387	82550387	+	Silent	SNP	A	A	G	rs4843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:82550387A>G	ENST00000313010.3	-	7	1196	c.1002T>C	c.(1000-1002)taT>taC	p.Y334Y	PRCP_ENST00000525772.1_5'UTR|PRCP_ENST00000393399.2_Silent_p.Y355Y|PRCP_ENST00000535099.1_Silent_p.Y229Y	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	334	SKS domain.				angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						AATAATTGTAATATACATTCA	0.378													A|||	525	0.104832	0.267	0.0418	5008	,	,		18163	0.005		0.0278	False		,,,				2504	0.1125				p.Y355Y		Atlas-SNP	.											.	PRCP	69	.	0			c.T1065C						PASS	.	A	,	1014,3392	375.4+/-321.6	108,798,1297	91.0	91.0	91.0		1002,1065	4.4	1.0	11	dbSNP_52	91	315,8285	112.1+/-172.3	5,305,3990	no	coding-synonymous,coding-synonymous	PRCP	NM_005040.2,NM_199418.2	,	113,1103,5287	GG,GA,AA		3.6628,23.0141,10.2184	,	334/497,355/518	82550387	1329,11677	2203	4300	6503	SO:0001819	synonymous_variant	5547	exon8			ATTGTAATATACA	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.1002T>C	11.37:g.82550387A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	55	37	0.672727	NM_199418	A8MU24|B2R7B7|B3KRK5|B5BU34	Silent	SNP	ENST00000313010.3	37	CCDS8262.1																																																																																			A|0.900;G|0.100	0.100	strong		0.378	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040	
GAS6	2621	hgsc.bcm.edu	37	13	114526504	114526504	+	Silent	SNP	G	G	A	rs74118435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114526504G>A	ENST00000327773.6	-	13	1643	c.1497C>T	c.(1495-1497)gtC>gtT	p.V499V	GAS6_ENST00000355761.4_Silent_p.V445V|GAS6-AS1_ENST00000458001.1_RNA|GAS6_ENST00000418959.3_Silent_p.V200V|GAS6_ENST00000357389.3_Silent_p.V542V|GAS6_ENST00000450766.1_Silent_p.V226V	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	542	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				activation of protein kinase B activity (GO:0032148)|apoptotic cell clearance (GO:0043277)|B cell chemotaxis (GO:0035754)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to interferon-alpha (GO:0035457)|cellular response to starvation (GO:0009267)|cellular response to vitamin K (GO:0071307)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|extracellular matrix assembly (GO:0085029)|fusion of virus membrane with host plasma membrane (GO:0019064)|hematopoietic stem cell migration to bone marrow (GO:0097241)|leukocyte migration (GO:0050900)|macrophage cytokine production (GO:0010934)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of oligodendrocyte apoptotic process (GO:1900142)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of renal albumin absorption (GO:2000533)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|peptidyl-serine phosphorylation (GO:0018105)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phagocytosis (GO:0050766)|positive regulation of protein export from nucleus (GO:0046827)|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 tyrosine kinase activity (GO:0061098)|positive regulation of TOR signaling (GO:0032008)|post-translational protein modification (GO:0043687)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein targeting to plasma membrane (GO:0072661)|proteolysis (GO:0006508)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|viral entry into host cell (GO:0046718)|viral genome replication (GO:0019079)	cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|platelet alpha granule lumen (GO:0031093)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|phosphatidylserine binding (GO:0001786)|protein tyrosine kinase activator activity (GO:0030296)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(4)|ovary(1)	5	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)				ATTCAGTCCCGACGTCCAGAG	0.627													G|||	111	0.0221645	0.0809	0.0058	5008	,	,		19406	0.0		0.0	False		,,,				2504	0.0				p.V499V		Atlas-SNP	.											.	GAS6	75	.	0			c.C1497T						PASS	.	G	,,	282,4122	157.4+/-190.3	8,266,1928	96.0	79.0	85.0		1497,678,600	-9.1	0.0	13	dbSNP_130	85	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS6	NM_000820.2,NM_001143945.1,NM_001143946.1	,,	8,269,6225	AA,AG,GG		0.0349,6.4033,2.1916	,,	499/679,226/406,200/380	114526504	285,12719	2202	4300	6502	SO:0001819	synonymous_variant	2621	exon13			AGTCCCGACGTCC		CCDS45072.1	13q34	2008-07-18			ENSG00000183087	ENSG00000183087			4168	protein-coding gene	gene with protein product	"""AXL stimulatory factor"""	600441		AXLLG		8336730	Standard	NM_000820		Approved	AXSF, FLJ34709, DKFZp666G247	uc001vud.3	Q14393	OTTHUMG00000017395	ENST00000327773.6:c.1497C>T	13.37:g.114526504G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	95	54	0.568421	NM_000820	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Silent	SNP	ENST00000327773.6	37	CCDS45072.1																																																																																			G|0.971;A|0.029	0.029	strong		0.627	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2	NM_000820	
EP400	57634	hgsc.bcm.edu	37	12	132514288	132514288	+	Silent	SNP	C	C	G	rs58319354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132514288C>G	ENST00000333577.4	+	29	5641	c.5532C>G	c.(5530-5532)tcC>tcG	p.S1844S	EP400_ENST00000332482.4_Silent_p.S1771S|EP400_ENST00000389561.2_Silent_p.S1808S|EP400_ENST00000389562.2_Silent_p.S1807S|SNORA49_ENST00000386157.1_RNA|EP400_ENST00000330386.6_Silent_p.S1727S			Q96L91	EP400_HUMAN	E1A binding protein p400	1844					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CACCCCCGTCCCTACGGGTGC	0.632													C|||	645	0.128794	0.3517	0.0389	5008	,	,		17812	0.0714		0.0447	False		,,,				2504	0.0368				p.S1808S		Atlas-SNP	.											.	EP400	370	.	0			c.C5424G						PASS	.	C		1344,3058		215,914,1072	37.0	41.0	40.0		5424	1.7	0.0	12	dbSNP_129	40	213,8377		3,207,4085	no	coding-synonymous	EP400	NM_015409.4		218,1121,5157	GG,GC,CC		2.4796,30.5316,11.9843		1808/3124	132514288	1557,11435	2201	4295	6496	SO:0001819	synonymous_variant	57634	exon28			CCCGTCCCTACGG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.5532C>G	12.37:g.132514288C>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	74	26	0.351351	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				C|0.882;G|0.118	0.118	strong		0.632	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
TTC3	7267	hgsc.bcm.edu	37	21	38524226	38524226	+	Silent	SNP	A	A	G	rs2835632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38524226A>G	ENST00000399017.2	+	26	5057	c.2310A>G	c.(2308-2310)aaA>aaG	p.K770K	TTC3_ENST00000540756.1_Silent_p.K460K|TTC3_ENST00000355666.1_Silent_p.K770K|TTC3_ENST00000354749.2_Silent_p.K770K|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	770					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AAGACAAAAAATTGAAGAGAA	0.338													A|||	528	0.105431	0.2466	0.1715	5008	,	,		18165	0.0407		0.003	False		,,,				2504	0.0399				p.K770K	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A2310G						PASS	.	A	,	912,3494	336.3+/-304.3	94,724,1385	67.0	66.0	66.0		2310,2310	0.3	0.2	21	dbSNP_100	66	16,8582	11.2+/-40.8	0,16,4283	no	coding-synonymous,coding-synonymous	TTC3	NM_001001894.1,NM_003316.3	,	94,740,5668	GG,GA,AA		0.1861,20.699,7.1363	,	770/2026,770/2026	38524226	928,12076	2203	4299	6502	SO:0001819	synonymous_variant	7267	exon26			CAAAAAATTGAAG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.2310A>G	21.37:g.38524226A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	192	105	0.546875	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1	197	0.0902014652014652	113	0.22967479674796748	51	0.1408839779005525	31	0.05419580419580419	2	0.002638522427440633	A	6.749	0.507112	0.12883	0.20699	0.001861	ENSG00000182670	ENST00000414818	.	.	.	5.42	0.33	0.15929	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25717	P	0.9854106	.	.	.	.	.	.	T	0.17561	-1.0365	3	.	.	.	-5.4385	8.4056	0.32612	0.6847:0.0:0.3153:0.0	rs2835632;rs3737425	.	.	.	S	134	.	.	N	+	2	0	TTC3	37446096	0.645000	0.27286	0.218000	0.23776	0.987000	0.75469	1.103000	0.31062	-0.103000	0.12175	-0.274000	0.10170	AAT	A|0.931;G|0.069	0.069	strong		0.338	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
ABCC11	85320	hgsc.bcm.edu	37	16	48250026	48250026	+	Splice_Site	SNP	G	G	T	rs11863236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48250026G>T	ENST00000394747.1	-	6	1299	c.950C>A	c.(949-951)gCg>gAg	p.A317E	ABCC11_ENST00000537808.1_Splice_Site_p.A317E|ABCC11_ENST00000356608.2_Splice_Site_p.A317E|ABCC11_ENST00000353782.5_Splice_Site_p.A317E|ABCC11_ENST00000394748.1_Splice_Site_p.A317E	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	317	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.		A -> E (in dbSNP:rs11863236). {ECO:0000269|PubMed:11591886}.		organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|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)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	AGACATTACCGCCAGTGGGAA	0.473													T|||	646	0.128994	0.298	0.0893	5008	,	,		21675	0.0446		0.1014	False		,,,				2504	0.044				p.A317E		Atlas-SNP	.											.	ABCC11	177	.	0			c.C950A						PASS	.	T	GLU/ALA,GLU/ALA,GLU/ALA	1109,3293	717.2+/-408.7	141,827,1233	119.0	124.0	122.0		950,950,950	2.3	0.7	16	dbSNP_120	122	758,7842	785.3+/-407.6	29,700,3571	yes	missense-near-splice,missense-near-splice,missense-near-splice	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	107,107,107	170,1527,4804	TT,TG,GG		8.814,25.1931,14.3593	benign,benign,benign	317/1383,317/1383,317/1345	48250026	1867,11135	2201	4300	6501	SO:0001630	splice_region_variant	85320	exon6			ATTACCGCCAGTG	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.951+1C>A	16.37:g.48250026G>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	260	0.11904761904761904	132	0.2682926829268293	37	0.10220994475138122	14	0.024475524475524476	77	0.10158311345646438	T	0.527	-0.859672	0.02610	0.251931	0.08814	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	D;D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08;-3.08	4.67	2.31	0.28768	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.215586	0.39544	N	0.001328	T	0.00012	0.0000	N	0.00538	-1.39	0.58432	P	9.99999999995449E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23619	-1.0183	9	0.36615	T	0.2	-7.7007	5.8459	0.18665	0.1607:0.0:0.3348:0.5044	rs11863236;rs52789697;rs11863236	317;317	Q96J66-2;Q96J66	.;ABCCB_HUMAN	E	317	ENSP00000311326:A317E;ENSP00000349017:A317E;ENSP00000378231:A317E;ENSP00000378230:A317E;ENSP00000438530:A317E	ENSP00000311326:A317E	A	-	2	0	ABCC11	46807527	0.999000	0.42202	0.706000	0.30403	0.030000	0.12068	1.236000	0.32683	-0.053000	0.13289	-0.256000	0.11100	GCG	G|0.864;T|0.136	0.136	strong		0.473	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	Missense_Mutation
HMCN1	83872	hgsc.bcm.edu	37	1	186057347	186057347	+	Silent	SNP	A	A	T	rs61745374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186057347A>T	ENST00000271588.4	+	62	9745	c.9516A>T	c.(9514-9516)acA>acT	p.T3172T	HMCN1_ENST00000367492.2_Silent_p.T3172T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3172	Ig-like C2-type 30.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGACATTAACATGTGATGCCA	0.428													A|||	206	0.0411342	0.1498	0.0101	5008	,	,		17561	0.0		0.001	False		,,,				2504	0.0				p.T3172T		Atlas-SNP	.											.	HMCN1	797	.	0			c.A9516T						PASS	.	A		558,3848	250.9+/-257.8	49,460,1694	98.0	87.0	91.0		9516	-11.3	0.0	1	dbSNP_129	91	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	HMCN1	NM_031935.2		49,466,5988	TT,TA,AA		0.0698,12.6645,4.3365		3172/5636	186057347	564,12442	2203	4300	6503	SO:0001819	synonymous_variant	83872	exon62			ATTAACATGTGAT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.9516A>T	1.37:g.186057347A>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	50	0.684932	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			A|0.953;T|0.047	0.047	strong		0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
CDH9	1007	hgsc.bcm.edu	37	5	26988328	26988328	+	Missense_Mutation	SNP	G	G	A	rs2288466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:26988328G>A	ENST00000231021.4	-	2	285	c.113C>T	c.(112-114)gCg>gTg	p.A38V		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	38			A -> V (in dbSNP:rs2288466). {ECO:0000269|PubMed:15489334}.		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						TGTCAGACCCGCTATCTTTTT	0.393													A|||	1910	0.38139	0.6936	0.2666	5008	,	,		15880	0.1508		0.4712	False		,,,				2504	0.1861				p.A38V	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											CDH9,NS,carcinoma,+1,1	CDH9	305	1	0			c.C113T						PASS	.	A	VAL/ALA	3019,1387	457.8+/-351.8	1046,927,230	139.0	135.0	136.0		113	3.3	0.0	5	dbSNP_100	136	4305,4295	576.0+/-390.3	1099,2107,1094	yes	missense	CDH9	NM_016279.3	64	2145,3034,1324	AA,AG,GG		49.9419,31.4798,43.6875	benign	38/790	26988328	7324,5682	2203	4300	6503	SO:0001583	missense	1007	exon2			AGACCCGCTATCT	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.113C>T	5.37:g.26988328G>A	ENSP00000231021:p.Ala38Val	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	179	81	0.452514	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	901	0.4125457875457875	324	0.6585365853658537	113	0.31215469613259667	98	0.17132867132867133	366	0.48284960422163586	A	3.005	-0.205196	0.06180	0.685202	0.500581	ENSG00000113100	ENST00000231021;ENST00000513289;ENST00000511822	T;T;T	0.57436	0.51;0.4;1.94	5.64	3.28	0.37604	.	1.138130	0.06392	N	0.717309	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.46091	-0.9216	8	.	.	.	.	8.4322	0.32764	0.6064:0.0:0.3936:0.0	rs2288466;rs17565545;rs52826250;rs57578097;rs2288466	38;38	E7EPN0;Q9ULB4	.;CADH9_HUMAN	V	38	ENSP00000231021:A38V;ENSP00000426239:A38V;ENSP00000422538:A38V	.	A	-	2	0	CDH9	27024085	0.000000	0.05858	0.014000	0.15608	0.685000	0.39939	0.479000	0.22228	0.109000	0.17891	-0.332000	0.08345	GCG	G|0.501;A|0.499	0.499	strong		0.393	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
PBK	55872	hgsc.bcm.edu	37	8	27679981	27679981	+	Missense_Mutation	SNP	T	T	C	rs3779620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27679981T>C	ENST00000301905.4	-	5	783	c.320A>G	c.(319-321)aAt>aGt	p.N107S	PBK_ENST00000522944.1_Missense_Mutation_p.N107S	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	107	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		N -> S (in dbSNP:rs3779620). {ECO:0000269|PubMed:10779557, ECO:0000269|PubMed:11378444, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.N107S(1)		endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		ACTGCCATCATTGGCTTCAGT	0.343													C|||	1116	0.222843	0.2837	0.1066	5008	,	,		18594	0.3611		0.1064	False		,,,				2504	0.2004				p.N107S		Atlas-SNP	.											PBK_ENST00000301905,NS,carcinoma,0,1	PBK	29	1	1	Substitution - Missense(1)	stomach(1)	c.A320G						PASS	.	C	SER/ASN	1095,3311	718.0+/-408.8	139,817,1247	65.0	59.0	61.0		320	2.2	1.0	8	dbSNP_107	61	873,7727	777.9+/-407.7	47,779,3474	yes	missense	PBK	NM_018492.2	46	186,1596,4721	CC,CT,TT		10.1512,24.8525,15.1315	benign	107/323	27679981	1968,11038	2203	4300	6503	SO:0001583	missense	55872	exon5			CCATCATTGGCTT	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"""T-LAK cell-originated protein kinase"", ""cancer/testis antigen 84"""	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.320A>G	8.37:g.27679981T>C	ENSP00000301905:p.Asn107Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Missense_Mutation	SNP	ENST00000301905.4	37	CCDS6063.1	442	0.20238095238095238	128	0.2601626016260163	42	0.11602209944751381	204	0.35664335664335667	68	0.08970976253298153	C	3.539	-0.094007	0.07053	0.248525	0.101512	ENSG00000168078	ENST00000301905;ENST00000522944	T;T	0.32988	1.43;1.43	5.46	2.21	0.28008	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.379039	0.34750	N	0.003715	T	0.00012	0.0000	N	0.12853	0.265	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.48055	-0.9068	9	0.12766	T	0.61	-6.1974	6.6419	0.22914	0.0:0.4885:0.0:0.5115	rs3779620;rs52820681;rs3779620	107;107	B4DX68;Q96KB5	.;TOPK_HUMAN	S	107	ENSP00000301905:N107S;ENSP00000428489:N107S	ENSP00000301905:N107S	N	-	2	0	PBK	27735900	0.772000	0.28567	0.995000	0.50966	0.757000	0.42996	0.748000	0.26305	0.378000	0.24764	-0.733000	0.03571	AAT	T|0.817;C|0.183	0.183	strong		0.343	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492	
ALKBH5	54890	hgsc.bcm.edu	37	17	18088094	18088094	+	Silent	SNP	C	C	T	rs11078411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000577847.1_RNA|RP11-258F1.1_ENST00000583062.1_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	83	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	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	
ALDH9A1	223	hgsc.bcm.edu	37	1	165649851	165649851	+	Missense_Mutation	SNP	C	C	G	rs1065756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:165649851C>G	ENST00000354775.4	-	5	966	c.662G>C	c.(661-663)aGt>aCt	p.S221T	ALDH9A1_ENST00000538148.1_Missense_Mutation_p.S127T|ALDH9A1_ENST00000461664.1_5'UTR	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	197					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)					ACCAGCCTCACTGTAGATTTC	0.498													G|||	177	0.0353435	0.0363	0.0548	5008	,	,		17777	0.0069		0.005	False		,,,				2504	0.0808				p.S221T	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.G662C						PASS	.	G	THR/SER	185,4221	810.1+/-416.0	6,173,2024	107.0	108.0	107.0		662	5.6	0.0	1	dbSNP_86	107	13,8587	818.7+/-406.8	0,13,4287	yes	missense	ALDH9A1	NM_000696.3	58	6,186,6311	GG,GC,CC		0.1512,4.1988,1.5224	benign	221/519	165649851	198,12808	2203	4300	6503	SO:0001583	missense	223	exon5			GCCTCACTGTAGA	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.662G>C	1.37:g.165649851C>G	ENSP00000346827:p.Ser221Thr	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	213	81	0.380282	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Missense_Mutation	SNP	ENST00000354775.4	37	CCDS1250.2	39	0.017857142857142856	21	0.042682926829268296	11	0.03038674033149171	5	0.008741258741258742	2	0.002638522427440633	G	0.018	-1.474171	0.01044	0.041988	0.001512	ENSG00000143149	ENST00000354775;ENST00000538148	T;T	0.76186	-1.0;-1.0	5.63	5.63	0.86233	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.330866	0.35677	N	0.003042	T	0.24736	0.0600	N	0.01705	-0.755	0.09310	P	1.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.11916	-1.0568	9	0.02654	T	1	.	14.5589	0.68120	0.0:0.1473:0.8527:0.0	rs1065756;rs52833383;rs58505705;rs1065756	127;211;197;221	B4DYY1;B4DX14;P49189;B9EKV4	.;.;AL9A1_HUMAN;.	T	221;127	ENSP00000346827:S221T;ENSP00000440026:S127T	ENSP00000346827:S221T	S	-	2	0	ALDH9A1	163916475	0.381000	0.25140	0.010000	0.14722	0.231000	0.25187	2.320000	0.43797	1.390000	0.46547	-0.120000	0.15030	AGT	C|0.978;G|0.022	0.022	strong		0.498	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1		
OR1N2	138882	hgsc.bcm.edu	37	9	125316350	125316350	+	Missense_Mutation	SNP	C	C	T	rs1411272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125316350C>T	ENST00000373688.2	+	1	960	c.902C>T	c.(901-903)aCg>aTg	p.T301M		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	301			T -> M (in dbSNP:rs1411272). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T301M(1)		breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						ATTATTCCCACGCTAAACCCA	0.393													T|||	2963	0.591653	0.6362	0.5994	5008	,	,		22233	0.6667		0.5457	False		,,,				2504	0.4959				p.T301M		Atlas-SNP	.											OR1N2,NS,carcinoma,0,1	OR1N2	51	1	1	Substitution - Missense(1)	stomach(1)	c.C902T						PASS	.	T	MET/THR	2739,1667	507.4+/-366.7	830,1079,294	138.0	138.0	138.0		902	4.6	1.0	9	dbSNP_88	138	4597,4003	553.7+/-386.4	1205,2187,908	yes	missense	OR1N2	NM_001004457.1	81	2035,3266,1202	TT,TC,CC		46.5465,37.8348,43.5953	benign	301/331	125316350	7336,5670	2203	4300	6503	SO:0001583	missense	138882	exon1			TTCCCACGCTAAA		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.902C>T	9.37:g.125316350C>T	ENSP00000362792:p.Thr301Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	145	50	0.344828	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Missense_Mutation	SNP	ENST00000373688.2	37	CCDS35123.1	1269	0.5810439560439561	292	0.5934959349593496	215	0.5939226519337016	355	0.6206293706293706	407	0.5369393139841688	T	0.802	-0.755023	0.03019	0.621652	0.534535	ENSG00000171501	ENST00000373688	T	0.36340	1.26	4.56	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000020	T	0.00012	0.0000	N	0.01464	-0.85	0.51233	P	8.099999999999774E-5	B	0.10296	0.003	B	0.04013	0.001	T	0.45145	-0.9281	9	0.02654	T	1	.	9.4731	0.38856	0.0:0.0857:0.0:0.9143	rs1411272;rs17446467;rs52827441;rs59353884;rs1411272	301	Q8NGR9	OR1N2_HUMAN	M	301	ENSP00000362792:T301M	ENSP00000362792:T301M	T	+	2	0	OR1N2	124356171	0.924000	0.31332	1.000000	0.80357	0.841000	0.47740	3.075000	0.50073	0.800000	0.34041	-0.268000	0.10319	ACG	C|0.431;N|0.000	.	strong		0.393	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
SLX4	84464	hgsc.bcm.edu	37	16	3640785	3640785	+	Missense_Mutation	SNP	C	C	T	rs59939128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3640785C>T	ENST00000294008.3	-	12	3494	c.2854G>A	c.(2854-2856)Gcg>Acg	p.A952T		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	952	Interaction with PLK1 and TERF2-TERF2IP.		A -> M (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TGGCCAAGCGCCTCCTCTGGC	0.647								Direct reversal of damage					C|||	336	0.0670927	0.0961	0.0764	5008	,	,		16756	0.0496		0.0646	False		,,,				2504	0.0419				p.A952T		Atlas-SNP	.											SLX4,NS,carcinoma,+2,1	SLX4	173	1	0			c.G2854A						PASS	.	C	THR/ALA	476,3918	215.1+/-234.2	27,422,1748	47.0	50.0	49.0		2854	-1.4	0.0	16	dbSNP_129	49	562,8038	137.9+/-194.8	14,534,3752	no	missense	SLX4	NM_032444.2	58	41,956,5500	TT,TC,CC		6.5349,10.833,7.9883	probably-damaging	952/1835	3640785	1038,11956	2197	4300	6497	SO:0001583	missense	84464	exon12			CAAGCGCCTCCTC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2854G>A	16.37:g.3640785C>T	ENSP00000294008:p.Ala952Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	152	79	0.519737	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	148	0.06776556776556776	53	0.10772357723577236	24	0.06629834254143646	23	0.04020979020979021	48	0.0633245382585752	C	9.916	1.210756	0.22289	0.10833	0.065349	ENSG00000188827	ENST00000294008	T	0.01369	4.97	4.64	-1.42	0.08913	.	1.163550	0.06146	N	0.673336	T	0.00039	0.0001	L	0.42245	1.32	0.09310	N	1	B	0.21452	0.056	B	0.19666	0.026	T	0.47799	-0.9089	10	0.27082	T	0.32	.	1.7256	0.02921	0.1415:0.4632:0.1378:0.2575	rs59939128	952	Q8IY92	SLX4_HUMAN	T	952	ENSP00000294008:A952T	ENSP00000294008:A952T	A	-	1	0	SLX4	3580786	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.014000	0.12656	-0.235000	0.09767	0.549000	0.68633	GCG	C|0.927;T|0.073	0.073	strong		0.647	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
DPP8	54878	hgsc.bcm.edu	37	15	65739303	65739303	+	Silent	SNP	C	C	A	rs11009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65739303C>A	ENST00000341861.5	-	20	4196	c.2616G>T	c.(2614-2616)tcG>tcT	p.S872S	DPP8_ENST00000321118.7_Silent_p.S823S|DPP8_ENST00000358939.4_Silent_p.S756S|DPP8_ENST00000321147.6_Silent_p.S821S|DPP8_ENST00000559233.1_Silent_p.S872S|DPP8_ENST00000300141.6_Silent_p.S856S|DPP8_ENST00000339244.5_Silent_p.S699S	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	872					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AATGTTCTCCCGATTCAGGAA	0.338													A|||	301	0.0601038	0.1044	0.0331	5008	,	,		17283	0.0446		0.0457	False		,,,				2504	0.0501				p.S872S		Atlas-SNP	.											.	DPP8	78	.	0			c.G2616T						PASS	.	A	,,,	423,3979	786.2+/-414.8	18,387,1796	143.0	141.0	141.0		2268,2568,2616,2463	-2.9	1.0	15	dbSNP_52	141	499,8099	796.4+/-407.5	16,467,3816	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DPP8	NM_017743.4,NM_130434.3,NM_197960.2,NM_197961.2	,,,	34,854,5612	AA,AC,CC		5.8037,9.6093,7.0923	,,,	756/783,856/883,872/899,821/848	65739303	922,12078	2201	4299	6500	SO:0001819	synonymous_variant	54878	exon21			TTCTCCCGATTCA	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"""dipeptidyl peptidase VIII"", ""dipeptidyl peptidase IV-related protein-1"", ""prolyl dipeptidase DPP8"""	606819	"""dipeptidylpeptidase 8"""			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.2616G>T	15.37:g.65739303C>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	86	32	0.372093	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Silent	SNP	ENST00000341861.5	37	CCDS10207.1																																																																																			C|0.936;A|0.064	0.064	strong		0.338	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743	
PSG2	5670	hgsc.bcm.edu	37	19	43579679	43579679	+	Missense_Mutation	SNP	T	T	A	rs1058086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43579679T>A	ENST00000406487.1	-	3	634	c.536A>T	c.(535-537)cAg>cTg	p.Q179L		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	179	Ig-like C2-type 1.		Q -> L (in dbSNP:rs1058086).		cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				CATCCACCACTGGTAGCTTGT	0.502													T|||	609	0.121605	0.056	0.2017	5008	,	,		19263	0.0893		0.1103	False		,,,				2504	0.1984				p.Q179L		Atlas-SNP	.											.	PSG2	84	.	0			c.A536T						PASS	.	T	LEU/GLN	303,4101		21,261,1920	245.0	247.0	246.0		536	-2.7	0.0	19	dbSNP_86	246	964,7630		57,850,3390	no	missense	PSG2	NM_031246.3	113	78,1111,5310	AA,AT,TT		11.2171,6.8801,9.7477		179/336	43579679	1267,11731	2202	4297	6499	SO:0001583	missense	5670	exon3			CACCACTGGTAGC		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.536A>T	19.37:g.43579679T>A	ENSP00000385706:p.Gln179Leu	Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	359	186	0.518106	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	231	0.10576923076923077	30	0.06097560975609756	61	0.1685082872928177	49	0.08566433566433566	91	0.12005277044854881	N	0	-2.587248	0.00128	0.068801	0.112171	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.14516	2.5	1.33	-2.66	0.06077	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.01076	-1.035	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.29305	-1.0016	8	0.02654	T	1	.	3.0717	0.06233	0.2961:0.4666:0.0:0.2373	rs1058086;rs3198696;rs16976416;rs57294777	179;179	B5MCM8;P11465	.;PSG2_HUMAN	L	179	ENSP00000385706:Q179L	ENSP00000332984:Q179L	Q	-	2	0	PSG2	48271519	0.001000	0.12720	0.005000	0.12908	0.005000	0.04900	-3.566000	0.00429	-1.108000	0.03000	-0.589000	0.04120	CAG	T|0.897;A|0.103	0.103	strong		0.502	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
ALKBH8	91801	hgsc.bcm.edu	37	11	107427616	107427616	+	Silent	SNP	C	C	G	rs17107135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:107427616C>G	ENST00000428149.2	-	3	394	c.243G>C	c.(241-243)ccG>ccC	p.P81P	ALKBH8_ENST00000429370.1_Silent_p.P81P|ALKBH8_ENST00000530933.1_5'UTR|ALKBH8_ENST00000389568.3_Silent_p.P81P|ALKBH8_ENST00000417449.2_Silent_p.P84P	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	81	RRM.				cellular response to DNA damage stimulus (GO:0006974)|tRNA methylation (GO:0030488)	cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|RNA binding (GO:0003723)|tRNA (uracil) methyltransferase activity (GO:0016300)			breast(2)|large_intestine(2)|lung(5)	9		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)		CAAATGAGTACGGCTTGTTAG	0.443													G|||	545	0.108826	0.3918	0.036	5008	,	,		14479	0.001		0.001	False		,,,				2504	0.0				p.P81P		Atlas-SNP	.											.	ALKBH8	88	.	0			c.G243C						PASS	.	G		1354,3048	692.3+/-405.5	220,914,1067	130.0	121.0	124.0		243	2.7	1.0	11	dbSNP_123	124	24,8572	818.1+/-406.9	0,24,4274	no	coding-synonymous	ALKBH8	NM_138775.2		220,938,5341	GG,GC,CC		0.2792,30.7587,10.6016		81/665	107427616	1378,11620	2201	4298	6499	SO:0001819	synonymous_variant	91801	exon3			TGAGTACGGCTTG	AF086489	CCDS8337.2, CCDS73376.1	11q22.3	2013-10-04			ENSG00000137760	ENSG00000137760	2.1.1.229	"""Alkylation repair homologs"", ""RNA binding motif (RRM) containing"""	25189	protein-coding gene	gene with protein product		613306				20123966	Standard	NM_138775		Approved	MGC10235	uc009yxp.3	Q96BT7	OTTHUMG00000157008	ENST00000428149.2:c.243G>C	11.37:g.107427616C>G		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_138775	B1Q2M0|B4DEF6|Q8N989	Silent	SNP	ENST00000428149.2	37	CCDS8337.2																																																																																			C|0.896;G|0.104	0.104	strong		0.443	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775	
RUFY4	285180	hgsc.bcm.edu	37	2	218953991	218953991	+	Missense_Mutation	SNP	T	T	G	rs201137688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218953991T>G	ENST00000344321.7	+	12	2037	c.1519T>G	c.(1519-1521)Tgg>Ggg	p.W507G	RUFY4_ENST00000441828.2_3'UTR|RUFY4_ENST00000374155.3_Missense_Mutation_p.W527G	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	507							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)		GGACCGCCTGTGGCAGAGGCT	0.527													T|||	2	0.000399361	0.0	0.0	5008	,	,		19104	0.0		0.001	False		,,,				2504	0.001				p.W507G		Atlas-SNP	.											.	RUFY4	59	.	0			c.T1519G						PASS	.	T	GLY/TRP	3,3833		0,3,1915	48.0	50.0	49.0		1519	4.9	1.0	2		49	14,8270		0,14,4128	yes	missense	RUFY4	NM_198483.3	184	0,17,6043	GG,GT,TT		0.169,0.0782,0.1403	probably-damaging	507/572	218953991	17,12103	1918	4142	6060	SO:0001583	missense	285180	exon12			CGCCTGTGGCAGA	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.1519T>G	2.37:g.218953991T>G	ENSP00000345900:p.Trp507Gly	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	183	74	0.404372	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	37		.	.	.	.	.	.	.	.	.	.	T	16.23	3.064752	0.55432	7.82E-4	0.00169	ENSG00000188282	ENST00000344321;ENST00000374155	T;T	0.66280	1.15;-0.2	4.92	4.92	0.64577	Zinc finger, FYVE/PHD-type (1);	0.000000	0.49305	D	0.000154	T	0.76842	0.4044	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.75545	-0.3280	10	0.27082	T	0.32	-16.7446	10.8813	0.46939	0.0:0.0:0.0:1.0	.	507	Q6ZNE9	RUFY4_HUMAN	G	507;527	ENSP00000345900:W507G;ENSP00000363270:W527G	ENSP00000345900:W507G	W	+	1	0	RUFY4	218662236	1.000000	0.71417	0.962000	0.40283	0.771000	0.43674	3.616000	0.54174	2.079000	0.62486	0.454000	0.30748	TGG	T|0.999;G|0.001	0.001	weak		0.527	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483	
TBL3	10607	hgsc.bcm.edu	37	16	2025411	2025411	+	Silent	SNP	G	G	C	rs12925447	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2025411G>C	ENST00000568546.1	+	9	905	c.777G>C	c.(775-777)ggG>ggC	p.G259G		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	259					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						AGTCCCCAGGGCTGTACTTTC	0.627													C|||	260	0.0519169	0.0787	0.0576	5008	,	,		18960	0.0		0.0964	False		,,,				2504	0.0194				p.G259G	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.G777C						PASS	.	C		330,4066	794.5+/-415.3	19,292,1887	100.0	104.0	103.0		777	3.0	0.9	16	dbSNP_121	103	808,7792	782.3+/-407.6	47,714,3539	no	coding-synonymous	TBL3	NM_006453.2		66,1006,5426	CC,CG,GG		9.3953,7.5068,8.7565		259/809	2025411	1138,11858	2198	4300	6498	SO:0001819	synonymous_variant	10607	exon9			CCCAGGGCTGTAC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.777G>C	16.37:g.2025411G>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	96	34	0.354167	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			G|0.918;C|0.082	0.082	strong		0.627	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
RAI14	26064	hgsc.bcm.edu	37	5	34811137	34811137	+	Silent	SNP	T	T	G	rs2271522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34811137T>G	ENST00000265109.3	+	8	758	c.471T>G	c.(469-471)ctT>ctG	p.L157L	RAI14_ENST00000506376.1_Silent_p.L149L|RAI14_ENST00000503673.1_Silent_p.L157L|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000515799.1_Silent_p.L160L|RAI14_ENST00000428746.2_Silent_p.L157L|RAI14_ENST00000512629.1_Silent_p.L157L|RAI14_ENST00000397449.1_Silent_p.L150L	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	157						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)					TACCGCTGCTTCTTGCTGTAC	0.423													T|||	1603	0.320088	0.0741	0.4928	5008	,	,		20093	0.3591		0.3907	False		,,,				2504	0.4172				p.L160L		Atlas-SNP	.											.	RAI14	100	.	0			c.T480G						PASS	.	T	,,,,,	549,3857	248.1+/-256.1	44,461,1698	291.0	283.0	286.0		471,471,471,447,480,471	-2.0	1.0	5	dbSNP_100	286	3077,5523	473.0+/-368.5	557,1963,1780	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	,,,,,	601,2424,3478	GG,GT,TT		35.7791,12.4603,27.8794	,,,,,	157/981,157/981,157/952,149/973,160/984,157/981	34811137	3626,9380	2203	4300	6503	SO:0001819	synonymous_variant	26064	exon10			GCTGCTTCTTGCT	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.471T>G	5.37:g.34811137T>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	143	75	0.524476	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Silent	SNP	ENST00000265109.3	37	CCDS34142.1																																																																																			T|0.715;G|0.285	0.285	strong		0.423	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
OR1L3	26735	hgsc.bcm.edu	37	9	125437769	125437769	+	Missense_Mutation	SNP	A	A	G	rs16912099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125437769A>G	ENST00000304820.2	+	1	455	c.361A>G	c.(361-363)Aac>Gac	p.N121D		NM_001005234.1	NP_001005234.1	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L, member 3	121			N -> D (in dbSNP:rs16912099).			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(2)|lung(6)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	16						TATGGCCATCAACCGCTGTGT	0.428													G|||	684	0.136581	0.4327	0.0331	5008	,	,		21908	0.0734		0.002	False		,,,				2504	0.0133				p.N121D		Atlas-SNP	.											.	OR1L3	51	.	0			c.A361G						PASS	.	G	ASP/ASN	1614,2792	662.4+/-401.0	291,1032,880	169.0	162.0	165.0		361	4.5	0.9	9	dbSNP_123	165	12,8588	818.8+/-406.8	0,12,4288	yes	missense	OR1L3	NM_001005234.1	23	291,1044,5168	GG,GA,AA		0.1395,36.6319,12.5019	benign	121/325	125437769	1626,11380	2203	4300	6503	SO:0001583	missense	26735	exon1			GCCATCAACCGCT		CCDS35128.1	9q33.2	2013-09-20			ENSG00000171481	ENSG00000171481		"""GPCR / Class A : Olfactory receptors"""	8215	protein-coding gene	gene with protein product							Standard	NM_001005234		Approved	OR9-D	uc011lzb.2	Q8NH93	OTTHUMG00000020619	ENST00000304820.2:c.361A>G	9.37:g.125437769A>G	ENSP00000302863:p.Asn121Asp	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	188	188	1	NM_001005234	B2RNF4|Q6IFN1	Missense_Mutation	SNP	ENST00000304820.2	37	CCDS35128.1	251	0.11492673992673992	190	0.3861788617886179	11	0.03038674033149171	48	0.08391608391608392	2	0.002638522427440633	G	2.296	-0.361332	0.05103	0.366319	0.001395	ENSG00000171481	ENST00000304820	T	0.00374	7.72	4.54	4.54	0.55810	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42172	N	0.000747	T	0.00012	0.0000	N	0.00001	-3.775	0.40266	P	0.021765000000000034	B	0.02656	0.0	B	0.01281	0.0	T	0.24728	-1.0152	9	0.02654	T	1	-4.8376	12.2785	0.54751	0.0841:0.0:0.9159:0.0	rs16912099;rs57092164;rs16912099	121	Q8NH93	OR1L3_HUMAN	D	121	ENSP00000302863:N121D	ENSP00000302863:N121D	N	+	1	0	OR1L3	124477590	1.000000	0.71417	0.915000	0.36163	0.122000	0.20287	7.536000	0.82023	1.312000	0.45043	-0.131000	0.14894	AAC	A|0.868;G|0.132	0.132	strong		0.428	OR1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053950.1		
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24261518	24261518	+	Silent	SNP	G	G	A	rs61731545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24261518G>A	ENST00000256412.4	+	13	1543	c.1323G>A	c.(1321-1323)gaG>gaA	p.E441E	ADAMDEC1_ENST00000538205.1_Silent_p.E362E|ADAMDEC1_ENST00000522298.1_Silent_p.E362E|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	441	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		CTTTGAAGGAGTGTACCAATC	0.433													A|||	87	0.0173722	0.0628	0.0058	5008	,	,		17414	0.0		0.0	False		,,,				2504	0.0				p.E441E	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.G1323A						PASS	.	A	,,	259,4147	802.9+/-415.7	10,239,1954	210.0	177.0	188.0		1086,1086,1323	-2.6	0.7	8	dbSNP_129	188	2,8598	818.9+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	10,241,6252	AA,AG,GG		0.0233,5.8783,2.0068	,,	362/392,362/392,441/471	24261518	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon13			GAAGGAGTGTACC	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.1323G>A	8.37:g.24261518G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	121	61	0.504132	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			G|0.979;A|0.021	0.021	strong		0.433	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
CARD9	64170	hgsc.bcm.edu	37	9	139264827	139264827	+	Silent	SNP	C	C	T	rs115057256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139264827C>T	ENST00000371732.5	-	6	1035	c.870G>A	c.(868-870)gcG>gcA	p.A290A	CARD9_ENST00000371734.3_Silent_p.A290A|CARD9_ENST00000460290.1_5'Flank|CARD9_ENST00000315908.7_Silent_p.A290A	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	290					defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|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 interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		GGTCCCGCAGCGCCTGCCGCC	0.687													C|||	50	0.00998403	0.0363	0.0029	5008	,	,		16294	0.0		0.0	False		,,,				2504	0.0				p.A290A		Atlas-SNP	.											CARD9,NS,NS,-1,1	CARD9	47	1	0			c.G870A						PASS	.	C	,	145,4233	94.8+/-133.5	2,141,2046	33.0	36.0	35.0		870,870	-8.2	0.2	9	dbSNP_132	35	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	CARD9	NM_052813.4,NM_052814.3	,	2,142,6343	TT,TC,CC		0.0116,3.312,1.1253	,	290/537,290/493	139264827	146,12828	2189	4298	6487	SO:0001819	synonymous_variant	64170	exon6			CCGCAGCGCCTGC	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.870G>A	9.37:g.139264827C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	71	0.78022	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Silent	SNP	ENST00000371732.5	37	CCDS6997.1																																																																																			C|0.989;T|0.011	0.011	strong		0.687	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
ATF4	468	hgsc.bcm.edu	37	22	39918323	39918323	+	Missense_Mutation	SNP	C	C	G	rs1803323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39918323C>G	ENST00000337304.2	+	2	1654	c.772C>G	c.(772-774)Ccc>Gcc	p.P258A	ATF4_ENST00000404241.2_Missense_Mutation_p.P258A|ATF4_ENST00000396680.1_Missense_Mutation_p.P258A	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	258			P -> A (in dbSNP:rs1803323).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	GTCTGCCCGTCCCAAACCTTA	0.522													C|||	86	0.0171725	0.0628	0.0043	5008	,	,		19286	0.0		0.0	False		,,,				2504	0.0				p.P258A		Atlas-SNP	.											.	ATF4	27	.	0			c.C772G						PASS	.	C	ALA/PRO,ALA/PRO	169,4237	99.8+/-138.5	5,159,2039	24.0	25.0	24.0		772,772	2.0	0.2	22	dbSNP_89	24	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ATF4	NM_001675.2,NM_182810.1	27,27	5,161,6337	GG,GC,CC		0.0233,3.8357,1.3148	possibly-damaging,possibly-damaging	258/352,258/352	39918323	171,12835	2203	4300	6503	SO:0001583	missense	468	exon2			GCCCGTCCCAAAC	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"""basic leucine zipper proteins"""	786	protein-coding gene	gene with protein product	"""tax-responsive enhancer element B67"""	604064	"""activating transcription factor 4 (tax-responsive enhancer element B67)"""	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.772C>G	22.37:g.39918323C>G	ENSP00000336790:p.Pro258Ala	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	329	178	0.541033	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	37	CCDS13996.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	10.09	1.255962	0.22965	0.038357	2.33E-4	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.24350	1.86;1.86;1.86	5.24	2.04	0.26737	.	0.251601	0.40640	N	0.001054	T	0.04998	0.0134	M	0.68952	2.095	0.28571	N	0.910626	P	0.48294	0.908	B	0.44224	0.444	T	0.03784	-1.1004	10	0.87932	D	0	-11.5679	9.0061	0.36113	0.0:0.6756:0.0:0.3244	rs1803323;rs52835171;rs1803323	258	P18848	ATF4_HUMAN	A	258	ENSP00000384587:P258A;ENSP00000336790:P258A;ENSP00000379912:P258A	ENSP00000336790:P258A	P	+	1	0	ATF4	38248269	0.003000	0.15002	0.178000	0.23040	0.066000	0.16364	0.129000	0.15830	0.219000	0.20840	0.462000	0.41574	CCC	C|0.987;G|0.013	0.013	strong		0.522	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675	
SLC22A25	387601	hgsc.bcm.edu	37	11	62996038	62996038	+	Splice_Site	SNP	T	T	C	rs1783657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62996038T>C	ENST00000306494.6	-	2	402		c.e2-2		SLC22A10_ENST00000535888.1_Intron|SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000525620.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						CAGATCCCACTGGAAGAAAAG	0.413													T|||	360	0.071885	0.2572	0.0173	5008	,	,		19271	0.0		0.004	False		,,,				2504	0.0041				.		Atlas-SNP	.											.	SLC22A25	87	.	0			c.403-2A>G						PASS	.	T		828,3574	329.3+/-301.0	75,678,1448	92.0	84.0	86.0			3.5	0.9	11	dbSNP_89	86	51,8545	31.2+/-83.2	0,51,4247	yes	splice-3	SLC22A25	NM_199352.3		75,729,5695	CC,CT,TT		0.5933,18.8096,6.7626			62996038	879,12119	2201	4298	6499	SO:0001630	splice_region_variant	387601	exon3			TCCCACTGGAAGA	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.403-2A>G	11.37:g.62996038T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_199352		Splice_Site	SNP	ENST00000306494.6	37	CCDS31592.1	118	0.05402930402930403	108	0.21951219512195122	6	0.016574585635359115	0	0.0	4	0.005277044854881266	T	11.87	1.766935	0.31320	0.188096	0.005933	ENSG00000196600	ENST00000306494;ENST00000451441	.	.	.	3.47	3.47	0.39725	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.356	0.43964	0.0:0.0:0.0:1.0	rs1783657;rs57074306;rs1783657	.	.	.	.	-1	.	.	.	-	.	.	SLC22A25	62752614	1.000000	0.71417	0.944000	0.38274	0.580000	0.36256	4.657000	0.61490	1.388000	0.46506	0.391000	0.25812	.	T|0.940;C|0.060	0.060	strong		0.413	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	Intron
DISP2	85455	hgsc.bcm.edu	37	15	40656141	40656141	+	Silent	SNP	T	T	C	rs12443160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	34	0	0		WXS	Illumina HiSeq	Phase_I	22	14	0.636364	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	
SPEM1	374768	hgsc.bcm.edu	37	17	7324340	7324340	+	Missense_Mutation	SNP	G	G	A	rs61741352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7324340G>A	ENST00000323675.3	+	3	371	c.346G>A	c.(346-348)Ggc>Agc	p.G116S	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	116					sperm individualization (GO:0007291)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	12		Prostate(122;0.173)				TCGCCGTCGAGGCTCTCCCAC	0.602													G|||	229	0.0457268	0.1672	0.0115	5008	,	,		18927	0.0		0.0	False		,,,				2504	0.0				p.G116S		Atlas-SNP	.											.	SPEM1	41	.	0			c.G346A						PASS	.	G	SER/GLY	547,3757		37,473,1642	70.0	76.0	74.0		346	2.7	0.0	17	dbSNP_129	74	3,8483		0,3,4240	yes	missense	SPEM1	NM_199339.2	56	37,476,5882	AA,AG,GG		0.0354,12.7091,4.3002	possibly-damaging	116/310	7324340	550,12240	2152	4243	6395	SO:0001583	missense	374768	exon3			CGTCGAGGCTCTC	AK097400	CCDS42254.1	17p13.1	2011-12-12	2008-02-04	2008-02-04	ENSG00000181323	ENSG00000181323			32429	protein-coding gene	gene with protein product		615116	"""chromosome 17 open reading frame 83"""	C17orf83		17426145, 20558241, 21184802	Standard	NM_199339		Approved	FLJ40081	uc002ggv.3	Q8N4L4		ENST00000323675.3:c.346G>A	17.37:g.7324340G>A	ENSP00000315554:p.Gly116Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	165	74	0.448485	NM_199339		Missense_Mutation	SNP	ENST00000323675.3	37	CCDS42254.1	83	0.038003663003663	78	0.15853658536585366	5	0.013812154696132596	0	0.0	0	0.0	G	10.79	1.449713	0.26074	0.127091	3.54E-4	ENSG00000181323	ENST00000323383;ENST00000323675	.	.	.	4.7	2.67	0.31697	.	1.055190	0.07527	N	0.911526	T	0.00109	0.0003	L	0.32530	0.975	0.09310	N	1	B	0.32829	0.386	B	0.31101	0.124	T	0.12528	-1.0544	9	0.46703	T	0.11	-0.4131	6.202	0.20581	0.1006:0.1883:0.7111:0.0	rs61741352	116	Q8N4L4	SPEM1_HUMAN	S	65;116	.	ENSP00000315511:G65S	G	+	1	0	SPEM1	7265064	0.004000	0.15560	0.001000	0.08648	0.146000	0.21551	1.315000	0.33608	0.566000	0.29273	0.655000	0.94253	GGC	G|0.962;A|0.038	0.038	strong		0.602	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339	
DIDO1	11083	hgsc.bcm.edu	37	20	61525488	61525488	+	Silent	SNP	A	A	G	rs112062101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61525488A>G	ENST00000266070.4	-	12	2956	c.2631T>C	c.(2629-2631)tcT>tcC	p.S877S	DIDO1_ENST00000395340.1_Silent_p.S877S|DIDO1_ENST00000395335.2_Silent_p.S877S|DIDO1_ENST00000395343.1_Silent_p.S877S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	877					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)					CTTTCTTAACAGAAGCTGACA	0.517													A|||	38	0.00758786	0.0265	0.0043	5008	,	,		19309	0.0		0.0	False		,,,				2504	0.0				p.S877S	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1,NS,carcinoma,-1,1	DIDO1	321	1	0			c.T2631C						PASS	.	A	,,,	111,4295	80.9+/-119.3	0,111,2092	102.0	117.0	112.0		2631,2631,2631,2631	-5.0	0.0	20	dbSNP_132	112	1,8593		0,1,4296	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_001193370.1,NM_033081.2,NM_080797.3	,,,	0,112,6388	GG,GA,AA		0.0116,2.5193,0.8615	,,,	877/2241,877/1190,877/2241,877/1190	61525488	112,12888	2203	4297	6500	SO:0001819	synonymous_variant	11083	exon12			CTTAACAGAAGCT	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.2631T>C	20.37:g.61525488A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			A|0.994;G|0.006	0.006	strong		0.517	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
GPRIN3	285513	hgsc.bcm.edu	37	4	90169025	90169025	+	Missense_Mutation	SNP	C	C	T	rs17015286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:90169025C>T	ENST00000609438.1	-	2	2755	c.2237G>A	c.(2236-2238)aGa>aAa	p.R746K	GPRIN3_ENST00000333209.4_Missense_Mutation_p.R746K	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	746			R -> K (in dbSNP:rs17015286).							breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CTGCCTTCCTCTGAGCTTCTT	0.468													T|||	299	0.0597045	0.2163	0.0173	5008	,	,		17742	0.0		0.0	False		,,,				2504	0.001				p.R746K		Atlas-SNP	.											.	GPRIN3	90	.	0			c.G2237A						PASS	.	T	LYS/ARG	800,3606	751.2+/-412.2	79,642,1482	108.0	110.0	109.0		2237	5.3	1.0	4	dbSNP_123	109	16,8584	818.7+/-406.8	0,16,4284	yes	missense	GPRIN3	NM_198281.2	26	79,658,5766	TT,TC,CC		0.186,18.1571,6.274	benign	746/777	90169025	816,12190	2203	4300	6503	SO:0001583	missense	285513	exon2			CTTCCTCTGAGCT	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.2237G>A	4.37:g.90169025C>T	ENSP00000476603:p.Arg746Lys	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	176	92	0.522727	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	112	0.05128205128205128	107	0.21747967479674796	5	0.013812154696132596	0	0.0	0	0.0	T	9.991	1.230900	0.22542	0.181571	0.00186	ENSG00000185477	ENST00000333209	T	0.19394	2.15	5.26	5.26	0.73747	.	0.000000	0.36234	N	0.002708	T	0.00012	0.0000	N	0.01228	-0.945	0.49130	P	2.4299999999999322E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	9	0.02654	T	1	-13.2449	11.2596	0.49074	0.0:0.0711:0.0:0.9289	rs17015286;rs52823204;rs56606122;rs61213802;rs17015286	746	Q6ZVF9	GRIN3_HUMAN	K	746	ENSP00000328672:R746K	ENSP00000328672:R746K	R	-	2	0	GPRIN3	90388048	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.662000	0.61525	1.023000	0.39654	-0.254000	0.11334	AGA	C|0.933;T|0.067	0.067	strong		0.468	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
PABPC1	26986	hgsc.bcm.edu	37	8	101721812	101721812	+	Missense_Mutation	SNP	G	G	A	rs200409148		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721812G>A	ENST00000318607.5	-	8	2248	c.1120C>T	c.(1120-1122)Cgc>Tgc	p.R374C	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519004.1_Missense_Mutation_p.R329C|PABPC1_ENST00000522387.1_Missense_Mutation_p.R342C|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	374					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TGAGCCTGGCGCTCTTCTTTG	0.502																																					p.R374C		Atlas-SNP	.											.	PABPC1	76	.	0			c.C1120T						PASS	.						144.0	123.0	130.0					8																	101721812		2203	4300	6503	SO:0001583	missense	26986	exon8			CCTGGCGCTCTTC	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.1120C>T	8.37:g.101721812G>A	ENSP00000313007:p.Arg374Cys	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	358	131	0.365922	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.154399|5.154399	0.94686|0.94686	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519596|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|T;T;T	.|0.06933	.|3.24;3.24;3.24	5.05|5.05	5.05|5.05	0.67936|0.67936	.|Nucleotide-binding, alpha-beta plait (1);	.|0.000000	.|0.64402	.|D	.|0.000006	T|T	0.24122|0.24122	0.0584|0.0584	L|L	0.58354|0.58354	1.805|1.805	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.69078	.|0.991;0.997;0.988	.|P;P;P	.|0.60012	.|0.641;0.867;0.852	T|T	0.00448|0.00448	-1.1733|-1.1733	5|10	.|0.87932	.|D	.|0	.|.	18.7718|18.7718	0.91894|0.91894	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|342;374;374	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	V|C	206|374;374;329;342	.|ENSP00000313007:R374C;ENSP00000429594:R329C;ENSP00000429395:R342C	.|ENSP00000313007:R374C	A|R	-|-	2|1	0|0	PABPC1|PABPC1	101790988|101790988	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.694000|6.694000	0.74587|0.74587	2.507000|2.507000	0.84556|0.84556	0.561000|0.561000	0.74099|0.74099	GCG|CGC	.	.	weak		0.502	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
ABCC11	85320	hgsc.bcm.edu	37	16	48265777	48265777	+	Missense_Mutation	SNP	C	C	T	rs16945988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48265777C>T	ENST00000394747.1	-	1	405	c.56G>A	c.(55-57)cGt>cAt	p.R19H	ABCC11_ENST00000537808.1_Missense_Mutation_p.R19H|ABCC11_ENST00000356608.2_Missense_Mutation_p.R19H|ABCC11_ENST00000353782.5_Missense_Mutation_p.R19H|ABCC11_ENST00000394748.1_Missense_Mutation_p.R19H	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	19			R -> H (in dbSNP:rs16945988).		organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|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)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	GTCGATGCCACGATTCACGAG	0.453													C|||	551	0.110024	0.2458	0.0893	5008	,	,		16838	0.0188		0.1014	False		,,,				2504	0.044				p.R19H		Atlas-SNP	.											ABCC11,NS,carcinoma,-1,1	ABCC11	177	1	0			c.G56A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	921,3479	354.4+/-312.6	98,725,1377	267.0	224.0	239.0		56,56,56	4.1	0.7	16	dbSNP_123	239	742,7858	178.5+/-227.8	28,686,3586	yes	missense,missense,missense	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	29,29,29	126,1411,4963	TT,TC,CC		8.6279,20.9318,12.7923	benign,benign,benign	19/1383,19/1383,19/1345	48265777	1663,11337	2200	4300	6500	SO:0001583	missense	85320	exon1			ATGCCACGATTCA	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.56G>A	16.37:g.48265777C>T	ENSP00000378230:p.Arg19His	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	264	141	0.534091	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	233	0.10668498168498168	114	0.23170731707317074	38	0.10497237569060773	5	0.008741258741258742	76	0.10026385224274406	C	10.62	1.400285	0.25291	0.209318	0.086279	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	D;D;D;D;D	0.92699	-2.89;-2.8;-2.8;-2.8;-3.09	5.2	4.11	0.48088	.	0.101083	0.38326	N	0.001730	T	0.00109	0.0003	N	0.08118	0	0.50813	P	1.0399999999999299E-4	P;P	0.44044	0.825;0.733	B;B	0.30855	0.121;0.057	T	0.19418	-1.0306	9	0.44086	T	0.13	-8.9094	9.2096	0.37311	0.8156:0.1844:0.0:0.0	rs16945988;rs59476528;rs16945988	19;19	Q96J66-2;Q96J66	.;ABCCB_HUMAN	H	19	ENSP00000311326:R19H;ENSP00000349017:R19H;ENSP00000378231:R19H;ENSP00000378230:R19H;ENSP00000438530:R19H	ENSP00000311326:R19H	R	-	2	0	ABCC11	46823278	0.951000	0.32395	0.733000	0.30861	0.148000	0.21650	2.218000	0.42889	0.827000	0.34685	-0.280000	0.10049	CGT	C|0.880;T|0.120	0.120	strong		0.453	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
GSDMC	56169	hgsc.bcm.edu	37	8	130762732	130762732	+	Missense_Mutation	SNP	T	T	C	rs76700535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:130762732T>C	ENST00000276708.4	-	11	1909	c.1028A>G	c.(1027-1029)tAc>tGc	p.Y343C		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	343						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						CAGGATACTGTAGAACATGAC	0.473													T|||	53	0.0105831	0.0393	0.0014	5008	,	,		20490	0.0		0.0	False		,,,				2504	0.0				p.Y343C		Atlas-SNP	.											.	GSDMC	71	.	0			c.A1028G						PASS	.	T	CYS/TYR	190,4216	120.0+/-157.7	6,178,2019	136.0	119.0	125.0		1028	-4.0	0.0	8	dbSNP_131	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GSDMC	NM_031415.2	194	6,179,6318	CC,CT,TT		0.0116,4.3123,1.4686	probably-damaging	343/509	130762732	191,12815	2203	4300	6503	SO:0001583	missense	56169	exon11			ATACTGTAGAACA	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"""melanoma-derived leucine zipper, extra-nuclear factor"""	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.1028A>G	8.37:g.130762732T>C	ENSP00000276708:p.Tyr343Cys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	117	47	0.401709	NM_031415	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	37	CCDS6360.1	25	0.011446886446886446	25	0.0508130081300813	0	0.0	0	0.0	0	0.0	T	9.583	1.124120	0.20959	0.043123	1.16E-4	ENSG00000147697	ENST00000276708	T	0.22134	1.97	5.14	-4.01	0.04045	.	1.565630	0.03508	N	0.219111	T	0.02688	0.0081	N	0.08118	0	0.09310	N	1	D	0.59357	0.985	P	0.55667	0.781	T	0.12993	-1.0526	10	0.38643	T	0.18	.	8.1941	0.31385	0.0:0.1621:0.5701:0.2678	.	343	Q9BYG8	GSDMC_HUMAN	C	343	ENSP00000276708:Y343C	ENSP00000276708:Y343C	Y	-	2	0	GSDMC	130831914	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.577000	0.05847	-0.432000	0.07297	-0.389000	0.06534	TAC	T|0.985;C|0.015	0.015	strong		0.473	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1		
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381957	39381957	+	Silent	SNP	C	C	T	rs150187552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39381957C>T	ENST00000333467.3	+	3	360	c.315C>T	c.(313-315)gcC>gcT	p.A105A	APOBEC3B_ENST00000407298.3_Silent_p.A105A|APOBEC3B_ENST00000402182.3_Silent_p.A105A	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	105					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)					CGAAGCTGGCCGAATTCCTGT	0.572													C|||	20	0.00399361	0.0151	0.0	5008	,	,		14653	0.0		0.0	False		,,,				2504	0.0				p.A105A		Atlas-SNP	.											.	APOBEC3B	32	.	0			c.C315T						PASS	.	C		28,4376		3,22,2177	156.0	149.0	151.0		315	-4.2	0.0	22	dbSNP_134	151	0,8596		0,0,4298	no	coding-synonymous	APOBEC3B	NM_004900.3		3,22,6475	TT,TC,CC		0.0,0.6358,0.2154		105/383	39381957	28,12972	2202	4298	6500	SO:0001819	synonymous_variant	9582	exon3			GCTGGCCGAATTC	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.315C>T	22.37:g.39381957C>T		Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	323	112	0.346749	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			C|0.998;T|0.002	0.002	strong		0.572	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
UGDH	7358	hgsc.bcm.edu	37	4	39510264	39510264	+	Silent	SNP	A	A	G	rs1129052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39510264A>G	ENST00000316423.6	-	7	1170	c.828T>C	c.(826-828)tgT>tgC	p.C276C	UGDH_ENST00000501493.2_Silent_p.C209C|UGDH_ENST00000506179.1_Silent_p.C276C|UGDH_ENST00000507089.1_Silent_p.C179C|UGDH_ENST00000515398.1_5'Flank	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	50	0	0		WXS	Illumina HiSeq	Phase_I	38	24	0.631579	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	
MKI67	4288	hgsc.bcm.edu	37	10	129901393	129901393	+	Missense_Mutation	SNP	T	T	C	rs11016071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129901393T>C	ENST00000368654.3	-	13	9086	c.8711A>G	c.(8710-8712)cAg>cGg	p.Q2904R	MKI67_ENST00000368653.3_Missense_Mutation_p.Q2544R	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2904	16 X 122 AA approximate repeats.		Q -> R (in dbSNP:rs11016071).		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)				TGCTCTTGGCTGTCTCCTGCT	0.537													C|||	1169	0.233427	0.3442	0.2291	5008	,	,		18105	0.2619		0.1571	False		,,,				2504	0.136				p.Q2904R		Atlas-SNP	.											.	MKI67	363	.	0			c.A8711G						PASS	.	C	ARG/GLN,ARG/GLN	1370,3036	690.7+/-405.3	209,952,1042	162.0	160.0	161.0		7631,8711	-7.3	0.0	10	dbSNP_120	161	1493,7107	749.0+/-407.4	138,1217,2945	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	43,43	347,2169,3987	CC,CT,TT		17.3605,31.094,22.0129	benign,benign	2544/2897,2904/3257	129901393	2863,10143	2203	4300	6503	SO:0001583	missense	4288	exon13			CTTGGCTGTCTCC	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.8711A>G	10.37:g.129901393T>C	ENSP00000357643:p.Gln2904Arg	Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	260	115	0.442308	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	488	0.22344322344322345	147	0.29878048780487804	68	0.1878453038674033	150	0.26223776223776224	123	0.16226912928759896	C	0.157	-1.084907	0.01888	0.31094	0.173605	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02301	4.35;4.35	4.28	-7.32	0.01436	.	.	.	.	.	T	0.00012	0.0000	N	0.04636	-0.2	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	0.48547	-0.9026	8	0.13470	T	0.59	.	7.3884	0.26895	0.2543:0.1277:0.0:0.6179	rs11016071;rs52808796;rs59734042;rs11016071	2903;2544;2904	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	R	2904;2544;2903	ENSP00000357643:Q2904R;ENSP00000357642:Q2544R	ENSP00000357642:Q2544R	Q	-	2	0	MKI67	129791383	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.024000	0.03603	-2.219000	0.00729	-1.082000	0.02213	CAG	T|0.781;C|0.219	0.219	strong		0.537	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
HLA-G	3135	hgsc.bcm.edu	37	6	29795913	29795913	+	Missense_Mutation	SNP	A	A	T	rs41551813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29795913A>T	ENST00000360323.6	+	2	187	c.163A>T	c.(163-165)Acg>Tcg	p.T55S	HLA-G_ENST00000428701.1_Missense_Mutation_p.T55S|HLA-G_ENST00000376828.2_Missense_Mutation_p.T60S|HLA-G_ENST00000376818.3_Missense_Mutation_p.T55S|HLA-G_ENST00000376815.3_Missense_Mutation_p.T55S			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	55	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)|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						CGTGGACGACACGCAGTTCGT	0.701													a|||	270	0.0539137	0.1127	0.0893	5008	,	,		12369	0.0079		0.0268	False		,,,				2504	0.0245				p.T55S		Atlas-SNP	.											.	HLA-G	90	.	0			c.A163T						PASS	.	A	SER/THR	279,2739		16,247,1246	35.0	26.0	29.0		163	-2.0	0.9	6	dbSNP_127	29	206,5210		4,198,2506	no	missense	HLA-G	NM_002127.5	58	20,445,3752	TT,TA,AA		3.8035,9.2445,5.7505	possibly-damaging	55/339	29795913	485,7949	1509	2708	4217	SO:0001583	missense	3135	exon3			GACGACACGCAGT		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.163A>T	6.37:g.29795913A>T	ENSP00000353472:p.Thr55Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	53	0.602273	NM_002127		Missense_Mutation	SNP	ENST00000360323.6	37	CCDS4668.1	107	0.04899267399267399	45	0.09146341463414634	34	0.09392265193370165	8	0.013986013986013986	20	0.026385224274406333	.	12.12	1.843036	0.32606	0.092445	0.038035	ENSG00000204632	ENST00000376828;ENST00000428701;ENST00000360323;ENST00000376818;ENST00000376815	T;T;T;T;T	0.00808	9.4;9.4;9.4;5.67;5.67	1.71	-2.02	0.07388	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.146220	0.07139	U	0.846876	T	0.03739	0.0106	H	0.98754	4.32	0.53005	P	3.399999999997849E-5	D;D;D;B	0.71674	0.994;0.997;0.998;0.049	D;D;D;B	0.85130	0.982;0.997;0.972;0.031	T	0.12993	-1.0526	9	0.87932	D	0	.	2.1121	0.03705	0.4076:0.2977:0.0:0.2947	rs41551813;rs61761352	55;60;55;55	Q29897;Q5RJ85;Q31611;P17693	.;.;.;HLAG_HUMAN	S	60;55;55;55;55	ENSP00000366024:T60S;ENSP00000412927:T55S;ENSP00000353472:T55S;ENSP00000366014:T55S;ENSP00000366011:T55S	ENSP00000353472:T55S	T	+	1	0	HLA-G	29903892	0.000000	0.05858	0.945000	0.38365	0.609000	0.37215	-0.523000	0.06230	-0.064000	0.13043	0.241000	0.17934	ACG	A|0.948;T|0.052	0.052	strong		0.701	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
TXLNB	167838	hgsc.bcm.edu	37	6	139564101	139564101	+	Silent	SNP	C	C	T	rs12529180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	103	0	0		WXS	Illumina HiSeq	Phase_I	116	50	0.431034	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	
METTL18	92342	hgsc.bcm.edu	37	1	169762807	169762807	+	Missense_Mutation	SNP	T	T	G	rs10489177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169762807T>G	ENST00000310392.4	-	2	383	c.30A>C	c.(28-30)gaA>gaC	p.E10D	C1orf112_ENST00000286031.6_5'Flank|C1orf112_ENST00000498289.1_Intron|C1orf112_ENST00000413811.2_5'Flank|C1orf112_ENST00000359326.4_5'Flank|C1orf112_ENST00000456684.1_5'Flank|METTL18_ENST00000303469.2_Missense_Mutation_p.E10D	NM_033418.2	NP_219486.1	O95568	MET18_HUMAN	methyltransferase like 18	10			E -> D (in dbSNP:rs10489177).			cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			kidney(1)|large_intestine(3)|lung(4)	8						CCAGATGGTCTTCTATAGTGA	0.358													T|||	1093	0.218251	0.2693	0.196	5008	,	,		17838	0.1657		0.164	False		,,,				2504	0.2751				p.E10D		Atlas-SNP	.											.	METTL18	23	.	0			c.A30C						PASS	.	T	ASP/GLU	1042,3364	382.3+/-324.4	138,766,1299	59.0	61.0	60.0		30	3.0	0.9	1	dbSNP_119	60	1353,7247	262.7+/-284.6	112,1129,3059	yes	missense	METTL18	NM_033418.1	45	250,1895,4358	GG,GT,TT		15.7326,23.6496,18.4146	benign	10/373	169762807	2395,10611	2203	4300	6503	SO:0001583	missense	92342	exon2			ATGGTCTTCTATA	AL035369	CCDS1284.1	1q24.2	2013-10-11	2011-03-02	2011-03-02	ENSG00000171806	ENSG00000171806			28793	protein-coding gene	gene with protein product	"""histidine protein methyltransferase 1"""	615255	"""chromosome 1 open reading frame 156"""	C1orf156		20864530	Standard	NM_033418		Approved	MGC9084, AsTP2, HPM1	uc001ggn.4	O95568	OTTHUMG00000035813	ENST00000310392.4:c.30A>C	1.37:g.169762807T>G	ENSP00000307975:p.Glu10Asp	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	146	73	0.5	NM_033418	B2R9T5	Missense_Mutation	SNP	ENST00000310392.4	37	CCDS1284.1	429	0.19642857142857142	146	0.2967479674796748	69	0.19060773480662985	92	0.16083916083916083	122	0.16094986807387862	T	11.11	1.543705	0.27563	0.236496	0.157326	ENSG00000171806	ENST00000310392;ENST00000303469;ENST00000454472	T;T;T	0.46063	2.48;2.48;0.88	5.45	3.01	0.34805	.	0.342769	0.23636	N	0.046072	T	0.16896	0.0406	L	0.50333	1.59	0.49389	P	2.1199999999998997E-4	B	0.12630	0.006	B	0.09377	0.004	T	0.05835	-1.0861	9	0.25751	T	0.34	1.9184	7.8622	0.29516	0.1337:0.0:0.1377:0.7286	rs10489177;rs12753424;rs16862688;rs52790921;rs57618261;rs10489177	10	O95568	MET18_HUMAN	D	10	ENSP00000307975:E10D;ENSP00000307077:E10D;ENSP00000402305:E10D	ENSP00000307077:E10D	E	-	3	2	METTL18	168029431	0.935000	0.31712	0.911000	0.35937	0.965000	0.64279	0.092000	0.15066	2.072000	0.62099	0.459000	0.35465	GAA	T|0.802;G|0.198	0.198	strong		0.358	METTL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087109.1	NM_033418	
OR5B3	441608	hgsc.bcm.edu	37	11	58170374	58170374	+	Missense_Mutation	SNP	T	T	C	rs12280114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58170374T>C	ENST00000309403.2	-	1	508	c.509A>G	c.(508-510)aAt>aGt	p.N170S		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	170			N -> S (in dbSNP:rs12280114).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N170S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ATGGACTTCATTGGACTTACA	0.448													T|||	1453	0.290136	0.3533	0.2695	5008	,	,		22324	0.1448		0.3628	False		,,,				2504	0.2945				p.N170S		Atlas-SNP	.											OR5B3,NS,carcinoma,0,1	OR5B3	65	1	1	Substitution - Missense(1)	stomach(1)	c.A509G						PASS	.	T	SER/ASN	1442,2960	467.9+/-355.0	229,984,988	107.0	99.0	102.0		509	1.7	0.0	11	dbSNP_120	102	3094,5496	473.6+/-368.6	550,1994,1751	yes	missense	OR5B3	NM_001005469.1	46	779,2978,2739	CC,CT,TT		36.0186,32.7578,34.9138	benign	170/315	58170374	4536,8456	2201	4295	6496	SO:0001583	missense	441608	exon1			ACTTCATTGGACT	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.509A>G	11.37:g.58170374T>C	ENSP00000308270:p.Asn170Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	655	0.2999084249084249	195	0.39634146341463417	89	0.24585635359116023	95	0.1660839160839161	276	0.3641160949868074	t	10.45	1.352391	0.24512	0.327578	0.360186	ENSG00000172769	ENST00000309403	T	0.00241	8.46	4.05	1.67	0.24075	GPCR, rhodopsin-like superfamily (1);	0.255793	0.27577	N	0.018745	T	0.00012	0.0000	M	0.91196	3.185	0.80722	P	0.0	P	0.44044	0.825	P	0.48524	0.58	T	0.17776	-1.0358	9	0.87932	D	0	-35.2106	7.5725	0.27915	0.0:0.1867:0.0:0.8133	rs12280114;rs52832394;rs57173256;rs12280114	170	Q8NH48	OR5B3_HUMAN	S	170	ENSP00000308270:N170S	ENSP00000308270:N170S	N	-	2	0	OR5B3	57926950	0.114000	0.22134	0.001000	0.08648	0.382000	0.30200	2.299000	0.43611	0.232000	0.21100	0.528000	0.53228	AAT	T|0.668;C|0.332	0.332	strong		0.448	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
USHBP1	83878	hgsc.bcm.edu	37	19	17367435	17367435	+	Missense_Mutation	SNP	T	T	C	rs9676419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17367435T>C	ENST00000252597.3	-	9	1488	c.1315A>G	c.(1315-1317)Atg>Gtg	p.M439V	USHBP1_ENST00000431146.2_Missense_Mutation_p.M375V|AC010646.3_ENST00000594059.1_5'Flank	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1									p.M439V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						AGAATCTTCATTAGAGAACGG	0.612													C|||	1650	0.329473	0.4735	0.3098	5008	,	,		18737	0.2758		0.2336	False		,,,				2504	0.3027				p.M439V		Atlas-SNP	.											USHBP1,NS,carcinoma,0,2	USHBP1	85	2	1	Substitution - Missense(1)	prostate(1)	c.A1315G						PASS	.	C	VAL/MET	1957,2449	622.4+/-393.9	428,1101,674	73.0	73.0	73.0		1315	-0.3	0.9	19	dbSNP_119	73	1879,6721	729.3+/-406.7	189,1501,2610	yes	missense	USHBP1	NM_031941.3	21	617,2602,3284	CC,CT,TT		21.8488,44.4167,29.4941	benign	439/704	17367435	3836,9170	2203	4300	6503	SO:0001583	missense	83878	exon9			TCTTCATTAGAGA	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1315A>G	19.37:g.17367435T>C	ENSP00000252597:p.Met439Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_031941		Missense_Mutation	SNP	ENST00000252597.3	37	CCDS12353.1	689	0.31547619047619047	264	0.5365853658536586	103	0.2845303867403315	150	0.26223776223776224	172	0.22691292875989447	C	0.006	-2.114278	0.00349	0.444167	0.218488	ENSG00000130307	ENST00000252597;ENST00000431146	T;T	0.10192	2.9;2.91	4.9	-0.346	0.12620	.	0.309917	0.24128	N	0.041292	T	0.00012	0.0000	N	0.00170	-1.935	0.09310	P	0.99999999854739	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36817	-0.9732	9	0.02654	T	1	-9.9883	6.3927	0.21595	0.0:0.4031:0.4212:0.1757	rs9676419;rs59052683;rs9676419	375;439	B4DUE8;Q8N6Y0	.;USBP1_HUMAN	V	439;375	ENSP00000252597:M439V;ENSP00000407902:M375V	ENSP00000252597:M439V	M	-	1	0	USHBP1	17228435	0.875000	0.30112	0.886000	0.34754	0.011000	0.07611	-0.030000	0.12308	-0.123000	0.11745	-0.119000	0.15052	ATG	T|0.693;C|0.307	0.307	strong		0.612	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
TTC14	151613	hgsc.bcm.edu	37	3	180325487	180325487	+	Silent	SNP	T	T	C	rs9858483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	73	0	0		WXS	Illumina HiSeq	Phase_I	88	36	0.409091	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	
CILP	8483	hgsc.bcm.edu	37	15	65496624	65496624	+	Missense_Mutation	SNP	C	C	G	rs140625947	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65496624C>G	ENST00000261883.4	-	6	1067	c.901G>C	c.(901-903)Gca>Cca	p.A301P		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	301					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						ACAAACTCTGCCTTGATGGTG	0.473													C|||	13	0.00259585	0.0008	0.0	5008	,	,		20367	0.0119		0.0	False		,,,				2504	0.0				p.A301P		Atlas-SNP	.											.	CILP	124	.	0			c.G901C						PASS	.	C	PRO/ALA	4,4398	8.1+/-20.4	0,4,2197	83.0	82.0	83.0		901	5.6	0.8	15	dbSNP_134	83	0,8598		0,0,4299	yes	missense	CILP	NM_003613.3	27	0,4,6496	GG,GC,CC		0.0,0.0909,0.0308	possibly-damaging	301/1185	65496624	4,12996	2201	4299	6500	SO:0001583	missense	8483	exon6			ACTCTGCCTTGAT	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.901G>C	15.37:g.65496624C>G	ENSP00000261883:p.Ala301Pro	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	164	75	0.457317	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	37	CCDS10203.1	7	0.003205128205128205	1	0.0020325203252032522	0	0.0	6	0.01048951048951049	0	0.0	C	18.99	3.738884	0.69304	9.09E-4	0.0	ENSG00000138615	ENST00000261883	T	0.40476	1.03	5.63	5.63	0.86233	.	0.163750	0.52532	D	0.000061	T	0.37019	0.0988	L	0.50333	1.59	0.43058	D	0.994673	P	0.50943	0.94	B	0.44044	0.439	T	0.44862	-0.9300	10	0.72032	D	0.01	-27.6493	18.6742	0.91523	0.0:1.0:0.0:0.0	.	301	O75339	CILP1_HUMAN	P	301	ENSP00000261883:A301P	ENSP00000261883:A301P	A	-	1	0	CILP	63283677	0.983000	0.35010	0.798000	0.32154	0.651000	0.38670	2.711000	0.47177	2.659000	0.90383	0.563000	0.77884	GCA	C|0.999;G|0.001	0.001	strong		0.473	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613	
MUC5B	727897	hgsc.bcm.edu	37	11	1265872	1265872	+	Missense_Mutation	SNP	G	G	A	rs200110372		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1265872G>A	ENST00000529681.1	+	31	7820	c.7762G>A	c.(7762-7764)Ggg>Agg	p.G2588R	MUC5B_ENST00000447027.1_Missense_Mutation_p.G2591R|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2588	11 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)		CACCACAACCGGGGCCACCGG	0.642																																					p.G2588R		Atlas-SNP	.											MUC5B,NS,carcinoma,0,6	MUC5B	473	6	0			c.G7762A						scavenged	.						108.0	134.0	126.0					11																	1265872		2035	4177	6212	SO:0001583	missense	727897	exon31			ACAACCGGGGCCA	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.7762G>A	11.37:g.1265872G>A	ENSP00000436812:p.Gly2588Arg	Somatic	432	0	0		WXS	Illumina HiSeq	Phase_I	460	58	0.126087	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.041|2.041	-0.419975|-0.419975	0.04734|0.04734	.|.	.|.	ENSG00000117983|ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844|ENST00000537836	T;T|.	0.24908|.	1.83;2.01|.	2.81|2.81	-5.62|-5.62	0.02481|0.02481	.|.	.|.	.|.	.|.	.|.	T|T	0.11665|0.11665	0.0284|0.0284	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	N|N	1|1	B;B|.	0.15719|.	0.014;0.008|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.07309|0.07309	-1.0779|-1.0779	9|6	0.87932|0.33141	D|T	0|0.24	.|.	1.8997|1.8997	0.03265|0.03265	0.1477:0.2336:0.3867:0.2321|0.1477:0.2336:0.3867:0.2321	.|.	3226;2591|.	A7Y9J9;E9PBJ0|.	.;.|.	R|Q	2588;2591;2560;2603|130	ENSP00000436812:G2588R;ENSP00000415793:G2591R|.	ENSP00000343037:G2560R|ENSP00000440615:R130Q	G|R	+|+	1|2	0|0	MUC5B|MUC5B	1222448|1222448	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.325000|-1.325000	0.02687|0.02687	-3.443000|-3.443000	0.00162|0.00162	-1.027000|-1.027000	0.02421|0.02421	GGG|CGG	.	.	weak		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144854608	144854608	+	Missense_Mutation	SNP	T	T	G	rs2798855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144854608T>G	ENST00000369354.3	-	42	7051	c.6862A>C	c.(6862-6864)Aaa>Caa	p.K2288Q	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.K2373Q|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.K2424Q|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.K2288Q|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.K2182Q			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2288					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)		CGCTCCTGTTTGGATACTTTG	0.502			T	PDGFRB	MPD																																p.K2288Q		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6862C						PASS	.	T	GLN/LYS,GLN/LYS,GLN/LYS	5,4401		0,5,2198	271.0	230.0	244.0		6862,6862,6544	-6.1	0.0	1	dbSNP_100	244	1,8599		0,1,4299	yes	missense,missense,missense	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1	53,53,53	0,6,6497	GG,GT,TT		0.0116,0.1135,0.0461	benign,benign,benign	2288/2347,2288/2363,2182/2241	144854608	6,13000	2203	4300	6503	SO:0001583	missense	9659	exon42			CCTGTTTGGATAC	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.6862A>C	1.37:g.144854608T>G	ENSP00000358360:p.Lys2288Gln	Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	394	61	0.154822	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	.	3.087	-0.187787	0.06299	0.001135	1.16E-4	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01538	4.79;4.91;4.93;4.89;4.9	4.0	-6.13	0.02118	.	.	.	.	.	T	0.00328	0.0010	N	0.16066	0.365	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.44605	-0.9317	9	0.19147	T	0.46	.	7.3378	0.26619	0.0:0.3913:0.4391:0.1695	rs2798855;rs4067565	2182;2288	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	Q	2182;2288;2288;2373;2424	ENSP00000327209:K2182Q;ENSP00000358360:K2288Q;ENSP00000358363:K2288Q;ENSP00000435654:K2373Q;ENSP00000358366:K2424Q	ENSP00000327209:K2182Q	K	-	1	0	PDE4DIP	143565965	0.499000	0.26083	0.000000	0.03702	0.211000	0.24417	0.536000	0.23129	-1.025000	0.03334	-1.007000	0.02485	AAA	T|0.980;G|0.020	0.020	strong		0.502	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
ELOVL5	60481	hgsc.bcm.edu	37	6	53159233	53159233	+	Intron	SNP	G	G	A	rs9474477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:53159233G>A	ENST00000542638.1	-	2	506				ELOVL5_ENST00000304434.6_Intron|ELOVL5_ENST00000486973.1_Intron|ELOVL5_ENST00000370918.4_Intron|ELOVL5_ENST00000541407.1_Intron|ELOVL5_ENST00000370913.5_Silent_p.L39L			Q9NYP7	ELOV5_HUMAN	ELOVL fatty acid elongase 5						alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7	Lung NSC(77;0.116)					agctgctgtagccatcctaca	0.453													G|||	126	0.0251597	0.0938	0.0014	5008	,	,		20012	0.0		0.001	False		,,,				2504	0.0				p.L39L		Atlas-SNP	.											.	ELOVL5	25	.	0			c.C115T						PASS	.	G	,,,	68,1520		1,66,727	3.0	3.0	3.0		,,115,	2.0	0.0	6	dbSNP_119	3	4,3590		0,4,1793	no	intron,intron,coding-synonymous,intron	ELOVL5	NM_001242828.1,NM_001242830.1,NM_001242831.1,NM_021814.4	,,,	1,70,2520	AA,AG,GG		0.1113,4.2821,1.3894	,,,	,,39/89,	53159233	72,5110	794	1797	2591	SO:0001627	intron_variant	60481	exon3			GCTGTAGCCATCC	AF052129	CCDS4951.1, CCDS56433.1, CCDS56434.1, CCDS75470.1	6p21.1-p12.1	2014-07-30	2011-05-25		ENSG00000012660	ENSG00000012660			21308	protein-coding gene	gene with protein product		611805	"""ELOVL family member 5, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"", ""spinocerebellar ataxia 38"""	SCA38		10970790, 25065913	Standard	NM_021814		Approved	HELO1, dJ483K16.1	uc011dwx.2	Q9NYP7	OTTHUMG00000016249	ENST00000542638.1:c.58+1206C>T	6.37:g.53159233G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	139	76	0.546763	NM_001242831	B4DZJ2|F6SH78|Q59EL3|Q5TGH5|Q6NXE7|Q7L2S5|Q8NCG4|Q9UI22	Silent	SNP	ENST00000542638.1	37	CCDS4951.1																																																																																			G|0.973;A|0.027	0.027	strong		0.453	ELOVL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043566.1	NM_021814	
RFX7	64864	hgsc.bcm.edu	37	15	56387421	56387421	+	Silent	SNP	T	T	C	rs34255389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56387421T>C	ENST00000559447.2	-	9	2485	c.2214A>G	c.(2212-2214)ctA>ctG	p.L738L	RFX7_ENST00000422057.1_Silent_p.L738L|RFX7_ENST00000317318.6_Silent_p.L835L|RFX7_ENST00000423270.1_Silent_p.L835L			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	738					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TCTGGCTATGTAGCTGCTGGC	0.393													T|||	16	0.00319489	0.0113	0.0014	5008	,	,		20635	0.0		0.0	False		,,,				2504	0.0				p.L835L		Atlas-SNP	.											.	RFX7	170	.	0			c.A2505G						PASS	.	T		40,3758		0,40,1859	115.0	113.0	114.0		2505	-10.9	0.0	15	dbSNP_126	114	0,8254		0,0,4127	no	coding-synonymous	RFX7	NM_022841.5		0,40,5986	CC,CT,TT		0.0,1.0532,0.3319		835/1461	56387421	40,12012	1899	4127	6026	SO:0001819	synonymous_variant	64864	exon9			GCTATGTAGCTGC			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.2214A>G	15.37:g.56387421T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	172	82	0.476744	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																				T|0.996;C|0.004	0.004	strong		0.393	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
WDR64	128025	hgsc.bcm.edu	37	1	241929542	241929542	+	Missense_Mutation	SNP	G	G	A	rs12095445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241929542G>A	ENST00000366552.2	+	15	2147	c.1940G>A	c.(1939-1941)cGa>cAa	p.R647Q	WDR64_ENST00000437684.2_Missense_Mutation_p.R647Q	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	647			R -> Q (in dbSNP:rs12095445).							breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GATTTATTACGAGTGAACTGC	0.373													G|||	551	0.110024	0.2194	0.1225	5008	,	,		16781	0.003		0.1541	False		,,,				2504	0.0184				p.R647Q		Atlas-SNP	.											WDR64_ENST00000366552,NS,carcinoma,+1,2	WDR64	234	2	0			c.G1940A						PASS	.	G	GLN/ARG	952,3454	360.1+/-315.1	94,764,1345	131.0	128.0	129.0		1940	0.7	0.2	1	dbSNP_120	129	1408,7192	271.6+/-289.6	121,1166,3013	yes	missense	WDR64	NM_144625.4	43	215,1930,4358	AA,AG,GG		16.3721,21.6069,18.1455	benign	647/1082	241929542	2360,10646	2203	4300	6503	SO:0001583	missense	128025	exon15			TATTACGAGTGAA	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"""WD repeat domain containing"""	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1940G>A	1.37:g.241929542G>A	ENSP00000355510:p.Arg647Gln	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	139	55	0.395683	NM_144625	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	37		262|262	0.11996336996336997|0.11996336996336997	101|101	0.20528455284552846|0.20528455284552846	51|51	0.1408839779005525|0.1408839779005525	2|2	0.0034965034965034965|0.0034965034965034965	108|108	0.1424802110817942|0.1424802110817942	G|G	7.315|7.315	0.615699|0.615699	0.14129|0.14129	0.216069|0.216069	0.163721|0.163721	ENSG00000162843|ENSG00000162843	ENST00000425826|ENST00000366552;ENST00000437684;ENST00000414635	.|T;T;T	.|0.39787	.|1.06;1.06;1.06	4.47|4.47	0.735|0.735	0.18300|0.18300	.|WD40 repeat-like-containing domain (1);	.|0.943557	.|0.08769	.|N	.|0.896536	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.48452|0.48452	P|P	3.4999999999996145E-4|3.4999999999996145E-4	.|B;B	.|0.23591	.|0.088;0.062	.|B;B	.|0.18871	.|0.023;0.005	T|T	0.31779|0.31779	-0.9931|-0.9931	4|9	.|0.22109	.|T	.|0.4	-0.0022|-0.0022	3.7563|3.7563	0.08586|0.08586	0.5957:0.1885:0.2158:0.0|0.5957:0.1885:0.2158:0.0	rs12095445;rs52808464;rs58881118;rs12095445|rs12095445;rs52808464;rs58881118;rs12095445	.|647;367	.|B1ANS9;D1MPS4	.|WDR64_HUMAN;.	K|Q	126|647;647;418	.|ENSP00000355510:R647Q;ENSP00000402446:R647Q;ENSP00000406656:R418Q	.|ENSP00000355510:R647Q	E|R	+|+	1|2	0|0	WDR64|WDR64	239996165|239996165	1.000000|1.000000	0.71417|0.71417	0.228000|0.228000	0.23943|0.23943	0.031000|0.031000	0.12232|0.12232	2.437000|2.437000	0.44828|0.44828	-0.072000|-0.072000	0.12864|0.12864	-1.283000|-1.283000	0.01379|0.01379	GAG|CGA	G|0.839;A|0.161	0.161	strong		0.373	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625	
SVEP1	79987	hgsc.bcm.edu	37	9	113149612	113149612	+	Missense_Mutation	SNP	T	T	C	rs114581956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113149612T>C	ENST00000401783.2	-	42	10349	c.10013A>G	c.(10012-10014)cAc>cGc	p.H3338R	SVEP1_ENST00000374469.1_Missense_Mutation_p.H3315R|SVEP1_ENST00000297826.5_Missense_Mutation_p.H1264R	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3338	Sushi 32. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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						TTCTGTGCAGTGTGCCTCAGA	0.468													T|||	47	0.00938498	0.0333	0.0029	5008	,	,		17065	0.0		0.001	False		,,,				2504	0.0				p.H3338R		Atlas-SNP	.											.	SVEP1	326	.	0			c.A10013G						PASS	.	T	ARG/HIS	94,3784		1,92,1846	140.0	140.0	140.0		10013	1.4	0.0	9	dbSNP_132	140	0,8258		0,0,4129	yes	missense	SVEP1	NM_153366.3	29	1,92,5975	CC,CT,TT		0.0,2.4239,0.7746	benign	3338/3572	113149612	94,12042	1939	4129	6068	SO:0001583	missense	79987	exon42			GTGCAGTGTGCCT	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.10013A>G	9.37:g.113149612T>C	ENSP00000384917:p.His3338Arg	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	241	80	0.33195	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	27	0.012362637362637362	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	3.480	-0.106077	0.06924	0.024239	0.0	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.63580	-0.05;-0.05;-0.05	5.09	1.42	0.22433	Complement control module (2);Sushi/SCR/CCP (3);	0.889971	0.09909	N	0.740049	T	0.08133	0.0203	N	0.11892	0.195	0.09310	N	0.999999	B	0.18013	0.025	B	0.22152	0.038	T	0.09662	-1.0664	10	0.21014	T	0.42	.	3.9589	0.09403	0.1226:0.0714:0.1426:0.6634	.	3338	Q4LDE5	SVEP1_HUMAN	R	3338;3315;1264	ENSP00000384917:H3338R;ENSP00000363593:H3315R;ENSP00000297826:H1264R	ENSP00000297826:H1264R	H	-	2	0	SVEP1	112189433	0.005000	0.15991	0.021000	0.16686	0.386000	0.30323	1.484000	0.35508	0.055000	0.16094	0.529000	0.55759	CAC	T|0.987;C|0.013	0.013	strong		0.468	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037424	33037424	+	Missense_Mutation	SNP	T	T	C	rs1126542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33037424T>C	ENST00000419277.1	-	3	469	c.340A>G	c.(340-342)Acc>Gcc	p.T114A	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.T114A	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	114	Alpha-1.		T -> A (in allele DPA1*01:05, allele DPA1*02:01, allele DPA1*02:02, allele DPA1*02:03, allele DPA1*02:04 and allele DPA1*04:01; dbSNP:rs1126542).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						GTACCGTTGGTGGCCTGAGTG	0.542													.|||	2199	0.439097	0.5802	0.2853	5008	,	,		19850	0.6796		0.1889	False		,,,				2504	0.3671				p.T114A		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.A340G						PASS	.						140.0	128.0	132.0					6																	33037424		1510	2709	4219	SO:0001583	missense	3113	exon2			CGTTGGTGGCCTG	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.340A>G	6.37:g.33037424T>C	ENSP00000393566:p.Thr114Ala	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	858	0.39285714285714285	270	0.5487804878048781	88	0.2430939226519337	370	0.6468531468531469	130	0.17150395778364116	C	0.073	-1.198952	0.01581	.	.	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000453337	T;T;T	0.00816	5.66;5.66;5.66	3.11	-6.22	0.02058	MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);Immunoglobulin-like fold (1);	1.036210	0.07665	N	0.934335	T	0.00328	0.0010	M	0.69523	2.12	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43861	-0.9365	9	0.34782	T	0.22	.	0.6691	0.00856	0.1954:0.1808:0.2729:0.351	rs1126542;rs2308922;rs3181639;rs12722008;rs17424589	114	P20036	DPA1_HUMAN	A	114	ENSP00000393566:T114A;ENSP00000402872:T114A;ENSP00000390929:T114A	ENSP00000393566:T114A	T	-	1	0	HLA-DPA1	33145402	0.000000	0.05858	0.063000	0.19743	0.003000	0.03518	-1.634000	0.02020	-3.515000	0.00149	-1.145000	0.01858	ACC	T|0.680;G|0.000;C|0.319;A|0.000	0.319	strong		0.542	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
NSUN2	54888	hgsc.bcm.edu	37	5	6600150	6600150	+	Silent	SNP	G	G	A	rs3822434	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:6600150G>A	ENST00000264670.6	-	19	2504	c.2193C>T	c.(2191-2193)gaC>gaT	p.D731D	NSUN2_ENST00000539938.1_Silent_p.D495D|NSUN2_ENST00000506139.1_Silent_p.D696D	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	731					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						CCTCAGTCACGTCATTGTCTG	0.572													C|||	869	0.173522	0.0825	0.2507	5008	,	,		18174	0.2321		0.1402	False		,,,				2504	0.2157				p.D731D		Atlas-SNP	.											NSUN2,colon,carcinoma,0,1	NSUN2	82	1	0			c.C2193T						PASS	.	C	,	411,3995		17,377,1809	182.0	144.0	157.0		2088,2193	-0.6	0.0	5	dbSNP_107	157	1279,7321		105,1069,3126	no	coding-synonymous,coding-synonymous	NSUN2	NM_001193455.1,NM_017755.5	,	122,1446,4935	AA,AG,GG		14.8721,9.3282,12.994	,	696/733,731/768	6600150	1690,11316	2203	4300	6503	SO:0001819	synonymous_variant	54888	exon19			AGTCACGTCATTG	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.2193C>T	5.37:g.6600150G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	169	81	0.47929	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	37	CCDS3869.1																																																																																			G|0.862;C|0.000;A|0.138	0.138	strong		0.572	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
UBD	10537	hgsc.bcm.edu	37	6	29524003	29524003	+	Missense_Mutation	SNP	A	A	G	rs2076484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29524003A>G	ENST00000377050.4	-	2	375	c.152T>C	c.(151-153)tTg>tCg	p.L51S	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	51	Ubiquitin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00214}.		L -> S (in dbSNP:rs2076484).		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						GGAGCCCAGCAAAAGAACCTG	0.463													a|||	1000	0.199681	0.4758	0.1052	5008	,	,		8373	0.1488		0.0268	False		,,,				2504	0.1237				p.L51S		Atlas-SNP	.											.	UBD	13	.	0			c.T152C						PASS	.	G	SER/LEU	1326,1696		277,772,462	73.0	63.0	66.0		152	-8.2	0.1	6	dbSNP_96	66	153,5265		2,149,2558	yes	missense	UBD	NM_006398.3	145	279,921,3020	GG,GA,AA		2.8239,43.8782,17.5237	benign	51/166	29524003	1479,6961	1511	2709	4220	SO:0001583	missense	10537	exon2			CCCAGCAAAAGAA	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.152T>C	6.37:g.29524003A>G	ENSP00000366249:p.Leu51Ser	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	144	71	0.493056	NM_006398	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Missense_Mutation	SNP	ENST00000377050.4	37	CCDS4662.1	393	0.17994505494505494	252	0.5121951219512195	41	0.1132596685082873	84	0.14685314685314685	16	0.021108179419525065	a	7.656	0.684031	0.14907	0.438782	0.028239	ENSG00000213886	ENST00000377050	T	0.74737	-0.87	5.05	-8.19	0.01049	Ubiquitin supergroup (1);Ubiquitin (2);	1.770580	0.04933	N	0.457201	T	0.33644	0.0870	L	0.33485	1.01	0.80722	P	0.0	B	0.21606	0.058	B	0.21360	0.034	T	0.27331	-1.0077	9	0.87932	D	0	-6.5613	1.2368	0.01955	0.2717:0.1124:0.1519:0.464	rs2076484;rs17177902;rs52796040;rs2076484	51	O15205	UBD_HUMAN	S	51	ENSP00000366249:L51S	ENSP00000366249:L51S	L	-	2	0	UBD	29631982	0.000000	0.05858	0.069000	0.20011	0.309000	0.27889	-0.213000	0.09305	-1.389000	0.02090	-0.308000	0.09152	TTG	A|0.820;G|0.180	0.180	strong		0.463	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076628.3		
CSNK1A1L	122011	hgsc.bcm.edu	37	13	37679268	37679268	+	Missense_Mutation	SNP	G	G	T	rs9576175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:37679268G>T	ENST00000379800.3	-	1	535	c.126C>A	c.(124-126)gaC>gaA	p.D42E		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	42	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> E (in dbSNP:rs9576175). {ECO:0000269|PubMed:15489334}.		cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.D42E(1)		NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		TCACTGCTACGTCCTCGCCGT	0.542													T|||	2989	0.596845	0.5567	0.5735	5008	,	,		18426	0.8135		0.494	False		,,,				2504	0.5501				p.D42E		Atlas-SNP	.											CSNK1A1L,NS,carcinoma,0,1	CSNK1A1L	69	1	1	Substitution - Missense(1)	prostate(1)	c.C126A						PASS	.	T	GLU/ASP	2388,2018	564.2+/-381.4	652,1084,467	153.0	132.0	139.0		126	0.8	0.3	13	dbSNP_119	139	4292,4308	577.9+/-390.6	1080,2132,1088	yes	missense	CSNK1A1L	NM_145203.5	45	1732,3216,1555	TT,TG,GG		49.907,45.8012,48.6391	benign	42/338	37679268	6680,6326	2203	4300	6503	SO:0001583	missense	122011	exon1			TGCTACGTCCTCG	BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.126C>A	13.37:g.37679268G>T	ENSP00000369126:p.Asp42Glu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_145203	Q5T2N2	Missense_Mutation	SNP	ENST00000379800.3	37	CCDS9363.1	1322	0.6053113553113553	269	0.5467479674796748	209	0.5773480662983426	463	0.8094405594405595	381	0.5026385224274407	T	0.004	-2.283595	0.00251	0.541988	0.49907	ENSG00000180138	ENST00000379800	T	0.17854	2.25	0.778	0.778	0.18543	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.055041	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00280	-1.71	0.58432	P	9.99999999995449E-6	B	0.02656	0.0	B	0.08055	0.003	T	0.25117	-1.0141	9	0.02654	T	1	.	4.8674	0.13615	0.0:0.0:0.3161:0.6839	rs9576175;rs17845861;rs17858836;rs52827977;rs61019247;rs9576175	42	Q8N752	KC1AL_HUMAN	E	42	ENSP00000369126:D42E	ENSP00000369126:D42E	D	-	3	2	CSNK1A1L	36577268	0.997000	0.39634	0.305000	0.25099	0.232000	0.25224	0.197000	0.17197	-0.206000	0.10203	-0.363000	0.07495	GAC	G|0.444;T|0.556	0.556	strong		0.542	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203	
FPR1	2357	hgsc.bcm.edu	37	19	52249947	52249947	+	Missense_Mutation	SNP	C	C	G	rs2070745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	143	0	0		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	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	
CAPN14	440854	hgsc.bcm.edu	37	2	31417290	31417290	+	Missense_Mutation	SNP	T	T	C	rs76523220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31417290T>C	ENST00000403897.3	-	9	1076	c.935A>G	c.(934-936)aAt>aGt	p.N312S	CAPN14_ENST00000444918.2_Missense_Mutation_p.N312S	NM_001145122.1	NP_001138594.1	A8MX76	CAN14_HUMAN	calpain 14	312	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|endometrium(2)|prostate(1)|skin(1)|stomach(2)	7						TTCTCCGTCATTGTCTTTCCT	0.448													T|||	210	0.0419329	0.1112	0.0245	5008	,	,		19529	0.0		0.0378	False		,,,				2504	0.0082				p.N312S		Atlas-SNP	.											.	CAPN14	36	.	0			c.A935G						PASS	.	T	SER/ASN	157,1227		12,133,547	87.0	80.0	82.0		935	3.6	0.5	2	dbSNP_131	82	92,3090		4,84,1503	yes	missense	CAPN14	NM_001145122.1	46	16,217,2050	CC,CT,TT		2.8913,11.3439,5.4534	benign	312/685	31417290	249,4317	692	1591	2283	SO:0001583	missense	440854	exon9			CCGTCATTGTCTT	AC015980	CCDS46254.1	2p23.1-p21	2013-01-10			ENSG00000214711	ENSG00000214711		"""EF-hand domain containing"""	16664	protein-coding gene	gene with protein product		610229				11675017	Standard	NM_001145122		Approved		uc010yms.2	A8MX76	OTTHUMG00000152039	ENST00000403897.3:c.935A>G	2.37:g.31417290T>C	ENSP00000385247:p.Asn312Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_001145122	B3KRU9	Missense_Mutation	SNP	ENST00000403897.3	37	CCDS46254.1	85	0.03891941391941392	45	0.09146341463414634	12	0.03314917127071823	0	0.0	28	0.036939313984168866	T	12.26	1.885840	0.33348	0.113439	0.028913	ENSG00000214711	ENST00000444918;ENST00000403897	D;D	0.97352	-4.35;-4.35	3.61	3.61	0.41365	Peptidase C2, calpain, catalytic domain (3);	0.309811	0.29046	U	0.013315	T	0.26702	0.0653	N	0.14661	0.345	0.32099	N	0.590856	B;B	0.30563	0.285;0.187	B;B	0.28916	0.096;0.04	T	0.75439	-0.3317	10	0.87932	D	0	.	12.5311	0.56115	0.0:0.0:0.0:1.0	.	312;136	A8MX76;A8MX76-2	CAN14_HUMAN;.	S	312	ENSP00000398670:N312S;ENSP00000385247:N312S	ENSP00000385247:N312S	N	-	2	0	CAPN14	31270794	0.993000	0.37304	0.453000	0.27007	0.636000	0.38137	5.177000	0.65032	1.411000	0.46957	0.533000	0.62120	AAT	T|0.964;C|0.036	0.036	strong		0.448	CAPN14-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325010.1	NM_001145122	
THAP4	51078	hgsc.bcm.edu	37	2	242572846	242572846	+	Silent	SNP	A	A	G	rs3208142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242572846A>G	ENST00000407315.1	-	2	1157	c.726T>C	c.(724-726)tcT>tcC	p.S242S		NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	242							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		GGGTGTGCTTAGAGGAGAAAC	0.537													G|||	2144	0.428115	0.41	0.3429	5008	,	,		19156	0.5665		0.3181	False		,,,				2504	0.4836				p.S242S		Atlas-SNP	.											.	THAP4	27	.	0			c.T726C						PASS	.	G		1638,2768	657.4+/-400.2	300,1038,865	70.0	80.0	76.0		726	2.1	1.0	2	dbSNP_105	76	2586,6006	687.2+/-404.2	410,1766,2120	no	coding-synonymous	THAP4	NM_015963.5		710,2804,2985	GG,GA,AA		30.0978,37.1766,32.4973		242/578	242572846	4224,8774	2203	4296	6499	SO:0001819	synonymous_variant	51078	exon2			GTGCTTAGAGGAG	AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946		"""THAP (C2CH-type zinc finger) domain containing"""	23187	protein-coding gene	gene with protein product		612533				12575992, 10810093	Standard	NM_015963		Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000407315.1:c.726T>C	2.37:g.242572846A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_015963	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Silent	SNP	ENST00000407315.1	37	CCDS2551.1																																																																																			A|0.650;G|0.350	0.350	strong		0.537	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963	
PPP2R3B	28227	hgsc.bcm.edu	37	X	295132	295132	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:295132T>C	ENST00000390665.3	-	13	1716	c.1698A>G	c.(1696-1698)gcA>gcG	p.A566A		NM_013239.4	NP_037371.2	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'', beta	566					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)				CGTCCCCGCATGCGTACTCGT	0.736													T|||	2715	0.542133	0.8351	0.4395	5008	,	,		11415	0.5278		0.4185	False		,,,				2504	0.3609				p.A566A		Atlas-SNP	.											.	PPP2R3B	43	.	0			c.A1698G						PASS	.	T		3373,977		1347,679,149	14.0	22.0	19.0		1698	-0.6	0.0	X	dbSNP_134	19	3489,5049		730,2029,1510	no	coding-synonymous	PPP2R3B	NM_013239.4		2077,2708,1659	CC,CT,TT		40.8644,22.4598,46.7567		566/576	295132	6862,6026	2175	4269	6444	SO:0001819	synonymous_variant	28227	exon13			CCCGCATGCGTAC	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.1698A>G	X.37:g.295132T>C		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_013239	Q6P4G9|Q7RTT1|Q96H01	Silent	SNP	ENST00000390665.3	37	CCDS14104.1																																																																																			T|0.485;C|0.515	0.515	strong		0.736	PPP2R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055577.2	NM_013239	
FBLIM1	54751	hgsc.bcm.edu	37	1	16091700	16091700	+	Silent	SNP	G	G	A	rs61733331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16091700G>A	ENST00000375766.3	+	3	862	c.222G>A	c.(220-222)ccG>ccA	p.P74P	FBLIM1_ENST00000332305.5_Silent_p.P74P|FBLIM1_ENST00000375771.1_Silent_p.P74P|FBLIM1_ENST00000441801.2_Silent_p.P74P|FBLIM1_ENST00000400773.1_Silent_p.P74P	NM_017556.2	NP_060026.2	Q8WUP2	FBLI1_HUMAN	filamin binding LIM protein 1	74	Intrinsically disordered.|Pro-rich.				cell junction assembly (GO:0034329)|regulation of cell shape (GO:0008360)|regulation of integrin activation (GO:0033623)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|stress fiber (GO:0001725)	filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	16		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|READ - Rectum adenocarcinoma(331;0.0649)|STAD - Stomach adenocarcinoma(313;0.138)		CCACAGTGCCGGCTGCACCTA	0.662													A|||	84	0.0167732	0.0477	0.0043	5008	,	,		13729	0.0069		0.002	False		,,,				2504	0.0092				p.P74P		Atlas-SNP	.											.	FBLIM1	46	.	0			c.G222A						PASS	.	A	,,	157,4227		2,153,2037	21.0	24.0	23.0		222,222,222	-2.8	0.0	1	dbSNP_129	23	18,8566		0,18,4274	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLIM1	NM_001024215.1,NM_001024216.1,NM_017556.2	,,	2,171,6311	AA,AG,GG		0.2097,3.5812,1.3495	,,	74/375,74/277,74/374	16091700	175,12793	2192	4292	6484	SO:0001819	synonymous_variant	54751	exon2			AGTGCCGGCTGCA		CCDS163.1, CCDS30609.1, CCDS44064.1	1p36.13	2014-04-07			ENSG00000162458	ENSG00000162458			24686	protein-coding gene	gene with protein product		607747				12679033, 12496242	Standard	XM_005245900		Approved	FBLP-1, CAL, migfilin	uc001axe.1	Q8WUP2	OTTHUMG00000003079	ENST00000375766.3:c.222G>A	1.37:g.16091700G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	123	67	0.544715	NM_001024215	B3KNY0|Q5VVE0|Q5VVE1|Q8IX23|Q96T00|Q9UFD6	Silent	SNP	ENST00000375766.3	37	CCDS163.1																																																																																			G|0.988;A|0.012	0.012	strong		0.662	FBLIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008511.3	NM_001024215	
SLC16A6	9120	hgsc.bcm.edu	37	17	66267734	66267734	+	Silent	SNP	T	T	C	rs61740584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66267734T>C	ENST00000327268.4	-	6	731	c.567A>G	c.(565-567)ctA>ctG	p.L189L	ARSG_ENST00000448504.2_Intron|SLC16A6_ENST00000580666.1_Silent_p.L189L	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	189					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	TGTTTAACTGTAGTAGGCCCA	0.473													T|||	118	0.0235623	0.087	0.0043	5008	,	,		18475	0.0		0.0	False		,,,				2504	0.0				p.L189L		Atlas-SNP	.											.	SLC16A6	56	.	0			c.A567G						PASS	.	T	,,	400,4006	199.1+/-222.7	18,364,1821	76.0	73.0	74.0		567,567,	-2.4	0.3	17	dbSNP_129	74	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	,,	18,365,6120	CC,CT,TT		0.0116,9.0785,3.0832	,,	189/524,189/524,	66267734	401,12605	2203	4300	6503	SO:0001819	synonymous_variant	9120	exon6			TAACTGTAGTAGG	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"""Solute carriers"""	10927	protein-coding gene	gene with protein product		603880	"""solute carrier family 16 (monocarboxylic acid transporters), member 6"", ""solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"""			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.567A>G	17.37:g.66267734T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_001174166	Q6P1X3	Silent	SNP	ENST00000327268.4	37	CCDS11675.1																																																																																			T|0.969;C|0.031	0.031	strong		0.473	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694	
CHD1L	9557	hgsc.bcm.edu	37	1	146763171	146763171	+	Missense_Mutation	SNP	T	T	A	rs61756300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:146763171T>A	ENST00000369258.4	+	20	2348	c.2328T>A	c.(2326-2328)agT>agA	p.S776R	CHD1L_ENST00000431239.1_Missense_Mutation_p.S682R|CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000361293.5_Missense_Mutation_p.S495R|CHD1L_ENST00000369259.3_Missense_Mutation_p.S572R	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	776	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					CAGACCTGAGTTTGGGAGGTG	0.403													T|||	101	0.0201677	0.0749	0.0029	5008	,	,		20473	0.0		0.0	False		,,,				2504	0.0				p.S776R		Atlas-SNP	.											.	CHD1L	72	.	0			c.T2328A						PASS	.	T	ARG/SER	265,4141	152.5+/-186.2	6,253,1944	196.0	162.0	173.0		2328	4.6	1.0	1	dbSNP_129	173	6,8594	4.3+/-15.6	0,6,4294	yes	missense	CHD1L	NM_004284.3	110	6,259,6238	AA,AT,TT		0.0698,6.0145,2.0837	benign	776/898	146763171	271,12735	2203	4300	6503	SO:0001583	missense	9557	exon20			CCTGAGTTTGGGA	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.2328T>A	1.37:g.146763171T>A	ENSP00000358262:p.Ser776Arg	Somatic	383	0	0		WXS	Illumina HiSeq	Phase_I	378	182	0.481481	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	37	CCDS927.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	T	12.55	1.970529	0.34754	0.060145	6.98E-4	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000361293	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.82	4.63	0.57726	Appr-1-p processing (1);	0.600804	0.20767	N	0.086044	T	0.11836	0.0288	N	0.25647	0.755	0.26362	N	0.977023	P;B;B	0.40476	0.718;0.063;0.032	B;B;B	0.35470	0.203;0.055;0.021	T	0.04650	-1.0936	10	0.23302	T	0.38	.	9.3476	0.38118	0.0:0.0:0.1803:0.8197	rs61756300	682;572;776	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	R	682;572;776;495	ENSP00000389031:S682R;ENSP00000358263:S572R;ENSP00000358262:S776R;ENSP00000355100:S495R	ENSP00000355100:S495R	S	+	3	2	CHD1L	145229795	0.305000	0.24481	1.000000	0.80357	0.902000	0.53008	0.451000	0.21779	2.223000	0.72356	0.454000	0.30748	AGT	T|0.984;A|0.016	0.016	strong		0.403	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284	
MIPEP	4285	hgsc.bcm.edu	37	13	24463414	24463414	+	Missense_Mutation	SNP	C	C	A	rs112735196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:24463414C>A	ENST00000382172.3	-	1	144	c.46G>T	c.(46-48)Gct>Tct	p.A16S	C1QTNF9B-AS1_ENST00000435039.2_RNA|C1QTNF9B_ENST00000556521.1_5'Flank|C1QTNF9B-AS1_ENST00000417034.1_RNA|C1QTNF9B-AS1_ENST00000382133.4_RNA|MIPEP_ENST00000469167.1_5'UTR	NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	16					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)		ggcggcAGAGCTGCTGCTCTG	0.692													C|||	24	0.00479233	0.0182	0.0	5008	,	,		11162	0.0		0.0	False		,,,				2504	0.0				p.A16S		Atlas-SNP	.											.	MIPEP	53	.	0			c.G46T						PASS	.						2.0	3.0	3.0					13																	24463414		1592	3189	4781	SO:0001583	missense	4285	exon1			GCAGAGCTGCTGC		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.46G>T	13.37:g.24463414C>A	ENSP00000371607:p.Ala16Ser	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	18	17	0.944444	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	c	11.93	1.786749	0.31593	.	.	ENSG00000027001	ENST00000382172	T	0.10005	2.92	4.11	2.28	0.28536	.	0.834312	0.10422	N	0.676614	T	0.04363	0.0120	L	0.36672	1.1	0.09310	N	1	B	0.20052	0.041	B	0.17098	0.017	T	0.26849	-1.0091	10	0.59425	D	0.04	-18.1677	7.5781	0.27948	0.0:0.7411:0.1649:0.094	.	16	Q99797	MIPEP_HUMAN	S	16	ENSP00000371607:A16S	ENSP00000371607:A16S	A	-	1	0	MIPEP	23361414	0.002000	0.14202	0.108000	0.21378	0.376000	0.30014	0.683000	0.25349	0.920000	0.36970	0.491000	0.48974	GCT	C|0.994;A|0.006	0.006	strong		0.692	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		
PSMC5	5705	hgsc.bcm.edu	37	17	61902011	61902011	+	5'Flank	SNP	C	C	T	rs9910549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61902011C>T	ENST00000310144.6	+	0	0				PSMC5_ENST00000580864.1_5'Flank|FTSJ3_ENST00000580295.1_5'Flank|FTSJ3_ENST00000427159.2_Silent_p.G301G	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						GCTCCTTGCGCCCCAACACTC	0.562													C|||	99	0.0197684	0.0734	0.0029	5008	,	,		19798	0.0		0.0	False		,,,				2504	0.0				p.G301G		Atlas-SNP	.											.	FTSJ3	63	.	0			c.G903A						PASS	.	C		211,4195	130.2+/-166.9	6,199,1998	191.0	171.0	178.0		903	0.5	1.0	17	dbSNP_119	178	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FTSJ3	NM_017647.3		6,201,6296	TT,TC,CC		0.0233,4.7889,1.6377		301/848	61902011	213,12793	2203	4300	6503	SO:0001631	upstream_gene_variant	117246	exon10			CTTGCGCCCCAAC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195			17.37:g.61902011C>T	Exception_encountered	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	207	103	0.497585	NM_017647	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Silent	SNP	ENST00000310144.6	37	CCDS11645.1																																																																																			C|0.976;T|0.024	0.024	strong		0.562	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
ZNF628	89887	hgsc.bcm.edu	37	19	55994975	55994975	+	Silent	SNP	G	G	T	rs114065657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55994975G>T	ENST00000598519.1	+	3	2968	c.2415G>T	c.(2413-2415)gtG>gtT	p.V805V	NAT14_ENST00000587400.1_5'Flank|NAT14_ENST00000591590.1_5'Flank|ZNF628_ENST00000391718.2_Silent_p.V801V|NAT14_ENST00000205194.4_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	805	Gly-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		TGCAGAATGTGGGGGGTGGGG	0.692													g|||	82	0.0163738	0.0598	0.0029	5008	,	,		13204	0.0		0.001	False		,,,				2504	0.0				p.V805V		Atlas-SNP	.											.	ZNF628	75	.	0			c.G2415T						PASS	.	G		212,4192		2,208,1992	32.0	41.0	38.0		2403	-1.7	0.8	19	dbSNP_132	38	2,8592		0,2,4295	no	coding-synonymous	ZNF628	NM_033113.2		2,210,6287	TT,TG,GG		0.0233,4.8138,1.6464		801/1056	55994975	214,12784	2202	4297	6499	SO:0001819	synonymous_variant	89887	exon3			GAATGTGGGGGGT	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.2415G>T	19.37:g.55994975G>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_033113	Q86X34	Silent	SNP	ENST00000598519.1	37	CCDS33116.3																																																																																			G|0.980;T|0.020	0.020	strong		0.692	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
GPRASP1	9737	hgsc.bcm.edu	37	X	101912465	101912465	+	Silent	SNP	G	G	T	rs1124050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101912465G>T	ENST00000361600.5	+	5	4425	c.3624G>T	c.(3622-3624)ccG>ccT	p.P1208P	GPRASP1_ENST00000537097.1_Silent_p.P1208P|RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000415986.1_Silent_p.P1208P|GPRASP1_ENST00000444152.1_Silent_p.P1208P	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	1208	OPRD1-binding.				endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						TTAATTATCCGTCCTCCCGAG	0.383													G|||	50	0.013245	0.0371	0.0014	3775	,	,		15018	0.0		0.0	False		,,,				2504	0.0				p.P1208P		Atlas-SNP	.											.	GPRASP1	140	.	0			c.G3624T						PASS	.	G	,,,,	148,3687		2,116,28,1514,543	103.0	93.0	97.0		3624,3624,3624,,3624	-5.8	0.1	X	dbSNP_86	97	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	GPRASP1,ARMCX5-GPRASP2	NM_001099410.1,NM_001099411.1,NM_001184727.1,NM_001199818.1,NM_014710.4	,,,,	2,116,28,3942,2415	TT,TG,T,GG,G		0.0,3.8592,1.4011	,,,,	1208/1396,1208/1396,1208/1396,,1208/1396	101912465	148,10415	2203	4300	6503	SO:0001819	synonymous_variant	9737	exon3			TTATCCGTCCTCC	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"""Armadillo repeat containing"""	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.3624G>T	X.37:g.101912465G>T		Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	293	107	0.365188	NM_001099411	O43168|Q96LA1	Silent	SNP	ENST00000361600.5	37	CCDS35352.1																																																																																			0|0.003;A|0.000;G|0.981;T|0.016	0.016	strong		0.383	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710	
MFSD1	64747	hgsc.bcm.edu	37	3	158520011	158520011	+	Missense_Mutation	SNP	C	C	T	rs28364680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:158520011C>T	ENST00000264266.8	+	1	132	c.70C>T	c.(70-72)Ccg>Tcg	p.P24S	RP11-379F4.9_ENST00000607044.1_RNA|MFSD1_ENST00000392813.4_Missense_Mutation_p.P73S|MFSD1_ENST00000415822.2_Missense_Mutation_p.P73S			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	24			P -> S (in dbSNP:rs28364680). {ECO:0000269|PubMed:14702039}.		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CAGAGGTGCCCCGGCCGCCCC	0.692													C|||	714	0.142572	0.1293	0.1282	5008	,	,		11497	0.1915		0.1501	False		,,,				2504	0.1125				p.P73S	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											.	MFSD1	88	.	0			c.C217T						PASS	.	C	SER/PRO,SER/PRO	517,3867		33,451,1708	13.0	15.0	14.0		217,217	3.2	0.0	3	dbSNP_125	14	968,7606		69,830,3388	no	missense,missense	MFSD1	NM_022736.2,NM_001167903.1	74,74	102,1281,5096	TT,TC,CC		11.2899,11.7929,11.4601	benign,benign	73/515,73/476	158520011	1485,11473	2192	4287	6479	SO:0001583	missense	64747	exon1			GGTGCCCCGGCCG	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.70C>T	3.37:g.158520011C>T	ENSP00000264266:p.Pro24Ser	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Missense_Mutation	SNP	ENST00000264266.8	37		343	0.15705128205128205	68	0.13821138211382114	52	0.143646408839779	107	0.18706293706293706	116	0.15303430079155672	C	17.11	3.306231	0.60305	0.117929	0.112899	ENSG00000118855	ENST00000415822;ENST00000392813;ENST00000264266;ENST00000361159	T;T;T	0.18502	2.27;2.21;2.33	5.04	3.15	0.36227	Major facilitator superfamily domain, general substrate transporter (1);	1.418460	0.04299	N	0.347069	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.001	T	0.34054	-0.9844	9	0.07325	T	0.83	.	4.8323	0.13447	0.1563:0.6111:0.1508:0.0818	rs28364680;rs59115350	73;24	C9JS94;Q9H3U5	.;MFSD1_HUMAN	S	73;73;24;24	ENSP00000403117:P73S;ENSP00000376560:P73S;ENSP00000264266:P24S	ENSP00000264266:P24S	P	+	1	0	MFSD1	160002705	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-1.207000	0.03008	1.105000	0.41606	0.563000	0.77884	CCG	C|0.842;T|0.158	0.158	strong		0.692	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736	
SLC6A17	388662	hgsc.bcm.edu	37	1	110740931	110740931	+	Silent	SNP	G	G	A	rs6685009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110740931G>A	ENST00000331565.4	+	12	2534	c.2049G>A	c.(2047-2049)gaG>gaA	p.E683E		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	683					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)			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)		TGCCCAGTGAGGCACCTTCCC	0.612													G|||	778	0.155351	0.5091	0.0375	5008	,	,		21398	0.0357		0.0278	False		,,,				2504	0.0153				p.E683E		Atlas-SNP	.											.	SLC6A17	86	.	0			c.G2049A						PASS	.	G		1893,2513	544.2+/-376.5	399,1095,709	121.0	98.0	106.0		2049	4.4	1.0	1	dbSNP_116	106	76,8524	44.9+/-103.4	1,74,4225	no	coding-synonymous	SLC6A17	NM_001010898.2		400,1169,4934	AA,AG,GG		0.8837,42.9641,15.1392		683/728	110740931	1969,11037	2203	4300	6503	SO:0001819	synonymous_variant	388662	exon12			CAGTGAGGCACCT		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.2049G>A	1.37:g.110740931G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Silent	SNP	ENST00000331565.4	37	CCDS30799.1																																																																																			G|0.845;A|0.155	0.155	strong		0.612	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60989243	60989243	+	Silent	SNP	T	T	C	rs34446012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60989243T>C	ENST00000252998.1	-	10	1320	c.1164A>G	c.(1162-1164)ctA>ctG	p.L388L		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	388						extracellular space (GO:0005615)											AGCCGACTGGTAGGGAGGGCA	0.701													T|||	25	0.00499201	0.0174	0.0029	5008	,	,		12717	0.0		0.0	False		,,,				2504	0.0				p.L388L		Atlas-SNP	.											.	.	.	.	0			c.A1164G						PASS	.	T		45,4287		0,45,2121	13.0	14.0	13.0		1164	-10.1	0.0	20	dbSNP_126	13	0,8462		0,0,4231	no	coding-synonymous	C20orf151	NM_080833.2		0,45,6352	CC,CT,TT		0.0,1.0388,0.3517		388/665	60989243	45,12749	2166	4231	6397	SO:0001819	synonymous_variant	140893	exon10			GACTGGTAGGGAG	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.1164A>G	20.37:g.60989243T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Silent	SNP	ENST00000252998.1	37	CCDS13498.1																																																																																			T|0.996;C|0.004	0.004	strong		0.701	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
NT5E	4907	hgsc.bcm.edu	37	6	86195098	86195098	+	Silent	SNP	C	C	T	rs35478984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:86195098C>T	ENST00000257770.3	+	4	946	c.897C>T	c.(895-897)aaC>aaT	p.N299N	NT5E_ENST00000369651.3_Silent_p.N299N	NM_002526.3	NP_002517.1	P21589	5NTD_HUMAN	5'-nucleotidase, ecto (CD73)	299					adenosine biosynthetic process (GO:0046086)|AMP catabolic process (GO:0006196)|dephosphorylation (GO:0016311)|DNA metabolic process (GO:0006259)|negative regulation of inflammatory response (GO:0050728)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Cytarabine(DB00987)|Pentoxifylline(DB00806)	AAAGAGGAAACGTCATCTCTT	0.438													C|||	97	0.019369	0.0703	0.0058	5008	,	,		20130	0.0		0.0	False		,,,				2504	0.0				p.N299N	Melanoma(140;797 1765 2035 2752 18208)	Atlas-SNP	.											.	NT5E	56	.	0			c.C897T						PASS	.	C	,	287,4119	159.6+/-192.1	8,271,1924	151.0	136.0	141.0		897,897	-0.1	0.9	6	dbSNP_126	141	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous	NT5E	NM_001204813.1,NM_002526.3	,	8,273,6222	TT,TC,CC		0.0233,6.5138,2.2221	,	299/525,299/575	86195098	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	4907	exon4			AGGAAACGTCATC	X55740	CCDS5002.1, CCDS56439.1	6q14-q21	2013-08-28	2002-04-18	2002-04-19	ENSG00000135318	ENSG00000135318	3.1.3.5	"""CD molecules"""	8021	protein-coding gene	gene with protein product		129190	"""5' nucleotidase (CD73)"""	NT5			Standard	NM_002526		Approved	CD73, eN, eNT, CALJA	uc003pko.4	P21589	OTTHUMG00000015139	ENST00000257770.3:c.897C>T	6.37:g.86195098C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_001204813	B3KQI8|O75520|Q5W116	Silent	SNP	ENST00000257770.3	37	CCDS5002.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	C	6.940	0.543124	0.13250	0.065138	2.33E-4	ENSG00000135318	ENST00000416334	.	.	.	5.36	-0.104	0.13605	.	.	.	.	.	T	0.44561	0.1299	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42732	-0.9434	4	.	.	.	-7.7038	11.3536	0.49602	0.0:0.1944:0.0:0.8056	rs35478984	.	.	.	M	64	.	.	T	+	2	0	NT5E	86251817	0.963000	0.33076	0.937000	0.37676	0.836000	0.47400	0.030000	0.13688	-0.211000	0.10124	-1.744000	0.00683	ACG	C|0.977;T|0.023	0.023	strong		0.438	NT5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041388.1		
COL5A1	1289	hgsc.bcm.edu	37	9	137619195	137619195	+	Silent	SNP	C	C	T	rs3124299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:137619195C>T	ENST00000371817.3	+	5	1152	c.738C>T	c.(736-738)acC>acT	p.T246T		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	246	Nonhelical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		ACTGTGACACCGCAGTACCTG	0.537													C|||	1716	0.342652	0.0424	0.5519	5008	,	,		18306	0.4077		0.4652	False		,,,				2504	0.407				p.T246T		Atlas-SNP	.											.	COL5A1	323	.	0			c.C738T						PASS	.	C		427,3979	204.8+/-226.9	33,361,1809	107.0	94.0	98.0		738	-8.4	0.0	9	dbSNP_103	98	3893,4707	545.0+/-384.7	895,2103,1302	yes	coding-synonymous	COL5A1	NM_000093.3		928,2464,3111	TT,TC,CC		45.2674,9.6913,33.2154		246/1839	137619195	4320,8686	2203	4300	6503	SO:0001819	synonymous_variant	1289	exon5			TGACACCGCAGTA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.738C>T	9.37:g.137619195C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	125	42	0.336	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			C|0.665;T|0.335	0.335	strong		0.537	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
GHITM	27069	hgsc.bcm.edu	37	10	85902479	85902479	+	Silent	SNP	A	A	T	rs146877821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85902479A>T	ENST00000372134.3	+	3	391	c.198A>T	c.(196-198)gcA>gcT	p.A66A	RP11-338I21.1_ENST00000606511.1_RNA	NM_014394.2	NP_055209.2	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein	66					apoptotic process (GO:0006915)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(2)	10						AAGAGGCAGCATTGGAACCAT	0.408													A|||	29	0.00579073	0.0212	0.0014	5008	,	,		15827	0.0		0.0	False		,,,				2504	0.0				p.A66A		Atlas-SNP	.											.	GHITM	30	.	0			c.A198T						PASS	.	A		53,3701		0,53,1824	100.0	102.0	101.0		198	-9.6	0.0	10	dbSNP_134	101	0,8224		0,0,4112	no	coding-synonymous	GHITM	NM_014394.2		0,53,5936	TT,TA,AA		0.0,1.4118,0.4425		66/346	85902479	53,11925	1877	4112	5989	SO:0001819	synonymous_variant	27069	exon3			GGCAGCATTGGAA	AB009685	CCDS41542.1	10q23.1	2008-02-01			ENSG00000165678	ENSG00000165678			17281	protein-coding gene	gene with protein product	"""transmembrane BAX inhibitor motif containing 5"""					8619474, 9110174	Standard	NM_014394		Approved	HSPC282, PTD010, DERP2, My021, TMBIM5	uc001kcs.1	Q9H3K2	OTTHUMG00000018637	ENST00000372134.3:c.198A>T	10.37:g.85902479A>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_014394	A8K9Z9|D3DWE0|O95894|Q5VT95|Q9H0P2	Silent	SNP	ENST00000372134.3	37	CCDS41542.1																																																																																			A|0.995;T|0.005	0.005	strong		0.408	GHITM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049125.1	NM_014394	
RHPN1	114822	hgsc.bcm.edu	37	8	144464073	144464073	+	Missense_Mutation	SNP	G	G	A	rs34746679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144464073G>A	ENST00000289013.6	+	14	1833	c.1732G>A	c.(1732-1734)Gcg>Acg	p.A578T		NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	603	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				signal transduction (GO:0007165)		small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(1)|lung(7)	9	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)			GCTGAAGGCTGCGGGAGAGGC	0.682													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		15201	0.0		0.0	False		,,,				2504	0.0				p.A578T		Atlas-SNP	.											RHPN1_ENST00000289013,NS,carcinoma,-1,2	RHPN1	76	2	0			c.G1732A						PASS	.	G	THR/ALA	90,4180		3,84,2048	29.0	46.0	41.0		1732	1.7	0.0	8	dbSNP_126	41	3,8489		0,3,4243	yes	missense	RHPN1	NM_052924.2	58	3,87,6291	AA,AG,GG		0.0353,2.1077,0.7287	benign	578/671	144464073	93,12669	2135	4246	6381	SO:0001583	missense	114822	exon14			AAGGCTGCGGGAG	AB067516	CCDS47927.1	8q24.3	2003-02-06			ENSG00000158106	ENSG00000158106			19973	protein-coding gene	gene with protein product		601031				11572484	Standard	NM_052924		Approved	KIAA1929, RHPN, ODF5	uc003yyb.3	Q8TCX5	OTTHUMG00000165006	ENST00000289013.6:c.1732G>A	8.37:g.144464073G>A	ENSP00000289013:p.Ala578Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	139	79	0.568345	NM_052924	Q8TAV1|Q96PV9	Missense_Mutation	SNP	ENST00000289013.6	37	CCDS47927.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	6.274	0.418750	0.11870	0.021077	3.53E-4	ENSG00000158106	ENST00000289013	T	0.27557	1.66	4.59	1.73	0.24493	.	0.587122	0.17709	N	0.164651	T	0.04092	0.0114	N	0.25789	0.76	0.09310	N	1	B	0.17852	0.024	B	0.17979	0.02	T	0.16719	-1.0393	10	0.25751	T	0.34	-10.2882	6.9391	0.24483	0.4169:0.0:0.5831:0.0	rs34746679	578	Q8TCX5-2	.	T	578	ENSP00000289013:A578T	ENSP00000289013:A578T	A	+	1	0	RHPN1	144535216	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	0.119000	0.15626	0.349000	0.23975	0.462000	0.41574	GCG	G|0.989;A|0.011	0.011	strong		0.682	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1		
PDE6A	5145	hgsc.bcm.edu	37	5	149323906	149323906	+	Silent	SNP	T	T	G	rs2277925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149323906T>G	ENST00000255266.5	-	1	450	c.331A>C	c.(331-333)Agg>Cgg	p.R111R		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	111	GAF 1.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)	p.R111R(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	TTGAAAAGCCTGGTGGCCAGC	0.562													G|||	1415	0.282548	0.3994	0.2363	5008	,	,		18477	0.246		0.167	False		,,,				2504	0.3139				p.R111R		Atlas-SNP	.											PDE6A,NS,carcinoma,0,1	PDE6A	98	1	1	Substitution - coding silent(1)	stomach(1)	c.A331C						PASS	.	G		1463,2943	680.2+/-403.8	237,989,977	82.0	82.0	82.0		331	2.2	0.9	5	dbSNP_100	82	1234,7366	761.9+/-407.6	102,1030,3168	no	coding-synonymous	PDE6A	NM_000440.2		339,2019,4145	GG,GT,TT		14.3488,33.2047,20.7366		111/861	149323906	2697,10309	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			AAAGCCTGGTGGC		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.331A>C	5.37:g.149323906T>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			T|0.786;G|0.214	0.214	strong		0.562	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
BPI	671	hgsc.bcm.edu	37	20	36954790	36954790	+	Missense_Mutation	SNP	G	G	A	rs5743524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36954790G>A	ENST00000262865.4	+	10	1218	c.1129G>A	c.(1129-1131)Gtc>Atc	p.V377I	CTD-2308N23.2_ENST00000437016.1_RNA|BPI_ENST00000489102.1_3'UTR	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	377			V -> I (in dbSNP:rs5743524).		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)				GGCCTTTGCCGTCCTCCCCAA	0.597													g|||	209	0.0417332	0.1475	0.0187	5008	,	,		19366	0.0		0.001	False		,,,				2504	0.0				p.V377I		Atlas-SNP	.											.	BPI	67	.	0			c.G1129A						PASS	.	A	ILE/VAL	508,3898	235.5+/-248.0	28,452,1723	90.0	70.0	77.0		1129	-3.8	0.0	20	dbSNP_114	77	8,8592	6.4+/-24.3	0,8,4292	yes	missense	BPI	NM_001725.2	29	28,460,6015	AA,AG,GG		0.093,11.5297,3.9674	benign	377/488	36954790	516,12490	2203	4300	6503	SO:0001583	missense	671	exon10			TTTGCCGTCCTCC	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.1129G>A	20.37:g.36954790G>A	ENSP00000262865:p.Val377Ile	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_001725	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Missense_Mutation	SNP	ENST00000262865.4	37	CCDS13303.1	85	0.03891941391941392	80	0.16260162601626016	5	0.013812154696132596	0	0.0	0	0.0	g	3.739	-0.053900	0.07362	0.115297	9.3E-4	ENSG00000101425	ENST00000262865	T	0.09163	3.01	4.39	-3.78	0.04333	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.053620	0.07393	N	0.889378	T	0.00039	0.0001	N	0.11927	0.2	0.53688	P	2.8000000000028002E-5	B	0.20988	0.05	B	0.11329	0.006	T	0.48175	-0.9058	9	0.06757	T	0.87	-18.082	13.0633	0.59020	0.743:0.0:0.257:0.0	rs5743524;rs5743524	377	P17213	BPI_HUMAN	I	377	ENSP00000262865:V377I	ENSP00000262865:V377I	V	+	1	0	BPI	36388204	0.008000	0.16893	0.003000	0.11579	0.011000	0.07611	-0.063000	0.11655	-0.933000	0.03737	-2.146000	0.00336	GTC	G|0.949;A|0.051	0.051	strong		0.597	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725	
KCNMB1	3779	hgsc.bcm.edu	37	5	169805956	169805956	+	Missense_Mutation	SNP	C	C	G	rs2301149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:169805956C>G	ENST00000274629.4	-	4	770	c.328G>C	c.(328-330)Gtg>Ctg	p.V110L	KCNIP1_ENST00000377360.4_Intron|KCNIP1_ENST00000518527.1_Intron	NM_004137.3	NP_004128.1	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 1	110			V -> L (in dbSNP:rs2301149).		blood coagulation (GO:0007596)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to calcium ion (GO:0051592)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			endometrium(1)|large_intestine(1)|lung(7)|ovary(2)	11	Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.175)	Miconazole(DB01110)|Procaine(DB00721)	TAATTGTCCACGCTGCCTGGG	0.547													G|||	617	0.123203	0.1316	0.111	5008	,	,		16028	0.1339		0.1004	False		,,,				2504	0.1329				p.E110Q		Atlas-SNP	.											KCNMB1,NS,carcinoma,0,1	KCNMB1	38	1	0			c.G328C						PASS	.	G	,LEU/VAL	466,3940	782.7+/-414.6	24,418,1761	62.0	64.0	63.0		,328	3.0	1.0	5	dbSNP_100	63	725,7875	785.9+/-407.6	36,653,3611	yes	intron,missense	KCNMB1,KCNIP1	NM_001034838.1,NM_004137.2	,32	60,1071,5372	GG,GC,CC		8.4302,10.5765,9.1573	,benign	,110/192	169805956	1191,11815	2203	4300	6503	SO:0001583	missense	3779	exon4			TGTCCACGCTGCC	AF035046	CCDS4373.1	5q34	2012-02-23			ENSG00000145936	ENSG00000145936		"""Potassium channels"""	6285	protein-coding gene	gene with protein product	"""BK channel beta subunit"""	603951				8799178, 9888999	Standard	NM_004137		Approved	hslo-beta	uc003maq.2	Q16558	OTTHUMG00000130439	ENST00000274629.4:c.328G>C	5.37:g.169805956C>G	ENSP00000274629:p.Val110Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_004137	O00707|O00708|P78475|Q53YR0|Q8TAX3|Q93005	Missense_Mutation	SNP	ENST00000274629.4	37	CCDS4373.1	235	0.10760073260073261	53	0.10772357723577236	47	0.1298342541436464	70	0.12237762237762238	65	0.08575197889182058	G	9.771	1.172679	0.21704	0.105765	0.084302	ENSG00000145936	ENST00000274629	T	0.08984	3.03	5.17	3.03	0.35002	.	0.407302	0.25175	N	0.032575	T	0.00039	0.0001	N	0.00347	-1.61	0.09310	P	0.99999999356255	B	0.02656	0.0	B	0.01281	0.0	T	0.38286	-0.9668	8	.	.	.	.	6.0615	0.19841	0.184:0.2949:0.5211:0.0	rs2301149;rs57496667;rs2301149	110	Q16558	KCMB1_HUMAN	L	110	ENSP00000274629:V110L	.	V	-	1	0	KCNMB1	169738534	1.000000	0.71417	0.996000	0.52242	0.461000	0.32589	1.632000	0.37102	0.580000	0.29522	-0.335000	0.08231	GTG	C|0.898;G|0.102	0.102	strong		0.547	KCNMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252830.3		
PTCH2	8643	hgsc.bcm.edu	37	1	45293518	45293518	+	Silent	SNP	A	A	G	rs7525308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:45293518A>G	ENST00000372192.3	-	14	2185	c.2055T>C	c.(2053-2055)gcT>gcC	p.A685A	PTCH2_ENST00000447098.2_Silent_p.A685A	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	685					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)					GTCTTACCTTAGCATGTGACT	0.617									Basal Cell Nevus syndrome				G|||	2231	0.445487	0.6021	0.4409	5008	,	,		21976	0.4911		0.3191	False		,,,				2504	0.32				p.A685A		Atlas-SNP	.											.	PTCH2	96	.	0			c.T2055C						PASS	.	G	,	2576,1830	533.1+/-373.6	765,1046,392	57.0	55.0	56.0		2055,2055	2.6	0.8	1	dbSNP_116	56	2944,5656	667.7+/-402.5	524,1896,1880	no	coding-synonymous,coding-synonymous	PTCH2	NM_001166292.1,NM_003738.4	,	1289,2942,2272	GG,GA,AA		34.2326,41.5343,42.4419	,	685/1147,685/1204	45293518	5520,7486	2203	4300	6503	SO:0001819	synonymous_variant	8643	exon14	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	TACCTTAGCATGT	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.2055T>C	1.37:g.45293518A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Silent	SNP	ENST00000372192.3	37	CCDS516.1																																																																																			A|0.574;G|0.426	0.426	strong		0.617	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
TG	7038	hgsc.bcm.edu	37	8	133953740	133953740	+	Missense_Mutation	SNP	A	A	C	rs61744749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133953740A>C	ENST00000220616.4	+	26	5226	c.5186A>C	c.(5185-5187)gAc>gCc	p.D1729A	TG_ENST00000377869.1_Missense_Mutation_p.D1672A|TG_ENST00000542445.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1729					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)		CTTGCATGCGACCGTGATCTG	0.527													A|||	140	0.0279553	0.1014	0.0086	5008	,	,		23318	0.0		0.0	False		,,,				2504	0.0				p.D1729A		Atlas-SNP	.											TG,NS,carcinoma,+1,1	TG	416	1	0			c.A5186C						PASS	.	A	ALA/ASP	382,4024	193.0+/-218.2	19,344,1840	176.0	141.0	153.0		5186	5.6	1.0	8	dbSNP_129	153	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TG	NM_003235.4	126	19,347,6137	CC,CA,AA		0.0349,8.67,2.9602	possibly-damaging	1729/2769	133953740	385,12621	2203	4300	6503	SO:0001583	missense	7038	exon26			CATGCGACCGTGA	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.5186A>C	8.37:g.133953740A>C	ENSP00000220616:p.Asp1729Ala	Somatic	292	1	0.00342466		WXS	Illumina HiSeq	Phase_I	311	147	0.472669	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	A	11.79	1.743661	0.30865	0.0867	3.49E-4	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;T	0.70282	-0.47;-0.47	5.61	5.61	0.85477	.	0.387653	0.24873	N	0.034902	T	0.02230	0.0069	M	0.72118	2.19	0.36596	D	0.874396	B	0.31581	0.329	B	0.27170	0.077	T	0.47898	-0.9081	10	0.66056	D	0.02	.	12.1945	0.54290	1.0:0.0:0.0:0.0	rs61744749	1729	P01266	THYG_HUMAN	A	1672;535;1729	ENSP00000367100:D1672A;ENSP00000220616:D1729A	ENSP00000220616:D1729A	D	+	2	0	TG	134022922	0.998000	0.40836	0.981000	0.43875	0.150000	0.21749	3.679000	0.54634	2.142000	0.66516	0.379000	0.24179	GAC	A|0.964;C|0.036	0.036	strong		0.527	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
ZNF790	388536	hgsc.bcm.edu	37	19	37309790	37309790	+	Missense_Mutation	SNP	T	T	A	rs4369791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37309790T>A	ENST00000356725.4	-	5	1576	c.1456A>T	c.(1456-1458)Acc>Tcc	p.T486S	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	486			T -> S (in dbSNP:rs4369791).		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)			CGAAAAAAGGTCTTTCCACAT	0.388													T|||	20	0.00399361	0.0151	0.0	5008	,	,		20361	0.0		0.0	False		,,,				2504	0.0				p.T486S		Atlas-SNP	.											.	ZNF790	89	.	0			c.A1456T						PASS	.	T	SER/THR,SER/THR,SER/THR,SER/THR	72,4334	65.3+/-102.7	1,70,2132	83.0	80.0	81.0		1456,1456,1456,1456	-1.0	0.0	19	dbSNP_111	81	0,8600		0,0,4300	yes	missense,missense,missense,missense	ZNF790	NM_001242800.1,NM_001242801.1,NM_001242802.1,NM_206894.3	58,58,58,58	1,70,6432	AA,AT,TT		0.0,1.6341,0.5536	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	486/637,486/637,486/637,486/637	37309790	72,12934	2203	4300	6503	SO:0001583	missense	388536	exon5			AAAAGGTCTTTCC	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.1456A>T	19.37:g.37309790T>A	ENSP00000349161:p.Thr486Ser	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_206894		Missense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	8.684	0.905767	0.17760	0.016341	0.0	ENSG00000197863	ENST00000356725	T	0.19105	2.17	3.14	-0.997	0.10215	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03477	0.0100	N	0.03903	-0.33	0.09310	N	1	B	0.22604	0.072	B	0.23018	0.043	T	0.32079	-0.9920	9	0.41790	T	0.15	.	4.173	0.10339	0.2887:0.4551:0.0:0.2562	rs4369791;rs52825956;rs4369791	486	Q6PG37	ZN790_HUMAN	S	486	ENSP00000349161:T486S	ENSP00000349161:T486S	T	-	1	0	ZNF790	42001630	0.000000	0.05858	0.034000	0.17996	0.389000	0.30415	0.069000	0.14552	-0.105000	0.12132	0.402000	0.26972	ACC	T|0.995;A|0.005	0.005	strong		0.388	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894	
SPRYD3	84926	hgsc.bcm.edu	37	12	53467230	53467230	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53467230G>T	ENST00000301463.4	-	6	619	c.533C>A	c.(532-534)tCc>tAc	p.S178Y	SPRYD3_ENST00000547837.1_Missense_Mutation_p.S215Y	NM_032840.2	NP_116229.1	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3	178	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.									central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						TCCATCTGGGGACATGGGCAT	0.607																																					p.S178Y		Atlas-SNP	.											.	SPRYD3	29	.	0			c.C533A						PASS	.						57.0	43.0	47.0					12																	53467230		2203	4292	6495	SO:0001583	missense	84926	exon6			TCTGGGGACATGG	AK074694	CCDS8845.1	12q13.13	2006-11-29		2006-02-02		ENSG00000167778			25920	protein-coding gene	gene with protein product						14702039	Standard	NM_032840		Approved	FLJ14800	uc001sbt.2	Q8NCJ5	OTTHUMG00000170101	ENST00000301463.4:c.533C>A	12.37:g.53467230G>T	ENSP00000301463:p.Ser178Tyr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_032840	B9EG99|Q96SK5	Missense_Mutation	SNP	ENST00000301463.4	37	CCDS8845.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.830680	0.71258	.	.	ENSG00000167778	ENST00000301463;ENST00000547837	T;T	0.60040	0.22;0.22	5.17	5.17	0.71159	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.060021	0.64402	D	0.000002	T	0.60143	0.2246	L	0.42245	1.32	0.53005	D	0.999964	D	0.56968	0.978	P	0.50708	0.648	T	0.59484	-0.7446	10	0.45353	T	0.12	-19.5437	16.5838	0.84722	0.0:0.0:1.0:0.0	.	178	Q8NCJ5	SPRY3_HUMAN	Y	178;215	ENSP00000301463:S178Y;ENSP00000449452:S215Y	ENSP00000301463:S178Y	S	-	2	0	SPRYD3	51753497	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.182000	0.94881	2.861000	0.98227	0.655000	0.94253	TCC	.	.	none		0.607	SPRYD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407264.1	NM_032840	
BPHL	670	hgsc.bcm.edu	37	6	3152760	3152760	+	Missense_Mutation	SNP	T	T	C	rs2231370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:3152760T>C	ENST00000380379.5	+	7	876	c.827T>C	c.(826-828)tTg>tCg	p.L276S	BPHL_ENST00000434640.1_Missense_Mutation_p.L259S|BPHL_ENST00000380375.3_Missense_Mutation_p.L259S|RP1-40E16.11_ENST00000447644.1_RNA|BPHL_ENST00000464040.1_3'UTR|BPHL_ENST00000380368.2_3'UTR|TUBB2A_ENST00000489942.1_5'Flank	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	276					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				AACCTGCATTTGCGTTTTGCA	0.438													T|||	250	0.0499201	0.1747	0.0173	5008	,	,		21159	0.001		0.005	False		,,,				2504	0.001				p.L276S		Atlas-SNP	.											.	BPHL	32	.	0			c.T827C						PASS	.	T	SER/LEU	588,3818	261.0+/-264.0	42,504,1657	168.0	153.0	158.0		827	4.7	0.1	6	dbSNP_98	158	31,8569	21.0+/-64.5	0,31,4269	yes	missense	BPHL	NM_004332.2	145	42,535,5926	CC,CT,TT		0.3605,13.3454,4.7593	probably-damaging	276/292	3152760	619,12387	2203	4300	6503	SO:0001583	missense	670	exon7			TGCATTTGCGTTT	X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"""breast epithelial mucin-associated antigen"""	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.827T>C	6.37:g.3152760T>C	ENSP00000369739:p.Leu276Ser	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	168	84	0.5	NM_004332	Q00306|Q13855|Q3KP51	Missense_Mutation	SNP	ENST00000380379.5	37	CCDS4483.2	104	0.047619047619047616	92	0.18699186991869918	5	0.013812154696132596	1	0.0017482517482517483	6	0.0079155672823219	T	19.10	3.761514	0.69763	0.133454	0.003605	ENSG00000137274	ENST00000434640;ENST00000380375;ENST00000380379	T;T;T	0.72051	-0.62;-0.62;-0.62	5.9	4.74	0.60224	.	0.069235	0.64402	D	0.000014	T	0.77061	0.4075	M	0.73430	2.235	0.22354	P	0.999176454	D;D	0.76494	0.999;0.999	D;D	0.79784	0.993;0.988	T	0.80801	-0.1220	9	0.56958	D	0.05	-17.8489	11.8569	0.52441	0.0:0.0677:0.0:0.9323	rs2231370;rs52831698;rs2231370	276;259	Q86WA6;Q86WA6-2	BPHL_HUMAN;.	S	259;259;276	ENSP00000390472:L259S;ENSP00000369734:L259S;ENSP00000369739:L276S	ENSP00000369734:L259S	L	+	2	0	BPHL	3097759	0.996000	0.38824	0.080000	0.20451	0.991000	0.79684	5.961000	0.70356	1.064000	0.40671	0.528000	0.53228	TTG	T|0.949;C|0.051	0.051	strong		0.438	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5		
PDE6A	5145	hgsc.bcm.edu	37	5	149323772	149323772	+	Silent	SNP	G	G	A	rs2277926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149323772G>A	ENST00000255266.5	-	1	584	c.465C>T	c.(463-465)aaC>aaT	p.N155N		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	155	GAF 1.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)	p.N155N(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CCTCCTCTGTGTTGGGGACGT	0.557													G|||	1247	0.249002	0.2761	0.2305	5008	,	,		17039	0.246		0.166	False		,,,				2504	0.3139				p.N155N		Atlas-SNP	.											PDE6A,NS,carcinoma,0,1	PDE6A	98	1	1	Substitution - coding silent(1)	stomach(1)	c.C465T						PASS	.	G		1052,3354	386.1+/-326.0	110,832,1261	151.0	129.0	136.0		465	4.5	1.0	5	dbSNP_100	136	1230,7370	247.2+/-275.4	103,1024,3173	no	coding-synonymous	PDE6A	NM_000440.2		213,1856,4434	AA,AG,GG		14.3023,23.8765,17.5457		155/861	149323772	2282,10724	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			CTCTGTGTTGGGG		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.465C>T	5.37:g.149323772G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	57	18	0.315789	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|0.807;A|0.193	0.193	strong		0.557	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
HOXD3	3232	hgsc.bcm.edu	37	2	177034130	177034130	+	Silent	SNP	G	G	A	rs77818566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:177034130G>A	ENST00000468418.3	+	3	2378	c.288G>A	c.(286-288)ggG>ggA	p.G96G	HOXD3_ENST00000249440.3_Silent_p.G96G|HOXD3_ENST00000410016.1_Silent_p.G96G			P31249	HXD3_HUMAN	homeobox D3	96					anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|embryonic skeletal system morphogenesis (GO:0048704)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		CGGGCACTGGGAACAGCCAGG	0.647													G|||	289	0.0577077	0.2133	0.0101	5008	,	,		14552	0.0		0.0	False		,,,				2504	0.0				p.G96G		Atlas-SNP	.											.	HOXD3	65	.	0			c.G288A						PASS	.	G		749,3657	262.5+/-264.9	73,603,1527	24.0	26.0	25.0		288	3.6	1.0	2	dbSNP_131	25	18,8582	9.8+/-36.6	0,18,4282	no	coding-synonymous	HOXD3	NM_006898.4		73,621,5809	AA,AG,GG		0.2093,16.9995,5.8973		96/433	177034130	767,12239	2203	4300	6503	SO:0001819	synonymous_variant	3232	exon2			CACTGGGAACAGC		CCDS2270.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128652	ENSG00000128652		"""Homeoboxes / ANTP class : HOXL subclass"""	5137	protein-coding gene	gene with protein product		142980	"""homeo box D3"""	HOX4A, HOX4, HOX1D		1973146, 1358459	Standard	NM_006898		Approved		uc002ukt.1	P31249	OTTHUMG00000132517	ENST00000468418.3:c.288G>A	2.37:g.177034130G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_006898	Q99955|Q9BSC5	Silent	SNP	ENST00000468418.3	37	CCDS2270.1																																																																																			G|0.949;A|0.051	0.051	strong		0.647	HOXD3-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334246.4		
RNF39	80352	hgsc.bcm.edu	37	6	30039240	30039240	+	Missense_Mutation	SNP	G	G	T	rs2301753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30039240G>T	ENST00000244360.6	-	4	1008	c.911C>A	c.(910-912)gCg>gAg	p.A304E	RNF39_ENST00000376751.3_Missense_Mutation_p.A304E	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	304	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		A -> E (in dbSNP:rs2301753). {ECO:0000269|PubMed:14574404}.			cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										CTCGTCGTCCGCATCCTCCCC	0.706													t|||	958	0.191294	0.2988	0.1744	5008	,	,		12945	0.1905		0.0954	False		,,,				2504	0.1575				p.A304E	NSCLC(8;188 360 1520 20207 31481)	Atlas-SNP	.											.	RNF39	27	.	0			c.C911A						PASS	.		GLU/ALA,GLU/ALA	753,2251		92,569,841	12.0	9.0	10.0		911,911	4.5	0.0	6	dbSNP_100	10	637,4757		52,533,2112	yes	missense,missense	RNF39	NM_025236.3,NM_170769.2	107,107	144,1102,2953	TT,TG,GG		11.8094,25.0666,16.5516	benign,benign	304/421,304/355	30039240	1390,7008	1502	2697	4199	SO:0001583	missense	80352	exon4			TCGTCCGCATCCT	AF238315	CCDS4673.1, CCDS4674.1	6p21.3	2013-01-09			ENSG00000204618	ENSG00000204618		"""RING-type (C3HC4) zinc fingers"""	18064	protein-coding gene	gene with protein product		607524				11130983, 11716498	Standard	NM_170769		Approved	HZFw1, LIRF	uc003npe.3	Q9H2S5	OTTHUMG00000031288	ENST00000244360.6:c.911C>A	6.37:g.30039240G>T	ENSP00000244360:p.Ala304Glu	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Missense_Mutation	SNP	ENST00000244360.6	37	CCDS4673.1	404	0.184981684981685	146	0.2967479674796748	72	0.19889502762430938	115	0.20104895104895104	71	0.09366754617414248	t	1.410	-0.575640	0.03882	0.250666	0.118094	ENSG00000204618	ENST00000376751;ENST00000244360	T;T	0.69306	0.03;-0.39	4.54	4.54	0.55810	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.151026	0.29653	N	0.011551	T	0.10637	0.0260	N	0.00707	-1.245	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15925	-1.0420	9	0.02654	T	1	-14.7253	9.8189	0.40869	0.0:0.0:0.1737:0.8263	rs2301753;rs60004051;rs2301753	304;304	Q9H2S5;Q9H2S5-2	RNF39_HUMAN;.	E	304	ENSP00000365942:A304E;ENSP00000244360:A304E	ENSP00000244360:A304E	A	-	2	0	RNF39	30147219	0.020000	0.18652	0.045000	0.18777	0.578000	0.36192	0.703000	0.25646	0.706000	0.31912	-1.106000	0.02097	GCG	G|0.804;T|0.196	0.196	strong		0.706	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769	
COL15A1	1306	hgsc.bcm.edu	37	9	101816873	101816873	+	Missense_Mutation	SNP	A	A	G	rs35642150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101816873A>G	ENST00000375001.3	+	32	3389	c.2966A>G	c.(2965-2967)aAa>aGa	p.K989R		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	989	Triple-helical region 6 (COL6).		K -> R (in dbSNP:rs35642150).		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)				AAAGGAGAGAAAGGATCCTGG	0.433													A|||	71	0.0141773	0.0514	0.0043	5008	,	,		19547	0.0		0.0	False		,,,				2504	0.0				p.K989R		Atlas-SNP	.											.	COL15A1	211	.	0			c.A2966G						PASS	.	A	ARG/LYS	123,4283	91.1+/-129.8	1,121,2081	79.0	84.0	82.0		2966	5.7	1.0	9	dbSNP_126	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense	COL15A1	NM_001855.3	26	1,122,6380	GG,GA,AA		0.0116,2.7916,0.9534	probably-damaging	989/1389	101816873	124,12882	2203	4300	6503	SO:0001583	missense	1306	exon32			GAGAGAAAGGATC	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.2966A>G	9.37:g.101816873A>G	ENSP00000364140:p.Lys989Arg	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	134	94	0.701493	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	A	16.86	3.239791	0.58995	0.027916	1.16E-4	ENSG00000204291	ENST00000375001	T	0.30448	1.53	5.67	5.67	0.87782	C-type lectin fold (1);	0.172969	0.41396	D	0.000883	T	0.13030	0.0316	L	0.33753	1.03	0.41059	D	0.985365	D	0.63880	0.993	D	0.72625	0.978	T	0.02560	-1.1141	10	0.20046	T	0.44	-17.3435	12.5857	0.56416	1.0:0.0:0.0:0.0	rs35642150	989	P39059	COFA1_HUMAN	R	989	ENSP00000364140:K989R	ENSP00000364140:K989R	K	+	2	0	COL15A1	100856694	0.999000	0.42202	1.000000	0.80357	0.990000	0.78478	1.712000	0.37940	2.288000	0.76882	0.533000	0.62120	AAA	A|0.988;G|0.012	0.012	strong		0.433	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
TMEM30B	161291	hgsc.bcm.edu	37	14	61747644	61747644	+	Silent	SNP	A	A	G	rs3196765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:61747644A>G	ENST00000555868.1	-	1	914	c.222T>C	c.(220-222)ggT>ggC	p.G74G	TMEM30B_ENST00000557163.1_5'UTR|TMEM30B_ENST00000355702.2_Silent_p.G74G	NM_001017970.2	NP_001017970.1	Q3MIR4	CC50B_HUMAN	transmembrane protein 30B	74					lipid transport (GO:0006869)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.107)|BRCA - Breast invasive adenocarcinoma(234;0.181)		CCGAGCAGTTACCGGTGCCCG	0.706													G|||	3905	0.779752	0.6528	0.7392	5008	,	,		11768	0.8591		0.8638	False		,,,				2504	0.8119				p.G74G		Atlas-SNP	.											.	TMEM30B	13	.	0			c.T222C						PASS	.	G		2664,1138		957,750,194	6.0	5.0	6.0		222	4.3	1.0	14	dbSNP_105	6	6522,954		2863,796,79	no	coding-synonymous	TMEM30B	NM_001017970.2		3820,1546,273	GG,GA,AA		12.7608,29.9316,18.5494		74/352	61747644	9186,2092	1901	3738	5639	SO:0001819	synonymous_variant	161291	exon1			GCAGTTACCGGTG	AK091169	CCDS32093.1	14q23.1	2006-09-20				ENSG00000182107			27254	protein-coding gene	gene with protein product		611029				15375526	Standard	NM_001017970		Approved	CDC50B	uc001xfl.3	Q3MIR4		ENST00000555868.1:c.222T>C	14.37:g.61747644A>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_001017970	B3KR84|Q14D00	Silent	SNP	ENST00000555868.1	37	CCDS32093.1																																																																																			A|0.214;G|0.786	0.786	strong		0.706	TMEM30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413358.1	XM_090844	
AHNAK2	113146	hgsc.bcm.edu	37	14	105410775	105410775	+	Silent	SNP	A	A	G	rs2819424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105410775A>G	ENST00000333244.5	-	7	11132	c.11013T>C	c.(11011-11013)gaT>gaC	p.D3671D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3671						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)			GGAGACTCACATCGGCTTCCA	0.582													.|||	2934	0.585863	0.7526	0.5202	5008	,	,		17655	0.4137		0.5358	False		,,,				2504	0.636				p.D3671D		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T11013C						PASS	.	G		2883,987		1074,735,126	142.0	150.0	147.0		11013	-7.9	0.0	14	dbSNP_100	147	4492,3782		1231,2030,876	no	coding-synonymous	AHNAK2	NM_138420.2		2305,2765,1002	GG,GA,AA		45.7095,25.5039,39.2704		3671/5796	105410775	7375,4769	1935	4137	6072	SO:0001819	synonymous_variant	113146	exon7			ACTCACATCGGCT	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.11013T>C	14.37:g.105410775A>G		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	258	257	0.996124	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.444;G|0.556	0.556	strong		0.582	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ZNF226	7769	hgsc.bcm.edu	37	19	44680489	44680489	+	Silent	SNP	G	G	A	rs2178342	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44680489G>A	ENST00000590089.1	+	7	1441	c.1074G>A	c.(1072-1074)acG>acA	p.T358T	ZNF226_ENST00000454662.2_Silent_p.T358T|ZNF226_ENST00000588883.1_3'UTR|ZNF226_ENST00000337433.5_Silent_p.T358T			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	358					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)						Prostate(69;0.0352)|all_neural(266;0.202)				AGGTCCACACGGCAGAGAAAC	0.468													G|||	879	0.175519	0.4614	0.2046	5008	,	,		21068	0.0952		0.0179	False		,,,				2504	0.0133				p.T358T	Pancreas(115;581 1665 13228 19278 50070)	Atlas-SNP	.											.	.	.	.	0			c.G1074A						PASS	.	G	,	1783,2613	486.7+/-360.7	362,1059,777	89.0	96.0	94.0		1074,1074	-8.6	0.0	19	dbSNP_96	94	62,8534	34.3+/-88.2	2,58,4238	no	coding-synonymous,coding-synonymous	ZNF226	NM_001032372.1,NM_001032373.1	,	364,1117,5015	AA,AG,GG		0.7213,40.5596,14.201	,	358/804,358/804	44680489	1845,11147	2198	4298	6496	SO:0001819	synonymous_variant	7769	exon6			CCACACGGCAGAG	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"""Zinc fingers, C2H2-type"", ""-"""	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.1074G>A	19.37:g.44680489G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_001032372	Q8WWE6|Q96TE6|Q9NS44	Silent	SNP	ENST00000590089.1	37	CCDS46102.1																																																																																			G|0.866;A|0.134	0.134	strong		0.468	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1		
FTO	79068	hgsc.bcm.edu	37	16	53922838	53922838	+	Missense_Mutation	SNP	C	C	T	rs16952624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53922838C>T	ENST00000471389.1	+	7	1436	c.1214C>T	c.(1213-1215)gCa>gTa	p.A405V	FTO_ENST00000431610.2_Missense_Mutation_p.A6V|FTO_ENST00000460382.1_Missense_Mutation_p.A6V|FTO_ENST00000394647.3_Missense_Mutation_p.A109V	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	405			A -> V (in dbSNP:rs16952624).		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						CAACTGGAAGCACTGTGGAAG	0.502													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		18970	0.0		0.0	False		,,,				2504	0.0				p.A405V		Atlas-SNP	.											FTO,NS,carcinoma,-1,1	FTO	51	1	0			c.C1214T						PASS	.	C	VAL/ALA	124,4272	93.0+/-131.7	4,116,2078	287.0	257.0	267.0		1214	-3.4	0.0	16	dbSNP_123	267	0,8600		0,0,4300	yes	missense	FTO	NM_001080432.2	64	4,116,6378	TT,TC,CC		0.0,2.8207,0.9541	benign	405/506	53922838	124,12872	2198	4300	6498	SO:0001583	missense	79068	exon7			TGGAAGCACTGTG	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.1214C>T	16.37:g.53922838C>T	ENSP00000418823:p.Ala405Val	Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	326	156	0.478528	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	37	CCDS32448.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	C	8.234	0.805364	0.16467	0.028207	0.0	ENSG00000140718	ENST00000471389;ENST00000394647;ENST00000431610;ENST00000460382;ENST00000476894	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.84	-3.41	0.04839	Alpha-ketoglutarate-dependent dioxygenase FTO, C-terminal (1);	0.513654	0.22753	N	0.056043	T	0.04724	0.0128	N	0.14661	0.345	0.09310	N	0.999998	B	0.18013	0.025	B	0.18871	0.023	T	0.06552	-1.0820	10	0.46703	T	0.11	-3.9788	7.7201	0.28727	0.3262:0.2045:0.4693:0.0	rs16952624;rs52815989;rs16952624	405	Q9C0B1	FTO_HUMAN	V	405;109;6;6;6	ENSP00000418823:A405V;ENSP00000378142:A109V;ENSP00000415636:A6V;ENSP00000417422:A6V	ENSP00000378142:A109V	A	+	2	0	FTO	52480339	0.643000	0.27269	0.004000	0.12327	0.166000	0.22503	0.621000	0.24418	-0.639000	0.05502	-0.275000	0.10095	GCA	C|0.988;T|0.012	0.012	strong		0.502	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432	
FBN2	2201	hgsc.bcm.edu	37	5	127873186	127873186	+	Silent	SNP	C	C	T	rs55715053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:127873186C>T	ENST00000508053.1	-	7	1085	c.111G>A	c.(109-111)ccG>ccA	p.P37P	FBN2_ENST00000508989.1_Silent_p.P37P|FBN2_ENST00000262464.4_Silent_p.P37P			P35556	FBN2_HUMAN	fibrillin 2	37					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)		GGGGCCGGGGCGGCTTGGGCG	0.706													C|||	690	0.13778	0.3555	0.062	5008	,	,		10249	0.005		0.0845	False		,,,				2504	0.089				p.P37P		Atlas-SNP	.											.	FBN2	858	.	0			c.G111A						PASS	.	C		1123,3175		145,833,1171	9.0	11.0	10.0		111	-0.7	0.6	5	dbSNP_129	10	716,7674		42,632,3521	no	coding-synonymous	FBN2	NM_001999.3		187,1465,4692	TT,TC,CC		8.534,26.1284,14.494		37/2913	127873186	1839,10849	2149	4195	6344	SO:0001819	synonymous_variant	2201	exon1			CCGGGGCGGCTTG	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.111G>A	5.37:g.127873186C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	27	26	0.962963	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			C|0.881;T|0.119	0.119	strong		0.706	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
PIEZO1	9780	hgsc.bcm.edu	37	16	88801457	88801457	+	Silent	SNP	G	G	A	rs115016757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88801457G>A	ENST00000301015.9	-	14	1920	c.1674C>T	c.(1672-1674)ccC>ccT	p.P558P	RP5-1142A6.2_ENST00000567968.1_RNA|RP5-1142A6.2_ENST00000440406.2_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	558					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						GCGTCCGCGTGGGCTCTGTGG	0.657													G|||	223	0.0445288	0.1611	0.0144	5008	,	,		14944	0.0		0.0	False		,,,				2504	0.0				p.P558P		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C1674T						PASS	.	G		155,1229		9,137,546	68.0	65.0	66.0		1674	3.0	1.0	16	dbSNP_132	66	2,3180		0,2,1589	no	coding-synonymous	PIEZO1	NM_001142864.2		9,139,2135	AA,AG,GG		0.0629,11.1994,3.4385		558/2522	88801457	157,4409	692	1591	2283	SO:0001819	synonymous_variant	9780	exon14			CCGCGTGGGCTCT	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.1674C>T	16.37:g.88801457G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	36	0.409091	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	58	0.026556776556776556	55	0.11178861788617886	3	0.008287292817679558	0	0.0	0	0.0	G	3.774	-0.047036	0.07407	0.111994	6.29E-4	ENSG00000103335	ENST00000451779	.	.	.	4.03	3.05	0.35203	.	.	.	.	.	T	0.00906	0.0030	.	.	.	0.09310	P	0.9999999968917	.	.	.	.	.	.	T	0.12293	-1.0553	3	.	.	.	-33.9642	6.4507	0.21902	0.0988:0.0:0.7192:0.1819	.	.	.	.	Y	504	.	.	H	-	1	0	FAM38A	87328958	0.271000	0.24162	0.986000	0.45419	0.301000	0.27625	0.787000	0.26858	0.786000	0.33708	0.313000	0.20887	CAC	G|0.966;A|0.034	0.034	strong		0.657	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
NCAPD3	23310	hgsc.bcm.edu	37	11	134048592	134048592	+	Missense_Mutation	SNP	G	G	T	rs34739733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134048592G>T	ENST00000534548.2	-	22	2783	c.2719C>A	c.(2719-2721)Ccc>Acc	p.P907T	RP11-700F16.3_ENST00000531710.1_RNA	NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	907			P -> T (in dbSNP:rs34739733).		mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		ACCTGGGGGGGTGGCTGAGAC	0.522													G|||	20	0.00399361	0.0136	0.0029	5008	,	,		18713	0.0		0.0	False		,,,				2504	0.0				p.P907T		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C2719A						PASS	.	G	THR/PRO	55,4347	54.2+/-90.2	0,55,2146	92.0	94.0	93.0		2719	4.1	0.0	11	dbSNP_126	93	0,8594		0,0,4297	yes	missense	NCAPD3	NM_015261.2	38	0,55,6443	TT,TG,GG		0.0,1.2494,0.4232	benign	907/1499	134048592	55,12941	2201	4297	6498	SO:0001583	missense	23310	exon22			GGGGGGGTGGCTG	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.2719C>A	11.37:g.134048592G>T	ENSP00000433681:p.Pro907Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	138	66	0.478261	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	8.015	0.758394	0.15846	0.012494	0.0	ENSG00000151503	ENST00000534548	T	0.21734	1.99	6.03	4.13	0.48395	Armadillo-like helical (1);Armadillo-type fold (1);	0.330969	0.32918	N	0.005489	T	0.09512	0.0234	L	0.31664	0.95	0.40749	D	0.982908	B	0.33413	0.411	B	0.29353	0.101	T	0.09530	-1.0670	10	0.14656	T	0.56	-4.2164	11.7991	0.52116	0.0:0.1196:0.6321:0.2483	rs34739733	907	P42695	CNDD3_HUMAN	T	907	ENSP00000433681:P907T	ENSP00000434168:P907T	P	-	1	0	NCAPD3	133553802	1.000000	0.71417	0.001000	0.08648	0.115000	0.19883	4.737000	0.62066	0.850000	0.35239	0.655000	0.94253	CCC	G|0.995;T|0.005	0.005	strong		0.522	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	
RGS13	6003	hgsc.bcm.edu	37	1	192628623	192628623	+	Missense_Mutation	SNP	G	G	C	rs16834603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:192628623G>C	ENST00000391995.2	+	7	738	c.450G>C	c.(448-450)ttG>ttC	p.L150F	RGS13_ENST00000543215.1_Missense_Mutation_p.L150F|RGS13_ENST00000482095.1_3'UTR	NM_002927.4	NP_002918.1	O14921	RGS13_HUMAN	regulator of G-protein signaling 13	150	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.		L -> F (in dbSNP:rs16834603). {ECO:0000269|Ref.2}.		G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of GTPase activity (GO:0043547)|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)			endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|skin(1)	19						AAAAACTTTTGAAAACTATGC	0.323													G|||	207	0.0413339	0.1513	0.0101	5008	,	,		16977	0.0		0.0	False		,,,				2504	0.0				p.L150F		Atlas-SNP	.											.	RGS13	31	.	0			c.G450C						PASS	.	G	PHE/LEU,PHE/LEU	577,3829	246.2+/-254.9	48,481,1674	46.0	45.0	45.0		450,450	2.7	1.0	1	dbSNP_123	45	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense	RGS13	NM_002927.4,NM_144766.2	22,22	48,485,5970	CC,CG,GG		0.0465,13.0958,4.4672	benign,benign	150/160,150/160	192628623	581,12425	2203	4300	6503	SO:0001583	missense	6003	exon7			ACTTTTGAAAACT	AF030107	CCDS1376.1	1q31.2	2008-02-05	2007-08-14		ENSG00000127074	ENSG00000127074		"""Regulators of G-protein signaling"""	9995	protein-coding gene	gene with protein product		607190	"""regulator of G-protein signalling 13"""			11875076	Standard	NM_144766		Approved		uc001gsk.3	O14921	OTTHUMG00000035601	ENST00000391995.2:c.450G>C	1.37:g.192628623G>C	ENSP00000375853:p.Leu150Phe	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	181	94	0.519337	NM_002927	Q6PGR2|Q8TD63|Q9BX45	Missense_Mutation	SNP	ENST00000391995.2	37	CCDS1376.1	71	0.03250915750915751	70	0.14227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	13.88	2.368730	0.42003	0.130958	4.65E-4	ENSG00000127074	ENST00000391995;ENST00000543215	T;T	0.36157	1.27;1.27	5.89	2.73	0.32206	Regulator of G protein signalling (2);Regulator of G protein signalling superfamily (1);	0.277274	0.34725	N	0.003740	T	0.00300	0.0009	M	0.75085	2.285	0.31991	P	0.6046279999999999	B	0.29531	0.247	B	0.35470	0.203	T	0.11743	-1.0575	9	0.62326	D	0.03	.	5.6215	0.17459	0.0815:0.1835:0.6077:0.1273	rs16834603;rs52813648;rs16834603	150	O14921	RGS13_HUMAN	F	150	ENSP00000375853:L150F;ENSP00000442837:L150F	ENSP00000375853:L150F	L	+	3	2	RGS13	190895246	0.082000	0.21442	1.000000	0.80357	0.888000	0.51559	0.259000	0.18405	1.497000	0.48584	0.591000	0.81541	TTG	G|0.955;C|0.045	0.045	strong		0.323	RGS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086400.1	NM_002927	
OR1E2	8388	hgsc.bcm.edu	37	17	3336699	3336699	+	Missense_Mutation	SNP	C	C	G	rs78339092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3336699C>G	ENST00000248384.1	-	1	436	c.437G>C	c.(436-438)aGc>aCc	p.S146T		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	146					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						GAGCATGGGGCTCATGATGGC	0.562													C|||	120	0.0239617	0.0885	0.0043	5008	,	,		19338	0.0		0.0	False		,,,				2504	0.0				p.S146T		Atlas-SNP	.											OR1E2,right_upper_lobe,carcinoma,+1,1	OR1E2	25	1	0			c.G437C						PASS	.																																			SO:0001583	missense	8388	exon1			ATGGGGCTCATGA	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"""GPCR / Class A : Olfactory receptors"""	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.437G>C	17.37:g.3336699C>G	ENSP00000248384:p.Ser146Thr	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	228	96	0.421053	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	37	CCDS11026.1	45	0.020604395604395604	45	0.09146341463414634	0	0.0	0	0.0	0	0.0	C	7.609	0.674467	0.14841	.	.	ENSG00000127780	ENST00000248384;ENST00000454364	T	0.03717	3.83	5.47	2.44	0.29823	GPCR, rhodopsin-like superfamily (1);	0.148993	0.48286	N	0.000187	T	0.00109	0.0003	N	0.08118	0	0.25052	N	0.99113	B	0.21225	0.053	B	0.26693	0.072	T	0.49495	-0.8934	10	0.33940	T	0.23	.	9.9959	0.41898	0.0:0.7793:0.0:0.2207	.	146	P47887	OR1E2_HUMAN	T	146;136	ENSP00000248384:S146T	ENSP00000248384:S146T	S	-	2	0	OR1E2	3283449	0.000000	0.05858	0.958000	0.39756	0.329000	0.28539	-0.448000	0.06820	0.439000	0.26476	0.650000	0.86243	AGC	C|0.987;G|0.013	0.013	strong		0.562	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1		
C6orf52	347744	hgsc.bcm.edu	37	6	10671764	10671764	+	Silent	SNP	G	G	A	rs3737278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10671764G>A	ENST00000426700.2	-	4	383	c.384C>T	c.(382-384)taC>taT	p.Y128Y	C6orf52_ENST00000379586.1_Silent_p.Y41Y|C6orf52_ENST00000460742.2_Silent_p.Y39Y|C6orf52_ENST00000467832.2_5'UTR|C6orf52_ENST00000259983.3_Silent_p.Y128Y|C6orf52_ENST00000503680.1_Silent_p.Y69Y			Q5T4I8	CF052_HUMAN	chromosome 6 open reading frame 52	128										endometrium(1)|prostate(1)	2						TGAGGGAGTCGTAGAGTTCTT	0.423													G|||	466	0.0930511	0.2731	0.013	5008	,	,		17160	0.0387		0.003	False		,,,				2504	0.0552				p.Y128Y		Atlas-SNP	.											C6orf52,colon,carcinoma,0,1	C6orf52	9	1	0			c.C384T						PASS	.						165.0	157.0	159.0					6																	10671764		692	1591	2283	SO:0001819	synonymous_variant	347744	exon5			GGAGTCGTAGAGT	BC016820	CCDS47371.1	6p24.2	2009-09-22	2007-06-07	2007-06-07	ENSG00000137434	ENSG00000137434			20881	protein-coding gene	gene with protein product						12477932	Standard	NM_001145020		Approved		uc011dij.2	Q5T4I8	OTTHUMG00000014240	ENST00000426700.2:c.384C>T	6.37:g.10671764G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	154	70	0.454545	NM_001145020	Q5T4I7|Q96AS6	Silent	SNP	ENST00000426700.2	37	CCDS47371.1																																																																																			G|0.907;A|0.093	0.093	strong		0.423	C6orf52-002	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039825.2	NM_001145020	
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69098115	69098115	+	Silent	SNP	A	A	G	rs10018067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:69098115A>G	ENST00000332644.5	-	6	650	c.489T>C	c.(487-489)tcT>tcC	p.S163S		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	163						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						TAAGCATTTCAGAAGCAGCCT	0.289													a|||	141	0.028155	0.1006	0.0086	5008	,	,		13924	0.0		0.0	False		,,,				2504	0.002				p.S163S		Atlas-SNP	.											.	TMPRSS11B	66	.	0			c.T489C						PASS	.	G		346,4054	754.8+/-412.5	17,312,1871	49.0	56.0	53.0		489	1.9	0.0	4	dbSNP_119	53	14,8572	810.0+/-407.1	0,14,4279	no	coding-synonymous	TMPRSS11B	NM_182502.3		17,326,6150	GG,GA,AA		0.1631,7.8636,2.7722		163/417	69098115	360,12626	2200	4293	6493	SO:0001819	synonymous_variant	132724	exon6			CATTTCAGAAGCA	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.489T>C	4.37:g.69098115A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	158	80	0.506329	NM_182502	A8K4D9	Silent	SNP	ENST00000332644.5	37	CCDS3521.1																																																																																			A|0.973;G|0.027	0.027	strong		0.289	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502	
DGKA	1606	hgsc.bcm.edu	37	12	56345408	56345408	+	Splice_Site	SNP	T	T	G	rs11834873	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56345408T>G	ENST00000331886.5	+	18	1882	c.1428T>G	c.(1426-1428)ggT>ggG	p.G476G	DGKA_ENST00000549079.2_3'UTR|DGKA_ENST00000394147.1_Splice_Site_p.G476G|DGKA_ENST00000551156.1_Splice_Site_p.G476G	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	476	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	CACTCCTAGGTTATGAAGGAC	0.502													G|||	539	0.107628	0.3805	0.0389	5008	,	,		21545	0.006		0.001	False		,,,				2504	0.002				p.G476G		Atlas-SNP	.											.	DGKA	70	.	0			c.T1428G						PASS	.	G	,,,	1383,3023	687.7+/-404.9	232,919,1052	113.0	106.0	108.0		1428,1428,1428,1428	-4.9	0.8	12	dbSNP_120	108	15,8585	818.5+/-406.9	0,15,4285	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	DGKA	NM_001345.4,NM_201444.2,NM_201445.1,NM_201554.1	,,,	232,934,5337	GG,GT,TT		0.1744,31.389,10.7489	,,,	476/736,476/736,476/736,476/736	56345408	1398,11608	2203	4300	6503	SO:0001630	splice_region_variant	1606	exon18			CCTAGGTTATGAA	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"""EF-hand domain containing"""	2849	protein-coding gene	gene with protein product		125855	"""diacylglycerol kinase, alpha (80kD)"""	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.1427-1T>G	12.37:g.56345408T>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Silent	SNP	ENST00000331886.5	37	CCDS8896.1																																																																																			T|0.889;G|0.111	0.111	strong		0.502	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1		Silent
SNAI1	6615	hgsc.bcm.edu	37	20	48600475	48600475	+	Missense_Mutation	SNP	C	C	T	rs34261470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48600475C>T	ENST00000244050.2	+	2	258	c.197C>T	c.(196-198)gCg>gTg	p.A66V		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	66			A -> V (in dbSNP:rs34261470).		cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|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 regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			TCTGTCCTGGCGCCCCAAGCC	0.657													C|||	140	0.0279553	0.093	0.0101	5008	,	,		14457	0.0		0.0	False		,,,				2504	0.0102				p.A66V		Atlas-SNP	.											.	SNAI1	28	.	0			c.C197T						PASS	.	C	VAL/ALA	321,4085	168.3+/-199.2	18,285,1900	45.0	50.0	48.0		197	1.8	0.9	20	dbSNP_126	48	7,8593	5.7+/-21.5	0,7,4293	no	missense	SNAI1	NM_005985.3	64	18,292,6193	TT,TC,CC		0.0814,7.2855,2.5219	benign	66/265	48600475	328,12678	2203	4300	6503	SO:0001583	missense	6615	exon2			TCCTGGCGCCCCA	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	11128	protein-coding gene	gene with protein product		604238	"""snail 1 (drosophila homolog), zinc finger protein"", ""snail homolog 1 (Drosophila)"""			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.197C>T	20.37:g.48600475C>T	ENSP00000244050:p.Ala66Val	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_005985	B2R842|Q9P113|Q9UBP7|Q9UHH7	Missense_Mutation	SNP	ENST00000244050.2	37	CCDS13423.1	38	0.0173992673992674	32	0.06504065040650407	6	0.016574585635359115	0	0.0	0	0.0	C	12.23	1.875633	0.33162	0.072855	8.14E-4	ENSG00000124216	ENST00000244050	T	0.20332	2.08	4.94	1.81	0.25067	.	1.159810	0.06133	N	0.670998	T	0.01061	0.0035	L	0.33485	1.01	0.23704	N	0.997068	B	0.11235	0.004	B	0.04013	0.001	T	0.32134	-0.9918	10	0.13853	T	0.58	-4.3384	7.28	0.26306	0.0:0.6314:0.0:0.3686	rs34261470	66	O95863	SNAI1_HUMAN	V	66	ENSP00000244050:A66V	ENSP00000244050:A66V	A	+	2	0	SNAI1	48033882	0.003000	0.15002	0.936000	0.37596	0.943000	0.58893	1.315000	0.33608	0.429000	0.26202	0.557000	0.71058	GCG	C|0.979;T|0.021	0.021	strong		0.657	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1		
ADAM19	8728	hgsc.bcm.edu	37	5	156964944	156964944	+	Missense_Mutation	SNP	G	G	C	rs11134804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156964944G>C	ENST00000517905.1	-	4	351	c.307C>G	c.(307-309)Caa>Gaa	p.Q103E	ADAM19_ENST00000257527.4_Missense_Mutation_p.Q103E|ADAM19_ENST00000430702.2_5'UTR|ADAM19_ENST00000394020.1_Missense_Mutation_p.Q105E			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	103					heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTGGTGGTTTGAGGGTTACCA	0.443													G|||	136	0.0271565	0.0968	0.0086	5008	,	,		18034	0.0		0.0	False		,,,				2504	0.002				p.Q103E		Atlas-SNP	.											.	ADAM19	216	.	0			c.C307G						PASS	.	G	GLU/GLN	377,4029	191.9+/-217.4	13,351,1839	207.0	192.0	197.0		307	5.2	1.0	5	dbSNP_120	197	4,8596	3.0+/-9.4	0,4,4296	yes	missense	ADAM19	NM_033274.3	29	13,355,6135	CC,CG,GG		0.0465,8.5565,2.9294	benign	103/919	156964944	381,12625	2203	4300	6503	SO:0001583	missense	8728	exon4			TGGTTTGAGGGTT	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"""ADAM metallopeptidase domain containing"""	197	protein-coding gene	gene with protein product	"""meltrin beta"""	603640	"""a disintegrin and metalloproteinase domain 19 (meltrin beta)"""			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.307C>G	5.37:g.156964944G>C	ENSP00000428654:p.Gln103Glu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		51	0.023351648351648352	47	0.09552845528455285	4	0.011049723756906077	0	0.0	0	0.0	G	14.59	2.579496	0.46006	0.085565	4.65E-4	ENSG00000135074	ENST00000257527;ENST00000394020;ENST00000517905	T;T;T	0.05199	3.48;3.48;3.48	5.17	5.17	0.71159	.	0.462253	0.20288	N	0.095302	T	0.00241	0.0007	L	0.41906	1.305	0.80722	D	1	B	0.23249	0.082	B	0.24394	0.053	T	0.39941	-0.9589	10	0.72032	D	0.01	.	14.5834	0.68308	0.0:0.0:1.0:0.0	rs11134804;rs56446321;rs11134804	103	Q9H013-2	.	E	103;105;103	ENSP00000257527:Q103E;ENSP00000377588:Q105E;ENSP00000428654:Q103E	ENSP00000257527:Q103E	Q	-	1	0	ADAM19	156897522	1.000000	0.71417	0.979000	0.43373	0.883000	0.51084	3.257000	0.51500	2.584000	0.87258	0.563000	0.77884	CAA	G|0.965;C|0.035	0.035	strong		0.443	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274	
LONRF2	164832	hgsc.bcm.edu	37	2	100915772	100915772	+	Missense_Mutation	SNP	A	A	G	rs4851287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:100915772A>G	ENST00000393437.3	-	6	1916	c.1277T>C	c.(1276-1278)cTt>cCt	p.L426P	LONRF2_ENST00000409647.1_Missense_Mutation_p.L183P	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	426			L -> P (in dbSNP:rs4851287). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.				ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						GCTCCTTTGAAGTGAGAGATC	0.433													G|||	3865	0.771765	0.8903	0.7363	5008	,	,		15374	0.9405		0.675	False		,,,				2504	0.5624				p.L426P		Atlas-SNP	.											.	LONRF2	62	.	0			c.T1277C						PASS	.	G	PRO/LEU	3671,735	299.3+/-285.7	1528,615,60	77.0	77.0	77.0		1277	4.0	0.0	2	dbSNP_111	77	5539,3061	465.4+/-366.5	1793,1953,554	yes	missense	LONRF2	NM_198461.3	98	3321,2568,614	GG,GA,AA		35.593,16.6818,29.1865	benign	426/755	100915772	9210,3796	2203	4300	6503	SO:0001583	missense	164832	exon6			CTTTGAAGTGAGA	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"""RING-type (C3HC4) zinc fingers"""	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1277T>C	2.37:g.100915772A>G	ENSP00000377086:p.Leu426Pro	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_198461	B9A006|Q6ZSR4	Missense_Mutation	SNP	ENST00000393437.3	37	CCDS2046.2	1709	0.7825091575091575	418	0.8495934959349594	245	0.6767955801104972	544	0.951048951048951	502	0.662269129287599	G	0.236	-1.017352	0.02078	0.833182	0.64407	ENSG00000170500	ENST00000393437;ENST00000409647	D;D	0.85556	-1.85;-2.0	3.96	3.96	0.45880	.	2.046660	0.02244	N	0.066060	T	0.00012	0.0000	N	0.00436	-1.5	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.50725	-0.8794	9	0.28530	T	0.3	-0.3994	7.1311	0.25502	0.0942:0.1715:0.7343:0.0	rs4851287;rs17438333;rs52819330;rs60152501;rs4851287	426	Q1L5Z9	LONF2_HUMAN	P	426;183	ENSP00000377086:L426P;ENSP00000386823:L183P	ENSP00000377086:L426P	L	-	2	0	LONRF2	100282204	0.972000	0.33761	0.014000	0.15608	0.001000	0.01503	1.729000	0.38115	0.878000	0.35920	-0.227000	0.12334	CTT	A|0.253;G|0.747	0.747	strong		0.433	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461	
OR6B2	389090	hgsc.bcm.edu	37	2	240969312	240969312	+	Missense_Mutation	SNP	A	A	G	rs10187574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	443	0	0		WXS	Illumina HiSeq	Phase_I	481	186	0.386694	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	
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145281413	145281413	+	Missense_Mutation	SNP	G	G	A	rs76765512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:145281413G>A	ENST00000369340.3	+	5	787	c.343G>A	c.(343-345)Gca>Aca	p.A115T	NOTCH2NL_ENST00000362074.6_Missense_Mutation_p.A115T|RP11-458D21.5_ENST00000468030.1_Missense_Mutation_p.A115T|NOTCH2NL_ENST00000344859.3_Missense_Mutation_p.A115T			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	115	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						TCATCCCTGTGCAAATGGAAG	0.502																																					p.A115T		Atlas-SNP	.											.	NOTCH2NL	100	.	0			c.G343A						PASS	.	G	THR/ALA	228,4178	115.4+/-153.4	0,228,1975	339.0	343.0	342.0		343	2.9	1.0	1	dbSNP_131	342	2,8596	1.2+/-3.3	0,2,4297	no	missense	NOTCH2NL	NM_203458.3	58	0,230,6272	AA,AG,GG		0.0233,5.1748,1.7687	possibly-damaging	115/237	145281413	230,12774	2203	4299	6502	SO:0001583	missense	388677	exon4			CCCTGTGCAAATG		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"""Notch homolog 2 (Drosophila) N-terminal like"""			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.343G>A	1.37:g.145281413G>A	ENSP00000358346:p.Ala115Thr	Somatic	1344	2	0.0014881		WXS	Illumina HiSeq	Phase_I	1480	388	0.262162	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Missense_Mutation	SNP	ENST00000369340.3	37	CCDS909.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.233634	0.79688	0.051748	2.33E-4	ENSG00000213240	ENST00000362074;ENST00000344859;ENST00000369340	D;D;D	0.87491	-2.26;-2.26;-2.26	2.87	2.87	0.33458	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.76835	0.4043	L	0.37507	1.11	0.32769	N	0.504048	P;P	0.49783	0.825;0.928	B;P	0.48571	0.342;0.582	T	0.70378	-0.4888	9	0.29301	T	0.29	.	11.5361	0.50639	0.0:0.0:1.0:0.0	.	115;115	Q7Z3S9-2;Q7Z3S9	.;NT2NL_HUMAN	T	115	ENSP00000354929:A115T;ENSP00000344557:A115T;ENSP00000358346:A115T	ENSP00000344557:A115T	A	+	1	0	NOTCH2NL	143992770	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	7.645000	0.83430	1.601000	0.50113	0.400000	0.26472	GCA	G|0.980;A|0.020	0.020	strong		0.502	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458	
ARSK	153642	hgsc.bcm.edu	37	5	94936744	94936744	+	Silent	SNP	G	G	A	rs61733083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:94936744G>A	ENST00000380009.4	+	7	1495	c.1290G>A	c.(1288-1290)tcG>tcA	p.S430S		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	430					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)		TAGCCTATTCGGATGGTGCAT	0.383													G|||	47	0.00938498	0.034	0.0029	5008	,	,		20862	0.0		0.0	False		,,,				2504	0.0				p.S430S		Atlas-SNP	.											.	ARSK	29	.	0			c.G1290A						PASS	.	G		120,4286	88.7+/-127.4	0,120,2083	125.0	119.0	121.0		1290	-1.4	0.7	5	dbSNP_129	121	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ARSK	NM_198150.2		0,121,6382	AA,AG,GG		0.0116,2.7236,0.9303		430/537	94936744	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	153642	exon7			CTATTCGGATGGT		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.1290G>A	5.37:g.94936744G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	130	56	0.430769	NM_198150	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Silent	SNP	ENST00000380009.4	37	CCDS4073.1																																																																																			G|0.990;A|0.010	0.010	strong		0.383	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150	
CDRT1	374286	hgsc.bcm.edu	37	17	15496727	15496727	+	Missense_Mutation	SNP	T	T	G	rs79385100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15496727T>G	ENST00000395906.3	-	11	1929	c.1930A>C	c.(1930-1932)Aat>Cat	p.N644H	RP11-385D13.1_ENST00000455584.2_Intron|CDRT1_ENST00000354433.3_Missense_Mutation_p.N144H|CDRT1_ENST00000583965.1_Intron	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	644				N -> H (in Ref. 1; AAC52034/AAD10830). {ECO:0000305}.						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)		CAGTTCCCATTGAAGAAATTG	0.512													.|||	987	0.197085	0.1936	0.281	5008	,	,		17558	0.2331		0.1213	False		,,,				2504	0.183				p.N644H		Atlas-SNP	.											.	CDRT1	83	.	0			c.A1930C						PASS	.	T	HIS/ASN	830,3576	318.5+/-295.7	75,680,1448	229.0	240.0	236.0		1930	3.6	1.0	17	dbSNP_131	236	1103,7497	221.0+/-258.6	72,959,3269	yes	missense	CDRT1	NM_006382.3	68	147,1639,4717	GG,GT,TT		12.8256,18.8379,14.8624	probably-damaging	644/753	15496727	1933,11073	2203	4300	6503	SO:0001583	missense	374286	exon11			TCCCATTGAAGAA	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.1930A>C	17.37:g.15496727T>G	ENSP00000379242:p.Asn644His	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	249	112	0.449799	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	398	0.18223443223443223	82	0.16666666666666666	94	0.2596685082872928	126	0.2202797202797203	96	0.1266490765171504	t	17.55	3.416430	0.62511	0.188379	0.128256	ENSG00000241322;ENSG00000251537;ENSG00000251537	ENST00000354433;ENST00000261644;ENST00000395906	T;T	0.19669	2.13;2.13	4.74	3.61	0.41365	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.00012	0.0000	M	0.61703	1.905	0.09310	P	0.9999999999999785	D	0.65815	0.995	P	0.62885	0.908	T	0.15521	-1.0434	7	.	.	.	.	9.886	0.41262	0.1521:0.0:0.0:0.8479	.	644	O95170	CDRT1_HUMAN	H	144;674;644	ENSP00000346416:N144H;ENSP00000379242:N644H	.	N	-	1	0	CDRT1;RP11-385D13.1	15437452	0.999000	0.42202	0.988000	0.46212	0.915000	0.54546	4.784000	0.62411	1.781000	0.52344	0.528000	0.53228	AAT	T|0.825;G|0.175	0.175	strong		0.512	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
TTN	7273	hgsc.bcm.edu	37	2	179611851	179611851	+	Intron	SNP	C	C	T	rs72648910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179611851C>T	ENST00000591111.1	-	46	10585				TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Silent_p.L5092L|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000578746.1_RNA			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						scavenged	.	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	283	3	0.0106007		WXS	Illumina HiSeq	Phase_I	275	146	0.530909	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	
SDAD1	55153	hgsc.bcm.edu	37	4	76878716	76878716	+	Missense_Mutation	SNP	G	G	C	rs2242471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:76878716G>C	ENST00000356260.5	-	19	1842	c.1724C>G	c.(1723-1725)tCc>tGc	p.S575C	SDAD1_ENST00000395711.4_Missense_Mutation_p.S538C|SDAD1_ENST00000513089.1_5'Flank	NM_018115.2	NP_060585.2	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	575			S -> C (in dbSNP:rs2242471). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		actin cytoskeleton organization (GO:0030036)|protein transport (GO:0015031)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal large subunit export from nucleus (GO:0000055)	nucleolus (GO:0005730)				breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	19			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			CCTCTTCTGGGATTTCCCGGG	0.458													G|||	1397	0.278954	0.2368	0.2089	5008	,	,		19049	0.0734		0.4225	False		,,,				2504	0.4499				p.S575C		Atlas-SNP	.											.	SDAD1	47	.	0			c.C1724G						PASS	.	G	CYS/SER	1104,3302	396.5+/-330.1	135,834,1234	137.0	138.0	138.0		1724	5.2	1.0	4	dbSNP_98	138	3365,5235	500.1+/-375.1	629,2107,1564	yes	missense	SDAD1	NM_018115.2	112	764,2941,2798	CC,CG,GG		39.1279,25.0567,34.3611	possibly-damaging	575/688	76878716	4469,8537	2203	4300	6503	SO:0001583	missense	55153	exon19			TTCTGGGATTTCC	AF132198	CCDS3573.2, CCDS75147.1	4q21.21	2010-11-24			ENSG00000198301	ENSG00000198301			25537	protein-coding gene	gene with protein product						11483580	Standard	NM_001288984		Approved	FLJ10498	uc003hje.4	Q9NVU7	OTTHUMG00000130111	ENST00000356260.5:c.1724C>G	4.37:g.76878716G>C	ENSP00000348596:p.Ser575Cys	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	233	121	0.519313	NM_018115	Q32Q11|Q68D52|Q7Z5U4|Q9H831|Q9H9P6	Missense_Mutation	SNP	ENST00000356260.5	37	CCDS3573.2	552	0.25274725274725274	107	0.21747967479674796	83	0.2292817679558011	37	0.06468531468531469	325	0.4287598944591029	G	17.93	3.509480	0.64522	0.250567	0.391279	ENSG00000198301	ENST00000356260;ENST00000395711	T;D	0.86432	1.89;-2.12	5.15	5.15	0.70609	SDA1 (1);	0.161367	0.56097	D	0.000037	T	0.00012	0.0000	L	0.46157	1.445	0.35218	P	0.22419699999999998	P;P	0.51057	0.941;0.602	P;B	0.49477	0.612;0.312	T	0.00888	-1.1526	9	0.59425	D	0.04	-4.1951	16.483	0.84163	0.0:0.0:1.0:0.0	rs2242471;rs3201420;rs11557433;rs17288280;rs52806783;rs2242471	538;575	E7EW05;Q9NVU7	.;SDA1_HUMAN	C	575;538	ENSP00000348596:S575C;ENSP00000379061:S538C	ENSP00000348596:S575C	S	-	2	0	SDAD1	77097740	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.973000	0.56845	2.581000	0.87130	0.650000	0.86243	TCC	G|0.688;C|0.312	0.312	strong		0.458	SDAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252418.3	NM_018115	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999385	46999385	+	Missense_Mutation	SNP	C	C	T	rs113256776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:46999385C>T	ENST00000374317.1	+	3	778	c.505C>T	c.(505-507)Cct>Tct	p.P169S	GPRIN2_ENST00000374314.4_Missense_Mutation_p.P169S	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	169										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TGGCCAGGCCCCTGCAGGCCT	0.637													C|||	128	0.0255591	0.09	0.0115	5008	,	,		39000	0.0		0.001	False		,,,				2504	0.0				p.P169S		Atlas-SNP	.											.	GPRIN2	94	.	0			c.C505T						PASS	.	C	SER/PRO	231,4175		0,231,1972	39.0	40.0	40.0		505	0.7	0.0	10	dbSNP_132	40	1,8599		0,1,4299	yes	missense	GPRIN2	NM_014696.3	74	0,232,6271	TT,TC,CC		0.0116,5.2429,1.7838	probably-damaging	169/459	46999385	232,12774	2203	4300	6503	SO:0001583	missense	9721	exon3			CAGGCCCCTGCAG	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.505C>T	10.37:g.46999385C>T	ENSP00000363436:p.Pro169Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	70	15	0.214286	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	.	.	.	.	.	.	.	.	.	.	C	9.805	1.181582	0.21787	0.052429	1.16E-4	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03330	3.97;3.97	4.71	0.695	0.18070	.	0.700953	0.12491	N	0.464220	T	0.00695	0.0023	M	0.63428	1.95	0.09310	N	1	B	0.22909	0.077	B	0.20767	0.031	T	0.39165	-0.9627	10	0.87932	D	0	-0.5548	3.3753	0.07235	0.1809:0.5265:0.0:0.2926	.	169	O60269	GRIN2_HUMAN	S	169	ENSP00000363436:P169S;ENSP00000363433:P169S	ENSP00000363433:P169S	P	+	1	0	GPRIN2	46419391	0.000000	0.05858	0.003000	0.11579	0.063000	0.16089	0.087000	0.14958	0.036000	0.15547	0.650000	0.86243	CCT	C|0.975;T|0.025	0.025	strong		0.637	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
STAG1	10274	hgsc.bcm.edu	37	3	136088038	136088038	+	Silent	SNP	G	G	A	rs9860801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:136088038G>A	ENST00000383202.2	-	24	2713	c.2457C>T	c.(2455-2457)ttC>ttT	p.F819F	STAG1_ENST00000434713.2_Silent_p.F593F|STAG1_ENST00000236698.5_Silent_p.F819F|STAG1_ENST00000536929.1_Silent_p.F403F	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	819					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						TATCTGGATTGAACACCAAAG	0.448													A|||	1517	0.302915	0.5522	0.2017	5008	,	,		15257	0.0585		0.3022	False		,,,				2504	0.2904				p.F819F		Atlas-SNP	.											.	STAG1	135	.	0			c.C2457T						PASS	.	A		2295,2111	576.3+/-384.2	609,1077,517	90.0	89.0	90.0		2457	3.0	1.0	3	dbSNP_119	90	2836,5764	675.1+/-403.2	465,1906,1929	no	coding-synonymous	STAG1	NM_005862.2		1074,2983,2446	AA,AG,GG		32.9767,47.9119,39.451		819/1259	136088038	5131,7875	2203	4300	6503	SO:0001819	synonymous_variant	10274	exon24			TGGATTGAACACC	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.2457C>T	3.37:g.136088038G>A		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_005862	O00539|Q6P275	Silent	SNP	ENST00000383202.2	37	CCDS3090.1																																																																																			G|0.655;A|0.344	0.344	strong		0.448	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862	
PSME4	23198	hgsc.bcm.edu	37	2	54120025	54120025	+	Missense_Mutation	SNP	A	A	T	rs805408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:54120025A>T	ENST00000404125.1	-	36	4166	c.4111T>A	c.(4111-4113)Tca>Aca	p.S1371T	PSME4_ENST00000421748.2_Missense_Mutation_p.S515T	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1371			S -> T (in dbSNP:rs805408).		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)			CTTTCATGTGAATCTGCAACC	0.373													A|||	1749	0.349241	0.2186	0.2522	5008	,	,		16857	0.4742		0.3002	False		,,,				2504	0.5164				p.S1371T		Atlas-SNP	.											.	PSME4	247	.	0			c.T4111A						PASS	.	A	THR/SER	931,3475	355.9+/-313.2	87,757,1359	102.0	100.0	101.0		4111	5.4	1.0	2	dbSNP_86	101	2595,6005	420.4+/-353.4	385,1825,2090	yes	missense	PSME4	NM_014614.2	58	472,2582,3449	TT,TA,AA		30.1744,21.1303,27.1106	benign	1371/1844	54120025	3526,9480	2203	4300	6503	SO:0001583	missense	23198	exon36			CATGTGAATCTGC	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.4111T>A	2.37:g.54120025A>T	ENSP00000384211:p.Ser1371Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	658	0.30128205128205127	102	0.2073170731707317	92	0.2541436464088398	230	0.4020979020979021	234	0.3087071240105541	A	9.975	1.226633	0.22542	0.211303	0.301744	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.66280	-0.2;-0.2	5.41	5.41	0.78517	Armadillo-like helical (1);Armadillo-type fold (1);	0.192762	0.47093	D	0.000251	T	0.00012	0.0000	N	0.04746	-0.17	0.21184	P	0.999767317	B;B;B	0.10296	0.003;0.0;0.002	B;B;B	0.11329	0.006;0.001;0.001	T	0.28267	-1.0049	9	0.15952	T	0.53	.	15.4442	0.75216	1.0:0.0:0.0:0.0	rs805408;rs52818353;rs805408	746;515;1371	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	T	515;1371	ENSP00000410830:S515T;ENSP00000384211:S1371T	ENSP00000384211:S1371T	S	-	1	0	PSME4	53973529	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.976000	0.63785	2.060000	0.61445	0.454000	0.30748	TCA	A|0.713;T|0.287	0.287	strong		0.373	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
EMID1	129080	hgsc.bcm.edu	37	22	29621128	29621128	+	Missense_Mutation	SNP	C	C	G	rs743920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:29621128C>G	ENST00000404820.3	+	4	453	c.326C>G	c.(325-327)gCt>gGt	p.A109G	EMID1_ENST00000404755.3_Missense_Mutation_p.A109G|EMID1_ENST00000334018.6_Missense_Mutation_p.A109G|EMID1_ENST00000484039.1_3'UTR			Q96A84	EMID1_HUMAN	EMI domain containing 1	107						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						TTAGTTGCAGCTTCCTCTGCC	0.637													G|||	2343	0.467851	0.7761	0.3646	5008	,	,		18937	0.6081		0.1143	False		,,,				2504	0.3436				p.A109G		Atlas-SNP	.											.	EMID1	33	.	0			c.C326G						PASS	.	G	GLY/ALA	2990,1416	461.5+/-352.9	1031,928,244	125.0	115.0	119.0		326	1.3	0.4	22	dbSNP_86	119	1108,7492	768.0+/-407.6	81,946,3273	yes	missense	EMID1	NM_133455.2	60	1112,1874,3517	GG,GC,CC		12.8837,32.138,31.5085	benign	109/444	29621128	4098,8908	2203	4300	6503	SO:0001583	missense	129080	exon4			TTGCAGCTTCCTC	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.326C>G	22.37:g.29621128C>G	ENSP00000384452:p.Ala109Gly	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_133455	B0QYK6|Q6ICG1|Q86SS7	Missense_Mutation	SNP	ENST00000404820.3	37		921	0.4217032967032967	382	0.7764227642276422	120	0.3314917127071823	331	0.5786713286713286	88	0.11609498680738786	G	0.286	-0.983016	0.02180	0.67862	0.128837	ENSG00000186998	ENST00000334018;ENST00000429226;ENST00000404755;ENST00000404820	D;T;D;D	0.89875	-2.58;0.93;-2.41;-2.56	4.62	1.28	0.21552	.	0.289804	0.24915	N	0.034589	T	0.00012	0.0000	N	0.00104	-2.125	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	0.42275	-0.9461	9	0.06625	T	0.88	-1.1286	7.6922	0.28575	0.0943:0.5032:0.4025:0.0	rs743920;rs5763064;rs17857319;rs57479276;rs743920	109;109;107;109	B0QYK4;B0QYK5;Q96A84;Q96A84-3	.;.;EMID1_HUMAN;.	G	109	ENSP00000335481:A109G;ENSP00000403816:A109G;ENSP00000385414:A109G;ENSP00000384452:A109G	ENSP00000335481:A109G	A	+	2	0	EMID1	27951128	0.754000	0.28360	0.352000	0.25734	0.003000	0.03518	0.813000	0.27225	0.250000	0.21479	-0.815000	0.03128	GCT	C|0.658;G|0.342	0.342	strong		0.637	EMID1-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321075.1	NM_133455	
ZNF30	90075	hgsc.bcm.edu	37	19	35422808	35422808	+	Missense_Mutation	SNP	C	C	T	rs10422961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35422808C>T	ENST00000601142.1	+	3	308	c.71C>T	c.(70-72)tCc>tTc	p.S24F	ZNF30_ENST00000601957.1_Missense_Mutation_p.S24F|ZNF30_ENST00000426813.2_5'UTR|ZNF30_ENST00000303586.7_Missense_Mutation_p.S24F|ZNF30_ENST00000439785.1_Missense_Mutation_p.S24F			P17039	ZNF30_HUMAN	zinc finger protein 30	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.			S -> F (in Ref. 1; BAG58432). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		ATAGCCTTCTCCCAGCAGGAG	0.463													C|||	1443	0.288139	0.2693	0.232	5008	,	,		20449	0.2202		0.3618	False		,,,				2504	0.3476				p.S24F		Atlas-SNP	.											ZNF30,colon,carcinoma,0,1	ZNF30	44	1	0			c.C71T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER	1094,3212		155,784,1214	79.0	85.0	83.0		71,71,71	1.5	1.0	19	dbSNP_119	83	2777,5777		466,1845,1966	yes	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	155,155,155	621,2629,3180	TT,TC,CC		32.4643,25.4064,30.1011	benign,benign,benign	24/625,24/625,24/624	35422808	3871,8989	2153	4277	6430	SO:0001583	missense	90075	exon3			CCTTCTCCCAGCA	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.71C>T	19.37:g.35422808C>T	ENSP00000469954:p.Ser24Phe	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	637	0.2916666666666667	128	0.2601626016260163	93	0.2569060773480663	136	0.23776223776223776	280	0.36939313984168864	C	11.43	1.637390	0.29157	0.254064	0.324643	ENSG00000168661	ENST00000439785;ENST00000303586	T;T	0.02944	4.1;4.1	1.55	1.55	0.23275	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	H	0.98701	4.305	0.09310	P	0.999999999831031	P;B	0.39903	0.694;0.031	B;B	0.41236	0.351;0.021	T	0.15235	-1.0444	8	0.72032	D	0.01	.	6.5714	0.22541	0.0:1.0:0.0:0.0	rs10422961;rs10422961	24;24	P17039-2;P17039	.;ZNF30_HUMAN	F	24	ENSP00000403441:S24F;ENSP00000303889:S24F	ENSP00000303889:S24F	S	+	2	0	ZNF30	40114648	0.676000	0.27567	0.991000	0.47740	0.971000	0.66376	1.149000	0.31626	1.167000	0.42706	0.514000	0.50259	TCC	C|0.700;T|0.300	0.300	strong		0.463	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
PCDHB4	56131	hgsc.bcm.edu	37	5	140503155	140503155	+	Silent	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140503155G>T	ENST00000194152.1	+	1	1575	c.1575G>T	c.(1573-1575)gcG>gcT	p.A525A	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	525	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTGCAGGCGTTCGAGTTCC	0.682																																					p.A525A		Atlas-SNP	.											PCDHB4,caecum,carcinoma,+1,1	PCDHB4	177	1	0			c.G1575T						scavenged	.						69.0	78.0	75.0					5																	140503155		2203	4298	6501	SO:0001819	synonymous_variant	56131	exon1			GCAGGCGTTCGAG	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1575G>T	5.37:g.140503155G>T		Somatic	370	2	0.00540541		WXS	Illumina HiSeq	Phase_I	444	13	0.0292793	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			.	.	none		0.682	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
CDH2	1000	hgsc.bcm.edu	37	18	25532304	25532304	+	Missense_Mutation	SNP	T	T	C	rs2289664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:25532304T>C	ENST00000269141.3	-	16	2957	c.2534A>G	c.(2533-2535)aAt>aGt	p.N845S	AC015933.2_ENST00000423367.1_RNA|CDH2_ENST00000399380.3_Missense_Mutation_p.N814S	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	845			N -> S (in dbSNP:rs2289664).		adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TGTGGGGTCATTGTCAGCCGC	0.448											OREG0003876	type=REGULATORY REGION|Gene=CDH2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	T|||	106	0.0211661	0.0015	0.013	5008	,	,		17916	0.0139		0.0338	False		,,,				2504	0.0481				p.N845S		Atlas-SNP	.											.	CDH2	194	.	0			c.A2534G						PASS	.	T	SER/ASN	31,4375	37.6+/-69.7	0,31,2172	90.0	87.0	88.0		2534	5.5	1.0	18	dbSNP_100	88	229,8371	94.2+/-156.2	3,223,4074	yes	missense	CDH2	NM_001792.3	46	3,254,6246	CC,CT,TT		2.6628,0.7036,1.9991	possibly-damaging	845/907	25532304	260,12746	2203	4300	6503	SO:0001583	missense	1000	exon16			GGGTCATTGTCAG	S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"""CD molecules"", ""Cadherins / Major cadherins"""	1759	protein-coding gene	gene with protein product	"""N-cadherin"""	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.2534A>G	18.37:g.25532304T>C	ENSP00000269141:p.Asn845Ser	Somatic	103	0	0	779	WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	38	0.0173992673992674	1	0.0020325203252032522	4	0.011049723756906077	9	0.015734265734265736	24	0.0316622691292876	T	10.82	1.458477	0.26248	0.007036	0.026628	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.77098	-1.07;-1.07	5.53	5.53	0.82687	Cadherin, cytoplasmic domain (1);	0.046462	0.85682	D	0.000000	T	0.64316	0.2587	L	0.39633	1.23	0.45452	D	0.998429	D;B	0.55385	0.971;0.251	D;B	0.64506	0.926;0.133	T	0.73180	-0.4064	10	0.28530	T	0.3	.	15.6593	0.77169	0.0:0.0:0.0:1.0	rs2289664;rs17445545;rs52812881;rs2289664	814;845	A8MWK3;P19022	.;CADH2_HUMAN	S	845;814	ENSP00000269141:N845S;ENSP00000382312:N814S	ENSP00000269141:N845S	N	-	2	0	CDH2	23786302	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.076000	0.57591	2.095000	0.63458	0.482000	0.46254	AAT	T|0.980;C|0.020	0.020	strong		0.448	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792	
MTG2	26164	hgsc.bcm.edu	37	20	60768615	60768615	+	Missense_Mutation	SNP	G	G	A	rs6062133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60768615G>A	ENST00000370823.3	+	2	157	c.139G>A	c.(139-141)Ggc>Agc	p.G47S	MTG2_ENST00000536470.1_Intron|MTG2_ENST00000436421.2_Missense_Mutation_p.G47S	NM_015666.3	NP_056481.1	Q9H4K7	MTG2_HUMAN	mitochondrial ribosome-associated GTPase 2	47	Localized in the mitochondria.|Not localized in the mitochondria.		G -> S (in dbSNP:rs6062133).		GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)										GCTCTCGGTCGGCCGTGCGGA	0.622													G|||	452	0.0902556	0.1399	0.0821	5008	,	,		16510	0.0228		0.1352	False		,,,				2504	0.0521				p.G47S		Atlas-SNP	.											.	GTPBP5	43	.	0			c.G139A						PASS	.	G	SER/GLY	608,3798	265.6+/-266.7	47,514,1642	45.0	48.0	47.0		139	-0.7	0.0	20	dbSNP_114	47	1233,7367	246.8+/-275.1	88,1057,3155	yes	missense	GTPBP5	NM_015666.3	56	135,1571,4797	AA,AG,GG		14.3372,13.7994,14.155	benign	47/407	60768615	1841,11165	2203	4300	6503	SO:0001583	missense	26164	exon2			TCGGTCGGCCGTG	AK001603	CCDS13492.1	20q13.33	2013-05-24	2013-05-24	2013-05-24	ENSG00000101181	ENSG00000101181			16239	protein-coding gene	gene with protein product		610919	"""GTP-binding protein 5 (putative)"", ""GTP binding protein 5 (putative)"""	GTPBP5		17054726, 23396448	Standard	NM_015666		Approved	FLJ10741, dJ1005F21.2, ObgH1		Q9H4K7	OTTHUMG00000032897	ENST00000370823.3:c.139G>A	20.37:g.60768615G>A	ENSP00000359859:p.Gly47Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	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	
KIAA0753	9851	hgsc.bcm.edu	37	17	6538355	6538355	+	Silent	SNP	G	G	A	rs2301873	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:6538355G>A	ENST00000361413.3	-	2	427	c.69C>T	c.(67-69)agC>agT	p.S23S	KIAA0753_ENST00000572370.1_Intron|KIAA0753_ENST00000542606.1_5'UTR	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	23						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		CTTTGGGGTCGCTCCTCCCAT	0.413													G|||	1684	0.336262	0.2655	0.3271	5008	,	,		16510	0.2897		0.4543	False		,,,				2504	0.365				p.S23S		Atlas-SNP	.											KIAA0753,NS,carcinoma,0,1	KIAA0753	63	1	0			c.C69T						PASS	.	G		1105,2703		158,789,957	108.0	98.0	101.0		69	0.3	0.0	17	dbSNP_100	101	3516,4718		754,2008,1355	no	coding-synonymous	KIAA0753	NM_014804.2		912,2797,2312	AA,AG,GG		42.701,29.0179,38.374		23/968	6538355	4621,7421	1904	4117	6021	SO:0001819	synonymous_variant	9851	exon2			GGGGTCGCTCCTC		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.69C>T	17.37:g.6538355G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Silent	SNP	ENST00000361413.3	37	CCDS42247.1																																																																																			G|0.637;A|0.363	0.363	strong		0.413	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
SLC2A8	29988	hgsc.bcm.edu	37	9	130162230	130162230	+	Silent	SNP	C	C	G	rs36057295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130162230C>G	ENST00000373371.3	+	4	560	c.471C>G	c.(469-471)ctC>ctG	p.L157L	SLC2A8_ENST00000373352.1_5'UTR|SLC2A8_ENST00000373360.3_Silent_p.L157L	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	157					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|male meiosis I (GO:0007141)|response to hypoxia (GO:0001666)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	glucose binding (GO:0005536)|glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	11						GGGGGTTGCTCGGCTCCTGTG	0.557													C|||	130	0.0259585	0.0968	0.0029	5008	,	,		17695	0.0		0.0	False		,,,				2504	0.0				p.L157L		Atlas-SNP	.											.	SLC2A8	27	.	0			c.C471G						PASS	.	C		315,4091	169.1+/-199.8	9,297,1897	137.0	134.0	135.0		471	-5.9	1.0	9	dbSNP_126	135	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC2A8	NM_014580.3		9,299,6195	GG,GC,CC		0.0233,7.1493,2.4373		157/478	130162230	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	29988	exon4			GTTGCTCGGCTCC	AJ245937	CCDS6870.1, CCDS65138.1, CCDS75903.1	9q33.3	2013-05-22	2008-09-02		ENSG00000136856	ENSG00000136856		"""Solute carriers"""	13812	protein-coding gene	gene with protein product		605245	"""solute carrier family 2 (facilitated glucose transporter) member 8"""			10671487, 10821868	Standard	NM_014580		Approved	GLUTX1, GLUT8	uc004bqu.4	Q9NY64	OTTHUMG00000020702	ENST00000373371.3:c.471C>G	9.37:g.130162230C>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	108	32	0.296296	NM_014580	Q8WUZ9|Q9NSC4	Silent	SNP	ENST00000373371.3	37	CCDS6870.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	C	1.094	-0.663174	0.03428	0.071493	2.33E-4	ENSG00000136856	ENST00000419132	.	.	.	5.35	-5.92	0.02261	.	.	.	.	.	T	0.04003	0.0112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40701	-0.9549	4	.	.	.	.	7.9566	0.30047	0.0948:0.1228:0.603:0.1794	rs36057295	.	.	.	W	67	.	.	S	+	2	0	SLC2A8	129202051	0.005000	0.15991	0.967000	0.41034	0.066000	0.16364	-2.012000	0.01451	-0.659000	0.05359	-0.302000	0.09304	TCG	C|0.975;G|0.025	0.025	strong		0.557	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580	
NARS2	79731	hgsc.bcm.edu	37	11	78279744	78279744	+	Silent	SNP	T	T	C	rs60510975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:78279744T>C	ENST00000281038.5	-	3	681	c.306A>G	c.(304-306)ccA>ccG	p.P102P	NARS2_ENST00000528850.1_5'UTR	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	102					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	GCCTTTTGGATGGACTTTTTA	0.333													T|||	225	0.0449281	0.1657	0.0072	5008	,	,		17073	0.0		0.001	False		,,,				2504	0.0				p.P102P		Atlas-SNP	.											NARS2,lower_third,carcinoma,-2,1	NARS2	62	1	0			c.A306G						PASS	.	T		604,3796	264.1+/-265.8	41,522,1637	182.0	174.0	177.0		306	-1.5	1.0	11	dbSNP_129	177	3,8579	3.0+/-9.4	0,3,4288	no	coding-synonymous	NARS2	NM_024678.5		41,525,5925	CC,CT,TT		0.035,13.7273,4.6757		102/478	78279744	607,12375	2200	4291	6491	SO:0001819	synonymous_variant	79731	exon3			TTTGGATGGACTT	BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"""Aminoacyl tRNA synthetases / Class II"""	26274	protein-coding gene	gene with protein product	"""asparagine tRNA ligase 2, mitochondrial (putative)"""	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.306A>G	11.37:g.78279744T>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	193	97	0.502591	NM_024678	G3V178	Silent	SNP	ENST00000281038.5	37	CCDS8261.1																																																																																			T|0.960;C|0.040	0.040	strong		0.333	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678	
DMKN	93099	hgsc.bcm.edu	37	19	36004171	36004171	+	Missense_Mutation	SNP	C	C	A	rs12460932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36004171C>A	ENST00000339686.3	-	1	383	c.207G>T	c.(205-207)gaG>gaT	p.E69D	DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Missense_Mutation_p.E69D|DMKN_ENST00000451297.2_Missense_Mutation_p.E69D|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000429837.1_Missense_Mutation_p.E69D|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.E69D|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.E69D|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.E69D|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.E69D	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	69	Gly-rich.		E -> D (in dbSNP:rs12460932).			extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GGCCAAGGGCCTCACTGACTT	0.627													C|||	1585	0.316494	0.3994	0.3357	5008	,	,		17452	0.3542		0.1431	False		,,,				2504	0.3303				p.E69D		Atlas-SNP	.											.	DMKN	116	.	0			c.G207T						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	1706,2700	516.7+/-369.2	344,1018,841	131.0	109.0	117.0		207,207,207,207,207,207,207	-5.7	0.0	19	dbSNP_120	117	1252,7348	250.3+/-277.2	106,1040,3154	yes	missense,missense,missense,missense,missense,missense,missense	DMKN	NM_001126056.2,NM_001126057.2,NM_001126058.2,NM_001190347.1,NM_001190348.1,NM_001190349.1,NM_033317.4	45,45,45,45,45,45,45	450,2058,3995	AA,AC,CC		14.5581,38.7199,22.7433	benign,benign,benign,benign,benign,benign,benign	69/466,69/399,69/387,69/450,69/437,69/370,69/477	36004171	2958,10048	2203	4300	6503	SO:0001583	missense	93099	exon1			AAGGGCCTCACTG	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.207G>T	19.37:g.36004171C>A	ENSP00000342012:p.Glu69Asp	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_001190347	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	592	0.27106227106227104	181	0.3678861788617886	98	0.27071823204419887	204	0.35664335664335667	109	0.1437994722955145	C	13.20	2.165566	0.38217	0.387199	0.145581	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000429837;ENST00000419602;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T;T;T	0.18016	2.75;2.51;2.51;2.27;2.27;2.26;2.26;2.24	2.87	-5.74	0.02391	.	1.443180	0.04827	N	0.438056	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B;D;D;B;B;B;B	0.56035	0.002;0.974;0.974;0.002;0.0;0.0;0.0	B;D;D;B;B;B;B	0.70487	0.0;0.969;0.969;0.0;0.0;0.0;0.0	T	0.17776	-1.0358	9	0.40728	T	0.16	0.0114	8.0196	0.30402	0.216:0.6689:0.1151:0.0	rs12460932;rs61157480;rs12460932	69;69;69;69;69;69;69	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;C9J4P6;Q6E0U4-4;Q6E0U4	.;.;.;.;.;.;DMKN_HUMAN	D	69	ENSP00000342012:E69D;ENSP00000405503:E69D;ENSP00000391036:E69D;ENSP00000394908:E69D;ENSP00000415277:E69D;ENSP00000414743:E69D;ENSP00000388404:E69D;ENSP00000409513:E69D	ENSP00000342012:E69D	E	-	3	2	DMKN	40696011	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.678000	0.05209	-0.832000	0.04251	-0.555000	0.04198	GAG	C|0.751;A|0.249	0.249	strong		0.627	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048539	33048539	+	Missense_Mutation	SNP	T	T	A	rs1042117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33048539T>A	ENST00000418931.2	+	2	307	c.191T>A	c.(190-192)tTc>tAc	p.F64Y	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.F64Y|HLA-DPA1_ENST00000419277.1_5'Flank	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	64	Beta-1.		F -> L (in allele DPB1*02:02, allele DPB1*02:03, allele DPB1*05:01, allele DPB1*15:02, allele DPB1*17:02, allele DPB1*19:02, allele DPB1*21:01, allele DPB1*21:01, allele DPB1*22:01, allele DPB1*34:01, allele DPB1*36:01, allele DPB1*38:01, allele DPB1*44:01, allele DPB1*48:01, allele DPB1*58:01, allele DPB1*62:01, allele DPB1*63:01, allele DPB1*95:01 and allele DPB1*97:01; dbSNP:rs9277348).|F -> Y (in allele DPB1*01:01, allele DPB1*01:02, allele DPB1*09:02, allele DPB1*11:01, allele DPB1*13:01, allele DPB1*15:01, allele DPB1*20:02, allele DPB1*21:02, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*27:01, allele DPB1*39:01, allele DPB1*40:01, allele DPB1*49:01, allele DPB1*53:01, allele DPB1*65:01, allele DPB1*74:01, allele DPB1*85:01, allele DPB1*89:01 and allele DPB1*96:01; dbSNP:rs1042117).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CGGGAGGAGTTCGCGCGCTTC	0.612													.|||	1045	0.208666	0.4781	0.1124	5008	,	,		14806	0.0863		0.0944	False		,,,				2504	0.1564				p.F64Y		Atlas-SNP	.											HLA-DPB1,rectum,carcinoma,-1,1	HLA-DPB1	28	1	0			c.T191A						PASS	.	A	,,TYR/PHE	1181,1841		220,741,550	69.0	70.0	69.0		,,191	-7.9	0.0	6	dbSNP_86	69	519,4899		24,471,2214	no	utr-5,utr-5,missense	HLA-DPA1,HLA-DPB1	NM_001242524.1,NM_001242525.1,NM_002121.5	,,22	244,1212,2764	AA,AT,TT		9.5792,39.0801,20.1422	,,benign	,,64/259	33048539	1700,6740	1511	2709	4220	SO:0001583	missense	3115	exon2			AGGAGTTCGCGCG		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.191T>A	6.37:g.33048539T>A	ENSP00000408146:p.Phe64Tyr	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	43	0.741379	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	386|386	0.17673992673992675|0.17673992673992675	233|233	0.4735772357723577|0.4735772357723577	41|41	0.1132596685082873|0.1132596685082873	39|39	0.06818181818181818|0.06818181818181818	73|73	0.09630606860158311|0.09630606860158311	A|A	0.008|0.008	-1.922143|-1.922143	0.00498|0.00498	0.390801|0.390801	0.095792|0.095792	ENSG00000223865|ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835|ENST00000416804	T;T;T|.	0.00262|.	8.4;8.4;8.4|.	3.94|3.94	-7.87|-7.87	0.01183|0.01183	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);|.	1.117700|.	0.06944|.	N|.	0.813382|.	T|T	0.02888|0.02888	0.0086|0.0086	N|N	0.04508|0.04508	-0.205|-0.205	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.10450|.	0.005;0.003|.	T|T	0.13388|0.13388	-1.0511|-1.0511	9|4	0.02654|.	T|.	1|.	.|.	6.7891|6.7891	0.23689|0.23689	0.5161:0.0:0.1925:0.2914|0.5161:0.0:0.1925:0.2914	rs1042117;rs3173298;rs16868592;rs17221108;rs58131392|rs1042117;rs3173298;rs16868592;rs17221108;rs58131392	74;64|.	Q59GY1;P04440|.	.;DPB1_HUMAN|.	Y|T	64;64;64;41|31	ENSP00000408146:F64Y;ENSP00000439674:F64Y;ENSP00000412654:F41Y|.	ENSP00000389210:F64Y|.	F|S	+|+	2|1	0|0	HLA-DPB1|HLA-DPB1	33156517|33156517	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-4.771000|-4.771000	0.00188|0.00188	-3.676000|-3.676000	0.00122|0.00122	-5.201000|-5.201000	0.00001|0.00001	TTC|TCG	T|0.803;A|0.197	0.197	strong		0.612	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
GTDC1	79712	hgsc.bcm.edu	37	2	144899559	144899559	+	Missense_Mutation	SNP	C	C	A	rs3731958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:144899559C>A	ENST00000392869.2	-	5	563	c.411G>T	c.(409-411)atG>atT	p.M137I	GTDC1_ENST00000409298.1_Missense_Mutation_p.M137I|GTDC1_ENST00000241391.5_Missense_Mutation_p.M137I|GTDC1_ENST00000344850.4_Missense_Mutation_p.M137I|GTDC1_ENST00000392867.3_Missense_Mutation_p.M137I|GTDC1_ENST00000542155.1_Missense_Mutation_p.M137I|GTDC1_ENST00000409214.1_Missense_Mutation_p.M137I|GTDC1_ENST00000463875.2_Missense_Mutation_p.M8I	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	137			M -> I (in dbSNP:rs3731958). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15068588}.		biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		TAAATTTTCCCATGGAAGTGA	0.408													A|||	3424	0.683706	0.7443	0.7104	5008	,	,		18668	0.8413		0.5447	False		,,,				2504	0.5634				p.M137I		Atlas-SNP	.											.	GTDC1	61	.	0			c.G411T						PASS	.	A	ILE/MET,ILE/MET,ILE/MET	3209,1197	415.0+/-337.0	1146,917,140	69.0	72.0	71.0		411,411,411	4.9	1.0	2	dbSNP_107	71	4206,4392	582.1+/-391.3	1036,2134,1129	yes	missense,missense,missense	GTDC1	NM_001006636.3,NM_001164629.2,NM_024659.4	10,10,10	2182,3051,1269	AA,AC,CC		48.9184,27.1675,42.9791	benign,benign,benign	137/459,137/459,137/374	144899559	7415,5589	2203	4299	6502	SO:0001583	missense	79712	exon6			TTTTCCCATGGAA	AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			ENSG00000121964	ENSG00000121964		"""Glycosyltransferase group 1 domain containing"""	20887	protein-coding gene	gene with protein product	"""mannosyltransferase-like"""	610165				15068588, 21821951	Standard	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	Q4AE62	OTTHUMG00000131835	ENST00000392869.2:c.411G>T	2.37:g.144899559C>A	ENSP00000376608:p.Met137Ile	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_001006636	A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Missense_Mutation	SNP	ENST00000392869.2	37	CCDS33300.1	1487	0.6808608058608059	364	0.7398373983739838	234	0.6464088397790055	473	0.8269230769230769	416	0.5488126649076517	A	5.380	0.255412	0.10185	0.728325	0.489184	ENSG00000121964	ENST00000392869;ENST00000409214;ENST00000392867;ENST00000409298;ENST00000542155;ENST00000241391;ENST00000344850;ENST00000463875;ENST00000437114	T;T;T;T;T;T;T;T;T	0.78707	1.15;1.15;1.15;-1.2;1.15;1.15;1.15;1.78;1.15	6.11	4.9	0.64082	Glycosyltransferase family 1, N-terminal (1);	0.046782	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00193	-1.875	0.50467	P	1.24000000000013E-4	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0	T	0.42832	-0.9428	9	0.02654	T	1	-19.5844	13.0113	0.58733	0.7461:0.2539:0.0:0.0	rs3731958;rs17690312;rs52829764;rs61347201;rs3731958	137;137;137;137;137	G1UFN1;Q4AE62-2;B8ZZ45;Q4AE62;Q4AE62-3	.;.;.;GTDC1_HUMAN;.	I	137;137;137;137;137;137;137;8;137	ENSP00000376608:M137I;ENSP00000386581:M137I;ENSP00000376606:M137I;ENSP00000386691:M137I;ENSP00000438323:M137I;ENSP00000241391:M137I;ENSP00000339750:M137I;ENSP00000437964:M8I;ENSP00000403869:M137I	ENSP00000241391:M137I	M	-	3	0	GTDC1	144616029	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	1.888000	0.39708	1.134000	0.42165	-0.256000	0.11100	ATG	C|0.374;A|0.625	0.625	strong		0.408	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2	NM_024659	
CHRNB4	1143	hgsc.bcm.edu	37	15	78922229	78922229	+	Missense_Mutation	SNP	T	T	C	rs56218866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:78922229T>C	ENST00000261751.3	-	5	529	c.418A>G	c.(418-420)Agc>Ggc	p.S140G	RP11-335K5.2_ENST00000559120.1_RNA|CHRNB4_ENST00000560511.1_5'Flank|CHRNB4_ENST00000412074.2_Intron	NM_000750.3	NP_000741.1	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4 (neuronal)	140			S -> G (in dbSNP:rs56218866). {ECO:0000269|PubMed:11450844}.		action potential (GO:0001508)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|regulation of neurotransmitter secretion (GO:0046928)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			endometrium(7)|kidney(1)|lung(13)|prostate(1)	22					Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)	CACAGGACGCTGCCGTTGGAC	0.577													T|||	173	0.0345447	0.0461	0.0029	5008	,	,		20109	0.0843		0.008	False		,,,				2504	0.0174				p.S140G		Atlas-SNP	.											.	CHRNB4	59	.	0			c.A418G						PASS	.	T	GLY/SER	196,4196	112.5+/-150.6	3,190,2003	40.0	44.0	42.0		418	5.0	1.0	15	dbSNP_129	42	55,8529	32.3+/-84.9	0,55,4237	yes	missense	CHRNB4	NM_000750.3	56	3,245,6240	CC,CT,TT		0.6407,4.4627,1.9343	possibly-damaging	140/499	78922229	251,12725	2196	4292	6488	SO:0001583	missense	1143	exon5			GGACGCTGCCGTT	U48861	CCDS10306.1, CCDS58392.1	15q24	2012-02-11	2012-02-07		ENSG00000117971	ENSG00000117971		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1964	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 4 (neuronal)"""	118509	"""cholinergic receptor, nicotinic, beta polypeptide 4"""			2004777	Standard	NM_000750		Approved		uc002bed.1	P30926	OTTHUMG00000143860	ENST00000261751.3:c.418A>G	15.37:g.78922229T>C	ENSP00000261751:p.Ser140Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	73	26	0.356164	NM_000750	A4FTX5|E9PHE8|Q16607|Q4VBA5|Q8WXC8|Q9BQR4	Missense_Mutation	SNP	ENST00000261751.3	37	CCDS10306.1	66	0.03021978021978022	14	0.028455284552845527	2	0.0055248618784530384	41	0.07167832167832168	9	0.011873350923482849	T	11.88	1.772142	0.31411	0.044627	0.006407	ENSG00000117971	ENST00000261751	T	0.80033	-1.33	4.97	4.97	0.65823	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.39200	0.1069	M	0.66506	2.035	0.80722	D	1	P	0.52061	0.95	P	0.56700	0.804	T	0.66905	-0.5805	10	0.33940	T	0.23	.	14.6367	0.68694	0.0:0.0:0.0:1.0	rs56218866;rs61737498	140	P30926	ACHB4_HUMAN	G	140	ENSP00000261751:S140G	ENSP00000261751:S140G	S	-	1	0	CHRNB4	76709284	1.000000	0.71417	0.994000	0.49952	0.117000	0.20001	4.107000	0.57811	1.864000	0.54056	0.533000	0.62120	AGC	T|0.982;C|0.018	0.018	strong		0.577	CHRNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290108.1		
PPP1R17	10842	hgsc.bcm.edu	37	7	31732089	31732089	+	Missense_Mutation	SNP	C	C	G	rs3735422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:31732089C>G	ENST00000342032.3	+	2	662	c.34C>G	c.(34-36)Ctc>Gtc	p.L12V	PPP1R17_ENST00000409146.3_Missense_Mutation_p.L12V	NM_006658.4	NP_006649.2	O96001	PPR17_HUMAN	protein phosphatase 1, regulatory subunit 17	12			L -> V (in dbSNP:rs3735422). {ECO:0000269|PubMed:10051666, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9920894}.		central nervous system development (GO:0007417)|intracellular signal transduction (GO:0035556)|regulation of phosphatase activity (GO:0010921)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)	p.L12V(1)									GCCACTGGAACTCTCAGAAGA	0.448													C|||	797	0.159145	0.2057	0.1095	5008	,	,		19782	0.2341		0.1153	False		,,,				2504	0.0992				p.L12V		Atlas-SNP	.											C7orf16,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.C34G						PASS	.	C	VAL/LEU,VAL/LEU	757,3649	308.0+/-290.3	61,635,1507	117.0	102.0	107.0		34,34	4.3	1.0	7	dbSNP_107	107	962,7638	210.3+/-251.2	55,852,3393	yes	missense,missense	C7orf16	NM_001145123.2,NM_006658.4	32,32	116,1487,4900	GG,GC,CC		11.186,17.1811,13.217	benign,benign	12/105,12/156	31732089	1719,11287	2203	4300	6503	SO:0001583	missense	10842	exon2			CTGGAACTCTCAG	AF071789	CCDS5436.1, CCDS47570.1	7p15	2012-04-17	2011-10-11	2011-10-11	ENSG00000106341	ENSG00000106341		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16973	protein-coding gene	gene with protein product	"""G-substrate"""	604088	"""chromosome 7 open reading frame 16"""	C7orf16		10051666, 9920894	Standard	NM_006658		Approved	GSBS	uc003tcl.3	O96001	OTTHUMG00000128629	ENST00000342032.3:c.34C>G	7.37:g.31732089C>G	ENSP00000340125:p.Leu12Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	117	44	0.376068	NM_006658	B4DE58|Q9UDQ0	Missense_Mutation	SNP	ENST00000342032.3	37	CCDS5436.1	337	0.1543040293040293	88	0.17886178861788618	37	0.10220994475138122	131	0.229020979020979	81	0.10686015831134564	C	12.87	2.068223	0.36470	0.171811	0.11186	ENSG00000106341	ENST00000342032;ENST00000409146	T;T	0.36157	1.27;1.28	6.16	4.32	0.51571	.	0.255877	0.33235	N	0.005132	T	0.00012	0.0000	L	0.47716	1.5	0.35108	P	0.23413399999999995	P;B	0.37207	0.587;0.3	B;B	0.35182	0.197;0.164	T	0.23368	-1.0190	9	0.46703	T	0.11	-1.8379	5.263	0.15584	0.2395:0.5777:0.1105:0.0722	rs3735422;rs17852495;rs3735422	12;12	B4DE58;O96001	.;PPR17_HUMAN	V	12	ENSP00000340125:L12V;ENSP00000386459:L12V	ENSP00000340125:L12V	L	+	1	0	C7orf16	31698614	1.000000	0.71417	0.999000	0.59377	0.844000	0.47949	2.986000	0.49370	0.886000	0.36113	0.650000	0.86243	CTC	C|0.856;G|0.144	0.144	strong		0.448	PPP1R17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250498.1	NM_006658	
MYOM1	8736	hgsc.bcm.edu	37	18	3168816	3168816	+	Splice_Site	SNP	G	G	A	rs2230167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3168816G>A	ENST00000356443.4	-	9	1671	c.1338C>T	c.(1336-1338)aaC>aaT	p.N446N	MYOM1_ENST00000261606.7_Splice_Site_p.N446N|MYOM1_ENST00000400569.3_Splice_Site_p.N446N	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	446	Ig-like C2-type 2.				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						AAGACTCACCGTTTCTGTACC	0.438													A|||	1413	0.282149	0.3313	0.2061	5008	,	,		18941	0.2798		0.2356	False		,,,				2504	0.32				p.N446N		Atlas-SNP	.											.	MYOM1	192	.	0			c.C1338T						PASS	.	A	,	1167,2591		170,827,882	106.0	99.0	101.0		1338,1338	4.4	1.0	18	dbSNP_98	101	2179,6049		287,1605,2222	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	MYOM1	NM_003803.3,NM_019856.1	,	457,2432,3104	AA,AG,GG		26.4827,31.0538,27.9159	,	446/1686,446/1590	3168816	3346,8640	1879	4114	5993	SO:0001630	splice_region_variant	8736	exon9			CTCACCGTTTCTG	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.1339+1C>T	18.37:g.3168816G>A		Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	158	158	1	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			T|0.125;G|0.436;C|0.285;A|0.154	0.154	strong		0.438	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	Silent
MDN1	23195	hgsc.bcm.edu	37	6	90461235	90461235	+	Missense_Mutation	SNP	T	T	C	rs115558420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90461235T>C	ENST00000369393.3	-	23	3257	c.3142A>G	c.(3142-3144)Aag>Gag	p.K1048E	MDN1_ENST00000428876.1_Missense_Mutation_p.K1048E			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1048					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GTAGGCTCCTTGTCTCCCACC	0.478													T|||	9	0.00179712	0.0068	0.0	5008	,	,		18332	0.0		0.0	False		,,,				2504	0.0				p.K1048E		Atlas-SNP	.											MDN1,NS,carcinoma,+2,1	MDN1	478	1	0			c.A3142G						PASS	.	T	GLU/LYS	41,4365	44.6+/-78.6	0,41,2162	155.0	133.0	140.0		3142	4.5	1.0	6	dbSNP_132	140	0,8600		0,0,4300	yes	missense	MDN1	NM_014611.1	56	0,41,6462	CC,CT,TT		0.0,0.9305,0.3152	possibly-damaging	1048/5597	90461235	41,12965	2203	4300	6503	SO:0001583	missense	23195	exon23			GCTCCTTGTCTCC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.3142A>G	6.37:g.90461235T>C	ENSP00000358400:p.Lys1048Glu	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	186	90	0.483871	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	T	15.19	2.759315	0.49468	0.009305	0.0	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.39592	1.07;1.07;1.07	5.71	4.48	0.54585	.	0.162096	0.53938	D	0.000057	T	0.13200	0.0320	N	0.22421	0.69	0.38581	D	0.950177	B;B	0.19331	0.035;0.003	B;B	0.15484	0.008;0.013	T	0.06409	-1.0828	10	0.14656	T	0.56	.	12.5357	0.56140	0.0:0.0:0.1389:0.8611	.	975;1048	Q5T795;Q9NU22	.;MDN1_HUMAN	E	1048;1048;975	ENSP00000358400:K1048E;ENSP00000413970:K1048E;ENSP00000409664:K975E	ENSP00000358400:K1048E	K	-	1	0	MDN1	90517956	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	3.063000	0.49978	2.172000	0.68678	0.533000	0.62120	AAG	T|0.997;C|0.003	0.003	strong		0.478	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
TTN	7273	hgsc.bcm.edu	37	2	179594590	179594590	+	Silent	SNP	T	T	A	rs66523653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179594590T>A	ENST00000591111.1	-	61	17663	c.17439A>T	c.(17437-17439)acA>acT	p.T5813T	TTN_ENST00000589042.1_Silent_p.T6130T|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.T4886T|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|RP11-171I2.1_ENST00000590024.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12614	Ig-like 39.				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)			TAGGAGTGCCTGTTATTTGGC	0.408													T|||	78	0.0155751	0.0537	0.0101	5008	,	,		18115	0.0		0.0	False		,,,				2504	0.0				p.T6130T		Atlas-SNP	.											.	TTN	18412	.	0			c.A18390T						PASS	.	T	,,,	168,3604		3,162,1721	58.0	56.0	57.0		,14658,,	2.1	1.0	2	dbSNP_130	57	1,8225		0,1,4112	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	3,163,5833	AA,AT,TT		0.0122,4.4539,1.4086	,,,	,4886/33424,,	179594590	169,11829	1886	4113	5999	SO:0001819	synonymous_variant	7273	exon63			AGTGCCTGTTATT	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.17439A>T	2.37:g.179594590T>A		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	237	118	0.49789	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|0.984;A|0.016	0.016	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
IHH	3549	hgsc.bcm.edu	37	2	219920565	219920565	+	Silent	SNP	C	C	T	rs3731878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219920565C>T	ENST00000295731.6	-	3	599	c.600G>A	c.(598-600)acG>acA	p.T200T	MIR3131_ENST00000583592.1_RNA	NM_002181.3	NP_002172.2	Q14623	IHH_HUMAN	indian hedgehog	200					bone resorption (GO:0045453)|camera-type eye photoreceptor cell fate commitment (GO:0060220)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|chondrocyte proliferation (GO:0035988)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint development (GO:0072498)|epithelial cell morphogenesis (GO:0003382)|epithelial cell-cell adhesion (GO:0090136)|head morphogenesis (GO:0060323)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intein-mediated protein splicing (GO:0016539)|maternal process involved in female pregnancy (GO:0060135)|multicellular organism growth (GO:0035264)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of eye pigmentation (GO:0048074)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell differentiation in thymus (GO:0033085)|neuron development (GO:0048666)|osteoblast differentiation (GO:0001649)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of growth (GO:0040008)|response to estradiol (GO:0032355)|retinal pigment epithelium development (GO:0003406)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|somite development (GO:0061053)|vitelline membrane formation (GO:0030704)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|patched binding (GO:0005113)|peptidase activity (GO:0008233)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000188)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCAGCCGCCCGTCTTGGCTG	0.672													C|||	551	0.110024	0.1104	0.0951	5008	,	,		16118	0.1617		0.0865	False		,,,				2504	0.091				p.T200T		Atlas-SNP	.											.	IHH	33	.	0			c.G600A						PASS	.	C		421,3975		30,361,1807	16.0	18.0	18.0		600	-5.4	1.0	2	dbSNP_107	18	670,7918		28,614,3652	no	coding-synonymous	IHH	NM_002181.3		58,975,5459	TT,TC,CC		7.8016,9.5769,8.4026		200/412	219920565	1091,11893	2198	4294	6492	SO:0001819	synonymous_variant	3549	exon3			GCCGCCCGTCTTG	L38517	CCDS33380.1	2q33-q35	2013-02-15	2013-02-15		ENSG00000163501	ENSG00000163501			5956	protein-coding gene	gene with protein product		600726	"""Indian hedgehog (Drosophila) homolog"", ""Indian hedgehog homolog (Drosophila)"""			7590746, 14770182	Standard	NM_002181		Approved	HHG2, BDA1	uc002vjo.2	Q14623	OTTHUMG00000154631	ENST00000295731.6:c.600G>A	2.37:g.219920565C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	48	27	0.5625	NM_002181	B9EGM5|O43322|Q8N4B9	Silent	SNP	ENST00000295731.6	37	CCDS33380.1																																																																																			C|0.902;T|0.098	0.098	strong		0.672	IHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336408.2	NM_002181	
RAET1G	353091	hgsc.bcm.edu	37	6	150240829	150240829	+	Missense_Mutation	SNP	G	G	C	rs9397449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:150240829G>C	ENST00000367360.2	-	2	276	c.209C>G	c.(208-210)aCa>aGa	p.T70R	RAET1E-AS1_ENST00000605899.1_RNA|RAET1E-AS1_ENST00000446954.2_RNA|RP11-244K5.8_ENST00000606915.1_RNA|RAET1G_ENST00000479265.1_Missense_Mutation_p.T70R	NM_001001788.2	NP_001001788.2			retinoic acid early transcript 1G											NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|urinary_tract(1)	13		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		GGGTGTGACTGTCTTGCTGCC	0.517													g|||	1132	0.226038	0.1021	0.111	5008	,	,		20972	0.5317		0.1501	False		,,,				2504	0.2382				p.T70R		Atlas-SNP	.											.	RAET1G	31	.	0			c.C209G						PASS	.	C	ARG/THR	492,3914	780.8+/-414.5	27,438,1738	278.0	261.0	267.0		209	-2.0	0.0	6	dbSNP_119	267	1130,7470	767.0+/-407.6	83,964,3253	no	missense	RAET1G	NM_001001788.2	71	110,1402,4991	CC,CG,GG		13.1395,11.1666,12.4712	benign	70/335	150240829	1622,11384	2203	4300	6503	SO:0001583	missense	353091	exon2			GTGACTGTCTTGC	AY172579	CCDS43514.1	6q24.1-25.1	2009-04-29	2004-11-22		ENSG00000203722	ENSG00000203722			16795	protein-coding gene	gene with protein product		609244	"""retinoic acid early transcript 1G pseudogene"""			11827464, 15240696	Standard	NM_001001788		Approved	ULBP5	uc010kii.1	Q6H3X3	OTTHUMG00000015802	ENST00000367360.2:c.209C>G	6.37:g.150240829G>C	ENSP00000356329:p.Thr70Arg	Somatic	916	1	0.0010917		WXS	Illumina HiSeq	Phase_I	891	333	0.373737	NM_001001788		Missense_Mutation	SNP	ENST00000367360.2	37	CCDS43514.1	503	0.2303113553113553	47	0.09552845528455285	46	0.1270718232044199	308	0.5384615384615384	102	0.1345646437994723	C	2.358	-0.347240	0.05208	0.111666	0.131395	ENSG00000203722	ENST00000367360;ENST00000479265	T;T	0.00626	6.13;6.13	2.4	-2.05	0.07321	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00144	0.0004	L	0.29908	0.895	0.80722	P	0.0	B	0.21688	0.059	B	0.26094	0.066	T	0.43540	-0.9385	8	0.02654	T	1	.	0.992	0.01459	0.1668:0.1581:0.398:0.2771	rs9397449;rs60358512;rs9397449	70	Q6H3X3	RET1G_HUMAN	R	70	ENSP00000356329:T70R;ENSP00000417503:T70R	ENSP00000356329:T70R	T	-	2	0	RAET1G	150282522	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.137000	0.01304	-0.955000	0.03636	-3.292000	0.00046	ACA	G|0.807;C|0.193	0.193	strong		0.517	RAET1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042668.2		
ASPG	374569	hgsc.bcm.edu	37	14	104563932	104563932	+	Silent	SNP	G	G	T	rs1465163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:104563932G>T	ENST00000551177.1	+	5	563	c.471G>T	c.(469-471)ctG>ctT	p.L157L	ASPG_ENST00000455920.2_Silent_p.L157L|ASPG_ENST00000546892.2_Silent_p.L157L	NM_001080464.2	NP_001073933.2	Q86U10	LPP60_HUMAN	asparaginase	157	Asparaginase.|Asparaginase/glutaminase. {ECO:0000255|PROSITE-ProRule:PRU01068}.				asparagine metabolic process (GO:0006528)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)		1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|asparaginase activity (GO:0004067)|lysophospholipase activity (GO:0004622)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	11						GTGAGAACCTGCTGGGGGCAC	0.672													G|||	1204	0.240415	0.2648	0.2133	5008	,	,		15130	0.37		0.0646	False		,,,				2504	0.274				p.L157L		Atlas-SNP	.											Q86U10_HUMAN,NS,carcinoma,0,2	ASPG	34	2	0			c.G471T						PASS	.	G		763,3163		64,635,1264	18.0	22.0	20.0		471	4.4	1.0	14	dbSNP_88	20	463,7791		13,437,3677	no	coding-synonymous	ASPG	NM_001080464.2		77,1072,4941	TT,TG,GG		5.6094,19.4345,10.0657		157/574	104563932	1226,10954	1963	4127	6090	SO:0001819	synonymous_variant	374569	exon5			GAACCTGCTGGGG		CCDS45170.1, CCDS45170.2	14q32.33	2014-03-14	2014-03-14	2008-11-06	ENSG00000166183	ENSG00000166183	3.1.1.5, 3.5.1.1	"""Ankyrin repeat domain containing"""	20123	protein-coding gene	gene with protein product	"""60-kDa-lysophospholipase"""		"""chromosome 14 open reading frame 76"", ""asparaginase homolog (S. cerevisiae)"""	C14orf76			Standard	NM_001080464		Approved		uc001yoq.2	Q86U10		ENST00000551177.1:c.471G>T	14.37:g.104563932G>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	172	81	0.47093	NM_001080464	B9EGQ2|Q8IV80	Silent	SNP	ENST00000551177.1	37	CCDS45170.2	469	0.21474358974358973	129	0.2621951219512195	80	0.22099447513812154	215	0.3758741258741259	45	0.059366754617414245	G	9.001	0.980146	0.18812	0.194345	0.056094	ENSG00000166183	ENST00000551170	.	.	.	4.38	4.38	0.52667	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22382	-1.0218	3	.	.	.	-15.8172	15.6926	0.77466	0.0:0.0:1.0:0.0	rs1465163;rs1744287;rs59169409;rs1465163	.	.	.	S	94	.	.	A	+	1	0	ASPG	103633685	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	1.245000	0.32790	1.966000	0.57179	0.563000	0.77884	GCT	G|0.778;T|0.222	0.222	strong		0.672	ASPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407005.1	NM_001080464	
TJP2	9414	hgsc.bcm.edu	37	9	71851080	71851080	+	Silent	SNP	C	C	T	rs12340440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:71851080C>T	ENST00000377245.4	+	13	2125	c.1917C>T	c.(1915-1917)gaC>gaT	p.D639D	TJP2_ENST00000539225.1_Silent_p.D670D|TJP2_ENST00000265384.7_Silent_p.D639D|TJP2_ENST00000535702.1_Silent_p.D643D|TJP2_ENST00000453658.2_Silent_p.D616D|TJP2_ENST00000348208.4_Silent_p.D639D	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	639	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						CACTGTATGACGGCAAGCTGG	0.502													C|||	75	0.014976	0.0545	0.0043	5008	,	,		19727	0.0		0.0	False		,,,				2504	0.0				p.D670D		Atlas-SNP	.											TJP2,colon,carcinoma,0,1	TJP2	120	1	0			c.C2010T						scavenged	.	C	,,,,,	188,4218	120.4+/-158.0	5,178,2020	106.0	97.0	100.0		1848,1929,2010,1917,1917,1917	-3.3	1.0	9	dbSNP_120	100	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,,,,	5,179,6319	TT,TC,CC		0.0116,4.2669,1.4532	,,,,,	616/1021,643/1158,670/1222,639/994,639/1191,639/1044	71851080	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	9414	exon13			GTATGACGGCAAG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1917C>T	9.37:g.71851080C>T		Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	57	36	0.631579	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	37	CCDS6627.1																																																																																			C|0.983;T|0.017	0.017	strong		0.502	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
SCML4	256380	hgsc.bcm.edu	37	6	108029109	108029109	+	Silent	SNP	T	T	C	rs3734754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:108029109T>C	ENST00000369020.3	-	7	1325	c.1080A>G	c.(1078-1080)ccA>ccG	p.P360P	SCML4_ENST00000369022.2_Silent_p.P302P|SCML4_ENST00000369025.2_Silent_p.P118P	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	360					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		CCAGAGCCTGTGGGTCGGCGT	0.632													C|||	1125	0.224641	0.1778	0.1354	5008	,	,		18716	0.369		0.1978	False		,,,				2504	0.2301				p.P360P		Atlas-SNP	.											SCML4_ENST00000369020,colon,carcinoma,0,1	SCML4	65	1	0			c.A1080G						PASS	.	C		272,1112		23,226,443	48.0	57.0	54.0		1080	-8.3	0.3	6	dbSNP_107	54	573,2609		54,465,1072	no	coding-synonymous	SCML4	NM_198081.3		77,691,1515	CC,CT,TT		18.0075,19.6532,18.5064		360/415	108029109	845,3721	692	1591	2283	SO:0001819	synonymous_variant	256380	exon7			AGCCTGTGGGTCG		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.1080A>G	6.37:g.108029109T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	162	72	0.444444	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Silent	SNP	ENST00000369020.3	37	CCDS5060.2																																																																																			T|0.784;C|0.216	0.216	strong		0.632	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
ZNF598	90850	hgsc.bcm.edu	37	16	2050151	2050151	+	Silent	SNP	A	A	G	rs114023844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2050151A>G	ENST00000563630.1	-	9	1476	c.1234T>C	c.(1234-1236)Ttg>Ctg	p.L412L	ZNF598_ENST00000431526.1_Silent_p.L467L|ZNF598_ENST00000562103.1_Silent_p.L412L|AC005606.15_ENST00000567515.1_lincRNA			Q86UK7	ZN598_HUMAN	zinc finger protein 598	467							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						GGCAGCGCCAACCCCACAGGG	0.687													A|||	137	0.0273562	0.0998	0.0072	5008	,	,		16236	0.0		0.0	False		,,,				2504	0.0				p.L467L		Atlas-SNP	.											.	ZNF598	55	.	0			c.T1399C						PASS	.	A		210,3608		6,198,1705	22.0	26.0	25.0		1401	-6.5	0.0	16	dbSNP_132	25	0,8050		0,0,4025	no	coding-synonymous	ZNF598	NM_178167.2		6,198,5730	GG,GA,AA		0.0,5.5003,1.7695		467/905	2050151	210,11658	1909	4025	5934	SO:0001819	synonymous_variant	90850	exon11			GCGCCAACCCCAC	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.1234T>C	16.37:g.2050151A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Silent	SNP	ENST00000563630.1	37																																																																																				A|0.978;G|0.022	0.022	strong		0.687	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
MAP1B	4131	hgsc.bcm.edu	37	5	71489695	71489695	+	Silent	SNP	C	C	T	rs2227915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71489695C>T	ENST00000296755.7	+	5	811	c.513C>T	c.(511-513)atC>atT	p.I171I		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	171					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		AAACCCAGATCGGGGAGTTAC	0.433													C|||	156	0.0311502	0.1135	0.0086	5008	,	,		20619	0.0		0.0	False		,,,				2504	0.0				p.I171I	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.C513T						PASS	.	C		353,4053	182.9+/-210.6	14,325,1864	48.0	47.0	48.0		513	2.3	1.0	5	dbSNP_123	48	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	MAP1B	NM_005909.3		14,329,6160	TT,TC,CC		0.0465,8.0118,2.7449		171/2469	71489695	357,12649	2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			CCAGATCGGGGAG	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.513C>T	5.37:g.71489695C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																			C|0.968;T|0.032	0.032	strong		0.433	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
ARL11	115761	hgsc.bcm.edu	37	13	50205165	50205165	+	Missense_Mutation	SNP	G	G	C	rs35835937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:50205165G>C	ENST00000282026.1	+	2	917	c.582G>C	c.(580-582)aaG>aaC	p.K194N	ARL11_ENST00000490932.1_Intron	NM_138450.5	NP_612459.1	Q969Q4	ARL11_HUMAN	ADP-ribosylation factor-like 11	194					hematopoietic progenitor cell differentiation (GO:0002244)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			kidney(1)|large_intestine(4)|ovary(1)	6		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00174)|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;0.119)|Kidney(9;0.169)	GBM - Glioblastoma multiforme(99;1.67e-09)		GAGACAGCAAGAGATCTTGAT	0.522													G|||	38	0.00758786	0.028	0.0014	5008	,	,		20145	0.0		0.0	False		,,,				2504	0.0				p.K194N		Atlas-SNP	.											.	ARL11	26	.	0			c.G582C						PASS	.	G	ASN/LYS	90,4200		1,88,2056	6.0	6.0	6.0		582	0.8	0.0	13	dbSNP_126	6	0,8320		0,0,4160	yes	missense	ARL11	NM_138450.5	94	1,88,6216	CC,CG,GG		0.0,2.0979,0.7137	benign	194/197	50205165	90,12520	2145	4160	6305	SO:0001583	missense	115761	exon2			CAGCAAGAGATCT	AF441378	CCDS9419.1	13q14.12	2014-05-09			ENSG00000152213	ENSG00000152213		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	24046	protein-coding gene	gene with protein product		609351				12477932	Standard	NM_138450		Approved	ARLTS1, FLJ33930	uc001vdf.2	Q969Q4	OTTHUMG00000016919	ENST00000282026.1:c.582G>C	13.37:g.50205165G>C	ENSP00000282026:p.Lys194Asn	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	160	91	0.56875	NM_138450		Missense_Mutation	SNP	ENST00000282026.1	37	CCDS9419.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	G	12.80	2.047801	0.36085	0.020979	0.0	ENSG00000152213	ENST00000282026	T	0.61158	0.13	4.85	0.84	0.18912	.	.	.	.	.	T	0.17280	0.0415	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.20140	-1.0284	9	0.87932	D	0	.	5.8114	0.18467	0.1723:0.2988:0.5288:0.0	rs35835937	194	Q969Q4	ARL11_HUMAN	N	194	ENSP00000282026:K194N	ENSP00000282026:K194N	K	+	3	2	ARL11	49103166	0.006000	0.16342	0.000000	0.03702	0.014000	0.08584	0.717000	0.25851	0.195000	0.20347	0.561000	0.74099	AAG	G|0.993;C|0.007	0.007	strong		0.522	ARL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044929.2	NM_138450	
CD207	50489	hgsc.bcm.edu	37	2	71061108	71061108	+	Silent	SNP	G	G	A	rs17662453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71061108G>A	ENST00000410009.3	-	3	279	c.234C>T	c.(232-234)gtC>gtT	p.V78V		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	78					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						TCAGCAACTGGACATTGGTCT	0.517													G|||	712	0.142173	0.1059	0.219	5008	,	,		19065	0.0972		0.1839	False		,,,				2504	0.1401				p.V78V		Atlas-SNP	.											.	CD207	47	.	0			c.C234T						PASS	.	T		473,3465		30,413,1526	46.0	41.0	42.0		234	-2.0	0.0	2	dbSNP_123	42	1789,6511		190,1409,2551	no	coding-synonymous	CD207	NM_015717.3		220,1822,4077	AA,AG,GG		21.5542,12.0112,18.4834		78/329	71061108	2262,9976	1969	4150	6119	SO:0001819	synonymous_variant	50489	exon3			CAACTGGACATTG	AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"""C-type lectin domain containing"", ""CD molecules"""	17935	protein-coding gene	gene with protein product		604862	"""CD207 antigen, langerin"""			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.234C>T	2.37:g.71061108G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	105	61	0.580952	NM_015717		Silent	SNP	ENST00000410009.3	37																																																																																				G|0.858;A|0.142	0.142	strong		0.517	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
IFNL1	282618	hgsc.bcm.edu	37	19	39789115	39789115	+	Missense_Mutation	SNP	A	A	G	rs30461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39789115A>G	ENST00000333625.2	+	5	659	c.562A>G	c.(562-564)Aac>Gac	p.N188D		NM_172140.1	NP_742152.1	Q8IU54	IFNL1_HUMAN	interferon, lambda 1	188			N -> D (in dbSNP:rs30461). {ECO:0000269|PubMed:15489334}.		defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of cell proliferation (GO:0008285)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of memory T cell differentiation (GO:0043381)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of immune response (GO:0050778)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-28 receptor complex (GO:0032002)	interleukin-28 receptor binding (GO:0032003)|receptor binding (GO:0005102)										GGCCGATGGGAACCTGTGTCT	0.557													G|||	1260	0.251597	0.711	0.134	5008	,	,		18650	0.0377		0.1123	False		,,,				2504	0.0777				p.N188D		Atlas-SNP	.											.	.	.	.	0			c.A562G						PASS	.	G	ASP/ASN	2730,1676	509.4+/-367.2	868,994,341	167.0	164.0	165.0		562	1.2	0.0	19	dbSNP_76	165	912,7688	777.9+/-407.7	44,824,3432	yes	missense	IL29	NM_172140.1	23	912,1818,3773	GG,GA,AA		10.6047,38.039,28.0025	benign	188/201	39789115	3642,9364	2203	4300	6503	SO:0001583	missense	282618	exon5			GATGGGAACCTGT	AY129150	CCDS12531.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000182393	ENSG00000182393		"""Interferons"""	18363	protein-coding gene	gene with protein product		607403	"""interleukin 29"", ""interleukin 29 (interferon, lambda 1)"""	IL29			Standard	NM_172140		Approved	IL-29	uc002okv.3	Q8IU54		ENST00000333625.2:c.562A>G	19.37:g.39789115A>G	ENSP00000329991:p.Asn188Asp	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	170	170	1	NM_172140	A0AV25|Q17R34	Missense_Mutation	SNP	ENST00000333625.2	37	CCDS12531.1	503	0.2303113553113553	335	0.6808943089430894	57	0.1574585635359116	24	0.04195804195804196	87	0.11477572559366754	G	0.047	-1.261791	0.01445	0.61961	0.106047	ENSG00000182393	ENST00000333625	T	0.08984	3.03	3.56	1.19	0.21007	.	0.790683	0.11368	N	0.571161	T	0.00012	0.0000	N	0.00071	-2.275	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33954	-0.9848	9	0.02654	T	1	-6.121	5.7718	0.18257	0.114:0.3789:0.5071:0.0	rs30461;rs519075;rs16973311;rs52793576;rs57286404;rs30461	188	Q8IU54	IL29_HUMAN	D	188	ENSP00000329991:N188D	ENSP00000329991:N188D	N	+	1	0	IL29	44480955	0.003000	0.15002	0.000000	0.03702	0.013000	0.08279	0.481000	0.22260	-0.017000	0.14103	-0.642000	0.03964	AAC	A|0.733;G|0.267	0.267	strong		0.557	IFNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463834.1	NM_172140	
KRT78	196374	hgsc.bcm.edu	37	12	53240025	53240025	+	Missense_Mutation	SNP	C	C	T	rs10876360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53240025C>T	ENST00000304620.4	-	4	775	c.712G>A	c.(712-714)Gct>Act	p.A238T	KRT78_ENST00000359499.4_Missense_Mutation_p.A128T	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	238	Coil 1B.|Rod.		A -> T (in dbSNP:rs10876360).			extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						TCTCTCAGAGCCTCCAGCTTG	0.552													T|||	912	0.182109	0.4418	0.0303	5008	,	,		18231	0.2282		0.0119	False		,,,				2504	0.0665				p.A238T		Atlas-SNP	.											.	KRT78	41	.	0			c.G712A						PASS	.	T	THR/ALA	1673,2733	654.8+/-399.8	327,1019,857	94.0	79.0	84.0		712	-2.1	0.0	12	dbSNP_120	84	101,8499	814.9+/-407.0	1,99,4200	yes	missense	KRT78	NM_173352.2	58	328,1118,5057	TT,TC,CC		1.1744,37.9709,13.6399	benign	238/521	53240025	1774,11232	2203	4300	6503	SO:0001583	missense	196374	exon4			TCAGAGCCTCCAG	AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.712G>A	12.37:g.53240025C>T	ENSP00000306261:p.Ala238Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Missense_Mutation	SNP	ENST00000304620.4	37	CCDS8840.1	333	0.15247252747252749	200	0.4065040650406504	9	0.024861878453038673	115	0.20104895104895104	9	0.011873350923482849	T	1.697	-0.502457	0.04261	0.379709	0.011744	ENSG00000170423	ENST00000359499;ENST00000304620;ENST00000539860;ENST00000547110	D;D;D	0.88277	-2.36;-2.36;-2.36	4.45	-2.12	0.07165	Filament (1);	.	.	.	.	T	0.00012	0.0000	N	0.02103	-0.685	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.12293	-1.0553	8	0.18710	T	0.47	.	5.0491	0.14499	0.4862:0.2819:0.0:0.2318	rs10876360;rs52810718;rs10876360	238	Q8N1N4	K2C78_HUMAN	T	128;238;9;9	ENSP00000352479:A128T;ENSP00000306261:A238T;ENSP00000447817:A9T	ENSP00000306261:A238T	A	-	1	0	KRT78	51526292	0.000000	0.05858	0.004000	0.12327	0.055000	0.15305	-2.571000	0.00913	-0.617000	0.05664	-1.419000	0.01111	GCT	C|0.848;T|0.152	0.152	strong		0.552	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352	
PSPH	5723	hgsc.bcm.edu	37	7	56088825	56088825	+	Missense_Mutation	SNP	T	T	A	rs74445297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:56088825T>A	ENST00000395471.3	-	4	886	c.81A>T	c.(79-81)agA>agT	p.R27S	PSPH_ENST00000275605.3_Missense_Mutation_p.R27S|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	27					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TTCCTTCTTCTCTGATGACCG	0.448																																					p.R27S		Atlas-SNP	.											.	PSPH	23	.	0			c.A81T						PASS	.						133.0	99.0	110.0					7																	56088825		2203	4300	6503	SO:0001583	missense	5723	exon4			TTCTTCTCTGATG	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.81A>T	7.37:g.56088825T>A	ENSP00000378854:p.Arg27Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	291	84	0.28866	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	702	0.32142857142857145	240	0.4878048780487805	94	0.2596685082872928	224	0.3916083916083916	144	0.18997361477572558	T	8.101	0.776745	0.16120	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626;ENST00000419984;ENST00000421312	D;D;D;D;D	0.83992	-1.58;-1.58;-1.58;-1.79;-1.79	5.6	0.722	0.18225	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.155391	0.64402	D	0.000020	T	0.00012	0.0000	L	0.48362	1.52	0.58432	D	0.999996	B;B	0.06786	0.001;0.001	B;B	0.14023	0.006;0.01	T	0.43327	-0.9398	10	0.27082	T	0.32	-15.084	8.7161	0.34411	0.0:0.4041:0.0:0.5959	.	27;27	Q53EY1;P78330	.;SERB_HUMAN	S	27	ENSP00000275605:R27S;ENSP00000378854:R27S;ENSP00000398653:R27S;ENSP00000399660:R27S;ENSP00000390952:R27S	ENSP00000275605:R27S	R	-	3	2	PSPH	56056319	0.997000	0.39634	0.998000	0.56505	0.198000	0.23893	0.542000	0.23222	0.108000	0.17862	0.482000	0.46254	AGA	T|0.752;A|0.248	0.248	strong		0.448	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
ZPBP2	124626	hgsc.bcm.edu	37	17	38028635	38028635	+	Silent	SNP	T	T	C	rs61737283	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38028635T>C	ENST00000348931.4	+	5	710	c.519T>C	c.(517-519)agT>agC	p.S173S	ZPBP2_ENST00000377940.3_Silent_p.S151S|ZPBP2_ENST00000584588.1_Intron	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	173			S -> I (in dbSNP:rs11557467). {ECO:0000269|PubMed:14702039}.		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)			TCTTGGATAGTCTAATTTCTG	0.358													T|||	148	0.0295527	0.1089	0.0058	5008	,	,		14981	0.0		0.0	False		,,,				2504	0.0				p.S173S		Atlas-SNP	.											.	ZPBP2	33	.	0			c.T519C						PASS	.																																			SO:0001819	synonymous_variant	124626	exon5			GGATAGTCTAATT	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.519T>C	17.37:g.38028635T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_199321	A8K8L8|Q6X783|Q86XL5	Silent	SNP	ENST00000348931.4	37	CCDS11352.1																																																																																			T|0.868;C|0.132	0.132	strong		0.358	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844	
QRICH2	84074	hgsc.bcm.edu	37	17	74289875	74289875	+	Silent	SNP	C	C	T	rs6501882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74289875C>T	ENST00000262765.5	-	4	614	c.435G>A	c.(433-435)ggG>ggA	p.G145G		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	145										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						GCTGCTGTCTCCCAGTACCAG	0.562													C|||	2351	0.469449	0.7073	0.3098	5008	,	,		19445	0.5724		0.2753	False		,,,				2504	0.3548				p.G145G		Atlas-SNP	.											.	QRICH2	143	.	0			c.G435A						PASS	.	C		2925,1481	678.2+/-403.5	977,971,255	57.0	59.0	58.0		435	-5.1	0.0	17	dbSNP_116	58	2485,6115	405.8+/-348.6	347,1791,2162	no	coding-synonymous	QRICH2	NM_032134.1		1324,2762,2417	TT,TC,CC		28.8953,33.6133,41.5962		145/1664	74289875	5410,7596	2203	4300	6503	SO:0001819	synonymous_variant	84074	exon4			CTGTCTCCCAGTA	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.435G>A	17.37:g.74289875C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	136	65	0.477941	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																			C|0.558;T|0.442	0.442	strong		0.562	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
DNAH6	1768	hgsc.bcm.edu	37	2	84924783	84924783	+	Missense_Mutation	SNP	G	G	C	rs73943384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:84924783G>C	ENST00000237449.6	+	46	7617	c.7609G>C	c.(7609-7611)Gag>Cag	p.E2537Q	DNAH6_ENST00000602588.1_Missense_Mutation_p.E509Q|DNAH6_ENST00000398278.2_Missense_Mutation_p.E2488Q|DNAH6_ENST00000389394.3_Missense_Mutation_p.E2537Q			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2537	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GGATGAACTGGAGCAGGTTTT	0.428													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		16198	0.0		0.0	False		,,,				2504	0.0				p.E2537Q		Atlas-SNP	.											.	DNAH6	194	.	0			c.G7609C						PASS	.	G	GLN/GLU	42,1342		0,42,650	138.0	126.0	130.0		7609	5.7	1.0	2	dbSNP_130	130	1,3181		0,1,1590	yes	missense	DNAH6	NM_001370.1	29	0,43,2240	CC,CG,GG		0.0314,3.0347,0.9417	probably-damaging	2537/4159	84924783	43,4523	692	1591	2283	SO:0001583	missense	1768	exon47			GAACTGGAGCAGG	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.7609G>C	2.37:g.84924783G>C	ENSP00000237449:p.Glu2537Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	G	25.4	4.630590	0.87660	0.030347	3.14E-4	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.56103	0.73;0.48;0.73	5.67	5.67	0.87782	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	.	.	.	.	T	0.38401	0.1039	L	0.57130	1.785	0.47949	D	0.999553	D;D	0.67145	0.996;0.99	D;D	0.70716	0.97;0.962	T	0.57751	-0.7757	9	0.49607	T	0.09	.	18.5426	0.91035	0.0:0.0:1.0:0.0	.	2537;2488	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	Q	2537;2488;2537	ENSP00000374045:E2537Q;ENSP00000381326:E2488Q;ENSP00000237449:E2537Q	ENSP00000237449:E2537Q	E	+	1	0	DNAH6	84778294	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.379000	0.59575	2.682000	0.91365	0.484000	0.47621	GAG	G|0.989;C|0.011	0.011	strong		0.428	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
GABRB1	2560	hgsc.bcm.edu	37	4	47408850	47408850	+	Silent	SNP	C	C	T	rs115114447	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:47408850C>T	ENST00000295454.3	+	8	1279	c.987C>T	c.(985-987)taC>taT	p.Y329Y	GABRB1_ENST00000538619.1_Silent_p.Y259Y	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	329					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|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)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					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)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|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)	TTGTAAATTACATCTTCTTTG	0.423													C|||	77	0.0153754	0.056	0.0043	5008	,	,		19488	0.0		0.0	False		,,,				2504	0.0				p.Y329Y		Atlas-SNP	.											GABRB1,colon,carcinoma,+1,1	GABRB1	107	1	0			c.C987T						PASS	.	C		236,4170	138.4+/-174.2	4,228,1971	167.0	161.0	163.0		987	1.1	1.0	4	dbSNP_132	163	4,8596	1.2+/-3.3	0,4,4296	no	coding-synonymous	GABRB1	NM_000812.3		4,232,6267	TT,TC,CC		0.0465,5.3563,1.8453		329/475	47408850	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	2560	exon8			AAATTACATCTTC		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4081	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 1"""	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.987C>T	4.37:g.47408850C>T		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	235	235	1	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Silent	SNP	ENST00000295454.3	37	CCDS3474.1																																																																																			C|0.982;T|0.018	0.018	strong		0.423	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1		
PASK	23178	hgsc.bcm.edu	37	2	242066314	242066314	+	Silent	SNP	T	T	C	rs2240542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242066314T>C	ENST00000405260.1	-	10	2714	c.2016A>G	c.(2014-2016)gcA>gcG	p.A672A	PASK_ENST00000544142.1_Silent_p.A486A|PASK_ENST00000358649.4_Silent_p.A672A|PASK_ENST00000539818.1_Silent_p.A456A|PASK_ENST00000403638.3_Silent_p.A672A|PASK_ENST00000234040.4_Silent_p.A672A	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	672					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		CCAGGGCTCCTGCAAGGCTCA	0.607													C|||	2145	0.428315	0.6331	0.415	5008	,	,		20173	0.4077		0.2575	False		,,,				2504	0.3579				p.A672A		Atlas-SNP	.											.	PASK	230	.	0			c.A2016G						PASS	.	C		2596,1810	526.5+/-371.9	755,1086,362	113.0	124.0	120.0		2016	-1.6	0.0	2	dbSNP_98	120	2553,6047	686.7+/-404.1	371,1811,2118	yes	coding-synonymous	PASK	NM_015148.2		1126,2897,2480	CC,CT,TT		29.686,41.0803,39.5894		672/1324	242066314	5149,7857	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon10			GGCTCCTGCAAGG	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2016A>G	2.37:g.242066314T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	128	45	0.351562	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			T|0.595;C|0.405	0.405	strong		0.607	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
PARM1	25849	hgsc.bcm.edu	37	4	75937971	75937971	+	Missense_Mutation	SNP	C	C	T	rs3822109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:75937971C>T	ENST00000307428.7	+	2	592	c.380C>T	c.(379-381)tCg>tTg	p.S127L	RP11-44F21.2_ENST00000513770.1_RNA|PARM1_ENST00000513238.1_Intron	NM_015393.3	NP_056208.2	Q6UWI2	PARM1_HUMAN	prostate androgen-regulated mucin-like protein 1	127			S -> L (in dbSNP:rs3822109). {ECO:0000269|PubMed:11230166}.		positive regulation of telomerase activity (GO:0051973)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)		p.S127L(1)		cervix(1)|endometrium(2)|lung(4)|ovary(1)	8						GAACACAGCTCGGGCACTCCT	0.582													C|||	1666	0.332668	0.2905	0.2767	5008	,	,		20761	0.1617		0.4612	False		,,,				2504	0.4734				p.S127L		Atlas-SNP	.											PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	1	Substitution - Missense(1)	stomach(1)	c.C380T						PASS	.	C	LEU/SER	1319,2921		213,893,1014	140.0	146.0	144.0		380	-3.3	0.0	4	dbSNP_107	144	3658,4810		809,2040,1385	yes	missense	PARM1	NM_015393.3	145	1022,2933,2399	TT,TC,CC		43.1979,31.1085,39.1643	benign	127/311	75937971	4977,7731	2120	4234	6354	SO:0001583	missense	25849	exon2			ACAGCTCGGGCAC	AK022311	CCDS47077.1	4q13.3-q21.3	2010-02-17	2009-09-28		ENSG00000169116	ENSG00000169116			24536	protein-coding gene	gene with protein product	"""Prostatic androgen-repressed message 1"", ""Castration-induced prostatic apoptosis-related protein 1"", ""WSC4, cell wall integrity and stress response component 4 homolog (S. cerevisiae)"""					10499539, 12772192, 18027867	Standard	NM_015393		Approved	DKFZP564O0823, Cipar1, WSC4	uc003hih.2	Q6UWI2	OTTHUMG00000160827	ENST00000307428.7:c.380C>T	4.37:g.75937971C>T	ENSP00000370224:p.Ser127Leu	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	165	83	0.50303	NM_015393	B3KMQ9|Q96DV8|Q9Y4S1	Missense_Mutation	SNP	ENST00000307428.7	37	CCDS47077.1	698	0.31959706959706957	142	0.2886178861788618	99	0.27348066298342544	88	0.15384615384615385	369	0.4868073878627968	C	8.244	0.807576	0.16467	0.311085	0.431979	ENSG00000169116	ENST00000307428	T	0.47869	0.83	5.34	-3.27	0.05048	.	1.740060	0.02914	N	0.137058	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39542	-0.9609	9	0.20519	T	0.43	7.3413	2.3283	0.04228	0.1265:0.2844:0.1241:0.465	rs3822109;rs17196707;rs52813318;rs59916458;rs3822109	127	Q6UWI2	PARM1_HUMAN	L	127	ENSP00000370224:S127L	ENSP00000370224:S127L	S	+	2	0	PARM1	76156995	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.478000	0.06575	-1.309000	0.02315	-0.993000	0.02533	TCG	C|0.691;T|0.309	0.309	strong		0.582	PARM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362494.1	NM_015393	
GNB5	10681	hgsc.bcm.edu	37	15	52446200	52446200	+	Silent	SNP	G	G	A	rs6493537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52446200G>A	ENST00000261837.7	-	4	377	c.312C>T	c.(310-312)caC>caT	p.H104H	GNB5_ENST00000396335.4_Silent_p.H62H|GNB5_ENST00000560116.1_Silent_p.H62H|GNB5_ENST00000358784.7_Silent_p.H62H	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	104					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		CTTTGTTCCCGTGGCCTTTGA	0.562													A|||	650	0.129792	0.3442	0.1167	5008	,	,		19422	0.0258		0.0417	False		,,,				2504	0.047				p.H104H		Atlas-SNP	.											.	GNB5	28	.	0			c.C312T						PASS	.	A	,	1362,3028	690.6+/-405.3	225,912,1058	152.0	129.0	137.0		186,312	-6.0	0.9	15	dbSNP_116	137	334,8252	803.8+/-407.3	5,324,3964	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	230,1236,5022	AA,AG,GG		3.8901,31.0251,13.0703	,	62/354,104/396	52446200	1696,11280	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon4			GTTCCCGTGGCCT	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"""WD repeat domain containing"""	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.312C>T	15.37:g.52446200G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			G|0.873;A|0.127	0.127	strong		0.562	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1		
DNAH10	196385	hgsc.bcm.edu	37	12	124417989	124417989	+	Missense_Mutation	SNP	C	C	T	rs61746561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124417989C>T	ENST00000409039.3	+	76	13079	c.13054C>T	c.(13054-13056)Cgc>Tgc	p.R4352C	DNAH10OS_ENST00000514254.2_Intron|RP11-380L11.3_ENST00000602292.1_RNA|CCDC92_ENST00000544798.1_Intron	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4352					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)		GCCACTGGACCGCTCCACCTT	0.617													C|||	70	0.0139776	0.0507	0.0014	5008	,	,		18672	0.0		0.001	False		,,,				2504	0.001				p.R4352C		Atlas-SNP	.											.	DNAH10	888	.	0			c.C13054T						PASS	.	C	CYS/ARG	149,3855		4,141,1857	40.0	43.0	42.0		13054	5.2	1.0	12	dbSNP_129	42	7,8303		0,7,4148	yes	missense	DNAH10	NM_207437.3	180	4,148,6005	TT,TC,CC		0.0842,3.7213,1.2669	probably-damaging	4352/4472	124417989	156,12158	2002	4155	6157	SO:0001583	missense	196385	exon76			CTGGACCGCTCCA	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.13054C>T	12.37:g.124417989C>T	ENSP00000386770:p.Arg4352Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	34	5.328033	0.95733	0.037213	8.42E-4	ENSG00000197653	ENST00000409039	T	0.09255	3.0	5.18	5.18	0.71444	Dynein heavy chain (1);	0.139800	0.49305	D	0.000149	T	0.11410	0.0278	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	T	0.02942	-1.1091	10	0.66056	D	0.02	.	18.3051	0.90177	0.0:1.0:0.0:0.0	rs61746561	4352	Q8IVF4	DYH10_HUMAN	C	4352	ENSP00000386770:R4352C	ENSP00000386770:R4352C	R	+	1	0	DNAH10	122983942	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.889000	0.69766	2.413000	0.81919	0.561000	0.74099	CGC	C|0.991;T|0.009	0.009	strong		0.617	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
CCDC54	84692	hgsc.bcm.edu	37	3	107096547	107096547	+	Missense_Mutation	SNP	G	G	A	rs709564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:107096547G>A	ENST00000261058.1	+	1	360	c.113G>A	c.(112-114)cGg>cAg	p.R38Q		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	38			R -> Q (in dbSNP:rs709564). {ECO:0000269|PubMed:15489334}.							NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						TGTAAGATTCGGCACCAAGAT	0.403													G|||	2500	0.499201	0.3442	0.5216	5008	,	,		21589	0.8919		0.2545	False		,,,				2504	0.5399				p.R38Q		Atlas-SNP	.											.	CCDC54	56	.	0			c.G113A						PASS	.	G	GLN/ARG	1442,2964	469.4+/-355.4	262,918,1023	138.0	138.0	138.0		113	-1.0	0.0	3	dbSNP_86	138	2032,6568	354.9+/-329.7	241,1550,2509	yes	missense	CCDC54	NM_032600.2	43	503,2468,3532	AA,AG,GG		23.6279,32.7281,26.7107	benign	38/329	107096547	3474,9532	2203	4300	6503	SO:0001583	missense	84692	exon1			AGATTCGGCACCA	AF367469	CCDS2949.1	3q13.12	2013-10-11			ENSG00000138483	ENSG00000138483			30703	protein-coding gene	gene with protein product	"""sperm protein 17"""					15257753	Standard	NM_032600		Approved	NYD-SP17, FLJ25362, SP17	uc003dwi.1	Q8NEL0	OTTHUMG00000159169	ENST00000261058.1:c.113G>A	3.37:g.107096547G>A	ENSP00000261058:p.Arg38Gln	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	163	90	0.552147	NM_032600	Q96A43	Missense_Mutation	SNP	ENST00000261058.1	37	CCDS2949.1	1018	0.4661172161172161	154	0.3130081300813008	163	0.45027624309392267	507	0.8863636363636364	194	0.2559366754617414	G	0.008	-1.878422	0.00537	0.327281	0.236279	ENSG00000138483	ENST00000261058	T	0.41065	1.01	5.44	-1.05	0.10036	.	1.036590	0.07686	N	0.937852	T	0.00012	0.0000	N	0.05280	-0.08	0.80722	P	0.0	B	0.12630	0.006	B	0.08055	0.003	T	0.28618	-1.0038	9	0.11794	T	0.64	1.0994	8.8703	0.35311	0.515:0.0:0.485:0.0	rs709564;rs17845930;rs17858909;rs52834280;rs60910251;rs709564	38	Q8NEL0	CCD54_HUMAN	Q	38	ENSP00000261058:R38Q	ENSP00000261058:R38Q	R	+	2	0	CCDC54	108579237	0.000000	0.05858	0.045000	0.18777	0.112000	0.19704	-0.131000	0.10482	-0.180000	0.10637	-0.482000	0.04802	CGG	G|0.632;A|0.368	0.368	strong		0.403	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1	NM_032600	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057635	46057635	+	Missense_Mutation	SNP	G	G	A	rs114397261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057635G>A	ENST00000380095.1	+	1	363	c.301G>A	c.(301-303)Gtg>Atg	p.V101M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	101	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						tgtctgctgtgtgcccgtctg	0.632													A|||	306	0.0611022	0.2118	0.0173	5008	,	,		18765	0.002		0.001	False		,,,				2504	0.0112				p.V101M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G301A						PASS	.	A	,MET/VAL	438,3968		76,286,1841	130.0	123.0	125.0		,301	-1.7	0.0	21	dbSNP_132	125	2,8594		0,2,4296	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,21	76,288,6137	AA,AG,GG		0.0233,9.941,3.3841	,possibly-damaging	,101/252	46057635	440,12562	2203	4298	6501	SO:0001583	missense	353333	exon1			TGCTGTGTGCCCG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.301G>A	21.37:g.46057635G>A	ENSP00000369438:p.Val101Met	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	273	120	0.43956	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	a	1.285	-0.609223	0.03690	0.09941	2.33E-4	ENSG00000221859	ENST00000380095	T	0.01430	4.9	2.86	-1.68	0.08212	.	.	.	.	.	T	0.00073	0.0002	L	0.36672	1.1	0.09310	N	1	B	0.26195	0.144	B	0.34452	0.183	T	0.44128	-0.9348	9	0.44086	T	0.13	.	9.7593	0.40522	0.4446:0.0:0.5554:0.0	.	101	P60014	KR10A_HUMAN	M	101	ENSP00000369438:V101M	ENSP00000369438:V101M	V	+	1	0	KRTAP10-10	44882063	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.140000	0.10342	-1.728000	0.01366	-2.786000	0.00116	GTG	G|0.928;A|0.072	0.072	strong		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103158278	103158278	+	Missense_Mutation	SNP	C	C	T	rs10895391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:103158278C>T	ENST00000375735.2	+	75	11183	c.11039C>T	c.(11038-11040)gCg>gTg	p.A3680V	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.A3687V	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3680			A -> V (in dbSNP:rs10895391). {ECO:0000269|PubMed:12056414}.		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)		GTAGTACAGGCGCTAAGACCG	0.328													C|||	1434	0.286342	0.1725	0.2464	5008	,	,		17114	0.3016		0.338	False		,,,				2504	0.3998				p.A3687V		Atlas-SNP	.											DYNC2H1_ENST00000398093,colon,carcinoma,-1,1	DYNC2H1	246	1	0			c.C11060T						PASS	.	C	VAL/ALA,VAL/ALA	742,2904		81,580,1162	89.0	83.0	85.0		11060,11039	5.8	1.0	11	dbSNP_120	85	2869,5279		511,1847,1716	yes	missense,missense	DYNC2H1	NM_001080463.1,NM_001377.2	64,64	592,2427,2878	TT,TC,CC		35.2111,20.3511,30.6173	benign,benign	3687/4315,3680/4308	103158278	3611,8183	1823	4074	5897	SO:0001583	missense	79659	exon76			TACAGGCGCTAAG	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.11039C>T	11.37:g.103158278C>T	ENSP00000364887:p.Ala3680Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	155	59	0.380645	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	608	0.2783882783882784	90	0.18292682926829268	102	0.281767955801105	157	0.2744755244755245	259	0.341688654353562	C	21.8	4.207195	0.79127	0.203511	0.352111	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.09911	2.93;2.93	5.79	5.79	0.91817	Dynein heavy chain (1);	0.054526	0.64402	D	0.000001	T	0.00012	0.0000	M	0.63428	1.95	0.09310	P	0.9999999859533	P;P	0.46656	0.596;0.882	B;B	0.38655	0.201;0.278	T	0.53143	-0.8480	9	0.45353	T	0.12	.	19.6264	0.95679	0.0:1.0:0.0:0.0	rs10895391;rs52827900;rs58780461;rs10895391	3680;3687	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	V	3680;3687	ENSP00000364887:A3680V;ENSP00000381167:A3687V	ENSP00000364887:A3680V	A	+	2	0	DYNC2H1	102663488	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	6.123000	0.71614	2.746000	0.94184	0.655000	0.94253	GCG	C|0.709;T|0.291	0.291	strong		0.328	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
PRDM14	63978	hgsc.bcm.edu	37	8	70967607	70967607	+	Silent	SNP	T	T	C	rs3750225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:70967607T>C	ENST00000276594.2	-	7	1617	c.1416A>G	c.(1414-1416)caA>caG	p.Q472Q		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	472					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|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(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			GGCTGGAAGATTGAGAGAAAC	0.393													C|||	3594	0.717652	0.8442	0.6282	5008	,	,		19026	0.7302		0.6143	False		,,,				2504	0.7035				p.Q472Q	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											.	PRDM14	102	.	0			c.A1416G						PASS	.	C		3575,831	329.9+/-301.2	1438,699,66	168.0	143.0	152.0		1416	3.3	1.0	8	dbSNP_107	152	5414,3186	482.2+/-370.8	1703,2008,589	no	coding-synonymous	PRDM14	NM_024504.2		3141,2707,655	CC,CT,TT		37.0465,18.8606,30.8857		472/572	70967607	8989,4017	2203	4300	6503	SO:0001819	synonymous_variant	63978	exon7			GGAAGATTGAGAG	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"""Zinc fingers, C2H2-type"""	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1416A>G	8.37:g.70967607T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_024504	Q86UX9	Silent	SNP	ENST00000276594.2	37	CCDS6206.1																																																																																			T|0.294;C|0.706	0.706	strong		0.393	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1		
UNC5B	219699	hgsc.bcm.edu	37	10	73039594	73039594	+	Silent	SNP	C	C	T	rs80333477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73039594C>T	ENST00000335350.6	+	2	512	c.96C>T	c.(94-96)agC>agT	p.S32S	UNC5B_ENST00000373192.4_Silent_p.S32S	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	32					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						ATTCTGGCAGCGAGGTGCTCC	0.657													C|||	79	0.0157748	0.0582	0.0029	5008	,	,		17163	0.0		0.0	False		,,,				2504	0.0				p.S32S		Atlas-SNP	.											.	UNC5B	123	.	0			c.C96T						PASS	.	C		186,4220	118.8+/-156.5	4,178,2021	37.0	32.0	34.0		96	-3.5	0.3	10	dbSNP_132	34	0,8600		0,0,4300	no	coding-synonymous	UNC5B	NM_170744.4		4,178,6321	TT,TC,CC		0.0,4.2215,1.4301		32/946	73039594	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	219699	exon2			TGGCAGCGAGGTG	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.96C>T	10.37:g.73039594C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	177	97	0.548023	NM_001244889	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																			C|0.987;T|0.013	0.013	strong		0.657	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
RPH3AL	9501	hgsc.bcm.edu	37	17	171137	171137	+	Silent	SNP	C	C	A	rs78269977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:171137C>A	ENST00000331302.7	-	4	454	c.147G>T	c.(145-147)ccG>ccT	p.P49P	RPH3AL_ENST00000576001.1_5'Flank|RP11-1260E13.1_ENST00000570501.1_RNA|RPH3AL_ENST00000323434.8_Silent_p.P49P|RPH3AL_ENST00000536489.2_Silent_p.P49P|RP11-1260E13.1_ENST00000572998.1_RNA	NM_001190411.1|NM_006987.3	NP_001177340.1|NP_008918.1	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	49	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of protein secretion (GO:0050714)|regulation of calcium ion-dependent exocytosis (GO:0017158)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|secretory granule membrane (GO:0030667)	cytoskeletal protein binding (GO:0008092)|metal ion binding (GO:0046872)			NS(2)|breast(1)|kidney(1)|large_intestine(1)|skin(1)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		CCACCTCCGCCGGGCTGAGGT	0.677													C|||	346	0.0690895	0.0832	0.0562	5008	,	,		14011	0.0288		0.0835	False		,,,				2504	0.0859				p.P49P		Atlas-SNP	.											.	RPH3AL	18	.	0			c.G147T						PASS	.	C	,,,	339,4067	178.3+/-207.1	17,305,1881	86.0	82.0	83.0		147,147,147,147	-10.1	0.0	17	dbSNP_131	83	823,7777	191.1+/-237.4	35,753,3512	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RPH3AL	NM_001190411.1,NM_001190412.1,NM_001190413.1,NM_006987.3	,,,	52,1058,5393	AA,AC,CC		9.5698,7.6941,8.9343	,,,	49/316,49/287,49/287,49/316	171137	1162,11844	2203	4300	6503	SO:0001819	synonymous_variant	9501	exon3			CTCCGCCGGGCTG		CCDS10994.1, CCDS54059.1	17p13.3	2014-07-02			ENSG00000181031	ENSG00000181031		"""Synaptotagmins"""	10296	protein-coding gene	gene with protein product		604881				10395805	Standard	NM_006987		Approved	Noc2	uc021tmx.1	Q9UNE2	OTTHUMG00000090273	ENST00000331302.7:c.147G>T	17.37:g.171137C>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	60	22	0.366667	NM_001190413	D3DTG7|Q9BSB3	Silent	SNP	ENST00000331302.7	37	CCDS10994.1																																																																																			C|0.917;A|0.083	0.083	strong		0.677	RPH3AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206597.2	NM_006987	
C5orf42	65250	hgsc.bcm.edu	37	5	37245935	37245935	+	Missense_Mutation	SNP	C	C	T	rs73750959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37245935C>T	ENST00000508244.1	-	2	187	c.94G>A	c.(94-96)Gtt>Att	p.V32I	C5orf42_ENST00000274258.7_5'UTR|C5orf42_ENST00000425232.2_Missense_Mutation_p.V32I|RN7SL37P_ENST00000490461.2_RNA			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	32						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			AAAAGAAAAACGGCTTCTTTT	0.328													C|||	152	0.0303514	0.1127	0.0043	5008	,	,		15998	0.0		0.0	False		,,,				2504	0.0				p.V32I		Atlas-SNP	.											.	C5orf42	422	.	0			c.G94A						PASS	.	C	ILE/VAL	145,1239		8,129,555	77.0	69.0	71.0		94	4.3	1.0	5	dbSNP_130	71	0,3176		0,0,1588	yes	missense	C5orf42	NM_023073.3	29	8,129,2143	TT,TC,CC		0.0,10.4769,3.1798	possibly-damaging	32/3198	37245935	145,4415	692	1588	2280	SO:0001583	missense	65250	exon3			GAAAAACGGCTTC		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.94G>A	5.37:g.37245935C>T	ENSP00000421690:p.Val32Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	C	12.59	1.983446	0.35036	0.104769	0.0	ENSG00000197603	ENST00000508244;ENST00000425232	T;T	0.51817	0.69;0.69	5.34	4.35	0.52113	.	0.391851	0.21991	U	0.066147	T	0.00724	0.0024	L	0.41824	1.3	0.80722	D	1	P	0.51351	0.944	B	0.37198	0.243	T	0.00783	-1.1568	10	0.59425	D	0.04	-10.2005	12.5366	0.56145	0.0:0.8874:0.0:0.1126	.	32	E9PH94	.	I	32	ENSP00000421690:V32I;ENSP00000389014:V32I	ENSP00000389014:V32I	V	-	1	0	C5orf42	37281692	1.000000	0.71417	1.000000	0.80357	0.430000	0.31655	3.683000	0.54663	2.497000	0.84241	0.313000	0.20887	GTT	C|0.980;T|0.020	0.020	strong		0.328	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
N4BP2	55728	hgsc.bcm.edu	37	4	40122377	40122377	+	Missense_Mutation	SNP	G	G	A	rs78767806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:40122377G>A	ENST00000261435.6	+	9	3062	c.2646G>A	c.(2644-2646)atG>atA	p.M882I		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	882					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TCAACATTATGGGTGACTGGC	0.388													G|||	127	0.0253594	0.0938	0.0043	5008	,	,		21899	0.0		0.0	False		,,,				2504	0.0				p.M882I		Atlas-SNP	.											.	N4BP2	166	.	0			c.G2646A						PASS	.	G	ILE/MET	297,4109	155.5+/-188.7	7,283,1913	55.0	56.0	55.0		2646	3.7	0.2	4	dbSNP_131	55	3,8595	2.2+/-6.3	0,3,4296	yes	missense	N4BP2	NM_018177.4	10	7,286,6209	AA,AG,GG		0.0349,6.7408,2.307	benign	882/1771	40122377	300,12704	2203	4299	6502	SO:0001583	missense	55728	exon9			CATTATGGGTGAC	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.2646G>A	4.37:g.40122377G>A	ENSP00000261435:p.Met882Ile	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	240	104	0.433333	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	44|44	0.020146520146520148|0.020146520146520148	42|42	0.08536585365853659|0.08536585365853659	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	6.953|6.953	0.545704|0.545704	0.13312|0.13312	0.067408|0.067408	3.49E-4|3.49E-4	ENSG00000078177|ENSG00000078177	ENST00000513269|ENST00000261435;ENST00000381804	.|T	.|0.16073	.|2.37	5.48|5.48	3.72|3.72	0.42706|0.42706	.|.	.|0.426709	.|0.19802	.|N	.|0.105727	T|T	0.00300|0.00300	0.0009|0.0009	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.06405	.|0.002;0.001	T|T	0.34502|0.34502	-0.9826|-0.9826	5|10	.|0.35671	.|T	.|0.21	-1.4935|-1.4935	5.7473|5.7473	0.18128|0.18128	0.1425:0.0:0.5811:0.2764|0.1425:0.0:0.5811:0.2764	.|.	.|882;882	.|Q86UW6-2;Q86UW6	.|.;N4BP2_HUMAN	R|I	529|882;802	.|ENSP00000261435:M882I	.|ENSP00000261435:M882I	G|M	+|+	1|3	0|0	N4BP2|N4BP2	39798772|39798772	0.070000|0.070000	0.21116|0.21116	0.168000|0.168000	0.22838|0.22838	0.735000|0.735000	0.41995|0.41995	0.254000|0.254000	0.18314|0.18314	0.778000|0.778000	0.33520|0.33520	0.655000|0.655000	0.94253|0.94253	GGG|ATG	G|0.975;A|0.025	0.025	strong		0.388	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
OTOF	9381	hgsc.bcm.edu	37	2	26699126	26699126	+	Silent	SNP	C	C	G	rs4335905|rs397515595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26699126C>G	ENST00000272371.2	-	23	2862	c.2736G>C	c.(2734-2736)ctG>ctC	p.L912L	OTOF_ENST00000339598.3_Silent_p.L165L|OTOF_ENST00000402415.3_Silent_p.L222L|OTOF_ENST00000338581.6_Silent_p.L165L|OTOF_ENST00000403946.3_Silent_p.L912L	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	912					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)	p.L165L(1)|p.L912L(1)		NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCACAGGTACAGCTCCACCT	0.687													G|||	3545	0.707867	0.7821	0.6657	5008	,	,		7877	0.9831		0.4722	False		,,,				2504	0.5961				p.L912L	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											OTOF_ENST00000361394,NS,lymphoid_neoplasm,0,2	OTOF	524	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.G2736C	GRCh37	CI084299	OTOF	I	rs4335905	PASS	.	G	,,,	3117,1283	406.2+/-333.8	1107,903,190	41.0	38.0	39.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	495,2736,666,495	-4.4	0.7	2	dbSNP_111	39	3765,4825	588.4+/-392.4	806,2153,1336	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	1913,3056,1526	GG,GC,CC		43.83,29.1591,47.0208	,,,	165/1231,912/1998,222/1308,165/1231	26699126	6882,6108	2200	4295	6495	SO:0001819	synonymous_variant	9381	exon23			CAGGTACAGCTCC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2736G>C	2.37:g.26699126C>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			C|0.421;G|0.579	0.579	strong		0.687	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
FANCA	2175	hgsc.bcm.edu	37	16	89857880	89857880	+	Silent	SNP	C	C	T	rs1800332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89857880C>T	ENST00000389301.3	-	14	1320	c.1290G>A	c.(1288-1290)gcG>gcA	p.A430A	FANCA_ENST00000568369.1_Silent_p.A430A	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	430					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)		CAACCAGGAACGCAGTGACCA	0.557			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	163	0.0325479	0.1195	0.0072	5008	,	,		20326	0.0		0.0	False		,,,				2504	0.0				p.A430A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,NS,lymphoid_neoplasm,-1,1	FANCA	99	1	0			c.G1290A						PASS	.	C		453,3943	217.1+/-235.6	20,413,1765	63.0	51.0	55.0		1290	-10.9	0.0	16	dbSNP_89	55	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	FANCA	NM_000135.2		20,415,6063	TT,TC,CC		0.0233,10.3048,3.5011		430/1456	89857880	455,12541	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CAGGAACGCAGTG	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.1290G>A	16.37:g.89857880C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	96	37	0.385417	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			C|0.967;T|0.033	0.033	strong		0.557	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
LMNA	4000	hgsc.bcm.edu	37	1	156105028	156105028	+	Silent	SNP	T	T	C	rs538089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156105028T>C	ENST00000368300.4	+	5	1073	c.861T>C	c.(859-861)gcT>gcC	p.A287A	LMNA_ENST00000392353.3_Silent_p.A206A|LMNA_ENST00000368297.1_Silent_p.A206A|LMNA_ENST00000448611.2_Silent_p.A175A|LMNA_ENST00000368301.2_Silent_p.A287A|LMNA_ENST00000361308.4_Silent_p.A287A|LMNA_ENST00000368299.3_Silent_p.A287A|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000473598.2_Silent_p.A188A|LMNA_ENST00000347559.2_Silent_p.A287A	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	287	Coil 2.|Rod.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					TGGTGGGGGCTGCCCACGAGG	0.632									Werner syndrome;Hutchinson-Gilford Progeria Syndrome				C|||	967	0.193091	0.5242	0.085	5008	,	,		16210	0.0228		0.0865	False		,,,				2504	0.1074				p.A287A		Atlas-SNP	.											.	LMNA	31	.	0			c.T861C						PASS	.	C	,,	1927,2479	623.6+/-394.2	411,1105,687	42.0	44.0	43.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	861,861,861	-11.0	0.4	1	dbSNP_83	43	646,7954	788.8+/-407.6	20,606,3674	no	coding-synonymous,coding-synonymous,coding-synonymous	LMNA	NM_005572.3,NM_170707.2,NM_170708.2	,,	431,1711,4361	CC,CT,TT		7.5116,43.7358,19.7832	,,	287/573,287/665,287/635	156105028	2573,10433	2203	4300	6503	SO:0001819	synonymous_variant	4000	exon5	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	GGGGGCTGCCCAC	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"""Intermediate filaments type V, lamins"""	6636	protein-coding gene	gene with protein product		150330	"""cardiomyopathy, dilated 1A (autosomal dominant)"", ""limb girdle muscular dystrophy 1B (autosomal dominant)"", ""progeria 1 (Hutchinson-Gilford type)"", ""lamin A/C-like 1"""	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.861T>C	1.37:g.156105028T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	203	201	0.990148	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	37	CCDS1129.1																																																																																			T|0.808;C|0.192	0.192	strong		0.632	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	
COL28A1	340267	hgsc.bcm.edu	37	7	7571420	7571420	+	Silent	SNP	T	T	C	rs17168526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:7571420T>C	ENST00000399429.3	-	3	380	c.240A>G	c.(238-240)caA>caG	p.Q80Q		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	80	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CAGGAGTCAATTGGAAAATCT	0.418													T|||	127	0.0253594	0.0923	0.0058	5008	,	,		18415	0.0		0.001	False		,,,				2504	0.0				p.Q80Q		Atlas-SNP	.											.	COL28A1	113	.	0			c.A240G						PASS	.	T		280,3454		9,262,1596	70.0	69.0	70.0		240	-8.4	0.0	7	dbSNP_123	70	6,8210		0,6,4102	no	coding-synonymous	COL28A1	NM_001037763.2		9,268,5698	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	0.073,7.4987,2.3933		80/1126	7571420	286,11664	1867	4108	5975	SO:0001819	synonymous_variant	340267	exon3			AGTCAATTGGAAA	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.240A>G	7.37:g.7571420T>C		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	318	131	0.41195	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	37	CCDS43553.1																																																																																			T|0.969;C|0.031	0.031	strong		0.418	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
FAM214A	56204	hgsc.bcm.edu	37	15	52901887	52901887	+	Silent	SNP	A	A	G	rs75512966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52901887A>G	ENST00000261844.7	-	6	1376	c.1224T>C	c.(1222-1224)ctT>ctC	p.L408L	FAM214A_ENST00000546305.2_Silent_p.L415L	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	408																	AAACCCGGAAAAGTTTTGAAT	0.403													A|||	99	0.0197684	0.0734	0.0029	5008	,	,		19310	0.0		0.0	False		,,,				2504	0.0				p.L408L		Atlas-SNP	.											.	.	.	.	0			c.T1224C						PASS	.	A		198,3438		6,186,1626	60.0	56.0	57.0		1224	0.5	0.0	15	dbSNP_132	57	1,8143		0,1,4071	no	coding-synonymous	KIAA1370	NM_019600.2		6,187,5697	GG,GA,AA		0.0123,5.4455,1.6893		408/1077	52901887	199,11581	1818	4072	5890	SO:0001819	synonymous_variant	56204	exon6			CCGGAAAAGTTTT	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.1224T>C	15.37:g.52901887A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			A|0.981;G|0.019	0.019	strong		0.403	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
ZNF225	7768	hgsc.bcm.edu	37	19	44636802	44636802	+	Missense_Mutation	SNP	A	A	T	rs16978738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44636802A>T	ENST00000262894.6	+	5	2315	c.2035A>T	c.(2035-2037)Aca>Tca	p.T679S	ZNF225_ENST00000590612.1_Missense_Mutation_p.T679S|ZNF225_ENST00000592780.1_3'UTR	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	679			T -> S (in dbSNP:rs16978738).		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.T679S(1)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				TGGAGAGAAAACATCTAAATG	0.403													A|||	344	0.0686901	0.0681	0.1599	5008	,	,		21420	0.0883		0.0139	False		,,,				2504	0.0409				p.T679S		Atlas-SNP	.											ZNF225,NS,carcinoma,0,1	ZNF225	41	1	1	Substitution - Missense(1)	stomach(1)	c.A2035T						PASS	.	A	SER/THR	209,4191	117.1+/-155.0	3,203,1994	47.0	47.0	47.0		2035	0.7	0.0	19	dbSNP_123	47	30,8566	19.8+/-62.0	1,28,4269	yes	missense	ZNF225	NM_013362.2	58	4,231,6263	TT,TA,AA		0.349,4.75,1.839	benign	679/707	44636802	239,12757	2200	4298	6498	SO:0001583	missense	7768	exon5			GAGAAAACATCTA	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"""Zinc fingers, C2H2-type"", ""-"""	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.2035A>T	19.37:g.44636802A>T	ENSP00000262894:p.Thr679Ser	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	179	98	0.547486	NM_013362	A8K8S2|Q53F12|Q9NS46|Q9UID8	Missense_Mutation	SNP	ENST00000262894.6	37	CCDS46100.1	147	0.0673076923076923	36	0.07317073170731707	53	0.1464088397790055	50	0.08741258741258741	8	0.010554089709762533	A	8.951	0.968102	0.18659	0.0475	0.00349	ENSG00000256294	ENST00000262894;ENST00000544184	T	0.14640	2.49	1.85	0.686	0.18015	Zinc finger, C2H2 (1);	.	.	.	.	T	0.00039	0.0001	N	0.05259	-0.085	0.52099	P	5.299999999996974E-5	B	0.02656	0.0	B	0.09377	0.004	T	0.33599	-0.9862	8	0.52906	T	0.07	.	8.2405	0.31658	0.2453:0.7547:0.0:0.0	rs16978738;rs16978738	679	Q9UK10	ZN225_HUMAN	S	679;643	ENSP00000262894:T679S	ENSP00000262894:T679S	T	+	1	0	ZNF225	49328642	0.000000	0.05858	0.003000	0.11579	0.015000	0.08874	-0.051000	0.11885	0.090000	0.17273	-0.677000	0.03784	ACA	A|0.937;T|0.063	0.063	strong		0.403	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1		
HDHD1	8226	hgsc.bcm.edu	37	X	6995417	6995417	+	Silent	SNP	C	C	T	rs2379207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:6995417C>T	ENST00000381077.5	-	3	430	c.354G>A	c.(352-354)gcG>gcA	p.A118A	HDHD1_ENST00000540122.1_Silent_p.A118A|HDHD1_ENST00000424830.2_Silent_p.A141A|HDHD1_ENST00000412827.2_Silent_p.A75A	NM_001178136.1|NM_012080.4	NP_001171607.1|NP_036212.3	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain containing 1	118					nucleotide metabolic process (GO:0009117)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)			breast(2)|large_intestine(1)|lung(3)	6						TATCGAACGACGCGGACCCCG	0.587													C|||	961	0.25457	0.0537	0.3372	3775	,	,		11649	0.2153		0.1779	False		,,,				2504	0.2658				p.A141A		Atlas-SNP	.											.	HDHD1	21	.	0			c.G423A						PASS	.	C	,,,	354,3193		16,254,68,1218,503	44.0	46.0	46.0		423,354,225,354	-1.5	0.0	X	dbSNP_100	46	1568,4975		152,846,418,1370,1389	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HDHD1	NM_001135565.1,NM_001178135.1,NM_001178136.1,NM_012080.4	,,,	168,1100,486,2588,1892	TT,TC,T,CC,C		23.9645,9.9803,19.0486	,,,	141/252,118/209,75/186,118/229	6995417	1922,8168	2059	4175	6234	SO:0001819	synonymous_variant	8226	exon4			GAACGACGCGGAC	M86934	CCDS48075.1, CCDS48076.1, CCDS55366.1, CCDS55367.1	Xp22.32	2010-07-21	2010-07-21	2010-07-21	ENSG00000130021	ENSG00000130021			16818	protein-coding gene	gene with protein product		306480	"""family with sequence similarity 16, member A, X-linked"", ""haloacid dehalogenase-like hydrolase domain containing 1A"""	FAM16AX, HDHD1A		1734713, 1284467	Standard	NM_012080		Approved	DXF68S1E, GS1	uc011mhm.1	Q08623	OTTHUMG00000021101	ENST00000381077.5:c.354G>A	X.37:g.6995417C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	187	97	0.518717	NM_001135565	B2R7X6|B4DV93|B7Z6Q3|E9PAV8|F5GWZ2|Q53F84|Q96EB8	Silent	SNP	ENST00000381077.5	37	CCDS48075.1																																																																																			C|0.748;0|0.031	.	strong		0.587	HDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055683.2	NM_012080	
KTN1	3895	hgsc.bcm.edu	37	14	56096686	56096686	+	Silent	SNP	A	A	C	rs74053638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:56096686A>C	ENST00000395314.3	+	7	1160	c.1092A>C	c.(1090-1092)acA>acC	p.T364T	KTN1_ENST00000395309.3_Silent_p.T364T|KTN1_ENST00000413890.2_Silent_p.T364T|KTN1_ENST00000395308.1_Silent_p.T364T|KTN1_ENST00000438792.2_Silent_p.T364T|KTN1_ENST00000395311.1_Silent_p.T364T|KTN1_ENST00000416613.1_Silent_p.T364T	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	364					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AAATGATGACAGAGAAAGAAA	0.274			T	RET	papillary thryoid								A|||	118	0.0235623	0.0825	0.0086	5008	,	,		20073	0.0		0.001	False		,,,				2504	0.002				p.T364T		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.A1092C						PASS	.	A	,,,	315,4091	165.1+/-196.6	12,291,1900	99.0	101.0	101.0		1092,1092,1092,1092	0.4	1.0	14	dbSNP_130	101	31,8569	21.0+/-64.5	0,31,4269	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	,,,	12,322,6169	CC,CA,AA		0.3605,7.1493,2.6603	,,,	364/1358,364/1307,364/1301,364/1358	56096686	346,12660	2203	4300	6503	SO:0001819	synonymous_variant	3895	exon7			GATGACAGAGAAA		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.1092A>C	14.37:g.56096686A>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	146	84	0.575342	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																			A|0.976;C|0.024	0.024	strong		0.274	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
ANKRD50	57182	hgsc.bcm.edu	37	4	125592440	125592440	+	Silent	SNP	T	T	C	rs3733472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:125592440T>C	ENST00000504087.1	-	4	3029	c.1992A>G	c.(1990-1992)ctA>ctG	p.L664L	ANKRD50_ENST00000515641.1_Silent_p.L485L	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	664										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						CGCCATGTTGTAGCAAATTCA	0.458													T|||	214	0.0427316	0.0492	0.0389	5008	,	,		24549	0.0208		0.0497	False		,,,				2504	0.0521				p.L664L		Atlas-SNP	.											.	ANKRD50	136	.	0			c.A1992G						PASS	.	T	,	215,4191	131.8+/-168.3	7,201,1995	193.0	163.0	173.0		1455,1992	-11.0	0.1	4	dbSNP_107	173	498,8102	143.7+/-199.7	7,484,3809	no	coding-synonymous,coding-synonymous	ANKRD50	NM_001167882.1,NM_020337.2	,	14,685,5804	CC,CT,TT		5.7907,4.8797,5.4821	,	485/1251,664/1430	125592440	713,12293	2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			ATGTTGTAGCAAA	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.1992A>G	4.37:g.125592440T>C		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	306	147	0.480392	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			T|0.948;C|0.052	0.052	strong		0.458	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
CYP39A1	51302	hgsc.bcm.edu	37	6	46563817	46563817	+	Missense_Mutation	SNP	A	A	T	rs7761731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46563817A>T	ENST00000275016.2	-	8	1175	c.972T>A	c.(970-972)aaT>aaA	p.N324K		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	324			N -> K (in dbSNP:rs7761731). {ECO:0000269|PubMed:10748047}.		bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						TTAGAAGGAGATTCTCCAGGT	0.353													T|||	2459	0.491014	0.7035	0.3833	5008	,	,		15400	0.3859		0.2684	False		,,,				2504	0.6176				p.N324K		Atlas-SNP	.											.	CYP39A1	41	.	0			c.T972A						PASS	.	T	LYS/ASN	2767,1639	496.9+/-363.7	869,1029,305	82.0	87.0	85.0		972	-0.5	1.0	6	dbSNP_116	85	2293,6307	703.7+/-405.4	312,1669,2319	yes	missense	CYP39A1	NM_016593.3	94	1181,2698,2624	TT,TA,AA		26.6628,37.1993,38.9051	benign	324/470	46563817	5060,7946	2203	4300	6503	SO:0001583	missense	51302	exon8			AAGGAGATTCTCC	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.972T>A	6.37:g.46563817A>T	ENSP00000275016:p.Asn324Lys	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	244	114	0.467213	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	914	0.4184981684981685	375	0.7621951219512195	135	0.3729281767955801	205	0.3583916083916084	199	0.262532981530343	T	1.157	-0.644802	0.03531	0.628007	0.266628	ENSG00000146233	ENST00000275016	D	0.84442	-1.85	5.64	-0.545	0.11843	.	0.191501	0.44285	N	0.000470	T	0.24314	0.0589	N	0.00788	-1.185	0.53005	P	3.100000000000325E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17776	-1.0358	9	0.02654	T	1	-12.3399	3.8072	0.08782	0.1147:0.4417:0.1896:0.254	rs7761731;rs52826280;rs61011153;rs7761731	304;324	B7Z786;Q9NYL5	.;CP39A_HUMAN	K	324	ENSP00000275016:N324K	ENSP00000275016:N324K	N	-	3	2	CYP39A1	46671776	0.973000	0.33851	0.964000	0.40570	0.654000	0.38779	-0.051000	0.11885	-0.349000	0.08274	-0.375000	0.07067	AAT	A|0.592;T|0.408	0.408	strong		0.353	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
FGGY	55277	hgsc.bcm.edu	37	1	59787350	59787350	+	Missense_Mutation	SNP	T	T	G	rs835409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:59787350T>G	ENST00000303721.7	+	2	303	c.129T>G	c.(127-129)aaT>aaG	p.N43K	FGGY_ENST00000474476.1_Intron|FGGY_ENST00000371212.1_Missense_Mutation_p.N43K|FGGY_ENST00000371218.4_Missense_Mutation_p.N43K	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	143	0	0		WXS	Illumina HiSeq	Phase_I	215	97	0.451163	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	
CFAP46	54777	hgsc.bcm.edu	37	10	134622046	134622046	+	Missense_Mutation	SNP	C	C	T	rs73387072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134622046C>T	ENST00000368586.5	-	58	8127	c.8027G>A	c.(8026-8028)cGt>cAt	p.R2676H	TTC40_ENST00000263170.5_Missense_Mutation_p.R837H	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CCAGCCCCGACGCAGACCCCA	0.677													C|||	131	0.0261581	0.0885	0.0173	5008	,	,		15164	0.0		0.002	False		,,,				2504	0.0				p.R2676H		Atlas-SNP	.											.	TTC40	100	.	0			c.G8027A						PASS	.	C	HIS/ARG	341,4065	166.9+/-198.0	17,307,1879	36.0	44.0	41.0		2963	0.2	0.0	10	dbSNP_130	41	9,8587	5.7+/-21.5	0,9,4289	yes	missense	C10orf92	NM_001200049.1	29	17,316,6168	TT,TC,CC		0.1047,7.7394,2.6919	possibly-damaging	988/1028	134622046	350,12652	2203	4298	6501	SO:0001583	missense	54777	exon58			CCCCGACGCAGAC																												ENST00000368586.5:c.8027G>A	10.37:g.134622046C>T	ENSP00000357575:p.Arg2676His	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	123	72	0.585366	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	51	0.023351648351648352	45	0.09146341463414634	6	0.016574585635359115	0	0.0	0	0.0	C	11.21	1.571070	0.28003	0.077394	0.001047	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.16073	2.71;2.37	1.36	0.248	0.15526	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	0.09310	N	0.999999	P	0.49559	0.925	B	0.29862	0.108	T	0.36744	-0.9735	9	0.87932	D	0	.	5.3024	0.15785	0.0:0.6333:0.3667:0.0	.	837	Q8IYW2	CJ092_HUMAN	H	2676;837	ENSP00000357575:R2676H;ENSP00000263170:R837H	ENSP00000263170:R837H	R	-	2	0	C10orf93	134472036	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.082000	0.03400	-0.076000	0.12775	-0.531000	0.04308	CGT	C|0.975;T|0.025	0.025	strong		0.677	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
CPA5	93979	hgsc.bcm.edu	37	7	129989878	129989878	+	Silent	SNP	T	T	C	rs7808823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:129989878T>C	ENST00000485477.1	+	4	1390	c.261T>C	c.(259-261)tcT>tcC	p.S87S	CPA5_ENST00000355388.3_Silent_p.S87S|CPA5_ENST00000461828.1_Silent_p.S87S|CPA5_ENST00000466363.2_Silent_p.S87S|CPA5_ENST00000393213.3_Silent_p.S87S|CPA5_ENST00000474905.1_Silent_p.S87S|CPA5_ENST00000431780.2_Silent_p.S87S			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	87						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					TTCCTTTCTCTGAACTGAAAG	0.527													C|||	2619	0.522963	0.4539	0.6311	5008	,	,		20994	0.5675		0.5219	False		,,,				2504	0.4949				p.S87S		Atlas-SNP	.											.	CPA5	61	.	0			c.T261C						PASS	.	C	,,	2066,2340	607.0+/-390.9	488,1090,625	123.0	124.0	124.0		261,261,261	-1.2	1.0	7	dbSNP_116	124	4384,4216	571.4+/-389.5	1128,2128,1044	yes	coding-synonymous,coding-synonymous,coding-synonymous	CPA5	NM_001127441.1,NM_001127442.1,NM_080385.4	,,	1616,3218,1669	CC,CT,TT		49.0233,46.8906,49.5925	,,	87/437,87/404,87/437	129989878	6450,6556	2203	4300	6503	SO:0001819	synonymous_variant	93979	exon5			TTTCTCTGAACTG	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.261T>C	7.37:g.129989878T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_080385	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Silent	SNP	ENST00000485477.1	37	CCDS5819.1																																																																																			C|0.512;N|0.000	0.512	strong		0.527	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441	
DNAJC7	7266	hgsc.bcm.edu	37	17	40142302	40142302	+	Silent	SNP	T	T	C	rs1127182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40142302T>C	ENST00000457167.4	-	6	815	c.579A>G	c.(577-579)ccA>ccG	p.P193P	DNAJC7_ENST00000426588.3_Silent_p.P137P|DNAJC7_ENST00000316603.7_Silent_p.P137P	NM_003315.3	NP_003306.3	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	193					chaperone cofactor-dependent protein refolding (GO:0070389)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)				ACTGTGCTTCTGGATAACGAC	0.498													T|||	660	0.131789	0.2224	0.0447	5008	,	,		19879	0.124		0.0726	False		,,,				2504	0.1401				p.P193P	Colon(63;618 1117 8600 10857 19751)	Atlas-SNP	.											.	DNAJC7	51	.	0			c.A579G						PASS	.	T	,	722,3230		60,602,1314	60.0	57.0	58.0		411,579	-2.8	1.0	17	dbSNP_86	58	540,7764		12,516,3624	no	coding-synonymous,coding-synonymous	DNAJC7	NM_001144766.2,NM_003315.3	,	72,1118,4938	CC,CT,TT		6.5029,18.2692,10.297	,	137/439,193/495	40142302	1262,10994	1976	4152	6128	SO:0001819	synonymous_variant	7266	exon6			TGCTTCTGGATAA	U46571	CCDS45677.1, CCDS45678.1	17q11.2	2013-01-10				ENSG00000168259		"""Heat shock proteins / DNAJ (HSP40)"", ""Tetratricopeptide (TTC) repeat domain containing"""	12392	protein-coding gene	gene with protein product		601964		TTC2		8836031, 11147971	Standard	NR_029431		Approved	TPR2	uc002hyo.3	Q99615		ENST00000457167.4:c.579A>G	17.37:g.40142302T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_003315	Q7Z784	Silent	SNP	ENST00000457167.4	37	CCDS45677.1																																																																																			T|0.894;C|0.106	0.106	strong		0.498	DNAJC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453366.2		
CCDC180	100499483	hgsc.bcm.edu	37	9	100087345	100087345	+	Silent	SNP	A	A	G	rs3747496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100087345A>G	ENST00000357054.1	+	28	2900	c.1965A>G	c.(1963-1965)tcA>tcG	p.S655S	CCDC180_ENST00000529487.1_Silent_p.S516S|CCDC180_ENST00000375202.2_Silent_p.S516S|CCDC180_ENST00000395220.1_Missense_Mutation_p.H627R|CCDC180_ENST00000411667.2_Silent_p.S513S|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000460482.2_3'UTR			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	78	0	0		WXS	Illumina HiSeq	Phase_I	90	66	0.733333	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	
OR2K2	26248	hgsc.bcm.edu	37	9	114089883	114089883	+	Silent	SNP	G	G	A	rs61748722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114089883G>A	ENST00000374428.1	-	1	917	c.918C>T	c.(916-918)taC>taT	p.Y306Y	OR2K2_ENST00000302681.1_Silent_p.Y277Y			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	306						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						TAAGCACTCCGTAAAGCAACG	0.383													A|||	74	0.0147764	0.053	0.0058	5008	,	,		22259	0.0		0.0	False		,,,				2504	0.0				p.Y277Y		Atlas-SNP	.											.	OR2K2	77	.	0			c.C831T						PASS	.	A		233,4173	805.1+/-415.8	5,223,1975	131.0	124.0	126.0		831	4.6	1.0	9	dbSNP_129	126	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	OR2K2	NM_205859.1		5,224,6274	AA,AG,GG		0.0116,5.2882,1.7992		277/317	114089883	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	26248	exon1			CACTCCGTAAAGC	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.918C>T	9.37:g.114089883G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	171	123	0.719298	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Silent	SNP	ENST00000374428.1	37																																																																																				G|0.982;A|0.018	0.018	strong		0.383	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859	
POLE	5426	hgsc.bcm.edu	37	12	133219831	133219831	+	Silent	SNP	T	T	C	rs5744944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133219831T>C	ENST00000320574.5	-	35	4573	c.4530A>G	c.(4528-4530)gcA>gcG	p.A1510A	POLE_ENST00000434528.3_5'Flank|POLE_ENST00000535270.1_Silent_p.A1483A	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1510					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)	CAAAGACGGATGCCCTGCGCT	0.602								DNA polymerases (catalytic subunits)					C|||	3031	0.605232	0.761	0.5317	5008	,	,		20994	0.6736		0.4304	False		,,,				2504	0.5562				p.A1510A		Atlas-SNP	.											.	POLE	416	.	0			c.A4530G						PASS	.	C		3091,1315	441.2+/-346.3	1076,939,188	101.0	91.0	94.0		4530	-11.9	0.1	12	dbSNP_114	94	3703,4897	619.4+/-396.9	797,2109,1394	no	coding-synonymous	POLE	NM_006231.2		1873,3048,1582	CC,CT,TT		43.0581,29.8457,47.7626		1510/2287	133219831	6794,6212	2203	4300	6503	SO:0001819	synonymous_variant	5426	exon35			GACGGATGCCCTG		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.4530A>G	12.37:g.133219831T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			T|0.448;C|0.552	0.552	strong		0.602	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
HLA-G	3135	hgsc.bcm.edu	37	6	29797696	29797696	+	Silent	SNP	A	A	G	rs1130363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29797696A>G	ENST00000360323.6	+	5	1023	c.999A>G	c.(997-999)agA>agG	p.R333R	HLA-G_ENST00000428701.1_Silent_p.R333R|HLA-G_ENST00000376828.2_Silent_p.R338R|HLA-G_ENST00000376818.3_Silent_p.R241R|HLA-G_ENST00000376815.3_Silent_p.R149R			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	333					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						TGCTGTGGAGAAAGAAGAGCT	0.567													N|||	2995	0.598043	0.621	0.5548	5008	,	,		20312	0.6101		0.4592	False		,,,				2504	0.728				p.R333R		Atlas-SNP	.											.	HLA-G	90	.	0			c.A999G						PASS	.	G		2670,1736		804,1062,337	79.0	72.0	74.0		999	1.3	0.0	6	dbSNP_86	74	4364,4236		1111,2142,1047	no	coding-synonymous	HLA-G	NM_002127.5		1915,3204,1384	GG,GA,AA		49.2558,39.4008,45.9173		333/339	29797696	7034,5972	2203	4300	6503	SO:0001819	synonymous_variant	3135	exon6			GTGGAGAAAGAAG		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.999A>G	6.37:g.29797696A>G		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	208	208	1	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			A|0.442;G|0.558	0.558	strong		0.567	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
MYH7B	57644	hgsc.bcm.edu	37	20	33565755	33565755	+	Missense_Mutation	SNP	G	G	A	rs11906160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33565755G>A	ENST00000262873.7	+	3	165	c.73G>A	c.(73-75)Gcc>Acc	p.A25T		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	0						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GCCTTGGGCCGCCTTGAACCT	0.602													G|||	782	0.15615	0.3041	0.1052	5008	,	,		13720	0.0863		0.1034	False		,,,				2504	0.1186				p.A25T		Atlas-SNP	.											.	MYH7B	145	.	0			c.G73A						PASS	.	G	THR/ALA	1039,3285		115,809,1238	119.0	129.0	126.0	http://www.ncbi.nlm.nih.gov/pubmed?term	73	-9.1	0.0	20	dbSNP_120	126	950,7582		50,850,3366	yes	missense	MYH7B	NM_020884.3	58	165,1659,4604	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	11.1346,24.0287,15.4714		25/1984	33565755	1989,10867	2162	4266	6428	SO:0001583	missense	57644	exon5			TGGGCCGCCTTGA	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.73G>A	20.37:g.33565755G>A	ENSP00000262873:p.Ala25Thr	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	40	14	0.35	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	311	0.1423992673992674	138	0.2804878048780488	46	0.1270718232044199	40	0.06993006993006994	87	0.11477572559366754	G	10.14	1.268479	0.23136	0.240287	0.111346	ENSG00000078814	ENST00000262873	D	0.86097	-2.07	4.52	-9.05	0.00730	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.02821	-1.1106	5	0.07030	T	0.85	.	10.2475	0.43350	0.5764:0.0:0.3366:0.087	rs11906160;rs61678150;rs11906160	.	.	.	T	25	ENSP00000262873:A25T	ENSP00000262873:A25T	A	+	1	0	MYH7B	33029416	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.052000	0.00627	-2.137000	0.00809	-1.421000	0.01109	GCC	G|0.858;A|0.142	0.142	strong		0.602	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
PKD1L1	168507	hgsc.bcm.edu	37	7	47925331	47925331	+	Missense_Mutation	SNP	C	C	G	rs10274334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47925331C>G	ENST00000289672.2	-	18	3208	c.3158G>C	c.(3157-3159)cGc>cCc	p.R1053P		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1053	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		R -> P (in dbSNP:rs10274334).		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						TCTCTCAGAGCGGCCAGTCAT	0.597													G|||	2931	0.585264	0.8094	0.5706	5008	,	,		18449	0.6359		0.4592	False		,,,				2504	0.3701				p.R1053P		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G3158C						PASS	.	G	PRO/ARG	3237,1169	395.1+/-329.5	1198,841,164	72.0	81.0	78.0		3158	-1.8	0.0	7	dbSNP_119	78	3619,4981	621.9+/-397.2	743,2133,1424	yes	missense	PKD1L1	NM_138295.3	103	1941,2974,1588	GG,GC,CC		42.0814,26.532,47.2859	benign	1053/2850	47925331	6856,6150	2203	4300	6503	SO:0001583	missense	168507	exon18			TCAGAGCGGCCAG	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.3158G>C	7.37:g.47925331C>G	ENSP00000289672:p.Arg1053Pro	Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	1306	0.597985347985348	394	0.8008130081300813	196	0.5414364640883977	370	0.6468531468531469	346	0.45646437994722955	G	7.105	0.574944	0.13623	0.73468	0.420814	ENSG00000158683	ENST00000289672	T	0.19250	2.16	4.04	-1.82	0.07857	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	4.615670	0.02220	N	0.063933	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	0.30679	-0.9970	9	0.14656	T	0.56	-7.6581	3.3665	0.07206	0.0888:0.3942:0.2495:0.2674	rs10274334;rs59743249;rs10274334	1053	Q8TDX9	PK1L1_HUMAN	P	1053	ENSP00000289672:R1053P	ENSP00000289672:R1053P	R	-	2	0	PKD1L1	47891856	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	-0.274000	0.08537	-0.514000	0.06488	-0.132000	0.14878	CGC	C|0.438;G|0.562	0.562	strong		0.597	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
ATP10A	57194	hgsc.bcm.edu	37	15	25928508	25928508	+	Silent	SNP	C	C	T	rs142960034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25928508C>T	ENST00000356865.6	-	17	3528	c.3417G>A	c.(3415-3417)ggG>ggA	p.G1139G		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1139					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TGTCCAGCACCCCAGTCACGA	0.537													C|||	19	0.00379393	0.0144	0.0	5008	,	,		17004	0.0		0.0	False		,,,				2504	0.0				p.G1139G		Atlas-SNP	.											.	ATP10A	270	.	0			c.G3417A						PASS	.	C		63,4343	59.3+/-96.0	0,63,2140	75.0	66.0	69.0		3417	2.5	1.0	15	dbSNP_134	69	0,8600		0,0,4300	no	coding-synonymous	ATP10A	NM_024490.3		0,63,6440	TT,TC,CC		0.0,1.4299,0.4844		1139/1500	25928508	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon17			CAGCACCCCAGTC	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3417G>A	15.37:g.25928508C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	148	73	0.493243	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			C|0.996;T|0.004	0.004	strong		0.537	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
PCDHA6	56142	hgsc.bcm.edu	37	5	140209429	140209429	+	Missense_Mutation	SNP	C	C	G	rs60309716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140209429C>G	ENST00000529310.1	+	1	1867	c.1753C>G	c.(1753-1755)Ctg>Gtg	p.L585V	PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	585	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.		L -> V (in dbSNP:rs60309716).		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)			GCCGCGGTCACTGGGTGCAGG	0.677													.|||	317	0.0632987	0.2322	0.013	5008	,	,		16721	0.0		0.001	False		,,,				2504	0.0				p.L585V		Atlas-SNP	.											.	PCDHA6	442	.	0			c.C1753G						PASS	.	G	,,,,,VAL/LEU,,VAL/LEU,	863,3543	743.4+/-411.5	78,707,1418	87.0	87.0	87.0		,,,,,1753,,1753,	1.0	0.0	5	dbSNP_129	87	2,8596	819.0+/-406.8	0,2,4297	no	intron,intron,intron,intron,intron,missense,intron,missense,intron	PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_031411.1,NM_031848.1,NM_031849.1	,,,,,32,,32,	78,709,5715	GG,GC,CC		0.0233,19.5869,6.6518	,,,,,,,,	,,,,,585/951,,585/804,	140209429	865,12139	2203	4299	6502	SO:0001583	missense	56142	exon1			CGGTCACTGGGTG	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.1753C>G	5.37:g.140209429C>G	ENSP00000433378:p.Leu585Val	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	274	141	0.514599	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	37	CCDS47281.1	96	0.04395604395604396	90	0.18292682926829268	6	0.016574585635359115	0	0.0	0	0.0	G	0.001	-3.111828	0.00032	0.195869	2.33E-4	ENSG00000081842	ENST00000529310	T	0.50001	0.76	3.87	0.98	0.19750	Cadherin (2);Cadherin-like (1);	0.000000	0.33199	N	0.005169	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.19484	-1.0304	9	0.07482	T	0.82	.	3.3104	0.07015	0.0814:0.2713:0.3691:0.2783	rs60309716;rs61730776	585;585	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	V	585	ENSP00000433378:L585V	ENSP00000433378:L585V	L	+	1	2	PCDHA6	140189613	0.013000	0.17824	0.005000	0.12908	0.002000	0.02628	1.103000	0.31062	-0.149000	0.11215	-0.671000	0.03813	CTG	C|0.940;G|0.060	0.060	strong		0.677	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
TEP1	7011	hgsc.bcm.edu	37	14	20852029	20852029	+	Missense_Mutation	SNP	A	A	G	rs1760904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20852029A>G	ENST00000262715.5	-	25	3623	c.3583T>C	c.(3583-3585)Tca>Cca	p.S1195P	TEP1_ENST00000545983.1_5'Flank|TEP1_ENST00000556935.1_Missense_Mutation_p.S1087P	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1195	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		S -> P (in dbSNP:rs1760904). {ECO:0000269|PubMed:9020079}.		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)		AAGACTAATGATGCCACCTTG	0.537													G|||	3462	0.691294	0.9644	0.6196	5008	,	,		21215	0.6181		0.4732	False		,,,				2504	0.6728				p.S1195P		Atlas-SNP	.											.	TEP1	224	.	0			c.T3583C						PASS	.	G	PRO/SER	3918,488	218.7+/-236.7	1749,420,34	40.0	46.0	44.0		3583	4.8	0.5	14	dbSNP_89	44	4060,4540	582.2+/-391.4	941,2178,1181	yes	missense	TEP1	NM_007110.4	74	2690,2598,1215	GG,GA,AA		47.2093,11.0758,38.6591	benign	1195/2628	20852029	7978,5028	2203	4300	6503	SO:0001583	missense	7011	exon25			CTAATGATGCCAC		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.3583T>C	14.37:g.20852029A>G	ENSP00000262715:p.Ser1195Pro	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	1384	0.6336996336996337	466	0.9471544715447154	211	0.5828729281767956	348	0.6083916083916084	359	0.4736147757255937	G	1.256	-0.617162	0.03663	0.889242	0.472093	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.78816	-1.21;-1.21	5.84	4.77	0.60923	NACHT nucleoside triphosphatase (1);	0.196582	0.44902	N	0.000417	T	0.00012	0.0000	N	0.02011	-0.69	0.44798	P	0.0021980000000000333	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38001	-0.9681	9	0.08599	T	0.76	-18.4575	9.2287	0.37423	0.1878:0.0:0.8122:0.0	rs1760904;rs2228038;rs17211362;rs52790546;rs60595270;rs1760904	1087;545;1195	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	P	1195;1195;1087	ENSP00000262715:S1195P;ENSP00000452574:S1087P	ENSP00000262715:S1195P	S	-	1	0	TEP1	19921869	0.410000	0.25376	0.493000	0.27502	0.915000	0.54546	0.938000	0.28965	1.489000	0.48450	-0.119000	0.15052	TCA	A|0.367;G|0.633	0.633	strong		0.537	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
EIF4G3	8672	hgsc.bcm.edu	37	1	21177800	21177800	+	Missense_Mutation	SNP	A	A	T	rs2230572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21177800A>T	ENST00000264211.8	-	22	3749	c.3555T>A	c.(3553-3555)gaT>gaA	p.D1185E	EIF4G3_ENST00000602326.1_Missense_Mutation_p.D1191E|EIF4G3_ENST00000374937.3_Missense_Mutation_p.D1191E|EIF4G3_ENST00000536266.1_Missense_Mutation_p.D789E|EIF4G3_ENST00000400422.1_Missense_Mutation_p.D1185E|EIF4G3_ENST00000374935.3_Missense_Mutation_p.D905E|EIF4G3_ENST00000537738.1_Missense_Mutation_p.D675E	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1185			D -> E (in dbSNP:rs2230572).		cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		TCCTCTCCACATCCACACCTC	0.498													A|||	14	0.00279553	0.0091	0.0029	5008	,	,		16789	0.0		0.0	False		,,,				2504	0.0				p.D1221E		Atlas-SNP	.											EIF4G3_ENST00000374937,NS,carcinoma,-2,2	EIF4G3	300	2	0			c.T3663A						PASS	.	A	GLU/ASP,GLU/ASP,GLU/ASP	50,4356	52.9+/-88.7	0,50,2153	163.0	147.0	152.0		3663,3573,3555	-7.4	0.0	1	dbSNP_98	152	0,8600		0,0,4300	yes	missense,missense,missense	EIF4G3	NM_001198801.1,NM_001198802.1,NM_003760.4	45,45,45	0,50,6453	TT,TA,AA		0.0,1.1348,0.3844	benign,benign,benign	1221/1622,1191/1592,1185/1586	21177800	50,12956	2203	4300	6503	SO:0001583	missense	8672	exon26			CTCCACATCCACA	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.3555T>A	1.37:g.21177800A>T	ENSP00000264211:p.Asp1185Glu	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	197	101	0.51269	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	37	CCDS214.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	A	14.94	2.685816	0.47991	0.011348	0.0	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266	T;T;T;T;T;T	0.06849	3.87;3.87;3.68;3.25;3.87;3.55	5.73	-7.44	0.01379	.	0.243758	0.46758	N	0.000265	T	0.01222	0.0040	N	0.14661	0.345	0.26519	N	0.974465	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.001;0.0	B;B;B;B;B	0.09377	0.001;0.001;0.001;0.004;0.002	T	0.39035	-0.9633	10	0.07644	T	0.81	-6.5184	6.1684	0.20404	0.2584:0.1981:0.4652:0.0783	rs2230572;rs35634957	1380;905;789;1191;1185	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	E	1185;1381;1185;905;675;1191;789	ENSP00000264211:D1185E;ENSP00000383274:D1185E;ENSP00000364071:D905E;ENSP00000442010:D675E;ENSP00000364073:D1191E;ENSP00000444693:D789E	ENSP00000264211:D1185E	D	-	3	2	EIF4G3	21050387	0.000000	0.05858	0.006000	0.13384	0.482000	0.33219	-2.045000	0.01410	-1.357000	0.02180	0.482000	0.46254	GAT	A|0.995;T|0.005	0.005	strong		0.498	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760	
C21orf2	755	hgsc.bcm.edu	37	21	45750725	45750725	+	Missense_Mutation	SNP	G	G	A	rs148023924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45750725G>A	ENST00000339818.4	-	6	830	c.623C>T	c.(622-624)tCg>tTg	p.S208L	C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000325223.7_Missense_Mutation_p.S207L|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000397956.3_Missense_Mutation_p.S207L|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	208					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)		GTGGCTGCTCGAGGCATCCCT	0.682													G|||	12	0.00239617	0.0068	0.0	5008	,	,		13283	0.0		0.001	False		,,,				2504	0.002				p.S208L		Atlas-SNP	.											.	C21orf2	10	.	0			c.C623T						PASS	.	G	LEU/SER	23,4355		0,23,2166	14.0	15.0	15.0		623	-5.4	0.0	21	dbSNP_134	15	0,8590		0,0,4295	yes	missense	C21orf2	NM_004928.2	145	0,23,6461	AA,AG,GG		0.0,0.5254,0.1774	benign	208/257	45750725	23,12945	2189	4295	6484	SO:0001583	missense	755	exon6			CTGCTCGAGGCAT	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.623C>T	21.37:g.45750725G>A	ENSP00000344566:p.Ser208Leu	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	160	79	0.49375	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	9.377	1.072041	0.20147	0.005254	0.0	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.35973	1.61;1.28;1.61	4.25	-5.4	0.02656	.	2.084300	0.02418	N	0.082253	T	0.08223	0.0205	N	0.02011	-0.69	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.04013	0.001;0.0;0.0;0.001	T	0.09292	-1.0681	10	0.28530	T	0.3	-0.0966	1.5726	0.02618	0.5044:0.1437:0.2077:0.1442	.	207;207;208;167	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	L	208;207;207	ENSP00000344566:S208L;ENSP00000381047:S207L;ENSP00000317302:S207L	ENSP00000317302:S207L	S	-	2	0	C21orf2	44575153	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.798000	0.04565	-0.617000	0.05664	-0.137000	0.14449	TCG	G|0.997;A|0.003	0.003	strong		0.682	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
SEC14L5	9717	hgsc.bcm.edu	37	16	5050678	5050678	+	Silent	SNP	C	C	T	rs61745575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5050678C>T	ENST00000251170.7	+	9	1173	c.993C>T	c.(991-993)ctC>ctT	p.L331L		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	331	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					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						TCTACATCCTCCGCCTGGGCC	0.632													C|||	132	0.0263578	0.0923	0.0115	5008	,	,		16872	0.0		0.002	False		,,,				2504	0.0				p.L331L		Atlas-SNP	.											SEC14L5,NS,carcinoma,+2,1	SEC14L5	79	1	0			c.C993T						PASS	.	C		191,3593		4,183,1705	11.0	12.0	12.0		993	1.2	1.0	16	dbSNP_129	12	2,7978		0,2,3988	no	coding-synonymous	SEC14L5	NM_014692.1		4,185,5693	TT,TC,CC		0.0251,5.0476,1.6406		331/697	5050678	193,11571	1892	3990	5882	SO:0001819	synonymous_variant	9717	exon9			CATCCTCCGCCTG	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.993C>T	16.37:g.5050678C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			C|0.975;T|0.025	0.025	strong		0.632	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
COL27A1	85301	hgsc.bcm.edu	37	9	116931445	116931445	+	Missense_Mutation	SNP	T	T	C	rs2808770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	83	0	0		WXS	Illumina HiSeq	Phase_I	101	60	0.594059	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	
TRIM67	440730	hgsc.bcm.edu	37	1	231298970	231298970	+	Silent	SNP	T	T	C	rs372035563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:231298970T>C	ENST00000366653.5	+	1	255	c.255T>C	c.(253-255)gcT>gcC	p.A85A	TRIM67_ENST00000444294.3_Silent_p.A85A|TRIM67_ENST00000366652.2_Silent_p.A85A|TRIM67_ENST00000449018.3_Silent_p.A45A			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	85	Gly-rich.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				GGAGTGCAGCTGGCGGCCTCG	0.756													T|||	20	0.00399361	0.0151	0.0	5008	,	,		9536	0.0		0.0	False		,,,				2504	0.0				p.A85A		Atlas-SNP	.											.	TRIM67	160	.	0			c.T255C						PASS	.	T		1,2915		0,1,1457	2.0	2.0	2.0		255	-8.1	0.0	1		2	0,6030		0,0,3015	no	coding-synonymous	TRIM67	NM_001004342.3		0,1,4472	CC,CT,TT		0.0,0.0343,0.0112		85/784	231298970	1,8945	1458	3015	4473	SO:0001819	synonymous_variant	440730	exon1			TGCAGCTGGCGGC	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"""Tripartite motif containing / Tripartite motif containing"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	31859	protein-coding gene	gene with protein product		610584	"""tripartite motif-containing 67"""				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.255T>C	1.37:g.231298970T>C		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	17	5	0.294118	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	37	CCDS44333.1																																																																																			.	.	none		0.756	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342	
FMN2	56776	hgsc.bcm.edu	37	1	240370935	240370935	+	Silent	SNP	A	A	C	rs71170718|rs562038978|rs188083977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:240370935A>C	ENST00000319653.9	+	5	3053	c.2823A>C	c.(2821-2823)ggA>ggC	p.G941G		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	941	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCGGAGCGGGAATACCTCCTC	0.701																																					p.G941G		Atlas-SNP	.											FMN2,NS,carcinoma,+1,3	FMN2	451	3	0			c.A2823C						scavenged	.						24.0	30.0	28.0					1																	240370935		2136	4208	6344	SO:0001819	synonymous_variant	56776	exon5			AGCGGGAATACCT	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.2823A>C	1.37:g.240370935A>C		Somatic	126	30	0.238095		WXS	Illumina HiSeq	Phase_I	199	25	0.125628	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			A|0.982;C|0.018	0.018	strong		0.701	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
SGMS2	166929	hgsc.bcm.edu	37	4	108816880	108816880	+	Silent	SNP	G	G	A	rs150784082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:108816880G>A	ENST00000394684.4	+	3	728	c.171G>A	c.(169-171)ccG>ccA	p.P57P	RP11-286E11.1_ENST00000513071.1_RNA|SGMS2_ENST00000359079.4_Silent_p.P57P|RP11-286E11.1_ENST00000499098.1_RNA|SGMS2_ENST00000394686.3_Silent_p.P57P	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	57					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		AAAAGTACCCGGACTATATCC	0.443													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		20353	0.0		0.0	False		,,,				2504	0.0				p.P57P		Atlas-SNP	.											.	SGMS2	39	.	0			c.G171A						PASS	.	G	,,	56,4350	55.5+/-91.7	0,56,2147	98.0	94.0	95.0		171,171,171	-5.7	0.7	4	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SGMS2	NM_001136257.1,NM_001136258.1,NM_152621.5	,,	0,57,6446	AA,AG,GG		0.0116,1.271,0.4383	,,	57/366,57/366,57/366	108816880	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	166929	exon2			GTACCCGGACTAT	BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.171G>A	4.37:g.108816880G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001136257	A8K2S9|B2RA61	Silent	SNP	ENST00000394684.4	37	CCDS3677.1																																																																																			G|0.996;A|0.004	0.004	strong		0.443	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621	
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24259600	24259600	+	Missense_Mutation	SNP	C	C	T	rs76707982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24259600C>T	ENST00000256412.4	+	12	1535	c.1315C>T	c.(1315-1317)Cct>Tct	p.P439S	ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.P360S|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.P360S|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	439	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TTGTGGCTCTCCTAAGGTATT	0.368													C|||	72	0.014377	0.053	0.0029	5008	,	,		16709	0.0		0.0	False		,,,				2504	0.0				p.P439S	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											ADAMDEC1_ENST00000256412,NS,malignant_melanoma,-1,1	ADAMDEC1	69	1	0			c.C1315T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	219,4187	127.8+/-164.7	6,207,1990	77.0	79.0	78.0		1078,1078,1315	3.4	1.0	8	dbSNP_131	78	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	74,74,74	6,208,6289	TT,TC,CC		0.0116,4.9705,1.6915	probably-damaging,probably-damaging,probably-damaging	360/392,360/392,439/471	24259600	220,12786	2203	4300	6503	SO:0001583	missense	27299	exon12			GGCTCTCCTAAGG	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.1315C>T	8.37:g.24259600C>T	ENSP00000256412:p.Pro439Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	61	39	0.639344	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	12.49	1.952501	0.34471	0.049705	1.16E-4	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.10860	2.83;2.83;2.83	6.16	3.43	0.39272	Blood coagulation inhibitor, Disintegrin (3);	0.377504	0.26176	N	0.025893	T	0.01156	0.0038	L	0.47190	1.495	0.44188	D	0.997006	P	0.35192	0.489	B	0.39935	0.314	T	0.20472	-1.0274	10	0.38643	T	0.18	-5.4888	8.4866	0.33076	0.0:0.7617:0.0:0.2383	.	439	O15204	ADEC1_HUMAN	S	439;360;360	ENSP00000256412:P439S;ENSP00000442592:P360S;ENSP00000428993:P360S	ENSP00000256412:P439S	P	+	1	0	ADAMDEC1	24315545	0.000000	0.05858	1.000000	0.80357	0.989000	0.77384	-0.002000	0.12924	0.486000	0.27676	0.650000	0.86243	CCT	C|0.983;T|0.017	0.017	strong		0.368	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
AMN	81693	hgsc.bcm.edu	37	14	103395212	103395212	+	Missense_Mutation	SNP	G	G	T	rs568801729		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103395212G>T	ENST00000299155.5	+	5	446	c.413G>T	c.(412-414)cGc>cTc	p.R138L		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	138					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|excretion (GO:0007588)|Golgi to plasma membrane protein transport (GO:0043001)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTGCCCTGCCGCCACGACGAC	0.706																																					p.R138L		Atlas-SNP	.											.	AMN	13	.	0			c.G413T						PASS	.						30.0	28.0	29.0					14																	103395212		2203	4297	6500	SO:0001583	missense	81693	exon5			CCTGCCGCCACGA	AF328788	CCDS9977.1	14q32.32	2014-09-17	2012-12-07		ENSG00000166126	ENSG00000166126			14604	protein-coding gene	gene with protein product		605799	"""amnionless homolog (mouse)"""			11279523	Standard	NM_030943		Approved	amnionless	uc001ymg.4	Q9BXJ7		ENST00000299155.5:c.413G>T	14.37:g.103395212G>T	ENSP00000299155:p.Arg138Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	93	54	0.580645	NM_030943	Q6UX83	Missense_Mutation	SNP	ENST00000299155.5	37	CCDS9977.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.570223	0.45798	.	.	ENSG00000166126	ENST00000299155;ENST00000541086	D	0.88664	-2.41	4.03	0.969	0.19686	.	0.560105	0.18314	U	0.145003	D	0.84083	0.5394	M	0.61703	1.905	0.26626	N	0.972569	P	0.38020	0.615	B	0.38954	0.286	T	0.76173	-0.3056	10	0.62326	D	0.03	-1.9881	2.5302	0.04701	0.11:0.1861:0.5126:0.1913	.	138	Q9BXJ7	AMNLS_HUMAN	L	138;84	ENSP00000299155:R138L	ENSP00000299155:R138L	R	+	2	0	AMN	102464965	0.003000	0.15002	0.737000	0.30932	0.919000	0.55068	0.296000	0.19083	-0.112000	0.11979	0.306000	0.20318	CGC	.	.	none		0.706	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1		
IL1RL2	8808	hgsc.bcm.edu	37	2	102808560	102808560	+	Missense_Mutation	SNP	G	G	A	rs138663033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102808560G>A	ENST00000264257.2	+	4	595	c.469G>A	c.(469-471)Ggt>Agt	p.G157S	IL1RL2_ENST00000539491.1_Missense_Mutation_p.G157S|IL1RL2_ENST00000481806.1_Intron|IL1RL2_ENST00000441515.2_Intron	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	157	Ig-like C2-type 2.				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						TTGTGTTTTGGGTCCAATAAA	0.308													G|||	9	0.00179712	0.0068	0.0	5008	,	,		16785	0.0		0.0	False		,,,				2504	0.0				p.G157S		Atlas-SNP	.											.	IL1RL2	118	.	0			c.G469A						PASS	.	G	SER/GLY	14,4392	22.3+/-47.3	0,14,2189	85.0	82.0	83.0		469	2.1	0.1	2	dbSNP_134	83	0,8600		0,0,4300	yes	missense	IL1RL2	NM_003854.2	56	0,14,6489	AA,AG,GG		0.0,0.3177,0.1076	benign	157/576	102808560	14,12992	2203	4300	6503	SO:0001583	missense	8808	exon4			GTTTTGGGTCCAA	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.469G>A	2.37:g.102808560G>A	ENSP00000264257:p.Gly157Ser	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	238	95	0.39916	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	6.404	0.442727	0.12164	0.003177	0.0	ENSG00000115598	ENST00000264257;ENST00000421464;ENST00000539491	T;T;T	0.76709	-1.04;2.76;-1.04	5.4	2.08	0.27032	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.759510	0.01061	N	0.004654	T	0.49677	0.1571	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.48502	-0.9030	10	0.17832	T	0.49	.	3.1289	0.06417	0.2457:0.0:0.5487:0.2056	.	157	Q9HB29	ILRL2_HUMAN	S	157	ENSP00000264257:G157S;ENSP00000387611:G157S;ENSP00000442184:G157S	ENSP00000264257:G157S	G	+	1	0	IL1RL2	102174992	0.674000	0.27549	0.060000	0.19600	0.002000	0.02628	0.829000	0.27449	0.752000	0.32923	-0.169000	0.13324	GGT	G|0.999;A|0.001	0.001	strong		0.308	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854	
ROGDI	79641	hgsc.bcm.edu	37	16	4849726	4849726	+	Missense_Mutation	SNP	G	G	C	rs143095485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4849726G>C	ENST00000322048.7	-	6	771	c.393C>G	c.(391-393)gaC>gaG	p.D131E	ROGDI_ENST00000586336.1_5'UTR	NM_024589.2	NP_078865.1	Q9GZN7	ROGDI_HUMAN	rogdi homolog (Drosophila)	131					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	intracellular (GO:0005622)|nucleus (GO:0005634)				endometrium(2)|lung(1)|ovary(1)|skin(1)	5						GGTAGCTCTGGTCCCGGCTGG	0.602													G|||	88	0.0175719	0.0643	0.0043	5008	,	,		12956	0.0		0.0	False		,,,				2504	0.0				p.D131E		Atlas-SNP	.											.	ROGDI	11	.	0			c.C393G						PASS	.	G	GLU/ASP	269,4125	152.5+/-186.2	5,259,1933	99.0	79.0	86.0		393	-9.8	0.4	16	dbSNP_134	86	0,8600		0,0,4300	yes	missense	ROGDI	NM_024589.1	45	5,259,6233	CC,CG,GG		0.0,6.122,2.0702	benign	131/288	4849726	269,12725	2197	4300	6497	SO:0001583	missense	79641	exon6			GCTCTGGTCCCGG	AK026039	CCDS10523.1	16p13.3	2014-09-17			ENSG00000067836	ENSG00000067836			29478	protein-coding gene	gene with protein product		614574				11230166	Standard	NM_024589		Approved	FLJ22386	uc002cxv.4	Q9GZN7	OTTHUMG00000129479	ENST00000322048.7:c.393C>G	16.37:g.4849726G>C	ENSP00000322832:p.Asp131Glu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	129	59	0.457364	NM_024589	Q6IA00	Missense_Mutation	SNP	ENST00000322048.7	37	CCDS10523.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	G	6.305	0.424431	0.11928	0.06122	0.0	ENSG00000067836	ENST00000322048	T	0.41065	1.01	4.91	-9.82	0.00484	.	0.057101	0.64402	D	0.000002	T	0.01870	0.0059	L	0.39020	1.185	0.32051	N	0.596972	B	0.10296	0.003	B	0.14023	0.01	T	0.11227	-1.0596	10	0.17369	T	0.5	1.2912	4.1989	0.10457	0.1965:0.3057:0.4049:0.0929	.	131	Q9GZN7	ROGDI_HUMAN	E	131	ENSP00000322832:D131E	ENSP00000322832:D131E	D	-	3	2	ROGDI	4789727	0.003000	0.15002	0.407000	0.26434	0.258000	0.26162	-0.702000	0.05069	-2.194000	0.00753	-0.254000	0.11334	GAC	G|0.980;C|0.020	0.020	strong		0.602	ROGDI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251643.3	NM_024589	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39913634	39913634	+	Missense_Mutation	SNP	G	G	A	rs10407035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39913634G>A	ENST00000409794.3	+	18	2790	c.1940G>A	c.(1939-1941)cGc>cAc	p.R647H	PLEKHG2_ENST00000425673.1_Missense_Mutation_p.R618H|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.R588H|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000378550.1_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	647			R -> H (in dbSNP:rs10407035). {ECO:0000269|PubMed:15489334}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			ATTCCCAGCCGCTGTGAAATT	0.522													G|||	1227	0.245008	0.202	0.1974	5008	,	,		19345	0.3909		0.1571	False		,,,				2504	0.2771				p.R647H		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G1940A						PASS	.	G	HIS/ARG	921,3485	353.6+/-312.2	86,749,1368	89.0	93.0	91.0		1940	-2.8	0.0	19	dbSNP_119	91	970,7630	210.5+/-251.4	54,862,3384	yes	missense	PLEKHG2	NM_022835.2	29	140,1611,4752	AA,AG,GG		11.2791,20.9033,14.5394	benign	647/1387	39913634	1891,11115	2203	4300	6503	SO:0001583	missense	64857	exon18			CCAGCCGCTGTGA	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.1940G>A	19.37:g.39913634G>A	ENSP00000386733:p.Arg647His	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	121	65	0.53719	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	493|493	0.22573260073260074|0.22573260073260074	111|111	0.22560975609756098|0.22560975609756098	63|63	0.17403314917127072|0.17403314917127072	208|208	0.36363636363636365|0.36363636363636365	111|111	0.14643799472295516|0.14643799472295516	G|G	7.223|7.223	0.597725|0.597725	0.13875|0.13875	0.209033|0.209033	0.112791|0.112791	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000458508	.|T;T;T	.|0.68479	.|-0.21;-0.21;-0.33	3.19|3.19	-2.84|-2.84	0.05751|0.05751	.|.	.|0.776000	.|0.10572	.|N	.|0.659076	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|P;P;D	.|0.53151	.|0.955;0.925;0.958	.|B;B;B	.|0.41723	.|0.365;0.2;0.27	T|T	0.18524|0.18524	-1.0334|-1.0334	4|9	.|0.41790	.|T	.|0.15	.|.	4.667|4.667	0.12671|0.12671	0.2592:0.0:0.3855:0.3552|0.2592:0.0:0.3855:0.3552	rs10407035;rs17845383;rs17858238;rs57929826;rs10407035|rs10407035;rs17845383;rs17858238;rs57929826;rs10407035	.|618;647;588	.|Q9H7P9-3;Q9H7P9;E7ESZ3	.|.;PKHG2_HUMAN;.	T|H	515|647;618;588	.|ENSP00000386733:R647H;ENSP00000392906:R618H;ENSP00000408857:R588H	.|ENSP00000386733:R647H	A|R	+|+	1|2	0|0	PLEKHG2|PLEKHG2	44605474|44605474	0.000000|0.000000	0.05858|0.05858	0.038000|0.038000	0.18304|0.18304	0.082000|0.082000	0.17680|0.17680	-0.547000|-0.547000	0.06055|0.06055	-0.311000|-0.311000	0.08754|0.08754	-1.250000|-1.250000	0.01514|0.01514	GCT|CGC	G|0.823;A|0.177	0.177	strong		0.522	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
HOXB8	3218	hgsc.bcm.edu	37	17	46690623	46690623	+	Missense_Mutation	SNP	G	G	C	rs112046402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:46690623G>C	ENST00000239144.4	-	2	907	c.673C>G	c.(673-675)Ctg>Gtg	p.L225V	HOXB7_ENST00000239165.7_5'Flank|HOXB8_ENST00000576562.1_Missense_Mutation_p.L224V|HOXB7_ENST00000567101.2_Intron	NM_024016.3	NP_076921.1	P17481	HXB8_HUMAN	homeobox B8	225					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|dorsal spinal cord development (GO:0021516)|embryonic skeletal system morphogenesis (GO:0048704)|grooming behavior (GO:0007625)|negative regulation of myeloid cell differentiation (GO:0045638)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(8)|urinary_tract(2)	11						GCCCGCTCCAGCTTCTGTTTC	0.612													G|||	155	0.0309505	0.1142	0.0058	5008	,	,		8098	0.0		0.0	False		,,,				2504	0.0				p.L225V		Atlas-SNP	.											.	HOXB8	26	.	0			c.C673G						PASS	.	G	VAL/LEU	341,4065	176.2+/-205.4	7,327,1869	81.0	83.0	83.0		673	1.9	1.0	17	dbSNP_132	83	1,8599		0,1,4299	yes	missense	HOXB8	NM_024016.3	32	7,328,6168	CC,CG,GG		0.0116,7.7394,2.6296	benign	225/244	46690623	342,12664	2203	4300	6503	SO:0001583	missense	3218	exon2			GCTCCAGCTTCTG		CCDS11533.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120068	ENSG00000120068		"""Homeoboxes / ANTP class : HOXL subclass"""	5119	protein-coding gene	gene with protein product		142963	"""homeo box B8"""	HOX2, HOX2D		1973146, 1358459	Standard	XM_005257286		Approved		uc002inw.3	P17481	OTTHUMG00000159904	ENST00000239144.4:c.673C>G	17.37:g.46690623G>C	ENSP00000239144:p.Leu225Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	NM_024016	Q9H1I2	Missense_Mutation	SNP	ENST00000239144.4	37	CCDS11533.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	G	7.810	0.715510	0.15306	0.077394	1.16E-4	ENSG00000120068	ENST00000239144	D	0.90324	-2.65	3.04	1.94	0.25998	.	0.473524	0.13687	U	0.369761	T	0.15046	0.0363	N	0.14661	0.345	0.25211	N	0.989973	B	0.12013	0.005	B	0.12156	0.007	T	0.43956	-0.9359	10	0.29301	T	0.29	.	8.2888	0.31946	0.0:0.0:0.4932:0.5068	.	225	P17481	HXB8_HUMAN	V	225	ENSP00000239144:L225V	ENSP00000239144:L225V	L	-	1	2	HOXB8	44045622	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.900000	0.48687	1.734000	0.51633	0.479000	0.44913	CTG	G|0.977;C|0.023	0.023	strong		0.612	HOXB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358092.3		
C19orf54	284325	hgsc.bcm.edu	37	19	41255603	41255603	+	Silent	SNP	G	G	A	rs2254338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41255603G>A	ENST00000378313.2	-	1	225	c.106C>T	c.(106-108)Ctg>Ttg	p.L36L	SNRPA_ENST00000243563.3_5'Flank|C19orf54_ENST00000470681.1_Intron|C19orf54_ENST00000339153.3_Intron|C19orf54_ENST00000598485.2_Intron|C19orf54_ENST00000598729.1_Intron	NM_198476.3	NP_940878.3	Q5BKX5	CS054_HUMAN	chromosome 19 open reading frame 54	36	Pro-rich.									breast(1)|lung(1)|urinary_tract(2)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GAAAAGTCCAGGGGACTTGGG	0.597													G|||	517	0.103235	0.1203	0.0432	5008	,	,		16282	0.2302		0.0467	False		,,,				2504	0.0501				p.L36L		Atlas-SNP	.											.	C19orf54	13	.	0			c.C106T						PASS	.						9.0	12.0	11.0					19																	41255603		691	1585	2276	SO:0001819	synonymous_variant	284325	exon1			AGTCCAGGGGACT	AK123126	CCDS12564.2	19q13.2	2012-10-26			ENSG00000188493	ENSG00000188493			24758	protein-coding gene	gene with protein product							Standard	NM_198476		Approved	FLJ41131	uc002oou.1	Q5BKX5	OTTHUMG00000150174	ENST00000378313.2:c.106C>T	19.37:g.41255603G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	159	89	0.559748	NM_198476	A8MSZ5|B4DNU7	Silent	SNP	ENST00000378313.2	37	CCDS12564.2																																																																																			G|0.877;A|0.123	0.123	strong		0.597	C19orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316701.1	NM_198476	
GABRG3	2567	hgsc.bcm.edu	37	15	27222266	27222266	+	Silent	SNP	A	A	G	rs35752220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:27222266A>G	ENST00000333743.6	+	2	425	c.171A>G	c.(169-171)gaA>gaG	p.E57E	GABRG3_ENST00000555083.1_Silent_p.E57E	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	57					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)	TGCTAAGAGAATATGATAAAA	0.348													A|||	182	0.0363419	0.1316	0.0101	5008	,	,		19188	0.0		0.001	False		,,,				2504	0.0				p.E57E	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.A171G						PASS	.	A		345,3291		16,313,1489	99.0	99.0	99.0		171	3.0	1.0	15	dbSNP_126	99	3,8149		0,3,4073	no	coding-synonymous	GABRG3	NM_033223.4		16,316,5562	GG,GA,AA		0.0368,9.4884,2.9522		57/468	27222266	348,11440	1818	4076	5894	SO:0001819	synonymous_variant	2567	exon2			AAGAGAATATGAT		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.171A>G	15.37:g.27222266A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_001270873	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1																																																																																			A|0.970;G|0.030	0.030	strong		0.348	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
FLG	2312	hgsc.bcm.edu	37	1	152276699	152276699	+	Missense_Mutation	SNP	A	A	G	rs12728605		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276699A>G	ENST00000368799.1	-	3	10698	c.10663T>C	c.(10663-10665)Tgg>Cgg	p.W3555R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3555	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)			GACCCAGACCACCTCTCAGAG	0.587									Ichthyosis																												p.W3555R		Atlas-SNP	.											.	FLG	900	.	0			c.T10663C						PASS	.						153.0	176.0	168.0					1																	152276699		2203	4297	6500	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CAGACCACCTCTC	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.10663T>C	1.37:g.152276699A>G	ENSP00000357789:p.Trp3555Arg	Somatic	460	1	0.00217391		WXS	Illumina HiSeq	Phase_I	481	257	0.534304	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	0.499	-0.871634	0.02570	.	.	ENSG00000143631	ENST00000368799	T	0.01560	4.77	2.05	-1.37	0.09056	.	.	.	.	.	T	0.00328	0.0010	N	0.11560	0.145	0.09310	N	1	B	0.24823	0.112	B	0.30646	0.118	T	0.36089	-0.9762	9	0.16420	T	0.52	.	3.8418	0.08917	0.1491:0.0:0.4879:0.3631	rs12728605	3555	P20930	FILA_HUMAN	R	3555	ENSP00000357789:W3555R	ENSP00000357789:W3555R	W	-	1	0	FLG	150543323	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.181000	0.03085	-0.764000	0.04651	-2.221000	0.00296	TGG	A|0.167;G|0.833	0.833	weak		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CEMIP	57214	hgsc.bcm.edu	37	15	81172064	81172064	+	Silent	SNP	G	G	A	rs35541581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81172064G>A	ENST00000394685.3	+	5	668	c.249G>A	c.(247-249)ctG>ctA	p.L83L	KIAA1199_ENST00000220244.3_Silent_p.L83L|KIAA1199_ENST00000356249.5_Silent_p.L83L			Q8WUJ3	CEMIP_HUMAN		83	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CAGGCAAGCTGGTCATTAAAG	0.527													A|||	357	0.0712859	0.2481	0.0389	5008	,	,		19880	0.0		0.002	False		,,,				2504	0.0				p.L83L		Atlas-SNP	.											.	KIAA1199	118	.	0			c.G249A						PASS	.	A		941,3465	736.2+/-410.7	102,737,1364	78.0	70.0	73.0		249	-12.1	0.0	15	dbSNP_126	73	29,8571	817.9+/-406.9	0,29,4271	no	coding-synonymous	KIAA1199	NM_018689.1		102,766,5635	AA,AG,GG		0.3372,21.3572,7.4581		83/1362	81172064	970,12036	2203	4300	6503	SO:0001819	synonymous_variant	57214	exon4			CAAGCTGGTCATT																												ENST00000394685.3:c.249G>A	15.37:g.81172064G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																			G|0.928;A|0.072	0.072	strong		0.527	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
MYLK	4638	hgsc.bcm.edu	37	3	123368013	123368013	+	Silent	SNP	A	A	G	rs1254392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:123368013A>G	ENST00000475616.1	-	22	4316	c.4317T>C	c.(4315-4317)gaT>gaC	p.D1439D	MYLK_ENST00000360304.3_Silent_p.D1439D|MYLK_ENST00000359169.1_Silent_p.D1439D|MYLK_ENST00000346322.5_Silent_p.D1370D|MYLK_ENST00000354792.5_Silent_p.D239D|MYLK_ENST00000360772.3_Silent_p.D1439D			Q15746	MYLK_HUMAN	myosin light chain kinase	1439	Actin-binding (calcium/calmodulin- insensitive). {ECO:0000250}.				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)		ACTCACCATCATCTGACACCT	0.592													G|||	1984	0.396166	0.5401	0.3285	5008	,	,		16095	0.6448		0.0895	False		,,,				2504	0.3088				p.D1439D		Atlas-SNP	.											.	MYLK	224	.	0			c.T4317C						PASS	.	G	,,,	2112,2294	600.7+/-389.6	506,1100,597	94.0	101.0	99.0		4317,4110,4317,4110	2.8	1.0	3	dbSNP_87	99	809,7791	782.2+/-407.6	47,715,3538	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	,,,	553,1815,4135	GG,GA,AA		9.407,47.9346,22.4589	,,,	1439/1915,1370/1846,1439/1864,1370/1795	123368013	2921,10085	2203	4300	6503	SO:0001819	synonymous_variant	4638	exon25			ACCATCATCTGAC	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.4317T>C	3.37:g.123368013A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	77	36	0.467532	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|0.731;G|0.269	0.269	strong		0.592	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
CYB561	1534	hgsc.bcm.edu	37	17	61513509	61513509	+	Silent	SNP	C	C	T	rs35447397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61513509C>T	ENST00000392976.1	-	3	506	c.207G>A	c.(205-207)ctG>ctA	p.L69L	CYB561_ENST00000542042.1_Silent_p.L136L|CYB561_ENST00000584031.1_Silent_p.L69L|CYB561_ENST00000392975.2_Silent_p.L69L|CYB561_ENST00000582297.1_Silent_p.L69L|CYB561_ENST00000581163.1_5'UTR|CYB561_ENST00000581573.1_Silent_p.L69L|CYB561_ENST00000582034.1_Silent_p.L40L|CYB561_ENST00000360793.3_Silent_p.L69L|CYB561_ENST00000448884.2_Silent_p.L69L|CYB561_ENST00000582997.1_Silent_p.L76L	NM_001017916.1	NP_001017916.1	P49447	CY561_HUMAN	cytochrome b561	69	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				electron transport chain (GO:0022900)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|transmembrane electron transfer carrier (GO:0022865)			lung(2)|ovary(1)|prostate(1)	4				READ - Rectum adenocarcinoma(1115;0.0689)		GGTAAACCAGCAGGGCTGTGG	0.607													C|||	41	0.0081869	0.031	0.0	5008	,	,		17487	0.0		0.0	False		,,,				2504	0.0				p.L69L		Atlas-SNP	.											.	CYB561	15	.	0			c.G207A						PASS	.	C	,,	114,4290	87.8+/-126.4	1,112,2089	128.0	94.0	106.0		207,207,207	3.9	1.0	17	dbSNP_126	106	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CYB561	NM_001017916.1,NM_001017917.1,NM_001915.3	,,	1,112,6389	TT,TC,CC		0.0,2.5886,0.8767	,,	69/252,69/252,69/252	61513509	114,12890	2202	4300	6502	SO:0001819	synonymous_variant	1534	exon3			AACCAGCAGGGCT		CCDS11636.1	17q23.3	2013-03-14	2013-03-14		ENSG00000008283	ENSG00000008283		"""Cytochrome b genes"""	2571	protein-coding gene	gene with protein product	"""ferric-chelate reductase 2"", ""cytochrome b561 family, member A1"""	600019				7959749, 23249217	Standard	XM_005257091		Approved	FRRS2, CYB561A1	uc002jas.3	P49447		ENST00000392976.1:c.207G>A	17.37:g.61513509C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001915	B2RE96|B7Z775|D3DU11|Q5BJG9|Q9BU05|Q9BWR9	Silent	SNP	ENST00000392976.1	37	CCDS11636.1																																																																																			C|0.989;T|0.011	0.011	strong		0.607	CYB561-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444843.1	NM_001915	
CFAP58	159686	hgsc.bcm.edu	37	10	106152111	106152111	+	Missense_Mutation	SNP	T	T	A	rs11192036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:106152111T>A	ENST00000369704.3	+	10	1620	c.1486T>A	c.(1486-1488)Tca>Aca	p.S496T		NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		496			S -> T (in dbSNP:rs11192036).			extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		AGCTGTGAGATCAGACAGAAA	0.303													T|||	1104	0.220447	0.2042	0.1945	5008	,	,		16246	0.2341		0.2634	False		,,,				2504	0.2025				p.S496T		Atlas-SNP	.											.	CCDC147	137	.	0			c.T1486A						PASS	.	T	THR/SER	872,3532	315.2+/-294.0	93,686,1423	54.0	61.0	59.0		1486	5.5	1.0	10	dbSNP_120	59	2203,6393	358.1+/-331.0	281,1641,2376	yes	missense	CCDC147	NM_001008723.1	58	374,2327,3799	AA,AT,TT		25.6282,19.8002,23.6538	benign	496/873	106152111	3075,9925	2202	4298	6500	SO:0001583	missense	159686	exon10			GTGAGATCAGACA																												ENST00000369704.3:c.1486T>A	10.37:g.106152111T>A	ENSP00000358718:p.Ser496Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	37	CCDS31282.1	519	0.23763736263736263	98	0.1991869918699187	75	0.20718232044198895	149	0.26048951048951047	197	0.2598944591029024	T	12.33	1.905796	0.33628	0.198002	0.256282	ENSG00000120051	ENST00000369704	T	0.44482	0.92	5.49	5.49	0.81192	.	0.260201	0.38897	N	0.001522	T	0.00012	0.0000	L	0.31804	0.96	0.09310	P	1.0	B	0.25521	0.128	B	0.25405	0.06	T	0.28396	-1.0045	9	0.17832	T	0.49	-4.5368	11.393	0.49825	0.1433:0.0:0.0:0.8567	rs11192036;rs17755504;rs52829473;rs11192036	496	Q5T655	CC147_HUMAN	T	496	ENSP00000358718:S496T	ENSP00000358718:S496T	S	+	1	0	CCDC147	106142101	0.999000	0.42202	0.994000	0.49952	0.920000	0.55202	2.502000	0.45398	2.093000	0.63338	0.533000	0.62120	TCA	T|0.767;A|0.233	0.233	strong		0.303	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1		
NOTCH3	4854	hgsc.bcm.edu	37	19	15290007	15290007	+	Missense_Mutation	SNP	C	C	T	rs10408676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15290007C>T	ENST00000263388.2	-	22	3622	c.3547G>A	c.(3547-3549)Gtg>Atg	p.V1183M		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1183	EGF-like 30; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		V -> M (in dbSNP:rs10408676). {ECO:0000269|PubMed:9388399}.		forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			ACCAGGTCCACGCAGGTGCCA	0.632													C|||	423	0.0844649	0.289	0.0259	5008	,	,		18528	0.0		0.007	False		,,,				2504	0.0164				p.V1183M		Atlas-SNP	.											.	NOTCH3	340	.	0			c.G3547A						PASS	.	C	MET/VAL	1066,3340	371.5+/-320.0	150,766,1287	35.0	40.0	38.0		3547	3.9	1.0	19	dbSNP_119	38	67,8533	38.3+/-94.2	0,67,4233	yes	missense	NOTCH3	NM_000435.2	21	150,833,5520	TT,TC,CC		0.7791,24.1943,8.7114	possibly-damaging	1183/2322	15290007	1133,11873	2203	4300	6503	SO:0001583	missense	4854	exon22			GGTCCACGCAGGT	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.3547G>A	19.37:g.15290007C>T	ENSP00000263388:p.Val1183Met	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	145	0.06639194139194139	125	0.2540650406504065	14	0.03867403314917127	0	0.0	6	0.0079155672823219	C	19.66	3.868866	0.72065	0.241943	0.007791	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.95103	-3.61	3.9	3.9	0.45041	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00356	0.0011	M	0.80183	2.485	0.21445	P	0.999688477	D;P	0.58620	0.983;0.698	P;B	0.54629	0.757;0.384	T	0.00000	-1.3391	8	0.56958	D	0.05	.	8.7049	0.34349	0.0:0.8903:0.0:0.1097	rs10408676;rs60652871;rs10408676	1134;1183	Q59FL3;Q9UM47	.;NOTC3_HUMAN	M	1183;1133	ENSP00000263388:V1183M	ENSP00000263388:V1183M	V	-	1	0	NOTCH3	15151007	0.965000	0.33210	0.992000	0.48379	0.925000	0.55904	2.324000	0.43831	1.720000	0.51447	0.561000	0.74099	GTG	C|0.924;T|0.076	0.076	strong		0.632	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
PTDSS2	81490	hgsc.bcm.edu	37	11	490036	490036	+	Silent	SNP	G	G	A	rs75782220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:490036G>A	ENST00000308020.5	+	11	1445	c.1269G>A	c.(1267-1269)gcG>gcA	p.A423A		NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	423					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	CCGTCCTGGCGCTCACCTGGA	0.657													G|||	347	0.0692891	0.0182	0.1282	5008	,	,		15765	0.1508		0.0258	False		,,,				2504	0.0573				p.A423A		Atlas-SNP	.											PTDSS2,caecum,carcinoma,0,3	PTDSS2	27	3	0			c.G1269A						PASS	.	G		107,4299	84.4+/-122.9	0,107,2096	88.0	59.0	69.0		1269	1.6	1.0	11	dbSNP_131	69	283,8317	105.0+/-166.0	9,265,4026	no	coding-synonymous	PTDSS2	NM_030783.1		9,372,6122	AA,AG,GG		3.2907,2.4285,2.9986		423/488	490036	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	81490	exon11			CCTGGCGCTCACC	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.1269G>A	11.37:g.490036G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	61	22	0.360656	NM_030783		Silent	SNP	ENST00000308020.5	37	CCDS7696.1																																																																																			G|0.960;A|0.040	0.040	strong		0.657	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2		
ALPK1	80216	hgsc.bcm.edu	37	4	113353285	113353285	+	Missense_Mutation	SNP	T	T	C	rs11726117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:113353285T>C	ENST00000458497.1	+	11	2861	c.2582T>C	c.(2581-2583)aTg>aCg	p.M861T	ALPK1_ENST00000177648.9_Missense_Mutation_p.M861T|ALPK1_ENST00000504176.2_Missense_Mutation_p.M783T	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	861			M -> T (in dbSNP:rs11726117). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.5}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CTCGACAGCATGGATGTTCCC	0.577													C|||	3298	0.658546	0.7481	0.5807	5008	,	,		20612	0.7014		0.6501	False		,,,				2504	0.5573				p.M861T		Atlas-SNP	.											ALPK1,NS,carcinoma,-1,1	ALPK1	125	1	0			c.T2582C						PASS	.	C	THR/MET,THR/MET	3195,1211	421.1+/-339.2	1157,881,165	55.0	52.0	53.0		2582,2582	1.7	0.0	4	dbSNP_120	53	5658,2942	457.6+/-364.4	1858,1942,500	yes	missense,missense	ALPK1	NM_001102406.1,NM_025144.3	81,81	3015,2823,665	CC,CT,TT		34.2093,27.4852,31.9314	benign,benign	861/1245,861/1245	113353285	8853,4153	2203	4300	6503	SO:0001583	missense	80216	exon11			ACAGCATGGATGT	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.2582T>C	4.37:g.113353285T>C	ENSP00000398048:p.Met861Thr	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	1473	0.6744505494505495	354	0.7195121951219512	209	0.5773480662983426	415	0.7255244755244755	495	0.6530343007915568	C	0.010	-1.766884	0.00651	0.725148	0.657907	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.02258	4.45;4.45;4.37	4.66	1.74	0.24563	.	0.519792	0.18510	N	0.139088	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14392	-1.0474	9	0.02654	T	1	0.2401	4.8695	0.13625	0.2163:0.5002:0.0:0.2834	rs11726117;rs52800541;rs58704414;rs11726117	783;861	F5H138;Q96QP1	.;ALPK1_HUMAN	T	861;861;783	ENSP00000398048:M861T;ENSP00000177648:M861T;ENSP00000426044:M783T	ENSP00000177648:M861T	M	+	2	0	ALPK1	113572734	0.000000	0.05858	0.004000	0.12327	0.012000	0.07955	-1.408000	0.02485	0.136000	0.18733	-0.726000	0.03593	ATG	C|0.679;N|0.000	0.679	strong		0.577	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
HS3ST6	64711	hgsc.bcm.edu	37	16	1961866	1961866	+	Silent	SNP	G	G	A	rs61742747	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1961866G>A	ENST00000293937.3	-	2	753	c.754C>T	c.(754-756)Ctg>Ttg	p.L252L	HS3ST6_ENST00000443547.1_Silent_p.L221L|HS3ST6_ENST00000454677.2_Silent_p.L269L			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	93	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	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	
ATF6B	1388	hgsc.bcm.edu	37	6	32093922	32093922	+	Silent	SNP	G	G	A	rs204894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32093922G>A	ENST00000375203.3	-	5	482	c.450C>T	c.(448-450)aaC>aaT	p.N150N	ATF6B_ENST00000468502.1_5'UTR|ATF6B_ENST00000375201.4_Silent_p.N147N	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	150					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						TGGGGATAACGTTGATCTGGA	0.512													G|||	244	0.048722	0.115	0.0648	5008	,	,		15085	0.001		0.0457	False		,,,				2504	0.0				p.N150N		Atlas-SNP	.											.	ATF6B	40	.	0			c.C450T						PASS	.	G	,	453,3953	216.4+/-235.1	21,411,1771	157.0	137.0	144.0		441,450	-0.3	1.0	6	dbSNP_79	144	404,8196	127.2+/-185.5	7,390,3903	yes	coding-synonymous,coding-synonymous	ATF6B	NM_001136153.1,NM_004381.4	,	28,801,5674	AA,AG,GG		4.6977,10.2814,6.5893	,	147/701,150/704	32093922	857,12149	2203	4300	6503	SO:0001819	synonymous_variant	1388	exon5			GATAACGTTGATC		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"""basic leucine zipper proteins"""	2349	protein-coding gene	gene with protein product		600984	"""cAMP responsive element binding protein-like 1"""	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.450C>T	6.37:g.32093922G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Silent	SNP	ENST00000375203.3	37	CCDS4737.1																																																																																			G|0.945;A|0.055	0.055	strong		0.512	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2		
LACC1	144811	hgsc.bcm.edu	37	13	44457925	44457925	+	Missense_Mutation	SNP	A	A	G	rs3764147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:44457925A>G	ENST00000441843.1	+	4	1245	c.760A>G	c.(760-762)Atc>Gtc	p.I254V	LACC1_ENST00000325686.6_Missense_Mutation_p.I254V	NM_001128303.1	NP_001121775.1	Q8IV20	LACC1_HUMAN	laccase (multicopper oxidoreductase) domain containing 1	254			I -> V (in dbSNP:rs3764147). {ECO:0000269|PubMed:14702039}.														TTCCAATGACATCTGGATTAT	0.378													A|||	1532	0.305911	0.3048	0.3646	5008	,	,		15919	0.3472		0.2266	False		,,,				2504	0.3047				p.I254V		Atlas-SNP	.											.	.	.	.	0			c.A760G						PASS	.	A	VAL/ILE,VAL/ILE	1297,3109	437.2+/-344.9	200,897,1106	88.0	85.0	86.0	http://omim.org/entry/613407|http://www.ncbi.nlm.nih.gov/pubmed?term	760,760	1.9	0.8	13	dbSNP_107	86	1981,6619	347.4+/-326.6	236,1509,2555	yes	missense,missense	LACC1	NM_001128303.1,NM_153218.2	29,29	436,2406,3661	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	23.0349,29.4371,25.2038	benign,benign	254/431,254/431	44457925	3278,9728	2203	4300	6503	SO:0001583	missense	144811	exon4			AATGACATCTGGA	AK096044	CCDS9391.1	13q14.11	2012-05-11	2011-08-09	2011-08-09	ENSG00000179630	ENSG00000179630			26789	protein-coding gene	gene with protein product		613409	"""chromosome 13 open reading frame 31"""	C13orf31		16740638, 22504414	Standard	NM_153218		Approved	FLJ38725	uc010acg.3	Q8IV20	OTTHUMG00000016826	ENST00000441843.1:c.760A>G	13.37:g.44457925A>G	ENSP00000391747:p.Ile254Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_001128303	A2A3Z6|Q8N8X5	Missense_Mutation	SNP	ENST00000441843.1	37	CCDS9391.1	660	0.3021978021978022	161	0.32723577235772355	134	0.3701657458563536	184	0.32167832167832167	181	0.23878627968337732	A	1.113	-0.657608	0.03454	0.294371	0.230349	ENSG00000179630	ENST00000441843;ENST00000325686	T;T	0.33216	1.42;1.42	5.7	1.94	0.25998	.	0.235834	0.42548	N	0.000690	T	0.00012	0.0000	N	0.01257	-0.925	0.39694	P	0.028919999999999946	B	0.06786	0.001	B	0.04013	0.001	T	0.47156	-0.9139	9	0.02654	T	1	-11.666	8.8558	0.35227	0.3187:0.0:0.6813:0.0	rs3764147;rs61264110;rs3764147	254	Q8IV20	LACC1_HUMAN	V	254	ENSP00000391747:I254V;ENSP00000317619:I254V	ENSP00000317619:I254V	I	+	1	0	LACC1	43355925	1.000000	0.71417	0.815000	0.32552	0.795000	0.44927	2.664000	0.46783	0.041000	0.15688	-0.242000	0.12053	ATC	A|0.722;G|0.278	0.278	strong		0.378	LACC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044726.3	NM_153218	
CDK12	51755	hgsc.bcm.edu	37	17	37682200	37682200	+	Missense_Mutation	SNP	A	A	G	rs61747430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37682200A>G	ENST00000447079.4	+	13	3424	c.3391A>G	c.(3391-3393)Atc>Gtc	p.I1131V	CDK12_ENST00000430627.2_Missense_Mutation_p.I1131V	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1131					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CGACCTGAGCATCCCTCAAAT	0.507			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)			A|||	43	0.00858626	0.0325	0.0	5008	,	,		19029	0.0		0.0	False		,,,				2504	0.0				p.I1131V		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	161	.	0			c.A3391G						PASS	.	A	VAL/ILE,VAL/ILE	148,4258	103.0+/-141.5	3,142,2058	88.0	75.0	80.0		3391,3391	2.6	1.0	17	dbSNP_129	80	1,8599		0,1,4299	yes	missense,missense	CDK12	NM_016507.2,NM_015083.1	29,29	3,143,6357	GG,GA,AA		0.0116,3.3591,1.1456	benign,benign	1131/1491,1131/1482	37682200	149,12857	2203	4300	6503	SO:0001583	missense	51755	exon13			CTGAGCATCCCTC	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.3391A>G	17.37:g.37682200A>G	ENSP00000398880:p.Ile1131Val	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	239	106	0.443515	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	A	4.981	0.182220	0.09495	0.033591	1.16E-4	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.67171	-0.23;-0.25	4.82	2.59	0.31030	.	0.151372	0.30374	N	0.009776	T	0.13457	0.0326	N	0.01668	-0.77	0.30087	N	0.808665	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.10917	-1.0609	10	0.30854	T	0.27	-6.9124	7.0706	0.25177	0.6741:0.0:0.3259:0.0	rs61747430	1130;1131;1131	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	V	1131	ENSP00000407720:I1131V;ENSP00000398880:I1131V	ENSP00000407720:I1131V	I	+	1	0	CDK12	34935726	0.995000	0.38212	0.998000	0.56505	0.771000	0.43674	1.586000	0.36611	0.811000	0.34303	-0.385000	0.06624	ATC	A|0.989;G|0.011	0.011	strong		0.507	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
WDR90	197335	hgsc.bcm.edu	37	16	711905	711905	+	Silent	SNP	A	A	G	rs2301426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	79	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	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	
NR1I2	8856	hgsc.bcm.edu	37	3	119530546	119530546	+	Silent	SNP	T	T	C	rs12721611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119530546T>C	ENST00000337940.4	+	4	657	c.609T>C	c.(607-609)acT>acC	p.T203T	NR1I2_ENST00000466380.1_Silent_p.T164T|NR1I2_ENST00000393716.2_Silent_p.T164T	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	164	Hinge.				drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|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)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	CCTTTGACACTACCTTCTCCC	0.527													T|||	76	0.0151757	0.0545	0.0058	5008	,	,		20683	0.0		0.0	False		,,,				2504	0.0				p.T203T		Atlas-SNP	.											.	NR1I2	44	.	0			c.T609C						PASS	.	T	,,	232,4174	136.5+/-172.5	3,226,1974	110.0	97.0	101.0		492,609,492	3.0	1.0	3	dbSNP_126	101	6,8594	2.2+/-6.3	1,4,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	NR1I2	NM_003889.3,NM_022002.2,NM_033013.2	,,	4,230,6269	CC,CT,TT		0.0698,5.2655,1.8299	,,	164/435,203/474,164/398	119530546	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	8856	exon4			TGACACTACCTTC	AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"""Nuclear hormone receptors"""	7968	protein-coding gene	gene with protein product	"""pregnane X receptor"", ""orphan nuclear receptor PXR"""	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	ENST00000337940.4:c.609T>C	3.37:g.119530546T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_022002	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Silent	SNP	ENST00000337940.4	37	CCDS2995.1																																																																																			T|0.981;C|0.019	0.019	strong		0.527	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1		
ZNF521	25925	hgsc.bcm.edu	37	18	22775185	22775185	+	Silent	SNP	C	C	T	rs1140026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:22775185C>T	ENST00000361524.3	-	5	3745	c.3597G>A	c.(3595-3597)aaG>aaA	p.K1199K	ZNF521_ENST00000584787.1_Silent_p.K979K|ZNF521_ENST00000538137.2_Silent_p.K1199K	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1199					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CCATCTGACACTTGATGCATT	0.323			T	PAX5	ALL								C|||	1135	0.226637	0.1316	0.2089	5008	,	,		19650	0.2768		0.2535	False		,,,				2504	0.2883				p.K1199K		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.G3597A						PASS	.	C		631,3773	271.6+/-270.3	33,565,1604	145.0	126.0	133.0		3597	5.6	1.0	18	dbSNP_86	133	2084,6516	357.9+/-330.9	254,1576,2470	no	coding-synonymous	ZNF521	NM_015461.2		287,2141,4074	TT,TC,CC		24.2326,14.3279,20.8782		1199/1312	22775185	2715,10289	2202	4300	6502	SO:0001819	synonymous_variant	25925	exon5			CTGACACTTGATG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3597G>A	18.37:g.22775185C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	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	
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156067	39156067	+	Silent	SNP	A	A	G	rs9890989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39156067A>G	ENST00000391587.1	-	1	71	c.39T>C	c.(37-39)acT>acC	p.T13T		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	13	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				TGGCAGGCCCAGTGGGGACAC	0.562													.|||	1497	0.298922	0.6112	0.2075	5008	,	,		17956	0.2302		0.1223	False		,,,				2504	0.1943				p.T13T		Atlas-SNP	.											.	KRTAP3-2	11	.	0			c.T39C						PASS	.	G		1929,2475		584,761,857	62.0	79.0	73.0		39	-5.6	0.8	17	dbSNP_119	73	635,7957		41,553,3702	no	coding-synonymous	KRTAP3-2	NM_031959.2		625,1314,4559	GG,GA,AA		7.3906,43.8011,19.7291		13/99	39156067	2564,10432	2202	4296	6498	SO:0001819	synonymous_variant	83897	exon1			AGGCCCAGTGGGG	AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"""Keratin associated proteins"""	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.39T>C	17.37:g.39156067A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	191	64	0.335079	NM_031959		Silent	SNP	ENST00000391587.1	37	CCDS32644.1																																																																																			A|0.750;G|0.250	0.250	strong		0.562	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257685.1		
GPR123	84435	hgsc.bcm.edu	37	10	134942832	134942832	+	Silent	SNP	G	G	A	rs45586231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134942832G>A	ENST00000392607.3	+	7	1936	c.1500G>A	c.(1498-1500)ccG>ccA	p.P500P	GPR123_ENST00000392606.2_Silent_p.P403P|GPR123_ENST00000607359.1_Silent_p.P1219P	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	500					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CCACGCAGCCGGGCAGGGAGG	0.706													G|||	1275	0.254593	0.2648	0.2421	5008	,	,		13293	0.4454		0.0905	False		,,,				2504	0.2219				p.P500P		Atlas-SNP	.											.	GPR123	118	.	0			c.G1500A						PASS	.	G		899,3391		95,709,1341	8.0	8.0	8.0		1500	-7.4	0.0	10	dbSNP_127	8	622,7836		33,556,3640	no	coding-synonymous	GPR123	NM_001083909.1		128,1265,4981	AA,AG,GG		7.354,20.9557,11.9313		500/561	134942832	1521,11227	2145	4229	6374	SO:0001819	synonymous_variant	84435	exon7			GCAGCCGGGCAGG	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"""-"", ""GPCR / Class B : Orphans"""	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.1500G>A	10.37:g.134942832G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	37	CCDS41580.1																																																																																			G|0.756;A|0.244	0.244	strong		0.706	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2		
FAM209B	388799	hgsc.bcm.edu	37	20	55111364	55111364	+	Missense_Mutation	SNP	A	A	C	rs2296129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:55111364A>C	ENST00000371325.1	+	2	482	c.386A>C	c.(385-387)gAa>gCa	p.E129A		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	129			E -> A (in dbSNP:rs2296129).			integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TTTGTGTCCGAAGTGCAGAAT	0.423													A|||	528	0.105431	0.0061	0.0331	5008	,	,		20202	0.4534		0.002	False		,,,				2504	0.0389				p.E129A		Atlas-SNP	.											.	.	.	.	0			c.A386C						PASS	.	A	ALA/GLU	37,4369	41.6+/-74.8	0,37,2166	98.0	97.0	97.0		386	1.2	1.0	20	dbSNP_100	97	10,8590	7.1+/-27.0	0,10,4290	yes	missense	C20orf107	NM_001013646.2	107	0,47,6456	CC,CA,AA		0.1163,0.8398,0.3614	benign	129/172	55111364	47,12959	2203	4300	6503	SO:0001583	missense	388799	exon2			TGTCCGAAGTGCA	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.386A>C	20.37:g.55111364A>C	ENSP00000360376:p.Glu129Ala	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	NM_001013646	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	37	CCDS33494.1	266	0.12179487179487179	0	0.0	10	0.027624309392265192	255	0.4458041958041958	1	0.0013192612137203166	A	6.202	0.405366	0.11754	0.008398	0.001163	ENSG00000213714	ENST00000371325	T	0.07908	3.15	3.55	1.2	0.21068	.	0.382680	0.21732	N	0.069953	T	0.00012	0.0000	N	0.08118	0	0.58432	P	9.000000000036756E-6	B	0.06786	0.001	B	0.06405	0.002	T	0.46414	-0.9193	9	0.66056	D	0.02	-10.4598	5.2781	0.15661	0.7472:0.0:0.2528:0.0	rs2296129;rs60361515;rs2296129	129	Q5JX69	CT107_HUMAN	A	129	ENSP00000360376:E129A	ENSP00000360376:E129A	E	+	2	0	C20orf107	54544771	1.000000	0.71417	0.963000	0.40424	0.029000	0.11900	1.033000	0.30191	0.123000	0.18342	0.454000	0.30748	GAA	A|0.951;C|0.049	0.049	strong		0.423	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
PCDHB2	56133	hgsc.bcm.edu	37	5	140475514	140475514	+	Missense_Mutation	SNP	C	C	A	rs73793576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140475514C>A	ENST00000194155.4	+	1	1288	c.1140C>A	c.(1138-1140)aaC>aaA	p.N380K		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	380	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCGGAGACAACGGAAGGATGG	0.473													C|||	44	0.00878594	0.0325	0.0014	5008	,	,		19966	0.0		0.0	False		,,,				2504	0.0				p.N380K		Atlas-SNP	.											.	PCDHB2	163	.	0			c.C1140A						PASS	.	C	LYS/ASN	116,4290	90.2+/-128.9	2,112,2089	81.0	73.0	76.0		1140	-1.8	1.0	5	dbSNP_130	76	0,8600		0,0,4300	yes	missense	PCDHB2	NM_018936.2	94	2,112,6389	AA,AC,CC		0.0,2.6328,0.8919	probably-damaging	380/799	140475514	116,12890	2203	4300	6503	SO:0001583	missense	56133	exon1			AGACAACGGAAGG	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1140C>A	5.37:g.140475514C>A	ENSP00000194155:p.Asn380Lys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	138	72	0.521739	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	C	11.52	1.663243	0.29515	0.026328	0.0	ENSG00000112852	ENST00000194155	T	0.59906	0.23	5.15	-1.8	0.07907	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.60945	0.2308	H	0.97390	3.995	0.35381	D	0.789909	D	0.71674	0.998	P	0.62435	0.902	T	0.82259	-0.0546	9	0.72032	D	0.01	.	12.3358	0.55067	0.0:0.4067:0.0:0.5933	.	380	Q9Y5E7	PCDB2_HUMAN	K	380	ENSP00000194155:N380K	ENSP00000194155:N380K	N	+	3	2	PCDHB2	140455698	0.014000	0.17966	0.990000	0.47175	0.260000	0.26232	-0.975000	0.03790	-0.310000	0.08766	0.655000	0.94253	AAC	C|0.991;A|0.009	0.009	strong		0.473	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
KCNJ2	3759	hgsc.bcm.edu	37	17	68172326	68172326	+	Silent	SNP	C	C	T	rs173135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:68172326C>T	ENST00000243457.3	+	2	1529	c.1146C>T	c.(1144-1146)ctC>ctT	p.L382L	KCNJ2_ENST00000535240.1_Silent_p.L382L	NM_000891.2	NP_000882.1	P63252	KCNJ2_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 2	382					cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|magnesium ion transport (GO:0015693)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of resting membrane potential (GO:0060075)|regulation of skeletal muscle contraction via regulation of action potential (GO:0014861)|relaxation of cardiac muscle (GO:0055119)|relaxation of skeletal muscle (GO:0090076)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of membrane (GO:0031224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(13)|skin(1)|urinary_tract(1)	25	Breast(10;1.64e-08)					AAGTTGCCCTCACAAGCAAAG	0.448													C|||	771	0.153954	0.1551	0.2392	5008	,	,		20815	0.131		0.1203	False		,,,				2504	0.1503				p.L382L		Atlas-SNP	.											.	KCNJ2	74	.	0			c.C1146T						PASS	.	C		574,3832	251.8+/-258.4	35,504,1664	121.0	123.0	122.0		1146	3.0	1.0	17	dbSNP_79	122	1020,7580	214.9+/-254.4	63,894,3343	no	coding-synonymous	KCNJ2	NM_000891.2		98,1398,5007	TT,TC,CC		11.8605,13.0277,12.2559		382/428	68172326	1594,11412	2203	4300	6503	SO:0001819	synonymous_variant	3759	exon2			TGCCCTCACAAGC	AF011904	CCDS11688.1	17q24.3	2014-09-17				ENSG00000123700		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6263	protein-coding gene	gene with protein product		600681				7696590, 11240146, 16382105	Standard	NM_000891		Approved	Kir2.1, IRK1, LQT7	uc002jir.3	P63252		ENST00000243457.3:c.1146C>T	17.37:g.68172326C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_000891	O15110|P48049	Silent	SNP	ENST00000243457.3	37	CCDS11688.1																																																																																			C|0.867;T|0.133	0.133	strong		0.448	KCNJ2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450889.1	NM_000891	
KIF5C	3800	hgsc.bcm.edu	37	2	149861927	149861927	+	Silent	SNP	G	G	A	rs184488465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:149861927G>A	ENST00000435030.1	+	22	2762	c.2394G>A	c.(2392-2394)ctG>ctA	p.L798L	KIF5C_ENST00000397413.1_Silent_p.L566L|KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000414838.2_Silent_p.L703L			O60282	KIF5C_HUMAN	kinesin family member 5C	798					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)		TGCAGACACTGCACAACCTTC	0.428													G|||	12	0.00239617	0.0091	0.0	5008	,	,		16356	0.0		0.0	False		,,,				2504	0.0				p.L798L		Atlas-SNP	.											.	KIF5C	166	.	0			c.G2394A						PASS	.	G		16,3708		0,16,1846	73.0	71.0	72.0		2105	-0.9	1.0	2		72	0,8218		0,0,4109	no	coding-synonymous	KIF5C	NM_004522.1		0,16,5955	AA,AG,GG		0.0,0.4296,0.134		798/958	149861927	16,11926	1862	4109	5971	SO:0001819	synonymous_variant	3800	exon22			GACACTGCACAAC	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.2394G>A	2.37:g.149861927G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	66	44	0.666667	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				G|0.999;A|0.001	0.001	strong		0.428	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522	
BRD7	29117	hgsc.bcm.edu	37	16	50368670	50368670	+	Missense_Mutation	SNP	C	C	A	rs113038433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50368670C>A	ENST00000394688.3	-	7	998	c.839G>T	c.(838-840)gGa>gTa	p.G280V	BRD7_ENST00000394689.2_Missense_Mutation_p.G280V			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	280					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				TTCGGCATCTCCAGAGTCCTC	0.473													C|||	60	0.0119808	0.0431	0.0043	5008	,	,		17122	0.0		0.0	False		,,,				2504	0.0				p.G280V		Atlas-SNP	.											.	BRD7	61	.	0			c.G839T						PASS	.	C	VAL/GLY,VAL/GLY	129,4267	94.4+/-133.1	1,127,2070	138.0	142.0	141.0		839,839	4.4	0.4	16	dbSNP_132	141	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	BRD7	NM_001173984.2,NM_013263.4	109,109	1,128,6369	AA,AC,CC		0.0116,2.9345,1.0003	benign,benign	280/653,280/652	50368670	130,12866	2198	4300	6498	SO:0001583	missense	29117	exon7			GCATCTCCAGAGT	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"""bromodomain-containing 7"""			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.839G>T	16.37:g.50368670C>A	ENSP00000378180:p.Gly280Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	192	59	0.307292	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	37	CCDS10742.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	C	10.22	1.289343	0.23478	0.029345	1.16E-4	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.30448	1.54;1.53	5.47	4.41	0.53225	.	0.486780	0.23583	N	0.046637	T	0.02193	0.0068	N	0.08118	0	0.24366	N	0.994853	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.07121	-1.0789	10	0.27082	T	0.32	-13.1079	10.8718	0.46887	0.3081:0.6919:0.0:0.0	.	280;280	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	V	280	ENSP00000378180:G280V;ENSP00000378181:G280V	ENSP00000378180:G280V	G	-	2	0	BRD7	48926171	0.945000	0.32115	0.424000	0.26647	0.782000	0.44232	2.285000	0.43487	2.733000	0.93635	0.650000	0.86243	GGA	C|0.988;A|0.012	0.012	strong		0.473	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263	
MICAL3	57553	hgsc.bcm.edu	37	22	18354766	18354766	+	Silent	SNP	C	C	T	rs9617630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:18354766C>T	ENST00000441493.2	-	17	2617	c.2265G>A	c.(2263-2265)ccG>ccA	p.P755P	MICAL3_ENST00000400561.2_Silent_p.P755P|MICAL3_ENST00000585038.1_Silent_p.P879P|MICAL3_ENST00000444520.1_Silent_p.P755P|MICAL3_ENST00000429452.1_Silent_p.P879P|MICAL3_ENST00000207726.7_Silent_p.P783P|MICAL3_ENST00000383094.3_Silent_p.P755P|MICAL3_ENST00000414725.2_Silent_p.P783P	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	755					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)		CCAGGTTCTGCGGGAACTCCT	0.627													c|||	897	0.179113	0.1785	0.2666	5008	,	,		20227	0.2014		0.0954	False		,,,				2504	0.181				p.P879P		Atlas-SNP	.											.	MICAL3	53	.	0			c.G2637A						PASS	.		,,	563,2573		57,449,1062	37.0	35.0	36.0		2265,2637,2265	-11.4	0.1	22	dbSNP_119	36	591,6569		19,553,3008	no	coding-synonymous,coding-synonymous,coding-synonymous	MICAL3	NM_001122731.1,NM_001136004.1,NM_015241.2	,,	76,1002,4070	TT,TC,CC		8.2542,17.9528,11.2082	,,	755/967,879/1074,755/2003	18354766	1154,9142	1568	3580	5148	SO:0001819	synonymous_variant	57553	exon21			GTTCTGCGGGAAC	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.2265G>A	22.37:g.18354766C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001136004	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1																																																																																			C|0.852;T|0.148	0.148	strong		0.627	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
PPP1R12C	54776	hgsc.bcm.edu	37	19	55607447	55607447	+	Silent	SNP	G	G	A	rs35641913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55607447G>A	ENST00000263433.3	-	8	1140	c.1125C>T	c.(1123-1125)gaC>gaT	p.D375D	PPP1R12C_ENST00000435544.2_Silent_p.D301D|PPP1R12C_ENST00000376393.2_Silent_p.D375D	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)		CCTCATCCTCGTCCTGGATGG	0.642													G|||	111	0.0221645	0.0825	0.0029	5008	,	,		14673	0.0		0.0	False		,,,				2504	0.0				p.D375D		Atlas-SNP	.											PPP1R12C,NS,carcinoma,0,1	PPP1R12C	46	1	0			c.C1125T						PASS	.	G		328,4078	163.6+/-195.4	9,310,1884	53.0	66.0	62.0		1125	-7.5	0.4	19	dbSNP_126	62	1,8595		0,1,4297	no	coding-synonymous	PPP1R12C	NM_017607.2		9,311,6181	AA,AG,GG		0.0116,7.4444,2.5304		375/783	55607447	329,12673	2203	4298	6501	SO:0001819	synonymous_variant	54776	exon8			ATCCTCGTCCTGG	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.1125C>T	19.37:g.55607447G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_017607		Silent	SNP	ENST00000263433.3	37	CCDS12916.1																																																																																			G|0.976;A|0.024	0.024	strong		0.642	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
ANGPT4	51378	hgsc.bcm.edu	37	20	854973	854973	+	Silent	SNP	T	T	G	rs62641668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:854973T>G	ENST00000381922.3	-	8	1407	c.1305A>C	c.(1303-1305)tcA>tcC	p.S435S	ANGPT4_ENST00000546022.1_Intron	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	435	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						GGTCGTTGTCTGAGTCAAGGG	0.612													T|||	75	0.014976	0.0416	0.0144	5008	,	,		20786	0.004		0.006	False		,,,				2504	0.0				p.S435S	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											ANGPT4,bladder,carcinoma,-1,1	ANGPT4	77	1	0			c.A1305C						PASS	.	T		163,4243	109.9+/-148.2	5,153,2045	123.0	93.0	103.0		1305	-10.3	0.0	20	dbSNP_129	103	52,8548	32.8+/-85.7	0,52,4248	no	coding-synonymous	ANGPT4	NM_015985.2		5,205,6293	GG,GT,TT		0.6047,3.6995,1.6531		435/504	854973	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	51378	exon8			GTTGTCTGAGTCA	AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"""Fibrinogen C domain containing"""	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.1305A>C	20.37:g.854973T>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	216	103	0.476852	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																			T|0.983;G|0.017	0.017	strong		0.612	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985	
SLC17A9	63910	hgsc.bcm.edu	37	20	61598731	61598731	+	Missense_Mutation	SNP	C	C	T	rs7271712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61598731C>T	ENST00000370351.4	+	13	1321	c.1190C>T	c.(1189-1191)aCg>aTg	p.T397M	SLC17A9_ENST00000370349.3_Missense_Mutation_p.T391M|SLC17A9_ENST00000488738.1_3'UTR	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	397			T -> M (in dbSNP:rs7271712).		exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						ATGGAGACCACGGGCTCCTGG	0.642													C|||	209	0.0417332	0.0923	0.0663	5008	,	,		16280	0.0		0.0378	False		,,,				2504	0.0031				p.T397M		Atlas-SNP	.											.	SLC17A9	54	.	0			c.C1190T						PASS	.	C	MET/THR	339,3741		11,317,1712	178.0	189.0	186.0		1190	2.6	1.0	20	dbSNP_116	186	237,8167		9,219,3974	yes	missense	SLC17A9	NM_022082.3	81	20,536,5686	TT,TC,CC		2.8201,8.3088,4.6139	probably-damaging	397/437	61598731	576,11908	2040	4202	6242	SO:0001583	missense	63910	exon13			AGACCACGGGCTC	AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"""Solute carriers"""	16192	protein-coding gene	gene with protein product		612107	"""chromosome 20 open reading frame 59"", ""solute carrier family 17, member 9"""	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.1190C>T	20.37:g.61598731C>T	ENSP00000359376:p.Thr397Met	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	238	126	0.529412	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Missense_Mutation	SNP	ENST00000370351.4	37	CCDS42901.1	99	0.04532967032967033	50	0.1016260162601626	22	0.06077348066298342	0	0.0	27	0.03562005277044855	C	15.68	2.906278	0.52333	0.083088	0.028201	ENSG00000101194	ENST00000370351;ENST00000370349	T;T	0.60548	0.18;0.18	4.6	2.6	0.31112	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.153499	0.64402	N	0.000019	T	0.04861	0.0131	M	0.76838	2.35	0.80722	D	1	D;D	0.64830	0.968;0.994	P;P	0.55965	0.619;0.788	T	0.13098	-1.0522	10	0.59425	D	0.04	.	9.7201	0.40297	0.0:0.7804:0.1415:0.0781	rs7271712;rs52790132;rs7271712	397;391	Q9BYT1;Q9BYT1-2	S17A9_HUMAN;.	M	397;391	ENSP00000359376:T397M;ENSP00000359374:T391M	ENSP00000359374:T391M	T	+	2	0	SLC17A9	61069176	0.991000	0.36638	0.957000	0.39632	0.822000	0.46500	2.977000	0.49297	0.451000	0.26802	0.561000	0.74099	ACG	C|0.952;T|0.048	0.048	strong		0.642	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082	
COL28A1	340267	hgsc.bcm.edu	37	7	7495735	7495735	+	Missense_Mutation	SNP	T	T	C	rs55745506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:7495735T>C	ENST00000399429.3	-	16	1451	c.1311A>G	c.(1309-1311)atA>atG	p.I437M		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	437			I -> M (in dbSNP:rs55745506).		cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCACAGGTCCTATATCCCCCT	0.408													C|||	1584	0.316294	0.5726	0.2522	5008	,	,		15221	0.2103		0.2107	False		,,,				2504	0.2331				p.I437M		Atlas-SNP	.											.	COL28A1	113	.	0			c.A1311G						PASS	.	C	MET/ILE	1760,1876		433,894,491	73.0	72.0	72.0		1311	1.4	1.0	7	dbSNP_129	72	1664,6492		155,1354,2569	yes	missense	COL28A1	NM_001037763.2	10	588,2248,3060	CC,CT,TT		20.4022,48.4048,29.0366	benign	437/1126	7495735	3424,8368	1818	4078	5896	SO:0001583	missense	340267	exon16			AGGTCCTATATCC	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.1311A>G	7.37:g.7495735T>C	ENSP00000382356:p.Ile437Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	69	40	0.57971	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	658	0.30128205128205127	292	0.5934959349593496	96	0.26519337016574585	115	0.20104895104895104	155	0.20448548812664907	C	8.864	0.947737	0.18356	0.484048	0.204022	ENSG00000215018	ENST00000399429;ENST00000399419	D	0.94280	-3.39	4.53	1.44	0.22558	.	2.249830	0.03373	N	0.199275	T	0.00012	0.0000	N	0.12611	0.24	0.48830	P	2.870000000000372E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37337	-0.9710	9	0.44086	T	0.13	0.4197	6.775	0.23615	0.0:0.5303:0.0:0.4697	rs55745506;rs59850353	437;437	Q2UY09-2;Q2UY09	.;COSA1_HUMAN	M	437	ENSP00000382356:I437M	ENSP00000382347:I437M	I	-	3	3	COL28A1	7462260	0.993000	0.37304	0.996000	0.52242	0.906000	0.53458	0.148000	0.16224	-0.044000	0.13491	-1.082000	0.02213	ATA	T|0.729;C|0.271	0.271	strong		0.408	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1808343	1808343	+	Silent	SNP	C	C	T	rs147914724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:1808343C>T	ENST00000398564.1	+	4	546	c.546C>T	c.(544-546)gaC>gaT	p.D182D	ARHGEF10_ENST00000398560.1_Silent_p.D182D|ARHGEF10_ENST00000262112.6_Silent_p.D182D|ARHGEF10_ENST00000520359.1_Silent_p.D158D|ARHGEF10_ENST00000349830.3_Silent_p.D158D|ARHGEF10_ENST00000518288.1_Silent_p.D182D			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	182					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)	p.D182D(1)		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)		CGTCCCTGGACGAAGAAGGTA	0.657													C|||	2	0.000399361	0.0008	0.0	5008	,	,		17485	0.0		0.0	False		,,,				2504	0.001				p.D158D		Atlas-SNP	.											ARHGEF10_ENST00000398564,colon,carcinoma,0,1	ARHGEF10	255	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C474T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	80.0	72.0	74.0		474	-10.6	0.0	8	dbSNP_134	74	0,8600		0,0,4300	no	coding-synonymous	ARHGEF10	NM_014629.2		0,14,6489	TT,TC,CC		0.0,0.3177,0.1076		158/1345	1808343	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon4			CCTGGACGAAGAA	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.546C>T	8.37:g.1808343C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				C|0.999;T|0.001	0.001	strong		0.657	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
LRRFIP1	9208	hgsc.bcm.edu	37	2	238671536	238671536	+	Missense_Mutation	SNP	A	A	G	rs61744755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238671536A>G	ENST00000392000.4	+	11	1297	c.1180A>G	c.(1180-1182)Atg>Gtg	p.M394V	LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000244815.5_Missense_Mutation_p.M370V|LRRFIP1_ENST00000289175.6_Missense_Mutation_p.M338V	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	394					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)		AAATGAGGTCATGGGTGCACC	0.498													A|||	211	0.0421326	0.1543	0.0086	5008	,	,		21148	0.0		0.001	False		,,,				2504	0.0				p.M394V		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.A1180G						PASS	.	A	,,VAL/MET,VAL/MET,VAL/MET	541,3865	245.9+/-254.7	45,451,1707	86.0	91.0	89.0		,,1180,1012,1108	-9.8	0.0	2	dbSNP_129	89	13,8587	9.8+/-36.6	0,13,4287	yes	intron,intron,missense,missense,missense	LRRFIP1	NM_001137550.1,NM_001137551.1,NM_001137552.1,NM_001137553.1,NM_004735.3	,,21,21,21	45,464,5994	GG,GA,AA		0.1512,12.2787,4.2596	,,benign,benign,benign	,,394/809,338/753,370/785	238671536	554,12452	2203	4300	6503	SO:0001583	missense	9208	exon11			GAGGTCATGGGTG	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.1180A>G	2.37:g.238671536A>G	ENSP00000375857:p.Met394Val	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	258	134	0.51938	NM_001137552	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	37	CCDS46552.1	108	0.04945054945054945	103	0.20934959349593496	5	0.013812154696132596	0	0.0	0	0.0	A	0.004	-2.380306	0.00205	0.122787	0.001512	ENSG00000124831	ENST00000289175;ENST00000244815;ENST00000392000	T;T;T	0.09163	3.01;3.01;3.01	4.89	-9.78	0.00496	.	3.686850	0.00754	N	0.001093	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.29274	-1.0017	9	0.13853	T	0.58	7.2432	3.7885	0.08710	0.1625:0.3152:0.3632:0.1592	rs61744755	338;394;370	Q32MZ4-3;Q32MZ4;Q32MZ4-2	.;LRRF1_HUMAN;.	V	338;370;394	ENSP00000289175:M338V;ENSP00000244815:M370V;ENSP00000375857:M394V	ENSP00000244815:M370V	M	+	1	0	LRRFIP1	238336275	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.652000	0.01988	-3.689000	0.00120	-2.196000	0.00310	ATG	A|0.948;G|0.052	0.052	strong		0.498	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
MYO10	4651	hgsc.bcm.edu	37	5	16673975	16673975	+	Missense_Mutation	SNP	C	C	G	rs25901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16673975C>G	ENST00000513610.1	-	36	5442	c.4988G>C	c.(4987-4989)aGc>aCc	p.S1663T	MYO10_ENST00000274203.9_Missense_Mutation_p.S1020T|MYO10_ENST00000427430.2_Missense_Mutation_p.S1020T|MYO10_ENST00000505695.1_Missense_Mutation_p.S1002T|MYO10_ENST00000515803.1_Missense_Mutation_p.S1002T	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1663	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.		S -> T (in dbSNP:rs25901). {ECO:0000269|PubMed:10984435, ECO:0000269|PubMed:11278607, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9872452}.		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						TTCCATCTCGCTTCCTGGAAA	0.468													G|||	4125	0.823682	0.9849	0.8055	5008	,	,		17976	0.7708		0.666	False		,,,				2504	0.8354				p.S1663T		Atlas-SNP	.											.	MYO10	198	.	0			c.G4988C						PASS	.	G	THR/SER	3508,246		1636,236,5	91.0	92.0	92.0		4988	5.4	1.0	5	dbSNP_76	92	5524,2722		1855,1814,454	yes	missense	MYO10	NM_012334.2	58	3491,2050,459	GG,GC,CC		33.0099,6.553,24.7333	benign	1663/2059	16673975	9032,2968	1877	4123	6000	SO:0001583	missense	4651	exon36			ATCTCGCTTCCTG	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.4988G>C	5.37:g.16673975C>G	ENSP00000421280:p.Ser1663Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	1718	0.7866300366300366	479	0.9735772357723578	282	0.7790055248618785	451	0.7884615384615384	506	0.6675461741424802	g	8.947	0.967253	0.18659	0.93447	0.669901	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	D;D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88;-2.88	5.41	5.41	0.78517	MyTH4 domain (3);	.	.	.	.	T	0.00012	0.0000	N	0.04355	-0.22	0.43930	P	0.003414000000000028	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.11329	0.006;0.002;0.003	T	0.46105	-0.9215	8	0.02654	T	1	.	16.4107	0.83712	0.0:0.1316:0.8684:0.0	rs25901;rs3892701;rs17429238;rs52818591;rs56807217;rs25901	542;1303;1663	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	T	1663;1002;1020;1002;1020	ENSP00000421280:S1663T;ENSP00000425051:S1002T;ENSP00000274203:S1020T;ENSP00000421170:S1002T;ENSP00000391106:S1020T	ENSP00000274203:S1020T	S	-	2	0	MYO10	16726975	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.033000	0.88852	1.291000	0.44653	-0.242000	0.12053	AGC	C|0.213;G|0.787	0.787	strong		0.468	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
HHLA2	11148	hgsc.bcm.edu	37	3	108081217	108081217	+	Missense_Mutation	SNP	C	C	A	rs3792332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108081217C>A	ENST00000357759.5	+	7	1446	c.1032C>A	c.(1030-1032)aaC>aaA	p.N344K	HHLA2_ENST00000467761.1_Missense_Mutation_p.N344K|HHLA2_ENST00000491820.1_Missense_Mutation_p.N344K|HHLA2_ENST00000489514.2_Missense_Mutation_p.N344K|HHLA2_ENST00000467562.1_Missense_Mutation_p.N280K	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	344			N -> K (in dbSNP:rs3792332).		positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						CTTCCCATAACAAAGGCTTAT	0.413													C|||	536	0.107029	0.1672	0.0735	5008	,	,		17654	0.1399		0.0417	False		,,,				2504	0.0828				p.N344K		Atlas-SNP	.											.	HHLA2	95	.	0			c.C1032A						PASS	.	C	LYS/ASN	503,3147		33,437,1355	114.0	101.0	105.0		1032	-1.6	0.0	3	dbSNP_107	105	340,7840		7,326,3757	yes	missense	HHLA2	NM_007072.2	94	40,763,5112	AA,AC,CC		4.1565,13.7808,7.126	benign	344/415	108081217	843,10987	1825	4090	5915	SO:0001583	missense	11148	exon7			CCATAACAAAGGC	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.1032C>A	3.37:g.108081217C>A	ENSP00000350402:p.Asn344Lys	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Missense_Mutation	SNP	ENST00000357759.5	37	CCDS46883.1	218|218	0.09981684981684982|0.09981684981684982	79|79	0.16056910569105692|0.16056910569105692	32|32	0.08839779005524862|0.08839779005524862	76|76	0.13286713286713286|0.13286713286713286	31|31	0.040897097625329816|0.040897097625329816	C|C	6.108|6.108	0.388214|0.388214	0.11581|0.11581	0.137808|0.137808	0.041565|0.041565	ENSG00000114455|ENSG00000114455	ENST00000491820;ENST00000467562;ENST00000357759;ENST00000467761;ENST00000489514|ENST00000482099	T;T;T;T;T|.	0.09817|.	5.12;2.94;5.08;5.08;5.08|.	1.58|1.58	-1.56|-1.56	0.08532|0.08532	.|.	.|.	.|.	.|.	.|.	T|T	0.00073|0.00073	0.0002|0.0002	N|N	0.14661|0.14661	0.345|0.345	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;0.001;0.001|.	T|T	0.26883|0.26883	-1.0090|-1.0090	8|4	0.66056|.	D|.	0.02|.	.|.	1.7016|1.7016	0.02873|0.02873	0.343:0.3055:0.0:0.3515|0.343:0.3055:0.0:0.3515	rs3792332;rs52801242;rs3792332|rs3792332;rs52801242;rs3792332	280;344;344|.	B4DKN2;C9J7D0;Q9UM44|.	.;.;HHLA2_HUMAN|.	K|K	344;280;344;344;344|247	ENSP00000418284:N344K;ENSP00000418345:N280K;ENSP00000350402:N344K;ENSP00000419207:N344K;ENSP00000417856:N344K|.	ENSP00000350402:N344K|.	N|Q	+|+	3|1	2|0	HHLA2|HHLA2	109563907|109563907	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.403000|0.403000	0.20982|0.20982	-0.452000|-0.452000	0.07087|0.07087	0.655000|0.655000	0.94253|0.94253	AAC|CAA	C|0.902;A|0.098	0.098	strong		0.413	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072	
EVPL	2125	hgsc.bcm.edu	37	17	74014628	74014628	+	Silent	SNP	G	G	A	rs2071193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	196	0	0		WXS	Illumina HiSeq	Phase_I	217	95	0.437788	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	
IL31RA	133396	hgsc.bcm.edu	37	5	55155402	55155402	+	Silent	SNP	C	C	T	rs1009639	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:55155402C>T	ENST00000447346.2	+	2	194	c.129C>T	c.(127-129)ccC>ccT	p.P43P	IL31RA_ENST00000297015.3_5'UTR|IL31RA_ENST00000396836.2_Silent_p.P43P|IL31RA_ENST00000490985.1_5'UTR|IL31RA_ENST00000396834.1_Silent_p.P24P|IL31RA_ENST00000359040.5_Silent_p.P43P|IL31RA_ENST00000354961.4_Silent_p.P24P	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	11	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				GGATGCTCCCCTCACTCTGCA	0.468													T|||	3147	0.628395	0.6543	0.4942	5008	,	,		20198	0.4544		0.7276	False		,,,				2504	0.7658				p.P43P		Atlas-SNP	.											.	IL31RA	84	.	0			c.C129T						PASS	.	T	,,,,	2918,1488		949,1020,234	183.0	158.0	167.0		72,129,72,,129	-0.8	0.1	5	dbSNP_86	167	6272,2328		2289,1694,317	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-5,coding-synonymous	IL31RA	NM_001242636.1,NM_001242637.1,NM_001242638.1,NM_001242639.1,NM_139017.5	,,,,	3238,2714,551	TT,TC,CC		27.0698,33.7721,29.3403	,,,,	24/746,43/682,24/663,,43/765	55155402	9190,3816	2203	4300	6503	SO:0001819	synonymous_variant	133396	exon2			GCTCCCCTCACTC	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.129C>T	5.37:g.55155402C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Silent	SNP	ENST00000447346.2	37	CCDS3970.2																																																																																			C|0.334;T|0.666	0.666	strong		0.468	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
C9orf66	157983	hgsc.bcm.edu	37	9	214908	214908	+	Silent	SNP	T	T	C	rs62533313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:214908T>C	ENST00000382387.2	-	1	985	c.489A>G	c.(487-489)agA>agG	p.R163R	DOCK8_ENST00000453981.1_5'UTR|DOCK8_ENST00000432829.2_5'UTR	NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	163										central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	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)		CCGCGGCTACTCTGCGGCGCG	0.692													T|||	437	0.0872604	0.1233	0.085	5008	,	,		11014	0.004		0.0974	False		,,,				2504	0.1155				p.R163R		Atlas-SNP	.											.	C9orf66	16	.	0			c.A489G						PASS	.	T	,	381,3313		13,355,1479	16.0	15.0	15.0		489,	0.2	0.0	9	dbSNP_129	15	658,6782		35,588,3097	no	coding-synonymous,utr-5	DOCK8,C9orf66	NM_152569.2,NM_203447.3	,	48,943,4576	CC,CT,TT		8.8441,10.314,9.3318	,	163/296,	214908	1039,10095	1847	3720	5567	SO:0001819	synonymous_variant	157983	exon1			GGCTACTCTGCGG	AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784			26436	protein-coding gene	gene with protein product							Standard	NM_152569		Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.489A>G	9.37:g.214908T>C		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_152569	Q96NB0	Silent	SNP	ENST00000382387.2	37	CCDS6439.1																																																																																			T|0.905;C|0.095	0.095	strong		0.692	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055436.1	NM_152569	
HRC	3270	hgsc.bcm.edu	37	19	49657582	49657582	+	Missense_Mutation	SNP	T	T	C	rs386810104|rs114040533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657582T>C	ENST00000252825.4	-	1	1099	c.913A>G	c.(913-915)Aat>Gat	p.N305D	HRC_ENST00000595625.1_Missense_Mutation_p.N305D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	305	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)	p.N305D(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		TCATCATCATTGTCATCTTCT	0.537													C|||	248	0.0495208	0.1657	0.0187	5008	,	,		26355	0.0		0.0099	False		,,,				2504	0.0061				p.N305D	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											HRC,NS,carcinoma,0,1	HRC	85	1	1	Substitution - Missense(1)	prostate(1)	c.A913G						scavenged	.						186.0	144.0	158.0					19																	49657582		2203	4300	6503	SO:0001583	missense	3270	exon1			CATCATTGTCATC		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.913A>G	19.37:g.49657582T>C	ENSP00000252825:p.Asn305Asp	Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	229	65	0.283843	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	37	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	C	0.080	-1.184868	0.01620	.	.	ENSG00000130528	ENST00000252825;ENST00000391863;ENST00000434964	T	0.30714	1.52	2.45	2.45	0.29901	.	.	.	.	.	T	0.05364	0.0142	N	0.00152	-1.975	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37596	-0.9699	9	0.02654	T	1	.	5.6115	0.17408	0.0:0.8276:0.0:0.1724	.	305	P23327	SRCH_HUMAN	D	305;4;275	ENSP00000252825:N305D	ENSP00000252825:N305D	N	-	1	0	HRC	54349394	0.000000	0.05858	0.012000	0.15200	0.038000	0.13279	0.339000	0.19875	0.177000	0.19895	-0.355000	0.07637	AAT	T|0.999;C|0.001	0.001	weak		0.537	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
XPO5	57510	hgsc.bcm.edu	37	6	43496662	43496662	+	Splice_Site	SNP	A	A	C	rs1106841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43496662A>C	ENST00000265351.7	-	24	2889	c.2679T>G	c.(2677-2679)cgT>cgG	p.R893R	POLR1C_ENST00000304004.3_Intron	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	893					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			TTACAAAGACACGTGCTGCAA	0.502													C|||	1956	0.390575	0.6354	0.4222	5008	,	,		17759	0.0565		0.3917	False		,,,				2504	0.3804				p.R893R		Atlas-SNP	.											XPO5,colon,carcinoma,0,2	XPO5	79	2	0			c.T2679G						PASS	.	C		2283,1575		693,897,339	41.0	44.0	43.0		2679	1.9	1.0	6	dbSNP_86	43	3187,5077		606,1975,1551	yes	coding-synonymous-near-splice	XPO5	NM_020750.2		1299,2872,1890	CC,CA,AA		38.5649,40.8243,45.1246		893/1205	43496662	5470,6652	1929	4132	6061	SO:0001630	splice_region_variant	57510	exon24			AAAGACACGTGCT	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.2678-1T>G	6.37:g.43496662A>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1																																																																																			A|0.635;C|0.365	0.365	strong		0.502	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	Silent
DNAH17	8632	hgsc.bcm.edu	37	17	76528790	76528790	+	Missense_Mutation	SNP	A	A	G	rs11651537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76528790A>G	ENST00000585328.1	-	20	3003	c.2879T>C	c.(2878-2880)aTa>aCa	p.I960T	RN7SL454P_ENST00000492744.2_RNA|DNAH17_ENST00000389840.5_Missense_Mutation_p.I963T	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	963	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)			CCTCATCTCTATGAGGTCTGT	0.522													A|||	2298	0.458866	0.5015	0.4179	5008	,	,		21569	0.4157		0.5318	False		,,,				2504	0.3998				p.I963T		Atlas-SNP	.											.	DNAH17	347	.	0			c.T2888C						PASS	.	A	THR/ILE	1965,1971		495,975,498	31.0	29.0	29.0		2888	3.0	1.0	17	dbSNP_120	29	4411,3897		1167,2077,910	yes	missense	DNAH17	NM_173628.3	89	1662,3052,1408	GG,GA,AA		46.9066,49.9238,47.9255		963/4463	76528790	6376,5868	1968	4154	6122	SO:0001583	missense	8632	exon20			ATCTCTATGAGGT	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.2879T>C	17.37:g.76528790A>G	ENSP00000465516:p.Ile960Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		1044	0.47802197802197804	226	0.45934959349593496	166	0.4585635359116022	235	0.41083916083916083	417	0.5501319261213721	A	0.466	-0.886596	0.02511	0.499238	0.530934	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.23552	1.9	5.2	2.99	0.34606	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	.	.	.	.	.	.	T	0.45483	-0.9258	6	0.16420	T	0.52	.	4.7212	0.12918	0.5964:0.1617:0.2418:0.0	rs11651537;rs59012278	.	.	.	T	960;963	ENSP00000374490:I963T	ENSP00000300671:I960T	I	-	2	0	DNAH17	74040385	0.000000	0.05858	0.968000	0.41197	0.233000	0.25261	0.453000	0.21811	1.947000	0.56498	0.379000	0.24179	ATA	A|0.513;G|0.487	0.487	strong		0.522	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
CCNG2	901	hgsc.bcm.edu	37	4	78079768	78079768	+	Missense_Mutation	SNP	A	A	G	rs4150051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:78079768A>G	ENST00000316355.5	+	2	439	c.83A>G	c.(82-84)gAa>gGa	p.E28G	CCNG2_ENST00000354403.5_Missense_Mutation_p.E28G|CCNG2_ENST00000395640.1_Missense_Mutation_p.E28G|CCNG2_ENST00000497512.1_3'UTR|CCNG2_ENST00000509972.1_Missense_Mutation_p.E28G|CCNG2_ENST00000502280.1_Missense_Mutation_p.E28G	NM_004354.2	NP_004345.1	Q16589	CCNG2_HUMAN	cyclin G2	28			E -> G (in dbSNP:rs4150051). {ECO:0000269|Ref.3}.		cell cycle checkpoint (GO:0000075)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)				breast(1)|kidney(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						CTGGAACAAGAAGAGAGATTC	0.502													A|||	22	0.00439297	0.0144	0.0043	5008	,	,		16831	0.0		0.0	False		,,,				2504	0.0				p.E28G		Atlas-SNP	.											.	CCNG2	27	.	0			c.A83G						PASS	.	A	GLY/GLU	67,4339	62.3+/-99.4	2,63,2138	112.0	112.0	112.0		83	5.6	1.0	4	dbSNP_110	112	1,8599		0,1,4299	yes	missense	CCNG2	NM_004354.2	98	2,64,6437	GG,GA,AA		0.0116,1.5207,0.5228	probably-damaging	28/345	78079768	68,12938	2203	4300	6503	SO:0001583	missense	901	exon2			AACAAGAAGAGAG	BC032518	CCDS3581.1	4q21.22	2009-05-07			ENSG00000138764	ENSG00000138764			1593	protein-coding gene	gene with protein product		603203				8806701	Standard	NM_004354		Approved		uc003hkq.4	Q16589	OTTHUMG00000130100	ENST00000316355.5:c.83A>G	4.37:g.78079768A>G	ENSP00000315743:p.Glu28Gly	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_004354	B4DF25|Q6FGA7|Q6FGC6	Missense_Mutation	SNP	ENST00000316355.5	37	CCDS3581.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	24.2	4.508863	0.85282	0.015207	1.16E-4	ENSG00000138764	ENST00000316355;ENST00000354403;ENST00000502280;ENST00000395640;ENST00000512918;ENST00000509972	T;T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;1.69;1.69	5.57	5.57	0.84162	Cyclin-like (1);	0.000000	0.85682	D	0.000000	T	0.64125	0.2570	M	0.88979	2.995	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.78046	-0.2357	10	0.87932	D	0	-16.452	15.3858	0.74699	1.0:0.0:0.0:0.0	rs4150051	28;28	B4DF25;Q16589	.;CCNG2_HUMAN	G	28	ENSP00000315743:E28G;ENSP00000346379:E28G;ENSP00000424665:E28G;ENSP00000379002:E28G;ENSP00000426085:E28G;ENSP00000426476:E28G	ENSP00000315743:E28G	E	+	2	0	CCNG2	78298792	1.000000	0.71417	1.000000	0.80357	0.550000	0.35303	7.252000	0.78309	2.126000	0.65437	0.459000	0.35465	GAA	A|0.996;G|0.004	0.004	strong		0.502	CCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252404.3	NM_004354	
SPPL2C	162540	hgsc.bcm.edu	37	17	43922535	43922535	+	Missense_Mutation	SNP	C	C	T	rs116482551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43922535C>T	ENST00000329196.5	+	1	280	c.263C>T	c.(262-264)cCc>cTc	p.P88L	MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	88	PA.					endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										AGCCAGCGGCCCCTCCGCCAG	0.682													C|||	19	0.00379393	0.0144	0.0	5008	,	,		15160	0.0		0.0	False		,,,				2504	0.0				p.P88L		Atlas-SNP	.											.	.	.	.	0			c.C263T						PASS	.	C	LEU/PRO	68,4338	56.2+/-92.4	1,66,2136	25.0	26.0	26.0		263	4.8	0.6	17	dbSNP_132	26	0,8598		0,0,4299	yes	missense	IMP5	NM_175882.2	98	1,66,6435	TT,TC,CC		0.0,1.5433,0.5229	probably-damaging	88/685	43922535	68,12936	2203	4299	6502	SO:0001583	missense	162540	exon1			AGCGGCCCCTCCG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.263C>T	17.37:g.43922535C>T	ENSP00000332488:p.Pro88Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	87	47	0.54023	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	15.63	2.890707	0.52014	0.015433	0.0	ENSG00000185294	ENST00000329196	T	0.06068	3.35	4.8	4.8	0.61643	Protease-associated domain, PA (1);	0.000000	0.42172	D	0.000759	T	0.10637	0.0260	M	0.73217	2.22	0.58432	D	0.999998	D	0.69078	0.997	D	0.68943	0.961	T	0.00203	-1.1924	10	0.33940	T	0.23	-5.2725	13.2146	0.59851	0.0:1.0:0.0:0.0	.	88	Q8IUH8	IMP5_HUMAN	L	88	ENSP00000332488:P88L	ENSP00000332488:P88L	P	+	2	0	AC217771.1	41278315	0.895000	0.30542	0.640000	0.29408	0.454000	0.32378	2.391000	0.44424	2.481000	0.83766	0.650000	0.86243	CCC	C|0.995;T|0.005	0.005	strong		0.682	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
ORC3	23595	hgsc.bcm.edu	37	6	88362943	88362943	+	Silent	SNP	C	C	T	rs2307393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88362943C>T	ENST00000392844.3	+	14	1540	c.1492C>T	c.(1492-1494)Ctg>Ttg	p.L498L	ORC3_ENST00000546266.1_Silent_p.L355L|ORC3_ENST00000257789.4_Silent_p.L498L|ORC3_ENST00000417380.2_3'UTR	NM_012381.3|NM_181837.2	NP_036513.2|NP_862820.1	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3	498					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						AGAGGAGTTCCTGGCCCAGTT	0.408													C|||	235	0.0469249	0.0953	0.0504	5008	,	,		17284	0.0099		0.0467	False		,,,				2504	0.0174				p.L498L		Atlas-SNP	.											.	ORC3	51	.	0			c.C1492T						PASS	.	C	,,	421,3985	203.8+/-226.2	21,379,1803	94.0	89.0	91.0		1063,1492,1492	4.8	1.0	6	dbSNP_100	91	395,8205	125.5+/-184.1	8,379,3913	no	coding-synonymous,coding-synonymous,coding-synonymous	ORC3	NM_001197259.1,NM_012381.3,NM_181837.2	,,	29,758,5716	TT,TC,CC		4.593,9.5552,6.274	,,	355/569,498/712,498/713	88362943	816,12190	2203	4300	6503	SO:0001819	synonymous_variant	23595	exon14			GAGTTCCTGGCCC	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.1492C>T	6.37:g.88362943C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_181837	A2A2T5|B4E025|Q13565|Q53GY6|Q5T159|Q6IUY7|Q86TN5|Q9UG44|Q9UNT6	Silent	SNP	ENST00000392844.3	37	CCDS43486.1																																																																																			C|0.945;T|0.055	0.055	strong		0.408	ORC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041452.2		
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39190973	39190973	+	Missense_Mutation	SNP	C	C	G	rs62624960		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39190973C>G	ENST00000344363.5	-	1	134	c.101G>C	c.(100-102)tGc>tCc	p.C34S		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	34			C -> S (in dbSNP:rs62624960). {ECO:0000269|PubMed:12228244}.			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCTGGCAGCAGCTGGTCTC	0.602																																					p.C34S		Atlas-SNP	.											.	KRTAP1-3	18	.	0			c.G101C						PASS	.						34.0	43.0	40.0					17																	39190973		1963	4159	6122	SO:0001583	missense	81850	exon1			TGGCAGCAGCTGG	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"""Keratin associated proteins"""	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.101G>C	17.37:g.39190973C>G	ENSP00000344420:p.Cys34Ser	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	228	51	0.223684	NM_030966	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	161	0.07371794871794872	55	0.11178861788617886	22	0.06077348066298342	68	0.11888111888111888	16	0.021108179419525065	C	10.25	1.297905	0.23650	.	.	ENSG00000221880	ENST00000344363	T	0.48522	0.81	3.51	1.46	0.22682	.	.	.	.	.	T	0.00552	0.0018	.	.	.	0.35701	D	0.815636	B	0.06786	0.001	B	0.12837	0.008	T	0.10776	-1.0615	8	0.66056	D	0.02	.	9.8065	0.40797	0.0:0.5894:0.4106:0.0	rs62624960	44	Q8IUG1	KRA13_HUMAN	S	34	ENSP00000344420:C34S	ENSP00000344420:C34S	C	-	2	0	KRTAP1-3	36444499	1.000000	0.71417	0.998000	0.56505	0.388000	0.30384	1.383000	0.34385	0.470000	0.27294	-0.217000	0.12591	TGC	C|0.926;G|0.074	0.074	strong		0.602	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1		
IGDCC4	57722	hgsc.bcm.edu	37	15	65676617	65676617	+	Silent	SNP	T	T	C	rs2292933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	83	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	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	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592265	1592265	+	Intron	SNP	A	A	G	rs45471597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1592265A>G	ENST00000381605.4	-	1	141				SIRPB1_ENST00000568365.1_Silent_p.T57T|SIRPB1_ENST00000279477.7_Silent_p.T57T|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000381596.1_5'UTR|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						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						GGATCAGGGAAGTCACAGTGC	0.557													N|||	3350	0.66893	0.739	0.5331	5008	,	,		8651	0.7669		0.5318	False		,,,				2504	0.7106				p.T57T		Atlas-SNP	.											.	SIRPB1	83	.	0			c.T171C						PASS	.						64.0	72.0	70.0					20																	1592265		447	1337	1784	SO:0001627	intron_variant	10326	exon2			CAGGGAAGTCACA	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.76+8249T>C	20.37:g.1592265A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	206	65	0.315534	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			A|0.417;G|0.583	0.583	strong		0.557	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
GBGT1	26301	hgsc.bcm.edu	37	9	136029474	136029474	+	Silent	SNP	C	C	T	rs35808997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136029474C>T	ENST00000372040.3	-	7	845	c.534G>A	c.(532-534)gaG>gaA	p.E178E	GBGT1_ENST00000372043.3_Missense_Mutation_p.R172K|GBGT1_ENST00000372038.3_3'UTR|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000540636.1_Silent_p.E161E	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	178					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		GCATGGATGTCTCCTCCCAGT	0.607													C|||	364	0.0726837	0.2632	0.0202	5008	,	,		17590	0.0		0.002	False		,,,				2504	0.0				p.E178E		Atlas-SNP	.											.	GBGT1	25	.	0			c.G534A						PASS	.	C		957,3449	360.1+/-315.1	109,739,1355	59.0	47.0	51.0		534	2.9	0.6	9	dbSNP_126	51	6,8592	4.3+/-15.6	0,6,4293	no	coding-synonymous	GBGT1	NM_021996.4		109,745,5648	TT,TC,CC		0.0698,21.7204,7.4054		178/348	136029474	963,12041	2203	4299	6502	SO:0001819	synonymous_variant	26301	exon7			GGATGTCTCCTCC	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.534G>A	9.37:g.136029474C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	118	69	0.584746	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	37	CCDS6960.1	115	0.052655677655677656	109	0.22154471544715448	6	0.016574585635359115	0	0.0	0	0.0	C	6.220	0.408804	0.11812	0.217204	6.98E-4	ENSG00000148288	ENST00000372043	T	0.22134	1.97	5.16	2.91	0.33838	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999742809	.	.	.	.	.	.	T	0.13575	-1.0504	5	0.87932	D	0	-9.1051	9.1909	0.37197	0.0:0.6371:0.2769:0.086	rs35808997;rs62638706	.	.	.	K	172	ENSP00000361113:R172K	ENSP00000361113:R172K	R	-	2	0	GBGT1	135019295	0.950000	0.32346	0.650000	0.29550	0.003000	0.03518	0.078000	0.14761	1.145000	0.42336	-0.479000	0.04858	AGA	C|0.934;T|0.066	0.066	strong		0.607	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
SYT8	90019	hgsc.bcm.edu	37	11	1858076	1858076	+	Missense_Mutation	SNP	C	C	T	rs115217397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1858076C>T	ENST00000381968.3	+	7	945	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	SYT8_ENST00000341958.3_Missense_Mutation_p.R259C|TNNI2_ENST00000252898.7_5'Flank|TNNI2_ENST00000381911.1_5'Flank|SYT8_ENST00000535046.1_3'UTR|TNNI2_ENST00000381906.1_5'Flank	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	273	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosome reaction (GO:0007340)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		TCGAGGCCTGCGTCCAGGACT	0.682													C|||	38	0.00758786	0.0272	0.0014	5008	,	,		16027	0.0		0.0	False		,,,				2504	0.001				p.R273C		Atlas-SNP	.											.	SYT8	29	.	0			c.C817T						PASS	.	C	CYS/ARG	108,4292	82.4+/-120.9	2,104,2094	37.0	38.0	38.0		817	0.6	0.2	11	dbSNP_132	38	1,8595	1.2+/-3.3	0,1,4297	yes	missense	SYT8	NM_138567.3	180	2,105,6391	TT,TC,CC		0.0116,2.4545,0.8387	probably-damaging	273/402	1858076	109,12887	2200	4298	6498	SO:0001583	missense	90019	exon7			GGCCTGCGTCCAG	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.817C>T	11.37:g.1858076C>T	ENSP00000371394:p.Arg273Cys	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	21	0.368421	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	17|17	0.007783882783882784|0.007783882783882784	17|17	0.034552845528455285|0.034552845528455285	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	c|c	13.17|13.17	2.156344|2.156344	0.38021|0.38021	0.024545|0.024545	1.16E-4|1.16E-4	ENSG00000149043|ENSG00000149043	ENST00000381978|ENST00000381968;ENST00000341958	.|T;T	.|0.69685	.|-0.42;-0.42	3.07|3.07	0.632|0.632	0.17705|0.17705	.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|.	.|.	.|.	.|.	T|T	0.35278|0.35278	0.0926|0.0926	L|L	0.33245|0.33245	0.995|0.995	0.18873|0.18873	N|N	0.999986|0.999986	.|D;D	.|0.63046	.|0.992;0.992	.|P;P	.|0.51918	.|0.684;0.684	T|T	0.40136|0.40136	-0.9579|-0.9579	5|9	.|0.87932	.|D	.|0	.|.	5.0271|5.0271	0.14391|0.14391	0.6967:0.1957:0.1076:0.0|0.6967:0.1957:0.1076:0.0	.|.	.|273;259	.|Q8NBV8;A6NCR4	.|SYT8_HUMAN;.	V|C	271|273;259	.|ENSP00000371394:R273C;ENSP00000343691:R259C	.|ENSP00000343691:R259C	A|R	+|+	2|1	0|0	SYT8|SYT8	1814652|1814652	0.012000|0.012000	0.17670|0.17670	0.210000|0.210000	0.23637|0.23637	0.473000|0.473000	0.32948|0.32948	-0.050000|-0.050000	0.11904|0.11904	0.015000|0.015000	0.14971|0.14971	0.313000|0.313000	0.20887|0.20887	GCG|CGT	C|0.991;T|0.009	0.009	strong		0.682	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4		
WHAMM	123720	hgsc.bcm.edu	37	15	83499665	83499665	+	Silent	SNP	G	G	A	rs3814282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83499665G>A	ENST00000286760.4	+	9	2055	c.1956G>A	c.(1954-1956)ccG>ccA	p.P652P		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	652	Mediates actin nucleation. {ECO:0000269|PubMed:18614018}.|Pro-rich.				actin filament organization (GO:0007015)|actin filament reorganization (GO:0090527)|ER to Golgi vesicle-mediated transport (GO:0006888)|focal adhesion assembly (GO:0048041)|lamellipodium assembly (GO:0030032)|membrane tubulation (GO:0097320)|positive regulation of actin nucleation (GO:0051127)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|Golgi membrane (GO:0000139)	Arp2/3 complex binding (GO:0071933)|GTP-Rho binding (GO:0017049)|microtubule binding (GO:0008017)			endometrium(6)|large_intestine(5)|lung(1)|prostate(1)	13						cgccgccaccgccgcccccac	0.572													G|||	888	0.177316	0.0923	0.1081	5008	,	,		9240	0.2044		0.1223	False		,,,				2504	0.3701				p.P652P		Atlas-SNP	.											.	WHAMM	63	.	0			c.G1956A						PASS	.	G		334,3466		22,290,1588	13.0	15.0	15.0		1956	-8.2	0.0	15	dbSNP_107	15	1101,7071		88,925,3073	no	coding-synonymous	WHAMM	NM_001080435.1		110,1215,4661	AA,AG,GG		13.4728,8.7895,11.9863		652/810	83499665	1435,10537	1900	4086	5986	SO:0001819	synonymous_variant	123720	exon9			GCCACCGCCGCCC	AK126887	CCDS45333.1	15q25.2	2009-02-18	2009-02-18	2009-02-18	ENSG00000156232	ENSG00000156232			30493	protein-coding gene	gene with protein product		612393	"""WAS protein homology region 2 domain containing 1"""	WHDC1		11853319, 18226259, 18614018, 18812086	Standard	XM_005272422		Approved	KIAA1971	uc002bje.3	Q8TF30		ENST00000286760.4:c.1956G>A	15.37:g.83499665G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	NM_001080435	Q8N1J9	Silent	SNP	ENST00000286760.4	37	CCDS45333.1																																																																																			G|0.863;A|0.137	0.137	strong		0.572	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1		
SMARCA4	6597	hgsc.bcm.edu	37	19	11094903	11094903	+	Missense_Mutation	SNP	G	G	A	rs145867502		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11094903G>A	ENST00000429416.3	+	3	357	c.76G>A	c.(76-78)Gcc>Acc	p.A26T	SMARCA4_ENST00000413806.3_Missense_Mutation_p.A26T|SMARCA4_ENST00000590574.1_Missense_Mutation_p.A26T|SMARCA4_ENST00000541122.2_Missense_Mutation_p.A26T|SMARCA4_ENST00000444061.3_Missense_Mutation_p.A26T|SMARCA4_ENST00000589677.1_Missense_Mutation_p.A26T|SMARCA4_ENST00000450717.3_Missense_Mutation_p.A26T|SMARCA4_ENST00000344626.4_Missense_Mutation_p.A26T|SMARCA4_ENST00000358026.2_Missense_Mutation_p.A26T	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	26	Necessary for interaction with SS18L1/CREST. {ECO:0000250}.				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)				TTCCCCTGGAGCCATGCTGGG	0.721			"""F, N, Mis"""		NSCLC								G|||	1	0.000199681	0.0008	0.0	5008	,	,		15706	0.0		0.0	False		,,,				2504	0.0				p.A26T		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.G76A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	12,4366		0,12,2177	19.0	24.0	23.0		76,76,76,76,76,76,76	4.9	1.0	19	dbSNP_134	23	0,8566		0,0,4283	no	missense,missense,missense,missense,missense,missense,missense	SMARCA4	NM_003072.3,NM_001128849.1,NM_001128848.1,NM_001128847.1,NM_001128846.1,NM_001128845.1,NM_001128844.1	58,58,58,58,58,58,58	0,12,6460	AA,AG,GG		0.0,0.2741,0.0927	benign,benign,benign,benign,benign,benign,benign	26/1648,26/1680,26/1614,26/1615,26/1617,26/1618,26/1648	11094903	12,12932	2189	4283	6472	SO:0001583	missense	6597	exon2			CCTGGAGCCATGC	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.76G>A	19.37:g.11094903G>A	ENSP00000395654:p.Ala26Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	21.4	4.144345	0.77888	0.002741	0.0	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.86956	-2.18;-2.19;-2.18;-2.17;-2.17;-2.18;-2.17	4.95	4.95	0.65309	.	0.130808	0.49305	D	0.000154	D	0.82879	0.5133	L	0.36672	1.1	0.48087	D	0.999582	B;B;B;B;B;B;B	0.10296	0.003;0.003;0.003;0.0;0.003;0.001;0.003	B;B;B;B;B;B;B	0.08055	0.003;0.003;0.003;0.001;0.003;0.001;0.003	T	0.79579	-0.1745	10	0.66056	D	0.02	-16.4285	17.1334	0.86732	0.0:0.0:1.0:0.0	.	26;26;26;26;26;26;26	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	T	26	ENSP00000395654:A26T;ENSP00000350720:A26T;ENSP00000343896:A26T;ENSP00000445036:A26T;ENSP00000392837:A26T;ENSP00000397783:A26T;ENSP00000414727:A26T	ENSP00000343896:A26T	A	+	1	0	SMARCA4	10955903	0.994000	0.37717	1.000000	0.80357	0.996000	0.88848	2.131000	0.42074	2.563000	0.86464	0.655000	0.94253	GCC	G|0.999;A|0.001	0.001	strong		0.721	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
PIGG	54872	hgsc.bcm.edu	37	4	533001	533001	+	Missense_Mutation	SNP	T	T	C	rs1127410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:533001T>C	ENST00000453061.2	+	13	2901	c.2795T>C	c.(2794-2796)tTc>tCc	p.F932S	PIGG_ENST00000504346.1_Missense_Mutation_p.F843S|PIGG_ENST00000383028.4_Missense_Mutation_p.F799S|PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000310340.5_Missense_Mutation_p.F924S	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	932			F -> S (in dbSNP:rs1127410).		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 (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						ATTCCAGTTTTCACGTACATC	0.388													C|||	1045	0.208666	0.3593	0.0994	5008	,	,		22096	0.2222		0.1282	False		,,,				2504	0.1513				p.F932S		Atlas-SNP	.											.	PIGG	86	.	0			c.T2795C						PASS	.	C	SER/PHE,SER/PHE	1425,2981	684.6+/-404.4	229,967,1007	191.0	167.0	175.0		2795,2771	5.9	0.0	4	dbSNP_86	175	1087,7513	768.9+/-407.6	74,939,3287	yes	missense,missense	PIGG	NM_001127178.1,NM_017733.3	155,155	303,1906,4294	CC,CT,TT		12.6395,32.3423,19.3142	benign,benign	932/984,924/976	533001	2512,10494	2203	4300	6503	SO:0001583	missense	54872	exon13			CAGTTTTCACGTA		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.2795T>C	4.37:g.533001T>C	ENSP00000415203:p.Phe932Ser	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	225	113	0.502222	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	453	0.20741758241758243	181	0.3678861788617886	40	0.11049723756906077	139	0.243006993006993	93	0.12269129287598944	C	2.913	-0.224932	0.06022	0.323423	0.126395	ENSG00000174227	ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028;ENST00000453065	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	5.91	5.91	0.95273	.	0.318324	0.33959	N	0.004399	T	0.00012	0.0000	N	0.00368	-1.59	0.09310	P	0.9999999999996261	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.36114	-0.9761	9	0.13853	T	0.58	-11.9767	13.132	0.59389	0.0:0.923:0.0:0.077	rs1127410;rs3183343;rs60748766;rs1127410	799;932;924	Q5H8A4-3;Q5H8A4;Q5H8A4-2	.;PIGG_HUMAN;.	S	924;932;843;799;88	ENSP00000311750:F924S;ENSP00000415203:F932S;ENSP00000424800:F843S;ENSP00000372494:F799S	ENSP00000311750:F924S	F	+	2	0	PIGG	523001	0.839000	0.29477	0.008000	0.14137	0.251000	0.25915	3.208000	0.51114	1.534000	0.49203	-0.119000	0.15052	TTC	T|0.790;C|0.210	0.210	strong		0.388	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
TSSK2	23617	hgsc.bcm.edu	37	22	19118992	19118992	+	Missense_Mutation	SNP	A	A	G	rs3747052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19118992A>G	ENST00000399635.2	+	1	672	c.80A>G	c.(79-81)aAa>aGa	p.K27R	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	27	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> R (may be associated with infertility; dbSNP:rs3747052). {ECO:0000269|PubMed:17344846}.		multicellular organismal development (GO:0007275)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(2)|lung(2)|prostate(4)|stomach(1)	11	Colorectal(54;0.0993)					GCAAAAGTCAAATCTGCCTAC	0.517													.|||	196	0.0391374	0.1165	0.0144	5008	,	,		22180	0.0198		0.008	False		,,,				2504	0.0041				p.K27R		Atlas-SNP	.											.	TSSK2	29	.	0			c.A80G						PASS	.	A	,ARG/LYS	482,3924	225.9+/-241.6	25,432,1746	82.0	70.0	74.0		,80	4.6	1.0	22	dbSNP_107	74	5,8595	3.7+/-12.6	0,5,4295	yes	utr-3,missense	DGCR14,TSSK2	NM_022719.2,NM_053006.4	,26	25,437,6041	GG,GA,AA		0.0581,10.9396,3.7444	,benign	,27/359	19118992	487,12519	2203	4300	6503	SO:0001583	missense	23617	exon1			AAGTCAAATCTGC	AF362953	CCDS13755.1	22q11.21	2007-01-30	2005-03-10	2005-03-12	ENSG00000206203	ENSG00000206203			11401	protein-coding gene	gene with protein product		610710	"""serine/threonine kinase 22B (spermiogenesis associated)"""	STK22B		10591208	Standard	NM_053006		Approved	SPOGA2, FLJ38613	uc002zow.2	Q96PF2	OTTHUMG00000150118	ENST00000399635.2:c.80A>G	22.37:g.19118992A>G	ENSP00000382544:p.Lys27Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	60	0.631579	NM_053006	Q8IY55	Missense_Mutation	SNP	ENST00000399635.2	37	CCDS13755.1	89	0.04075091575091575	63	0.12804878048780488	6	0.016574585635359115	13	0.022727272727272728	7	0.009234828496042216	A	16.33	3.091896	0.55968	0.109396	5.81E-4	ENSG00000206203	ENST00000399635	D	0.82619	-1.63	5.62	4.56	0.56223	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	0.53938	D	0.000060	T	0.02727	0.0082	N	0.13327	0.33	0.32898	D	0.51277	B	0.23185	0.081	B	0.42882	0.401	T	0.58446	-0.7635	10	0.72032	D	0.01	.	9.692	0.40134	0.845:0.0:0.0:0.155	rs3747052;rs3747052	27	Q96PF2	TSSK2_HUMAN	R	27	ENSP00000382544:K27R	ENSP00000382544:K27R	K	+	2	0	TSSK2	17498992	1.000000	0.71417	0.984000	0.44739	0.986000	0.74619	5.829000	0.69316	0.912000	0.36772	0.460000	0.39030	AAA	A|0.959;G|0.041	0.041	strong		0.517	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1		
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39280234	39280234	+	Silent	SNP	C	C	T	rs611651		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39280234C>T	ENST00000394014.1	-	1	185	c.141G>A	c.(139-141)agG>agA	p.R47R		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	47	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].					keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCACTGGGGCCTGCAGCAGC	0.687																																					p.R47R		Atlas-SNP	.											.	KRTAP4-12	32	.	0			c.G141A						PASS	.						27.0	50.0	42.0					17																	39280234		2006	4274	6280	SO:0001819	synonymous_variant	83755	exon1			CTGGGGCCTGCAG	AJ406943	CCDS32649.1	17q21.2	2013-06-25			ENSG00000213416	ENSG00000213416		"""Keratin associated proteins"""	16776	protein-coding gene	gene with protein product						11279113	Standard	NM_031854		Approved	KAP4.12	uc002hwa.3	Q9BQ66	OTTHUMG00000133632	ENST00000394014.1:c.141G>A	17.37:g.39280234C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	73	71	0.972603	NM_031854	A3KMC5|Q495I0	Silent	SNP	ENST00000394014.1	37	CCDS32649.1																																																																																			C|0.333;T|0.667	0.667	weak		0.687	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1		
DHRS2	10202	hgsc.bcm.edu	37	14	24114490	24114490	+	3'UTR	SNP	G	G	A	rs7150155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24114490G>A	ENST00000250383.6	+	0	1347				DHRS2_ENST00000344777.7_Silent_p.V294V	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2						C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		GCGTAGCTGTGGTCCCAGGCC	0.597													g|||	370	0.0738818	0.267	0.0216	5008	,	,		17143	0.0		0.002	False		,,,				2504	0.0				p.V294V		Atlas-SNP	.											DHRS2_ENST00000344777,NS,carcinoma,+1,1	DHRS2	78	1	0			c.G882A						scavenged	.		,	963,3443	362.4+/-316.1	113,737,1353	58.0	60.0	59.0		,882	2.3	0.0	14	dbSNP_116	59	13,8587	9.1+/-34.3	0,13,4287	no	utr-3,coding-synonymous	DHRS2	NM_005794.3,NM_182908.4	,	113,750,5640	AA,AG,GG		0.1512,21.8566,7.5042	,	,294/301	24114490	976,12030	2203	4300	6503	SO:0001624	3_prime_UTR_variant	10202	exon9			AGCTGTGGTCCCA		CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18349	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 1"""	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.*28G>A	14.37:g.24114490G>A		Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	71	39	0.549296	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Silent	SNP	ENST00000250383.6	37	CCDS9604.1																																																																																			G|0.966;A|0.034	0.034	strong		0.597	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908	
DNAH17	8632	hgsc.bcm.edu	37	17	76472768	76472768	+	Silent	SNP	G	G	A	rs7405830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76472768G>A	ENST00000585328.1	-	52	8149	c.8025C>T	c.(8023-8025)ctC>ctT	p.L2675L	DNAH17_ENST00000389840.5_Silent_p.L2666L|DNAH17_ENST00000586052.1_Intron	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2666					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)			AAAGGCGGACGAGGTCCAGTG	0.507													A|||	1881	0.375599	0.761	0.2435	5008	,	,		20560	0.2798		0.1909	False		,,,				2504	0.2372				p.L2680L		Atlas-SNP	.											.	DNAH17	347	.	0			c.C8040T						PASS	.	A		2623,1379		873,877,251	110.0	124.0	119.0		8040	-9.5	0.4	17	dbSNP_116	119	1610,6712		158,1294,2709	no	coding-synonymous	DNAH17	NM_173628.3		1031,2171,2960	AA,AG,GG		19.3463,34.4578,34.3476		2680/4463	76472768	4233,8091	2001	4161	6162	SO:0001819	synonymous_variant	8632	exon52			GCGGACGAGGTCC	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.8025C>T	17.37:g.76472768G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	261	260	0.996169	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.641;A|0.359	0.359	strong		0.507	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
KIF21B	23046	hgsc.bcm.edu	37	1	200971353	200971353	+	Silent	SNP	A	A	G	rs61740482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200971353A>G	ENST00000422435.2	-	9	1654	c.1338T>C	c.(1336-1338)gaT>gaC	p.D446D	KIF21B_ENST00000332129.2_Silent_p.D446D|KIF21B_ENST00000360529.5_Silent_p.D446D|KIF21B_ENST00000461742.2_Silent_p.D446D	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	446					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)	p.D446D(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TGTTGATGGCATCGATGGCCT	0.612													g|||	384	0.0766773	0.0998	0.0504	5008	,	,		18587	0.125		0.005	False		,,,				2504	0.0879				p.D446D		Atlas-SNP	.											KIF21B,NS,carcinoma,0,1	KIF21B	208	1	1	Substitution - coding silent(1)	stomach(1)	c.T1338C						PASS	.			432,3974	786.5+/-414.8	21,390,1792	157.0	128.0	138.0		1338	-0.3	1.0	1	dbSNP_129	138	22,8578	818.4+/-406.9	0,22,4278	no	coding-synonymous	KIF21B	NM_017596.2		21,412,6070	GG,GA,AA		0.2558,9.8048,3.4907		446/1625	200971353	454,12552	2203	4300	6503	SO:0001819	synonymous_variant	23046	exon9			GATGGCATCGATG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.1338T>C	1.37:g.200971353A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	150	81	0.54	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	37	CCDS58056.1																																																																																			A|0.959;G|0.041	0.041	strong		0.612	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
DDX47	51202	hgsc.bcm.edu	37	12	12967127	12967127	+	Silent	SNP	C	C	T	rs1051374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:12967127C>T	ENST00000358007.3	+	2	172	c.150C>T	c.(148-150)atC>atT	p.I50I	DDX47_ENST00000352940.4_Silent_p.I50I	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	50					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		CCACCAAGATCCAGATTGAAG	0.398													C|||	1937	0.386781	0.2511	0.4121	5008	,	,		23125	0.5992		0.2734	False		,,,				2504	0.4499				p.I50I		Atlas-SNP	.											.	DDX47	37	.	0			c.C150T						PASS	.	C	,	1166,3240	412.4+/-336.1	168,830,1205	308.0	290.0	296.0		150,150	5.3	1.0	12	dbSNP_86	296	2385,6215	397.3+/-345.7	330,1725,2245	yes	coding-synonymous,coding-synonymous	DDX47	NM_016355.3,NM_201224.1	,	498,2555,3450	TT,TC,CC		27.7326,26.4639,27.3028	,	50/456,50/407	12967127	3551,9455	2203	4300	6503	SO:0001819	synonymous_variant	51202	exon2			CAAGATCCAGATT	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"""DEAD-boxes"""	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.150C>T	12.37:g.12967127C>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	202	91	0.450495	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Silent	SNP	ENST00000358007.3	37	CCDS8655.1																																																																																			C|0.686;T|0.314	0.314	strong		0.398	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355	
GFM1	85476	hgsc.bcm.edu	37	3	158372389	158372389	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:158372389A>C	ENST00000486715.1	+	8	1409	c.1052A>C	c.(1051-1053)cAc>cCc	p.H351P	GFM1_ENST00000478576.1_Missense_Mutation_p.H351P|GFM1_ENST00000264263.5_Missense_Mutation_p.H370P	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			GACAATTCCCACCCATTTGTA	0.308																																					p.H351P		Atlas-SNP	.											.	GFM1	83	.	0			c.A1052C						PASS	.																																			SO:0001583	missense	85476	exon8			ATTCCCACCCATT	AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"""G translation elongation factor, mitochondrial"""			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.1052A>C	3.37:g.158372389A>C	ENSP00000419038:p.His351Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_024996		Missense_Mutation	SNP	ENST00000486715.1	37	CCDS33885.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.225950	0.39300	.	.	ENSG00000168827	ENST00000486715;ENST00000478576;ENST00000264263;ENST00000312756	T;T;T	0.79845	-1.31;-1.31;-1.31	5.66	5.66	0.87406	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.216872	0.49305	D	0.000147	T	0.72930	0.3522	N	0.22421	0.69	0.80722	D	1	B;B;B	0.34161	0.439;0.203;0.047	B;B;B	0.39660	0.306;0.162;0.112	T	0.75445	-0.3315	10	0.72032	D	0.01	-10.9205	11.6275	0.51153	0.867:0.0:0.0:0.133	.	370;351;351	Q96RP9-2;Q96RP9;C9IZ01	.;EFGM_HUMAN;.	P	351;351;370;85	ENSP00000419038:H351P;ENSP00000418755:H351P;ENSP00000264263:H370P	ENSP00000264263:H370P	H	+	2	0	GFM1	159855083	0.996000	0.38824	0.988000	0.46212	0.739000	0.42172	5.152000	0.64882	2.140000	0.66376	0.533000	0.62120	CAC	.	.	none		0.308	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996	
POM121L12	285877	hgsc.bcm.edu	37	7	53104078	53104078	+	Silent	SNP	G	G	A	rs72598686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:53104078G>A	ENST00000408890.4	+	1	730	c.714G>A	c.(712-714)ccG>ccA	p.P238P		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	238										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CTCTGAAGCCGAGCCTCGGCC	0.647													G|||	1659	0.33127	0.2209	0.2464	5008	,	,		12613	0.4315		0.2982	False		,,,				2504	0.4714				p.P238P		Atlas-SNP	.											POM121L12,NS,carcinoma,0,1	POM121L12	146	1	0			c.G714A						PASS	.	G		847,3087		94,659,1214	44.0	52.0	50.0		714	-3.7	0.0	7	dbSNP_130	50	2247,6031		281,1685,2173	no	coding-synonymous	POM121L12	NM_182595.3		375,2344,3387	AA,AG,GG		27.1442,21.5302,25.3357		238/297	53104078	3094,9118	1967	4139	6106	SO:0001819	synonymous_variant	285877	exon1			GAAGCCGAGCCTC		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.714G>A	7.37:g.53104078G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	95	37	0.389474	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			G|0.706;A|0.294	0.294	strong		0.647	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
USP10	9100	hgsc.bcm.edu	37	16	84778261	84778261	+	Silent	SNP	G	G	A	rs77170713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84778261G>A	ENST00000219473.7	+	4	287	c.174G>A	c.(172-174)gaG>gaA	p.E58E	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Silent_p.E62E	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	58	Interaction with p53/TP53.				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						AGAGAATTGAGTTTGGTGTCG	0.403													G|||	27	0.00539137	0.0204	0.0	5008	,	,		16411	0.0		0.0	False		,,,				2504	0.0				p.E62E		Atlas-SNP	.											.	USP10	51	.	0			c.G186A						PASS	.	G		55,3637		0,55,1791	45.0	43.0	43.0		174	-3.0	1.0	16	dbSNP_131	43	1,8163		0,1,4081	no	coding-synonymous	USP10	NM_005153.2		0,56,5872	AA,AG,GG		0.0122,1.4897,0.4723		58/799	84778261	56,11800	1846	4082	5928	SO:0001819	synonymous_variant	9100	exon5			AATTGAGTTTGGT	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.174G>A	16.37:g.84778261G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	145	77	0.531034	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	12.78	2.039111	0.35989	0.014897	1.22E-4	ENSG00000103194	ENST00000540269	.	.	.	5.06	-3.04	0.05412	.	.	.	.	.	T	0.59609	0.2206	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67538	-0.5645	5	0.66056	D	0.02	-22.7486	11.4442	0.50114	0.7447:0.0:0.2553:0.0	.	.	.	.	N	38	.	ENSP00000445589:S38N	S	+	2	0	USP10	83335762	1.000000	0.71417	0.969000	0.41365	0.892000	0.51952	0.653000	0.24902	-0.665000	0.05317	-0.339000	0.08088	AGT	G|0.997;A|0.003	0.003	strong		0.403	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
ZNF763	284390	hgsc.bcm.edu	37	19	12089704	12089704	+	Missense_Mutation	SNP	G	G	A	rs79043756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12089704G>A	ENST00000358987.3	+	4	1092	c.965G>A	c.(964-966)cGt>cAt	p.R322H	ZNF763_ENST00000343949.5_Missense_Mutation_p.R325H|ZNF763_ENST00000538752.1_Missense_Mutation_p.R342H|ZNF763_ENST00000590798.1_Missense_Mutation_p.R342H|ZNF763_ENST00000545530.1_Missense_Mutation_p.R200H			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	322					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)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						AAAGCATTCCGTAGTTACAGA	0.408													g|||	82	0.0163738	0.0582	0.0043	5008	,	,		21314	0.0		0.001	False		,,,				2504	0.001				p.R325H		Atlas-SNP	.											.	ZNF763	31	.	0			c.G974A						PASS	.	G	HIS/ARG	264,4122	737.1+/-410.8	5,254,1934	72.0	75.0	74.0		974	-2.6	0.0	19	dbSNP_131	74	7,8589	799.1+/-407.4	0,7,4291	no	missense	ZNF763	NM_001012753.1	29	5,261,6225	AA,AG,GG		0.0814,6.0192,2.0875		325/398	12089704	271,12711	2193	4298	6491	SO:0001583	missense	284390	exon4			CATTCCGTAGTTA	AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"""Zinc fingers, C2H2-type"", ""-"""	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.965G>A	19.37:g.12089704G>A	ENSP00000402017:p.Arg322His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_001012753	B3KRU3|B4DRE7	Missense_Mutation	SNP	ENST00000358987.3	37		45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	a	0.005	-2.195045	0.00299	0.060192	8.14E-4	ENSG00000197054	ENST00000538752;ENST00000343949;ENST00000545530;ENST00000358987	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	1.31	-2.62	0.06152	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00328	0.0010	N	0.25426	0.745	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.33701	-0.9858	9	0.13108	T	0.6	.	4.5111	0.11912	0.2955:0.3236:0.3809:0.0	.	342;322;325	F5H0A9;Q0D2J5;Q0D2J5-2	.;ZN763_HUMAN;.	H	342;325;200;322	ENSP00000438117:R342H;ENSP00000369774:R325H;ENSP00000446166:R200H;ENSP00000402017:R322H	ENSP00000369774:R325H	R	+	2	0	ZNF763	11950704	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-7.131000	0.00043	-2.876000	0.00321	-2.047000	0.00414	CGT	G|0.979;A|0.021	0.021	strong		0.408	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753	
PPP2R3B	28227	hgsc.bcm.edu	37	X	299360	299360	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	124	0	0		WXS	Illumina HiSeq	Phase_I	145	68	0.468966	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	
NUP88	4927	hgsc.bcm.edu	37	17	5291126	5291126	+	Missense_Mutation	SNP	T	T	C	rs149760662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5291126T>C	ENST00000573584.1	-	12	2251	c.1742A>G	c.(1741-1743)gAc>gGc	p.D581G	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	581					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)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						CTTTGCCAAGTCCTGTTTGAG	0.522													T|||	5	0.000998403	0.0	0.0014	5008	,	,		15835	0.0		0.003	False		,,,				2504	0.001				p.D581G		Atlas-SNP	.											.	NUP88	47	.	0			c.A1742G						PASS	.	T	GLY/ASP	6,4400	11.4+/-27.6	0,6,2197	96.0	96.0	96.0		1742	4.8	1.0	17	dbSNP_134	96	44,8556	27.9+/-77.7	0,44,4256	yes	missense	NUP88	NM_002532.4	94	0,50,6453	CC,CT,TT		0.5116,0.1362,0.3844	benign	581/742	5291126	50,12956	2203	4300	6503	SO:0001583	missense	4927	exon12			GCCAAGTCCTGTT	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1742A>G	17.37:g.5291126T>C	ENSP00000458954:p.Asp581Gly	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_002532	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	37	CCDS11070.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	19.11	3.764327	0.69878	0.001362	0.005116	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	4.76	4.76	0.60689	.	0.047661	0.85682	D	0.000000	T	0.48822	0.1521	L	0.38838	1.175	0.52501	D	0.999951	P;B	0.52692	0.955;0.046	P;B	0.51615	0.675;0.04	T	0.51196	-0.8736	9	0.32370	T	0.25	-20.571	13.9189	0.63919	0.0:0.0:0.0:1.0	.	466;581	B4DP20;Q99567	.;NUP88_HUMAN	G	581;466	.	ENSP00000225696:D581G	D	-	2	0	NUP88	5231850	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.299000	0.65716	2.137000	0.66172	0.454000	0.30748	GAC	T|0.998;C|0.002	0.002	strong		0.522	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10527404	10527404	+	Missense_Mutation	SNP	G	G	A	rs141089693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:10527404G>A	ENST00000396560.2	+	4	1085	c.858G>A	c.(856-858)atG>atA	p.M286I	ATF7IP2_ENST00000356427.2_Missense_Mutation_p.M286I|ATF7IP2_ENST00000324570.5_Missense_Mutation_p.M286I|ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Missense_Mutation_p.M286I	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	286					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AGAAGAGGATGTTTTCAGAAA	0.338													G|||	5	0.000998403	0.0038	0.0	5008	,	,		21095	0.0		0.0	False		,,,				2504	0.0				p.M286I		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.G858A						PASS	.	G	ILE/MET	30,4362	32.6+/-62.9	1,28,2167	54.0	56.0	55.0		858	1.8	1.0	16	dbSNP_134	55	0,8598		0,0,4299	yes	missense	ATF7IP2	NM_024997.2	10	1,28,6466	AA,AG,GG		0.0,0.6831,0.2309	possibly-damaging	286/683	10527404	30,12960	2196	4299	6495	SO:0001583	missense	80063	exon4			GAGGATGTTTTCA	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.858G>A	16.37:g.10527404G>A	ENSP00000379808:p.Met286Ile	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	159	81	0.509434	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	37	CCDS10540.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	13.62	2.292811	0.40594	0.006831	0.0	ENSG00000166669	ENST00000396559;ENST00000396560;ENST00000535850;ENST00000356427;ENST00000324570	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.02	1.79	0.24919	.	0.492757	0.20948	N	0.082817	T	0.25269	0.0614	L	0.55481	1.735	0.21822	N	0.999525	B;B	0.27656	0.184;0.161	B;B	0.29353	0.101;0.053	T	0.13522	-1.0506	10	0.33940	T	0.23	-6.0402	5.1577	0.15044	0.1856:0.0:0.6499:0.1645	.	286;286	Q5U623-2;Q5U623	.;MCAF2_HUMAN	I	286	ENSP00000379807:M286I;ENSP00000379808:M286I;ENSP00000440791:M286I;ENSP00000348799:M286I;ENSP00000322811:M286I	ENSP00000322811:M286I	M	+	3	0	ATF7IP2	10434905	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.462000	0.35266	0.648000	0.30732	-0.145000	0.13849	ATG	G|0.999;A|0.001	0.001	strong		0.338	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
SLC22A3	6581	hgsc.bcm.edu	37	6	160769811	160769811	+	Silent	SNP	C	C	T	rs668871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160769811C>T	ENST00000275300.2	+	1	512	c.360C>T	c.(358-360)cgC>cgT	p.R120R	SLC22A3_ENST00000392145.1_Silent_p.R120R	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	120					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	TCCCCAACCGCTCGGCTCCCC	0.741													T|||	2161	0.43151	0.5605	0.4424	5008	,	,		12151	0.2857		0.4742	False		,,,				2504	0.3558				p.R120R		Atlas-SNP	.											.	SLC22A3	58	.	0			c.C360T						PASS	.	T		2015,1197		677,661,268	4.0	4.0	4.0		360	2.8	0.5	6	dbSNP_83	4	3611,3005		1085,1441,782	no	coding-synonymous	SLC22A3	NM_021977.2		1762,2102,1050	TT,TC,CC		45.4202,37.2665,42.7554		120/557	160769811	5626,4202	1606	3308	4914	SO:0001819	synonymous_variant	6581	exon1			CAACCGCTCGGCT	AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477		"""Solute carriers"""	10967	protein-coding gene	gene with protein product		604842	"""solute carrier family 22 (extraneuronal monoamine transporter), member 3"""			9632645, 9933568	Standard	NM_021977		Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.360C>T	6.37:g.160769811C>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_021977	Q5SYN6|Q9UP02	Silent	SNP	ENST00000275300.2	37	CCDS5277.1																																																																																			T|0.369;G|0.002;C|0.629	0.369	strong		0.741	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042953.1	NM_021977	
IL4R	3566	hgsc.bcm.edu	37	16	27356271	27356271	+	Silent	SNP	T	T	C	rs112497527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27356271T>C	ENST00000395762.2	+	5	550	c.291T>C	c.(289-291)gaT>gaC	p.D97D	IL4R_ENST00000170630.2_Silent_p.D97D|IL4R_ENST00000543915.2_Silent_p.D97D|IL4R_ENST00000380922.3_Silent_p.D82D|IL4R_ENST00000449195.1_Silent_p.D97D	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	97		Major IL4 binding determinant.			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						TCAGTGCGGATAACTATACAC	0.642													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		14225	0.0		0.0	False		,,,				2504	0.0				p.D97D		Atlas-SNP	.											.	IL4R	70	.	0			c.T291C						PASS	.	C	,	198,4196	807.2+/-415.9	3,192,2002	108.0	92.0	98.0		291,291	2.4	0.0	16	dbSNP_132	98	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous	IL4R	NM_000418.2,NM_001008699.1	,	3,194,6300	CC,CT,TT		0.0233,4.5061,1.5392	,	97/826,97/228	27356271	200,12794	2197	4300	6497	SO:0001819	synonymous_variant	3566	exon5			TGCGGATAACTAT	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.291T>C	16.37:g.27356271T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Silent	SNP	ENST00000395762.2	37	CCDS10629.1																																																																																			T|0.988;C|0.012	0.012	strong		0.642	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
NTSR1	4923	hgsc.bcm.edu	37	20	61386231	61386231	+	Silent	SNP	C	C	T	rs6010685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	35	0	0		WXS	Illumina HiSeq	Phase_I	29	19	0.655172	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		
MRPL28	10573	hgsc.bcm.edu	37	16	417691	417691	+	Missense_Mutation	SNP	C	C	G	rs114486517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:417691C>G	ENST00000199706.8	-	6	790	c.755G>C	c.(754-756)aGa>aCa	p.R252T	MRPL28_ENST00000429738.1_Intron|MRPL28_ENST00000389675.2_Missense_Mutation_p.R252T	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	252				R -> T (in Ref. 6; AAC50181). {ECO:0000305}.	translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				GCCACTGGCTCTCTTCTGCAC	0.617													C|||	327	0.0652955	0.2194	0.0303	5008	,	,		18217	0.0		0.008	False		,,,				2504	0.0082				p.R252T		Atlas-SNP	.											.	MRPL28	15	.	0			c.G755C						PASS	.	C	THR/ARG	811,3595	316.1+/-294.4	77,657,1469	53.0	48.0	50.0		755	-3.0	0.0	16	dbSNP_132	50	57,8543	33.3+/-86.6	1,55,4244	yes	missense	MRPL28	NM_006428.4	71	78,712,5713	GG,GC,CC		0.6628,18.4067,6.6738	benign	252/257	417691	868,12138	2203	4300	6503	SO:0001583	missense	10573	exon6			CTGGCTCTCTTCT	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"""Mitochondrial ribosomal proteins / large subunits"""	14484	protein-coding gene	gene with protein product		604853	"""melanoma-associated antigen recognised by cytotoxic T lymphocytes"""	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.755G>C	16.37:g.417691C>G	ENSP00000199706:p.Arg252Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	134	69	0.514925	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Missense_Mutation	SNP	ENST00000199706.8	37	CCDS32349.1	109	0.04990842490842491	98	0.1991869918699187	9	0.024861878453038673	0	0.0	2	0.002638522427440633	C	8.839	0.941748	0.18281	0.184067	0.006628	ENSG00000086504	ENST00000397735;ENST00000199706;ENST00000397734;ENST00000389675	T;T	0.23950	1.88;1.88	4.86	-2.96	0.05547	.	0.400839	0.27000	N	0.021425	T	0.00012	0.0000	L	0.31294	0.92	0.80722	P	0.0	B;B	0.22003	0.063;0.063	B;B	0.15484	0.013;0.013	T	0.23940	-1.0174	9	0.49607	T	0.09	-0.0185	4.4593	0.11659	0.0:0.2928:0.309:0.3982	.	252;252	Q13084;Q4TT38	RM28_HUMAN;.	T	252	ENSP00000199706:R252T;ENSP00000374326:R252T	ENSP00000199706:R252T	R	-	2	0	MRPL28	357692	0.007000	0.16637	0.004000	0.12327	0.779000	0.44077	-0.411000	0.07142	-0.118000	0.11851	0.637000	0.83480	AGA	C|0.937;G|0.063	0.063	strong		0.617	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2		
INSC	387755	hgsc.bcm.edu	37	11	15170686	15170686	+	Missense_Mutation	SNP	G	G	A	rs61877970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:15170686G>A	ENST00000379554.3	+	2	153	c.107G>A	c.(106-108)cGc>cAc	p.R36H	INSC_ENST00000424273.1_De_novo_Start_OutOfFrame|INSC_ENST00000525218.1_De_novo_Start_OutOfFrame|INSC_ENST00000379556.3_De_novo_Start_OutOfFrame|INSC_ENST00000528567.1_De_novo_Start_OutOfFrame|INSC_ENST00000530161.1_De_novo_Start_OutOfFrame	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	36					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						GGTCACGACCGCTGCAAGCAG	0.562													G|||	198	0.0395367	0.0424	0.0605	5008	,	,		20792	0.0159		0.0646	False		,,,				2504	0.0194				p.R36H		Atlas-SNP	.											.	INSC	104	.	0			c.G107A						PASS	.	G	HIS/ARG,	255,4143	134.1+/-170.4	16,223,1960	61.0	62.0	62.0		107,	0.9	0.1	11	dbSNP_129	62	615,7967	158.5+/-212.0	28,559,3704	yes	missense,utr-5	INSC	NM_001031853.3,NM_001042536.1	29,	44,782,5664	AA,AG,GG		7.1662,5.7981,6.7026	possibly-damaging,	36/580,	15170686	870,12110	2199	4291	6490	SO:0001583	missense	387755	exon2			ACGACCGCTGCAA	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.107G>A	11.37:g.15170686G>A	ENSP00000368872:p.Arg36His	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Missense_Mutation	SNP	ENST00000379554.3	37	CCDS41621.1	105	0.04807692307692308	20	0.04065040650406504	20	0.055248618784530384	13	0.022727272727272728	52	0.06860158311345646	G	3.156	-0.173145	0.06421	0.057981	0.071662	ENSG00000188487	ENST00000379554	T	0.33654	1.4	4.99	0.942	0.19525	.	.	.	.	.	T	0.01254	0.0041	N	0.08118	0	0.19775	N	0.99995	B	0.02656	0.0	B	0.01281	0.0	T	0.13845	-1.0494	9	0.56958	D	0.05	-0.8183	6.8675	0.24102	0.3934:0.0:0.6066:0.0	rs61877970	36	Q1MX18	INSC_HUMAN	H	36	ENSP00000368872:R36H	ENSP00000368872:R36H	R	+	2	0	INSC	15127262	0.036000	0.19791	0.100000	0.21137	0.019000	0.09904	0.086000	0.14935	0.015000	0.14971	0.561000	0.74099	CGC	G|0.946;A|0.054	0.054	strong		0.562	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853	
NUP88	4927	hgsc.bcm.edu	37	17	5289580	5289580	+	Silent	SNP	A	A	G	rs11209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5289580A>G	ENST00000573584.1	-	17	2681	c.2172T>C	c.(2170-2172)caT>caC	p.H724H	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	724					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)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						TTTCCCTTATATGTTCACCCC	0.358													G|||	2887	0.576478	0.5061	0.4308	5008	,	,		17870	0.8244		0.4165	False		,,,				2504	0.684				p.H724H		Atlas-SNP	.											.	NUP88	47	.	0			c.T2172C						PASS	.	G		2220,2186	586.2+/-386.4	558,1104,541	224.0	208.0	214.0		2172	4.0	1.0	17	dbSNP_52	214	3248,5352	649.5+/-400.6	606,2036,1658	no	coding-synonymous	NUP88	NM_002532.4		1164,3140,2199	GG,GA,AA		37.7674,49.6142,42.0421		724/742	5289580	5468,7538	2203	4300	6503	SO:0001819	synonymous_variant	4927	exon17			CCTTATATGTTCA	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.2172T>C	17.37:g.5289580A>G		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	232	119	0.512931	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			A|0.526;G|0.474	0.474	strong		0.358	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
KRT81	3887	hgsc.bcm.edu	37	12	52685213	52685213	+	Missense_Mutation	SNP	T	T	G	rs79897879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52685213T>G	ENST00000327741.5	-	1	105	c.37A>C	c.(37-39)Agc>Cgc	p.S13R	KRT86_ENST00000544024.1_Intron|KRT86_ENST00000423955.2_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	13	Head.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		GAGATGCAGCTGAAGGCGCGC	0.672													t|||	501	0.10004	0.2284	0.0216	5008	,	,		12312	0.1141		0.003	False		,,,				2504	0.0675				p.S13R		Atlas-SNP	.											KRT81,NS,carcinoma,0,2	KRT81	46	2	0			c.A37C						scavenged	.	T	ARG/SER	878,3490		86,706,1392	22.0	27.0	25.0		37	5.2	1.0	12	dbSNP_131	25	27,8441		0,27,4207	yes	missense	KRT81	NM_002281.3	110	86,733,5599	GG,GT,TT		0.3188,20.1007,7.0505	probably-damaging	13/506	52685213	905,11931	2184	4234	6418	SO:0001583	missense	3887	exon1			TGCAGCTGAAGGC	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6458	protein-coding gene	gene with protein product	"""hard keratin type II 1"""	602153	"""keratin, hair, basic, 1"""	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.37A>C	12.37:g.52685213T>G	ENSP00000369349:p.Ser13Arg	Somatic	43	1	0.0232558		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Missense_Mutation	SNP	ENST00000327741.5	37	CCDS31805.1	195	0.08928571428571429	117	0.23780487804878048	8	0.022099447513812154	67	0.11713286713286714	3	0.00395778364116095	T	17.99	3.523540	0.64747	0.201007	0.003188	ENSG00000205426	ENST00000327741;ENST00000389388	D	0.83163	-1.69	5.17	5.17	0.71159	.	0.181068	0.26563	U	0.023676	T	0.00210	0.0006	M	0.75777	2.31	0.29183	P	0.876332	D	0.59357	0.985	D	0.65323	0.934	T	0.00002	-1.2612	9	0.72032	D	0.01	.	15.0178	0.71600	0.0:0.0:0.0:1.0	.	13	Q14533	KRT81_HUMAN	R	13	ENSP00000369349:S13R	ENSP00000369349:S13R	S	-	1	0	KRT81	50971480	1.000000	0.71417	1.000000	0.80357	0.576000	0.36127	3.117000	0.50407	1.943000	0.56356	0.448000	0.29417	AGC	T|0.923;G|0.077	0.077	strong		0.672	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281	
CCDC73	493860	hgsc.bcm.edu	37	11	32622233	32622233	+	IGR	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:32622233A>T	ENST00000335185.5	-	0	3849				EIF3M_ENST00000531120.1_Splice_Site|EIF3M_ENST00000524896.1_Splice_Site	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73											NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TCTGTTTTCTAGGCCTGTTAC	0.333																																					.		Atlas-SNP	.											.	EIF3M	37	.	0			c.800-2A>T						PASS	.						65.0	63.0	63.0					11																	32622233		2202	4299	6501	SO:0001628	intergenic_variant	10480	exon9			TTTTCTAGGCCTG	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279		11.37:g.32622233A>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	108	12	0.111111	NM_006360	Q6P5Q7|Q6ZMW0|Q86WE7	Splice_Site	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	A	31	5.076612	0.94000	.	.	ENSG00000149100	ENST00000531120;ENST00000524896;ENST00000526267	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3871	0.83514	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF3M	32578809	1.000000	0.71417	0.634000	0.29324	0.673000	0.39480	8.701000	0.91331	2.270000	0.75569	0.482000	0.46254	.	.	.	none		0.333	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	
ST8SIA2	8128	hgsc.bcm.edu	37	15	92987938	92987938	+	Silent	SNP	C	C	G	rs2305561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	100	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	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	
LHFPL2	10184	hgsc.bcm.edu	37	5	77784810	77784810	+	Silent	SNP	A	A	C	rs35110604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:77784810A>C	ENST00000515007.2	-	3	907	c.597T>G	c.(595-597)gcT>gcG	p.A199A	LHFPL2_ENST00000380345.2_Silent_p.A199A			Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2	199						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	6		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)		CAGAGAAGACAGCACAGATGA	0.473													A|||	116	0.0231629	0.0825	0.0101	5008	,	,		21336	0.0		0.0	False		,,,				2504	0.0				p.A199A		Atlas-SNP	.											.	LHFPL2	9	.	0			c.T597G						PASS	.	A		282,4124	157.4+/-190.3	7,268,1928	134.0	131.0	132.0		597	-4.5	1.0	5	dbSNP_126	132	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	LHFPL2	NM_005779.2		7,271,6225	CC,CA,AA		0.0349,6.4004,2.1913		199/229	77784810	285,12721	2203	4300	6503	SO:0001819	synonymous_variant	10184	exon5			GAAGACAGCACAG	D86961	CCDS4042.1	5q13	2008-02-05			ENSG00000145685	ENSG00000145685			6588	protein-coding gene	gene with protein product		609718				10329012	Standard	NM_005779		Approved	KIAA0206	uc003kfo.3	Q6ZUX7	OTTHUMG00000107579	ENST00000515007.2:c.597T>G	5.37:g.77784810A>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	167	83	0.497006	NM_005779	B2RMQ6|Q7Z5P0|Q92605	Silent	SNP	ENST00000515007.2	37	CCDS4042.1																																																																																			A|0.982;C|0.018	0.018	strong		0.473	LHFPL2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369098.2	NM_005779	
MBLAC2	153364	hgsc.bcm.edu	37	5	89769834	89769834	+	Silent	SNP	G	G	A	rs9293544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:89769834G>A	ENST00000316610.6	-	1	751	c.276C>T	c.(274-276)ctC>ctT	p.L92L	MBLAC2_ENST00000514906.1_Silent_p.L92L|POLR3G_ENST00000504930.1_5'Flank|POLR3G_ENST00000399107.1_5'Flank|POLR3G_ENST00000514483.1_5'Flank	NM_203406.1	NP_981951	Q68D91	MBLC2_HUMAN	metallo-beta-lactamase domain containing 2	92						extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			kidney(1)|liver(1)|lung(3)	5						CGAACTGGTAGAGGCCGCCGG	0.692													G|||	234	0.0467252	0.1672	0.0173	5008	,	,		15521	0.0		0.001	False		,,,				2504	0.0				p.L92L		Atlas-SNP	.											.	MBLAC2	9	.	0			c.C276T						PASS	.	G		658,3730		45,568,1581	16.0	17.0	17.0		276	2.4	1.0	5	dbSNP_119	17	3,8583		0,3,4290	no	coding-synonymous	MBLAC2	NM_203406.1		45,571,5871	AA,AG,GG		0.0349,14.9954,5.0948		92/280	89769834	661,12313	2194	4293	6487	SO:0001819	synonymous_variant	153364	exon1			CTGGTAGAGGCCG	BC038230	CCDS4067.1	5q14.3	2009-04-08	2009-04-08		ENSG00000176055	ENSG00000176055			33711	protein-coding gene	gene with protein product							Standard	NM_203406		Approved	DKFZp686P15118, MGC46734	uc003kjp.3	Q68D91	OTTHUMG00000131327	ENST00000316610.6:c.276C>T	5.37:g.89769834G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	83	49	0.590361	NM_203406	D6RJI1|Q8IY16|Q8N8D8	Silent	SNP	ENST00000316610.6	37	CCDS4067.1																																																																																			G|0.951;A|0.049	0.049	strong		0.692	MBLAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254098.2	NM_203406	
TMEM232	642987	hgsc.bcm.edu	37	5	109904249	109904249	+	Missense_Mutation	SNP	C	C	T	rs61734250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:109904249C>T	ENST00000455884.2	-	11	1404	c.1354G>A	c.(1354-1356)Gaa>Aaa	p.E452K	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Missense_Mutation_p.E452K			C9JQI7	TM232_HUMAN	transmembrane protein 232	452						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						TCCTGTTCTTCGTCTCCTTGA	0.363													C|||	109	0.0217652	0.0802	0.0029	5008	,	,		17280	0.0		0.001	False		,,,				2504	0.0				p.E452K		Atlas-SNP	.											TMEM232_ENST00000455884,rectum,carcinoma,0,2	TMEM232	57	2	0			c.G1354A						PASS	.	C	LYS/GLU	71,1313		2,67,623	443.0	343.0	373.0		1354	3.1	0.7	5	dbSNP_129	373	0,3182		0,0,1591	yes	missense	TMEM232	NM_001039763.3	56	2,67,2214	TT,TC,CC		0.0,5.1301,1.555	benign	452/658	109904249	71,4495	692	1591	2283	SO:0001583	missense	642987	exon11			GTTCTTCGTCTCC	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.1354G>A	5.37:g.109904249C>T	ENSP00000401477:p.Glu452Lys	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	201	97	0.482587	NM_001039763	B4DKF4	Missense_Mutation	SNP	ENST00000455884.2	37	CCDS47253.2	43	0.019688644688644688	42	0.08536585365853659	1	0.0027624309392265192	0	0.0	0	0.0	C	11.26	1.584993	0.28268	0.051301	0.0	ENSG00000186952	ENST00000429839;ENST00000455884	.	.	.	5.88	3.09	0.35607	.	0.688144	0.13800	N	0.361872	T	0.00695	0.0023	N	0.21448	0.665	0.21290	N	0.999739	B;B;B	0.27971	0.196;0.055;0.03	B;B;B	0.17722	0.019;0.011;0.007	T	0.13522	-1.0506	8	.	.	.	-3.5222	5.5928	0.17311	0.0:0.6568:0.1618:0.1814	.	452;452;334	C9JQI7;C9JQI7-2;E9PFK0	TM232_HUMAN;.;.	K	452	.	.	E	-	1	0	TMEM232	109932148	0.949000	0.32298	0.655000	0.29622	0.924000	0.55760	0.721000	0.25911	0.364000	0.24374	0.557000	0.71058	GAA	C|0.977;T|0.023	0.023	strong		0.363	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
FAM155B	27112	hgsc.bcm.edu	37	X	68725640	68725640	+	Missense_Mutation	SNP	T	T	C	rs1171942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:68725640T>C	ENST00000252338.4	+	1	557	c.515T>C	c.(514-516)cTt>cCt	p.L172P	AL158069.1_ENST00000579664.1_RNA	NM_015686.2	NP_056501.2	O75949	F155B_HUMAN	family with sequence similarity 155, member B	172			L -> P (in dbSNP:rs1171942). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)	16						CCTGACTCCCTTTCCCGTGCC	0.592													c|||	2428	0.643179	0.6664	0.5029	3775	,	,		7543	0.6111		0.2336	False		,,,				2504	0.3548				p.L172P		Atlas-SNP	.											.	FAM155B	44	.	0			c.T515C						PASS	.		PRO/LEU	3216,615		1162,411,481,58,88	24.0	30.0	28.0		515	1.7	0.9	X	dbSNP_87	28	2199,4526		270,1044,615,1113,1256	yes	missense	FAM155B	NM_015686.2	98	1432,1455,1096,1171,1344	CC,CT,C,TT,T		32.6989,16.0532,48.7022	benign	172/473	68725640	5415,5141	2200	4298	6498	SO:0001583	missense	27112	exon1			ACTCCCTTTCCCG	AF087142	CCDS35317.1	Xq13.1	2008-04-15	2008-04-15	2008-04-15	ENSG00000130054	ENSG00000130054			30701	protein-coding gene	gene with protein product			"""transmembrane protein 28"", ""chromosome X open reading frame 63"""	TMEM28, CXorf63			Standard	NM_015686		Approved	TED	uc004dxk.3	O75949	OTTHUMG00000021756	ENST00000252338.4:c.515T>C	X.37:g.68725640T>C	ENSP00000252338:p.Leu172Pro	Somatic	261	1	0.00383142		WXS	Illumina HiSeq	Phase_I	270	269	0.996296	NM_015686	B1ALV6|B9EGK1|D3DVU1	Missense_Mutation	SNP	ENST00000252338.4	37	CCDS35317.1	1017	0.6130198915009042	214	0.722972972972973	115	0.4637096774193548	234	0.6964285714285714	127	0.19538461538461538	C	0.003	-2.570916	0.00133	0.839468	0.326989	ENSG00000130054	ENST00000252338	T	0.42131	0.98	4.7	1.72	0.24424	.	0.680336	0.13754	N	0.365088	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	0.16897	-1.0387	9	0.22109	T	0.4	2.301	4.9816	0.14168	0.0:0.5568:0.1525:0.2907	rs1171942;rs16989158	172	O75949-2	.	P	172	ENSP00000252338:L172P	ENSP00000252338:L172P	L	+	2	0	FAM155B	68642365	0.067000	0.21026	0.877000	0.34402	0.392000	0.30506	1.452000	0.35156	-0.005000	0.14395	-1.324000	0.01287	CTT	T|0.456;C|0.544	0.544	strong		0.592	FAM155B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057037.1	NM_015686	
ABL1	25	hgsc.bcm.edu	37	9	133761001	133761001	+	Silent	SNP	A	A	G	rs1056171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	122	122	1	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	
AKTIP	64400	hgsc.bcm.edu	37	16	53526366	53526366	+	Silent	SNP	T	T	C	rs16952272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53526366T>C	ENST00000394657.7	-	10	1011	c.837A>G	c.(835-837)tcA>tcG	p.S279S	AKTIP_ENST00000300245.4_Silent_p.S280S|AKTIP_ENST00000570004.1_Silent_p.S279S	NM_001012398.1|NM_022476.2	NP_001012398.1|NP_071921.1	Q9H8T0	AKTIP_HUMAN	AKT interacting protein	279					apoptotic process (GO:0006915)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|protein transport (GO:0015031)	FHF complex (GO:0070695)|plasma membrane (GO:0005886)	acid-amino acid ligase activity (GO:0016881)			large_intestine(1)|lung(2)|prostate(2)	5		all_cancers(37;0.14)				AAGGCTGTACTGAGCCAGGCT	0.433													T|||	36	0.0071885	0.025	0.0029	5008	,	,		20673	0.0		0.001	False		,,,				2504	0.0				p.S279S		Atlas-SNP	.											.	AKTIP	16	.	0			c.A837G						PASS	.	T	,	119,4277	89.2+/-127.9	2,115,2081	115.0	112.0	113.0		837,837	1.3	1.0	16	dbSNP_123	113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	AKTIP	NM_001012398.1,NM_022476.2	,	2,116,6380	CC,CT,TT		0.0116,2.707,0.9234	,	279/293,279/293	53526366	120,12876	2198	4300	6498	SO:0001819	synonymous_variant	64400	exon10			CTGTACTGAGCCA	AK023320	CCDS10749.1	16q12.2	2010-01-14	2007-01-16	2007-01-16	ENSG00000166971	ENSG00000166971		"""Ubiquitin-conjugating enzymes E2"""	16710	protein-coding gene	gene with protein product		608483	"""fused toes (mouse) homolog"", ""fused toes homolog (mouse)"""	FTS		7818539, 8626685	Standard	XM_005256094		Approved	FLJ13258	uc002ehl.3	Q9H8T0	OTTHUMG00000133199	ENST00000394657.7:c.837A>G	16.37:g.53526366T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	184	87	0.472826	NM_022476	Q503B1|Q53H38	Silent	SNP	ENST00000394657.7	37	CCDS10749.1																																																																																			T|0.990;C|0.010	0.010	strong		0.433	AKTIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256909.4	NM_022476	
SEMA6D	80031	hgsc.bcm.edu	37	15	48063076	48063076	+	Silent	SNP	T	T	C	rs568215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:48063076T>C	ENST00000316364.5	+	19	2755	c.2316T>C	c.(2314-2316)ccT>ccC	p.P772P	SEMA6D_ENST00000537942.1_Silent_p.P710P|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000389428.3_Silent_p.P697P|SEMA6D_ENST00000536845.2_Silent_p.P772P|SEMA6D_ENST00000389432.2_Silent_p.P729P|SEMA6D_ENST00000389433.2_Silent_p.P753P|SEMA6D_ENST00000358066.4_Silent_p.P710P|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000354744.4_Silent_p.P716P|SEMA6D_ENST00000558014.1_Silent_p.P710P	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	88	0	0		WXS	Illumina HiSeq	Phase_I	101	40	0.39604	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	
EXOC3L1	283849	hgsc.bcm.edu	37	16	67219107	67219107	+	Missense_Mutation	SNP	G	G	C	rs9939768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67219107G>C	ENST00000314586.6	-	11	1921	c.1681C>G	c.(1681-1683)Caa>Gaa	p.Q561E	KIAA0895L_ENST00000290881.7_5'Flank|KIAA0895L_ENST00000563831.2_5'Flank|KIAA0895L_ENST00000561621.1_5'Flank|KIAA0895L_ENST00000563902.1_5'Flank|EXOC3L1_ENST00000562887.1_5'Flank	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	561			Q -> E (in dbSNP:rs9939768).		exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						CACACACTTTGCAGGAGCTCA	0.642													C|||	1001	0.19988	0.5113	0.0735	5008	,	,		17024	0.0248		0.0686	False		,,,				2504	0.184				p.Q561E		Atlas-SNP	.											.	EXOC3L1	52	.	0			c.C1681G						PASS	.	C	GLU/GLN	1842,2554	608.3+/-391.1	395,1052,751	45.0	56.0	52.0		1681	3.7	0.7	16	dbSNP_119	52	595,8005	777.5+/-407.7	28,539,3733	yes	missense	EXOC3L1	NM_178516.3	29	423,1591,4484	CC,CG,GG		6.9186,41.9017,18.7519	benign	561/747	67219107	2437,10559	2198	4300	6498	SO:0001583	missense	283849	exon11			CACTTTGCAGGAG	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"""exocyst complex component 3-like"""	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.1681C>G	16.37:g.67219107G>C	ENSP00000325674:p.Gln561Glu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	122	49	0.401639	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	326	0.14926739926739926	233	0.4735772357723577	33	0.09116022099447514	12	0.02097902097902098	48	0.0633245382585752	C	5.850	0.340979	0.11069	0.419017	0.069186	ENSG00000179044	ENST00000314586;ENST00000545725;ENST00000314553	T;T	0.05649	3.41;3.41	5.6	3.66	0.41972	.	0.572106	0.19996	N	0.101441	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	0.04013	0.0;0.0;0.001	T	0.42258	-0.9462	9	0.06236	T	0.91	-7.604	6.6796	0.23113	0.0:0.6955:0.1467:0.1578	rs9939768;rs52823978;rs9939768	458;458;561	F5H4W1;B7Z6U0;Q86VI1	.;.;EX3L1_HUMAN	E	561;458;463	ENSP00000325674:Q561E;ENSP00000439910:Q458E	ENSP00000325008:Q463E	Q	-	1	0	EXOC3L1	65776608	0.110000	0.22057	0.717000	0.30585	0.064000	0.16182	0.707000	0.25704	0.334000	0.23590	-0.215000	0.12644	CAA	G|0.838;C|0.162	0.162	strong		0.642	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102463407	102463407	+	Silent	SNP	A	A	G	rs12893215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102463407A>G	ENST00000360184.4	+	16	3764	c.3600A>G	c.(3598-3600)caA>caG	p.Q1200Q		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1200	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.Q1200Q(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TGGAAAAGCAAAGGTTCCAGT	0.413													A|||	1010	0.201677	0.2685	0.1585	5008	,	,		20106	0.251		0.0905	False		,,,				2504	0.2055				p.Q1200Q		Atlas-SNP	.											DYNC1H1,NS,carcinoma,0,1	DYNC1H1	395	1	1	Substitution - coding silent(1)	stomach(1)	c.A3600G						PASS	.	A		1059,3347	380.6+/-323.8	133,793,1277	49.0	50.0	49.0		3600	1.4	1.0	14	dbSNP_121	49	958,7642	208.3+/-249.8	59,840,3401	no	coding-synonymous	DYNC1H1	NM_001376.4		192,1633,4678	GG,GA,AA		11.1395,24.0354,15.5082		1200/4647	102463407	2017,10989	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon16			AAAGCAAAGGTTC	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.3600A>G	14.37:g.102463407A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	195	110	0.564103	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			A|0.836;G|0.164	0.164	strong		0.413	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
SLC9A4	389015	hgsc.bcm.edu	37	2	103148868	103148868	+	Silent	SNP	G	G	A	rs59687519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:103148868G>A	ENST00000295269.4	+	12	2575	c.2118G>A	c.(2116-2118)gaG>gaA	p.E706E		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	706					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						AGAAGCAAGAGGCACAAGAAA	0.468													G|||	88	0.0175719	0.062	0.0086	5008	,	,		21876	0.0		0.0	False		,,,				2504	0.0				p.E706E		Atlas-SNP	.											.	SLC9A4	115	.	0			c.G2118A						PASS	.	G		265,4141	150.3+/-184.3	9,247,1947	93.0	90.0	91.0		2118	0.7	0.0	2	dbSNP_129	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC9A4	NM_001011552.3		9,249,6245	AA,AG,GG		0.0233,6.0145,2.0529		706/799	103148868	267,12739	2203	4300	6503	SO:0001819	synonymous_variant	389015	exon12			GCAAGAGGCACAA		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.2118G>A	2.37:g.103148868G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	102	59	0.578431	NM_001011552	Q69YK0	Silent	SNP	ENST00000295269.4	37	CCDS33264.1																																																																																			G|0.981;A|0.019	0.019	strong		0.468	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
TRPS1	7227	hgsc.bcm.edu	37	8	116631902	116631902	+	Silent	SNP	C	C	A	rs7823278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:116631902C>A	ENST00000220888.5	-	2	543	c.384G>T	c.(382-384)ccG>ccT	p.P128P	TRPS1_ENST00000520276.1_Silent_p.P132P|TRPS1_ENST00000395715.3_Silent_p.P141P|TRPS1_ENST00000519076.1_Silent_p.P82P|TRPS1_ENST00000519674.1_Silent_p.P128P			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	128					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CTGCTCTTTGCGGAGACTTCA	0.522									Langer-Giedion syndrome				A|||	844	0.16853	0.5734	0.049	5008	,	,		18881	0.0		0.002	False		,,,				2504	0.0511				p.P141P		Atlas-SNP	.											TRPS1_ENST00000395715,NS,carcinoma,-1,2	TRPS1	516	2	0			c.G423T						PASS	.	A		1632,2214		341,950,632	58.0	58.0	58.0		423	5.8	1.0	8	dbSNP_116	58	20,8250		0,20,4115	no	coding-synonymous	TRPS1	NM_014112.2		341,970,4747	AA,AC,CC		0.2418,42.4337,13.6349		141/1295	116631902	1652,10464	1923	4135	6058	SO:0001819	synonymous_variant	7227	exon3	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	TCTTTGCGGAGAC	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"""GATA zinc finger domain containing"", ""Zinc fingers, C2H2-type"""	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.384G>T	8.37:g.116631902C>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																				C|0.873;A|0.127	0.127	strong		0.522	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112	
RNF208	727800	hgsc.bcm.edu	37	9	140115554	140115554	+	Silent	SNP	G	G	A	rs144152667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140115554G>A	ENST00000392827.1	-	2	279	c.111C>T	c.(109-111)caC>caT	p.H37H	RNF208_ENST00000391553.1_Silent_p.H37H			Q9H0X6	RN208_HUMAN	ring finger protein 208	37					protein autoubiquitination (GO:0051865)		ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			lung(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		ACTTTTCAGGGTGGACAATCT	0.667													G|||	151	0.0301518	0.0507	0.0634	5008	,	,		10373	0.0129		0.0209	False		,,,				2504	0.0061				p.H37H		Atlas-SNP	.											.	RNF208	11	.	0			c.C111T						PASS	.	G		190,3734		6,178,1778	17.0	21.0	20.0		111	0.2	1.0	9	dbSNP_134	20	157,8129		2,153,3988	no	coding-synonymous	RNF208	NM_031297.4		8,331,5766	AA,AG,GG		1.8948,4.842,2.8419		37/262	140115554	347,11863	1962	4143	6105	SO:0001819	synonymous_variant	727800	exon1			TTCAGGGTGGACA	AF416715	CCDS7037.2	9q34.3	2007-01-19				ENSG00000212864		"""RING-type (C3HC4) zinc fingers"""	25420	protein-coding gene	gene with protein product						11230166	Standard	NM_031297		Approved	DKFZP761H1710	uc004clz.2	Q9H0X6		ENST00000392827.1:c.111C>T	9.37:g.140115554G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	156	48	0.307692	NM_031297	A2BFA0	Silent	SNP	ENST00000392827.1	37	CCDS7037.2																																																																																			G|0.964;A|0.036	0.036	strong		0.667	RNF208-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254714.1	NM_031297	
SLC25A22	79751	hgsc.bcm.edu	37	11	800186	800186	+	5'Flank	SNP	C	C	T	rs148849040		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:800186C>T	ENST00000531214.1	-	0	0				PIDD_ENST00000347755.5_Missense_Mutation_p.R740Q|PIDD_ENST00000411829.2_Missense_Mutation_p.R723Q	NM_001191060.1	NP_001177989.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22						L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTTCCTCTGCCGGGCAGCCTC	0.692													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14878	0.0		0.0	False		,,,				2504	0.0				p.R740Q	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											.	PIDD	76	.	0			c.G2219A						PASS	.	C	GLN/ARG,GLN/ARG	5,4369		0,5,2182	15.0	17.0	16.0		2219,2168	3.3	1.0	11	dbSNP_134	16	0,8574		0,0,4287	yes	missense,missense	PIDD	NM_145886.3,NM_145887.3	43,43	0,5,6469	TT,TC,CC		0.0,0.1143,0.0386	probably-damaging,probably-damaging	740/911,723/894	800186	5,12943	2187	4287	6474	SO:0001631	upstream_gene_variant	55367	exon14			CTCTGCCGGGCAG	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310		11.37:g.800186C>T	Exception_encountered	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	60	41	0.683333	NM_145886	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Missense_Mutation	SNP	ENST00000531214.1	37	CCDS7715.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.238462	0.79800	0.001143	0.0	ENSG00000177595	ENST00000411829;ENST00000347755	T;T	0.48201	0.82;0.94	4.24	3.29	0.37713	.	0.138436	0.46145	N	0.000315	T	0.49236	0.1545	L	0.29908	0.895	0.32961	D	0.521066	D;D;D;D	0.76494	0.999;0.999;0.996;0.999	D;P;P;D	0.64776	0.929;0.886;0.806;0.928	T	0.58429	-0.7638	10	0.54805	T	0.06	.	7.9393	0.29948	0.0:0.7476:0.0:0.2524	.	451;740;583;723	Q9HB75-5;Q9HB75;Q9HB75-3;Q9HB75-2	.;PIDD_HUMAN;.;.	Q	723;740	ENSP00000416801:R723Q;ENSP00000337797:R740Q	ENSP00000337797:R740Q	R	-	2	0	PIDD	790186	1.000000	0.71417	0.999000	0.59377	0.828000	0.46876	1.731000	0.38135	2.193000	0.70182	0.462000	0.41574	CGG	C|1.000;T|0.000	0.000	weak		0.692	SLC25A22-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384124.1		
FREM2	341640	hgsc.bcm.edu	37	13	39265558	39265558	+	Silent	SNP	T	T	A	rs41292757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39265558T>A	ENST00000280481.7	+	1	4293	c.4077T>A	c.(4075-4077)ggT>ggA	p.G1359G		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1359					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)		AACCTACTGGTGCCTTTGAAA	0.398													T|||	59	0.0117812	0.0008	0.0216	5008	,	,		21033	0.0		0.0378	False		,,,				2504	0.0051				p.G1359G		Atlas-SNP	.											.	FREM2	385	.	0			c.T4077A						PASS	.	T		43,4363	44.6+/-78.6	0,43,2160	63.0	64.0	63.0		4077	0.2	0.8	13	dbSNP_127	63	324,8276	114.8+/-174.7	5,314,3981	no	coding-synonymous	FREM2	NM_207361.4		5,357,6141	AA,AT,TT		3.7674,0.9759,2.8218		1359/3170	39265558	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			TACTGGTGCCTTT	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.4077T>A	13.37:g.39265558T>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			T|0.972;A|0.028	0.028	strong		0.398	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
UBR5	51366	hgsc.bcm.edu	37	8	103311153	103311153	+	Silent	SNP	C	C	T	rs61752302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103311153C>T	ENST00000520539.1	-	25	3855	c.3249G>A	c.(3247-3249)gcG>gcA	p.A1083A	UBR5_ENST00000521922.1_Silent_p.A1077A|UBR5_ENST00000220959.4_Silent_p.A1083A	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	1083					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)			AATGAGCATTCGCCTTTCGAT	0.373													C|||	85	0.0169728	0.0514	0.0	5008	,	,		19740	0.0		0.0129	False		,,,				2504	0.0041				p.A1083A	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.G3249A						PASS	.	C		243,4163	141.5+/-176.9	10,223,1970	137.0	126.0	130.0		3249	-0.1	1.0	8	dbSNP_129	130	176,8424	80.9+/-143.5	2,172,4126	no	coding-synonymous	UBR5	NM_015902.5		12,395,6096	TT,TC,CC		2.0465,5.5152,3.2216		1083/2800	103311153	419,12587	2203	4300	6503	SO:0001819	synonymous_variant	51366	exon25			AGCATTCGCCTTT	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.3249G>A	8.37:g.103311153C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	125	54	0.432	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	37	CCDS34933.1	27	0.012362637362637362	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	11.39	1.625663	0.28889	0.055152	0.020465	ENSG00000104517	ENST00000520898;ENST00000519365	.	.	.	5.96	-0.0952	0.13642	.	.	.	.	.	T	0.11067	0.0270	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.07195	-1.0785	4	.	.	.	.	7.0141	0.24879	0.0:0.2623:0.1432:0.5945	rs61752302	.	.	.	K	173;182	.	.	E	-	1	0	UBR5	103380329	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	1.243000	0.32767	-0.029000	0.13827	0.585000	0.79938	GAA	C|0.972;T|0.028	0.028	strong		0.373	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	
PMFBP1	83449	hgsc.bcm.edu	37	16	72156842	72156842	+	Missense_Mutation	SNP	T	T	G	rs16973716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:72156842T>G	ENST00000537792.1	-	3	236	c.237A>C	c.(235-237)aaA>aaC	p.K79N	PMFBP1_ENST00000355636.6_Missense_Mutation_p.K768N|PMFBP1_ENST00000237353.10_Missense_Mutation_p.K913N|PMFBP1_ENST00000537465.1_Missense_Mutation_p.K918N			Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	918						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TGGCAATGTATTTCACCTGCT	0.537													T|||	2412	0.481629	0.6263	0.3112	5008	,	,		20099	0.3413		0.4105	False		,,,				2504	0.6247				p.K913N		Atlas-SNP	.											.	PMFBP1	101	.	0			c.A2739C						PASS	.	T	ASN/LYS,ASN/LYS	2428,1968	619.0+/-393.3	681,1066,451	90.0	87.0	88.0		2304,2739	3.8	1.0	16	dbSNP_123	88	3631,4969	522.4+/-380.1	781,2069,1450	yes	missense,missense	PMFBP1	NM_001160213.1,NM_031293.2	94,94	1462,3135,1901	GG,GT,TT		42.2209,44.768,46.622	probably-damaging,probably-damaging	768/883,913/1008	72156842	6059,6937	2198	4300	6498	SO:0001583	missense	83449	exon19			AATGTATTTCACC	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000537792.1:c.237A>C	16.37:g.72156842T>G	ENSP00000443366:p.Lys79Asn	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000537792.1	37		939	0.42994505494505497	291	0.5914634146341463	126	0.34806629834254144	203	0.3548951048951049	319	0.420844327176781	T	17.71	3.456390	0.63401	0.55232	0.422209	ENSG00000118557	ENST00000537792;ENST00000537465;ENST00000237353;ENST00000355636	T;T;T;T	0.58506	0.33;2.27;2.3;2.11	4.87	3.78	0.43462	.	0.000000	0.51477	D	0.000097	T	0.00012	0.0000	M	0.68317	2.08	0.36865	P	0.11140700000000003	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.83275	0.996;0.948;0.994	T	0.50162	-0.8860	9	0.54805	T	0.06	-21.4562	7.1271	0.25477	0.0:0.1004:0.0:0.8996	rs16973716;rs16973716	918;913;918	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	N	79;918;913;768	ENSP00000443366:K79N;ENSP00000443817:K918N;ENSP00000237353:K913N;ENSP00000347854:K768N	ENSP00000237353:K913N	K	-	3	2	PMFBP1	70714343	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	1.490000	0.35573	0.893000	0.36288	0.477000	0.44152	AAA	T|0.542;G|0.458	0.458	strong		0.537	PMFBP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000396523.1	NM_031293	
CD3EAP	10849	hgsc.bcm.edu	37	19	45912736	45912736	+	Missense_Mutation	SNP	C	C	A	rs3212986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45912736C>A	ENST00000309424.3	+	3	1998	c.1510C>A	c.(1510-1512)Cag>Aag	p.Q504K	ERCC1_ENST00000588738.1_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.Q506K|ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000423698.2_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	504	Poly-Gln.		Q -> K (in dbSNP:rs3212986). {ECO:0000269|PubMed:15489334}.		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)		GAAGCGGAAGCAGCAGCAGCA	0.617													A|||	1478	0.295128	0.2912	0.3545	5008	,	,		14891	0.2986		0.2505	False		,,,				2504	0.3006				p.Q504K		Atlas-SNP	.											.	CD3EAP	27	.	0			c.C1510A	GRCh37	CM005461	CD3EAP	M	rs3212986	PASS	.	A	,,LYS/GLN	1274,3100		195,884,1108	15.0	16.0	16.0		,,1510	2.7	0.0	19	dbSNP_106	16	2109,6467		259,1591,2438	yes	utr-3,utr-3,missense	ERCC1,CD3EAP	NM_001166049.1,NM_001983.3,NM_012099.1	,,53	454,2475,3546	AA,AC,CC		24.5919,29.1267,26.1236	,,benign	,,504/511	45912736	3383,9567	2187	4288	6475	SO:0001583	missense	10849	exon3			CGGAAGCAGCAGC	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.1510C>A	19.37:g.45912736C>A	ENSP00000310966:p.Gln504Lys	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	24	8	0.333333	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	641	0.2934981684981685	151	0.30691056910569103	125	0.3453038674033149	162	0.28321678321678323	203	0.2678100263852243	A	0.114	-1.133957	0.01742	0.291267	0.245919	ENSG00000117877	ENST00000309424	T	0.08984	3.03	4.82	2.68	0.31781	.	0.765358	0.10689	N	0.645497	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.47611	-0.9104	9	0.02654	T	1	.	5.6432	0.17575	0.5816:0.3274:0.091:0.0	rs3212986;rs60333438;rs3212986	506;504	O15446-2;O15446	.;RPA34_HUMAN	K	504	ENSP00000310966:Q504K	ENSP00000310966:Q504K	Q	+	1	0	CD3EAP	50604576	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.397000	0.02511	0.209000	0.20645	-2.053000	0.00404	CAG	C|0.723;A|0.277	0.277	strong		0.617	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
PRRG2	5639	hgsc.bcm.edu	37	19	50086806	50086806	+	Silent	SNP	C	C	T	rs3745474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50086806C>T	ENST00000246794.5	+	3	262	c.93C>T	c.(91-93)ttC>ttT	p.F31F	NOSIP_ENST00000339093.3_5'Flank|NOSIP_ENST00000596358.1_5'Flank|PRRG2_ENST00000596700.1_Intron	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	60	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	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	
OR10G9	219870	hgsc.bcm.edu	37	11	123894246	123894246	+	Missense_Mutation	SNP	A	A	G	rs79669172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123894246A>G	ENST00000375024.1	+	1	527	c.527A>G	c.(526-528)tAt>tGt	p.Y176C		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	176						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(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)		ATCCAGCACTATTTGTGTGAT	0.557													A|||	437	0.0872604	0.1067	0.1556	5008	,	,		22802	0.1438		0.007	False		,,,				2504	0.0368				p.Y176C		Atlas-SNP	.											.	OR10G9	80	.	0			c.A527G						PASS	.	A	CYS/TYR	392,4010	194.3+/-219.2	19,354,1828	276.0	235.0	249.0		527	2.3	0.9	11	dbSNP_131	249	31,8567	20.4+/-63.3	0,31,4268	no	missense	OR10G9	NM_001001953.1	194	19,385,6096	GG,GA,AA		0.3605,8.905,3.2538	probably-damaging	176/312	123894246	423,12577	2201	4299	6500	SO:0001583	missense	219870	exon1			AGCACTATTTGTG	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.527A>G	11.37:g.123894246A>G	ENSP00000364164:p.Tyr176Cys	Somatic	415	0	0		WXS	Illumina HiSeq	Phase_I	500	267	0.534	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	192	0.08791208791208792	47	0.09552845528455285	59	0.16298342541436464	81	0.14160839160839161	5	0.006596306068601583	A	7.146	0.582843	0.13749	0.08905	0.003605	ENSG00000236981	ENST00000375024	T	0.00158	8.65	3.48	2.29	0.28610	GPCR, rhodopsin-like superfamily (1);	0.172945	0.27901	N	0.017397	T	0.00012	0.0000	L	0.57536	1.79	0.58432	P	1.0000000000287557E-6	D	0.69078	0.997	D	0.73708	0.981	T	0.55127	-0.8189	9	0.87932	D	0	.	4.0431	0.09760	0.4862:0.1812:0.0:0.3326	.	176	Q8NGN4	O10G9_HUMAN	C	176	ENSP00000364164:Y176C	ENSP00000364164:Y176C	Y	+	2	0	OR10G9	123399456	0.003000	0.15002	0.923000	0.36655	0.026000	0.11368	-0.026000	0.12392	0.495000	0.27882	0.533000	0.62120	TAT	A|0.952;G|0.048	0.048	strong		0.557	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
C4orf22	255119	hgsc.bcm.edu	37	4	81866010	81866010	+	Missense_Mutation	SNP	A	A	C	rs201959026		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:81866010A>C	ENST00000358105.3	+	5	572	c.523A>C	c.(523-525)Aac>Cac	p.N175H	C4orf22_ENST00000508675.1_Missense_Mutation_p.N192H	NM_152770.2	NP_689983.2	Q6V702	CD022_HUMAN	chromosome 4 open reading frame 22	175										NS(1)|large_intestine(3)|lung(5)|prostate(1)|skin(5)	15						TTCAAGTCCCAACTATCAAGT	0.313													A|||	1	0.000199681	0.0008	0.0	5008	,	,		16588	0.0		0.0	False		,,,				2504	0.0				p.N192H		Atlas-SNP	.											.	C4orf22	35	.	0			c.A574C						PASS	.	A	HIS/ASN,HIS/ASN	8,4396	12.9+/-30.5	0,8,2194	70.0	71.0	71.0		574,523	5.8	1.0	4		71	0,8594		0,0,4297	yes	missense,missense	C4orf22	NM_001206997.1,NM_152770.2	68,68	0,8,6491	CC,CA,AA		0.0,0.1817,0.0615	possibly-damaging,possibly-damaging	192/251,175/234	81866010	8,12990	2202	4297	6499	SO:0001583	missense	255119	exon6			AGTCCCAACTATC	BC034296	CCDS3587.1, CCDS56336.1	4q21.21	2008-02-05			ENSG00000197826	ENSG00000197826			28554	protein-coding gene	gene with protein product						12477932	Standard	NM_152770		Approved		uc010ijp.3	Q6V702	OTTHUMG00000130289	ENST00000358105.3:c.523A>C	4.37:g.81866010A>C	ENSP00000350818:p.Asn175His	Somatic	282	1	0.0035461		WXS	Illumina HiSeq	Phase_I	328	148	0.451219	NM_001206997	E7EQ13|Q6ZQY4|Q8N4G9	Missense_Mutation	SNP	ENST00000358105.3	37	CCDS3587.1	.	.	.	.	.	.	.	.	.	.	A	17.34	3.364872	0.61513	0.001817	0.0	ENSG00000197826	ENST00000358105;ENST00000508675	T;T	0.36878	1.23;1.23	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.55609	0.1931	M	0.77616	2.38	0.46203	D	0.998921	P;D	0.54397	0.956;0.966	P;P	0.55667	0.73;0.781	T	0.60010	-0.7346	10	0.56958	D	0.05	.	15.1462	0.72653	1.0:0.0:0.0:0.0	.	192;175	E7EQ13;Q6V702	.;CD022_HUMAN	H	175;192	ENSP00000350818:N175H;ENSP00000425786:N192H	ENSP00000350818:N175H	N	+	1	0	C4orf22	82085034	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	6.456000	0.73501	2.216000	0.71823	0.533000	0.62120	AAC	.	.	weak		0.313	C4orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252629.2	NM_152770	
PSPH	5723	hgsc.bcm.edu	37	7	56088902	56088902	+	Missense_Mutation	SNP	C	C	T	rs77329757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:56088902C>T	ENST00000395471.3	-	4	809	c.4G>A	c.(4-6)Gtc>Atc	p.V2I	PSPH_ENST00000275605.3_Missense_Mutation_p.V2I|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	2				V -> I (in Ref. 1; CAA71318). {ECO:0000305}.	cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GAGTGGGAGACCATCGCTGGA	0.403																																					p.V2I		Atlas-SNP	.											PSPH,rectum,carcinoma,0,1	PSPH	23	1	0			c.G4A						PASS	.						59.0	49.0	53.0					7																	56088902		2203	4300	6503	SO:0001583	missense	5723	exon4			GGGAGACCATCGC	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.4G>A	7.37:g.56088902C>T	ENSP00000378854:p.Val2Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	187	44	0.235294	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.870338	0.33069	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626;ENST00000419984;ENST00000421312;ENST00000424596;ENST00000413218;ENST00000416592	D;D;D;T;T	0.82619	-1.63;-1.63;-1.63;-1.11;-1.11	5.5	4.62	0.57501	.	0.498508	0.22451	N	0.059892	T	0.76586	0.4008	L	0.43152	1.355	0.25991	N	0.982243	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.004	T	0.62821	-0.6773	10	0.26408	T	0.33	-18.3475	13.3091	0.60370	0.0:0.9237:0.0:0.0763	.	2;2	Q53EY1;P78330	.;SERB_HUMAN	I	2	ENSP00000275605:V2I;ENSP00000378854:V2I;ENSP00000398653:V2I;ENSP00000399660:V2I;ENSP00000390952:V2I	ENSP00000275605:V2I	V	-	1	0	PSPH	56056396	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	1.602000	0.36783	1.325000	0.45301	0.591000	0.81541	GTC	C|0.996;T|0.004	0.004	strong		0.403	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
WBSCR28	135886	hgsc.bcm.edu	37	7	73279361	73279361	+	Silent	SNP	C	C	T	rs61742124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73279361C>T	ENST00000320531.2	+	2	147	c.111C>T	c.(109-111)ctC>ctT	p.L37L		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	37						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				ATTTCCTGCTCCTCAAGATCA	0.582													C|||	1049	0.209465	0.3268	0.219	5008	,	,		16536	0.0784		0.2028	False		,,,				2504	0.1861				p.L37L		Atlas-SNP	.											.	WBSCR28	24	.	0			c.C111T						PASS	.	C		1004,2802		144,716,1043	263.0	271.0	269.0		111	-6.3	0.8	7	dbSNP_129	269	1622,6604		168,1286,2659	no	coding-synonymous	WBSCR28	NM_182504.3		312,2002,3702	TT,TC,CC		19.718,26.3794,21.8251		37/266	73279361	2626,9406	1903	4113	6016	SO:0001819	synonymous_variant	135886	exon2			CCTGCTCCTCAAG	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.111C>T	7.37:g.73279361C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	217	91	0.419355	NM_182504	Q6UE04|Q8NHP4	Silent	SNP	ENST00000320531.2	37	CCDS43597.1																																																																																			C|0.789;T|0.211	0.211	strong		0.582	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504	
CRYZ	1429	hgsc.bcm.edu	37	1	75175886	75175886	+	Missense_Mutation	SNP	T	T	C	rs3819946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:75175886T>C	ENST00000340866.5	-	6	613	c.526A>G	c.(526-528)Att>Gtt	p.I176V	CRYZ_ENST00000492102.1_5'Flank|CRYZ_ENST00000370871.3_Missense_Mutation_p.I176V|CRYZ_ENST00000370872.3_Missense_Mutation_p.I39V|CRYZ_ENST00000417775.1_Missense_Mutation_p.I176V	NM_001889.3	NP_001880.2	Q08257	QOR_HUMAN	crystallin, zeta (quinone reductase)	176			I -> V (in dbSNP:rs3819946). {ECO:0000269|Ref.4}.		protein homotetramerization (GO:0051289)|visual perception (GO:0007601)|xenobiotic catabolic process (GO:0042178)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	mRNA 3'-UTR binding (GO:0003730)|NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)	10					Dicoumarol(DB00266)	GTGCCCAAAATCTTTAAGCCA	0.368													C|||	2307	0.460663	0.525	0.3386	5008	,	,		15728	0.7669		0.1421	False		,,,				2504	0.4724				p.I176V		Atlas-SNP	.											.	CRYZ	28	.	0			c.A526G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1978,2428	616.5+/-392.8	445,1088,670	75.0	76.0	75.0		526,526,115,526	5.5	1.0	1	dbSNP_107	75	1123,7477	767.3+/-407.6	74,975,3251	yes	missense,missense,missense,missense	CRYZ	NM_001130042.1,NM_001130043.1,NM_001134759.1,NM_001889.3	29,29,29,29	519,2063,3921	CC,CT,TT		13.0581,44.8933,23.8428	benign,benign,benign,benign	176/330,176/296,39/193,176/330	75175886	3101,9905	2203	4300	6503	SO:0001583	missense	1429	exon6			CCAAAATCTTTAA		CCDS665.1, CCDS44162.1, CCDS44163.1	1p31.1	2013-02-14			ENSG00000116791	ENSG00000116791			2419	protein-coding gene	gene with protein product		123691					Standard	NM_001889		Approved		uc001dgj.3	Q08257	OTTHUMG00000009620	ENST00000340866.5:c.526A>G	1.37:g.75175886T>C	ENSP00000339399:p.Ile176Val	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	260	121	0.465385	NM_001130043	A6NN60|D3DQ76|Q53FT0|Q59EU7|Q5HYE7|Q6NSK9	Missense_Mutation	SNP	ENST00000340866.5	37	CCDS665.1	914	0.4184981684981685	236	0.4796747967479675	111	0.30662983425414364	445	0.777972027972028	122	0.16094986807387862	C	3.968	-0.008900	0.07727	0.448933	0.130581	ENSG00000116791	ENST00000340866;ENST00000370872;ENST00000417775;ENST00000370871;ENST00000370870;ENST00000441120	T;T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;4.15;4.15	5.54	5.54	0.83059	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	N	0.000000	T	0.01189	0.0039	N	0.00563	-1.375	0.53005	P	3.399999999997849E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.42344	-0.9457	9	0.02654	T	1	.	11.7379	0.51775	0.0:0.8555:0.0:0.1445	rs3819946;rs52802695;rs56521451;rs60828006;rs3819946	39;176;176	Q5HYE7;A6NN60;Q08257	.;.;QOR_HUMAN	V	176;39;176;176;176;176	ENSP00000339399:I176V;ENSP00000359909:I39V;ENSP00000399805:I176V;ENSP00000359908:I176V;ENSP00000359907:I176V;ENSP00000404289:I176V	ENSP00000339399:I176V	I	-	1	0	CRYZ	74948474	1.000000	0.71417	0.997000	0.53966	0.556000	0.35491	4.095000	0.57728	1.488000	0.48433	-0.213000	0.12676	ATT	C|0.339;N|0.000	0.339	strong		0.368	CRYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026514.1		
DNAH14	127602	hgsc.bcm.edu	37	1	225152298	225152298	+	Missense_Mutation	SNP	A	A	T	rs79645812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225152298A>T	ENST00000445597.2	+	6	866	c.866A>T	c.(865-867)aAg>aTg	p.K289M	DNAH14_ENST00000366850.3_Missense_Mutation_p.K162M|DNAH14_ENST00000366848.1_Missense_Mutation_p.K162M|DNAH14_ENST00000366849.1_Missense_Mutation_p.K162M|DNAH14_ENST00000400952.3_Missense_Mutation_p.K162M|DNAH14_ENST00000430092.1_Missense_Mutation_p.K162M|DNAH14_ENST00000439375.2_Missense_Mutation_p.K162M			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	289					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						GCAATTCAGAAGATTACTTTA	0.259													A|||	28	0.00559105	0.0204	0.0014	5008	,	,		13586	0.0		0.0	False		,,,				2504	0.0				p.K162M		Atlas-SNP	.											.	DNAH14	300	.	0			c.A485T						PASS	.	A	MET/LYS,MET/LYS,MET/LYS	82,3478		0,82,1698	70.0	69.0	69.0		485,485,485	4.2	0.0	1	dbSNP_131	69	0,8100		0,0,4050	yes	missense,missense,missense	DNAH14	NM_001145154.1,NM_001373.1,NM_144989.2	95,95,95	0,82,5748	TT,TA,AA		0.0,2.3034,0.7033	probably-damaging,probably-damaging,probably-damaging	162/454,162/4516,162/229	225152298	82,11578	1780	4050	5830	SO:0001583	missense	127602	exon5			TTCAGAAGATTAC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.866A>T	1.37:g.225152298A>T	ENSP00000409472:p.Lys289Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_144989	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		10|10	0.004578754578754579|0.004578754578754579	10|10	0.02032520325203252|0.02032520325203252	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	15.26|15.26	2.781749|2.781749	0.49891|0.49891	0.023034|0.023034	0.0|0.0	ENSG00000185842|ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000366850;ENST00000400952;ENST00000366849;ENST00000366848;ENST00000439375|ENST00000433124	T;T;T;T;T;T;T|.	0.36878|.	2.32;1.42;1.23;1.26;1.27;1.23;1.42|.	5.33|5.33	4.17|4.17	0.49024|0.49024	.|.	0.553031|.	0.17085|.	N|.	0.187621|.	T|.	0.22859|.	0.0552|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	D;D;D;D|.	0.89917|.	0.999;1.0;1.0;0.999|.	D;D;D;D|.	0.76071|.	0.912;0.987;0.967;0.927|.	T|.	0.12091|.	-1.0561|.	9|.	0.87932|.	D|.	0|.	.|.	9.497|9.497	0.38995|0.38995	0.9159:0.0:0.0841:0.0|0.9159:0.0:0.0841:0.0	.|.	162;162;162;289|.	Q0VDD8-4;Q0VDD8-3;Q0VDD8-2;Q0VDD8|.	.;.;.;DYH14_HUMAN|.	M|X	289;162;162;162;162;162;162|60	ENSP00000409472:K289M;ENSP00000414402:K162M;ENSP00000355815:K162M;ENSP00000383737:K162M;ENSP00000355814:K162M;ENSP00000355813:K162M;ENSP00000392061:K162M|.	ENSP00000355813:K162M|.	K|R	+|+	2|1	0|2	DNAH14|DNAH14	223218921|223218921	0.789000|0.789000	0.28775|0.28775	0.040000|0.040000	0.18447|0.18447	0.068000|0.068000	0.16541|0.16541	1.785000|1.785000	0.38684|0.38684	0.929000|0.929000	0.37192|0.37192	0.413000|0.413000	0.27773|0.27773	AAG|AGA	A|0.995;T|0.005	0.005	strong		0.259	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
FAM188B	84182	hgsc.bcm.edu	37	7	30915262	30915262	+	Silent	SNP	C	C	T	rs10215354|rs386711774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30915262C>T	ENST00000265299.6	+	15	2039	c.1962C>T	c.(1960-1962)aaC>aaT	p.N654N	INMT-FAM188B_ENST00000458257.1_3'UTR|AQP1_ENST00000509504.1_Silent_p.N117N|AQP1_ENST00000434909.2_5'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	654										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGCATTACAACATGTGCCAGG	0.512													C|||	1506	0.300719	0.6195	0.0893	5008	,	,		21536	0.2927		0.0567	False		,,,				2504	0.2791				p.N654N		Atlas-SNP	.											.	FAM188B	62	.	0			c.C1962T						PASS	.	C		1412,2644		461,490,1077	169.0	170.0	169.0		1962	-11.3	0.2	7	dbSNP_119	169	231,8189		23,185,4002	no	coding-synonymous	FAM188B	NM_032222.2		484,675,5079	TT,TC,CC		2.7435,34.8126,13.1693		654/758	30915262	1643,10833	2028	4210	6238	SO:0001819	synonymous_variant	84182	exon15			TTACAACATGTGC	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.1962C>T	7.37:g.30915262C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_032222	Q71AZ7|Q9H6D2	Silent	SNP	ENST00000265299.6	37	CCDS43565.1																																																																																			C|0.858;T|0.142	0.142	strong		0.512	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
GPR112	139378	hgsc.bcm.edu	37	X	135426968	135426968	+	Missense_Mutation	SNP	C	C	A	rs5930931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:135426968C>A	ENST00000394143.1	+	6	1394	c.1103C>A	c.(1102-1104)cCt>cAt	p.P368H	GPR112_ENST00000412101.1_Missense_Mutation_p.P163H|GPR112_ENST00000370652.1_Missense_Mutation_p.P368H|GPR112_ENST00000287534.4_Missense_Mutation_p.P305H|GPR112_ENST00000394141.1_Missense_Mutation_p.P163H	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	368			P -> H (in dbSNP:rs5930931). {ECO:0000269|Ref.2}.		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)	p.P368L(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TTTCAACCACCTACACCTTCT	0.368													c|||	1700	0.450331	0.4213	0.3545	3775	,	,		16744	0.2024		0.3738	False		,,,				2504	0.3241				p.P368H		Atlas-SNP	.											.	GPR112	459	.	1	Substitution - Missense(1)	prostate(1)	c.C1103A						PASS	.		HIS/PRO	2081,1754		479,816,307,337,264	84.0	78.0	80.0		1103	2.1	0.0	X	dbSNP_114	80	3200,3528		554,1184,908,690,964	yes	missense	GPR112	NM_153834.3	77	1033,2000,1215,1027,1228	AA,AC,A,CC,C		47.5624,45.7366,49.9953	possibly-damaging	368/3081	135426968	5281,5282	2203	4300	6503	SO:0001583	missense	139378	exon6			AACCACCTACACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1103C>A	X.37:g.135426968C>A	ENSP00000377699:p.Pro368His	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	111	68	0.612613	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	706	0.4255575647980711	138	0.3689839572192513	80	0.27972027972027974	76	0.15702479338842976	186	0.3174061433447099	c	2.747	-0.260836	0.05791	0.542634	0.475624	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.29397	1.61;1.61;1.57;1.71;1.57	3.95	2.08	0.27032	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;P;P	0.55605	0.972;0.924;0.875	P;P;B	0.49047	0.599;0.46;0.271	T	0.44544	-0.9321	8	0.66056	D	0.02	.	8.6564	0.34066	0.3924:0.6076:0.0:0.0	rs5930931;rs58573078;rs5930931	305;163;368	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	H	368;368;163;305;163	ENSP00000377699:P368H;ENSP00000359686:P368H;ENSP00000416526:P163H;ENSP00000287534:P305H;ENSP00000377697:P163H	ENSP00000287534:P305H	P	+	2	0	GPR112	135254634	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.303000	0.19210	0.238000	0.21222	-0.519000	0.04390	CCT	0|0.025;A|0.455	0.455	strong		0.368	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
PRDM15	63977	hgsc.bcm.edu	37	21	43236176	43236176	+	Silent	SNP	G	G	A	rs4075967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43236176G>A	ENST00000269844.3	-	26	3485	c.3375C>T	c.(3373-3375)caC>caT	p.H1125H	PRDM15_ENST00000422911.1_Silent_p.H816H|PRDM15_ENST00000447207.2_Silent_p.H759H|PRDM15_ENST00000398548.1_Silent_p.H796H|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	136	0	0		WXS	Illumina HiSeq	Phase_I	175	88	0.502857	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	
PEPD	5184	hgsc.bcm.edu	37	19	33968991	33968991	+	Missense_Mutation	SNP	T	T	A	rs61748998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33968991T>A	ENST00000244137.7	-	7	542	c.509A>T	c.(508-510)gAa>gTa	p.E170V	PEPD_ENST00000397032.4_Missense_Mutation_p.E170V|PEPD_ENST00000436370.3_Missense_Mutation_p.E106V	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	170					cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					ATTGTTGACTTCGAACCTGTA	0.488													T|||	77	0.0153754	0.0567	0.0	5008	,	,		21814	0.0		0.002	False		,,,				2504	0.0				p.E170V		Atlas-SNP	.											.	PEPD	48	.	0			c.A509T						PASS	.	T	VAL/GLU,VAL/GLU,VAL/GLU	155,3897		4,147,1875	87.0	88.0	88.0		509,509,317	3.6	1.0	19	dbSNP_129	88	1,8361		0,1,4180	yes	missense,missense,missense	PEPD	NM_000285.3,NM_001166056.1,NM_001166057.1	121,121,121	4,148,6055	AA,AT,TT		0.012,3.8253,1.2566	benign,benign,benign	170/494,170/453,106/430	33968991	156,12258	2026	4181	6207	SO:0001583	missense	5184	exon7			TTGACTTCGAACC	BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"""prolidase"""	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.509A>T	19.37:g.33968991T>A	ENSP00000244137:p.Glu170Val	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	157	80	0.509554	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Missense_Mutation	SNP	ENST00000244137.7	37	CCDS42544.1	19	0.0086996336996337	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	8.903	0.956821	0.18507	0.038253	1.2E-4	ENSG00000124299	ENST00000244137;ENST00000397032;ENST00000436370	T;T;T	0.79749	-1.03;-0.93;-1.3	5.7	3.56	0.40772	.	0.722777	0.15080	N	0.281739	T	0.32194	0.0821	N	0.13168	0.305	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.31052	-0.9957	10	0.24483	T	0.36	-4.3759	10.1383	0.42719	0.0:0.0:0.3228:0.6772	rs61748998	106;170;170	E9PCE8;A8MX47;P12955	.;.;PEPD_HUMAN	V	170;170;106	ENSP00000244137:E170V;ENSP00000380226:E170V;ENSP00000391890:E106V	ENSP00000244137:E170V	E	-	2	0	PEPD	38660831	1.000000	0.71417	0.994000	0.49952	0.574000	0.36063	0.933000	0.28897	0.387000	0.25024	0.533000	0.62120	GAA	T|0.978;A|0.022	0.022	strong		0.488	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285	
LRGUK	136332	hgsc.bcm.edu	37	7	133881794	133881794	+	Silent	SNP	T	T	C	rs35258804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:133881794T>C	ENST00000285928.2	+	13	1551	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	494	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						ATGGATTAAATAGGGACACCG	0.358													T|||	188	0.0375399	0.1324	0.013	5008	,	,		18959	0.0		0.001	False		,,,				2504	0.0031				p.N494N		Atlas-SNP	.											.	LRGUK	113	.	0			c.T1482C						PASS	.	T		484,3922	226.9+/-242.2	40,404,1759	164.0	154.0	158.0		1482	0.7	0.4	7	dbSNP_126	158	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	LRGUK	NM_144648.1		40,426,6037	CC,CT,TT		0.2558,10.985,3.8905		494/826	133881794	506,12500	2203	4300	6503	SO:0001819	synonymous_variant	136332	exon13			ATTAAATAGGGAC	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1482T>C	7.37:g.133881794T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	37	CCDS5830.1																																																																																			T|0.963;C|0.037	0.037	strong		0.358	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	
RPA1	6117	hgsc.bcm.edu	37	17	1795180	1795180	+	Silent	SNP	T	T	C	rs2230931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1795180T>C	ENST00000254719.5	+	15	1715	c.1605T>C	c.(1603-1605)tcT>tcC	p.S535S		NM_002945.3	NP_002936.1	P27694	RFA1_HUMAN	replication protein A1, 70kDa	535					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						TCCAGGAGTCTGCTGAAGCTA	0.323								Nucleotide excision repair (NER)					T|||	1472	0.29393	0.3654	0.304	5008	,	,		17399	0.252		0.1799	False		,,,				2504	0.3507				p.S535S		Atlas-SNP	.											.	RPA1	48	.	0			c.T1605C	GRCh37	CM995272	RPA1	M	rs2230931	PASS	.	T		1567,2839	490.8+/-361.9	273,1021,909	86.0	89.0	88.0		1605	2.2	1.0	17	dbSNP_98	88	1533,7067	288.6+/-298.9	135,1263,2902	no	coding-synonymous	RPA1	NM_002945.3		408,2284,3811	CC,CT,TT		17.8256,35.5651,23.8352		535/617	1795180	3100,9906	2203	4300	6503	SO:0001819	synonymous_variant	6117	exon15			GGAGTCTGCTGAA	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.1605T>C	17.37:g.1795180T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	34	0.548387	NM_002945	A8K0Y9|Q59ES9	Silent	SNP	ENST00000254719.5	37	CCDS11014.1																																																																																			T|0.751;C|0.249	0.249	strong		0.323	RPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207118.2	NM_002945	
SPTBN5	51332	hgsc.bcm.edu	37	15	42179424	42179424	+	Missense_Mutation	SNP	C	C	T	rs890499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42179424C>T	ENST00000320955.6	-	6	1102	c.875G>A	c.(874-876)aGg>aAg	p.R292K		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	292					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)		AGTGAGTCTCCTCTGGACAGT	0.612													C|||	306	0.0611022	0.2239	0.013	5008	,	,		19925	0.0		0.001	False		,,,				2504	0.0				p.R257K		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G770A						PASS	.	C	LYS/ARG	563,2887		35,493,1197	25.0	33.0	30.0		770	1.1	0.8	15	dbSNP_86	30	9,6849		0,9,3420	yes	missense	SPTBN5	NM_016642.2	26	35,502,4617	TT,TC,CC		0.1312,16.3188,5.5491	possibly-damaging	257/3640	42179424	572,9736	1725	3429	5154	SO:0001583	missense	51332	exon6			AGTCTCCTCTGGA	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.875G>A	15.37:g.42179424C>T	ENSP00000317790:p.Arg292Lys	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	274	140	0.510949	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		106	0.048534798534798536	103	0.20934959349593496	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	5.966	0.362219	0.11296	0.163188	0.001312	ENSG00000137877	ENST00000320955	T	0.69806	-0.43	4.49	1.08	0.20341	.	0.076889	0.48286	D	0.000197	T	0.00039	0.0001	N	0.05383	-0.06	0.43540	P	0.00416099999999997	P	0.35612	0.512	B	0.24541	0.054	T	0.22906	-1.0203	9	0.02654	T	1	.	5.7068	0.17913	0.0:0.3579:0.0:0.6421	rs890499;rs1704358;rs890499	292	Q9NRC6	SPTN5_HUMAN	K	292	ENSP00000317790:R292K	ENSP00000317790:R292K	R	-	2	0	SPTBN5	39966716	0.982000	0.34865	0.797000	0.32132	0.954000	0.61252	0.676000	0.25247	0.357000	0.24183	0.591000	0.81541	AGG	C|0.929;T|0.071	0.071	strong		0.612	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
URB2	9816	hgsc.bcm.edu	37	1	229783361	229783361	+	Silent	SNP	C	C	T	rs137900306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229783361C>T	ENST00000258243.2	+	7	4147	c.4011C>T	c.(4009-4011)atC>atT	p.I1337I		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1337						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						AGGAGGCCATCGGCAACCCCC	0.612													C|||	5	0.000998403	0.0038	0.0	5008	,	,		14676	0.0		0.0	False		,,,				2504	0.0				p.I1337I		Atlas-SNP	.											.	URB2	152	.	0			c.C4011T						PASS	.	C		11,4395	17.9+/-39.9	0,11,2192	90.0	74.0	79.0		4011	-0.1	0.1	1	dbSNP_134	79	0,8600		0,0,4300	no	coding-synonymous	URB2	NM_014777.2		0,11,6492	TT,TC,CC		0.0,0.2497,0.0846		1337/1525	229783361	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	9816	exon7			GGCCATCGGCAAC	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.4011C>T	1.37:g.229783361C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_014777	Q5VYC9	Silent	SNP	ENST00000258243.2	37	CCDS31052.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
INPPL1	3636	hgsc.bcm.edu	37	11	71948536	71948536	+	Missense_Mutation	SNP	C	C	G	rs11548491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71948536C>G	ENST00000298229.2	+	26	3452	c.3248C>G	c.(3247-3249)gCt>gGt	p.A1083G	INPPL1_ENST00000541756.1_Missense_Mutation_p.A841G|INPPL1_ENST00000538751.1_Missense_Mutation_p.A841G|PHOX2A_ENST00000544057.1_5'Flank	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1083	Pro-rich.		A -> G (in dbSNP:rs11548491). {ECO:0000269|PubMed:15687335}.		actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CGTGGTGGGGCTGAGGCCCGT	0.687													G|||	784	0.15655	0.298	0.1196	5008	,	,		15497	0.1498		0.0746	False		,,,				2504	0.0828				p.A1083G		Atlas-SNP	.											.	INPPL1	120	.	0			c.C3248G						PASS	.	G	GLY/ALA	1109,3287		153,803,1242	17.0	18.0	18.0		3248	2.6	1.0	11	dbSNP_120	18	501,8083		13,475,3804	yes	missense	INPPL1	NM_001567.3	60	166,1278,5046	GG,GC,CC		5.8364,25.2275,12.4037	benign	1083/1259	71948536	1610,11370	2198	4292	6490	SO:0001583	missense	3636	exon26			GTGGGGCTGAGGC	Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"""Sterile alpha motif (SAM) domain containing"", ""SH2 domain containing"""	6080	protein-coding gene	gene with protein product	"""51C protein"""	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.3248C>G	11.37:g.71948536C>G	ENSP00000298229:p.Ala1083Gly	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	158	78	0.493671	NM_001567	B2RTX5|Q13577|Q13578	Missense_Mutation	SNP	ENST00000298229.2	37	CCDS8213.1	320	0.14652014652014653	142	0.2886178861788618	53	0.1464088397790055	70	0.12237762237762238	55	0.07255936675461741	N	2.288	-0.363144	0.05103	0.252275	0.058364	ENSG00000165458	ENST00000298229;ENST00000541756;ENST00000538751;ENST00000541752	D;D;D;T	0.96619	-2.95;-4.07;-4.07;1.47	4.66	2.62	0.31277	.	0.242758	0.33732	N	0.004607	T	0.00039	0.0001	N	0.08118	0	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.12630	-1.0540	9	0.19590	T	0.45	.	9.1488	0.36951	0.0:0.2732:0.5708:0.156	rs11548491;rs17847211;rs61512395	1083	O15357	SHIP2_HUMAN	G	1083;841;841;96	ENSP00000298229:A1083G;ENSP00000446360:A841G;ENSP00000444619:A841G;ENSP00000441094:A96G	ENSP00000298229:A1083G	A	+	2	0	INPPL1	71626184	0.992000	0.36948	0.988000	0.46212	0.014000	0.08584	0.104000	0.15313	0.594000	0.29761	-1.089000	0.02181	GCT	C|0.871;G|0.129	0.129	strong		0.687	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567	
TNXB	7148	hgsc.bcm.edu	37	6	32032689	32032689	+	Silent	SNP	C	C	T	rs35206129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32032689C>T	ENST00000375244.3	-	19	6951	c.6750G>A	c.(6748-6750)tcG>tcA	p.S2250S	TNXB_ENST00000375247.2_Silent_p.S2250S			P22105	TENX_HUMAN	tenascin XB	2322	Fibronectin type-III 14. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GCTCCAGGCCCGAGATGGTGA	0.612													C|||	18	0.00359425	0.0129	0.0014	5008	,	,		17765	0.0		0.0	False		,,,				2504	0.0				p.S2250S		Atlas-SNP	.											.	TNXB	553	.	0			c.G6750A						PASS	.	C		11,2531		0,11,1260	49.0	55.0	53.0		6750	-9.6	0.7	6	dbSNP_126	53	0,5100		0,0,2550	no	coding-synonymous	TNXB	NM_019105.6		0,11,3810	TT,TC,CC		0.0,0.4327,0.1439		2250/4243	32032689	11,7631	1271	2550	3821	SO:0001819	synonymous_variant	7148	exon19			CAGGCCCGAGATG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.6750G>A	6.37:g.32032689C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				C|0.995;T|0.005	0.005	strong		0.612	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
KEAP1	9817	hgsc.bcm.edu	37	19	10610236	10610236	+	Silent	SNP	A	A	G	rs1048287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10610236A>G	ENST00000171111.5	-	2	1021	c.474T>C	c.(472-474)ggT>ggC	p.G158G	KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Silent_p.G158G	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	158					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	ACATGACAGCACCGTTCATGA	0.582													G|||	409	0.0816693	0.1914	0.0562	5008	,	,		21654	0.001		0.1074	False		,,,				2504	0.0082				p.G158G		Atlas-SNP	.											.	KEAP1	182	.	0			c.T474C						PASS	.	G	,	798,3608	750.7+/-412.1	68,662,1473	184.0	145.0	158.0		474,474	-9.6	0.1	19	dbSNP_86	158	822,7778	782.1+/-407.6	42,738,3520	no	coding-synonymous,coding-synonymous	KEAP1	NM_012289.3,NM_203500.1	,	110,1400,4993	GG,GA,AA		9.5581,18.1117,12.4558	,	158/625,158/625	10610236	1620,11386	2203	4300	6503	SO:0001819	synonymous_variant	9817	exon2			GACAGCACCGTTC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.474T>C	19.37:g.10610236A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Silent	SNP	ENST00000171111.5	37	CCDS12239.1																																																																																			A|0.885;G|0.115	0.115	strong		0.582	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
FLG	2312	hgsc.bcm.edu	37	1	152285137	152285137	+	Missense_Mutation	SNP	G	G	T	rs3120654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152285137G>T	ENST00000368799.1	-	3	2260	c.2225C>A	c.(2224-2226)tCc>tAc	p.S742Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	742	Ser-rich.		S -> Y (in dbSNP:rs3120654).		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)			ACTACCACTGGACCCTCGGTG	0.587									Ichthyosis				-|||	606	0.121006	0.4009	0.0317	5008	,	,		20663	0.0496		0.001	False		,,,				2504	0.0031				p.S742Y		Atlas-SNP	.											.	FLG	900	.	0			c.C2225A						PASS	.	G	TYR/SER	1475,2931		245,985,973	359.0	372.0	367.0		2225	3.2	0.0	1	dbSNP_103	367	19,8581		0,19,4281	no	missense	FLG	NM_002016.1	144	245,1004,5254	TT,TG,GG		0.2209,33.4771,11.487	benign	742/4062	152285137	1494,11512	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCACTGGACCCTC	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.2225C>A	1.37:g.152285137G>T	ENSP00000357789:p.Ser742Tyr	Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	231	228	0.987013	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	197	0.0902014652014652	156	0.3170731707317073	17	0.04696132596685083	23	0.04020979020979021	1	0.0013192612137203166	-	6.498	0.460047	0.12342	0.334771	0.002209	ENSG00000143631	ENST00000368799	T	0.09073	3.02	4.17	3.25	0.37280	.	.	.	.	.	T	0.04815	0.0130	L	0.39397	1.21	0.80722	P	0.0	D	0.71674	0.998	D	0.64144	0.922	T	0.04991	-1.0913	8	0.02654	T	1	-2.0E-4	7.4925	0.27471	0.1191:0.0:0.8809:0.0	.	742	P20930	FILA_HUMAN	Y	742	ENSP00000357789:S742Y	ENSP00000357789:S742Y	S	-	2	0	FLG	150551761	0.004000	0.15560	0.003000	0.11579	0.002000	0.02628	1.429000	0.34903	0.971000	0.38288	0.485000	0.47835	TCC	G|0.892;T|0.108	0.108	strong		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
DHX9	1660	hgsc.bcm.edu	37	1	182844020	182844020	+	Silent	SNP	C	C	T	rs11332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182844020C>T	ENST00000367549.3	+	16	1856	c.1746C>T	c.(1744-1746)acC>acT	p.T582T		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	582					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						TTCAGATGACCCACTTTGTTC	0.383													C|||	900	0.179712	0.3449	0.1254	5008	,	,		19735	0.1181		0.0746	False		,,,				2504	0.1667				p.T582T	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.C1746T						PASS	.	C		1131,2635		160,811,912	129.0	134.0	132.0		1746	3.5	1.0	1	dbSNP_52	132	652,7578		23,606,3486	no	coding-synonymous	DHX9	NM_001357.4		183,1417,4398	TT,TC,CC		7.9222,30.0319,14.8633		582/1271	182844020	1783,10213	1883	4115	5998	SO:0001819	synonymous_variant	1660	exon16			GATGACCCACTTT	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.1746C>T	1.37:g.182844020C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	32	0.376471	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Silent	SNP	ENST00000367549.3	37	CCDS41444.1																																																																																			C|0.865;T|0.135	0.135	strong		0.383	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
NEBL	10529	hgsc.bcm.edu	37	10	21134282	21134282	+	Missense_Mutation	SNP	C	C	G	rs41277370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:21134282C>G	ENST00000377122.4	-	12	1528	c.1132G>C	c.(1132-1134)Gat>Cat	p.D378H	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	378			D -> H (in dbSNP:rs41277370).		cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.D378H(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TTCTCAAAATCCTCTTTGTAA	0.348													C|||	193	0.0385383	0.0053	0.0461	5008	,	,		16267	0.0268		0.0835	False		,,,				2504	0.044				p.D378H		Atlas-SNP	.											NEBL,NS,carcinoma,0,1	NEBL	199	1	1	Substitution - Missense(1)	stomach(1)	c.G1132C						PASS	.	C	,HIS/ASP,	81,4325	69.8+/-107.6	1,79,2123	113.0	110.0	111.0		,1132,	4.2	1.0	10	dbSNP_127	111	712,7886	174.2+/-224.5	27,658,3614	yes	intron,missense,intron	NEBL	NM_001173484.1,NM_006393.2,NM_213569.2	,81,	28,737,5737	GG,GC,CC		8.281,1.8384,6.0981	,probably-damaging,	,378/1015,	21134282	793,12211	2203	4299	6502	SO:0001583	missense	10529	exon12			CAAAATCCTCTTT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1132G>C	10.37:g.21134282C>G	ENSP00000366326:p.Asp378His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	64	26	0.40625	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	37	CCDS7134.1	102	0.046703296703296704	8	0.016260162601626018	20	0.055248618784530384	15	0.026223776223776224	59	0.07783641160949868	C	16.21	3.059222	0.55325	0.018384	0.08281	ENSG00000078114	ENST00000377122	T	0.54071	0.59	6.14	4.24	0.50183	.	0.284706	0.36409	N	0.002617	T	0.12263	0.0298	M	0.86097	2.795	0.80722	D	1	P	0.48589	0.912	P	0.62298	0.9	T	0.47959	-0.9076	10	0.72032	D	0.01	.	9.0226	0.36209	0.0:0.8194:0.0:0.1806	rs41277370	378	O76041	NEBL_HUMAN	H	378	ENSP00000366326:D378H	ENSP00000366326:D378H	D	-	1	0	NEBL	21174288	0.999000	0.42202	0.978000	0.43139	0.719000	0.41307	3.614000	0.54160	0.869000	0.35703	-0.145000	0.13849	GAT	C|0.937;G|0.063	0.063	strong		0.348	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	
KIAA0319	9856	hgsc.bcm.edu	37	6	24551664	24551664	+	Missense_Mutation	SNP	T	T	C	rs807534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24551664T>C	ENST00000378214.3	-	20	3562	c.3038A>G	c.(3037-3039)tAt>tGt	p.Y1013C	KIAA0319_ENST00000430948.2_Missense_Mutation_p.Y968C|KIAA0319_ENST00000537886.1_Intron|KIAA0319_ENST00000543707.1_Missense_Mutation_p.Y1013C|KIAA0319_ENST00000535378.1_Missense_Mutation_p.Y1004C	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	1013			Y -> C (in dbSNP:rs807534).		negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						TGTCTTACCATATTTGGGCCT	0.423													T|||	485	0.096845	0.0832	0.0922	5008	,	,		20835	0.0764		0.1272	False		,,,				2504	0.1084				p.Y1013C		Atlas-SNP	.											.	KIAA0319	117	.	0			c.A3038G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR,,CYS/TYR	415,3991	202.1+/-225.0	20,375,1808	351.0	275.0	301.0		3011,3038,2903,,3038	0.2	1.0	6	dbSNP_86	301	1149,7451	235.7+/-268.2	75,999,3226	yes	missense,missense,missense,intron,missense	KIAA0319	NM_001168374.1,NM_001168375.1,NM_001168376.1,NM_001168377.1,NM_014809.3	194,194,194,,194	95,1374,5034	CC,CT,TT		13.3605,9.419,12.0252	probably-damaging,probably-damaging,probably-damaging,,probably-damaging	1004/1064,1013/1073,968/1028,,1013/1073	24551664	1564,11442	2203	4300	6503	SO:0001583	missense	9856	exon20			TTACCATATTTGG	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.3038A>G	6.37:g.24551664T>C	ENSP00000367459:p.Tyr1013Cys	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	314	314	1	NM_001168375	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	220	0.10073260073260074	43	0.08739837398373984	40	0.11049723756906077	38	0.06643356643356643	99	0.13060686015831136	T	14.94	2.686305	0.47991	0.09419	0.133605	ENSG00000137261	ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T	0.07021	3.23;3.23;3.23;3.23	4.56	0.197	0.15164	.	0.307026	0.26855	N	0.022150	T	0.08403	0.0209	L	0.48362	1.52	0.28285	P	0.9238074000000001	D;D	0.89917	1.0;0.999	D;P	0.65874	0.939;0.87	T	0.09640	-1.0665	9	0.38643	T	0.18	-14.3463	10.4006	0.44227	0.3848:0.0:0.0:0.6152	rs807534;rs52812688;rs56987247;rs807534	1004;1013	Q5VV43-2;Q5VV43	.;K0319_HUMAN	C	1004;968;1013;1013	ENSP00000442403:Y1004C;ENSP00000401086:Y968C;ENSP00000367459:Y1013C;ENSP00000437656:Y1013C	ENSP00000367459:Y1013C	Y	-	2	0	KIAA0319	24659643	1.000000	0.71417	0.990000	0.47175	0.960000	0.62799	1.674000	0.37544	0.216000	0.20781	0.454000	0.30748	TAT	T|0.886;C|0.114	0.114	strong		0.423	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
TENM2	57451	hgsc.bcm.edu	37	5	167689296	167689296	+	Silent	SNP	C	C	T	rs17632540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:167689296C>T	ENST00000518659.1	+	29	7845	c.7806C>T	c.(7804-7806)aaC>aaT	p.N2602N	TENM2_ENST00000403607.2_Silent_p.N2426N|TENM2_ENST00000545108.1_Silent_p.N2601N|TENM2_ENST00000519204.1_Silent_p.N2481N|TENM2_ENST00000520394.1_Silent_p.N2363N	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2602					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TGCTGAACAACGCCTACTACC	0.562													C|||	999	0.199481	0.1536	0.1556	5008	,	,		20212	0.002		0.3022	False		,,,				2504	0.3906				p.N2593N		Atlas-SNP	.											.	.	.	.	0			c.C7779T						PASS	.	C		684,3574		58,568,1503	43.0	48.0	47.0		7779	0.5	1.0	5	dbSNP_123	47	2524,5976		397,1730,2123	no	coding-synonymous	ODZ2	NM_001122679.1		455,2298,3626	TT,TC,CC		29.6941,16.0639,25.145		2593/2766	167689296	3208,9550	2129	4250	6379	SO:0001819	synonymous_variant	57451	exon29			GAACAACGCCTAC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.7806C>T	5.37:g.167689296C>T		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				C|0.820;T|0.180	0.180	strong		0.562	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
TNN	63923	hgsc.bcm.edu	37	1	175097864	175097864	+	Silent	SNP	G	G	A	rs12022593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:175097864G>A	ENST00000239462.4	+	15	3425	c.3312G>A	c.(3310-3312)acG>acA	p.T1104T		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	1104	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		ACATGGAAACGGACGGAGGTG	0.592													G|||	879	0.175519	0.1082	0.1643	5008	,	,		17883	0.2609		0.1948	False		,,,				2504	0.1667				p.T1104T		Atlas-SNP	.											TNN,right_upper_lobe,carcinoma,+1,1	TNN	297	1	0			c.G3312A						PASS	.	G		525,3881	240.6+/-251.3	24,477,1702	97.0	92.0	94.0		3312	-2.3	0.9	1	dbSNP_120	94	1856,6744	331.6+/-319.7	212,1432,2656	no	coding-synonymous	TNN	NM_022093.1		236,1909,4358	AA,AG,GG		21.5814,11.9156,18.3069		1104/1300	175097864	2381,10625	2203	4300	6503	SO:0001819	synonymous_variant	63923	exon15			GGAAACGGACGGA	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.3312G>A	1.37:g.175097864G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	37	CCDS30943.1																																																																																			G|0.813;A|0.187	0.187	strong		0.592	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
CD6	923	hgsc.bcm.edu	37	11	60776103	60776103	+	Silent	SNP	T	T	C	rs61899223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000545105.1_Intron|CD6_ENST00000452451.2_Silent_p.T189T|CD6_ENST00000352009.5_Silent_p.T189T|CD6_ENST00000346437.4_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	98	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	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	
RXRB	6257	hgsc.bcm.edu	37	6	33162507	33162507	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33162507G>A	ENST00000374680.3	-	10	1765	c.1554C>T	c.(1552-1554)atC>atT	p.I518I	RXRB_ENST00000374685.4_Silent_p.I522I|RXRB_ENST00000544186.1_Silent_p.I332I|COL11A2_ENST00000374712.1_5'Flank|COL11A2_ENST00000395197.1_5'Flank|COL11A2_ENST00000361917.1_5'Flank|COL11A2_ENST00000341947.2_5'Flank|COL11A2_ENST00000395194.1_5'Flank|COL11A2_ENST00000357486.1_5'Flank|COL11A2_ENST00000374714.1_5'Flank|COL11A2_ENST00000374713.1_5'Flank|COL11A2_ENST00000374708.4_5'Flank	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	518	Ligand-binding. {ECO:0000250}.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|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)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	GGAAGGTGTCGATGGGGGTGT	0.547																																					p.I522I		Atlas-SNP	.											RXRB,colon,carcinoma,0,1	RXRB	34	1	0			c.C1566T						PASS	.						97.0	88.0	91.0					6																	33162507		1511	2709	4220	SO:0001819	synonymous_variant	6257	exon10			GGTGTCGATGGGG	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"""Nuclear hormone receptors"""	10478	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 2"""	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.1554C>T	6.37:g.33162507G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_001270401	P28703|Q59G65|Q5JP92|Q5STQ1	Silent	SNP	ENST00000374680.3	37	CCDS4768.1																																																																																			.	.	none		0.547	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976	
OR5B3	441608	hgsc.bcm.edu	37	11	58170025	58170025	+	Silent	SNP	C	C	G	rs12271646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58170025C>G	ENST00000309403.2	-	1	857	c.858G>C	c.(856-858)ctG>ctC	p.L286L		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, 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)	p.L286L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GACTATAGACCAGAGGGTTCA	0.438													C|||	1453	0.290136	0.3533	0.2695	5008	,	,		20773	0.1448		0.3628	False		,,,				2504	0.2945				p.L286L		Atlas-SNP	.											OR5B3,NS,carcinoma,0,1	OR5B3	65	1	1	Substitution - coding silent(1)	stomach(1)	c.G858C						scavenged	.	C		1442,2960	468.3+/-355.1	229,984,988	140.0	121.0	127.0		858	-0.6	0.2	11	dbSNP_120	127	3093,5497	473.2+/-368.5	550,1993,1752	no	coding-synonymous	OR5B3	NM_001005469.1		779,2977,2740	GG,GC,CC		36.007,32.7578,34.9061		286/315	58170025	4535,8457	2201	4295	6496	SO:0001819	synonymous_variant	441608	exon1			ATAGACCAGAGGG	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.858G>C	11.37:g.58170025C>G		Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	217	105	0.483871	NM_001005469	Q6IEV6	Silent	SNP	ENST00000309403.2	37	CCDS31549.1																																																																																			C|0.665;G|0.335	0.335	strong		0.438	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656246	46656246	+	Missense_Mutation	SNP	T	T	G	rs7291444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46656246T>G	ENST00000253255.5	-	1	2973	c.2974A>C	c.(2974-2976)Aca>Cca	p.T992P		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	992			T -> P (in dbSNP:rs7291444).		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)		CTAAGCACTGTGCTGTCCACT	0.507													T|||	1065	0.21266	0.5575	0.1297	5008	,	,		21694	0.001		0.16	False		,,,				2504	0.0777				p.T992P		Atlas-SNP	.											.	PKDREJ	195	.	0			c.A2974C						PASS	.	T	PRO/THR	2031,2375	562.8+/-381.0	571,889,743	147.0	140.0	142.0		2974	-1.3	0.0	22	dbSNP_116	142	1254,7346	251.0+/-277.6	88,1078,3134	yes	missense	PKDREJ	NM_006071.1	38	659,1967,3877	GG,GT,TT		14.5814,46.0962,25.2576	benign	992/2254	46656246	3285,9721	2203	4300	6503	SO:0001583	missense	10343	exon1			GCACTGTGCTGTC	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.2974A>C	22.37:g.46656246T>G	ENSP00000253255:p.Thr992Pro	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	148	73	0.493243	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	449	0.20558608058608058	281	0.5711382113821138	55	0.15193370165745856	0	0.0	113	0.14907651715039577	T	9.836	1.189664	0.21954	0.460962	0.145814	ENSG00000130943	ENST00000253255	T	0.36340	1.26	4.65	-1.26	0.09376	.	1.107710	0.06788	N	0.786461	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.20368	0.044	B	0.16722	0.016	T	0.47355	-0.9124	9	0.30078	T	0.28	0.8913	5.6541	0.17633	0.0:0.2993:0.1343:0.5664	rs7291444;rs52836498;rs57430542;rs7291444	992	Q9NTG1	PKDRE_HUMAN	P	992	ENSP00000253255:T992P	ENSP00000253255:T992P	T	-	1	0	PKDREJ	45034910	0.000000	0.05858	0.000000	0.03702	0.187000	0.23431	-1.782000	0.01772	-0.425000	0.07371	0.533000	0.62120	ACA	A|0.001;G|0.248;T|0.751	0.248	strong		0.507	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
NSFL1C	55968	hgsc.bcm.edu	37	20	1433171	1433171	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1433171T>C	ENST00000216879.4	-	7	1619	c.752A>G	c.(751-753)aAa>aGa	p.K251R	NSFL1C_ENST00000353088.2_Missense_Mutation_p.K220R|NSFL1C_ENST00000461211.1_5'UTR|NSFL1C_ENST00000476071.1_Missense_Mutation_p.K253R|NSFL1C_ENST00000350991.4_Missense_Mutation_p.K253R|NSFL1C_ENST00000381658.4_Missense_Mutation_p.K140R	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)	251						chromosome (GO:0005694)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	16						AGTGAAGGCTTTGAAGGCTCC	0.577																																					p.K251R		Atlas-SNP	.											.	NSFL1C	38	.	0			c.A752G						PASS	.						158.0	139.0	146.0					20																	1433171		2203	4300	6503	SO:0001583	missense	55968	exon7			AAGGCTTTGAAGG	AF112211	CCDS13015.1, CCDS13016.1, CCDS56175.1	20p13	2011-06-28			ENSG00000088833	ENSG00000088833		"""UBX domain containing"""	15912	protein-coding gene	gene with protein product	"""SHP1 homolog (S. cerevisiae)"", ""UBX domain protein 2C"""	606610				11042152	Standard	NM_016143		Approved	dJ776F14.1, p47, UBXD10, UBX1, UBXN2C	uc002wfc.3	Q9UNZ2	OTTHUMG00000031665	ENST00000216879.4:c.752A>G	20.37:g.1433171T>C	ENSP00000216879:p.Lys251Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	96	34	0.354167	NM_016143	A2A2L1|B2RD74|Q5JXA4|Q5JXA5|Q7Z533|Q9H102|Q9NVL9|Q9UI06	Missense_Mutation	SNP	ENST00000216879.4	37	CCDS13015.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.076548	0.55753	.	.	ENSG00000088833	ENST00000353088;ENST00000476071;ENST00000216879;ENST00000381658;ENST00000350991	T;T;T;T;T	0.49432	0.79;0.78;0.78;0.82;0.78	5.13	2.85	0.33270	SEP domain (3);	0.000000	0.85682	D	0.000000	T	0.42337	0.1198	M	0.62016	1.91	0.58432	D	0.999995	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.12156	0.007;0.005;0.005	T	0.30937	-0.9961	10	0.51188	T	0.08	-10.0824	8.1784	0.31296	0.0:0.294:0.0:0.706	.	220;140;251	Q9UNZ2-4;Q9UNZ2-6;Q9UNZ2	.;.;NSF1C_HUMAN	R	220;253;251;140;253	ENSP00000338643:K220R;ENSP00000418529:K253R;ENSP00000216879:K251R;ENSP00000371074:K140R;ENSP00000202584:K253R	ENSP00000216879:K251R	K	-	2	0	NSFL1C	1381171	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.908000	0.28545	0.503000	0.28060	0.533000	0.62120	AAA	.	.	none		0.577	NSFL1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077525.2	NM_016143	
PAK2	5062	hgsc.bcm.edu	37	3	196509522	196509522	+	Missense_Mutation	SNP	C	C	G	rs67093638		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196509522C>G	ENST00000327134.3	+	2	327	c.5C>G	c.(4-6)tCt>tGt	p.S2C	RNU6-42P_ENST00000384165.1_RNA	NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	2					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)	p.S2C(2)		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)		TGAATCATGTCTGATAACGGA	0.408																																					p.S2C		Atlas-SNP	.											PAK2_ENST00000327134,NS,carcinoma,0,4	PAK2	113	4	2	Substitution - Missense(2)	prostate(2)	c.C5G						scavenged	.						81.0	87.0	85.0					3																	196509522		2203	4300	6503	SO:0001583	missense	5062	exon2			TCATGTCTGATAA	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.5C>G	3.37:g.196509522C>G	ENSP00000314067:p.Ser2Cys	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	168	2	0.0119048	NM_002577	Q13154|Q6ISC3	Missense_Mutation	SNP	ENST00000327134.3	37	CCDS3321.1	42	0.019230769230769232	6	0.012195121951219513	0	0.0	7	0.012237762237762238	29	0.03825857519788918	C	14.90	2.672409	0.47781	.	.	ENSG00000180370	ENST00000327134	T	0.70631	-0.5	5.21	5.21	0.72293	.	0.055816	0.64402	D	0.000001	T	0.30417	0.0764	N	0.25426	0.745	0.54753	D	0.999985	B	0.15141	0.012	B	0.20577	0.03	T	0.51284	-0.8725	10	0.62326	D	0.03	.	18.756	0.91833	0.0:1.0:0.0:0.0	.	2	Q13177	PAK2_HUMAN	C	2	ENSP00000314067:S2C	ENSP00000314067:S2C	S	+	2	0	PAK2	197993919	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.961000	0.49168	2.456000	0.83038	0.655000	0.94253	TCT	C|0.986;G|0.014	0.014	strong		0.408	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
OR4D11	219986	hgsc.bcm.edu	37	11	59271637	59271637	+	Missense_Mutation	SNP	T	T	C	rs7120079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	431	3	0.00696056		WXS	Illumina HiSeq	Phase_I	427	220	0.515222	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	
AP4E1	23431	hgsc.bcm.edu	37	15	51233881	51233881	+	Missense_Mutation	SNP	A	A	G	rs58909326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51233881A>G	ENST00000261842.5	+	10	1191	c.1085A>G	c.(1084-1086)tAt>tGt	p.Y362C	AP4E1_ENST00000560508.1_Missense_Mutation_p.Y287C	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	362					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		GCTCTTACCTATGTTATCCAA	0.353													A|||	72	0.014377	0.053	0.0029	5008	,	,		16104	0.0		0.0	False		,,,				2504	0.0				p.Y362C		Atlas-SNP	.											.	AP4E1	78	.	0			c.A1085G						PASS	.	A	CYS/TYR	216,4176	131.8+/-168.3	5,206,1985	147.0	137.0	141.0		1085	4.9	1.0	15	dbSNP_129	141	2,8586	2.2+/-6.3	0,2,4292	yes	missense	AP4E1	NM_007347.3	194	5,208,6277	GG,GA,AA		0.0233,4.918,1.6795	benign	362/1138	51233881	218,12762	2196	4294	6490	SO:0001583	missense	23431	exon10			TTACCTATGTTAT	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.1085A>G	15.37:g.51233881A>G	ENSP00000261842:p.Tyr362Cys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	35	0.016025641025641024	35	0.07113821138211382	0	0.0	0	0.0	0	0.0	A	11.86	1.763436	0.31228	0.04918	2.33E-4	ENSG00000081014	ENST00000261842	T	0.25414	1.8	6.04	4.93	0.64822	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.061436	0.64402	D	0.000002	T	0.01029	0.0034	N	0.16098	0.37	0.58432	D	0.999997	B	0.22800	0.075	B	0.21917	0.037	T	0.10823	-1.0613	10	0.37606	T	0.19	-17.2068	9.7604	0.40528	0.8689:0.0:0.1311:0.0	rs58909326	362	Q9UPM8	AP4E1_HUMAN	C	362	ENSP00000261842:Y362C	ENSP00000261842:Y362C	Y	+	2	0	AP4E1	49021173	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.930000	0.63462	2.317000	0.78254	0.460000	0.39030	TAT	A|0.982;G|0.018	0.018	strong		0.353	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
SLCO4A1	28231	hgsc.bcm.edu	37	20	61292475	61292475	+	Missense_Mutation	SNP	C	C	T	rs201057493		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61292475C>T	ENST00000370507.1	+	4	1165	c.1069C>T	c.(1069-1071)Cgt>Tgt	p.R357C	RP11-93B14.5_ENST00000433126.1_RNA|RP11-93B14.5_ENST00000411824.1_RNA|RP11-93B14.5_ENST00000451648.1_RNA|SLCO4A1_ENST00000217159.1_Missense_Mutation_p.R357C			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	357					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)	GGACAGCAGCCGTGGGGAGGC	0.622													c|||	1	0.000199681	0.0	0.0	5008	,	,		11244	0.0		0.001	False		,,,				2504	0.0				p.R357C	Pancreas(168;741 2006 10379 40139 45334)	Atlas-SNP	.											SLCO4A1,uveal_tract,malignant_melanoma,0,1	SLCO4A1	65	1	0			c.C1069T						PASS	.		CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	89.0	80.0	83.0		1069	3.2	0.0	20		83	0,8600		0,0,4300	no	missense	SLCO4A1	NM_016354.3	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	357/723	61292475	1,13005	2203	4300	6503	SO:0001583	missense	28231	exon5			AGCAGCCGTGGGG	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.1069C>T	20.37:g.61292475C>T	ENSP00000359538:p.Arg357Cys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Missense_Mutation	SNP	ENST00000370507.1	37	CCDS13501.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	6.688	0.495496	0.12762	2.27E-4	0.0	ENSG00000101187	ENST00000217159;ENST00000370512;ENST00000370507	T;T	0.41400	1.0;1.0	4.25	3.22	0.36961	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	6.950440	0.00447	N	0.000090	T	0.42810	0.1219	L	0.54323	1.7	0.19300	N	0.999972	B	0.15473	0.013	B	0.15484	0.013	T	0.30707	-0.9969	10	0.56958	D	0.05	.	7.3638	0.26762	0.0:0.7375:0.1713:0.0912	.	357	Q96BD0	SO4A1_HUMAN	C	357	ENSP00000217159:R357C;ENSP00000359538:R357C	ENSP00000217159:R357C	R	+	1	0	SLCO4A1	60762920	0.092000	0.21681	0.008000	0.14137	0.002000	0.02628	2.568000	0.45965	1.940000	0.56252	0.450000	0.29827	CGT	C|1.000;T|0.000	0.000	strong		0.622	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354	
SYT8	90019	hgsc.bcm.edu	37	11	1857762	1857762	+	Silent	SNP	C	C	T	rs3741230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1857762C>T	ENST00000381968.3	+	6	794	c.666C>T	c.(664-666)acC>acT	p.T222T	SYT8_ENST00000341958.3_Silent_p.T208T|TNNI2_ENST00000381911.1_5'Flank|SYT8_ENST00000535046.1_3'UTR|TNNI2_ENST00000381906.1_5'Flank	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	112	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	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		
GPR144	347088	hgsc.bcm.edu	37	9	127230864	127230864	+	Missense_Mutation	SNP	G	G	A	rs7854446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127230864G>A	ENST00000334810.1	+	14	2221	c.2221G>A	c.(2221-2223)Gtg>Atg	p.V741M				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	741					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						CTGGATGCTGGTGGAGGGGCT	0.637													G|||	92	0.0183706	0.0666	0.0058	5008	,	,		17950	0.0		0.0	False		,,,				2504	0.0				p.V741M		Atlas-SNP	.											.	GPR144	33	.	0			c.G2221A						PASS	.	G	MET/VAL	114,1270		6,102,584	100.0	88.0	92.0		2221	4.7	1.0	9	dbSNP_116	92	1,3181		0,1,1590	yes	missense	GPR144	NM_001161808.1	21	6,103,2174	AA,AG,GG		0.0314,8.237,2.5186	probably-damaging	741/964	127230864	115,4451	692	1591	2283	SO:0001583	missense	347088	exon14			ATGCTGGTGGAGG	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.2221G>A	9.37:g.127230864G>A	ENSP00000335156:p.Val741Met	Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	121	119	0.983471	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	39|39	0.017857142857142856|0.017857142857142856	37|37	0.07520325203252033|0.07520325203252033	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	21.8|21.8	4.205019|4.205019	0.79127|0.79127	0.08237|0.08237	3.14E-4|3.14E-4	ENSG00000180264|ENSG00000180264	ENST00000446588|ENST00000334810	.|T	.|0.41400	.|1.0	4.7|4.7	4.7|4.7	0.59300|0.59300	.|GPCR, family 2-like (1);	.|.	.|.	.|.	.|.	T|T	0.09202|0.09202	0.0227|0.0227	M|M	0.76170|0.76170	2.325|2.325	0.49582|0.49582	D|D	0.999802|0.999802	D|D	0.89917|0.89917	1.0|1.0	D|D	0.91635|0.91635	0.999|0.999	T|T	0.45249|0.45249	-0.9274|-0.9274	8|9	0.87932|0.72032	D|D	0|0.01	.|.	16.2217|16.2217	0.82262|0.82262	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs7854446;rs7854446|rs7854446;rs7854446	9|741	A1E4E8|Q7Z7M1	.|GP144_HUMAN	D|M	9|741	.|ENSP00000335156:V741M	ENSP00000414478:G9D|ENSP00000335156:V741M	G|V	+|+	2|1	0|0	GPR144|GPR144	126270685|126270685	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.838000|0.838000	0.47535|0.47535	6.672000|6.672000	0.74477|0.74477	2.147000|2.147000	0.66899|0.66899	0.561000|0.561000	0.74099|0.74099	GGT|GTG	G|0.967;A|0.033	0.033	strong		0.637	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
MUC4	4585	hgsc.bcm.edu	37	3	195513540	195513540	+	Silent	SNP	A	A	G	rs201447574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513540A>G	ENST00000463781.3	-	2	5370	c.4911T>C	c.(4909-4911)aaT>aaC	p.N1637N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.N1637N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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.N1637_T1652delNASSLSTGHATPLHVT(2)|p.N1637N(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)		ATGAGGAAGCATTGGTGACAG	0.577																																					p.N1637N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	3	Deletion - In frame(2)|Substitution - coding silent(1)	stomach(2)|kidney(1)	c.T4911C						scavenged	.						35.0	41.0	39.0					3																	195513540		689	1581	2270	SO:0001819	synonymous_variant	4585	exon2			GGAAGCATTGGTG	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.4911T>C	3.37:g.195513540A>G		Somatic	663	11	0.0165913		WXS	Illumina HiSeq	Phase_I	599	13	0.0217028	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|0.990;G|0.010	0.010	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CASP4	837	hgsc.bcm.edu	37	11	104819333	104819333	+	Missense_Mutation	SNP	C	C	A	rs55901059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:104819333C>A	ENST00000444739.2	-	6	1762	c.852G>T	c.(850-852)gaG>gaT	p.E284D	CASP4_ENST00000531333.1_5'Flank|CASP4_ENST00000393150.3_Missense_Mutation_p.E228D	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	284			E -> D (in dbSNP:rs55901059).		apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		CCTCTAGGTTCTCAGATGACT	0.493													c|||	93	0.0185703	0.0688	0.0029	5008	,	,		19215	0.0		0.0	False		,,,				2504	0.0				p.E284D		Atlas-SNP	.											.	CASP4	57	.	0			c.G852T						PASS	.	C	ASP/GLU,ASP/GLU	287,4117	157.8+/-190.6	12,263,1927	157.0	117.0	131.0		852,684	-2.6	0.0	11	dbSNP_129	131	1,8597		0,1,4298	yes	missense,missense	CASP4	NM_001225.3,NM_033306.2	45,45	12,264,6225	AA,AC,CC		0.0116,6.5168,2.215	benign,benign	284/378,228/322	104819333	288,12714	2202	4299	6501	SO:0001583	missense	837	exon6			TAGGTTCTCAGAT	U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"""Caspases"""	1505	protein-coding gene	gene with protein product		602664	"""caspase 4, apoptosis-related cysteine protease"""			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.852G>T	11.37:g.104819333C>A	ENSP00000388566:p.Glu284Asp	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	141	86	0.609929	NM_001225	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	37	CCDS8327.1	43	0.019688644688644688	42	0.08536585365853659	1	0.0027624309392265192	0	0.0	0	0.0	C	9.595	1.127085	0.20959	0.065168	1.16E-4	ENSG00000196954	ENST00000444739;ENST00000393150;ENST00000355546	T;T	0.20738	2.05;2.05	5.08	-2.61	0.06171	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);	1.203310	0.05999	N	0.647483	T	0.00580	0.0019	L	0.37800	1.135	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.32587	-0.9901	10	0.19590	T	0.45	.	12.8207	0.57692	0.0:0.3484:0.58:0.0716	rs55901059;rs61735787	284	P49662	CASP4_HUMAN	D	284;228;237	ENSP00000388566:E284D;ENSP00000376857:E228D	ENSP00000347741:E237D	E	-	3	2	CASP4	104324543	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.270000	0.02831	-0.407000	0.07576	-0.494000	0.04653	GAG	C|0.979;A|0.021	0.021	strong		0.493	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225	
SMAD9	4093	hgsc.bcm.edu	37	13	37453576	37453576	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:37453576C>T	ENST00000399275.2	-	1	390	c.251G>A	c.(250-252)cGc>cAc	p.R84H	SMAD9_ENST00000483941.1_5'Flank|SMAD9_ENST00000379826.4_Missense_Mutation_p.R84H|SMAD9_ENST00000350148.5_Missense_Mutation_p.R84H			O15198	SMAD9_HUMAN	SMAD family member 9	84	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cartilage development (GO:0051216)|cellular response to organic cyclic compound (GO:0071407)|hindbrain development (GO:0030902)|intracellular signal transduction (GO:0035556)|midbrain development (GO:0030901)|Mullerian duct regression (GO:0001880)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)	18		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)		CAGGCCCTTGCGGTGGGACAC	0.657																																					p.R84H		Atlas-SNP	.											SMAD9_ENST00000379826,NS,carcinoma,-1,2	SMAD9	91	2	0			c.G251A						scavenged	.						36.0	40.0	39.0					13																	37453576		2203	4300	6503	SO:0001583	missense	4093	exon2			CCCTTGCGGTGGG		CCDS9360.1, CCDS45032.1	13q12-q14	2014-09-17	2006-11-06	2004-05-26	ENSG00000120693	ENSG00000120693		"""SMADs"""	6774	protein-coding gene	gene with protein product		603295	"""MAD, mothers against decapentaplegic homolog 9 (Drosophila)"", ""SMAD, mothers against DPP homolog 9 (Drosophila)"""	MADH6, MADH9		9205116	Standard	NM_001127217		Approved		uc001uvw.3	O15198	OTTHUMG00000016740	ENST00000399275.2:c.251G>A	13.37:g.37453576C>T	ENSP00000382216:p.Arg84His	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	2	0.0273973	NM_005905	A2A2Y6|O14989|Q5TBA1	Missense_Mutation	SNP	ENST00000399275.2	37	CCDS45032.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.098209	0.76870	.	.	ENSG00000120693	ENST00000399275;ENST00000350148;ENST00000379826	T;T;T	0.77750	-1.12;-1.12;-1.12	5.53	5.53	0.82687	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.89076	0.6612	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74023	0.981;0.982	D	0.90040	0.4141	10	0.66056	D	0.02	.	18.4517	0.90705	0.0:1.0:0.0:0.0	.	84;84	O15198-2;O15198	.;SMAD9_HUMAN	H	84	ENSP00000382216:R84H;ENSP00000239885:R84H;ENSP00000369154:R84H	ENSP00000239885:R84H	R	-	2	0	SMAD9	36351576	1.000000	0.71417	1.000000	0.80357	0.574000	0.36063	7.762000	0.85270	2.599000	0.87857	0.563000	0.77884	CGC	.	.	none		0.657	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905	
BRDT	676	hgsc.bcm.edu	37	1	92445179	92445179	+	Missense_Mutation	SNP	G	G	A	rs114276662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:92445179G>A	ENST00000362005.3	+	9	1570	c.1152G>A	c.(1150-1152)atG>atA	p.M384I	BRDT_ENST00000399546.2_Missense_Mutation_p.M384I|BRDT_ENST00000394530.3_Missense_Mutation_p.M338I|BRDT_ENST00000370389.2_Missense_Mutation_p.M311I|BRDT_ENST00000402388.1_Missense_Mutation_p.M384I	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	384					cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		TTGAGAGTATGCCTTTATGTT	0.348													G|||	22	0.00439297	0.0144	0.0029	5008	,	,		16690	0.0		0.001	False		,,,				2504	0.0				p.M388I		Atlas-SNP	.											.	BRDT	133	.	0			c.G1164A						PASS	.	G	ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	67,4339	61.7+/-98.7	0,67,2136	103.0	103.0	103.0		1152,1164,1014,1014,933,1152,1152	3.5	0.0	1	dbSNP_133	103	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	10,10,10,10,10,10,10	0,67,6436	AA,AG,GG		0.0,1.5207,0.5151	benign,benign,benign,benign,benign,benign,benign	384/948,388/952,338/902,338/902,311/875,384/948,384/948	92445179	67,12939	2203	4300	6503	SO:0001583	missense	676	exon8			GAGTATGCCTTTA	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.1152G>A	1.37:g.92445179G>A	ENSP00000354568:p.Met384Ile	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	206	92	0.446602	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	7.998	0.754682	0.15778	0.015207	0.0	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000394530;ENST00000426141;ENST00000402388	T;T;T;T;T;T	0.09163	3.33;3.34;3.33;3.38;3.01;3.33	5.41	3.49	0.39957	Bromodomain (1);	0.456653	0.24005	N	0.042435	T	0.02230	0.0069	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.18863	0.031;0.031;0.0;0.031	B;B;B;B	0.09377	0.004;0.004;0.002;0.002	T	0.43032	-0.9416	10	0.38643	T	0.18	-0.2883	5.9499	0.19239	0.1483:0.0:0.5637:0.288	.	338;338;388;384	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	I	384;311;384;384;338;384;384	ENSP00000354568:M384I;ENSP00000359416:M311I;ENSP00000387822:M384I;ENSP00000378038:M338I;ENSP00000404969:M384I;ENSP00000384051:M384I	ENSP00000354568:M384I	M	+	3	0	BRDT	92217767	0.008000	0.16893	0.016000	0.15963	0.543000	0.35085	1.606000	0.36826	0.631000	0.30412	0.655000	0.94253	ATG	G|0.995;A|0.005	0.005	strong		0.348	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
UBA5	79876	hgsc.bcm.edu	37	3	132384704	132384704	+	Missense_Mutation	SNP	G	G	A	rs61748106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:132384704G>A	ENST00000356232.4	+	2	1271	c.199G>A	c.(199-201)Gac>Aac	p.D67N	UBA5_ENST00000493720.2_Missense_Mutation_p.D67N|UBA5_ENST00000473651.1_Missense_Mutation_p.D67N|UBA5_ENST00000494238.2_Missense_Mutation_p.D11N|UBA5_ENST00000264991.4_Missense_Mutation_p.D11N	NM_024818.3	NP_079094.1	Q9GZZ9	UBA5_HUMAN	ubiquitin-like modifier activating enzyme 5	67					protein ufmylation (GO:0071569)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|UFM1 activating enzyme activity (GO:0071566)			breast(2)|endometrium(4)|kidney(4)|large_intestine(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						AATTGTAAGCGACTATGAGGT	0.303													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18495	0.0		0.0	False		,,,				2504	0.0				p.D67N		Atlas-SNP	.											UBA5,colon,carcinoma,0,1	UBA5	33	1	0			c.G199A						PASS	.	G	ASN/ASP,ASN/ASP	7,4399	12.9+/-30.5	0,7,2196	90.0	98.0	96.0		199,31	4.3	0.7	3	dbSNP_129	96	0,8600		0,0,4300	yes	missense,missense	UBA5	NM_024818.3,NM_198329.2	23,23	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	benign,benign	67/405,11/349	132384704	7,12999	2203	4300	6503	SO:0001583	missense	79876	exon2			GTAAGCGACTATG	AY253672	CCDS3076.1, CCDS3077.1	3q22	2007-11-30	2007-11-30	2007-11-30	ENSG00000081307	ENSG00000081307		"""Ubiquitin-like modifier activating enzymes"""	23230	protein-coding gene	gene with protein product	"""UBA5, ubiquitin-activating enzyme E1 homolog (yeast)"""	610552	"""ubiquitin-activating enzyme E1-domain containing 1"""	UBE1DC1		11230166, 15071506	Standard	NM_198329		Approved	FLJ23251	uc003epa.4	Q9GZZ9	OTTHUMG00000159759	ENST00000356232.4:c.199G>A	3.37:g.132384704G>A	ENSP00000348565:p.Asp67Asn	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_024818	A6NJL3|D3DNC8|Q96ST1	Missense_Mutation	SNP	ENST00000356232.4	37	CCDS3076.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	4.515	0.095620	0.08681	0.001589	0.0	ENSG00000081307	ENST00000264991;ENST00000356232;ENST00000493720;ENST00000468022;ENST00000473651;ENST00000494238;ENST00000489361	T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58	6.03	4.26	0.50523	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.14056	0.0340	N	0.04959	-0.14	0.80722	D	1	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.002	T	0.07616	-1.0763	10	0.12103	T	0.63	-19.1821	11.318	0.49403	0.1873:0.0:0.8127:0.0	rs61748106	67;67	E7EWE1;Q9GZZ9	.;UBA5_HUMAN	N	11;67;67;11;67;11;11	ENSP00000264991:D11N;ENSP00000348565:D67N;ENSP00000417879:D67N;ENSP00000418569:D11N;ENSP00000424984:D67N;ENSP00000418807:D11N;ENSP00000417905:D11N	ENSP00000264991:D11N	D	+	1	0	UBA5	133867394	1.000000	0.71417	0.700000	0.30305	0.868000	0.49771	4.654000	0.61469	0.898000	0.36418	-0.794000	0.03295	GAC	G|0.999;A|0.001	0.001	strong		0.303	UBA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357187.2	NM_024818	
PXDNL	137902	hgsc.bcm.edu	37	8	52321293	52321293	+	Missense_Mutation	SNP	T	T	A	rs562911693		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:52321293T>A	ENST00000356297.4	-	17	2991	c.2891A>T	c.(2890-2892)cAt>cTt	p.H964L	PXDNL_ENST00000543296.1_Missense_Mutation_p.H964L	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	964					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CAGAGCCAGATGCTCGTTGGC	0.647																																					p.H964L		Atlas-SNP	.											.	PXDNL	414	.	0			c.A2891T						PASS	.						13.0	15.0	14.0					8																	52321293		1980	4147	6127	SO:0001583	missense	137902	exon17			GCCAGATGCTCGT		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2891A>T	8.37:g.52321293T>A	ENSP00000348645:p.His964Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.567|7.567	0.665851|0.665851	0.14710|0.14710	.|.	.|.	ENSG00000147485|ENSG00000147485	ENST00000356297;ENST00000543296|ENST00000522933	T;T|.	0.71698|.	-0.59;-0.59|.	3.73|3.73	1.18|1.18	0.20946|0.20946	.|.	0.164545|.	0.29508|.	N|.	0.011960|.	T|T	0.19208|0.19208	0.0461|0.0461	N|N	0.17082|0.17082	0.46|0.46	0.26667|0.26667	N|N	0.971805|0.971805	B|.	0.11235|.	0.004|.	B|.	0.17979|.	0.02|.	T|T	0.24657|0.24657	-1.0154|-1.0154	10|5	0.59425|.	D|.	0.04|.	.|.	3.9824|3.9824	0.09501|0.09501	0.1835:0.1097:0.0:0.7068|0.1835:0.1097:0.0:0.7068	.|.	964|.	A1KZ92|.	PXDNL_HUMAN|.	L|F	964|83	ENSP00000348645:H964L;ENSP00000444865:H964L|.	ENSP00000348645:H964L|.	H|I	-|-	2|1	0|0	PXDNL|PXDNL	52483846|52483846	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	5.173000|5.173000	0.65010|0.65010	-0.052000|-0.052000	0.13311|0.13311	-0.371000|-0.371000	0.07208|0.07208	CAT|ATC	.	.	none		0.647	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
ZNF439	90594	hgsc.bcm.edu	37	19	11978898	11978898	+	Silent	SNP	T	T	C	rs113442649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11978898T>C	ENST00000304030.2	+	3	1214	c.1014T>C	c.(1012-1014)ctT>ctC	p.L338L	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Silent_p.L202L	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	338					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						TATCCTCTCTTACAAGTTTTC	0.388													t|||	36	0.0071885	0.0257	0.0029	5008	,	,		23879	0.0		0.0	False		,,,				2504	0.0				p.L338L		Atlas-SNP	.											.	ZNF439	67	.	0			c.T1014C						PASS	.	T		123,4283	90.6+/-129.3	0,123,2080	98.0	99.0	98.0		1014	-1.1	0.0	19	dbSNP_132	98	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous	ZNF439	NM_152262.2		0,128,6375	CC,CT,TT		0.0581,2.7916,0.9842		338/500	11978898	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	90594	exon3			CTCTCTTACAAGT	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.1014T>C	19.37:g.11978898T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	108	71	0.657407	NM_152262	Q8IYZ7|Q96SU1	Silent	SNP	ENST00000304030.2	37	CCDS12268.1																																																																																			T|0.989;C|0.011	0.011	strong		0.388	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1		
ANK1	286	hgsc.bcm.edu	37	8	41547748	41547748	+	Silent	SNP	G	G	A	rs7816734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:41547748G>A	ENST00000347528.4	-	33	4184	c.4101C>T	c.(4099-4101)gcC>gcT	p.A1367A	ANK1_ENST00000379758.2_Silent_p.A1367A|ANK1_ENST00000265709.8_Silent_p.A1408A|ANK1_ENST00000352337.4_Silent_p.A1367A|ANK1_ENST00000289734.7_Silent_p.A1367A|ANK1_ENST00000396945.1_Silent_p.A1367A|ANK1_ENST00000396942.1_Silent_p.A1367A	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1367					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)			AGCTCACCTTGGCGCAGGGGG	0.627													G|||	938	0.1873	0.5439	0.0576	5008	,	,		17004	0.0764		0.0606	False		,,,				2504	0.0419				p.A1408A		Atlas-SNP	.											.	ANK1	497	.	0			c.C4224T						PASS	.	G	,,,,	2010,2396	562.1+/-380.9	470,1070,663	93.0	75.0	81.0		4101,4224,4101,4101,4101	2.2	1.0	8	dbSNP_116	81	495,8105	142.3+/-198.5	12,471,3817	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	,,,,	482,1541,4480	AA,AG,GG		5.7558,45.6196,19.2603	,,,,	1367/1881,1408/1898,1367/1857,1367/1882,1367/1720	41547748	2505,10501	2203	4300	6503	SO:0001819	synonymous_variant	286	exon34			CACCTTGGCGCAG	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.4101C>T	8.37:g.41547748G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	372	0.17032967032967034	266	0.540650406504065	19	0.052486187845303865	43	0.07517482517482517	44	0.05804749340369393	G	9.953	1.220573	0.22457	0.456196	0.057558	ENSG00000029534	ENST00000520299	.	.	.	5.08	2.17	0.27698	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8844	0.13696	0.0756:0.2822:0.4961:0.146	rs7816734;rs7816734	.	.	.	X	689	.	.	Q	-	1	0	ANK1	41666905	1.000000	0.71417	0.992000	0.48379	0.858000	0.48976	2.444000	0.44890	0.261000	0.21753	0.563000	0.77884	CAA	G|0.811;A|0.189	0.189	strong		0.627	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
MT-ND4L	4539	hgsc.bcm.edu	37	M	10688	10688	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10688G>A	ENST00000361335.1	+	1	219	c.219G>A	c.(217-219)gtG>gtA	p.V73V	MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03901	NU4LM_HUMAN	mitochondrially encoded NADH dehydrogenase 4L	73					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(2)|kidney(2)	5						GAAGCAGCGGTGGGCCTAGCC	0.458																																					p.V73V		Atlas-SNP	.											.	.	.	.	0			c.G219A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			AGCGGTGGGCCTA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000212907	ENSG00000212907	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7460	protein-coding gene	gene with protein product	"""complex I ND4L subunit"", ""NADH-ubiquinone oxidoreductase chain 4L"""	516004	"""NADH dehydrogenase 4L"""	MTND4L			Standard			Approved	ND4L, NAD4L		P03901		ENST00000361335.1:c.219G>A	M.37:g.10688G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	ENST00000361335		Silent	SNP	ENST00000361335.1	37																																																																																				.	.	none		0.458	MT-ND4L-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024034	
SUN1	23353	hgsc.bcm.edu	37	7	883105	883105	+	Silent	SNP	C	C	T	rs113652875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:883105C>T	ENST00000405266.1	+	5	630	c.606C>T	c.(604-606)ccC>ccT	p.P202P	SUN1_ENST00000457378.2_Silent_p.P223P|SUN1_ENST00000425407.2_Silent_p.P152P|SUN1_ENST00000401592.1_Silent_p.P202P|SUN1_ENST00000403868.1_Silent_p.P202P|SUN1_ENST00000389574.3_Silent_p.P152P|SUN1_ENST00000452783.2_Intron|SUN1_ENST00000456758.2_Silent_p.P260P			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	202					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)		p.P152P(1)|p.P223P(1)|p.P202P(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CGGCGCACCCCGCGGCCCCCG	0.577													.|||	108	0.0215655	0.0318	0.0303	5008	,	,		14218	0.0		0.0368	False		,,,				2504	0.0082				p.P223P		Atlas-SNP	.											.	SUN1	157	.	3	Substitution - coding silent(3)	lung(3)	c.C669T						PASS	.	C	,,,,	123,3783		3,117,1833	93.0	110.0	105.0		606,,669,606,456	-8.3	0.0	7	dbSNP_132	105	395,7857		5,385,3736	no	coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	SUN1	NM_001130965.2,NM_001171944.1,NM_001171945.1,NM_001171946.1,NM_025154.5	,,,,	8,502,5569	TT,TC,CC		4.7867,3.149,4.2606	,,,,	202/786,,223/279,202/258,152/703	883105	518,11640	1953	4126	6079	SO:0001819	synonymous_variant	23353	exon7			GCACCCCGCGGCC	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.606C>T	7.37:g.883105C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	52	0.619048	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Silent	SNP	ENST00000405266.1	37		54	0.024725274725274724	10	0.02032520325203252	19	0.052486187845303865	0	0.0	25	0.032981530343007916	C	5.914	0.352670	0.11182	0.03149	0.047867	ENSG00000164828	ENST00000419312	T	0.45668	0.89	4.16	-8.32	0.00996	.	0.484707	0.23375	N	0.048878	T	0.07188	0.0182	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.35251	-0.9796	7	0.72032	D	0.01	-0.6632	8.7454	0.34583	0.0929:0.1:0.0927:0.7143	.	.	.	.	L	43	ENSP00000414279:P43L	ENSP00000414279:P43L	P	+	2	0	SUN1	849631	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.997000	0.01470	-2.012000	0.00950	-0.218000	0.12543	CCG	C|0.969;T|0.031	0.031	strong		0.577	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
AHNAK2	113146	hgsc.bcm.edu	37	14	105407208	105407208	+	Silent	SNP	T	T	C	rs11851053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105407208T>C	ENST00000333244.5	-	7	14699	c.14580A>G	c.(14578-14580)gtA>gtG	p.V4860V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4860						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)			TAGGAAAAGATACCTGACCAA	0.493													C|||	2779	0.554912	0.6437	0.5115	5008	,	,		20513	0.4107		0.5338	False		,,,				2504	0.636				p.V4860V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A14580G						PASS	.	C		2565,1247		870,825,211	30.0	31.0	31.0		14580	-0.4	0.0	14	dbSNP_120	31	4484,3794		1234,2016,889	no	coding-synonymous	AHNAK2	NM_138420.2		2104,2841,1100	CC,CT,TT		45.8323,32.7125,41.6956		4860/5796	105407208	7049,5041	1906	4139	6045	SO:0001819	synonymous_variant	113146	exon7			AAAAGATACCTGA	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.14580A>G	14.37:g.105407208T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			T|0.457;C|0.543	0.543	strong		0.493	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SPSB4	92369	hgsc.bcm.edu	37	3	140785175	140785175	+	Silent	SNP	C	C	A	rs890529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	28	0	0		WXS	Illumina HiSeq	Phase_I	35	25	0.714286	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	
IGSF22	283284	hgsc.bcm.edu	37	11	18738281	18738281	+	Missense_Mutation	SNP	C	C	T	rs10766494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18738281C>T	ENST00000513874.1	-	10	1379	c.1240G>A	c.(1240-1242)Gtt>Att	p.V414I	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	414			V -> I (in dbSNP:rs10766494). {ECO:0000269|PubMed:14702039}.							NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TCACGGTCAACAGTGAGCTGG	0.522													T|||	3751	0.749002	0.8298	0.7032	5008	,	,		20180	0.8125		0.7724	False		,,,				2504	0.5828				p.V414I		Atlas-SNP	.											.	IGSF22	211	.	0			c.G1240A						PASS	.	T	ILE/VAL	3124,792		1252,620,86	95.0	93.0	94.0		1240	3.8	0.9	11	dbSNP_120	94	6169,2135		2291,1587,274	yes	missense	IGSF22	NM_173588.3	29	3543,2207,360	TT,TC,CC		25.7105,20.2247,23.9525	benign	414/1327	18738281	9293,2927	1958	4152	6110	SO:0001583	missense	283284	exon10			GGTCAACAGTGAG	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1240G>A	11.37:g.18738281C>T	ENSP00000421191:p.Val414Ile	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	1711	0.7834249084249084	405	0.823170731707317	264	0.7292817679558011	461	0.8059440559440559	581	0.7664907651715039	T	7.426	0.637650	0.14386	0.797753	0.742895	ENSG00000179057	ENST00000513874	T	0.62788	0.0	4.88	3.75	0.43078	.	0.210848	0.23519	N	0.047319	T	0.00012	0.0000	M	0.80183	2.485	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.27571	-1.0070	9	0.37606	T	0.19	.	7.7518	0.28901	0.0:0.1664:0.0:0.8336	rs10766494;rs57990712;rs10766494	414	D6RGV7	.	I	414	ENSP00000421191:V414I	ENSP00000322422:V414I	V	-	1	0	IGSF22	18694857	0.975000	0.34042	0.895000	0.35142	0.719000	0.41307	1.514000	0.35834	0.237000	0.21200	-0.254000	0.11334	GTT	C|0.232;T|0.768	0.768	strong		0.522	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
PKMYT1	9088	hgsc.bcm.edu	37	16	3023185	3023185	+	Missense_Mutation	SNP	G	G	A	rs150931982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3023185G>A	ENST00000262300.8	-	8	1850	c.1342C>T	c.(1342-1344)Cgg>Tgg	p.R448W	PKMYT1_ENST00000440027.2_Silent_p.P460P|PKMYT1_ENST00000571102.1_5'Flank|PAQR4_ENST00000293978.8_3'UTR|PAQR4_ENST00000318782.8_3'UTR|PKMYT1_ENST00000573944.1_Missense_Mutation_p.R439W|PAQR4_ENST00000572687.1_3'UTR|PKMYT1_ENST00000431515.2_Missense_Mutation_p.R448W|PKMYT1_ENST00000574385.1_Missense_Mutation_p.R439W|PKMYT1_ENST00000574730.1_Missense_Mutation_p.R379W	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	448	Interaction with CDC2-CCNB1.|Interaction with PIN1.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						CCCACAGTCCGGGCCAGGACA	0.657													G|||	17	0.00339457	0.0129	0.0	5008	,	,		15724	0.0		0.0	False		,,,				2504	0.0				p.R448W		Atlas-SNP	.											.	PKMYT1	23	.	0			c.C1342T						PASS	.	G	TRP/ARG,,	34,4316		0,34,2141	28.0	27.0	28.0		1342,,1380	2.5	0.8	16	dbSNP_134	28	0,8560		0,0,4280	yes	missense,utr-3,coding-synonymous	PKMYT1,PAQR4	NM_004203.4,NM_152341.3,NM_182687.2	101,,	0,34,6421	AA,AG,GG		0.0,0.7816,0.2634	probably-damaging,,	448/500,,460/481	3023185	34,12876	2175	4280	6455	SO:0001583	missense	9088	exon8			CAGTCCGGGCCAG	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"""membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase"", ""protein phosphatase 1, regulatory subunit 126"""	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.1342C>T	16.37:g.3023185G>A	ENSP00000262300:p.Arg448Trp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_004203	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000262300.8	37	CCDS10486.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	13.73	2.324957	0.41197	0.007816	0.0	ENSG00000127564	ENST00000431515;ENST00000262300;ENST00000402679	T;T	0.62941	-0.01;0.15	4.75	2.47	0.30058	.	0.463681	0.22806	N	0.055404	T	0.41719	0.1171	L	0.32530	0.975	0.80722	D	1	D;D	0.60575	0.988;0.988	P;P	0.52424	0.698;0.698	T	0.53514	-0.8428	10	0.59425	D	0.04	-16.2832	9.4789	0.38889	0.0:0.0:0.6461:0.3539	.	379;448	B4DXD4;Q99640	.;PMYT1_HUMAN	W	448	ENSP00000392855:R448W;ENSP00000262300:R448W	ENSP00000262300:R448W	R	-	1	2	PKMYT1	2963186	0.954000	0.32549	0.808000	0.32385	0.023000	0.10783	1.549000	0.36212	1.104000	0.41587	0.655000	0.94253	CGG	G|0.995;A|0.005	0.005	strong		0.657	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203	
B3GNT7	93010	hgsc.bcm.edu	37	2	232263127	232263127	+	Missense_Mutation	SNP	G	G	A	rs2290130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	174	0	0		WXS	Illumina HiSeq	Phase_I	201	113	0.562189	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	
OR5V1	81696	hgsc.bcm.edu	37	6	29323655	29323655	+	Silent	SNP	G	G	A	rs7761746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29323655G>A	ENST00000377154.1	-	4	617	c.318C>T	c.(316-318)ttC>ttT	p.F106F	OR5V1_ENST00000543825.1_Silent_p.F106F			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	106						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(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ATCCTACAAAGAAAACAAATG	0.423													G|||	314	0.0626997	0.1846	0.049	5008	,	,		21979	0.0139		0.0189	False		,,,				2504	0.0031				p.F106F	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											.	OR5V1	63	.	0			c.C318T						PASS	.	G		789,3617	307.5+/-290.0	69,651,1483	65.0	67.0	67.0		318	2.6	1.0	6	dbSNP_116	67	128,8470	64.2+/-126.4	0,128,4171	no	coding-synonymous	OR5V1	NM_030876.5		69,779,5654	AA,AG,GG		1.4887,17.9074,7.0517		106/322	29323655	917,12087	2203	4299	6502	SO:0001819	synonymous_variant	81696	exon1			TACAAAGAAAACA		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"""GPCR / Class A : Olfactory receptors"""	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.318C>T	6.37:g.29323655G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	105	56	0.533333	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Silent	SNP	ENST00000377154.1	37	CCDS4657.1																																																																																			G|0.926;A|0.074	0.074	strong		0.423	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3		
NTSR2	23620	hgsc.bcm.edu	37	2	11798675	11798675	+	Missense_Mutation	SNP	G	G	A	rs61753869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11798675G>A	ENST00000306928.5	-	4	1197	c.1163C>T	c.(1162-1164)cCg>cTg	p.P388L		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	388					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	CTGGGGCTTCGGGGGTAACCG	0.547													G|||	438	0.0874601	0.3139	0.0317	5008	,	,		18790	0.0		0.001	False		,,,				2504	0.0				p.P388L		Atlas-SNP	.											NTSR2,NS,carcinoma,-1,1	NTSR2	36	1	0			c.C1163T						PASS	.	G	LEU/PRO	1267,3139	432.6+/-343.3	190,887,1126	72.0	76.0	75.0		1163	-8.2	0.0	2	dbSNP_129	75	11,8589	5.7+/-21.5	0,11,4289	yes	missense	NTSR2	NM_012344.3	98	190,898,5415	AA,AG,GG		0.1279,28.7562,9.8262	benign	388/411	11798675	1278,11728	2203	4300	6503	SO:0001583	missense	23620	exon4			GGCTTCGGGGGTA	Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"""GPCR / Class A : Neurotensin receptors"""	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.1163C>T	2.37:g.11798675G>A	ENSP00000303686:p.Pro388Leu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	152	69	0.453947	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Missense_Mutation	SNP	ENST00000306928.5	37	CCDS1681.1	173	0.07921245421245421	161	0.32723577235772355	12	0.03314917127071823	0	0.0	0	0.0	G	3.400	-0.122456	0.06795	0.287562	0.001279	ENSG00000169006	ENST00000306928	T	0.37235	1.21	4.1	-8.2	0.01045	.	15.571800	0.00166	N	0.000000	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	0.13818	-1.0495	9	0.27082	T	0.32	.	2.7725	0.05338	0.0979:0.1785:0.2918:0.4318	.	388	O95665	NTR2_HUMAN	L	388	ENSP00000303686:P388L	ENSP00000303686:P388L	P	-	2	0	NTSR2	11716126	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.423000	0.01030	-3.062000	0.00256	-3.395000	0.00039	CCG	G|0.911;A|0.089	0.089	strong		0.547	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1		
MUC4	4585	hgsc.bcm.edu	37	3	195515079	195515079	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515079G>A	ENST00000463781.3	-	2	3831	c.3372C>T	c.(3370-3372)acC>acT	p.T1124T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T1124T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	563					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)		AGGAAGTGTCGGTGACAGGAA	0.557																																					p.T1124T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C3372T						scavenged	.						12.0	8.0	9.0					3																	195515079		671	1535	2206	SO:0001819	synonymous_variant	4585	exon2			AGTGTCGGTGACA	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.3372C>T	3.37:g.195515079G>A		Somatic	174	4	0.0229885		WXS	Illumina HiSeq	Phase_I	396	15	0.0378788	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																																																																																			.	.	none		0.557	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RASGRF2	5924	hgsc.bcm.edu	37	5	80390736	80390736	+	Silent	SNP	C	C	T	rs34039392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80390736C>T	ENST00000265080.4	+	12	1747	c.1680C>T	c.(1678-1680)gaC>gaT	p.D560D		NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	560	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)			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)		AGCCTCCTGACGCTGCCGCCT	0.463													C|||	296	0.0591054	0.2171	0.0086	5008	,	,		16224	0.0		0.003	False		,,,				2504	0.0				p.D560D		Atlas-SNP	.											.	RASGRF2	165	.	0			c.C1680T						PASS	.	C		740,3666	303.8+/-288.1	64,612,1527	102.0	103.0	102.0		1680	-4.2	0.0	5	dbSNP_126	102	23,8577	15.3+/-51.7	0,23,4277	no	coding-synonymous	RASGRF2	NM_006909.1		64,635,5804	TT,TC,CC		0.2674,16.7953,5.8665		560/1238	80390736	763,12243	2203	4300	6503	SO:0001819	synonymous_variant	5924	exon12			TCCTGACGCTGCC	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.1680C>T	5.37:g.80390736C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_006909	B9EG89|Q9UK56	Silent	SNP	ENST00000265080.4	37	CCDS4052.1																																																																																			C|0.946;T|0.054	0.054	strong		0.463	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909	
NCAN	1463	hgsc.bcm.edu	37	19	19339285	19339285	+	Silent	SNP	G	G	A	rs10406347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19339285G>A	ENST00000252575.6	+	8	2955	c.2856G>A	c.(2854-2856)ccG>ccA	p.P952P	NCAN_ENST00000538881.1_Silent_p.P403P	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	952					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|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)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	CTACGGTACCGTGGGACCCCT	0.642													G|||	197	0.0393371	0.0885	0.0043	5008	,	,		17300	0.0526		0.001	False		,,,				2504	0.0235				p.P952P		Atlas-SNP	.											.	NCAN	277	.	0			c.G2856A						PASS	.	G		325,4081	166.9+/-198.0	9,307,1887	101.0	104.0	103.0		2856	-7.5	0.0	19	dbSNP_119	103	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	NCAN	NM_004386.2		9,311,6183	AA,AG,GG		0.0465,7.3763,2.5296		952/1322	19339285	329,12677	2203	4300	6503	SO:0001819	synonymous_variant	1463	exon8			GGTACCGTGGGAC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.2856G>A	19.37:g.19339285G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_004386	Q9UPK6	Silent	SNP	ENST00000252575.6	37	CCDS12397.1																																																																																			G|0.970;A|0.030	0.030	strong		0.642	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
IGF2R	3482	hgsc.bcm.edu	37	6	160482929	160482929	+	Missense_Mutation	SNP	C	C	G	rs8191844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160482929C>G	ENST00000356956.1	+	25	3699	c.3551C>G	c.(3550-3552)aCc>aGc	p.T1184S		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1184			T -> S (in dbSNP:rs8191844). {ECO:0000269|Ref.5}.		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)	CGCTTCTCCACCAGGATCACG	0.522													C|||	40	0.00798722	0.0287	0.0029	5008	,	,		18416	0.0		0.0	False		,,,				2504	0.0				p.T1184S		Atlas-SNP	.											.	IGF2R	251	.	0			c.C3551G						PASS	.	C	SER/THR	127,4279	93.0+/-131.7	1,125,2077	159.0	148.0	152.0		3551	5.5	1.0	6	dbSNP_117	152	0,8600		0,0,4300	yes	missense	IGF2R	NM_000876.2	58	1,125,6377	GG,GC,CC		0.0,2.8824,0.9765	probably-damaging	1184/2492	160482929	127,12879	2203	4300	6503	SO:0001583	missense	3482	exon25			TCTCCACCAGGAT	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.3551C>G	6.37:g.160482929C>G	ENSP00000349437:p.Thr1184Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	23.0	4.365286	0.82463	0.028824	0.0	ENSG00000197081	ENST00000356956	T	0.04275	3.66	5.5	5.5	0.81552	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.14270	0.0345	M	0.75615	2.305	0.52501	D	0.999957	D	0.89917	1.0	D	0.87578	0.998	T	0.01810	-1.1269	10	0.32370	T	0.25	-13.6676	17.5389	0.87841	0.0:1.0:0.0:0.0	rs8191844;rs52837912;rs8191844	1184	P11717	MPRI_HUMAN	S	1184	ENSP00000349437:T1184S	ENSP00000349437:T1184S	T	+	2	0	IGF2R	160402919	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.514000	0.67043	2.735000	0.93741	0.655000	0.94253	ACC	C|0.991;G|0.009	0.009	strong		0.522	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
TAS2R50	259296	hgsc.bcm.edu	37	12	11138852	11138852	+	Missense_Mutation	SNP	C	C	T	rs1376251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11138852C>T	ENST00000506868.1	-	1	659	c.608G>A	c.(607-609)tGt>tAt	p.C203Y	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	203			C -> Y (in dbSNP:rs1376251). {ECO:0000269|PubMed:12379855}.		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						GAGATGTTTACACAGAGAACA	0.413													C|||	2055	0.410343	0.056	0.3775	5008	,	,		20640	0.755		0.3579	False		,,,				2504	0.6115				p.C203Y		Atlas-SNP	.											.	TAS2R50	37	.	0			c.G608A	GRCh37	CM053427	TAS2R50	M	rs1376251	PASS	.	C	TYR/CYS	420,3986	204.8+/-226.9	20,380,1803	140.0	132.0	135.0		608	1.2	0.1	12	dbSNP_88	135	2878,5722	451.3+/-362.6	495,1888,1917	yes	missense	TAS2R50	NM_176890.2	194	515,2268,3720	TT,TC,CC		33.4651,9.5325,25.3575	benign	203/300	11138852	3298,9708	2203	4300	6503	SO:0001583	missense	259296	exon1			TGTTTACACAGAG	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.608G>A	12.37:g.11138852C>T	ENSP00000424040:p.Cys203Tyr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	139	61	0.438849	NM_176890	P59545|Q2M255|Q645Y0	Missense_Mutation	SNP	ENST00000506868.1	37	CCDS8638.1	868	0.3974358974358974	26	0.052845528455284556	150	0.4143646408839779	426	0.7447552447552448	266	0.35092348284960423	C	7.954	0.745525	0.15710	0.095325	0.334651	ENSG00000212126	ENST00000506868	T	0.36520	1.25	2.19	1.22	0.21188	.	0.531082	0.16393	U	0.216373	T	0.00012	0.0000	M	0.86028	2.79	0.58432	P	1.0000000000287557E-6	B	0.19583	0.037	B	0.27608	0.081	T	0.26985	-1.0087	9	0.27785	T	0.31	.	7.5054	0.27542	0.2586:0.7414:0.0:0.0	rs1376251;rs52810970;rs57200136;rs1376251	203	P59544	T2R50_HUMAN	Y	203	ENSP00000424040:C203Y	ENSP00000424040:C203Y	C	-	2	0	TAS2R50	11030119	0.336000	0.24757	0.078000	0.20375	0.492000	0.33523	1.588000	0.36633	0.217000	0.20800	0.313000	0.20887	TGT	C|0.687;A|0.002	.	strong		0.413	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890	
GIPC3	126326	hgsc.bcm.edu	37	19	3586543	3586543	+	Silent	SNP	G	G	A	rs8113232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3586543G>A	ENST00000322315.5	+	2	321	c.276G>A	c.(274-276)ctG>ctA	p.L92L		NM_133261.2	NP_573568.1	Q8TF64	GIPC3_HUMAN	GIPC PDZ domain containing family, member 3	92										breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)		AGAAGCTCCTGGGGGGTCAGA	0.577											OREG0025154	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1136	0.226837	0.5643	0.1066	5008	,	,		14480	0.0367		0.1392	False		,,,				2504	0.1421				p.L92L		Atlas-SNP	.											.	GIPC3	27	.	0			c.G276A						PASS	.	A		2272,2134	576.6+/-384.3	581,1110,512	76.0	77.0	76.0		276	1.3	1.0	19	dbSNP_116	76	1105,7495	766.9+/-407.6	75,955,3270	no	coding-synonymous	GIPC3	NM_133261.2		656,2065,3782	AA,AG,GG		12.8488,48.434,25.9649		92/313	3586543	3377,9629	2203	4300	6503	SO:0001819	synonymous_variant	126326	exon2			GCTCCTGGGGGGT	AB073738	CCDS32871.1	19p13.3	2011-11-29				ENSG00000179855			18183	protein-coding gene	gene with protein product		608792	"""chromosome 19 open reading frame 64"", ""deafness, autosomal recessive 72"", ""deafness, autosomal recessive 15"""	C19orf64, DFNB72, DFNB15		11836571, 21326233	Standard	NM_133261		Approved	DFNB95	uc002lyd.4	Q8TF64		ENST00000322315.5:c.276G>A	19.37:g.3586543G>A		Somatic	120	0	0	612	WXS	Illumina HiSeq	Phase_I	118	118	1	NM_133261	O75227	Silent	SNP	ENST00000322315.5	37	CCDS32871.1																																																																																			G|0.758;A|0.242	0.242	strong		0.577	GIPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394577.1	NM_133261	
SKA1	220134	hgsc.bcm.edu	37	18	47911631	47911631	+	Silent	SNP	A	A	G	rs11538068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47911631A>G	ENST00000285116.3	+	5	568	c.357A>G	c.(355-357)gaA>gaG	p.E119E	SKA1_ENST00000417656.2_Intron|SKA1_ENST00000488454.1_Intron|SKA1_ENST00000398452.2_Silent_p.E119E	NM_001039535.2|NM_145060.3	NP_001034624.1|NP_659497.1	Q96BD8	SKA1_HUMAN	spindle and kinetochore associated complex subunit 1	119					cell division (GO:0051301)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|spindle microtubule (GO:0005876)	microtubule binding (GO:0008017)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(1)|prostate(1)	13						TCAAAGTTGAAGAACCTGAAC	0.373													G|||	427	0.0852636	0.2383	0.0245	5008	,	,		16172	0.0794		0.0129	False		,,,				2504	0.002				p.E119E		Atlas-SNP	.											.	SKA1	21	.	0			c.A357G						PASS	.	G	,	869,3537	743.6+/-411.5	80,709,1414	139.0	144.0	142.0		357,357	1.2	0.6	18	dbSNP_120	142	14,8586	818.7+/-406.8	0,14,4286	no	coding-synonymous,coding-synonymous	SKA1	NM_001039535.2,NM_145060.3	,	80,723,5700	GG,GA,AA		0.1628,19.7231,6.7892	,	119/256,119/256	47911631	883,12123	2203	4300	6503	SO:0001819	synonymous_variant	220134	exon5			AGTTGAAGAACCT	BC015706	CCDS11946.1	18q21.1	2013-01-17	2009-08-19	2009-08-19	ENSG00000154839	ENSG00000154839			28109	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 24"""	C18orf24		17093495	Standard	NM_145060		Approved	MGC10200	uc002leu.3	Q96BD8	OTTHUMG00000132685	ENST00000285116.3:c.357A>G	18.37:g.47911631A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	82	25	0.304878	NM_001039535	B2R9Y6|B4E0P4	Silent	SNP	ENST00000285116.3	37	CCDS11946.1																																																																																			A|0.920;G|0.080	0.080	strong		0.373	SKA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255982.2	NM_145060	
DNAH5	1767	hgsc.bcm.edu	37	5	13841066	13841066	+	Silent	SNP	G	G	A	rs6880264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13841066G>A	ENST00000265104.4	-	34	5762	c.5658C>T	c.(5656-5658)taC>taT	p.Y1886Y		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1886	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)					TCAGAGTCTCGTATTTCACTC	0.388									Kartagener syndrome				G|||	74	0.0147764	0.0545	0.0029	5008	,	,		19415	0.0		0.0	False		,,,				2504	0.0				p.Y1886Y		Atlas-SNP	.											.	DNAH5	868	.	0			c.C5658T						PASS	.	G		192,4214	122.9+/-160.3	2,188,2013	149.0	136.0	141.0		5658	-2.4	1.0	5	dbSNP_116	141	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	DNAH5	NM_001369.2		2,191,6310	AA,AG,GG		0.0349,4.3577,1.4993		1886/4625	13841066	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon34	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGTCTCGTATTTC	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.5658C>T	5.37:g.13841066G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	141	63	0.446809	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			G|0.985;A|0.015	0.015	strong		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
GAL3ST4	79690	hgsc.bcm.edu	37	7	99758136	99758136	+	Silent	SNP	T	T	G	rs3800951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99758136T>G	ENST00000360039.4	-	4	1268	c.876A>C	c.(874-876)gcA>gcC	p.A292A	GAL3ST4_ENST00000411994.1_Missense_Mutation_p.H191P|C7orf43_ENST00000457641.1_5'Flank|C7orf43_ENST00000316937.3_5'Flank|GAL3ST4_ENST00000413800.1_Silent_p.A292A|C7orf43_ENST00000419841.1_5'Flank|GAL3ST4_ENST00000423751.1_Missense_Mutation_p.H191P|GAL3ST4_ENST00000426974.2_Silent_p.A230A	NM_024637.4	NP_078913.3	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	292					cell-cell signaling (GO:0007267)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(5)|prostate(1)|upper_aerodigestive_tract(1)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGTCCAGCCATGCCAGACCCC	0.527													G|||	2721	0.543331	0.4622	0.4366	5008	,	,		20997	0.6438		0.5606	False		,,,				2504	0.6074				p.A292A		Atlas-SNP	.											.	GAL3ST4	59	.	0			c.A876C						PASS	.	G		2219,2187		551,1117,535	97.0	89.0	92.0		876	0.7	1.0	7	dbSNP_107	92	4919,3681		1421,2077,802	no	coding-synonymous	GAL3ST4	NM_024637.4		1972,3194,1337	GG,GT,TT		42.8023,49.6369,45.1176		292/487	99758136	7138,5868	2203	4300	6503	SO:0001819	synonymous_variant	79690	exon4			CAGCCATGCCAGA	AF316113	CCDS5688.1	7q22.1	2007-04-02			ENSG00000197093	ENSG00000197093		"""Sulfotransferases, membrane-bound"""	24145	protein-coding gene	gene with protein product		608235				11333265	Standard	NM_024637		Approved	FLJ12116	uc003utu.3	Q96RP7	OTTHUMG00000154885	ENST00000360039.4:c.876A>C	7.37:g.99758136T>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_024637	A4D2A8|B4DWL8|D6W5U5|Q8N3P7|Q8WZ17|Q96E33|Q9HA78	Silent	SNP	ENST00000360039.4	37	CCDS5688.1	1132	0.5183150183150184	204	0.4146341463414634	155	0.4281767955801105	343	0.5996503496503497	430	0.5672823218997362	G	9.010	0.982263	0.18889	0.503631	0.571977	ENSG00000197093	ENST00000423751;ENST00000411994	.	.	.	4.82	0.712	0.18167	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999823277	.	.	.	.	.	.	T	0.43877	-0.9364	4	0.87932	D	0	-9.2138	3.645	0.08181	0.269:0.0:0.4415:0.2895	rs3800951;rs17845360;rs17858211;rs56997718;rs3800951	.	.	.	P	191	.	ENSP00000414733:H191P	H	-	2	0	GAL3ST4	99596072	0.108000	0.22018	0.991000	0.47740	0.906000	0.53458	-0.016000	0.12613	-0.279000	0.09167	-0.285000	0.09966	CAT	T|0.464;G|0.536	0.536	strong		0.527	GAL3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337495.2	NM_024637	
OR10G3	26533	hgsc.bcm.edu	37	14	22038525	22038525	+	Silent	SNP	G	G	T	rs11626693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	142	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	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		
MUC16	94025	hgsc.bcm.edu	37	19	9063594	9063594	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9063594C>T	ENST00000397910.4	-	3	24055	c.23852G>A	c.(23851-23853)aGg>aAg	p.R7951K		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7953	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						AGGACCCCTCCTCATAAGAGT	0.463																																					p.R7951K		Atlas-SNP	.											MUC16_ENST00000397910,bladder,carcinoma,-1,3	MUC16	4315	3	0			c.G23852A						scavenged	.						137.0	128.0	130.0					19																	9063594		1977	4160	6137	SO:0001583	missense	94025	exon3			CCCCTCCTCATAA	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.23852G>A	19.37:g.9063594C>T	ENSP00000381008:p.Arg7951Lys	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	197	3	0.0152284	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	5.652	0.304911	0.10678	.	.	ENSG00000181143	ENST00000397910	T	0.21031	2.03	2.67	-2.99	0.05497	.	.	.	.	.	T	0.08846	0.0219	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.25779	-1.0122	8	0.87932	D	0	.	4.1679	0.10315	0.1632:0.4799:0.0:0.3569	.	7951	B5ME49	.	K	7951	ENSP00000381008:R7951K	ENSP00000381008:R7951K	R	-	2	0	MUC16	8924594	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.984000	0.03755	-0.888000	0.03956	-1.509000	0.00949	AGG	.	.	none		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LRRFIP2	9209	hgsc.bcm.edu	37	3	37154417	37154417	+	Missense_Mutation	SNP	T	T	C	rs34902788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37154417T>C	ENST00000336686.4	-	8	507	c.427A>G	c.(427-429)Aaa>Gaa	p.K143E	LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.K143E|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000396428.2_Missense_Mutation_p.K112E|LRRFIP2_ENST00000354379.4_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	143	DVL3-binding.|Ser-rich.		K -> E (in dbSNP:rs34902788).		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						AGTAGGTCTTTATGAGAATCA	0.368													T|||	72	0.014377	0.0514	0.0058	5008	,	,		18111	0.0		0.0	False		,,,				2504	0.0				p.K143E		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.A427G						PASS	.	T	,GLU/LYS,	190,4216	120.4+/-158.0	7,176,2020	128.0	128.0	128.0		,427,	4.3	1.0	3	dbSNP_126	128	2,8598	1.2+/-3.3	0,2,4298	yes	intron,missense,intron	LRRFIP2	NM_001134369.1,NM_006309.2,NM_017724.2	,56,	7,178,6318	CC,CT,TT		0.0233,4.3123,1.4762	,possibly-damaging,	,143/722,	37154417	192,12814	2203	4300	6503	SO:0001583	missense	9209	exon9			GGTCTTTATGAGA	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.427A>G	3.37:g.37154417T>C	ENSP00000338727:p.Lys143Glu	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	46	16	0.347826	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	T	10.81	1.454776	0.26161	0.043123	2.33E-4	ENSG00000093167	ENST00000421307;ENST00000336686;ENST00000396428	T;T;T	0.48201	0.82;0.82;0.87	5.52	4.29	0.51040	.	0.266541	0.34959	N	0.003544	T	0.06554	0.0168	N	0.08118	0	0.29065	N	0.883669	B;B	0.27853	0.076;0.191	B;B	0.28465	0.077;0.09	T	0.04153	-1.0973	10	0.12766	T	0.61	-16.635	12.8465	0.57833	0.0:0.0:0.1352:0.8648	rs34902788	112;143	A8MXR0;Q9Y608	.;LRRF2_HUMAN	E	143;143;112	ENSP00000392217:K143E;ENSP00000338727:K143E;ENSP00000379705:K112E	ENSP00000338727:K143E	K	-	1	0	LRRFIP2	37129421	1.000000	0.71417	0.981000	0.43875	0.935000	0.57460	3.954000	0.56708	2.232000	0.73038	0.482000	0.46254	AAA	T|0.987;C|0.013	0.013	strong		0.368	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	
ATP2A3	489	hgsc.bcm.edu	37	17	3839685	3839685	+	Silent	SNP	G	G	A	rs1062683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3839685G>A	ENST00000352011.3	-	16	2454	c.2400C>T	c.(2398-2400)gaC>gaT	p.D800D	ATP2A3_ENST00000397041.3_Silent_p.D800D|ATP2A3_ENST00000397043.3_Silent_p.D800D|ATP2A3_ENST00000309890.7_Silent_p.D800D|ATP2A3_ENST00000397035.3_Silent_p.D800D|ATP2A3_ENST00000397039.1_De_novo_Start_OutOfFrame|ATP2A3_ENST00000359983.3_Silent_p.D800D			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	800					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		CAGGTAGGCCGTCTGTCACCA	0.622													G|||	849	0.169529	0.2194	0.1585	5008	,	,		17621	0.0655		0.1918	False		,,,				2504	0.1943				p.D800D	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.C2400T						PASS	.	G	,,,,,,	946,3460	360.9+/-315.4	98,750,1355	78.0	80.0	79.0		2400,2400,2400,2400,2400,2400,2400	0.7	1.0	17	dbSNP_86	79	1710,6890	312.5+/-310.9	156,1398,2746	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	254,2148,4101	AA,AG,GG		19.8837,21.4707,20.4213	,,,,,,	800/1000,800/1053,800/1045,800/1044,800/1030,800/999,800/1030	3839685	2656,10350	2203	4300	6503	SO:0001819	synonymous_variant	489	exon16			TAGGCCGTCTGTC		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.2400C>T	17.37:g.3839685G>A		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	233	134	0.575107	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			T|0.000;G|0.815;C|0.000;A|0.184	0.184	strong		0.622	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
PDIA6	10130	hgsc.bcm.edu	37	2	10933249	10933249	+	Silent	SNP	C	C	T	rs4799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10933249C>T	ENST00000272227.3	-	5	573	c.426G>A	c.(424-426)cgG>cgA	p.R142R	PDIA6_ENST00000381611.4_Silent_p.R147R|PDIA6_ENST00000404371.2_Silent_p.R194R|PDIA6_ENST00000404824.2_Silent_p.R190R|PDIA6_ENST00000540494.1_Silent_p.R139R	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	142					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)		ATCCTCCGCTCCGTCCCCCGA	0.483													C|||	1934	0.386182	0.1619	0.4784	5008	,	,		18105	0.4583		0.4781	False		,,,				2504	0.455				p.R142R	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											.	PDIA6	31	.	0			c.G426A						PASS	.	C		947,3459	358.4+/-314.3	118,711,1374	102.0	93.0	96.0		426	1.5	0.0	2	dbSNP_52	96	4355,4245	581.0+/-391.2	1093,2169,1038	no	coding-synonymous	PDIA6	NM_005742.2		1211,2880,2412	TT,TC,CC		49.3605,21.4934,40.7658		142/441	10933249	5302,7704	2203	4300	6503	SO:0001819	synonymous_variant	10130	exon5			TCCGCTCCGTCCC	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.426G>A	2.37:g.10933249C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	165	76	0.460606	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	37	CCDS1675.1																																																																																			C|0.592;T|0.408	0.408	strong		0.483	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742	
C9orf135	138255	hgsc.bcm.edu	37	9	72472831	72472831	+	Silent	SNP	C	C	T	rs10780682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:72472831C>T	ENST00000377197.3	+	4	474	c.387C>T	c.(385-387)acC>acT	p.T129T	C9orf135_ENST00000466872.2_3'UTR|C9orf135_ENST00000527647.1_Silent_p.T129T	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	71	0	0		WXS	Illumina HiSeq	Phase_I	57	13	0.22807	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	
DSG1	1828	hgsc.bcm.edu	37	18	28919884	28919884	+	Missense_Mutation	SNP	A	A	C	rs16961689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28919884A>C	ENST00000257192.4	+	11	1795	c.1583A>C	c.(1582-1584)tAt>tCt	p.Y528S		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	528			Y -> S (in dbSNP:rs16961689).		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)			AGCCAAGTATATTCTTCTGAA	0.418													T|||	745	0.148762	0.2428	0.0994	5008	,	,		16518	0.0645		0.0845	False		,,,				2504	0.2096				p.Y528S		Atlas-SNP	.											.	DSG1	176	.	0			c.A1583C						PASS	.	T	SER/TYR	790,3616		73,644,1486	112.0	112.0	112.0		1583	-7.3	0.0	18	dbSNP_123	112	613,7987		29,555,3716	yes	missense	DSG1	NM_001942.2	144	102,1199,5202	CC,CA,AA		7.1279,17.9301,10.7873	benign	528/1050	28919884	1403,11603	2203	4300	6503	SO:0001583	missense	1828	exon11			AAGTATATTCTTC	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.1583A>C	18.37:g.28919884A>C	ENSP00000257192:p.Tyr528Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	252	0.11538461538461539	120	0.24390243902439024	40	0.11049723756906077	34	0.05944055944055944	58	0.07651715039577836	T	0	-2.792046	0.00077	0.179301	0.071279	ENSG00000134760	ENST00000257192	T	0.56103	0.48	3.66	-7.33	0.01431	.	64.773800	0.00166	N	0.000000	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	0.14868	-1.0457	9	0.45353	T	0.12	.	0.6084	0.00757	0.3335:0.2049:0.266:0.1956	rs16961689;rs52817095;rs16961689	528	Q02413	DSG1_HUMAN	S	528	ENSP00000257192:Y528S	ENSP00000257192:Y528S	Y	+	2	0	DSG1	27173882	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.182000	0.01256	-4.536000	0.00043	-5.634000	0.00000	TAT	A|0.885;C|0.115	0.115	strong		0.418	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
NR1D1	9572	hgsc.bcm.edu	37	17	38253469	38253469	+	Silent	SNP	G	G	A	rs9905506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38253469G>A	ENST00000246672.3	-	2	849	c.219C>T	c.(217-219)ccC>ccT	p.P73P		NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	73	Crucial for activation of GJA1. {ECO:0000250}.|Modulating.				cell differentiation (GO:0030154)|cellular response to lipopolysaccharide (GO:0071222)|circadian regulation of gene expression (GO:0032922)|circadian temperature homeostasis (GO:0060086)|gene expression (GO:0010467)|glycogen biosynthetic process (GO:0005978)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of bile acid biosynthetic process (GO:0070859)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasomal protein catabolic process (GO:0010498)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of lipid metabolic process (GO:0019216)|regulation of type B pancreatic cell proliferation (GO:0061469)|response to leptin (GO:0044321)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|heme binding (GO:0020037)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|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)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|transcription corepressor binding (GO:0001222)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	11	Colorectal(19;0.000442)					CACTCAGGCTGGGTGGAATGC	0.607													G|||	123	0.0245607	0.0908	0.0043	5008	,	,		18042	0.0		0.0	False		,,,				2504	0.0				p.P73P		Atlas-SNP	.											.	NR1D1	45	.	0			c.C219T						PASS	.	G		290,4116	160.3+/-192.7	5,280,1918	75.0	76.0	76.0		219	1.6	1.0	17	dbSNP_119	76	0,8600		0,0,4300	no	coding-synonymous	NR1D1	NM_021724.3		5,280,6218	AA,AG,GG		0.0,6.5819,2.2297		73/615	38253469	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	9572	exon2			CAGGCTGGGTGGA	X72631	CCDS11361.1	17q11.2	2013-01-16			ENSG00000126368	ENSG00000126368		"""Nuclear hormone receptors"""	7962	protein-coding gene	gene with protein product		602408		THRAL		1971514	Standard	NM_021724		Approved	ear-1, hRev, Rev-ErbAalpha, THRA1	uc002htz.3	P20393	OTTHUMG00000133327	ENST00000246672.3:c.219C>T	17.37:g.38253469G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	176	84	0.477273	NM_021724	Q0P5Z4|Q15304	Silent	SNP	ENST00000246672.3	37	CCDS11361.1																																																																																			G|0.979;A|0.021	0.021	strong		0.607	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1		
PAK2	5062	hgsc.bcm.edu	37	3	196544948	196544948	+	Silent	SNP	T	T	C	rs56172538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196544948T>C	ENST00000327134.3	+	12	1396	c.1074T>C	c.(1072-1074)ttT>ttC	p.F358F		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	358	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		CATTGGAGTTTTTACATGCTA	0.398													T|||	494	0.0986422	0.2844	0.0519	5008	,	,		15485	0.0		0.0378	False		,,,				2504	0.045				p.F358F		Atlas-SNP	.											.	PAK2	113	.	0			c.T1074C						PASS	.	T		1136,3270	405.5+/-333.5	142,852,1209	116.0	103.0	107.0		1074	5.8	1.0	3	dbSNP_129	107	382,8218	123.8+/-182.6	12,358,3930	no	coding-synonymous	PAK2	NM_002577.4		154,1210,5139	CC,CT,TT		4.4419,25.783,11.6715		358/525	196544948	1518,11488	2203	4300	6503	SO:0001819	synonymous_variant	5062	exon12			GGAGTTTTTACAT	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.1074T>C	3.37:g.196544948T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1	160	0.07326007326007326	116	0.23577235772357724	17	0.04696132596685083	0	0.0	27	0.03562005277044855	T	10.14	1.268826	0.23136	0.25783	0.044419	ENSG00000180370	ENST00000426668	T	0.68025	-0.3	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.39981	-0.9587	6	0.66056	D	0.02	.	6.417	0.21721	0.0:0.1886:0.0:0.8114	rs56172538;rs61735863	.	.	.	S	101	ENSP00000402927:F101S	ENSP00000402927:F101S	F	+	2	0	PAK2	198029345	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.134000	0.31442	2.326000	0.78906	0.533000	0.62120	TTT	T|0.896;C|0.104	0.104	strong		0.398	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
POLD1	5424	hgsc.bcm.edu	37	19	50905762	50905762	+	Silent	SNP	T	T	C	rs1143666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50905762T>C	ENST00000440232.2	+	7	863	c.810T>C	c.(808-810)gcT>gcC	p.A270A	POLD1_ENST00000599857.1_Silent_p.A270A|POLD1_ENST00000595904.1_Silent_p.A270A	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	270					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		AGCTCCCAGCTGGGAAATACG	0.672								DNA polymerases (catalytic subunits)					C|||	693	0.138379	0.4418	0.0605	5008	,	,		14079	0.006		0.004	False		,,,				2504	0.0583				p.A270A		Atlas-SNP	.											.	POLD1	174	.	0			c.T810C						PASS	.	C		1617,2777		305,1007,885	20.0	20.0	20.0		810	-5.7	0.0	19	dbSNP_86	20	22,8574		1,20,4277	no	coding-synonymous	POLD1	NM_002691.2		306,1027,5162	CC,CT,TT		0.2559,36.8002,12.6174		270/1108	50905762	1639,11351	2197	4298	6495	SO:0001819	synonymous_variant	5424	exon7			CCCAGCTGGGAAA		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.810T>C	19.37:g.50905762T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	144	67	0.465278	NM_002691	Q8NER3|Q96H98	Silent	SNP	ENST00000440232.2	37	CCDS12795.1																																																																																			T|0.880;C|0.120	0.120	strong		0.672	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
MEGF6	1953	hgsc.bcm.edu	37	1	3413868	3413868	+	Missense_Mutation	SNP	C	C	G	rs4648506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	32	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	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	
DDX51	317781	hgsc.bcm.edu	37	12	132625884	132625884	+	Missense_Mutation	SNP	C	C	T	rs142395492	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132625884C>T	ENST00000397333.3	-	8	1224	c.1186G>A	c.(1186-1188)Gag>Aag	p.E396K		NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	396	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		GCGGGGTCCTCGCTCTGGAAG	0.682													C|||	46	0.0091853	0.0318	0.0043	5008	,	,		14725	0.0		0.001	False		,,,				2504	0.0				p.E396K		Atlas-SNP	.											.	DDX51	33	.	0			c.G1186A						PASS	.	C	LYS/GLU	117,3883		6,105,1889	43.0	54.0	51.0		1186	1.9	0.0	12	dbSNP_134	51	5,8245		0,5,4120	no	missense	DDX51	NM_175066.3	56	6,110,6009	TT,TC,CC		0.0606,2.925,0.9959	benign	396/667	132625884	122,12128	2000	4125	6125	SO:0001583	missense	317781	exon8			GGTCCTCGCTCTG	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"""DEAD-boxes"""	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.1186G>A	12.37:g.132625884C>T	ENSP00000380495:p.Glu396Lys	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	28	18	0.642857	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	37	CCDS41865.1	18	0.008241758241758242	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	11.56	1.674865	0.29783	0.02925	6.06E-4	ENSG00000185163	ENST00000397333	T	0.12255	2.7	4.79	1.92	0.25849	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.770658	0.12492	N	0.464146	T	0.01661	0.0053	N	0.08118	0	0.09310	N	1	B	0.24721	0.11	B	0.20184	0.028	T	0.44221	-0.9342	10	0.14252	T	0.57	-14.9068	5.9048	0.18986	0.0:0.6566:0.1608:0.1826	.	396	Q8N8A6	DDX51_HUMAN	K	396	ENSP00000380495:E396K	ENSP00000380495:E396K	E	-	1	0	DDX51	131191837	0.000000	0.05858	0.005000	0.12908	0.004000	0.04260	0.982000	0.29539	0.438000	0.26450	-0.229000	0.12294	GAG	C|0.992;T|0.008	0.008	strong		0.682	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
DYNC1I1	1780	hgsc.bcm.edu	37	7	95499234	95499234	+	Silent	SNP	A	A	G	rs3757697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:95499234A>G	ENST00000324972.6	+	6	658	c.465A>G	c.(463-465)caA>caG	p.Q155Q	DYNC1I1_ENST00000537881.1_Silent_p.Q118Q|DYNC1I1_ENST00000457059.1_Silent_p.Q138Q|DYNC1I1_ENST00000447467.2_Silent_p.Q138Q|DYNC1I1_ENST00000437599.1_Silent_p.Q135Q|DYNC1I1_ENST00000359388.4_Silent_p.Q118Q	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	155					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			AGGTCACCCAAGTGGATTTCC	0.458													a|||	609	0.121605	0.1104	0.0865	5008	,	,		20328	0.121		0.0805	False		,,,				2504	0.2045				p.Q155Q		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.A465G						PASS	.	G	,,	492,3914	228.1+/-243.1	18,456,1729	140.0	126.0	130.0		414,354,465	-2.5	1.0	7	dbSNP_107	130	857,7743	194.9+/-240.2	37,783,3480	no	coding-synonymous,coding-synonymous,coding-synonymous	DYNC1I1	NM_001135556.1,NM_001135557.1,NM_004411.4	,,	55,1239,5209	GG,GA,AA		9.9651,11.1666,10.3721	,,	138/629,118/609,155/646	95499234	1349,11657	2203	4300	6503	SO:0001819	synonymous_variant	1780	exon6			CACCCAAGTGGAT	AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"""Cytoplasmic dyneins"", ""WD repeat domain containing"""	2963	protein-coding gene	gene with protein product		603772	"""dynein, cytoplasmic, intermediate polypeptide 1"""	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.465A>G	7.37:g.95499234A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	139	68	0.489209	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Silent	SNP	ENST00000324972.6	37	CCDS5644.1																																																																																			A|0.899;G|0.101	0.101	strong		0.458	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411	
NCAM2	4685	hgsc.bcm.edu	37	21	22790831	22790831	+	Silent	SNP	T	T	C	rs986371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:22790831T>C	ENST00000400546.1	+	11	1671	c.1422T>C	c.(1420-1422)aaT>aaC	p.N474N	NCAM2_ENST00000284894.7_Silent_p.N332N	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	474	Ig-like C2-type 5.				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)		GACGCTATAATTGCACAGCCA	0.299													T|||	30	0.00599042	0.0204	0.0043	5008	,	,		16315	0.0		0.0	False		,,,				2504	0.0				p.N474N		Atlas-SNP	.											.	NCAM2	220	.	0			c.T1422C						PASS	.	T		102,3546		0,102,1722	110.0	109.0	109.0		1422	-3.3	1.0	21	dbSNP_86	109	0,8166		0,0,4083	no	coding-synonymous	NCAM2	NM_004540.3		0,102,5805	CC,CT,TT		0.0,2.7961,0.8634		474/838	22790831	102,11712	1824	4083	5907	SO:0001819	synonymous_variant	4685	exon11			CTATAATTGCACA		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.1422T>C	21.37:g.22790831T>C		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	290	139	0.47931	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Silent	SNP	ENST00000400546.1	37	CCDS42910.1																																																																																			T|0.992;C|0.008	0.008	strong		0.299	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540	
AHCTF1	25909	hgsc.bcm.edu	37	1	247021085	247021085	+	Silent	SNP	G	G	C	rs41308162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247021085G>C	ENST00000391829.2	-	30	4287	c.4164C>G	c.(4162-4164)ctC>ctG	p.L1388L	AHCTF1_ENST00000326225.3_Silent_p.L1397L|AHCTF1_ENST00000366508.1_Silent_p.L1423L|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1388	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				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)			CTGCAACTAAGAGATCCTTTG	0.343													G|||	913	0.182308	0.4728	0.0821	5008	,	,		17161	0.0079		0.0875	False		,,,				2504	0.138				p.L1397L	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											AHCTF1,NS,carcinoma,0,1	AHCTF1	187	1	0			c.C4191G						PASS	.	G		1838,2568	522.5+/-370.8	388,1062,753	61.0	62.0	62.0		4191	2.3	0.0	1	dbSNP_127	62	738,7862	178.5+/-227.8	32,674,3594	no	coding-synonymous	AHCTF1	NM_015446.4		420,1736,4347	CC,CG,GG		8.5814,41.7158,19.8062		1397/2276	247021085	2576,10430	2203	4300	6503	SO:0001819	synonymous_variant	25909	exon30			AACTAAGAGATCC		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.4164C>G	1.37:g.247021085G>C		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	258	118	0.457364	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	37																																																																																				G|0.826;C|0.174	0.174	strong		0.343	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
CEACAM20	125931	hgsc.bcm.edu	37	19	45029208	45029208	+	RNA	SNP	G	G	A	rs10408247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45029208G>A	ENST00000454753.1	-	0	400							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				ACTTTGGGTGGCATCAAGTGG	0.567													G|||	1455	0.290535	0.6445	0.2911	5008	,	,		18869	0.1815		0.0765	False		,,,				2504	0.1442				p.A41V		Atlas-SNP	.											.	CEACAM20	31	.	0			c.C122T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	2132,2024		560,1012,506	115.0	123.0	120.0		122,122,122,122	0.0	0.0	19	dbSNP_119	120	731,7695		31,669,3513	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	64,64,64,64	591,1681,4019	AA,AG,GG		8.6755,48.7007,22.7547	benign,benign,benign,benign	41/597,41/492,41/504,41/585	45029208	2863,9719	2078	4213	6291			125931	exon2			TGGGTGGCATCAA	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45029208G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	165	164	0.993939	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				G|0.725;A|0.275	0.275	strong		0.567	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
KIAA1211	57482	hgsc.bcm.edu	37	4	57180563	57180563	+	Missense_Mutation	SNP	G	G	C	rs59615456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57180563G>C	ENST00000504228.1	+	6	1000	c.895G>C	c.(895-897)Ggt>Cgt	p.G299R	KIAA1211_ENST00000264229.6_Missense_Mutation_p.G299R|KIAA1211_ENST00000541073.1_Missense_Mutation_p.G292R			Q6ZU35	K1211_HUMAN	KIAA1211	299	Glu-rich.			G -> R (in Ref. 2; BAC86392). {ECO:0000305}.						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)					GGAAGCGCCAGGTTGGGAGGA	0.716													G|||	1138	0.227236	0.1505	0.2262	5008	,	,		13699	0.2589		0.3429	False		,,,				2504	0.18				p.G299R		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G895C						PASS	.	G	ARG/GLY	622,3124		63,496,1314	5.0	7.0	7.0		895	0.0	0.0	4	dbSNP_129	7	2434,5116		429,1576,1770	no	missense	KIAA1211	NM_020722.1	125	492,2072,3084	CC,CG,GG		32.2384,16.6044,27.0538	benign	299/1234	57180563	3056,8240	1873	3775	5648	SO:0001583	missense	57482	exon8			GCGCCAGGTTGGG	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.895G>C	4.37:g.57180563G>C	ENSP00000423366:p.Gly299Arg	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	571	0.26144688644688646	75	0.1524390243902439	91	0.2513812154696133	148	0.25874125874125875	257	0.3390501319261214	G	7.864	0.726788	0.15439	0.166044	0.322384	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.11063	2.82;2.82;2.81	4.58	0.0276	0.14155	.	.	.	.	.	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B;B	0.11235	0.004;0.004	B;B	0.14578	0.011;0.011	T	0.42732	-0.9434	8	0.36615	T	0.2	-0.8935	3.6126	0.08066	0.4628:0.2149:0.3223:0.0	rs59615456;rs62310634	292;299	F5H1N7;Q6ZU35	.;K1211_HUMAN	R	299;299;292;209	ENSP00000264229:G299R;ENSP00000423366:G299R;ENSP00000444006:G292R	ENSP00000264229:G299R	G	+	1	0	KIAA1211	56875320	0.003000	0.15002	0.000000	0.03702	0.029000	0.11900	1.610000	0.36869	0.107000	0.17824	0.462000	0.41574	GGT	G|0.738;C|0.262	0.262	strong		0.716	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3674170	3674170	+	Silent	SNP	G	G	A	rs61734520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3674170G>A	ENST00000344754.4	-	13	3431	c.3432C>T	c.(3430-3432)gcC>gcT	p.A1144A	SIGLEC1_ENST00000202578.4_Silent_p.A1144A	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1144	Ig-like C2-type 11.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						GGTAGGAGGTGGCATCCCTGA	0.662													G|||	103	0.0205671	0.0772	0.0014	5008	,	,		15685	0.0		0.0	False		,,,				2504	0.0				p.A1144A		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C3432T						PASS	.	G		233,4173	136.9+/-172.8	7,219,1977	53.0	47.0	49.0		3432	-3.0	0.7	20	dbSNP_129	49	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	SIGLEC1	NM_023068.3		7,223,6273	AA,AG,GG		0.0465,5.2882,1.8222		1144/1710	3674170	237,12769	2203	4300	6503	SO:0001819	synonymous_variant	6614	exon13			GGAGGTGGCATCC	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.3432C>T	20.37:g.3674170G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	119	69	0.579832	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1																																																																																			G|0.980;A|0.020	0.020	strong		0.662	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
UNC80	285175	hgsc.bcm.edu	37	2	210818971	210818971	+	Silent	SNP	G	G	A	rs16843977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:210818971G>A	ENST00000439458.1	+	47	7316	c.7236G>A	c.(7234-7236)ttG>ttA	p.L2412L	UNC80_ENST00000272845.6_Silent_p.L2407L	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	2412					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						AGGCCCTTTTGTACAGTGTAG	0.458													A|||	496	0.0990415	0.2148	0.0331	5008	,	,		16877	0.004		0.0219	False		,,,				2504	0.1667				p.L2412L		Atlas-SNP	.											.	UNC80	280	.	0			c.G7236A						PASS	.	A	,	247,1137		22,203,467	93.0	102.0	99.0		7236,7221	-8.9	0.0	2	dbSNP_123	99	66,3116		0,66,1525	no	coding-synonymous,coding-synonymous	UNC80	NM_032504.1,NM_182587.3	,	22,269,1992	AA,AG,GG		2.0742,17.8468,6.855	,	2412/3259,2407/3235	210818971	313,4253	692	1591	2283	SO:0001819	synonymous_variant	285175	exon47			CCTTTTGTACAGT	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.7236G>A	2.37:g.210818971G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Silent	SNP	ENST00000439458.1	37	CCDS46504.1																																																																																			G|0.937;A|0.063	0.063	strong		0.458	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
LIPF	8513	hgsc.bcm.edu	37	10	90438207	90438207	+	Silent	SNP	A	A	G	rs1228187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90438207A>G	ENST00000238983.4	+	10	1012	c.966A>G	c.(964-966)caA>caG	p.Q322Q	LIPF_ENST00000355843.2_Silent_p.Q299Q|LIPF_ENST00000394375.3_Silent_p.Q332Q|LIPF_ENST00000608620.1_Silent_p.Q289Q	NM_004190.3	NP_004181.1	P07098	LIPG_HUMAN	lipase, gastric	322					lipid catabolic process (GO:0016042)|malate metabolic process (GO:0006108)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)	lipid binding (GO:0008289)|malate dehydrogenase activity (GO:0016615)|triglyceride lipase activity (GO:0004806)			NS(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(6)	13		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)	Orlistat(DB01083)	TCTAGTCCCAACCTCCCTACT	0.448													A|||	1144	0.228435	0.1248	0.3069	5008	,	,		19364	0.3274		0.2107	False		,,,				2504	0.229				p.Q332Q		Atlas-SNP	.											.	LIPF	62	.	0			c.A996G						PASS	.	A	,,,	618,3788	268.9+/-268.7	43,532,1628	186.0	170.0	175.0		867,996,897,966	-9.7	0.0	10	dbSNP_87	175	1777,6823	321.5+/-315.1	196,1385,2719	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LIPF	NM_001198828.1,NM_001198829.1,NM_001198830.1,NM_004190.3	,,,	239,1917,4347	GG,GA,AA		20.6628,14.0263,18.4146	,,,	289/366,332/409,299/376,322/399	90438207	2395,10611	2203	4300	6503	SO:0001819	synonymous_variant	8513	exon11			GTCCCAACCTCCC	X05997	CCDS7389.1, CCDS55718.1, CCDS55719.1, CCDS65896.1	10q23	2005-10-30			ENSG00000182333	ENSG00000182333	3.1.1.3		6622	protein-coding gene	gene with protein product		601980				3304425, 9186906	Standard	NM_004190		Approved	HGL, HLAL	uc010qmt.2	P07098	OTTHUMG00000018695	ENST00000238983.4:c.966A>G	10.37:g.90438207A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	143	72	0.503497	NM_001198829	B7Z723|F5H1P4|Q2M1P6|Q5VXI7|Q5VXI8|Q658L8	Silent	SNP	ENST00000238983.4	37	CCDS7389.1																																																																																			A|0.799;G|0.201	0.201	strong		0.448	LIPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049256.1		
NAV2	89797	hgsc.bcm.edu	37	11	20070349	20070349	+	Silent	SNP	C	C	T	rs78806867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:20070349C>T	ENST00000396087.3	+	16	4146	c.4047C>T	c.(4045-4047)tcC>tcT	p.S1349S	NAV2_ENST00000360655.4_Silent_p.S1262S|NAV2_ENST00000527559.2_Silent_p.S1278S|NAV2-AS2_ENST00000533767.1_RNA|NAV2_ENST00000540292.1_Silent_p.S1280S|NAV2_ENST00000396085.1_Silent_p.S1326S|NAV2_ENST00000349880.4_Silent_p.S1326S|NAV2_ENST00000311043.8_Silent_p.S412S|NAV2_ENST00000533917.1_Silent_p.S412S	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1349					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TGGTCATCTCCAATCCTCATG	0.522													C|||	63	0.0125799	0.0454	0.0014	5008	,	,		21187	0.0		0.002	False		,,,				2504	0.0				p.S1349S		Atlas-SNP	.											.	NAV2	255	.	0			c.C4047T						PASS	.	C	,,,	145,4261	101.2+/-139.8	5,135,2063	136.0	113.0	121.0		3786,1236,3978,3978	1.9	1.0	11	dbSNP_131	121	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	5,136,6362	TT,TC,CC		0.0116,3.291,1.1226	,,,	1262/2366,412/1494,1326/2430,1326/2433	20070349	146,12860	2203	4300	6503	SO:0001819	synonymous_variant	89797	exon16			CATCTCCAATCCT	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.4047C>T	11.37:g.20070349C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			C|0.988;T|0.012	0.012	strong		0.522	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
ANKRD16	54522	hgsc.bcm.edu	37	10	5920244	5920244	+	Missense_Mutation	SNP	T	T	C	rs61729846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5920244T>C	ENST00000380094.5	-	7	1478	c.935A>G	c.(934-936)cAt>cGt	p.H312R	ANKRD16_ENST00000191063.8_Missense_Mutation_p.I286V|ANKRD16_ENST00000380092.4_Missense_Mutation_p.H312R	NM_019046.2	NP_061919.1	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16	312										breast(1)|endometrium(1)|large_intestine(5)|lung(3)|stomach(2)	12						ACAGGCCAGATGCAGGGCTGA	0.502													T|||	310	0.061901	0.2247	0.0173	5008	,	,		19150	0.0		0.001	False		,,,				2504	0.0				p.H312R		Atlas-SNP	.											.	ANKRD16	32	.	0			c.A935G						PASS	.	T	ARG/HIS,VAL/ILE,ARG/HIS	885,3521	343.8+/-307.8	98,689,1416	67.0	66.0	66.0		935,856,935	5.0	1.0	10	dbSNP_129	66	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense	ANKRD16	NM_001009941.2,NM_001009943.2,NM_019046.2	29,29,29	98,694,5711	CC,CT,TT		0.0581,20.0862,6.843	probably-damaging,probably-damaging,probably-damaging	312/362,286/305,312/362	5920244	890,12116	2203	4300	6503	SO:0001583	missense	54522	exon7			GCCAGATGCAGGG	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.935A>G	10.37:g.5920244T>C	ENSP00000369436:p.His312Arg	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	47	30	0.638298	NM_001009941	A6NEF0|F8WEI4|Q9NT01	Missense_Mutation	SNP	ENST00000380094.5	37	CCDS31136.1	102|102	0.046703296703296704|0.046703296703296704	96|96	0.1951219512195122|0.1951219512195122	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	0|0	0.0|0.0	T|T	12.88|12.88	2.071823|2.071823	0.36566|0.36566	0.200862|0.200862	5.81E-4|5.81E-4	ENSG00000134461|ENSG00000134461	ENST00000380094;ENST00000380092|ENST00000191063	T;T|T	0.71461|0.58797	-0.57;-0.57|0.31	4.97|4.97	4.97|4.97	0.65823|0.65823	Ankyrin repeat-containing domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00144|0.00144	0.0004|0.0004	M|M	0.85099|0.85099	2.735|2.735	0.35597|0.35597	P|P	0.192465|0.192465	D|B	0.89917|0.19073	1.0|0.033	D|B	0.91635|0.21917	0.999|0.037	T|T	0.20672|0.20672	-1.0268|-1.0268	9|8	0.51188|0.62326	T|D	0.08|0.03	-15.6176|-15.6176	13.4896|13.4896	0.61386|0.61386	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	312|286	Q6P6B7|F8WEI4	ANR16_HUMAN|.	R|V	312|286	ENSP00000369436:H312R;ENSP00000369434:H312R|ENSP00000352361:I286V	ENSP00000369434:H312R|ENSP00000352361:I286V	H|I	-|-	2|1	0|0	ANKRD16|ANKRD16	5960250|5960250	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.852000|0.852000	0.48524|0.48524	6.409000|6.409000	0.73289|0.73289	1.858000|1.858000	0.53909|0.53909	0.254000|0.254000	0.18369|0.18369	CAT|ATC	T|0.928;C|0.072	0.072	strong		0.502	ANKRD16-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046611.2	XM_166138	
FASTKD1	79675	hgsc.bcm.edu	37	2	170403106	170403106	+	Silent	SNP	G	G	A	rs16857030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170403106G>A	ENST00000453153.2	-	8	1669	c.1323C>T	c.(1321-1323)gcC>gcT	p.A441A	FASTKD1_ENST00000453929.2_Silent_p.A441A	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	441					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						GTGGTAAAACGGCTTCAATTC	0.428													G|||	494	0.0986422	0.2496	0.0764	5008	,	,		19180	0.003		0.0636	False		,,,				2504	0.045				p.A441A		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C1323T						PASS	.	G		878,3528	338.9+/-305.5	90,698,1415	70.0	72.0	72.0		1323	-1.6	0.9	2	dbSNP_123	72	483,8117	139.5+/-196.2	10,463,3827	no	coding-synonymous	FASTKD1	NM_024622.3		100,1161,5242	AA,AG,GG		5.6163,19.9274,10.4644		441/848	170403106	1361,11645	2203	4300	6503	SO:0001819	synonymous_variant	79675	exon8			TAAAACGGCTTCA	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.1323C>T	2.37:g.170403106G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	173	70	0.404624	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			G|0.902;A|0.098	0.098	strong		0.428	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
MTMR3	8897	hgsc.bcm.edu	37	22	30403307	30403307	+	Splice_Site	SNP	C	C	T	rs146523702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30403307C>T	ENST00000401950.2	+	10	1218	c.876C>T	c.(874-876)ttC>ttT	p.F292F	MTMR3_ENST00000406629.1_Splice_Site_p.F292F|MTMR3_ENST00000333027.3_Splice_Site_p.F292F|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000323630.5_Splice_Site_p.F156F|MTMR3_ENST00000351488.3_Splice_Site_p.F292F	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	292	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			ACGTGGAGTTCGGTAAGGTGC	0.458													C|||	12	0.00239617	0.0091	0.0	5008	,	,		21375	0.0		0.0	False		,,,				2504	0.0				p.F292F		Atlas-SNP	.											MTMR3_ENST00000401950,NS,lymphoid_neoplasm,+2,1	MTMR3	106	1	0			c.C876T						PASS	.	C	,,	47,4359	46.0+/-80.4	0,47,2156	46.0	40.0	42.0		876,876,876	-3.0	1.0	22	dbSNP_134	42	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	MTMR3	NM_021090.3,NM_153050.2,NM_153051.2	,,	0,49,6454	TT,TC,CC		0.0233,1.0667,0.3767	,,	292/1199,292/1171,292/1162	30403307	49,12957	2203	4300	6503	SO:0001630	splice_region_variant	8897	exon10			GGAGTTCGGTAAG	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.877+1C>T	22.37:g.30403307C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Silent	SNP	ENST00000401950.2	37	CCDS13870.1																																																																																			C|0.997;T|0.003	0.003	strong		0.458	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090	Silent
CYP4F11	57834	hgsc.bcm.edu	37	19	16024605	16024605	+	Silent	SNP	C	C	G	rs75284625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16024605C>G	ENST00000402119.4	-	12	1938	c.1512G>C	c.(1510-1512)ctG>ctC	p.L504L	CYP4F11_ENST00000248041.8_Silent_p.L504L|CYP4F11_ENST00000591841.1_Silent_p.L179L|CYP4F11_ENST00000326742.8_3'UTR	NM_021187.3	NP_067010.3			cytochrome P450, family 4, subfamily F, polypeptide 11											NS(1)|breast(3)|endometrium(4)|large_intestine(2)|lung(11)|ovary(1)|skin(3)	25						CGCGCAATATCAGCTCGGGTT	0.632													.|||	36	0.0071885	0.0257	0.0029	5008	,	,		15991	0.0		0.0	False		,,,				2504	0.0				p.L504L		Atlas-SNP	.											.	CYP4F11	83	.	0			c.G1512C						PASS	.	C	,	190,4216	120.8+/-158.4	8,174,2021	62.0	57.0	59.0		1512,1512	1.6	0.2	19	dbSNP_132	59	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CYP4F11	NM_001128932.1,NM_021187.3	,	8,175,6320	GG,GC,CC		0.0116,4.3123,1.4686	,	504/525,504/525	16024605	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	57834	exon13			CAATATCAGCTCG	AF236085	CCDS12337.1	19p13.1	2011-07-29	2003-01-14		ENSG00000171903	ENSG00000171903		"""Cytochrome P450s"""	13265	protein-coding gene	gene with protein product		611517	"""cytochrome P450, subfamily IVF, polypeptide 11"""			10964514, 9068972	Standard	NM_021187		Approved		uc002nbu.2	Q9HBI6		ENST00000402119.4:c.1512G>C	19.37:g.16024605C>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	150	81	0.54	NM_001128932		Silent	SNP	ENST00000402119.4	37	CCDS12337.1																																																																																			C|0.990;G|0.010	0.010	strong		0.632	CYP4F11-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460385.2	NM_021187	
TMEM203	94107	hgsc.bcm.edu	37	9	140099675	140099675	+	Silent	SNP	G	G	A	rs113235610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140099675G>A	ENST00000343666.5	-	1	415	c.192C>T	c.(190-192)acC>acT	p.T64T	NDOR1_ENST00000371521.4_5'Flank|NDOR1_ENST00000427047.2_5'Flank|TPRN_ENST00000541945.1_5'Flank|TMEM203_ENST00000537254.1_Silent_p.T64T|NDOR1_ENST00000458322.2_5'Flank|NDOR1_ENST00000344894.5_5'Flank	NM_053045.1	NP_444273.1	Q969S6	TM203_HUMAN	transmembrane protein 203	64						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(1)	2	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		ACACGATGGTGGTGAAGTAGG	0.617													G|||	33	0.00658946	0.0212	0.0072	5008	,	,		15733	0.0		0.0	False		,,,				2504	0.0				p.T64T		Atlas-SNP	.											TMEM203,NS,carcinoma,0,1	TMEM203	8	1	0			c.C192T						PASS	.	G		83,4319	70.3+/-108.2	1,81,2119	45.0	47.0	46.0		192	3.1	1.0	9	dbSNP_132	46	0,8584		0,0,4292	no	coding-synonymous	TMEM203	NM_053045.1		1,81,6411	AA,AG,GG		0.0,1.8855,0.6391		64/137	140099675	83,12903	2201	4292	6493	SO:0001819	synonymous_variant	94107	exon1			GATGGTGGTGAAG	BC009283	CCDS35185.1	9q34.3	2007-12-18			ENSG00000187713	ENSG00000187713			28217	protein-coding gene	gene with protein product	"""HBeAg-binding protein 1"""					12477932	Standard	NM_053045		Approved	MGC14327, HBEBP1	uc004clv.3	Q969S6	OTTHUMG00000020985	ENST00000343666.5:c.192C>T	9.37:g.140099675G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	80	56	0.7	NM_053045	Q6NW08	Silent	SNP	ENST00000343666.5	37	CCDS35185.1																																																																																			G|0.992;A|0.008	0.008	strong		0.617	TMEM203-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055325.2	NM_053045	
HECTD1	25831	hgsc.bcm.edu	37	14	31619392	31619392	+	Silent	SNP	T	T	C	rs11620816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:31619392T>C	ENST00000399332.1	-	13	2456	c.1968A>G	c.(1966-1968)caA>caG	p.Q656Q	HECTD1_ENST00000553700.1_Silent_p.Q656Q	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	656			Q -> H (in dbSNP:rs11620816).		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)		GTTTACCTTGTTGCAATTCTT	0.338													C|||	1468	0.293131	0.5053	0.1585	5008	,	,		17711	0.2907		0.1074	False		,,,				2504	0.2955				p.Q656Q		Atlas-SNP	.											.	HECTD1	159	.	0			c.A1968G						PASS	.	C		1599,2143		354,891,626	250.0	232.0	238.0		1968	6.0	1.0	14	dbSNP_120	238	1060,7164		60,940,3112	no	coding-synonymous	HECTD1	NM_015382.2		414,1831,3738	CC,CT,TT		12.8891,42.7312,22.2213		656/2611	31619392	2659,9307	1871	4112	5983	SO:0001819	synonymous_variant	25831	exon13			ACCTTGTTGCAAT	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.1968A>G	14.37:g.31619392T>C		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	184	79	0.429348	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1																																																																																			C|0.246;T|0.754	0.246	strong		0.338	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
CAAP1	79886	hgsc.bcm.edu	37	9	26842506	26842506	+	Silent	SNP	G	G	A	rs10967558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:26842506G>A	ENST00000333916.5	-	6	967	c.879C>T	c.(877-879)gaC>gaT	p.D293D	CAAP1_ENST00000520187.1_3'UTR|CAAP1_ENST00000535437.1_Silent_p.D148D	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	293					apoptotic process (GO:0006915)												CTTTCTCCAGGTCATCTATCT	0.502													G|||	242	0.0483227	0.1747	0.0144	5008	,	,		18187	0.0		0.001	False		,,,				2504	0.0				p.D293D		Atlas-SNP	.											.	.	.	.	0			c.C879T						PASS	.	G	,	585,3821	259.5+/-263.1	32,521,1650	244.0	228.0	233.0		444,879	2.9	1.0	9	dbSNP_120	233	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	C9orf82	NM_001167575.1,NM_024828.3	,	32,525,5946	AA,AG,GG		0.0465,13.2773,4.5287	,	148/217,293/362	26842506	589,12417	2203	4300	6503	SO:0001819	synonymous_variant	79886	exon6			CTCCAGGTCATCT	BC014658	CCDS6516.1	9p21.2	2012-04-20	2012-04-20	2012-04-20	ENSG00000120159	ENSG00000120159			25834	protein-coding gene	gene with protein product	"""conserved anti-apoptotic protein"""		"""chromosome 9 open reading frame 82"""	C9orf82		21980415	Standard	NM_024828		Approved	FLJ13657, CAAP	uc003zqc.3	Q9H8G2	OTTHUMG00000019706	ENST00000333916.5:c.879C>T	9.37:g.26842506G>A		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	295	140	0.474576	NM_024828	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Silent	SNP	ENST00000333916.5	37	CCDS6516.1																																																																																			G|0.941;A|0.059	0.059	strong		0.502	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051954.1	NM_024828	
BPTF	2186	hgsc.bcm.edu	37	17	65914911	65914911	+	Silent	SNP	T	T	C	rs80201495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65914911T>C	ENST00000321892.4	+	14	5824	c.5763T>C	c.(5761-5763)gaT>gaC	p.D1921D	BPTF_ENST00000306378.6_Silent_p.D1795D|BPTF_ENST00000424123.3_Silent_p.D1782D|BPTF_ENST00000335221.5_Silent_p.D1921D			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1921					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GATGGGATGATATGGCGGCCA	0.458													C|||	95	0.0189696	0.0666	0.0086	5008	,	,		16414	0.0		0.001	False		,,,				2504	0.0				p.D1921D		Atlas-SNP	.											.	BPTF	415	.	0			c.T5763C						PASS	.	C	,	247,4159	804.1+/-415.7	7,233,1963	149.0	145.0	147.0		5763,5385	3.2	1.0	17	dbSNP_131	147	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	BPTF	NM_004459.6,NM_182641.3	,	7,241,6255	CC,CT,TT		0.093,5.606,1.9606	,	1921/2904,1795/2921	65914911	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	2186	exon14			GGATGATATGGCG	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.5763T>C	17.37:g.65914911T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	148	76	0.513514	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	37																																																																																				T|0.981;C|0.019	0.019	strong		0.458	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
GOLGA3	2802	hgsc.bcm.edu	37	12	133398638	133398638	+	Missense_Mutation	SNP	G	G	A	rs141852501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133398638G>A	ENST00000450791.2	-	1	260	c.77C>T	c.(76-78)gCc>gTc	p.A26V	GOLGA3_ENST00000456883.2_Missense_Mutation_p.A26V|GOLGA3_ENST00000545875.1_Missense_Mutation_p.A26V|GOLGA3_ENST00000204726.3_Missense_Mutation_p.A26V|GOLGA3_ENST00000537452.1_Missense_Mutation_p.A26V			Q08378	GOGA3_HUMAN	golgin A3	26	Pro-rich.				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)		CTTCAGTGGGGCCTCGGGGAG	0.647													G|||	8	0.00159744	0.0061	0.0	5008	,	,		14431	0.0		0.0	False		,,,				2504	0.0				p.A26V		Atlas-SNP	.											.	GOLGA3	234	.	0			c.C77T						PASS	.	G	VAL/ALA,VAL/ALA	28,4378	32.6+/-62.9	0,28,2175	44.0	47.0	46.0		77,77	-3.7	0.0	12	dbSNP_134	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	GOLGA3	NM_001172557.1,NM_005895.3	64,64	0,29,6474	AA,AG,GG		0.0116,0.6355,0.223	benign,benign	26/1135,26/1499	133398638	29,12977	2203	4300	6503	SO:0001583	missense	2802	exon2			AGTGGGGCCTCGG	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.77C>T	12.37:g.133398638G>A	ENSP00000410378:p.Ala26Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	111	58	0.522523	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	11.20	1.568083	0.28003	0.006355	1.16E-4	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.32988	1.86;1.86;1.86;1.43;1.43	5.4	-3.7	0.04437	.	1.125330	0.06702	N	0.771525	T	0.16896	0.0406	L	0.44542	1.39	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.33574	-0.9863	10	0.41790	T	0.15	.	7.4989	0.27505	0.069:0.4444:0.3435:0.1431	.	26;26;26	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	V	26	ENSP00000204726:A26V;ENSP00000410378:A26V;ENSP00000409303:A26V;ENSP00000442143:A26V;ENSP00000442603:A26V	ENSP00000204726:A26V	A	-	2	0	GOLGA3	131908711	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.762000	0.04745	-0.565000	0.06061	-2.362000	0.00238	GCC	G|0.997;A|0.003	0.003	strong		0.647	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
ATP2A3	489	hgsc.bcm.edu	37	17	3845927	3845927	+	Silent	SNP	A	A	G	rs17846889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3845927A>G	ENST00000352011.3	-	12	1572	c.1518T>C	c.(1516-1518)acT>acC	p.T506T	ATP2A3_ENST00000397041.3_Silent_p.T506T|ATP2A3_ENST00000397043.3_Silent_p.T506T|ATP2A3_ENST00000309890.7_Silent_p.T506T|ATP2A3_ENST00000397035.3_Silent_p.T506T|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000359983.3_Silent_p.T506T			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	506					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		TGCCCTGGCCAGTAGGGTGAG	0.642													a|||	1927	0.384784	0.584	0.4712	5008	,	,		16766	0.0873		0.4553	False		,,,				2504	0.2883				p.T506T	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T1518C						PASS	.	G	,,,,,,	2512,1894	629.2+/-395.2	714,1084,405	78.0	68.0	72.0		1518,1518,1518,1518,1518,1518,1518	-7.9	0.0	17	dbSNP_123	72	3954,4646	550.0+/-385.7	933,2088,1279	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	1647,3172,1684	GG,GA,AA		45.9767,42.9868,49.7155	,,,,,,	506/1000,506/1053,506/1045,506/1044,506/1030,506/999,506/1030	3845927	6466,6540	2203	4300	6503	SO:0001819	synonymous_variant	489	exon12			CTGGCCAGTAGGG		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1518T>C	17.37:g.3845927A>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			G|0.461;C|0.000;A|0.539	0.461	strong		0.642	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39279921	39279921	+	Missense_Mutation	SNP	A	A	G	rs623410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39279921A>G	ENST00000394014.1	-	1	498	c.454T>C	c.(454-456)Tgc>Cgc	p.C152R		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	152	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].					keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			caagaggggcagcagctgctg	0.657													G|||	968	0.193291	0.5121	0.1455	5008	,	,		14860	0.1498		0.0179	False		,,,				2504	0.0215				p.C152R		Atlas-SNP	.											.	KRTAP4-12	32	.	0			c.T454C						PASS	.	G	ARG/CYS	1750,2646		365,1020,813	17.0	23.0	21.0		454	0.0	0.0	17	dbSNP_83	21	129,8447		5,119,4164	no	missense	KRTAP4-12	NM_031854.2	180	370,1139,4977	GG,GA,AA		1.5042,39.8089,14.485	benign	152/202	39279921	1879,11093	2198	4288	6486	SO:0001583	missense	83755	exon1			AGGGGCAGCAGCT	AJ406943	CCDS32649.1	17q21.2	2013-06-25			ENSG00000213416	ENSG00000213416		"""Keratin associated proteins"""	16776	protein-coding gene	gene with protein product						11279113	Standard	NM_031854		Approved	KAP4.12	uc002hwa.3	Q9BQ66	OTTHUMG00000133632	ENST00000394014.1:c.454T>C	17.37:g.39279921A>G	ENSP00000377582:p.Cys152Arg	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	131	128	0.977099	NM_031854	A3KMC5|Q495I0	Missense_Mutation	SNP	ENST00000394014.1	37	CCDS32649.1	398	0.18223443223443223	242	0.491869918699187	45	0.12430939226519337	97	0.16958041958041958	14	0.018469656992084433	.	0.005	-2.206372	0.00292	0.398089	0.015042	ENSG00000213416	ENST00000394014	T	0.01185	5.21	4.99	0.0438	0.14223	.	.	.	.	.	T	0.00012	0.0000	N	0.00031	-2.6	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.30446	-0.9978	8	0.02654	T	1	.	6.0206	0.19626	0.0815:0.506:0.2817:0.1308	rs623410	152	Q9BQ66	KR412_HUMAN	R	152	ENSP00000377582:C152R	ENSP00000377582:C152R	C	-	1	0	KRTAP4-12	36533447	0.000000	0.05858	0.004000	0.12327	0.147000	0.21601	-1.047000	0.03521	-0.041000	0.13558	-0.320000	0.08662	TGC	A|0.835;G|0.165	0.165	strong		0.657	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1		
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802621	31802621	+	Missense_Mutation	SNP	T	T	A	rs73899382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31802621T>A	ENST00000334068.2	+	1	50	c.28T>A	c.(28-30)Ttc>Atc	p.F10I		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	10						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						CTCTAGAAACTTCTCCTCCCG	0.542													-|||	32	0.00638978	0.0234	0.0014	5008	,	,		18495	0.0		0.0	False		,,,				2504	0.0				p.F10I	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.T28A						PASS	.	T	ILE/PHE	90,4316	74.7+/-112.8	1,88,2114	112.0	113.0	113.0		28	2.5	1.0	21	dbSNP_130	113	0,8600		0,0,4300	yes	missense	KRTAP13-4	NM_181600.1	21	1,88,6414	AA,AT,TT		0.0,2.0427,0.692	probably-damaging	10/161	31802621	90,12916	2203	4300	6503	SO:0001583	missense	284827	exon1			AGAAACTTCTCCT	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.28T>A	21.37:g.31802621T>A	ENSP00000334834:p.Phe10Ile	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	238	102	0.428571	NM_181600	A2RRL3	Missense_Mutation	SNP	ENST00000334068.2	37	CCDS13592.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	t	14.16	2.452391	0.43531	0.020427	0.0	ENSG00000186971	ENST00000334068	T	0.03496	3.91	4.95	2.47	0.30058	.	0.000000	0.46442	D	0.000291	T	0.06096	0.0158	M	0.87971	2.92	0.26406	N	0.976344	D	0.89917	1.0	D	0.91635	0.999	T	0.01345	-1.1379	10	0.66056	D	0.02	.	9.5117	0.39080	0.0:0.0:0.3442:0.6558	.	10	Q3LI77	KR134_HUMAN	I	10	ENSP00000334834:F10I	ENSP00000334834:F10I	F	+	1	0	KRTAP13-4	30724492	0.999000	0.42202	0.996000	0.52242	0.025000	0.11179	1.211000	0.32382	0.388000	0.25054	-0.321000	0.08615	TTC	T|0.992;A|0.008	0.008	strong		0.542	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1		
ATPAF2	91647	hgsc.bcm.edu	37	17	17924447	17924447	+	Missense_Mutation	SNP	T	T	C	rs34607655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17924447T>C	ENST00000474627.3	-	7	876	c.722A>G	c.(721-723)gAg>gGg	p.E241G	ATPAF2_ENST00000469327.1_5'UTR|ATPAF2_ENST00000585101.1_Intron	NM_145691.3	NP_663729.1	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2	241					proton-transporting ATP synthase complex assembly (GO:0043461)	mitochondrion (GO:0005739)|nuclear speck (GO:0016607)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	8	all_neural(463;0.228)					CTGGTACTCCTCCTCCAGGCG	0.577													T|||	19	0.00379393	0.0136	0.0014	5008	,	,		20341	0.0		0.0	False		,,,				2504	0.0				p.E241G		Atlas-SNP	.											.	ATPAF2	15	.	0			c.A722G						PASS	.	T	GLY/GLU	39,4367	41.6+/-74.8	0,39,2164	43.0	35.0	38.0		722	5.7	1.0	17	dbSNP_126	38	0,8600		0,0,4300	yes	missense	ATPAF2	NM_145691.3	98	0,39,6464	CC,CT,TT		0.0,0.8852,0.2999	probably-damaging	241/290	17924447	39,12967	2203	4300	6503	SO:0001583	missense	91647	exon7			TACTCCTCCTCCA	AF052185	CCDS32585.1	17p11.2	2012-10-12			ENSG00000171953	ENSG00000171953		"""Mitochondrial respiratory chain complex assembly factors"""	18802	protein-coding gene	gene with protein product		608918				11410595, 11997338	Standard	NM_145691		Approved	Atp12p, ATP12, LP3663, MGC29736	uc002gse.1	Q8N5M1	OTTHUMG00000059354	ENST00000474627.3:c.722A>G	17.37:g.17924447T>C	ENSP00000417190:p.Glu241Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_145691	A6NDE5|A8K2J2|Q6XYC7	Missense_Mutation	SNP	ENST00000474627.3	37	CCDS32585.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	T	28.0	4.877445	0.91664	0.008852	0.0	ENSG00000171953	ENST00000474627	T	0.81330	-1.48	5.7	5.7	0.88788	ATPase assembly, ATP12, domain (1);	0.000000	0.85682	D	0.000000	D	0.84982	0.5593	M	0.88105	2.93	0.80722	D	1	D	0.57257	0.979	P	0.52554	0.702	D	0.88744	0.3245	10	0.66056	D	0.02	-18.6937	15.9482	0.79809	0.0:0.0:0.0:1.0	rs34607655	241	Q8N5M1	ATPF2_HUMAN	G	241	ENSP00000417190:E241G	ENSP00000417190:E241G	E	-	2	0	ATPAF2	17865172	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.945000	0.87732	2.170000	0.68504	0.528000	0.53228	GAG	T|0.996;C|0.004	0.004	strong		0.577	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3	NM_145691	
MUC17	140453	hgsc.bcm.edu	37	7	100679760	100679760	+	Missense_Mutation	SNP	G	G	A	rs73168394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100679760G>A	ENST00000306151.4	+	3	5127	c.5063G>A	c.(5062-5064)gGa>gAa	p.G1688E		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1688	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)					TATACTGAAGGAAGAACTCCT	0.478																																					p.G1688E		Atlas-SNP	.											MUC17,caecum,carcinoma,0,2	MUC17	804	2	0			c.G5063A						PASS	.						187.0	202.0	197.0					7																	100679760		2203	4300	6503	SO:0001583	missense	140453	exon3			CTGAAGGAAGAAC	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.5063G>A	7.37:g.100679760G>A	ENSP00000302716:p.Gly1688Glu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	122	21	0.172131	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.044	-1.274900	0.01410	.	.	ENSG00000169876	ENST00000306151	T	0.06068	3.35	0.579	-1.16	0.09678	.	.	.	.	.	T	0.02649	0.0080	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.46062	-0.9218	8	0.02654	T	1	.	.	.	.	.	1688	Q685J3	MUC17_HUMAN	E	1688	ENSP00000302716:G1688E	ENSP00000302716:G1688E	G	+	2	0	MUC17	100466480	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.758000	0.00374	-0.992000	0.03472	-1.407000	0.01130	GGA	G|0.989;A|0.011	0.011	strong		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
LYST	1130	hgsc.bcm.edu	37	1	235933535	235933535	+	Missense_Mutation	SNP	C	C	G	rs6665568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235933535C>G	ENST00000389794.3	-	20	6021	c.5847G>C	c.(5845-5847)caG>caC	p.Q1949H	LYST_ENST00000389793.2_Missense_Mutation_p.Q1949H|LYST_ENST00000536965.1_3'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1949			Q -> H (in dbSNP:rs6665568).		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)			TAAACATCTGCTGGTGGTGAT	0.388													C|||	308	0.0615016	0.2194	0.0245	5008	,	,		17686	0.0		0.001	False		,,,				2504	0.0				p.Q1949H		Atlas-SNP	.											.	LYST	370	.	0			c.G5847C						PASS	.	C	HIS/GLN	828,3578	327.5+/-300.1	76,676,1451	128.0	132.0	131.0		5847	0.8	0.7	1	dbSNP_116	131	10,8590	6.4+/-24.3	0,10,4290	yes	missense	LYST	NM_000081.2	24	76,686,5741	GG,GC,CC		0.1163,18.7926,6.4432	benign	1949/3802	235933535	838,12168	2203	4300	6503	SO:0001583	missense	1130	exon20			CATCTGCTGGTGG	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.5847G>C	1.37:g.235933535C>G	ENSP00000374444:p.Gln1949His	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	154	74	0.480519	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	115	0.052655677655677656	108	0.21951219512195122	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	8.986	0.976514	0.18736	0.187926	0.001163	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.61158	0.13;0.13	5.48	0.809	0.18725	.	0.630262	0.18067	N	0.152750	T	0.00012	0.0000	N	0.17082	0.46	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.11966	-1.0566	9	0.13853	T	0.58	.	2.9878	0.05973	0.217:0.4875:0.1067:0.1888	rs6665568;rs52790740;rs6665568	1949	Q99698	LYST_HUMAN	H	1949	ENSP00000374444:Q1949H;ENSP00000374443:Q1949H	ENSP00000374443:Q1949H	Q	-	3	2	LYST	234000158	0.152000	0.22762	0.656000	0.29637	0.957000	0.61999	-0.438000	0.06905	0.266000	0.21894	0.650000	0.86243	CAG	C|0.943;G|0.057	0.057	strong		0.388	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
ABCA9	10350	hgsc.bcm.edu	37	17	67031882	67031882	+	Silent	SNP	A	A	G	rs16973534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:67031882A>G	ENST00000340001.4	-	7	1072	c.861T>C	c.(859-861)ctT>ctC	p.L287L	ABCA9_ENST00000370732.2_Silent_p.L287L|ABCA9_ENST00000453985.2_Silent_p.L287L	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	287					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					ATTTTACAATAAGAGCCATTA	0.423													A|||	141	0.028155	0.1036	0.0058	5008	,	,		16263	0.0		0.0	False		,,,				2504	0.0				p.L287L		Atlas-SNP	.											.	ABCA9	192	.	0			c.T861C						PASS	.	A		442,3964	213.8+/-233.3	27,388,1788	71.0	67.0	68.0		861	-1.6	0.0	17	dbSNP_123	68	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ABCA9	NM_080283.3		27,391,6085	GG,GA,AA		0.0349,10.0318,3.4215		287/1625	67031882	445,12561	2203	4300	6503	SO:0001819	synonymous_variant	10350	exon7			TACAATAAGAGCC	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"""ATP binding cassette transporters / subfamily A"""	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.861T>C	17.37:g.67031882A>G		Somatic	435	0	0		WXS	Illumina HiSeq	Phase_I	430	196	0.455814	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Silent	SNP	ENST00000340001.4	37	CCDS11681.1																																																																																			A|0.970;G|0.030	0.030	strong		0.423	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386	
ASH1L	55870	hgsc.bcm.edu	37	1	155451343	155451343	+	Missense_Mutation	SNP	A	A	C	rs114218266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155451343A>C	ENST00000368346.3	-	3	1957	c.1318T>G	c.(1318-1320)Tgt>Ggt	p.C440G	ASH1L_ENST00000392403.3_Missense_Mutation_p.C440G|ASH1L_ENST00000548830.1_3'UTR			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	440					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTTGTACTACAAGAAGCCTTA	0.423													A|||	103	0.0205671	0.0734	0.0058	5008	,	,		19464	0.002		0.0	False		,,,				2504	0.0				p.C440G		Atlas-SNP	.											.	ASH1L	279	.	0			c.T1318G						PASS	.	A	GLY/CYS	299,4107	155.5+/-188.7	12,275,1916	61.0	60.0	60.0		1318	3.6	1.0	1	dbSNP_132	60	2,8598	1.2+/-3.3	0,2,4298	yes	missense	ASH1L	NM_018489.2	159	12,277,6214	CC,CA,AA		0.0233,6.7862,2.3143	possibly-damaging	440/2965	155451343	301,12705	2203	4300	6503	SO:0001583	missense	55870	exon3			TACTACAAGAAGC	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.1318T>G	1.37:g.155451343A>C	ENSP00000357330:p.Cys440Gly	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	179	77	0.430168	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	A	15.65	2.897292	0.52121	0.067862	2.33E-4	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.91407	-2.84;-2.83	4.73	3.6	0.41247	.	0.327762	0.30538	N	0.009409	T	0.74772	0.3760	N	0.14661	0.345	0.80722	D	1	P;P	0.50528	0.895;0.936	B;P	0.44477	0.264;0.451	T	0.78445	-0.2201	10	0.72032	D	0.01	.	7.8358	0.29369	0.8353:0.0:0.1647:0.0	.	440;440	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	G	440	ENSP00000357330:C440G;ENSP00000376204:C440G	ENSP00000357330:C440G	C	-	1	0	ASH1L	153717967	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.294000	0.59043	0.936000	0.37367	0.460000	0.39030	TGT	A|0.981;C|0.019	0.019	strong		0.423	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
PLCD4	84812	hgsc.bcm.edu	37	2	219483526	219483526	+	Missense_Mutation	SNP	G	G	C	rs200863393		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219483526G>C	ENST00000450993.2	+	4	745	c.406G>C	c.(406-408)Gac>Cac	p.D136H	PLCD4_ENST00000417849.1_Missense_Mutation_p.D136H|U3_ENST00000516996.1_RNA|PLCD4_ENST00000432688.1_Missense_Mutation_p.D136H	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	136	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGAGCGCCTGGACCAGTATCG	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		20288	0.0		0.001	False		,,,				2504	0.0				p.D136H		Atlas-SNP	.											.	PLCD4	51	.	0			c.G406C						PASS	.	G	HIS/ASP	0,4162		0,0,2081	18.0	18.0	18.0		406	4.9	1.0	2		18	2,8408		0,2,4203	yes	missense	PLCD4	NM_032726.3	81	0,2,6284	CC,CG,GG		0.0238,0.0,0.0159	probably-damaging	136/763	219483526	2,12570	2081	4205	6286	SO:0001583	missense	84812	exon4			CGCCTGGACCAGT	AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"""EF-hand domain containing"""	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.406G>C	2.37:g.219483526G>C	ENSP00000388631:p.Asp136His	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	37	CCDS46516.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	18.34	3.603570	0.66445	0.0	2.38E-4	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000457426;ENST00000417849;ENST00000432688	T;T;T	0.43688	0.94;0.94;0.94	4.89	4.89	0.63831	.	1.041430	0.07513	N	0.909165	T	0.69441	0.3111	M	0.76838	2.35	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.61063	-0.7138	10	0.51188	T	0.08	.	16.8055	0.85626	0.0:0.0:1.0:0.0	.	83;136	B4DN84;Q9BRC7	.;PLCD4_HUMAN	H	136	ENSP00000388631:D136H;ENSP00000396942:D136H;ENSP00000396185:D136H	ENSP00000251959:D136H	D	+	1	0	PLCD4	219191770	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.473000	0.97714	2.553000	0.86117	0.655000	0.94253	GAC	G|1.000;C|0.000	0.000	strong		0.582	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1		
SPAG9	9043	hgsc.bcm.edu	37	17	49043640	49043640	+	Missense_Mutation	SNP	T	T	C	rs9896965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:49043640T>C	ENST00000262013.7	-	30	4167	c.3959A>G	c.(3958-3960)aAt>aGt	p.N1320S	SPAG9_ENST00000510283.1_Missense_Mutation_p.N1176S|SPAG9_ENST00000357122.4_Missense_Mutation_p.N1306S|SPAG9_ENST00000509724.1_5'Flank|SPAG9_ENST00000505279.1_Missense_Mutation_p.N1310S	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	1320			N -> S (in dbSNP:rs9896965).		activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GGCTCACTCATTGCCATACAT	0.443													C|||	348	0.0694888	0.2451	0.0245	5008	,	,		18804	0.0		0.005	False		,,,				2504	0.002				p.N1320S		Atlas-SNP	.											.	SPAG9	151	.	0			c.A3959G						PASS	.	C	SER/ASN,SER/ASN	1032,3374	727.1+/-409.8	120,792,1291	200.0	187.0	191.0		3959,3917	0.2	1.0	17	dbSNP_119	191	46,8554	817.3+/-406.9	0,46,4254	yes	missense,missense	SPAG9	NM_001130528.2,NM_003971.5	46,46	120,838,5545	CC,CT,TT		0.5349,23.4226,8.2885	benign,benign	1320/1322,1306/1308	49043640	1078,11928	2203	4300	6503	SO:0001583	missense	9043	exon30			CACTCATTGCCAT	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.3959A>G	17.37:g.49043640T>C	ENSP00000262013:p.Asn1320Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	136	0.06227106227106227	122	0.24796747967479674	10	0.027624309392265192	0	0.0	4	0.005277044854881266	C	0.006	-2.086087	0.00371	0.234226	0.005349	ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	T;T;T;T	0.20738	2.05;2.05;2.06;2.06	5.65	0.179	0.15063	.	0.530266	0.24511	N	0.037894	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.46638	-0.9177	9	0.15952	T	0.53	-3.8897	10.9806	0.47492	0.0:0.6111:0.0:0.3889	rs9896965;rs52825432;rs9896965	1310;1320;1306;1176	O60271-2;O60271;O60271-4;E7ENU2	.;JIP4_HUMAN;.;.	S	1320;1077;1067;1176;1310;1306;918	ENSP00000262013:N1320S;ENSP00000423165:N1176S;ENSP00000426900:N1310S;ENSP00000349636:N1306S	ENSP00000262013:N1320S	N	-	2	0	SPAG9	46398639	0.101000	0.21875	0.984000	0.44739	0.012000	0.07955	-0.236000	0.09003	-0.064000	0.13043	-0.790000	0.03334	AAT	T|0.917;C|0.083	0.083	strong		0.443	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971	
TMC8	147138	hgsc.bcm.edu	37	17	76134237	76134237	+	Missense_Mutation	SNP	G	G	A	rs11651675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76134237G>A	ENST00000318430.5	+	12	1875	c.1501G>A	c.(1501-1503)Gtc>Atc	p.V501I	TMC8_ENST00000589691.1_Missense_Mutation_p.V278I	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	501			V -> I (in dbSNP:rs11651675).		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)			GCTGAATAGCGTCTTCCTCTT	0.612													G|||	214	0.0427316	0.0287	0.0144	5008	,	,		17634	0.0089		0.0278	False		,,,				2504	0.1319				p.V501I		Atlas-SNP	.											.	TMC8	44	.	0			c.G1501A						PASS	.	G	ILE/VAL	98,4308	78.8+/-117.2	0,98,2105	81.0	82.0	82.0		1501	-6.6	0.0	17	dbSNP_120	82	332,8268	115.2+/-175.0	5,322,3973	yes	missense	TMC8	NM_152468.4	29	5,420,6078	AA,AG,GG		3.8605,2.2242,3.3062	benign	501/727	76134237	430,12576	2203	4300	6503	SO:0001583	missense	147138	exon12			AATAGCGTCTTCC	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.1501G>A	17.37:g.76134237G>A	ENSP00000325561:p.Val501Ile	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Missense_Mutation	SNP	ENST00000318430.5	37	CCDS32749.1	43	0.019688644688644688	11	0.022357723577235773	6	0.016574585635359115	3	0.005244755244755245	23	0.030343007915567283	G	7.442	0.640821	0.14386	0.022242	0.038605	ENSG00000167895	ENST00000318430	T	0.63913	-0.07	4.57	-6.58	0.01836	.	1.053430	0.07340	N	0.880564	T	0.09379	0.0231	N	0.03304	-0.355	0.09310	N	0.999997	B	0.11235	0.004	B	0.06405	0.002	T	0.31613	-0.9937	10	0.12430	T	0.62	-17.6016	14.016	0.64525	0.6643:0.0:0.3357:0.0	rs11651675;rs11651675	501	Q8IU68	TMC8_HUMAN	I	501	ENSP00000325561:V501I	ENSP00000325561:V501I	V	+	1	0	TMC8	73645832	0.000000	0.05858	0.018000	0.16275	0.929000	0.56500	-1.675000	0.01947	-1.222000	0.02587	-1.008000	0.02478	GTC	G|0.969;A|0.031	0.031	strong		0.612	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3		
FLG	2312	hgsc.bcm.edu	37	1	152283975	152283975	+	Silent	SNP	A	A	G	rs66831674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152283975A>G	ENST00000368799.1	-	3	3422	c.3387T>C	c.(3385-3387)tcT>tcC	p.S1129S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1129	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)			GCCCATGGGCAGACTCAGACT	0.602									Ichthyosis				A|||	2319	0.463059	0.5204	0.4524	5008	,	,		19772	0.6558		0.172	False		,,,				2504	0.4939				p.S1129S		Atlas-SNP	.											.	FLG	900	.	0			c.T3387C						PASS	.	A		2011,2395	553.3+/-378.7	471,1069,663	169.0	206.0	193.0		3387	-6.3	0.0	1	dbSNP_130	193	1417,7181	270.4+/-288.9	125,1167,3007	no	coding-synonymous	FLG	NM_002016.1		596,2236,3670	GG,GA,AA		16.4806,45.6423,26.3611		1129/4062	152283975	3428,9576	2203	4299	6502	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ATGGGCAGACTCA	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.3387T>C	1.37:g.152283975A>G		Somatic	438	1	0.0022831		WXS	Illumina HiSeq	Phase_I	445	443	0.995506	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			.	.	weak		0.602	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TENM3	55714	hgsc.bcm.edu	37	4	183594275	183594275	+	Missense_Mutation	SNP	T	T	C	rs201144002		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:183594275T>C	ENST00000511685.1	+	7	1352	c.1229T>C	c.(1228-1230)aTt>aCt	p.I410T	TENM3_ENST00000406950.2_Missense_Mutation_p.I410T			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	410					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CAGCTCTTCATTGATCAGCCA	0.438																																					p.I410T		Atlas-SNP	.											.	.	.	.	0			c.T1229C						PASS	.	T	THR/ILE	0,3630		0,0,1815	63.0	59.0	60.0		1229	4.9	1.0	4		60	1,8189		0,1,4094	yes	missense	ODZ3	NM_001080477.1	89	0,1,5909	CC,CT,TT		0.0122,0.0,0.0085	possibly-damaging	410/2700	183594275	1,11819	1815	4095	5910	SO:0001583	missense	55714	exon6			TCTTCATTGATCA	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.1229T>C	4.37:g.183594275T>C	ENSP00000424226:p.Ile410Thr	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	195	100	0.512821	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	T	17.79	3.476907	0.63849	0.0	1.22E-4	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.29397	1.57;1.57	4.91	4.91	0.64330	.	.	.	.	.	T	0.31765	0.0807	M	0.67397	2.05	0.53688	D	0.999978	B	0.33694	0.421	B	0.26864	0.074	T	0.15780	-1.0425	9	0.44086	T	0.13	.	15.0662	0.71996	0.0:0.0:0.0:1.0	.	410	Q9P273	TEN3_HUMAN	T	410	ENSP00000424226:I410T;ENSP00000385276:I410T	ENSP00000385276:I410T	I	+	2	0	ODZ3	183831269	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.822000	0.86651	2.197000	0.70478	0.456000	0.33151	ATT	.	.	weak		0.438	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
OR52J3	119679	hgsc.bcm.edu	37	11	5068177	5068177	+	Missense_Mutation	SNP	A	A	T	rs2500018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5068177A>T	ENST00000380370.1	+	1	422	c.422A>T	c.(421-423)cAa>cTa	p.Q141L		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	141			Q -> L (in dbSNP:rs2500018). {ECO:0000269|PubMed:14983052, ECO:0000269|Ref.1, ECO:0000269|Ref.3}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTGACATCCCAAGTGTTGGTG	0.493													A|||	2442	0.48762	0.5915	0.4971	5008	,	,		21422	0.2619		0.508	False		,,,				2504	0.5521				p.Q141L		Atlas-SNP	.											OR52J3,NS,carcinoma,-1,1	OR52J3	77	1	0			c.A422T						PASS	.	A	LEU/GLN	2444,1958	621.1+/-393.7	688,1068,445	182.0	118.0	139.0		422	-5.2	0.0	11	dbSNP_100	139	4304,4292	578.0+/-390.6	1067,2170,1061	yes	missense	OR52J3	NM_001001916.2	113	1755,3238,1506	TT,TA,AA		49.9302,44.4798,48.0843	benign	141/312	5068177	6748,6250	2201	4298	6499	SO:0001583	missense	119679	exon1			CATCCCAAGTGTT	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.422A>T	11.37:g.5068177A>T	ENSP00000369728:p.Gln141Leu	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	299	163	0.545151	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	995	0.4555860805860806	290	0.5894308943089431	170	0.4696132596685083	149	0.26048951048951047	386	0.5092348284960422	A	1.867	-0.461166	0.04508	0.555202	0.500698	ENSG00000205495	ENST00000380370	T	0.11277	2.79	4.19	-5.19	0.02832	GPCR, rhodopsin-like superfamily (1);	1.059250	0.07502	N	0.907470	T	0.00012	0.0000	L	0.33293	1	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.43621	-0.9380	9	0.46703	T	0.11	.	7.2722	0.26262	0.4249:0.2007:0.3744:0.0	rs2500018;rs17259473;rs52831001;rs60936519;rs2500018	141	Q8NH60	O52J3_HUMAN	L	141	ENSP00000369728:Q141L	ENSP00000369728:Q141L	Q	+	2	0	OR52J3	5024753	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.528000	0.02225	-0.989000	0.03485	-2.338000	0.00246	CAA	A|0.494;T|0.506	0.506	strong		0.493	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
CTXN3	613212	hgsc.bcm.edu	37	5	126993262	126993262	+	Missense_Mutation	SNP	G	G	A	rs386692235|rs61743797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:126993262G>A	ENST00000379445.3	+	3	600	c.49G>A	c.(49-51)Gaa>Aaa	p.E17K	CTC-548H10.2_ENST00000512352.1_RNA|CTXN3_ENST00000395322.3_Missense_Mutation_p.E17K	NM_001048252.2	NP_001041717.1	Q4LDR2	CTXN3_HUMAN	cortexin 3	17			E -> V (in dbSNP:rs248709). {ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0128)|COAD - Colon adenocarcinoma(49;0.0234)|OV - Ovarian serous cystadenocarcinoma(64;0.038)		CCTTGGGAACGAATCAGCAGA	0.478													G|||	11	0.00219649	0.0076	0.0	5008	,	,		21036	0.0		0.001	False		,,,				2504	0.0				p.E17K		Atlas-SNP	.											.	CTXN3	19	.	0			c.G49A						PASS	.						128.0	111.0	117.0					5																	126993262		2203	4300	6503	SO:0001583	missense	613212	exon3			GGGAACGAATCAG	AB219764	CCDS34221.1	5q23.2	2006-09-21				ENSG00000205279			31110	protein-coding gene	gene with protein product							Standard	NM_001048252		Approved		uc003kum.4	Q4LDR2		ENST00000379445.3:c.49G>A	5.37:g.126993262G>A	ENSP00000368758:p.Glu17Lys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	83	49	0.590361	NM_001048252	B2RV32|D3DQ82	Missense_Mutation	SNP	ENST00000379445.3	37	CCDS34221.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	1.635	-0.518074	0.04171	.	.	ENSG00000205279	ENST00000379445;ENST00000395322	T;T	0.30714	1.52;1.52	4.52	-5.44	0.02624	.	1.776230	0.02356	N	0.076391	T	0.08670	0.0215	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17623	-1.0363	9	0.09084	T	0.74	0.374	4.8394	0.13483	0.4246:0.0873:0.3994:0.0887	rs61743797	17	Q4LDR2	CTXN3_HUMAN	K	17	ENSP00000368758:E17K;ENSP00000378732:E17K	ENSP00000368758:E17K	E	+	1	0	CTXN3	127021161	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.490000	0.02304	-1.410000	0.02035	-0.940000	0.02684	GAA	G|0.998;A|0.002	0.002	strong		0.478	CTXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372467.1	XM_932841	
KIAA1244	57221	hgsc.bcm.edu	37	6	138645228	138645228	+	Silent	SNP	G	G	A	rs3734301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138645228G>A	ENST00000251691.4	+	31	5104	c.4938G>A	c.(4936-4938)gcG>gcA	p.A1646A		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		TGCGAGTGGCGGCCCCGTCCT	0.642													G|||	1143	0.228235	0.6142	0.1484	5008	,	,		18962	0.1151		0.0626	False		,,,				2504	0.0501				p.A1646A		Atlas-SNP	.											KIAA1244,NS,carcinoma,+1,1	KIAA1244	236	1	0			c.G4938A						PASS	.	G		2271,2135	557.4+/-379.7	599,1073,531	42.0	48.0	46.0		4938	-10.9	0.2	6	dbSNP_107	46	535,8065	143.6+/-199.6	18,499,3783	no	coding-synonymous	KIAA1244	NM_020340.4		617,1572,4314	AA,AG,GG		6.2209,48.4567,21.5747		1646/2178	138645228	2806,10200	2203	4300	6503	SO:0001819	synonymous_variant	57221	exon31			AGTGGCGGCCCCG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.4938G>A	6.37:g.138645228G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_020340		Silent	SNP	ENST00000251691.4	37	CCDS5189.2																																																																																			G|0.789;A|0.211	0.211	strong		0.642	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
KRT84	3890	hgsc.bcm.edu	37	12	52777580	52777580	+	Silent	SNP	A	A	C	rs386763043|rs1613929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52777580A>C	ENST00000257951.3	-	2	615	c.549T>G	c.(547-549)gtT>gtG	p.V183V	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	183	Coil 1A.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CTAGGAACCGAACCTAAATCC	0.493													C|||	1664	0.332268	0.6172	0.3199	5008	,	,		22989	0.1954		0.2068	False		,,,				2504	0.226				p.V183V		Atlas-SNP	.											.	KRT84	61	.	0			c.T549G						PASS	.	C		2127,2279		715,697,791	54.0	55.0	55.0		549	1.2	1.0	12	dbSNP_89	55	1290,7310		180,930,3190	yes	coding-synonymous	KRT84	NM_033045.3		895,1627,3981	CC,CA,AA		15.0,48.2751,26.2725		183/601	52777580	3417,9589	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon2			GAACCGAACCTAA	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.549T>G	12.37:g.52777580A>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.686;C|0.314	0.314	strong		0.493	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
LIPM	340654	hgsc.bcm.edu	37	10	90580023	90580023	+	Missense_Mutation	SNP	C	C	T	rs61735049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90580023C>T	ENST00000404743.4	+	9	1204	c.1037C>T	c.(1036-1038)aCg>aTg	p.T346M	ANKRD22_ENST00000476963.1_5'Flank|LIPM_ENST00000539337.1_Missense_Mutation_p.T306M	NM_001128215.1	NP_001121687.1	Q5VYY2	LIPM_HUMAN	lipase, family member M	346					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)|skin(1)	7						AGAGATATGACGGTCCCTACA	0.433													C|||	32	0.00638978	0.0219	0.0029	5008	,	,		21943	0.0		0.001	False		,,,				2504	0.0				p.T346M		Atlas-SNP	.											.	LIPM	17	.	0			c.C1037T						PASS	.	C	MET/THR,	21,1363		0,21,671	99.0	81.0	86.0		1037,	1.8	0.5	10	dbSNP_129	86	2,3180		0,2,1589	yes	missense,utr-3	ANKRD22,LIPM	NM_001128215.1,NM_144590.2	81,	0,23,2260	TT,TC,CC		0.0629,1.5173,0.5037	benign,	346/424,	90580023	23,4543	692	1591	2283	SO:0001583	missense	340654	exon9			ATATGACGGTCCC		CCDS44457.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000173239	ENSG00000173239			23455	protein-coding gene	gene with protein product		613923	"""lipase-like, ab-hydrolase domain containing 3"""	LIPL3			Standard	NM_001128215		Approved	bA304I5.1	uc009xtm.1	Q5VYY2	OTTHUMG00000018698	ENST00000404743.4:c.1037C>T	10.37:g.90580023C>T	ENSP00000383901:p.Thr346Met	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_001128215	A6PVS3|B2RXK7|B5MCR3	Missense_Mutation	SNP	ENST00000404743.4	37	CCDS44457.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	C	10.78	1.446521	0.25987	0.015173	6.29E-4	ENSG00000173239	ENST00000404743;ENST00000539337	T;T	0.72725	-0.68;-0.68	5.75	1.84	0.25277	Alpha/beta hydrolase fold-1 (1);	0.453160	0.22674	N	0.057035	T	0.43986	0.1272	M	0.86268	2.805	0.19300	N	0.999977	B;B	0.21452	0.037;0.056	B;B	0.26202	0.067;0.028	T	0.55976	-0.8055	10	0.41790	T	0.15	-6.7851	2.5727	0.04798	0.1166:0.4893:0.1138:0.2802	rs61735049	306;346	B2RXK7;Q5VYY2	.;LIPM_HUMAN	M	346;306	ENSP00000383901:T346M;ENSP00000440375:T306M	ENSP00000383901:T346M	T	+	2	0	LIPM	90570003	0.000000	0.05858	0.475000	0.27278	0.925000	0.55904	-2.177000	0.01261	0.079000	0.16929	-0.126000	0.14955	ACG	C|0.994;T|0.006	0.006	strong		0.433	LIPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049261.3	XM_291663	
CELSR1	9620	hgsc.bcm.edu	37	22	46777896	46777896	+	Missense_Mutation	SNP	C	C	G	rs7287089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46777896C>G	ENST00000262738.3	-	21	6934	c.6935G>C	c.(6934-6936)cGc>cCc	p.R2312P		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2312			R -> P (does not affect protein localization to the cell membrane; dbSNP:rs7287089). {ECO:0000269|PubMed:22095531}.		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)		AGGCCCCGGGCGCGTGGTCTG	0.682													.|||	85	0.0169728	0.0605	0.0072	5008	,	,		12386	0.0		0.0	False		,,,				2504	0.0				p.R2312P		Atlas-SNP	.											.	CELSR1	242	.	0			c.G6935C						PASS	.	C	PRO/ARG	163,4111		1,161,1975	8.0	9.0	9.0		6935	-3.2	0.0	22	dbSNP_116	9	2,8374		0,2,4186	no	missense	CELSR1	NM_014246.1	103	1,163,6161	GG,GC,CC		0.0239,3.8138,1.3043	benign	2312/3015	46777896	165,12485	2137	4188	6325	SO:0001583	missense	9620	exon21			CCCGGGCGCGTGG	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.6935G>C	22.37:g.46777896C>G	ENSP00000262738:p.Arg2312Pro	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	29	12	0.413793	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	C	9.166	1.020045	0.19433	0.038138	2.39E-4	ENSG00000075275	ENST00000262738	T	0.67698	-0.28	4.89	-3.18	0.05186	Domain of unknown function DUF3497 (1);	1.362770	0.05247	N	0.513271	T	0.05777	0.0151	N	0.08118	0	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.002	T	0.04413	-1.0953	10	0.20519	T	0.43	.	3.427	0.07414	0.1112:0.33:0.384:0.1748	rs7287089	633;2312	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	P	2312	ENSP00000262738:R2312P	ENSP00000262738:R2312P	R	-	2	0	CELSR1	45156560	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.121000	0.03270	-0.119000	0.11830	0.555000	0.69702	CGC	C|0.985;G|0.015	0.015	strong		0.682	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
CEP55	55165	hgsc.bcm.edu	37	10	95278683	95278683	+	Missense_Mutation	SNP	G	G	A	rs75139274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	251	110	0.438247	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	
BSPRY	54836	hgsc.bcm.edu	37	9	116122954	116122954	+	Silent	SNP	A	A	G	rs752757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116122954A>G	ENST00000374183.4	+	3	507	c.468A>G	c.(466-468)aaA>aaG	p.K156K	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	156					calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						CGCTGCAGAAACTTGACACCA	0.617													G|||	1825	0.364417	0.5393	0.3343	5008	,	,		17996	0.3919		0.1978	False		,,,				2504	0.2924				p.K156K		Atlas-SNP	.											BSPRY,NS,carcinoma,0,2	BSPRY	21	2	0			c.A468G						PASS	.	G		1966,2332		424,1118,607	36.0	42.0	40.0		468	5.1	1.0	9	dbSNP_86	40	1813,6705		192,1429,2638	no	coding-synonymous	BSPRY	NM_017688.2		616,2547,3245	GG,GA,AA		21.2843,45.7422,29.4866		156/403	116122954	3779,9037	2149	4259	6408	SO:0001819	synonymous_variant	54836	exon3			GCAGAAACTTGAC	AJ276691	CCDS43868.1	9q33.1	2008-02-05			ENSG00000119411	ENSG00000119411			18232	protein-coding gene	gene with protein product						10978534, 11099500	Standard	NM_017688		Approved	FLJ20150	uc004bhg.4	Q5W0U4	OTTHUMG00000021006	ENST00000374183.4:c.468A>G	9.37:g.116122954A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	85	19	0.223529	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Silent	SNP	ENST00000374183.4	37	CCDS43868.1																																																																																			G|0.353;C|0.000;N|0.000;A|0.647	0.353	strong		0.617	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688	
ZBTB3	79842	hgsc.bcm.edu	37	11	62519565	62519565	+	Missense_Mutation	SNP	G	G	C	rs544641	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	44	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	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	
DHX8	1659	hgsc.bcm.edu	37	17	41570819	41570819	+	Silent	SNP	G	G	A	rs146528228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41570819G>A	ENST00000262415.3	+	7	942	c.870G>A	c.(868-870)cgG>cgA	p.R290R	DHX8_ENST00000540306.1_Silent_p.R290R	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	290	S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		TCAGGAAGCGGTGGGAAGGCC	0.512													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19930	0.0		0.0	False		,,,				2504	0.0				p.R290R	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.G870A						PASS	.	G		31,4375	36.8+/-68.6	0,31,2172	96.0	92.0	93.0		870	0.8	1.0	17	dbSNP_134	93	0,8600		0,0,4300	no	coding-synonymous	DHX8	NM_004941.1		0,31,6472	AA,AG,GG		0.0,0.7036,0.2384		290/1221	41570819	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	1659	exon7			GAAGCGGTGGGAA	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.870G>A	17.37:g.41570819G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_004941		Silent	SNP	ENST00000262415.3	37	CCDS11464.1																																																																																			G|0.998;A|0.002	0.002	strong		0.512	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1		
PPP1R16B	26051	hgsc.bcm.edu	37	20	37534665	37534665	+	Silent	SNP	C	C	T	rs4812332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:37534665C>T	ENST00000299824.1	+	7	939	c.750C>T	c.(748-750)gaC>gaT	p.D250D	PPP1R16B_ENST00000373331.2_Intron	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	250					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				TCCTCCTGGACCATGGAGTGC	0.612													C|||	1729	0.345248	0.2995	0.3746	5008	,	,		17452	0.4167		0.336	False		,,,				2504	0.3221				p.D250D		Atlas-SNP	.											.	PPP1R16B	103	.	0			c.C750T						PASS	.	C	,	1402,3004	460.0+/-352.4	212,978,1013	106.0	95.0	98.0		,750	2.5	1.0	20	dbSNP_111	98	2770,5830	440.9+/-359.6	409,1952,1939	no	intron,coding-synonymous	PPP1R16B	NM_001172735.1,NM_015568.2	,	621,2930,2952	TT,TC,CC		32.2093,31.8202,32.0775	,	,250/568	37534665	4172,8834	2203	4300	6503	SO:0001819	synonymous_variant	26051	exon7			CCTGGACCATGGA	AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	15850	protein-coding gene	gene with protein product	"""TGF-beta-inhibited membrane-associated protein"", ""ankyrin repeat domain protein 4"""	613275	"""protein phosphatase 1, regulatory (inhibitor) subunit 16B"""			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.750C>T	20.37:g.37534665C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_015568	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Silent	SNP	ENST00000299824.1	37	CCDS13309.1																																																																																			C|0.671;T|0.329	0.329	strong		0.612	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568	
CLEC1B	51266	hgsc.bcm.edu	37	12	10150961	10150961	+	Missense_Mutation	SNP	G	G	A	rs2273987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:10150961G>A	ENST00000298527.6	-	2	262	c.83C>T	c.(82-84)tCc>tTc	p.S28F	CLEC1B_ENST00000348658.4_Intron|CLEC1B_ENST00000428126.2_Intron	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	28			S -> F (in dbSNP:rs2273987).		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.S28F(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						ACGCCACCAGGAGGAGGATGC	0.562													G|||	450	0.0898562	0.0522	0.0504	5008	,	,		18063	0.1706		0.0865	False		,,,				2504	0.089				p.S28F		Atlas-SNP	.											CLEC1B,NS,carcinoma,+1,2	CLEC1B	39	2	1	Substitution - Missense(1)	stomach(1)	c.C83T						PASS	.	G	,PHE/SER	212,3992		9,194,1899	99.0	106.0	104.0		,83	4.4	0.4	12	dbSNP_100	104	683,7739		23,637,3551	yes	intron,missense	CLEC1B	NM_001099431.1,NM_016509.3	,155	32,831,5450	AA,AG,GG		8.1097,5.0428,7.0885	,possibly-damaging	,28/230	10150961	895,11731	2102	4211	6313	SO:0001583	missense	51266	exon2			CACCAGGAGGAGG	AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"""C-type lectin domain containing"""	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.83C>T	12.37:g.10150961G>A	ENSP00000298527:p.Ser28Phe	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	193	94	0.487047	NM_016509	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	37	CCDS41752.1	214	0.09798534798534798	25	0.0508130081300813	15	0.04143646408839779	113	0.19755244755244755	61	0.08047493403693931	G	13.74	2.328352	0.41197	0.050428	0.081097	ENSG00000165682	ENST00000298527	T	0.01516	4.81	4.37	4.37	0.52481	.	0.418107	0.20454	N	0.092030	T	0.00012	0.0000	M	0.76838	2.35	0.20489	P	0.999893407	D	0.61080	0.989	P	0.57283	0.817	T	0.49679	-0.8914	9	0.40728	T	0.16	.	12.3952	0.55380	0.0:0.0:1.0:0.0	rs2273987;rs61392058;rs2273987	28	Q9P126	CLC1B_HUMAN	F	28	ENSP00000298527:S28F	ENSP00000298527:S28F	S	-	2	0	CLEC1B	10042228	0.177000	0.23109	0.430000	0.26722	0.414000	0.31173	4.546000	0.60705	1.968000	0.57251	0.305000	0.20034	TCC	G|0.909;A|0.091	0.091	strong		0.562	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509	
CLEC12B	387837	hgsc.bcm.edu	37	12	10163381	10163381	+	Missense_Mutation	SNP	C	C	T	rs11833101|rs386760228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:10163381C>T	ENST00000338896.5	+	1	151	c.23C>T	c.(22-24)gCg>gTg	p.A8V	CLEC1B_ENST00000428126.2_Intron|CLEC12B_ENST00000396502.1_Missense_Mutation_p.A8V	NM_001129998.1	NP_001123470.1	Q2HXU8	CL12B_HUMAN	C-type lectin domain family 12, member B	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|large_intestine(2)|lung(5)	9						GTGACCTACGCGACACTCACA	0.398													C|||	160	0.0319489	0.1135	0.0144	5008	,	,		20629	0.0		0.0	False		,,,				2504	0.0				p.A8V		Atlas-SNP	.											.	CLEC12B	25	.	0			c.C23T						PASS	.	C	VAL/ALA,VAL/ALA	334,4072	170.1+/-200.6	12,310,1881	61.0	58.0	59.0		23,23	4.0	0.3	12	dbSNP_120	59	0,8600		0,0,4300	yes	missense,missense	CLEC12B	NM_001129998.1,NM_205852.2	64,64	12,310,6181	TT,TC,CC		0.0,7.5806,2.568	possibly-damaging,possibly-damaging	8/277,8/233	10163381	334,12672	2203	4300	6503	SO:0001583	missense	387837	exon1			CCTACGCGACACT	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.23C>T	12.37:g.10163381C>T	ENSP00000344563:p.Ala8Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	28	0.363636	NM_001129998	Q6UWF2|Q6ZRG0	Missense_Mutation	SNP	ENST00000338896.5	37	CCDS44830.1	60	0.027472527472527472	54	0.10975609756097561	6	0.016574585635359115	0	0.0	0	0.0	C	12.83	2.054910	0.36277	0.075806	0.0	ENSG00000256660	ENST00000396502;ENST00000338896	T;T	0.01629	4.72;5.01	4.88	4.0	0.46444	.	0.368895	0.22840	N	0.054991	T	0.00073	0.0002	M	0.69823	2.125	0.18873	N	0.999986	B;P;P	0.44690	0.206;0.454;0.841	B;B;B	0.33690	0.022;0.049;0.168	T	0.50841	-0.8780	10	0.62326	D	0.03	.	9.8308	0.40941	0.0:0.9025:0.0:0.0975	rs11833101;rs56980128	8;8;8	Q2HXU8;Q2HXU8-2;F5H4H7	CL12B_HUMAN;.;.	V	8	ENSP00000379759:A8V;ENSP00000344563:A8V	ENSP00000344563:A8V	A	+	2	0	CLEC12B	10054648	0.000000	0.05858	0.322000	0.25334	0.601000	0.36947	0.634000	0.24614	1.390000	0.46547	0.561000	0.74099	GCG	C|0.976;T|0.024	0.024	strong		0.398	CLEC12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399554.2	NM_205852	
ZNF444	55311	hgsc.bcm.edu	37	19	56669889	56669889	+	Silent	SNP	G	G	A	rs61736530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56669889G>A	ENST00000337080.3	+	4	691	c.324G>A	c.(322-324)tcG>tcA	p.S108S	ZNF444_ENST00000592171.1_3'UTR|ZNF444_ENST00000592949.1_Silent_p.S108S	NM_001253792.1|NM_018337.3	NP_001240721.1|NP_060807.2	Q8N0Y2	ZN444_HUMAN	zinc finger protein 444	108					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)			NS(1)|endometrium(1)|lung(5)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0531)		CCGATGGGTCGTCAGCAACGA	0.597													g|||	64	0.0127796	0.0461	0.0014	5008	,	,		17153	0.001		0.001	False		,,,				2504	0.0				p.S108S		Atlas-SNP	.											.	ZNF444	15	.	0			c.G324A						PASS	.	A		220,4186	131.8+/-168.3	3,214,1986	74.0	64.0	68.0		324	-5.4	0.0	19	dbSNP_129	68	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	ZNF444	NM_018337.2		3,216,6284	AA,AG,GG		0.0233,4.9932,1.7069		108/328	56669889	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	55311	exon4			TGGGTCGTCAGCA	AB052954	CCDS12939.1, CCDS59426.1	19q13.43	2013-01-09			ENSG00000167685	ENSG00000167685		"""-"", ""Zinc fingers, C2H2-type"""	16052	protein-coding gene	gene with protein product		607874				11978792, 19760602	Standard	NM_001253792		Approved	ZSCAN17, FLJ11137, EZF2	uc002qmm.3	Q8N0Y2		ENST00000337080.3:c.324G>A	19.37:g.56669889G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	214	214	1	NM_001253792	Q8TEQ9|Q8WU35|Q9NUU1	Silent	SNP	ENST00000337080.3	37	CCDS12939.1																																																																																			G|0.981;A|0.019	0.019	strong		0.597	ZNF444-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457503.1	NM_018337	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595183	140595183	+	Silent	SNP	G	G	T	rs2910330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	279	1	0.00358423		WXS	Illumina HiSeq	Phase_I	298	145	0.486577	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	
PLXNA4	91584	hgsc.bcm.edu	37	7	132192949	132192949	+	Silent	SNP	T	T	C	rs156962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:132192949T>C	ENST00000359827.3	-	2	1466	c.504A>G	c.(502-504)tcA>tcG	p.S168S	PLXNA4_ENST00000423507.2_Silent_p.S168S|PLXNA4_ENST00000378539.5_Silent_p.S168S|PLXNA4_ENST00000321063.4_Silent_p.S168S			Q9HCM2	PLXA4_HUMAN	plexin A4	168	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)	p.S168S(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CTCCAAAGACTGAGCCGCTCT	0.542													C|||	1970	0.393371	0.5159	0.3588	5008	,	,		19381	0.2718		0.3917	False		,,,				2504	0.3793				p.S168S		Atlas-SNP	.											PLXNA4_ENST00000359827,NS,carcinoma,0,2	PLXNA4	873	2	2	Substitution - coding silent(2)	stomach(2)	c.A504G						PASS	.	C	,,	2117,2289	600.1+/-389.4	512,1093,598	110.0	98.0	102.0		504,504,504	-10.5	0.1	7	dbSNP_79	102	3346,5254	642.8+/-399.9	639,2068,1593	no	coding-synonymous,coding-synonymous,coding-synonymous	PLXNA4	NM_001105543.1,NM_020911.1,NM_181775.3	,,	1151,3161,2191	CC,CT,TT		38.907,48.0481,42.0037	,,	168/493,168/1895,168/523	132192949	5463,7543	2203	4300	6503	SO:0001819	synonymous_variant	91584	exon2			AAAGACTGAGCCG	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.504A>G	7.37:g.132192949T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	130	71	0.546154	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			T|0.598;C|0.402	0.402	strong		0.542	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
ALLC	55821	hgsc.bcm.edu	37	2	3729254	3729254	+	Missense_Mutation	SNP	C	C	T	rs13426642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:3729254C>T	ENST00000252505.3	+	6	491	c.329C>T	c.(328-330)aCc>aTc	p.T110I		NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	129					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		GAAAGAGGAACCAGGACAGGA	0.443										HNSCC(21;0.051)			T|||	958	0.191294	0.3487	0.1326	5008	,	,		18597	0.13		0.174	False		,,,				2504	0.1012				p.T110I		Atlas-SNP	.											.	ALLC	61	.	0			c.C329T						PASS	.	T	ILE/THR	1109,2681		150,809,936	53.0	56.0	55.0		329	-1.7	0.0	2	dbSNP_121	55	1577,6649		159,1259,2695	yes	missense	ALLC	NM_018436.3	89	309,2068,3631	TT,TC,CC		19.1709,29.2612,22.3535	benign	110/392	3729254	2686,9330	1895	4113	6008	SO:0001583	missense	55821	exon6			GAGGAACCAGGAC	AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.329C>T	2.37:g.3729254C>T	ENSP00000252505:p.Thr110Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_018436	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	37	CCDS46223.1	428	0.19597069597069597	175	0.3556910569105691	53	0.1464088397790055	69	0.12062937062937062	131	0.17282321899736147	T	2.425	-0.332270	0.05314	0.292612	0.191709	ENSG00000151360	ENST00000252505	.	.	.	4.98	-1.69	0.08186	Allantoicase domain (1);Galactose-binding domain-like (1);	1.431930	0.04091	N	0.311285	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.40403	-0.9565	8	0.36615	T	0.2	-6.0446	1.6428	0.02756	0.148:0.3466:0.153:0.3524	rs13426642;rs17856846;rs59065366;rs13426642	129	Q8N6M5	ALLC_HUMAN	I	110	.	ENSP00000252505:T110I	T	+	2	0	ALLC	3707129	0.000000	0.05858	0.005000	0.12908	0.006000	0.05464	-0.729000	0.04920	-0.411000	0.07530	-0.269000	0.10298	ACC	C|0.801;T|0.199	0.199	strong		0.443	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1		
BLZF1	8548	hgsc.bcm.edu	37	1	169345883	169345883	+	Missense_Mutation	SNP	A	A	G	rs112226207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169345883A>G	ENST00000367808.3	+	3	557	c.134A>G	c.(133-135)cAt>cGt	p.H45R	BLZF1_ENST00000367807.3_Missense_Mutation_p.H45R|BLZF1_ENST00000329281.2_Missense_Mutation_p.H45R			Q9H2G9	GO45_HUMAN	basic leucine zipper nuclear factor 1	45					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|mitotic cell cycle (GO:0000278)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	14	all_hematologic(923;0.208)					AGAAAGCATCATAGTCTTCAG	0.453													A|||	8	0.00159744	0.0053	0.0014	5008	,	,		18203	0.0		0.0	False		,,,				2504	0.0				p.H45R		Atlas-SNP	.											.	BLZF1	57	.	0			c.A134G						PASS	.	A	ARG/HIS	30,4376	36.0+/-67.5	0,30,2173	95.0	95.0	95.0		134	-1.9	0.0	1	dbSNP_132	95	0,8600		0,0,4300	yes	missense	BLZF1	NM_003666.2	29	0,30,6473	GG,GA,AA		0.0,0.6809,0.2307	benign	45/401	169345883	30,12976	2203	4300	6503	SO:0001583	missense	8548	exon3			AGCATCATAGTCT	U79751	CCDS1278.1	1q24	2008-08-01	2008-08-01		ENSG00000117475	ENSG00000117475			1065	protein-coding gene	gene with protein product		608692				9129147	Standard	NM_003666		Approved	JEM-1	uc001gfy.3	Q9H2G9	OTTHUMG00000035453	ENST00000367808.3:c.134A>G	1.37:g.169345883A>G	ENSP00000356782:p.His45Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	144	71	0.493056	NM_003666	O15298|Q5T531|Q5T533|Q9GZX4	Missense_Mutation	SNP	ENST00000367808.3	37	CCDS1278.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	A	4.096	0.015897	0.07959	0.006809	0.0	ENSG00000117475	ENST00000367808;ENST00000329281;ENST00000367807;ENST00000420531;ENST00000426663	T;T;T;T;T	0.42513	1.57;1.57;0.97;0.97;1.57	5.27	-1.89	0.07689	.	0.566329	0.20243	N	0.096258	T	0.07234	0.0183	N	0.22421	0.69	0.26193	N	0.979556	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.001;0.001;0.003	T	0.34279	-0.9835	9	0.09590	T	0.72	-2.9441	6.7849	0.23668	0.5046:0.3627:0.1328:0.0	.	45;45;45	A8K6R0;Q9H2G9;Q9H2G9-2	.;GO45_HUMAN;.	R	45	ENSP00000356782:H45R;ENSP00000327541:H45R;ENSP00000356781:H45R;ENSP00000414668:H45R;ENSP00000404408:H45R	ENSP00000327541:H45R	H	+	2	0	BLZF1	167612507	0.001000	0.12720	0.000000	0.03702	0.695000	0.40330	0.633000	0.24598	-0.247000	0.09597	-0.389000	0.06534	CAT	A|0.997;G|0.003	0.003	strong		0.453	BLZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086109.1	NM_003666	
CLEC10A	10462	hgsc.bcm.edu	37	17	6979179	6979179	+	Silent	SNP	A	A	G	rs364569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:6979179A>G	ENST00000254868.4	-	7	874	c.546T>C	c.(544-546)ccT>ccC	p.P182P	CLEC10A_ENST00000571664.1_Silent_p.P158P|CLEC10A_ENST00000416562.2_Silent_p.P155P|CLEC10A_ENST00000576617.1_Silent_p.P155P	NM_182906.2	NP_878910.1	Q8IUN9	CLC10_HUMAN	C-type lectin domain family 10, member A	182					endocytosis (GO:0006897)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						CCCAGTTGACAGGGCAGCAGG	0.597													g|||	2125	0.424321	0.6936	0.3127	5008	,	,		18008	0.3294		0.3569	False		,,,				2504	0.3067				p.P182P		Atlas-SNP	.											.	CLEC10A	40	.	0			c.T546C						PASS	.	G	,	2888,1518	481.2+/-359.0	945,998,260	78.0	76.0	77.0		474,546	-1.1	0.0	17	dbSNP_80	77	3040,5560	661.6+/-401.9	546,1948,1806	no	coding-synonymous,coding-synonymous	CLEC10A	NM_006344.2,NM_182906.2	,	1491,2946,2066	GG,GA,AA		35.3488,34.453,45.579	,	158/293,182/317	6979179	5928,7078	2203	4300	6503	SO:0001819	synonymous_variant	10462	exon7			GTTGACAGGGCAG	D50532	CCDS11087.1, CCDS45597.1	17p13.2	2014-05-20	2005-02-09	2005-02-11		ENSG00000132514		"""C-type lectin domain containing"", ""CD molecules"""	16916	protein-coding gene	gene with protein product	"""macrophage lectin 2 (calcium dependent)"""	605999	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 14 (macrophage-derived)"""	CLECSF13, CLECSF14		8598452	Standard	XM_005256411		Approved	HML2, HML, CD301	uc002gej.3	Q8IUN9		ENST00000254868.4:c.546T>C	17.37:g.6979179A>G		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_182906	A8K8J8|Q14538|Q6PIW3	Silent	SNP	ENST00000254868.4	37	CCDS11087.1																																																																																			A|0.544;G|0.456	0.456	strong		0.597	CLEC10A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439837.2	NM_006344	
ALOX15B	247	hgsc.bcm.edu	37	17	7950394	7950394	+	Splice_Site	SNP	G	G	A	rs9895916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7950394G>A	ENST00000380183.4	+	10	1596	c.1457G>A	c.(1456-1458)cGc>cAc	p.R486H	ALOX15B_ENST00000573359.1_Intron|ALOX15B_ENST00000572022.1_Splice_Site_p.R486H|ALOX15B_ENST00000380173.2_Splice_Site_p.R457H	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	486	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		R -> H (in dbSNP:rs9895916). {ECO:0000269|PubMed:11839751}.		apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						GCAGTGGAACGGTGAGGGGCC	0.627													G|||	586	0.117013	0.2337	0.0288	5008	,	,		17866	0.0645		0.0119	False		,,,				2504	0.184				p.R486H		Atlas-SNP	.											ALOX15B,caecum,carcinoma,+1,2	ALOX15B	66	2	0			c.G1457A						PASS	.	G	HIS/ARG,,HIS/ARG	888,3518	342.8+/-307.3	91,706,1406	60.0	61.0	61.0		1370,,1457	0.2	0.1	17	dbSNP_119	61	168,8432	78.9+/-141.6	2,164,4134	yes	missense-near-splice,intron,missense-near-splice	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	29,,29	93,870,5540	AA,AG,GG		1.9535,20.1543,8.1193	benign,,benign	457/648,,486/677	7950394	1056,11950	2203	4300	6503	SO:0001630	splice_region_variant	247	exon10			TGGAACGGTGAGG	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1457+1G>A	17.37:g.7950394G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	161	0.07371794871794872	99	0.20121951219512196	14	0.03867403314917127	41	0.07167832167832168	7	0.009234828496042216	G	15.53	2.859695	0.51376	0.201543	0.019535	ENSG00000179593	ENST00000380173;ENST00000380183	D;D	0.90324	-2.65;-2.65	4.69	0.219	0.15274	Lipoxygenase, C-terminal (3);	0.391636	0.31673	N	0.007255	T	0.00384	0.0012	L	0.51914	1.62	0.28434	P	0.9171212	B;B;B	0.29862	0.259;0.218;0.164	B;B;B	0.27715	0.056;0.049;0.082	T	0.19353	-1.0308	9	0.48119	T	0.1	-1.7759	5.3026	0.15785	0.2424:0.0:0.616:0.1417	rs9895916	486;457;486	B4DNW8;O15296-4;O15296	.;.;LX15B_HUMAN	H	457;486	ENSP00000369520:R457H;ENSP00000369530:R486H	ENSP00000369520:R457H	R	+	2	0	ALOX15B	7891119	1.000000	0.71417	0.121000	0.21740	0.892000	0.51952	3.649000	0.54417	-0.093000	0.12396	0.655000	0.94253	CGC	G|0.923;A|0.077	0.077	strong		0.627	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		Missense_Mutation
TRIM7	81786	hgsc.bcm.edu	37	5	180626927	180626927	+	Missense_Mutation	SNP	A	A	G	rs416574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180626927A>G	ENST00000274773.7	-	3	834	c.773T>C	c.(772-774)gTt>gCt	p.V258A	TRIM7_ENST00000393315.1_Missense_Mutation_p.V50A|CTC-338M12.6_ENST00000502812.2_RNA|CTC-338M12.6_ENST00000511517.1_RNA|CTC-338M12.6_ENST00000512508.1_RNA|CTC-338M12.6_ENST00000514784.1_RNA|CTC-338M12.6_ENST00000509080.1_RNA|TRIM7_ENST00000422067.2_Missense_Mutation_p.V50A|TRIM7_ENST00000361809.3_Missense_Mutation_p.V50A|CTC-338M12.6_ENST00000419707.2_RNA|TRIM7_ENST00000393319.3_Missense_Mutation_p.V76A|TRIM7_ENST00000504241.1_5'Flank	NM_203293.1	NP_976038.1	Q9C029	TRIM7_HUMAN	tripartite motif containing 7	258			V -> A (in dbSNP:rs416574).			cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.V258A(1)		NS(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|stomach(1)	17	all_cancers(89;6.03e-06)|all_epithelial(37;7.1e-07)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000172)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;2e-06)|Epithelial(171;1.35e-05)|OV - Ovarian serous cystadenocarcinoma(192;0.000128)|Kidney(146;0.0674)|GBM - Glioblastoma multiforme(465;0.0802)		GGTGATCTCAACCCCGAGCTG	0.607													G|||	2669	0.532947	0.9455	0.2709	5008	,	,		19203	0.4732		0.2893	False		,,,				2504	0.4734				p.V258A	Esophageal Squamous(128;2258 2308 35507 48647)	Atlas-SNP	.											TRIM7,NS,carcinoma,0,1	TRIM7	56	1	1	Substitution - Missense(1)	stomach(1)	c.T773C						PASS	.	G	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	3651,755	307.7+/-290.2	1516,619,68	75.0	63.0	67.0		773,149,149,149,227	-0.9	0.0	5	dbSNP_80	67	2492,6108	694.6+/-404.7	360,1772,2168	yes	missense,missense,missense,missense,missense	TRIM7	NM_203293.1,NM_203294.1,NM_203295.1,NM_203296.1,NM_203297.1	64,64,64,64,64	1876,2391,2236	GG,GA,AA		28.9767,17.1357,47.232	benign,benign,benign,benign,benign	258/512,50/304,50/304,50/304,76/330	180626927	6143,6863	2203	4300	6503	SO:0001583	missense	81786	exon3			ATCTCAACCCCGA	AF220032	CCDS4462.1, CCDS4463.1, CCDS4464.1, CCDS43414.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146054	ENSG00000146054		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16278	protein-coding gene	gene with protein product	"""glycogenin-interacting protein"", ""tripartite motif protein TRIM7"""	609315	"""tripartite motif-containing 7"""			11331580	Standard	NM_203294		Approved	RNF90, GNIP	uc003mmz.1	Q9C029	OTTHUMG00000130963	ENST00000274773.7:c.773T>C	5.37:g.180626927A>G	ENSP00000274773:p.Val258Ala	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_203293	A2RUE4|D3DWR7|Q969F5|Q96F67|Q96J89|Q96J90	Missense_Mutation	SNP	ENST00000274773.7	37	CCDS4462.1	1022	0.46794871794871795	461	0.9369918699186992	96	0.26519337016574585	254	0.44405594405594406	211	0.2783641160949868	G	2.916	-0.224239	0.06061	0.828643	0.289767	ENSG00000146054	ENST00000274773;ENST00000393315;ENST00000361809;ENST00000393319;ENST00000422067	T;T;T;T;T	0.04454	3.62;3.62;3.62;3.62;3.62	5.34	-0.916	0.10489	.	0.865708	0.10169	N	0.707336	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.06570	-1.0819	9	0.23302	T	0.38	.	2.2804	0.04112	0.1231:0.2807:0.3711:0.2251	rs416574;rs59917988;rs416574	258;76	Q9C029;Q9C029-4	TRIM7_HUMAN;.	A	258;50;50;76;50	ENSP00000274773:V258A;ENSP00000376991:V50A;ENSP00000355059:V50A;ENSP00000376994:V76A;ENSP00000391458:V50A	ENSP00000274773:V258A	V	-	2	0	TRIM7	180559533	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.072000	0.11486	-0.899000	0.03901	-1.794000	0.00625	GTT	A|0.532;G|0.468	0.468	strong		0.607	TRIM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253569.3	NM_203296	
CSF1	1435	hgsc.bcm.edu	37	1	110466776	110466776	+	Silent	SNP	C	C	T	rs3208449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110466776C>T	ENST00000329608.6	+	6	1924	c.1533C>T	c.(1531-1533)gcC>gcT	p.A511A	CSF1_ENST00000369801.1_Silent_p.A395A|CSF1_ENST00000369802.3_Silent_p.A511A|CSF1_ENST00000344188.5_Silent_p.A395A|CSF1_ENST00000420111.2_Silent_p.A213A	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	511					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|developmental process involved in reproduction (GO:0003006)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary duct terminal end bud growth (GO:0060763)|mammary gland fat development (GO:0060611)|monocyte activation (GO:0042117)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|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 cellular protein metabolic process (GO:0032270)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of macrophage derived foam cell differentiation (GO:0010743)|regulation of ossification (GO:0030278)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|macrophage colony-stimulating factor receptor binding (GO:0005157)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		TCTTGCTGGCCGTCGGAGGCC	0.637													C|||	14	0.00279553	0.0106	0.0	5008	,	,		16807	0.0		0.0	False		,,,				2504	0.0				p.A511A		Atlas-SNP	.											.	CSF1	40	.	0			c.C1533T						PASS	.	C	,,,	28,4376		0,28,2174	34.0	34.0	34.0		1533,1185,639,1533	-8.4	0.1	1	dbSNP_105	34	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CSF1	NM_000757.5,NM_172210.2,NM_172211.2,NM_172212.2	,,,	0,29,6473	TT,TC,CC		0.0116,0.6358,0.223	,,,	511/555,395/439,213/257,511/555	110466776	29,12975	2202	4300	6502	SO:0001819	synonymous_variant	1435	exon6			GCTGGCCGTCGGA	BC021117	CCDS816.1, CCDS817.1, CCDS30797.1	1p13.3	2012-09-20			ENSG00000184371	ENSG00000184371			2432	protein-coding gene	gene with protein product		120420				1540160	Standard	NM_172210		Approved	M-CSF, MCSF, MGC31930	uc001dyw.4	P09603	OTTHUMG00000011646	ENST00000329608.6:c.1533C>T	1.37:g.110466776C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_000757	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Silent	SNP	ENST00000329608.6	37	CCDS816.1																																																																																			C|0.996;T|0.004	0.004	strong		0.637	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757	
UMODL1	89766	hgsc.bcm.edu	37	21	43531325	43531325	+	Intron	SNP	C	C	T	rs114358105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43531325C>T	ENST00000408910.2	+	11	1899				UMODL1_ENST00000400427.1_Nonsense_Mutation_p.Q593*|UMODL1_ENST00000400424.2_Intron|UMODL1_ENST00000408989.2_Nonsense_Mutation_p.Q665*|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						GAGCCTCAGACAGGAGAGTAC	0.716													C|||	102	0.0203674	0.0378	0.0144	5008	,	,		10893	0.0		0.0119	False		,,,				2504	0.0307				p.Q665X	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C1993T						PASS	.	C	,stop/GLN,,stop/GLN	85,3533		0,85,1724	5.0	8.0	7.0		,1777,,1993	-0.5	0.0	21	dbSNP_132	7	101,7793		0,101,3846	no	intron,stop-gained,intron,stop-gained	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	0,186,5570	TT,TC,CC		1.2795,2.3494,1.6157	,,,	,593/1375,,665/1447	43531325	186,11326	1809	3947	5756	SO:0001627	intron_variant	89766	exon11			CTCAGACAGGAGA		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.1899+94C>T	21.37:g.43531325C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Nonsense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	34	0.015567765567765568	18	0.036585365853658534	7	0.019337016574585635	0	0.0	9	0.011873350923482849	C	24.3	4.516105	0.85495	0.023494	0.012795	ENSG00000177398	ENST00000400427;ENST00000408989	.	.	.	1.9	-0.51	0.11973	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	.	3.6921	0.08350	0.0:0.3661:0.4365:0.1973	.	.	.	.	X	593;665	.	ENSP00000383279:Q593X	Q	+	1	0	UMODL1	42404394	0.032000	0.19561	0.000000	0.03702	0.001000	0.01503	0.967000	0.29344	0.138000	0.18790	0.609000	0.83330	CAG	C|0.985;T|0.015	0.015	strong		0.716	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
PASK	23178	hgsc.bcm.edu	37	2	242065635	242065635	+	Missense_Mutation	SNP	A	A	G	rs77674262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242065635A>G	ENST00000405260.1	-	10	3393	c.2695T>C	c.(2695-2697)Tac>Cac	p.Y899H	PASK_ENST00000544142.1_Missense_Mutation_p.Y713H|PASK_ENST00000358649.4_Missense_Mutation_p.Y899H|PASK_ENST00000539818.1_Missense_Mutation_p.Y683H|PASK_ENST00000403638.3_Missense_Mutation_p.Y899H|PASK_ENST00000234040.4_Missense_Mutation_p.Y899H	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	899				Y -> H (in Ref. 1; AAK69752). {ECO:0000305}.	negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		TCTCGATGGTAGCAGCTCCCG	0.637													A|||	109	0.0217652	0.0764	0.0115	5008	,	,		17584	0.0		0.0	False		,,,				2504	0.0				p.Y899H		Atlas-SNP	.											.	PASK	230	.	0			c.T2695C						PASS	.	A	HIS/TYR	255,4151	142.3+/-177.5	10,235,1958	70.0	56.0	61.0		2695	2.4	0.9	2	dbSNP_131	61	0,8600		0,0,4300	yes	missense	PASK	NM_015148.2	83	10,235,6258	GG,GA,AA		0.0,5.7876,1.9606	benign	899/1324	242065635	255,12751	2203	4300	6503	SO:0001583	missense	23178	exon10			GATGGTAGCAGCT	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2695T>C	2.37:g.242065635A>G	ENSP00000384016:p.Tyr899His	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	143	74	0.517483	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	42	0.019230769230769232	38	0.07723577235772358	4	0.011049723756906077	0	0.0	0	0.0	A	6.136	0.393272	0.11638	0.057876	0.0	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.33;-0.37;0.57	4.94	2.43	0.29744	.	0.703722	0.12909	N	0.429094	T	0.06872	0.0175	M	0.62723	1.935	0.28200	N	0.927392	B;B;B;B;B	0.18013	0.014;0.025;0.025;0.015;0.014	B;B;B;B;B	0.18561	0.01;0.022;0.022;0.022;0.01	T	0.24440	-1.0160	10	0.45353	T	0.12	.	5.2611	0.15573	0.758:0.0:0.0873:0.1548	.	864;713;899;899;899	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	H	899;713;899;899;683;899	ENSP00000234040:Y899H;ENSP00000441374:Y713H;ENSP00000384016:Y899H;ENSP00000351475:Y899H;ENSP00000443083:Y683H;ENSP00000384438:Y899H	ENSP00000234040:Y899H	Y	-	1	0	PASK	241714308	1.000000	0.71417	0.911000	0.35937	0.022000	0.10575	2.054000	0.41335	0.734000	0.32515	-0.411000	0.06167	TAC	A|0.979;G|0.021	0.021	strong		0.637	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
STAMBPL1	57559	hgsc.bcm.edu	37	10	90681048	90681048	+	Silent	SNP	C	C	T	rs34083181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90681048C>T	ENST00000371926.3	+	9	2008	c.1050C>T	c.(1048-1050)ccC>ccT	p.P350P	STAMBPL1_ENST00000371922.1_Silent_p.P184P|STAMBPL1_ENST00000371924.1_Silent_p.P350P|STAMBPL1_ENST00000371927.3_Silent_p.P350P	NM_020799.3	NP_065850.1	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	350	MPN.					membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(2)|endometrium(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(1)	11		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		AGACACATCCCACTCAAACTG	0.368													C|||	133	0.0265575	0.0272	0.0101	5008	,	,		19700	0.0387		0.0089	False		,,,				2504	0.0429				p.P350P		Atlas-SNP	.											.	STAMBPL1	63	.	0			c.C1050T						PASS	.	C		87,4319	75.2+/-113.4	0,87,2116	110.0	103.0	105.0		1050	-10.0	0.7	10	dbSNP_126	105	72,8528	42.6+/-100.3	0,72,4228	no	coding-synonymous	STAMBPL1	NM_020799.2		0,159,6344	TT,TC,CC		0.8372,1.9746,1.2225		350/437	90681048	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	57559	exon9			ACATCCCACTCAA	AB037794	CCDS7391.1	10q23.32	2006-11-08			ENSG00000138134	ENSG00000138134			24105	protein-coding gene	gene with protein product	"""associated molecule with the SH3 domain of STAM (AMSH) like protein"", ""associated molecule with the SH3 domain of STAM (AMSH) - Family Protein"""	612352				12810066, 12943674	Standard	NM_020799		Approved	AMSH-LP, KIAA1373, AMSH-FP, FLJ31524, ALMalpha, bA399O19.2	uc001kfk.4	Q96FJ0	OTTHUMG00000018702	ENST00000371926.3:c.1050C>T	10.37:g.90681048C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_020799	B3KPA7|Q5T9N4|Q5T9N9|Q7Z420|Q9P2H4	Silent	SNP	ENST00000371926.3	37	CCDS7391.1																																																																																			C|0.982;T|0.018	0.018	strong		0.368	STAMBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049283.1	NM_020799	
AAMDC	28971	hgsc.bcm.edu	37	11	77553638	77553638	+	Silent	SNP	T	T	C	rs585721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77553638T>C	ENST00000526415.1	+	3	269	c.96T>C	c.(94-96)ggT>ggC	p.G32G	RP11-91P24.7_ENST00000525594.1_RNA|AAMDC_ENST00000533193.1_Silent_p.G32G|AAMDC_ENST00000525409.1_Silent_p.G32G|AAMDC_ENST00000532481.1_Silent_p.G32G|AAMDC_ENST00000525034.1_Silent_p.G51G|AAMDC_ENST00000393427.2_Silent_p.G32G|AAMDC_ENST00000527134.1_Silent_p.G32G|AAMDC_ENST00000304716.8_Silent_p.G32G			Q9H7C9	AAMDC_HUMAN	adipogenesis associated, Mth938 domain containing	32	MTH138-like domain. {ECO:0000250}.				negative regulation of apoptotic process (GO:0043066)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)		p.G32G(1)									GGCCAGGGGGTAGTCGGACTT	0.433													C|||	1957	0.390775	0.5265	0.3948	5008	,	,		17605	0.2688		0.3688	False		,,,				2504	0.3528				p.G32G		Atlas-SNP	.											C11orf67,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.T96C						PASS	.	C		2296,2104	575.6+/-384.0	583,1130,487	69.0	67.0	68.0		96	-1.8	1.0	11	dbSNP_83	68	3162,5422	653.5+/-401.1	586,1990,1716	no	coding-synonymous	C11orf67	NM_024684.2		1169,3120,2203	CC,CT,TT		36.836,47.8182,42.0364		32/123	77553638	5458,7526	2200	4292	6492	SO:0001819	synonymous_variant	28971	exon2			AGGGGGTAGTCGG	BC016854	CCDS8254.1	11q14.1	2012-10-08	2012-10-08	2012-10-08	ENSG00000087884	ENSG00000087884			30205	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 67"""	C11orf67		12477932	Standard	NM_024684		Approved	PTD015, FLJ21035, CK067	uc001oyq.3	Q9H7C9	OTTHUMG00000166651	ENST00000526415.1:c.96T>C	11.37:g.77553638T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	34	0.377778	NM_024684	Q96AQ4|Q9Y6B1	Silent	SNP	ENST00000526415.1	37	CCDS8254.1																																																																																			T|0.588;C|0.412	0.412	strong		0.433	AAMDC-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390976.1	NM_024684	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59500255	59500255	+	Silent	SNP	C	C	T	rs61740133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:59500255C>T	ENST00000307144.4	+	1	1214	c.1116C>T	c.(1114-1116)ctC>ctT	p.L372L	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	372					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						CAAAAACACTCTGGGAAATTC	0.358													T|||	529	0.105631	0.2216	0.0865	5008	,	,		18846	0.0397		0.0517	False		,,,				2504	0.0859				p.L372L		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.C1116T						PASS	.	T	,	691,3509		54,583,1463	47.0	53.0	51.0		,1116	1.5	0.1	15	dbSNP_129	51	468,8016		15,438,3789	no	intron,coding-synonymous	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,	69,1021,5252	TT,TC,CC		5.5163,16.4524,9.1375	,	,372/382	59500255	1159,11525	2100	4242	6342	SO:0001819	synonymous_variant	92483	exon1			AACACTCTGGGAA	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.1116C>T	15.37:g.59500255C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_033195	Q6DUY4|Q96LI2	Silent	SNP	ENST00000307144.4	37	CCDS10171.1																																																																																			C|0.923;T|0.077	0.077	strong		0.358	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
USP46	64854	hgsc.bcm.edu	37	4	53494283	53494283	+	Silent	SNP	G	G	A	rs115007179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:53494283G>A	ENST00000441222.3	-	3	349	c.165C>T	c.(163-165)ttC>ttT	p.F55F	USP46_ENST00000508499.1_Silent_p.F48F|USP46_ENST00000504078.1_5'Flank|USP46_ENST00000451218.2_Silent_p.F28F	NM_022832.3	NP_073743.2	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46	55	USP.				adult feeding behavior (GO:0008343)|behavioral fear response (GO:0001662)|behavioral response to ethanol (GO:0048149)|protein deubiquitination (GO:0016579)|regulation of synaptic transmission, GABAergic (GO:0032228)|righting reflex (GO:0060013)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)	12			LUSC - Lung squamous cell carcinoma(32;0.0295)			ATGGACGGCAGAAGTACAATG	0.522													G|||	43	0.00858626	0.031	0.0029	5008	,	,		21730	0.0		0.0	False		,,,				2504	0.0				p.F55F		Atlas-SNP	.											.	USP46	38	.	0			c.C165T						PASS	.	G	,	110,3966		2,106,1930	90.0	85.0	86.0		144,165	5.2	1.0	4	dbSNP_132	86	3,8385		0,3,4191	no	coding-synonymous,coding-synonymous	USP46	NM_001134223.1,NM_022832.3	,	2,109,6121	AA,AG,GG		0.0358,2.6987,0.9066	,	48/360,55/367	53494283	113,12351	2038	4194	6232	SO:0001819	synonymous_variant	64854	exon3			ACGGCAGAAGTAC	AK022614	CCDS47053.1, CCDS47054.1	4q12	2008-02-05	2005-08-08		ENSG00000109189	ENSG00000109189		"""Ubiquitin-specific peptidases"""	20075	protein-coding gene	gene with protein product		612849	"""ubiquitin specific protease 46"""			12838346	Standard	NM_022832		Approved	FLJ12552	uc003gzn.3	P62068	OTTHUMG00000160640	ENST00000441222.3:c.165C>T	4.37:g.53494283G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	102	101	0.990196	NM_022832	B7Z3Y7|B7Z675|B7Z7S3|G8ACC7|Q80V95|Q9H7U4|Q9H9T8	Silent	SNP	ENST00000441222.3	37	CCDS47053.1																																																																																			G|0.997;A|0.003	0.003	strong		0.522	USP46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361516.2	NM_022832	
TTC17	55761	hgsc.bcm.edu	37	11	43413028	43413028	+	Missense_Mutation	SNP	A	A	C	rs12099204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:43413028A>C	ENST00000039989.4	+	4	447	c.433A>C	c.(433-435)Ata>Cta	p.I145L	RP11-484D2.4_ENST00000394183.2_RNA|TTC17_ENST00000299240.6_Missense_Mutation_p.I145L	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	145			I -> L (in dbSNP:rs12099204).		actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						TGAAGATTATATAGACACAGA	0.328													A|||	528	0.105431	0.382	0.0317	5008	,	,		16846	0.0		0.001	False		,,,				2504	0.0				p.I145L		Atlas-SNP	.											.	TTC17	112	.	0			c.A433C						PASS	.	A	LEU/ILE	1459,2947	469.6+/-355.5	256,947,1000	80.0	82.0	82.0		433	5.2	1.0	11	dbSNP_120	82	9,8591	6.4+/-24.3	0,9,4291	yes	missense	TTC17	NM_018259.5	5	256,956,5291	CC,CA,AA		0.1047,33.1139,11.2871	benign	145/1142	43413028	1468,11538	2203	4300	6503	SO:0001583	missense	55761	exon4			GATTATATAGACA	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"""Tetratricopeptide (TTC) repeat domain containing"""	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.433A>C	11.37:g.43413028A>C	ENSP00000039989:p.Ile145Leu	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	203	203	1	NM_018259	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	37	CCDS31466.1	202	0.0924908424908425	193	0.39227642276422764	9	0.024861878453038673	0	0.0	0	0.0	A	12.70	2.015330	0.35511	0.331139	0.001047	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.31510	1.49;1.59	5.2	5.2	0.72013	.	0.264075	0.45606	D	0.000357	T	0.00012	0.0000	N	0.08118	0	0.34987	P	0.245382	B;B;B	0.16802	0.011;0.007;0.019	B;B;B	0.17433	0.008;0.006;0.018	T	0.41088	-0.9528	9	0.09338	T	0.73	-16.7019	9.8335	0.40956	0.9228:0.0:0.0772:0.0	rs12099204;rs12099204	145;145;145	Q8NEC0;Q96AE7;G3XAB3	.;TTC17_HUMAN;.	L	145	ENSP00000299240:I145L;ENSP00000039989:I145L	ENSP00000039989:I145L	I	+	1	0	TTC17	43369604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.614000	0.36911	2.091000	0.63221	0.460000	0.39030	ATA	A|0.883;C|0.117	0.117	strong		0.328	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259	
PRPF8	10594	hgsc.bcm.edu	37	17	1553003	1553003	+	IGR	SNP	G	G	T	rs9896488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1553003G>T	ENST00000572621.1	-	0	7445				PRPF8_ENST00000575116.1_5'Flank|RILP_ENST00000301336.6_Silent_p.A32A			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8						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)		CCAGGGCCCCGGCTAGATGGT	0.751													G|||	392	0.0782748	0.2073	0.0231	5008	,	,		10869	0.0873		0.003	False		,,,				2504	0.0112				p.A32A		Atlas-SNP	.											.	RILP	24	.	0			c.C96A						PASS	.			510,3290		20,470,1410	5.0	7.0	6.0		96	-2.2	1.0	17	dbSNP_119	6	32,7890		0,32,3929	no	coding-synonymous	RILP	NM_031430.2		20,502,5339	TT,TG,GG		0.4039,13.4211,4.6238		32/402	1553003	542,11180	1900	3961	5861	SO:0001628	intergenic_variant	83547	exon1			GGCCCCGGCTAGA	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		17.37:g.1553003G>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_031430	O14547|O75965	Silent	SNP	ENST00000572621.1	37	CCDS11010.1																																																																																			G|0.922;T|0.078	0.078	strong		0.751	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
DAAM1	23002	hgsc.bcm.edu	37	14	59797373	59797373	+	Silent	SNP	G	G	A	rs28927674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:59797373G>A	ENST00000395125.1	+	12	1550	c.1527G>A	c.(1525-1527)gcG>gcA	p.A509A	DAAM1_ENST00000360909.3_Silent_p.A509A|DAAM1_ENST00000351081.1_Silent_p.A509A	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	509					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AGCAGGTGGCGGACCTCACAG	0.522													G|||	153	0.0305511	0.0053	0.0375	5008	,	,		19108	0.0109		0.0924	False		,,,				2504	0.0164				p.A509A		Atlas-SNP	.											DAAM1,colon,carcinoma,+1,1	DAAM1	95	1	0			c.G1527A						PASS	.	G		70,4336	66.4+/-103.9	0,70,2133	71.0	71.0	71.0		1527	-12.0	0.4	14	dbSNP_125	71	814,7786	188.9+/-235.7	33,748,3519	no	coding-synonymous	DAAM1	NM_014992.1		33,818,5652	AA,AG,GG		9.4651,1.5887,6.7969		509/1079	59797373	884,12122	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon13			GGTGGCGGACCTC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.1527G>A	14.37:g.59797373G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	177	76	0.429379	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.939;A|0.061	0.061	strong		0.522	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18499629	18499629	+	Missense_Mutation	SNP	A	A	T	rs77656456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18499629A>T	ENST00000266497.5	+	10	1522	c.1484A>T	c.(1483-1485)aAt>aTt	p.N495I	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.N495I|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.N495I|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.N495I			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	495	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				CAGCTAATCAATGTCTACTGT	0.418													A|||	9	0.00179712	0.0061	0.0014	5008	,	,		17734	0.0		0.0	False		,,,				2504	0.0				p.N495I		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A1484T						PASS	.	A	ILE/ASN	17,3835		0,17,1909	183.0	183.0	183.0		1484	1.6	0.0	12	dbSNP_131	183	0,8256		0,0,4128	yes	missense	PIK3C2G	NM_004570.4	149	0,17,6037	TT,TA,AA		0.0,0.4413,0.1404	benign	495/1446	18499629	17,12091	1926	4128	6054	SO:0001583	missense	5288	exon11			TAATCAATGTCTA	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1484A>T	12.37:g.18499629A>T	ENSP00000266497:p.Asn495Ile	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	10.11	1.260049	0.23051	0.004413	0.0	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.60797	1.49;0.17;0.17;0.16	3.98	1.61	0.23674	Phosphoinositide 3-kinase, C2 (1);	1.592470	0.03319	N	0.191731	T	0.30727	0.0774	N	0.08118	0	0.09310	N	1	B;B;B	0.30281	0.04;0.066;0.275	B;B;B	0.28232	0.033;0.073;0.087	T	0.35871	-0.9771	10	0.66056	D	0.02	-1.4578	6.9084	0.24321	0.6849:0.0:0.3151:0.0	.	494;495;495	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	I	495	ENSP00000443850:N495I;ENSP00000404845:N495I;ENSP00000266497:N495I;ENSP00000445381:N495I	ENSP00000266497:N495I	N	+	2	0	PIK3C2G	18390896	0.000000	0.05858	0.019000	0.16419	0.908000	0.53690	0.199000	0.17237	0.344000	0.23847	0.454000	0.30748	AAT	A|0.998;T|0.002	0.002	strong		0.418	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557486	32557486	+	Missense_Mutation	SNP	T	T	A	rs201540428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32557486T>A	ENST00000360004.5	-	1	139	c.34A>T	c.(34-36)Atg>Ttg	p.M12L		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	12					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						AGCGCTGTCATGCAGGAGCCT	0.577										Multiple Myeloma(14;0.17)			T|||	371	0.0740815	0.1225	0.0389	5008	,	,		26616	0.0585		0.0417	False		,,,				2504	0.0828				p.M12L		Atlas-SNP	.											HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	0			c.A34T						PASS	.						86.0	104.0	97.0					6																	32557486		1511	2709	4220	SO:0001583	missense	3123	exon1			CTGTCATGCAGGA	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.34A>T	6.37:g.32557486T>A	ENSP00000353099:p.Met12Leu	Somatic	370	0	0		WXS	Illumina HiSeq	Phase_I	267	22	0.082397	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	12.35	1.912089	0.33721	.	.	ENSG00000196126	ENST00000360004	T	0.00211	8.54	4.4	-0.756	0.11057	MHC classes I/II-like antigen recognition protein (1);	3.037640	0.01196	N	0.007449	T	0.00039	0.0001	L	0.39898	1.24	0.09310	N	1	B	0.31435	0.323	B	0.23716	0.048	T	0.30563	-0.9974	10	0.62326	D	0.03	.	0.4245	0.00461	0.1798:0.2114:0.1864:0.4224	rs3179205	12	P01911	2B1F_HUMAN	L	12	ENSP00000353099:M12L	ENSP00000353099:M12L	M	-	1	0	HLA-DRB1	32665464	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.388000	0.07352	-0.281000	0.09141	-0.530000	0.04314	ATG	T|0.848;A|0.152	0.152	strong		0.577	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
NWD1	284434	hgsc.bcm.edu	37	19	16860685	16860685	+	Missense_Mutation	SNP	C	C	T	rs61998161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860685C>T	ENST00000552788.1	+	4	1232	c.1232C>T	c.(1231-1233)aCc>aTc	p.T411I	NWD1_ENST00000379808.3_Missense_Mutation_p.T411I|NWD1_ENST00000339803.6_Missense_Mutation_p.T276I|NWD1_ENST00000549814.1_Missense_Mutation_p.T411I|NWD1_ENST00000524140.2_Missense_Mutation_p.T411I|NWD1_ENST00000523826.1_Missense_Mutation_p.T205I			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	411	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GACGCCCACACCAGGGTGGTC	0.587													c|||	120	0.0239617	0.0825	0.0101	5008	,	,		18238	0.0		0.001	False		,,,				2504	0.0031				p.T411I		Atlas-SNP	.											.	NWD1	303	.	0			c.C1232T						PASS	.		ILE/THR	266,4134		5,256,1939	55.0	56.0	56.0		1232	-8.4	0.0	19	dbSNP_129	56	10,8590		0,10,4290	yes	missense	NWD1	NM_001007525.3	89	5,266,6229	TT,TC,CC		0.1163,6.0455,2.1231	benign	411/1433	16860685	276,12724	2200	4300	6500	SO:0001583	missense	284434	exon6			CCCACACCAGGGT	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1232C>T	19.37:g.16860685C>T	ENSP00000447224:p.Thr411Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		49	0.022435897435897436	42	0.08536585365853659	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	c	5.508	0.278633	0.10458	0.060455	0.001163	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45;-1.45	4.77	-8.37	0.00976	.	1.739930	0.02884	N	0.133179	T	0.07234	0.0183	N	0.19112	0.55	0.09310	N	1	P;B;P	0.39022	0.655;0.435;0.491	B;B;B	0.37198	0.243;0.157;0.243	T	0.48547	-0.9026	10	0.33940	T	0.23	-0.9905	16.403	0.83649	0.0991:0.1543:0.7466:0.0	rs61998161	411;411;276	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	I	276;411;411;411;205;411;276	ENSP00000428579:T411I;ENSP00000447548:T411I;ENSP00000369136:T411I;ENSP00000428955:T205I;ENSP00000447224:T411I;ENSP00000340159:T276I	ENSP00000340159:T276I	T	+	2	0	NWD1	16721685	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.167000	0.09940	-0.626000	0.05596	-0.194000	0.12790	ACC	C|0.979;T|0.021	0.021	strong		0.587	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
SSPO	23145	hgsc.bcm.edu	37	7	149499254	149499254	+	RNA	SNP	G	G	A	rs59522380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149499254G>A	ENST00000378016.2	+	0	7622							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)			CCGCGTGACCGGTTCCGAAGC	0.687													G|||	298	0.0595048	0.2171	0.0159	5008	,	,		15602	0.0		0.0	False		,,,				2504	0.0				p.R2541Q		Atlas-SNP	.											.	.	.	.	0			c.G7622A						PASS	.	G		441,3035		13,415,1310	4.0	6.0	5.0		7626	-4.0	0.0	7	dbSNP_129	5	7,7421		0,7,3707	no	coding-notMod3	SSPO	NM_198455.2		13,422,5017	AA,AG,GG		0.0942,12.687,4.1086			149499254	448,10456	1738	3714	5452			23145	exon51			GTGACCGGTTCCG	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.149499254G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.945;A|0.055	0.055	strong		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
OR4A47	403253	hgsc.bcm.edu	37	11	48510654	48510654	+	Missense_Mutation	SNP	A	A	C	rs7103557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48510654A>C	ENST00000446524.1	+	1	386	c.310A>C	c.(310-312)Att>Ctt	p.I104L		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	104			I -> L (in dbSNP:rs7103557).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						TATCGAGCACATTTTCGGTGG	0.438													C|||	2406	0.480431	0.3767	0.5922	5008	,	,		20770	0.4474		0.6451	False		,,,				2504	0.4059				p.I104L		Atlas-SNP	.											.	OR4A47	72	.	0			c.A310C						PASS	.	C	LEU/ILE	1937,2465		433,1071,697	102.0	96.0	98.0		310	1.0	0.2	11	dbSNP_116	98	5345,3251		1663,2019,616	yes	missense	OR4A47	NM_001005512.2	5	2096,3090,1313	CC,CA,AA		37.8199,44.0027,43.976	benign	104/310	48510654	7282,5716	2201	4298	6499	SO:0001583	missense	403253	exon1			GAGCACATTTTCG	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"""GPCR / Class A : Olfactory receptors"""	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.310A>C	11.37:g.48510654A>C	ENSP00000412752:p.Ile104Leu	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	183	98	0.535519	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	1177	0.5389194139194139	182	0.3699186991869919	225	0.6215469613259669	282	0.493006993006993	488	0.6437994722955145	N	0.005	-2.152709	0.00325	0.440027	0.621801	ENSG00000237388	ENST00000446524	T	0.00695	5.83	4.82	1.05	0.20165	GPCR, rhodopsin-like superfamily (1);	0.394443	0.22074	N	0.064984	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03249	-1.1056	8	0.17369	T	0.5	.	4.3157	0.10991	0.1398:0.2725:0.0:0.5876	rs7103557;rs7103557	104	Q6IF82	O4A47_HUMAN	L	104	ENSP00000412752:I104L	ENSP00000412752:I104L	I	+	1	0	OR4A47	48467230	0.000000	0.05858	0.174000	0.22961	0.013000	0.08279	-2.133000	0.01308	-0.063000	0.13065	-1.375000	0.01183	ATT	A|0.441;C|0.559	0.559	strong		0.438	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512	
PTPRA	5786	hgsc.bcm.edu	37	20	2969015	2969015	+	Silent	SNP	C	C	G	rs61742610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2969015C>G	ENST00000216877.6	+	8	1006	c.606C>G	c.(604-606)tcC>tcG	p.S202S	PTPRA_ENST00000425918.2_Silent_p.S222S|PTPRA_ENST00000380393.3_Silent_p.S211S|PTPRA_ENST00000399903.2_Silent_p.S211S|PTPRA_ENST00000318266.5_Silent_p.S202S|PTPRA_ENST00000356147.3_Silent_p.S202S|PTPRA_ENST00000358719.4_Silent_p.S67S	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	211					axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TGGCCAGATCCCCAAGCACCA	0.547													C|||	147	0.029353	0.0802	0.0231	5008	,	,		17950	0.001		0.003	False		,,,				2504	0.0215				p.S211S		Atlas-SNP	.											.	PTPRA	75	.	0			c.C633G						PASS	.	C	,,	279,4127	155.5+/-188.7	9,261,1933	96.0	95.0	96.0		633,606,606	0.8	1.0	20	dbSNP_129	96	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRA	NM_002836.3,NM_080840.2,NM_080841.2	,,	9,277,6217	GG,GC,CC		0.186,6.3323,2.2682	,,	211/803,202/794,202/794	2969015	295,12711	2203	4300	6503	SO:0001819	synonymous_variant	5786	exon13			CAGATCCCCAAGC		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.606C>G	20.37:g.2969015C>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	145	80	0.551724	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Silent	SNP	ENST00000216877.6	37	CCDS13039.1																																																																																			C|0.977;G|0.023	0.023	strong		0.547	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3		
TMPRSS15	5651	hgsc.bcm.edu	37	21	19687517	19687517	+	Missense_Mutation	SNP	T	T	G	rs11088674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:19687517T>G	ENST00000284885.3	-	17	2011	c.1978A>C	c.(1978-1980)Aat>Cat	p.N660H		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	660	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.		N -> H (in dbSNP:rs11088674).			brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TCACAGAGATTCACCAGTGGA	0.393													T|||	274	0.0547125	0.1982	0.0159	5008	,	,		17865	0.0		0.001	False		,,,				2504	0.0				p.N660H		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A1978C						PASS	.	T	HIS/ASN	811,3595	324.2+/-298.5	69,673,1461	171.0	142.0	152.0		1978	5.3	0.9	21	dbSNP_120	152	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TMPRSS15	NM_002772.2	68	69,674,5760	GG,GT,TT		0.0116,18.4067,6.2433	benign	660/1020	19687517	812,12194	2203	4300	6503	SO:0001583	missense	5651	exon17			AGAGATTCACCAG		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1978A>C	21.37:g.19687517T>G	ENSP00000284885:p.Asn660His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	86	0.039377289377289376	82	0.16666666666666666	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	T	3.323	-0.138326	0.06669	0.184067	1.16E-4	ENSG00000154646	ENST00000284885	D	0.95377	-3.69	5.27	5.27	0.74061	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.247388	0.42053	D	0.000763	T	0.01387	0.0045	N	0.26130	0.795	0.28774	N	0.900214	B	0.21225	0.053	B	0.25405	0.06	T	0.28427	-1.0044	9	.	.	.	.	7.7237	0.28746	0.0:0.0912:0.0:0.9088	rs11088674;rs11088674	660	P98073	ENTK_HUMAN	H	660	ENSP00000284885:N660H	.	N	-	1	0	TMPRSS15	18609388	0.975000	0.34042	0.869000	0.34112	0.027000	0.11550	2.212000	0.42835	2.221000	0.72209	0.528000	0.53228	AAT	T|0.943;G|0.057	0.057	strong		0.393	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
FAM65B	9750	hgsc.bcm.edu	37	6	24848345	24848345	+	Missense_Mutation	SNP	C	C	A	rs35254980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24848345C>A	ENST00000259698.4	-	12	1160	c.985G>T	c.(985-987)Gct>Tct	p.A329S	FAM65B_ENST00000538035.1_Missense_Mutation_p.A358S|FAM65B_ENST00000378023.4_Missense_Mutation_p.A329S|FAM65B_ENST00000540914.1_Missense_Mutation_p.A329S|FAM65B_ENST00000510784.2_Missense_Mutation_p.A363S	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	329					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						TTGTTCCCAGCGCCTGAGGAT	0.522													C|||	109	0.0217652	0.0772	0.0043	5008	,	,		19094	0.0		0.004	False		,,,				2504	0.0				p.A329S		Atlas-SNP	.											.	FAM65B	134	.	0			c.G985T						PASS	.	C	SER/ALA,SER/ALA	255,3715		6,243,1736	78.0	77.0	77.0		985,985	-3.5	0.0	6	dbSNP_126	77	8,8346		0,8,4169	yes	missense,missense	FAM65B	NM_014722.2,NM_015864.2	99,99	6,251,5905	AA,AC,CC		0.0958,6.4232,2.134	benign,benign	329/1069,329/592	24848345	263,12061	1985	4177	6162	SO:0001583	missense	9750	exon12			TCCCAGCGCCTGA	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"""myogenesis-related and NCAM-associated protein homolog (chicken)"""	611410	"""chromosome 6 open reading frame 32"""	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.985G>T	6.37:g.24848345C>A	ENSP00000259698:p.Ala329Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_015864	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	39	0.017857142857142856	32	0.06504065040650407	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	7.015	0.557535	0.13436	0.064232	9.58E-4	ENSG00000111913	ENST00000259698;ENST00000538035;ENST00000378023;ENST00000540914;ENST00000510784	T;T;T;T;T	0.01998	4.51;4.51;4.51;4.51;4.51	5.48	-3.49	0.04724	.	0.396788	0.30704	N	0.009044	T	0.00300	0.0009	N	0.01576	-0.805	0.09310	N	1	B;B;B;B	0.20780	0.048;0.048;0.027;0.027	B;B;B;B	0.24269	0.034;0.052;0.021;0.052	T	0.32719	-0.9896	10	0.19147	T	0.46	-1.0033	9.8918	0.41294	0.0:0.1236:0.128:0.7485	rs35254980	363;358;329;329	B7Z6U4;F5GX51;Q9Y4F9-2;Q9Y4F9	.;.;.;FA65B_HUMAN	S	329;358;329;329;363	ENSP00000259698:A329S;ENSP00000441138:A358S;ENSP00000367262:A329S;ENSP00000438425:A329S;ENSP00000441305:A363S	ENSP00000259698:A329S	A	-	1	0	FAM65B	24956324	0.630000	0.27155	0.001000	0.08648	0.822000	0.46500	0.993000	0.29680	-0.569000	0.06030	0.563000	0.77884	GCT	C|0.985;A|0.015	0.015	strong		0.522	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
LMF1	64788	hgsc.bcm.edu	37	16	961054	961054	+	Silent	SNP	C	C	T	rs2277892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:961054C>T	ENST00000262301.11	-	4	558	c.540G>A	c.(538-540)acG>acA	p.T180T	LMF1_ENST00000543238.1_Intron|LMF1_ENST00000539379.1_3'UTR|LMF1_ENST00000568897.1_5'UTR|LMF1_ENST00000399843.2_Silent_p.T180T	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	180					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)		p.T180T(1)		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)				CCAGGAACCCCGTCTCCAGAA	0.532													C|||	1255	0.250599	0.4107	0.2421	5008	,	,		16912	0.244		0.0924	False		,,,				2504	0.2096				p.T180T		Atlas-SNP	.											LMF1,NS,carcinoma,0,1	LMF1	42	1	1	Substitution - coding silent(1)	stomach(1)	c.G540A						PASS	.	C		1382,2584		228,926,829	44.0	51.0	49.0		540	-9.1	0.2	16	dbSNP_100	49	894,7386		51,792,3297	no	coding-synonymous	LMF1	NM_022773.2		279,1718,4126	TT,TC,CC		10.7971,34.8462,18.5857		180/568	961054	2276,9970	1983	4140	6123	SO:0001819	synonymous_variant	64788	exon4			GAACCCCGTCTCC	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.540G>A	16.37:g.961054C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			C|0.774;T|0.226	0.226	strong		0.532	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
NCF4	4689	hgsc.bcm.edu	37	22	37271802	37271802	+	Silent	SNP	C	C	T	rs2072712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37271802C>T	ENST00000248899.6	+	8	919	c.735C>T	c.(733-735)taC>taT	p.Y245Y	NCF4_ENST00000397147.4_Silent_p.Y245Y	NM_000631.4	NP_000622.2	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4, 40kDa	245	OPR.				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)|immune response (GO:0006955)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of catalytic activity (GO:0043085)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|membrane (GO:0016020)|NADPH oxidase complex (GO:0043020)|phagolysosome (GO:0032010)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein dimerization activity (GO:0046983)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16					Dextromethorphan(DB00514)	GCTACTACTACGAAGACACCA	0.597													C|||	659	0.131589	0.2549	0.1383	5008	,	,		15260	0.0645		0.0656	False		,,,				2504	0.0971				p.Y245Y		Atlas-SNP	.											.	NCF4	66	.	0			c.C735T						PASS	.	C	,	930,3476	354.1+/-312.5	88,754,1361	141.0	123.0	129.0		735,735	-9.1	0.3	22	dbSNP_96	129	592,8008	157.7+/-211.4	21,550,3729	no	coding-synonymous,coding-synonymous	NCF4	NM_000631.4,NM_013416.3	,	109,1304,5090	TT,TC,CC		6.8837,21.1076,11.7023	,	245/340,245/349	37271802	1522,11484	2203	4300	6503	SO:0001819	synonymous_variant	4689	exon8			CTACTACGAAGAC	X77094	CCDS13934.1, CCDS13935.1	22q13.1	2014-09-17	2002-08-29		ENSG00000100365	ENSG00000100365			7662	protein-coding gene	gene with protein product	"""neutrophil NADPH oxidase factor 4"""	601488	"""neutrophil cytosolic factor 4 (40kD)"""			8839867	Standard	NM_013416		Approved	p40phox, SH3PXD4	uc003apy.4	Q15080	OTTHUMG00000150548	ENST00000248899.6:c.735C>T	22.37:g.37271802C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	86	55	0.639535	NM_000631	A8K4F9|O60808|Q86U56|Q9BU98|Q9NP45	Silent	SNP	ENST00000248899.6	37	CCDS13934.1	245	0.11217948717948718	112	0.22764227642276422	52	0.143646408839779	33	0.057692307692307696	48	0.0633245382585752	C	6.651	0.488624	0.12641	0.211076	0.068837	ENSG00000100365	ENST00000415063	.	.	.	4.57	-9.15	0.00698	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999750706	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.3163	13.8809	0.63682	0.0:0.1141:0.0991:0.7868	rs2072712;rs11552116;rs35958880;rs58864041;rs2072712	.	.	.	X	109	.	.	R	+	1	2	NCF4	35601748	0.008000	0.16893	0.333000	0.25482	0.823000	0.46562	-1.907000	0.01589	-2.252000	0.00699	-0.827000	0.03088	CGA	C|0.886;T|0.114	0.114	strong		0.597	NCF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318863.1	NM_000631	
FGFRL1	53834	hgsc.bcm.edu	37	4	1018705	1018705	+	Missense_Mutation	SNP	C	C	A	rs4647930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1018705C>A	ENST00000398484.2	+	8	1665	c.1085C>A	c.(1084-1086)cCa>cAa	p.P362Q	FGFRL1_ENST00000510644.1_Missense_Mutation_p.P362Q|RP11-460I19.2_ENST00000503095.1_lincRNA|FGFRL1_ENST00000264748.6_Missense_Mutation_p.P362Q|FGFRL1_ENST00000504138.1_Missense_Mutation_p.P362Q			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	362			P -> Q (in dbSNP:rs4647930). {ECO:0000269|PubMed:11031111, ECO:0000269|PubMed:11267671, ECO:0000269|PubMed:15489334}.		diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCAAAACCGCCAGGGCCACCT	0.662													c|||	686	0.136981	0.031	0.1383	5008	,	,		13718	0.0823		0.2674	False		,,,				2504	0.2014				p.P362Q		Atlas-SNP	.											.	FGFRL1	77	.	0			c.C1085A						PASS	.		GLN/PRO,GLN/PRO,GLN/PRO	326,4068		16,294,1887	26.0	31.0	29.0		1085,1085,1085	3.9	0.9	4	dbSNP_111	29	2315,6269		345,1625,2322	yes	missense,missense,missense	FGFRL1	NM_001004356.2,NM_001004358.1,NM_021923.3	76,76,76	361,1919,4209	AA,AC,CC		26.9688,7.4192,20.3498	benign,benign,benign	362/505,362/505,362/505	1018705	2641,10337	2197	4292	6489	SO:0001583	missense	53834	exon7			AACCGCCAGGGCC		CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418		"""Immunoglobulin superfamily / I-set domain containing"""	3693	protein-coding gene	gene with protein product		605830					Standard	NM_021923		Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.1085C>A	4.37:g.1018705C>A	ENSP00000381498:p.Pro362Gln	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	25	12	0.48	NM_001004356	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Missense_Mutation	SNP	ENST00000398484.2	37	CCDS3344.1	311	0.1423992673992674	14	0.028455284552845527	56	0.15469613259668508	40	0.06993006993006994	201	0.26517150395778366	c	14.70	2.614939	0.46631	0.074192	0.269688	ENSG00000127418	ENST00000398484;ENST00000542622;ENST00000510644;ENST00000504138;ENST00000264748	D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89	4.71	3.86	0.44501	.	0.055638	0.64402	D	0.000001	T	0.00039	0.0001	L	0.43152	1.355	0.09310	P	0.9999999153122	B	0.24533	0.105	B	0.20577	0.03	T	0.03095	-1.1073	9	0.40728	T	0.16	-4.2415	11.9103	0.52735	0.0:0.9146:0.0:0.0854	rs4647930;rs4647930	362	Q8N441	FGRL1_HUMAN	Q	362;332;362;362;362	ENSP00000381498:P362Q;ENSP00000425025:P362Q;ENSP00000423091:P362Q;ENSP00000264748:P362Q	ENSP00000264748:P362Q	P	+	2	0	FGFRL1	1008705	0.920000	0.31207	0.879000	0.34478	0.714000	0.41099	2.056000	0.41355	0.988000	0.38734	0.651000	0.88453	CCA	C|0.820;A|0.180	0.180	strong		0.662	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923	
MS4A14	84689	hgsc.bcm.edu	37	11	60183401	60183401	+	Missense_Mutation	SNP	G	G	T	rs376669252		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60183401G>T	ENST00000300187.6	+	5	1237	c.960G>T	c.(958-960)ttG>ttT	p.L320F	MS4A14_ENST00000395005.2_Missense_Mutation_p.L303F|MS4A14_ENST00000531783.1_Missense_Mutation_p.L353F|MS4A14_ENST00000395001.1_3'UTR|MS4A14_ENST00000531787.1_Missense_Mutation_p.L208F	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	320						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						CTGAAGACTTGCCATCCCAAG	0.448																																					p.L353F		Atlas-SNP	.											.	MS4A14	120	.	0			c.G1059T						PASS	.	G	PHE/LEU,PHE/LEU	1,4405	2.1+/-5.4	0,1,2202	99.0	91.0	94.0		909,960	-0.6	0.0	11		94	0,8600		0,0,4300	no	missense,missense	MS4A14	NM_001079692.1,NM_032597.3	22,22	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	303/663,320/680	60183401	1,13005	2203	4300	6503	SO:0001583	missense	84689	exon6			AGACTTGCCATCC	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.960G>T	11.37:g.60183401G>T	ENSP00000300187:p.Leu320Phe	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	164	77	0.469512	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	G	9.851	1.193578	0.22037	2.27E-4	0.0	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.39787	1.07;2.31;1.06;2.67	3.83	-0.63	0.11530	.	3.820730	0.00986	N	0.003454	T	0.32071	0.0817	L	0.36672	1.1	0.09310	N	1	P;P	0.40107	0.703;0.578	B;B	0.35413	0.202;0.099	T	0.27331	-1.0077	10	0.52906	T	0.07	-0.0477	5.6589	0.17658	0.0999:0.0:0.3621:0.5381	.	303;320	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	F	208;320;303;353	ENSP00000437222:L208F;ENSP00000300187:L320F;ENSP00000378453:L303F;ENSP00000433761:L353F	ENSP00000300187:L320F	L	+	3	2	MS4A14	59939977	0.000000	0.05858	0.007000	0.13788	0.081000	0.17604	-0.924000	0.03996	-0.103000	0.12175	-0.143000	0.13931	TTG	.	.	weak		0.448	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
LBP	3929	hgsc.bcm.edu	37	20	36982785	36982785	+	Missense_Mutation	SNP	C	C	G	rs2232586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36982785C>G	ENST00000217407.2	+	4	631	c.470C>G	c.(469-471)tCc>tGc	p.S157C		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	157			S -> C (in dbSNP:rs2232586).	VTAS -> GYCL (in Ref. 1; AAA59493). {ECO:0000305}.	acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				GTTACTGCCTCCAGCTGCAGC	0.592													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		17413	0.0		0.0	False		,,,				2504	0.0				p.S157C		Atlas-SNP	.											.	LBP	60	.	0			c.C470G						PASS	.	C	CYS/SER	45,4361	46.7+/-81.2	1,43,2159	66.0	56.0	59.0		470	3.8	0.2	20	dbSNP_98	59	0,8600		0,0,4300	yes	missense	LBP	NM_004139.2	112	1,43,6459	GG,GC,CC		0.0,1.0213,0.346	probably-damaging	157/482	36982785	45,12961	2203	4300	6503	SO:0001583	missense	3929	exon4			CTGCCTCCAGCTG		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.470C>G	20.37:g.36982785C>G	ENSP00000217407:p.Ser157Cys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	11.79	1.743153	0.30865	0.010213	0.0	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.07688	3.17	4.77	3.75	0.43078	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.281808	0.30437	N	0.009628	T	0.10766	0.0263	M	0.85041	2.73	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.00759	-1.1578	10	0.62326	D	0.03	-21.3368	9.7646	0.40552	0.2055:0.7945:0.0:0.0	rs2232586	157	P18428	LBP_HUMAN	C	157	ENSP00000217407:S157C	ENSP00000217407:S157C	S	+	2	0	LBP	36416199	0.012000	0.17670	0.193000	0.23327	0.108000	0.19459	2.151000	0.42263	2.648000	0.89879	0.561000	0.74099	TCC	C|0.994;G|0.006	0.006	strong		0.592	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
PSAPL1	768239	hgsc.bcm.edu	37	4	7436151	7436151	+	Silent	SNP	T	T	C	rs61738663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:7436151T>C	ENST00000319098.4	-	1	549	c.456A>G	c.(454-456)ccA>ccG	p.P152P	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)	152					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						CTTTGGAGAGTGGCCTCAGGG	0.662													T|||	233	0.0465256	0.1634	0.0231	5008	,	,		16972	0.0		0.0	False		,,,				2504	0.001				p.P152P		Atlas-SNP	.											.	PSAPL1	51	.	0			c.A456G						PASS	.	T	,	545,3441		36,473,1484	11.0	13.0	12.0		456,	-5.4	0.0	4	dbSNP_129	12	3,8305		0,3,4151	no	coding-synonymous,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	,	36,476,5635	CC,CT,TT		0.0361,13.6729,4.4575	,	152/522,	7436151	548,11746	1993	4154	6147	SO:0001819	synonymous_variant	768239	exon1			GGAGAGTGGCCTC	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.456A>G	4.37:g.7436151T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_001085382	A0A184|Q8N7T4	Silent	SNP	ENST00000319098.4	37	CCDS47009.1																																																																																			T|0.963;C|0.037	0.037	strong		0.662	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
PCSK5	5125	hgsc.bcm.edu	37	9	78936358	78936358	+	Missense_Mutation	SNP	G	G	A	rs1110222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:78936358G>A	ENST00000545128.1	+	30	4362	c.3824G>A	c.(3823-3825)gGc>gAc	p.G1275D		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1275	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						GCAGAAGACGGCATATGTGAA	0.527													G|||	1598	0.319089	0.4592	0.2378	5008	,	,		15572	0.1369		0.341	False		,,,				2504	0.3528				p.G1275D		Atlas-SNP	.											.	PCSK5	329	.	0			c.G3824A						PASS	.	G	ASP/GLY	775,977		182,411,283	174.0	138.0	149.0		3824	4.6	0.0	9	dbSNP_86	149	1314,2668		221,872,898	yes	missense	PCSK5	NM_001190482.1	94	403,1283,1181	AA,AG,GG		32.9985,44.2352,36.4318	benign	1275/1861	78936358	2089,3645	876	1991	2867	SO:0001583	missense	5125	exon30			AAGACGGCATATG		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.3824G>A	9.37:g.78936358G>A	ENSP00000446280:p.Gly1275Asp	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	49	0.7	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	670	0.3067765567765568	234	0.47560975609756095	99	0.27348066298342544	76	0.13286713286713286	261	0.34432717678100266	G	8.856	0.945778	0.18356	0.442352	0.329985	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.32023	1.52;1.47	5.5	4.61	0.57282	.	0.338727	0.30732	N	0.008997	T	0.00012	0.0000	M	0.70595	2.14	0.80722	P	0.0	.	.	.	.	.	.	T	0.50250	-0.8850	7	0.21014	T	0.42	-7.5297	8.5591	0.33501	0.1743:0.0:0.8257:0.0	rs1110222;rs2803425;rs60377265;rs1110222	.	.	.	D	1275;1005;975	ENSP00000446280:G1275D;ENSP00000411654:G975D	ENSP00000365945:G1005D	G	+	2	0	PCSK5	78126178	0.005000	0.15991	0.002000	0.10522	0.004000	0.04260	0.922000	0.28734	1.334000	0.45468	0.561000	0.74099	GGC	G|0.679;A|0.321	0.321	strong		0.527	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
RGPD3	653489	hgsc.bcm.edu	37	2	107041612	107041612	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:107041612A>C	ENST00000409886.3	-	20	2898	c.2811T>G	c.(2809-2811)agT>agG	p.S937R	RGPD3_ENST00000304514.7_Missense_Mutation_p.S937R	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	937					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						GAGGCTTTTCACTTTTCTTTT	0.403																																					p.S937R		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	2	0			c.T2811G						scavenged	.						86.0	76.0	79.0					2																	107041612		692	1590	2282	SO:0001583	missense	653489	exon20			CTTTTCACTTTTC		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.2811T>G	2.37:g.107041612A>C	ENSP00000386588:p.Ser937Arg	Somatic	1034	0	0		WXS	Illumina HiSeq	Phase_I	1268	108	0.0851735	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	.	.	.	.	.	.	.	.	.	.	.	5.022	0.189738	0.09547	.	.	ENSG00000153165	ENST00000409886;ENST00000452099;ENST00000304514	T;T	0.40756	1.03;1.02	2.35	1.1	0.20463	.	.	.	.	.	T	0.34366	0.0895	L	0.54323	1.7	0.09310	N	1	P	0.49559	0.925	B	0.43575	0.424	T	0.16188	-1.0411	9	0.22706	T	0.39	-2.0278	5.5415	0.17041	0.844:0.0:0.156:0.0	.	937	A6NKT7	RGPD3_HUMAN	R	937;695;937	ENSP00000386588:S937R;ENSP00000303659:S937R	ENSP00000303659:S937R	S	-	3	2	RGPD3	106408044	0.541000	0.26417	0.031000	0.17742	0.516000	0.34256	1.090000	0.30902	0.167000	0.19631	0.156000	0.16432	AGT	.	.	weak		0.403	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
USP2	9099	hgsc.bcm.edu	37	11	119243912	119243912	+	Silent	SNP	C	C	T	rs536224379|rs79464246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119243912C>T	ENST00000260187.2	-	2	573	c.279G>A	c.(277-279)gaG>gaA	p.E93E	RP11-334E6.3_ENST00000530918.2_RNA|USP2_ENST00000455332.2_Intron	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	93	Necessary for interaction with MDM4.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		GGGTCTGGCTCTCTGCCCGCT	0.657													C|||	40	0.00798722	0.0265	0.0072	5008	,	,		16244	0.0		0.0	False		,,,				2504	0.0				p.E93E		Atlas-SNP	.											.	USP2	71	.	0			c.G279A						PASS	.	C		107,4291	82.9+/-121.4	2,103,2094	67.0	76.0	73.0		279	4.3	1.0	11	dbSNP_132	73	1,8589		0,1,4294	no	coding-synonymous	USP2	NM_004205.4		2,104,6388	TT,TC,CC		0.0116,2.4329,0.8315		93/606	119243912	108,12880	2199	4295	6494	SO:0001819	synonymous_variant	9099	exon2			CTGGCTCTCTGCC	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.279G>A	11.37:g.119243912C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	37	CCDS8422.1																																																																																			C|0.991;T|0.009	0.009	strong		0.657	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997	
GPRC5D	55507	hgsc.bcm.edu	37	12	13103196	13103196	+	Silent	SNP	G	G	A	rs150759739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:13103196G>A	ENST00000228887.1	-	1	122	c.123C>T	c.(121-123)ctC>ctT	p.L41L	RP11-392P7.6_ENST00000394742.3_RNA|RP11-392P7.6_ENST00000538231.1_RNA|RP11-392P7.6_ENST00000543515.2_RNA|RP11-392P7.6_ENST00000545914.1_RNA|RP11-392P7.6_ENST00000536029.1_RNA|GPRC5D_ENST00000396333.3_Silent_p.L41L|RP11-392P7.6_ENST00000540198.1_RNA|RP11-392P7.6_ENST00000542078.1_RNA	NM_018654.1	NP_061124.1	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, class C, group 5, member D	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			kidney(2)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		GAAATGCTAAGAGTAGCAGAA	0.547													G|||	16	0.00319489	0.0106	0.0014	5008	,	,		20686	0.001		0.0	False		,,,				2504	0.0				p.L41L		Atlas-SNP	.											.	GPRC5D	23	.	0			c.C123T						PASS	.	G		39,4367	44.6+/-78.6	0,39,2164	98.0	91.0	94.0		123	5.2	1.0	12	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	GPRC5D	NM_018654.1		0,39,6464	AA,AG,GG		0.0,0.8852,0.2999		41/346	13103196	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	55507	exon1			TGCTAAGAGTAGC	AF209923	CCDS8658.1	12p13.3	2014-01-30	2014-01-30		ENSG00000111291	ENSG00000111291		"""GPCR / Class C : Orphans"""	13310	protein-coding gene	gene with protein product		607437	"""G protein-coupled receptor, family C, group 5, member D"""				Standard	XM_005253421		Approved		uc010shp.2	Q9NZD1	OTTHUMG00000168711	ENST00000228887.1:c.123C>T	12.37:g.13103196G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	70	48	0.685714	NM_018654	Q3KNV3|Q7Z5J9|Q8TDS6	Silent	SNP	ENST00000228887.1	37	CCDS8658.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	GPRC5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400687.1		
DVL1	1855	hgsc.bcm.edu	37	1	1277183	1277183	+	Missense_Mutation	SNP	C	C	T	rs61735963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1277183C>T	ENST00000378888.5	-	5	753	c.469G>A	c.(469-471)Gcc>Acc	p.A157T	DVL1_ENST00000378891.5_Missense_Mutation_p.A157T			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	157				A -> P (in Ref. 1; AAB65242). {ECO:0000305}.	axon extension (GO:0048675)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|collateral sprouting (GO:0048668)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|cytoplasmic microtubule organization (GO:0031122)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|negative regulation of protein binding (GO:0032091)|negative regulation of protein kinase activity (GO:0006469)|neural tube development (GO:0021915)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prepulse inhibition (GO:0060134)|protein localization to microtubule (GO:0035372)|protein localization to nucleus (GO:0034504)|receptor clustering (GO:0043113)|regulation of neurotransmitter levels (GO:0001505)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|social behavior (GO:0035176)|synapse organization (GO:0050808)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	axon (GO:0030424)|cell cortex (GO:0005938)|clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|growth cone (GO:0030426)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	enzyme binding (GO:0019899)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|Rac GTPase binding (GO:0048365)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TTGGTCCGGGCGGCTGTGGGG	0.687													c|||	329	0.0656949	0.2375	0.0202	5008	,	,		17330	0.0		0.001	False		,,,				2504	0.0				p.A157T		Atlas-SNP	.											.	DVL1	36	.	0			c.G469A						PASS	.	C	THR/ALA	898,3474		85,728,1373	14.0	14.0	14.0		469	-3.4	0.0	1	dbSNP_129	14	9,8557		0,9,4274	yes	missense	DVL1	NM_004421.2	58	85,737,5647	TT,TC,CC		0.1051,20.5398,7.0104	benign	157/671	1277183	907,12031	2186	4283	6469	SO:0001583	missense	1855	exon5			TCCGGGCGGCTGT	AF006011	CCDS22.1	1p36	2013-05-22	2013-05-22		ENSG00000107404	ENSG00000107404		"""Dishevelled homologs"""	3084	protein-coding gene	gene with protein product		601365	"""dishevelled 1 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 1 (Drosophila)"""			8817329	Standard	NM_004421		Approved		uc001aer.4	O14640	OTTHUMG00000003069	ENST00000378888.5:c.469G>A	1.37:g.1277183C>T	ENSP00000368166:p.Ala157Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_004421	Q5TA33|Q5TA35	Missense_Mutation	SNP	ENST00000378888.5	37		122	0.055860805860805864	114	0.23170731707317074	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	8.305	0.820817	0.16678	0.205398	0.001051	ENSG00000107404	ENST00000378891;ENST00000378888;ENST00000345100	T;T	0.04917	3.53;3.53	4.02	-3.44	0.04796	.	0.469288	0.22130	N	0.064219	T	0.00012	0.0000	N	0.04880	-0.145	0.45621	P	0.0014420000000000543	B	0.02656	0.0	B	0.04013	0.001	T	0.37572	-0.9700	9	0.07813	T	0.8	.	0.2996	0.00271	0.3245:0.167:0.1548:0.3536	.	157	O14640-2	.	T	157	ENSP00000368169:A157T;ENSP00000368166:A157T	ENSP00000340031:A157T	A	-	1	0	DVL1	1267046	0.188000	0.23250	0.019000	0.16419	0.398000	0.30690	0.396000	0.20867	-0.463000	0.06973	0.205000	0.17691	GCC	C|0.931;T|0.069	0.069	strong		0.687	DVL1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008490.1	NM_004421	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262103	39262103	+	Missense_Mutation	SNP	A	A	T	rs374629799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39262103A>T	ENST00000391415.1	+	1	520	c.463A>T	c.(463-465)Agc>Tgc	p.S155C		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	155	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						ccccagctgcagcatctccag	0.672													a|||	152	0.0303514	0.0893	0.0216	5008	,	,		18051	0.001		0.0139	False		,,,				2504	0.0041				p.S155C		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	2	0			c.A463T						PASS	.						6.0	9.0	8.0					17																	39262103		679	1572	2251	SO:0001583	missense	100132386	exon1			AGCTGCAGCATCT	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.463A>T	17.37:g.39262103A>T	ENSP00000375234:p.Ser155Cys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	186	42	0.225806	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	0.091	-1.167638	0.01660	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00584	6.4	3.1	-1.38	0.09027	.	.	.	.	.	T	0.00109	0.0003	N	0.00041	-2.485	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48186	-0.9057	9	0.02654	T	1	.	0.2915	0.00259	0.1968:0.2502:0.1975:0.3554	.	155	Q9BYQ8	KRA49_HUMAN	C	143;155;146	ENSP00000375234:S155C	ENSP00000334461:S146C	S	+	1	0	KRTAP4-9	36515629	0.946000	0.32159	0.002000	0.10522	0.205000	0.24178	1.056000	0.30480	-0.110000	0.12022	-1.044000	0.02363	AGC	.	.	weak		0.672	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
UMODL1	89766	hgsc.bcm.edu	37	21	43536047	43536047	+	Silent	SNP	C	C	T	rs141581454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43536047C>T	ENST00000408910.2	+	14	2427	c.2427C>T	c.(2425-2427)aaC>aaT	p.N809N	UMODL1_ENST00000400427.1_Silent_p.N865N|UMODL1_ENST00000400424.2_Silent_p.N737N|UMODL1_ENST00000408989.2_Silent_p.N937N	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	809	SEA 2. {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						CCTTTCGCAACGCAAGCAGCC	0.468													C|||	6	0.00119808	0.0038	0.0014	5008	,	,		17984	0.0		0.0	False		,,,				2504	0.0				p.N937N	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C2811T						PASS	.	C	,,,	20,3852		0,20,1916	96.0	98.0	97.0		2427,2595,2211,2811	-6.4	0.0	21	dbSNP_134	97	0,8284		0,0,4142	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	0,20,6058	TT,TC,CC		0.0,0.5165,0.1645	,,,	809/1319,865/1375,737/1247,937/1447	43536047	20,12136	1936	4142	6078	SO:0001819	synonymous_variant	89766	exon13			TCGCAACGCAAGC		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.2427C>T	21.37:g.43536047C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	233	116	0.497854	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			C|0.998;T|0.002	0.002	strong		0.468	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
C4orf6	10141	hgsc.bcm.edu	37	4	5527102	5527102	+	Missense_Mutation	SNP	C	C	A	rs886532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:5527102C>A	ENST00000195455.2	+	1	220	c.45C>A	c.(43-45)aaC>aaA	p.N15K	C4orf6_ENST00000515342.1_Intron	NM_005750.2	NP_005741.1	Q99440	CD006_HUMAN	chromosome 4 open reading frame 6	15			N -> K (in dbSNP:rs886532).		nervous system development (GO:0007399)					large_intestine(1)|prostate(1)	2						attcaaagaaccaatttttta	0.368													C|||	338	0.067492	0.1732	0.013	5008	,	,		17380	0.0645		0.003	False		,,,				2504	0.0327				p.N15K		Atlas-SNP	.											.	C4orf6	6	.	0			c.C45A						PASS	.	C	LYS/ASN	623,3781		36,551,1615	33.0	36.0	35.0		45	-0.4	0.1	4	dbSNP_86	35	13,8573		0,13,4280	yes	missense	C4orf6	NM_005750.2	94	36,564,5895	AA,AC,CC		0.1514,14.1462,4.8961	benign	15/94	5527102	636,12354	2202	4293	6495	SO:0001583	missense	10141	exon1			AAAGAACCAATTT	D82070	CCDS3381.1	4p16	2012-02-24			ENSG00000082929	ENSG00000082929			13716	protein-coding gene	gene with protein product						9016955	Standard	NM_005750		Approved	aC1	uc003gii.3	Q99440	OTTHUMG00000125492	ENST00000195455.2:c.45C>A	4.37:g.5527102C>A	ENSP00000195455:p.Asn15Lys	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	122	71	0.581967	NM_005750	Q17R65	Missense_Mutation	SNP	ENST00000195455.2	37	CCDS3381.1	130	0.05952380952380952	83	0.16869918699186992	4	0.011049723756906077	40	0.06993006993006994	3	0.00395778364116095	C	2.778	-0.254175	0.05829	0.141462	0.001514	ENSG00000082929	ENST00000195455	T	0.53206	0.63	0.225	-0.451	0.12214	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.80722	P	0.0	D	0.54772	0.968	P	0.59546	0.859	T	0.13045	-1.0524	6	0.87932	D	0	.	.	.	.	rs886532;rs52825485;rs886532	15	Q99440	CD006_HUMAN	K	15	ENSP00000195455:N15K	ENSP00000195455:N15K	N	+	3	2	C4orf6	5578003	0.164000	0.22935	0.132000	0.22025	0.130000	0.20726	-0.711000	0.05019	-0.709000	0.05008	-0.704000	0.03662	AAC	C|0.932;A|0.068	0.068	strong		0.368	C4orf6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246818.1	NM_005750	
NDNL2	56160	hgsc.bcm.edu	37	15	29561467	29561467	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:29561467T>G	ENST00000332303.4	-	1	566	c.443A>C	c.(442-444)aAg>aCg	p.K148T	FAM189A1_ENST00000261275.4_Intron	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN	necdin-like 2	148	Interaction with NSMCE1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)				breast(3)|large_intestine(2)|lung(3)	8		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		AGTGTTGCTCTTGGGTTCAAG	0.582																																					p.K148T		Atlas-SNP	.											.	NDNL2	19	.	0			c.A443C						PASS	.						81.0	74.0	76.0					15																	29561467		2203	4300	6503	SO:0001583	missense	56160	exon1			TTGCTCTTGGGTT	AF490510	CCDS10023.1	15q13.1	2008-02-01			ENSG00000185115	ENSG00000185115			7677	protein-coding gene	gene with protein product		608243				18086888	Standard	NM_138704		Approved	HCA4, MAGEG1, MAGEL3, NSE3, NSMCE3	uc001zco.3	Q96MG7	OTTHUMG00000129261	ENST00000332303.4:c.443A>C	15.37:g.29561467T>G	ENSP00000330694:p.Lys148Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_138704	Q8IW16|Q8TEI6|Q9H214	Missense_Mutation	SNP	ENST00000332303.4	37	CCDS10023.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.238898	0.58995	.	.	ENSG00000185115	ENST00000332303	T	0.05717	3.4	3.91	-1.44	0.08856	.	0.124104	0.52532	U	0.000070	T	0.03305	0.0096	N	0.20807	0.61	0.09310	N	0.999997	P	0.36712	0.566	B	0.42959	0.403	T	0.35051	-0.9804	10	0.02654	T	1	.	4.0573	0.09823	0.0:0.3563:0.1937:0.45	.	148	Q96MG7	MAGG1_HUMAN	T	148	ENSP00000330694:K148T	ENSP00000330694:K148T	K	-	2	0	NDNL2	27348759	1.000000	0.71417	0.007000	0.13788	0.969000	0.65631	0.975000	0.29449	-0.271000	0.09272	0.460000	0.39030	AAG	.	.	none		0.582	NDNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251370.1	NM_138704	
TRANK1	9881	hgsc.bcm.edu	37	3	36898699	36898699	+	Silent	SNP	G	G	A	rs187740236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:36898699G>A	ENST00000429976.2	-	12	2629	c.2382C>T	c.(2380-2382)tgC>tgT	p.C794C	TRANK1_ENST00000301807.6_Silent_p.C244C|TRANK1_ENST00000428977.2_Silent_p.C244C	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	794							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						TTTCTGAAGTGCACTCGATCT	0.502													G|||	14	0.00279553	0.0106	0.0	5008	,	,		20254	0.0		0.0	False		,,,				2504	0.0				p.C794C		Atlas-SNP	.											.	TRANK1	398	.	0			c.C2382T						PASS	.	G		34,4008		1,32,1988	243.0	235.0	238.0		2382	-3.4	0.7	3		238	0,8392		0,0,4196	yes	coding-synonymous	TRANK1	NM_014831.2		1,32,6184	AA,AG,GG		0.0,0.8412,0.2734		794/2926	36898699	34,12400	2021	4196	6217	SO:0001819	synonymous_variant	9881	exon12			TGAAGTGCACTCG	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.2382C>T	3.37:g.36898699G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_014831	Q8N8K0	Silent	SNP	ENST00000429976.2	37	CCDS46789.2																																																																																			G|0.998;A|0.002	0.002	strong		0.502	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
PIGZ	80235	hgsc.bcm.edu	37	3	196674916	196674916	+	Silent	SNP	A	A	C	rs1147240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196674916A>C	ENST00000412723.1	-	3	998	c.852T>G	c.(850-852)gcT>gcG	p.A284A		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	284					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		TCCTGGATGTAGCGGGGCTGG	0.607													A|||	2891	0.577276	0.6672	0.4568	5008	,	,		18756	0.7698		0.3976	False		,,,				2504	0.5276				p.A284A		Atlas-SNP	.											.	PIGZ	34	.	0			c.T852G						PASS	.	A		2723,1683	639.9+/-397.2	832,1059,312	104.0	110.0	108.0		852	-8.1	0.0	3	dbSNP_87	108	3228,5372	471.3+/-368.1	617,1994,1689	no	coding-synonymous	PIGZ	NM_025163.2		1449,3053,2001	CC,CA,AA		37.5349,38.1979,45.7558		284/580	196674916	5951,7055	2203	4300	6503	SO:0001819	synonymous_variant	80235	exon3			GGATGTAGCGGGG	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	30596	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 4"", ""dol-P-Man dependent GPI mannosyltransferase"""	611671	"""phosphatidylinositol glycan, class Z"""			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.852T>G	3.37:g.196674916A>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_025163	Q9H9G6	Silent	SNP	ENST00000412723.1	37	CCDS3324.1																																																																																			A|0.479;C|0.521	0.521	strong		0.607	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
HAVCR1	26762	hgsc.bcm.edu	37	5	156479583	156479583	+	Silent	SNP	C	C	G	rs192652646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156479583C>G	ENST00000339252.3	-	3	994	c.462G>C	c.(460-462)acG>acC	p.T154T	HAVCR1_ENST00000425854.1_Silent_p.T154T|HAVCR1_ENST00000522693.1_Silent_p.T154T|HAVCR1_ENST00000544197.1_Silent_p.T154T|HAVCR1_ENST00000523175.1_Silent_p.T154T	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)			endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTGGAACAGTCGTTGTCGTTG	0.473																																					p.T154T		Atlas-SNP	.											HAVCR1,colon,carcinoma,-1,2	HAVCR1	84	2	0			c.G462C						scavenged	.						511.0	502.0	505.0					5																	156479583		2137	4231	6368	SO:0001819	synonymous_variant	26762	exon4			AACAGTCGTTGTC	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"""Immunoglobulin superfamily / V-set domain containing"""	17866	protein-coding gene	gene with protein product	"""T-cell immunoglobulin mucin family member 1"""	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.462G>C	5.37:g.156479583C>G		Somatic	421	0	0		WXS	Illumina HiSeq	Phase_I	457	5	0.0109409	NM_001099414	O43656	Silent	SNP	ENST00000339252.3	37	CCDS43392.1																																																																																			C|0.981;G|0.019	0.019	strong		0.473	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
GRM5	2915	hgsc.bcm.edu	37	11	88338074	88338074	+	Silent	SNP	G	G	A	rs61745770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:88338074G>A	ENST00000305447.4	-	4	1355	c.1206C>T	c.(1204-1206)aaC>aaT	p.N402N	GRM5_ENST00000418177.2_Silent_p.N402N|GRM5_ENST00000305432.5_Silent_p.N402N|GRM5_ENST00000393297.1_Silent_p.N402N|GRM5_ENST00000455756.2_Silent_p.N402N	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	402					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	AATAGATGGCGTTGATCACAA	0.458													g|||	136	0.0271565	0.0946	0.0144	5008	,	,		20660	0.0		0.001	False		,,,				2504	0.0				p.N402N		Atlas-SNP	.											.	GRM5	414	.	0			c.C1206T						PASS	.	A	,	353,4049	183.3+/-210.9	14,325,1862	101.0	86.0	91.0		1206,1206	-2.1	1.0	11	dbSNP_129	91	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	GRM5	NM_000842.3,NM_001143831.2	,	14,325,6161	AA,AG,GG		0.0,8.0191,2.7154	,	402/1181,402/1213	88338074	353,12647	2201	4299	6500	SO:0001819	synonymous_variant	2915	exon5			GATGGCGTTGATC	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4597	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 86"""	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1206C>T	11.37:g.88338074G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_000842	Q6J164	Silent	SNP	ENST00000305447.4	37	CCDS44694.1																																																																																			G|0.971;A|0.029	0.029	strong		0.458	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842	
ABCA13	154664	hgsc.bcm.edu	37	7	48452147	48452147	+	Silent	SNP	G	G	A	rs369363967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:48452147G>A	ENST00000435803.1	+	41	12450	c.12426G>A	c.(12424-12426)acG>acA	p.T4142T		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4142					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						TGCACCTGACGGGCTATGGGA	0.478													G|||	4	0.000798722	0.0023	0.0014	5008	,	,		17632	0.0		0.0	False		,,,				2504	0.0				p.T4142T		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G12426A						PASS	.	G		24,3846		0,24,1911	80.0	75.0	77.0		12426	-9.9	0.0	7		77	0,8308		0,0,4154	no	coding-synonymous	ABCA13	NM_152701.3		0,24,6065	AA,AG,GG		0.0,0.6202,0.1971		4142/5059	48452147	24,12154	1935	4154	6089	SO:0001819	synonymous_variant	154664	exon41			CCTGACGGGCTAT	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.12426G>A	7.37:g.48452147G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	152	85	0.559211	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			.	.	weak		0.478	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
FMR1	2332	hgsc.bcm.edu	37	X	147010320	147010320	+	Silent	SNP	G	G	A	rs25707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:147010320G>A	ENST00000370475.4	+	5	542	c.414G>A	c.(412-414)cgG>cgA	p.R138R	FMR1_ENST00000370470.1_Silent_p.R138R|FMR1_ENST00000218200.8_Silent_p.R138R|FMR1_ENST00000370471.3_Silent_p.R138R|FMR1_ENST00000334557.6_Silent_p.R138R|FMR1_ENST00000440235.2_5'Flank|FMR1_ENST00000370477.1_Silent_p.R138R|FMR1_ENST00000439526.2_Silent_p.R138R	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	138			R -> Q (rare variant found in a developmentally delayed male; unknown pathological significance). {ECO:0000269|PubMed:20799337}.		central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					AAGACTTACGGCAAATGTAAG	0.333									Fragile X syndrome				A|||	376	0.0996026	0.1467	0.0303	3775	,	,		11597	0.001		0.0815	False		,,,				2504	0.0798				p.R138R		Atlas-SNP	.											.	FMR1	93	.	0			c.G414A						PASS	.	A	,,,,	639,3195		43,457,96,1132,474	86.0	77.0	80.0		414,414,414,414,414	-1.7	0.9	X	dbSNP_76	80	540,6188		14,363,149,2051,1723	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FMR1	NM_001185075.1,NM_001185076.1,NM_001185081.1,NM_001185082.1,NM_002024.5	,,,,	57,820,245,3183,2197	AA,AG,A,GG,G		8.0262,16.6667,11.1627	,,,,	138/538,138/612,138/517,138/587,138/633	147010320	1179,9383	2202	4300	6502	SO:0001819	synonymous_variant	2332	exon5	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	CTTACGGCAAATG	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"""premature ovarian failure 1"""	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.414G>A	X.37:g.147010320G>A		Somatic	241	1	0.00414938		WXS	Illumina HiSeq	Phase_I	290	182	0.627586	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Silent	SNP	ENST00000370475.4	37	CCDS14682.1																																																																																			0|0.002;A|0.101	0.101	strong		0.333	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024	
ZNF844	284391	hgsc.bcm.edu	37	19	12187475	12187475	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12187475C>G	ENST00000439326.3	+	4	1715	c.1540C>G	c.(1540-1542)Cat>Gat	p.H514D	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	514					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.H514D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						AAAGCCTTCACATCTGCCTCA	0.408																																					p.H514D		Atlas-SNP	.											ZNF844,NS,carcinoma,0,6	ZNF844	69	6	1	Substitution - Missense(1)	endometrium(1)	c.C1540G						scavenged	.						87.0	81.0	83.0					19																	12187475		692	1591	2283	SO:0001583	missense	284391	exon4			CCTTCACATCTGC	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1540C>G	19.37:g.12187475C>G	ENSP00000392024:p.His514Asp	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	83	3	0.0361446	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	.	.	.	.	.	.	.	.	.	.	c	0.059	-1.227642	0.01518	.	.	ENSG00000223547	ENST00000439326;ENST00000541708	T	0.06371	3.31	2.45	-4.91	0.03085	.	.	.	.	.	T	0.02649	0.0080	N	0.04387	-0.21	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44019	-0.9355	9	0.25106	T	0.35	.	9.0916	0.36614	0.0:0.4133:0.4132:0.1735	.	514	Q08AG5	ZN844_HUMAN	D	514	ENSP00000392024:H514D	ENSP00000392024:H514D	H	+	1	0	ZNF844	12048475	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-4.066000	0.00302	-2.826000	0.00341	-1.839000	0.00587	CAT	.	.	none		0.408	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
MYH11	4629	hgsc.bcm.edu	37	16	15808861	15808861	+	Silent	SNP	G	G	A	rs587781070|rs149566621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:15808861G>A	ENST00000300036.5	-	40	5800	c.5691C>T	c.(5689-5691)aaC>aaT	p.N1897N	NDE1_ENST00000396355.1_Intron|MYH11_ENST00000576790.2_Silent_p.N1897N|MYH11_ENST00000396324.3_Silent_p.N1904N|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000452625.2_Silent_p.N1904N|NDE1_ENST00000342673.5_Intron	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1897					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGCGGTTGGCGTTGATGCGCT	0.632			T	CBFB	AML								G|||	10	0.00199681	0.0076	0.0	5008	,	,		13948	0.0		0.0	False		,,,				2504	0.0				p.N1904N		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.C5712T						PASS	.	G	,,,,,	31,4363	37.6+/-69.7	0,31,2166	133.0	125.0	128.0		5712,5712,,5691,,5691	-3.5	1.0	16	dbSNP_134	128	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	,,,,,	0,35,6462	AA,AG,GG		0.0465,0.7055,0.2694	,,,,,	1904/1946,1904/1980,,1897/1973,,1897/1939	15808861	35,12959	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon41			GTTGGCGTTGATG	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5691C>T	16.37:g.15808861G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			G|0.998;A|0.002	0.002	strong		0.632	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
CEP55	55165	hgsc.bcm.edu	37	10	95262980	95262980	+	Silent	SNP	C	C	T	rs62642530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:95262980C>T	ENST00000371485.3	+	3	598	c.294C>T	c.(292-294)acC>acT	p.T98T		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	98					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)				ATAGTACTACCACATTGCTTG	0.443													C|||	20	0.00399361	0.0129	0.0014	5008	,	,		19829	0.0		0.0	False		,,,				2504	0.002				p.T98T		Atlas-SNP	.											.	CEP55	35	.	0			c.C294T						PASS	.	C	,	38,4368	16.8+/-37.8	0,38,2165	147.0	131.0	136.0		294,294	-10.7	0.0	10	dbSNP_129	136	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CEP55	NM_001127182.1,NM_018131.4	,	0,38,6465	TT,TC,CC		0.0,0.8625,0.2922	,	98/465,98/465	95262980	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	55165	exon3			TACTACCACATTG	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.294C>T	10.37:g.95262980C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Silent	SNP	ENST00000371485.3	37	CCDS7428.1																																																																																			C|0.996;T|0.004	0.004	strong		0.443	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131	
TTN	7273	hgsc.bcm.edu	37	2	179528378	179528378	+	Intron	SNP	C	C	T	rs2163008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179528378C>T	ENST00000591111.1	-	154	34489				TTN_ENST00000589042.1_Missense_Mutation_p.E12170K|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_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)			ACTTCAGGCTCTTTAGGAGGA	0.388													T|||	1298	0.259185	0.503	0.2277	5008	,	,		18311	0.1339		0.0755	False		,,,				2504	0.2699				p.E12170K		Atlas-SNP	.											.	TTN	18412	.	0			c.G36508A						PASS	.	T	,,,	829,923		198,433,245	301.0	308.0	306.0		,,,	3.8	1.0	2	dbSNP_96	306	223,3759		7,209,1775	no	intron,intron,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	205,642,2020	TT,TC,CC		5.6002,47.3174,18.3467	,,,	,,,	179528378	1052,4682	876	1991	2867	SO:0001627	intron_variant	7273	exon171			CAGGCTCTTTAGG	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.34265-4857G>A	2.37:g.179528378C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	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		440	0.20146520146520147	243	0.49390243902439024	78	0.2154696132596685	64	0.11188811188811189	55	0.07255936675461741	T	1.005	-0.689738	0.03328	0.473174	0.056002	ENSG00000155657	ENST00000541862;ENST00000392423	.	.	.	4.92	3.77	0.43336	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999998224	.	.	.	.	.	.	T	0.44907	-0.9297	4	0.02654	T	1	.	7.9799	0.30177	0.0:0.3269:0.0:0.6731	rs2163008;rs59956680	.	.	.	K	444;296	.	ENSP00000376219:E296K	E	-	1	0	TTN	179236623	0.001000	0.12720	0.999000	0.59377	0.604000	0.37047	-0.251000	0.08818	0.340000	0.23745	-0.535000	0.04281	GAG	C|0.832;T|0.168	0.168	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
N4BP2	55728	hgsc.bcm.edu	37	4	40144467	40144467	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:40144467T>C	ENST00000261435.6	+	15	5376	c.4960T>C	c.(4960-4962)Ttt>Ctt	p.F1654L		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1654					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TGTCGCCACCTTTTATGCCCA	0.393																																					p.F1654L		Atlas-SNP	.											N4BP2,NS,carcinoma,0,1	N4BP2	166	1	0			c.T4960C						scavenged	.						75.0	75.0	75.0					4																	40144467		2203	4300	6503	SO:0001583	missense	55728	exon15			GCCACCTTTTATG	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.4960T>C	4.37:g.40144467T>C	ENSP00000261435:p.Phe1654Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	121	3	0.0247934	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.0|26.0	4.691963|4.691963	0.88735|0.88735	.|.	.|.	ENSG00000078177|ENSG00000078177	ENST00000261435;ENST00000381804|ENST00000513269	T|.	0.19105|.	2.17|.	5.48|5.48	5.48|5.48	0.80851|0.80851	Domain of unknown function DUF1771 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70500|0.70500	0.3231|0.3231	L|L	0.59436|0.59436	1.845|1.845	0.53688|0.53688	D|D	0.999971|0.999971	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.77557|.	0.983;0.99|.	T|T	0.69355|0.69355	-0.5167|-0.5167	10|5	0.72032|.	D|.	0.01|.	-18.3881|-18.3881	15.5702|15.5702	0.76330|0.76330	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1637;1654|.	Q86UW6-2;Q86UW6|.	.;N4BP2_HUMAN|.	L|P	1654;1574|1283	ENSP00000261435:F1654L|.	ENSP00000261435:F1654L|.	F|L	+|+	1|2	0|0	N4BP2|N4BP2	39820862|39820862	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.789000|0.789000	0.44602|0.44602	7.442000|7.442000	0.80503|0.80503	2.084000|2.084000	0.62774|0.62774	0.379000|0.379000	0.24179|0.24179	TTT|CTT	.	.	none		0.393	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
OR4L1	122742	hgsc.bcm.edu	37	14	20528207	20528207	+	Missense_Mutation	SNP	G	G	A	rs1958715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20528207G>A	ENST00000315683.1	+	1	4	c.4G>A	c.(4-6)Gat>Aat	p.D2N		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	2			D -> N (in dbSNP:rs1958715).			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(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		TGAGTAAATGGATCTTAAAAA	0.299													g|||	2688	0.536741	0.4902	0.5562	5008	,	,		17781	0.5734		0.3857	False		,,,				2504	0.7035				p.D2N		Atlas-SNP	.											.	OR4L1	98	.	0			c.G4A						PASS	.		ASN/ASP	2146,2260		521,1104,578	103.0	112.0	109.0		4	1.4	0.8	14	dbSNP_92	109	3457,5141		730,1997,1572	yes	missense	OR4L1	NM_001004717.1	23	1251,3101,2150	AA,AG,GG		40.207,48.7063,43.0867	possibly-damaging	2/313	20528207	5603,7401	2203	4299	6502	SO:0001583	missense	122742	exon1			TAAATGGATCTTA		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.4G>A	14.37:g.20528207G>A	ENSP00000319217:p.Asp2Asn	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_001004717	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	1083	0.4958791208791209	255	0.5182926829268293	192	0.5303867403314917	320	0.5594405594405595	316	0.41688654353562005	.	8.093	0.775042	0.16051	0.487063	0.40207	ENSG00000176246	ENST00000315683	T	0.03004	4.08	3.28	1.4	0.22301	.	0.569745	0.15717	N	0.248106	T	0.00012	0.0000	L	0.33245	0.995	0.39736	P	0.02832199999999996	B	0.09022	0.002	B	0.10450	0.005	T	0.20739	-1.0266	9	0.25751	T	0.34	.	6.4376	0.21831	0.1113:0.1873:0.7014:0.0	rs1958715;rs17126014;rs52801958;rs61492536;rs1958715	2	Q8NH43	OR4L1_HUMAN	N	2	ENSP00000319217:D2N	ENSP00000319217:D2N	D	+	1	0	OR4L1	19598047	0.000000	0.05858	0.786000	0.31890	0.504000	0.33889	-0.124000	0.10595	0.395000	0.25257	0.639000	0.83563	GAT	G|0.535;A|0.465	0.465	strong		0.299	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
PRDM12	59335	hgsc.bcm.edu	37	9	133553993	133553993	+	Silent	SNP	C	C	T	rs7021384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133553993C>T	ENST00000253008.2	+	4	708	c.648C>T	c.(646-648)ccC>ccT	p.P216P		NM_021619.2	NP_067632.2	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	216					neurogenesis (GO:0022008)|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)			kidney(2)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)		OV - Ovarian serous cystadenocarcinoma(145;0.000344)		CAGGTGTGCCCGGGCTAGAGG	0.592													C|||	1893	0.377995	0.3336	0.451	5008	,	,		18722	0.4722		0.3211	False		,,,				2504	0.3476				p.P216P		Atlas-SNP	.											.	PRDM12	24	.	0			c.C648T						PASS	.	C		1542,2864	486.4+/-360.6	264,1014,925	89.0	85.0	86.0		648	-11.5	0.0	9	dbSNP_116	86	2733,5867	436.9+/-358.5	436,1861,2003	no	coding-synonymous	PRDM12	NM_021619.2		700,2875,2928	TT,TC,CC		31.7791,34.9977,32.8694		216/368	133553993	4275,8731	2203	4300	6503	SO:0001819	synonymous_variant	59335	exon4			TGTGCCCGGGCTA	AY004252	CCDS6934.1	9q33-q34	2013-01-08			ENSG00000130711	ENSG00000130711		"""Zinc fingers, C2H2-type"""	13997	protein-coding gene	gene with protein product	"""PR-domain containing protein 12"", ""PR-domain zinc finger protein 12"""					14523459	Standard	NM_021619		Approved		uc004bzt.1	Q9H4Q4	OTTHUMG00000020808	ENST00000253008.2:c.648C>T	9.37:g.133553993C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_021619	A3KFK9	Silent	SNP	ENST00000253008.2	37	CCDS6934.1																																																																																			C|0.650;T|0.350	0.350	strong		0.592	PRDM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054664.1	NM_021619	
NRAP	4892	hgsc.bcm.edu	37	10	115375528	115375528	+	Silent	SNP	C	C	A	rs11196397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115375528C>A	ENST00000359988.3	-	27	3265	c.3021G>T	c.(3019-3021)ccG>ccT	p.P1007P	NRAP_ENST00000369360.3_Silent_p.P980P|NRAP_ENST00000369358.4_Silent_p.P1015P|NRAP_ENST00000360478.3_Silent_p.P972P	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.P1007P(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)		GGTCAGCAGTCGGTGTGTAAT	0.498													C|||	1140	0.227636	0.0802	0.2507	5008	,	,		20885	0.3958		0.2783	False		,,,				2504	0.1851				p.P1007P		Atlas-SNP	.											NRAP,NS,carcinoma,0,1	NRAP	208	1	1	Substitution - coding silent(1)	stomach(1)	c.G3021T						PASS	.	C	,	450,3956	217.4+/-235.8	30,390,1783	386.0	288.0	321.0		2916,3021	1.9	0.6	10	dbSNP_120	321	2318,6282	389.1+/-342.8	312,1694,2294	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	342,2084,4077	AA,AC,CC		26.9535,10.2133,21.2825	,	972/1696,1007/1731	115375528	2768,10238	2203	4300	6503	SO:0001819	synonymous_variant	4892	exon27			AGCAGTCGGTGTG		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.3021G>T	10.37:g.115375528C>A		Somatic	449	0	0		WXS	Illumina HiSeq	Phase_I	444	221	0.497748	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			C|0.772;A|0.228	0.228	strong		0.498	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
MYH1	4619	hgsc.bcm.edu	37	17	10404766	10404766	+	Silent	SNP	C	C	T	rs61730793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10404766C>T	ENST00000226207.5	-	27	3493	c.3399G>A	c.(3397-3399)cgG>cgA	p.R1133R	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1133					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CTGCTTTGGCCCGGGAGGCCC	0.572													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		16908	0.0		0.0	False		,,,				2504	0.0				p.R1133R		Atlas-SNP	.											.	MYH1	403	.	0			c.G3399A						PASS	.	C		90,4316		1,88,2114	40.0	45.0	44.0		3399	3.3	1.0	17	dbSNP_129	44	0,8588		0,0,4294	no	coding-synonymous	MYH1	NM_005963.3		1,88,6408	TT,TC,CC		0.0,2.0427,0.6926		1133/1940	10404766	90,12904	2203	4294	6497	SO:0001819	synonymous_variant	4619	exon27			TTTGGCCCGGGAG		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3399G>A	17.37:g.10404766C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	160	86	0.5375	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	37	CCDS11155.1																																																																																			C|0.994;T|0.006	0.006	strong		0.572	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919263	51919263	+	Missense_Mutation	SNP	G	G	T	rs7258951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51919263G>T	ENST00000339313.5	-	5	1029	c.913C>A	c.(913-915)Ccc>Acc	p.P305T	SIGLEC10_ENST00000432469.2_Missense_Mutation_p.P222T|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.P247T|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.P305T|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.P247T|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.P257T|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.P305T|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	305	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		AGCCCCAGGGGTCTAGGGCCC	0.682																																					p.P305T		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C913A						PASS	.						27.0	32.0	30.0					19																	51919263		2203	4300	6503	SO:0001583	missense	89790	exon5			CCAGGGGTCTAGG	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.913C>A	19.37:g.51919263G>T	ENSP00000345243:p.Pro305Thr	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	180	31	0.172222	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	0.970	-0.700547	0.03279	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	4.37	-8.73	0.00841	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.075820	0.02035	N	0.048846	T	0.14098	0.0341	N	0.00041	-2.485	0.09310	N	1	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	0.14023	0.004;0.001;0.001;0.002;0.001;0.01	T	0.24190	-1.0167	10	0.02654	T	1	.	4.0774	0.09911	0.0833:0.1276:0.315:0.474	rs7258951	257;305;305;247;247;305	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	T	305;222;305;247;247;257;305;119	ENSP00000342389:P305T;ENSP00000396742:P222T;ENSP00000348646:P305T;ENSP00000408387:P247T;ENSP00000389132:P247T;ENSP00000414324:P257T;ENSP00000345243:P305T;ENSP00000435281:P119T	ENSP00000345243:P305T	P	-	1	0	SIGLEC10	56611075	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-4.629000	0.00206	-5.012000	0.00024	-2.282000	0.00269	CCC	G|0.718;T|0.282	0.282	strong		0.682	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
POP5	51367	hgsc.bcm.edu	37	12	121019009	121019009	+	Silent	SNP	G	G	C	rs74750729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121019009G>C	ENST00000357500.4	-	2	107	c.72C>G	c.(70-72)ctC>ctG	p.L24L	POP5_ENST00000341039.2_Silent_p.L24L|POP5_ENST00000542776.1_5'UTR	NM_015918.3	NP_057002.2	Q969H6	POP5_HUMAN	processing of precursor 5, ribonuclease P/MRP subunit (S. cerevisiae)	24					tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)	ribonuclease P activity (GO:0004526)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	7	all_neural(191;0.077)|Medulloblastoma(191;0.0922)					CTCGGTCATCGAGGCTTAGGC	0.672													G|||	8	0.00159744	0.0061	0.0	5008	,	,		16752	0.0		0.0	False		,,,				2504	0.0				p.L24L		Atlas-SNP	.											.	POP5	14	.	0			c.C72G						PASS	.	G	,	43,4363	44.6+/-78.6	0,43,2160	44.0	46.0	45.0		72,72	1.7	1.0	12	dbSNP_131	45	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	POP5	NM_015918.3,NM_198202.1	,	0,43,6460	CC,CG,GG		0.0,0.9759,0.3306	,	24/164,24/114	121019009	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	51367	exon2			GTCATCGAGGCTT	AJ306296	CCDS9202.1, CCDS9203.1	12q24.31	2012-05-21			ENSG00000167272	ENSG00000167272			17689	protein-coding gene	gene with protein product		609992				11413139	Standard	NM_198202		Approved		uc001tys.3	Q969H6	OTTHUMG00000169023	ENST00000357500.4:c.72C>G	12.37:g.121019009G>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_198202	A6NL80|Q53FS5|Q9Y2Q6	Silent	SNP	ENST00000357500.4	37	CCDS9202.1																																																																																			G|0.998;C|0.002	0.002	strong		0.672	POP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401993.1	NM_015918	
MATN3	4148	hgsc.bcm.edu	37	2	20205680	20205680	+	Silent	SNP	C	C	T	rs28401180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20205680C>T	ENST00000407540.3	-	2	677	c.615G>A	c.(613-615)gaG>gaA	p.E205E	AC079145.4_ENST00000416575.1_RNA|MATN3_ENST00000421259.2_Silent_p.E205E	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	205	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGCCGCCACCTCATTCACCT	0.597													C|||	2626	0.524361	0.528	0.4625	5008	,	,		17859	0.619		0.4026	False		,,,				2504	0.591				p.E205E		Atlas-SNP	.											.	MATN3	28	.	0			c.G615A						PASS	.	C		1964,2134		494,976,579	21.0	25.0	23.0		615	3.5	1.0	2	dbSNP_125	23	3408,4988		716,1976,1506	no	coding-synonymous	MATN3	NM_002381.4		1210,2952,2085	TT,TC,CC		40.5908,47.9258,42.9966		205/487	20205680	5372,7122	2049	4198	6247	SO:0001819	synonymous_variant	4148	exon2			CGCCACCTCATTC	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.615G>A	2.37:g.20205680C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_002381	B2CPU0|Q4ZG02	Silent	SNP	ENST00000407540.3	37	CCDS46226.1																																																																																			C|0.513;T|0.487	0.487	strong		0.597	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381	
LILRA2	11027	hgsc.bcm.edu	37	19	55098742	55098742	+	Missense_Mutation	SNP	G	G	T	rs73939008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55098742G>T	ENST00000251377.3	+	9	1514	c.1381G>T	c.(1381-1383)Gtg>Ttg	p.V461L	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA2_ENST00000391738.3_Missense_Mutation_p.V461L|CTB-83J4.2_ENST00000596330.1_lincRNA|LILRA2_ENST00000391737.1_Missense_Mutation_p.V432L|LILRA2_ENST00000251376.3_Missense_Mutation_p.V444L|LILRB1_ENST00000418536.2_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	461					defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		CTTGGTCCTGGTGGTCCTCGG	0.562													g|||	51	0.0101837	0.0378	0.0014	5008	,	,		17380	0.0		0.0	False		,,,				2504	0.0				p.V461L		Atlas-SNP	.											LILRA2,right_upper_lobe,carcinoma,0,1	LILRA2	99	1	0			c.G1381T						PASS	.	G	LEU/VAL,LEU/VAL	100,4306	78.3+/-116.7	0,100,2103	111.0	96.0	101.0		1381,1330	-4.3	0.0	19	dbSNP_130	101	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	LILRA2	NM_001130917.1,NM_006866.2	32,32	0,102,6401	TT,TG,GG		0.0233,2.2696,0.7843	,	461/484,444/467	55098742	102,12904	2203	4300	6503	SO:0001583	missense	11027	exon8			GTCCTGGTGGTCC	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.1381G>T	19.37:g.55098742G>T	ENSP00000251377:p.Val461Leu	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	253	109	0.43083	NM_001130917	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	10.21	1.287724	0.23478	0.022696	2.33E-4	ENSG00000239998	ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T	0.00529	6.98;6.98;6.86;6.78	2.74	-4.29	0.03721	.	22.652400	0.00166	N	0.000016	T	0.00109	0.0003	N	0.25094	0.71	0.09310	N	0.999998	B;B;P	0.45126	0.341;0.09;0.851	B;B;P	0.47402	0.066;0.026;0.546	T	0.55755	-0.8091	10	0.02654	T	1	.	5.1841	0.15174	0.0:0.3589:0.2798:0.3612	.	432;461;444	A8MZH0;Q8N149;Q8N149-2	.;LIRA2_HUMAN;.	L	461;461;444;432	ENSP00000251377:V461L;ENSP00000375618:V461L;ENSP00000251376:V444L;ENSP00000375617:V432L	ENSP00000251376:V444L	V	+	1	0	LILRA2	59790554	0.003000	0.15002	0.035000	0.18076	0.160000	0.22226	-1.113000	0.03296	-0.357000	0.08175	0.609000	0.83330	GTG	G|0.991;T|0.009	0.009	strong		0.562	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2		
DMD	1756	hgsc.bcm.edu	37	X	32466654	32466654	+	Silent	SNP	G	G	A	rs143628111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:32466654G>A	ENST00000357033.4	-	27	3911	c.3705C>T	c.(3703-3705)gcC>gcT	p.A1235A	DMD_ENST00000378677.2_Silent_p.A1231A	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	1235					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)				CCTTTTTTAAGGCCTCTTGTG	0.438													G|||	71	0.0188079	0.0537	0.0	3775	,	,		13391	0.0		0.0	False		,,,				2504	0.0				p.A1235A		Atlas-SNP	.											.	DMD	2127	.	0			c.C3705T						PASS	.	G	,,,,	183,3650		3,143,34,1485,537	199.0	158.0	172.0		3681,3705,3336,3693,3336	4.0	1.0	X	dbSNP_134	172	2,6725		0,2,0,2426,1871	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	3,145,34,3911,2408	AA,AG,A,GG,G		0.0297,4.7743,1.7519	,,,,	1227/3678,1235/3686,1112/3563,1231/3682,1112/3563	32466654	185,10375	2202	4299	6501	SO:0001819	synonymous_variant	1756	exon27			TTTTAAGGCCTCT	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.3705C>T	X.37:g.32466654G>A		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	258	127	0.492248	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																			G|0.983;A|0.017	0.017	strong		0.438	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
TG	7038	hgsc.bcm.edu	37	8	133953673	133953673	+	Missense_Mutation	SNP	C	C	T	rs61744678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133953673C>T	ENST00000220616.4	+	26	5159	c.5119C>T	c.(5119-5121)Ccc>Tcc	p.P1707S	TG_ENST00000377869.1_Missense_Mutation_p.P1650S|TG_ENST00000542445.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1707					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)		ATTGTACAACCCCATTGTGTT	0.498													C|||	380	0.0758786	0.2655	0.0331	5008	,	,		22960	0.0		0.005	False		,,,				2504	0.001				p.P1707S		Atlas-SNP	.											TG,right_upper_lobe,carcinoma,-1,1	TG	416	1	0			c.C5119T						PASS	.	C	SER/PRO	1029,3377	380.4+/-323.7	118,793,1292	171.0	145.0	154.0		5119	-1.3	0.0	8	dbSNP_129	154	27,8573	18.5+/-59.3	0,27,4273	yes	missense	TG	NM_003235.4	74	118,820,5565	TT,TC,CC		0.314,23.3545,8.1193	benign	1707/2769	133953673	1056,11950	2203	4300	6503	SO:0001583	missense	7038	exon26			TACAACCCCATTG	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.5119C>T	8.37:g.133953673C>T	ENSP00000220616:p.Pro1707Ser	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	274	135	0.492701	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	132	0.06043956043956044	118	0.23983739837398374	11	0.03038674033149171	0	0.0	3	0.00395778364116095	C	0.010	-1.779518	0.00634	0.233545	0.00314	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;T	0.65549	-0.16;-0.16	5.81	-1.31	0.09230	.	0.444137	0.21467	N	0.074067	T	0.00012	0.0000	N	0.26130	0.795	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.10613	-1.0622	9	0.15066	T	0.55	.	4.487	0.11794	0.0:0.307:0.3029:0.3901	rs61744678	1707	P01266	THYG_HUMAN	S	1650;513;1707	ENSP00000367100:P1650S;ENSP00000220616:P1707S	ENSP00000220616:P1707S	P	+	1	0	TG	134022855	0.000000	0.05858	0.004000	0.12327	0.053000	0.15095	-0.195000	0.09546	-0.120000	0.11809	0.462000	0.41574	CCC	C|0.929;T|0.071	0.071	strong		0.498	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
FLG	2312	hgsc.bcm.edu	37	1	152279729	152279729	+	Missense_Mutation	SNP	C	C	T	rs3126072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152279729C>T	ENST00000368799.1	-	3	7668	c.7633G>A	c.(7633-7635)Gga>Aga	p.G2545R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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						scavenged	.	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	379	4	0.0105541		WXS	Illumina HiSeq	Phase_I	552	550	0.996377	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	
HMMR	3161	hgsc.bcm.edu	37	5	162909716	162909716	+	Missense_Mutation	SNP	C	C	T	rs299295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162909716C>T	ENST00000358715.3	+	13	1487	c.1451C>T	c.(1450-1452)gCg>gTg	p.A484V	HMMR_ENST00000432118.2_Missense_Mutation_p.A398V|HMMR_ENST00000393915.4_Missense_Mutation_p.A485V|RP11-80G7.1_ENST00000521666.1_RNA|RP11-80G7.1_ENST00000514724.2_RNA|HMMR_ENST00000353866.3_Missense_Mutation_p.A469V			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	317	0	0		WXS	Illumina HiSeq	Phase_I	369	177	0.479675	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	
TG	7038	hgsc.bcm.edu	37	8	134144113	134144113	+	Silent	SNP	C	C	T	rs2294024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134144113C>T	ENST00000220616.4	+	46	7960	c.7920C>T	c.(7918-7920)taC>taT	p.Y2640Y	TG_ENST00000377869.1_Silent_p.Y2583Y|TG_ENST00000519543.1_Silent_p.Y773Y|TG_ENST00000542445.1_Silent_p.Y1010Y	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2640					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)		p.Y2640Y(1)		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)		ACCCAGCCTACGAGGGGCAGT	0.498													C|||	2030	0.405351	0.5885	0.4928	5008	,	,		17458	0.1657		0.4841	False		,,,				2504	0.2618				p.Y2640Y		Atlas-SNP	.											TG,NS,carcinoma,0,1	TG	416	1	1	Substitution - coding silent(1)	stomach(1)	c.C7920T						PASS	.	C		2536,1870	631.6+/-395.7	737,1062,404	94.0	94.0	94.0		7920	0.1	0.0	8	dbSNP_100	94	4238,4362	571.7+/-389.6	1070,2098,1132	no	coding-synonymous	TG	NM_003235.4		1807,3160,1536	TT,TC,CC		49.2791,42.4421,47.9163		2640/2769	134144113	6774,6232	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon46			AGCCTACGAGGGG	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.7920C>T	8.37:g.134144113C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	166	88	0.53012	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	926	0.423992673992674	276	0.5609756097560976	191	0.5276243093922652	97	0.16958041958041958	362	0.47757255936675463	C	6.383	0.438787	0.12104	0.575579	0.492791	ENSG00000042832	ENST00000519178	.	.	.	5.32	0.0514	0.14297	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8924	0.13733	0.0:0.4075:0.1533:0.4392	rs2294024;rs2294024	.	.	.	X	1096	.	.	R	+	1	2	TG	134213295	0.002000	0.14202	0.013000	0.15412	0.986000	0.74619	-0.075000	0.11431	0.254000	0.21573	0.491000	0.48974	CGA	C|0.522;T|0.478	0.478	strong		0.498	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
PIK3C2A	5286	hgsc.bcm.edu	37	11	17191019	17191019	+	Silent	SNP	A	A	G	rs214936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:17191019A>G	ENST00000265970.7	-	1	269	c.270T>C	c.(268-270)atT>atC	p.I90I	PIK3C2A_ENST00000540361.1_Intron|PIK3C2A_ENST00000531428.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	90	Interaction with clathrin; sufficient to induce clathrin assemby.				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						TTTCTACATCAATATCTAATG	0.378													a|||	1823	0.364018	0.3744	0.3847	5008	,	,		21861	0.1845		0.497	False		,,,				2504	0.3834				p.I90I		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T270C						PASS	.	A		1680,2720	509.6+/-367.3	318,1044,838	182.0	181.0	182.0		270	2.0	1.0	11	dbSNP_79	182	3973,4613	552.3+/-386.1	900,2173,1220	no	coding-synonymous	PIK3C2A	NM_002645.2		1218,3217,2058	GG,GA,AA		46.273,38.1818,43.5315		90/1687	17191019	5653,7333	2200	4293	6493	SO:0001819	synonymous_variant	5286	exon1			TACATCAATATCT	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.270T>C	11.37:g.17191019A>G		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	292	139	0.476027	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Silent	SNP	ENST00000265970.7	37	CCDS7824.1																																																																																			A|0.601;G|0.399	0.399	strong		0.378	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
TICRR	90381	hgsc.bcm.edu	37	15	90167610	90167610	+	Missense_Mutation	SNP	G	G	T	rs115865608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90167610G>T	ENST00000268138.7	+	20	4174	c.4069G>T	c.(4069-4071)Gtt>Ttt	p.V1357F	KIF7_ENST00000558928.1_Intron|TICRR_ENST00000560985.1_Missense_Mutation_p.V1356F			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1357	Pro-rich.				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)										CTCCTGCCCTGTTCCCTCAAC	0.517													G|||	15	0.00299521	0.0098	0.0029	5008	,	,		20300	0.0		0.0	False		,,,				2504	0.0				p.V1357F		Atlas-SNP	.											.	.	.	.	0			c.G4069T						PASS	.	G	PHE/VAL	47,4353	48.9+/-83.8	1,45,2154	129.0	129.0	129.0		4069	0.1	0.0	15	dbSNP_132	129	0,8598		0,0,4299	yes	missense	C15orf42	NM_152259.3	50	1,45,6453	TT,TG,GG		0.0,1.0682,0.3616	possibly-damaging	1357/1911	90167610	47,12951	2200	4299	6499	SO:0001583	missense	90381	exon20			TGCCCTGTTCCCT	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.4069G>T	15.37:g.90167610G>T	ENSP00000268138:p.Val1357Phe	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	3	0.0013736263736263737	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	0	0.0	G	8.278	0.814810	0.16607	0.010682	0.0	ENSG00000140534	ENST00000268138	T	0.08984	3.03	4.59	0.12	0.14691	.	1.919780	0.02660	N	0.107408	T	0.09598	0.0236	L	0.50333	1.59	0.09310	N	1	P	0.43701	0.815	P	0.46389	0.515	T	0.26883	-1.0090	10	0.40728	T	0.16	0.4344	7.2402	0.26092	0.2249:0.1216:0.6535:0.0	.	1357	Q7Z2Z1	TICRR_HUMAN	F	1357	ENSP00000268138:V1357F	ENSP00000268138:V1357F	V	+	1	0	C15orf42	87968614	0.003000	0.15002	0.002000	0.10522	0.216000	0.24613	0.321000	0.19558	0.118000	0.18165	-0.140000	0.14226	GTT	G|0.996;T|0.004	0.004	strong		0.517	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
INSR	3643	hgsc.bcm.edu	37	19	7166388	7166388	+	Silent	SNP	G	G	A	rs2229429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7166388G>A	ENST00000302850.5	-	8	1780	c.1638C>T	c.(1636-1638)gaC>gaT	p.D546D	INSR_ENST00000341500.5_Silent_p.D546D	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	546					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)"""	CATCCTGCCCGTCGAACTCCG	0.547													G|||	1285	0.256589	0.4834	0.1441	5008	,	,		19189	0.0655		0.1909	False		,,,				2504	0.2945				p.D546D		Atlas-SNP	.											.	INSR	265	.	0			c.C1638T						PASS	.	G	,	1901,2505	545.4+/-376.8	403,1095,705	84.0	61.0	69.0		1638,1638	-4.5	0.8	19	dbSNP_98	69	1710,6890	311.2+/-310.2	165,1380,2755	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	568,2475,3460	AA,AG,GG		19.8837,43.1457,27.7641	,	546/1383,546/1371	7166388	3611,9395	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon8			CTGCCCGTCGAAC	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.1638C>T	19.37:g.7166388G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			T|0.000;G|0.746;C|0.000;A|0.254	0.254	strong		0.547	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
C1orf112	55732	hgsc.bcm.edu	37	1	169796859	169796859	+	Silent	SNP	A	A	C	rs149832132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169796859A>C	ENST00000286031.6	+	12	1705	c.1005A>C	c.(1003-1005)ccA>ccC	p.P335P	C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000413811.2_Intron|C1orf112_ENST00000359326.4_Silent_p.P335P	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	335										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)					AAGACCTGCCATGTGAACTGC	0.398													A|||	14	0.00279553	0.0106	0.0	5008	,	,		19847	0.0		0.0	False		,,,				2504	0.0				p.P335P		Atlas-SNP	.											.	C1orf112	74	.	0			c.A1005C						PASS	.	A		42,4364	45.3+/-79.5	0,42,2161	348.0	345.0	346.0		1005	-10.8	0.0	1	dbSNP_134	346	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C1orf112	NM_018186.2		0,43,6460	CC,CA,AA		0.0116,0.9532,0.3306		335/854	169796859	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	55732	exon12			CCTGCCATGTGAA	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.1005A>C	1.37:g.169796859A>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	76	26	0.342105	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	37	CCDS1285.1																																																																																			A|0.997;C|0.003	0.003	strong		0.398	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
MUC5B	727897	hgsc.bcm.edu	37	11	1267562	1267562	+	Missense_Mutation	SNP	C	C	T	rs60268710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	342	1	0.00292398		WXS	Illumina HiSeq	Phase_I	392	193	0.492347	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	
SEZ6	124925	hgsc.bcm.edu	37	17	27284443	27284443	+	Missense_Mutation	SNP	A	A	G	rs12941884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27284443A>G	ENST00000317338.12	-	12	2845	c.2417T>C	c.(2416-2418)aTg>aCg	p.M806T	SEZ6_ENST00000442608.3_Missense_Mutation_p.M806T|SEZ6_ENST00000360295.9_Missense_Mutation_p.M806T|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000335960.6_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	806	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.		M -> T (in dbSNP:rs12941884). {ECO:0000269|PubMed:14702039}.		adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|negative regulation of dendrite development (GO:2000171)|positive regulation of dendrite development (GO:1900006)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	apical dendrite (GO:0097440)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	29	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			GGAGCTGCCCATCAGCACAAA	0.582													G|||	954	0.190495	0.2224	0.1859	5008	,	,		17489	0.123		0.1213	False		,,,				2504	0.2914				p.M806T		Atlas-SNP	.											.	SEZ6	61	.	0			c.T2417C						PASS	.	G	THR/MET,THR/MET	773,3133		88,597,1268	88.0	98.0	95.0		2417,2417	3.7	1.0	17	dbSNP_121	95	1033,7269		63,907,3181	yes	missense,missense	SEZ6	NM_001098635.1,NM_178860.4	81,81	151,1504,4449	GG,GA,AA		12.4428,19.7901,14.7936	benign,benign	806/994,806/995	27284443	1806,10402	1953	4151	6104	SO:0001583	missense	124925	exon12			CTGCCCATCAGCA	AY038048	CCDS45638.1, CCDS45639.1	17q11.2	2008-03-06	2001-11-28		ENSG00000063015	ENSG00000063015			15955	protein-coding gene	gene with protein product			"""seizure related gene 6 (mouse) homolog"""			17086543	Standard	NM_178860		Approved		uc002hdp.2	Q53EL9	OTTHUMG00000168010	ENST00000317338.12:c.2417T>C	17.37:g.27284443A>G	ENSP00000312942:p.Met806Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	141	77	0.546099	NM_001098635	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Missense_Mutation	SNP	ENST00000317338.12	37	CCDS45639.1	311	0.1423992673992674	101	0.20528455284552846	56	0.15469613259668508	59	0.10314685314685315	95	0.12532981530343007	G	1.337	-0.595139	0.03771	0.197901	0.124428	ENSG00000063015	ENST00000442608;ENST00000360295;ENST00000317338;ENST00000541381	T;T	0.64618	-0.11;-0.11	5.69	3.65	0.41850	Complement control module (2);Sushi/SCR/CCP (3);	0.060679	0.64402	N	0.000004	T	0.00039	0.0001	N	0.01048	-1.04	0.09310	P	0.9999999999999786	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.08452	-1.0721	9	0.10636	T	0.68	.	8.0263	0.30438	0.1504:0.1309:0.7186:0.0	rs12941884;rs52816964;rs61301981;rs12941884	806;681;806	Q53EL9-3;Q53EL9-2;Q53EL9	.;.;SEZ6_HUMAN	T	806;806;681;806	ENSP00000403784:M806T;ENSP00000353440:M806T	ENSP00000312942:M681T	M	-	2	0	SEZ6	24308569	0.992000	0.36948	0.999000	0.59377	0.783000	0.44284	2.085000	0.41634	0.763000	0.33175	-0.642000	0.03964	ATG	A|0.847;G|0.153	0.153	strong		0.582	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3		
C16orf82	162083	hgsc.bcm.edu	37	16	27078705	27078705	+	lincRNA	SNP	T	T	C	rs115398674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27078705T>C	ENST00000505035.1	+	0	678				RP11-673P17.2_ENST00000565783.1_RNA			Q7Z2V1	TNT_HUMAN	chromosome 16 open reading frame 82																		CTGGGCTCCATAGACCCTCCC	0.652													C|||	96	0.0191693	0.0711	0.0014	5008	,	,		17209	0.0		0.001	False		,,,				2504	0.0				p.I130T		Atlas-SNP	.											.	.	.	.	0			c.T389C						PASS	.	C	THR/ILE	203,3827		4,195,1816	8.0	12.0	10.0		389	-4.4	0.0	16	dbSNP_132	10	4,8292		0,4,4144	yes	missense	C16orf82	NM_001145545.1	89	4,199,5960	CC,CT,TT		0.0482,5.0372,1.6794	benign	130/155	27078705	207,12119	2015	4148	6163			162083	exon1			GCTCCATAGACCC	BC031257		16p12.1	2013-01-24			ENSG00000234186	ENSG00000234186			30755	other	unknown						12477932	Standard	NM_001145545		Approved	TNT	uc010vcm.2	Q7Z2V1	OTTHUMG00000161986		16.37:g.27078705T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	74	26	0.351351	NM_001145545	B9EGC2|Q8NEF0	Missense_Mutation	SNP	ENST00000505035.1	37																																																																																				T|0.980;C|0.020	0.020	strong		0.652	C16orf82-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000366634.1	NM_001145545	
OBSCN	84033	hgsc.bcm.edu	37	1	228476414	228476414	+	Silent	SNP	G	G	A	rs3795791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228476414G>A	ENST00000422127.1	+	38	10208	c.10164G>A	c.(10162-10164)gcG>gcA	p.A3388A	OBSCN_ENST00000359599.6_Silent_p.A2235A|OBSCN_ENST00000284548.11_Silent_p.A3388A|OBSCN_ENST00000570156.2_Silent_p.A3817A|OBSCN_ENST00000366709.4_Silent_p.A507A|OBSCN_ENST00000366707.4_Silent_p.A507A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3388	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)				TGAGCAAGGCGGCCCCCGTGG	0.627													G|||	470	0.0938498	0.0439	0.013	5008	,	,		20753	0.3175		0.0258	False		,,,				2504	0.0583				p.A3817A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G11451A						PASS	.	G	,	193,3981		5,183,1899	88.0	97.0	94.0		10164,10164	-4.2	0.0	1	dbSNP_107	94	156,8232		0,156,4038	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	5,339,5937	AA,AG,GG		1.8598,4.6239,2.7782	,	3388/7969,3388/6621	228476414	349,12213	2087	4194	6281	SO:0001819	synonymous_variant	84033	exon43			CAAGGCGGCCCCC	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.10164G>A	1.37:g.228476414G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	186	85	0.456989	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																																																																																			G|0.910;A|0.090	0.090	strong		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
NID2	22795	hgsc.bcm.edu	37	14	52493996	52493996	+	Missense_Mutation	SNP	C	C	T	rs28507587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:52493996C>T	ENST00000216286.5	-	12	2596	c.2597G>A	c.(2596-2598)cGg>cAg	p.R866Q	NID2_ENST00000541773.1_Intron	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	866	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.		R -> Q (in dbSNP:rs28507587).		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)					GTGAACACACCGGGCCTGCCC	0.587													c|||	116	0.0231629	0.0847	0.0058	5008	,	,		19977	0.0		0.0	False		,,,				2504	0.0				p.R866Q		Atlas-SNP	.											NID2,NS,carcinoma,-1,1	NID2	201	1	0			c.G2597A						PASS	.	C	GLN/ARG	293,4113	160.3+/-192.7	12,269,1922	41.0	37.0	38.0		2597	-0.7	1.0	14	dbSNP_125	38	5,8595	3.0+/-9.4	0,5,4295	yes	missense	NID2	NM_007361.3	43	12,274,6217	TT,TC,CC		0.0581,6.65,2.2913	possibly-damaging	866/1376	52493996	298,12708	2203	4300	6503	SO:0001583	missense	22795	exon12			ACACACCGGGCCT	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.2597G>A	14.37:g.52493996C>T	ENSP00000216286:p.Arg866Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	38	0.0173992673992674	35	0.07113821138211382	3	0.008287292817679558	0	0.0	0	0.0	C	9.202	1.028739	0.19512	0.0665	5.81E-4	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000395707	T	0.71934	-0.61	5.98	-0.687	0.11320	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.509728	0.21782	N	0.069185	T	0.05181	0.0138	L	0.33339	1.005	0.53688	D	0.999977	B;P;B	0.45044	0.012;0.849;0.04	B;B;B	0.26094	0.011;0.066;0.025	T	0.28138	-1.0053	10	0.10902	T	0.67	.	12.2116	0.54383	0.0:0.5941:0.0:0.4059	rs28507587;rs28507587	460;868;866	E7EPP3;Q5CZI2;Q14112	.;.;NID2_HUMAN	Q	866;460;868	ENSP00000216286:R866Q	ENSP00000216286:R866Q	R	-	2	0	NID2	51563746	0.000000	0.05858	0.956000	0.39512	0.155000	0.21991	-1.056000	0.03489	-0.047000	0.13423	-0.222000	0.12452	CGG	C|0.979;T|0.021	0.021	strong		0.587	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
GNA12	2768	hgsc.bcm.edu	37	7	2834577	2834577	+	Silent	SNP	T	T	C	rs2230878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2834577T>C	ENST00000275364.3	-	2	672	c.510A>G	c.(508-510)agA>agG	p.R170R	GNA12_ENST00000544127.1_Silent_p.R94R|GNA12_ENST00000407904.3_Silent_p.R111R	NM_007353.2	NP_031379.2	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein) alpha 12	170					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic digit morphogenesis (GO:0042733)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|platelet activation (GO:0030168)|regulation of cell shape (GO:0008360)|regulation of fibroblast migration (GO:0010762)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)|response to drug (GO:0042493)|Rho protein signal transduction (GO:0007266)	brush border membrane (GO:0031526)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		GAAACTCGCTTCTCCGGCTGA	0.547													C|||	99	0.0197684	0.0514	0.0101	5008	,	,		18315	0.0		0.0159	False		,,,				2504	0.0082				p.R170R		Atlas-SNP	.											.	GNA12	35	.	0			c.A510G						PASS	.	C		208,4198	807.3+/-415.9	7,194,2002	66.0	64.0	65.0		510	2.7	1.0	7	dbSNP_123	65	77,8523	815.8+/-406.9	1,75,4224	yes	coding-synonymous	GNA12	NM_007353.2		8,269,6226	CC,CT,TT		0.8953,4.7208,2.1913		170/382	2834577	285,12721	2203	4300	6503	SO:0001819	synonymous_variant	2768	exon2			CTCGCTTCTCCGG	L01694	CCDS5335.1, CCDS64584.1, CCDS64583.1	7p22.3	2006-07-08			ENSG00000146535	ENSG00000146535			4380	protein-coding gene	gene with protein product		604394				8423800, 16247467	Standard	NM_007353		Approved	gep	uc003smu.3	Q03113	OTTHUMG00000023064	ENST00000275364.3:c.510A>G	7.37:g.2834577T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_007353	A4D204|B3KXS2|B7Z3F7|Q2T9L1|Q5PPR5|Q86UM8|Q8TD71|Q9UDU9	Silent	SNP	ENST00000275364.3	37	CCDS5335.1																																																																																			T|0.980;C|0.020	0.020	strong		0.547	GNA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241608.1	NM_007353	
PROSER1	80209	hgsc.bcm.edu	37	13	39586343	39586343	+	Silent	SNP	G	G	C	rs9576697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39586343G>C	ENST00000352251.3	-	12	3422	c.2589C>G	c.(2587-2589)ggC>ggG	p.G863G	PROSER1_ENST00000350125.3_Silent_p.G841G|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	863																	AAACAGAACTGCCTGCAGCTT	0.413													G|||	1124	0.224441	0.2511	0.1599	5008	,	,		17836	0.2183		0.162	False		,,,				2504	0.3047				p.G863G		Atlas-SNP	.											.	.	.	.	0			c.C2589G						PASS	.	G	,	1093,3313	391.0+/-327.9	117,859,1227	130.0	147.0	141.0		2589,2523	2.7	1.0	13	dbSNP_119	141	1209,7391	242.9+/-272.7	92,1025,3183	no	coding-synonymous,coding-synonymous	PROSER1	NM_025138.3,NM_170719.2	,	209,1884,4410	CC,CG,GG		14.0581,24.8071,17.6995	,	863/945,841/923	39586343	2302,10704	2203	4300	6503	SO:0001819	synonymous_variant	80209	exon12			AGAACTGCCTGCA	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.2589C>G	13.37:g.39586343G>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	170	83	0.488235	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																			G|0.818;C|0.182	0.182	strong		0.413	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412542	105412542	+	Silent	SNP	A	A	G	rs386781092|rs12433815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105412542A>G	ENST00000333244.5	-	7	9365	c.9246T>C	c.(9244-9246)gaT>gaC	p.D3082D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3082						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)			GGCCCTTGACATCTATCTGGG	0.627													.|||	2592	0.517572	0.584	0.4669	5008	,	,		14237	0.3978		0.4861	False		,,,				2504	0.6196				p.D3082D		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T9246C						PASS	.	A		1158,2452		482,194,1129	65.0	75.0	72.0		9246	-2.2	0.0	14	dbSNP_120	72	1886,6184		794,298,2943	no	coding-synonymous	AHNAK2	NM_138420.2		1276,492,4072	GG,GA,AA		23.3705,32.0776,26.0616		3082/5796	105412542	3044,8636	1805	4035	5840	SO:0001819	synonymous_variant	113146	exon7			CTTGACATCTATC	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.9246T>C	14.37:g.105412542A>G		Somatic	262	2	0.00763359		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.668;G|0.332	0.332	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
HK2	3099	hgsc.bcm.edu	37	2	75116527	75116527	+	Missense_Mutation	SNP	G	G	A	rs2229629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:75116527G>A	ENST00000290573.2	+	17	3131	c.2531G>A	c.(2530-2532)aGg>aAg	p.R844K	HK2_ENST00000409174.1_Missense_Mutation_p.R816K	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	844	Catalytic.|Hexokinase type-2 2.		R -> K (in dbSNP:rs2229629). {ECO:0000269|PubMed:7883123, 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						GTGGTGGACAGGATACGAGAA	0.607													A|||	1045	0.208666	0.6346	0.0447	5008	,	,		17870	0.1131		0.0139	False		,,,				2504	0.0481				p.R844K		Atlas-SNP	.											.	HK2	85	.	0			c.G2531A	GRCh37	CM950635	HK2	M	rs2229629	PASS	.	A	LYS/ARG	2314,2092	570.9+/-383.0	597,1120,486	97.0	87.0	91.0		2531	5.0	1.0	2	dbSNP_98	91	106,8494	814.3+/-407.0	0,106,4194	no	missense	HK2	NM_000189.4	26	597,1226,4680	AA,AG,GG		1.2326,47.4807,18.6068	benign	844/918	75116527	2420,10586	2203	4300	6503	SO:0001583	missense	3099	exon17			TGGACAGGATACG		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.2531G>A	2.37:g.75116527G>A	ENSP00000290573:p.Arg844Lys	Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	205	205	1	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	37	CCDS1956.1	413	0.1891025641025641	306	0.6219512195121951	19	0.052486187845303865	79	0.1381118881118881	9	0.011873350923482849	A	9.674	1.147434	0.21288	0.525193	0.012326	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.95853	-3.83;-3.83	4.97	4.97	0.65823	Hexokinase, C-terminal (1);	0.094115	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00403	-1.54	0.48696	P	3.069999999999462E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.42292	-0.9460	9	0.02654	T	1	-8.0119	8.985	0.35988	0.9122:0.0:0.0878:0.0	rs2229629;rs2279426;rs17847150;rs57447301	844	P52789	HXK2_HUMAN	K	844;844;816	ENSP00000290573:R844K;ENSP00000387140:R816K	ENSP00000290573:R844K	R	+	2	0	HK2	74970035	1.000000	0.71417	0.997000	0.53966	0.957000	0.61999	7.291000	0.78721	0.933000	0.37291	-0.361000	0.07541	AGG	G|0.805;A|0.195	0.195	strong		0.607	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
SELP	6403	hgsc.bcm.edu	37	1	169566326	169566326	+	Silent	SNP	G	G	A	rs6135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169566326G>A	ENST00000263686.6	-	11	1831	c.1794C>T	c.(1792-1794)tgC>tgT	p.C598C	SELP_ENST00000367788.2_Silent_p.C536C|SELP_ENST00000367786.2_Silent_p.C536C|SELP_ENST00000367794.2_Silent_p.C536C|SELP_ENST00000367792.2_Intron|SELP_ENST00000367791.2_Intron|SELP_ENST00000458599.2_Intron|SELP_ENST00000367793.2_Silent_p.C536C	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	204	0	0		WXS	Illumina HiSeq	Phase_I	187	81	0.433155	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	
ATP2A1	487	hgsc.bcm.edu	37	16	28898793	28898793	+	Silent	SNP	T	T	C	rs6565259	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:28898793T>C	ENST00000357084.3	+	8	945	c.678T>C	c.(676-678)acT>acC	p.T226T	ATP2A1_ENST00000536376.1_Silent_p.T101T|ATP2A1_ENST00000395503.4_Silent_p.T226T	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	226					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						TGGCCACCACTGGTGTGGGCA	0.602													t|||	1697	0.338858	0.5189	0.4942	5008	,	,		18719	0.1617		0.3131	False		,,,				2504	0.1943				p.T226T		Atlas-SNP	.											.	ATP2A1	116	.	0			c.T678C						PASS	.	C	,	2225,2169	590.6+/-387.4	538,1149,510	97.0	93.0	94.0		678,678	-11.0	0.0	16	dbSNP_116	94	3020,5580	464.7+/-366.3	540,1940,1820	no	coding-synonymous,coding-synonymous	ATP2A1	NM_004320.4,NM_173201.3	,	1078,3089,2330	CC,CT,TT		35.1163,49.3628,40.3648	,	226/995,226/1002	28898793	5245,7749	2197	4300	6497	SO:0001819	synonymous_variant	487	exon8			CACCACTGGTGTG		CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.678T>C	16.37:g.28898793T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																			T|0.631;C|0.369	0.369	strong		0.602	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
FBXW9	84261	hgsc.bcm.edu	37	19	12800597	12800597	+	Missense_Mutation	SNP	T	T	C	rs73921601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12800597T>C	ENST00000380339.3	-	7	1250	c.1214A>G	c.(1213-1215)aAc>aGc	p.N405S	CTD-2659N19.2_ENST00000585742.1_RNA|CTD-2192J16.26_ENST00000593554.1_lincRNA|FBXW9_ENST00000587955.1_Missense_Mutation_p.N395S|FBXW9_ENST00000393261.3_Missense_Mutation_p.N375S|FBXW9_ENST00000544494.1_Missense_Mutation_p.N113S			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	405					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						GAAGCAGCCGTTGCGGTTGGC	0.652													T|||	245	0.0489217	0.1679	0.0187	5008	,	,		17279	0.0		0.0099	False		,,,				2504	0.0				p.N375S		Atlas-SNP	.											FBXW9_ENST00000393261,caecum,carcinoma,+1,3	FBXW9	30	3	0			c.A1124G						PASS	.	T	SER/ASN	686,3720	270.4+/-269.6	52,582,1569	60.0	63.0	62.0		1124	-0.8	0.0	19	dbSNP_130	62	125,8475	61.3+/-123.2	0,125,4175	yes	missense	FBXW9	NM_032301.2	46	52,707,5744	CC,CT,TT		1.4535,15.5697,6.2356	benign	375/459	12800597	811,12195	2203	4300	6503	SO:0001583	missense	84261	exon7			CAGCCGTTGCGGT	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.1214A>G	19.37:g.12800597T>C	ENSP00000369696:p.Asn405Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	29	0.345238	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		87	0.03983516483516483	73	0.1483739837398374	7	0.019337016574585635	0	0.0	7	0.009234828496042216	T	4.791	0.147100	0.09134	0.155697	0.014535	ENSG00000132004	ENST00000544494;ENST00000393261;ENST00000380339	T;T;T	0.75154	-0.91;-0.91;-0.91	4.32	-0.772	0.10998	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	2.425580	0.01961	N	0.043380	T	0.00384	0.0012	L	0.27053	0.805	0.80722	P	0.0	B;B;B	0.11235	0.001;0.004;0.001	B;B;B	0.12156	0.003;0.007;0.001	T	0.02326	-1.1176	9	0.21540	T	0.41	2.9217	4.636	0.12525	0.0:0.4404:0.1963:0.3633	.	395;405;375	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	S	113;375;405	ENSP00000442714:N113S;ENSP00000376945:N375S;ENSP00000369696:N405S	ENSP00000369696:N405S	N	-	2	0	FBXW9	12661597	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	-0.137000	0.10389	0.154000	0.19237	0.397000	0.26171	AAC	T|0.944;C|0.056	0.056	strong		0.652	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
CDKAL1	54901	hgsc.bcm.edu	37	6	21201493	21201493	+	Silent	SNP	G	G	A	rs9465994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:21201493G>A	ENST00000378610.1	+	13	1546	c.1536G>A	c.(1534-1536)tcG>tcA	p.S512S	CDKAL1_ENST00000378624.4_Silent_p.S421S|CDKAL1_ENST00000476517.1_3'UTR|CDKAL1_ENST00000274695.4_Silent_p.S512S			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	512					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			GAGAAGTCTCGGGTTTGACAA	0.458													A|||	2662	0.53155	0.8139	0.5937	5008	,	,		18594	0.4018		0.4503	False		,,,				2504	0.3231				p.S512S		Atlas-SNP	.											CDKAL1,NS,carcinoma,+1,1	CDKAL1	55	1	0			c.G1536A						PASS	.	A		3311,1095	395.8+/-329.8	1254,803,146	107.0	88.0	94.0		1536	-12.3	0.0	6	dbSNP_119	94	3915,4685	605.4+/-395.0	895,2125,1280	no	coding-synonymous	CDKAL1	NM_017774.3		2149,2928,1426	AA,AG,GG		45.5233,24.8525,44.441		512/580	21201493	7226,5780	2203	4300	6503	SO:0001819	synonymous_variant	54901	exon15			AGTCTCGGGTTTG	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.1536G>A	6.37:g.21201493G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Silent	SNP	ENST00000378610.1	37	CCDS4546.1																																																																																			G|0.451;A|0.549	0.549	strong		0.458	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774	
UBR4	23352	hgsc.bcm.edu	37	1	19451090	19451090	+	Missense_Mutation	SNP	T	T	C	rs183578825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19451090T>C	ENST00000375254.3	-	65	9560	c.9533A>G	c.(9532-9534)aAt>aGt	p.N3178S	UBR4_ENST00000375226.2_Missense_Mutation_p.N3154S|UBR4_ENST00000375267.2_Missense_Mutation_p.N3178S|UBR4_ENST00000375217.2_Missense_Mutation_p.N3171S	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3178					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)			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)		GATTCGAGAATTGGTGTCAGT	0.468													T|||	3	0.000599042	0.0023	0.0	5008	,	,		19837	0.0		0.0	False		,,,				2504	0.0				p.N3178S		Atlas-SNP	.											UBR4,NS,carcinoma,0,1	UBR4	415	1	0			c.A9533G						PASS	.						201.0	183.0	189.0					1																	19451090		2203	4300	6503	SO:0001583	missense	23352	exon65			CGAGAATTGGTGT	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.9533A>G	1.37:g.19451090T>C	ENSP00000364403:p.Asn3178Ser	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	167	79	0.473054	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	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	13.60	2.286447	0.40494	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000425413;ENST00000417040	T;T;T;T	0.21543	2.0;2.0;2.01;2.01	6.07	3.29	0.37713	.	0.196102	0.52532	N	0.000075	T	0.07999	0.0200	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24693	-1.0153	10	0.16896	T	0.51	.	7.8597	0.29504	0.0:0.303:0.0:0.697	.	3178	Q5T4S7	UBR4_HUMAN	S	3178;3178;3171;3154;786;1864	ENSP00000364403:N3178S;ENSP00000364416:N3178S;ENSP00000364365:N3171S;ENSP00000364374:N3154S	ENSP00000364365:N3171S	N	-	2	0	UBR4	19323677	1.000000	0.71417	0.990000	0.47175	0.842000	0.47809	3.890000	0.56220	0.348000	0.23949	0.533000	0.62120	AAT	T|0.999;C|0.001	0.001	strong		0.468	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
ZDHHC19	131540	hgsc.bcm.edu	37	3	195935346	195935346	+	Missense_Mutation	SNP	C	C	T	rs75505676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195935346C>T	ENST00000296326.3	-	4	573	c.494G>A	c.(493-495)tGc>tAc	p.C165Y	ZDHHC19_ENST00000488508.1_5'UTR	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	165						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)		CGAGTAGAGGCACAGGGACAG	0.602													C|||	15	0.00299521	0.0098	0.0029	5008	,	,		16054	0.0		0.0	False		,,,				2504	0.0				p.C165Y		Atlas-SNP	.											.	ZDHHC19	25	.	0			c.G494A						PASS	.	C	TYR/CYS	41,4341		0,41,2150	117.0	137.0	130.0		494	4.7	1.0	3	dbSNP_131	130	0,8560		0,0,4280	yes	missense	ZDHHC19	NM_001039617.1	194	0,41,6430	TT,TC,CC		0.0,0.9356,0.3168	probably-damaging	165/310	195935346	41,12901	2191	4280	6471	SO:0001583	missense	131540	exon4			TAGAGGCACAGGG	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.494G>A	3.37:g.195935346C>T	ENSP00000296326:p.Cys165Tyr	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	244	116	0.47541	NM_001039617	A8MSY6|B3KVI1	Missense_Mutation	SNP	ENST00000296326.3	37	CCDS43190.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	19.39	3.817947	0.71028	0.009356	0.0	ENSG00000163958	ENST00000296326	T	0.24350	1.86	5.61	4.72	0.59763	Zinc finger, DHHC-type, palmitoyltransferase (1);	0.000000	0.64402	D	0.000008	T	0.44912	0.1316	M	0.93328	3.405	0.36364	D	0.860879	P	0.52463	0.953	P	0.54544	0.755	T	0.69262	-0.5191	10	0.66056	D	0.02	-33.5711	11.8273	0.52275	0.1753:0.8247:0.0:0.0	.	165	Q8WVZ1	ZDH19_HUMAN	Y	165	ENSP00000296326:C165Y	ENSP00000296326:C165Y	C	-	2	0	ZDHHC19	197419743	0.937000	0.31787	0.983000	0.44433	0.650000	0.38633	0.889000	0.28282	1.342000	0.45619	0.561000	0.74099	TGC	C|0.996;T|0.004	0.004	strong		0.602	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341533.1	NM_144637	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713099	32713099	+	Silent	SNP	G	G	A	rs9469266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32713099G>A	ENST00000374940.3	+	2	348	c.246G>A	c.(244-246)ccG>ccA	p.P82P		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	82	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)|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)"""	GTTTTGACCCGCAGAGTGCAC	0.468													G|||	371	0.0740815	0.2337	0.0548	5008	,	,		21011	0.0		0.0159	False		,,,				2504	0.0082				p.P82P		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.G246A						PASS	.	G		635,2387		65,505,941	128.0	124.0	126.0		246	-4.1	1.0	6	dbSNP_119	126	71,5347		1,69,2639	no	coding-synonymous	HLA-DQA2	NM_020056.4		66,574,3580	AA,AG,GG		1.3104,21.0126,8.3649		82/256	32713099	706,7734	1511	2709	4220	SO:0001819	synonymous_variant	3118	exon2			TGACCCGCAGAGT		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.246G>A	6.37:g.32713099G>A		Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	37	CCDS4753.1																																																																																			G|0.926;A|0.074	0.074	strong		0.468	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
MUC6	4588	hgsc.bcm.edu	37	11	1016849	1016849	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1016849C>G	ENST00000421673.2	-	31	6002	c.5952G>C	c.(5950-5952)atG>atC	p.M1984I		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1984	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.M1984I(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ATGTTGCAGTCATAGGACCTG	0.582																																					p.M1984I		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	2	Substitution - Missense(2)	lung(2)	c.G5952C						scavenged	.						1544.0	1533.0	1537.0					11																	1016849		2203	4298	6501	SO:0001583	missense	4588	exon31			TGCAGTCATAGGA	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.5952G>C	11.37:g.1016849C>G	ENSP00000406861:p.Met1984Ile	Somatic	1941	41	0.0211231		WXS	Illumina HiSeq	Phase_I	2201	89	0.0404362	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	c	0.326	-0.959077	0.02267	.	.	ENSG00000184956	ENST00000421673	T	0.17691	2.26	2.64	-5.29	0.02747	.	.	.	.	.	T	0.09598	0.0236	L	0.43152	1.355	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.27839	-1.0062	9	0.14656	T	0.56	.	1.5757	0.02624	0.1743:0.1847:0.3717:0.2692	.	1984	Q6W4X9	MUC6_HUMAN	I	1984	ENSP00000406861:M1984I	ENSP00000406861:M1984I	M	-	3	0	MUC6	1006849	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.496000	0.02291	-4.003000	0.00082	-2.547000	0.00178	ATG	.	.	none		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
BRWD1	54014	hgsc.bcm.edu	37	21	40590176	40590176	+	Silent	SNP	G	G	T	rs76171323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:40590176G>T	ENST00000333229.2	-	31	3888	c.3561C>A	c.(3559-3561)ggC>ggA	p.G1187G	BRWD1_ENST00000342449.3_Silent_p.G1187G|BRWD1_ENST00000380800.3_Silent_p.G1187G|BRWD1-IT1_ENST00000435608.1_RNA	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1187	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				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)				AATCAACAGGGCCTGCAAAAG	0.378													G|||	75	0.014976	0.0545	0.0014	5008	,	,		15406	0.0		0.002	False		,,,				2504	0.0				p.G1187G	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											BRWD1_ENST00000333229,NS,lymphoid_neoplasm,0,2	BRWD1	325	2	0			c.C3561A						PASS	.	G	,	182,4224	118.8+/-156.5	1,180,2022	108.0	107.0	107.0		3561,3561	-0.7	1.0	21	dbSNP_131	107	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	1,181,6321	TT,TG,GG		0.0116,4.1307,1.407	,	1187/2321,1187/2270	40590176	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon31			AACAGGGCCTGCA	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.3561C>A	21.37:g.40590176G>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	66	0.589286	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1	40	0.018315018315018316	40	0.08130081300813008	0	0.0	0	0.0	0	0.0	G	9.823	1.186196	0.21870	0.041307	1.16E-4	ENSG00000185658	ENST00000424441	.	.	.	5.56	-0.669	0.11388	.	.	.	.	.	T	0.04861	0.0131	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.04115	-1.0976	4	.	.	.	-8.3462	7.2761	0.26286	0.5235:0.1169:0.3596:0.0	.	.	.	.	T	173	.	.	P	-	1	0	BRWD1	39512046	0.888000	0.30383	0.993000	0.49108	0.904000	0.53231	0.108000	0.15396	-0.032000	0.13758	0.462000	0.41574	CCC	G|0.984;T|0.016	0.016	strong		0.378	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
WDR4	10785	hgsc.bcm.edu	37	21	44273691	44273691	+	Silent	SNP	G	G	A	rs146863277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44273691G>A	ENST00000398208.2	-	9	1022	c.963C>T	c.(961-963)ggC>ggT	p.G321G	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Silent_p.G321G	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)		GCCACTGGTCGCCCACAGGCC	0.622													G|||	23	0.00459265	0.0151	0.0029	5008	,	,		15951	0.0		0.001	False		,,,				2504	0.0				p.G321G		Atlas-SNP	.											.	WDR4	35	.	0			c.C963T						PASS	.	G	,	65,4339	56.2+/-92.4	1,63,2138	26.0	26.0	26.0		963,963	-6.0	0.0	21	dbSNP_134	26	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	WDR4	NM_018669.4,NM_033661.3	,	1,66,6435	AA,AG,GG		0.0349,1.4759,0.5229	,	321/413,321/413	44273691	68,12936	2202	4300	6502	SO:0001819	synonymous_variant	10785	exon9			CTGGTCGCCCACA	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.963C>T	21.37:g.44273691G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	43	0.623188	NM_018669		Silent	SNP	ENST00000398208.2	37	CCDS13691.1																																																																																			G|0.995;A|0.005	0.005	strong		0.622	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
LRP3	4037	hgsc.bcm.edu	37	19	33696897	33696897	+	Silent	SNP	C	C	T	rs11084712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	62	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	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		
ZNF780A	284323	hgsc.bcm.edu	37	19	40580426	40580426	+	Silent	SNP	A	A	G	rs399405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40580426A>G	ENST00000595687.2	-	6	2132	c.1923T>C	c.(1921-1923)tcT>tcC	p.S641S	ZNF780A_ENST00000340963.5_Silent_p.S641S|ZNF780A_ENST00000594395.1_Silent_p.S642S|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000455521.1_Silent_p.S642S|ZNF780A_ENST00000450241.2_Silent_p.S607S|ZNF780A_ENST00000414720.2_Intron	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	641					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(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTTACATTCAAGATGCCTTCT	0.418													a|||	547	0.109225	0.3449	0.0403	5008	,	,		22537	0.0069		0.0109	False		,,,				2504	0.046				p.S642S		Atlas-SNP	.											.	ZNF780A	156	.	0			c.T1926C						PASS	.	A	,,,	1370,3036	454.7+/-350.8	220,930,1053	153.0	148.0	150.0		1923,1926,1923,	-2.3	0.0	19	dbSNP_80	150	68,8532	41.7+/-99.0	1,66,4233	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	221,996,5286	GG,GA,AA		0.7907,31.094,11.0564	,,,	641/642,642/643,641/642,	40580426	1438,11568	2203	4300	6503	SO:0001819	synonymous_variant	284323	exon6			CATTCAAGATGCC	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"""Zinc fingers, C2H2-type"", ""-"""	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.1923T>C	19.37:g.40580426A>G		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	268	268	1	NM_001142577	E9PB48|Q6ZN87	Silent	SNP	ENST00000595687.2	37	CCDS33026.2																																																																																			A|0.899;G|0.101	0.101	strong		0.418	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144871829	144871829	+	Silent	SNP	C	C	T	rs111761861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144871829C>T	ENST00000369354.3	-	32	5322	c.5133G>A	c.(5131-5133)ttG>ttA	p.L1711L	PDE4DIP_ENST00000530740.1_Silent_p.L1796L|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369359.4_Silent_p.L1847L|PDE4DIP_ENST00000369356.4_Silent_p.L1711L|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1711					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)		GAGCTGAGGGCAATGGTGCCT	0.527			T	PDGFRB	MPD								.|||	214	0.0427316	0.0605	0.0144	5008	,	,		40094	0.0734		0.0179	False		,,,				2504	0.0327				p.L1711L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G5133A						PASS	.	C	,,	199,4207	112.5+/-150.6	0,199,2004	99.0	103.0	101.0		,5133,5133	4.2	1.0	1	dbSNP_132	101	137,8455	63.9+/-126.0	0,137,4159	no	intron,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,336,6163	TT,TC,CC		1.5945,4.5166,2.585	,,	,1711/2363,1711/2347	144871829	336,12662	2203	4296	6499	SO:0001819	synonymous_variant	9659	exon32			TGAGGGCAATGGT	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.5133G>A	1.37:g.144871829C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	135	26	0.192593	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1																																																																																			C|0.969;T|0.031	0.031	strong		0.527	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
SLC35C1	55343	hgsc.bcm.edu	37	11	45832509	45832509	+	Missense_Mutation	SNP	A	A	G	rs7130656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:45832509A>G	ENST00000314134.3	+	2	2114	c.718A>G	c.(718-720)Atc>Gtc	p.I240V	SLC35C1_ENST00000442528.2_Missense_Mutation_p.I227V|SLC35C1_ENST00000456334.1_Missense_Mutation_p.I227V|CTD-2210P24.6_ENST00000534128.1_lincRNA	NM_018389.4	NP_060859.4	Q96A29	FUCT1_HUMAN	solute carrier family 35 (GDP-fucose transporter), member C1	240			I -> V (in dbSNP:rs7130656).		carbohydrate transport (GO:0008643)|lipid glycosylation (GO:0030259)|negative regulation of Notch signaling pathway (GO:0045746)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10				GBM - Glioblastoma multiforme(35;0.227)		CAACGCCTGCATCCTCTTCCT	0.632													G|||	515	0.102835	0.2337	0.0677	5008	,	,		19582	0.001		0.1382	False		,,,				2504	0.0194				p.I240V		Atlas-SNP	.											SLC35C1,NS,carcinoma,0,2	SLC35C1	23	2	0			c.A718G						PASS	.	G	VAL/ILE,VAL/ILE,VAL/ILE	906,3500	738.9+/-411.0	86,734,1383	57.0	54.0	55.0		679,679,718	1.1	1.0	11	dbSNP_116	55	959,7639	774.1+/-407.7	68,823,3408	yes	missense,missense,missense	SLC35C1	NM_001145265.1,NM_001145266.1,NM_018389.4	29,29,29	154,1557,4791	GG,GA,AA		11.1538,20.5629,14.3417	benign,benign,benign	227/352,227/352,240/365	45832509	1865,11139	2203	4299	6502	SO:0001583	missense	55343	exon2			GCCTGCATCCTCT		CCDS7914.1, CCDS44575.1	11p11.2	2014-09-17	2013-07-17			ENSG00000181830		"""Solute carriers"""	20197	protein-coding gene	gene with protein product		605881	"""solute carrier family 35, member C1"""			11326279, 11326280	Standard	NM_018389		Approved	FUCT1, FLJ11320	uc010rgm.2	Q96A29		ENST00000314134.3:c.718A>G	11.37:g.45832509A>G	ENSP00000313318:p.Ile240Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_018389	B2RDB2|Q9BV76|Q9NUJ8	Missense_Mutation	SNP	ENST00000314134.3	37	CCDS7914.1	259	0.11858974358974358	119	0.241869918699187	34	0.09392265193370165	0	0.0	106	0.13984168865435356	G	2.482	-0.319429	0.05386	0.205629	0.111538	ENSG00000181830	ENST00000442528;ENST00000456334;ENST00000530670;ENST00000314134;ENST00000540685	T;T;T	0.65916	-0.18;-0.18;-0.18	6.17	1.14	0.20703	Domain of unknown function DUF250 (1);	0.522394	0.21103	N	0.080121	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.13415	-1.0510	9	0.07175	T	0.84	-22.5421	5.0846	0.14675	0.2866:0.0:0.5:0.2134	rs7130656;rs17725077;rs57668458;rs7130656	240	Q96A29	FUCT1_HUMAN	V	227;227;161;240;240	ENSP00000412408:I227V;ENSP00000399779:I227V;ENSP00000313318:I240V	ENSP00000313318:I240V	I	+	1	0	SLC35C1	45789085	0.391000	0.25221	0.969000	0.41365	0.663000	0.39108	0.551000	0.23361	0.186000	0.20125	-1.617000	0.00794	ATC	A|0.866;G|0.134	0.134	strong		0.632	SLC35C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390139.1	NM_018389	
TRIP11	9321	hgsc.bcm.edu	37	14	92441066	92441066	+	Missense_Mutation	SNP	C	C	T	rs1051340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:92441066C>T	ENST00000267622.4	-	19	5852	c.5479G>A	c.(5479-5481)Ggt>Agt	p.G1827S		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1827			G -> S (in dbSNP:rs1051340). {ECO:0000269|PubMed:10189370, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7776974, ECO:0000269|PubMed:9373237}.		protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		CTGGTAACACCGCCCTGATCG	0.368			T	PDGFRB	AML								C|||	1359	0.271366	0.2095	0.1643	5008	,	,		15466	0.3065		0.3131	False		,,,				2504	0.3517				p.G1827S	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.G5479A						PASS	.	C	SER/GLY	983,3423	368.6+/-318.7	100,783,1320	67.0	60.0	63.0		5479	3.9	0.6	14	dbSNP_86	63	2832,5768	445.8+/-361.1	497,1838,1965	yes	missense	TRIP11	NM_004239.3	56	597,2621,3285	TT,TC,CC		32.9302,22.3105,29.3326	probably-damaging	1827/1980	92441066	3815,9191	2203	4300	6503	SO:0001583	missense	9321	exon19			TAACACCGCCCTG	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.5479G>A	14.37:g.92441066C>T	ENSP00000267622:p.Gly1827Ser	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	187	97	0.518717	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	600|600	0.27472527472527475|0.27472527472527475	98|98	0.1991869918699187|0.1991869918699187	63|63	0.17403314917127072|0.17403314917127072	193|193	0.3374125874125874|0.3374125874125874	246|246	0.3245382585751979|0.3245382585751979	C|C	17.62|17.62	3.433947|3.433947	0.62955|0.62955	0.223105|0.223105	0.329302|0.329302	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.04970|.	3.52|.	5.71|5.71	3.9|3.9	0.45041|0.45041	.|.	0.050236|.	0.85682|.	D|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.27053|0.27053	0.805|0.805	0.21915|0.21915	P|P	0.999473102|0.999473102	D;P|.	0.55800|.	0.973;0.903|.	B;B|.	0.41236|.	0.322;0.351|.	T|T	0.36939|0.36939	-0.9727|-0.9727	9|4	0.56958|.	D|.	0.05|.	.|.	12.3669|12.3669	0.55234|0.55234	0.0:0.8639:0.0:0.1361|0.0:0.8639:0.0:0.1361	rs1051340;rs3191717;rs8014538;rs11554399;rs17806291;rs61645330;rs1051340|rs1051340;rs3191717;rs8014538;rs11554399;rs17806291;rs61645330;rs1051340	1563;1827|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	S|Q	1827;1563|1542	ENSP00000267622:G1827S|.	ENSP00000267622:G1827S|.	G|R	-|-	1|2	0|0	TRIP11|TRIP11	91510819|91510819	0.962000|0.962000	0.33011|0.33011	0.632000|0.632000	0.29296|0.29296	0.597000|0.597000	0.36814|0.36814	2.209000|2.209000	0.42806|0.42806	0.770000|0.770000	0.33336|0.33336	-0.136000|-0.136000	0.14681|0.14681	GGT|CGG	C|0.709;T|0.291	0.291	strong		0.368	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249152	71249152	+	Silent	SNP	C	C	T	rs112809261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	284	0	0		WXS	Illumina HiSeq	Phase_I	226	88	0.389381	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	
FLG	2312	hgsc.bcm.edu	37	1	152285188	152285188	+	Missense_Mutation	SNP	G	G	A	rs3120655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152285188G>A	ENST00000368799.1	-	3	2209	c.2174C>T	c.(2173-2175)aCt>aTt	p.T725I	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	725	Ser-rich.		T -> I (in dbSNP:rs3120655).		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)			TCCGTGCCCAGTGCCTGAGTG	0.567									Ichthyosis				-|||	562	0.11222	0.407	0.0331	5008	,	,		21307	0.0		0.001	False		,,,				2504	0.0				p.T725I		Atlas-SNP	.											.	FLG	900	.	0			c.C2174T						PASS	.	G	ILE/THR	1483,2923		249,985,969	379.0	400.0	393.0		2174	3.0	0.0	1	dbSNP_103	393	19,8581		0,19,4281	no	missense	FLG	NM_002016.1	89	249,1004,5250	AA,AG,GG		0.2209,33.6586,11.5485	possibly-damaging	725/4062	152285188	1502,11504	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGCCCAGTGCCTG	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.2174C>T	1.37:g.152285188G>A	ENSP00000357789:p.Thr725Ile	Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	274	272	0.992701	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	165	0.07554945054945054	152	0.3089430894308943	12	0.03314917127071823	1	0.0017482517482517483	0	0.0	-	6.095	0.385885	0.11524	0.336586	0.002209	ENSG00000143631	ENST00000368799	T	0.03358	3.96	3.89	2.97	0.34412	.	.	.	.	.	T	0.00580	0.0019	N	0.03281	-0.365	0.80722	P	0.0	B	0.14805	0.011	B	0.17979	0.02	T	0.46317	-0.9200	8	0.16896	T	0.51	1.9131	8.0676	0.30669	0.1154:0.0:0.8846:0.0	.	725	P20930	FILA_HUMAN	I	725	ENSP00000357789:T725I	ENSP00000357789:T725I	T	-	2	0	FLG	150551812	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.408000	0.07169	0.832000	0.34804	-0.663000	0.03849	ACT	.	.	weak		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ATP13A4	84239	hgsc.bcm.edu	37	3	193210768	193210768	+	Silent	SNP	A	A	G	rs2130407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:193210768A>G	ENST00000342695.4	-	5	793	c.471T>C	c.(469-471)ctT>ctC	p.L157L	ATP13A4_ENST00000295548.3_Silent_p.L157L|ATP13A4_ENST00000392443.3_Silent_p.L157L	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	157						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		TGGCAGAACTAAGCCAGTCTT	0.318													G|||	2641	0.527356	0.6573	0.5029	5008	,	,		16069	0.5476		0.4036	False		,,,				2504	0.4755				p.L157L		Atlas-SNP	.											.	ATP13A4	154	.	0			c.T471C						PASS	.	G		2708,1698	511.9+/-367.9	814,1080,309	134.0	129.0	131.0		471	1.5	1.0	3	dbSNP_96	131	3530,5068	629.8+/-398.3	746,2038,1515	no	coding-synonymous	ATP13A4	NM_032279.2		1560,3118,1824	GG,GA,AA		41.0561,38.5384,47.9699		157/1197	193210768	6238,6766	2203	4299	6502	SO:0001819	synonymous_variant	84239	exon5			AGAACTAAGCCAG	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.471T>C	3.37:g.193210768A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	96	38	0.395833	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			A|0.508;G|0.492	0.492	strong		0.318	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
EFEMP1	2202	hgsc.bcm.edu	37	2	56145110	56145110	+	Silent	SNP	G	G	T	rs12292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:56145110G>T	ENST00000394555.2	-	4	642	c.207C>A	c.(205-207)ctC>ctA	p.L69L	EFEMP1_ENST00000355426.3_Silent_p.L69L|EFEMP1_ENST00000424836.2_Silent_p.L11L|EFEMP1_ENST00000394554.1_Silent_p.L69L	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	69	EGF-like 1; atypical. {ECO:0000255|PROSITE-ProRule:PRU00076}.				epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TCGGAAGGCAGAGGTATCCTC	0.458													G|||	193	0.0385383	0.1369	0.0159	5008	,	,		21544	0.0		0.001	False		,,,				2504	0.0				p.L69L	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.C207A						PASS	.	G	,	526,3880	239.6+/-250.7	28,470,1705	111.0	112.0	112.0		207,207	1.7	1.0	2	dbSNP_52	112	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	EFEMP1	NM_001039348.2,NM_001039349.2	,	28,473,6002	TT,TG,GG		0.0349,11.9383,4.0674	,	69/494,69/494	56145110	529,12477	2203	4300	6503	SO:0001819	synonymous_variant	2202	exon4			AAGGCAGAGGTAT	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"""Fibulins"""	3218	protein-coding gene	gene with protein product	"""fibulin 3"""	601548	"""fibrillin-like"", ""EGF-containing fibulin-like extracellular matrix protein 1"""	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.207C>A	2.37:g.56145110G>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	229	122	0.532751	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Silent	SNP	ENST00000394555.2	37	CCDS1857.1	58	0.026556776556776556	53	0.10772357723577236	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	9.474	1.096510	0.20552	0.119383	3.49E-4	ENSG00000115380	ENST00000405693	.	.	.	5.68	1.67	0.24075	.	.	.	.	.	T	0.00695	0.0023	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01600	-1.1315	5	0.27785	T	0.31	.	3.1782	0.06576	0.1297:0.1199:0.5058:0.2445	rs12292;rs12292	.	.	.	Y	5	.	ENSP00000384951:S5Y	S	-	2	0	EFEMP1	55998614	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.101000	0.31037	0.288000	0.22398	0.650000	0.86243	TCT	G|0.951;T|0.049	0.049	strong		0.458	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2		
APPBP2	10513	hgsc.bcm.edu	37	17	58603185	58603185	+	Silent	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:58603185G>C	ENST00000083182.3	-	1	395	c.108C>G	c.(106-108)ccC>ccG	p.P36P	RP11-15E18.1_ENST00000558027.1_RNA|RP11-15E18.1_ENST00000559739.1_RNA	NM_001282476.1|NM_006380.2	NP_001269405.1|NP_006371.2	Q92624	APBP2_HUMAN	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	36					intracellular protein transport (GO:0006886)|intracellular transport (GO:0046907)|metabolic process (GO:0008152)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	microtubule motor activity (GO:0003777)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(17)|pancreas(1)|urinary_tract(1)	25	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			GGATGTTCTCGGGCAAGGAGC	0.602																																					p.P36P		Atlas-SNP	.											.	APPBP2	48	.	0			c.C108G						PASS	.						136.0	110.0	119.0					17																	58603185		2203	4300	6503	SO:0001819	synonymous_variant	10513	exon1			GTTCTCGGGCAAG	AF017782	CCDS32699.1	17q23.2	2012-09-20	2001-11-28		ENSG00000062725	ENSG00000062725			622	protein-coding gene	gene with protein product	"""protein interacting with APP tail 1"""	605324	"""amyloid beta precursor protein (cytoplasmic tail)-binding protein 2"""			9843960	Standard	NM_006380		Approved	KIAA0228, Hs.84084, PAT1	uc002iys.1	Q92624		ENST00000083182.3:c.108C>G	17.37:g.58603185G>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	134	73	0.544776	NM_006380	A8K862|O95095|Q8WVC9	Silent	SNP	ENST00000083182.3	37	CCDS32699.1																																																																																			.	.	none		0.602	APPBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449465.1	NM_006380	
NDUFA10	4705	hgsc.bcm.edu	37	2	240961728	240961728	+	Silent	SNP	T	T	C	rs2083411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240961728T>C	ENST00000252711.2	-	2	205	c.105A>G	c.(103-105)aaA>aaG	p.K35K	NDUFA10_ENST00000404554.1_Silent_p.K35K|NDUFA10_ENST00000307300.4_Silent_p.K35K|NDUFA10_ENST00000407129.3_Silent_p.K35K	NM_004544.3	NP_004535.1	O95299	NDUAA_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42kDa	35					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)		CATAGCGCAGTTTGCACTGCA	0.428													C|||	3518	0.702476	0.8011	0.6311	5008	,	,		14147	0.7867		0.6779	False		,,,				2504	0.5583				p.K35K		Atlas-SNP	.											.	NDUFA10	40	.	0			c.A105G						PASS	.	C		3465,941	358.1+/-314.2	1376,713,114	129.0	110.0	116.0		105	3.6	0.0	2	dbSNP_96	116	5568,3032	468.3+/-367.3	1831,1906,563	no	coding-synonymous	NDUFA10	NM_004544.3		3207,2619,677	CC,CT,TT		35.2558,21.3572,30.5474		35/356	240961728	9033,3973	2203	4300	6503	SO:0001819	synonymous_variant	4705	exon2			GCGCAGTTTGCAC	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.105A>G	2.37:g.240961728T>C		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	215	215	1	NM_004544	Q8WXC9	Silent	SNP	ENST00000252711.2	37	CCDS2531.1																																																																																			T|0.299;C|0.701	0.701	strong		0.428	NDUFA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257180.2	NM_004544	
NRD1	4898	hgsc.bcm.edu	37	1	52344245	52344245	+	Silent	SNP	T	T	G	rs72901974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:52344245T>G	ENST00000354831.7	-	1	232	c.43A>C	c.(43-45)Agg>Cgg	p.R15R	NRD1_ENST00000352171.7_Silent_p.R15R|NRD1_ENST00000544028.1_Intron|NRD1_ENST00000539524.1_5'Flank	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	15					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						CACAACTTCCTCCGGGTGGCA	0.627													T|||	252	0.0503195	0.0582	0.0043	5008	,	,		15741	0.0556		0.0089	False		,,,				2504	0.1094				p.R15R		Atlas-SNP	.											.	NRD1	89	.	0			c.A43C						PASS	.	T	,	265,4141	138.8+/-174.5	5,255,1943	26.0	26.0	26.0		43,43	4.0	1.0	1	dbSNP_130	26	62,8538	35.3+/-89.8	0,62,4238	no	coding-synonymous,coding-synonymous	NRD1	NM_001101662.1,NM_002525.2	,	5,317,6181	GG,GT,TT		0.7209,6.0145,2.5142	,	15/1152,15/1220	52344245	327,12679	2203	4300	6503	SO:0001819	synonymous_variant	4898	exon1			ACTTCCTCCGGGT	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.43A>C	1.37:g.52344245T>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Silent	SNP	ENST00000354831.7	37	CCDS559.1																																																																																			T|0.972;G|0.028	0.028	strong		0.627	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	
TUBA3D	113457	hgsc.bcm.edu	37	2	132238286	132238286	+	Silent	SNP	C	C	T	rs111626841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:132238286C>T	ENST00000321253.6	+	4	1127	c.1020C>T	c.(1018-1020)acC>acT	p.T340T		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	340					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		CCAAGCGCACCATCCAGTTTG	0.562													.|||	839	0.167532	0.4592	0.1037	5008	,	,		15998	0.004		0.0924	False		,,,				2504	0.0644				p.T340T	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											.	TUBA3D	60	.	0			c.C1020T						PASS	.	T		1721,2685	627.4+/-394.9	382,957,864	78.0	81.0	80.0		1020	1.5	1.0	2	dbSNP_132	80	712,7888	779.9+/-407.7	41,630,3629	no	coding-synonymous	TUBA3D	NM_080386.2		423,1587,4493	TT,TC,CC		8.2791,39.0604,18.7068		340/451	132238286	2433,10573	2203	4300	6503	SO:0001819	synonymous_variant	113457	exon4			GCGCACCATCCAG	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"""Tubulins"""	24071	protein-coding gene	gene with protein product	"""alpha-tubulin isotype H2-alpha"""					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.1020C>T	2.37:g.132238286C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	150	61	0.406667	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000321253.6	37	CCDS33290.1																																																																																			C|0.831;T|0.169	0.169	strong		0.562	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386	
AEBP1	165	hgsc.bcm.edu	37	7	44146151	44146151	+	Missense_Mutation	SNP	C	C	T	rs75107445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44146151C>T	ENST00000223357.3	+	2	565	c.260C>T	c.(259-261)cCg>cTg	p.P87L		NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	87	Pro-rich.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						ACAGTGCCTCCGGAAAAGACC	0.587													C|||	9	0.00179712	0.0061	0.0	5008	,	,		15644	0.0		0.0	False		,,,				2504	0.001				p.P87L		Atlas-SNP	.											AEBP1,larynx,carcinoma,-1,1	AEBP1	102	1	0			c.C260T						PASS	.	C	LEU/PRO	23,4365	26.2+/-53.5	0,23,2171	36.0	45.0	42.0		260	1.9	0.1	7	dbSNP_131	42	0,8586		0,0,4293	yes	missense	AEBP1	NM_001129.3	98	0,23,6464	TT,TC,CC		0.0,0.5242,0.1773	benign	87/1159	44146151	23,12951	2194	4293	6487	SO:0001583	missense	165	exon2			TGCCTCCGGAAAA	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"""aortic carboxypeptidase-like protein"", ""adipocyte enhancer binding protein 1"""	602981	"""AE-binding protein 1"""			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.260C>T	7.37:g.44146151C>T	ENSP00000223357:p.Pro87Leu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	CCDS5476.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	16.09	3.025082	0.54683	0.005242	0.0	ENSG00000106624	ENST00000223357;ENST00000449162	D	0.94828	-3.53	4.9	1.92	0.25849	.	0.598172	0.14954	N	0.288777	D	0.84853	0.5564	L	0.27053	0.805	0.34323	D	0.68679	B	0.14805	0.011	B	0.08055	0.003	T	0.81575	-0.0870	10	0.87932	D	0	-1.0442	6.299	0.21101	0.0:0.6427:0.0:0.3573	.	87	Q8IUX7	AEBP1_HUMAN	L	87;3	ENSP00000223357:P87L	ENSP00000223357:P87L	P	+	2	0	AEBP1	44112676	0.000000	0.05858	0.071000	0.20095	0.651000	0.38670	0.214000	0.17541	0.079000	0.16929	0.462000	0.41574	CCG	C|0.999;T|0.001	0.001	strong		0.587	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129	
MUC17	140453	hgsc.bcm.edu	37	7	100677285	100677285	+	Missense_Mutation	SNP	G	G	A	rs74852422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677285G>A	ENST00000306151.4	+	3	2652	c.2588G>A	c.(2587-2589)gGa>gAa	p.G863E		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	863	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)					TATAGTGAAGGAAGAACTCCT	0.493																																					p.G863E		Atlas-SNP	.											.	MUC17	804	.	0			c.G2588A						PASS	.						302.0	284.0	290.0					7																	100677285		2203	4300	6503	SO:0001583	missense	140453	exon3			GTGAAGGAAGAAC	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.2588G>A	7.37:g.100677285G>A	ENSP00000302716:p.Gly863Glu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	212	53	0.25	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	1.492	-0.554404	0.03996	.	.	ENSG00000169876	ENST00000306151	T	0.03553	3.89	1.14	-2.29	0.06805	.	.	.	.	.	T	0.01905	0.0060	L	0.29908	0.895	0.09310	N	1	B	0.24186	0.099	B	0.12837	0.008	T	0.47509	-0.9112	9	0.02654	T	1	.	2.5676	0.04787	0.2144:0.0:0.3644:0.4212	.	863	Q685J3	MUC17_HUMAN	E	863	ENSP00000302716:G863E	ENSP00000302716:G863E	G	+	2	0	MUC17	100464005	0.004000	0.15560	0.000000	0.03702	0.003000	0.03518	0.987000	0.29603	-0.747000	0.04759	0.196000	0.17591	GGA	G|0.988;A|0.013	0.013	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PKMYT1	9088	hgsc.bcm.edu	37	16	3026956	3026956	+	Silent	SNP	T	T	C	rs4149786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3026956T>C	ENST00000262300.8	-	3	595	c.87A>G	c.(85-87)ccA>ccG	p.P29P	PKMYT1_ENST00000440027.2_Silent_p.P29P|PKMYT1_ENST00000573944.1_Silent_p.P20P|PKMYT1_ENST00000431515.2_Silent_p.P29P|PKMYT1_ENST00000574385.1_Silent_p.P20P|PKMYT1_ENST00000574730.1_Intron	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	29	Pro-rich.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						GGAAGTAGGCTGGGACTGGGA	0.692													C|||	5	0.000998403	0.0	0.0	5008	,	,		16125	0.0		0.0	False		,,,				2504	0.0051				p.P29P		Atlas-SNP	.											.	PKMYT1	23	.	0			c.A87G						PASS	.	C	,	10,4286		0,10,2138	12.0	15.0	14.0		87,87	-3.7	1.0	16	dbSNP_110	14	0,8510		0,0,4255	no	coding-synonymous,coding-synonymous	PKMYT1	NM_004203.4,NM_182687.2	,	0,10,6393	CC,CT,TT		0.0,0.2328,0.0781	,	29/500,29/481	3026956	10,12796	2148	4255	6403	SO:0001819	synonymous_variant	9088	exon3			GTAGGCTGGGACT	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"""membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase"", ""protein phosphatase 1, regulatory subunit 126"""	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.87A>G	16.37:g.3026956T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	21	0.323077	NM_182687	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000262300.8	37	CCDS10486.1																																																																																			T|0.993;C|0.007	0.007	strong		0.692	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203	
TTC7A	57217	hgsc.bcm.edu	37	2	47301029	47301029	+	Silent	SNP	A	A	G	rs3739099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47301029A>G	ENST00000319190.5	+	20	2912	c.2544A>G	c.(2542-2544)gtA>gtG	p.V848V	TTC7A_ENST00000394850.2_Silent_p.V872V|TTC7A_ENST00000409245.1_Silent_p.V814V|AC073283.7_ENST00000421759.1_RNA|RP11-761B3.1_ENST00000422269.1_Intron|TTC7A_ENST00000263737.6_Silent_p.V494V|C2orf61_ENST00000464527.2_Intron	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	848					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GCAGCCCTGTACTGCCCTTCT	0.687													G|||	1665	0.332468	0.3064	0.2507	5008	,	,		17841	0.6577		0.0885	False		,,,				2504	0.3415				p.V848V		Atlas-SNP	.											TTC7A,NS,carcinoma,0,1	TTC7A	80	1	0			c.A2544G						PASS	.	G		1221,3183	692.2+/-405.5	177,867,1158	41.0	35.0	37.0		2544	1.0	1.0	2	dbSNP_107	37	641,7959	780.6+/-407.7	30,581,3689	no	coding-synonymous	TTC7A	NM_020458.2		207,1448,4847	GG,GA,AA		7.4535,27.7248,14.3187		848/859	47301029	1862,11142	2202	4300	6502	SO:0001819	synonymous_variant	57217	exon20			CCCTGTACTGCCC	AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"""Tetratricopeptide (TTC) repeat domain containing"""	19750	protein-coding gene	gene with protein product		609332	"""tetratricopeptide repeat domain 7"""	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.2544A>G	2.37:g.47301029A>G		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	223	104	0.466368	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																			A|0.774;G|0.226	0.226	strong		0.687	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
LILRA3	11026	hgsc.bcm.edu	37	19	54803141	54803141	+	Missense_Mutation	SNP	C	C	T	rs147561158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54803141C>T	ENST00000251390.3	-	4	627	c.536G>A	c.(535-537)cGg>cAg	p.R179Q	LILRA3_ENST00000391745.1_Missense_Mutation_p.R196Q|LILRA3_ENST00000391744.3_Intron	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	179	Ig-like C2-type 2.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GAAGATGGCCCGGGATGACCC	0.567													.|||	5	0.000998403	0.0038	0.0	5008	,	,		15432	0.0		0.0	False		,,,				2504	0.0				p.R179Q		Atlas-SNP	.											LILRA3,right_upper_lobe,carcinoma,0,2	LILRA3	65	2	0			c.G536A						scavenged	.	C	,GLN/ARG	25,4365		1,23,2171	139.0	115.0	123.0		,536	-0.2	0.0	19	dbSNP_134	123	0,8332		0,0,4166	yes	intron,missense	LILRA3	NM_001172654.1,NM_006865.3	,43	1,23,6337	TT,TC,CC		0.0,0.5695,0.1965	,	,179/440	54803141	25,12697	2195	4166	6361	SO:0001583	missense	11026	exon4			ATGGCCCGGGATG	U91926		19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.536G>A	19.37:g.54803141C>T	ENSP00000251390:p.Arg179Gln	Somatic	315	2	0.00634921		WXS	Illumina HiSeq	Phase_I	346	167	0.482659	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	37	CCDS12887.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	0.015	-1.559568	0.00910	0.005695	0.0	ENSG00000170866	ENST00000251390;ENST00000391745	T;T	0.02890	4.12;4.12	2.07	-0.183	0.13284	Immunoglobulin-like fold (1);	0.611757	0.12604	N	0.454468	T	0.00695	0.0023	N	0.02391	-0.57	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.46693	-0.9173	10	0.02654	T	1	.	4.3936	0.11351	0.0:0.4019:0.0:0.5981	.	179	Q8N6C8	LIRA3_HUMAN	Q	179;196	ENSP00000251390:R179Q;ENSP00000375625:R196Q	ENSP00000251390:R179Q	R	-	2	0	LILRA3	59494953	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.534000	0.06150	-0.089000	0.12484	-0.350000	0.07774	CGG	C|0.998;T|0.002	0.002	strong		0.567	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
GLRA3	8001	hgsc.bcm.edu	37	4	175688141	175688141	+	Silent	SNP	G	G	A	rs12651268|rs201682361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:175688141G>A	ENST00000274093.3	-	3	742	c.240C>T	c.(238-240)agC>agT	p.S80S	GLRA3_ENST00000340217.5_Silent_p.S80S	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	80					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)|Ivermectin(DB00602)|Lindane(DB00431)	TAGAGCCAAAGCTGTTGATGA	0.353													G|||	1696	0.338658	0.1142	0.3242	5008	,	,		16006	0.5198		0.3708	False		,,,				2504	0.4325				p.S80S		Atlas-SNP	.											.	GLRA3	76	.	0			c.C240T						PASS	.	G	,	53,4353		24,5,2174	168.0	160.0	163.0		240,240	4.8	1.0	4	dbSNP_120	163	621,7979		243,135,3922	no	coding-synonymous,coding-synonymous	GLRA3	NM_001042543.1,NM_006529.2	,	267,140,6096	AA,AG,GG		7.2209,1.2029,5.1822	,	80/450,80/465	175688141	674,12332	2203	4300	6503	SO:0001819	synonymous_variant	8001	exon3			GCCAAAGCTGTTG	AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"""Ligand-gated ion channels / Glycine receptors"""	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.240C>T	4.37:g.175688141G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_001042543	D3DP44|O75816|Q5D0E3	Silent	SNP	ENST00000274093.3	37	CCDS3822.1																																																																																			G|0.704;A|0.296	0.296	strong		0.353	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1		
HIP1	3092	hgsc.bcm.edu	37	7	75211414	75211414	+	Silent	SNP	A	A	G	rs237238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75211414A>G	ENST00000336926.6	-	6	545	c.519T>C	c.(517-519)gcT>gcC	p.A173A	RN7SL642P_ENST00000581382.1_RNA|HIP1_ENST00000434438.2_Silent_p.A173A	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	173					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CACTTTCTCCAGCCTCGTCCA	0.552			T	PDGFRB	CMML								A|||	488	0.0974441	0.1074	0.0793	5008	,	,		19934	0.0754		0.0795	False		,,,				2504	0.138				p.A173A		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	HIP1,NS,carcinoma,-1,1	HIP1	91	1	0			c.T519C						PASS	.	A		411,3995	203.5+/-225.9	24,363,1816	92.0	69.0	77.0	http://www.ncbi.nlm.nih.gov/pubmed?term	519	-10.8	0.7	7	dbSNP_79	77	621,7979	161.4+/-214.4	26,569,3705	no	coding-synonymous	HIP1	NM_005338.5		50,932,5521	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	7.2209,9.3282,7.9348		173/1038	75211414	1032,11974	2203	4300	6503	SO:0001819	synonymous_variant	3092	exon6			TTCTCCAGCCTCG	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.519T>C	7.37:g.75211414A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			A|0.912;G|0.088	0.088	strong		0.552	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
COL11A1	1301	hgsc.bcm.edu	37	1	103491461	103491461	+	Intron	SNP	T	T	G	rs12731843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:103491461T>G	ENST00000370096.3	-	7	1210				COL11A1_ENST00000353414.4_Intron|COL11A1_ENST00000512756.1_Intron|COL11A1_ENST00000358392.2_Missense_Mutation_p.K276N	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1						cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTTCCTTTGATTTAGTAGCCA	0.348													G|||	397	0.0792732	0.121	0.0418	5008	,	,		18459	0.0675		0.0696	False		,,,				2504	0.0716				p.K276N		Atlas-SNP	.											.	COL11A1	972	.	0			c.A828C						PASS	.	G	,,,ASN/LYS	493,3911	775.0+/-414.1	26,441,1735	115.0	122.0	120.0		,,,828	0.9	1.0	1	dbSNP_121	120	547,8051	792.8+/-407.5	17,513,3769	yes	intron,intron,intron,missense	COL11A1	NM_001190709.1,NM_001854.3,NM_080630.3,NM_080629.2	,,,94	43,954,5504	GG,GT,TT		6.3619,11.1944,7.9988	,,,benign	,,,276/1819	103491461	1040,11962	2202	4299	6501	SO:0001627	intron_variant	1301	exon6			CTTTGATTTAGTA	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.898-292A>C	1.37:g.103491461T>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	55	35	0.636364	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	165	0.07554945054945054	50	0.1016260162601626	18	0.049723756906077346	40	0.06993006993006994	57	0.07519788918205805	G	7.104	0.574635	0.13623	0.111944	0.063619	ENSG00000060718	ENST00000358392;ENST00000427239	T;T	0.71934	-0.55;-0.61	5.5	0.879	0.19155	.	2.666740	0.00918	N	0.002557	T	0.27798	0.0684	N	0.17474	0.49	0.09310	P	0.999999999999109	B	0.02656	0.0	B	0.01281	0.0	T	0.05517	-1.0880	9	0.17832	T	0.49	.	4.3926	0.11348	0.0677:0.2714:0.3471:0.3138	rs12731843;rs52837620;rs12731843	276	P12107-2	.	N	276	ENSP00000351163:K276N;ENSP00000408640:K276N	ENSP00000351163:K276N	K	-	3	2	COL11A1	103264049	0.987000	0.35691	0.997000	0.53966	0.993000	0.82548	0.028000	0.13644	0.034000	0.15491	-0.137000	0.14449	AAA	T|0.922;G|0.078	0.078	strong		0.348	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
DUS3L	56931	hgsc.bcm.edu	37	19	5789565	5789565	+	Missense_Mutation	SNP	T	T	C	rs2436487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5789565T>C	ENST00000309061.7	-	3	649	c.553A>G	c.(553-555)Agg>Ggg	p.R185G	DUS3L_ENST00000320699.8_Intron|DUS3L_ENST00000590681.1_5'UTR	NM_020175.2	NP_064560.2	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like (S. cerevisiae)	185			R -> G (in dbSNP:rs2436487). {ECO:0000269|PubMed:15489334}.				flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA dihydrouridine synthase activity (GO:0017150)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(2)	14						CCCTCGGGCCTCAGGTGGGCC	0.721													C|||	2304	0.460064	0.8177	0.2349	5008	,	,		13189	0.5496		0.1948	False		,,,				2504	0.317				p.R185G		Atlas-SNP	.											DUS3L,NS,carcinoma,0,1	DUS3L	42	1	0			c.A553G						PASS	.	C	,GLY/ARG	2891,1425		1024,843,291	7.0	12.0	10.0		,553	4.5	0.9	19	dbSNP_100	10	1496,6988		140,1216,2886	no	intron,missense	DUS3L	NM_001161619.1,NM_020175.2	,125	1164,2059,3177	CC,CT,TT		17.6332,33.0167,34.2734	,benign	,185/651	5789565	4387,8413	2158	4242	6400	SO:0001583	missense	56931	exon3			CGGGCCTCAGGTG		CCDS32880.1, CCDS54202.1	19p13.3	2014-02-12			ENSG00000141994	ENSG00000141994			26920	protein-coding gene	gene with protein product						12477932	Standard	NM_020175		Approved	DUS3, FLJ13896	uc002mdc.3	Q96G46	OTTHUMG00000162311	ENST00000309061.7:c.553A>G	19.37:g.5789565T>C	ENSP00000311977:p.Arg185Gly	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	14	6	0.428571	NM_020175	Q96HM5|Q9BSU4|Q9H877|Q9NPR1	Missense_Mutation	SNP	ENST00000309061.7	37	CCDS32880.1	905	0.4143772893772894	385	0.782520325203252	93	0.2569060773480663	281	0.49125874125874125	146	0.19261213720316622	C	0.773	-0.765146	0.02996	0.669833	0.176332	ENSG00000141994	ENST00000309061	T	0.17370	2.28	4.51	4.51	0.55191	Zinc finger, CCCH-type (1);	0.127872	0.53938	N	0.000056	T	0.00012	0.0000	N	0.00864	-1.135	0.51767	P	6.099999999997774E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.17167	-1.0378	9	0.12766	T	0.61	-2.8966	10.5357	0.45002	0.0:0.9026:0.0:0.0974	rs2436487;rs3760777;rs17845247;rs17858066;rs58221162;rs2436487	185	Q96G46	DUS3L_HUMAN	G	185	ENSP00000311977:R185G	ENSP00000311977:R185G	R	-	1	2	DUS3L	5740565	0.996000	0.38824	0.894000	0.35097	0.121000	0.20230	2.069000	0.41481	0.902000	0.36520	-0.320000	0.08662	AGG	T|0.554;C|0.446	0.446	strong		0.721	DUS3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451870.2	NM_020175	
PLEKHA4	57664	hgsc.bcm.edu	37	19	49368843	49368843	+	Missense_Mutation	SNP	T	T	C	rs506425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49368843T>C	ENST00000263265.6	-	3	664	c.109A>G	c.(109-111)Atc>Gtc	p.I37V	PLEKHA4_ENST00000355496.5_Missense_Mutation_p.I37V	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	37			I -> V (in dbSNP:rs506425). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		AAGGCGTGGATCTTGTTTACT	0.597													C|||	2192	0.4377	0.8661	0.3242	5008	,	,		16677	0.1111		0.3032	False		,,,				2504	0.4141				p.I37V		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.A109G						PASS	.	C	VAL/ILE,VAL/ILE	3475,931	357.6+/-314.0	1375,725,103	123.0	95.0	105.0		109,109	4.0	1.0	19	dbSNP_83	105	2607,5993	689.4+/-404.4	396,1815,2089	yes	missense,missense	PLEKHA4	NM_001161354.1,NM_020904.2	29,29	1771,2540,2192	CC,CT,TT		30.314,21.1303,46.763	benign,benign	37/584,37/780	49368843	6082,6924	2203	4300	6503	SO:0001583	missense	57664	exon3			CGTGGATCTTGTT	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.109A>G	19.37:g.49368843T>C	ENSP00000263265:p.Ile37Val	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_001161354	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	831	0.3804945054945055	407	0.8272357723577236	123	0.3397790055248619	67	0.11713286713286714	234	0.3087071240105541	C	4.078	0.012294	0.07912	0.788697	0.30314	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.11385	2.78;2.78	5.04	3.98	0.46160	.	0.000000	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00382	-1.575	0.45035	P	0.0019419999999999993	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31586	-0.9938	9	0.02654	T	1	.	10.4978	0.44788	0.0:0.8265:0.0:0.1735	rs506425;rs17855917;rs57752905;rs506425	37;37	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	V	37	ENSP00000263265:I37V;ENSP00000347683:I37V	ENSP00000263265:I37V	I	-	1	0	PLEKHA4	54060655	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.044000	0.49830	1.270000	0.44297	-0.213000	0.12676	ATC	T|0.549;G|0.003	.	strong		0.597	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		
OTC	5009	hgsc.bcm.edu	37	X	38260570	38260570	+	Silent	SNP	T	T	C	rs145777402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38260570T>C	ENST00000039007.4	+	5	581	c.429T>C	c.(427-429)taT>taC	p.Y143Y	TM4SF2_ENST00000465127.1_Intron|OTC_ENST00000488812.1_3'UTR	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	143					ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	CTCGAGTGTATAAACAATCAG	0.393													T|||	12	0.00317881	0.0091	0.0	3775	,	,		10235	0.0		0.0	False		,,,				2504	0.0				p.Y143Y		Atlas-SNP	.											.	OTC	60	.	0			c.T429C						PASS	.	T		45,3788		0,40,5,1591,566	103.0	78.0	86.0		429	-0.4	1.0	X	dbSNP_134	86	0,6728		0,0,0,2428,1872	no	coding-synonymous	OTC	NM_000531.5		0,40,5,4019,2438	CC,CT,C,TT,T		0.0,1.174,0.4261		143/355	38260570	45,10516	2202	4300	6502	SO:0001819	synonymous_variant	5009	exon5			AGTGTATAAACAA	K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.429T>C	X.37:g.38260570T>C		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	179	74	0.413408	NM_000531	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Silent	SNP	ENST00000039007.4	37	CCDS14247.1																																																																																			T|0.994;C|0.006	0.006	strong		0.393	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2		
OR52E6	390078	hgsc.bcm.edu	37	11	5863113	5863113	+	Silent	SNP	G	G	A	rs10742810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	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	
ODF1	4956	hgsc.bcm.edu	37	8	103573024	103573024	+	Missense_Mutation	SNP	G	G	A	rs568456031|rs143802899|rs111689913|rs58232162|rs386728348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103573024G>A	ENST00000285402.3	+	2	821	c.665G>A	c.(664-666)aGc>aAc	p.S222N	ODF1_ENST00000518835.1_Missense_Mutation_p.S15N	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	222	C-X-P repeat region.		Missing. {ECO:0000269|PubMed:8111388}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.C218_P226delCNPCSPCNP(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			aacccctgcagcccctgcaac	0.567													A|||	442	0.0882588	0.3011	0.0303	5008	,	,		16173	0.0129		0.0099	False		,,,				2504	0.0				p.S222N		Atlas-SNP	.											.	ODF1	55	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G665A						PASS	.	A	ASN/SER	1013,3353		178,657,1348	60.0	59.0	59.0		665	-4.1	0.0	8	dbSNP_132	59	30,8398		1,28,4185	no	missense	ODF1	NM_024410.3	46	179,685,5533	AA,AG,GG		0.356,23.202,8.1523	benign	222/251	103573024	1043,11751	2183	4214	6397	SO:0001583	missense	4956	exon2			CCTGCAGCCCCTG	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"""Heat shock proteins / HSPB"""	8113	protein-coding gene	gene with protein product	"""cancer/testis antigen 133"""	182878	"""outer dense fibre of sperm tails 1"""			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.665G>A	8.37:g.103573024G>A	ENSP00000285402:p.Ser222Asn	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_024410	Q3SX72	Missense_Mutation	SNP	ENST00000285402.3	37	CCDS6293.1	188	0.08608058608058608	164	0.3333333333333333	11	0.03038674033149171	9	0.015734265734265736	4	0.005277044854881266	A	0.034	-1.317862	0.01320	0.23202	0.00356	ENSG00000155087	ENST00000285402;ENST00000518835	D;T	0.86164	-2.08;1.89	4.92	-4.11	0.03928	.	1.048210	0.07416	N	0.893166	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	0.00688	-1.1609	10	0.22706	T	0.39	-12.522	13.0969	0.59197	0.6974:0.0:0.3026:0.0	.	222	Q14990	ODFP1_HUMAN	N	222;15	ENSP00000285402:S222N;ENSP00000430023:S15N	ENSP00000285402:S222N	S	+	2	0	ODF1	103642200	0.004000	0.15560	0.004000	0.12327	0.002000	0.02628	-1.097000	0.03349	-1.135000	0.02895	-1.581000	0.00855	AGC	G|0.893;A|0.107	0.107	strong		0.567	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1		
VLDLR	7436	hgsc.bcm.edu	37	9	2648773	2648773	+	Silent	SNP	A	A	G	rs6148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2648773A>G	ENST00000382100.3	+	14	2423	c.2067A>G	c.(2065-2067)caA>caG	p.Q689Q	VLDLR_ENST00000382099.2_Silent_p.Q689Q	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	689					cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		ATGATGCCCAAGACATCATTG	0.443													A|||	370	0.0738818	0.0265	0.0793	5008	,	,		22594	0.002		0.2068	False		,,,				2504	0.0716				p.Q689Q		Atlas-SNP	.											.	VLDLR	68	.	0			c.A2067G						PASS	.	A	,	213,4193	130.2+/-166.9	5,203,1995	122.0	110.0	114.0		2067,2067	1.2	1.0	9	dbSNP_52	114	1609,6991	299.4+/-304.4	169,1271,2860	no	coding-synonymous,coding-synonymous	VLDLR	NM_001018056.1,NM_003383.3	,	174,1474,4855	GG,GA,AA		18.7093,4.8343,14.0089	,	689/846,689/874	2648773	1822,11184	2203	4300	6503	SO:0001819	synonymous_variant	7436	exon14			TGCCCAAGACATC		CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"""Low density lipoprotein receptors"""	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.2067A>G	9.37:g.2648773A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	201	95	0.472637	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	Silent	SNP	ENST00000382100.3	37	CCDS6446.1																																																																																			A|0.874;G|0.126	0.126	strong		0.443	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383	
DEFB129	140881	hgsc.bcm.edu	37	20	210306	210306	+	Missense_Mutation	SNP	C	C	G	rs1053783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:210306C>G	ENST00000246105.4	+	2	477	c.446C>G	c.(445-447)aCc>aGc	p.T149S		NM_080831.3	NP_543021.1	Q9H1M3	DB129_HUMAN	defensin, beta 129	149			T -> S (in dbSNP:rs1053783).		defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|stomach(1)	9		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)			AAGAGTAACACCAAAGAAAGC	0.502													C|||	1248	0.249201	0.469	0.1196	5008	,	,		18729	0.2351		0.0915	False		,,,				2504	0.2209				p.T149S		Atlas-SNP	.											.	DEFB129	24	.	0			c.C446G						PASS	.	C	SER/THR	1840,2566	536.8+/-374.6	389,1062,752	136.0	123.0	127.0		446	2.3	0.0	20	dbSNP_86	127	774,7826	183.5+/-231.7	37,700,3563	yes	missense	DEFB129	NM_080831.3	58	426,1762,4315	GG,GC,CC		9.0,41.7612,20.0984	probably-damaging	149/184	210306	2614,10392	2203	4300	6503	SO:0001583	missense	140881	exon2			GTAACACCAAAGA	AY358186	CCDS12992.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125903	ENSG00000125903		"""Defensins, beta"""	16218	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 87"""	C20orf87		11854508	Standard	NM_080831		Approved	bA530N10.3, DEFB-29	uc002wda.3	Q9H1M3	OTTHUMG00000031618	ENST00000246105.4:c.446C>G	20.37:g.210306C>G	ENSP00000246105:p.Thr149Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_080831	Q8NES7	Missense_Mutation	SNP	ENST00000246105.4	37	CCDS12992.1	459	0.21016483516483517	222	0.45121951219512196	43	0.11878453038674033	127	0.22202797202797203	67	0.08839050131926121	C	14.43	2.533782	0.45073	0.417612	0.09	ENSG00000125903	ENST00000246105	T	0.38401	1.14	4.25	2.27	0.28462	.	0.739381	0.12150	N	0.494997	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P	0.41978	0.767	B	0.33196	0.159	T	0.48175	-0.9058	9	0.49607	T	0.09	-9.4267	6.8928	0.24238	0.0:0.7886:0.0:0.2114	rs1053783;rs3194381;rs52805850;rs59902862;rs1053783	149	Q9H1M3	DB129_HUMAN	S	149	ENSP00000246105:T149S	ENSP00000246105:T149S	T	+	2	0	DEFB129	158306	0.001000	0.12720	0.018000	0.16275	0.084000	0.17831	0.085000	0.14912	0.725000	0.32318	0.462000	0.41574	ACC	C|0.798;G|0.202	0.202	strong		0.502	DEFB129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077430.2	NM_080831	
KRT74	121391	hgsc.bcm.edu	37	12	52966390	52966390	+	Missense_Mutation	SNP	A	A	T	rs11170176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52966390A>T	ENST00000305620.2	-	2	580	c.533T>A	c.(532-534)cTg>cAg	p.L178Q	KRT74_ENST00000549343.1_Missense_Mutation_p.L178Q	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	178	Linker 1.|Rod.		L -> Q (in dbSNP:rs11170176).		intermediate filament cytoskeleton organization (GO:0045104)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	keratin filament binding (GO:1990254)|structural molecule activity (GO:0005198)			kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	28				BRCA - Breast invasive adenocarcinoma(357;0.191)		GTTCAGGTCCAGCTGCTGCAG	0.557													A|||	1108	0.221246	0.2761	0.098	5008	,	,		20769	0.376		0.1193	False		,,,				2504	0.18				p.L178Q		Atlas-SNP	.											.	KRT74	67	.	0			c.T533A						PASS	.	A	GLN/LEU	1196,3210	417.4+/-337.9	170,856,1177	129.0	118.0	122.0		533	4.7	1.0	12	dbSNP_120	122	1086,7514	227.1+/-262.6	68,950,3282	no	missense	KRT74	NM_175053.3	113	238,1806,4459	TT,TA,AA		12.6279,27.1448,17.5457	benign	178/530	52966390	2282,10724	2203	4300	6503	SO:0001583	missense	121391	exon2			AGGTCCAGCTGCT	BK000977	CCDS8832.1	12q13.13	2013-06-25			ENSG00000170484	ENSG00000170484		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28929	protein-coding gene	gene with protein product		608248				12648212, 16831889	Standard	NM_175053		Approved	K6IRS4, KRT5C, KRT6IRS4	uc001sap.1	Q7RTS7	OTTHUMG00000169658	ENST00000305620.2:c.533T>A	12.37:g.52966390A>T	ENSP00000307240:p.Leu178Gln	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	271	148	0.546125	NM_175053	B5MD61|Q86Y45	Missense_Mutation	SNP	ENST00000305620.2	37	CCDS8832.1	456	0.2087912087912088	126	0.25609756097560976	42	0.11602209944751381	189	0.3304195804195804	99	0.13060686015831136	A	15.55	2.865720	0.51588	0.271448	0.126279	ENSG00000170484	ENST00000549343;ENST00000305620	D;D	0.87491	-2.26;-2.26	4.71	4.71	0.59529	Filament (1);	0.324202	0.17383	N	0.176247	T	0.00012	0.0000	N	0.00113	-2.09	0.29642	P	0.844674	P	0.40578	0.722	P	0.46452	0.517	T	0.48547	-0.9026	9	0.02654	T	1	.	5.812	0.18471	0.6142:0.1334:0.0:0.2524	rs11170176	178	Q7RTS7	K2C74_HUMAN	Q	178	ENSP00000447447:L178Q;ENSP00000307240:L178Q	ENSP00000307240:L178Q	L	-	2	0	KRT74	51252657	0.974000	0.33945	1.000000	0.80357	0.981000	0.71138	2.808000	0.47963	2.066000	0.61787	0.528000	0.53228	CTG	A|0.812;T|0.188	0.188	strong		0.557	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053	
MAP3K5	4217	hgsc.bcm.edu	37	6	136977568	136977568	+	Silent	SNP	T	T	C	rs2076260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:136977568T>C	ENST00000359015.4	-	10	1917	c.1557A>G	c.(1555-1557)ttA>ttG	p.L519L	MAP3K5_ENST00000355845.4_5'UTR	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	519					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GCTTATATATTAAAATTGTCT	0.403													C|||	2199	0.439097	0.7254	0.2997	5008	,	,		16911	0.5565		0.171	False		,,,				2504	0.3057				p.L519L		Atlas-SNP	.											MAP3K5,NS,carcinoma,0,1	MAP3K5	136	1	0			c.A1557G						PASS	.	C		2853,1553	487.8+/-361.0	929,995,279	115.0	109.0	111.0		1557	5.7	1.0	6	dbSNP_96	111	1499,7101	748.6+/-407.3	122,1255,2923	no	coding-synonymous	MAP3K5	NM_005923.3		1051,2250,3202	CC,CT,TT		17.4302,35.2474,33.4615		519/1375	136977568	4352,8654	2203	4300	6503	SO:0001819	synonymous_variant	4217	exon10			ATATATTAAAATT	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.1557A>G	6.37:g.136977568T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	74	46	0.621622	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	37	CCDS5179.1																																																																																			T|0.613;C|0.387	0.387	strong		0.403	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
ARHGEF15	22899	hgsc.bcm.edu	37	17	8215534	8215534	+	Silent	SNP	C	C	T	rs3744651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	297	0	0		WXS	Illumina HiSeq	Phase_I	341	181	0.530792	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	
CSMD2	114784	hgsc.bcm.edu	37	1	34238283	34238283	+	Missense_Mutation	SNP	T	T	C	rs474474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:34238283T>C	ENST00000338325.1	-	7	969	c.557A>G	c.(556-558)cAc>cGc	p.H186R	CSMD2_ENST00000373381.4_Missense_Mutation_p.H578R			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	538	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTCACCGTGGTGAAACCGGGA	0.537													C|||	1901	0.379593	0.5333	0.317	5008	,	,		19833	0.2659		0.2406	False		,,,				2504	0.4765				p.H538R		Atlas-SNP	.											.	CSMD2	946	.	0			c.A1613G						PASS	.	C	ARG/HIS	2143,2263	596.7+/-388.7	525,1093,585	111.0	105.0	107.0		1613	-1.3	0.9	1	dbSNP_83	107	2291,6309	706.5+/-405.5	301,1689,2310	yes	missense	CSMD2	NM_052896.3	29	826,2782,2895	CC,CT,TT		26.6395,48.6382,34.092	benign	538/3488	34238283	4434,8572	2203	4300	6503	SO:0001583	missense	114784	exon13			CCGTGGTGAAACC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000338325.1:c.557A>G	1.37:g.34238283T>C	ENSP00000340311:p.His186Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	88	58	0.659091	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000338325.1	37		682	0.31227106227106227	238	0.483739837398374	96	0.26519337016574585	168	0.2937062937062937	180	0.23746701846965698	C	9.737	1.163742	0.21538	0.486382	0.266395	ENSG00000121904	ENST00000373381;ENST00000338325	T;T	0.62941	-0.01;-0.01	6.06	-1.29	0.09288	Complement control module (2);Sushi/SCR/CCP (3);	0.180087	0.50627	N	0.000119	T	0.00012	0.0000	N	0.01284	-0.91	0.09310	P	0.999999999946275	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41197	-0.9522	9	0.10636	T	0.68	.	6.7188	0.23318	0.1097:0.4467:0.0:0.4436	rs474474;rs56977083;rs474474	538;578	Q7Z408;E7EUA6	CSMD2_HUMAN;.	R	578;186	ENSP00000362479:H578R;ENSP00000340311:H186R	ENSP00000241312:H538R	H	-	2	0	CSMD2	34010870	0.032000	0.19561	0.934000	0.37439	0.987000	0.75469	-0.069000	0.11542	-0.514000	0.06488	-0.733000	0.03571	CAC	T|0.662;C|0.338	0.338	strong		0.537	CSMD2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000036404.2	NM_052896	
TSC22D2	9819	hgsc.bcm.edu	37	3	150176316	150176316	+	Missense_Mutation	SNP	C	C	A	rs149526922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150176316C>A	ENST00000361875.3	+	4	3252	c.2236C>A	c.(2236-2238)Cca>Aca	p.P746T	TSC22D2_ENST00000361136.2_Missense_Mutation_p.P722T	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	746					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ATCCCAACTCCCAACCCAACA	0.438													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19128	0.0		0.0	False		,,,				2504	0.0				p.P746T		Atlas-SNP	.											.	TSC22D2	42	.	0			c.C2236A						PASS	.	C	THR/PRO	9,4397	15.5+/-35.6	0,9,2194	117.0	113.0	115.0		2236	4.3	1.0	3	dbSNP_134	115	0,8600		0,0,4300	yes	missense	TSC22D2	NM_014779.2	38	0,9,6494	AA,AC,CC		0.0,0.2043,0.0692	possibly-damaging	746/781	150176316	9,12997	2203	4300	6503	SO:0001583	missense	9819	exon4			CAACTCCCAACCC	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.2236C>A	3.37:g.150176316C>A	ENSP00000354543:p.Pro746Thr	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	275	129	0.469091	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Missense_Mutation	SNP	ENST00000361875.3	37	CCDS3149.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	0.007|0.007	-1.972930|-1.972930	0.00452|0.00452	0.002043|0.002043	0.0|0.0	ENSG00000196428|ENSG00000196428	ENST00000466814|ENST00000543241;ENST00000361875;ENST00000361136	.|T;T	.|0.29917	.|1.55;1.56	5.38|5.38	4.27|4.27	0.50696|0.50696	.|.	0.273316|0.273316	0.25256|0.25256	N|N	0.031991|0.031991	T|T	0.09949|0.09949	0.0244|0.0244	N|N	0.04508|0.04508	-0.205|-0.205	0.28151|0.28151	N|N	0.92938|0.92938	.|B;B	.|0.33919	.|0.037;0.432	.|B;B	.|0.33196	.|0.023;0.159	T|T	0.35871|0.35871	-0.9771|-0.9771	6|10	.|0.02654	.|T	.|1	.|.	4.617|4.617	0.12432|0.12432	0.0:0.765:0.0:0.235|0.0:0.765:0.0:0.235	.|.	.|722;746	.|O75157-2;O75157	.|.;T22D2_HUMAN	H|T	169|195;746;722	.|ENSP00000354543:P746T;ENSP00000354893:P722T	.|ENSP00000354893:P722T	P|P	+|+	2|1	0|0	TSC22D2|TSC22D2	151659006|151659006	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.032000|0.032000	0.12392|0.12392	0.943000|0.943000	0.29030|0.29030	2.693000|2.693000	0.91896|0.91896	0.655000|0.655000	0.94253|0.94253	CCC|CCA	C|0.999;A|0.001	0.001	strong		0.438	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779	
CARD11	84433	hgsc.bcm.edu	37	7	2946461	2946461	+	Silent	SNP	T	T	C	rs1124581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2946461T>C	ENST00000396946.4	-	25	3679	c.3276A>G	c.(3274-3276)cgA>cgG	p.R1092R		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	1092	Guanylate kinase-like.				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)		CCGTCTCAGGTCGGGGCAGCA	0.682			Mis		DLBCL								C|||	2987	0.596446	0.7012	0.5274	5008	,	,		15696	0.6508		0.4742	False		,,,				2504	0.5736				p.R1092R		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.A3276G						PASS	.	C		2889,1517	463.0+/-353.4	971,947,285	34.0	29.0	31.0		3276	3.0	0.1	7	dbSNP_86	31	4220,4380	566.9+/-388.7	1067,2086,1147	no	coding-synonymous	CARD11	NM_032415.4		2038,3033,1432	CC,CT,TT		49.0698,34.4303,45.3406		1092/1155	2946461	7109,5897	2203	4300	6503	SO:0001819	synonymous_variant	84433	exon25			CTCAGGTCGGGGC	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.3276A>G	7.37:g.2946461T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	200	200	1	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																			T|0.439;C|0.561	0.561	strong		0.682	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
FAM207A	85395	hgsc.bcm.edu	37	21	46380068	46380068	+	Missense_Mutation	SNP	G	G	A	rs141593051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46380068G>A	ENST00000291634.6	+	3	385	c.337G>A	c.(337-339)Gag>Aag	p.E113K	FAM207A_ENST00000397826.3_Missense_Mutation_p.E98K|FAM207A_ENST00000479127.1_3'UTR	NM_058190.2	NP_478070.1	Q9NSI2	F207A_HUMAN	family with sequence similarity 207, member A	113																	GCTGAGGCGTGAGCAATGGTT	0.572													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21685	0.0		0.0	False		,,,				2504	0.0				p.E113K		Atlas-SNP	.											.	.	.	.	0			c.G337A						PASS	.	G	LYS/GLU	5,4401	11.4+/-27.6	0,5,2198	128.0	101.0	110.0		337	3.2	0.4	21	dbSNP_134	110	0,8600		0,0,4300	yes	missense	FAM207A	NM_058190.2	56	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	benign	113/231	46380068	5,13001	2203	4300	6503	SO:0001583	missense	85395	exon3			AGGCGTGAGCAAT		CCDS13718.1	21q22.3	2011-08-15	2011-08-15	2011-08-15	ENSG00000160256	ENSG00000160256			15811	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 70"""	C21orf70			Standard	NM_058190		Approved	PRED56	uc002zgl.3	Q9NSI2	OTTHUMG00000090293	ENST00000291634.6:c.337G>A	21.37:g.46380068G>A	ENSP00000291634:p.Glu113Lys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_058190		Missense_Mutation	SNP	ENST00000291634.6	37	CCDS13718.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	10.04	1.240186	0.22711	0.001135	0.0	ENSG00000160256	ENST00000291634;ENST00000397826;ENST00000458015	T;T;T	0.47177	0.85;0.85;0.85	3.24	3.24	0.37175	.	0.168860	0.50627	D	0.000105	T	0.36276	0.0961	L	0.55743	1.74	0.40834	D	0.983615	P;B	0.46142	0.873;0.021	B;B	0.44044	0.439;0.037	T	0.48281	-0.9049	10	0.62326	D	0.03	-19.5017	10.2398	0.43305	0.0:0.0:1.0:0.0	.	98;113	Q9NSI2-2;Q9NSI2	.;F207A_HUMAN	K	113;98;98	ENSP00000291634:E113K;ENSP00000380926:E98K;ENSP00000404964:E98K	ENSP00000291634:E113K	E	+	1	0	C21orf70	45204496	0.782000	0.28689	0.427000	0.26684	0.158000	0.22134	2.095000	0.41729	2.110000	0.64415	0.650000	0.86243	GAG	G|0.999;A|0.001	0.001	strong		0.572	FAM207A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206639.1	NM_058190	
BZRAP1	9256	hgsc.bcm.edu	37	17	56383744	56383744	+	Missense_Mutation	SNP	T	T	C	rs11079346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	70	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	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	
PSME2	5721	hgsc.bcm.edu	37	14	24615435	24615435	+	Silent	SNP	T	T	C	rs4575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24615435T>C	ENST00000216802.5	-	2	702	c.63A>G	c.(61-63)agA>agG	p.R21R	RNF31_ENST00000324103.6_5'Flank|RNF31_ENST00000382687.3_5'Flank|PSME2_ENST00000560410.1_Intron|PSME2_ENST00000471700.2_5'UTR|RNF31_ENST00000559275.1_5'Flank	NM_002818.2	NP_002809.2	Q9UL46	PSME2_HUMAN	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	21					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502)				endometrium(1)|lung(3)|prostate(2)	6				GBM - Glioblastoma multiforme(265;0.00839)		AAAGATTCTGTCTGAAGACCT	0.507													C|||	2844	0.567891	0.7905	0.5447	5008	,	,		17071	0.6369		0.3231	False		,,,				2504	0.4642				p.R21R		Atlas-SNP	.											.	PSME2	21	.	0			c.A63G						PASS	.	C		3076,1330	445.5+/-347.7	1085,906,212	96.0	97.0	97.0		63	4.0	1.0	14	dbSNP_52	97	2376,6224	701.4+/-405.2	338,1700,2262	no	coding-synonymous	PSME2	NM_002818.2		1423,2606,2474	CC,CT,TT		27.6279,30.1861,41.9191		21/240	24615435	5452,7554	2203	4300	6503	SO:0001819	synonymous_variant	5721	exon2			ATTCTGTCTGAAG		CCDS9614.1	14q11.2	2010-03-10			ENSG00000100911	ENSG00000100911		"""Proteasome (prosome, macropain) subunits"""	9569	protein-coding gene	gene with protein product		602161				7789512	Standard	NM_002818		Approved	PA28beta	uc001wmj.3	Q9UL46	OTTHUMG00000028797	ENST00000216802.5:c.63A>G	14.37:g.24615435T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_002818	Q15129	Silent	SNP	ENST00000216802.5	37	CCDS9614.1																																																																																			T|0.531;C|0.469	0.469	strong		0.507	PSME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071918.3	NM_002818	
LEFTY1	10637	hgsc.bcm.edu	37	1	226076598	226076598	+	Missense_Mutation	SNP	C	C	T	rs35273824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226076598C>T	ENST00000272134.5	-	1	248	c.169G>A	c.(169-171)Gtg>Atg	p.V57M	LEFTY1_ENST00000492457.1_Intron|RP4-559A3.7_ENST00000432920.2_Intron	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	57			V -> M (in dbSNP:rs35273824).		cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					TGGGCCCTCACGTGGGTGGGG	0.697													C|||	194	0.038738	0.1346	0.0216	5008	,	,		17711	0.0		0.0	False		,,,				2504	0.001				p.V57M		Atlas-SNP	.											.	LEFTY1	30	.	0			c.G169A						PASS	.	C	MET/VAL	581,3825	246.8+/-255.3	33,515,1655	30.0	32.0	31.0		169	1.0	0.1	1	dbSNP_126	31	0,8598		0,0,4299	yes	missense	LEFTY1	NM_020997.3	21	33,515,5954	TT,TC,CC		0.0,13.1866,4.4679	probably-damaging	57/367	226076598	581,12423	2203	4299	6502	SO:0001583	missense	10637	exon1			CCCTCACGTGGGT	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"""left-right determination, factor B"""	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.169G>A	1.37:g.226076598C>T	ENSP00000272134:p.Val57Met	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	194	103	0.530928	NM_020997	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	78	0.03571428571428571	70	0.14227642276422764	8	0.022099447513812154	0	0.0	0	0.0	c	11.47	1.647249	0.29246	0.131866	0.0	ENSG00000243709	ENST00000272134	T	0.58940	0.3	4.18	0.96	0.19631	Transforming growth factor-beta, N-terminal (1);	0.188005	0.47093	D	0.000242	T	0.00967	0.0032	M	0.74881	2.28	0.44789	P	0.0022060000000000413	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	T	0.29305	-1.0016	9	0.34782	T	0.22	.	4.8349	0.13460	0.0:0.613:0.177:0.21	rs35273824	57;57	B2R7U0;O75610	.;LFTY1_HUMAN	M	57	ENSP00000272134:V57M	ENSP00000272134:V57M	V	-	1	0	LEFTY1	224143221	0.997000	0.39634	0.125000	0.21846	0.032000	0.12392	2.679000	0.46909	0.249000	0.21456	0.313000	0.20887	GTG	C|0.956;T|0.044	0.044	strong		0.697	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997	
APOF	319	hgsc.bcm.edu	37	12	56755058	56755058	+	Missense_Mutation	SNP	A	A	G	rs4301822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56755058A>G	ENST00000398189.3	-	2	1009	c.932T>C	c.(931-933)aTa>aCa	p.I311T	APOF_ENST00000541105.1_Missense_Mutation_p.I293T|STAT2_ENST00000557235.1_5'Flank|STAT2_ENST00000418572.2_5'Flank|STAT2_ENST00000314128.4_5'Flank	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	311					cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|high-density lipoprotein particle (GO:0034364)|low-density lipoprotein particle (GO:0034362)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)|receptor binding (GO:0005102)			breast(1)|lung(3)|prostate(1)|stomach(1)	6						GCTCTTGATTATGGCCCACCC	0.433													A|||	860	0.171725	0.618	0.0605	5008	,	,		19267	0.0		0.001	False		,,,				2504	0.0				p.I311T		Atlas-SNP	.											.	APOF	13	.	0			c.T932C						PASS	.	A	THR/ILE	2014,1714		552,910,402	63.0	62.0	62.0		932	-0.8	0.0	12	dbSNP_111	62	37,8135		0,37,4049	yes	missense	APOF	NM_001638.2	89	552,947,4451	GG,GA,AA		0.4528,45.9764,17.2353	benign	311/327	56755058	2051,9849	1864	4086	5950	SO:0001583	missense	319	exon2			TTGATTATGGCCC	L27050	CCDS44923.1	12q13	2013-01-24				ENSG00000175336		"""Apolipoproteins"""	615	protein-coding gene	gene with protein product		107760				8093033	Standard	NM_001638		Approved		uc001sle.1	Q13790		ENST00000398189.3:c.932T>C	12.37:g.56755058A>G	ENSP00000381250:p.Ile311Thr	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	NM_001638	Q8TC13	Missense_Mutation	SNP	ENST00000398189.3	37	CCDS44923.1	313	0.1433150183150183	292	0.5934959349593496	20	0.055248618784530384	0	0.0	1	0.0013192612137203166	A	11.19	1.566097	0.27915	0.540236	0.004528	ENSG00000175336	ENST00000398189;ENST00000541105	T;T	0.46819	0.86;0.87	4.35	-0.826	0.10805	.	1.635310	0.04195	N	0.329013	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.15719	0.014	B	0.18871	0.023	T	0.47182	-0.9137	9	0.56958	D	0.05	2.3357	3.2021	0.06653	0.4939:0.0:0.3248:0.1813	rs4301822;rs52837142;rs4301822	311	Q13790	APOF_HUMAN	T	311;293	ENSP00000381250:I311T;ENSP00000440997:I293T	ENSP00000381250:I311T	I	-	2	0	APOF	55041325	0.000000	0.05858	0.000000	0.03702	0.300000	0.27592	-0.010000	0.12743	-0.126000	0.11682	-0.256000	0.11100	ATA	A|0.818;G|0.182	0.182	strong		0.433	APOF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410076.1		
MAP1A	4130	hgsc.bcm.edu	37	15	43818052	43818052	+	Missense_Mutation	SNP	G	G	A	rs2245715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43818052G>A	ENST00000300231.5	+	4	4831	c.4381G>A	c.(4381-4383)Gat>Aat	p.D1461N	MAP1A_ENST00000382031.1_Missense_Mutation_p.D1699N|MAP1A_ENST00000399453.1_Missense_Mutation_p.D1461N			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1461			D -> N (in dbSNP:rs2245715).		microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	AGAACAAAAGGATACAGCCCT	0.448													G|||	1837	0.366813	0.6831	0.2147	5008	,	,		20781	0.4167		0.1044	False		,,,				2504	0.2658				p.D1461N		Atlas-SNP	.											.	MAP1A	189	.	0			c.G4381A						PASS	.	G	ASN/ASP	2194,1530		656,882,324	81.0	82.0	82.0		4381	3.0	0.1	15	dbSNP_100	82	839,7353		48,743,3305	yes	missense	MAP1A	NM_002373.5	23	704,1625,3629	AA,AG,GG		10.2417,41.0849,25.4532	possibly-damaging	1461/2804	43818052	3033,8883	1862	4096	5958	SO:0001583	missense	4130	exon4			CAAAAGGATACAG	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.4381G>A	15.37:g.43818052G>A	ENSP00000300231:p.Asp1461Asn	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	747	0.34203296703296704	329	0.6686991869918699	76	0.20994475138121546	270	0.47202797202797203	72	0.09498680738786279	G	14.00	2.405007	0.42613	0.589151	0.102417	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.21543	2.31;2.0;2.0	3.98	3.02	0.34903	.	.	.	.	.	T	0.00012	0.0000	L	0.49126	1.545	0.80722	P	0.0	B	0.26195	0.144	B	0.33042	0.157	T	0.21143	-1.0254	8	0.37606	T	0.19	-0.0114	13.2141	0.59849	0.0:0.1619:0.8381:0.0	rs2245715;rs60336985;rs2245715	1461	P78559	MAP1A_HUMAN	N	1699;1461;1461	ENSP00000371462:D1699N;ENSP00000382380:D1461N;ENSP00000300231:D1461N	ENSP00000300231:D1461N	D	+	1	0	MAP1A	41605344	0.004000	0.15560	0.077000	0.20336	0.498000	0.33706	1.414000	0.34736	0.947000	0.37659	0.563000	0.77884	GAT	G|0.669;A|0.331	0.331	strong		0.448	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
MUC17	140453	hgsc.bcm.edu	37	7	100677572	100677572	+	Missense_Mutation	SNP	A	A	G	rs60940057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677572A>G	ENST00000306151.4	+	3	2939	c.2875A>G	c.(2875-2877)Act>Gct	p.T959A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	959	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)					GACCACTTCTACTGAAGCCAC	0.498																																					p.T959A		Atlas-SNP	.											.	MUC17	804	.	0			c.A2875G						PASS	.	A	ALA/THR	293,4113	129.4+/-166.1	0,293,1910	305.0	290.0	295.0		2875	-2.4	0.0	7	dbSNP_129	295	277,8319	80.6+/-143.3	0,277,4021	no	missense	MUC17	NM_001040105.1	58	0,570,5931	GG,GA,AA		3.2224,6.65,4.3839	benign	959/4494	100677572	570,12432	2203	4298	6501	SO:0001583	missense	140453	exon3			ACTTCTACTGAAG	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.2875A>G	7.37:g.100677572A>G	ENSP00000302716:p.Thr959Ala	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	232	55	0.237069	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	1.937	-0.444524	0.04604	0.0665	0.032224	ENSG00000169876	ENST00000306151	T	0.02258	4.37	1.19	-2.38	0.06622	.	.	.	.	.	T	0.00144	0.0004	N	0.17082	0.46	0.09310	N	1	B	0.17667	0.023	B	0.09377	0.004	T	0.46721	-0.9171	9	0.23302	T	0.38	.	4.0165	0.09646	0.2761:0.4:0.3239:0.0	rs60940057	959	Q685J3	MUC17_HUMAN	A	959	ENSP00000302716:T959A	ENSP00000302716:T959A	T	+	1	0	MUC17	100464292	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-2.865000	0.00724	-1.347000	0.02208	0.113000	0.15668	ACT	A|0.946;G|0.054	0.054	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FGF4	2249	hgsc.bcm.edu	37	11	69588798	69588798	+	Silent	SNP	A	A	G	rs61738964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:69588798A>G	ENST00000168712.1	-	2	756	c.438T>C	c.(436-438)taT>taC	p.Y146Y	AP001888.1_ENST00000602104.1_5'Flank|FGF4_ENST00000538040.1_Intron	NM_002007.2	NP_001998.1	P08620	FGF4_HUMAN	fibroblast growth factor 4	146					apoptotic process involved in morphogenesis (GO:0060561)|cartilage condensation (GO:0001502)|cell-cell signaling (GO:0007267)|chondroblast differentiation (GO:0060591)|cranial suture morphogenesis (GO:0060363)|embryonic hindlimb morphogenesis (GO:0035116)|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)|mesenchymal cell proliferation (GO:0010463)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)	cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			lung(3)	3	Melanoma(5;1.89e-05)		LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)		Pentosan Polysulfate(DB00686)	TCACCGAGCCATAGAGCTTGC	0.657													A|||	31	0.0061901	0.0212	0.0043	5008	,	,		17189	0.0		0.0	False		,,,				2504	0.0				p.Y146Y		Atlas-SNP	.											.	FGF4	13	.	0			c.T438C						PASS	.	A		100,4300	77.8+/-116.1	3,94,2103	38.0	34.0	35.0		438	1.5	1.0	11	dbSNP_129	35	0,8588		0,0,4294	no	coding-synonymous	FGF4	NM_002007.2		3,94,6397	GG,GA,AA		0.0,2.2727,0.7699		146/207	69588798	100,12888	2200	4294	6494	SO:0001819	synonymous_variant	2249	exon2			CGAGCCATAGAGC	M17446	CCDS8194.1	11q13.3	2014-01-30	2008-08-01		ENSG00000075388	ENSG00000075388		"""Endogenous ligands"""	3682	protein-coding gene	gene with protein product	"""human stomach cancer, transforming factor from FGF-related oncogene"", ""kaposi sarcoma oncogene"", ""transforming protein KS3"""	164980	"""heparin secretory transforming protein 1"""	HSTF1		1611909	Standard	NM_002007		Approved	K-FGF, HBGF-4, HST, HST-1, KFGF	uc001opg.1	P08620	OTTHUMG00000167887	ENST00000168712.1:c.438T>C	11.37:g.69588798A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	174	83	0.477012	NM_002007	B7U994	Silent	SNP	ENST00000168712.1	37	CCDS8194.1																																																																																			A|0.994;G|0.006	0.006	strong		0.657	FGF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396834.2	NM_002007	
APC2	10297	hgsc.bcm.edu	37	19	1469078	1469078	+	Silent	SNP	G	G	A	rs79021820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1469078G>A	ENST00000535453.1	+	14	7491	c.5778G>A	c.(5776-5778)tcG>tcA	p.S1926S	APC2_ENST00000238483.4_Silent_p.S1652S|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000233607.2_Silent_p.S1926S			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGCAGAGATCGCCCGTGCGGA	0.771													G|||	198	0.0395367	0.1475	0.0043	5008	,	,		6607	0.0		0.0	False		,,,				2504	0.0				p.S1926S		Atlas-SNP	.											.	APC2	50	.	0			c.G5778A						PASS	.	G		162,2148		1,160,994	1.0	2.0	2.0		5778	-7.8	0.5	19	dbSNP_131	2	3,5457		0,3,2727	no	coding-synonymous	APC2	NM_005883.2		1,163,3721	AA,AG,GG		0.0549,7.013,2.1236		1926/2304	1469078	165,7605	1155	2730	3885	SO:0001819	synonymous_variant	10297	exon15			GAGATCGCCCGTG		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"""Armadillo repeat containing"""	24036	protein-coding gene	gene with protein product	"""adenomatous polyposis coli like"""	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.5778G>A	19.37:g.1469078G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	29	19	0.655172	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	37	CCDS12068.1																																																																																			G|0.949;A|0.051	0.051	strong		0.771	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883	
TAS1R2	80834	hgsc.bcm.edu	37	1	19166893	19166893	+	Missense_Mutation	SNP	C	C	T	rs6662276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19166893C>T	ENST00000375371.3	-	6	1741	c.1720G>A	c.(1720-1722)Gcc>Acc	p.A574T		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	574			A -> T (in dbSNP:rs6662276).		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)	AAGCCCAGGGCGGCCAGCAGG	0.612													C|||	456	0.0910543	0.0575	0.0274	5008	,	,		18237	0.1141		0.0557	False		,,,				2504	0.1943				p.A574T		Atlas-SNP	.											TAS1R2,NS,carcinoma,+1,1	TAS1R2	134	1	0			c.G1720A						PASS	.	C	THR/ALA	292,4114	159.2+/-191.8	13,266,1924	49.0	51.0	50.0		1720	-2.4	0.0	1	dbSNP_116	50	398,8202	125.6+/-184.2	14,370,3916	yes	missense	TAS1R2	NM_152232.2	58	27,636,5840	TT,TC,CC		4.6279,6.6273,5.3052	benign	574/840	19166893	690,12316	2203	4300	6503	SO:0001583	missense	80834	exon6			CCAGGGCGGCCAG		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.1720G>A	1.37:g.19166893C>T	ENSP00000364520:p.Ala574Thr	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	150	0.06868131868131869	38	0.07723577235772358	8	0.022099447513812154	63	0.11013986013986014	41	0.05408970976253298	C	0.507	-0.868442	0.02590	0.066273	0.046279	ENSG00000179002	ENST00000375371	D	0.89050	-2.46	5.48	-2.4	0.06583	GPCR, family 3, C-terminal (1);	1.393920	0.04634	N	0.404173	T	0.03827	0.0108	N	0.08118	0	0.80722	P	0.0	B	0.24618	0.107	B	0.12156	0.007	T	0.42275	-0.9461	9	0.14656	T	0.56	.	0.2745	0.00236	0.2947:0.1946:0.1462:0.3645	rs6662276;rs6662276	574	Q8TE23	TS1R2_HUMAN	T	574	ENSP00000364520:A574T	ENSP00000364520:A574T	A	-	1	0	TAS1R2	19039480	0.000000	0.05858	0.003000	0.11579	0.012000	0.07955	-0.804000	0.04535	-0.254000	0.09500	-0.878000	0.02970	GCC	C|0.937;T|0.063	0.063	strong		0.612	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
SH3BP4	23677	hgsc.bcm.edu	37	2	235950284	235950284	+	Silent	SNP	A	A	C	rs3731648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:235950284A>C	ENST00000409212.1	+	4	1378	c.871A>C	c.(871-873)Agg>Cgg	p.R291R	SH3BP4_ENST00000392011.2_Silent_p.R291R|SH3BP4_ENST00000344528.4_Silent_p.R291R			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	291					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)	p.R291R(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		GCTAAACCACAGGAAGCTGGC	0.582													C|||	1494	0.298323	0.2867	0.3256	5008	,	,		17048	0.4077		0.0915	False		,,,				2504	0.3947				p.R291R		Atlas-SNP	.											SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	1	Substitution - coding silent(1)	stomach(1)	c.A871C						PASS	.	C		1115,3287		134,847,1220	40.0	50.0	46.0		871	4.6	1.0	2	dbSNP_107	46	888,7712		47,794,3459	no	coding-synonymous	SH3BP4	NM_014521.2		181,1641,4679	CC,CA,AA		10.3256,25.3294,15.4053		291/964	235950284	2003,10999	2201	4300	6501	SO:0001819	synonymous_variant	23677	exon4			AACCACAGGAAGC	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.871A>C	2.37:g.235950284A>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	CCDS2513.1																																																																																			A|0.797;C|0.203	0.203	strong		0.582	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
CCDC15	80071	hgsc.bcm.edu	37	11	124908352	124908352	+	Missense_Mutation	SNP	T	T	C	rs7107487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124908352T>C	ENST00000344762.5	+	14	2696	c.2437T>C	c.(2437-2439)Tgt>Cgt	p.C813R	CCDC15_ENST00000530061.1_3'UTR|CCDC15_ENST00000529051.1_Missense_Mutation_p.C813R	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	813			C -> R (in dbSNP:rs7107487).			centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		AGAGCAAGAATGTTATGCTGC	0.308													C|||	1149	0.229433	0.3616	0.1398	5008	,	,		16654	0.1825		0.1481	False		,,,				2504	0.2464				p.C813R		Atlas-SNP	.											.	CCDC15	134	.	0			c.T2437C						PASS	.	C	ARG/CYS	1185,2417		202,781,818	34.0	30.0	32.0		2437	3.1	1.0	11	dbSNP_116	32	1268,6866		97,1074,2896	yes	missense	CCDC15	NM_025004.2	180	299,1855,3714	CC,CT,TT		15.5889,32.8984,20.9015	benign	813/952	124908352	2453,9283	1801	4067	5868	SO:0001583	missense	80071	exon14			CAAGAATGTTATG	BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.2437T>C	11.37:g.124908352T>C	ENSP00000341684:p.Cys813Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	112	29	0.258929	NM_025004	Q9H8U7	Missense_Mutation	SNP	ENST00000344762.5	37	CCDS44756.1	461	0.21108058608058608	181	0.3678861788617886	59	0.16298342541436464	106	0.1853146853146853	115	0.1517150395778364	C	0.627	-0.818673	0.02776	0.328984	0.155889	ENSG00000149548	ENST00000529051;ENST00000344762	T;T	0.20332	2.16;2.08	5.0	3.11	0.35812	.	.	.	.	.	T	0.00012	0.0000	N	0.00152	-1.975	0.29734	P	0.8376250000000001	B	0.02656	0.0	B	0.01281	0.0	T	0.46162	-0.9211	8	0.02654	T	1	-0.3039	5.8186	0.18514	0.1537:0.6807:0.0:0.1656	rs7107487;rs52832936;rs60393511;rs7107487	813	Q0P6D6	CCD15_HUMAN	R	813	ENSP00000435403:C813R;ENSP00000341684:C813R	ENSP00000341684:C813R	C	+	1	0	CCDC15	124413562	0.991000	0.36638	0.973000	0.42090	0.926000	0.56050	1.147000	0.31602	0.244000	0.21351	-0.349000	0.07799	TGT	T|0.779;C|0.221	0.221	strong		0.308	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
SLC17A1	6568	hgsc.bcm.edu	37	6	25813150	25813150	+	Missense_Mutation	SNP	G	G	A	rs1165196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:25813150G>A	ENST00000244527.4	-	8	921	c.806C>T	c.(805-807)aCt>aTt	p.T269I	SLC17A1_ENST00000468082.1_Intron|SLC17A1_ENST00000427328.1_Intron|SLC17A1_ENST00000476801.1_Missense_Mutation_p.T269I	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	269			T -> I (in dbSNP:rs1165196). {ECO:0000269|PubMed:7826357, ECO:0000269|PubMed:8288239}.		ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						AAAACTACCAGTGGAAATAGC	0.368													A|||	3601	0.71905	0.9213	0.7003	5008	,	,		22291	0.8165		0.5646	False		,,,				2504	0.5174				p.T269I		Atlas-SNP	.											.	SLC17A1	71	.	0			c.C806T	GRCh37	CM086146	SLC17A1	M	rs1165196	PASS	.	A	ILE/THR	3795,611	265.9+/-266.9	1637,521,45	77.0	77.0	77.0	http://www.ncbi.nlm.nih.gov/pubmed?term	806	3.7	0.0	6	dbSNP_87	77	4698,3902	545.1+/-384.7	1271,2156,873	yes	missense	SLC17A1	NM_005074.3	89	2908,2677,918	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	45.3721,13.8675,34.6994	benign	269/468	25813150	8493,4513	2203	4300	6503	SO:0001583	missense	6568	exon8			CTACCAGTGGAAA		CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"""Solute carriers"""	10929	protein-coding gene	gene with protein product		182308	"""solute carrier family 17 (sodium phosphate), member 1"""	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.806C>T	6.37:g.25813150G>A	ENSP00000244527:p.Thr269Ile	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Missense_Mutation	SNP	ENST00000244527.4	37	CCDS4565.1	1617	0.7403846153846154	454	0.9227642276422764	250	0.6906077348066298	480	0.8391608391608392	433	0.5712401055408971	A	4.386	0.071267	0.08436	0.861325	0.546279	ENSG00000124568	ENST00000244527;ENST00000476801	T;T	0.55588	0.51;0.51	3.67	3.67	0.42095	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	2.163280	0.02119	N	0.055446	T	0.08358	0.0208	N	0.01140	-0.99	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.21793	-1.0235	9	0.15952	T	0.53	.	5.9435	0.19205	0.8822:0.0:0.1178:0.0	rs1165196;rs1747529;rs17342465;rs60458507;rs1165196	269	Q14916	NPT1_HUMAN	I	269	ENSP00000244527:T269I;ENSP00000420614:T269I	ENSP00000244527:T269I	T	-	2	0	SLC17A1	25921129	0.003000	0.15002	0.001000	0.08648	0.022000	0.10575	1.880000	0.39628	0.777000	0.33496	-0.254000	0.11334	ACT	G|0.298;T|0.002	.	strong		0.368	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2		
C8A	731	hgsc.bcm.edu	37	1	57383315	57383315	+	Missense_Mutation	SNP	G	G	C	rs1342440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57383315G>C	ENST00000361249.3	+	11	1777	c.1681G>C	c.(1681-1683)Gag>Cag	p.E561Q		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	561	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.		E -> Q (in dbSNP:rs1342440).		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						AAGGAGAAGAGAGTGTGACAA	0.582													G|||	683	0.136382	0.2617	0.1326	5008	,	,		18028	0.0407		0.0477	False		,,,				2504	0.1595				p.E561Q		Atlas-SNP	.											.	C8A	103	.	0			c.G1681C						PASS	.	G	GLN/GLU	903,3503	347.7+/-309.6	90,723,1390	68.0	67.0	67.0		1681	2.7	1.0	1	dbSNP_88	67	407,8193	128.2+/-186.4	8,391,3901	yes	missense	C8A	NM_000562.2	29	98,1114,5291	CC,CG,GG		4.7326,20.4948,10.0723	benign	561/585	57383315	1310,11696	2203	4300	6503	SO:0001583	missense	731	exon11			AGAAGAGAGTGTG	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"""Complement system"""	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1681G>C	1.37:g.57383315G>C	ENSP00000354458:p.Glu561Gln	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	277	145	0.523466	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	226	0.10347985347985347	120	0.24390243902439024	39	0.10773480662983426	34	0.05944055944055944	33	0.04353562005277045	G	10.21	1.287220	0.23478	0.204948	0.047326	ENSG00000157131	ENST00000361249	T	0.53640	0.61	4.82	2.73	0.32206	.	0.664639	0.16161	N	0.226732	T	0.00012	0.0000	N	0.04335	-0.225	0.43942	P	0.0033919999999999506	B	0.22003	0.063	B	0.22152	0.038	T	0.27905	-1.0060	9	0.18276	T	0.48	-17.6438	8.0533	0.30591	0.0973:0.3433:0.5594:0.0	rs1342440;rs1628730;rs52814302;rs60984479;rs1342440	561	P07357	CO8A_HUMAN	Q	561	ENSP00000354458:E561Q	ENSP00000354458:E561Q	E	+	1	0	C8A	57155903	0.989000	0.36119	1.000000	0.80357	0.865000	0.49528	1.024000	0.30077	1.199000	0.43173	0.563000	0.77884	GAG	G|0.901;C|0.099	0.099	strong		0.582	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
FRAS1	80144	hgsc.bcm.edu	37	4	79351542	79351542	+	Missense_Mutation	SNP	C	C	T	rs34271211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79351542C>T	ENST00000325942.6	+	37	5380	c.4940C>T	c.(4939-4941)aCa>aTa	p.T1647I	FRAS1_ENST00000264895.6_Missense_Mutation_p.T1647I	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1647					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						CTTAAGCATACAGCTGAGTTC	0.498													C|||	41	0.0081869	0.031	0.0	5008	,	,		19131	0.0		0.0	False		,,,				2504	0.0				p.T1647I		Atlas-SNP	.											.	FRAS1	779	.	0			c.C4940T						PASS	.	C	ILE/THR,ILE/THR	123,3785		2,119,1833	59.0	61.0	61.0		4940,4940	4.0	0.0	4	dbSNP_126	61	0,8324		0,0,4162	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	89,89	2,119,5995	TT,TC,CC		0.0,3.1474,1.0056	possibly-damaging,possibly-damaging	1647/1977,1647/4013	79351542	123,12109	1954	4162	6116	SO:0001583	missense	80144	exon37			AGCATACAGCTGA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.4940C>T	4.37:g.79351542C>T	ENSP00000326330:p.Thr1647Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	C	13.88	2.368547	0.42003	0.031474	0.0	ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000545316	T;T	0.26810	1.71;1.71	5.68	3.98	0.46160	.	0.367128	0.29307	N	0.012540	T	0.04272	0.0118	L	0.57536	1.79	0.09310	N	1	P;P	0.47302	0.565;0.893	B;B	0.39876	0.205;0.312	T	0.10613	-1.0622	10	0.20046	T	0.44	.	2.3609	0.04307	0.2218:0.458:0.1775:0.1427	rs34271211	1647;1647	E9PHH6;A2RRR8	.;.	I	1647;1647;67	ENSP00000326330:T1647I;ENSP00000264895:T1647I	ENSP00000264895:T1647I	T	+	2	0	FRAS1	79570566	0.019000	0.18553	0.003000	0.11579	0.001000	0.01503	2.837000	0.48191	0.883000	0.36040	-0.229000	0.12294	ACA	C|0.992;T|0.008	0.008	strong		0.498	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
LRFN3	79414	hgsc.bcm.edu	37	19	36430798	36430798	+	Silent	SNP	A	A	G	rs1057265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	24	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	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	
CAAP1	79886	hgsc.bcm.edu	37	9	26861106	26861106	+	Missense_Mutation	SNP	C	C	T	rs12342214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:26861106C>T	ENST00000333916.5	-	5	785	c.697G>A	c.(697-699)Gtg>Atg	p.V233M	CAAP1_ENST00000495958.1_5'UTR|CAAP1_ENST00000520187.1_Intron|CAAP1_ENST00000535437.1_Missense_Mutation_p.V88M	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	233			V -> M (in dbSNP:rs12342214).		apoptotic process (GO:0006915)												TTCTCTCTCACGGATGAAGCA	0.318													T|||	257	0.0513179	0.1868	0.013	5008	,	,		15800	0.0		0.001	False		,,,				2504	0.0				p.V233M		Atlas-SNP	.											.	.	.	.	0			c.G697A						PASS	.	T	MET/VAL,MET/VAL	602,3804	769.0+/-413.6	30,542,1631	95.0	104.0	101.0		262,697	0.6	0.4	9	dbSNP_120	101	3,8597	818.4+/-406.9	0,3,4297	yes	missense,missense	C9orf82	NM_001167575.1,NM_024828.3	21,21	30,545,5928	TT,TC,CC		0.0349,13.6632,4.6517	benign,benign	88/217,233/362	26861106	605,12401	2203	4300	6503	SO:0001583	missense	79886	exon5			CTCTCACGGATGA	BC014658	CCDS6516.1	9p21.2	2012-04-20	2012-04-20	2012-04-20	ENSG00000120159	ENSG00000120159			25834	protein-coding gene	gene with protein product	"""conserved anti-apoptotic protein"""		"""chromosome 9 open reading frame 82"""	C9orf82		21980415	Standard	NM_024828		Approved	FLJ13657, CAAP	uc003zqc.3	Q9H8G2	OTTHUMG00000019706	ENST00000333916.5:c.697G>A	9.37:g.26861106C>T	ENSP00000369431:p.Val233Met	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	170	72	0.423529	NM_024828	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Missense_Mutation	SNP	ENST00000333916.5	37	CCDS6516.1	94	0.04304029304029304	89	0.18089430894308944	5	0.013812154696132596	0	0.0	0	0.0	T	11.16	1.556553	0.27827	0.136632	3.49E-4	ENSG00000120159	ENST00000333916;ENST00000535437	T;T	0.44881	0.91;0.92	5.71	0.612	0.17591	.	0.254994	0.31381	N	0.007741	T	0.00039	0.0001	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.06405	0.002	T	0.18272	-1.0342	9	0.33940	T	0.23	0.0412	1.6248	0.02721	0.1489:0.2564:0.3337:0.261	rs12342214;rs52805377;rs12342214	233	Q9H8G2	CI082_HUMAN	M	233;88	ENSP00000369431:V233M;ENSP00000444885:V88M	ENSP00000369431:V233M	V	-	1	0	C9orf82	26851106	0.831000	0.29352	0.434000	0.26772	0.937000	0.57800	-0.048000	0.11944	-0.404000	0.07610	-1.904000	0.00526	GTG	C|0.939;T|0.061	0.061	strong		0.318	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051954.1	NM_024828	
TXNDC5	81567	hgsc.bcm.edu	37	6	7883386	7883386	+	Silent	SNP	G	G	A	rs9502656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7883386G>A	ENST00000379757.4	-	10	1327	c.1290C>T	c.(1288-1290)gaC>gaT	p.D430D	BLOC1S5-TXNDC5_ENST00000439343.2_3'UTR|TXNDC5_ENST00000539054.1_Silent_p.D358D|TXNDC5_ENST00000473453.1_Silent_p.D322D	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	430					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)					CCTAAAGTTCGTCTTTCGCTT	0.557													G|||	375	0.0748802	0.2466	0.0331	5008	,	,		17755	0.0		0.0209	False		,,,				2504	0.0051				p.D430D	Ovarian(119;1430 1625 3928 26125 34589)	Atlas-SNP	.											.	TXNDC5	33	.	0			c.C1290T						PASS	.	G	,	895,3511	345.9+/-308.8	94,707,1402	159.0	117.0	131.0		966,1290	-10.3	0.0	6	dbSNP_119	131	184,8416	82.9+/-145.4	4,176,4120	no	coding-synonymous,coding-synonymous	TXNDC5	NM_001145549.2,NM_030810.3	,	98,883,5522	AA,AG,GG		2.1395,20.3132,8.2962	,	322/325,430/433	7883386	1079,11927	2203	4300	6503	SO:0001819	synonymous_variant	81567	exon10			AAGTTCGTCTTTC	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.1290C>T	6.37:g.7883386G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_030810	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Silent	SNP	ENST00000379757.4	37	CCDS4505.1																																																																																			G|0.920;A|0.080	0.080	strong		0.557	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810	
PGAM2	5224	hgsc.bcm.edu	37	7	44104805	44104805	+	Silent	SNP	C	C	T	rs112828964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44104805C>T	ENST00000297283.3	-	1	381	c.324G>A	c.(322-324)ggG>ggA	p.G108G	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	108					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						CCTGCTCCTCCCCGTGCTTGG	0.632													C|||	159	0.0317492	0.1188	0.0029	5008	,	,		16305	0.0		0.0	False		,,,				2504	0.0				p.G108G		Atlas-SNP	.											.	PGAM2	20	.	0			c.G324A						PASS	.	C		422,3984	206.5+/-228.1	19,384,1800	62.0	61.0	62.0		324	-4.1	0.9	7	dbSNP_132	62	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PGAM2	NM_000290.3		19,386,6098	TT,TC,CC		0.0233,9.5778,3.26		108/254	44104805	424,12582	2203	4300	6503	SO:0001819	synonymous_variant	5224	exon1			CTCCTCCCCGTGC		CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.324G>A	7.37:g.44104805C>T		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	280	131	0.467857	NM_000290		Silent	SNP	ENST00000297283.3	37	CCDS34624.1																																																																																			C|0.968;T|0.032	0.032	strong		0.632	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1		
PUM2	23369	hgsc.bcm.edu	37	2	20508156	20508156	+	Silent	SNP	C	C	T	rs34057700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20508156C>T	ENST00000361078.2	-	5	730	c.708G>A	c.(706-708)caG>caA	p.Q236Q	PUM2_ENST00000403432.1_Silent_p.Q236Q|PUM2_ENST00000536417.1_Silent_p.Q180Q|PUM2_ENST00000420234.1_5'Flank|PUM2_ENST00000319801.5_Silent_p.Q236Q|PUM2_ENST00000338086.5_Silent_p.Q236Q			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	236	Interaction with SNAPIN.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATAGTCAAACTGTAAGGATT	0.408													C|||	145	0.0289537	0.1021	0.013	5008	,	,		17612	0.0		0.001	False		,,,				2504	0.0				p.Q236Q		Atlas-SNP	.											.	PUM2	91	.	0			c.G708A						PASS	.	C		404,4002	200.8+/-224.0	18,368,1817	83.0	81.0	81.0		708	5.2	1.0	2	dbSNP_126	81	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PUM2	NM_015317.1		18,370,6115	TT,TC,CC		0.0233,9.1693,3.1216		236/1065	20508156	406,12600	2203	4300	6503	SO:0001819	synonymous_variant	23369	exon5			GTCAAACTGTAAG	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"""pumilio (Drosphila) homolog 2"", ""pumilio homolog 2 (Drosophila)"""			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.708G>A	2.37:g.20508156C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	180	85	0.472222	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Silent	SNP	ENST00000361078.2	37																																																																																				C|0.974;T|0.026	0.026	strong		0.408	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317	
FAT1	2195	hgsc.bcm.edu	37	4	187542432	187542432	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187542432A>G	ENST00000441802.2	-	10	5517	c.5308T>C	c.(5308-5310)Tat>Cat	p.Y1770H		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1770	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						AGTCCTGTATATTCTGCCTGC	0.443										HNSCC(5;0.00058)																											p.Y1770H	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T5308C						PASS	.						106.0	99.0	101.0					4																	187542432		1947	4150	6097	SO:0001583	missense	2195	exon10			CTGTATATTCTGC	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.5308T>C	4.37:g.187542432A>G	ENSP00000406229:p.Tyr1770His	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	264	125	0.473485	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.471201	0.43942	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.66638	-0.22	5.5	5.5	0.81552	Cadherin (2);Cadherin-like (1);	0.055265	0.85682	D	0.000000	D	0.85517	0.5715	H	0.94542	3.55	0.58432	D	0.999999	D	0.67145	0.996	D	0.63381	0.914	D	0.89615	0.3844	10	0.72032	D	0.01	.	15.7759	0.78214	1.0:0.0:0.0:0.0	.	1770	Q14517	FAT1_HUMAN	H	1770;1772	ENSP00000406229:Y1770H	ENSP00000260147:Y1772H	Y	-	1	0	FAT1	187779426	1.000000	0.71417	0.279000	0.24732	0.057000	0.15508	9.139000	0.94554	2.308000	0.77769	0.533000	0.62120	TAT	.	.	none		0.443	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
RNF207	388591	hgsc.bcm.edu	37	1	6278425	6278425	+	Missense_Mutation	SNP	G	G	A	rs61746089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6278425G>A	ENST00000377939.4	+	17	1856	c.1729G>A	c.(1729-1731)Gcc>Acc	p.A577T	RNF207_ENST00000483336.1_3'UTR|RNF207_ENST00000377948.2_3'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	577						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		CGCGGCCTCAGCCAGGTAAAG	0.577													G|||	29	0.00579073	0.0204	0.0029	5008	,	,		20029	0.0		0.0	False		,,,				2504	0.0				p.A577T		Atlas-SNP	.											.	RNF207	45	.	0			c.G1729A						PASS	.	G	THR/ALA	79,4175		0,79,2048	59.0	70.0	66.0		1729	-1.1	0.7	1	dbSNP_129	66	0,8490		0,0,4245	yes	missense	RNF207	NM_207396.2	58	0,79,6293	AA,AG,GG		0.0,1.8571,0.6199	benign	577/635	6278425	79,12665	2127	4245	6372	SO:0001583	missense	388591	exon17			GCCTCAGCCAGGT	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1729G>A	1.37:g.6278425G>A	ENSP00000367173:p.Ala577Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Missense_Mutation	SNP	ENST00000377939.4	37	CCDS59.2	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	G	12.17	1.856674	0.32791	0.018571	0.0	ENSG00000158286	ENST00000377939	T	0.17691	2.26	5.1	-1.12	0.09808	.	1.899990	0.03308	N	0.190106	T	0.02807	0.0084	N	0.16478	0.41	0.53005	D	0.999968	B	0.06786	0.001	B	0.08055	0.003	T	0.39502	-0.9611	10	0.13470	T	0.59	-18.452	4.6334	0.12513	0.3114:0.3955:0.293:0.0	rs61746089	577	Q6ZRF8	RN207_HUMAN	T	577	ENSP00000367173:A577T	ENSP00000367173:A577T	A	+	1	0	RNF207	6201012	0.008000	0.16893	0.657000	0.29651	0.042000	0.13812	-0.175000	0.09825	0.123000	0.18342	-0.222000	0.12452	GCC	G|0.991;A|0.009	0.009	strong		0.577	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
ANKRD36B	57730	hgsc.bcm.edu	37	2	98206012	98206012	+	RNA	SNP	G	G	A	rs185401750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98206012G>A	ENST00000443455.1	-	0	315							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		TCTCTTATTGGCGTCATAATA	0.522													.|||	73	0.0145767	0.0469	0.0043	5008	,	,		11591	0.006		0.001	False		,,,				2504	0.001				p.A46V		Atlas-SNP	.											.	.	.	.	0			c.C137T						PASS	.	G	VAL/ALA	41,1343		2,37,653	106.0	82.0	89.0		137	0.8	0.0	2		89	0,3182		0,0,1591	no	missense	ANKRD36B	NM_025190.3	64	2,37,2244	AA,AG,GG		0.0,2.9624,0.8979	benign	46/1354	98206012	41,4525	692	1591	2283			57730	exon1			TTATTGGCGTCAT	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98206012G>A		Somatic	292	1	0.00342466		WXS	Illumina HiSeq	Phase_I	259	124	0.478764	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				G|0.989;A|0.011	0.011	strong		0.522	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
PIP4K2B	8396	hgsc.bcm.edu	37	17	36926731	36926731	+	Silent	SNP	T	T	G	rs228289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36926731T>G	ENST00000269554.3	-	9	1608	c.1128A>C	c.(1126-1128)acA>acC	p.T376T		NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	376	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						CTTTCTTCTTTGTATCGTATG	0.542													C|||	2013	0.401957	0.5068	0.3559	5008	,	,		17056	0.3591		0.2306	False		,,,				2504	0.5133				p.T376T		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.A1128C						PASS	.	C		1964,2442		433,1098,672	240.0	213.0	222.0		1128	-4.9	0.1	17	dbSNP_79	222	2018,6582		250,1518,2532	no	coding-synonymous	PIP4K2B	NM_003559.4		683,2616,3204	GG,GT,TT		23.4651,44.5756,30.6166		376/417	36926731	3982,9024	2203	4300	6503	SO:0001819	synonymous_variant	8396	exon9			CTTCTTTGTATCG	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"""phosphatidylinositol-4-phosphate 5-kinase, type II, beta"""	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.1128A>C	17.37:g.36926731T>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	184	96	0.521739	NM_003559	Q5U0E8|Q8TBP2	Silent	SNP	ENST00000269554.3	37	CCDS11329.1																																																																																			T|0.663;G|0.337	0.337	strong		0.542	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559	
SEMA3E	9723	hgsc.bcm.edu	37	7	83035289	83035289	+	Silent	SNP	A	A	G	rs28505908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:83035289A>G	ENST00000307792.3	-	8	1367	c.900T>C	c.(898-900)aaT>aaC	p.N300N	SEMA3E_ENST00000427262.1_Silent_p.N240N	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	300	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TGTCAATTCCATTCATTCCTG	0.353													A|||	60	0.0119808	0.0454	0.0	5008	,	,		18888	0.0		0.0	False		,,,				2504	0.0				p.N300N		Atlas-SNP	.											.	SEMA3E	125	.	0			c.T900C						PASS	.	A	,	154,4252	106.0+/-144.5	1,152,2050	159.0	145.0	150.0		720,900	3.3	1.0	7	dbSNP_125	150	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	SEMA3E	NM_001178129.1,NM_012431.2	,	1,154,6348	GG,GA,AA		0.0233,3.4952,1.1994	,	240/716,300/776	83035289	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	9723	exon8			AATTCCATTCATT	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.900T>C	7.37:g.83035289A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	37	CCDS34674.1																																																																																			A|0.987;G|0.013	0.013	strong		0.353	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
OR2L3	391192	hgsc.bcm.edu	37	1	248224754	248224754	+	Silent	SNP	T	T	C	rs55893924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248224754T>C	ENST00000359959.3	+	1	771	c.771T>C	c.(769-771)acT>acC	p.T257T	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	257						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(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	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;0.0278)			TTGTCTACACTTATCTACGTC	0.488													N|||	1555	0.310503	0.7398	0.1326	5008	,	,		20515	0.254		0.1481	False		,,,				2504	0.0818				p.T257T		Atlas-SNP	.											.	OR2L3	97	.	0			c.T771C						PASS	.	C	,	2706,1700	500.3+/-364.7	826,1054,323	121.0	115.0	117.0		771,	-4.0	0.0	1	dbSNP_129	117	1145,7449	760.4+/-407.6	69,1007,3221	no	coding-synonymous,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	,	895,2061,3544	CC,CT,TT		13.3232,38.5837,29.6231	,	257/313,	248224754	3851,9149	2203	4297	6500	SO:0001819	synonymous_variant	391192	exon1			CTACACTTATCTA	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"""GPCR / Class A : Olfactory receptors"""	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.771T>C	1.37:g.248224754T>C		Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	266	107	0.402256	NM_001004687	B9EH44	Silent	SNP	ENST00000359959.3	37	CCDS31104.1																																																																																			.	.	weak		0.488	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
TPSB2	64499	hgsc.bcm.edu	37	16	1279623	1279623	+	RNA	SNP	G	G	A	rs72633259	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1279623G>A	ENST00000339687.6	-	0	199				TPSB2_ENST00000430512.2_RNA|TPSB2_ENST00000445910.1_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				GGGAGCCCCCGCAGAAGTGCA	0.682													G|||	1997	0.398762	0.3192	0.2579	5008	,	,		10589	0.6766		0.333	False		,,,				2504	0.3875				p.C59C		Atlas-SNP	.											.	TPSB2	8	.	0			c.C177T						PASS	.	G		1338,2956		285,768,1094	32.0	42.0	39.0		177	-6.4	0.0	16	dbSNP_130	39	2505,6089		372,1761,2164	no	coding-synonymous	TPSB2	NM_024164.5		657,2529,3258	AA,AG,GG		29.1482,31.1598,29.8184		59/276	1279623	3843,9045	2147	4297	6444			64499	exon3			GCCCCCGCAGAAG	AF099143		16p13.3	2009-11-20	2009-11-18		ENSG00000197253	ENSG00000197253			14120	protein-coding gene	gene with protein product	"""tryptase beta II"", ""tryptase beta III"""	191081	"""tryptase beta 2"""			19748655	Standard	NM_024164		Approved		uc002cky.3	P20231	OTTHUMG00000155926		16.37:g.1279623G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	134	53	0.395522	NM_024164	D2E6S0|D2E6S2|O95827|Q15664|Q9UQI6|Q9UQI7	Silent	SNP	ENST00000339687.6	37																																																																																				G|0.650;A|0.350	0.350	strong		0.682	TPSB2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000342364.1	NM_024164	
HYI	81888	hgsc.bcm.edu	37	1	43917098	43917098	+	Missense_Mutation	SNP	C	C	G	rs79439514	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43917098C>G	ENST00000372425.4	-	7	938	c.743G>C	c.(742-744)tGt>tCt	p.C248S	SZT2_ENST00000372442.1_3'UTR|HYI_ENST00000372432.1_Splice_Site|HYI_ENST00000583037.1_Missense_Mutation_p.C175S|HYI_ENST00000372426.1_Missense_Mutation_p.C200S|HYI_ENST00000486909.1_Missense_Mutation_p.C248S|HYI-AS1_ENST00000444386.1_RNA|SZT2-AS1_ENST00000396885.2_RNA|HYI_ENST00000372434.1_Missense_Mutation_p.C273S|SZT2_ENST00000562955.1_3'UTR			Q5T013	HYI_HUMAN	hydroxypyruvate isomerase (putative)	248							hydroxypyruvate isomerase activity (GO:0008903)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	6	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTGATACTCACAGCCCACGAA	0.627													C|||	146	0.0291534	0.1051	0.0086	5008	,	,		18840	0.0		0.001	False		,,,				2504	0.0				p.C248S		Atlas-SNP	.											.	HYI	23	.	0			c.G743C						PASS	.	C	SER/CYS,,	377,4029	189.5+/-215.6	21,335,1847	61.0	66.0	64.0		743,,	5.5	1.0	1	dbSNP_131	64	2,8598	2.2+/-6.3	0,2,4298	yes	missense,utr-3,splice-5	SZT2,HYI	NM_001190880.2,NM_015284.3,NM_031207.5	112,,	21,337,6145	GG,GC,CC		0.0233,8.5565,2.914	probably-damaging,,	248/278,,	43917098	379,12627	2203	4300	6503	SO:0001583	missense	81888	exon7			TACTCACAGCCCA		CCDS488.1, CCDS488.2, CCDS53309.1, CCDS72771.1	1p34.2	2010-06-24	2010-06-24		ENSG00000178922	ENSG00000178922	5.3.1.22		26948	protein-coding gene	gene with protein product			"""hydroxypyruvate isomerase homolog (E. coli)"""			10561547	Standard	NM_031207		Approved	HT036	uc001cjo.3	Q5T013	OTTHUMG00000007502	ENST00000372425.4:c.743G>C	1.37:g.43917098C>G	ENSP00000361502:p.Cys248Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_001190880	D3DPX4|D3DPX5|Q5Q9A2|Q7Z778|Q96S83|Q9BZR3|Q9BZR4	Missense_Mutation	SNP	ENST00000372425.4	37	CCDS53309.1	56|56	0.02564102564102564|0.02564102564102564	54|54	0.10975609756097561|0.10975609756097561	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	20.9|20.9	4.070255|4.070255	0.76301|0.76301	0.085565|0.085565	2.33E-4|2.33E-4	ENSG00000178922|ENSG00000178922	ENST00000372425;ENST00000372434;ENST00000372430;ENST00000372426;ENST00000486909|ENST00000470662	T;T;T|.	0.43294|.	0.95;0.95;0.95|.	5.52|5.52	5.52|5.52	0.82312|0.82312	Xylose isomerase-like, TIM barrel domain (2);|.	.|.	.|.	.|.	.|.	T|T	0.17492|0.17492	0.0420|0.0420	M|M	0.93638|0.93638	3.44|3.44	0.09310|0.09310	P|P	0.9999999792184|0.9999999792184	D|.	0.54601|.	0.967|.	P|.	0.56865|.	0.808|.	T|T	0.69239|0.69239	-0.5197|-0.5197	8|4	0.87932|.	D|.	0|.	.|.	19.8124|19.8124	0.96553|0.96553	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	248|.	Q5T013|.	HYI_HUMAN|.	S|L	248;200;175;200;248|157	ENSP00000361502:C248S;ENSP00000361503:C200S;ENSP00000428399:C248S|.	ENSP00000361502:C248S|.	C|V	-|-	2|1	0|0	HYI|HYI	43689685|43689685	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.785000|0.785000	0.44390|0.44390	7.729000|7.729000	0.84864|0.84864	2.764000|2.764000	0.94973|0.94973	0.563000|0.563000	0.77884|0.77884	TGT|GTG	C|0.974;G|0.026	0.026	strong		0.627	HYI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031207	
SMARCA2	6595	hgsc.bcm.edu	37	9	2039776	2039776	+	Silent	SNP	A	A	G	rs376509101|rs13296987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2039776A>G	ENST00000382203.1	+	4	875	c.666A>G	c.(664-666)caA>caG	p.Q222Q	RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000349721.2_Silent_p.Q222Q|SMARCA2_ENST00000491574.1_3'UTR|SMARCA2_ENST00000357248.2_Silent_p.Q222Q|SMARCA2_ENST00000382194.1_Silent_p.Q222Q			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	222	Poly-Gln.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|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)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		agcagcagcaacagcagcagc	0.637													A|||	80	0.0159744	0.0333	0.0029	5008	,	,		13171	0.001		0.004	False		,,,				2504	0.0297				p.Q222Q		Atlas-SNP	.											SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	0			c.A666G						scavenged	.						12.0	14.0	13.0					9																	2039776		2197	4275	6472	SO:0001819	synonymous_variant	6595	exon4			GCAGCAACAGCAG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.666A>G	9.37:g.2039776A>G		Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			A|0.750;G|0.250	0.250	strong		0.637	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
KMT2B	9757	hgsc.bcm.edu	37	19	36224705	36224705	+	Missense_Mutation	SNP	A	A	G	rs231591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36224705A>G	ENST00000222270.7	+	30	7091	c.7091A>G	c.(7090-7092)gAt>gGt	p.D2364G	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.D2364G	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2364			D -> G (in dbSNP:rs231591).		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)										CTTCCGGAAGATGGTCCTCCC	0.637													G|||	3107	0.620407	0.848	0.428	5008	,	,		16478	0.505		0.4811	False		,,,				2504	0.7117				p.D2364G		Atlas-SNP	.											.	MLL4	229	.	0			c.A7091G						PASS	.	G	GLY/ASP	3099,773		1233,633,70	60.0	66.0	64.0		7091	1.7	0.3	19	dbSNP_79	64	3932,4336		924,2084,1126	yes	missense	MLL4	NM_014727.1	94	2157,2717,1196	GG,GA,AA		47.5568,19.9638,42.084	benign	2364/2716	36224705	7031,5109	1936	4134	6070	SO:0001583	missense	8085	exon30			CGGAAGATGGTCC	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.7091A>G	19.37:g.36224705A>G	ENSP00000222270:p.Asp2364Gly	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	1231	0.5636446886446886	402	0.8170731707317073	164	0.4530386740331492	298	0.5209790209790209	367	0.4841688654353562	G	0.154	-1.088329	0.01873	0.800362	0.475568	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.82711	-1.64;-1.64	5.24	1.66	0.24008	.	0.496643	0.17023	N	0.190057	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	0.39522	-0.9610	9	0.09338	T	0.73	.	3.7383	0.08520	0.0871:0.3105:0.4424:0.16	rs231591;rs661098;rs58885664;rs231591	2364	Q9UMN6	MLL4_HUMAN	G	2364	ENSP00000222270:D2364G;ENSP00000398837:D2364G	ENSP00000222270:D2364G	D	+	2	0	AD000671.1	40916545	0.826000	0.29277	0.293000	0.24932	0.148000	0.21650	0.097000	0.15168	0.219000	0.20840	-0.215000	0.12644	GAT	A|0.441;G|0.559	0.559	strong		0.637	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
BCLAF1	9774	hgsc.bcm.edu	37	6	136589425	136589425	+	Missense_Mutation	SNP	G	G	T	rs77081633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:136589425G>T	ENST00000531224.1	-	10	2524	c.2272C>A	c.(2272-2274)Cct>Act	p.P758T	BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000392348.2_Missense_Mutation_p.P756T|BCLAF1_ENST00000530767.1_Missense_Mutation_p.P585T|BCLAF1_ENST00000527759.1_Missense_Mutation_p.P756T|BCLAF1_ENST00000031135.9_5'UTR|BCLAF1_ENST00000527536.1_Missense_Mutation_p.P758T|BCLAF1_ENST00000353331.4_Missense_Mutation_p.P756T	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	758	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)		GGAGAAGAAGGTGATGCTGAA	0.343													G|||	12	0.00239617	0.0	0.0014	5008	,	,		20171	0.0		0.0099	False		,,,				2504	0.001				p.P758T	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.C2272A						PASS	.						134.0	118.0	123.0					6																	136589425		2203	4300	6503	SO:0001583	missense	9774	exon10			AAGAAGGTGATGC	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.2272C>A	6.37:g.136589425G>T	ENSP00000435210:p.Pro758Thr	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	263	48	0.18251	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	44	0.020146520146520148	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	37	0.048812664907651716	G	8.714	0.912737	0.17907	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348	T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22	4.87	3.74	0.42951	.	0.107851	0.41396	D	0.000887	T	0.04318	0.0119	N	0.14661	0.345	0.80722	D	1	B;P;B;B;B	0.36909	0.042;0.573;0.137;0.042;0.042	B;B;B;B;B	0.36666	0.031;0.23;0.031;0.031;0.031	T	0.14476	-1.0471	10	0.66056	D	0.02	-4.4078	6.3907	0.21585	0.2287:0.0:0.7713:0.0	.	756;86;756;758;585	Q9NYF8-2;B7Z8J9;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;.;BCLF1_HUMAN;.	T	758;756;758;585;756;756	ENSP00000435210:P758T;ENSP00000229446:P756T;ENSP00000435441:P758T;ENSP00000436501:P585T;ENSP00000434826:P756T;ENSP00000376159:P756T	ENSP00000229446:P756T	P	-	1	0	BCLAF1	136631118	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	3.955000	0.56715	2.431000	0.82371	0.484000	0.47621	CCT	G|0.976;T|0.024	0.024	strong		0.343	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	
TJP2	9414	hgsc.bcm.edu	37	9	71841018	71841018	+	Silent	SNP	A	A	G	rs17062695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:71841018A>G	ENST00000377245.4	+	7	1345	c.1137A>G	c.(1135-1137)ctA>ctG	p.L379L	TJP2_ENST00000539225.1_Silent_p.L410L|TJP2_ENST00000265384.7_Silent_p.L379L|TJP2_ENST00000535702.1_Silent_p.L383L|TJP2_ENST00000453658.2_Silent_p.L356L|TJP2_ENST00000348208.4_Silent_p.L379L	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	379	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						AACTACAGCTAGTGGTGTTGA	0.408													A|||	558	0.111422	0.1596	0.1066	5008	,	,		18995	0.1151		0.0616	False		,,,				2504	0.0971				p.L410L		Atlas-SNP	.											.	TJP2	120	.	0			c.A1230G						PASS	.	A	,,,,,	623,3783	272.8+/-271.0	39,545,1619	73.0	71.0	72.0		1068,1149,1230,1137,1137,1137	-12.1	0.2	9	dbSNP_123	72	522,8078	147.4+/-202.8	13,496,3791	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,,,,	52,1041,5410	GG,GA,AA		6.0698,14.1398,8.8036	,,,,,	356/1021,383/1158,410/1222,379/994,379/1191,379/1044	71841018	1145,11861	2203	4300	6503	SO:0001819	synonymous_variant	9414	exon7			ACAGCTAGTGGTG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1137A>G	9.37:g.71841018A>G		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	218	71	0.325688	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	37	CCDS6627.1																																																																																			A|0.907;G|0.093	0.093	strong		0.408	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
OR2T4	127074	hgsc.bcm.edu	37	1	248525780	248525780	+	Missense_Mutation	SNP	C	C	T	rs28698997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248525780C>T	ENST00000366475.1	+	1	898	c.898C>T	c.(898-900)Cct>Tct	p.P300S		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	300						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTACCACACCCCTGAGAAGGA	0.507													c|||	1474	0.294329	0.2405	0.2709	5008	,	,		20748	0.4276		0.1799	False		,,,				2504	0.364				p.P300S		Atlas-SNP	.											OR2T4,NS,carcinoma,-1,1	OR2T4	126	1	0			c.C898T						scavenged	.	C	SER/PRO	1063,3343	386.5+/-326.1	140,783,1280	143.0	142.0	142.0		898	0.7	1.0	1	dbSNP_125	142	1400,7200	271.1+/-289.3	113,1174,3013	no	missense	OR2T4	NM_001004696.1	74	253,1957,4293	TT,TC,CC		16.2791,24.1262,18.9374	benign	300/349	248525780	2463,10543	2203	4300	6503	SO:0001583	missense	127074	exon1			CACACCCCTGAGA	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.898C>T	1.37:g.248525780C>T	ENSP00000355431:p.Pro300Ser	Somatic	1097	3	0.00273473		WXS	Illumina HiSeq	Phase_I	1140	587	0.514912	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	605	0.27701465201465203	136	0.2764227642276423	84	0.23204419889502761	238	0.4160839160839161	147	0.19393139841688653	C	10.26	1.299887	0.23650	0.241262	0.162791	ENSG00000196944	ENST00000366475	T	0.00183	8.6	3.0	0.732	0.18283	GPCR, rhodopsin-like superfamily (1);	0.309688	0.23494	N	0.047579	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.31790	0.34	B	0.38683	0.279	T	0.03193	-1.1062	9	0.54805	T	0.06	.	4.7106	0.12870	0.0:0.4376:0.3575:0.2049	rs28698997	300	Q8NH00	OR2T4_HUMAN	S	300	ENSP00000355431:P300S	ENSP00000355431:P300S	P	+	1	0	OR2T4	246592403	0.000000	0.05858	0.953000	0.39169	0.941000	0.58515	-0.266000	0.08631	0.407000	0.25591	0.585000	0.79938	CCT	.	.	weak		0.507	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
DNAH10	196385	hgsc.bcm.edu	37	12	124288264	124288264	+	Missense_Mutation	SNP	G	G	A	rs77491573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124288264G>A	ENST00000409039.3	+	16	2342	c.2317G>A	c.(2317-2319)Gtc>Atc	p.V773I		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	773	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)		TGAGTCTCTCGTCCACCAGAT	0.398													G|||	563	0.11242	0.2958	0.0648	5008	,	,		18722	0.0446		0.0358	False		,,,				2504	0.047				p.V773I		Atlas-SNP	.											.	DNAH10	888	.	0			c.G2317A						PASS	.	G	ILE/VAL	1124,3282	400.8+/-331.7	147,830,1226	63.0	57.0	59.0		2317	4.1	0.7	12	dbSNP_131	59	340,8260	116.5+/-176.2	2,336,3962	yes	missense	DNAH10	NM_207437.3	29	149,1166,5188	AA,AG,GG		3.9535,25.5107,11.2563	benign	773/4472	124288264	1464,11542	2203	4300	6503	SO:0001583	missense	196385	exon16			TCTCTCGTCCACC	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.2317G>A	12.37:g.124288264G>A	ENSP00000386770:p.Val773Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	234	0.10714285714285714	140	0.2845528455284553	34	0.09392265193370165	32	0.055944055944055944	28	0.036939313984168866	G	10.29	1.310301	0.23821	0.255107	0.039535	ENSG00000197653	ENST00000409039	T	0.26957	1.7	5.0	4.11	0.48088	.	0.117816	0.32106	N	0.006580	T	0.00012	0.0000	M	0.80028	2.48	0.34062	P	0.342557	P;P;B	0.49358	0.923;0.874;0.122	P;B;B	0.45449	0.481;0.288;0.028	T	0.36939	-0.9727	9	0.21540	T	0.41	.	11.1297	0.48339	0.1507:0.0:0.8493:0.0	.	773;648;773	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	I	773	ENSP00000386770:V773I	ENSP00000386770:V773I	V	+	1	0	DNAH10	122854217	1.000000	0.71417	0.689000	0.30133	0.134000	0.20937	4.785000	0.62418	1.236000	0.43740	0.655000	0.94253	GTC	G|0.882;A|0.118	0.118	strong		0.398	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
UBA1	7317	hgsc.bcm.edu	37	X	47070468	47070468	+	Missense_Mutation	SNP	A	A	C	rs143044923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47070468A>C	ENST00000335972.6	+	20	2491	c.2308A>C	c.(2308-2310)Aac>Cac	p.N770H	UBA1_ENST00000377269.3_Missense_Mutation_p.N218H|UBA1_ENST00000377351.4_Missense_Mutation_p.N770H	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	770					cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GGCTGCTGCCAACCTGTTTGC	0.622													A|||	15	0.00397351	0.0106	0.0014	3775	,	,		14662	0.0		0.0	False		,,,				2504	0.0				p.N770H		Atlas-SNP	.											.	UBA1	89	.	0			c.A2308C						PASS	.	A	HIS/ASN,HIS/ASN	80,3755		1,63,15,1568,556	94.0	71.0	79.0		2308,2308	4.7	1.0	X	dbSNP_134	79	1,6727		0,1,0,2427,1872	yes	missense,missense	UBA1	NM_003334.3,NM_153280.2	68,68	1,64,15,3995,2428	CC,CA,C,AA,A		0.0149,2.086,0.7668	probably-damaging,probably-damaging	770/1059,770/1059	47070468	81,10482	2203	4300	6503	SO:0001583	missense	7317	exon20			GCTGCCAACCTGT	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"""Ubiquitin-like modifier activating enzymes"""	12469	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog (yeast)"", ""POC20 centriolar protein homolog (Chlamydomonas)"""	314370	"""ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)"", ""ubiquitin-activating enzyme E1"""	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.2308A>C	X.37:g.47070468A>C	ENSP00000338413:p.Asn770His	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	37	CCDS14275.1	5	0.0030138637733574444	2	0.004098360655737705	0	0.0	0	0.0	0	0.0	A	21.3	4.124412	0.77436	0.02086	1.49E-4	ENSG00000130985	ENST00000377351;ENST00000335972;ENST00000377269	T;T;T	0.74632	-0.86;-0.86;-0.86	4.66	4.66	0.58398	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.043287	0.85682	D	0.000000	T	0.82125	0.4969	H	0.95114	3.625	0.58432	D	0.999996	D;D	0.89917	0.999;1.0	D;D	0.91635	0.985;0.999	D	0.87031	0.2135	10	0.40728	T	0.16	-28.4035	12.3807	0.55305	1.0:0.0:0.0:0.0	.	218;770	Q5JRR6;P22314	.;UBA1_HUMAN	H	770;770;218	ENSP00000366568:N770H;ENSP00000338413:N770H;ENSP00000366481:N218H	ENSP00000338413:N770H	N	+	1	0	UBA1	46955412	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.197000	0.51028	1.837000	0.53436	0.430000	0.28490	AAC	A|0.994;C|0.006	0.006	strong		0.622	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	
UNC5B	219699	hgsc.bcm.edu	37	10	72972770	72972770	+	Missense_Mutation	SNP	G	G	T	rs61757568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72972770G>T	ENST00000335350.6	+	1	444	c.28G>T	c.(28-30)Gcg>Tcg	p.A10S	AL359832.1_ENST00000401185.1_RNA|UNC5B_ENST00000373192.4_Missense_Mutation_p.A10S	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	10					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						AGCTCGGGGCGCGCTGCTGCT	0.751													g|||	77	0.0153754	0.0537	0.0072	5008	,	,		10768	0.0		0.001	False		,,,				2504	0.0				p.A10S		Atlas-SNP	.											.	UNC5B	123	.	0			c.G28T						PASS	.	G	SER/ALA	40,4190		3,34,2078	6.0	8.0	7.0		28	4.3	1.0	10	dbSNP_129	7	2,8392		0,2,4195	no	missense	UNC5B	NM_170744.4	99	3,36,6273	TT,TG,GG		0.0238,0.9456,0.3327	possibly-damaging	10/946	72972770	42,12582	2115	4197	6312	SO:0001583	missense	219699	exon1			CGGGGCGCGCTGC	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.28G>T	10.37:g.72972770G>T	ENSP00000334329:p.Ala10Ser	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_001244889	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	g	10.46	1.355935	0.24598	0.009456	2.38E-4	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.48836	0.86;0.8	4.28	4.28	0.50868	.	0.385350	0.22088	U	0.064791	T	0.08358	0.0208	N	0.11560	0.145	0.29489	N	0.855747	P;P	0.50156	0.932;0.889	P;B	0.45167	0.472;0.281	T	0.01848	-1.1261	10	0.22109	T	0.4	-12.4358	12.2354	0.54512	0.0:0.0:1.0:0.0	rs61757568	10;10	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	S	10	ENSP00000334329:A10S;ENSP00000362288:A10S	ENSP00000334329:A10S	A	+	1	0	UNC5B	72642776	1.000000	0.71417	1.000000	0.80357	0.247000	0.25773	4.071000	0.57556	1.946000	0.56461	0.298000	0.19748	GCG	G|0.986;T|0.014	0.014	strong		0.751	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
POM121L12	285877	hgsc.bcm.edu	37	7	53103540	53103540	+	Missense_Mutation	SNP	C	C	G	rs78135827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:53103540C>G	ENST00000408890.4	+	1	192	c.176C>G	c.(175-177)aCt>aGt	p.T59S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	59										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						AGGTCCCTGACTCAGAGCCAT	0.706													C|||	168	0.0335463	0.1248	0.0043	5008	,	,		12626	0.0		0.0	False		,,,				2504	0.0				p.T59S		Atlas-SNP	.											POM121L12,NS,carcinoma,0,1	POM121L12	146	1	0			c.C176G						PASS	.	C	SER/THR	438,3494		27,384,1555	29.0	35.0	33.0		176	-1.1	0.0	7	dbSNP_131	33	4,8306		0,4,4151	yes	missense	POM121L12	NM_182595.3	58	27,388,5706	GG,GC,CC		0.0481,11.1394,3.6105	probably-damaging	59/297	53103540	442,11800	1966	4155	6121	SO:0001583	missense	285877	exon1			CCCTGACTCAGAG		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.176C>G	7.37:g.53103540C>G	ENSP00000386133:p.Thr59Ser	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	74	0.03388278388278388	71	0.1443089430894309	2	0.0055248618784530384	1	0.0017482517482517483	0	0.0	C	0.374	-0.932216	0.02359	0.111394	4.81E-4	ENSG00000221900	ENST00000408890	T	0.22539	1.95	1.81	-1.11	0.09840	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.16603	0.018	B	0.20767	0.031	T	0.41052	-0.9530	8	0.22109	T	0.4	.	2.491	0.04610	0.0:0.3885:0.2856:0.3259	.	59	Q8N7R1	P1L12_HUMAN	S	59	ENSP00000386133:T59S	ENSP00000386133:T59S	T	+	2	0	POM121L12	53071034	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.353000	0.20130	-0.287000	0.09064	0.313000	0.20887	ACT	C|0.965;G|0.035	0.035	strong		0.706	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
SLC7A6OS	84138	hgsc.bcm.edu	37	16	68344696	68344696	+	Missense_Mutation	SNP	C	C	T	rs3803650	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:68344696C>T	ENST00000263997.6	-	1	152	c.134G>A	c.(133-135)gGt>gAt	p.G45D	PRMT7_ENST00000441236.1_5'Flank|PRMT7_ENST00000339507.5_5'Flank|PRMT7_ENST00000348497.4_5'Flank|snoU13_ENST00000458872.1_RNA|PRMT7_ENST00000449359.3_5'Flank	NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	45			G -> D (in dbSNP:rs3803650). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)		TCTCTCCAAACCCTCCGACGT	0.627													c|||	3347	0.668331	0.7746	0.6816	5008	,	,		16642	0.7728		0.5437	False		,,,				2504	0.5358				p.G45D		Atlas-SNP	.											SLC7A6OS,NS,carcinoma,0,1	SLC7A6OS	22	1	0			c.G134A						scavenged	.	T	ASP/GLY	3273,1123	715.1+/-408.4	1227,819,152	75.0	62.0	66.0		134	-5.3	0.0	16	dbSNP_107	66	5011,3589	627.2+/-397.9	1450,2111,739	yes	missense	SLC7A6OS	NM_032178.2	94	2677,2930,891	TT,TC,CC		41.7326,25.546,36.2573	benign	45/310	68344696	8284,4712	2198	4300	6498	SO:0001583	missense	84138	exon1			TCCAAACCCTCCG		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.134G>A	16.37:g.68344696C>T	ENSP00000263997:p.Gly45Asp	Somatic	202	2	0.00990099		WXS	Illumina HiSeq	Phase_I	226	110	0.486726	NM_032178	Q8TCZ3|Q9H8R8	Missense_Mutation	SNP	ENST00000263997.6	37	CCDS10865.1	1518	0.695054945054945	402	0.8170731707317073	241	0.6657458563535912	455	0.7954545454545454	420	0.554089709762533	c	8.395	0.840662	0.16891	0.74454	0.582674	ENSG00000103061	ENST00000263997	T	0.18016	2.24	5.14	-5.34	0.02705	.	0.784649	0.12366	N	0.475201	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.09022	0.002	B	0.11329	0.006	T	0.31251	-0.9950	9	0.12103	T	0.63	0.0062	7.5123	0.27581	0.0:0.2759:0.1293:0.5949	rs3803650;rs17554596;rs17554603;rs17845399;rs17858256;rs60471765;rs3803650	45	Q96CW6	S7A6O_HUMAN	D	45	ENSP00000263997:G45D	ENSP00000263997:G45D	G	-	2	0	SLC7A6OS	66902197	0.184000	0.23200	0.002000	0.10522	0.276000	0.26787	-0.287000	0.08388	-0.806000	0.04398	-0.124000	0.14976	GGT	C|0.334;T|0.666	0.666	strong		0.627	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178	
MUC16	94025	hgsc.bcm.edu	37	19	9024994	9024994	+	Missense_Mutation	SNP	C	C	T	rs67631215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	168	0	0		WXS	Illumina HiSeq	Phase_I	169	81	0.47929	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	
GGA3	23163	hgsc.bcm.edu	37	17	73236124	73236124	+	Silent	SNP	A	A	G	rs28641831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73236124A>G	ENST00000245541.6	-	13	1545	c.1329T>C	c.(1327-1329)gaT>gaC	p.D443D	GGA3_ENST00000578348.1_Silent_p.D321D|GGA3_ENST00000582486.1_Silent_p.D371D|GGA3_ENST00000351904.7_Silent_p.D410D|GGA3_ENST00000582717.1_Silent_p.D371D|GGA3_ENST00000538886.1_Silent_p.D321D	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	443	Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			GCAGAGGAGCATCGGAGGCGC	0.662													G|||	905	0.180711	0.4894	0.0922	5008	,	,		13055	0.1002		0.003	False		,,,				2504	0.092				p.D443D		Atlas-SNP	.											.	GGA3	54	.	0			c.T1329C						PASS	.	G	,,,	1529,2757		270,989,884	14.0	16.0	16.0		1113,963,1230,1329	-9.3	0.0	17	dbSNP_125	16	30,8378		0,30,4174	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GGA3	NM_001172703.1,NM_001172704.1,NM_014001.3,NM_138619.2	,,,	270,1019,5058	GG,GA,AA		0.3568,35.6743,12.2814	,,,	371/652,321/593,410/691,443/724	73236124	1559,11135	2143	4204	6347	SO:0001819	synonymous_variant	23163	exon13			AGGAGCATCGGAG	AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.1329T>C	17.37:g.73236124A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_138619	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Silent	SNP	ENST00000245541.6	37	CCDS11717.1																																																																																			A|0.857;G|0.143	0.143	strong		0.662	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619	
LYST	1130	hgsc.bcm.edu	37	1	235945294	235945294	+	Silent	SNP	T	T	C	rs6696123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235945294T>C	ENST00000389794.3	-	15	5130	c.4956A>G	c.(4954-4956)ttA>ttG	p.L1652L	LYST_ENST00000389793.2_Silent_p.L1652L|LYST_ENST00000536965.1_3'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1652					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)			CTTGGGATGATAAACAATGGC	0.393													T|||	1520	0.303514	0.4879	0.2997	5008	,	,		15207	0.0655		0.4254	False		,,,				2504	0.1769				p.L1652L		Atlas-SNP	.											.	LYST	370	.	0			c.A4956G						PASS	.	T		2237,2169	593.4+/-388.0	570,1097,536	108.0	106.0	107.0		4956	-6.4	0.4	1	dbSNP_116	107	3435,5165	506.2+/-376.5	679,2077,1544	no	coding-synonymous	LYST	NM_000081.2		1249,3174,2080	CC,CT,TT		39.9419,49.2283,43.6106		1652/3802	235945294	5672,7334	2203	4300	6503	SO:0001819	synonymous_variant	1130	exon15			GGATGATAAACAA	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.4956A>G	1.37:g.235945294T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			T|0.614;C|0.386	0.386	strong		0.393	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
C2orf16	84226	hgsc.bcm.edu	37	2	27804691	27804691	+	Missense_Mutation	SNP	A	A	G	rs573591891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27804691A>G	ENST00000408964.2	+	1	5303	c.5252A>G	c.(5251-5253)cAc>cGc	p.H1751R	ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000355467.4_5'Flank|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000413371.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|RP11-158I13.2_ENST00000505973.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1751	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					AGAAGACATCACAGTCCCTCT	0.552													A|||	8	0.00159744	0.0053	0.0	5008	,	,		20961	0.001		0.0	False		,,,				2504	0.0				p.H1751R		Atlas-SNP	.											.	C2orf16	357	.	0			c.A5252G						PASS	.						192.0	196.0	195.0					2																	27804691		1917	4144	6061	SO:0001583	missense	84226	exon1			GACATCACAGTCC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.5252A>G	2.37:g.27804691A>G	ENSP00000386190:p.His1751Arg	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	157	13	0.0828025	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.199397	0.00299	.	.	ENSG00000221843	ENST00000408964	T	0.04706	3.57	3.97	-7.95	0.01148	.	.	.	.	.	T	0.01592	0.0051	N	0.01729	-0.75	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.42682	-0.9437	9	0.02654	T	1	.	14.4295	0.67240	0.7984:0.0:0.1133:0.0882	.	1751	Q68DN1	CB016_HUMAN	R	1751	ENSP00000386190:H1751R	ENSP00000386190:H1751R	H	+	2	0	C2orf16	27658195	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-11.276000	0.00004	-2.917000	0.00306	-1.919000	0.00516	CAC	.	.	none		0.552	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
HSD17B13	345275	hgsc.bcm.edu	37	4	88243832	88243832	+	Silent	SNP	A	A	G	rs137887488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88243832A>G	ENST00000328546.4	-	1	226	c.162T>C	c.(160-162)taT>taC	p.Y54Y	RP11-529H2.2_ENST00000508163.1_RNA|HSD17B13_ENST00000302219.6_Silent_p.Y54Y	NM_178135.3	NP_835236.2	Q7Z5P4	DHB13_HUMAN	hydroxysteroid (17-beta) dehydrogenase 13	54						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	8		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.000308)		TTGCAAATTCATAAGTAGTCT	0.388													A|||	10	0.00199681	0.0068	0.0014	5008	,	,		20127	0.0		0.0	False		,,,				2504	0.0				p.Y54Y		Atlas-SNP	.											.	HSD17B13	27	.	0			c.T162C						PASS	.	A	,	39,4367	43.1+/-76.7	0,39,2164	109.0	110.0	110.0		162,162	-0.3	1.0	4	dbSNP_134	110	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	HSD17B13	NM_001136230.1,NM_178135.3	,	0,39,6464	GG,GA,AA		0.0,0.8852,0.2999	,	54/265,54/301	88243832	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	345275	exon1			AAATTCATAAGTA		CCDS3618.1, CCDS47097.1	4q22.1	2011-09-20			ENSG00000170509	ENSG00000170509	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	18685	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 16C, member 3"""	612127				19027726	Standard	NM_178135		Approved	SCDR9, SDR16C3	uc003hqo.2	Q7Z5P4	OTTHUMG00000130602	ENST00000328546.4:c.162T>C	4.37:g.88243832A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	186	89	0.478495	NM_178135	A8K9R9|Q2M1L5|Q86W22|Q86W23	Silent	SNP	ENST00000328546.4	37	CCDS3618.1																																																																																			A|0.996;G|0.004	0.004	strong		0.388	HSD17B13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253052.1	NM_178135	
CD200R1	131450	hgsc.bcm.edu	37	3	112647832	112647832	+	Missense_Mutation	SNP	A	A	C	rs9826308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112647832A>C	ENST00000471858.1	-	4	763	c.531T>G	c.(529-531)caT>caG	p.H177Q	CD200R1_ENST00000490004.1_3'UTR|CD200R1_ENST00000308611.3_Missense_Mutation_p.H200Q|CD200R1_ENST00000295863.4_Missense_Mutation_p.H155Q|CD200R1_ENST00000440122.2_3'UTR	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	177	Ig-like C2-type.		Q -> H (in allele 2; dbSNP:rs9826308). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15274657, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.7}.		regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TCCAGGAGATATGCGCAGCTG	0.502													C|||	3263	0.651558	0.7216	0.6066	5008	,	,		18584	0.7024		0.5328	False		,,,				2504	0.6585				p.H200Q		Atlas-SNP	.											.	CD200R1	91	.	0			c.T600G						PASS	.	C	GLN/HIS,,,GLN/HIS	3012,1394	460.5+/-352.6	1023,966,214	107.0	89.0	95.0		600,,,531	3.6	0.7	3	dbSNP_119	95	4581,4019	555.7+/-386.7	1224,2133,943	yes	missense,utr-3,utr-3,missense	CD200R1	NM_138806.3,NM_138939.2,NM_138940.2,NM_170780.2	24,,,24	2247,3099,1157	CC,CA,AA		46.7326,31.6387,41.6193	benign,,,benign	200/349,,,177/326	112647832	7593,5413	2203	4300	6503	SO:0001583	missense	131450	exon5			GGAGATATGCGCA	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.531T>G	3.37:g.112647832A>C	ENSP00000418928:p.His177Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	37	CCDS2970.1	1375	0.6295787545787546	342	0.6951219512195121	222	0.6132596685082873	398	0.6958041958041958	413	0.5448548812664907	C	0.033	-1.319975	0.01320	0.683613	0.532674	ENSG00000163606	ENST00000471858;ENST00000308611;ENST00000295863	T;T;T	0.73897	-0.79;-0.79;-0.79	5.43	3.59	0.41128	.	0.651463	0.14922	N	0.290632	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999209259	.	.	.	.	.	.	T	0.42682	-0.9437	6	0.02654	T	1	.	9.9902	0.41865	0.1423:0.5516:0.3061:0.0	rs9826308;rs52825592;rs9826308	.	.	.	Q	177;200;155	ENSP00000418928:H177Q;ENSP00000311035:H200Q;ENSP00000295863:H155Q	ENSP00000295863:H155Q	H	-	3	2	CD200R1	114130522	0.179000	0.23135	0.707000	0.30419	0.196000	0.23810	0.343000	0.19944	0.241000	0.21283	-0.988000	0.02552	CAT	A|0.408;C|0.592	0.592	strong		0.502	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
SPHK2	56848	hgsc.bcm.edu	37	19	49131317	49131317	+	Silent	SNP	G	G	T	rs116785119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49131317G>T	ENST00000245222.4	+	5	1113	c.747G>T	c.(745-747)ctG>ctT	p.L249L	SPHK2_ENST00000601712.1_Silent_p.L213L|SPHK2_ENST00000600537.1_Silent_p.L190L|SPHK2_ENST00000443164.1_Silent_p.L311L|SPHK2_ENST00000340932.3_Silent_p.L213L|SPHK2_ENST00000599029.1_Silent_p.L213L|SPHK2_ENST00000599748.1_Silent_p.L213L|SPHK2_ENST00000598088.1_Silent_p.L249L	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	249	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				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)		GAGACGGGCTGCTCCATGAGG	0.647													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		16367	0.0		0.0	False		,,,				2504	0.0				p.L249L		Atlas-SNP	.											.	SPHK2	62	.	0			c.G747T						PASS	.	G	,,,	56,4350	55.5+/-91.7	1,54,2148	55.0	60.0	58.0		570,747,639,747	4.6	1.0	19	dbSNP_132	58	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK2	NM_001204158.2,NM_001204159.2,NM_001204160.2,NM_020126.4	,,,	1,54,6448	TT,TG,GG		0.0,1.271,0.4306	,,,	190/596,249/655,213/619,249/655	49131317	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	56848	exon5			CGGGCTGCTCCAT	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.747G>T	19.37:g.49131317G>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Silent	SNP	ENST00000245222.4	37	CCDS12727.1																																																																																			G|0.996;T|0.004	0.004	strong		0.647	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
ZNF611	81856	hgsc.bcm.edu	37	19	53209554	53209554	+	Missense_Mutation	SNP	G	G	T	rs4085565|rs34846371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53209554G>T	ENST00000319783.1	-	7	1070	c.754C>A	c.(754-756)Ccc>Acc	p.P252T	ZNF611_ENST00000540744.1_Missense_Mutation_p.P252T|ZNF611_ENST00000453741.2_Missense_Mutation_p.P183T|ZNF611_ENST00000543227.1_Missense_Mutation_p.P252T|ZNF611_ENST00000602162.1_Missense_Mutation_p.P183T|ZNF611_ENST00000595798.1_Missense_Mutation_p.P183T|ZNF611_ENST00000602046.1_5'Flank	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	252			P -> I (requires 2 nucleotide substitutions; dbSNP:rs34846371). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.|P -> L (in dbSNP:rs4085566).|P -> T (in dbSNP:rs4085565).		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(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		CCTAAATGGGGTATCTGGTGT	0.383													-|||	2197	0.438698	0.7012	0.3285	5008	,	,		21189	0.3681		0.4105	False		,,,				2504	0.2638				p.P252T		Atlas-SNP	.											ZNF611,NS,carcinoma,+1,1	ZNF611	72	1	0			c.C754A						PASS	.	T	THR/PRO,THR/PRO,THR/PRO,THR/PRO	2862,1544		1004,854,345	137.0	145.0	142.0		754,754,547,754	1.2	0.0	19	dbSNP_108	142	3197,5397		725,1747,1825	no	missense,missense,missense,missense	ZNF611	NM_001161499.1,NM_001161500.1,NM_001161501.1,NM_030972.3	38,38,38,38	1729,2601,2170	TT,TG,GG		37.2004,35.0431,46.6077	benign,benign,benign,benign	252/706,252/706,183/637,252/706	53209554	6059,6941	2203	4297	6500	SO:0001583	missense	81856	exon7			AATGGGGTATCTG	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.754C>A	19.37:g.53209554G>T	ENSP00000322427:p.Pro252Thr	Somatic	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	193	107	0.554404	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	930	0.4258241758241758	314	0.6382113821138211	126	0.34806629834254144	214	0.3741258741258741	276	0.3641160949868074	.	1.705	-0.500665	0.04261	0.649569	0.372004	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	1.2	1.2	0.21068	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00595	-1.35	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.18178	-1.0345	8	0.39692	T	0.17	.	6.3535	0.21389	0.0:0.0:0.5087:0.4913	rs4085565;rs60261865;rs4085565	252	Q8N823	ZN611_HUMAN	T	252;252;183;252	ENSP00000437616:P252T;ENSP00000439211:P252T;ENSP00000443505:P183T;ENSP00000322427:P252T	ENSP00000322427:P252T	P	-	1	0	ZNF611	57901366	0.000000	0.05858	0.010000	0.14722	0.004000	0.04260	0.006000	0.13152	-0.306000	0.08818	-1.228000	0.01579	CCC	.	.	weak		0.383	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972	
SVEP1	79987	hgsc.bcm.edu	37	9	113169816	113169816	+	Silent	SNP	T	T	C	rs116159392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113169816T>C	ENST00000401783.2	-	38	8400	c.8064A>G	c.(8062-8064)ggA>ggG	p.G2688G	SVEP1_ENST00000374469.1_Silent_p.G2665G|SVEP1_ENST00000297826.5_Silent_p.G614G	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2688	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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						GAAGTTCATATCCTGGATTAC	0.453													T|||	207	0.0413339	0.149	0.0144	5008	,	,		22581	0.0		0.0	False		,,,				2504	0.0				p.G2688G		Atlas-SNP	.											SVEP1,NS,carcinoma,0,1	SVEP1	326	1	0			c.A8064G						PASS	.	T		461,3353		27,407,1473	169.0	166.0	167.0		8064	-6.8	0.9	9	dbSNP_132	167	5,8265		0,5,4130	no	coding-synonymous	SVEP1	NM_153366.3		27,412,5603	CC,CT,TT		0.0605,12.087,3.8563		2688/3572	113169816	466,11618	1907	4135	6042	SO:0001819	synonymous_variant	79987	exon38			TTCATATCCTGGA	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.8064A>G	9.37:g.113169816T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	118	75	0.635593	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			T|0.959;C|0.041	0.041	strong		0.453	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PARD3B	117583	hgsc.bcm.edu	37	2	205990353	205990353	+	Silent	SNP	C	C	T	rs2276676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000349953.3_Silent_p.T442T|PARD3B_ENST00000351153.1_Silent_p.T442T|PARD3B_ENST00000462231.1_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	104	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	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	
FLG	2312	hgsc.bcm.edu	37	1	152280900	152280900	+	Missense_Mutation	SNP	T	T	G	rs74129452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152280900T>G	ENST00000368799.1	-	3	6497	c.6462A>C	c.(6460-6462)caA>caC	p.Q2154H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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						PASS	.						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	450	1	0.00222222		WXS	Illumina HiSeq	Phase_I	783	344	0.439336	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	
OR52L1	338751	hgsc.bcm.edu	37	11	6007680	6007680	+	Missense_Mutation	SNP	A	A	G	rs4436524|rs386750238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6007680A>G	ENST00000332249.4	-	1	535	c.481T>C	c.(481-483)Tgc>Cgc	p.C161R		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	161			C -> R (in dbSNP:rs4436524). {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)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATTCCGATGCACCCTATGACC	0.517													.|||	3759	0.750599	0.562	0.8357	5008	,	,		23293	0.8631		0.8171	False		,,,				2504	0.7607				p.C161R	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											OR52L1_ENST00000332249,NS,carcinoma,0,2	OR52L1	100	2	0			c.T481C						PASS	.	G	ARG/CYS	2544,1520		834,876,322	74.0	71.0	72.0		481	0.2	0.0	11	dbSNP_111	72	6656,1726		2648,1360,183	no	missense	OR52L1	NM_001005173.2	180	3482,2236,505	GG,GA,AA		20.5917,37.4016,26.0807	benign	161/330	6007680	9200,3246	2032	4191	6223	SO:0001583	missense	338751	exon1			CGATGCACCCTAT	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"""GPCR / Class A : Olfactory receptors"""	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.481T>C	11.37:g.6007680A>G	ENSP00000330338:p.Cys161Arg	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	160	71	0.44375	NM_001005173	B2RPA6|Q6IFK9	Missense_Mutation	SNP	ENST00000332249.4	37	CCDS44529.1	1698	0.7774725274725275	278	0.5650406504065041	296	0.8176795580110497	507	0.8863636363636364	617	0.8139841688654353	G	0	-2.730502	0.00089	0.625984	0.794083	ENSG00000183313	ENST00000332249	T	0.35973	1.28	3.85	0.241	0.15494	GPCR, rhodopsin-like superfamily (1);	0.486110	0.17495	N	0.172195	T	0.00012	0.0000	N	0.01228	-0.945	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14811	-1.0459	9	0.15952	T	0.53	.	2.2228	0.03977	0.2875:0.1684:0.431:0.1131	rs4436524;rs17265708;rs52827577;rs61074917;rs4436524	161	Q8NGH7	O52L1_HUMAN	R	161	ENSP00000330338:C161R	ENSP00000330338:C161R	C	-	1	0	OR52L1	5964256	0.000000	0.05858	0.012000	0.15200	0.002000	0.02628	-4.145000	0.00286	-0.371000	0.08004	-3.149000	0.00058	TGC	A|0.245;G|0.755;T|0.000	0.755	strong		0.517	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173	
SCIN	85477	hgsc.bcm.edu	37	7	12675713	12675713	+	Missense_Mutation	SNP	T	T	C	rs17166250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12675713T>C	ENST00000297029.5	+	10	1464	c.1363T>C	c.(1363-1365)Ttc>Ctc	p.F455L	SCIN_ENST00000445618.2_Missense_Mutation_p.F208L|SCIN_ENST00000519209.1_Missense_Mutation_p.F208L	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	455	Ca(2+)-dependent actin binding.		F -> L (in dbSNP:rs17166250).		actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		AACATCTGCGTTCCTGACTGT	0.453													T|||	163	0.0325479	0.0416	0.0346	5008	,	,		19999	0.0		0.0567	False		,,,				2504	0.0276				p.F455L		Atlas-SNP	.											.	SCIN	105	.	0			c.T1363C						PASS	.	T	LEU/PHE,LEU/PHE	180,3844		1,178,1833	94.0	93.0	94.0		1363,622	5.6	1.0	7	dbSNP_123	94	369,8015		10,349,3833	yes	missense,missense	SCIN	NM_001112706.2,NM_033128.3	22,22	11,527,5666	CC,CT,TT		4.4012,4.4732,4.4246	benign,benign	455/716,208/469	12675713	549,11859	2012	4192	6204	SO:0001583	missense	85477	exon10			TCTGCGTTCCTGA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.1363T>C	7.37:g.12675713T>C	ENSP00000297029:p.Phe455Leu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	122	62	0.508197	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	61	0.027930402930402932	13	0.026422764227642278	10	0.027624309392265192	0	0.0	38	0.05013192612137203	T	14.43	2.533963	0.45073	0.044732	0.044012	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.49432	0.78;0.78;0.78	5.55	5.55	0.83447	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	T	0.14485	0.0350	N	0.17312	0.475	0.53688	D	0.999979	D	0.65815	0.995	D	0.68192	0.956	T	0.23404	-1.0189	10	0.30078	T	0.28	-15.794	15.6872	0.77421	0.0:0.0:0.0:1.0	rs17166250;rs52793594;rs17166250	455	Q9Y6U3	ADSV_HUMAN	L	455;208;208	ENSP00000297029:F455L;ENSP00000430997:F208L;ENSP00000390189:F208L	ENSP00000297029:F455L	F	+	1	0	SCIN	12642238	1.000000	0.71417	0.971000	0.41717	0.460000	0.32559	3.816000	0.55658	2.100000	0.63781	0.533000	0.62120	TTC	T|0.970;C|0.030	0.030	strong		0.453	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
ATP11B	23200	hgsc.bcm.edu	37	3	182614493	182614493	+	Silent	SNP	T	T	C	rs4859142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:182614493T>C	ENST00000323116.5	+	26	3248	c.2988T>C	c.(2986-2988)ttT>ttC	p.F996F		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	996					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TTTAGATGTTTGGAAACTGGA	0.323													T|||	719	0.14357	0.3472	0.1081	5008	,	,		17954	0.0417		0.0895	False		,,,				2504	0.0542				p.F996F		Atlas-SNP	.											.	ATP11B	115	.	0			c.T2988C						PASS	.	T		1361,3045	452.6+/-350.1	208,945,1050	252.0	246.0	248.0		2988	4.5	1.0	3	dbSNP_111	248	858,7740	195.2+/-240.5	39,780,3480	no	coding-synonymous	ATP11B	NM_014616.1		247,1725,4530	CC,CT,TT		9.9791,30.8897,17.064		996/1178	182614493	2219,10785	2203	4299	6502	SO:0001819	synonymous_variant	23200	exon26			GATGTTTGGAAAC	AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"""ATPases / P-type"""	13553	protein-coding gene	gene with protein product		605869	"""ATPase, Class VI, type 11B"""			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.2988T>C	3.37:g.182614493T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_014616	Q96FN1|Q9UKK7	Silent	SNP	ENST00000323116.5	37	CCDS33896.1	294	0.1346153846153846	156	0.3170731707317073	38	0.10497237569060773	25	0.043706293706293704	75	0.09894459102902374	T	9.681	1.149424	0.21288	0.308897	0.099791	ENSG00000058063	ENST00000498086	.	.	.	5.66	4.5	0.54988	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.20207	-1.0282	3	.	.	.	.	11.301	0.49306	0.0:0.0712:0.0:0.9288	rs4859142;rs56539343;rs4859142	.	.	.	S	797	.	.	L	+	2	0	ATP11B	184097187	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.720000	0.68470	0.979000	0.38497	0.455000	0.32223	TTG	T|0.842;C|0.158	0.158	strong		0.323	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616	
ATG2A	23130	hgsc.bcm.edu	37	11	64665444	64665444	+	Missense_Mutation	SNP	G	G	A	rs61740228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64665444G>A	ENST00000377264.3	-	35	4973	c.4861C>T	c.(4861-4863)Cgc>Tgc	p.R1621C	ATG2A_ENST00000421419.2_Missense_Mutation_p.R1623C	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1621					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GTCTCGGGGCGAGCTAGGGGA	0.687													G|||	271	0.0541134	0.1891	0.0259	5008	,	,		14801	0.0		0.003	False		,,,				2504	0.0				p.R1621C		Atlas-SNP	.											.	ATG2A	133	.	0			c.C4861T						PASS	.	G	CYS/ARG	712,3680		63,586,1547	31.0	39.0	36.0		4861	2.5	0.4	11	dbSNP_129	36	4,8578		0,4,4287	yes	missense	ATG2A	NM_015104.2	180	63,590,5834	AA,AG,GG		0.0466,16.2113,5.5187	probably-damaging	1621/1939	64665444	716,12258	2196	4291	6487	SO:0001583	missense	23130	exon35			CGGGGCGAGCTAG		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.4861C>T	11.37:g.64665444G>A	ENSP00000366475:p.Arg1621Cys	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	86|86	0.039377289377289376|0.039377289377289376	77|77	0.1565040650406504|0.1565040650406504	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	0|0	0.0|0.0	G|G	9.496|9.496	1.101947|1.101947	0.20632|0.20632	0.162113|0.162113	4.66E-4|4.66E-4	ENSG00000110046|ENSG00000110046	ENST00000421419;ENST00000377264|ENST00000418259	T;T|.	0.07327|.	3.2;3.2|.	4.38|4.38	2.5|2.5	0.30297|0.30297	.|.	1.153450|.	0.06390|.	N|.	0.716880|.	T|T	0.00178|0.00178	0.0005|0.0005	L|L	0.34521|0.34521	1.04|1.04	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.10359|0.10359	-1.0633|-1.0633	9|4	0.54805|.	T|.	0.06|.	.|.	6.7746|6.7746	0.23613|0.23613	0.2147:0.0:0.7853:0.0|0.2147:0.0:0.7853:0.0	.|.	1621;1623|.	Q2TAZ0;Q2TAZ0-3|.	ATG2A_HUMAN;.|.	C|L	1623;1621|1424	ENSP00000410522:R1623C;ENSP00000366475:R1621C|.	ENSP00000366475:R1621C|.	R|S	-|-	1|2	0|0	ATG2A|ATG2A	64422020|64422020	0.987000|0.987000	0.35691|0.35691	0.426000|0.426000	0.26672|0.26672	0.016000|0.016000	0.09150|0.09150	2.246000|2.246000	0.43142|0.43142	0.594000|0.594000	0.29761|0.29761	-0.258000|-0.258000	0.10820|0.10820	CGC|TCG	G|0.957;A|0.043	0.043	strong		0.687	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
MYO10	4651	hgsc.bcm.edu	37	5	16701717	16701717	+	Silent	SNP	C	C	T	rs149110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16701717C>T	ENST00000513610.1	-	25	3241	c.2787G>A	c.(2785-2787)agG>agA	p.R929R	MYO10_ENST00000274203.9_Silent_p.R286R|MYO10_ENST00000427430.2_Silent_p.R286R|MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000505695.1_Silent_p.R268R|MYO10_ENST00000515803.1_Silent_p.R268R	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	929	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						CCTCCTCCAGCCTGCGGAGCT	0.637													C|||	327	0.0652955	0.2277	0.0288	5008	,	,		13912	0.0		0.006	False		,,,				2504	0.0				p.R929R		Atlas-SNP	.											.	MYO10	198	.	0			c.G2787A						PASS	.	C		850,3468		77,696,1386	24.0	29.0	27.0		2787	3.2	0.9	5	dbSNP_79	27	49,8505		1,47,4229	no	coding-synonymous	MYO10	NM_012334.2		78,743,5615	TT,TC,CC		0.5728,19.685,6.9842		929/2059	16701717	899,11973	2159	4277	6436	SO:0001819	synonymous_variant	4651	exon25			CTCCAGCCTGCGG	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.2787G>A	5.37:g.16701717C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			C|0.928;T|0.072	0.072	strong		0.637	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
CAP2	10486	hgsc.bcm.edu	37	6	17507504	17507504	+	Silent	SNP	C	C	G	rs146710056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:17507504C>G	ENST00000229922.2	+	5	937	c.405C>G	c.(403-405)gcC>gcG	p.A135A	CAP2_ENST00000489374.1_Intron|CAP2_ENST00000465994.1_Silent_p.A135A|CAP2_ENST00000493172.1_Intron|CAP2_ENST00000378990.2_Silent_p.A109A	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	135					activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			ATCTTTCGGCCGTCAGCGAAA	0.483													C|||	4	0.000798722	0.003	0.0	5008	,	,		19667	0.0		0.0	False		,,,				2504	0.0				p.A135A		Atlas-SNP	.											.	CAP2	61	.	0			c.C405G						PASS	.	C		18,4388	26.2+/-53.5	0,18,2185	128.0	102.0	111.0		405	-3.8	0.8	6	dbSNP_134	111	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CAP2	NM_006366.2		0,19,6484	GG,GC,CC		0.0116,0.4085,0.1461		135/478	17507504	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	10486	exon5			TTCGGCCGTCAGC	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.405C>G	6.37:g.17507504C>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	37	CCDS4539.1																																																																																			C|0.998;G|0.002	0.002	strong		0.483	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
RNF213	57674	hgsc.bcm.edu	37	17	78263486	78263486	+	Missense_Mutation	SNP	T	T	C	rs17853989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78263486T>C	ENST00000582970.1	+	6	1105	c.962T>C	c.(961-963)aTg>aCg	p.M321T	RNF213_ENST00000319921.4_Missense_Mutation_p.M321T|RNF213_ENST00000456466.1_Missense_Mutation_p.M321T|RNF213_ENST00000508628.2_Missense_Mutation_p.M370T	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	321				M -> T (in Ref. 4; AAH36891/AAH40341). {ECO:0000305}.	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)	p.M321T(1)|p.M370T(1)		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)			AAGGACGAGATGGCTGCTGCT	0.473													t|||	1101	0.219848	0.4531	0.1268	5008	,	,		16968	0.0665		0.165	False		,,,				2504	0.1851				p.M321T		Atlas-SNP	.											RNF213_ENST00000411702,NS,carcinoma,0,2	RNF213	766	2	2	Substitution - Missense(2)	stomach(2)	c.T962C						PASS	.	T	THR/MET,THR/MET	1746,2660	517.3+/-369.4	354,1038,811	60.0	66.0	64.0		1109,962	-8.7	0.0	17	dbSNP_123	64	1624,6976	299.3+/-304.4	153,1318,2829	yes	missense,missense	RNF213	NM_020914.4,NM_020954.2	81,81	507,2356,3640	CC,CT,TT		18.8837,39.6278,25.9111	benign,benign	370/5257,321/1064	78263486	3370,9636	2203	4300	6503	SO:0001583	missense	57674	exon6			ACGAGATGGCTGC	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.962T>C	17.37:g.78263486T>C	ENSP00000464087:p.Met321Thr	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	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	433	0.19826007326007325	213	0.4329268292682927	45	0.12430939226519337	37	0.06468531468531469	138	0.1820580474934037	t	4.375	0.069242	0.08436	0.396278	0.188837	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.39229	1.09;1.09	4.4	-8.69	0.00855	.	615.921000	0.00166	N	0.000012	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14117	-1.0484	9	0.06891	T	0.86	-2.4186	4.0565	0.09819	0.3513:0.2506:0.0:0.3981	rs17853989;rs17857133	321;321	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	T	321;370;321;321	ENSP00000392123:M321T;ENSP00000324392:M321T	ENSP00000324392:M321T	M	+	2	0	RNF213	75878081	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.421000	0.02455	-2.102000	0.00845	-2.512000	0.00187	ATG	T|0.759;C|0.241	0.241	strong		0.473	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
ATP8B1	5205	hgsc.bcm.edu	37	18	55334339	55334339	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:55334339T>C	ENST00000283684.4	-	19	2269	c.2270A>G	c.(2269-2271)tAt>tGt	p.Y757C	RP11-35G9.5_ENST00000588925.1_RNA|ATP8B1_ENST00000536015.1_Missense_Mutation_p.Y757C|RP11-35G9.3_ENST00000599199.1_RNA|RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.3_ENST00000591854.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	757					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				ATCCTCCCCATAGCAGATGGT	0.368																																					p.Y757C		Atlas-SNP	.											.	ATP8B1	126	.	0			c.A2270G						PASS	.						114.0	107.0	109.0					18																	55334339		2203	4300	6503	SO:0001583	missense	5205	exon20			TCCCCATAGCAGA	AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"""ATPases / P-type"""	3706	protein-coding gene	gene with protein product		602397	"""ATPase, Class I, type 8B, member 1"", ""ATPase, class I, type 8B, member 1"""	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.2270A>G	18.37:g.55334339T>C	ENSP00000283684:p.Tyr757Cys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	95	4	0.0421053	NM_005603	Q9BTP8	Missense_Mutation	SNP	ENST00000283684.4	37	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	T	15.76	2.928583	0.52759	.	.	ENSG00000081923	ENST00000283684;ENST00000536015	T;T	0.67698	-0.28;-0.28	5.15	5.15	0.70609	HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.77738	0.4175	L	0.59436	1.845	0.80722	D	1	D	0.65815	0.995	D	0.65773	0.938	T	0.79999	-0.1566	10	0.66056	D	0.02	.	14.945	0.71023	0.0:0.0:0.0:1.0	.	757	O43520	AT8B1_HUMAN	C	757	ENSP00000283684:Y757C;ENSP00000445359:Y757C	ENSP00000283684:Y757C	Y	-	2	0	ATP8B1	53485337	1.000000	0.71417	0.990000	0.47175	0.593000	0.36681	5.781000	0.68964	2.063000	0.61619	0.528000	0.53228	TAT	.	.	none		0.368	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603	
CT47B1	643311	hgsc.bcm.edu	37	X	120008932	120008932	+	Missense_Mutation	SNP	T	T	C	rs193289998		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:120008932T>C	ENST00000371311.3	-	1	847	c.593A>G	c.(592-594)gAg>gGg	p.E198G		NM_001145718.1	NP_001139190.1	P0C2W7	CT47B_HUMAN	cancer/testis antigen family 47, member B1	198										breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|lung(9)|ovary(1)|skin(1)	22						CGACGCGGCCTCCTGGACCGA	0.711													N|||	78	0.0206623	0.053	0.0115	3775	,	,		9887	0.0		0.0	False		,,,				2504	0.0				p.E198G		Atlas-SNP	.											.	CT47B1	67	.	0			c.A593G						PASS	.	T	GLY/GLU	86,1123		1,78,6,438,169	28.0	28.0	28.0		593	0.7	0.0	X		28	0,2389		0,0,0,800,789	no	missense	CT47B1	NM_001145718.1	98	1,78,6,1238,958	CC,CT,C,TT,T		0.0,7.1133,2.3902	benign	198/300	120008932	86,3512	692	1589	2281	SO:0001583	missense	643311	exon1			GCGGCCTCCTGGA		CCDS48161.1	Xq24	2014-05-06	2011-03-24		ENSG00000236446	ENSG00000236446			33293	protein-coding gene	gene with protein product	"""cancer/testis CT47 family, member 13"""	300790				16382448	Standard	NM_001145718		Approved	CT47.13	uc011muc.2	P0C2W7	OTTHUMG00000187483	ENST00000371311.3:c.593A>G	X.37:g.120008932T>C	ENSP00000360360:p.Glu198Gly	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	77	22	0.285714	NM_001145718	A6NM97	Missense_Mutation	SNP	ENST00000371311.3	37	CCDS48161.1	25	0.015069318866787222	15	0.03125	2	0.00558659217877095	0	0.0	0	0.0	T	10.45	1.352922	0.24512	0.071133	0.0	ENSG00000236446	ENST00000371311	.	.	.	1.89	0.714	0.18180	.	.	.	.	.	T	0.01029	0.0034	N	0.08118	0	0.80722	P	0.0	B	0.19817	0.039	B	0.08055	0.003	T	0.15492	-1.0435	7	0.35671	T	0.21	.	3.0134	0.06052	0.0:0.4121:0.0:0.5879	.	198	P0C2W7	CT47B_HUMAN	G	198	.	ENSP00000360360:E198G	E	-	2	0	CT47B1	119892960	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-1.020000	0.03618	0.129000	0.18514	0.143000	0.16000	GAG	T|0.985;C|0.015	0.015	strong		0.711	CT47B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058121.1	NM_001145718	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464558	39464558	+	Silent	SNP	G	G	A	rs72828117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39464558G>A	ENST00000391352.1	-	1	947	c.948C>T	c.(946-948)ccC>ccT	p.P316P		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	316						keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						AGCAGGGGCTGGGCTCAGAGC	0.572													G|||	454	0.090655	0.2027	0.0504	5008	,	,		23500	0.0506		0.0785	False		,,,				2504	0.0215				p.P316P		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.C948T						PASS	.																																			SO:0001819	synonymous_variant	100505753	exon1			GGGGCTGGGCTCA	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.948C>T	17.37:g.39464558G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_001146182		Silent	SNP	ENST00000391352.1	37	CCDS56032.1																																																																																			G|0.900;A|0.100	0.100	strong		0.572	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
TMPRSS5	80975	hgsc.bcm.edu	37	11	113565322	113565322	+	Silent	SNP	C	C	A	rs17115841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:113565322C>A	ENST00000299882.5	-	8	811	c.663G>T	c.(661-663)ggG>ggT	p.G221G	TMPRSS5_ENST00000538955.1_Silent_p.G177G|TMPRSS5_ENST00000540540.1_5'UTR|TMPRSS5_ENST00000545579.1_Silent_p.G212G|TMPRSS5_ENST00000544476.1_Intron|TMPRSS5_ENST00000544634.1_Intron|TMPRSS5_ENST00000545265.1_5'Flank|TMPRSS5_ENST00000536856.1_5'UTR	NM_030770.2	NP_110397.2	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	221	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)		CCACAGACTGCCCACCAACTA	0.642													C|||	448	0.0894569	0.2186	0.0908	5008	,	,		15182	0.0		0.0746	False		,,,				2504	0.0215				p.G221G		Atlas-SNP	.											TMPRSS5_ENST00000299882,NS,neuroblastoma,-2,2	TMPRSS5	69	2	0			c.G663T						PASS	.	C		655,3211		43,569,1321	11.0	16.0	14.0		663	1.3	1.0	11	dbSNP_123	14	509,7585		13,483,3551	no	coding-synonymous	TMPRSS5	NM_030770.2		56,1052,4872	AA,AC,CC		6.2886,16.9426,9.7324		221/458	113565322	1164,10796	1933	4047	5980	SO:0001819	synonymous_variant	80975	exon8			AGACTGCCCACCA	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.663G>T	11.37:g.113565322C>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	64	42	0.65625	NM_030770		Silent	SNP	ENST00000299882.5	37	CCDS44735.1																																																																																			C|0.913;A|0.087	0.087	strong		0.642	TMPRSS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398652.1	NM_030770	
CMYA5	202333	hgsc.bcm.edu	37	5	79033306	79033306	+	Missense_Mutation	SNP	A	A	C	rs2278239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79033306A>C	ENST00000446378.2	+	2	8749	c.8718A>C	c.(8716-8718)aaA>aaC	p.K2906N		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2906			K -> N (in dbSNP:rs2278239).		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)		ATGCTGATAAAATGGTTTCTA	0.408													A|||	1339	0.267372	0.5605	0.0807	5008	,	,		19741	0.3621		0.0815	False		,,,				2504	0.0971				p.K2906N		Atlas-SNP	.											.	CMYA5	643	.	0			c.A8718C						PASS	.	A	ASN/LYS	1801,1927		446,909,509	65.0	61.0	62.0		8718	-0.1	0.0	5	dbSNP_100	62	715,7481		39,637,3422	yes	missense	CMYA5	NM_153610.3	94	485,1546,3931	CC,CA,AA		8.7238,48.3101,21.1003	benign	2906/4070	79033306	2516,9408	1864	4098	5962	SO:0001583	missense	202333	exon2			TGATAAAATGGTT	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.8718A>C	5.37:g.79033306A>C	ENSP00000394770:p.Lys2906Asn	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	106	106	1	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	614	0.28113553113553114	294	0.5975609756097561	29	0.08011049723756906	232	0.40559440559440557	59	0.07783641160949868	A	5.559	0.287917	0.10513	0.483101	0.087238	ENSG00000164309	ENST00000446378	T	0.38077	1.16	6.07	-0.131	0.13494	.	0.712405	0.13179	N	0.407696	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.26195	0.144	B	0.21546	0.035	T	0.40001	-0.9586	9	0.49607	T	0.09	.	2.2812	0.04114	0.3041:0.1227:0.3893:0.184	rs2278239;rs52812215;rs58612098;rs2278239	2906	Q8N3K9	CMYA5_HUMAN	N	2906	ENSP00000394770:K2906N	ENSP00000394770:K2906N	K	+	3	2	CMYA5	79069062	0.000000	0.05858	0.000000	0.03702	0.340000	0.28889	0.658000	0.24979	-0.026000	0.13895	-0.256000	0.11100	AAA	A|0.698;C|0.302	0.302	strong		0.408	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
ABCC3	8714	hgsc.bcm.edu	37	17	48734136	48734136	+	Missense_Mutation	SNP	G	G	A	rs35777968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48734136G>A	ENST00000285238.8	+	3	376	c.296G>A	c.(295-297)cGg>cAg	p.R99Q	ABCC3_ENST00000427699.1_Missense_Mutation_p.R99Q	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	99					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)	GTCCATGGCCGGGCCCCTGCC	0.617													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		16262	0.0		0.0	False		,,,				2504	0.0				p.R99Q		Atlas-SNP	.											.	ABCC3	138	.	0			c.G296A						PASS	.	G	GLN/ARG,GLN/ARG	157,4249	103.4+/-141.9	2,153,2048	70.0	71.0	71.0		296,296	-2.1	0.0	17	dbSNP_126	71	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ABCC3	NM_001144070.1,NM_003786.3	43,43	2,155,6346	AA,AG,GG		0.0233,3.5633,1.2225	benign,benign	99/573,99/1528	48734136	159,12847	2203	4300	6503	SO:0001583	missense	8714	exon3			ATGGCCGGGCCCC	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.296G>A	17.37:g.48734136G>A	ENSP00000285238:p.Arg99Gln	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	G	11.08	1.534357	0.27475	0.035633	2.33E-4	ENSG00000108846	ENST00000427699;ENST00000285238	T;T	0.35236	1.32;1.32	5.53	-2.14	0.07123	.	1.579970	0.03817	N	0.266872	T	0.04137	0.0115	N	0.12182	0.205	0.09310	N	1	B;B	0.17038	0.01;0.02	B;B	0.13407	0.002;0.009	T	0.12372	-1.0550	10	0.12430	T	0.62	0.3777	6.1119	0.20106	0.4088:0.2585:0.3327:0.0	rs35777968;rs45584534;rs59497545	99;99	O15438;O15438-5	MRP3_HUMAN;.	Q	99	ENSP00000395160:R99Q;ENSP00000285238:R99Q	ENSP00000285238:R99Q	R	+	2	0	ABCC3	46089135	0.000000	0.05858	0.018000	0.16275	0.347000	0.29111	0.356000	0.20181	-0.007000	0.14345	0.591000	0.81541	CGG	G|0.987;A|0.013	0.013	strong		0.617	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
CAPN3	825	hgsc.bcm.edu	37	15	42652099	42652099	+	Silent	SNP	T	T	C	rs1801496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42652099T>C	ENST00000397163.3	+	1	315	c.96T>C	c.(94-96)acT>acC	p.T32T	CAPN3_ENST00000356316.3_Intron|CAPN3_ENST00000349748.3_Silent_p.T32T|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000357568.3_Silent_p.T32T|CAPN3_ENST00000318023.7_Silent_p.T32T	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	32					apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		GCAAGGCCACTGAGGCTGGGG	0.572													C|||	472	0.0942492	0.1392	0.062	5008	,	,		15952	0.002		0.0845	False		,,,				2504	0.1616				p.T32T		Atlas-SNP	.											.	CAPN3	172	.	0			c.T96C						PASS	.	C	,,	611,3795	763.1+/-413.2	45,521,1637	92.0	107.0	102.0		96,96,96	-9.6	0.0	15	dbSNP_89	102	693,7905	783.3+/-407.6	31,631,3637	no	coding-synonymous,coding-synonymous,coding-synonymous	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1	,,	76,1152,5274	CC,CT,TT		8.06,13.8675,10.0277	,,	32/822,32/816,32/730	42652099	1304,11700	2203	4299	6502	SO:0001819	synonymous_variant	825	exon1			GGCCACTGAGGCT	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"""EF-hand domain containing"""	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.96T>C	15.37:g.42652099T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																			T|0.910;C|0.090	0.090	strong		0.572	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		
NLRC4	58484	hgsc.bcm.edu	37	2	32475109	32475109	+	Silent	SNP	G	G	A	rs455060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32475109G>A	ENST00000404025.2	-	5	2312	c.1824C>T	c.(1822-1824)gcC>gcT	p.A608A	NLRC4_ENST00000360906.5_Silent_p.A608A|NLRC4_ENST00000342905.6_Intron|NLRC4_ENST00000402280.1_Silent_p.A608A			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	608					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)	p.A608A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TGAAGTCCAGGGCACTTGCAC	0.433													A|||	2966	0.592252	0.7201	0.6556	5008	,	,		19989	0.4633		0.6173	False		,,,				2504	0.4816				p.A608A		Atlas-SNP	.											NLRC4,NS,carcinoma,0,1	NLRC4	165	1	1	Substitution - coding silent(1)	stomach(1)	c.C1824T						PASS	.	A	,,	2993,1413	462.6+/-353.3	1022,949,232	125.0	135.0	132.0		1824,1824,1824	-5.5	0.8	2	dbSNP_80	132	5197,3403	502.2+/-375.6	1574,2049,677	no	coding-synonymous,coding-synonymous,coding-synonymous	NLRC4	NM_001199138.1,NM_001199139.1,NM_021209.4	,,	2596,2998,909	AA,AG,GG		39.5698,32.0699,37.0291	,,	608/1025,608/1025,608/1025	32475109	8190,4816	2203	4300	6503	SO:0001819	synonymous_variant	58484	exon4			GTCCAGGGCACTT	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"""Nucleotide-binding domain and leucine rich repeat containing"""	16412	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4"", ""NOD-like receptor C4"""	606831	"""caspase recruitment domain family, member 12"""	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.1824C>T	2.37:g.32475109G>A		Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Silent	SNP	ENST00000404025.2	37	CCDS33174.1																																																																																			G|0.383;A|0.617	0.617	strong		0.433	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209	
CCL11	6356	hgsc.bcm.edu	37	17	32612894	32612894	+	Missense_Mutation	SNP	G	G	A	rs1129844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:32612894G>A	ENST00000305869.3	+	1	208	c.67G>A	c.(67-69)Gct>Act	p.A23T		NM_002986.2	NP_002977.1	P51671	CCL11_HUMAN	chemokine (C-C motif) ligand 11	23			A -> T (in clone 53; dbSNP:rs1129844).		actin filament organization (GO:0007015)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|chronic inflammatory response (GO:0002544)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mammary duct terminal end bud growth (GO:0060763)|mast cell chemotaxis (GO:0002551)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of Rac GTPase activity (GO:0032855)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|response to interleukin-4 (GO:0070670)|response to radiation (GO:0009314)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			breast(1)|lung(1)|prostate(1)	3	Breast(3;0.00224)	Breast(31;0.151)|Ovarian(249;0.17)		BRCA - Breast invasive adenocarcinoma(366;0.155)		CCAGGGGCTCGCTGGGCCAGG	0.552													G|||	723	0.144369	0.084	0.1369	5008	,	,		17118	0.1974		0.17	False		,,,				2504	0.1503				p.A23T		Atlas-SNP	.											.	CCL11	12	.	0			c.G67A	GRCh37	CM072923	CCL11	M	rs1129844	PASS	.	G	THR/ALA	412,3994	204.1+/-226.4	21,370,1812	94.0	96.0	95.0		67	-1.5	0.5	17	dbSNP_86	95	1535,7065	288.9+/-299.0	135,1265,2900	yes	missense	CCL11	NM_002986.2	58	156,1635,4712	AA,AG,GG		17.8488,9.3509,14.97	benign	23/98	32612894	1947,11059	2203	4300	6503	SO:0001583	missense	6356	exon1			GGGCTCGCTGGGC	AB063614	CCDS11279.1	17q21.1-q21.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000172156	ENSG00000172156		"""Chemokine ligands"", ""Endogenous ligands"""	10610	protein-coding gene	gene with protein product	"""eotaxin-1"""	601156	"""small inducible cytokine subfamily A (Cys-Cys), member 11 (eotaxin)"""	SCYA11		9169149	Standard	NM_002986		Approved	eotaxin, MGC22554	uc002hia.1	P51671	OTTHUMG00000132884	ENST00000305869.3:c.67G>A	17.37:g.32612894G>A	ENSP00000302234:p.Ala23Thr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_002986	P50877|Q92490|Q92491	Missense_Mutation	SNP	ENST00000305869.3	37	CCDS11279.1	305	0.13965201465201466	47	0.09552845528455285	47	0.1298342541436464	88	0.15384615384615385	123	0.16226912928759896	G	11.38	1.621023	0.28889	0.093509	0.178488	ENSG00000172156	ENST00000305869	T	0.02812	4.15	4.48	-1.52	0.08637	Chemokine interleukin-8-like domain (1);	0.572486	0.15716	N	0.248132	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.33883	0.43	B	0.30179	0.112	T	0.49153	-0.8969	8	0.48119	T	0.1	.	5.8131	0.18477	0.2623:0.0:0.6012:0.1365	rs1129844;rs3188137;rs3744508;rs17412369;rs3744508	23	P51671	CCL11_HUMAN	T	23	ENSP00000302234:A23T	ENSP00000302234:A23T	A	+	1	0	CCL11	29637007	0.027000	0.19231	0.536000	0.28039	0.069000	0.16628	0.232000	0.17891	-0.280000	0.09154	-1.871000	0.00553	GCT	A|0.126;C|0.145;G|0.706;T|0.023	0.126	strong		0.552	CCL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256377.2	NM_002986	
OTUD4	54726	hgsc.bcm.edu	37	4	146059006	146059006	+	Missense_Mutation	SNP	G	G	A	rs558808115		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:146059006G>A	ENST00000447906.2	-	21	3108	c.2921C>T	c.(2920-2922)aCt>aTt	p.T974I	OTUD4_ENST00000454497.2_Missense_Mutation_p.T909I|OTUD4_ENST00000455611.2_Intron			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	974					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)					AACAGGCACAGTTTCTCTCTC	0.463																																					p.T909I		Atlas-SNP	.											OTUD4,NS,carcinoma,0,5	OTUD4	120	5	0			c.C2726T						scavenged	.						128.0	133.0	131.0					4																	146059006		2203	4300	6503	SO:0001583	missense	54726	exon21			GGCACAGTTTCTC		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.2921C>T	4.37:g.146059006G>A	ENSP00000395487:p.Thr974Ile	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	253	4	0.0158103	NM_001102653	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	37		.	.	.	.	.	.	.	.	.	.	G	13.28	2.191504	0.38707	.	.	ENSG00000164164	ENST00000454497;ENST00000447906	T;T	0.34275	1.37;1.37	6.17	5.33	0.75918	.	1.059000	0.07258	N	0.867023	T	0.32793	0.0841	N	0.24115	0.695	0.80722	D	1	B;B	0.13145	0.007;0.004	B;B	0.14023	0.01;0.004	T	0.02275	-1.1184	10	0.59425	D	0.04	-0.3286	15.5098	0.75772	0.0658:0.0:0.9342:0.0	.	974;973	G3V0I6;Q01804	.;OTUD4_HUMAN	I	909;974	ENSP00000409279:T909I;ENSP00000395487:T974I	ENSP00000395487:T974I	T	-	2	0	OTUD4	146278456	0.027000	0.19231	0.108000	0.21378	0.880000	0.50808	2.210000	0.42816	1.621000	0.50320	0.655000	0.94253	ACT	.	.	none		0.463	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493	
PSG4	5672	hgsc.bcm.edu	37	19	43699417	43699417	+	Missense_Mutation	SNP	A	A	G	rs3859474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43699417A>G	ENST00000405312.3	-	4	955	c.718T>C	c.(718-720)Tcc>Ccc	p.S240P	PSG4_ENST00000244295.9_Intron|PSG4_ENST00000433626.2_Missense_Mutation_p.S147P	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	100	1	0.01		WXS	Illumina HiSeq	Phase_I	186	186	1	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	
KMT2D	8085	hgsc.bcm.edu	37	12	49433356	49433356	+	Silent	SNP	G	G	A	rs116686402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49433356G>A	ENST00000301067.7	-	32	8090	c.8091C>T	c.(8089-8091)cgC>cgT	p.R2697R	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2697					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)										GCAGGGTGTTGCGCTGGATCT	0.587													G|||	93	0.0185703	0.0696	0.0014	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.R2697R		Atlas-SNP	.											.	MLL2	1173	.	0			c.C8091T						PASS	.	G		239,3787		8,223,1782	17.0	19.0	18.0		8091	0.2	1.0	12	dbSNP_132	18	2,8382		0,2,4190	no	coding-synonymous	MLL2	NM_003482.3		8,225,5972	AA,AG,GG		0.0239,5.9364,1.942		2697/5538	49433356	241,12169	2013	4192	6205	SO:0001819	synonymous_variant	8085	exon32			GGTGTTGCGCTGG	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.8091C>T	12.37:g.49433356G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	43	17	0.395349	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			G|0.986;A|0.014	0.014	strong		0.587	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
ALDH16A1	126133	hgsc.bcm.edu	37	19	49969522	49969522	+	Silent	SNP	C	C	T	rs116631301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49969522C>T	ENST00000293350.4	+	14	2083	c.1920C>T	c.(1918-1920)gcC>gcT	p.A640A	ALDH16A1_ENST00000433981.2_Silent_p.A475A|ALDH16A1_ENST00000540132.1_Silent_p.A477A|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000455361.2_Silent_p.A589A	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	640						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)		GGGTGCAGGCCCAAGGCCACA	0.701													C|||	44	0.00878594	0.031	0.0043	5008	,	,		14666	0.0		0.0	False		,,,				2504	0.0				p.A640A		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.C1920T						PASS	.	C	,	145,4033		0,145,1944	7.0	9.0	8.0		1767,1920	3.3	1.0	19	dbSNP_132	8	3,8237		0,3,4117	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	0,148,6061	TT,TC,CC		0.0364,3.4706,1.1918	,	589/752,640/803	49969522	148,12270	2089	4120	6209	SO:0001819	synonymous_variant	126133	exon14			GCAGGCCCAAGGC	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.1920C>T	19.37:g.49969522C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			C|0.992;T|0.008	0.008	strong		0.701	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
MUC17	140453	hgsc.bcm.edu	37	7	100680370	100680370	+	Silent	SNP	C	C	T	rs201762013|rs10257974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100680370C>T	ENST00000306151.4	+	3	5737	c.5673C>T	c.(5671-5673)ccC>ccT	p.P1891P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1891	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)					CAACAACTCCCGCTGTCACCA	0.502													-|||	800	0.159744	0.2814	0.0879	5008	,	,		24145	0.0972		0.1193	False		,,,				2504	0.1524				p.P1891P		Atlas-SNP	.											.	MUC17	804	.	0			c.C5673T						PASS	.	T		1063,3333		193,677,1328	237.0	251.0	246.0		5673	-0.2	0.0	7	dbSNP_119	246	987,7613		56,875,3369	no	coding-synonymous	MUC17	NM_001040105.1		249,1552,4697	TT,TC,CC		11.4767,24.1811,15.7741		1891/4494	100680370	2050,10946	2198	4300	6498	SO:0001819	synonymous_variant	140453	exon3			AACTCCCGCTGTC	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.5673C>T	7.37:g.100680370C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			C|0.861;T|0.139	0.139	strong		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
KIF12	113220	hgsc.bcm.edu	37	9	116856481	116856481	+	Missense_Mutation	SNP	C	C	A	rs35719524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116856481C>A	ENST00000374118.3	-	10	1116	c.879G>T	c.(877-879)atG>atT	p.M293I	KIF12_ENST00000473174.1_Intron	NM_138424.1	NP_612433.1	Q96FN5	KIF12_HUMAN	kinesin family member 12	426	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	17						CATTCTCTAGCATGAACTCCT	0.627													C|||	485	0.096845	0.1218	0.1052	5008	,	,		16353	0.001		0.164	False		,,,				2504	0.0869				p.M293I		Atlas-SNP	.											.	KIF12	35	.	0			c.G879T						PASS	.	C	ILE/MET	678,3728	286.3+/-278.7	58,562,1583	63.0	66.0	65.0		879	5.6	1.0	9	dbSNP_126	65	1541,7059	289.0+/-299.1	132,1277,2891	yes	missense	KIF12	NM_138424.1	10	190,1839,4474	AA,AC,CC		17.9186,15.3881,17.0614	benign	293/514	116856481	2219,10787	2203	4300	6503	SO:0001583	missense	113220	exon10			CTCTAGCATGAAC	BC010626	CCDS6801.1	9q33.1	2008-02-05			ENSG00000136883	ENSG00000136883		"""Kinesins"""	21495	protein-coding gene	gene with protein product		611278					Standard	NM_138424		Approved		uc004bif.3	Q96FN5	OTTHUMG00000020533	ENST00000374118.3:c.879G>T	9.37:g.116856481C>A	ENSP00000363232:p.Met293Ile	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	46	0.638889	NM_138424	Q5TBE0	Missense_Mutation	SNP	ENST00000374118.3	37	CCDS6801.1	236	0.10805860805860806	69	0.1402439024390244	42	0.11602209944751381	1	0.0017482517482517483	124	0.16358839050131926	C	17.41	3.382259	0.61845	0.153881	0.179186	ENSG00000136883	ENST00000374118;ENST00000259410	T	0.73681	-0.77	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000001	T	0.00241	0.0007	L	0.34521	1.04	0.25332	P	0.9890252	B	0.33266	0.404	B	0.32533	0.147	T	0.10132	-1.0643	9	0.36615	T	0.2	.	15.0246	0.71659	0.0:1.0:0.0:0.0	rs35719524;rs62556539	426	Q96FN5	KIF12_HUMAN	I	293;426	ENSP00000363232:M293I	ENSP00000259410:M426I	M	-	3	0	KIF12	115896302	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.060000	0.41394	2.608000	0.88229	0.655000	0.94253	ATG	C|0.851;A|0.149	0.149	strong		0.627	KIF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053751.1	NM_138424	
BEGAIN	57596	hgsc.bcm.edu	37	14	101004432	101004432	+	Silent	SNP	G	G	A	rs7493484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101004432G>A	ENST00000355173.2	-	7	1727	c.1656C>T	c.(1654-1656)gcC>gcT	p.A552A	CTD-2062F14.3_ENST00000553301.1_lincRNA|BEGAIN_ENST00000556751.1_Silent_p.A488A|BEGAIN_ENST00000443071.2_Silent_p.A552A	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	552						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				TTTCCGGGGAGGCCTCCATGG	0.711													G|||	335	0.066893	0.2057	0.0144	5008	,	,		11513	0.0417		0.002	False		,,,				2504	0.0092				p.A552A	NSCLC(159;1889 2010 9965 27479 40101)	Atlas-SNP	.											.	BEGAIN	32	.	0			c.C1656T						PASS	.	G	,	723,3651		49,625,1513	11.0	13.0	12.0		1656,1656	-1.3	1.0	14	dbSNP_116	12	22,8540		0,22,4259	no	coding-synonymous,coding-synonymous	BEGAIN	NM_001159531.1,NM_020836.3	,	49,647,5772	AA,AG,GG		0.2569,16.5295,5.7591	,	552/594,552/594	101004432	745,12191	2187	4281	6468	SO:0001819	synonymous_variant	57596	exon7			CGGGGAGGCCTCC	BC002607	CCDS9962.1	14q32.2	2012-12-07	2012-12-07			ENSG00000183092			24163	protein-coding gene	gene with protein product			"""brain-enriched guanylate kinase-associated homolog (rat)"""			10819331	Standard	NM_020836		Approved	KIAA1446	uc010txa.2	Q9BUH8		ENST00000355173.2:c.1656C>T	14.37:g.101004432G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_020836	Q9NPU3|Q9P282	Silent	SNP	ENST00000355173.2	37	CCDS9962.1																																																																																			G|0.933;A|0.067	0.067	strong		0.711	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836	
ANKRD36B	57730	hgsc.bcm.edu	37	2	98165920	98165920	+	RNA	SNP	A	A	G	rs200418218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98165920A>G	ENST00000443455.1	-	0	1549							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		TTCTCTGGCTATATTCAAAAC	0.313													.|||	330	0.0658946	0.1808	0.0216	5008	,	,		39278	0.0556		0.0089	False		,,,				2504	0.0112				p.I480T		Atlas-SNP	.											.	.	.	.	0			c.T1439C						PASS	.	G	THR/ILE	466,3072		34,398,1337	51.0	20.0	30.0		1439	-1.1	0.0	2	dbSNP_134	30	107,7547		0,107,3720	no	missense	ANKRD36B	NM_025190.3	89	34,505,5057	GG,GA,AA		1.398,13.1713,5.1197	probably-damaging	480/1354	98165920	573,10619	1769	3827	5596			57730	exon20			CTGGCTATATTCA	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98165920A>G		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				A|0.983;G|0.017	0.017	strong		0.313	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
HLA-A	3105	hgsc.bcm.edu	37	6	29910340	29910340	+	Missense_Mutation	SNP	A	A	G	rs79326316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29910340A>G	ENST00000396634.1	+	3	351	c.10A>G	c.(10-12)Atg>Gtg	p.M4V	HLA-A_ENST00000376809.5_Missense_Mutation_p.M4V|HLA-A_ENST00000376802.2_Missense_Mutation_p.M4V|HLA-A_ENST00000376806.5_Missense_Mutation_p.M4V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	4					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						GATGGCCGTCATGGCGCCCCG	0.677									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.M4V		Atlas-SNP	.											.	HLA-A	89	.	0			c.A10G						PASS	.						36.0	38.0	37.0					6																	29910340		2201	4295	6496	SO:0001583	missense	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCCGTCATGGCGC	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.10A>G	6.37:g.29910340A>G	ENSP00000379873:p.Met4Val	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	266	54	0.203008	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	4.992	0.184267	0.09495	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00644	6.02;6.01;6.02;6.07	2.84	-5.68	0.02436	.	3.605040	0.01925	U	0.040781	T	0.00637	0.0021	M	0.76170	2.325	0.09310	N	1	P;B;B;B	0.42203	0.773;0.0;0.0;0.0	P;B;B;B	0.50270	0.636;0.001;0.001;0.001	T	0.11108	-1.0601	10	0.87932	D	0	.	5.9599	0.19293	0.2488:0.3159:0.4353:0.0	.	4;4;4;4	Q5SRN7;P16188;Q5SRN5;P04439	.;1A30_HUMAN;.;1A03_HUMAN	V	4	ENSP00000379873:M4V;ENSP00000366002:M4V;ENSP00000366005:M4V;ENSP00000365998:M4V	ENSP00000348012:M4V	M	+	1	0	HLA-A	30018319	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.865000	0.01649	-1.630000	0.01545	-0.537000	0.04273	ATG	A|0.971;G|0.029	0.029	strong		0.677	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SOX10	6663	hgsc.bcm.edu	37	22	38379543	38379543	+	Silent	SNP	G	G	A	rs73415876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38379543G>A	ENST00000396884.2	-	2	531	c.249C>T	c.(247-249)taC>taT	p.Y83Y	SOX10_ENST00000470555.1_Intron|SOX10_ENST00000360880.2_Silent_p.Y83Y|POLR2F_ENST00000405557.1_Intron|POLR2F_ENST00000407936.1_Intron	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	83					anatomical structure morphogenesis (GO:0009653)|cell maturation (GO:0048469)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|enteric nervous system development (GO:0048484)|in utero embryonic development (GO:0001701)|melanocyte differentiation (GO:0030318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system development (GO:0007422)|positive regulation of gliogenesis (GO:0014015)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extrinsic component of mitochondrial outer membrane (GO:0031315)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|transcription coactivator activity (GO:0003713)			NS(6)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|skin(2)	20	Melanoma(58;0.045)					GCGTCCAGTCGTAGCCGCTGA	0.657													G|||	205	0.0409345	0.152	0.0043	5008	,	,		11391	0.0		0.001	False		,,,				2504	0.0				p.Y83Y	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)	Atlas-SNP	.											.	SOX10	48	.	0			c.C249T	GRCh37	CM981855	SOX10	M	rs73415876	PASS	.	G		496,3910	215.5+/-234.4	22,452,1729	64.0	40.0	48.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	249	1.1	1.0	22	dbSNP_130	48	7,8591	4.3+/-15.6	0,7,4292	no	coding-synonymous	SOX10	NM_006941.3		22,459,6021	AA,AG,GG		0.0814,11.2574,3.868		83/467	38379543	503,12501	2203	4299	6502	SO:0001819	synonymous_variant	6663	exon2			CCAGTCGTAGCCG		CCDS13964.1	22q13.1	2014-09-17			ENSG00000100146	ENSG00000100146		"""SRY (sex determining region Y)-boxes"""	11190	protein-coding gene	gene with protein product	"""dominant megacolon, mouse, human homolog of"""	602229				9462749, 10441344, 12944398	Standard	NM_006941		Approved	DOM, WS4, WS2E	uc003aun.1	P56693	OTTHUMG00000149913	ENST00000396884.2:c.249C>T	22.37:g.38379543G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	120	65	0.541667	NM_006941	B4DV62|Q6FHW7	Silent	SNP	ENST00000396884.2	37	CCDS13964.1																																																																																			A|0.044;G|0.956	0.044	strong		0.657	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941	
CLCN6	1185	hgsc.bcm.edu	37	1	11884586	11884586	+	Silent	SNP	G	G	A	rs60602304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11884586G>A	ENST00000346436.6	+	8	676	c.624G>A	c.(622-624)tcG>tcA	p.S208S	CLCN6_ENST00000376496.3_Silent_p.S208S|CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000312413.6_Silent_p.S208S|CLCN6_ENST00000376487.3_Silent_p.S186S	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	208					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	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;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		ACAGTGGTTCGGTGGTGGGAG	0.597													G|||	115	0.0229633	0.0794	0.0043	5008	,	,		18300	0.004		0.001	False		,,,				2504	0.002				p.S208S		Atlas-SNP	.											.	CLCN6	77	.	0			c.G624A						PASS	.	G	,,,	421,3985	204.8+/-226.9	19,383,1801	75.0	68.0	71.0		624,624,624,624	-11.6	0.1	1	dbSNP_129	71	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLCN6	NM_001286.2,NM_021735.2,NM_021736.2,NM_021737.2	,,,	19,391,6093	AA,AG,GG		0.093,9.5552,3.2985	,,,	208/870,208/321,208/354,208/309	11884586	429,12577	2203	4300	6503	SO:0001819	synonymous_variant	1185	exon8			TGGTTCGGTGGTG	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.624G>A	1.37:g.11884586G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	99	53	0.535354	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Silent	SNP	ENST00000346436.6	37	CCDS138.1																																																																																			G|0.970;A|0.030	0.030	strong		0.597	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
HNRNPH3	3189	hgsc.bcm.edu	37	10	70101417	70101417	+	Missense_Mutation	SNP	G	G	C	rs16925347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70101417G>C	ENST00000265866.7	+	8	1016	c.851G>C	c.(850-852)gGc>gCc	p.G284A	HNRNPH3_ENST00000354695.5_Missense_Mutation_p.G269A|HNRNPH3_ENST00000469172.1_3'UTR|HNRNPH3_ENST00000441000.2_Missense_Mutation_p.G176A	NM_012207.2|NM_021644.3	NP_036339.1|NP_067676.2	P31942	HNRH3_HUMAN	heterogeneous nuclear ribonucleoprotein H3 (2H9)	284	Gly-rich.		G -> A (in dbSNP:rs16925347).		epithelial cell differentiation (GO:0030855)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)	11						GGAATGGGAGGCTACGGAAGA	0.368													G|||	183	0.0365415	0.003	0.098	5008	,	,		17232	0.001		0.0845	False		,,,				2504	0.0256				p.G284A		Atlas-SNP	.											.	HNRNPH3	33	.	0			c.G851C						PASS	.	G	ALA/GLY,ALA/GLY	89,4317	74.1+/-112.3	2,85,2116	95.0	101.0	99.0		851,806	4.8	1.0	10	dbSNP_123	99	787,7813	185.3+/-233.1	39,709,3552	yes	missense,missense	HNRNPH3	NM_012207.2,NM_021644.3	60,60	41,794,5668	CC,CG,GG		9.1512,2.02,6.7354	probably-damaging,probably-damaging	284/347,269/332	70101417	876,12130	2203	4300	6503	SO:0001583	missense	3189	exon8			TGGGAGGCTACGG		CCDS7278.1, CCDS7279.1	10q22	2013-02-12		2008-04-18	ENSG00000096746	ENSG00000096746		"""RNA binding motif (RRM) containing"""	5043	protein-coding gene	gene with protein product		602324		HNRPH3		8999868	Standard	NM_021644		Approved	2H9	uc001jnw.4	P31942	OTTHUMG00000018349	ENST00000265866.7:c.851G>C	10.37:g.70101417G>C	ENSP00000265866:p.Gly284Ala	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_012207	A8K682|B3KRE1|Q9BSX1|Q9NP53|Q9NP96|Q9NPA7|Q9NPI4|Q9UFU4|Q9Y4J5	Missense_Mutation	SNP	ENST00000265866.7	37	CCDS7278.1	113	0.051739926739926737	1	0.0020325203252032522	41	0.1132596685082873	1	0.0017482517482517483	70	0.09234828496042216	G	11.23	1.577265	0.28092	0.0202	0.091512	ENSG00000096746	ENST00000265866;ENST00000441000;ENST00000354695	T;T;T	0.16196	2.7;2.36;2.55	5.68	4.77	0.60923	Nucleotide-binding, alpha-beta plait (1);	0.071468	0.64402	D	0.000018	T	0.00356	0.0011	L	0.52011	1.625	0.09310	P	0.9999999999804431	B;B;B	0.10296	0.001;0.003;0.002	B;B;B	0.08055	0.001;0.003;0.002	T	0.11842	-1.0571	9	0.20046	T	0.44	.	16.8329	0.85949	0.0:0.1285:0.8715:0.0	rs16925347;rs52833498;rs16925347	176;269;284	B4DHY1;P31942-2;P31942	.;.;HNRH3_HUMAN	A	284;176;269	ENSP00000265866:G284A;ENSP00000409869:G176A;ENSP00000346726:G269A	ENSP00000265866:G284A	G	+	2	0	HNRNPH3	69771423	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.872000	0.56085	1.390000	0.46547	0.563000	0.77884	GGC	G|0.943;C|0.057	0.057	strong		0.368	HNRNPH3-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090165.1		
GRIN2A	2903	hgsc.bcm.edu	37	16	9916204	9916204	+	Silent	SNP	C	C	G	rs9806806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:9916204C>G	ENST00000396573.2	-	11	2394	c.2085G>C	c.(2083-2085)cgG>cgC	p.R695R	GRIN2A_ENST00000396575.2_Silent_p.R695R|GRIN2A_ENST00000404927.2_Silent_p.R695R|GRIN2A_ENST00000330684.3_Silent_p.R695R|GRIN2A_ENST00000535259.1_Silent_p.R538R|GRIN2A_ENST00000562109.1_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	282	1	0.0035461		WXS	Illumina HiSeq	Phase_I	279	145	0.519713	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		
LCN8	138307	hgsc.bcm.edu	37	9	139649612	139649612	+	Splice_Site	SNP	C	C	A	rs2282258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139649612C>A	ENST00000371688.3	-	6	717	c.422G>T	c.(421-423)gGg>gTg	p.G141V	LCN8_ENST00000482893.1_5'UTR	NM_178469.3	NP_848564.2	Q6JVE9	LCN8_HUMAN	lipocalin 8	164					response to hormone (GO:0009725)|transport (GO:0006810)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	10	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)		GGCACACCGCCCTGCAGGATA	0.716													C|||	776	0.154952	0.1467	0.2363	5008	,	,		14332	0.1518		0.1292	False		,,,				2504	0.138				p.G141V		Atlas-SNP	.											LCN8,colon,carcinoma,0,1	LCN8	14	1	0			c.G422T						PASS	.	C	VAL/GLY	616,3770		43,530,1620	23.0	25.0	24.0		422	2.7	1.0	9	dbSNP_100	24	1184,7410		84,1016,3197	yes	missense-near-splice	LCN8	NM_178469.3	109	127,1546,4817	AA,AC,CC		13.7771,14.0447,13.8675	probably-damaging	141/153	139649612	1800,11180	2193	4297	6490	SO:0001630	splice_region_variant	138307	exon6			CACCGCCCTGCAG	AK124003	CCDS35183.1	9q34.3	2011-10-24	2005-01-11		ENSG00000204001	ENSG00000204001		"""Lipocalins"""	27038	protein-coding gene	gene with protein product		612902	"""chromosome 9 open reading frame 137"", ""lipocalin 5"""	LCN5			Standard	XM_005266058		Approved		uc004cjb.1	Q6JVE9	OTTHUMG00000020942	ENST00000371688.3:c.422-1G>T	9.37:g.139649612C>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	156	104	0.666667	NM_178469	A1L4A8|A6NMN9|Q5T5R4	Missense_Mutation	SNP	ENST00000371688.3	37	CCDS35183.1	350	0.16025641025641027	98	0.1991869918699187	73	0.20165745856353592	83	0.1451048951048951	96	0.1266490765171504	C	10.47	1.358374	0.24598	0.140447	0.137771	ENSG00000204001	ENST00000371688	T	0.52295	0.67	2.74	2.74	0.32292	.	.	.	.	.	T	0.00073	0.0002	L	0.27053	0.805	0.19575	P	0.999969191	D	0.89917	1.0	D	0.91635	0.999	T	0.03829	-1.1000	8	0.28530	T	0.3	.	9.1522	0.36971	0.0:1.0:0.0:0.0	rs2282258	141	Q6JVE9-2	.	V	141	ENSP00000360753:G141V	ENSP00000360753:G141V	G	-	2	0	LCN8	138769433	0.896000	0.30565	0.962000	0.40283	0.010000	0.07245	1.807000	0.38902	1.850000	0.53721	0.561000	0.74099	GGG	C|0.851;A|0.149	0.149	strong		0.716	LCN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055109.1	NM_178469	Missense_Mutation
PSG11	5680	hgsc.bcm.edu	37	19	43519362	43519362	+	Silent	SNP	C	C	T	rs11083680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43519362C>T	ENST00000401740.1	-	4	973	c.870G>A	c.(868-870)caG>caA	p.Q290Q	PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000403486.1_Silent_p.Q168Q|PSG11_ENST00000320078.7_Silent_p.Q290Q|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						PASS	.	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	184	0	0		WXS	Illumina HiSeq	Phase_I	189	87	0.460317	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	
RAPGEF3	10411	hgsc.bcm.edu	37	12	48134768	48134768	+	Missense_Mutation	SNP	A	A	T	rs80097705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48134768A>T	ENST00000449771.2	-	20	2067	c.1979T>A	c.(1978-1980)cTg>cAg	p.L660Q	RAPGEF3_ENST00000549151.1_Missense_Mutation_p.L618Q|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.L569Q|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.L618Q|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.L660Q|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.L618Q			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	660					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)		GGCACTCACCAGGTCCAGCCC	0.657													A|||	149	0.0297524	0.1059	0.0115	5008	,	,		15902	0.0		0.001	False		,,,				2504	0.0				p.L660Q		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.T1979A						PASS	.	A	GLN/LEU,GLN/LEU,GLN/LEU	441,3965	204.5+/-226.7	16,409,1778	28.0	26.0	27.0		1979,1853,1853	2.8	1.0	12	dbSNP_131	27	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	113,113,113	16,412,6075	TT,TA,AA		0.0349,10.0091,3.4138	benign,benign,benign	660/924,618/882,618/882	48134768	444,12562	2203	4300	6503	SO:0001583	missense	10411	exon20			CTCACCAGGTCCA	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.1979T>A	12.37:g.48134768A>T	ENSP00000395708:p.Leu660Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	64	0.029304029304029304	60	0.12195121951219512	4	0.011049723756906077	0	0.0	0	0.0	A	15.33	2.801075	0.50315	0.100091	3.49E-4	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	4.0	2.85	0.33270	Guanine-nucleotide dissociation stimulator CDC25 (2);Ras guanine nucleotide exchange factor, domain (1);	0.318780	0.26567	N	0.023652	T	0.00271	0.0008	N	0.25332	0.735	0.25580	P	0.9868038	B	0.13145	0.007	B	0.15484	0.013	T	0.05007	-1.0912	9	0.52906	T	0.07	.	7.9374	0.29937	0.898:0.0:0.102:0.0	.	660	O95398	RPGF3_HUMAN	Q	618;660;307;618;618;618;660;623;569	ENSP00000384521:L618Q;ENSP00000395708:L660Q;ENSP00000448619:L618Q;ENSP00000171000:L618Q;ENSP00000373864:L660Q;ENSP00000448480:L569Q	ENSP00000171000:L618Q	L	-	2	0	RAPGEF3	46421035	0.352000	0.24895	1.000000	0.80357	0.997000	0.91878	1.101000	0.31037	1.609000	0.50190	0.459000	0.35465	CTG	A|0.965;T|0.035	0.035	strong		0.657	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
RANBP2	5903	hgsc.bcm.edu	37	2	109384665	109384665	+	Missense_Mutation	SNP	A	A	G	rs145613015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:109384665A>G	ENST00000283195.6	+	20	7796	c.7670A>G	c.(7669-7671)aAt>aGt	p.N2557S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2557					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						AAAAGTAACAATAGTGAAACT	0.363													A|||	10	0.00199681	0.0068	0.0014	5008	,	,		20419	0.0		0.0	False		,,,				2504	0.0				p.N2557S		Atlas-SNP	.											.	RANBP2	488	.	0			c.A7670G						PASS	.	A	SER/ASN	27,4379	30.8+/-60.4	1,25,2177	84.0	98.0	93.0		7670	-1.0	0.0	2	dbSNP_134	93	0,8594		0,0,4297	no	missense	RANBP2	NM_006267.4	46	1,25,6474	GG,GA,AA		0.0,0.6128,0.2077	benign	2557/3225	109384665	27,12973	2203	4297	6500	SO:0001583	missense	5903	exon20			GTAACAATAGTGA	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.7670A>G	2.37:g.109384665A>G	ENSP00000283195:p.Asn2557Ser	Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	378	186	0.492063	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	A	0.024	-1.385684	0.01194	0.006128	0.0	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.25250	1.81	5.31	-1.03	0.10102	.	.	.	.	.	T	0.04679	0.0127	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39292	-0.9621	9	0.07644	T	0.81	-6.4079	10.0576	0.42255	0.5205:0.0:0.4795:0.0	.	2557	P49792	RBP2_HUMAN	S	1581;2557	ENSP00000283195:N2557S	ENSP00000283195:N2557S	N	+	2	0	RANBP2	108751097	0.000000	0.05858	0.007000	0.13788	0.682000	0.39822	-0.668000	0.05268	-0.097000	0.12307	0.377000	0.23210	AAT	.	.	weak		0.363	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
OR10T2	128360	hgsc.bcm.edu	37	1	158368846	158368846	+	Missense_Mutation	SNP	T	T	C	rs6662382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158368846T>C	ENST00000334438.1	-	1	410	c.411A>G	c.(409-411)atA>atG	p.I137M		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	137			I -> M (in dbSNP:rs6662382).			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)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					GCCTTTTGTTTATGATGAGTG	0.458													C|||	1829	0.365216	0.4191	0.3055	5008	,	,		20669	0.2262		0.3131	False		,,,				2504	0.5317				p.I137M		Atlas-SNP	.											.	OR10T2	76	.	0			c.A411G						PASS	.	C	MET/ILE	1732,2674	649.7+/-398.9	336,1060,807	107.0	106.0	106.0		411	2.6	0.2	1	dbSNP_116	106	2674,5926	685.0+/-404.0	402,1870,2028	yes	missense	OR10T2	NM_001004475.1	10	738,2930,2835	CC,CT,TT		31.093,39.31,33.8767	benign	137/315	158368846	4406,8600	2203	4300	6503	SO:0001583	missense	128360	exon1			TTTGTTTATGATG	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.411A>G	1.37:g.158368846T>C	ENSP00000334115:p.Ile137Met	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	702	0.32142857142857145	212	0.43089430894308944	98	0.27071823204419887	147	0.256993006993007	245	0.3232189973614776	C	0.005	-2.191600	0.00302	0.3931	0.31093	ENSG00000186306	ENST00000334438	T	0.16073	2.37	4.57	2.64	0.31445	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	N	0.000099	T	0.00666	0.0022	N	0.00074	-2.255	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46952	-0.9154	9	0.02654	T	1	.	9.2914	0.37789	0.0:0.507:0.4123:0.0807	rs6662382;rs52805250;rs60803248;rs6662382	137	Q8NGX3	O10T2_HUMAN	M	137	ENSP00000334115:I137M	ENSP00000334115:I137M	I	-	3	3	OR10T2	156635470	1.000000	0.71417	0.223000	0.23860	0.373000	0.29922	2.066000	0.41452	0.164000	0.19529	-0.119000	0.15052	ATA	T|0.659;C|0.341	0.341	strong		0.458	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
TTC21B	79809	hgsc.bcm.edu	37	2	166770120	166770120	+	Silent	SNP	A	A	G	rs10176588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	203	0	0		WXS	Illumina HiSeq	Phase_I	197	97	0.492386	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	
PALD1	27143	hgsc.bcm.edu	37	10	72294192	72294192	+	Missense_Mutation	SNP	C	C	T	rs141167395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72294192C>T	ENST00000263563.6	+	9	1302	c.1034C>T	c.(1033-1035)aCg>aTg	p.T345M		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	345						cytosol (GO:0005829)											GCTGCCCCCACGCAGGCCAAG	0.622													C|||	6	0.00119808	0.0038	0.0	5008	,	,		16332	0.001		0.0	False		,,,				2504	0.0				p.T345M		Atlas-SNP	.											.	.	.	.	0			c.C1034T						PASS	.	C	MET/THR	13,4391	20.2+/-43.8	0,13,2189	38.0	35.0	36.0		1034	-4.0	0.0	10	dbSNP_134	36	0,8598		0,0,4299	yes	missense	KIAA1274	NM_014431.2	81	0,13,6488	TT,TC,CC		0.0,0.2952,0.1	benign	345/857	72294192	13,12989	2202	4299	6501	SO:0001583	missense	27143	exon9			CCCCCACGCAGGC	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.1034C>T	10.37:g.72294192C>T	ENSP00000263563:p.Thr345Met	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	9.315	1.056639	0.19907	0.002952	0.0	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.24908	1.83	4.62	-3.99	0.04069	.	1.808830	0.02724	N	0.114334	T	0.13628	0.0330	N	0.11201	0.11	0.09310	N	1	B	0.18610	0.029	B	0.15052	0.012	T	0.23619	-1.0183	10	0.45353	T	0.12	0.2671	6.7714	0.23596	0.1154:0.3697:0.0:0.5148	.	345	Q9ULE6	PALD_HUMAN	M	345	ENSP00000263563:T345M	ENSP00000263563:T345M	T	+	2	0	KIAA1274	71964198	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.206000	0.01231	-1.208000	0.02634	-0.448000	0.05591	ACG	C|0.999;T|0.001	0.001	strong		0.622	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
SLC43A2	124935	hgsc.bcm.edu	37	17	1494660	1494660	+	Silent	SNP	G	G	A	rs73976240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1494660G>A	ENST00000301335.5	-	8	922	c.834C>T	c.(832-834)tcC>tcT	p.S278S	SLC43A2_ENST00000574274.1_5'UTR|SLC43A2_ENST00000412517.3_Silent_p.S141S|SLC43A2_ENST00000571650.1_Silent_p.S278S|SLC43A2_ENST00000382147.4_Silent_p.S278S	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	278					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CACTCCTCATGGAGCTGCCCA	0.622													G|||	129	0.0257588	0.0961	0.0029	5008	,	,		10550	0.0		0.0	False		,,,				2504	0.0				p.S278S		Atlas-SNP	.											.	SLC43A2	37	.	0			c.C834T						PASS	.	G		311,4095	167.3+/-198.3	13,285,1905	76.0	70.0	72.0		834	5.1	1.0	17	dbSNP_130	72	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	SLC43A2	NM_152346.1		13,288,6202	AA,AG,GG		0.0349,7.0586,2.4143		278/570	1494660	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	124935	exon8			CCTCATGGAGCTG	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.834C>T	17.37:g.1494660G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	48	0.578313	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																			G|0.971;A|0.029	0.029	strong		0.622	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346	
INSL4	3641	hgsc.bcm.edu	37	9	5231712	5231712	+	Silent	SNP	T	T	A	rs12720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	88	0	0		WXS	Illumina HiSeq	Phase_I	100	40	0.4	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	
APLNR	187	hgsc.bcm.edu	37	11	57003581	57003581	+	Missense_Mutation	SNP	C	C	T	rs7943508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57003581C>T	ENST00000606794.1	-	1	1094	c.898G>A	c.(898-900)Gtc>Atc	p.V300I		NM_005161.4	NP_005152.1	P35414	APJ_HUMAN	apelin receptor	300			V -> I (in dbSNP:rs7943508).		G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation (GO:0007369)|heart development (GO:0007507)|regulation of body fluid levels (GO:0050878)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)	p.V300F(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CAGCTGTTGACGTAGCTGATG	0.597													C|||	71	0.0141773	0.0492	0.0086	5008	,	,		22043	0.0		0.0	False		,,,				2504	0.0				p.V300I		Atlas-SNP	.											APLNR,caecum,carcinoma,0,2	APLNR	62	2	1	Substitution - Missense(1)	lung(1)	c.G898A						PASS	.	C	ILE/VAL	180,4222	112.5+/-150.6	4,172,2025	115.0	62.0	80.0		898	2.6	1.0	11	dbSNP_116	80	3,8589	1.2+/-3.3	0,3,4293	yes	missense	APLNR	NM_005161.4	29	4,175,6318	TT,TC,CC		0.0349,4.0891,1.4083	benign	300/381	57003581	183,12811	2201	4296	6497	SO:0001583	missense	187	exon1			TGTTGACGTAGCT	U03642	CCDS7950.1	11q12.1	2012-08-08	2008-05-12	2008-05-12	ENSG00000134817	ENSG00000134817			339	protein-coding gene	gene with protein product	"""APJ (apelin) receptor"""	600052	"""angiotensin II receptor-like 1"""	AGTRL1		8294032, 14622440	Standard	NM_005161		Approved	FLJ90771, APJ, APJR	uc001njo.3	P35414	OTTHUMG00000167021	ENST00000606794.1:c.898G>A	11.37:g.57003581C>T	ENSP00000475344:p.Val300Ile	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	152	86	0.565789	NM_005161		Missense_Mutation	SNP	ENST00000606794.1	37	CCDS7950.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	C	7.586	0.669656	0.14776	0.040891	3.49E-4	ENSG00000134817	ENST00000257254;ENST00000326830;ENST00000444275	T	0.37411	1.2	5.46	2.62	0.31277	GPCR, rhodopsin-like superfamily (1);	0.326514	0.28067	N	0.016724	T	0.01558	0.0050	L	0.31845	0.965	0.26372	N	0.976879	B	0.30824	0.296	B	0.23852	0.049	T	0.07654	-1.0761	10	0.20519	T	0.43	-43.2768	8.7044	0.34345	0.0:0.6322:0.0:0.3678	rs7943508;rs52819082;rs7943508	300	P35414	APJ_HUMAN	I	300;181;219	ENSP00000257254:V300I	ENSP00000257254:V300I	V	-	1	0	APLNR	56760157	0.163000	0.22920	1.000000	0.80357	0.982000	0.71751	-0.359000	0.07632	0.292000	0.22492	-0.751000	0.03497	GTC	C|0.986;T|0.014	0.014	strong		0.597	APLNR-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470575.1	NM_005161	
SLC4A8	9498	hgsc.bcm.edu	37	12	51855009	51855009	+	Silent	SNP	T	T	G	rs150970094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:51855009T>G	ENST00000453097.2	+	9	1252	c.1035T>G	c.(1033-1035)ggT>ggG	p.G345G	SLC4A8_ENST00000514353.3_Silent_p.G292G|SLC4A8_ENST00000535225.2_Silent_p.G292G|SLC4A8_ENST00000358657.3_Silent_p.G372G|SLC4A8_ENST00000394856.1_Silent_p.G292G	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		TCTTATTGGGTCCAGTAGGGA	0.398													T|||	18	0.00359425	0.0136	0.0	5008	,	,		18676	0.0		0.0	False		,,,				2504	0.0				p.G345G		Atlas-SNP	.											SLC4A8,back,malignant_melanoma,+2,1	SLC4A8	292	1	0			c.T1035G						PASS	.	T	,	38,4368	42.3+/-75.8	0,38,2165	155.0	142.0	147.0		1035,1035	-2.6	1.0	12	dbSNP_134	147	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC4A8	NM_001039960.1,NM_004858.2	,	0,38,6465	GG,GT,TT		0.0,0.8625,0.2922	,	345/1094,345/1045	51855009	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	9498	exon9			ATTGGGTCCAGTA	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"""Solute carriers"""	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1035T>G	12.37:g.51855009T>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	164	78	0.47561	NM_001039960		Silent	SNP	ENST00000453097.2	37	CCDS44890.1																																																																																			T|0.997;G|0.003	0.003	strong		0.398	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858	
DLG5	9231	hgsc.bcm.edu	37	10	79556301	79556301	+	Missense_Mutation	SNP	A	A	G	rs74140333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79556301A>G	ENST00000372391.2	-	28	5221	c.5216T>C	c.(5215-5217)cTg>cCg	p.L1739P	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Missense_Mutation_p.L1399P	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1739	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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)			GACAGGCCTCAGAGCGGTGCA	0.602													A|||	68	0.0135783	0.0499	0.0014	5008	,	,		20065	0.0		0.001	False		,,,				2504	0.0				p.L1739P		Atlas-SNP	.											.	DLG5	154	.	0			c.T5216C						PASS	.	A	PRO/LEU	150,4256	104.3+/-142.8	2,146,2055	100.0	85.0	90.0		5216	3.6	1.0	10	dbSNP_130	90	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DLG5	NM_004747.3	98	2,148,6353	GG,GA,AA		0.0233,3.4044,1.1687	benign	1739/1920	79556301	152,12854	2203	4300	6503	SO:0001583	missense	9231	exon28			GGCCTCAGAGCGG	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.5216T>C	10.37:g.79556301A>G	ENSP00000361467:p.Leu1739Pro	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	211	98	0.464455	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	37	CCDS7353.2	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	12.73	2.026468	0.35701	0.034044	2.33E-4	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.20598	2.06;2.06;2.06	5.97	3.63	0.41609	Guanylate kinase/L-type calcium channel (1);	0.000000	0.31519	N	0.007516	T	0.00784	0.0026	N	0.00652	-1.29	0.58432	D	0.999999	B;B	0.10296	0.001;0.003	B;B	0.17433	0.002;0.018	T	0.31586	-0.9938	10	0.24483	T	0.36	.	4.6381	0.12534	0.5759:0.0:0.4241:0.0	.	1739;1399	Q8TDM6;Q8TDM6-2	DLG5_HUMAN;.	P	1739;700;1399	ENSP00000361467:L1739P;ENSP00000394797:L700P;ENSP00000361464:L1399P	ENSP00000361464:L1399P	L	-	2	0	DLG5	79226307	1.000000	0.71417	0.970000	0.41538	0.687000	0.40016	4.450000	0.60041	1.069000	0.40788	0.533000	0.62120	CTG	A|0.989;G|0.011	0.011	strong		0.602	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
SPECC1L	23384	hgsc.bcm.edu	37	22	24761502	24761502	+	Silent	SNP	G	G	A	rs139166286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24761502G>A	ENST00000314328.9	+	13	3171	c.2886G>A	c.(2884-2886)tcG>tcA	p.S962S	SPECC1L_ENST00000437398.1_Silent_p.S962S|SPECC1L_ENST00000541492.1_Silent_p.S962S|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	962					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						AGGGAGCGTCGCCAGCCTCTC	0.502																																					p.S962S		Atlas-SNP	.											.	SPECC1L	85	.	0			c.G2886A						PASS	.	G	,	18,4388	25.3+/-52.1	0,18,2185	109.0	84.0	92.0		2886,2886	-11.1	0.0	22	dbSNP_134	92	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SPECC1L	NM_001145468.1,NM_015330.2	,	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	,	962/1118,962/1118	24761502	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	23384	exon12			AGCGTCGCCAGCC	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"""cytokinesis and spindle organization A"", ""cytospin A"""	614140	"""SPECC1-like"""			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.2886G>A	22.37:g.24761502G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_001145468	B7Z758|F5H1H6|O15081	Silent	SNP	ENST00000314328.9	37	CCDS33619.1																																																																																			A|0.002;G|0.998	0.002	strong		0.502	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330	
RGPD4	285190	hgsc.bcm.edu	37	2	108496435	108496435	+	Missense_Mutation	SNP	T	T	A	rs832352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:108496435T>A	ENST00000408999.3	+	21	5013	c.4936T>A	c.(4936-4938)Tgg>Agg	p.W1646R	RGPD4_ENST00000354986.4_Missense_Mutation_p.W1646R	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1646					protein targeting to Golgi (GO:0000042)			p.W1646R(1)		breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						GCCTCCATTATGGCATGCTGA	0.358													t|||	2779	0.554912	0.5204	0.4914	5008	,	,		18442	0.3472		0.7008	False		,,,				2504	0.7106				p.W1646R		Atlas-SNP	.											RGPD4,NS,carcinoma,0,1	RGPD4	112	1	1	Substitution - Missense(1)	kidney(1)	c.T4936A						PASS	.						42.0	36.0	38.0					2																	108496435		692	1578	2270	SO:0001583	missense	285190	exon21			CCATTATGGCATG	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.4936T>A	2.37:g.108496435T>A	ENSP00000386810:p.Trp1646Arg	Somatic	498	1	0.00200803		WXS	Illumina HiSeq	Phase_I	478	415	0.868201	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	CCDS46381.1	1139	0.5215201465201466	247	0.5020325203252033	187	0.5165745856353591	197	0.34440559440559443	508	0.6701846965699209	t	10.26	1.301807	0.23736	.	.	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.42513	0.97;0.97	0.854	0.854	0.19007	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.36921	P	0.10862300000000003	D	0.64830	0.994	D	0.67725	0.953	T	0.35176	-0.9799	8	0.21540	T	0.41	-0.4067	7.1387	0.25543	0.0:0.0:0.0:1.0	rs832352;rs3820958	1646	Q7Z3J3	RGPD4_HUMAN	R	1646;1646;1013	ENSP00000347081:W1646R;ENSP00000386810:W1646R	ENSP00000347081:W1646R	W	+	1	0	RGPD4	107862867	1.000000	0.71417	0.997000	0.53966	0.893000	0.52053	3.939000	0.56591	0.641000	0.30601	0.327000	0.21459	TGG	T|0.446;A|0.554	0.554	strong		0.358	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
CDC27	996	hgsc.bcm.edu	37	17	45214623	45214623	+	Missense_Mutation	SNP	G	G	A	rs75637741		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45214623G>A	ENST00000066544.3	-	14	1901	c.1808C>T	c.(1807-1809)gCc>gTc	p.A603V	CDC27_ENST00000531206.1_Missense_Mutation_p.A609V|CDC27_ENST00000527547.1_Missense_Mutation_p.A602V|CDC27_ENST00000446365.2_Missense_Mutation_p.A542V	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	603					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAGAGTATAGGCATAAGCGTA	0.383																																					p.A609V		Atlas-SNP	.											CDC27_ENST00000531206,rectum,carcinoma,0,2	CDC27	337	2	0			c.C1826T						scavenged	.																																			SO:0001583	missense	996	exon14			GTATAGGCATAAG	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1808C>T	17.37:g.45214623G>A	ENSP00000066544:p.Ala603Val	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	36	8	0.222222	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	36	5.873394	0.97049	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.81	5.81	0.92471	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.74382	0.3709	M	0.93594	3.435	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.993;0.993;0.994	T	0.80863	-0.1192	10	0.87932	D	0	-9.797	17.5633	0.87913	0.0:0.0:1.0:0.0	.	542;602;609;603	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	V	603;609;542;602	ENSP00000066544:A603V;ENSP00000434614:A609V;ENSP00000392802:A542V;ENSP00000437339:A602V	ENSP00000066544:A603V	A	-	2	0	CDC27	42569622	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.761000	0.94854	0.585000	0.79938	GCC	.	.	weak		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
ATP6V1C1	528	hgsc.bcm.edu	37	8	104054603	104054603	+	Silent	SNP	T	T	C	rs7009365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104054603T>C	ENST00000395862.3	+	3	327	c.168T>C	c.(166-168)gaT>gaC	p.D56D	ATP6V1C1_ENST00000521514.1_5'UTR|ATP6V1C1_ENST00000518857.1_Intron|ATP6V1C1_ENST00000518738.1_Silent_p.D56D	NM_001695.4	NP_001686.1	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1	56					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)			GCTTGTCAGATGAACTGGCTA	0.373													T|||	382	0.076278	0.2685	0.0375	5008	,	,		19747	0.0		0.0	False		,,,				2504	0.001				p.D56D		Atlas-SNP	.											.	ATP6V1C1	33	.	0			c.T168C						PASS	.	T		917,3489	353.1+/-312.0	113,691,1399	226.0	216.0	220.0		168	0.8	1.0	8	dbSNP_116	220	10,8590	4.3+/-15.6	1,8,4291	no	coding-synonymous	ATP6V1C1	NM_001695.4		114,699,5690	CC,CT,TT		0.1163,20.8125,7.1275		56/383	104054603	927,12079	2203	4300	6503	SO:0001819	synonymous_variant	528	exon3			GTCAGATGAACTG	X69151	CCDS6296.1	8p22.3	2011-05-24	2006-01-13	2002-05-10	ENSG00000155097	ENSG00000155097	3.6.3.14	"""ATPases / V-type"""	856	protein-coding gene	gene with protein product		603097	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) 42kD"", ""ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1"""	ATP6D, ATP6C		8250920, 14580332	Standard	NM_001695		Approved	VATC, Vma5	uc003ykz.4	P21283	OTTHUMG00000164761	ENST00000395862.3:c.168T>C	8.37:g.104054603T>C		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	157	82	0.522293	NM_001695		Silent	SNP	ENST00000395862.3	37	CCDS6296.1																																																																																			T|0.922;C|0.078	0.078	strong		0.373	ATP6V1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380101.1	NM_001695	
DST	667	hgsc.bcm.edu	37	6	56505063	56505063	+	Silent	SNP	A	A	G	rs2144407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:56505063A>G	ENST00000361203.3	-	14	1742	c.1735T>C	c.(1735-1737)Ttg>Ctg	p.L579L	DST_ENST00000312431.6_Silent_p.L579L|DST_ENST00000370788.2_Silent_p.L579L|DST_ENST00000421834.2_Silent_p.L579L|DST_ENST00000370769.4_Silent_p.L579L|DST_ENST00000244364.6_Silent_p.L253L|DST_ENST00000370754.5_Silent_p.L757L|DST_ENST00000370765.6_Silent_p.L253L|DST_ENST00000518935.1_Silent_p.L253L|DST_ENST00000446842.2_Silent_p.L253L			Q03001	DYST_HUMAN	dystonin	579					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)			ATCAACTTCAAAGTTTGCAAT	0.388													G|||	660	0.131789	0.4281	0.0418	5008	,	,		19856	0.0179		0.0288	False		,,,				2504	0.0184				p.L253L		Atlas-SNP	.											.	DST	1427	.	0			c.T757C						PASS	.	G	,	1704,2702	651.3+/-399.2	335,1034,834	76.0	79.0	78.0		757,757	4.9	0.9	6	dbSNP_96	78	381,8219	801.6+/-407.4	10,361,3929	no	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	345,1395,4763	GG,GA,AA		4.4302,38.6745,16.0311	,	253/2650,253/5172	56505063	2085,10921	2203	4300	6503	SO:0001819	synonymous_variant	667	exon4			ACTTCAAAGTTTG	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.1735T>C	6.37:g.56505063A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	158	74	0.468354	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																				A|0.854;C|0.000;G|0.146	0.146	strong		0.388	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
IL4R	3566	hgsc.bcm.edu	37	16	27373915	27373915	+	Silent	SNP	G	G	T	rs2234898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27373915G>T	ENST00000395762.2	+	11	1501	c.1242G>T	c.(1240-1242)ctG>ctT	p.L414L	IL4R_ENST00000170630.2_Silent_p.L414L|IL4R_ENST00000543915.2_Silent_p.L414L|IL4R_ENST00000380922.3_Silent_p.L399L	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	79	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	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		
PCDHB6	56130	hgsc.bcm.edu	37	5	140530534	140530534	+	Missense_Mutation	SNP	G	G	C	rs10076554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140530534G>C	ENST00000231136.1	+	1	696	c.696G>C	c.(694-696)ttG>ttC	p.L232F	PCDHB6_ENST00000543635.1_Missense_Mutation_p.L96F	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	232	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		L -> F (in dbSNP:rs10076554).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCAGGTTTTGGACATCAATG	0.587													G|||	73	0.0145767	0.0537	0.0029	5008	,	,		17505	0.0		0.0	False		,,,				2504	0.0				p.L232F		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G696C						PASS	.	G	PHE/LEU	193,4213	121.3+/-158.8	4,185,2014	44.0	48.0	47.0		696	0.6	0.5	5	dbSNP_119	47	0,8600		0,0,4300	yes	missense	PCDHB6	NM_018939.2	22	4,185,6314	CC,CG,GG		0.0,4.3804,1.4839	possibly-damaging	232/795	140530534	193,12813	2203	4300	6503	SO:0001583	missense	56130	exon1			GGTTTTGGACATC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.696G>C	5.37:g.140530534G>C	ENSP00000231136:p.Leu232Phe	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	G	14.12	2.441466	0.43326	0.043804	0.0	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.01804	4.63;4.63	4.85	0.653	0.17828	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.01320	0.0043	M	0.93106	3.38	0.26654	N	0.97205	D	0.57571	0.98	D	0.63381	0.914	T	0.08432	-1.0722	9	0.72032	D	0.01	.	3.9631	0.09420	0.3108:0.0:0.4427:0.2466	rs10076554;rs61376880;rs10076554	232	Q9Y5E3	PCDB6_HUMAN	F	96;232;17	ENSP00000438466:L96F;ENSP00000231136:L232F	ENSP00000231136:L232F	L	+	3	2	PCDHB6	140510718	0.118000	0.22208	0.455000	0.27031	0.888000	0.51559	-0.354000	0.07681	0.178000	0.19917	0.561000	0.74099	TTG	G|0.986;C|0.014	0.014	strong		0.587	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
DBNL	28988	hgsc.bcm.edu	37	7	44096482	44096482	+	Missense_Mutation	SNP	G	G	A	rs61735009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44096482G>A	ENST00000448521.1	+	5	552	c.454G>A	c.(454-456)Gtg>Atg	p.V152M	DBNL_ENST00000490734.2_Missense_Mutation_p.V57M|DBNL_ENST00000494774.1_Missense_Mutation_p.V152M|DBNL_ENST00000497184.1_3'UTR|DBNL_ENST00000468694.1_Missense_Mutation_p.V152M|DBNL_ENST00000456905.1_Intron|DBNL_ENST00000440166.1_Missense_Mutation_p.V49M|DBNL_ENST00000452943.1_Missense_Mutation_p.V127M	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	152					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|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)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)	p.V152L(1)		breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						CTTCCAGGACGTGGGACCCCA	0.617													G|||	73	0.0145767	0.0552	0.0	5008	,	,		19626	0.0		0.0	False		,,,				2504	0.0				p.V152M	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											.	DBNL	26	.	1	Substitution - Missense(1)	lung(1)	c.G454A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	188,4218	120.8+/-158.4	4,180,2019	101.0	93.0	96.0		454,454,454	-6.3	0.0	7	dbSNP_129	96	0,8600		0,0,4300	yes	missense,missense,missense	DBNL	NM_001014436.2,NM_001122956.1,NM_014063.6	21,21,21	4,180,6319	AA,AG,GG		0.0,4.2669,1.4455	benign,benign,benign	152/431,152/440,152/432	44096482	188,12818	2203	4300	6503	SO:0001583	missense	28988	exon5			CAGGACGTGGGAC	AF151364	CCDS34622.1, CCDS34623.1, CCDS47579.1, CCDS64633.1, CCDS64634.1	7p13	2004-07-22			ENSG00000136279	ENSG00000136279			2696	protein-coding gene	gene with protein product		610106				10087302	Standard	NM_014063		Approved	SH3P7, HIP-55	uc003tjq.4	Q9UJU6	OTTHUMG00000155350	ENST00000448521.1:c.454G>A	7.37:g.44096482G>A	ENSP00000411701:p.Val152Met	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	104	45	0.432692	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Missense_Mutation	SNP	ENST00000448521.1	37	CCDS34623.1	23|23	0.010531135531135532|0.010531135531135532	23|23	0.046747967479674794|0.046747967479674794	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	6.385|6.385	0.439110|0.439110	0.12104|0.12104	0.042669|0.042669	0.0|0.0	ENSG00000136279|ENSG00000136279	ENST00000432854|ENST00000448521;ENST00000440166;ENST00000452943;ENST00000468694;ENST00000494774;ENST00000490734;ENST00000539475	.|T;T;T;T;T;T	.|0.30714	.|1.91;2.23;2.23;1.52;1.91;2.22	4.9|4.9	-6.34|-6.34	0.01982|0.01982	.|.	.|1.052620	.|0.07283	.|N	.|0.871083	T|T	0.02230|0.02230	0.0069|0.0069	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;B;B	.|0.25772	.|0.021;0.021;0.02;0.134;0.082;0.119;0.005;0.012	.|B;B;B;B;B;B;B;B	.|0.15052	.|0.005;0.003;0.005;0.012;0.003;0.008;0.001;0.004	T|T	0.25502|0.25502	-1.0130|-1.0130	5|10	.|0.41790	.|T	.|0.15	0.0525|0.0525	8.2112|8.2112	0.31483|0.31483	0.2474:0.0:0.6024:0.1502|0.2474:0.0:0.6024:0.1502	rs61735009|rs61735009	.|49;100;82;57;127;152;152;152	.|B4DEM2;B4DXL9;B4DDU5;C9J7P1;B4DDD6;Q9UJU6-3;Q9UJU6;Q9UJU6-2	.|.;.;.;.;.;.;DBNL_HUMAN;.	H|M	80|152;49;127;152;152;57;82	.|ENSP00000411701:V152M;ENSP00000415173:V49M;ENSP00000405343:V127M;ENSP00000417653:V152M;ENSP00000419992:V152M;ENSP00000417749:V57M	.|ENSP00000415173:V49M	R|V	+|+	2|1	0|0	DBNL|DBNL	44063007|44063007	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.088000|0.088000	0.18126|0.18126	-0.206000|-0.206000	0.09398|0.09398	-0.667000|-0.667000	0.05303|0.05303	-0.696000|-0.696000	0.03686|0.03686	CGT|GTG	A|0.013;C|0.000;G|0.987	0.013	strong		0.617	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063	
SMOC1	64093	hgsc.bcm.edu	37	14	70477508	70477508	+	Silent	SNP	C	C	T	rs3825739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:70477508C>T	ENST00000381280.4	+	8	955	c.702C>T	c.(700-702)gcC>gcT	p.A234A	SMOC1_ENST00000361956.3_Silent_p.A234A	NM_001034852.2|NM_022137.5	NP_001030024.1|NP_071420.1	Q9H4F8	SMOC1_HUMAN	SPARC related modular calcium binding 1	234	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165)	basement membrane (GO:0005604)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GGCAGAGTGCCCTGGAAGAGG	0.537													C|||	1030	0.205671	0.0061	0.3213	5008	,	,		19744	0.4196		0.173	False		,,,				2504	0.2065				p.A234A		Atlas-SNP	.											SMOC1,colon,carcinoma,+1,1	SMOC1	61	1	0			c.C702T						PASS	.	C	,	212,4194	131.0+/-167.6	10,192,2001	111.0	118.0	116.0		702,702	4.6	1.0	14	dbSNP_107	116	1567,7033	295.1+/-302.2	143,1281,2876	no	coding-synonymous,coding-synonymous	SMOC1	NM_001034852.2,NM_022137.5	,	153,1473,4877	TT,TC,CC		18.2209,4.8116,13.6783	,	234/436,234/435	70477508	1779,11227	2203	4300	6503	SO:0001819	synonymous_variant	64093	exon8			GAGTGCCCTGGAA	AJ249900	CCDS9798.1, CCDS32110.1	14q24.1	2010-08-05			ENSG00000198732	ENSG00000198732			20318	protein-coding gene	gene with protein product		608488				12130637	Standard	NM_001034852		Approved		uc001xlt.2	Q9H4F8		ENST00000381280.4:c.702C>T	14.37:g.70477508C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	102	54	0.529412	NM_001034852	A8K1S3|B2R7P5|Q96F78	Silent	SNP	ENST00000381280.4	37	CCDS9798.1																																																																																			C|0.825;T|0.175	0.175	strong		0.537	SMOC1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412467.1		
FREM2	341640	hgsc.bcm.edu	37	13	39263422	39263422	+	Silent	SNP	C	C	T	rs41292751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39263422C>T	ENST00000280481.7	+	1	2157	c.1941C>T	c.(1939-1941)gaC>gaT	p.D647D		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	647					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)		AGCAGCAGGACATAACAGAGG	0.532													C|||	61	0.0121805	0.0008	0.0216	5008	,	,		17077	0.0		0.0378	False		,,,				2504	0.0072				p.D647D		Atlas-SNP	.											.	FREM2	385	.	0			c.C1941T						PASS	.	C		43,4363	45.3+/-79.5	0,43,2160	72.0	66.0	68.0		1941	5.1	1.0	13	dbSNP_127	68	324,8276	114.8+/-174.7	5,314,3981	no	coding-synonymous	FREM2	NM_207361.4		5,357,6141	TT,TC,CC		3.7674,0.9759,2.8218		647/3170	39263422	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			GCAGGACATAACA	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.1941C>T	13.37:g.39263422C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|0.973;T|0.027	0.027	strong		0.532	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
VWCE	220001	hgsc.bcm.edu	37	11	61048322	61048322	+	Silent	SNP	G	G	C	rs61744427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61048322G>C	ENST00000335613.5	-	8	1559	c.1173C>G	c.(1171-1173)gcC>gcG	p.A391A		NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	391	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						ATTCATGCATGGCTCCCAGGT	0.662													G|||	142	0.0283546	0.0613	0.0058	5008	,	,		17203	0.0268		0.001	False		,,,				2504	0.0297				p.A391A		Atlas-SNP	.											.	VWCE	84	.	0			c.C1173G						PASS	.	G		240,4164		3,234,1965	12.0	14.0	13.0		1173	1.2	0.5	11	dbSNP_129	13	3,8587		0,3,4292	no	coding-synonymous	VWCE	NM_152718.2		3,237,6257	CC,CG,GG		0.0349,5.4496,1.8701		391/956	61048322	243,12751	2202	4295	6497	SO:0001819	synonymous_variant	220001	exon8			ATGCATGGCTCCC	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.1173C>G	11.37:g.61048322G>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	37	CCDS8002.1																																																																																			G|0.971;C|0.029	0.029	strong		0.662	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718	
MFAP3L	9848	hgsc.bcm.edu	37	4	170912685	170912685	+	Silent	SNP	T	T	C	rs61740817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:170912685T>C	ENST00000361618.3	-	3	1381	c.1074A>G	c.(1072-1074)gaA>gaG	p.E358E	MFAP3L_ENST00000393704.3_Silent_p.E255E|RP11-6E9.4_ENST00000508955.1_RNA	NM_021647.6	NP_067679.6	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like	358						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		CGGTAGAAGGTTCTGCAGTTT	0.512													.|||	324	0.0646965	0.239	0.0101	5008	,	,		19333	0.0		0.001	False		,,,				2504	0.0				p.E358E		Atlas-SNP	.											MFAP3L,NS,carcinoma,-2,1	MFAP3L	59	1	0			c.A1074G						PASS	.	C	,	788,3618	751.8+/-412.2	79,630,1494	191.0	160.0	170.0		765,1074	2.5	1.0	4	dbSNP_129	170	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	MFAP3L	NM_001009554.2,NM_021647.6	,	79,638,5786	CC,CT,TT		0.093,17.8847,6.1203	,	255/307,358/410	170912685	796,12210	2203	4300	6503	SO:0001819	synonymous_variant	9848	exon3			AGAAGGTTCTGCA	AB014526	CCDS34103.1, CCDS43281.1	4q33	2014-08-12			ENSG00000198948	ENSG00000198948		"""Immunoglobulin superfamily / I-set domain containing"""	29083	protein-coding gene	gene with protein product						9734811	Standard	XM_005263366		Approved	KIAA0626, NYD-sp9	uc003isp.4	O75121	OTTHUMG00000160942	ENST00000361618.3:c.1074A>G	4.37:g.170912685T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	213	105	0.492958	NM_021647	A8K1X6|D3DP35|Q4W5N7|Q4W5N9|Q6TNA8|Q9BVE1|Q9BXK0	Silent	SNP	ENST00000361618.3	37	CCDS34103.1																																																																																			T|0.933;C|0.067	0.067	strong		0.512	MFAP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363043.2	NM_021647	
HLA-A	3105	hgsc.bcm.edu	37	6	29910583	29910583	+	Silent	SNP	C	C	T	rs386698550|rs1059426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29910583C>T	ENST00000396634.1	+	4	464	c.123C>T	c.(121-123)cgC>cgT	p.R41R	HLA-A_ENST00000376809.5_Silent_p.R41R|HLA-A_ENST00000376802.2_Silent_p.R41R|HLA-A_ENST00000376806.5_Silent_p.R41R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	41	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.R41fs*31(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						GGCCCGGCCGCGGGGAGCCCC	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|||	623	0.124401	0.2368	0.1225	5008	,	,		14781	0.1042		0.0577	False		,,,				2504	0.0634				p.R41R		Atlas-SNP	.											.	HLA-A	89	.	1	Deletion - Frameshift(1)	ovary(1)	c.C123T						PASS	.						19.0	19.0	19.0					6																	29910583		2193	4286	6479	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGGCCGCGGGGAG	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.123C>T	6.37:g.29910583C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	97	20	0.206186	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.911;T|0.089	0.089	strong		0.711	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
LGI4	163175	hgsc.bcm.edu	37	19	35616316	35616316	+	Silent	SNP	C	C	T	rs12610234|rs36102542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35616316C>T	ENST00000310123.3	-	9	1914	c.1395G>A	c.(1393-1395)caG>caA	p.Q465Q	LGI4_ENST00000392225.3_Missense_Mutation_p.S491N|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	465					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			GGATGGCCAGCTGGTCCCTGG	0.667													C|||	1804	0.360224	0.3132	0.2493	5008	,	,		14380	0.2679		0.3698	False		,,,				2504	0.5879				p.Q465Q		Atlas-SNP	.											.	LGI4	32	.	0			c.G1395A						PASS	.	C		1450,2956		229,992,982	22.0	22.0	22.0		1395	5.1	1.0	19	dbSNP_120	22	3054,5544		529,1996,1774	no	coding-synonymous	LGI4	NM_139284.2		758,2988,2756	TT,TC,CC		35.5199,32.9097,34.6355		465/538	35616316	4504,8500	2203	4299	6502	SO:0001819	synonymous_variant	163175	exon9			GGCCAGCTGGTCC	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.1395G>A	19.37:g.35616316C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	180	180	1	NM_139284	B2RN53|B9EGS7|Q5M8T1	Silent	SNP	ENST00000310123.3	37	CCDS12444.1	601	0.2751831501831502	143	0.29065040650406504	78	0.2154696132596685	125	0.21853146853146854	255	0.33641160949868076	C	15.04	2.716225	0.48622	0.329097	0.355199	ENSG00000153902	ENST00000392225	T	0.68025	-0.3	5.09	5.09	0.68999	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.27938	-1.0059	5	0.87932	D	0	.	9.5979	0.39584	0.0:0.9042:0.0:0.0958	rs12610234	.	.	.	N	491	ENSP00000376059:S491N	ENSP00000376059:S491N	S	-	2	0	LGI4	40308156	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	1.746000	0.38288	2.363000	0.80096	0.484000	0.47621	AGC	C|0.678;T|0.322	0.322	strong		0.667	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1		
RAI14	26064	hgsc.bcm.edu	37	5	34814745	34814745	+	Missense_Mutation	SNP	T	T	C	rs150350937		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34814745T>C	ENST00000265109.3	+	12	1197	c.910T>C	c.(910-912)Tcg>Ccg	p.S304P	RAI14_ENST00000506376.1_Missense_Mutation_p.S296P|RAI14_ENST00000503673.1_Missense_Mutation_p.S304P|RAI14_ENST00000515799.1_Missense_Mutation_p.S307P|RAI14_ENST00000428746.2_Missense_Mutation_p.S304P|RAI14_ENST00000512629.1_Missense_Mutation_p.S275P|RAI14_ENST00000397449.1_Missense_Mutation_p.S297P	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	304						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)					GGGAAAGGAATCGGTATTTTT	0.318																																					p.S307P		Atlas-SNP	.											RAI14,scalp,malignant_melanoma,-1,1	RAI14	100	1	0			c.T919C						PASS	.	T	PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER	8,4398	12.9+/-30.5	0,8,2195	174.0	155.0	162.0		910,910,823,886,919,910	3.4	1.0	5	dbSNP_134	162	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	RAI14	NM_001145520.1,NM_001145521.1,NM_001145522.1,NM_001145523.1,NM_001145525.1,NM_015577.2	74,74,74,74,74,74	0,8,6495	CC,CT,TT		0.0,0.1816,0.0615	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	304/981,304/981,275/952,296/973,307/984,304/981	34814745	8,12998	2203	4300	6503	SO:0001583	missense	26064	exon14			AAGGAATCGGTAT	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.910T>C	5.37:g.34814745T>C	ENSP00000265109:p.Ser304Pro	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	291	150	0.515464	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.050617	0.36181	0.001816	0.0	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.38077	1.21;1.16;1.21;1.21;1.22;1.26;1.25	5.86	3.44	0.39384	.	.	.	.	.	T	0.20007	0.0481	N	0.14661	0.345	0.27353	N	0.956195	B;B;B;B	0.09022	0.001;0.001;0.002;0.001	B;B;B;B	0.09377	0.004;0.001;0.004;0.001	T	0.14309	-1.0477	9	0.31617	T	0.26	-4.3706	6.5518	0.22438	0.0:0.3208:0.0:0.6792	.	296;275;307;304	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	P	304;275;304;304;307;296;297	ENSP00000265109:S304P;ENSP00000422377:S275P;ENSP00000388725:S304P;ENSP00000422942:S304P;ENSP00000427123:S307P;ENSP00000423854:S296P;ENSP00000380591:S297P	ENSP00000265109:S304P	S	+	1	0	RAI14	34850502	0.963000	0.33076	0.987000	0.45799	0.933000	0.57130	0.571000	0.23669	1.139000	0.42245	0.528000	0.53228	TCG	T|1.000;C|0.000	0.000	weak		0.318	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
MT-CO3	4514	hgsc.bcm.edu	37	M	9540	9540	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:9540T>C	ENST00000362079.2	+	1	334	c.334T>C	c.(334-336)Tta>Cta	p.L112L	MT-TS1_ENST00000387416.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-ND3_ENST00000361227.2_5'Flank			P00414	COX3_HUMAN	mitochondrially encoded cytochrome c oxidase III	112					aerobic electron transport chain (GO:0019646)|cellular metabolic process (GO:0044237)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(10)|kidney(14)|lung(1)|urinary_tract(1)	27						CTACCCCCCAACTAGGAGGGC	0.493																																					p.L112L		Atlas-SNP	.											.	.	.	.	0			c.T334C						PASS	.																																			SO:0001819	synonymous_variant	5742	exon1			CCCCAATTAGGAG			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198938	ENSG00000198938		"""Mitochondrial respiratory chain complex / Complex IV"""	7422	protein-coding gene	gene with protein product		516050	"""cytochrome c oxidase III"""	MTCO3			Standard			Approved	COX3, COIII, CO3		P00414		ENST00000362079.2:c.334T>C	M.37:g.9540T>C		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	ENST00000362079	Q14Y83	Silent	SNP	ENST00000362079.2	37																																																																																				.	.	none		0.493	MT-CO3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024032	
MIA3	375056	hgsc.bcm.edu	37	1	222825568	222825568	+	Splice_Site	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:222825568A>G	ENST00000344922.5	+	13	4006		c.e13-1		MIA3_ENST00000340535.7_Splice_Site|MIA3_ENST00000344507.1_Intron|MIA3_ENST00000344441.6_Splice_Site	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3						chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.?(1)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		GTTTTGCATTAGGTTCAGATT	0.338																																					.		Atlas-SNP	.											MIA3,NS,carcinoma,0,1	MIA3	167	1	1	Unknown(1)	endometrium(1)	c.3982-2A>G						scavenged	.						129.0	124.0	126.0					1																	222825568		1845	4083	5928	SO:0001630	splice_region_variant	375056	exon13			TGCATTAGGTTCA		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.3982-1A>G	1.37:g.222825568A>G		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	180	3	0.0166667	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Splice_Site	SNP	ENST00000344922.5	37	CCDS41470.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.121351	0.77436	.	.	ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000340535;ENST00000284471	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2829	0.82707	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MIA3	220892191	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	6.113000	0.71553	2.248000	0.74166	0.533000	0.62120	.	.	.	none		0.338	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	Intron
MUC4	4585	hgsc.bcm.edu	37	3	195512820	195512820	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512820G>A	ENST00000463781.3	-	2	6090	c.5631C>T	c.(5629-5631)gaC>gaT	p.D1877D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D1877D	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		CTGAGGAAGCGTCGGTGACAA	0.567																																					p.D1877D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C5631T						scavenged	.																																			SO:0001819	synonymous_variant	4585	exon2			GGAAGCGTCGGTG	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.5631C>T	3.37:g.195512820G>A		Somatic	400	0	0		WXS	Illumina HiSeq	Phase_I	321	9	0.0280374	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																																																																																			.	.	none		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ANKRD65	441869	hgsc.bcm.edu	37	1	1354515	1354515	+	Missense_Mutation	SNP	C	C	G	rs534554090|rs904589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1354515C>G	ENST00000537107.1	-	4	1302	c.1165G>C	c.(1165-1167)Gag>Cag	p.E389Q	ANKRD65_ENST00000520296.1_3'UTR|ANKRD65_ENST00000454272.1_5'UTR|ANKRD65_ENST00000427211.1_3'UTR|RP4-758J18.7_ENST00000428932.1_RNA	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	202	0	0		WXS	Illumina HiSeq	Phase_I	207	95	0.458937	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			
ZNF808	388558	hgsc.bcm.edu	37	19	53057031	53057031	+	Missense_Mutation	SNP	A	A	G	rs116132766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53057031A>G	ENST00000359798.4	+	5	1042	c.862A>G	c.(862-864)Aag>Gag	p.K288E		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	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)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		GAAACCTTACAAGTGTAAAGA	0.398													A|||	13	0.00259585	0.0083	0.0029	5008	,	,		22244	0.0		0.0	False		,,,				2504	0.0				p.K288E		Atlas-SNP	.											.	ZNF808	81	.	0			c.A862G						PASS	.	A	GLU/LYS	56,4350		0,56,2147	147.0	148.0	148.0		862	-1.1	0.0	19	dbSNP_132	148	1,8599		0,1,4299	no	missense	ZNF808	NM_001039886.3	56	0,57,6446	GG,GA,AA		0.0116,1.271,0.4383	possibly-damaging	288/904	53057031	57,12949	2203	4300	6503	SO:0001583	missense	388558	exon5			CCTTACAAGTGTA	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"""Zinc fingers, C2H2-type"", ""-"""	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.862A>G	19.37:g.53057031A>G	ENSP00000352846:p.Lys288Glu	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	151	53	0.350993	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	37	CCDS46167.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	.	0.202	-1.043775	0.01997	0.01271	1.16E-4	ENSG00000198482	ENST00000359798	T	0.16196	2.36	1.38	-1.15	0.09709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09730	0.0239	L	0.49350	1.555	0.09310	N	1	P	0.42941	0.794	B	0.43754	0.43	T	0.20974	-1.0259	9	0.13470	T	0.59	.	3.8277	0.08861	0.6228:0.2188:0.1583:0.0	.	288	Q8N4W9	ZN808_HUMAN	E	288	ENSP00000352846:K288E	ENSP00000352846:K288E	K	+	1	0	ZNF808	57748843	0.000000	0.05858	0.009000	0.14445	0.029000	0.11900	-1.383000	0.02544	-0.207000	0.10187	-1.020000	0.02445	AAG	A|0.996;G|0.004	0.004	strong		0.398	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886	
ESPL1	9700	hgsc.bcm.edu	37	12	53675381	53675381	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53675381C>T	ENST00000257934.4	+	13	2681	c.2590C>T	c.(2590-2592)Cga>Tga	p.R864*	ESPL1_ENST00000552462.1_Nonsense_Mutation_p.R864*	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	864					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TGATCTGCTTCGAAGTCAACT	0.453																																					p.R864X	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											ESPL1,colon,carcinoma,-1,1	ESPL1	158	1	0			c.C2590T						scavenged	.						172.0	150.0	157.0					12																	53675381		2203	4300	6503	SO:0001587	stop_gained	9700	exon13			CTGCTTCGAAGTC	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.2590C>T	12.37:g.53675381C>T	ENSP00000257934:p.Arg864*	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	2	0.0169492	NM_012291		Nonsense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	C	40	8.003819	0.98605	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	.	.	.	5.1	3.2	0.36748	.	1.005060	0.07997	N	0.988111	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3292	0.32175	0.1963:0.6443:0.1594:0.0	.	.	.	.	X	864;539;864	.	ENSP00000257934:R864X	R	+	1	2	ESPL1	51961648	0.007000	0.16637	0.001000	0.08648	0.968000	0.65278	0.665000	0.25083	0.763000	0.33175	0.561000	0.74099	CGA	.	.	none		0.453	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
FBXO34	55030	hgsc.bcm.edu	37	14	55818514	55818514	+	Missense_Mutation	SNP	C	C	T	rs59719421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55818514C>T	ENST00000313833.4	+	2	1651	c.1406C>T	c.(1405-1407)tCc>tTc	p.S469F	FBXO34_ENST00000440021.1_Missense_Mutation_p.S469F	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	469										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						GACCAGCCTTCCATTTTAAAC	0.433													C|||	74	0.0147764	0.053	0.0058	5008	,	,		20569	0.0		0.0	False		,,,				2504	0.0				p.S469F		Atlas-SNP	.											.	FBXO34	61	.	0			c.C1406T						PASS	.	C	PHE/SER,PHE/SER	247,4159	143.1+/-178.2	7,233,1963	117.0	113.0	114.0		1406,1406	4.6	0.0	14	dbSNP_129	114	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	155,155	7,236,6260	TT,TC,CC		0.0349,5.606,1.9222	possibly-damaging,possibly-damaging	469/712,469/712	55818514	250,12756	2203	4300	6503	SO:0001583	missense	55030	exon2			AGCCTTCCATTTT	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1406C>T	14.37:g.55818514C>T	ENSP00000313159:p.Ser469Phe	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	223	97	0.434978	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	C	9.052	0.992345	0.18966	0.05606	3.49E-4	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.19938	2.11;2.11	5.48	4.6	0.57074	.	0.393578	0.20036	N	0.100616	T	0.04003	0.0112	L	0.51422	1.61	0.09310	N	1	D	0.53462	0.96	P	0.55965	0.788	T	0.01130	-1.1442	10	0.62326	D	0.03	-11.2954	9.7892	0.40695	0.0:0.7856:0.1416:0.0728	rs59719421	469	Q9NWN3	FBX34_HUMAN	F	469	ENSP00000313159:S469F;ENSP00000394117:S469F	ENSP00000313159:S469F	S	+	2	0	FBXO34	54888267	0.215000	0.23574	0.006000	0.13384	0.072000	0.16883	1.083000	0.30815	1.573000	0.49748	-0.127000	0.14921	TCC	C|0.979;T|0.021	0.021	strong		0.433	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
SYBU	55638	hgsc.bcm.edu	37	8	110587222	110587222	+	Silent	SNP	A	A	G	rs35039797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110587222A>G	ENST00000422135.1	-	8	2420	c.1905T>C	c.(1903-1905)ccT>ccC	p.P635P	SYBU_ENST00000529175.1_Silent_p.P429P|SYBU_ENST00000399066.3_Silent_p.P632P|SYBU_ENST00000533065.1_Silent_p.P516P|SYBU_ENST00000433638.1_Silent_p.P635P|SYBU_ENST00000276646.9_Silent_p.P635P|SYBU_ENST00000527707.1_5'Flank|SYBU_ENST00000533895.1_Silent_p.P634P|SYBU_ENST00000528647.1_Silent_p.P634P|SYBU_ENST00000528331.1_Silent_p.P516P|SYBU_ENST00000424158.2_Silent_p.P640P|SYBU_ENST00000532779.1_Silent_p.P567P|SYBU_ENST00000408889.3_Silent_p.P516P|SYBU_ENST00000419099.1_Silent_p.P634P|SYBU_ENST00000440310.1_Silent_p.P635P|SYBU_ENST00000533171.1_Silent_p.P635P|SYBU_ENST00000408908.2_Silent_p.P635P|SYBU_ENST00000529690.1_Silent_p.P505P|SYBU_ENST00000446070.2_Silent_p.P634P	NM_001099744.1	NP_001093214.1	Q9NX95	SYBU_HUMAN	syntabulin (syntaxin-interacting)	635					regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|dense body (GO:0097433)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	30						TGTTATACACAGGATCCGTTC	0.587													A|||	288	0.057508	0.208	0.0144	5008	,	,		17399	0.0		0.003	False		,,,				2504	0.0				p.P635P		Atlas-SNP	.											.	SYBU	71	.	0			c.T1905C						PASS	.	A	,,,,,,,,,,,,,,	706,3390		44,618,1386	75.0	87.0	83.0		1902,1905,1905,1548,1902,1905,1548,1905,1902,1905,1902,1905,1548,1896,1902	-8.9	0.5	8	dbSNP_126	83	8,8354		0,8,4173	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	SYBU	NM_001099743.1,NM_001099744.1,NM_001099745.1,NM_001099746.1,NM_001099747.1,NM_001099748.1,NM_001099749.1,NM_001099750.1,NM_001099751.1,NM_001099752.1,NM_001099753.1,NM_001099754.1,NM_001099755.1,NM_001099756.1,NM_017786.5	,,,,,,,,,,,,,,	44,626,5559	GG,GA,AA		0.0957,17.2363,5.7313	,,,,,,,,,,,,,,	634/663,635/664,635/664,516/545,634/663,635/664,516/545,635/664,634/663,635/664,634/663,635/664,516/545,632/661,634/663	110587222	714,11744	2048	4181	6229	SO:0001819	synonymous_variant	55638	exon8			ATACACAGGATCC	AB040905	CCDS43763.1, CCDS43764.1, CCDS47912.1, CCDS55271.1	8q23.2	2010-08-27				ENSG00000147642			26011	protein-coding gene	gene with protein product	"""syntaphilin-like"""	611568				17611281, 16750881, 16157705, 15656992, 15459722	Standard	NM_001099743		Approved	FLJ20366, GOLSYN, KIAA1472, OCSYN, SNPHL	uc003ynj.4	Q9NX95		ENST00000422135.1:c.1905T>C	8.37:g.110587222A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_001099752	A8K354|B3KQX3|B3KU61|Q5R1T1|Q5R1T2|Q5R1T3|Q5Y2M6|Q8ND49|Q8TCR6|Q96D80|Q9P256	Silent	SNP	ENST00000422135.1	37	CCDS47912.1																																																																																			A|0.972;G|0.028	0.028	strong		0.587	SYBU-204	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385501.1	NM_017786	
DHX36	170506	hgsc.bcm.edu	37	3	154002774	154002774	+	Silent	SNP	G	G	A	rs114098462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:154002774G>A	ENST00000496811.1	-	18	2114	c.2034C>T	c.(2032-2034)aaC>aaT	p.N678N	DHX36_ENST00000308361.6_Silent_p.N678N|DHX36_ENST00000329463.5_Silent_p.N664N|DHX36_ENST00000544526.1_Silent_p.N664N	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	678					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TATCCAAAGCGTTCTGTAAAG	0.373													G|||	46	0.0091853	0.0325	0.0029	5008	,	,		19458	0.0		0.001	False		,,,				2504	0.0				p.N678N		Atlas-SNP	.											.	DHX36	98	.	0			c.C2034T						PASS	.	G	,	114,4292	87.8+/-126.4	1,112,2090	102.0	101.0	101.0		1992,2034	-4.6	0.8	3	dbSNP_132	101	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DHX36	NM_001114397.1,NM_020865.2	,	1,112,6390	AA,AG,GG		0.0,2.5874,0.8765	,	664/995,678/1009	154002774	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	170506	exon18			CAAAGCGTTCTGT	AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"""DEAH-boxes"""	14410	protein-coding gene	gene with protein product		612767	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"""	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.2034C>T	3.37:g.154002774G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	172	75	0.436047	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Silent	SNP	ENST00000496811.1	37	CCDS3171.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	G	9.279	1.047589	0.19827	0.025874	0.0	ENSG00000174953	ENST00000469977	.	.	.	5.6	-4.64	0.03349	.	.	.	.	.	T	0.41096	0.1144	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61113	-0.7128	4	.	.	.	.	15.9172	0.79531	0.4712:0.0:0.5288:0.0	.	.	.	.	M	125	.	.	T	-	2	0	DHX36	155485468	0.990000	0.36364	0.828000	0.32881	0.775000	0.43874	0.509000	0.22707	-1.147000	0.02851	-0.880000	0.02959	ACG	G|0.992;A|0.008	0.008	strong		0.373	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865	
SLC29A3	55315	hgsc.bcm.edu	37	10	73082563	73082563	+	Missense_Mutation	SNP	A	A	G	rs2277257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73082563A>G	ENST00000373189.5	+	2	104	c.52A>G	c.(52-54)Aga>Gga	p.R18G	snoU13_ENST00000459444.1_RNA	NM_001174098.1|NM_018344.5	NP_001167569.1|NP_060814.4	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 3	18			R -> G (in dbSNP:rs2277257). {ECO:0000269|PubMed:12975309}.		transmembrane transport (GO:0055085)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	15						CTCCACCTACAGAACCACAAG	0.587													A|||	2350	0.469249	0.7005	0.3444	5008	,	,		19962	0.3601		0.4006	False		,,,				2504	0.4284				p.R18G	Esophageal Squamous(200;1319 2142 18949 31248 39672)	Atlas-SNP	.											.	SLC29A3	51	.	0			c.A52G						PASS	.	A	GLY/ARG,GLY/ARG	2802,1604	663.8+/-401.3	894,1014,295	128.0	129.0	129.0		52,52	1.2	0.4	10	dbSNP_100	129	3537,5063	515.4+/-378.6	725,2087,1488	yes	missense,missense	SLC29A3	NM_001174098.1,NM_018344.5	125,125	1619,3101,1783	GG,GA,AA		41.1279,36.4049,48.739	possibly-damaging,possibly-damaging	18/259,18/476	73082563	6339,6667	2203	4300	6503	SO:0001583	missense	55315	exon2			ACCTACAGAACCA	AF326987	CCDS7310.1	10q22.2	2013-07-17	2013-07-17		ENSG00000198246	ENSG00000198246		"""Solute carriers"""	23096	protein-coding gene	gene with protein product		612373	"""solute carrier family 29 (nucleoside transporters), member 3"""			11396612	Standard	NM_018344		Approved	ENT3, FLJ11160	uc001jrr.4	Q9BZD2	OTTHUMG00000018424	ENST00000373189.5:c.52A>G	10.37:g.73082563A>G	ENSP00000362285:p.Arg18Gly	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_018344	B2RB50|B4E2Z9|B7ZA37|Q0VAM9|Q5T465|Q7RTT8|Q8IVZ0|Q9BWI2|Q9NUS9	Missense_Mutation	SNP	ENST00000373189.5	37	CCDS7310.1	983	0.4500915750915751	334	0.6788617886178862	132	0.36464088397790057	219	0.38286713286713286	298	0.39313984168865435	A	6.233	0.411183	0.11812	0.635951	0.411279	ENSG00000198246	ENST00000373189	T	0.68331	-0.32	5.15	1.21	0.21127	.	0.644976	0.15117	N	0.279597	T	0.00012	0.0000	M	0.63428	1.95	0.26705	P	0.971088	B	0.06786	0.001	B	0.06405	0.002	T	0.41627	-0.9498	9	0.39692	T	0.17	-3.3134	7.3753	0.26825	0.5473:0.3726:0.0801:0.0	rs2277257;rs17629116;rs52808361;rs56776781;rs2277257	18	Q9BZD2	S29A3_HUMAN	G	18	ENSP00000362285:R18G	ENSP00000362285:R18G	R	+	1	2	SLC29A3	72752569	0.324000	0.24652	0.394000	0.26270	0.007000	0.05969	0.728000	0.26013	0.363000	0.24346	-0.321000	0.08615	AGA	A|0.527;G|0.473	0.473	strong		0.587	SLC29A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048544.1	NM_018344	
TRIOBP	11078	hgsc.bcm.edu	37	22	38129311	38129311	+	Silent	SNP	C	C	T	rs200990219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38129311C>T	ENST00000406386.3	+	8	4209	c.3954C>T	c.(3952-3954)tcC>tcT	p.S1318S		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1318					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)					ATAGGAAGTCCGAGGCAGCGG	0.652													C|||	10	0.00199681	0.0076	0.0	5008	,	,		15854	0.0		0.0	False		,,,				2504	0.0				p.S1318S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C3954T						PASS	.	C		12,3732		0,12,1860	8.0	14.0	12.0		3954	-1.1	1.0	22		12	0,7806		0,0,3903	no	coding-synonymous	TRIOBP	NM_001039141.2		0,12,5763	TT,TC,CC		0.0,0.3205,0.1039		1318/2366	38129311	12,11538	1872	3903	5775	SO:0001819	synonymous_variant	11078	exon8			GAAGTCCGAGGCA	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.3954C>T	22.37:g.38129311C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	170	80	0.470588	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.998;T|0.002	0.002	strong		0.652	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
PCDHGB1	56104	hgsc.bcm.edu	37	5	140731159	140731159	+	Silent	SNP	T	T	C	rs78745319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140731159T>C	ENST00000523390.1	+	1	1332	c.1332T>C	c.(1330-1332)aaT>aaC	p.N444N	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	444	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAACGACAATGCACCTGTTT	0.552													.|||	258	0.0515176	0.1664	0.013	5008	,	,		19775	0.0		0.0258	False		,,,				2504	0.0031				p.N444N		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.T1332C						PASS	.	T	,,,,	559,3789		39,481,1654	86.0	98.0	94.0		,,,1332,1332	-3.5	0.1	5	dbSNP_132	94	145,8401		1,143,4129	no	intron,intron,intron,coding-synonymous,coding-synonymous	PCDHGB1,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018922.2,NM_032095.1	,,,,	40,624,5783	CC,CT,TT		1.6967,12.8565,5.4599	,,,,	,,,444/928,444/811	140731159	704,12190	2174	4273	6447	SO:0001819	synonymous_variant	56104	exon1			CGACAATGCACCT	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1332T>C	5.37:g.140731159T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	144	70	0.486111	NM_018922	Q3SY75|Q9Y5C8	Silent	SNP	ENST00000523390.1	37	CCDS54923.1																																																																																			T|0.959;C|0.041	0.041	strong		0.552	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
PRIMA1	145270	hgsc.bcm.edu	37	14	94187816	94187816	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94187816C>G	ENST00000393140.1	-	5	538	c.436G>C	c.(436-438)Gta>Cta	p.V146L	PRIMA1_ENST00000393143.1_Missense_Mutation_p.V146L|PRIMA1_ENST00000316227.3_3'UTR	NM_178013.3	NP_821092.1	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1	146					establishment of localization in cell (GO:0051649)|neurotransmitter catabolic process (GO:0042135)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|synapse (GO:0045202)				endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		TTCACGTCTACTCCTTTGTTG	0.577																																					p.V146L		Atlas-SNP	.											.	PRIMA1	21	.	0			c.G436C						PASS	.						142.0	101.0	115.0					14																	94187816		2203	4300	6503	SO:0001583	missense	145270	exon5			CGTCTACTCCTTT		CCDS9912.1	14q32.13	2008-08-29			ENSG00000175785	ENSG00000175785			18319	protein-coding gene	gene with protein product	"""membrane anchor of acetylcholinesterase"""	613851				11804574	Standard	NM_178013		Approved	PRIMA	uc001ybw.1	Q86XR5	OTTHUMG00000141313	ENST00000393140.1:c.436G>C	14.37:g.94187816C>G	ENSP00000376848:p.Val146Leu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_178013	Q86XR6	Missense_Mutation	SNP	ENST00000393140.1	37	CCDS9912.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815771	0.50527	.	.	ENSG00000175785	ENST00000393140;ENST00000393143	.	.	.	4.65	3.72	0.42706	.	0.948209	0.08632	N	0.916915	T	0.45736	0.1357	L	0.27053	0.805	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36407	-0.9749	9	0.49607	T	0.09	-3.289	10.1546	0.42814	0.1979:0.8021:0.0:0.0	.	146	Q86XR5	PRIMA_HUMAN	L	146	.	ENSP00000376848:V146L	V	-	1	0	PRIMA1	93257569	1.000000	0.71417	0.998000	0.56505	0.070000	0.16714	2.628000	0.46477	2.135000	0.66039	0.591000	0.81541	GTA	.	.	none		0.577	PRIMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280658.1	NM_178013	
UNC5D	137970	hgsc.bcm.edu	37	8	35624434	35624434	+	Silent	SNP	C	C	A	rs16884404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:35624434C>A	ENST00000404895.2	+	15	2656	c.2328C>A	c.(2326-2328)tcC>tcA	p.S776S	UNC5D_ENST00000287272.2_Silent_p.S707S|UNC5D_ENST00000420357.1_Silent_p.S709S|UNC5D_ENST00000416672.1_Silent_p.S781S|UNC5D_ENST00000453357.2_Silent_p.S771S|UNC5D_ENST00000449677.1_Silent_p.S352S	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	776					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		TCCCGTTCTCCCGCGTGTGGT	0.567													C|||	511	0.102037	0.3215	0.036	5008	,	,		18566	0.0		0.0099	False		,,,				2504	0.0521				p.S776S		Atlas-SNP	.											.	UNC5D	393	.	0			c.C2328A						PASS	.	C		1129,3277	403.5+/-332.8	162,805,1236	88.0	76.0	80.0		2328	2.4	1.0	8	dbSNP_123	80	121,8479	62.8+/-124.8	2,117,4181	no	coding-synonymous	UNC5D	NM_080872.2		164,922,5417	AA,AC,CC		1.407,25.6241,9.6109		776/954	35624434	1250,11756	2203	4300	6503	SO:0001819	synonymous_variant	137970	exon15			GTTCTCCCGCGTG	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"""Immunoglobulin superfamily / I-set domain containing"""	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.2328C>A	8.37:g.35624434C>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	122	51	0.418033	NM_080872	Q8WYP7	Silent	SNP	ENST00000404895.2	37	CCDS6093.2																																																																																			C|0.891;A|0.109	0.109	strong		0.567	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2		
CCDC183	84960	hgsc.bcm.edu	37	9	139698977	139698977	+	Silent	SNP	G	G	A	rs11145892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139698977G>A	ENST00000338005.6	+	7	725	c.690G>A	c.(688-690)gcG>gcA	p.A230A	KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA|KIAA1984-AS1_ENST00000414656.1_RNA|RP11-216L13.18_ENST00000471502.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		230										biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		AAAGGGAGGCGTCCTTCATCG	0.612													G|||	64	0.0127796	0.0424	0.0058	5008	,	,		18627	0.0		0.002	False		,,,				2504	0.002				p.A230A		Atlas-SNP	.											.	KIAA1984	39	.	0			c.G690A						PASS	.	G		120,3832		1,118,1857	39.0	44.0	42.0		690	-5.7	0.4	9	dbSNP_120	42	37,8243		0,37,4103	no	coding-synonymous	KIAA1984	NM_001039374.4		1,155,5960	AA,AG,GG		0.4469,3.0364,1.2835		230/535	139698977	157,12075	1976	4140	6116	SO:0001819	synonymous_variant	84960	exon7			GGAGGCGTCCTTC																												ENST00000338005.6:c.690G>A	9.37:g.139698977G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	40	27	0.675	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Silent	SNP	ENST00000338005.6	37	CCDS43906.1																																																																																			G|0.993;A|0.007	0.007	strong		0.612	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
PRRC2A	7916	hgsc.bcm.edu	37	6	31603189	31603189	+	Missense_Mutation	SNP	G	G	A	rs11538264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31603189G>A	ENST00000376033.2	+	23	5554	c.5320G>A	c.(5320-5322)Gtg>Atg	p.V1774M	PRRC2A_ENST00000376007.4_Missense_Mutation_p.V1774M	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1774	4 X 57 AA type A repeats.		V -> M (in dbSNP:rs11538264).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CTTACGCCTAGTGGTAGGAGA	0.498													G|||	232	0.0463259	0.1006	0.0634	5008	,	,		24475	0.0179		0.0219	False		,,,				2504	0.0153				p.V1774M		Atlas-SNP	.											.	PRRC2A	152	.	0			c.G5320A						PASS	.	G	MET/VAL,MET/VAL	257,2765		10,237,1264	121.0	109.0	113.0		5320,5320	3.7	1.0	6	dbSNP_120	113	147,5271		1,145,2563	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	21,21	11,382,3827	AA,AG,GG		2.7132,8.5043,4.7867	probably-damaging,probably-damaging	1774/2158,1774/2158	31603189	404,8036	1511	2709	4220	SO:0001583	missense	7916	exon23			CGCCTAGTGGTAG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5320G>A	6.37:g.31603189G>A	ENSP00000365201:p.Val1774Met	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	221	110	0.497738	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	111	0.050824175824175824	55	0.11178861788617886	24	0.06629834254143646	16	0.027972027972027972	16	0.021108179419525065	G	5.652	0.304984	0.10678	0.085043	0.027132	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01647	4.71;4.71	5.51	3.71	0.42584	.	0.246078	0.28971	N	0.013543	T	0.00552	0.0018	N	0.22421	0.69	0.37881	P	0.06961200000000001	B	0.10296	0.003	B	0.09377	0.004	T	0.47983	-0.9074	9	0.87932	D	0	-3.1123	4.9425	0.13973	0.1686:0.0:0.6615:0.1699	rs11538264;rs17207253;rs11538264	1774	P48634	PRC2A_HUMAN	M	1768;1757;1774;1774;999	ENSP00000365175:V1774M;ENSP00000365201:V1774M	ENSP00000365175:V1774M	V	+	1	0	PRRC2A	31711168	0.924000	0.31332	0.977000	0.42913	0.401000	0.30781	2.140000	0.42159	0.863000	0.35553	-0.258000	0.10820	GTG	G|0.943;A|0.057	0.057	strong		0.498	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
CSF1R	1436	hgsc.bcm.edu	37	5	149460544	149460544	+	Silent	SNP	G	G	A	rs41424646		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149460544G>A	ENST00000286301.3	-	3	384	c.93C>T	c.(91-93)gtC>gtT	p.V31V	CSF1R_ENST00000543093.1_Silent_p.V31V	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	31	Ig-like C2-type 1.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	CTGGCTTCACGACCAGCTCAG	0.607																																					p.V31V		Atlas-SNP	.											CSF1R_ENST00000286301,caecum,carcinoma,-1,2	CSF1R	250	2	0			c.C93T						scavenged	.	G		6,4400	11.4+/-27.6	0,6,2197	98.0	69.0	78.0		93	-11.5	0.1	5	dbSNP_127	78	0,8600		0,0,4300	no	coding-synonymous	CSF1R	NM_005211.3		0,6,6497	AA,AG,GG		0.0,0.1362,0.0461		31/973	149460544	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon3			CTTCACGACCAGC	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.93C>T	5.37:g.149460544G>A		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	186	94	0.505376	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			T|0.000;G|0.999;A|0.001	0.001	strong		0.607	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	
ZNF407	55628	hgsc.bcm.edu	37	18	72344238	72344238	+	Silent	SNP	C	C	T	rs17817969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:72344238C>T	ENST00000299687.5	+	1	1263	c.1263C>T	c.(1261-1263)ctC>ctT	p.L421L	ZNF407_ENST00000309902.6_Silent_p.L421L|ZNF407_ENST00000577538.1_Silent_p.L421L|ZNF407_ENST00000582337.1_Silent_p.L421L	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	421					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAAATATTCTCGTGTTGGGTA	0.438													C|||	340	0.0678914	0.112	0.0663	5008	,	,		21706	0.002		0.1064	False		,,,				2504	0.0378				p.L421L		Atlas-SNP	.											.	ZNF407	231	.	0			c.C1263T						PASS	.	C	,,	387,3373		18,351,1511	63.0	65.0	64.0		1263,1263,1263	-7.7	0.0	18	dbSNP_123	64	1145,7097		88,969,3064	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	106,1320,4575	TT,TC,CC		13.8923,10.2926,12.7645	,,	421/1816,421/1661,421/2249	72344238	1532,10470	1880	4121	6001	SO:0001819	synonymous_variant	55628	exon1			TATTCTCGTGTTG	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1263C>T	18.37:g.72344238C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			C|0.907;T|0.093	0.093	strong		0.438	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
TBX22	50945	hgsc.bcm.edu	37	X	79283509	79283509	+	Silent	SNP	T	T	C	rs195293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:79283509T>C	ENST00000373294.5	+	7	911	c.883T>C	c.(883-885)Tta>Cta	p.L295L	TBX22_ENST00000373296.3_Silent_p.L295L|TBX22_ENST00000373291.1_Silent_p.L175L|TBX22_ENST00000442340.1_Silent_p.L175L	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	295					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						GGATGGGCTTTTAGAGACCTA	0.363													T|||	383	0.101457	0.2723	0.0317	3775	,	,		12527	0.0		0.001	False		,,,				2504	0.0				p.L295L		Atlas-SNP	.											.	TBX22	118	.	0			c.T883C						PASS	.	T	,,	1214,2621		158,708,190,766,381	94.0	86.0	89.0		883,523,883	3.9	1.0	X	dbSNP_79	89	9,6719		0,7,2,2421,1870	no	coding-synonymous,coding-synonymous,coding-synonymous	TBX22	NM_001109878.1,NM_001109879.1,NM_016954.2	,,	158,715,192,3187,2251	CC,CT,C,TT,T		0.1338,31.6558,11.5782	,,	295/521,175/401,295/521	79283509	1223,9340	2203	4300	6503	SO:0001819	synonymous_variant	50945	exon7			GGGCTTTTAGAGA	AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"""T-boxes"""	11600	protein-coding gene	gene with protein product		300307	"""cleft palate and/or ankyloglossia"""	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.883T>C	X.37:g.79283509T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_016954	Q5JZ06|Q96LC0|Q9HBF1	Silent	SNP	ENST00000373294.5	37	CCDS14445.1																																																																																			T|0.847;0|0.016	.	strong		0.363	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954	
CDK11A	728642	hgsc.bcm.edu	37	1	1635565	1635565	+	Silent	SNP	C	C	T	rs11488591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1635565C>T	ENST00000378633.1	-	16	1795	c.1716G>A	c.(1714-1716)gcG>gcA	p.A572A	CDK11A_ENST00000495016.1_Intron|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000378638.2_Silent_p.A535A|CDK11A_ENST00000357760.2_Silent_p.A568A|CDK11A_ENST00000356200.3_Silent_p.A535A|CDK11A_ENST00000358779.5_Silent_p.A559A|CDK11A_ENST00000404249.3_Silent_p.A569A			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	572	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.A568A(1)|p.A584A(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						CGTACTCCCGCGCCAGCCCAA	0.682													-|||	1232	0.246006	0.5	0.1167	5008	,	,		13745	0.2183		0.0646	False		,,,				2504	0.2096				p.A569A	Pancreas(186;965 2119 30274 40311 50569)	Atlas-SNP	.											CDK11B,NS,carcinoma,0,2	CDK11A	38	2	2	Substitution - coding silent(2)	stomach(2)	c.G1707A						PASS	.	C	,	1678,2272		402,874,699	36.0	43.0	41.0		1707,1677	-5.3	0.0	1	dbSNP_120	41	451,7805		33,385,3710	no	coding-synonymous,coding-synonymous	CDK11A	NM_024011.2,NM_033529.2	,	435,1259,4409	TT,TC,CC		5.4627,42.481,17.4422	,	569/781,559/771	1635565	2129,10077	1975	4128	6103	SO:0001819	synonymous_variant	728642	exon16			CTCCCGCGCCAGC	AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128		"""Cyclin-dependent kinases"""	1730	protein-coding gene	gene with protein product		116951	"""cell division cycle 2-like 2"", ""cell division cycle 2-like 2 (PITSLRE proteins)"""	CDC2L3, CDC2L2		7920654, 9750192, 19884882	Standard	NM_033529		Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000378633.1:c.1716G>A	1.37:g.1635565C>T		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	248	132	0.532258	NM_024011	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	Silent	SNP	ENST00000378633.1	37																																																																																				C|0.822;T|0.178	0.178	strong		0.682	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51918135	51918135	+	Missense_Mutation	SNP	G	G	T	rs1833785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51918135G>T	ENST00000339313.5	-	8	1674	c.1558C>A	c.(1558-1560)Cgc>Agc	p.R520S	SIGLEC10_ENST00000432469.2_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.R462S|SIGLEC10_ENST00000353836.5_Intron|SIGLEC10_ENST00000441969.3_Intron|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.R520S|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	520			R -> S (in dbSNP:rs1833785).		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)		GCCTCACAGCGGAGCCTGAGG	0.667													t|||	1217	0.243011	0.3828	0.1974	5008	,	,		15822	0.2113		0.1501	False		,,,				2504	0.2147				p.R520S		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C1558A						PASS	.	T	SER/ARG,,,,,,SER/ARG	1520,2884		258,1004,940	44.0	52.0	49.0		1384,,,,,,1558	-2.3	0.8	19	dbSNP_92	49	1283,7315		99,1085,3115	yes	missense,intron,intron,intron,intron,intron,missense	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	110,,,,,,110	357,2089,4055	TT,TG,GG		14.9221,34.5141,21.5582	benign,,,,,,benign	462/640,,,,,,520/698	51918135	2803,10199	2202	4299	6501	SO:0001583	missense	89790	exon8			CACAGCGGAGCCT	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.1558C>A	19.37:g.51918135G>T	ENSP00000345243:p.Arg520Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_033130	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	461	0.21108058608058608	178	0.3617886178861789	65	0.17955801104972377	108	0.1888111888111888	110	0.14511873350923482	.	2.864	-0.235411	0.05983	0.345141	0.149221	ENSG00000142512	ENST00000356298;ENST00000439889;ENST00000339313	D;D;D	0.85484	-1.99;-1.99;-1.99	4.83	-2.29	0.06805	.	0.523323	0.19200	N	0.120203	T	0.00012	0.0000	N	0.00385	-1.57	0.58432	P	9.000000000036756E-6	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.12243	-1.0555	9	0.02654	T	1	.	11.8093	0.52173	0.0:0.086:0.7091:0.2048	rs1833785;rs3810100;rs16982678	462;520	Q96LC7-3;Q96LC7	.;SIG10_HUMAN	S	520;462;520	ENSP00000348646:R520S;ENSP00000389132:R462S;ENSP00000345243:R520S	ENSP00000345243:R520S	R	-	1	0	SIGLEC10	56609947	0.006000	0.16342	0.838000	0.33150	0.003000	0.03518	-0.988000	0.03739	-0.803000	0.04415	-1.915000	0.00519	CGC	G|0.776;T|0.224	0.224	strong		0.667	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
ZNF765	91661	hgsc.bcm.edu	37	19	53901281	53901281	+	Missense_Mutation	SNP	C	C	G	rs141876832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53901281C>G	ENST00000396408.3	+	2	130	c.13C>G	c.(13-15)Cag>Gag	p.Q5E	ZNF765_ENST00000594030.1_Missense_Mutation_p.Q5E	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	5					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)		GGCTCTTCCTCAGGTGAGATG	0.433													.|||	88	0.0175719	0.0651	0.0029	5008	,	,		21689	0.0		0.0	False		,,,				2504	0.0				p.Q5E		Atlas-SNP	.											ZNF765_ENST00000396408,NS,carcinoma,-2,1	ZNF765	61	1	0			c.C13G						PASS	.	C	GLU/GLN	237,4169	139.2+/-174.8	4,229,1970	183.0	155.0	164.0		13	0.9	0.0	19	dbSNP_134	164	2,8598	2.2+/-6.3	0,2,4298	no	missense	ZNF765	NM_001040185.1	29	4,231,6268	GG,GC,CC		0.0233,5.379,1.8376	benign	5/524	53901281	239,12767	2203	4300	6503	SO:0001583	missense	91661	exon2			CTTCCTCAGGTGA	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.13C>G	19.37:g.53901281C>G	ENSP00000379689:p.Gln5Glu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Missense_Mutation	SNP	ENST00000396408.3	37	CCDS46171.1	83	0.038003663003663	44	0.08943089430894309	11	0.03038674033149171	14	0.024475524475524476	14	0.018469656992084433	C	2.310	-0.358135	0.05138	0.05379	2.33E-4	ENSG00000196417	ENST00000396408	T	0.00940	5.52	0.924	0.924	0.19418	Krueppel-associated box (1);	.	.	.	.	T	0.00073	0.0002	M	0.72894	2.215	0.09310	N	1	D	0.54772	0.968	P	0.44732	0.459	T	0.53078	-0.8489	9	0.66056	D	0.02	.	5.23	0.15416	0.0:1.0:0.0:0.0	.	5	Q7L2R6	ZN765_HUMAN	E	5	ENSP00000379689:Q5E	ENSP00000379689:Q5E	Q	+	1	0	ZNF765	58593093	0.446000	0.25665	0.033000	0.17914	0.161000	0.22273	0.533000	0.23082	0.829000	0.34733	0.194000	0.17425	CAG	C|0.962;G|0.038	0.038	strong		0.433	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372	
NEUROG1	4762	hgsc.bcm.edu	37	5	134871280	134871280	+	Missense_Mutation	SNP	C	C	T	rs34137563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134871280C>T	ENST00000314744.4	-	1	359	c.101G>A	c.(100-102)aGa>aAa	p.R34K		NM_006161.2	NP_006152.2	Q92886	NGN1_HUMAN	neurogenin 1	34					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)			CTGTTGGAGTCTGGCACAGTC	0.692													C|||	30	0.00599042	0.0212	0.0029	5008	,	,		13642	0.0		0.0	False		,,,				2504	0.0				p.R34K		Atlas-SNP	.											.	NEUROG1	18	.	0			c.G101A						PASS	.	C	LYS/ARG	63,4167		2,59,2054	13.0	12.0	12.0		101	3.8	1.0	5	dbSNP_126	12	0,8264		0,0,4132	yes	missense	NEUROG1	NM_006161.2	26	2,59,6186	TT,TC,CC		0.0,1.4894,0.5042	possibly-damaging	34/238	134871280	63,12431	2115	4132	6247	SO:0001583	missense	4762	exon1			TGGAGTCTGGCAC	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.101G>A	5.37:g.134871280C>T	ENSP00000317580:p.Arg34Lys	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	NM_006161	Q5U0Q9|Q96HE1	Missense_Mutation	SNP	ENST00000314744.4	37	CCDS4187.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	12.13	1.847045	0.32606	0.014894	0.0	ENSG00000181965	ENST00000314744	D	0.95103	-3.61	4.7	3.83	0.44106	.	0.656928	0.13766	N	0.364252	T	0.74489	0.3723	N	0.24115	0.695	0.26416	N	0.976176	P	0.37864	0.61	B	0.37989	0.262	T	0.72606	-0.4242	10	0.06099	T	0.92	-0.0177	10.6463	0.45621	0.0:0.904:0.0:0.096	rs34137563	34	Q92886	NGN1_HUMAN	K	34	ENSP00000317580:R34K	ENSP00000317580:R34K	R	-	2	0	NEUROG1	134899179	1.000000	0.71417	0.958000	0.39756	0.312000	0.27988	2.898000	0.48672	0.977000	0.38444	-0.258000	0.10820	AGA	C|0.993;T|0.007	0.007	strong		0.692	NEUROG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251192.1	NM_006161	
GEMIN5	25929	hgsc.bcm.edu	37	5	154275786	154275786	+	Missense_Mutation	SNP	G	G	A	rs6865950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:154275786G>A	ENST00000285873.7	-	24	3538	c.3463C>T	c.(3463-3465)Cct>Tct	p.P1155S		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	1155			P -> S (in dbSNP:rs6865950).		gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCCACGAAAGGCCCTTCGGTG	0.532													G|||	600	0.119808	0.1778	0.196	5008	,	,		19517	0.0526		0.0895	False		,,,				2504	0.0879				p.P1155S		Atlas-SNP	.											.	GEMIN5	120	.	0			c.C3463T						PASS	.	G	SER/PRO	736,3670	303.8+/-288.1	65,606,1532	133.0	114.0	121.0		3463	1.3	0.7	5	dbSNP_116	121	640,7960	163.8+/-216.2	18,604,3678	yes	missense	GEMIN5	NM_015465.3	74	83,1210,5210	AA,AG,GG		7.4419,16.7045,10.5797	benign	1155/1509	154275786	1376,11630	2203	4300	6503	SO:0001583	missense	25929	exon24			CGAAAGGCCCTTC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"""WD repeat domain containing"""	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.3463C>T	5.37:g.154275786G>A	ENSP00000285873:p.Pro1155Ser	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	182	96	0.527473	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	37	CCDS4330.1	245	0.11217948717948718	97	0.19715447154471544	55	0.15193370165745856	27	0.0472027972027972	66	0.0870712401055409	G	0.007	-1.991013	0.00439	0.167045	0.074419	ENSG00000082516	ENST00000285873	T	0.68903	-0.36	5.44	1.31	0.21738	.	0.530450	0.21762	N	0.069489	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.04607	-1.0939	9	0.06891	T	0.86	-2.351	4.098	0.10000	0.2196:0.1119:0.5488:0.1197	rs6865950;rs6865950	1154;1155	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	S	1155	ENSP00000285873:P1155S	ENSP00000285873:P1155S	P	-	1	0	GEMIN5	154255979	0.015000	0.18098	0.674000	0.29902	0.174000	0.22865	0.229000	0.17833	0.616000	0.30141	0.462000	0.41574	CCT	G|0.891;A|0.109	0.109	strong		0.532	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1		
INMT	11185	hgsc.bcm.edu	37	7	30793532	30793532	+	Missense_Mutation	SNP	G	G	A	rs76338133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30793532G>A	ENST00000013222.5	+	2	356	c.340G>A	c.(340-342)Gcc>Acc	p.A114T	INMT-FAM188B_ENST00000458257.1_Missense_Mutation_p.A113T|INMT_ENST00000409539.1_Missense_Mutation_p.A113T|INMT_ENST00000484180.1_3'UTR	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	114					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						GGTGAAATTCGCCTGTGAGCT	0.577													G|||	66	0.0131789	0.0461	0.0072	5008	,	,		19308	0.0		0.0	False		,,,				2504	0.0				p.A114T		Atlas-SNP	.											.	INMT	38	.	0			c.G340A						PASS	.	G	THR/ALA,THR/ALA	191,4215	118.8+/-156.5	1,189,2013	55.0	63.0	60.0		337,340	3.0	0.1	7	dbSNP_131	60	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	58,58	1,191,6311	AA,AG,GG		0.0233,4.335,1.4839	possibly-damaging,possibly-damaging	113/263,114/264	30793532	193,12813	2203	4300	6503	SO:0001583	missense	11185	exon2			AAATTCGCCTGTG		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.340G>A	7.37:g.30793532G>A	ENSP00000013222:p.Ala114Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	27	0.012362637362637362	23	0.046747967479674794	4	0.011049723756906077	0	0.0	0	0.0	G	20.3	3.970206	0.74246	0.04335	2.33E-4	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.03745	3.82;3.82	3.94	3.01	0.34805	.	0.359516	0.21052	N	0.080972	T	0.00524	0.0017	L	0.47716	1.5	0.26856	N	0.968062	P;P	0.42993	0.797;0.797	B;B	0.30855	0.121;0.121	T	0.44190	-0.9344	10	0.62326	D	0.03	-22.6315	8.8685	0.35300	0.1195:0.0:0.8805:0.0	.	113;114	B8ZZ69;O95050	.;INMT_HUMAN	T	114;113	ENSP00000013222:A114T;ENSP00000386961:A113T	ENSP00000013222:A114T	A	+	1	0	INMT	30760057	0.724000	0.28038	0.090000	0.20809	0.481000	0.33189	3.811000	0.55620	0.927000	0.37143	0.561000	0.74099	GCC	G|0.984;A|0.016	0.016	strong		0.577	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
TIMELESS	8914	hgsc.bcm.edu	37	12	56815717	56815717	+	Missense_Mutation	SNP	T	T	C	rs61733875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56815717T>C	ENST00000553532.1	-	21	2758	c.2608A>G	c.(2608-2610)Atg>Gtg	p.M870V	TIMELESS_ENST00000229201.4_Missense_Mutation_p.M869V|TIMELESS_ENST00000554616.1_Missense_Mutation_p.M367V					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						GCCAGTCCCATCTGTACCAGA	0.557													T|||	255	0.0509185	0.1823	0.0187	5008	,	,		21890	0.0		0.001	False		,,,				2504	0.0				p.M870V		Atlas-SNP	.											.	TIMELESS	107	.	0			c.A2608G						PASS	.	T	VAL/MET	704,3702	295.3+/-283.6	47,610,1546	140.0	127.0	131.0		2608	1.3	0.8	12	dbSNP_129	131	4,8596	3.0+/-9.4	0,4,4296	yes	missense	TIMELESS	NM_003920.3	21	47,614,5842	CC,CT,TT		0.0465,15.9782,5.4436	benign	870/1209	56815717	708,12298	2203	4300	6503	SO:0001583	missense	8914	exon21			GTCCCATCTGTAC	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.2608A>G	12.37:g.56815717T>C	ENSP00000450607:p.Met870Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	111	0.050824175824175824	108	0.21951219512195122	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	7.065	0.567067	0.13560	0.159782	4.65E-4	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.11604	2.76;2.76;2.76	5.29	1.26	0.21427	Timeless C-terminal (1);	0.478535	0.21599	N	0.071972	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B	0.17852	0.024	B	0.20955	0.032	T	0.35325	-0.9793	9	0.51188	T	0.08	-2.3118	3.9116	0.09205	0.0713:0.2456:0.3032:0.3798	.	870	Q9UNS1	TIM_HUMAN	V	869;870;367	ENSP00000229201:M869V;ENSP00000450607:M870V;ENSP00000450848:M367V	ENSP00000229201:M870V	M	-	1	0	TIMELESS	55101984	0.560000	0.26570	0.789000	0.31954	0.285000	0.27093	0.692000	0.25482	0.031000	0.15407	-0.973000	0.02599	ATG	T|0.947;C|0.053	0.053	strong		0.557	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
SEMA4B	10509	hgsc.bcm.edu	37	15	90760810	90760810	+	Silent	SNP	C	C	T	rs74037028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90760810C>T	ENST00000411539.2	+	2	557	c.297C>T	c.(295-297)ttC>ttT	p.F99F	SEMA4B_ENST00000332496.6_Silent_p.F99F|SEMA4B_ENST00000379122.3_Silent_p.F94F	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	94	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)			ACCTCAGCTTCCTGCCAGGCG	0.597													C|||	159	0.0317492	0.1142	0.0101	5008	,	,		19548	0.0		0.001	False		,,,				2504	0.0				p.F99F		Atlas-SNP	.											.	SEMA4B	51	.	0			c.C297T						PASS	.	C	,	336,3682		14,308,1687	57.0	58.0	58.0		297,297	5.6	1.0	15	dbSNP_130	58	16,8334		1,14,4160	no	coding-synonymous,coding-synonymous	SEMA4B	NM_020210.3,NM_198925.2	,	15,322,5847	TT,TC,CC		0.1916,8.3624,2.8461	,	99/838,99/838	90760810	352,12016	2009	4175	6184	SO:0001819	synonymous_variant	10509	exon3			CAGCTTCCTGCCA	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.297C>T	15.37:g.90760810C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_020210	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Silent	SNP	ENST00000411539.2	37	CCDS45347.1																																																																																			C|0.977;T|0.023	0.023	strong		0.597	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925	
ATAD3B	83858	hgsc.bcm.edu	37	1	1421531	1421531	+	Silent	SNP	C	C	A	rs819976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1421531C>A	ENST00000308647.7	+	10	1121	c.1005C>A	c.(1003-1005)acC>acA	p.T335T		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	335						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)		CCATAGCAACCAGGAACACCA	0.642													N|||	2417	0.482628	0.8502	0.3228	5008	,	,		17732	0.622		0.0924	False		,,,				2504	0.3569				p.T335T		Atlas-SNP	.											.	ATAD3B	68	.	0			c.C1005A						PASS	.	A		3215,1191		1192,831,180	79.0	91.0	87.0		1005	1.1	0.7	1	dbSNP_86	87	617,7981		35,547,3717	no	coding-synonymous	ATAD3B	NM_031921.4		1227,1378,3897	AA,AC,CC		7.1761,27.0313,29.4679		335/649	1421531	3832,9172	2203	4299	6502	SO:0001819	synonymous_variant	83858	exon10			AGCAACCAGGAAC	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.1005C>A	1.37:g.1421531C>A		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	206	90	0.436893	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Silent	SNP	ENST00000308647.7	37	CCDS30.1																																																																																			C|0.587;A|0.413	0.413	strong		0.642	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
RPE65	6121	hgsc.bcm.edu	37	1	68904645	68904645	+	Silent	SNP	C	C	A	rs61752907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:68904645C>A	ENST00000262340.5	-	9	1031	c.978G>T	c.(976-978)gtG>gtT	p.V326V		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	326					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						AGCAGAGATCCACAATCAGAA	0.418													C|||	12	0.00239617	0.0083	0.0	5008	,	,		18772	0.0		0.001	False		,,,				2504	0.0				p.V326V		Atlas-SNP	.											.	RPE65	87	.	0			c.G978T						PASS	.	C		17,4389	25.3+/-52.1	0,17,2186	281.0	279.0	280.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	978	3.0	1.0	1	dbSNP_129	280	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	RPE65	NM_000329.2		0,21,6482	AA,AC,CC		0.0465,0.3858,0.1615		326/534	68904645	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	6121	exon9			GAGATCCACAATC	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.978G>T	1.37:g.68904645C>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	143	72	0.503497	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	37	CCDS643.1																																																																																			C|0.998;A|0.002	0.002	strong		0.418	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
OR6Y1	391112	hgsc.bcm.edu	37	1	158517099	158517099	+	Missense_Mutation	SNP	C	C	A	rs113154921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158517099C>A	ENST00000302617.3	-	1	796	c.797G>T	c.(796-798)cGt>cTt	p.R266L		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	266						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)					GAGTTTGGGACGGGCATAGGT	0.483													C|||	99	0.0197684	0.0719	0.0043	5008	,	,		24161	0.0		0.001	False		,,,				2504	0.0				p.R266L		Atlas-SNP	.											.	OR6Y1	73	.	0			c.G797T						PASS	.	C	LEU/ARG	264,4142	148.4+/-182.8	11,242,1950	208.0	195.0	200.0		797	3.5	1.0	1	dbSNP_132	200	5,8595	5.0+/-18.6	0,5,4295	yes	missense	OR6Y1	NM_001005189.1	102	11,247,6245	AA,AC,CC		0.0581,5.9918,2.0683	probably-damaging	266/326	158517099	269,12737	2203	4300	6503	SO:0001583	missense	391112	exon1			TTGGGACGGGCAT	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.797G>T	1.37:g.158517099C>A	ENSP00000304807:p.Arg266Leu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	142	68	0.478873	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	37	CCDS30899.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	18.23	3.577221	0.65878	0.059918	5.81E-4	ENSG00000197532	ENST00000302617	T	0.36699	1.24	5.34	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42172	D	0.000750	T	0.35740	0.0942	M	0.73319	2.225	0.09310	N	1	D	0.64830	0.994	P	0.58660	0.843	T	0.18681	-1.0329	10	0.87932	D	0	.	8.5271	0.33311	0.0:0.7603:0.0:0.2397	.	266	Q8NGX8	OR6Y1_HUMAN	L	266	ENSP00000304807:R266L	ENSP00000304807:R266L	R	-	2	0	OR6Y1	156783723	0.000000	0.05858	0.983000	0.44433	0.927000	0.56198	-0.100000	0.10990	0.822000	0.34565	0.655000	0.94253	CGT	A|0.018;C|0.982;G|0.000	0.018	strong		0.483	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189	
SELP	6403	hgsc.bcm.edu	37	1	169566308	169566308	+	Silent	SNP	G	G	A	rs6132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169566308G>A	ENST00000263686.6	-	11	1849	c.1812C>T	c.(1810-1812)aaC>aaT	p.N604N	SELP_ENST00000367788.2_Silent_p.N542N|SELP_ENST00000367786.2_Silent_p.N542N|SELP_ENST00000367794.2_Silent_p.N542N|SELP_ENST00000367792.2_Intron|SELP_ENST00000367791.2_Intron|SELP_ENST00000458599.2_Intron|SELP_ENST00000367793.2_Silent_p.N542N	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	194	0	0		WXS	Illumina HiSeq	Phase_I	198	92	0.464646	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	
C8orf31	286122	hgsc.bcm.edu	37	8	144126087	144126087	+	Missense_Mutation	SNP	C	C	A	rs73717943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144126087C>A	ENST00000395172.1	+	4	560	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	C8orf31_ENST00000517653.1_3'UTR	NM_173687.2	NP_775958.1	Q8N9H6	CH031_HUMAN	chromosome 8 open reading frame 31	70										breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10	all_cancers(97;1.89e-10)|all_epithelial(106;8.73e-09)|Lung NSC(106;0.000161)|all_lung(105;0.000447)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TGCCCTGGCACCCCAGGGACT	0.627													c|||	115	0.0229633	0.084	0.0058	5008	,	,		14974	0.0		0.0	False		,,,				2504	0.0				p.P70T		Atlas-SNP	.											.	C8orf31	18	.	0			c.C208A						PASS	.	C	THR/PRO	323,4083	170.1+/-200.6	7,309,1887	69.0	60.0	63.0		208	-2.7	0.0	8	dbSNP_130	63	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C8orf31	NM_173687.2	38	7,311,6185	AA,AC,CC		0.0233,7.3309,2.4988	benign	70/133	144126087	325,12681	2203	4300	6503	SO:0001583	missense	286122	exon4			CTGGCACCCCAGG		CCDS6395.1	8q24.3	2012-04-11			ENSG00000177335	ENSG00000177335			26731	protein-coding gene	gene with protein product							Standard	NM_173687		Approved	FLJ37131	uc003yxp.1	Q8N9H6	OTTHUMG00000164771	ENST00000395172.1:c.208C>A	8.37:g.144126087C>A	ENSP00000378601:p.Pro70Thr	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_173687	Q6GMU7	Missense_Mutation	SNP	ENST00000395172.1	37	CCDS6395.1	46	0.021062271062271064	43	0.08739837398373984	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	c	0.019	-1.466214	0.01053	0.073309	2.33E-4	ENSG00000177335	ENST00000395172	T	0.57595	0.39	1.37	-2.73	0.05950	.	.	.	.	.	T	0.00875	0.0029	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.05500	-1.0881	9	0.87932	D	0	.	0.828	0.01124	0.2674:0.3758:0.1668:0.19	.	70	Q8N9H6	CH031_HUMAN	T	70	ENSP00000378601:P70T	ENSP00000378601:P70T	P	+	1	0	C8orf31	144197462	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.991000	0.01478	-2.249000	0.00702	-1.735000	0.00691	CCC	C|0.973;A|0.027	0.027	strong		0.627	C8orf31-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380167.1	NM_173687	
FAM179A	165186	hgsc.bcm.edu	37	2	29240783	29240783	+	Missense_Mutation	SNP	A	A	G	rs1109758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29240783A>G	ENST00000379558.4	+	10	1672	c.1321A>G	c.(1321-1323)Atc>Gtc	p.I441V	FAM179A_ENST00000465300.1_Intron|FAM179A_ENST00000403861.2_Intron	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	441			I -> V (in dbSNP:rs1109758).							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						CAGCATCCCCATCAGCCGGCA	0.677													G|||	2010	0.401358	0.6679	0.304	5008	,	,		15556	0.3224		0.341	False		,,,				2504	0.2536				p.I441V		Atlas-SNP	.											.	FAM179A	106	.	0			c.A1321G						PASS	.	G	VAL/ILE	2212,1698		640,932,383	13.0	18.0	16.0		1321	1.1	0.1	2	dbSNP_86	16	2639,5645		431,1777,1934	yes	missense	FAM179A	NM_199280.2	29	1071,2709,2317	GG,GA,AA		31.8566,43.4271,39.7819	benign	441/1020	29240783	4851,7343	1955	4142	6097	SO:0001583	missense	165186	exon10			ATCCCCATCAGCC	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.1321A>G	2.37:g.29240783A>G	ENSP00000368876:p.Ile441Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	124	48	0.387097	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	888	0.4065934065934066	337	0.6849593495934959	113	0.31215469613259667	181	0.31643356643356646	257	0.3390501319261214	G	0	-2.582335	0.00129	0.565729	0.318566	ENSG00000189350	ENST00000379558	T	0.04502	3.61	4.26	1.07	0.20283	.	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.38475	P	0.052425000000000055	B	0.02656	0.0	B	0.01281	0.0	T	0.10847	-1.0612	8	0.08599	T	0.76	.	8.8404	0.35137	0.4176:0.0:0.5824:0.0	rs1109758;rs4420672;rs17007448;rs58321497;rs1109758	441	Q6ZUX3	F179A_HUMAN	V	441	ENSP00000368876:I441V	ENSP00000368876:I441V	I	+	1	0	FAM179A	29094287	0.064000	0.20934	0.083000	0.20561	0.007000	0.05969	0.232000	0.17891	-0.122000	0.11766	-0.914000	0.02751	ATC	A|0.599;G|0.401	0.401	strong		0.677	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
USP10	9100	hgsc.bcm.edu	37	16	84778694	84778694	+	Missense_Mutation	SNP	T	T	C	rs2326391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84778694T>C	ENST00000219473.7	+	4	720	c.607T>C	c.(607-609)Tca>Cca	p.S203P	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Missense_Mutation_p.S207P	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	203			S -> P (in dbSNP:rs2326391). {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						CATGCCCCCGTCAGTTACGCC	0.547													T|||	1406	0.280751	0.2337	0.121	5008	,	,		17497	0.4107		0.1531	False		,,,				2504	0.455				p.S207P		Atlas-SNP	.											.	USP10	51	.	0			c.T619C						PASS	.	T	PRO/SER	824,3138		80,664,1237	30.0	29.0	29.0		607	-2.2	0.0	16	dbSNP_100	29	1157,7163		83,991,3086	no	missense	USP10	NM_005153.2	74	163,1655,4323	CC,CT,TT		13.9062,20.7976,16.1293	benign	203/799	84778694	1981,10301	1981	4160	6141	SO:0001583	missense	9100	exon5			CCCCCGTCAGTTA	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.607T>C	16.37:g.84778694T>C	ENSP00000219473:p.Ser203Pro	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	209	105	0.502392	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	T	4.094	0.015431	0.07959	0.207976	0.139063	ENSG00000103194	ENST00000219473	T	0.08282	3.11	5.17	-2.15	0.07102	.	1.297810	0.05133	N	0.492893	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.47649	-0.9101	9	0.42905	T	0.14	3.5779	7.0558	0.25099	0.0:0.4462:0.1418:0.4121	rs2326391;rs17855998	207;203	Q14694-3;Q14694	.;UBP10_HUMAN	P	203	ENSP00000219473:S203P	ENSP00000219473:S203P	S	+	1	0	USP10	83336195	0.000000	0.05858	0.000000	0.03702	0.181000	0.23173	-0.193000	0.09573	-0.758000	0.04690	0.402000	0.26972	TCA	T|0.774;C|0.226	0.226	strong		0.547	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
HDHD1	8226	hgsc.bcm.edu	37	X	6995315	6995315	+	Silent	SNP	C	C	T	rs2379206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:6995315C>T	ENST00000381077.5	-	3	532	c.456G>A	c.(454-456)ccG>ccA	p.P152P	HDHD1_ENST00000540122.1_Silent_p.P152P|HDHD1_ENST00000424830.2_Silent_p.P175P|HDHD1_ENST00000412827.2_Silent_p.P109P	NM_001178136.1|NM_012080.4	NP_001171607.1|NP_036212.3	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain containing 1	152					nucleotide metabolic process (GO:0009117)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)			breast(2)|large_intestine(1)|lung(3)	6						GGAAGATGTCCGGGTCTGGCT	0.557													C|||	2503	0.663046	0.559	0.5187	3775	,	,		15252	0.4524		0.4185	False		,,,				2504	0.5389				p.P175P		Atlas-SNP	.											.	HDHD1	21	.	0			c.G525A						PASS	.	C	,,,	2638,926		837,565,399,95,171	35.0	36.0	36.0		525,456,327,456	-7.8	0.0	X	dbSNP_100	36	3887,2671		870,1118,1029,387,779	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HDHD1	NM_001135565.1,NM_001178135.1,NM_001178136.1,NM_012080.4	,,,	1707,1683,1428,482,950	TT,TC,T,CC,C		40.7289,25.982,35.5365	,,,	175/252,152/209,109/186,152/229	6995315	6525,3597	2067	4183	6250	SO:0001819	synonymous_variant	8226	exon4			GATGTCCGGGTCT	M86934	CCDS48075.1, CCDS48076.1, CCDS55366.1, CCDS55367.1	Xp22.32	2010-07-21	2010-07-21	2010-07-21	ENSG00000130021	ENSG00000130021			16818	protein-coding gene	gene with protein product		306480	"""family with sequence similarity 16, member A, X-linked"", ""haloacid dehalogenase-like hydrolase domain containing 1A"""	FAM16AX, HDHD1A		1734713, 1284467	Standard	NM_012080		Approved	DXF68S1E, GS1	uc011mhm.1	Q08623	OTTHUMG00000021101	ENST00000381077.5:c.456G>A	X.37:g.6995315C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	233	112	0.480687	NM_001135565	B2R7X6|B4DV93|B7Z6Q3|E9PAV8|F5GWZ2|Q53F84|Q96EB8	Silent	SNP	ENST00000381077.5	37	CCDS48075.1																																																																																			C|0.347;T|0.653	0.653	strong		0.557	HDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055683.2	NM_012080	
DSPP	1834	hgsc.bcm.edu	37	4	88535832	88535832	+	Missense_Mutation	SNP	A	A	G	rs201553143|rs142316753		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88535832A>G	ENST00000282478.7	+	4	2051	c.2018A>G	c.(2017-2019)gAt>gGt	p.D673G	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D673G			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	673	Asp/Ser-rich.			D -> DSSDSSS (in Ref. 1; AAF42472). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gacagcagtgatagcagtgac	0.488																																					p.D673G		Atlas-SNP	.											.	DSPP	174	.	0			c.A2018G						PASS	.						122.0	139.0	133.0					4																	88535832		1702	3108	4810	SO:0001583	missense	1834	exon5			GCAGTGATAGCAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2018A>G	4.37:g.88535832A>G	ENSP00000282478:p.Asp673Gly	Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	364	58	0.159341	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	-	0.506	-0.868666	0.02570	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87650	-2.28;-2.28	2.58	1.3	0.21679	.	.	.	.	.	T	0.78972	0.4368	L	0.43923	1.385	0.09310	N	0.999992	B	0.13145	0.007	B	0.09377	0.004	T	0.62492	-0.6843	9	0.29301	T	0.29	-9.092	4.9808	0.14164	0.6876:0.0:0.3124:0.0	.	673	Q9NZW4	DSPP_HUMAN	G	673	ENSP00000382213:D673G;ENSP00000282478:D673G	ENSP00000282478:D673G	D	+	2	0	DSPP	88754856	0.507000	0.26146	0.889000	0.34880	0.021000	0.10359	1.818000	0.39012	0.190000	0.20209	0.139000	0.15985	GAT	.	.	weak		0.488	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
C2CD4C	126567	hgsc.bcm.edu	37	19	408200	408200	+	Silent	SNP	G	G	C	rs7252178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:408200G>C	ENST00000332235.6	-	2	335	c.162C>G	c.(160-162)ccC>ccG	p.P54P		NM_001136263.1	NP_001129735.1	Q8TF44	C2C4C_HUMAN	C2 calcium-dependent domain containing 4C	54										large_intestine(1)|pancreas(1)	2						AGGGCAGCTTGGGGGGGATGA	0.716													g|||	158	0.0315495	0.1165	0.0058	5008	,	,		10623	0.0		0.0	False		,,,				2504	0.0				p.P54P		Atlas-SNP	.											C2CD4C,NS,carcinoma,0,1	C2CD4C	13	1	0			c.C162G						PASS	.						19.0	24.0	23.0					19																	408200		692	1589	2281	SO:0001819	synonymous_variant	126567	exon2			CAGCTTGGGGGGG	AB075837	CCDS45890.1	19p13.3	2009-09-28	2009-09-28	2009-09-28		ENSG00000183186			29417	protein-coding gene	gene with protein product	"""nuclear localized factor 3"""	610336	"""KIAA1957"", ""family with sequence similarity 148, member C"""	KIAA1957, FAM148C		11853319	Standard	NM_001136263		Approved	NLF3	uc002loo.3	Q8TF44		ENST00000332235.6:c.162C>G	19.37:g.408200G>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	180	98	0.544444	NM_001136263	Q8N3H7	Silent	SNP	ENST00000332235.6	37	CCDS45890.1																																																																																			G|0.971;C|0.029	0.029	strong		0.716	C2CD4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451789.2	XM_065166	
TRIM3	10612	hgsc.bcm.edu	37	11	6477831	6477831	+	Silent	SNP	C	C	T	rs10606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6477831C>T	ENST00000525074.1	-	6	1519	c.1125G>A	c.(1123-1125)ccG>ccA	p.P375P	TRIM3_ENST00000537602.1_Silent_p.P297P|TRIM3_ENST00000345851.3_Silent_p.P375P|TRIM3_ENST00000536344.1_Silent_p.P256P|TRIM3_ENST00000359518.3_Silent_p.P375P|TRIM3_ENST00000529058.1_5'UTR	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	375					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P375P(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCACTGGCACCGGAAGGCGCG	0.637													C|||	940	0.1877	0.2973	0.1772	5008	,	,		18660	0.0188		0.1849	False		,,,				2504	0.2239				p.P375P	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											TRIM3,NS,lymphoid_neoplasm,0,1	TRIM3	67	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1125A						PASS	.	C	,	1261,3125		180,901,1112	31.0	31.0	31.0		1125,1125	-10.3	0.0	11	dbSNP_52	31	1738,6816		198,1342,2737	no	coding-synonymous,coding-synonymous	TRIM3	NM_006458.2,NM_033278.2	,	378,2243,3849	TT,TC,CC		20.318,28.7506,23.1762	,	375/745,375/745	6477831	2999,9941	2193	4277	6470	SO:0001819	synonymous_variant	10612	exon6			TGGCACCGGAAGG	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.1125G>A	11.37:g.6477831C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																			C|0.791;T|0.209	0.209	strong		0.637	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
PIP4K2B	8396	hgsc.bcm.edu	37	17	36936846	36936846	+	Silent	SNP	C	C	T	rs16968328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36936846C>T	ENST00000269554.3	-	4	846	c.366G>A	c.(364-366)acG>acA	p.T122T	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	122	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						GGGCGCTGCGCGTCACTGAAT	0.572													C|||	323	0.0644968	0.2352	0.013	5008	,	,		19211	0.001		0.002	False		,,,				2504	0.0				p.T122T		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.G366A						PASS	.	C		767,3639	313.0+/-292.9	60,647,1496	79.0	73.0	75.0		366	-6.1	0.9	17	dbSNP_123	75	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	PIP4K2B	NM_003559.4		60,655,5788	TT,TC,CC		0.093,17.4081,5.9588		122/417	36936846	775,12231	2203	4300	6503	SO:0001819	synonymous_variant	8396	exon4			GCTGCGCGTCACT	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"""phosphatidylinositol-4-phosphate 5-kinase, type II, beta"""	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.366G>A	17.37:g.36936846C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_003559	Q5U0E8|Q8TBP2	Silent	SNP	ENST00000269554.3	37	CCDS11329.1																																																																																			C|0.931;T|0.069	0.069	strong		0.572	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559	
DPP8	54878	hgsc.bcm.edu	37	15	65793060	65793060	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65793060G>A	ENST00000341861.5	-	4	2058	c.478C>T	c.(478-480)Cgc>Tgc	p.R160C	DPP8_ENST00000321118.7_Missense_Mutation_p.R160C|DPP8_ENST00000358939.4_Missense_Mutation_p.R144C|DPP8_ENST00000321147.6_Missense_Mutation_p.R160C|Y_RNA_ENST00000516408.1_RNA|DPP8_ENST00000559233.1_Missense_Mutation_p.R160C|DPP8_ENST00000300141.6_Missense_Mutation_p.R144C|DPP8_ENST00000339244.5_Missense_Mutation_p.R160C	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	160					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GTTCCAATGCGTTTTCTTTCT	0.393																																					p.R160C		Atlas-SNP	.											DPP8,colon,carcinoma,+1,1	DPP8	78	1	0			c.C478T						PASS	.						204.0	196.0	199.0					15																	65793060		2201	4299	6500	SO:0001583	missense	54878	exon5			CAATGCGTTTTCT	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"""dipeptidyl peptidase VIII"", ""dipeptidyl peptidase IV-related protein-1"", ""prolyl dipeptidase DPP8"""	606819	"""dipeptidylpeptidase 8"""			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.478C>T	15.37:g.65793060G>A	ENSP00000339208:p.Arg160Cys	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	179	62	0.346369	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Missense_Mutation	SNP	ENST00000341861.5	37	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.943085	0.92526	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000339244;ENST00000395652	T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.58864	0.2152	M	0.72479	2.2	0.40608	D	0.981643	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.996;1.0;1.0	T	0.60047	-0.7339	10	0.87932	D	0	-17.8264	20.2885	0.98538	0.0:0.0:1.0:0.0	.	144;144;160;160	Q6V1X1-3;Q6V1X1-4;Q6V1X1-2;Q6V1X1	.;.;.;DPP8_HUMAN	C	160;144;144;160;160;160;160	ENSP00000339208:R160C;ENSP00000351817:R144C;ENSP00000300141:R144C;ENSP00000318111:R160C;ENSP00000316373:R160C;ENSP00000341230:R160C;ENSP00000379013:R160C	ENSP00000300141:R144C	R	-	1	0	DPP8	63580113	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.896000	0.87350	2.791000	0.96007	0.650000	0.86243	CGC	.	.	none		0.393	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743	
PLCG2	5336	hgsc.bcm.edu	37	16	81960783	81960783	+	Splice_Site	SNP	G	G	A	rs115583707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81960783G>A	ENST00000359376.3	+	23	2728	c.2514G>A	c.(2512-2514)caG>caA	p.Q838Q		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	838					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						TAGAAAAGCAGGTGAGTCCCC	0.512													G|||	54	0.0107827	0.0356	0.0101	5008	,	,		20557	0.0		0.0	False		,,,				2504	0.0				p.Q838Q		Atlas-SNP	.											.	PLCG2	276	.	0			c.G2514A						PASS	.	G		149,3837		3,143,1847	109.0	107.0	107.0		2514	5.3	1.0	16	dbSNP_132	107	1,8337		0,1,4168	yes	coding-synonymous-near-splice	PLCG2	NM_002661.3		3,144,6015	AA,AG,GG		0.012,3.7381,1.2171		838/1266	81960783	150,12174	1993	4169	6162	SO:0001630	splice_region_variant	5336	exon23			AAAGCAGGTGAGT		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.2514+1G>A	16.37:g.81960783G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			G|0.984;A|0.016	0.016	strong		0.512	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		Silent
GPR171	29909	hgsc.bcm.edu	37	3	150917000	150917000	+	Silent	SNP	T	T	G	rs3773614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150917000T>G	ENST00000309180.5	-	3	404	c.174A>C	c.(172-174)acA>acC	p.T58T	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_013308.3	NP_037440.3	O14626	GP171_HUMAN	G protein-coupled receptor 171	58					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)			endometrium(1)|kidney(4)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	15			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GGAAATCGGCTGTAAGCAAAT	0.413													T|||	591	0.118011	0.2194	0.085	5008	,	,		18283	0.0704		0.0666	False		,,,				2504	0.1063				p.T58T		Atlas-SNP	.											.	GPR171	36	.	0			c.A174C						PASS	.	T	,	897,3509	346.7+/-309.1	88,721,1394	85.0	83.0	84.0		174,	-6.9	0.0	3	dbSNP_107	84	608,7992	160.0+/-213.2	17,574,3709	no	coding-synonymous,intron	GPR171,MED12L	NM_013308.3,NM_053002.4	,	105,1295,5103	GG,GT,TT		7.0698,20.3586,11.5716	,	58/320,	150917000	1505,11501	2203	4300	6503	SO:0001819	synonymous_variant	29909	exon3			ATCGGCTGTAAGC	AF002986	CCDS3155.1	3q25.1	2012-08-21			ENSG00000174946	ENSG00000174946		"""GPCR / Class A : Orphans"""	30057	protein-coding gene	gene with protein product	"""platelet activating receptor homolog"""					9370294	Standard	NM_013308		Approved	H963	uc003eyq.4	O14626	OTTHUMG00000159861	ENST00000309180.5:c.174A>C	3.37:g.150917000T>G		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	173	88	0.508671	NM_013308	D3DNJ4|Q8IV06	Silent	SNP	ENST00000309180.5	37	CCDS3155.1																																																																																			T|0.882;G|0.118	0.118	strong		0.413	GPR171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357793.1	NM_013308	
NFATC1	4772	hgsc.bcm.edu	37	18	77170477	77170477	+	Missense_Mutation	SNP	C	C	A	rs1051978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:77170477C>A	ENST00000427363.2	+	2	202	c.202C>A	c.(202-204)Ccg>Acg	p.P68T	NFATC1_ENST00000587635.1_Missense_Mutation_p.P68T|NFATC1_ENST00000586434.1_Missense_Mutation_p.P55T|NFATC1_ENST00000397790.2_Intron|NFATC1_ENST00000253506.5_Missense_Mutation_p.P68T|NFATC1_ENST00000592223.1_Missense_Mutation_p.P55T|NFATC1_ENST00000329101.4_Missense_Mutation_p.P55T|NFATC1_ENST00000545796.1_Intron|NFATC1_ENST00000318065.5_Missense_Mutation_p.P55T|NFATC1_ENST00000591814.1_Missense_Mutation_p.P68T|NFATC1_ENST00000542384.1_Missense_Mutation_p.P68T			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	68			P -> T (in dbSNP:rs1051978).		calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	CCTGCCGGCCCCGTGCCACAA	0.652													C|||	234	0.0467252	0.0068	0.1527	5008	,	,		14100	0.0		0.0934	False		,,,				2504	0.0256				p.P68T	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C202A						PASS	.	C	THR/PRO,THR/PRO,,THR/PRO,THR/PRO	100,4306	77.8+/-116.1	1,98,2104	59.0	68.0	65.0		202,163,,163,202	3.5	0.0	18	dbSNP_86	65	935,7663	205.9+/-248.2	54,827,3418	yes	missense,missense,intron,missense,missense	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	38,38,,38,38	55,925,5522	AA,AC,CC		10.8746,2.2696,7.9591	possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	68/826,55/931,,55/813,68/717	77170477	1035,11969	2203	4299	6502	SO:0001583	missense	4772	exon2			CCGGCCCCGTGCC	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.202C>A	18.37:g.77170477C>A	ENSP00000389377:p.Pro68Thr	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		128	0.05860805860805861	4	0.008130081300813009	50	0.13812154696132597	0	0.0	74	0.09762532981530343	C	10.32	1.318656	0.23994	0.022696	0.108746	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000542384;ENST00000329101;ENST00000427363;ENST00000397794	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	4.39	3.49	0.39957	.	0.118056	0.64402	D	0.000016	T	0.00328	0.0010	M	0.70275	2.135	0.09310	P	1.0	B;B;B;B;B;B;B	0.34181	0.306;0.306;0.306;0.306;0.306;0.44;0.306	B;B;B;B;B;B;B	0.30646	0.08;0.118;0.05;0.08;0.08;0.08;0.05	T	0.10543	-1.0625	9	0.66056	D	0.02	-10.9661	8.6371	0.33955	0.0:0.7533:0.1611:0.0856	rs1051978;rs2230114;rs16958940;rs1051978	55;55;68;68;68;55;68	B5B2M7;B5B2N1;B5B2M6;O95644;B5B2M4;B5B2M5;Q2M1S3	.;.;.;NFAC1_HUMAN;.;.;.	T	68;68;68;55;55;32	ENSP00000316553:P68T;ENSP00000253506:P68T;ENSP00000442435:P68T;ENSP00000327850:P55T	ENSP00000253506:P68T	P	+	1	0	NFATC1	75271465	0.236000	0.23804	0.006000	0.13384	0.137000	0.21094	2.714000	0.47202	1.013000	0.39391	0.561000	0.74099	CCG	C|0.931;A|0.069	0.069	strong		0.652	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
C2orf91	400950	hgsc.bcm.edu	37	2	42165754	42165754	+	Splice_Site	SNP	C	C	T	rs10192292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:42165754C>T	ENST00000378711.2	-	4	475		c.e4-1			NM_001242815.1	NP_001229744.1	Q6ZV80	CB091_HUMAN	chromosome 2 open reading frame 91																		CAGGTGGAACCTGCAAGAAAG	0.522													C|||	1263	0.252196	0.2557	0.3703	5008	,	,		18626	0.2381		0.2773	False		,,,				2504	0.1524				.		Atlas-SNP	.											.	.	.	.	0			c.386-1G>A						PASS	.																																			SO:0001630	splice_region_variant	400950	exon5			TGGAACCTGCAAG		CCDS56116.1	2p21	2012-02-17			ENSG00000205086	ENSG00000205086			42966	protein-coding gene	gene with protein product							Standard	NM_001242815		Approved		uc002rsf.1	Q6ZV80	OTTHUMG00000152307	ENST00000378711.2:c.386-1G>A	2.37:g.42165754C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	188	102	0.542553	NM_001242815		Splice_Site	SNP	ENST00000378711.2	37	CCDS56116.1	607	0.27793040293040294	115	0.23373983739837398	138	0.3812154696132597	149	0.26048951048951047	205	0.2704485488126649	C	13.75	2.330050	0.41297	.	.	ENSG00000205086	ENST00000378711	.	.	.	3.16	-0.673	0.11373	.	.	.	.	.	.	.	.	.	.	.	0.47737	P	4.96000000000052E-4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.3978	0.07312	0.0:0.4572:0.208:0.3348	rs10192292;rs56746019	.	.	.	.	-1	.	.	.	-	.	.	AC013480.1	42019258	0.000000	0.05858	0.005000	0.12908	0.873000	0.50193	-0.302000	0.08221	-0.124000	0.11724	0.561000	0.74099	.	C|0.732;T|0.268	0.268	strong		0.522	C2orf91-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000325755.1	NM_001242815	Intron
SVEP1	79987	hgsc.bcm.edu	37	9	113169116	113169116	+	Missense_Mutation	SNP	T	T	C	rs16914996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113169116T>C	ENST00000401783.2	-	38	9100	c.8764A>G	c.(8764-8766)Atc>Gtc	p.I2922V	SVEP1_ENST00000374469.1_Missense_Mutation_p.I2899V|SVEP1_ENST00000297826.5_Missense_Mutation_p.I848V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2922	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.		I -> V (in dbSNP:rs16914996).		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						CCGTGCAAGATGTAGCCCTCG	0.527													T|||	207	0.0413339	0.149	0.0144	5008	,	,		21879	0.0		0.0	False		,,,				2504	0.0				p.I2922V		Atlas-SNP	.											.	SVEP1	326	.	0			c.A8764G						PASS	.	T	VAL/ILE	495,3643		27,441,1601	141.0	142.0	141.0		8764	-1.4	0.0	9	dbSNP_123	141	5,8423		0,5,4209	yes	missense	SVEP1	NM_153366.3	29	27,446,5810	CC,CT,TT		0.0593,11.9623,3.979	benign	2922/3572	113169116	500,12066	2069	4214	6283	SO:0001583	missense	79987	exon38			GCAAGATGTAGCC	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.8764A>G	9.37:g.113169116T>C	ENSP00000384917:p.Ile2922Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	74	52	0.702703	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	74	0.03388278388278388	71	0.1443089430894309	3	0.008287292817679558	0	0.0	0	0.0	T	0.008	-1.879969	0.00537	0.119623	5.93E-4	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.61859	0.07;0.07;0.07	5.41	-1.41	0.08941	Complement control module (2);Sushi/SCR/CCP (3);	1.252220	0.05177	N	0.500598	T	0.00178	0.0005	N	0.01146	-0.985	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03651	-1.1016	9	0.17369	T	0.5	.	6.9527	0.24554	0.1169:0.3452:0.0:0.5379	rs16914996;rs52792614;rs16914996	2922	Q4LDE5	SVEP1_HUMAN	V	2922;2899;848	ENSP00000384917:I2922V;ENSP00000363593:I2899V;ENSP00000297826:I848V	ENSP00000297826:I848V	I	-	1	0	SVEP1	112208937	0.000000	0.05858	0.002000	0.10522	0.079000	0.17450	-1.006000	0.03671	-0.630000	0.05567	-0.326000	0.08463	ATC	T|0.943;C|0.057	0.057	strong		0.527	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
NAV2	89797	hgsc.bcm.edu	37	11	19735325	19735325	+	Silent	SNP	C	C	A	rs11828836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:19735325C>A	ENST00000396087.3	+	1	183	c.84C>A	c.(82-84)ccC>ccA	p.P28P	RP11-359E10.1_ENST00000603468.1_lincRNA|NAV2_ENST00000360655.4_Intron|NAV2_ENST00000396085.1_Silent_p.P28P|NAV2_ENST00000349880.4_Silent_p.P28P	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	28					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TGCACGTgcccccggcccggg	0.662													C|||	112	0.0223642	0.0825	0.0043	5008	,	,		13608	0.0		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											.	NAV2	255	.	0			c.C84A						PASS	.	C	,,	269,4121		8,253,1934	20.0	22.0	21.0		,84,84	4.4	1.0	11	dbSNP_120	21	5,8571		0,5,4283	no	intron,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	8,258,6217	AA,AC,CC		0.0583,6.1276,2.1132	,,	,28/2430,28/2433	19735325	274,12692	2195	4288	6483	SO:0001819	synonymous_variant	89797	exon1			CGTGCCCCCGGCC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.84C>A	11.37:g.19735325C>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	38	28	0.736842	NM_145117	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			C|0.975;A|0.025	0.025	strong		0.662	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
OLFML2B	25903	hgsc.bcm.edu	37	1	161993192	161993192	+	Missense_Mutation	SNP	T	T	C	rs12130792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161993192T>C	ENST00000294794.3	-	1	452	c.29A>G	c.(28-30)tAc>tGc	p.Y10C	OLFML2B_ENST00000367940.2_Missense_Mutation_p.Y10C	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	10			Y -> C (in dbSNP:rs12130792).		extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			CAGAGCGAAGTAGAGAACTAG	0.627													T|||	488	0.0974441	0.1604	0.0375	5008	,	,		17425	0.1419		0.0726	False		,,,				2504	0.0348				p.Y10C		Atlas-SNP	.											.	OLFML2B	114	.	0			c.A29G						PASS	.	T	CYS/TYR	629,3777	269.5+/-269.1	50,529,1624	56.0	56.0	56.0		29	2.8	0.6	1	dbSNP_120	56	648,7952	165.9+/-218.0	23,602,3675	yes	missense	OLFML2B	NM_015441.1	194	73,1131,5299	CC,CT,TT		7.5349,14.276,9.8185	benign	10/751	161993192	1277,11729	2203	4300	6503	SO:0001583	missense	25903	exon1			GCGAAGTAGAGAA	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.29A>G	1.37:g.161993192T>C	ENSP00000294794:p.Tyr10Cys	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	134	132	0.985075	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	37	CCDS1236.1	239	0.10943223443223443	84	0.17073170731707318	14	0.03867403314917127	85	0.1486013986013986	56	0.07387862796833773	T	5.529	0.282591	0.10458	0.14276	0.075349	ENSG00000162745	ENST00000294794;ENST00000367940	D;D	0.86432	-2.12;-2.12	4.85	2.76	0.32466	.	.	.	.	.	T	0.37919	0.1021	N	0.01576	-0.805	0.23645	P	0.99722	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10894	-1.0610	8	0.02654	T	1	.	6.6908	0.23169	0.0:0.7575:0.0:0.2425	rs12130792;rs58683497;rs12130792	10;10	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	C	10	ENSP00000294794:Y10C;ENSP00000356917:Y10C	ENSP00000294794:Y10C	Y	-	2	0	OLFML2B	160259816	0.782000	0.28689	0.575000	0.28536	0.084000	0.17831	0.741000	0.26202	0.501000	0.28013	-0.366000	0.07423	TAC	T|0.895;C|0.105	0.105	strong		0.627	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441	
JPH3	57338	hgsc.bcm.edu	37	16	87717863	87717863	+	Missense_Mutation	SNP	C	C	T	rs138328691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:87717863C>T	ENST00000284262.2	+	3	1518	c.1276C>T	c.(1276-1278)Cgg>Tgg	p.R426W	JPH3_ENST00000563609.1_3'UTR	NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	426					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		CTTCCAGCACCGGGAAAACGG	0.647																																					p.R426W		Atlas-SNP	.											JPH3,NS,carcinoma,-2,1	JPH3	95	1	0			c.C1276T						PASS	.	C	TRP/ARG	4,4392	6.2+/-15.9	0,4,2194	73.0	60.0	64.0		1276	-4.8	0.9	16	dbSNP_134	64	0,8600		0,0,4300	yes	missense	JPH3	NM_020655.2	101	0,4,6494	TT,TC,CC		0.0,0.091,0.0308	probably-damaging	426/749	87717863	4,12992	2198	4300	6498	SO:0001583	missense	57338	exon3			CAGCACCGGGAAA	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.1276C>T	16.37:g.87717863C>T	ENSP00000284262:p.Arg426Trp	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	218	121	0.555046	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Missense_Mutation	SNP	ENST00000284262.2	37	CCDS10962.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.641510	0.67244	9.1E-4	0.0	ENSG00000154118	ENST00000537256;ENST00000284262	T	0.49720	0.77	4.64	-4.8	0.03190	.	0.326711	0.28371	N	0.015584	T	0.51517	0.1679	L	0.50333	1.59	0.43617	D	0.995991	D	0.76494	0.999	P	0.55871	0.786	T	0.57797	-0.7749	10	0.56958	D	0.05	.	16.5936	0.84789	0.5065:0.4935:0.0:0.0	.	426	Q8WXH2	JPH3_HUMAN	W	289;426	ENSP00000284262:R426W	ENSP00000284262:R426W	R	+	1	2	JPH3	86275364	0.404000	0.25328	0.947000	0.38551	0.966000	0.64601	-0.364000	0.07583	-1.153000	0.02829	-0.181000	0.13052	CGG	C|0.999;T|0.001	0.001	strong		0.647	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
VWDE	221806	hgsc.bcm.edu	37	7	12420145	12420145	+	Silent	SNP	T	T	C	rs146236000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12420145T>C	ENST00000275358.3	-	5	944	c.756A>G	c.(754-756)gaA>gaG	p.E252E		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	252						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TGCCATCAAGTTCTAAAAGAG	0.368													T|||	39	0.00778754	0.0287	0.0014	5008	,	,		14891	0.0		0.0	False		,,,				2504	0.0				p.E252E		Atlas-SNP	.											VWDE_ENST00000275358,NS,carcinoma,-2,1	VWDE	123	1	0			c.A756G						PASS	.	T		32,1352		1,30,661	62.0	55.0	57.0		756	-0.3	1.0	7	dbSNP_134	57	1,3181		0,1,1590	no	coding-synonymous	VWDE	NM_001135924.1		1,31,2251	CC,CT,TT		0.0314,2.3121,0.7227		252/1591	12420145	33,4533	692	1591	2283	SO:0001819	synonymous_variant	221806	exon5			ATCAAGTTCTAAA		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.756A>G	7.37:g.12420145T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_001135924	B7ZM77|Q96SQ3	Silent	SNP	ENST00000275358.3	37	CCDS47544.1																																																																																			T|0.994;C|0.006	0.006	strong		0.368	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
ZNF91	7644	hgsc.bcm.edu	37	19	23556550	23556550	+	Missense_Mutation	SNP	G	G	A	rs148956643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:23556550G>A	ENST00000300619.7	-	3	452	c.247C>T	c.(247-249)Ccc>Tcc	p.P83S	ZNF91_ENST00000599743.1_Missense_Mutation_p.P83S|ZNF91_ENST00000397082.2_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	83	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)				CTACCTGTGGGTTCATCCACC	0.438													G|||	73	0.0145767	0.0514	0.0072	5008	,	,		12954	0.0		0.0	False		,,,				2504	0.0				p.P83S		Atlas-SNP	.											.	ZNF91	349	.	0			c.C247T						PASS	.	G	SER/PRO	210,4192	127.8+/-164.7	4,202,1995	75.0	78.0	77.0		247	-0.3	0.0	19	dbSNP_134	77	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF91	NM_003430.2	74	4,203,6294	AA,AG,GG		0.0116,4.7706,1.6228	benign	83/1192	23556550	211,12791	2201	4300	6501	SO:0001583	missense	7644	exon3			CTGTGGGTTCATC	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.247C>T	19.37:g.23556550G>A	ENSP00000300619:p.Pro83Ser	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	G	0.005	-2.230572	0.00280	0.047706	1.16E-4	ENSG00000167232	ENST00000300619	T	0.05855	3.38	0.158	-0.317	0.12736	Krueppel-associated box (1);	.	.	.	.	T	0.00815	0.0027	L	0.59436	1.845	0.09310	N	1	B	0.24533	0.105	B	0.17979	0.02	T	0.46582	-0.9181	8	0.17369	T	0.5	.	.	.	.	.	83	Q05481	ZNF91_HUMAN	S	83	ENSP00000300619:P83S	ENSP00000300619:P83S	P	-	1	0	ZNF91	23348390	0.002000	0.14202	0.005000	0.12908	0.006000	0.05464	-0.167000	0.09940	-1.052000	0.03222	-1.038000	0.02383	CCC	G|0.992;A|0.008	0.008	strong		0.438	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
TAF2	6873	hgsc.bcm.edu	37	8	120803654	120803654	+	Silent	SNP	C	C	T	rs11996390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120803654C>T	ENST00000378164.2	-	11	1621	c.1323G>A	c.(1321-1323)ctG>ctA	p.L441L		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	441					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			ATTCCCAGGACAGTGTATGTG	0.328													C|||	879	0.175519	0.3079	0.1427	5008	,	,		18326	0.0268		0.1968	False		,,,				2504	0.1513				p.L441L		Atlas-SNP	.											.	TAF2	204	.	0			c.G1323A						PASS	.	C		1341,3065	449.0+/-348.9	214,913,1076	108.0	102.0	104.0		1323	-9.6	0.0	8	dbSNP_120	104	1966,6632	344.2+/-325.2	203,1560,2536	no	coding-synonymous	TAF2	NM_003184.3		417,2473,3612	TT,TC,CC		22.8658,30.4358,25.4306		441/1200	120803654	3307,9697	2203	4299	6502	SO:0001819	synonymous_variant	6873	exon11			CCAGGACAGTGTA	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.1323G>A	8.37:g.120803654C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Silent	SNP	ENST00000378164.2	37	CCDS34937.1	381	0.17445054945054944	168	0.34146341463414637	51	0.1408839779005525	13	0.022727272727272728	149	0.19656992084432717	C	4.330	0.060658	0.08339	0.304358	0.228658	ENSG00000064313	ENST00000523904	.	.	.	4.79	-9.59	0.00556	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999670865	.	.	.	.	.	.	T	0.17561	-1.0365	3	.	.	.	-39.2558	13.4587	0.61214	0.2386:0.6286:0.0746:0.0582	rs11996390;rs57077905;rs11996390	.	.	.	Y	134	.	.	C	-	2	0	TAF2	120872835	0.001000	0.12720	0.002000	0.10522	0.717000	0.41224	-1.603000	0.02077	-3.771000	0.00109	-0.499000	0.04595	TGT	C|0.777;T|0.223	0.223	strong		0.328	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
PPP1R3A	5506	hgsc.bcm.edu	37	7	113519267	113519267	+	Missense_Mutation	SNP	C	C	T	rs35067467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:113519267C>T	ENST00000284601.3	-	4	1948	c.1880G>A	c.(1879-1881)aGg>aAg	p.R627K		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	627			R -> K (in dbSNP:rs35067467).		glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						ATAATCATTCCTCAAAACATT	0.393													C|||	187	0.0373403	0.1339	0.0115	5008	,	,		20272	0.0		0.002	False		,,,				2504	0.0				p.R627K		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.G1880A						PASS	.	C	LYS/ARG	455,3951	213.5+/-233.1	22,411,1770	83.0	81.0	82.0		1880	-3.9	0.0	7	dbSNP_126	82	9,8591	6.4+/-24.3	0,9,4291	yes	missense	PPP1R3A	NM_002711.3	26	22,420,6061	TT,TC,CC		0.1047,10.3268,3.5676	benign	627/1123	113519267	464,12542	2203	4300	6503	SO:0001583	missense	5506	exon4			TCATTCCTCAAAA	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9291	protein-coding gene	gene with protein product	"""glycogen-associated regulatory subunit of protein phosphatase-1"", ""protein phosphatase 1 regulatory subunit GM"""	600917	"""protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)"", ""protein phosphatase 1, regulatory (inhibitor) subunit 3A"""	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1880G>A	7.37:g.113519267C>T	ENSP00000284601:p.Arg627Lys	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	238	121	0.508403	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	68	0.031135531135531136	61	0.12398373983739837	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	0.023	-1.404787	0.01155	0.103268	0.001047	ENSG00000154415	ENST00000284601	T	0.15256	2.44	6.02	-3.93	0.04143	.	1.218990	0.05550	N	0.567306	T	0.00178	0.0005	L	0.31294	0.92	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39881	-0.9592	9	0.15499	T	0.54	-0.3547	9.053	0.36387	0.0:0.3009:0.11:0.5891	rs35067467	627	Q16821	PPR3A_HUMAN	K	627	ENSP00000284601:R627K	ENSP00000284601:R627K	R	-	2	0	PPP1R3A	113306503	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	-0.502000	0.06390	-0.652000	0.05408	-1.106000	0.02097	AGG	C|0.959;T|0.041	0.041	strong		0.393	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711	
PATZ1	23598	hgsc.bcm.edu	37	22	31737436	31737436	+	Intron	SNP	G	G	A	rs62236170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31737436G>A	ENST00000266269.5	-	2	1965				PATZ1_ENST00000405309.3_Intron|PATZ1_ENST00000351933.4_Intron|PATZ1_ENST00000215919.3_Silent_p.T523T	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1						male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)		EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						CCTCTGGGGTGGTCCAGCCCT	0.607													G|||	129	0.0257588	0.0424	0.0173	5008	,	,		15931	0.0089		0.0408	False		,,,				2504	0.0112				p.T523T		Atlas-SNP	.											.	PATZ1	24	.	0			c.C1569T						PASS	.	G	,,,	136,4270	97.1+/-135.8	3,130,2070	55.0	63.0	60.0		,,1569,	-2.7	0.2	22	dbSNP_129	60	445,8155	133.1+/-190.7	10,425,3865	no	intron,intron,coding-synonymous,intron	PATZ1	NM_014323.2,NM_032050.1,NM_032051.1,NM_032052.1	,,,	13,555,5935	AA,AG,GG		5.1744,3.0867,4.4672	,,,	,,523/538,	31737436	581,12425	2203	4300	6503	SO:0001627	intron_variant	23598	exon3			TGGGGTGGTCCAG	AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13071	protein-coding gene	gene with protein product		605165	"""zinc finger protein 278"""	ZNF278		10591208, 18241078, 18401526	Standard	NM_014323		Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.1335+1446C>T	22.37:g.31737436G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	120	45	0.375	NM_032051	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Silent	SNP	ENST00000266269.5	37	CCDS13894.1																																																																																			G|0.963;A|0.037	0.037	strong		0.607	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052	
SVIL	6840	hgsc.bcm.edu	37	10	29783908	29783908	+	Missense_Mutation	SNP	A	A	G	rs78773460		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:29783908A>G	ENST00000355867.4	-	20	4528	c.3776T>C	c.(3775-3777)aTg>aCg	p.M1259T	SVIL_ENST00000538146.1_Missense_Mutation_p.M51T|SVIL_ENST00000375398.2_Missense_Mutation_p.M1259T|SVIL_ENST00000375400.3_Missense_Mutation_p.M833T|SVIL_ENST00000535393.1_Missense_Mutation_p.M173T	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1259					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.M1259T(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)				TTCTAACTGCATATCTGGTCT	0.502																																					p.M1259T		Atlas-SNP	.											SVIL,NS,carcinoma,0,2	SVIL	226	2	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.T3776C						PASS	.						180.0	172.0	175.0					10																	29783908		2203	4300	6503	SO:0001583	missense	6840	exon20			AACTGCATATCTG	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.3776T>C	10.37:g.29783908A>G	ENSP00000348128:p.Met1259Thr	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	263	71	0.269962	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	A	17.38	3.374630	0.61735	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;T	0.27557	2.68;2.67;2.67;2.59;1.66	4.41	4.41	0.53225	.	0.084190	0.85682	D	0.000000	T	0.39937	0.1097	M	0.71581	2.175	0.47476	D	0.999433	B;P;B;P	0.44429	0.336;0.835;0.104;0.774	B;B;B;P	0.45913	0.268;0.295;0.054;0.497	T	0.33497	-0.9866	10	0.40728	T	0.16	-28.221	13.8415	0.63441	1.0:0.0:0.0:0.0	.	173;51;833;1259	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	T	833;1259;1259;173;213;51	ENSP00000364549:M833T;ENSP00000364547:M1259T;ENSP00000348128:M1259T;ENSP00000445472:M173T;ENSP00000440343:M51T	ENSP00000348128:M1259T	M	-	2	0	SVIL	29823914	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	8.642000	0.91036	1.854000	0.53819	0.254000	0.18369	ATG	A|0.500;G|0.500	0.500	strong		0.502	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
MCM5	4174	hgsc.bcm.edu	37	22	35806815	35806815	+	Silent	SNP	T	T	C	rs133417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:35806815T>C	ENST00000216122.4	+	7	985	c.831T>C	c.(829-831)acT>acC	p.T277T	MCM5_ENST00000382011.5_Silent_p.T234T	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	277					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						TTGGCCTGACTACCAGCAGGG	0.577													C|||	602	0.120208	0.2587	0.0576	5008	,	,		20903	0.0466		0.0417	False		,,,				2504	0.1339				p.T277T		Atlas-SNP	.											.	MCM5	54	.	0			c.T831C						PASS	.	C		888,3518	742.3+/-411.4	85,718,1400	144.0	121.0	129.0		831	3.2	0.5	22	dbSNP_78	129	382,8218	802.6+/-407.3	9,364,3927	no	coding-synonymous	MCM5	NM_006739.3		94,1082,5327	CC,CT,TT		4.4419,20.1543,9.7647		277/735	35806815	1270,11736	2203	4300	6503	SO:0001819	synonymous_variant	4174	exon7			CCTGACTACCAGC		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"""minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)"", ""MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"""	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.831T>C	22.37:g.35806815T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	190	92	0.484211	NM_006739	O60785|Q14578|Q9BTJ4|Q9BWL8	Silent	SNP	ENST00000216122.4	37	CCDS13915.1																																																																																			T|0.893;C|0.107	0.107	strong		0.577	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3		
PLK2	10769	hgsc.bcm.edu	37	5	57751443	57751443	+	Silent	SNP	A	A	G	rs1042994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:57751443A>G	ENST00000274289.3	-	11	1848	c.1548T>C	c.(1546-1548)ttT>ttC	p.F516F	PLK2_ENST00000502671.1_Intron	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	516	POLO box 1. {ECO:0000255|PROSITE- ProRule:PRU00154}.				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)		GCTGGTACCCAAAGCCATATT	0.443													G|||	607	0.121206	0.205	0.2061	5008	,	,		18616	0.0		0.1282	False		,,,				2504	0.0654				p.F516F		Atlas-SNP	.											.	PLK2	71	.	0			c.T1548C						PASS	.	G		836,3570	747.2+/-411.8	103,630,1470	85.0	80.0	82.0		1548	-1.1	1.0	5	dbSNP_86	82	957,7643	775.2+/-407.7	55,847,3398	no	coding-synonymous	PLK2	NM_006622.2		158,1477,4868	GG,GA,AA		11.1279,18.9741,13.7859		516/686	57751443	1793,11213	2203	4300	6503	SO:0001819	synonymous_variant	10769	exon11			GTACCCAAAGCCA		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.1548T>C	5.37:g.57751443A>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	204	93	0.455882	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	37	CCDS3974.1																																																																																			A|0.873;G|0.127	0.127	strong		0.443	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622	
FAM71B	153745	hgsc.bcm.edu	37	5	156589937	156589937	+	Missense_Mutation	SNP	G	G	A	rs115938677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156589937G>A	ENST00000302938.4	-	2	1434	c.1339C>T	c.(1339-1341)Cgc>Tgc	p.R447C		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	447						nucleus (GO:0005634)		p.R447G(1)		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)			CCTGCCTTGCGGTGATGAGAA	0.498													G|||	32	0.00638978	0.0182	0.0014	5008	,	,		20598	0.0		0.0	False		,,,				2504	0.0072				p.R447C		Atlas-SNP	.											FAM71B,NS,carcinoma,0,1	FAM71B	145	1	1	Substitution - Missense(1)	lung(1)	c.C1339T						PASS	.	G	CYS/ARG	87,4319	72.5+/-110.5	2,83,2118	171.0	162.0	165.0		1339	3.8	0.6	5	dbSNP_132	165	1,8599	1.2+/-3.3	0,1,4299	yes	missense	FAM71B	NM_130899.2	180	2,84,6417	AA,AG,GG		0.0116,1.9746,0.6766	probably-damaging	447/606	156589937	88,12918	2203	4300	6503	SO:0001583	missense	153745	exon2			CCTTGCGGTGATG		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.1339C>T	5.37:g.156589937G>A	ENSP00000305596:p.Arg447Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	64	24	0.375	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	16.74	3.208131	0.58343	0.019746	1.16E-4	ENSG00000170613	ENST00000302938	T	0.19394	2.15	4.64	3.76	0.43208	.	1.354870	0.05270	N	0.517312	T	0.21387	0.0515	M	0.65498	2.005	0.37788	D	0.927243	D	0.69078	0.997	P	0.50490	0.642	T	0.08743	-1.0707	10	0.87932	D	0	-0.0752	10.7971	0.46466	0.0:0.0:0.8103:0.1897	.	447	Q8TC56	FA71B_HUMAN	C	447	ENSP00000305596:R447C	ENSP00000305596:R447C	R	-	1	0	FAM71B	156522515	0.960000	0.32886	0.566000	0.28421	0.204000	0.24138	1.831000	0.39141	1.241000	0.43820	0.655000	0.94253	CGC	G|0.995;A|0.005	0.005	strong		0.498	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899	
TNRC18	84629	hgsc.bcm.edu	37	7	5410814	5410814	+	Silent	SNP	G	G	C	rs114987874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5410814G>C	ENST00000430969.1	-	11	3759	c.3411C>G	c.(3409-3411)ccC>ccG	p.P1137P	TNRC18_ENST00000399537.4_Silent_p.P1137P	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1137	Pro-rich.						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)		TGATCTTGGAGGGGGACAAGC	0.697													G|||	122	0.024361	0.0847	0.0101	5008	,	,		13301	0.0		0.003	False		,,,				2504	0.0				p.P1137P		Atlas-SNP	.											.	TNRC18	311	.	0			c.C3411G						PASS	.	G		322,3598		8,306,1646	15.0	17.0	16.0		3411	0.2	1.0	7	dbSNP_132	16	16,8234		0,16,4109	no	coding-synonymous	TNRC18	NM_001080495.2		8,322,5755	CC,CG,GG		0.1939,8.2143,2.7773		1137/2969	5410814	338,11832	1960	4125	6085	SO:0001819	synonymous_variant	84629	exon11			CTTGGAGGGGGAC	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.3411C>G	7.37:g.5410814G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	83	33	0.39759	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.984;C|0.016	0.016	strong		0.697	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PCDHA6	56142	hgsc.bcm.edu	37	5	140209593	140209593	+	Silent	SNP	A	A	G	rs61730636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140209593A>G	ENST00000529310.1	+	1	2031	c.1917A>G	c.(1915-1917)gaA>gaG	p.E639E	PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	639	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTGGACGAAGCGGACTCTC	0.667													.|||	317	0.0632987	0.2322	0.013	5008	,	,		16276	0.0		0.001	False		,,,				2504	0.0				p.E639E		Atlas-SNP	.											PCDHA6_ENST00000529310,NS,carcinoma,+2,6	PCDHA6	442	6	0			c.A1917G						scavenged	.	A	,,,,,,,,	857,3549	328.0+/-300.3	78,701,1424	58.0	66.0	64.0		,,,,,1917,,1917,	0.9	0.6	5	dbSNP_129	64	2,8596	2.2+/-6.3	0,2,4297	no	intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous,intron	PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_031411.1,NM_031848.1,NM_031849.1	,,,,,,,,	78,703,5721	GG,GA,AA		0.0233,19.4507,6.6057	,,,,,,,,	,,,,,639/951,,639/804,	140209593	859,12145	2203	4299	6502	SO:0001819	synonymous_variant	56142	exon1			GGACGAAGCGGAC	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.1917A>G	5.37:g.140209593A>G		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	CCDS47281.1																																																																																			A|0.940;G|0.060	0.060	strong		0.667	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
GRIN3A	116443	hgsc.bcm.edu	37	9	104335682	104335682	+	Missense_Mutation	SNP	C	C	T	rs3739722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:104335682C>T	ENST00000361820.3	-	9	3722	c.3122G>A	c.(3121-3123)cGg>cAg	p.R1041Q		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	1041			R -> Q (in dbSNP:rs3739722). {ECO:0000269|PubMed:11853319, ECO:0000269|PubMed:15489334}.		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)	CTGGTGGATCCGGATGCCCAG	0.522													C|||	933	0.186302	0.2171	0.2046	5008	,	,		20654	0.2579		0.1173	False		,,,				2504	0.1288				p.R1041Q		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G3122A						PASS	.	C	GLN/ARG	933,3473	356.9+/-313.7	104,725,1374	152.0	139.0	144.0		3122	-4.0	0.0	9	dbSNP_107	144	1126,7474	233.0+/-266.5	88,950,3262	yes	missense	GRIN3A	NM_133445.2	43	192,1675,4636	TT,TC,CC		13.093,21.1757,15.8312	benign	1041/1116	104335682	2059,10947	2203	4300	6503	SO:0001583	missense	116443	exon9			TGGATCCGGATGC		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.3122G>A	9.37:g.104335682C>T	ENSP00000355155:p.Arg1041Gln	Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	251	154	0.613546	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	421	0.19276556776556777	111	0.22560975609756098	63	0.17403314917127072	150	0.26223776223776224	97	0.1279683377308707	C	10.40	1.340250	0.24339	0.211757	0.13093	ENSG00000198785	ENST00000361820	T	0.09911	2.93	5.46	-3.96	0.04106	.	0.924765	0.09105	N	0.847883	T	0.00012	0.0000	M	0.66939	2.045	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42155	-0.9468	9	0.18710	T	0.47	.	13.8051	0.63225	0.0:0.3847:0.0:0.6153	rs3739722;rs52800836;rs59648517;rs3739722	1041	Q8TCU5	NMD3A_HUMAN	Q	1041	ENSP00000355155:R1041Q	ENSP00000355155:R1041Q	R	-	2	0	GRIN3A	103375503	0.000000	0.05858	0.000000	0.03702	0.866000	0.49608	-1.991000	0.01478	-0.711000	0.04995	-0.136000	0.14681	CGG	C|0.831;T|0.169	0.169	strong		0.522	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
CIT	11113	hgsc.bcm.edu	37	12	120139701	120139701	+	Silent	SNP	T	T	G	rs34140357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:120139701T>G	ENST00000261833.7	-	41	5293	c.5241A>C	c.(5239-5241)ggA>ggC	p.G1747G	CIT_ENST00000392521.2_Silent_p.G1789G|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1747	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		ATTTATTGGTTCCAATGAGGA	0.512													T|||	252	0.0503195	0.1823	0.0159	5008	,	,		21657	0.0		0.0	False		,,,				2504	0.0				p.G1789G		Atlas-SNP	.											.	CIT	535	.	0			c.A5367C						PASS	.	T	,	639,3767	274.0+/-271.7	50,539,1614	203.0	195.0	198.0		5367,5241	-0.1	1.0	12	dbSNP_126	198	8,8592	4.3+/-15.6	0,8,4292	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	50,547,5906	GG,GT,TT		0.093,14.503,4.9746	,	1789/2070,1747/2028	120139701	647,12359	2203	4300	6503	SO:0001819	synonymous_variant	11113	exon42			ATTGGTTCCAATG	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.5241A>C	12.37:g.120139701T>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	141	60	0.425532	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	97	0.044413919413919416	89	0.18089430894308944	8	0.022099447513812154	0	0.0	0	0.0	T	11.11	1.542516	0.27563	0.14503	9.3E-4	ENSG00000122966	ENST00000392520	.	.	.	5.68	-0.123	0.13527	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14504	-1.0470	3	.	.	.	.	7.4878	0.27443	0.0:0.2091:0.1194:0.6715	rs34140357	.	.	.	A	1360	.	.	E	-	2	0	CIT	118624084	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	1.220000	0.32491	0.060000	0.16281	0.528000	0.53228	GAA	T|0.947;G|0.053	0.053	strong		0.512	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
MISP	126353	hgsc.bcm.edu	37	19	757354	757354	+	Silent	SNP	G	G	A	rs35090443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:757354G>A	ENST00000215582.6	+	2	511	c.408G>A	c.(406-408)ctG>ctA	p.L136L		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	136					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CCAGGAGGCTGTGTGACCTGG	0.672													G|||	94	0.01877	0.0681	0.0058	5008	,	,		17272	0.0		0.0	False		,,,				2504	0.0				p.L136L		Atlas-SNP	.											.	C19orf21	56	.	0			c.G408A						PASS	.	G		230,4172	124.5+/-161.8	8,214,1979	41.0	39.0	40.0		408	-8.1	0.0	19	dbSNP_126	40	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	C19orf21	NM_173481.2		8,215,6276	AA,AG,GG		0.0116,5.2249,1.7772		136/680	757354	231,12767	2201	4298	6499	SO:0001819	synonymous_variant	126353	exon2			GAGGCTGTGTGAC	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"""mitotic interactor and substrate of Plk1"""	615289	"""chromosome 19 open reading frame 21"""	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.408G>A	19.37:g.757354G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_173481		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			G|0.982;A|0.018	0.018	strong		0.672	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481	
SYTL2	54843	hgsc.bcm.edu	37	11	85435730	85435730	+	Intron	SNP	C	C	T	rs550404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:85435730C>T	ENST00000528231.1	-	7	1737				SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000354566.3_Silent_p.P590P|SYTL2_ENST00000525423.1_Silent_p.P590P|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000359152.5_Silent_p.P1114P	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.P590P(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CAGTTATTAACGGAGCCTCGG	0.438													C|||	3013	0.601637	0.6483	0.5461	5008	,	,		18027	0.6042		0.6541	False		,,,				2504	0.5215				p.P590P		Atlas-SNP	.											.	SYTL2	231	.	1	Substitution - coding silent(1)	prostate(1)	c.G1770A						PASS	.	C	,,,,	2856,1550	664.5+/-401.4	929,998,276	66.0	64.0	65.0		,,,1770,1770	-7.0	0.0	11	dbSNP_83	65	5644,2954	665.0+/-402.2	1877,1890,532	yes	intron,intron,intron,coding-synonymous,coding-synonymous	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,,	2806,2888,808	TT,TC,CC		34.3568,35.1793,34.6355	,,,,	,,,590/1273,590/1257	85435730	8500,4504	2203	4299	6502	SO:0001627	intron_variant	54843	exon1			TATTAACGGAGCC	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+3208G>A	11.37:g.85435730C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			C|0.366;T|0.634	0.634	strong		0.438	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
UBA6	55236	hgsc.bcm.edu	37	4	68500171	68500171	+	Silent	SNP	A	A	G	rs10008910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:68500171A>G	ENST00000322244.5	-	21	1967	c.1908T>C	c.(1906-1908)caT>caC	p.H636H		NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	636					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						ACTGTATGGTATGTTCAATAG	0.333													A|||	783	0.15635	0.1581	0.1182	5008	,	,		15380	0.1052		0.165	False		,,,				2504	0.2249				p.H636H		Atlas-SNP	.											.	UBA6	98	.	0			c.T1908C						PASS	.	A		748,3656	282.8+/-276.7	73,602,1527	65.0	73.0	70.0		1908	0.7	1.0	4	dbSNP_119	70	1202,7394	238.5+/-269.9	80,1042,3176	no	coding-synonymous	UBA6	NM_018227.5		153,1644,4703	GG,GA,AA		13.9832,16.9846,15.0		636/1053	68500171	1950,11050	2202	4298	6500	SO:0001819	synonymous_variant	55236	exon21			TATGGTATGTTCA	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"""Ubiquitin-like modifier activating enzymes"""	25581	protein-coding gene	gene with protein product	"""UBA6, ubiquitin-activating enzyme E1"""	611361	"""ubiquitin-activating enzyme E1-like 2"""	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.1908T>C	4.37:g.68500171A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	37	31	0.837838	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Silent	SNP	ENST00000322244.5	37	CCDS3516.1	325	0.1488095238095238	77	0.1565040650406504	48	0.13259668508287292	72	0.1258741258741259	128	0.16886543535620052	A	8.494	0.862714	0.17178	0.169846	0.139832	ENSG00000033178	ENST00000505673	.	.	.	5.79	0.723	0.18231	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.10451	-1.0629	3	.	.	.	-16.826	9.1465	0.36937	0.7147:0.0:0.2853:0.0	rs10008910	.	.	.	T	170	.	.	I	-	2	0	UBA6	68182766	0.996000	0.38824	0.998000	0.56505	0.920000	0.55202	0.482000	0.22276	-0.075000	0.12798	0.482000	0.46254	ATA	A|0.851;G|0.149	0.149	strong		0.333	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	
DYX1C1	161582	hgsc.bcm.edu	37	15	55722882	55722882	+	Nonsense_Mutation	SNP	C	C	A	rs57809907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55722882C>A	ENST00000321149.3	-	10	1616	c.1249G>T	c.(1249-1251)Gaa>Taa	p.E417*	DYX1C1_ENST00000380679.1_Intron|DYX1C1_ENST00000457155.2_3'UTR|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000348518.3_3'UTR|DYX1C1_ENST00000448430.2_Intron	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	417					cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		GATTTTAGTTCTGTTCCTTGA	0.338													C|||	879	0.175519	0.4818	0.0706	5008	,	,		13441	0.0089		0.0865	False		,,,				2504	0.0992				p.E417X		Atlas-SNP	.											DYX1C1,NS,carcinoma,+2,1	DYX1C1	54	1	0			c.G1249T	GRCh37	CM035520	DYX1C1	M	rs57809907	PASS	.	C	,,stop/GLU	1825,2559	532.5+/-373.5	383,1059,750	107.0	107.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,1249	4.7	1.0	15	dbSNP_129	107	765,7809	181.3+/-230.0	28,709,3550	yes	utr-3,intron,stop-gained	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	,,	411,1768,4300	AA,AC,CC		8.9223,41.6286,19.9877	,,	,,417/421	55722882	2590,10368	2192	4287	6479	SO:0001587	stop_gained	161582	exon10			TTAGTTCTGTTCC		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.1249G>T	15.37:g.55722882C>A	ENSP00000323275:p.Glu417*	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	78	32	0.410256	NM_130810	Q6P5Y9|Q8N1S6	Nonsense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	344	0.1575091575091575	243	0.49390243902439024	26	0.0718232044198895	6	0.01048951048951049	69	0.09102902374670185	C	38	7.101446	0.98063	0.416286	0.089223	ENSG00000256061	ENST00000321149	.	.	.	5.6	4.68	0.58851	.	0.670270	0.13414	U	0.389654	.	.	.	.	.	.	0.09310	P	0.9999999862604	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	7.7377	0.28823	0.0:0.717:0.1348:0.1483	rs57809907	.	.	.	X	417	.	ENSP00000323275:E417X	E	-	1	0	DYX1C1	53510174	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	-0.079000	0.11357	1.350000	0.45770	0.558000	0.71614	GAA	C|0.819;A|0.181	0.181	strong		0.338	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
IL17REL	400935	hgsc.bcm.edu	37	22	50439194	50439194	+	Missense_Mutation	SNP	C	C	T	rs9617090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50439194C>T	ENST00000389983.2	-	5	472	c.208G>A	c.(208-210)Ggg>Agg	p.G70R	IL17REL_ENST00000341280.5_Missense_Mutation_p.G70R	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	70			G -> R (in dbSNP:rs9617090).	GGQ -> RGR (in Ref. 1; BAC85743). {ECO:0000305}.						endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		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;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		TGCTGCCCCCCCTGCTGCCGG	0.701													C|||	1328	0.265176	0.1384	0.2968	5008	,	,		17292	0.3343		0.4115	False		,,,				2504	0.1922				p.G70R		Atlas-SNP	.											.	IL17REL	21	.	0			c.G208A						PASS	.		ARG/GLY	810,3588		87,636,1476	15.0	18.0	17.0		208	-0.7	0.0	22	dbSNP_119	17	3580,5004		761,2058,1473	yes	missense	IL17REL	NM_001001694.2	125	848,2694,2949	TT,TC,CC		41.7055,18.4175,33.8161	benign	70/337	50439194	4390,8592	2199	4292	6491	SO:0001583	missense	400935	exon5			GCCCCCCCTGCTG	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.208G>A	22.37:g.50439194C>T	ENSP00000374633:p.Gly70Arg	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_001001694	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	37	CCDS33679.1	672	0.3076923076923077	66	0.13414634146341464	106	0.292817679558011	198	0.34615384615384615	302	0.39841688654353563	c	4.275	0.050173	0.08243	0.184175	0.417055	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.13420	2.59;2.59	3.36	-0.699	0.11277	.	1.046010	0.07618	U	0.926515	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	0.48258	-0.9051	9	0.15952	T	0.53	.	3.7209	0.08456	0.4232:0.4475:0.0:0.1293	rs9617090	70	Q6ZVW7	I17EL_HUMAN	R	70	ENSP00000374633:G70R;ENSP00000342520:G70R	ENSP00000342520:G70R	G	-	1	0	IL17REL	48781321	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.148000	0.10219	0.068000	0.16574	-0.127000	0.14921	GGG	C|0.696;T|0.304	0.304	strong		0.701	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694	
ZNF836	162962	hgsc.bcm.edu	37	19	52658510	52658510	+	Missense_Mutation	SNP	T	T	C	rs8113504	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52658510T>C	ENST00000322146.8	-	5	2947	c.2426A>G	c.(2425-2427)aAt>aGt	p.N809S	ZNF836_ENST00000597252.1_Missense_Mutation_p.N809S|CTC-471J1.8_ENST00000594362.1_RNA	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	809			N -> S (in dbSNP:rs8113504). {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(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GCCACACTCATTACACACGTA	0.393													t|||	1468	0.293131	0.4856	0.1744	5008	,	,		22147	0.4018		0.1252	False		,,,				2504	0.1779				p.N809S		Atlas-SNP	.											.	ZNF836	158	.	0			c.A2426G						PASS	.	T	SER/ASN	1885,2519	500.8+/-364.8	418,1049,735	145.0	155.0	152.0		2426	0.8	0.5	19	dbSNP_116	152	1163,7435	231.2+/-265.3	76,1011,3212	no	missense	ZNF836	NM_001102657.1	46	494,2060,3947	CC,CT,TT		13.5264,42.802,23.4425	possibly-damaging	809/937	52658510	3048,9954	2202	4299	6501	SO:0001583	missense	162962	exon5			CACTCATTACACA	BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"""Zinc fingers, C2H2-type"", ""-"""	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.2426A>G	19.37:g.52658510T>C	ENSP00000325038:p.Asn809Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001102657		Missense_Mutation	SNP	ENST00000322146.8	37	CCDS46162.1	636	0.29120879120879123	270	0.5487804878048781	56	0.15469613259668508	210	0.36713286713286714	100	0.13192612137203166	T	8.209	0.799993	0.16397	0.42802	0.135264	ENSG00000196267	ENST00000322146	T	0.16324	2.35	1.9	0.76	0.18442	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00823	-1.155	0.58432	P	8.000000000008E-6	B	0.24963	0.115	B	0.23419	0.046	T	0.35748	-0.9776	8	0.11182	T	0.66	.	2.9668	0.05910	0.4271:0.0:0.2163:0.3566	rs8113504;rs52823453;rs59799043;rs8113504	809	Q6ZNA1	ZN836_HUMAN	S	809	ENSP00000325038:N809S	ENSP00000325038:N809S	N	-	2	0	ZNF836	57350322	0.000000	0.05858	0.537000	0.28052	0.918000	0.54935	-5.565000	0.00113	-0.004000	0.14419	0.397000	0.26171	AAT	T|0.735;C|0.265	0.265	strong		0.393	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657	
CCNB2	9133	hgsc.bcm.edu	37	15	59406674	59406674	+	Missense_Mutation	SNP	T	T	C	rs16941036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:59406674T>C	ENST00000288207.2	+	4	490	c.299T>C	c.(298-300)aTg>aCg	p.M100T	CCNB2_ENST00000559622.1_Missense_Mutation_p.M19T	NM_004701.3	NP_004692.1	O95067	CCNB2_HUMAN	cyclin B2	100			M -> T (in dbSNP:rs16941036). {ECO:0000269|Ref.5}.		G2/M transition of mitotic cell cycle (GO:0000086)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				kidney(4)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9						GATGTCTCCATGAAGGAAGAG	0.473													T|||	17	0.00339457	0.0121	0.0014	5008	,	,		20124	0.0		0.0	False		,,,				2504	0.0				p.M100T		Atlas-SNP	.											.	CCNB2	23	.	0			c.T299C						PASS	.	T	THR/MET	72,4310	64.1+/-101.4	0,72,2119	92.0	85.0	87.0		299	4.2	1.0	15	dbSNP_123	87	1,8581	1.2+/-3.3	0,1,4290	yes	missense	CCNB2	NM_004701.3	81	0,73,6409	CC,CT,TT		0.0117,1.6431,0.5631	benign	100/399	59406674	73,12891	2191	4291	6482	SO:0001583	missense	9133	exon4			TCTCCATGAAGGA	AF002822	CCDS10170.1	15q21.3	2004-01-19			ENSG00000157456	ENSG00000157456			1580	protein-coding gene	gene with protein product		602755					Standard	NM_004701		Approved	HsT17299	uc002afz.3	O95067	OTTHUMG00000132715	ENST00000288207.2:c.299T>C	15.37:g.59406674T>C	ENSP00000288207:p.Met100Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_004701	B3KM93|Q6FI99	Missense_Mutation	SNP	ENST00000288207.2	37	CCDS10170.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	T	8.119	0.780523	0.16120	0.016431	1.17E-4	ENSG00000157456	ENST00000288207	T	0.13538	2.58	5.3	4.17	0.49024	.	0.590246	0.19354	N	0.116311	T	0.08133	0.0203	M	0.75777	2.31	0.43457	D	0.995659	B;B	0.19935	0.017;0.04	B;B	0.20384	0.029;0.029	T	0.03524	-1.1028	10	0.13853	T	0.58	.	10.3592	0.43982	0.0:0.0774:0.0:0.9226	rs16941036;rs52827002;rs16941036	100;100	Q53HG9;O95067	.;CCNB2_HUMAN	T	100	ENSP00000288207:M100T	ENSP00000288207:M100T	M	+	2	0	CCNB2	57193966	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.612000	0.46343	0.862000	0.35528	0.459000	0.35465	ATG	T|0.994;C|0.006	0.006	strong		0.473	CCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256016.1	NM_004701	
ARID1B	57492	hgsc.bcm.edu	37	6	157505478	157505478	+	Silent	SNP	G	G	A	rs61745451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:157505478G>A	ENST00000350026.5	+	12	3421	c.3420G>A	c.(3418-3420)gaG>gaA	p.E1140E	ARID1B_ENST00000367148.1_Silent_p.E1193E|ARID1B_ENST00000275248.4_Silent_p.E1135E|ARID1B_ENST00000346085.5_Silent_p.E1153E	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1140	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		TTGCCTTTGAGTGCAAGATCG	0.567													G|||	68	0.0135783	0.0492	0.0014	5008	,	,		18188	0.0		0.002	False		,,,				2504	0.0				p.E1153E		Atlas-SNP	.											.	ARID1B	320	.	0			c.G3459A						PASS	.	G	,	141,4265	99.8+/-138.5	1,139,2063	80.0	77.0	78.0		3420,3459	5.9	1.0	6	dbSNP_129	78	3,8589	3.0+/-9.4	0,3,4293	no	coding-synonymous,coding-synonymous	ARID1B	NM_017519.2,NM_020732.3	,	1,142,6356	AA,AG,GG		0.0349,3.2002,1.1079	,	1140/2237,1153/2250	157505478	144,12854	2203	4296	6499	SO:0001819	synonymous_variant	57492	exon13			CTTTGAGTGCAAG	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3420G>A	6.37:g.157505478G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	162	75	0.462963	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	37	CCDS5251.2																																																																																			G|0.989;A|0.011	0.011	strong		0.567	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
STH	246744	hgsc.bcm.edu	37	17	44076711	44076711	+	Silent	SNP	G	G	A	rs73317018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:44076711G>A	ENST00000537309.1	+	1	96	c.66G>A	c.(64-66)ccG>ccA	p.P22P	MAPT_ENST00000351559.5_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000415613.2_Intron|MAPT_ENST00000571987.1_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000334239.8_Intron	NM_001007532.2	NP_001007533.1	Q8IWL8	STH_HUMAN	saitohin	22						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						gcaggtggccggccctcattg	0.537													G|||	178	0.0355431	0.1271	0.0144	5008	,	,		18789	0.0		0.0	False		,,,				2504	0.0				p.P22P		Atlas-SNP	.											.	STH	14	.	0			c.G66A						PASS	.	G	,,,,,,,,	452,3442		19,414,1514	66.0	65.0	65.0		66,,,,,,,,	-2.5	0.0	17	dbSNP_132	65	1,8263		0,1,4131	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron	MAPT,STH	NM_001007532.2,NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	,,,,,,,,	19,415,5645	AA,AG,GG		0.0121,11.6076,3.7259	,,,,,,,,	22/129,,,,,,,,	44076711	453,11705	1947	4132	6079	SO:0001819	synonymous_variant	246744	exon1			GTGGCCGGCCCTC	AA325304	CCDS54136.1	17q21.1	2008-01-22				ENSG00000256762			18839	protein-coding gene	gene with protein product	"""microtubule-associated protein tau (MAPT) intronic transcript"""	607067				12032355, 16186110	Standard	NM_001007532		Approved	MAPTIT	uc002ijy.2	Q8IWL8		ENST00000537309.1:c.66G>A	17.37:g.44076711G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	180	90	0.5	NM_001007532	A1L3X7	Silent	SNP	ENST00000537309.1	37	CCDS54136.1																																																																																			A|0.027;C|0.000;G|0.972;T|0.000	0.027	strong		0.537	STH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400444.1		
VLDLR	7436	hgsc.bcm.edu	37	9	2645719	2645719	+	Silent	SNP	C	C	T	rs6143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2645719C>T	ENST00000382100.3	+	10	1814	c.1458C>T	c.(1456-1458)gcC>gcT	p.A486A	VLDLR_ENST00000382099.2_Silent_p.A486A	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	486					cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		TATTCTGGGCCGATCTAAGCC	0.428													T|||	238	0.047524	0.1566	0.0173	5008	,	,		20951	0.0119		0.006	False		,,,				2504	0.001				p.A486A		Atlas-SNP	.											.	VLDLR	68	.	0			c.C1458T						PASS	.	T	,	593,3813	771.5+/-413.8	36,521,1646	156.0	159.0	158.0		1458,1458	2.4	1.0	9	dbSNP_52	158	12,8588	818.6+/-406.8	0,12,4288	no	coding-synonymous,coding-synonymous	VLDLR	NM_001018056.1,NM_003383.3	,	36,533,5934	TT,TC,CC		0.1395,13.4589,4.6517	,	486/846,486/874	2645719	605,12401	2203	4300	6503	SO:0001819	synonymous_variant	7436	exon10			CTGGGCCGATCTA		CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"""Low density lipoprotein receptors"""	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.1458C>T	9.37:g.2645719C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	51	0.579545	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	Silent	SNP	ENST00000382100.3	37	CCDS6446.1																																																																																			C|0.945;T|0.055	0.055	strong		0.428	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383	
IRS4	8471	hgsc.bcm.edu	37	X	107978343	107978343	+	Missense_Mutation	SNP	C	C	T	rs375938401|rs41307415|rs1800993	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:107978343C>T	ENST00000372129.2	-	1	1308	c.1232G>A	c.(1231-1233)cGa>cAa	p.R411Q	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	411					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						CAGTCTTCCTCGCCTGGAGTG	0.642													C|||	171	0.045298	0.0401	0.0562	3775	,	,		13032	0.002		0.0398	False		,,,				2504	0.0378				p.R411Q		Atlas-SNP	.											.	IRS4	253	.	0			c.G1232A						PASS	.	C	GLN/ARG	10,3825		0,0,10,1632,561	49.0	42.0	45.0		1232	2.2	0.0	X	dbSNP_127	45	30,6698		2,1,25,2425,1847	yes	missense	IRS4	NM_003604.2	43	2,1,35,4057,2408	TT,TC,T,CC,C		0.4459,0.2608,0.3787	benign	411/1258	107978343	40,10523	2203	4300	6503	SO:0001583	missense	8471	exon1			CTTCCTCGCCTGG	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1232G>A	X.37:g.107978343C>T	ENSP00000361202:p.Arg411Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	115	67	0.582609	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	66	0.039783001808318265	23	0.046747967479674794	13	0.036931818181818184	0	0.0	17	0.02309782608695652	C	7.661	0.684931	0.14973	0.002608	0.004459	ENSG00000133124	ENST00000372129	T	0.36520	1.25	4.93	2.23	0.28157	.	1.025260	0.07794	N	0.955471	T	0.03959	0.0111	L	0.32530	0.975	0.80722	P	0.0	B	0.29508	0.246	B	0.12837	0.008	T	0.13629	-1.0502	9	0.42905	T	0.14	-0.9947	5.2258	0.15393	0.0:0.4248:0.2889:0.2862	rs41307415	411	O14654	IRS4_HUMAN	Q	411	ENSP00000361202:R411Q	ENSP00000361202:R411Q	R	-	2	0	IRS4	107864999	0.758000	0.28405	0.046000	0.18839	0.146000	0.21551	-0.020000	0.12525	0.157000	0.19338	-0.192000	0.12808	CGA	C|0.950;T|0.050	0.050	strong		0.642	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
CDC16	8881	hgsc.bcm.edu	37	13	115002305	115002305	+	Silent	SNP	G	G	A	rs8002514	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:115002305G>A	ENST00000356221.3	+	3	243	c.135G>A	c.(133-135)caG>caA	p.Q45Q	CDC16_ENST00000375308.1_5'UTR|CDC16_ENST00000252457.5_Silent_p.Q44Q|CDC16_ENST00000375312.3_5'UTR|CDC16_ENST00000252458.6_5'UTR|CDC16_ENST00000375310.1_5'UTR|CDC16_ENST00000360383.3_Silent_p.Q45Q			Q13042	CDC16_HUMAN	cell division cycle 16	45					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)			GGTTGGCTCAGTGTCTTTACC	0.413													A|||	1711	0.341653	0.5825	0.2767	5008	,	,		14511	0.1587		0.2584	False		,,,				2504	0.3364				p.Q45Q		Atlas-SNP	.											.	CDC16	50	.	0			c.G135A						PASS	.	A	,	2277,2129	579.4+/-384.9	577,1123,503	118.0	116.0	117.0		135,135	2.4	1.0	13	dbSNP_116	117	1991,6609	722.8+/-406.4	230,1531,2539	no	coding-synonymous,coding-synonymous	CDC16	NM_001078645.1,NM_003903.3	,	807,2654,3042	AA,AG,GG		23.1512,48.3205,32.8156	,	45/621,45/621	115002305	4268,8738	2203	4300	6503	SO:0001819	synonymous_variant	8881	exon3			GGCTCAGTGTCTT	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.135G>A	13.37:g.115002305G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																			G|0.678;A|0.322	0.322	strong		0.413	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	
WSB2	55884	hgsc.bcm.edu	37	12	118474238	118474238	+	Silent	SNP	G	G	A	rs34253698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:118474238G>A	ENST00000315436.3	-	6	879	c.738C>T	c.(736-738)gaC>gaT	p.D246D	WSB2_ENST00000544233.1_Silent_p.D36D|WSB2_ENST00000441406.2_Silent_p.D263D|WSB2_ENST00000536738.1_5'UTR|WSB2_ENST00000542304.1_Silent_p.D21D|WSB2_ENST00000535496.1_Silent_p.D248D	NM_001278557.1|NM_018639.3	NP_001265486.1|NP_061109.1	Q9NYS7	WSB2_HUMAN	WD repeat and SOCS box containing 2	246					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGGGGGAGAAGTCACAAGAGA	0.512													G|||	77	0.0153754	0.056	0.0043	5008	,	,		19879	0.0		0.0	False		,,,				2504	0.0				p.D246D		Atlas-SNP	.											.	WSB2	32	.	0			c.C738T						PASS	.	G		183,4223	117.1+/-155.0	4,175,2024	176.0	156.0	163.0		738	3.8	1.0	12	dbSNP_126	163	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	WSB2	NM_018639.3		4,178,6321	AA,AG,GG		0.0349,4.1534,1.4301		246/405	118474238	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	55884	exon6			GGAGAAGTCACAA	AF038187	CCDS9186.1, CCDS61251.1, CCDS61252.1	12q24.23	2013-01-09	2011-01-25		ENSG00000176871	ENSG00000176871		"""WD repeat domain containing"""	19222	protein-coding gene	gene with protein product			"""WD repeat and SOCS box-containing 2"""			12076535	Standard	NM_018639		Approved	SBA2, MGC10210	uc001twr.2	Q9NYS7	OTTHUMG00000168885	ENST00000315436.3:c.738C>T	12.37:g.118474238G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_018639	B4DIE6|B4DPV6|Q9NRX9	Silent	SNP	ENST00000315436.3	37	CCDS9186.1																																																																																			G|0.985;A|0.015	0.015	strong		0.512	WSB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401515.1	NM_018639	
CHTF18	63922	hgsc.bcm.edu	37	16	846012	846012	+	Silent	SNP	C	C	T	rs114461038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:846012C>T	ENST00000262315.9	+	18	2454	c.2391C>T	c.(2389-2391)ctC>ctT	p.L797L	CHTF18_ENST00000317063.6_Silent_p.L1006L|CHTF18_ENST00000455171.2_Silent_p.L825L	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	797					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)				GCACGATGCTCGCTTACAGCC	0.642													c|||	89	0.0177716	0.0643	0.0058	5008	,	,		14732	0.0		0.0	False		,,,				2504	0.0				p.L797L		Atlas-SNP	.											.	CHTF18	52	.	0			c.C2391T						PASS	.			175,4107		8,159,1974	29.0	36.0	34.0		2391	-8.6	0.6	16	dbSNP_132	34	3,8505		0,3,4251	no	coding-synonymous	CHTF18	NM_022092.2		8,162,6225	TT,TC,CC		0.0353,4.0869,1.3917		797/976	846012	178,12612	2141	4254	6395	SO:0001819	synonymous_variant	63922	exon18			GATGCTCGCTTAC	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.2391C>T	16.37:g.846012C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	37	CCDS45371.1																																																																																			C|0.979;T|0.021	0.021	strong		0.642	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
HYPM	25763	hgsc.bcm.edu	37	X	37850385	37850385	+	Missense_Mutation	SNP	C	C	T	rs61737321		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37850385C>T	ENST00000341016.3	+	1	316	c.293C>T	c.(292-294)gCt>gTt	p.A98V	TM4SF2_ENST00000465127.1_Intron	NM_012274.1	NP_036406.1	O75409	HYPM_HUMAN		98										central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(2)	8						CCCCACAGCGCTGAGAGTGAT	0.527													C|||	50	0.013245	0.0356	0.0043	3775	,	,		15106	0.0		0.0	False		,,,				2504	0.0				p.A98V		Atlas-SNP	.											.	CXorf27	14	.	0			c.C293T						PASS	.	C	VAL/ALA	116,3567		3,85,25,1468,546	99.0	104.0	102.0		293	-6.5	0.0	X	dbSNP_129	102	0,6600		0,0,0,2392,1816	yes	missense	CXorf27	NM_012274.1	64	3,85,25,3860,2362	TT,TC,T,CC,C		0.0,3.1496,1.1281	benign	98/118	37850385	116,10167	2127	4208	6335	SO:0001583	missense	25763	exon1			ACAGCGCTGAGAG																												ENST00000341016.3:c.293C>T	X.37:g.37850385C>T	ENSP00000339511:p.Ala98Val	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	209	105	0.502392	NM_012274	A1A4D3	Missense_Mutation	SNP	ENST00000341016.3	37	CCDS43929.1	10	0.006027727546714889	5	0.010245901639344262	2	0.005555555555555556	0	0.0	0	0.0	C	4.372	0.068603	0.08436	0.031496	0.0	ENSG00000187516	ENST00000341016	T	0.39787	1.06	3.24	-6.47	0.01902	Histone-fold (1);	.	.	.	.	T	0.04952	0.0133	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.13202	-1.0518	9	0.25751	T	0.34	.	1.5554	0.02583	0.1509:0.3307:0.3038:0.2146	rs61737321	98	O75409	HYPM_HUMAN	V	98	ENSP00000339511:A98V	ENSP00000339511:A98V	A	+	2	0	CXorf27	37735329	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.422000	0.02453	-1.678000	0.01454	-0.505000	0.04504	GCT	C|0.994;T|0.006	0.006	strong		0.527	CXorf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080888.1		
WDR18	57418	hgsc.bcm.edu	37	19	991968	991968	+	Silent	SNP	T	T	C	rs1127043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:991968T>C	ENST00000251289.5	+	8	968	c.945T>C	c.(943-945)aaT>aaC	p.N315N	WDR18_ENST00000587001.2_Silent_p.N315N	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	315					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)		CAGTCACCAATGCCGCCATCC	0.706													N|||	1975	0.394369	0.4758	0.2738	5008	,	,		7631	0.4107		0.2962	False		,,,				2504	0.454				p.N315N		Atlas-SNP	.											.	WDR18	20	.	0			c.T945C						PASS	.	C		1912,2278		470,972,653	8.0	9.0	9.0		945	-0.6	0.9	19	dbSNP_86	9	2388,5854		417,1554,2150	no	coding-synonymous	WDR18	NM_024100.3		887,2526,2803	CC,CT,TT		28.9736,45.6325,34.5882		315/433	991968	4300,8132	2095	4121	6216	SO:0001819	synonymous_variant	57418	exon8			CACCAATGCCGCC		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.945T>C	19.37:g.991968T>C		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	23	6	0.26087	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	37	CCDS12051.1																																																																																			T|0.651;C|0.349	0.349	strong		0.706	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
AHNAK2	113146	hgsc.bcm.edu	37	14	105414629	105414629	+	Missense_Mutation	SNP	G	G	A	rs72702027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105414629G>A	ENST00000333244.5	-	7	7278	c.7159C>T	c.(7159-7161)Cca>Tca	p.P2387S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2387						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)		p.K2385fs*18(1)		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)			GGGCCCTCTGGGAGTTTCACA	0.637													.|||	2664	0.531949	0.5673	0.5101	5008	,	,		16631	0.4048		0.5328	False		,,,				2504	0.6299				p.P2387S		Atlas-SNP	.											.	AHNAK2	719	.	1	Deletion - Frameshift(1)	ovary(1)	c.C7159T						PASS	.	G	SER/PRO	2290,1486		726,838,324	104.0	117.0	113.0		7159	0.8	0.0	14	dbSNP_131	113	4464,3752		1227,2010,871	no	missense	AHNAK2	NM_138420.2	74	1953,2848,1195	AA,AG,GG		45.667,39.3538,43.6791	possibly-damaging	2387/5796	105414629	6754,5238	1888	4108	5996	SO:0001583	missense	113146	exon7			CCTCTGGGAGTTT	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.7159C>T	14.37:g.105414629G>A	ENSP00000353114:p.Pro2387Ser	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	229	229	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1113	0.5096153846153846	297	0.6036585365853658	201	0.5552486187845304	217	0.3793706293706294	398	0.525065963060686	-	15.77	2.932190	0.52866	0.606462	0.54333	ENSG00000185567	ENST00000333244	T	0.03242	4.0	4.0	0.756	0.18421	.	.	.	.	.	T	0.00012	0.0000	M	0.90870	3.155	0.80722	P	0.0	P	0.44344	0.833	P	0.52758	0.708	T	0.27938	-1.0059	8	0.45353	T	0.12	.	16.3569	0.83237	0.0:0.575:0.425:0.0	.	2387	Q8IVF2	AHNK2_HUMAN	S	2387	ENSP00000353114:P2387S	ENSP00000353114:P2387S	P	-	1	0	AHNAK2	104485674	0.002000	0.14202	0.001000	0.08648	0.010000	0.07245	0.145000	0.16157	0.151000	0.19162	0.485000	0.47835	CCA	G|0.479;A|0.521	0.521	strong		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CHMP6	79643	hgsc.bcm.edu	37	17	78972902	78972902	+	Silent	SNP	C	C	T	rs35687235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78972902C>T	ENST00000325167.5	+	8	633	c.555C>T	c.(553-555)aaC>aaT	p.N185N	CTD-2561B21.7_ENST00000576215.1_RNA|CTD-2561B21.7_ENST00000577061.2_RNA	NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	185					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein N-terminus binding (GO:0047485)			lung(2)|ovary(1)	3	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0175)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CCACAGAAAACGTCCCTGTCA	0.622													C|||	144	0.028754	0.1059	0.0043	5008	,	,		19893	0.0		0.001	False		,,,				2504	0.0				p.N185N		Atlas-SNP	.											.	CHMP6	16	.	0			c.C555T						PASS	.	C		370,4036	187.1+/-213.8	18,334,1851	129.0	108.0	115.0		555	1.3	0.1	17	dbSNP_126	115	0,8600		0,0,4300	no	coding-synonymous	CHMP6	NM_024591.4		18,334,6151	TT,TC,CC		0.0,8.3976,2.8448		185/202	78972902	370,12636	2203	4300	6503	SO:0001819	synonymous_variant	79643	exon8			AGAAAACGTCCCT	BC010108	CCDS11774.1	17q25.3	2014-08-13	2011-09-21		ENSG00000176108	ENSG00000176108		"""Charged multivesicular body proteins"""	25675	protein-coding gene	gene with protein product		610901	"""chromatin modifying protein 6"""			11559748, 15511219	Standard	NM_024591		Approved	FLJ11749, VPS20	uc002jyw.4	Q96FZ7	OTTHUMG00000177645	ENST00000325167.5:c.555C>T	17.37:g.78972902C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	89	52	0.58427	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Silent	SNP	ENST00000325167.5	37	CCDS11774.1																																																																																			C|0.968;T|0.032	0.032	strong		0.622	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591	
TBC1D4	9882	hgsc.bcm.edu	37	13	75861001	75861001	+	Missense_Mutation	SNP	A	A	G	rs557337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:75861001A>G	ENST00000377636.3	-	21	4170	c.3824T>C	c.(3823-3825)gTc>gCc	p.V1275A	TBC1D4_ENST00000431480.2_Missense_Mutation_p.V1267A|TBC1D4_ENST00000425511.1_Missense_Mutation_p.V439A|TBC1D4_ENST00000377625.2_Missense_Mutation_p.V1212A	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1275			V -> A (in dbSNP:rs557337). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19077034, ECO:0000269|PubMed:9628581}.		cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GTCACAATTGACTAGAGCATC	0.463													G|||	873	0.174321	0.556	0.0778	5008	,	,		16760	0.0		0.0666	False		,,,				2504	0.0174				p.V1275A		Atlas-SNP	.											.	TBC1D4	142	.	0			c.T3824C						PASS	.	G	ALA/VAL	1770,2058		428,914,572	104.0	107.0	106.0		3824	3.9	0.0	13	dbSNP_83	106	484,7778		13,458,3660	yes	missense	TBC1D4	NM_014832.2	64	441,1372,4232	GG,GA,AA		5.8581,46.2382,18.6435	benign	1275/1299	75861001	2254,9836	1914	4131	6045	SO:0001583	missense	9882	exon21			CAATTGACTAGAG	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.3824T>C	13.37:g.75861001A>G	ENSP00000366863:p.Val1275Ala	Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	333	166	0.498498	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	333	0.15247252747252749	256	0.5203252032520326	32	0.08839779005524862	0	0.0	45	0.059366754617414245	G	0.218	-1.030972	0.02029	0.462382	0.058581	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.03358	4.23;4.23;4.23;3.96	5.63	3.87	0.44632	.	0.297360	0.28841	N	0.013979	T	0.00012	0.0000	N	0.02011	-0.69	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;0.001;0.0;0.0	T	0.38329	-0.9666	9	0.02654	T	1	-5.6523	10.4567	0.44555	0.2148:0.0:0.7852:0.0	rs557337;rs52811417;rs60191388;rs557337	439;1212;1267;1275	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	A	1275;1267;1212;439	ENSP00000366863:V1275A;ENSP00000395986:V1267A;ENSP00000366852:V1212A;ENSP00000390654:V439A	ENSP00000366852:V1212A	V	-	2	0	TBC1D4	74759002	1.000000	0.71417	0.008000	0.14137	0.004000	0.04260	4.134000	0.57990	0.847000	0.35167	-0.119000	0.15052	GTC	A|0.827;G|0.173	0.173	strong		0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
DENND1C	79958	hgsc.bcm.edu	37	19	6480013	6480013	+	Missense_Mutation	SNP	C	C	T	rs10416003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6480013C>T	ENST00000381480.2	-	2	179	c.67G>A	c.(67-69)Gcc>Acc	p.A23T	DENND1C_ENST00000591030.1_Intron|DENND1C_ENST00000543576.1_Intron	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	23	UDENN.		A -> T (in dbSNP:rs10416003).		positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						TGCAGGGAGGCAGGGCAGGCC	0.607													c|||	50	0.00998403	0.0363	0.0014	5008	,	,		16807	0.0		0.001	False		,,,				2504	0.0				p.A23T		Atlas-SNP	.											.	DENND1C	93	.	0			c.G67A						PASS	.	C	THR/ALA	144,3742		2,140,1801	34.0	39.0	37.0		67	-1.7	0.1	19	dbSNP_119	37	1,8255		0,1,4127	yes	missense	DENND1C	NM_024898.2	58	2,141,5928	TT,TC,CC		0.0121,3.7056,1.1942	benign	23/802	6480013	145,11997	1943	4128	6071	SO:0001583	missense	79958	exon2			GGGAGGCAGGGCA	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.67G>A	19.37:g.6480013C>T	ENSP00000370889:p.Ala23Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	145	77	0.531034	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	18	0.008241758241758242	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	c	9.626	1.135185	0.21123	0.037056	1.21E-4	ENSG00000205744	ENST00000381480	T	0.08193	3.12	4.95	-1.69	0.08186	uDENN (3);	0.538503	0.18725	N	0.132907	T	0.00695	0.0023	N	0.08118	0	0.09310	N	0.999995	B	0.16396	0.017	B	0.13407	0.009	T	0.44360	-0.9333	10	0.18710	T	0.47	-2.0715	5.3304	0.15930	0.0:0.4706:0.1479:0.3814	rs10416003;rs10416003	23	Q8IV53	DEN1C_HUMAN	T	23	ENSP00000370889:A23T	ENSP00000370889:A23T	A	-	1	0	DENND1C	6431013	0.003000	0.15002	0.132000	0.22025	0.862000	0.49288	-0.763000	0.04740	-0.080000	0.12685	0.558000	0.71614	GCC	C|0.991;T|0.009	0.009	strong		0.607	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
NPY	4852	hgsc.bcm.edu	37	7	24329133	24329133	+	Silent	SNP	C	C	T	rs5574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:24329133C>T	ENST00000407573.1	+	4	494	c.204C>T	c.(202-204)tcC>tcT	p.S68S	NPY_ENST00000242152.2_Silent_p.S68S|NPY_ENST00000405982.1_Silent_p.S68S			P01303	NPY_HUMAN	neuropeptide Y	68					adult feeding behavior (GO:0008343)|behavior (GO:0007610)|blood circulation (GO:0008015)|calcium ion transport (GO:0006816)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of appetite (GO:0032100)|regulation of blood pressure (GO:0008217)|synaptic transmission (GO:0007268)	cell (GO:0005623)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			breast(1)|kidney(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	9						GAAAACGATCCAGCCCAGAGA	0.398													T|||	1874	0.374201	0.3343	0.4308	5008	,	,		16610	0.3452		0.4702	False		,,,				2504	0.319				p.S68S		Atlas-SNP	.											.	NPY	25	.	0			c.C204T						PASS	.	T		1569,2837	668.4+/-402.0	290,989,924	109.0	104.0	106.0		204	-1.0	1.0	7	dbSNP_52	106	4029,4571	596.9+/-393.7	934,2161,1205	no	coding-synonymous	NPY	NM_000905.3		1224,3150,2129	TT,TC,CC		46.8488,35.6105,43.0417		68/98	24329133	5598,7408	2203	4300	6503	SO:0001819	synonymous_variant	4852	exon3			ACGATCCAGCCCA	K01911	CCDS5387.1	7p15.3	2013-02-26			ENSG00000122585	ENSG00000122585		"""Endogenous ligands"""	7955	protein-coding gene	gene with protein product	"""prepro-neuropeptide Y"""	162640					Standard	NM_000905		Approved	PYY4	uc003sww.2	P01303	OTTHUMG00000022973	ENST00000407573.1:c.204C>T	7.37:g.24329133C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_000905		Silent	SNP	ENST00000407573.1	37	CCDS5387.1																																																																																			C|0.579;A|0.002	.	strong		0.398	NPY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326748.1	NM_000905	
EAF1	85403	hgsc.bcm.edu	37	3	15476011	15476011	+	Silent	SNP	C	C	G	rs1563415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:15476011C>G	ENST00000396842.2	+	4	917	c.492C>G	c.(490-492)ccC>ccG	p.P164P	EAF1_ENST00000432764.2_Silent_p.P63P|EAF1-AS1_ENST00000597949.1_RNA|RNU6-1024P_ENST00000384199.1_RNA	NM_033083.6	NP_149074.3	Q96JC9	EAF1_HUMAN	ELL associated factor 1	164	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ELL-EAF complex (GO:0032783)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	7						AAGATAACCCCTCACCTGAAC	0.478													C|||	1040	0.207668	0.0144	0.2363	5008	,	,		19515	0.2917		0.2485	False		,,,				2504	0.32				p.P164P		Atlas-SNP	.											.	EAF1	16	.	0			c.C492G						PASS	.	C		245,4161	142.7+/-177.9	6,233,1964	231.0	218.0	222.0		492	0.2	1.0	3	dbSNP_88	222	2268,6332	384.1+/-341.0	278,1712,2310	no	coding-synonymous	EAF1	NM_033083.6		284,1945,4274	GG,GC,CC		26.3721,5.5606,19.3219		164/269	15476011	2513,10493	2203	4300	6503	SO:0001819	synonymous_variant	85403	exon4			TAACCCCTCACCT	AF272973	CCDS2626.1	3p25.1	2011-06-10			ENSG00000144597	ENSG00000144597			20907	protein-coding gene	gene with protein product		608315				11418481	Standard	NM_033083		Approved		uc003bzu.3	Q96JC9	OTTHUMG00000162544	ENST00000396842.2:c.492C>G	3.37:g.15476011C>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_033083	B4E3F5|Q8IW10	Silent	SNP	ENST00000396842.2	37	CCDS2626.1																																																																																			C|0.796;G|0.204	0.204	strong		0.478	EAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252100.4	NM_033083	
ZNF99	7652	hgsc.bcm.edu	37	19	22940659	22940659	+	Silent	SNP	C	C	T	rs59621958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22940659C>T	ENST00000596209.1	-	4	2142	c.2052G>A	c.(2050-2052)aaG>aaA	p.K684K	ZNF99_ENST00000397104.3_Silent_p.K593K|CTC-451A6.4_ENST00000442497.2_lincRNA	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	684					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GGTTAAAAGCCTTGCCACATT	0.378													T|||	1087	0.217053	0.4213	0.1326	5008	,	,		20012	0.1726		0.1362	False		,,,				2504	0.1299				p.K684K		Atlas-SNP	.											.	ZNF99	273	.	0			c.G2052A						PASS	.	T		1486,2718		256,974,872	46.0	49.0	48.0		1779	0.2	0.0	19	dbSNP_129	48	980,7520		67,846,3337	no	coding-synonymous	ZNF99	NM_001080409.2		323,1820,4209	TT,TC,CC		11.5294,35.3473,19.4112		593/912	22940659	2466,10238	2102	4250	6352	SO:0001819	synonymous_variant	7652	exon4			AAAAGCCTTGCCA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2052G>A	19.37:g.22940659C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_001080409	M0R335	Silent	SNP	ENST00000596209.1	37	CCDS59369.1																																																																																			C|0.826;T|0.174	0.174	strong		0.378	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
GPATCH1	55094	hgsc.bcm.edu	37	19	33600764	33600764	+	Missense_Mutation	SNP	T	T	C	rs2287679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33600764T>C	ENST00000170564.2	+	11	1741	c.1427T>C	c.(1426-1428)cTc>cCc	p.L476P		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	476			L -> P (in dbSNP:rs2287679). {ECO:0000269|PubMed:17974005}.		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)					AGAGCCCAGCTCTCCCCTGCA	0.552													C|||	2672	0.533546	0.8003	0.2867	5008	,	,		16368	0.5079		0.2416	False		,,,				2504	0.6748				p.L476P	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.T1427C						PASS	.	C	PRO/LEU	3203,1203	401.0+/-331.8	1159,885,159	39.0	40.0	40.0		1427	5.7	0.1	19	dbSNP_100	40	2297,6303	678.3+/-403.4	281,1735,2284	yes	missense	GPATCH1	NM_018025.2	98	1440,2620,2443	CC,CT,TT		26.7093,27.3037,42.2882	benign	476/932	33600764	5500,7506	2203	4300	6503	SO:0001583	missense	55094	exon11			CCCAGCTCTCCCC	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.1427T>C	19.37:g.33600764T>C	ENSP00000170564:p.Leu476Pro	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Missense_Mutation	SNP	ENST00000170564.2	37	CCDS12428.1	970	0.4441391941391941	386	0.7845528455284553	107	0.2955801104972376	285	0.4982517482517482	192	0.2532981530343008	C	2.963	-0.214135	0.06101	0.726963	0.267093	ENSG00000076650	ENST00000170564	T	0.30182	1.54	5.74	5.74	0.90152	.	0.773566	0.12715	N	0.445174	T	0.00012	0.0000	N	0.01081	-1.03	0.41672	P	0.010757000000000017	B	0.02656	0.0	B	0.04013	0.001	T	0.30679	-0.9970	9	0.30078	T	0.28	-0.2351	9.4371	0.38646	0.0:0.7817:0.0:0.2183	rs2287679;rs57097144;rs2287679	476	Q9BRR8	GPTC1_HUMAN	P	476	ENSP00000170564:L476P	ENSP00000170564:L476P	L	+	2	0	GPATCH1	38292604	0.001000	0.12720	0.127000	0.21898	0.004000	0.04260	1.138000	0.31491	1.454000	0.47793	-0.119000	0.15052	CTC	T|0.541;C|0.459	0.459	strong		0.552	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
SEC62	7095	hgsc.bcm.edu	37	3	169700525	169700525	+	Silent	SNP	C	C	G	rs35176867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:169700525C>G	ENST00000337002.4	+	4	340	c.282C>G	c.(280-282)gcC>gcG	p.A94A	SEC62_ENST00000480708.1_Silent_p.A94A|SEC62-AS1_ENST00000479626.1_RNA	NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	94					cotranslational protein targeting to membrane (GO:0006613)|posttranslational protein targeting to membrane (GO:0006620)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	9						TTCACCGAGCCCTAAAAGTAA	0.323													C|||	102	0.0203674	0.0749	0.0043	5008	,	,		16024	0.0		0.0	False		,,,				2504	0.0				p.A94A		Atlas-SNP	.											.	SEC62	27	.	0			c.C282G						PASS	.	C		246,4122	129.0+/-165.8	11,224,1949	63.0	75.0	71.0		282	-2.3	0.9	3	dbSNP_126	71	0,8592		0,0,4296	no	coding-synonymous	SEC62	NM_003262.3		11,224,6245	GG,GC,CC		0.0,5.6319,1.8981		94/400	169700525	246,12714	2184	4296	6480	SO:0001819	synonymous_variant	7095	exon4			CCGAGCCCTAAAA	D87127	CCDS3210.1	3q26.2	2008-04-22	2008-04-22	2008-04-22	ENSG00000008952	ENSG00000008952			11846	protein-coding gene	gene with protein product		602173	"""translocation protein 1"""	TLOC1		9020021, 10799540	Standard	NM_003262		Approved	Dtrp1, HTP1	uc003fgh.3	Q99442	OTTHUMG00000158753	ENST00000337002.4:c.282C>G	3.37:g.169700525C>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	195	98	0.502564	NM_003262	D3DNQ0|O00682|O00729	Silent	SNP	ENST00000337002.4	37	CCDS3210.1																																																																																			C|0.983;G|0.017	0.017	strong		0.323	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352043.1		
PRKCG	5582	hgsc.bcm.edu	37	19	54410114	54410114	+	Missense_Mutation	SNP	A	A	G	rs73937614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54410114A>G	ENST00000263431.3	+	18	2341	c.2059A>G	c.(2059-2061)Agc>Ggc	p.S687G	CACNG7_ENST00000391767.1_5'Flank|PRKCG_ENST00000542049.1_Missense_Mutation_p.S538G|PRKCG_ENST00000540413.1_Missense_Mutation_p.S687G	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	687					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)			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)	GGATGCCCGCAGCCCCACCAG	0.677											OREG0025667	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	58	0.0115815	0.0408	0.0058	5008	,	,		12287	0.0		0.0	False		,,,				2504	0.0				p.S687G		Atlas-SNP	.											.	PRKCG	246	.	0			c.A2059G						PASS	.	A	GLY/SER	118,4288	81.9+/-120.4	1,116,2086	38.0	48.0	45.0		2059	2.1	1.0	19	dbSNP_130	45	1,8597		0,1,4298	yes	missense	PRKCG	NM_002739.3	56	1,117,6384	GG,GA,AA		0.0116,2.6782,0.9151	possibly-damaging	687/698	54410114	119,12885	2203	4299	6502	SO:0001583	missense	5582	exon18			GCCCGCAGCCCCA	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.2059A>G	19.37:g.54410114A>G	ENSP00000263431:p.Ser687Gly	Somatic	180	0	0	1000	WXS	Illumina HiSeq	Phase_I	208	89	0.427885	NM_002739	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	A	16.20	3.056968	0.55325	0.026782	1.16E-4	ENSG00000126583	ENST00000540413;ENST00000263431;ENST00000542049	T;T;T	0.70631	-0.5;-0.5;-0.5	4.23	2.1	0.27182	.	.	.	.	.	T	0.33527	0.0866	L	0.43152	1.355	0.24531	N	0.994117	B;B;B	0.26876	0.118;0.041;0.162	B;B;B	0.24394	0.017;0.004;0.053	T	0.45041	-0.9288	9	0.59425	D	0.04	.	4.5914	0.12307	0.7265:0.0:0.0996:0.1739	.	538;687;687	B7Z8Q0;F5H5C4;P05129	.;.;KPCG_HUMAN	G	687;687;538	ENSP00000443493:S687G;ENSP00000263431:S687G;ENSP00000438090:S538G	ENSP00000263431:S687G	S	+	1	0	PRKCG	59101926	0.991000	0.36638	1.000000	0.80357	0.980000	0.70556	1.765000	0.38481	0.752000	0.32923	-0.496000	0.04628	AGC	A|0.993;G|0.007	0.007	strong		0.677	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739	
MUC4	4585	hgsc.bcm.edu	37	3	195505863	195505863	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195505863G>A	ENST00000463781.3	-	2	13047	c.12588C>T	c.(12586-12588)acC>acT	p.T4196T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T4196T	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.T4196T(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)		AGGAAGTGTCGGTGACAGGAA	0.607																																					p.T4196T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	prostate(1)	c.C12588T						scavenged	.						19.0	14.0	16.0					3																	195505863		689	1578	2267	SO:0001819	synonymous_variant	4585	exon2			AGTGTCGGTGACA	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.12588C>T	3.37:g.195505863G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	297	15	0.050505	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		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TTN	7273	hgsc.bcm.edu	37	2	179428061	179428061	+	Missense_Mutation	SNP	C	C	T	rs11896637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179428061C>T	ENST00000591111.1	-	276	78099	c.77875G>A	c.(77875-77877)Gca>Aca	p.A25959T	TTN_ENST00000589042.1_Missense_Mutation_p.A27600T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A18535T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A25032T|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A18660T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A18727T|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25959	Fibronectin type-III 89. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTAACAGGTGCGCCACCATCA	0.493													C|||	178	0.0355431	0.1256	0.0159	5008	,	,		21438	0.0		0.001	False		,,,				2504	0.0				p.A27600T		Atlas-SNP	.											.	TTN	18412	.	0			c.G82798A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	398,3684		21,356,1664	72.0	71.0	71.0		56179,55978,75094,55603	3.9	0.3	2	dbSNP_120	71	8,8402		0,8,4197	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	58,58,58,58	21,364,5861	TT,TC,CC		0.0951,9.7501,3.2501	benign,benign,benign,benign	18727/27119,18660/27052,25032/33424,18535/26927	179428061	406,12086	2041	4205	6246	SO:0001583	missense	7273	exon326			CAGGTGCGCCACC	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.77875G>A	2.37:g.179428061C>T	ENSP00000465570:p.Ala25959Thr	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	238	115	0.483193	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		85	0.03891941391941392	77	0.1565040650406504	8	0.022099447513812154	0	0.0	0	0.0	C	18.20	3.570710	0.65765	0.097501	9.51E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.74	3.93	0.45458	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00241	0.0007	L	0.47190	1.495	0.19300	P	0.9999757677	B;B;B;B	0.22414	0.069;0.069;0.069;0.02	B;B;B;B	0.17433	0.018;0.018;0.018;0.018	T	0.06481	-1.0824	8	0.87932	D	0	.	12.9829	0.58575	0.0:0.8666:0.0:0.1334	rs11896637;rs52798942;rs11896637	18535;18660;18727;25959	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	25032;18535;18727;18660;18533	ENSP00000343764:A25032T;ENSP00000434586:A18535T;ENSP00000340554:A18727T;ENSP00000352154:A18660T	ENSP00000340554:A18727T	A	-	1	0	TTN	179136307	0.999000	0.42202	0.344000	0.25628	0.992000	0.81027	4.111000	0.57838	0.755000	0.32990	0.563000	0.77884	GCA	C|0.965;T|0.035	0.035	strong		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KIF26B	55083	hgsc.bcm.edu	37	1	245530282	245530282	+	Silent	SNP	G	G	A	rs61734839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:245530282G>A	ENST00000407071.2	+	3	1052	c.612G>A	c.(610-612)acG>acA	p.T204T	KIF26B_ENST00000479506.1_3'UTR	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	204					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)			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)			TGGTGCTGACGTTGGAGCAGG	0.647													G|||	335	0.066893	0.1914	0.0317	5008	,	,		18212	0.0		0.0179	False		,,,				2504	0.0429				p.T204T		Atlas-SNP	.											.	KIF26B	343	.	0			c.G612A						PASS	.	G		673,3695		52,569,1563	37.0	41.0	40.0		612	0.2	0.9	1	dbSNP_129	40	157,8367		2,153,4107	yes	coding-synonymous	KIF26B	NM_018012.3		54,722,5670	AA,AG,GG		1.8419,15.4075,6.4381		204/2109	245530282	830,12062	2184	4262	6446	SO:0001819	synonymous_variant	55083	exon3			GCTGACGTTGGAG	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.612G>A	1.37:g.245530282G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	114	62	0.54386	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																			G|0.953;A|0.047	0.047	strong		0.647	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
EGR4	1961	hgsc.bcm.edu	37	2	73518716	73518716	+	Missense_Mutation	SNP	C	C	T	rs141733943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73518716C>T	ENST00000545030.1	-	2	1713	c.1639G>A	c.(1639-1641)Ggc>Agc	p.G547S	EGR4_ENST00000436467.2_Missense_Mutation_p.G444S	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	547					cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|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)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AAGCGGCGGCCGCACACGTCG	0.662													C|||	2	0.000399361	0.0015	0.0	5008	,	,		12645	0.0		0.0	False		,,,				2504	0.0				p.G547S		Atlas-SNP	.											.	EGR4	52	.	0			c.G1639A						PASS	.	C	SER/GLY	2,4404		0,2,2201	24.0	28.0	27.0		1639	4.8	1.0	2	dbSNP_134	27	0,8596		0,0,4298	no	missense	EGR4	NM_001965.3	56	0,2,6499	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	547/590	73518716	2,13000	2203	4298	6501	SO:0001583	missense	1961	exon2			GGCGGCCGCACAC		CCDS1925.2	2p13	2013-01-08			ENSG00000135625	ENSG00000135625		"""Zinc fingers, C2H2-type"""	3241	protein-coding gene	gene with protein product		128992				1584812	Standard	NM_001965		Approved	NGFI-C, PAT133	uc010yrj.2	Q05215	OTTHUMG00000129774	ENST00000545030.1:c.1639G>A	2.37:g.73518716C>T	ENSP00000445626:p.Gly547Ser	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	176	99	0.5625	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Missense_Mutation	SNP	ENST00000545030.1	37	CCDS1925.2	.	.	.	.	.	.	.	.	.	.	C	31	5.103602	0.94245	4.54E-4	0.0	ENSG00000135625	ENST00000545030;ENST00000436467	T;T	0.07216	3.21;3.21	4.79	4.79	0.61399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000005	T	0.20780	0.0500	L	0.37897	1.145	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.77557	0.989;0.99	T	0.00715	-1.1597	10	0.87932	D	0	-21.0702	16.5595	0.84535	0.0:1.0:0.0:0.0	.	444;547	Q05215;G3V1T5	EGR4_HUMAN;.	S	547;444	ENSP00000445626:G547S;ENSP00000419687:G444S	ENSP00000419687:G444S	G	-	1	0	EGR4	73372224	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.631000	0.83237	2.478000	0.83669	0.655000	0.94253	GGC	C|1.000;T|0.000	0.000	weak		0.662	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965	
MSH5	4439	hgsc.bcm.edu	37	6	31729359	31729359	+	Silent	SNP	A	A	G	rs707938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31729359A>G	ENST00000375755.3	+	22	2434	c.2148A>G	c.(2146-2148)caA>caG	p.Q716Q	SAPCD1_ENST00000425424.1_5'Flank|MSH5-SAPCD1_ENST00000491552.1_3'UTR|SAPCD1-AS1_ENST00000419679.1_RNA|SAPCD1_ENST00000415669.2_5'Flank|MSH5_ENST00000431848.2_Silent_p.Q415Q|MSH5_ENST00000534153.4_Silent_p.Q733Q|MSH5_ENST00000375750.3_Silent_p.Q716Q|MSH5_ENST00000395853.1_Silent_p.Q390Q|MSH5-SAPCD1_ENST00000493662.2_Silent_p.Q733Q|MSH5_ENST00000375742.3_Silent_p.Q733Q|MSH5_ENST00000375740.3_Silent_p.Q734Q|MSH5_ENST00000375703.3_Silent_p.Q717Q	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	716					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						TTCAGCTACAACTGCTGCCAC	0.607								Direct reversal of damage;Mismatch excision repair (MMR)					G|||	2340	0.467252	0.6929	0.4236	5008	,	,		17393	0.3512		0.3191	False		,,,				2504	0.4652				p.Q734Q		Atlas-SNP	.											.	MSH5	108	.	0			c.A2202G						PASS	.	G	,,,	2847,1559		925,997,281	47.0	53.0	51.0		2148,2202,2151,2148	2.6	1.0	6	dbSNP_86	51	2724,5876		455,1814,2031	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MSH5	NM_002441.4,NM_025259.5,NM_172165.3,NM_172166.3	,,,	1380,2811,2312	GG,GA,AA		31.6744,35.3836,42.8341	,,,	716/835,734/823,717/836,716/835	31729359	5571,7435	2203	4300	6503	SO:0001819	synonymous_variant	4439	exon22			GCTACAACTGCTG	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.2148A>G	6.37:g.31729359A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	58	0.644444	NM_025259	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Silent	SNP	ENST00000375755.3	37	CCDS4720.1																																																																																			A|0.573;G|0.427	0.427	strong		0.607	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4		
TNXB	7148	hgsc.bcm.edu	37	6	32041621	32041621	+	Missense_Mutation	SNP	G	G	A	rs6910390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32041621G>A	ENST00000375244.3	-	12	4685	c.4484C>T	c.(4483-4485)aCa>aTa	p.T1495I	TNXB_ENST00000375247.2_Missense_Mutation_p.T1495I			P22105	TENX_HUMAN	tenascin XB	1582	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CTCGGGGACTGTCCAGGAGAG	0.627													G|||	27	0.00539137	0.0159	0.0058	5008	,	,		13775	0.0		0.002	False		,,,				2504	0.0				p.T1495I		Atlas-SNP	.											.	TNXB	553	.	0			c.C4484T						PASS	.	G	ILE/THR	33,2523		1,31,1246	29.0	31.0	30.0		4484	1.5	0.1	6	dbSNP_116	30	30,5096		0,30,2533	yes	missense	TNXB	NM_019105.6	89	1,61,3779	AA,AG,GG		0.5853,1.2911,0.8201	benign	1495/4243	32041621	63,7619	1278	2563	3841	SO:0001583	missense	7148	exon12			GGGACTGTCCAGG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.4484C>T	6.37:g.32041621G>A	ENSP00000364393:p.Thr1495Ile	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	190	100	0.526316	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		18	0.008241758241758242	11	0.022357723577235773	3	0.008287292817679558	1	0.0017482517482517483	3	0.00395778364116095	G	4.859	0.159720	0.09287	0.012911	0.005853	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.59083	0.29;0.29	5.46	1.54	0.23209	.	0.993930	0.08149	N	0.990366	T	0.44456	0.1294	M	0.82823	2.61	0.19945	N	0.999944	B	0.28552	0.215	B	0.36845	0.234	T	0.51934	-0.8642	10	0.38643	T	0.18	.	7.6751	0.28481	0.3741:0.0:0.6259:0.0	rs6910390	1495	P22105-3	.	I	1495	ENSP00000364393:T1495I;ENSP00000364396:T1495I	ENSP00000364393:T1495I	T	-	2	0	TNXB	32149599	0.384000	0.25164	0.076000	0.20297	0.007000	0.05969	0.499000	0.22546	-0.013000	0.14199	-1.178000	0.01721	ACA	G|0.992;A|0.008	0.008	strong		0.627	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
SPINK1	6690	hgsc.bcm.edu	37	5	147207605	147207605	+	Silent	SNP	G	G	A	rs35737774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147207605G>A	ENST00000296695.5	-	3	382	c.174C>T	c.(172-174)tgC>tgT	p.C58C	SPINK1_ENST00000510027.2_Silent_p.C58C	NM_003122.3	NP_003113.2	P00995	ISK1_HUMAN	serine peptidase inhibitor, Kazal type 1	58	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				negative regulation of calcium ion import (GO:0090281)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of serine-type endopeptidase activity (GO:1900004)|regulation of acrosome reaction (GO:0060046)|regulation of store-operated calcium entry (GO:2001256)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACATAACACGCATTCATTGG	0.323									Hereditary Pancreatitis																												p.C58C		Atlas-SNP	.											.	SPINK1	9	.	0			c.C174T						PASS	.	G		624,3782	272.5+/-270.8	42,540,1621	102.0	95.0	97.0		174	-1.0	0.0	5	dbSNP_126	97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SPINK1	NM_003122.3		42,541,5920	AA,AG,GG		0.0116,14.1625,4.8055		58/80	147207605	625,12381	2203	4300	6503	SO:0001819	synonymous_variant	6690	exon3	Familial Cancer Database		TAACACGCATTCA		CCDS4286.1	5q32	2011-08-31	2005-08-17		ENSG00000164266	ENSG00000164266		"""Serine peptidase inhibitors, Kazal type"""	11244	protein-coding gene	gene with protein product		167790	"""serine protease inhibitor, Kazal type 1"""				Standard	XM_005268501		Approved	Spink3, PCTT, PSTI, TATI	uc003los.2	P00995	OTTHUMG00000129730	ENST00000296695.5:c.174C>T	5.37:g.147207605G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_003122		Silent	SNP	ENST00000296695.5	37	CCDS4286.1																																																																																			G|0.956;A|0.044	0.044	strong		0.323	SPINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251940.2	NM_003122	
CSNK2A3	283106	hgsc.bcm.edu	37	11	11373631	11373631	+	Missense_Mutation	SNP	C	C	T	rs74507390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:11373631C>T	ENST00000528848.2	-	1	1273	c.1036G>A	c.(1036-1038)Gtc>Atc	p.V346I	RP11-567I13.1_ENST00000526867.1_RNA|GALNT18_ENST00000227756.4_Intron	NM_001256686.1	NP_001243615.1	Q8NEV1	CSK23_HUMAN	casein kinase 2, alpha 3 polypeptide	346					positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)										GCGCTGCTGACGGGCGTACTG	0.567													-|||	208	0.0415335	0.1483	0.0173	5008	,	,		18472	0.0		0.0	False		,,,				2504	0.0				p.V346I		Atlas-SNP	.											.	.	.	.	0			c.G1036A						PASS	.																																			SO:0001583	missense	283106	exon1			TGCTGACGGGCGT	X64692	CCDS59224.1	11p15.3	2013-01-18	2013-01-17	2013-01-17	ENSG00000254598	ENSG00000254598			2458	protein-coding gene	gene with protein product			"""casein kinase 2, alpha 1 polypeptide pseudogene"""	CSNK2A1P		12102635, 1610905, 20625391	Standard	NM_001256686		Approved		uc001mjp.4	Q8NEV1	OTTHUMG00000165708	ENST00000528848.2:c.1036G>A	11.37:g.11373631C>T	ENSP00000473553:p.Val346Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_001256686		Missense_Mutation	SNP	ENST00000528848.2	37	CCDS59224.1																																																																																			C|0.965;T|0.035	0.035	strong		0.567	CSNK2A3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385850.3	NM_001256686	
MYH9	4627	hgsc.bcm.edu	37	22	36678816	36678816	+	Silent	SNP	C	C	A	rs80050551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36678816C>A	ENST00000216181.5	-	41	6011	c.5781G>T	c.(5779-5781)ccG>ccT	p.P1927P	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1927					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)	p.P1927P(1)		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						GCACGACAAACGGCAGGTCCC	0.672			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				.|||	138	0.0275559	0.0991	0.0101	5008	,	,		14735	0.0		0.0	False		,,,				2504	0.0				p.P1927P		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	MYH9,NS,NS,0,1	MYH9	225	1	1	Substitution - coding silent(1)	pancreas(1)	c.G5781T						PASS	.			364,4042	178.0+/-206.8	14,336,1853	34.0	30.0	32.0		5781	-7.5	0.7	22	dbSNP_131	32	5,8593	3.0+/-9.4	0,5,4294	no	coding-synonymous	MYH9	NM_002473.4		14,341,6147	AA,AC,CC		0.0582,8.2615,2.8376		1927/1961	36678816	369,12635	2203	4299	6502	SO:0001819	synonymous_variant	4627	exon41	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GACAAACGGCAGG		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.5781G>T	22.37:g.36678816C>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	42	26	0.619048	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			C|0.969;A|0.031	0.031	strong		0.672	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
DCTN4	51164	hgsc.bcm.edu	37	5	150097883	150097883	+	Missense_Mutation	SNP	G	G	C	rs11954652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150097883G>C	ENST00000447998.2	-	11	1141	c.1026C>G	c.(1024-1026)ttC>ttG	p.F342L	DCTN4_ENST00000424236.1_Missense_Mutation_p.F285L|DCTN4_ENST00000446090.2_Missense_Mutation_p.F349L	NM_016221.3	NP_057305.1	Q9UJW0	DCTN4_HUMAN	dynactin 4 (p62)	342			F -> L (in dbSNP:rs11954652). {ECO:0000269|PubMed:14702039}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	10		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTCACACTCGAAGAGAGTCA	0.522													C|||	1356	0.270767	0.6142	0.0893	5008	,	,		19789	0.2589		0.0606	False		,,,				2504	0.1636				p.F349L		Atlas-SNP	.											.	DCTN4	35	.	0			c.C1047G						PASS	.	C	LEU/PHE,LEU/PHE,LEU/PHE	2334,2072	568.8+/-382.5	638,1058,507	138.0	119.0	125.0		1026,855,1047	4.1	1.0	5	dbSNP_120	125	410,8190	801.0+/-407.4	6,398,3896	yes	missense,missense,missense	DCTN4	NM_016221.3,NM_001135644.1,NM_001135643.1	22,22,22	644,1456,4403	CC,CG,GG		4.7674,47.0268,21.098	benign,benign,benign	342/461,285/404,349/468	150097883	2744,10262	2203	4300	6503	SO:0001583	missense	51164	exon12			ACACTCGAAGAGA	AF195120	CCDS4310.1, CCDS47310.1, CCDS47311.1	5q31-q32	2008-05-23			ENSG00000132912	ENSG00000132912			15518	protein-coding gene	gene with protein product		614758				10843801, 16554302	Standard	NM_016221		Approved		uc010jhi.3	Q9UJW0	OTTHUMG00000130079	ENST00000447998.2:c.1026C>G	5.37:g.150097883G>C	ENSP00000416968:p.Phe342Leu	Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_001135643	B3KWW0|D3DQH0|E5RGT5|Q8TAN8	Missense_Mutation	SNP	ENST00000447998.2	37	CCDS4310.1	509	0.23305860805860806	281	0.5711382113821138	37	0.10220994475138122	146	0.25524475524475526	45	0.059366754617414245	C	5.578	0.291418	0.10567	0.529732	0.047674	ENSG00000132912	ENST00000447998;ENST00000424236;ENST00000446090	T;T;T	0.21734	1.99;1.99;1.99	5.83	4.05	0.47172	.	0.448446	0.25192	N	0.032456	T	0.00012	0.0000	N	0.00258	-1.755	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43426	-0.9392	9	0.06236	T	0.91	-1.0278	5.3363	0.15959	0.1213:0.636:0.1168:0.1258	rs11954652;rs11954652	349;342	Q9UJW0-3;Q9UJW0	.;DCTN4_HUMAN	L	342;285;349	ENSP00000416968:F342L;ENSP00000411251:F285L;ENSP00000414906:F349L	ENSP00000411251:F285L	F	-	3	2	DCTN4	150078076	0.994000	0.37717	0.970000	0.41538	0.976000	0.68499	0.443000	0.21644	0.487000	0.27698	-0.125000	0.14975	TTC	G|0.780;C|0.220	0.220	strong		0.522	DCTN4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252372.1		
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45993990	45993990	+	Missense_Mutation	SNP	T	T	C	rs79601471		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45993990T>C	ENST00000400374.3	+	1	385	c.355T>C	c.(355-357)Tgc>Cgc	p.C119R	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_5'Flank	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	119	36 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CAAGACTGTCTGCTGCAAGCC	0.647																																					p.C119R		Atlas-SNP	.											.	KRTAP10-4	44	.	0			c.T355C						PASS	.	T	ARG/CYS,	498,3906		0,498,1704	117.0	107.0	111.0		355,	3.2	0.5	21	dbSNP_131	111	2,8590		0,2,4294	no	missense,intron	TSPEAR,KRTAP10-4	NM_198687.1,NM_144991.2	180,	0,500,5998	CC,CT,TT		0.0233,11.3079,3.8473	probably-damaging,	119/402,	45993990	500,12496	2202	4296	6498	SO:0001583	missense	386672	exon1			ACTGTCTGCTGCA	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.355T>C	21.37:g.45993990T>C	ENSP00000383225:p.Cys119Arg	Somatic	575	0	0		WXS	Illumina HiSeq	Phase_I	530	140	0.264151	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	97	0.044413919413919416	86	0.17479674796747968	11	0.03038674033149171	0	0.0	0	0.0	N	6.327	0.428441	0.11987	0.113079	2.33E-4	ENSG00000215454	ENST00000400374	T	0.01043	5.41	4.37	3.18	0.36537	.	.	.	.	.	T	0.00012	0.0000	M	0.90870	3.155	0.23780	P	0.99686138	D	0.54772	0.968	P	0.50970	0.655	T	0.16928	-1.0386	8	0.87932	D	0	.	7.1933	0.25839	0.3572:0.0:0.0:0.6428	.	119	P60372	KR104_HUMAN	R	119	ENSP00000383225:C119R	ENSP00000383225:C119R	C	+	1	0	KRTAP10-4	44818418	0.622000	0.27085	0.456000	0.27044	0.149000	0.21700	0.699000	0.25586	0.514000	0.28300	0.386000	0.25728	TGC	T|0.955;C|0.045	0.045	strong		0.647	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
HLA-B	3106	hgsc.bcm.edu	37	6	31324516	31324516	+	Missense_Mutation	SNP	C	C	A	rs1131215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31324516C>A	ENST00000412585.2	-	2	320	c.292G>T	c.(292-294)Gac>Tac	p.D98Y		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	98	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						CTCTCTCGGTCAGTCTGTGCC	0.682									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	3525	0.703874	0.7163	0.7507	5008	,	,		6748	0.6419		0.5954	False		,,,				2504	0.8292				p.D98Y		Atlas-SNP	.											HLA-B,colon,carcinoma,0,1	HLA-B	54	1	0			c.G292T						scavenged	.	A	TYR/ASP	2329,1909		891,547,681	50.0	52.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	292	-6.4	0.0	6	dbSNP_86	52	3737,4619		1270,1197,1711	no	missense	HLA-B	NM_005514.6	160	2161,1744,2392	AA,AC,CC		44.7224,45.0448,48.1658		98/363	31324516	6066,6528	2119	4178	6297	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CTCGGTCAGTCTG	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.292G>T	6.37:g.31324516C>A	ENSP00000399168:p.Asp98Tyr	Somatic	40	40	1		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	1363	0.6240842490842491	310	0.6300813008130082	257	0.7099447513812155	374	0.6538461538461539	422	0.5567282321899736	N	3.390	-0.124570	0.06795	0.549552	0.447224	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00009	9.52;9.52	3.2	-6.41	0.01938	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	6.155240	0.01158	U	0.006566	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;D	0.89917	0.354;0.057;1.0	B;B;D	0.97110	0.291;0.083;1.0	T	0.62120	-0.6921	9	0.02654	T	1	.	2.0223	0.03512	0.3366:0.364:0.0893:0.21	rs1131215;rs3177922;rs3190915;rs9266166;rs17413622	98;98;73	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	Y	98;109	ENSP00000399168:D98Y;ENSP00000405931:D109Y	ENSP00000399168:D98Y	D	-	1	0	HLA-B	31432495	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.850000	0.01670	-2.027000	0.00932	-6.206000	0.00000	GAC	C|0.415;A|0.585	0.585	strong		0.682	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
OPN4	94233	hgsc.bcm.edu	37	10	88416963	88416963	+	Intron	SNP	G	G	A	rs7901458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:88416963G>A	ENST00000241891.5	+	3	457				OPN4_ENST00000372071.2_Missense_Mutation_p.R101H	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 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						gctgtgcttcgtggagtcact	0.542													G|||	236	0.0471246	0.1346	0.0144	5008	,	,		22029	0.0119		0.0149	False		,,,				2504	0.0215				p.R101H		Atlas-SNP	.											OPN4,NS,carcinoma,+1,1	OPN4	61	1	0			c.G302A						PASS	.	G	HIS/ARG,	500,3906	230.7+/-244.8	27,446,1730	235.0	162.0	187.0		302,	-4.8	0.0	10	dbSNP_116	187	140,8460	69.4+/-131.9	1,138,4161	yes	missense,intron	OPN4	NM_001030015.2,NM_033282.3	29,	28,584,5891	AA,AG,GG		1.6279,11.3482,4.9208	benign,	101/490,	88416963	640,12366	2203	4300	6503	SO:0001627	intron_variant	94233	exon3			TGCTTCGTGGAGT	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.291-826G>A	10.37:g.88416963G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	37	CCDS7376.1	91	0.041666666666666664	73	0.1483739837398374	6	0.016574585635359115	5	0.008741258741258742	7	0.009234828496042216	G	9.031	0.987272	0.18889	0.113482	0.016279	ENSG00000122375	ENST00000372071;ENST00000443292	T;T	0.19938	2.11;2.11	3.66	-4.79	0.03200	.	2.203020	0.03070	N	0.157117	T	0.00039	0.0001	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	0.24941	-1.0146	9	0.25751	T	0.34	.	1.278	0.02034	0.2835:0.1229:0.1084:0.4851	rs7901458;rs56530469;rs7901458	101;101	C9JWU6;Q9UHM6-2	.;.	H	101	ENSP00000361141:R101H;ENSP00000393132:R101H	ENSP00000361141:R101H	R	+	2	0	OPN4	88406943	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.680000	0.01939	-0.849000	0.04158	-0.247000	0.11927	CGT	G|0.949;A|0.051	0.051	strong		0.542	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
VWA2	340706	hgsc.bcm.edu	37	10	116032519	116032519	+	Missense_Mutation	SNP	A	A	G	rs597371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116032519A>G	ENST00000392982.3	+	6	642	c.392A>G	c.(391-393)gAa>gGa	p.E131G	VWA2_ENST00000603594.1_Missense_Mutation_p.E131G			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	131	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.		E -> G (in dbSNP:rs597371). {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)		ACGGAGACGGAACTTGCTCTG	0.517													G|||	2790	0.557109	0.8782	0.4741	5008	,	,		21147	0.3373		0.4324	False		,,,				2504	0.5368				p.E131G		Atlas-SNP	.											.	VWA2	64	.	0			c.A392G						PASS	.	G	GLY/GLU	3526,880	342.0+/-307.0	1402,722,79	108.0	109.0	109.0		392	4.3	0.5	10	dbSNP_83	109	3700,4900	620.6+/-397.1	802,2096,1402	yes	missense	VWA2	NM_198496.1	98	2204,2818,1481	GG,GA,AA		43.0233,19.9728,44.441	benign	131/726	116032519	7226,5780	2203	4300	6503	SO:0001583	missense	340706	exon6			AGACGGAACTTGC	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.392A>G	10.37:g.116032519A>G	ENSP00000376708:p.Glu131Gly	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		1102	0.5045787545787546	423	0.8597560975609756	166	0.4585635359116022	195	0.3409090909090909	318	0.41952506596306066	G	1.007	-0.689115	0.03328	0.800272	0.430233	ENSG00000165816	ENST00000392982;ENST00000298715	T	0.80033	-1.33	5.2	4.28	0.50868	von Willebrand factor, type A (3);	0.120923	0.56097	N	0.000030	T	0.00012	0.0000	N	0.00000	-4.035	0.39718	P	0.02856599999999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48525	-0.9028	9	0.02654	T	1	.	9.0543	0.36397	0.079:0.1468:0.7743:0.0	rs597371;rs59737203;rs597371	131;131	Q5GFL6;Q5GFL6-2	VWA2_HUMAN;.	G	131	ENSP00000376708:E131G	ENSP00000298715:E131G	E	+	2	0	VWA2	116022509	1.000000	0.71417	0.454000	0.27019	0.223000	0.24884	5.047000	0.64232	0.556000	0.29098	-0.119000	0.15052	GAA	A|0.454;G|0.546	0.546	strong		0.517	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3670646	3670646	+	Silent	SNP	C	C	T	rs8115679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3670646C>T	ENST00000344754.4	-	18	4856	c.4857G>A	c.(4855-4857)ctG>ctA	p.L1619L	SIGLEC1_ENST00000202578.4_Silent_p.L1619L	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1619	Ig-like C2-type 16.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						AGGCAGAGCCCAGGACATTTG	0.597													C|||	117	0.0233626	0.0862	0.0043	5008	,	,		19707	0.0		0.0	False		,,,				2504	0.0				p.L1619L		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.G4857A						PASS	.	C		310,4094	164.4+/-196.0	11,288,1903	44.0	38.0	40.0		4857	4.6	1.0	20	dbSNP_116	40	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SIGLEC1	NM_023068.3		11,290,6201	TT,TC,CC		0.0233,7.0391,2.3993		1619/1710	3670646	312,12692	2202	4300	6502	SO:0001819	synonymous_variant	6614	exon18			AGAGCCCAGGACA	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.4857G>A	20.37:g.3670646C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	178	75	0.421348	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	C	8.307	0.821130	0.16678	0.070391	2.33E-4	ENSG00000088827	ENST00000419548	.	.	.	5.55	4.6	0.57074	.	.	.	.	.	T	0.12305	0.0299	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21211	-1.0252	4	.	.	.	.	12.3752	0.55275	0.0:0.8305:0.1695:0.0	rs8115679;rs8115679	.	.	.	R	433	.	.	G	-	1	0	SIGLEC1	3618646	1.000000	0.71417	0.996000	0.52242	0.785000	0.44390	1.377000	0.34317	1.320000	0.45209	0.561000	0.74099	GGG	C|0.974;T|0.026	0.026	strong		0.597	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
RAI14	26064	hgsc.bcm.edu	37	5	34687817	34687817	+	Intron	SNP	T	T	C	rs10521016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34687817T>C	ENST00000265109.3	+	2	323				RAI14_ENST00000506376.1_Start_Codon_SNP_p.M1T|RAI14_ENST00000503673.1_Intron|RAI14_ENST00000515799.1_Intron|RAI14_ENST00000428746.2_Intron|RAI14_ENST00000512629.1_Intron	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14							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)					GGGAATTAGATGGAAGCCAAG	0.413													T|||	143	0.0285543	0.1044	0.0072	5008	,	,		19536	0.0		0.0	False		,,,				2504	0.0				p.M1T		Atlas-SNP	.											.	RAI14	100	.	0			c.T2C						PASS	.						187.0	157.0	166.0					5																	34687817		692	1591	2283	SO:0001627	intron_variant	26064	exon1			ATTAGATGGAAGC	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.36+757T>C	5.37:g.34687817T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	181	180	0.994475	NM_001145523	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	67	0.030677655677655676	65	0.13211382113821138	2	0.0055248618784530384	0	0.0	0	0.0	T	7.737	0.700548	0.15106	.	.	ENSG00000039560	ENST00000506376	T	0.33654	1.4	5.19	-0.0796	0.13710	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.21518	-1.0243	8	0.56958	D	0.05	.	0.6567	0.00835	0.1705:0.1874:0.1658:0.4763	rs10521016;rs56487933;rs10521016	1	Q9P0K7-3	.	T	1	ENSP00000423854:M1T	ENSP00000423854:M1T	M	+	2	0	RAI14	34723574	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.023000	0.12456	-0.143000	0.11334	-1.087000	0.02190	ATG	T|0.955;C|0.045	0.045	strong		0.413	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
NTF3	4908	hgsc.bcm.edu	37	12	5603632	5603632	+	Silent	SNP	G	G	A	rs6332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:5603632G>A	ENST00000331010.6	+	1	335	c.252G>A	c.(250-252)ccG>ccA	p.P84P	NTF3_ENST00000423158.3_Silent_p.P97P|NTF3_ENST00000535299.1_Intron	NM_002527.4	NP_002518.1	P20783	NTF3_HUMAN	neurotrophin 3	84					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell-cell signaling (GO:0007267)|enteric nervous system development (GO:0048484)|epidermis development (GO:0008544)|glial cell fate determination (GO:0007403)|induction of positive chemotaxis (GO:0050930)|mechanoreceptor differentiation (GO:0042490)|myelination (GO:0042552)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive chemotaxis (GO:0050918)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of synaptic transmission (GO:0050804)|signal transduction (GO:0007165)|smooth muscle cell differentiation (GO:0051145)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular region (GO:0005576)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(3)|upper_aerodigestive_tract(1)	22						CATTCCAGCCGGTGATTGCAA	0.622													A|||	2445	0.488219	0.5325	0.438	5008	,	,		16459	0.4583		0.503	False		,,,				2504	0.4796				p.P97P	GBM(194;1104 2182 8339 9578 18493)	Atlas-SNP	.											.	NTF3	50	.	0			c.G291A						PASS	.	A	,	2328,2078	560.3+/-380.4	627,1074,502	47.0	54.0	52.0		291,252	-11.0	0.0	12	dbSNP_52	52	4394,4206	561.4+/-387.8	1126,2142,1032	yes	coding-synonymous,coding-synonymous	NTF3	NM_001102654.1,NM_002527.4	,	1753,3216,1534	AA,AG,GG		48.907,47.163,48.3162	,	97/271,84/258	5603632	6722,6284	2203	4300	6503	SO:0001819	synonymous_variant	4908	exon2			CCAGCCGGTGATT		CCDS8538.1, CCDS44806.1	12p13	2014-01-30			ENSG00000185652	ENSG00000185652		"""Endogenous ligands"""	8023	protein-coding gene	gene with protein product		162660				1889806	Standard	NM_002527		Approved	NGF2	uc001qnk.4	P20783	OTTHUMG00000168649	ENST00000331010.6:c.252G>A	12.37:g.5603632G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_001102654	B7Z1T5|Q6FH50	Silent	SNP	ENST00000331010.6	37	CCDS8538.1																																																																																			G|0.498;A|0.502	0.502	strong		0.622	NTF3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400486.1		
PCNT	5116	hgsc.bcm.edu	37	21	47754449	47754449	+	Missense_Mutation	SNP	G	G	A	rs59183158		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47754449G>A	ENST00000359568.5	+	3	513	c.406G>A	c.(406-408)Ggt>Agt	p.G136S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	136					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)					GTTCACAGTCGGTGACCACCC	0.552																																					p.G136S		Atlas-SNP	.											PCNT,NS,carcinoma,0,1	PCNT	283	1	0			c.G406A						scavenged	.						180.0	121.0	141.0					21																	47754449		2203	4300	6503	SO:0001583	missense	5116	exon3			ACAGTCGGTGACC	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.406G>A	21.37:g.47754449G>A	ENSP00000352572:p.Gly136Ser	Somatic	262	2	0.00763359		WXS	Illumina HiSeq	Phase_I	301	14	0.0465116	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	a	0.003	-2.400549	0.00195	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01279	5.06	0.158	-0.317	0.12736	.	.	.	.	.	T	0.00637	0.0021	N	0.01874	-0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49969	-0.8882	8	0.41790	T	0.15	.	.	.	.	rs59183158	18;136	O95613-2;O95613	.;PCNT_HUMAN	S	136	ENSP00000352572:G136S	ENSP00000338675:G136S	G	+	1	0	PCNT	46578877	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.839000	0.00738	-2.864000	0.00326	-2.902000	0.00092	GGT	.	.	weak		0.552	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
EMR1	2015	hgsc.bcm.edu	37	19	6896483	6896483	+	Missense_Mutation	SNP	G	G	A	rs330877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6896483G>A	ENST00000312053.4	+	3	206	c.169G>A	c.(169-171)Gct>Act	p.A57T	EMR1_ENST00000250572.8_Missense_Mutation_p.A57T|EMR1_ENST00000601198.1_3'UTR|AC020895.1_ENST00000580648.1_RNA|EMR1_ENST00000381407.5_Missense_Mutation_p.A57T|EMR1_ENST00000450315.3_Missense_Mutation_p.A57T|EMR1_ENST00000381404.4_Missense_Mutation_p.A57T	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	57	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.		A -> T (in dbSNP:rs330877). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7601460}.		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)					TTACTATTGCGCTTGCAAACA	0.463													g|||	1693	0.338059	0.3903	0.3934	5008	,	,		20636	0.3403		0.2674	False		,,,				2504	0.2986				p.A57T		Atlas-SNP	.											EMR1,NS,carcinoma,-1,1	EMR1	153	1	0			c.G169A						scavenged	.	A	THR/ALA	1595,2811	496.0+/-363.4	292,1011,900	176.0	143.0	154.0		169	-3.3	0.0	19	dbSNP_79	154	2512,6088	411.9+/-350.6	356,1800,2144	yes	missense	EMR1	NM_001974.3	58	648,2811,3044	AA,AG,GG		29.2093,36.2006,31.5777	benign	57/887	6896483	4107,8899	2203	4300	6503	SO:0001583	missense	2015	exon3			TATTGCGCTTGCA	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.169G>A	19.37:g.6896483G>A	ENSP00000311545:p.Ala57Thr	Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	NM_001256252	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	728	0.3333333333333333	167	0.3394308943089431	147	0.40607734806629836	210	0.36713286713286714	204	0.2691292875989446	g	0.072	-1.200768	0.01581	0.362006	0.292093	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	D;D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93;-2.93	3.91	-3.26	0.05064	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	N	0.00510	-1.415	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.001;0.0;0.001	T	0.04140	-1.0974	8	0.05351	T	0.99	.	4.3996	0.11379	0.5505:0.0:0.2083:0.2412	rs330877;rs2228536;rs330877	57;57;57;57;57	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	T	57	ENSP00000311545:A57T;ENSP00000370811:A57T;ENSP00000250572:A57T;ENSP00000370814:A57T;ENSP00000405974:A57T	ENSP00000250572:A57T	A	+	1	0	EMR1	6847483	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.030000	0.03581	-1.051000	0.03226	-2.703000	0.00135	GCT	G|0.675;A|0.325	0.325	strong		0.463	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
DCHS2	54798	hgsc.bcm.edu	37	4	155219373	155219373	+	Silent	SNP	A	A	G	rs17031391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155219373A>G	ENST00000357232.4	-	18	4727	c.4728T>C	c.(4726-4728)gtT>gtC	p.V1576V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1576	Cadherin 13. {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)		CATTGTCATTAACATCAGTGA	0.438													A|||	405	0.0808706	0.2602	0.0418	5008	,	,		19929	0.0109		0.0179	False		,,,				2504	0.0031				p.V1576V		Atlas-SNP	.											.	DCHS2	594	.	0			c.T4728C						PASS	.	A		945,3461	361.4+/-315.7	116,713,1374	103.0	102.0	102.0		4728	-1.4	1.0	4	dbSNP_123	102	148,8452	72.6+/-135.2	3,142,4155	no	coding-synonymous	DCHS2	NM_017639.3		119,855,5529	GG,GA,AA		1.7209,21.448,8.4038		1576/2917	155219373	1093,11913	2203	4300	6503	SO:0001819	synonymous_variant	54798	exon18			GTCATTAACATCA	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.4728T>C	4.37:g.155219373A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	214	98	0.457944	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			A|0.913;G|0.087	0.087	strong		0.438	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
OR5B2	390190	hgsc.bcm.edu	37	11	58190228	58190228	+	Silent	SNP	G	G	A	rs77952368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58190228G>A	ENST00000302581.2	-	1	558	c.507C>T	c.(505-507)tcC>tcT	p.S169S		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	169						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)				GTACCAGATTGGATTTACAGA	0.453													G|||	26	0.00519169	0.0182	0.0029	5008	,	,		22719	0.0		0.0	False		,,,				2504	0.0				p.S169S		Atlas-SNP	.											OR5B2,NS,carcinoma,-1,1	OR5B2	75	1	0			c.C507T						PASS	.	G		59,4343	56.2+/-92.4	1,57,2143	61.0	57.0	58.0		507	1.8	0.0	11	dbSNP_131	58	1,8589		0,1,4294	no	coding-synonymous	OR5B2	NM_001005566.2		1,58,6437	AA,AG,GG		0.0116,1.3403,0.4618		169/310	58190228	60,12932	2201	4295	6496	SO:0001819	synonymous_variant	390190	exon1			CAGATTGGATTTA	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.507C>T	11.37:g.58190228G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	72	43	0.597222	NM_001005566	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Silent	SNP	ENST00000302581.2	37	CCDS31550.1																																																																																			G|0.993;A|0.007	0.007	strong		0.453	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566	
IFNA5	3442	hgsc.bcm.edu	37	9	21305048	21305048	+	Missense_Mutation	SNP	G	G	C	rs138121530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21305048G>C	ENST00000259555.4	-	1	264	c.208C>G	c.(208-210)Cag>Gag	p.Q70E		NM_002169.2	NP_002160.1	P01569	IFNA5_HUMAN	interferon, alpha 5	70					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	7				Lung(24;2.34e-24)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		TTCTGGAACTGGTTGCCATCA	0.473													G|||	60	0.0119808	0.0439	0.0029	5008	,	,		23310	0.0		0.0	False		,,,				2504	0.0				p.Q70E		Atlas-SNP	.											.	IFNA5	21	.	0			c.C208G						PASS	.	G	GLU/GLN	212,4194	131.0+/-167.6	3,206,1994	139.0	130.0	133.0		208	4.2	0.0	9	dbSNP_134	133	2,8598	2.2+/-6.3	0,2,4298	no	missense	IFNA5	NM_002169.2	29	3,208,6292	CC,CG,GG		0.0233,4.8116,1.6454	benign	70/190	21305048	214,12792	2203	4300	6503	SO:0001583	missense	3442	exon1			GGAACTGGTTGCC		CCDS6502.1	9p22	2010-08-24			ENSG00000147873	ENSG00000147873		"""Interferons"""	5426	protein-coding gene	gene with protein product		147565				1385305	Standard	NM_002169		Approved	IFN-alphaG	uc011lnh.2	P01569	OTTHUMG00000019664	ENST00000259555.4:c.208C>G	9.37:g.21305048G>C	ENSP00000259555:p.Gln70Glu	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	288	138	0.479167	NM_002169	Q52LX3	Missense_Mutation	SNP	ENST00000259555.4	37	CCDS6502.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	G	13.34	2.206733	0.39003	0.048116	2.33E-4	ENSG00000147873	ENST00000259555	T	0.04275	3.66	4.16	4.16	0.48862	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.474897	0.22261	N	0.062416	T	0.02610	0.0079	M	0.85373	2.75	0.09310	N	1	B	0.25743	0.133	P	0.45712	0.491	T	0.02596	-1.1136	10	0.72032	D	0.01	.	10.4841	0.44711	0.0:0.1982:0.8018:0.0	.	70	P01569	IFNA5_HUMAN	E	70	ENSP00000259555:Q70E	ENSP00000259555:Q70E	Q	-	1	0	IFNA5	21295048	0.002000	0.14202	0.014000	0.15608	0.007000	0.05969	1.019000	0.30014	2.052000	0.61016	0.537000	0.68136	CAG	G|0.984;C|0.016	0.016	strong		0.473	IFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051893.1	NM_002169	
OPRM1	4988	hgsc.bcm.edu	37	6	154428666	154428666	+	Intron	SNP	C	C	T	rs677830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:154428666C>T	ENST00000330432.7	+	4	1401				OPRM1_ENST00000435918.2_Intron|OPRM1_ENST00000419506.2_Nonsense_Mutation_p.Q411*|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000337049.4_Intron|OPRM1_ENST00000452687.2_Intron|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000522555.1_Intron|OPRM1_ENST00000414028.2_Intron|OPRM1_ENST00000434900.2_Intron|OPRM1_ENST00000522236.1_Intron|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	70	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	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	
NUDT8	254552	hgsc.bcm.edu	37	11	67397251	67397251	+	Silent	SNP	G	G	C	rs17851655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67397251G>C	ENST00000376693.2	-	1	141	c.132C>G	c.(130-132)gtC>gtG	p.V44V	RP11-655M14.13_ENST00000533311.1_lincRNA|NUDT8_ENST00000301490.4_Silent_p.V44V	NM_001243750.1	NP_001230679.1	Q8WV74	NUDT8_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 8	44	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						GCAGCGCCGGGACCCCACGCA	0.766													G|||	750	0.14976	0.289	0.0937	5008	,	,		9332	0.0704		0.0944	False		,,,				2504	0.1401				p.V44V		Atlas-SNP	.											.	NUDT8	12	.	0			c.C132G						PASS	.	G		762,3106		62,638,1234	7.0	6.0	6.0		132	0.8	1.0	11	dbSNP_123	6	742,6910		41,660,3125	no	coding-synonymous	NUDT8	NM_181843.2		103,1298,4359	CC,CG,GG		9.6968,19.7001,13.0556		44/141	67397251	1504,10016	1934	3826	5760	SO:0001819	synonymous_variant	254552	exon1			CGCCGGGACCCCA	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.132C>G	11.37:g.67397251G>C		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_181843	Q6ZW59	Silent	SNP	ENST00000376693.2	37	CCDS58151.1																																																																																			G|0.869;C|0.131	0.131	strong		0.766	NUDT8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394036.1	NM_181843	
CAPN14	440854	hgsc.bcm.edu	37	2	31399988	31399988	+	Missense_Mutation	SNP	C	C	T	rs4592896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31399988C>T	ENST00000403897.3	-	20	2017	c.1876G>A	c.(1876-1878)Gtc>Atc	p.V626I	CAPN14_ENST00000444918.2_Missense_Mutation_p.V626I	NM_001145122.1	NP_001138594.1	A8MX76	CAN14_HUMAN	calpain 14	626	Domain IV.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|endometrium(2)|prostate(1)|skin(1)|stomach(2)	7						AGCTGACAGACGTCATCACTG	0.557													C|||	1826	0.364617	0.6278	0.4481	5008	,	,		17954	0.1736		0.2256	False		,,,				2504	0.2894				p.V626I		Atlas-SNP	.											.	CAPN14	36	.	0			c.G1876A						PASS	.	C	ILE/VAL	760,624		206,348,138	45.0	48.0	47.0		1876	2.4	0.0	2	dbSNP_111	47	711,2471		75,561,955	yes	missense	CAPN14	NM_001145122.1	29	281,909,1093	TT,TC,CC		22.3444,45.0867,32.2164	benign	626/685	31399988	1471,3095	692	1591	2283	SO:0001583	missense	440854	exon20			GACAGACGTCATC	AC015980	CCDS46254.1	2p23.1-p21	2013-01-10			ENSG00000214711	ENSG00000214711		"""EF-hand domain containing"""	16664	protein-coding gene	gene with protein product		610229				11675017	Standard	NM_001145122		Approved		uc010yms.2	A8MX76	OTTHUMG00000152039	ENST00000403897.3:c.1876G>A	2.37:g.31399988C>T	ENSP00000385247:p.Val626Ile	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	179	178	0.994413	NM_001145122	B3KRU9	Missense_Mutation	SNP	ENST00000403897.3	37	CCDS46254.1	725	0.33195970695970695	293	0.5955284552845529	151	0.4171270718232044	104	0.18181818181818182	177	0.23350923482849603	C	8.452	0.853364	0.17106	0.549133	0.223444	ENSG00000214711	ENST00000444918;ENST00000403897	T;T	0.29655	1.56;1.56	5.29	2.38	0.29361	EF-hand-like domain (1);	0.385688	0.21440	U	0.074519	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B	0.32350	0.251;0.366	B;B	0.21546	0.015;0.035	T	0.42498	-0.9448	9	0.30854	T	0.27	.	6.4197	0.21736	0.0:0.6626:0.0:0.3374	rs4592896;rs52814384;rs59685902;rs4592896	626;450	A8MX76;A8MX76-2	CAN14_HUMAN;.	I	626	ENSP00000398670:V626I;ENSP00000385247:V626I	ENSP00000385247:V626I	V	-	1	0	CAPN14	31253492	0.158000	0.22850	0.049000	0.19019	0.056000	0.15407	0.273000	0.18662	0.179000	0.19938	0.561000	0.74099	GTC	C|0.689;T|0.311	0.311	strong		0.557	CAPN14-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325010.1	NM_001145122	
CD33	945	hgsc.bcm.edu	37	19	51729594	51729594	+	Missense_Mutation	SNP	T	T	C	rs11882250|rs201473304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51729594T>C	ENST00000262262.4	+	4	748	c.727T>C	c.(727-729)Ttt>Ctt	p.F243L	CD33_ENST00000421133.2_Missense_Mutation_p.F116L|CD33_ENST00000391796.3_Missense_Mutation_p.F243L|CD33_ENST00000436584.2_Missense_Mutation_p.F116L	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	243			F -> L (in dbSNP:rs11882250).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	AACTGGTATCTTTCCAGGAGA	0.502													t|||	186	0.0371406	0.1271	0.0245	5008	,	,		18721	0.0		0.001	False		,,,				2504	0.0				p.F243L		Atlas-SNP	.											.	CD33	55	.	0			c.T727C						PASS	.	T	LEU/PHE,LEU/PHE,LEU/PHE	478,3928		26,426,1751	92.0	86.0	88.0		346,727,727	2.9	0.0	19	dbSNP_120	88	4,8596		0,4,4296	yes	missense,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	22,22,22	26,430,6047	CC,CT,TT		0.0465,10.8488,3.706	benign,benign,benign	116/238,243/311,243/365	51729594	482,12524	2203	4300	6503	SO:0001583	missense	945	exon4			GGTATCTTTCCAG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.727T>C	19.37:g.51729594T>C	ENSP00000262262:p.Phe243Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	64	0.029304029304029304	51	0.10365853658536585	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	.	9.409	1.079972	0.20309	0.108488	4.65E-4	ENSG00000105383	ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796	T;T;T;T	0.34667	1.35;2.53;1.55;2.36	2.88	2.88	0.33553	.	.	.	.	.	T	0.00496	0.0016	L	0.40543	1.245	0.80722	P	0.0	B;B;B	0.26975	0.066;0.165;0.048	B;B;B	0.23852	0.028;0.049;0.023	T	0.06935	-1.0799	8	0.33141	T	0.24	.	7.4754	0.27374	0.0:0.0:0.0:1.0	rs11882250;rs52835930;rs56510285;rs57266763;rs11882250	116;243;243	C9JEN7;F8WAL2;P20138	.;.;CD33_HUMAN	L	116;243;116;243	ENSP00000403331:F116L;ENSP00000262262:F243L;ENSP00000410126:F116L;ENSP00000375673:F243L	ENSP00000262262:F243L	F	+	1	0	CD33	56421406	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.212000	0.17497	1.322000	0.45245	0.379000	0.24179	TTT	T|0.958;C|0.042	0.042	strong		0.502	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
PDE3A	5139	hgsc.bcm.edu	37	12	20522487	20522487	+	Missense_Mutation	SNP	A	A	G	rs372953537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:20522487A>G	ENST00000359062.3	+	1	309	c.269A>G	c.(268-270)gAg>gGg	p.E90G	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	90					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	TGTGACCTGGAGCAGTGTAAG	0.716													A|||	5	0.000998403	0.0038	0.0	5008	,	,		11878	0.0		0.0	False		,,,				2504	0.0				p.E90G		Atlas-SNP	.											.	PDE3A	184	.	0			c.A269G						PASS	.	A	GLY/GLU	6,4166		0,6,2080	5.0	5.0	5.0		269	-0.0	0.5	12		5	0,8264		0,0,4132	no	missense	PDE3A	NM_000921.4	98	0,6,6212	GG,GA,AA		0.0,0.1438,0.0482	possibly-damaging	90/1142	20522487	6,12430	2086	4132	6218	SO:0001583	missense	5139	exon1			ACCTGGAGCAGTG		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.269A>G	12.37:g.20522487A>G	ENSP00000351957:p.Glu90Gly	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.182736	0.57800	0.001438	0.0	ENSG00000172572	ENST00000359062	T	0.64260	-0.09	5.03	-0.0284	0.13922	.	4.081800	0.00633	N	0.000487	T	0.46639	0.1403	N	0.19112	0.55	0.25845	N	0.984007	B	0.02656	0.0	B	0.01281	0.0	T	0.35871	-0.9771	10	0.59425	D	0.04	.	3.9386	0.09316	0.5223:0.1842:0.2935:0.0	.	90	Q14432	PDE3A_HUMAN	G	90	ENSP00000351957:E90G	ENSP00000351957:E90G	E	+	2	0	PDE3A	20413754	0.929000	0.31497	0.519000	0.27824	0.703000	0.40648	0.632000	0.24583	-0.019000	0.14055	0.449000	0.29647	GAG	.	.	weak		0.716	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		
ITPR2	3709	hgsc.bcm.edu	37	12	26774089	26774089	+	Missense_Mutation	SNP	T	T	G	rs2230373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26774089T>G	ENST00000381340.3	-	26	3845	c.3429A>C	c.(3427-3429)gaA>gaC	p.E1143D	RP11-666F17.1_ENST00000414098.2_RNA|ITPR2_ENST00000545902.1_5'Flank	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1143			E -> D (in dbSNP:rs16931091).		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)	TCACTTGACTTTCCCCTATTT	0.413													T|||	203	0.0405351	0.149	0.0072	5008	,	,		18812	0.0		0.001	False		,,,				2504	0.0				p.E1143D		Atlas-SNP	.											.	ITPR2	270	.	0			c.A3429C						PASS	.	T	ASP/GLU	488,3302		24,440,1431	380.0	359.0	366.0		3429	-0.8	0.6	12	dbSNP_123	366	1,8249		0,1,4124	yes	missense	ITPR2	NM_002223.2	45	24,441,5555	GG,GT,TT		0.0121,12.876,4.0615	benign	1143/2702	26774089	489,11551	1895	4125	6020	SO:0001583	missense	3709	exon26			TTGACTTTCCCCT	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.3429A>C	12.37:g.26774089T>G	ENSP00000370744:p.Glu1143Asp	Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	281	139	0.494662	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	82	0.037545787545787544	81	0.16463414634146342	1	0.0027624309392265192	0	0.0	0	0.0	T	9.713	1.157689	0.21454	0.12876	1.21E-4	ENSG00000123104	ENST00000381340	D	0.91996	-2.95	4.36	-0.782	0.10961	.	0.222293	0.40554	N	0.001063	T	0.00754	0.0025	N	0.05574	-0.02	0.31748	P	0.634949	B	0.02656	0.0	B	0.01281	0.0	T	0.23726	-1.0180	9	0.14656	T	0.56	.	1.8975	0.03261	0.1237:0.3347:0.2527:0.2889	rs16931091;rs56635647;rs16931091	1143	Q14571	ITPR2_HUMAN	D	1143	ENSP00000370744:E1143D	ENSP00000370744:E1143D	E	-	3	2	ITPR2	26665356	0.003000	0.15002	0.552000	0.28243	0.721000	0.41392	-0.083000	0.11286	-0.216000	0.10048	0.454000	0.30748	GAA	T|0.944;G|0.056	0.056	strong		0.413	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
PLA2G4E	123745	hgsc.bcm.edu	37	15	42289456	42289456	+	Splice_Site	SNP	G	G	C	rs79040960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42289456G>C	ENST00000399518.3	-	11	1462	c.976C>G	c.(976-978)Cct>Gct	p.P326A	PLA2G4E_ENST00000413860.2_Splice_Site_p.P297A|CTD-2382E5.1_ENST00000499478.2_RNA	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	314	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)		AGTGTCTCAGGGCTGGAGGGA	0.607													G|||	125	0.0249601	0.0885	0.0115	5008	,	,		19005	0.0		0.0	False		,,,				2504	0.0				p.P326A		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.C976G						PASS	.	G	ALA/PRO	214,3522		2,210,1656	11.0	14.0	13.0		976	-0.7	0.2	15	dbSNP_131	13	2,7470		0,2,3734	yes	missense-near-splice	PLA2G4E	NM_001206670.1	27	2,212,5390	CC,CG,GG		0.0268,5.7281,1.9272	benign	326/869	42289456	216,10992	1868	3736	5604	SO:0001630	splice_region_variant	123745	exon11			TCTCAGGGCTGGA		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.975-1C>G	15.37:g.42289456G>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_001206670	Q6ZSC0	Missense_Mutation	SNP	ENST00000399518.3	37	CCDS55962.1	33	0.01510989010989011	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	0	0.0	G	12.97	2.097162	0.37048	0.057281	2.68E-4	ENSG00000188089	ENST00000399518;ENST00000413860	T;T	0.01599	4.86;4.74	5.68	-0.726	0.11170	.	0.499688	0.17527	U	0.171007	T	0.00356	0.0011	M	0.72118	2.19	0.22656	N	0.998886	B	0.32731	0.382	B	0.32677	0.15	T	0.37033	-0.9723	10	0.51188	T	0.08	-4.1952	10.0101	0.41981	0.4735:0.0:0.5265:0.0	.	297	C9JK77	.	A	326;297	ENSP00000382434:P326A;ENSP00000413897:P297A	ENSP00000382434:P326A	P	-	1	0	PLA2G4E	40076748	0.130000	0.22417	0.193000	0.23327	0.022000	0.10575	-0.429000	0.06982	0.048000	0.15891	-0.251000	0.11542	CCT	G|0.982;C|0.018	0.018	strong		0.607	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442	Missense_Mutation
FBXO39	162517	hgsc.bcm.edu	37	17	6690161	6690161	+	Silent	SNP	C	C	T	rs17853331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:6690161C>T	ENST00000321535.4	+	3	1216	c.1086C>T	c.(1084-1086)atC>atT	p.I362I		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	362										NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	26						ACCTCCTCATCATATCCTGCA	0.463													C|||	1544	0.308307	0.1944	0.3026	5008	,	,		18317	0.5823		0.2038	False		,,,				2504	0.2914				p.I362I		Atlas-SNP	.											.	FBXO39	50	.	0			c.C1086T						PASS	.	C		844,3562	333.1+/-302.8	95,654,1454	110.0	97.0	102.0		1086	3.5	1.0	17	dbSNP_123	102	1817,6783	326.6+/-317.4	195,1427,2678	no	coding-synonymous	FBXO39	NM_153230.2		290,2081,4132	TT,TC,CC		21.1279,19.1557,20.4598		362/443	6690161	2661,10345	2203	4300	6503	SO:0001819	synonymous_variant	162517	exon3			CCTCATCATATCC	BC034782	CCDS11082.1	17p13.2	2014-01-21			ENSG00000177294	ENSG00000177294		"""F-boxes /  ""other"""""	28565	protein-coding gene	gene with protein product		609106				12477932	Standard	NM_153230		Approved	MGC35179, Fbx39, CT144	uc010vtg.2	Q8N4B4	OTTHUMG00000102062	ENST00000321535.4:c.1086C>T	17.37:g.6690161C>T		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	212	104	0.490566	NM_153230		Silent	SNP	ENST00000321535.4	37	CCDS11082.1																																																																																			C|0.771;T|0.229	0.229	strong		0.463	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230	
ZP4	57829	hgsc.bcm.edu	37	1	238049143	238049143	+	Missense_Mutation	SNP	G	G	A	rs34811980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:238049143G>A	ENST00000366570.4	-	7	1041	c.883C>T	c.(883-885)Cca>Tca	p.P295S	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	295	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		P -> S (in dbSNP:rs34811980).		acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			ACATTGATTGGGAGAGAGTTG	0.502													G|||	157	0.0313498	0.1112	0.013	5008	,	,		18469	0.0		0.001	False		,,,				2504	0.0				p.P295S	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.C883T						PASS	.	G	SER/PRO	393,4013	196.4+/-220.7	14,365,1824	167.0	161.0	163.0		883	4.8	0.1	1	dbSNP_126	163	6,8594	4.3+/-15.6	0,6,4294	yes	missense	ZP4	NM_021186.3	74	14,371,6118	AA,AG,GG		0.0698,8.9197,3.0678	probably-damaging	295/541	238049143	399,12607	2203	4300	6503	SO:0001583	missense	57829	exon7			TGATTGGGAGAGA	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.883C>T	1.37:g.238049143G>A	ENSP00000355529:p.Pro295Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	18.15	3.560913	0.65538	0.089197	6.98E-4	ENSG00000116996	ENST00000366570	T	0.81163	-1.46	4.85	4.85	0.62838	Zona pellucida sperm-binding protein (3);	0.124427	0.53938	D	0.000041	T	0.13841	0.0335	M	0.70275	2.135	0.09310	N	1	D	0.76494	0.999	D	0.74023	0.982	T	0.48514	-0.9029	10	0.34782	T	0.22	-14.4465	10.7036	0.45942	0.0:0.0:0.8094:0.1905	rs34811980	295	Q12836	ZP4_HUMAN	S	295	ENSP00000355529:P295S	ENSP00000355529:P295S	P	-	1	0	ZP4	236115766	0.999000	0.42202	0.076000	0.20297	0.635000	0.38103	3.598000	0.54038	2.242000	0.73789	0.650000	0.86243	CCA	G|0.973;A|0.027	0.027	strong		0.502	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
PHPT1	29085	hgsc.bcm.edu	37	9	139745012	139745012	+	Intron	SNP	G	G	T	rs149543778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139745012G>T	ENST00000247665.10	+	3	622				MAMDC4_ENST00000317446.2_5'Flank|MAMDC4_ENST00000445819.1_5'Flank|PHPT1_ENST00000545326.1_Splice_Site_p.G114C|PHPT1_ENST00000371661.1_Splice_Site_p.G114C|PHPT1_ENST00000492540.1_3'UTR	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1						negative regulation of ATP citrate synthase activity (GO:2000984)|negative regulation of lyase activity (GO:0051350)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-histidine dephosphorylation (GO:0035971)|positive regulation of cell motility (GO:2000147)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|protein dephosphorylation (GO:0006470)|regulation of actin cytoskeleton reorganization (GO:2000249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium channel inhibitor activity (GO:0019855)|ion channel binding (GO:0044325)|phosphohistidine phosphatase activity (GO:0008969)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|large_intestine(1)|lung(1)	3	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CCACCATCAAGGTTTGCTTGC	0.637													G|||	26	0.00519169	0.0159	0.0072	5008	,	,		18692	0.0		0.0	False		,,,				2504	0.0				p.G114C		Atlas-SNP	.											.	PHPT1	14	.	0			c.G340T						PASS	.	G	CYS/GLY,	37,3091		0,37,1527	37.0	38.0	38.0		340,	1.5	0.0	9	dbSNP_134	38	0,7150		0,0,3575	yes	missense-near-splice,intron	PHPT1	NM_001135861.1,NM_014172.4	159,	0,37,5102	TT,TG,GG		0.0,1.1829,0.36	,	114/125,	139745012	37,10241	1564	3575	5139	SO:0001627	intron_variant	29085	exon3			CATCAAGGTTTGC	AF131857	CCDS7009.1, CCDS48060.1	9q34.3	2008-02-05			ENSG00000054148	ENSG00000054148	3.1.3.-		30033	protein-coding gene	gene with protein product	"""phosphohistidine phosphatase 14kDa"", "" sex-regulated protein janus-a"""	610167				11042152, 8619474	Standard	NM_014172		Approved	PHP14, HSPC141, CGI-202, DKFZp564M173, bA216L13.10	uc004cjq.4	Q9NRX4	OTTHUMG00000020950	ENST00000247665.10:c.286-195G>T	9.37:g.139745012G>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	36	0.590164	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Missense_Mutation	SNP	ENST00000247665.10	37	CCDS7009.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	.	11.23	1.576676	0.28092	0.011829	0.0	ENSG00000054148	ENST00000371661;ENST00000545326	.	.	.	1.54	1.54	0.23209	.	.	.	.	.	T	0.54549	0.1865	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.41875	-0.9484	7	0.54805	T	0.06	.	9.0668	0.36469	0.0:0.0:1.0:0.0	.	114	Q9NRX4-2	.	C	114	.	ENSP00000360724:G114C	G	+	1	0	PHPT1	138864833	0.000000	0.05858	0.002000	0.10522	0.044000	0.14063	0.167000	0.16602	1.174000	0.42811	0.462000	0.41574	GGC	G|0.996;T|0.004	0.004	strong		0.637	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172	
PRSS35	167681	hgsc.bcm.edu	37	6	84233325	84233325	+	Silent	SNP	G	G	A	rs147168330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84233325G>A	ENST00000369700.3	+	2	342	c.165G>A	c.(163-165)aaG>aaA	p.K55K	PRSS35_ENST00000536636.1_Silent_p.K55K	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	55						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)		CAGATGCTAAGATGATGGTAA	0.453													G|||	19	0.00379393	0.0144	0.0	5008	,	,		18836	0.0		0.0	False		,,,				2504	0.0				p.K55K		Atlas-SNP	.											.	PRSS35	60	.	0			c.G165A						PASS	.	G	,	32,4374	38.4+/-70.7	0,32,2171	129.0	127.0	128.0		165,165	2.0	0.0	6	dbSNP_134	128	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PRSS35	NM_001170423.1,NM_153362.2	,	0,32,6471	AA,AG,GG		0.0,0.7263,0.246	,	55/414,55/414	84233325	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	167681	exon2			TGCTAAGATGATG	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.165G>A	6.37:g.84233325G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	198	84	0.424242	NM_153362	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	37	CCDS4999.1																																																																																			G|0.997;A|0.003	0.003	strong		0.453	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362	
SLC5A9	200010	hgsc.bcm.edu	37	1	48697713	48697713	+	Missense_Mutation	SNP	C	C	T	rs140292897	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:48697713C>T	ENST00000438567.2	+	7	839	c.787C>T	c.(787-789)Cgg>Tgg	p.R263W	SLC5A9_ENST00000420136.2_Intron|RP5-1024N4.4_ENST00000606809.1_RNA|SLC5A9_ENST00000533824.1_Missense_Mutation_p.R284W|SLC5A9_ENST00000236495.5_Missense_Mutation_p.R288W	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	263					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						TCACCTCCCACGGCCCGATGC	0.617													C|||	7	0.00139776	0.0045	0.0	5008	,	,		20299	0.0		0.001	False		,,,				2504	0.0				p.R288W		Atlas-SNP	.											.	SLC5A9	82	.	0			c.C862T						PASS	.	C	TRP/ARG,TRP/ARG	27,4379	34.3+/-65.2	0,27,2176	124.0	113.0	117.0		787,862	5.0	0.8	1	dbSNP_134	117	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	SLC5A9	NM_001011547.2,NM_001135181.1	101,101	0,30,6473	TT,TC,CC		0.0349,0.6128,0.2307	probably-damaging,probably-damaging	263/682,288/707	48697713	30,12976	2203	4300	6503	SO:0001583	missense	200010	exon8			CTCCCACGGCCCG	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.787C>T	1.37:g.48697713C>T	ENSP00000401730:p.Arg263Trp	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	233	232	0.995708	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	28.2	4.897309	0.91962	0.006128	3.49E-4	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	D;D;D	0.89415	-2.46;-2.44;-2.51	5.95	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.94401	0.8199	M	0.93420	3.415	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.94931	0.8082	10	0.87932	D	0	.	15.4795	0.75514	0.1395:0.8605:0.0:0.0	.	284;263;288	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	W	284;263;288	ENSP00000431900:R284W;ENSP00000401730:R263W;ENSP00000236495:R288W	ENSP00000236495:R288W	R	+	1	2	SLC5A9	48470300	0.998000	0.40836	0.828000	0.32881	0.985000	0.73830	3.906000	0.56340	1.485000	0.48380	0.563000	0.77884	CGG	C|0.998;T|0.002	0.002	strong		0.617	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
FER	2241	hgsc.bcm.edu	37	5	108294979	108294979	+	Silent	SNP	T	T	C	rs34869483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:108294979T>C	ENST00000281092.4	+	13	1971	c.1587T>C	c.(1585-1587)gaT>gaC	p.D529D	FER_ENST00000438717.2_Silent_p.D354D|FER_ENST00000536402.1_3'UTR	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	529	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		AACTTATAGATCATCACTATA	0.363													T|||	30	0.00599042	0.0015	0.0043	5008	,	,		15833	0.0		0.0119	False		,,,				2504	0.0133				p.D529D	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.T1587C						PASS	.	T		14,4390	21.2+/-45.6	0,14,2188	138.0	131.0	133.0		1587	-7.7	0.9	5	dbSNP_126	133	193,8405	84.8+/-147.2	4,185,4110	no	coding-synonymous	FER	NM_005246.2		4,199,6298	CC,CT,TT		2.2447,0.3179,1.5921		529/823	108294979	207,12795	2202	4299	6501	SO:0001819	synonymous_variant	2241	exon13			TATAGATCATCAC	J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	3655	protein-coding gene	gene with protein product	"""phosphoprotein NCP94"", ""protein phosphatase 1, regulatory subunit 74"""	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.1587T>C	5.37:g.108294979T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	112	44	0.392857	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	37	CCDS4098.1																																																																																			T|0.988;C|0.012	0.012	strong		0.363	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
ADAM8	101	hgsc.bcm.edu	37	10	135077265	135077265	+	Missense_Mutation	SNP	A	A	G	rs3008319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135077265A>G	ENST00000445355.3	-	22	2374	c.2324T>C	c.(2323-2325)aTc>aCc	p.I775T	ADAM8_ENST00000415217.3_Silent_p.H719H|ADAM8_ENST00000485491.2_Intron	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	775			I -> T (in dbSNP:rs3008319).		activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)	p.I775T(1)		central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		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)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		CGTTGGCTTGATGACCTGGGA	0.642													A|||	341	0.0680911	0.2421	0.0288	5008	,	,		15527	0.0		0.001	False		,,,				2504	0.0				p.I775T		Atlas-SNP	.											ADAM8,NS,carcinoma,0,1	ADAM8	41	1	1	Substitution - Missense(1)	prostate(1)	c.T2324C						PASS	.	A	THR/ILE,,	990,3408		102,786,1311	41.0	39.0	40.0		2324,2157,	1.0	0.1	10	dbSNP_101	40	12,8580		0,12,4284	yes	missense,coding-synonymous,intron	ADAM8	NM_001109.4,NM_001164489.1,NM_001164490.1	89,,	102,798,5595	GG,GA,AA		0.1397,22.5102,7.7136	benign,,	775/825,719/743,	135077265	1002,11988	2199	4296	6495	SO:0001583	missense	101	exon22			GGCTTGATGACCT	D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	215	protein-coding gene	gene with protein product		602267	"""a disintegrin and metalloproteinase domain 8"""			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.2324T>C	10.37:g.135077265A>G	ENSP00000453302:p.Ile775Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	52	22	0.423077	NM_001109	B4DVM6|H0YL36|H0YLR0|H0YN39	Missense_Mutation	SNP	ENST00000445355.3	37	CCDS31319.2																																																																																			A|0.917;G|0.083	0.083	strong		0.642	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109	
MICA	100507436	hgsc.bcm.edu	37	6	31380194	31380194	+	Missense_Mutation	SNP	T	T	C	rs41554412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31380194T>C	ENST00000449934.2	+	5	1039	c.985T>C	c.(985-987)Tgt>Cgt	p.C329R	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)				TTATTTTCTATGTCCGTTGTT	0.468													t|||	1266	0.252796	0.3616	0.2853	5008	,	,		18607	0.1776		0.1779	False		,,,				2504	0.2372				p.C329R		Atlas-SNP	.											MICA,NS,carcinoma,-2,1	MICA	21	1	0			c.T985C						PASS	.						163.0	154.0	156.0					6																	31380194		692	1591	2283	SO:0001583	missense	100507436	exon5			TTTCTATGTCCGT	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.985T>C	6.37:g.31380194T>C	ENSP00000413079:p.Cys329Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	528	0.24175824175824176	172	0.34959349593495936	113	0.31215469613259667	94	0.16433566433566432	149	0.19656992084432717	-	7.095	0.572964	0.13623	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.01438	5.44;4.89	1.49	0.201	0.15186	.	.	.	.	.	T	0.01029	0.0034	L	0.34521	1.04	0.80722	P	0.0	D;D	0.63046	0.992;0.992	P;P	0.59703	0.74;0.862	T	0.54098	-0.8344	8	0.87932	D	0	.	3.6509	0.08203	0.3419:0.0:0.0:0.6581	rs41554412;rs61738276	191;329	Q5SS58;Q96QC4	.;.	R	191;329;286;329;220	ENSP00000413079:C329R;ENSP00000402410:C220R	ENSP00000365394:C329R	C	+	1	0	MICA	31488173	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.397000	0.07269	0.086000	0.17137	0.310000	0.20435	TGT	T|0.773;C|0.227	0.227	strong		0.468	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
MYH15	22989	hgsc.bcm.edu	37	3	108147543	108147543	+	Silent	SNP	C	C	A	rs61745179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108147543C>A	ENST00000273353.3	-	28	3614	c.3558G>T	c.(3556-3558)ctG>ctT	p.L1186L		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1186						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						TGTCTCGGTGCAGCTTCTGGA	0.507													C|||	262	0.0523163	0.0696	0.0504	5008	,	,		18064	0.0		0.0915	False		,,,				2504	0.044				p.L1186L		Atlas-SNP	.											.	MYH15	223	.	0			c.G3558T						PASS	.	C		240,3694		4,232,1731	138.0	134.0	135.0		3558	1.3	0.1	3	dbSNP_129	135	694,7632		30,634,3499	no	coding-synonymous	MYH15	NM_014981.1		34,866,5230	AA,AC,CC		8.3353,6.1007,7.6183		1186/1947	108147543	934,11326	1967	4163	6130	SO:0001819	synonymous_variant	22989	exon28			TCGGTGCAGCTTC	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.3558G>T	3.37:g.108147543C>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	232	125	0.538793	NM_014981		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																			C|0.934;A|0.066	0.066	strong		0.507	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
ARFGEF1	10565	hgsc.bcm.edu	37	8	68178397	68178397	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:68178397G>A	ENST00000262215.3	-	14	2356	c.1967C>T	c.(1966-1968)cCt>cTt	p.P656L	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.P110L	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	656					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)	p.P656H(1)		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)			TATTGTCTCAGGGTGTTTGAT	0.373																																					p.P656L		Atlas-SNP	.											ARFGEF1,NS,carcinoma,0,1	ARFGEF1	196	1	1	Substitution - Missense(1)	endometrium(1)	c.C1967T						scavenged	.						133.0	123.0	127.0					8																	68178397		2202	4300	6502	SO:0001583	missense	10565	exon14			GTCTCAGGGTGTT	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.1967C>T	8.37:g.68178397G>A	ENSP00000262215:p.Pro656Leu	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	303	4	0.0132013	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.746050	0.49151	.	.	ENSG00000066777	ENST00000520381;ENST00000262215	T;T	0.20738	2.92;2.05	5.83	5.83	0.93111	Armadillo-type fold (1);	0.106577	0.64402	D	0.000003	T	0.12860	0.0312	N	0.04820	-0.15	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.20672	-1.0268	10	0.17832	T	0.49	.	20.1099	0.97909	0.0:0.0:1.0:0.0	.	656;110	Q9Y6D6;E5RIF2	BIG1_HUMAN;.	L	110;656	ENSP00000428429:P110L;ENSP00000262215:P656L	ENSP00000262215:P656L	P	-	2	0	ARFGEF1	68340951	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.771000	0.98977	2.753000	0.94483	0.585000	0.79938	CCT	.	.	none		0.373	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421	
ZFPM2	23414	hgsc.bcm.edu	37	8	106815517	106815517	+	Silent	SNP	C	C	T	rs11995760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:106815517C>T	ENST00000407775.2	+	8	3457	c.3207C>T	c.(3205-3207)caC>caT	p.H1069H	ZFPM2_ENST00000520492.1_Silent_p.H937H|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000521622.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000509144.2_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000520433.1_RNA|ZFPM2_ENST00000517361.1_Silent_p.H937H|ZFPM2_ENST00000378472.4_Silent_p.H800H|RP11-152P17.2_ENST00000520594.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	1069					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			ATCCTCAGCACGAAGACGACC	0.478													T|||	628	0.125399	0.3858	0.0548	5008	,	,		18650	0.0069		0.0288	False		,,,				2504	0.045				p.H1069H		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C3207T						PASS	.	T		1181,2705		171,839,933	67.0	66.0	66.0		3207	-4.7	0.3	8	dbSNP_120	66	196,8078		3,190,3944	no	coding-synonymous	ZFPM2	NM_012082.3		174,1029,4877	TT,TC,CC		2.3689,30.3911,11.324		1069/1152	106815517	1377,10783	1943	4137	6080	SO:0001819	synonymous_variant	23414	exon8			TCAGCACGAAGAC	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.3207C>T	8.37:g.106815517C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	135	56	0.414815	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Silent	SNP	ENST00000407775.2	37	CCDS47908.1																																																																																			C|0.884;T|0.116	0.116	strong		0.478	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
NES	10763	hgsc.bcm.edu	37	1	156641537	156641537	+	Missense_Mutation	SNP	C	C	T	rs951781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156641537C>T	ENST00000368223.3	-	4	2575	c.2443G>A	c.(2443-2445)Gta>Ata	p.V815I		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	815	Tail.		V -> I (in dbSNP:rs951781). {ECO:0000269|PubMed:12880961}.		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)	p.V815I(1)		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)					ACTGCCTCTACGCTCTCTTCT	0.418													C|||	1023	0.204273	0.0363	0.2738	5008	,	,		19193	0.12		0.3439	False		,,,				2504	0.3252				p.V815I		Atlas-SNP	.											NES,NS,carcinoma,0,1	NES	196	1	1	Substitution - Missense(1)	stomach(1)	c.G2443A						scavenged	.	C	ILE/VAL	401,4005	199.1+/-222.7	19,363,1821	105.0	96.0	99.0		2443	-4.9	0.0	1	dbSNP_92	99	3050,5550	468.2+/-367.2	579,1892,1829	yes	missense	NES	NM_006617.1	29	598,2255,3650	TT,TC,CC		35.4651,9.1012,26.5339	benign	815/1622	156641537	3451,9555	2203	4300	6503	SO:0001583	missense	10763	exon4			CCTCTACGCTCTC	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.2443G>A	1.37:g.156641537C>T	ENSP00000357206:p.Val815Ile	Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	189	94	0.497355	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	37	CCDS1151.1	460	0.21062271062271062	18	0.036585365853658534	105	0.2900552486187845	73	0.12762237762237763	264	0.3482849604221636	C	11.39	1.624057	0.28889	0.091012	0.354651	ENSG00000132688	ENST00000368223	D	0.85258	-1.96	5.4	-4.93	0.03066	.	1.551100	0.04567	N	0.392662	T	0.58991	0.2161	L	0.38838	1.175	0.80722	P	0.0	B	0.18166	0.026	B	0.04013	0.001	T	0.52238	-0.8602	9	0.38643	T	0.18	.	7.4335	0.27141	0.0:0.2352:0.1919:0.5728	rs951781;rs17393839;rs57478265;rs951781	815	P48681	NEST_HUMAN	I	815	ENSP00000357206:V815I	ENSP00000357206:V815I	V	-	1	0	NES	154908161	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-1.666000	0.01963	-0.441000	0.07201	-0.251000	0.11542	GTA	C|0.783;T|0.217	0.217	strong		0.418	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
LY75	4065	hgsc.bcm.edu	37	2	160737717	160737717	+	Silent	SNP	G	G	A	rs79199281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160737717G>A	ENST00000263636.4	-	8	1308	c.1281C>T	c.(1279-1281)aaC>aaT	p.N427N	LY75-CD302_ENST00000505052.1_Silent_p.N427N|LY75_ENST00000554112.1_Silent_p.N427N|LY75-CD302_ENST00000504764.1_Silent_p.N427N|LY75_ENST00000553424.1_Silent_p.N427N	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	427	C-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GTATGTTTATGTTCTTAAGGC	0.323													G|||	26	0.00519169	0.0197	0.0	5008	,	,		19352	0.0		0.0	False		,,,				2504	0.0				p.N427N		Atlas-SNP	.											.	LY75	151	.	0			c.C1281T						PASS	.	G	,,	59,4347	58.1+/-94.6	0,59,2144	177.0	164.0	168.0		1281,1281,1281	1.9	1.0	2	dbSNP_131	168	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	0,59,6444	AA,AG,GG		0.0,1.3391,0.4536	,,	427/1874,427/1818,427/1723	160737717	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon8			GTTTATGTTCTTA	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.1281C>T	2.37:g.160737717G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	89	23	0.258427	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			G|0.994;A|0.006	0.006	strong		0.323	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
BANK1	55024	hgsc.bcm.edu	37	4	102751276	102751276	+	Silent	SNP	C	C	T	rs10516486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:102751276C>T	ENST00000322953.4	+	2	656	c.382C>T	c.(382-384)Cta>Tta	p.L128L	BANK1_ENST00000508653.1_Intron|BANK1_ENST00000444316.2_Silent_p.L98L|BANK1_ENST00000428908.1_Intron|BANK1_ENST00000504592.1_Silent_p.L113L	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	128	Interaction with ITPR2.				B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		CTATGAATTACTAAATATCTC	0.373													T|||	2706	0.540335	0.7564	0.4813	5008	,	,		15791	0.504		0.3887	False		,,,				2504	0.4836				p.L128L		Atlas-SNP	.											.	BANK1	95	.	0			c.C382T						PASS	.	T	,,	3056,1350	427.2+/-341.4	1066,924,213	59.0	66.0	64.0		292,,382	-0.0	0.0	4	dbSNP_119	64	3299,5301	642.6+/-399.8	632,2035,1633	no	coding-synonymous,intron,coding-synonymous	BANK1	NM_001083907.2,NM_001127507.2,NM_017935.4	,,	1698,2959,1846	TT,TC,CC		38.3605,30.64,48.8621	,,	98/756,,128/786	102751276	6355,6651	2203	4300	6503	SO:0001819	synonymous_variant	55024	exon2			GAATTACTAAATA	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"""Ankyrin repeat domain containing"""	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.382C>T	4.37:g.102751276C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	68	25	0.367647	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Silent	SNP	ENST00000322953.4	37	CCDS34038.1																																																																																			C|0.514;T|0.486	0.486	strong		0.373	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	
MT-ND4	4538	hgsc.bcm.edu	37	M	11164	11164	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11164A>G	ENST00000361381.2	+	1	405	c.405A>G	c.(403-405)cgA>cgG	p.R135R	MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	135					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						ATCATCACCCGATGAGGCAAC	0.443																																					p.R135R		Atlas-SNP	.											.	.	.	.	0			c.A405G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CACCCGATGAGGC			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.405A>G	M.37:g.11164A>G		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.443	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
MUC17	140453	hgsc.bcm.edu	37	7	100678988	100678988	+	Missense_Mutation	SNP	G	G	A	rs71286276		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678988G>A	ENST00000306151.4	+	3	4355	c.4291G>A	c.(4291-4293)Gct>Act	p.A1431T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1431	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.A1431T(1)		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)					GACCACTTCTGCTGAAGCCAC	0.488																																					p.A1431T		Atlas-SNP	.											MUC17,NS,carcinoma,0,2	MUC17	804	2	1	Substitution - Missense(1)	kidney(1)	c.G4291A						scavenged	.						207.0	222.0	217.0					7																	100678988		2203	4300	6503	SO:0001583	missense	140453	exon3			ACTTCTGCTGAAG	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.4291G>A	7.37:g.100678988G>A	ENSP00000302716:p.Ala1431Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	135	5	0.037037	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	3.722	-0.057377	0.07317	.	.	ENSG00000169876	ENST00000306151	T	0.02656	4.21	0.982	-0.425	0.12317	.	.	.	.	.	T	0.01558	0.0050	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48779	-0.9005	9	0.02654	T	1	.	4.4511	0.11621	0.488:0.0:0.512:0.0	.	1431	Q685J3	MUC17_HUMAN	T	1431	ENSP00000302716:A1431T	ENSP00000302716:A1431T	A	+	1	0	MUC17	100465708	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-2.968000	0.00669	-0.790000	0.04492	-1.616000	0.00795	GCT	.	.	none		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CACNA2D3	55799	hgsc.bcm.edu	37	3	55108149	55108149	+	Silent	SNP	A	A	G	rs17054785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:55108149A>G	ENST00000474759.1	+	38	3240	c.3192A>G	c.(3190-3192)gcA>gcG	p.A1064A	CACNA2D3_ENST00000490478.1_Silent_p.A970A|CACNA2D3_ENST00000478261.1_3'UTR|CACNA2D3_ENST00000415676.2_Silent_p.A1064A|CACNA2D3_ENST00000288197.5_Silent_p.A1064A	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	1064						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)	AGGAGAATGCAAGGGAGTGTG	0.537													A|||	505	0.100839	0.174	0.0965	5008	,	,		18872	0.0		0.1541	False		,,,				2504	0.0542				p.A1064A		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.A3192G						PASS	.	A		692,3350		67,558,1396	122.0	120.0	121.0		3192	-10.0	0.4	3	dbSNP_123	121	1254,7058		97,1060,2999	no	coding-synonymous	CACNA2D3	NM_018398.2		164,1618,4395	GG,GA,AA		15.0866,17.1202,15.752		1064/1092	55108149	1946,10408	2021	4156	6177	SO:0001819	synonymous_variant	55799	exon38			GAATGCAAGGGAG	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.3192A>G	3.37:g.55108149A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_018398	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	37	CCDS54598.1																																																																																			A|0.895;G|0.105	0.105	strong		0.537	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		
FCGBP	8857	hgsc.bcm.edu	37	19	40363926	40363926	+	Missense_Mutation	SNP	C	C	G	rs3746013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40363926C>G	ENST00000221347.6	-	31	14723	c.14716G>C	c.(14716-14718)Gat>Cat	p.D4906H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4906	VWFD 12. {ECO:0000255|PROSITE- ProRule:PRU00580}.		D -> H (in dbSNP:rs3746013). {ECO:0000269|PubMed:9182547}.			extracellular vesicular exosome (GO:0070062)		p.D4906H(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)			CGTTGGAGATCTCCAGCTGCA	0.597													C|||	1444	0.288339	0.23	0.1614	5008	,	,		21074	0.5387		0.1998	False		,,,				2504	0.2904				p.D4906H		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	stomach(1)	c.G14716C						PASS	.	C	HIS/ASP	1012,3394	376.8+/-322.2	113,786,1304	95.0	77.0	83.0		14716	-1.0	0.0	19	dbSNP_107	83	1829,6771	327.7+/-318.0	189,1451,2660	yes	missense	FCGBP	NM_003890.2	81	302,2237,3964	GG,GC,CC		21.2674,22.9687,21.8438	probably-damaging	4906/5406	40363926	2841,10165	2203	4300	6503	SO:0001583	missense	8857	exon31			GGAGATCTCCAGC	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.14716G>C	19.37:g.40363926C>G	ENSP00000221347:p.Asp4906His	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	146	52	0.356164	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	648	0.2967032967032967	109	0.22154471544715448	63	0.17403314917127072	321	0.5611888111888111	155	0.20448548812664907	C	9.033	0.987678	0.18966	0.229687	0.212674	ENSG00000090920	ENST00000221347	T	0.59502	0.26	5.34	-1.04	0.10068	von Willebrand factor, type D domain (3);	0.249576	0.34046	U	0.004304	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	D	0.69078	0.997	D	0.74674	0.984	T	0.45571	-0.9252	9	0.14656	T	0.56	.	6.206	0.20604	0.0:0.5518:0.2287:0.2194	rs3746013;rs61020961;rs3746013	4906	Q9Y6R7	FCGBP_HUMAN	H	4906	ENSP00000221347:D4906H	ENSP00000221347:D4906H	D	-	1	0	FCGBP	45055766	0.000000	0.05858	0.005000	0.12908	0.014000	0.08584	0.392000	0.20801	-0.030000	0.13804	0.313000	0.20887	GAT	C|0.746;G|0.254	0.254	strong		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF512	84450	hgsc.bcm.edu	37	2	27838058	27838058	+	Silent	SNP	C	C	A	rs11127071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27838058C>A	ENST00000355467.4	+	11	1238	c.1155C>A	c.(1153-1155)ctC>ctA	p.L385L	ZNF512_ENST00000556601.1_Silent_p.L254L|ZNF512_ENST00000379717.1_Silent_p.L384L|ZNF512_ENST00000416005.2_Silent_p.L356L|ZNF512_ENST00000413371.2_Silent_p.L308L|RP11-158I13.2_ENST00000505973.1_RNA	NM_001271287.1|NM_001271288.1|NM_001271289.1|NM_001271318.1|NM_032434.3	NP_001258216.1|NP_001258217.1|NP_001258218.1|NP_001258247.1|NP_115810.2	Q96ME7	ZN512_HUMAN	zinc finger protein 512	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)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)					GTCCAGGGCTCCCTACCTTCA	0.378													A|||	3269	0.652756	0.7148	0.6873	5008	,	,		17541	0.8452		0.497	False		,,,				2504	0.5061				p.L385L		Atlas-SNP	.											.	ZNF512	54	.	0			c.C1155A						PASS	.	A		2965,1441	466.0+/-354.4	979,1007,217	176.0	168.0	170.0		1155	-6.0	0.4	2	dbSNP_120	170	4252,4348	581.1+/-391.2	1064,2124,1112	no	coding-synonymous	ZNF512	NM_032434.2		2043,3131,1329	AA,AC,CC		49.4419,32.7054,44.5102		385/568	27838058	7217,5789	2203	4300	6503	SO:0001819	synonymous_variant	84450	exon11			AGGGCTCCCTACC	AL833748	CCDS1758.1, CCDS59428.1, CCDS59429.1	2p23	2008-02-05			ENSG00000243943	ENSG00000243943		"""Zinc fingers, C2H2-type"""	29380	protein-coding gene	gene with protein product						11347906	Standard	NM_032434		Approved	KIAA1805	uc002rla.4	Q96ME7	OTTHUMG00000097786	ENST00000355467.4:c.1155C>A	2.37:g.27838058C>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_032434	B4DSM5|Q53RZ7|Q86XK6|Q96JM0	Silent	SNP	ENST00000355467.4	37	CCDS1758.1																																																																																			C|0.399;A|0.601	0.601	strong		0.378	ZNF512-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215029.2	NM_032434	
RREB1	6239	hgsc.bcm.edu	37	6	7246994	7246994	+	Silent	SNP	C	C	T	rs187908583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7246994C>T	ENST00000349384.6	+	11	4460	c.4146C>T	c.(4144-4146)ggC>ggT	p.G1382G	RREB1_ENST00000379938.2_Silent_p.G1437G|RREB1_ENST00000379933.3_Silent_p.G1382G|RREB1_ENST00000334984.6_Intron	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1382					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)				GCGAGGCAGGCGCCGGGGGCG	0.692													C|||	33	0.00658946	0.025	0.0	5008	,	,		11874	0.0		0.0	False		,,,				2504	0.0				p.G1437G		Atlas-SNP	.											.	RREB1	242	.	0			c.C4311T						PASS	.	C	,,,	60,4166		0,60,2053	11.0	13.0	13.0		4146,4311,,4146	-3.5	0.0	6		13	1,8303		0,1,4151	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	,,,	0,61,6204	TT,TC,CC		0.012,1.4198,0.4868	,,,	1382/1688,1437/1743,,1382/1688	7246994	61,12469	2113	4152	6265	SO:0001819	synonymous_variant	6239	exon12			GGCAGGCGCCGGG	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.4146C>T	6.37:g.7246994C>T		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	CCDS34336.1																																																																																			C|0.993;T|0.007	0.007	strong		0.692	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
LRRIQ3	127255	hgsc.bcm.edu	37	1	74575141	74575141	+	Silent	SNP	G	G	A	rs182798407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:74575141G>A	ENST00000395089.1	-	4	803	c.804C>T	c.(802-804)ctC>ctT	p.L268L	LRRIQ3_ENST00000468759.1_5'UTR|LRRIQ3_ENST00000354431.4_Silent_p.L268L|LRRIQ3_ENST00000370909.2_Silent_p.L160L			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	268										NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						GATCCTTAAGGAGCTTATCTT	0.289													G|||	15	0.00299521	0.0113	0.0	5008	,	,		12152	0.0		0.0	False		,,,				2504	0.0				p.L268L		Atlas-SNP	.											LRRIQ3,right_upper_lobe,carcinoma,-1,1	LRRIQ3	146	1	0			c.C804T						PASS	.	G		41,3525		2,37,1744	100.0	83.0	88.0		804	2.0	0.0	1		88	0,8096		0,0,4048	no	coding-synonymous	LRRIQ3	NM_001105659.1		2,37,5792	AA,AG,GG		0.0,1.1497,0.3516		268/625	74575141	41,11621	1783	4048	5831	SO:0001819	synonymous_variant	127255	exon5			CTTAAGGAGCTTA	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.804C>T	1.37:g.74575141G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Silent	SNP	ENST00000395089.1	37	CCDS41350.1																																																																																			G|0.997;A|0.003	0.003	strong		0.289	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258	
SCN5A	6331	hgsc.bcm.edu	37	3	38592406	38592406	+	Silent	SNP	A	A	G	rs1805126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38592406A>G	ENST00000333535.4	-	28	5606	c.5457T>C	c.(5455-5457)gaT>gaC	p.D1819D	SCN5A_ENST00000413689.1_Silent_p.D1819D|SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000451551.2_Silent_p.D1765D|SCN5A_ENST00000425664.1_Silent_p.D1801D|SCN5A_ENST00000450102.2_Silent_p.D1765D|SCN5A_ENST00000414099.2_Silent_p.D1801D|SCN5A_ENST00000443581.1_Silent_p.D1818D|SCN5A_ENST00000455624.2_Silent_p.D1786D|SCN5A_ENST00000423572.2_Silent_p.D1818D|SCN5A_ENST00000449557.2_Silent_p.D1765D			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1819			D -> N (in LQT3; digenic; associated with Gly-100 mutation on the KCNH2 gene). {ECO:0000269|PubMed:16922724}.		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)	CAGACAGGGCATCGGCAAAGT	0.517													A|||	2466	0.492412	0.7042	0.4265	5008	,	,		20365	0.5784		0.3648	False		,,,				2504	0.2955				p.D1819D		Atlas-SNP	.											.	SCN5A	634	.	0			c.T5457C	GRCh37	CM057565	SCN5A	M	rs1805126	PASS	.	A	,,,,,	2694,1612		858,978,317	58.0	65.0	63.0		5454,5457,5403,5358,5295,5457	-8.1	0.4	3	dbSNP_89	63	2850,5694		489,1872,1911	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN5A	NM_000335.4,NM_001099404.1,NM_001099405.1,NM_001160160.1,NM_001160161.1,NM_198056.2	,,,,,	1347,2850,2228	GG,GA,AA		33.3567,37.4361,43.144	,,,,,	1818/2016,1819/2017,1801/1999,1786/1984,1765/1963,1819/2017	38592406	5544,7306	2153	4272	6425	SO:0001819	synonymous_variant	6331	exon28			CAGGGCATCGGCA	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.5457T>C	3.37:g.38592406A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_198056	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	37	CCDS46796.1																																																																																			A|0.498;G|0.502	0.502	strong		0.517	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
HLA-A	3105	hgsc.bcm.edu	37	6	29911086	29911086	+	Missense_Mutation	SNP	T	T	C	rs1136700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29911086T>C	ENST00000396634.1	+	5	726	c.385T>C	c.(385-387)Tcg>Ccg	p.S129P	HLA-A_ENST00000376809.5_Missense_Mutation_p.S129P|HLA-A_ENST00000376802.2_Missense_Mutation_p.S129P|HLA-A_ENST00000376806.5_Missense_Mutation_p.S129P			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	129	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						CGACGTGGGGTCGGACGGGCG	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|||	1516	0.302716	0.289	0.1599	5008	,	,		11361	0.3264		0.2803	False		,,,				2504	0.4213				p.S129P		Atlas-SNP	.											HLA-A,NS,carcinoma,-1,1	HLA-A	89	1	0			c.T385C						PASS	.	T	PRO/SER	803,2195		163,477,859	27.0	21.0	23.0		385	-0.5	0.3	6	dbSNP_86	23	1878,3516		404,1070,1223	no	missense	HLA-A	NM_002116.7	74	567,1547,2082	CC,CT,TT		34.8165,26.7845,31.9471	benign	129/366	29911086	2681,5711	1499	2697	4196	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTGGGGTCGGACG	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.385T>C	6.37:g.29911086T>C	ENSP00000379873:p.Ser129Pro	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	71	44	0.619718	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	585	0.26785714285714285	142	0.2886178861788618	58	0.16022099447513813	164	0.2867132867132867	221	0.29155672823219	.	6.812	0.518971	0.13005	0.267845	0.348165	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00009	9.47;9.47;9.47;9.47	3.78	-0.459	0.12179	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	3.406660	0.02719	N	0.113799	T	0.00012	0.0000	N	0.00808	-1.17	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0	T	0.08680	-1.0710	9	0.02654	T	1	.	5.9403	0.19189	0.0:0.3406:0.4626:0.1968	rs1136700;rs3179190;rs3200177;rs9260153;rs17423992;rs41563619	8;129;129;129;129	B4DVB9;Q5SRN7;P16188;Q5SRN5;P04439	.;.;1A30_HUMAN;.;1A03_HUMAN	P	129	ENSP00000379873:S129P;ENSP00000366002:S129P;ENSP00000366005:S129P;ENSP00000365998:S129P	ENSP00000348012:S129P	S	+	1	0	HLA-A	30019065	0.000000	0.05858	0.258000	0.24420	0.545000	0.35147	-0.115000	0.10741	-0.232000	0.09811	-0.388000	0.06559	TCG	C|0.299;T|0.701	0.299	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
LILRA1	11024	hgsc.bcm.edu	37	19	55107336	55107336	+	Silent	SNP	C	C	T	rs34058364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55107336C>T	ENST00000251372.3	+	6	1076	c.894C>T	c.(892-894)tcC>tcT	p.S298S	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	298	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		ACAGATGCTCCGGTGCATACA	0.677													c|||	1456	0.290735	0.5166	0.268	5008	,	,		14602	0.2758		0.0974	False		,,,				2504	0.2157				p.S298S		Atlas-SNP	.											.	LILRA1	105	.	0			c.C894T						PASS	.						37.0	54.0	48.0					19																	55107336		2196	4300	6496	SO:0001819	synonymous_variant	11024	exon6			ATGCTCCGGTGCA	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.894C>T	19.37:g.55107336C>T		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	185	172	0.92973	NM_006863	O75018|Q3MJA6	Silent	SNP	ENST00000251372.3	37	CCDS12901.1																																																																																			C|0.851;T|0.149	0.149	strong		0.677	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
TRPM6	140803	hgsc.bcm.edu	37	9	77415284	77415284	+	Silent	SNP	A	A	C	rs7859201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:77415284A>C	ENST00000360774.1	-	17	2361	c.2124T>G	c.(2122-2124)ctT>ctG	p.L708L	RN7SKP47_ENST00000365347.1_RNA|TRPM6_ENST00000376864.4_Silent_p.L708L|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000361255.3_Silent_p.L703L|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000451710.3_Silent_p.L708L|TRPM6_ENST00000449912.2_Silent_p.L703L	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	708			L -> P (in HOMG1; loss of function; no effect on cell membrane localization). {ECO:0000269|PubMed:23942199}.		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						CGGCCAGTTTAAGGCAGGTCG	0.498													C|||	2308	0.460863	0.7436	0.3415	5008	,	,		18117	0.3482		0.3728	False		,,,				2504	0.3701				p.L708L		Atlas-SNP	.											.	TRPM6	377	.	0			c.T2124G						PASS	.	C	,,	2924,1482	475.3+/-357.3	973,978,252	130.0	106.0	114.0		2109,2109,2124	3.2	0.8	9	dbSNP_116	114	3264,5336	648.3+/-400.5	607,2050,1643	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	1580,3028,1895	CC,CA,AA		37.9535,33.636,47.578	,,	703/2018,703/2018,708/2023	77415284	6188,6818	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon17			CAGTTTAAGGCAG	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.2124T>G	9.37:g.77415284A>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	127	81	0.637795	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																			A|0.532;C|0.468	0.468	strong		0.498	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
ABCC6	368	hgsc.bcm.edu	37	16	16248791	16248791	+	Missense_Mutation	SNP	C	C	T	rs57695665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16248791C>T	ENST00000205557.7	-	28	4009	c.3980G>A	c.(3979-3981)gGg>gAg	p.G1327E		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1327	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	AATGGGGACCCCGTCGATCCA	0.672													C|||	27	0.00539137	0.0197	0.0014	5008	,	,		16551	0.0		0.0	False		,,,				2504	0.0				p.G1327E		Atlas-SNP	.											.	ABCC6	110	.	0			c.G3980A						PASS	.	C	GLU/GLY	51,4343		0,51,2146	29.0	25.0	26.0		3980	3.6	1.0	16	dbSNP_129	26	1,8597		0,1,4298	yes	missense	ABCC6	NM_001171.5	98	0,52,6444	TT,TC,CC		0.0116,1.1607,0.4002	probably-damaging	1327/1504	16248791	52,12940	2197	4299	6496	SO:0001583	missense	368	exon28			GGGACCCCGTCGA	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.3980G>A	16.37:g.16248791C>T	ENSP00000205557:p.Gly1327Glu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	18.13	3.554991	0.65425	0.011607	1.16E-4	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.92149	-2.98	4.53	3.57	0.40892	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.47852	U	0.000212	D	0.90232	0.6946	M	0.84773	2.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90118	0.4197	10	0.62326	D	0.03	.	12.2401	0.54538	0.0:0.9153:0.0:0.0847	rs57695665	1327;1327	O95255;A8Y988	MRP6_HUMAN;.	E	1327;265	ENSP00000205557:G1327E	ENSP00000205557:G1327E	G	-	2	0	ABCC6	16156292	0.891000	0.30450	0.957000	0.39632	0.594000	0.36715	2.702000	0.47102	0.901000	0.36495	0.465000	0.42564	GGG	C|0.994;T|0.006	0.006	strong		0.672	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
RBBP4	5928	hgsc.bcm.edu	37	1	33134865	33134865	+	Silent	SNP	A	A	C	rs11551266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:33134865A>C	ENST00000373493.5	+	7	954	c.795A>C	c.(793-795)ccA>ccC	p.P265P	RBBP4_ENST00000373485.1_Silent_p.P265P|RBBP4_ENST00000414241.3_Silent_p.P264P|RBBP4_ENST00000544435.1_Silent_p.P13P|RBBP4_ENST00000458695.2_Silent_p.P230P	NM_001135255.1|NM_005610.2	NP_001128727.1|NP_005601.1	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4	265					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin assembly (GO:0031497)|chromatin remodeling (GO:0006338)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|nucleosome assembly (GO:0006334)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|NURF complex (GO:0016589)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				CTTCCAAACCAAGCCACTCAG	0.383													A|||	409	0.0816693	0.2927	0.0303	5008	,	,		17140	0.0		0.001	False		,,,				2504	0.0				p.P265P		Atlas-SNP	.											.	RBBP4	38	.	0			c.A795C						PASS	.	A	,,	1061,3345	373.0+/-320.6	139,783,1281	63.0	62.0	62.0		792,690,795	4.1	1.0	1	dbSNP_120	62	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	RBBP4	NM_001135255.1,NM_001135256.1,NM_005610.2	,,	139,794,5570	CC,CA,AA		0.1279,24.0808,8.2423	,,	264/425,230/391,265/426	33134865	1072,11934	2203	4300	6503	SO:0001819	synonymous_variant	5928	exon7			CAAACCAAGCCAC	BC053904	CCDS366.1, CCDS44105.1, CCDS44106.1	1p35.1	2014-07-17	2001-11-28		ENSG00000162521	ENSG00000162521		"""WD repeat domain containing"""	9887	protein-coding gene	gene with protein product		602923	"""retinoblastoma-binding protein 4"""			8350924, 14609955, 17531812	Standard	NM_005610		Approved	RbAp48, NURF55, lin-53	uc001bvr.3	Q09028	OTTHUMG00000007998	ENST00000373493.5:c.795A>C	1.37:g.33134865A>C		Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	215	94	0.437209	NM_005610	B2R6G9|B4DRH0|D3DPQ3|P31149|Q53H02|Q96BV9	Silent	SNP	ENST00000373493.5	37	CCDS366.1	158|158	0.07234432234432235|0.07234432234432235	151|151	0.30691056910569103|0.30691056910569103	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	0|0	0.0|0.0	A|A	8.870|8.870	0.948970|0.948970	0.18356|0.18356	0.240808|0.240808	0.001279|0.001279	ENSG00000162521|ENSG00000162521	ENST00000475321|ENST00000463378	.|.	.|.	.|.	5.23|5.23	4.08|4.08	0.47627|0.47627	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.34153|0.34153	-0.9840|-0.9840	3|3	.|.	.|.	.|.	.|.	6.6964|6.6964	0.23201|0.23201	0.5947:0.2729:0.0:0.1324|0.5947:0.2729:0.0:0.1324	rs11551266;rs17849722;rs56732244|rs11551266;rs17849722;rs56732244	.|.	.|.	.|.	Q|P	68|25	.|.	.|.	K|Q	+|+	1|2	0|0	RBBP4|RBBP4	32907452|32907452	0.838000|0.838000	0.29461|0.29461	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	0.081000|0.081000	0.14823|0.14823	0.910000|0.910000	0.36722|0.36722	0.402000|0.402000	0.26972|0.26972	AAG|CAA	A|0.925;C|0.075	0.075	strong		0.383	RBBP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021957.3	NM_005610	
NMT1	4836	hgsc.bcm.edu	37	17	43171154	43171154	+	Silent	SNP	C	C	T	rs1132898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43171154C>T	ENST00000592782.1	+	5	618	c.487C>T	c.(487-489)Ctg>Ttg	p.L163L	NMT1_ENST00000258960.2_Silent_p.L163L|NMT1_ENST00000590114.1_3'UTR			P30419	NMT1_HUMAN	N-myristoyltransferase 1	163					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)				TGCTTTGGACCTGGGCGATCG	0.592													C|||	997	0.199081	0.3616	0.134	5008	,	,		16891	0.0367		0.1769	False		,,,				2504	0.2157				p.L163L		Atlas-SNP	.											.	NMT1	31	.	0			c.C487T						PASS	.	C		1432,2974	464.5+/-353.9	247,938,1018	79.0	65.0	70.0		487	4.1	1.0	17	dbSNP_86	70	1747,6853	316.3+/-312.7	170,1407,2723	no	coding-synonymous	NMT1	NM_021079.3		417,2345,3741	TT,TC,CC		20.314,32.5011,24.4426		163/497	43171154	3179,9827	2203	4300	6503	SO:0001819	synonymous_variant	4836	exon4			TTGGACCTGGGCG		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.487C>T	17.37:g.43171154C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	NM_021079	A8K7C1|Q9UE09	Silent	SNP	ENST00000592782.1	37	CCDS11494.1																																																																																			C|0.785;G|0.000;T|0.215	0.215	strong		0.592	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079	
MAST1	22983	hgsc.bcm.edu	37	19	12978556	12978556	+	Silent	SNP	C	C	G	rs202159363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12978556C>G	ENST00000251472.4	+	20	2370	c.2331C>G	c.(2329-2331)tcC>tcG	p.S777S		NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1											NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						AGCGATTCTCCGCGTCCGAGG	0.687													C|||	59	0.0117812	0.0431	0.0029	5008	,	,		13407	0.0		0.0	False		,,,				2504	0.0				p.S777S		Atlas-SNP	.											.	MAST1	214	.	0			c.C2331G						PASS	.	C		118,4146		0,118,2014	7.0	7.0	7.0		2331	-9.0	0.1	19		7	1,8357		0,1,4178	no	coding-synonymous	MAST1	NM_014975.2		0,119,6192	GG,GC,CC		0.012,2.7674,0.9428		777/1571	12978556	119,12503	2132	4179	6311	SO:0001819	synonymous_variant	22983	exon20			ATTCTCCGCGTCC	AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.2331C>G	19.37:g.12978556C>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_014975		Silent	SNP	ENST00000251472.4	37	CCDS32921.1																																																																																			C|0.995;G|0.005	0.005	strong		0.687	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975	
PSG9	5678	hgsc.bcm.edu	37	19	43773532	43773532	+	Missense_Mutation	SNP	G	G	C	rs8101191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43773532G>C	ENST00000270077.3	-	1	148	c.52C>G	c.(52-54)Ctc>Gtc	p.L18V	PSG9_ENST00000593948.1_Missense_Mutation_p.L18V|PSG9_ENST00000596730.1_Missense_Mutation_p.L18V|PSG9_ENST00000418820.2_Missense_Mutation_p.L18V|PSG9_ENST00000291752.5_Missense_Mutation_p.L18V|PSG9_ENST00000244293.7_Missense_Mutation_p.L18V|PSG9_ENST00000443718.3_Missense_Mutation_p.L18V	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	18			L -> V (in dbSNP:rs8101191).		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				GTGAGCAGGAGCCCCTTCCAG	0.602													g|||	953	0.190296	0.2148	0.1484	5008	,	,		16929	0.38		0.0835	False		,,,				2504	0.1012				p.L18V		Atlas-SNP	.											.	PSG9	77	.	0			c.C52G						PASS	.	A	VAL/LEU	883,3523	343.3+/-307.6	83,717,1403	96.0	94.0	95.0		52	-3.2	0.0	19	dbSNP_116	95	525,8075	146.8+/-202.3	24,477,3799	no	missense	PSG9	NM_002784.3	32	107,1194,5202	CC,CG,GG		6.1047,20.0409,10.8258	benign	18/427	43773532	1408,11598	2203	4300	6503	SO:0001583	missense	5678	exon1			GCAGGAGCCCCTT	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.52C>G	19.37:g.43773532G>C	ENSP00000270077:p.Leu18Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	67	24	0.358209	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	37	CCDS12618.1	431	0.19734432234432234	94	0.1910569105691057	54	0.14917127071823205	229	0.40034965034965037	54	0.0712401055408971	g	3.947	-0.013044	0.07727	0.200409	0.061047	ENSG00000183668	ENST00000270077;ENST00000291752;ENST00000443718;ENST00000435220;ENST00000244293	T;T;T;T	0.53206	0.63;2.1;2.46;1.47	2.17	-3.23	0.05109	.	.	.	.	.	T	0.00012	0.0000	L	0.46614	1.455	0.80722	P	0.0	B;P;P;B;B	0.38335	0.076;0.494;0.627;0.001;0.002	B;B;B;B;B	0.37346	0.034;0.125;0.247;0.008;0.005	T	0.33033	-0.9884	8	0.54805	T	0.06	.	6.1349	0.20225	0.6288:0.0:0.3712:0.0	rs8101191	18;18;18;18;18	E7EW65;Q15227;G3XAA7;Q6LEU7;Q00887	.;.;.;.;PSG9_HUMAN	V	18	ENSP00000270077:L18V;ENSP00000291752:L18V;ENSP00000396753:L18V;ENSP00000244293:L18V	ENSP00000244293:L18V	L	-	1	0	PSG9	48465372	0.022000	0.18835	0.015000	0.15790	0.061000	0.15899	-0.421000	0.07053	-0.493000	0.06678	-1.906000	0.00525	CTC	G|0.866;C|0.134	0.134	strong		0.602	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
PNPLA3	80339	hgsc.bcm.edu	37	22	44322922	44322922	+	Missense_Mutation	SNP	T	T	G	rs2076213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44322922T>G	ENST00000216180.3	+	2	468	c.295T>G	c.(295-297)Tgc>Ggc	p.C99G	PNPLA3_ENST00000478713.1_3'UTR|PNPLA3_ENST00000423180.2_Missense_Mutation_p.C95G	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	99	Patatin.		C -> G (in dbSNP:rs2076213). {ECO:0000269|PubMed:15489334}.		acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				ACAGGGTCTCTGCAAATGCCT	0.522													T|||	362	0.0722843	0.0393	0.1628	5008	,	,		20589	0.0268		0.0855	False		,,,				2504	0.0859				p.C99G		Atlas-SNP	.											.	PNPLA3	53	.	0			c.T295G						PASS	.	T	GLY/CYS	203,4203	126.6+/-163.6	3,197,2003	91.0	79.0	83.0		295	-2.1	0.0	22	dbSNP_96	83	838,7762	192.3+/-238.3	38,762,3500	yes	missense	PNPLA3	NM_025225.2	159	41,959,5503	GG,GT,TT		9.7442,4.6074,8.004	benign	99/482	44322922	1041,11965	2203	4300	6503	SO:0001583	missense	80339	exon2			GGTCTCTGCAAAT		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"""Patatin-like phospholipase domain containing"""	18590	protein-coding gene	gene with protein product		609567	"""chromosome 22 open reading frame 20"", ""adiponutrin"""	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.295T>G	22.37:g.44322922T>G	ENSP00000216180:p.Cys99Gly	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	150	84	0.56	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Missense_Mutation	SNP	ENST00000216180.3	37	CCDS14054.1	166	0.076007326007326	21	0.042682926829268296	61	0.1685082872928177	19	0.033216783216783216	65	0.08575197889182058	T	7.556	0.663724	0.14710	0.046074	0.097442	ENSG00000100344	ENST00000216180;ENST00000423180	T;T	0.78816	-1.21;-0.99	5.68	-2.13	0.07144	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	1.465370	0.03714	N	0.250817	T	0.00144	0.0004	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03306	-1.1050	9	0.25751	T	0.34	-1.4464	0.6504	0.00826	0.2984:0.2845:0.1077:0.3094	rs2076213;rs17493955;rs17855951;rs57129774;rs2076213	99	Q9NST1	PLPL3_HUMAN	G	99;95	ENSP00000216180:C99G;ENSP00000397987:C95G	ENSP00000216180:C99G	C	+	1	0	PNPLA3	42654255	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.512000	0.06313	0.008000	0.14787	-0.263000	0.10527	TGC	T|0.924;G|0.076;C|0.000	0.076	strong		0.522	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225	
NEB	4703	hgsc.bcm.edu	37	2	152527608	152527608	+	Missense_Mutation	SNP	C	C	T	rs34577613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152527608C>T	ENST00000172853.10	-	38	4582	c.4435G>A	c.(4435-4437)Gtc>Atc	p.V1479I	NEB_ENST00000603639.1_Missense_Mutation_p.V1479I|NEB_ENST00000409198.1_Missense_Mutation_p.V1479I|NEB_ENST00000604864.1_Missense_Mutation_p.V1479I|NEB_ENST00000397345.3_Missense_Mutation_p.V1479I|NEB_ENST00000427231.2_Missense_Mutation_p.V1479I			P20929	NEBU_HUMAN	nebulin	1479			V -> I (in dbSNP:rs34577613).		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)	p.V1479I(1)		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)		GTGAACTTGACGGTATCTGGG	0.483													T|||	1679	0.335264	0.4546	0.1095	5008	,	,		21763	0.5754		0.1223	False		,,,				2504	0.3057				p.V1479I		Atlas-SNP	.											NEB,NS,carcinoma,0,1	NEB	1697	1	1	Substitution - Missense(1)	stomach(1)	c.G4435A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL	1503,2705		261,981,862	164.0	163.0	163.0		4435,4435,4435	4.2	1.0	2	dbSNP_126	163	920,7532		58,804,3364	yes	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	29,29,29	319,1785,4226	TT,TC,CC		10.885,35.7177,19.139	benign,benign,benign	1479/8526,1479/8526,1479/6670	152527608	2423,10237	2104	4226	6330	SO:0001583	missense	4703	exon38			ACTTGACGGTATC	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.4435G>A	2.37:g.152527608C>T	ENSP00000172853:p.Val1479Ile	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	255	253	0.992157	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		700	0.32051282051282054	243	0.49390243902439024	46	0.1270718232044199	322	0.5629370629370629	89	0.11741424802110818	T	5.418	0.262254	0.10239	0.357177	0.10885	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.05081	3.5;3.53;3.53;3.54	5.42	4.25	0.50352	.	0.288297	0.32671	N	0.005787	T	0.00012	0.0000	N	0.00707	-1.245	0.09310	P	0.9999999999754821	B	0.02656	0.0	B	0.04013	0.001	T	0.26883	-1.0090	9	0.10902	T	0.67	.	7.0714	0.25181	0.0:0.138:0.1258:0.7362	rs34577613;rs60727639	1479	P20929	NEBU_HUMAN	I	1479	ENSP00000386259:V1479I;ENSP00000380505:V1479I;ENSP00000416578:V1479I;ENSP00000172853:V1479I	ENSP00000172853:V1479I	V	-	1	0	NEB	152235854	0.007000	0.16637	1.000000	0.80357	0.802000	0.45316	0.019000	0.13444	0.997000	0.38969	-0.254000	0.11334	GTC	C|0.705;T|0.295	0.295	strong		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEDD9	4739	hgsc.bcm.edu	37	6	11190859	11190859	+	Missense_Mutation	SNP	G	G	A	rs61755989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:11190859G>A	ENST00000379446.5	-	5	1409	c.1243C>T	c.(1243-1245)Cgg>Tgg	p.R415W	NEDD9_ENST00000504387.1_Missense_Mutation_p.R415W|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	415					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)			TGCTGGAGCCGCTGAAGTCTC	0.537													G|||	104	0.0207668	0.0741	0.0072	5008	,	,		19658	0.0		0.001	False		,,,				2504	0.0				p.R415W		Atlas-SNP	.											.	NEDD9	191	.	0			c.C1243T						PASS	.	G	TRP/ARG,TRP/ARG	272,4134	152.9+/-186.6	8,256,1939	68.0	64.0	65.0		1243,1243	3.2	0.3	6	dbSNP_129	65	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	NEDD9	NM_001142393.1,NM_006403.3	101,101	8,258,6237	AA,AG,GG		0.0233,6.1734,2.1067	benign,benign	415/835,415/835	11190859	274,12732	2203	4300	6503	SO:0001583	missense	4739	exon6			GGAGCCGCTGAAG	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.1243C>T	6.37:g.11190859G>A	ENSP00000368759:p.Arg415Trp	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Missense_Mutation	SNP	ENST00000379446.5	37	CCDS4520.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	G	8.301	0.819834	0.16678	0.061734	2.33E-4	ENSG00000111859	ENST00000379446;ENST00000504387	T;T	0.27256	1.68;1.68	5.92	3.16	0.36331	Serine rich protein interaction (1);	0.147556	0.64402	N	0.000009	T	0.12689	0.0308	M	0.77103	2.36	0.80722	D	1	B;B;B	0.33512	0.415;0.294;0.403	B;B;B	0.29176	0.081;0.099;0.045	T	0.02966	-1.1088	10	0.59425	D	0.04	-11.9291	5.1672	0.15092	0.1975:0.0:0.5527:0.2498	.	415;415;415	G5E9Y9;A8K9G7;Q14511	.;.;CASL_HUMAN	W	415	ENSP00000368759:R415W;ENSP00000422871:R415W	ENSP00000368759:R415W	R	-	1	2	NEDD9	11298845	0.969000	0.33509	0.350000	0.25708	0.084000	0.17831	1.794000	0.38774	0.395000	0.25257	-0.182000	0.12963	CGG	G|0.981;A|0.019	0.019	strong		0.537	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403	
TNN	63923	hgsc.bcm.edu	37	1	175105996	175105996	+	Missense_Mutation	SNP	C	C	T	rs2072036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:175105996C>T	ENST00000239462.4	+	17	3580	c.3467C>T	c.(3466-3468)gCg>gTg	p.A1156V		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	1156	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		A -> V (in dbSNP:rs2072036).		axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GGCACTCCAGCGCGGTATGAG	0.453													C|||	608	0.121406	0.0961	0.1052	5008	,	,		19829	0.2123		0.0905	False		,,,				2504	0.1053				p.A1156V		Atlas-SNP	.											TNN,bladder,carcinoma,-1,1	TNN	297	1	0			c.C3467T						PASS	.	C	VAL/ALA	405,4001	201.8+/-224.7	22,361,1820	84.0	78.0	80.0		3467	1.9	0.0	1	dbSNP_96	80	770,7830	183.2+/-231.5	26,718,3556	yes	missense	TNN	NM_022093.1	64	48,1079,5376	TT,TC,CC		8.9535,9.192,9.0343	benign	1156/1300	175105996	1175,11831	2203	4300	6503	SO:0001583	missense	63923	exon17			CTCCAGCGCGGTA	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.3467C>T	1.37:g.175105996C>T	ENSP00000239462:p.Ala1156Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	293	0.13415750915750915	55	0.11178861788617886	34	0.09392265193370165	136	0.23776223776223776	68	0.08970976253298153	C	2.604	-0.292295	0.05568	0.09192	0.089535	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.26223	1.75	5.27	1.92	0.25849	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.397573	0.29730	N	0.011357	T	0.00012	0.0000	L	0.33624	1.015	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.26573	-1.0099	9	0.52906	T	0.07	.	4.2092	0.10503	0.0:0.5171:0.1689:0.314	rs2072036;rs52836593;rs2072036	1156	Q9UQP3	TENN_HUMAN	V	1156;979	ENSP00000239462:A1156V	ENSP00000239462:A1156V	A	+	2	0	TNN	173372619	0.000000	0.05858	0.020000	0.16555	0.006000	0.05464	0.590000	0.23954	0.750000	0.32877	-0.710000	0.03640	GCG	C|0.889;T|0.111	0.111	strong		0.453	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
LMF1	64788	hgsc.bcm.edu	37	16	1004554	1004554	+	Silent	SNP	C	C	T	rs3751667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1004554C>T	ENST00000262301.11	-	2	324	c.306G>A	c.(304-306)acG>acA	p.T102T	LMF1_ENST00000543238.1_Intron|LMF1_ENST00000539379.1_Silent_p.T95T|LMF1_ENST00000568897.1_5'UTR|LMF1_ENST00000399843.2_Silent_p.T102T	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	102					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)				CTTCCCAGCTCGTCCTGTCCT	0.557													C|||	1807	0.360823	0.4274	0.2608	5008	,	,		20519	0.4127		0.2078	False		,,,				2504	0.4458				p.T102T		Atlas-SNP	.											LMF1,NS,carcinoma,-1,3	LMF1	42	3	0			c.G306A						PASS	.	C		1550,2552		292,966,793	51.0	53.0	53.0		306	-11.1	0.0	16	dbSNP_107	53	1918,6470		220,1478,2496	no	coding-synonymous	LMF1	NM_022773.2		512,2444,3289	TT,TC,CC		22.866,37.7864,27.7662		102/568	1004554	3468,9022	2051	4194	6245	SO:0001819	synonymous_variant	64788	exon2			CCAGCTCGTCCTG	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.306G>A	16.37:g.1004554C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			C|0.674;T|0.326	0.326	strong		0.557	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
IGSF9B	22997	hgsc.bcm.edu	37	11	133815981	133815981	+	Silent	SNP	C	C	G	rs10894768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:133815981C>G	ENST00000321016.8	-	2	467	c.237G>C	c.(235-237)ccG>ccC	p.P79P	IGSF9B_ENST00000533871.2_Silent_p.P79P			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	79	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CCACGTGCGGCGGGTAGTAGC	0.617													G|||	1776	0.354633	0.3011	0.438	5008	,	,		16482	0.5208		0.2992	False		,,,				2504	0.2536				p.P79P		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G237C						PASS	.	G		1154,3082		154,846,1118	48.0	59.0	55.0		237	-11.4	0.0	11	dbSNP_120	55	2510,5934		370,1770,2082	no	coding-synonymous	IGSF9B	NM_014987.1		524,2616,3200	GG,GC,CC		29.7252,27.2427,28.8959		79/1350	133815981	3664,9016	2118	4222	6340	SO:0001819	synonymous_variant	22997	exon2			GTGCGGCGGGTAG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.237G>C	11.37:g.133815981C>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	146	59	0.40411	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				C|0.633;G|0.367	0.367	strong		0.617	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786888	75786888	+	Missense_Mutation	SNP	C	C	T	rs1615736		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75786888C>T	ENST00000478296.1	-	4	2012	c.1736G>A	c.(1735-1737)cGt>cAt	p.R579H	ZNF717_ENST00000422325.1_Missense_Mutation_p.R629H|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.R622H|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	622					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TGACTTCTGACGAAAGGTTTT	0.403																																					p.R629H		Atlas-SNP	.											.	ZNF717	160	.	0			c.G1886A						PASS	.						20.0	24.0	23.0					3																	75786888		631	1552	2183	SO:0001583	missense	100131827	exon5			TTCTGACGAAAGG	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1736G>A	3.37:g.75786888C>T	ENSP00000419377:p.Arg579His	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		834	0.38186813186813184	149	0.30284552845528456	158	0.43646408839779005	217	0.3793706293706294	310	0.40897097625329815	.	5.928	0.355334	0.11239	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.08102	3.13;3.13;3.13	1.9	-3.81	0.04294	.	.	.	.	.	T	0.00012	0.0000	L	0.42744	1.35	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46512	-0.9186	8	0.23891	T	0.37	.	5.2238	0.15383	0.0:0.1993:0.3294:0.4713	rs1615736	629	C9JSV9	.	H	579;629;622	ENSP00000419377:R579H;ENSP00000409514:R629H;ENSP00000383643:R622H	ENSP00000383643:R622H	R	-	2	0	ZNF717	75869578	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.218000	0.00553	-1.710000	0.01397	-1.132000	0.01976	CGT	C|0.618;T|0.382	0.382	strong		0.403	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
KCNK18	338567	hgsc.bcm.edu	37	10	118969353	118969353	+	Missense_Mutation	SNP	C	C	T	rs363360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:118969353C>T	ENST00000334549.1	+	3	698	c.698C>T	c.(697-699)gCg>gTg	p.A233V		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	233			A -> V (in dbSNP:rs363360). {ECO:0000269|PubMed:20871611}.		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)		AGATCTCATGCGCTAGAGAAA	0.527													C|||	163	0.0325479	0.1165	0.013	5008	,	,		20294	0.0		0.0	False		,,,				2504	0.0				p.A233V		Atlas-SNP	.											KCNK18,colon,carcinoma,0,1	KCNK18	70	1	0			c.C698T						scavenged	.	C	VAL/ALA	421,3985	204.1+/-226.4	22,377,1804	103.0	99.0	100.0		698	2.8	0.0	10	dbSNP_79	100	3,8597	2.2+/-6.3	0,3,4297	no	missense	KCNK18	NM_181840.1	64	22,380,6101	TT,TC,CC		0.0349,9.5552,3.26	benign	233/385	118969353	424,12582	2203	4300	6503	SO:0001583	missense	338567	exon3			CTCATGCGCTAGA	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.698C>T	10.37:g.118969353C>T	ENSP00000334650:p.Ala233Val	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_181840	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	37	CCDS7598.1	67	0.030677655677655676	59	0.11991869918699187	8	0.022099447513812154	0	0.0	0	0.0	C	4.454	0.084176	0.08583	0.095552	3.49E-4	ENSG00000186795	ENST00000334549	T	0.14640	2.49	4.87	2.83	0.33086	.	0.649699	0.15587	N	0.254599	T	0.00144	0.0004	L	0.32530	0.975	0.09310	N	1	P	0.36010	0.532	B	0.27380	0.079	T	0.37957	-0.9683	10	0.31617	T	0.26	.	9.2831	0.37740	0.0:0.648:0.2759:0.0761	rs363360;rs363360	233	Q7Z418	KCNKI_HUMAN	V	233	ENSP00000334650:A233V	ENSP00000334650:A233V	A	+	2	0	KCNK18	118959343	0.289000	0.24334	0.002000	0.10522	0.001000	0.01503	1.454000	0.35178	1.379000	0.46325	0.655000	0.94253	GCG	A|0.000;C|0.963;T|0.037	0.037	strong		0.527	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840	
PZP	5858	hgsc.bcm.edu	37	12	9334571	9334571	+	Splice_Site	SNP	C	C	T	rs3741849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9334571C>T	ENST00000261336.2	-	14	1717	c.1689G>A	c.(1687-1689)aaG>aaA	p.K563K	PZP_ENST00000381997.2_Splice_Site_p.K432K	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	563					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						AATCGCTCACCTTGTTGGCTA	0.358													C|||	475	0.0948482	0.1831	0.0548	5008	,	,		-128	0.0337		0.0934	False		,,,				2504	0.0685				p.K563K	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											PZP_ENST00000381997,colon,carcinoma,-1,2	PZP	422	2	0			c.G1689A						PASS	.	C		696,3710	266.8+/-267.5	51,594,1558	48.0	51.0	50.0		1689	3.9	0.9	12	dbSNP_107	50	872,7728	186.3+/-233.8	42,788,3470	yes	coding-synonymous-near-splice	PZP	NM_002864.2		93,1382,5028	TT,TC,CC		10.1395,15.7966,12.056		563/1483	9334571	1568,11438	2203	4300	6503	SO:0001630	splice_region_variant	5858	exon14			GCTCACCTTGTTG	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.1689+1G>A	12.37:g.9334571C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	134	76	0.567164	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Silent	SNP	ENST00000261336.2	37	CCDS8600.1																																																																																			C|0.886;T|0.114	0.114	strong		0.358	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	Silent
RSF1	51773	hgsc.bcm.edu	37	11	77413223	77413223	+	Missense_Mutation	SNP	T	T	C	rs78433827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77413223T>C	ENST00000308488.6	-	6	1353	c.1051A>G	c.(1051-1053)Atc>Gtc	p.I351V	RSF1_ENST00000360355.2_Missense_Mutation_p.I320V|RSF1_ENST00000480887.1_Missense_Mutation_p.I99V			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	351	Glu-rich.				CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			CCAAATTCGATCCTTTCAGGC	0.398													T|||	29	0.00579073	0.0197	0.0043	5008	,	,		18269	0.0		0.0	False		,,,				2504	0.0				p.I351V		Atlas-SNP	.											RSF1,caecum,carcinoma,+2,1	RSF1	105	1	0			c.A1051G						PASS	.	T	VAL/ILE	110,4290	86.8+/-125.4	1,108,2091	149.0	147.0	148.0		1051	-0.2	0.0	11	dbSNP_131	148	2,8582	2.2+/-6.3	0,2,4290	yes	missense	RSF1	NM_016578.3	29	1,110,6381	CC,CT,TT		0.0233,2.5,0.8626	benign	351/1442	77413223	112,12872	2200	4292	6492	SO:0001583	missense	51773	exon6			ATTCGATCCTTTC	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.1051A>G	11.37:g.77413223T>C	ENSP00000311513:p.Ile351Val	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	288	162	0.5625	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	37	CCDS8253.1	9	0.004120879120879121	6	0.012195121951219513	3	0.008287292817679558	0	0.0	0	0.0	T	0.003	-2.567968	0.00133	0.025	2.33E-4	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000526324;ENST00000528095	D;D;D;D;T	0.84589	-1.85;-1.85;-1.87;-1.86;1.6	5.9	-0.187	0.13268	.	1.083410	0.07199	N	0.857181	T	0.41026	0.1141	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41124	-0.9526	10	0.21014	T	0.42	3.5725	1.2586	0.01996	0.175:0.2018:0.3389:0.2843	.	351	Q96T23	RSF1_HUMAN	V	351;99;320;152;350	ENSP00000311513:I351V;ENSP00000434509:I99V;ENSP00000353511:I320V;ENSP00000432022:I152V;ENSP00000436408:I350V	ENSP00000311513:I351V	I	-	1	0	RSF1	77090871	0.000000	0.05858	0.014000	0.15608	0.387000	0.30353	-0.043000	0.12043	0.057000	0.16193	-0.313000	0.08912	ATC	T|0.992;C|0.008	0.008	strong		0.398	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
QRICH2	84074	hgsc.bcm.edu	37	17	74287389	74287389	+	Missense_Mutation	SNP	T	T	C	rs2279053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74287389T>C	ENST00000262765.5	-	4	3100	c.2921A>G	c.(2920-2922)cAt>cGt	p.H974R		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	974			H -> R (in dbSNP:rs2279053).							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						AGGAATTCCATGTCGGTCCGA	0.527													C|||	2350	0.469249	0.7065	0.3098	5008	,	,		19962	0.5734		0.2744	False		,,,				2504	0.3548				p.H974R		Atlas-SNP	.											.	QRICH2	143	.	0			c.A2921G						PASS	.	C	ARG/HIS	2927,1479	472.8+/-356.5	979,969,255	68.0	68.0	68.0		2921	-9.4	0.0	17	dbSNP_100	68	2483,6117	696.2+/-404.9	348,1787,2165	yes	missense	QRICH2	NM_032134.1	29	1327,2756,2420	CC,CT,TT		28.8721,33.5679,41.5962	benign	974/1664	74287389	5410,7596	2203	4300	6503	SO:0001583	missense	84074	exon4			ATTCCATGTCGGT	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.2921A>G	17.37:g.74287389T>C	ENSP00000262765:p.His974Arg	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	126	74	0.587302	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	984	0.45054945054945056	350	0.7113821138211383	106	0.292817679558011	333	0.5821678321678322	195	0.25725593667546176	C	2.659	-0.280104	0.05642	0.664321	0.288721	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08102	3.13	4.68	-9.36	0.00629	.	.	.	.	.	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	0.31696	-0.9934	8	0.19147	T	0.46	9.8215	1.7269	0.02924	0.4102:0.2666:0.0962:0.2269	rs2279053;rs56708258;rs2279053	974;974	B5MD94;Q9H0J4	.;QRIC2_HUMAN	R	974	ENSP00000262765:H974R	ENSP00000262765:H974R	H	-	2	0	QRICH2	71798984	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.988000	0.03739	-2.936000	0.00299	-3.824000	0.00019	CAT	T|0.545;C|0.455	0.455	strong		0.527	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
FAM86C1	55199	hgsc.bcm.edu	37	11	71507186	71507186	+	Missense_Mutation	SNP	T	T	C	rs74830167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71507186T>C	ENST00000359244.4	+	4	408	c.385T>C	c.(385-387)Tgt>Cgt	p.C129R	FAM86C1_ENST00000426628.2_Missense_Mutation_p.C122R|FAM86C1_ENST00000346333.6_Missense_Mutation_p.C95R	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	129										lung(1)	1						AACCCAGAGATGTGCCAGCTG	0.632																																					p.C129R		Atlas-SNP	.											FAM86C1_ENST00000426628,brain,glioma,0,3	FAM86C1	27	3	0			c.T385C						scavenged	.						117.0	127.0	124.0					11																	71507186		2200	4293	6493	SO:0001583	missense	55199	exon4			CAGAGATGTGCCA	AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"""family with sequence similarity 86, member C"""	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.385T>C	11.37:g.71507186T>C	ENSP00000352182:p.Cys129Arg	Somatic	238	2	0.00840336		WXS	Illumina HiSeq	Phase_I	295	22	0.0745763	NM_018172	Q8N5D3	Missense_Mutation	SNP	ENST00000359244.4	37	CCDS41686.1	.	.	.	.	.	.	.	.	.	.	.	0.042	-1.281242	0.01398	.	.	ENSG00000158483	ENST00000346333;ENST00000359244;ENST00000426628;ENST00000528685	T;T;T;T	0.17213	2.34;2.58;2.34;2.29	1.49	1.49	0.22878	.	.	.	.	.	T	0.06005	0.0156	.	.	.	0.30869	N	0.732718	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41716	-0.9493	8	0.06236	T	0.91	.	4.112	0.10063	0.0:0.7698:0.0:0.2302	.	122;95;129	G3V0F7;Q9NVL1-2;Q9NVL1	.;.;FA86C_HUMAN	R	95;129;122;95	ENSP00000325662:C95R;ENSP00000352182:C129R;ENSP00000391329:C122R;ENSP00000436598:C95R	ENSP00000325662:C95R	C	+	1	0	FAM86C1	71184834	0.987000	0.35691	0.038000	0.18304	0.002000	0.02628	3.044000	0.49830	0.199000	0.20427	-1.160000	0.01791	TGT	T|0.940;C|0.060	0.060	strong		0.632	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563	
UTRN	7402	hgsc.bcm.edu	37	6	145051594	145051594	+	Silent	SNP	G	G	A	rs4305737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:145051594G>A	ENST00000367545.3	+	53	7911	c.7911G>A	c.(7909-7911)gaG>gaA	p.E2637E	UTRN_ENST00000367526.4_Silent_p.E192E	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2637					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		CCCCTGAAGAGCCAAGAAGAA	0.443													A|||	3219	0.642772	0.9123	0.6225	5008	,	,		13715	0.8681		0.2286	False		,,,				2504	0.4867				p.E2637E		Atlas-SNP	.											.	UTRN	327	.	0			c.G7911A						PASS	.	A		3479,927	354.6+/-312.7	1376,727,100	67.0	73.0	71.0		7911	2.7	1.0	6	dbSNP_111	71	2174,6426	712.7+/-405.9	280,1614,2406	no	coding-synonymous	UTRN	NM_007124.2		1656,2341,2506	AA,AG,GG		25.2791,21.0395,43.4646		2637/3434	145051594	5653,7353	2203	4300	6503	SO:0001819	synonymous_variant	7402	exon53			TGAAGAGCCAAGA	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.7911G>A	6.37:g.145051594G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	35	6	0.171429	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	37	CCDS34547.1																																																																																			G|0.490;A|0.510	0.510	strong		0.443	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
TSHZ3	57616	hgsc.bcm.edu	37	19	31768491	31768491	+	Silent	SNP	G	G	A	rs139947200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:31768491G>A	ENST00000240587.4	-	2	2535	c.2208C>T	c.(2206-2208)gcC>gcT	p.A736A		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	736					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					AGGGCTTGGCGGCCTTGCCCA	0.627													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17340	0.0		0.0	False		,,,				2504	0.0				p.A736A		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C2208T						PASS	.	G		17,4389	22.3+/-47.3	0,17,2186	58.0	59.0	59.0		2208	-10.7	0.3	19	dbSNP_134	59	0,8600		0,0,4300	no	coding-synonymous	TSHZ3	NM_020856.2		0,17,6486	AA,AG,GG		0.0,0.3858,0.1307		736/1082	31768491	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CTTGGCGGCCTTG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2208C>T	19.37:g.31768491G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.999;A|0.001	0.001	strong		0.627	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
SWAP70	23075	hgsc.bcm.edu	37	11	9769483	9769483	+	Silent	SNP	C	C	T	rs34696762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9769483C>T	ENST00000318950.6	+	10	1537	c.1434C>T	c.(1432-1434)acC>acT	p.T478T	SWAP70_ENST00000447399.2_Silent_p.T420T	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	478					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)		TTCAGACAACCGAGGCGGAGA	0.552													C|||	917	0.183107	0.3351	0.1599	5008	,	,		16981	0.3075		0.008	False		,,,				2504	0.046				p.T478T		Atlas-SNP	.											.	SWAP70	40	.	0			c.C1434T						PASS	.	C		1151,3251	410.6+/-335.4	151,849,1201	99.0	95.0	96.0		1434	-11.7	0.0	11	dbSNP_126	96	65,8523	37.8+/-93.5	0,65,4229	no	coding-synonymous	SWAP70	NM_015055.2		151,914,5430	TT,TC,CC		0.7569,26.1472,9.361		478/586	9769483	1216,11774	2201	4294	6495	SO:0001819	synonymous_variant	23075	exon10			GACAACCGAGGCG	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.1434C>T	11.37:g.9769483C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	130	61	0.469231	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Silent	SNP	ENST00000318950.6	37	CCDS31426.1																																																																																			C|0.889;T|0.111	0.111	strong		0.552	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055	
CSF2RA	1438	hgsc.bcm.edu	37	X	1401646	1401646	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1401646C>G	ENST00000381524.3	+	3	236	c.50C>G	c.(49-51)gCa>gGa	p.A17G	CSF2RA_ENST00000355432.3_Missense_Mutation_p.A17G|CSF2RA_ENST00000361536.3_Missense_Mutation_p.A17G|CSF2RA_ENST00000381500.1_Missense_Mutation_p.A17G|CSF2RA_ENST00000355805.2_Missense_Mutation_p.A17G|CSF2RA_ENST00000494969.2_Missense_Mutation_p.A17G|CSF2RA_ENST00000432318.2_Missense_Mutation_p.A17G|CSF2RA_ENST00000417535.2_Missense_Mutation_p.A17G|CSF2RA_ENST00000381509.3_Missense_Mutation_p.A17G|CSF2RA_ENST00000381529.3_Missense_Mutation_p.A17G|CSF2RA_ENST00000501036.2_5'UTR			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	17					response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	CCACACCCAGCATTCCTCCTG	0.527													c|||	1070	0.213658	0.6914	0.0749	5008	,	,		20490	0.0308		0.0477	False		,,,				2504	0.0256				p.A17G	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.C50G						PASS	.	C	GLY/ALA,GLY/ALA,GLY/ALA,,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	2532,1874		717,1098,388	260.0	267.0	264.0		50,50,50,,50,50,50,50,50	0.2	0.0	X	dbSNP_134	264	358,8234		12,334,3950	yes	missense,missense,missense,utr-5,missense,missense,missense,missense,missense	CSF2RA	NM_001161529.1,NM_001161530.1,NM_001161531.1,NM_001161532.1,NM_006140.4,NM_172245.2,NM_172246.2,NM_172247.2,NM_172249.2	60,60,60,,60,60,60,60,60	729,1432,4338	GG,GC,CC		4.1667,42.5329,22.2342	possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	17/401,17/435,17/411,,17/401,17/401,17/378,17/334,17/234	1401646	2890,10108	2203	4296	6499	SO:0001583	missense	1438	exon1			ACCCAGCATTCCT	M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"""CD molecules"", ""Pseudoautosomal regions / PAR1"""	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.50C>G	X.37:g.1401646C>G	ENSP00000370935:p.Ala17Gly	Somatic	589	0	0		WXS	Illumina HiSeq	Phase_I	593	281	0.473862	NM_172247	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Missense_Mutation	SNP	ENST00000381524.3	37	CCDS35191.1	395	0.18086080586080586	317	0.6443089430894309	25	0.06906077348066299	16	0.027972027972027972	37	0.048812664907651716	.	8.761	0.923502	0.18056	0.574671	0.041667	ENSG00000198223	ENST00000381529;ENST00000432318;ENST00000361536;ENST00000381507;ENST00000381524;ENST00000412290;ENST00000419094;ENST00000381509;ENST00000355805;ENST00000355432;ENST00000417535;ENST00000381500	D;D;D;D;T;T;D;T;T;D;D	0.95238	-3.32;-3.32;-3.65;-3.32;0.61;1.55;-3.45;0.54;0.77;-3.17;-3.65	1.21	0.191	0.15130	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20563	N	0.999885	D;P;D;D;D;P	0.61697	0.972;0.953;0.978;0.99;0.99;0.953	P;P;P;P;P;P	0.59948	0.866;0.739;0.649;0.763;0.719;0.739	T	0.24154	-1.0168	8	0.25751	T	0.34	.	3.6875	0.08334	0.0:0.7058:0.0:0.2942	.	17;17;17;17;17;17	P15509-2;A7J003;P15509-3;P15509-6;P15509-5;P15509	.;.;.;.;.;CSF2R_HUMAN	G	17	ENSP00000370940:A17G;ENSP00000416437:A17G;ENSP00000354836:A17G;ENSP00000370935:A17G;ENSP00000410667:A17G;ENSP00000397452:A17G;ENSP00000370920:A17G;ENSP00000348058:A17G;ENSP00000347606:A17G;ENSP00000394227:A17G;ENSP00000370911:A17G	ENSP00000347606:A17G	A	+	2	0	CSF2RA	1361646	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.182000	0.16900	-0.211000	0.10124	0.350000	0.21858	GCA	C|0.794;G|0.206	0.206	strong		0.527	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2		
FBXO44	93611	hgsc.bcm.edu	37	1	11721321	11721321	+	Silent	SNP	G	G	A	rs12057383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11721321G>A	ENST00000251547.5	+	6	841	c.759G>A	c.(757-759)ccG>ccA	p.P253P	FBXO6_ENST00000376753.4_5'Flank|FBXO44_ENST00000251546.4_Missense_Mutation_p.A212T|FBXO44_ENST00000376768.1_Missense_Mutation_p.A244T|FBXO44_ENST00000376762.4_Missense_Mutation_p.A212T|FBXO44_ENST00000376770.1_Silent_p.P253P|FBXO44_ENST00000376760.1_Missense_Mutation_p.A212T	NM_033182.5	NP_149438.2	Q9H4M3	FBX44_HUMAN	F-box protein 44	253						SCF ubiquitin ligase complex (GO:0019005)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8	Ovarian(185;0.249)	Lung NSC(185;4.15e-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;5.41e-06)|COAD - Colon adenocarcinoma(227;0.000255)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000758)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		TCGGGCCCCCGCTGCCCTGAC	0.637													G|||	406	0.0810703	0.2784	0.0187	5008	,	,		15749	0.002		0.007	False		,,,				2504	0.0164				p.A212T		Atlas-SNP	.											.	FBXO44	20	.	0			c.G634A						PASS	.	G	,,THR/ALA,THR/ALA	1089,3317	394.7+/-329.4	130,829,1244	66.0	70.0	69.0		759,759,634,634	-4.8	0.9	1	dbSNP_120	69	33,8567	22.8+/-68.1	0,33,4267	yes	coding-synonymous,coding-synonymous,missense,missense	FBXO44	NM_001014765.1,NM_033182.5,NM_183412.2,NM_183413.2	,,58,58	130,862,5511	AA,AG,GG		0.3837,24.7163,8.6268	,,,	253/256,253/256,212/225,212/225	11721321	1122,11884	2203	4300	6503	SO:0001819	synonymous_variant	93611	exon5			GCCCCCGCTGCCC	AY040878	CCDS131.1, CCDS132.1	1p36.21	2008-03-26			ENSG00000132879	ENSG00000132879		"""F-boxes /  ""other"""""	24847	protein-coding gene	gene with protein product		609111				12383498	Standard	XM_005263535		Approved	FBX30, FBG3, MGC14140, Fbxo6a, Fbx44	uc001asm.3	Q9H4M3	OTTHUMG00000002071	ENST00000251547.5:c.759G>A	1.37:g.11721321G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	NM_183412	B3KNZ2|B7Z743|Q5TGX2|Q5TGX4|Q5TGX5|Q68DJ9|Q8WWY2	Missense_Mutation	SNP	ENST00000251547.5	37	CCDS132.1	145	0.06639194139194139	135	0.27439024390243905	4	0.011049723756906077	0	0.0	6	0.0079155672823219	G	11.75	1.732499	0.30684	0.247163	0.003837	ENSG00000132879	ENST00000251546;ENST00000376768;ENST00000376762;ENST00000376760	T;T;T;T	0.38401	1.2;1.14;1.2;1.2	4.82	-4.76	0.03229	.	0.998809	0.08102	N	0.997570	T	0.00012	0.0000	.	.	.	0.23696	P	0.9970848	B;B	0.10296	0.0;0.003	B;B	0.06405	0.001;0.002	T	0.31251	-0.9950	8	0.62326	D	0.03	-13.878	10.7614	0.46266	0.1572:0.1065:0.7363:0.0	rs12057383;rs56815691	244;212	B7Z1P2;Q9H4M3-2	.;.	T	212;244;212;212	ENSP00000251546:A212T;ENSP00000365959:A244T;ENSP00000365953:A212T;ENSP00000365951:A212T	ENSP00000251546:A212T	A	+	1	0	FBXO44	11643908	0.000000	0.05858	0.924000	0.36721	0.260000	0.26232	-0.672000	0.05244	-1.124000	0.02936	-0.258000	0.10820	GCT	G|0.924;A|0.076	0.076	strong		0.637	FBXO44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005761.1	NM_183412	
CCDC17	149483	hgsc.bcm.edu	37	1	46086588	46086588	+	Missense_Mutation	SNP	T	T	C	rs16832629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46086588T>C	ENST00000528266.1	-	11	1733	c.1586A>G	c.(1585-1587)aAt>aGt	p.N529S	CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000421127.2_Missense_Mutation_p.N520S|CCDC17_ENST00000343901.2_Missense_Mutation_p.N497S|CCDC17_ENST00000464739.1_5'Flank			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	529										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					AGGAATCCCATTCAGCTGCCC	0.577													T|||	32	0.00638978	0.0227	0.0029	5008	,	,		22169	0.0		0.0	False		,,,				2504	0.0				p.N529S		Atlas-SNP	.											.	CCDC17	54	.	0			c.A1586G						PASS	.	T	SER/ASN,SER/ASN	81,4325	68.7+/-106.4	0,81,2122	49.0	44.0	46.0		1586,1559	4.8	0.8	1	dbSNP_123	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	CCDC17	NM_001114938.2,NM_001190182.1	46,46	0,82,6421	CC,CT,TT		0.0116,1.8384,0.6305	probably-damaging,probably-damaging	529/623,520/614	46086588	82,12924	2203	4300	6503	SO:0001583	missense	149483	exon11			ATCCCATTCAGCT		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.1586A>G	1.37:g.46086588T>C	ENSP00000432172:p.Asn529Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	140	57	0.407143	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Missense_Mutation	SNP	ENST00000528266.1	37	CCDS44131.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	20.8	4.050511	0.75960	0.018384	1.16E-4	ENSG00000159588	ENST00000421127;ENST00000343901;ENST00000528266	T;T;T	0.48201	0.82;0.82;0.82	5.92	4.77	0.60923	.	0.130657	0.52532	D	0.000077	T	0.49389	0.1554	M	0.71581	2.175	0.36900	D	0.890378	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.70227	0.954;0.968;0.954	T	0.68492	-0.5394	10	0.87932	D	0	-5.1285	11.5274	0.50588	0.1344:0.0:0.0:0.8656	rs16832629	529;520;497	Q96LX7;Q96LX7-5;F2Z395	CCD17_HUMAN;.;.	S	520;497;529	ENSP00000389415:N520S;ENSP00000341451:N497S;ENSP00000432172:N529S	ENSP00000341451:N497S	N	-	2	0	CCDC17	45859175	0.991000	0.36638	0.794000	0.32065	0.951000	0.60555	2.283000	0.43470	1.021000	0.39600	0.533000	0.62120	AAT	T|0.993;C|0.007	0.007	strong		0.577	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	
URB1	9875	hgsc.bcm.edu	37	21	33755763	33755763	+	Silent	SNP	G	G	A	rs2833795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33755763G>A	ENST00000382751.3	-	4	650	c.535C>T	c.(535-537)Ctg>Ttg	p.L179L		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	179						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						AGGGTGTACAGGGTCTTTTTA	0.562													A|||	2780	0.555112	0.944	0.4078	5008	,	,		18168	0.5813		0.2684	False		,,,				2504	0.4018				p.L179L		Atlas-SNP	.											URB1_ENST00000382751,NS,carcinoma,0,2	URB1	176	2	0			c.C535T						PASS	.	A		1164,220		499,166,27	79.0	82.0	81.0		535	1.8	1.0	21	dbSNP_100	81	843,2339		102,639,850	no	coding-synonymous	URB1	NM_014825.2		601,805,877	AA,AG,GG		26.4928,15.896,43.9553		179/2272	33755763	2007,2559	692	1591	2283	SO:0001819	synonymous_variant	9875	exon4			TGTACAGGGTCTT	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.535C>T	21.37:g.33755763G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																			G|0.471;A|0.529	0.529	strong		0.562	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
ENOX1	55068	hgsc.bcm.edu	37	13	43987003	43987003	+	Missense_Mutation	SNP	C	C	G	rs7338624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:43987003C>G	ENST00000261488.6	-	4	625	c.48G>C	c.(46-48)gaG>gaC	p.E16D	ENOX1_ENST00000412891.1_Missense_Mutation_p.E16D	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	16			E -> D (in dbSNP:rs7338624). {ECO:0000269|PubMed:19055324}.		rhythmic process (GO:0048511)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(3)|large_intestine(7)|lung(18)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(1)	34		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		TCTGAGGAAGCTCCTGGGGAA	0.498													C|||	242	0.0483227	0.1778	0.0101	5008	,	,		16486	0.0		0.0	False		,,,				2504	0.0				p.E16D		Atlas-SNP	.											.	ENOX1	158	.	0			c.G48C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	677,3729	286.3+/-278.7	49,579,1575	125.0	111.0	116.0		48,48,48	2.9	0.9	13	dbSNP_116	116	9,8591	5.7+/-21.5	0,9,4291	yes	missense,missense,missense	ENOX1	NM_001127615.1,NM_001242863.1,NM_017993.3	45,45,45	49,588,5866	GG,GC,CC		0.1047,15.3654,5.2745	benign,benign,benign	16/644,16/644,16/644	43987003	686,12320	2203	4300	6503	SO:0001583	missense	55068	exon4			AGGAAGCTCCTGG	EF432052	CCDS9389.1	13q14.11	2013-02-12			ENSG00000120658	ENSG00000120658		"""RNA binding motif (RRM) containing"""	25474	protein-coding gene	gene with protein product		610914				11360993	Standard	NM_001127615		Approved	FLJ10094, PIG38, CNOX, cCNOX	uc001uza.4	Q8TC92	OTTHUMG00000016818	ENST00000261488.6:c.48G>C	13.37:g.43987003C>G	ENSP00000261488:p.Glu16Asp	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	37	CCDS9389.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	C	11.61	1.690096	0.29962	0.153654	0.001047	ENSG00000120658	ENST00000261488;ENST00000412891	T;T	0.44083	0.93;0.93	5.91	2.88	0.33553	.	0.688144	0.14119	N	0.340181	T	0.00109	0.0003	N	0.08118	0	0.09310	P	0.99999166027	B	0.02656	0.0	B	0.01281	0.0	T	0.18241	-1.0343	9	0.19590	T	0.45	-0.328	2.7291	0.05222	0.2036:0.4159:0.0:0.3805	rs7338624;rs52798713;rs7338624	16	Q8TC92	ENOX1_HUMAN	D	16	ENSP00000261488:E16D;ENSP00000415054:E16D	ENSP00000261488:E16D	E	-	3	2	ENOX1	42885003	0.996000	0.38824	0.871000	0.34182	0.975000	0.68041	1.058000	0.30504	0.842000	0.35045	0.655000	0.94253	GAG	C|0.955;G|0.045	0.045	strong		0.498	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993	
FBLN2	2199	hgsc.bcm.edu	37	3	13671402	13671402	+	Silent	SNP	C	C	T	rs41283999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:13671402C>T	ENST00000295760.7	+	13	2853	c.2784C>T	c.(2782-2784)tgC>tgT	p.C928C	FBLN2_ENST00000535798.1_Silent_p.C954C|FBLN2_ENST00000492059.1_Silent_p.C975C|FBLN2_ENST00000404922.3_Silent_p.C975C	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	928	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)			GCTGTTCCTGCGCCTCCGGGT	0.647													C|||	193	0.0385383	0.1369	0.0159	5008	,	,		19750	0.0		0.001	False		,,,				2504	0.0				p.C975C		Atlas-SNP	.											.	FBLN2	137	.	0			c.C2925T						PASS	.	C	,,	426,3860		15,396,1732	21.0	25.0	24.0		2925,2925,2784	-1.2	0.2	3	dbSNP_127	24	4,8484		0,4,4240	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLN2	NM_001004019.1,NM_001165035.1,NM_001998.2	,,	15,400,5972	TT,TC,CC		0.0471,9.9393,3.3662	,,	975/1232,975/1232,928/1185	13671402	430,12344	2143	4244	6387	SO:0001819	synonymous_variant	2199	exon14			TTCCTGCGCCTCC	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.2784C>T	3.37:g.13671402C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	164	78	0.47561	NM_001004019	B7Z9C5|Q8IUI0|Q8IUI1	Silent	SNP	ENST00000295760.7	37	CCDS46762.1																																																																																			C|0.965;T|0.035	0.035	strong		0.647	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019	
STAG3	10734	hgsc.bcm.edu	37	7	99796146	99796146	+	Silent	SNP	A	A	C	rs3735241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99796146A>C	ENST00000426455.1	+	13	1700	c.1293A>C	c.(1291-1293)ccA>ccC	p.P431P	STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000543273.1_RNA|STAG3_ENST00000317296.5_Silent_p.P431P|STAG3_ENST00000394018.2_Silent_p.P373P	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	431					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCGTCTACCCAGTTGTGTATG	0.522													C|||	2504	0.5	0.3654	0.6254	5008	,	,		19600	0.6815		0.498	False		,,,				2504	0.408				p.P431P		Atlas-SNP	.											.	STAG3	121	.	0			c.A1293C						PASS	.	C		1816,2590		363,1090,750	142.0	123.0	130.0		1293	-6.2	0.1	7	dbSNP_107	130	4281,4319		1082,2117,1101	no	coding-synonymous	STAG3	NM_012447.2		1445,3207,1851	CC,CA,AA		49.7791,41.2165,46.8784		431/1226	99796146	6097,6909	2203	4300	6503	SO:0001819	synonymous_variant	10734	exon13			CTACCCAGTTGTG	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.1293A>C	7.37:g.99796146A>C		Somatic	347	0	0		WXS	Illumina HiSeq	Phase_I	410	207	0.504878	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Silent	SNP	ENST00000426455.1	37	CCDS34703.1																																																																																			C|0.482;N|0.000	0.482	strong		0.522	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
CGN	57530	hgsc.bcm.edu	37	1	151493098	151493098	+	Silent	SNP	C	C	T	rs141884525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151493098C>T	ENST00000271636.7	+	5	1204	c.1071C>T	c.(1069-1071)gcC>gcT	p.A357A		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	351	Interacts with ZO-2.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			CTACTAAGGCCGTGGCAGGGC	0.557													C|||	28	0.00559105	0.0106	0.0	5008	,	,		19386	0.0129		0.0	False		,,,				2504	0.001				p.A357A		Atlas-SNP	.											.	CGN	106	.	0			c.C1071T						PASS	.	C		31,4375	36.8+/-68.6	0,31,2172	76.0	68.0	71.0		1071	3.0	0.0	1	dbSNP_134	71	0,8600		0,0,4300	no	coding-synonymous	CGN	NM_020770.2		0,31,6472	TT,TC,CC		0.0,0.7036,0.2384		357/1204	151493098	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	57530	exon5			TAAGGCCGTGGCA	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.1071C>T	1.37:g.151493098C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	196	101	0.515306	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Silent	SNP	ENST00000271636.7	37	CCDS999.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	3	0.005244755244755245	0	0.0	C	1.548	-0.540081	0.04053	0.007036	0.0	ENSG00000143375	ENST00000416743	.	.	.	4.97	3.02	0.34903	.	.	.	.	.	T	0.20495	0.0493	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.18461	-1.0336	4	.	.	.	0.3924	10.9367	0.47249	0.0:0.6821:0.2427:0.0752	.	.	.	.	L	66	.	.	P	+	2	0	CGN	149759722	0.026000	0.19158	0.030000	0.17652	0.001000	0.01503	0.384000	0.20668	0.266000	0.21894	-0.797000	0.03246	CCG	C|0.997;T|0.003	0.003	strong		0.557	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
UNC5A	90249	hgsc.bcm.edu	37	5	176305523	176305523	+	Silent	SNP	C	C	T	rs146460064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176305523C>T	ENST00000329542.4	+	13	2341	c.2067C>T	c.(2065-2067)caC>caT	p.H689H	UNC5A_ENST00000261961.3_Silent_p.H649H	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	689					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	all_cancers(89;0.000119)|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)			GGTACTTGCACTGCACCTTCA	0.602													C|||	8	0.00159744	0.0061	0.0	5008	,	,		20146	0.0		0.0	False		,,,				2504	0.0				p.H689H		Atlas-SNP	.											.	UNC5A	76	.	0			c.C2067T						PASS	.	C		41,4365	44.6+/-78.6	0,41,2162	107.0	83.0	91.0		2067	3.8	1.0	5	dbSNP_134	91	0,8600		0,0,4300	no	coding-synonymous	UNC5A	NM_133369.2		0,41,6462	TT,TC,CC		0.0,0.9305,0.3152		689/843	176305523	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	90249	exon13			CTTGCACTGCACC	AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"""Immunoglobulin superfamily / I-set domain containing"""	12567	protein-coding gene	gene with protein product		607869	"""unc5 (C.elegans homolog) a"""				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.2067C>T	5.37:g.176305523C>T		Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	222	116	0.522523	NM_133369	B2RXE6|Q8TF26|Q96GP4	Silent	SNP	ENST00000329542.4	37	CCDS34299.1																																																																																			C|0.996;T|0.004	0.004	strong		0.602	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300	
SPATA4	132851	hgsc.bcm.edu	37	4	177113956	177113956	+	Silent	SNP	A	A	G	rs2291244	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	60	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	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	
IFT80	57560	hgsc.bcm.edu	37	3	159997061	159997061	+	Missense_Mutation	SNP	T	T	A	rs6778728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	182	0	0		WXS	Illumina HiSeq	Phase_I	180	75	0.416667	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	
CCDC84	338657	hgsc.bcm.edu	37	11	118886117	118886117	+	Silent	SNP	C	C	T	rs10111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118886117C>T	ENST00000334418.1	+	10	962	c.906C>T	c.(904-906)cgC>cgT	p.R302R	RPS25_ENST00000528547.1_5'Flank	NM_198489.1	NP_940891.1	Q86UT8	CCD84_HUMAN	coiled-coil domain containing 84	302										breast(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		CTTTTGGCCGCGTCTGGAATA	0.547													C|||	1261	0.251797	0.3517	0.2334	5008	,	,		15190	0.0685		0.2286	False		,,,				2504	0.3425				p.R302R		Atlas-SNP	.											.	CCDC84	21	.	0			c.C906T						PASS	.	C		1486,2914	454.5+/-350.7	253,980,967	39.0	41.0	40.0		906	-9.9	0.7	11	dbSNP_52	40	1934,6654	321.7+/-315.2	221,1492,2581	no	coding-synonymous	CCDC84	NM_198489.1		474,2472,3548	TT,TC,CC		22.5198,33.7727,26.332		302/333	118886117	3420,9568	2200	4294	6494	SO:0001819	synonymous_variant	338657	exon10			TGGCCGCGTCTGG	AB094093	CCDS8405.1	11q23.3	2006-03-13			ENSG00000186166	ENSG00000186166			30460	protein-coding gene	gene with protein product							Standard	NM_198489		Approved	DLNB14	uc001pul.3	Q86UT8	OTTHUMG00000166348	ENST00000334418.1:c.906C>T	11.37:g.118886117C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	128	55	0.429688	NM_198489		Silent	SNP	ENST00000334418.1	37	CCDS8405.1																																																																																			C|0.763;T|0.237	0.237	strong		0.547	CCDC84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389315.1	NM_198489	
COPE	11316	hgsc.bcm.edu	37	19	19017862	19017862	+	Missense_Mutation	SNP	G	G	A	rs10330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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|COPE_ENST00000598969.1_Intron|AC002985.3_ENST00000596918.1_3'UTR|COPE_ENST00000349893.4_Missense_Mutation_p.T117I	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	117			T -> I (in dbSNP:rs10330). {ECO:0000269|PubMed:10469566, ECO:0000269|PubMed:14702039}.		COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						CAGGAAGGTGGTGTTGGTCAC	0.647													G|||	1041	0.207867	0.413	0.1239	5008	,	,		18826	0.0754		0.1332	False		,,,				2504	0.2035				p.T117I		Atlas-SNP	.											.	COPE	26	.	0			c.C350T						PASS	.	G	ILE/THR,,ILE/THR	1575,2829	456.9+/-351.5	267,1041,894	130.0	72.0	92.0		350,,350	4.8	1.0	19	dbSNP_52	92	1004,7594	203.2+/-246.3	60,884,3355	yes	missense,intron,missense	COPE	NM_007263.3,NM_199442.1,NM_199444.1	89,,89	327,1925,4249	AA,AG,GG		11.6771,35.7629,19.8354	benign,,benign	117/309,,117/257	19017862	2579,10423	2202	4299	6501	SO:0001583	missense	11316	exon4			AAGGTGGTGTTGG	AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669			2234	protein-coding gene	gene with protein product		606942				10469566	Standard	NM_007263		Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.350C>T	19.37:g.19017862G>A	ENSP00000262812:p.Thr117Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	105	59	0.561905	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	
C10orf71	118461	hgsc.bcm.edu	37	10	50532155	50532155	+	Missense_Mutation	SNP	T	T	G	rs61453891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50532155T>G	ENST00000374144.3	+	3	1853	c.1565T>G	c.(1564-1566)gTg>gGg	p.V522G	C10orf71_ENST00000323868.4_Missense_Mutation_p.V522G			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	522			V -> G (in dbSNP:rs61453891).							endometrium(1)	1						CTCTTGAAAGTGCTTGATGAG	0.502													T|||	150	0.0299521	0.1067	0.0115	5008	,	,		21076	0.0		0.001	False		,,,				2504	0.0				p.V522G		Atlas-SNP	.											.	C10orf71	179	.	0			c.T1565G						PASS	.	T	GLY/VAL,GLY/VAL	381,3695		19,343,1676	71.0	75.0	74.0		1565,1565	3.6	0.7	10	dbSNP_129	74	6,8358		0,6,4176	yes	missense,missense	C10orf71	NM_001135196.1,NM_199459.3	109,109	19,349,5852	GG,GT,TT		0.0717,9.3474,3.1109	benign,benign	522/1436,522/720	50532155	387,12053	2038	4182	6220	SO:0001583	missense	118461	exon3			TGAAAGTGCTTGA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.1565T>G	10.37:g.50532155T>G	ENSP00000363259:p.Val522Gly	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	49	0.022435897435897436	44	0.08943089430894309	5	0.013812154696132596	0	0.0	0	0.0	T	0.006	-2.028060	0.00410	0.093474	7.17E-4	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.13196	2.61;3.75	5.52	3.62	0.41486	.	0.465425	0.15896	N	0.239327	T	0.00109	0.0003	N	0.00170	-1.935	0.37892	D	0.930737	B	0.02656	0.0	B	0.01281	0.0	T	0.35001	-0.9806	10	0.08599	T	0.76	.	4.4351	0.11547	0.071:0.3245:0.3604:0.2441	rs61453891	522	Q711Q0-3	.	G	522	ENSP00000318713:V522G;ENSP00000363259:V522G	ENSP00000318713:V522G	V	+	2	0	C10orf71	50202161	0.998000	0.40836	0.723000	0.30687	0.214000	0.24535	1.664000	0.37439	0.651000	0.30788	-0.202000	0.12741	GTG	T|0.977;G|0.023	0.023	strong		0.502	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
KCNMA1	3778	hgsc.bcm.edu	37	10	78944590	78944590	+	Silent	SNP	G	G	A	rs1131824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:78944590G>A	ENST00000286628.8	-	4	686	c.687C>T	c.(685-687)ttC>ttT	p.F229F	KCNMA1_ENST00000286627.5_Silent_p.F229F|KCNMA1_ENST00000406533.3_Silent_p.F229F|KCNMA1_ENST00000404771.3_Silent_p.F229F|KCNMA1_ENST00000354353.5_Silent_p.F229F|KCNMA1_ENST00000404857.1_Silent_p.F229F|KCNMA1_ENST00000372440.1_Silent_p.F229F|KCNMA1_ENST00000372443.1_Silent_p.F229F	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	229					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	CCCGCAAGCCGAAGTAGAGAA	0.468													A|||	2033	0.40595	0.705	0.2695	5008	,	,		18937	0.249		0.335	False		,,,				2504	0.3333				p.F229F		Atlas-SNP	.											.	KCNMA1	370	.	0			c.C687T						PASS	.	A	,,,	2735,1671	508.4+/-367.0	857,1021,325	155.0	140.0	145.0		687,687,687,687	5.3	1.0	10	dbSNP_86	145	3109,5491	658.9+/-401.6	549,2011,1740	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNMA1	NM_001014797.2,NM_001161352.1,NM_001161353.1,NM_002247.3	,,,	1406,3032,2065	AA,AG,GG		36.1512,37.9256,44.9331	,,,	229/1183,229/1237,229/1220,229/1179	78944590	5844,7162	2203	4300	6503	SO:0001819	synonymous_variant	3778	exon4			CAAGCCGAAGTAG	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6284	protein-coding gene	gene with protein product	"""BK channel alpha subunit"""	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.687C>T	10.37:g.78944590G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_001161352	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Silent	SNP	ENST00000286628.8	37		835|835	0.3823260073260073|0.3823260073260073	335|335	0.6808943089430894|0.6808943089430894	108|108	0.2983425414364641|0.2983425414364641	138|138	0.24125874125874125|0.24125874125874125	254|254	0.33509234828496043|0.33509234828496043	A|A	6.974|6.974	0.549742|0.549742	0.13374|0.13374	0.620744|0.620744	0.361512|0.361512	ENSG00000156113|ENSG00000156113	ENST00000372421|ENST00000372403	.|.	.|.	.|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.45366|0.45366	-0.9266|-0.9266	3|3	.|.	.|.	.|.	-11.1608|-11.1608	10.553|10.553	0.45101|0.45101	0.8628:0.0:0.1372:0.0|0.8628:0.0:0.1372:0.0	rs1131824;rs2227912;rs2296678;rs3192016;rs7098260;rs17414082;rs17482985;rs41318619;rs57078861;rs1131824|rs1131824;rs2227912;rs2296678;rs3192016;rs7098260;rs17414082;rs17482985;rs41318619;rs57078861;rs1131824	.|.	.|.	.|.	W|L	218|180	.|.	.|.	R|S	-|-	1|2	2|0	KCNMA1|KCNMA1	78614596|78614596	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.952000|0.952000	0.60782|0.60782	1.408000|1.408000	0.34668|0.34668	1.101000|1.101000	0.41535|0.41535	-0.254000|-0.254000	0.11334|0.11334	CGG|TCG	G|0.579;A|0.421	0.421	strong		0.468	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247	
BIRC6	57448	hgsc.bcm.edu	37	2	32822957	32822957	+	Silent	SNP	G	G	A	rs2710625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32822957G>A	ENST00000421745.2	+	69	13886	c.13752G>A	c.(13750-13752)acG>acA	p.T4584T		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4584	Ubiquitin-conjugating.				apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.T4584T(1)|p.T4556T(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AAGCTGTGACGCTTTCAACCT	0.438													A|||	1667	0.332867	0.3207	0.3674	5008	,	,		15901	0.2956		0.4344	False		,,,				2504	0.2587				p.T4584T	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,NS,carcinoma,0,2	BIRC6	838	2	2	Substitution - coding silent(2)	stomach(2)	c.G13752A						PASS	.	A		1392,3014	688.7+/-405.0	208,976,1019	122.0	100.0	108.0		13752	-9.8	0.0	2	dbSNP_100	108	3646,4954	623.3+/-397.4	773,2100,1427	no	coding-synonymous	BIRC6	NM_016252.3		981,3076,2446	AA,AG,GG		42.3953,31.5933,38.736		4584/4858	32822957	5038,7968	2203	4300	6503	SO:0001819	synonymous_variant	57448	exon69			TGTGACGCTTTCA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.13752G>A	2.37:g.32822957G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	67	25	0.373134	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			G|0.624;A|0.376	0.376	strong		0.438	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
C6orf223	221416	hgsc.bcm.edu	37	6	43970658	43970658	+	Missense_Mutation	SNP	T	T	A	rs115402675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43970658T>A	ENST00000336600.5	+	4	544	c.524T>A	c.(523-525)cTt>cAt	p.L175H	C6orf223_ENST00000448947.2_3'UTR|RP5-1120P11.1_ENST00000422059.1_RNA|C6orf223_ENST00000439969.2_3'UTR|RP5-1120P11.1_ENST00000607590.1_RNA|C6orf223_ENST00000442114.2_Missense_Mutation_p.L155H	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	175								p.L175H(1)		central_nervous_system(1)|lung(2)|pancreas(1)|prostate(1)|urinary_tract(1)	6	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)			GAGTCCCTTCTTCGCGGCCTC	0.731													T|||	243	0.0485224	0.0711	0.0403	5008	,	,		9653	0.0476		0.0457	False		,,,				2504	0.0276				p.L175H		Atlas-SNP	.											C6orf223,NS,carcinoma,0,1	C6orf223	14	1	1	Substitution - Missense(1)	pancreas(1)	c.T524A						PASS	.	T	HIS/LEU,	261,4095		7,247,1924	11.0	15.0	14.0		524,	-4.4	0.0	6	dbSNP_132	14	263,8263		4,255,4004	yes	missense,utr-3	C6orf223	NM_153246.4,NM_001171992.1	99,	11,502,5928	AA,AT,TT		3.0847,5.9917,4.0677	probably-damaging,	175/243,	43970658	524,12358	2178	4263	6441	SO:0001583	missense	221416	exon4			CCCTTCTTCGCGG	BC032706	CCDS34459.1, CCDS55016.1	6p21.1	2012-09-05			ENSG00000181577	ENSG00000181577			28692	protein-coding gene	gene with protein product						12477932	Standard	NM_153246		Approved	MGC45491	uc003own.3	Q8N319	OTTHUMG00000014753	ENST00000336600.5:c.524T>A	6.37:g.43970658T>A	ENSP00000426159:p.Leu175His	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_153246	E9PB59|Q8N575	Missense_Mutation	SNP	ENST00000336600.5	37	CCDS34459.1	112	0.05128205128205128	34	0.06910569105691057	18	0.049723756906077346	23	0.04020979020979021	37	0.048812664907651716	T	10.08	1.252805	0.22965	0.059917	0.030847	ENSG00000181577	ENST00000336600	T	0.44482	0.92	3.15	-4.4	0.03600	.	1.404370	0.05315	N	0.525593	T	0.12646	0.0307	N	0.08118	0	0.09310	N	0.999996	D	0.55385	0.971	P	0.50490	0.642	T	0.07693	-1.0759	10	0.87932	D	0	.	5.4409	0.16509	0.0:0.218:0.5041:0.2779	.	175	Q8N319	CF223_HUMAN	H	175	ENSP00000426159:L175H	ENSP00000426159:L175H	L	+	2	0	C6orf223	44078636	0.000000	0.05858	0.000000	0.03702	0.235000	0.25334	0.573000	0.23699	-0.896000	0.03915	-0.496000	0.04628	CTT	T|0.955;A|0.045	0.045	strong		0.731	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246	
ZNF229	7772	hgsc.bcm.edu	37	19	44934653	44934653	+	Silent	SNP	T	T	C	rs8113370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44934653T>C	ENST00000588931.1	-	6	736	c.303A>G	c.(301-303)aaA>aaG	p.K101K	CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000291187.4_Silent_p.K95K|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	101	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				AGGAGAGCTCTTTGTGTGAAA	0.413													T|||	817	0.163139	0.1906	0.3228	5008	,	,		20023	0.1558		0.1074	False		,,,				2504	0.0777				p.K101K		Atlas-SNP	.											.	ZNF229	123	.	0			c.A303G						PASS	.	T		625,3057		51,523,1267	61.0	58.0	59.0		303	0.9	0.0	19	dbSNP_116	59	905,7281		54,797,3242	no	coding-synonymous	ZNF229	NM_014518.2		105,1320,4509	CC,CT,TT		11.0555,16.9745,12.8918		101/826	44934653	1530,10338	1841	4093	5934	SO:0001819	synonymous_variant	7772	exon6			GAGCTCTTTGTGT	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.303A>G	19.37:g.44934653T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_014518	B2RWN3|Q59FV2|Q86WL9	Silent	SNP	ENST00000588931.1	37	CCDS42574.1																																																																																			T|0.846;C|0.154	0.154	strong		0.413	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
SLC22A14	9389	hgsc.bcm.edu	37	3	38347633	38347633	+	Missense_Mutation	SNP	G	G	A	rs34043027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38347633G>A	ENST00000273173.4	+	1	207	c.116G>A	c.(115-117)cGc>cAc	p.R39H	RNU6-235P_ENST00000362644.1_RNA|SLC22A14_ENST00000448498.1_Missense_Mutation_p.R39H	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	39					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)		ATGCTGTTACGCAGATTGAGG	0.537													G|||	376	0.0750799	0.0726	0.0605	5008	,	,		22758	0.1617		0.0596	False		,,,				2504	0.0153				p.R39H		Atlas-SNP	.											SLC22A14,NS,lymphoid_neoplasm,+1,1	SLC22A14	64	1	0			c.G116A						PASS	.	G	HIS/ARG	320,4086	172.3+/-202.3	14,292,1897	187.0	166.0	173.0		116	-4.6	0.0	3	dbSNP_126	173	405,8195	129.5+/-187.6	12,381,3907	yes	missense	SLC22A14	NM_004803.3	29	26,673,5804	AA,AG,GG		4.7093,7.2628,5.5744	benign	39/595	38347633	725,12281	2203	4300	6503	SO:0001583	missense	9389	exon1			TGTTACGCAGATT	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.116G>A	3.37:g.38347633G>A	ENSP00000273173:p.Arg39His	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	171	87	0.508772	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	197	0.0902014652014652	42	0.08536585365853659	19	0.052486187845303865	85	0.1486013986013986	51	0.06728232189973615	G	7.254	0.603853	0.14002	0.072628	0.047093	ENSG00000144671	ENST00000448498;ENST00000423219;ENST00000273173	T;T	0.36520	1.25;1.25	4.33	-4.6	0.03390	.	6.492390	0.00622	N	0.000455	T	0.00144	0.0004	L	0.32530	0.975	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.09751	-1.0660	9	0.30078	T	0.28	.	6.9982	0.24795	0.5288:0.0:0.356:0.1152	rs34043027	39	Q9Y267	S22AE_HUMAN	H	39	ENSP00000396283:R39H;ENSP00000273173:R39H	ENSP00000273173:R39H	R	+	2	0	SLC22A14	38322637	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.755000	0.04782	-1.068000	0.03156	-1.817000	0.00601	CGC	G|0.933;A|0.067	0.067	strong		0.537	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632744	32632744	+	Silent	SNP	C	C	T	rs1049082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32632744C>T	ENST00000399084.1	-	3	388	c.210G>A	c.(208-210)gcG>gcA	p.A70A	HLA-DQB1_ENST00000399079.3_Silent_p.A70A|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000374943.4_Silent_p.A70A|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Silent_p.A70A			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	41	0	0		WXS	Illumina HiSeq	Phase_I	20	20	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																																																																																			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	
HIST3H3	8290	hgsc.bcm.edu	37	1	228612934	228612934	+	Silent	SNP	A	A	G	rs61740979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228612934A>G	ENST00000366696.1	-	1	92	c.93T>C	c.(91-93)ccT>ccC	p.P31P		NM_003493.2	NP_003484.1	Q16695	H31T_HUMAN	histone cluster 3, H3	31					telomere maintenance (GO:0000723)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(2)|prostate(2)|skin(1)	6		Prostate(94;0.0724)				CGCCAGTGGCAGGTGCGCTCT	0.667													g|||	80	0.0159744	0.0567	0.0058	5008	,	,		13386	0.0		0.001	False		,,,				2504	0.0				p.P31P		Atlas-SNP	.											.	HIST3H3	20	.	0			c.T93C						PASS	.	C		240,4162		1,238,1962	36.0	43.0	41.0		93	-6.5	0.0	1	dbSNP_129	41	0,8594		0,0,4297	no	coding-synonymous	HIST3H3	NM_003493.2		1,238,6259	GG,GA,AA		0.0,5.4521,1.8467		31/137	228612934	240,12756	2201	4297	6498	SO:0001819	synonymous_variant	8290	exon1			AGTGGCAGGTGCG	Z49861	CCDS1572.1	1q42.13	2012-09-19	2006-10-11	2003-02-21	ENSG00000168148	ENSG00000168148		"""Histones / Replication-dependent"""	4778	protein-coding gene	gene with protein product		602820	"""H3 histone family, member T"", ""histone 3, H3"""	H3FT		8834248, 12408966	Standard	NM_003493		Approved	H3t, H3/g, H3.4	uc001hsx.1	Q16695	OTTHUMG00000040044	ENST00000366696.1:c.93T>C	1.37:g.228612934A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	64	24	0.375	NM_003493	B2R5K3|Q6FGU4	Silent	SNP	ENST00000366696.1	37	CCDS1572.1																																																																																			A|0.981;G|0.019	0.019	strong		0.667	HIST3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096595.2	NM_003493	
UPK1A	11045	hgsc.bcm.edu	37	19	36168914	36168914	+	Missense_Mutation	SNP	T	T	C	rs2285421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36168914T>C	ENST00000222275.2	+	7	770	c.770T>C	c.(769-771)aTg>aCg	p.M257T	UPK1A_ENST00000379013.2_3'UTR	NM_007000.2	NP_008931.1	O00322	UPK1A_HUMAN	uroplakin 1A	257			M -> T (in dbSNP:rs2285421). {ECO:0000269|PubMed:15489334}.		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)			TTCTACACCATGCTCTGAGGG	0.647													C|||	3299	0.658746	0.8359	0.5029	5008	,	,		14729	0.6161		0.5	False		,,,				2504	0.7372				p.M257T		Atlas-SNP	.											.	UPK1A	23	.	0			c.T770C						PASS	.	C	THR/MET	3461,943	337.3+/-304.8	1355,751,96	47.0	49.0	48.0		770	0.5	0.1	19	dbSNP_100	48	4165,4435	555.1+/-386.6	982,2201,1117	yes	missense	UPK1A	NM_007000.2	81	2337,2952,1213	CC,CT,TT		48.4302,21.4124,41.3565	benign	257/259	36168914	7626,5378	2202	4300	6502	SO:0001583	missense	11045	exon7			ACACCATGCTCTG	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.770T>C	19.37:g.36168914T>C	ENSP00000222275:p.Met257Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_007000	Q3KNU5|Q3KNU6	Missense_Mutation	SNP	ENST00000222275.2	37	CCDS12470.1	1339	0.6130952380952381	401	0.8150406504065041	188	0.5193370165745856	361	0.6311188811188811	389	0.5131926121372031	C	7.118	0.577334	0.13686	0.785876	0.484302	ENSG00000105668	ENST00000222275	T	0.05025	3.51	5.22	0.485	0.16830	.	.	.	.	.	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	0.11470	-1.0586	8	0.09843	T	0.71	.	4.7632	0.13118	0.1406:0.4845:0.0:0.3749	rs2285421;rs17652127;rs52810906;rs58866560;rs2285421	257	O00322	UPK1A_HUMAN	T	257	ENSP00000222275:M257T	ENSP00000222275:M257T	M	+	2	0	UPK1A	40860754	0.015000	0.18098	0.101000	0.21167	0.255000	0.26057	-0.031000	0.12287	0.085000	0.17107	-0.929000	0.02709	ATG	T|0.391;C|0.609	0.609	strong		0.647	UPK1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109486.3		
OBSCN	84033	hgsc.bcm.edu	37	1	228494696	228494696	+	Silent	SNP	G	G	A	rs4653939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228494696G>A	ENST00000422127.1	+	45	12065	c.12021G>A	c.(12019-12021)gcG>gcA	p.A4007A	OBSCN_ENST00000284548.11_Silent_p.A4007A|OBSCN_ENST00000570156.2_Silent_p.A4964A|OBSCN_ENST00000366709.4_Silent_p.A1126A|OBSCN_ENST00000366707.4_Silent_p.A1641A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4007	Ig-like 41.				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)				GGGCGGGTGCGAGCGTGGAGT	0.652													G|||	1545	0.308506	0.3714	0.2925	5008	,	,		20661	0.497		0.1869	False		,,,				2504	0.1656				p.A4964A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G14892A						PASS	.	G	,	1627,2743		313,1001,871	40.0	48.0	45.0		12021,12021	-5.7	0.0	1	dbSNP_111	45	1661,6879		162,1337,2771	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	475,2338,3642	AA,AG,GG		19.4496,37.2311,25.4686	,	4007/7969,4007/6621	228494696	3288,9622	2185	4270	6455	SO:0001819	synonymous_variant	84033	exon56			GGGTGCGAGCGTG	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.12021G>A	1.37:g.228494696G>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	269	269	1	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																																																																																			G|0.667;A|0.333	0.333	strong		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SECTM1	6398	hgsc.bcm.edu	37	17	80280054	80280054	+	Missense_Mutation	SNP	A	A	C	rs61738919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80280054A>C	ENST00000269389.3	-	5	1080	c.730T>G	c.(730-732)Tat>Gat	p.Y244D	SECTM1_ENST00000580437.1_3'UTR	NM_003004.2	NP_002995.1	Q8WVN6	SCTM1_HUMAN	secreted and transmembrane 1	244					immune response (GO:0006955)|mesoderm development (GO:0007498)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine activity (GO:0005125)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(2)|lung(1)	4	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00928)|BRCA - Breast invasive adenocarcinoma(99;0.0833)			TCTGCGGCATATGGAAACAAG	0.657													C|||	241	0.048123	0.1097	0.0562	5008	,	,		16080	0.0		0.0398	False		,,,				2504	0.0174				p.Y244D		Atlas-SNP	.											.	SECTM1	14	.	0			c.T730G						PASS	.	C	ASP/TYR	478,3928	781.3+/-414.5	24,430,1749	64.0	67.0	66.0		730	-0.8	0.0	17	dbSNP_129	66	414,8186	800.7+/-407.4	12,390,3898	yes	missense	SECTM1	NM_003004.2	160	36,820,5647	CC,CA,AA		4.814,10.8488,6.8584	benign	244/249	80280054	892,12114	2203	4300	6503	SO:0001583	missense	6398	exon5			CGGCATATGGAAA	U77643	CCDS11808.1	17q25	2008-07-18				ENSG00000141574			10707	protein-coding gene	gene with protein product	"""K12 protein"", ""type 1a transmembrane protein"""	602602				9480746	Standard	NM_003004		Approved	K12	uc002keo.3	Q8WVN6		ENST00000269389.3:c.730T>G	17.37:g.80280054A>C	ENSP00000269389:p.Tyr244Asp	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_003004	B2R7H0|O00466	Missense_Mutation	SNP	ENST00000269389.3	37	CCDS11808.1	111	0.050824175824175824	59	0.11991869918699187	20	0.055248618784530384	0	0.0	32	0.04221635883905013	C	0.004	-2.337026	0.00224	0.108488	0.04814	ENSG00000141574	ENST00000269389	.	.	.	0.64	-0.758	0.11049	.	.	.	.	.	T	0.00144	0.0004	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	0.18999	-1.0319	6	0.02654	T	1	.	.	.	.	.	244;244	Q8WVN6;A8K3U3	SCTM1_HUMAN;.	D	244	.	ENSP00000269389:Y244D	Y	-	1	0	SECTM1	77873343	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.176000	0.09811	-1.026000	0.03330	-0.648000	0.03929	TAT	A|0.935;C|0.065	0.065	strong		0.657	SECTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442856.1	NM_003004	
INMT	11185	hgsc.bcm.edu	37	7	30795146	30795146	+	Silent	SNP	C	C	T	rs6966180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30795146C>T	ENST00000013222.5	+	3	487	c.471C>T	c.(469-471)gcC>gcT	p.A157A	INMT-FAM188B_ENST00000458257.1_Intron|INMT_ENST00000409539.1_Silent_p.A156A|INMT_ENST00000484180.1_3'UTR	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	157					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						TGCCTCTCGCCGACTGTGTGC	0.657													C|||	187	0.0373403	0.1346	0.013	5008	,	,		19119	0.0		0.0	False		,,,				2504	0.0				p.A157A		Atlas-SNP	.											.	INMT	38	.	0			c.C471T						PASS	.	C	,	515,3891	239.0+/-250.2	33,449,1721	85.0	72.0	76.0		468,471	-8.1	0.0	7	dbSNP_116	76	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	INMT	NM_001199219.1,NM_006774.4	,	33,453,6017	TT,TC,CC		0.0465,11.6886,3.9905	,	156/263,157/264	30795146	519,12487	2203	4300	6503	SO:0001819	synonymous_variant	11185	exon3			TCTCGCCGACTGT		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.471C>T	7.37:g.30795146C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Silent	SNP	ENST00000013222.5	37	CCDS5430.1																																																																																			C|0.962;T|0.038	0.038	strong		0.657	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
OR5T2	219464	hgsc.bcm.edu	37	11	55999879	55999879	+	Silent	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55999879C>A	ENST00000313264.4	-	1	858	c.783G>T	c.(781-783)ctG>ctT	p.L261L		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					GAATGGCCAACAGAATCAAAC	0.438																																					p.L261L		Atlas-SNP	.											OR5T2,NS,carcinoma,0,1	OR5T2	107	1	0			c.G783T						scavenged	.						129.0	120.0	123.0					11																	55999879		2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			GGCCAACAGAATC	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.783G>T	11.37:g.55999879C>A		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	219	94	0.429224	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	37	CCDS31523.1																																																																																			.	.	none		0.438	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
LMTK3	114783	hgsc.bcm.edu	37	19	49001600	49001600	+	Missense_Mutation	SNP	A	A	G	rs61745738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49001600A>G	ENST00000600059.1	-	11	2953	c.2726T>C	c.(2725-2727)gTc>gCc	p.V909A	LMTK3_ENST00000270238.3_Missense_Mutation_p.V938A			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	909	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		GTTGCCCAGGACTGTCGGGTC	0.667													G|||	503	0.100439	0.2398	0.0634	5008	,	,		13447	0.0079		0.0527	False		,,,				2504	0.0828				p.V938A		Atlas-SNP	.											.	LMTK3	125	.	0			c.T2813C						PASS	.	G	ALA/VAL	764,3070		85,594,1238	27.0	31.0	30.0		2813	-0.0	0.2	19	dbSNP_129	30	354,7868		9,336,3766	yes	missense	LMTK3	NM_001080434.1	64	94,930,5004	GG,GA,AA		4.3055,19.927,9.2734	benign	938/1490	49001600	1118,10938	1917	4111	6028	SO:0001583	missense	114783	exon12			CCCAGGACTGTCG	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 101"""						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.2726T>C	19.37:g.49001600A>G	ENSP00000472020:p.Val909Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_001080434	Q4G0U1	Missense_Mutation	SNP	ENST00000600059.1	37		185	0.08470695970695971	110	0.22357723577235772	28	0.07734806629834254	6	0.01048951048951049	41	0.05408970976253298	a	0	-2.762715	0.00082	0.19927	0.043055	ENSG00000142235	ENST00000270238	T	0.79033	-1.23	3.89	-0.00579	0.14016	.	1.029000	0.07801	N	0.956498	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	0.02721	-1.1119	9	0.02654	T	1	.	7.0955	0.25307	0.5615:0.0:0.4385:0.0	.	909	Q96Q04	LMTK3_HUMAN	A	938	ENSP00000270238:V938A	ENSP00000270238:V938A	V	-	2	0	LMTK3	53693412	0.045000	0.20229	0.186000	0.23195	0.001000	0.01503	0.353000	0.20130	-0.400000	0.07656	-0.386000	0.06593	GTC	A|0.922;G|0.078	0.078	strong		0.667	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895	
GRHL1	29841	hgsc.bcm.edu	37	2	10101289	10101289	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10101289C>T	ENST00000324907.9	+	4	529	c.393C>T	c.(391-393)ggC>ggT	p.G131G	GRHL1_ENST00000324883.5_5'UTR|GRHL1_ENST00000405379.2_Silent_p.G131G	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	131					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)		ACCAGCTGGGCATTGATAAGA	0.498																																					p.G131G		Atlas-SNP	.											.	GRHL1	95	.	0			c.C393T						PASS	.						77.0	84.0	81.0					2																	10101289		1327	2309	3636	SO:0001819	synonymous_variant	29841	exon4			GCTGGGCATTGAT	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.393C>T	2.37:g.10101289C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	181	80	0.441989	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Silent	SNP	ENST00000324907.9	37	CCDS33144.2																																																																																			.	.	none		0.498	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552	
MYO19	80179	hgsc.bcm.edu	37	17	34856697	34856697	+	Missense_Mutation	SNP	A	A	G	rs56919948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34856697A>G	ENST00000431794.3	-	23	2872	c.2350T>C	c.(2350-2352)Tgg>Cgg	p.W784R	MYO19_ENST00000268852.9_Missense_Mutation_p.W584R	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	784	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					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)		ACGGCCCGCCACTGCCGCTCC	0.637													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		18434	0.0		0.0	False		,,,				2504	0.0				p.W784R		Atlas-SNP	.											.	MYO19	130	.	0			c.T2350C						PASS	.	G	ARG/TRP,ARG/TRP	74,4174		1,72,2051	14.0	18.0	17.0		2350,1750	2.8	0.4	17	dbSNP_129	17	0,8448		0,0,4224	yes	missense,missense	MYO19	NM_001163735.1,NM_025109.5	101,101	1,72,6275	GG,GA,AA		0.0,1.742,0.5829	benign,benign	784/971,584/771	34856697	74,12622	2124	4224	6348	SO:0001583	missense	80179	exon24			CCCGCCACTGCCG	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.2350T>C	17.37:g.34856697A>G	ENSP00000409936:p.Trp784Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	0.005	-2.234560	0.00277	0.01742	0.0	ENSG00000141140	ENST00000431794;ENST00000268852	T;T	0.53640	0.61;0.61	5.12	2.82	0.32997	.	0.000000	0.42548	N	0.000694	T	0.04770	0.0129	N	0.00197	-1.87	0.24385	N	0.994776	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33727	-0.9857	10	0.05959	T	0.93	.	6.7399	0.23431	0.1403:0.0:0.3167:0.543	rs56919948;rs61753952	784;584	Q96H55;Q96H55-4	MYO19_HUMAN;.	R	784;584	ENSP00000409936:W784R;ENSP00000268852:W584R	ENSP00000268852:W584R	W	-	1	0	MYO19	31930810	0.989000	0.36119	0.423000	0.26634	0.007000	0.05969	1.804000	0.38873	0.033000	0.15463	-1.507000	0.00952	TGG	A|0.996;G|0.004	0.004	strong		0.637	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33588874	33588874	+	IGR	SNP	G	G	A	rs76931580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33588874G>A	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Silent_p.T1838T			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein						calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			TGGAGCAGACGGTGCGCGAGC	0.647													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		17893	0.0		0.0	False		,,,				2504	0.0				p.T1838T		Atlas-SNP	.											.	MYH7B	145	.	0			c.G5514A						PASS	.	G		149,4255	97.1+/-135.8	0,149,2053	40.0	50.0	47.0		5514	-9.1	0.1	20	dbSNP_131	47	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	MYH7B	NM_020884.3		0,151,6351	AA,AG,GG		0.0233,3.3833,1.1612		1838/1984	33588874	151,12853	2202	4300	6502	SO:0001628	intergenic_variant	57644	exon41			GCAGACGGTGCGC	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319		20.37:g.33588874G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	192	85	0.442708	NM_020884	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			G|0.996;A|0.004	0.004	strong		0.647	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
SCN5A	6331	hgsc.bcm.edu	37	3	38592356	38592356	+	Missense_Mutation	SNP	A	A	G	rs45563942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38592356A>G	ENST00000333535.4	-	28	5656	c.5507T>C	c.(5506-5508)aTc>aCc	p.I1836T	SCN5A_ENST00000413689.1_Missense_Mutation_p.I1836T|SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000451551.2_Missense_Mutation_p.I1782T|SCN5A_ENST00000425664.1_Missense_Mutation_p.I1818T|SCN5A_ENST00000450102.2_Missense_Mutation_p.I1782T|SCN5A_ENST00000414099.2_Missense_Mutation_p.I1818T|SCN5A_ENST00000443581.1_Missense_Mutation_p.I1835T|SCN5A_ENST00000455624.2_Missense_Mutation_p.I1803T|SCN5A_ENST00000423572.2_Missense_Mutation_p.I1835T|SCN5A_ENST00000449557.2_Missense_Mutation_p.I1782T			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1836					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)	GTCCATGTTGATGAGGCTTAT	0.552													A|||	8	0.00159744	0.0061	0.0	5008	,	,		21013	0.0		0.0	False		,,,				2504	0.0				p.I1836T		Atlas-SNP	.											.	SCN5A	634	.	0			c.T5507C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE	11,4249		0,11,2119	85.0	92.0	90.0		5504,5507,5453,5408,5345,5507	4.8	1.0	3	dbSNP_127	90	0,8484		0,0,4242	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	89,89,89,89,89,89	0,11,6361	GG,GA,AA		0.0,0.2582,0.0863	benign,benign,benign,benign,benign,benign	1835/2016,1836/2017,1818/1999,1803/1984,1782/1963,1836/2017	38592356	11,12733	2130	4242	6372	SO:0001583	missense	6331	exon28			ATGTTGATGAGGC	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.5507T>C	3.37:g.38592356A>G	ENSP00000328968:p.Ile1836Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_198056	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	16.43	3.122483	0.56613	0.002582	0.0	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.96427	-3.92;-3.93;-3.93;-4.0;-3.93;-3.92;-3.93;-4.01;-4.0;-4.0	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.97539	0.9194	M	0.89095	3.005	0.49213	D	0.999767	B;P;B;B;B;B	0.50710	0.146;0.938;0.07;0.17;0.065;0.261	B;D;B;P;B;P	0.73380	0.379;0.98;0.265;0.547;0.351;0.734	D	0.96083	0.9055	10	0.66056	D	0.02	.	14.5421	0.68002	1.0:0.0:0.0:0.0	rs45563942	1782;1803;1818;1836;1835;1836	E9PEF3;E9PHB6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;SCN5A_HUMAN;.;.	T	1818;1835;1836;1782;1835;1818;1836;1803;1782;1782	ENSP00000398962:I1818T;ENSP00000398266:I1835T;ENSP00000410257:I1836T;ENSP00000388797:I1782T;ENSP00000397915:I1835T;ENSP00000416634:I1818T;ENSP00000328968:I1836T;ENSP00000399524:I1803T;ENSP00000403355:I1782T;ENSP00000413996:I1782T	ENSP00000328968:I1836T	I	-	2	0	SCN5A	38567360	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.133000	0.94460	2.025000	0.59659	0.460000	0.39030	ATC	A|0.999;G|0.001	0.001	strong		0.552	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
GALM	130589	hgsc.bcm.edu	37	2	38916970	38916970	+	Missense_Mutation	SNP	A	A	T	rs6741892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	175	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	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	
EIF2B3	8891	hgsc.bcm.edu	37	1	45444038	45444038	+	Silent	SNP	G	G	A	rs11556200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	113	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	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	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34831866	34831866	+	Silent	SNP	G	G	A	rs3734264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:34831866G>A	ENST00000192788.5	+	15	3474	c.3303G>A	c.(3301-3303)acG>acA	p.T1101T	UHRF1BP1_ENST00000452449.2_Silent_p.T1101T	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	1101							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						TGAAGAGGACGGTATCTCAAC	0.507													A|||	2321	0.463458	0.7723	0.3112	5008	,	,		19112	0.4573		0.338	False		,,,				2504	0.2894				p.T1101T		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.G3303A						PASS	.	A		2641,1405		881,879,263	133.0	140.0	138.0		3303	-9.9	0.0	6	dbSNP_107	138	2865,5493		495,1875,1809	no	coding-synonymous	UHRF1BP1	NM_017754.3		1376,2754,2072	AA,AG,GG		34.2785,34.7257,44.3889		1101/1441	34831866	5506,6898	2023	4179	6202	SO:0001819	synonymous_variant	54887	exon15			GAGGACGGTATCT	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.3303G>A	6.37:g.34831866G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	128	49	0.382812	NM_017754	Q9NXE0	Silent	SNP	ENST00000192788.5	37	CCDS43455.1																																																																																			G|0.537;A|0.463	0.463	strong		0.507	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
SIDT1	54847	hgsc.bcm.edu	37	3	113285272	113285272	+	Silent	SNP	A	A	C	rs61734094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113285272A>C	ENST00000264852.4	+	2	954	c.228A>C	c.(226-228)acA>acC	p.T76T	SIDT1_ENST00000393830.3_Silent_p.T76T	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	76					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						TGCAGGTGACAGCCGTGAGGG	0.507													C|||	101	0.0201677	0.0545	0.0086	5008	,	,		19117	0.0079		0.0099	False		,,,				2504	0.0051				p.T76T		Atlas-SNP	.											.	SIDT1	99	.	0			c.A228C						PASS	.	C		265,4141	802.1+/-415.6	10,245,1948	246.0	191.0	210.0		228	-11.2	0.0	3	dbSNP_129	210	60,8540	816.6+/-406.9	2,56,4242	no	coding-synonymous	SIDT1	NM_017699.2		12,301,6190	CC,CA,AA		0.6977,6.0145,2.4988		76/828	113285272	325,12681	2203	4300	6503	SO:0001819	synonymous_variant	54847	exon2			GGTGACAGCCGTG	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.228A>C	3.37:g.113285272A>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_017699	Q17RR4	Silent	SNP	ENST00000264852.4	37	CCDS2974.1																																																																																			A|0.978;C|0.022	0.022	strong		0.507	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855647	12855647	+	Silent	SNP	C	C	T	rs200536957		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12855647C>T	ENST00000332296.7	+	4	1030	c.927C>T	c.(925-927)gaC>gaT	p.D309D	PRAMEF1_ENST00000400814.3_Silent_p.D64D	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	309					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					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)		TGGAAGAAGACATGAAGTGTC	0.498																																					p.D309D		Atlas-SNP	.											PRAMEF1,NS,carcinoma,+2,2	PRAMEF1	78	2	0			c.C927T						scavenged	.						43.0	48.0	46.0					1																	12855647		2197	4275	6472	SO:0001819	synonymous_variant	65121	exon4			AGAAGACATGAAG	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.927C>T	1.37:g.12855647C>T		Somatic	376	61	0.162234		WXS	Illumina HiSeq	Phase_I	426	39	0.0915493	NM_023013	Q9UQP2	Silent	SNP	ENST00000332296.7	37	CCDS148.1																																																																																			C|0.999;T|0.001	0.001	weak		0.498	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
MNS1	55329	hgsc.bcm.edu	37	15	56735674	56735674	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56735674T>C	ENST00000260453.3	-	7	1129	c.965A>G	c.(964-966)gAa>gGa	p.E322G	TEX9_ENST00000352903.2_Intron|TEX9_ENST00000537232.1_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	322	Glu-rich.				cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		CTGGTATAATTCTTGTCGCAC	0.294																																					p.E322G		Atlas-SNP	.											MNS1,colon,carcinoma,-1,1	MNS1	39	1	0			c.A965G						scavenged	.						132.0	125.0	128.0					15																	56735674		2192	4291	6483	SO:0001583	missense	55329	exon7			TATAATTCTTGTC	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"""spermatogenesis associated 40"""	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.965A>G	15.37:g.56735674T>C	ENSP00000260453:p.Glu322Gly	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	108	2	0.0185185	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	37	CCDS10158.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.772713	0.90108	.	.	ENSG00000138587	ENST00000260453	T	0.11169	2.8	5.76	5.76	0.90799	.	0.045312	0.85682	D	0.000000	T	0.32734	0.0839	M	0.80183	2.485	0.80722	D	1	D	0.71674	0.998	D	0.63113	0.911	T	0.08066	-1.0740	10	0.72032	D	0.01	-24.5326	13.8137	0.63278	0.0:0.0:0.0:1.0	.	322	Q8NEH6	MNS1_HUMAN	G	322	ENSP00000260453:E322G	ENSP00000260453:E322G	E	-	2	0	MNS1	54522966	1.000000	0.71417	0.955000	0.39395	0.974000	0.67602	6.843000	0.75384	2.175000	0.68902	0.519000	0.50382	GAA	.	.	none		0.294	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365	
CTDP1	9150	hgsc.bcm.edu	37	18	77473127	77473127	+	Missense_Mutation	SNP	C	C	T	rs2279103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:77473127C>T	ENST00000299543.7	+	7	1166	c.1019C>T	c.(1018-1020)aCg>aTg	p.T340M	CTDP1_ENST00000075430.7_Missense_Mutation_p.T340M	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	340	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.		T -> M (in dbSNP:rs2279103).		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)		GAATCTCAGACGAGAAAGAAA	0.433													C|||	414	0.0826677	0.0045	0.0677	5008	,	,		16222	0.1389		0.169	False		,,,				2504	0.0521				p.T340M		Atlas-SNP	.											.	CTDP1	67	.	0			c.C1019T						PASS	.	C	MET/THR,MET/THR,MET/THR	170,4236	109.5+/-147.8	7,156,2040	54.0	53.0	54.0		662,1019,1019	0.3	0.0	18	dbSNP_100	54	1538,7062	288.6+/-298.9	139,1260,2901	yes	missense,missense,missense	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	81,81,81	146,1416,4941	TT,TC,CC		17.8837,3.8584,13.1324	benign,benign,benign	221/843,340/962,340/868	77473127	1708,11298	2203	4300	6503	SO:0001583	missense	9150	exon7			CTCAGACGAGAAA	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.1019C>T	18.37:g.77473127C>T	ENSP00000299543:p.Thr340Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	110	65	0.590909	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	37	CCDS12017.1	245	0.11217948717948718	7	0.014227642276422764	28	0.07734806629834254	70	0.12237762237762238	140	0.18469656992084432	C	2.918	-0.223925	0.06061	0.038584	0.178837	ENSG00000060069	ENST00000299543;ENST00000075430	T;T	0.09817	2.97;2.94	4.82	0.332	0.15938	NLI interacting factor (1);	0.670270	0.15369	N	0.265948	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.30114	0.165;0.269;0.103	B;B;B	0.17979	0.013;0.02;0.006	T	0.45877	-0.9231	9	0.40728	T	0.16	-3.9704	3.0092	0.06039	0.2026:0.2918:0.0:0.5055	rs2279103;rs61656723;rs2279103	221;340;340	Q9Y5B0-3;Q9Y5B0-4;Q9Y5B0	.;.;CTDP1_HUMAN	M	340	ENSP00000299543:T340M;ENSP00000075430:T340M	ENSP00000075430:T340M	T	+	2	0	CTDP1	75574115	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	0.099000	0.15210	0.186000	0.20125	-0.122000	0.15005	ACG	C|0.885;T|0.115	0.115	strong		0.433	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
C15orf43	145645	hgsc.bcm.edu	37	15	45253735	45253735	+	Missense_Mutation	SNP	A	A	T	rs77033860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45253735A>T	ENST00000340827.3	+	4	318	c.301A>T	c.(301-303)Att>Ttt	p.I101F	RNU6-1332P_ENST00000516666.1_RNA	NM_152448.2	NP_689661.1	Q8NHR7	CO043_HUMAN	chromosome 15 open reading frame 43	101										NS(1)|breast(2)|large_intestine(1)|lung(2)|skin(2)	8		all_cancers(109;3.68e-08)|all_epithelial(112;1.05e-06)|Lung NSC(122;1.42e-05)|all_lung(180;0.000112)|Melanoma(134;0.0192)		all cancers(107;7.64e-17)|GBM - Glioblastoma multiforme(94;2.03e-06)		AAGAAGAAAAATTGGTAGTTT	0.289																																					p.I101F		Atlas-SNP	.											C15orf43,NS,haematopoietic_neoplasm,0,2	C15orf43	19	2	0			c.A301T						scavenged	.						63.0	60.0	61.0					15																	45253735		2198	4293	6491	SO:0001583	missense	145645	exon4			AGAAAAATTGGTA	BC029537	CCDS10115.1	15q21.1	2006-02-03			ENSG00000167014	ENSG00000167014			28520	protein-coding gene	gene with protein product							Standard	NM_152448		Approved	MGC33951	uc001zuk.4	Q8NHR7	OTTHUMG00000131264	ENST00000340827.3:c.301A>T	15.37:g.45253735A>T	ENSP00000340644:p.Ile101Phe	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	184	10	0.0543478	NM_152448		Missense_Mutation	SNP	ENST00000340827.3	37	CCDS10115.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.274786	0.40194	.	.	ENSG00000167014	ENST00000340827	T	0.49139	0.79	4.4	3.26	0.37387	.	0.243069	0.31909	N	0.006868	T	0.35008	0.0917	L	0.29908	0.895	0.37417	D	0.913478	P	0.35383	0.498	B	0.37943	0.261	T	0.30621	-0.9972	10	0.48119	T	0.1	.	8.141	0.31082	0.7769:0.2231:0.0:0.0	.	101	Q8NHR7	CO043_HUMAN	F	101	ENSP00000340644:I101F	ENSP00000340644:I101F	I	+	1	0	C15orf43	43041027	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.732000	0.26072	0.650000	0.30769	0.448000	0.29417	ATT	A|0.989;T|0.011	0.011	strong		0.289	C15orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254032.1	NM_152448	
FURIN	5045	hgsc.bcm.edu	37	15	91419098	91419098	+	Missense_Mutation	SNP	C	C	T	rs16944971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91419098C>T	ENST00000268171.3	+	2	407	c.128C>T	c.(127-129)gCg>gTg	p.A43V		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	43			A -> V (in dbSNP:rs16944971).		cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GGAGGCCCAGCGGTGGCCAAC	0.622													C|||	143	0.0285543	0.0938	0.0173	5008	,	,		18737	0.0		0.007	False		,,,				2504	0.0				p.A43V		Atlas-SNP	.											.	FURIN	85	.	0			c.C128T						PASS	.	C	VAL/ALA	340,4048		9,322,1863	54.0	39.0	44.0		128	3.8	0.0	15	dbSNP_123	44	30,8546		0,30,4258	yes	missense	FURIN	NM_002569.2	64	9,352,6121	TT,TC,CC		0.3498,7.7484,2.8541	benign	43/795	91419098	370,12594	2194	4288	6482	SO:0001583	missense	5045	exon2			GCCCAGCGGTGGC	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.128C>T	15.37:g.91419098C>T	ENSP00000268171:p.Ala43Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	37	CCDS10364.1	52	0.023809523809523808	38	0.07723577235772358	11	0.03038674033149171	0	0.0	3	0.00395778364116095	C	3.280	-0.147217	0.06627	0.077484	0.003498	ENSG00000140564	ENST00000268171	T	0.31510	1.49	4.77	3.85	0.44370	Proteinase inhibitor, propeptide (1);	0.284147	0.31963	N	0.006784	T	0.00936	0.0031	L	0.35487	1.065	0.09310	N	1	B	0.14438	0.01	B	0.12156	0.007	T	0.09443	-1.0674	10	0.32370	T	0.25	-14.4547	4.2077	0.10497	0.2574:0.5633:0.0:0.1793	rs16944971;rs16944971	43	P09958	FURIN_HUMAN	V	43	ENSP00000268171:A43V	ENSP00000268171:A43V	A	+	2	0	FURIN	89220102	0.000000	0.05858	0.004000	0.12327	0.036000	0.12997	0.595000	0.24029	1.257000	0.44085	0.555000	0.69702	GCG	C|0.968;T|0.032	0.032	strong		0.622	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
VPS54	51542	hgsc.bcm.edu	37	2	64189566	64189566	+	Silent	SNP	A	A	G	rs17028275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:64189566A>G	ENST00000272322.4	-	7	790	c.636T>C	c.(634-636)taT>taC	p.Y212Y	VPS54_ENST00000354504.3_Silent_p.Y95Y|VPS54_ENST00000409558.4_Silent_p.Y200Y			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	212					growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						CAATATCCAGATAATGGCTCA	0.358													A|||	622	0.124201	0.3389	0.0447	5008	,	,		21239	0.006		0.0338	False		,,,				2504	0.1053				p.Y212Y		Atlas-SNP	.											.	VPS54	57	.	0			c.T636C						PASS	.	A	,	1289,3117	437.2+/-344.9	191,907,1105	61.0	58.0	59.0		600,636	4.6	1.0	2	dbSNP_123	59	294,8306	107.8+/-168.5	6,282,4012	no	coding-synonymous,coding-synonymous	VPS54	NM_001005739.1,NM_016516.2	,	197,1189,5117	GG,GA,AA		3.4186,29.2556,12.1713	,	200/966,212/978	64189566	1583,11423	2203	4300	6503	SO:0001819	synonymous_variant	51542	exon7			ATCCAGATAATGG	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 164"""	614633	"""vacuolar protein sorting 54 (yeast)"""			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.636T>C	2.37:g.64189566A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Silent	SNP	ENST00000272322.4	37	CCDS33208.1																																																																																			A|0.893;G|0.107	0.107	strong		0.358	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516	
STAB2	55576	hgsc.bcm.edu	37	12	104089586	104089586	+	Silent	SNP	C	C	T	rs17034395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:104089586C>T	ENST00000388887.2	+	33	3750	c.3546C>T	c.(3544-3546)atC>atT	p.I1182I		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						ACAATGCCATCGAGAATTACA	0.403													.|||	380	0.0758786	0.2269	0.0231	5008	,	,		24489	0.0		0.0	False		,,,				2504	0.0654				p.I1182I		Atlas-SNP	.											.	STAB2	370	.	0			c.C3546T						PASS	.	C		855,3551	335.5+/-303.9	98,659,1446	112.0	110.0	110.0		3546	-1.1	1.0	12	dbSNP_123	110	19,8581	12.6+/-44.7	0,19,4281	no	coding-synonymous	STAB2	NM_017564.9		98,678,5727	TT,TC,CC		0.2209,19.4054,6.72		1182/2552	104089586	874,12132	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon33			TGCCATCGAGAAT	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.3546C>T	12.37:g.104089586C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.930;T|0.070	0.070	strong		0.403	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
MAPK13	5603	hgsc.bcm.edu	37	6	36104468	36104468	+	Silent	SNP	C	C	G	rs115013068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36104468C>G	ENST00000211287.4	+	7	793	c.531C>G	c.(529-531)gcC>gcG	p.A177A	MAPK13_ENST00000373766.5_Silent_p.A177A|MAPK13_ENST00000373761.6_Silent_p.A167A|MAPK13_ENST00000373759.1_Silent_p.A99A	NM_002754.4	NP_002745.1	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	177	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 production (GO:0032755)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|prostate(2)|skin(1)	12						ATGCAGACGCCGAGATGACTG	0.577													C|||	54	0.0107827	0.034	0.013	5008	,	,		20219	0.0		0.0	False		,,,				2504	0.0				p.A177A		Atlas-SNP	.											.	MAPK13	65	.	0			c.C531G						PASS	.	C		134,4272	94.4+/-133.1	3,128,2072	29.0	29.0	29.0		531	-10.2	0.0	6	dbSNP_132	29	0,8600		0,0,4300	no	coding-synonymous	MAPK13	NM_002754.3		3,128,6372	GG,GC,CC		0.0,3.0413,1.0303		177/366	36104468	134,12872	2203	4300	6503	SO:0001819	synonymous_variant	5603	exon7			AGACGCCGAGATG	Y10488	CCDS4818.1	6p21	2011-06-09			ENSG00000156711	ENSG00000156711	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6875	protein-coding gene	gene with protein product		602899		PRKM13		9295308, 9218798	Standard	NM_002754		Approved	SAPK4, p38delta	uc003ols.4	O15264	OTTHUMG00000014587	ENST00000211287.4:c.531C>G	6.37:g.36104468C>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	187	98	0.524064	NM_002754	O14739|O15124|Q5U4A5|Q6FI46|Q9UNU0	Silent	SNP	ENST00000211287.4	37	CCDS4818.1																																																																																			C|0.990;G|0.010	0.010	strong		0.577	MAPK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040328.1		
USP8	9101	hgsc.bcm.edu	37	15	50776525	50776525	+	Silent	SNP	T	T	C	rs10220843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:50776525T>C	ENST00000396444.3	+	12	2195	c.1857T>C	c.(1855-1857)ttT>ttC	p.F619F	USP8_ENST00000307179.4_Silent_p.F619F|USP8_ENST00000433963.1_Silent_p.F619F|USP8_ENST00000425032.3_Intron	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	619					cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		CAGGAACTTTTAGAGAGGATA	0.299													T|||	555	0.110823	0.3245	0.0634	5008	,	,		17432	0.0179		0.0328	False		,,,				2504	0.0317				p.F619F		Atlas-SNP	.											.	USP8	90	.	0			c.T1857C						PASS	.	T	,,	1075,3317	373.7+/-320.9	139,797,1260	61.0	64.0	63.0		1857,1857,1857	2.7	1.0	15	dbSNP_119	63	272,8306	101.6+/-162.9	8,256,4025	no	coding-synonymous,coding-synonymous,coding-synonymous	USP8	NM_001128610.1,NM_001128611.1,NM_005154.3	,,	147,1053,5285	CC,CT,TT		3.1709,24.4763,10.3855	,,	619/1119,619/1119,619/1119	50776525	1347,11623	2196	4289	6485	SO:0001819	synonymous_variant	9101	exon12			AACTTTTAGAGAG	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"""Ubiquitin-specific peptidases"""	12631	protein-coding gene	gene with protein product		603158	"""ubiquitin specific protease 8"""			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.1857T>C	15.37:g.50776525T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Silent	SNP	ENST00000396444.3	37	CCDS10137.1																																																																																			T|0.906;C|0.094	0.094	strong		0.299	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154	
DEFB136	613210	hgsc.bcm.edu	37	8	11831557	11831557	+	Silent	SNP	G	G	A	rs73538682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11831557G>A	ENST00000382209.2	-	2	125	c.126C>T	c.(124-126)ttC>ttT	p.F42F		NM_001033018.2	NP_001028190.2	Q30KP8	DB136_HUMAN	defensin, beta 136	42					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(2)|large_intestine(1)|lung(4)	7			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.163)		GCGGACACCCGAAGAAACATA	0.473													G|||	147	0.029353	0.1067	0.0058	5008	,	,		20997	0.0		0.002	False		,,,				2504	0.0				p.F42F		Atlas-SNP	.											.	DEFB136	16	.	0			c.C126T						PASS	.	G		356,3638		15,326,1656	169.0	174.0	173.0		126	-2.5	0.7	8	dbSNP_130	173	5,8353		0,5,4174	no	coding-synonymous	DEFB136	NM_001033018.2		15,331,5830	AA,AG,GG		0.0598,8.9134,2.9226		42/79	11831557	361,11991	1997	4179	6176	SO:0001819	synonymous_variant	613210	exon2			ACACCCGAAGAAA	DQ012026	CCDS43709.1	8p23.1	2011-07-19			ENSG00000205884	ENSG00000205884		"""Defensins, beta"""	34433	protein-coding gene	gene with protein product						16033865	Standard	NM_001033018		Approved	DEFB137	uc011kxm.2	Q30KP8	OTTHUMG00000158720	ENST00000382209.2:c.126C>T	8.37:g.11831557G>A		Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_001033018	Q4QY36	Silent	SNP	ENST00000382209.2	37	CCDS43709.1																																																																																			G|0.980;A|0.020	0.020	strong		0.473	DEFB136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351889.1	NM_001033018	
POTEE	445582	hgsc.bcm.edu	37	2	132020983	132020983	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:132020983G>A	ENST00000356920.5	+	15	2049	c.1955G>A	c.(1954-1956)cGg>cAg	p.R652Q	POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	652					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											AGTACGTTGCGGGAAGAAATT	0.353																																					p.R652Q		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,+1,1	.	.	1	0			c.G1955A						scavenged	.						22.0	23.0	23.0					2																	132020983		1916	4147	6063	SO:0001583	missense	445582	exon15			CGTTGCGGGAAGA	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.1955G>A	2.37:g.132020983G>A	ENSP00000439189:p.Arg652Gln	Somatic	573	1	0.0017452		WXS	Illumina HiSeq	Phase_I	694	85	0.122478	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	3.449	-0.112491	0.06881	.	.	ENSG00000188219	ENST00000356920	T	0.10192	2.9	0.993	0.993	0.19825	.	.	.	.	.	T	0.01976	0.0062	N	0.00392	-1.555	0.09310	N	0.999997	B	0.06786	0.001	B	0.01281	0.0	T	0.43956	-0.9359	9	0.02654	T	1	.	4.4834	0.11778	0.7821:0.0:0.2179:0.0	.	652	Q6S8J3	POTEE_HUMAN	Q	652	ENSP00000439189:R652Q	ENSP00000439189:R652Q	R	+	2	0	AC131180.1	131737453	0.003000	0.15002	0.337000	0.25536	0.033000	0.12548	0.069000	0.14552	-0.094000	0.12374	-1.451000	0.01035	CGG	.	.	none		0.353	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
HSD17B4	3295	hgsc.bcm.edu	37	5	118860938	118860938	+	Missense_Mutation	SNP	T	T	C	rs11539471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118860938T>C	ENST00000256216.6	+	18	1664	c.1531T>C	c.(1531-1533)Tgg>Cgg	p.W511R	HSD17B4_ENST00000504811.1_Missense_Mutation_p.W536R|HSD17B4_ENST00000510025.1_Missense_Mutation_p.W487R|HSD17B4_ENST00000515320.1_Missense_Mutation_p.W493R|HSD17B4_ENST00000522415.1_3'UTR|HSD17B4_ENST00000414835.2_Missense_Mutation_p.W371R|HSD17B4_ENST00000509514.1_Missense_Mutation_p.W249R|HSD17B4_ENST00000513628.1_Missense_Mutation_p.W374R	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	511	(3R)-3-hydroxydecanoyl-CoA binding. {ECO:0000250}.|Enoyl-CoA hydratase 2.|MaoC-like.		W -> R (in dbSNP:rs11539471). {ECO:0000269|PubMed:10400999}.		alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		CAGTGGAGACTGGAATCCCTT	0.333													T|||	655	0.130791	0.3585	0.0951	5008	,	,		16611	0.003		0.0646	False		,,,				2504	0.0481				p.W536R	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.T1606C						PASS	.	T	ARG/TRP,ARG/TRP,ARG/TRP	1324,3080	444.3+/-347.3	200,924,1078	113.0	106.0	108.0		1531,1606,1477	5.6	1.0	5	dbSNP_120	108	664,7934	166.8+/-218.7	26,612,3661	yes	missense,missense,missense	HSD17B4	NM_000414.3,NM_001199291.1,NM_001199292.1	101,101,101	226,1536,4739	CC,CT,TT		7.7227,30.0636,15.29	benign,benign,benign	511/737,536/762,493/719	118860938	1988,11014	2202	4299	6501	SO:0001583	missense	3295	exon19			GGAGACTGGAATC		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.1531T>C	5.37:g.118860938T>C	ENSP00000256216:p.Trp511Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Missense_Mutation	SNP	ENST00000256216.6	37	CCDS4126.1	230	0.10531135531135531	151	0.30691056910569103	30	0.08287292817679558	2	0.0034965034965034965	47	0.06200527704485488	T	17.31	3.356754	0.61293	0.300636	0.077227	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628;ENST00000509514	T;T;T;T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28;-1.28;-1.28;-1.28	5.61	5.61	0.85477	MaoC-like dehydratase (1);	0.051342	0.85682	D	0.000000	T	0.00012	0.0000	N	0.10782	0.045	0.09310	P	0.999999485192	B;B;B;B;B	0.26547	0.152;0.01;0.008;0.032;0.01	B;B;B;B;B	0.20767	0.03;0.01;0.017;0.031;0.01	T	0.04165	-1.0972	9	0.20046	T	0.44	-4.7889	14.0394	0.64665	0.0:0.0:0.0:1.0	rs11539471;rs17145454;rs52813715;rs57299690;rs11539471	536;493;487;249;511	F5HE57;E9PB82;E7EWE5;E7EPL9;P51659	.;.;.;.;DHB4_HUMAN	R	511;493;487;536;371;374;249	ENSP00000256216:W511R;ENSP00000424613:W493R;ENSP00000424940:W487R;ENSP00000420914:W536R;ENSP00000411960:W371R;ENSP00000425993:W374R;ENSP00000426272:W249R	ENSP00000256216:W511R	W	+	1	0	HSD17B4	118888837	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.293000	0.72731	2.266000	0.75297	0.533000	0.62120	TGG	T|0.864;C|0.136	0.136	strong		0.333	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	
PHYH	5264	hgsc.bcm.edu	37	10	13330402	13330402	+	Silent	SNP	T	T	C	rs473407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:13330402T>C	ENST00000263038.4	-	6	694	c.636A>G	c.(634-636)acA>acG	p.T212T	PHYH_ENST00000396913.2_Silent_p.T112T|PHYH_ENST00000396920.3_Silent_p.T195T	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	212					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|isoprenoid metabolic process (GO:0006720)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|electron carrier activity (GO:0009055)|L-ascorbic acid binding (GO:0031418)|metal ion binding (GO:0046872)|phytanoyl-CoA dioxygenase activity (GO:0048244)			NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	AGCCCTTGTGTGTGCCTGGGA	0.587													T|||	1197	0.239018	0.4312	0.1686	5008	,	,		16570	0.124		0.2286	False		,,,				2504	0.1585				p.T212T		Atlas-SNP	.											.	PHYH	50	.	0			c.A636G						PASS	.	T	,	1709,2697	509.9+/-367.4	339,1031,833	57.0	55.0	56.0		336,636	-5.6	0.3	10	dbSNP_83	56	2192,6408	372.2+/-336.6	278,1636,2386	no	coding-synonymous,coding-synonymous	PHYH	NM_001037537.1,NM_006214.3	,	617,2667,3219	CC,CT,TT		25.4884,38.788,29.9938	,	112/239,212/339	13330402	3901,9105	2203	4300	6503	SO:0001819	synonymous_variant	5264	exon6			CTTGTGTGTGCCT		CCDS7097.1, CCDS41489.1	10p13	2010-04-27	2006-01-09		ENSG00000107537	ENSG00000107537	1.14.11.18		8940	protein-coding gene	gene with protein product	"""Refsum disease"", ""phytanoyl-CoA dioxygenase"""	602026	"""phytanoyl-CoA hydroxylase (Refsum disease)"", ""phytanoyl-CoA hydroxylase"""			9326939	Standard	XM_005252469		Approved	PAHX, RD, PHYH1	uc001imf.3	O14832	OTTHUMG00000017693	ENST00000263038.4:c.636A>G	10.37:g.13330402T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_006214	A8MTS8|B1ALH5	Silent	SNP	ENST00000263038.4	37	CCDS7097.1																																																																																			T|0.728;C|0.272	0.272	strong		0.587	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2		
TET1	80312	hgsc.bcm.edu	37	10	70406747	70406747	+	Missense_Mutation	SNP	A	A	G	rs144156611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70406747A>G	ENST00000373644.4	+	4	4470	c.4261A>G	c.(4261-4263)Acc>Gcc	p.T1421A		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1421					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TGAACTGCCCACCTGCAGCTG	0.368													A|||	43	0.00858626	0.0008	0.0504	5008	,	,		19982	0.0		0.005	False		,,,				2504	0.002				p.T1421A		Atlas-SNP	.											.	TET1	255	.	0			c.A4261G						PASS	.	A	ALA/THR	4,4402	8.1+/-20.4	0,4,2199	61.0	58.0	59.0		4261	-10.4	0.0	10	dbSNP_134	59	39,8561	24.6+/-71.5	0,39,4261	yes	missense	TET1	NM_030625.2	58	0,43,6460	GG,GA,AA		0.4535,0.0908,0.3306	benign	1421/2137	70406747	43,12963	2203	4300	6503	SO:0001583	missense	80312	exon4			CTGCCCACCTGCA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.4261A>G	10.37:g.70406747A>G	ENSP00000362748:p.Thr1421Ala	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	127	54	0.425197	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	22	0.010073260073260074	0	0.0	19	0.052486187845303865	0	0.0	3	0.00395778364116095	A	11.19	1.565969	0.27915	9.08E-4	0.004535	ENSG00000138336	ENST00000373644	T	0.20881	2.04	5.22	-10.4	0.00318	TET cysteine-rich domain (1);	2.737390	0.01161	N	0.006653	T	0.01661	0.0053	L	0.31926	0.97	0.09310	N	1	B	0.14012	0.009	B	0.14023	0.01	T	0.14392	-1.0474	10	0.66056	D	0.02	.	0.6454	0.00817	0.1857:0.2739:0.184:0.3564	.	1421	Q8NFU7	TET1_HUMAN	A	1421	ENSP00000362748:T1421A	ENSP00000362748:T1421A	T	+	1	0	TET1	70076753	0.001000	0.12720	0.000000	0.03702	0.862000	0.49288	-0.836000	0.04382	-2.685000	0.00406	0.455000	0.32223	ACC	A|0.995;G|0.005	0.005	strong		0.368	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
EMX2	2018	hgsc.bcm.edu	37	10	119305282	119305282	+	Silent	SNP	C	C	A	rs424112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:119305282C>A	ENST00000553456.3	+	2	1370	c.546C>A	c.(544-546)gcC>gcA	p.A182A	EMX2_ENST00000546446.1_3'UTR|EMX2_ENST00000442245.4_Intron|EMX2OS_ENST00000551288.1_RNA	NM_004098.3	NP_004089.1	Q04743	EMX2_HUMAN	empty spiracles homeobox 2	182					anterior/posterior pattern specification (GO:0009952)|cell proliferation in forebrain (GO:0021846)|cerebral cortex regionalization (GO:0021796)|dentate gyrus development (GO:0021542)|forebrain cell migration (GO:0021885)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|renal system development (GO:0072001)|response to drug (GO:0042493)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(2)	12		Colorectal(252;0.109)|Lung NSC(174;0.179)|all_lung(145;0.22)		all cancers(201;0.0133)		TGGTGGGCGCCGAAAGGAAGC	0.642													C|||	191	0.038139	0.1354	0.0159	5008	,	,		15931	0.0		0.001	False		,,,				2504	0.0				p.A182A		Atlas-SNP	.											.	EMX2	25	.	0			c.C546A						PASS	.	C	,	469,3937	219.7+/-237.4	28,413,1762	46.0	44.0	45.0		,546	-3.2	1.0	10	dbSNP_80	45	4,8596	3.7+/-12.6	0,4,4296	no	intron,coding-synonymous	EMX2	NM_001165924.1,NM_004098.3	,	28,417,6058	AA,AC,CC		0.0465,10.6446,3.6368	,	,182/253	119305282	473,12533	2203	4300	6503	SO:0001819	synonymous_variant	2018	exon2			GGGCGCCGAAAGG	AF301598	CCDS7601.1, CCDS53583.1	10q26.11	2011-06-20	2007-02-15		ENSG00000170370	ENSG00000170370		"""Homeoboxes / ANTP class : NKL subclass"""	3341	protein-coding gene	gene with protein product		600035	"""empty spiracles homolog 2 (Drosophila)"""			7959790	Standard	NM_004098		Approved		uc001ldh.4	Q04743	OTTHUMG00000019123	ENST00000553456.3:c.546C>A	10.37:g.119305282C>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	178	95	0.533708	NM_004098	G3V305|Q96NN8|Q9BQF4	Silent	SNP	ENST00000553456.3	37	CCDS7601.1																																																																																			C|0.962;A|0.038	0.038	strong		0.642	EMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050569.4	NM_004098	
PTPRE	5791	hgsc.bcm.edu	37	10	129866449	129866449	+	Silent	SNP	C	C	G	rs7100666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129866449C>G	ENST00000254667.3	+	12	1185	c.906C>G	c.(904-906)ccC>ccG	p.P302P	PTPRE_ENST00000430713.2_3'UTR|PTPRE_ENST00000306042.5_Silent_p.P244P|PTPRE_ENST00000419012.2_Silent_p.P302P	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	302	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	CCAGCTGGCCCGACTTCGGAG	0.607													C|||	876	0.17492	0.1528	0.1585	5008	,	,		17460	0.2609		0.0835	False		,,,				2504	0.2219				p.P302P	Colon(52;977 1184 20575 41685)	Atlas-SNP	.											PTPRE_ENST00000306042,NS,carcinoma,0,4	PTPRE	132	4	0			c.C906G						PASS	.	C	,	697,3709	291.5+/-281.6	60,577,1566	56.0	54.0	55.0		906,732	-5.1	1.0	10	dbSNP_116	55	720,7880	174.8+/-225.0	34,652,3614	no	coding-synonymous,coding-synonymous	PTPRE	NM_006504.4,NM_130435.3	,	94,1229,5180	GG,GC,CC		8.3721,15.8193,10.895	,	302/701,244/643	129866449	1417,11589	2203	4300	6503	SO:0001819	synonymous_variant	5791	exon12			CTGGCCCGACTTC	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.906C>G	10.37:g.129866449C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_006504	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Silent	SNP	ENST00000254667.3	37	CCDS7657.1																																																																																			C|0.880;G|0.120	0.120	strong		0.607	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1		
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464437	39464437	+	Missense_Mutation	SNP	G	G	C	rs72828116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39464437G>C	ENST00000391352.1	-	1	1068	c.1069C>G	c.(1069-1071)Ctt>Gtt	p.L357V		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	357						keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						CTGCAGGAAAGAGGTCGGCAG	0.547													G|||	454	0.090655	0.2027	0.0504	5008	,	,		22172	0.0506		0.0785	False		,,,				2504	0.0215				p.L357V		Atlas-SNP	.											KRTAP16-1,NS,carcinoma,0,1	KRTAP16-1	12	1	0			c.C1069G						PASS	.																																			SO:0001583	missense	100505753	exon1			AGGAAAGAGGTCG	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.1069C>G	17.37:g.39464437G>C	ENSP00000375147:p.Leu357Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_001146182		Missense_Mutation	SNP	ENST00000391352.1	37	CCDS56032.1	224	0.10256410256410256	105	0.21341463414634146	23	0.06353591160220995	31	0.05419580419580419	65	0.08575197889182058	G	0	-2.661978	0.00107	.	.	ENSG00000212657	ENST00000391352	T	0.00801	5.68	4.82	2.76	0.32466	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.52099	P	5.3999999999998494E-5	.	.	.	.	.	.	T	0.47100	-0.9143	6	0.21540	T	0.41	.	6.864	0.24082	0.0943:0.3648:0.5409:0.0	.	.	.	.	V	357	ENSP00000375147:L357V	ENSP00000375147:L357V	L	-	1	0	KRTAP16-1	36717963	0.888000	0.30383	0.643000	0.29450	0.022000	0.10575	2.824000	0.48088	0.592000	0.29728	0.491000	0.48974	CTT	G|0.900;C|0.100	0.100	strong		0.547	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
ISY1	57461	hgsc.bcm.edu	37	3	128853738	128853738	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:128853738A>G	ENST00000393295.3	-	8	795	c.478T>C	c.(478-480)Tat>Cat	p.Y160H	ISY1-RAB43_ENST00000418265.1_Missense_Mutation_p.Y160H|ISY1_ENST00000273541.8_Missense_Mutation_p.Y182H|ISY1_ENST00000393292.3_Missense_Mutation_p.Y160H|ISY1_ENST00000471497.1_Intron	NM_001199469.1|NM_020701.3	NP_001186398.1|NP_065752.1	Q9ULR0	ISY1_HUMAN	ISY1 splicing factor homolog (S. cerevisiae)	160					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|skin(1)	15						AGGTAACCATAGTACTCAAAA	0.398																																					p.Y182H		Atlas-SNP	.											ISY1,NS,carcinoma,+1,1	ISY1	36	1	0			c.T544C						scavenged	.						143.0	136.0	138.0					3																	128853738		1929	4155	6084	SO:0001583	missense	57461	exon9			AACCATAGTACTC		CCDS43149.1, CCDS56277.1	3q21.3	2008-11-25			ENSG00000240682	ENSG00000240682			29201	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 33"""	612764				16103217	Standard	NM_020701		Approved	KIAA1160, fSAP33		Q9ULR0	OTTHUMG00000137365	ENST00000393295.3:c.478T>C	3.37:g.128853738A>G	ENSP00000376973:p.Tyr160His	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	196	4	0.0204082	NM_001199469	Q96IL2|Q9BT05	Missense_Mutation	SNP	ENST00000393295.3	37	CCDS43149.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.632049	0.87660	.	.	ENSG00000240682	ENST00000418265;ENST00000393295;ENST00000273541;ENST00000496163;ENST00000393292	T	0.60548	0.18	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.81569	0.4850	H	0.95114	3.625	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.998	D	0.85685	0.1303	10	0.56958	D	0.05	.	11.5753	0.50858	1.0:0.0:0.0:0.0	.	182;160;160	Q9ULR0-2;Q9ULR0;Q9ULR0-1	.;ISY1_HUMAN;.	H	160;160;182;98;160	ENSP00000273541:Y182H	ENSP00000273541:Y182H	Y	-	1	0	ISY1	130336428	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	8.138000	0.89613	2.042000	0.60477	0.383000	0.25322	TAT	.	.	none		0.398	ISY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267856.1	NM_020701	
KRTAP25-1	100131902	hgsc.bcm.edu	37	21	31661691	31661691	+	Missense_Mutation	SNP	A	A	G	rs8127420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31661691A>G	ENST00000416044.1	-	1	141	c.118T>C	c.(118-120)Tcc>Ccc	p.S40P		NM_001128598.1	NP_001122070.1	Q3LHN0	KR251_HUMAN	keratin associated protein 25-1	40			S -> P (in dbSNP:rs8127420).			intermediate filament (GO:0005882)				breast(1)	1						CAGGTCCTGGACACAAAATTC	0.403													A|||	2591	0.517372	0.6392	0.5014	5008	,	,		19139	0.5853		0.327	False		,,,				2504	0.4898				p.S40P		Atlas-SNP	.											.	KRTAP25-1	13	.	0			c.T118C						PASS	.	A	PRO/SER	837,547		251,335,106	131.0	124.0	126.0		118	-2.9	0.0	21	dbSNP_116	126	926,2256		137,652,802	yes	missense	KRTAP25-1	NM_001128598.1	74	388,987,908	GG,GA,AA		29.1012,39.5231,38.6115	possibly-damaging	40/103	31661691	1763,2803	692	1591	2283	SO:0001583	missense	100131902	exon1			TCCTGGACACAAA		CCDS46640.1	21q22.1	2010-10-18	2008-02-26	2008-04-22	ENSG00000232263	ENSG00000232263		"""Keratin associated proteins"""	34003	protein-coding gene	gene with protein product							Standard	NM_001128598		Approved	KAP25.1	uc010glr.1	Q3LHN0	OTTHUMG00000125482	ENST00000416044.1:c.118T>C	21.37:g.31661691A>G	ENSP00000398619:p.Ser40Pro	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	246	99	0.402439	NM_001128598		Missense_Mutation	SNP	ENST00000416044.1	37	CCDS46640.1	1092	0.5	327	0.6646341463414634	175	0.48342541436464087	341	0.5961538461538461	249	0.32849604221635886	A	11.25	1.583312	0.28268	0.604769	0.291012	ENSG00000232263	ENST00000416044	T	0.05081	3.5	3.54	-2.86	0.05717	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.29378	0.243	B	0.32393	0.145	T	0.24835	-1.0149	8	0.87932	D	0	.	0.5677	0.00690	0.4339:0.1749:0.2209:0.1703	rs8127420	40	Q3LHN0	KR251_HUMAN	P	40	ENSP00000398619:S40P	ENSP00000398619:S40P	S	-	1	0	KRTAP25-1	30583562	0.000000	0.05858	0.000000	0.03702	0.161000	0.22273	-0.077000	0.11394	-0.665000	0.05317	0.346000	0.21813	TCC	A|0.520;G|0.480	0.480	strong		0.403	KRTAP25-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246805.1	NM_001128598	
FLG	2312	hgsc.bcm.edu	37	1	152276659	152276659	+	Missense_Mutation	SNP	T	T	C	rs7532285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276659T>C	ENST00000368799.1	-	3	10738	c.10703A>G	c.(10702-10704)cAg>cGg	p.Q3568R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	507	1	0.00197239		WXS	Illumina HiSeq	Phase_I	501	97	0.193613	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	
SERPINB2	5055	hgsc.bcm.edu	37	18	61565014	61565014	+	Silent	SNP	C	C	T	rs6106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61565014C>T	ENST00000299502.4	+	5	551	c.471C>T	c.(469-471)gaC>gaT	p.D157D	SERPINB2_ENST00000482254.1_3'UTR|SERPINB2_ENST00000457692.1_Silent_p.D157D	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	157					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	AGGCAGTAGACTTCCTAGAAT	0.343													C|||	313	0.0625	0.2216	0.0259	5008	,	,		19658	0.0		0.002	False		,,,				2504	0.0				p.D157D		Atlas-SNP	.											.	SERPINB2	63	.	0			c.C471T						PASS	.	C	,	781,3625	308.0+/-290.3	67,647,1489	62.0	67.0	65.0		471,471	2.9	0.9	18	dbSNP_52	65	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	SERPINB2	NM_001143818.1,NM_002575.2	,	67,659,5777	TT,TC,CC		0.1395,17.7258,6.0972	,	157/416,157/416	61565014	793,12213	2203	4300	6503	SO:0001819	synonymous_variant	5055	exon5			AGTAGACTTCCTA	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.471C>T	18.37:g.61565014C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	214	106	0.495327	NM_002575	Q96E96	Silent	SNP	ENST00000299502.4	37	CCDS11989.1	130	0.05952380952380952	117	0.23780487804878048	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	C	8.325	0.825088	0.16678	0.177258	0.001395	ENSG00000242550	ENST00000397996;ENST00000418725	.	.	.	5.6	2.87	0.33458	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09552	-1.0669	3	.	.	.	.	8.4939	0.33117	0.0:0.7035:0.0:0.2965	rs6106;rs6106	.	.	.	F	34	.	.	L	+	1	0	SERPINB10	59715994	1.000000	0.71417	0.946000	0.38457	0.866000	0.49608	0.916000	0.28651	0.418000	0.25898	-0.142000	0.14014	CTT	C|0.933;T|0.067	0.067	strong		0.343	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
KNTC1	9735	hgsc.bcm.edu	37	12	123030788	123030788	+	Missense_Mutation	SNP	G	G	T	rs7968222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123030788G>T	ENST00000333479.7	+	9	912	c.735G>T	c.(733-735)aaG>aaT	p.K245N	KNTC1_ENST00000450485.2_Missense_Mutation_p.K208N	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	245			K -> N (in dbSNP:rs7968222).		mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		TGACAGTTAAGAACCTTATTG	0.308													G|||	672	0.134185	0.3011	0.0735	5008	,	,		16728	0.006		0.1014	False		,,,				2504	0.1176				p.K245N		Atlas-SNP	.											.	KNTC1	182	.	0			c.G735T						PASS	.	G	ASN/LYS	976,2648		137,702,973	52.0	50.0	50.0		735	4.6	1.0	12	dbSNP_116	50	852,7294		31,790,3252	yes	missense	KNTC1	NM_014708.4	94	168,1492,4225	TT,TG,GG		10.4591,26.9316,15.531	possibly-damaging	245/2210	123030788	1828,9942	1812	4073	5885	SO:0001583	missense	9735	exon9			AGTTAAGAACCTT		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.735G>T	12.37:g.123030788G>T	ENSP00000328236:p.Lys245Asn	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	142	63	0.443662	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	270	0.12362637362637363	153	0.31097560975609756	34	0.09392265193370165	2	0.0034965034965034965	81	0.10686015831134564	G	12.80	2.047297	0.36085	0.269316	0.104591	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.44482	0.92;0.92	5.51	4.61	0.57282	.	0.362044	0.29995	N	0.010674	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	0.9999999999940533	B;P	0.48764	0.421;0.915	B;B	0.36922	0.157;0.236	T	0.40924	-0.9537	9	0.21540	T	0.41	-15.7297	7.5578	0.27835	0.249:0.0:0.751:0.0	rs7968222;rs17883020;rs52834023;rs61051270;rs7968222	208;245	E7ES84;P50748	.;KNTC1_HUMAN	N	208;245	ENSP00000397992:K208N;ENSP00000328236:K245N	ENSP00000328236:K245N	K	+	3	2	KNTC1	121596741	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.372000	0.34261	1.322000	0.45245	0.650000	0.86243	AAG	G|0.867;T|0.133	0.133	strong		0.308	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
SEMA6D	80031	hgsc.bcm.edu	37	15	48058071	48058071	+	Missense_Mutation	SNP	G	G	A	rs532598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:48058071G>A	ENST00000316364.5	+	14	1872	c.1433G>A	c.(1432-1434)aGt>aAt	p.S478N	SEMA6D_ENST00000537942.1_Missense_Mutation_p.S478N|SEMA6D_ENST00000355997.3_Missense_Mutation_p.S478N|SEMA6D_ENST00000389428.3_Missense_Mutation_p.S478N|SEMA6D_ENST00000536845.2_Missense_Mutation_p.S478N|SEMA6D_ENST00000389432.2_Missense_Mutation_p.S478N|SEMA6D_ENST00000389433.2_Missense_Mutation_p.S478N|SEMA6D_ENST00000358066.4_Missense_Mutation_p.S478N|SEMA6D_ENST00000558816.1_Missense_Mutation_p.S478N|SEMA6D_ENST00000354744.4_Missense_Mutation_p.S478N|SEMA6D_ENST00000558014.1_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	124	0	0		WXS	Illumina HiSeq	Phase_I	126	52	0.412698	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	
ERCC4	2072	hgsc.bcm.edu	37	16	14038659	14038659	+	Missense_Mutation	SNP	T	T	C	rs2020955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:14038659T>C	ENST00000311895.7	+	10	1993	c.1984T>C	c.(1984-1986)Tct>Cct	p.S662P		NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	662	Nuclease.		S -> P (in dbSNP:rs2020955). {ECO:0000269|Ref.2}.		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						AGGCACAGCATCTGCAGATGT	0.488			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				T|||	306	0.0611022	0.2209	0.0187	5008	,	,		19375	0.0		0.001	False		,,,				2504	0.0				p.S662P		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.T1984C						PASS	.	T	PRO/SER	845,3549	335.7+/-304.0	79,687,1431	103.0	93.0	97.0		1984	0.9	0.0	16	dbSNP_94	97	11,8589	8.4+/-32.0	0,11,4289	yes	missense	ERCC4	NM_005236.2	74	79,698,5720	CC,CT,TT		0.1279,19.2308,6.5877	benign	662/917	14038659	856,12138	2197	4300	6497	SO:0001583	missense	2072	exon10	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ACAGCATCTGCAG	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.1984T>C	16.37:g.14038659T>C	ENSP00000310520:p.Ser662Pro	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Missense_Mutation	SNP	ENST00000311895.7	37	CCDS32390.1	106	0.048534798534798536	100	0.2032520325203252	6	0.016574585635359115	0	0.0	0	0.0	T	8.372	0.835596	0.16820	0.192308	0.001279	ENSG00000175595	ENST00000311895;ENST00000389138	T	0.62105	0.05	5.8	0.884	0.19182	.	0.401079	0.30732	N	0.008982	T	0.00039	0.0001	N	0.05414	-0.055	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.06162	-1.0842	9	0.27082	T	0.32	-7.9859	1.9232	0.03312	0.1348:0.1162:0.2951:0.4539	rs2020955;rs2020955	662	Q92889	XPF_HUMAN	P	662;650	ENSP00000310520:S662P	ENSP00000310520:S662P	S	+	1	0	ERCC4	13946160	0.014000	0.17966	0.001000	0.08648	0.041000	0.13682	0.464000	0.21988	0.084000	0.17077	0.533000	0.62120	TCT	T|0.934;C|0.066	0.066	strong		0.488	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236	
MUC4	4585	hgsc.bcm.edu	37	3	195507060	195507060	+	Missense_Mutation	SNP	G	G	T	rs202129071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507060G>T	ENST00000463781.3	-	2	11850	c.11391C>A	c.(11389-11391)gaC>gaA	p.D3797E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3797E	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)		CTGAGGAAGTGTCGGTGACAG	0.602																																					p.D3797E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	0			c.C11391A						scavenged	.						7.0	7.0	7.0					3																	195507060		641	1487	2128	SO:0001583	missense	4585	exon2			GGAAGTGTCGGTG	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.11391C>A	3.37:g.195507060G>T	ENSP00000417498:p.Asp3797Glu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	157	15	0.0955414	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	8.187	0.795093	0.16327	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.55;1.55	.	.	.	.	0.282130	0.14041	U	0.345384	T	0.15349	0.0370	N	0.19112	0.55	0.09310	N	0.999997	B	0.15141	0.012	B	0.06405	0.002	T	0.25537	-1.0129	8	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3669	E7ESK3	.	E	3797	ENSP00000417498:D3797E;ENSP00000420243:D3797E	.	D	-	3	2	MUC4	196991839	0.001000	0.12720	0.041000	0.18516	0.041000	0.13682	0.608000	0.24223	0.064000	0.16427	0.064000	0.15345	GAC	G|0.956;A|0.044	.	alt		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CATSPER3	347732	hgsc.bcm.edu	37	5	134343766	134343766	+	Missense_Mutation	SNP	T	T	G	rs3896260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134343766T>G	ENST00000282611.6	+	4	698	c.612T>G	c.(610-612)aaT>aaG	p.N204K		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	204			N -> K (in dbSNP:rs3896260).		calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTCCAGACAATGGTGACCATG	0.552													G|||	646	0.128994	0.4584	0.0461	5008	,	,		15472	0.0		0.007	False		,,,				2504	0.001				p.N204K		Atlas-SNP	.											.	CATSPER3	38	.	0			c.T612G						PASS	.	G	LYS/ASN	1758,2648	644.5+/-398.0	347,1064,792	184.0	145.0	158.0		612	-2.1	0.0	5	dbSNP_108	158	24,8576	818.1+/-406.9	0,24,4276	yes	missense	CATSPER3	NM_178019.2	94	347,1088,5068	GG,GT,TT		0.2791,39.9001,13.7014	benign	204/399	134343766	1782,11224	2203	4300	6503	SO:0001583	missense	347732	exon4			AGACAATGGTGAC	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.612T>G	5.37:g.134343766T>G	ENSP00000282611:p.Asn204Lys	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	303	145	0.478548	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	241	0.11034798534798534	221	0.4491869918699187	17	0.04696132596685083	0	0.0	3	0.00395778364116095	G	0.003	-2.468589	0.00169	0.399001	0.002791	ENSG00000152705	ENST00000282611	D	0.97553	-4.43	4.33	-2.08	0.07254	Ion transport (1);	1.918400	0.01976	N	0.044466	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	0.50440	-0.8828	8	.	.	.	1.4415	0.1834	0.00126	0.2523:0.1883:0.202:0.3574	rs3896260;rs52815255;rs60117234;rs3896260	204	Q86XQ3	CTSR3_HUMAN	K	204	ENSP00000282611:N204K	.	N	+	3	2	CATSPER3	134371665	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.154000	0.03166	-0.973000	0.03555	-0.358000	0.07595	AAT	T|0.860;G|0.140	0.140	strong		0.552	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
ZNF618	114991	hgsc.bcm.edu	37	9	116810204	116810204	+	Silent	SNP	G	G	A	rs12378906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116810204G>A	ENST00000374126.5	+	14	1377	c.1278G>A	c.(1276-1278)caG>caA	p.Q426Q	ZNF618_ENST00000288466.7_Silent_p.Q333Q|ZNF618_ENST00000470105.1_3'UTR			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	426					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						CCTCCAACCAGTCCCGATCGC	0.532													G|||	329	0.0656949	0.1203	0.0605	5008	,	,		21014	0.0		0.0885	False		,,,				2504	0.0399				p.Q333Q		Atlas-SNP	.											.	ZNF618	184	.	0			c.G999A						PASS	.	G		467,3649		17,433,1608	75.0	78.0	77.0		999	3.6	1.0	9	dbSNP_120	77	715,7715		33,649,3533	yes	coding-synonymous	ZNF618	NM_133374.2		50,1082,5141	AA,AG,GG		8.4816,11.346,9.4213		333/862	116810204	1182,11364	2058	4215	6273	SO:0001819	synonymous_variant	114991	exon13			CAACCAGTCCCGA	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.1278G>A	9.37:g.116810204G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	121	57	0.471074	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				G|0.927;A|0.073	0.073	strong		0.532	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
SMYD1	150572	hgsc.bcm.edu	37	2	88396213	88396213	+	Silent	SNP	G	G	A	rs13403507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:88396213G>A	ENST00000419482.2	+	6	883	c.798G>A	c.(796-798)ctG>ctA	p.L266L	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.L253L	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	266					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						AGAGGCAGCTGAAGAAGCAGT	0.493													G|||	44	0.00878594	0.0333	0.0	5008	,	,		22022	0.0		0.0	False		,,,				2504	0.0				p.L266L		Atlas-SNP	.											.	SMYD1	95	.	0			c.G798A						PASS	.	G		105,4301	84.4+/-122.9	0,105,2098	106.0	98.0	101.0		798	-0.6	1.0	2	dbSNP_121	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SMYD1	NM_198274.3		0,106,6397	AA,AG,GG		0.0116,2.3831,0.815		266/491	88396213	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon6			GCAGCTGAAGAAG	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.798G>A	2.37:g.88396213G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			G|0.992;A|0.008	0.008	strong		0.493	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
ZNF804B	219578	hgsc.bcm.edu	37	7	88964000	88964000	+	Silent	SNP	C	C	T	rs801839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88964000C>T	ENST00000333190.4	+	4	2313	c.1704C>T	c.(1702-1704)ttC>ttT	p.F568F		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	568							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AATATACTTTCAGTGCAAATG	0.353										HNSCC(36;0.09)			T|||	2553	0.509784	0.7345	0.3401	5008	,	,		19433	0.7153		0.2336	False		,,,				2504	0.3988				p.F568F		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C1704T						PASS	.	T		2816,1566		895,1026,270	42.0	45.0	44.0		1704	4.3	0.5	7	dbSNP_86	44	2011,6581		238,1535,2523	no	coding-synonymous	ZNF804B	NM_181646.2		1133,2561,2793	TT,TC,CC		23.4055,35.7371,37.2052		568/1350	88964000	4827,8147	2191	4296	6487	SO:0001819	synonymous_variant	219578	exon4			TACTTTCAGTGCA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1704C>T	7.37:g.88964000C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	37	CCDS5613.1																																																																																			C|0.493;T|0.507	0.507	strong		0.353	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
MUC17	140453	hgsc.bcm.edu	37	7	100677944	100677944	+	Missense_Mutation	SNP	T	T	C	rs10264727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677944T>C	ENST00000306151.4	+	3	3311	c.3247T>C	c.(3247-3249)Tct>Cct	p.S1083P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1083	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)					CAGTTCATCTTCTACAACTGC	0.507																																					p.S1083P		Atlas-SNP	.											.	MUC17	804	.	0			c.T3247C						PASS	.	C	PRO/SER	1107,3299		5,1097,1101	457.0	379.0	405.0		3247	-1.5	0.0	7	dbSNP_119	405	933,7667		0,933,3367	no	missense	MUC17	NM_001040105.1	74	5,2030,4468	CC,CT,TT		10.8488,25.1248,15.6851	benign	1083/4494	100677944	2040,10966	2203	4300	6503	SO:0001583	missense	140453	exon3			TCATCTTCTACAA	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.3247T>C	7.37:g.100677944T>C	ENSP00000302716:p.Ser1083Pro	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	344	203	0.590116	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.509	-0.867515	0.02590	0.251248	0.108488	ENSG00000169876	ENST00000306151	T	0.02656	4.21	0.74	-1.48	0.08745	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30679	-0.9970	9	0.02654	T	1	.	2.5705	0.04793	0.3829:0.1792:0.0:0.4379	rs10264727	1083	Q685J3	MUC17_HUMAN	P	1083	ENSP00000302716:S1083P	ENSP00000302716:S1083P	S	+	1	0	MUC17	100464664	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.501000	0.00450	-2.418000	0.00566	-1.386000	0.01163	TCT	T|0.902;C|0.098	0.098	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PREX1	57580	hgsc.bcm.edu	37	20	47261017	47261017	+	Silent	SNP	T	T	C	rs6066802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47261017T>C	ENST00000371941.3	-	27	3553	c.3531A>G	c.(3529-3531)cgA>cgG	p.R1177R	PREX1_ENST00000396220.1_Silent_p.R1177R|PREX1_ENST00000496915.1_5'Flank	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1177					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.R1177R(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)			GGACCGAGTCTCGATTGCTGT	0.592													C|||	1605	0.320487	0.2118	0.3559	5008	,	,		17511	0.369		0.2624	False		,,,				2504	0.4519				p.R1177R		Atlas-SNP	.											PREX1,NS,carcinoma,0,1	PREX1	441	1	1	Substitution - coding silent(1)	stomach(1)	c.A3531G						PASS	.	C		973,3433	733.1+/-410.4	100,773,1330	95.0	76.0	82.0		3531	1.5	1.0	20	dbSNP_114	82	2242,6358	707.8+/-405.6	289,1664,2347	no	coding-synonymous	PREX1	NM_020820.3		389,2437,3677	CC,CT,TT		26.0698,22.0835,24.7194		1177/1660	47261017	3215,9791	2203	4300	6503	SO:0001819	synonymous_variant	57580	exon27			CGAGTCTCGATTG	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.3531A>G	20.37:g.47261017T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			T|0.728;C|0.272	0.272	strong		0.592	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
GSDMC	56169	hgsc.bcm.edu	37	8	130762324	130762324	+	Silent	SNP	A	A	G	rs35085916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:130762324A>G	ENST00000276708.4	-	12	2006	c.1125T>C	c.(1123-1125)ggT>ggC	p.G375G		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	375						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						TTAGGATGGCACCACCAGGGC	0.368													A|||	87	0.0173722	0.0628	0.0058	5008	,	,		18988	0.0		0.0	False		,,,				2504	0.0				p.G375G		Atlas-SNP	.											.	GSDMC	71	.	0			c.T1125C						PASS	.	A		286,4120	153.3+/-186.9	9,268,1926	36.0	36.0	36.0		1125	0.7	0.0	8	dbSNP_126	36	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	GSDMC	NM_031415.2		9,272,6222	GG,GA,AA		0.0465,6.4911,2.2297		375/509	130762324	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	56169	exon12			GATGGCACCACCA	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"""melanoma-derived leucine zipper, extra-nuclear factor"""	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.1125T>C	8.37:g.130762324A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	111	67	0.603604	NM_031415	Q5XKF3|Q6P494	Silent	SNP	ENST00000276708.4	37	CCDS6360.1																																																																																			A|0.981;G|0.019	0.019	strong		0.368	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1		
HEG1	57493	hgsc.bcm.edu	37	3	124731689	124731689	+	Missense_Mutation	SNP	T	T	A	rs78680419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124731689T>A	ENST00000311127.4	-	6	2801	c.2734A>T	c.(2734-2736)Act>Tct	p.T912S	HEG1_ENST00000477536.1_5'Flank	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	912					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						ATCAATCCAGTGGTAGCATCC	0.488													T|||	1425	0.284545	0.3449	0.2896	5008	,	,		25262	0.4633		0.0905	False		,,,				2504	0.2147				p.T912S		Atlas-SNP	.											.	HEG1	109	.	0			c.A2734T						PASS	.	T	SER/THR	1233,2799		179,875,962	156.0	159.0	158.0		2734	2.3	0.0	3	dbSNP_131	158	738,7614		44,650,3482	yes	missense	HEG1	NM_020733.1	58	223,1525,4444	AA,AT,TT		8.8362,30.5804,15.9157	benign	912/1382	124731689	1971,10413	2016	4176	6192	SO:0001583	missense	57493	exon6			ATCCAGTGGTAGC	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.2734A>T	3.37:g.124731689T>A	ENSP00000311502:p.Thr912Ser	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	318	157	0.493711	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	571	0.26144688644688646	163	0.3313008130081301	85	0.23480662983425415	249	0.4353146853146853	74	0.09762532981530343	T	11.12	1.544628	0.27563	0.305804	0.088362	ENSG00000173706	ENST00000311127	D	0.89552	-2.53	4.78	2.31	0.28768	.	0.382752	0.18394	N	0.142573	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.31318	0.319;0.214	B;B	0.31686	0.134;0.063	T	0.23583	-1.0184	9	0.49607	T	0.09	.	4.9603	0.14063	0.1617:0.0872:0.0:0.7511	.	912;912	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	S	912	ENSP00000311502:T912S	ENSP00000311502:T912S	T	-	1	0	HEG1	126214379	0.938000	0.31826	0.001000	0.08648	0.064000	0.16182	0.798000	0.27014	0.381000	0.24851	0.533000	0.62120	ACT	T|0.772;A|0.228	0.228	strong		0.488	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
CDK12	51755	hgsc.bcm.edu	37	17	37619038	37619038	+	Silent	SNP	G	G	A	rs35896550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37619038G>A	ENST00000447079.4	+	1	747	c.714G>A	c.(712-714)tcG>tcA	p.S238S	CDK12_ENST00000430627.2_Silent_p.S238S	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	238					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						ATAGCCCCTCGGGAGCTTCTT	0.483			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)			G|||	291	0.058107	0.2073	0.0159	5008	,	,		18736	0.0		0.003	False		,,,				2504	0.0031				p.S238S		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	CDK12,NS,carcinoma,+1,1	CDK12	161	1	0			c.G714A						PASS	.	G	,	772,3634	306.9+/-289.7	55,662,1486	102.0	112.0	109.0		714,714	-9.9	0.3	17	dbSNP_126	109	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	CDK12	NM_015083.1,NM_016507.2	,	55,665,5783	AA,AG,GG		0.0349,17.5216,5.9588	,	238/1482,238/1491	37619038	775,12231	2203	4300	6503	SO:0001819	synonymous_variant	51755	exon1			CCCCTCGGGAGCT	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.714G>A	17.37:g.37619038G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Silent	SNP	ENST00000447079.4	37	CCDS11337.1																																																																																			G|0.933;A|0.067	0.067	strong		0.483	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
ETV7	51513	hgsc.bcm.edu	37	6	36341251	36341251	+	Missense_Mutation	SNP	G	G	A	rs9470262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36341251G>A	ENST00000340181.4	-	4	653	c.412C>T	c.(412-414)Cac>Tac	p.H138Y	ETV7_ENST00000373737.4_Missense_Mutation_p.H138Y|ETV7_ENST00000538992.1_5'UTR|ETV7_ENST00000373738.1_Missense_Mutation_p.H83Y|ETV7_ENST00000339796.5_Missense_Mutation_p.H138Y	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	138			H -> Y (in dbSNP:rs9470262).		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						ACTGGAGAGTGCTGGGTGGGC	0.602													G|||	59	0.0117812	0.0446	0.0	5008	,	,		11025	0.0		0.0	False		,,,				2504	0.0				p.H138Y		Atlas-SNP	.											.	ETV7	31	.	0			c.C412T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS,,TYR/HIS	156,4250		3,150,2050	27.0	25.0	25.0		412,247,235,412,247,169,,412	2.4	0.0	6	dbSNP_119	25	0,8598		0,0,4299	yes	missense,missense,missense,missense,missense,missense,utr-5,missense	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	83,83,83,83,83,83,,83	3,150,6349	AA,AG,GG		0.0,3.5406,1.1996	benign,benign,benign,benign,benign,benign,,benign	138/318,83/287,79/283,138/265,83/263,57/261,,138/342	36341251	156,12848	2203	4299	6502	SO:0001583	missense	51513	exon4			GAGAGTGCTGGGT	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.412C>T	6.37:g.36341251G>A	ENSP00000341843:p.His138Tyr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	142	63	0.443662	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Missense_Mutation	SNP	ENST00000340181.4	37	CCDS4819.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	9.065	0.995354	0.19043	0.035406	0.0	ENSG00000010030	ENST00000339796;ENST00000340181;ENST00000373737;ENST00000373738	T;T;T;T	0.13538	2.96;2.96;2.58;2.68	3.37	2.43	0.29744	.	7.870880	0.00616	U	0.000429	T	0.02727	0.0082	N	0.24115	0.695	0.34145	D	0.66687	B;B;B;B;B;B	0.33135	0.399;0.167;0.255;0.091;0.263;0.34	B;B;B;B;B;B	0.31686	0.134;0.065;0.041;0.105;0.044;0.134	T	0.34825	-0.9813	10	0.02654	T	1	.	9.2275	0.37416	0.0:0.0:0.503:0.497	rs9470262;rs52802542;rs9470262	79;138;83;138;83;138	Q9Y603-2;Q9Y603-7;Q9Y603-4;Q9Y603;Q9Y603-6;Q9Y603-5	.;.;.;ETV7_HUMAN;.;.	Y	138;138;138;83	ENSP00000342260:H138Y;ENSP00000341843:H138Y;ENSP00000362842:H138Y;ENSP00000362843:H83Y	ENSP00000342260:H138Y	H	-	1	0	ETV7	36449229	0.000000	0.05858	0.007000	0.13788	0.022000	0.10575	0.108000	0.15396	1.446000	0.47643	0.456000	0.33151	CAC	G|0.988;A|0.012	0.012	strong		0.602	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135	
XRN1	54464	hgsc.bcm.edu	37	3	142123841	142123841	+	Silent	SNP	C	C	T	rs2306700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:142123841C>T	ENST00000264951.4	-	16	1908	c.1791G>A	c.(1789-1791)gaG>gaA	p.E597E	RNU6-1294P_ENST00000515995.1_RNA|XRN1_ENST00000392981.2_Silent_p.E597E	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	597					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)			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						ACATTAGGCACTCACTATGTT	0.408													C|||	609	0.121605	0.1604	0.0965	5008	,	,		18450	0.1002		0.1481	False		,,,				2504	0.0818				p.E597E		Atlas-SNP	.											.	XRN1	138	.	0			c.G1791A						PASS	.	C	,	645,3761	277.8+/-273.9	46,553,1604	169.0	152.0	158.0		1791,1791	-0.4	1.0	3	dbSNP_100	158	1196,7404	242.6+/-272.5	79,1038,3183	no	coding-synonymous,coding-synonymous	XRN1	NM_001042604.1,NM_019001.3	,	125,1591,4787	TT,TC,CC		13.907,14.6391,14.155	,	597/1694,597/1707	142123841	1841,11165	2203	4300	6503	SO:0001819	synonymous_variant	54464	exon16			TAGGCACTCACTA	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.1791G>A	3.37:g.142123841C>T		Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	294	134	0.455782	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	37	CCDS3123.1																																																																																			C|0.867;T|0.133	0.133	strong		0.408	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	
PIWIL3	440822	hgsc.bcm.edu	37	22	25119210	25119210	+	Silent	SNP	A	A	C	rs56199175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25119210A>C	ENST00000332271.5	-	19	2687	c.2271T>G	c.(2269-2271)gcT>gcG	p.A757A	PIWIL3_ENST00000527701.1_Silent_p.A639A|PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000533313.1_Silent_p.A639A	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	757	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						CCACAATGAAAGCTAGAGTGA	0.333													a|||	400	0.0798722	0.0681	0.0548	5008	,	,		21989	0.0893		0.0467	False		,,,				2504	0.138				p.A757A		Atlas-SNP	.											.	PIWIL3	115	.	0			c.T2271G						PASS	.	A		287,4119	156.6+/-189.7	10,267,1926	88.0	82.0	84.0		2271	1.6	0.8	22	dbSNP_129	84	429,8169	132.0+/-189.7	8,413,3878	no	coding-synonymous	PIWIL3	NM_001008496.2		18,680,5804	CC,CA,AA		4.9895,6.5138,5.506		757/883	25119210	716,12288	2203	4299	6502	SO:0001819	synonymous_variant	440822	exon19			AATGAAAGCTAGA	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"""Argonaute/PIWI family"""	18443	protein-coding gene	gene with protein product		610314	"""piwi-like 3 (Drosophila)"""			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.2271T>G	22.37:g.25119210A>C		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_001008496		Silent	SNP	ENST00000332271.5	37	CCDS33623.1																																																																																			A|0.945;C|0.055	0.055	strong		0.333	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496	
FOCAD	54914	hgsc.bcm.edu	37	9	20764870	20764870	+	Missense_Mutation	SNP	T	T	C	rs10511687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:20764870T>C	ENST00000380249.1	+	9	861	c.497T>C	c.(496-498)tTa>tCa	p.L166S	FOCAD_ENST00000338382.6_Missense_Mutation_p.L166S	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	166			L -> S (in dbSNP:rs10511687).			focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											TCTTATAGGTTAGAAGTTTCA	0.353													C|||	1407	0.28095	0.3094	0.2795	5008	,	,		24115	0.0437		0.3767	False		,,,				2504	0.3896				p.L166S		Atlas-SNP	.											.	.	.	.	0			c.T497C						PASS	.	C	SER/LEU	1420,2986	685.3+/-404.5	220,980,1003	123.0	116.0	118.0		497	6.0	1.0	9	dbSNP_119	118	3143,5457	656.3+/-401.3	579,1985,1736	yes	missense	KIAA1797	NM_017794.3	145	799,2965,2739	CC,CT,TT		36.5465,32.2288,35.0838	benign	166/1802	20764870	4563,8443	2203	4300	6503	SO:0001583	missense	54914	exon9			ATAGGTTAGAAGT	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.497T>C	9.37:g.20764870T>C	ENSP00000369599:p.Leu166Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	560	0.2564102564102564	145	0.29471544715447157	106	0.292817679558011	33	0.057692307692307696	276	0.3641160949868074	C	8.211	0.800362	0.16397	0.322288	0.365465	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.22945	1.93;1.93	5.98	5.98	0.97165	Domain of unknown function DUF3730 (1);	0.550410	0.19445	N	0.114095	T	0.00012	0.0000	N	0.01874	-0.695	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.38845	-0.9642	9	0.02654	T	1	-24.8529	8.723	0.34452	0.2532:0.6767:0.0:0.0701	rs10511687;rs52817455;rs58837776;rs10511687	166	Q5VW36	K1797_HUMAN	S	166	ENSP00000369599:L166S;ENSP00000344307:L166S	ENSP00000344307:L166S	L	+	2	0	KIAA1797	20754870	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	1.741000	0.38238	1.555000	0.49500	-0.186000	0.12905	TTA	T|0.745;C|0.255	0.255	strong		0.353	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
LRP6	4040	hgsc.bcm.edu	37	12	12336966	12336966	+	Silent	SNP	A	A	G	rs7978064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:12336966A>G	ENST00000261349.4	-	5	1000	c.924T>C	c.(922-924)tgT>tgC	p.C308C	LRP6_ENST00000543091.1_Silent_p.C308C	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	308	EGF-like 1.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|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 Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TGGGGCAAGCACACTGATAAA	0.378													A|||	692	0.138179	0.3359	0.1744	5008	,	,		18561	0.0079		0.0875	False		,,,				2504	0.0317				p.C308C		Atlas-SNP	.											.	LRP6	170	.	0			c.T924C						PASS	.	A		1249,3157	427.6+/-341.6	183,883,1137	99.0	95.0	96.0		924	3.4	1.0	12	dbSNP_116	96	803,7797	188.9+/-235.7	46,711,3543	no	coding-synonymous	LRP6	NM_002336.2		229,1594,4680	GG,GA,AA		9.3372,28.3477,15.7773		308/1614	12336966	2052,10954	2203	4300	6503	SO:0001819	synonymous_variant	4040	exon5			GCAAGCACACTGA	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.924T>C	12.37:g.12336966A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	134	76	0.567164	NM_002336	Q17RZ2	Silent	SNP	ENST00000261349.4	37	CCDS8647.1																																																																																			A|0.850;G|0.150	0.150	strong		0.378	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
AMOTL1	154810	hgsc.bcm.edu	37	11	94533373	94533373	+	Silent	SNP	C	C	T	rs2303960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94533373C>T	ENST00000433060.2	+	3	1158	c.1017C>T	c.(1015-1017)ccC>ccT	p.P339P	AMOTL1_ENST00000317829.8_Silent_p.P289P|AMOTL1_ENST00000317837.9_Silent_p.P339P	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	59	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	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	
SEMA6C	10500	hgsc.bcm.edu	37	1	151107277	151107277	+	Missense_Mutation	SNP	C	C	T	rs149398166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151107277C>T	ENST00000341697.3	-	16	3346	c.1655G>A	c.(1654-1656)gGt>gAt	p.G552D	SEMA6C_ENST00000479820.1_5'Flank			Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	552					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|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)			CACTTACCCACCAGATCCCCT	0.527													C|||	19	0.00379393	0.0144	0.0	5008	,	,		19859	0.0		0.0	False		,,,				2504	0.0				p.G552D		Atlas-SNP	.											.	SEMA6C	70	.	0			c.G1655A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY	40,4366	43.8+/-77.6	2,36,2165	134.0	121.0	125.0		1655,1535,1655	3.2	1.0	1	dbSNP_134	125	0,8600		0,0,4300	yes	missense,missense,missense	SEMA6C	NM_001178061.1,NM_001178062.1,NM_030913.4	94,94,94	2,36,6465	TT,TC,CC		0.0,0.9079,0.3076	possibly-damaging,possibly-damaging,possibly-damaging	552/963,512/923,552/931	151107277	40,12966	2203	4300	6503	SO:0001583	missense	10500	exon16			TACCCACCAGATC	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"""Semaphorins"""	10740	protein-coding gene	gene with protein product	"""m-Sema Y2"""	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.1655G>A	1.37:g.151107277C>T	ENSP00000344148:p.Gly552Asp	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	206	107	0.519417	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	37	CCDS984.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	11.28	1.593364	0.28357	0.009079	0.0	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.25	3.22	0.36961	.	3.389920	0.00550	N	0.000248	T	0.33498	0.0865	L	0.44542	1.39	0.32800	D	0.500067	B;D;B;D	0.54772	0.002;0.96;0.1;0.968	B;P;B;P	0.50934	0.01;0.523;0.257;0.654	T	0.06232	-1.0838	10	0.37606	T	0.19	.	11.5843	0.50910	0.0:0.527:0.473:0.0	.	552;512;552;552	B4DZD4;Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;.;SEM6C_HUMAN	D	552;512;552;552	ENSP00000357910:G552D;ENSP00000357908:G512D;ENSP00000357909:G552D;ENSP00000344148:G552D	ENSP00000344148:G552D	G	-	2	0	SEMA6C	149373901	0.981000	0.34729	1.000000	0.80357	0.599000	0.36880	1.049000	0.30392	1.349000	0.45751	0.561000	0.74099	GGT	C|0.995;T|0.005	0.005	strong		0.527	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913	
INCENP	3619	hgsc.bcm.edu	37	11	61906397	61906397	+	Missense_Mutation	SNP	A	A	G	rs138049815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61906397A>G	ENST00000394818.3	+	7	1413	c.1211A>G	c.(1210-1212)aAt>aGt	p.N404S	INCENP_ENST00000278849.4_Missense_Mutation_p.N404S	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	404					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						TGGCCCCACAATGACACGGAG	0.587													A|||	13	0.00259585	0.0098	0.0	5008	,	,		17407	0.0		0.0	False		,,,				2504	0.0				p.N404S		Atlas-SNP	.											.	INCENP	122	.	0			c.A1211G						PASS	.	A	SER/ASN,SER/ASN	48,4356	49.6+/-84.7	0,48,2154	133.0	122.0	125.0		1211,1211	1.4	0.1	11	dbSNP_134	125	1,8597		0,1,4298	yes	missense,missense	INCENP	NM_020238.2,NM_001040694.1	46,46	0,49,6452	GG,GA,AA		0.0116,1.0899,0.3769	benign,benign	404/915,404/919	61906397	49,12953	2202	4299	6501	SO:0001583	missense	3619	exon7			CCCACAATGACAC	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.1211A>G	11.37:g.61906397A>G	ENSP00000378295:p.Asn404Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	124	68	0.548387	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	A	0.939	-0.710017	0.03230	0.010899	1.16E-4	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.13196	2.61;2.61	5.24	1.43	0.22495	.	0.301301	0.29113	N	0.013114	T	0.02156	0.0067	N	0.01410	-0.885	0.09310	N	1	B;B;B	0.18610	0.029;0.0;0.0	B;B;B	0.18871	0.023;0.001;0.001	T	0.44605	-0.9317	10	0.07325	T	0.83	.	6.0369	0.19712	0.4261:0.0:0.5739:0.0	.	404;404;404	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	S	404	ENSP00000378295:N404S;ENSP00000278849:N404S	ENSP00000278849:N404S	N	+	2	0	INCENP	61662973	0.048000	0.20356	0.068000	0.19968	0.006000	0.05464	0.392000	0.20801	0.558000	0.29135	-0.242000	0.12053	AAT	A|0.996;G|0.004	0.004	strong		0.587	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
ICT1	3396	hgsc.bcm.edu	37	17	73008804	73008804	+	Missense_Mutation	SNP	G	G	T	rs3744206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73008804G>T	ENST00000301585.5	+	1	36	c.23G>T	c.(22-24)cGc>cTc	p.R8L		NM_001545.1	NP_001536.1	Q14197	ICT1_HUMAN	immature colon carcinoma transcript 1	8			R -> P (in dbSNP:rs3744206).		mitochondrial translational termination (GO:0070126)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	aminoacyl-tRNA hydrolase activity (GO:0004045)|translation release factor activity, codon nonspecific (GO:0016150)			NS(1)|central_nervous_system(1)|lung(2)|ovary(1)|urinary_tract(1)	6	all_lung(278;0.226)					AGGTGCCTGCGCTGGGGCCTG	0.697											OREG0024724	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	118	0.0235623	0.0703	0.0101	5008	,	,		10726	0.0		0.0179	False		,,,				2504	0.0				p.R8L		Atlas-SNP	.											ICT1,NS,carcinoma,0,1	ICT1	17	1	0			c.G23T						PASS	.	G	LEU/ARG	223,4091		3,217,1937	10.0	9.0	9.0		23	2.2	0.8	17	dbSNP_107	9	274,8156		5,264,3946	no	missense	ICT1	NM_001545.1	102	8,481,5883	TT,TG,GG		3.2503,5.1692,3.8999	benign	8/207	73008804	497,12247	2157	4215	6372	SO:0001583	missense	3396	exon1			GCCTGCGCTGGGG	X81788	CCDS11711.1	17q25	2014-02-12				ENSG00000167862			5359	protein-coding gene	gene with protein product		603000				8575443, 20186120	Standard	NM_001545		Approved	DS-1	uc002jmm.3	Q14197		ENST00000301585.5:c.23G>T	17.37:g.73008804G>T	ENSP00000301585:p.Arg8Leu	Somatic	9	0	0	1142	WXS	Illumina HiSeq	Phase_I	17	14	0.823529	NM_001545	B2RAD1|Q53HM7|Q53Y11	Missense_Mutation	SNP	ENST00000301585.5	37	CCDS11711.1	.	.	.	.	.	.	.	.	.	.	G	9.452	1.090738	0.20471	0.051692	0.032503	ENSG00000167862	ENST00000301585	T	0.25749	1.78	5.58	2.2	0.27929	.	0.565130	0.17342	N	0.177719	T	0.01940	0.0061	N	0.14661	0.345	0.09310	N	0.999991	B	0.02656	0.0	B	0.01281	0.0	T	0.16689	-1.0394	10	0.44086	T	0.13	-4.1944	7.6743	0.28476	0.0:0.1266:0.4103:0.4631	rs3744206	8	Q14197	ICT1_HUMAN	L	8	ENSP00000301585:R8L	ENSP00000301585:R8L	R	+	2	0	ICT1	70520399	0.005000	0.15991	0.830000	0.32933	0.026000	0.11368	0.131000	0.15870	0.674000	0.31244	0.655000	0.94253	CGC	C|0.010;G|0.987;T|0.003	0.003	strong		0.697	ICT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445314.1	NM_001545	
CCR2	729230	hgsc.bcm.edu	37	3	46401243	46401243	+	Silent	SNP	A	A	G	rs3918386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46401243A>G	ENST00000400888.2	+	2	1056	c.1017A>G	c.(1015-1017)ccA>ccG	p.P339P	CCR2_ENST00000292301.4_Silent_p.P339P			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	339					blood vessel remodeling (GO:0001974)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular homeostasis (GO:0019725)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JAK-STAT cascade (GO:0007259)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of angiogenesis (GO:0016525)|negative regulation of eosinophil degranulation (GO:0043310)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of astrocyte chemotaxis (GO:2000464)|positive regulation of CD8-positive, alpha-beta T cell extravasation (GO:2000451)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of monocyte extravasation (GO:2000439)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of vascular endothelial growth factor production (GO:0010574)|response to wounding (GO:0009611)|T-helper 17 cell chemotaxis (GO:0035705)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|CCR2 chemokine receptor binding (GO:0031727)|chemokine receptor activity (GO:0004950)|protein homodimerization activity (GO:0042803)			breast(3)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)	14				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)		GAGTGAGACCAGGAAAGAATG	0.498													A|||	356	0.0710863	0.2595	0.0187	5008	,	,		19407	0.0		0.0	False		,,,				2504	0.0				p.P339P		Atlas-SNP	.											.	CCR2	103	.	0			c.A1017G						PASS	.	A		597,2539		60,477,1031	119.0	108.0	111.0		1017	-4.7	0.0	3	dbSNP_108	111	7,7157		0,7,3575	no	coding-synonymous	CCR2	NM_001123041.2		60,484,4606	GG,GA,AA		0.0977,19.037,5.8641		339/375	46401243	604,9696	1568	3582	5150	SO:0001819	synonymous_variant	729230	exon3			GAGACCAGGAAAG		CCDS43078.1, CCDS46813.1	3p21	2012-08-08			ENSG00000121807	ENSG00000121807		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1603	protein-coding gene	gene with protein product		601267		CMKBR2		8146186	Standard	NM_001123041		Approved	CC-CKR-2, CKR2, MCP-1-R, CD192, FLJ78302	uc003cpn.4	P41597	OTTHUMG00000156466	ENST00000400888.2:c.1017A>G	3.37:g.46401243A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Silent	SNP	ENST00000400888.2	37	CCDS43078.1																																																																																			A|0.940;G|0.060	0.060	strong		0.498	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647	
CLEC14A	161198	hgsc.bcm.edu	37	14	38724043	38724043	+	Silent	SNP	G	G	A	rs530380827|rs78287081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:38724043G>A	ENST00000342213.2	-	1	1531	c.1185C>T	c.(1183-1185)tcC>tcT	p.S395S		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	395						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		CCACGGCAGAGGAGGAGTCGA	0.502													G|||	44	0.00878594	0.0333	0.0	5008	,	,		19714	0.0		0.0	False		,,,				2504	0.0				p.S395S		Atlas-SNP	.											.	CLEC14A	83	.	0			c.C1185T						PASS	.	G		119,4287	88.2+/-126.9	2,115,2086	52.0	49.0	50.0		1185	-0.7	0.9	14	dbSNP_132	50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CLEC14A	NM_175060.1		2,116,6385	AA,AG,GG		0.0116,2.7009,0.9227		395/491	38724043	120,12886	2203	4300	6503	SO:0001819	synonymous_variant	161198	exon1			GGCAGAGGAGGAG		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"""C-type lectin domain containing"""	19832	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 27"""	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.1185C>T	14.37:g.38724043G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_175060	Q695G9|Q6PWT6|Q8N5V5	Silent	SNP	ENST00000342213.2	37	CCDS9667.1																																																																																			G|0.992;A|0.008	0.008	strong		0.502	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060	
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316482	39316482	+	Missense_Mutation	SNP	C	C	G	rs366700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39316482C>G	ENST00000390661.3	-	1	501	c.462G>C	c.(460-462)agG>agC	p.R154S		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	154	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		R -> S (in dbSNP:rs366700).			keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GCCTGTAGCACCTGGACACAC	0.617													c|||	523	0.104433	0.379	0.0288	5008	,	,		20637	0.0		0.002	False		,,,				2504	0.0				p.R154S		Atlas-SNP	.											.	KRTAP4-4	21	.	0			c.G462C						PASS	.	G	SER/ARG	1375,3019		224,927,1046	39.0	46.0	44.0		462	1.5	1.0	17	dbSNP_80	44	7,8585		0,7,4289	yes	missense	KRTAP4-4	NM_032524.1	110	224,934,5335	GG,GC,CC		0.0815,31.2927,10.6422	benign	154/167	39316482	1382,11604	2197	4296	6493	SO:0001583	missense	84616	exon1			GTAGCACCTGGAC	AJ406936	CCDS11383.1	17q21.2	2013-06-25			ENSG00000171396	ENSG00000171396		"""Keratin associated proteins"""	16928	protein-coding gene	gene with protein product			"""keratin associated protein 4-13"""	KRTAP4-13		11279113	Standard	NM_032524		Approved	KAP4.4, KAP4.13	uc002hwc.3	Q9BYR3	OTTHUMG00000133428	ENST00000390661.3:c.462G>C	17.37:g.39316482C>G	ENSP00000375076:p.Arg154Ser	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	251	250	0.996016	NM_032524	Q9BYU7	Missense_Mutation	SNP	ENST00000390661.3	37	CCDS11383.1	190	0.08699633699633699	179	0.3638211382113821	11	0.03038674033149171	0	0.0	0	0.0	.	2.548	-0.304815	0.05495	0.312927	8.15E-4	ENSG00000171396	ENST00000390661	T	0.00571	6.5	4.79	1.5	0.22942	.	0.286046	0.18063	U	0.152889	T	0.00012	0.0000	N	0.00159	-1.955	0.54753	P	1.8999999999991246E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.03068	-1.1076	9	0.19147	T	0.46	.	4.8968	0.13755	0.2534:0.289:0.4576:0.0	rs366700;rs52806510;rs366700	154	Q9BYR3	KRA44_HUMAN	S	154	ENSP00000375076:R154S	ENSP00000375076:R154S	R	-	3	2	KRTAP4-4	36570008	0.000000	0.05858	0.990000	0.47175	0.502000	0.33828	-0.971000	0.03806	0.113000	0.18004	-0.335000	0.08231	AGG	C|0.938;G|0.062	0.062	strong		0.617	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1		
DSE	29940	hgsc.bcm.edu	37	6	116758004	116758004	+	Silent	SNP	C	C	T	rs367781233		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116758004C>T	ENST00000331677.3	+	7	2817	c.2373C>T	c.(2371-2373)gaC>gaT	p.D791D	DSE_ENST00000452085.3_Silent_p.D791D|DSE_ENST00000537543.1_Silent_p.D810D|DSE_ENST00000359564.2_Silent_p.D791D			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	791					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)		AGGCCATTGACAGGATTTTTG	0.473																																					p.D791D		Atlas-SNP	.											.	DSE	98	.	0			c.C2373T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	68.0	72.0	70.0		2373,2373	1.9	1.0	6		70	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DSE	NM_001080976.1,NM_013352.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	791/959,791/959	116758004	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	29940	exon6			CATTGACAGGATT	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.2373C>T	6.37:g.116758004C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	142	64	0.450704	NM_001080976	Q5R3K6	Silent	SNP	ENST00000331677.3	37	CCDS5107.1																																																																																			.	.	weak		0.473	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
CCDC180	100499483	hgsc.bcm.edu	37	9	100128003	100128003	+	Missense_Mutation	SNP	C	C	G	rs148165882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100128003C>G	ENST00000357054.1	+	42	4931	c.3996C>G	c.(3994-3996)aaC>aaG	p.N1332K	CCDC180_ENST00000529487.1_Missense_Mutation_p.N1387K|MIR1302-8_ENST00000408342.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.N1387K|CCDC180_ENST00000395220.1_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1332						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											GCAGTGAGAACCTGCTGACAG	0.587													C|||	16	0.00319489	0.0008	0.0014	5008	,	,		17985	0.0		0.0129	False		,,,				2504	0.001				p.N1387K		Atlas-SNP	.											KIAA1529,NS,haematopoietic_neoplasm,0,2	.	.	2	0			c.C4161G						PASS	.	C	LYS/ASN	10,4396	16.8+/-37.8	0,10,2193	132.0	126.0	128.0		4161	-3.1	0.1	9	dbSNP_134	128	67,8533	40.3+/-97.0	0,67,4233	yes	missense	C9orf174	NM_020893.2	94	0,77,6426	GG,GC,CC		0.7791,0.227,0.592	possibly-damaging	1387/1702	100128003	77,12929	2203	4300	6503	SO:0001583	missense	0	exon30			TGAGAACCTGCTG	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.3996C>G	9.37:g.100128003C>G	ENSP00000349562:p.Asn1332Lys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	110	37	0.336364	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		13	0.005952380952380952	1	0.0020325203252032522	0	0.0	0	0.0	12	0.0158311345646438	C	10.99	1.508248	0.27036	0.00227	0.007791	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	T;T;T	0.07567	3.19;3.18;3.18	4.73	-3.11	0.05299	.	0.520038	0.17321	N	0.178515	T	0.01627	0.0052	N	0.19112	0.55	0.20074	N	0.999931	B;P	0.49559	0.257;0.925	B;B	0.43478	0.074;0.421	T	0.33904	-0.9850	10	0.05721	T	0.95	-0.9292	5.5431	0.17049	0.0:0.2861:0.3182:0.3956	.	1526;1332	B7ZMG3;Q9P1Z9	.;CI174_HUMAN	K	1332;1387;1387	ENSP00000349562:N1332K;ENSP00000364348:N1387K;ENSP00000434727:N1387K	ENSP00000349562:N1332K	N	+	3	2	C9orf174	99167824	0.001000	0.12720	0.142000	0.22268	0.006000	0.05464	-0.935000	0.03950	-0.344000	0.08338	-0.302000	0.09304	AAC	C|0.994;G|0.006	0.006	strong		0.587	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
TGM2	7052	hgsc.bcm.edu	37	20	36770588	36770588	+	Silent	SNP	C	C	T	rs2076390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36770588C>T	ENST00000361475.2	-	7	1046	c.873G>A	c.(871-873)ctG>ctA	p.L291L	TGM2_ENST00000536701.1_Silent_p.L210L|TGM2_ENST00000536724.1_Silent_p.L231L	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	291					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)	TAGGGATGCCCAGGCACCTCA	0.597													C|||	1012	0.202077	0.2141	0.1196	5008	,	,		18709	0.2718		0.1392	False		,,,				2504	0.2372				p.L291L		Atlas-SNP	.											.	TGM2	88	.	0			c.G873A						PASS	.	C	,	833,3573	329.6+/-301.1	85,663,1455	175.0	141.0	152.0		873,873	-10.3	0.5	20	dbSNP_96	152	1208,7392	244.7+/-273.8	77,1054,3169	no	coding-synonymous,coding-synonymous	TGM2	NM_004613.2,NM_198951.1	,	162,1717,4624	TT,TC,CC		14.0465,18.906,15.6928	,	291/688,291/549	36770588	2041,10965	2203	4300	6503	SO:0001819	synonymous_variant	7052	exon7			GATGCCCAGGCAC	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.873G>A	20.37:g.36770588C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	198	110	0.555556	NM_198951	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Silent	SNP	ENST00000361475.2	37	CCDS13302.1																																																																																			C|0.831;T|0.169	0.169	strong		0.597	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951	
GIMAP8	155038	hgsc.bcm.edu	37	7	150163837	150163837	+	Silent	SNP	A	A	G	rs2140595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	78	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	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	
ATG2A	23130	hgsc.bcm.edu	37	11	64675074	64675074	+	Missense_Mutation	SNP	G	G	A	rs61741398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64675074G>A	ENST00000377264.3	-	18	2682	c.2570C>T	c.(2569-2571)gCc>gTc	p.A857V	ATG2A_ENST00000421419.2_Missense_Mutation_p.A857V	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	857					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						CGAGGGCTGGGCGGCGGGGTC	0.627													G|||	108	0.0215655	0.0756	0.0086	5008	,	,		12877	0.0		0.002	False		,,,				2504	0.0				p.A857V		Atlas-SNP	.											.	ATG2A	133	.	0			c.C2570T						PASS	.	G	VAL/ALA	297,4069		13,271,1899	14.0	15.0	15.0		2570	3.3	0.0	11	dbSNP_129	15	0,8564		0,0,4282	yes	missense	ATG2A	NM_015104.2	64	13,271,6181	AA,AG,GG		0.0,6.8026,2.297	benign	857/1939	64675074	297,12633	2183	4282	6465	SO:0001583	missense	23130	exon18			GGCTGGGCGGCGG		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.2570C>T	11.37:g.64675074G>A	ENSP00000366475:p.Ala857Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	118	47	0.398305	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	G	8.222	0.802766	0.16397	0.068026	0.0	ENSG00000110046	ENST00000421419;ENST00000377264	T;T	0.45668	0.89;0.89	4.19	3.27	0.37495	.	0.651391	0.14546	N	0.312930	T	0.02767	0.0083	L	0.47716	1.5	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.01692	-1.1294	10	0.41790	T	0.15	.	7.2311	0.26043	0.1175:0.0:0.8825:0.0	.	857	Q2TAZ0	ATG2A_HUMAN	V	857	ENSP00000410522:A857V;ENSP00000366475:A857V	ENSP00000366475:A857V	A	-	2	0	ATG2A	64431650	0.021000	0.18746	0.009000	0.14445	0.008000	0.06430	1.467000	0.35321	2.350000	0.79820	0.655000	0.94253	GCC	G|0.984;A|0.016	0.016	strong		0.627	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
CIAPIN1	57019	hgsc.bcm.edu	37	16	57468110	57468110	+	Silent	SNP	G	G	A	rs77773186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57468110G>A	ENST00000569979.1	-	4	448	c.402C>T	c.(400-402)ccC>ccT	p.P134P	CIAPIN1_ENST00000569246.1_5'UTR|CIAPIN1_ENST00000569370.1_Silent_p.P134P|CIAPIN1_ENST00000567518.1_Silent_p.P121P|CIAPIN1_ENST00000568940.1_Silent_p.P134P|CIAPIN1_ENST00000394391.4_Silent_p.P134P|CIAPIN1_ENST00000565961.1_Silent_p.P107P					cytokine induced apoptosis inhibitor 1											cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						CAGGGGTTAGGGGCTCCCGCT	0.443													G|||	24	0.00479233	0.0182	0.0	5008	,	,		20722	0.0		0.0	False		,,,				2504	0.0				p.P134P		Atlas-SNP	.											.	CIAPIN1	17	.	0			c.C402T						PASS	.	G		40,3776		0,40,1868	108.0	102.0	104.0		402	2.2	0.1	16	dbSNP_131	104	1,8231		0,1,4115	no	coding-synonymous	CIAPIN1	NM_020313.2		0,41,5983	AA,AG,GG		0.0121,1.0482,0.3403		134/313	57468110	41,12007	1908	4116	6024	SO:0001819	synonymous_variant	57019	exon5			GGTTAGGGGCTCC	AF248964	CCDS10781.2	16q21	2012-09-20			ENSG00000005194	ENSG00000005194			28050	protein-coding gene	gene with protein product		608943				10493829, 11230166	Standard	XM_005256061		Approved	Anamorsin	uc002ell.1	Q6FI81	OTTHUMG00000133457	ENST00000569979.1:c.402C>T	16.37:g.57468110G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	96	56	0.583333	NM_020313		Silent	SNP	ENST00000569979.1	37																																																																																				G|0.993;A|0.007	0.007	strong		0.443	CIAPIN1-010	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432580.1	NM_020313	
SALL3	27164	hgsc.bcm.edu	37	18	76754367	76754367	+	Silent	SNP	C	C	T	rs2927258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:76754367C>T	ENST00000537592.2	+	2	2376	c.2376C>T	c.(2374-2376)acC>acT	p.T792T	SALL3_ENST00000536229.3_Silent_p.T659T|SALL3_ENST00000575389.2_Silent_p.T792T	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	792					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)		ACGCGGAGACCCTGAGCAGCT	0.647													C|||	363	0.072484	0.1513	0.0389	5008	,	,		15540	0.0605		0.0398	False		,,,				2504	0.0358				p.T792T		Atlas-SNP	.											SALL3,NS,carcinoma,0,1	SALL3	162	1	0			c.C2376T						PASS	.	C		504,3898	228.5+/-243.3	34,436,1731	64.0	64.0	64.0		2376	-1.1	0.0	18	dbSNP_101	64	491,8109	142.2+/-198.4	19,453,3828	no	coding-synonymous	SALL3	NM_171999.2		53,889,5559	TT,TC,CC		5.7093,11.4493,7.6527		792/1301	76754367	995,12007	2201	4300	6501	SO:0001819	synonymous_variant	27164	exon2			GGAGACCCTGAGC	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.2376C>T	18.37:g.76754367C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	94	55	0.585106	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	37	CCDS12013.1																																																																																			C|0.930;T|0.070	0.070	strong		0.647	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
FAM114A2	10827	hgsc.bcm.edu	37	5	153382518	153382518	+	Silent	SNP	G	G	A	rs34136150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:153382518G>A	ENST00000351797.4	-	10	1081	c.1005C>T	c.(1003-1005)acC>acT	p.T335T	FAM114A2_ENST00000522858.1_Silent_p.T335T|FAM114A2_ENST00000520313.1_Silent_p.T265T|FAM114A2_ENST00000520667.1_Silent_p.T335T	NM_018691.2	NP_061161.2	Q9NRY5	F1142_HUMAN	family with sequence similarity 114, member A2	335							purine nucleotide binding (GO:0017076)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)|urinary_tract(1)	18						ATTCGTGGGCGGTATTTCTTG	0.393													G|||	466	0.0930511	0.1891	0.0764	5008	,	,		16772	0.0179		0.1143	False		,,,				2504	0.0307				p.T335T		Atlas-SNP	.											.	FAM114A2	51	.	0			c.C1005T						PASS	.	G		689,3717	292.1+/-281.9	61,567,1575	133.0	130.0	131.0		1005	-7.1	0.1	5	dbSNP_126	131	1048,7552	222.2+/-259.3	53,942,3305	no	coding-synonymous	FAM114A2	NM_018691.2		114,1509,4880	AA,AG,GG		12.186,15.6378,13.3554		335/506	153382518	1737,11269	2203	4300	6503	SO:0001819	synonymous_variant	10827	exon10			GTGGGCGGTATTT	AF159700	CCDS4323.1	5q31-q33	2008-06-13	2008-06-13	2008-06-13	ENSG00000055147	ENSG00000055147			1333	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 3"""	C5orf3		10843801	Standard	XM_005268359		Approved	133K02	uc003lvc.3	Q9NRY5	OTTHUMG00000130147	ENST00000351797.4:c.1005C>T	5.37:g.153382518G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_018691	B2R8D8|Q9H7E0	Silent	SNP	ENST00000351797.4	37	CCDS4323.1																																																																																			G|0.880;A|0.120	0.120	strong		0.393	FAM114A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252455.1	NM_018691	
C1orf127	148345	hgsc.bcm.edu	37	1	11008594	11008594	+	Missense_Mutation	SNP	A	A	T	rs1281016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11008594A>T	ENST00000377008.4	-	11	1543	c.1097T>A	c.(1096-1098)gTc>gAc	p.V366D	C1orf127_ENST00000377004.4_Missense_Mutation_p.V533D			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	366			V -> D (in dbSNP:rs1281016).							NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TGGTCCTGAGACCAGAAGTGA	0.612													A|||	346	0.0690895	0.2035	0.0144	5008	,	,		19200	0.004		0.0427	False		,,,				2504	0.0204				p.V533D		Atlas-SNP	.											.	C1orf127	134	.	0			c.T1598A						PASS	.	A	ASP/VAL	735,3671	303.5+/-288.0	65,605,1533	56.0	53.0	54.0		1598	0.5	0.0	1	dbSNP_87	54	343,8257	116.3+/-176.0	4,335,3961	yes	missense	C1orf127	NM_001170754.1	152	69,940,5494	TT,TA,AA		3.9884,16.6818,8.2885	probably-damaging	533/824	11008594	1078,11928	2203	4300	6503	SO:0001583	missense	148345	exon12			CCTGAGACCAGAA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1097T>A	1.37:g.11008594A>T	ENSP00000366207:p.Val366Asp	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	179	86	0.480447	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		167|167	0.07646520146520147|0.07646520146520147	123|123	0.25|0.25	4|4	0.011049723756906077|0.011049723756906077	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	A|A	13.05|13.05	2.122259|2.122259	0.37436|0.37436	0.166818|0.166818	0.039884|0.039884	ENSG00000175262|ENSG00000175262	ENST00000418570;ENST00000520253|ENST00000377004;ENST00000377008	.|T;T	.|0.26518	.|1.73;1.73	4.15|4.15	0.48|0.48	0.16804|0.16804	.|.	.|0.956786	.|0.08574	.|N	.|0.925628	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	P|P	0.0|0.0	.|P;P;P	.|0.46512	.|0.879;0.879;0.879	.|B;B;B	.|0.42163	.|0.378;0.378;0.378	T|T	0.19484|0.19484	-1.0304|-1.0304	4|9	.|0.15952	.|T	.|0.53	-5.9143|-5.9143	0.8883|0.8883	0.01249|0.01249	0.3866:0.3152:0.136:0.1622|0.3866:0.3152:0.136:0.1622	rs1281016;rs52819154;rs1281016|rs1281016;rs52819154;rs1281016	.|384;358;366	.|B7ZLG7;Q8N9H9-2;Q8N9H9	.|.;.;CA127_HUMAN	T|D	368;485|533;366	.|ENSP00000366203:V533D;ENSP00000366207:V366D	.|ENSP00000366203:V533D	S|V	-|-	1|2	0|0	C1orf127|C1orf127	10931181|10931181	0.000000|0.000000	0.05858|0.05858	0.008000|0.008000	0.14137|0.14137	0.057000|0.057000	0.15508|0.15508	-0.110000|-0.110000	0.10824|0.10824	0.317000|0.317000	0.23160|0.23160	0.402000|0.402000	0.26972|0.26972	TCT|GTC	A|0.922;T|0.078	0.078	strong		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3481531	3481531	+	Silent	SNP	T	T	C	rs11548215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:3481531T>C	ENST00000324266.5	+	10	2037	c.1842T>C	c.(1840-1842)gaT>gaC	p.D614D	TRAPPC12_ENST00000382110.2_Silent_p.D614D	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	614					vesicle-mediated transport (GO:0016192)												AGAAATTAGATGGACTACAGG	0.328													T|||	476	0.0950479	0.1657	0.0692	5008	,	,		18454	0.0496		0.0944	False		,,,				2504	0.0654				p.D614D		Atlas-SNP	.											.	.	.	.	0			c.T1842C						PASS	.	T		730,3676	296.7+/-284.4	65,600,1538	69.0	73.0	71.0		1842	-2.6	1.0	2	dbSNP_120	71	844,7756	191.4+/-237.6	37,770,3493	no	coding-synonymous	TTC15	NM_016030.5		102,1370,5031	CC,CT,TT		9.814,16.5683,12.1021		614/736	3481531	1574,11432	2203	4300	6503	SO:0001819	synonymous_variant	51112	exon10			ATTAGATGGACTA	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.1842T>C	2.37:g.3481531T>C		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	276	115	0.416667	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	CCDS1652.1	223	0.1021062271062271	93	0.18902439024390244	24	0.06629834254143646	30	0.05244755244755245	76	0.10026385224274406	T	6.540	0.467960	0.12402	0.165683	0.09814	ENSG00000171853	ENST00000452495	.	.	.	5.66	-2.59	0.06209	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.999999999880938	.	.	.	.	.	.	T	0.23154	-1.0196	3	.	.	.	.	11.3558	0.49615	0.0:0.4395:0.0:0.5605	rs11548215;rs17851117	.	.	.	R	16	.	.	W	+	1	0	TTC15	3460538	0.124000	0.22315	0.986000	0.45419	0.633000	0.38033	-0.755000	0.04782	-0.353000	0.08224	-0.280000	0.10049	TGG	T|0.889;C|0.111	0.111	strong		0.328	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
ZBTB24	9841	hgsc.bcm.edu	37	6	109787596	109787596	+	Missense_Mutation	SNP	C	C	T	rs2232448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:109787596C>T	ENST00000230122.3	-	7	1719	c.1552G>A	c.(1552-1554)Gct>Act	p.A518T	MICAL1_ENST00000368952.4_5'Flank	NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	518			A -> T (in dbSNP:rs2232448).		hematopoietic progenitor cell differentiation (GO:0002244)|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(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		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;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		GCATCTGAAGCATGCTTCTCC	0.463													C|||	418	0.0834665	0.2776	0.0346	5008	,	,		19894	0.0		0.0099	False		,,,				2504	0.0174				p.A518T		Atlas-SNP	.											.	ZBTB24	64	.	0			c.G1552A						PASS	.	C	THR/ALA	1041,3365	383.0+/-324.7	128,785,1290	120.0	111.0	114.0		1552	0.9	0.0	6	dbSNP_98	114	129,8471	64.9+/-127.2	0,129,4171	yes	missense	ZBTB24	NM_014797.2	58	128,914,5461	TT,TC,CC		1.5,23.6269,8.9958	benign	518/698	109787596	1170,11836	2203	4300	6503	SO:0001583	missense	9841	exon7			CTGAAGCATGCTT	AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	21143	protein-coding gene	gene with protein product	"""POZ (BTB) and AT hook containing zinc finger 2"""	614064	"""zinc finger protein 450"""	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.1552G>A	6.37:g.109787596C>T	ENSP00000230122:p.Ala518Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	132	77	0.583333	NM_014797	Q17RC6|Q5TED5|Q8N455	Missense_Mutation	SNP	ENST00000230122.3	37	CCDS34509.1	150	0.06868131868131869	131	0.266260162601626	14	0.03867403314917127	0	0.0	5	0.006596306068601583	C	5.706	0.314802	0.10789	0.236269	0.015	ENSG00000112365	ENST00000230122	T	0.11277	2.79	6.06	0.896	0.19253	.	1.043490	0.07456	N	0.899772	T	0.01189	0.0039	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47420	-0.9119	9	0.62326	D	0.03	0.2747	0.4792	0.00545	0.2407:0.3331:0.1937:0.2325	rs2232448;rs52798886;rs57567548;rs2232448	518	O43167	ZBT24_HUMAN	T	518	ENSP00000230122:A518T	ENSP00000230122:A518T	A	-	1	0	ZBTB24	109894289	0.000000	0.05858	0.000000	0.03702	0.170000	0.22686	0.142000	0.16096	0.444000	0.26612	0.655000	0.94253	GCT	C|0.918;T|0.082	0.082	strong		0.463	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797	
OR2A2	442361	hgsc.bcm.edu	37	7	143806688	143806688	+	Missense_Mutation	SNP	C	C	A	rs10230228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143806688C>A	ENST00000408979.2	+	1	82	c.13C>A	c.(13-15)Cag>Aag	p.Q5K		NM_001005480.2	NP_001005480.2	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A, member 2	5			Q -> K (in dbSNP:rs10230228).			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)					GGAAGGCAACCAGACATGGAT	0.498													.|||	780	0.155751	0.3888	0.1297	5008	,	,		18028	0.0		0.166	False		,,,				2504	0.0092				p.Q5K		Atlas-SNP	.											OR2A2,rectum,carcinoma,-2,1	OR2A2	48	1	0			c.C13A						PASS	.	C	LYS/GLN	1435,2573		247,941,816	106.0	103.0	104.0		13	2.7	1.0	7	dbSNP_119	104	1680,6692		156,1368,2662	yes	missense	OR2A2	NM_001005480.2	53	403,2309,3478	AA,AC,CC		20.0669,35.8034,25.1616	benign	5/319	143806688	3115,9265	2004	4186	6190	SO:0001583	missense	442361	exon1			GGCAACCAGACAT		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.13C>A	7.37:g.143806688C>A	ENSP00000386209:p.Gln5Lys	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	285	127	0.445614	NM_001005480	B2RN85|Q8NGT6	Missense_Mutation	SNP	ENST00000408979.2	37	CCDS43671.1	364	0.16666666666666666	193	0.39227642276422764	51	0.1408839779005525	0	0.0	120	0.158311345646438	C	11.74	1.729249	0.30684	0.358034	0.200669	ENSG00000221989	ENST00000408979	T	0.00625	6.14	3.61	2.68	0.31781	.	.	.	.	.	T	0.00012	0.0000	L	0.54908	1.71	0.80722	P	0.0	B	0.15719	0.014	B	0.17433	0.018	T	0.29941	-0.9995	8	0.45353	T	0.12	.	8.8126	0.34976	0.0:0.7679:0.2321:0.0	rs10230228	5	Q6IF42	OR2A2_HUMAN	K	5	ENSP00000386209:Q5K	ENSP00000386209:Q5K	Q	+	1	0	OR2A2	143437621	0.002000	0.14202	0.996000	0.52242	0.990000	0.78478	-0.074000	0.11450	0.802000	0.34089	0.609000	0.83330	CAG	C|0.826;A|0.174	0.174	strong		0.498	OR2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349978.1		
ZNF432	9668	hgsc.bcm.edu	37	19	52538278	52538278	+	Silent	SNP	A	A	C	rs6509616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52538278A>C	ENST00000594154.1	-	5	866	c.654T>G	c.(652-654)tcT>tcG	p.S218S	ZNF432_ENST00000221315.5_Silent_p.S218S			O94892	ZN432_HUMAN	zinc finger protein 432	218					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	29		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)		CAGTGAGCTGAGACTTCTTGA	0.403													A|||	239	0.0477236	0.1203	0.0317	5008	,	,		19205	0.005		0.0408	False		,,,				2504	0.0123				p.S218S		Atlas-SNP	.											.	ZNF432	172	.	0			c.T654G						PASS	.	A		392,4014	195.7+/-220.2	13,366,1824	107.0	105.0	106.0		654	2.0	1.0	19	dbSNP_116	106	217,8383	90.9+/-153.0	2,213,4085	no	coding-synonymous	ZNF432	NM_014650.2		15,579,5909	CC,CA,AA		2.5233,8.897,4.6825		218/653	52538278	609,12397	2203	4300	6503	SO:0001819	synonymous_variant	9668	exon5			GAGCTGAGACTTC	AB018341	CCDS12848.1	19q13.41	2013-01-08				ENSG00000256087		"""Zinc fingers, C2H2-type"", ""-"""	20810	protein-coding gene	gene with protein product						9872452	Standard	NM_014650		Approved	KIAA0798	uc002pyk.3	O94892		ENST00000594154.1:c.654T>G	19.37:g.52538278A>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_014650		Silent	SNP	ENST00000594154.1	37	CCDS12848.1																																																																																			A|0.946;C|0.054	0.054	strong		0.403	ZNF432-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462410.1	NM_014650	
OR5L1	219437	hgsc.bcm.edu	37	11	55578991	55578991	+	Silent	SNP	C	C	T	rs61732387|rs386753698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55578991C>T	ENST00000333973.2	+	1	138	c.49C>T	c.(49-51)Cta>Tta	p.L17L		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L17L(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TCTCCTTGGACTATCAGATGT	0.438													N|||	525	0.104832	0.1884	0.0461	5008	,	,		18141	0.0813		0.0924	False		,,,				2504	0.0706				p.L17L		Atlas-SNP	.											OR5L1,NS,carcinoma,0,1	OR5L1	145	1	1	Substitution - coding silent(1)	stomach(1)	c.C49T						PASS	.	T		670,3730	763.4+/-413.2	63,544,1593	208.0	196.0	200.0		49	-2.0	0.0	11	dbSNP_130	200	724,7862	785.1+/-407.6	32,660,3601	no	coding-synonymous	OR5L1	NM_001004738.1		95,1204,5194	TT,TC,CC		8.4323,15.2273,10.7346		17/312	55578991	1394,11592	2200	4293	6493	SO:0001819	synonymous_variant	219437	exon1			CTTGGACTATCAG	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.49C>T	11.37:g.55578991C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	117	66	0.564103	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			C|0.899;T|0.101	0.101	strong		0.438	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
ENDOG	2021	hgsc.bcm.edu	37	9	131584649	131584649	+	Silent	SNP	C	C	T	rs55985529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131584649C>T	ENST00000372642.4	+	3	865	c.654C>T	c.(652-654)atC>atT	p.I218I	C9orf114_ENST00000361256.5_3'UTR	NM_004435.2	NP_004426.2	Q14249	NUCG_HUMAN	endonuclease G	218					apoptotic DNA fragmentation (GO:0006309)|DNA recombination (GO:0006310)|in utero embryonic development (GO:0001701)|positive regulation of apoptotic process (GO:0043065)|response to antibiotic (GO:0046677)|response to tumor necrosis factor (GO:0034612)	mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|nucleic acid binding (GO:0003676)										ACCAGGTCATCGGCAAGAACC	0.592													C|||	136	0.0271565	0.0961	0.0101	5008	,	,		20205	0.0		0.002	False		,,,				2504	0.0				p.I218I		Atlas-SNP	.											.	ENDOG	8	.	0			c.C654T						PASS	.	C	,	338,4068	177.3+/-206.3	10,318,1875	88.0	78.0	82.0		654,	-11.3	0.0	9	dbSNP_129	82	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,utr-3	ENDOG,C9orf114	NM_004435.2,NM_016390.2	,	10,323,6170	TT,TC,CC		0.0581,7.6714,2.6372	,	218/298,	131584649	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	2021	exon3			GGTCATCGGCAAG	X79444	CCDS6912.1	9q34.1	2008-06-04			ENSG00000167136	ENSG00000167136			3346	protein-coding gene	gene with protein product		600440				7789991	Standard	NM_004435		Approved		uc004bwc.3	Q14249	OTTHUMG00000020763	ENST00000372642.4:c.654C>T	9.37:g.131584649C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	107	66	0.616822	NM_004435	Q5T281|Q9BSP2	Silent	SNP	ENST00000372642.4	37	CCDS6912.1																																																																																			C|0.970;T|0.030	0.030	strong		0.592	ENDOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054505.1	NM_004435	
ABCB11	8647	hgsc.bcm.edu	37	2	169824983	169824983	+	Missense_Mutation	SNP	T	T	C	rs11568364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:169824983T>C	ENST00000263817.6	-	17	2153	c.2029A>G	c.(2029-2031)Atg>Gtg	p.M677V		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	677			M -> V (does not affect transport capacity for taurocholate; dbSNP:rs11568364). {ECO:0000269|PubMed:15077010, ECO:0000269|PubMed:16763017, ECO:0000269|PubMed:16799996, ECO:0000269|PubMed:17264802}.		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)	CTCGCAAGCATGTCATCTTCA	0.398													T|||	286	0.0571086	0.1831	0.0331	5008	,	,		17934	0.0		0.0159	False		,,,				2504	0.0051				p.M677V		Atlas-SNP	.											.	ABCB11	136	.	0			c.A2029G						PASS	.	T	VAL/MET	618,3164		47,524,1320	98.0	90.0	92.0		2029	-2.0	0.0	2	dbSNP_126	92	165,8103		1,163,3970	yes	missense	ABCB11	NM_003742.2	21	48,687,5290	CC,CT,TT		1.9956,16.3406,6.4979	benign	677/1322	169824983	783,11267	1891	4134	6025	SO:0001583	missense	8647	exon17			CAAGCATGTCATC	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.2029A>G	2.37:g.169824983T>C	ENSP00000263817:p.Met677Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	132	58	0.439394	NM_003742	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	37	CCDS46444.1	107	0.04899267399267399	84	0.17073170731707318	12	0.03314917127071823	0	0.0	11	0.014511873350923483	T	4.271	0.049489	0.08243	0.163406	0.019956	ENSG00000073734	ENST00000263817	D	0.85955	-2.05	5.46	-2.01	0.07410	.	159.533000	0.00166	N	0.000000	T	0.00468	0.0015	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	0.13202	-1.0518	9	0.29301	T	0.29	-7.6669	2.5783	0.04812	0.4676:0.0824:0.0965:0.3535	rs11568364;rs45576536;rs52799939;rs59217356;rs11568364	119;677	B4DZQ8;O95342	.;ABCBB_HUMAN	V	677	ENSP00000263817:M677V	ENSP00000263817:M677V	M	-	1	0	ABCB11	169533229	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.041000	0.13927	-0.572000	0.06006	-1.109000	0.02080	ATG	T|0.937;C|0.063	0.063	strong		0.398	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
OR6P1	128366	hgsc.bcm.edu	37	1	158533140	158533140	+	Silent	SNP	A	A	G	rs12080815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	79	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	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		
CPAMD8	27151	hgsc.bcm.edu	37	19	17049245	17049245	+	Silent	SNP	G	G	A	rs61133226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17049245G>A	ENST00000443236.1	-	23	2977	c.2946C>T	c.(2944-2946)gtC>gtT	p.V982V		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	935						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						ACGCCCGGGGGACTCCTTCCG	0.607													G|||	319	0.0636981	0.1778	0.0331	5008	,	,		18994	0.0387		0.002	False		,,,				2504	0.0204				p.V982V		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C2946T						PASS	.	G		597,3501		42,513,1494	41.0	45.0	44.0		2946	-4.8	0.0	19	dbSNP_129	44	8,8392		0,8,4192	no	coding-synonymous	CPAMD8	NM_015692.2		42,521,5686	AA,AG,GG		0.0952,14.5681,4.8408		982/1933	17049245	605,11893	2049	4200	6249	SO:0001819	synonymous_variant	27151	exon23			CCGGGGGACTCCT	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.2946C>T	19.37:g.17049245G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	122	0.055860805860805864	89	0.18089430894308944	11	0.03038674033149171	21	0.03671328671328671	1	0.0013192612137203166	G	2.180	-0.387755	0.04932	0.145681	9.52E-4	ENSG00000160111	ENST00000443236	.	.	.	2.39	-4.78	0.03209	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.37885	P	0.06947800000000004	.	.	.	.	.	.	T	0.19811	-1.0294	3	.	.	.	.	0.9916	0.01458	0.3747:0.0965:0.2404:0.2883	rs61133226;rs61745099	.	.	.	F	993	.	.	S	-	2	0	CPAMD8	16910245	0.410000	0.25376	0.002000	0.10522	0.045000	0.14185	-0.383000	0.07398	-2.191000	0.00756	-2.576000	0.00170	TCC	G|0.961;A|0.039	0.039	strong		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
CHL1	10752	hgsc.bcm.edu	37	3	361508	361508	+	Missense_Mutation	SNP	C	C	T	rs2272522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:361508C>T	ENST00000256509.2	+	3	691	c.49C>T	c.(49-51)Ctc>Ttc	p.L17F	CHL1_ENST00000397491.2_Missense_Mutation_p.L17F	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	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)	p.L17F(1)		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)		TCTAATGTTCCTCCTGTTAAA	0.338													T|||	1763	0.352037	0.5643	0.2378	5008	,	,		16826	0.3085		0.2048	False		,,,				2504	0.3425				p.L17F		Atlas-SNP	.											CHL1,caecum,carcinoma,0,2	CHL1	242	2	1	Substitution - Missense(1)	stomach(1)	c.C49T	GRCh37	CM023348	CHL1	M	rs2272522	PASS	.	T	PHE/LEU	2278,2126	572.4+/-383.3	567,1144,491	63.0	66.0	65.0		49	-2.0	0.0	3	dbSNP_100	65	1740,6860	732.3+/-406.8	185,1370,2745	yes	missense	CHL1	NM_006614.2	22	752,2514,3236	TT,TC,CC		20.2326,48.2743,30.8982	benign	17/1225	361508	4018,8986	2202	4300	6502	SO:0001583	missense	10752	exon1			ATGTTCCTCCTGT	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.49C>T	3.37:g.361508C>T	ENSP00000256509:p.Leu17Phe	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	678	0.31043956043956045	272	0.5528455284552846	84	0.23204419889502761	176	0.3076923076923077	146	0.19261213720316622	T	0.103	-1.149599	0.01714	0.517257	0.202326	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000427688;ENST00000421198;ENST00000435603;ENST00000449294	T;T;T;T;T;T	0.65732	0.16;0.19;1.01;0.21;0.13;-0.17	4.78	-2.03	0.07365	.	0.510152	0.20101	N	0.099240	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;0.001	T	0.36286	-0.9754	9	0.02654	T	1	.	10.7653	0.46291	0.0:0.4333:0.0:0.5667	rs2272522;rs57759025;rs2272522	17;17;17	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	F	17	ENSP00000256509:L17F;ENSP00000380628:L17F;ENSP00000403311:L17F;ENSP00000413628:L17F;ENSP00000397445:L17F;ENSP00000390440:L17F	ENSP00000256509:L17F	L	+	1	0	CHL1	336508	0.756000	0.28383	0.003000	0.11579	0.135000	0.20990	-0.166000	0.09954	-0.954000	0.03640	-1.197000	0.01672	CTC	C|0.678;T|0.322	0.322	strong		0.338	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
LRRTM1	347730	hgsc.bcm.edu	37	2	80529706	80529706	+	Silent	SNP	A	A	G	rs35054232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:80529706A>G	ENST00000295057.3	-	2	1895	c.1239T>C	c.(1237-1239)ctT>ctC	p.L413L	CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000496558.1_Intron|LRRTM1_ENST00000409148.1_Silent_p.L413L|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000361291.4_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	413					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						CGCCGCCTGGAAGAGCCACGG	0.682										HNSCC(69;0.2)			G|||	228	0.0455272	0.1604	0.0115	5008	,	,		16729	0.004		0.001	False		,,,				2504	0.0031				p.L413L		Atlas-SNP	.											.	LRRTM1	251	.	0			c.T1239C						PASS	.	G	,,	569,3833	754.3+/-412.4	41,487,1673	49.0	45.0	47.0		,,1239	2.0	1.0	2	dbSNP_126	47	37,8557	806.0+/-407.3	0,37,4260	no	intron,intron,coding-synonymous	CTNNA2,LRRTM1	NM_001164883.1,NM_004389.3,NM_178839.4	,,	41,524,5933	GG,GA,AA		0.4305,12.9259,4.663	,,	,,413/523	80529706	606,12390	2201	4297	6498	SO:0001819	synonymous_variant	347730	exon2			GCCTGGAAGAGCC	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.1239T>C	2.37:g.80529706A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	NM_178839	A8K397|D6W5K1|Q96DN1	Silent	SNP	ENST00000295057.3	37	CCDS1966.1																																																																																			A|0.958;G|0.042	0.042	strong		0.682	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
GPAM	57678	hgsc.bcm.edu	37	10	113935379	113935379	+	Missense_Mutation	SNP	T	T	C	rs10787428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:113935379T>C	ENST00000348367.4	-	6	589	c.392A>G	c.(391-393)gAa>gGa	p.E131G	GPAM_ENST00000369425.1_Missense_Mutation_p.E131G|GPAM_ENST00000423155.1_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	87	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	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	
DPYSL4	10570	hgsc.bcm.edu	37	10	134017388	134017388	+	Silent	SNP	C	C	G	rs1052556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134017388C>G	ENST00000338492.4	+	13	1748	c.1584C>G	c.(1582-1584)gtC>gtG	p.V528V	DPYSL4_ENST00000368629.1_Silent_p.V368V|DPYSL4_ENST00000368627.1_Silent_p.V368V	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	528					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		AGATCTCCGTCCCTCCTGTGC	0.682													C|||	761	0.151957	0.0756	0.1153	5008	,	,		16346	0.372		0.1262	False		,,,				2504	0.0808				p.V528V		Atlas-SNP	.											.	DPYSL4	91	.	0			c.C1584G						PASS	.	C		434,3972	208.8+/-229.8	22,390,1791	98.0	94.0	95.0		1584	-0.6	0.3	10	dbSNP_86	95	999,7601	215.2+/-254.6	64,871,3365	no	coding-synonymous	DPYSL4	NM_006426.2		86,1261,5156	GG,GC,CC		11.6163,9.8502,11.018		528/573	134017388	1433,11573	2203	4300	6503	SO:0001819	synonymous_variant	10570	exon13			CTCCGTCCCTCCT	AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.1584C>G	10.37:g.134017388C>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	177	67	0.378531	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Silent	SNP	ENST00000338492.4	37	CCDS7665.1																																																																																			C|0.865;G|0.135	0.135	strong		0.682	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2		
BPIFB4	149954	hgsc.bcm.edu	37	20	31671318	31671318	+	Silent	SNP	T	T	C	rs144729538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31671318T>C	ENST00000375483.3	+	3	315	c.315T>C	c.(313-315)taT>taC	p.Y105Y		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	105						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										AATACCGATATGGTGAGATCC	0.527													T|||	68	0.0135783	0.0469	0.0058	5008	,	,		14628	0.0		0.002	False		,,,				2504	0.0				p.Y105Y		Atlas-SNP	.											.	.	.	.	0			c.T315C						PASS	.	T		184,4222	118.8+/-156.5	5,174,2024	82.0	74.0	77.0		315	-4.4	1.0	20	dbSNP_134	77	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BPIFB4	NM_182519.2		5,175,6323	CC,CT,TT		0.0116,4.1761,1.4224		105/615	31671318	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	149954	exon3			CCGATATGGTGAG	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.315T>C	20.37:g.31671318T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	131	74	0.564885	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	37	CCDS13213.2																																																																																			T|0.986;C|0.014	0.014	strong		0.527	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
SEMG1	6406	hgsc.bcm.edu	37	20	43836237	43836237	+	Missense_Mutation	SNP	T	T	A	rs61729393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43836237T>A	ENST00000372781.3	+	2	356	c.299T>A	c.(298-300)cTa>cAa	p.L100Q	SEMG1_ENST00000244069.6_Missense_Mutation_p.L100Q	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	100	Repeat-rich region. {ECO:0000250}.			L -> Q (in Ref. 3; AAP82463). {ECO:0000305}.	insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				CAACGACATCTAGGTGGAAGT	0.393													T|||	63	0.0125799	0.0371	0.0086	5008	,	,		22065	0.0		0.004	False		,,,				2504	0.0041				p.L100Q		Atlas-SNP	.											.	SEMG1	71	.	0			c.T299A						PASS	.	T	GLN/LEU	144,4262	100.7+/-139.4	1,142,2060	143.0	123.0	130.0		299	-2.1	0.0	20	dbSNP_129	130	18,8582	12.6+/-44.7	0,18,4282	yes	missense	SEMG1	NM_003007.3	113	1,160,6342	AA,AT,TT		0.2093,3.2683,1.2456		100/463	43836237	162,12844	2203	4300	6503	SO:0001583	missense	6406	exon2			GACATCTAGGTGG		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"""semen coagulating protein"", ""cancer/testis antigen 103"""	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.299T>A	20.37:g.43836237T>A	ENSP00000361867:p.Leu100Gln	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	193	92	0.476684	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	23	0.010531135531135532	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	T	10.92	1.485748	0.26686	0.032683	0.002093	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.09445	2.98;2.98	1.07	-2.13	0.07144	.	.	.	.	.	T	0.07007	0.0178	L	0.54323	1.7	0.09310	N	1	D;D;D	0.63880	0.985;0.993;0.988	P;D;P	0.71414	0.693;0.973;0.796	T	0.08513	-1.0718	9	0.62326	D	0.03	.	4.0698	0.09877	0.0:0.4746:0.0:0.5254	rs61729393	100;100;100	P04279-2;P04279;E7EPD3	.;SEMG1_HUMAN;.	Q	100	ENSP00000244069:L100Q;ENSP00000361867:L100Q	ENSP00000244069:L100Q	L	+	2	0	SEMG1	43269651	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.238000	0.01199	-0.505000	0.06568	-0.321000	0.08615	CTA	T|0.988;A|0.012	0.012	strong		0.393	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
ABCC8	6833	hgsc.bcm.edu	37	11	17419279	17419279	+	Silent	SNP	C	C	T	rs1799859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:17419279C>T	ENST00000389817.3	-	31	3887	c.3819G>A	c.(3817-3819)agG>agA	p.R1273R	ABCC8_ENST00000302539.4_Silent_p.R1274R			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1273	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	CAGAGAGCTCCCTGTGCAGGG	0.652													C|||	1958	0.390974	0.77	0.4236	5008	,	,		18243	0.0873		0.2704	False		,,,				2504	0.2924				p.R1273R		Atlas-SNP	.											.	ABCC8	170	.	0			c.G3819A	GRCh37	CM981881	ABCC8	M	rs1799859	PASS	.	C		3006,1394	686.5+/-404.7	1022,962,216	90.0	84.0	86.0		3819	-0.4	1.0	11	dbSNP_89	86	2314,6272	389.5+/-342.9	307,1700,2286	no	coding-synonymous	ABCC8	NM_000352.3		1329,2662,2502	TT,TC,CC		26.9509,31.6818,40.9672		1273/1582	17419279	5320,7666	2200	4293	6493	SO:0001819	synonymous_variant	6833	exon31			GAGCTCCCTGTGC	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"""ATP binding cassette transporters / subfamily C"""	59	protein-coding gene	gene with protein product	"""sulfonylurea receptor (hyperinsulinemia)"""	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.3819G>A	11.37:g.17419279C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Silent	SNP	ENST00000389817.3	37	CCDS31437.1	723	0.33104395604395603	322	0.6544715447154471	144	0.39779005524861877	56	0.0979020979020979	201	0.26517150395778366	C	9.687	1.150834	0.21371	0.683182	0.269509	ENSG00000006071	ENST00000528374	.	.	.	5.12	-0.368	0.12537	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27281	P	0.9580932	.	.	.	.	.	.	T	0.35549	-0.9784	3	.	.	.	.	0.9041	0.01281	0.1595:0.2632:0.1952:0.3822	rs1799859;rs2229689;rs4148643;rs12787564;rs17846763;rs57092202;rs1799859	.	.	.	R	97	.	.	G	-	1	0	ABCC8	17375855	0.983000	0.35010	0.977000	0.42913	0.974000	0.67602	0.311000	0.19380	0.034000	0.15491	0.555000	0.69702	GGA	C|0.611;T|0.389	0.389	strong		0.652	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
ZNF683	257101	hgsc.bcm.edu	37	1	26691174	26691174	+	Missense_Mutation	SNP	C	C	A	rs11247933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26691174C>A	ENST00000436292.1	-	4	983	c.863G>T	c.(862-864)cGt>cTt	p.R288L	ZNF683_ENST00000349618.3_Missense_Mutation_p.R288L|ZNF683_ENST00000374204.1_Missense_Mutation_p.R288L|ZNF683_ENST00000403843.1_Missense_Mutation_p.R288L			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	288			R -> L (in dbSNP:rs11247933).		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)		CATGCCACCACGCTCCAGGCC	0.617													C|||	1319	0.263379	0.1233	0.4193	5008	,	,		16688	0.2778		0.341	False		,,,				2504	0.2474				p.R288L		Atlas-SNP	.											.	ZNF683	51	.	0			c.G863T						PASS	.	C	LEU/ARG,LEU/ARG	720,3686	295.9+/-283.9	58,604,1541	75.0	77.0	76.0		863,863	-7.0	0.0	1	dbSNP_120	76	3089,5511	470.5+/-367.8	547,1995,1758	yes	missense,missense	ZNF683	NM_001114759.1,NM_173574.2	102,102	605,2599,3299	AA,AC,CC		35.9186,16.3414,29.2865	benign,benign	288/505,288/505	26691174	3809,9197	2203	4300	6503	SO:0001583	missense	257101	exon4			CCACCACGCTCCA	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.863G>T	1.37:g.26691174C>A	ENSP00000388792:p.Arg288Leu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_173574	Q5T141|Q5T146|Q5T147|Q5T149|Q8NEN4	Missense_Mutation	SNP	ENST00000436292.1	37		620	0.2838827838827839	64	0.13008130081300814	144	0.39779005524861877	147	0.256993006993007	265	0.3496042216358839	C	7.602	0.672902	0.14776	0.163414	0.359186	ENSG00000176083	ENST00000403843;ENST00000436292;ENST00000374204;ENST00000349618	T;T;T;T	0.09630	3.01;3.01;2.96;2.96	3.52	-7.04	0.01578	.	2.010380	0.02183	N	0.060622	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.12630	0.006;0.003	B;B	0.17098	0.017;0.008	T	0.44467	-0.9326	9	0.10377	T	0.69	3.2031	3.8651	0.09013	0.1064:0.2623:0.1055:0.5259	rs11247933;rs52829071;rs59372706;rs11247933	288;288	Q8IZ20-2;Q8IZ20	.;ZN683_HUMAN	L	288	ENSP00000384782:R288L;ENSP00000388792:R288L;ENSP00000363320:R288L;ENSP00000344095:R288L	ENSP00000344095:R288L	R	-	2	0	ZNF683	26563761	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.192000	0.01245	-2.439000	0.00551	-1.134000	0.01955	CGT	C|0.728;A|0.272	0.272	strong		0.617	ZNF683-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009794.2	NM_173574	
AGT	183	hgsc.bcm.edu	37	1	230846305	230846305	+	Missense_Mutation	SNP	C	C	T	rs11568032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230846305C>T	ENST00000366667.4	-	2	506	c.292G>A	c.(292-294)Gaa>Aaa	p.E98K	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	98			E -> K (in dbSNP:rs11568032).		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)		AACTTGTCTTCGGTGTCAAGT	0.562													C|||	17	0.00339457	0.0113	0.0029	5008	,	,		21719	0.0		0.0	False		,,,				2504	0.0				p.E98K		Atlas-SNP	.											.	AGT	62	.	0			c.G292A						PASS	.	C	LYS/GLU	62,4344	58.1+/-94.6	0,62,2141	90.0	88.0	89.0		292	4.2	0.0	1	dbSNP_120	89	0,8600		0,0,4300	yes	missense	AGT	NM_000029.3	56	0,62,6441	TT,TC,CC		0.0,1.4072,0.4767	benign	98/486	230846305	62,12944	2203	4300	6503	SO:0001583	missense	183	exon2			TGTCTTCGGTGTC	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.292G>A	1.37:g.230846305C>T	ENSP00000355627:p.Glu98Lys	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	183	86	0.469945	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	9	0.004120879120879121	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	C	8.409	0.843741	0.16963	0.014072	0.0	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.87412	-2.25	5.09	4.18	0.49190	Serpin domain (1);	0.637587	0.16103	N	0.229456	T	0.73621	0.3610	M	0.62723	1.935	0.09310	N	1	P;P;P	0.40794	0.685;0.729;0.685	B;B;B	0.29785	0.107;0.101;0.107	T	0.66135	-0.5999	10	0.23302	T	0.38	.	5.7631	0.18211	0.1411:0.6438:0.1367:0.0785	rs11568032;rs52801258;rs59896600;rs11568032	98;98;98	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	K	98	ENSP00000355627:E98K	ENSP00000355627:E98K	E	-	1	0	AGT	228912928	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.721000	0.25911	1.276000	0.44395	0.491000	0.48974	GAA	C|0.994;T|0.006	0.006	strong		0.562	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029	
MKI67	4288	hgsc.bcm.edu	37	10	129901722	129901722	+	Silent	SNP	G	G	A	rs10082432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129901722G>A	ENST00000368654.3	-	13	8757	c.8382C>T	c.(8380-8382)gcC>gcT	p.A2794A	MKI67_ENST00000368653.3_Silent_p.A2434A	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2794	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)				CTATGGCTTGGGCACTTTCCC	0.493													G|||	1162	0.232029	0.3404	0.2277	5008	,	,		17212	0.2599		0.1581	False		,,,				2504	0.136				p.A2794A		Atlas-SNP	.											.	MKI67	363	.	0			c.C8382T						PASS	.	G	,	1359,3047	450.8+/-349.5	207,945,1051	94.0	89.0	91.0		7302,8382	-5.2	0.0	10	dbSNP_119	91	1489,7111	282.0+/-295.3	136,1217,2947	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	343,2162,3998	AA,AG,GG		17.314,30.8443,21.8976	,	2434/2897,2794/3257	129901722	2848,10158	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			GGCTTGGGCACTT	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.8382C>T	10.37:g.129901722G>A		Somatic	281	1	0.00355872		WXS	Illumina HiSeq	Phase_I	238	106	0.445378	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			G|0.782;A|0.218	0.218	strong		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
PTPRF	5792	hgsc.bcm.edu	37	1	44086831	44086831	+	Silent	SNP	C	C	T	rs1143702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44086831C>T	ENST00000359947.4	+	33	5923	c.5583C>T	c.(5581-5583)taC>taT	p.Y1861Y	PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000438120.1_Silent_p.Y1852Y|PTPRF_ENST00000372414.3_Silent_p.Y1861Y|PTPRF_ENST00000422171.2_Silent_p.Y1220Y|PTPRF_ENST00000372413.3_Silent_p.Y1852Y	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1861	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)				GCATGCGCTACGAGGGCGTGG	0.617													c|||	2857	0.570487	0.5507	0.5014	5008	,	,		22363	0.6855		0.6441	False		,,,				2504	0.4519				p.Y1861Y		Atlas-SNP	.											.	PTPRF	172	.	0			c.C5583T						PASS	.	T	,	2561,1845	634.9+/-396.3	749,1063,391	85.0	67.0	73.0		5583,5556	-9.5	0.2	1	dbSNP_86	73	5727,2873	672.1+/-402.9	1938,1851,511	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	2687,2914,902	TT,TC,CC		33.407,41.8747,36.2756	,	1861/1908,1852/1899	44086831	8288,4718	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon33			GCGCTACGAGGGC	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.5583C>T	1.37:g.44086831C>T		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	267	267	1	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	1276|1276	0.5842490842490843|0.5842490842490843	270|270	0.5487804878048781|0.5487804878048781	199|199	0.5497237569060773|0.5497237569060773	357|357	0.6241258741258742|0.6241258741258742	450|450	0.5936675461741425|0.5936675461741425	c|c	7.649|7.649	0.682443|0.682443	0.14907|0.14907	0.581253|0.581253	0.66593|0.66593	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	4.76|4.76	-9.52|-9.52	0.00578|0.00578	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.01202	.|-1.1420	.|3	.|.	.|.	.|.	.|.	15.3071|15.3071	0.74001|0.74001	0.0:0.3821:0.0:0.6179|0.0:0.3821:0.0:0.6179	rs1143702;rs7517450;rs17849120;rs1143702|rs1143702;rs7517450;rs17849120;rs1143702	.|.	.|.	.|.	X|M	1245;1286|1507	.|.	.|.	R|T	+|+	1|2	2|0	PTPRF|PTPRF	43859418|43859418	0.000000|0.000000	0.05858|0.05858	0.150000|0.150000	0.22450|0.22450	0.932000|0.932000	0.56968|0.56968	-2.838000|-2.838000	0.00739|0.00739	-2.452000|-2.452000	0.00542|0.00542	-2.203000|-2.203000	0.00303|0.00303	CGA|ACG	A|0.000;C|0.380;T|0.620	0.620	strong		0.617	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
ARHGEF2	9181	hgsc.bcm.edu	37	1	155931630	155931630	+	Silent	SNP	G	G	A	rs143812169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155931630G>A	ENST00000361247.4	-	11	1389	c.1290C>T	c.(1288-1290)gaC>gaT	p.D430D	ARHGEF2_ENST00000462460.2_Silent_p.D475D|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000313667.4_Silent_p.D429D|ARHGEF2_ENST00000368316.1_Silent_p.D402D|ARHGEF2_ENST00000313695.7_Silent_p.D402D|ARHGEF2_ENST00000368315.4_Silent_p.D431D	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	430	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					AAATACCCTCGTCCACATTGG	0.632													G|||	21	0.00419329	0.0136	0.0	5008	,	,		17097	0.0		0.0	False		,,,				2504	0.0031				p.D430D	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.C1290T						PASS	.	G	,,	90,4316	73.6+/-111.7	1,88,2114	74.0	73.0	73.0		1290,1287,1206	4.0	1.0	1	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF2	NM_001162383.1,NM_001162384.1,NM_004723.3	,,	1,89,6413	AA,AG,GG		0.0116,2.0427,0.6997	,,	430/987,429/986,402/959	155931630	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	9181	exon11			ACCCTCGTCCACA	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	682	protein-coding gene	gene with protein product		607560	"""rho/rac guanine nucleotide exchange factor (GEF) 2"""			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.1290C>T	1.37:g.155931630G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	189	95	0.502645	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Silent	SNP	ENST00000361247.4	37	CCDS53376.1																																																																																			G|0.995;A|0.005	0.005	strong		0.632	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723	
PITX1	5307	hgsc.bcm.edu	37	5	134364996	134364996	+	Silent	SNP	G	G	T	rs1131611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134364996G>T	ENST00000265340.7	-	3	834	c.418C>A	c.(418-420)Cgg>Agg	p.R140R	PITX1_ENST00000506438.1_Silent_p.R140R	NM_002653.4	NP_002644.4	P78337	PITX1_HUMAN	paired-like homeodomain 1	140					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)		TTGGCTCGCCGGTTCTTGAAC	0.687													G|||	898	0.179313	0.4554	0.2061	5008	,	,		15649	0.001		0.1054	False		,,,				2504	0.047				p.R140R		Atlas-SNP	.											.	PITX1	31	.	0			c.C418A						PASS	.	G		1784,2618		370,1044,787	37.0	42.0	40.0		418	3.5	1.0	5	dbSNP_86	40	929,7665		57,815,3425	no	coding-synonymous	PITX1	NM_002653.4		427,1859,4212	TT,TG,GG		10.8099,40.527,20.8757		140/315	134364996	2713,10283	2201	4297	6498	SO:0001819	synonymous_variant	5307	exon3			CTCGCCGGTTCTT	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.418C>A	5.37:g.134364996G>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_002653	A8K3M0|D3DQB0|O14677|O60425|Q9BTI5	Silent	SNP	ENST00000265340.7	37	CCDS4182.1																																																																																			G|0.809;T|0.191	0.191	strong		0.687	PITX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251195.3		
SPOCK1	6695	hgsc.bcm.edu	37	5	136448208	136448208	+	Silent	SNP	A	A	G	rs17170968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:136448208A>G	ENST00000394945.1	-	5	559	c.390T>C	c.(388-390)ccT>ccC	p.P130P	SPOCK1_ENST00000282223.7_Silent_p.P130P	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	130	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCAAATTCGAAGGTCCAACCC	0.498													A|||	379	0.0756789	0.2769	0.0187	5008	,	,		18879	0.0		0.0	False		,,,				2504	0.0				p.P130P		Atlas-SNP	.											.	SPOCK1	58	.	0			c.T390C						PASS	.	A		1146,3260	407.3+/-334.2	151,844,1208	101.0	97.0	98.0		390	-1.0	1.0	5	dbSNP_123	98	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	SPOCK1	NM_004598.3		151,854,5498	GG,GA,AA		0.1163,26.01,8.8882		130/440	136448208	1156,11850	2203	4300	6503	SO:0001819	synonymous_variant	6695	exon5			ATTCGAAGGTCCA	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"""sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"""	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.390T>C	5.37:g.136448208A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Silent	SNP	ENST00000394945.1	37	CCDS4191.1																																																																																			A|0.924;G|0.076	0.076	strong		0.498	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598	
ABHD2	11057	hgsc.bcm.edu	37	15	89738475	89738475	+	Missense_Mutation	SNP	A	A	C	rs147106119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89738475A>C	ENST00000352732.5	+	11	1619	c.1099A>C	c.(1099-1101)Atg>Ctg	p.M367L	ABHD2_ENST00000355100.3_Missense_Mutation_p.M367L|ABHD2_ENST00000565973.1_Missense_Mutation_p.M367L	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	367					negative regulation of cell migration (GO:0030336)|response to wounding (GO:0009611)	integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|soft_tissue(1)	23	Lung NSC(78;0.0472)|all_lung(78;0.089)					AGAGAACGTCATGTTTGTGCT	0.557													A|||	5	0.000998403	0.0038	0.0	5008	,	,		20328	0.0		0.0	False		,,,				2504	0.0				p.M367L	Colon(11;252 417 24570 33239 41878)	Atlas-SNP	.											.	ABHD2	55	.	0			c.A1099C						PASS	.	A	LEU/MET,LEU/MET	16,4384	23.3+/-48.9	0,16,2184	142.0	124.0	130.0		1099,1099	4.6	1.0	15	dbSNP_134	130	0,8598		0,0,4299	yes	missense,missense	ABHD2	NM_007011.7,NM_152924.4	15,15	0,16,6483	CC,CA,AA		0.0,0.3636,0.1231	benign,benign	367/426,367/426	89738475	16,12982	2200	4299	6499	SO:0001583	missense	11057	exon15			AACGTCATGTTTG	X12433	CCDS10348.1	15q26.1	2006-10-06			ENSG00000140526	ENSG00000140526		"""Abhydrolase domain containing"""	18717	protein-coding gene	gene with protein product		612196					Standard	NM_152924		Approved	LABH2	uc002bnk.2	P08910	OTTHUMG00000148684	ENST00000352732.5:c.1099A>C	15.37:g.89738475A>C	ENSP00000268129:p.Met367Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_007011	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Missense_Mutation	SNP	ENST00000352732.5	37	CCDS10348.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	5.968	0.362642	0.11296	0.003636	0.0	ENSG00000140526	ENST00000352732;ENST00000355100	T;T	0.60299	0.2;0.2	5.75	4.6	0.57074	Alpha/beta hydrolase fold-1 (1);	0.166180	0.64402	D	0.000008	T	0.34019	0.0883	N	0.16307	0.4	0.41422	D	0.987801	B	0.10296	0.003	B	0.15052	0.012	T	0.10847	-1.0612	10	0.08179	T	0.78	-14.589	6.6357	0.22881	0.7918:0.0:0.0709:0.1373	.	367	P08910	ABHD2_HUMAN	L	367	ENSP00000268129:M367L;ENSP00000347217:M367L	ENSP00000268129:M367L	M	+	1	0	ABHD2	87539479	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.877000	0.63086	0.974000	0.38366	0.533000	0.62120	ATG	A|0.999;C|0.001	0.001	strong		0.557	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2		
GOT2	2806	hgsc.bcm.edu	37	16	58743454	58743454	+	Missense_Mutation	SNP	A	A	C	rs30842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58743454A>C	ENST00000245206.5	-	9	1165	c.1037T>G	c.(1036-1038)gTc>gGc	p.V346G	GOT2_ENST00000434819.2_Missense_Mutation_p.V303G	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	346			V -> G (in dbSNP:rs30842). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:3207426, ECO:0000269|PubMed:4052435}.		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)	GTCAGCCATGACTTTCACTTC	0.502													C|||	3782	0.755192	0.8994	0.7824	5008	,	,		19314	0.6607		0.7097	False		,,,				2504	0.6851				p.V346G		Atlas-SNP	.											.	GOT2	42	.	0			c.T1037G						PASS	.	C	GLY/VAL	3785,611	265.6+/-266.7	1627,531,40	253.0	247.0	249.0		1037	5.3	1.0	16	dbSNP_76	249	5901,2699	433.0+/-357.3	2034,1833,433	yes	missense	GOT2	NM_002080.2	109	3661,2364,473	CC,CA,AA		31.3837,13.899,25.4694	benign	346/431	58743454	9686,3310	2198	4300	6498	SO:0001583	missense	2806	exon9			GCCATGACTTTCA		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.1037T>G	16.37:g.58743454A>C	ENSP00000245206:p.Val346Gly	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	90	54	0.6	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Missense_Mutation	SNP	ENST00000245206.5	37	CCDS10801.1	1611	0.7376373626373627	438	0.8902439024390244	277	0.7651933701657458	376	0.6573426573426573	520	0.6860158311345647	C	3.270	-0.149293	0.06585	0.86101	0.686163	ENSG00000125166	ENST00000245206;ENST00000434819	D;D	0.90261	-2.64;-2.64	5.31	5.31	0.75309	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.162273	0.53938	N	0.000059	T	0.00012	0.0000	N	0.00327	-1.64	0.33927	P	0.35837300000000005	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42649	-0.9439	8	.	.	.	5.2238	14.6551	0.68828	0.1464:0.8536:0.0:0.0	rs30842;rs17821579;rs56935811;rs30842	303;346	E7ERW2;P00505	.;AATM_HUMAN	G	346;303	ENSP00000245206:V346G;ENSP00000394100:V303G	.	V	-	2	0	GOT2	57300955	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.160000	0.50739	1.252000	0.44001	-0.127000	0.14921	GTC	A|0.252;C|0.748	0.748	strong		0.502	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
CST5	1473	hgsc.bcm.edu	37	20	23860178	23860178	+	Missense_Mutation	SNP	A	A	G	rs1799841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	109	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	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	
KNG1	3827	hgsc.bcm.edu	37	3	186459475	186459475	+	Missense_Mutation	SNP	C	C	G	rs5030084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186459475C>G	ENST00000265023.4	+	10	1502	c.1290C>G	c.(1288-1290)gaC>gaG	p.D430E	RP11-573D15.8_ENST00000609726.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000596329.1_RNA|KNG1_ENST00000287611.2_Intron	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	430	His-rich.		D -> E (in dbSNP:rs5030084).		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		GTAGACATGACTGGGGCCATG	0.483													C|||	166	0.033147	0.0613	0.0375	5008	,	,		21946	0.0129		0.0258	False		,,,				2504	0.0204				p.D430E		Atlas-SNP	.											.	KNG1	129	.	0			c.C1290G						PASS	.	C	,GLU/ASP,	270,4096		4,262,1917	100.0	101.0	101.0		,1290,	3.0	0.7	3	dbSNP_113	101	239,8339		5,229,4055	yes	intron,missense,intron	KNG1	NM_000893.3,NM_001102416.2,NM_001166451.1	,45,	9,491,5972	GG,GC,CC		2.7862,6.1842,3.9323	,benign,	,430/645,	186459475	509,12435	2183	4289	6472	SO:0001583	missense	3827	exon10			ACATGACTGGGGC		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"""Endogenous ligands"""	6383	protein-coding gene	gene with protein product	"""alpha-2-thiol proteinase inhibitor"", ""bradykinin"""	612358	"""kininogen"""	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.1290C>G	3.37:g.186459475C>G	ENSP00000265023:p.Asp430Glu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	119	48	0.403361	NM_001102416	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	37	CCDS43183.1	70	0.03205128205128205	26	0.052845528455284556	17	0.04696132596685083	7	0.012237762237762238	20	0.026385224274406333	C	11.14	1.549816	0.27652	0.061842	0.027862	ENSG00000113889	ENST00000265023	T	0.58210	0.35	4.79	2.98	0.34508	.	0.379044	0.23049	N	0.052505	T	0.04907	0.0132	L	0.46157	1.445	0.80722	D	1	P	0.42827	0.791	B	0.31946	0.138	T	0.00995	-1.1487	9	.	.	.	-0.6577	6.9085	0.24323	0.0:0.7335:0.1741:0.0924	rs5030084;rs52817760;rs61657557;rs5030084	430	P01042	KNG1_HUMAN	E	430	ENSP00000265023:D430E	.	D	+	3	2	KNG1	187942169	0.988000	0.35896	0.682000	0.30024	0.381000	0.30169	-0.157000	0.10085	0.923000	0.37045	0.655000	0.94253	GAC	C|0.964;G|0.036	0.036	strong		0.483	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416	
UNC5B	219699	hgsc.bcm.edu	37	10	73051440	73051440	+	Missense_Mutation	SNP	G	G	A	rs10509332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73051440G>A	ENST00000335350.6	+	10	1962	c.1546G>A	c.(1546-1548)Gcc>Acc	p.A516T	UNC5B_ENST00000373192.4_Missense_Mutation_p.A505T	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	516			A -> T (in dbSNP:rs10509332).		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						TAGCGATTTCGCCCGGGACAC	0.682													g|||	174	0.0347444	0.0923	0.013	5008	,	,		16797	0.0		0.0169	False		,,,				2504	0.0266				p.A516T		Atlas-SNP	.											.	UNC5B	123	.	0			c.G1546A						PASS	.		THR/ALA	326,4080	175.9+/-205.1	12,302,1889	49.0	51.0	50.0		1546	-7.4	0.0	10	dbSNP_119	50	235,8363	96.3+/-158.1	3,229,4067	yes	missense	UNC5B	NM_170744.4	58	15,531,5956	AA,AG,GG		2.7332,7.399,4.3141	benign	516/946	73051440	561,12443	2203	4299	6502	SO:0001583	missense	219699	exon10			GATTTCGCCCGGG	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.1546G>A	10.37:g.73051440G>A	ENSP00000334329:p.Ala516Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	66	0.03021978021978022	44	0.08943089430894309	6	0.016574585635359115	0	0.0	16	0.021108179419525065	g	0.003	-2.576838	0.00131	0.07399	0.027332	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.48836	0.86;0.8	3.71	-7.42	0.01388	.	1.034760	0.07589	N	0.921713	T	0.00754	0.0025	N	0.22421	0.69	0.09310	N	1	B;B	0.24483	0.104;0.063	B;B	0.15870	0.014;0.006	T	0.04128	-1.0975	10	0.14656	T	0.56	-3.517	0.8807	0.01233	0.1728:0.2213:0.3114:0.2946	rs10509332;rs10509332	505;516	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	T	516;505	ENSP00000334329:A516T;ENSP00000362288:A505T	ENSP00000334329:A516T	A	+	1	0	UNC5B	72721446	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.641000	0.02007	-3.747000	0.00112	-2.851000	0.00103	GCC	G|0.960;A|0.040	0.040	strong		0.682	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
FRAS1	80144	hgsc.bcm.edu	37	4	78987157	78987157	+	Missense_Mutation	SNP	A	A	G	rs4859905	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:78987157A>G	ENST00000325942.6	+	2	535	c.95A>G	c.(94-96)gAt>gGt	p.D32G	FRAS1_ENST00000264895.6_Missense_Mutation_p.D32G|FRAS1_ENST00000264899.6_Missense_Mutation_p.D32G	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	32	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.		D -> G (in dbSNP:rs4859905).		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						GTCTATCAGGATTCCTTGTTG	0.408													G|||	2762	0.551518	0.7519	0.4654	5008	,	,		18692	0.5407		0.4195	False		,,,				2504	0.4888				p.D32G		Atlas-SNP	.											.	FRAS1	779	.	0			c.A95G						PASS	.	G	GLY/ASP,GLY/ASP	2527,1199		884,759,220	232.0	215.0	220.0		95,95	5.9	1.0	4	dbSNP_111	220	3285,4913		664,1957,1478	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	94,94	1548,2716,1698	GG,GA,AA		40.0707,32.1793,48.742	benign,benign	32/1977,32/4013	78987157	5812,6112	1863	4099	5962	SO:0001583	missense	80144	exon2			ATCAGGATTCCTT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.95A>G	4.37:g.78987157A>G	ENSP00000326330:p.Asp32Gly	Somatic	402	1	0.00248756		WXS	Illumina HiSeq	Phase_I	394	182	0.461929	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	1127	0.5160256410256411	352	0.7154471544715447	173	0.47790055248618785	301	0.5262237762237763	301	0.3970976253298153	G	5.385	0.256325	0.10185	0.678207	0.400707	ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000264899;ENST00000380674	T;T;T	0.56611	0.45;0.45;0.45	5.9	5.9	0.94986	.	0.162317	0.41194	N	0.000924	T	0.00012	0.0000	.	.	.	0.45261	P	0.0017329999999999846	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35201	-0.9798	8	0.02654	T	1	.	12.5489	0.56216	0.0777:0.0:0.9222:0.0	rs4859905;rs58160615;rs4859905	32;32	E9PHH6;A2RRR8	.;.	G	32	ENSP00000326330:D32G;ENSP00000264895:D32G;ENSP00000264899:D32G	ENSP00000264895:D32G	D	+	2	0	FRAS1	79206181	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	2.691000	0.47010	1.517000	0.48917	-0.213000	0.12676	GAT	A|0.473;G|0.527	0.527	strong		0.408	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
LRRC18	474354	hgsc.bcm.edu	37	10	50121785	50121785	+	Missense_Mutation	SNP	G	G	A	rs11101561|rs386743529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50121785G>A	ENST00000374160.3	-	1	492	c.416C>T	c.(415-417)aCa>aTa	p.T139I	WDFY4_ENST00000413659.2_Intron|RP11-523O18.7_ENST00000430438.1_RNA|LRRC18_ENST00000298124.3_Missense_Mutation_p.T139I|WDFY4_ENST00000325239.5_Intron	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						GGCCCCCAGTGTGGTGGGCAC	0.592													G|||	639	0.127596	0.3994	0.085	5008	,	,		19487	0.0		0.0258	False		,,,				2504	0.0266				p.T139I		Atlas-SNP	.											.	LRRC18	52	.	0			c.C416T						PASS	.	G	ILE/THR,	1405,3001		269,867,1067	75.0	75.0	75.0		416,	6.0	1.0	10	dbSNP_120	75	190,8410		4,182,4114	yes	missense,intron	WDFY4,LRRC18	NM_001006939.3,NM_020945.1	89,	273,1049,5181	AA,AG,GG		2.2093,31.8883,12.2636	probably-damaging,	139/262,	50121785	1595,11411	2203	4300	6503	SO:0001583	missense	474354	exon1			CCCAGTGTGGTGG	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.416C>T	10.37:g.50121785G>A	ENSP00000363275:p.Thr139Ile	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	146	62	0.424658	NM_001006939	Q6UY02	Missense_Mutation	SNP	ENST00000374160.3	37	CCDS31197.1	183	0.08379120879120878	142	0.2886178861788618	25	0.06906077348066299	0	0.0	16	0.021108179419525065	G	18.40	3.616785	0.66672	0.318883	0.022093	ENSG00000165383	ENST00000374160;ENST00000298124	T;T	0.17054	2.3;2.3	5.98	5.98	0.97165	.	0.102656	0.64402	D	0.000002	T	0.00012	0.0000	M	0.85099	2.735	0.22342	P	0.999185278	D	0.59767	0.986	P	0.53649	0.731	T	0.03875	-1.0996	8	.	.	.	.	20.4434	0.99119	0.0:0.0:1.0:0.0	rs11101561;rs61200891	139	Q8N456	LRC18_HUMAN	I	139	ENSP00000363275:T139I;ENSP00000298124:T139I	.	T	-	2	0	LRRC18	49791791	0.986000	0.35501	0.969000	0.41365	0.830000	0.47004	1.869000	0.39519	2.838000	0.97847	0.655000	0.94253	ACA	G|0.891;A|0.109	0.109	strong		0.592	LRRC18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047964.1	NM_001006939	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34825662	34825662	+	Silent	SNP	T	T	C	rs16894959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:34825662T>C	ENST00000192788.5	+	13	1906	c.1735T>C	c.(1735-1737)Ttg>Ctg	p.L579L	UHRF1BP1_ENST00000452449.2_Silent_p.L579L	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	579							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						AGATGAACACTTGGACATCCG	0.443													T|||	693	0.138379	0.3071	0.0994	5008	,	,		20564	0.0119		0.1262	False		,,,				2504	0.0808				p.L579L		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.T1735C						PASS	.	T		878,2966		98,682,1142	117.0	109.0	112.0		1735	-10.2	0.3	6	dbSNP_123	112	1244,7018		101,1042,2988	no	coding-synonymous	UHRF1BP1	NM_017754.3		199,1724,4130	CC,CT,TT		15.0569,22.8408,17.5285		579/1441	34825662	2122,9984	1922	4131	6053	SO:0001819	synonymous_variant	54887	exon13			GAACACTTGGACA	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.1735T>C	6.37:g.34825662T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_017754	Q9NXE0	Silent	SNP	ENST00000192788.5	37	CCDS43455.1																																																																																			T|0.852;C|0.148	0.148	strong		0.443	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
PXDN	7837	hgsc.bcm.edu	37	2	1647186	1647186	+	Silent	SNP	G	G	A	rs111450110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1647186G>A	ENST00000252804.4	-	19	3956	c.3906C>T	c.(3904-3906)gaC>gaT	p.D1302D		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1302					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)		TGGGGATCTCGTCACAGCTGC	0.612													G|||	57	0.0113818	0.0393	0.0072	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.D1302D		Atlas-SNP	.											.	PXDN	255	.	0			c.C3906T						PASS	.	G		167,4063		5,157,1953	65.0	76.0	72.0		3906	-9.0	0.0	2	dbSNP_132	72	1,8443		0,1,4221	yes	coding-synonymous	PXDN	NM_012293.1		5,158,6174	AA,AG,GG		0.0118,3.948,1.3255		1302/1480	1647186	168,12506	2115	4222	6337	SO:0001819	synonymous_variant	7837	exon19			GATCTCGTCACAG	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.3906C>T	2.37:g.1647186G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1																																																																																			G|0.992;A|0.008	0.008	strong		0.612	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
PSPH	5723	hgsc.bcm.edu	37	7	56088786	56088786	+	Silent	SNP	A	A	T	rs202027697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:56088786A>T	ENST00000395471.3	-	4	925	c.120T>A	c.(118-120)gtT>gtA	p.V40V	PSPH_ENST00000275605.3_Silent_p.V40V|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	40					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CCGCGTCCTCAACGCCACAGA	0.423																																					p.V40V		Atlas-SNP	.											.	PSPH	23	.	0			c.T120A						PASS	.						151.0	116.0	128.0					7																	56088786		2203	4300	6503	SO:0001819	synonymous_variant	5723	exon4			GTCCTCAACGCCA	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.120T>A	7.37:g.56088786A>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	228	66	0.289474	NM_004577	B2RCR5|Q7Z3S5	Silent	SNP	ENST00000395471.3	37	CCDS5522.1																																																																																			A|0.749;T|0.251	0.251	strong		0.423	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
CCT5	22948	hgsc.bcm.edu	37	5	10262607	10262607	+	Silent	SNP	G	G	A	rs113262482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:10262607G>A	ENST00000280326.4	+	9	1614	c.1194G>A	c.(1192-1194)gcG>gcA	p.A398A	CCT5_ENST00000503026.1_Silent_p.A377A|CCT5_ENST00000515390.1_Silent_p.A343A|CCT5_ENST00000506600.1_Silent_p.A305A|CCT5_ENST00000515676.1_Silent_p.A360A|CTD-2256P15.4_ENST00000606194.1_RNA	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	398					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						TTGAGGAGGCGAAACGATCCC	0.468													G|||	40	0.00798722	0.0295	0.0	5008	,	,		20572	0.0		0.001	False		,,,				2504	0.0				p.A398A		Atlas-SNP	.											.	CCT5	49	.	0			c.G1194A						PASS	.	G		99,4307	79.3+/-117.8	1,97,2105	160.0	131.0	141.0		1194	-7.7	0.9	5	dbSNP_132	141	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous	CCT5	NM_012073.3		1,100,6402	AA,AG,GG		0.0349,2.2469,0.7843		398/542	10262607	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	22948	exon9			GGAGGCGAAACGA	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"""Heat Shock Proteins / Chaperonins"""	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.1194G>A	5.37:g.10262607G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_012073	A8JZY8|A8K2X8|B4DYD8	Silent	SNP	ENST00000280326.4	37	CCDS3877.1																																																																																			G|0.992;A|0.008	0.008	strong		0.468	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2		
PCDHB14	56122	hgsc.bcm.edu	37	5	140603248	140603248	+	Silent	SNP	G	G	A	rs7713000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140603248G>A	ENST00000239449.4	+	1	171	c.171G>A	c.(169-171)gaG>gaA	p.E57E	PCDHB14_ENST00000515856.2_Intron	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	57	Cadherin 1. {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)			TGGGGGTGGAGGAGCTGTCTT	0.478													g|||	103	0.0205671	0.0734	0.0072	5008	,	,		17325	0.0		0.001	False		,,,				2504	0.0				p.E57E	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G171A						PASS	.	G		278,4128		6,266,1931	90.0	93.0	92.0		171	1.0	0.6	5	dbSNP_116	92	0,8600		0,0,4300	no	coding-synonymous	PCDHB14	NM_018934.2		6,266,6231	AA,AG,GG		0.0,6.3096,2.1375		57/799	140603248	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	56122	exon1			GGTGGAGGAGCTG	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.171G>A	5.37:g.140603248G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	205	106	0.517073	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			G|0.975;A|0.025	0.025	strong		0.478	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
GALNT10	55568	hgsc.bcm.edu	37	5	153792453	153792453	+	Missense_Mutation	SNP	G	G	A	rs142635658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:153792453G>A	ENST00000297107.6	+	10	1528	c.1391G>A	c.(1390-1392)cGa>cAa	p.R464Q	GALNT10_ENST00000377657.3_Missense_Mutation_p.R137Q|GALNT10_ENST00000377661.2_Missense_Mutation_p.R402Q|SAP30L-AS1_ENST00000519727.1_RNA|SAP30L-AS1_ENST00000524264.1_RNA	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	464	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)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			TTTCAGATCCGAAATGTGGGC	0.612													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18983	0.0		0.0	False		,,,				2504	0.0				p.R464Q		Atlas-SNP	.											.	GALNT10	70	.	0			c.G1391A						PASS	.	G	GLN/ARG	41,4365	44.6+/-78.6	0,41,2162	85.0	84.0	85.0		1391	3.8	0.4	5	dbSNP_134	85	0,8600		0,0,4300	yes	missense	GALNT10	NM_198321.3	43	0,41,6462	AA,AG,GG		0.0,0.9305,0.3152	benign	464/604	153792453	41,12965	2203	4300	6503	SO:0001583	missense	55568	exon10			AGATCCGAAATGT	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19873	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 10"""	608043	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"""			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.1391G>A	5.37:g.153792453G>A	ENSP00000297107:p.Arg464Gln	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Missense_Mutation	SNP	ENST00000297107.6	37	CCDS4325.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	12.24	1.879954	0.33162	0.009305	0.0	ENSG00000164574	ENST00000297107;ENST00000377661;ENST00000377657	T;T;T	0.28666	1.6;1.6;1.6	5.56	3.77	0.43336	Ricin B-related lectin (1);Ricin B lectin (2);	0.091610	0.85682	D	0.000000	T	0.17492	0.0420	L	0.49256	1.55	0.48571	D	0.99967	B;B;B	0.31752	0.054;0.338;0.04	B;B;B	0.22152	0.013;0.038;0.005	T	0.02736	-1.1117	10	0.26408	T	0.33	.	10.6774	0.45794	0.2076:0.0:0.7924:0.0	.	402;135;464	Q86SR1-2;D6R8Y1;Q86SR1	.;.;GLT10_HUMAN	Q	464;402;137	ENSP00000297107:R464Q;ENSP00000366889:R402Q;ENSP00000366885:R137Q	ENSP00000297107:R464Q	R	+	2	0	GALNT10	153772646	1.000000	0.71417	0.392000	0.26245	0.899000	0.52679	2.936000	0.48971	0.706000	0.31912	0.655000	0.94253	CGA	G|0.997;A|0.003	0.003	strong		0.612	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321	
ZNF600	162966	hgsc.bcm.edu	37	19	53270460	53270460	+	Silent	SNP	G	G	A	rs4614842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53270460G>A	ENST00000338230.3	-	3	816	c.549C>T	c.(547-549)ccC>ccT	p.P183P		NM_198457.2	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	183					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(2)|kidney(4)|large_intestine(9)|liver(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		CTCCTAAATGGGGTATCTGGT	0.373													-|||	589	0.117612	0.0439	0.1167	5008	,	,		21331	0.1855		0.0676	False		,,,				2504	0.1994				p.P183P	Esophageal Squamous(196;1235 2112 2375 33339 34207)	Atlas-SNP	.											.	ZNF600	75	.	0			c.C549T						PASS	.	G		190,4216		1,188,2014	117.0	124.0	122.0		549	-3.0	0.0	19	dbSNP_111	122	751,7843		36,679,3582	no	coding-synonymous	ZNF600	NM_198457.2		37,867,5596	AA,AG,GG		8.7387,4.3123,7.2385		183/723	53270460	941,12059	2203	4297	6500	SO:0001819	synonymous_variant	162966	exon3			TAAATGGGGTATC	U52096	CCDS12856.1	19q13.42	2013-01-08				ENSG00000189190		"""Zinc fingers, C2H2-type"""	30951	protein-coding gene	gene with protein product						12576331	Standard	NM_198457		Approved	KR-ZNF1, DKFZp686F06123	uc002qab.4	Q6ZNG1		ENST00000338230.3:c.549C>T	19.37:g.53270460G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	180	72	0.4	NM_198457	Q6MZR0	Silent	SNP	ENST00000338230.3	37	CCDS12856.1																																																																																			.	.	weak		0.373	ZNF600-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463093.1	NM_198457	
CEP78	84131	hgsc.bcm.edu	37	9	80881357	80881357	+	Splice_Site	SNP	G	G	C	rs146563928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:80881357G>C	ENST00000424347.2	+	15	2086		c.e15-1		CEP78_ENST00000415759.2_Splice_Site|CEP78_ENST00000376598.2_Splice_Site|CEP78_ENST00000277082.5_Splice_Site|CEP78_ENST00000376597.4_Splice_Site			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa						G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						TTTCCTTCTAGTTTCAGAAAA	0.378													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18264	0.0		0.001	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CEP78	79	.	0			c.1849-1G>C						PASS	.	G	,	1,3681		0,1,1840	40.0	40.0	40.0		,	4.0	1.0	9	dbSNP_134	40	21,8139		0,21,4059	yes	splice-3,splice-3	CEP78	NM_001098802.1,NM_032171.1	,	0,22,5899	CC,CG,GG		0.2574,0.0272,0.1858	,	,	80881357	22,11820	1841	4080	5921	SO:0001630	splice_region_variant	84131	exon16			CTTCTAGTTTCAG	BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 81"""	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.1798-1G>C	9.37:g.80881357G>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	29	10	0.344828	NM_001098802	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Splice_Site	SNP	ENST00000424347.2	37		2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	14.72	2.618270	0.46736	2.72E-4	0.002574	ENSG00000148019	ENST00000424347;ENST00000415085;ENST00000415759;ENST00000376597;ENST00000277082;ENST00000376598	.	.	.	6.07	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3193	0.26517	0.1296:0.1641:0.7063:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CEP78	80071177	0.987000	0.35691	0.999000	0.59377	0.943000	0.58893	1.038000	0.30254	2.885000	0.99019	0.655000	0.94253	.	G|0.999;C|0.001	0.001	strong		0.378	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991	Intron
ADAMTS17	170691	hgsc.bcm.edu	37	15	100821576	100821576	+	Missense_Mutation	SNP	G	G	A	rs7496668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	46	0	0		WXS	Illumina HiSeq	Phase_I	46	45	0.978261	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	
AGMO	392636	hgsc.bcm.edu	37	7	15458194	15458194	+	Missense_Mutation	SNP	T	T	A	rs146442781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:15458194T>A	ENST00000342526.3	-	5	767	c.598A>T	c.(598-600)Atc>Ttc	p.I200F		NM_001004320.1	NP_001004320.1	Q6ZNB7	ALKMO_HUMAN	alkylglycerol monooxygenase	200					ether lipid metabolic process (GO:0046485)|fatty acid biosynthetic process (GO:0006633)|membrane lipid metabolic process (GO:0006643)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glyceryl-ether monooxygenase activity (GO:0050479)|iron ion binding (GO:0005506)	p.I200V(1)		breast(1)|kidney(1)|large_intestine(6)|liver(1)|lung(30)|prostate(1)|skin(2)	42						TCTGTATGGATCCAAAATTGG	0.348													T|||	22	0.00439297	0.0151	0.0029	5008	,	,		13274	0.0		0.0	False		,,,				2504	0.0				p.I200F		Atlas-SNP	.											AGMO,NS,carcinoma,0,1	AGMO	98	1	1	Substitution - Missense(1)	prostate(1)	c.A598T						scavenged	.	T	PHE/ILE	50,4350		0,50,2150	35.0	42.0	40.0		598	5.8	1.0	7	dbSNP_134	40	0,8574		0,0,4287	yes	missense	AGMO	NM_001004320.1	21	0,50,6437	AA,AT,TT		0.0,1.1364,0.3854	probably-damaging	200/446	15458194	50,12924	2200	4287	6487	SO:0001583	missense	392636	exon5			TATGGATCCAAAA		CCDS34604.1	7p21.1	2013-03-04	2011-01-31	2011-01-31	ENSG00000187546	ENSG00000187546	1.14.16.5	"""Fatty acid hydroxylase domain containing"""	33784	protein-coding gene	gene with protein product		613738	"""transmembrane protein 195"""	TMEM195		20643956	Standard	NM_001004320		Approved	FLJ16237	uc003stb.1	Q6ZNB7	OTTHUMG00000152387	ENST00000342526.3:c.598A>T	7.37:g.15458194T>A	ENSP00000341662:p.Ile200Phe	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	162	81	0.5	NM_001004320	A4D114|A6NCH5	Missense_Mutation	SNP	ENST00000342526.3	37	CCDS34604.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	T	22.8	4.342517	0.81911	0.011364	0.0	ENSG00000187546	ENST00000342526	D	0.84730	-1.89	5.8	5.8	0.92144	Fatty acid hydroxylase (1);	0.000000	0.85682	D	0.000000	D	0.91751	0.7391	M	0.93462	3.42	0.80722	D	1	D	0.56035	0.974	P	0.61328	0.887	D	0.93409	0.6767	10	0.72032	D	0.01	-30.639	16.1416	0.81528	0.0:0.0:0.0:1.0	.	200	Q6ZNB7	ALKMO_HUMAN	F	200	ENSP00000341662:I200F	ENSP00000341662:I200F	I	-	1	0	AGMO	15424719	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.600000	0.67599	2.209000	0.71365	0.482000	0.46254	ATC	T|0.997;A|0.003	0.003	strong		0.348	AGMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326049.2	NM_001004320	
DEFB1	1672	hgsc.bcm.edu	37	8	6728298	6728298	+	Missense_Mutation	SNP	C	C	T	rs2738047|rs397732952	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:6728298C>T	ENST00000297439.3	-	2	276	c.112G>A	c.(112-114)Gtc>Atc	p.V38I		NM_005218.3	NP_005209.1	P60022	DEFB1_HUMAN	defensin, beta 1	38			V -> I (in dbSNP:rs2738047).		acute inflammatory response (GO:0002526)|antibacterial humoral response (GO:0019731)|chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|response to bacterium (GO:0009617)|response to testosterone (GO:0033574)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(1)	1			STAD - Stomach adenocarcinoma(24;0.0984)	COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.128)		CCACTGCTGACGCAATTGTAA	0.498													C|||	199	0.0397364	0.1384	0.0043	5008	,	,		18887	0.0069		0.002	False		,,,				2504	0.0041				p.V38I	Pancreas(35;916 948 9612 33610 36642)	Atlas-SNP	.											.	DEFB1	4	.	0			c.G112A	GRCh37	CM020372	DEFB1	M	rs2738047	PASS	.	C	ILE/VAL	545,3861	249.6+/-257.0	36,473,1694	122.0	99.0	107.0		112	2.2	0.0	8	dbSNP_100	107	6,8594	5.0+/-18.6	0,6,4294	yes	missense	DEFB1	NM_005218.3	29	36,479,5988	TT,TC,CC		0.0698,12.3695,4.2365	benign	38/69	6728298	551,12455	2203	4300	6503	SO:0001583	missense	1672	exon2			TGCTGACGCAATT	X92744	CCDS5959.1	8p23.1	2012-03-27			ENSG00000164825	ENSG00000164825		"""Defensins, beta"""	2766	protein-coding gene	gene with protein product		602056				7628632	Standard	NM_005218		Approved	HBD-1, DEFB-1, DEFB101, HBD1, BD1, MGC51822	uc003wqs.2	P60022	OTTHUMG00000090367	ENST00000297439.3:c.112G>A	8.37:g.6728298C>T	ENSP00000297439:p.Val38Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	128	71	0.554688	NM_005218	Q09753	Missense_Mutation	SNP	ENST00000297439.3	37	CCDS5959.1	62	0.028388278388278388	56	0.11382113821138211	0	0.0	6	0.01048951048951049	0	0.0	C	13.89	2.373486	0.42105	0.123695	6.98E-4	ENSG00000164825	ENST00000297439	T	0.21543	2.0	4.24	2.16	0.27623	.	1.226530	0.06201	N	0.683220	T	0.00178	0.0005	.	.	.	0.09310	N	1	P	0.49696	0.927	B	0.29440	0.102	T	0.28870	-1.0030	9	0.41790	T	0.15	-4.8641	9.8265	0.40914	0.0:0.589:0.411:0.0	rs2738047;rs52816296;rs60091306;rs2738047	38	P60022	DEFB1_HUMAN	I	38	ENSP00000297439:V38I	ENSP00000297439:V38I	V	-	1	0	DEFB1	6715708	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.025000	0.13577	1.041000	0.40125	0.563000	0.77884	GTC	T|0.041;C|0.959	0.041	strong		0.498	DEFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251292.1	NM_005218	
STK31	56164	hgsc.bcm.edu	37	7	23751736	23751736	+	Silent	SNP	A	A	G	rs7779633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:23751736A>G	ENST00000355870.3	+	2	188	c.69A>G	c.(67-69)caA>caG	p.Q23Q	STK31_ENST00000433467.2_Silent_p.Q23Q|STK31_ENST00000354639.3_5'UTR|STK31_ENST00000428484.1_5'UTR	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	23						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						GAATTGTTCAAATGGATGAAG	0.279													A|||	1928	0.384984	0.503	0.353	5008	,	,		17811	0.3571		0.3519	False		,,,				2504	0.3108				p.Q23Q		Atlas-SNP	.											STK31,NS,carcinoma,+1,1	STK31	175	1	0			c.A69G						PASS	.	A	,,	2059,2347	565.2+/-381.6	493,1073,637	138.0	139.0	138.0		,69,	-2.3	1.0	7	dbSNP_116	138	2910,5690	452.7+/-363.0	472,1966,1862	no	utr-5,coding-synonymous,utr-5	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	,,	965,3039,2499	GG,GA,AA		33.8372,46.7317,38.2054	,,	,23/1020,	23751736	4969,8037	2203	4300	6503	SO:0001819	synonymous_variant	56164	exon2			TGTTCAAATGGAT	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.69A>G	7.37:g.23751736A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																			A|0.618;G|0.382	0.382	strong		0.279	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
CCDC183	84960	hgsc.bcm.edu	37	9	139694521	139694521	+	Missense_Mutation	SNP	T	T	G	rs4546744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139694521T>G	ENST00000338005.6	+	4	373	c.338T>G	c.(337-339)cTg>cGg	p.L113R	KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.L143R|RP11-216L13.18_ENST00000471502.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		113			L -> R (in dbSNP:rs4546744).							biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		CTGATCCACCTGGTGCGGCGG	0.667													T|||	1327	0.264976	0.3003	0.2954	5008	,	,		10067	0.2421		0.2177	False		,,,				2504	0.2679				p.L113R		Atlas-SNP	.											KIAA1984,NS,carcinoma,0,1	KIAA1984	39	1	0			c.T338G						scavenged	.	T	ARG/LEU	1040,3066		153,734,1166	14.0	17.0	16.0		338	4.8	1.0	9	dbSNP_111	16	1716,6654		209,1298,2678	yes	missense	KIAA1984	NM_001039374.4	102	362,2032,3844	GG,GT,TT		20.5018,25.3288,22.0904	probably-damaging	113/535	139694521	2756,9720	2053	4185	6238	SO:0001583	missense	84960	exon4			TCCACCTGGTGCG																												ENST00000338005.6:c.338T>G	9.37:g.139694521T>G	ENSP00000338013:p.Leu113Arg	Somatic	28	1	0.0357143		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	513	0.2348901098901099	132	0.2682926829268293	98	0.27071823204419887	124	0.21678321678321677	159	0.20976253298153033	T	20.4	3.987669	0.74589	0.253288	0.205018	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.11495	2.77	4.85	4.85	0.62838	.	0.569511	0.13099	U	0.413906	T	0.00012	0.0000	M	0.61703	1.905	0.24583	P	0.99386576	D	0.57257	0.979	P	0.59487	0.858	T	0.37549	-0.9701	9	0.15952	T	0.53	-15.2278	10.827	0.46638	0.0:0.0:0.0:1.0	rs4546744;rs60974315;rs4546744	113	Q5T5S1	K1984_HUMAN	R	113	ENSP00000338013:L113R	ENSP00000338013:L113R	L	+	2	0	KIAA1984	138814342	0.931000	0.31567	1.000000	0.80357	0.960000	0.62799	0.669000	0.25142	1.808000	0.52836	0.379000	0.24179	CTG	T|0.772;G|0.228	0.228	strong		0.667	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
SSPO	23145	hgsc.bcm.edu	37	7	149498945	149498945	+	RNA	SNP	C	C	T	rs73727615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149498945C>T	ENST00000378016.2	+	0	7397							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)			CTCTGTTCCCCGAGCCAGCTG	0.657													C|||	90	0.0179712	0.0635	0.0086	5008	,	,		18616	0.0		0.0	False		,,,				2504	0.0				p.P2466L		Atlas-SNP	.											.	.	.	.	0			c.C7397T						PASS	.	C		208,4004		3,202,1901	31.0	34.0	33.0		7401	2.5	0.1	7	dbSNP_130	33	3,8429		0,3,4213	no	coding-notMod3	SSPO	NM_198455.2		3,205,6114	TT,TC,CC		0.0356,4.9383,1.6688			149498945	211,12433	2106	4216	6322			23145	exon50			GTTCCCCGAGCCA	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.149498945C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.982;T|0.018	0.018	strong		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CHRNB4	1143	hgsc.bcm.edu	37	15	78921762	78921762	+	Silent	SNP	G	G	A	rs3743072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:78921762G>A	ENST00000261751.3	-	5	996	c.885C>T	c.(883-885)atC>atT	p.I295I	RP11-335K5.2_ENST00000559120.1_RNA|CHRNB4_ENST00000560511.1_5'Flank|CHRNB4_ENST00000412074.2_Intron	NM_000750.3	NP_000741.1	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4 (neuronal)	295					action potential (GO:0001508)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|regulation of neurotransmitter secretion (GO:0046928)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			endometrium(7)|kidney(1)|lung(13)|prostate(1)	22					Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)	GGTACTTGCCGATGAGAGGCA	0.567													G|||	275	0.0549121	0.1233	0.0101	5008	,	,		22662	0.0813		0.008	False		,,,				2504	0.0153				p.I295I		Atlas-SNP	.											.	CHRNB4	59	.	0			c.C885T						PASS	.	G		435,3957	210.2+/-230.7	24,387,1785	159.0	124.0	136.0		885	-3.9	0.8	15	dbSNP_107	136	56,8530	35.9+/-90.5	0,56,4237	no	coding-synonymous	CHRNB4	NM_000750.3		24,443,6022	AA,AG,GG		0.6522,9.9044,3.7833		295/499	78921762	491,12487	2196	4293	6489	SO:0001819	synonymous_variant	1143	exon5			CTTGCCGATGAGA	U48861	CCDS10306.1, CCDS58392.1	15q24	2012-02-11	2012-02-07		ENSG00000117971	ENSG00000117971		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1964	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 4 (neuronal)"""	118509	"""cholinergic receptor, nicotinic, beta polypeptide 4"""			2004777	Standard	NM_000750		Approved		uc002bed.1	P30926	OTTHUMG00000143860	ENST00000261751.3:c.885C>T	15.37:g.78921762G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_000750	A4FTX5|E9PHE8|Q16607|Q4VBA5|Q8WXC8|Q9BQR4	Silent	SNP	ENST00000261751.3	37	CCDS10306.1																																																																																			G|0.962;A|0.038	0.038	strong		0.567	CHRNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290108.1		
LAMB4	22798	hgsc.bcm.edu	37	7	107738948	107738948	+	Silent	SNP	G	G	A	rs451252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107738948G>A	ENST00000388781.3	-	11	1343	c.1260C>T	c.(1258-1260)gcC>gcT	p.A420A	LAMB4_ENST00000418464.1_Silent_p.A420A|LAMB4_ENST00000414450.2_Silent_p.A420A|LAMB4_ENST00000388780.3_Silent_p.A420A|LAMB4_ENST00000205386.4_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	144	0	0		WXS	Illumina HiSeq	Phase_I	139	73	0.52518	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	
CLDN6	9074	hgsc.bcm.edu	37	16	3065924	3065924	+	Silent	SNP	G	G	A	rs2269911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3065924G>A	ENST00000396925.1	-	3	527	c.99C>T	c.(97-99)acC>acT	p.T33T	CLDN6_ENST00000572154.1_Intron|TNFRSF12A_ENST00000573001.1_5'Flank|CLDN6_ENST00000328796.4_Silent_p.T33T			P56747	CLD6_HUMAN	claudin 6	33					calcium-independent cell-cell adhesion (GO:0016338)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.T33T(1)		kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	10						CGATGAAAGCGGTCACCTTCC	0.632													G|||	1154	0.230431	0.1399	0.1585	5008	,	,		22170	0.4028		0.1978	False		,,,				2504	0.2597				p.T33T		Atlas-SNP	.											CLDN6,NS,carcinoma,0,1	CLDN6	31	1	1	Substitution - coding silent(1)	stomach(1)	c.C99T						scavenged	.	G		609,3787	265.3+/-266.6	44,521,1633	129.0	101.0	111.0		99	-2.5	1.0	16	dbSNP_100	111	1637,6963	301.7+/-305.6	161,1315,2824	no	coding-synonymous	CLDN6	NM_021195.4		205,1836,4457	AA,AG,GG		19.0349,13.8535,17.2822		33/221	3065924	2246,10750	2198	4300	6498	SO:0001819	synonymous_variant	9074	exon2			GAAAGCGGTCACC	AJ249735	CCDS10488.1	16p13.3	2008-08-01			ENSG00000184697	ENSG00000184697		"""Claudins"""	2048	protein-coding gene	gene with protein product		615798				9892664, 18234789	Standard	NM_021195		Approved		uc002csu.4	P56747	OTTHUMG00000128999	ENST00000396925.1:c.99C>T	16.37:g.3065924G>A		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	236	106	0.449153	NM_021195	B3KQP9|D3DUA5	Silent	SNP	ENST00000396925.1	37	CCDS10488.1																																																																																			G|0.811;A|0.189	0.189	strong		0.632	CLDN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250988.1	NM_021195	
FAM179A	165186	hgsc.bcm.edu	37	2	29226417	29226417	+	Silent	SNP	C	C	T	rs76285160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29226417C>T	ENST00000379558.4	+	6	1050	c.699C>T	c.(697-699)ggC>ggT	p.G233G	FAM179A_ENST00000403861.2_Silent_p.G233G	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	233										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						AGTCCCTGGGCGCCATCGTGA	0.637													C|||	371	0.0740815	0.1225	0.0231	5008	,	,		19082	0.1508		0.0109	False		,,,				2504	0.0307				p.G233G		Atlas-SNP	.											.	FAM179A	106	.	0			c.C699T						PASS	.	C		385,3749		10,365,1692	40.0	46.0	44.0		699	-10.3	0.0	2	dbSNP_132	44	24,8338		0,24,4157	no	coding-synonymous	FAM179A	NM_199280.2		10,389,5849	TT,TC,CC		0.287,9.313,3.273		233/1020	29226417	409,12087	2067	4181	6248	SO:0001819	synonymous_variant	165186	exon6			CCTGGGCGCCATC	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.699C>T	2.37:g.29226417C>T		Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	241	125	0.518672	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			C|0.929;T|0.071	0.071	strong		0.637	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
ALPI	248	hgsc.bcm.edu	37	2	233323000	233323000	+	Silent	SNP	C	C	T	rs10195208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233323000C>T	ENST00000295463.3	+	9	1142	c.1065C>T	c.(1063-1065)gaC>gaT	p.D355D		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	355					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		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;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TGTTCGACGACGCCATTGAGA	0.627													C|||	253	0.0505192	0.1884	0.0058	5008	,	,		17694	0.0		0.0	False		,,,				2504	0.0				p.D355D		Atlas-SNP	.											ALPI,NS,carcinoma,+2,1	ALPI	64	1	0			c.C1065T						PASS	.	C		624,3782	271.6+/-270.3	39,546,1618	86.0	76.0	79.0		1065	-8.9	0.0	2	dbSNP_119	79	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	ALPI	NM_001631.3		39,554,5910	TT,TC,CC		0.093,14.1625,4.8593		355/529	233323000	632,12374	2203	4300	6503	SO:0001819	synonymous_variant	248	exon9			CGACGACGCCATT	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.1065C>T	2.37:g.233323000C>T		Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	266	128	0.481203	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Silent	SNP	ENST00000295463.3	37	CCDS2492.1																																																																																			C|0.950;T|0.050	0.050	strong		0.627	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
ANKRD50	57182	hgsc.bcm.edu	37	4	125591687	125591687	+	Silent	SNP	A	A	G	rs3733471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	237	0	0		WXS	Illumina HiSeq	Phase_I	235	103	0.438298	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	
ADIPOQ	9370	hgsc.bcm.edu	37	3	186570951	186570951	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186570951C>T	ENST00000412955.2	+	2	245	c.104C>T	c.(103-105)gCc>gTc	p.A35V	ADIPOQ_ENST00000320741.2_Missense_Mutation_p.A35V|ADIPOQ-AS1_ENST00000422718.1_RNA|ADIPOQ_ENST00000444204.2_Missense_Mutation_p.A35V			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	35					adiponectin-activated signaling pathway (GO:0033211)|brown fat cell differentiation (GO:0050873)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to insulin stimulus (GO:0032869)|circadian rhythm (GO:0007623)|detection of oxidative stress (GO:0070994)|fatty acid beta-oxidation (GO:0006635)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|low-density lipoprotein particle clearance (GO:0034383)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of hormone secretion (GO:0046888)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular protein transport (GO:0090317)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metanephric mesenchymal cell migration (GO:2000590)|negative regulation of phagocytosis (GO:0050765)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of receptor binding (GO:1900121)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of synaptic transmission (GO:0050805)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|positive regulation of blood pressure (GO:0045777)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of metanephric glomerular visceral epithelial cell development (GO:2000478)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myeloid cell apoptotic process (GO:0033034)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal albumin absorption (GO:2000534)|positive regulation of signal transduction (GO:0009967)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|regulation of glucose metabolic process (GO:0010906)|response to activity (GO:0014823)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to linoleic acid (GO:0070543)|response to nutrient (GO:0007584)|response to sucrose (GO:0009744)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|sialic acid binding (GO:0033691)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(2)	16	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)		CCCAAGGGGGCCTGCACAGGT	0.627																																					p.A35V		Atlas-SNP	.											.	ADIPOQ	35	.	0			c.C104T						PASS	.						51.0	52.0	51.0					3																	186570951		2203	4300	6503	SO:0001583	missense	9370	exon3			AGGGGGCCTGCAC	D45371	CCDS3284.1	3q27	2013-02-26	2005-01-24	2005-01-27	ENSG00000181092	ENSG00000181092		"""Endogenous ligands"""	13633	protein-coding gene	gene with protein product	"""adipose most abundant gene transcript 1"", ""adiponectin precursor"""	605441	"""adipocyte, C1Q and collagen domain containing"""	ACDC		7592907, 8631877	Standard	NM_001177800		Approved	ACRP30, AdipoQ, apM1, GBP28, adiponectin	uc003fra.3	Q15848	OTTHUMG00000156521	ENST00000412955.2:c.104C>T	3.37:g.186570951C>T	ENSP00000405611:p.Ala35Val	Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	241	128	0.53112	NM_001177800	Q58EX9	Missense_Mutation	SNP	ENST00000412955.2	37	CCDS3284.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.627218	0.46944	.	.	ENSG00000181092	ENST00000412955;ENST00000320741;ENST00000444204	D;D;D	0.90676	-2.71;-2.71;-2.71	5.21	0.744	0.18353	.	0.825880	0.10698	N	0.644378	T	0.80396	0.4615	N	0.24115	0.695	0.19300	N	0.999976	B	0.06786	0.001	B	0.08055	0.003	T	0.64326	-0.6434	10	0.27082	T	0.32	.	4.1548	0.10256	0.139:0.4701:0.2975:0.0934	.	35	Q15848	ADIPO_HUMAN	V	35	ENSP00000405611:A35V;ENSP00000320709:A35V;ENSP00000389814:A35V	ENSP00000320709:A35V	A	+	2	0	ADIPOQ	188053645	0.068000	0.21057	0.807000	0.32361	0.936000	0.57629	1.784000	0.38674	0.213000	0.20722	0.655000	0.94253	GCC	.	.	none		0.627	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344490.2	NM_004797	
FHOD1	29109	hgsc.bcm.edu	37	16	67265360	67265360	+	Silent	SNP	C	C	A	rs6499118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67265360C>A	ENST00000258201.4	-	16	2725	c.2478G>T	c.(2476-2478)gcG>gcT	p.A826A		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	826	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		AGTTGCCCACCGCTAGGAGGG	0.567													A|||	1312	0.261981	0.7368	0.0922	5008	,	,		20718	0.0238		0.0706	False		,,,				2504	0.183				p.A826A		Atlas-SNP	.											.	FHOD1	86	.	0			c.G2478T						PASS	.	A		2657,1739	520.2+/-370.2	812,1033,353	112.0	104.0	107.0		2478	4.3	1.0	16	dbSNP_116	107	604,7996	792.3+/-407.5	28,548,3724	no	coding-synonymous	FHOD1	NM_013241.2		840,1581,4077	AA,AC,CC		7.0233,39.5587,25.0923		826/1165	67265360	3261,9735	2198	4300	6498	SO:0001819	synonymous_variant	29109	exon16			GCCCACCGCTAGG	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.2478G>T	16.37:g.67265360C>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	162	80	0.493827	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Silent	SNP	ENST00000258201.4	37	CCDS10834.1																																																																																			C|0.755;A|0.245	0.245	strong		0.567	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2		
SSPO	23145	hgsc.bcm.edu	37	7	149486726	149486726	+	RNA	SNP	T	T	C	rs855695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149486726T>C	ENST00000378016.2	+	0	4500							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)			TGTCCTGTGTTGATGGCACCT	0.637													C|||	161	0.0321486	0.1059	0.0115	5008	,	,		18130	0.004		0.0	False		,,,				2504	0.0092				p.V1500V		Atlas-SNP	.											.	.	.	.	0			c.T4500C						PASS	.	C		300,3736		11,278,1729	24.0	31.0	29.0		4504	-9.6	0.0	7	dbSNP_86	29	6,8338		0,6,4166	yes	coding-notMod3	SSPO	NM_198455.2		11,284,5895	CC,CT,TT		0.0719,7.4331,2.4717			149486726	306,12074	2018	4172	6190			23145	exon31			CTGTGTTGATGGC	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.149486726T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	127	77	0.606299	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				T|0.974;C|0.026	0.026	strong		0.637	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CFAP74	85452	hgsc.bcm.edu	37	1	1916890	1916890	+	IGR	SNP	C	C	T	rs3795280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1916890C>T	ENST00000434971.2	-	0	339							Q69YW0	CA222_HUMAN												breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)	11	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)		GCTCTGCAAACAGGCGTCTGG	0.662													c|||	2196	0.438498	0.6573	0.2795	5008	,	,		18797	0.4335		0.3082	False		,,,				2504	0.3947				p.L145L		Atlas-SNP	.											.	KIAA1751	92	.	0			c.G435A						PASS	.	T		2382,1730		693,996,367	67.0	73.0	71.0		435	2.8	0.6	1	dbSNP_107	71	2744,5634		450,1844,1895	no	coding-synonymous	KIAA1751	NM_001080484.1		1143,2840,2262	TT,TC,CC		32.7524,42.072,41.0408		145/763	1916890	5126,7364	2056	4189	6245	SO:0001628	intergenic_variant	85452	exon6			TGCAAACAGGCGT																													1.37:g.1916890C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	157	86	0.547771	NM_001080484		Silent	SNP	ENST00000434971.2	37																																																																																				C|0.606;T|0.394	0.394	strong		0.662	C1orf222-201	KNOWN	basic	protein_coding	protein_coding			
PLA2G4B	100137049	hgsc.bcm.edu	37	15	42138572	42138572	+	Missense_Mutation	SNP	C	C	T	rs36126315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42138572C>T	ENST00000452633.1	+	18	2124	c.1772C>T	c.(1771-1773)aCa>aTa	p.T591I	PLA2G4B_ENST00000542534.2_Missense_Mutation_p.T822I|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.T822I|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.T822I|PLA2G4B_ENST00000458483.1_Missense_Mutation_p.T591I			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	591	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		T -> I (in dbSNP:rs36126315).		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)		CACTTCTCCACATGGAAAGGT	0.547													C|||	76	0.0151757	0.0552	0.0029	5008	,	,		20192	0.0		0.001	False		,,,				2504	0.0				p.T822I		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.C2465T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR	194,4212		8,178,2017	99.0	97.0	98.0		1772,2465,2465	3.0	0.6	15	dbSNP_126	98	3,8597		0,3,4297	yes	missense,missense,missense	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	89,89,89	8,181,6314	TT,TC,CC		0.0349,4.4031,1.5147	benign,benign,benign	591/782,822/894,822/1013	42138572	197,12809	2203	4300	6503	SO:0001583	missense	8681	exon22			TCTCCACATGGAA	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.1772C>T	15.37:g.42138572C>T	ENSP00000396045:p.Thr591Ile	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	24	0.01098901098901099	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	15.97	2.990575	0.54041	0.044031	3.49E-4	ENSG00000168970;ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000382448;ENST00000342159;ENST00000458483;ENST00000452633	T;T;T;T	0.12984	2.63;2.63;2.63;2.63	4.96	3.05	0.35203	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	1.072970	0.07218	N	0.860326	T	0.04452	0.0122	L	0.49778	1.585	0.23454	N	0.997645	P;B;B	0.45283	0.855;0.078;0.178	P;B;B	0.47470	0.548;0.055;0.086	T	0.16928	-1.0386	10	0.40728	T	0.16	-4.9065	7.2416	0.26100	0.0:0.6949:0.144:0.1611	rs36126315	591;822;822	P0C869;P0C869-7;P0C869-6	PA24B_HUMAN;.;.	I	822;822;591;591	ENSP00000371886:T822I;ENSP00000342785:T822I;ENSP00000416610:T591I;ENSP00000396045:T591I	ENSP00000342785:T822I	T	+	2	0	JMJD7-PLA2G4B;PLA2G4B	39925864	0.227000	0.23707	0.645000	0.29479	0.900000	0.52787	0.800000	0.27042	0.727000	0.32360	0.655000	0.94253	ACA	C|0.985;T|0.015	0.015	strong		0.547	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633	
IMP4	92856	hgsc.bcm.edu	37	2	131103479	131103479	+	Silent	SNP	C	C	T	rs34942992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131103479C>T	ENST00000259239.3	+	6	1275	c.567C>T	c.(565-567)caC>caT	p.H189H	IMP4_ENST00000409935.1_Silent_p.H189H	NM_033416.1	NP_219484.1	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein	189	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				rRNA processing (GO:0006364)	nucleolus (GO:0005730)|ribonucleoprotein complex (GO:0030529)				central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	18	Colorectal(110;0.1)					TCATCACACACGGCTTCTCCT	0.627													C|||	317	0.0632987	0.2186	0.0303	5008	,	,		16824	0.0		0.007	False		,,,				2504	0.0				p.H189H		Atlas-SNP	.											.	IMP4	35	.	0			c.C567T						PASS	.	C		923,3483	350.8+/-311.0	93,737,1373	68.0	64.0	65.0		567	-6.4	0.5	2	dbSNP_126	65	18,8582	14.0+/-48.4	0,18,4282	no	coding-synonymous	IMP4	NM_033416.1		93,755,5655	TT,TC,CC		0.2093,20.9487,7.2351		189/292	131103479	941,12065	2203	4300	6503	SO:0001819	synonymous_variant	92856	exon6			CACACACGGCTTC	BC010042	CCDS2160.1	2q21.1	2014-02-19	2014-02-19		ENSG00000136718	ENSG00000136718			30856	protein-coding gene	gene with protein product		612981	"""IMP4, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""			8619474, 9110174, 12655004	Standard	NM_033416		Approved	MGC19606, BXDC4	uc002tra.1	Q96G21	OTTHUMG00000131627	ENST00000259239.3:c.567C>T	2.37:g.131103479C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	167	83	0.497006	NM_033416	Q3ZTT3	Silent	SNP	ENST00000259239.3	37	CCDS2160.1	106	0.048534798534798536	88	0.17886178861788618	15	0.04143646408839779	0	0.0	3	0.00395778364116095	C	4.046	0.006106	0.07866	0.209487	0.002093	ENSG00000136718	ENST00000452955	.	.	.	5.54	-6.4	0.01944	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999999991	.	.	.	.	.	.	T	0.41088	-0.9528	3	.	.	.	-30.9456	20.4249	0.99070	0.0:0.7431:0.0:0.2569	rs34942992	.	.	.	M	178	.	.	T	+	2	0	IMP4	130819949	0.838000	0.29461	0.510000	0.27712	0.459000	0.32528	-0.168000	0.09925	-1.766000	0.01302	-1.851000	0.00568	ACG	C|0.934;T|0.066	0.066	strong		0.627	IMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254520.2	NM_033416	
TRPM6	140803	hgsc.bcm.edu	37	9	77376647	77376647	+	Missense_Mutation	SNP	T	T	C	rs2274924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:77376647T>C	ENST00000360774.1	-	27	4987	c.4750A>G	c.(4750-4752)Aag>Gag	p.K1584E	TRPM6_ENST00000376864.4_Missense_Mutation_p.K1584E|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000361255.3_Missense_Mutation_p.K1579E|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000451710.3_Missense_Mutation_p.K1584E|TRPM6_ENST00000449912.2_Missense_Mutation_p.K1579E	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1584			K -> E (in dbSNP:rs2274924). {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)	p.K1584E(1)		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						TTCTTTTTCTTTGACAGTCTC	0.428													T|||	1477	0.294928	0.4463	0.147	5008	,	,		18536	0.3155		0.1571	False		,,,				2504	0.316				p.K1584E		Atlas-SNP	.											TRPM6,caecum,carcinoma,+2,2	TRPM6	377	2	1	Substitution - Missense(1)	stomach(1)	c.A4750G						PASS	.	T	GLU/LYS,GLU/LYS,GLU/LYS	1727,2679	519.0+/-369.9	333,1061,809	204.0	177.0	186.0		4735,4735,4750	4.6	0.6	9	dbSNP_100	186	1335,7265	261.9+/-284.1	91,1153,3056	yes	missense,missense,missense	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	56,56,56	424,2214,3865	CC,CT,TT		15.5233,39.1966,23.543	benign,benign,benign	1579/2018,1579/2018,1584/2023	77376647	3062,9944	2203	4300	6503	SO:0001583	missense	140803	exon27			TTTTCTTTGACAG	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.4750A>G	9.37:g.77376647T>C	ENSP00000354006:p.Lys1584Glu	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	205	135	0.658537	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	544	0.2490842490842491	190	0.3861788617886179	46	0.1270718232044199	182	0.3181818181818182	126	0.1662269129287599	T	16.64	3.179714	0.57800	0.391966	0.155233	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864	T;T;T;T;T	0.56444	0.55;0.55;0.56;0.55;0.46	5.77	4.64	0.57946	.	0.437410	0.27039	N	0.021226	T	0.00012	0.0000	L	0.59436	1.845	0.34496	P	0.294519	P;P;P	0.42692	0.682;0.675;0.787	B;B;P	0.46758	0.326;0.426;0.526	T	0.36187	-0.9758	9	0.62326	D	0.03	.	10.7405	0.46149	0.0:0.0749:0.0:0.9251	rs2274924;rs61238454;rs2274924	1584;1579;1579	Q9BX84;Q9BX84-3;Q9BX84-2	TRPM6_HUMAN;.;.	E	1584;1584;1579;1579;1584	ENSP00000354006:K1584E;ENSP00000407341:K1584E;ENSP00000396672:K1579E;ENSP00000354962:K1579E;ENSP00000366060:K1584E	ENSP00000354006:K1584E	K	-	1	0	TRPM6	76566467	0.888000	0.30383	0.558000	0.28319	0.405000	0.30901	1.602000	0.36783	1.131000	0.42111	0.528000	0.53228	AAG	T|0.756;C|0.244	0.244	strong		0.428	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
SRRM2	23524	hgsc.bcm.edu	37	16	2813177	2813177	+	Missense_Mutation	SNP	C	C	G	rs17136053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2813177C>G	ENST00000301740.8	+	11	3197	c.2648C>G	c.(2647-2649)tCt>tGt	p.S883C		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	883	Ser-rich.		S -> C (in dbSNP:rs17136053).		mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						GAGTTGAAATCTAGGACCCCT	0.517													C|||	127	0.0253594	0.0923	0.0072	5008	,	,		19890	0.0		0.0	False		,,,				2504	0.0				p.S883C		Atlas-SNP	.											.	SRRM2	263	.	0			c.C2648G						PASS	.	C	CYS/SER	373,4023	189.5+/-215.6	16,341,1841	82.0	74.0	77.0		2648	2.2	0.7	16	dbSNP_123	77	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SRRM2	NM_016333.3	112	16,343,6139	GG,GC,CC		0.0233,8.485,2.8855	possibly-damaging	883/2753	2813177	375,12621	2198	4300	6498	SO:0001583	missense	23524	exon11			TGAAATCTAGGAC	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2648C>G	16.37:g.2813177C>G	ENSP00000301740:p.Ser883Cys	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	56	0.02564102564102564	53	0.10772357723577236	3	0.008287292817679558	0	0.0	0	0.0	C	4.788	0.146546	0.09134	0.08485	2.33E-4	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933;ENST00000426305	T	0.31247	1.5	5.37	2.21	0.28008	.	0.094270	0.47852	N	0.000215	T	0.00524	0.0017	L	0.58101	1.795	0.28061	N	0.932955	B	0.09022	0.002	B	0.04013	0.001	T	0.05354	-1.0890	10	0.59425	D	0.04	-0.8628	8.8449	0.35164	0.0:0.6364:0.2835:0.0801	rs17136053;rs52826498;rs17136053	883	Q9UQ35	SRRM2_HUMAN	C	883;883;135;848	ENSP00000301740:S883C	ENSP00000301740:S883C	S	+	2	0	SRRM2	2753178	0.942000	0.31987	0.690000	0.30148	0.967000	0.64934	1.873000	0.39558	0.215000	0.20761	0.650000	0.86243	TCT	C|0.969;G|0.031	0.031	strong		0.517	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
HSPB8	26353	hgsc.bcm.edu	37	12	119631654	119631654	+	Silent	SNP	C	C	T	rs4628742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:119631654C>T	ENST00000281938.2	+	3	1253	c.582C>T	c.(580-582)acC>acT	p.T194T		NM_014365.2	NP_055180.1	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	194					cell death (GO:0008219)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	14	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGAAGTCACCTGTACCTGAG	0.502													C|||	412	0.0822684	0.2867	0.0159	5008	,	,		18743	0.0169		0.001	False		,,,				2504	0.0041				p.T194T		Atlas-SNP	.											.	HSPB8	45	.	0			c.C582T						PASS	.	C		1050,3356	383.5+/-324.9	125,800,1278	89.0	84.0	86.0		582	1.4	1.0	12	dbSNP_111	86	9,8591	4.3+/-15.6	0,9,4291	no	coding-synonymous	HSPB8	NM_014365.2		125,809,5569	TT,TC,CC		0.1047,23.8311,8.1424		194/197	119631654	1059,11947	2203	4300	6503	SO:0001819	synonymous_variant	26353	exon3			AGTCACCTGTACC	AF191017	CCDS9189.1	12q24.23	2014-09-17	2004-04-23					"""Heat shock proteins / HSPB"""	30171	protein-coding gene	gene with protein product		608014	"""heat shock 27kDa protein 8"""			10833516, 11085516	Standard	NM_014365		Approved	H11, E2IG1, HSP22, HspB8	uc001txb.3	Q9UJY1		ENST00000281938.2:c.582C>T	12.37:g.119631654C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	160	74	0.4625	NM_014365	B2R6A6|Q6FIH3|Q9UKS3	Silent	SNP	ENST00000281938.2	37	CCDS9189.1																																																																																			C|0.917;T|0.083	0.083	strong		0.502	HSPB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401647.1	NM_014365	
CAPN14	440854	hgsc.bcm.edu	37	2	31410653	31410653	+	Missense_Mutation	SNP	C	C	T	rs7422120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31410653C>T	ENST00000403897.3	-	15	1699	c.1558G>A	c.(1558-1560)Gat>Aat	p.D520N	CAPN14_ENST00000444918.2_Missense_Mutation_p.D520N	NM_001145122.1	NP_001138594.1	A8MX76	CAN14_HUMAN	calpain 14	520	Domain IV.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|endometrium(2)|prostate(1)|skin(1)|stomach(2)	7						AAGAATTCATCCTGCCTTTCA	0.423													T|||	1644	0.328275	0.5908	0.389	5008	,	,		17909	0.1558		0.1899	False		,,,				2504	0.2505				p.D520N		Atlas-SNP	.											.	CAPN14	36	.	0			c.G1558A						PASS	.	T	ASN/ASP	716,668		183,350,159	121.0	121.0	121.0		1558	-0.2	0.0	2	dbSNP_116	121	530,2652		50,430,1111	yes	missense	CAPN14	NM_001145122.1	23	233,780,1270	TT,TC,CC		16.6562,48.2659,27.2887	benign	520/685	31410653	1246,3320	692	1591	2283	SO:0001583	missense	440854	exon15			ATTCATCCTGCCT	AC015980	CCDS46254.1	2p23.1-p21	2013-01-10			ENSG00000214711	ENSG00000214711		"""EF-hand domain containing"""	16664	protein-coding gene	gene with protein product		610229				11675017	Standard	NM_001145122		Approved		uc010yms.2	A8MX76	OTTHUMG00000152039	ENST00000403897.3:c.1558G>A	2.37:g.31410653C>T	ENSP00000385247:p.Asp520Asn	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_001145122	B3KRU9	Missense_Mutation	SNP	ENST00000403897.3	37	CCDS46254.1	648	0.2967032967032967	273	0.5548780487804879	131	0.36187845303867405	94	0.16433566433566432	150	0.19788918205804748	T	0.077	-1.191270	0.01607	0.517341	0.166562	ENSG00000214711	ENST00000444918;ENST00000403897	T;T	0.28895	1.59;1.59	3.54	-0.241	0.13043	EF-hand-like domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.46527	-0.9185	8	0.40728	T	0.16	.	11.185	0.48650	0.0:0.6894:0.0:0.3106	rs7422120;rs52813309;rs7422120	520;344	A8MX76;A8MX76-2	CAN14_HUMAN;.	N	520	ENSP00000398670:D520N;ENSP00000385247:D520N	ENSP00000385247:D520N	D	-	1	0	CAPN14	31264157	0.461000	0.25783	0.001000	0.08648	0.007000	0.05969	-0.095000	0.11077	-1.004000	0.03421	-2.680000	0.00142	GAT	C|0.732;T|0.268	0.268	strong		0.423	CAPN14-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325010.1	NM_001145122	
VWA3B	200403	hgsc.bcm.edu	37	2	98709684	98709684	+	Silent	SNP	T	T	C	rs298917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98709684T>C	ENST00000477737.1	+	2	333	c.129T>C	c.(127-129)caT>caC	p.H43H	VWA3B_ENST00000451075.2_5'UTR|VWA3B_ENST00000435344.1_Silent_p.H43H	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	43										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TTCAACTGCATGGGCTTAAGA	0.458													T|||	535	0.106829	0.0877	0.1427	5008	,	,		17580	0.0407		0.1938	False		,,,				2504	0.0859				p.H43H		Atlas-SNP	.											.	VWA3B	138	.	0			c.T129C						PASS	.	T		380,3546		24,332,1607	126.0	117.0	120.0		129	-1.3	0.9	2	dbSNP_79	120	1680,6646		174,1332,2657	no	coding-synonymous	VWA3B	NM_144992.4		198,1664,4264	CC,CT,TT		20.1778,9.6791,16.8136		43/1295	98709684	2060,10192	1963	4163	6126	SO:0001819	synonymous_variant	200403	exon2			ACTGCATGGGCTT	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.129T>C	2.37:g.98709684T>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	197	92	0.467005	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Silent	SNP	ENST00000477737.1	37	CCDS42718.1																																																																																			T|0.871;C|0.129	0.129	strong		0.458	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
GJA4	2701	hgsc.bcm.edu	37	1	35259961	35259961	+	Silent	SNP	A	A	G	rs1764390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35259961A>G	ENST00000342280.4	+	2	235	c.147A>G	c.(145-147)caA>caG	p.Q49Q		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	49					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)				GTGACGAGCAATCAGATTTCG	0.602													G|||	3112	0.621406	0.8533	0.513	5008	,	,		18874	0.4841		0.6481	False		,,,				2504	0.499				p.Q49Q		Atlas-SNP	.											.	GJA4	25	.	0			c.A147G						PASS	.	G		3620,786	318.0+/-295.4	1493,634,76	176.0	151.0	160.0		147	4.6	1.0	1	dbSNP_89	160	5564,3036	467.5+/-367.1	1788,1988,524	no	coding-synonymous	GJA4	NM_002060.2		3281,2622,600	GG,GA,AA		35.3023,17.8393,29.3864		49/334	35259961	9184,3822	2203	4300	6503	SO:0001819	synonymous_variant	2701	exon2			CGAGCAATCAGAT	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.147A>G	1.37:g.35259961A>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	164	163	0.993902	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Silent	SNP	ENST00000342280.4	37	CCDS30669.1																																																																																			A|0.319;C|0.000;G|0.681;T|0.000	0.681	strong		0.602	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060	
TET2	54790	hgsc.bcm.edu	37	4	106155751	106155751	+	Missense_Mutation	SNP	G	G	A	rs6843141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:106155751G>A	ENST00000540549.1	+	3	1512	c.652G>A	c.(652-654)Gtg>Atg	p.V218M	TET2_ENST00000394764.1_Missense_Mutation_p.V218M|TET2_ENST00000305737.2_Missense_Mutation_p.V218M|TET2_ENST00000380013.4_Missense_Mutation_p.V218M|TET2_ENST00000413648.2_Missense_Mutation_p.V218M|TET2_ENST00000513237.1_Missense_Mutation_p.V239M|TET2_ENST00000545826.1_Missense_Mutation_p.V218M			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	218			V -> M (in dbSNP:rs6843141). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:19483684}.		5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TGCCTCTTCCGTGGAACACAC	0.418			"""Mis N, F"""		MDS								A|||	518	0.103435	0.2882	0.0274	5008	,	,		24127	0.0615		0.0239	False		,,,				2504	0.0327				p.V218M		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.G652A						PASS	.	A	MET/VAL,MET/VAL	1253,3153	703.3+/-407.0	194,865,1144	85.0	75.0	78.0		652,652	2.4	1.0	4	dbSNP_116	78	180,8420	810.9+/-407.1	2,176,4122	yes	missense,missense	TET2	NM_001127208.2,NM_017628.4	21,21	196,1041,5266	AA,AG,GG		2.093,28.4385,11.018	benign,benign	218/2003,218/1166	106155751	1433,11573	2203	4300	6503	SO:0001583	missense	54790	exon3			TCTTCCGTGGAAC	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.652G>A	4.37:g.106155751G>A	ENSP00000442788:p.Val218Met	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	225	0.10302197802197802	157	0.31910569105691056	13	0.03591160220994475	39	0.06818181818181818	16	0.021108179419525065	A	0.111	-1.138831	0.01742	0.284385	0.02093	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648;ENST00000535110	T;T;T;T;T;T;T	0.03496	3.91;4.49;3.91;4.49;4.49;3.91;3.92	4.95	2.44	0.29823	.	1.590140	0.04491	N	0.379479	T	0.00012	0.0000	N	0.04203	-0.255	0.58432	P	1.0000000000287557E-6	B;B;B	0.09022	0.0;0.0;0.002	B;B;B	0.04013	0.0;0.0;0.001	T	0.43507	-0.9387	9	0.02654	T	1	.	5.3304	0.15930	0.6876:0.1492:0.1631:0.0	rs6843141;rs52821391;rs57504518;rs6843141	239;218;218	E7EQS8;Q6N021;Q6N021-2	.;TET2_HUMAN;.	M	218;218;218;239;218;218;218;218	ENSP00000306705:V218M;ENSP00000442788:V218M;ENSP00000442867:V218M;ENSP00000425443:V239M;ENSP00000369351:V218M;ENSP00000378245:V218M;ENSP00000391448:V218M	ENSP00000265149:V218M	V	+	1	0	TET2	106375200	0.998000	0.40836	0.997000	0.53966	0.995000	0.86356	0.756000	0.26419	-0.034000	0.13713	-0.254000	0.11334	GTG	G|0.879;A|0.121	0.121	strong		0.418	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46058043	46058043	+	Missense_Mutation	SNP	C	C	T	rs77109703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46058043C>T	ENST00000380095.1	+	1	771	c.709C>T	c.(709-711)Cgc>Tgc	p.R237C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	237						keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CGTGTGCTCCCGCCCTGCCTG	0.692																																					p.R237C		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C709T						PASS	.	C	,CYS/ARG	389,4017	164.7+/-196.3	0,389,1814	49.0	53.0	52.0		,709	-1.5	0.0	21	dbSNP_131	52	4,8590	1.2+/-3.3	0,4,4293	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,180	0,393,6107	TT,TC,CC		0.0465,8.8289,3.0231	,benign	,237/252	46058043	393,12607	2203	4297	6500	SO:0001583	missense	353333	exon1			TGCTCCCGCCCTG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.709C>T	21.37:g.46058043C>T	ENSP00000369438:p.Arg237Cys	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	380	84	0.221053	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	48	0.02197802197802198	47	0.09552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	c	4.111	0.018755	0.07959	0.088289	4.65E-4	ENSG00000221859	ENST00000380095	T	0.01422	4.91	3.52	-1.53	0.08611	.	.	.	.	.	T	0.00073	0.0002	M	0.78285	2.405	0.36787	D	0.884654	B	0.28636	0.218	B	0.18871	0.023	T	0.50466	-0.8825	9	0.66056	D	0.02	.	4.2298	0.10597	0.3112:0.4801:0.0:0.2088	.	237	P60014	KR10A_HUMAN	C	237	ENSP00000369438:R237C	ENSP00000369438:R237C	R	+	1	0	KRTAP10-10	44882471	0.000000	0.05858	0.038000	0.18304	0.008000	0.06430	-1.152000	0.03172	-0.202000	0.10268	-0.444000	0.05651	CGC	C|0.966;T|0.034	0.034	strong		0.692	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
SOGA3	387104	hgsc.bcm.edu	37	6	127797389	127797389	+	Silent	SNP	C	C	T	rs61741826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:127797389C>T	ENST00000525778.1	-	6	2527	c.1782G>A	c.(1780-1782)gtG>gtA	p.V594V	SOGA3_ENST00000465909.2_Silent_p.V594V|SOGA3_ENST00000368268.2_Silent_p.V594V|SOGA3_ENST00000556132.1_Silent_p.V594V|SOGA3_ENST00000474293.2_5'Flank|SOGA3_ENST00000481848.2_Silent_p.V594V			Q5TF21	SOGA3_HUMAN	SOGA family member 3	594					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CTTCTTCCTCCACCAGCCTTA	0.577													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18875	0.0		0.0	False		,,,				2504	0.0				p.V594V		Atlas-SNP	.											.	.	.	.	0			c.G1782A						PASS	.	C		14,4244		0,14,2115	120.0	129.0	126.0		1782	4.7	1.0	6	dbSNP_129	126	0,8480		0,0,4240	no	coding-synonymous	C6orf174	NM_001012279.2		0,14,6355	TT,TC,CC		0.0,0.3288,0.1099		594/948	127797389	14,12724	2129	4240	6369	SO:0001819	synonymous_variant	387104	exon6			TTCCTCCACCAGC	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1782G>A	6.37:g.127797389C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_001012279		Silent	SNP	ENST00000525778.1	37	CCDS43505.1																																																																																			C|0.999;T|0.001	0.001	strong		0.577	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
LY6H	4062	hgsc.bcm.edu	37	8	144239859	144239859	+	Silent	SNP	A	A	G	rs10109061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144239859A>G	ENST00000430474.2	-	4	396	c.231T>C	c.(229-231)tgT>tgC	p.C77C	LY6H_ENST00000414417.2_Silent_p.C98C|LY6H_ENST00000342752.4_Silent_p.C98C	NM_002347.4	NP_002338.3	O94772	LY6H_HUMAN	lymphocyte antigen 6 complex, locus H	77	UPAR/Ly6.				nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.C77C(1)		endometrium(1)|lung(1)|stomach(2)	4	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TAACGAAGTCACAGGAGGAGG	0.537													G|||	2194	0.438099	0.7156	0.3343	5008	,	,		20246	0.2827		0.4036	False		,,,				2504	0.3323				p.C98C		Atlas-SNP	.											LY6H,NS,carcinoma,0,1	LY6H	12	1	1	Substitution - coding silent(1)	stomach(1)	c.T294C						scavenged	.	G	,,	2878,1528	484.6+/-360.1	947,984,272	107.0	106.0	107.0		294,294,231	-6.0	0.4	8	dbSNP_119	107	3756,4844	616.1+/-396.5	813,2130,1357	no	coding-synonymous,coding-synonymous,coding-synonymous	LY6H	NM_001130478.1,NM_001135655.1,NM_002347.4	,,	1760,3114,1629	GG,GA,AA		43.6744,34.68,48.9928	,,	98/162,98/162,77/141	144239859	6634,6372	2203	4300	6503	SO:0001819	synonymous_variant	4062	exon4			GAAGTCACAGGAG	AB012293	CCDS6396.1, CCDS47926.1	8q24.3	2008-08-01			ENSG00000176956	ENSG00000176956			6728	protein-coding gene	gene with protein product		603625				9799603	Standard	NM_001130478		Approved	NMLY6	uc011lkb.2	O94772	OTTHUMG00000154890	ENST00000430474.2:c.231T>C	8.37:g.144239859A>G		Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_001135655	B2RAD2|J3KQI0|Q6IAX0	Silent	SNP	ENST00000430474.2	37	CCDS6396.1																																																																																			A|0.509;G|0.491	0.491	strong		0.537	LY6H-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337535.1		
TRIM41	90933	hgsc.bcm.edu	37	5	180661274	180661274	+	Missense_Mutation	SNP	C	C	G	rs78013120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180661274C>G	ENST00000315073.5	+	6	2102	c.1392C>G	c.(1390-1392)gaC>gaG	p.D464E	TRIM41_ENST00000510072.1_3'UTR|TRIM41_ENST00000351937.5_Missense_Mutation_p.D464E	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	464	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGTTGCTGACCATCCCAAGC	0.726													C|||	23	0.00459265	0.0174	0.0	5008	,	,		8455	0.0		0.0	False		,,,				2504	0.0				p.D464E		Atlas-SNP	.											.	TRIM41	96	.	0			c.C1392G						PASS	.	C	GLU/ASP,GLU/ASP	72,4296		0,72,2112	21.0	24.0	23.0		1392,1392	3.1	1.0	5	dbSNP_133	23	0,8498		0,0,4249	yes	missense,missense	TRIM41	NM_033549.3,NM_201627.1	45,45	0,72,6361	GG,GC,CC		0.0,1.6484,0.5596	possibly-damaging,possibly-damaging	464/631,464/519	180661274	72,12794	2184	4249	6433	SO:0001583	missense	90933	exon6			TGCTGACCATCCC	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19013	protein-coding gene	gene with protein product	"""RING-finger protein that interacts with C kinase"""	610530	"""tripartite motif-containing 41"""			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.1392C>G	5.37:g.180661274C>G	ENSP00000320869:p.Asp464Glu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_201627	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	37	CCDS4466.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	18.88	3.716930	0.68844	0.016484	0.0	ENSG00000146063	ENST00000515499;ENST00000351937;ENST00000315073;ENST00000438174	T;T;T	0.14391	2.51;2.51;2.51	4.97	3.14	0.36123	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	0.183072	0.38837	N	0.001552	T	0.09247	0.0228	M	0.62088	1.915	0.26095	N	0.980893	P;B	0.51791	0.948;0.001	P;B	0.48627	0.584;0.005	T	0.04386	-1.0955	10	0.48119	T	0.1	.	7.2565	0.26179	0.1752:0.7342:0.0:0.0907	.	464;464	Q8WV44;Q8WV44-2	TRI41_HUMAN;.	E	174;464;464;149	ENSP00000426803:D174E;ENSP00000336749:D464E;ENSP00000320869:D464E	ENSP00000320869:D464E	D	+	3	2	TRIM41	180593880	0.827000	0.29292	1.000000	0.80357	0.981000	0.71138	1.423000	0.34837	0.645000	0.30675	0.557000	0.71058	GAC	C|0.995;G|0.005	0.005	strong		0.726	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627	
TMEM204	79652	hgsc.bcm.edu	37	16	1584294	1584294	+	Silent	SNP	C	C	T	rs79579867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1584294C>T	ENST00000566264.1	+	1	721	c.18C>T	c.(16-18)ctC>ctT	p.L6L	TMEM204_ENST00000253934.5_Silent_p.L6L|IFT140_ENST00000426508.2_Intron|IFT140_ENST00000361339.5_5'Flank	NM_024600.5	NP_078876.2	Q9BSN7	TM204_HUMAN	transmembrane protein 204	6					lymph vessel development (GO:0001945)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to stress (GO:0006950)|smooth muscle cell differentiation (GO:0051145)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|cervix(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Hepatocellular(780;0.219)				TGCAGAGACTCGTGGCCGCGG	0.672													C|||	103	0.0205671	0.0764	0.0029	5008	,	,		15087	0.0		0.0	False		,,,				2504	0.0				p.L6L		Atlas-SNP	.											.	TMEM204	29	.	0			c.C18T						PASS	.	C	,	263,3993		4,255,1869	32.0	39.0	37.0		,18	-10.6	0.1	16	dbSNP_131	37	2,8484		0,2,4241	no	intron,coding-synonymous	IFT140,TMEM204	NM_014714.3,NM_024600.4	,	4,257,6110	TT,TC,CC		0.0236,6.1795,2.0797	,	,6/227	1584294	265,12477	2128	4243	6371	SO:0001819	synonymous_variant	79652	exon1			GAGACTCGTGGCC		CCDS42098.1	16p13.3	2008-02-05	2008-01-08	2008-01-08		ENSG00000131634			14158	protein-coding gene	gene with protein product		611002	"""chromosome 16 open reading frame 30"""	C16orf30			Standard	NM_024600		Approved	FLJ20898	uc002cmc.3	Q9BSN7		ENST00000566264.1:c.18C>T	16.37:g.1584294C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	202	98	0.485149	NM_024600	D3DU76|Q3KRC1|Q9H7G5	Silent	SNP	ENST00000566264.1	37	CCDS42098.1																																																																																			C|0.979;T|0.021	0.021	strong		0.672	TMEM204-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432610.1	NM_024600	
ABCA12	26154	hgsc.bcm.edu	37	2	215876371	215876371	+	Silent	SNP	T	T	C	rs10198064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	253	0	0		WXS	Illumina HiSeq	Phase_I	221	112	0.506787	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	
ZBTB38	253461	hgsc.bcm.edu	37	3	141163975	141163975	+	Silent	SNP	G	G	A	rs61732448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141163975G>A	ENST00000514251.1	+	4	3024	c.2745G>A	c.(2743-2745)ccG>ccA	p.P915P	ZBTB38_ENST00000441582.2_Silent_p.P915P|ZBTB38_ENST00000321464.5_Silent_p.P916P					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						CTGACAAACCGTGGCGCCCTT	0.502													G|||	120	0.0239617	0.0461	0.0014	5008	,	,		19160	0.0298		0.002	False		,,,				2504	0.0266				p.P915P		Atlas-SNP	.											ZBTB38,NS,carcinoma,0,1	ZBTB38	92	1	0			c.G2745A						PASS	.	G		192,3740		8,176,1782	50.0	51.0	51.0		2745	-8.4	0.8	3	dbSNP_129	51	4,8306		0,4,4151	no	coding-synonymous	ZBTB38	NM_001080412.2		8,180,5933	AA,AG,GG		0.0481,4.883,1.601		915/1196	141163975	196,12046	1966	4155	6121	SO:0001819	synonymous_variant	253461	exon8			CAAACCGTGGCGC	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.2745G>A	3.37:g.141163975G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_001080412		Silent	SNP	ENST00000514251.1	37	CCDS43157.1																																																																																			G|0.989;A|0.011	0.011	strong		0.502	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
OR2T4	127074	hgsc.bcm.edu	37	1	248525647	248525647	+	Silent	SNP	C	C	A	rs28405645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248525647C>A	ENST00000366475.1	+	1	765	c.765C>A	c.(763-765)ctC>ctA	p.L255L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCATCCTCCTCACCATCCACG	0.517													c|||	1468	0.293131	0.239	0.2709	5008	,	,		22286	0.4256		0.1799	False		,,,				2504	0.362				p.L255L		Atlas-SNP	.											.	OR2T4	126	.	0			c.C765A						PASS	.	C		1061,3345	385.4+/-325.7	140,781,1282	129.0	127.0	128.0		765	-0.0	0.1	1	dbSNP_125	128	1395,7205	269.1+/-288.2	112,1171,3017	no	coding-synonymous	OR2T4	NM_001004696.1		252,1952,4299	AA,AC,CC		16.2209,24.0808,18.8836		255/349	248525647	2456,10550	2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			CCTCCTCACCATC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.765C>A	1.37:g.248525647C>A		Somatic	890	1	0.0011236		WXS	Illumina HiSeq	Phase_I	919	438	0.476605	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			C|0.790;A|0.210	0.210	strong		0.517	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
CYP4F3	4051	hgsc.bcm.edu	37	19	15763721	15763721	+	Silent	SNP	G	G	A	rs1805042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	171	0	0		WXS	Illumina HiSeq	Phase_I	192	79	0.411458	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	
OR10V1	390201	hgsc.bcm.edu	37	11	59481016	59481016	+	Silent	SNP	C	C	T	rs537595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59481016C>T	ENST00000307552.2	-	1	321	c.303G>A	c.(301-303)caG>caA	p.Q101Q	STX3_ENST00000300150.7_5'UTR	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, member 1	101						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)|liver(1)|lung(10)|skin(1)	16						AGAAAAACATCTGGGTGCCAC	0.478													T|||	591	0.118011	0.3064	0.1527	5008	,	,		22641	0.0367		0.0189	False		,,,				2504	0.0245				p.Q101Q		Atlas-SNP	.											.	OR10V1	40	.	0			c.G303A						PASS	.	T		1037,3365	726.4+/-409.7	160,717,1324	74.0	66.0	69.0		303	-5.8	0.9	11	dbSNP_83	69	156,8434	811.8+/-407.1	3,150,4142	no	coding-synonymous	OR10V1	NM_001005324.1		163,867,5466	TT,TC,CC		1.8161,23.5575,9.1826		101/310	59481016	1193,11799	2201	4295	6496	SO:0001819	synonymous_variant	390201	exon1			AAACATCTGGGTG	AB065807	CCDS31565.1	11q12.1	2012-08-09			ENSG00000172289	ENSG00000172289		"""GPCR / Class A : Olfactory receptors"""	15136	protein-coding gene	gene with protein product							Standard	NM_001005324		Approved		uc001nof.1	Q8NGI7	OTTHUMG00000167406	ENST00000307552.2:c.303G>A	11.37:g.59481016C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_001005324	Q6IFD9|Q96R50	Silent	SNP	ENST00000307552.2	37	CCDS31565.1																																																																																			C|0.894;T|0.106	0.106	strong		0.478	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656511	46656511	+	Silent	SNP	A	A	G	rs9627324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	115	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	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	
LDLR	3949	hgsc.bcm.edu	37	19	11224265	11224265	+	Silent	SNP	A	A	G	rs5930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11224265A>G	ENST00000558518.1	+	10	1600	c.1413A>G	c.(1411-1413)agA>agG	p.R471R	LDLR_ENST00000558013.1_Silent_p.R471R|LDLR_ENST00000557933.1_Silent_p.R471R|LDLR_ENST00000455727.2_Silent_p.R303R|LDLR_ENST00000545707.1_Silent_p.R344R|LDLR_ENST00000535915.1_Silent_p.R430R	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	471			R -> G (found in a patient with hypercholesterolemia). {ECO:0000269|PubMed:21418584}.		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	TCATCAGCAGAGACATCCAGG	0.607													G|||	3280	0.654952	0.7504	0.7147	5008	,	,		18170	0.5952		0.5785	False		,,,				2504	0.6237				p.R471R	GBM(18;201 575 7820 21545)	Atlas-SNP	.											LDLR,NS,carcinoma,0,1	LDLR	72	1	1	Unknown(1)	lung(1)	c.A1413G						PASS	.	G	,,,,,	3241,1165	409.1+/-334.9	1190,861,152	48.0	46.0	47.0		1413,1413,1290,909,1050,1032	-2.2	0.0	19	dbSNP_52	47	5299,3301	491.0+/-373.0	1628,2043,629	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LDLR	NM_000527.4,NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195802.1,NM_001195803.1	,,,,,	2818,2904,781	GG,GA,AA		38.3837,26.4412,34.338	,,,,,	471/861,471/859,430/820,303/693,350/740,344/683	11224265	8540,4466	2203	4300	6503	SO:0001819	synonymous_variant	3949	exon10			CAGCAGAGACATC	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1413A>G	19.37:g.11224265A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Silent	SNP	ENST00000558518.1	37	CCDS12254.1																																																																																			A|0.345;G|0.655	0.655	strong		0.607	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
ARHGEF40	55701	hgsc.bcm.edu	37	14	21546354	21546354	+	Missense_Mutation	SNP	C	C	T	rs61744857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21546354C>T	ENST00000298694.4	+	9	2180	c.2053C>T	c.(2053-2055)Cgc>Tgc	p.R685C	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.R685C			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	685						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						AAGGCTATGTCGCCTGTGCCA	0.562													C|||	301	0.0601038	0.1218	0.0447	5008	,	,		20293	0.0526		0.0437	False		,,,				2504	0.0123				p.R685C		Atlas-SNP	.											ARHGEF40_ENST00000298694,NS,carcinoma,-1,1	ARHGEF40	84	1	0			c.C2053T						PASS	.	C	CYS/ARG	431,3975	209.5+/-230.2	23,385,1795	74.0	67.0	70.0		2053	3.0	0.4	14	dbSNP_129	70	386,8214	125.8+/-184.4	6,374,3920	yes	missense	ARHGEF40	NM_018071.3	180	29,759,5715	TT,TC,CC		4.4884,9.7821,6.2817	possibly-damaging	685/1520	21546354	817,12189	2203	4300	6503	SO:0001583	missense	55701	exon9			CTATGTCGCCTGT		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.2053C>T	14.37:g.21546354C>T	ENSP00000298694:p.Arg685Cys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	58	0.585859	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	37	CCDS32041.1	132	0.06043956043956044	61	0.12398373983739837	14	0.03867403314917127	26	0.045454545454545456	31	0.040897097625329816	C	12.85	2.061252	0.36373	0.097821	0.044884	ENSG00000165801	ENST00000298694;ENST00000298693	T;T	0.02525	4.33;4.26	4.91	2.97	0.34412	.	1.299180	0.05059	N	0.479560	T	0.00039	0.0001	L	0.34521	1.04	0.80722	P	0.0	P	0.40931	0.733	B	0.28709	0.093	T	0.48536	-0.9027	9	0.66056	D	0.02	.	6.6462	0.22936	0.2581:0.584:0.1578:0.0	rs61744857	685	Q8TER5	ARH40_HUMAN	C	685	ENSP00000298694:R685C;ENSP00000298693:R685C	ENSP00000298693:R685C	R	+	1	0	ARHGEF40	20616194	0.001000	0.12720	0.425000	0.26659	0.960000	0.62799	0.193000	0.17116	0.573000	0.29400	0.558000	0.71614	CGC	C|0.939;T|0.061	0.061	strong		0.562	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
FAM135A	57579	hgsc.bcm.edu	37	6	71248046	71248046	+	Silent	SNP	A	A	G	rs9455152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71248046A>G	ENST00000418814.2	+	20	4784	c.4170A>G	c.(4168-4170)acA>acG	p.T1390T	FAM135A_ENST00000457062.2_Silent_p.T1177T|FAM135A_ENST00000361499.3_Silent_p.T1194T|FAM135A_ENST00000370479.3_Silent_p.T1177T|FAM135A_ENST00000505769.1_Silent_p.T970T|FAM135A_ENST00000505868.1_Silent_p.T1390T	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1390										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						TGCAGCTGACATGTCGAGATC	0.323													A|||	101	0.0201677	0.0726	0.0043	5008	,	,		14384	0.0		0.002	False		,,,				2504	0.0				p.T1390T		Atlas-SNP	.											.	FAM135A	181	.	0			c.A4170G						PASS	.	A	,,	299,4107	162.5+/-194.5	7,285,1911	59.0	61.0	60.0		3582,4170,3531	2.9	1.0	6	dbSNP_119	60	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	7,289,6207	GG,GA,AA		0.0465,6.7862,2.3297	,,	1194/1320,1390/1516,1177/1303	71248046	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	57579	exon18			GCTGACATGTCGA	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.4170A>G	6.37:g.71248046A>G		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	174	96	0.551724	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			A|0.974;G|0.026	0.026	strong		0.323	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
HEATR5B	54497	hgsc.bcm.edu	37	2	37280711	37280711	+	Silent	SNP	T	T	C	rs10202107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37280711T>C	ENST00000233099.5	-	17	2534	c.2439A>G	c.(2437-2439)caA>caG	p.Q813Q	HEATR5B_ENST00000354531.2_Silent_p.Q813Q	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	813						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)				CACCTTTAGCTTGTTTAACAC	0.313													T|||	56	0.0111821	0.0416	0.0014	5008	,	,		17495	0.0		0.0	False		,,,				2504	0.0				p.Q813Q		Atlas-SNP	.											.	HEATR5B	185	.	0			c.A2439G						PASS	.	T		121,4285	91.1+/-129.8	2,117,2084	56.0	57.0	57.0		2439	2.3	1.0	2	dbSNP_119	57	0,8600		0,0,4300	no	coding-synonymous	HEATR5B	NM_019024.1		2,117,6384	CC,CT,TT		0.0,2.7463,0.9303		813/2072	37280711	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	54497	exon17			TTTAGCTTGTTTA	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.2439A>G	2.37:g.37280711T>C		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	196	101	0.515306	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																			T|0.989;C|0.011	0.011	strong		0.313	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
DLK1	8788	hgsc.bcm.edu	37	14	101201219	101201219	+	Missense_Mutation	SNP	G	G	C	rs115349979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101201219G>C	ENST00000341267.4	+	5	1380	c.1138G>C	c.(1138-1140)Gac>Cac	p.D380H	DLK1_ENST00000331224.6_Missense_Mutation_p.D307H|RP11-566J3.4_ENST00000608876.1_lincRNA	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	380					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)				GGAGGCCGGCGACGAGGAGAT	0.552													G|||	62	0.0123802	0.0469	0.0	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.D380H		Atlas-SNP	.											DLK1,NS,carcinoma,-2,2	DLK1	57	2	0			c.G1138C						PASS	.	G	HIS/ASP	130,4276	94.8+/-133.5	3,124,2076	85.0	86.0	86.0		1138	0.9	0.2	14	dbSNP_132	86	0,8600		0,0,4300	yes	missense	DLK1	NM_003836.5	81	3,124,6376	CC,CG,GG		0.0,2.9505,0.9995	benign	380/384	101201219	130,12876	2203	4300	6503	SO:0001583	missense	8788	exon5			GCCGGCGACGAGG	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.1138G>C	14.37:g.101201219G>C	ENSP00000340292:p.Asp380His	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_003836	P15803|Q96DW5	Missense_Mutation	SNP	ENST00000341267.4	37	CCDS9963.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	G	9.764	1.170865	0.21621	0.029505	0.0	ENSG00000185559	ENST00000341267;ENST00000331224	D;D	0.88431	-2.38;-2.32	4.41	0.928	0.19443	.	1.200000	0.06159	N	0.675641	T	0.57844	0.2081	N	0.08118	0	0.09310	N	1	P;P	0.46220	0.874;0.8	P;P	0.54460	0.753;0.571	T	0.69351	-0.5168	10	0.87932	D	0	.	0.6745	0.00864	0.2119:0.1565:0.3728:0.2589	.	307;380	P80370-2;P80370	.;DLK1_HUMAN	H	380;307	ENSP00000340292:D380H;ENSP00000331081:D307H	ENSP00000331081:D307H	D	+	1	0	DLK1	100270972	0.002000	0.14202	0.191000	0.23289	0.049000	0.14656	0.031000	0.13710	0.860000	0.35481	-0.332000	0.08345	GAC	G|0.988;C|0.012	0.012	strong		0.552	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
GHRHR	2692	hgsc.bcm.edu	37	7	31008686	31008686	+	Missense_Mutation	SNP	G	G	A	rs4988496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:31008686G>A	ENST00000326139.2	+	3	215	c.169G>A	c.(169-171)Gcg>Acg	p.A57T	GHRHR_ENST00000409904.3_5'Flank|GHRHR_ENST00000409316.1_5'Flank	NM_000823.3	NP_000814.2	Q02643	GHRHR_HUMAN	growth hormone releasing hormone receptor	57			A -> T (in dbSNP:rs4988496).		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP-mediated signaling (GO:0019933)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|determination of adult lifespan (GO:0008340)|growth hormone secretion (GO:0030252)|hormone metabolic process (GO:0042445)|lactation (GO:0007595)|multicellular organismal reproductive process (GO:0048609)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of intracellular steroid hormone receptor signaling pathway (GO:0033143)|regulation of protein metabolic process (GO:0051246)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|somatotropin secreting cell development (GO:0060133)|water homeostasis (GO:0030104)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nuclear matrix (GO:0016363)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	G-protein coupled receptor activity (GO:0004930)|growth factor binding (GO:0019838)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35					Sermorelin(DB00010)|Tesamorelin(DB08869)	AGGCTGCCCTGCGACCTGGGA	0.612													A|||	638	0.127396	0.3427	0.049	5008	,	,		17335	0.0615		0.0616	False		,,,				2504	0.0276				p.A57T		Atlas-SNP	.											.	GHRHR	55	.	0			c.G169A	GRCh37	CM005494	GHRHR	M	rs4988496	PASS	.	A	THR/ALA	1204,3198		167,870,1164	20.0	20.0	20.0		169	-7.8	0.0	7	dbSNP_113	20	492,8100		16,460,3820	yes	missense	GHRHR	NM_000823.3	58	183,1330,4984	AA,AG,GG		5.7263,27.3512,13.0522	benign	57/424	31008686	1696,11298	2201	4296	6497	SO:0001583	missense	2692	exon3			TGCCCTGCGACCT		CCDS5432.1	7p14	2012-08-10			ENSG00000106128	ENSG00000106128		"""GPCR / Class B : Glucagon receptors"""	4266	protein-coding gene	gene with protein product		139191				7680413, 7514564	Standard	NM_000823		Approved		uc003tbx.3	Q02643	OTTHUMG00000152801	ENST00000326139.2:c.169G>A	7.37:g.31008686G>A	ENSP00000320180:p.Ala57Thr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_000823	Q99863	Missense_Mutation	SNP	ENST00000326139.2	37	CCDS5432.1	255	0.11675824175824176	161	0.32723577235772355	17	0.04696132596685083	30	0.05244755244755245	47	0.06200527704485488	A	7.039	0.562074	0.13498	0.273512	0.057263	ENSG00000106128	ENST00000326139	T	0.63580	-0.05	4.64	-7.79	0.01218	GPCR, family 2, secretin-like, conserved site (1);GPCR, family 2, extracellular hormone receptor domain (3);	.	.	.	.	T	0.00012	0.0000	N	0.03115	-0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.15492	-1.0435	8	0.37606	T	0.19	.	2.4739	0.04571	0.1537:0.2235:0.4024:0.2204	rs4988496;rs52803549;rs58388240;rs4988496	57	Q02643	GHRHR_HUMAN	T	57	ENSP00000320180:A57T	ENSP00000320180:A57T	A	+	1	0	GHRHR	30975211	0.000000	0.05858	0.000000	0.03702	0.350000	0.29205	-0.548000	0.06048	-2.403000	0.00577	-0.260000	0.10688	GCG	G|0.861;A|0.139	0.139	strong		0.612	GHRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327967.2		
ZFP36	7538	hgsc.bcm.edu	37	19	39898667	39898667	+	Silent	SNP	C	C	T	rs3746083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39898667C>T	ENST00000248673.3	+	2	367	c.309C>T	c.(307-309)cgC>cgT	p.R103R	ZFP36_ENST00000594045.1_3'UTR|MIR4530_ENST00000581459.1_RNA|ZFP36_ENST00000597629.1_Silent_p.R109R	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	103					3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of inflammatory response (GO:0050728)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|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)|regulation of tumor necrosis factor production (GO:0032680)|response to starvation (GO:0042594)|RNA destabilization (GO:0050779)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|AU-rich element binding (GO:0017091)|C-C chemokine binding (GO:0019957)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(5)|pancreas(1)	7	all_cancers(60;6.54e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.53e-06)|Ovarian(47;0.0512)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CCCCCTCGCGCTACAAGACTG	0.687													C|||	180	0.0359425	0.0333	0.0418	5008	,	,		15495	0.0347		0.0477	False		,,,				2504	0.0245				p.R109R	NSCLC(67;1164 1324 12056 21056 30097)	Atlas-SNP	.											.	ZFP36	19	.	0			c.C327T						PASS	.	C		154,4250		2,150,2050	56.0	63.0	60.0		309	-5.3	1.0	19	dbSNP_107	60	362,8232		10,342,3945	no	coding-synonymous	ZFP36	NM_003407.2		12,492,5995	TT,TC,CC		4.2122,3.4968,3.9698		103/327	39898667	516,12482	2202	4297	6499	SO:0001819	synonymous_variant	7538	exon2			CTCGCGCTACAAG	M63625	CCDS12534.1, CCDS12534.2	19q13.1	2012-11-27	2012-11-27			ENSG00000128016		"""RING-type (C3HC4) zinc fingers"""	12862	protein-coding gene	gene with protein product		190700	"""zinc finger protein 36, C3H type, homolog (mouse)"""			1699942	Standard	NM_003407		Approved	RNF162A, TIS11, G0S24, TTP, NUP475, tristetraprolin	uc002olh.2	P26651		ENST00000248673.3:c.309C>T	19.37:g.39898667C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_003407	B2RA54	Silent	SNP	ENST00000248673.3	37																																																																																				A|0.000;C|0.959;G|0.000;T|0.041	0.041	strong		0.687	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
HELQ	113510	hgsc.bcm.edu	37	4	84350870	84350870	+	Silent	SNP	A	A	G	rs59255439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84350870A>G	ENST00000295488.3	-	12	2487	c.2325T>C	c.(2323-2325)caT>caC	p.H775H	HELQ_ENST00000510985.1_Silent_p.H708H	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	775					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						CATTCATGAAATGATAGATGT	0.328								Other identified genes with known or suspected DNA repair function					G|||	497	0.0992412	0.3563	0.036	5008	,	,		15251	0.0		0.001	False		,,,				2504	0.0				p.H775H		Atlas-SNP	.											.	HELQ	95	.	0			c.T2325C						PASS	.	G		1348,3052	683.1+/-404.2	191,966,1043	43.0	39.0	40.0		2325	1.2	1.0	4	dbSNP_129	40	18,8578	810.1+/-407.1	0,18,4280	no	coding-synonymous	HELQ	NM_133636.2		191,984,5323	GG,GA,AA		0.2094,30.6364,10.5109		775/1102	84350870	1366,11630	2200	4298	6498	SO:0001819	synonymous_variant	113510	exon12			CATGAAATGATAG	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.2325T>C	4.37:g.84350870A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																			A|0.908;G|0.092	0.092	strong		0.328	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
PLXND1	23129	hgsc.bcm.edu	37	3	129291751	129291751	+	Silent	SNP	T	T	C	rs2244708	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129291751T>C	ENST00000324093.4	-	14	3049	c.2871A>G	c.(2869-2871)ccA>ccG	p.P957P	PLXND1_ENST00000393239.1_Silent_p.P957P	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	957	IPT/TIG 1.				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						CACCTGAGAGTGGTCCTGGGG	0.677													C|||	2155	0.430312	0.6036	0.2911	5008	,	,		15878	0.5119		0.3479	False		,,,				2504	0.2955				p.P957P	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											PLXND1,colon,carcinoma,0,1	PLXND1	149	1	0			c.A2871G						PASS	.	C		2532,1872	537.5+/-374.7	728,1076,398	62.0	52.0	55.0		2871	-6.7	0.0	3	dbSNP_100	55	2726,5874	680.0+/-403.6	445,1836,2019	yes	coding-synonymous	PLXND1	NM_015103.2		1173,2912,2417	CC,CT,TT		31.6977,42.5068,40.4337		957/1926	129291751	5258,7746	2202	4300	6502	SO:0001819	synonymous_variant	23129	exon14			TGAGAGTGGTCCT	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.2871A>G	3.37:g.129291751T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			T|0.572;C|0.428	0.428	strong		0.677	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057636	46057636	+	Missense_Mutation	SNP	T	T	A	rs115298124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057636T>A	ENST00000380095.1	+	1	364	c.302T>A	c.(301-303)gTg>gAg	p.V101E	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	101	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						gtctgctgtgtgcccgtctgc	0.627													A|||	306	0.0611022	0.2118	0.0173	5008	,	,		19037	0.002		0.001	False		,,,				2504	0.0112				p.V101E		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.T302A						PASS	.	A	,GLU/VAL	550,3856		77,396,1730	131.0	124.0	126.0		,302	-5.7	0.0	21	dbSNP_132	126	2,8594		0,2,4296	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,121	77,398,6026	AA,AT,TT		0.0233,12.483,4.2455	,benign	,101/252	46057636	552,12450	2203	4298	6501	SO:0001583	missense	353333	exon1			GCTGTGTGCCCGT	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.302T>A	21.37:g.46057636T>A	ENSP00000369438:p.Val101Glu	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	273	120	0.43956	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	a	0.032	-1.330391	0.01298	0.12483	2.33E-4	ENSG00000221859	ENST00000380095	T	0.01323	5.01	2.86	-5.72	0.02406	.	.	.	.	.	T	0.00012	0.0000	N	0.10874	0.06	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39165	-0.9627	9	0.22706	T	0.39	.	1.3737	0.02215	0.2016:0.1241:0.184:0.4903	.	101	P60014	KR10A_HUMAN	E	101	ENSP00000369438:V101E	ENSP00000369438:V101E	V	+	2	0	KRTAP10-10	44882064	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.107000	0.03316	-4.925000	0.00027	-3.683000	0.00024	GTG	T|0.928;A|0.072	0.072	strong		0.627	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
DMXL2	23312	hgsc.bcm.edu	37	15	51795172	51795172	+	Silent	SNP	G	G	A	rs12592889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	79	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	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	
CELF2	10659	hgsc.bcm.edu	37	10	11356160	11356160	+	Silent	SNP	C	C	T	rs2246449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:11356160C>T	ENST00000379261.4	+	10	1106	c.1014C>T	c.(1012-1014)ctC>ctT	p.L338L	CELF2_ENST00000450189.1_Silent_p.L345L|CELF2_ENST00000609692.1_Silent_p.L314L|CELF2_ENST00000354440.2_Silent_p.L314L|CELF2_ENST00000537122.1_Silent_p.L227L|CELF2_ENST00000417956.2_Silent_p.L314L|CELF2_ENST00000354897.3_Silent_p.L314L|CELF2-AS1_ENST00000379256.3_RNA|CELF2_ENST00000399850.3_Silent_p.L314L|CELF2_ENST00000315874.4_Silent_p.L314L|CELF2_ENST00000542579.1_Silent_p.L345L|CELF2_ENST00000416382.2_Silent_p.L338L|CELF2_ENST00000427450.1_Silent_p.L314L|CELF2_ENST00000608830.1_Silent_p.L314L	NM_001025077.2	NP_001020248.1	O95319	CELF2_HUMAN	CUGBP, Elav-like family member 2	338	Ala-rich.				mRNA processing (GO:0006397)|regulation of heart contraction (GO:0008016)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	16						TGACCTCTCTCGGGACTCTGC	0.507													T|||	2259	0.451078	0.6377	0.2594	5008	,	,		19547	0.4871		0.2684	False		,,,				2504	0.4857				p.L345L		Atlas-SNP	.											.	CELF2	78	.	0			c.C1035T						PASS	.	T	,,,	2154,1694		611,932,381	101.0	99.0	100.0		942,1014,942,1035	-10.4	0.5	10	dbSNP_100	100	2162,6106		300,1562,2272	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CELF2	NM_001025076.2,NM_001025077.2,NM_001083591.1,NM_006561.3	,,,	911,2494,2653	TT,TC,CC		26.149,44.0229,35.6223	,,,	314/491,338/509,314/489,345/522	11356160	4316,7800	1924	4134	6058	SO:0001819	synonymous_variant	10659	exon10			CTCTCTCGGGACT	U69546	CCDS41488.1, CCDS44354.1, CCDS44355.1, CCDS44356.1	10p13	2013-02-12	2010-02-19	2010-02-19	ENSG00000048740	ENSG00000048740		"""RNA binding motif (RRM) containing"""	2550	protein-coding gene	gene with protein product		602538	"""CUG triplet repeat, RNA-binding protein 2"", ""CUG triplet repeat, RNA binding protein 2"""	CUGBP2		7869393, 9887331	Standard	NM_006561		Approved	Etr-3, NAPOR-2, BRUNOL3	uc001ikl.4	O95319	OTTHUMG00000017668	ENST00000379261.4:c.1014C>T	10.37:g.11356160C>T		Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	175	94	0.537143	NM_006561	B7ZAN9|Q7KYU4|Q8N499|Q92950|Q96NW9|Q96RQ5|Q96RQ6|Q9UL67	Silent	SNP	ENST00000379261.4	37	CCDS44354.1																																																																																			C|0.603;T|0.397	0.397	strong		0.507	CELF2-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
KLHL32	114792	hgsc.bcm.edu	37	6	97512577	97512577	+	Missense_Mutation	SNP	A	A	G	rs2294763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:97512577A>G	ENST00000369261.4	+	5	749	c.386A>G	c.(385-387)aAt>aGt	p.N129S	KLHL32_ENST00000544166.1_5'UTR|KLHL32_ENST00000539200.1_Intron|KLHL32_ENST00000536676.1_Missense_Mutation_p.N93S	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	129			N -> S (in dbSNP:rs2294763).					p.N129S(1)		breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		GAGCTTCTCAATTTATGCTCC	0.468													A|||	301	0.0601038	0.1157	0.0288	5008	,	,		18851	0.0804		0.0179	False		,,,				2504	0.0297				p.N129S		Atlas-SNP	.											KLHL32,NS,carcinoma,0,1	KLHL32	85	1	1	Substitution - Missense(1)	stomach(1)	c.A386G						PASS	.	A	SER/ASN	474,3932	224.3+/-240.5	20,434,1749	145.0	108.0	120.0		386	1.9	0.9	6	dbSNP_100	120	190,8410	85.3+/-147.7	2,186,4112	yes	missense	KLHL32	NM_052904.3	46	22,620,5861	GG,GA,AA		2.2093,10.7581,5.1053	benign	129/621	97512577	664,12342	2203	4300	6503	SO:0001583	missense	114792	exon5			TTCTCAATTTATG	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.386A>G	6.37:g.97512577A>G	ENSP00000358265:p.Asn129Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	150	64	0.426667	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	37	CCDS5038.1	135	0.061813186813186816	58	0.11788617886178862	12	0.03314917127071823	53	0.09265734265734266	12	0.0158311345646438	A	13.41	2.227809	0.39399	0.107581	0.022093	ENSG00000186231	ENST00000369255;ENST00000369261;ENST00000536676;ENST00000369254;ENST00000447886	T;T;T;T	0.67523	-0.27;1.98;-0.27;1.94	5.54	1.89	0.25635	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.179966	0.64402	N	0.000016	T	0.24353	0.0590	N	0.11023	0.085	0.09310	P	1.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.001;0.002	T	0.03315	-1.1049	9	0.51188	T	0.08	.	8.4836	0.33059	0.6357:0.0:0.3643:0.0	rs2294763;rs52827164;rs56862294;rs2294763	93;129;129	B7Z346;Q96NJ5;Q6IQ08	.;KLH32_HUMAN;.	S	55;129;93;129;25	ENSP00000358265:N129S;ENSP00000440382:N93S;ENSP00000358258:N129S;ENSP00000389310:N25S	ENSP00000358258:N129S	N	+	2	0	KLHL32	97619298	0.997000	0.39634	0.912000	0.35992	0.995000	0.86356	2.070000	0.41491	0.185000	0.20105	0.528000	0.53228	AAT	A|0.940;G|0.060	0.060	strong		0.468	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904	
LBP	3929	hgsc.bcm.edu	37	20	36997655	36997655	+	Missense_Mutation	SNP	C	C	T	rs2232613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36997655C>T	ENST00000217407.2	+	10	1159	c.998C>T	c.(997-999)cCc>cTc	p.P333L		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	333			P -> L (abolishes lipopolysaccharide binding and causes increased proteolytic degradation of the protein; dbSNP:rs2232613). {ECO:0000269|PubMed:24120359}.		acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				AGGCTCTACCCCAACATGAAC	0.507													C|||	276	0.0551118	0.0983	0.0418	5008	,	,		19010	0.001		0.0726	False		,,,				2504	0.044				p.P333L		Atlas-SNP	.											.	LBP	60	.	0			c.C998T						PASS	.	C	LEU/PRO	423,3983	205.8+/-227.6	28,367,1808	95.0	93.0	94.0		998	4.6	1.0	20	dbSNP_98	94	689,7911	171.7+/-222.6	34,621,3645	yes	missense	LBP	NM_004139.2	98	62,988,5453	TT,TC,CC		8.0116,9.6005,8.5499	probably-damaging	333/482	36997655	1112,11894	2203	4300	6503	SO:0001583	missense	3929	exon10			TCTACCCCAACAT		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.998C>T	20.37:g.36997655C>T	ENSP00000217407:p.Pro333Leu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	125	0.05723443223443223	53	0.10772357723577236	17	0.04696132596685083	1	0.0017482517482517483	54	0.0712401055408971	C	20.2	3.950249	0.73787	0.096005	0.080116	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.27890	1.64	5.54	4.58	0.56647	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.000000	0.64402	D	0.000001	T	0.02047	0.0064	M	0.87097	2.86	0.09310	P	0.99999750602	D	0.89917	1.0	D	0.97110	1.0	T	0.37619	-0.9698	9	0.40728	T	0.16	-36.9081	14.0635	0.64815	0.0:0.8481:0.1518:0.0	rs2232613;rs60019947;rs2232613	333	P18428	LBP_HUMAN	L	333	ENSP00000217407:P333L	ENSP00000217407:P333L	P	+	2	0	LBP	36431069	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.338000	0.59316	1.537000	0.49254	0.655000	0.94253	CCC	C|0.926;T|0.074	0.074	strong		0.507	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
RHOT2	89941	hgsc.bcm.edu	37	16	720152	720152	+	Silent	SNP	T	T	C	rs3752487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:720152T>C	ENST00000315082.4	+	6	420	c.306T>C	c.(304-306)aaT>aaC	p.N102N	RHOT2_ENST00000569943.2_3'UTR	NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	102	Miro 1.				cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				CACTGGTGAATGGGGGGACCA	0.632													T|||	887	0.177117	0.2307	0.1484	5008	,	,		18540	0.2887		0.0795	False		,,,				2504	0.1104				p.N102N		Atlas-SNP	.											.	RHOT2	35	.	0			c.T306C						PASS	.	T		908,3486	341.0+/-306.5	94,720,1383	39.0	42.0	41.0		306	2.8	1.0	16	dbSNP_107	41	784,7812	182.8+/-231.1	32,720,3546	no	coding-synonymous	RHOT2	NM_138769.1		126,1440,4929	CC,CT,TT		9.1205,20.6645,13.0254		102/619	720152	1692,11298	2197	4298	6495	SO:0001819	synonymous_variant	89941	exon6			GGTGAATGGGGGG	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.306T>C	16.37:g.720152T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Silent	SNP	ENST00000315082.4	37	CCDS10417.1																																																																																			T|0.850;C|0.150	0.150	strong		0.632	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769	
ALDH7A1	501	hgsc.bcm.edu	37	5	125928395	125928395	+	Silent	SNP	A	A	G	rs60720055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125928395A>G	ENST00000409134.3	-	3	492	c.273T>C	c.(271-273)acT>acC	p.T91T	ALDH7A1_ENST00000413020.1_5'UTR|ALDH7A1_ENST00000553117.1_Silent_p.T91T|ALDH7A1_ENST00000447989.2_Silent_p.T118T	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	91					cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|glycine betaine biosynthetic process from choline (GO:0019285)|lysine catabolic process (GO:0006554)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|betaine-aldehyde dehydrogenase activity (GO:0008802)|L-aminoadipate-semialdehyde dehydrogenase activity (GO:0004043)			endometrium(1)|kidney(4)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)		CTTTCTTTACAGTTTCTTCAT	0.368													A|||	302	0.0603035	0.1717	0.0274	5008	,	,		18399	0.0		0.0288	False		,,,				2504	0.0276				p.T118T		Atlas-SNP	.											.	ALDH7A1	57	.	0			c.T354C						PASS	.	A	,,	657,3749	278.1+/-274.1	42,573,1588	111.0	105.0	107.0		273,189,354	-9.2	0.1	5	dbSNP_129	107	214,8386	88.9+/-151.2	2,210,4088	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH7A1	NM_001182.4,NM_001201377.1,NM_001202404.1	,,	44,783,5676	GG,GA,AA		2.4884,14.9115,6.6969	,,	91/540,63/512,118/503	125928395	871,12135	2203	4300	6503	SO:0001819	synonymous_variant	501	exon3			CTTTACAGTTTCT	S74728	CCDS4137.2, CCDS56380.1	5q31	2013-06-03			ENSG00000164904	ENSG00000164904	1.2.1.31	"""Aldehyde dehydrogenases"""	877	protein-coding gene	gene with protein product	"""antiquitin 1"", ""26g turgor protein homolog"", ""alpha-aminoadipic semialdehyde dehydrogenase"", ""alpha-AASA dehydrogenase"", ""delta1-piperideine-6-carboxylate dehydrogenease"", ""P6c dehydrogenase"""	107323		ATQ1		9417906	Standard	NM_001182		Approved	EPD, PDE	uc003ktx.3	P49419	OTTHUMG00000128942	ENST00000409134.3:c.273T>C	5.37:g.125928395A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_001202404	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Silent	SNP	ENST00000409134.3	37	CCDS4137.2																																																																																			A|0.941;G|0.059	0.059	strong		0.368	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182	
RINT1	60561	hgsc.bcm.edu	37	7	105177041	105177041	+	Missense_Mutation	SNP	A	A	T	rs11556986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:105177041A>T	ENST00000257700.2	+	3	349	c.118A>T	c.(118-120)Agt>Tgt	p.S40C		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	40			S -> C (in dbSNP:rs11556986).		G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TCTTATTGGAAGTAAACAAGT	0.313													A|||	959	0.191494	0.2738	0.17	5008	,	,		16236	0.0218		0.1948	False		,,,				2504	0.2669				p.S40C		Atlas-SNP	.											RINT1,NS,carcinoma,-2,1	RINT1	65	1	0			c.A118T						PASS	.	A	CYS/SER	1117,3289	400.8+/-331.7	135,847,1221	178.0	184.0	182.0		118	2.8	0.0	7	dbSNP_120	182	1548,7052	292.3+/-300.8	159,1230,2911	yes	missense	RINT1	NM_021930.4	112	294,2077,4132	TT,TA,AA		18.0,25.3518,20.4905	possibly-damaging	40/793	105177041	2665,10341	2203	4300	6503	SO:0001583	missense	60561	exon3			ATTGGAAGTAAAC	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.118A>T	7.37:g.105177041A>T	ENSP00000257700:p.Ser40Cys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	37	CCDS34726.1	353	0.16163003663003664	122	0.24796747967479674	62	0.1712707182320442	8	0.013986013986013986	161	0.21240105540897097	A	9.350	1.065381	0.20067	0.253518	0.18	ENSG00000135249	ENST00000257700	T	0.25414	1.8	5.2	2.75	0.32379	.	0.525534	0.21062	N	0.080810	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.23084	-1.0198	9	0.56958	D	0.05	-3.7725	6.7224	0.23338	0.7888:0.0:0.0754:0.1358	rs11556986;rs52812744	40	Q6NUQ1	RINT1_HUMAN	C	40	ENSP00000257700:S40C	ENSP00000257700:S40C	S	+	1	0	RINT1	104964277	0.884000	0.30299	0.018000	0.16275	0.252000	0.25951	1.413000	0.34725	0.279000	0.22186	0.402000	0.26972	AGT	A|0.809;T|0.191	0.191	strong		0.313	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930	
KDM3B	51780	hgsc.bcm.edu	37	5	137708434	137708434	+	Silent	SNP	C	C	T	rs4835678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:137708434C>T	ENST00000314358.5	+	2	464	c.264C>T	c.(262-264)atC>atT	p.I88I		NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	88					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						AGGAAGTTATCGTGCTTCTGC	0.498													T|||	3380	0.67492	0.5598	0.6715	5008	,	,		17856	0.8482		0.5934	False		,,,				2504	0.7382				p.I88I		Atlas-SNP	.											.	KDM3B	177	.	0			c.C264T						PASS	.	T		2530,1876	539.9+/-375.4	711,1108,384	109.0	103.0	105.0		264	3.9	1.0	5	dbSNP_111	105	5019,3581	519.3+/-379.4	1473,2073,754	no	coding-synonymous	KDM3B	NM_016604.3		2184,3181,1138	TT,TC,CC		41.6395,42.5783,41.9576		88/1762	137708434	7549,5457	2203	4300	6503	SO:0001819	synonymous_variant	51780	exon2			AGTTATCGTGCTT	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.264C>T	5.37:g.137708434C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	211	100	0.473934	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	37	CCDS34242.1																																																																																			C|0.379;T|0.621	0.621	strong		0.498	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
KIAA1244	57221	hgsc.bcm.edu	37	6	138584014	138584014	+	Missense_Mutation	SNP	C	C	G	rs116596107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138584014C>G	ENST00000251691.4	+	12	1560	c.1394C>G	c.(1393-1395)gCt>gGt	p.A465G		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		AAGGATGGGGCTGAGTGGAGC	0.612													C|||	4	0.000798722	0.003	0.0	5008	,	,		21357	0.0		0.0	False		,,,				2504	0.0				p.A465G		Atlas-SNP	.											.	KIAA1244	236	.	0			c.C1394G						PASS	.	C	GLY/ALA	37,4369	42.3+/-75.8	0,37,2166	94.0	72.0	80.0		1394	1.7	0.1	6	dbSNP_132	80	0,8600		0,0,4300	yes	missense	KIAA1244	NM_020340.4	60	0,37,6466	GG,GC,CC		0.0,0.8398,0.2845	benign	465/2178	138584014	37,12969	2203	4300	6503	SO:0001583	missense	57221	exon12			ATGGGGCTGAGTG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.1394C>G	6.37:g.138584014C>G	ENSP00000251691:p.Ala465Gly	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	9.329	1.060068	0.19987	0.008398	0.0	ENSG00000112379	ENST00000251691	T	0.18960	2.18	5.62	1.68	0.24146	.	0.330121	0.29544	N	0.011855	T	0.05456	0.0144	L	0.36672	1.1	0.20074	N	0.999932	B	0.02656	0.0	B	0.04013	0.001	T	0.39761	-0.9598	10	0.23302	T	0.38	-25.5355	11.5601	0.50772	0.0:0.4804:0.4521:0.0675	.	465	Q5TH69	BIG3_HUMAN	G	465	ENSP00000251691:A465G	ENSP00000251691:A465G	A	+	2	0	KIAA1244	138625707	0.965000	0.33210	0.081000	0.20488	0.953000	0.61014	2.466000	0.45084	0.266000	0.21894	0.655000	0.94253	GCT	C|0.998;G|0.002	0.002	strong		0.612	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
MED13	9969	hgsc.bcm.edu	37	17	60040329	60040329	+	Silent	SNP	C	C	T	rs2278812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60040329C>T	ENST00000397786.2	-	21	4924	c.4848G>A	c.(4846-4848)acG>acA	p.T1616T		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1616					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|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)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	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 coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CCCGATCCATCGTGCTAAAAT	0.398													C|||	1427	0.284944	0.3828	0.2046	5008	,	,		16521	0.5248		0.1223	False		,,,				2504	0.1299				p.T1616T		Atlas-SNP	.											MED13,colon,carcinoma,0,1	MED13	181	1	0			c.G4848A						PASS	.	C		1233,2471		201,831,820	69.0	67.0	68.0		4848	-10.9	0.3	17	dbSNP_100	68	962,7234		62,838,3198	no	coding-synonymous	MED13	NM_005121.2		263,1669,4018	TT,TC,CC		11.7374,33.2883,18.4454		1616/2175	60040329	2195,9705	1852	4098	5950	SO:0001819	synonymous_variant	9969	exon21			ATCCATCGTGCTA	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.4848G>A	17.37:g.60040329C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_005121	B2RU05|O60334	Silent	SNP	ENST00000397786.2	37	CCDS42366.1																																																																																			C|0.741;T|0.259	0.259	strong		0.398	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
GPRC6A	222545	hgsc.bcm.edu	37	6	117113653	117113653	+	Silent	SNP	T	T	C	rs615199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117113653T>C	ENST00000310357.3	-	6	2454	c.2433A>G	c.(2431-2433)ccA>ccG	p.P811P	GPRC6A_ENST00000368549.3_Silent_p.P740P|GPRC6A_ENST00000530250.1_Silent_p.P636P	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	811					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P811P(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TCTCCACAGCTGGTACATATT	0.343													T|||	1534	0.30631	0.1452	0.3674	5008	,	,		24347	0.5228		0.3082	False		,,,				2504	0.2556				p.P811P		Atlas-SNP	.											GPRC6A,NS,carcinoma,0,1	GPRC6A	152	1	1	Substitution - coding silent(1)	stomach(1)	c.A2433G						PASS	.	T		744,3662	304.1+/-288.3	65,614,1524	79.0	81.0	81.0		2433	-5.8	0.3	6	dbSNP_83	81	2838,5762	446.6+/-361.3	459,1920,1921	no	coding-synonymous	GPRC6A	NM_148963.2		524,2534,3445	CC,CT,TT		33.0,16.8861,27.5411		811/927	117113653	3582,9424	2203	4300	6503	SO:0001819	synonymous_variant	222545	exon6			CACAGCTGGTACA	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2433A>G	6.37:g.117113653T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			C|0.301;N|0.000	0.301	strong		0.343	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
ARHGAP17	55114	hgsc.bcm.edu	37	16	24965975	24965975	+	Silent	SNP	C	C	G	rs111986765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24965975C>G	ENST00000289968.6	-	10	870	c.801G>C	c.(799-801)ctG>ctC	p.L267L	ARHGAP17_ENST00000303665.5_Silent_p.L267L|ARHGAP17_ENST00000575975.1_5'Flank|ARHGAP17_ENST00000441763.2_3'UTR	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	267	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)		CTTCAATGGGCAGCGCAATCT	0.542													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18487	0.0		0.0	False		,,,				2504	0.0				p.L267L		Atlas-SNP	.											.	ARHGAP17	138	.	0			c.G801C						PASS	.	C	,	1,4393	2.1+/-5.4	0,1,2196	138.0	132.0	134.0		801,801	-10.4	0.1	16	dbSNP_132	134	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ARHGAP17	NM_001006634.1,NM_018054.4	,	0,1,6496	GG,GC,CC		0.0,0.0228,0.0077	,	267/882,267/804	24965975	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	55114	exon10			AATGGGCAGCGCA	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.801G>C	16.37:g.24965975C>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Silent	SNP	ENST00000289968.6	37	CCDS32409.1																																																																																			C|0.999;G|0.001	0.001	strong		0.542	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054	
MT-ATP8	4509	hgsc.bcm.edu	37	M	8468	8468	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:8468C>T	ENST00000361851.1	+	1	103	c.103C>T	c.(103-105)Cta>Tta	p.L35L	MT-TS1_ENST00000387416.2_RNA|MT-TN_ENST00000387400.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TY_ENST00000387409.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-ATP6_ENST00000361899.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-ND3_ENST00000361227.2_5'Flank			P03928	ATP8_HUMAN	mitochondrially encoded ATP synthase 8	35					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)										CAAACTACCACCTACCTCCCT	0.393																																					p.L35L		Atlas-SNP	.											.	.	.	.	0			c.C103T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TACCACCTACCTC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000228253	ENSG00000228253		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7415	protein-coding gene	gene with protein product		516070	"""ATP synthase 8"""	MTATP8			Standard			Approved	ATP8, A6L		P03928		ENST00000361851.1:c.103C>T	M.37:g.8468C>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	6	6	1	ENST00000361851	Q34771	Silent	SNP	ENST00000361851.1	37																																																																																				.	.	none		0.393	MT-ATP8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024030	
UQCC1	55245	hgsc.bcm.edu	37	20	33981906	33981906	+	Missense_Mutation	SNP	G	G	C	rs75909303	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33981906G>C	ENST00000374385.5	-	2	295	c.118C>G	c.(118-120)Cgc>Ggc	p.R40G	UQCC1_ENST00000374377.5_Missense_Mutation_p.S20W|UQCC1_ENST00000374384.2_Missense_Mutation_p.R40G|UQCC1_ENST00000397554.1_Missense_Mutation_p.R40G|UQCC1_ENST00000397556.3_5'UTR|UQCC1_ENST00000349714.5_Missense_Mutation_p.R40G|UQCC1_ENST00000407996.2_Missense_Mutation_p.R40G|UQCC1_ENST00000491125.1_5'UTR|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000542501.1_Missense_Mutation_p.R40G|UQCC1_ENST00000359226.2_Missense_Mutation_p.R40G|UQCC1_ENST00000374380.2_Missense_Mutation_p.R40G	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	40						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											TGGGAAGTGCGAGACAGAGCC	0.433													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		19195	0.0		0.0	False		,,,				2504	0.0				p.R40G		Atlas-SNP	.											UQCC,NS,carcinoma,0,1	UQCC	41	1	0			c.C118G						PASS	.	C	GLY/ARG,GLY/ARG,GLY/ARG	95,4311	817.7+/-416.3	2,91,2110	124.0	117.0	120.0		118,118,118	4.8	1.0	20	dbSNP_131	120	0,8600		0,0,4300	yes	missense,missense,missense	UQCC	NM_001184977.1,NM_018244.4,NM_199487.2	125,125,125	2,91,6410	CC,CG,GG		0.0,2.1562,0.7304	benign,benign,benign	40/232,40/300,40/274	33981906	95,12911	2203	4300	6503	SO:0001583	missense	55245	exon2			AAGTGCGAGACAG	AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"""Mitochondrial respiratory chain complex assembly factors"""	15891	protein-coding gene	gene with protein product	"""Basic FGF-repressed Zic-binding protein"", ""cytochrome B protein synthesis 3 homolog (S. cerevisiae)"""	611797	"""chromosome 20 open reading frame 44"", ""ubiquinol-cytochrome c reductase complex chaperone"""	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.118C>G	20.37:g.33981906G>C	ENSP00000363506:p.Arg40Gly	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Missense_Mutation	SNP	ENST00000374385.5	37	CCDS13252.1	8|8	0.003663003663003663|0.003663003663003663	8|8	0.016260162601626018|0.016260162601626018	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	2.061|2.061	-0.415323|-0.415323	0.04766|0.04766	0.021562|0.021562	0.0|0.0	ENSG00000101019|ENSG00000101019	ENST00000349714;ENST00000359226;ENST00000374384;ENST00000374380;ENST00000374385;ENST00000407996;ENST00000424405;ENST00000542501;ENST00000438533;ENST00000397554|ENST00000374377	T;T;T;T;T;T;T;T;T;T|.	0.05382|.	3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45|.	4.76|4.76	4.76|4.76	0.60689|0.60689	.|.	0.246918|.	0.36034|.	N|.	0.002824|.	T|T	0.03959|0.03959	0.0111|0.0111	N|N	0.00182|0.00182	-1.905|-1.905	0.09310|0.09310	N|N	0.999994|0.999994	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0;0.0|.	T|T	0.12863|0.12863	-1.0531|-1.0531	10|6	0.02654|0.87932	T|D	1|0	0.7758|0.7758	11.0424|11.0424	0.47838|0.47838	0.0:0.8127:0.1873:0.0|0.0:0.8127:0.1873:0.0	.|.	40;40;40;40;40|.	B1AKV5;B7Z7J8;B7ZBG3;B7ZBG4;Q9NVA1|.	.;.;.;.;UQCC_HUMAN|.	G|W	40|20	ENSP00000335364:R40G;ENSP00000352161:R40G;ENSP00000363505:R40G;ENSP00000363501:R40G;ENSP00000363506:R40G;ENSP00000386064:R40G;ENSP00000399713:R40G;ENSP00000445059:R40G;ENSP00000398531:R40G;ENSP00000380686:R40G|.	ENSP00000335364:R40G|ENSP00000363497:S20W	R|S	-|-	1|2	0|0	UQCC|UQCC	33445320|33445320	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.857000|0.857000	0.48899|0.48899	1.417000|1.417000	0.34770|0.34770	1.248000|1.248000	0.43934|0.43934	-0.127000|-0.127000	0.14921|0.14921	CGC|TCG	G|0.994;C|0.006	0.006	strong		0.433	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244	
PNPO	55163	hgsc.bcm.edu	37	17	46023295	46023295	+	Silent	SNP	C	C	G	rs35974730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:46023295C>G	ENST00000225573.4	+	5	591	c.486C>G	c.(484-486)ccC>ccG	p.P162P	PNPO_ENST00000434554.2_Intron|PNPO_ENST00000544840.1_Silent_p.P144P|RP11-6N17.6_ENST00000582142.1_RNA|PNPO_ENST00000534893.1_Silent_p.P67P|RP11-6N17.9_ENST00000582262.1_RNA|RP11-6N17.6_ENST00000580372.1_RNA	NM_018129.3	NP_060599.1	Q9NVS9	PNPO_HUMAN	pyridoxamine 5'-phosphate oxidase	162					pyridoxine biosynthetic process (GO:0008615)|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)	FMN binding (GO:0010181)|pyridoxamine-phosphate oxidase activity (GO:0004733)			endometrium(2)|large_intestine(1)|lung(1)|urinary_tract(1)	5						ACTCCCGCCCCAAGAGCAGCC	0.607													C|||	93	0.0185703	0.0681	0.0029	5008	,	,		19973	0.0		0.001	False		,,,				2504	0.0				p.P162P		Atlas-SNP	.											.	PNPO	18	.	0			c.C486G						PASS	.	C		274,4132	155.9+/-189.0	10,254,1939	70.0	69.0	69.0		486	2.1	1.0	17	dbSNP_126	69	14,8586	9.1+/-34.3	0,14,4286	yes	coding-synonymous	PNPO	NM_018129.3		10,268,6225	GG,GC,CC		0.1628,6.2188,2.2144		162/262	46023295	288,12718	2203	4300	6503	SO:0001819	synonymous_variant	55163	exon5			CCGCCCCAAGAGC	AF468030	CCDS11522.1	17q21.32	2008-11-27	2006-07-12			ENSG00000108439	1.4.3.5		30260	protein-coding gene	gene with protein product		603287	"""pyridoxine 5'-phosphate oxidase"""			9601034, 15182361	Standard	NM_018129		Approved	PDXPO	uc002imo.3	Q9NVS9		ENST00000225573.4:c.486C>G	17.37:g.46023295C>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_018129	B4E0V0|B4E152|B4E1D7|D3DTT9	Silent	SNP	ENST00000225573.4	37	CCDS11522.1																																																																																			C|0.980;G|0.020	0.020	strong		0.607	PNPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441407.1	NM_018129	
OR2T4	127074	hgsc.bcm.edu	37	1	248525657	248525657	+	Missense_Mutation	SNP	G	G	A	rs28718027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248525657G>A	ENST00000366475.1	+	1	775	c.775G>A	c.(775-777)Ggg>Agg	p.G259R		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACCATCCACGGGATGAACTC	0.507													a|||	1476	0.294728	0.2405	0.2709	5008	,	,		21255	0.4296		0.1799	False		,,,				2504	0.364				p.G259R		Atlas-SNP	.											OR2T4,right_upper_lobe,carcinoma,-1,1	OR2T4	126	1	0			c.G775A						scavenged	.	A	ARG/GLY	1056,3350	722.6+/-409.3	140,776,1287	128.0	126.0	127.0		775	0.2	0.8	1	dbSNP_125	127	1386,7214	752.1+/-407.4	111,1164,3025	no	missense	OR2T4	NM_001004696.1	125	251,1940,4312	AA,AG,GG		16.1163,23.9673,18.7759	benign	259/349	248525657	2442,10564	2203	4300	6503	SO:0001583	missense	127074	exon1			ATCCACGGGATGA	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.775G>A	1.37:g.248525657G>A	ENSP00000355431:p.Gly259Arg	Somatic	902	2	0.00221729		WXS	Illumina HiSeq	Phase_I	927	457	0.492988	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	539	0.2467948717948718	113	0.22967479674796748	73	0.20165745856353592	221	0.38636363636363635	132	0.1741424802110818	A	0.003	-2.467723	0.00169	0.239673	0.161163	ENSG00000196944	ENST00000366475	T	0.00019	9.06	3.09	0.223	0.15292	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	N	0.000181	T	0.00012	0.0000	N	0.00101	-2.135	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38436	-0.9661	9	0.02654	T	1	.	5.6019	0.17359	0.5788:0.3259:0.0954:0.0	rs28718027	259	Q8NH00	OR2T4_HUMAN	R	259	ENSP00000355431:G259R	ENSP00000355431:G259R	G	+	1	0	OR2T4	246592280	0.000000	0.05858	0.777000	0.31699	0.114000	0.19823	0.443000	0.21644	-0.098000	0.12285	-0.340000	0.08031	GGG	G|0.795;A|0.205	0.205	strong		0.507	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
TNC	3371	hgsc.bcm.edu	37	9	117810651	117810651	+	Silent	SNP	G	G	A	rs146504512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117810651G>A	ENST00000350763.4	-	16	5151	c.4740C>T	c.(4738-4740)acC>acT	p.T1580T	TNC_ENST00000341037.4_Intron|TNC_ENST00000535648.1_Intron|TNC_ENST00000542877.1_Intron|TNC_ENST00000340094.3_Silent_p.T1216T|TNC_ENST00000537320.1_Intron|TNC_ENST00000423613.2_Intron|TNC_ENST00000481475.1_5'UTR|TNC_ENST00000346706.3_Intron|TNC_ENST00000345230.3_Intron	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1580	Fibronectin type-III 11. {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						GCTTCCTCTGGGTTCCTGAAA	0.527													G|||	26	0.00519169	0.0144	0.0072	5008	,	,		18220	0.0		0.001	False		,,,				2504	0.001				p.T1580T		Atlas-SNP	.											.	TNC	282	.	0			c.C4740T						PASS	.	G		39,4367	43.8+/-77.6	0,39,2164	89.0	82.0	84.0		4740	3.1	1.0	9	dbSNP_134	84	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	TNC	NM_002160.3		0,47,6456	AA,AG,GG		0.093,0.8852,0.3614		1580/2202	117810651	47,12959	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon16			CCTCTGGGTTCCT		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.4740C>T	9.37:g.117810651G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																			G|0.996;A|0.004	0.004	strong		0.527	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
IRAK3	11213	hgsc.bcm.edu	37	12	66641813	66641813	+	Silent	SNP	C	C	T	rs11465988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:66641813C>T	ENST00000261233.4	+	12	2074	c.1653C>T	c.(1651-1653)tcC>tcT	p.S551S	IRAK3_ENST00000457197.2_Silent_p.S490S	NM_007199.2	NP_009130.2			interleukin-1 receptor-associated kinase 3											breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(28;0.0203)		TAGTTCCATCCCAGGACTTAA	0.463													C|||	187	0.0373403	0.118	0.0288	5008	,	,		18571	0.001		0.0089	False		,,,				2504	0.001				p.S551S		Atlas-SNP	.											.	IRAK3	75	.	0			c.C1653T						PASS	.	C	,	402,4004	199.8+/-223.2	23,356,1824	121.0	131.0	127.0		1470,1653	2.7	0.6	12	dbSNP_120	127	26,8574	17.3+/-56.4	0,26,4274	no	coding-synonymous,coding-synonymous	IRAK3	NM_001142523.1,NM_007199.2	,	23,382,6098	TT,TC,CC		0.3023,9.1239,3.2908	,	490/536,551/597	66641813	428,12578	2203	4300	6503	SO:0001819	synonymous_variant	11213	exon12			TCCATCCCAGGAC	AF113136	CCDS8975.1, CCDS44937.1	12q13.13	2008-05-02			ENSG00000090376	ENSG00000090376			17020	protein-coding gene	gene with protein product		604459				10383454	Standard	NM_001142523		Approved	IRAK-M	uc001sth.3	Q9Y616	OTTHUMG00000169002	ENST00000261233.4:c.1653C>T	12.37:g.66641813C>T		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_007199		Silent	SNP	ENST00000261233.4	37	CCDS8975.1																																																																																			C|0.968;T|0.032	0.032	strong		0.463	IRAK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401908.1		
AQP8	343	hgsc.bcm.edu	37	16	25228566	25228566	+	Silent	SNP	G	G	A	rs139992979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:25228566G>A	ENST00000219660.5	+	2	185	c.60G>A	c.(58-60)ccG>ccA	p.P20P	AQP8_ENST00000566125.1_Silent_p.P14P	NM_001169.2	NP_001160.2	O94778	AQP8_HUMAN	aquaporin 8	20					canalicular bile acid transport (GO:0015722)|cellular response to cAMP (GO:0071320)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)			NS(1)|breast(1)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	16				GBM - Glioblastoma multiforme(48;0.044)		CCAGGGAGCCGAGCGTGGGTG	0.577													G|||	50	0.00998403	0.031	0.0115	5008	,	,		18800	0.0		0.001	False		,,,				2504	0.0				p.P20P		Atlas-SNP	.											.	AQP8	75	.	0			c.G60A						PASS	.	G		105,4289	82.4+/-120.9	2,101,2094	190.0	187.0	188.0		60	-9.9	0.0	16	dbSNP_134	188	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	AQP8	NM_001169.2		2,106,6389	AA,AG,GG		0.0581,2.3896,0.8465		20/262	25228566	110,12884	2197	4300	6497	SO:0001819	synonymous_variant	343	exon2			GGAGCCGAGCGTG	BC040630	CCDS10626.1	16p12	2008-02-05			ENSG00000103375	ENSG00000103375		"""Ion channels / Aquaporins"""	642	protein-coding gene	gene with protein product		603750				9806845, 10393433	Standard	NM_001169		Approved		uc002doc.3	O94778	OTTHUMG00000097013	ENST00000219660.5:c.60G>A	16.37:g.25228566G>A		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	238	111	0.466387	NM_001169	Q8IUU3|Q9UIA4	Silent	SNP	ENST00000219660.5	37	CCDS10626.1																																																																																			G|0.993;A|0.007	0.007	strong		0.577	AQP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214102.2	NM_001169	
OR3A2	4995	hgsc.bcm.edu	37	17	3181677	3181677	+	Missense_Mutation	SNP	G	G	C	rs73977611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3181677G>C	ENST00000408891.2	-	1	591	c.553C>G	c.(553-555)Cac>Gac	p.H185D	RP11-64J4.2_ENST00000573491.1_RNA	NM_002551.3	NP_002542.3	P47893	OR3A2_HUMAN	olfactory receptor, family 3, subfamily A, member 2	185					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			ovary(1)	1						CAGTAGAAGTGATTGACCTCA	0.562													G|||	81	0.0161741	0.0575	0.0072	5008	,	,		21392	0.0		0.0	False		,,,				2504	0.0				p.H185D	GBM(166;478 2018 3875 5042 31983)|Esophageal Squamous(77;407 1232 1405 14297 15272)	Atlas-SNP	.											.	OR3A2	36	.	0			c.C553G						PASS	.	G	ASP/HIS	188,4216	120.8+/-158.4	4,180,2018	71.0	59.0	63.0		553	2.8	1.0	17	dbSNP_130	63	1,8559		0,1,4279	no	missense	OR3A2	NM_002551.3	81	4,181,6297	CC,CG,GG		0.0117,4.2688,1.4579	probably-damaging	185/322	3181677	189,12775	2202	4280	6482	SO:0001583	missense	4995	exon1			AGAAGTGATTGAC	U04713	CCDS42233.1	17p13.3	2012-08-09				ENSG00000221882		"""GPCR / Class A : Olfactory receptors"""	8283	protein-coding gene	gene with protein product						8921386, 10673334	Standard	NM_002551		Approved	OLFRA04, OR228, OR17-228	uc002fvg.3	P47893		ENST00000408891.2:c.553C>G	17.37:g.3181677G>C	ENSP00000386180:p.His185Asp	Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	295	140	0.474576	NM_002551	Q6IFM3|Q9P1Q3	Missense_Mutation	SNP	ENST00000408891.2	37	CCDS42233.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	G	15.06	2.721441	0.48728	0.042688	1.17E-4	ENSG00000221882	ENST00000408891	T	0.00174	8.62	4.9	2.85	0.33270	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000069	T	0.00144	0.0004	M	0.90425	3.115	0.31106	N	0.710527	D	0.59357	0.985	D	0.68039	0.955	T	0.03335	-1.1047	10	0.87932	D	0	-23.7752	13.1298	0.59375	0.0:0.0:0.7099:0.2901	.	185	P47893	OR3A2_HUMAN	D	185	ENSP00000386180:H185D	ENSP00000386180:H185D	H	-	1	0	OR3A2	3128427	0.630000	0.27155	0.983000	0.44433	0.377000	0.30045	1.081000	0.30791	0.745000	0.32763	0.561000	0.74099	CAC	G|0.991;C|0.009	0.009	strong		0.562	OR3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438370.1		
PODXL	5420	hgsc.bcm.edu	37	7	131190696	131190696	+	Silent	SNP	T	T	C	rs6651125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:131190696T>C	ENST00000378555.3	-	8	1657	c.1410A>G	c.(1408-1410)gcA>gcG	p.A470A	PODXL_ENST00000537928.1_Silent_p.A438A|PODXL_ENST00000541194.1_Silent_p.A472A|PODXL_ENST00000322985.9_Silent_p.A438A			O00592	PODXL_HUMAN	podocalyxin-like	470					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					GCAGGAATGATGCCATGCAGA	0.627													C|||	1787	0.356829	0.3661	0.4207	5008	,	,		16011	0.3026		0.3877	False		,,,				2504	0.3231				p.A470A		Atlas-SNP	.											.	PODXL	53	.	0			c.A1410G						PASS	.	C	,	1476,2930		247,982,974	45.0	37.0	40.0		1410,1314	-10.4	0.0	7	dbSNP_116	40	3025,5575		529,1967,1804	no	coding-synonymous,coding-synonymous	PODXL	NM_001018111.2,NM_005397.3	,	776,2949,2778	CC,CT,TT		35.1744,33.4998,34.6071	,	470/559,438/527	131190696	4501,8505	2203	4300	6503	SO:0001819	synonymous_variant	5420	exon8			GAATGATGCCATG		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.1410A>G	7.37:g.131190696T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	37	CCDS34755.1																																																																																			T|0.657;C|0.343	0.343	strong		0.627	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
KCNG4	93107	hgsc.bcm.edu	37	16	84256410	84256410	+	Missense_Mutation	SNP	C	C	T	rs7196482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84256410C>T	ENST00000308251.4	-	3	1041	c.973G>A	c.(973-975)Ggg>Agg	p.G325R		NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	325			G -> R (in dbSNP:rs7196482).		protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						TAGGAGCTCCCGCTCGGCCTC	0.677													C|||	885	0.176717	0.2156	0.1686	5008	,	,		17359	0.0506		0.2266	False		,,,				2504	0.2086				p.G325R		Atlas-SNP	.											.	KCNG4	71	.	0			c.G973A						PASS	.	C	ARG/GLY	942,3458	340.2+/-306.1	109,724,1367	30.0	33.0	32.0		973	-2.7	0.0	16	dbSNP_116	32	1922,6678	321.7+/-315.2	212,1498,2590	no	missense	KCNG4	NM_172347.2	125	321,2222,3957	TT,TC,CC		22.3488,21.4091,22.0308	probably-damaging	325/520	84256410	2864,10136	2200	4300	6500	SO:0001583	missense	93107	exon3			AGCTCCCGCTCGG	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.973G>A	16.37:g.84256410C>T	ENSP00000312129:p.Gly325Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	369	0.16895604395604397	101	0.20528455284552846	63	0.17403314917127072	26	0.045454545454545456	179	0.23614775725593667	C	8.185	0.794792	0.16327	0.214091	0.223488	ENSG00000168418	ENST00000308251	D	0.97041	-4.22	5.61	-2.74	0.05932	Ion transport (1);	0.310951	0.34268	N	0.004108	T	0.00552	0.0018	M	0.75085	2.285	0.58432	P	6.999999999979245E-6	D	0.56521	0.976	P	0.51516	0.672	T	0.50642	-0.8804	9	0.72032	D	0.01	.	8.1708	0.31254	0.0:0.3567:0.1088:0.5345	rs7196482;rs59048729;rs7196482	325	Q8TDN1	KCNG4_HUMAN	R	325	ENSP00000312129:G325R	ENSP00000312129:G325R	G	-	1	0	KCNG4	82813911	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.117000	0.10708	-0.433000	0.07286	0.655000	0.94253	GGG	C|0.810;T|0.190	0.190	strong		0.677	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
MAT1A	4143	hgsc.bcm.edu	37	10	82040052	82040052	+	Silent	SNP	A	A	G	rs1143694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:82040052A>G	ENST00000372213.3	-	5	686	c.426T>C	c.(424-426)gcT>gcC	p.A142A		NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	142					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	TCTCGTCGGTAGCATAGCCGA	0.627													G|||	4324	0.863419	0.9743	0.7968	5008	,	,		17860	0.9722		0.669	False		,,,				2504	0.8487				p.A142A		Atlas-SNP	.											.	MAT1A	52	.	0			c.T426C						PASS	.	G		4058,348	181.5+/-209.5	1870,318,15	72.0	71.0	71.0		426	2.2	0.9	10	dbSNP_86	71	5676,2924	456.3+/-364.0	1904,1868,528	no	coding-synonymous	MAT1A	NM_000429.2		3774,2186,543	GG,GA,AA		34.0,7.8983,25.1576		142/396	82040052	9734,3272	2203	4300	6503	SO:0001819	synonymous_variant	4143	exon5			GTCGGTAGCATAG		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"""S-adenosylmethionine synthetase"""	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.426T>C	10.37:g.82040052A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_000429	D3DWD5|Q5QP09	Silent	SNP	ENST00000372213.3	37	CCDS7365.1																																																																																			A|0.209;G|0.791	0.791	strong		0.627	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429	
SOCS6	9306	hgsc.bcm.edu	37	18	67992279	67992279	+	Silent	SNP	G	G	A	rs2231562	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:67992279G>A	ENST00000397942.3	+	2	691	c.375G>A	c.(373-375)acG>acA	p.T125T	SOCS6_ENST00000582322.1_Silent_p.T125T	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	125					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				TAAGGTCCACGTCGCTCCGCA	0.607													C|||	497	0.0992412	0.0862	0.0922	5008	,	,		17508	0.0833		0.163	False		,,,				2504	0.0726				p.T125T	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-SNP	.											.	SOCS6	54	.	0			c.G375A						PASS	.	C		339,4067		10,319,1874	37.0	39.0	38.0		375	-10.2	0.0	18	dbSNP_98	38	1321,7273		102,1117,3078	no	coding-synonymous	SOCS6	NM_004232.3		112,1436,4952	AA,AG,GG		15.3712,7.6941,12.7692		125/536	67992279	1660,11340	2203	4297	6500	SO:0001819	synonymous_variant	9306	exon2			GTCCACGTCGCTC	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	16833	protein-coding gene	gene with protein product		605118	"""suppressor of cytokine signaling 4"""	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.375G>A	18.37:g.67992279G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	16	0.280702	NM_004232	Q8WUM3	Silent	SNP	ENST00000397942.3	37	CCDS11998.1																																																																																			G|0.878;A|0.122	0.122	strong		0.607	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2		
SLC26A11	284129	hgsc.bcm.edu	37	17	78199666	78199666	+	Missense_Mutation	SNP	C	C	G	rs115961261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78199666C>G	ENST00000361193.3	+	6	824	c.544C>G	c.(544-546)Ccg>Gcg	p.P182A	SLC26A11_ENST00000572725.1_Missense_Mutation_p.P182A|SLC26A11_ENST00000411502.3_Missense_Mutation_p.P182A|SLC26A11_ENST00000546047.2_Missense_Mutation_p.P182A	NM_001166347.1|NM_173626.3	NP_001159819.1|NP_775897.3			solute carrier family 26 (anion exchanger), member 11											central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	28	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CATCCCCAGGCCGTTCTTCCT	0.562													C|||	44	0.00878594	0.0333	0.0	5008	,	,		16297	0.0		0.0	False		,,,				2504	0.0				p.P182A		Atlas-SNP	.											SLC26A11,NS,carcinoma,-1,2	SLC26A11	60	2	0			c.C544G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	141,4265	101.6+/-140.2	5,131,2067	200.0	158.0	173.0		544,544,544,544	4.1	1.0	17	dbSNP_132	173	0,8600		0,0,4300	yes	missense,missense,missense,missense	SLC26A11	NM_001166347.1,NM_001166348.1,NM_001166349.1,NM_173626.3	27,27,27,27	5,131,6367	GG,GC,CC		0.0,3.2002,1.0841	benign,benign,benign,benign	182/607,182/607,182/607,182/607	78199666	141,12865	2203	4300	6503	SO:0001583	missense	284129	exon6			CCCAGGCCGTTCT		CCDS11771.2	17q25	2013-07-18	2013-07-18		ENSG00000181045	ENSG00000181045		"""Solute carriers"""	14471	protein-coding gene	gene with protein product		610117	"""solute carrier family 26, member 11"""				Standard	NM_001166347		Approved		uc010dhv.2	Q86WA9	OTTHUMG00000133419	ENST00000361193.3:c.544C>G	17.37:g.78199666C>G	ENSP00000355384:p.Pro182Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_173626		Missense_Mutation	SNP	ENST00000361193.3	37	CCDS11771.2	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	9.192	1.026307	0.19512	0.032002	0.0	ENSG00000181045	ENST00000411502;ENST00000546047;ENST00000361193	D;D;D	0.92647	-3.08;-3.08;-3.08	4.09	4.09	0.47781	Sulphate transporter (1);	0.424346	0.25997	N	0.026961	T	0.70413	0.3221	N	0.25286	0.73	0.24628	N	0.993634	B	0.22080	0.064	B	0.27170	0.077	T	0.66015	-0.6028	10	0.20519	T	0.43	-11.6618	12.7028	0.57043	0.0:0.8328:0.1672:0.0	.	182	Q86WA9	S2611_HUMAN	A	182	ENSP00000403998:P182A;ENSP00000440724:P182A;ENSP00000355384:P182A	ENSP00000355384:P182A	P	+	1	0	SLC26A11	75814261	0.998000	0.40836	0.970000	0.41538	0.955000	0.61496	3.003000	0.49505	1.811000	0.52892	0.467000	0.42956	CCG	C|0.990;G|0.010	0.010	strong		0.562	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1		
BUB1B	701	hgsc.bcm.edu	37	15	40498503	40498503	+	Missense_Mutation	SNP	T	T	C	rs1801528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40498503T>C	ENST00000287598.6	+	15	2048	c.1853T>C	c.(1852-1854)gTa>gCa	p.V618A	BUB1B_ENST00000412359.3_Missense_Mutation_p.V632A	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	618			V -> A (in colorectal cancer; dbSNP:rs1801528). {ECO:0000269|PubMed:10366450, ECO:0000269|PubMed:17344846}.		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)		GCTCGTTTTGTATCCACTCCT	0.448			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				T|||	465	0.0928514	0.3389	0.0245	5008	,	,		19876	0.0		0.0	False		,,,				2504	0.0				p.V618A		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	BUB1B,NS,carcinoma,+1,1	BUB1B	71	1	0			c.T1853C						PASS	.	T	ALA/VAL	1117,3289	402.2+/-332.3	135,847,1221	95.0	96.0	96.0		1853	-0.5	1.0	15	dbSNP_89	96	18,8582	13.3+/-46.6	0,18,4282	yes	missense	BUB1B	NM_001211.5	64	135,865,5503	CC,CT,TT		0.2093,25.3518,8.7267	benign	618/1051	40498503	1135,11871	2203	4300	6503	SO:0001583	missense	701	exon15	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GTTTTGTATCCAC	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.1853T>C	15.37:g.40498503T>C	ENSP00000287598:p.Val618Ala	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	176	86	0.488636	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Missense_Mutation	SNP	ENST00000287598.6	37	CCDS10053.1	179	0.08195970695970696	169	0.3434959349593496	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	T	5.086	0.201529	0.09652	0.253518	0.002093	ENSG00000156970	ENST00000287598;ENST00000412359	T;T	0.11277	2.79;2.8	5.51	-0.494	0.12034	.	0.391035	0.23252	N	0.050240	T	0.00012	0.0000	N	0.01874	-0.695	0.44409	P	0.0026760000000000117	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48490	-0.9031	9	0.02654	T	1	-0.8963	13.1761	0.59629	0.0:0.7666:0.0:0.2334	rs1801528;rs52836029	632;618	O60566-3;O60566	.;BUB1B_HUMAN	A	618;632	ENSP00000287598:V618A;ENSP00000398470:V632A	ENSP00000287598:V618A	V	+	2	0	BUB1B	38285795	0.999000	0.42202	0.961000	0.40146	0.990000	0.78478	0.726000	0.25984	-0.099000	0.12263	0.482000	0.46254	GTA	T|0.917;C|0.083	0.083	strong		0.448	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
MTFR2	113115	hgsc.bcm.edu	37	6	136570221	136570221	+	Missense_Mutation	SNP	T	T	C	rs147085272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:136570221T>C	ENST00000420702.1	-	2	406	c.17A>G	c.(16-18)aAt>aGt	p.N6S	MTFR2_ENST00000451457.2_Missense_Mutation_p.N6S|MTFR2_ENST00000445767.2_5'UTR	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	6					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											TCTTAAGATATTCAGTATGAG	0.358													T|||	49	0.00978435	0.0356	0.0029	5008	,	,		19511	0.0		0.0	False		,,,				2504	0.0				p.N6S		Atlas-SNP	.											.	.	.	.	0			c.A17G						PASS	.	T	SER/ASN,SER/ASN	124,4282	91.6+/-130.3	5,114,2084	81.0	76.0	78.0		17,17	1.0	0.1	6	dbSNP_134	78	0,8600		0,0,4300	yes	missense,missense	FAM54A	NM_001099286.1,NM_138419.3	46,46	5,114,6384	CC,CT,TT		0.0,2.8143,0.9534	benign,benign	6/386,6/386	136570221	124,12882	2203	4300	6503	SO:0001583	missense	113115	exon2			AAGATATTCAGTA	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"""DUF729 domain containing 1"", ""family with sequence similarity 54, member A"""	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.17A>G	6.37:g.136570221T>C	ENSP00000395232:p.Asn6Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	42	16	0.380952	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Missense_Mutation	SNP	ENST00000420702.1	37	CCDS5176.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	T	12.20	1.867291	0.32977	0.028143	0.0	ENSG00000146410	ENST00000451457;ENST00000420702	T;T	0.42900	0.96;0.96	4.85	0.955	0.19602	.	0.442859	0.25285	N	0.031765	T	0.11793	0.0287	L	0.36672	1.1	0.25226	N	0.989865	B	0.14438	0.01	B	0.12156	0.007	T	0.23226	-1.0194	10	0.87932	D	0	-9.0671	3.8762	0.09058	0.0:0.2276:0.1828:0.5896	.	6	Q6P444	FA54A_HUMAN	S	6	ENSP00000407010:N6S;ENSP00000395232:N6S	ENSP00000356758:N6S	N	-	2	0	FAM54A	136611914	0.991000	0.36638	0.053000	0.19242	0.995000	0.86356	0.177000	0.16801	-0.006000	0.14370	0.482000	0.46254	AAT	T|0.988;C|0.012	0.012	strong		0.358	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419	
CDK7	1022	hgsc.bcm.edu	37	5	68531253	68531253	+	Silent	SNP	C	C	T	rs2972388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68531253C>T	ENST00000256443.3	+	2	202	c.99C>T	c.(97-99)aaC>aaT	p.N33N	CDK7_ENST00000513629.1_3'UTR|CDK7_ENST00000502604.1_5'UTR|CDK7_ENST00000514676.1_Silent_p.N33N	NM_001799.3	NP_001790.1	P50613	CDK7_HUMAN	cyclin-dependent kinase 7	33	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				7-methylguanosine mRNA capping (GO:0006370)|androgen receptor signaling pathway (GO:0030521)|ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|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)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|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)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|DNA-dependent ATPase activity (GO:0008094)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription coactivator activity (GO:0003713)			endometrium(1)|lung(2)	3		Lung NSC(167;7.26e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.98e-56)|Epithelial(20;3.54e-52)|all cancers(19;9.11e-48)|Lung(70;0.0185)		GAGATAAGAACACCAACCAAA	0.323								Nucleotide excision repair (NER)					T|||	3154	0.629792	0.7693	0.6427	5008	,	,		20512	0.499		0.5427	False		,,,				2504	0.6564				p.N33N		Atlas-SNP	.											.	CDK7	48	.	0			c.C99T						PASS	.	T		3116,1290	438.2+/-345.2	1097,922,184	135.0	148.0	143.0		99	4.0	1.0	5	dbSNP_101	143	4639,3961	551.9+/-386.0	1273,2093,934	no	coding-synonymous	CDK7	NM_001799.3		2370,3015,1118	TT,TC,CC		46.0581,29.2783,40.3737		33/347	68531253	7755,5251	2203	4300	6503	SO:0001819	synonymous_variant	1022	exon2			TAAGAACACCAAC		CCDS3999.1	5q12.1	2012-11-05	2007-11-21		ENSG00000134058	ENSG00000134058		"""Cyclin-dependent kinases"", ""General transcription factor IIH complex subunits"""	1778	protein-coding gene	gene with protein product		601955	"""cyclin-dependent kinase 7 (homolog of Xenopus MO15 cdk-activating kinase)"", ""cyclin-dependent kinase 7 (MO15 homolog, Xenopus laevis, cdk-activating kinase)"""			8069918	Standard	NM_001799		Approved	CAK1, CDKN7, MO15, STK1, CAK	uc003jvs.4	P50613	OTTHUMG00000099358	ENST00000256443.3:c.99C>T	5.37:g.68531253C>T		Somatic	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	311	310	0.996785	NM_001799	Q9BS60|Q9UE19	Silent	SNP	ENST00000256443.3	37	CCDS3999.1																																																																																			C|0.407;T|0.593	0.593	strong		0.323	CDK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216802.3	NM_001799	
CMYA5	202333	hgsc.bcm.edu	37	5	79025317	79025317	+	Silent	SNP	A	A	G	rs1366270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79025317A>G	ENST00000446378.2	+	2	760	c.729A>G	c.(727-729)caA>caG	p.Q243Q		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	243					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)		TTCCTCTACAATTTTATGGAA	0.318													A|||	1389	0.277356	0.5961	0.085	5008	,	,		18869	0.3621		0.0815	False		,,,				2504	0.0971				p.Q243Q		Atlas-SNP	.											.	CMYA5	643	.	0			c.A729G						PASS	.	A		1856,1772		487,882,445	42.0	42.0	42.0		729	-4.5	0.6	5	dbSNP_88	42	710,7430		39,632,3399	no	coding-synonymous	CMYA5	NM_153610.3		526,1514,3844	GG,GA,AA		8.7224,48.8423,21.8049		243/4070	79025317	2566,9202	1814	4070	5884	SO:0001819	synonymous_variant	202333	exon2			TCTACAATTTTAT	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.729A>G	5.37:g.79025317A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	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|0.700;G|0.300	0.300	strong		0.318	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
NWD1	284434	hgsc.bcm.edu	37	19	16860087	16860087	+	Missense_Mutation	SNP	G	G	A	rs61750949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860087G>A	ENST00000552788.1	+	4	634	c.634G>A	c.(634-636)Gcg>Acg	p.A212T	NWD1_ENST00000379808.3_Missense_Mutation_p.A212T|NWD1_ENST00000339803.6_Missense_Mutation_p.A77T|NWD1_ENST00000549814.1_Missense_Mutation_p.A212T|NWD1_ENST00000524140.2_Missense_Mutation_p.A212T|NWD1_ENST00000523826.1_Missense_Mutation_p.A6T			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	212							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GGACCGGCTCGCGGATGGCTG	0.592													G|||	120	0.0239617	0.0825	0.0101	5008	,	,		16617	0.0		0.001	False		,,,				2504	0.0031				p.A212T		Atlas-SNP	.											.	NWD1	303	.	0			c.G634A						PASS	.						74.0	56.0	62.0					19																	16860087		2203	4300	6503	SO:0001583	missense	284434	exon6			CGGCTCGCGGATG	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.634G>A	19.37:g.16860087G>A	ENSP00000447224:p.Ala212Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		49	0.022435897435897436	42	0.08536585365853659	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	g	5.285	0.237974	0.10023	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.58940	1.72;1.72;1.72;0.3;1.72;0.44	4.52	-3.02	0.05446	.	0.678723	0.14068	N	0.343619	T	0.01287	0.0042	N	0.24115	0.695	0.09310	N	1	P;P;P	0.48230	0.716;0.907;0.85	B;B;B	0.31495	0.041;0.131;0.062	T	0.04946	-1.0916	10	0.17832	T	0.49	-0.4805	16.5319	0.84362	0.0:0.7256:0.2744:0.0	rs61750949	212;212;77	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	T	77;212;212;212;6;212;77	ENSP00000428579:A212T;ENSP00000447548:A212T;ENSP00000369136:A212T;ENSP00000428955:A6T;ENSP00000447224:A212T;ENSP00000340159:A77T	ENSP00000340159:A77T	A	+	1	0	NWD1	16721087	0.000000	0.05858	0.005000	0.12908	0.210000	0.24377	0.594000	0.24014	-0.722000	0.04922	-0.337000	0.08149	GCG	G|0.983;A|0.017	0.017	strong		0.592	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
DNAH10	196385	hgsc.bcm.edu	37	12	124360032	124360032	+	Silent	SNP	C	C	T	rs11834289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124360032C>T	ENST00000409039.3	+	46	7864	c.7839C>T	c.(7837-7839)caC>caT	p.H2613H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2613	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)		TGAAAGGCCACACCTCGGTAA	0.438													T|||	462	0.0922524	0.2806	0.0418	5008	,	,		17889	0.0506		0.0089	False		,,,				2504	0.002				p.H2613H		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7839T						PASS	.	T		909,2825		110,689,1068	108.0	100.0	103.0		7839	-6.8	0.4	12	dbSNP_120	103	88,8104		1,86,4009	no	coding-synonymous	DNAH10	NM_207437.3		111,775,5077	TT,TC,CC		1.0742,24.3439,8.3599		2613/4472	124360032	997,10929	1867	4096	5963	SO:0001819	synonymous_variant	196385	exon46			AGGCCACACCTCG	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.7839C>T	12.37:g.124360032C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.924;T|0.076	0.076	strong		0.438	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
CRISP2	7180	hgsc.bcm.edu	37	6	49666100	49666100	+	Missense_Mutation	SNP	T	T	C	rs34457011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49666100T>C	ENST00000339139.4	-	7	628	c.392A>G	c.(391-393)aAt>aGt	p.N131S		NM_001142407.2|NM_001142408.2|NM_001142417.2|NM_001142435.2|NM_001261822.1|NM_003296.3	NP_001135879.1|NP_001135880.1|NP_001135889.1|NP_001135907.1|NP_001248751.1|NP_003287.1	P16562	CRIS2_HUMAN	cysteine-rich secretory protein 2	131	SCP.		N -> S (in dbSNP:rs34457011).		single organismal cell-cell adhesion (GO:0016337)	extracellular space (GO:0005615)				kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	19	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			AACAACTGCATTGGGACTCTT	0.408													T|||	35	0.00698882	0.0257	0.0014	5008	,	,		19608	0.0		0.0	False		,,,				2504	0.0				p.N131S		Atlas-SNP	.											.	CRISP2	53	.	0			c.A392G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	102,4304	82.4+/-120.9	2,98,2103	124.0	114.0	117.0		392,392,392,392,392	-1.4	0.0	6	dbSNP_126	117	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	CRISP2	NM_001142407.1,NM_001142408.1,NM_001142417.1,NM_001142435.1,NM_003296.2	46,46,46,46,46	2,98,6403	CC,CT,TT		0.0,2.315,0.7843	benign,benign,benign,benign,benign	131/244,131/244,131/244,131/244,131/244	49666100	102,12904	2203	4300	6503	SO:0001583	missense	7180	exon7			ACTGCATTGGGAC	X95239	CCDS4928.1	6p12.3	2009-03-12	2003-09-03	2003-09-05	ENSG00000124490	ENSG00000124490			12024	protein-coding gene	gene with protein product	"""cancer/testis antigen 36"""	187430	"""testis specific protein 1 (probe H4-1 p3-1)"""	GAPDL5, TPX1		2613236, 8665901	Standard	NM_003296		Approved	CRISP-2, CT36	uc003ozo.3	P16562	OTTHUMG00000014822	ENST00000339139.4:c.392A>G	6.37:g.49666100T>C	ENSP00000339155:p.Asn131Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	NM_001142408	A8K8M0|Q53FF2|Q5U8Z9|Q7Z7B2	Missense_Mutation	SNP	ENST00000339139.4	37	CCDS4928.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	T	9.996	1.232230	0.22626	0.02315	0.0	ENSG00000124490	ENST00000339139;ENST00000211238	T	0.09630	2.96	5.26	-1.44	0.08856	CAP domain (3);	0.986209	0.08313	N	0.965097	T	0.02230	0.0069	L	0.33189	0.99	0.09310	N	1	B;B	0.20052	0.02;0.041	B;B	0.22152	0.038;0.038	T	0.47598	-0.9105	10	0.33940	T	0.23	.	5.0274	0.14393	0.0:0.3052:0.282:0.4128	rs34457011	131;131	Q7Z7B2;P16562	.;CRIS2_HUMAN	S	131	ENSP00000339155:N131S	ENSP00000211238:N131S	N	-	2	0	CRISP2	49774059	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.986000	0.03747	-0.396000	0.07703	-0.379000	0.06801	AAT	T|0.991;C|0.009	0.009	strong		0.408	CRISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040870.2	NM_003296	
DQX1	165545	hgsc.bcm.edu	37	2	74746322	74746322	+	Silent	SNP	A	A	T	rs6546909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74746322A>T	ENST00000404568.3	-	11	2061	c.1842T>A	c.(1840-1842)ctT>ctA	p.L614L	DQX1_ENST00000393951.2_Silent_p.L614L	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	614						nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						GGGTTAGGAGAAGGTAATTTC	0.493													T|||	2620	0.523163	0.8101	0.3213	5008	,	,		19600	0.8185		0.16	False		,,,				2504	0.3476				p.L614L		Atlas-SNP	.											.	DQX1	95	.	0			c.T1842A						PASS	.	T		3057,1349	447.7+/-348.4	1084,889,230	88.0	93.0	91.0		1842	2.6	0.9	2	dbSNP_116	91	1324,7276	758.0+/-407.5	109,1106,3085	no	coding-synonymous	DQX1	NM_133637.2		1193,1995,3315	TT,TA,AA		15.3953,30.6173,33.6845		614/718	74746322	4381,8625	2203	4300	6503	SO:0001819	synonymous_variant	165545	exon11			TAGGAGAAGGTAA	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"""DEAQ box polypeptide 1 (RNA-dependent ATPase)"""				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.1842T>A	2.37:g.74746322A>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	148	147	0.993243	NM_133637	Q6B017|Q8NAM8	Silent	SNP	ENST00000404568.3	37	CCDS1949.2																																																																																			A|0.580;T|0.420	0.420	strong		0.493	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415299	105415299	+	Silent	SNP	A	A	G	rs59107644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105415299A>G	ENST00000333244.5	-	7	6608	c.6489T>C	c.(6487-6489)ttT>ttC	p.F2163F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2163						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)			CAGACACCCCAAACGACGGCA	0.587													.|||	957	0.191094	0.23	0.1758	5008	,	,		16361	0.0665		0.2714	False		,,,				2504	0.1953				p.F2163F		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T6489C						PASS	.	G		695,3171		131,433,1369	219.0	155.0	178.0		6489	-4.9	0.0	14	dbSNP_129	178	318,6684		21,276,3204	no	coding-synonymous	AHNAK2	NM_138420.2		152,709,4573	GG,GA,AA		4.5416,17.9772,9.3209		2163/5796	105415299	1013,9855	1933	3501	5434	SO:0001819	synonymous_variant	113146	exon7			CACCCCAAACGAC	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.6489T>C	14.37:g.105415299A>G		Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	358	185	0.51676	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.823;G|0.177	0.177	strong		0.587	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
USP44	84101	hgsc.bcm.edu	37	12	95927087	95927087	+	Missense_Mutation	SNP	C	C	G	rs7305024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:95927087C>G	ENST00000258499.3	-	2	1234	c.946G>C	c.(946-948)Gag>Cag	p.E316Q	USP44_ENST00000552440.1_Missense_Mutation_p.E316Q|USP44_ENST00000393091.2_Missense_Mutation_p.E316Q|USP44_ENST00000537435.2_Missense_Mutation_p.E316Q	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	316	USP.		E -> Q (in dbSNP:rs7305024).		mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						CTTGTCTTCTCGCTAGCAGTC	0.368													C|||	251	0.0501198	0.1808	0.0159	5008	,	,		21981	0.0		0.001	False		,,,				2504	0.0				p.E316Q		Atlas-SNP	.											.	USP44	83	.	0			c.G946C						PASS	.	C	GLN/GLU,GLN/GLU	667,3739	282.2+/-276.4	46,575,1582	59.0	56.0	57.0		946,946	5.0	0.5	12	dbSNP_116	57	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	USP44	NM_001042403.1,NM_032147.2	29,29	46,580,5877	GG,GC,CC		0.0581,15.1384,5.1668	benign,benign	316/713,316/713	95927087	672,12334	2203	4300	6503	SO:0001583	missense	84101	exon2			TCTTCTCGCTAGC	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.946G>C	12.37:g.95927087C>G	ENSP00000258499:p.Glu316Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_032147	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	37	CCDS9053.1	103	0.04716117216117216	97	0.19715447154471544	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	3.204	-0.163026	0.06502	0.151384	5.81E-4	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	4.96	4.96	0.65561	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.473004	0.24200	N	0.040632	T	0.00039	0.0001	N	0.24115	0.695	0.44899	P	0.0020879999999999788	B	0.27264	0.173	B	0.35114	0.196	T	0.27054	-1.0085	9	0.16896	T	0.51	.	18.5826	0.91177	0.0:1.0:0.0:0.0	rs7305024;rs52829293;rs7305024	316	Q9H0E7	UBP44_HUMAN	Q	316	ENSP00000258499:E316Q;ENSP00000376806:E316Q;ENSP00000448670:E316Q;ENSP00000442629:E316Q	ENSP00000258499:E316Q	E	-	1	0	USP44	94451218	1.000000	0.71417	0.477000	0.27303	0.042000	0.13812	2.166000	0.42406	2.457000	0.83068	0.561000	0.74099	GAG	C|0.955;G|0.045	0.045	strong		0.368	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	
IL4R	3566	hgsc.bcm.edu	37	16	27373872	27373872	+	Missense_Mutation	SNP	A	A	C	rs1805011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27373872A>C	ENST00000395762.2	+	11	1458	c.1199A>C	c.(1198-1200)gAg>gCg	p.E400A	IL4R_ENST00000170630.2_Missense_Mutation_p.E400A|IL4R_ENST00000543915.2_Missense_Mutation_p.E400A|IL4R_ENST00000380922.3_Missense_Mutation_p.E385A	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	92	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	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		
FANCA	2175	hgsc.bcm.edu	37	16	89849480	89849480	+	Missense_Mutation	SNP	C	C	T	rs2239359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89849480C>T	ENST00000389301.3	-	16	1531	c.1501G>A	c.(1501-1503)Ggc>Agc	p.G501S	FANCA_ENST00000568369.1_Missense_Mutation_p.G501S	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	501			G -> S (common polymorphism; dbSNP:rs2239359). {ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:8896563, ECO:0000269|PubMed:9169126, ECO:0000269|PubMed:9371798, ECO:0000269|PubMed:9399890, ECO:0000269|PubMed:9721219, 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)		CGGTACTTGCCGGGAACCAGG	0.597			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				T|||	3125	0.624002	0.6997	0.5821	5008	,	,		18307	0.8671		0.4066	False		,,,				2504	0.5245				p.G501S		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.G1501A						PASS	.	T	SER/GLY	2991,1405	460.2+/-352.5	1010,971,217	178.0	136.0	150.0		1501	-4.6	0.0	16	dbSNP_98	150	3277,5323	648.0+/-400.4	626,2025,1649	yes	missense	FANCA	NM_000135.2	56	1636,2996,1866	TT,TC,CC		38.1047,31.9609,48.2302	benign	501/1456	89849480	6268,6728	2198	4300	6498	SO:0001583	missense	2175	exon16	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ACTTGCCGGGAAC	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.1501G>A	16.37:g.89849480C>T	ENSP00000373952:p.Gly501Ser	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	230	112	0.486957	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	1326	0.6071428571428571	333	0.676829268292683	196	0.5414364640883977	476	0.8321678321678322	321	0.4234828496042216	T	0.018	-1.467911	0.01053	0.680391	0.381047	ENSG00000187741	ENST00000389301	D	0.82803	-1.65	5.5	-4.64	0.03349	.	1.404820	0.04079	N	0.309285	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40308	-0.9570	9	0.02654	T	1	0.0	14.5434	0.68013	0.0:0.6757:0.0904:0.2339	rs2239359;rs17232721;rs17745942;rs52816520;rs60434029;rs2239359	501;501	B4DRI7;O15360	.;FANCA_HUMAN	S	501	ENSP00000373952:G501S	ENSP00000373952:G501S	G	-	1	0	FANCA	88376981	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.038000	0.12144	-1.689000	0.01434	-1.234000	0.01563	GGC	C|0.439;N|0.001	.	strong		0.597	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
VWA5B1	127731	hgsc.bcm.edu	37	1	20662938	20662938	+	Missense_Mutation	SNP	A	A	G	rs10916769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:20662938A>G	ENST00000375079.2	+	13	2097	c.1901A>G	c.(1900-1902)aAa>aGa	p.K634R	VWA5B1_ENST00000525343.1_3'UTR|VWA5B1_ENST00000375083.4_Missense_Mutation_p.K634R|VWA5B1_ENST00000289815.8_Missense_Mutation_p.K634R|VWA5B1_ENST00000289825.4_Missense_Mutation_p.K351R	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	634			K -> R (in dbSNP:rs10916769).			extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						GGGCAGGCCAAAAATGCCCGG	0.572													A|||	1122	0.224042	0.1641	0.2046	5008	,	,		17994	0.3601		0.172	False		,,,				2504	0.2321				p.K634R		Atlas-SNP	.											.	VWA5B1	44	.	0			c.A1901G						PASS	.	A	ARG/LYS	237,1147		15,207,470	43.0	43.0	43.0		1901	-2.1	0.1	1	dbSNP_120	43	603,2579		54,495,1042	yes	missense	VWA5B1	NM_001039500.2	26	69,702,1512	GG,GA,AA		18.9503,17.1243,18.3968	benign	634/1216	20662938	840,3726	692	1591	2283	SO:0001583	missense	127731	exon13			AGGCCAAAAATGC	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.1901A>G	1.37:g.20662938A>G	ENSP00000364220:p.Lys634Arg	Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	228	123	0.539474	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	ENST00000375079.2	37		513	0.2348901098901099	63	0.12804878048780488	76	0.20994475138121546	238	0.4160839160839161	136	0.17941952506596306	A	9.750	1.167284	0.21621	0.171243	0.189503	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375083;ENST00000289825;ENST00000375079	T;T;T;T	0.14144	2.53;2.53;2.53;2.53	4.86	-2.08	0.07254	.	0.980503	0.08362	N	0.957506	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B;B;B	0.24823	0.013;0.053;0.112;0.007	B;B;B;B	0.18561	0.003;0.015;0.022;0.004	T	0.48559	-0.9025	9	0.11182	T	0.66	-3.5749	4.4993	0.11856	0.3297:0.348:0.3222:0.0	rs10916769;rs56608920;rs58762752;rs10916769	634;634;634;351	Q5TIE3;Q5TIE3-5;Q5TIE3-2;Q5TIE3-3	VW5B1_HUMAN;.;.;.	R	634;634;634;351;634	ENSP00000289815:K634R;ENSP00000364224:K634R;ENSP00000289825:K351R;ENSP00000364220:K634R	ENSP00000289815:K634R	K	+	2	0	VWA5B1	20535525	0.000000	0.05858	0.113000	0.21522	0.054000	0.15201	0.025000	0.13577	-0.008000	0.14320	0.443000	0.29094	AAA	A|0.767;G|0.233	0.233	strong		0.572	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
AHCTF1	25909	hgsc.bcm.edu	37	1	247021040	247021040	+	Silent	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247021040C>A	ENST00000391829.2	-	30	4332	c.4209G>T	c.(4207-4209)ccG>ccT	p.P1403P	AHCTF1_ENST00000326225.3_Silent_p.P1412P|AHCTF1_ENST00000366508.1_Silent_p.P1438P|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1403	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				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)			TTCCTTGAACCGGGCTTAAGT	0.343																																					p.P1412P	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											AHCTF1,NS,carcinoma,-1,1	AHCTF1	187	1	0			c.G4236T						scavenged	.						59.0	60.0	59.0					1																	247021040		2203	4300	6503	SO:0001819	synonymous_variant	25909	exon30			TTGAACCGGGCTT		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.4209G>T	1.37:g.247021040C>A		Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	299	4	0.0133779	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	37																																																																																				.	.	none		0.343	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
CD207	50489	hgsc.bcm.edu	37	2	71058184	71058184	+	Silent	SNP	C	C	T	rs13421115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71058184C>T	ENST00000410009.3	-	6	1029	c.984G>A	c.(982-984)ccG>ccA	p.P328P		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	328					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						TGTCCTGTCACGGTTCTGATG	0.488													T|||	812	0.162141	0.1959	0.1744	5008	,	,		19961	0.004		0.2734	False		,,,				2504	0.1564				p.P328P		Atlas-SNP	.											.	CD207	47	.	0			c.G984A						PASS	.	T		844,3040		89,666,1187	75.0	71.0	72.0		984	-2.8	0.0	2	dbSNP_121	72	2258,6028		309,1640,2194	no	coding-synonymous	CD207	NM_015717.3		398,2306,3381	TT,TC,CC		27.2508,21.7302,25.4889		328/329	71058184	3102,9068	1942	4143	6085	SO:0001819	synonymous_variant	50489	exon6			CTGTCACGGTTCT	AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"""C-type lectin domain containing"", ""CD molecules"""	17935	protein-coding gene	gene with protein product		604862	"""CD207 antigen, langerin"""			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.984G>A	2.37:g.71058184C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	104	42	0.403846	NM_015717		Silent	SNP	ENST00000410009.3	37																																																																																				C|0.806;T|0.194	0.194	strong		0.488	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
DNAH10	196385	hgsc.bcm.edu	37	12	124323011	124323011	+	Silent	SNP	T	T	C	rs116167096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124323011T>C	ENST00000409039.3	+	28	4582	c.4557T>C	c.(4555-4557)ggT>ggC	p.G1519G		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1519	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)		AGATCATGGGTGAGACCTTAA	0.567													T|||	94	0.01877	0.0688	0.0043	5008	,	,		17334	0.0		0.0	False		,,,				2504	0.0				p.G1519G		Atlas-SNP	.											.	DNAH10	888	.	0			c.T4557C						PASS	.	T		189,3859		4,181,1839	33.0	34.0	34.0		4557	-10.4	0.0	12	dbSNP_132	34	1,8343		0,1,4171	no	coding-synonymous	DNAH10	NM_207437.3		4,182,6010	CC,CT,TT		0.012,4.669,1.5332		1519/4472	124323011	190,12202	2024	4172	6196	SO:0001819	synonymous_variant	196385	exon28			CATGGGTGAGACC	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.4557T>C	12.37:g.124323011T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			T|0.983;C|0.017	0.017	strong		0.567	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
PCDHA2	56146	hgsc.bcm.edu	37	5	140176840	140176840	+	Missense_Mutation	SNP	C	C	T	rs6858913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140176840C>T	ENST00000526136.1	+	1	2291	c.2291C>T	c.(2290-2292)cCc>cTc	p.P764L	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000378132.1_Missense_Mutation_p.P764L|PCDHA2_ENST00000520672.2_Missense_Mutation_p.P764L|PCDHA1_ENST00000504120.2_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	764	5 X 4 AA repeats of P-X-X-P.		P -> L (in dbSNP:rs6858913).		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(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGGAGGACCCCCCCAAGACG	0.617													.|||	71	0.0141773	0.053	0.0014	5008	,	,		14850	0.0		0.0	False		,,,				2504	0.0				p.P764L		Atlas-SNP	.											.	PCDHA2	404	.	0			c.C2291T						PASS	.	C	,LEU/PRO,,LEU/PRO	225,4181	134.9+/-171.1	9,207,1987	47.0	51.0	49.0		,2291,,2291	1.0	0.7	5	dbSNP_116	49	1,8599	1.2+/-3.3	0,1,4299	yes	intron,missense,intron,missense	PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_031411.1,NM_031495.1	,98,,98	9,208,6286	TT,TC,CC		0.0116,5.1067,1.7377	,,,	,764/949,,764/825	140176840	226,12780	2203	4300	6503	SO:0001583	missense	56146	exon1			AGGACCCCCCCAA	AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"""Cadherins / Protocadherins : Clustered"""	8668	other	complex locus constituent	"""KIAA0345-like 12"""	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.2291C>T	5.37:g.140176840C>T	ENSP00000431748:p.Pro764Leu	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	305	143	0.468852	NM_031495	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	37	CCDS54914.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	c	5.110	0.205978	0.09704	0.051067	1.16E-4	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.11930	2.73;2.73;2.73	4.0	1.05	0.20165	.	2.011240	0.03846	N	0.271521	T	0.01940	0.0061	L	0.42487	1.325	0.09310	N	1	B;B;B	0.13594	0.008;0.001;0.007	B;B;B	0.15052	0.012;0.003;0.012	T	0.29792	-1.0000	10	0.35671	T	0.21	.	6.6028	0.22710	0.0:0.6237:0.131:0.2453	rs6858913;rs52809059;rs6858913	764;764;764	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	L	764	ENSP00000430584:P764L;ENSP00000367372:P764L;ENSP00000431748:P764L	ENSP00000367372:P764L	P	+	2	0	PCDHA2	140157024	0.000000	0.05858	0.736000	0.30914	0.471000	0.32888	0.336000	0.19823	0.265000	0.21872	-0.225000	0.12378	CCC	C|0.982;T|0.018	0.018	strong		0.617	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905	
VIPR1	7433	hgsc.bcm.edu	37	3	42568929	42568929	+	Silent	SNP	T	T	C	rs2229722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:42568929T>C	ENST00000325123.4	+	5	557	c.444T>C	c.(442-444)atT>atC	p.I148I	VIPR1-AS1_ENST00000602176.1_RNA|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1_ENST00000543411.1_Silent_p.I100I|VIPR1-AS1_ENST00000593611.1_RNA|VIPR1_ENST00000438259.2_Intron|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1-AS1_ENST00000593621.1_RNA|VIPR1_ENST00000433647.1_Silent_p.I107I|VIPR1_ENST00000473575.1_3'UTR	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	148					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		GCTACACCATTGGCTACGGCC	0.607													C|||	1859	0.371206	0.4667	0.2839	5008	,	,		16535	0.5784		0.1511	False		,,,				2504	0.317				p.I148I		Atlas-SNP	.											.	VIPR1	45	.	0			c.T444C						PASS	.	C		1915,2491	627.0+/-394.8	389,1137,677	122.0	108.0	113.0		444	0.6	0.8	3	dbSNP_98	113	1389,7211	754.1+/-407.5	107,1175,3018	no	coding-synonymous	VIPR1	NM_004624.3		496,2312,3695	CC,CT,TT		16.1512,43.4635,25.4037		148/458	42568929	3304,9702	2203	4300	6503	SO:0001819	synonymous_variant	7433	exon5			CACCATTGGCTAC	AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12694	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 1"""	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.444T>C	3.37:g.42568929T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Silent	SNP	ENST00000325123.4	37	CCDS2698.1																																																																																			T|0.722;C|0.278	0.278	strong		0.607	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624	
ZBTB22	9278	hgsc.bcm.edu	37	6	33283945	33283945	+	Missense_Mutation	SNP	C	C	G	rs35663442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33283945C>G	ENST00000431845.2	-	2	900	c.749G>C	c.(748-750)gGa>gCa	p.G250A	TAPBP_ENST00000489157.1_5'Flank|ZBTB22_ENST00000418724.1_Missense_Mutation_p.G250A|TAPBP_ENST00000475304.1_5'Flank|TAPBP_ENST00000426633.2_5'Flank|TAPBP_ENST00000434618.2_5'Flank|TAPBP_ENST00000456592.2_5'Flank	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	250			G -> A (in dbSNP:rs35663442).		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)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(3)	21						TGTGGCCCCTCCACTGCCAAC	0.627													C|||	54	0.0107827	0.0393	0.0029	5008	,	,		17213	0.0		0.0	False		,,,				2504	0.0				p.G250A		Atlas-SNP	.											.	ZBTB22	48	.	0			c.G749C						PASS	.	C	ALA/GLY,ALA/GLY	144,4262	101.2+/-139.8	5,134,2064	47.0	46.0	46.0		749,749	2.1	0.5	6	dbSNP_126	46	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	ZBTB22	NM_001145338.1,NM_005453.4	60,60	5,138,6360	GG,GC,CC		0.0465,3.2683,1.1379	benign,benign	250/635,250/635	33283945	148,12858	2203	4300	6503	SO:0001583	missense	9278	exon2			GCCCCTCCACTGC	Z97183	CCDS4775.1	6p21.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000236104	ENSG00000236104		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13085	protein-coding gene	gene with protein product		611439	"""zinc finger protein 297"""	ZNF297			Standard	NM_005453		Approved	BING1, ZNF297A, fruitless, fru, ZBTB22A	uc010juu.3	O15209	OTTHUMG00000031110	ENST00000431845.2:c.749G>C	6.37:g.33283945C>G	ENSP00000407545:p.Gly250Ala	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	72	25	0.347222	NM_001145338	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Missense_Mutation	SNP	ENST00000431845.2	37	CCDS4775.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	C	2.540	-0.306538	0.05458	0.032683	4.65E-4	ENSG00000236104	ENST00000418724;ENST00000431845	T;T	0.07800	3.16;3.16	3.99	2.14	0.27477	.	0.253027	0.20824	N	0.085014	T	0.00875	0.0029	N	0.12182	0.205	0.28027	N	0.934308	B	0.06786	0.001	B	0.04013	0.001	T	0.46721	-0.9171	10	0.06757	T	0.87	.	4.0063	0.09603	0.0:0.5646:0.2105:0.2249	rs35663442	250	O15209	ZBT22_HUMAN	A	250	ENSP00000404403:G250A;ENSP00000407545:G250A	ENSP00000404403:G250A	G	-	2	0	ZBTB22	33391923	0.000000	0.05858	0.470000	0.27216	0.392000	0.30506	0.632000	0.24583	0.325000	0.23359	0.297000	0.19635	GGA	C|0.989;G|0.011	0.011	strong		0.627	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2		
GJA4	2701	hgsc.bcm.edu	37	1	35260760	35260760	+	Missense_Mutation	SNP	G	G	A	rs140949366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35260760G>A	ENST00000342280.4	+	2	1034	c.946G>A	c.(946-948)Ggc>Agc	p.G316S		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	316					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)				CCCTCAGAATGGCCAAAAACC	0.577													G|||	40	0.00798722	0.0295	0.0014	5008	,	,		17399	0.0		0.0	False		,,,				2504	0.0				p.G316S		Atlas-SNP	.											.	GJA4	25	.	0			c.G946A						PASS	.	G	SER/GLY	121,4285	88.7+/-127.4	4,113,2086	42.0	40.0	41.0		946	3.4	0.0	1	dbSNP_134	41	0,8600		0,0,4300	yes	missense	GJA4	NM_002060.2	56	4,113,6386	AA,AG,GG		0.0,2.7463,0.9303	probably-damaging	316/334	35260760	121,12885	2203	4300	6503	SO:0001583	missense	2701	exon2			CAGAATGGCCAAA	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.946G>A	1.37:g.35260760G>A	ENSP00000343676:p.Gly316Ser	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Missense_Mutation	SNP	ENST00000342280.4	37	CCDS30669.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	2.239	-0.374329	0.05034	0.027463	0.0	ENSG00000187513	ENST00000342280	D	0.97186	-4.28	5.25	3.39	0.38822	.	0.791228	0.11561	N	0.551774	D	0.85448	0.5699	L	0.44542	1.39	0.09310	N	0.999995	B	0.06786	0.001	B	0.04013	0.001	T	0.78170	-0.2308	10	0.11794	T	0.64	.	7.8674	0.29545	0.1462:0.1332:0.7206:0.0	.	316	P35212	CXA4_HUMAN	S	316	ENSP00000343676:G316S	ENSP00000343676:G316S	G	+	1	0	GJA4	35033347	0.002000	0.14202	0.009000	0.14445	0.026000	0.11368	0.960000	0.29253	0.603000	0.29913	0.561000	0.74099	GGC	G|0.989;A|0.011	0.011	strong		0.577	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060	
CIT	11113	hgsc.bcm.edu	37	12	120145987	120145987	+	Silent	SNP	G	G	C	rs56158046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:120145987G>C	ENST00000261833.7	-	39	5134	c.5082C>G	c.(5080-5082)ggC>ggG	p.G1694G	CIT_ENST00000392521.2_Silent_p.G1736G|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1694	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		AGCTTACCTTGCCTGCCCCAA	0.527													G|||	555	0.110823	0.3661	0.0476	5008	,	,		17588	0.0		0.0199	False		,,,				2504	0.0184				p.G1736G		Atlas-SNP	.											.	CIT	535	.	0			c.C5208G						PASS	.	G	,	1273,3133	432.4+/-343.3	191,891,1121	89.0	83.0	85.0		5208,5082	4.2	1.0	12	dbSNP_129	85	133,8467	67.3+/-129.8	1,131,4168	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	192,1022,5289	CC,CG,GG		1.5465,28.8924,10.8104	,	1736/2070,1694/2028	120145987	1406,11600	2203	4300	6503	SO:0001819	synonymous_variant	11113	exon40			TACCTTGCCTGCC	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.5082C>G	12.37:g.120145987G>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	199	0.09111721611721611	166	0.33739837398373984	20	0.055248618784530384	0	0.0	13	0.017150395778364115	G	3.445	-0.113195	0.06881	0.288924	0.015465	ENSG00000122966	ENST00000392520	.	.	.	5.08	4.18	0.49190	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.31971	-0.9924	3	.	.	.	.	10.8926	0.47004	0.0:0.1414:0.7117:0.1469	rs56158046;rs58511553	.	.	.	G	1307	.	.	A	-	2	0	CIT	118630370	1.000000	0.71417	1.000000	0.80357	0.424000	0.31475	1.849000	0.39318	1.264000	0.44198	0.462000	0.41574	GCA	G|0.901;C|0.099	0.099	strong		0.527	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
AGL	178	hgsc.bcm.edu	37	1	100335977	100335977	+	Missense_Mutation	SNP	A	A	G	rs17121403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100335977A>G	ENST00000294724.4	+	6	1164	c.686A>G	c.(685-687)cAg>cGg	p.Q229R	AGL_ENST00000361302.3_Missense_Mutation_p.Q213R|AGL_ENST00000361915.3_Missense_Mutation_p.Q229R|AGL_ENST00000361522.4_Missense_Mutation_p.Q212R|AGL_ENST00000370161.2_Missense_Mutation_p.Q213R|AGL_ENST00000370165.3_Missense_Mutation_p.Q229R|AGL_ENST00000370163.3_Missense_Mutation_p.Q229R	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	229			Q -> R (in dbSNP:rs17121403).		carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		AAATGGATCCAGGAACATCCA	0.383													A|||	242	0.0483227	0.0998	0.0778	5008	,	,		16767	0.0288		0.0119	False		,,,				2504	0.0153				p.Q229R		Atlas-SNP	.											.	AGL	137	.	0			c.A686G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	386,4020	194.0+/-219.0	16,354,1833	83.0	82.0	83.0	http://www.ncbi.nlm.nih.gov/pubmed?term	686,686,686,686,635,638	4.2	1.0	1	dbSNP_123	83	162,8438	76.0+/-138.7	3,156,4141	yes	missense,missense,missense,missense,missense,missense	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000645.2,NM_000646.2	43,43,43,43,43,43	19,510,5974	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	1.8837,8.7608,4.2134	benign,benign,benign,benign,benign,benign	229/1533,229/1533,229/1533,229/1533,212/1516,213/1517	100335977	548,12458	2203	4300	6503	SO:0001583	missense	178	exon6			GGATCCAGGAACA	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.686A>G	1.37:g.100335977A>G	ENSP00000294724:p.Gln229Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	148	74	0.5	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	81	0.03708791208791209	32	0.06504065040650407	22	0.06077348066298342	18	0.03146853146853147	9	0.011873350923482849	a	4.697	0.129685	0.08981	0.087608	0.018837	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	5.37	4.23	0.50019	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.366516	0.30620	N	0.009224	T	0.37839	0.1018	N	0.11313	0.125	0.25527	N	0.987316	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.27365	-1.0076	10	0.11182	T	0.66	.	3.3885	0.07281	0.6434:0.1418:0.0787:0.1361	rs17121403;rs52817380;rs17121403	212;213;229	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	R	229;229;229;229;213;213;212	ENSP00000355106:Q229R;ENSP00000359184:Q229R;ENSP00000359182:Q229R;ENSP00000294724:Q229R;ENSP00000354971:Q213R;ENSP00000359180:Q213R;ENSP00000354635:Q212R	ENSP00000294724:Q229R	Q	+	2	0	AGL	100108565	0.282000	0.24268	0.996000	0.52242	0.994000	0.84299	1.669000	0.37492	0.943000	0.37553	0.477000	0.44152	CAG	A|0.959;G|0.041	0.041	strong		0.383	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
EQTN	54586	hgsc.bcm.edu	37	9	27296705	27296705	+	Silent	SNP	A	A	G	rs3824406	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:27296705A>G	ENST00000380032.3	-	2	191	c.108T>C	c.(106-108)gaT>gaC	p.D36D	EQTN_ENST00000537675.1_Silent_p.D36D|EQTN_ENST00000380031.1_Silent_p.D36D|EQTN_ENST00000484994.1_5'UTR	NM_020641.2	NP_065692.2	Q9NQ60	EQTN_HUMAN	equatorin, sperm acrosome associated	36					acrosomal vesicle exocytosis (GO:0060478)|endocytosis (GO:0006897)|fusion of sperm to egg plasma membrane (GO:0007342)	early endosome (GO:0005769)|inner acrosomal membrane (GO:0002079)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|outer acrosomal membrane (GO:0002081)|plasma membrane (GO:0005886)											GCTTATTAACATCTTCATTTA	0.294													A|||	611	0.122005	0.0129	0.0807	5008	,	,		17016	0.1994		0.1889	False		,,,				2504	0.1503				p.D36D		Atlas-SNP	.											.	.	.	.	0			c.T108C						PASS	.	A	,	164,4242	108.6+/-147.0	2,160,2041	86.0	83.0	84.0		108,108	1.3	0.0	9	dbSNP_107	84	1478,7102	279.5+/-294.0	122,1234,2934	no	coding-synonymous,coding-synonymous	C9orf11	NM_001161585.1,NM_020641.2	,	124,1394,4975	GG,GA,AA		17.2261,3.7222,12.6444	,	36/266,36/295	27296705	1642,11344	2203	4290	6493	SO:0001819	synonymous_variant	54586	exon2			ATTAACATCTTCA	AJ278482	CCDS35001.1, CCDS55300.1	9p21	2012-09-20	2012-09-20	2012-09-20	ENSG00000120160	ENSG00000120160			1359	protein-coding gene	gene with protein product	"""Acr formation associated factor"", ""Acrosome formation associated factor"", ""sperm acrosome associated 8"""		"""chromosome 9 open reading frame 11"", ""equatorin"""	C9orf11			Standard	NM_020641		Approved	AFAF, SPACA8, equatorin	uc003zql.3	Q9NQ60	OTTHUMG00000021033	ENST00000380032.3:c.108T>C	9.37:g.27296705A>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	211	106	0.50237	NM_001161585	B2RPB3|B7ZMK1|Q5TCU1|Q96L22	Silent	SNP	ENST00000380032.3	37	CCDS35001.1																																																																																			A|0.873;G|0.127	0.127	strong		0.294	EQTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055499.1	NM_020641	
FRMPD1	22844	hgsc.bcm.edu	37	9	37745562	37745562	+	Missense_Mutation	SNP	C	C	T	rs62640016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:37745562C>T	ENST00000539465.1	+	16	4126	c.3533C>T	c.(3532-3534)cCt>cTt	p.P1178L	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.P1178L			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1178						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.P1178H(1)		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)		CCACATCCCCCTAGAGACCCT	0.483													C|||	81	0.0161741	0.0605	0.0014	5008	,	,		19697	0.0		0.0	False		,,,				2504	0.0				p.P1178L		Atlas-SNP	.											FRMPD1,scalp,carcinoma,+1,1	FRMPD1	237	1	1	Substitution - Missense(1)	lung(1)	c.C3533T						PASS	.	C	LEU/PRO	164,4242	104.7+/-143.2	3,158,2042	52.0	55.0	54.0		3533	3.2	0.0	9	dbSNP_129	54	0,8598		0,0,4299	yes	missense	FRMPD1	NM_014907.2	98	3,158,6341	TT,TC,CC		0.0,3.7222,1.2612	possibly-damaging	1178/1579	37745562	164,12840	2203	4299	6502	SO:0001583	missense	22844	exon16			ATCCCCCTAGAGA	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.3533C>T	9.37:g.37745562C>T	ENSP00000444411:p.Pro1178Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	11.39	1.625940	0.28889	0.037222	0.0	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.06768	3.26;3.26	4.24	3.24	0.37175	.	1.039780	0.07531	N	0.912167	T	0.00998	0.0033	N	0.24115	0.695	0.19300	N	0.999977	B	0.06786	0.001	B	0.04013	0.001	T	0.15925	-1.0420	10	0.56958	D	0.05	-9.9948	8.5566	0.33485	0.2299:0.7701:0.0:0.0	rs62640016	1178	Q5SYB0	FRPD1_HUMAN	L	1178	ENSP00000366995:P1178L;ENSP00000444411:P1178L	ENSP00000366995:P1178L	P	+	2	0	FRMPD1	37735562	0.005000	0.15991	0.037000	0.18230	0.034000	0.12701	1.541000	0.36126	2.298000	0.77334	0.561000	0.74099	CCT	C|0.986;T|0.014	0.014	strong		0.483	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
C1orf52	148423	hgsc.bcm.edu	37	1	85724328	85724328	+	Silent	SNP	C	C	T	rs4949926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:85724328C>T	ENST00000471115.1	-	2	362	c.354G>A	c.(352-354)ccG>ccA	p.P118P	C1orf52_ENST00000294661.4_5'UTR|C1orf52_ENST00000344356.5_Silent_p.P118P	NM_198077.3	NP_932343.1	Q8N6N3	CA052_HUMAN	chromosome 1 open reading frame 52	118							poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)	10				all cancers(265;0.0105)|Epithelial(280;0.0293)		GCTCTGGAGGCGGAGGCTTCT	0.428													C|||	1126	0.22484	0.1271	0.3156	5008	,	,		13049	0.2956		0.2078	False		,,,				2504	0.2372				p.P118P		Atlas-SNP	.											.	C1orf52	16	.	0			c.G354A						PASS	.	C		598,3808	261.0+/-264.0	36,526,1641	141.0	133.0	135.0		354	-3.8	0.2	1	dbSNP_111	135	1747,6853	319.5+/-314.2	169,1409,2722	no	coding-synonymous	C1orf52	NM_198077.3		205,1935,4363	TT,TC,CC		20.314,13.5724,18.0301		118/183	85724328	2345,10661	2203	4300	6503	SO:0001819	synonymous_variant	148423	exon2			TGGAGGCGGAGGC	BC029538	CCDS703.1	1p22.3	2008-02-05			ENSG00000162642	ENSG00000162642			24871	protein-coding gene	gene with protein product						11891061	Standard	NM_198077		Approved	gm117, FLJ44982	uc001dkv.3	Q8N6N3	OTTHUMG00000009966	ENST00000471115.1:c.354G>A	1.37:g.85724328C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	93	34	0.365591	NM_198077	B3KX89|Q8TDK5|Q8TDK6	Silent	SNP	ENST00000471115.1	37	CCDS703.1																																																																																			C|0.810;T|0.190	0.190	strong		0.428	C1orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027616.2	NM_198077	
MTERF3	51001	hgsc.bcm.edu	37	8	97263180	97263180	+	Missense_Mutation	SNP	T	T	G	rs112357919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:97263180T>G	ENST00000287025.3	-	4	729	c.631A>C	c.(631-633)Aaa>Caa	p.K211Q	MTERFD1_ENST00000523821.1_Missense_Mutation_p.K211Q|MTERFD1_ENST00000522822.1_Missense_Mutation_p.K90Q|MTERFD1_ENST00000524341.1_Missense_Mutation_p.K21Q	NM_015942.3	NP_057026.3	Q96E29	MTEF3_HUMAN		211					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)	transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	24	Breast(36;5.16e-05)					GCATGATTTTTTGTCAGGAAT	0.363													T|||	215	0.0429313	0.1566	0.0101	5008	,	,		12111	0.0		0.001	False		,,,				2504	0.0				p.K211Q		Atlas-SNP	.											.	MTERFD1	50	.	0			c.A631C						PASS	.	T	GLN/LYS	602,3804	263.1+/-265.3	36,530,1637	113.0	116.0	115.0		631	6.0	1.0	8	dbSNP_132	115	3,8597	3.0+/-9.4	0,3,4297	yes	missense	MTERFD1	NM_015942.3	53	36,533,5934	GG,GT,TT		0.0349,13.6632,4.6517	probably-damaging	211/418	97263180	605,12401	2203	4300	6503	SO:0001583	missense	51001	exon4			GATTTTTTGTCAG																												ENST00000287025.3:c.631A>C	8.37:g.97263180T>G	ENSP00000287025:p.Lys211Gln	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	163	82	0.503067	NM_015942	B3KMG6|G3V130|Q9Y301	Missense_Mutation	SNP	ENST00000287025.3	37	CCDS6270.1	79	0.036172161172161175	76	0.15447154471544716	3	0.008287292817679558	0	0.0	0	0.0	T	22.3	4.273758	0.80580	0.136632	3.49E-4	ENSG00000156469	ENST00000523821;ENST00000522822;ENST00000524341;ENST00000287025	T;T;T;T	0.17213	2.73;2.73;2.29;2.73	5.98	5.98	0.97165	.	0.191366	0.51477	D	0.000091	T	0.00210	0.0006	M	0.69823	2.125	0.20821	P	0.999846152	D;D	0.65815	0.995;0.995	P;P	0.58820	0.846;0.799	T	0.01298	-1.1392	9	0.33940	T	0.23	-9.9875	15.0407	0.71788	0.0:0.0:0.0:1.0	.	211;211	E5RIK9;Q96E29	.;MTER1_HUMAN	Q	211;90;21;211	ENSP00000429400:K211Q;ENSP00000430138:K90Q;ENSP00000429267:K21Q;ENSP00000287025:K211Q	ENSP00000287025:K211Q	K	-	1	0	MTERFD1	97332356	1.000000	0.71417	0.963000	0.40424	0.946000	0.59487	4.381000	0.59587	2.289000	0.77006	0.482000	0.46254	AAA	T|0.958;G|0.042	0.042	strong		0.363	MTERFD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379876.1		
FMNL3	91010	hgsc.bcm.edu	37	12	50043687	50043687	+	Silent	SNP	A	A	G	rs61733848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50043687A>G	ENST00000293590.5	-	18	2255	c.2022T>C	c.(2020-2022)ccT>ccC	p.P674P	FMNL3_ENST00000550488.1_Silent_p.P674P|FMNL3_ENST00000352151.5_Silent_p.P623P|FMNL3_ENST00000335154.5_Silent_p.P674P			Q8IVF7	FMNL3_HUMAN	formin-like 3	674	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						CGAAGTCCACAGGTAGTGTCT	0.567													A|||	72	0.014377	0.0348	0.0043	5008	,	,		21632	0.001		0.0149	False		,,,				2504	0.0072				p.P674P		Atlas-SNP	.											FMNL3,face,carcinoma,-2,1	FMNL3	137	1	0			c.T2022C						scavenged	.	A	,	139,4045		1,137,1954	29.0	31.0	31.0		2022,1869	-10.9	0.2	12	dbSNP_129	31	119,8347		2,115,4116	no	coding-synonymous,coding-synonymous	FMNL3	NM_175736.4,NM_198900.2	,	3,252,6070	GG,GA,AA		1.4056,3.3222,2.0395	,	674/1028,623/977	50043687	258,12392	2092	4233	6325	SO:0001819	synonymous_variant	91010	exon18			GTCCACAGGTAGT	AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.2022T>C	12.37:g.50043687A>G		Somatic	35	1	0.0285714		WXS	Illumina HiSeq	Phase_I	58	39	0.672414	NM_175736	B0JZA7|Q6ZRJ1	Silent	SNP	ENST00000293590.5	37																																																																																				A|0.985;G|0.015	0.015	strong		0.567	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736	
ZNF813	126017	hgsc.bcm.edu	37	19	53994083	53994083	+	Silent	SNP	T	T	C	rs150664026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53994083T>C	ENST00000396403.4	+	4	725	c.597T>C	c.(595-597)tcT>tcC	p.S199S	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	199					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)	1				GBM - Glioblastoma multiforme(134;0.00619)		TCCGGAATTCTTCGTTACTCA	0.368													.|||	12	0.00239617	0.0083	0.0014	5008	,	,		20858	0.0		0.0	False		,,,				2504	0.0				p.S199S		Atlas-SNP	.											ZNF813_ENST00000396403,NS,carcinoma,+1,1	ZNF813	81	1	0			c.T597C						PASS	.	T		31,4353		0,31,2161	79.0	87.0	84.0		597	0.5	0.0	19	dbSNP_134	84	2,8584		0,2,4291	no	coding-synonymous	ZNF813	NM_001004301.3		0,33,6452	CC,CT,TT		0.0233,0.7071,0.2544		199/618	53994083	33,12937	2192	4293	6485	SO:0001819	synonymous_variant	126017	exon4			GAATTCTTCGTTA	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.597T>C	19.37:g.53994083T>C		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	248	119	0.479839	NM_001004301		Silent	SNP	ENST00000396403.4	37	CCDS46172.1																																																																																			T|0.999;C|0.001	0.001	strong		0.368	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
LILRA1	11024	hgsc.bcm.edu	37	19	55107357	55107357	+	Silent	SNP	C	C	T	rs35066441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55107357C>T	ENST00000251372.3	+	6	1097	c.915C>T	c.(913-915)tcC>tcT	p.S305S	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	305	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		ACCTCTCCTCCGAGTGGTCGG	0.682													c|||	808	0.161342	0.4009	0.0994	5008	,	,		14575	0.0079		0.0924	False		,,,				2504	0.1104				p.S305S		Atlas-SNP	.											.	LILRA1	105	.	0			c.C915T						PASS	.						31.0	46.0	41.0					19																	55107357		2200	4299	6499	SO:0001819	synonymous_variant	11024	exon6			CTCCTCCGAGTGG	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.915C>T	19.37:g.55107357C>T		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	153	68	0.444444	NM_006863	O75018|Q3MJA6	Silent	SNP	ENST00000251372.3	37	CCDS12901.1																																																																																			C|0.920;T|0.080	0.080	strong		0.682	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
TMEM206	55248	hgsc.bcm.edu	37	1	212538572	212538572	+	Silent	SNP	C	C	T	rs12087727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:212538572C>T	ENST00000261455.4	-	8	1175	c.1038G>A	c.(1036-1038)acG>acA	p.T346T	TMEM206_ENST00000535273.1_Silent_p.T407T	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	346						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)		TTATGTGGCTCGTTGCCTGAC	0.413													C|||	517	0.103235	0.3767	0.0259	5008	,	,		16867	0.0		0.001	False		,,,				2504	0.0				p.T407T		Atlas-SNP	.											TMEM206,NS,carcinoma,-1,1	TMEM206	41	1	0			c.G1221A						PASS	.	C	,	1385,3021	459.2+/-352.2	228,929,1046	215.0	199.0	205.0		1221,1038	-11.8	0.0	1	dbSNP_120	205	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,coding-synonymous	TMEM206	NM_001198862.1,NM_018252.2	,	228,950,5325	TT,TC,CC		0.2442,31.4344,10.8104	,	407/412,346/351	212538572	1406,11600	2203	4300	6503	SO:0001819	synonymous_variant	55248	exon9			GTGGCTCGTTGCC	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.1038G>A	1.37:g.212538572C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	136	59	0.433824	NM_001198862	B7Z4D6|Q6IA87|Q9NV85	Silent	SNP	ENST00000261455.4	37	CCDS1504.1																																																																																			C|0.908;T|0.092	0.092	strong		0.413	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252	
VPS41	27072	hgsc.bcm.edu	37	7	38860809	38860809	+	Silent	SNP	G	G	T	rs77229707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:38860809G>T	ENST00000310301.4	-	6	432	c.378C>A	c.(376-378)ccC>ccA	p.P126P	VPS41_ENST00000395969.2_Silent_p.P101P	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	126					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						TTACTTTAATGGGACAGTCAA	0.348													G|||	78	0.0155751	0.0333	0.013	5008	,	,		17185	0.0		0.0119	False		,,,				2504	0.0133				p.P126P		Atlas-SNP	.											.	VPS41	102	.	0			c.C378A						PASS	.	G	,	197,4209	123.7+/-161.0	4,189,2010	87.0	91.0	90.0		378,303	-0.3	1.0	7	dbSNP_132	90	125,8475	64.9+/-127.2	1,123,4176	no	coding-synonymous,coding-synonymous	VPS41	NM_014396.3,NM_080631.3	,	5,312,6186	TT,TG,GG		1.4535,4.4712,2.4758	,	126/855,101/830	38860809	322,12684	2203	4300	6503	SO:0001819	synonymous_variant	27072	exon6			TTTAATGGGACAG	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.378C>A	7.37:g.38860809G>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	75	43	0.573333	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	37	CCDS5457.1																																																																																			G|0.978;T|0.022	0.022	strong		0.348	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
CHPF	79586	hgsc.bcm.edu	37	2	220404648	220404648	+	Silent	SNP	C	C	T	rs1043833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220404648C>T	ENST00000243776.6	-	4	2033	c.1785G>A	c.(1783-1785)ctG>ctA	p.L595L	CHPF_ENST00000535926.1_Silent_p.L433L	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	595					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)|mitochondrion (GO:0005739)	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(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CCATGAGGCGCAGTGGTGAGG	0.652													C|||	1534	0.30631	0.1884	0.4841	5008	,	,		17935	0.2748		0.4523	False		,,,				2504	0.2219				p.L595L		Atlas-SNP	.											.	CHPF	56	.	0			c.G1785A						PASS	.	C	,	1096,3310		126,844,1233	53.0	59.0	57.0		1299,1785	-0.6	0.8	2	dbSNP_86	57	3967,4625		933,2101,1262	no	coding-synonymous,coding-synonymous	CHPF	NM_001195731.1,NM_024536.5	,	1059,2945,2495	TT,TC,CC		46.1709,24.8752,38.9521	,	433/614,595/776	220404648	5063,7935	2203	4296	6499	SO:0001819	synonymous_variant	79586	exon4			GAGGCGCAGTGGT	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24291	protein-coding gene	gene with protein product	"""chondroitin sulfate synthase 2"""	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1785G>A	2.37:g.220404648C>T		Somatic	227	2	0.00881057		WXS	Illumina HiSeq	Phase_I	235	235	1	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Silent	SNP	ENST00000243776.6	37	CCDS2443.1																																																																																			C|0.645;T|0.355	0.355	strong		0.652	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536	
VN1R4	317703	hgsc.bcm.edu	37	19	53770846	53770846	+	Missense_Mutation	SNP	C	C	G	rs112743505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53770846C>G	ENST00000311170.4	-	1	126	c.73G>C	c.(73-75)Gtt>Ctt	p.V25L	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	25					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)		TGGAGAAGAACAGAGAAGCTC	0.493										HNSCC(26;0.072)			G|||	256	0.0511182	0.1831	0.0159	5008	,	,		19164	0.002		0.001	False		,,,				2504	0.0				p.V25L		Atlas-SNP	.											.	VN1R4	65	.	0			c.G73C						PASS	.	G	LEU/VAL	706,3700	745.0+/-411.6	70,566,1567	57.0	63.0	61.0		73	1.2	0.0	19	dbSNP_134	61	8,8592	817.1+/-406.9	0,8,4292	yes	missense	VN1R4	NM_173857.2	32	70,574,5859	GG,GC,CC		0.093,16.0236,5.4898	benign	25/302	53770846	714,12292	2203	4300	6503	SO:0001583	missense	317703	exon1			GAAGAACAGAGAA	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.73G>C	19.37:g.53770846C>G	ENSP00000310856:p.Val25Leu	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	394	192	0.48731	NM_173857	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Missense_Mutation	SNP	ENST00000311170.4	37	CCDS33099.1	93	0.042582417582417584	75	0.1524390243902439	8	0.022099447513812154	4	0.006993006993006993	6	0.0079155672823219	G	0.008	-1.870615	0.00542	0.160236	9.3E-4	ENSG00000228567	ENST00000311170	T	0.44482	0.92	2.26	1.19	0.21007	GPCR, rhodopsin-like superfamily (1);	0.610624	0.12496	N	0.463795	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24905	-1.0147	9	0.02654	T	1	.	3.7996	0.08753	0.1549:0.2523:0.5928:0.0	.	25	Q7Z5H5	VN1R4_HUMAN	L	25	ENSP00000310856:V25L	ENSP00000310856:V25L	V	-	1	0	VN1R4	58462658	0.016000	0.18221	0.008000	0.14137	0.008000	0.06430	0.420000	0.21263	0.090000	0.17273	-0.275000	0.10095	GTT	C|0.953;G|0.047	0.047	strong		0.493	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857	
ZCCHC2	54877	hgsc.bcm.edu	37	18	60227833	60227833	+	Silent	SNP	T	T	C	rs17070100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:60227833T>C	ENST00000269499.5	+	8	1924	c.1506T>C	c.(1504-1506)caT>caC	p.H502H	ZCCHC2_ENST00000586834.1_Silent_p.H181H	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	502						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						TGTTGCAGCATGCCATAATCC	0.353													t|||	566	0.113019	0.2322	0.0908	5008	,	,		18793	0.003		0.1103	False		,,,				2504	0.0838				p.H502H		Atlas-SNP	.											.	ZCCHC2	64	.	0			c.T1506C						PASS	.	T		822,2894		95,632,1131	196.0	168.0	177.0		1506	-1.0	0.8	18	dbSNP_123	177	939,7267		59,821,3223	no	coding-synonymous	ZCCHC2	NM_017742.4		154,1453,4354	CC,CT,TT		11.4428,22.1206,14.771		502/1179	60227833	1761,10161	1858	4103	5961	SO:0001819	synonymous_variant	54877	exon8			GCAGCATGCCATA	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.1506T>C	18.37:g.60227833T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	160	74	0.4625	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Silent	SNP	ENST00000269499.5	37	CCDS45880.1																																																																																			T|0.893;C|0.107	0.107	strong		0.353	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742	
DPY19L1	23333	hgsc.bcm.edu	37	7	34978926	34978926	+	Silent	SNP	G	G	A	rs377307859		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:34978926G>A	ENST00000310974.4	-	20	1851	c.1707C>T	c.(1705-1707)ccC>ccT	p.P569P	MIR548N_ENST00000408742.1_RNA	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	569						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						GATTCACAATGGGCCGAAGTG	0.507																																					p.P569P		Atlas-SNP	.											.	DPY19L1	56	.	0			c.C1707T						PASS	.	G		1,4179		0,1,2089	120.0	112.0	115.0		1707	-0.4	0.0	7		115	0,8478		0,0,4239	no	coding-synonymous	DPY19L1	NM_015283.1		0,1,6328	AA,AG,GG		0.0,0.0239,0.0079		569/676	34978926	1,12657	2090	4239	6329	SO:0001819	synonymous_variant	23333	exon20			CACAATGGGCCGA	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.1707C>T	7.37:g.34978926G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	138	71	0.514493	NM_015283	O94954|Q4G151	Silent	SNP	ENST00000310974.4	37	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	G	9.689	1.151487	0.21371	2.39E-4	0.0	ENSG00000173852	ENST00000428054	.	.	.	5.9	-0.415	0.12355	.	.	.	.	.	T	0.41282	0.1152	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21109	-1.0255	4	.	.	.	-12.4763	1.5429	0.02559	0.2774:0.217:0.3812:0.1244	.	.	.	.	Y	19	.	.	H	-	1	0	DPY19L1	34945451	0.075000	0.21258	0.018000	0.16275	0.856000	0.48823	0.068000	0.14531	-0.382000	0.07870	-0.150000	0.13652	CAT	.	.	weak		0.507	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1		
LPA	4018	hgsc.bcm.edu	37	6	161032668	161032668	+	Silent	SNP	A	A	G	rs113727842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:161032668A>G	ENST00000316300.5	-	16	2573	c.2529T>C	c.(2527-2529)acT>acC	p.T843T	LPA_ENST00000447678.1_Silent_p.T843T			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3351	Kringle 8. {ECO:0000255|PROSITE- ProRule:PRU00121}.				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)	p.T843T(1)		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)	AGGTTCTTCCAGTGACAGTGG	0.498													-|||	1977	0.394768	0.466	0.268	5008	,	,		24720	0.4345		0.3966	False		,,,				2504	0.3456				p.T843T		Atlas-SNP	.											LPA,NS,carcinoma,0,1	LPA	237	1	1	Substitution - coding silent(1)	prostate(1)	c.T2529C						scavenged	.	T		1097,1337		269,559,389	146.0	158.0	154.0		2529	0.8	0.0	6	dbSNP_132	154	1749,3323		338,1073,1125	no	coding-synonymous	LPA	NM_005577.2		607,1632,1514	GG,GA,AA		34.4834,45.0698,37.9163		843/2041	161032668	2846,4660	1217	2536	3753	SO:0001819	synonymous_variant	4018	exon17			TCTTCCAGTGACA	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.2529T>C	6.37:g.161032668A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	29	8	0.275862	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																			A|0.250;G|0.750	0.750	weak		0.498	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
ALPK3	57538	hgsc.bcm.edu	37	15	85403104	85403104	+	Missense_Mutation	SNP	G	G	A	rs114686452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85403104G>A	ENST00000258888.5	+	8	4836	c.4669G>A	c.(4669-4671)Gcc>Acc	p.A1557T		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1557	Ig-like 2.		A -> D (in dbSNP:rs34775428). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GCACGGCTCGGCCTCCACCGA	0.687													G|||	11	0.00219649	0.0083	0.0	5008	,	,		16937	0.0		0.0	False		,,,				2504	0.0				p.A1557T		Atlas-SNP	.											.	ALPK3	289	.	0			c.G4669A						PASS	.	G	THR/ALA	17,4389	24.3+/-50.5	0,17,2186	57.0	55.0	55.0		4669	3.6	0.6	15	dbSNP_132	55	0,8598		0,0,4299	yes	missense	ALPK3	NM_020778.4	58	0,17,6485	AA,AG,GG		0.0,0.3858,0.1307	possibly-damaging	1557/1908	85403104	17,12987	2203	4299	6502	SO:0001583	missense	57538	exon8			GGCTCGGCCTCCA	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.4669G>A	15.37:g.85403104G>A	ENSP00000258888:p.Ala1557Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	4	0.0018315018315018315	3	0.006097560975609756	0	0.0	0	0.0	1	0.0013192612137203166	G	22.4	4.289118	0.80914	0.003858	0.0	ENSG00000136383	ENST00000258888	T	0.06687	3.27	5.52	3.62	0.41486	Immunoglobulin-like (1);Protein kinase-like domain (1);Immunoglobulin-like fold (1);	0.331817	0.30383	N	0.009744	T	0.07863	0.0197	L	0.34521	1.04	0.26266	N	0.978497	D	0.60575	0.988	P	0.54590	0.756	T	0.12344	-1.0551	10	0.27082	T	0.32	-10.6766	9.2405	0.37493	0.0811:0.1467:0.7721:0.0	.	1557	Q96L96	ALPK3_HUMAN	T	1557	ENSP00000258888:A1557T	ENSP00000258888:A1557T	A	+	1	0	ALPK3	83204108	1.000000	0.71417	0.556000	0.28293	0.972000	0.66771	3.919000	0.56439	0.680000	0.31366	0.563000	0.77884	GCC	G|0.998;A|0.002	0.002	strong		0.687	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
HDGFRP2	84717	hgsc.bcm.edu	37	19	4488718	4488718	+	Missense_Mutation	SNP	G	G	A	rs147061912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4488718G>A	ENST00000301284.4	+	4	398	c.334G>A	c.(334-336)Gac>Aac	p.D112N	HDGFRP2_ENST00000586684.1_Missense_Mutation_p.D112N	NM_001001520.1|NM_032631.2	NP_001001520|NP_116020.1	Q7Z4V5	HDGR2_HUMAN		112					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										CAACCCCGCCGACGGCAGTGA	0.677													G|||	37	0.00738818	0.028	0.0	5008	,	,		14427	0.0		0.0	False		,,,				2504	0.0				p.D112N		Atlas-SNP	.											.	.	.	.	0			c.G334A						PASS	.	G	ASN/ASP,ASN/ASP	96,4038		1,94,1972	11.0	15.0	13.0		334,334	2.5	0.0	19	dbSNP_134	13	0,8302		0,0,4151	yes	missense,missense	HDGFRP2	NM_032631.2,NM_001001520.1	23,23	1,94,6123	AA,AG,GG		0.0,2.3222,0.772	benign,benign	112/676,112/677	4488718	96,12340	2067	4151	6218	SO:0001583	missense	0	exon4			CCCGCCGACGGCA																												ENST00000301284.4:c.334G>A	19.37:g.4488718G>A	ENSP00000301284:p.Asp112Asn	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_032631	I3L080|K7EQZ6|Q96GI5|Q9BW08	Missense_Mutation	SNP	ENST00000301284.4	37	CCDS42472.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	4.364	0.067010	0.08388	0.023222	0.0	ENSG00000167674	ENST00000301284;ENST00000398364	T	0.46451	0.87	4.86	2.5	0.30297	.	0.387710	0.23889	N	0.043579	T	0.10852	0.0265	L	0.38175	1.15	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.01281	0.0;0.0	T	0.08229	-1.0732	10	0.21014	T	0.42	.	8.9678	0.35887	0.0:0.1609:0.6729:0.1662	.	112;112	C9JEE1;Q7Z4V5	.;HDGR2_HUMAN	N	112;98	ENSP00000301284:D112N	ENSP00000301284:D112N	D	+	1	0	AC011498.1	4439718	0.052000	0.20516	0.003000	0.11579	0.006000	0.05464	2.427000	0.44740	1.143000	0.42306	0.555000	0.69702	GAC	G|0.994;A|0.006	0.006	strong		0.677	HDGFRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458642.1		
DUSP13	51207	hgsc.bcm.edu	37	10	76855412	76855412	+	Silent	SNP	G	G	A	rs3740317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76855412G>A	ENST00000472493.2	-	3	393	c.315C>T	c.(313-315)gaC>gaT	p.D105D	DUSP13_ENST00000478873.2_Silent_p.D241D|DUSP13_ENST00000491677.2_Silent_p.D234D|DUSP13_ENST00000607131.1_Silent_p.D198D|DUSP13_ENST00000372702.3_3'UTR|DUSP13_ENST00000464872.1_Intron|DUSP13_ENST00000372700.3_Silent_p.D155D|DUSP13_ENST00000605915.1_Silent_p.D127D|DUSP13_ENST00000607009.1_5'Flank	NM_016364.3	NP_057448.3	Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	105					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)	p.D234D(1)		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)					AGGGGTTGTCGTCCGCCTCGA	0.552													A|||	2110	0.421326	0.4289	0.4424	5008	,	,		21230	0.6379		0.2773	False		,,,				2504	0.3211				p.D198D	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											DUSP13_ENST00000356369,NS,carcinoma,0,1	DUSP13	82	1	1	Substitution - coding silent(1)	stomach(1)	c.C594T						scavenged	.	A	,,,	1849,2557	634.9+/-396.3	383,1083,737	263.0	210.0	228.0		,465,594,315	2.7	1.0	10	dbSNP_107	228	2298,6302	705.7+/-405.5	303,1692,2305	no	utr-3,coding-synonymous,coding-synonymous,coding-synonymous	DUSP13	NM_001007271.1,NM_001007272.1,NM_001007273.1,NM_016364.3	,,,	686,2775,3042	AA,AG,GG		26.7209,41.9655,31.8853	,,,	,155/249,198/292,105/199	76855412	4147,8859	2203	4300	6503	SO:0001819	synonymous_variant	51207	exon5			GTTGTCGTCCGCC	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.315C>T	10.37:g.76855412G>A		Somatic	122	2	0.0163934		WXS	Illumina HiSeq	Phase_I	125	124	0.992	NM_001007273	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Silent	SNP	ENST00000472493.2	37	CCDS7346.1																																																																																			G|0.642;A|0.358	0.358	strong		0.552	DUSP13-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048786.3		
SNED1	25992	hgsc.bcm.edu	37	2	242004866	242004866	+	Silent	SNP	A	A	G	rs2286321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242004866A>G	ENST00000310397.8	+	21	2865	c.2865A>G	c.(2863-2865)acA>acG	p.T955T	SNED1_ENST00000342631.6_Silent_p.T955T|SNED1_ENST00000401884.1_Silent_p.T955T|SNED1_ENST00000405547.3_Silent_p.T955T|AC005237.4_ENST00000458377.1_RNA	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	955	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		ACCGCCGCACAGACTTTGTGG	0.622													G|||	1910	0.38139	0.6596	0.2795	5008	,	,		16152	0.4097		0.2008	False		,,,				2504	0.2342				p.T955T		Atlas-SNP	.											.	SNED1	76	.	0			c.A2865G						PASS	.	G		2180,1854		610,960,447	46.0	58.0	54.0		2865	-9.6	0.1	2	dbSNP_100	54	1446,6904		135,1176,2864	no	coding-synonymous	SNED1	NM_001080437.1		745,2136,3311	GG,GA,AA		17.3174,45.9593,29.2797		955/1414	242004866	3626,8758	2017	4175	6192	SO:0001819	synonymous_variant	25992	exon21			CCGCACAGACTTT	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.2865A>G	2.37:g.242004866A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																			A|0.630;G|0.370	0.370	strong		0.622	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
C5orf46	389336	hgsc.bcm.edu	37	5	147286013	147286013	+	Missense_Mutation	SNP	A	A	T	rs7722926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147286013A>T	ENST00000318315.4	-	1	52	c.52T>A	c.(52-54)Ttc>Atc	p.F18I	C5orf46_ENST00000515291.1_Missense_Mutation_p.F18I|C5orf46_ENST00000510432.1_5'UTR	NM_206966.2	NP_996849.2	Q6UWT4	CE046_HUMAN	chromosome 5 open reading frame 46	18			F -> I (in dbSNP:rs7722926). {ECO:0000269|PubMed:14702039}.			extracellular vesicular exosome (GO:0070062)				NS(1)|lung(1)|prostate(1)	3						CAGGTCAGGAATAAGACAAGC	0.458													T|||	1475	0.294529	0.6619	0.147	5008	,	,		17834	0.2232		0.0905	False		,,,				2504	0.1861				p.F18I		Atlas-SNP	.											.	C5orf46	8	.	0			c.T52A						PASS	.	T	ILE/PHE	2689,1717	514.9+/-368.7	819,1051,333	99.0	87.0	91.0		52	3.7	0.9	5	dbSNP_116	91	901,7699	777.8+/-407.7	52,797,3451	yes	missense	C5orf46	NM_206966.2	21	871,1848,3784	TT,TA,AA		10.4767,38.9696,27.6026	benign	18/88	147286013	3590,9416	2203	4300	6503	SO:0001583	missense	389336	exon1			TCAGGAATAAGAC		CCDS34267.1	5q33.1	2013-12-13			ENSG00000178776	ENSG00000178776			33768	protein-coding gene	gene with protein product	"""skin and saliva secreted protein 1"""						Standard	NM_206966		Approved	MGC23985, SSSP1	uc003lou.3	Q6UWT4	OTTHUMG00000163420	ENST00000318315.4:c.52T>A	5.37:g.147286013A>T	ENSP00000315370:p.Phe18Ile	Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	368	368	1	NM_206966	A8K038|Q8WU04	Missense_Mutation	SNP	ENST00000318315.4	37	CCDS34267.1	576	0.26373626373626374	326	0.6626016260162602	56	0.15469613259668508	127	0.22202797202797203	67	0.08839050131926121	T	5.187	0.220059	0.09863	0.610304	0.104767	ENSG00000178776	ENST00000318315;ENST00000515291	T;T	0.36340	1.26;1.26	4.88	3.7	0.42460	.	0.000000	0.49305	N	0.000160	T	0.00012	0.0000	.	.	.	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46359	-0.9197	8	0.02654	T	1	-13.5441	5.7677	0.18235	0.1688:0.0:0.177:0.6542	rs7722926;rs56595669;rs7722926	18	Q6UWT4	CE046_HUMAN	I	18	ENSP00000315370:F18I;ENSP00000425984:F18I	ENSP00000315370:F18I	F	-	1	0	C5orf46	147266206	0.993000	0.37304	0.941000	0.38009	0.994000	0.84299	1.300000	0.33436	0.443000	0.26582	-0.257000	0.10917	TTC	A|0.710;T|0.290	0.290	strong		0.458	C5orf46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373314.1	NM_206966	
MYOM1	8736	hgsc.bcm.edu	37	18	3188976	3188976	+	Missense_Mutation	SNP	A	A	G	rs1962519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3188976A>G	ENST00000356443.4	-	4	874	c.541T>C	c.(541-543)Tct>Cct	p.S181P	RP13-270P17.2_ENST00000580139.1_RNA|MYOM1_ENST00000261606.7_Missense_Mutation_p.S181P|MYOM1_ENST00000400569.3_Missense_Mutation_p.S181P	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	181			S -> P (in dbSNP:rs1962519). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505783}.		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						GACTGTTTAGATGTTGTGATT	0.488													A|||	2220	0.443291	0.1641	0.402	5008	,	,		17012	0.8363		0.4026	False		,,,				2504	0.4867				p.S181P		Atlas-SNP	.											.	MYOM1	192	.	0			c.T541C						PASS	.	A	PRO/SER,PRO/SER	747,3251		72,603,1324	325.0	297.0	306.0		541,541	1.3	0.6	18	dbSNP_92	306	3467,4881		745,1977,1452	yes	missense,missense	MYOM1	NM_003803.3,NM_019856.1	74,74	817,2580,2776	GG,GA,AA		41.5309,18.6843,34.1325	benign,benign	181/1686,181/1590	3188976	4214,8132	1999	4174	6173	SO:0001583	missense	8736	exon4			GTTTAGATGTTGT	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.541T>C	18.37:g.3188976A>G	ENSP00000348821:p.Ser181Pro	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	203	83	0.408867	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	1011	0.46291208791208793	85	0.17276422764227642	139	0.3839779005524862	477	0.833916083916084	310	0.40897097625329815	A	12.33	1.904802	0.33628	0.186843	0.415309	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.54479	0.73;0.74;0.57	4.27	1.27	0.21489	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	6.999999999979245E-6	D;P	0.56968	0.978;0.856	P;B	0.53146	0.719;0.312	T	0.31806	-0.9930	8	0.27082	T	0.32	.	7.6383	0.28280	0.5186:0.0:0.0:0.4814	rs1962519;rs17531602;rs60425523;rs1962519	181;181	P52179-2;P52179	.;MYOM1_HUMAN	P	181	ENSP00000348821:S181P;ENSP00000383413:S181P;ENSP00000261606:S181P	ENSP00000261606:S181P	S	-	1	0	MYOM1	3178976	0.077000	0.21312	0.612000	0.29024	0.571000	0.35966	-0.165000	0.09968	0.370000	0.24538	0.491000	0.48974	TCT	A|0.536;G|0.464	0.464	strong		0.488	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
TSKS	60385	hgsc.bcm.edu	37	19	50248556	50248556	+	Missense_Mutation	SNP	C	C	T	rs34082111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50248556C>T	ENST00000246801.3	-	7	1172	c.1090G>A	c.(1090-1092)Ggc>Agc	p.G364S	TSKS_ENST00000358830.3_Missense_Mutation_p.G164S	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	364					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		CCTAGGAAGCCGTCGACCCTG	0.706													C|||	54	0.0107827	0.0401	0.0014	5008	,	,		13851	0.0		0.0	False		,,,				2504	0.0				p.G364S		Atlas-SNP	.											.	TSKS	97	.	0			c.G1090A						PASS	.	C	SER/GLY	120,4282		3,114,2084	23.0	23.0	23.0		1090	3.8	1.0	19	dbSNP_126	23	1,8595		0,1,4297	yes	missense	TSKS	NM_021733.1	56	3,115,6381	TT,TC,CC		0.0116,2.726,0.9309	probably-damaging	364/593	50248556	121,12877	2201	4298	6499	SO:0001583	missense	60385	exon7			GGAAGCCGTCGAC	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 161"""	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.1090G>A	19.37:g.50248556C>T	ENSP00000246801:p.Gly364Ser	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	61	38	0.622951	NM_021733	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	25.2	4.614167	0.87359	0.02726	1.16E-4	ENSG00000126467	ENST00000246801;ENST00000358830	T;T	0.55588	0.51;0.51	4.89	3.84	0.44239	.	0.000000	0.53938	D	0.000058	T	0.14227	0.0344	L	0.29908	0.895	0.34627	D	0.719177	P	0.39964	0.697	B	0.32393	0.145	T	0.40403	-0.9565	10	0.35671	T	0.21	-19.1441	10.8376	0.46696	0.0:0.91:0.0:0.09	rs34082111	364	Q9UJT2	TSKS_HUMAN	S	364;164	ENSP00000246801:G364S;ENSP00000351691:G164S	ENSP00000246801:G364S	G	-	1	0	TSKS	54940368	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.050000	0.41297	1.273000	0.44346	0.561000	0.74099	GGC	C|0.991;T|0.009	0.009	strong		0.706	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	
AHNAK2	113146	hgsc.bcm.edu	37	14	105408315	105408315	+	Silent	SNP	T	T	C	rs28600075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105408315T>C	ENST00000333244.5	-	7	13592	c.13473A>G	c.(13471-13473)ccA>ccG	p.P4491P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4491						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)			CCTCCATCTTTGGCGCAGACA	0.577													-|||	2782	0.555511	0.646	0.5115	5008	,	,		20612	0.4117		0.5338	False		,,,				2504	0.635				p.P4491P		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A13473G						PASS	.	C		2760,1322		941,878,222	158.0	166.0	163.0		13473	-1.1	0.0	14	dbSNP_125	163	4533,3827		1246,2041,893	no	coding-synonymous	AHNAK2	NM_138420.2		2187,2919,1115	CC,CT,TT		45.7775,32.3861,41.384		4491/5796	105408315	7293,5149	2041	4180	6221	SO:0001819	synonymous_variant	113146	exon7			CATCTTTGGCGCA	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.13473A>G	14.37:g.105408315T>C		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	249	249	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			T|0.466;C|0.534	0.534	strong		0.577	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SNED1	25992	hgsc.bcm.edu	37	2	242021742	242021742	+	Missense_Mutation	SNP	G	G	T	rs2108485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242021742G>T	ENST00000310397.8	+	29	4084	c.4084G>T	c.(4084-4086)Gcc>Tcc	p.A1362S	SNED1_ENST00000342631.6_Missense_Mutation_p.A1329S|SNED1_ENST00000405547.3_Missense_Mutation_p.A1329S|MTERFD2_ENST00000464344.2_Intron	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1362			A -> S (in dbSNP:rs2108485). {ECO:0000269|PubMed:15489334}.		cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		CGAGACAAAGGCCTTTCCAGT	0.572													T|||	2132	0.425719	0.7511	0.3545	5008	,	,		18972	0.5546		0.168	False		,,,				2504	0.1687				p.A1362S		Atlas-SNP	.											.	SNED1	76	.	0			c.G4084T						PASS	.	T	SER/ALA	2626,1462		858,910,276	203.0	220.0	215.0		4084	3.3	0.8	2	dbSNP_96	215	1345,7043		100,1145,2949	yes	missense	SNED1	NM_001080437.1	99	958,2055,3225	TT,TG,GG		16.0348,35.7632,31.8291	benign	1362/1414	242021742	3971,8505	2044	4194	6238	SO:0001583	missense	25992	exon29			ACAAAGGCCTTTC	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.4084G>T	2.37:g.242021742G>T	ENSP00000308893:p.Ala1362Ser	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	117	115	0.982906	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	919	0.4207875457875458	357	0.725609756097561	118	0.3259668508287293	321	0.5611888111888111	123	0.16226912928759896	T	1.878	-0.458563	0.04508	0.642368	0.160348	ENSG00000162804	ENST00000405547;ENST00000310397;ENST00000342631	T;D;T	0.81739	-1.41;-1.53;-1.4	4.48	3.31	0.37934	.	0.172481	0.27768	N	0.017929	T	0.00012	0.0000	N	0.01493	-0.835	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.46162	-0.9211	9	0.02654	T	1	.	9.5049	0.39040	0.0:0.0:0.3742:0.6258	rs2108485;rs17856779;rs52791508;rs57854954;rs2108485	1329;1362	B5MEF5;Q8TER0	.;SNED1_HUMAN	S	1329;1362;1329	ENSP00000386007:A1329S;ENSP00000308893:A1362S;ENSP00000342992:A1329S	ENSP00000308893:A1362S	A	+	1	0	SNED1	241670415	0.999000	0.42202	0.796000	0.32109	0.768000	0.43524	1.115000	0.31209	0.137000	0.18759	-0.525000	0.04345	GCC	G|0.576;T|0.424	0.424	strong		0.572	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
ZC3H4	23211	hgsc.bcm.edu	37	19	47575279	47575279	+	Silent	SNP	G	G	C	rs76187449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47575279G>C	ENST00000253048.5	-	13	1939	c.1902C>G	c.(1900-1902)ccC>ccG	p.P634P	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	634	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		ggtgcatgtcggggtgcatgt	0.672													g|||	134	0.0267572	0.0938	0.0115	5008	,	,		17976	0.0		0.002	False		,,,				2504	0.0				p.P634P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.C1902G						PASS	.						31.0	36.0	35.0					19																	47575279		2097	4223	6320	SO:0001819	synonymous_variant	23211	exon13			CATGTCGGGGTGC	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1902C>G	19.37:g.47575279G>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			.	.	weak		0.672	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
MBOAT2	129642	hgsc.bcm.edu	37	2	8998971	8998971	+	Silent	SNP	T	T	C	rs35943010	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:8998971T>C	ENST00000305997.3	-	13	1599	c.1401A>G	c.(1399-1401)aaA>aaG	p.K467K	MBOAT2_ENST00000486484.1_5'Flank	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	467					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTCTTTGAGTTTTTTTCACTG	0.318													T|||	74	0.0147764	0.0227	0.0086	5008	,	,		17674	0.003		0.004	False		,,,				2504	0.0317				p.K467K	Ovarian(194;1699 3813 22401)	Atlas-SNP	.											.	MBOAT2	36	.	0			c.A1401G						PASS	.	T		69,4337	61.7+/-98.7	1,67,2135	77.0	79.0	78.0		1401	1.2	0.8	2	dbSNP_126	78	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	MBOAT2	NM_138799.2		1,81,6421	CC,CT,TT		0.1628,1.566,0.6382		467/521	8998971	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	129642	exon13			TTGAGTTTTTTTC	BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"""O-acyltransferase (membrane bound) domain containing 2"""	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.1401A>G	2.37:g.8998971T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Silent	SNP	ENST00000305997.3	37	CCDS1660.1																																																																																			T|0.994;C|0.006	0.006	strong		0.318	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799	
CHST5	23563	hgsc.bcm.edu	37	16	75563746	75563746	+	Silent	SNP	T	T	G	rs8048818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75563746T>G	ENST00000336257.3	-	3	1931	c.537A>C	c.(535-537)ccA>ccC	p.P179P	RP11-77K12.7_ENST00000460606.1_3'UTR|CHST5_ENST00000541075.1_Silent_p.P185P	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	179					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)	24						CCAGGCTGAATGGCTGCCGCG	0.672													G|||	1012	0.202077	0.3359	0.1441	5008	,	,		14472	0.2073		0.1998	False		,,,				2504	0.0593				p.P179P		Atlas-SNP	.											.	CHST5	47	.	0			c.A537C						PASS	.	G		1407,2989	676.5+/-403.2	236,935,1027	93.0	101.0	98.0		537	2.7	1.0	16	dbSNP_116	98	1688,6910	730.9+/-406.8	182,1324,2793	no	coding-synonymous	CHST5	NM_024533.4		418,2259,3820	GG,GT,TT		19.6325,32.0064,23.8187		179/412	75563746	3095,9899	2198	4299	6497	SO:0001819	synonymous_variant	23563	exon3			GCTGAATGGCTGC	AF176839	CCDS10919.1	16q23.1	2008-02-05			ENSG00000135702	ENSG00000135702		"""Sulfotransferases, membrane-bound"""	1973	protein-coding gene	gene with protein product		604817				10491328, 11017086	Standard	NM_024533		Approved	I-GLCNAC-6-ST, FLJ22167	uc002fei.3	Q9GZS9	OTTHUMG00000137610	ENST00000336257.3:c.537A>C	16.37:g.75563746T>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	21	0.368421	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Silent	SNP	ENST00000336257.3	37	CCDS10919.1																																																																																			T|0.771;G|0.229	0.229	strong		0.672	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126	
LILRB3	11025	hgsc.bcm.edu	37	19	54725019	54725019	+	Silent	SNP	G	G	A	rs78279726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54725019G>A	ENST00000391750.1	-	6	1027	c.891C>T	c.(889-891)taC>taT	p.Y297Y	LILRB3_ENST00000245620.9_Silent_p.Y297Y|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000407860.2_Silent_p.Y297Y|LILRB3_ENST00000346401.6_Silent_p.Y297Y|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Silent_p.Y297Y|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000424807.1_Silent_p.Y297Y			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	297	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGTGTGCACCGTAGCACCTGT	0.682													.|||	1595	0.31849	0.2345	0.3069	5008	,	,		6728	0.5506		0.3211	False		,,,				2504	0.1984				p.Y297Y		Atlas-SNP	.											.	LILRB3	67	.	0			c.C891T						PASS	.	G	,	679,2939		111,457,1241	24.0	22.0	23.0		891,891	-3.6	0.1	19	dbSNP_131	23	369,3609		134,101,1754	no	coding-synonymous,coding-synonymous	LILRB3	NM_001081450.1,NM_006864.2	,	245,558,2995	AA,AG,GG		9.276,18.7673,13.7967	,	297/633,297/632	54725019	1048,6548	1809	1989	3798	SO:0001819	synonymous_variant	11025	exon5			TGCACCGTAGCAC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.891C>T	19.37:g.54725019G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	300	122	0.406667	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			G|0.702;A|0.298	0.298	strong		0.682	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
BDP1	55814	hgsc.bcm.edu	37	5	70858194	70858194	+	Silent	SNP	C	C	T	rs277941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70858194C>T	ENST00000358731.4	+	38	7853	c.7590C>T	c.(7588-7590)cgC>cgT	p.R2530R	BDP1_ENST00000380675.2_3'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2530					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)		GTAAGAAACGCCTAAAACCTC	0.373													.|||	1621	0.323682	0.1067	0.4928	5008	,	,		15735	0.505		0.335	False		,,,				2504	0.2986				p.R2530R		Atlas-SNP	.											.	BDP1	204	.	0			c.C7590T						PASS	.	C		549,3081		38,473,1304	74.0	69.0	71.0		7590	-0.1	0.4	5	dbSNP_79	71	2805,5341		509,1787,1777	no	coding-synonymous	BDP1	NM_018429.2		547,2260,3081	TT,TC,CC		34.4341,15.124,28.4817		2530/2625	70858194	3354,8422	1815	4073	5888	SO:0001819	synonymous_variant	55814	exon38			GAAACGCCTAAAA	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.7590C>T	5.37:g.70858194C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Silent	SNP	ENST00000358731.4	37	CCDS43328.1																																																																																			C|0.662;T|0.338	0.338	strong		0.373	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
DSPP	1834	hgsc.bcm.edu	37	4	88536460	88536460	+	Silent	SNP	C	C	T	rs199691318		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88536460C>T	ENST00000282478.7	+	4	2679	c.2646C>T	c.(2644-2646)agC>agT	p.S882S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S882S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	882	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcagtgatagcagtgacagca	0.498																																					p.S882S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2646T						PASS	.						73.0	87.0	82.0					4																	88536460		1617	2929	4546	SO:0001819	synonymous_variant	1834	exon5			TGATAGCAGTGAC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2646C>T	4.37:g.88536460C>T		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	327	29	0.088685	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
CPAMD8	27151	hgsc.bcm.edu	37	19	17088299	17088299	+	Missense_Mutation	SNP	T	T	C	rs1824152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17088299T>C	ENST00000443236.1	-	15	1809	c.1778A>G	c.(1777-1779)cAt>cGt	p.H593R	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	546						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						CACGGCCAGATGAAGAGAGGT	0.592													t|||	2839	0.566893	0.9213	0.3963	5008	,	,		17909	0.5625		0.3777	False		,,,				2504	0.408				p.H593R		Atlas-SNP	.											.	CPAMD8	192	.	0			c.A1778G						PASS	.	C	ARG/HIS	3115,813		1259,597,108	39.0	45.0	43.0		1778	-5.2	0.0	19	dbSNP_92	43	2825,5453		475,1875,1789	no	missense	CPAMD8	NM_015692.2	29	1734,2472,1897	CC,CT,TT		34.1266,20.6976,48.6646	benign	593/1933	17088299	5940,6266	1964	4139	6103	SO:0001583	missense	27151	exon15			GCCAGATGAAGAG	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.1778A>G	19.37:g.17088299T>C	ENSP00000402505:p.His593Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	1126|1126	0.5155677655677655|0.5155677655677655	415|415	0.8434959349593496|0.8434959349593496	136|136	0.3756906077348066|0.3756906077348066	306|306	0.534965034965035|0.534965034965035	269|269	0.3548812664907652|0.3548812664907652	t|t	0.001|0.001	-2.964973|-2.964973	0.00049|0.00049	0.793024|0.793024	0.341266|0.341266	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	2.62|2.62	-5.24|-5.24	0.02789|0.02789	Alpha-2-macroglobulin, N-terminal 2 (1);|.	1.028330|.	0.07794|.	N|.	0.955448|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.10664|0.10664	0.02|0.02	0.21604|0.21604	P|P	0.999620117|0.999620117	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.10847|0.10847	-1.0612|-1.0612	8|4	0.15066|.	T|.	0.55|.	.|.	8.2718|8.2718	0.31849|0.31849	0.1001:0.314:0.0:0.5859|0.1001:0.314:0.0:0.5859	rs1824152;rs3745334;rs60607898;rs1824152|rs1824152;rs3745334;rs60607898;rs1824152	546|.	Q8IZJ3|.	CPMD8_HUMAN|.	R|V	593|604	.|.	ENSP00000291440:H593R|.	H|I	-|-	2|1	0|0	CPAMD8|CPAMD8	16949299|16949299	0.003000|0.003000	0.15002|0.15002	0.004000|0.004000	0.12327|0.12327	0.081000|0.081000	0.17604|0.17604	-0.493000|-0.493000	0.06459|0.06459	-3.135000|-3.135000	0.00235|0.00235	-4.516000|-4.516000	0.00005|0.00005	CAT|ATC	.	.	weak		0.592	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
GBX1	2636	hgsc.bcm.edu	37	7	150846188	150846188	+	Missense_Mutation	SNP	C	C	T	rs11975799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150846188C>T	ENST00000297537.4	-	2	579	c.580G>A	c.(580-582)Gca>Aca	p.A194T	GBX1_ENST00000475831.1_5'Flank	NM_001098834.1	NP_001092304.1	Q14549	GBX1_HUMAN	gastrulation brain homeobox 1	194			A -> T (in dbSNP:rs11975799).		adult walking behavior (GO:0007628)|neuron fate commitment (GO:0048663)|proprioception (GO:0019230)|regulation of transcription, DNA-templated (GO:0006355)|sensory neuron axon guidance (GO:0097374)|spinal cord motor neuron differentiation (GO:0021522)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(5)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCTGCTGATGCCTCCAGCTTC	0.582													C|||	117	0.0233626	0.0764	0.0072	5008	,	,		16501	0.006		0.0	False		,,,				2504	0.0051				p.A194T		Atlas-SNP	.											.	GBX1	21	.	0			c.G580A						PASS	.	C	THR/ALA	219,3991		9,201,1895	204.0	220.0	215.0		580	0.8	0.8	7	dbSNP_120	215	4,8462		0,4,4229	yes	missense	GBX1	NM_001098834.1	58	9,205,6124	TT,TC,CC		0.0472,5.2019,1.7592	benign	194/364	150846188	223,12453	2105	4233	6338	SO:0001583	missense	2636	exon2			CTGATGCCTCCAG	L11239	CCDS43682.1	7q36.1	2012-03-09	2005-12-22		ENSG00000164900	ENSG00000164900		"""Homeoboxes / ANTP class : HOXL subclass"""	4185	protein-coding gene	gene with protein product		603354	"""gastrulation brain homeo box 1"""			7903253	Standard	NM_001098834		Approved		uc011kvg.2	Q14549	OTTHUMG00000158751	ENST00000297537.4:c.580G>A	7.37:g.150846188C>T	ENSP00000297537:p.Ala194Thr	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_001098834		Missense_Mutation	SNP	ENST00000297537.4	37	CCDS43682.1	41	0.018772893772893772	33	0.06707317073170732	4	0.011049723756906077	4	0.006993006993006993	0	0.0	C	13.43	2.233908	0.39498	0.052019	4.72E-4	ENSG00000164900	ENST00000297537	D	0.91894	-2.93	4.95	0.769	0.18492	.	0.952841	0.08341	U	0.960876	T	0.27489	0.0675	N	0.08118	0	0.42774	D	0.993847	B	0.10296	0.003	B	0.06405	0.002	T	0.57165	-0.7858	10	0.19147	T	0.46	-4.7045	3.1719	0.06555	0.1248:0.4649:0.2571:0.1532	rs11975799;rs11975799	194	Q14549	GBX1_HUMAN	T	194	ENSP00000297537:A194T	ENSP00000297537:A194T	A	-	1	0	GBX1	150477121	0.997000	0.39634	0.847000	0.33407	0.987000	0.75469	1.560000	0.36331	0.141000	0.18875	-0.373000	0.07131	GCA	C|0.979;T|0.021	0.021	strong		0.582	GBX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352029.1		
LY75	4065	hgsc.bcm.edu	37	2	160673405	160673405	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160673405C>T	ENST00000263636.4	-	30	4319	c.4292G>A	c.(4291-4293)aGc>aAc	p.S1431N	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.S1431N|LY75_ENST00000554112.1_Missense_Mutation_p.S1431N|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.S1431N|LY75_ENST00000553424.1_Missense_Mutation_p.S1431N	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1431	C-type lectin 9. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GTTGTGAACGCTTGCCAAGTG	0.388																																					p.S1431N		Atlas-SNP	.											LY75,NS,carcinoma,-1,1	LY75	151	1	0			c.G4292A						scavenged	.						156.0	153.0	154.0					2																	160673405		2203	4300	6503	SO:0001583	missense	4065	exon30			TGAACGCTTGCCA	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.4292G>A	2.37:g.160673405C>T	ENSP00000263636:p.Ser1431Asn	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	146	3	0.0205479	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.453325	0.84209	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	5.89	5.89	0.94794	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.41294	D	0.000908	T	0.61540	0.2355	H	0.94306	3.52	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.91635	0.999;0.999;0.994	T	0.71705	-0.4512	10	0.87932	D	0	-22.4771	19.8311	0.96636	0.0:1.0:0.0:0.0	.	1431;1431;1431	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	N	1431	ENSP00000451511:S1431N;ENSP00000451446:S1431N;ENSP00000263636:S1431N;ENSP00000423463:S1431N;ENSP00000421035:S1431N	ENSP00000423463:S1431N	S	-	2	0	LY75;LY75-CD302	160381651	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	3.614000	0.54160	2.787000	0.95880	0.650000	0.86243	AGC	.	.	none		0.388	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
SLC36A3	285641	hgsc.bcm.edu	37	5	150657173	150657173	+	Silent	SNP	T	T	C	rs56998614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150657173T>C	ENST00000335230.3	-	10	1605	c.1194A>G	c.(1192-1194)gtA>gtG	p.V398V	SLC36A3_ENST00000377713.3_Silent_p.V439V	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	398						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)			TCACGGAGCCTACCAGGGAGA	0.537													C|||	638	0.127396	0.3245	0.049	5008	,	,		18658	0.0863		0.005	False		,,,				2504	0.0849				p.V439V		Atlas-SNP	.											.	SLC36A3	54	.	0			c.A1317G						PASS	.	C	,	1108,3298	718.1+/-408.8	157,794,1252	61.0	56.0	58.0		1317,1194	3.8	1.0	5	dbSNP_129	58	23,8577	818.2+/-406.9	1,21,4278	no	coding-synonymous,coding-synonymous	SLC36A3	NM_001145017.1,NM_181774.3	,	158,815,5530	CC,CT,TT		0.2674,25.1475,8.696	,	439/512,398/471	150657173	1131,11875	2203	4300	6503	SO:0001819	synonymous_variant	285641	exon11			GGAGCCTACCAGG	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.1194A>G	5.37:g.150657173T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Silent	SNP	ENST00000335230.3	37	CCDS4314.1																																																																																			T|0.911;C|0.089	0.089	strong		0.537	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
SHISA6	388336	hgsc.bcm.edu	37	17	11461483	11461483	+	Silent	SNP	C	C	T	rs148413919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11461483C>T	ENST00000409168.3	+	4	1365	c.1365C>T	c.(1363-1365)taC>taT	p.Y455Y	SHISA6_ENST00000432116.3_Silent_p.Y487Y|SHISA6_ENST00000441885.3_Silent_p.Y506Y	NM_001173461.1	NP_001166932.1	Q6ZSJ9	SHSA6_HUMAN	shisa family member 6	455						alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)				breast(1)|endometrium(4)	5						ATAACTCATACGCCACCCTGG	0.612													C|||	33	0.00658946	0.025	0.0	5008	,	,		16338	0.0		0.0	False		,,,				2504	0.0				p.Y506Y		Atlas-SNP	.											.	SHISA6	44	.	0			c.C1518T						PASS	.	C	,,	34,1350		0,34,658	65.0	62.0	63.0		1365,1461,1518	0.2	1.0	17	dbSNP_134	63	1,3181		0,1,1590	no	coding-synonymous,coding-synonymous,coding-synonymous	SHISA6	NM_001173461.1,NM_001173462.1,NM_207386.3	,,	0,35,2248	TT,TC,CC		0.0314,2.4566,0.7665	,,	455/501,487/533,506/552	11461483	35,4531	692	1591	2283	SO:0001819	synonymous_variant	388336	exon6			CTCATACGCCACC	AK127379, AK128003	CCDS45615.1, CCDS54089.1, CCDS54090.1	17p13.1-p12	2013-07-31	2013-07-31		ENSG00000188803	ENSG00000188803		"""Shisa homologs"""	34491	protein-coding gene	gene with protein product			"""shisa homolog 6 (Xenopus laevis)"""				Standard	NM_207386		Approved	FLJ45455	uc002gnc.2	Q6ZSJ9	OTTHUMG00000154121	ENST00000409168.3:c.1365C>T	17.37:g.11461483C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_207386	B3KXV5|Q4PL63	Silent	SNP	ENST00000409168.3	37	CCDS54090.1																																																																																			C|0.994;T|0.006	0.006	strong		0.612	SHISA6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000333970.2	NM_207386	
FBN2	2201	hgsc.bcm.edu	37	5	127624905	127624905	+	Missense_Mutation	SNP	T	T	A	rs149071226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:127624905T>A	ENST00000508053.1	-	58	7525	c.6551A>T	c.(6550-6552)aAt>aTt	p.N2184I	FBN2_ENST00000262464.4_Missense_Mutation_p.N2184I			P35556	FBN2_HUMAN	fibrillin 2	2184	EGF-like 36; 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)		ACATTGACCATTTGAACAAAT	0.453													T|||	3	0.000599042	0.0023	0.0	5008	,	,		18157	0.0		0.0	False		,,,				2504	0.0				p.N2184I		Atlas-SNP	.											.	FBN2	858	.	0			c.A6551T						PASS	.	T	ILE/ASN	19,4387	26.2+/-53.5	0,19,2184	161.0	152.0	155.0		6551	5.8	1.0	5	dbSNP_134	155	0,8600		0,0,4300	yes	missense	FBN2	NM_001999.3	149	0,19,6484	AA,AT,TT		0.0,0.4312,0.1461	possibly-damaging	2184/2913	127624905	19,12987	2203	4300	6503	SO:0001583	missense	2201	exon52			TGACCATTTGAAC	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.6551A>T	5.37:g.127624905T>A	ENSP00000424571:p.Asn2184Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	110	43	0.390909	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.385239	0.82792	0.004312	0.0	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.92647	-3.08;-3.08	5.76	5.76	0.90799	Matrix fibril-associated (1);EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000002	D	0.95768	0.8623	M	0.89030	3	0.58432	D	0.999995	D	0.58620	0.983	P	0.60012	0.867	D	0.96209	0.9151	10	0.87932	D	0	.	12.1851	0.54234	0.0:0.0683:0.0:0.9317	.	2184	P35556	FBN2_HUMAN	I	2184	ENSP00000262464:N2184I;ENSP00000424571:N2184I	ENSP00000262464:N2184I	N	-	2	0	FBN2	127652804	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.317000	0.51968	2.324000	0.78689	0.533000	0.62120	AAT	T|0.998;A|0.002	0.002	strong		0.453	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
ACSM2B	348158	hgsc.bcm.edu	37	16	20554582	20554582	+	Missense_Mutation	SNP	T	T	G	rs142632912		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20554582T>G	ENST00000329697.6	-	11	1452	c.1284A>C	c.(1282-1284)gaA>gaC	p.E428D	ACSM2B_ENST00000567288.1_5'Flank|ACSM2B_ENST00000565232.1_Missense_Mutation_p.E428D|ACSM2B_ENST00000567001.1_Missense_Mutation_p.E428D|ACSM2B_ENST00000565322.1_Missense_Mutation_p.E349D	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	428					fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						TGTCGGGATTTTCCTGGTGAC	0.488																																					p.E428D		Atlas-SNP	.											ACSM2B,NS,carcinoma,-2,1	ACSM2B	121	1	0			c.A1284C						scavenged	.						80.0	137.0	118.0					16																	20554582		2089	4300	6389	SO:0001583	missense	348158	exon12			GGGATTTTCCTGG	AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813		"""Acyl-CoA synthetase family"""	30931	protein-coding gene	gene with protein product	"""xenobiotic/medium chain fatty acid:CoA ligase"""	614359	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2		12616642	Standard	NM_182617		Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.1284A>C	16.37:g.20554582T>G	ENSP00000327453:p.Glu428Asp	Somatic	366	48	0.131148		WXS	Illumina HiSeq	Phase_I	257	110	0.428016	NM_182617	Q86YT1	Missense_Mutation	SNP	ENST00000329697.6	37	CCDS10586.1	212	0.09706959706959707	104	0.21138211382113822	22	0.06077348066298342	25	0.043706293706293704	61	0.08047493403693931	G	0.003	-2.499652	0.00157	.	.	ENSG00000066813	ENST00000329697	T	0.47177	0.85	3.26	1.14	0.20703	AMP-dependent synthetase/ligase (1);	0.721394	0.11798	N	0.528403	T	0.00012	0.0000	N	0.02830	-0.485	0.21020	P	0.999801927	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.22138	-1.0225	9	0.02654	T	1	-0.0081	2.4769	0.04578	0.333:0.0:0.2965:0.3705	.	428;428	A8K051;Q68CK6	.;ACS2B_HUMAN	D	428	ENSP00000327453:E428D	ENSP00000327453:E428D	E	-	3	2	ACSM2B	20462083	1.000000	0.71417	0.025000	0.17156	0.005000	0.04900	1.211000	0.32382	-0.079000	0.12707	-0.917000	0.02746	GAA	.	.	weak		0.488	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254417.2	NM_182617	
GNAI1	2770	hgsc.bcm.edu	37	7	79840339	79840339	+	Silent	SNP	C	C	T	rs12721454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:79840339C>T	ENST00000351004.3	+	6	1018	c.645C>T	c.(643-645)ttC>ttT	p.F215F	GNAI1_ENST00000457358.2_Silent_p.F163F	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	215					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						TTCATTGCTTCGAAGGAGTGA	0.413													C|||	376	0.0750799	0.2731	0.0187	5008	,	,		18249	0.0		0.002	False		,,,				2504	0.0				p.F215F		Atlas-SNP	.											.	GNAI1	44	.	0			c.C645T						PASS	.	C		888,3518	344.6+/-308.2	93,702,1408	170.0	141.0	151.0		645	-3.1	1.0	7	dbSNP_123	151	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous	GNAI1	NM_002069.5		93,705,5705	TT,TC,CC		0.0349,20.1543,6.8507		215/355	79840339	891,12115	2203	4300	6503	SO:0001819	synonymous_variant	2770	exon6			TTGCTTCGAAGGA	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"""Gi1 protein alpha subunit"""	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.645C>T	7.37:g.79840339C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	145	85	0.586207	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Silent	SNP	ENST00000351004.3	37	CCDS5595.1																																																																																			C|0.935;T|0.065	0.065	strong		0.413	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069	
OBSCN	84033	hgsc.bcm.edu	37	1	228560181	228560181	+	Silent	SNP	G	G	A	rs62640372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228560181G>A	ENST00000422127.1	+	94	21746	c.21702G>A	c.(21700-21702)tcG>tcA	p.S7234S	OBSCN_ENST00000570156.2_Silent_p.S8191S|OBSCN_ENST00000366707.4_Silent_p.S4868S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7234					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)				AGTCCCAGTCGGAGGAGCAGC	0.692													G|||	32	0.00638978	0.0227	0.0014	5008	,	,		15712	0.001		0.0	False		,,,				2504	0.0				p.S8191S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G24573A						PASS	.	G		93,4067		0,93,1987	13.0	16.0	15.0		21702	-2.1	0.6	1	dbSNP_129	15	0,8404		0,0,4202	no	coding-synonymous	OBSCN	NM_001098623.1		0,93,6189	AA,AG,GG		0.0,2.2356,0.7402		7234/7969	228560181	93,12471	2080	4202	6282	SO:0001819	synonymous_variant	84033	exon105			CCAGTCGGAGGAG	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.21702G>A	1.37:g.228560181G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	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	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	6.630	0.484618	0.12641	0.022356	0.0	ENSG00000154358	ENST00000441106	.	.	.	1.05	-2.1	0.07210	.	.	.	.	.	T	0.09774	0.0240	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24835	-1.0149	4	.	.	.	.	2.4475	0.04509	0.0:0.253:0.2936:0.4534	rs62640372	.	.	.	R	1851	.	.	G	+	1	0	OBSCN	226626804	0.013000	0.17824	0.600000	0.28864	0.363000	0.29612	-0.971000	0.03806	0.119000	0.18210	0.121000	0.15741	GGA	G|0.996;A|0.004	0.004	strong		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CDAN1	146059	hgsc.bcm.edu	37	15	43028592	43028592	+	Silent	SNP	G	G	A	rs7167392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43028592G>A	ENST00000356231.3	-	2	500	c.477C>T	c.(475-477)ccC>ccT	p.P159P		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	159					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)		TGGGGCGGCTGGGGCTGCCAG	0.736													G|||	1305	0.260583	0.4365	0.1427	5008	,	,		10276	0.0546		0.2227	False		,,,				2504	0.3579				p.P159P		Atlas-SNP	.											.	CDAN1	70	.	0			c.C477T						PASS	.	G		1658,2690		315,1028,831	16.0	19.0	18.0		477	-2.9	0.3	15	dbSNP_116	18	1804,6730		201,1402,2664	no	coding-synonymous	CDAN1	NM_138477.2		516,2430,3495	AA,AG,GG		21.139,38.1325,26.8747		159/1228	43028592	3462,9420	2174	4267	6441	SO:0001819	synonymous_variant	146059	exon2			GCGGCTGGGGCTG	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.477C>T	15.37:g.43028592G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Silent	SNP	ENST00000356231.3	37	CCDS32209.1																																																																																			G|0.766;A|0.234	0.234	strong		0.736	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
TCN2	6948	hgsc.bcm.edu	37	22	31011350	31011350	+	Missense_Mutation	SNP	C	C	T	rs35838082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31011350C>T	ENST00000215838.3	+	5	1137	c.643C>T	c.(643-645)Cgg>Tgg	p.R215W	TCN2_ENST00000405742.3_Missense_Mutation_p.R211W|TCN2_ENST00000407817.3_Missense_Mutation_p.R188W			P20062	TCO2_HUMAN	transcobalamin II	215			R -> W (in dbSNP:rs35838082).		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)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|prostate(2)|urinary_tract(1)	22					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAACCCTGGTCGGAGACAACG	0.557													C|||	365	0.0728834	0.2443	0.0159	5008	,	,		21382	0.001		0.006	False		,,,				2504	0.0245				p.R215W		Atlas-SNP	.											.	TCN2	44	.	0			c.C643T						PASS	.	C	TRP/ARG,TRP/ARG	1044,3362	382.1+/-324.3	124,796,1283	87.0	77.0	81.0		643,562	5.8	0.0	22	dbSNP_126	81	58,8542	35.9+/-90.5	0,58,4242	yes	missense,missense	TCN2	NM_000355.3,NM_001184726.1	101,101	124,854,5525	TT,TC,CC		0.6744,23.695,8.473	probably-damaging,probably-damaging	215/428,188/401	31011350	1102,11904	2203	4300	6503	SO:0001583	missense	6948	exon5			CCTGGTCGGAGAC		CCDS13881.1, CCDS54519.1	22q12.2	2014-09-17	2010-05-11		ENSG00000185339	ENSG00000185339			11653	protein-coding gene	gene with protein product	"""macrocytic anemia"""	613441	"""transcobalamin II; macrocytic anemia"""			1708393, 7742531	Standard	NM_000355		Approved	D22S676, D22S750, TC2	uc003aip.2	P20062	OTTHUMG00000151095	ENST00000215838.3:c.643C>T	22.37:g.31011350C>T	ENSP00000215838:p.Arg215Trp	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	208	208	1	NM_000355	Q96FD4|Q9BVI8|Q9UCI5|Q9UCI6|Q9UDM0	Missense_Mutation	SNP	ENST00000215838.3	37	CCDS13881.1	126	0.057692307692307696	115	0.23373983739837398	5	0.013812154696132596	0	0.0	6	0.0079155672823219	C	20.4	3.985921	0.74589	0.23695	0.006744	ENSG00000185339	ENST00000215838;ENST00000405742;ENST00000407817	T;T;T	0.15952	2.38;2.38;2.38	5.82	5.82	0.92795	.	0.978539	0.08426	N	0.947638	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999999691	D;D;D	0.60575	0.975;0.988;0.988	P;P;P	0.51229	0.663;0.559;0.559	T	0.48525	-0.9028	9	0.62326	D	0.03	-1.0E-4	17.0097	0.86403	0.0:1.0:0.0:0.0	rs35838082;rs61224137	188;211;215	Q96FD4;B5MBX2;P20062	.;.;TCO2_HUMAN	W	215;211;188	ENSP00000215838:R215W;ENSP00000385914:R211W;ENSP00000384914:R188W	ENSP00000215838:R215W	R	+	1	2	TCN2	29341350	0.001000	0.12720	0.009000	0.14445	0.013000	0.08279	1.271000	0.33098	2.756000	0.94617	0.561000	0.74099	CGG	C|0.925;T|0.075	0.075	strong		0.557	TCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321282.2	NM_000355	
MB	4151	hgsc.bcm.edu	37	22	36007075	36007075	+	Silent	SNP	C	C	T	rs7293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36007075C>T	ENST00000397326.2	-	2	372	c.174G>A	c.(172-174)gcG>gcA	p.A58A	MB_ENST00000397328.1_Silent_p.A58A|MB_ENST00000406324.1_Silent_p.A58A|MB_ENST00000401702.1_Silent_p.A3A|MB_ENST00000359787.1_Silent_p.A58A	NM_005368.2	NP_005359.1	P02144	MYG_HUMAN	myoglobin	58					brown fat cell differentiation (GO:0050873)|enucleate erythrocyte differentiation (GO:0043353)|heart development (GO:0007507)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|slow-twitch skeletal muscle fiber contraction (GO:0031444)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			lung(1)	1						AGTCCTCAGACGCCTTCATCT	0.552													C|||	2659	0.53095	0.4501	0.4712	5008	,	,		21677	0.747		0.4483	False		,,,				2504	0.545				p.A58A	GBM(49;694 1113 16998 18419)|Esophageal Squamous(101;120 1973 10459 37086)	Atlas-SNP	.											MB_ENST00000447607,caecum,carcinoma,0,2	MB	7	2	0			c.G174A						PASS	.	C	,,	1974,2432	556.7+/-379.6	421,1132,650	139.0	110.0	120.0		174,174,174	-11.0	0.0	22	dbSNP_52	120	4016,4584	555.6+/-386.7	954,2108,1238	no	coding-synonymous,coding-synonymous,coding-synonymous	MB	NM_005368.2,NM_203377.1,NM_203378.1	,,	1375,3240,1888	TT,TC,CC		46.6977,44.8025,46.0557	,,	58/155,58/155,58/155	36007075	5990,7016	2203	4300	6503	SO:0001819	synonymous_variant	4151	exon3			CTCAGACGCCTTC		CCDS13917.1	22q13.1	2012-10-02			ENSG00000198125	ENSG00000198125			6915	protein-coding gene	gene with protein product		160000				10591208, 2989088	Standard	NM_005368		Approved	PVALB	uc003anz.3	P02144	OTTHUMG00000150606	ENST00000397326.2:c.174G>A	22.37:g.36007075C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_203377	Q52H51|Q5THY7	Silent	SNP	ENST00000397326.2	37	CCDS13917.1																																																																																			C|0.504;T|0.496	0.496	strong		0.552	MB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319057.2	NM_203377	
MUC17	140453	hgsc.bcm.edu	37	7	100683156	100683156	+	Missense_Mutation	SNP	C	C	T	rs79046921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100683156C>T	ENST00000306151.4	+	3	8523	c.8459C>T	c.(8458-8460)aCg>aTg	p.T2820M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2820	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)					GTCAACCACACGCCAGTGGCC	0.493																																					p.T2820M		Atlas-SNP	.											MUC17,colon,carcinoma,-1,2	MUC17	804	2	0			c.C8459T						scavenged	.	C	MET/THR	620,3786	270.1+/-269.4	46,528,1629	241.0	247.0	245.0		8459	0.9	0.0	7	dbSNP_131	245	6,8594	3.0+/-9.4	0,6,4294	yes	missense	MUC17	NM_001040105.1	81	46,534,5923	TT,TC,CC		0.0698,14.0717,4.8132	probably-damaging	2820/4494	100683156	626,12380	2203	4300	6503	SO:0001583	missense	140453	exon3			ACCACACGCCAGT	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.8459C>T	7.37:g.100683156C>T	ENSP00000302716:p.Thr2820Met	Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	143	77	0.538462	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	77	0.035256410256410256	74	0.15040650406504066	3	0.008287292817679558	0	0.0	0	0.0	C	6.722	0.501948	0.12822	0.140717	6.98E-4	ENSG00000169876	ENST00000306151	T	0.02015	4.5	0.911	0.911	0.19343	.	.	.	.	.	T	0.00039	0.0001	N	0.20986	0.625	0.80722	P	0.0	D	0.76494	0.999	D	0.64877	0.93	T	0.53265	-0.8463	8	0.62326	D	0.03	.	7.81	0.29226	0.0:1.0:0.0:0.0	.	2820	Q685J3	MUC17_HUMAN	M	2820	ENSP00000302716:T2820M	ENSP00000302716:T2820M	T	+	2	0	MUC17	100469876	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.791000	0.26915	0.801000	0.34066	0.134000	0.15878	ACG	A|0.000;C|0.960;T|0.040	0.040	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TBC1D31	93594	hgsc.bcm.edu	37	8	124138855	124138855	+	Silent	SNP	G	G	A	rs16898012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124138855G>A	ENST00000287380.1	+	13	1902	c.1812G>A	c.(1810-1812)ctG>ctA	p.L604L	TBC1D31_ENST00000309336.3_Silent_p.L604L|TBC1D31_ENST00000522420.1_Silent_p.L499L|TBC1D31_ENST00000378080.2_Silent_p.L499L|TBC1D31_ENST00000327098.5_Silent_p.L604L|TBC1D31_ENST00000521676.1_Silent_p.L481L|TBC1D31_ENST00000518805.1_Silent_p.L237L	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	604						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										CCTTCCTTCTGATGACTGTTG	0.423													G|||	1490	0.297524	0.3858	0.3732	5008	,	,		15646	0.1815		0.2525	False		,,,				2504	0.2904				p.L604L		Atlas-SNP	.											.	WDR67	97	.	0			c.G1812A						PASS	.	G	,	1691,2715	513.1+/-368.2	325,1041,837	126.0	120.0	122.0		1812,1812	1.8	1.0	8	dbSNP_123	122	2218,6382	378.1+/-338.8	277,1664,2359	no	coding-synonymous,coding-synonymous	WDR67	NM_001145088.1,NM_145647.3	,	602,2705,3196	AA,AG,GG		25.7907,38.3795,30.0554	,	604/971,604/1067	124138855	3909,9097	2203	4300	6503	SO:0001819	synonymous_variant	93594	exon13			CCTTCTGATGACT	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.1812G>A	8.37:g.124138855G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	162	88	0.54321	NM_001145088	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Silent	SNP	ENST00000287380.1	37	CCDS6338.1																																																																																			G|0.705;A|0.295	0.295	strong		0.423	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	
EPB41L1	2036	hgsc.bcm.edu	37	20	34782171	34782171	+	Silent	SNP	T	T	C	rs2295568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34782171T>C	ENST00000338074.2	+	12	1499	c.1338T>C	c.(1336-1338)caT>caC	p.H446H	EPB41L1_ENST00000373941.1_Silent_p.H446H|EPB41L1_ENST00000441639.1_Silent_p.H384H|EPB41L1_ENST00000202028.5_Silent_p.H384H|EPB41L1_ENST00000373946.3_Silent_p.H415H|EPB41L1_ENST00000373950.2_Silent_p.H349H	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	446					cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					GCGAGAACCATGATGCAGGGC	0.602													C|||	648	0.129393	0.3086	0.0692	5008	,	,		20818	0.1349		0.0139	False		,,,				2504	0.0429				p.H446H		Atlas-SNP	.											.	EPB41L1	111	.	0			c.T1338C						PASS	.	C	,	1155,3251	712.4+/-408.1	157,841,1205	66.0	55.0	59.0		1338,1152	-7.2	0.0	20	dbSNP_100	59	85,8515	815.4+/-407.0	1,83,4216	no	coding-synonymous,coding-synonymous	EPB41L1	NM_012156.2,NM_177996.1	,	158,924,5421	CC,CT,TT		0.9884,26.2143,9.5341	,	446/882,384/780	34782171	1240,11766	2203	4300	6503	SO:0001819	synonymous_variant	2036	exon13			GAACCATGATGCA	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.1338T>C	20.37:g.34782171T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	184	87	0.472826	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Silent	SNP	ENST00000338074.2	37	CCDS13271.1	262	0.11996336996336997	155	0.3150406504065041	29	0.08011049723756906	68	0.11888111888111888	10	0.013192612137203167	C	1.666	-0.510210	0.04231	0.262143	0.009884	ENSG00000088367	ENST00000451082	.	.	.	5.35	-7.15	0.01521	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999801478	.	.	.	.	.	.	T	0.15636	-1.0430	3	.	.	.	.	20.2067	0.98280	0.0:0.6792:0.0:0.3208	rs2295568;rs56428251;rs61316391;rs2295568	.	.	.	T	24	.	.	M	+	2	0	EPB41L1	34245585	0.001000	0.12720	0.042000	0.18584	0.230000	0.25150	-2.445000	0.01011	-1.906000	0.01089	-2.133000	0.00342	ATG	T|0.886;C|0.114	0.114	strong		0.602	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156	
ZNF492	57615	hgsc.bcm.edu	37	19	22848028	22848028	+	Missense_Mutation	SNP	G	G	C	rs3745115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	779	0	0		WXS	Illumina HiSeq	Phase_I	561	299	0.532977	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	
LPP	4026	hgsc.bcm.edu	37	3	188326955	188326955	+	Missense_Mutation	SNP	A	A	G	rs35417432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:188326955A>G	ENST00000312675.4	+	6	682	c.436A>G	c.(436-438)Act>Gct	p.T146A	LPP_ENST00000471917.1_3'UTR|LPP_ENST00000448637.1_Missense_Mutation_p.T146A|LPP_ENST00000543006.1_Missense_Mutation_p.T146A	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	146	Pro-rich.		T -> A (in dbSNP:rs35417432).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TTAGAGCTCCACTGGTTCAAC	0.388			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								A|||	270	0.0539137	0.1899	0.0231	5008	,	,		16335	0.0		0.003	False		,,,				2504	0.0				p.T146A		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	LPP	72	.	0			c.A436G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	779,3627	315.2+/-294.0	66,647,1490	96.0	96.0	96.0		436,436,436	-2.5	0.2	3	dbSNP_126	96	10,8590	5.0+/-18.6	0,10,4290	yes	missense,missense,missense	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	58,58,58	66,657,5780	GG,GA,AA		0.1163,17.6804,6.0664	benign,benign,benign	146/613,146/466,146/613	188326955	789,12217	2203	4300	6503	SO:0001583	missense	4026	exon6			AGCTCCACTGGTT	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.436A>G	3.37:g.188326955A>G	ENSP00000318089:p.Thr146Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	109	46	0.422018	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	37	CCDS3291.1	99	0.04532967032967033	89	0.18089430894308944	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	A	3.408	-0.120818	0.06838	0.176804	0.001163	ENSG00000145012	ENST00000448637;ENST00000416784;ENST00000312675;ENST00000543006	T;T;T;T	0.52057	2.06;1.09;0.68;0.68	5.64	-2.45	0.06481	.	0.868823	0.09583	N	0.782522	T	0.00039	0.0001	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.15930	0.015;0.0;0.0	B;B;B	0.10450	0.005;0.002;0.0	T	0.35001	-0.9806	9	0.07482	T	0.82	.	15.6517	0.77099	0.2645:0.0:0.7355:0.0	rs35417432	146;146;146	B7Z8W0;C9JUT4;Q93052	.;.;LPP_HUMAN	A	146	ENSP00000393602:T146A;ENSP00000410340:T146A;ENSP00000318089:T146A;ENSP00000438891:T146A	ENSP00000318089:T146A	T	+	1	0	LPP	189809649	0.000000	0.05858	0.211000	0.23655	0.179000	0.23085	-0.288000	0.08377	-0.925000	0.03775	0.533000	0.62120	ACT	A|0.939;G|0.061	0.061	strong		0.388	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
HDAC8	55869	hgsc.bcm.edu	37	X	71791912	71791912	+	Silent	SNP	C	C	T	rs11093377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:71791912C>T	ENST00000373573.3	-	2	500	c.159G>A	c.(157-159)caG>caA	p.Q53Q	HDAC8_ENST00000373571.1_Silent_p.Q53Q|HDAC8_ENST00000373556.3_Silent_p.Q53Q|HDAC8_ENST00000373560.2_Silent_p.Q53Q|HDAC8_ENST00000373559.4_Silent_p.Q53Q|HDAC8_ENST00000373554.1_Silent_p.Q53Q|HDAC8_ENST00000439122.2_Silent_p.Q53Q|HDAC8_ENST00000373583.1_Silent_p.Q53Q|HDAC8_ENST00000429103.2_5'UTR|HDAC8_ENST00000373589.4_Silent_p.Q53Q|HDAC8_ENST00000478743.1_5'UTR|HDAC8_ENST00000373561.4_Silent_p.Q53Q	NM_018486.2	NP_060956.1	Q9BY41	HDAC8_HUMAN	histone deacetylase 8	53	Histone deacetylase.				chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cohesin localization to chromatin (GO:0071922)|sister chromatid cohesion (GO:0007062)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|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)|transcription factor binding (GO:0008134)			breast(3)|cervix(1)|endometrium(1)|lung(4)|prostate(1)	10	Renal(35;0.156)				Vorinostat(DB02546)	CTTACCTCATCTGCTTATGCA	0.383													T|||	1576	0.417483	0.5219	0.2867	3775	,	,		13458	0.498		0.0149	False		,,,				2504	0.1738				p.Q53Q		Atlas-SNP	.											.	HDAC8	18	.	0			c.G159A						PASS	.	T	,,,,,	2372,1463		633,761,345,238,226	109.0	85.0	93.0		159,159,159,159,159,159	0.1	1.0	X	dbSNP_120	93	68,6660		1,54,12,2373,1860	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HDAC8	NM_001166418.1,NM_001166419.1,NM_001166420.1,NM_001166422.1,NM_001166448.1,NM_018486.2	,,,,,	634,815,357,2611,2086	TT,TC,T,CC,C		1.0107,38.1486,23.0995	,,,,,	53/287,53/257,53/147,53/159,53/140,53/378	71791912	2440,8123	2203	4300	6503	SO:0001819	synonymous_variant	55869	exon2			CCTCATCTGCTTA	AF230097	CCDS14420.1, CCDS55448.1, CCDS55449.1, CCDS55450.1, CCDS55451.1, CCDS55452.1	Xq13	2014-01-29	2002-09-02	2002-09-06	ENSG00000147099	ENSG00000147099			13315	protein-coding gene	gene with protein product		300269	"""histone deacetylase-like 1"", ""Wilson-Turner X-linked mental retardation syndrome"""	HDACL1, WTS, MRXS6		10756090, 10922473, 22889856	Standard	NM_001166448		Approved	RPD3	uc004eau.3	Q9BY41	OTTHUMG00000021814	ENST00000373573.3:c.159G>A	X.37:g.71791912C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	273	133	0.487179	NM_018486	A6ND12|A6ND61|A6NET3|A6NJR3|A8MQ62|B4DKN0|B4DV22|Q86VC8|Q9NP76|Q9NYH4	Silent	SNP	ENST00000373573.3	37	CCDS14420.1																																																																																			C|0.654;0|0.003	.	strong		0.383	HDAC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057193.2	NM_018486	
RPS6KB2	6199	hgsc.bcm.edu	37	11	67200819	67200819	+	Silent	SNP	C	C	T	rs4930427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67200819C>T	ENST00000312629.5	+	10	852	c.807C>T	c.(805-807)ttC>ttT	p.F269F	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	269	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)	p.F269F(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			AGCCGCCCTTCACCGCAGAGA	0.637													C|||	1783	0.35603	0.3283	0.5389	5008	,	,		17222	0.3264		0.4225	False		,,,				2504	0.226				p.F269F		Atlas-SNP	.											RPS6KB2_ENST00000312629,NS,carcinoma,0,1	RPS6KB2	92	1	1	Substitution - coding silent(1)	stomach(1)	c.C807T						PASS	.	C		1221,2719		198,825,947	89.0	100.0	97.0		807	0.6	1.0	11	dbSNP_111	97	3473,4791		759,1955,1418	no	coding-synonymous	RPS6KB2	NM_003952.2		957,2780,2365	TT,TC,CC		42.0257,30.9898,38.4628		269/483	67200819	4694,7510	1970	4132	6102	SO:0001819	synonymous_variant	6199	exon10			GCCCTTCACCGCA	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"""ribosomal protein S6 kinase, 70kD, polypeptide 2"""			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.807C>T	11.37:g.67200819C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Silent	SNP	ENST00000312629.5	37	CCDS41677.1																																																																																			A|0.000;C|0.599;T|0.400	0.400	strong		0.637	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952	
C10orf12	26148	hgsc.bcm.edu	37	10	98742088	98742088	+	Missense_Mutation	SNP	T	T	C	rs7082522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98742088T>C	ENST00000286067.2	+	1	1048	c.941T>C	c.(940-942)cTt>cCt	p.L314P		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	314			L -> P (in dbSNP:rs7082522).							NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		CCTGCTCACCTTCCTGAAGAG	0.572													T|||	42	0.00838658	0.0234	0.0101	5008	,	,		19340	0.0		0.004	False		,,,				2504	0.0				p.L314P		Atlas-SNP	.											.	C10orf12	94	.	0			c.T941C						PASS	.	T	PRO/LEU	82,4324	69.8+/-107.6	0,82,2121	66.0	67.0	67.0		941	2.5	0.1	10	dbSNP_116	67	19,8581	12.6+/-44.7	0,19,4281	yes	missense	C10orf12	NM_015652.2	98	0,101,6402	CC,CT,TT		0.2209,1.8611,0.7766	benign	314/1248	98742088	101,12905	2203	4300	6503	SO:0001583	missense	26148	exon1			CTCACCTTCCTGA	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.941T>C	10.37:g.98742088T>C	ENSP00000286067:p.Leu314Pro	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	37	CCDS7452.1	9	0.004120879120879121	5	0.01016260162601626	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	T	6.674	0.492926	0.12702	0.018611	0.002209	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.08720	3.06	6.05	2.49	0.30216	.	0.311072	0.22801	N	0.055461	T	0.02156	0.0067	N	0.14661	0.345	0.20638	N	0.999875	B;B	0.17038	0.006;0.02	B;B	0.16722	0.009;0.016	T	0.40850	-0.9541	10	0.33141	T	0.24	0.0135	8.0912	0.30801	0.0:0.3649:0.0:0.6351	rs7082522;rs7082522	148;314	A0PJI9;Q8N655	.;CJ012_HUMAN	P	314;148	ENSP00000286067:L314P	ENSP00000286067:L314P	L	+	2	0	C10orf12	98732078	0.000000	0.05858	0.055000	0.19348	0.931000	0.56810	-0.378000	0.07446	0.189000	0.20188	0.533000	0.62120	CTT	T|0.994;C|0.006	0.006	strong		0.572	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
AP1G2	8906	hgsc.bcm.edu	37	14	24033027	24033027	+	Missense_Mutation	SNP	G	G	A	rs12897422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24033027G>A	ENST00000308724.5	-	11	1885	c.1130C>T	c.(1129-1131)tCc>tTc	p.S377F	RP11-66N24.3_ENST00000555968.1_RNA|AP1G2_ENST00000556277.1_5'Flank|AP1G2_ENST00000397120.3_Missense_Mutation_p.S377F	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	113	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	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	
EPHB3	2049	hgsc.bcm.edu	37	3	184299167	184299167	+	Silent	SNP	T	T	C	rs1138510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184299167T>C	ENST00000330394.2	+	15	3311	c.2859T>C	c.(2857-2859)tcT>tcC	p.S953S	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	953	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			GGTTTGCATCTTTTGACCTGG	0.587													C|||	1660	0.33147	0.5499	0.2435	5008	,	,		18837	0.1677		0.3469	False		,,,				2504	0.2515				p.S953S		Atlas-SNP	.											.	EPHB3	114	.	0			c.T2859C						PASS	.	C		2312,2094	571.9+/-383.2	591,1130,482	93.0	75.0	81.0		2859	3.3	1.0	3	dbSNP_86	81	2718,5882	680.6+/-403.7	437,1844,2019	no	coding-synonymous	EPHB3	NM_004443.3		1028,2974,2501	CC,CT,TT		31.6047,47.5261,38.6745		953/999	184299167	5030,7976	2203	4300	6503	SO:0001819	synonymous_variant	2049	exon15			TGCATCTTTTGAC	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.2859T>C	3.37:g.184299167T>C		Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	306	305	0.996732	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			T|0.632;C|0.368	0.368	strong		0.587	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
SP1	6667	hgsc.bcm.edu	37	12	53777171	53777171	+	Silent	SNP	A	A	G	rs3741651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53777171A>G	ENST00000327443.4	+	3	1538	c.1440A>G	c.(1438-1440)caA>caG	p.Q480Q	SP1_ENST00000426431.2_Silent_p.Q473Q	NM_001251825.1|NM_138473.2	NP_001238754.1|NP_612482.2	P08047	SP1_HUMAN	Sp1 transcription factor	480	Transactivation domain B (Gln-rich).				cellular lipid metabolic process (GO:0044255)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|gene expression (GO:0010467)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|ossification (GO:0001503)|positive regulation by host of viral transcription (GO:0043923)|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)|rhythmic process (GO:0048511)|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)|trophectodermal cell differentiation (GO:0001829)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	bHLH transcription factor binding (GO:0043425)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|histone deacetylase binding (GO:0042826)|HMG box domain binding (GO:0071837)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|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 positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.00527)		CACAAGCCCAAACAATCACCT	0.557													G|||	941	0.187899	0.2216	0.2147	5008	,	,		21711	0.1796		0.162	False		,,,				2504	0.1585				p.Q480Q		Atlas-SNP	.											.	SP1	57	.	0			c.A1440G						PASS	.	G	,	884,3522	742.6+/-411.4	95,694,1414	169.0	162.0	164.0		1419,1440	4.7	1.0	12	dbSNP_107	164	1506,7094	748.0+/-407.3	126,1254,2920	no	coding-synonymous,coding-synonymous	SP1	NM_003109.1,NM_138473.2	,	221,1948,4334	GG,GA,AA		17.5116,20.0635,18.3761	,	473/779,480/786	53777171	2390,10616	2203	4300	6503	SO:0001819	synonymous_variant	6667	exon3			AGCCCAAACAATC	J03133	CCDS8857.1, CCDS44898.1	12q13.1	2013-01-08						"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11205	protein-coding gene	gene with protein product	"""specificity protein 1"""	189906				1662663	Standard	NM_003109		Approved		uc001scw.3	P08047	OTTHUMG00000170047	ENST00000327443.4:c.1440A>G	12.37:g.53777171A>G		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	159	72	0.45283	NM_138473	E4Z9M7|G5E9M8|Q86TN8|Q9H3Q5|Q9NR51|Q9NY21|Q9NYE7	Silent	SNP	ENST00000327443.4	37	CCDS8857.1																																																																																			A|0.814;G|0.186	0.186	strong		0.557	SP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407044.1		
NUP155	9631	hgsc.bcm.edu	37	5	37310765	37310765	+	Silent	SNP	A	A	G	rs53429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37310765A>G	ENST00000231498.3	-	23	2720	c.2517T>C	c.(2515-2517)gcT>gcC	p.A839A	NUP155_ENST00000513532.1_Intron|NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000381843.2_Silent_p.A780A	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	839					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)			TGATAAGAGAAGCAATTAATG	0.398													A|||	150	0.0299521	0.1112	0.0043	5008	,	,		14358	0.0		0.0	False		,,,				2504	0.0				p.A839A		Atlas-SNP	.											.	NUP155	116	.	0			c.T2517C						PASS	.	A	,	438,3968	210.5+/-231.0	24,390,1789	152.0	152.0	152.0		2340,2517	1.6	1.0	5	dbSNP_80	152	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NUP155	NM_004298.2,NM_153485.1	,	24,391,6088	GG,GA,AA		0.0116,9.941,3.3754	,	780/1333,839/1392	37310765	439,12567	2203	4300	6503	SO:0001819	synonymous_variant	9631	exon23			AAGAGAAGCAATT	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.2517T>C	5.37:g.37310765A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_153485	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	37	CCDS3921.1																																																																																			A|0.962;C|0.000	.	strong		0.398	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298	
TDP2	51567	hgsc.bcm.edu	37	6	24653273	24653273	+	Missense_Mutation	SNP	G	G	C	rs2294689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24653273G>C	ENST00000378198.4	-	6	915	c.745C>G	c.(745-747)Caa>Gaa	p.Q249E	TDP2_ENST00000478285.1_5'Flank|TDP2_ENST00000341060.3_Missense_Mutation_p.Q191E|TDP2_ENST00000545995.1_Missense_Mutation_p.Q279E			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	249			Q -> E (in dbSNP:rs2294689). {ECO:0000269|Ref.5}.		cell surface receptor signaling pathway (GO:0007166)|double-strand break repair (GO:0006302)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|PML body (GO:0016605)	5'-tyrosyl-DNA phosphodiesterase activity (GO:0070260)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)|tyrosyl-RNA phosphodiesterase activity (GO:0036317)			kidney(2)|large_intestine(1)|lung(5)|ovary(1)	9						GGAGCCTCTTGCATTTTCTTT	0.423								Direct reversal of damage					G|||	1222	0.24401	0.2579	0.3026	5008	,	,		17788	0.4623		0.0378	False		,,,				2504	0.1708				p.Q249E		Atlas-SNP	.											.	TDP2	29	.	0			c.C745G						PASS	.	G	GLU/GLN	897,3509	348.5+/-309.9	93,711,1399	203.0	212.0	209.0		745	5.3	1.0	6	dbSNP_100	209	381,8219	123.9+/-182.7	9,363,3928	yes	missense	TDP2	NM_016614.2	29	102,1074,5327	CC,CG,GG		4.4302,20.3586,9.8262	possibly-damaging	249/363	24653273	1278,11728	2203	4300	6503	SO:0001583	missense	51567	exon6			CCTCTTGCATTTT	AJ269473	CCDS4557.1	6p22.3-p22.1	2010-05-07	2010-05-07	2010-05-07	ENSG00000111802	ENSG00000111802	3.1.4.-		17768	protein-coding gene	gene with protein product		605764	"""TRAF and TNF receptor associated protein"""	TTRAP		11478795	Standard	NM_016614		Approved		uc003nej.3	O95551	OTTHUMG00000014360	ENST00000378198.4:c.745C>G	6.37:g.24653273G>C	ENSP00000367440:p.Gln249Glu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Missense_Mutation	SNP	ENST00000378198.4	37	CCDS4557.1	483	0.22115384615384615	112	0.22764227642276422	100	0.27624309392265195	243	0.42482517482517484	28	0.036939313984168866	G	9.939	1.216996	0.22373	0.203586	0.044302	ENSG00000111802	ENST00000378198;ENST00000545995;ENST00000545780;ENST00000341060	T;T;T	0.80304	-1.36;-1.36;-1.36	5.33	5.33	0.75918	Endonuclease/exonuclease/phosphatase (2);	0.225081	0.46758	D	0.000269	T	0.57695	0.2071	L	0.44542	1.39	0.29930	P	0.8219920000000001	B;B	0.23806	0.074;0.091	B;B	0.29663	0.064;0.105	T	0.50625	-0.8806	9	0.06099	T	0.92	-11.0751	12.9775	0.58546	0.0:0.0:0.718:0.282	rs2294689;rs3181241;rs17243381;rs60616684;rs2294689	279;249	O95551-2;O95551	.;TYDP2_HUMAN	E	249;279;171;191	ENSP00000367440:Q249E;ENSP00000437637:Q279E;ENSP00000345345:Q191E	ENSP00000345345:Q191E	Q	-	1	0	TDP2	24761252	1.000000	0.71417	0.969000	0.41365	0.828000	0.46876	3.045000	0.49838	2.654000	0.90174	0.655000	0.94253	CAA	G|0.830;C|0.170	0.170	strong		0.423	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1		
LAMA1	284217	hgsc.bcm.edu	37	18	7033037	7033037	+	Silent	SNP	G	G	A	rs621993	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:7033037G>A	ENST00000389658.3	-	15	2202	c.2109C>T	c.(2107-2109)gcC>gcT	p.A703A		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	703	Laminin IV type A 1. {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)				CCACATCAGCGGCCACCACCA	0.512													G|||	2036	0.40655	0.708	0.3905	5008	,	,		18010	0.1319		0.4036	False		,,,				2504	0.2965				p.A703A		Atlas-SNP	.											LAMA1,brain,glioma,-1,1	LAMA1	458	1	0			c.C2109T						PASS	.	G		2823,1583	657.4+/-400.2	894,1035,274	107.0	78.0	88.0		2109	-0.5	0.0	18	dbSNP_83	88	3478,5122	495.4+/-374.0	690,2098,1512	no	coding-synonymous	LAMA1	NM_005559.3		1584,3133,1786	AA,AG,GG		40.4419,35.9283,48.4469		703/3076	7033037	6301,6705	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon15			ATCAGCGGCCACC	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.2109C>T	18.37:g.7033037G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.542;A|0.458	0.458	strong		0.512	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
C22orf42	150297	hgsc.bcm.edu	37	22	32554985	32554985	+	Missense_Mutation	SNP	A	A	G	rs5998267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32554985A>G	ENST00000382097.3	-	1	290	c.218T>C	c.(217-219)cTg>cCg	p.L73P	RP1-90G24.8_ENST00000426354.1_lincRNA	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	73			L -> P (in dbSNP:rs5998267).							NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						GGACATCTTCAGCATCTTCGG	0.557													.|||	2917	0.582468	0.8495	0.4193	5008	,	,		17928	0.4167		0.4831	False		,,,				2504	0.6104				p.L73P		Atlas-SNP	.											.	C22orf42	37	.	0			c.T218C						PASS	.	G	PRO/LEU	3508,898	336.3+/-304.3	1393,722,88	159.0	158.0	158.0		218		0.0	22	dbSNP_114	158	3969,4631	583.1+/-391.5	947,2075,1278	yes	missense	C22orf42	NM_001010859.1	98	2340,2797,1366	GG,GA,AA		46.1512,20.3813,42.5111	benign	73/252	32554985	7477,5529	2203	4300	6503	SO:0001583	missense	150297	exon1			ATCTTCAGCATCT	BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.218T>C	22.37:g.32554985A>G	ENSP00000371529:p.Leu73Pro	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	297	296	0.996633	NM_001010859	A4QPH5	Missense_Mutation	SNP	ENST00000382097.3	37	CCDS33639.1	1168	0.5347985347985348	409	0.8313008130081301	157	0.43370165745856354	234	0.4090909090909091	368	0.48548812664907653	G	0.016	-1.533546	0.00951	0.796187	0.461512	ENSG00000205856	ENST00000382097	T	0.34472	1.36	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31052	-0.9957	6	0.41790	T	0.15	.	.	.	.	rs5998267;rs8141156;rs52829159;rs56619140;rs59525772;rs5998267	73	Q6IC83	CV042_HUMAN	P	73	ENSP00000371529:L73P	ENSP00000371529:L73P	L	-	2	0	C22orf42	30884985	0.003000	0.15002	0.021000	0.16686	0.021000	0.10359	-1.336000	0.02660	-2.036000	0.00922	-2.094000	0.00368	CTG	A|0.432;G|0.568	0.568	strong		0.557	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859	
NEB	4703	hgsc.bcm.edu	37	2	152511874	152511874	+	Missense_Mutation	SNP	A	A	C	rs78733601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152511874A>C	ENST00000172853.10	-	51	6864	c.6717T>G	c.(6715-6717)atT>atG	p.I2239M	NEB_ENST00000603639.1_Missense_Mutation_p.I2239M|NEB_ENST00000409198.1_Missense_Mutation_p.I2239M|NEB_ENST00000604864.1_Missense_Mutation_p.I2239M|NEB_ENST00000397345.3_Missense_Mutation_p.I2239M|NEB_ENST00000427231.2_Missense_Mutation_p.I2239M			P20929	NEBU_HUMAN	nebulin	2239					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)		TATTCCAATCAATGGTGTATA	0.313													A|||	134	0.0267572	0.0333	0.0043	5008	,	,		13884	0.0843		0.001	False		,,,				2504	0.001				p.I2239M		Atlas-SNP	.											.	NEB	1697	.	0			c.T6717G						PASS	.	A	MET/ILE,MET/ILE,MET/ILE	98,3528		0,98,1715	88.0	76.0	80.0		6717,6717,6717	3.5	1.0	2	dbSNP_131	80	3,8165		0,3,4081	yes	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	10,10,10	0,101,5796	CC,CA,AA		0.0367,2.7027,0.8564	benign,benign,benign	2239/8526,2239/8526,2239/6670	152511874	101,11693	1813	4084	5897	SO:0001583	missense	4703	exon51			CCAATCAATGGTG	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.6717T>G	2.37:g.152511874A>C	ENSP00000172853:p.Ile2239Met	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	27	8	0.296296	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		64	0.029304029304029304	23	0.046747967479674794	2	0.0055248618784530384	38	0.06643356643356643	1	0.0013192612137203166	A	12.63	1.996087	0.35226	0.027027	3.67E-4	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.81	3.48	0.39840	.	1.181470	0.05975	N	0.643070	T	0.02418	0.0074	N	0.08118	0	0.54753	D	0.999985	B	0.23442	0.085	B	0.40101	0.319	T	0.46317	-0.9200	10	0.54805	T	0.06	.	1.0374	0.01551	0.4314:0.2178:0.2206:0.1302	.	2239	P20929	NEBU_HUMAN	M	2239	ENSP00000386259:I2239M;ENSP00000380505:I2239M;ENSP00000416578:I2239M;ENSP00000172853:I2239M	ENSP00000172853:I2239M	I	-	3	3	NEB	152220120	0.967000	0.33354	0.989000	0.46669	0.983000	0.72400	1.167000	0.31847	1.042000	0.40150	0.477000	0.44152	ATT	A|0.970;C|0.030	0.030	strong		0.313	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEIL3	55247	hgsc.bcm.edu	37	4	178262683	178262683	+	Silent	SNP	T	T	C	rs17676249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:178262683T>C	ENST00000264596.3	+	6	874	c.756T>C	c.(754-756)ccT>ccC	p.P252P	RP11-376O6.2_ENST00000506895.1_RNA	NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	252					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)		ACAAGCGTCCTAATTGTGGTC	0.388								Base excision repair (BER), DNA glycosylases					T|||	728	0.145367	0.1437	0.1268	5008	,	,		16258	0.1091		0.2048	False		,,,				2504	0.137				p.P252P		Atlas-SNP	.											.	NEIL3	89	.	0			c.T756C						PASS	.	T		753,3653	309.1+/-290.9	69,615,1519	90.0	84.0	86.0		756	3.0	1.0	4	dbSNP_123	86	1837,6763	328.8+/-318.4	194,1449,2657	no	coding-synonymous	NEIL3	NM_018248.2		263,2064,4176	CC,CT,TT		21.3605,17.0903,19.9139		252/606	178262683	2590,10416	2203	4300	6503	SO:0001819	synonymous_variant	55247	exon6			GCGTCCTAATTGT	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.756T>C	4.37:g.178262683T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Silent	SNP	ENST00000264596.3	37	CCDS3828.1																																																																																			T|0.826;C|0.174	0.174	strong		0.388	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
OSBPL7	114881	hgsc.bcm.edu	37	17	45885756	45885756	+	Silent	SNP	C	C	T	rs9911983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45885756C>T	ENST00000007414.3	-	23	2621	c.2430G>A	c.(2428-2430)acG>acA	p.T810T	OSBPL7_ENST00000392507.3_Silent_p.T810T	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	810					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						CGCTGCTATCCGTCTGCCGCC	0.627													T|||	2374	0.474042	0.7005	0.4352	5008	,	,		19535	0.1528		0.5298	False		,,,				2504	0.4693				p.T810T		Atlas-SNP	.											OSBPL7,colon,carcinoma,-1,1	OSBPL7	65	1	0			c.G2430A						PASS	.	T		3093,1313	444.5+/-347.4	1094,905,204	61.0	56.0	58.0		2430	-8.4	0.8	17	dbSNP_119	58	4785,3815	538.2+/-383.4	1362,2061,877	no	coding-synonymous	OSBPL7	NM_145798.2		2456,2966,1081	TT,TC,CC		44.3605,29.8003,39.428		810/843	45885756	7878,5128	2203	4300	6503	SO:0001819	synonymous_variant	114881	exon23			GCTATCCGTCTGC	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.2430G>A	17.37:g.45885756C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	37	CCDS11515.1																																																																																			C|0.449;T|0.551	0.551	strong		0.627	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
DOCK4	9732	hgsc.bcm.edu	37	7	111512589	111512589	+	Silent	SNP	G	G	A	rs10257550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:111512589G>A	ENST00000437633.1	-	18	2032	c.1776C>T	c.(1774-1776)acC>acT	p.T592T	DOCK4_ENST00000476846.1_5'UTR|DOCK4_ENST00000428084.1_Silent_p.T592T	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	592					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				TGTCTGGGTGGGTTCTCCATT	0.358													G|||	371	0.0740815	0.1112	0.049	5008	,	,		18816	0.005		0.0666	False		,,,				2504	0.1207				p.T592T		Atlas-SNP	.											.	DOCK4	365	.	0			c.C1776T						PASS	.	G		343,3311		19,305,1503	63.0	57.0	59.0		1776	1.8	1.0	7	dbSNP_119	59	558,7610		21,516,3547	no	coding-synonymous	DOCK4	NM_014705.3		40,821,5050	AA,AG,GG		6.8315,9.387,7.6214		592/1967	111512589	901,10921	1827	4084	5911	SO:0001819	synonymous_variant	9732	exon18			TGGGTGGGTTCTC		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.1776C>T	7.37:g.111512589G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_014705	O14584|O94824|Q8NB45	Silent	SNP	ENST00000437633.1	37	CCDS47688.1	116	0.05311355311355311	48	0.0975609756097561	20	0.055248618784530384	2	0.0034965034965034965	46	0.06068601583113457	G	8.267	0.812398	0.16537	0.09387	0.068315	ENSG00000128512	ENST00000423057;ENST00000445943	.	.	.	4.57	1.78	0.24846	.	.	.	.	.	T	0.01189	0.0039	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.12811	-1.0533	3	.	.	.	.	6.3219	0.21223	0.2321:0.1354:0.6325:0.0	rs10257550;rs10257550	.	.	.	L	44;580	.	.	P	-	2	0	DOCK4	111299825	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.500000	0.22562	0.657000	0.30906	0.650000	0.86243	CCC	G|0.930;A|0.070	0.070	strong		0.358	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
WNK1	65125	hgsc.bcm.edu	37	12	988894	988894	+	Silent	SNP	G	G	A	rs9804992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:988894G>A	ENST00000315939.6	+	11	3172	c.2529G>A	c.(2527-2529)caG>caA	p.Q843Q	WNK1_ENST00000340908.4_Silent_p.Q436Q|WNK1_ENST00000537687.1_Intron|WNK1_ENST00000530271.2_Silent_p.Q1341Q|WNK1_ENST00000535572.1_Intron	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	843					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.Q843Q(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CTGTCTCTCAGATTCCCATAT	0.547													A|||	730	0.145767	0.1203	0.2003	5008	,	,		19266	0.1091		0.1382	False		,,,				2504	0.1871				p.Q843Q	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											WNK1,NS,carcinoma,0,2	WNK1	403	2	1	Substitution - coding silent(1)	stomach(1)	c.G2529A						PASS	.	A	,,,	573,3833	773.5+/-414.0	34,505,1664	204.0	176.0	185.0		,,2529,	-4.9	0.8	12	dbSNP_119	185	1349,7251	756.1+/-407.5	103,1143,3054	no	intron,intron,coding-synonymous,intron	WNK1	NM_001184985.1,NM_014823.2,NM_018979.3,NM_213655.4	,,,	137,1648,4718	AA,AG,GG		15.686,13.005,14.7778	,,,	,,843/2383,	988894	1922,11084	2203	4300	6503	SO:0001819	synonymous_variant	65125	exon11			CTCTCAGATTCCC	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.2529G>A	12.37:g.988894G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	178	82	0.460674	NM_018979	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																			G|0.860;A|0.140	0.140	strong		0.547	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
SREBF2	6721	hgsc.bcm.edu	37	22	42276742	42276742	+	Missense_Mutation	SNP	G	G	C	rs2228314	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42276742G>C	ENST00000361204.4	+	10	1950	c.1784G>C	c.(1783-1785)gGc>gCc	p.G595A		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	595			G -> A (in dbSNP:rs2228314). {ECO:0000269|PubMed:7903453}.		cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						GCTGCTGCCGGCAACCTACAA	0.557													C|||	2032	0.405751	0.6165	0.5893	5008	,	,		16039	0.2004		0.2316	False		,,,				2504	0.3814				p.G595A		Atlas-SNP	.											SREBF2,NS,carcinoma,+1,1	SREBF2	99	1	0			c.G1784C						PASS	.	C	ALA/GLY	2515,1891	535.8+/-374.3	739,1037,427	66.0	76.0	72.0		1784	4.9	0.9	22	dbSNP_98	72	2288,6312	697.2+/-404.9	328,1632,2340	yes	missense	SREBF2	NM_004599.2	60	1067,2669,2767	CC,CG,GG		26.6047,42.9187,36.9291	benign	595/1142	42276742	4803,8203	2203	4300	6503	SO:0001583	missense	6721	exon10			CTGCCGGCAACCT	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.1784G>C	22.37:g.42276742G>C	ENSP00000354476:p.Gly595Ala	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	225	112	0.497778	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	37	CCDS14023.1	800	0.3663003663003663	303	0.6158536585365854	197	0.5441988950276243	130	0.22727272727272727	170	0.22427440633245382	C	5.347	0.249403	0.10130	0.570813	0.266047	ENSG00000198911	ENST00000361204;ENST00000457567	T	0.18016	2.24	4.95	4.95	0.65309	.	0.513362	0.22633	N	0.057556	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38045	-0.9679	9	0.06625	T	0.88	-8.3867	6.5586	0.22474	0.0:0.6932:0.1526:0.1542	rs2228314;rs4822063;rs11547819;rs4822063	595	Q12772	SRBP2_HUMAN	A	595	ENSP00000354476:G595A	ENSP00000354476:G595A	G	+	2	0	SREBF2	40606688	0.687000	0.27671	0.866000	0.34008	0.887000	0.51463	1.148000	0.31614	1.094000	0.41399	-0.345000	0.07892	GGC	G|0.627;C|0.373	0.373	strong		0.557	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	
MEGF8	1954	hgsc.bcm.edu	37	19	42863035	42863035	+	Missense_Mutation	SNP	A	A	G	rs1206038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42863035A>G	ENST00000251268.6	+	30	5272	c.5272A>G	c.(5272-5274)Aag>Gag	p.K1758E	MEGF8_ENST00000334370.4_Missense_Mutation_p.K1691E	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1758					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				AGTCAGGAAGAAGATGGCTCT	0.562													G|||	549	0.109625	0.1543	0.1009	5008	,	,		14115	0.0645		0.0567	False		,,,				2504	0.1564				p.K1758E		Atlas-SNP	.											.	MEGF8	358	.	0			c.A5272G						PASS	.	G	GLU/LYS	616,3790	760.6+/-413.0	52,512,1639	57.0	55.0	55.0		5071	1.9	0.0	19	dbSNP_87	55	463,8137	792.1+/-407.5	12,439,3849	yes	missense	MEGF8	NM_001410.2	56	64,951,5488	GG,GA,AA		5.3837,13.9809,8.2962	benign	1691/2779	42863035	1079,11927	2203	4300	6503	SO:0001583	missense	1954	exon30			AGGAAGAAGATGG	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.5272A>G	19.37:g.42863035A>G	ENSP00000251268:p.Lys1758Glu	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	239	123	0.514644	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	37		210	0.09615384615384616	94	0.1910569105691057	43	0.11878453038674033	28	0.04895104895104895	45	0.059366754617414245	G	3.628	-0.076126	0.07184	0.139809	0.053837	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.20332	2.08;2.08	3.33	1.91	0.25777	Galactose oxidase/kelch, beta-propeller (1);	0.716490	0.10923	N	0.619185	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	0.42310	-0.9459	9	0.28530	T	0.3	-0.6821	4.8396	0.13483	0.4425:0.0:0.5575:0.0	rs1206038;rs56716653;rs1206038	1758;1691	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	E	1691;1758	ENSP00000334219:K1691E;ENSP00000251268:K1758E	ENSP00000251268:K1758E	K	+	1	0	MEGF8	47554875	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-0.070000	0.11523	-0.050000	0.13356	-0.355000	0.07637	AAG	A|0.900;G|0.100	0.100	strong		0.562	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
CLCNKA	1187	hgsc.bcm.edu	37	1	16354590	16354590	+	Missense_Mutation	SNP	A	A	T	rs12126269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16354590A>T	ENST00000331433.4	+	10	963	c.944A>T	c.(943-945)tAc>tTc	p.Y315F	CLCNKA_ENST00000420078.1_Missense_Mutation_p.Y315F|CLCNKA_ENST00000375692.1_Missense_Mutation_p.Y315F|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000439316.2_Missense_Mutation_p.Y272F			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	220	0	0		WXS	Illumina HiSeq	Phase_I	237	106	0.447257	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		
MST1L	11223	hgsc.bcm.edu	37	1	17084066	17084066	+	RNA	SNP	G	G	A	rs201206414		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17084066G>A	ENST00000455405.2	-	0	646							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										TCGCTCTCCCGCACATGTCCT	0.602																																					p.R619W		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	0			c.C1855T						scavenged	.																																					11223	exon14			TCTCCCGCACATG	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.17084066G>A		Somatic	1264	1	0.000791139		WXS	Illumina HiSeq	Phase_I	1552	122	0.0786082	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	12.75	2.032090	0.35893	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.166530	0.06656	N	0.763598	T	0.54679	0.1873	.	.	.	.	.	.	D;D	0.76494	0.999;0.998	P;D	0.65443	0.888;0.935	T	0.47911	-0.9080	6	0.66056	D	0.02	.	2.9647	0.05903	0.3885:0.0:0.6115:0.0	.	619;645	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	W	619;645	.	ENSP00000439273:R619W	R	-	1	2	MST1P9	16956653	1.000000	0.71417	0.403000	0.26384	0.000000	0.00434	0.941000	0.29005	0.502000	0.28037	0.000000	0.15137	CGG	G|0.999;A|0.001	0.001	weak		0.602	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
EGFLAM	133584	hgsc.bcm.edu	37	5	38370537	38370537	+	Missense_Mutation	SNP	T	T	C	rs1465567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38370537T>C	ENST00000354891.3	+	6	1031	c.685T>C	c.(685-687)Tgg>Cgg	p.W229R	EGFLAM_ENST00000322350.5_Missense_Mutation_p.W229R	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	229	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		W -> R (in dbSNP:rs1465567).		extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)	p.W229R(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					CCCCCGCAGCTGGCCCAGTGA	0.567													T|||	1288	0.257188	0.4372	0.1354	5008	,	,		17182	0.1796		0.2038	False		,,,				2504	0.2352				p.W229R	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											EGFLAM,NS,carcinoma,0,1	EGFLAM	302	1	1	Substitution - Missense(1)	stomach(1)	c.T685C						PASS	.	T	ARG/TRP,ARG/TRP	1746,2660	520.6+/-370.3	349,1048,806	43.0	42.0	42.0		685,685	-2.0	0.0	5	dbSNP_88	42	1663,6937	305.6+/-307.5	175,1313,2812	yes	missense,missense	EGFLAM	NM_001205301.1,NM_152403.3	101,101	524,2361,3618	CC,CT,TT		19.3372,39.6278,26.211	benign,benign	229/1018,229/1010	38370537	3409,9597	2203	4300	6503	SO:0001583	missense	133584	exon6			CGCAGCTGGCCCA	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"""Fibronectin type III domain containing"""	26810	protein-coding gene	gene with protein product	"""pikachurin"", ""agrin-like"""					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.685T>C	5.37:g.38370537T>C	ENSP00000346964:p.Trp229Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	565	0.2586996336996337	239	0.48577235772357724	58	0.16022099447513813	118	0.2062937062937063	150	0.19788918205804748	T	7.093	0.572574	0.13623	0.396278	0.193372	ENSG00000164318	ENST00000354891;ENST00000322350	T;T	0.52057	0.68;0.68	5.82	-2.02	0.07388	Fibronectin, type III (2);Immunoglobulin-like fold (1);	2.059790	0.01504	N	0.017616	T	0.00012	0.0000	N	0.01761	-0.735	0.53688	P	2.6999999999999247E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35847	-0.9772	9	0.06625	T	0.88	-0.0747	5.516	0.16906	0.0841:0.6017:0.2313:0.083	rs1465567;rs1465567	229;229	Q63HQ2;Q63HQ2-2	EGFLA_HUMAN;.	R	229	ENSP00000346964:W229R;ENSP00000313084:W229R	ENSP00000313084:W229R	W	+	1	0	EGFLAM	38406294	0.000000	0.05858	0.016000	0.15963	0.941000	0.58515	-0.353000	0.07691	-0.389000	0.07786	-0.379000	0.06801	TGG	T|0.741;C|0.259	0.259	strong		0.567	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	
PPP1R10	5514	hgsc.bcm.edu	37	6	30570374	30570374	+	Silent	SNP	G	G	A	rs35689098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30570374G>A	ENST00000376511.2	-	19	2604	c.2052C>T	c.(2050-2052)ggC>ggT	p.G684G		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	684	Gly-rich.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						GCATAGGGTCGCCCGGGCCAT	0.677													G|||	138	0.0275559	0.0915	0.0159	5008	,	,		15303	0.001		0.001	False		,,,				2504	0.0041				p.G684G		Atlas-SNP	.											.	PPP1R10	60	.	0			c.C2052T						PASS	.	G		164,2534		1,162,1186	7.0	10.0	9.0		2052	-0.1	0.9	6	dbSNP_126	9	11,5013		0,11,2501	no	coding-synonymous	PPP1R10	NM_002714.2		1,173,3687	AA,AG,GG		0.2189,6.0786,2.2663		684/941	30570374	175,7547	1349	2512	3861	SO:0001819	synonymous_variant	5514	exon19			AGGGTCGCCCGGG	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9284	protein-coding gene	gene with protein product	"""phosphatase 1 nuclear targeting subunit"", ""HLA-C associated transcript 53"""	603771	"""protein phosphatase 1, regulatory (inhibitor) subunit 10"""			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.2052C>T	6.37:g.30570374G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_002714	O00405	Silent	SNP	ENST00000376511.2	37	CCDS4681.1																																																																																			G|0.970;A|0.030	0.030	strong		0.677	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714	
CHCHD10	400916	hgsc.bcm.edu	37	22	24108438	24108438	+	Missense_Mutation	SNP	G	G	T	rs111677724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24108438G>T	ENST00000484558.2	-	3	854	c.286C>A	c.(286-288)Ccc>Acc	p.P96T	CHCHD10_ENST00000401675.3_Missense_Mutation_p.P103T|CHCHD10_ENST00000520222.1_Missense_Mutation_p.S22R			Q8WYQ3	CHC10_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 10	96	CHCH.				ATP biosynthetic process (GO:0006754)|negative regulation of ATP citrate synthase activity (GO:2000984)|oxidative phosphorylation (GO:0006119)	mitochondrion (GO:0005739)				large_intestine(2)|lung(1)	3						ATCTGCAGGGGCTGGGGGGCA	0.652													G|||	296	0.0591054	0.2141	0.0173	5008	,	,		6897	0.0		0.001	False		,,,				2504	0.0				p.P96T		Atlas-SNP	.											.	CHCHD10	4	.	0			c.C286A						PASS	.	G	THR/PRO	764,3590		66,632,1479	8.0	6.0	7.0		286	4.2	0.4	22	dbSNP_132	7	10,8454		0,10,4222	no	missense	CHCHD10	NM_213720.1	38	66,642,5701	TT,TG,GG		0.1181,17.5471,6.0384	possibly-damaging	96/143	24108438	774,12044	2177	4232	6409	SO:0001583	missense	400916	exon3			GCAGGGGCTGGGG	AB050774	CCDS13815.1	22q11.23	2011-03-28	2008-06-13	2008-06-13	ENSG00000250479	ENSG00000250479		"""Coiled-coil-helix-coiled-coil-helix domain containing"""	15559	protein-coding gene	gene with protein product		615903	"""chromosome 22 open reading frame 16"""	C22orf16			Standard	XM_006724241		Approved	N27C7-4	uc002zxw.3	Q8WYQ3	OTTHUMG00000150736	ENST00000484558.2:c.286C>A	22.37:g.24108438G>T	ENSP00000418428:p.Pro96Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_213720	A8K0J5	Missense_Mutation	SNP	ENST00000484558.2	37	CCDS13815.1	92|92	0.04212454212454213|0.04212454212454213	87|87	0.17682926829268292|0.17682926829268292	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	17.64|17.64	3.440254|3.440254	0.63067|0.63067	0.175471|0.175471	0.001181|0.001181	ENSG00000250479|ENSG00000250479	ENST00000401675;ENST00000484558|ENST00000520222	T;T|.	0.42131|.	0.98;0.98|.	4.15|4.15	4.15|4.15	0.48705|0.48705	.|.	0.257192|.	0.31134|.	N|.	0.008183|.	T|T	0.00210|0.00210	0.0006|0.0006	L|L	0.40543|0.40543	1.245|1.245	0.18873|0.18873	P|P	0.9999844086|0.9999844086	P|.	0.47762|.	0.9|.	B|.	0.39419|.	0.299|.	T|T	0.13791|0.13791	-1.0496|-1.0496	9|5	0.20519|0.87932	T|D	0.43|0	-10.8797|-10.8797	14.7977|14.7977	0.69889|0.69889	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	96|.	Q8WYQ3|.	CHC10_HUMAN|.	T|R	103;96|22	ENSP00000384973:P103T;ENSP00000418428:P96T|.	ENSP00000384973:P103T|ENSP00000430042:S22R	P|S	-|-	1|3	0|2	CHCHD10|CHCHD10	22438438|22438438	1.000000|1.000000	0.71417|0.71417	0.380000|0.380000	0.26093|0.26093	0.805000|0.805000	0.45488|0.45488	4.807000|4.807000	0.62576|0.62576	2.253000|2.253000	0.74438|0.74438	0.485000|0.485000	0.47835|0.47835	CCC|AGC	G|0.957;T|0.043	0.043	strong		0.652	CHCHD10-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000319870.2	NM_213720	
CDA	978	hgsc.bcm.edu	37	1	20945055	20945055	+	Silent	SNP	C	C	T	rs1048977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	94	0	0		WXS	Illumina HiSeq	Phase_I	94	39	0.414894	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	
DGCR14	8220	hgsc.bcm.edu	37	22	19121872	19121872	+	Missense_Mutation	SNP	G	G	A	rs712965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19121872G>A	ENST00000252137.6	-	10	1311	c.1268C>T	c.(1267-1269)gCa>gTa	p.A423V		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	423			A -> V (in dbSNP:rs712965). {ECO:0000269|PubMed:9063747}.		mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					GGTGGAGCGTGCTGGGGATGG	0.687													G|||	515	0.102835	0.1694	0.0865	5008	,	,		15034	0.1062		0.0547	False		,,,				2504	0.0706				p.A423V		Atlas-SNP	.											.	DGCR14	43	.	0			c.C1268T						PASS	.	G	VAL/ALA	736,3670	299.8+/-286.0	62,612,1529	78.0	71.0	74.0		1268	3.2	1.0	22	dbSNP_86	74	493,8107	141.4+/-197.7	18,457,3825	yes	missense	DGCR14	NM_022719.2	64	80,1069,5354	AA,AG,GG		5.7326,16.7045,9.4495	benign	423/477	19121872	1229,11777	2203	4300	6503	SO:0001583	missense	8220	exon10			GAGCGTGCTGGGG	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"""DiGeorge syndrome critical region gene 13"""	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.1268C>T	22.37:g.19121872G>A	ENSP00000252137:p.Ala423Val	Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	351	165	0.470085	NM_022719	Q49AH7|Q9BTZ4	Missense_Mutation	SNP	ENST00000252137.6	37	CCDS13756.1	199	0.09111721611721611	67	0.13617886178861788	35	0.09668508287292818	59	0.10314685314685315	38	0.05013192612137203	G	13.24	2.178402	0.38511	0.167045	0.057326	ENSG00000100056	ENST00000252137	T	0.24151	1.87	4.32	3.23	0.37069	.	0.278460	0.33496	N	0.004843	T	0.00039	0.0001	L	0.27053	0.805	0.38802	D	0.955227	B	0.09022	0.002	B	0.09377	0.004	T	0.33292	-0.9874	10	0.25106	T	0.35	-14.0916	12.4077	0.55449	0.0988:0.0:0.9011:0.0	rs712965;rs59275056;rs712965	423	Q96DF8	DGC14_HUMAN	V	423	ENSP00000252137:A423V	ENSP00000252137:A423V	A	-	2	0	DGCR14	17501872	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.499000	0.60380	2.241000	0.73720	0.484000	0.47621	GCA	G|0.894;T|0.002	.	strong		0.687	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2		
TXLNB	167838	hgsc.bcm.edu	37	6	139576736	139576736	+	Missense_Mutation	SNP	C	C	T	rs17068451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139576736C>T	ENST00000358430.3	-	7	1274	c.1042G>A	c.(1042-1044)Gtg>Atg	p.V348M		NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	348			V -> M (in dbSNP:rs17068451). {ECO:0000269|PubMed:17974005}.			cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		TCCTTCAGCACTTTCGCCTGA	0.527													C|||	1061	0.211861	0.5492	0.1311	5008	,	,		16958	0.0327		0.1501	False		,,,				2504	0.0613				p.V348M		Atlas-SNP	.											.	TXLNB	96	.	0			c.G1042A						PASS	.	C	MET/VAL	2131,2275	578.8+/-384.8	506,1119,578	106.0	86.0	93.0		1042	4.6	1.0	6	dbSNP_123	93	1334,7266	261.0+/-283.6	103,1128,3069	yes	missense	TXLNB	NM_153235.3	21	609,2247,3647	TT,TC,CC		15.5116,48.3659,26.6416	benign	348/685	139576736	3465,9541	2203	4300	6503	SO:0001583	missense	167838	exon7			TCAGCACTTTCGC		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.1042G>A	6.37:g.139576736C>T	ENSP00000351206:p.Val348Met	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Missense_Mutation	SNP	ENST00000358430.3	37	CCDS34545.1	447|447	0.20467032967032966|0.20467032967032966	261|261	0.5304878048780488|0.5304878048780488	51|51	0.1408839779005525|0.1408839779005525	14|14	0.024475524475524476|0.024475524475524476	121|121	0.15963060686015831|0.15963060686015831	C|C	11.17|11.17	1.560642|1.560642	0.27827|0.27827	0.483659|0.483659	0.155116|0.155116	ENSG00000164440|ENSG00000164440	ENST00000367652|ENST00000358430	.|T	.|0.29397	.|1.57	5.73|5.73	4.64|4.64	0.57946|0.57946	.|.	.|0.246085	.|0.45606	.|D	.|0.000351	T|T	0.04003|0.04003	0.0112|0.0112	N|N	0.03238|0.03238	-0.38|-0.38	0.36836|0.36836	P|P	0.11283299999999996|0.11283299999999996	.|B	.|0.29232	.|0.238	.|B	.|0.27380	.|0.079	T|T	0.30297|0.30297	-0.9983|-0.9983	4|8	.|.	.|.	.|.	-27.3255|-27.3255	4.2605|4.2605	0.10739|0.10739	0.0:0.6977:0.0:0.3023|0.0:0.6977:0.0:0.3023	rs17068451;rs56592445;rs58721508;rs17068451|rs17068451;rs56592445;rs58721508;rs17068451	.|348	.|Q8N3L3	.|TXLNB_HUMAN	N|M	60|348	.|ENSP00000351206:V348M	.|.	S|V	-|-	2|1	0|0	TXLNB|TXLNB	139618429|139618429	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.735000|0.735000	0.41995|0.41995	1.465000|1.465000	0.35299|0.35299	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	AGT|GTG	C|0.754;T|0.246	0.246	strong		0.527	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235	
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31691993	31691993	+	Missense_Mutation	SNP	C	C	T	rs77018583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31691993C>T	ENST00000360542.3	-	1	614	c.361G>A	c.(361-363)Ggc>Agc	p.G121S		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	121						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GGACGACAGCCGCTGGACACA	0.547													C|||	50	0.00998403	0.0325	0.0029	5008	,	,		20333	0.004		0.0	False		,,,				2504	0.001				p.G121S		Atlas-SNP	.											KRTAP26-1,colon,carcinoma,+1,1	KRTAP26-1	58	1	0			c.G361A						PASS	.	C	SER/GLY	138,4268	98.9+/-137.6	0,138,2065	116.0	119.0	118.0		361	-5.4	0.0	21	dbSNP_131	118	0,8600		0,0,4300	yes	missense	KRTAP26-1	NM_203405.1	56	0,138,6365	TT,TC,CC		0.0,3.1321,1.061	benign	121/211	31691993	138,12868	2203	4300	6503	SO:0001583	missense	388818	exon1			GACAGCCGCTGGA	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"""Keratin associated proteins"""	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.361G>A	21.37:g.31691993C>T	ENSP00000353742:p.Gly121Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	150	77	0.513333	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	20	0.009157509157509158	16	0.032520325203252036	2	0.0055248618784530384	2	0.0034965034965034965	0	0.0	C	0.014	-1.585008	0.00872	0.031321	0.0	ENSG00000197683	ENST00000360542	T	0.01902	4.57	5.21	-5.39	0.02664	.	1.102650	0.07134	N	0.846044	T	0.00356	0.0011	N	0.04132	-0.27	0.09310	N	1	B	0.14438	0.01	B	0.09377	0.004	T	0.48747	-0.9008	10	0.16896	T	0.51	0.1935	1.5488	0.02571	0.1297:0.3086:0.2657:0.2961	.	121	Q6PEX3	KR261_HUMAN	S	121	ENSP00000353742:G121S	ENSP00000353742:G121S	G	-	1	0	KRTAP26-1	30613864	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.339000	0.02652	-0.734000	0.04843	-0.290000	0.09829	GGC	C|0.989;T|0.011	0.011	strong		0.547	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405	
ARSG	22901	hgsc.bcm.edu	37	17	66364804	66364804	+	Missense_Mutation	SNP	T	T	C	rs1558878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66364804T>C	ENST00000448504.2	+	7	1616	c.820T>C	c.(820-822)Tgg>Cgg	p.W274R	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Missense_Mutation_p.W110R	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	274			W -> R (in dbSNP:rs1558878).		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)			TGCAGGGCTCTGGGAGATGGA	0.542													C|||	1800	0.359425	0.3185	0.4424	5008	,	,		21144	0.2351		0.4831	False		,,,				2504	0.3569				p.W274R		Atlas-SNP	.											.	ARSG	55	.	0			c.T820C						PASS	.	C	ARG/TRP	1524,2882	673.2+/-402.8	268,988,947	117.0	109.0	112.0		820	4.3	0.4	17	dbSNP_88	112	4276,4324	579.7+/-390.9	1066,2144,1090	yes	missense	ARSG	NM_014960.3	101	1334,3132,2037	CC,CT,TT		49.7209,34.5892,44.5948	benign	274/526	66364804	5800,7206	2203	4300	6503	SO:0001583	missense	22901	exon7			GGGCTCTGGGAGA	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.820T>C	17.37:g.66364804T>C	ENSP00000407193:p.Trp274Arg	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	108	46	0.425926	NM_001267727	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	37	CCDS11676.1	807	0.3695054945054945	146	0.2967479674796748	153	0.42265193370165743	144	0.2517482517482518	364	0.48021108179419525	C	0.021	-1.427426	0.01117	0.345892	0.497209	ENSG00000141337	ENST00000452479;ENST00000448504	.	.	.	5.26	4.28	0.50868	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.780131	0.12215	N	0.488911	T	0.00012	0.0000	N	0.00325	-1.645	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47142	-0.9140	8	0.15499	T	0.54	.	5.0112	0.14313	0.25:0.5859:0.0:0.1641	rs1558878;rs3744299;rs52799630;rs61503778;rs1558878	274	Q96EG1	ARSG_HUMAN	R	274;173	.	ENSP00000407193:W173R	W	+	1	0	ARSG	63876399	0.021000	0.18746	0.385000	0.26158	0.028000	0.11728	0.486000	0.22340	1.467000	0.48044	-0.119000	0.15052	TGG	T|0.602;C|0.398	0.398	strong		0.542	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
G6PD	2539	hgsc.bcm.edu	37	X	153763492	153763492	+	Missense_Mutation	SNP	T	T	C	rs1050829|rs34233392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153763492T>C	ENST00000393564.2	-	5	488	c.376A>G	c.(376-378)Aat>Gat	p.N126D	G6PD_ENST00000393562.2_Missense_Mutation_p.N156D|G6PD_ENST00000369620.2_Missense_Mutation_p.N126D|G6PD_ENST00000497281.1_5'UTR	NM_001042351.1	NP_001035810.1	P11413	G6PD_HUMAN	glucose-6-phosphate dehydrogenase	126			N -> D (in A(+), A(-), Santa Maria; class IV and in Mount Sinai; class I; dbSNP:rs1050829). {ECO:0000269|PubMed:12524354, ECO:0000269|PubMed:1889820, ECO:0000269|PubMed:2836867, ECO:0000269|PubMed:3446582, ECO:0000269|PubMed:8733135, ECO:0000269|PubMed:9452072}.		carbohydrate metabolic process (GO:0005975)|cellular response to oxidative stress (GO:0034599)|cholesterol biosynthetic process (GO:0006695)|cytokine production (GO:0001816)|erythrocyte maturation (GO:0043249)|glucose 6-phosphate metabolic process (GO:0051156)|glutathione metabolic process (GO:0006749)|lipid metabolic process (GO:0006629)|NADP metabolic process (GO:0006739)|NADPH regeneration (GO:0006740)|negative regulation of protein glutathionylation (GO:0010734)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|regulation of neuron apoptotic process (GO:0043523)|response to ethanol (GO:0045471)|response to food (GO:0032094)|response to organic cyclic compound (GO:0014070)|ribose phosphate biosynthetic process (GO:0046390)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	glucose binding (GO:0005536)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(3)|ovary(4)	18	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)					TGGAGGGCATTCATGTGGCTG	0.592													T|||	357	0.0945695	0.2564	0.0216	3775	,	,		14707	0.0		0.003	False		,,,				2504	0.0				p.N156D		Atlas-SNP	.											.	G6PD	73	.	0			c.A466G	GRCh37	CM880030	G6PD	M	rs1050829	PASS	.	T	ASP/ASN,ASP/ASN	1195,2640		161,694,179,777,392	126.0	94.0	105.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	466,376	0.5	0.0	X	dbSNP_86	105	4,6724		0,2,2,2426,1870	yes	missense,missense	G6PD	NM_000402.3,NM_001042351.1	23,23	161,696,181,3203,2262	CC,CT,C,TT,T		0.0595,31.1604,11.3509	benign,benign	156/546,126/516	153763492	1199,9364	2203	4300	6503	SO:0001583	missense	2539	exon5			GGGCATTCATGTG	X03674	CCDS14756.2, CCDS44023.1	Xq28	2014-09-17			ENSG00000160211	ENSG00000160211	1.1.1.49		4057	protein-coding gene	gene with protein product		305900				3012556, 2428611	Standard	NM_000402		Approved	G6PD1	uc004flx.1	P11413	OTTHUMG00000024237	ENST00000393564.2:c.376A>G	X.37:g.153763492T>C	ENSP00000377194:p.Asn126Asp	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	235	78	0.331915	NM_000402	D3DWX9|Q16000|Q16765|Q8IU70|Q8IU88|Q8IUA6|Q96PQ2	Missense_Mutation	SNP	ENST00000393564.2	37	CCDS44023.1	135	0.081374321880651	85	0.20432692307692307	9	0.025	0	0.0	2	0.0026455026455026454	T	4.463	0.085705	0.08583	0.311604	5.95E-4	ENSG00000160211	ENST00000393562;ENST00000291567;ENST00000393564;ENST00000369620;ENST00000439227;ENST00000440967;ENST00000433845	D;D;D;D;D;D	0.99394	-5.82;-5.82;-5.82;-5.82;-5.82;-5.82	5.67	0.495	0.16890	NAD(P)-binding domain (1);Glucose-6-phosphate dehydrogenase, NAD-binding (1);	0.730689	0.13899	N	0.355051	T	0.00039	0.0001	N	0.05510	-0.035	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.53933	-0.8368	9	0.20046	T	0.44	.	4.889	0.13717	0.0:0.2505:0.147:0.6025	rs1050829;rs2230035;rs3191189	126;156	P11413;P11413-3	G6PD_HUMAN;.	D	156;126;126;126;126;126;126	ENSP00000377192:N156D;ENSP00000377194:N126D;ENSP00000358633:N126D;ENSP00000395599:N126D;ENSP00000400648:N126D;ENSP00000394690:N126D	ENSP00000291567:N126D	N	-	1	0	G6PD	153416686	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.234000	0.09028	-0.267000	0.09325	0.486000	0.48141	AAT	T|0.844;0|0.051	.	strong		0.592	G6PD-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061170.3	NM_000402	
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458476	39458476	+	Missense_Mutation	SNP	A	A	T	rs1001191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	118	0	0		WXS	Illumina HiSeq	Phase_I	123	54	0.439024	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		
MUC4	4585	hgsc.bcm.edu	37	3	195515126	195515126	+	Missense_Mutation	SNP	C	C	A	rs529638482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515126C>A	ENST00000463781.3	-	2	3784	c.3325G>T	c.(3325-3327)Gac>Tac	p.D1109Y	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D1109Y	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	540					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)		GAGGAAGTGTCGGTGACAGGA	0.577													.|||	144	0.028754	0.0983	0.013	5008	,	,		17471	0.0		0.002	False		,,,				2504	0.0031				p.D1109Y		Atlas-SNP	.											.	MUC4	1505	.	0			c.G3325T						PASS	.						9.0	6.0	7.0					3																	195515126		654	1463	2117	SO:0001583	missense	4585	exon2			AAGTGTCGGTGAC	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.3325G>T	3.37:g.195515126C>A	ENSP00000417498:p.Asp1109Tyr	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	353	37	0.104816	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	.	.	.	.	.	.	.	.	.	.	-	3.781	-0.045714	0.07452	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.43;1.42	0.814	-1.63	0.08345	.	.	.	.	.	T	0.28863	0.0716	N	0.19112	0.55	0.09310	N	1	D	0.69078	0.997	P	0.62560	0.904	T	0.17837	-1.0356	8	.	.	.	.	5.2224	0.15375	0.0:0.4002:0.0:0.5998	.	1109	E7ESK3	.	Y	1109	ENSP00000417498:D1109Y;ENSP00000420243:D1109Y	.	D	-	1	0	MUC4	196999521	0.000000	0.05858	0.001000	0.08648	0.296000	0.27459	-0.592000	0.05747	-0.657000	0.05373	0.064000	0.15345	GAC	.	.	none		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DHRS4	10901	hgsc.bcm.edu	37	14	24423007	24423007	+	Missense_Mutation	SNP	G	G	A	rs17099455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24423007G>A	ENST00000313250.5	+	1	213	c.10G>A	c.(10-12)Gcg>Acg	p.A4T	DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000397075.3_Missense_Mutation_p.A4T|DHRS4_ENST00000397073.2_5'UTR|DHRS4_ENST00000382761.3_5'UTR|DHRS4_ENST00000397074.3_Missense_Mutation_p.A4T|DHRS4_ENST00000559632.1_Missense_Mutation_p.A4T|DHRS4_ENST00000543741.2_Missense_Mutation_p.A4T|DHRS4_ENST00000308178.8_5'UTR|DHRS4_ENST00000558263.1_Missense_Mutation_p.A4T|DHRS4_ENST00000421831.1_5'UTR|DHRS4_ENST00000558581.1_Missense_Mutation_p.A4T	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	69	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	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		
CLDN16	10686	hgsc.bcm.edu	37	3	190106074	190106074	+	Missense_Mutation	SNP	G	G	C	rs386669518|rs3214506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:190106074G>C	ENST00000264734.2	+	1	414	c.166G>C	c.(166-168)Gct>Cct	p.A56P	CLDN16_ENST00000468220.1_Intron|CLDN16_ENST00000456423.1_Missense_Mutation_p.A56P	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	56					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		TGGGGCCAGGGCTGGTGTCTG	0.507													G|||	586	0.117013	0.0681	0.1455	5008	,	,		20600	0.0208		0.2336	False		,,,				2504	0.1421				p.A56P		Atlas-SNP	.											.	CLDN16	59	.	0			c.G166C						PASS	.						161.0	140.0	147.0					3																	190106074		2203	4300	6503	SO:0001583	missense	10686	exon1			GCCAGGGCTGGTG	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"""Claudins"""	2037	protein-coding gene	gene with protein product	"""paracellin-1"", ""hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"""	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.166G>C	3.37:g.190106074G>C	ENSP00000264734:p.Ala56Pro	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	239	106	0.443515	NM_006580		Missense_Mutation	SNP	ENST00000264734.2	37	CCDS3296.1	.	.	.	.	.	.	.	.	.	.	G	6.438	0.448874	0.12223	.	.	ENSG00000113946	ENST00000264734;ENST00000456423	D;D	0.93659	-2.9;-3.26	5.39	-3.93	0.04143	.	1.665760	0.03286	N	0.186971	D	0.84234	0.5427	N	0.19112	0.55	0.09310	N	1	B;B	0.12630	0.006;0.0	B;B	0.16289	0.015;0.002	T	0.70167	-0.4946	10	0.36615	T	0.2	-13.3321	0.4429	0.00489	0.347:0.1211:0.2211:0.3108	.	56;56	A0SDD8;Q9Y5I7	.;CLD16_HUMAN	P	56	ENSP00000264734:A56P;ENSP00000414136:A56P	ENSP00000264734:A56P	A	+	1	0	CLDN16	191588768	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-0.121000	0.10643	-0.435000	0.07264	-0.535000	0.04281	GCT	G|0.753;C|0.247	0.247	strong		0.507	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580	
CYP11B1	1584	hgsc.bcm.edu	37	8	143957163	143957163	+	Silent	SNP	C	C	G	rs6403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143957163C>G	ENST00000292427.4	-	6	1118	c.1086G>C	c.(1084-1086)ctG>ctC	p.L362L	CYP11B1_ENST00000377675.3_Silent_p.L433L|CYP11B1_ENST00000517471.1_Silent_p.L362L	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	362					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	GCAGCAAGGGCAGCTCGGTGG	0.697									Familial Hyperaldosteronism type I				.|||	729	0.145567	0.0144	0.0965	5008	,	,		16691	0.4395		0.0179	False		,,,				2504	0.1861				p.L362L		Atlas-SNP	.											.	CYP11B1	128	.	0			c.G1086C						PASS	.	C	,	88,4318		0,88,2115	68.0	70.0	70.0		1086,1086	1.3	1.0	8	dbSNP_52	70	169,8431		5,159,4136	no	coding-synonymous,coding-synonymous	CYP11B1	NM_000497.3,NM_001026213.1	,	5,247,6251	GG,GC,CC		1.9651,1.9973,1.976	,	362/504,362/438	143957163	257,12749	2203	4300	6503	SO:0001819	synonymous_variant	1584	exon6	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	CAAGGGCAGCTCG	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"""Cytochrome P450s"""	2591	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	610613	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"""	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.1086G>C	8.37:g.143957163C>G		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	267	148	0.554307	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	37	CCDS6392.1																																																																																			C|0.948;G|0.052	0.052	strong		0.697	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		
GRB10	2887	hgsc.bcm.edu	37	7	50672017	50672017	+	Silent	SNP	G	G	A	rs200886440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:50672017G>A	ENST00000401949.1	-	16	1916	c.1447C>T	c.(1447-1449)Cta>Tta	p.L483L	GRB10_ENST00000357271.5_Silent_p.L437L|GRB10_ENST00000398812.2_Silent_p.L483L|GRB10_ENST00000398810.2_Silent_p.L425L|GRB10_ENST00000335866.3_Silent_p.L425L|GRB10_ENST00000402578.1_Silent_p.L425L|GRB10_ENST00000403097.1_Silent_p.L477L|GRB10_ENST00000439599.1_Silent_p.L477L|GRB10_ENST00000407526.1_Silent_p.L425L|GRB10_ENST00000402497.1_Silent_p.L425L|GRB10_ENST00000406641.1_Silent_p.L425L			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	483					insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					CCTGTACTTAGGGTAGAAGGG	0.493									Russell-Silver syndrome				G|||	3	0.000599042	0.0023	0.0	5008	,	,		21445	0.0		0.0	False		,,,				2504	0.0				p.L483L		Atlas-SNP	.											.	GRB10	155	.	0			c.C1447T						PASS	.	G	,,,	2,4002		0,2,2000	140.0	141.0	141.0		1309,1273,1273,1447	1.1	0.3	7		141	0,8338		0,0,4169	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRB10	NM_001001549.2,NM_001001550.2,NM_001001555.2,NM_005311.4	,,,	0,2,6169	AA,AG,GG		0.0,0.05,0.0162	,,,	437/549,425/537,425/537,483/595	50672017	2,12340	2002	4169	6171	SO:0001819	synonymous_variant	2887	exon13	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	TACTTAGGGTAGA		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.1447C>T	7.37:g.50672017G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_005311	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Silent	SNP	ENST00000401949.1	37	CCDS43582.1																																																																																			G|0.999;A|0.001	0.001	strong		0.493	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1		
GPR110	266977	hgsc.bcm.edu	37	6	46976924	46976924	+	Silent	SNP	G	G	A	rs45511696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46976924G>A	ENST00000371253.2	-	11	2462	c.2247C>T	c.(2245-2247)gtC>gtT	p.V749V	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Silent_p.V552V	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	749					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						CCAGTGCAGGGACAACAAAAG	0.493													G|||	186	0.0371406	0.0787	0.0389	5008	,	,		22252	0.0		0.0447	False		,,,				2504	0.0102				p.V749V		Atlas-SNP	.											.	GPR110	102	.	0			c.C2247T						PASS	.	G		375,4031	188.5+/-214.9	14,347,1842	92.0	97.0	95.0		2247	1.2	0.5	6	dbSNP_127	95	328,8272	115.3+/-175.2	7,314,3979	no	coding-synonymous	GPR110	NM_153840.2		21,661,5821	AA,AG,GG		3.814,8.5111,5.4052		749/911	46976924	703,12303	2203	4300	6503	SO:0001819	synonymous_variant	266977	exon11			TGCAGGGACAACA	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.2247C>T	6.37:g.46976924G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	135	69	0.511111	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	37	CCDS34471.1																																																																																			G|0.952;A|0.048	0.048	strong		0.493	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
KANK2	25959	hgsc.bcm.edu	37	19	11289129	11289129	+	Intron	SNP	G	G	A	rs114414326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11289129G>A	ENST00000586659.1	-	6	1732				KANK2_ENST00000432929.2_Missense_Mutation_p.P479L|KANK2_ENST00000589894.1_Intron|KANK2_ENST00000589359.1_Missense_Mutation_p.P479L|KANK2_ENST00000355150.5_Intron			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2						apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CCCGCCTGGAGGGGAGGACAG	0.677													G|||	79	0.0157748	0.0575	0.0043	5008	,	,		11402	0.0		0.0	False		,,,				2504	0.0				p.P479L		Atlas-SNP	.											.	KANK2	47	.	0			c.C1436T						PASS	.	G	,LEU/PRO	191,4215		4,183,2016	20.0	25.0	23.0		,1436	4.4	0.0	19	dbSNP_132	23	4,8590		0,4,4293	yes	intron,missense	KANK2	NM_001136191.2,NM_015493.6	,98	4,187,6309	AA,AG,GG		0.0465,4.335,1.5	,	,479/860	11289129	195,12805	2203	4297	6500	SO:0001627	intron_variant	25959	exon4			CCTGGAGGGGAGG	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	29300	protein-coding gene	gene with protein product		614610	"""matrix-remodelling associated 3"", ""ankyrin repeat domain 25"""	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.1418-6C>T	19.37:g.11289129G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	G	15.34	2.803527	0.50315	0.04335	4.65E-4	ENSG00000197256	ENST00000432929	T	0.34472	1.36	5.45	4.39	0.52855	.	.	.	.	.	T	0.04092	0.0114	.	.	.	0.26307	N	0.977885	P	0.38827	0.649	B	0.32677	0.15	T	0.01776	-1.1276	8	0.31617	T	0.26	.	11.8895	0.52620	0.0841:0.0:0.9159:0.0	.	479	Q63ZY3-2	.	L	479	ENSP00000395650:P479L	ENSP00000395650:P479L	P	-	2	0	KANK2	11150129	0.745000	0.28261	0.002000	0.10522	0.180000	0.23129	1.956000	0.40382	1.283000	0.44513	0.655000	0.94253	CCT	G|0.990;A|0.010	0.010	strong		0.677	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
PSEN2	5664	hgsc.bcm.edu	37	1	227076671	227076671	+	Silent	SNP	T	T	C	rs61730652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227076671T>C	ENST00000366783.3	+	8	1144	c.708T>C	c.(706-708)agT>agC	p.S236S	PSEN2_ENST00000340188.4_Silent_p.S236S|PSEN2_ENST00000366782.1_Silent_p.S269S|PSEN2_ENST00000472139.2_Silent_p.S92S|PSEN2_ENST00000391872.2_Silent_p.S269S|PSEN2_ENST00000422240.2_Silent_p.S236S	NM_000447.2|NM_012486.2	NP_000438.2|NP_036618.2	P49810	PSN2_HUMAN	presenilin 2	236					amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|brain morphogenesis (GO:0048854)|calcium ion transport (GO:0006816)|cardiac muscle contraction (GO:0060048)|cell fate specification (GO:0001708)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|forebrain development (GO:0030900)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|locomotion (GO:0040011)|lung alveolus development (GO:0048286)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|memory (GO:0007613)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of protein phosphorylation (GO:0001933)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of synaptic plasticity (GO:0048167)|response to hypoxia (GO:0001666)|somitogenesis (GO:0001756)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear inner membrane (GO:0005637)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|urinary_tract(1)	20		Prostate(94;0.0771)				TCATGATCAGTGCGCTCATGG	0.602													T|||	146	0.0291534	0.0893	0.0101	5008	,	,		18772	0.0		0.0129	False		,,,				2504	0.0082				p.S236S		Atlas-SNP	.											.	PSEN2	55	.	0			c.T708C						PASS	.	T	,	378,4028	190.5+/-216.4	16,346,1841	153.0	125.0	135.0		708,708	-4.3	0.9	1	dbSNP_129	135	63,8537	39.3+/-95.6	0,63,4237	no	coding-synonymous,coding-synonymous	PSEN2	NM_000447.2,NM_012486.2	,	16,409,6078	CC,CT,TT		0.7326,8.5792,3.3907	,	236/449,236/448	227076671	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	5664	exon8			GATCAGTGCGCTC	BC006365	CCDS1556.1, CCDS44324.1	1q42.13	2014-09-17	2014-02-24		ENSG00000143801	ENSG00000143801			9509	protein-coding gene	gene with protein product		600759	"""Alzheimer disease 4"""	AD4		7638621	Standard	NM_000447		Approved	AD3L, STM2, PS2	uc009xeo.1	P49810	OTTHUMG00000037563	ENST00000366783.3:c.708T>C	1.37:g.227076671T>C		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	295	141	0.477966	NM_012486	A8K8D4|B1AP21|Q96P32	Silent	SNP	ENST00000366783.3	37	CCDS1556.1																																																																																			T|0.969;C|0.031	0.031	strong		0.602	PSEN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091539.1	NM_000447	
GAPVD1	26130	hgsc.bcm.edu	37	9	128099784	128099784	+	Missense_Mutation	SNP	C	C	T	rs62637637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:128099784C>T	ENST00000495955.1	+	17	3081	c.2791C>T	c.(2791-2793)Cca>Tca	p.P931S	GAPVD1_ENST00000297933.6_Missense_Mutation_p.P931S|GAPVD1_ENST00000312123.9_Missense_Mutation_p.P910S|GAPVD1_ENST00000265956.4_Missense_Mutation_p.P905S|GAPVD1_ENST00000394083.2_Missense_Mutation_p.P910S|GAPVD1_ENST00000394105.2_Missense_Mutation_p.P958S|GAPVD1_ENST00000394104.2_Missense_Mutation_p.P931S|GAPVD1_ENST00000470056.1_Missense_Mutation_p.P931S			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	931				P -> S (in Ref. 6; AAH13635). {ECO:0000305}.	endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						AGAACTCCCTCCAGCTGCAGC	0.532													C|||	30	0.00599042	0.0219	0.0014	5008	,	,		18533	0.0		0.0	False		,,,				2504	0.0				p.P958S		Atlas-SNP	.											.	GAPVD1	124	.	0			c.C2872T						PASS	.	C	SER/PRO	68,4338	62.9+/-100.1	1,66,2136	70.0	69.0	70.0		2872	5.3	0.9	9	dbSNP_129	70	0,8600		0,0,4300	yes	missense	GAPVD1	NM_015635.2	74	1,66,6436	TT,TC,CC		0.0,1.5433,0.5228	benign	958/1488	128099784	68,12938	2203	4300	6503	SO:0001583	missense	26130	exon16			CTCCCTCCAGCTG		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.2791C>T	9.37:g.128099784C>T	ENSP00000419063:p.Pro931Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	136	33	0.242647	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	37		14|14	0.00641025641025641|0.00641025641025641	13|13	0.026422764227642278|0.026422764227642278	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	8.329|8.329	0.826071|0.826071	0.16749|0.16749	0.015433|0.015433	0.0|0.0	ENSG00000165219|ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000467750;ENST00000297933;ENST00000312123|ENST00000436712	.|.	.|.	.|.	6.17|6.17	5.26|5.26	0.73747|0.73747	.|.	0.267957|.	0.43416|.	D|.	0.000568|.	T|T	0.15955|0.15955	0.0384|0.0384	N|N	0.19112|0.19112	0.55|0.55	0.32006|0.32006	N|N	0.602735|0.602735	B;B;B;B;B;B|.	0.15930|.	0.002;0.002;0.001;0.001;0.001;0.015|.	B;B;B;B;B;B|.	0.12837|.	0.006;0.004;0.004;0.004;0.004;0.008|.	T|T	0.35895|0.35895	-0.9770|-0.9770	9|5	0.15066|.	T|.	0.55|.	.|.	11.4079|11.4079	0.49908|0.49908	0.1307:0.6166:0.2527:0.0|0.1307:0.6166:0.2527:0.0	rs62637637|rs62637637	905;931;931;910;931;958|.	Q14C86-5;Q14C86;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6|.	.;GAPD1_HUMAN;.;.;.;.|.	S|F	931;958;931;905;910;931;931;931;910|767	.|.	ENSP00000265956:P905S|.	P|S	+|+	1|2	0|0	GAPVD1|GAPVD1	127139605|127139605	0.914000|0.914000	0.31030|0.31030	0.948000|0.948000	0.38648|0.38648	0.162000|0.162000	0.22319|0.22319	2.148000|2.148000	0.42235|0.42235	1.586000|1.586000	0.49944|0.49944	0.655000|0.655000	0.94253|0.94253	CCA|TCC	C|0.993;T|0.007	0.007	strong		0.532	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1		
CUBN	8029	hgsc.bcm.edu	37	10	16979661	16979661	+	Silent	SNP	T	T	C	rs1801234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:16979661T>C	ENST00000377833.4	-	39	5921	c.5856A>G	c.(5854-5856)tcA>tcG	p.S1952S		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1952	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATCCCTTCCCTGAGATTGAAG	0.438													C|||	2711	0.541334	0.7542	0.5548	5008	,	,		14518	0.4911		0.4175	False		,,,				2504	0.4233				p.S1952S		Atlas-SNP	.											.	CUBN	515	.	0			c.A5856G						PASS	.	C		3022,1384	454.4+/-350.6	1029,964,210	62.0	66.0	65.0		5856	-4.0	0.2	10	dbSNP_89	65	3622,4978	625.2+/-397.7	782,2058,1460	no	coding-synonymous	CUBN	NM_001081.3		1811,3022,1670	CC,CT,TT		42.1163,31.4117,48.9159		1952/3624	16979661	6644,6362	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon39			CTTCCCTGAGATT	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.5856A>G	10.37:g.16979661T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	70	40	0.571429	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			T|0.475;C|0.525	0.525	strong		0.438	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
NRIP1	8204	hgsc.bcm.edu	37	21	16338814	16338814	+	Missense_Mutation	SNP	T	T	C	rs9975169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:16338814T>C	ENST00000400202.1	-	3	2412	c.1700A>G	c.(1699-1701)aAt>aGt	p.N567S	NRIP1_ENST00000400199.1_Missense_Mutation_p.N567S|AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Missense_Mutation_p.N567S			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	567	Repression domain 2.		N -> S (in dbSNP:rs9975169).		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)		TTGAGAGAGATTGATGGGAGA	0.443													T|||	116	0.0231629	0.0809	0.013	5008	,	,		20094	0.0		0.0	False		,,,				2504	0.0				p.N567S		Atlas-SNP	.											.	NRIP1	103	.	0			c.A1700G						PASS	.	T	SER/ASN	356,4050	183.6+/-211.2	17,322,1864	240.0	238.0	238.0		1700	6.0	1.0	21	dbSNP_119	238	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NRIP1	NM_003489.3	46	17,323,6163	CC,CT,TT		0.0116,8.0799,2.7449	probably-damaging	567/1159	16338814	357,12649	2203	4300	6503	SO:0001583	missense	8204	exon4			GAGAGATTGATGG	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.1700A>G	21.37:g.16338814T>C	ENSP00000383063:p.Asn567Ser	Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	232	118	0.508621	NM_003489	Q8IWE8	Missense_Mutation	SNP	ENST00000400202.1	37	CCDS13568.1	39	0.017857142857142856	35	0.07113821138211382	4	0.011049723756906077	0	0.0	0	0.0	T	17.23	3.337615	0.60963	0.080799	1.16E-4	ENSG00000180530	ENST00000400199;ENST00000400202;ENST00000318948	T;T;T	0.20200	2.09;2.09;2.09	6.02	6.02	0.97574	.	0.204155	0.42172	D	0.000750	T	0.02455	0.0075	L	0.53249	1.67	0.45490	D	0.998455	D	0.59767	0.986	P	0.58520	0.84	T	0.00019	-1.2359	10	0.62326	D	0.03	-19.3161	16.5446	0.84426	0.0:0.0:0.0:1.0	rs9975169;rs52814028;rs9975169	567	P48552	NRIP1_HUMAN	S	567	ENSP00000383060:N567S;ENSP00000383063:N567S;ENSP00000327213:N567S	ENSP00000327213:N567S	N	-	2	0	NRIP1	15260685	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.714000	0.61902	2.311000	0.77944	0.533000	0.62120	AAT	T|0.973;C|0.027	0.027	strong		0.443	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
CARD11	84433	hgsc.bcm.edu	37	7	2959172	2959172	+	Silent	SNP	G	G	A	rs3735126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2959172G>A	ENST00000396946.4	-	18	2747	c.2344C>T	c.(2344-2346)Ctg>Ttg	p.L782L		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	782					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)		GAGATGTTCAGGTTCAGCCGG	0.592			Mis		DLBCL								G|||	818	0.163339	0.2882	0.1527	5008	,	,		20869	0.1548		0.0288	False		,,,				2504	0.1493				p.L782L		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.C2344T						PASS	.	G		1177,3229	412.6+/-336.2	157,863,1183	123.0	78.0	93.0		2344	4.2	1.0	7	dbSNP_107	93	183,8417	81.8+/-144.4	1,181,4118	no	coding-synonymous	CARD11	NM_032415.4		158,1044,5301	AA,AG,GG		2.1279,26.7136,10.4567		782/1155	2959172	1360,11646	2203	4300	6503	SO:0001819	synonymous_variant	84433	exon18			TGTTCAGGTTCAG	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.2344C>T	7.37:g.2959172G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	195	99	0.507692	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																			G|0.880;A|0.120	0.120	strong		0.592	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
PTPRN2	5799	hgsc.bcm.edu	37	7	157931151	157931151	+	Missense_Mutation	SNP	C	C	G	rs150508509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157931151C>G	ENST00000389418.4	-	7	976	c.967G>C	c.(967-969)Ggc>Cgc	p.G323R	PTPRN2_ENST00000409483.1_Missense_Mutation_p.G285R|PTPRN2_ENST00000389416.4_Missense_Mutation_p.G306R|PTPRN2_ENST00000389413.3_Missense_Mutation_p.G323R|PTPRN2_ENST00000404321.2_Missense_Mutation_p.G346R	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	323				G -> R (in Ref. 2; CAA69880). {ECO:0000305}.	negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CCACTCAGGCCCCTCACCTCA	0.632													C|||	93	0.0185703	0.053	0.0058	5008	,	,		19317	0.0		0.0	False		,,,				2504	0.0194				p.G323R		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G967C						PASS	.		ARG/GLY,ARG/GLY,ARG/GLY	217,4189	127.0+/-164.0	3,211,1989	62.0	64.0	64.0		967,916,967	-4.9	0.0	7	dbSNP_134	64	1,8599		0,1,4299	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	125,125,125	3,212,6288	GG,GC,CC		0.0116,4.9251,1.6761	benign,benign,benign	323/1016,306/999,323/987	157931151	218,12788	2203	4300	6503	SO:0001583	missense	5799	exon7			TCAGGCCCCTCAC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.967G>C	7.37:g.157931151C>G	ENSP00000374069:p.Gly323Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	101	35	0.346535	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	C	3.517	-0.098660	0.07010	0.049251	1.16E-4	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02552	4.25;4.27;4.26;4.26;4.25	4.11	-4.94	0.03057	.	.	.	.	.	T	0.00271	0.0008	N	0.12746	0.255	0.09310	N	1	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.0;0.0	T	0.48269	-0.9050	9	0.15499	T	0.54	.	5.6925	0.17837	0.0:0.3821:0.1927:0.4252	.	346;285;323;306;323	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	R	285;323;306;323;346	ENSP00000387114:G285R;ENSP00000374064:G323R;ENSP00000374067:G306R;ENSP00000374069:G323R;ENSP00000385464:G346R	ENSP00000374064:G323R	G	-	1	0	PTPRN2	157623912	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.128000	0.15810	-1.148000	0.02847	-0.312000	0.09012	GGC	C|0.981;G|0.019	0.019	strong		0.632	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
TTN	7273	hgsc.bcm.edu	37	2	179598399	179598399	+	Silent	SNP	C	C	T	rs72648932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179598399C>T	ENST00000591111.1	-	51	14990	c.14766G>A	c.(14764-14766)acG>acA	p.T4922T	TTN_ENST00000589042.1_Silent_p.T5239T|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.T3995T|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	12314	Ig-like 29.				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)			CAGCCAGGCACGTGTATTTGC	0.378													C|||	120	0.0239617	0.0877	0.0058	5008	,	,		20602	0.0		0.0	False		,,,				2504	0.0				p.T5239T		Atlas-SNP	.											.	TTN	18412	.	0			c.G15717A						PASS	.	C	,,,	223,3501		8,207,1647	136.0	130.0	132.0		,11985,,	-7.5	1.0	2	dbSNP_130	132	7,8189		0,7,4091	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	8,214,5738	TT,TC,CC		0.0854,5.9882,1.9295	,,,	,3995/33424,,	179598399	230,11690	1862	4098	5960	SO:0001819	synonymous_variant	7273	exon53			CAGGCACGTGTAT	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.14766G>A	2.37:g.179598399C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	153	82	0.535948	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|0.980;T|0.020	0.020	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
EPPK1	83481	hgsc.bcm.edu	37	8	144941181	144941181	+	Missense_Mutation	SNP	G	G	C	rs7839934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144941181G>C	ENST00000525985.1	-	2	6312	c.6241C>G	c.(6241-6243)Ctg>Gtg	p.L2081V				P58107	EPIPL_HUMAN	epiplakin 1	2081						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGGAACAGCAGCCAGCCCGTG	0.592													g|||	1432	0.285942	0.2254	0.2997	5008	,	,		20148	0.2669		0.2575	False		,,,				2504	0.407				p.L2081V		Atlas-SNP	.											.	EPPK1	199	.	0			c.C6241G						PASS	.	C	VAL/LEU	960,3348		104,752,1298	66.0	73.0	71.0		6241	-1.8	0.0	8	dbSNP_116	71	2179,6351		285,1609,2371	yes	missense	EPPK1	NM_031308.1	32	389,2361,3669	CC,CG,GG		25.5451,22.2841,24.4508	benign	2081/2420	144941181	3139,9699	2154	4265	6419	SO:0001583	missense	83481	exon1			ACAGCAGCCAGCC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6241C>G	8.37:g.144941181G>C	ENSP00000436337:p.Leu2081Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		567	0.25961538461538464	116	0.23577235772357724	104	0.287292817679558	148	0.25874125874125875	199	0.262532981530343	g	3.474	-0.107219	0.06924	0.222841	0.255451	ENSG00000227184	ENST00000525985	T	0.69040	-0.37	4.41	-1.77	0.07982	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17440	-1.0369	7	0.15952	T	0.53	.	5.5162	0.16908	0.0:0.3982:0.2789:0.3229	rs7839934;rs7839934	2081	E9PPU0	.	V	2081	ENSP00000436337:L2081V	ENSP00000436337:L2081V	L	-	1	2	EPPK1	145013169	0.000000	0.05858	0.005000	0.12908	0.000000	0.00434	-2.297000	0.01141	-0.861000	0.04094	-3.661000	0.00025	CTG	G|0.737;C|0.263	0.263	strong		0.592	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
SLC14A1	6563	hgsc.bcm.edu	37	18	43307246	43307246	+	Intron	SNP	C	C	T	rs11877062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:43307246C>T	ENST00000321925.4	+	2	211				RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000436407.3_Missense_Mutation_p.R4W|SLC14A1_ENST00000415427.3_Missense_Mutation_p.R4W|SLC14A1_ENST00000402943.2_Intron|SLC14A1_ENST00000502059.2_5'UTR|SLC14A1_ENST00000535474.1_Intron|SLC14A1_ENST00000586142.1_5'Flank	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)						transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						GATGAATGGACGGTCTTTGAT	0.517													C|||	2013	0.401957	0.1846	0.5115	5008	,	,		19904	0.5188		0.5089	False		,,,				2504	0.3875				p.R4W		Atlas-SNP	.											.	SLC14A1	84	.	0			c.C10T						PASS	.	C	TRP/ARG,,TRP/ARG,	293,1091		28,237,427	63.0	52.0	55.0		10,,10,	2.8	0.9	18	dbSNP_120	55	1567,1615		399,769,423	yes	missense,intron,missense,intron	SLC14A1	NM_001128588.3,NM_001146036.2,NM_001146037.1,NM_015865.6	101,,101,	427,1006,850	TT,TC,CC		49.2458,21.1705,40.7359	probably-damaging,,probably-damaging,	4/446,,4/446,	43307246	1860,2706	692	1591	2283	SO:0001627	intron_variant	6563	exon1			AATGGACGGTCTT	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"""Blood group antigens"", ""Solute carriers"""	10918	protein-coding gene	gene with protein product		613868	"""Kidd blood group"", ""solute carrier family 14 (urea transporter), member 1"""	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.-22+2268C>T	18.37:g.43307246C>T		Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Missense_Mutation	SNP	ENST00000321925.4	37	CCDS11925.1	961	0.440018315018315	92	0.18699186991869918	188	0.5193370165745856	296	0.5174825174825175	385	0.5079155672823219	C	17.05	3.288793	0.59976	0.211705	0.492458	ENSG00000141469	ENST00000415427;ENST00000436407	T;T	0.48836	0.8;0.8	4.61	2.81	0.32909	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	0.99999776371	D	0.63880	0.993	P	0.47705	0.555	T	0.48127	-0.9062	8	0.72032	D	0.01	.	6.976	0.24674	0.0:0.7872:0.0:0.2128	rs11877062;rs11877062	4	Q13336-2	.	W	4	ENSP00000412309:R4W;ENSP00000390637:R4W	ENSP00000412309:R4W	R	+	1	2	SLC14A1	41561244	0.376000	0.25098	0.918000	0.36340	0.911000	0.54048	0.567000	0.23608	0.488000	0.27723	0.467000	0.42956	CGG	C|0.593;T|0.407	0.407	strong		0.517	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865	
TRIM49B	283116	hgsc.bcm.edu	37	11	49053390	49053390	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:49053390T>C	ENST00000332682.7	+	2	267	c.239T>C	c.(238-240)gTc>gCc	p.V80A		NM_001206626.1	NP_001193555.1	A6NDI0	TR49B_HUMAN	tripartite motif containing 49B	80						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			lung(8)	8						GCTAGAAAAGTCAGTCTCTGG	0.458																																					p.V80A		Atlas-SNP	.											TRIM49B,NS,NS,-1,1	TRIM49B	27	1	0			c.T239C						scavenged	.																																			SO:0001583	missense	283116	exon1			GAAAAGTCAGTCT		CCDS55762.1	11p11.12	2014-02-17			ENSG00000182053	ENSG00000182053		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	42955	protein-coding gene	gene with protein product							Standard	NM_001206626		Approved		uc021qix.1	A6NDI0		ENST00000332682.7:c.239T>C	11.37:g.49053390T>C	ENSP00000330216:p.Val80Ala	Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	288	4	0.0138889	NM_001206626		Missense_Mutation	SNP	ENST00000332682.7	37	CCDS55762.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.970469	0.00048	.	.	ENSG00000182053	ENST00000332682	D	0.84516	-1.86	0.49	-0.979	0.10276	.	.	.	.	.	T	0.62258	0.2413	N	0.08118	0	0.09310	N	0.999994	.	.	.	.	.	.	T	0.43327	-0.9398	7	0.09590	T	0.72	.	3.3156	0.07032	0.0:0.4841:0.2642:0.2517	.	.	.	.	A	80	ENSP00000330216:V80A	ENSP00000330216:V80A	V	+	2	0	AC084851.1	49009966	0.001000	0.12720	0.043000	0.18650	0.016000	0.09150	0.032000	0.13732	-1.832000	0.01196	-1.194000	0.01681	GTC	.	.	none		0.458	TRIM49B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ZNF638	27332	hgsc.bcm.edu	37	2	71654175	71654175	+	Missense_Mutation	SNP	G	G	A	rs1804020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71654175G>A	ENST00000409544.1	+	24	5806	c.5176G>A	c.(5176-5178)Gtg>Atg	p.V1726M	ZNF638_ENST00000264447.4_Missense_Mutation_p.V1726M|ZNF638_ENST00000409407.1_Missense_Mutation_p.V666M|ZNF638_ENST00000355812.3_3'UTR	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						PASS	.	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	125	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	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	
ZNF510	22869	hgsc.bcm.edu	37	9	99522508	99522508	+	Missense_Mutation	SNP	C	C	T	rs61731162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99522508C>T	ENST00000375231.1	-	6	1254	c.604G>A	c.(604-606)Ggt>Agt	p.G202S	ZNF510_ENST00000472201.1_5'Flank|ZNF510_ENST00000223428.4_Missense_Mutation_p.G202S			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	202					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(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				TTACCGCAACCTATTTTCTTT	0.294													C|||	172	0.034345	0.1263	0.0072	5008	,	,		17618	0.0		0.0	False		,,,				2504	0.0				p.G202S		Atlas-SNP	.											.	ZNF510	59	.	0			c.G604A						PASS	.	C	SER/GLY	441,3957	195.0+/-219.7	22,397,1780	39.0	44.0	42.0		604	0.0	0.0	9	dbSNP_129	42	2,8588	2.2+/-6.3	0,2,4293	yes	missense	ZNF510	NM_014930.1	56	22,399,6073	TT,TC,CC		0.0233,10.0273,3.4108	benign	202/684	99522508	443,12545	2199	4295	6494	SO:0001583	missense	22869	exon6			CGCAACCTATTTT	AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"""Zinc fingers, C2H2-type"", ""-"""	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.604G>A	9.37:g.99522508C>T	ENSP00000364379:p.Gly202Ser	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	108	67	0.62037	NM_014930	Q5SZP5	Missense_Mutation	SNP	ENST00000375231.1	37	CCDS35074.1	53	0.024267399267399268	50	0.1016260162601626	3	0.008287292817679558	0	0.0	0	0.0	c	10.85	1.467776	0.26335	0.100273	2.33E-4	ENSG00000081386	ENST00000375231;ENST00000223428	T;T	0.05139	3.49;3.49	3.02	0.0252	0.14144	.	.	.	.	.	T	0.00109	0.0003	N	0.12569	0.235	0.09310	N	1	B	0.26002	0.139	B	0.19946	0.027	T	0.48305	-0.9047	9	0.18710	T	0.47	.	2.8749	0.05628	0.3758:0.3954:0.0:0.2288	.	202	Q9Y2H8	ZN510_HUMAN	S	202	ENSP00000364379:G202S;ENSP00000223428:G202S	ENSP00000223428:G202S	G	-	1	0	ZNF510	98562329	0.000000	0.05858	0.001000	0.08648	0.318000	0.28184	0.101000	0.15251	0.012000	0.14892	0.655000	0.94253	GGT	C|0.973;T|0.027	0.027	strong		0.294	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930	
DST	667	hgsc.bcm.edu	37	6	56483852	56483852	+	Silent	SNP	T	T	G	rs2230863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:56483852T>G	ENST00000370765.6	-	23	5087	c.4980A>C	c.(4978-4980)gtA>gtC	p.V1660V	DST_ENST00000312431.6_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000446842.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	3730					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)			TAAATTCACTTACCAAATTTT	0.353													T|||	185	0.0369409	0.1218	0.0029	5008	,	,		19604	0.0198		0.002	False		,,,				2504	0.0				p.V1660V		Atlas-SNP	.											.	DST	1427	.	0			c.A4980C						PASS	.	T	,	432,3974	209.8+/-230.5	20,392,1791	121.0	130.0	127.0		4980,	-7.7	0.8	6	dbSNP_98	127	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous,intron	DST	NM_001723.5,NM_015548.4	,	20,402,6081	GG,GT,TT		0.1163,9.8048,3.3984	,	1660/2650,	56483852	442,12564	2203	4300	6503	SO:0001819	synonymous_variant	667	exon23			TTCACTTACCAAA	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.4980A>C	6.37:g.56483852T>G		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	205	103	0.502439	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000370765.6	37	CCDS4959.1																																																																																			T|0.957;G|0.043	0.043	strong		0.353	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723	
LIPM	340654	hgsc.bcm.edu	37	10	90575251	90575251	+	Silent	SNP	T	T	C	rs61737049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90575251T>C	ENST00000404743.4	+	6	1016	c.849T>C	c.(847-849)aaT>aaC	p.N283N	LIPM_ENST00000539337.1_Silent_p.N243N	NM_001128215.1	NP_001121687.1	Q5VYY2	LIPM_HUMAN	lipase, family member M	283					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)|skin(1)	7						ACACCAACAATATGAACATGG	0.438													T|||	79	0.0157748	0.0575	0.0043	5008	,	,		19878	0.0		0.0	False		,,,				2504	0.0				p.N283N		Atlas-SNP	.											.	LIPM	17	.	0			c.T849C						PASS	.						145.0	117.0	125.0					10																	90575251		692	1591	2283	SO:0001819	synonymous_variant	340654	exon6			CAACAATATGAAC		CCDS44457.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000173239	ENSG00000173239			23455	protein-coding gene	gene with protein product		613923	"""lipase-like, ab-hydrolase domain containing 3"""	LIPL3			Standard	NM_001128215		Approved	bA304I5.1	uc009xtm.1	Q5VYY2	OTTHUMG00000018698	ENST00000404743.4:c.849T>C	10.37:g.90575251T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	115	46	0.4	NM_001128215	A6PVS3|B2RXK7|B5MCR3	Silent	SNP	ENST00000404743.4	37	CCDS44457.1																																																																																			T|0.985;C|0.015	0.015	strong		0.438	LIPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049261.3	XM_291663	
HEPH	9843	hgsc.bcm.edu	37	X	65427124	65427124	+	Silent	SNP	A	A	G	rs809363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:65427124A>G	ENST00000343002.2	+	13	3043	c.2379A>G	c.(2377-2379)acA>acG	p.T793T	HEPH_ENST00000441993.2_Silent_p.T796T|HEPH_ENST00000336279.5_Silent_p.T526T|HEPH_ENST00000519389.1_Silent_p.T847T|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	124	0	0		WXS	Illumina HiSeq	Phase_I	104	104	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	
ALOX15B	247	hgsc.bcm.edu	37	17	7951878	7951878	+	Missense_Mutation	SNP	A	A	G	rs7225107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7951878A>G	ENST00000380183.4	+	14	2165	c.2026A>G	c.(2026-2028)Atc>Gtc	p.I676V	ALOX15B_ENST00000573359.1_Missense_Mutation_p.I602V|ALOX15B_ENST00000572022.1_Missense_Mutation_p.I664V|ALOX15B_ENST00000380173.2_Missense_Mutation_p.I647V	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	676	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		I -> V (in dbSNP:rs7225107).		apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)	p.I676V(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						CAGCGTCTCCATCTAAATCCC	0.577													A|||	537	0.107228	0.2587	0.0346	5008	,	,		17657	0.12		0.0129	False		,,,				2504	0.0378				p.I676V		Atlas-SNP	.											ALOX15B,NS,carcinoma,-2,2	ALOX15B	66	2	1	Substitution - Missense(1)	stomach(1)	c.A2026G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	937,3469	358.1+/-314.2	100,737,1366	88.0	87.0	87.0		1939,1804,2026	3.8	1.0	17	dbSNP_116	87	108,8492	58.3+/-119.8	0,108,4192	yes	missense,missense,missense	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	29,29,29	100,845,5558	GG,GA,AA		1.2558,21.2665,8.0348	possibly-damaging,possibly-damaging,possibly-damaging	647/648,602/603,676/677	7951878	1045,11961	2203	4300	6503	SO:0001583	missense	247	exon14			GTCTCCATCTAAA	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.2026A>G	17.37:g.7951878A>G	ENSP00000369530:p.Ile676Val	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	209	0.09569597069597069	113	0.22967479674796748	13	0.03591160220994475	74	0.12937062937062938	9	0.011873350923482849	A	16.88	3.244410	0.59103	0.212665	0.012558	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	D;D	0.94576	-3.46;-3.46	3.76	3.76	0.43208	Lipoxygenase, C-terminal (2);	0.049400	0.85682	D	0.000000	T	0.00580	0.0019	M	0.76727	2.345	0.22819	P	0.99869436	P;D;P;P	0.54397	0.942;0.966;0.808;0.709	P;P;P;B	0.51266	0.463;0.664;0.54;0.338	T	0.00000	-1.3585	9	0.51188	T	0.08	.	11.8713	0.52520	1.0:0.0:0.0:0.0	rs7225107;rs7225107	664;602;647;676	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	V	647;602;676	ENSP00000369520:I647V;ENSP00000369530:I676V	ENSP00000344337:I602V	I	+	1	0	ALOX15B	7892603	1.000000	0.71417	0.997000	0.53966	0.842000	0.47809	2.800000	0.47900	1.701000	0.51217	0.379000	0.24179	ATC	A|0.907;G|0.093	0.093	strong		0.577	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
KIAA1024	23251	hgsc.bcm.edu	37	15	79749447	79749447	+	Missense_Mutation	SNP	G	G	T	rs11634652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	99	0	0		WXS	Illumina HiSeq	Phase_I	123	54	0.439024	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	
FLG	2312	hgsc.bcm.edu	37	1	152284576	152284576	+	Missense_Mutation	SNP	C	C	A	rs143382793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284576C>A	ENST00000368799.1	-	3	2821	c.2786G>T	c.(2785-2787)gGc>gTc	p.G929V	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	929	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)			TTGTCCCTGGCCTGCCTGTGA	0.557									Ichthyosis																												p.G929V		Atlas-SNP	.											.	FLG	900	.	0			c.G2786T						PASS	.						327.0	313.0	318.0					1																	152284576		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCCTGGCCTGCCT	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.2786G>T	1.37:g.152284576C>A	ENSP00000357789:p.Gly929Val	Somatic	591	1	0.00169205		WXS	Illumina HiSeq	Phase_I	745	145	0.194631	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	1.719	-0.497190	0.04291	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.06528	3.29	1.17	0.0422	0.14216	.	.	.	.	.	T	0.06142	0.0159	M	0.77820	2.39	0.09310	N	1	D	0.67145	0.996	P	0.58970	0.849	T	0.24977	-1.0145	9	0.21014	T	0.42	.	4.8967	0.13753	0.0:0.6064:0.3936:0.0	.	929	P20930	FILA_HUMAN	V	929;136	ENSP00000357789:G929V	ENSP00000357789:G929V	G	-	2	0	FLG	150551200	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.167000	0.09940	0.033000	0.15463	0.479000	0.44913	GGC	C|0.993;A|0.007	0.007	strong		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TECPR1	25851	hgsc.bcm.edu	37	7	97873994	97873994	+	Silent	SNP	G	G	A	rs1874344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:97873994G>A	ENST00000447648.2	-	5	719	c.420C>T	c.(418-420)taC>taT	p.Y140Y	TECPR1_ENST00000542604.1_Silent_p.Y61Y|TECPR1_ENST00000379795.3_Silent_p.Y140Y			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	140					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						AGTCGATGGCGTACGTCCACC	0.587													g|||	1513	0.302117	0.2126	0.3285	5008	,	,		18002	0.4534		0.2744	False		,,,				2504	0.2771				p.Y140Y		Atlas-SNP	.											TECPR1,NS,carcinoma,0,2	TECPR1	77	2	0			c.C420T						PASS	.	A		774,3230		69,636,1297	91.0	96.0	94.0		420	-3.8	0.4	7	dbSNP_92	94	1969,6335		244,1481,2427	no	coding-synonymous	TECPR1	NM_015395.1		313,2117,3724	AA,AG,GG		23.7115,19.3307,22.2863		140/1166	97873994	2743,9565	2002	4152	6154	SO:0001819	synonymous_variant	25851	exon5			GATGGCGTACGTC		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.420C>T	7.37:g.97873994G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	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	
TINF2	26277	hgsc.bcm.edu	37	14	24709351	24709351	+	Silent	SNP	C	C	T	rs10141326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24709351C>T	ENST00000267415.7	-	8	1481	c.1140G>A	c.(1138-1140)ccG>ccA	p.P380P	TINF2_ENST00000538777.1_3'UTR|TINF2_ENST00000540705.1_Silent_p.P345P|TINF2_ENST00000558510.1_5'Flank|TINF2_ENST00000399423.4_3'UTR|TINF2_ENST00000558566.1_3'UTR	NM_001099274.1	NP_001092744.1	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2	380					negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of protein ADP-ribosylation (GO:0010836)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of telomere maintenance (GO:0032206)|protein localization to chromosome (GO:0034502)|protein localization to chromosome, telomeric region (GO:0070198)|telomere assembly (GO:0032202)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	chromosome, telomeric region (GO:0000781)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinucleolar chromocenter (GO:0010370)	telomeric DNA binding (GO:0042162)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|prostate(1)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0185)		TGCACAGAGACGGAGGACACA	0.502									Congenital Dyskeratosis;Ataxia Pancytopenia syndrome				T|||	299	0.0597045	0.2209	0.0101	5008	,	,		21880	0.0		0.0	False		,,,				2504	0.0				p.P380P		Atlas-SNP	.											.	TINF2	61	.	0			c.G1140A						PASS	.	T	,	753,3255		77,599,1328	164.0	172.0	169.0		1140,	1.7	0.0	14	dbSNP_119	169	10,8338		0,10,4164	no	coding-synonymous,utr-3	TINF2	NM_001099274.1,NM_012461.2	,	77,609,5492	TT,TC,CC		0.1198,18.7874,6.1751	,	380/452,	24709351	763,11593	2004	4174	6178	SO:0001819	synonymous_variant	26277	exon8	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita;Myelocerebellar disorder	CAGAGACGGAGGA	AF195512	CCDS41936.1, CCDS41937.1	14q12	2008-07-29				ENSG00000092330			11824	protein-coding gene	gene with protein product		604319				10581025, 18252230	Standard	NM_012461		Approved	TIN2	uc001woa.4	Q9BSI4		ENST00000267415.7:c.1140G>A	14.37:g.24709351C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_001099274	B3W5Q7|Q9H904|Q9UHC2	Silent	SNP	ENST00000267415.7	37	CCDS41936.1																																																																																			C|0.944;T|0.056	0.056	strong		0.502	TINF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415406.2		
FASLG	356	hgsc.bcm.edu	37	1	172628521	172628521	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:172628521G>A	ENST00000367721.2	+	1	364	c.180G>A	c.(178-180)ccG>ccA	p.P60P	FASLG_ENST00000340030.3_Silent_p.P60P	NM_000639.1	NP_000630.1	P48023	TNFL6_HUMAN	Fas ligand (TNF superfamily, member 6)	60	Poly-Pro.|Pro-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cellular chloride ion homeostasis (GO:0030644)|endosomal lumen acidification (GO:0048388)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|immune response (GO:0006955)|inflammatory cell apoptotic process (GO:0006925)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of angiogenesis (GO:0016525)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|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 neuron apoptotic process (GO:0043525)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to growth factor (GO:0070848)|response to lipopolysaccharide (GO:0032496)|retinal cell programmed cell death (GO:0046666)|signal transduction (GO:0007165)|T cell apoptotic process (GO:0070231)|transcription, DNA-templated (GO:0006351)	caveola (GO:0005901)|cytoplasmic membrane-bounded vesicle (GO:0016023)|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)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|skin(1)	19						cgccgccgccgccaccactgc	0.617																																					p.P60P	Ovarian(28;486 876 30334 44033)	Atlas-SNP	.											FASLG,colon,carcinoma,0,2	FASLG	44	2	0			c.G180A						scavenged	.						74.0	69.0	71.0					1																	172628521		2203	4299	6502	SO:0001819	synonymous_variant	356	exon1			GCCGCCGCCACCA	U11821	CCDS1304.1	1q23	2014-09-17	2005-01-07	2005-01-07	ENSG00000117560	ENSG00000117560		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"", ""Endogenous ligands"""	11936	protein-coding gene	gene with protein product		134638	"""tumor necrosis factor (ligand) superfamily, member 6"""	APT1LG1, TNFSF6		7826947, 9022072	Standard	NM_000639		Approved	FasL, CD178	uc001gis.3	P48023	OTTHUMG00000034841	ENST00000367721.2:c.180G>A	1.37:g.172628521G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	171	2	0.0116959	NM_000639	Q9BZP9	Silent	SNP	ENST00000367721.2	37	CCDS1304.1																																																																																			.	.	none		0.617	FASLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084276.1		
TIAM2	26230	hgsc.bcm.edu	37	6	155486535	155486535	+	Missense_Mutation	SNP	A	A	G	rs62621836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:155486535A>G	ENST00000461783.3	+	11	3626	c.2353A>G	c.(2353-2355)Ata>Gta	p.I785V	TIAM2_ENST00000456144.1_Missense_Mutation_p.I785V|TIAM2_ENST00000529824.2_Missense_Mutation_p.I785V|TIAM2_ENST00000360366.4_Missense_Mutation_p.I785V|TIAM2_ENST00000528391.2_Missense_Mutation_p.I97V|TIAM2_ENST00000367174.2_Missense_Mutation_p.I137V|TIAM2_ENST00000456877.2_Missense_Mutation_p.I97V|TIAM2_ENST00000318981.5_Missense_Mutation_p.I785V			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	785					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)		GAGACCTTCTATAACTCAGGT	0.448													A|||	100	0.0199681	0.0719	0.0072	5008	,	,		19834	0.0		0.0	False		,,,				2504	0.0				p.I785V		Atlas-SNP	.											.	TIAM2	161	.	0			c.A2353G						PASS	.	A	VAL/ILE	301,4105	165.4+/-196.9	7,287,1909	68.0	64.0	65.0		2353	-4.4	0.0	6	dbSNP_129	65	2,8598	1.2+/-3.3	0,2,4298	yes	missense	TIAM2	NM_012454.3	29	7,289,6207	GG,GA,AA		0.0233,6.8316,2.3297	benign	785/1702	155486535	303,12703	2203	4300	6503	SO:0001583	missense	26230	exon8			CCTTCTATAACTC		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.2353A>G	6.37:g.155486535A>G	ENSP00000437188:p.Ile785Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	A	10.77	1.443893	0.25987	0.068316	2.33E-4	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391	T;T;T;T;T;T;T;T;T	0.06142	3.48;3.39;3.44;3.48;3.4;3.57;3.44;3.34;3.4	5.01	-4.42	0.03579	.	0.494314	0.23646	N	0.045965	T	0.01558	0.0050	M	0.61703	1.905	0.20196	N	0.999928	B;B;B;B	0.10296	0.0;0.003;0.003;0.002	B;B;B;B	0.12837	0.008;0.006;0.003;0.003	T	0.48670	-0.9015	10	0.17832	T	0.49	.	6.285	0.21029	0.3957:0.2475:0.3568:0.0	rs62621836	97;785;785;785	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	V	785;1031;785;785;785;137;785;785;97;97	ENSP00000437188:I785V;ENSP00000434901:I785V;ENSP00000407746:I785V;ENSP00000327315:I785V;ENSP00000356142:I137V;ENSP00000353528:I785V;ENSP00000433348:I785V;ENSP00000407183:I97V;ENSP00000435335:I97V	ENSP00000327315:I785V	I	+	1	0	TIAM2	155528227	0.000000	0.05858	0.010000	0.14722	0.881000	0.50899	-0.215000	0.09279	-1.006000	0.03412	-0.274000	0.10170	ATA	A|0.979;G|0.021	0.021	strong		0.448	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
QRICH2	84074	hgsc.bcm.edu	37	17	74287204	74287204	+	Missense_Mutation	SNP	C	C	G	rs2279052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74287204C>G	ENST00000262765.5	-	4	3285	c.3106G>C	c.(3106-3108)Gag>Cag	p.E1036Q		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1036			E -> Q (in dbSNP:rs2279052). {ECO:0000269|PubMed:14702039}.							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						CTACTGAGCTCTCCCATCAGA	0.532													C|||	2082	0.415735	0.5113	0.2939	5008	,	,		19627	0.5734		0.2753	False		,,,				2504	0.3548				p.E1036Q		Atlas-SNP	.											.	QRICH2	143	.	0			c.G3106C						PASS	.	C	GLN/GLU	2167,2239	585.7+/-386.3	531,1105,567	115.0	112.0	113.0		3106	5.5	0.3	17	dbSNP_100	113	2475,6125	406.0+/-348.7	346,1783,2171	yes	missense	QRICH2	NM_032134.1	29	877,2888,2738	GG,GC,CC		28.7791,49.1829,35.6912	probably-damaging	1036/1664	74287204	4642,8364	2203	4300	6503	SO:0001583	missense	84074	exon4			TGAGCTCTCCCAT	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.3106G>C	17.37:g.74287204C>G	ENSP00000262765:p.Glu1036Gln	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	895	0.4097985347985348	265	0.5386178861788617	101	0.27900552486187846	333	0.5821678321678322	196	0.25857519788918204	C	11.06	1.528788	0.27387	0.491829	0.287791	ENSG00000129646	ENST00000262765;ENST00000447564;ENST00000301613	T;T	0.53857	2.7;0.6	5.54	5.54	0.83059	.	.	.	.	.	T	0.00012	0.0000	N	0.20986	0.625	0.37391	P	0.08755999999999997	D;P	0.55605	0.972;0.938	D;P	0.65140	0.932;0.636	T	0.49322	-0.8952	8	0.45353	T	0.12	-19.3391	14.9968	0.71439	0.0:1.0:0.0:0.0	rs2279052;rs52800512;rs2279052	1036;1036	B5MD94;Q9H0J4	.;QRIC2_HUMAN	Q	1036;44;1036	ENSP00000262765:E1036Q;ENSP00000394461:E44Q	ENSP00000262765:E1036Q	E	-	1	0	QRICH2	71798799	0.976000	0.34144	0.280000	0.24747	0.101000	0.19017	3.799000	0.55529	2.610000	0.88304	0.555000	0.69702	GAG	C|0.613;G|0.387	0.387	strong		0.532	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
ECM2	1842	hgsc.bcm.edu	37	9	95267938	95267938	+	Silent	SNP	T	T	C	rs35161698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95267938T>C	ENST00000344604.5	-	7	1490	c.1341A>G	c.(1339-1341)ggA>ggG	p.G447G	CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Silent_p.G425G	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	447					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						TGAGATTGTTTCCTTCCAATT	0.323													T|||	117	0.0233626	0.0802	0.0159	5008	,	,		15033	0.0		0.0	False		,,,				2504	0.0				p.G447G		Atlas-SNP	.											.	ECM2	147	.	0			c.A1341G						PASS	.	T	,,,	294,4112	144.2+/-179.2	6,282,1915	80.0	85.0	83.0		,1275,1275,1341	5.8	1.0	9	dbSNP_126	83	8,8592	5.7+/-21.5	0,8,4292	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECM2,CENPP	NM_001012267.1,NM_001197295.1,NM_001197296.1,NM_001393.3	,,,	6,290,6207	CC,CT,TT		0.093,6.6727,2.322	,,,	,425/678,425/644,447/700	95267938	302,12704	2203	4300	6503	SO:0001819	synonymous_variant	1842	exon7			ATTGTTTCCTTCC	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.1341A>G	9.37:g.95267938T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	99	62	0.626263	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Silent	SNP	ENST00000344604.5	37	CCDS6698.1																																																																																			T|0.978;C|0.022	0.022	strong		0.323	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393	
MED12L	116931	hgsc.bcm.edu	37	3	151127074	151127074	+	Missense_Mutation	SNP	G	G	A	rs78970280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151127074G>A	ENST00000474524.1	+	38	5797	c.5759G>A	c.(5758-5760)cGg>cAg	p.R1920Q	MED12L_ENST00000273432.4_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1920	Gln-rich.					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)			GCGCAAGCACGGCCCTCCCCT	0.527													G|||	36	0.0071885	0.0265	0.0014	5008	,	,		14258	0.0		0.0	False		,,,				2504	0.0				p.R1920Q		Atlas-SNP	.											MED12L,colon,carcinoma,-1,1	MED12L	271	1	0			c.G5759A						PASS	.	G	GLN/ARG	74,4332	66.4+/-103.9	1,72,2130	74.0	76.0	76.0		5759	5.8	1.0	3	dbSNP_132	76	0,8600		0,0,4300	yes	missense	MED12L	NM_053002.4	43	1,72,6430	AA,AG,GG		0.0,1.6795,0.569	probably-damaging	1920/2146	151127074	74,12932	2203	4300	6503	SO:0001583	missense	116931	exon38			AAGCACGGCCCTC	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.5759G>A	3.37:g.151127074G>A	ENSP00000417235:p.Arg1920Gln	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	15.65	2.896847	0.52121	0.016795	0.0	ENSG00000144893	ENST00000474524	T	0.55588	0.51	5.75	5.75	0.90469	Mediator complex, subunit Med12, catenin-binding (1);	0.133081	0.51477	D	0.000099	T	0.44582	0.1300	L	0.57536	1.79	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	T	0.52734	-0.8536	10	0.23891	T	0.37	-27.2348	17.7294	0.88373	0.0:0.0:1.0:0.0	.	1920	Q86YW9	MD12L_HUMAN	Q	1920	ENSP00000417235:R1920Q	ENSP00000417235:R1920Q	R	+	2	0	MED12L	152609764	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.424000	0.52764	2.708000	0.92522	0.650000	0.86243	CGG	G|0.993;A|0.007	0.007	strong		0.527	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
MINPP1	9562	hgsc.bcm.edu	37	10	89312046	89312046	+	Silent	SNP	T	T	C	rs2233169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:89312046T>C	ENST00000371996.4	+	5	1316	c.1275T>C	c.(1273-1275)gcT>gcC	p.A425A	MINPP1_ENST00000371994.4_3'UTR|MINPP1_ENST00000536010.1_Silent_p.A224A|MINPP1_ENST00000472891.1_3'UTR	NM_004897.4	NP_004888.2	Q9UNW1	MINP1_HUMAN	multiple inositol-polyphosphate phosphatase 1	425					bone mineralization (GO:0030282)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|ossification (GO:0001503)|polyphosphate metabolic process (GO:0006797)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|bisphosphoglycerate 3-phosphatase activity (GO:0034417)|inositol hexakisphosphate 2-phosphatase activity (GO:0052826)|phosphohistidine phosphatase activity (GO:0008969)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|urinary_tract(2)	5		Colorectal(252;0.122)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00123)		GTGAAAATGCTAAGACTCCTA	0.368													T|||	142	0.0283546	0.0998	0.0086	5008	,	,		20648	0.0		0.002	False		,,,				2504	0.002				p.A425A		Atlas-SNP	.											.	MINPP1	22	.	0			c.T1275C						PASS	.	T	,,	354,4052	181.5+/-209.5	14,326,1863	126.0	123.0	124.0		,672,1275	-4.7	1.0	10	dbSNP_98	124	11,8589	7.7+/-29.5	0,11,4289	no	utr-3,coding-synonymous,coding-synonymous	MINPP1	NM_001178117.1,NM_001178118.1,NM_004897.4	,,	14,337,6152	CC,CT,TT		0.1279,8.0345,2.8064	,,	,224/287,425/488	89312046	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	9562	exon5			AAATGCTAAGACT	AF046915	CCDS7384.1, CCDS53551.1, CCDS53552.1	10q23	2010-05-04	2010-05-04		ENSG00000107789	ENSG00000107789	3.1.3.62		7102	protein-coding gene	gene with protein product		605391	"""multiple inositol polyphosphate histidine phosphatase, 1"""			10087200	Standard	NM_004897		Approved	MIPP	uc001keu.3	Q9UNW1	OTTHUMG00000018678	ENST00000371996.4:c.1275T>C	10.37:g.89312046T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	137	61	0.445255	NM_004897	F5H683|O95172|O95286|Q59EJ2|Q9UGA3	Silent	SNP	ENST00000371996.4	37	CCDS7384.1																																																																																			T|0.975;C|0.025	0.025	strong		0.368	MINPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049221.1		
COL17A1	1308	hgsc.bcm.edu	37	10	105824332	105824332	+	Silent	SNP	C	C	T	rs149012179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105824332C>T	ENST00000353479.5	-	10	920	c.630G>A	c.(628-630)acG>acA	p.T210T	COL17A1_ENST00000393211.3_Silent_p.T210T|COL17A1_ENST00000369733.3_Silent_p.T210T	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	210	Necessary for interaction with DST and for the recruitment of DST to hemidesmosome.|Nonhelical region (NC16).		T -> M (in dbSNP:rs805708). {ECO:0000269|PubMed:15489334}.		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)		CATCCAGGATCGTTGCATCGT	0.547													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		15732	0.0		0.0	False		,,,				2504	0.0				p.T210T		Atlas-SNP	.											.	COL17A1	149	.	0			c.G630A						PASS	.	C		90,4316	74.7+/-112.8	0,90,2113	119.0	81.0	94.0		630	-8.0	0.1	10	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	COL17A1	NM_000494.3		0,90,6413	TT,TC,CC		0.0,2.0427,0.692		210/1498	105824332	90,12916	2203	4300	6503	SO:0001819	synonymous_variant	1308	exon10			CAGGATCGTTGCA	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.630G>A	10.37:g.105824332C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	156	79	0.50641	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	37	CCDS7554.1																																																																																			C|0.993;T|0.007	0.007	strong		0.547	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	155059	155059	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:155059G>A	ENST00000283426.6	+	6	1044	c.994G>A	c.(994-996)Gac>Aac	p.D332N		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	332							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		CGCAGACCTCGACGGCTCCTT	0.577																																					p.D332N		Atlas-SNP	.											PLEKHG4B_ENST00000283426,NS,carcinoma,-2,2	PLEKHG4B	167	2	0			c.G994A						scavenged	.						86.0	77.0	80.0					5																	155059		2203	4300	6503	SO:0001583	missense	153478	exon6			GACCTCGACGGCT	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.994G>A	5.37:g.155059G>A	ENSP00000283426:p.Asp332Asn	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	71	3	0.0422535	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	.	10.59	1.394085	0.25205	.	.	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.59083	0.29;0.29	3.88	3.01	0.34805	.	.	.	.	.	T	0.66015	0.2747	L	0.60455	1.87	0.09310	N	1	D	0.76494	0.999	P	0.61275	0.886	T	0.53961	-0.8364	9	0.62326	D	0.03	.	7.3764	0.26831	0.126:0.0:0.874:0.0	.	332	Q96PX9	PKH4B_HUMAN	N	332;246	ENSP00000283426:D332N;ENSP00000422493:D246N	ENSP00000283426:D332N	D	+	1	0	PLEKHG4B	208059	1.000000	0.71417	0.000000	0.03702	0.106000	0.19336	4.161000	0.58170	0.623000	0.30267	0.460000	0.39030	GAC	.	.	none		0.577	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
KREMEN2	79412	hgsc.bcm.edu	37	16	3017854	3017854	+	Missense_Mutation	SNP	G	G	C	rs11866302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3017854G>C	ENST00000303746.5	+	9	1799	c.1222G>C	c.(1222-1224)Gct>Cct	p.A408P	KREMEN2_ENST00000572045.1_3'UTR|PKMYT1_ENST00000571102.1_5'Flank|KREMEN2_ENST00000575769.1_3'UTR|KREMEN2_ENST00000571007.1_Missense_Mutation_p.A369P|PAQR4_ENST00000293978.8_5'Flank|PAQR4_ENST00000318782.8_5'Flank|PAQR4_ENST00000572687.1_5'Flank|KREMEN2_ENST00000319500.6_Silent_p.G381G|KREMEN2_ENST00000575885.1_Silent_p.G342G|PAQR4_ENST00000576565.1_5'Flank			Q8NCW0	KREM2_HUMAN	kringle containing transmembrane protein 2	408			A -> P (in dbSNP:rs11866302).		Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|large_intestine(1)	4						GGCGCTGGGGGCTTCCAGGGG	0.701													C|||	609	0.121605	0.4009	0.0519	5008	,	,		11404	0.0		0.0338	False		,,,				2504	0.0092				p.A408P		Atlas-SNP	.											.	KREMEN2	13	.	0			c.G1222C						PASS	.	C	,PRO/ALA	988,3056		100,788,1134	5.0	6.0	6.0		1143,1222	-0.3	0.9	16	dbSNP_120	6	143,7957		2,139,3909	yes	coding-synonymous,missense	KREMEN2	NM_024507.2,NM_172229.1	,27	102,927,5043	CC,CG,GG		1.7654,24.4313,9.3132	,benign	381/421,408/463	3017854	1131,11013	2022	4050	6072	SO:0001583	missense	79412	exon9			CTGGGGGCTTCCA	BC003533	CCDS10483.1, CCDS10484.1, CCDS58412.1, CCDS58413.1	16p13.11	2008-08-04			ENSG00000131650	ENSG00000131650			18797	protein-coding gene	gene with protein product		609899				12050670	Standard	NM_172229		Approved	MGC10791, KRM2	uc002csg.3	Q8NCW0	OTTHUMG00000128976	ENST00000303746.5:c.1222G>C	16.37:g.3017854G>C	ENSP00000304422:p.Ala408Pro	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	116	45	0.387931	NM_172229	B4DXF6|I3L2S2|Q8N2J4|Q8NCW1|Q96GL8|Q9BTP9	Missense_Mutation	SNP	ENST00000303746.5	37	CCDS10483.1	229	0.10485347985347986	186	0.3780487804878049	24	0.06629834254143646	0	0.0	19	0.025065963060686015	C	0.013	-1.614260	0.00835	0.244313	0.017654	ENSG00000131650	ENST00000303746	T	0.54866	0.55	4.69	-0.35	0.12606	.	0.182647	0.26446	N	0.024339	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999700303	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35895	-0.9770	8	0.02654	T	1	.	7.3415	0.26640	0.4372:0.277:0.2858:0.0	rs11866302	369;408	B4DXF6;Q8NCW0	.;KREM2_HUMAN	P	408	ENSP00000304422:A408P	ENSP00000304422:A408P	A	+	1	0	KREMEN2	2957855	0.995000	0.38212	0.888000	0.34837	0.079000	0.17450	0.061000	0.14366	-0.131000	0.11578	-0.232000	0.12228	GCT	G|0.891;C|0.109	0.109	strong		0.701	KREMEN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250964.2	NM_145347	
SPEN	23013	hgsc.bcm.edu	37	1	16262404	16262404	+	Silent	SNP	C	C	T	rs61749277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16262404C>T	ENST00000375759.3	+	11	9873	c.9669C>T	c.(9667-9669)agC>agT	p.S3223S		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	3223	Pro-rich.				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)		CACCAGCCAGCAAGGCCCCTC	0.667													C|||	607	0.121206	0.0212	0.2392	5008	,	,		10601	0.2242		0.0984	False		,,,				2504	0.09				p.S3223S		Atlas-SNP	.											.	SPEN	374	.	0			c.C9669T						PASS	.	C		169,4229		5,159,2035	28.0	30.0	29.0		9669	5.1	1.0	1	dbSNP_129	29	820,7756		41,738,3509	no	coding-synonymous	SPEN	NM_015001.2		46,897,5544	TT,TC,CC		9.5616,3.8427,7.6229		3223/3665	16262404	989,11985	2199	4288	6487	SO:0001819	synonymous_variant	23013	exon11			AGCCAGCAAGGCC		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.9669C>T	1.37:g.16262404C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	37	CCDS164.1																																																																																			C|0.902;G|0.000;T|0.098	0.098	strong		0.667	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
STOM	2040	hgsc.bcm.edu	37	9	124110368	124110368	+	Silent	SNP	C	C	T	rs115702601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124110368C>T	ENST00000286713.2	-	6	602	c.585G>A	c.(583-585)aaG>aaA	p.K195K	AL161784.1_ENST00000594963.1_Silent_p.S46S|STOM_ENST00000347359.2_Intron|STOM_ENST00000538954.1_Silent_p.K144K	NM_001270526.1|NM_004099.5	NP_001257455.1|NP_004090.4	P27105	STOM_HUMAN	stomatin	195					protein homooligomerization (GO:0051260)|regulation of acid-sensing ion channel activity (GO:1901585)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|vesicle (GO:0031982)				endometrium(1)|large_intestine(1)|lung(3)|urinary_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)		GTTTCACATCCTTAATTTCCA	0.493													C|||	19	0.00379393	0.0136	0.0	5008	,	,		16533	0.0		0.001	False		,,,				2504	0.0				p.K195K		Atlas-SNP	.											.	STOM	15	.	0			c.G585A						PASS	.	C	,	50,4356	52.3+/-87.9	0,50,2153	123.0	121.0	122.0		585,	1.5	1.0	9	dbSNP_132	122	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous,intron	STOM	NM_004099.4,NM_198194.1	,	0,51,6452	TT,TC,CC		0.0116,1.1348,0.3921	,	195/289,	124110368	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	2040	exon6			CACATCCTTAATT		CCDS6830.1, CCDS6831.1, CCDS75892.1	9q34.1	2008-07-21	2002-11-11	2002-11-15	ENSG00000148175	ENSG00000148175			3383	protein-coding gene	gene with protein product		133090	"""erythrocyte membrane protein band 7.2 (stomatin)"""	EPB7, EPB72		1883838	Standard	NM_198194		Approved	BND7	uc004blh.4	P27105	OTTHUMG00000020590	ENST00000286713.2:c.585G>A	9.37:g.124110368C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	NM_001270526	B1AM77|Q14087|Q15609|Q5VX96|Q96FK4	Silent	SNP	ENST00000286713.2	37	CCDS6830.1																																																																																			C|0.996;T|0.004	0.004	strong		0.493	STOM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053889.1	NM_004099	
TAF5L	27097	hgsc.bcm.edu	37	1	229750089	229750089	+	Splice_Site	SNP	T	T	C	rs144626601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229750089T>C	ENST00000366676.1	-	1	140	c.141A>G	c.(139-141)acA>acG	p.T47T	TAF5L_ENST00000366675.3_Splice_Site_p.T47T|TAF5L_ENST00000477957.1_5'UTR|TAF5L_ENST00000366674.1_Silent_p.T47T|TAF5L_ENST00000258281.2_Splice_Site_p.T47T			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	47					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)				CACCATTACCTGTTAGATTGG	0.557													T|||	17	0.00339457	0.0129	0.0	5008	,	,		20513	0.0		0.0	False		,,,				2504	0.0				p.T47T		Atlas-SNP	.											.	TAF5L	76	.	0			c.A141G						PASS	.	T	,	51,4355	53.6+/-89.4	0,51,2152	105.0	95.0	99.0		141,141	3.5	1.0	1	dbSNP_134	99	0,8600		0,0,4300	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	TAF5L	NM_001025247.1,NM_014409.3	,	0,51,6452	CC,CT,TT		0.0,1.1575,0.3921	,	47/326,47/590	229750089	51,12955	2203	4300	6503	SO:0001630	splice_region_variant	27097	exon2			ATTACCTGTTAGA	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.142+1A>G	1.37:g.229750089T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	156	65	0.416667	NM_001025247	Q5TDI5|Q5TDI6|Q8IW31	Silent	SNP	ENST00000366676.1	37	CCDS1581.1																																																																																			T|0.997;C|0.003	0.003	strong		0.557	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409	Silent
RP11-93K22.13	0	hgsc.bcm.edu	37	3	129810973	129810973	+	lincRNA	SNP	G	G	A	rs114865400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129810973G>A	ENST00000514010.1	-	0	157				ALG1L2_ENST00000507643.1_RNA																							GACACAGAGCGGTCGGCCTTC	0.632													N|||	155	0.0309505	0.1029	0.0086	5008	,	,		17255	0.0089		0.001	False		,,,				2504	0.0031				p.R54Q		Atlas-SNP	.											.	.	.	.	0			c.G161A						PASS	.	C	GLN/ARG	117,1267		4,109,579	18.0	20.0	19.0		161	-2.4	0.0	3	dbSNP_132	19	1,3181		0,1,1590	no	missense	ALG1L2	NM_001136152.1	43	4,110,2169	AA,AG,GG		0.0314,8.4538,2.5843	benign	54/216	129810973	118,4448	692	1591	2283			644974	exon3			CAGAGCGGTCGGC																													3.37:g.129810973G>A		Somatic	493	0	0		WXS	Illumina HiSeq	Phase_I	556	273	0.491007	NM_001136152		Missense_Mutation	SNP	ENST00000514010.1	37																																																																																				G|0.968;A|0.032	0.032	strong		0.632	RP11-93K22.13-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000358040.1		
TTN	7273	hgsc.bcm.edu	37	2	179659912	179659912	+	Missense_Mutation	SNP	G	G	A	rs16866538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179659912G>A	ENST00000591111.1	-	7	1206	c.982C>T	c.(982-984)Cgt>Tgt	p.R328C	TTN_ENST00000589042.1_Missense_Mutation_p.R328C|TTN_ENST00000460472.2_Missense_Mutation_p.R328C|TTN_ENST00000342992.6_Missense_Mutation_p.R328C|TTN_ENST00000360870.5_Missense_Mutation_p.R328C|TTN_ENST00000359218.5_Missense_Mutation_p.R328C|TTN_ENST00000342175.6_Missense_Mutation_p.R328C			Q8WZ42	TITIN_HUMAN	titin	0	ZIS1.		R -> C (in dbSNP:rs16866538). {ECO:0000269|PubMed:11846417, 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)			TGAGTCTTACGCATGAGCAAT	0.547													G|||	1182	0.236022	0.1974	0.098	5008	,	,		20301	0.5883		0.0477	False		,,,				2504	0.2168				p.R328C		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,+1,16	TTN	18412	16	0			c.C982T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	689,3717	289.5+/-280.5	54,581,1568	102.0	93.0	96.0		982,982,982,982,982	5.3	0.1	2	dbSNP_123	96	457,8143	136.5+/-193.6	16,425,3859	yes	missense,missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133379.3,NM_133378.4,NM_003319.4	180,180,180,180,180	70,1006,5427	AA,AG,GG		5.314,15.6378,8.8113	benign,benign,benign,benign,benign	328/27119,328/27052,328/5605,328/33424,328/26927	179659912	1146,11860	2203	4300	6503	SO:0001583	missense	7273	exon7			TCTTACGCATGAG	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.982C>T	2.37:g.179659912G>A	ENSP00000465570:p.Arg328Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	52	0.58427	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		506	0.2316849816849817	101	0.20528455284552846	34	0.09392265193370165	337	0.5891608391608392	34	0.044854881266490766	G	8.050	0.765811	0.15983	0.156378	0.05314	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.72942	-0.7;-0.33;-0.38;-0.39;-0.36	6.17	5.3	0.74995	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.24831	P	0.99252889	B;B;B;B;P	0.41947	0.08;0.08;0.08;0.14;0.766	B;B;B;B;B	0.33121	0.01;0.01;0.01;0.01;0.158	T	0.49670	-0.8915	8	0.87932	D	0	.	11.7311	0.51737	0.1343:0.0:0.8657:0.0	rs16866538;rs52818462;rs57423160;rs16866538	328;328;328;328;328	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	C	328	ENSP00000343764:R328C;ENSP00000434586:R328C;ENSP00000340554:R328C;ENSP00000352154:R328C;ENSP00000354117:R328C	ENSP00000340554:R328C	R	-	1	0	TTN	179368157	1.000000	0.71417	0.102000	0.21198	0.028000	0.11728	5.683000	0.68189	1.626000	0.50381	0.655000	0.94253	CGT	G|0.845;A|0.155	0.155	strong		0.547	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
WNT2B	7482	hgsc.bcm.edu	37	1	113063125	113063125	+	Silent	SNP	A	A	G	rs910697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113063125A>G	ENST00000369684.4	+	5	1655	c.1170A>G	c.(1168-1170)caA>caG	p.Q390Q	WNT2B_ENST00000256640.5_Silent_p.Q298Q|RP4-671G15.2_ENST00000608357.1_RNA|WNT2B_ENST00000369686.5_Silent_p.Q371Q	NM_024494.2	NP_078613.1	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family, member 2B	390					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to starvation (GO:0009267)|chondrocyte differentiation (GO:0002062)|cornea development in camera-type eye (GO:0061303)|forebrain regionalization (GO:0021871)|hematopoietic stem cell proliferation (GO:0071425)|iris morphogenesis (GO:0061072)|lens development in camera-type eye (GO:0002088)|lung induction (GO:0060492)|male gonad development (GO:0008584)|mesenchymal-epithelial cell signaling (GO:0060638)|neuron differentiation (GO:0030182)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|stomach(1)	18	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-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)		GGCTGGACCAAACCTGAACAC	0.517													G|||	2421	0.483427	0.5371	0.4438	5008	,	,		19029	0.6151		0.4612	False		,,,				2504	0.3262				p.Q390Q		Atlas-SNP	.											.	WNT2B	51	.	0			c.A1170G						PASS	.	G	,	2267,2139	577.5+/-384.5	593,1081,529	119.0	103.0	108.0		1113,1170	5.3	1.0	1	dbSNP_86	108	3921,4679	602.9+/-394.6	902,2117,1281	no	coding-synonymous,coding-synonymous	WNT2B	NM_004185.3,NM_024494.2	,	1495,3198,1810	GG,GA,AA		45.593,48.5474,47.578	,	371/373,390/392	113063125	6188,6818	2203	4300	6503	SO:0001819	synonymous_variant	7482	exon5			GGACCAAACCTGA	AB045116	CCDS847.1, CCDS846.1	1p13	2008-07-18			ENSG00000134245	ENSG00000134245		"""Wingless-type MMTV integration sites"""	12781	protein-coding gene	gene with protein product	"""XWNT2, Xenopus, homolog of"", ""wingless-type MMTV integration site family, member 13"""	601968		WNT13		8761309, 10944466	Standard	NM_024494		Approved	XWNT2	uc001ecb.3	Q93097	OTTHUMG00000011157	ENST00000369684.4:c.1170A>G	1.37:g.113063125A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_024494	O14903|Q5TEH9|Q5TEI2|Q9HDC1|Q9HDC2	Silent	SNP	ENST00000369684.4	37	CCDS847.1																																																																																			A|0.500;C|0.000;G|0.499;T|0.001	0.499	strong		0.517	WNT2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030692.1	NM_004185	
MAATS1	89876	hgsc.bcm.edu	37	3	119445092	119445092	+	Missense_Mutation	SNP	T	T	A	rs9817771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119445092T>A	ENST00000273390.5	+	7	834	c.757T>A	c.(757-759)Tct>Act	p.S253T		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	253			S -> T (in dbSNP:rs9817771).			mitochondrion (GO:0005739)											TTGGGAAGCCTCTCTCCCCGC	0.542													A|||	70	0.0139776	0.0514	0.0014	5008	,	,		19226	0.0		0.0	False		,,,				2504	0.001				p.S253T		Atlas-SNP	.											.	.	.	.	0			c.T757A						PASS	.	A	THR/SER	209,4197	807.3+/-415.9	3,203,1997	57.0	55.0	56.0		757	4.4	0.8	3	dbSNP_119	56	4,8596	819.2+/-406.8	1,2,4297	yes	missense	C3orf15	NM_033364.3	58	4,205,6294	AA,AT,TT		0.0465,4.7435,1.6377	benign	253/768	119445092	213,12793	2203	4300	6503	SO:0001583	missense	89876	exon7			GAAGCCTCTCTCC	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.757T>A	3.37:g.119445092T>A	ENSP00000273390:p.Ser253Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	A	1.705	-0.500484	0.04291	0.047435	4.65E-4	ENSG00000183833	ENST00000273390	T	0.23147	1.92	5.62	4.44	0.53790	.	0.293168	0.41938	N	0.000789	T	0.00815	0.0027	N	0.00630	-1.315	0.80722	D	1	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.0;0.0	T	0.26430	-1.0103	10	0.02654	T	1	-7.7599	5.0067	0.14291	0.6979:0.1217:0.0641:0.1163	rs9817771;rs52835037;rs9817771	253;14;191;253;253	Q7Z4T9;Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	AAT1_HUMAN;.;.;.;.	T	253	ENSP00000273390:S253T	ENSP00000273390:S253T	S	+	1	0	C3orf15	120927782	1.000000	0.71417	0.839000	0.33178	0.385000	0.30292	3.898000	0.56281	0.484000	0.27630	-0.265000	0.10407	TCT	T|0.984;A|0.016	0.016	strong		0.542	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
DLG4	1742	hgsc.bcm.edu	37	17	7099811	7099811	+	Silent	SNP	G	G	A	rs17203281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7099811G>A	ENST00000399506.2	-	10	1358	c.1167C>T	c.(1165-1167)atC>atT	p.I389I	DLG4_ENST00000399510.2_Silent_p.I432I|DLG4_ENST00000302955.6_Silent_p.I386I			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	389	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	TATACTGAGCGATGATCGTGA	0.542													G|||	1232	0.246006	0.1831	0.2349	5008	,	,		22199	0.3155		0.331	False		,,,				2504	0.18				p.I432I		Atlas-SNP	.											.	DLG4	110	.	0			c.C1296T						PASS	.	G	,	781,3401		71,639,1381	76.0	72.0	74.0		1158,1296	-2.8	1.0	17	dbSNP_123	74	2570,5840		396,1778,2031	no	coding-synonymous,coding-synonymous	DLG4	NM_001128827.1,NM_001365.3	,	467,2417,3412	AA,AG,GG		30.5589,18.6753,26.6121	,	386/722,432/768	7099811	3351,9241	2091	4205	6296	SO:0001819	synonymous_variant	1742	exon12			CTGAGCGATGATC	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.1167C>T	17.37:g.7099811G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_001365	B7Z1S1|G5E939|Q92941|Q9UKK8	Silent	SNP	ENST00000399506.2	37																																																																																				G|0.742;A|0.258	0.258	strong		0.542	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365	
MUC4	4585	hgsc.bcm.edu	37	3	195511937	195511937	+	Missense_Mutation	SNP	C	C	T	rs201509113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511937C>T	ENST00000463781.3	-	2	6973	c.6514G>A	c.(6514-6516)Ggt>Agt	p.G2172S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G2172S	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)		GTGGCGTGACCTGTGGATGCT	0.577																																					p.G2172S		Atlas-SNP	.											.	MUC4	1505	.	0			c.G6514A						PASS	.						12.0	15.0	14.0					3																	195511937		652	1533	2185	SO:0001583	missense	4585	exon2			CGTGACCTGTGGA	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.6514G>A	3.37:g.195511937C>T	ENSP00000417498:p.Gly2172Ser	Somatic	473	0	0		WXS	Illumina HiSeq	Phase_I	355	58	0.16338	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	7.497	0.651958	0.14516	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28666	1.6;1.67	.	.	.	.	.	.	.	.	T	0.29976	0.0750	N	0.19112	0.55	0.09310	N	0.999998	D	0.56746	0.977	D	0.63488	0.915	T	0.11084	-1.0602	7	.	.	.	.	3.4513	0.07499	0.4478:0.552:1.0E-4:1.0E-4	.	2172	E7ESK3	.	S	2172	ENSP00000417498:G2172S;ENSP00000420243:G2172S	.	G	-	1	0	MUC4	196996332	0.229000	0.23729	0.002000	0.10522	0.068000	0.16541	1.016000	0.29976	0.488000	0.27723	0.064000	0.15345	GGT	C|0.953;T|0.047	0.047	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
THEM5	284486	hgsc.bcm.edu	37	1	151825991	151825991	+	Silent	SNP	G	G	T	rs7556386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151825991G>T	ENST00000368817.5	-	1	182	c.51C>A	c.(49-51)ggC>ggA	p.G17G		NM_182578.3	NP_872384	Q8N1Q8	ACO15_HUMAN	thioesterase superfamily member 5	17					cardiolipin acyl-chain remodeling (GO:0035965)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)	mitochondrial matrix (GO:0005759)	palmitoyl-CoA hydrolase activity (GO:0016290)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CCTCAAGAAGGCCTCTGTGGT	0.582													G|||	3138	0.626597	0.7421	0.562	5008	,	,		17329	0.6567		0.6859	False		,,,				2504	0.4243				p.G17G		Atlas-SNP	.											.	THEM5	41	.	0			c.C51A						PASS	.	G		3178,1228	706.0+/-407.3	1154,870,179	105.0	106.0	106.0		51	1.9	0.0	1	dbSNP_116	106	5822,2778	678.3+/-403.5	1984,1854,462	no	coding-synonymous	THEM5	NM_182578.3		3138,2724,641	TT,TG,GG		32.3023,27.8711,30.8012		17/248	151825991	9000,4006	2203	4300	6503	SO:0001819	synonymous_variant	284486	exon1			AAGAAGGCCTCTG	AK095283	CCDS1005.1	1q21.3	2008-02-05			ENSG00000196407	ENSG00000196407			26755	protein-coding gene	gene with protein product		615653					Standard	NM_182578		Approved	FLJ37964	uc021oyw.1	Q8N1Q8	OTTHUMG00000013070	ENST00000368817.5:c.51C>A	1.37:g.151825991G>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_182578	Q5T1C3	Silent	SNP	ENST00000368817.5	37	CCDS1005.1																																																																																			G|0.330;T|0.670	0.670	strong		0.582	THEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036678.2	NM_182578	
ZNF106	64397	hgsc.bcm.edu	37	15	42729508	42729508	+	Silent	SNP	G	G	A	rs4924677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42729508G>A	ENST00000263805.4	-	10	4925	c.4599C>T	c.(4597-4599)gcC>gcT	p.A1533A	ZNF106_ENST00000565380.1_Silent_p.A761A|ZNF106_ENST00000565611.1_Silent_p.A718A	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	1533					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)										TTGCATTTACGGCAGCTTGGT	0.403													G|||	609	0.121605	0.1589	0.2522	5008	,	,		7129	0.1012		0.0109	False		,,,				2504	0.1135				p.A1533A		Atlas-SNP	.											.	ZFP106	117	.	0			c.C4599T						PASS	.	G		612,3794	266.5+/-267.3	45,522,1636	140.0	132.0	135.0		4599	-6.9	1.0	15	dbSNP_111	135	97,8501	54.0+/-114.7	1,95,4203	no	coding-synonymous	ZFP106	NM_022473.1		46,617,5839	AA,AG,GG		1.1282,13.8901,5.4522		1533/1884	42729508	709,12295	2203	4299	6502	SO:0001819	synonymous_variant	64397	exon10			ATTTACGGCAGCT	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.4599C>T	15.37:g.42729508G>A		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	272	137	0.503676	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Silent	SNP	ENST00000263805.4	37	CCDS32208.1																																																																																			G|0.933;A|0.067	0.067	strong		0.403	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
WDR90	197335	hgsc.bcm.edu	37	16	705795	705795	+	Silent	SNP	C	C	T	rs12599798	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:705795C>T	ENST00000293879.4	+	17	1872	c.1872C>T	c.(1870-1872)agC>agT	p.S624S	LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Silent_p.S624S			Q96KV7	WDR90_HUMAN	WD repeat domain 90	624										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCATCAGCAGCCTCAGCGTCT	0.682													C|||	1233	0.246206	0.4123	0.1758	5008	,	,		17229	0.3026		0.1163	False		,,,				2504	0.1472				p.S624S		Atlas-SNP	.											.	WDR90	107	.	0			c.C1872T						PASS	.	C		1492,2804		264,964,920	22.0	25.0	24.0		1872	4.6	1.0	16	dbSNP_120	24	1094,7372		62,970,3201	no	coding-synonymous	WDR90	NM_145294.4		326,1934,4121	TT,TC,CC		12.9223,34.73,20.2633		624/1749	705795	2586,10176	2148	4233	6381	SO:0001819	synonymous_variant	197335	exon17			CAGCAGCCTCAGC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.1872C>T	16.37:g.705795C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	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	
GKN2	200504	hgsc.bcm.edu	37	2	69172570	69172570	+	Missense_Mutation	SNP	G	G	A	rs73935451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69172570G>A	ENST00000328895.4	-	6	593	c.485C>T	c.(484-486)gCt>gTt	p.A162V	GKN2_ENST00000481498.1_3'UTR	NM_182536.2	NP_872342.2	Q86XP6	GKN2_HUMAN	gastrokine 2	162						extracellular region (GO:0005576)				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(1)	15						ACAGCCTCCAGCACCGACATT	0.343													G|||	95	0.0189696	0.0703	0.0029	5008	,	,		14842	0.0		0.0	False		,,,				2504	0.0				p.A162V		Atlas-SNP	.											.	GKN2	28	.	0			c.C485T						PASS	.	G	VAL/ALA	192,4214	117.5+/-155.4	5,182,2016	86.0	98.0	94.0		485	4.6	0.0	2	dbSNP_130	94	3,8597	3.0+/-9.4	0,3,4297	yes	missense	GKN2	NM_182536.2	64	5,185,6313	AA,AG,GG		0.0349,4.3577,1.4993	benign	162/185	69172570	195,12811	2203	4300	6503	SO:0001583	missense	200504	exon6			CCTCCAGCACCGA	AF494509	CCDS33215.1	2p14	2012-10-10			ENSG00000183607	ENSG00000183607		"""BRICHOS domain containing"""	24588	protein-coding gene	gene with protein product	"""down regulated in gastric cancer GDDR"", ""BRICHOS domain containing 1B"""					15774165, 15924415, 16888721	Standard	NM_182536		Approved	TFIZ1, PRO813, VLTI465, blottin, GDDR, BRICD1B	uc002sfa.3	Q86XP6	OTTHUMG00000152655	ENST00000328895.4:c.485C>T	2.37:g.69172570G>A	ENSP00000329292:p.Ala162Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	152	85	0.559211	NM_182536	Q6UWS6	Missense_Mutation	SNP	ENST00000328895.4	37	CCDS33215.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	G	16.09	3.023294	0.54683	0.043577	3.49E-4	ENSG00000183607	ENST00000328895	T	0.45668	0.89	5.48	4.61	0.57282	.	0.626420	0.16479	N	0.212605	T	0.02688	0.0081	L	0.50333	1.59	0.25024	N	0.991315	P	0.48294	0.908	B	0.34138	0.176	T	0.06075	-1.0847	10	0.66056	D	0.02	-5.4299	9.8712	0.41175	0.0908:0.0:0.9092:0.0	.	162	Q86XP6	GKN2_HUMAN	V	162	ENSP00000329292:A162V	ENSP00000329292:A162V	A	-	2	0	GKN2	69026074	0.014000	0.17966	0.006000	0.13384	0.410000	0.31052	1.135000	0.31454	1.562000	0.49601	0.650000	0.86243	GCT	G|0.983;A|0.017	0.017	strong		0.343	GKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327191.1	NM_182536	
MUC4	4585	hgsc.bcm.edu	37	3	195515257	195515257	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515257G>T	ENST00000463781.3	-	2	3653	c.3194C>A	c.(3193-3195)gCa>gAa	p.A1065E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1065E	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	498					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.A1065E(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)		ACCTGTGGATGCTGAGGAAGT	0.562																																					p.A1065E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	NS(2)|endometrium(1)	c.C3194A						PASS	.						24.0	18.0	20.0					3																	195515257		690	1590	2280	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	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.3194C>A	3.37:g.195515257G>T	ENSP00000417498:p.Ala1065Glu	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	265	62	0.233962	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	.	.	.	.	.	.	.	.	.	.	-	6.830	0.522392	0.13066	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.44;1.44	0.573	-1.15	0.09709	.	.	.	.	.	T	0.14960	0.0361	N	0.19112	0.55	0.09310	N	1	B	0.19200	0.034	B	0.14023	0.01	T	0.28744	-1.0034	8	.	.	.	.	4.0999	0.10009	0.5176:0.0:0.4824:0.0	.	1065	E7ESK3	.	E	1065	ENSP00000417498:A1065E;ENSP00000420243:A1065E	.	A	-	2	0	MUC4	196999652	.	.	0.002000	0.10522	0.032000	0.12392	.	.	-0.302000	0.08869	-2.092000	0.00371	GCA	G|0.500;A|0.500	.	alt		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SAMD13	148418	hgsc.bcm.edu	37	1	84791374	84791374	+	Silent	SNP	C	C	T	rs55638637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:84791374C>T	ENST00000370671.3	+	3	227	c.168C>T	c.(166-168)gtC>gtT	p.V56V	SAMD13_ENST00000394834.3_Silent_p.V36V|SAMD13_ENST00000370669.1_Silent_p.V36V|SAMD13_ENST00000370670.2_Silent_p.V36V|SAMD13_ENST00000370668.3_Silent_p.V36V|SAMD13_ENST00000370673.3_Silent_p.V50V			Q5VXD3	SAM13_HUMAN	sterile alpha motif domain containing 13	56	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									lung(4)	4				all cancers(265;0.00667)|Epithelial(280;0.0219)|OV - Ovarian serous cystadenocarcinoma(397;0.136)		TGATGGATGTCGTCAATTATT	0.478													C|||	213	0.0425319	0.0741	0.0202	5008	,	,		21412	0.001		0.0338	False		,,,				2504	0.0675				p.V50V		Atlas-SNP	.											.	SAMD13	5	.	0			c.C150T						PASS	.	C	,,	279,4127	155.2+/-188.4	12,255,1936	175.0	148.0	157.0		150,108,108	-3.6	1.0	1	dbSNP_129	157	264,8336	102.3+/-163.5	4,256,4040	no	coding-synonymous,coding-synonymous,coding-synonymous	SAMD13	NM_001010971.2,NM_001134663.1,NM_001134664.1	,,	16,511,5976	TT,TC,CC		3.0698,6.3323,4.175	,,	50/117,36/103,36/103	84791374	543,12463	2203	4300	6503	SO:0001819	synonymous_variant	148418	exon3			GGATGTCGTCAAT		CCDS30760.1, CCDS44166.1	1p31.1	2013-01-10			ENSG00000203943	ENSG00000203943		"""Sterile alpha motif (SAM) domain containing"""	24582	protein-coding gene	gene with protein product							Standard	NM_001010971		Approved		uc001djr.3	Q5VXD3	OTTHUMG00000009859	ENST00000370671.3:c.168C>T	1.37:g.84791374C>T		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	235	108	0.459574	NM_001010971	B3KPW8|D3DT11|Q53AI4|Q5VXD2|Q5VXD4	Silent	SNP	ENST00000370671.3	37																																																																																				C|0.962;T|0.038	0.038	strong		0.478	SAMD13-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027243.1	NM_001010971	
SUMF1	285362	hgsc.bcm.edu	37	3	4403837	4403837	+	Silent	SNP	A	A	G	rs2633852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:4403837A>G	ENST00000272902.5	-	9	1151	c.1116T>C	c.(1114-1116)acT>acC	p.T372T	SUMF1_ENST00000534863.1_Intron|SUMF1_ENST00000458465.2_Silent_p.T240T|SUMF1_ENST00000405420.2_Silent_p.T352T|SUMF1_ENST00000383843.5_Silent_p.T347T	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	372					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)		GTCAGTCCATAGTGGGCAGGC	0.522													G|||	3808	0.760383	0.9206	0.6945	5008	,	,		20130	0.7609		0.5905	False		,,,				2504	0.7648				p.T372T		Atlas-SNP	.											.	SUMF1	23	.	0			c.T1116C						PASS	.	G	,,	3754,652	277.2+/-273.6	1603,548,52	64.0	62.0	63.0		1041,1056,1116	0.6	0.0	3	dbSNP_100	63	4747,3853	541.5+/-384.0	1316,2115,869	no	coding-synonymous,coding-synonymous,coding-synonymous	SUMF1	NM_001164674.1,NM_001164675.1,NM_182760.3	,,	2919,2663,921	GG,GA,AA		44.8023,14.798,34.6379	,,	347/350,352/355,372/375	4403837	8501,4505	2203	4300	6503	SO:0001819	synonymous_variant	285362	exon9			GTCCATAGTGGGC	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.1116T>C	3.37:g.4403837A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_182760	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Silent	SNP	ENST00000272902.5	37	CCDS2564.1																																																																																			A|0.307;G|0.693	0.693	strong		0.522	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377086	49377086	+	Missense_Mutation	SNP	T	T	C	rs611251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49377086T>C	ENST00000200453.5	+	2	865	c.596T>C	c.(595-597)gTa>gCa	p.V199A		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	199	Glu-rich.		V -> A (in dbSNP:rs611251).		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		GAAGAAGCTGTAAAGAAAGAA	0.532													T|||	1368	0.273163	0.534	0.2262	5008	,	,		18625	0.0933		0.1521	False		,,,				2504	0.2638				p.V199A		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.T596C						PASS	.	T	ALA/VAL	2102,2304	573.6+/-383.6	513,1076,614	149.0	161.0	157.0		596	0.4	0.0	19	dbSNP_83	157	1245,7355	249.3+/-276.6	74,1097,3129	yes	missense	PPP1R15A	NM_014330.3	64	587,2173,3743	CC,CT,TT		14.4767,47.7077,25.7343	probably-damaging	199/675	49377086	3347,9659	2203	4300	6503	SO:0001583	missense	23645	exon2			AAGCTGTAAAGAA	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.596T>C	19.37:g.49377086T>C	ENSP00000200453:p.Val199Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	513	0.2348901098901099	259	0.5264227642276422	81	0.22375690607734808	57	0.09965034965034965	116	0.15303430079155672	T	10.91	1.483851	0.26598	0.477077	0.144767	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.04194	3.68	4.06	0.39	0.16275	.	1.686450	0.03645	N	0.240170	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B	0.26363	0.147	B	0.19666	0.026	T	0.44159	-0.9346	9	0.02654	T	1	-1.0388	2.3232	0.04216	0.2168:0.2659:0.0:0.5173	rs611251;rs3177847;rs3826819;rs52819950;rs58000193;rs611251	199	O75807	PR15A_HUMAN	A	199;39;157	ENSP00000200453:V199A	ENSP00000200453:V199A	V	+	2	0	PPP1R15A	54068898	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.145000	0.16157	0.236000	0.21180	0.418000	0.28097	GTA	T|0.735;G|0.004	.	strong		0.532	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
BEGAIN	57596	hgsc.bcm.edu	37	14	101005236	101005236	+	Silent	SNP	A	A	G	rs12892571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101005236A>G	ENST00000355173.2	-	7	923	c.852T>C	c.(850-852)caT>caC	p.H284H	CTD-2062F14.3_ENST00000553301.1_lincRNA|BEGAIN_ENST00000556751.1_Silent_p.H220H|BEGAIN_ENST00000443071.2_Silent_p.H284H	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	284						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				GGAAGGCCTCATGCTGGAAGC	0.701													G|||	3226	0.644169	0.9697	0.621	5008	,	,		12984	0.7054		0.4115	False		,,,				2504	0.3967				p.H284H	NSCLC(159;1889 2010 9965 27479 40101)	Atlas-SNP	.											.	BEGAIN	32	.	0			c.T852C						PASS	.	G	,	3855,541		1702,451,45	18.0	23.0	21.0		852,852	2.5	0.6	14	dbSNP_121	21	3359,5239		679,2001,1619	no	coding-synonymous,coding-synonymous	BEGAIN	NM_001159531.1,NM_020836.3	,	2381,2452,1664	GG,GA,AA		39.0672,12.3066,44.4821	,	284/594,284/594	101005236	7214,5780	2198	4299	6497	SO:0001819	synonymous_variant	57596	exon7			GGCCTCATGCTGG	BC002607	CCDS9962.1	14q32.2	2012-12-07	2012-12-07			ENSG00000183092			24163	protein-coding gene	gene with protein product			"""brain-enriched guanylate kinase-associated homolog (rat)"""			10819331	Standard	NM_020836		Approved	KIAA1446	uc010txa.2	Q9BUH8		ENST00000355173.2:c.852T>C	14.37:g.101005236A>G		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_020836	Q9NPU3|Q9P282	Silent	SNP	ENST00000355173.2	37	CCDS9962.1																																																																																			A|0.415;G|0.585	0.585	strong		0.701	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836	
EVC2	132884	hgsc.bcm.edu	37	4	5624670	5624670	+	Missense_Mutation	SNP	T	T	C	rs730469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:5624670T>C	ENST00000344408.5	-	14	2148	c.2095A>G	c.(2095-2097)Acg>Gcg	p.T699A	EVC2_ENST00000310917.2_Missense_Mutation_p.T619A|EVC2_ENST00000344938.1_Missense_Mutation_p.T699A	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	699			T -> A (in dbSNP:rs730469).		smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TCCTCAACCGTTCGGAAGGCC	0.632													C|||	2592	0.517572	0.8775	0.3963	5008	,	,		15234	0.62		0.2555	False		,,,				2504	0.2812				p.T699A		Atlas-SNP	.											EVC2,colon,carcinoma,+2,1	EVC2	202	1	0			c.A2095G						PASS	.	C	ALA/THR,ALA/THR	3407,999		1328,751,124	49.0	55.0	53.0		1855,2095	0.4	0.0	4	dbSNP_86	53	2393,6207		340,1713,2247	yes	missense,missense	EVC2	NM_001166136.1,NM_147127.4	58,58	1668,2464,2371	CC,CT,TT		27.8256,22.6736,44.5948	benign,benign	619/1229,699/1309	5624670	5800,7206	2203	4300	6503	SO:0001583	missense	132884	exon14			CAACCGTTCGGAA	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2095A>G	4.37:g.5624670T>C	ENSP00000342144:p.Thr699Ala	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	168	74	0.440476	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	1097	0.5022893772893773	421	0.8556910569105691	141	0.38950276243093923	334	0.583916083916084	201	0.26517150395778366	C	0.004	-2.288290	0.00248	0.773264	0.278256	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.73897	-0.79;-0.78;-0.79	5.0	0.373	0.16178	.	0.802333	0.11785	N	0.529747	T	0.00012	0.0000	N	0.04297	-0.235	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39603	-0.9606	9	0.06757	T	0.87	-0.5273	1.4581	0.02390	0.1583:0.1958:0.1568:0.489	rs730469;rs58423551;rs730469	699	Q86UK5	LBN_HUMAN	A	699;619;699	ENSP00000339954:T699A;ENSP00000311683:T619A;ENSP00000342144:T699A	ENSP00000311683:T619A	T	-	1	0	EVC2	5675571	0.205000	0.23458	0.000000	0.03702	0.003000	0.03518	1.480000	0.35464	-0.092000	0.12417	-0.642000	0.03964	ACG	T|0.515;C|0.485	0.485	strong		0.632	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
CCDC107	203260	hgsc.bcm.edu	37	9	35660901	35660901	+	Missense_Mutation	SNP	C	C	T	rs2275420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35660901C>T	ENST00000426546.2	+	5	635	c.569C>T	c.(568-570)tCt>tTt	p.S190F	CCDC107_ENST00000378406.1_3'UTR|CCDC107_ENST00000421582.2_3'UTR|RMRP_ENST00000602361.1_lincRNA|ARHGEF39_ENST00000490970.1_5'Flank|ARHGEF39_ENST00000378387.3_3'UTR|CCDC107_ENST00000378407.3_3'UTR|ARHGEF39_ENST00000378395.2_3'UTR|ARHGEF39_ENST00000343259.3_3'UTR|CCDC107_ENST00000378409.3_Intron|CCDC107_ENST00000327351.2_Intron	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	190			S -> F (in dbSNP:rs2275420).			integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GACAAAGTCTCTGAAACTGGA	0.542													C|||	758	0.151358	0.3336	0.0879	5008	,	,		19570	0.0427		0.1312	False		,,,				2504	0.0828				p.S190F		Atlas-SNP	.											.	CCDC107	12	.	0			c.C569T						PASS	.	C	PHE/SER,,,,	1323,3083	445.1+/-347.6	206,911,1086	120.0	128.0	126.0		569,,,,	1.2	0.0	9	dbSNP_100	126	1168,7432	238.5+/-269.9	79,1010,3211	yes	missense,intron,intron,utr-3,utr-3	C9orf100,CCDC107	NM_174923.2,NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2	155,,,,	285,1921,4297	TT,TC,CC		13.5814,30.0272,19.1527	probably-damaging,,,,	190/284,,,,	35660901	2491,10515	2203	4300	6503	SO:0001583	missense	203260	exon5			AAGTCTCTGAAAC	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.569C>T	9.37:g.35660901C>T	ENSP00000414964:p.Ser190Phe	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Missense_Mutation	SNP	ENST00000426546.2	37	CCDS6583.1	327	0.14972527472527472	163	0.3313008130081301	32	0.08839779005524862	26	0.045454545454545456	106	0.13984168865435356	C	9.796	1.179221	0.21787	0.300272	0.135814	ENSG00000159884	ENST00000426546	T	0.25085	1.82	5.44	1.16	0.20824	.	1.492810	0.03871	N	0.275557	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	D	0.55605	0.972	P	0.53549	0.729	T	0.25187	-1.0139	9	0.59425	D	0.04	-0.0036	3.0663	0.06215	0.3277:0.434:0.15:0.0883	rs2275420;rs52801812;rs59963800;rs2275420	190	Q8WV48	CC107_HUMAN	F	190	ENSP00000414964:S190F	ENSP00000414964:S190F	S	+	2	0	CCDC107	35650901	0.000000	0.05858	0.000000	0.03702	0.248000	0.25809	0.104000	0.15313	0.358000	0.24211	0.655000	0.94253	TCT	C|0.831;T|0.169	0.169	strong		0.542	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923	
CCHCR1	54535	hgsc.bcm.edu	37	6	31122500	31122500	+	Missense_Mutation	SNP	G	G	A	rs130065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31122500G>A	ENST00000376266.5	-	4	429	c.307C>T	c.(307-309)Cgg>Tgg	p.R103W	CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000396268.3_Missense_Mutation_p.R192W|CCHCR1_ENST00000396263.2_Missense_Mutation_p.R103W|CCHCR1_ENST00000451521.2_Missense_Mutation_p.R156W	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	103			R -> W (in allele HCR*WWCC; associated with psoriasis; dbSNP:rs130065). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14574404}.		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						TCCTCCAGCCGCCGCAGCTCT	0.657													G|||	598	0.119409	0.1241	0.0793	5008	,	,		18354	0.0387		0.1918	False		,,,				2504	0.1503				p.R192W		Atlas-SNP	.											.	CCHCR1	68	.	0			c.C574T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	410,2604		29,352,1126	31.0	36.0	34.0		466,574,307	4.4	1.0	6	dbSNP_78	34	1110,4304		120,870,1717	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	101,101,101	149,1222,2843	AA,AG,GG		20.5024,13.6032,18.0351	benign,benign,benign	156/836,192/872,103/783	31122500	1520,6908	1507	2707	4214	SO:0001583	missense	54535	exon4			CCAGCCGCCGCAG	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.307C>T	6.37:g.31122500G>A	ENSP00000365442:p.Arg103Trp	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	265	0.12133699633699634	62	0.12601626016260162	27	0.07458563535911603	26	0.045454545454545456	150	0.19788918205804748	G	18.11	3.550954	0.65311	0.136032	0.205024	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521;ENST00000448141;ENST00000508683;ENST00000448162;ENST00000513222;ENST00000503420;ENST00000515274;ENST00000507751;ENST00000455279;ENST00000412245;ENST00000503934;ENST00000426967;ENST00000502557;ENST00000507829	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.07327	3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2	5.33	4.37	0.52481	.	0.450693	0.21536	N	0.072963	T	0.05227	0.0139	M	0.69823	2.125	0.31057	P	0.7145239999999999	B;B;B;B;B	0.27997	0.019;0.019;0.019;0.197;0.066	B;B;B;B;B	0.25405	0.002;0.002;0.002;0.06;0.017	T	0.05178	-1.0901	9	0.59425	D	0.04	-22.3718	9.5976	0.39584	0.0:0.0:0.7385:0.2615	rs130065;rs3173361;rs17840019;rs58977051	103;103;103;156;192	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	W	192;103;103;103;156;67;67;103;77;67;103;103;103;129;103;201;103;103	ENSP00000379566:R192W;ENSP00000365442:R103W;ENSP00000379561:R103W;ENSP00000401039:R156W;ENSP00000414323:R67W;ENSP00000421393:R67W;ENSP00000390027:R103W;ENSP00000425682:R77W;ENSP00000421992:R67W;ENSP00000420941:R103W;ENSP00000398715:R103W;ENSP00000425595:R103W;ENSP00000402432:R201W;ENSP00000425377:R103W;ENSP00000420911:R103W	ENSP00000365442:R103W	R	-	1	2	CCHCR1	31230479	0.987000	0.35691	1.000000	0.80357	0.768000	0.43524	1.439000	0.35013	2.510000	0.84645	0.638000	0.83543	CGG	G|0.836;A|0.164	0.164	strong		0.657	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
MYO7B	4648	hgsc.bcm.edu	37	2	128341904	128341904	+	Silent	SNP	G	G	A	rs61743462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128341904G>A	ENST00000409816.2	+	12	1583	c.1551G>A	c.(1549-1551)ccG>ccA	p.P517P	MYO7B_ENST00000389524.4_Silent_p.P517P|MYO7B_ENST00000428314.1_Silent_p.P517P			Q6PIF6	MYO7B_HUMAN	myosin VIIB	517	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GCCGCTTCCCGCAGGTGTGTG	0.602													G|||	54	0.0107827	0.0393	0.0029	5008	,	,		18661	0.0		0.0	False		,,,				2504	0.0				p.P517P		Atlas-SNP	.											.	MYO7B	359	.	0			c.G1551A						PASS	.	G		144,3842		1,142,1850	55.0	59.0	57.0		1551	-6.6	0.9	2	dbSNP_129	57	1,8289		0,1,4144	no	coding-synonymous	MYO7B	NM_001080527.1		1,143,5994	AA,AG,GG		0.0121,3.6126,1.1812		517/2117	128341904	145,12131	1993	4145	6138	SO:0001819	synonymous_variant	4648	exon13			CTTCCCGCAGGTG		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.1551G>A	2.37:g.128341904G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	37	CCDS46405.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
APH1B	83464	hgsc.bcm.edu	37	15	63597857	63597857	+	Missense_Mutation	SNP	T	T	G	rs1047552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:63597857T>G	ENST00000261879.5	+	6	721	c.651T>G	c.(649-651)ttT>ttG	p.F217L	APH1B_ENST00000560716.1_3'UTR|APH1B_ENST00000380343.4_Missense_Mutation_p.F176L	NM_001145646.1|NM_031301.3	NP_001139118.1|NP_112591.2	Q8WW43	APH1B_HUMAN	APH1B gamma secretase subunit	217			F -> L (in dbSNP:rs1047552).		apoptotic signaling pathway (GO:0097190)|membrane protein intracellular domain proteolysis (GO:0031293)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	peptidase activity (GO:0008233)	p.F217L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	12						CGTCAGCATTTATAATCCTGG	0.443													T|||	401	0.0800719	0.0575	0.1167	5008	,	,		19199	0.1637		0.0388	False		,,,				2504	0.0409				p.F217L		Atlas-SNP	.											APH1B,NS,carcinoma,0,1	APH1B	27	1	1	Substitution - Missense(1)	stomach(1)	c.T651G	GRCh37	CM086277	APH1B	M	rs1047552	PASS	.	T	LEU/PHE,LEU/PHE	244,4162	141.9+/-177.2	10,224,1969	70.0	74.0	73.0		528,651	0.0	0.0	15	dbSNP_86	73	259,8341	100.8+/-162.1	6,247,4047	yes	missense,missense	APH1B	NM_001145646.1,NM_031301.3	22,22	16,471,6016	GG,GT,TT		3.0116,5.5379,3.8674	benign,benign	176/217,217/258	63597857	503,12503	2203	4300	6503	SO:0001583	missense	83464	exon6			AGCATTTATAATC	AY358698	CCDS10184.1, CCDS45276.1	15q22.2	2013-05-01	2013-05-01		ENSG00000138613	ENSG00000138613			24080	protein-coding gene	gene with protein product		607630	"""anterior pharynx defective 1 homolog B (C. elegans)"""			12110170, 11230166	Standard	NM_031301		Approved	PSFL, APH-1B, DKFZp564D0372	uc002ama.3	Q8WW43	OTTHUMG00000132863	ENST00000261879.5:c.651T>G	15.37:g.63597857T>G	ENSP00000261879:p.Phe217Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_031301	A8K589|Q564N3|Q6UWQ1|Q9H0S0	Missense_Mutation	SNP	ENST00000261879.5	37	CCDS10184.1	222	0.10164835164835165	43	0.08739837398373984	36	0.09944751381215469	117	0.20454545454545456	26	0.03430079155672823	T	8.914	0.959432	0.18507	0.055379	0.030116	ENSG00000138613	ENST00000380343;ENST00000261879	T;T	0.41065	1.01;1.01	4.93	0.0142	0.14099	.	0.068865	0.64402	D	0.000012	T	0.00039	0.0001	N	0.24115	0.695	0.54753	P	1.799999999996249E-5	B;B	0.20671	0.047;0.047	B;B	0.25506	0.061;0.061	T	0.14896	-1.0456	9	0.45353	T	0.12	-7.5573	7.3785	0.26841	0.0:0.487:0.0:0.513	rs1047552;rs3187561;rs52837075;rs1047552	176;217	Q564N3;Q8WW43	.;APH1B_HUMAN	L	176;217	ENSP00000369700:F176L;ENSP00000261879:F217L	ENSP00000261879:F217L	F	+	3	2	APH1B	61384910	0.121000	0.22262	0.002000	0.10522	0.030000	0.12068	-0.118000	0.10692	-0.029000	0.13827	-0.475000	0.04921	TTT	G|0.065;T|0.935	0.065	strong		0.443	APH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256337.1	NM_031301	
TEP1	7011	hgsc.bcm.edu	37	14	20837033	20837033	+	Missense_Mutation	SNP	T	T	C	rs2104978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20837033T>C	ENST00000262715.5	-	54	7725	c.7685A>G	c.(7684-7686)cAt>cGt	p.H2562R	TEP1_ENST00000556935.1_Missense_Mutation_p.H2454R	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2562			H -> R (in dbSNP:rs2104978).		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)		AGGTAGCACATGGAGGGCTGT	0.527													T|||	173	0.0345447	0.003	0.0317	5008	,	,		16457	0.002		0.0656	False		,,,				2504	0.0808				p.H2562R		Atlas-SNP	.											.	TEP1	224	.	0			c.A7685G						PASS	.	T	ARG/HIS	62,4344	60.5+/-97.4	0,62,2141	87.0	67.0	74.0		7685	5.8	1.0	14	dbSNP_96	74	570,8030	153.6+/-207.9	17,536,3747	yes	missense	TEP1	NM_007110.4	29	17,598,5888	CC,CT,TT		6.6279,1.4072,4.8593	probably-damaging	2562/2628	20837033	632,12374	2203	4300	6503	SO:0001583	missense	7011	exon54			AGCACATGGAGGG		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.7685A>G	14.37:g.20837033T>C	ENSP00000262715:p.His2562Arg	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	198	81	0.409091	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	63	0.028846153846153848	0	0.0	12	0.03314917127071823	0	0.0	51	0.06728232189973615	T	21.4	4.151048	0.78001	0.014072	0.066279	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.58210	0.35;0.35	5.81	5.81	0.92471	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.181219	0.42964	D	0.000629	T	0.10594	0.0259	L	0.39898	1.24	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.72338	0.961;0.977	T	0.22556	-1.0213	10	0.13108	T	0.6	-17.9579	13.6839	0.62504	0.0:0.0:0.0:1.0	rs2104978;rs2228033;rs17277305;rs52818387;rs2104978	2454;2562	G3V5X7;Q99973	.;TEP1_HUMAN	R	2562;2554;2454	ENSP00000262715:H2562R;ENSP00000452574:H2454R	ENSP00000262715:H2562R	H	-	2	0	TEP1	19906873	0.998000	0.40836	1.000000	0.80357	0.986000	0.74619	3.917000	0.56424	2.226000	0.72624	0.482000	0.46254	CAT	T|0.957;C|0.043	0.043	strong		0.527	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
PTPN3	5774	hgsc.bcm.edu	37	9	112219474	112219474	+	Missense_Mutation	SNP	C	C	G	rs3793524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	123	0	0		WXS	Illumina HiSeq	Phase_I	129	91	0.705426	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		
SAMD15	161394	hgsc.bcm.edu	37	14	77843920	77843920	+	Silent	SNP	A	A	G	rs61729313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:77843920A>G	ENST00000216471.4	+	1	445	c.159A>G	c.(157-159)caA>caG	p.Q53Q	SAMD15_ENST00000533095.2_Intron|TMED8_ENST00000216468.7_5'Flank	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	53										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						AGATTTACCAAGAGCCACAGC	0.532													A|||	324	0.0646965	0.2368	0.0159	5008	,	,		18476	0.0		0.0	False		,,,				2504	0.0				p.Q53Q		Atlas-SNP	.											.	SAMD15	60	.	0			c.A159G						PASS	.	A		744,3662	304.4+/-288.4	66,612,1525	68.0	69.0	69.0		159	0.9	0.0	14	dbSNP_129	69	5,8595	2.2+/-6.3	0,5,4295	no	coding-synonymous	SAMD15	NM_001010860.1		66,617,5820	GG,GA,AA		0.0581,16.8861,5.7589		53/675	77843920	749,12257	2203	4300	6503	SO:0001819	synonymous_variant	161394	exon1			TTACCAAGAGCCA	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.159A>G	14.37:g.77843920A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	54	0.529412	NM_001010860	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																			A|0.932;G|0.068	0.068	strong		0.532	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
MED7	9443	hgsc.bcm.edu	37	5	156565839	156565839	+	Missense_Mutation	SNP	C	C	T	rs151231455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156565839C>T	ENST00000286317.5	-	2	985	c.604G>A	c.(604-606)Gaa>Aaa	p.E202K	MED7_ENST00000420343.1_Missense_Mutation_p.E202K	NM_004270.4	NP_004261.1	O43513	MED7_HUMAN	mediator complex subunit 7	202					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(1)|lung(3)|urinary_tract(2)	7	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTTGATGTTCATTCTGTCCA	0.388													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		20059	0.0		0.0	False		,,,				2504	0.0				p.E202K		Atlas-SNP	.											.	MED7	18	.	0			c.G604A						PASS	.	C	LYS/GLU,LYS/GLU	127,4279	93.0+/-131.7	4,119,2080	178.0	165.0	170.0		604,604	4.0	1.0	5	dbSNP_134	170	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	MED7	NM_001100816.1,NM_004270.4	56,56	4,120,6379	TT,TC,CC		0.0116,2.8824,0.9842	benign,benign	202/234,202/234	156565839	128,12878	2203	4300	6503	SO:0001583	missense	9443	exon2			GATGTTCATTCTG	AF104251	CCDS4334.1	5q33.3	2008-02-05	2007-07-30	2007-07-30	ENSG00000155868	ENSG00000155868			2378	protein-coding gene	gene with protein product		605045	"""cofactor required for Sp1 transcriptional activation, subunit 9, 33kDa"""	CRSP9		9989412	Standard	NM_004270		Approved	CRSP33	uc003lwm.4	O43513	OTTHUMG00000130243	ENST00000286317.5:c.604G>A	5.37:g.156565839C>T	ENSP00000286317:p.Glu202Lys	Somatic	348	1	0.00287356		WXS	Illumina HiSeq	Phase_I	319	149	0.467085	NM_001100816		Missense_Mutation	SNP	ENST00000286317.5	37	CCDS4334.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	8.966	0.971874	0.18736	0.028824	1.16E-4	ENSG00000155868	ENST00000286317;ENST00000420343	.	.	.	5.81	4.04	0.47022	.	0.530450	0.21352	N	0.075941	T	0.19005	0.0456	N	0.25647	0.755	0.35254	D	0.778968	B	0.06786	0.001	B	0.04013	0.001	T	0.29397	-1.0013	9	0.18710	T	0.47	-16.0444	11.7459	0.51819	0.0:0.8027:0.1305:0.0668	.	202	O43513	MED7_HUMAN	K	202	.	ENSP00000286317:E202K	E	-	1	0	MED7	156498417	0.986000	0.35501	0.999000	0.59377	0.951000	0.60555	1.750000	0.38329	0.791000	0.33826	-0.137000	0.14449	GAA	C|0.991;T|0.009	0.009	strong		0.388	MED7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252567.2	NM_004270	
SLIT3	6586	hgsc.bcm.edu	37	5	168180081	168180081	+	Missense_Mutation	SNP	C	C	T	rs10036727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:168180081C>T	ENST00000519560.1	-	18	2271	c.1852G>A	c.(1852-1854)Ggc>Agc	p.G618S	SLIT3_ENST00000332966.8_Missense_Mutation_p.G618S|SLIT3_ENST00000404867.3_Missense_Mutation_p.G618S	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	618			G -> S (in dbSNP:rs10036727). {ECO:0000269|PubMed:12975309}.		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)			CTCACACAGCCGATCAAGTTA	0.557													T|||	2859	0.570887	0.705	0.5072	5008	,	,		22384	0.5258		0.5258	False		,,,				2504	0.5276				p.G618S	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.G1852A						PASS	.	T	SER/GLY	3059,1347	449.0+/-348.9	1069,921,213	111.0	79.0	90.0		1852	5.3	1.0	5	dbSNP_119	90	4411,4189	568.4+/-389.0	1155,2101,1044	yes	missense	SLIT3	NM_003062.2	56	2224,3022,1257	TT,TC,CC		48.7093,30.5719,42.565	benign	618/1524	168180081	7470,5536	2203	4300	6503	SO:0001583	missense	6586	exon18			CACAGCCGATCAA	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.1852G>A	5.37:g.168180081C>T	ENSP00000430333:p.Gly618Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	157	70	0.44586	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	1229	0.5627289377289377	328	0.6666666666666666	185	0.511049723756906	325	0.5681818181818182	391	0.5158311345646438	T	10.40	1.339436	0.24339	0.694281	0.512907	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.56103	0.48;0.48;0.48	5.34	5.34	0.76211	.	0.157308	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00793	-1.18	0.47214	P	6.439999999999779E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.44159	-0.9346	9	0.02654	T	1	.	11.2503	0.49022	0.0:0.0718:0.0:0.9282	rs10036727;rs17634699;rs52808264;rs58822677;rs10036727	618	O75094	SLIT3_HUMAN	S	618	ENSP00000430333:G618S;ENSP00000332164:G618S;ENSP00000384890:G618S	ENSP00000332164:G618S	G	-	1	0	SLIT3	168112659	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	6.302000	0.72788	0.879000	0.35944	-0.254000	0.11334	GGC	C|0.423;N|0.000	.	strong		0.557	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
THTPA	79178	hgsc.bcm.edu	37	14	24026174	24026174	+	Missense_Mutation	SNP	G	G	T	rs141465409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24026174G>T	ENST00000288014.6	+	1	944	c.208G>T	c.(208-210)Gca>Tca	p.A70S	RP11-66N24.4_ENST00000553985.1_RNA|THTPA_ENST00000554970.1_Missense_Mutation_p.A70S|THTPA_ENST00000554789.1_Missense_Mutation_p.A70S|RP11-66N24.4_ENST00000556354.1_RNA|THTPA_ENST00000404535.3_Missense_Mutation_p.A70S|RP11-66N24.4_ENST00000555446.1_RNA|THTPA_ENST00000556015.1_Missense_Mutation_p.A70S			Q9BU02	THTPA_HUMAN	thiamine triphosphatase	70	CYTH. {ECO:0000255|PROSITE- ProRule:PRU01044}.				dephosphorylation (GO:0016311)|generation of precursor metabolites and energy (GO:0006091)|small molecule metabolic process (GO:0044281)|thiamine diphosphate metabolic process (GO:0042357)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)|thiamin-triphosphatase activity (GO:0050333)			large_intestine(1)|prostate(2)	3	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)		TCCTGGAGCAGCAGGTGTCTT	0.582													G|||	6	0.00119808	0.0045	0.0	5008	,	,		18740	0.0		0.0	False		,,,				2504	0.0				p.A70S		Atlas-SNP	.											.	THTPA	11	.	0			c.G208T						PASS	.	G	SER/ALA,SER/ALA	5,4401	9.9+/-24.2	0,5,2198	84.0	71.0	75.0		208,208	-2.0	0.0	14	dbSNP_134	75	0,8600		0,0,4300	yes	missense,missense	THTPA	NM_001126339.1,NM_024328.3	99,99	0,5,6498	TT,TG,GG		0.0,0.1135,0.0384	benign,benign	70/231,70/231	24026174	5,13001	2203	4300	6503	SO:0001583	missense	79178	exon2			GGAGCAGCAGGTG	AF432862	CCDS32053.1, CCDS58306.1, CCDS58307.1	14q11.2	2011-04-28					3.6.1.28		18987	protein-coding gene	gene with protein product		611612				11827967	Standard	NR_046051		Approved	THTPASE	uc001wkh.5	Q9BU02		ENST00000288014.6:c.208G>T	14.37:g.24026174G>T	ENSP00000288014:p.Ala70Ser	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	215	115	0.534884	NM_001256321	D3DS50|G3V4J3	Missense_Mutation	SNP	ENST00000288014.6	37	CCDS32053.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	7.575	0.667592	0.14710	0.001135	0.0	ENSG00000157306	ENST00000404535;ENST00000288014;ENST00000557630;ENST00000556015;ENST00000554970;ENST00000554789	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	5.91	-1.95	0.07548	CYTH domain (2);CYTH-like domain (1);	1.127190	0.06371	N	0.713610	T	0.24431	0.0592	L	0.41573	1.285	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.12156	0.007;0.003	T	0.22452	-1.0216	10	0.05959	T	0.93	0.0017	1.2016	0.01886	0.2075:0.3314:0.2356:0.2254	.	70;70	G3V4J3;Q9BU02	.;THTPA_HUMAN	S	70	ENSP00000384580:A70S;ENSP00000288014:A70S;ENSP00000452281:A70S;ENSP00000451835:A70S;ENSP00000452465:A70S;ENSP00000450459:A70S	ENSP00000288014:A70S	A	+	1	0	THTPA	23096014	0.000000	0.05858	0.000000	0.03702	0.989000	0.77384	-0.268000	0.08607	-0.725000	0.04901	0.655000	0.94253	GCA	G|0.999;T|0.001	0.001	strong		0.582	THTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413800.2		
PCSK7	9159	hgsc.bcm.edu	37	11	117079687	117079687	+	Silent	SNP	G	G	A	rs148329047	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117079687G>A	ENST00000320934.3	-	13	2247	c.1617C>T	c.(1615-1617)cgC>cgT	p.R539R	PCSK7_ENST00000540028.1_Silent_p.R180R|PCSK7_ENST00000529458.1_5'Flank	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	539					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CCAAGCTGCCGCGCCGTGGGT	0.617			T	IGH@	MLCLS								G|||	44	0.00878594	0.031	0.0029	5008	,	,		24069	0.0		0.001	False		,,,				2504	0.0				p.R539R		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.C1617T						PASS	.	G		81,4321	62.3+/-99.4	0,81,2120	41.0	42.0	41.0		1617	-9.1	0.2	11	dbSNP_134	41	0,8590		0,0,4295	no	coding-synonymous	PCSK7	NM_004716.2		0,81,6415	AA,AG,GG		0.0,1.8401,0.6235		539/786	117079687	81,12911	2201	4295	6496	SO:0001819	synonymous_variant	9159	exon13			GCTGCCGCGCCGT	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.1617C>T	11.37:g.117079687G>A		Somatic	393	0	0		WXS	Illumina HiSeq	Phase_I	246	92	0.373984	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			G|0.991;A|0.009	0.009	strong		0.617	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
PRSS41	360226	hgsc.bcm.edu	37	16	2849542	2849542	+	RNA	SNP	C	C	T	rs6500613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2849542C>T	ENST00000399677.1	+	0	552							Q7RTY9	PRS41_HUMAN	protease, serine, 41							anchored component of membrane (GO:0031225)|intracellular organelle (GO:0043229)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)										GCTGGGTGACCGGCTGGGGGT	0.612													C|||	107	0.0213658	0.0809	0.0	5008	,	,		17014	0.0		0.0	False		,,,				2504	0.0				p.T184T		Atlas-SNP	.											.	.	.	.	0			c.C552T						PASS	.	C		65,1319		1,63,628	86.0	65.0	72.0		552	-9.1	0.8	16	dbSNP_116	72	0,3182		0,0,1591	no	coding-synonymous	PRSS41	NM_001135086.1		1,63,2219	TT,TC,CC		0.0,4.6965,1.4236		184/319	2849542	65,4501	692	1591	2283			360226	exon3			GGTGACCGGCTGG			16p13.3	2014-04-01			ENSG00000215148	ENSG00000215148		"""Serine peptidases / Serine peptidases"""	30715	other	unknown	"""testis serine protease 1"""					12838346	Standard	NM_001135086		Approved	TESSP1	uc010uwi.2	Q7RTY9	OTTHUMG00000128932		16.37:g.2849542C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_001135086		Silent	SNP	ENST00000399677.1	37																																																																																				C|0.978;T|0.022	0.022	strong		0.612	PRSS41-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000436450.1	NM_183379	
ASB15	142685	hgsc.bcm.edu	37	7	123269280	123269280	+	Missense_Mutation	SNP	T	T	C	rs73718442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:123269280T>C	ENST00000451558.1	+	12	1753	c.1232T>C	c.(1231-1233)aTg>aCg	p.M411T	ASB15_ENST00000451215.1_Missense_Mutation_p.M411T|ASB15_ENST00000434204.1_Missense_Mutation_p.M411T|ASB15_ENST00000275699.3_Missense_Mutation_p.M411T|ASB15_ENST00000540573.1_Missense_Mutation_p.M411T			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	411					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						TGTTATTTTATGCATGTGAAT	0.418													T|||	42	0.00838658	0.0303	0.0	5008	,	,		21984	0.001		0.001	False		,,,				2504	0.0				p.M411T		Atlas-SNP	.											.	ASB15	94	.	0			c.T1232C						PASS	.	T	THR/MET	102,4304	81.9+/-120.4	1,100,2102	151.0	134.0	140.0		1232	6.2	1.0	7	dbSNP_130	140	1,8599		0,1,4299	yes	missense	ASB15	NM_080928.3	81	1,101,6401	CC,CT,TT		0.0116,2.315,0.7919	benign	411/589	123269280	103,12903	2203	4300	6503	SO:0001583	missense	142685	exon8			ATTTTATGCATGT	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.1232T>C	7.37:g.123269280T>C	ENSP00000397655:p.Met411Thr	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	37	CCDS34742.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	T	6.119	0.390139	0.11581	0.02315	1.16E-4	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000275699	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	6.17	6.17	0.99709	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.25827	0.0629	L	0.43152	1.355	0.37857	D	0.929585	B	0.15473	0.013	B	0.09377	0.004	T	0.40739	-0.9547	10	0.06625	T	0.88	-21.3197	12.4321	0.55578	0.1256:0.0:0.0:0.8744	.	411	Q8WXK1	ASB15_HUMAN	T	411;411;411;411;200;411	ENSP00000397655:M411T;ENSP00000390963:M411T;ENSP00000416433:M411T;ENSP00000438643:M411T;ENSP00000275699:M411T	ENSP00000275699:M411T	M	+	2	0	ASB15	123056516	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.015000	0.29963	2.371000	0.80710	0.533000	0.62120	ATG	T|0.992;C|0.008	0.008	strong		0.418	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1		
CLRN3	119467	hgsc.bcm.edu	37	10	129676520	129676520	+	Missense_Mutation	SNP	T	T	C	rs34656572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129676520T>C	ENST00000368671.3	-	3	736	c.574A>G	c.(574-576)Ata>Gta	p.I192V		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	192						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)				ACAGTGACTATATTTAGAAGA	0.458													T|||	45	0.00898562	0.0333	0.0014	5008	,	,		22782	0.0		0.0	False		,,,				2504	0.0				p.I192V		Atlas-SNP	.											.	CLRN3	27	.	0			c.A574G						PASS	.	T	VAL/ILE	169,4237	113.3+/-151.4	3,163,2037	220.0	190.0	200.0		574	-6.1	0.0	10	dbSNP_126	200	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CLRN3	NM_152311.3	29	3,165,6335	CC,CT,TT		0.0233,3.8357,1.3148	benign	192/227	129676520	171,12835	2203	4300	6503	SO:0001583	missense	119467	exon3			TGACTATATTTAG	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.574A>G	10.37:g.129676520T>C	ENSP00000357660:p.Ile192Val	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_152311	Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	37	CCDS7656.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	T	4.071	0.010943	0.07912	0.038357	2.33E-4	ENSG00000180745	ENST00000368671	T	0.75154	-0.91	4.48	-6.08	0.02151	.	0.505264	0.18944	N	0.126863	T	0.21761	0.0524	N	0.21448	0.665	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.24941	-1.0146	10	0.10377	T	0.69	.	16.6501	0.85187	0.0:0.7096:0.0:0.2904	rs34656572	192;124	Q8NCR9;Q8NCR9-2	CLRN3_HUMAN;.	V	192	ENSP00000357660:I192V	ENSP00000357660:I192V	I	-	1	0	CLRN3	129566510	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.443000	0.01013	-1.177000	0.02744	-0.263000	0.10527	ATA	T|0.989;C|0.011	0.011	strong		0.458	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311	
MT-ND4	4538	hgsc.bcm.edu	37	M	11654	11654	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11654A>G	ENST00000361381.2	+	1	895	c.895A>G	c.(895-897)Aca>Gca	p.T299A	MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	299					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						CCCTCGTAGTAACAGCCATTC	0.468																																					p.T299A		Atlas-SNP	.											.	.	.	.	0			c.A895G						PASS	.																																			SO:0001583	missense	0	exon1			GTAGTAACAGCCA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.895A>G	M.37:g.11654A>G	ENSP00000354961:p.Thr299Ala	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.468	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
TNRC18	84629	hgsc.bcm.edu	37	7	5352731	5352731	+	Silent	SNP	G	G	A	rs114222264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5352731G>A	ENST00000430969.1	-	27	8139	c.7791C>T	c.(7789-7791)acC>acT	p.T2597T	TNRC18_ENST00000399537.4_Silent_p.T2597T	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2597	Ser-rich.						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)		TACGGCCCCCGGTGCCGCAGC	0.682													G|||	191	0.038139	0.1407	0.0029	5008	,	,		7259	0.0		0.003	False		,,,				2504	0.0				p.T2597T		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7791T						PASS	.	G		243,2437		9,225,1106	7.0	12.0	11.0		7791	-3.8	0.0	7	dbSNP_132	11	2,6206		0,2,3102	no	coding-synonymous	TNRC18	NM_001080495.2		9,227,4208	AA,AG,GG		0.0322,9.0672,2.7565		2597/2969	5352731	245,8643	1340	3104	4444	SO:0001819	synonymous_variant	84629	exon27			GCCCCCGGTGCCG	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.7791C>T	7.37:g.5352731G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	23	8	0.347826	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.964;A|0.036	0.036	strong		0.682	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PPFIA1	8500	hgsc.bcm.edu	37	11	70185325	70185325	+	Silent	SNP	C	C	T	rs1061328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	190	0	0		WXS	Illumina HiSeq	Phase_I	200	199	0.995	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	
ATP2A3	489	hgsc.bcm.edu	37	17	3848013	3848013	+	Silent	SNP	A	A	C	rs1800911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3848013A>C	ENST00000352011.3	-	10	1326	c.1272T>G	c.(1270-1272)gcT>gcG	p.A424A	ATP2A3_ENST00000397041.3_Silent_p.A424A|ATP2A3_ENST00000397043.3_Silent_p.A424A|ATP2A3_ENST00000309890.7_Silent_p.A424A|ATP2A3_ENST00000397035.3_Silent_p.A424A|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000359983.3_Silent_p.A424A			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	424					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		TGTAGTCCAGAGCCGAGTCGT	0.657													C|||	1684	0.336262	0.4062	0.4597	5008	,	,		11878	0.0843		0.4573	False		,,,				2504	0.2894				p.A424A	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T1272G						PASS	.	C	,,,,,,	1739,2667	636.6+/-396.6	349,1041,813	51.0	42.0	45.0		1272,1272,1272,1272,1272,1272,1272	-4.1	0.5	17	dbSNP_89	45	3945,4651	593.9+/-393.2	927,2091,1280	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	1276,3132,2093	CC,CA,AA		45.8934,39.4689,43.7164	,,,,,,	424/1000,424/1053,424/1045,424/1044,424/1030,424/999,424/1030	3848013	5684,7318	2203	4298	6501	SO:0001819	synonymous_variant	489	exon10			GTCCAGAGCCGAG		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1272T>G	17.37:g.3848013A>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			A|0.610;C|0.390	0.390	strong		0.657	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
CUL9	23113	hgsc.bcm.edu	37	6	43154064	43154064	+	Silent	SNP	C	C	T	rs79828871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43154064C>T	ENST00000252050.4	+	4	1206	c.1122C>T	c.(1120-1122)ggC>ggT	p.G374G	CUL9_ENST00000354495.3_Silent_p.G374G|CUL9_ENST00000372647.2_Silent_p.G374G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	374					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						GCCGTAGTGGCTATGGAGAAT	0.577													C|||	187	0.0373403	0.1331	0.0144	5008	,	,		19600	0.0		0.001	False		,,,				2504	0.0				p.G374G		Atlas-SNP	.											.	CUL9	248	.	0			c.C1122T						PASS	.	C		441,3965	212.8+/-232.6	12,417,1774	74.0	73.0	73.0		1122	3.7	1.0	6	dbSNP_131	73	0,8600		0,0,4300	no	coding-synonymous	CUL9	NM_015089.2		12,417,6074	TT,TC,CC		0.0,10.0091,3.3907		374/2518	43154064	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon4			TAGTGGCTATGGA	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.1122C>T	6.37:g.43154064C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	140	58	0.414286	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.967;T|0.033	0.033	strong		0.577	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
THADA	63892	hgsc.bcm.edu	37	2	43518843	43518843	+	Missense_Mutation	SNP	A	A	G	rs17030648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:43518843A>G	ENST00000405006.4	-	34	5353	c.5002T>C	c.(5002-5004)Tgt>Cgt	p.C1668R	THADA_ENST00000405975.2_Missense_Mutation_p.C1668R|THADA_ENST00000330266.7_Intron|THADA_ENST00000415080.2_Missense_Mutation_p.C1349R	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1668			C -> R (in dbSNP:rs17030648).							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)				ACCTCCACACATGTCTGCATG	0.393													A|||	159	0.0317492	0.1157	0.0086	5008	,	,		16790	0.0		0.0	False		,,,				2504	0.0				p.C1668R		Atlas-SNP	.											.	THADA	131	.	0			c.T5002C						PASS	.	A	ARG/CYS,ARG/CYS	351,3379		16,319,1530	62.0	58.0	59.0		5002,5002	-5.8	0.0	2	dbSNP_123	59	7,8131		0,7,4062	yes	missense,missense	THADA	NM_001083953.1,NM_022065.4	180,180	16,326,5592	GG,GA,AA		0.086,9.4102,3.0165	benign,benign	1668/1954,1668/1954	43518843	358,11510	1865	4069	5934	SO:0001583	missense	63892	exon34			CCACACATGTCTG	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.5002T>C	2.37:g.43518843A>G	ENSP00000385995:p.Cys1668Arg	Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	213	118	0.553991	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	62	0.028388278388278388	61	0.12398373983739837	1	0.0027624309392265192	0	0.0	0	0.0	A	0.081	-1.182910	0.01620	0.094102	8.6E-4	ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006	T;T;T	0.67698	-0.28;-0.28;-0.28	4.52	-5.84	0.02318	.	1.778280	0.02439	N	0.084348	T	0.01092	0.0036	L	0.35723	1.085	0.58432	P	9.99999999995449E-6	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.15292	-1.0442	9	0.13108	T	0.6	-12.3615	13.0032	0.58687	0.3567:0.0:0.6433:0.0	rs17030648;rs52831994;rs17030648	1595;1668	B6ZDQ0;Q6YHU6	.;THADA_HUMAN	R	1668;1595;1349;1668	ENSP00000386088:C1668R;ENSP00000416048:C1349R;ENSP00000385995:C1668R	ENSP00000349464:C1595R	C	-	1	0	THADA	43372347	0.000000	0.05858	0.000000	0.03702	0.183000	0.23260	-2.041000	0.01415	-1.081000	0.03105	-0.384000	0.06662	TGT	A|0.958;G|0.042	0.042	strong		0.393	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
PLEC	5339	hgsc.bcm.edu	37	8	145006866	145006866	+	Silent	SNP	G	G	A	rs185978075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145006866G>A	ENST00000322810.4	-	15	2332	c.2163C>T	c.(2161-2163)ccC>ccT	p.P721P	PLEC_ENST00000345136.3_Silent_p.P584P|PLEC_ENST00000398774.2_Silent_p.P552P|PLEC_ENST00000356346.3_Silent_p.P570P|PLEC_ENST00000527096.1_Silent_p.P607P|PLEC_ENST00000354589.3_Silent_p.P584P|PLEC_ENST00000357649.2_Silent_p.P588P|PLEC_ENST00000436759.2_Silent_p.P611P|PLEC_ENST00000354958.2_Silent_p.P562P	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	721	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CCCGGGTGGCGGGGGAGAGCT	0.716													A|||	61	0.0121805	0.0424	0.0072	5008	,	,		14613	0.0		0.0	False		,,,				2504	0.0				p.P721P		Atlas-SNP	.											.	PLEC	1144	.	0			c.C2163T						PASS	.	A	,,,,,,,	99,3883		3,93,1895	10.0	14.0	13.0		1833,1710,1686,2163,1656,1752,1764,1752	-9.7	0.0	8		13	2,8238		0,2,4118	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	,,,,,,,	3,95,6013	AA,AG,GG		0.0243,2.4862,0.8264	,,,,,,,	611/4575,570/4534,562/4526,721/4685,552/4516,584/4548,588/4552,584/4548	145006866	101,12121	1991	4120	6111	SO:0001819	synonymous_variant	5339	exon15			GGTGGCGGGGGAG	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.2163C>T	8.37:g.145006866G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.994;A|0.006	0.006	strong		0.716	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
TNRC6A	27327	hgsc.bcm.edu	37	16	24802245	24802245	+	Missense_Mutation	SNP	T	T	G	rs112027699		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24802245T>G	ENST00000395799.3	+	6	2411	c.2282T>G	c.(2281-2283)tTt>tGt	p.F761C	TNRC6A_ENST00000315183.7_Missense_Mutation_p.F761C	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	761	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)		ACACAGACTTTTAACTCAGGG	0.488													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19808	0.0		0.0	False		,,,				2504	0.0				p.F761C		Atlas-SNP	.											.	TNRC6A	171	.	0			c.T2282G						PASS	.	T	CYS/PHE	2,4390	2.1+/-5.4	0,2,2194	46.0	51.0	50.0		2282	4.7	1.0	16	dbSNP_132	50	0,8600		0,0,4300	no	missense	TNRC6A	NM_014494.2	205	0,2,6494	GG,GT,TT		0.0,0.0455,0.0154	benign	761/1963	24802245	2,12990	2196	4300	6496	SO:0001583	missense	27327	exon6			AGACTTTTAACTC	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.2282T>G	16.37:g.24802245T>G	ENSP00000379144:p.Phe761Cys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	T	9.930	1.214512	0.22289	4.55E-4	0.0	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.11495	2.77;2.78	5.82	4.71	0.59529	.	0.329999	0.31859	N	0.006945	T	0.05410	0.0143	N	0.08118	0	0.80722	D	1	P;P;P	0.45078	0.687;0.681;0.85	B;B;B	0.42282	0.382;0.181;0.258	T	0.24440	-1.0160	10	0.56958	D	0.05	-1.2962	3.6846	0.08323	0.0:0.2795:0.0:0.7205	.	508;761;761	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	C	761	ENSP00000326900:F761C;ENSP00000379144:F761C	ENSP00000326900:F761C	F	+	2	0	TNRC6A	24709746	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.281000	0.33214	2.225000	0.72522	0.460000	0.39030	TTT	T|0.999;G|0.001	0.001	strong		0.488	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
COLEC12	81035	hgsc.bcm.edu	37	18	334742	334742	+	Splice_Site	SNP	C	C	T	rs17857498|rs2305027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	103	0	0		WXS	Illumina HiSeq	Phase_I	147	53	0.360544	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
SLC5A12	159963	hgsc.bcm.edu	37	11	26700344	26700344	+	Silent	SNP	G	G	C	rs150900623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:26700344G>C	ENST00000396005.3	-	13	1803	c.1494C>G	c.(1492-1494)acC>acG	p.T498T		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	498					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						TCGAGTACCAGGTATCAGCTA	0.453													G|||	42	0.00838658	0.031	0.0014	5008	,	,		16935	0.0		0.0	False		,,,				2504	0.0				p.T498T		Atlas-SNP	.											.	SLC5A12	134	.	0			c.C1494G						PASS	.	G		75,3887		0,75,1906	116.0	114.0	115.0		1494	0.2	0.8	11	dbSNP_134	115	0,8338		0,0,4169	no	coding-synonymous	SLC5A12	NM_178498.3		0,75,6075	CC,CG,GG		0.0,1.893,0.6098		498/619	26700344	75,12225	1981	4169	6150	SO:0001819	synonymous_variant	159963	exon13			GTACCAGGTATCA	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.1494C>G	11.37:g.26700344G>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			G|0.994;C|0.006	0.006	strong		0.453	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498	
UPF1	5976	hgsc.bcm.edu	37	19	18958562	18958562	+	Silent	SNP	A	A	T	rs73526913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18958562A>T	ENST00000599848.1	+	3	590	c.381A>T	c.(379-381)ggA>ggT	p.G127G	UPF1_ENST00000262803.5_Silent_p.G127G			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	127	Sufficient for interaction with RENT2.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						GTTACTGTGGAATACACGATC	0.428											OREG0025373	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	43	0.00858626	0.0318	0.0014	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.G127G		Atlas-SNP	.											.	UPF1	88	.	0			c.A381T						PASS	.	A		130,4276	95.7+/-134.4	3,124,2076	128.0	120.0	123.0		381	-7.9	0.8	19	dbSNP_130	123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	UPF1	NM_002911.3		3,125,6375	TT,TA,AA		0.0116,2.9505,1.0072		127/1119	18958562	131,12875	2203	4300	6503	SO:0001819	synonymous_variant	5976	exon3			CTGTGGAATACAC	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"""UP Frameshift 1"", ""smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	601430	"""regulator of nonsense transcripts 1"""	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.381A>T	19.37:g.18958562A>T		Somatic	146	0	0	729	WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_002911	O00239|O43343|Q86Z25|Q92842	Silent	SNP	ENST00000599848.1	37																																																																																				A|0.991;T|0.009	0.009	strong		0.428	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911	
MUC4	4585	hgsc.bcm.edu	37	3	195511214	195511214	+	Missense_Mutation	SNP	G	G	C	rs202190300		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511214G>C	ENST00000463781.3	-	2	7696	c.7237C>G	c.(7237-7239)Cac>Gac	p.H2413D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H2413D	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.H2413D(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)		TGGGTGGCGTGACCTGTGGAT	0.592																																					p.H2413D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+2,3	MUC4	1505	3	1	Substitution - Missense(1)	kidney(1)	c.C7237G						PASS	.						41.0	42.0	42.0					3																	195511214		668	1588	2256	SO:0001583	missense	4585	exon2			TGGCGTGACCTGT	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.7237C>G	3.37:g.195511214G>C	ENSP00000417498:p.His2413Asp	Somatic	747	0	0		WXS	Illumina HiSeq	Phase_I	272	11	0.0404412	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	2.114	-0.403051	0.04865	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29397	1.58;1.57	.	.	.	.	.	.	.	.	T	0.14743	0.0356	N	0.19112	0.55	0.09310	N	1	B	0.15141	0.012	B	0.01281	0.0	T	0.27502	-1.0072	7	.	.	.	.	4.69	0.12776	1.0E-4:0.0:0.6456:0.3543	.	2413	E7ESK3	.	D	2413	ENSP00000417498:H2413D;ENSP00000420243:H2413D	.	H	-	1	0	MUC4	196995609	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-1.963000	0.01513	-0.914000	0.03827	0.000000	0.15137	CAC	G|0.999;C|0.001	0.001	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
XIRP2	129446	hgsc.bcm.edu	37	2	168100280	168100280	+	Missense_Mutation	SNP	G	G	A	rs201184820		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:168100280G>A	ENST00000409195.1	+	9	2467	c.2378G>A	c.(2377-2379)cGa>cAa	p.R793Q	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R793Q|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R571Q|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	618					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						AAAGTTGTCCGAGGAATATCC	0.408													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18882	0.0		0.0	False		,,,				2504	0.0				p.R793Q		Atlas-SNP	.											XIRP2,larynx,carcinoma,+1,2	XIRP2	914	2	0			c.G2378A						PASS	.	G	GLN/ARG,GLN/ARG,,,	4,3694		0,4,1845	72.0	70.0	70.0		1712,2378,,,	5.9	1.0	2		70	0,8182		0,0,4091	yes	missense,missense,intron,intron,intron	XIRP2	NM_001199144.1,NM_152381.5,NM_001079810.3,NM_001199143.1,NM_001199145.1	43,43,,,	0,4,5936	AA,AG,GG		0.0,0.1082,0.0337	probably-damaging,probably-damaging,,,	571/3328,793/3550,,,	168100280	4,11876	1849	4091	5940	SO:0001583	missense	129446	exon9			TTGTCCGAGGAAT	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.2378G>A	2.37:g.168100280G>A	ENSP00000386840:p.Arg793Gln	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	140	83	0.592857	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.752177	0.69533	0.001082	0.0	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.04234	3.68;3.68;3.67	5.92	5.92	0.95590	.	0.058183	0.64402	D	0.000001	T	0.24851	0.0603	M	0.80422	2.495	0.39027	D	0.959861	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69479	0.92;0.964;0.964	T	0.00270	-1.1860	10	0.49607	T	0.09	-12.8648	20.3213	0.98679	0.0:0.0:1.0:0.0	.	618;618;571	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Q	793;793;571	ENSP00000386840:R793Q;ENSP00000295237:R793Q;ENSP00000387255:R571Q	ENSP00000295237:R793Q	R	+	2	0	XIRP2	167808526	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.728000	0.54991	2.810000	0.96702	0.650000	0.86243	CGA	.	.	weak		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
SLC35G6	643664	hgsc.bcm.edu	37	17	7386301	7386301	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7386301A>C	ENST00000412468.2	+	2	1113	c.998A>C	c.(997-999)gAa>gCa	p.E333A	ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	333						integral component of membrane (GO:0016021)		p.E333A(1)									TGTGAGAGGGAAGGGAAGGTG	0.557																																					p.E333A		Atlas-SNP	.											POLR2A_ENST00000412468,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	prostate(1)	c.A998C						scavenged	.						60.0	58.0	59.0					17																	7386301		2203	4300	6503	SO:0001583	missense	643664	exon2			AGAGGGAAGGGAA		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.998A>C	17.37:g.7386301A>C	ENSP00000396523:p.Glu333Ala	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	175	5	0.0285714	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	A	2.913	-0.225018	0.06022	.	.	ENSG00000181222	ENST00000412468	T	0.26067	1.76	4.69	1.0	0.19881	.	.	.	.	.	T	0.15609	0.0376	N	0.25647	0.755	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.22626	-1.0211	9	0.36615	T	0.2	-0.2286	5.7938	0.18375	0.4278:0.471:0.1012:0.0	.	333	P0C7Q6	S35G6_HUMAN	A	333	ENSP00000396523:E333A	ENSP00000396523:E333A	E	+	2	0	SLC35G6	7327025	0.886000	0.30341	0.428000	0.26697	0.484000	0.33280	1.649000	0.37281	0.732000	0.32470	0.477000	0.44152	GAA	.	.	none		0.557	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
DST	667	hgsc.bcm.edu	37	6	56507489	56507489	+	Missense_Mutation	SNP	A	A	G	rs1024196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:56507489A>G	ENST00000244364.6	-	1	305	c.98T>C	c.(97-99)tTg>tCg	p.L33S	DST_ENST00000312431.6_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370765.6_Missense_Mutation_p.L33S|DST_ENST00000518935.1_Missense_Mutation_p.L33S|DST_ENST00000446842.2_Missense_Mutation_p.L33S	NM_001144769.2|NM_001144770.1|NM_015548.4|NM_183380.3	NP_001138241.1|NP_001138242.1|NP_056363.2|NP_899236.1	Q03001	DYST_HUMAN	dystonin	0					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ACAATGAACCAAGAGAAGATT	0.398													G|||	660	0.131789	0.4281	0.0418	5008	,	,		21129	0.0179		0.0288	False		,,,				2504	0.0184				p.L33S		Atlas-SNP	.											.	DST	1427	.	0			c.T98C						PASS	.	G	SER/LEU,SER/LEU	1704,2702	652.5+/-399.4	335,1034,834	127.0	116.0	120.0		98,98	5.9	0.9	6	dbSNP_86	120	379,8221	802.5+/-407.3	9,361,3930	yes	missense,missense	DST	NM_001723.5,NM_015548.4	145,145	344,1395,4764	GG,GA,AA		4.407,38.6745,16.0157	,	33/2650,33/5172	56507489	2083,10923	2203	4300	6503	SO:0001583	missense	667	exon1			TGAACCAAGAGAA	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	ENST00000244364.6:c.98T>C	6.37:g.56507489A>G	ENSP00000244364:p.Leu33Ser	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	160	72	0.45	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000244364.6	37	CCDS47443.1	258	0.11813186813186813	214	0.4349593495934959	17	0.04696132596685083	9	0.015734265734265736	18	0.023746701846965697	G	5.858	0.342578	0.11069	0.386745	0.04407	ENSG00000151914	ENST00000244364;ENST00000446842;ENST00000439203;ENST00000370765;ENST00000518935	T;T;T;T;T	0.75154	1.07;0.87;-0.39;-0.91;-0.38	5.86	5.86	0.93980	.	.	.	.	.	T	0.29850	0.0746	N	0.02011	-0.69	0.20307	P	0.999917	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	0.14952	-1.0454	8	0.12430	T	0.62	.	15.6237	0.76833	0.0658:0.0:0.9342:0.0	rs1024196;rs58963769;rs1024196	33;33;33;33	Q6P0N6;Q03001-3;Q03001-9;Q03001-8	.;.;.;.	S	33	ENSP00000244364:L33S;ENSP00000393645:L33S;ENSP00000404924:L33S;ENSP00000359801:L33S;ENSP00000431003:L33S	ENSP00000244364:L33S	L	-	2	0	DST	56615448	1.000000	0.71417	0.901000	0.35422	0.306000	0.27790	5.320000	0.65841	1.638000	0.50547	-0.128000	0.14901	TTG	A|0.848;G|0.152	0.152	strong		0.398	DST-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041022.4	NM_001723	
FBXO34	55030	hgsc.bcm.edu	37	14	55818403	55818403	+	Missense_Mutation	SNP	T	T	C	rs35070799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55818403T>C	ENST00000313833.4	+	2	1540	c.1295T>C	c.(1294-1296)gTt>gCt	p.V432A	FBXO34_ENST00000440021.1_Missense_Mutation_p.V432A	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	432			V -> A (in dbSNP:rs35070799).							breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						ACAGATGCTGTTGATTGTATG	0.418													T|||	230	0.0459265	0.0008	0.0807	5008	,	,		21205	0.006		0.0805	False		,,,				2504	0.0879				p.V432A		Atlas-SNP	.											.	FBXO34	61	.	0			c.T1295C						PASS	.	T	ALA/VAL,ALA/VAL	65,4341	60.5+/-97.4	0,65,2138	138.0	129.0	132.0		1295,1295	0.4	0.0	14	dbSNP_126	132	690,7910	171.2+/-222.1	24,642,3634	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	64,64	24,707,5772	CC,CT,TT		8.0233,1.4753,5.805	benign,benign	432/712,432/712	55818403	755,12251	2203	4300	6503	SO:0001583	missense	55030	exon2			ATGCTGTTGATTG	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1295T>C	14.37:g.55818403T>C	ENSP00000313159:p.Val432Ala	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	156	80	0.512821	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	96	0.04395604395604396	1	0.0020325203252032522	38	0.10497237569060773	2	0.0034965034965034965	55	0.07255936675461741	T	2.813	-0.246439	0.05867	0.014753	0.080233	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.24908	1.83;1.83	5.48	0.452	0.16634	.	0.665108	0.13820	N	0.360485	T	0.00468	0.0015	L	0.56769	1.78	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.33803	-0.9854	10	0.06236	T	0.91	0.0061	6.0301	0.19675	0.0:0.1949:0.2462:0.559	rs35070799;rs61755585	432	Q9NWN3	FBX34_HUMAN	A	432	ENSP00000313159:V432A;ENSP00000394117:V432A	ENSP00000313159:V432A	V	+	2	0	FBXO34	54888156	0.001000	0.12720	0.000000	0.03702	0.376000	0.30014	0.337000	0.19841	-0.058000	0.13177	0.528000	0.53228	GTT	T|0.945;C|0.055	0.055	strong		0.418	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276876	71276876	+	Silent	SNP	A	A	G	rs12788123		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71276876A>G	ENST00000398531.1	+	1	268	c.243A>G	c.(241-243)aaA>aaG	p.K81K	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	81	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.K81K(1)		endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GGGGCTCCAAAGGGGGCTGTG	0.682																																					p.K81K		Atlas-SNP	.											KRTAP5-10,NS,carcinoma,0,1	KRTAP5-10	37	1	1	Substitution - coding silent(1)	endometrium(1)	c.A243G						scavenged	.						51.0	72.0	65.0					11																	71276876		2140	4257	6397	SO:0001819	synonymous_variant	387273	exon1			CTCCAAAGGGGGC	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.243A>G	11.37:g.71276876A>G		Somatic	162	20	0.123457		WXS	Illumina HiSeq	Phase_I	177	24	0.135593	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			A|0.998;G|0.002	0.002	weak		0.682	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
RYR3	6263	hgsc.bcm.edu	37	15	34105084	34105084	+	Silent	SNP	A	A	G	rs16958093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34105084A>G	ENST00000389232.4	+	73	10348	c.10278A>G	c.(10276-10278)aaA>aaG	p.K3426K	RYR3_ENST00000415757.3_Silent_p.K3421K	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3426					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)		CAGCTGTAAAATGGCAACTGA	0.428													A|||	198	0.0395367	0.1362	0.0101	5008	,	,		21062	0.006		0.0	False		,,,				2504	0.0051				p.K3426K		Atlas-SNP	.											.	RYR3	760	.	0			c.A10278G						PASS	.	A		360,3396		26,308,1544	88.0	85.0	86.0		10278	0.6	1.0	15	dbSNP_123	86	4,8238		0,4,4117	no	coding-synonymous	RYR3	NM_001036.3		26,312,5661	GG,GA,AA		0.0485,9.5847,3.0338		3426/4871	34105084	364,11634	1878	4121	5999	SO:0001819	synonymous_variant	6263	exon73			TGTAAAATGGCAA		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.10278A>G	15.37:g.34105084A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			A|0.955;G|0.045	0.045	strong		0.428	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
PSG4	5672	hgsc.bcm.edu	37	19	43699336	43699336	+	Missense_Mutation	SNP	T	T	C	rs1058718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43699336T>C	ENST00000405312.3	-	4	1036	c.799A>G	c.(799-801)Aag>Gag	p.K267E	PSG4_ENST00000244295.9_Intron|PSG4_ENST00000433626.2_Missense_Mutation_p.K174E	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	81	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	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	
KIAA0556	23247	hgsc.bcm.edu	37	16	27692835	27692835	+	Silent	SNP	G	G	A	rs12923861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27692835G>A	ENST00000261588.4	+	8	943	c.924G>A	c.(922-924)caG>caA	p.Q308Q	CTD-2049O4.1_ENST00000564893.1_RNA|KIAA0556_ENST00000567894.1_3'UTR	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	308						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						TCCCAGACCAGGAGAGGATGT	0.587													G|||	531	0.10603	0.1528	0.1902	5008	,	,		19008	0.001		0.1541	False		,,,				2504	0.0419				p.Q308Q		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G924A						PASS	.	G		658,3736	279.0+/-274.6	48,562,1587	114.0	121.0	119.0		924	1.8	1.0	16	dbSNP_121	119	1281,7319	252.8+/-278.7	90,1101,3109	no	coding-synonymous	KIAA0556	NM_015202.2		138,1663,4696	AA,AG,GG		14.8953,14.975,14.9223		308/1619	27692835	1939,11055	2197	4300	6497	SO:0001819	synonymous_variant	23247	exon8			AGACCAGGAGAGG	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.924G>A	16.37:g.27692835G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_015202	A7E2C2	Silent	SNP	ENST00000261588.4	37	CCDS32415.1																																																																																			G|0.863;A|0.137	0.137	strong		0.587	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
MICA	100507436	hgsc.bcm.edu	37	6	31379773	31379773	+	Silent	SNP	C	C	T	rs1051796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31379773C>T	ENST00000449934.2	+	4	717	c.663C>T	c.(661-663)atC>atT	p.I221I	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)				AGGGCAACATCACCGTGACAT	0.602													c|||	1821	0.363618	0.4766	0.4049	5008	,	,		20346	0.3006		0.3141	False		,,,				2504	0.2975				p.I221I		Atlas-SNP	.											.	MICA	21	.	0			c.C663T						PASS	.	C		579,805		132,315,245	31.0	34.0	33.0		663	1.6	0.0	6	dbSNP_86	33	913,2269		126,661,804	no	coding-synonymous	MICA	NM_001177519.1		258,976,1049	TT,TC,CC		28.6926,41.8353,32.6763		221/333	31379773	1492,3074	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon4			CAACATCACCGTG	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.663C>T	6.37:g.31379773C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			.	.	weak		0.602	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
OR51B6	390058	hgsc.bcm.edu	37	11	5373114	5373114	+	Missense_Mutation	SNP	G	G	A	rs5006888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5373114G>A	ENST00000380219.1	+	1	377	c.377G>A	c.(376-378)aGc>aAc	p.S126N	HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	126			S -> N (in dbSNP:rs5006888).	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)		ACCATCCGCAGCCCCTTAAGA	0.468													A|||	3037	0.60643	0.587	0.5692	5008	,	,		23218	0.5446		0.6054	False		,,,				2504	0.7239				p.S126N		Atlas-SNP	.											.	OR51B6	53	.	0			c.G377A						PASS	.	A	ASN/SER	2560,1842	534.4+/-373.9	757,1046,398	127.0	116.0	120.0		377	2.7	0.0	11	dbSNP_113	120	5070,3524	511.0+/-377.6	1515,2040,742	yes	missense	OR51B6	NM_001004750.1	46	2272,3086,1140	AA,AG,GG		41.0054,41.8446,41.2896	benign	126/313	5373114	7630,5366	2201	4297	6498	SO:0001583	missense	390058	exon1			TCCGCAGCCCCTT		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.377G>A	11.37:g.5373114G>A	ENSP00000369568:p.Ser126Asn	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	248	246	0.991935	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	1268	0.5805860805860806	288	0.5853658536585366	218	0.6022099447513812	315	0.5506993006993007	447	0.5897097625329816	A	0	-2.607379	0.00121	0.581554	0.589946	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00532	6.75	5.01	2.67	0.31697	GPCR, rhodopsin-like superfamily (1);	0.101582	0.42964	N	0.000623	T	0.00012	0.0000	N	0.00217	-1.83	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.13980	-1.0489	9	0.02654	T	1	.	4.9735	0.14129	0.5439:0.2965:0.1596:0.0	rs5006888;rs59241671	126	Q9H340	O51B6_HUMAN	N	125;126	ENSP00000369568:S126N	ENSP00000369568:S126N	S	+	2	0	OR51B6	5329690	0.008000	0.16893	0.040000	0.18447	0.030000	0.12068	2.394000	0.44450	0.070000	0.16634	-0.556000	0.04195	AGC	G|0.408;A|0.592	0.592	strong		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
LILRB4	11006	hgsc.bcm.edu	37	19	55179145	55179145	+	Missense_Mutation	SNP	A	A	T	rs61738946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55179145A>T	ENST00000391736.1	+	13	1416	c.1101A>T	c.(1099-1101)agA>agT	p.R367S	LILRB4_ENST00000270452.2_Missense_Mutation_p.R367S|LILRB4_ENST00000391733.3_Missense_Mutation_p.R368S|LILRB4_ENST00000391734.3_Intron|LILRB4_ENST00000430952.2_Missense_Mutation_p.R366S	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	367					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)		AACACTCCAGACCTAGGAGAG	0.567																																					p.R367S		Atlas-SNP	.											LILRB4,NS,carcinoma,+2,1	LILRB4	86	1	0			c.A1101T						scavenged	.						116.0	118.0	117.0					19																	55179145		2203	4300	6503	SO:0001583	missense	11006	exon11			CTCCAGACCTAGG	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.1101A>T	19.37:g.55179145A>T	ENSP00000375616:p.Arg367Ser	Somatic	370	7	0.0189189		WXS	Illumina HiSeq	Phase_I	432	21	0.0486111	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	23	0.010531135531135532	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	6.892	0.534167	0.13188	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391733;ENST00000434286	T;T;T;T;T	0.00505	6.93;6.93;7.0;6.94;6.93	1.73	1.73	0.24493	.	.	.	.	.	T	0.00144	0.0004	L	0.41710	1.295	0.09310	N	1	B;B;B;B	0.23490	0.002;0.086;0.086;0.043	B;B;B;B	0.12837	0.0;0.008;0.008;0.007	T	0.40627	-0.9553	9	0.27785	T	0.31	.	5.5252	0.16955	1.0:0.0:0.0:0.0	rs61738946	366;368;366;367	C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	S	367;367;366;368;366	ENSP00000375616:R367S;ENSP00000270452:R367S;ENSP00000408995:R366S;ENSP00000375613:R368S;ENSP00000401962:R366S	ENSP00000270452:R367S	R	+	3	2	LILRB4	59870957	0.002000	0.14202	0.018000	0.16275	0.021000	0.10359	0.274000	0.18680	1.054000	0.40438	0.459000	0.35465	AGA	A|0.990;T|0.010	0.010	strong		0.567	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
OR10X1	128367	hgsc.bcm.edu	37	1	158549492	158549492	+	Nonsense_Mutation	SNP	C	C	T	rs863362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	134	0	0		WXS	Illumina HiSeq	Phase_I	140	66	0.471429	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	
C15orf40	123207	hgsc.bcm.edu	37	15	83680313	83680313	+	Missense_Mutation	SNP	T	T	G	rs114478510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83680313T>G	ENST00000513601.2	-	1	54	c.47A>C	c.(46-48)aAt>aCt	p.N16T	C15orf40_ENST00000451195.3_Missense_Mutation_p.N16T|RP11-382A20.7_ENST00000570202.1_RNA|C15orf40_ENST00000538348.2_Missense_Mutation_p.N16T|C15orf40_ENST00000304177.5_5'UTR|RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000565712.1_Missense_Mutation_p.N16T			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40	16										large_intestine(3)|lung(2)|skin(1)	6						GCCCCGAGTATTGGGTGTTGC	0.692											OREG0023391	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	50	0.00998403	0.028	0.0144	5008	,	,		14631	0.0		0.003	False		,,,				2504	0.0				p.N16T		Atlas-SNP	.											.	C15orf40	18	.	0			c.A47C						PASS	.	T	THR/ASN,THR/ASN,THR/ASN,THR/ASN,THR/ASN	69,4335		0,69,2133	21.0	22.0	22.0		47,47,47,47,47	1.6	0.0	15	dbSNP_132	22	5,8595		0,5,4295	yes	missense,missense,missense,missense,missense	C15orf40	NM_144597.2,NM_001160116.1,NM_001160115.1,NM_001160114.1,NM_001160113.1	65,65,65,65,65	0,74,6428	GG,GT,TT		0.0581,1.5668,0.5691	benign,benign,benign,benign,benign	16/154,16/150,16/168,16/154,16/168	83680313	74,12930	2202	4300	6502	SO:0001583	missense	123207	exon1			CGAGTATTGGGTG	BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.47A>C	15.37:g.83680313T>G	ENSP00000424666:p.Asn16Thr	Somatic	37	0	0	1223	WXS	Illumina HiSeq	Phase_I	30	9	0.3	NM_001160116	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Missense_Mutation	SNP	ENST00000513601.2	37	CCDS32312.2	24	0.01098901098901099	16	0.032520325203252036	6	0.016574585635359115	0	0.0	2	0.002638522427440633	T	9.731	1.162258	0.21538	0.015668	5.81E-4	ENSG00000169609	ENST00000538348;ENST00000451195;ENST00000513601	.	.	.	3.61	1.58	0.23477	.	.	.	.	.	T	0.05823	0.0152	N	0.08118	0	0.20764	N	0.99985	B;B;B	0.17038	0.02;0.02;0.008	B;B;B	0.11329	0.006;0.006;0.006	T	0.15350	-1.0440	8	0.42905	T	0.14	.	5.5455	0.17061	0.0:0.7421:0.0:0.2579	.	16;16;16	F8WD31;F5GX92;G5EA00	.;.;.	T	16	.	ENSP00000403987:N16T	N	-	2	0	C15orf40	81471317	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.131000	0.10482	0.499000	0.27970	-0.624000	0.04008	AAT	T|0.992;G|0.008	0.008	strong		0.692	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597	
PLCD1	5333	hgsc.bcm.edu	37	3	38052725	38052725	+	Missense_Mutation	SNP	C	C	T	rs933135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38052725C>T	ENST00000334661.4	-	5	992	c.770G>A	c.(769-771)cGc>cAc	p.R257H	PLCD1_ENST00000463876.1_Missense_Mutation_p.R278H|PLCD1_ENST00000479619.1_5'Flank	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	257			R -> H (in dbSNP:rs933135).		angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		GGGCTCGTAGCGCTCAATGAG	0.672													C|||	316	0.063099	0.0	0.0303	5008	,	,		16535	0.1825		0.0149	False		,,,				2504	0.0982				p.R278H		Atlas-SNP	.											.	PLCD1	87	.	0			c.G833A	GRCh37	CM067709	PLCD1	M	rs933135	PASS	.	C	HIS/ARG,HIS/ARG	16,4390		0,16,2187	28.0	29.0	29.0		833,770	4.9	1.0	3	dbSNP_86	29	152,8444		0,152,4146	yes	missense,missense	PLCD1	NM_001130964.1,NM_006225.3	29,29	0,168,6333	TT,TC,CC		1.7683,0.3631,1.2921	possibly-damaging,possibly-damaging	278/778,257/757	38052725	168,12834	2203	4298	6501	SO:0001583	missense	5333	exon5			TCGTAGCGCTCAA		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"""EF-hand domain containing"""	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.770G>A	3.37:g.38052725C>T	ENSP00000335600:p.Arg257His	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	59	20	0.338983	NM_001130964	B3KR14|Q86VN8	Missense_Mutation	SNP	ENST00000334661.4	37	CCDS2671.1	124	0.056776556776556776	1	0.0020325203252032522	8	0.022099447513812154	100	0.17482517482517482	15	0.01978891820580475	C	18.23	3.577339	0.65878	0.003631	0.017683	ENSG00000187091	ENST00000463876;ENST00000334661	T;T	0.46451	0.87;0.87	4.95	4.95	0.65309	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);EF-hand-like domain (1);	0.102292	0.64402	D	0.000003	T	0.00271	0.0008	M	0.75615	2.305	0.26759	P	0.9700436	D;P	0.62365	0.991;0.792	P;B	0.61201	0.885;0.132	T	0.15723	-1.0427	9	0.62326	D	0.03	.	9.8655	0.41140	0.0:0.8434:0.0:0.1566	rs933135;rs52803102;rs933135	257;278	P51178;B3KR14	PLCD1_HUMAN;.	H	278;257	ENSP00000430344:R278H;ENSP00000335600:R257H	ENSP00000335600:R257H	R	-	2	0	PLCD1	38027729	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.560000	0.36331	2.677000	0.91161	0.655000	0.94253	CGC	C|0.958;A|0.000	.	strong		0.672	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2		
MDN1	23195	hgsc.bcm.edu	37	6	90482397	90482397	+	Missense_Mutation	SNP	T	T	C	rs12110451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90482397T>C	ENST00000369393.3	-	14	2093	c.1978A>G	c.(1978-1980)Atc>Gtc	p.I660V	MDN1_ENST00000428876.1_Missense_Mutation_p.I660V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	660			I -> V (in dbSNP:rs12110451).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AGCTGCTCGATGAGAACAGAG	0.512													T|||	822	0.164137	0.1793	0.1398	5008	,	,		16706	0.2163		0.1809	False		,,,				2504	0.09				p.I660V		Atlas-SNP	.											.	MDN1	478	.	0			c.A1978G						PASS	.	T	VAL/ILE	848,3558	333.3+/-302.9	87,674,1442	107.0	110.0	109.0		1978	4.5	1.0	6	dbSNP_120	109	1539,7061	290.5+/-299.9	142,1255,2903	yes	missense	MDN1	NM_014611.1	29	229,1929,4345	CC,CT,TT		17.8953,19.2465,18.3531	benign	660/5597	90482397	2387,10619	2203	4300	6503	SO:0001583	missense	23195	exon14			GCTCGATGAGAAC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.1978A>G	6.37:g.90482397T>C	ENSP00000358400:p.Ile660Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	410	0.18772893772893773	93	0.18902439024390244	46	0.1270718232044199	127	0.22202797202797203	144	0.18997361477572558	T	11.71	1.718341	0.30503	0.192465	0.178953	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.40476	1.03;1.03;1.03	5.65	4.47	0.54385	.	0.212692	0.41605	D	0.000848	T	0.12135	0.0295	N	0.11201	0.11	0.35477	P	0.20219200000000004	B;B	0.18610	0.007;0.029	B;B	0.20384	0.011;0.029	T	0.04855	-1.0922	9	0.62326	D	0.03	.	11.8001	0.52122	0.0:0.0:0.2879:0.7121	rs12110451;rs52821586;rs60532094;rs12110451	587;660	Q5T795;Q9NU22	.;MDN1_HUMAN	V	660;660;587	ENSP00000358400:I660V;ENSP00000413970:I660V;ENSP00000409664:I587V	ENSP00000358400:I660V	I	-	1	0	MDN1	90539118	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.720000	0.47252	0.953000	0.37825	0.528000	0.53228	ATC	T|0.817;C|0.183	0.183	strong		0.512	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
PRR12	57479	hgsc.bcm.edu	37	19	50099422	50099422	+	Silent	SNP	C	C	T	rs73058052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50099422C>T	ENST00000418929.2	+	4	1842	c.1830C>T	c.(1828-1830)gcC>gcT	p.A610A		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)		GCTATGCAGCCGGAGCAGGTG	0.657													C|||	718	0.143371	0.1407	0.0778	5008	,	,		14479	0.0208		0.168	False		,,,				2504	0.2945				p.A610A		Atlas-SNP	.											.	PRR12	157	.	0			c.C1830T						PASS	.	C		564,3410		49,466,1472	22.0	29.0	27.0		1830	-7.6	0.4	19	dbSNP_130	27	1406,6916		105,1196,2860	no	coding-synonymous	PRR12	NM_020719.1		154,1662,4332	TT,TC,CC		16.895,14.1922,16.0215		610/2037	50099422	1970,10326	1987	4161	6148	SO:0001819	synonymous_variant	57479	exon4			TGCAGCCGGAGCA	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.1830C>T	19.37:g.50099422C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	94	38	0.404255	NM_020719	E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	37	CCDS46143.1																																																																																			C|0.876;T|0.124	0.124	strong		0.657	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719	
WDR78	79819	hgsc.bcm.edu	37	1	67327986	67327986	+	Splice_Site	SNP	C	C	G	rs144890566		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:67327986C>G	ENST00000371026.3	-	7	996		c.e7-1		WDR78_ENST00000431318.1_Splice_Site|WDR78_ENST00000493572.1_5'UTR|WDR78_ENST00000371023.3_Splice_Site	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78						hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						GACATTATGCCTAGATAAAGA	0.318																																					.		Atlas-SNP	.											.	WDR78	102	.	0			c.941-1G>C						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	65.0	65.0	65.0		,	4.8	0.6	1	dbSNP_134	65	0,8600		0,0,4300	no	splice-3,splice-3	WDR78	NM_024763.4,NM_207014.2	,	0,2,6501	GG,GC,CC		0.0,0.0454,0.0154	,	,	67327986	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	79819	exon8			TTATGCCTAGATA	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.941-1G>C	1.37:g.67327986C>G		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	178	93	0.522472	NM_024763	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Splice_Site	SNP	ENST00000371026.3	37	CCDS635.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.64|17.64	3.440343|3.440343	0.63067|0.63067	4.54E-4|4.54E-4	0.0|0.0	ENSG00000152763|ENSG00000152763	ENST00000371026;ENST00000431318;ENST00000464352;ENST00000371023;ENST00000469450|ENST00000531552	.|T	.|0.55413	.|0.52	5.67|5.67	4.76|4.76	0.60689|0.60689	.|.	.|.	.|.	.|.	.|.	.|T	.|0.47544	.|0.1451	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.47262	.|-0.9131	.|5	.|.	.|.	.|.	.|.	12.3988|12.3988	0.55402|0.55402	0.0:0.9183:0.0:0.0817|0.0:0.9183:0.0:0.0817	.|.	.|.	.|.	.|.	.|R	-1|1	.|ENSP00000433037:G1R	.|.	.|G	-|-	.|1	.|0	WDR78|WDR78	67100574|67100574	1.000000|1.000000	0.71417|0.71417	0.631000|0.631000	0.29282|0.29282	0.826000|0.826000	0.46750|0.46750	4.397000|4.397000	0.59690|0.59690	1.393000|1.393000	0.46605|0.46605	0.591000|0.591000	0.81541|0.81541	.|GGC	C|1.000;G|0.000	0.000	weak		0.318	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	Intron
NPAP1	23742	hgsc.bcm.edu	37	15	24922407	24922407	+	Missense_Mutation	SNP	C	C	T	rs79339610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:24922407C>T	ENST00000329468.2	+	1	1867	c.1393C>T	c.(1393-1395)Ctt>Ttt	p.L465F		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	465	Pro-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											TCCTCTGGCTCTTCCTGCTGA	0.502													C|||	18	0.00359425	0.0121	0.0	5008	,	,		20216	0.0		0.002	False		,,,				2504	0.0				p.L465F		Atlas-SNP	.											C15orf2,colon,carcinoma,0,1	.	.	1	0			c.C1393T						PASS	.	C	PHE/LEU	56,4350		1,54,2148	191.0	185.0	187.0		1393	-4.1	0.0	15	dbSNP_131	187	1,8599		0,1,4299	yes	missense	C15orf2	NM_018958.2	22	1,55,6447	TT,TC,CC		0.0116,1.271,0.4383	probably-damaging	465/1157	24922407	57,12949	2203	4300	6503	SO:0001583	missense	23742	exon1			CTGGCTCTTCCTG	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.1393C>T	15.37:g.24922407C>T	ENSP00000333735:p.Leu465Phe	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	107	41	0.383178	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	6	0.0027472527472527475	5	0.01016260162601626	0	0.0	0	0.0	1	0.0013192612137203166	.	12.35	1.912039	0.33721	0.01271	1.16E-4	ENSG00000185823	ENST00000329468	T	0.10860	2.83	2.07	-4.13	0.03904	.	2.992630	0.01188	N	0.007259	T	0.04952	0.0133	L	0.29908	0.895	0.09310	N	1	B	0.31383	0.321	B	0.31614	0.133	T	0.14615	-1.0466	10	0.24483	T	0.36	.	2.191	0.03899	0.2812:0.1844:0.4144:0.12	.	465	Q9NZP6	CO002_HUMAN	F	465	ENSP00000333735:L465F	ENSP00000333735:L465F	L	+	1	0	C15orf2	22473500	0.000000	0.05858	0.000000	0.03702	0.366000	0.29705	-2.799000	0.00762	-2.586000	0.00459	0.313000	0.20887	CTT	C|0.996;T|0.004	0.004	strong		0.502	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
EPHB3	2049	hgsc.bcm.edu	37	3	184298663	184298663	+	Silent	SNP	G	G	A	rs11719912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184298663G>A	ENST00000330394.2	+	13	2987	c.2535G>A	c.(2533-2535)caG>caA	p.Q845Q	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	845	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TGAGCAACCAGGATGTGAGTG	0.567													G|||	331	0.0660942	0.1067	0.0735	5008	,	,		20851	0.0		0.1203	False		,,,				2504	0.0184				p.Q845Q		Atlas-SNP	.											.	EPHB3	114	.	0			c.G2535A						PASS	.	G		441,3965	213.1+/-232.8	26,389,1788	134.0	126.0	128.0		2535	3.2	1.0	3	dbSNP_120	128	876,7724	197.5+/-242.1	51,774,3475	no	coding-synonymous	EPHB3	NM_004443.3		77,1163,5263	AA,AG,GG		10.186,10.0091,10.1261		845/999	184298663	1317,11689	2203	4300	6503	SO:0001819	synonymous_variant	2049	exon13			CAACCAGGATGTG	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.2535G>A	3.37:g.184298663G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			G|0.909;A|0.091	0.091	strong		0.567	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
PLIN4	729359	hgsc.bcm.edu	37	19	4511746	4511746	+	Missense_Mutation	SNP	A	A	T	rs62115192		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4511746A>T	ENST00000301286.3	-	3	2183	c.2184T>A	c.(2182-2184)aaT>aaA	p.N728K		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	728	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						CTTTGGCCACATTCGCAGCAC	0.577																																					p.N728K		Atlas-SNP	.											.	PLIN4	191	.	0			c.T2184A						PASS	.						148.0	134.0	138.0					19																	4511746		2024	4170	6194	SO:0001583	missense	729359	exon3			GGCCACATTCGCA	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.2184T>A	19.37:g.4511746A>T	ENSP00000301286:p.Asn728Lys	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	433	52	0.120092	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	a	14.30	2.495348	0.44352	.	.	ENSG00000167676	ENST00000301286	T	0.05382	3.45	4.56	-9.13	0.00704	.	0.915443	0.08968	N	0.867615	T	0.13415	0.0325	M	0.82323	2.585	0.80722	P	0.0	P	0.52316	0.952	P	0.53649	0.731	T	0.00557	-1.1672	9	0.36615	T	0.2	-4.9999	8.1871	0.31346	0.2655:0.0976:0.541:0.0959	rs62115192	728	Q96Q06	PLIN4_HUMAN	K	728	ENSP00000301286:N728K	ENSP00000301286:N728K	N	-	3	2	PLIN4	4462746	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.931000	0.00169	-2.908000	0.00309	-1.193000	0.01689	AAT	A|0.333;T|0.667	0.667	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
HDX	139324	hgsc.bcm.edu	37	X	83591879	83591879	+	Missense_Mutation	SNP	T	T	C	rs77791258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:83591879T>C	ENST00000297977.5	-	7	1781	c.1670A>G	c.(1669-1671)aAt>aGt	p.N557S	HDX_ENST00000373177.2_Missense_Mutation_p.N557S|HDX_ENST00000506585.2_Missense_Mutation_p.N499S	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	557						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						AACAACTTCATTGGGCTCTTC	0.333													t|||	172	0.0455629	0.1188	0.0216	3775	,	,		12736	0.0		0.0	False		,,,				2504	0.0				p.N557S	Pancreas(53;231 1169 36156 43751 51139)	Atlas-SNP	.											.	HDX	124	.	0			c.A1670G						PASS	.	C	SER/ASN,SER/ASN,SER/ASN	503,3330		35,338,95,1258,476	86.0	72.0	76.0		1496,1670,1670	-7.3	0.4	X	dbSNP_131	76	4,6720		0,4,0,2423,1870	yes	missense,missense,missense	HDX	NM_001177478.1,NM_001177479.1,NM_144657.4	46,46,46	35,342,95,3681,2346	CC,CT,C,TT,T		0.0595,13.1229,4.8025	benign,benign,benign	499/633,557/691,557/691	83591879	507,10050	2202	4297	6499	SO:0001583	missense	139324	exon7			ACTTCATTGGGCT	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.1670A>G	X.37:g.83591879T>C	ENSP00000297977:p.Asn557Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	60	0.03616636528028933	39	0.08369098712446352	4	0.011363636363636364	0	0.0	0	0.0	T	0.666	-0.803647	0.02841	0.131229	5.95E-4	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.27557	1.66;1.66;1.66	5.33	-7.27	0.01461	.	0.753578	0.13237	N	0.403154	T	0.00144	0.0004	N	0.11560	0.145	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.31888	-0.9927	9	0.06757	T	0.87	-14.8311	16.4567	0.84019	0.0:0.6124:0.0:0.3876	.	557	Q7Z353	HDX_HUMAN	S	557;499;557	ENSP00000297977:N557S;ENSP00000362272:N499S;ENSP00000423670:N557S	ENSP00000297977:N557S	N	-	2	0	HDX	83478535	0.008000	0.16893	0.432000	0.26747	0.605000	0.37080	-2.080000	0.01368	-1.696000	0.01421	0.409000	0.27619	AAT	T|0.950;C|0.050	0.050	strong		0.333	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657	
IL4R	3566	hgsc.bcm.edu	37	16	27373972	27373972	+	Silent	SNP	T	T	C	rs2234900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27373972T>C	ENST00000395762.2	+	11	1558	c.1299T>C	c.(1297-1299)ctT>ctC	p.L433L	IL4R_ENST00000170630.2_Silent_p.L433L|IL4R_ENST00000543915.2_Silent_p.L433L|IL4R_ENST00000380922.3_Silent_p.L418L	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	79	0	0		WXS	Illumina HiSeq	Phase_I	97	30	0.309278	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		
WNK4	65266	hgsc.bcm.edu	37	17	40947320	40947320	+	Missense_Mutation	SNP	C	C	T	rs2290041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40947320C>T	ENST00000246914.5	+	14	2902	c.2881C>T	c.(2881-2883)Cct>Tct	p.P961S		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	961			P -> S (in dbSNP:rs2290041).		chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		TAGTCCCCTCCCTAGCCTGCC	0.622													C|||	515	0.102835	0.2557	0.0231	5008	,	,		15268	0.0387		0.004	False		,,,				2504	0.1207				p.P961S	Esophageal Squamous(6;201 374 4964 23855 42828)	Atlas-SNP	.											.	WNK4	182	.	0			c.C2881T						PASS	.	C	SER/PRO	1003,3403	372.2+/-320.3	117,769,1317	63.0	61.0	62.0		2881	4.7	0.1	17	dbSNP_100	62	11,8589	8.4+/-32.0	0,11,4289	yes	missense	WNK4	NM_032387.4	74	117,780,5606	TT,TC,CC		0.1279,22.7644,7.7964	possibly-damaging	961/1244	40947320	1014,11992	2203	4300	6503	SO:0001583	missense	65266	exon14			CCCCTCCCTAGCC	AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.2881C>T	17.37:g.40947320C>T	ENSP00000246914:p.Pro961Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Missense_Mutation	SNP	ENST00000246914.5	37	CCDS11439.1	144	0.06593406593406594	112	0.22764227642276422	7	0.019337016574585635	22	0.038461538461538464	3	0.00395778364116095	C	0.472	-0.883791	0.02530	0.227644	0.001279	ENSG00000126562	ENST00000246914	T	0.72725	-0.68	5.62	4.65	0.58169	.	0.153235	0.30667	N	0.009130	T	0.00039	0.0001	L	0.32530	0.975	0.09310	P	0.9999999663314	B;B;P	0.35507	0.176;0.11;0.506	B;B;B	0.28849	0.095;0.024;0.074	T	0.09250	-1.0683	9	0.15499	T	0.54	-6.1739	9.9084	0.41390	0.1386:0.7885:0.0:0.0728	rs2290041;rs52823239;rs56682713	961;961;961	Q96J92-3;B0LPI0;Q96J92	.;.;WNK4_HUMAN	S	961	ENSP00000246914:P961S	ENSP00000246914:P961S	P	+	1	0	WNK4	38200846	0.000000	0.05858	0.052000	0.19188	0.169000	0.22640	0.290000	0.18975	1.370000	0.46153	0.591000	0.81541	CCT	C|0.927;T|0.073	0.073	strong		0.622	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
PRRC2A	7916	hgsc.bcm.edu	37	6	31599594	31599594	+	Silent	SNP	A	A	G	rs10947220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31599594A>G	ENST00000376033.2	+	16	3378	c.3144A>G	c.(3142-3144)ggA>ggG	p.G1048G	PRRC2A_ENST00000376007.4_Silent_p.G1048G	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1048	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GAGGGCGGGGAGCCCGAAGCC	0.647													A|||	233	0.0465256	0.1006	0.0634	5008	,	,		12424	0.0179		0.0219	False		,,,				2504	0.0164				p.G1048G		Atlas-SNP	.											PRRC2A,NS,neuroblastoma,0,1	PRRC2A	152	1	0			c.A3144G						PASS	.	A	,	170,2840		4,162,1339	15.0	16.0	15.0		3144,3144	-0.8	1.0	6	dbSNP_120	15	114,5284		0,114,2585	no	coding-synonymous,coding-synonymous	PRRC2A	NM_004638.3,NM_080686.2	,	4,276,3924	GG,GA,AA		2.1119,5.6478,3.3777	,	1048/2158,1048/2158	31599594	284,8124	1505	2699	4204	SO:0001819	synonymous_variant	7916	exon16			GCGGGGAGCCCGA	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3144A>G	6.37:g.31599594A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																			A|0.949;G|0.050;T|0.000	0.050	strong		0.647	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
OGDHL	55753	hgsc.bcm.edu	37	10	50954850	50954850	+	Silent	SNP	G	G	A	rs75974530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50954850G>A	ENST00000374103.4	-	10	1327	c.1242C>T	c.(1240-1242)agC>agT	p.S414S	OGDHL_ENST00000419399.1_Silent_p.S357S|OGDHL_ENST00000432695.1_Silent_p.S205S	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	414					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						AGGGCAGGTCGCTCAGGTGGA	0.617													G|||	88	0.0175719	0.062	0.0072	5008	,	,		22610	0.0		0.001	False		,,,				2504	0.0				p.S414S		Atlas-SNP	.											.	OGDHL	149	.	0			c.C1242T						PASS	.	G	,,	299,4107	164.4+/-196.0	9,281,1913	151.0	102.0	119.0		1071,615,1242	-11.5	0.2	10	dbSNP_131	119	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	,,	9,290,6204	AA,AG,GG		0.1047,6.7862,2.3681	,,	357/954,205/802,414/1011	50954850	308,12698	2203	4300	6503	SO:0001819	synonymous_variant	55753	exon10			CAGGTCGCTCAGG	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.1242C>T	10.37:g.50954850G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	126	66	0.52381	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																			G|0.976;A|0.024	0.024	strong		0.617	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
SYNE2	23224	hgsc.bcm.edu	37	14	64612858	64612858	+	Missense_Mutation	SNP	C	C	A	rs10151658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64612858C>A	ENST00000344113.4	+	84	15768	c.15556C>A	c.(15556-15558)Ctg>Atg	p.L5186M	SYNE2_ENST00000554584.1_Missense_Mutation_p.L5103M|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.L1820M|SYNE2_ENST00000358025.3_Missense_Mutation_p.L5186M|SYNE2_ENST00000357395.3_Missense_Mutation_p.L1571M|SYNE2_ENST00000394768.2_Missense_Mutation_p.L1571M	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						PASS	.	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	195	0	0		WXS	Illumina HiSeq	Phase_I	204	93	0.455882	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	
PTPRN	5798	hgsc.bcm.edu	37	2	220164886	220164886	+	Missense_Mutation	SNP	A	A	C	rs35314717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220164886A>C	ENST00000295718.2	-	9	1497	c.1257T>G	c.(1255-1257)agT>agG	p.S419R	PTPRN_ENST00000409251.3_Missense_Mutation_p.S419R|AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Missense_Mutation_p.S329R	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	419			S -> R (in dbSNP:rs35314717).		cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		GCTGGACTTCACTGGAGGTAG	0.627													A|||	162	0.0323482	0.1172	0.0101	5008	,	,		16965	0.0		0.0	False		,,,				2504	0.0				p.S419R		Atlas-SNP	.											.	PTPRN	138	.	0			c.T1257G						PASS	.	A	ARG/SER,ARG/SER,ARG/SER	475,3931	223.9+/-240.3	29,417,1757	67.0	76.0	73.0		1257,987,1257	-2.4	0.0	2	dbSNP_126	73	6,8594	4.3+/-15.6	0,6,4294	yes	missense,missense,missense	PTPRN	NM_001199763.1,NM_001199764.1,NM_002846.3	110,110,110	29,423,6051	CC,CA,AA		0.0698,10.7808,3.6983	benign,benign,benign	419/951,329/890,419/980	220164886	481,12525	2203	4300	6503	SO:0001583	missense	5798	exon9			GACTTCACTGGAG		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.1257T>G	2.37:g.220164886A>C	ENSP00000295718:p.Ser419Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	89	53	0.595506	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	63	0.028846153846153848	61	0.12398373983739837	2	0.0055248618784530384	0	0.0	0	0.0	A	4.756	0.140493	0.09083	0.107808	6.98E-4	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.27104	1.69;1.69;1.69	4.27	-2.38	0.06622	.	1.386960	0.04458	N	0.373874	T	0.00210	0.0006	N	0.24115	0.695	0.80722	P	0.0	B;B	0.23735	0.09;0.09	B;B	0.21360	0.034;0.015	T	0.23619	-1.0183	9	0.16420	T	0.52	.	7.6045	0.28095	0.276:0.1662:0.5578:0.0	rs35314717;rs60827710	419;419	Q6NSL1;Q16849	.;PTPRN_HUMAN	R	419;419;419;329	ENSP00000386638:S419R;ENSP00000295718:S419R;ENSP00000444244:S329R	ENSP00000295718:S419R	S	-	3	2	PTPRN	219873130	0.000000	0.05858	0.001000	0.08648	0.379000	0.30106	-0.764000	0.04735	-0.686000	0.05170	0.459000	0.35465	AGT	A|0.966;C|0.034	0.034	strong		0.627	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2		
OBSCN	84033	hgsc.bcm.edu	37	1	228505204	228505204	+	Missense_Mutation	SNP	G	G	A	rs4653942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228505204G>A	ENST00000422127.1	+	52	13645	c.13601G>A	c.(13600-13602)cGc>cAc	p.R4534H	OBSCN_ENST00000284548.11_Missense_Mutation_p.R4534H|OBSCN_ENST00000570156.2_Missense_Mutation_p.R5491H|OBSCN_ENST00000366709.4_Missense_Mutation_p.R1653H|OBSCN_ENST00000366707.4_Missense_Mutation_p.R2168H	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4534	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H (in dbSNP:rs4653942). {ECO:0000269|PubMed:11448995}.		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)				GTGGTGGCTCGCAGCAGCCAC	0.657													g|||	1579	0.315296	0.3941	0.2954	5008	,	,		15262	0.499		0.1869	False		,,,				2504	0.1656				p.R5491H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G16472A						PASS	.		HIS/ARG,HIS/ARG	1547,2561		304,939,811	28.0	32.0	31.0		13601,13601	2.4	0.0	1	dbSNP_111	31	1632,6764		158,1316,2724	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	29,29	462,2255,3535	AA,AG,GG		19.4378,37.6582,25.4239	probably-damaging,probably-damaging	4534/7969,4534/6621	228505204	3179,9325	2054	4198	6252	SO:0001583	missense	84033	exon63			TGGCTCGCAGCAG	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.13601G>A	1.37:g.228505204G>A	ENSP00000409493:p.Arg4534His	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	198	196	0.989899	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	735	0.33653846153846156	188	0.3821138211382114	111	0.30662983425414364	288	0.5034965034965035	148	0.19525065963060687	g	13.05	2.120013	0.37436	0.376582	0.194378	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	4.42	2.36	0.29203	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.565277	0.16104	N	0.229422	T	0.00012	0.0000	L	0.28649	0.875	0.80722	P	0.0	P;D	0.64830	0.702;0.994	B;P	0.52672	0.295;0.706	T	0.44513	-0.9323	9	0.45353	T	0.12	.	2.8707	0.05616	0.3981:0.2307:0.3712:0.0	rs4653942;rs4653942	4534;4534	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	H	4534;4534;2168;1653	ENSP00000284548:R4534H;ENSP00000409493:R4534H;ENSP00000355668:R2168H;ENSP00000355670:R1653H	ENSP00000284548:R4534H	R	+	2	0	OBSCN	226571827	0.043000	0.20138	0.007000	0.13788	0.029000	0.11900	1.330000	0.33781	1.099000	0.41499	0.479000	0.44913	CGC	G|0.671;A|0.329	0.329	strong		0.657	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-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:108366734G>A	ENST00000223528.2	+	5	732	c.608G>A	c.(607-609)cGa>cAa	p.R203Q	FKTN_ENST00000448551.2_Missense_Mutation_p.R203Q|FKTN_ENST00000357998.5_Missense_Mutation_p.R203Q|FKTN_ENST00000602661.1_Missense_Mutation_p.R203Q|FKTN_ENST00000540160.1_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	66	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	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	
ATP2B2	491	hgsc.bcm.edu	37	3	10420087	10420087	+	Silent	SNP	T	T	C	rs751122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:10420087T>C	ENST00000352432.4	-	9	1119	c.1050A>G	c.(1048-1050)caA>caG	p.Q350Q	ATP2B2_ENST00000360273.2_Silent_p.Q350Q|ATP2B2_ENST00000343816.4_Silent_p.Q336Q|ATP2B2_ENST00000397077.1_Silent_p.Q305Q|ATP2B2_ENST00000383800.4_Silent_p.Q305Q			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	350					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						CCCCGTCCTGTTGTTTGGCTG	0.617													C|||	2470	0.493211	0.4418	0.317	5008	,	,		20457	0.6994		0.3708	False		,,,				2504	0.6012				p.Q350Q	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A1050G						PASS	.	C	,	1731,2675	643.1+/-397.8	338,1055,810	55.0	53.0	54.0		1050,915	3.9	1.0	3	dbSNP_86	54	2964,5636	658.6+/-401.6	506,1952,1842	no	coding-synonymous,coding-synonymous	ATP2B2	NM_001001331.2,NM_001683.3	,	844,3007,2652	CC,CT,TT		34.4651,39.2873,36.0987	,	350/1244,305/1199	10420087	4695,8311	2203	4300	6503	SO:0001819	synonymous_variant	491	exon10			GTCCTGTTGTTTG	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.1050A>G	3.37:g.10420087T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_001001331	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	CCDS33701.1																																																																																			T|0.596;C|0.404	0.404	strong		0.617	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
OC90	729330	hgsc.bcm.edu	37	8	133044172	133044172	+	Silent	SNP	G	G	A	rs6989686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133044172G>A	ENST00000443356.2	-	13	1121	c.1035C>T	c.(1033-1035)taC>taT	p.Y345Y	OC90_ENST00000603859.1_Silent_p.Y329Y|OC90_ENST00000254627.3_Silent_p.Y329Y|OC90_ENST00000262283.5_Silent_p.Y541Y			Q02509	OC90_HUMAN	otoconin 90	345	Phospholipase A2-like 2.				lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			CTTGTCCACAGTAACAGCCAT	0.542													G|||	45	0.00898562	0.0325	0.0029	5008	,	,		19082	0.0		0.0	False		,,,				2504	0.0				p.Y329Y		Atlas-SNP	.											.	OC90	163	.	0			c.C987T						PASS	.	G		111,3919		1,109,1905	57.0	60.0	59.0		987	4.1	1.0	8	dbSNP_116	59	1,8369		0,1,4184	no	coding-synonymous	OC90	NM_001080399.2		1,110,6089	AA,AG,GG		0.0119,2.7543,0.9032		329/478	133044172	112,12288	2015	4185	6200	SO:0001819	synonymous_variant	729330	exon12			TCCACAGTAACAG	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.1035C>T	8.37:g.133044172G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	144	65	0.451389	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				G|0.994;A|0.006	0.006	strong		0.542	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	
PLXNB2	23654	hgsc.bcm.edu	37	22	50718941	50718941	+	Silent	SNP	C	C	T	rs73891209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50718941C>T	ENST00000449103.1	-	25	4292	c.4152G>A	c.(4150-4152)aaG>aaA	p.K1384K	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Silent_p.K1384K			O15031	PLXB2_HUMAN	plexin B2	1384					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)		GCTTGGGGTTCTTGGCCACCA	0.692													C|||	222	0.0443291	0.1619	0.0115	5008	,	,		9618	0.0		0.0	False		,,,				2504	0.0				p.K1384K		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G4152A						PASS	.	C		556,3828		45,466,1681	75.0	80.0	78.0		4152	4.3	1.0	22	dbSNP_130	78	1,8583		0,1,4291	no	coding-synonymous	PLXNB2	NM_012401.3		45,467,5972	TT,TC,CC		0.0116,12.6825,4.2952		1384/1839	50718941	557,12411	2192	4292	6484	SO:0001819	synonymous_variant	23654	exon25			GGGGTTCTTGGCC		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.4152G>A	22.37:g.50718941C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1																																																																																			C|0.976;G|0.000;T|0.024	0.024	strong		0.692	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
TRIM55	84675	hgsc.bcm.edu	37	8	67064654	67064654	+	Missense_Mutation	SNP	A	A	G	rs7843605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:67064654A>G	ENST00000315962.4	+	8	1401	c.1028A>G	c.(1027-1029)aAa>aGa	p.K343R	TRIM55_ENST00000350034.4_Intron|TRIM55_ENST00000353317.5_Missense_Mutation_p.K343R|TRIM55_ENST00000276573.7_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	26	0	0		WXS	Illumina HiSeq	Phase_I	27	11	0.407407	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	
MUC17	140453	hgsc.bcm.edu	37	7	100675367	100675367	+	Missense_Mutation	SNP	A	A	G	rs116801454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100675367A>G	ENST00000306151.4	+	3	734	c.670A>G	c.(670-672)Agc>Ggc	p.S224G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	224	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)					TATGCCTGCCAGCACCATGAA	0.473													A|||	67	0.0133786	0.0492	0.0029	5008	,	,		23907	0.0		0.0	False		,,,				2504	0.0				p.S224G		Atlas-SNP	.											.	MUC17	804	.	0			c.A670G						PASS	.	A	GLY/SER	208,4198	127.8+/-164.7	5,198,2000	175.0	178.0	177.0		670	-0.9	0.0	7	dbSNP_132	177	2,8598	1.2+/-3.3	0,2,4298	yes	missense	MUC17	NM_001040105.1	56	5,200,6298	GG,GA,AA		0.0233,4.7208,1.6146	possibly-damaging	224/4494	100675367	210,12796	2203	4300	6503	SO:0001583	missense	140453	exon3			CCTGCCAGCACCA	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.670A>G	7.37:g.100675367A>G	ENSP00000302716:p.Ser224Gly	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	107	46	0.429907	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	A	1.401	-0.578226	0.03854	0.047208	2.33E-4	ENSG00000169876	ENST00000306151	T	0.02552	4.25	0.801	-0.886	0.10590	.	.	.	.	.	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	P	0.51933	0.949	B	0.34138	0.176	T	0.46843	-0.9162	9	0.23302	T	0.38	.	2.6539	0.05007	0.5677:0.0:0.0:0.4323	.	224	Q685J3	MUC17_HUMAN	G	224	ENSP00000302716:S224G	ENSP00000302716:S224G	S	+	1	0	MUC17	100462087	0.006000	0.16342	0.000000	0.03702	0.006000	0.05464	0.201000	0.17276	-0.273000	0.09246	0.165000	0.16767	AGC	A|0.987;G|0.013	0.013	strong		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CFAP53	220136	hgsc.bcm.edu	37	18	47788535	47788535	+	Missense_Mutation	SNP	G	G	A	rs138060809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47788535G>A	ENST00000398545.4	-	2	241	c.124C>T	c.(124-126)Cgc>Tgc	p.R42C		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)		TGATGGCTGCGTCGGATTCTT	0.433													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0				p.R42C		Atlas-SNP	.											.	CCDC11	59	.	0			c.C124T						PASS	.	G	CYS/ARG	8,3834		0,8,1913	118.0	113.0	115.0		124	4.2	0.0	18	dbSNP_134	115	0,8250		0,0,4125	yes	missense	CCDC11	NM_145020.3	180	0,8,6038	AA,AG,GG		0.0,0.2082,0.0662	probably-damaging	42/515	47788535	8,12084	1921	4125	6046	SO:0001583	missense	220136	exon2			GGCTGCGTCGGAT																												ENST00000398545.4:c.124C>T	18.37:g.47788535G>A	ENSP00000381553:p.Arg42Cys	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_145020		Missense_Mutation	SNP	ENST00000398545.4	37	CCDS11940.2	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	6.779	0.512676	0.12944	0.002082	0.0	ENSG00000172361	ENST00000398545	T	0.35789	1.29	5.12	4.24	0.50183	.	0.138507	0.22268	U	0.062301	T	0.37237	0.0996	L	0.58101	1.795	0.09310	N	0.999996	D	0.64830	0.994	P	0.44477	0.451	T	0.35001	-0.9806	10	0.72032	D	0.01	0.0534	11.0958	0.48143	0.0:0.0:0.8151:0.1849	.	42	Q96M91	CCD11_HUMAN	C	42	ENSP00000381553:R42C	ENSP00000381553:R42C	R	-	1	0	CCDC11	46042533	0.058000	0.20735	0.003000	0.11579	0.110000	0.19582	3.065000	0.49994	1.503000	0.48686	-0.309000	0.09137	CGC	G|0.999;A|0.001	0.001	strong		0.433	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3		
FAM118A	55007	hgsc.bcm.edu	37	22	45723807	45723807	+	Missense_Mutation	SNP	G	G	C	rs11556482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45723807G>C	ENST00000216214.3	+	5	1219	c.385G>C	c.(385-387)Gtg>Ctg	p.V129L	FAM118A_ENST00000441876.2_Missense_Mutation_p.V129L|FAM118A_ENST00000405673.1_Missense_Mutation_p.V129L|FAM118A_ENST00000405548.3_5'Flank	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	129			V -> L (in dbSNP:rs11556482). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CCGGAGTCCTGTGGTGCTGCA	0.592													C|||	2691	0.53734	0.8548	0.402	5008	,	,		19525	0.5258		0.2932	False		,,,				2504	0.4673				p.V129L		Atlas-SNP	.											.	FAM118A	32	.	0			c.G385C						PASS	.	C	LEU/VAL,LEU/VAL	3325,1081	392.4+/-328.5	1262,801,140	70.0	59.0	63.0		385,385	-0.0	0.1	22	dbSNP_120	63	2445,6155	697.2+/-404.9	354,1737,2209	yes	missense,missense	FAM118A	NM_001104595.1,NM_017911.2	32,32	1616,2538,2349	CC,CG,GG		28.4302,24.5347,44.3641	benign,benign	129/358,129/358	45723807	5770,7236	2203	4300	6503	SO:0001583	missense	55007	exon4			AGTCCTGTGGTGC	BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 8"""	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.385G>C	22.37:g.45723807G>C	ENSP00000216214:p.Val129Leu	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	156	86	0.551282	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Missense_Mutation	SNP	ENST00000216214.3	37	CCDS14065.1	1086	0.49725274725274726	414	0.8414634146341463	153	0.42265193370165743	299	0.5227272727272727	220	0.29023746701846964	C	0.889	-0.726183	0.03158	0.754653	0.284302	ENSG00000100376	ENST00000216214;ENST00000441876;ENST00000405673;ENST00000427777	T;T;T;T	0.42131	1.03;1.03;0.98;0.99	5.12	-0.0348	0.13895	.	0.968722	0.08538	N	0.930981	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36163	-0.9759	9	0.27785	T	0.31	-20.5793	13.0846	0.59133	0.0917:0.3886:0.5197:0.0	rs11556482;rs17845392;rs17858249	129	Q9NWS6	F118A_HUMAN	L	129	ENSP00000216214:V129L;ENSP00000395892:V129L;ENSP00000385231:V129L;ENSP00000395194:V129L	ENSP00000216214:V129L	V	+	1	0	FAM118A	44102471	0.935000	0.31712	0.119000	0.21687	0.190000	0.23558	1.400000	0.34577	0.124000	0.18369	-0.335000	0.08231	GTG	G|0.539;C|0.461	0.461	strong		0.592	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
GPR108	56927	hgsc.bcm.edu	37	19	6735929	6735929	+	Missense_Mutation	SNP	C	C	T	rs11539588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6735929C>T	ENST00000264080.7	-	3	307	c.281G>A	c.(280-282)cGc>cAc	p.R94H	TRIP10_ENST00000600428.1_5'Flank|GPR108_ENST00000430424.4_5'UTR	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	94						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						TGAATAGGAGCGAACTCTGCC	0.597											OREG0025202	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	303	0.0605032	0.1384	0.0663	5008	,	,		15640	0.0437		0.0169	False		,,,				2504	0.0133				p.R94H		Atlas-SNP	.											.	GPR108	35	.	0			c.G281A						PASS	.	C	HIS/ARG	379,3415		17,345,1535	37.0	41.0	40.0		281	-0.9	0.0	19	dbSNP_120	40	138,8084		0,138,3973	yes	missense	GPR108	NM_001080452.1	29	17,483,5508	TT,TC,CC		1.6784,9.9895,4.3026	possibly-damaging	94/544	6735929	517,11499	1897	4111	6008	SO:0001583	missense	56927	exon3			TAGGAGCGAACTC		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.281G>A	19.37:g.6735929C>T	ENSP00000264080:p.Arg94His	Somatic	63	0	0	636	WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001080452	B9EJD7	Missense_Mutation	SNP	ENST00000264080.7	37	CCDS42479.1	144	0.06593406593406594	73	0.1483739837398374	24	0.06629834254143646	33	0.057692307692307696	14	0.018469656992084433	C	1.254	-0.617668	0.03663	0.099895	0.016784	ENSG00000125734	ENST00000264080	T	0.23147	1.92	4.23	-0.876	0.10624	.	0.836337	0.09852	N	0.747434	T	0.00073	0.0002	N	0.25890	0.77	0.58432	P	2.9999999999752447E-6	B	0.11235	0.004	B	0.06405	0.002	T	0.25950	-1.0117	9	0.54805	T	0.06	-36.7302	4.5388	0.12047	0.1523:0.599:0.149:0.0997	rs11539588	94	Q9NPR9	GP108_HUMAN	H	94	ENSP00000264080:R94H	ENSP00000264080:R94H	R	-	2	0	GPR108	6686929	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-1.072000	0.03434	-0.255000	0.09486	-0.959000	0.02639	CGC	C|0.952;T|0.048	0.048	strong		0.597	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2		
PLA2G4C	8605	hgsc.bcm.edu	37	19	48558159	48558159	+	Silent	SNP	G	G	A	rs2307280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48558159G>A	ENST00000599921.1	-	15	1762	c.1405C>T	c.(1405-1407)Ctg>Ttg	p.L469L	PLA2G4C_ENST00000413144.2_Silent_p.L469L|PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000599111.1_Silent_p.L479L|PLA2G4C_ENST00000354276.3_Silent_p.L469L			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	469	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				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)		ATGTTGAACAGGGGAAAATGC	0.517													g|||	408	0.0814696	0.2965	0.0231	5008	,	,		18425	0.0		0.0	False		,,,				2504	0.0				p.L479L		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.C1435T						PASS	.	G	,,	996,3410	372.2+/-320.3	116,764,1323	110.0	102.0	105.0		1435,1405,1405	1.9	0.9	19	dbSNP_100	105	12,8588	7.7+/-29.5	0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	,,	116,776,5611	AA,AG,GG		0.1395,22.6055,7.7503	,,	479/552,469/528,469/542	48558159	1008,11998	2203	4300	6503	SO:0001819	synonymous_variant	8605	exon15			TGAACAGGGGAAA	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.1405C>T	19.37:g.48558159G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Silent	SNP	ENST00000599921.1	37	CCDS12710.1																																																																																			G|0.926;A|0.074	0.074	strong		0.517	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
PIGG	54872	hgsc.bcm.edu	37	4	520853	520853	+	Missense_Mutation	SNP	G	G	A	rs13114026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:520853G>A	ENST00000453061.2	+	10	2201	c.2095G>A	c.(2095-2097)Gtc>Atc	p.V699I	PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000383028.4_Missense_Mutation_p.V566I|PIGG_ENST00000504346.1_Missense_Mutation_p.V610I|PIGG_ENST00000310340.5_Missense_Mutation_p.V691I	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	699			V -> I (in dbSNP:rs13114026). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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 (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)	p.L689_A694delLSVLAA(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						CGAGCTCTCTGTCCTGGCTGC	0.552													G|||	893	0.178315	0.2413	0.0908	5008	,	,		14770	0.2054		0.1292	False		,,,				2504	0.1779				p.V699I		Atlas-SNP	.											.	PIGG	86	.	1	Deletion - In frame(1)	ovary(1)	c.G2095A						PASS	.	G	ILE/VAL,ILE/VAL	1003,3403	370.8+/-319.7	117,769,1317	62.0	49.0	53.0		2095,2071	3.4	0.0	4	dbSNP_121	53	1035,7565	219.7+/-257.6	66,903,3331	yes	missense,missense	PIGG	NM_001127178.1,NM_017733.3	29,29	183,1672,4648	AA,AG,GG		12.0349,22.7644,15.6697	benign,benign	699/984,691/976	520853	2038,10968	2203	4300	6503	SO:0001583	missense	54872	exon10			CTCTCTGTCCTGG		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.2095G>A	4.37:g.520853G>A	ENSP00000415203:p.Val699Ile	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	269	133	0.494424	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	396	0.1813186813186813	132	0.2682926829268293	37	0.10220994475138122	130	0.22727272727272727	97	0.1279683377308707	G	2.896	-0.228623	0.06022	0.227644	0.120349	ENSG00000174227	ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028	T;T;T;T	0.09255	3.32;3.33;3.0;3.0	6.06	3.39	0.38822	.	0.669240	0.16139	N	0.227810	T	0.00012	0.0000	L	0.52011	1.625	0.58432	P	1.0000000000287557E-6	B;B;B	0.30236	0.274;0.022;0.169	B;B;B	0.30401	0.115;0.01;0.086	T	0.42932	-0.9422	9	0.12766	T	0.61	-2.4778	5.1107	0.14808	0.1524:0.0:0.5552:0.2924	rs13114026;rs59899952;rs13114026	566;699;691	Q5H8A4-3;Q5H8A4;Q5H8A4-2	.;PIGG_HUMAN;.	I	691;699;610;566	ENSP00000311750:V691I;ENSP00000415203:V699I;ENSP00000424800:V610I;ENSP00000372494:V566I	ENSP00000311750:V691I	V	+	1	0	PIGG	510853	0.063000	0.20901	0.004000	0.12327	0.216000	0.24613	0.374000	0.20501	0.437000	0.26423	-0.145000	0.13849	GTC	G|0.827;A|0.173	0.173	strong		0.552	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
MRPS9	64965	hgsc.bcm.edu	37	2	105665808	105665808	+	Splice_Site	SNP	C	C	T	rs11538197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	69	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	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
LACTB	114294	hgsc.bcm.edu	37	15	63433785	63433785	+	Silent	SNP	G	G	A	rs4775629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:63433785G>A	ENST00000261893.4	+	6	1497	c.1425G>A	c.(1423-1425)tcG>tcA	p.S475S	RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	475						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)	p.S475S(1)		NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						CGTATGGTTCGTGTAGAAAGC	0.483													G|||	615	0.122804	0.1921	0.0922	5008	,	,		20324	0.1677		0.0308	False		,,,				2504	0.0992				p.S475S	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											LACTB,NS,carcinoma,0,1	LACTB	29	1	1	Substitution - coding silent(1)	stomach(1)	c.G1425A						PASS	.	G		735,3671	304.1+/-288.3	72,591,1540	77.0	67.0	70.0		1425	-5.8	0.9	15	dbSNP_111	70	206,8394	88.6+/-150.9	2,202,4096	no	coding-synonymous	LACTB	NM_032857.3		74,793,5636	AA,AG,GG		2.3953,16.6818,7.2351		475/548	63433785	941,12065	2203	4300	6503	SO:0001819	synonymous_variant	114294	exon6			TGGTTCGTGTAGA	AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"""Mitochondrial ribosomal proteins / large subunits"""	16468	protein-coding gene	gene with protein product		608440	"""mitochondrial ribosomal protein L56"""	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.1425G>A	15.37:g.63433785G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	173	78	0.450867	NM_032857	P83096	Silent	SNP	ENST00000261893.4	37	CCDS10182.1																																																																																			G|0.904;A|0.096	0.096	strong		0.483	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857	
SLC22A12	116085	hgsc.bcm.edu	37	11	64367862	64367862	+	Silent	SNP	T	T	C	rs7932775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64367862T>C	ENST00000377574.1	+	8	2056	c.1309T>C	c.(1309-1311)Ttg>Ctg	p.L437L	SLC22A12_ENST00000473690.1_Silent_p.L216L|SLC22A12_ENST00000336464.7_Silent_p.L403L|SLC22A12_ENST00000377567.2_Silent_p.L329L|SLC22A12_ENST00000377572.1_Silent_p.L329L	NM_144585.2	NP_653186.2	Q96S37	S22AC_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 12	437					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)	GCGCTCAGCCTTGGCCGTGCT	0.647													C|||	1990	0.397364	0.674	0.255	5008	,	,		14174	0.5129		0.2018	False		,,,				2504	0.2065				p.L437L		Atlas-SNP	.											.	SLC22A12	68	.	0			c.T1309C						PASS	.	C	,	2545,1845		746,1053,396	14.0	17.0	16.0		1309,646	2.9	1.0	11	dbSNP_116	16	1592,6994		173,1246,2874	no	coding-synonymous,coding-synonymous	SLC22A12	NM_144585.2,NM_153378.1	,	919,2299,3270	CC,CT,TT		18.5418,42.0273,31.8819	,	437/554,216/333	64367862	4137,8839	2195	4293	6488	SO:0001819	synonymous_variant	116085	exon8			TCAGCCTTGGCCG	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.1309T>C	11.37:g.64367862T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_144585	B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2	Silent	SNP	ENST00000377574.1	37	CCDS8075.1																																																																																			T|0.629;C|0.371	0.371	strong		0.647	SLC22A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104966.2	NM_144585	
LGR5	8549	hgsc.bcm.edu	37	12	71977787	71977787	+	Missense_Mutation	SNP	T	T	C	rs17109924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:71977787T>C	ENST00000266674.5	+	18	2308	c.1997T>C	c.(1996-1998)gTg>gCg	p.V666A	LGR5_ENST00000540815.2_Missense_Mutation_p.V642A|LGR5_ENST00000536515.1_Missense_Mutation_p.V594A|RP11-186F10.2_ENST00000546601.1_RNA			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	666			V -> A (in dbSNP:rs17109924). {ECO:0000269|PubMed:15489334}.		G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						GGGTTCTCTGTGAAATATTCT	0.458													T|||	357	0.0712859	0.1172	0.0648	5008	,	,		22071	0.003		0.0606	False		,,,				2504	0.0951				p.V666A		Atlas-SNP	.											LGR5,bladder,carcinoma,-1,1	LGR5	103	1	0			c.T1997C						PASS	.	T	ALA/VAL	456,3950	218.1+/-236.3	25,406,1772	136.0	134.0	135.0		1997	4.7	1.0	12	dbSNP_123	135	657,7943	165.9+/-218.0	20,617,3663	yes	missense	LGR5	NM_003667.2	64	45,1023,5435	CC,CT,TT		7.6395,10.3495,8.5576	possibly-damaging	666/908	71977787	1113,11893	2203	4300	6503	SO:0001583	missense	8549	exon18			TCTCTGTGAAATA	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"""GPCR / Class A : Orphans"""	4504	protein-coding gene	gene with protein product		606667	"""G protein-coupled receptor 49"", ""leucine-rich repeat-containing G protein-coupled receptor 5"""	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.1997T>C	12.37:g.71977787T>C	ENSP00000266674:p.Val666Ala	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	179	177	0.988827	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Missense_Mutation	SNP	ENST00000266674.5	37	CCDS9000.1	130	0.05952380952380952	56	0.11382113821138211	26	0.0718232044198895	1	0.0017482517482517483	47	0.06200527704485488	T	10.78	1.446347	0.25987	0.103495	0.076395	ENSG00000139292	ENST00000266674;ENST00000451585;ENST00000536515;ENST00000540815	T;T;T	0.77620	-1.11;-1.11;-1.11	5.85	4.71	0.59529	GPCR, rhodopsin-like superfamily (1);	0.250903	0.28504	N	0.015110	T	0.03651	0.0104	L	0.45051	1.395	0.37532	D	0.917956	B;B	0.19331	0.028;0.035	B;B	0.26864	0.044;0.074	T	0.30119	-0.9989	10	0.18276	T	0.48	.	11.8686	0.52507	0.0:0.068:0.0:0.932	rs17109924;rs56488504;rs61507334;rs17109924	642;666	O75473-2;O75473	.;LGR5_HUMAN	A	666;666;594;642	ENSP00000266674:V666A;ENSP00000443033:V594A;ENSP00000441035:V642A	ENSP00000266674:V666A	V	+	2	0	LGR5	70264054	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	3.325000	0.52030	1.044000	0.40200	0.533000	0.62120	GTG	T|0.922;C|0.078	0.078	strong		0.458	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667	
PABPC3	5042	hgsc.bcm.edu	37	13	25671786	25671786	+	Missense_Mutation	SNP	G	G	A	rs113301206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25671786G>A	ENST00000281589.3	+	1	1487	c.1450G>A	c.(1450-1452)Gtg>Atg	p.V484M		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	484					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AACACAGACAGTGGGTCCACG	0.537													g|||	617	0.123203	0.1876	0.1081	5008	,	,		22365	0.0655		0.0666	False		,,,				2504	0.1646				p.V484M		Atlas-SNP	.											PABPC3,brain,glioma,0,1	PABPC3	129	1	0			c.G1450A						scavenged	.						64.0	58.0	60.0					13																	25671786		2203	4300	6503	SO:0001583	missense	5042	exon1			CAGACAGTGGGTC	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1450G>A	13.37:g.25671786G>A	ENSP00000281589:p.Val484Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	110	5	0.0454545	NM_030979	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	4.651	0.121106	0.08881	.	.	ENSG00000151846	ENST00000281589	T	0.26957	1.7	0.875	-0.771	0.11002	.	0.098881	0.40908	N	0.000987	T	0.04363	0.0120	N	0.00197	-1.87	0.23421	N	0.997711	B	0.02656	0.0	B	0.09377	0.004	T	0.38243	-0.9670	10	0.30854	T	0.27	.	4.3022	0.10930	0.7031:0.0:0.2969:0.0	.	484	Q9H361	PABP3_HUMAN	M	484	ENSP00000281589:V484M	ENSP00000281589:V484M	V	+	1	0	PABPC3	24569786	0.402000	0.25311	0.468000	0.27192	0.114000	0.19823	0.521000	0.22893	-0.307000	0.08804	0.313000	0.20887	GTG	G|0.938;A|0.062	0.062	strong		0.537	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
C2CD3	26005	hgsc.bcm.edu	37	11	73759254	73759254	+	Missense_Mutation	SNP	C	C	A	rs1632245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73759254C>A	ENST00000334126.7	-	28	5717	c.5491G>T	c.(5491-5493)Ggg>Tgg	p.G1831W	C2CD3_ENST00000313663.7_Missense_Mutation_p.G1831W			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1831			G -> W (in dbSNP:rs1632245).		brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					ACTCACCTCCCAGGAGAGGAG	0.443													C|||	243	0.0485224	0.1778	0.0115	5008	,	,		19111	0.0		0.0	False		,,,				2504	0.0				p.G1831W		Atlas-SNP	.											C2CD3_ENST00000334126,NS,carcinoma,+2,2	C2CD3	288	2	0			c.G5491T						PASS	.						58.0	53.0	55.0					11																	73759254		2200	4293	6493	SO:0001583	missense	26005	exon28			ACCTCCCAGGAGA	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.5491G>T	11.37:g.73759254C>A	ENSP00000334379:p.Gly1831Trp	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		76|76	0.0347985347985348|0.0347985347985348	71|71	0.1443089430894309|0.1443089430894309	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	C|C	12.63|12.63	1.994257|1.994257	0.35226|0.35226	.|.	.|.	ENSG00000168014|ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160|ENST00000538361	T;T;T|.	0.14266|.	2.91;2.93;2.52|.	4.75|4.75	0.796|0.796	0.18648|0.18648	.|.	0.878366|.	0.10272|.	N|.	0.694613|.	T|T	0.00328|0.00328	0.0010|0.0010	L|L	0.47716|0.47716	1.5|1.5	0.42535|0.42535	P|P	0.006946000000000008|0.006946000000000008	D|.	0.60575|.	0.988|.	P|.	0.62089|.	0.898|.	T|T	0.09640|0.09640	-1.0665|-1.0665	9|4	0.72032|.	D|.	0.01|.	.|.	3.8081|3.8081	0.08786|0.08786	0.0:0.518:0.1836:0.2984|0.0:0.518:0.1836:0.2984	rs1632245;rs52791226;rs1632245|rs1632245;rs52791226;rs1632245	1831|.	Q4AC94-1|.	.|.	W|L	1831;1831;1812;639|64	ENSP00000334379:G1831W;ENSP00000323339:G1831W;ENSP00000388750:G639W|.	ENSP00000323339:G1831W|.	G|W	-|-	1|2	0|0	C2CD3|C2CD3	73436902|73436902	0.919000|0.919000	0.31177|0.31177	0.959000|0.959000	0.39883|0.39883	0.175000|0.175000	0.22909|0.22909	0.834000|0.834000	0.27518|0.27518	0.312000|0.312000	0.23038|0.23038	0.655000|0.655000	0.94253|0.94253	GGG|TGG	A|0.037;C|0.963	0.037	strong		0.443	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
P2RX7	5027	hgsc.bcm.edu	37	12	121622115	121622115	+	Missense_Mutation	SNP	C	C	T	rs28360459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121622115C>T	ENST00000546057.1	+	13	1441	c.1298C>T	c.(1297-1299)gCg>gTg	p.A433V	P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000328963.5_Missense_Mutation_p.A263V|P2RX7_ENST00000541446.1_Missense_Mutation_p.A144V|P2RX7_ENST00000535250.1_Missense_Mutation_p.A343V	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	433			A -> V (in dbSNP:rs28360459).		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)					CAGAGACCTGCGATGGACTTC	0.453													C|||	177	0.0353435	0.1278	0.0115	5008	,	,		17958	0.0		0.0	False		,,,				2504	0.0				p.A433V		Atlas-SNP	.											.	P2RX7	53	.	0			c.C1298T						PASS	.	C	VAL/ALA	510,3896	235.5+/-248.0	29,452,1722	68.0	71.0	70.0		1298	-5.1	0.0	12	dbSNP_125	70	6,8594	3.7+/-12.6	0,6,4294	yes	missense	P2RX7	NM_002562.5	64	29,458,6016	TT,TC,CC		0.0698,11.5751,3.9674	benign	433/596	121622115	516,12490	2203	4300	6503	SO:0001583	missense	5027	exon13			GACCTGCGATGGA	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.1298C>T	12.37:g.121622115C>T	ENSP00000442349:p.Ala433Val	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	28	11	0.392857	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	63	0.028846153846153848	58	0.11788617886178862	5	0.013812154696132596	0	0.0	0	0.0	C	2.926	-0.222035	0.06061	0.115751	6.98E-4	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.05139	4.39;4.0;4.17;3.49	5.21	-5.06	0.02946	.	2.346980	0.01797	N	0.032678	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.14805	0.011;0.001;0.011;0.003	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.42865	-0.9426	9	0.39692	T	0.17	0.4342	1.6799	0.02830	0.4149:0.2708:0.0915:0.2229	rs28360459	263;144;343;433	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	V	433;263;343;144	ENSP00000442349:A433V;ENSP00000330696:A263V;ENSP00000442572:A343V;ENSP00000437471:A144V	ENSP00000330696:A263V	A	+	2	0	P2RX7	120106498	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.486000	0.06513	-0.443000	0.07180	-0.218000	0.12543	GCG	C|0.965;T|0.035	0.035	strong		0.453	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
TTN	7273	hgsc.bcm.edu	37	2	179435887	179435887	+	Missense_Mutation	SNP	A	A	G	rs744427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179435887A>G	ENST00000591111.1	-	276	70273	c.70049T>C	c.(70048-70050)aTt>aCt	p.I23350T	TTN_ENST00000589042.1_Missense_Mutation_p.I24991T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I15926T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I22423T|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I16051T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I16118T|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23350	Fibronectin type-III 69. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CGGCTTGCCAATGCCCACGAT	0.438													A|||	82	0.0163738	0.0582	0.0072	5008	,	,		22831	0.0		0.0	False		,,,				2504	0.0				p.I24991T		Atlas-SNP	.											.	TTN	18412	.	0			c.T74972C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE	193,3777		5,183,1797	107.0	108.0	107.0		48353,48152,67268,47777	4.1	0.9	2	dbSNP_86	107	1,8337		0,1,4168	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	5,184,5965	GG,GA,AA		0.012,4.8615,1.5762	benign,benign,benign,benign	16118/27119,16051/27052,22423/33424,15926/26927	179435887	194,12114	1985	4169	6154	SO:0001583	missense	7273	exon326			TTGCCAATGCCCA	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.70049T>C	2.37:g.179435887A>G	ENSP00000465570:p.Ile23350Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	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		42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	A	9.233	1.036446	0.19669	0.048615	1.2E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.28	4.13	0.48395	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02418	0.0074	L	0.33093	0.98	0.25488	N	0.987672	B;B;B;B	0.09022	0.0;0.0;0.002;0.002	B;B;B;B	0.09377	0.001;0.001;0.004;0.004	T	0.05419	-1.0886	9	0.87932	D	0	.	11.1794	0.48618	0.9275:0.0:0.0725:0.0	rs744427;rs52837048;rs744427	15926;16051;16118;23350	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	22423;15926;16118;16051;15924	ENSP00000343764:I22423T;ENSP00000434586:I15926T;ENSP00000340554:I16118T;ENSP00000352154:I16051T	ENSP00000340554:I16118T	I	-	2	0	TTN	179144133	1.000000	0.71417	0.915000	0.36163	0.984000	0.73092	6.333000	0.72939	0.959000	0.37980	-0.256000	0.11100	ATT	A|0.984;G|0.016	0.016	strong		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TGFBR3	7049	hgsc.bcm.edu	37	1	92177938	92177938	+	Silent	SNP	A	A	G	rs1805113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:92177938A>G	ENST00000525962.1	-	12	2089	c.2028T>C	c.(2026-2028)ttT>ttC	p.F676F	TGFBR3_ENST00000370399.2_Silent_p.F675F|TGFBR3_ENST00000212355.4_Silent_p.F676F			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	676	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				blastocyst development (GO:0001824)|blood vessel development (GO:0001568)|BMP signaling pathway (GO:0030509)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cell growth (GO:0016049)|cell migration (GO:0016477)|definitive erythrocyte differentiation (GO:0060318)|definitive hemopoiesis (GO:0060216)|epithelial to mesenchymal transition (GO:0001837)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|negative regulation of cellular component movement (GO:0051271)|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 transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of protein binding (GO:0043393)|response to follicle-stimulating hormone (GO:0032354)|response to hypoxia (GO:0001666)|response to luteinizing hormone (GO:0034699)|response to prostaglandin E (GO:0034695)|transforming growth factor beta receptor complex assembly (GO:0007181)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	coreceptor activity (GO:0015026)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|PDZ domain binding (GO:0030165)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type III (GO:0070123)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(24)|ovary(3)|prostate(4)|skin(1)|stomach(1)|urinary_tract(3)	55		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		GCGGGATAGGAAAGTGCACTC	0.428													A|||	1401	0.279752	0.3101	0.2882	5008	,	,		20898	0.0863		0.4304	False		,,,				2504	0.2771				p.F676F		Atlas-SNP	.											.	TGFBR3	103	.	0			c.T2028C						PASS	.	A	,,	1515,2891	481.0+/-359.0	255,1005,943	156.0	150.0	152.0		2025,2025,2028	-0.4	1.0	1	dbSNP_89	152	3750,4850	533.3+/-382.4	822,2106,1372	no	coding-synonymous,coding-synonymous,coding-synonymous	TGFBR3	NM_001195683.1,NM_001195684.1,NM_003243.4	,,	1077,3111,2315	GG,GA,AA		43.6047,34.3849,40.4813	,,	675/851,675/851,676/852	92177938	5265,7741	2203	4300	6503	SO:0001819	synonymous_variant	7049	exon13			GATAGGAAAGTGC	L07594	CCDS30770.1, CCDS55614.1	1p33-p32	2008-02-05	2007-02-15		ENSG00000069702	ENSG00000069702		"""Proteoglycans / Cell surface : Other"""	11774	protein-coding gene	gene with protein product	"""betaglycan proteoglycan"""	600742	"""transforming growth factor, beta receptor III (betaglycan, 300kDa)"""			1333192, 1319842	Standard	NM_001195684		Approved	betaglycan, BGCAN	uc001doh.3	Q03167	OTTHUMG00000010097	ENST00000525962.1:c.2028T>C	1.37:g.92177938A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	152	76	0.5	NM_003243	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Silent	SNP	ENST00000525962.1	37	CCDS30770.1																																																																																			A|0.655;G|0.345	0.345	strong		0.428	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634373	32634373	+	Silent	SNP	C	C	T	rs9274522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32634373C>T	ENST00000399082.3	-	1	56	c.12G>A	c.(10-12)aaG>aaA	p.K4K	HLA-DQB1_ENST00000399079.3_Silent_p.K4K|HLA-DQB1_ENST00000399084.1_Silent_p.K4K|HLA-DQB1_ENST00000374943.4_Silent_p.K4K|HLA-DQB1_ENST00000434651.2_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	36	0	0		WXS	Illumina HiSeq	Phase_I	10	10	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|0.670;T|0.330	0.330	strong		0.532	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
MT-ND5	4540	hgsc.bcm.edu	37	M	12477	12477	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:12477T>C	ENST00000361567.2	+	1	141	c.141T>C	c.(139-141)agT>agC	p.S47S	MT-TS2_ENST00000387449.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	47					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TTTATTATCAGTCTCTTCCCC	0.438																																					p.S47S		Atlas-SNP	.											.	.	.	.	0			c.T141C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TATCAGTCTCTTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.141T>C	M.37:g.12477T>C		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.438	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
OR2W5	441932	hgsc.bcm.edu	37	1	247655275	247655275	+	RNA	SNP	T	T	C	rs12141850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247655275T>C	ENST00000522351.1	+	0	906							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 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)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	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;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			ACCATCGTCATTCCCAGCATC	0.522													C|||	1620	0.323482	0.4629	0.2406	5008	,	,		16411	0.2619		0.3241	False		,,,				2504	0.2566				p.H282H		Atlas-SNP	.											.	OR2W5	97	.	0			c.T846C						PASS	.	C		1982,2424	618.2+/-393.1	459,1064,680	114.0	104.0	107.0		846	3.1	0.4	1	dbSNP_120	107	2614,5986	688.3+/-404.3	397,1820,2083	no	coding-synonymous	OR2W5	NM_001004698.2		856,2884,2763	CC,CT,TT		30.3953,44.9841,35.3375		282/321	247655275	4596,8410	2203	4300	6503			441932	exon1			TCGTCATTCCCAG			1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"""GPCR / Class A : Olfactory receptors"""	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		1.37:g.247655275T>C		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	191	85	0.445026	NM_001004698	B9EH85	Silent	SNP	ENST00000522351.1	37																																																																																				T|0.648;C|0.352	0.352	strong		0.522	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
MUC5B	727897	hgsc.bcm.edu	37	11	1267917	1267917	+	Silent	SNP	T	T	C	rs3021163		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1267917T>C	ENST00000529681.1	+	31	9865	c.9807T>C	c.(9805-9807)tcT>tcC	p.S3269S	MUC5B_ENST00000447027.1_Silent_p.S3272S|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3269	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)		CACCCTCCTCTACTCCAGAGA	0.647																																					p.S3269S		Atlas-SNP	.											MUC5B,NS,neuroblastoma,0,2	MUC5B	473	2	0			c.T9807C						PASS	.						107.0	138.0	128.0					11																	1267917		2063	4169	6232	SO:0001819	synonymous_variant	727897	exon31			CTCCTCTACTCCA	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.9807T>C	11.37:g.1267917T>C		Somatic	395	1	0.00253165		WXS	Illumina HiSeq	Phase_I	377	141	0.374005	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|1.000;|0.000	1.000	weak		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
WWOX	51741	hgsc.bcm.edu	37	16	78148935	78148935	+	Missense_Mutation	SNP	C	C	T	rs144601717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:78148935C>T	ENST00000566780.1	+	4	659	c.293C>T	c.(292-294)cCg>cTg	p.P98L	WWOX_ENST00000402655.2_Missense_Mutation_p.P98L|WWOX_ENST00000408984.3_Missense_Mutation_p.P98L|WWOX_ENST00000355860.3_Missense_Mutation_p.P98L|WWOX_ENST00000406884.2_Missense_Mutation_p.P98L|WWOX_ENST00000539474.2_Missense_Mutation_p.P98L	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	98			P -> L (in dbSNP:rs144601717). {ECO:0000269|PubMed:11572989}.		cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)			large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		GATGATAATCCGACCAAGCCA	0.502													C|||	54	0.0107827	0.0182	0.0086	5008	,	,		15548	0.0		0.0179	False		,,,				2504	0.0061				p.P98L		Atlas-SNP	.											.	WWOX	98	.	0			c.C293T						PASS	.	C	LEU/PRO,LEU/PRO	64,3644		0,64,1790	144.0	141.0	142.0		293,293	5.6	1.0	16	dbSNP_134	142	118,8072		0,118,3977	yes	missense,missense	WWOX	NM_016373.2,NM_130791.2	98,98	0,182,5767	TT,TC,CC		1.4408,1.726,1.5297	benign,benign	98/415,98/190	78148935	182,11716	1854	4095	5949	SO:0001583	missense	51741	exon4			ATAATCCGACCAA	AF187015	CCDS42196.1, CCDS42197.1	16q23.3-q24.1	2012-08-15	2002-01-14		ENSG00000186153	ENSG00000186153	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	12799	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 41C, member 1"""	605131	"""WW domain-containing oxidoreductase"""			10786676, 10861292, 19027726	Standard	XR_243411		Approved	FOR, WOX1, SDR41C1	uc002ffk.3	Q9NZC7	OTTHUMG00000176851	ENST00000566780.1:c.293C>T	16.37:g.78148935C>T	ENSP00000457230:p.Pro98Leu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	190	100	0.526316	NM_130791	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	37	CCDS42196.1	25	0.011446886446886446	10	0.02032520325203252	4	0.011049723756906077	0	0.0	11	0.014511873350923483	C	16.10	3.026678	0.54683	0.01726	0.014408	ENSG00000186153	ENST00000408984;ENST00000355860;ENST00000402655;ENST00000406884;ENST00000539474	T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34	5.6	5.6	0.85130	.	0.205378	0.43416	D	0.000569	T	0.29976	0.0750	L	0.50333	1.59	0.58432	D	0.999999	B;P;P;B	0.48764	0.152;0.915;0.602;0.09	B;B;B;B	0.35510	0.057;0.204;0.032;0.01	T	0.36286	-0.9754	10	0.30078	T	0.28	.	19.9823	0.97331	0.0:1.0:0.0:0.0	.	98;98;98;98	Q9NZC7-6;Q9NZC7-5;Q9NZC7;Q9NZC7-3	.;.;WWOX_HUMAN;.	L	98	ENSP00000386161:P98L;ENSP00000348119:P98L;ENSP00000384238:P98L;ENSP00000384495:P98L;ENSP00000445210:P98L	ENSP00000348119:P98L	P	+	2	0	WWOX	76706436	0.998000	0.40836	0.960000	0.40013	0.158000	0.22134	4.066000	0.57520	2.788000	0.95919	0.650000	0.86243	CCG	C|0.985;T|0.015	0.015	strong		0.502	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1		
CATSPER3	347732	hgsc.bcm.edu	37	5	134343661	134343661	+	Silent	SNP	C	C	T	rs10044000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134343661C>T	ENST00000282611.6	+	4	593	c.507C>T	c.(505-507)gcC>gcT	p.A169A		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	169					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.A169A(1)		NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGATCACCGCCGTGGGGCAGA	0.592													C|||	1358	0.271166	0.1467	0.2911	5008	,	,		13373	0.2569		0.4254	False		,,,				2504	0.2812				p.A169A		Atlas-SNP	.											CATSPER3,NS,carcinoma,0,1	CATSPER3	38	1	1	Substitution - coding silent(1)	stomach(1)	c.C507T						PASS	.	C		813,3593	324.8+/-298.8	65,683,1455	190.0	138.0	156.0		507	-2.0	0.0	5	dbSNP_119	156	3585,5015	518.2+/-379.2	751,2083,1466	no	coding-synonymous	CATSPER3	NM_178019.2		816,2766,2921	TT,TC,CC		41.686,18.4521,33.8152		169/399	134343661	4398,8608	2203	4300	6503	SO:0001819	synonymous_variant	347732	exon4			CACCGCCGTGGGG	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.507C>T	5.37:g.134343661C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	211	120	0.56872	NM_178019	Q86XS6	Silent	SNP	ENST00000282611.6	37	CCDS4181.1																																																																																			C|0.678;T|0.322	0.322	strong		0.592	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
NMRK2	27231	hgsc.bcm.edu	37	19	3942110	3942110	+	Missense_Mutation	SNP	G	G	A	rs16992131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3942110G>A	ENST00000168977.2	+	8	822	c.532G>A	c.(532-534)Gag>Aag	p.E178K	NMRK2_ENST00000593949.1_Missense_Mutation_p.E183K|NMRK2_ENST00000599576.1_Missense_Mutation_p.G109E	NM_170678.2	NP_733778.1	Q9NPI5	NRK2_HUMAN	nicotinamide riboside kinase 2	178			E -> K (in dbSNP:rs16992131).		NAD biosynthetic process (GO:0009435)|negative regulation of myoblast differentiation (GO:0045662)	intracellular (GO:0005622)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|ribosylnicotinamide kinase activity (GO:0050262)										GTCCCGAGAGGAGCTCTTCCG	0.642													G|||	117	0.0233626	0.084	0.0072	5008	,	,		15546	0.0		0.001	False		,,,				2504	0.0				p.E178K		Atlas-SNP	.											.	.	.	.	0			c.G532A						PASS	.	G	LYS/GLU	299,4107	154.4+/-187.8	9,281,1913	47.0	47.0	47.0		532	2.8	0.0	19	dbSNP_123	47	7,8593	5.0+/-18.6	0,7,4293	yes	missense	ITGB1BP3	NM_170678.2	56	9,288,6206	AA,AG,GG		0.0814,6.7862,2.3528	benign	178/231	3942110	306,12700	2203	4300	6503	SO:0001583	missense	27231	exon8			CGAGAGGAGCTCT	AF190819	CCDS12115.1, CCDS74259.1	19p13.3	2013-10-28	2012-05-31	2012-05-31	ENSG00000077009	ENSG00000077009			17871	protein-coding gene	gene with protein product	"""muscle-specific beta 1 integrin binding protein"", ""nicotinamide riboside kinase 2"""	608705	"""integrin beta 1 binding protein 3"""	ITGB1BP3		10613898, 15137942	Standard	NM_170678		Approved	MIBP, NRK2	uc002lyz.4	Q9NPI5	OTTHUMG00000181758	ENST00000168977.2:c.532G>A	19.37:g.3942110G>A	ENSP00000168977:p.Glu178Lys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_170678	B7ZKR3|Q52M81|Q9NZK3	Missense_Mutation	SNP	ENST00000168977.2	37	CCDS12115.1	41	0.018772893772893772	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	0	0.0	G	11.37	1.619506	0.28801	0.067862	8.14E-4	ENSG00000077009	ENST00000168977;ENST00000395034	T	0.59502	0.26	3.83	2.76	0.32466	.	0.214037	0.37437	U	0.002089	T	0.03959	0.0111	L	0.42245	1.32	0.31116	N	0.709375	B;P	0.37423	0.444;0.594	B;B	0.41412	0.356;0.231	T	0.08994	-1.0695	10	0.18710	T	0.47	-9.412	9.3096	0.37895	0.0:0.2212:0.7788:0.0	rs16992131;rs16992131	183;178	B7ZKR3;Q9NPI5	.;NRK2_HUMAN	K	178;134	ENSP00000168977:E178K	ENSP00000168977:E178K	E	+	1	0	ITGB1BP3	3893110	1.000000	0.71417	0.005000	0.12908	0.070000	0.16714	4.069000	0.57541	0.585000	0.29608	0.485000	0.47835	GAG	G|0.977;A|0.023	0.023	strong		0.642	NMRK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457492.1	NM_014446, NM_170678	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261717	39261717	+	Missense_Mutation	SNP	G	G	A	rs149483591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39261717G>A	ENST00000391415.1	+	1	134	c.77G>A	c.(76-78)cGc>cAc	p.R26H		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	26	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						ACCTGCTGCCGCCCCAGCTGC	0.647													G|||	272	0.0543131	0.1959	0.0173	5008	,	,		18818	0.0		0.001	False		,,,				2504	0.0				p.R26H		Atlas-SNP	.											KRTAP4-9,NS,carcinoma,+1,1	KRTAP4-9	110	1	0			c.G77A						scavenged	.	G	HIS/ARG	218,1166		12,194,486	16.0	21.0	19.0		77	-0.7	1.0	17	dbSNP_134	19	2,3178		0,2,1588	no	missense	KRTAP4-9	NM_001146041.1	29	12,196,2074	AA,AG,GG		0.0629,15.7514,4.8203	benign	26/211	39261717	220,4344	692	1590	2282	SO:0001583	missense	100132386	exon1			GCTGCCGCCCCAG	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.77G>A	17.37:g.39261717G>A	ENSP00000375234:p.Arg26His	Somatic	129	2	0.0155039		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	95	0.043498168498168496	89	0.18089430894308944	6	0.016574585635359115	0	0.0	0	0.0	.	10.53	1.376288	0.24857	0.157514	6.29E-4	ENSG00000212722	ENST00000391415;ENST00000333994	T	0.32515	1.45	3.31	-0.714	0.11219	.	.	.	.	.	T	0.00073	0.0002	M	0.79614	2.46	0.52099	P	5.999999999994898E-5	B	0.25521	0.128	B	0.20767	0.031	T	0.08310	-1.0728	8	0.37606	T	0.19	.	6.5459	0.22406	0.5339:0.0:0.4661:0.0	.	26	Q9BYQ8	KRA49_HUMAN	H	26	ENSP00000375234:R26H	ENSP00000334461:R26H	R	+	2	0	KRTAP4-9	36515243	0.000000	0.05858	0.986000	0.45419	0.476000	0.33039	-1.656000	0.01980	-0.101000	0.12219	0.194000	0.17425	CGC	G|0.956;A|0.044	0.044	strong		0.647	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
ITGA2B	3674	hgsc.bcm.edu	37	17	42457120	42457120	+	Silent	SNP	C	C	T	rs5912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42457120C>T	ENST00000262407.5	-	18	1846	c.1815G>A	c.(1813-1815)ccG>ccA	p.P605P	ITGA2B_ENST00000353281.4_Silent_p.P605P	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	605					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	CCTCCGTGGGCGGTAGGGACA	0.617													C|||	59	0.0117812	0.0318	0.0159	5008	,	,		19144	0.0		0.006	False		,,,				2504	0.0				p.P605P		Atlas-SNP	.											ITGA2B,colon,carcinoma,-1,1	ITGA2B	88	1	0			c.G1815A						PASS	.	C		174,4232	111.6+/-149.8	4,166,2033	94.0	82.0	86.0		1815	-3.7	0.0	17	dbSNP_52	86	67,8533	39.8+/-96.3	0,67,4233	no	coding-synonymous	ITGA2B	NM_000419.3		4,233,6266	TT,TC,CC		0.7791,3.9492,1.853		605/1040	42457120	241,12765	2203	4300	6503	SO:0001819	synonymous_variant	3674	exon18			CGTGGGCGGTAGG		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.1815G>A	17.37:g.42457120C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	37	CCDS32665.1																																																																																			C|0.982;T|0.018	0.018	strong		0.617	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		
OR52L1	338751	hgsc.bcm.edu	37	11	6007272	6007272	+	Missense_Mutation	SNP	A	A	G	rs4237768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6007272A>G	ENST00000332249.4	-	1	943	c.889T>C	c.(889-891)Tgg>Cgg	p.W297R		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	297			W -> R (in dbSNP:rs4237768). {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)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGGAGATACCATGTGGCCAGA	0.493													.|||	4152	0.829073	0.7821	0.8703	5008	,	,		22363	0.8681		0.8489	False		,,,				2504	0.8027				p.W297R	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											.	OR52L1	100	.	0			c.T889C						PASS	.	G	ARG/TRP	3295,887		1294,707,90	83.0	84.0	83.0		889	2.6	0.9	11	dbSNP_111	83	6994,1490		2886,1222,134	yes	missense	OR52L1	NM_001005173.2	101	4180,1929,224	GG,GA,AA		17.5625,21.2099,18.7668	benign	297/330	6007272	10289,2377	2091	4242	6333	SO:0001583	missense	338751	exon1			GATACCATGTGGC	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"""GPCR / Class A : Olfactory receptors"""	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.889T>C	11.37:g.6007272A>G	ENSP00000330338:p.Trp297Arg	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	140	67	0.478571	NM_001005173	B2RPA6|Q6IFK9	Missense_Mutation	SNP	ENST00000332249.4	37	CCDS44529.1	1845	0.8447802197802198	381	0.774390243902439	312	0.861878453038674	512	0.8951048951048951	640	0.8443271767810027	G	1.924	-0.447696	0.04572	0.787901	0.824375	ENSG00000183313	ENST00000332249	T	0.00084	8.75	3.54	2.62	0.31277	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39020	N	0.001486	T	0.00012	0.0000	M	0.94101	3.495	0.58432	P	1.999999999946489E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.48681	-0.9014	9	0.66056	D	0.02	.	5.0625	0.14564	0.1965:0.0:0.6388:0.1647	rs4237768;rs17265701;rs52807381;rs57331053;rs4237768	297	Q8NGH7	O52L1_HUMAN	R	297	ENSP00000330338:W297R	ENSP00000330338:W297R	W	-	1	0	OR52L1	5963848	0.000000	0.05858	0.947000	0.38551	0.008000	0.06430	-2.451000	0.01006	0.318000	0.23185	-1.803000	0.00618	TGG	A|0.165;G|0.835	0.835	strong		0.493	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173	
ZHX1	11244	hgsc.bcm.edu	37	8	124265676	124265676	+	Silent	SNP	C	C	T	rs34145851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124265676C>T	ENST00000522655.1	-	3	3051	c.2511G>A	c.(2509-2511)gaG>gaA	p.E837E	ZHX1_ENST00000522595.1_5'Flank|ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000395571.3_Silent_p.E837E|ZHX1_ENST00000297857.2_Silent_p.E837E			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	837	Required for repressor activity.				cell differentiation (GO:0030154)|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)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			CTTCATCTTCCTCCTCATTTT	0.398													C|||	69	0.013778	0.0514	0.0014	5008	,	,		18508	0.0		0.0	False		,,,				2504	0.0				p.E837E		Atlas-SNP	.											ZHX1,NS,carcinoma,-2,1	ZHX1	89	1	0			c.G2511A						PASS	.	C	,,	194,4212	122.9+/-160.3	4,186,2013	210.0	202.0	205.0		2511,,2511	1.6	1.0	8	dbSNP_126	205	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,coding-synonymous	ZHX1,ZHX1-C8ORF76	NM_001017926.2,NM_001204180.1,NM_007222.4	,,	4,187,6312	TT,TC,CC		0.0116,4.4031,1.4993	,,	837/874,,837/874	124265676	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	11244	exon3			ATCTTCCTCCTCA	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	12871	protein-coding gene	gene with protein product		604764	"""zinc-fingers and homeoboxes 1"""			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.2511G>A	8.37:g.124265676C>T		Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	311	149	0.4791	NM_007222	Q8IWD8	Silent	SNP	ENST00000522655.1	37	CCDS6342.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	5.662	0.306815	0.10733	0.044031	1.16E-4	ENSG00000165156	ENST00000520474	.	.	.	5.95	1.57	0.23409	.	.	.	.	.	T	0.20170	0.0485	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.09997	-1.0649	4	.	.	.	-14.7224	5.1468	0.14989	0.1123:0.5612:0.198:0.1285	rs34145851	.	.	.	K	522	.	.	R	-	2	0	ZHX1	124334857	0.995000	0.38212	0.997000	0.53966	0.983000	0.72400	0.381000	0.20619	0.384000	0.24942	0.491000	0.48974	AGG	C|0.986;T|0.014	0.014	strong		0.398	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1		
ITGA2	3673	hgsc.bcm.edu	37	5	52351377	52351377	+	Silent	SNP	T	T	C	rs1139484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	74	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	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	
OR8G5	219865	hgsc.bcm.edu	37	11	124135481	124135481	+	Silent	SNP	C	C	T	rs2466701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124135481C>T	ENST00000524943.2	+	1	759	c.759C>T	c.(757-759)taC>taT	p.Y253Y	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		TCAGCTCTTACATCTTCATCA	0.458													c|||	2196	0.438498	0.292	0.5591	5008	,	,		21111	0.5833		0.5527	False		,,,				2504	0.2843				p.Y253Y	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.C759T						PASS	.	C		1450,2878		253,944,967	134.0	132.0	133.0		759	-3.9	0.0	11	dbSNP_100	133	4688,3878		1298,2092,893	no	coding-synonymous	OR8G5	NM_001005198.1		1551,3036,1860	TT,TC,CC		45.272,33.5028,47.6035		253/347	124135481	6138,6756	2164	4283	6447	SO:0001819	synonymous_variant	219865	exon1			CTCTTACATCTTC	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.759C>T	11.37:g.124135481C>T		Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	268	268	1	NM_001005198	B2RND3|Q6IEU6	Silent	SNP	ENST00000524943.2	37																																																																																				C|0.521;T|0.479	0.479	strong		0.458	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
MED28	80306	hgsc.bcm.edu	37	4	17616349	17616349	+	Silent	SNP	G	G	A	rs146036794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:17616349G>A	ENST00000237380.7	+	1	96	c.72G>A	c.(70-72)ccG>ccA	p.P24P	AC006160.5_ENST00000511010.1_RNA	NM_025205.3	NP_079481.2	Q9H204	MED28_HUMAN	mediator complex subunit 28	24					negative regulation of smooth muscle cell differentiation (GO:0051151)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cortical actin cytoskeleton (GO:0030864)|mediator complex (GO:0016592)|membrane (GO:0016020)				lung(6)|skin(2)	8						CGGGCCTTCCGGGCCAAGCTT	0.587													G|||	27	0.00539137	0.0204	0.0	5008	,	,		14224	0.0		0.0	False		,,,				2504	0.0				p.P24P		Atlas-SNP	.											.	MED28	16	.	0			c.G72A						PASS	.	G		68,4338	54.9+/-90.9	1,66,2136	51.0	60.0	57.0		72	2.6	1.0	4	dbSNP_134	57	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MED28	NM_025205.3		1,68,6434	AA,AG,GG		0.0233,1.5433,0.5382		24/179	17616349	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	80306	exon1			CCTTCCGGGCCAA	AF317678	CCDS33963.1	4p16	2007-07-30	2007-07-30		ENSG00000118579	ENSG00000118579			24628	protein-coding gene	gene with protein product		610311	"""mediator of RNA polymerase II transcription, subunit 28 homolog (S. cerevisiae)"""			11779215, 15467741	Standard	NM_025205		Approved	EG1, DKFZP434N185, magicin	uc003gpi.1	Q9H204	OTTHUMG00000161980	ENST00000237380.7:c.72G>A	4.37:g.17616349G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_025205	Q9BZJ5	Silent	SNP	ENST00000237380.7	37	CCDS33963.1																																																																																			G|0.996;A|0.004	0.004	strong		0.587	MED28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360055.3	NM_025205	
SEL1L3	23231	hgsc.bcm.edu	37	4	25806319	25806319	+	Silent	SNP	C	C	T	rs34954596	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:25806319C>T	ENST00000399878.3	-	10	1742	c.1620G>A	c.(1618-1620)aaG>aaA	p.K540K	SEL1L3_ENST00000502949.1_Silent_p.K387K|SEL1L3_ENST00000264868.5_Silent_p.K505K	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	540						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						TCTTTACAGCCTTCTCAAATA	0.418													C|||	92	0.0183706	0.0015	0.0144	5008	,	,		19601	0.0188		0.0318	False		,,,				2504	0.0297				p.K540K		Atlas-SNP	.											.	SEL1L3	62	.	0			c.G1620A						PASS	.	C		20,3708		0,20,1844	113.0	107.0	109.0		1620	1.4	1.0	4	dbSNP_126	109	250,7988		5,240,3874	no	coding-synonymous	SEL1L3	NM_015187.3		5,260,5718	TT,TC,CC		3.0347,0.5365,2.2564		540/1133	25806319	270,11696	1864	4119	5983	SO:0001819	synonymous_variant	23231	exon10			TACAGCCTTCTCA	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.1620G>A	4.37:g.25806319C>T		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	270	130	0.481481	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Silent	SNP	ENST00000399878.3	37	CCDS47037.1																																																																																			C|0.978;T|0.022	0.022	strong		0.418	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994488	45994488	+	Missense_Mutation	SNP	G	G	T	rs396912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45994488G>T	ENST00000400374.3	+	1	883	c.853G>T	c.(853-855)Ggc>Tgc	p.G285C	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_5'Flank	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	285	36 X 5 AA repeats of C-C-X(3).		G -> C (in dbSNP:rs396912).			keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CAAGCCTGTCGGCTCTGTGCC	0.642													.|||	931	0.185903	0.3812	0.0937	5008	,	,		22814	0.2054		0.0368	False		,,,				2504	0.1207				p.G285C		Atlas-SNP	.											KRTAP10-4,colon,carcinoma,-1,1	KRTAP10-4	44	1	0			c.G853T						PASS	.	T	,CYS/GLY	1527,2879	669.8+/-402.2	259,1009,935	115.0	120.0	118.0		,853	1.9	0.0	21	dbSNP_80	118	266,8334	803.6+/-407.3	4,258,4038	no	intron,missense	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,159	263,1267,4973	TT,TG,GG		3.093,34.6573,13.7859	,benign	,285/402	45994488	1793,11213	2203	4300	6503	SO:0001583	missense	386672	exon1			CCTGTCGGCTCTG	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.853G>T	21.37:g.45994488G>T	ENSP00000383225:p.Gly285Cys	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	280	279	0.996429	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	365|365	0.1671245421245421|0.1671245421245421	181|181	0.3678861788617886|0.3678861788617886	33|33	0.09116022099447514|0.09116022099447514	130|130	0.22727272727272727|0.22727272727272727	21|21	0.027704485488126648|0.027704485488126648	T|t	0.403|0.403	-0.917088|-0.917088	0.02415|0.02415	0.346573|0.346573	0.03093|0.03093	ENSG00000215454|ENSG00000215454	ENST00000334871|ENST00000400374	.|T	.|0.00686	.|5.85	4.38|4.38	1.89|1.89	0.25635|0.25635	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	N|N	0.00019|0.00019	-2.79|-2.79	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	.|T	.|0.41698	.|-0.9494	.|8	.|0.02654	.|T	.|1	.|.	1.2795|1.2795	0.02037|0.02037	0.299:0.0913:0.154:0.4556|0.299:0.0913:0.154:0.4556	rs396912;rs396912|rs396912;rs396912	.|285	.|P60372	.|KR104_HUMAN	.|C	-1|285	.|ENSP00000383225:G285C	.|ENSP00000383225:G285C	.|G	+|+	.|1	.|0	KRTAP10-4|KRTAP10-4	44818916|44818916	0.040000|0.040000	0.19996|0.19996	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-0.499000|-0.499000	0.06413|0.06413	0.160000|0.160000	0.19432|0.19432	-0.320000|-0.320000	0.08662|0.08662	.|GGC	G|0.785;T|0.215	0.215	strong		0.642	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105924699	105924699	+	Silent	SNP	G	G	A	rs115690647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:105924699G>A	ENST00000393359.2	-	2	486	c.60C>T	c.(58-60)ggC>ggT	p.G20G	TGFBRAP1_ENST00000258449.1_Silent_p.G20G			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	20					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						GCTCCTTGTCGCCCATCAGCA	0.547													G|||	39	0.00778754	0.0295	0.0	5008	,	,		18930	0.0		0.0	False		,,,				2504	0.0				p.G20G	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C60T						PASS	.	G	,	101,4305	80.4+/-118.8	0,101,2102	42.0	41.0	42.0		60,60	-3.4	0.2	2	dbSNP_132	42	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TGFBRAP1	NM_001142621.1,NM_004257.4	,	0,101,6402	AA,AG,GG		0.0,2.2923,0.7766	,	20/861,20/861	105924699	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	9392	exon2			CTTGTCGCCCATC	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.60C>T	2.37:g.105924699G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_004257	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	37	CCDS2067.1																																																																																			G|0.990;A|0.010	0.010	strong		0.547	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
KIRREL2	84063	hgsc.bcm.edu	37	19	36349736	36349736	+	Silent	SNP	G	G	C	rs34006827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36349736G>C	ENST00000360202.5	+	4	690	c.492G>C	c.(490-492)ggG>ggC	p.G164G	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Silent_p.G164G|KIRREL2_ENST00000347900.6_Silent_p.G114G|KIRREL2_ENST00000262625.7_Silent_p.G164G	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	164	Ig-like C2-type 2.				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)			TCCGAGATGGGGTCCTGTTGG	0.577													G|||	187	0.0373403	0.0703	0.0259	5008	,	,		18578	0.0119		0.0258	False		,,,				2504	0.0389				p.G164G		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G492C						PASS	.	G	,,	274,4132	153.3+/-186.9	12,250,1941	107.0	103.0	104.0		492,342,492	2.1	1.0	19	dbSNP_126	104	288,8312	106.8+/-167.6	2,284,4014	no	coding-synonymous,coding-synonymous,coding-synonymous	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	,,	14,534,5955	CC,CG,GG		3.3488,6.2188,4.3211	,,	164/634,114/584,164/709	36349736	562,12444	2203	4300	6503	SO:0001819	synonymous_variant	84063	exon4			AGATGGGGTCCTG	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.492G>C	19.37:g.36349736G>C		Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	209	100	0.478469	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	37	CCDS12481.1																																																																																			G|0.963;C|0.037	0.037	strong		0.577	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
OR52E6	390078	hgsc.bcm.edu	37	11	5863013	5863013	+	Missense_Mutation	SNP	T	T	C	rs4362173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	154	0	0		WXS	Illumina HiSeq	Phase_I	175	94	0.537143	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	
NUMA1	4926	hgsc.bcm.edu	37	11	71718413	71718413	+	Missense_Mutation	SNP	C	C	T	rs149588226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71718413C>T	ENST00000393695.3	-	21	5616	c.5285G>A	c.(5284-5286)cGc>cAc	p.R1762H	NUMA1_ENST00000358965.6_Missense_Mutation_p.R1748H|NUMA1_ENST00000351960.6_Missense_Mutation_p.R626H	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						GGGGGGCAGGCGCTGGGAGAT	0.622			T	RARA	APL								C|||	14	0.00279553	0.0106	0.0	5008	,	,		17501	0.0		0.0	False		,,,				2504	0.0				p.R1762H		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.G5285A						PASS	.	C	HIS/ARG	72,4328	63.5+/-100.7	1,70,2129	40.0	43.0	42.0		5285	4.6	1.0	11	dbSNP_134	42	0,8586		0,0,4293	yes	missense	NUMA1	NM_006185.2	29	1,70,6422	TT,TC,CC		0.0,1.6364,0.5544	probably-damaging	1762/2116	71718413	72,12914	2200	4293	6493	SO:0001583	missense	4926	exon21			GGCAGGCGCTGGG	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.5285G>A	11.37:g.71718413C>T	ENSP00000377298:p.Arg1762His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	28	0.329412	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	4|4	0.0018315018315018315|0.0018315018315018315	4|4	0.008130081300813009|0.008130081300813009	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	20.5|20.5	3.994037|3.994037	0.74703|0.74703	0.016364|0.016364	0.0|0.0	ENSG00000137497|ENSG00000137497	ENST00000541584|ENST00000351960;ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	.|T;T;T	.|0.21543	.|2.0;2.46;2.46	4.58|4.58	4.58|4.58	0.56647|0.56647	.|.	.|0.000000	.|0.56097	.|D	.|0.000035	T|T	0.13329|0.13329	0.0323|0.0323	N|N	0.24115|0.24115	0.695|0.695	0.40559|0.40559	D|D	0.981196|0.981196	.|D;D;D;D	.|0.89917	.|0.999;0.999;0.999;1.0	.|P;D;P;D	.|0.67231	.|0.897;0.95;0.855;0.938	T|T	0.01587|0.01587	-1.1318|-1.1318	5|10	.|0.52906	.|T	.|0.07	.|.	6.077|6.077	0.19921|0.19921	0.0:0.7688:0.0:0.2312|0.0:0.7688:0.0:0.2312	.|.	.|1768;1748;1762;626	.|Q4LE64;Q14980-2;Q14980;Q9BTE9	.|.;.;NUMA1_HUMAN;.	T|H	611|626;1748;1762;1311;735	.|ENSP00000260051:R626H;ENSP00000351851:R1748H;ENSP00000377298:R1762H	.|ENSP00000260051:R626H	A|R	-|-	1|2	0|0	NUMA1|NUMA1	71396061|71396061	0.995000|0.995000	0.38212|0.38212	0.999000|0.999000	0.59377|0.59377	0.988000|0.988000	0.76386|0.76386	1.062000|1.062000	0.30555|0.30555	2.527000|2.527000	0.85204|0.85204	0.561000|0.561000	0.74099|0.74099	GCC|CGC	C|0.995;T|0.005	0.005	strong		0.622	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
EVPLL	645027	hgsc.bcm.edu	37	17	18284263	18284263	+	Silent	SNP	C	C	T	rs116412205|rs386795970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18284263C>T	ENST00000399134.4	+	2	370	c.12C>T	c.(10-12)agC>agT	p.S4S	RP1-37N7.1_ENST00000579352.1_RNA	NM_001145127.1	NP_001138599.1	A8MZ36	EVPLL_HUMAN	envoplakin-like	4			S -> N (in dbSNP:rs570145). {ECO:0000269|PubMed:14702039}.							NS(1)|endometrium(1)|large_intestine(1)|lung(2)	5						TGCAAGCCAGCGCCGACCAGG	0.657													.|||	71	0.0141773	0.0507	0.0058	5008	,	,		17727	0.0		0.0	False		,,,				2504	0.0				p.S4S		Atlas-SNP	.											.	EVPLL	10	.	0			c.C12T						PASS	.	C		32,1352		3,26,663	99.0	101.0	100.0		12	-0.7	1.0	17	dbSNP_132	100	0,3182		0,0,1591	no	coding-synonymous	EVPLL	NM_001145127.1		3,26,2254	TT,TC,CC		0.0,2.3121,0.7008		4/302	18284263	32,4534	692	1591	2283	SO:0001819	synonymous_variant	645027	exon2			AGCCAGCGCCGAC		CCDS45626.1	17p11.2	2009-08-25			ENSG00000214860	ENSG00000214860			35236	protein-coding gene	gene with protein product							Standard	NM_001145127		Approved		uc002gte.3	A8MZ36	OTTHUMG00000059095	ENST00000399134.4:c.12C>T	17.37:g.18284263C>T		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	242	100	0.413223	NM_001145127	B4DPD4	Silent	SNP	ENST00000399134.4	37	CCDS45626.1																																																																																			C|0.993;T|0.007	0.007	strong		0.657	EVPLL-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130836.2	NM_001145127	
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69094472	69094472	+	Silent	SNP	A	A	T	rs34044450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:69094472A>T	ENST00000332644.5	-	9	1238	c.1077T>A	c.(1075-1077)gcT>gcA	p.A359A		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	359	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.A359A(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						GACATGCATCAGCTTCTCCTG	0.323													A|||	48	0.00958466	0.0356	0.0014	5008	,	,		19437	0.0		0.0	False		,,,				2504	0.0				p.A359A		Atlas-SNP	.											TMPRSS11B,NS,carcinoma,0,1	TMPRSS11B	66	1	1	Substitution - coding silent(1)	lung(1)	c.T1077A						PASS	.	A		116,4290	88.2+/-126.9	2,112,2089	131.0	120.0	124.0		1077	-5.8	0.0	4	dbSNP_126	124	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	TMPRSS11B	NM_182502.3		2,120,6381	TT,TA,AA		0.093,2.6328,0.9534		359/417	69094472	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	132724	exon9			TGCATCAGCTTCT	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.1077T>A	4.37:g.69094472A>T		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	252	114	0.452381	NM_182502	A8K4D9	Silent	SNP	ENST00000332644.5	37	CCDS3521.1																																																																																			A|0.990;T|0.010	0.010	strong		0.323	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502	
SSPO	23145	hgsc.bcm.edu	37	7	149512267	149512267	+	RNA	SNP	C	C	T	rs142728666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149512267C>T	ENST00000378016.2	+	0	10587							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)			GCGTAGACTGCGGGGGTGGCC	0.667													C|||	46	0.0091853	0.0219	0.0029	5008	,	,		17602	0.0		0.002	False		,,,				2504	0.0133				p.C3529C		Atlas-SNP	.											.	.	.	.	0			c.C10587T						PASS	.	C		80,4040		1,78,1981	37.0	44.0	42.0		10597	-3.0	0.8	7	dbSNP_134	42	16,8358		0,16,4171	yes	coding-notMod3	SSPO	NM_198455.2		1,94,6152	TT,TC,CC		0.1911,1.9417,0.7684			149512267	96,12398	2060	4187	6247			23145	exon75			AGACTGCGGGGGT	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.149512267C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.996;T|0.004	0.004	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
ABCB11	8647	hgsc.bcm.edu	37	2	169842746	169842746	+	Silent	SNP	T	T	C	rs7563233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:169842746T>C	ENST00000263817.6	-	10	1081	c.957A>G	c.(955-957)ggA>ggG	p.G319G		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	319	ABC transmembrane type-1 1. {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)			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)	CCATCACTATTCCTTTTCTAA	0.438													C|||	610	0.121805	0.3964	0.049	5008	,	,		17824	0.001		0.0179	False		,,,				2504	0.0337				p.G319G		Atlas-SNP	.											.	ABCB11	136	.	0			c.A957G						PASS	.	C		1159,2621		179,801,910	146.0	138.0	141.0		957	-2.4	0.8	2	dbSNP_116	141	189,8051		3,183,3934	no	coding-synonymous	ABCB11	NM_003742.2		182,984,4844	CC,CT,TT		2.2937,30.6614,11.2146		319/1322	169842746	1348,10672	1890	4120	6010	SO:0001819	synonymous_variant	8647	exon10			CACTATTCCTTTT	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.957A>G	2.37:g.169842746T>C		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	37	CCDS46444.1																																																																																			T|0.885;C|0.115	0.115	strong		0.438	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
ITPR1	3708	hgsc.bcm.edu	37	3	4856234	4856234	+	Silent	SNP	G	G	A	rs901854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:4856234G>A	ENST00000443694.2	+	55	7644	c.7644G>A	c.(7642-7644)aaG>aaA	p.K2548K	ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000456211.2_Silent_p.K2500K|AC018816.3_ENST00000441894.1_Intron|AC018816.3_ENST00000449914.1_Intron|AC018816.3_ENST00000489771.1_Intron|ITPR1_ENST00000423119.2_Silent_p.K2515K|ITPR1_ENST00000544951.1_Silent_p.K526K|ITPR1_ENST00000354582.6_Silent_p.K2548K|ITPR1_ENST00000302640.8_Silent_p.K2548K|ITPR1_ENST00000357086.4_Silent_p.K2515K			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	102	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	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	
BRCA2	675	hgsc.bcm.edu	37	13	32912299	32912299	+	Silent	SNP	T	T	C	rs543304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:32912299T>C	ENST00000380152.3	+	11	4040	c.3807T>C	c.(3805-3807)gtT>gtC	p.V1269V	BRCA2_ENST00000544455.1_Silent_p.V1269V			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1269					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		ATGATTCTGTTGTTTCAATGT	0.274			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			T|||	842	0.168131	0.1846	0.1527	5008	,	,		19007	0.1726		0.1998	False		,,,				2504	0.1196				p.V1269V	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.T3807C						PASS	.	T		874,3532	313.0+/-292.9	86,702,1415	27.0	28.0	28.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3807	1.6	0.0	13	dbSNP_83	28	1610,6982	278.0+/-293.2	150,1310,2836	no	coding-synonymous	BRCA2	NM_000059.3		236,2012,4251	CC,CT,TT		18.7384,19.8366,19.1106		1269/3419	32912299	2484,10514	2203	4296	6499	SO:0001819	synonymous_variant	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TTCTGTTGTTTCA	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.3807T>C	13.37:g.32912299T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																			C|0.187;N|0.000;T|0.813	0.187	strong		0.274	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
KDM4C	23081	hgsc.bcm.edu	37	9	7013874	7013874	+	Silent	SNP	C	C	T	rs35006356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:7013874C>T	ENST00000381309.3	+	14	2620	c.2055C>T	c.(2053-2055)ctC>ctT	p.L685L	KDM4C_ENST00000428870.2_Silent_p.L372L|KDM4C_ENST00000442236.2_Silent_p.L430L|KDM4C_ENST00000535193.1_Silent_p.L707L|KDM4C_ENST00000543771.1_Silent_p.L685L|KDM4C_ENST00000381306.3_Silent_p.L685L|KDM4C_ENST00000536108.1_Silent_p.L504L	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	685					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						CTAAGCCCCTCATACCAGAGA	0.388													C|||	36	0.0071885	0.0265	0.0	5008	,	,		19797	0.0		0.001	False		,,,				2504	0.0				p.L707L		Atlas-SNP	.											.	KDM4C	186	.	0			c.C2121T						PASS	.	C	,,,	96,4310	77.8+/-116.1	1,94,2108	118.0	114.0	115.0		2055,2055,2121,2055	1.3	1.0	9	dbSNP_126	115	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	,,,	1,94,6408	TT,TC,CC		0.0,2.1788,0.7381	,,,	685/1048,685/814,707/836,685/1057	7013874	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	23081	exon14			GCCCCTCATACCA	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.2055C>T	9.37:g.7013874C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Silent	SNP	ENST00000381309.3	37	CCDS6471.1																																																																																			C|0.993;T|0.007	0.007	strong		0.388	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
KRT84	3890	hgsc.bcm.edu	37	12	52777513	52777513	+	Missense_Mutation	SNP	T	T	C	rs2245203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52777513T>C	ENST00000257951.3	-	2	682	c.616A>G	c.(616-618)Atc>Gtc	p.I206V	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	206	Linker 1.|Rod.		I -> V (in dbSNP:rs2245203).		hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TTGCTCCTGATACATTTCTGC	0.537													C|||	1664	0.332268	0.6172	0.3199	5008	,	,		21008	0.1954		0.2068	False		,,,				2504	0.226				p.I206V		Atlas-SNP	.											.	KRT84	61	.	0			c.A616G						PASS	.	C	VAL/ILE	2466,1940	551.8+/-378.4	717,1032,454	77.0	76.0	76.0		616	3.1	1.0	12	dbSNP_100	76	1804,6796	733.1+/-406.9	180,1444,2676	yes	missense	KRT84	NM_033045.3	29	897,2476,3130	CC,CT,TT		20.9767,44.0309,32.831	benign	206/601	52777513	4270,8736	2203	4300	6503	SO:0001583	missense	3890	exon2			TCCTGATACATTT	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.616A>G	12.37:g.52777513T>C	ENSP00000257951:p.Ile206Val	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	664	0.304029304029304	288	0.5853658536585366	100	0.27624309392265195	117	0.20454545454545456	159	0.20976253298153033	C	8.846	0.943350	0.18281	0.559691	0.209767	ENSG00000161849	ENST00000257951	D	0.88354	-2.37	5.32	3.07	0.35406	Filament (1);	0.423150	0.20341	N	0.094240	T	0.00012	0.0000	N	0.01515	-0.825	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45381	-0.9265	9	0.14656	T	0.56	.	9.4999	0.39011	0.0:0.735:0.0:0.265	rs2245203;rs58066728;rs2245203	206	Q9NSB2	KRT84_HUMAN	V	206	ENSP00000257951:I206V	ENSP00000257951:I206V	I	-	1	0	KRT84	51063780	0.006000	0.16342	0.989000	0.46669	0.760000	0.43138	0.122000	0.15687	0.440000	0.26502	-0.119000	0.15052	ATC	T|0.684;C|0.316	0.316	strong		0.537	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
LEKR1	389170	hgsc.bcm.edu	37	3	156763279	156763279	+	Silent	SNP	C	C	T	rs73873779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:156763279C>T	ENST00000470811.1	+	14	2242	c.907C>T	c.(907-909)Cta>Tta	p.L303L	LEKR1_ENST00000356539.4_Silent_p.L607L			Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1	303										breast(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	11			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CAAGGGCAGCCTAACCTCCCC	0.522													C|||	1012	0.202077	0.4788	0.0562	5008	,	,		19648	0.1617		0.0129	False		,,,				2504	0.1677				p.L607L		Atlas-SNP	.											.	LEKR1	66	.	0			c.C1819T						PASS	.	C		1765,2641	525.2+/-371.5	357,1051,795	87.0	88.0	88.0		1819	3.3	0.6	3	dbSNP_130	88	115,8485	59.8+/-121.6	1,113,4186	no	coding-synonymous	LEKR1	NM_001004316.2		358,1164,4981	TT,TC,CC		1.3372,40.059,14.4549		607/693	156763279	1880,11126	2203	4300	6503	SO:0001819	synonymous_variant	389170	exon13			GGCAGCCTAACCT	AK131473	CCDS54660.1	3q25.31	2014-02-12	2008-02-21		ENSG00000197980	ENSG00000197980			33765	protein-coding gene	gene with protein product		613536					Standard	NM_001004316		Approved	FLJ16641	uc021xgh.1	Q6ZMV7	OTTHUMG00000160130	ENST00000470811.1:c.907C>T	3.37:g.156763279C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_001004316		Silent	SNP	ENST00000470811.1	37																																																																																				C|0.852;T|0.148	0.148	strong		0.522	LEKR1-010	KNOWN	upstream_ATG|basic	protein_coding	protein_coding	OTTHUMT00000351625.3	NM_001004316	
OR6K3	391114	hgsc.bcm.edu	37	1	158687163	158687163	+	Missense_Mutation	SNP	G	G	A	rs28568406	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158687163G>A	ENST00000368146.1	-	1	790	c.791C>T	c.(790-792)cCg>cTg	p.P264L	OR6K3_ENST00000368145.1_Missense_Mutation_p.P248L			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	264			P -> L (in dbSNP:rs28568406). {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)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					AAAGAATATCGGGAAGACCAT	0.453													A|||	1948	0.388978	0.4773	0.4323	5008	,	,		22981	0.4474		0.3966	False		,,,				2504	0.1708				p.P248L		Atlas-SNP	.											.	OR6K3	101	.	0			c.C743T						PASS	.	A	LEU/PRO	2096,2310	603.5+/-390.1	496,1104,603	131.0	112.0	118.0		743	3.8	0.0	1	dbSNP_125	118	3256,5344	649.7+/-400.6	613,2030,1657	yes	missense	OR6K3	NM_001005327.2	98	1109,3134,2260	AA,AG,GG		37.8605,47.5715,41.1502	benign	248/316	158687163	5352,7654	2203	4300	6503	SO:0001583	missense	391114	exon1			AATATCGGGAAGA	AB065633	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			ENSG00000203757	ENSG00000203757		"""GPCR / Class A : Olfactory receptors"""	15030	protein-coding gene	gene with protein product							Standard	NM_001005327		Approved		uc021pbn.1	Q8NGY3	OTTHUMG00000022770	ENST00000368146.1:c.791C>T	1.37:g.158687163G>A	ENSP00000357128:p.Pro264Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	134	132	0.985075	NM_001005327	Q5VUV0|Q6IFR5	Missense_Mutation	SNP	ENST00000368146.1	37		913	0.41804029304029305	225	0.4573170731707317	152	0.4198895027624309	238	0.4160839160839161	298	0.39313984168865435	A	1.380	-0.583678	0.03827	0.475715	0.378605	ENSG00000203757	ENST00000368145;ENST00000368146	T;T	0.32988	1.43;1.43	3.77	3.77	0.43336	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01092	0.0036	N	0.00022	-2.74	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.43196	-0.9406	8	0.07325	T	0.83	.	8.466	0.32956	0.9021:0.0:0.0979:0.0	rs28568406;rs52822126;rs57495154	264	Q8NGY3	OR6K3_HUMAN	L	248;264	ENSP00000357127:P248L;ENSP00000357128:P264L	ENSP00000357127:P248L	P	-	2	0	OR6K3	156953787	0.000000	0.05858	0.001000	0.08648	0.446000	0.32137	0.037000	0.13840	0.606000	0.29965	-0.516000	0.04426	CCG	G|0.585;A|0.415	0.415	strong		0.453	OR6K3-201	KNOWN	basic	protein_coding	protein_coding			
CDC20B	166979	hgsc.bcm.edu	37	5	54420799	54420799	+	Silent	SNP	A	A	C	rs382402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:54420799A>C	ENST00000381375.2	-	9	1192	c.1047T>G	c.(1045-1047)gtT>gtG	p.V349V	CDC20B_ENST00000334206.5_3'UTR|CDC20B_ENST00000296733.1_Silent_p.V349V|CDC20B_ENST00000322374.6_Silent_p.V349V			Q86Y33	CD20B_HUMAN	cell division cycle 20B	349								p.V349V(1)		kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			GAAGTGTTCCAACATGATGCT	0.507													A|||	858	0.171326	0.0424	0.147	5008	,	,		17943	0.1915		0.2147	False		,,,				2504	0.2975				p.V349V		Atlas-SNP	.											CDC20B,NS,carcinoma,0,1	CDC20B	61	1	1	Substitution - coding silent(1)	stomach(1)	c.T1047G						PASS	.	A	,,	288,4118	160.7+/-193.0	15,258,1930	140.0	120.0	127.0		1047,1047,1047	-9.3	0.0	5	dbSNP_80	127	1641,6959	302.4+/-305.9	160,1321,2819	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC20B	NM_001145734.2,NM_001170402.1,NM_152623.2	,,	175,1579,4749	CC,CA,AA		19.0814,6.5365,14.8316	,,	349/478,349/520,349/516	54420799	1929,11077	2203	4300	6503	SO:0001819	synonymous_variant	166979	exon9			TGTTCCAACATGA	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.1047T>G	5.37:g.54420799A>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Silent	SNP	ENST00000381375.2	37	CCDS54852.1																																																																																			A|0.851;C|0.149	0.149	strong		0.507	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
C16orf82	162083	hgsc.bcm.edu	37	16	27078545	27078545	+	lincRNA	SNP	C	C	T	rs386790113|rs185409807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27078545C>T	ENST00000505035.1	+	0	518				RP11-673P17.2_ENST00000565783.1_RNA			Q7Z2V1	TNT_HUMAN	chromosome 16 open reading frame 82																		CGTGCAGCACCCGAGGCCAGA	0.652													C|||	96	0.0191693	0.0711	0.0014	5008	,	,		16664	0.0		0.001	False		,,,				2504	0.0				p.P77S		Atlas-SNP	.											.	.	.	.	0			c.C229T						PASS	.						23.0	31.0	28.0					16																	27078545		2188	4290	6478			162083	exon1			CAGCACCCGAGGC	BC031257		16p12.1	2013-01-24			ENSG00000234186	ENSG00000234186			30755	other	unknown						12477932	Standard	NM_001145545		Approved	TNT	uc010vcm.2	Q7Z2V1	OTTHUMG00000161986		16.37:g.27078545C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_001145545	B9EGC2|Q8NEF0	Missense_Mutation	SNP	ENST00000505035.1	37																																																																																				C|0.982;T|0.018	0.018	strong		0.652	C16orf82-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000366634.1	NM_001145545	
IGJ	3512	hgsc.bcm.edu	37	4	71522999	71522999	+	Silent	SNP	C	C	T	rs75928327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71522999C>T	ENST00000254801.4	-	3	367	c.198G>A	c.(196-198)ctG>ctA	p.L66L	IGJ_ENST00000543780.1_Silent_p.L82L|ENAM_ENST00000472903.1_Intron	NM_144646.3	NP_653247.1	P01591	IGJ_HUMAN	immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides	66					adaptive immune response (GO:0002250)|antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of respiratory burst (GO:0060267)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|dimeric IgA immunoglobulin complex (GO:0071750)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|pentameric IgM immunoglobulin complex (GO:0071756)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7			Lung(101;0.235)			CCCTGTTGTTCAGAGGAACAC	0.328													C|||	45	0.00898562	0.034	0.0	5008	,	,		16873	0.0		0.0	False		,,,				2504	0.0				p.L66L		Atlas-SNP	.											.	IGJ	13	.	0			c.G198A						PASS	.	C		103,4303	82.9+/-121.4	0,103,2100	81.0	77.0	78.0		198	4.7	1.0	4	dbSNP_132	78	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	IGJ	NM_144646.3		0,105,6396	TT,TC,CC		0.0233,2.3377,0.8076		66/160	71522999	105,12897	2203	4298	6501	SO:0001819	synonymous_variant	3512	exon3			GTTGTTCAGAGGA	M12759	CCDS3545.1	4q21	2012-10-02			ENSG00000132465	ENSG00000132465		"""Immunoglobulins / IGJ linker"""	5713	protein-coding gene	gene with protein product	"""immunoglobulin J chain"", ""IgJ chain"""	147790				3016707, 2984306	Standard	NM_144646		Approved	IGCJ, JCH	uc003hfn.4	P01591	OTTHUMG00000129909	ENST00000254801.4:c.198G>A	4.37:g.71522999C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_144646		Silent	SNP	ENST00000254801.4	37	CCDS3545.1																																																																																			C|0.990;T|0.010	0.010	strong		0.328	IGJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252160.1	NM_144646	
RANBP2	5903	hgsc.bcm.edu	37	2	109347314	109347314	+	Missense_Mutation	SNP	C	C	G	rs144278795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:109347314C>G	ENST00000283195.6	+	3	351	c.225C>G	c.(223-225)aaC>aaG	p.N75K		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	75					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TGGAAGAAAACACAGACAAAG	0.353													C|||	16	0.00319489	0.0083	0.0058	5008	,	,		16939	0.0		0.001	False		,,,				2504	0.0				p.N75K		Atlas-SNP	.											.	RANBP2	488	.	0			c.C225G						PASS	.	C	LYS/ASN	19,2931		0,19,1456	102.0	123.0	115.0		225	-0.8	0.8	2	dbSNP_134	115	0,5138		0,0,2569	no	missense	RANBP2	NM_006267.4	94	0,19,4025	GG,GC,CC		0.0,0.6441,0.2349	probably-damaging	75/3225	109347314	19,8069	1475	2569	4044	SO:0001583	missense	5903	exon3			AGAAAACACAGAC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.225C>G	2.37:g.109347314C>G	ENSP00000283195:p.Asn75Lys	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	296	142	0.47973	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.833077	0.50951	0.006441	0.0	ENSG00000153201	ENST00000409491;ENST00000283195;ENST00000456637	T	0.61392	0.11	4.24	-0.825	0.10809	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.	.	.	.	T	0.56645	0.1999	L	0.55103	1.725	0.27121	N	0.962148	D	0.61080	0.989	P	0.62435	0.902	T	0.55854	-0.8075	9	0.45353	T	0.12	-19.048	9.7309	0.40361	0.0:0.4107:0.0:0.5893	.	75	P49792	RBP2_HUMAN	K	75;75;49	ENSP00000283195:N75K	ENSP00000283195:N75K	N	+	3	2	RANBP2	108713746	0.342000	0.24809	0.759000	0.31340	0.848000	0.48234	-0.351000	0.07711	-0.299000	0.08909	-0.237000	0.12165	AAC	C|0.996;G|0.004	0.004	strong		0.353	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
NRP1	8829	hgsc.bcm.edu	37	10	33469181	33469181	+	Silent	SNP	A	A	G	rs1048804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:33469181A>G	ENST00000265371.4	-	18	3120	c.2595T>C	c.(2593-2595)agT>agC	p.S865S	NRP1_ENST00000374867.2_Silent_p.S865S|NRP1_ENST00000395995.1_Silent_p.S848S|NRP1_ENST00000374875.1_Silent_p.S677S			O14786	NRP1_HUMAN	neuropilin 1	865					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.S865S(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)	CCCCCAGGGCACTCATGGCTA	0.532													G|||	2125	0.424321	0.5666	0.2061	5008	,	,		18341	0.622		0.2455	False		,,,				2504	0.3671				p.S865S	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											NRP1,NS,carcinoma,0,1	NRP1	126	1	1	Substitution - coding silent(1)	stomach(1)	c.T2595C						PASS	.	G		2210,2196	585.1+/-386.2	574,1062,567	187.0	177.0	181.0		2595	-4.9	0.8	10	dbSNP_86	181	2024,6576	721.1+/-406.3	223,1578,2499	no	coding-synonymous	NRP1	NM_003873.5		797,2640,3066	GG,GA,AA		23.5349,49.8411,32.5542		865/924	33469181	4234,8772	2203	4300	6503	SO:0001819	synonymous_variant	8829	exon17			CAGGGCACTCATG	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.2595T>C	10.37:g.33469181A>G		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	304	157	0.516447	NM_003873	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Silent	SNP	ENST00000265371.4	37	CCDS7177.1																																																																																			A|0.634;G|0.366	0.366	strong		0.532	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
MICA	100507436	hgsc.bcm.edu	37	6	31379795	31379795	+	Missense_Mutation	SNP	A	A	G	rs1131898|rs386699191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31379795A>G	ENST00000449934.2	+	4	739	c.685A>G	c.(685-687)Agc>Ggc	p.S229G	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)				CAGGGCTTCCAGCTTCTATCC	0.587													g|||	1823	0.364018	0.4773	0.4063	5008	,	,		19594	0.2996		0.3141	False		,,,				2504	0.2986				p.S229G		Atlas-SNP	.											.	MICA	21	.	0			c.A685G						PASS	.						20.0	24.0	23.0					6																	31379795		692	1591	2283	SO:0001583	missense	100507436	exon4			GCTTCCAGCTTCT	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.685A>G	6.37:g.31379795A>G	ENSP00000413079:p.Ser229Gly	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	664	0.304029304029304	188	0.3821138211382114	147	0.40607734806629836	134	0.23426573426573427	195	0.25725593667546176	N	0.013	-1.630927	0.00813	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.09163	3.01;3.01	2.52	-1.92	0.07618	.	1.300610	0.05734	N	0.600057	T	0.00967	0.0032	.	.	.	0.80722	P	0.0	B;B	0.14012	0.009;0.003	B;B	0.08055	0.003;0.001	T	0.43310	-0.9399	8	0.02654	T	1	.	8.8893	0.35423	0.6127:0.0:0.3873:0.0	rs1131898;rs3192173;rs17206701;rs17883642	91;229	Q5SS58;Q96QC4	.;.	G	91;229;186;229;120	ENSP00000413079:S229G;ENSP00000402410:S120G	ENSP00000365394:S229G	S	+	1	0	MICA	31487774	0.015000	0.18098	0.001000	0.08648	0.014000	0.08584	0.171000	0.16685	-0.782000	0.04541	-1.366000	0.01203	AGC	A|0.700;G|0.300	0.300	strong		0.587	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
NEB	4703	hgsc.bcm.edu	37	2	152496526	152496526	+	Missense_Mutation	SNP	A	A	G	rs6713162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152496526A>G	ENST00000172853.10	-	62	8881	c.8734T>C	c.(8734-8736)Tcc>Ccc	p.S2912P	NEB_ENST00000603639.1_Missense_Mutation_p.S2912P|NEB_ENST00000409198.1_Missense_Mutation_p.S2912P|NEB_ENST00000604864.1_Missense_Mutation_p.S2912P|NEB_ENST00000397345.3_Missense_Mutation_p.S2912P|NEB_ENST00000427231.2_Missense_Mutation_p.S2912P			P20929	NEBU_HUMAN	nebulin	2912			S -> P (in dbSNP:rs6713162).		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)	p.S2912P(1)		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)		GAGCCAATGGACACCCAGCCA	0.393													G|||	2230	0.445288	0.7201	0.1628	5008	,	,		19009	0.6339		0.174	False		,,,				2504	0.3589				p.S2912P		Atlas-SNP	.											NEB,NS,carcinoma,0,1	NEB	1697	1	1	Substitution - Missense(1)	stomach(1)	c.T8734C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER	2256,1518		681,894,312	113.0	121.0	118.0		8734,8734,8734	5.5	1.0	2	dbSNP_116	118	1358,6874		124,1110,2882	yes	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	74,74,74	805,2004,3194	GG,GA,AA		16.4966,40.2226,30.1016	benign,benign,benign	2912/8526,2912/8526,2912/6670	152496526	3614,8392	1887	4116	6003	SO:0001583	missense	4703	exon62			CAATGGACACCCA	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.8734T>C	2.37:g.152496526A>G	ENSP00000172853:p.Ser2912Pro	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		907	0.4152930402930403	355	0.7215447154471545	70	0.19337016574585636	354	0.6188811188811189	128	0.16886543535620052	G	7.903	0.734863	0.15574	0.597774	0.164966	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.04234	3.73;3.67;3.68;3.97	5.46	5.46	0.80206	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00029	-2.615	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36601	-0.9741	9	0.02654	T	1	.	14.4749	0.67539	0.0707:0.0:0.9293:0.0	rs6713162;rs52824461;rs57895848;rs6713162	2912	P20929	NEBU_HUMAN	P	2912	ENSP00000386259:S2912P;ENSP00000380505:S2912P;ENSP00000416578:S2912P;ENSP00000172853:S2912P	ENSP00000172853:S2912P	S	-	1	0	NEB	152204772	1.000000	0.71417	0.995000	0.50966	0.961000	0.63080	5.546000	0.67243	1.332000	0.45431	-0.119000	0.15052	TCC	A|0.570;G|0.430	0.430	strong		0.393	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
DOCK8	81704	hgsc.bcm.edu	37	9	382646	382646	+	Silent	SNP	C	C	T	rs116523732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:382646C>T	ENST00000453981.1	+	22	2851	c.2739C>T	c.(2737-2739)tcC>tcT	p.S913S	DOCK8_ENST00000382331.1_Silent_p.S215S|DOCK8_ENST00000382329.1_Silent_p.S380S|DOCK8_ENST00000469391.1_Silent_p.S845S|DOCK8_ENST00000432829.2_Silent_p.S845S			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	913					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)		GGACACACTCCGCAGCAGACG	0.507													C|||	56	0.0111821	0.0386	0.0072	5008	,	,		20060	0.0		0.0	False		,,,				2504	0.0				p.S913S		Atlas-SNP	.											.	DOCK8	401	.	0			c.C2739T						PASS	.	C	,,	139,4267	98.9+/-137.6	2,135,2066	61.0	53.0	56.0		2535,2535,2739	-6.7	0.0	9	dbSNP_132	56	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	2,137,6364	TT,TC,CC		0.0233,3.1548,1.0841	,,	845/2000,845/2032,913/2100	382646	141,12865	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon22			ACACTCCGCAGCA	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.2739C>T	9.37:g.382646C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			C|0.991;T|0.009	0.009	strong		0.507	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
EMC1	23065	hgsc.bcm.edu	37	1	19565344	19565344	+	Missense_Mutation	SNP	C	C	G	rs709683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19565344C>G	ENST00000477853.1	-	10	1076	c.1034G>C	c.(1033-1035)aGt>aCt	p.S345T	EMC1_ENST00000375199.3_Missense_Mutation_p.S344T|RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375208.3_Missense_Mutation_p.S323T	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	345			S -> T (in dbSNP:rs709683). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16303743}.			ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											AGAACTGCTACTTTTCTGCTA	0.458													G|||	2866	0.572284	0.7315	0.5101	5008	,	,		18872	0.7401		0.3469	False		,,,				2504	0.4601				p.S345T		Atlas-SNP	.											.	.	.	.	0			c.G1034C						PASS	.	G	THR/SER	3012,1394	458.0+/-351.8	1047,918,238	116.0	124.0	121.0		1034	5.2	0.9	1	dbSNP_86	121	3095,5505	659.4+/-401.7	566,1963,1771	yes	missense	KIAA0090	NM_015047.1	58	1613,2881,2009	GG,GC,CC		35.9884,31.6387,46.9553	benign	345/994	19565344	6107,6899	2203	4300	6503	SO:0001583	missense	23065	exon10			CTGCTACTTTTCT		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.1034G>C	1.37:g.19565344C>G	ENSP00000420608:p.Ser345Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_001271428	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	37	CCDS190.1	1224|1224	0.5604395604395604|0.5604395604395604	361|361	0.733739837398374|0.733739837398374	167|167	0.4613259668508287|0.4613259668508287	431|431	0.7534965034965035|0.7534965034965035	265|265	0.3496042216358839|0.3496042216358839	G|G	7.688|7.688	0.690412|0.690412	0.15039|0.15039	0.683613|0.683613	0.359884|0.359884	ENSG00000127463|ENSG00000127463	ENST00000375197|ENST00000477853;ENST00000375199;ENST00000375208	.|T;T;T	.|0.23147	.|1.98;1.92;1.98	6.17|6.17	5.22|5.22	0.72569|0.72569	.|.	.|0.708347	.|0.15080	.|N	.|0.281698	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.58432|0.58432	P|P	4.000000000004E-6|4.000000000004E-6	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.01281	.|0.0;0.0;0.0;0.0	T|T	0.16217|0.16217	-1.0410|-1.0410	5|9	0.39692|0.12430	T|T	0.17|0.62	-7.2019|-7.2019	16.2834|16.2834	0.82708|0.82708	0.0:0.2663:0.7337:0.0|0.0:0.2663:0.7337:0.0	rs709683;rs57408009;rs709683|rs709683;rs57408009;rs709683	.|323;344;345;345	.|Q8N766-4;Q8N766-2;Q8N766-3;Q8N766	.|.;.;.;K0090_HUMAN	N|T	78|345;344;323	.|ENSP00000420608:S345T;ENSP00000364345:S344T;ENSP00000364354:S323T	ENSP00000364343:K78N|ENSP00000364345:S344T	K|S	-|-	3|2	2|0	KIAA0090|KIAA0090	19437931|19437931	0.934000|0.934000	0.31675|0.31675	0.868000|0.868000	0.34077|0.34077	0.804000|0.804000	0.45430|0.45430	2.667000|2.667000	0.46808|0.46808	1.643000|1.643000	0.50594|0.50594	-0.120000|-0.120000	0.15030|0.15030	AAG|AGT	C|0.506;G|0.494	0.494	strong		0.458	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047	
HRNR	388697	hgsc.bcm.edu	37	1	152191052	152191052	+	Missense_Mutation	SNP	G	G	T	rs115232928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152191052G>T	ENST00000368801.2	-	3	3128	c.3053C>A	c.(3052-3054)tCc>tAc	p.S1018Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1018					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)			AGACTGCCCGGAACCAGACCC	0.607													G|||	95	0.0189696	0.0696	0.0043	5008	,	,		21165	0.0		0.0	False		,,,				2504	0.0				p.S1018Y		Atlas-SNP	.											.	HRNR	403	.	0			c.C3053A						PASS	.	G	TYR/SER	190,4216	121.3+/-158.8	4,182,2017	135.0	149.0	145.0		3053	-0.1	0.0	1	dbSNP_132	145	0,8600		0,0,4300	no	missense	HRNR	NM_001009931.1	144	4,182,6317	TT,TG,GG		0.0,4.3123,1.4609	probably-damaging	1018/2851	152191052	190,12816	2203	4300	6503	SO:0001583	missense	388697	exon3			TGCCCGGAACCAG	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.3053C>A	1.37:g.152191052G>T	ENSP00000357791:p.Ser1018Tyr	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	264	122	0.462121	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	4.651	0.121012	0.08881	0.043123	0.0	ENSG00000197915	ENST00000368801	T	0.02472	4.28	3.24	-0.0513	0.13827	.	.	.	.	.	T	0.01695	0.0054	L	0.29908	0.895	0.09310	N	1	D	0.69078	0.997	D	0.65987	0.94	T	0.44832	-0.9302	9	0.28530	T	0.3	.	3.0366	0.06124	0.2539:0.0:0.536:0.21	.	1018	Q86YZ3	HORN_HUMAN	Y	1018	ENSP00000357791:S1018Y	ENSP00000357791:S1018Y	S	-	2	0	HRNR	150457676	0.008000	0.16893	0.000000	0.03702	0.002000	0.02628	0.817000	0.27281	-0.110000	0.12022	0.558000	0.71614	TCC	G|0.985;T|0.015	0.015	strong		0.607	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
TRIM4	89122	hgsc.bcm.edu	37	7	99500911	99500911	+	Silent	SNP	A	A	G	rs2247761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99500911A>G	ENST00000355947.2	-	6	978	c.849T>C	c.(847-849)tcT>tcC	p.S283S	TRIM4_ENST00000354241.5_Silent_p.S257S|TRIM4_ENST00000349062.2_Silent_p.S257S	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	283					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				CAGCTTCAAGAGAATAGTTCA	0.478													G|||	2898	0.578674	0.9039	0.4597	5008	,	,		21033	0.2976		0.5338	False		,,,				2504	0.5593				p.S283S		Atlas-SNP	.											.	TRIM4	33	.	0			c.T849C						PASS	.	G	,	3721,685	286.6+/-278.8	1574,573,56	126.0	120.0	122.0		849,771	1.2	0.0	7	dbSNP_100	122	5016,3584	518.2+/-379.2	1452,2112,736	no	coding-synonymous,coding-synonymous	TRIM4	NM_033017.3,NM_033091.2	,	3026,2685,792	GG,GA,AA		41.6744,15.547,32.8233	,	283/501,257/475	99500911	8737,4269	2203	4300	6503	SO:0001819	synonymous_variant	89122	exon6			TTCAAGAGAATAG	AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16275	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM4"", ""tripartite motif protein 4"""		"""tripartite motif-containing 4"""			11331580	Standard	NM_033017		Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.849T>C	7.37:g.99500911A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Silent	SNP	ENST00000355947.2	37	CCDS5679.1	1194	0.5467032967032966	440	0.8943089430894309	181	0.5	158	0.2762237762237762	415	0.5474934036939314	G	0.012	-1.669101	0.00765	0.84453	0.583256	ENSG00000146833	ENST00000447480	T	0.03358	3.96	2.16	1.25	0.21368	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.29058	-1.0024	5	0.02654	T	1	.	8.2152	0.31507	0.1842:0.0:0.8158:0.0	rs2247761;rs10386374;rs17212140;rs2247761	.	.	.	P	159	ENSP00000396229:S159P	ENSP00000396229:S159P	S	-	1	0	TRIM4	99338847	0.002000	0.14202	0.001000	0.08648	0.000000	0.00434	-0.126000	0.10563	-0.206000	0.10203	-1.820000	0.00599	TCT	A|0.383;G|0.617	0.617	strong		0.478	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017	
PSG2	5670	hgsc.bcm.edu	37	19	43585286	43585286	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43585286G>A	ENST00000406487.1	-	2	275	c.177C>T	c.(175-177)ccC>ccT	p.P59P	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	59	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				TAAGATTCTGGGGCAAATTGT	0.458																																					p.P59P		Atlas-SNP	.											PSG2,colon,carcinoma,-2,4	PSG2	84	4	0			c.C177T						scavenged	.						113.0	116.0	115.0					19																	43585286		2203	4296	6499	SO:0001819	synonymous_variant	5670	exon2			ATTCTGGGGCAAA		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.177C>T	19.37:g.43585286G>A		Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	357	15	0.0420168	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			.	.	none		0.458	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
CXCL1	2919	hgsc.bcm.edu	37	4	74735244	74735244	+	Silent	SNP	A	A	G	rs2071425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	23	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	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		
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970718	45970718	+	Silent	SNP	C	C	T	rs233238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45970718C>T	ENST00000391621.1	-	1	670	c.624G>A	c.(622-624)ccG>ccA	p.P208P	TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	208	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						GCTGGCAGCACGGAGAGGAAG	0.642													C|||	1331	0.265775	0.357	0.1715	5008	,	,		20976	0.3641		0.2068	False		,,,				2504	0.1687				p.P208P		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.G624A						PASS	.	C	,	1465,2941	472.6+/-356.4	247,971,985	119.0	126.0	124.0		,624	-5.0	0.0	21	dbSNP_79	124	1696,6904	311.7+/-310.5	158,1380,2762	no	intron,coding-synonymous	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,	405,2351,3747	TT,TC,CC		19.7209,33.2501,24.3042	,	,208/256	45970718	3161,9845	2203	4300	6503	SO:0001819	synonymous_variant	386679	exon1			GCAGCACGGAGAG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.624G>A	21.37:g.45970718C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	229	108	0.471616	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			C|0.742;T|0.258	0.258	strong		0.642	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
TCEB3B	51224	hgsc.bcm.edu	37	18	44561069	44561069	+	Silent	SNP	G	G	T	rs139088020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44561069G>T	ENST00000332567.4	-	1	919	c.567C>A	c.(565-567)ccC>ccA	p.P189P	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	189					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GTTGCTTCCCGGGCGCAGCGG	0.701													G|||	8	0.00159744	0.0053	0.0014	5008	,	,		13286	0.0		0.0	False		,,,				2504	0.0				p.P189P		Atlas-SNP	.											.	TCEB3B	141	.	0			c.C567A						PASS	.	G	,	20,4348		0,20,2164	24.0	28.0	27.0		567,	-0.2	0.0	18	dbSNP_134	27	0,8562		0,0,4281	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	0,20,6445	TT,TG,GG		0.0,0.4579,0.1547	,	189/754,	44561069	20,12910	2184	4281	6465	SO:0001819	synonymous_variant	51224	exon1			CTTCCCGGGCGCA	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.567C>A	18.37:g.44561069G>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	70	41	0.585714	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			G|0.998;T|0.002	0.002	strong		0.701	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
PDZD3	79849	hgsc.bcm.edu	37	11	119059404	119059404	+	Missense_Mutation	SNP	G	G	A	rs1815811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119059404G>A	ENST00000531114.1	+	7	1862	c.1313G>A	c.(1312-1314)cGg>cAg	p.R438Q	PDZD3_ENST00000392817.2_Missense_Mutation_p.R438Q|PDZD3_ENST00000322712.4_Missense_Mutation_p.R358Q|PDZD3_ENST00000525131.1_Missense_Mutation_p.R359Q|PDZD3_ENST00000355547.5_Missense_Mutation_p.R372Q			Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	438				R -> Q (in Ref. 2; BAC76050 and 5; AAH29042). {ECO:0000305}.	cGMP-mediated signaling (GO:0019934)|ion transport (GO:0006811)|negative regulation of cGMP biosynthetic process (GO:0030827)|negative regulation of guanylate cyclase activity (GO:0031283)|receptor guanylyl cyclase signaling pathway (GO:0007168)|response to toxic substance (GO:0009636)|water transport (GO:0006833)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|subapical complex (GO:0035003)	guanylate cyclase inhibitor activity (GO:0030251)|ion channel inhibitor activity (GO:0008200)|protein C-terminus binding (GO:0008022)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	14	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)		GCCTCGCCCCGGGGCAGCAGC	0.607													A|||	3330	0.664936	0.6014	0.4251	5008	,	,		17325	0.879		0.5716	False		,,,				2504	0.7965				p.R372Q		Atlas-SNP	.											.	PDZD3	42	.	0			c.G1115A						PASS	.	A	GLN/ARG,GLN/ARG	2590,1810	529.0+/-372.6	778,1034,388	58.0	54.0	56.0		1115,1073	-1.8	0.0	11	dbSNP_92	56	4672,3918	545.1+/-384.7	1256,2160,879	yes	missense,missense	PDZD3	NM_001168468.1,NM_024791.3	43,43	2034,3194,1267	AA,AG,GG		45.6112,41.1364,44.0955	benign,benign	372/506,358/492	119059404	7262,5728	2200	4295	6495	SO:0001583	missense	79849	exon9			CGCCCCGGGGCAG	AK091966	CCDS8417.1, CCDS53719.1	11q23.3	2008-02-05	2006-01-24	2006-01-24	ENSG00000172367	ENSG00000172367			19891	protein-coding gene	gene with protein product		607146	"""PDZ domain containing 2"""	PDZK2		11950846	Standard	NM_024791		Approved	FLJ22756, IKEPP	uc001pvz.3	Q86UT5	OTTHUMG00000166224	ENST00000531114.1:c.1313G>A	11.37:g.119059404G>A	ENSP00000431164:p.Arg438Gln	Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_001168468	Q8N6R4|Q8NAW7|Q8NEX7|Q9H5Z3	Missense_Mutation	SNP	ENST00000531114.1	37		1384	0.6336996336996337	297	0.6036585365853658	170	0.4696132596685083	493	0.8618881118881119	424	0.5593667546174143	A	3.171	-0.170042	0.06461	0.588636	0.543888	ENSG00000172367	ENST00000525131;ENST00000531114;ENST00000355547;ENST00000322712;ENST00000454065;ENST00000392817	T;T;T;T;T	0.73047	1.61;1.58;1.62;-0.71;1.58	5.21	-1.83	0.07833	PDZ/DHR/GLGF (1);	1.300320	0.05375	N	0.536080	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B;B	0.09022	0.0;0.002;0.001;0.001	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.27773	-1.0064	9	0.09338	T	0.73	0.0036	6.3572	0.21408	0.3089:0.3595:0.3317:0.0	rs1815811;rs4127379;rs17545150;rs17845869;rs17858844;rs60088554;rs1815811	359;438;372;358	E9PPZ1;Q86UT5;Q86UT5-2;B0YJ61	.;NHRF4_HUMAN;.;.	Q	359;438;372;358;372;438	ENSP00000434559:R359Q;ENSP00000431164:R438Q;ENSP00000347742:R372Q;ENSP00000327107:R358Q;ENSP00000376564:R438Q	ENSP00000327107:R358Q	R	+	2	0	PDZD3	118564614	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.042000	0.13949	-0.564000	0.06070	-0.254000	0.11334	CGG	G|0.395;A|0.605	0.605	strong		0.607	PDZD3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388471.1	NM_024791	
PRR21	643905	hgsc.bcm.edu	37	2	240981362	240981362	+	Silent	SNP	T	T	C	rs115420937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240981362T>C	ENST00000408934.1	-	1	1037	c.1038A>G	c.(1036-1038)ctA>ctG	p.L346L		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	346										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						TGAAGAGGCGTAGATGAAGAG	0.562													t|||	43	0.00858626	0.031	0.0029	5008	,	,		22045	0.0		0.0	False		,,,				2504	0.0				p.L346L		Atlas-SNP	.											.	PRR21	53	.	0			c.A1038G						PASS	.	T		100,4306	80.4+/-118.8	3,94,2106	145.0	128.0	134.0		1038	-1.0	0.0	2	dbSNP_132	134	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	PRR21	NM_001080835.1		3,98,6402	CC,CT,TT		0.0465,2.2696,0.7996		346/390	240981362	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	643905	exon1			GAGGCGTAGATGA	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.1038A>G	2.37:g.240981362T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			T|0.992;C|0.008	0.008	strong		0.562	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
DMD	1756	hgsc.bcm.edu	37	X	31496431	31496431	+	Missense_Mutation	SNP	T	T	A	rs41305353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:31496431T>A	ENST00000357033.4	-	59	8935	c.8729A>T	c.(8728-8730)gAg>gTg	p.E2910V	DMD_ENST00000378707.3_Missense_Mutation_p.E450V|DMD_ENST00000541735.1_Missense_Mutation_p.E450V|DMD_ENST00000378677.2_Missense_Mutation_p.E2906V|DMD_ENST00000445312.1_5'Flank|DMD_ENST00000343523.2_Missense_Mutation_p.E450V|DMD_ENST00000474231.1_Missense_Mutation_p.E450V|DMD_ENST00000359836.1_Missense_Mutation_p.E450V	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	2910			E -> V (in dbSNP:rs41305353). {ECO:0000269|PubMed:12359139}.		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)				AGTATTGACCTCCTCAGCCTG	0.488													T|||	135	0.0357616	0.059	0.0202	3775	,	,		14080	0.0308		0.0099	False		,,,				2504	0.002				p.E2910V		Atlas-SNP	.											.	DMD	2127	.	0			c.A8729T	GRCh37	CM940360	DMD	M	rs41305353	PASS	.	T	VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU	263,3570		7,210,39,1414,532	73.0	69.0	70.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	8705,8729,8360,8717,8360,4706,4697,1349,542,1349,1349,1349,1349	5.4	1.0	X	dbSNP_127	70	57,6671		0,39,18,2389,1854	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3,NM_004011.3,NM_004012.3,NM_004013.2,NM_004014.2,NM_004020.3,NM_004021.2,NM_004022.2,NM_004023.2	121,121,121,121,121,121,121,121,121,121,121,121,121	7,249,57,3803,2386	AA,AT,A,TT,T		0.8472,6.8615,3.03	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	2902/3678,2910/3686,2787/3563,2906/3682,2787/3563,1569/2345,1566/2342,450/1226,181/957,450/1116,450/1244,450/1231,450/1134	31496431	320,10241	2202	4300	6502	SO:0001583	missense	1756	exon59			TTGACCTCCTCAG	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.8729A>T	X.37:g.31496431T>A	ENSP00000354923:p.Glu2910Val	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	207	95	0.458937	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	65	0.03918022905364678	23	0.04852320675105485	6	0.016853932584269662	9	0.01601423487544484	8	0.010610079575596816	T	23.5	4.422122	0.83559	0.068615	0.008472	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231	T;T;T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18	5.4	5.4	0.78164	.	0.192432	0.24391	U	0.038930	T	0.02688	0.0081	N	0.12471	0.22	0.21861	P	0.999507306	B;P;D;P;P;B;B;B;P;D;P	0.57899	0.119;0.93;0.981;0.93;0.93;0.005;0.075;0.075;0.93;0.958;0.481	B;P;P;B;B;B;B;B;P;P;B	0.52109	0.268;0.462;0.69;0.368;0.368;0.007;0.061;0.083;0.462;0.663;0.316	T	0.16424	-1.0403	9	0.38643	T	0.18	.	14.6815	0.69020	0.0:0.0:0.0:1.0	rs41305353	2902;2910;2906;1569;1566;450;450;450;450;450;2787	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3	.;DMD_HUMAN;.;.;.;.;.;.;.;.;.	V	2902;1569;1566;606;2906;2910;450;450;2910;2787;450;450;450	ENSP00000350765:E606V;ENSP00000367948:E2906V;ENSP00000354923:E2910V;ENSP00000352894:E450V;ENSP00000340057:E450V;ENSP00000367979:E450V;ENSP00000444119:E450V;ENSP00000417123:E450V	ENSP00000340057:E450V	E	-	2	0	DMD	31406352	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.655000	0.83696	1.916000	0.55485	0.430000	0.28490	GAG	T|0.792;A|0.208	0.208	strong		0.488	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
CACNA1F	778	hgsc.bcm.edu	37	X	49070329	49070329	+	Missense_Mutation	SNP	C	C	T	rs34308720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49070329C>T	ENST00000376265.2	-	31	3836	c.3775G>A	c.(3775-3777)Gct>Act	p.A1259T	CACNA1F_ENST00000323022.5_Missense_Mutation_p.A1248T|CACNA1F_ENST00000376251.1_Missense_Mutation_p.A1194T	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1259			A -> T (in dbSNP:rs34308720).		axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	ACAATAAGAGCGTCAAACGTG	0.512													c|||	16	0.00423841	0.0121	0.0	3775	,	,		15638	0.0		0.0	False		,,,				2504	0.0				p.A1259T		Atlas-SNP	.											.	CACNA1F	218	.	0			c.G3775A						PASS	.	C	THR/ALA	73,3762		0,64,9,1568,562	135.0	88.0	104.0		3775	5.0	1.0	X	dbSNP_126	104	0,6728		0,0,0,2428,1872	yes	missense	CACNA1F	NM_005183.2	58	0,64,9,3996,2434	TT,TC,T,CC,C		0.0,1.9035,0.6911	possibly-damaging	1259/1978	49070329	73,10490	2203	4300	6503	SO:0001583	missense	778	exon31			TAAGAGCGTCAAA	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.3775G>A	X.37:g.49070329C>T	ENSP00000365441:p.Ala1259Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	117	55	0.470085	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	4	0.0024110910186859553	3	0.006122448979591836	0	0.0	0	0.0	0	0.0	C	22.4	4.288051	0.80803	0.019035	0.0	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	D;D;D	0.98400	-4.91;-4.91;-4.91	4.97	4.97	0.65823	Ion transport (1);	0.053644	0.64402	D	0.000001	D	0.96002	0.8698	L	0.28014	0.82	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.973	D	0.94804	0.7973	10	0.72032	D	0.01	.	16.1084	0.81241	0.0:1.0:0.0:0.0	rs34308720	1248;1259	F5CIQ9;O60840	.;CAC1F_HUMAN	T	1194;1248;1259	ENSP00000365427:A1194T;ENSP00000321618:A1248T;ENSP00000365441:A1259T	ENSP00000321618:A1248T	A	-	1	0	CACNA1F	48957273	0.995000	0.38212	1.000000	0.80357	0.634000	0.38068	1.260000	0.32968	2.053000	0.61076	0.529000	0.55759	GCT	C|0.993;T|0.007	0.007	strong		0.512	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
ZNF646	9726	hgsc.bcm.edu	37	16	31092629	31092629	+	Missense_Mutation	SNP	G	G	A	rs370035952		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31092629G>A	ENST00000394979.2	+	1	5407	c.4984G>A	c.(4984-4986)Gga>Aga	p.G1662R	ZNF646_ENST00000300850.5_Missense_Mutation_p.G1662R			O15015	ZN646_HUMAN	zinc finger protein 646	1662					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						AGCCAGGGGAGGACAAGCGGT	0.662																																					p.G1662R		Atlas-SNP	.											.	ZNF646	133	.	0			c.G4984A						PASS	.	G	ARG/GLY	1,4393	2.1+/-5.4	0,1,2196	63.0	73.0	70.0		4984	2.8	0.0	16		70	0,8598		0,0,4299	no	missense	ZNF646	NM_014699.3	125	0,1,6495	AA,AG,GG		0.0,0.0228,0.0077	benign	1662/1833	31092629	1,12991	2197	4299	6496	SO:0001583	missense	9726	exon2			AGGGGAGGACAAG	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"""Zinc fingers, C2H2-type"""	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.4984G>A	16.37:g.31092629G>A	ENSP00000378429:p.Gly1662Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	144	83	0.576389	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		.	.	.	.	.	.	.	.	.	.	G	5.858	0.342448	0.11069	2.28E-4	0.0	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.09445	2.98;3.04	5.8	2.76	0.32466	.	.	.	.	.	T	0.07007	0.0178	L	0.29908	0.895	0.09310	N	1	B	0.15930	0.015	B	0.16289	0.015	T	0.40831	-0.9542	9	0.20519	T	0.43	-7.682	4.3737	0.11260	0.2498:0.1703:0.5798:0.0	.	1662	O15015-2	.	R	1662	ENSP00000300850:G1662R;ENSP00000378429:G1662R	ENSP00000300850:G1662R	G	+	1	0	ZNF646	31000130	0.133000	0.22466	0.003000	0.11579	0.061000	0.15899	1.546000	0.36179	0.783000	0.33636	0.655000	0.94253	GGA	.	.	weak		0.662	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
MYOM1	8736	hgsc.bcm.edu	37	18	3075746	3075746	+	Silent	SNP	G	G	A	rs1143657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3075746G>A	ENST00000356443.4	-	35	4995	c.4662C>T	c.(4660-4662)gcC>gcT	p.A1554A	MYOM1_ENST00000261606.7_Silent_p.A1458A|MYOM1_ENST00000400569.3_Silent_p.A1554A	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1554					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.A1554A(3)		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						ATTCAGCATAGGCCTCATCGT	0.443													G|||	919	0.183506	0.1747	0.183	5008	,	,		18427	0.1875		0.2008	False		,,,				2504	0.1738				p.A1554A		Atlas-SNP	.											MYOM1,NS,carcinoma,0,2	MYOM1	192	2	3	Substitution - coding silent(3)	prostate(2)|stomach(1)	c.C4662T						PASS	.	G	,	525,3227		38,449,1389	58.0	58.0	58.0		4662,4374	4.2	1.0	18	dbSNP_123	58	1395,6825		108,1179,2823	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	146,1628,4212	AA,AG,GG		16.9708,13.9925,16.0374	,	1554/1686,1458/1590	3075746	1920,10052	1876	4110	5986	SO:0001819	synonymous_variant	8736	exon35			AGCATAGGCCTCA	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.4662C>T	18.37:g.3075746G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			G|0.810;A|0.190	0.190	strong		0.443	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
GKN2	200504	hgsc.bcm.edu	37	2	69173570	69173570	+	Missense_Mutation	SNP	C	C	T	rs1128272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69173570C>T	ENST00000328895.4	-	5	446	c.338G>A	c.(337-339)aGc>aAc	p.S113N	GKN2_ENST00000481498.1_Missense_Mutation_p.S113N	NM_182536.2	NP_872342.2	Q86XP6	GKN2_HUMAN	gastrokine 2	113	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.		S -> N (in dbSNP:rs1128272). {ECO:0000269|PubMed:12975309}.			extracellular region (GO:0005576)				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(1)	15						GGTGTATTTGCTGGAGAACAT	0.398													T|||	1568	0.313099	0.4985	0.1585	5008	,	,		20062	0.378		0.1183	False		,,,				2504	0.3057				p.S113N		Atlas-SNP	.											.	GKN2	28	.	0			c.G338A						PASS	.	T	ASN/SER	1931,2475	623.6+/-394.2	418,1095,690	161.0	152.0	155.0		338	-4.5	0.0	2	dbSNP_86	155	804,7796	783.1+/-407.6	51,702,3547	yes	missense	GKN2	NM_182536.2	46	469,1797,4237	TT,TC,CC		9.3488,43.8266,21.0288	benign	113/185	69173570	2735,10271	2203	4300	6503	SO:0001583	missense	200504	exon5			TATTTGCTGGAGA	AF494509	CCDS33215.1	2p14	2012-10-10			ENSG00000183607	ENSG00000183607		"""BRICHOS domain containing"""	24588	protein-coding gene	gene with protein product	"""down regulated in gastric cancer GDDR"", ""BRICHOS domain containing 1B"""					15774165, 15924415, 16888721	Standard	NM_182536		Approved	TFIZ1, PRO813, VLTI465, blottin, GDDR, BRICD1B	uc002sfa.3	Q86XP6	OTTHUMG00000152655	ENST00000328895.4:c.338G>A	2.37:g.69173570C>T	ENSP00000329292:p.Ser113Asn	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_182536	Q6UWS6	Missense_Mutation	SNP	ENST00000328895.4	37	CCDS33215.1	575	0.2632783882783883	238	0.483739837398374	58	0.16022099447513813	186	0.32517482517482516	93	0.12269129287598944	T	0.840	-0.742144	0.03088	0.438266	0.093488	ENSG00000183607	ENST00000328895;ENST00000481498	T;T	0.79554	-1.28;-1.28	4.73	-4.54	0.03452	BRICHOS (2);	2.019600	0.02252	N	0.066721	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.27971	-1.0058	9	0.02654	T	1	-18.1259	8.2576	0.31766	0.0:0.2615:0.5461:0.1924	rs1128272;rs3185051;rs6745497;rs17409490;rs52793439;rs57180184;rs1128272	113;113	E5RHQ8;Q86XP6	.;GKN2_HUMAN	N	113	ENSP00000329292:S113N;ENSP00000428538:S113N	ENSP00000329292:S113N	S	-	2	0	GKN2	69027074	0.000000	0.05858	0.000000	0.03702	0.081000	0.17604	-1.786000	0.01766	-0.988000	0.03489	-0.381000	0.06696	AGC	C|0.754;T|0.246	0.246	strong		0.398	GKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327191.1	NM_182536	
PCYOX1	51449	hgsc.bcm.edu	37	2	70485332	70485332	+	Silent	SNP	G	G	A	rs114523411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70485332G>A	ENST00000433351.2	+	1	64	c.36G>A	c.(34-36)ctG>ctA	p.L12L	PCYOX1_ENST00000545138.1_5'Flank|PCYOX1_ENST00000264441.5_Silent_p.L12L|PCYOX1_ENST00000505044.2_Intron	NM_016297.3	NP_057381.3	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1	12					prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)	15						TCTCCTCGCTGCTGGGGTTGT	0.706													G|||	23	0.00459265	0.0174	0.0	5008	,	,		9844	0.0		0.0	False		,,,				2504	0.0				p.L12L		Atlas-SNP	.											.	PCYOX1	34	.	0			c.G36A						PASS	.	G		49,4355	50.9+/-86.3	0,49,2153	38.0	39.0	39.0		36	-3.9	0.0	2	dbSNP_132	39	0,8600		0,0,4300	no	coding-synonymous	PCYOX1	NM_016297.3		0,49,6453	AA,AG,GG		0.0,1.1126,0.3768		12/506	70485332	49,12955	2202	4300	6502	SO:0001819	synonymous_variant	51449	exon1			CTCGCTGCTGGGG	AB020715	CCDS1902.1	2p13.3	2008-02-05			ENSG00000116005	ENSG00000116005	1.8.3.5		20588	protein-coding gene	gene with protein product		610995				10585463, 12186880	Standard	NM_016297		Approved	KIAA0908, PCL1	uc002sgn.4	Q9UHG3	OTTHUMG00000129671	ENST00000433351.2:c.36G>A	2.37:g.70485332G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	111	40	0.36036	NM_016297	B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8	Silent	SNP	ENST00000433351.2	37	CCDS1902.1																																																																																			G|0.995;A|0.005	0.005	strong		0.706	PCYOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251872.3	NM_016297	
POTEE	445582	hgsc.bcm.edu	37	2	132021539	132021539	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:132021539G>A	ENST00000356920.5	+	15	2605	c.2511G>A	c.(2509-2511)caG>caA	p.Q837Q	POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	837	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											TGGCCATCCAGGCCGTGCCGT	0.607																																					p.Q837Q		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,+2,2	.	.	2	0			c.G2511A						scavenged	.						149.0	151.0	150.0					2																	132021539		2203	4300	6503	SO:0001819	synonymous_variant	445582	exon15			CATCCAGGCCGTG	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.2511G>A	2.37:g.132021539G>A		Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	352	4	0.0113636	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Silent	SNP	ENST00000356920.5	37	CCDS46414.1																																																																																			.	.	none		0.607	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
PLXNA4	91584	hgsc.bcm.edu	37	7	132193225	132193225	+	Silent	SNP	G	G	A	rs78248128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:132193225G>A	ENST00000359827.3	-	2	1190	c.228C>T	c.(226-228)agC>agT	p.S76S	PLXNA4_ENST00000423507.2_Silent_p.S76S|PLXNA4_ENST00000378539.5_Silent_p.S76S|PLXNA4_ENST00000321063.4_Silent_p.S76S			Q9HCM2	PLXA4_HUMAN	plexin A4	76	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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						CCTTCAGGTCGCTGGAGAGCT	0.587													G|||	189	0.0377396	0.1293	0.013	5008	,	,		18830	0.0		0.004	False		,,,				2504	0.0051				p.S76S		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C228T						PASS	.	G	,,	450,3956	214.8+/-234.0	26,398,1779	57.0	60.0	59.0		228,228,228	-4.6	1.0	7	dbSNP_131	59	23,8577	16.0+/-53.3	1,21,4278	no	coding-synonymous,coding-synonymous,coding-synonymous	PLXNA4	NM_001105543.1,NM_020911.1,NM_181775.3	,,	27,419,6057	AA,AG,GG		0.2674,10.2133,3.6368	,,	76/493,76/1895,76/523	132193225	473,12533	2203	4300	6503	SO:0001819	synonymous_variant	91584	exon2			CAGGTCGCTGGAG	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.228C>T	7.37:g.132193225G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	158	92	0.582278	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			G|0.966;A|0.034	0.034	strong		0.587	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
PDE6A	5145	hgsc.bcm.edu	37	5	149245754	149245754	+	Silent	SNP	A	A	G	rs17110644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149245754A>G	ENST00000255266.5	-	20	2456	c.2337T>C	c.(2335-2337)ttT>ttC	p.F779F		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	779					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	AGGTGCAAACAAAGTCAATGA	0.458													A|||	274	0.0547125	0.1044	0.0865	5008	,	,		20697	0.005		0.0278	False		,,,				2504	0.044				p.F779F		Atlas-SNP	.											.	PDE6A	98	.	0			c.T2337C						PASS	.	A		404,4002	201.5+/-224.5	22,360,1821	161.0	147.0	152.0		2337	-6.7	0.4	5	dbSNP_123	152	318,8282	113.7+/-173.7	6,306,3988	no	coding-synonymous	PDE6A	NM_000440.2		28,666,5809	GG,GA,AA		3.6977,9.1693,5.5513		779/861	149245754	722,12284	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon20			GCAAACAAAGTCA		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.2337T>C	5.37:g.149245754A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			A|0.946;G|0.054	0.054	strong		0.458	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
MKLN1	4289	hgsc.bcm.edu	37	7	131128450	131128450	+	Silent	SNP	T	T	C	rs10224156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:131128450T>C	ENST00000352689.6	+	11	1424	c.1384T>C	c.(1384-1386)Tta>Cta	p.L462L	MKLN1_ENST00000421797.2_Silent_p.L370L	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	462					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					ACACTGCATGTTATTCCACTC	0.398													C|||	239	0.0477236	0.1702	0.0187	5008	,	,		23230	0.0		0.001	False		,,,				2504	0.0				p.L462L		Atlas-SNP	.											.	MKLN1	67	.	0			c.T1384C						PASS	.	C	,	707,3699	760.0+/-412.9	54,599,1550	95.0	85.0	89.0		1315,1384	4.1	1.0	7	dbSNP_119	89	13,8587	818.8+/-406.8	0,13,4287	no	coding-synonymous,coding-synonymous	MKLN1	NM_001145354.1,NM_013255.4	,	54,612,5837	CC,CT,TT		0.1512,16.0463,5.5359	,	439/713,462/736	131128450	720,12286	2203	4300	6503	SO:0001819	synonymous_variant	4289	exon11			TGCATGTTATTCC	AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.1384T>C	7.37:g.131128450T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	157	89	0.566879	NM_013255	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Silent	SNP	ENST00000352689.6	37	CCDS34754.1																																																																																			T|0.948;C|0.052	0.052	strong		0.398	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255	
C1orf127	148345	hgsc.bcm.edu	37	1	11008497	11008497	+	Silent	SNP	G	G	C	rs1281017	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11008497G>C	ENST00000377008.4	-	11	1640	c.1194C>G	c.(1192-1194)ggC>ggG	p.G398G	C1orf127_ENST00000377004.4_Silent_p.G565G			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	398										NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CGCTTGACAAGCCTCTCAGCA	0.632													C|||	1627	0.32488	0.4009	0.2867	5008	,	,		17686	0.2371		0.1849	False		,,,				2504	0.4836				p.G565G		Atlas-SNP	.											.	C1orf127	134	.	0			c.C1695G						PASS	.	C		1487,2919	659.8+/-400.6	267,953,983	31.0	33.0	32.0		1695	-5.1	0.0	1	dbSNP_87	32	1519,7081	730.0+/-406.7	142,1235,2923	no	coding-synonymous	C1orf127	NM_001170754.1		409,2188,3906	CC,CG,GG		17.6628,33.7494,23.1124		565/824	11008497	3006,10000	2203	4300	6503	SO:0001819	synonymous_variant	148345	exon12			TGACAAGCCTCTC	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1194C>G	1.37:g.11008497G>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	158	80	0.506329	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		599	0.2742673992673993	206	0.4186991869918699	98	0.27071823204419887	142	0.24825174825174826	153	0.20184696569920843	C	3.508	-0.100345	0.06967	0.337494	0.176628	ENSG00000175262	ENST00000418570;ENST00000520253	.	.	.	4.61	-5.09	0.02920	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.42749	-0.9433	3	.	.	.	0.0012	4.3862	0.11318	0.1211:0.1502:0.1199:0.6088	rs1281017	.	.	.	G	400;517	.	.	A	-	2	0	C1orf127	10931084	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.893000	0.04127	-1.335000	0.02241	-1.145000	0.01858	GCT	G|0.745;C|0.255	0.255	strong		0.632	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
TMEM132D	121256	hgsc.bcm.edu	37	12	129559557	129559557	+	Silent	SNP	C	C	T	rs10773594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:129559557C>T	ENST00000422113.2	-	9	2489	c.2163G>A	c.(2161-2163)acG>acA	p.T721T	TMEM132D_ENST00000389441.4_Silent_p.T259T	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	721					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TATCCAAGGGCGTGACTGAGC	0.463													T|||	3226	0.644169	0.6278	0.6888	5008	,	,		19697	0.5645		0.6769	False		,,,				2504	0.683				p.T721T		Atlas-SNP	.											TMEM132D,bladder,carcinoma,-2,2	TMEM132D	299	2	0			c.G2163A						PASS	.	T		2873,1533	478.5+/-358.2	967,939,297	61.0	56.0	57.0		2163	-8.6	0.8	12	dbSNP_120	57	5923,2677	416.9+/-352.3	2035,1853,412	no	coding-synonymous	TMEM132D	NM_133448.2		3002,2792,709	TT,TC,CC		31.1279,34.7935,32.3697		721/1100	129559557	8796,4210	2203	4300	6503	SO:0001819	synonymous_variant	121256	exon9			CAAGGGCGTGACT	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.2163G>A	12.37:g.129559557C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	39	13	0.333333	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																			C|0.337;T|0.663	0.663	strong		0.463	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
HDAC4	9759	hgsc.bcm.edu	37	2	240111556	240111556	+	Silent	SNP	G	G	A	rs6740794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240111556G>A	ENST00000345617.3	-	4	1103	c.312C>T	c.(310-312)caC>caT	p.H104H	HDAC4_ENST00000541256.1_Silent_p.H73H	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	104					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)		GCTGCGCCTCGTGCTGCCGGG	0.677													g|||	239	0.0477236	0.171	0.0173	5008	,	,		14486	0.0		0.001	False		,,,				2504	0.0				p.H104H		Atlas-SNP	.											HDAC4,colon,carcinoma,0,1	HDAC4	127	1	0			c.C312T						PASS	.	A		671,3735	265.6+/-266.7	50,571,1582	30.0	27.0	28.0		312	-0.9	1.0	2	dbSNP_116	28	12,8588	7.1+/-27.0	0,12,4288	no	coding-synonymous	HDAC4	NM_006037.3		50,583,5870	AA,AG,GG		0.1395,15.2292,5.2514		104/1085	240111556	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon4			CGCCTCGTGCTGC	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.312C>T	2.37:g.240111556G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.938;A|0.062	0.062	strong		0.677	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
XKR5	389610	hgsc.bcm.edu	37	8	6690276	6690276	+	RNA	SNP	T	T	C	rs2741098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:6690276T>C	ENST00000518724.1	-	0	355				GS1-24F4.2_ENST00000500823.2_lincRNA			Q6UX68	XKR5_HUMAN	XK, Kell blood group complex subunit-related family, member 5							integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)	3			STAD - Stomach adenocarcinoma(24;0.0984)	READ - Rectum adenocarcinoma(644;0.137)|COAD - Colon adenocarcinoma(149;0.166)		TGCAGCATCATCAAGGAGCAA	0.577													C|||	3352	0.669329	0.9123	0.513	5008	,	,		18947	0.5516		0.5368	False		,,,				2504	0.7096				p.M69V		Atlas-SNP	.											.	XKR5	20	.	0			c.A205G						PASS	.	C	VAL/MET	3532,648		1493,546,51	96.0	107.0	103.0		205	0.5	0.0	8	dbSNP_100	103	4446,3982		1176,2094,944	yes	missense	XKR5	NM_207411.4	21	2669,2640,995	CC,CT,TT		47.2473,15.5024,36.7227	benign	69/687	6690276	7978,4630	2090	4214	6304			389610	exon2			GCATCATCAAGGA	AY358489		8p23.1	2006-01-12	2006-01-12		ENSG00000186530	ENSG00000275591			20782	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 5"""				Standard	NM_207411		Approved		uc022aqv.1	Q6UX68	OTTHUMG00000153652		8.37:g.6690276T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_207411	Q5GH74	Missense_Mutation	SNP	ENST00000518724.1	37																																																																																				T|0.360;C|0.640	0.640	strong		0.577	XKR5-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000331969.2	NM_207411	
EP400	57634	hgsc.bcm.edu	37	12	132547096	132547096	+	Silent	SNP	G	G	A	rs74479394|rs113304321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132547096G>A	ENST00000333577.4	+	48	8401	c.8292G>A	c.(8290-8292)caG>caA	p.Q2764Q	EP400_ENST00000389561.2_Silent_p.Q2728Q|EP400_ENST00000389562.2_Silent_p.Q2727Q|EP400_ENST00000330386.6_Silent_p.Q2647Q|EP400_ENST00000332482.4_Silent_p.Q2691Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2764	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcaacaacagcagcagcagc	0.567													G|||	734	0.146565	0.3215	0.0432	5008	,	,		15582	0.1111		0.0417	False		,,,				2504	0.1278				p.Q2728Q		Atlas-SNP	.											EP400,colon,carcinoma,0,3	EP400	370	3	0			c.G8184A						PASS	.	G		0,4324		0,0,2162	24.0	29.0	27.0		8184	0.5	0.9	12	dbSNP_131	27	1,8349		0,1,4174	no	coding-synonymous	EP400	NM_015409.4		0,1,6336	AA,AG,GG		0.012,0.0,0.0079		2728/3124	132547096	1,12673	2162	4175	6337	SO:0001819	synonymous_variant	57634	exon47			ACAACAGCAGCAG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8292G>A	12.37:g.132547096G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	128	17	0.132812	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				.	.	weak		0.567	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
SNRPA1	6627	hgsc.bcm.edu	37	15	101835306	101835306	+	Silent	SNP	G	G	C	rs61738984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:101835306G>C	ENST00000254193.6	-	1	150	c.78C>G	c.(76-78)ctC>ctG	p.L26L	RP11-299G20.2_ENST00000558838.1_RNA|SNRPA1_ENST00000560856.1_5'UTR	NM_003090.2	NP_003081.2	P09661	RU2A_HUMAN	small nuclear ribonucleoprotein polypeptide A'	26					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U2 snRNP (GO:0005686)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	Lung NSC(78;0.00156)|all_lung(78;0.00195)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00113)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ACTCACCCCGGAGGTCCAGCT	0.721													G|||	442	0.0882588	0.2829	0.0749	5008	,	,		11636	0.001		0.007	False		,,,				2504	0.0082				p.L26L		Atlas-SNP	.											.	SNRPA1	11	.	0			c.C78G						PASS	.	G		774,3286		49,676,1305	5.0	5.0	5.0		78	-8.1	0.2	15	dbSNP_129	5	29,7973		1,27,3973	no	coding-synonymous	SNRPA1	NM_003090.2		50,703,5278	CC,CG,GG		0.3624,19.064,6.6573		26/256	101835306	803,11259	2030	4001	6031	SO:0001819	synonymous_variant	6627	exon1			ACCCCGGAGGTCC	AJ130971	CCDS10391.1	15q26.3	2011-10-11			ENSG00000131876	ENSG00000131876			11152	protein-coding gene	gene with protein product		603521				2928112	Standard	NM_003090		Approved	Lea1	uc002bww.3	P09661	OTTHUMG00000149871	ENST00000254193.6:c.78C>G	15.37:g.101835306G>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_003090	B2R5I6|Q8TBD2	Silent	SNP	ENST00000254193.6	37	CCDS10391.1																																																																																			G|0.906;C|0.094	0.094	strong		0.721	SNRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313621.2	NM_003090	
RANBP6	26953	hgsc.bcm.edu	37	9	6012658	6012658	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:6012658T>G	ENST00000259569.5	-	1	2960	c.2950A>C	c.(2950-2952)Ata>Cta	p.I984L	RANBP6_ENST00000485372.1_5'Flank	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	984					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.I984L(4)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		ATCTTCCCTATTGCTGAGATA	0.363																																					p.I984L		Atlas-SNP	.											RANBP6,bladder,carcinoma,0,7	RANBP6	127	7	4	Substitution - Missense(4)	lung(2)|endometrium(1)|kidney(1)	c.A2950C						scavenged	.						110.0	103.0	106.0					9																	6012658		2203	4300	6503	SO:0001583	missense	26953	exon1			TCCCTATTGCTGA	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.2950A>C	9.37:g.6012658T>G	ENSP00000259569:p.Ile984Leu	Somatic	181	2	0.0110497		WXS	Illumina HiSeq	Phase_I	249	6	0.0240964	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Missense_Mutation	SNP	ENST00000259569.5	37	CCDS6467.1	.	.	.	.	.	.	.	.	.	.	T	10.80	1.451466	0.26074	.	.	ENSG00000137040	ENST00000259569	T	0.08807	3.05	4.79	2.63	0.31362	Armadillo-like helical (1);Armadillo-type fold (1);	0.121890	0.53938	D	0.000050	T	0.03263	0.0095	N	0.11341	0.13	0.36993	D	0.894861	B;B;B	0.17268	0.021;0.012;0.021	B;B;B	0.16722	0.016;0.011;0.016	T	0.36648	-0.9739	10	0.06891	T	0.86	-4.4735	5.2001	0.15258	0.0:0.4849:0.0:0.5151	.	151;572;984	B4E340;B4DTX6;O60518	.;.;RNBP6_HUMAN	L	984	ENSP00000259569:I984L	ENSP00000259569:I984L	I	-	1	0	RANBP6	6002658	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.090000	0.50191	0.682000	0.31407	0.533000	0.62120	ATA	.	.	none		0.363	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416	
PPP6R2	9701	hgsc.bcm.edu	37	22	50874851	50874851	+	Silent	SNP	G	G	A	rs78837601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50874851G>A	ENST00000216061.5	+	15	1942	c.1572G>A	c.(1570-1572)acG>acA	p.T524T	PPP6R2_ENST00000395741.3_Silent_p.T525T|PPP6R2_ENST00000395744.3_Silent_p.T524T|PPP6R2_ENST00000359139.3_Silent_p.T524T			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	524						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						AGACGCTGACGGAGACGAACC	0.687													G|||	105	0.0209665	0.0719	0.0086	5008	,	,		17157	0.004		0.0	False		,,,				2504	0.0				p.T525T		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G1575A						PASS	.	G	,,,	322,4064		9,304,1880	53.0	34.0	41.0		1572,1575,1572,1572	-9.1	0.0	22	dbSNP_131	41	2,8584		0,2,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP6R2	NM_001242898.1,NM_001242899.1,NM_001242900.1,NM_014678.4	,,,	9,306,6171	AA,AG,GG		0.0233,7.3415,2.4977	,,,	524/960,525/934,524/928,524/933	50874851	324,12648	2193	4293	6486	SO:0001819	synonymous_variant	9701	exon14			GCTGACGGAGACG	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	19253	protein-coding gene	gene with protein product		610877	"""KIAA0685"", ""SAPS domain family, member 2"""	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.1572G>A	22.37:g.50874851G>A		Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	342	166	0.48538	NM_001242899	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Silent	SNP	ENST00000216061.5	37																																																																																				G|0.976;A|0.024	0.024	strong		0.687	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678	
MYO5C	55930	hgsc.bcm.edu	37	15	52553259	52553259	+	Missense_Mutation	SNP	C	C	G	rs200784696		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52553259C>G	ENST00000261839.7	-	10	1274	c.1113G>C	c.(1111-1113)caG>caC	p.Q371H	MYO5C_ENST00000443683.2_Missense_Mutation_p.Q314H|MYO5C_ENST00000541028.1_5'UTR	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	371	Myosin motor.					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)		TGCACAGCCACTGAGCAACTC	0.557													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19769	0.0		0.0	False		,,,				2504	0.0				p.Q371H		Atlas-SNP	.											.	MYO5C	162	.	0			c.G1113C						PASS	.	C	HIS/GLN	2,4080		0,2,2039	67.0	71.0	70.0		1113	4.6	1.0	15		70	0,8416		0,0,4208	yes	missense	MYO5C	NM_018728.3	24	0,2,6247	GG,GC,CC		0.0,0.049,0.016	benign	371/1743	52553259	2,12496	2041	4208	6249	SO:0001583	missense	55930	exon10			CAGCCACTGAGCA	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.1113G>C	15.37:g.52553259C>G	ENSP00000261839:p.Gln371His	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	C	6.117	0.389752	0.11581	4.9E-4	0.0	ENSG00000128833	ENST00000261839;ENST00000443683	D;D	0.95238	-3.65;-2.21	5.51	4.59	0.56863	Myosin head, motor domain (2);	0.190704	0.47852	D	0.000217	D	0.87047	0.6080	N	0.05050	-0.12	0.47737	D	0.999502	B	0.09022	0.002	B	0.11329	0.006	T	0.81245	-0.1020	10	0.23302	T	0.38	.	16.3026	0.82830	0.0:0.8673:0.1327:0.0	.	371	Q9NQX4	MYO5C_HUMAN	H	371;314	ENSP00000261839:Q371H;ENSP00000410582:Q314H	ENSP00000261839:Q371H	Q	-	3	2	MYO5C	50340551	1.000000	0.71417	0.999000	0.59377	0.071000	0.16799	0.860000	0.27871	1.325000	0.45301	-0.175000	0.13238	CAG	.	.	weak		0.557	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
LAMB4	22798	hgsc.bcm.edu	37	7	107745029	107745029	+	Silent	SNP	A	A	G	rs2074748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107745029A>G	ENST00000388781.3	-	9	989	c.906T>C	c.(904-906)gaT>gaC	p.D302D	LAMB4_ENST00000418464.1_Silent_p.D302D|LAMB4_ENST00000388780.3_Silent_p.D302D|LAMB4_ENST00000414450.2_Silent_p.D302D|LAMB4_ENST00000205386.4_Silent_p.D302D	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	302	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						AGTTCGGACCATCTGTATTGT	0.512													A|||	376	0.0750799	0.093	0.0375	5008	,	,		17505	0.1369		0.0129	False		,,,				2504	0.0777				p.D302D		Atlas-SNP	.											.	LAMB4	253	.	0			c.T906C						PASS	.	A		329,4077	174.1+/-203.8	11,307,1885	243.0	216.0	225.0		906	-5.1	0.7	7	dbSNP_96	225	114,8486	60.2+/-122.0	1,112,4187	no	coding-synonymous	LAMB4	NM_007356.2		12,419,6072	GG,GA,AA		1.3256,7.4671,3.4061		302/1762	107745029	443,12563	2203	4300	6503	SO:0001819	synonymous_variant	22798	exon9			CGGACCATCTGTA	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.906T>C	7.37:g.107745029A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			A|0.944;G|0.056	0.056	strong		0.512	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
COL15A1	1306	hgsc.bcm.edu	37	9	101778272	101778272	+	Missense_Mutation	SNP	A	A	C	rs35250850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	101	0	0		WXS	Illumina HiSeq	Phase_I	116	28	0.241379	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	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377054	168377054	+	lincRNA	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:168377054G>T	ENST00000538528.1	-	0	565																											CAGTGTGGGGGGAGGAGAAGA	0.642																																					p.S93S		Atlas-SNP	.											.	.	.	.	0			c.C279A						PASS	.						3.0	4.0	4.0					6																	168377054		618	1453	2071			0	exon1			GTGGGGGGAGGAG																													6.37:g.168377054G>T		Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	331	52	0.1571	NM_001129895		Silent	SNP	ENST00000538528.1	37																																																																																				.	.	none		0.642	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
LPL	4023	hgsc.bcm.edu	37	8	19818436	19818436	+	Silent	SNP	C	C	A	rs316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:19818436C>A	ENST00000311322.8	+	8	1634	c.1164C>A	c.(1162-1164)acC>acA	p.T388T		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	388	Heparin-binding. {ECO:0000250}.|PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	CAAATAAGACCTACTCCTTCC	0.403													A|||	764	0.152556	0.2368	0.1455	5008	,	,		14705	0.1121		0.1203	False		,,,				2504	0.1186				p.T388T		Atlas-SNP	.											.	LPL	78	.	0			c.C1164A						PASS	.	A		1008,3398	728.4+/-409.9	116,776,1311	104.0	103.0	104.0		1164	-11.3	0.4	8	dbSNP_36	104	1055,7545	770.4+/-407.7	56,943,3301	no	coding-synonymous	LPL	NM_000237.2		172,1719,4612	AA,AC,CC		12.2674,22.8779,15.8619		388/476	19818436	2063,10943	2203	4300	6503	SO:0001819	synonymous_variant	4023	exon8			TAAGACCTACTCC		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.1164C>A	8.37:g.19818436C>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	71	23	0.323944	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Silent	SNP	ENST00000311322.8	37	CCDS6012.1																																																																																			C|0.846;A|0.154	0.154	strong		0.403	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3		
KRT71	112802	hgsc.bcm.edu	37	12	52946424	52946424	+	Silent	SNP	G	G	A	rs61729863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52946424G>A	ENST00000267119.5	-	1	507	c.438C>T	c.(436-438)gaC>gaT	p.D146D		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	146	Coil 1A.|Rod.				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)		GACCCACCTTGTCGATGAAGG	0.537													G|||	187	0.0373403	0.1339	0.0144	5008	,	,		19941	0.0		0.0	False		,,,				2504	0.0				p.D146D		Atlas-SNP	.											.	KRT71	70	.	0			c.C438T						PASS	.	G		431,3975	208.5+/-229.5	28,375,1800	94.0	92.0	92.0		438	0.9	1.0	12	dbSNP_129	92	0,8600		0,0,4300	no	coding-synonymous	KRT71	NM_033448.2		28,375,6100	AA,AG,GG		0.0,9.7821,3.3139		146/524	52946424	431,12575	2203	4300	6503	SO:0001819	synonymous_variant	112802	exon1			CACCTTGTCGATG	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.438C>T	12.37:g.52946424G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	208	87	0.418269	NM_033448	B3KVC1|Q3SY85|Q96DU2	Silent	SNP	ENST00000267119.5	37	CCDS8831.1																																																																																			G|0.970;A|0.030	0.030	strong		0.537	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448	
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692346	31692346	+	Missense_Mutation	SNP	C	C	T	rs115381362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31692346C>T	ENST00000360542.3	-	1	261	c.8G>A	c.(7-9)tGc>tAc	p.C3Y		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	3						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GTAGTTGGGGCAAGACATAGT	0.512													C|||	25	0.00499201	0.0182	0.0014	5008	,	,		17989	0.0		0.0	False		,,,				2504	0.0				p.C3Y		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.G8A						PASS	.	C	TYR/CYS	90,4308		0,90,2109	31.0	34.0	33.0		8	2.9	0.9	21	dbSNP_132	33	1,8591		0,1,4295	yes	missense	KRTAP26-1	NM_203405.1	194	0,91,6404	TT,TC,CC		0.0116,2.0464,0.7005	probably-damaging	3/211	31692346	91,12899	2199	4296	6495	SO:0001583	missense	388818	exon1			TTGGGGCAAGACA	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"""Keratin associated proteins"""	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.8G>A	21.37:g.31692346C>T	ENSP00000353742:p.Cys3Tyr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	C	15.21	2.765058	0.49574	0.020464	1.16E-4	ENSG00000197683	ENST00000360542	T	0.16073	2.37	4.95	2.91	0.33838	.	1.072940	0.07352	U	0.882550	T	0.07863	0.0197	N	0.08118	0	0.22975	N	0.998487	D	0.65815	0.995	D	0.66497	0.944	T	0.44081	-0.9351	10	0.72032	D	0.01	-3.9981	10.796	0.46461	0.0:0.6254:0.3746:0.0	.	3	Q6PEX3	KR261_HUMAN	Y	3	ENSP00000353742:C3Y	ENSP00000353742:C3Y	C	-	2	0	KRTAP26-1	30614217	0.953000	0.32496	0.911000	0.35937	0.718000	0.41266	0.656000	0.24948	1.347000	0.45714	0.655000	0.94253	TGC	C|0.993;T|0.007	0.007	strong		0.512	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405	
CCDC173	129881	hgsc.bcm.edu	37	2	170537661	170537661	+	Silent	SNP	A	A	G	rs145389999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170537661A>G	ENST00000447353.1	-	2	255	c.150T>C	c.(148-150)atT>atC	p.I50I		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	50																	CATCGTGTGGAATTATGGTGA	0.393													A|||	52	0.0103834	0.0356	0.0072	5008	,	,		17148	0.0		0.0	False		,,,				2504	0.0				p.I50I		Atlas-SNP	.											.	.	.	.	0			c.T150C						PASS	.	A		89,3817		1,87,1865	161.0	153.0	156.0		150	3.2	1.0	2	dbSNP_134	156	0,8292		0,0,4146	no	coding-synonymous	C2orf77	NM_001085447.1		1,87,6011	GG,GA,AA		0.0,2.2785,0.7296		50/553	170537661	89,12109	1953	4146	6099	SO:0001819	synonymous_variant	129881	exon2			GTGTGGAATTATG	BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"""hypothetical LOC129881"""		"""chromosome 2 open reading frame 77"""	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.150T>C	2.37:g.170537661A>G		Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	202	108	0.534653	NM_001085447	Q6PJF6	Silent	SNP	ENST00000447353.1	37	CCDS46445.1																																																																																			A|0.993;G|0.007	0.007	strong		0.393	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447	
CHRDL2	25884	hgsc.bcm.edu	37	11	74415606	74415606	+	Missense_Mutation	SNP	T	T	C	rs59876990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:74415606T>C	ENST00000376332.3	-	7	1172	c.676A>G	c.(676-678)Atc>Gtc	p.I226V	CHRDL2_ENST00000263671.5_Missense_Mutation_p.I226V|CHRDL2_ENST00000534159.1_5'UTR	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	226					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|ossification (GO:0001503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)|skin(2)	15	Hepatocellular(1;0.098)					TGGCGAGGGATGAAGCTCAGA	0.582													T|||	102	0.0203674	0.0756	0.0029	5008	,	,		14376	0.0		0.0	False		,,,				2504	0.0				p.I226V		Atlas-SNP	.											.	CHRDL2	47	.	0			c.A676G						PASS	.	T	VAL/ILE	246,4154	144.6+/-179.5	7,232,1961	65.0	62.0	63.0		676	-1.4	1.0	11	dbSNP_129	63	0,8586		0,0,4293	yes	missense	CHRDL2	NM_015424.3	29	7,232,6254	CC,CT,TT		0.0,5.5909,1.8943	benign	226/452	74415606	246,12740	2200	4293	6493	SO:0001583	missense	25884	exon7			GAGGGATGAAGCT	AL110168	CCDS8234.1, CCDS60893.1	11q13.4	2013-09-20			ENSG00000054938	ENSG00000054938			24168	protein-coding gene	gene with protein product		613127				12853144, 12975309	Standard	NM_015424		Approved	BNF1	uc001ovh.3	Q6WN34	OTTHUMG00000165623	ENST00000376332.3:c.676A>G	11.37:g.74415606T>C	ENSP00000365510:p.Ile226Val	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	229	102	0.445415	NM_015424	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Missense_Mutation	SNP	ENST00000376332.3	37		42	0.019230769230769232	41	0.08333333333333333	1	0.0027624309392265192	0	0.0	0	0.0	T	12.53	1.964712	0.34659	0.055909	0.0	ENSG00000054938	ENST00000263671;ENST00000376332;ENST00000376323;ENST00000393519;ENST00000528789	T;T;T	0.62105	0.94;0.98;0.05	5.39	-1.36	0.09085	.	0.361824	0.31472	N	0.007600	T	0.03871	0.0109	L	0.56769	1.78	0.27110	N	0.962407	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.09377	0.001;0.002;0.004	T	0.06232	-1.0838	10	0.19147	T	0.46	-7.7366	6.1715	0.20421	0.0:0.1511:0.3979:0.451	rs59876990	226;226;226	E9PCG7;Q6WN34;Q6WN34-2	.;CRDL2_HUMAN;.	V	226;226;112;110;226	ENSP00000263671:I226V;ENSP00000365510:I226V;ENSP00000431380:I226V	ENSP00000263671:I226V	I	-	1	0	CHRDL2	74093254	0.983000	0.35010	0.996000	0.52242	0.980000	0.70556	-0.008000	0.12788	-0.250000	0.09555	0.379000	0.24179	ATC	T|0.978;C|0.022	0.022	strong		0.582	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1		
ATP6AP2	10159	hgsc.bcm.edu	37	X	40460040	40460040	+	Silent	SNP	T	T	C	rs7691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40460040T>C	ENST00000378438.4	+	8	923	c.765T>C	c.(763-765)taT>taC	p.Y255Y	ATP6AP2_ENST00000486558.1_3'UTR|ATP6AP2_ENST00000535539.1_Silent_p.Y223Y|ATP6AP2_ENST00000535777.1_Silent_p.Y177Y|ATP6AP2_ENST00000544975.1_Silent_p.Y179Y	NM_005765.2	NP_005756.2	O75787	RENR_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 2	255					angiotensin maturation (GO:0002003)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|eye pigmentation (GO:0048069)|head morphogenesis (GO:0060323)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of Wnt signaling pathway (GO:0030177)|proteolysis (GO:0006508)|regulation of MAPK cascade (GO:0043408)|rostrocaudal neural tube patterning (GO:0021903)	cell body (GO:0044297)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(2)	4						ACAGTCTTTATGGTGGGAATG	0.353													T|||	583	0.154437	0.2526	0.1859	3775	,	,		12735	0.1091		0.001	False		,,,				2504	0.0092				p.Y255Y		Atlas-SNP	.											.	ATP6AP2	45	.	0			c.T765C						PASS	.	T		1149,2686		144,692,169,796,402	120.0	94.0	102.0		765	1.5	1.0	X	dbSNP_52	102	42,6686		0,28,14,2400,1858	no	coding-synonymous	ATP6AP2	NM_005765.2		144,720,183,3196,2260	CC,CT,C,TT,T		0.6243,29.9609,11.2752		255/351	40460040	1191,9372	2203	4300	6503	SO:0001819	synonymous_variant	10159	exon8			TCTTTATGGTGGG	AF248966	CCDS14252.1	Xp11.4	2014-06-17	2003-08-28	2003-08-29	ENSG00000182220	ENSG00000182220			18305	protein-coding gene	gene with protein product	"""prorenin receptor"", ""renin receptor"""	300556	"""ATPase, H+ transporting, lysosomal interacting protein 2"""	ATP6IP2		9556572, 11590366	Standard	NM_005765		Approved	M8-9, APT6M8-9, ATP6M8-9, PRR, RENR	uc004det.3	O75787	OTTHUMG00000024103	ENST00000378438.4:c.765T>C	X.37:g.40460040T>C		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	227	226	0.995595	NM_005765	B7Z9I3|Q5QTQ7|Q6T7F5|Q8NBP3|Q8NG15|Q96FV6|Q96LB5|Q9H2P8|Q9UG89	Silent	SNP	ENST00000378438.4	37	CCDS14252.1	247|247	0.14888487040385776|0.14888487040385776	78|78	0.1902439024390244|0.1902439024390244	46|46	0.1393939393939394|0.1393939393939394	46|46	0.08614232209737828|0.08614232209737828	1|1	0.0013192612137203166|0.0013192612137203166	T|T	8.602|8.602	0.887101|0.887101	0.17540|0.17540	0.299609|0.299609	0.006243|0.006243	ENSG00000182220|ENSG00000182220	ENST00000447485|ENST00000423649	.|.	.|.	.|.	5.23|5.23	1.55|1.55	0.23275|0.23275	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24368|0.24368	-1.0162|-1.0162	3|3	.|.	.|.	.|.	-44.4115|-44.4115	9.1043|9.1043	0.36687|0.36687	0.0:0.3009:0.0:0.6991|0.0:0.3009:0.0:0.6991	rs7691;rs1059871;rs3200729;rs5963811;rs6520665;rs57415406;rs7691|rs7691;rs1059871;rs3200729;rs5963811;rs6520665;rs57415406;rs7691	.|.	.|.	.|.	T|R	230|196	.|.	.|.	M|W	+|+	2|1	0|0	ATP6AP2|ATP6AP2	40344984|40344984	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.979000|0.979000	0.70002|0.70002	0.578000|0.578000	0.23773|0.23773	0.180000|0.180000	0.19960|0.19960	0.417000|0.417000	0.27973|0.27973	ATG|TGG	0|0.015;C|0.145	0.145	strong		0.353	ATP6AP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060679.1	NM_005765	
XIRP1	165904	hgsc.bcm.edu	37	3	39228514	39228514	+	Missense_Mutation	SNP	G	G	A	rs61736154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39228514G>A	ENST00000340369.3	-	2	2651	c.2423C>T	c.(2422-2424)tCg>tTg	p.S808L	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Missense_Mutation_p.S808L	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	808					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)		CCCTGTGCCCGAGAGCACATA	0.612													G|||	103	0.0205671	0.0719	0.0058	5008	,	,		19504	0.0		0.0	False		,,,				2504	0.0041				p.S808L		Atlas-SNP	.											.	XIRP1	173	.	0			c.C2423T						PASS	.	G	LEU/SER,LEU/SER	316,4090	169.1+/-199.8	13,290,1900	64.0	65.0	65.0		2423,2423	3.2	0.6	3	dbSNP_129	65	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	XIRP1	NM_001198621.1,NM_194293.2	145,145	13,293,6197	AA,AG,GG		0.0349,7.172,2.4527	benign,benign	808/1122,808/1844	39228514	319,12687	2203	4300	6503	SO:0001583	missense	165904	exon2			GTGCCCGAGAGCA	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.2423C>T	3.37:g.39228514G>A	ENSP00000343140:p.Ser808Leu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	G	3.312	-0.140545	0.06669	0.07172	3.49E-4	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.04862	3.54;3.95	4.11	3.23	0.37069	.	0.252041	0.37178	N	0.002208	T	0.00356	0.0011	N	0.14661	0.345	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41034	-0.9531	10	0.56958	D	0.05	.	10.0728	0.42343	0.1005:0.0:0.8995:0.0	.	808;808	Q702N8;Q702N8-2	XIRP1_HUMAN;.	L	808	ENSP00000379550:S808L;ENSP00000343140:S808L	ENSP00000343140:S808L	S	-	2	0	XIRP1	39203518	0.352000	0.24895	0.624000	0.29186	0.033000	0.12548	1.016000	0.29976	1.099000	0.41499	-0.244000	0.11960	TCG	G|0.977;A|0.023	0.023	strong		0.612	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
CREB3L3	84699	hgsc.bcm.edu	37	19	4154910	4154910	+	Silent	SNP	C	C	T	rs35474881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4154910C>T	ENST00000078445.2	+	2	189	c.42C>T	c.(40-42)gcC>gcT	p.A14A	CREB3L3_ENST00000252587.3_Silent_p.A5A|CREB3L3_ENST00000602147.1_Silent_p.A14A|CREB3L3_ENST00000595923.1_Silent_p.A14A|CREB3L3_ENST00000602257.1_Silent_p.A14A	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	14					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTCTGCTGCCTGCTCCATGG	0.622													C|||	429	0.0856629	0.0855	0.0821	5008	,	,		18561	0.0308		0.1431	False		,,,				2504	0.0859				p.A14A		Atlas-SNP	.											CREB3L3,NS,carcinoma,+1,2	CREB3L3	53	2	0			c.C42T						PASS	.	C		403,4003	199.4+/-223.0	24,355,1824	96.0	79.0	85.0		42	0.7	0.0	19	dbSNP_126	85	1175,7425	239.0+/-270.3	90,995,3215	no	coding-synonymous	CREB3L3	NM_032607.1		114,1350,5039	TT,TC,CC		13.6628,9.1466,12.1329		14/462	4154910	1578,11428	2203	4300	6503	SO:0001819	synonymous_variant	84699	exon2			TGCTGCCTGCTCC		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"""basic leucine zipper proteins"""	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.42C>T	19.37:g.4154910C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	164	91	0.554878	NM_001271997	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	37	CCDS12121.1																																																																																			C|0.881;T|0.119	0.119	strong		0.622	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	
PCDHGA7	56108	hgsc.bcm.edu	37	5	140763029	140763029	+	Missense_Mutation	SNP	A	A	G	rs2072315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140763029A>G	ENST00000518325.1	+	1	563	c.563A>G	c.(562-564)gAa>gGa	p.E188G	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	188	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> G (in dbSNP:rs2072315).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGACGATGAAACTAAGTAC	0.627													.|||	2720	0.543131	0.8495	0.6254	5008	,	,		17317	0.3264		0.4225	False		,,,				2504	0.4182				p.E188G		Atlas-SNP	.											.	PCDHGA7	130	.	0			c.A563G						PASS	.	G	,,,,,,GLY/GLU,,,,GLY/GLU	3433,813		1403,627,93	23.0	28.0	26.0		,,,,,,563,,,,563	4.2	0.9	5	dbSNP_96	26	3661,4845		784,2093,1376	yes	intron,intron,intron,intron,intron,intron,missense,intron,intron,intron,missense	PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032087.1	,,,,,,98,,,,98	2187,2720,1469	GG,GA,AA		43.0402,19.1474,44.3695	,,,,,,,,,,	,,,,,,188/933,,,,188/818	140763029	7094,5658	2123	4253	6376	SO:0001583	missense	56108	exon1			ACGATGAAACTAA	AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"""Cadherins / Protocadherins : Clustered"""	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.563A>G	5.37:g.140763029A>G	ENSP00000430024:p.Glu188Gly	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	1144	0.5238095238095238	399	0.8109756097560976	218	0.6022099447513812	189	0.3304195804195804	338	0.44591029023746703	.	0.867	-0.733271	0.03135	0.808526	0.430402	ENSG00000253537	ENST00000518325	T	0.19532	2.14	5.11	4.23	0.50019	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00005	-3.27	0.37323	P	0.09037799999999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39375	-0.9617	8	0.02654	T	1	.	12.4703	0.55783	0.1437:0.0:0.8563:0.0	rs2072315;rs17603026;rs52792598;rs57573292;rs2072315	188;188	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	G	188	ENSP00000430024:E188G	ENSP00000430024:E188G	E	+	2	0	PCDHGA7	140743213	0.916000	0.31088	0.908000	0.35775	0.368000	0.29767	1.416000	0.34759	1.290000	0.44636	-0.119000	0.15052	GAA	A|0.473;G|0.527	0.527	strong		0.627	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920	
C10orf62	414157	hgsc.bcm.edu	37	10	99350128	99350128	+	Silent	SNP	A	A	G	rs7093643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99350128A>G	ENST00000370640.3	+	1	679	c.474A>G	c.(472-474)ctA>ctG	p.L158L	HOGA1_ENST00000370647.4_Intron|HOGA1_ENST00000370646.4_Intron|PI4K2A_ENST00000370649.3_Intron|PI4K2A_ENST00000555577.1_Intron	NM_001009997.2	NP_001009997.2	Q5T681	CJ062_HUMAN	chromosome 10 open reading frame 62	158										endometrium(2)|kidney(1)|lung(1)	4		Colorectal(252;0.162)		Epithelial(162;9.58e-11)|all cancers(201;8.62e-09)		CAGGTCACCTAGAGTCCAAGG	0.587													G|||	1392	0.277955	0.3548	0.2968	5008	,	,		20226	0.1369		0.3091	False		,,,				2504	0.274				p.L158L		Atlas-SNP	.											C10orf62,colon,carcinoma,0,1	C10orf62	14	1	0			c.A474G						scavenged	.	G	,,	1611,2795	663.3+/-401.2	295,1021,887	75.0	74.0	75.0		474,,	2.0	0.9	10	dbSNP_116	75	2716,5884	681.7+/-403.7	422,1872,2006	no	coding-synonymous,intron,intron	HOGA1,C10orf62	NM_001009997.2,NM_001134670.1,NM_138413.3	,,	717,2893,2893	GG,GA,AA		31.5814,36.5638,33.2693	,,	158/224,,	99350128	4327,8679	2203	4300	6503	SO:0001819	synonymous_variant	414157	exon1			TCACCTAGAGTCC		CCDS31261.1	10q24.2	2012-05-31			ENSG00000203942	ENSG00000203942			23294	protein-coding gene	gene with protein product							Standard	NM_001009997		Approved	bA548K23.1	uc001koa.3	Q5T681	OTTHUMG00000018858	ENST00000370640.3:c.474A>G	10.37:g.99350128A>G		Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_001009997	Q49A70|Q8N3Y6	Silent	SNP	ENST00000370640.3	37	CCDS31261.1																																																																																			A|0.704;G|0.296	0.296	strong		0.587	C10orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049723.1	NM_001009997	
TET2	54790	hgsc.bcm.edu	37	4	106156983	106156983	+	Silent	SNP	G	G	A	rs35695427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:106156983G>A	ENST00000540549.1	+	3	2744	c.1884G>A	c.(1882-1884)gaG>gaA	p.E628E	TET2_ENST00000394764.1_Silent_p.E628E|TET2_ENST00000305737.2_Silent_p.E628E|TET2_ENST00000380013.4_Silent_p.E628E|TET2_ENST00000413648.2_Silent_p.E628E|TET2_ENST00000513237.1_Silent_p.E649E|TET2_ENST00000545826.1_Silent_p.E628E			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	628	Gln-rich.				5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		CACAGCTGGAGCACAAGTCAC	0.478			"""Mis N, F"""		MDS								G|||	65	0.0129792	0.0484	0.0014	5008	,	,		20615	0.0		0.0	False		,,,				2504	0.0				p.E628E		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2_ENST00000305737,bladder,carcinoma,+2,2	TET2	1762	2	0			c.G1884A						PASS	.	G	,	225,4181	136.1+/-172.1	11,203,1989	70.0	71.0	71.0		1884,1884	0.0	0.1	4	dbSNP_126	71	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	TET2	NM_001127208.2,NM_017628.4	,	11,205,6287	AA,AG,GG		0.0233,5.1067,1.7453	,	628/2003,628/1166	106156983	227,12779	2203	4300	6503	SO:0001819	synonymous_variant	54790	exon3			GCTGGAGCACAAG	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.1884G>A	4.37:g.106156983G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	136	71	0.522059	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	37	CCDS47120.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	G	0.008	-1.911390	0.00508	0.051067	2.33E-4	ENSG00000168769	ENST00000535110	.	.	.	5.59	-0.00446	0.14022	.	.	.	.	.	T	0.02380	0.0073	.	.	.	0.48341	D	0.999636	.	.	.	.	.	.	T	0.27157	-1.0082	5	0.02654	T	1	.	1.5409	0.02555	0.3344:0.1288:0.389:0.1477	rs35695427	.	.	.	N	628	.	ENSP00000438851:S628N	S	+	2	0	TET2	106376432	0.996000	0.38824	0.083000	0.20561	0.103000	0.19146	0.236000	0.17967	0.243000	0.21327	-0.143000	0.13931	AGC	G|0.982;A|0.018	0.018	strong		0.478	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
CCDC142	84865	hgsc.bcm.edu	37	2	74708454	74708454	+	Missense_Mutation	SNP	A	A	C	rs142978072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74708454A>C	ENST00000393965.3	-	3	1550	c.1154T>G	c.(1153-1155)cTt>cGt	p.L385R	CCDC142_ENST00000290418.4_Missense_Mutation_p.L385R|TTC31_ENST00000233623.5_5'Flank|TTC31_ENST00000410003.1_5'Flank|TTC31_ENST00000442235.2_5'Flank|CCDC142_ENST00000471713.1_5'UTR	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	385										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						GGATGTGGGAAGGCTGCTCTG	0.552													A|||	19	0.00379393	0.0144	0.0	5008	,	,		19474	0.0		0.0	False		,,,				2504	0.0				p.L385R		Atlas-SNP	.											.	CCDC142	40	.	0			c.T1154G						PASS	.	A	ARG/LEU	32,4374	37.6+/-69.7	0,32,2171	111.0	127.0	121.0		1154	-2.0	0.1	2	dbSNP_134	121	0,8600		0,0,4300	yes	missense	CCDC142	NM_032779.3	102	0,32,6471	CC,CA,AA		0.0,0.7263,0.246	possibly-damaging	385/744	74708454	32,12974	2203	4300	6503	SO:0001583	missense	84865	exon3			GTGGGAAGGCTGC	AK075543	CCDS1945.1	2p13.1	2008-02-05			ENSG00000135637	ENSG00000135637			25889	protein-coding gene	gene with protein product							Standard	NM_032779		Approved	FLJ14397	uc002slq.3	Q17RM4	OTTHUMG00000129962	ENST00000393965.3:c.1154T>G	2.37:g.74708454A>C	ENSP00000377537:p.Leu385Arg	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	145	56	0.386207	NM_032779	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Missense_Mutation	SNP	ENST00000393965.3	37		6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	A	2.527	-0.309466	0.05458	0.007263	0.0	ENSG00000135637	ENST00000393965;ENST00000290418	T;T	0.43688	0.94;0.94	4.74	-2.0	0.07433	.	1.069320	0.07370	N	0.885599	T	0.32376	0.0827	L	0.41236	1.265	0.09310	N	1	P;P;P	0.47677	0.899;0.899;0.899	P;P;P	0.51355	0.466;0.466;0.667	T	0.36578	-0.9742	10	0.52906	T	0.07	0.0723	5.5768	0.17228	0.3761:0.1645:0.4594:0.0	.	385;385;385	Q17RM4;Q17RM4-2;Q17RM4-3	CC142_HUMAN;.;.	R	385	ENSP00000377537:L385R;ENSP00000290418:L385R	ENSP00000290418:L385R	L	-	2	0	CCDC142	74561962	0.003000	0.15002	0.052000	0.19188	0.399000	0.30720	0.052000	0.14163	-0.208000	0.10171	0.460000	0.39030	CTT	A|0.997;C|0.003	0.003	strong		0.552	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2413788	2413788	+	Missense_Mutation	SNP	G	G	A	rs147023760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2413788G>A	ENST00000332578.3	+	9	1243	c.1243G>A	c.(1243-1245)Gcc>Acc	p.A415T		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	415	Peptidase S1 1. {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)		GTGTGCGGAAGCCCGGCGTCC	0.652													G|||	78	0.0155751	0.0575	0.0029	5008	,	,		16111	0.0		0.0	False		,,,				2504	0.0				p.A415T		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.G1243A						PASS	.	G	THR/ALA	191,4215	119.2+/-156.9	7,177,2019	56.0	60.0	59.0		1243	2.9	0.0	19	dbSNP_134	59	0,8600		0,0,4300	yes	missense	TMPRSS9	NM_182973.1	58	7,177,6319	AA,AG,GG		0.0,4.335,1.4686	possibly-damaging	415/1060	2413788	191,12815	2203	4300	6503	SO:0001583	missense	360200	exon9			GCGGAAGCCCGGC	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.1243G>A	19.37:g.2413788G>A	ENSP00000330264:p.Ala415Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	9.621	1.133714	0.21123	0.04335	0.0	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.88664	-2.41	3.93	2.87	0.33458	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.157070	0.29806	N	0.011145	T	0.54711	0.1875	N	0.25647	0.755	0.09310	N	1	D;P	0.76494	0.999;0.587	D;P	0.79108	0.992;0.486	T	0.69367	-0.5164	10	0.15066	T	0.55	.	12.189	0.54257	0.0:0.1739:0.8261:0.0	.	415;449	Q7Z410;E7EMP4	TMPS9_HUMAN;.	T	449;415	ENSP00000330264:A415T	ENSP00000330264:A415T	A	+	1	0	TMPRSS9	2364788	0.674000	0.27549	0.004000	0.12327	0.000000	0.00434	2.621000	0.46418	0.637000	0.30526	-0.314000	0.08810	GCC	G|0.983;A|0.017	0.017	strong		0.652	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
MYH7	4625	hgsc.bcm.edu	37	14	23892888	23892888	+	Silent	SNP	A	A	G	rs7157716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	309	2	0.00647249		WXS	Illumina HiSeq	Phase_I	307	144	0.469055	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29910562	29910562	+	Silent	SNP	A	A	C	rs281864725|rs1059418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29910562A>C	ENST00000396634.1	+	4	443	c.102A>C	c.(100-102)acA>acC	p.T34T	HLA-A_ENST00000376809.5_Silent_p.T34T|HLA-A_ENST00000376802.2_Silent_p.T34T|HLA-A_ENST00000376806.5_Silent_p.T34T			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	34	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						ATTTCTTCACATCCGTGTCCC	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)			a|||	1002	0.20008	0.1641	0.1182	5008	,	,		13677	0.3284		0.1282	False		,,,				2504	0.2485				p.T34T		Atlas-SNP	.											.	HLA-A	89	.	0			c.A102C						PASS	.						17.0	16.0	16.0					6																	29910562		2189	4275	6464	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CTTCACATCCGTG	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.102A>C	6.37:g.29910562A>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	15	0.205479	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			A|0.837;C|0.159;T|0.004	0.159	strong		0.721	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
INSRR	3645	hgsc.bcm.edu	37	1	156814884	156814884	+	Silent	SNP	C	C	T	rs149474857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156814884C>T	ENST00000368195.3	-	12	2817	c.2421G>A	c.(2419-2421)gcG>gcA	p.A807A	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	807					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCATGGTGCGCGCAAAGACGA	0.617													C|||	36	0.0071885	0.0272	0.0	5008	,	,		16306	0.0		0.0	False		,,,				2504	0.0				p.A807A		Atlas-SNP	.											.	INSRR	309	.	0			c.G2421A						PASS	.	C	,	104,4302	78.3+/-116.7	0,104,2099	23.0	22.0	22.0		,2421	-4.1	0.9	1	dbSNP_134	22	1,8599		0,1,4299	no	intron,coding-synonymous	INSRR,NTRK1	NM_001007792.1,NM_014215.2	,	0,105,6398	TT,TC,CC		0.0116,2.3604,0.8073	,	,807/1298	156814884	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	3645	exon12			GGTGCGCGCAAAG	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"""Fibronectin type III domain containing"""	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2421G>A	1.37:g.156814884C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_014215	O60724|Q5VZS3	Silent	SNP	ENST00000368195.3	37	CCDS1160.1																																																																																			C|0.991;T|0.009	0.009	strong		0.617	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215	
MUC4	4585	hgsc.bcm.edu	37	3	195513590	195513590	+	Missense_Mutation	SNP	C	C	T	rs74192533		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513590C>T	ENST00000463781.3	-	2	5320	c.4861G>A	c.(4861-4863)Gac>Aac	p.D1621N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D1621N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)		GAGGAAGTGTCGGTGACAGGA	0.572																																					p.D1621N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.G4861A						scavenged	.						16.0	21.0	19.0					3																	195513590		684	1562	2246	SO:0001583	missense	4585	exon2			AAGTGTCGGTGAC	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.4861G>A	3.37:g.195513590C>T	ENSP00000417498:p.Asp1621Asn	Somatic	567	4	0.00705467		WXS	Illumina HiSeq	Phase_I	488	9	0.0184426	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	.	.	.	.	.	.	.	.	.	.	-	6.630	0.484649	0.12641	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35421	1.31;1.33	.	.	.	.	.	.	.	.	T	0.12774	0.0310	N	0.08118	0	0.09310	N	1	P	0.47545	0.897	B	0.35312	0.2	T	0.11690	-1.0577	7	.	.	.	.	3.6132	0.08067	2.0E-4:0.5026:0.4969:2.0E-4	.	1621	E7ESK3	.	N	1621	ENSP00000417498:D1621N;ENSP00000420243:D1621N	.	D	-	1	0	MUC4	196997985	0.000000	0.05858	0.018000	0.16275	0.018000	0.09664	-0.145000	0.10265	0.088000	0.17205	0.089000	0.15464	GAC	CGGTGACAG|0.500;TGGTGACAA|0.500	.	alt		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF157	7712	hgsc.bcm.edu	37	X	47272480	47272480	+	Silent	SNP	G	G	A	rs61736399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47272480G>A	ENST00000377073.3	+	4	1094	c.1008G>A	c.(1006-1008)ggG>ggA	p.G336G		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	336					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)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						GTGAATGTGGGAAATTCTTCC	0.418													G|||	23	0.00609272	0.0144	0.0043	3775	,	,		15735	0.0		0.001	False		,,,				2504	0.0				p.G336G		Atlas-SNP	.											.	ZNF157	46	.	0			c.G1008A						PASS	.	G		119,3716		3,94,19,1535,552	39.0	37.0	38.0		1008	0.3	0.6	X	dbSNP_129	38	1,6726		0,1,0,2427,1871	no	coding-synonymous	ZNF157	NM_003446.3		3,95,19,3962,2423	AA,AG,A,GG,G		0.0149,3.103,1.1361		336/507	47272480	120,10442	2203	4299	6502	SO:0001819	synonymous_variant	7712	exon4			ATGTGGGAAATTC	U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"""Zinc fingers, C2H2-type"", ""-"""	12942	protein-coding gene	gene with protein product		300024	"""zinc finger protein 157 (HZF22)"""			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.1008G>A	X.37:g.47272480G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	81	27	0.333333	NM_003446	Q96LE9	Silent	SNP	ENST00000377073.3	37	CCDS14278.1																																																																																			G|0.990;A|0.010	0.010	strong		0.418	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446	
TOM1L2	146691	hgsc.bcm.edu	37	17	17786042	17786042	+	Missense_Mutation	SNP	G	G	T	rs146710625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17786042G>T	ENST00000379504.3	-	6	720	c.637C>A	c.(637-639)Ccc>Acc	p.P213T	TOM1L2_ENST00000581396.1_Missense_Mutation_p.P163T|TOM1L2_ENST00000535933.1_Intron|TOM1L2_ENST00000542206.1_Intron|TOM1L2_ENST00000395739.4_Missense_Mutation_p.P168T|TOM1L2_ENST00000318094.10_Missense_Mutation_p.P168T|TOM1L2_ENST00000540946.1_Intron	NM_001082968.1	NP_001076437.1	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 (chicken)	213					intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	clathrin binding (GO:0030276)|protein kinase binding (GO:0019901)			endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(2)	10	all_neural(463;0.228)					GCTGTGATGGGGCCAGTCACA	0.557																																					p.P213T	Melanoma(192;2505 2909 14455 25269)	Atlas-SNP	.											.	TOM1L2	54	.	0			c.C637A						PASS	.	G	THR/PRO,THR/PRO	11,4395	17.9+/-39.9	0,11,2192	96.0	89.0	91.0		487,637	4.7	1.0	17	dbSNP_134	91	0,8600		0,0,4300	yes	missense,missense	TOM1L2	NM_001033551.2,NM_001082968.1	38,38	0,11,6492	TT,TG,GG		0.0,0.2497,0.0846	benign,benign	163/458,213/508	17786042	11,12995	2203	4300	6503	SO:0001583	missense	146691	exon6			TGATGGGGCCAGT	AJ230803	CCDS32584.1, CCDS42270.1, CCDS74000.1, CCDS74001.1, CCDS74002.1, CCDS74003.1	17p11.2	2008-07-03	2001-11-28		ENSG00000175662	ENSG00000175662			11984	protein-coding gene	gene with protein product		615519	"""target of myb1 (chicken) homolog-like 1"""			10036180	Standard	NM_001082968		Approved		uc002grz.4	Q6ZVM7	OTTHUMG00000059353	ENST00000379504.3:c.637C>A	17.37:g.17786042G>T	ENSP00000368818:p.Pro213Thr	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	192	85	0.442708	NM_001082968	B7Z2L7|B7Z7F4|Q86V61|Q8TDE7|Q96M88	Missense_Mutation	SNP	ENST00000379504.3	37	CCDS42270.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.282146	0.80692	0.002497	0.0	ENSG00000175662	ENST00000379504;ENST00000318094;ENST00000395739;ENST00000537091	T;T	0.41065	1.01;1.01	5.7	4.73	0.59995	.	0.096186	0.85682	D	0.000000	T	0.56292	0.1975	M	0.79926	2.475	0.80722	D	1	B;P;B;B	0.50369	0.104;0.934;0.081;0.326	B;P;B;B	0.49361	0.059;0.608;0.067;0.142	T	0.61917	-0.6964	10	0.41790	T	0.15	-7.6658	16.772	0.85541	0.0:0.129:0.871:0.0	.	163;168;213;163	B7Z8F0;Q6ZVM7-3;Q6ZVM7;Q6ZVM7-2	.;.;TM1L2_HUMAN;.	T	213;163;168;163	ENSP00000368818:P213T;ENSP00000379088:P168T	ENSP00000312860:P163T	P	-	1	0	TOM1L2	17726767	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	5.571000	0.67404	1.388000	0.46506	0.655000	0.94253	CCC	G|0.999;T|0.001	0.001	strong		0.557	TOM1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131928.1		
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305800	39305800	+	Missense_Mutation	SNP	T	T	A	rs141998775		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.						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	132	0	0		WXS	Illumina HiSeq	Phase_I	109	16	0.146789	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		
DOCK1	1793	hgsc.bcm.edu	37	10	128795081	128795081	+	Silent	SNP	G	G	A	rs79043452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:128795081G>A	ENST00000280333.6	+	7	652	c.543G>A	c.(541-543)acG>acA	p.T181T		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	181					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)		TAACTAGCACGATTAGTCTCT	0.368													G|||	19	0.00379393	0.0144	0.0	5008	,	,		20216	0.0		0.0	False		,,,				2504	0.0				p.T181T		Atlas-SNP	.											.	DOCK1	188	.	0			c.G543A						PASS	.	G		40,3640		0,40,1800	214.0	203.0	206.0		498	-10.2	0.0	10	dbSNP_133	206	1,8191		0,1,4095	no	coding-synonymous	DOCK1	NM_001380.3		0,41,5895	AA,AG,GG		0.0122,1.087,0.3454		166/1851	128795081	41,11831	1840	4096	5936	SO:0001819	synonymous_variant	1793	exon7			TAGCACGATTAGT	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.543G>A	10.37:g.128795081G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	159	79	0.496855	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				G|0.997;A|0.003	0.003	strong		0.368	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
CCDC8	83987	hgsc.bcm.edu	37	19	46915182	46915182	+	Missense_Mutation	SNP	C	C	T	rs11880658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46915182C>T	ENST00000307522.3	-	1	1659	c.886G>A	c.(886-888)Ggg>Agg	p.G296R		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	296			G -> R (in dbSNP:rs11880658).		microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;4.66e-05)|all cancers(93;0.000582)|Epithelial(262;0.00428)|GBM - Glioblastoma multiforme(486;0.0421)		GCCTCTCCCCCCTGATCAGCC	0.642													C|||	215	0.0429313	0.1558	0.0101	5008	,	,		16994	0.0		0.002	False		,,,				2504	0.0				p.G296R		Atlas-SNP	.											.	CCDC8	56	.	0			c.G886A						PASS	.	C	ARG/GLY	511,3895	229.4+/-244.0	26,459,1718	85.0	85.0	85.0		886	-0.9	0.2	19	dbSNP_120	85	4,8596	2.2+/-6.3	0,4,4296	yes	missense	CCDC8	NM_032040.3	125	26,463,6014	TT,TC,CC		0.0465,11.5978,3.9597	benign	296/539	46915182	515,12491	2203	4300	6503	SO:0001583	missense	83987	exon1			CTCCCCCCTGATC	BC025243	CCDS12685.1	19q13.33	2012-04-17			ENSG00000169515	ENSG00000169515		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25367	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 20"""	614145				11230166	Standard	NM_032040		Approved	DKFZp564K0322, 3M3, PPP1R20	uc002pep.3	Q9H0W5	OTTHUMG00000162348	ENST00000307522.3:c.886G>A	19.37:g.46915182C>T	ENSP00000303158:p.Gly296Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_032040	Q8TB26	Missense_Mutation	SNP	ENST00000307522.3	37	CCDS12685.1	80	0.03663003663003663	76	0.15447154471544716	4	0.011049723756906077	0	0.0	0	0.0	C	4.694	0.129001	0.08981	0.115978	4.65E-4	ENSG00000169515	ENST00000307522	T	0.10668	2.85	3.87	-0.89	0.10577	.	0.845492	0.09922	N	0.738356	T	0.00039	0.0001	N	0.02011	-0.69	0.29953	N	0.820099	B	0.06786	0.001	B	0.08055	0.003	T	0.48007	-0.9072	10	0.11485	T	0.65	-2.0588	8.1056	0.30883	0.0:0.5064:0.0:0.4936	rs11880658	296	Q9H0W5	CCDC8_HUMAN	R	296	ENSP00000303158:G296R	ENSP00000303158:G296R	G	-	1	0	CCDC8	51607022	0.000000	0.05858	0.194000	0.23346	0.165000	0.22458	-0.753000	0.04792	-0.122000	0.11766	0.655000	0.94253	GGG	C|0.962;T|0.038	0.038	strong		0.642	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	NM_032040	
CARD11	84433	hgsc.bcm.edu	37	7	2957005	2957005	+	Silent	SNP	T	T	C	rs3735124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	59	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	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	
KLHL33	123103	hgsc.bcm.edu	37	14	20897676	20897676	+	Missense_Mutation	SNP	T	T	C	rs1953225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20897676T>C	ENST00000344581.4	-	3	1256	c.1034A>G	c.(1033-1035)gAg>gGg	p.E345G		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	345			E -> G (in dbSNP:rs1953225).									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)		GACATTGAGCTCAGGGTTGTA	0.498													T|||	1298	0.259185	0.3812	0.134	5008	,	,		20948	0.2718		0.2097	False		,,,				2504	0.2209				p.E345G		Atlas-SNP	.											.	KLHL33	37	.	0			c.A1034G						PASS	.	T	GLY/GLU	448,936		84,280,328	187.0	163.0	170.0		1034	5.3	1.0	14	dbSNP_92	170	605,2577		57,491,1043	yes	missense	KLHL33	NM_001109997.2	98	141,771,1371	CC,CT,TT		19.0132,32.3699,23.0618	probably-damaging	345/534	20897676	1053,3513	692	1591	2283	SO:0001583	missense	123103	exon3			TTGAGCTCAGGGT		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.1034A>G	14.37:g.20897676T>C	ENSP00000341549:p.Glu345Gly	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_001109997		Missense_Mutation	SNP	ENST00000344581.4	37	CCDS53882.1	526	0.24084249084249085	173	0.3516260162601626	50	0.13812154696132597	153	0.2674825174825175	150	0.19788918205804748	T	8.186	0.795008	0.16327	0.323699	0.190132	ENSG00000185271	ENST00000344581	T	0.79554	-1.28	5.34	5.34	0.76211	Kelch-type beta propeller (1);	0.269175	0.36034	N	0.002825	T	0.00012	0.0000	L	0.39085	1.19	0.80722	P	0.0	B	0.16603	0.018	B	0.18871	0.023	T	0.05115	-1.0905	9	0.56958	D	0.05	.	12.9404	0.58340	0.0:0.0:0.0:1.0	rs1953225;rs17242641;rs57704167;rs1953225	345	A6NCF5	KLH33_HUMAN	G	345	ENSP00000341549:E345G	ENSP00000341549:E345G	E	-	2	0	KLHL33	19967516	0.003000	0.15002	0.986000	0.45419	0.965000	0.64279	1.324000	0.33712	2.242000	0.73789	0.533000	0.62120	GAG	T|0.747;C|0.253	0.253	strong		0.498	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
SAA1	6288	hgsc.bcm.edu	37	11	18290866	18290866	+	Silent	SNP	T	T	C	rs1136745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18290866T>C	ENST00000405158.2	+	3	400	c.216T>C	c.(214-216)gcT>gcC	p.A72A	RNA5SP334_ENST00000364825.1_RNA|SAA1_ENST00000532858.1_Silent_p.A72A|SAA1_ENST00000356524.4_Silent_p.A72A	NM_000331.4	NP_000322	P0DJI8	SAA1_HUMAN	serum amyloid A1	72					acute-phase response (GO:0006953)|innate immune response (GO:0045087)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of inflammatory response (GO:0050728)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of interleukin-1 secretion (GO:0050716)|regulation of protein secretion (GO:0050708)	endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	G-protein coupled receptor binding (GO:0001664)|heparin binding (GO:0008201)	p.A72A(1)		endometrium(1)|large_intestine(3)|lung(2)|stomach(3)	9					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	GTGCCTGGGCTGCAGAAGTGA	0.562																																					p.A72A		Atlas-SNP	.											SAA1,NS,carcinoma,0,1	SAA1	14	1	1	Substitution - coding silent(1)	stomach(1)	c.T216C						scavenged	.						20.0	21.0	20.0					11																	18290866		2190	4260	6450	SO:0001819	synonymous_variant	6288	exon3			CTGGGCTGCAGAA	M10906	CCDS7835.1	11p15.1	2014-01-30			ENSG00000173432	ENSG00000173432		"""Endogenous ligands"""	10513	protein-coding gene	gene with protein product		104750		SAA		2595451, 9305847	Standard	NM_199161		Approved	PIG4, TP53I4	uc021qeo.1	P0DJI8	OTTHUMG00000166147	ENST00000405158.2:c.216T>C	11.37:g.18290866T>C		Somatic	138	14	0.101449		WXS	Illumina HiSeq	Phase_I	129	22	0.170543	NM_199161	P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Silent	SNP	ENST00000405158.2	37	CCDS7835.1																																																																																			C|1.000;|0.000	1.000	weak		0.562	SAA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395864.1	NM_199161	
ZNF792	126375	hgsc.bcm.edu	37	19	35449409	35449409	+	Silent	SNP	G	G	A	rs2651081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35449409G>A	ENST00000404801.1	-	4	1736	c.1350C>T	c.(1348-1350)caC>caT	p.H450H	ZNF792_ENST00000605484.1_Silent_p.H383H	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	450					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.H371H(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CACCACACCCGTGAGGCCGCT	0.502													G|||	1639	0.327276	0.4841	0.1859	5008	,	,		21139	0.2034		0.329	False		,,,				2504	0.3415				p.H450H	GBM(1;7 183 21053 22581 22847)	Atlas-SNP	.											FLJ38451,NS,carcinoma,0,1	ZNF792	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C1350T						PASS	.	G		1953,2453	554.8+/-379.1	408,1137,658	117.0	115.0	116.0		1350	-0.8	0.0	19	dbSNP_100	116	2546,6054	416.0+/-352.0	383,1780,2137	no	coding-synonymous	ZNF792	NM_175872.4		791,2917,2795	AA,AG,GG		29.6047,44.3259,34.5917		450/633	35449409	4499,8507	2203	4300	6503	SO:0001819	synonymous_variant	126375	exon4			ACACCCGTGAGGC	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.1350C>T	19.37:g.35449409G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Silent	SNP	ENST00000404801.1	37	CCDS12440.2																																																																																			G|0.659;A|0.341	0.341	strong		0.502	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
TARBP1	6894	hgsc.bcm.edu	37	1	234546245	234546245	+	Silent	SNP	C	C	T	rs1141264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:234546245C>T	ENST00000040877.1	-	23	3737	c.3738G>A	c.(3736-3738)acG>acA	p.T1246T	TARBP1_ENST00000483404.1_5'Flank	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1246					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)			CTGCTAAAAACGTACAAATGC	0.284													T|||	1688	0.337061	0.211	0.3847	5008	,	,		18371	0.3958		0.3907	False		,,,				2504	0.3579				p.T1246T		Atlas-SNP	.											.	TARBP1	111	.	0			c.G3738A						PASS	.	T		1057,3343	692.5+/-405.5	132,793,1275	53.0	57.0	55.0		3738	-0.3	1.0	1	dbSNP_86	55	3311,5281	633.0+/-398.7	618,2075,1603	no	coding-synonymous	TARBP1	NM_005646.3		750,2868,2878	TT,TC,CC		38.5358,24.0227,33.6207		1246/1622	234546245	4368,8624	2200	4296	6496	SO:0001819	synonymous_variant	6894	exon23			TAAAAACGTACAA		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.3738G>A	1.37:g.234546245C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	186	89	0.478495	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			C|0.658;T|0.342	0.342	strong		0.284	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
RAD9A	5883	hgsc.bcm.edu	37	11	67160961	67160961	+	Intron	SNP	A	A	G	rs2066496|rs386754479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67160961A>G	ENST00000307980.2	+	4	327				RNU6-1238P_ENST00000517215.1_RNA	NM_001243224.1|NM_004584.2	NP_001230153.1|NP_004575.1	Q99638	RAD9A_HUMAN	RAD9 homolog A (S. pombe)						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)|DNA replication checkpoint (GO:0000076)|intra-S DNA damage checkpoint (GO:0031573)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|enzyme binding (GO:0019899)|exodeoxyribonuclease III activity (GO:0008853)|histone deacetylase binding (GO:0042826)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			lung(7)|upper_aerodigestive_tract(1)	8			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			GTCTTATCCCATGCAGTCTTT	0.562								Other conserved DNA damage response genes					a|||	869	0.173522	0.3328	0.1081	5008	,	,		18773	0.2292		0.0775	False		,,,				2504	0.046				p.M1V		Atlas-SNP	.											.	RAD9A	15	.	0			c.A1G						PASS	.	G		1244,3156	426.2+/-341.1	170,904,1126	79.0	72.0	74.0			-7.3	0.0	11	dbSNP_98	74	597,7993	158.8+/-212.2	14,569,3712	no	intron	RAD9A	NM_004584.2		184,1473,4838	GG,GA,AA		6.9499,28.2727,14.1724			67160961	1841,11149	2200	4295	6495	SO:0001627	intron_variant	5883	exon1			TATCCCATGCAGT	U53174	CCDS8159.1	11q13.1-q13.2	2008-02-05	2003-07-21	2003-07-23	ENSG00000172613	ENSG00000172613			9827	protein-coding gene	gene with protein product		603761	"""RAD9 (S. pombe) homolog"""	RAD9		8943031	Standard	NM_004584		Approved		uc001okr.3	Q99638	OTTHUMG00000167670	ENST00000307980.2:c.235-6A>G	11.37:g.67160961A>G		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_001243224	B2RCZ8|Q6FI29|Q96C41	Missense_Mutation	SNP	ENST00000307980.2	37	CCDS8159.1																																																																																			A|0.819;G|0.181	0.181	strong		0.562	RAD9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395481.2	NM_004584	
KY	339855	hgsc.bcm.edu	37	3	134322814	134322814	+	Silent	SNP	G	G	C	rs2293294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:134322814G>C	ENST00000423778.2	-	11	1654	c.1593C>G	c.(1591-1593)ggC>ggG	p.G531G	KY_ENST00000508956.1_Silent_p.G510G|KY_ENST00000503669.1_3'UTR	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	531					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)	p.G531G(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGGCAAACTTGCCTGCATGGG	0.527													G|||	1482	0.295927	0.413	0.2349	5008	,	,		20559	0.1101		0.33	False		,,,				2504	0.3374				p.G531G		Atlas-SNP	.											KY_ENST00000423778,NS,carcinoma,0,1	KY	92	1	1	Substitution - coding silent(1)	stomach(1)	c.C1593G						PASS	.	G		1556,2496		331,894,801	79.0	81.0	80.0		1593	3.8	1.0	3	dbSNP_100	80	2993,5407		564,1865,1771	no	coding-synonymous	KY	NM_178554.4		895,2759,2572	CC,CG,GG		35.631,38.4008,36.5323		531/662	134322814	4549,7903	2026	4200	6226	SO:0001819	synonymous_variant	339855	exon11			AAACTTGCCTGCA	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.1593C>G	3.37:g.134322814G>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	90	52	0.577778	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			G|0.694;C|0.306	0.306	strong		0.527	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
THBS1	7057	hgsc.bcm.edu	37	15	39874092	39874092	+	Silent	SNP	C	C	T	rs35248254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39874092C>T	ENST00000260356.5	+	2	199	c.34C>T	c.(34-36)Ctg>Ttg	p.L12L		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	12					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CGTCCTGTTCCTGATGCATGT	0.592											OREG0023050	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	78	0.0155751	0.0552	0.0072	5008	,	,		18818	0.0		0.0	False		,,,				2504	0.0				p.L12L		Atlas-SNP	.											.	THBS1	106	.	0			c.C34T						PASS	.	C		165,4235	110.4+/-148.6	3,159,2038	121.0	101.0	108.0		34	4.0	1.0	15	dbSNP_126	108	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	THBS1	NM_003246.2		3,160,6334	TT,TC,CC		0.0116,3.75,1.2775		12/1171	39874092	166,12828	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon2			CTGTTCCTGATGC		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.34C>T	15.37:g.39874092C>T		Somatic	128	0	0	889	WXS	Illumina HiSeq	Phase_I	125	57	0.456	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.985;T|0.015	0.015	strong		0.592	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
SCG2	7857	hgsc.bcm.edu	37	2	224462714	224462714	+	Silent	SNP	G	G	A	rs721233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:224462714G>A	ENST00000305409.2	-	2	1519	c.1287C>T	c.(1285-1287)gaC>gaT	p.D429D		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|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)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		CACTGAGCCCGTCTGGTAGGG	0.468													G|||	277	0.0553115	0.1604	0.0346	5008	,	,		19418	0.001		0.0189	False		,,,				2504	0.0215				p.D429D		Atlas-SNP	.											.	SCG2	99	.	0			c.C1287T						PASS	.	G		663,3743	279.3+/-274.7	49,565,1589	78.0	78.0	78.0		1287	-3.1	0.2	2	dbSNP_86	78	173,8427	78.6+/-141.3	3,167,4130	no	coding-synonymous	SCG2	NM_003469.4		52,732,5719	AA,AG,GG		2.0116,15.0477,6.4278		429/618	224462714	836,12170	2203	4300	6503	SO:0001819	synonymous_variant	7857	exon2			GAGCCCGTCTGGT	M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"""secretoneurin"", ""chromogranin C"""	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.1287C>T	2.37:g.224462714G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_003469	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Silent	SNP	ENST00000305409.2	37	CCDS2457.1																																																																																			G|0.932;A|0.068	0.068	strong		0.468	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469	
OR10G7	390265	hgsc.bcm.edu	37	11	123909638	123909638	+	Missense_Mutation	SNP	G	G	A	rs148218442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909638G>A	ENST00000330487.5	-	1	79	c.71C>T	c.(70-72)cCc>cTc	p.P24L		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		TCCAAAGAGGGGGGCGTCCAG	0.572													G|||	62	0.0123802	0.0416	0.0101	5008	,	,		16260	0.0		0.0	False		,,,				2504	0.0				p.P24L		Atlas-SNP	.											OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	0			c.C71T						scavenged	.	G	LEU/PRO	70,4330	56.8+/-93.2	0,70,2130	96.0	92.0	94.0		71	-3.2	0.0	11	dbSNP_134	94	4,8594	3.0+/-9.4	0,4,4295	no	missense	OR10G7	NM_001004463.1	98	0,74,6425	AA,AG,GG		0.0465,1.5909,0.5693	benign	24/312	123909638	74,12924	2200	4299	6499	SO:0001583	missense	390265	exon1			AAGAGGGGGGCGT	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.71C>T	11.37:g.123909638G>A	ENSP00000329689:p.Pro24Leu	Somatic	408	2	0.00490196		WXS	Illumina HiSeq	Phase_I	229	109	0.475983	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	20	0.009157509157509158	12	0.024390243902439025	4	0.011049723756906077	0	0.0	4	0.005277044854881266	G	0.023	-1.397240	0.01175	0.015909	4.65E-4	ENSG00000182634	ENST00000330487	T	0.00036	8.86	3.38	-3.23	0.05109	.	1.833280	0.02752	N	0.117583	T	0.00039	0.0001	N	0.01096	-1.015	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33954	-0.9848	10	0.02654	T	1	.	10.6967	0.45903	0.7947:0.0:0.2053:0.0	.	24	Q8NGN6	O10G7_HUMAN	L	24	ENSP00000329689:P24L	ENSP00000329689:P24L	P	-	2	0	OR10G7	123414848	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.678000	0.05209	-0.661000	0.05345	-0.232000	0.12228	CCC	G|0.992;A|0.008	0.008	strong		0.572	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
ALAS2	212	hgsc.bcm.edu	37	X	55035751	55035751	+	Silent	SNP	C	C	T	rs6612251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:55035751C>T	ENST00000330807.5	-	11	1763	c.1626G>A	c.(1624-1626)gcG>gcA	p.A542A	ALAS2_ENST00000396198.3_Silent_p.A529A|ALAS2_ENST00000498636.1_5'UTR|ALAS2_ENST00000335854.4_Silent_p.A505A	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	542					cellular iron ion homeostasis (GO:0006879)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|hemoglobin biosynthetic process (GO:0042541)|oxygen homeostasis (GO:0032364)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5-aminolevulinate synthase activity (GO:0003870)|coenzyme binding (GO:0050662)|glycine binding (GO:0016594)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)	17					Glycine(DB00145)	GCAGCCCCACCGCAGTCCAAG	0.542													C|||	36	0.00953642	0.025	0.0	3775	,	,		12374	0.001		0.001	False		,,,				2504	0.001				p.A542A		Atlas-SNP	.											.	ALAS2	163	.	0			c.G1626A						PASS	.	C	,,	202,3631		3,164,32,1465,537	23.0	20.0	21.0		1626,1515,1587	-5.1	0.7	X	dbSNP_116	21	1,6722		0,0,1,2427,1868	no	coding-synonymous,coding-synonymous,coding-synonymous	ALAS2	NM_000032.4,NM_001037967.3,NM_001037968.3	,,	3,164,33,3892,2405	TT,TC,T,CC,C		0.0149,5.27,1.9231	,,	542/588,505/551,529/575	55035751	203,10353	2201	4296	6497	SO:0001819	synonymous_variant	212	exon11			CCCCACCGCAGTC		CCDS14366.1, CCDS35303.1, CCDS43960.1	Xp11.21	2008-02-05	2008-02-04		ENSG00000158578	ENSG00000158578	2.3.1.37		397	protein-coding gene	gene with protein product	"""sideroblastic/hypochromic anemia"""	301300	"""aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)"""	ASB		1577484	Standard	NM_000032		Approved		uc004dua.4	P22557	OTTHUMG00000021641	ENST00000330807.5:c.1626G>A	X.37:g.55035751C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	256	130	0.507812	NM_000032	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Silent	SNP	ENST00000330807.5	37	CCDS14366.1																																																																																			C|0.974;0|0.006	.	strong		0.542	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032	
TTLL12	23170	hgsc.bcm.edu	37	22	43568512	43568512	+	Missense_Mutation	SNP	C	C	T	rs34074034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:43568512C>T	ENST00000216129.6	-	10	1453	c.1390G>A	c.(1390-1392)Gtg>Atg	p.V464M	TTLL12_ENST00000484118.1_5'Flank|TTLL12_ENST00000494035.1_5'Flank	NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	464	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.		V -> M (in dbSNP:rs34074034).		cellular protein modification process (GO:0006464)					central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				ACCTTTCCCACGTCTTCTCGA	0.572													C|||	1014	0.202476	0.0598	0.1643	5008	,	,		16640	0.2351		0.2465	False		,,,				2504	0.3436				p.V464M		Atlas-SNP	.											.	TTLL12	50	.	0			c.G1390A						PASS	.	C	MET/VAL	385,4021	193.6+/-218.7	16,353,1834	209.0	150.0	170.0		1390	5.3	1.0	22	dbSNP_126	170	2043,6557	356.5+/-330.3	249,1545,2506	yes	missense	TTLL12	NM_015140.3	21	265,1898,4340	TT,TC,CC		23.7558,8.7381,18.6683	probably-damaging	464/645	43568512	2428,10578	2203	4300	6503	SO:0001583	missense	23170	exon10			TTCCCACGTCTTC	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"""Tubulin tyrosine ligase-like family"""	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.1390G>A	22.37:g.43568512C>T	ENSP00000216129:p.Val464Met	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	178	82	0.460674	NM_015140	Q20WK5|Q9UGU3	Missense_Mutation	SNP	ENST00000216129.6	37	CCDS14047.1	436	0.19963369963369965	39	0.07926829268292683	67	0.1850828729281768	132	0.23076923076923078	198	0.2612137203166227	C	22.3	4.264974	0.80358	0.087381	0.237558	ENSG00000100304	ENST00000216129;ENST00000423379	T	0.08193	3.12	5.31	5.31	0.75309	.	0.059184	0.64402	D	0.000002	T	0.00012	0.0000	M	0.82323	2.585	0.09310	P	0.9999999844361	D;D	0.76494	0.999;0.999	D;D	0.75484	0.971;0.986	T	0.00883	-1.1528	9	0.87932	D	0	-21.7077	18.9677	0.92702	0.0:1.0:0.0:0.0	rs34074034;rs60598679	464;464	B1AH89;Q14166	.;TTL12_HUMAN	M	464	ENSP00000216129:V464M	ENSP00000216129:V464M	V	-	1	0	TTLL12	41898456	1.000000	0.71417	0.985000	0.45067	0.367000	0.29736	5.546000	0.67243	2.466000	0.83321	0.561000	0.74099	GTG	C|0.803;G|0.000;T|0.197	0.197	strong		0.572	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
RET	5979	hgsc.bcm.edu	37	10	43615094	43615094	+	Silent	SNP	C	C	T	rs1800862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:43615094C>T	ENST00000355710.3	+	14	2740	c.2508C>T	c.(2506-2508)agC>agT	p.S836S	RET_ENST00000340058.5_Silent_p.S836S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	836	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	GCAACTCCAGCTCCCTGGACC	0.642		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				C|||	180	0.0359425	0.0129	0.0303	5008	,	,		15331	0.0		0.0586	False		,,,				2504	0.0849				p.S836S	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	.	RET	916	.	0			c.C2508T	GRCh37	CM012798	RET	M	rs1800862	PASS	.	C	,	117,4289	83.9+/-122.4	2,113,2088	36.0	35.0	35.0		2508,2508	2.5	1.0	10	dbSNP_89	35	435,8163	128.3+/-186.6	17,401,3881	no	coding-synonymous,coding-synonymous	RET	NM_020630.4,NM_020975.4	,	19,514,5969	TT,TC,CC		5.0593,2.6555,4.2448	,	836/1073,836/1115	43615094	552,12452	2203	4299	6502	SO:0001819	synonymous_variant	5979	exon14	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	CTCCAGCTCCCTG	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2508C>T	10.37:g.43615094C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	37	CCDS7200.1																																																																																			C|0.960;T|0.040	0.040	strong		0.642	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
TRPM3	80036	hgsc.bcm.edu	37	9	73150984	73150984	+	Missense_Mutation	SNP	C	C	T	rs6560142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:73150984C>T	ENST00000377110.3	-	25	5252	c.5009G>A	c.(5008-5010)cGa>cAa	p.R1670Q	TRPM3_ENST00000377106.1_Missense_Mutation_p.R1542Q|TRPM3_ENST00000358082.3_Missense_Mutation_p.R1532Q|TRPM3_ENST00000357533.2_Missense_Mutation_p.R1674Q|TRPM3_ENST00000396285.1_Missense_Mutation_p.R1529Q|TRPM3_ENST00000360823.2_Missense_Mutation_p.R1532Q|TRPM3_ENST00000408909.2_Missense_Mutation_p.R1529Q|TRPM3_ENST00000396280.5_Missense_Mutation_p.R1519Q|TRPM3_ENST00000377105.1_Missense_Mutation_p.R1529Q|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396292.4_Missense_Mutation_p.R1542Q|TRPM3_ENST00000423814.3_Missense_Mutation_p.R1697Q			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1695					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						GAAGGGATTTCGCAGGCTTGC	0.562													C|||	3009	0.600839	0.6278	0.5764	5008	,	,		18907	0.7937		0.5835	False		,,,				2504	0.4008				p.R1670Q		Atlas-SNP	.											.	TRPM3	700	.	0			c.G5009A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	2735,1671	657.4+/-400.2	862,1011,330	167.0	162.0	163.0		5009,4550,4586,4520,4556,4625,4595	5.8	1.0	9	dbSNP_116	163	4741,3859	609.1+/-395.5	1312,2117,871	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	43,43,43,43,43,43,43	2174,3128,1201	TT,TC,CC		44.8721,37.9256,42.5188	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1670/1708,1517/1555,1529/1567,1507/1545,1519/1557,1542/1580,1532/1570	73150984	7476,5530	2203	4300	6503	SO:0001583	missense	80036	exon25			GGATTTCGCAGGC	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.5009G>A	9.37:g.73150984C>T	ENSP00000366314:p.Arg1670Gln	Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	167	166	0.994012	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	1406	0.6437728937728938	301	0.6117886178861789	194	0.5359116022099447	466	0.8146853146853147	445	0.5870712401055409	C	26.7	4.765198	0.90020	0.620744	0.551279	ENSG00000083067	ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	T;T;T;T;T;T;T;T;T;T	0.59638	0.36;0.27;0.27;0.25;0.36;0.25;0.28;0.27;0.27;0.35	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.24115	0.695	0.21386	P	0.999701503	D;D;P;D;D;D;D	0.71674	0.998;0.998;0.913;0.984;0.998;0.998;0.997	D;D;B;B;D;D;D	0.75484	0.986;0.979;0.233;0.381;0.979;0.979;0.953	T	0.31308	-0.9948	9	0.32370	T	0.25	-8.4256	19.9981	0.97395	0.0:1.0:0.0:0.0	rs6560142;rs17535977;rs52826401;rs60325149;rs6560142	1670;1660;1674;1532;1529;1642;1529	Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.;.;.;.;.;.;.	Q	1670;1542;1532;1529;1674;1529;1529;1542;1532;1697	ENSP00000366314:R1670Q;ENSP00000366310:R1542Q;ENSP00000354066:R1532Q;ENSP00000366309:R1529Q;ENSP00000350140:R1674Q;ENSP00000386127:R1529Q;ENSP00000379581:R1529Q;ENSP00000379587:R1542Q;ENSP00000350791:R1532Q;ENSP00000389542:R1697Q	ENSP00000350140:R1674Q	R	-	2	0	TRPM3	72340804	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	2.729000	0.93468	0.655000	0.94253	CGA	C|0.396;T|0.604	0.604	strong		0.562	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945	
CCDC7	79741	hgsc.bcm.edu	37	10	32832249	32832249	+	Nonsense_Mutation	SNP	C	C	T	rs201935164		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:32832249C>T	ENST00000362006.5	+	13	1558	c.1015C>T	c.(1015-1017)Cga>Tga	p.R339*	CCDC7_ENST00000277657.6_Nonsense_Mutation_p.R339*	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	339										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				TACAAATAATCGAACAAAGAA	0.264													C|||	1	0.000199681	0.0	0.0	5008	,	,		14861	0.001		0.0	False		,,,				2504	0.0				p.R339X		Atlas-SNP	.											CCDC7,colon,carcinoma,-1,1	CCDC7	47	1	0			c.C1015T						scavenged	.						28.0	29.0	29.0					10																	32832249		2186	4257	6443	SO:0001587	stop_gained	221016	exon13			AATAATCGAACAA	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.1015C>T	10.37:g.32832249C>T	ENSP00000355078:p.Arg339*	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	213	3	0.0140845	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Nonsense_Mutation	SNP	ENST00000362006.5	37	CCDS7173.1	.	.	.	.	.	.	.	.	.	.	C	35	5.419212	0.96092	.	.	ENSG00000216937	ENST00000277657;ENST00000362006;ENST00000435402	.	.	.	3.47	2.56	0.30785	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-4.3315	8.3553	0.32327	0.2342:0.7658:0.0:0.0	.	.	.	.	X	339;339;8	.	ENSP00000277657:R339X	R	+	1	2	CCDC7	32872255	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-0.047000	0.11963	1.058000	0.40530	-0.278000	0.10074	CGA	C|0.999;T|0.001	0.001	weak		0.264	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023	
PCSK5	5125	hgsc.bcm.edu	37	9	78853916	78853916	+	Missense_Mutation	SNP	G	G	C	rs17062264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:78853916G>C	ENST00000545128.1	+	23	3446	c.2908G>C	c.(2908-2910)Gga>Cga	p.G970R		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	970	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						GGGAGAGTGTGGAGATAGCTG	0.537													C|||	687	0.137181	0.2156	0.1282	5008	,	,		18750	0.0099		0.1243	False		,,,				2504	0.182				p.G970R		Atlas-SNP	.											.	PCSK5	329	.	0			c.G2908C						PASS	.	C	ARG/GLY	321,1431		26,269,581	40.0	35.0	36.0		2908	4.5	0.6	9	dbSNP_123	36	475,3507		31,413,1547	yes	missense	PCSK5	NM_001190482.1	125	57,682,2128	CC,CG,GG		11.9287,18.3219,13.8821		970/1861	78853916	796,4938	876	1991	2867	SO:0001583	missense	5125	exon23			GAGTGTGGAGATA		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.2908G>C	9.37:g.78853916G>C	ENSP00000446280:p.Gly970Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	240	0.10989010989010989	96	0.1951219512195122	46	0.1270718232044199	3	0.005244755244755245	95	0.12532981530343007	C	0.020	-1.435645	0.01108	0.183219	0.119287	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.28666	1.6;1.6	5.54	4.53	0.55603	.	0.496439	0.19738	N	0.107185	T	0.00012	0.0000	N	0.01431	-0.87	0.58432	P	2.9999999999752447E-6	.	.	.	.	.	.	T	0.32134	-0.9918	7	0.16420	T	0.52	0.1669	3.0125	0.06048	0.2711:0.4904:0.14:0.0985	rs17062264;rs56482229;rs58574166;rs17062264	.	.	.	R	970;673;643	ENSP00000446280:G970R;ENSP00000411654:G643R	ENSP00000365945:G673R	G	+	1	0	PCSK5	78043736	0.332000	0.24722	0.620000	0.29132	0.123000	0.20343	1.157000	0.31724	0.523000	0.28482	-0.195000	0.12781	GGA	G|0.882;C|0.118	0.118	strong		0.537	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ABCC10	89845	hgsc.bcm.edu	37	6	43411700	43411700	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43411700C>T	ENST00000372530.4	+	11	2661	c.2446C>T	c.(2446-2448)Caa>Taa	p.Q816*	ABCC10_ENST00000244533.3_Nonsense_Mutation_p.Q788*	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	816	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	GCCACTGGTACAAGCTGTCCC	0.542																																					p.Q816X		Atlas-SNP	.											.	ABCC10	118	.	0			c.C2446T						PASS	.						150.0	145.0	147.0					6																	43411700		2203	4300	6503	SO:0001587	stop_gained	89845	exon11			CTGGTACAAGCTG	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.2446C>T	6.37:g.43411700C>T	ENSP00000361608:p.Gln816*	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Nonsense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	42	9.524227	0.99195	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	.	.	.	5.67	5.67	0.87782	.	0.128063	0.52532	D	0.000071	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-28.5185	13.6285	0.62181	0.0:0.7989:0.2011:0.0	.	.	.	.	X	816;788	.	ENSP00000244533:Q788X	Q	+	1	0	ABCC10	43519678	0.921000	0.31238	0.981000	0.43875	0.798000	0.45092	3.288000	0.51739	2.673000	0.90976	0.655000	0.94253	CAA	.	.	none		0.542	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
SBSPON	157869	hgsc.bcm.edu	37	8	74005179	74005179	+	Silent	SNP	T	T	G	rs114228241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:74005179T>G	ENST00000297354.6	-	1	328	c.124A>C	c.(124-126)Agg>Cgg	p.R42R	SBSPON_ENST00000519697.1_Intron	NM_153225.3	NP_694957.3	Q8IVN8	SBSPO_HUMAN	somatomedin B and thrombospondin, type 1 domain containing	42	SMB. {ECO:0000255|PROSITE- ProRule:PRU00350}.				immune response (GO:0006955)	proteinaceous extracellular matrix (GO:0005578)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)										CTGTCCAGCCTCCAGCCGCGG	0.741													T|||	588	0.117412	0.171	0.0461	5008	,	,		7673	0.251		0.0089	False		,,,				2504	0.0695				p.R42R		Atlas-SNP	.											.	.	.	.	0			c.A124C						PASS	.	T		372,3366		23,326,1520	14.0	22.0	20.0		124	2.7	1.0	8	dbSNP_132	20	36,8130		0,36,4047	no	coding-synonymous	C8orf84	NM_153225.3		23,362,5567	GG,GT,TT		0.4409,9.9518,3.4274		42/265	74005179	408,11496	1869	4083	5952	SO:0001819	synonymous_variant	157869	exon1			CCAGCCTCCAGCC		CCDS43747.2	8q21.11	2013-08-07	2012-05-15	2012-05-15	ENSG00000164764	ENSG00000164764			30362	protein-coding gene	gene with protein product	"""RPE spondin"", ""rpe-spondin"""		"""chromosome 8 open reading frame 84"""	C8orf84		12107410	Standard	NM_153225		Approved	RPESP	uc003xzf.3	Q8IVN8	OTTHUMG00000157144	ENST00000297354.6:c.124A>C	8.37:g.74005179T>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	62	23	0.370968	NM_153225	A8KAA5|Q96J64	Silent	SNP	ENST00000297354.6	37	CCDS43747.2																																																																																			T|0.913;G|0.087	0.087	strong		0.741	SBSPON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347584.2	NM_153225	
FMO3	2328	hgsc.bcm.edu	37	1	171076888	171076888	+	Missense_Mutation	SNP	G	G	C	rs12072582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171076888G>C	ENST00000367755.4	+	4	505	c.394G>C	c.(394-396)Gat>Cat	p.D132H	FMO3_ENST00000392085.2_Missense_Mutation_p.D132H|FMO3_ENST00000538429.1_Missense_Mutation_p.D69H|FMO3_ENST00000542847.1_Missense_Mutation_p.D112H	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	132			D -> H (in dbSNP:rs12072582). {ECO:0000269|PubMed:12527699, ECO:0000269|Ref.4}.		drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CACTGAAAGGGATGGTAAAAA	0.413													G|||	73	0.0145767	0.0522	0.0058	5008	,	,		15662	0.0		0.0	False		,,,				2504	0.0				p.D132H		Atlas-SNP	.											.	FMO3	73	.	0			c.G394C	GRCh37	CM033905	FMO3	M	rs12072582	PASS	.	G	HIS/ASP,HIS/ASP	176,4230	113.8+/-151.8	2,172,2029	132.0	133.0	133.0		394,394	-2.1	0.0	1	dbSNP_120	133	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	FMO3	NM_001002294.2,NM_006894.5	81,81	2,173,6328	CC,CG,GG		0.0116,3.9946,1.3609	benign,benign	132/533,132/533	171076888	177,12829	2203	4300	6503	SO:0001583	missense	2328	exon4			GAAAGGGATGGTA	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.394G>C	1.37:g.171076888G>C	ENSP00000356729:p.Asp132His	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	189	73	0.386243	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	37	CCDS1292.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	G	8.560	0.877541	0.17395	0.039946	1.16E-4	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	4.84	-2.13	0.07144	.	0.100095	0.64402	N	0.000003	T	0.26085	0.0636	M	0.65677	2.01	0.34737	D	0.730401	B;B;B	0.26512	0.151;0.09;0.036	B;B;B	0.31245	0.126;0.069;0.078	T	0.02588	-1.1137	10	0.49607	T	0.09	-2.9075	3.4783	0.07593	0.1388:0.3402:0.4052:0.1158	rs12072582;rs52790216;rs58199544;rs12072582	69;112;132	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	H	132;132;112;69	ENSP00000356729:D132H;ENSP00000375935:D132H;ENSP00000444073:D112H;ENSP00000439500:D69H	ENSP00000356729:D132H	D	+	1	0	FMO3	169343512	0.005000	0.15991	0.035000	0.18076	0.054000	0.15201	0.421000	0.21280	-0.407000	0.07576	0.591000	0.81541	GAT	G|0.983;C|0.017	0.017	strong		0.413	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	
IDS	3423	hgsc.bcm.edu	37	X	148579705	148579705	+	Missense_Mutation	SNP	G	G	A	rs61736892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:148579705G>A	ENST00000340855.6	-	5	850	c.641C>T	c.(640-642)aCg>aTg	p.T214M	IDS_ENST00000422081.2_Missense_Mutation_p.T3M|IDS_ENST00000541269.1_Missense_Mutation_p.T3M|IDS_ENST00000370441.4_Missense_Mutation_p.T214M|IDS_ENST00000370443.4_Missense_Mutation_p.T214M|IDS_ENST00000490775.1_5'UTR	NM_000202.5|NM_001166550.1	NP_000193.1|NP_001160022.1	P22304	IDS_HUMAN	iduronate 2-sulfatase	214					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	lysosomal lumen (GO:0043202)	iduronate-2-sulfatase activity (GO:0004423)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(5)|large_intestine(2)|lung(8)|prostate(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					ACTGGCTGACGTTTTCATCTT	0.527													G|||	60	0.015894	0.0439	0.0029	3775	,	,		14709	0.0		0.0	False		,,,				2504	0.0				p.T214M		Atlas-SNP	.											.	IDS	46	.	0			c.C641T	GRCh37	CS961600	IDS	S	rs61736892	PASS	.	G	MET/THR,MET/THR,MET/THR	184,3651		7,143,27,1482,544	160.0	136.0	144.0		641,371,641	1.7	0.2	X	dbSNP_129	144	0,6728		0,0,0,2428,1872	yes	missense,missense,missense	IDS	NM_000202.5,NM_001166550.1,NM_006123.4	81,81,81	7,143,27,3910,2416	AA,AG,A,GG,G		0.0,4.7979,1.7419	benign,benign,benign	214/551,124/461,214/344	148579705	184,10379	2203	4300	6503	SO:0001583	missense	3423	exon5			GCTGACGTTTTCA	M58342	CCDS14685.1, CCDS14686.1	Xq27.3-q28	2012-10-02	2008-08-01		ENSG00000010404	ENSG00000010404	3.1.6.13		5389	protein-coding gene	gene with protein product	"""Hunter syndrome"""	300823		SIDS			Standard	NM_006123		Approved		uc011mxe.2	P22304	OTTHUMG00000022615	ENST00000340855.6:c.641C>T	X.37:g.148579705G>A	ENSP00000339801:p.Thr214Met	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	234	110	0.470085	NM_006123	D3DWT4|Q14604|Q9BRM3	Missense_Mutation	SNP	ENST00000340855.6	37	CCDS14685.1	24	0.014466546112115732	17	0.035416666666666666	1	0.0027624309392265192	0	0.0	0	0.0	G	13.84	2.358547	0.41801	0.047979	0.0	ENSG00000010404	ENST00000340855;ENST00000541269;ENST00000370441;ENST00000370443	D;D;D;D	0.99900	-7.62;-5.85;-7.62;-7.62	5.12	1.68	0.24146	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.624103	0.18240	N	0.147268	D	0.97676	0.9238	L	0.56340	1.77	0.80722	P	0.0	D;D;D	0.61697	0.987;0.973;0.99	P;P;P	0.59595	0.781;0.806;0.86	D	0.90347	0.4363	9	0.46703	T	0.11	.	3.6256	0.08112	0.0979:0.1075:0.4765:0.318	.	214;124;214	P22304-2;B4DGD7;P22304	.;.;IDS_HUMAN	M	214;3;214;214	ENSP00000339801:T214M;ENSP00000441261:T3M;ENSP00000359470:T214M;ENSP00000359472:T214M	ENSP00000339801:T214M	T	-	2	0	IDS	148387610	0.031000	0.19500	0.151000	0.22473	0.933000	0.57130	0.398000	0.20899	0.865000	0.35603	-0.395000	0.06472	ACG	G|0.982;A|0.018	0.018	strong		0.527	IDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058677.3		
SMCHD1	23347	hgsc.bcm.edu	37	18	2728559	2728559	+	Missense_Mutation	SNP	A	A	G	rs9961682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2728559A>G	ENST00000320876.6	+	23	3216	c.2878A>G	c.(2878-2880)Ata>Gta	p.I960V	SMCHD1_ENST00000609587.1_3'UTR|RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.I960V	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	960			I -> V (in dbSNP:rs9961682).		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						ATCAGACAACATAACAGCACA	0.358													A|||	154	0.0307508	0.1097	0.0101	5008	,	,		17853	0.001		0.001	False		,,,				2504	0.0				p.I960V		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A2878G						PASS	.	A	VAL/ILE	409,3315		26,357,1479	104.0	100.0	101.0		2878	-3.5	0.9	18	dbSNP_119	101	7,8193		0,7,4093	yes	missense	SMCHD1	NM_015295.2	29	26,364,5572	GG,GA,AA		0.0854,10.9828,3.4888	benign	960/2006	2728559	416,11508	1862	4100	5962	SO:0001583	missense	23347	exon23			GACAACATAACAG	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.2878A>G	18.37:g.2728559A>G	ENSP00000326603:p.Ile960Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	58	36	0.62069	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	52	0.023809523809523808	46	0.09349593495934959	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	A	10.45	1.352273	0.24512	0.109828	8.54E-4	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.24908	1.83;1.84	5.84	-3.46	0.04767	.	0.509376	0.22250	N	0.062565	T	0.00241	0.0007	N	0.14661	0.345	0.26418	N	0.976158	B	0.02656	0.0	B	0.01281	0.0	T	0.16364	-1.0405	10	0.32370	T	0.25	-4.6572	9.6361	0.39809	0.3166:0.2087:0.4747:0.0	rs9961682;rs52802941;rs9961682	960	A6NHR9	SMHD1_HUMAN	V	960	ENSP00000326603:I960V;ENSP00000261598:I960V	ENSP00000261598:I960V	I	+	1	0	SMCHD1	2718559	0.830000	0.29337	0.936000	0.37596	0.999000	0.98932	-0.076000	0.11412	-0.889000	0.03950	0.528000	0.53228	ATA	A|0.969;G|0.031	0.031	strong		0.358	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
B4GALNT4	338707	hgsc.bcm.edu	37	11	379598	379598	+	Silent	SNP	A	A	G	rs1134699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:379598A>G	ENST00000329962.6	+	15	2385	c.2385A>G	c.(2383-2385)gaA>gaG	p.E795E		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	795					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)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		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)		AAAGTCCCGAACCCGCTCCCG	0.731													.|||	2497	0.498602	0.6664	0.464	5008	,	,		10232	0.4911		0.4026	False		,,,				2504	0.4029				p.E795E		Atlas-SNP	.											B4GALNT4,rectum,carcinoma,0,1	B4GALNT4	83	1	0			c.A2385G						scavenged	.	G		2237,1841		675,887,477	5.0	7.0	7.0		2385	2.7	0.3	11	dbSNP_86	7	2925,5275		621,1683,1796	no	coding-synonymous	B4GALNT4	NM_178537.4		1296,2570,2273	GG,GA,AA		35.6707,45.1447,42.0427		795/1040	379598	5162,7116	2039	4100	6139	SO:0001819	synonymous_variant	338707	exon15			TCCCGAACCCGCT	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2385A>G	11.37:g.379598A>G		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_178537	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																			A|0.483;G|0.517	0.517	strong		0.731	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
CLEC4C	170482	hgsc.bcm.edu	37	12	7894056	7894056	+	Missense_Mutation	SNP	G	G	A	rs73056605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	143	0	0		WXS	Illumina HiSeq	Phase_I	144	74	0.513889	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	
CDRT1	374286	hgsc.bcm.edu	37	17	15510988	15510988	+	Missense_Mutation	SNP	T	T	C	rs62070402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15510988T>C	ENST00000395906.3	-	6	1131	c.1132A>G	c.(1132-1134)Aac>Gac	p.N378D	RP11-385D13.1_ENST00000455584.2_Missense_Mutation_p.N688D	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	378										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)		GTCCACAGGTTGTACTCATTC	0.483													T|||	1466	0.292732	0.264	0.2767	5008	,	,		20919	0.4514		0.1511	False		,,,				2504	0.3252				p.N378D		Atlas-SNP	.											.	CDRT1	83	.	0			c.A1132G						PASS	.	T	ASP/ASN	1076,3330	382.5+/-324.5	143,790,1270	80.0	76.0	78.0		1132	2.7	1.0	17	dbSNP_129	78	1443,7153	270.4+/-288.9	125,1193,2980	no	missense	CDRT1	NM_006382.3	23	268,1983,4250	CC,CT,TT		16.7869,24.4212,19.3739	possibly-damaging	378/753	15510988	2519,10483	2203	4298	6501	SO:0001583	missense	374286	exon6			ACAGGTTGTACTC	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.1132A>G	17.37:g.15510988T>C	ENSP00000379242:p.Asn378Asp	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	192	81	0.421875	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	T	13.75	2.328938	0.41197	0.244212	0.167869	ENSG00000251537	ENST00000261644;ENST00000395906	T	0.21734	1.99	4.99	2.69	0.31865	F-box domain, Skp2-like (1);	0.557353	0.14804	U	0.297455	T	0.00012	0.0000	M	0.69823	2.125	0.09310	P	0.9999999699041	P;B	0.42827	0.791;0.421	B;B	0.32677	0.15;0.107	T	0.30297	-0.9983	9	0.35671	T	0.21	.	5.8404	0.18630	0.0:0.0906:0.1708:0.7386	rs62070402	378;702	O95170;Q59EB2	CDRT1_HUMAN;.	D	408;378	ENSP00000379242:N378D	ENSP00000261644:N408D	N	-	1	0	RP11-385D13.1	15451713	0.998000	0.40836	0.993000	0.49108	0.814000	0.46013	1.550000	0.36223	0.824000	0.34613	0.459000	0.35465	AAC	T|0.810;C|0.190	0.190	strong		0.483	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
PDE6B	5158	hgsc.bcm.edu	37	4	660340	660340	+	Silent	SNP	G	G	A	rs61739716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:660340G>A	ENST00000496514.1	+	20	2310	c.2289G>A	c.(2287-2289)aaG>aaA	p.K763K	PDE6B_ENST00000255622.6_Silent_p.K763K|PDE6B_ENST00000429163.2_Silent_p.K484K			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	763					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	ACCGGAACAAGGCGGCCGAGC	0.652													.|||	53	0.0105831	0.0378	0.0014	5008	,	,		15996	0.0		0.001	False		,,,				2504	0.001				p.K763K	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.G2289A						PASS	.	G	,,	159,4247	108.2+/-146.6	2,155,2046	96.0	78.0	84.0		2289,2289,1452	1.0	1.0	4	dbSNP_129	84	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE6B	NM_000283.3,NM_001145291.1,NM_001145292.1	,,	2,155,6346	AA,AG,GG		0.0,3.6087,1.2225	,,	763/855,763/854,484/576	660340	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	5158	exon20			GAACAAGGCGGCC	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"""Phosphodiesterases"""	8786	protein-coding gene	gene with protein product	"""congenital stationary night blindness 3, autosomal dominant"""	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.2289G>A	4.37:g.660340G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Silent	SNP	ENST00000496514.1	37	CCDS33932.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	G	9.994	1.231604	0.22626	0.036087	0.0	ENSG00000133256	ENST00000461490	.	.	.	4.26	0.984	0.19773	.	.	.	.	.	T	0.22282	0.0537	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.13150	-1.0520	4	.	.	.	.	6.8943	0.24247	0.5241:0.0:0.4759:0.0	rs61739716	.	.	.	K	44	.	.	R	+	2	0	PDE6B	650340	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	1.242000	0.32755	0.120000	0.18254	0.650000	0.86243	AGG	G|0.990;A|0.010	0.010	strong		0.652	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283	
DENND1C	79958	hgsc.bcm.edu	37	19	6468331	6468331	+	Missense_Mutation	SNP	T	T	C	rs62107586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6468331T>C	ENST00000381480.2	-	22	1817	c.1705A>G	c.(1705-1707)Atg>Gtg	p.M569V	DENND1C_ENST00000543576.1_Missense_Mutation_p.M525V	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	569					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						TTGGCTCCCATGCTAAGACTG	0.582													C|||	1147	0.229034	0.3245	0.245	5008	,	,		17696	0.003		0.3877	False		,,,				2504	0.1585				p.M569V		Atlas-SNP	.											.	DENND1C	93	.	0			c.A1705G						PASS	.	C	VAL/MET	1327,2747		224,879,934	50.0	52.0	51.0		1705	-5.2	0.0	19	dbSNP_129	51	3596,4782		756,2084,1349	yes	missense	DENND1C	NM_024898.2	21	980,2963,2283	CC,CT,TT		42.9219,32.5724,39.5358	benign	569/802	6468331	4923,7529	2037	4189	6226	SO:0001583	missense	79958	exon22			CTCCCATGCTAAG	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1705A>G	19.37:g.6468331T>C	ENSP00000370889:p.Met569Val	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	241	121	0.502075	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	560	0.2564102564102564	176	0.35772357723577236	99	0.27348066298342544	2	0.0034965034965034965	283	0.3733509234828496	C	0.015	-1.565636	0.00903	0.325724	0.429219	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.08546	3.25;3.08	4.75	-5.17	0.02849	.	1.339980	0.05292	N	0.521292	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	0.46555	-0.9183	9	0.02654	T	1	0.2663	6.0997	0.20041	0.0:0.22:0.2458:0.5342	rs62107586	569	Q8IV53	DEN1C_HUMAN	V	569;525	ENSP00000370889:M569V;ENSP00000437805:M525V	ENSP00000370889:M569V	M	-	1	0	DENND1C	6419331	0.000000	0.05858	0.000000	0.03702	0.392000	0.30506	-1.413000	0.02473	-0.799000	0.04439	-0.684000	0.03749	ATG	A|0.000;C|0.295;G|0.000;T|0.705	0.295	strong		0.582	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
TRIM45	80263	hgsc.bcm.edu	37	1	117656088	117656088	+	Missense_Mutation	SNP	A	A	G	rs1289658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117656088A>G	ENST00000256649.4	-	5	2013	c.1487T>C	c.(1486-1488)aTg>aCg	p.M496T	TRIM45_ENST00000369464.3_Missense_Mutation_p.M478T|TRIM45_ENST00000369461.3_Missense_Mutation_p.M439T	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	496			M -> T (in dbSNP:rs1289658). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15351693, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		bone development (GO:0060348)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|prostate(1)	23	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		TCTCCTCACCATCACAGTGAA	0.557													G|||	2229	0.445088	0.6793	0.4755	5008	,	,		22011	0.1865		0.4364	False		,,,				2504	0.3824				p.M496T		Atlas-SNP	.											.	TRIM45	55	.	0			c.T1487C						PASS	.	G	THR/MET,THR/MET	2732,1674	508.8+/-367.0	873,986,344	66.0	61.0	62.0		1433,1487	4.0	0.6	1	dbSNP_87	62	3455,5145	636.3+/-399.1	680,2095,1525	yes	missense,missense	TRIM45	NM_001145635.1,NM_025188.3	81,81	1553,3081,1869	GG,GA,AA		40.1744,37.9936,47.5704	benign,benign	478/563,496/581	117656088	6187,6819	2203	4300	6503	SO:0001583	missense	80263	exon5			CTCACCATCACAG		CCDS893.1, CCDS44200.1	1p13.1	2011-04-20	2011-01-25		ENSG00000134253	ENSG00000134253		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19018	protein-coding gene	gene with protein product		609318	"""tripartite motif-containing 45"""			15351693	Standard	NM_025188		Approved	FLJ13181, RNF99	uc001egz.2	Q9H8W5	OTTHUMG00000012119	ENST00000256649.4:c.1487T>C	1.37:g.117656088A>G	ENSP00000256649:p.Met496Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_025188	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	909	0.41620879120879123	317	0.6443089430894309	169	0.46685082872928174	93	0.16258741258741258	330	0.43535620052770446	G	0.005	-2.228181	0.00280	0.620064	0.401744	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	T;T;T	0.39406	2.08;1.08;2.08	4.96	3.99	0.46301	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.522971	0.20258	N	0.095923	T	0.02929	0.0087	N	0.00823	-1.155	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39663	-0.9603	9	0.07030	T	0.85	-10.0408	3.8833	0.09088	0.1845:0.0:0.4103:0.4052	rs1289658;rs17524007;rs52814348;rs60516003;rs1289658	478;496	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	T	496;478;439	ENSP00000256649:M496T;ENSP00000358476:M478T;ENSP00000358473:M439T	ENSP00000256649:M496T	M	-	2	0	TRIM45	117457611	0.023000	0.18921	0.629000	0.29254	0.342000	0.28953	0.149000	0.16243	0.562000	0.29204	-0.213000	0.12676	ATG	A|0.549;G|0.451	0.451	strong		0.557	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188	
ASTN1	460	hgsc.bcm.edu	37	1	176915087	176915087	+	Missense_Mutation	SNP	C	C	T	rs138686233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:176915087C>T	ENST00000367654.3	-	13	2459	c.2248G>A	c.(2248-2250)Gga>Aga	p.G750R	ASTN1_ENST00000361833.2_Missense_Mutation_p.G742R|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Missense_Mutation_p.G742R|ASTN1_ENST00000367657.3_Missense_Mutation_p.G742R	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	750					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)		p.G742*(1)		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						AGCACCTGTCCGGCAGCCACT	0.463													C|||	8	0.00159744	0.0061	0.0	5008	,	,		19496	0.0		0.0	False		,,,				2504	0.0				p.G742R		Atlas-SNP	.											ASTN1,NS,carcinoma,0,1	ASTN1	314	1	1	Substitution - Nonsense(1)	lung(1)	c.G2224A						PASS	.	C	ARG/GLY,ARG/GLY	37,4369	41.6+/-74.8	0,37,2166	110.0	118.0	115.0		2224,2224	5.2	1.0	1	dbSNP_134	115	0,8600		0,0,4300	yes	missense,missense	ASTN1	NM_004319.1,NM_207108.1	125,125	0,37,6466	TT,TC,CC		0.0,0.8398,0.2845	possibly-damaging,possibly-damaging	742/1295,742/1217	176915087	37,12969	2203	4300	6503	SO:0001583	missense	460	exon13			CCTGTCCGGCAGC	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.2248G>A	1.37:g.176915087C>T	ENSP00000356626:p.Gly750Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	82	49	0.597561	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	25.9	4.687682	0.88639	0.008398	0.0	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.17370	2.28;2.7;2.7;2.29	5.25	5.25	0.73442	.	0.107853	0.64402	D	0.000004	T	0.15478	0.0373	L	0.27053	0.805	0.58432	D	0.999998	D;D;D	0.67145	0.996;0.993;0.993	P;P;P	0.54856	0.762;0.762;0.762	T	0.00555	-1.1673	10	0.87932	D	0	-17.5766	11.9089	0.52727	0.0:0.9195:0.0:0.0805	.	750;742;742	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	R	742;742;750;742;742	ENSP00000356629:G742R;ENSP00000354536:G742R;ENSP00000356626:G750R;ENSP00000395041:G742R	ENSP00000354536:G742R	G	-	1	0	ASTN1	175181710	1.000000	0.71417	0.951000	0.38953	0.992000	0.81027	5.539000	0.67199	2.467000	0.83353	0.655000	0.94253	GGA	C|0.998;T|0.002	0.002	strong		0.463	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
CXorf30	645090	hgsc.bcm.edu	37	X	36371719	36371719	+	Missense_Mutation	SNP	T	T	A	rs41309695		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:36371719T>A	ENST00000378657.4	+	14	1760	c.1112T>A	c.(1111-1113)tTt>tAt	p.F371Y		NM_001098843.4	NP_001092313.2	A6PW82	CX030_HUMAN	chromosome X open reading frame 30	371								p.F913Y(1)		breast(1)|lung(2)|stomach(1)	4						TTTTTCGGATTTAGTCTTACT	0.378													A|||	676	0.179073	0.0605	0.2161	3775	,	,		12485	0.1895		0.0716	False		,,,				2504	0.1871				p.F371Y		Atlas-SNP	.											.	CXorf30	76	.	1	Substitution - Missense(1)	stomach(1)	c.T1112A						PASS	.	A	TYR/PHE	116,1093		3,99,11,415,164	153.0	112.0	125.0		1112	-5.8	0.0	X	dbSNP_127	125	168,2223		7,97,57,696,734	yes	missense	CXorf30	NM_001098843.3	22	10,196,68,1111,898	AA,AT,A,TT,T		7.0263,9.5947,7.8889	benign	371/634	36371719	284,3316	692	1591	2283	SO:0001583	missense	645090	exon15			TCGGATTTAGTCT		CCDS55396.1	Xp21.1	2014-08-07			ENSG00000205081	ENSG00000205081			27298	protein-coding gene	gene with protein product							Standard	NM_001098843		Approved		uc011mkc.3	A6PW82	OTTHUMG00000021353	ENST00000378657.4:c.1112T>A	X.37:g.36371719T>A	ENSP00000367926:p.Phe371Tyr	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	168	86	0.511905	NM_001098843		Missense_Mutation	SNP	ENST00000378657.4	37	CCDS55396.1	270	0.162748643761302	20	0.04291845493562232	49	0.1484848484848485	77	0.15587044534412955	41	0.05631868131868132	A	0.016	-1.522087	0.00967	0.095947	0.070263	ENSG00000205081	ENST00000378653;ENST00000378657	T;T	0.22336	1.96;1.96	4.41	-5.76	0.02376	.	3.928160	0.00424	N	0.000065	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.28170	-1.0052	9	0.02654	T	1	5.0939	1.8918	0.03249	0.3022:0.3148:0.076:0.307	rs41309695;rs62592536	371	A6PW82	CX030_HUMAN	Y	656;371	ENSP00000367922:F656Y;ENSP00000367926:F371Y	ENSP00000367922:F656Y	F	+	2	0	CXorf30	36281640	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.289000	0.02780	-2.710000	0.00394	-4.120000	0.00011	TTT	T|0.835;A|0.165	0.165	strong		0.378	CXorf30-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NP_001092313	
NRK	203447	hgsc.bcm.edu	37	X	105168689	105168689	+	Missense_Mutation	SNP	C	C	A	rs16984889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:105168689C>A	ENST00000243300.9	+	19	3281	c.2978C>A	c.(2977-2979)gCa>gAa	p.A993E	NRK_ENST00000428173.2_Missense_Mutation_p.A994E	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	993			A -> E (in dbSNP:rs16984889).		activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						GTTGTCAGGGCAAGCTATGGC	0.408										HNSCC(51;0.14)			C|||	462	0.122384	0.3306	0.0331	3775	,	,		16586	0.0		0.002	False		,,,				2504	0.0				p.A993E		Atlas-SNP	.											.	NRK	321	.	0			c.C2978A						PASS	.	C	GLU/ALA	1205,2084		184,619,218,559,347	26.0	24.0	25.0		2978	1.8	0.1	X	dbSNP_123	25	9,6498		0,8,1,2351,1788	yes	missense	NRK	NM_198465.2	107	184,627,219,2910,2135	AA,AC,A,CC,C		0.1383,36.6373,12.3928	benign	993/1583	105168689	1214,8582	1927	4148	6075	SO:0001583	missense	203447	exon19			TCAGGGCAAGCTA	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.2978C>A	X.37:g.105168689C>A	ENSP00000434830:p.Ala993Glu	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	267	163	0.610487	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		168	0.10126582278481013	109	0.2794871794871795	4	0.011299435028248588	0	0.0	0	0.0	C	12.01	1.808484	0.31961	0.366373	0.001383	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.79554	-1.27;-1.28	4.85	1.79	0.24919	.	0.766382	0.11121	N	0.597389	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	9.99999999995449E-6	B;B	0.30281	0.275;0.037	B;B	0.27796	0.083;0.011	T	0.14671	-1.0464	9	0.62326	D	0.03	.	1.9029	0.03271	0.212:0.4677:0.2021:0.1183	rs16984889;rs52799695;rs16984889	661;993	Q7Z2Y5-2;Q7Z2Y5	.;NRK_HUMAN	E	993;994	ENSP00000434830:A993E;ENSP00000438378:A994E	ENSP00000434830:A993E	A	+	2	0	NRK	105055345	0.038000	0.19896	0.138000	0.22173	0.767000	0.43475	-0.107000	0.10873	0.901000	0.36495	0.513000	0.50165	GCA	0|0.008;A|0.143	0.143	strong		0.408	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465	
C3orf30	152405	hgsc.bcm.edu	37	3	118865615	118865615	+	Missense_Mutation	SNP	G	G	C	rs9859242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:118865615G>C	ENST00000295622.1	+	1	619	c.579G>C	c.(577-579)caG>caC	p.Q193H	IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	193			Q -> H (in dbSNP:rs9859242).							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)		CTTCCGAGCAGATGGACCGCA	0.512													G|||	113	0.0225639	0.084	0.0029	5008	,	,		22926	0.0		0.0	False		,,,				2504	0.0				p.Q193H		Atlas-SNP	.											.	C3orf30	64	.	0			c.G579C						PASS	.	G	HIS/GLN	361,4045	184.3+/-211.7	17,327,1859	97.0	100.0	99.0		579	2.2	0.0	3	dbSNP_119	99	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C3orf30	NM_152539.2	24	17,329,6157	CC,CG,GG		0.0233,8.1934,2.791	possibly-damaging	193/537	118865615	363,12643	2203	4300	6503	SO:0001583	missense	152405	exon1			CGAGCAGATGGAC	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.579G>C	3.37:g.118865615G>C	ENSP00000295622:p.Gln193His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	112	48	0.428571	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	29|29	0.013278388278388278|0.013278388278388278	28|28	0.056910569105691054|0.056910569105691054	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.18|13.18	2.160413|2.160413	0.38119|0.38119	0.081934|0.081934	2.33E-4|2.33E-4	ENSG00000163424|ENSG00000163424	ENST00000460150|ENST00000295622;ENST00000470341	.|T	.|0.26223	.|1.75	4.09|4.09	2.24|2.24	0.28232|0.28232	.|.	.|1.043520	.|0.07559	.|N	.|0.916758	T|T	0.02767|0.02767	0.0083|0.0083	L|L	0.52573|0.52573	1.65|1.65	0.09310|0.09310	N|N	1|1	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.74023	.|0.982;0.971	T|T	0.04128|0.04128	-1.0975|-1.0975	5|10	.|0.41790	.|T	.|0.15	0.0286|0.0286	6.1512|6.1512	0.20313|0.20313	0.1027:0.3712:0.5262:0.0|0.1027:0.3712:0.5262:0.0	rs9859242;rs9859242|rs9859242;rs9859242	.|193;193	.|E9PFE5;Q96M34	.|.;CC030_HUMAN	H|H	157|193	.|ENSP00000295622:Q193H	.|ENSP00000295622:Q193H	D|Q	+|+	1|3	0|2	C3orf30|C3orf30	120348305|120348305	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	-0.341000|-0.341000	0.07811|0.07811	0.661000|0.661000	0.30985|0.30985	0.514000|0.514000	0.50259|0.50259	GAT|CAG	G|0.977;C|0.023	0.023	strong		0.512	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
INHA	3623	hgsc.bcm.edu	37	2	220439700	220439700	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220439700G>T	ENST00000243786.2	+	2	733	c.553G>T	c.(553-555)Gct>Tct	p.A185S	INHA_ENST00000489456.1_3'UTR	NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	185					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)		GGCCACCTCTGCTCTCTCTCT	0.687																																					p.A185S		Atlas-SNP	.											INHA,right_upper_lobe,carcinoma,-1,1	INHA	30	1	0			c.G553T						scavenged	.						86.0	80.0	82.0					2																	220439700		2203	4300	6503	SO:0001583	missense	3623	exon2			ACCTCTGCTCTCT		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.553G>T	2.37:g.220439700G>T	ENSP00000243786:p.Ala185Ser	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	89	2	0.0224719	NM_002191	A8K8H5	Missense_Mutation	SNP	ENST00000243786.2	37	CCDS2444.1	.	.	.	.	.	.	.	.	.	.	G	7.113	0.576509	0.13686	.	.	ENSG00000123999	ENST00000243786	D	0.85088	-1.94	5.37	4.43	0.53597	.	0.488362	0.22115	N	0.064422	D	0.85474	0.5705	M	0.85099	2.735	0.22199	N	0.999294	P	0.36222	0.544	B	0.34093	0.175	T	0.81754	-0.0788	10	0.62326	D	0.03	-16.9786	12.8035	0.57598	0.0:0.0:0.651:0.349	.	185	P05111	INHA_HUMAN	S	185	ENSP00000243786:A185S	ENSP00000243786:A185S	A	+	1	0	INHA	220147944	0.108000	0.22018	0.625000	0.29200	0.033000	0.12548	1.688000	0.37690	2.504000	0.84457	0.561000	0.74099	GCT	.	.	none		0.687	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1		
ZNF200	7752	hgsc.bcm.edu	37	16	3282468	3282468	+	Missense_Mutation	SNP	G	G	A	rs9302870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3282468G>A	ENST00000431561.3	-	4	1031	c.419C>T	c.(418-420)aCg>aTg	p.T140M	ZNF200_ENST00000396868.3_Missense_Mutation_p.T139M|ZNF200_ENST00000396870.4_Missense_Mutation_p.T140M|ZNF200_ENST00000414144.2_Missense_Mutation_p.T140M|ZNF200_ENST00000396871.4_Missense_Mutation_p.T140M|ZNF200_ENST00000575948.1_Missense_Mutation_p.T140M	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	140			T -> M (in dbSNP:rs9302870).		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)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						CTTCTCTGACGTGAGTTGTTG	0.463													G|||	346	0.0690895	0.2504	0.0173	5008	,	,		21841	0.0		0.003	False		,,,				2504	0.0				p.T140M		Atlas-SNP	.											.	ZNF200	36	.	0			c.C419T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	817,3577	326.7+/-299.7	77,663,1457	237.0	211.0	220.0		419,419,419,419,416,419	2.7	0.6	16	dbSNP_119	220	10,8590	7.1+/-27.0	0,10,4290	yes	missense,missense,missense,missense,missense,missense	ZNF200	NM_001145446.1,NM_001145447.1,NM_001145448.1,NM_003454.3,NM_198087.2,NM_198088.2	81,81,81,81,81,81	77,673,5747	AA,AG,GG		0.1163,18.5935,6.3645	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	140/395,140/395,140/395,140/396,139/395,140/396	3282468	827,12167	2197	4300	6497	SO:0001583	missense	7752	exon4			TCTGACGTGAGTT	AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"""Zinc fingers, C2H2-type"""	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.419C>T	16.37:g.3282468G>A	ENSP00000395723:p.Thr140Met	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	128	68	0.53125	NM_003454	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Missense_Mutation	SNP	ENST00000431561.3	37	CCDS10497.1	139	0.06364468864468864	133	0.2703252032520325	6	0.016574585635359115	0	0.0	0	0.0	G	12.60	1.986342	0.35036	0.185935	0.001163	ENSG00000010539	ENST00000396870;ENST00000396868;ENST00000396871;ENST00000414144;ENST00000431561	T;T;T;T;T	0.06449	3.3;3.33;3.3;3.39;3.39	4.84	2.73	0.32206	.	0.395014	0.18653	N	0.134956	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P;P;P	0.42039	0.658;0.658;0.769	B;B;B	0.43082	0.23;0.23;0.407	T	0.49273	-0.8957	9	0.62326	D	0.03	-13.3741	8.5959	0.33714	0.2043:0.0:0.7957:0.0	rs9302870;rs9302870	140;140;139	D3DUB7;P98182;P98182-2	.;ZN200_HUMAN;.	M	140;139;140;140;140	ENSP00000380079:T140M;ENSP00000380077:T139M;ENSP00000380080:T140M;ENSP00000405786:T140M;ENSP00000395723:T140M	ENSP00000380077:T139M	T	-	2	0	ZNF200	3222469	0.179000	0.23135	0.574000	0.28523	0.226000	0.24999	0.021000	0.13489	1.257000	0.44085	0.555000	0.69702	ACG	G|0.914;A|0.086	0.086	strong		0.463	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1		
CLTA	1211	hgsc.bcm.edu	37	9	36197564	36197564	+	Silent	SNP	A	A	G	rs138682143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:36197564A>G	ENST00000242285.6	+	2	354	c.234A>G	c.(232-234)gtA>gtG	p.V78V	CLTA_ENST00000470744.1_Silent_p.V78V|CLTA_ENST00000396603.2_Silent_p.V78V|CLTA_ENST00000538225.1_Silent_p.V78V|CLTA_ENST00000540080.1_Intron|CLTA_ENST00000466396.1_Intron|CLTA_ENST00000433436.2_Silent_p.V78V|CLTA_ENST00000345519.5_Silent_p.V78V			P09496	CLCA_HUMAN	clathrin, light chain A	78					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	clathrin heavy chain binding (GO:0032050)|peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	6			STAD - Stomach adenocarcinoma(86;0.228)			TTGATGGAGTAATGAATGGTG	0.383																																					p.V78V		Atlas-SNP	.											.	CLTA	18	.	0			c.A234G						PASS	.	A	,,,,,	10,4396	16.8+/-37.8	0,10,2193	254.0	237.0	243.0		234,234,234,,234,234	0.6	1.0	9	dbSNP_134	243	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous	CLTA	NM_001076677.2,NM_001184760.1,NM_001184761.1,NM_001184762.1,NM_001833.3,NM_007096.3	,,,,,	0,10,6493	GG,GA,AA		0.0,0.227,0.0769	,,,,,	78/237,78/231,78/169,,78/219,78/249	36197564	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	1211	exon2			TGGAGTAATGAAT		CCDS6600.1, CCDS6601.1, CCDS43802.1, CCDS55306.1, CCDS55307.1	9p13.3	2010-05-11	2010-05-11		ENSG00000122705	ENSG00000122705			2090	protein-coding gene	gene with protein product		118960	"""clathrin, light polypeptide (Lca)"""			7713494	Standard	NM_007096		Approved	Lca	uc003zzc.3	P09496	OTTHUMG00000019896	ENST00000242285.6:c.234A>G	9.37:g.36197564A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	189	109	0.57672	NM_001184761	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Silent	SNP	ENST00000242285.6	37	CCDS6601.1																																																																																			A|0.998;G|0.002	0.002	strong		0.383	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096	
ZNF28	7576	hgsc.bcm.edu	37	19	53304448	53304448	+	Missense_Mutation	SNP	C	C	T	rs143289804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53304448C>T	ENST00000457749.2	-	4	769	c.650G>A	c.(649-651)tGt>tAt	p.C217Y	ZNF28_ENST00000414252.2_Missense_Mutation_p.C164Y|ZNF28_ENST00000438150.2_Missense_Mutation_p.C164Y|ZNF28_ENST00000360272.4_Missense_Mutation_p.C164Y	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	217					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		ACTCTCAATACATTGGAAAGA	0.328													-|||	6	0.00119808	0.0045	0.0	5008	,	,		21480	0.0		0.0	False		,,,				2504	0.0				p.C217Y		Atlas-SNP	.											.	ZNF28	191	.	0			c.G650A						PASS	.	C	TYR/CYS	22,4384		0,22,2181	118.0	121.0	120.0		650	-3.5	0.0	19	dbSNP_134	120	0,8600		0,0,4300	yes	missense	ZNF28	NM_006969.3	194	0,22,6481	TT,TC,CC		0.0,0.4993,0.1692	benign	217/719	53304448	22,12984	2203	4300	6503	SO:0001583	missense	7576	exon4			TCAATACATTGGA	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"""Zinc fingers, C2H2-type"", ""-"""	13073	protein-coding gene	gene with protein product			"""zinc finger protein 28 (KOX 24)"""				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.650G>A	19.37:g.53304448C>T	ENSP00000397693:p.Cys217Tyr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	37	CCDS33093.2	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	-	3.805	-0.040964	0.07452	0.004993	0.0	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34	1.74	-3.48	0.04739	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49236	0.1545	H	0.94183	3.505	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55885	-0.8070	9	0.66056	D	0.02	.	5.4015	0.16299	0.0:0.5647:0.168:0.2673	.	217	P17035	ZNF28_HUMAN	Y	164;217;164;164;164	ENSP00000412143:C164Y;ENSP00000397693:C217Y;ENSP00000353410:C164Y;ENSP00000444965:C164Y;ENSP00000375661:C164Y	ENSP00000353410:C164Y	C	-	2	0	ZNF28	57996260	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	1.019000	0.30014	-1.136000	0.02892	-1.497000	0.00963	TGT	C|0.998;T|0.002	0.002	strong		0.328	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969	
OR10R2	343406	hgsc.bcm.edu	37	1	158450314	158450314	+	Missense_Mutation	SNP	A	A	G	rs6679056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	216	2	0.00925926		WXS	Illumina HiSeq	Phase_I	228	110	0.482456	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	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118187528	118187528	+	Missense_Mutation	SNP	C	C	T	rs10885929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:118187528C>T	ENST00000369230.3	+	1	150	c.4C>T	c.(4-6)Ctt>Ttt	p.L2F		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	2			L -> F (in dbSNP:rs10885929).		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		AGCTTAGATGCTTGGAATTTG	0.284													C|||	219	0.04373	0.0484	0.1282	5008	,	,		15738	0.0298		0.0219	False		,,,				2504	0.0143				p.L2F		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.C4T						PASS	.	C	PHE/LEU	191,4215	119.6+/-157.3	3,185,2015	72.0	80.0	77.0		4	-1.3	1.0	10	dbSNP_120	77	204,8394	85.0+/-147.5	2,200,4097	yes	missense	PNLIPRP3	NM_001011709.2	22	5,385,6112	TT,TC,CC		2.3726,4.335,3.0375	benign	2/468	118187528	395,12609	2203	4299	6502	SO:0001583	missense	119548	exon1			TAGATGCTTGGAA	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.4C>T	10.37:g.118187528C>T	ENSP00000358232:p.Leu2Phe	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_001011709		Missense_Mutation	SNP	ENST00000369230.3	37	CCDS31292.1	112	0.05128205128205128	30	0.06097560975609756	48	0.13259668508287292	20	0.03496503496503497	14	0.018469656992084433	C	8.735	0.917534	0.17982	0.04335	0.023726	ENSG00000203837	ENST00000369230	D	0.87650	-2.28	5.32	-1.27	0.09347	.	0.534295	0.16670	N	0.204387	T	0.01905	0.0060	N	0.20574	0.59	0.47659	P	5.169999999999897E-4	B	0.18166	0.026	B	0.20767	0.031	T	0.18777	-1.0326	9	0.44086	T	0.13	.	3.3014	0.06984	0.287:0.2116:0.0:0.5013	rs10885929;rs10885929	2	Q17RR3	LIPR3_HUMAN	F	2	ENSP00000358232:L2F	ENSP00000358232:L2F	L	+	1	0	PNLIPRP3	118177518	0.984000	0.35163	0.963000	0.40424	0.921000	0.55340	-0.158000	0.10070	-0.490000	0.06707	-0.218000	0.12543	CTT	C|0.961;T|0.039	0.039	strong		0.284	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
AKAP1	8165	hgsc.bcm.edu	37	17	55183716	55183716	+	Silent	SNP	T	T	C	rs1050515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:55183716T>C	ENST00000337714.3	+	2	1124	c.891T>C	c.(889-891)gaT>gaC	p.D297D	AKAP1_ENST00000571629.1_Silent_p.D297D|AKAP1_ENST00000572557.1_Silent_p.D297D|AKAP1_ENST00000314126.3_Silent_p.D297D|AKAP1_ENST00000539273.1_Silent_p.D297D	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	297					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					AAGCCCAGGATAGAGGTGTCG	0.552													C|||	2958	0.590655	0.587	0.549	5008	,	,		18274	0.8115		0.5318	False		,,,				2504	0.4581				p.D297D		Atlas-SNP	.											.	AKAP1	73	.	0			c.T891C						PASS	.	C	,,	2509,1897	545.2+/-376.7	719,1071,413	77.0	84.0	81.0		891,891,891	-11.5	0.0	17	dbSNP_86	81	4525,4075	560.0+/-387.5	1187,2151,962	no	coding-synonymous,coding-synonymous,coding-synonymous	AKAP1	NM_001242902.1,NM_001242903.1,NM_003488.3	,,	1906,3222,1375	CC,CT,TT		47.3837,43.0549,45.9173	,,	297/904,297/904,297/904	55183716	7034,5972	2203	4300	6503	SO:0001819	synonymous_variant	8165	exon3			CCAGGATAGAGGT	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Tudor domain containing"""	367	protein-coding gene	gene with protein product	"""protein kinase anchoring protein 1"", ""dual specificity A-kinase-anchoring protein 1"", ""protein phosphatase 1, regulatory subunit 43"", ""tudor domain containing 17"""	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.891T>C	17.37:g.55183716T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Silent	SNP	ENST00000337714.3	37	CCDS11594.1																																																																																			C|0.565;G|0.000;T|0.435	0.565	strong		0.552	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1		
OR4K15	81127	hgsc.bcm.edu	37	14	20443943	20443943	+	Missense_Mutation	SNP	A	A	G	rs4060024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20443943A>G	ENST00000305051.5	+	1	341	c.266A>G	c.(265-267)aAc>aGc	p.N89S		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	89			N -> S (in dbSNP:rs4060024). {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)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTGCTTGCAAACCTGTCATTT	0.443													A|||	1880	0.375399	0.7451	0.2017	5008	,	,		22854	0.1498		0.2435	False		,,,				2504	0.3671				p.N89S		Atlas-SNP	.											.	OR4K15	82	.	0			c.A266G						PASS	.	A	SER/ASN	3031,1375		1039,953,211	90.0	102.0	98.0		266	1.1	0.4	14	dbSNP_108	98	2424,6172		335,1754,2209	no	missense	OR4K15	NM_001005486.1	46	1374,2707,2420	GG,GA,AA		28.1992,31.2074,41.9551	probably-damaging	89/349	20443943	5455,7547	2203	4298	6501	SO:0001583	missense	81127	exon1			TTGCAAACCTGTC		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.266A>G	14.37:g.20443943A>G	ENSP00000304077:p.Asn89Ser	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	697	0.3191391941391941	353	0.717479674796748	70	0.19337016574585636	82	0.14335664335664336	192	0.2532981530343008	.	9.577	1.122587	0.20877	0.687926	0.281992	ENSG00000169488	ENST00000305051	T	0.12774	2.65	3.61	1.12	0.20585	GPCR, rhodopsin-like superfamily (1);	0.110120	0.40302	N	0.001124	T	0.00012	0.0000	M	0.71206	2.165	0.41247	P	0.013314999999999966	D	0.61080	0.989	P	0.53401	0.725	T	0.38394	-0.9663	9	0.62326	D	0.03	.	0.8705	0.01213	0.4864:0.2021:0.1155:0.196	rs4060024;rs7159237;rs57980873;rs4060024	89	Q8NH41	OR4KF_HUMAN	S	89	ENSP00000304077:N89S	ENSP00000304077:N89S	N	+	2	0	OR4K15	19513783	0.235000	0.23794	0.398000	0.26321	0.129000	0.20672	1.917000	0.39996	0.030000	0.15379	-0.468000	0.05107	AAC	.	.	weak		0.443	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
FAM114A1	92689	hgsc.bcm.edu	37	4	38907222	38907222	+	Silent	SNP	A	A	G	rs17501308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38907222A>G	ENST00000358869.2	+	5	692	c.516A>G	c.(514-516)ggA>ggG	p.G172G	FAM114A1_ENST00000515037.1_5'UTR	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	172						cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						CTTCTGAAGGAGCCCAACCAA	0.433													G|||	37	0.00738818	0.0257	0.0014	5008	,	,		17480	0.0		0.0	False		,,,				2504	0.002				p.G172G		Atlas-SNP	.											.	FAM114A1	42	.	0			c.A516G						PASS	.	G		110,4296	816.0+/-416.2	1,108,2094	100.0	102.0	101.0		516	2.0	0.2	4	dbSNP_123	101	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	FAM114A1	NM_138389.2		1,109,6393	GG,GA,AA		0.0116,2.4966,0.8535		172/564	38907222	111,12895	2203	4300	6503	SO:0001819	synonymous_variant	92689	exon5			TGAAGGAGCCCAA		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.516A>G	4.37:g.38907222A>G		Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	171	96	0.561404	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Silent	SNP	ENST00000358869.2	37	CCDS3447.1																																																																																			A|0.990;G|0.010	0.010	strong		0.433	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	
FBXO34	55030	hgsc.bcm.edu	37	14	55817708	55817708	+	Silent	SNP	T	T	C	rs10144418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55817708T>C	ENST00000313833.4	+	2	845	c.600T>C	c.(598-600)taT>taC	p.Y200Y	FBXO34_ENST00000440021.1_Silent_p.Y200Y	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	200								p.Y200Y(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						ATGGAGTCTATGCTGGGAGGC	0.502													T|||	1597	0.31889	0.2073	0.3012	5008	,	,		22020	0.3185		0.4155	False		,,,				2504	0.3834				p.Y200Y		Atlas-SNP	.											FBXO34,NS,carcinoma,0,1	FBXO34	61	1	1	Substitution - coding silent(1)	stomach(1)	c.T600C						scavenged	.	T	,	1078,3328	392.1+/-328.4	130,818,1255	103.0	90.0	95.0		600,600	-3.2	0.0	14	dbSNP_119	95	3534,5066	514.5+/-378.4	751,2032,1517	no	coding-synonymous,coding-synonymous	FBXO34	NM_017943.3,NM_152231.1	,	881,2850,2772	CC,CT,TT		41.093,24.4666,35.4606	,	200/712,200/712	55817708	4612,8394	2203	4300	6503	SO:0001819	synonymous_variant	55030	exon2			AGTCTATGCTGGG	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.600T>C	14.37:g.55817708T>C		Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	183	85	0.464481	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Silent	SNP	ENST00000313833.4	37	CCDS32086.1																																																																																			T|0.655;C|0.345	0.345	strong		0.502	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
NDUFAF2	91942	hgsc.bcm.edu	37	5	60448734	60448734	+	Silent	SNP	T	T	C	rs77878573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:60448734T>C	ENST00000296597.5	+	4	589	c.462T>C	c.(460-462)ttT>ttC	p.F154F	NDUFAF2_ENST00000511107.1_3'UTR|NDUFAF2_ENST00000512623.1_3'UTR	NM_174889.4	NP_777549.1	Q8N183	MIMIT_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 2	154					negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)	mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|ovary(1)	6		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)				GTAAAACCTTTCAGCCAGGAT	0.443													T|||	89	0.0177716	0.0658	0.0029	5008	,	,		13669	0.0		0.0	False		,,,				2504	0.0				p.F154F		Atlas-SNP	.											.	NDUFAF2	10	.	0			c.T462C						PASS	.	T		242,4162	130.2+/-166.9	6,230,1966	33.0	28.0	30.0		462	-4.8	1.0	5	dbSNP_131	30	4,8592	3.0+/-9.4	0,4,4294	no	coding-synonymous	NDUFAF2	NM_174889.4		6,234,6260	CC,CT,TT		0.0465,5.495,1.8923		154/170	60448734	246,12754	2202	4298	6500	SO:0001819	synonymous_variant	91942	exon4			AACCTTTCAGCCA	AB183433	CCDS3979.1	5q12.1	2012-10-12	2012-05-08	2008-02-15	ENSG00000164182	ENSG00000164182		"""Mitochondrial respiratory chain complex assembly factors"""	28086	protein-coding gene	gene with protein product	"""Myc-induced mitochondrial protein"""	609653	"""NDUFA12-like"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 2"""	NDUFA12L		15774466, 16200211, 17383918	Standard	NM_174889		Approved	B17.2L, MMTN, mimitin	uc003jsp.4	Q8N183	OTTHUMG00000131221	ENST00000296597.5:c.462T>C	5.37:g.60448734T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	143	71	0.496504	NM_174889	A8K5I1	Silent	SNP	ENST00000296597.5	37	CCDS3979.1																																																																																			T|0.981;C|0.019	0.019	strong		0.443	NDUFAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253965.1	NM_174889	
AGPAT2	10555	hgsc.bcm.edu	37	9	139571560	139571560	+	Silent	SNP	G	G	A	rs73668354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139571560G>A	ENST00000371696.2	-	3	410	c.345C>T	c.(343-345)tgC>tgT	p.C115C	AGPAT2_ENST00000538402.1_Silent_p.C115C|AGPAT2_ENST00000371694.3_Silent_p.C115C	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	115					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)		CGATCTGCACGCAGCGCTCCG	0.637													G|||	72	0.014377	0.0461	0.013	5008	,	,		15024	0.0		0.002	False		,,,				2504	0.0				p.C115C		Atlas-SNP	.											AGPAT2,NS,carcinoma,0,1	AGPAT2	17	1	0			c.C345T						PASS	.	A	,	183,4223	115.0+/-153.0	2,179,2022	50.0	57.0	54.0		345,345	-3.2	0.7	9	dbSNP_130	54	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	AGPAT2	NM_001012727.1,NM_006412.3	,	2,185,6316	AA,AG,GG		0.0698,4.1534,1.4532	,	115/247,115/279	139571560	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	10555	exon3			CTGCACGCAGCGC	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.345C>T	9.37:g.139571560G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	116	85	0.732759	NM_001012727	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Silent	SNP	ENST00000371696.2	37	CCDS7003.1																																																																																			G|0.982;A|0.018	0.018	strong		0.637	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412	
CMTR2	55783	hgsc.bcm.edu	37	16	71318577	71318577	+	Missense_Mutation	SNP	T	T	C	rs3803704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71318577T>C	ENST00000338099.5	-	3	1583	c.1247A>G	c.(1246-1248)aAt>aGt	p.N416S	CMTR2_ENST00000434935.2_Missense_Mutation_p.N416S			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	416			N -> S (in dbSNP:rs3803704). {ECO:0000269|PubMed:14702039}.		7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										TAGCCAATTATTTCTGGAAAG	0.308													T|||	1392	0.277955	0.2852	0.4784	5008	,	,		19429	0.2103		0.2485	False		,,,				2504	0.226				p.N416S		Atlas-SNP	.											FTSJD1,NS,carcinoma,0,1	FTSJD1	70	1	0			c.A1247G						PASS	.	T	SER/ASN,SER/ASN	1132,3258		165,802,1228	29.0	31.0	30.0		1247,1247	2.5	1.0	16	dbSNP_107	30	2152,6412		279,1594,2409	yes	missense,missense	FTSJD1	NM_001099642.1,NM_018348.5	46,46	444,2396,3637	CC,CT,TT		25.1284,25.7859,25.3512	benign,benign	416/771,416/771	71318577	3284,9670	2195	4282	6477	SO:0001583	missense	55783	exon3			CAATTATTTCTGG	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.1247A>G	16.37:g.71318577T>C	ENSP00000337512:p.Asn416Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	643	0.2944139194139194	149	0.30284552845528456	164	0.4530386740331492	132	0.23076923076923078	198	0.2612137203166227	T	0.906	-0.720809	0.03182	0.257859	0.251284	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.13307	2.6;2.6	5.95	2.53	0.30540	.	0.329703	0.36200	N	0.002739	T	0.00012	0.0000	L	0.46157	1.445	0.33937	P	0.35721899999999995	B	0.06786	0.001	B	0.06405	0.002	T	0.46303	-0.9201	9	0.11794	T	0.64	0.0132	8.9128	0.35563	0.0:0.2118:0.0:0.7882	rs3803704;rs52799996;rs60429579;rs3803704	416	Q8IYT2	FTSJ1_HUMAN	S	416	ENSP00000337512:N416S;ENSP00000411148:N416S	ENSP00000337512:N416S	N	-	2	0	FTSJD1	69876078	0.994000	0.37717	1.000000	0.80357	0.989000	0.77384	0.147000	0.16202	0.503000	0.28060	0.402000	0.26972	AAT	T|0.735;C|0.265	0.265	strong		0.308	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
SLC13A2	9058	hgsc.bcm.edu	37	17	26824156	26824156	+	Missense_Mutation	SNP	A	A	G	rs11567842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26824156A>G	ENST00000314669.5	+	12	2068	c.1648A>G	c.(1648-1650)Atc>Gtc	p.I550V	SLC13A2_ENST00000545060.1_Missense_Mutation_p.I507V|SLC13A2_ENST00000537681.1_Missense_Mutation_p.I479V|SLC13A2_ENST00000444914.3_Missense_Mutation_p.I599V	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	550			I -> V (in dbSNP:rs11567842). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17470169}.		dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)	p.I550V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	TGGAGTCCTGATCATCGCACT	0.612													G|||	2371	0.473442	0.6415	0.5346	5008	,	,		19203	0.3452		0.3698	False		,,,				2504	0.4417				p.I599V		Atlas-SNP	.											SLC13A2,NS,carcinoma,0,1	SLC13A2	125	1	1	Substitution - Missense(1)	stomach(1)	c.A1795G						PASS	.	G	VAL/ILE,VAL/ILE,VAL/ILE	2552,1854	538.7+/-375.1	761,1030,412	153.0	125.0	135.0		1648,1519,1795	3.2	1.0	17	dbSNP_120	135	2975,5625	667.1+/-402.4	526,1923,1851	yes	missense,missense,missense	SLC13A2	NM_003984.3,NM_001145976.1,NM_001145975.1	29,29,29	1287,2953,2263	GG,GA,AA		34.593,42.079,42.4958	benign,benign,benign	550/593,507/550,599/642	26824156	5527,7479	2203	4300	6503	SO:0001583	missense	9058	exon12			GTCCTGATCATCG	U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"""Solute carriers"""	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.1648A>G	17.37:g.26824156A>G	ENSP00000316202:p.Ile550Val	Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	298	298	1	NM_001145975	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	37	CCDS11231.1	1012	0.4633699633699634	330	0.6707317073170732	193	0.5331491712707183	223	0.38986013986013984	266	0.35092348284960423	G	0.131	-1.113770	0.01799	0.57921	0.34593	ENSG00000007216	ENST00000314669;ENST00000444914;ENST00000545060;ENST00000537681	T;T;T;T	0.03272	3.99;3.99;3.99;3.99	5.27	3.21	0.36854	.	0.772693	0.12195	N	0.490860	T	0.00012	0.0000	N	0.00504	-1.425	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.27054	-1.0085	9	0.02654	T	1	-21.18	8.1201	0.30965	0.4377:0.0:0.5623:0.0	rs11567842;rs11568454;rs52804705;rs56617498;rs57825258;rs11567842	507;599;479;550	F5GWV6;E7ETH5;G3V1L2;Q13183	.;.;.;S13A2_HUMAN	V	550;599;507;479	ENSP00000316202:I550V;ENSP00000392411:I599V;ENSP00000441935:I507V;ENSP00000440802:I479V	ENSP00000316202:I550V	I	+	1	0	SLC13A2	23848283	0.529000	0.26322	1.000000	0.80357	0.420000	0.31355	0.555000	0.23422	0.590000	0.29694	-0.215000	0.12644	ATC	A|0.560;G|0.440	0.440	strong		0.612	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984	
TARBP1	6894	hgsc.bcm.edu	37	1	234529519	234529519	+	Silent	SNP	C	C	T	rs1802871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:234529519C>T	ENST00000040877.1	-	27	4307	c.4308G>A	c.(4306-4308)ccG>ccA	p.P1436P	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1436					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)			GACTGTTCCACGGGATAATCT	0.468													C|||	1147	0.229034	0.5401	0.1844	5008	,	,		17469	0.0853		0.0875	False		,,,				2504	0.1339				p.P1436P		Atlas-SNP	.											TARBP1,caecum,carcinoma,0,1	TARBP1	111	1	0			c.G4308A						PASS	.	C		2025,2381	564.2+/-381.4	474,1077,652	97.0	101.0	100.0		4308	-8.7	0.1	1	dbSNP_89	100	710,7890	173.7+/-224.2	32,646,3622	no	coding-synonymous	TARBP1	NM_005646.3		506,1723,4274	TT,TC,CC		8.2558,45.9601,21.0288		1436/1622	234529519	2735,10271	2203	4300	6503	SO:0001819	synonymous_variant	6894	exon27			GTTCCACGGGATA		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.4308G>A	1.37:g.234529519C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	154	68	0.441558	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			C|0.797;T|0.203	0.203	strong		0.468	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39908215	39908215	+	Silent	SNP	G	G	A	rs142309421		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39908215G>A	ENST00000409794.3	+	8	1615	c.765G>A	c.(763-765)gcG>gcA	p.A255A	PLEKHG2_ENST00000425673.1_Silent_p.A255A|PLEKHG2_ENST00000458508.2_Silent_p.A196A|PLEKHG2_ENST00000409797.2_Silent_p.A255A|PLEKHG2_ENST00000378550.1_Silent_p.A255A	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	255	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGCACTGGGCGGAGGGCCCAG	0.572																																					p.A255A		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G765A						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	56.0	50.0	52.0		765	-9.4	0.0	19	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous	PLEKHG2	NM_022835.2		0,4,6499	AA,AG,GG		0.0,0.0908,0.0308		255/1387	39908215	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	64857	exon8			CTGGGCGGAGGGC	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.765G>A	19.37:g.39908215G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	G	0.870	-0.732282	0.03135	9.08E-4	0.0	ENSG00000090924	ENST00000205135	.	.	.	4.68	-9.36	0.00629	.	.	.	.	.	T	0.33760	0.0874	.	.	.	0.46901	D	0.999249	.	.	.	.	.	.	T	0.52064	-0.8625	4	.	.	.	.	1.5973	0.02666	0.2022:0.2901:0.2917:0.216	.	.	.	.	Q	152	.	.	R	+	2	0	PLEKHG2	44600055	0.000000	0.05858	0.019000	0.16419	0.184000	0.23303	-5.033000	0.00158	-4.337000	0.00055	-2.075000	0.00382	CGG	G|1.000;A|0.000	0.000	weak		0.572	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
BEGAIN	57596	hgsc.bcm.edu	37	14	101005215	101005215	+	Silent	SNP	T	T	C	rs12893951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101005215T>C	ENST00000355173.2	-	7	944	c.873A>G	c.(871-873)gcA>gcG	p.A291A	CTD-2062F14.3_ENST00000553301.1_lincRNA|BEGAIN_ENST00000556751.1_Silent_p.A227A|BEGAIN_ENST00000443071.2_Silent_p.A291A	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	291						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				GCAGTGAGCCTGCGTAGCTGG	0.706													C|||	3260	0.650958	0.969	0.6254	5008	,	,		13674	0.7093		0.4274	False		,,,				2504	0.409				p.A291A	NSCLC(159;1889 2010 9965 27479 40101)	Atlas-SNP	.											.	BEGAIN	32	.	0			c.A873G						PASS	.	C	,	3873,527		1715,443,42	23.0	26.0	25.0		873,873	1.5	0.9	14	dbSNP_121	25	3508,5090		752,2004,1543	no	coding-synonymous,coding-synonymous	BEGAIN	NM_001159531.1,NM_020836.3	,	2467,2447,1585	CC,CT,TT		40.8002,11.9773,43.2143	,	291/594,291/594	101005215	7381,5617	2200	4299	6499	SO:0001819	synonymous_variant	57596	exon7			TGAGCCTGCGTAG	BC002607	CCDS9962.1	14q32.2	2012-12-07	2012-12-07			ENSG00000183092			24163	protein-coding gene	gene with protein product			"""brain-enriched guanylate kinase-associated homolog (rat)"""			10819331	Standard	NM_020836		Approved	KIAA1446	uc010txa.2	Q9BUH8		ENST00000355173.2:c.873A>G	14.37:g.101005215T>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	22	20	0.909091	NM_020836	Q9NPU3|Q9P282	Silent	SNP	ENST00000355173.2	37	CCDS9962.1																																																																																			T|0.388;C|0.612	0.612	strong		0.706	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836	
SNX18	112574	hgsc.bcm.edu	37	5	53815560	53815560	+	Missense_Mutation	SNP	A	A	C	rs13162502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	126	0	0		WXS	Illumina HiSeq	Phase_I	115	42	0.365217	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		
CASC1	55259	hgsc.bcm.edu	37	12	25311489	25311489	+	Missense_Mutation	SNP	G	G	T	rs10842496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25311489G>T	ENST00000320267.9	-	3	178	c.97C>A	c.(97-99)Cgt>Agt	p.R33S	CASC1_ENST00000395990.2_5'UTR|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000537577.1_Intron|CASC1_ENST00000395987.3_Missense_Mutation_p.R39S|CASC1_ENST00000545133.1_Intron|CASC1_ENST00000354189.5_Missense_Mutation_p.R97S	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	33	Glu-rich.		R -> S (in dbSNP:rs10842496). {ECO:0000269|PubMed:16410263}.							breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			TATTTCAAACGGGCTTCCTCT	0.303													G|||	1271	0.253794	0.1293	0.3487	5008	,	,		19737	0.1925		0.3757	False		,,,				2504	0.2924				p.R97S		Atlas-SNP	.											.	CASC1	146	.	0			c.C289A						PASS	.	G	SER/ARG,SER/ARG,SER/ARG,,	681,3725	284.6+/-277.7	52,577,1574	79.0	77.0	78.0		289,97,115,,	5.4	1.0	12	dbSNP_120	78	3109,5487	470.9+/-367.9	564,1981,1753	yes	missense,missense,missense,intron,utr-5	CASC1	NM_001082972.1,NM_001082973.1,NM_018272.3,NM_001204101.1,NM_001204102.1	110,110,110,,	616,2558,3327	TT,TG,GG		36.168,15.4562,29.1494	probably-damaging,probably-damaging,probably-damaging,,	97/691,33/717,39/723,,	25311489	3790,9212	2203	4298	6501	SO:0001583	missense	55259	exon4			TCAAACGGGCTTC	AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 54"""					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.97C>A	12.37:g.25311489G>T	ENSP00000313141:p.Arg33Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_001082972	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Missense_Mutation	SNP	ENST00000320267.9	37	CCDS41762.1	598|598	0.27380952380952384|0.27380952380952384	67|67	0.13617886178861788|0.13617886178861788	111|111	0.30662983425414364|0.30662983425414364	138|138	0.24125874125874125|0.24125874125874125	282|282	0.3720316622691293|0.3720316622691293	G|G	17.49|17.49	3.401556|3.401556	0.62288|0.62288	0.154562|0.154562	0.36168|0.36168	ENSG00000118307|ENSG00000118307	ENST00000556006|ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395992	.|T;T;T	.|0.44881	.|1.99;0.91;0.92	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.69823|0.69823	2.125|2.125	0.09310|0.09310	P|P	1.0|1.0	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.997;0.999	T|T	0.20706|0.20706	-1.0267|-1.0267	4|9	.|0.66056	.|D	.|0.02	-17.9944|-17.9944	14.7255|14.7255	0.69341|0.69341	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs10842496;rs10842496|rs10842496;rs10842496	.|97;33;39	.|Q6TDU7-3;Q6TDU7;F8W8F9	.|.;CASC1_HUMAN;.	Q|S	8|97;39;33;39	.|ENSP00000346126:R97S;ENSP00000379310:R39S;ENSP00000313141:R33S	.|ENSP00000313141:R33S	P|R	-|-	2|1	0|0	CASC1|CASC1	25202756|25202756	1.000000|1.000000	0.71417|0.71417	0.971000|0.971000	0.41717|0.41717	0.990000|0.990000	0.78478|0.78478	3.836000|3.836000	0.55813|0.55813	2.535000|2.535000	0.85469|0.85469	0.573000|0.573000	0.79308|0.79308	CCG|CGT	G|0.728;T|0.272	0.272	strong		0.303	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272	
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43654194	43654194	+	Silent	SNP	A	A	G	rs35718664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:43654194A>G	ENST00000374466.3	+	3	1028	c.693A>G	c.(691-693)acA>acG	p.T231T	CSGALNACT2_ENST00000374464.1_Silent_p.T231T	NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	231					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)			endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						ATAAGGGCACACAGTATGAAC	0.403													G|||	189	0.0377396	0.0121	0.0317	5008	,	,		16738	0.0		0.0636	False		,,,				2504	0.089				p.T231T		Atlas-SNP	.											.	CSGALNACT2	67	.	0			c.A693G						PASS	.	G		112,4294	815.6+/-416.2	3,106,2094	101.0	96.0	97.0		693	-4.9	0.7	10	dbSNP_126	97	511,8089	796.1+/-407.5	22,467,3811	no	coding-synonymous	CSGALNACT2	NM_018590.3		25,573,5905	GG,GA,AA		5.9419,2.542,4.7901		231/543	43654194	623,12383	2203	4300	6503	SO:0001819	synonymous_variant	55454	exon3			GGGCACACAGTAT	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"""Beta 4-glycosyltransferases"""	24292	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"""					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.693A>G	10.37:g.43654194A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	101	57	0.564356	NM_018590	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Silent	SNP	ENST00000374466.3	37	CCDS7201.1																																																																																			A|0.955;G|0.045	0.045	strong		0.403	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590	
SPNS3	201305	hgsc.bcm.edu	37	17	4351534	4351534	+	Missense_Mutation	SNP	G	G	C	rs61740736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4351534G>C	ENST00000355530.2	+	6	986	c.706G>C	c.(706-708)Ggg>Cgg	p.G236R	SPNS3_ENST00000576069.1_3'UTR|SPNS3_ENST00000333476.2_Missense_Mutation_p.G109R	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	236					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						CGAGACACAGGGGGAGGGGGC	0.637													G|||	77	0.0153754	0.0552	0.0058	5008	,	,		17510	0.0		0.0	False		,,,				2504	0.0				p.G236R		Atlas-SNP	.											.	SPNS3	52	.	0			c.G706C						PASS	.	G	ARG/GLY	160,4246	104.3+/-142.8	3,154,2046	33.0	31.0	32.0		706	1.9	0.2	17	dbSNP_129	32	0,8600		0,0,4300	yes	missense	SPNS3	NM_182538.4	125	3,154,6346	CC,CG,GG		0.0,3.6314,1.2302	benign	236/513	4351534	160,12846	2203	4300	6503	SO:0001583	missense	201305	exon6			ACACAGGGGGAGG		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.706G>C	17.37:g.4351534G>C	ENSP00000347721:p.Gly236Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	103	43	0.417476	NM_182538	Q8IZ31	Missense_Mutation	SNP	ENST00000355530.2	37	CCDS11045.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	G	3.051	-0.195356	0.06259	0.036314	0.0	ENSG00000182557	ENST00000355530;ENST00000333476	T;T	0.58797	0.31;0.31	5.42	1.9	0.25705	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.357041	0.32343	N	0.006225	T	0.05960	0.0155	N	0.17312	0.475	0.09310	N	0.999999	B;B	0.15141	0.001;0.012	B;B	0.23852	0.002;0.049	T	0.04153	-1.0973	10	0.11485	T	0.65	-3.8842	3.2294	0.06744	0.3204:0.0:0.4977:0.1819	rs61740736	109;236	Q6ZMD2-2;Q6ZMD2	.;SPNS3_HUMAN	R	236;109	ENSP00000347721:G236R;ENSP00000333207:G109R	ENSP00000333207:G109R	G	+	1	0	SPNS3	4298283	0.202000	0.23423	0.212000	0.23672	0.006000	0.05464	0.900000	0.28431	0.794000	0.33899	-0.217000	0.12591	GGG	G|0.989;C|0.011	0.011	strong		0.637	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305785	39305785	+	Missense_Mutation	SNP	A	A	T	rs411367		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305785A>T	ENST00000343246.4	-	1	269	c.235T>A	c.(235-237)Tgc>Agc	p.C79S		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	79	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)			tggcagcagcaggggcggcag	0.657																																					p.C79S		Atlas-SNP	.											KRTAP4-5,colon,carcinoma,0,3	KRTAP4-5	34	3	0			c.T235A						PASS	.						12.0	18.0	16.0					17																	39305785		2089	4172	6261	SO:0001583	missense	85289	exon1			AGCAGCAGGGGCG	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.235T>A	17.37:g.39305785A>T	ENSP00000340546:p.Cys79Ser	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	99	28	0.282828	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	773	0.35393772893772896	210	0.4268292682926829	126	0.34806629834254144	175	0.30594405594405594	262	0.34564643799472294	.	0.010	-1.763522	0.00651	.	.	ENSG00000198271	ENST00000343246	T	0.00534	6.74	2.78	-5.56	0.02529	.	0.768893	0.10092	N	0.717076	T	0.00012	0.0000	N	0.01431	-0.87	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23297	-1.0192	9	0.02654	T	1	.	5.4481	0.16548	0.6146:0.0:0.1542:0.2312	rs411367;rs6503604	79	Q9BYR2	KRA45_HUMAN	S	79	ENSP00000340546:C79S	ENSP00000340546:C79S	C	-	1	0	KRTAP4-5	36559311	0.977000	0.34250	0.000000	0.03702	0.000000	0.00434	-0.260000	0.08708	-1.272000	0.02427	-2.057000	0.00402	TGC	A|0.646;T|0.354	0.354	strong		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
OGFOD3	79701	hgsc.bcm.edu	37	17	80364341	80364341	+	Silent	SNP	C	C	T	rs34315006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80364341C>T	ENST00000313056.5	-	5	592	c.441G>A	c.(439-441)ttG>ttA	p.L147L	OGFOD3_ENST00000329197.5_Silent_p.L147L	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	147						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)										CCCCTGAGTGCAAGTCCAGAA	0.532													C|||	8	0.00159744	0.0	0.0072	5008	,	,		18395	0.0		0.002	False		,,,				2504	0.001				p.L147L		Atlas-SNP	.											.	.	.	.	0			c.G441A						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	107.0	93.0	98.0		441,441	3.7	1.0	17	dbSNP_126	98	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous,coding-synonymous	C17orf101	NM_024648.2,NM_175902.4	,	0,36,6467	TT,TC,CC		0.3953,0.0454,0.2768	,	147/320,147/332	80364341	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	79701	exon5			TGAGTGCAAGTCC	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.441G>A	17.37:g.80364341C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Silent	SNP	ENST00000313056.5	37	CCDS11811.1																																																																																			C|0.997;T|0.003	0.003	strong		0.532	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077755	19077755	+	Silent	SNP	A	A	C	rs11024969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:19077755A>C	ENST00000329773.2	-	2	282	c.195T>G	c.(193-195)tcT>tcG	p.S65S		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	65					positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)	p.S65S(1)		NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						GGACGTAGACAGAGAAGGCGT	0.557													A|||	566	0.113019	0.1944	0.036	5008	,	,		18324	0.1468		0.0656	False		,,,				2504	0.0716				p.S65S	GBM(198;1966 2199 4849 37227 49954)	Atlas-SNP	.											MRGPRX2,NS,carcinoma,0,1	MRGPRX2	42	1	1	Substitution - coding silent(1)	stomach(1)	c.T195G						PASS	.	A		701,3697		61,579,1559	84.0	92.0	89.0		195	-4.8	0.0	11	dbSNP_120	89	428,8158		7,414,3872	no	coding-synonymous	MRGPRX2	NM_054030.2		68,993,5431	CC,CA,AA		4.9849,15.9391,8.6953		65/331	19077755	1129,11855	2199	4293	6492	SO:0001819	synonymous_variant	117194	exon2			GTAGACAGAGAAG		CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"""GPCR / Class A : Orphans"""	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.195T>G	11.37:g.19077755A>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_054030	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Silent	SNP	ENST00000329773.2	37	CCDS7847.1																																																																																			A|0.900;C|0.100	0.100	strong		0.557	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030	
ANKRD36	375248	hgsc.bcm.edu	37	2	97877478	97877478	+	Splice_Site	SNP	G	G	A	rs10194525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:97877478G>A	ENST00000461153.2	+	58	3713	c.3469G>A	c.(3469-3471)Gtg>Atg	p.V1157M	ANKRD36_ENST00000420699.2_Splice_Site_p.V1157M			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	1157								p.V1157M(1)|p.V987M(1)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						ATCTGGGACAGGTAATTTTGC	0.398																																					p.V1157M		Atlas-SNP	.											ANKRD36_ENST00000420699,NS,carcinoma,0,2	ANKRD36	170	2	2	Substitution - Missense(2)	endometrium(2)	c.G3469A						PASS	.						126.0	121.0	123.0					2																	97877478		692	1591	2283	SO:0001630	splice_region_variant	375248	exon58			GGGACAGGTAATT	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.3469+1G>A	2.37:g.97877478G>A		Somatic	417	0	0		WXS	Illumina HiSeq	Phase_I	503	172	0.341948	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	.	11.89	1.775024	0.31411	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000461694	T;T	0.21191	2.02;2.02	1.17	1.17	0.20885	.	.	.	.	.	T	0.21509	0.0518	L	0.39898	1.24	0.20307	N	0.999911	P	0.51240	0.943	P	0.49361	0.608	T	0.11060	-1.0603	9	0.66056	D	0.02	.	5.763	0.18211	0.0:0.0:1.0:0.0	rs10194525;rs58967241	1157	A6QL64	AN36A_HUMAN	M	1157;1157;417	ENSP00000419530:V1157M;ENSP00000391950:V1157M	ENSP00000391950:V1157M	V	+	1	0	ANKRD36	97241205	0.997000	0.39634	0.147000	0.22382	0.056000	0.15407	1.868000	0.39509	0.949000	0.37715	0.436000	0.28706	GTG	G|0.500;A|0.500	0.500	strong		0.398	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		Missense_Mutation
DCAF12L2	340578	hgsc.bcm.edu	37	X	125299188	125299188	+	Silent	SNP	T	T	G	rs12014937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:125299188T>G	ENST00000360028.2	-	1	746	c.720A>C	c.(718-720)ccA>ccC	p.P240P	DCAF12L2_ENST00000538699.1_Silent_p.P240P			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	240										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						GGGCATATACTGGGAGACCCA	0.642													G|||	2050	0.543046	0.587	0.4236	3775	,	,		12575	0.3859		0.2495	False		,,,				2504	0.3476				p.P240P		Atlas-SNP	.											.	DCAF12L2	157	.	0			c.A720C						PASS	.	G		2758,1077		841,669,407,122,164	29.0	32.0	31.0		720	-7.7	0.0	X	dbSNP_120	31	1994,4730		220,988,566,1219,1304	no	coding-synonymous	DCAF12L2	NM_001013628.2		1061,1657,973,1341,1468	GG,GT,G,TT,T		29.655,28.0834,45.0043		240/464	125299188	4752,5807	2203	4297	6500	SO:0001819	synonymous_variant	340578	exon1			ATATACTGGGAGA	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"""WD repeat domain containing"""	32950	protein-coding gene	gene with protein product			"""WD repeat domain 40C"""	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.720A>C	X.37:g.125299188T>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_001013628	B2RN42	Silent	SNP	ENST00000360028.2	37	CCDS43991.1																																																																																			T|0.485;G|0.515	0.515	strong		0.642	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628	
ZNF100	163227	hgsc.bcm.edu	37	19	21909548	21909548	+	Silent	SNP	A	A	G	rs371600049		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21909548A>G	ENST00000358296.6	-	5	1764	c.1566T>C	c.(1564-1566)ttT>ttC	p.F522F	ZNF100_ENST00000305570.6_Silent_p.F458F	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	522					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						GGGACTGGTTAAAGTCTTTAC	0.368													N|||	1	0.000199681	0.0008	0.0	5008	,	,		19310	0.0		0.0	False		,,,				2504	0.0				p.F522F		Atlas-SNP	.											.	ZNF100	62	.	0			c.T1566C						PASS	.	A		3,4315		0,3,2156	71.0	80.0	77.0		1566	-0.4	0.3	19		77	0,8552		0,0,4276	no	coding-synonymous	ZNF100	NM_173531.3		0,3,6432	GG,GA,AA		0.0,0.0695,0.0233		522/543	21909548	3,12867	2159	4276	6435	SO:0001819	synonymous_variant	163227	exon5			CTGGTTAAAGTCT	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.1566T>C	19.37:g.21909548A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	36	27	0.75	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			.	.	weak		0.368	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
OR51F1	256892	hgsc.bcm.edu	37	11	4790471	4790471	+	Missense_Mutation	SNP	G	G	A	rs1030723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4790471G>A	ENST00000380383.1	-	1	697	c.698C>T	c.(697-699)tCt>tTt	p.S233F	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.S226F			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	233			S -> F (in dbSNP:rs1030723).			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)		TCTGAGGACAGAGTGAATAAT	0.453													G|||	837	0.167133	0.4418	0.1052	5008	,	,		23334	0.0		0.1292	False		,,,				2504	0.0511				p.S226F		Atlas-SNP	.											.	OR51F1	60	.	0			c.C677T						PASS	.	G	PHE/SER	1745,2657	520.2+/-370.2	356,1033,812	126.0	123.0	124.0		677	4.3	0.8	11	dbSNP_86	124	1019,7577	217.8+/-256.4	74,871,3353	yes	missense	OR51F1	NM_001004752.1	155	430,1904,4165	AA,AG,GG		11.8544,39.6411,21.2648	probably-damaging	226/313	4790471	2764,10234	2201	4298	6499	SO:0001583	missense	256892	exon1			AGGACAGAGTGAA	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.698C>T	11.37:g.4790471G>A	ENSP00000369744:p.Ser233Phe	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	142	63	0.443662	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		330	0.1510989010989011	217	0.4410569105691057	34	0.09392265193370165	0	0.0	79	0.10422163588390501	G	13.37	2.217842	0.39201	0.396411	0.118544	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00158	8.65;8.65	5.24	4.32	0.51571	GPCR, rhodopsin-like superfamily (1);	0.378221	0.23017	N	0.052898	T	0.00012	0.0000	M	0.92317	3.295	0.34571	P	0.28654900000000005	D	0.89917	1.0	D	0.97110	1.0	T	0.08166	-1.0735	9	0.87932	D	0	.	9.1496	0.36955	0.0805:0.1504:0.7692:0.0	rs1030723;rs52810044;rs57519163;rs1030723	233	A6NGY5	O51F1_HUMAN	F	226;233	ENSP00000345163:S226F;ENSP00000369744:S233F	ENSP00000345163:S226F	S	-	2	0	OR51F1	4747047	0.651000	0.27340	0.821000	0.32701	0.348000	0.29142	3.919000	0.56439	1.428000	0.47296	0.655000	0.94253	TCT	G|0.798;A|0.202	0.202	strong		0.453	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
OR51F1	256892	hgsc.bcm.edu	37	11	4790951	4790951	+	Missense_Mutation	SNP	A	A	G	rs11033801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4790951A>G	ENST00000380383.1	-	1	217	c.218T>C	c.(217-219)tTc>tCc	p.F73S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.F66S			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	73			F -> S (in dbSNP:rs11033801).			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)		TGATAGCCTGAAGAGGAAATA	0.443													G|||	1080	0.215655	0.4569	0.2017	5008	,	,		21639	0.0		0.2704	False		,,,				2504	0.0654				p.F66S		Atlas-SNP	.											.	OR51F1	60	.	0			c.T197C						PASS	.	G	SER/PHE	1966,2436	617.7+/-393.0	443,1080,678	67.0	63.0	65.0		197	4.8	1.0	11	dbSNP_120	65	2164,6432	712.0+/-405.9	286,1592,2420	yes	missense	OR51F1	NM_001004752.1	155	729,2672,3098	GG,GA,AA		25.1745,44.6615,31.7741	benign	66/313	4790951	4130,8868	2201	4298	6499	SO:0001583	missense	256892	exon1			AGCCTGAAGAGGA	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.218T>C	11.37:g.4790951A>G	ENSP00000369744:p.Phe73Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		494	0.2261904761904762	225	0.4573170731707317	82	0.2265193370165746	0	0.0	187	0.24670184696569922	G	0.026	-1.367725	0.01225	0.446615	0.251745	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00449	7.37;7.37	4.81	4.81	0.61882	GPCR, rhodopsin-like superfamily (1);	0.133054	0.34580	N	0.003857	T	0.00012	0.0000	N	0.00186	-1.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06643	-1.0815	9	0.02654	T	1	.	7.3933	0.26921	0.0863:0.0:0.7488:0.1649	rs11033801;rs52802475;rs58778978;rs11033801	73	A6NGY5	O51F1_HUMAN	S	66;73	ENSP00000345163:F66S;ENSP00000369744:F73S	ENSP00000345163:F66S	F	-	2	0	OR51F1	4747527	0.352000	0.24895	0.965000	0.40720	0.712000	0.41017	0.483000	0.22292	1.271000	0.44313	-0.197000	0.12766	TTC	A|0.702;G|0.298	0.298	strong		0.443	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
ADRB1	153	hgsc.bcm.edu	37	10	115804206	115804206	+	Silent	SNP	G	G	T	rs7921133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115804206G>T	ENST00000369295.2	+	1	401	c.315G>T	c.(313-315)ctG>ctT	p.L105L		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	105					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	GCGCCGACCTGGTCATGGGGC	0.662													G|||	144	0.028754	0.1044	0.0086	5008	,	,		15320	0.0		0.0	False		,,,				2504	0.0				p.L105L		Atlas-SNP	.											.	ADRB1	16	.	0			c.G315T						PASS	.	G		447,3959	205.8+/-227.6	24,399,1780	57.0	67.0	63.0		315	4.1	1.0	10	dbSNP_116	63	8,8590	6.4+/-24.3	0,8,4291	no	coding-synonymous	ADRB1	NM_000684.2		24,407,6071	TT,TG,GG		0.093,10.1453,3.4989		105/478	115804206	455,12549	2203	4299	6502	SO:0001819	synonymous_variant	153	exon1			CGACCTGGTCATG	J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"""GPCR / Class A : Adrenoceptors : beta"""	285	protein-coding gene	gene with protein product		109630	"""adrenergic, beta-1-, receptor"""	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.315G>T	10.37:g.115804206G>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_000684	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Silent	SNP	ENST00000369295.2	37	CCDS7586.1																																																																																			G|0.963;T|0.037	0.037	strong		0.662	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1		
SFRP4	6424	hgsc.bcm.edu	37	7	37947103	37947103	+	Missense_Mutation	SNP	C	C	T	rs1802074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:37947103C>T	ENST00000436072.2	-	6	1396	c.1019G>A	c.(1018-1020)aGa>aAa	p.R340K	EPDR1_ENST00000476620.1_Intron	NM_003014.3	NP_003005.2	Q6FHJ7	SFRP4_HUMAN	secreted frizzled-related protein 4	340			R -> K (in dbSNP:rs1802074). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		brain development (GO:0007420)|cell differentiation (GO:0030154)|decidualization (GO:0046697)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|menstrual cycle phase (GO:0022601)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of sodium-dependent phosphate transport (GO:2000119)|phosphate ion homeostasis (GO:0055062)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of receptor internalization (GO:0002092)|response to hormone (GO:0009725)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						CGGGTTTGTTCTCTTCTGGGC	0.507													C|||	1267	0.252995	0.3979	0.1772	5008	,	,		19455	0.2619		0.2217	False		,,,				2504	0.1339				p.R340K		Atlas-SNP	.											.	SFRP4	66	.	0			c.G1019A						PASS	.	C	LYS/ARG	1503,2903	480.6+/-358.9	262,979,962	194.0	193.0	193.0		1019	0.9	0.0	7	dbSNP_89	193	1651,6949	304.1+/-306.8	145,1361,2794	yes	missense	SFRP4	NM_003014.3	26	407,2340,3756	TT,TC,CC		19.1977,34.1126,24.2503	benign	340/347	37947103	3154,9852	2203	4300	6503	SO:0001583	missense	6424	exon6			TTTGTTCTCTTCT	AF026692	CCDS5453.1	7p14.1	2008-07-18			ENSG00000106483	ENSG00000106483		"""Secreted frizzled-related proteins"""	10778	protein-coding gene	gene with protein product		606570				10211996	Standard	NM_003014		Approved	frpHE, FRP-4, FRPHE	uc003tfo.4	Q6FHJ7	OTTHUMG00000023026	ENST00000436072.2:c.1019G>A	7.37:g.37947103C>T	ENSP00000410715:p.Arg340Lys	Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	349	349	1	NM_003014	B4DYC1|O14877|Q05BG7|Q1ZYW2|Q4G124|Q6FHM0|Q6PD64	Missense_Mutation	SNP	ENST00000436072.2	37	CCDS5453.1	606	0.2774725274725275	194	0.3943089430894309	82	0.2265193370165746	153	0.2674825174825175	177	0.23350923482849603	C	0.488	-0.876652	0.02550	0.341126	0.191977	ENSG00000106483	ENST00000436072;ENST00000446575	T	0.62105	0.05	5.68	0.881	0.19166	.	0.557844	0.18393	N	0.142610	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	0.40496	-0.9560	9	0.12430	T	0.62	.	9.5666	0.39402	0.0:0.492:0.0:0.508	rs1802074;rs52828267;rs60194202;rs1802074	340	Q6FHJ7	SFRP4_HUMAN	K	340;337	ENSP00000410715:R340K	ENSP00000410715:R340K	R	-	2	0	SFRP4	37913628	0.603000	0.26924	0.016000	0.15963	0.085000	0.17905	0.505000	0.22642	-0.071000	0.12886	-1.193000	0.01689	AGA	C|0.744;T|0.256	0.256	strong		0.507	SFRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220017.2	NM_003014	
RBP1	5947	hgsc.bcm.edu	37	3	139258508	139258508	+	Missense_Mutation	SNP	G	G	A	rs2071386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:139258508G>A	ENST00000483943.2	-	1	53	c.53C>T	c.(52-54)cCg>cTg	p.P18L	RP11-319G6.1_ENST00000515247.1_RNA|RBP1_ENST00000232219.2_Missense_Mutation_p.P18L|RP11-319G6.1_ENST00000381790.3_RNA|RBP1_ENST00000492918.1_Missense_Mutation_p.P18L	NM_001130993.1	NP_001124465.1	P09455	RET1_HUMAN	retinol binding protein 1, cellular	0					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	5					Acitretin(DB00459)|Vitamin A(DB00162)	GGGGCTCTGCGGGGCGGCGAC	0.746													G|||	851	0.169928	0.2943	0.232	5008	,	,		12066	0.13		0.0716	False		,,,				2504	0.1002				p.P18L		Atlas-SNP	.											.	RBP1	39	.	0			c.C53T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	304,1066		35,234,416	6.0	10.0	9.0		53,53,53	2.1	0.9	3	dbSNP_96	9	195,2969		4,187,1391	yes	missense,missense,missense	RBP1	NM_001130992.1,NM_001130993.1,NM_002899.3	98,98,98	39,421,1807	AA,AG,GG		6.1631,22.1898,11.0057	possibly-damaging,possibly-damaging,possibly-damaging	18/158,18/154,18/198	139258508	499,4035	685	1582	2267	SO:0001583	missense	5947	exon1			CTCTGCGGGGCGG		CCDS3110.2, CCDS46925.1, CCDS46926.1	3q21-q23	2013-03-01	2001-11-28		ENSG00000114115	ENSG00000114115		"""Fatty acid binding protein family"""	9919	protein-coding gene	gene with protein product		180260	"""retinol-binding protein 1, cellular"""			1654334, 9858824	Standard	NM_002899		Approved	CRABP-I, CRBP1, CRBP, RBPC, CRBPI	uc003eti.2	P09455	OTTHUMG00000155751	ENST00000483943.2:c.53C>T	3.37:g.139258508G>A	ENSP00000424813:p.Pro18Leu	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	11	5	0.454545	NM_002899	A8K2Q0|B7Z7A0|E7EWV0|F2Z2F2|Q6FGX8	Missense_Mutation	SNP	ENST00000483943.2	37	CCDS46925.1	333	0.15247252747252749	130	0.26422764227642276	80	0.22099447513812154	74	0.12937062937062938	49	0.06464379947229551	G	5.283	0.237637	0.10023	0.221898	0.061631	ENSG00000114115	ENST00000232219;ENST00000483943;ENST00000492918	T;T;T	0.28454	1.86;1.63;1.61	4.11	2.1	0.27182	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.37949	P	0.06740500000000005	P;P	0.47545	0.897;0.897	B;B	0.35278	0.199;0.199	T	0.37619	-0.9698	8	0.20519	T	0.43	.	8.5086	0.33204	0.0:0.0:0.5782:0.4218	rs2071386;rs57968945	18;18	F2Z2F2;E7EWV0	.;.	L	18	ENSP00000232219:P18L;ENSP00000424813:P18L;ENSP00000429166:P18L	ENSP00000232219:P18L	P	-	2	0	RBP1	140741198	0.807000	0.29009	0.909000	0.35828	0.480000	0.33159	0.082000	0.14847	1.049000	0.40321	-0.182000	0.12963	CCG	G|0.850;A|0.150	0.150	strong		0.746	RBP1-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341497.2	NM_002899	
MTUS1	57509	hgsc.bcm.edu	37	8	17513414	17513414	+	Silent	SNP	G	G	A	rs12224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17513414G>A	ENST00000262102.6	-	9	3290	c.3066C>T	c.(3064-3066)taC>taT	p.Y1022Y	MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000400046.1_Silent_p.Y94Y|MTUS1_ENST00000297488.6_Silent_p.Y188Y|MTUS1_ENST00000381861.3_Silent_p.Y269Y|MTUS1_ENST00000544260.1_Silent_p.Y167Y|MTUS1_ENST00000519263.1_Silent_p.Y968Y|MTUS1_ENST00000381869.3_Silent_p.Y968Y	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	1022					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)		CTTCTTCAATGTAAGTGTCCC	0.463													G|||	386	0.0770767	0.1263	0.0548	5008	,	,		19300	0.0208		0.0726	False		,,,				2504	0.089				p.Y1022Y		Atlas-SNP	.											.	MTUS1	144	.	0			c.C3066T						PASS	.	G	,,,,	420,3332		22,376,1478	180.0	164.0	169.0		3066,2904,807,501,564	2.3	0.6	8	dbSNP_52	169	739,7503		28,683,3410	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	,,,,	50,1059,4888	AA,AG,GG		8.9663,11.194,9.6632	,,,,	1022/1271,968/1217,269/518,167/416,188/437	17513414	1159,10835	1876	4121	5997	SO:0001819	synonymous_variant	57509	exon9			TTCAATGTAAGTG	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.3066C>T	8.37:g.17513414G>A		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	215	102	0.474419	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			G|0.920;A|0.080	0.080	strong		0.463	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
PSTK	118672	hgsc.bcm.edu	37	10	124742858	124742858	+	Silent	SNP	G	G	A	rs45498396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:124742858G>A	ENST00000368887.3	+	3	1019	c.579G>A	c.(577-579)agG>agA	p.R193R	PSTK_ENST00000405485.1_Silent_p.R193R|PSTK_ENST00000497219.1_3'UTR	NM_153336.2	NP_699167.2	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	193					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|tRNA binding (GO:0000049)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|skin(1)|stomach(2)	13		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		ATGGCCAGAGGCCACAGGCAC	0.453													G|||	563	0.11242	0.1785	0.1254	5008	,	,		17620	0.0099		0.1869	False		,,,				2504	0.0429				p.R193R		Atlas-SNP	.											.	PSTK	34	.	0			c.G579A						PASS	.	G		648,3758	277.5+/-273.7	59,530,1614	71.0	71.0	71.0		579	-2.4	0.0	10	dbSNP_127	71	1557,7043	292.6+/-300.9	140,1277,2883	no	coding-synonymous	PSTK	NM_153336.2		199,1807,4497	AA,AG,GG		18.1047,14.7072,16.9537		193/349	124742858	2205,10801	2203	4300	6503	SO:0001819	synonymous_variant	118672	exon3			CCAGAGGCCACAG	AK127173	CCDS7633.1	10q26.13	2007-04-17	2007-04-17	2007-04-17	ENSG00000179988	ENSG00000179988			28578	protein-coding gene	gene with protein product		611310	"""chromosome 10 open reading frame 89"""	C10orf89		15317934	Standard	NM_153336		Approved	MGC35392	uc001lgy.1	Q8IV42	OTTHUMG00000019191	ENST00000368887.3:c.579G>A	10.37:g.124742858G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	103	58	0.563107	NM_153336	Q6ZSS9	Silent	SNP	ENST00000368887.3	37	CCDS7633.1	270	0.12362637362637363	71	0.1443089430894309	54	0.14917127071823205	5	0.008741258741258742	140	0.18469656992084432	G	7.080	0.569992	0.13560	0.147072	0.181047	ENSG00000179988	ENST00000406217	.	.	.	5.86	-2.41	0.06562	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	P	0.99999999577586	.	.	.	.	.	.	T	0.30736	-0.9968	3	.	.	.	-11.4716	15.141	0.72609	0.3487:0.0:0.6513:0.0	rs45498396;rs61744313	.	.	.	D	194	.	.	G	+	2	0	PSTK	124732848	0.019000	0.18553	0.020000	0.16555	0.948000	0.59901	0.213000	0.17521	-0.708000	0.05015	-0.471000	0.05019	GGC	G|0.842;A|0.158	0.158	strong		0.453	PSTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050811.1	NM_153336	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329779	24329779	+	IGR	SNP	C	C	G	rs189357682		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24329779C>G								AC096509.1 (24985 upstream) : AC004552.1 (37146 downstream)																							GTGGGGCGCCCGGCAGCTGGA	0.652													G|||	354	0.0937748	0.2345	0.0447	3775	,	,		10876	0.001		0.0099	False		,,,				2504	0.002				p.G552R		Atlas-SNP	.											.	.	.	.	0			c.G1654C						PASS	.	G	ARG/GLY	735,1889		88,404,155,566,353	11.0	12.0	12.0		1654	1.1	0.0	X		12	111,5382		0,78,33,1838,1628	yes	missense	FAM48B2	NM_001136233.1	125	88,482,188,2404,1981	GG,GC,G,CC,C		2.0208,28.0107,10.4226	benign	552/818	24329779	846,7271	1566	3577	5143	SO:0001628	intergenic_variant	170067	exon1			GGCGCCCGGCAGC																													X.37:g.24329779C>G		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	221	130	0.588235	NM_001136233		Missense_Mutation	SNP		37																																																																																				C|0.927;G|0.073	0.073	strong	0	0.652								
AHR	196	hgsc.bcm.edu	37	7	17379110	17379110	+	Missense_Mutation	SNP	G	G	A	rs2066853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:17379110G>A	ENST00000242057.4	+	10	2304	c.1661G>A	c.(1660-1662)aGa>aAa	p.R554K	AHR_ENST00000492120.1_3'UTR	NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	554			R -> K (in dbSNP:rs2066853). {ECO:0000269|PubMed:10739168, ECO:0000269|PubMed:11698344, ECO:0000269|PubMed:7550366}.		apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|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)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	GAAGACATCAGACACATGCAG	0.378													A|||	1356	0.270767	0.4622	0.1729	5008	,	,		21674	0.37		0.1083	False		,,,				2504	0.1462				p.R554K		Atlas-SNP	.											.	AHR	89	.	0			c.G1661A	GRCh37	CM005460	AHR	M	rs2066853	PASS	.	A	LYS/ARG	1957,2449	598.6+/-389.1	423,1111,669	61.0	69.0	66.0		1661	0.6	0.1	7	dbSNP_94	66	870,7730	769.9+/-407.6	50,770,3480	yes	missense	AHR	NM_001621.4	26	473,1881,4149	AA,AG,GG		10.1163,44.4167,21.7361	benign	554/849	17379110	2827,10179	2203	4300	6503	SO:0001583	missense	196	exon10			ACATCAGACACAT	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"""Basic helix-loop-helix proteins"""	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.1661G>A	7.37:g.17379110G>A	ENSP00000242057:p.Arg554Lys	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	37	CCDS5366.1	598	0.27380952380952384	218	0.44308943089430897	56	0.15469613259668508	237	0.4143356643356643	87	0.11477572559366754	A	1.860	-0.462934	0.04476	0.444167	0.101163	ENSG00000106546	ENST00000242057	T	0.18810	2.19	6.02	0.604	0.17547	.	0.511408	0.22840	N	0.054999	T	0.00012	0.0000	N	0.01076	-1.035	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48948	-0.8989	9	0.02654	T	1	.	11.5999	0.50997	0.6648:0.0:0.3352:0.0	rs2066853;rs10330845;rs17137606;rs52789584;rs59985413;rs2066853	554	P35869	AHR_HUMAN	K	554	ENSP00000242057:R554K	ENSP00000242057:R554K	R	+	2	0	AHR	17345635	0.019000	0.18553	0.146000	0.22360	0.819000	0.46315	1.476000	0.35420	-0.048000	0.13401	-0.269000	0.10298	AGA	G|0.757;A|0.243	0.243	strong		0.378	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621	
SLC7A5	8140	hgsc.bcm.edu	37	16	87902684	87902684	+	Silent	SNP	G	G	T	rs17853938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:87902684G>T	ENST00000261622.4	-	1	410	c.345C>A	c.(343-345)ggC>ggA	p.G115G		NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	115					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)	AGGCGTAGTCGCCGCCCGATT	0.662													G|||	755	0.150759	0.3941	0.0692	5008	,	,		15492	0.005		0.0994	False		,,,				2504	0.0828				p.G115G		Atlas-SNP	.											.	SLC7A5	28	.	0			c.C345A						PASS	.	G		1558,2836	465.5+/-354.2	268,1022,907	38.0	35.0	36.0		345	1.2	1.0	16	dbSNP_123	36	954,7644	200.7+/-244.4	64,826,3409	no	coding-synonymous	SLC7A5	NM_003486.5		332,1848,4316	TT,TG,GG		11.0956,35.4574,19.335		115/508	87902684	2512,10480	2197	4299	6496	SO:0001819	synonymous_variant	8140	exon1			GTAGTCGCCGCCC	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.345C>A	16.37:g.87902684G>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	110	62	0.563636	NM_003486	Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Silent	SNP	ENST00000261622.4	37	CCDS10964.1																																																																																			G|0.835;T|0.165	0.165	strong		0.662	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486	
ADCK4	79934	hgsc.bcm.edu	37	19	41198210	41198210	+	Silent	SNP	A	A	G	rs17851001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41198210A>G	ENST00000324464.3	-	15	1666	c.1365T>C	c.(1363-1365)taT>taC	p.Y455Y	ADCK4_ENST00000243583.6_Silent_p.Y414Y|NUMBL_ENST00000540131.1_5'Flank|NUMBL_ENST00000598779.1_5'Flank|ADCK4_ENST00000450541.1_Silent_p.Y414Y|NUMBL_ENST00000599594.1_5'Flank|NUMBL_ENST00000252891.4_5'Flank	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	455						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)			ACCCAAAGTCATAAGGGCCCT	0.672													A|||	68	0.0135783	0.0484	0.0058	5008	,	,		15061	0.0		0.0	False		,,,				2504	0.0				p.Y455Y		Atlas-SNP	.											.	ADCK4	92	.	0			c.T1365C						PASS	.	A	,	195,4211	116.3+/-154.2	5,185,2013	27.0	27.0	27.0		1242,1365	-10.1	0.4	19	dbSNP_123	27	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	ADCK4	NM_001142555.2,NM_024876.3	,	5,185,6312	GG,GA,AA		0.0,4.4258,1.4995	,	414/504,455/545	41198210	195,12809	2203	4299	6502	SO:0001819	synonymous_variant	79934	exon15			AAAGTCATAAGGG	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.1365T>C	19.37:g.41198210A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	94	38	0.404255	NM_024876	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	37	CCDS12562.1																																																																																			A|0.986;G|0.014	0.014	strong		0.672	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
FAM186A	121006	hgsc.bcm.edu	37	12	50746166	50746166	+	Silent	SNP	G	G	C	rs368983791		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50746166G>C	ENST00000327337.5	-	4	4448	c.4449C>G	c.(4447-4449)ctC>ctG	p.L1483L	FAM186A_ENST00000543096.1_5'Flank|FAM186A_ENST00000543111.1_Silent_p.L1483L	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1483								p.L1483L(2)									GCGGAGGGATGAGAGGGATCC	0.647																																					p.L1483L	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,3	FAM186A	181	3	2	Substitution - coding silent(2)	endometrium(2)	c.C4449G						scavenged	.						22.0	21.0	21.0					12																	50746166		692	1591	2283	SO:0001819	synonymous_variant	121006	exon4			AGGGATGAGAGGG		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4449C>G	12.37:g.50746166G>C		Somatic	376	2	0.00531915		WXS	Illumina HiSeq	Phase_I	400	8	0.02	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			.	.	weak		0.647	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
CCDC114	93233	hgsc.bcm.edu	37	19	48807367	48807367	+	Silent	SNP	C	C	A	rs28582401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48807367C>A	ENST00000315396.7	-	7	1267	c.585G>T	c.(583-585)ctG>ctT	p.L195L		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	195					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)		CGCGCTCCCGCAGCAAGCCCA	0.682													C|||	771	0.153954	0.1422	0.0965	5008	,	,		15049	0.124		0.1988	False		,,,				2504	0.1953				p.L195L		Atlas-SNP	.											.	CCDC114	100	.	0			c.G585T						PASS	.	C		744,3662	296.7+/-284.4	66,612,1525	43.0	43.0	43.0		585	-0.5	1.0	19	dbSNP_125	43	1589,7011	285.2+/-297.1	159,1271,2870	no	coding-synonymous	CCDC114	NM_144577.3		225,1883,4395	AA,AC,CC		18.4767,16.8861,17.9379		195/671	48807367	2333,10673	2203	4300	6503	SO:0001819	synonymous_variant	93233	exon7			CTCCCGCAGCAAG	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.585G>T	19.37:g.48807367C>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Silent	SNP	ENST00000315396.7	37	CCDS12714.2																																																																																			C|0.817;A|0.183	0.183	strong		0.682	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
SLC7A13	157724	hgsc.bcm.edu	37	8	87229948	87229948	+	Silent	SNP	T	T	A	rs4621787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87229948T>A	ENST00000297524.3	-	3	1033	c.930A>T	c.(928-930)tcA>tcT	p.S310S	SLC7A13_ENST00000419776.2_Silent_p.S301S|SLC7A13_ENST00000520624.1_5'UTR	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	310						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						TTGGTCTCGATGATTTAAATA	0.388													T|||	843	0.168331	0.1921	0.2363	5008	,	,		15021	0.1419		0.0845	False		,,,				2504	0.2014				p.S310S		Atlas-SNP	.											.	SLC7A13	97	.	0			c.A930T						PASS	.	T		797,3609	283.1+/-276.9	114,569,1520	82.0	95.0	91.0		930	-1.8	0.0	8	dbSNP_111	91	774,7818	179.5+/-228.6	31,712,3553	no	coding-synonymous	SLC7A13	NM_138817.2		145,1281,5073	AA,AT,TT		9.0084,18.089,12.0865		310/471	87229948	1571,11427	2203	4296	6499	SO:0001819	synonymous_variant	157724	exon3			TCTCGATGATTTA	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.930A>T	8.37:g.87229948T>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_138817	Q05C37|Q08AH9|Q96N84	Silent	SNP	ENST00000297524.3	37	CCDS34917.1																																																																																			A|0.126;G|0.000;T|0.873	0.126	strong		0.388	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
CD300E	342510	hgsc.bcm.edu	37	17	72613589	72613589	+	Missense_Mutation	SNP	T	T	G	rs581157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72613589T>G	ENST00000328630.3	-	2	96	c.56A>C	c.(55-57)aAg>aCg	p.K19T	CD300E_ENST00000392619.1_Missense_Mutation_p.K46T|CD300E_ENST00000426295.2_Missense_Mutation_p.K60T			Q496F6	CLM2_HUMAN	CD300e molecule	19	Ig-like V-type.		K -> T (in dbSNP:rs581157). {ECO:0000269|PubMed:15557162}.		innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						GCCGGGGCCCTTCAGAGACAA	0.552													G|||	2172	0.433706	0.618	0.3501	5008	,	,		18373	0.3532		0.4294	False		,,,				2504	0.3313				p.K19T		Atlas-SNP	.											.	CD300E	70	.	0			c.A56C						PASS	.	G	THR/LYS	2563,1843	529.0+/-372.6	744,1075,384	41.0	37.0	38.0		56	-3.7	0.0	17	dbSNP_83	38	3781,4819	612.2+/-395.9	842,2097,1361	yes	missense	CD300E	NM_181449.2	78	1586,3172,1745	GG,GT,TT		43.9651,41.8293,48.7775	benign	19/206	72613589	6344,6662	2203	4300	6503	SO:0001583	missense	342510	exon2			GGGCCCTTCAGAG	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.56A>C	17.37:g.72613589T>G	ENSP00000329942:p.Lys19Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_181449	B4DNS1|Q7Z7I3	Missense_Mutation	SNP	ENST00000328630.3	37	CCDS11702.1	969	0.44368131868131866	315	0.6402439024390244	126	0.34806629834254144	198	0.34615384615384615	330	0.43535620052770446	G	3.490	-0.104128	0.06967	0.581707	0.439651	ENSG00000186407	ENST00000392619;ENST00000426295;ENST00000328630;ENST00000412268	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	4.62	-3.69	0.04450	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.315838	0.22719	N	0.056466	T	0.00012	0.0000	N	0.00633	-1.31	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42932	-0.9422	9	0.22109	T	0.4	-6.1244	4.5509	0.12112	0.1653:0.5134:0.2025:0.1188	rs581157;rs17470415;rs52818557;rs59897598;rs581157	19	Q496F6	CLM2_HUMAN	T	46;60;19;21	ENSP00000376395:K46T;ENSP00000416642:K60T;ENSP00000329942:K19T;ENSP00000415488:K21T	ENSP00000329942:K19T	K	-	2	0	CD300E	70125184	0.000000	0.05858	0.002000	0.10522	0.157000	0.22087	-3.607000	0.00416	-0.592000	0.05851	-1.623000	0.00790	AAG	T|0.531;G|0.469	0.469	strong		0.552	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449	
MAP3K9	4293	hgsc.bcm.edu	37	14	71202692	71202692	+	Silent	SNP	T	T	C	rs78155813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:71202692T>C	ENST00000554752.2	-	9	1898	c.1899A>G	c.(1897-1899)ccA>ccG	p.P633P	MAP3K9_ENST00000553414.1_Intron|MAP3K9_ENST00000554146.1_Intron|MAP3K9_ENST00000555993.2_Silent_p.P633P|MAP3K9_ENST00000381250.4_Intron	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	633					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		AGTGGAAATGTGGAGATTCTG	0.453													T|||	59	0.0117812	0.0408	0.0072	5008	,	,		21579	0.0		0.0	False		,,,				2504	0.0				p.P633P	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.A1899G						PASS	.	T		85,4321	72.0+/-110.0	1,83,2119	173.0	148.0	156.0		1899	3.2	1.0	14	dbSNP_132	156	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MAP3K9	NM_033141.2		1,84,6418	CC,CT,TT		0.0116,1.9292,0.6612		633/1119	71202692	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	4293	exon9			GAAATGTGGAGAT	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.1899A>G	14.37:g.71202692T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Silent	SNP	ENST00000554752.2	37																																																																																				T|0.989;C|0.011	0.011	strong		0.453	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2		
RLBP1	6017	hgsc.bcm.edu	37	15	89762198	89762198	+	Missense_Mutation	SNP	T	T	G	rs146844731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89762198T>G	ENST00000268125.5	-	3	448	c.9A>C	c.(7-9)gaA>gaC	p.E3D		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	3					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)	TACTTACCCCTTCTGACATGT	0.542													T|||	10	0.00199681	0.0076	0.0	5008	,	,		19219	0.0		0.0	False		,,,				2504	0.0				p.E3D		Atlas-SNP	.											RLBP1,NS,carcinoma,-2,1	RLBP1	34	1	0			c.A9C						PASS	.	T	ASP/GLU	26,4374	32.6+/-62.9	0,26,2174	146.0	125.0	132.0		9	-3.2	1.0	15	dbSNP_134	132	0,8598		0,0,4299	yes	missense	RLBP1	NM_000326.4	45	0,26,6473	GG,GT,TT		0.0,0.5909,0.2	benign	3/318	89762198	26,12972	2200	4299	6499	SO:0001583	missense	6017	exon3			TACCCCTTCTGAC	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.9A>C	15.37:g.89762198T>G	ENSP00000268125:p.Glu3Asp	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	38	0.603175	NM_000326	B2R667	Missense_Mutation	SNP	ENST00000268125.5	37	CCDS32324.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	9.490	1.100449	0.20552	0.005909	0.0	ENSG00000140522	ENST00000268125	T	0.79141	-1.24	5.17	-3.21	0.05140	.	0.467603	0.23298	N	0.049703	T	0.42359	0.1199	N	0.14661	0.345	0.26969	N	0.965636	B	0.02656	0.0	B	0.01281	0.0	T	0.30001	-0.9993	10	0.16420	T	0.52	-10.8678	5.1979	0.15249	0.0:0.2661:0.2778:0.4561	.	3	P12271	RLBP1_HUMAN	D	3	ENSP00000268125:E3D	ENSP00000268125:E3D	E	-	3	2	RLBP1	87563202	0.925000	0.31364	0.968000	0.41197	0.138000	0.21146	-0.148000	0.10219	-0.417000	0.07461	-1.276000	0.01395	GAA	T|0.998;G|0.002	0.002	strong		0.542	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326	
GPRASP2	114928	hgsc.bcm.edu	37	X	101970877	101970877	+	Silent	SNP	T	T	C	rs113906002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101970877T>C	ENST00000535209.1	+	4	1911	c.1080T>C	c.(1078-1080)acT>acC	p.T360T	GPRASP2_ENST00000543253.1_Silent_p.T360T|GPRASP2_ENST00000332262.5_Silent_p.T360T			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	360						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						ATCCTAATACTGCCTTGAAAC	0.463													.|||	50	0.013245	0.0371	0.0014	3775	,	,		14732	0.0		0.0	False		,,,				2504	0.0				p.T360T		Atlas-SNP	.											.	GPRASP2	89	.	0			c.T1080C						PASS	.	C	,,,,,	148,3687		2,116,28,1514,543	90.0	84.0	86.0		1080,1080,1080,1080,1080,1080	0.1	0.0	X	dbSNP_132	86	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPRASP2,ARMCX5-GPRASP2	NM_001004051.3,NM_001184874.2,NM_001184875.2,NM_001184876.2,NM_001199818.1,NM_138437.5	,,,,,	2,116,28,3942,2415	CC,CT,C,TT,T		0.0,3.8592,1.4011	,,,,,	360/839,360/839,360/839,360/839,360/839,360/839	101970877	148,10415	2203	4300	6503	SO:0001819	synonymous_variant	114928	exon4			TAATACTGCCTTG	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"""Armadillo repeat containing"""	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.1080T>C	X.37:g.101970877T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	113	38	0.336283	NM_138437	D3DXA0|Q8NAB4	Silent	SNP	ENST00000535209.1	37	CCDS14501.1																																																																																			T|0.986;C|0.014	0.014	strong		0.463	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
SLC2A1	6513	hgsc.bcm.edu	37	1	43396414	43396414	+	Silent	SNP	G	G	A	rs11537641	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43396414G>A	ENST00000426263.3	-	4	577	c.399C>T	c.(397-399)tgC>tgT	p.C133C	SLC2A1_ENST00000372500.3_Silent_p.C133C|SLC2A1_ENST00000475162.1_5'UTR|SLC2A1_ENST00000415851.2_Intron	NM_006516.2	NP_006507.2	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 1	133					carbohydrate metabolic process (GO:0005975)|cellular response to glucose starvation (GO:0042149)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|protein complex assembly (GO:0006461)|regulation of insulin secretion (GO:0050796)|response to osmotic stress (GO:0006970)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|female pronucleus (GO:0001939)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|midbody (GO:0030496)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|identical protein binding (GO:0042802)|protein self-association (GO:0043621)|xenobiotic transporter activity (GO:0042910)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|pancreas(2)	13	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)	TGGTCAGGCCGCAGTACACAC	0.622													G|||	708	0.141374	0.0802	0.2133	5008	,	,		21408	0.1022		0.1909	False		,,,				2504	0.1626				p.C133C		Atlas-SNP	.											.	SLC2A1	36	.	0			c.C399T	GRCh37	CM044065	SLC2A1	M	rs11537641	PASS	.	G		423,3983	204.1+/-226.4	17,389,1797	66.0	59.0	61.0		399	-6.7	0.8	1	dbSNP_120	61	1709,6891	311.3+/-310.3	167,1375,2758	no	coding-synonymous	SLC2A1	NM_006516.2		184,1764,4555	AA,AG,GG		19.8721,9.6005,16.3924		133/493	43396414	2132,10874	2203	4300	6503	SO:0001819	synonymous_variant	6513	exon4			CAGGCCGCAGTAC	K03195	CCDS477.1	1p34.2	2013-05-22			ENSG00000117394	ENSG00000117394		"""Solute carriers"""	11005	protein-coding gene	gene with protein product		138140	"""human T-cell leukemia virus (I and II) receptor"""	GLUT1, GLUT, HTLVR		8839927, 14622599, 18451999	Standard	NM_006516		Approved	DYT18	uc001cik.2	P11166	OTTHUMG00000007657	ENST00000426263.3:c.399C>T	1.37:g.43396414G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_006516	A8K9S6|B2R620|D3DPX0|O75535|Q147X2	Silent	SNP	ENST00000426263.3	37	CCDS477.1																																																																																			G|0.840;A|0.160	0.160	strong		0.622	SLC2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020358.2	NM_006516	
DENND2A	27147	hgsc.bcm.edu	37	7	140221878	140221878	+	Silent	SNP	G	G	A	rs61737088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140221878G>A	ENST00000275884.6	-	17	3105	c.2688C>T	c.(2686-2688)aaC>aaT	p.N896N	DENND2A_ENST00000496613.1_Silent_p.N896N|DENND2A_ENST00000537639.1_Silent_p.N896N			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	896	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				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)					ACACCACCTCGTTCAAGGGGC	0.582													G|||	62	0.0123802	0.0446	0.0029	5008	,	,		15621	0.0		0.001	False		,,,				2504	0.0				p.N896N		Atlas-SNP	.											.	DENND2A	132	.	0			c.C2688T						PASS	.	G		141,3909		3,135,1887	49.0	53.0	52.0		2688	-3.1	0.7	7	dbSNP_129	52	3,8365		0,3,4181	no	coding-synonymous	DENND2A	NM_015689.3		3,138,6068	AA,AG,GG		0.0359,3.4815,1.1596		896/1010	140221878	144,12274	2025	4184	6209	SO:0001819	synonymous_variant	27147	exon16			CACCTCGTTCAAG	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.2688C>T	7.37:g.140221878G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1																																																																																			G|0.993;A|0.007	0.007	strong		0.582	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
MCMDC2	157777	hgsc.bcm.edu	37	8	67809160	67809160	+	Missense_Mutation	SNP	C	C	G	rs35595089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:67809160C>G	ENST00000422365.2	+	12	1763	c.1592C>G	c.(1591-1593)gCt>gGt	p.A531G	MCMDC2_ENST00000396592.3_Missense_Mutation_p.A531G|MCMDC2_ENST00000313616.5_Missense_Mutation_p.A531G|MCMDC2_ENST00000541540.1_Missense_Mutation_p.A468G	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	531					DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						TTTTATGCGGCTTCTAGACAG	0.408													C|||	30	0.00599042	0.0227	0.0	5008	,	,		13579	0.0		0.0	False		,,,				2504	0.0				p.A531G		Atlas-SNP	.											.	MCMDC2	84	.	0			c.C1592G						PASS	.	C	GLY/ALA,GLY/ALA,GLY/ALA	93,4313	76.2+/-114.5	2,89,2112	100.0	100.0	100.0		1592,1592,1592	4.6	1.0	8	dbSNP_126	100	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	C8orf45	NM_001136160.1,NM_001136161.1,NM_173518.4	60,60,60	2,90,6411	GG,GC,CC		0.0116,2.1108,0.7227	possibly-damaging,possibly-damaging,possibly-damaging	531/633,531/591,531/682	67809160	94,12912	2203	4300	6503	SO:0001583	missense	157777	exon12			ATGCGGCTTCTAG	BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460			26368	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 45"""	C8orf45			Standard	NM_173518		Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068	ENST00000422365.2:c.1592C>G	8.37:g.67809160C>G	ENSP00000413632:p.Ala531Gly	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Missense_Mutation	SNP	ENST00000422365.2	37	CCDS6197.2	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	10.04	1.240474	0.22711	0.021108	1.16E-4	ENSG00000178460	ENST00000396592;ENST00000422365;ENST00000313616;ENST00000541540	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.51	4.57	0.56435	.	0.315894	0.33075	N	0.005315	T	0.12944	0.0314	L	0.40543	1.245	0.26863	N	0.967917	P;P;P	0.36354	0.493;0.549;0.549	B;B;B	0.41036	0.234;0.346;0.272	T	0.07233	-1.0783	10	0.22706	T	0.39	-9.108	6.8758	0.24147	0.1753:0.7144:0.0:0.1103	rs35595089;rs57404017	468;531;531	Q4G0Z9-4;Q4G0Z9;B4DXX4	.;CH045_HUMAN;.	G	531;531;531;468	ENSP00000379837:A531G;ENSP00000413632:A531G;ENSP00000317234:A531G;ENSP00000445629:A468G	ENSP00000317234:A531G	A	+	2	0	C8orf45	67971714	0.967000	0.33354	0.996000	0.52242	0.225000	0.24961	2.515000	0.45512	2.763000	0.94921	0.650000	0.86243	GCT	C|0.993;G|0.007	0.007	strong		0.408	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518	
MRPL22	29093	hgsc.bcm.edu	37	5	154346259	154346259	+	Silent	SNP	A	A	G	rs14922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:154346259A>G	ENST00000523037.1	+	7	464	c.423A>G	c.(421-423)tcA>tcG	p.S141S	MRPL22_ENST00000522038.1_Silent_p.S147S|MRPL22_ENST00000439747.3_Silent_p.S167S|MRPL22_ENST00000518364.1_3'UTR|MRPL22_ENST00000265229.8_Silent_p.S61S	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	141					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AGTCCACCTCAGGACGAGGCC	0.468													A|||	611	0.122005	0.0961	0.2219	5008	,	,		21141	0.0645		0.1252	False		,,,				2504	0.1421				p.S141S		Atlas-SNP	.											.	MRPL22	18	.	0			c.A423G						PASS	.	A	,	468,3938	221.0+/-238.3	24,420,1759	119.0	111.0	114.0		183,423	-2.7	0.9	5	dbSNP_52	114	1034,7566	219.1+/-257.3	49,936,3315	no	coding-synonymous,coding-synonymous	MRPL22	NM_001014990.2,NM_014180.3	,	73,1356,5074	GG,GA,AA		12.0233,10.6219,11.5485	,	61/127,141/207	154346259	1502,11504	2203	4300	6503	SO:0001819	synonymous_variant	29093	exon7			CACCTCAGGACGA	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"""Mitochondrial ribosomal proteins / large subunits"""	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.423A>G	5.37:g.154346259A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	147	71	0.482993	NM_014180	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Silent	SNP	ENST00000523037.1	37	CCDS4331.1																																																																																			T|0.168;G|0.092	0.092	strong		0.468	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2		
NWD1	284434	hgsc.bcm.edu	37	19	16918459	16918459	+	Missense_Mutation	SNP	C	C	T	rs78570914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16918459C>T	ENST00000552788.1	+	16	3799	c.3799C>T	c.(3799-3801)Cgc>Tgc	p.R1267C	NWD1_ENST00000379808.3_Missense_Mutation_p.R1267C|NWD1_ENST00000339803.6_Missense_Mutation_p.R1132C|NWD1_ENST00000549814.1_Missense_Mutation_p.R1225C|NWD1_ENST00000524140.2_Missense_Mutation_p.R1267C|NWD1_ENST00000523826.1_Missense_Mutation_p.R1061C			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1267							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TGCTGAGCAGCGCAAGCTCCT	0.562													C|||	17	0.00339457	0.0121	0.0014	5008	,	,		18437	0.0		0.0	False		,,,				2504	0.0				p.R1267C		Atlas-SNP	.											NWD1_ENST00000524140,NS,carcinoma,-1,3	NWD1	303	3	0			c.C3799T						PASS	.	C	CYS/ARG	34,4372	40.0+/-72.8	1,32,2170	91.0	95.0	94.0		3799	-1.5	0.0	19	dbSNP_131	94	0,8600		0,0,4300	yes	missense	NWD1	NM_001007525.3	180	1,32,6470	TT,TC,CC		0.0,0.7717,0.2614	benign	1267/1433	16918459	34,12972	2203	4300	6503	SO:0001583	missense	284434	exon18			GAGCAGCGCAAGC	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.3799C>T	19.37:g.16918459C>T	ENSP00000447224:p.Arg1267Cys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	123	54	0.439024	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	C	7.773	0.707922	0.15239	0.007717	0.0	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.70749	-0.19;-0.51;-0.19;2.21;1.55;2.21	5.27	-1.54	0.08584	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	1.389700	0.04604	N	0.399111	T	0.39436	0.1078	N	0.14661	0.345	0.09310	N	1	P;P;P	0.38922	0.519;0.651;0.519	B;B;B	0.34722	0.057;0.188;0.057	T	0.42716	-0.9435	10	0.72032	D	0.01	-0.223	1.2256	0.01932	0.3166:0.3553:0.1858:0.1423	.	1267;1267;1132	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	C	1132;1267;1225;1267;1061;1267;1132	ENSP00000428579:R1267C;ENSP00000447548:R1225C;ENSP00000369136:R1267C;ENSP00000428955:R1061C;ENSP00000447224:R1267C;ENSP00000340159:R1132C	ENSP00000340159:R1132C	R	+	1	0	NWD1	16779459	0.911000	0.30947	0.011000	0.14972	0.055000	0.15305	1.787000	0.38704	-0.087000	0.12528	-0.140000	0.14226	CGC	C|0.997;T|0.003	0.003	strong		0.562	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
EPHB6	2051	hgsc.bcm.edu	37	7	142562011	142562011	+	Silent	SNP	C	C	T	rs8177141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142562011C>T	ENST00000392957.2	+	7	1240	c.453C>T	c.(451-453)cgC>cgT	p.R151R	EPHB6_ENST00000442129.1_Silent_p.R151R|EPHB6_ENST00000411471.2_Intron	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	151	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					ACCTCAAACGCTGGACCAAGG	0.627													C|||	122	0.024361	0.0847	0.0144	5008	,	,		17524	0.0		0.0	False		,,,				2504	0.0				p.R151R		Atlas-SNP	.											EPHB6,right_lower_lobe,carcinoma,-2,1	EPHB6	168	1	0			c.C453T						PASS	.	C		332,4074	168.3+/-199.2	19,294,1890	58.0	62.0	61.0		453	4.7	1.0	7	dbSNP_117	61	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	EPHB6	NM_004445.3		19,297,6187	TT,TC,CC		0.0349,7.5352,2.5757		151/1022	142562011	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	2051	exon7			CAAACGCTGGACC	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.453C>T	7.37:g.142562011C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	106	60	0.566038	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	CCDS5873.2																																																																																			C|0.970;T|0.030	0.030	strong		0.627	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1		
LONRF2	164832	hgsc.bcm.edu	37	2	100911980	100911980	+	Silent	SNP	C	C	T	rs116227203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:100911980C>T	ENST00000393437.3	-	8	2151	c.1512G>A	c.(1510-1512)ctG>ctA	p.L504L	LONRF2_ENST00000409647.1_Silent_p.L261L	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	504							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						ATTCTTCGGCCAGAACAGTTA	0.343													C|||	73	0.0145767	0.0522	0.0043	5008	,	,		19323	0.0		0.001	False		,,,				2504	0.0				p.L504L		Atlas-SNP	.											.	LONRF2	62	.	0			c.G1512A						PASS	.	C		200,4206	124.5+/-161.8	1,198,2004	95.0	93.0	94.0		1512	3.3	0.2	2	dbSNP_132	94	0,8600		0,0,4300	no	coding-synonymous	LONRF2	NM_198461.3		1,198,6304	TT,TC,CC		0.0,4.5393,1.5378		504/755	100911980	200,12806	2203	4300	6503	SO:0001819	synonymous_variant	164832	exon8			TTCGGCCAGAACA	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"""RING-type (C3HC4) zinc fingers"""	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1512G>A	2.37:g.100911980C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_198461	B9A006|Q6ZSR4	Silent	SNP	ENST00000393437.3	37	CCDS2046.2																																																																																			C|0.986;T|0.014	0.014	strong		0.343	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461	
C9orf171	389799	hgsc.bcm.edu	37	9	135418389	135418389	+	Silent	SNP	G	G	A	rs61308567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135418389G>A	ENST00000343036.2	+	6	843	c.795G>A	c.(793-795)ccG>ccA	p.P265P	C9orf171_ENST00000393216.2_Silent_p.P229P	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	265										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						AGTACAAGCCGCCCGTGAAGC	0.602													G|||	245	0.0489217	0.1762	0.0173	5008	,	,		16308	0.0		0.0	False		,,,				2504	0.0				p.P265P		Atlas-SNP	.											.	C9orf171	53	.	0			c.G795A						PASS	.	G		590,3816	262.2+/-264.8	37,516,1650	156.0	136.0	143.0		795	-5.2	0.9	9	dbSNP_129	143	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	C9orf171	NM_207417.1		37,521,5945	AA,AG,GG		0.0581,13.3908,4.5748		265/321	135418389	595,12411	2203	4300	6503	SO:0001819	synonymous_variant	389799	exon6			CAAGCCGCCCGTG	AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.795G>A	9.37:g.135418389G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_207417	Q147X1	Silent	SNP	ENST00000343036.2	37	CCDS6949.1																																																																																			G|0.948;A|0.052	0.052	strong		0.602	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417	
SLC4A1AP	22950	hgsc.bcm.edu	37	2	27886820	27886820	+	Silent	SNP	G	G	T	rs58106741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27886820G>T	ENST00000326019.6	+	1	483	c.201G>T	c.(199-201)tcG>tcT	p.S67S	SUPT7L_ENST00000464789.2_5'Flank|SUPT7L_ENST00000406540.1_5'Flank|SUPT7L_ENST00000405491.1_5'Flank|SUPT7L_ENST00000404798.2_5'Flank|SUPT7L_ENST00000337768.5_5'Flank	NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	67						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					CCCTGGCGTCGCAAGACCTCA	0.592													G|||	334	0.0666933	0.2315	0.0187	5008	,	,		16985	0.0		0.0129	False		,,,				2504	0.002				p.S67S		Atlas-SNP	.											.	SLC4A1AP	63	.	0			c.G201T						PASS	.	G		771,3635	315.5+/-294.2	77,617,1509	77.0	76.0	76.0		201	-2.8	0.0	2	dbSNP_129	76	68,8532	40.3+/-97.0	0,68,4232	no	coding-synonymous	SLC4A1AP	NM_018158.2		77,685,5741	TT,TG,GG		0.7907,17.4989,6.4509		67/797	27886820	839,12167	2203	4300	6503	SO:0001819	synonymous_variant	22950	exon1			GGCGTCGCAAGAC		CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"""lung cancer oncogene 3"""	602655	"""solute carrier family 4 (anion exchanger), member 1, adapter protein"""			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.201G>T	2.37:g.27886820G>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_018158	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Silent	SNP	ENST00000326019.6	37	CCDS33166.1																																																																																			G|0.940;T|0.060	0.060	strong		0.592	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1	NM_018158	
AGO3	192669	hgsc.bcm.edu	37	1	36521340	36521340	+	Silent	SNP	C	C	T	rs61743816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36521340C>T	ENST00000373191.4	+	19	2926	c.2577C>T	c.(2575-2577)ttC>ttT	p.F859F	AGO3_ENST00000246314.6_Silent_p.F625F	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	859					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)|mRNA catabolic process (GO:0006402)|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)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										CAATGTACTTCGCTTAAATAG	0.428													C|||	48	0.00958466	0.034	0.0	5008	,	,		20951	0.0		0.003	False		,,,				2504	0.0				p.F859F		Atlas-SNP	.											.	.	.	.	0			c.C2577T						PASS	.	C	,	105,4301	81.9+/-120.4	2,101,2100	139.0	115.0	123.0		2577,1875	1.9	1.0	1	dbSNP_129	123	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	EIF2C3	NM_024852.3,NM_177422.2	,	2,106,6395	TT,TC,CC		0.0581,2.3831,0.8458	,	859/861,625/627	36521340	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	192669	exon19			GTACTTCGCTTAA	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"""Argonaute/PIWI family"""	18421	protein-coding gene	gene with protein product	"""argonaute 3"""	607355	"""eukaryotic translation initiation factor 2C, 3"""	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.2577C>T	1.37:g.36521340C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Silent	SNP	ENST00000373191.4	37	CCDS399.1																																																																																			C|0.992;T|0.008	0.008	strong		0.428	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852	
MRAP2	112609	hgsc.bcm.edu	37	6	84799185	84799185	+	Silent	SNP	C	C	T	rs2875382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84799185C>T	ENST00000257776.4	+	4	738	c.603C>T	c.(601-603)caC>caT	p.H201H		NM_138409.2	NP_612418.2	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	201					energy homeostasis (GO:0097009)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|positive regulation of cAMP biosynthetic process (GO:0030819)|protein localization to cell surface (GO:0034394)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	corticotropin hormone receptor binding (GO:0031780)|identical protein binding (GO:0042802)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)|type 5 melanocortin receptor binding (GO:0031783)	p.H201H(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(4)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	19						AGACCTCACACAAAGACCTGG	0.413													T|||	1749	0.349241	0.711	0.2666	5008	,	,		20311	0.1736		0.2306	False		,,,				2504	0.2219				p.H201H		Atlas-SNP	.											MRAP2,NS,carcinoma,0,1	MRAP2	40	1	1	Substitution - coding silent(1)	stomach(1)	c.C603T						PASS	.	T		2840,1566	489.9+/-361.6	915,1010,278	94.0	100.0	98.0		603	-0.5	0.0	6	dbSNP_101	98	1802,6798	732.8+/-406.9	196,1410,2694	no	coding-synonymous	MRAP2	NM_138409.2		1111,2420,2972	TT,TC,CC		20.9535,35.5424,35.6912		201/206	84799185	4642,8364	2203	4300	6503	SO:0001819	synonymous_variant	112609	exon4			CTCACACAAAGAC	AK090775	CCDS5001.1	6q14.3	2009-10-06	2008-07-16	2008-07-16	ENSG00000135324	ENSG00000135324			21232	protein-coding gene	gene with protein product		615410	"""chromosome 6 open reading frame 117"""	C6orf117			Standard	NM_138409		Approved	bA51G5.2	uc003pkg.4	Q96G30	OTTHUMG00000015121	ENST00000257776.4:c.603C>T	6.37:g.84799185C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_138409	A8K9M1|Q8IXM9|Q8N2D1	Silent	SNP	ENST00000257776.4	37	CCDS5001.1																																																																																			C|0.654;T|0.346	0.346	strong		0.413	MRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041367.1	NM_138409	
LILRA6	79168	hgsc.bcm.edu	37	19	54744195	54744195	+	Missense_Mutation	SNP	G	G	A	rs1132604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54744195G>A	ENST00000396365.2	-	6	1252	c.1213C>T	c.(1213-1215)Cac>Tac	p.H405Y	LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.H405Y|LILRA6_ENST00000245621.5_Missense_Mutation_p.H405Y	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	405	Ig-like C2-type 2.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.H405N(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)		GACAGCAGGTGGGGGTTGGAG	0.612													.|||	491	0.0980431	0.2927	0.049	5008	,	,		26348	0.0		0.0229	False		,,,				2504	0.0481				p.H405Y		Atlas-SNP	.											LILRA6,colon,carcinoma,+1,1	LILRA6	75	1	1	Substitution - Missense(1)	lung(1)	c.C1213T						scavenged	.						89.0	125.0	113.0					19																	54744195		2196	4300	6496	SO:0001583	missense	79168	exon6			GCAGGTGGGGGTT	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.1213C>T	19.37:g.54744195G>A	ENSP00000379651:p.His405Tyr	Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	301	43	0.142857	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	102	0.046703296703296704	85	0.17276422764227642	10	0.027624309392265192	0	0.0	7	0.009234828496042216	G	0	-2.632637	0.00115	.	.	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.00669	5.9;5.9;5.9	2.71	0.427	0.16489	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.167250	0.06702	N	0.771663	T	0.00012	0.0000	N	0.00413	-1.525	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.38845	-0.9642	10	0.02654	T	1	.	5.898	0.18949	0.7984:0.0:0.2016:0.0	.	405;405;405	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	Y	405	ENSP00000411227:H405Y;ENSP00000379651:H405Y;ENSP00000245621:H405Y	ENSP00000245621:H405Y	H	-	1	0	LILRA6	59436007	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.810000	0.01729	-0.152000	0.11156	-2.766000	0.00121	CAC	G|0.954;A|0.046	0.046	strong		0.612	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
FAM129A	116496	hgsc.bcm.edu	37	1	184765072	184765072	+	Missense_Mutation	SNP	A	A	G	rs28927681	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:184765072A>G	ENST00000367511.3	-	14	2019	c.1826T>C	c.(1825-1827)cTg>cCg	p.L609P	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	609				L -> P (in Ref. 7; BAB84965). {ECO:0000305}.	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						CTCACTACCCAGAACTCCTGG	0.547													a|||	1011	0.201877	0.5477	0.0908	5008	,	,		18374	0.0823		0.0825	False		,,,				2504	0.0593				p.L609P		Atlas-SNP	.											FAM129A,NS,carcinoma,-1,2	FAM129A	98	2	0			c.T1826C						PASS	.	G	PRO/LEU	2016,2390	533.1+/-373.6	468,1080,655	63.0	69.0	67.0		1826	-3.5	0.0	1	dbSNP_125	67	625,7975	156.6+/-210.4	22,581,3697	yes	missense	FAM129A	NM_052966.2	98	490,1661,4352	GG,GA,AA		7.2674,45.7558,20.306	benign	609/929	184765072	2641,10365	2203	4300	6503	SO:0001583	missense	116496	exon14			CTACCCAGAACTC	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.1826T>C	1.37:g.184765072A>G	ENSP00000356481:p.Leu609Pro	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	37	CCDS1364.1	395	0.18086080586080586	257	0.5223577235772358	37	0.10220994475138122	41	0.07167832167832168	60	0.079155672823219	a	7.583	0.669083	0.14776	0.457558	0.072674	ENSG00000135842	ENST00000367511	T	0.09911	2.93	5.67	-3.55	0.04639	.	2.968870	0.00698	N	0.000769	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.46803	-0.9165	9	0.07325	T	0.83	3.6762	14.2079	0.65746	0.6039:0.0:0.3961:0.0	rs28927681;rs56623820;rs28927681	609	Q9BZQ8	NIBAN_HUMAN	P	609	ENSP00000356481:L609P	ENSP00000356481:L609P	L	-	2	0	FAM129A	183031695	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.348000	0.07740	-1.574000	0.01657	-2.676000	0.00143	CTG	G|0.177;A|0.823	0.177	strong		0.547	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1		
COL4A3	1285	hgsc.bcm.edu	37	2	228118867	228118867	+	Missense_Mutation	SNP	G	G	A	rs80109666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228118867G>A	ENST00000396578.3	+	14	967	c.805G>A	c.(805-807)Gag>Aag	p.E269K	AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000606119.1_RNA|AC097662.2_ENST00000437673.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	269	Triple-helical region.				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)		AGCAATGGGCGAGCCTGGACC	0.418													G|||	304	0.0607029	0.0855	0.0115	5008	,	,		18214	0.1438		0.0129	False		,,,				2504	0.0256				p.E269K		Atlas-SNP	.											.	COL4A3	293	.	0			c.G805A						PASS	.	G	LYS/GLU	253,3543		16,221,1661	102.0	112.0	109.0		805	-5.1	0.0	2	dbSNP_131	109	20,8204		0,20,4092	yes	missense	COL4A3	NM_000091.4	56	16,241,5753	AA,AG,GG		0.2432,6.6649,2.2712	benign	269/1671	228118867	273,11747	1898	4112	6010	SO:0001583	missense	1285	exon14			ATGGGCGAGCCTG		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.805G>A	2.37:g.228118867G>A	ENSP00000379823:p.Glu269Lys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	145	0.06639194139194139	44	0.08943089430894309	7	0.019337016574585635	85	0.1486013986013986	9	0.011873350923482849	G	8.865	0.947951	0.18356	0.066649	0.002432	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.94184	-3.37	5.62	-5.14	0.02875	.	1.289780	0.05378	N	0.536580	T	0.02342	0.0072	L	0.28608	0.87	0.80722	P	0.0	P;P;P;P	0.44139	0.803;0.803;0.827;0.751	B;B;B;B	0.38327	0.064;0.151;0.271;0.095	T	0.59150	-0.7508	9	0.09843	T	0.71	.	7.9227	0.29857	0.3598:0.3879:0.2523:0.0	.	269;269;269;269	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	K	269	ENSP00000379823:E269K	ENSP00000323334:E269K	E	+	1	0	COL4A3	227827111	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-1.206000	0.03011	-1.518000	0.01778	-2.498000	0.00192	GAG	G|0.956;A|0.044	0.044	strong		0.418	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
OR6P1	128366	hgsc.bcm.edu	37	1	158533224	158533224	+	Silent	SNP	A	A	G	rs12081915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	96	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	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		
ITSN2	50618	hgsc.bcm.edu	37	2	24524958	24524958	+	Missense_Mutation	SNP	C	C	T	rs7603997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:24524958C>T	ENST00000355123.4	-	10	1314	c.871G>A	c.(871-873)Gtt>Att	p.V291I	ITSN2_ENST00000361999.3_Missense_Mutation_p.V291I|ITSN2_ENST00000406921.3_Missense_Mutation_p.V291I	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	291	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.		V -> I (in dbSNP:rs7603997). {ECO:0000269|PubMed:14702039}.		endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCACCATCAACGTCAGCCAGA	0.353													T|||	1463	0.292133	0.388	0.2075	5008	,	,		15878	0.1915		0.3509	False		,,,				2504	0.2658				p.V291I		Atlas-SNP	.											.	ITSN2	224	.	0			c.G871A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL	1863,2543	632.7+/-395.9	407,1049,747	87.0	80.0	83.0		871,871,871	2.1	1.0	2	dbSNP_116	83	2841,5759	673.9+/-403.1	462,1917,1921	yes	missense,missense,missense	ITSN2	NM_006277.2,NM_019595.3,NM_147152.2	29,29,29	869,2966,2668	TT,TC,CC		33.0349,42.2833,36.1679	benign,benign,benign	291/1698,291/1671,291/1250	24524958	4704,8302	2203	4300	6503	SO:0001583	missense	50618	exon10			CATCAACGTCAGC	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.871G>A	2.37:g.24524958C>T	ENSP00000347244:p.Val291Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	664	0.304029304029304	200	0.4065040650406504	84	0.23204419889502761	111	0.19405594405594406	269	0.3548812664907652	T	3.130	-0.178539	0.06380	0.422833	0.330349	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	4.44	2.11	0.27256	EPS15 homology (EH) (2);EF-hand-like domain (1);	0.000000	0.37483	N	0.002070	T	0.00012	0.0000	N	0.04508	-0.205	0.52501	P	4.899999999996574E-5	P;P;P;P	0.51791	0.911;0.911;0.948;0.622	P;P;P;B	0.48952	0.496;0.496;0.596;0.275	T	0.11867	-1.0570	9	0.02654	T	1	.	9.1297	0.36837	0.0:0.2282:0.0:0.7718	rs7603997;rs17845626;rs17858557;rs52793399;rs59754072;rs7603997	291;291;291;291	Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3	.;.;.;ITSN2_HUMAN	I	291;291;291;315;291;316	ENSP00000354561:V291I;ENSP00000347244:V291I;ENSP00000370250:V291I;ENSP00000384499:V291I;ENSP00000391224:V316I	ENSP00000347244:V291I	V	-	1	0	ITSN2	24378462	0.991000	0.36638	0.999000	0.59377	0.973000	0.67179	0.343000	0.19944	0.338000	0.23692	-0.524000	0.04348	GTT	C|0.652;N|0.000	.	strong		0.353	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
KIF1A	547	hgsc.bcm.edu	37	2	241713646	241713646	+	Silent	SNP	A	A	G	rs1063353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241713646A>G	ENST00000320389.7	-	12	1149	c.991T>C	c.(991-993)Ttg>Ctg	p.L331L	KIF1A_ENST00000498729.2_Silent_p.L331L	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	331	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		GCAGGACTCAAGGCTGCCACC	0.592													G|||	2572	0.513578	0.7428	0.3631	5008	,	,		13128	0.622		0.3618	False		,,,				2504	0.3548				p.L331L		Atlas-SNP	.											.	KIF1A	152	.	0			c.T991C						PASS	.	G		2789,1501		909,971,265	72.0	77.0	75.0		991	4.3	1.0	2	dbSNP_86	75	2940,5542		516,1908,1817	no	coding-synonymous	KIF1A	NM_004321.5		1425,2879,2082	GG,GA,AA		34.6616,34.9883,44.8559		331/1691	241713646	5729,7043	2145	4241	6386	SO:0001819	synonymous_variant	547	exon12			GACTCAAGGCTGC	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.991T>C	2.37:g.241713646A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	205	105	0.512195	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Silent	SNP	ENST00000320389.7	37	CCDS46561.1	1092	0.5	354	0.7195121951219512	115	0.31767955801104975	349	0.6101398601398601	274	0.36147757255936674	G	5.440	0.266237	0.10294	0.650117	0.346616	ENSG00000130294	ENST00000428768	.	.	.	4.33	4.33	0.51752	.	0.000000	0.64402	U	0.000002	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40403	-0.9565	4	.	.	.	.	12.0657	0.53586	0.0862:0.0:0.9138:0.0	rs1063353;rs3204419	.	.	.	P	138	.	.	L	-	2	0	KIF1A	241362319	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	6.463000	0.73530	0.820000	0.34516	-0.374000	0.07098	CTT	A|0.528;G|0.472	0.472	strong		0.592	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201951	32201951	+	RNA	SNP	A	A	G	rs9982775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:32201951A>G	ENST00000452750.1	-	0	127							Q8IUC3	KRA71_HUMAN	keratin associated protein 7-1 (gene/pseudogene)							intermediate filament (GO:0005882)											TGAAGGTCCCATGGAAGTTGG	0.522													G|||	2557	0.510583	0.4266	0.6614	5008	,	,		19883	0.4454		0.5278	False		,,,				2504	0.5665				p.H22H		Atlas-SNP	.											.	.	.	.	0			c.T66C						PASS	.	G		622,762		146,330,216	69.0	71.0	70.0		67	-1.2	0.0	21	dbSNP_119	70	1536,1646		359,818,414	yes	coding-synonymous	KRTAP7-1	NM_181606.2		505,1148,630	GG,GA,AA		48.2715,44.9422,47.2624		22/88	32201951	2158,2408	692	1591	2283			337878	exon2			GGTCCCATGGAAG	AJ457063	CCDS74780.1	21q22.1	2014-04-10	2010-03-12		ENSG00000184586	ENSG00000274749		"""Keratin associated proteins"""	18934	protein-coding gene	gene with protein product			"""keratin associated protein 7-1"""			12359730	Standard	NM_181606		Approved	KAP7.1	uc011adj.2	Q8IUC3	OTTHUMG00000188305		21.37:g.32201951A>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	207	103	0.497585	NM_181606	Q3LI56	Silent	SNP	ENST00000452750.1	37																																																																																				A|0.490;G|0.510	0.510	strong		0.522	KRTAP7-1-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000128248.3	NM_181606	
GSAP	54103	hgsc.bcm.edu	37	7	77010661	77010661	+	Silent	SNP	T	T	C	rs17152629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:77010661T>C	ENST00000257626.7	-	8	615	c.537A>G	c.(535-537)caA>caG	p.Q179Q		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	179					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										GGATACGAAATTGTTCAATAT	0.284													T|||	157	0.0313498	0.1104	0.0144	5008	,	,		18372	0.001		0.0	False		,,,				2504	0.0				p.Q179Q		Atlas-SNP	.											.	PION	74	.	0			c.A537G						PASS	.	T		349,3271		20,309,1481	66.0	63.0	64.0		537	-1.6	0.2	7	dbSNP_123	64	3,8131		0,3,4064	no	coding-synonymous	PION	NM_017439.3		20,312,5545	CC,CT,TT		0.0369,9.6409,2.9947		179/855	77010661	352,11402	1810	4067	5877	SO:0001819	synonymous_variant	54103	exon8			ACGAAATTGTTCA		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"""pigeon homolog (Drosophila)"""	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.537A>G	7.37:g.77010661T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Silent	SNP	ENST00000257626.7	37	CCDS34672.2																																																																																			T|0.965;C|0.035	0.035	strong		0.284	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
FYB	2533	hgsc.bcm.edu	37	5	39202911	39202911	+	Missense_Mutation	SNP	G	G	A	rs1642515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:39202911G>A	ENST00000351578.6	-	2	342	c.152C>T	c.(151-153)cCc>cTc	p.P51L	FYB_ENST00000515010.1_Missense_Mutation_p.P51L|FYB_ENST00000505428.1_Missense_Mutation_p.P51L|FYB_ENST00000540520.1_Missense_Mutation_p.P61L|FYB_ENST00000512982.1_Missense_Mutation_p.P51L	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	51			P -> L (in dbSNP:rs1642515).		immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			TACATTGCTGGGTCCTGCAGG	0.502													G|||	182	0.0363419	0.1331	0.0086	5008	,	,		17552	0.0		0.0	False		,,,				2504	0.0				p.P61L		Atlas-SNP	.											.	FYB	354	.	0			c.C182T						PASS	.	G	LEU/PRO,LEU/PRO	449,3361		21,407,1477	60.0	58.0	58.0		152,152	3.4	0.5	5	dbSNP_89	58	5,8235		0,5,4115	yes	missense,missense	FYB	NM_001465.4,NM_199335.3	98,98	21,412,5592	AA,AG,GG		0.0607,11.7848,3.7676	benign,benign	51/830,51/784	39202911	454,11596	1905	4120	6025	SO:0001583	missense	2533	exon2			TTGCTGGGTCCTG	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"""FYN-binding protein (FYB-120/130)"""			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.152C>T	5.37:g.39202911G>A	ENSP00000316460:p.Pro51Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	37	CCDS47200.1	64	0.029304029304029304	60	0.12195121951219512	4	0.011049723756906077	0	0.0	0	0.0	G	12.15	1.852358	0.32699	0.117848	6.07E-4	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542;ENST00000510188;ENST00000512138	T;T;T;T;T;T;T	0.73897	0.51;0.51;0.57;0.57;0.56;-0.79;-0.14	6.17	3.39	0.38822	.	0.680112	0.15332	N	0.267922	T	0.01695	0.0054	L	0.43701	1.375	0.20403	P	0.9999089434	B;B	0.20887	0.049;0.007	B;B	0.15052	0.012;0.006	T	0.30504	-0.9976	9	0.56958	D	0.05	-0.0459	5.9531	0.19259	0.2021:0.0:0.6538:0.1441	rs1642515;rs1642515	61;51	B4DLN2;O15117	.;FYB_HUMAN	L	51;51;51;51;61;51;51;51	ENSP00000316460:P51L;ENSP00000426346:P51L;ENSP00000425845:P51L;ENSP00000427114:P51L;ENSP00000442840:P61L;ENSP00000426597:P51L;ENSP00000424919:P51L	ENSP00000316460:P51L	P	-	2	0	FYB	39238668	0.961000	0.32948	0.518000	0.27811	0.688000	0.40055	1.158000	0.31737	0.444000	0.26612	0.655000	0.94253	CCC	G|0.959;A|0.041	0.041	strong		0.502	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465	
FXYD3	5349	hgsc.bcm.edu	37	19	35612168	35612168	+	Intron	SNP	T	T	A	rs1688016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35612168T>A	ENST00000344013.6	+	5	293				FXYD3_ENST00000604804.1_Intron|FXYD3_ENST00000454903.2_Missense_Mutation_p.L39H|FXYD3_ENST00000406242.3_Intron|FXYD3_ENST00000535103.1_Intron|FXYD3_ENST00000604255.1_Intron|FXYD3_ENST00000605550.1_Intron|FXYD3_ENST00000605552.1_Missense_Mutation_p.L39H|FXYD3_ENST00000603449.1_Missense_Mutation_p.L39H|FXYD3_ENST00000346446.5_Intron|FXYD3_ENST00000406988.1_Intron|FXYD3_ENST00000604621.1_Intron|FXYD3_ENST00000604404.1_Intron|FXYD3_ENST00000603181.1_Intron|FXYD3_ENST00000605677.1_Intron|FXYD3_ENST00000603524.1_Intron|FXYD3_ENST00000435734.2_Intron			Q14802	FXYD3_HUMAN	FXYD domain containing ion transport regulator 3						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of catalytic activity (GO:0050790)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.L39H(1)		endometrium(1)|lung(2)|prostate(1)	4	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CCGTGCCCCCTTTCCCCTCCC	0.517													A|||	1783	0.35603	0.2958	0.2493	5008	,	,		16537	0.2679		0.3698	False		,,,				2504	0.59				p.L39H		Atlas-SNP	.											.	FXYD3	15	.	1	Substitution - Missense(1)	kidney(1)	c.T116A						PASS	.	A	,,HIS/LEU,HIS/LEU,,,,	1396,3010	687.1+/-404.8	215,966,1022	69.0	73.0	71.0		,,116,116,,,,	0.7	0.0	19	dbSNP_89	71	3066,5534	658.0+/-401.5	527,2012,1761	yes	intron,intron,missense,missense,intron,intron,intron,intron	FXYD3	NM_001136007.1,NM_001136008.1,NM_001136009.1,NM_001136010.1,NM_001136011.1,NM_001136012.1,NM_005971.3,NM_021910.2	,,99,99,,,,	742,2978,2783	AA,AT,TT		35.6512,31.6841,34.3072	,,,,,,,	,,39/62,39/62,,,,	35612168	4462,8544	2203	4300	6503	SO:0001627	intron_variant	5349	exon5			GCCCCCTTTCCCC	X93036	CCDS12442.1, CCDS12443.1, CCDS46048.1, CCDS46049.1, CCDS46050.1	19q13.11-q13.12	2008-05-14	2002-01-14			ENSG00000089356			4027	protein-coding gene	gene with protein product		604996	"""FXYD domain-containing ion transport regulator 3"""	PLML		7836447, 10950925	Standard	NM_005971		Approved	MAT-8	uc010xsm.2	Q14802		ENST00000344013.6:c.97+19T>A	19.37:g.35612168T>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	250	248	0.992	NM_001136010	A6NDE0|C9JDU2|F5H174|F8WB34|Q13211|Q6IB59	Missense_Mutation	SNP	ENST00000344013.6	37	CCDS12442.1	668	0.3058608058608059	157	0.31910569105691056	85	0.23480662983425415	137	0.2395104895104895	289	0.3812664907651715	A	2.768	-0.256355	0.05829	0.316841	0.356512	ENSG00000089356	ENST00000454903	.	.	.	2.85	0.693	0.18056	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45745	-0.9240	5	.	.	.	.	2.5324	0.04706	0.2797:0.4271:0.0:0.2932	rs1688016	39	C9JDU2	.	H	39	.	.	L	+	2	0	FXYD3	40304008	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.057000	0.11768	-0.034000	0.13713	-0.336000	0.08194	CTT	T|0.672;A|0.328	0.328	strong		0.517	FXYD3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000468985.1	NM_021910	
MMP21	118856	hgsc.bcm.edu	37	10	127456150	127456150	+	Missense_Mutation	SNP	G	G	A	rs28381319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:127456150G>A	ENST00000368808.3	-	6	1360	c.1361C>T	c.(1360-1362)gCg>gTg	p.A454V		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	454			A -> V (in dbSNP:rs28381319). {ECO:0000269|Ref.3}.		hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	GTCATAAAACGCCGTGTCTAG	0.443													G|||	174	0.0347444	0.1225	0.013	5008	,	,		19942	0.001		0.0	False		,,,				2504	0.002				p.A454V		Atlas-SNP	.											.	MMP21	46	.	0			c.C1361T						PASS	.	G	VAL/ALA	372,4034	189.2+/-215.4	8,356,1839	152.0	146.0	148.0		1361	5.8	1.0	10	dbSNP_125	148	2,8598	1.2+/-3.3	0,2,4298	yes	missense	MMP21	NM_147191.1	64	8,358,6137	AA,AG,GG		0.0233,8.443,2.8756	possibly-damaging	454/570	127456150	374,12632	2203	4300	6503	SO:0001583	missense	118856	exon6			TAAAACGCCGTGT	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"""matrix metalloproteinase 21"""			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1361C>T	10.37:g.127456150G>A	ENSP00000357798:p.Ala454Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_147191	Q5VZP9|Q8NG02	Missense_Mutation	SNP	ENST00000368808.3	37	CCDS7647.1	77	0.035256410256410256	72	0.14634146341463414	5	0.013812154696132596	0	0.0	0	0.0	G	18.53	3.643997	0.67244	0.08443	2.33E-4	ENSG00000154485	ENST00000368808	T	0.04194	3.68	5.75	5.75	0.90469	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	M	0.80616	2.505	0.09310	P	0.99999826623	D	0.59767	0.986	B	0.43360	0.417	T	0.14587	-1.0467	9	0.54805	T	0.06	-14.0558	17.4385	0.87559	0.0:0.0:1.0:0.0	rs28381319	454	Q8N119	MMP21_HUMAN	V	454	ENSP00000357798:A454V	ENSP00000357798:A454V	A	-	2	0	MMP21	127446140	1.000000	0.71417	0.957000	0.39632	0.017000	0.09413	8.132000	0.89603	2.719000	0.93026	0.655000	0.94253	GCG	G|0.956;A|0.044	0.044	strong		0.443	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1		
ZNF844	284391	hgsc.bcm.edu	37	19	12187210	12187210	+	Silent	SNP	A	A	G	rs6511764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12187210A>G	ENST00000439326.3	+	4	1450	c.1275A>G	c.(1273-1275)gtA>gtG	p.V425V	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	425					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						TAAGCAGTGTAGTAAAGCCTT	0.428													.|||	1455	0.290535	0.73	0.1455	5008	,	,		23733	0.0853		0.161	False		,,,				2504	0.1442				p.V425V		Atlas-SNP	.											ZNF844,right_upper_lobe,carcinoma,0,2	ZNF844	69	2	0			c.A1275G						scavenged	.	G		883,501		287,309,96	54.0	57.0	56.0		1275	0.5	0.0	19	dbSNP_116	56	413,2769		25,363,1203	no	coding-synonymous	ZNF844	NM_001136501.1		312,672,1299	GG,GA,AA		12.9793,36.1994,28.3837		425/667	12187210	1296,3270	692	1591	2283	SO:0001819	synonymous_variant	284391	exon4			CAGTGTAGTAAAG	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1275A>G	19.37:g.12187210A>G		Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001136501	Q5JPI8	Silent	SNP	ENST00000439326.3	37	CCDS45985.1																																																																																			A|0.772;G|0.228	0.228	strong		0.428	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
PCDHGA11	56105	hgsc.bcm.edu	37	5	140801104	140801104	+	Missense_Mutation	SNP	T	T	C	rs11167744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140801104T>C	ENST00000398587.2	+	1	343	c.310T>C	c.(310-312)Ttt>Ctt	p.F104L	PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000518882.1_Missense_Mutation_p.F104L|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	104	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		F -> L (in dbSNP:rs11167744).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCCTCCTGTTTTTTAAATAT	0.498													t|||	567	0.113219	0.1195	0.1499	5008	,	,		17586	0.1181		0.0596	False		,,,				2504	0.1288				p.F104L		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.T310C						PASS	.	T	,,,LEU/PHE,,,,,,,,,,,,,,,LEU/PHE,LEU/PHE	469,3667		25,419,1624	32.0	37.0	36.0		,,,310,,,,,,,,,,,,,,,310,310	-3.1	1.0	5	dbSNP_120	36	624,7896		25,574,3661	yes	intron,intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032091.1,NM_032092.1	,,,22,,,,,,,,,,,,,,,22,22	50,993,5285	CC,CT,TT		7.3239,11.3395,8.6362	,,,,,,,,,,,,,,,,,,,	,,,104/936,,,,,,,,,,,,,,,104/838,104/751	140801104	1093,11563	2068	4260	6328	SO:0001583	missense	56105	exon1			TCCTGTTTTTTAA	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"""Cadherins / Protocadherins : Clustered"""	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.310T>C	5.37:g.140801104T>C	ENSP00000381589:p.Phe104Leu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_032091	B7ZVY8|Q9Y5D8|Q9Y5D9	Missense_Mutation	SNP	ENST00000398587.2	37	CCDS47294.1	220	0.10073260073260074	53	0.10772357723577236	47	0.1298342541436464	69	0.12062937062937062	51	0.06728232189973615	t	2.098	-0.406756	0.04832	0.113395	0.073239	ENSG00000253873	ENST00000398587;ENST00000518882	T;T	0.24350	1.86;1.86	5.93	-3.06	0.05379	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	1.496170	0.06373	N	0.713909	T	0.00039	0.0001	N	0.00300	-1.685	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	0.32824	-0.9892	9	0.02654	T	1	.	0.9188	0.01310	0.4206:0.1385:0.1628:0.2782	rs11167744;rs61342402;rs11167744	104;104;104	Q9Y5H2;Q9Y5H2-3;Q9Y5H2-2	PCDGB_HUMAN;.;.	L	104	ENSP00000381589:F104L;ENSP00000428333:F104L	ENSP00000381589:F104L	F	+	1	0	PCDHGA11	140781288	0.000000	0.05858	0.979000	0.43373	0.990000	0.78478	-3.692000	0.00391	-0.129000	0.11620	0.482000	0.46254	TTT	T|0.896;C|0.104	0.104	strong		0.498	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914	
PIWIL4	143689	hgsc.bcm.edu	37	11	94320237	94320237	+	Silent	SNP	T	T	C	rs7110167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94320237T>C	ENST00000299001.6	+	7	949	c.738T>C	c.(736-738)ttT>ttC	p.F246F	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	246					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GGCCTGGGTTTGCCATTTCTG	0.358													T|||	2772	0.553514	0.8124	0.4524	5008	,	,		19065	0.5		0.4016	False		,,,				2504	0.4867				p.F246F		Atlas-SNP	.											PIWIL4,NS,carcinoma,+2,1	PIWIL4	70	1	0			c.T738C						PASS	.	T		3284,1118	717.2+/-408.7	1239,806,156	144.0	153.0	150.0		738	-0.4	0.2	11	dbSNP_116	150	3427,5169	504.7+/-376.2	705,2017,1576	no	coding-synonymous	PIWIL4	NM_152431.2		1944,2823,1732	CC,CT,TT		39.8674,25.3975,48.369		246/853	94320237	6711,6287	2201	4298	6499	SO:0001819	synonymous_variant	143689	exon7			TGGGTTTGCCATT	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.738T>C	11.37:g.94320237T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	21	0.362069	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			T|0.476;C|0.524	0.524	strong		0.358	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
DAAM2	23500	hgsc.bcm.edu	37	6	39847153	39847153	+	Missense_Mutation	SNP	C	C	A	rs150676991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:39847153C>A	ENST00000398904.2	+	14	1927	c.1745C>A	c.(1744-1746)cCt>cAt	p.P582H	DAAM2_ENST00000538976.1_Missense_Mutation_p.P582H|RP11-61I13.3_ENST00000607675.1_RNA|DAAM2_ENST00000274867.4_Missense_Mutation_p.P582H			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	582	FH1.|Pro-rich.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					CTGCCCCTCCCTCAGGACCCC	0.652													C|||	2	0.000399361	0.0015	0.0	5008	,	,		12540	0.0		0.0	False		,,,				2504	0.0				p.P582H		Atlas-SNP	.											.	DAAM2	101	.	0			c.C1745A						PASS	.	C	HIS/PRO,HIS/PRO	8,3826		0,8,1909	44.0	46.0	45.0		1745,1745	5.2	0.9	6	dbSNP_134	45	14,8208		0,14,4097	yes	missense,missense	DAAM2	NM_001201427.1,NM_015345.3	77,77	0,22,6006	AA,AC,CC		0.1703,0.2087,0.1825	benign,benign	582/1069,582/1068	39847153	22,12034	1917	4111	6028	SO:0001583	missense	23500	exon14			CCCTCCCTCAGGA	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.1745C>A	6.37:g.39847153C>A	ENSP00000381876:p.Pro582His	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	250	110	0.44	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	16.94	3.261074	0.59431	0.002087	0.001703	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	D;D;D	0.84146	-1.81;-1.81;-1.79	5.15	5.15	0.70609	Actin-binding FH2 (1);	0.215647	0.39407	N	0.001370	T	0.65302	0.2678	N	0.08118	0	0.80722	D	1	P;B	0.40875	0.731;0.38	B;B	0.42555	0.391;0.159	T	0.73799	-0.3869	10	0.46703	T	0.11	.	13.0249	0.58808	0.0:0.9199:0.0:0.0801	.	582;582	G5EA45;Q86T65	.;DAAM2_HUMAN	H	582	ENSP00000274867:P582H;ENSP00000381876:P582H;ENSP00000437808:P582H	ENSP00000274867:P582H	P	+	2	0	DAAM2	39955131	0.989000	0.36119	0.881000	0.34555	0.838000	0.47535	3.359000	0.52292	2.383000	0.81215	0.650000	0.86243	CCT	C|0.998;A|0.002	0.002	strong		0.652	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
SYNE2	23224	hgsc.bcm.edu	37	14	64519053	64519053	+	Silent	SNP	C	C	T	rs35960129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64519053C>T	ENST00000344113.4	+	48	8634	c.8422C>T	c.(8422-8424)Cta>Tta	p.L2808L	SYNE2_ENST00000554584.1_Silent_p.L2841L|SYNE2_ENST00000358025.3_Silent_p.L2808L|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2808					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)		AAATAATACCCTAGAGGACTT	0.383													C|||	120	0.0239617	0.087	0.0072	5008	,	,		20674	0.0		0.0	False		,,,				2504	0.0				p.L2808L		Atlas-SNP	.											.	SYNE2	577	.	0			c.C8422T						PASS	.	C	,	260,3436		11,238,1599	73.0	68.0	70.0		8422,8422	4.0	0.9	14	dbSNP_126	70	0,8182		0,0,4091	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	11,238,5690	TT,TC,CC		0.0,7.0346,2.1889	,	2808/6886,2808/6908	64519053	260,11618	1848	4091	5939	SO:0001819	synonymous_variant	23224	exon48			AATACCCTAGAGG	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.8422C>T	14.37:g.64519053C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			C|0.990;T|0.010	0.010	strong		0.383	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
UGT2B11	10720	hgsc.bcm.edu	37	4	70078393	70078393	+	Nonsense_Mutation	SNP	C	C	T	rs138593124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:70078393C>T	ENST00000446444.1	-	2	776	c.768G>A	c.(766-768)tgG>tgA	p.W256*	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	256					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						TTCGCATAAGCCATATGTCAG	0.388													.|||	22	0.00439297	0.0159	0.0014	5008	,	,		14009	0.0		0.0	False		,,,				2504	0.0				p.W256X		Atlas-SNP	.											.	UGT2B11	92	.	0			c.G768A						PASS	.	C	stop/TRP	83,4323		1,81,2121	141.0	147.0	145.0		768	2.0	0.2	4	dbSNP_134	145	0,8598		0,0,4299	no	stop-gained	UGT2B11	NM_001073.1		1,81,6420	TT,TC,CC		0.0,1.8838,0.6383		256/530	70078393	83,12921	2203	4299	6502	SO:0001587	stop_gained	10720	exon2			CATAAGCCATATG	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.768G>A	4.37:g.70078393C>T	ENSP00000387683:p.Trp256*	Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	336	151	0.449405	NM_001073	Q3KNV9	Nonsense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	-	12.43	1.936842	0.34189	0.018838	0.0	ENSG00000213759	ENST00000446444	.	.	.	1.96	1.96	0.26148	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5515	0.39313	0.0:1.0:0.0:0.0	.	.	.	.	X	256	.	ENSP00000387683:W256X	W	-	3	0	UGT2B11	70112982	1.000000	0.71417	0.183000	0.23137	0.044000	0.14063	4.939000	0.63526	1.087000	0.41251	0.184000	0.17185	TGG	C|0.993;T|0.007	0.007	strong		0.388	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
TBX3	6926	hgsc.bcm.edu	37	12	115118722	115118722	+	Silent	SNP	G	G	A	rs35069811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:115118722G>A	ENST00000257566.3	-	2	1008	c.619C>T	c.(619-621)Ctg>Ttg	p.L207L	TBX3_ENST00000349155.2_Silent_p.L207L	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	207					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|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)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		GTGAGTTTCAGTTTGTGGAAA	0.463													G|||	73	0.0145767	0.0537	0.0029	5008	,	,		19262	0.0		0.0	False		,,,				2504	0.0				p.L207L		Atlas-SNP	.											.	TBX3	106	.	0			c.C619T						PASS	.	G	,	256,4150	146.9+/-181.5	7,242,1954	147.0	139.0	142.0		619,619	4.9	1.0	12	dbSNP_126	142	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	TBX3	NM_005996.3,NM_016569.3	,	7,246,6250	AA,AG,GG		0.0465,5.8103,1.9991	,	207/724,207/744	115118722	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	6926	exon2			GTTTCAGTTTGTG	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.619C>T	12.37:g.115118722G>A		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	256	118	0.460938	NM_005996	Q8TB20|Q9UKF8	Silent	SNP	ENST00000257566.3	37	CCDS9176.1																																																																																			G|0.979;A|0.021	0.021	strong		0.463	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996	
EXPH5	23086	hgsc.bcm.edu	37	11	108384857	108384857	+	Silent	SNP	T	T	C	rs116565594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108384857T>C	ENST00000265843.4	-	6	1487	c.1377A>G	c.(1375-1377)agA>agG	p.R459R	EXPH5_ENST00000443411.1_Silent_p.R271R|EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Silent_p.R383R|EXPH5_ENST00000525344.1_Silent_p.R452R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	459					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TGAAGAAAGATCTGGTAAATG	0.438													T|||	64	0.0127796	0.0477	0.0014	5008	,	,		22659	0.0		0.0	False		,,,				2504	0.0				p.R459R		Atlas-SNP	.											.	EXPH5	193	.	0			c.A1377G						PASS	.	T		168,4234	112.5+/-150.6	0,168,2033	158.0	150.0	152.0		1377	2.5	1.0	11	dbSNP_132	152	0,8596		0,0,4298	no	coding-synonymous	EXPH5	NM_015065.2		0,168,6331	CC,CT,TT		0.0,3.8164,1.2925		459/1990	108384857	168,12830	2201	4298	6499	SO:0001819	synonymous_variant	23086	exon6			GAAAGATCTGGTA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.1377A>G	11.37:g.108384857T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	37	CCDS8341.1																																																																																			T|0.987;C|0.013	0.013	strong		0.438	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
RECQL5	9400	hgsc.bcm.edu	37	17	73627539	73627539	+	Missense_Mutation	SNP	T	T	C	rs820196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73627539T>C	ENST00000317905.5	-	9	1598	c.1439A>G	c.(1438-1440)gAc>gGc	p.D480G	RECQL5_ENST00000443199.2_5'UTR|SMIM5_ENST00000375215.3_5'Flank|RECQL5_ENST00000423245.2_Missense_Mutation_p.D453G	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	173	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	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	
FASTKD1	79675	hgsc.bcm.edu	37	2	170428198	170428198	+	Silent	SNP	G	G	A	rs113959605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170428198G>A	ENST00000453153.2	-	2	688	c.342C>T	c.(340-342)gaC>gaT	p.D114D	FASTKD1_ENST00000453929.2_Silent_p.D114D	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	114					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						CCAGGGTATCGTCATTCATTA	0.279													G|||	37	0.00738818	0.0265	0.0014	5008	,	,		17370	0.0		0.001	False		,,,				2504	0.0				p.D114D		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C342T						PASS	.	G		89,4315	68.7+/-106.4	2,85,2115	46.0	45.0	45.0		342	-5.3	0.0	2	dbSNP_132	45	1,8599		0,1,4299	no	coding-synonymous	FASTKD1	NM_024622.3		2,86,6414	AA,AG,GG		0.0116,2.0209,0.6921		114/848	170428198	90,12914	2202	4300	6502	SO:0001819	synonymous_variant	79675	exon2			GGTATCGTCATTC	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.342C>T	2.37:g.170428198G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			G|0.993;A|0.007	0.007	strong		0.279	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
LCN1	3933	hgsc.bcm.edu	37	9	138413373	138413373	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138413373T>C	ENST00000263598.2	+	1	90	c.30T>C	c.(28-30)ctT>ctC	p.L10L	LCN1_ENST00000371781.3_Silent_p.L10L	NM_001252617.1|NM_001252618.1|NM_001252619.1|NM_002297.3	NP_001239546.1|NP_001239547.1|NP_001239548.1|NP_002288.1	P31025	LCN1_HUMAN	lipocalin 1	10					negative regulation of endopeptidase activity (GO:0010951)|proteolysis (GO:0006508)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|sensory perception of taste (GO:0050909)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.L10L(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)	13		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.54e-08)|Epithelial(140;5.25e-08)|all cancers(34;9.27e-07)|READ - Rectum adenocarcinoma(205;0.155)		CCGTCAGCCTTGGCCTCATTG	0.667																																					p.L10L		Atlas-SNP	.											LCN1,NS,carcinoma,0,3	LCN1	21	3	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.T30C						scavenged	.																																			SO:0001819	synonymous_variant	3933	exon1			CAGCCTTGGCCTC		CCDS6991.1	9q34	2011-11-14	2011-11-01		ENSG00000160349	ENSG00000160349		"""Lipocalins"""	6525	protein-coding gene	gene with protein product	"""Von Ebner gland protein"", ""tear lipocalin"", ""lipocalin 1-like 2"", ""tear prealbumin"""	151675	"""lipocalin 1 (protein migrating faster than albumin, tear prealbumin)"", ""lipocalin 1 (tear prealbumin)"""			8276406	Standard	NM_002297		Approved	VEGP, TP, PMFA, MGC71975, TLC	uc022bpk.1	P31025	OTTHUMG00000020908	ENST00000263598.2:c.30T>C	9.37:g.138413373T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	214	11	0.0514019	NM_001252617	Q5T8A1	Silent	SNP	ENST00000263598.2	37	CCDS6991.1																																																																																			.	.	none		0.667	LCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054992.1	NM_002297	
RPL5	6125	hgsc.bcm.edu	37	1	93299193	93299193	+	Silent	SNP	G	G	A	rs58263806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:93299193G>A	ENST00000370321.3	+	3	255	c.165G>A	c.(163-165)gtG>gtA	p.V55V		NM_000969.3	NP_000960.2	P46777	RL5_HUMAN	ribosomal protein L5	55					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)		TAGTTCGTGTGACAAACAGAG	0.368													A|||	121	0.0241613	0.0877	0.0058	5008	,	,		18734	0.0		0.001	False		,,,				2504	0.0				p.V55V		Atlas-SNP	.											.	RPL5	38	.	0			c.G165A						PASS	.	A		313,4093	796.5+/-415.4	11,291,1901	62.0	68.0	66.0		165	1.1	1.0	1	dbSNP_129	66	4,8596	818.7+/-406.8	0,4,4296	no	coding-synonymous	RPL5	NM_000969.3		11,295,6197	AA,AG,GG		0.0465,7.1039,2.4373		55/298	93299193	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	6125	exon3			TCGTGTGACAAAC	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.165G>A	1.37:g.93299193G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	25	0.357143	NM_000969	Q32LZ3|Q53HH6|Q9H3F4	Silent	SNP	ENST00000370321.3	37	CCDS741.1																																																																																			G|0.977;A|0.023	0.023	strong		0.368	RPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030058.2	NM_000969	
CDK5R1	8851	hgsc.bcm.edu	37	17	30815208	30815208	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:30815208G>A	ENST00000313401.3	+	2	1259	c.570G>A	c.(568-570)tgG>tgA	p.W190*		NM_003885.2	NP_003876.1	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	190					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|brain development (GO:0007420)|cell proliferation (GO:0008283)|cerebellum development (GO:0021549)|embryo development (GO:0009790)|ephrin receptor signaling pathway (GO:0048013)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|hippocampus development (GO:0021766)|ionotropic glutamate receptor signaling pathway (GO:0035235)|layer formation in cerebral cortex (GO:0021819)|negative regulation of axon extension (GO:0030517)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of neuron differentiation (GO:0045664)|rhythmic process (GO:0048511)|serine phosphorylation of STAT3 protein (GO:0033136)|superior olivary nucleus maturation (GO:0021722)	axon (GO:0030424)|contractile fiber (GO:0043292)|cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|cyclin-dependent protein kinase 5 activator activity (GO:0016534)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)			cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)			TGCAGGGCTGGCAGGACCAGG	0.652																																					p.W190X		Atlas-SNP	.											.	CDK5R1	30	.	0			c.G570A						PASS	.						68.0	71.0	70.0					17																	30815208		2203	4300	6503	SO:0001587	stop_gained	8851	exon2			GGGCTGGCAGGAC	X80343	CCDS11273.1	17q12	2006-03-28			ENSG00000176749	ENSG00000176749			1775	protein-coding gene	gene with protein product		603460				8090221	Standard	NM_003885		Approved	p35nck5a, Nck5a	uc002hhn.3	Q15078	OTTHUMG00000132814	ENST00000313401.3:c.570G>A	17.37:g.30815208G>A	ENSP00000318486:p.Trp190*	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	131	20	0.152672	NM_003885	E1P664|Q5U0G3	Nonsense_Mutation	SNP	ENST00000313401.3	37	CCDS11273.1	.	.	.	.	.	.	.	.	.	.	G	43	10.067794	0.99329	.	.	ENSG00000176749	ENST00000313401	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.2883	16.9953	0.86366	0.0:0.0:1.0:0.0	.	.	.	.	X	190	.	ENSP00000318486:W190X	W	+	3	0	CDK5R1	27839321	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.759000	0.98931	2.609000	0.88269	0.557000	0.71058	TGG	.	.	none		0.652	CDK5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256264.1	NM_003885	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887546	9887546	+	Missense_Mutation	SNP	G	G	A	rs2240906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9887546G>A	ENST00000306084.6	+	2	1269	c.1070G>A	c.(1069-1071)gGt>gAt	p.G357D	TXNDC2_ENST00000536353.2_3'UTR|TXNDC2_ENST00000357775.5_Missense_Mutation_p.G290D	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	357	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.		G -> D (in dbSNP:rs2240906). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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						CCCAAGAAGGGTGACATCCCC	0.572													g|||	2412	0.481629	0.3548	0.4481	5008	,	,		22318	0.8155		0.4185	False		,,,				2504	0.3978				p.G357D		Atlas-SNP	.											TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	0			c.G1070A						PASS	.	G	ASP/GLY,ASP/GLY	1660,2746		314,1032,857	151.0	142.0	145.0		1070,869	0.9	0.0	18	dbSNP_98	145	3635,4965		796,2043,1461	no	missense,missense	TXNDC2	NM_001098529.1,NM_032243.5	94,94	1110,3075,2318	AA,AG,GG		42.2674,37.6759,40.712	benign,benign	357/554,290/487	9887546	5295,7711	2203	4300	6503	SO:0001583	missense	84203	exon2			AGAAGGGTGACAT	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.1070G>A	18.37:g.9887546G>A	ENSP00000304908:p.Gly357Asp	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	1104	0.5054945054945055	165	0.3353658536585366	156	0.430939226519337	458	0.8006993006993007	325	0.4287598944591029	-	3.140	-0.176442	0.06380	0.376759	0.422674	ENSG00000168454	ENST00000536353;ENST00000357775;ENST00000306084;ENST00000426718	T;T	0.32988	1.43;1.43	3.74	0.852	0.18995	.	.	.	.	.	T	0.00012	0.0000	N	0.25485	0.75	0.80722	P	0.0	B	0.17667	0.023	B	0.24155	0.051	T	0.16928	-1.0386	7	.	.	.	-0.4401	6.3628	0.21437	0.1838:0.2762:0.54:0.0	rs2240906;rs60707091;rs2240906	357	Q86VQ3	TXND2_HUMAN	D	155;290;357;342	ENSP00000350419:G290D;ENSP00000304908:G357D	.	G	+	2	0	TXNDC2	9877546	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.783000	0.01770	-0.049000	0.13379	-0.813000	0.03139	GGT	G|0.562;A|0.438	0.438	strong		0.572	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
SKA1	220134	hgsc.bcm.edu	37	18	47918536	47918536	+	Silent	SNP	C	C	T	rs16951872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47918536C>T	ENST00000285116.3	+	7	898	c.687C>T	c.(685-687)caC>caT	p.H229H	SKA1_ENST00000417656.2_Silent_p.H183H|SKA1_ENST00000488454.1_Silent_p.H78H|SKA1_ENST00000398452.2_Silent_p.H229H	NM_001039535.2|NM_145060.3	NP_001034624.1|NP_659497.1	Q96BD8	SKA1_HUMAN	spindle and kinetochore associated complex subunit 1	229					cell division (GO:0051301)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|spindle microtubule (GO:0005876)	microtubule binding (GO:0008017)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(1)|prostate(1)	13						AGAAGTTTCACGTGTTACTGA	0.378													C|||	392	0.0782748	0.2133	0.0216	5008	,	,		13624	0.0794		0.0129	False		,,,				2504	0.002				p.H229H		Atlas-SNP	.											.	SKA1	21	.	0			c.C687T						PASS	.	C	,	786,3620	316.6+/-294.7	63,660,1480	93.0	93.0	93.0		687,687	-5.2	0.2	18	dbSNP_123	93	14,8586	9.1+/-34.3	0,14,4286	no	coding-synonymous,coding-synonymous	SKA1	NM_001039535.2,NM_145060.3	,	63,674,5766	TT,TC,CC		0.1628,17.8393,6.151	,	229/256,229/256	47918536	800,12206	2203	4300	6503	SO:0001819	synonymous_variant	220134	exon7			GTTTCACGTGTTA	BC015706	CCDS11946.1	18q21.1	2013-01-17	2009-08-19	2009-08-19	ENSG00000154839	ENSG00000154839			28109	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 24"""	C18orf24		17093495	Standard	NM_145060		Approved	MGC10200	uc002leu.3	Q96BD8	OTTHUMG00000132685	ENST00000285116.3:c.687C>T	18.37:g.47918536C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_001039535	B2R9Y6|B4E0P4	Silent	SNP	ENST00000285116.3	37	CCDS11946.1																																																																																			C|0.925;T|0.075	0.075	strong		0.378	SKA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255982.2	NM_145060	
HLA-C	3107	hgsc.bcm.edu	37	6	31239449	31239449	+	Missense_Mutation	SNP	C	C	G	rs28626310	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31239449C>G	ENST00000376228.5	-	2	284	c.270G>C	c.(268-270)aaG>aaC	p.K90N	HLA-C_ENST00000383329.3_Missense_Mutation_p.K90N	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	90	Alpha-1.		K -> N (in dbSNP:rs28626310).		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						GGCGCTTGTACTTCTGTGTCT	0.701													c|||	710	0.141773	0.1452	0.1282	5008	,	,		12148	0.0516		0.168	False		,,,				2504	0.2127				p.K90N		Atlas-SNP	.											.	HLA-C	92	.	0			c.G270C						PASS	.	C	ASN/LYS	438,2584		26,386,1099	48.0	49.0	48.0		270	-5.5	0.0	6	dbSNP_125	48	999,4419		91,817,1801	no	missense	HLA-C	NM_002117.5	94	117,1203,2900	GG,GC,CC		18.4385,14.4937,17.0261	benign	90/367	31239449	1437,7003	1511	2709	4220	SO:0001583	missense	3107	exon2			CTTGTACTTCTGT	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.270G>C	6.37:g.31239449C>G	ENSP00000365402:p.Lys90Asn	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	283	142	0.501767	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	260|260	0.11904761904761904|0.11904761904761904	60|60	0.12195121951219512|0.12195121951219512	47|47	0.1298342541436464|0.1298342541436464	26|26	0.045454545454545456|0.045454545454545456	127|127	0.16754617414248021|0.16754617414248021	-|-	0.008|0.008	-1.894729|-1.894729	0.00522|0.00522	0.144937|0.144937	0.184385|0.184385	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.48;9.48|.	2.75|2.75	-5.49|-5.49	0.02584|0.02584	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	2211.810000|.	0.00541|.	N|.	0.000226|.	T|T	0.01489|0.01489	0.0048|0.0048	N|N	0.01751|0.01751	-0.74|-0.74	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.10296|.	0.003;0.003;0.001;0.003|.	B;B;B;B|.	0.21151|.	0.033;0.033;0.033;0.022|.	T|T	0.22941|0.22941	-1.0202|-1.0202	9|4	0.36615|.	T|.	0.2|.	.|.	3.7958|3.7958	0.08738|0.08738	0.0845:0.197:0.1701:0.5485|0.0845:0.197:0.1701:0.5485	rs28626310;rs41555912|rs28626310;rs41555912	90;90;90;90|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	N|L	90;90;90;127|90	ENSP00000365402:K90N;ENSP00000372819:K90N|.	ENSP00000365402:K90N|.	K|V	-|-	3|1	2|0	HLA-C|HLA-C	31347428|31347428	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-9.984000|-9.984000	0.00008|0.00008	-6.044000|-6.044000	0.00007|0.00007	-3.594000|-3.594000	0.00028|0.00028	AAG|GTA	C|0.840;G|0.160	0.160	strong		0.701	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
KALRN	8997	hgsc.bcm.edu	37	3	124352728	124352728	+	Silent	SNP	G	G	A	rs652863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124352728G>A	ENST00000291478.5	+	3	565	c.402G>A	c.(400-402)ccG>ccA	p.P134P	KALRN_ENST00000428018.2_Silent_p.P134P|KALRN_ENST00000360013.3_Silent_p.P1831P|KALRN_ENST00000393496.1_Silent_p.P204P	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1831	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				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						AAGATGAGCCGGATGAAGAGT	0.438													G|||	350	0.0698882	0.1974	0.0389	5008	,	,		20051	0.0		0.0457	False		,,,				2504	0.0164				p.P1831P		Atlas-SNP	.											TRAD,NS,carcinoma,+1,2	KALRN	556	2	0			c.G5493A						PASS	.	G	,	726,3680	301.0+/-286.6	68,590,1545	127.0	107.0	113.0		5493,402	-0.6	1.0	3	dbSNP_83	113	320,8280	112.3+/-172.5	9,302,3989	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_007064.3	,	77,892,5534	AA,AG,GG		3.7209,16.4775,8.0424	,	1831/2987,134/1290	124352728	1046,11960	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon36			TGAGCCGGATGAA	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	ENST00000291478.5:c.402G>A	3.37:g.124352728G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	82	47	0.573171	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	37	CCDS3028.1	142	0.06501831501831502	96	0.1951219512195122	13	0.03591160220994475	0	0.0	33	0.04353562005277045	G	9.418	1.082387	0.20309	0.164775	0.037209	ENSG00000160145	ENST00000354186	.	.	.	4.74	-0.623	0.11556	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.23368	-1.0190	3	.	.	.	.	3.6533	0.08212	0.4502:0.0:0.152:0.3978	rs652863;rs652863	.	.	.	Q	1800	.	.	R	+	2	0	KALRN	125835418	0.998000	0.40836	0.997000	0.53966	0.992000	0.81027	0.599000	0.24089	-0.173000	0.10761	-0.367000	0.07326	CGG	G|0.917;A|0.083	0.083	strong		0.438	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947	
CLYBL	171425	hgsc.bcm.edu	37	13	100425097	100425097	+	Missense_Mutation	SNP	G	G	T	rs17577293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:100425097G>T	ENST00000376360.1	+	2	109	c.82G>T	c.(82-84)Gat>Tat	p.D28Y	CLYBL_ENST00000376355.3_Missense_Mutation_p.D28Y|CLYBL_ENST00000444838.2_Missense_Mutation_p.D28Y|CLYBL_ENST00000376354.1_Missense_Mutation_p.D28Y|CLYBL_ENST00000339105.4_Missense_Mutation_p.D28Y			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	28			D -> Y (in dbSNP:rs17577293).			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)					TCTAGCAGCTGATATCCCCAG	0.393													G|||	38	0.00758786	0.0	0.0029	5008	,	,		17913	0.0		0.0298	False		,,,				2504	0.0061				p.D28Y		Atlas-SNP	.											.	CLYBL	48	.	0			c.G82T						PASS	.	G	TYR/ASP	28,4378	35.2+/-66.4	0,28,2175	145.0	138.0	140.0		82	3.2	0.0	13	dbSNP_123	140	267,8333	102.3+/-163.5	7,253,4040	yes	missense	CLYBL	NM_206808.2	160	7,281,6215	TT,TG,GG		3.1047,0.6355,2.2682	possibly-damaging	28/341	100425097	295,12711	2203	4300	6503	SO:0001583	missense	171425	exon2			GCAGCTGATATCC	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.82G>T	13.37:g.100425097G>T	ENSP00000365538:p.Asp28Tyr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_206808	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	37	CCDS32002.1	21	0.009615384615384616	0	0.0	0	0.0	0	0.0	21	0.027704485488126648	G	12.73	2.024971	0.35701	0.006355	0.031047	ENSG00000125246	ENST00000376355;ENST00000376360;ENST00000444838;ENST00000376354;ENST00000339105	T;T;T;T;T	0.25085	1.85;1.82;1.85;1.85;1.82	5.0	3.21	0.36854	.	1.112960	0.06569	N	0.748186	T	0.04588	0.0125	N	0.08118	0	0.09310	N	1	P;P;P	0.42785	0.79;0.785;0.454	B;B;B	0.38500	0.275;0.26;0.135	T	0.11616	-1.0580	10	0.59425	D	0.04	.	6.0792	0.19933	0.1735:0.1526:0.6739:0.0	rs17577293;rs52796069;rs17577293	28;28;28	B4DU60;Q8N0X4-2;Q8N0X4	.;.;CLYBL_HUMAN	Y	28	ENSP00000365533:D28Y;ENSP00000365538:D28Y;ENSP00000404768:D28Y;ENSP00000365532:D28Y;ENSP00000342991:D28Y	ENSP00000342991:D28Y	D	+	1	0	CLYBL	99223098	0.123000	0.22298	0.001000	0.08648	0.074000	0.17049	0.748000	0.26305	1.074000	0.40909	0.462000	0.41574	GAT	G|0.982;T|0.018	0.018	strong		0.393	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1		
DIDO1	11083	hgsc.bcm.edu	37	20	61542863	61542863	+	Silent	SNP	G	G	A	rs11907248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61542863G>A	ENST00000266070.4	-	3	427	c.102C>T	c.(100-102)atC>atT	p.I34I	DIDO1_ENST00000370368.1_Silent_p.I34I|DIDO1_ENST00000354665.4_Silent_p.I34I|DIDO1_ENST00000266071.5_Silent_p.I34I|DIDO1_ENST00000370371.4_Silent_p.I34I|DIDO1_ENST00000370366.1_Silent_p.I34I|DIDO1_ENST00000395340.1_Silent_p.I34I|DIDO1_ENST00000395335.2_Silent_p.I34I|DIDO1_ENST00000395343.1_Silent_p.I34I	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	34					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)					CTCGCTTGGCGATAGTGGTCC	0.637													G|||	330	0.0658946	0.1218	0.0447	5008	,	,		17396	0.0238		0.0497	False		,,,				2504	0.0654				p.I34I	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C102T						PASS	.	G	,,,,,	535,3869	232.6+/-246.1	32,471,1699	66.0	67.0	67.0		102,102,102,102,102,102	-10.8	0.0	20	dbSNP_120	67	481,8119	136.7+/-193.7	13,455,3832	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_001193370.1,NM_022105.4,NM_033081.2,NM_080796.3,NM_080797.3	,,,,,	45,926,5531	AA,AG,GG		5.593,12.148,7.813	,,,,,	34/2241,34/1190,34/563,34/2241,34/563,34/1190	61542863	1016,11988	2202	4300	6502	SO:0001819	synonymous_variant	11083	exon3			CTTGGCGATAGTG	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.102C>T	20.37:g.61542863G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	183	93	0.508197	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			G|0.924;A|0.076	0.076	strong		0.637	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
SERPINB8	5271	hgsc.bcm.edu	37	18	61654297	61654297	+	Missense_Mutation	SNP	A	A	G	rs3169983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61654297A>G	ENST00000397985.2	+	7	1166	c.910A>G	c.(910-912)Act>Gct	p.T304A	SERPINB8_ENST00000542677.1_Missense_Mutation_p.T122A|SERPINB8_ENST00000353706.2_Missense_Mutation_p.T304A|SERPINB8_ENST00000493661.1_Intron	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	304			T -> A (in dbSNP:rs3169983). {ECO:0000269|PubMed:17974005}.		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)				TGGAATGTCAACTGAGAAGAA	0.498													A|||	889	0.177516	0.2648	0.0663	5008	,	,		19756	0.1756		0.0716	False		,,,				2504	0.2495				p.T304A		Atlas-SNP	.											.	SERPINB8	42	.	0			c.A910G						PASS	.	A	ALA/THR,ALA/THR	941,3465	358.6+/-314.5	109,723,1371	116.0	98.0	104.0		910,910	-1.0	0.0	18	dbSNP_105	104	785,7815	185.3+/-233.1	45,695,3560	yes	missense,missense	SERPINB8	NM_002640.3,NM_198833.1	58,58	154,1418,4931	GG,GA,AA		9.1279,21.3572,13.2708	benign,benign	304/375,304/375	61654297	1726,11280	2203	4300	6503	SO:0001583	missense	5271	exon7			ATGTCAACTGAGA	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.910A>G	18.37:g.61654297A>G	ENSP00000381072:p.Thr304Ala	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_198833	B4DTW2|Q7Z2V6|Q8N178	Missense_Mutation	SNP	ENST00000397985.2	37	CCDS11991.1	314	0.14377289377289376	109	0.22154471544715448	26	0.0718232044198895	127	0.22202797202797203	52	0.06860158311345646	A	5.544	0.285312	0.10513	0.213572	0.091279	ENSG00000166401	ENST00000397985;ENST00000353706;ENST00000542677	D;D;T	0.82255	-1.59;-1.59;2.81	5.65	-1.01	0.10169	Serpin domain (3);	0.744591	0.13300	N	0.398299	T	0.00039	0.0001	N	0.05199	-0.095	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.02821	-1.1106	9	0.09338	T	0.73	.	1.3588	0.02187	0.323:0.1099:0.3293:0.2378	rs3169983;rs3744957;rs3169983	304	P50452	SPB8_HUMAN	A	304;304;122	ENSP00000381072:T304A;ENSP00000331368:T304A;ENSP00000438328:T122A	ENSP00000331368:T304A	T	+	1	0	SERPINB8	59805277	0.000000	0.05858	0.001000	0.08648	0.870000	0.49936	0.113000	0.15499	-0.053000	0.13289	0.533000	0.62120	ACT	A|0.851;G|0.149	0.149	strong		0.498	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848	
CYTH4	27128	hgsc.bcm.edu	37	22	37693632	37693632	+	Silent	SNP	C	C	T	rs73887105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37693632C>T	ENST00000248901.6	+	5	449	c.262C>T	c.(262-264)Ctg>Ttg	p.L88L	CYTH4_ENST00000405206.3_Silent_p.L88L|CYTH4_ENST00000439667.1_3'UTR|CYTH4_ENST00000402997.1_Silent_p.L88L	NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	88	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						TGAGCACAAGCTGCTGACCCC	0.572													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		20239	0.0		0.0	False		,,,				2504	0.0				p.L88L		Atlas-SNP	.											.	CYTH4	51	.	0			c.C262T						PASS	.	C		102,4304	81.4+/-119.9	1,100,2102	74.0	68.0	70.0		262	4.0	1.0	22	dbSNP_130	70	0,8600		0,0,4300	no	coding-synonymous	CYTH4	NM_013385.3		1,100,6402	TT,TC,CC		0.0,2.315,0.7843		88/395	37693632	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	27128	exon5			CACAAGCTGCTGA	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.262C>T	22.37:g.37693632C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_013385	Q5R3F9|Q9UGT6	Silent	SNP	ENST00000248901.6	37	CCDS13946.1																																																																																			C|0.992;T|0.008	0.008	strong		0.572	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1		
PANK4	55229	hgsc.bcm.edu	37	1	2441358	2441358	+	Missense_Mutation	SNP	T	T	C	rs2494620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:2441358T>C	ENST00000378466.3	-	18	2063	c.2051A>G	c.(2050-2052)cAg>cGg	p.Q684R	PANK4_ENST00000435556.3_Missense_Mutation_p.Q645R	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	684			Q -> R (in dbSNP:rs2494620). {ECO:0000269|Ref.2}.		coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)	p.Q684R(1)		breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CCTCTCTTCCTGGAGCGCAGA	0.657													C|||	2313	0.461861	0.7148	0.3444	5008	,	,		17094	0.4702		0.2127	False		,,,				2504	0.4509				p.Q684R		Atlas-SNP	.											PANK4,NS,lymphoid_neoplasm,0,2	PANK4	64	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A2051G						PASS	.	C	ARG/GLN	2888,1508	461.7+/-353.0	962,964,272	46.0	55.0	52.0		2051	-0.2	0.0	1	dbSNP_100	52	1916,6676	711.8+/-405.9	210,1496,2590	yes	missense	PANK4	NM_018216.1	43	1172,2460,2862	CC,CT,TT		22.2998,34.3039,36.988	benign	684/774	2441358	4804,8184	2198	4296	6494	SO:0001583	missense	55229	exon18			TCTTCCTGGAGCG	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.2051A>G	1.37:g.2441358T>C	ENSP00000367727:p.Gln684Arg	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	199	102	0.512563	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	852	0.3901098901098901	341	0.693089430894309	114	0.3149171270718232	242	0.4230769230769231	155	0.20448548812664907	C	4.722	0.134313	0.09032	0.656961	0.222998	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.06371	3.31;3.31	5.03	-0.23	0.13090	Domain of unknown function DUF89 (2);	0.544208	0.20048	N	0.100373	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.10613	-1.0622	9	0.10902	T	0.67	-0.009	10.247	0.43347	0.0:0.5005:0.0:0.4995	rs2494620;rs11541160;rs58437041;rs2494620	645;684	E9PHT6;Q9NVE7	.;PANK4_HUMAN	R	684;645	ENSP00000367727:Q684R;ENSP00000421433:Q645R	ENSP00000367727:Q684R	Q	-	2	0	PANK4	2431218	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.488000	0.02308	-0.299000	0.08909	-0.994000	0.02522	CAG	T|0.615;C|0.385	0.385	strong		0.657	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1		
FH	2271	hgsc.bcm.edu	37	1	241676972	241676972	+	Silent	SNP	G	G	A	rs10926501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241676972G>A	ENST00000366560.3	-	3	347	c.309C>T	c.(307-309)gcC>gcT	p.A103A	FH_ENST00000493477.1_5'Flank	NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	103					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		TTACTTCAGCGGCCGCTCGCT	0.353			"""Mis, N, F"""			"""lieomyomatosis, renal"""			Hereditary Leiomyomatosis and Renal Cell Cancer				G|||	169	0.033746	0.1241	0.0072	5008	,	,		16468	0.0		0.0	False		,,,				2504	0.0				p.A103A	Melanoma(148;1573 2486 7381 46575)	Atlas-SNP	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"""E, M"""	FH,NS,carcinoma,0,2	FH	64	2	0			c.C309T						PASS	.	G		386,4020	191.6+/-217.2	18,350,1835	121.0	123.0	122.0		309	0.9	1.0	1	dbSNP_120	122	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	FH	NM_000143.3		18,353,6132	AA,AG,GG		0.0349,8.7608,2.9909		103/511	241676972	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	2271	exon3	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	TTCAGCGGCCGCT	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.309C>T	1.37:g.241676972G>A		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	273	141	0.516484	NM_000143	B1ANK7	Silent	SNP	ENST00000366560.3	37	CCDS1617.1																																																																																			G|0.975;A|0.025	0.025	strong		0.353	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143	
CCDC94	55702	hgsc.bcm.edu	37	19	4251069	4251069	+	Silent	SNP	T	T	C	rs1045750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4251069T>C	ENST00000262962.7	+	3	239	c.171T>C	c.(169-171)aaT>aaC	p.N57N		NM_018074.4	NP_060544.2	Q9BW85	CCD94_HUMAN	coiled-coil domain containing 94	57								p.N57N(1)		NS(1)|endometrium(1)|lung(2)|ovary(1)|stomach(2)	7				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)		AGAAATTCAATGCTCGGAAGG	0.567													C|||	2385	0.476238	0.7262	0.2795	5008	,	,		18805	0.4464		0.3022	False		,,,				2504	0.4877				p.N57N		Atlas-SNP	.											CCDC94,NS,carcinoma,0,1	CCDC94	28	1	1	Substitution - coding silent(1)	stomach(1)	c.T171C						PASS	.	C		2936,1470	472.4+/-356.4	974,988,241	124.0	121.0	122.0		171	-2.0	0.5	19	dbSNP_86	122	2458,6142	697.2+/-404.9	374,1710,2216	no	coding-synonymous	CCDC94	NM_018074.4		1348,2698,2457	CC,CT,TT		28.5814,33.3636,41.4732		57/324	4251069	5394,7612	2203	4300	6503	SO:0001819	synonymous_variant	55702	exon3			ATTCAATGCTCGG	AK001236	CCDS12124.1	19p13.3	2008-02-05				ENSG00000105248			25518	protein-coding gene	gene with protein product						12477932	Standard	NM_018074		Approved	FLJ10374	uc002lzv.4	Q9BW85		ENST00000262962.7:c.171T>C	19.37:g.4251069T>C		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	155	155	1	NM_018074	O75270|Q9H862|Q9NW16	Silent	SNP	ENST00000262962.7	37	CCDS12124.1																																																																																			T|0.563;C|0.437	0.437	strong		0.567	CCDC94-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458007.2	NM_018074	
PHAX	51808	hgsc.bcm.edu	37	5	125944131	125944131	+	Silent	SNP	G	G	C	rs61747690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125944131G>C	ENST00000297540.4	+	3	1481	c.786G>C	c.(784-786)ctG>ctC	p.L262L		NM_032177.3	NP_115553.2	Q9H814	PHAX_HUMAN	phosphorylated adaptor for RNA export	262	Necessary for interaction with CBP80. {ECO:0000250}.|Sufficient for poly U RNA-binding.				gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein transport (GO:0015031)|RNA metabolic process (GO:0016070)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA binding (GO:0003723)|toxic substance binding (GO:0015643)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	8						TTGAACTTCTGATGGAAACCG	0.348													G|||	184	0.0367412	0.1324	0.0086	5008	,	,		18871	0.0		0.003	False		,,,				2504	0.0				p.L262L		Atlas-SNP	.											.	PHAX	20	.	0			c.G786C						PASS	.	G		471,3935	222.6+/-239.4	27,417,1759	159.0	167.0	164.0		786	0.7	1.0	5	dbSNP_129	164	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous	PHAX	NM_032177.3		27,429,6047	CC,CG,GG		0.1395,10.69,3.7137		262/395	125944131	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	51808	exon3			ACTTCTGATGGAA	AK023255	CCDS4138.1	5q23.2	2011-05-24	2008-10-01	2008-10-01	ENSG00000164902	ENSG00000164902			10241	protein-coding gene	gene with protein product		604924	"""RNA U, small nuclear RNA export adaptor (phosphorylation regulated)"""	RNUXA		10786834	Standard	NM_032177		Approved	FLJ13193	uc003kua.2	Q9H814	OTTHUMG00000163273	ENST00000297540.4:c.786G>C	5.37:g.125944131G>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_032177	Q9H8W1	Silent	SNP	ENST00000297540.4	37	CCDS4138.1																																																																																			G|0.963;C|0.037	0.037	strong		0.348	PHAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250924.1	NM_032177	
CCDC69	26112	hgsc.bcm.edu	37	5	150567017	150567017	+	Missense_Mutation	SNP	A	A	G	rs386693598|rs61745454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150567017A>G	ENST00000355417.2	-	5	497	c.323T>C	c.(322-324)cTc>cCc	p.L108P	CCDC69_ENST00000521308.1_5'UTR	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	108										haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGAGGCCCGGAGGACTGTAGG	0.557													A|||	161	0.0321486	0.0545	0.0216	5008	,	,		18674	0.0		0.0437	False		,,,				2504	0.0307				p.L108P		Atlas-SNP	.											.	CCDC69	30	.	0			c.T323C						PASS	.	A	PRO/LEU	224,4182	134.1+/-170.4	3,218,1982	76.0	77.0	77.0		323	2.3	0.8	5	dbSNP_129	77	322,8278	112.3+/-172.5	10,302,3988	yes	missense	CCDC69	NM_015621.2	98	13,520,5970	GG,GA,AA		3.7442,5.084,4.1981	benign	108/297	150567017	546,12460	2203	4300	6503	SO:0001583	missense	26112	exon5			GCCCGGAGGACTG		CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.323T>C	5.37:g.150567017A>G	ENSP00000347586:p.Leu108Pro	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_015621	A8K9X6	Missense_Mutation	SNP	ENST00000355417.2	37	CCDS4312.1	70	0.03205128205128205	30	0.06097560975609756	6	0.016574585635359115	0	0.0	34	0.044854881266490766	A	10.99	1.507812	0.27036	0.05084	0.037442	ENSG00000198624	ENST00000355417	T	0.10099	2.91	4.75	2.35	0.29111	.	0.380247	0.22617	N	0.057742	T	0.00998	0.0033	L	0.61218	1.895	0.58432	D	0.999996	B	0.32653	0.379	B	0.30029	0.11	T	0.20472	-1.0274	10	0.62326	D	0.03	-5.8364	3.7638	0.08615	0.7113:0.0:0.1003:0.1884	.	108	A6NI79	CCD69_HUMAN	P	108	ENSP00000347586:L108P	ENSP00000347586:L108P	L	-	2	0	CCDC69	150547210	1.000000	0.71417	0.811000	0.32455	0.993000	0.82548	1.738000	0.38207	0.325000	0.23359	0.454000	0.30748	CTC	A|0.960;G|0.040	0.040	strong		0.557	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621	
PRSS12	8492	hgsc.bcm.edu	37	4	119237348	119237348	+	Silent	SNP	T	T	C	rs2292597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:119237348T>C	ENST00000296498.3	-	6	1563	c.1281A>G	c.(1279-1281)caA>caG	p.Q427Q		NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	427	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.Q427Q(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						TAAATCCCAATTGTCGACAAA	0.378													C|||	2731	0.545327	0.4516	0.5692	5008	,	,		17615	0.5843		0.5626	False		,,,				2504	0.5971				p.Q427Q		Atlas-SNP	.											PRSS12,NS,carcinoma,0,1	PRSS12	71	1	1	Substitution - coding silent(1)	stomach(1)	c.A1281G						PASS	.	C		2088,2318	604.1+/-390.3	516,1056,631	102.0	95.0	97.0		1281	3.5	0.9	4	dbSNP_100	97	4726,3874	544.2+/-384.5	1306,2114,880	no	coding-synonymous	PRSS12	NM_003619.3		1822,3170,1511	CC,CT,TT		45.0465,47.3899,47.6088		427/876	119237348	6814,6192	2203	4300	6503	SO:0001819	synonymous_variant	8492	exon6			TCCCAATTGTCGA	AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"""Serine peptidases / Serine peptidases"""	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.1281A>G	4.37:g.119237348T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_003619	Q9UP16	Silent	SNP	ENST00000296498.3	37	CCDS3709.1																																																																																			T|0.467;C|0.533	0.533	strong		0.378	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2		
SLC17A3	10786	hgsc.bcm.edu	37	6	25849620	25849620	+	Silent	SNP	A	A	G	rs942379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:25849620A>G	ENST00000360657.3	-	10	1395	c.1110T>C	c.(1108-1110)agT>agC	p.S370S	SLC17A3_ENST00000397060.4_Silent_p.S448S|SLC17A3_ENST00000361703.6_Silent_p.S370S			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	370					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						GAAGAAATCCACTGACAGTGG	0.418													G|||	3521	0.703075	0.9198	0.6902	5008	,	,		15514	0.8105		0.5388	False		,,,				2504	0.4775				p.S448S		Atlas-SNP	.											.	SLC17A3	95	.	0			c.T1344C						PASS	.	G	,	3764,642	275.2+/-272.4	1612,540,51	74.0	71.0	72.0		1344,1110	-0.8	0.1	6	dbSNP_86	72	4553,4047	554.6+/-386.5	1190,2173,937	no	coding-synonymous,coding-synonymous	SLC17A3	NM_001098486.1,NM_006632.3	,	2802,2713,988	GG,GA,AA		47.0581,14.571,36.0526	,	448/499,370/421	25849620	8317,4689	2203	4300	6503	SO:0001819	synonymous_variant	10786	exon11			AAATCCACTGACA	U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"""Solute carriers"""	10931	protein-coding gene	gene with protein product		611034	"""solute carrier family 17 (sodium phosphate), member 3"""			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.1110T>C	6.37:g.25849620A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_001098486	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Silent	SNP	ENST00000360657.3	37	CCDS4566.2	1584	0.7252747252747253	454	0.9227642276422764	247	0.6823204419889503	476	0.8321678321678322	407	0.5369393139841688	G	4.510	0.094579	0.08632	0.85429	0.529419	ENSG00000124564	ENST00000481949	.	.	.	4.55	-0.836	0.10770	.	.	.	.	.	T	0.12732	0.0309	.	.	.	0.25770	P	0.9848456	.	.	.	.	.	.	T	0.23762	-1.0179	3	.	.	.	.	4.0301	0.09705	0.5185:0.1813:0.3002:0.0	rs942379;rs1747553;rs3736878;rs17270953;rs17851585;rs57863386;rs942379	.	.	.	A	49	.	.	V	-	2	0	SLC17A3	25957599	0.000000	0.05858	0.128000	0.21923	0.014000	0.08584	-1.080000	0.03407	-0.075000	0.12798	-0.266000	0.10368	GTG	A|0.326;G|0.674	0.674	strong		0.418	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2		
KLHL32	114792	hgsc.bcm.edu	37	6	97580539	97580539	+	Silent	SNP	A	A	G	rs13208956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:97580539A>G	ENST00000369261.4	+	10	1980	c.1617A>G	c.(1615-1617)gaA>gaG	p.E539E	KLHL32_ENST00000544166.1_Silent_p.E95E|KLHL32_ENST00000539200.1_Silent_p.E470E|KLHL32_ENST00000536676.1_Silent_p.E503E	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	539										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		GCCAAAATGAATCTGGAGTTG	0.343													A|||	154	0.0307508	0.0484	0.0202	5008	,	,		17594	0.001		0.0298	False		,,,				2504	0.046				p.E539E		Atlas-SNP	.											KLHL32,neck,malignant_melanoma,+2,1	KLHL32	85	1	0			c.A1617G						PASS	.	A		178,4228	115.0+/-153.0	5,168,2030	108.0	108.0	108.0		1617	5.6	1.0	6	dbSNP_121	108	340,8260	117.2+/-176.8	2,336,3962	no	coding-synonymous	KLHL32	NM_052904.3		7,504,5992	GG,GA,AA		3.9535,4.0399,3.9828		539/621	97580539	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	114792	exon10			AAATGAATCTGGA	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.1617A>G	6.37:g.97580539A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	56	28	0.5	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Silent	SNP	ENST00000369261.4	37	CCDS5038.1																																																																																			A|0.967;G|0.033	0.033	strong		0.343	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904	
VAV2	7410	hgsc.bcm.edu	37	9	136633606	136633606	+	Silent	SNP	G	G	A	rs9722384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136633606G>A	ENST00000371850.3	-	29	2578	c.2547C>T	c.(2545-2547)atC>atT	p.I849I	VAV2_ENST00000371851.1_Silent_p.I839I|VAV2_ENST00000406606.3_Silent_p.I810I	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	849	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		GGTCTCCGCCGATGCGGCTGT	0.662													G|||	487	0.0972444	0.3086	0.0461	5008	,	,		17818	0.003		0.0308	False		,,,				2504	0.0133				p.I849I		Atlas-SNP	.											.	VAV2	165	.	0			c.C2547T						PASS	.	G	,	1178,3228	413.3+/-336.4	166,846,1191	84.0	78.0	80.0		2547,2430	-3.2	1.0	9	dbSNP_119	80	280,8320	104.4+/-165.4	8,264,4028	no	coding-synonymous,coding-synonymous	VAV2	NM_001134398.1,NM_003371.3	,	174,1110,5219	AA,AG,GG		3.2558,26.7363,11.2102	,	849/879,810/840	136633606	1458,11548	2203	4300	6503	SO:0001819	synonymous_variant	7410	exon29			TCCGCCGATGCGG		CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12658	protein-coding gene	gene with protein product		600428	"""vav 2 oncogene"""			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.2547C>T	9.37:g.136633606G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	95	68	0.715789	NM_001134398	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Silent	SNP	ENST00000371850.3	37	CCDS48053.1																																																																																			G|0.895;A|0.105	0.105	strong		0.662	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1		
DCLK1	9201	hgsc.bcm.edu	37	13	36385031	36385031	+	Silent	SNP	G	G	T	rs2322807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:36385031G>T	ENST00000360631.3	-	12	1840	c.1629C>A	c.(1627-1629)ccC>ccA	p.P543P	DCLK1_ENST00000255448.4_Silent_p.P543P|DCLK1_ENST00000379893.1_Silent_p.P236P			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	543	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		CTGTGTACAGGGGGCCGTCTA	0.458													G|||	1492	0.297923	0.4289	0.2421	5008	,	,		16326	0.2778		0.2296	False		,,,				2504	0.2515				p.P543P		Atlas-SNP	.											.	DCLK1	350	.	0			c.C1629A						PASS	.	G	,,	1867,2539	539.6+/-375.3	401,1065,737	170.0	164.0	166.0		708,708,1629	1.0	1.0	13	dbSNP_100	166	1842,6758	329.8+/-318.9	187,1468,2645	no	coding-synonymous,coding-synonymous,coding-synonymous	DCLK1	NM_001195415.1,NM_001195416.1,NM_004734.4	,,	588,2533,3382	TT,TG,GG		21.4186,42.374,28.5176	,,	236/423,236/434,543/730	36385031	3709,9297	2203	4300	6503	SO:0001819	synonymous_variant	9201	exon12			GTACAGGGGGCCG	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"""doublecortin and CaM kinase-like 1"""	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1629C>A	13.37:g.36385031G>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	37																																																																																				G|0.713;T|0.287	0.287	strong		0.458	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
DNAH12	201625	hgsc.bcm.edu	37	3	57469151	57469151	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:57469151T>C	ENST00000351747.2	-	13	1782	c.1602A>G	c.(1600-1602)gtA>gtG	p.V534V	DNAH12_ENST00000389536.4_Silent_p.V534V	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	534	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(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						GGGCTTTTTCTACATAAGATA	0.318																																					p.V534V		Atlas-SNP	.											.	DNAH12	182	.	0			c.A1602G						PASS	.						269.0	210.0	228.0					3																	57469151		692	1591	2283	SO:0001819	synonymous_variant	201625	exon13			TTTTTCTACATAA	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.1602A>G	3.37:g.57469151T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	155	79	0.509677	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Silent	SNP	ENST00000351747.2	37																																																																																				.	.	none		0.318	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
PHRF1	57661	hgsc.bcm.edu	37	11	609577	609577	+	Missense_Mutation	SNP	C	C	T	rs7123948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:609577C>T	ENST00000264555.5	+	14	4249	c.4121C>T	c.(4120-4122)gCg>gTg	p.A1374V	PHRF1_ENST00000533464.1_Missense_Mutation_p.A1370V|PHRF1_ENST00000413872.2_Missense_Mutation_p.A1372V|PHRF1_ENST00000416188.2_Missense_Mutation_p.A1373V	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1374			A -> V (in dbSNP:rs7123948).		mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						AGCCCCTCTGCGAGTGGGAGG	0.677													T|||	425	0.0848642	0.2474	0.0476	5008	,	,		12381	0.001		0.0427	False		,,,				2504	0.0215				p.A1373V		Atlas-SNP	.											.	PHRF1	188	.	0			c.C4118T						PASS	.	T	VAL/ALA	734,3328		68,598,1365	15.0	21.0	19.0		4118	-6.4	0.0	11	dbSNP_116	19	345,7995		14,317,3839	yes	missense	PHRF1	NM_020901.2	64	82,915,5204	TT,TC,CC		4.1367,18.0699,8.7002	benign	1373/1649	609577	1079,11323	2031	4170	6201	SO:0001583	missense	57661	exon14			CCTCTGCGAGTGG	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.4121C>T	11.37:g.609577C>T	ENSP00000264555:p.Ala1374Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	37		169	0.07738095238095238	116	0.23577235772357724	20	0.055248618784530384	0	0.0	33	0.04353562005277045	T	3.357	-0.131373	0.06753	0.180699	0.041367	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21	3.21	-6.43	0.01926	.	.	.	.	.	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	0.01281	0.0;0.0;0.0;0.0	T	0.02104	-1.1213	8	0.23891	T	0.37	1.1815	3.0647	0.06211	0.2082:0.457:0.105:0.2298	rs7123948;rs7123948	1370;1372;1373;1374	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	V	1374;1372;1373;1370	ENSP00000264555:A1374V;ENSP00000388589:A1372V;ENSP00000410626:A1373V;ENSP00000431870:A1370V	ENSP00000264555:A1374V	A	+	2	0	PHRF1	599577	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.142000	0.03203	-3.050000	0.00260	-2.422000	0.00218	GCG	C|0.902;T|0.098	0.098	strong		0.677	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552092	32552092	+	Missense_Mutation	SNP	A	A	T	rs16822516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32552092A>T	ENST00000360004.5	-	2	269	c.164T>A	c.(163-165)tTc>tAc	p.F55Y		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	55	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						TCTGTCCAGGAACCGCACCCG	0.627										Multiple Myeloma(14;0.17)			A|||	1450	0.289537	0.2511	0.3501	5008	,	,		8224	0.2609		0.3091	False		,,,				2504	0.3078				p.F55Y		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.T164A						PASS	.						30.0	28.0	29.0					6																	32552092		2180	4243	6423	SO:0001583	missense	3123	exon2			TCCAGGAACCGCA	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.164T>A	6.37:g.32552092A>T	ENSP00000353099:p.Phe55Tyr	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	65	22	0.338462	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	471	0.21565934065934067	116	0.23577235772357724	88	0.2430939226519337	90	0.15734265734265734	177	0.23350923482849603	.	3.972	-0.008199	0.07773	.	.	ENSG00000196126	ENST00000360004	T	0.00357	7.89	3.52	-7.04	0.01578	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);	1.314130	0.04757	N	0.425694	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.09314	-1.0680	8	0.22109	T	0.4	.	9.1989	0.37246	0.1654:0.1127:0.0:0.7219	rs16822516;rs17881894	55	P01911	2B1F_HUMAN	Y	55	ENSP00000353099:F55Y	ENSP00000353099:F55Y	F	-	2	0	HLA-DRB1	32660070	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.670000	0.01956	-2.006000	0.00958	-3.056000	0.00068	TTC	A|0.778;T|0.222	0.222	strong		0.627	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
NUMBL	9253	hgsc.bcm.edu	37	19	41190455	41190455	+	Missense_Mutation	SNP	G	G	T	rs143941883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41190455G>T	ENST00000252891.4	-	3	283	c.116C>A	c.(115-117)gCg>gAg	p.A39E	NUMBL_ENST00000540131.1_5'UTR|NUMBL_ENST00000598779.1_5'UTR|NUMBL_ENST00000599594.1_5'UTR	NM_004756.3	NP_004747.1	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	39					adherens junction organization (GO:0034332)|axonogenesis (GO:0007409)|cytokine-mediated signaling pathway (GO:0019221)|lateral ventricle development (GO:0021670)|nervous system development (GO:0007399)|neuroblast division in subventricular zone (GO:0021849)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of neurogenesis (GO:0050769)|protein metabolic process (GO:0019538)	cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)	16			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			CATGGTGCCCGCCCCGTCTGG	0.662													G|||	74	0.0147764	0.053	0.0058	5008	,	,		12097	0.0		0.0	False		,,,				2504	0.0				p.A39E		Atlas-SNP	.											.	NUMBL	49	.	0			c.C116A						PASS	.	G	GLU/ALA	198,4208	112.9+/-151.0	5,188,2010	20.0	20.0	20.0		116	4.1	1.0	19	dbSNP_134	20	0,8600		0,0,4300	yes	missense	NUMBL	NM_004756.3	107	5,188,6310	TT,TG,GG		0.0,4.4939,1.5224	benign	39/610	41190455	198,12808	2203	4300	6503	SO:0001583	missense	9253	exon3			GTGCCCGCCCCGT	AF015401	CCDS12561.1	19q13.13-q13.2	2008-07-17	2001-11-28			ENSG00000105245			8061	protein-coding gene	gene with protein product		604018	"""numb (Drosophila) homolog-like"""			9225980, 9303539	Standard	XM_006723471		Approved	NUMB-R, CTG3a, CAG3A, TNRC23, NUMBR, NUMBLIKE	uc002oon.3	Q9Y6R0		ENST00000252891.4:c.116C>A	19.37:g.41190455G>T	ENSP00000252891:p.Ala39Glu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	147	58	0.394558	NM_004756	Q7Z4J9	Missense_Mutation	SNP	ENST00000252891.4	37	CCDS12561.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	G	20.8	4.045316	0.75846	0.044939	0.0	ENSG00000105245	ENST00000252891	T	0.56776	0.44	5.17	4.14	0.48551	.	0.189579	0.32287	N	0.006318	T	0.08935	0.0221	N	0.08118	0	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.04440	-1.0951	10	0.66056	D	0.02	-15.7799	11.0624	0.47955	0.0867:0.0:0.9133:0.0	.	39;39	A8K033;Q9Y6R0	.;NUMBL_HUMAN	E	39	ENSP00000252891:A39E	ENSP00000252891:A39E	A	-	2	0	NUMBL	45882295	0.627000	0.27129	0.999000	0.59377	0.995000	0.86356	1.270000	0.33086	1.423000	0.47198	0.591000	0.81541	GCG	G|0.987;T|0.013	0.013	strong		0.662	NUMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462749.2	NM_004756	
VWDE	221806	hgsc.bcm.edu	37	7	12410362	12410362	+	Silent	SNP	C	C	T	rs1072557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12410362C>T	ENST00000275358.3	-	11	1904	c.1716G>A	c.(1714-1716)ccG>ccA	p.P572P		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	572	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						AATCATTTTCCGGATTTTCAT	0.373													T|||	951	0.189896	0.2821	0.0951	5008	,	,		14280	0.2024		0.1034	False		,,,				2504	0.2086				p.P572P		Atlas-SNP	.											VWDE_ENST00000275358,colon,carcinoma,0,1	VWDE	123	1	0			c.G1716A						PASS	.	T		386,998		58,270,364	53.0	45.0	47.0		1716	2.1	1.0	7	dbSNP_86	47	365,2817		20,325,1246	no	coding-synonymous	VWDE	NM_001135924.1		78,595,1610	TT,TC,CC		11.4708,27.8902,16.4477		572/1591	12410362	751,3815	692	1591	2283	SO:0001819	synonymous_variant	221806	exon11			ATTTTCCGGATTT		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.1716G>A	7.37:g.12410362C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	170	100	0.588235	NM_001135924	B7ZM77|Q96SQ3	Silent	SNP	ENST00000275358.3	37	CCDS47544.1																																																																																			T|0.098;G|0.321;C|0.497;A|0.083	0.098	strong		0.373	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
SYCE1	93426	hgsc.bcm.edu	37	10	135368590	135368590	+	Missense_Mutation	SNP	T	T	C	rs3737031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135368590T>C	ENST00000343131.5	-	13	1066	c.962A>G	c.(961-963)cAc>cGc	p.H321R	SYCE1_ENST00000432597.2_Intron|SYCE1_ENST00000368517.3_Intron|SPRN_ENST00000541506.1_Intron	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	321				H -> R (in Ref. 5; AAH34821). {ECO:0000305}.	synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.H321R(1)		breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		CCCTGCTTGGTGTGCAGCTCC	0.552													t|||	775	0.154752	0.0454	0.1715	5008	,	,		20610	0.2698		0.1093	False		,,,				2504	0.2188				p.H321R		Atlas-SNP	.											SYCE1_ENST00000343131,NS,carcinoma,0,1	SYCE1	81	1	1	Substitution - Missense(1)	stomach(1)	c.A962G						PASS	.	A	,ARG/HIS,	76,1308		3,70,619	167.0	139.0	147.0		,962,	-0.0	0.0	10	dbSNP_107	147	282,2900		10,262,1319	yes	intron,missense,intron	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	,29,	13,332,1938	CC,CT,TT		8.8624,5.4913,7.8406	,benign,	,321/352,	135368590	358,4208	692	1591	2283	SO:0001583	missense	93426	exon13			GCTTGGTGTGCAG	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.962A>G	10.37:g.135368590T>C	ENSP00000341282:p.His321Arg	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	179	85	0.47486	NM_001143764	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	37	CCDS44501.1	329	0.15064102564102563	24	0.04878048780487805	62	0.1712707182320442	153	0.2674825174825175	90	0.11873350923482849	t	5.594	0.294345	0.10567	0.054913	0.088624	ENSG00000171772	ENST00000343131	T	0.08634	3.07	3.84	-0.0272	0.13927	.	2.080430	0.01972	N	0.044198	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.11235	0.004	B	0.10450	0.005	T	0.46373	-0.9196	9	0.46703	T	0.11	4.5253	1.2555	0.01990	0.1808:0.104:0.1877:0.5274	rs3737031;rs17846112;rs17859115;rs52813729;rs3737031	321	Q8N0S2	SYCE1_HUMAN	R	321	ENSP00000341282:H321R	ENSP00000341282:H321R	H	-	2	0	SYCE1	135218580	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.269000	0.18589	-0.003000	0.14444	-0.364000	0.07487	CAC	T|0.856;C|0.144	0.144	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
PIGG	54872	hgsc.bcm.edu	37	4	517622	517622	+	Silent	SNP	C	C	T	rs13150531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:517622C>T	ENST00000453061.2	+	9	2095	c.1989C>T	c.(1987-1989)gcC>gcT	p.A663A	PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000383028.4_Silent_p.A530A|PIGG_ENST00000504346.1_Silent_p.A574A|PIGG_ENST00000310340.5_Silent_p.A655A	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	663					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 (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						TAATACTGGCCTGCTGCCGGC	0.652													C|||	1123	0.224241	0.3964	0.0994	5008	,	,		16572	0.2202		0.1302	False		,,,				2504	0.181				p.A663A		Atlas-SNP	.											.	PIGG	86	.	0			c.C1989T						PASS	.	C	,	1447,2925		254,939,993	18.0	17.0	17.0		1989,1965	2.8	0.7	4	dbSNP_121	17	1018,7520		65,888,3316	no	coding-synonymous,coding-synonymous	PIGG	NM_001127178.1,NM_017733.3	,	319,1827,4309	TT,TC,CC		11.9232,33.097,19.0937	,	663/984,655/976	517622	2465,10445	2186	4269	6455	SO:0001819	synonymous_variant	54872	exon9			ACTGGCCTGCTGC		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.1989C>T	4.37:g.517622C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Silent	SNP	ENST00000453061.2	37	CCDS46992.1																																																																																			C|0.779;T|0.221	0.221	strong		0.652	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
NLRC3	197358	hgsc.bcm.edu	37	16	3599220	3599220	+	RNA	SNP	C	C	T	rs373104014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3599220C>T	ENST00000301749.7	-	0	2930				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGAGTTTTCTCGAAGGCTGAA	0.562													C|||	11	0.00219649	0.0083	0.0	5008	,	,		19418	0.0		0.0	False		,,,				2504	0.0				p.R842Q		Atlas-SNP	.											.	NLRC3	103	.	0			c.G2525A						PASS	.	C	GLN/ARG	10,3958		0,10,1974	36.0	37.0	37.0		2526	4.9	0.6	16		37	0,8318		0,0,4159	no	missense	NLRC3	NM_178844.2	43	0,10,6133	TT,TC,CC		0.0,0.252,0.0814	probably-damaging	842/1066	3599220	10,12276	1984	4159	6143			197358	exon14			TTTTCTCGAAGGC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3599220C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	C	18.58	3.655008	0.67472	0.00252	0.0	ENSG00000167984	ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.54071	0.59;0.6;0.59	4.95	4.95	0.65309	.	0.000000	0.64402	D	0.000001	T	0.52370	0.1730	N	0.13003	0.285	0.23227	N	0.998083	D;D	0.69078	0.997;0.961	D;P	0.76071	0.987;0.818	T	0.45542	-0.9254	10	0.15499	T	0.54	.	13.7484	0.62890	0.0:1.0:0.0:0.0	.	842;888	Q7RTR2;C9JLH9	NLRC3_HUMAN;.	Q	842;841;888	ENSP00000301749:R842Q;ENSP00000352039:R841Q;ENSP00000414415:R888Q	ENSP00000301749:R842Q	R	-	2	0	NLRC3	3539221	1.000000	0.71417	0.612000	0.29024	0.688000	0.40055	4.089000	0.57685	2.313000	0.78055	0.558000	0.71614	CGA	.	.	weak		0.562	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
CETP	1071	hgsc.bcm.edu	37	16	57017279	57017279	+	Missense_Mutation	SNP	G	G	A	rs2228667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57017279G>A	ENST00000566128.1	+	15	1435	c.1168G>A	c.(1168-1170)Gtg>Atg	p.V390M	CETP_ENST00000379780.2_Missense_Mutation_p.V395M|CETP_ENST00000200676.3_Missense_Mutation_p.V455M					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						CAGCAAAGGCGTGAGCCTCTT	0.607																																					p.V455M		Atlas-SNP	.											CETP,NS,carcinoma,-1,1	CETP	50	1	0			c.G1363A						PASS	.		MET/VAL	3,4393		0,3,2195	103.0	95.0	98.0		1363	3.2	1.0	16	dbSNP_98	98	0,8600		0,0,4300	no	missense	CETP	NM_000078.2	21	0,3,6495	AA,AG,GG		0.0,0.0682,0.0231	benign	455/494	57017279	3,12993	2198	4300	6498	SO:0001583	missense	1071	exon15			AAAGGCGTGAGCC	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.1168G>A	16.37:g.57017279G>A	ENSP00000456276:p.Val390Met	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		.	.	.	.	.	.	.	.	.	.	c	14.33	2.503998	0.44558	6.82E-4	0.0	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.11712	2.75;2.75	3.16	3.16	0.36331	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.497607	0.16291	U	0.220905	T	0.04272	0.0118	N	0.08118	0	0.24408	N	0.994677	B;P	0.44380	0.049;0.834	B;B	0.30029	0.026;0.11	T	0.31833	-0.9929	10	0.66056	D	0.02	0.0425	8.4085	0.32629	0.0:0.7577:0.2423:0.0	rs2228667	395;455	P11597-2;P11597	.;CETP_HUMAN	M	455;395	ENSP00000200676:V455M;ENSP00000369106:V395M	ENSP00000200676:V455M	V	+	1	0	CETP	55574780	0.996000	0.38824	1.000000	0.80357	0.010000	0.07245	0.994000	0.29693	0.668000	0.31126	-0.225000	0.12378	GTG	A|0.002;G|0.998	0.002	strong		0.607	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
RPTOR	57521	hgsc.bcm.edu	37	17	78896529	78896529	+	Silent	SNP	C	C	T	rs2271603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78896529C>T	ENST00000306801.3	+	22	2888	c.2526C>T	c.(2524-2526)acC>acT	p.T842T	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Silent_p.T684T	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	842					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CCTAGGCCACCGTGAACGCCC	0.697													C|||	1229	0.245407	0.1536	0.2911	5008	,	,		15181	0.1964		0.3241	False		,,,				2504	0.3067				p.T842T		Atlas-SNP	.											RPTOR,NS,carcinoma,0,1	RPTOR	122	1	0			c.C2526T						PASS	.	C	,	760,3606		64,632,1487	22.0	23.0	23.0		2052,2526	-9.6	0.4	17	dbSNP_100	23	2767,5805		446,1875,1965	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	510,2507,3452	TT,TC,CC		32.2795,17.4072,27.2608	,	684/1178,842/1336	78896529	3527,9411	2183	4286	6469	SO:0001819	synonymous_variant	57521	exon22			GGCCACCGTGAAC		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.2526C>T	17.37:g.78896529C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			C|0.748;T|0.252	0.252	strong		0.697	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
PCSK5	5125	hgsc.bcm.edu	37	9	78937974	78937974	+	Missense_Mutation	SNP	C	C	T	rs3001772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:78937974C>T	ENST00000545128.1	+	31	4566	c.4028C>T	c.(4027-4029)aCg>aTg	p.T1343M		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1343	CRM (Cys-rich motif).				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						CCAGAGTGCACGCCTGAGTTC	0.552													T|||	2451	0.489417	0.6846	0.4337	5008	,	,		18793	0.2093		0.5487	False		,,,				2504	0.4928				p.T1343M		Atlas-SNP	.											.	PCSK5	329	.	0			c.C4028T						PASS	.	T	MET/THR	1139,613		375,389,112	21.0	18.0	19.0		4028	5.7	1.0	9	dbSNP_101	19	2170,1812		603,964,424	yes	missense	PCSK5	NM_001190482.1	81	978,1353,536	TT,TC,CC		45.5048,34.9886,42.2916	benign	1343/1861	78937974	3309,2425	876	1991	2867	SO:0001583	missense	5125	exon31			AGTGCACGCCTGA		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.4028C>T	9.37:g.78937974C>T	ENSP00000446280:p.Thr1343Met	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	75	54	0.72	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	1020	0.46703296703296704	326	0.6626016260162602	164	0.4530386740331492	110	0.19230769230769232	420	0.554089709762533	T	10.28	1.305791	0.23736	0.650114	0.544952	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.30714	1.54;1.52	5.65	5.65	0.86999	.	0.444025	0.27340	N	0.019810	T	0.00012	0.0000	N	0.03071	-0.42	0.58432	P	6.999999999979245E-6	.	.	.	.	.	.	T	0.10019	-1.0648	7	0.40728	T	0.16	-8.0846	10.9166	0.47139	0.0:0.0746:0.0:0.9254	rs3001772;rs58696668	.	.	.	M	1343;1073;1043	ENSP00000446280:T1343M;ENSP00000411654:T1043M	ENSP00000365945:T1073M	T	+	2	0	PCSK5	78127794	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	1.767000	0.38501	0.976000	0.38417	-0.269000	0.10298	ACG	C|0.517;T|0.483	0.483	strong		0.552	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
F5	2153	hgsc.bcm.edu	37	1	169529826	169529826	+	Silent	SNP	C	C	A	rs6022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169529826C>A	ENST00000367797.3	-	4	753	c.552G>T	c.(550-552)tcG>tcT	p.S184S	F5_ENST00000367796.3_Silent_p.S184S|F5_ENST00000546081.1_Silent_p.S47S	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	184	F5/8 type A 1.|Plastocyanin-like 1.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	CAATCAGCCCCGAGTTGAAAT	0.468													A|||	2092	0.417732	0.6543	0.2911	5008	,	,		17222	0.6647		0.1819	False		,,,				2504	0.1759				p.S184S		Atlas-SNP	.											.	F5	301	.	0			c.G552T						PASS	.	A		2531,1875	539.3+/-375.2	737,1057,409	125.0	122.0	123.0		552	-1.7	1.0	1	dbSNP_52	123	1517,7083	748.0+/-407.3	132,1253,2915	no	coding-synonymous	F5	NM_000130.4		869,2310,3324	AA,AC,CC		17.6395,42.5556,31.1241		184/2225	169529826	4048,8958	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon4			CAGCCCCGAGTTG	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.552G>T	1.37:g.169529826C>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	195	194	0.994872	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	
SPINT4	391253	hgsc.bcm.edu	37	20	44351095	44351095	+	Missense_Mutation	SNP	C	C	A	rs16990631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44351095C>A	ENST00000279058.3	+	1	106	c.89C>A	c.(88-90)gCg>gAg	p.A30E		NM_178455.1	NP_848550.1	Q6UDR6	SPIT4_HUMAN	serine peptidase inhibitor, Kunitz type 4	30			A -> E (in dbSNP:rs16990631).			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			lung(6)|ovary(1)|skin(1)	8		Myeloproliferative disorder(115;0.028)				AATAAAATTGCGGAGAAGATA	0.403													C|||	130	0.0259585	0.0212	0.0389	5008	,	,		22012	0.0		0.0398	False		,,,				2504	0.0358				p.A30E		Atlas-SNP	.											.	SPINT4	17	.	0			c.C89A						PASS	.	C	GLU/ALA	102,4304	80.4+/-118.8	1,100,2102	146.0	137.0	140.0		89	-3.5	0.0	20	dbSNP_123	140	406,8194	128.8+/-187.0	13,380,3907	yes	missense	SPINT4	NM_178455.1	107	14,480,6009	AA,AC,CC		4.7209,2.315,3.9059	benign	30/100	44351095	508,12498	2203	4300	6503	SO:0001583	missense	391253	exon1			AAATTGCGGAGAA	AY372174	CCDS33477.1	20q13.12	2012-08-20	2005-10-18	2005-10-25	ENSG00000149651	ENSG00000149651			16130	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 137"", ""serine peptidase inhibitor, Kunitz type 4"""	C20orf137		21988899	Standard	NM_178455		Approved	dJ601O1.1	uc002xpe.1	Q6UDR6	OTTHUMG00000130153	ENST00000279058.3:c.89C>A	20.37:g.44351095C>A	ENSP00000279058:p.Ala30Glu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	192	99	0.515625	NM_178455	Q9BQN3	Missense_Mutation	SNP	ENST00000279058.3	37	CCDS33477.1	49	0.022435897435897436	12	0.024390243902439025	12	0.03314917127071823	0	0.0	25	0.032981530343007916	C	9.484	1.098836	0.20552	0.02315	0.047209	ENSG00000149651	ENST00000279058	T	0.54675	0.56	3.97	-3.46	0.04767	.	1.136080	0.06683	N	0.768367	T	0.05777	0.0151	.	.	.	0.09310	N	1	B	0.31077	0.307	B	0.23419	0.046	T	0.11690	-1.0577	9	0.66056	D	0.02	0.4807	0.4623	0.00518	0.2335:0.3326:0.1375:0.2964	rs16990631;rs16990631	30	Q6UDR6	SPIT4_HUMAN	E	30	ENSP00000279058:A30E	ENSP00000279058:A30E	A	+	2	0	SPINT4	43784509	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.705000	0.05052	-0.636000	0.05524	-0.143000	0.13931	GCG	C|0.963;A|0.037	0.037	strong		0.403	SPINT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252463.2	XM_372869	
SPATA13	221178	hgsc.bcm.edu	37	13	24797333	24797333	+	Intron	SNP	G	G	C	rs1220545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:24797333G>C	ENST00000382095.4	+	2	185				RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.R89P|SPATA13_ENST00000382108.3_Missense_Mutation_p.R89P|SPATA13_ENST00000424834.2_Missense_Mutation_p.R89P	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						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)		CACCCCGAGCGGCCCCACTCC	0.607													.|||	15	0.00299521	0.0113	0.0	5008	,	,		18093	0.0		0.0	False		,,,				2504	0.0				p.R89P		Atlas-SNP	.											.	SPATA13	92	.	0			c.G266C						PASS	.	G	PRO/ARG,	25,1359		0,25,667	29.0	32.0	31.0		266,	5.2	1.0	13	dbSNP_87	31	0,3182		0,0,1591	no	missense,intron	SPATA13	NM_001166271.1,NM_153023.2	103,	0,25,2258	CC,CG,GG		0.0,1.8064,0.5475	benign,	89/1278,	24797333	25,4541	692	1591	2283	SO:0001627	intron_variant	221178	exon2			CCGAGCGGCCCCA	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.-222-26282G>C	13.37:g.24797333G>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	79	50	0.632911	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	37	CCDS9305.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	14.69	2.610495	0.46527	0.018064	0.0	ENSG00000182957	ENST00000382108	T	0.81330	-1.48	5.25	5.25	0.73442	.	0.000000	0.39475	U	0.001355	T	0.75280	0.3828	L	0.46157	1.445	0.80722	D	1	.	.	.	.	.	.	T	0.82309	-0.0521	8	0.87932	D	0	.	18.2627	0.90041	0.0:0.0:1.0:0.0	rs1220545	.	.	.	P	89	ENSP00000371542:R89P	ENSP00000371542:R89P	R	+	2	0	SPATA13	23695333	1.000000	0.71417	0.995000	0.50966	0.021000	0.10359	5.152000	0.64882	2.644000	0.89710	0.478000	0.44815	CGG	G|0.997;C|0.003	0.003	strong		0.607	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
DDI1	414301	hgsc.bcm.edu	37	11	103908517	103908517	+	Missense_Mutation	SNP	G	G	A	rs116423827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:103908517G>A	ENST00000302259.3	+	1	1210	c.967G>A	c.(967-969)Gat>Aat	p.D323N	PDGFD_ENST00000302251.5_Intron|PDGFD_ENST00000393158.2_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	323							aspartic-type endopeptidase activity (GO:0004190)			central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		CATACTTGAGGATCAACCCAT	0.448													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		19982	0.0		0.0	False		,,,				2504	0.0				p.D323N		Atlas-SNP	.											.	DDI1	222	.	0			c.G967A						PASS	.	G	ASN/ASP,,	55,4349	54.9+/-90.9	1,53,2148	139.0	129.0	133.0		967,,	5.2	1.0	11	dbSNP_132	133	1,8597	1.2+/-3.3	0,1,4298	yes	missense,intron,intron	PDGFD,DDI1	NM_001001711.2,NM_025208.4,NM_033135.3	23,,	1,54,6446	AA,AG,GG		0.0116,1.2489,0.4307	possibly-damaging,,	323/397,,	103908517	56,12946	2202	4299	6501	SO:0001583	missense	414301	exon1			CTTGAGGATCAAC		CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"""				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.967G>A	11.37:g.103908517G>A	ENSP00000302805:p.Asp323Asn	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	117	41	0.350427	NM_001001711	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	37	CCDS31660.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	11.40	1.628901	0.28978	0.012489	1.16E-4	ENSG00000170967	ENST00000302259	T	0.43688	0.94	5.21	5.21	0.72293	Peptidase aspartic (1);Peptidase aspartic, eukaryotic predicted (1);Peptidase aspartic, catalytic (1);	0.165679	0.52532	D	0.000074	T	0.19765	0.0475	N	0.11364	0.135	0.47862	D	0.999536	B	0.26547	0.152	B	0.32090	0.14	T	0.06197	-1.0840	10	0.10636	T	0.68	-21.2941	16.6709	0.85266	0.0:0.0:1.0:0.0	.	323	Q8WTU0	DDI1_HUMAN	N	323	ENSP00000302805:D323N	ENSP00000302805:D323N	D	+	1	0	DDI1	103413727	1.000000	0.71417	0.954000	0.39281	0.097000	0.18754	9.016000	0.93645	2.884000	0.98904	0.655000	0.94253	GAT	G|0.995;A|0.005	0.005	strong		0.448	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711	
RAB40AL	282808	hgsc.bcm.edu	37	X	102192330	102192330	+	Silent	SNP	T	T	C	rs386826706|rs61745025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192330T>C	ENST00000218249.5	+	1	131	c.84T>C	c.(82-84)agT>agC	p.S28S	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	28					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						TAGGCAAGAGTGAGATCCTGG	0.672													.|||	989	0.261987	0.4085	0.0677	3775	,	,		10110	0.1171		0.005	False		,,,				2504	0.2853				p.S28S		Atlas-SNP	.											.	RAB40AL	33	.	0			c.T84C						PASS	.	C		1501,2333		328,575,270,729,300	56.0	74.0	68.0		84	-2.0	0.3	X	dbSNP_129	68	31,6697		0,23,8,2405,1864	no	coding-synonymous	RAB40AL	NM_001031834.1		328,598,278,3134,2164	CC,CT,C,TT,T		0.4608,39.1497,14.5048		28/279	102192330	1532,9030	2202	4300	6502	SO:0001819	synonymous_variant	282808	exon1			CAAGAGTGAGATC	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"""Ras like GTPase"""	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.84T>C	X.37:g.102192330T>C		Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	279	278	0.996416	NM_001031834	Q495H3	Silent	SNP	ENST00000218249.5	37	CCDS35353.1																																																																																			T|0.823;C|0.177	0.177	strong		0.672	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834	
SLC52A1	55065	hgsc.bcm.edu	37	17	4936336	4936336	+	Silent	SNP	A	A	T	rs72822610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4936336A>T	ENST00000424747.1	-	5	1975	c.1263T>A	c.(1261-1263)ctT>ctA	p.L421L	SLC52A1_ENST00000254853.5_Silent_p.L421L|SLC52A1_ENST00000512825.2_3'UTR	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	421					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										CACCGGCACCAAGCAGGGAGC	0.617													A|||	501	0.10004	0.1445	0.1066	5008	,	,		19163	0.0605		0.1441	False		,,,				2504	0.0307				p.L421L		Atlas-SNP	.											.	.	.	.	0			c.T1263A						PASS	.	A	,	598,3808	263.1+/-265.3	43,512,1648	83.0	79.0	81.0		1263,1263	-1.7	0.1	17	dbSNP_130	81	1231,7369	246.8+/-275.1	83,1065,3152	no	coding-synonymous,coding-synonymous	GPR172B	NM_001104577.1,NM_017986.3	,	126,1577,4800	TT,TA,AA		14.314,13.5724,14.0627	,	421/449,421/449	4936336	1829,11177	2203	4300	6503	SO:0001819	synonymous_variant	55065	exon5			GGCACCAAGCAGG	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"""Solute carriers"""	30225	protein-coding gene	gene with protein product	"""riboflavin transporter 1"""	607883	"""G protein-coupled receptor 172B"""	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.1263T>A	17.37:g.4936336A>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Silent	SNP	ENST00000424747.1	37	CCDS11066.1																																																																																			A|0.868;T|0.132	0.132	strong		0.617	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986	
IGF2R	3482	hgsc.bcm.edu	37	6	160468278	160468278	+	Silent	SNP	A	A	G	rs998075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160468278A>G	ENST00000356956.1	+	16	2287	c.2139A>G	c.(2137-2139)acA>acG	p.T713T		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	713					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)	GAGGCGGCACACCCTATAACA	0.463													G|||	2892	0.577476	0.6384	0.4899	5008	,	,		19164	0.6925		0.4841	False		,,,				2504	0.5348				p.T713T		Atlas-SNP	.											.	IGF2R	251	.	0			c.A2139G						PASS	.	G		2695,1711	513.7+/-368.4	840,1015,348	134.0	126.0	129.0		2139	-11.0	0.0	6	dbSNP_86	129	4025,4575	597.0+/-393.7	919,2187,1194	no	coding-synonymous	IGF2R	NM_000876.2		1759,3202,1542	GG,GA,AA		46.8023,38.8334,48.3315		713/2492	160468278	6720,6286	2203	4300	6503	SO:0001819	synonymous_variant	3482	exon16			CGGCACACCCTAT	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.2139A>G	6.37:g.160468278A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			A|0.458;G|0.542	0.542	strong		0.463	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
RPS24	6229	hgsc.bcm.edu	37	10	79814747	79814747	+	Silent	SNP	C	C	T	rs76653255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79814747C>T	ENST00000440692.1	+	5	991	c.849C>T	c.(847-849)tgC>tgT	p.C283C		NM_001142285.1	NP_001135757.1	P62847	RS24_HUMAN	ribosomal protein S24	0					cellular protein metabolic process (GO:0044267)|erythrocyte homeostasis (GO:0034101)|gene expression (GO:0010467)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|translation initiation factor binding (GO:0031369)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(2)|skin(1)	5	all_cancers(46;0.0343)|all_epithelial(25;0.000959)|Breast(12;0.00113)|Prostate(51;0.0095)		Epithelial(14;0.00128)|OV - Ovarian serous cystadenocarcinoma(4;0.00248)|all cancers(16;0.00428)			caccttcctgcctctctggtc	0.542													C|||	318	0.0634984	0.2231	0.0202	5008	,	,		17984	0.0		0.0089	False		,,,				2504	0.0				p.C283C		Atlas-SNP	.											.	RPS24	23	.	0			c.C849T						PASS	.	C		237,1147		17,203,472	37.0	35.0	35.0		849	-4.1	0.0	10	dbSNP_132	35	7,3175		0,7,1584	yes	coding-synonymous	RPS24	NM_001142285.1		17,210,2056	TT,TC,CC		0.22,17.1243,5.3438		283/290	79814747	244,4322	692	1591	2283	SO:0001819	synonymous_variant	6229	exon5			TTCCTGCCTCTCT	AB007159	CCDS7355.1, CCDS7356.1, CCDS44443.1	10q22	2011-04-06			ENSG00000138326	ENSG00000138326		"""S ribosomal proteins"""	10411	protein-coding gene	gene with protein product		602412				9027498, 9582194	Standard	NM_001142283		Approved	S24	uc001jzs.3	P62847	OTTHUMG00000018549	ENST00000440692.1:c.849C>T	10.37:g.79814747C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	NM_001142285	E7EPK6|P16632|Q5T0P7|Q5T0P8|Q7Z3D1	Silent	SNP	ENST00000440692.1	37	CCDS44443.1																																																																																			C|0.947;T|0.053	0.053	strong		0.542	RPS24-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001026	
ZFAT	57623	hgsc.bcm.edu	37	8	135613947	135613947	+	Missense_Mutation	SNP	C	C	T	rs35003767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:135613947C>T	ENST00000377838.3	-	6	2189	c.2015G>A	c.(2014-2016)aGg>aAg	p.R672K	ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000429442.2_Missense_Mutation_p.R660K|ZFAT_ENST00000520214.1_Missense_Mutation_p.R660K|ZFAT_ENST00000523399.1_Missense_Mutation_p.R610K|ZFAT_ENST00000520727.1_Missense_Mutation_p.R660K|ZFAT_ENST00000520356.1_Missense_Mutation_p.R660K	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	672			R -> K (in dbSNP:rs35003767).		hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			CCTGAGACACCTGCTGGGATC	0.602													C|||	119	0.023762	0.0855	0.0086	5008	,	,		19293	0.0		0.0	False		,,,				2504	0.0				p.R672K		Atlas-SNP	.											.	ZFAT	265	.	0			c.G2015A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	224,3798		7,210,1794	60.0	66.0	64.0		1979,1979,1829,1979,2015	-2.1	0.0	8	dbSNP_126	64	2,8378		0,2,4188	yes	missense,missense,missense,missense,missense	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	26,26,26,26,26	7,212,5982	TT,TC,CC		0.0239,5.5694,1.8223	benign,benign,benign,benign,benign	660/1232,660/1232,610/1182,660/1146,672/1244	135613947	226,12176	2011	4190	6201	SO:0001583	missense	57623	exon6			AGACACCTGCTGG	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.2015G>A	8.37:g.135613947C>T	ENSP00000367069:p.Arg672Lys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	59	0.027014652014652016	56	0.11382113821138211	3	0.008287292817679558	0	0.0	0	0.0	C	0.009	-1.816281	0.00595	0.055694	2.39E-4	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399;ENST00000398946	T;T;T;T;T;T	0.08282	3.18;3.12;3.13;3.11;3.12;3.12	4.76	-2.14	0.07123	.	1.175010	0.06093	N	0.663981	T	0.00109	0.0003	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.16396	0.001;0.017;0.002;0.001	B;B;B;B	0.15870	0.001;0.014;0.002;0.0	T	0.37731	-0.9693	10	0.05436	T	0.98	-1.7605	2.7057	0.05161	0.1238:0.3172:0.3665:0.1925	rs35003767	610;660;660;672	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	K	660;660;660;672;660;559;610;660	ENSP00000427879:R660K;ENSP00000427831:R660K;ENSP00000394501:R660K;ENSP00000367069:R672K;ENSP00000428483:R660K;ENSP00000429091:R610K	ENSP00000326997:R559K	R	-	2	0	ZFAT	135683129	0.000000	0.05858	0.000000	0.03702	0.217000	0.24651	-2.263000	0.01174	-0.055000	0.13244	0.561000	0.74099	AGG	C|0.971;T|0.029	0.029	strong		0.602	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
PLCD1	5333	hgsc.bcm.edu	37	3	38051941	38051941	+	Silent	SNP	T	T	C	rs9857730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38051941T>C	ENST00000334661.4	-	6	1125	c.903A>G	c.(901-903)ccA>ccG	p.P301P	PLCD1_ENST00000463876.1_Silent_p.P322P|PLCD1_ENST00000479619.1_5'Flank	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	301	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		AGTGGCTAAGTGGCTGGCCCA	0.612													C|||	1336	0.266773	0.5053	0.1657	5008	,	,		19691	0.0863		0.1769	False		,,,				2504	0.2945				p.P322P		Atlas-SNP	.											PLCD1_ENST00000463876,NS,carcinoma,0,2	PLCD1	87	2	0			c.A966G						PASS	.	C	,	2062,2344	607.3+/-390.9	479,1104,620	55.0	56.0	56.0		966,903	-5.7	0.8	3	dbSNP_119	56	1808,6792	731.9+/-406.8	181,1446,2673	no	coding-synonymous,coding-synonymous	PLCD1	NM_001130964.1,NM_006225.3	,	660,2550,3293	CC,CT,TT		21.0233,46.7998,29.7555	,	322/778,301/757	38051941	3870,9136	2203	4300	6503	SO:0001819	synonymous_variant	5333	exon6			GCTAAGTGGCTGG		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"""EF-hand domain containing"""	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.903A>G	3.37:g.38051941T>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	159	75	0.471698	NM_001130964	B3KR14|Q86VN8	Silent	SNP	ENST00000334661.4	37	CCDS2671.1																																																																																			T|0.725;C|0.275	0.275	strong		0.612	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2		
LTF	4057	hgsc.bcm.edu	37	3	46496854	46496854	+	Missense_Mutation	SNP	G	G	A	rs60938611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46496854G>A	ENST00000231751.4	-	5	873	c.578C>T	c.(577-579)gCg>gTg	p.A193V	LTF_ENST00000426532.2_Missense_Mutation_p.A149V|LTF_ENST00000417439.1_Missense_Mutation_p.A193V	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	193	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		CCCTGTCCCCGCACACAGGCG	0.552													G|||	324	0.0646965	0.2337	0.0216	5008	,	,		22455	0.0		0.0	False		,,,				2504	0.0				p.A193V		Atlas-SNP	.											.	LTF	98	.	0			c.C578T						PASS	.	G	VAL/ALA,VAL/ALA	726,3680	299.6+/-285.9	64,598,1541	140.0	115.0	124.0		446,578	-5.2	0.0	3	dbSNP_129	124	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	LTF	NM_001199149.1,NM_002343.3	64,64	64,603,5836	AA,AG,GG		0.0581,16.4775,5.6205	benign,benign	149/667,193/711	46496854	731,12275	2203	4300	6503	SO:0001583	missense	4057	exon5			GTCCCCGCACACA		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.578C>T	3.37:g.46496854G>A	ENSP00000231751:p.Ala193Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	141	68	0.482269	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	102|102	0.046703296703296704|0.046703296703296704	92|92	0.18699186991869918|0.18699186991869918	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	G|G	7.510|7.510	0.654550|0.654550	0.14580|0.14580	0.164775|0.164775	5.81E-4|5.81E-4	ENSG00000012223|ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496|ENST00000443743	T;T;T;T|.	0.34667|.	1.35;1.35;1.35;1.35|.	4.79|4.79	-5.21|-5.21	0.02815|0.02815	.|.	1.046820|.	0.07391|.	N|.	0.889107|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.25245|0.25245	0.725|0.725	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.15473|.	0.013;0.011;0.013|.	B;B;B|.	0.08055|.	0.002;0.003;0.002|.	T|T	0.29761|0.29761	-1.0001|-1.0001	9|5	0.10377|0.87932	T|D	0.69|0	0.3304|0.3304	5.6254|5.6254	0.17480|0.17480	0.3945:0.0:0.398:0.2075|0.3945:0.0:0.398:0.2075	rs60938611;rs61740469|rs60938611;rs61740469	193;180;193|.	E7ER44;E7EQB2;P02788|.	.;.;TRFL_HUMAN|.	V|W	193;149;193;180|126	ENSP00000231751:A193V;ENSP00000405719:A149V;ENSP00000405546:A193V;ENSP00000397427:A180V|.	ENSP00000231751:A193V|ENSP00000393737:R126W	A|R	-|-	2|1	0|2	LTF|LTF	46471858|46471858	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-0.754000|-0.754000	0.04787|0.04787	-0.692000|-0.692000	0.05128|0.05128	-1.728000|-1.728000	0.00702|0.00702	GCG|CGG	G|0.949;A|0.051	0.051	strong		0.552	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
FAM9B	171483	hgsc.bcm.edu	37	X	8997440	8997440	+	Missense_Mutation	SNP	G	G	A	rs141078293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:8997440G>A	ENST00000327220.5	-	6	665	c.301C>T	c.(301-303)Cat>Tat	p.H101Y	FAM9B_ENST00000362066.3_Missense_Mutation_p.H141Y|FAM9B_ENST00000428477.1_Missense_Mutation_p.H101Y			Q8IZU0	FAM9B_HUMAN	family with sequence similarity 9, member B	101						nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|urinary_tract(1)	11		Hepatocellular(5;0.219)				TTCAGAGAATGTATATAATCA	0.368													G|||	11	0.00291391	0.0	0.0	3775	,	,		14758	0.0		0.0109	False		,,,				2504	0.0				p.H101Y		Atlas-SNP	.											.	FAM9B	32	.	0			c.C301T						PASS	.	G	TYR/HIS	2,3833		0,2,0,1630,571	190.0	146.0	161.0		301	-0.6	0.0	X	dbSNP_134	161	84,6644		0,61,23,2367,1849	yes	missense	FAM9B	NM_205849.2	83	0,63,23,3997,2420	AA,AG,A,GG,G		1.2485,0.0522,0.8142	possibly-damaging	101/187	8997440	86,10477	2203	4300	6503	SO:0001583	missense	171483	exon5			GAGAATGTATATA		CCDS14132.1	Xp22.31	2014-02-17			ENSG00000177138	ENSG00000177138			18404	protein-coding gene	gene with protein product	"""testis expressed 39B"""	300478				12213195, 21085121, 21998597, 22936694	Standard	XM_005274456		Approved	TEX39B	uc011mhu.2	Q8IZU0	OTTHUMG00000021114	ENST00000327220.5:c.301C>T	X.37:g.8997440G>A	ENSP00000318716:p.His101Tyr	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	190	75	0.394737	NM_205849	Q0IJ68|Q8N7Z8	Missense_Mutation	SNP	ENST00000327220.5	37	CCDS14132.1	9	0.0054249547920434	0	0.0	0	0.0	0	0.0	7	0.009283819628647215	G	0.008	-1.907334	0.00512	5.22E-4	0.012485	ENSG00000177138	ENST00000362066;ENST00000327220;ENST00000428477	.	.	.	0.43	-0.548	0.11833	.	.	.	.	.	T	0.17959	0.0431	N	0.15975	0.35	0.09310	N	1	P;P	0.43431	0.807;0.807	P;P	0.53518	0.728;0.728	T	0.09907	-1.0653	7	0.02654	T	1	.	.	.	.	.	101;141	Q8IZU0;Q8N7Z8	FAM9B_HUMAN;.	Y	141;101;101	.	ENSP00000318716:H101Y	H	-	1	0	FAM9B	8957440	0.004000	0.15560	0.003000	0.11579	0.003000	0.03518	-0.210000	0.09345	-0.426000	0.07360	-0.422000	0.05995	CAT	G|0.993;A|0.007	0.007	strong		0.368	FAM9B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055702.2	NM_205849	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257381	114257381	+	Missense_Mutation	SNP	T	T	G	rs13428956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:114257381T>G	ENST00000306507.5	+	1	721	c.548T>G	c.(547-549)cTg>cGg	p.L183R		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	183					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						TACTGGAGCCTGGACCCCGCC	0.652													.|||	306	0.0611022	0.2216	0.0159	5008	,	,		10688	0.0		0.0	False		,,,				2504	0.002				p.L183R		Atlas-SNP	.											.	FOXD4L1	48	.	0			c.T548G						PASS	.	T	ARG/LEU	727,3503		131,465,1519	54.0	72.0	66.0		548	2.6	1.0	2	dbSNP_121	66	3,8201		0,3,4099	no	missense	FOXD4L1	NM_012184.4	102	131,468,5618	GG,GT,TT		0.0366,17.1868,5.871	probably-damaging	183/409	114257381	730,11704	2115	4102	6217	SO:0001583	missense	200350	exon1			GGAGCCTGGACCC	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.548T>G	2.37:g.114257381T>G	ENSP00000302756:p.Leu183Arg	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	174	82	0.471264	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	91	0.041666666666666664	90	0.18292682926829268	1	0.0027624309392265192	0	0.0	0	0.0	.	17.71	3.456701	0.63401	0.171868	3.66E-4	ENSG00000184492	ENST00000306507	D	0.97041	-4.22	2.57	2.57	0.30868	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.27841	U	0.017640	T	0.15219	0.0367	M	0.93854	3.465	0.09310	P	0.99999539299	D	0.76494	0.999	D	0.81914	0.995	T	0.05886	-1.0858	9	0.87932	D	0	.	8.6531	0.34046	0.0:0.0:0.0:1.0	rs13428956	183	Q9NU39	FX4L1_HUMAN	R	183	ENSP00000302756:L183R	ENSP00000302756:L183R	L	+	2	0	FOXD4L1	113973851	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	7.431000	0.80335	1.190000	0.43042	0.155000	0.16302	CTG	T|0.973;G|0.027	0.027	strong		0.652	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
HAP1	9001	hgsc.bcm.edu	37	17	39884065	39884065	+	Missense_Mutation	SNP	C	C	A	rs35612698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39884065C>A	ENST00000310778.5	-	8	1233	c.1224G>T	c.(1222-1224)ttG>ttT	p.L408F	HAP1_ENST00000347901.4_Missense_Mutation_p.L408F|JUP_ENST00000540235.1_Intron|HAP1_ENST00000341193.5_Intron|RN7SL399P_ENST00000471648.2_RNA|HAP1_ENST00000393939.2_Intron			P54257	HAP1_HUMAN	huntingtin-associated protein 1	408	Glu-rich.|HAP1 N-terminal.		L -> F (in dbSNP:rs35612698).		anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			GCTGCTTCTGCAACTTTTCAG	0.602													C|||	1184	0.236422	0.1793	0.2493	5008	,	,		20399	0.1935		0.4016	False		,,,				2504	0.1789				p.L408F		Atlas-SNP	.											.	HAP1	48	.	0			c.G1224T						PASS	.	C	,,PHE/LEU	939,3467	354.6+/-312.7	107,725,1371	48.0	42.0	44.0		,,1224	1.3	0.9	17	dbSNP_126	44	3381,5219	496.5+/-374.3	634,2113,1553	yes	intron,intron,missense	HAP1	NM_001079870.1,NM_001079871.1,NM_177977.2	,,22	741,2838,2924	AA,AC,CC		39.314,21.3118,33.2154	,,probably-damaging	,,408/620	39884065	4320,8686	2203	4300	6503	SO:0001583	missense	9001	exon8			CTTCTGCAACTTT	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"""neuroan 1"""	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.1224G>T	17.37:g.39884065C>A	ENSP00000309392:p.Leu408Phe	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_177977	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	37		570	0.260989010989011	85	0.17276422764227642	105	0.2900552486187845	84	0.14685314685314685	296	0.39050131926121373	C	14.34	2.505980	0.44558	0.213118	0.39314	ENSG00000173805	ENST00000310778;ENST00000347901	T;T	0.35605	1.3;1.3	3.45	1.28	0.21552	.	.	.	.	.	T	0.00012	0.0000	M	0.79475	2.455	0.31296	P	0.68889	D;D	0.61697	0.99;0.986	P;P	0.62382	0.901;0.894	T	0.36237	-0.9756	8	0.72032	D	0.01	-4.5459	3.4576	0.07521	0.2534:0.6089:0.0:0.1377	rs35612698;rs62065872	408;408	P54257-2;P54257	.;HAP1_HUMAN	F	408	ENSP00000309392:L408F;ENSP00000334002:L408F	ENSP00000309392:L408F	L	-	3	2	HAP1	37137591	0.980000	0.34600	0.928000	0.36995	0.592000	0.36648	0.135000	0.15952	1.809000	0.52856	0.549000	0.68633	TTG	C|0.692;A|0.308	0.308	strong		0.602	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949	
ATAD2	29028	hgsc.bcm.edu	37	8	124357302	124357302	+	Missense_Mutation	SNP	C	C	T	rs78548009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124357302C>T	ENST00000287394.5	-	19	2647	c.2540G>A	c.(2539-2541)cGt>cAt	p.R847H	RNU6-875P_ENST00000516488.1_RNA|MIR548AA1_ENST00000384971.2_RNA|ATAD2_ENST00000521903.1_Missense_Mutation_p.R165H	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	847					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R847H(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			CTTAGCTTCACGAATCACCTA	0.398													C|||	7	0.00139776	0.0015	0.0	5008	,	,		17101	0.0		0.0	False		,,,				2504	0.0051				p.R847H		Atlas-SNP	.											ATAD2,NS,carcinoma,0,1	ATAD2	160	1	1	Substitution - Missense(1)	endometrium(1)	c.G2540A						PASS	.	C	HIS/ARG	8,4398	14.3+/-33.2	0,8,2195	175.0	150.0	159.0		2540	4.7	1.0	8	dbSNP_131	159	0,8600		0,0,4300	yes	missense	ATAD2	NM_014109.3	29	0,8,6495	TT,TC,CC		0.0,0.1816,0.0615	probably-damaging	847/1391	124357302	8,12998	2203	4300	6503	SO:0001583	missense	29028	exon19			GCTTCACGAATCA	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.2540G>A	8.37:g.124357302C>T	ENSP00000287394:p.Arg847His	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	37	CCDS6343.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	19.10	3.761292	0.69763	0.001816	0.0	ENSG00000156802	ENST00000287394;ENST00000521903	D;D	0.82803	-1.65;-1.65	5.58	4.7	0.59300	.	0.888358	0.09837	N	0.749398	D	0.87783	0.6264	L	0.58101	1.795	0.37045	D	0.897316	D	0.63880	0.993	P	0.56514	0.8	D	0.85289	0.1066	10	0.46703	T	0.11	-4.8315	14.7146	0.69257	0.0:0.9301:0.0:0.0699	.	847	Q6PL18	ATAD2_HUMAN	H	847;165	ENSP00000287394:R847H;ENSP00000429213:R165H	ENSP00000287394:R847H	R	-	2	0	ATAD2	124426483	0.983000	0.35010	1.000000	0.80357	0.436000	0.31835	0.289000	0.18957	1.359000	0.45940	0.655000	0.94253	CGT	C|0.999;T|0.001	0.001	strong		0.398	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109	
MCF2L2	23101	hgsc.bcm.edu	37	3	182994744	182994744	+	Splice_Site	SNP	C	C	T	rs61731401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:182994744C>T	ENST00000328913.3	-	15	2075	c.1778G>A	c.(1777-1779)aGt>aAt	p.S593N	MCF2L2_ENST00000447025.2_Splice_Site_p.S593N|MCF2L2_ENST00000414362.2_Splice_Site_p.S593N|MCF2L2_ENST00000473233.1_Splice_Site_p.S593N	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	593							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)			GATTTCTTCACTCTGAAGTGA	0.443													T|||	136	0.0271565	0.0983	0.0072	5008	,	,		13396	0.0		0.001	False		,,,				2504	0.0				p.S593N		Atlas-SNP	.											MCF2L2,brain,glioma,0,1	MCF2L2	164	1	0			c.G1778A						PASS	.	T	ASN/SER	379,4027	769.4+/-413.7	24,331,1848	23.0	23.0	23.0		1778	3.7	1.0	3	dbSNP_129	23	2,8598	800.0+/-407.4	0,2,4298	yes	missense-near-splice	MCF2L2	NM_015078.2	46	24,333,6146	TT,TC,CC		0.0233,8.6019,2.9294	benign	593/1115	182994744	381,12625	2203	4300	6503	SO:0001630	splice_region_variant	23101	exon15			TCTTCACTCTGAA	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.1777-1G>A	3.37:g.182994744C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	T	0.017	-1.489466	0.01018	0.086019	2.33E-4	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000437431;ENST00000414362	T;T;T;T	0.04603	4.59;4.6;3.71;3.59	4.9	3.66	0.41972	.	0.531863	0.17868	N	0.159298	T	0.00109	0.0003	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.57394	-0.7819	10	0.31617	T	0.26	.	4.0278	0.09695	0.1805:0.097:0.0:0.7224	.	593;593	Q86YR7-2;Q86YR7	.;MF2L2_HUMAN	N	593;593;593;129;593	ENSP00000328118:S593N;ENSP00000420070:S593N;ENSP00000388190:S593N;ENSP00000414131:S593N	ENSP00000328118:S593N	S	-	2	0	MCF2L2	184477438	1.000000	0.71417	1.000000	0.80357	0.162000	0.22319	1.042000	0.30303	1.010000	0.39314	-0.360000	0.07572	AGT	C|0.975;T|0.025	0.025	strong		0.443	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	Missense_Mutation
HSD17B12	51144	hgsc.bcm.edu	37	11	43876698	43876698	+	Missense_Mutation	SNP	C	C	T	rs11555762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	128	0	0		WXS	Illumina HiSeq	Phase_I	132	62	0.469697	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		
NDUFA13	51079	hgsc.bcm.edu	37	19	19626087	19626087	+	5'Flank	SNP	C	C	T	rs150432013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19626087C>T	ENST00000507754.4	+	0	0				TSSK6_ENST00000360913.3_Silent_p.P50P|TSSK6_ENST00000585580.3_Silent_p.P50P|NDUFA13_ENST00000503283.1_5'Flank|YJEFN3_ENST00000608404.1_5'Flank|NDUFA13_ENST00000252576.5_5'Flank|NDUFA13_ENST00000428459.2_5'Flank|NDUFA13_ENST00000512771.3_5'Flank|CTC-260F20.3_ENST00000555938.1_5'Flank			Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13						apoptotic signaling pathway (GO:0097190)|cellular metabolic process (GO:0044237)|cellular response to interferon-beta (GO:0035458)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of peptidase activity (GO:0010952)|positive regulation of protein catabolic process (GO:0045732)|protein import into mitochondrial inner membrane (GO:0045039)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	12						TGACGAAGTCCGGGGGCGCTC	0.617													C|||	18	0.00359425	0.0136	0.0	5008	,	,		15387	0.0		0.0	False		,,,				2504	0.0				p.P50P		Atlas-SNP	.											.	TSSK6	32	.	0			c.G150A						PASS	.	C		42,4364	44.6+/-78.6	0,42,2161	55.0	51.0	52.0		150	-9.9	0.9	19	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous	TSSK6	NM_032037.2		0,42,6461	TT,TC,CC		0.0,0.9532,0.3229		50/274	19626087	42,12964	2203	4300	6503	SO:0001631	upstream_gene_variant	83983	exon1			GAAGTCCGGGGGC	AF261134	CCDS12404.1, CCDS12404.2	19p13.11	2011-07-04			ENSG00000186010	ENSG00000186010		"""Mitochondrial respiratory chain complex / Complex I"""	17194	protein-coding gene	gene with protein product	"""complex I B16.6 subunit"""	609435				12837546, 10924506, 15367666	Standard	NM_015965		Approved	CGI-39, CDA016, GRIM-19, GRIM19, B16.6		Q9P0J0	OTTHUMG00000162211		19.37:g.19626087C>T	Exception_encountered	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_032037	B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327	Silent	SNP	ENST00000507754.4	37	CCDS12404.2																																																																																			C|0.996;T|0.004	0.004	strong		0.617	NDUFA13-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367916.6	NM_015965	
ZRANB3	84083	hgsc.bcm.edu	37	2	135988236	135988236	+	Nonsense_Mutation	SNP	G	G	A	rs200823309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:135988236G>A	ENST00000264159.6	-	13	1917	c.1801C>T	c.(1801-1803)Cga>Tga	p.R601*	ZRANB3_ENST00000401392.1_Nonsense_Mutation_p.R601*|ZRANB3_ENST00000412849.1_5'UTR|ZRANB3_ENST00000536680.1_Nonsense_Mutation_p.R601*	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	601					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		AGTGGAGTTCGGATTTGCTTG	0.507													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19706	0.0		0.0	False		,,,				2504	0.0				p.R601X		Atlas-SNP	.											.	ZRANB3	109	.	0			c.C1801T						PASS	.	G	stop/ARG	10,3932		0,10,1961	158.0	155.0	156.0		1801	-0.6	0.0	2		156	1,8297		0,1,4148	yes	stop-gained	ZRANB3	NM_032143.2		0,11,6109	AA,AG,GG		0.0121,0.2537,0.0899		601/1080	135988236	11,12229	1971	4149	6120	SO:0001587	stop_gained	84083	exon13			GAGTTCGGATTTG	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"""Zinc fingers, RAN-binding domain containing"""	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.1801C>T	2.37:g.135988236G>A	ENSP00000264159:p.Arg601*	Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	323	145	0.448916	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Nonsense_Mutation	SNP	ENST00000264159.6	37	CCDS46419.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	36	5.734207	0.96865	0.002537	1.21E-4	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	.	.	.	4.8	-0.643	0.11482	.	1.959680	0.01762	N	0.030630	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.5281	2.7512	0.05281	0.137:0.0772:0.2876:0.4982	.	.	.	.	X	66;66;601;601;601	.	ENSP00000264159:R601X	R	-	1	2	ZRANB3	135704706	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.257000	0.18369	-0.270000	0.09285	-0.375000	0.07067	CGA	G|1.000;A|0.000	0.000	strong		0.507	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143	
BIN3	55909	hgsc.bcm.edu	37	8	22481449	22481449	+	Silent	SNP	A	A	G	rs1871900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22481449A>G	ENST00000276416.6	-	8	662	c.594T>C	c.(592-594)ttT>ttC	p.F198F	BIN3_ENST00000399977.4_Silent_p.F150F|BIN3_ENST00000519335.1_5'UTR|BIN3_ENST00000519513.1_Silent_p.F144F	NM_018688.4	NP_061158.1	Q9NQY0	BIN3_HUMAN	bridging integrator 3	198	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				actin filament organization (GO:0007015)|barrier septum assembly (GO:0000917)|cytokinesis (GO:0000910)|myoblast migration involved in skeletal muscle regeneration (GO:0014839)|protein localization (GO:0008104)|regulation of lamellipodium assembly (GO:0010591)|skeletal muscle fiber development (GO:0048741)|unidimensional cell growth (GO:0009826)	actin filament (GO:0005884)|cytoplasm (GO:0005737)	cytoskeletal adaptor activity (GO:0008093)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	9		Prostate(55;0.0424)|Breast(100;0.102)|all_epithelial(46;0.143)		BRCA - Breast invasive adenocarcinoma(99;0.00664)|Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		TGAGGGACTCAAAGCTGGGCT	0.622													a|||	2490	0.497204	0.6067	0.3977	5008	,	,		15483	0.3978		0.4394	False		,,,				2504	0.5818				p.F198F		Atlas-SNP	.											.	BIN3	16	.	0			c.T594C						PASS	.	G		2138,1810		583,972,419	21.0	27.0	25.0		594	-11.0	0.2	8	dbSNP_92	25	3451,4843		723,2005,1419	no	coding-synonymous	BIN3	NM_018688.4		1306,2977,1838	GG,GA,AA		41.6084,45.846,45.6543		198/254	22481449	5589,6653	1974	4147	6121	SO:0001819	synonymous_variant	55909	exon8			GGACTCAAAGCTG		CCDS47825.1	8p21.2	2008-07-04			ENSG00000147439	ENSG00000147439			1054	protein-coding gene	gene with protein product		606396				16524918	Standard	NM_018688		Approved		uc003xcl.3	Q9NQY0	OTTHUMG00000163844	ENST00000276416.6:c.594T>C	8.37:g.22481449A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_018688	Q9BVG2|Q9NVY9	Silent	SNP	ENST00000276416.6	37	CCDS47825.1																																																																																			G|0.475;C|0.000;A|0.525	0.475	strong		0.622	BIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375895.1		
RASA2	5922	hgsc.bcm.edu	37	3	141327474	141327474	+	Silent	SNP	G	G	A	rs295323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141327474G>A	ENST00000452898.1	+	21	2198	c.2163G>A	c.(2161-2163)ctG>ctA	p.L721L	RASA2_ENST00000286364.3_Silent_p.L720L|RASA2_ENST00000509118.1_3'UTR	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	721					intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.L720L(1)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						CTGTGTATCTGAACGGAAATT	0.438													A|||	2256	0.450479	0.7315	0.4625	5008	,	,		21103	0.2937		0.3797	False		,,,				2504	0.2965				p.L720L		Atlas-SNP	.											RASA2_ENST00000286364,NS,carcinoma,0,1	RASA2	169	1	1	Substitution - coding silent(1)	stomach(1)	c.G2160A						PASS	.	A		2958,1448	467.4+/-354.8	999,960,244	123.0	124.0	124.0		2160	-10.8	0.0	3	dbSNP_79	124	3341,5259	643.9+/-400.0	601,2139,1560	no	coding-synonymous	RASA2	NM_006506.2		1600,3099,1804	AA,AG,GG		38.8488,32.8643,48.4315		720/850	141327474	6299,6707	2203	4300	6503	SO:0001819	synonymous_variant	5922	exon21			GTATCTGAACGGA	AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"""Pleckstrin homology (PH) domain containing"""	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.2163G>A	3.37:g.141327474G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	221	113	0.511312	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Silent	SNP	ENST00000452898.1	37																																																																																				G|0.523;A|0.477	0.477	strong		0.438	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506	
KIF5C	3800	hgsc.bcm.edu	37	2	149806388	149806388	+	Silent	SNP	C	C	T	rs60169973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:149806388C>T	ENST00000435030.1	+	9	1118	c.750C>T	c.(748-750)gaC>gaT	p.D250D	KIF5C_ENST00000414838.2_Silent_p.D155D|KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000397413.1_Silent_p.D18D			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	128	0	0		WXS	Illumina HiSeq	Phase_I	118	50	0.423729	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	
OR6N2	81442	hgsc.bcm.edu	37	1	158746847	158746847	+	Silent	SNP	A	A	G	rs16841094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158746847A>G	ENST00000339258.1	-	1	578	c.579T>C	c.(577-579)tcT>tcC	p.S193S		NM_001005278.1	NP_001005278.1	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N, member 2	193						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(6)|lung(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(112;0.0378)					GAATGTTAGCAGATGTGTCCT	0.418													G|||	942	0.188099	0.2254	0.0548	5008	,	,		24908	0.1925		0.0746	False		,,,				2504	0.3446				p.S193S		Atlas-SNP	.											.	OR6N2	78	.	0			c.T579C						PASS	.	G		807,3599	749.0+/-412.0	69,669,1465	48.0	47.0	47.0		579	-0.3	0.5	1	dbSNP_123	47	605,7995	791.7+/-407.5	28,549,3723	no	coding-synonymous	OR6N2	NM_001005278.1		97,1218,5188	GG,GA,AA		7.0349,18.3159,10.8565		193/318	158746847	1412,11594	2203	4300	6503	SO:0001819	synonymous_variant	81442	exon1			GTTAGCAGATGTG	BK004200	CCDS30906.1	1q23.1	2012-08-09			ENSG00000188340	ENSG00000188340		"""GPCR / Class A : Olfactory receptors"""	15035	protein-coding gene	gene with protein product							Standard	NM_001005278		Approved		uc010pir.2	Q8NGY6	OTTHUMG00000022775	ENST00000339258.1:c.579T>C	1.37:g.158746847A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_001005278	Q6IFR2	Silent	SNP	ENST00000339258.1	37	CCDS30906.1																																																																																			A|0.870;G|0.130	0.130	strong		0.418	OR6N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059068.1		
MAP10	54627	hgsc.bcm.edu	37	1	232942028	232942028	+	Missense_Mutation	SNP	A	A	G	rs61739198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232942028A>G	ENST00000418460.1	+	1	1386	c.1259A>G	c.(1258-1260)aAt>aGt	p.N420S		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	278					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										GGTGCTGGCAATGGGAGAAAT	0.408													A|||	291	0.058107	0.1755	0.0159	5008	,	,		20419	0.0367		0.0	False		,,,				2504	0.0112				p.N420S		Atlas-SNP	.											.	.	.	.	0			c.A1259G						PASS	.	A	SER/ASN	564,3334		34,496,1419	270.0	276.0	274.0		1259	0.1	0.0	1	dbSNP_129	274	10,8292		0,10,4141	yes	missense	KIAA1383	NM_019090.2	46	34,506,5560	GG,GA,AA		0.1205,14.469,4.7049	benign	420/1048	232942028	574,11626	1949	4151	6100	SO:0001583	missense	54627	exon1			CTGGCAATGGGAG	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.1259A>G	1.37:g.232942028A>G	ENSP00000403208:p.Asn420Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	77	0.035256410256410256	59	0.11991869918699187	6	0.016574585635359115	12	0.02097902097902098	0	0.0	A	0.010	-1.770792	0.00645	0.14469	0.001205	ENSG00000212916	ENST00000418460	.	.	.	4.1	0.0565	0.14319	.	1.494600	0.04801	N	0.433460	T	0.00073	0.0002	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.19516	-1.0303	8	0.06625	T	0.88	0.6958	6.8928	0.24238	0.3994:0.0:0.6006:0.0	rs61739198	278	Q9P2G4	K1383_HUMAN	S	420	.	ENSP00000403208:N420S	N	+	2	0	KIAA1383	231008651	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.330000	0.19715	0.030000	0.15379	-1.864000	0.00558	AAT	A|0.970;G|0.030	0.030	strong		0.408	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
FAM136A	84908	hgsc.bcm.edu	37	2	70528092	70528092	+	Silent	SNP	G	G	A	rs72904358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70528092G>A	ENST00000037869.3	-	2	186	c.108C>T	c.(106-108)agC>agT	p.S36S	AC022201.5_ENST00000445084.1_RNA|FAM136A_ENST00000430566.1_Silent_p.S143S|FAM136A_ENST00000450256.1_Missense_Mutation_p.R102C	NM_032822.2	NP_116211.2	Q96C01	F136A_HUMAN	family with sequence similarity 136, member A	36						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						AACAGCTGGCGCTGCACCGGA	0.577													G|||	492	0.0982428	0.3124	0.0202	5008	,	,		19465	0.001		0.003	False		,,,				2504	0.0624				p.S36S		Atlas-SNP	.											FAM136A,caecum,carcinoma,0,1	FAM136A	14	1	0			c.C108T						scavenged	.	G		1006,3400	373.9+/-321.0	116,774,1313	75.0	76.0	76.0		108	-1.5	1.0	2	dbSNP_130	76	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous	FAM136A	NM_032822.2		116,799,5588	AA,AG,GG		0.2907,22.8325,7.9271		36/139	70528092	1031,11975	2203	4300	6503	SO:0001819	synonymous_variant	84908	exon2			GCTGGCGCTGCAC	BC014975	CCDS1904.1	2p14	2014-02-12	2007-07-10		ENSG00000035141	ENSG00000035141			25911	protein-coding gene	gene with protein product	"""hypothetical protein FLJ14668"""					12477932	Standard	NM_032822		Approved	FLJ14668	uc002sgq.4	Q96C01	OTTHUMG00000129668	ENST00000037869.3:c.108C>T	2.37:g.70528092G>A		Somatic	217	2	0.00921659		WXS	Illumina HiSeq	Phase_I	225	113	0.502222	NM_032822	Q96SS3	Silent	SNP	ENST00000037869.3	37	CCDS1904.1	165	0.07554945054945054	151	0.30691056910569103	9	0.024861878453038673	1	0.0017482517482517483	4	0.005277044854881266	G	13.18	2.160192	0.38119	0.228325	0.002907	ENSG00000035141	ENST00000450256	.	.	.	5.01	-1.49	0.08718	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.34030	-0.9845	4	0.87932	D	0	.	10.957	0.47364	0.4179:0.0:0.5821:0.0	.	.	.	.	C	102	.	ENSP00000391468:R102C	R	-	1	0	FAM136A	70381596	0.992000	0.36948	0.966000	0.40874	0.969000	0.65631	0.199000	0.17237	-0.250000	0.09555	-0.263000	0.10527	CGC	G|0.921;A|0.079	0.079	strong		0.577	FAM136A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251869.2	NM_032822	
TOX3	27324	hgsc.bcm.edu	37	16	52478215	52478215	+	Silent	SNP	C	C	T	rs3743797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	94	60	0.638298	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	
TESK1	7016	hgsc.bcm.edu	37	9	35608962	35608962	+	Silent	SNP	C	C	T	rs148341917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35608962C>T	ENST00000336395.5	+	10	1354	c.1104C>T	c.(1102-1104)ccC>ccT	p.P368P	TESK1_ENST00000498522.1_3'UTR|CD72_ENST00000490239.1_5'Flank|MIR4667_ENST00000578933.1_RNA	NM_006285.2	NP_006276.2	Q15569	TESK1_HUMAN	testis-specific kinase 1	368					cell junction assembly (GO:0034329)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	27			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGAATCACCCCCCAACTGGG	0.607													C|||	30	0.00599042	0.0129	0.0014	5008	,	,		17980	0.001		0.002	False		,,,				2504	0.0092				p.P368P		Atlas-SNP	.											.	TESK1	46	.	0			c.C1104T						PASS	.	C		63,4343	58.7+/-95.3	0,63,2140	63.0	70.0	68.0		1104	3.4	1.0	9	dbSNP_134	68	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous	TESK1	NM_006285.2		0,88,6415	TT,TC,CC		0.2907,1.4299,0.6766		368/627	35608962	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	7016	exon10			ATCACCCCCCAAC	D50863	CCDS6580.1	9p13	2010-04-27			ENSG00000107140	ENSG00000107140	2.7.12.1		11731	protein-coding gene	gene with protein product	"""testis-specific kinase-1"", ""testis specific kinase-1"""	601782				8537404	Standard	NM_006285		Approved		uc003zxa.3	Q15569	OTTHUMG00000019863	ENST00000336395.5:c.1104C>T	9.37:g.35608962C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_006285	Q8IXZ8	Silent	SNP	ENST00000336395.5	37	CCDS6580.1																																																																																			C|0.994;T|0.006	0.006	strong		0.607	TESK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052314.1	NM_006285	
FIBCD1	84929	hgsc.bcm.edu	37	9	133787225	133787225	+	Silent	SNP	A	A	G	rs6597650	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133787225A>G	ENST00000372338.4	-	5	1142	c.900T>C	c.(898-900)gaT>gaC	p.D300D	FIBCD1_ENST00000253018.4_Silent_p.D142D|FIBCD1_ENST00000372337.2_Silent_p.D142D|FIBCD1_ENST00000448616.1_Silent_p.D300D	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	300	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		CTCGGTACGCATCCCAGCCCC	0.672													G|||	3010	0.601038	0.8381	0.5965	5008	,	,		16495	0.6121		0.4046	False		,,,				2504	0.4744				p.D300D		Atlas-SNP	.											.	FIBCD1	34	.	0			c.T900C						PASS	.	G	,	3424,974		1338,748,113	47.0	39.0	42.0		900,900	-2.0	0.7	9	dbSNP_116	42	3425,5175		682,2061,1557	no	coding-synonymous,coding-synonymous	FIBCD1	NM_001145106.1,NM_032843.4	,	2020,2809,1670	GG,GA,AA		39.8256,22.1464,47.3073	,	300/462,300/462	133787225	6849,6149	2199	4300	6499	SO:0001819	synonymous_variant	84929	exon6			GTACGCATCCCAG	AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"""Fibrinogen C domain containing"""	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.900T>C	9.37:g.133787225A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	130	51	0.392308	NM_001145106	A3KFK0|Q6UXK6|Q96SJ7	Silent	SNP	ENST00000372338.4	37	CCDS6937.1	1262	0.5778388278388278	404	0.8211382113821138	185	0.511049723756906	362	0.6328671328671329	311	0.4102902374670185	G	3.545	-0.092788	0.07053	0.778536	0.398256	ENSG00000130720	ENST00000444139	.	.	.	5.06	-1.98	0.07480	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999850689	.	.	.	.	.	.	T	0.23655	-1.0182	3	.	.	.	.	1.5364	0.02546	0.2048:0.2805:0.3178:0.1969	rs6597650;rs59798032;rs6597650	.	.	.	T	254	.	.	M	-	2	0	FIBCD1	132777046	0.000000	0.05858	0.664000	0.29753	0.275000	0.26752	-1.838000	0.01687	-0.680000	0.05211	-1.535000	0.00915	ATG	A|0.442;G|0.558	0.558	strong		0.672	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843	
SLC28A2	9153	hgsc.bcm.edu	37	15	45556163	45556163	+	Silent	SNP	T	T	C	rs8023604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45556163T>C	ENST00000347644.3	+	6	596	c.531T>C	c.(529-531)ttT>ttC	p.F177F	CTD-2651B20.3_ENST00000560344.1_RNA|CTD-2651B20.3_ENST00000561404.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	177					nucleobase-containing compound metabolic process (GO:0006139)|purine nucleoside transmembrane transport (GO:0015860)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside:sodium symporter activity (GO:0005415)|purine nucleoside transmembrane transporter activity (GO:0015211)			NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1)	26		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)	Mercaptopurine(DB01033)	TGATCCCCTTTGCAGGAATCT	0.507													C|||	866	0.172923	0.5734	0.0533	5008	,	,		19479	0.0		0.002	False		,,,				2504	0.0706				p.F177F	NSCLC(92;493 1501 26361 28917 47116)	Atlas-SNP	.											.	SLC28A2	64	.	0			c.T531C						PASS	.	C		2273,2123	578.0+/-384.6	611,1051,536	196.0	159.0	171.0		531	-6.4	0.5	15	dbSNP_116	171	13,8583	818.5+/-406.9	0,13,4285	no	coding-synonymous	SLC28A2	NM_004212.3		611,1064,4821	CC,CT,TT		0.1512,48.2939,17.5954		177/659	45556163	2286,10706	2198	4298	6496	SO:0001819	synonymous_variant	9153	exon6			CCCCTTTGCAGGA	U84392	CCDS10121.1	15q15	2013-07-17	2013-07-17		ENSG00000137860	ENSG00000137860		"""Solute carriers"""	11002	protein-coding gene	gene with protein product		606208	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"""			9435697	Standard	NM_004212		Approved	CNT2, SPNT1, HCNT2, HsT17153	uc001zva.2	O43868	OTTHUMG00000131426	ENST00000347644.3:c.531T>C	15.37:g.45556163T>C		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	177	82	0.463277	NM_004212	A8K7F9|O43239|Q52LZ0	Silent	SNP	ENST00000347644.3	37	CCDS10121.1																																																																																			T|0.841;C|0.159	0.159	strong		0.507	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212	
C8orf74	203076	hgsc.bcm.edu	37	8	10555263	10555263	+	Missense_Mutation	SNP	C	C	G	rs147047803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10555263C>G	ENST00000304519.5	+	3	425	c.396C>G	c.(394-396)gaC>gaG	p.D132E	RP1L1_ENST00000329335.3_Intron	NM_001040032.1	NP_001035121	Q6P047	CH074_HUMAN	chromosome 8 open reading frame 74	132										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13				COAD - Colon adenocarcinoma(149;0.0811)		TGGGCCAGGACCAGCAGGTCG	0.622													C|||	11	0.00219649	0.0083	0.0	5008	,	,		17486	0.0		0.0	False		,,,				2504	0.0				p.D132E		Atlas-SNP	.											.	C8orf74	28	.	0			c.C396G						PASS	.	C	GLU/ASP	33,4233		0,33,2100	163.0	169.0	167.0		396	-3.2	0.2	8	dbSNP_134	167	0,8450		0,0,4225	yes	missense	C8orf74	NM_001040032.1	45	0,33,6325	GG,GC,CC		0.0,0.7736,0.2595	benign	132/295	10555263	33,12683	2133	4225	6358	SO:0001583	missense	203076	exon3			CCAGGACCAGCAG	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.396C>G	8.37:g.10555263C>G	ENSP00000307129:p.Asp132Glu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_001040032	A2RUD6	Missense_Mutation	SNP	ENST00000304519.5	37	CCDS47800.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	0.118	-1.129786	0.01756	0.007736	0.0	ENSG00000171060	ENST00000304519	T	0.28666	1.6	5.2	-3.25	0.05079	.	0.639609	0.15360	N	0.266446	T	0.08133	0.0203	N	0.16656	0.425	0.09310	N	1	B	0.14012	0.009	B	0.11329	0.006	T	0.22695	-1.0209	10	0.15499	T	0.54	.	2.1908	0.03898	0.1217:0.2888:0.3579:0.2316	.	132	Q6P047	CH074_HUMAN	E	132	ENSP00000307129:D132E	ENSP00000307129:D132E	D	+	3	2	C8orf74	10592673	0.006000	0.16342	0.207000	0.23584	0.043000	0.13939	-1.025000	0.03600	-0.299000	0.08909	-1.334000	0.01262	GAC	C|0.997;G|0.003	0.003	strong		0.622	C8orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375675.1	NM_001040032	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4448389	4448389	+	Missense_Mutation	SNP	G	G	T	rs72830101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4448389G>T	ENST00000254718.4	-	17	2548	c.2242C>A	c.(2242-2244)Cgc>Agc	p.R748S	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.R748S			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	748	Glu-rich.				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						tccccgtcgcgctcctcctcc	0.662													G|||	10	0.00199681	0.0	0.0043	5008	,	,		8617	0.0		0.007	False		,,,				2504	0.0				p.R748S		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C2242A						PASS	.	G	SER/ARG,SER/ARG	11,4391		0,11,2190	257.0	178.0	205.0		2242,2242	5.2	0.1	17	dbSNP_130	205	85,8503		1,83,4210	yes	missense,missense	MYBBP1A	NM_001105538.1,NM_014520.3	110,110	1,94,6400	TT,TG,GG		0.9898,0.2499,0.739	probably-damaging,probably-damaging	748/1333,748/1329	4448389	96,12894	2201	4294	6495	SO:0001583	missense	10514	exon17			CGTCGCGCTCCTC	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.2242C>A	17.37:g.4448389G>T	ENSP00000254718:p.Arg748Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	g	12.87	2.068082	0.36470	0.002499	0.009898	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.40756	1.02;1.02	5.22	5.22	0.72569	Armadillo-type fold (1);	0.309217	0.33401	N	0.004955	T	0.41488	0.1161	L	0.60455	1.87	0.09310	N	1	P;D	0.61697	0.506;0.99	B;P	0.55303	0.189;0.773	T	0.37454	-0.9705	10	0.21014	T	0.42	-13.6044	11.7659	0.51930	0.0:0.0:0.8245:0.1755	.	748;748	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	S	748	ENSP00000370968:R748S;ENSP00000254718:R748S	ENSP00000254718:R748S	R	-	1	0	MYBBP1A	4395138	0.003000	0.15002	0.081000	0.20488	0.383000	0.30230	0.387000	0.20718	2.606000	0.88127	0.542000	0.68232	CGC	G|0.995;T|0.005	0.005	strong		0.662	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
ASB16	92591	hgsc.bcm.edu	37	17	42254165	42254165	+	Missense_Mutation	SNP	A	A	G	rs146134954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42254165A>G	ENST00000293414.1	+	3	713	c.629A>G	c.(628-630)cAg>cGg	p.Q210R	ASB16-AS1_ENST00000591166.1_RNA|ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000585457.1_RNA|ASB16-AS1_ENST00000592897.1_RNA	NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	210					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GGCGAGAGCCAGGAGACGCCC	0.672													A|||	65	0.0129792	0.0477	0.0029	5008	,	,		13770	0.0		0.0	False		,,,				2504	0.0				p.Q210R		Atlas-SNP	.											.	ASB16	34	.	0			c.A629G						PASS	.	A	ARG/GLN,	154,4252	103.4+/-141.9	4,146,2053	52.0	51.0	52.0		629,456	4.7	0.1	17	dbSNP_134	52	2,8598	2.2+/-6.3	0,2,4298	yes	missense,coding-synonymous	ASB16,C17orf65	NM_080863.4,NM_178542.3	43,	4,148,6351	GG,GA,AA		0.0233,3.4952,1.1994	benign,	210/454,152/194	42254165	156,12850	2203	4300	6503	SO:0001583	missense	92591	exon3			AGAGCCAGGAGAC	AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"""Ankyrin repeat domain containing"""	19768	protein-coding gene	gene with protein product		615056	"""ankyrin repeat and SOCS box-containing 16"""			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.629A>G	17.37:g.42254165A>G	ENSP00000293414:p.Gln210Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	19	0.316667	NM_080863	B2RBC0|Q8WXK0	Missense_Mutation	SNP	ENST00000293414.1	37	CCDS11478.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	A	2.058	-0.416098	0.04766	0.034952	2.33E-4	ENSG00000161664	ENST00000293414	T	0.63913	-0.07	4.73	4.73	0.59995	Ankyrin repeat-containing domain (3);	0.305652	0.34067	N	0.004299	T	0.05456	0.0144	N	0.16602	0.42	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04650	-1.0936	10	0.10902	T	0.67	-8.7467	5.8244	0.18546	0.8141:0.0:0.1859:0.0	.	210	Q96NS5	ASB16_HUMAN	R	210	ENSP00000293414:Q210R	ENSP00000293414:Q210R	Q	+	2	0	ASB16	39609691	0.009000	0.17119	0.120000	0.21714	0.087000	0.18053	1.072000	0.30678	1.985000	0.57927	0.374000	0.22700	CAG	A|0.987;G|0.013	0.013	strong		0.672	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1		
GGCX	2677	hgsc.bcm.edu	37	2	85780131	85780131	+	Silent	SNP	G	G	A	rs2592551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85780131G>A	ENST00000233838.4	-	9	1298	c.1218C>T	c.(1216-1218)cgC>cgT	p.R406R	GGCX_ENST00000473665.1_5'UTR|GGCX_ENST00000430215.3_Silent_p.R349R	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	406					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)	p.R406R(1)		endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	GCTGGTGGGAGCGGGAGTGCA	0.537													G|||	1432	0.285942	0.3903	0.2219	5008	,	,		19279	0.3095		0.3111	False		,,,				2504	0.1401				p.R406R		Atlas-SNP	.											GGCX,NS,carcinoma,0,1	GGCX	44	1	1	Substitution - coding silent(1)	stomach(1)	c.C1218T						PASS	.	G	,	1547,2859	486.9+/-360.8	280,987,936	188.0	165.0	173.0		1218,1047	4.7	1.0	2	dbSNP_100	173	2388,6212	396.6+/-345.4	334,1720,2246	no	coding-synonymous,coding-synonymous	GGCX	NM_000821.5,NM_001142269.2	,	614,2707,3182	AA,AG,GG		27.7674,35.1112,30.2553	,	406/759,349/702	85780131	3935,9071	2203	4300	6503	SO:0001819	synonymous_variant	2677	exon9			GTGGGAGCGGGAG		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.1218C>T	2.37:g.85780131G>A		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	305	140	0.459016	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Silent	SNP	ENST00000233838.4	37	CCDS1978.1																																																																																			G|0.693;A|0.307	0.307	strong		0.537	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
TTC21B	79809	hgsc.bcm.edu	37	2	166758389	166758389	+	Missense_Mutation	SNP	C	C	T	rs76726265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166758389C>T	ENST00000243344.7	-	20	2737	c.2600G>A	c.(2599-2601)cGt>cAt	p.R867H		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	867			R -> C (in JBTS11; functionally null mutation in vitro). {ECO:0000269|PubMed:21258341}.|R -> H (found in a patient with Meckel- Gruber syndrome also carrying a homozygous variant in CC2D2A; functionally null mutation in vitro; dbSNP:rs76726265). {ECO:0000269|PubMed:21258341}.		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						CATCTGAACACGTTTTAGTAC	0.378													C|||	6	0.00119808	0.0038	0.0014	5008	,	,		14632	0.0		0.0	False		,,,				2504	0.0				p.R867H		Atlas-SNP	.											TTC21B,NS,carcinoma,-1,1	TTC21B	130	1	0			c.G2600A						PASS	.	C	HIS/ARG	25,4381	31.7+/-61.6	0,25,2178	59.0	55.0	56.0		2600	5.7	1.0	2	dbSNP_131	56	0,8600		0,0,4300	yes	missense	TTC21B	NM_024753.3	29	0,25,6478	TT,TC,CC		0.0,0.5674,0.1922	probably-damaging	867/1317	166758389	25,12981	2203	4300	6503	SO:0001583	missense	79809	exon20			TGAACACGTTTTA	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.2600G>A	2.37:g.166758389C>T	ENSP00000243344:p.Arg867His	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	181	80	0.441989	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	37	CCDS33315.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	34	5.320668	0.95682	0.005674	0.0	ENSG00000123607	ENST00000243344	T	0.55234	0.53	5.7	5.7	0.88788	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.68054	0.2959	M	0.75884	2.315	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.73297	-0.4027	10	0.62326	D	0.03	-13.8163	19.8381	0.96666	0.0:1.0:0.0:0.0	.	867	Q7Z4L5	TT21B_HUMAN	H	867	ENSP00000243344:R867H	ENSP00000243344:R867H	R	-	2	0	TTC21B	166466635	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.061000	0.71148	2.692000	0.91855	0.650000	0.86243	CGT	C|0.998;T|0.002	0.002	strong		0.378	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	
ZNF519	162655	hgsc.bcm.edu	37	18	14106039	14106039	+	Missense_Mutation	SNP	T	T	C	rs62086326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:14106039T>C	ENST00000590202.1	-	3	652	c.500A>G	c.(499-501)aAt>aGt	p.N167S	RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589203.1_Intron|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	48	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	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	
SLC35D1	23169	hgsc.bcm.edu	37	1	67518534	67518534	+	Missense_Mutation	SNP	C	C	T	rs10157422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:67518534C>T	ENST00000235345.5	-	3	329	c.244G>A	c.(244-246)Gcc>Acc	p.A82T	SLC35D1_ENST00000506472.2_Missense_Mutation_p.A3T	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	82			A -> T (in dbSNP:rs10157422).		carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						GCCACTGTGGCCACCATCTGT	0.433													C|||	522	0.104233	0.267	0.062	5008	,	,		18937	0.0		0.0577	False		,,,				2504	0.0695				p.A82T		Atlas-SNP	.											SLC35D1,NS,carcinoma,+2,1	SLC35D1	22	1	0			c.G244A						scavenged	.	C	THR/ALA	1031,3375	381.1+/-324.0	102,827,1274	136.0	128.0	131.0		244	5.1	1.0	1	dbSNP_119	131	567,8033	153.0+/-207.5	11,545,3744	yes	missense	SLC35D1	NM_015139.2	58	113,1372,5018	TT,TC,CC		6.593,23.3999,12.2866	possibly-damaging	82/356	67518534	1598,11408	2203	4300	6503	SO:0001583	missense	23169	exon3			CTGTGGCCACCAT	AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"""Solute carriers"""	20800	protein-coding gene	gene with protein product		610804	"""solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"""			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.244G>A	1.37:g.67518534C>T	ENSP00000235345:p.Ala82Thr	Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_015139	A8K185|B7Z3X2|Q52LU5|Q92548	Missense_Mutation	SNP	ENST00000235345.5	37	CCDS636.1	189	0.08653846153846154	119	0.241869918699187	26	0.0718232044198895	0	0.0	44	0.05804749340369393	C	29.6	5.022245	0.93462	0.233999	0.06593	ENSG00000116704	ENST00000235345;ENST00000506472	T;T	0.65178	-0.14;0.28	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.43523	0.1251	M	0.62723	1.935	0.09310	P	0.9999999999186048	B;B	0.33212	0.103;0.402	B;B	0.29942	0.061;0.109	T	0.48514	-0.9029	9	0.14656	T	0.56	-31.2119	17.1609	0.86803	0.0:1.0:0.0:0.0	rs10157422;rs52821602;rs57934810;rs10157422	3;82	B7Z3X2;Q9NTN3	.;S35D1_HUMAN	T	82;3	ENSP00000235345:A82T;ENSP00000445189:A3T	ENSP00000235345:A82T	A	-	1	0	SLC35D1	67291122	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.390000	0.79816	2.342000	0.79632	0.561000	0.74099	GCC	C|0.884;T|0.116	0.116	strong		0.433	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139	
MYOZ3	91977	hgsc.bcm.edu	37	5	150056296	150056296	+	Missense_Mutation	SNP	C	C	T	rs57761602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150056296C>T	ENST00000520112.1	+	2	474	c.364C>T	c.(364-366)Cgt>Tgt	p.R122C	MYOZ3_ENST00000297130.4_Silent_p.L205L|MYOZ3_ENST00000456566.2_3'UTR|MYOZ3_ENST00000517768.1_Silent_p.L205L					myozenin 3											large_intestine(2)|lung(1)|skin(2)	5		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGGACCCCTCGTGGGGGGCA	0.622													C|||	576	0.115016	0.3434	0.0202	5008	,	,		14340	0.0853		0.002	False		,,,				2504	0.0204				p.L205L		Atlas-SNP	.											MYOZ3,colon,carcinoma,0,1	MYOZ3	21	1	0			c.C615T						PASS	.	C	,	1240,3166	403.5+/-332.8	166,908,1129	61.0	72.0	68.0		615,615	-3.6	0.0	5	dbSNP_129	68	23,8577	16.6+/-54.9	0,23,4277	no	coding-synonymous,coding-synonymous	MYOZ3	NM_001122853.1,NM_133371.3	,	166,931,5406	TT,TC,CC		0.2674,28.1434,9.7109	,	205/252,205/252	150056296	1263,11743	2203	4300	6503	SO:0001583	missense	91977	exon7			ACCCCTCGTGGGG	AF480443	CCDS4309.1	5q33.2	2008-07-18			ENSG00000164591	ENSG00000164591			18565	protein-coding gene	gene with protein product	"""calsarcin 3"", ""FATZ related protein 3"""	610735				11842093	Standard	NM_001122853		Approved	CS-3, CS3, FRP3	uc003lsr.3	Q8TDC0	OTTHUMG00000130077	ENST00000520112.1:c.364C>T	5.37:g.150056296C>T	ENSP00000429439:p.Arg122Cys	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_001122853		Silent	SNP	ENST00000520112.1	37		230	0.10531135531135531	169	0.3434959349593496	9	0.024861878453038673	52	0.09090909090909091	0	0.0	C	2.543	-0.305838	0.05458	0.281434	0.002674	ENSG00000164591	ENST00000520112	.	.	.	5.2	-3.63	0.04529	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.33111	-0.9881	4	0.87932	D	0	-10.7574	2.871	0.05617	0.1018:0.218:0.4072:0.273	rs57761602;rs61745516	.	.	.	C	122	.	ENSP00000429439:R122C	R	+	1	0	MYOZ3	150036489	0.000000	0.05858	0.018000	0.16275	0.013000	0.08279	-0.196000	0.09532	-1.205000	0.02645	-0.136000	0.14681	CGT	C|0.902;T|0.098	0.098	strong		0.622	MYOZ3-007	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000374429.1	NM_001122853	
SLC35C1	55343	hgsc.bcm.edu	37	11	45827783	45827783	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:45827783A>G	ENST00000314134.3	+	1	1827	c.431A>G	c.(430-432)aAt>aGt	p.N144S	SLC35C1_ENST00000442528.2_Missense_Mutation_p.N131S|SLC35C1_ENST00000456334.1_Missense_Mutation_p.N131S	NM_018389.4	NP_060859.4	Q96A29	FUCT1_HUMAN	solute carrier family 35 (GDP-fucose transporter), member C1	144					carbohydrate transport (GO:0008643)|lipid glycosylation (GO:0030259)|negative regulation of Notch signaling pathway (GO:0045746)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10				GBM - Glioblastoma multiforme(35;0.227)		GCCTTCTACAATGTGGGCCGC	0.587																																					p.N144S		Atlas-SNP	.											.	SLC35C1	23	.	0			c.A431G						PASS	.						137.0	96.0	110.0					11																	45827783		2203	4299	6502	SO:0001583	missense	55343	exon1			TCTACAATGTGGG		CCDS7914.1, CCDS44575.1	11p11.2	2014-09-17	2013-07-17			ENSG00000181830		"""Solute carriers"""	20197	protein-coding gene	gene with protein product		605881	"""solute carrier family 35, member C1"""			11326279, 11326280	Standard	NM_018389		Approved	FUCT1, FLJ11320	uc010rgm.2	Q96A29		ENST00000314134.3:c.431A>G	11.37:g.45827783A>G	ENSP00000313318:p.Asn144Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	77	4	0.0519481	NM_018389	B2RDB2|Q9BV76|Q9NUJ8	Missense_Mutation	SNP	ENST00000314134.3	37	CCDS7914.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.323167	0.41096	.	.	ENSG00000181830	ENST00000442528;ENST00000456334;ENST00000530670;ENST00000314134;ENST00000530471;ENST00000540685	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	4.64	4.64	0.57946	Drug/metabolite transporter (1);	0.049836	0.85682	D	0.000000	T	0.28732	0.0712	L	0.39898	1.24	0.42596	D	0.993269	B	0.22909	0.077	B	0.26614	0.071	T	0.08289	-1.0729	10	0.23302	T	0.38	-24.5504	10.2877	0.43577	0.8343:0.1656:0.0:0.0	.	144	Q96A29	FUCT1_HUMAN	S	131;131;65;144;131;144	ENSP00000412408:N131S;ENSP00000399779:N131S;ENSP00000313318:N144S;ENSP00000432669:N131S	ENSP00000313318:N144S	N	+	2	0	SLC35C1	45784359	0.978000	0.34361	1.000000	0.80357	0.992000	0.81027	4.671000	0.61590	1.738000	0.51689	0.460000	0.39030	AAT	.	.	none		0.587	SLC35C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390139.1	NM_018389	
ETNPPL	64850	hgsc.bcm.edu	37	4	109674116	109674116	+	Missense_Mutation	SNP	A	A	G	rs1377210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:109674116A>G	ENST00000296486.3	-	6	707	c.553T>C	c.(553-555)Tca>Cca	p.S185P	ETNPPL_ENST00000512646.1_Missense_Mutation_p.S127P|ETNPPL_ENST00000411864.2_Missense_Mutation_p.S179P|ETNPPL_ENST00000510706.1_Missense_Mutation_p.S145P	NM_001146590.1|NM_031279.3	NP_001140062.1|NP_112569.2	Q8TBG4	AT2L1_HUMAN	ethanolamine-phosphate phospho-lyase	185			S -> P (in dbSNP:rs1377210).			mitochondrion (GO:0005739)	ethanolamine-phosphate phospho-lyase activity (GO:0050459)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)										GCACTGGCTGAGTCTGCATGG	0.378													G|||	1329	0.265375	0.2988	0.1499	5008	,	,		19676	0.498		0.0805	False		,,,				2504	0.2526				p.S185P		Atlas-SNP	.											.	AGXT2L1	67	.	0			c.T553C	GRCh37	CM064956	AGXT2L1	M	rs1377210	PASS	.	G	PRO/SER,PRO/SER,PRO/SER	1204,3202	709.0+/-407.7	164,876,1163	172.0	162.0	165.0		535,379,553	4.6	0.8	4	dbSNP_88	165	757,7843	784.9+/-407.6	36,685,3579	yes	missense,missense,missense	AGXT2L1	NM_001146590.1,NM_001146627.1,NM_031279.3	74,74,74	200,1561,4742	GG,GA,AA		8.8023,27.3264,15.0777	benign,benign,benign	179/494,127/442,185/500	109674116	1961,11045	2203	4300	6503	SO:0001583	missense	64850	exon6			TGGCTGAGTCTGC	AJ298293	CCDS3682.1, CCDS54792.1, CCDS54793.1	4q25	2013-06-12	2013-06-12	2013-06-12	ENSG00000164089	ENSG00000164089	4.2.3.2		14404	protein-coding gene	gene with protein product		614682	"""alanine-glyoxylate aminotransferase 2-like 1"""	AGXT2L1		7592550, 22241472	Standard	NM_031279		Approved		uc003hzc.3	Q8TBG4	OTTHUMG00000161036	ENST00000296486.3:c.553T>C	4.37:g.109674116A>G	ENSP00000296486:p.Ser185Pro	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_031279	B7Z1Y0|E9PBY0|Q9H174	Missense_Mutation	SNP	ENST00000296486.3	37	CCDS3682.1	562	0.2573260073260073	158	0.32113821138211385	44	0.12154696132596685	298	0.5209790209790209	62	0.08179419525065963	G	0.840	-0.742376	0.03088	0.273264	0.088023	ENSG00000164089	ENST00000296486;ENST00000411864;ENST00000512646;ENST00000510706	D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16	5.46	4.61	0.57282	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.048916	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00637	-1.305	0.44309	P	0.0028129999999999544	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.37865	-0.9687	8	.	.	.	-5.6589	10.6615	0.45704	0.0686:0.0:0.7992:0.1322	rs1377210;rs3733621;rs52805159;rs60825583;rs1377210	127;179;185	E9PBY0;Q8TBG4-2;Q8TBG4	.;.;AT2L1_HUMAN	P	185;179;127;145	ENSP00000296486:S185P;ENSP00000392269:S179P;ENSP00000427065:S127P;ENSP00000423240:S145P	.	S	-	1	0	AGXT2L1	109893565	1.000000	0.71417	0.761000	0.31378	0.203000	0.24098	4.751000	0.62169	0.665000	0.31066	-0.119000	0.15052	TCA	A|0.791;G|0.209	0.209	strong		0.378	ETNPPL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363508.1	NM_031279	
MUC4	4585	hgsc.bcm.edu	37	3	195508382	195508382	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508382G>A	ENST00000463781.3	-	2	10528	c.10069C>T	c.(10069-10071)Cac>Tac	p.H3357Y	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3357Y	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)		GGGGTGGCGTGACCTGTGGAT	0.602																																					p.H3357Y		Atlas-SNP	.											.	MUC4	1505	.	0			c.C10069T						PASS	.						38.0	30.0	32.0					3																	195508382		689	1583	2272	SO:0001583	missense	4585	exon2			TGGCGTGACCTGT	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.10069C>T	3.37:g.195508382G>A	ENSP00000417498:p.His3357Tyr	Somatic	417	0	0		WXS	Illumina HiSeq	Phase_I	354	69	0.194915	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	0.904	-0.721432	0.03182	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.51;1.49	1.03	-2.05	0.07321	.	.	.	.	.	T	0.13884	0.0336	N	0.14661	0.345	0.09310	N	1	B	0.15141	0.012	B	0.01281	0.0	T	0.29518	-1.0009	8	.	.	.	.	5.4087	0.16336	0.0:0.0:0.5637:0.4363	.	3229	E7ESK3	.	Y	3357	ENSP00000417498:H3357Y;ENSP00000420243:H3357Y	.	H	-	1	0	MUC4	196993161	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-2.033000	0.01425	-0.784000	0.04528	0.089000	0.15464	CAC	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LRTOMT	220074	hgsc.bcm.edu	37	11	71806515	71806515	+	Silent	SNP	A	A	G	rs150245488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71806515A>G	ENST00000289488.2	+	6	906	c.528A>G	c.(526-528)aaA>aaG	p.K176K	LRTOMT_ENST00000539587.1_Missense_Mutation_p.N42S|LAMTOR1_ENST00000545249.1_Intron|LRTOMT_ENST00000419228.1_Intron|LRTOMT_ENST00000423494.2_Silent_p.K158K|LRTOMT_ENST00000324866.7_3'UTR|LRTOMT_ENST00000447974.1_Intron|LAMTOR1_ENST00000539797.1_5'Flank|LAMTOR1_ENST00000535107.1_Intron|LRTOMT_ENST00000538478.1_Silent_p.K176K|LRTOMT_ENST00000539271.1_Missense_Mutation_p.N42S|LRTOMT_ENST00000307198.7_Intron|LRTOMT_ENST00000541614.1_Intron|LRTOMT_ENST00000439209.1_Intron|LRTOMT_ENST00000440313.2_Intron|LRTOMT_ENST00000435085.1_Intron	NM_001271471.2|NM_145309.5	NP_001258400.1|NP_660352.1	Q96E66	LRC51_HUMAN	leucine rich transmembrane and O-methyltransferase domain containing	176						cytoplasm (GO:0005737)				large_intestine(2)|lung(1)|ovary(1)	4						AAGTCTGGAAACGCATGAACA	0.537													A|||	14	0.00279553	0.0106	0.0	5008	,	,		20529	0.0		0.0	False		,,,				2504	0.0				p.K176K		Atlas-SNP	.											.	LRTOMT	20	.	0			c.A528G						PASS	.	A	,,,	72,4328	64.7+/-102.0	1,70,2129	96.0	69.0	78.0		,,474,528	0.6	1.0	11	dbSNP_134	78	0,8586		0,0,4293	no	intron,intron,coding-synonymous,coding-synonymous	LRTOMT	NM_001145307.2,NM_001145308.2,NM_001205138.1,NM_145309.3	,,,	1,70,6422	GG,GA,AA		0.0,1.6364,0.5544	,,,	,,158/175,176/193	71806515	72,12914	2200	4293	6493	SO:0001819	synonymous_variant	220074	exon6			CTGGAAACGCATG		CCDS8208.1, CCDS44667.1, CCDS44668.1, CCDS55778.1, CCDS59227.1	11q13.4	2014-09-05	2013-08-19	2008-11-27	ENSG00000184154	ENSG00000184154			25033	protein-coding gene	gene with protein product		612414	"""leucine rich repeat containing 51"", ""deafness, autosomal recessive 63"""	LRRC51, DFNB63		18794526, 18953341	Standard	NM_145309		Approved	COMT2, CFAP111	uc010rqw.2	Q8WZ04	OTTHUMG00000154887	ENST00000289488.2:c.528A>G	11.37:g.71806515A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	149	81	0.543624	NM_145309	B2R7X1|B6CZ35|B6CZ36|B6CZ37|B6CZ38|B6CZ39|B7Z5I4	Silent	SNP	ENST00000289488.2	37	CCDS8208.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	14.26	2.483004	0.44147	0.016364	0.0	ENSG00000184154	ENST00000539271;ENST00000539587	.	.	.	5.9	0.652	0.17823	.	.	.	.	.	T	0.47395	0.1443	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58446	-0.7635	5	0.87932	D	0	-16.0144	8.9883	0.36008	0.4707:0.0:0.5292:0.0	.	.	.	.	S	42	.	ENSP00000442267:N42S	N	+	2	0	LRTOMT	71484163	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.340000	0.19892	0.072000	0.16694	0.496000	0.49642	AAC	A|0.995;G|0.005	0.005	strong		0.537	LRTOMT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337504.1	NM_145309	
GPATCH1	55094	hgsc.bcm.edu	37	19	33579128	33579128	+	Silent	SNP	T	T	C	rs7259333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33579128T>C	ENST00000170564.2	+	2	476	c.162T>C	c.(160-162)agT>agC	p.S54S		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	54					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)					GGGCCTTTAGTGGAGGTTTCT	0.363													C|||	2674	0.533946	0.8018	0.2867	5008	,	,		13444	0.5099		0.2416	False		,,,				2504	0.6728				p.S54S	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.T162C						PASS	.	C		3204,1202	416.7+/-337.7	1159,886,158	96.0	101.0	99.0		162	-4.0	0.7	19	dbSNP_116	99	2313,6287	705.1+/-405.5	284,1745,2271	no	coding-synonymous	GPATCH1	NM_018025.2		1443,2631,2429	CC,CT,TT		26.8953,27.281,42.4189		54/932	33579128	5517,7489	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon2			CTTTAGTGGAGGT	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.162T>C	19.37:g.33579128T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			T|0.549;C|0.451	0.451	strong		0.363	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
H6PD	9563	hgsc.bcm.edu	37	1	9324670	9324670	+	Silent	SNP	A	A	G	rs9434743	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	143	0	0		WXS	Illumina HiSeq	Phase_I	157	65	0.414013	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	
CEP192	55125	hgsc.bcm.edu	37	18	13055915	13055915	+	Missense_Mutation	SNP	A	A	C	rs11080623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13055915A>C	ENST00000325971.8	+	17	3131	c.1538A>C	c.(1537-1539)cAg>cCg	p.Q513P	CEP192_ENST00000506447.1_Missense_Mutation_p.Q1109P|CEP192_ENST00000430049.2_Missense_Mutation_p.Q634P			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	513			Q -> P (in dbSNP:rs11080623).		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TCTATTATCCAGAATAACTCT	0.393													A|||	39	0.00778754	0.0008	0.0187	5008	,	,		21179	0.0		0.0239	False		,,,				2504	0.001				p.Q1109P		Atlas-SNP	.											.	CEP192	340	.	0			c.A3326C						PASS	.	A	PRO/GLN	22,4384	28.1+/-56.4	0,22,2181	60.0	59.0	59.0		3326	-0.5	0.1	18	dbSNP_120	59	276,8324	103.6+/-164.7	3,270,4027	yes	missense	CEP192	NM_032142.3	76	3,292,6208	CC,CA,AA		3.2093,0.4993,2.2913	benign	1109/2538	13055915	298,12708	2203	4300	6503	SO:0001583	missense	55125	exon19			TTATCCAGAATAA	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.1538A>C	18.37:g.13055915A>C	ENSP00000317156:p.Gln513Pro	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		31	0.014194139194139194	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	22	0.029023746701846966	A	9.745	1.165868	0.21538	0.004993	0.032093	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.24538	1.85;1.85;1.85	4.41	-0.462	0.12168	.	0.484808	0.17160	N	0.184713	T	0.06234	0.0161	L	0.47716	1.5	0.09310	N	1	B;B;B	0.17465	0.011;0.011;0.022	B;B;B	0.15484	0.007;0.007;0.013	T	0.19811	-1.0294	10	0.23891	T	0.37	-1.5367	7.8859	0.29651	0.5467:0.3343:0.0:0.119	rs11080623;rs52829180;rs11080623	634;1109;513	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	P	1109;513;513;634	ENSP00000427550:Q1109P;ENSP00000317156:Q513P;ENSP00000389190:Q634P	ENSP00000317156:Q513P	Q	+	2	0	CEP192	13045915	0.013000	0.17824	0.147000	0.22382	0.076000	0.17211	1.283000	0.33237	0.132000	0.18615	0.460000	0.39030	CAG	A|0.980;C|0.020	0.020	strong		0.393	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
TARS2	80222	hgsc.bcm.edu	37	1	150470182	150470182	+	Silent	SNP	A	A	G	rs115388015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150470182A>G	ENST00000369064.3	+	10	1231	c.1197A>G	c.(1195-1197)acA>acG	p.T399T	TARS2_ENST00000369054.2_Silent_p.T269T|TARS2_ENST00000463555.1_3'UTR|TARS2_ENST00000438568.2_3'UTR|TARS2_ENST00000606933.1_Silent_p.T317T	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	399					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	GGCATATCACAGATACACTCG	0.512													A|||	83	0.0165735	0.059	0.0072	5008	,	,		16357	0.0		0.0	False		,,,				2504	0.0				p.T399T		Atlas-SNP	.											.	TARS2	91	.	0			c.A1197G						PASS	.	A		210,4196	128.6+/-165.4	9,192,2002	56.0	49.0	51.0		1197	-0.3	0.0	1	dbSNP_132	51	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	TARS2	NM_025150.3		9,195,6299	GG,GA,AA		0.0349,4.7662,1.6377		399/719	150470182	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	80222	exon10			TATCACAGATACA	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	30740	protein-coding gene	gene with protein product	"""threonine tRNA ligase 2, mitochondrial"""	612805	"""threonyl-tRNA synthetase-like 1"""	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.1197A>G	1.37:g.150470182A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_025150	Q53GW7|Q96I50|Q9H9V2	Silent	SNP	ENST00000369064.3	37	CCDS952.1																																																																																			A|0.981;G|0.019	0.019	strong		0.512	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150	
MMS22L	253714	hgsc.bcm.edu	37	6	97613163	97613163	+	Silent	SNP	T	T	C	rs1209290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:97613163T>C	ENST00000275053.4	-	21	3445	c.3180A>G	c.(3178-3180)ccA>ccG	p.P1060P	MMS22L_ENST00000369251.2_Silent_p.P1020P	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1060					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						ATGATATTGGTGGAATAGTGG	0.353													C|||	2558	0.510783	0.7209	0.4078	5008	,	,		16517	0.246		0.497	False		,,,				2504	0.5869				p.P1060P		Atlas-SNP	.											.	MMS22L	102	.	0			c.A3180G						PASS	.	C		2983,1423	464.9+/-354.0	1004,975,224	107.0	109.0	109.0		3180	-3.8	0.0	6	dbSNP_87	109	4410,4190	568.3+/-389.0	1135,2140,1025	no	coding-synonymous	MMS22L	NM_198468.2		2139,3115,1249	CC,CT,TT		48.7209,32.2969,43.157		1060/1244	97613163	7393,5613	2203	4300	6503	SO:0001819	synonymous_variant	253714	exon21			TATTGGTGGAATA		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"""chromosome 6 open reading frame 167"""	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3180A>G	6.37:g.97613163T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Silent	SNP	ENST00000275053.4	37	CCDS5039.1																																																																																			T|0.475;C|0.525	0.525	strong		0.353	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468	
MUC4	4585	hgsc.bcm.edu	37	3	195513468	195513468	+	Missense_Mutation	SNP	G	G	C	rs76596008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513468G>C	ENST00000463781.3	-	2	5442	c.4983C>G	c.(4981-4983)caC>caG	p.H1661Q	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H1661Q	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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.H1661Q(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)		GAGGGGTGGCGTGACCTGTGG	0.587																																					p.H1661Q		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	kidney(1)|endometrium(1)	c.C4983G						scavenged	.						26.0	31.0	30.0					3																	195513468		688	1577	2265	SO:0001583	missense	4585	exon2			GGTGGCGTGACCT	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.4983C>G	3.37:g.195513468G>C	ENSP00000417498:p.His1661Gln	Somatic	601	2	0.00332779		WXS	Illumina HiSeq	Phase_I	627	8	0.0127592	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	.	.	.	.	.	.	.	.	.	.	-	3.800	-0.041898	0.07452	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28255	1.66;1.62	0.595	-0.863	0.10669	.	.	.	.	.	T	0.16685	0.0401	N	0.02539	-0.55	0.09310	N	1	P	0.49358	0.923	P	0.53518	0.728	T	0.14868	-1.0457	8	.	.	.	.	5.1757	0.15133	0.2702:0.0:0.7298:0.0	.	1661	E7ESK3	.	Q	1661	ENSP00000417498:H1661Q;ENSP00000420243:H1661Q	.	H	-	3	2	MUC4	196997863	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	0.163000	0.16520	-0.313000	0.08728	0.089000	0.15464	CAC	A|0.004;C|0.007;G|0.989	0.007	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NEU2	4759	hgsc.bcm.edu	37	2	233899148	233899148	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233899148T>C	ENST00000233840.3	+	2	524	c.524T>C	c.(523-525)gTg>gCg	p.V175A		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	175					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	CGGAGCCTGGTGGTGCCCGCC	0.657																																					p.V175A		Atlas-SNP	.											.	NEU2	42	.	0			c.T524C						PASS	.																																			SO:0001583	missense	4759	exon2			GCCTGGTGGTGCC	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"""N-acetyl-alpha-neuraminidase 2"""	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.524T>C	2.37:g.233899148T>C	ENSP00000233840:p.Val175Ala	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	37	CCDS2501.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.120495	0.77323	.	.	ENSG00000115488	ENST00000233840	D	0.85955	-2.05	4.88	4.88	0.63580	Neuraminidase (2);	0.234313	0.29707	N	0.011404	D	0.90113	0.6911	L	0.60455	1.87	0.38849	D	0.956227	D	0.65815	0.995	D	0.70487	0.969	D	0.91831	0.5475	10	0.87932	D	0	-13.5728	13.6972	0.62587	0.0:0.0:0.0:1.0	.	175	Q9Y3R4	NEUR2_HUMAN	A	175	ENSP00000233840:V175A	ENSP00000233840:V175A	V	+	2	0	NEU2	233607392	1.000000	0.71417	0.994000	0.49952	0.610000	0.37248	7.783000	0.85696	1.821000	0.53095	0.459000	0.35465	GTG	.	.	none		0.657	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383	
ADAM32	203102	hgsc.bcm.edu	37	8	39141120	39141120	+	Missense_Mutation	SNP	C	C	A	rs28705715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39141120C>A	ENST00000379907.4	+	24	2461	c.2334C>A	c.(2332-2334)gaC>gaA	p.D778E	ADAM32_ENST00000524303.1_3'UTR|ADAM32_ENST00000437682.2_Missense_Mutation_p.D679E|ADAM32_ENST00000519315.1_Missense_Mutation_p.D620E	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	778			D -> E (in dbSNP:rs28705715).			integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			AATCACAGGACAGTACCCAAA	0.269													A|||	648	0.129393	0.4357	0.0375	5008	,	,		14029	0.0377		0.006	False		,,,				2504	0.002				p.D778E		Atlas-SNP	.											.	ADAM32	70	.	0			c.C2334A						PASS	.	A	GLU/ASP	1238,2366		234,770,798	67.0	69.0	69.0		2334	2.8	0.2	8	dbSNP_125	69	32,8104		1,30,4037	yes	missense	ADAM32	NM_145004.5	45	235,800,4835	AA,AC,CC		0.3933,34.3507,10.8177	benign	778/788	39141120	1270,10470	1802	4068	5870	SO:0001583	missense	203102	exon24			ACAGGACAGTACC	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.2334C>A	8.37:g.39141120C>A	ENSP00000369238:p.Asp778Glu	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	195	193	0.989744	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	37	CCDS47846.1	236	0.10805860805860806	201	0.40853658536585363	14	0.03867403314917127	18	0.03146853146853147	3	0.00395778364116095	A	1.791	-0.479607	0.04383	0.343507	0.003933	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907	D;D;D	0.87256	-2.18;-2.23;-2.18	3.99	2.85	0.33270	.	.	.	.	.	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	0.16541	-1.0399	8	0.02654	T	1	.	4.1598	0.10278	0.6831:0.2098:0.1071:0.0	rs28705715	679;150;620;778	E7EPX8;Q6ZP86;E7ER82;Q8TC27	.;.;.;ADA32_HUMAN	E	679;620;778	ENSP00000405978:D679E;ENSP00000429422:D620E;ENSP00000369238:D778E	ENSP00000369238:D778E	D	+	3	2	ADAM32	39260277	0.000000	0.05858	0.152000	0.22495	0.456000	0.32438	-0.152000	0.10159	0.373000	0.24621	-0.256000	0.11100	GAC	C|0.914;A|0.086	0.086	strong		0.269	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
FPGT	8790	hgsc.bcm.edu	37	1	74670277	74670277	+	Silent	SNP	G	G	A	rs139749795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:74670277G>A	ENST00000609362.1	+	4	583	c.546G>A	c.(544-546)agG>agA	p.R182R	FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000370894.5_Intron|FPGT_ENST00000534056.1_Intron|FPGT_ENST00000524915.1_Intron|FPGT_ENST00000467578.2_3'UTR|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT_ENST00000370898.3_Silent_p.R195R|FPGT-TNNI3K_ENST00000557284.2_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	182					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)	p.R182R(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						AGTTTATTAGGTTTGACAAAC	0.353													G|||	15	0.00299521	0.0113	0.0	5008	,	,		17320	0.0		0.0	False		,,,				2504	0.0				p.R182R		Atlas-SNP	.											FPGT,NS,carcinoma,0,1	FPGT	77	1	1	Substitution - coding silent(1)	lung(1)	c.G546A						PASS	.	G	,,,,	49,4357	51.6+/-87.1	2,45,2156	113.0	111.0	111.0		,,,,546	-11.1	0.0	1	dbSNP_134	111	0,8600		0,0,4300	no	intron,intron,intron,intron,coding-synonymous	FPGT,FPGT-TNNI3K	NM_001112808.2,NM_001199327.1,NM_001199328.1,NM_001199329.1,NM_003838.3	,,,,	2,45,6456	AA,AG,GG		0.0,1.1121,0.3767	,,,,	,,,,182/595	74670277	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	8790	exon4			TATTAGGTTTGAC	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.546G>A	1.37:g.74670277G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	166	78	0.46988	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Silent	SNP	ENST00000609362.1	37	CCDS663.1																																																																																			G|0.996;A|0.004	0.004	strong		0.353	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SMC2	10592	hgsc.bcm.edu	37	9	106888978	106888978	+	Silent	SNP	C	C	T	rs6479217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:106888978C>T	ENST00000286398.7	+	19	2796	c.2508C>T	c.(2506-2508)taC>taT	p.Y836Y	SMC2_ENST00000374787.3_Silent_p.Y836Y|SMC2_ENST00000374793.3_Silent_p.Y836Y|SMC2_ENST00000303219.8_Silent_p.Y836Y	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	836					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						ATACATCTTACAAACAACAGC	0.348													C|||	326	0.0650958	0.2209	0.013	5008	,	,		16974	0.0129		0.007	False		,,,				2504	0.0051				p.Y836Y		Atlas-SNP	.											.	SMC2	127	.	0			c.C2508T						PASS	.	C	,,	745,3661	303.5+/-288.0	55,635,1513	82.0	83.0	83.0		2508,2508,2508	-0.1	0.0	9	dbSNP_116	83	62,8538	38.8+/-94.9	0,62,4238	no	coding-synonymous,coding-synonymous,coding-synonymous	SMC2	NM_001042550.1,NM_001042551.1,NM_006444.2	,,	55,697,5751	TT,TC,CC		0.7209,16.9088,6.2048	,,	836/1198,836/1198,836/1198	106888978	807,12199	2203	4300	6503	SO:0001819	synonymous_variant	10592	exon19			ATCTTACAAACAA	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"""Structural maintenance of chromosomes proteins"""	14011	protein-coding gene	gene with protein product		605576	"""SMC2 (structural maintenance of chromosomes 2, yeast)-like 1"", ""SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"""	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.2508C>T	9.37:g.106888978C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	41	8	0.195122	NM_006444	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	37	CCDS35086.1																																																																																			C|0.935;T|0.065	0.065	strong		0.348	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1		
FZD1	8321	hgsc.bcm.edu	37	7	90895944	90895944	+	Silent	SNP	C	C	T	rs2232161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:90895944C>T	ENST00000287934.2	+	1	2162	c.1749C>T	c.(1747-1749)caC>caT	p.H583H		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	583					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			CCTGCCCTCACCTCCAGGCGG	0.637													C|||	85	0.0169728	0.0605	0.0072	5008	,	,		13904	0.0		0.0	False		,,,				2504	0.0				p.H583H		Atlas-SNP	.											FZD1,NS,carcinoma,0,2	FZD1	64	2	0			c.C1749T						PASS	.	C		238,4168	130.2+/-166.9	9,220,1974	30.0	28.0	29.0		1749	2.9	1.0	7	dbSNP_98	29	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FZD1	NM_003505.1		9,221,6273	TT,TC,CC		0.0116,5.4017,1.8376		583/648	90895944	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	8321	exon1			CCCTCACCTCCAG	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"""GPCR / Class F : Frizzled receptors"""	4038	protein-coding gene	gene with protein product	"""Wnt receptor"", ""frizzled, Drosophila, homolog of, 1"""	603408	"""frizzled (Drosophila) homolog 1"", ""frizzled homolog 1 (Drosophila)"", ""frizzled 1, seven transmembrane spanning receptor"", ""frizzled family receptor 1"""			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.1749C>T	7.37:g.90895944C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_003505	A4D1E8|O94815|Q549T8	Silent	SNP	ENST00000287934.2	37	CCDS5620.1																																																																																			C|0.983;T|0.017	0.017	strong		0.637	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505	
POM121L2	94026	hgsc.bcm.edu	37	6	27279185	27279185	+	Silent	SNP	A	A	T	rs16897553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27279185A>T	ENST00000444565.1	-	1	764	c.765T>A	c.(763-765)gcT>gcA	p.A255A	POM121L2_ENST00000377451.2_Silent_p.A255A	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	255										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						AGCTGCCAATAGCATTCCTTT	0.498													A|||	151	0.0301518	0.0983	0.0159	5008	,	,		18721	0.001		0.005	False		,,,				2504	0.0041				p.A255A		Atlas-SNP	.											.	POM121L2	61	.	0			c.T765A						PASS	.	A		118,1266		4,110,578	21.0	18.0	19.0		765	-8.0	0.0	6	dbSNP_123	19	38,3144		0,38,1553	no	coding-synonymous	POM121L2	NM_033482.3		4,148,2131	TT,TA,AA		1.1942,8.526,3.4166		255/1036	27279185	156,4410	692	1591	2283	SO:0001819	synonymous_variant	94026	exon1			GCCAATAGCATTC	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.765T>A	6.37:g.27279185A>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_033482	C9J1I7	Silent	SNP	ENST00000444565.1	37	CCDS59497.1																																																																																			A|0.953;T|0.047	0.047	strong		0.498	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
ZNF594	84622	hgsc.bcm.edu	37	17	5085245	5085245	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085245G>A	ENST00000399604.4	-	1	2447	c.2307C>T	c.(2305-2307)acC>acT	p.T769T	ZNF594_ENST00000575779.1_Silent_p.T769T			Q96JF6	ZN594_HUMAN	zinc finger protein 594	769					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)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TGCCCTGGAAGGTCCTACTAC	0.413																																					p.T769T		Atlas-SNP	.											.	ZNF594	89	.	0			c.C2307T						PASS	.						205.0	206.0	206.0					17																	5085245		1989	4182	6171	SO:0001819	synonymous_variant	84622	exon2			CTGGAAGGTCCTA	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.2307C>T	17.37:g.5085245G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	100	18	0.18	NM_032530	Q6RFS0	Silent	SNP	ENST00000399604.4	37	CCDS42241.1																																																																																			.	.	none		0.413	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
COL6A3	1293	hgsc.bcm.edu	37	2	238283605	238283605	+	Silent	SNP	G	G	A	rs12622093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238283605G>A	ENST00000295550.4	-	8	3581	c.3129C>T	c.(3127-3129)ggC>ggT	p.G1043G	COL6A3_ENST00000472056.1_Silent_p.G436G|COL6A3_ENST00000409809.1_Silent_p.G837G|COL6A3_ENST00000346358.4_Silent_p.G843G|COL6A3_ENST00000392003.2_Silent_p.G636G|COL6A3_ENST00000347401.3_Silent_p.G842G|COL6A3_ENST00000353578.4_Silent_p.G837G|COL6A3_ENST00000392004.3_Silent_p.G837G	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1043	Nonhelical region.|VWFA 6. {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)		ACAGAGGGAAGCCGCTCCTGA	0.587													G|||	1081	0.215855	0.1082	0.2536	5008	,	,		19171	0.2698		0.2465	False		,,,				2504	0.2474				p.G1043G		Atlas-SNP	.											COL6A3_ENST00000392004,NS,carcinoma,0,2	COL6A3	608	2	0			c.C3129T						PASS	.	G	,,,,	568,3838	248.7+/-256.4	42,484,1677	46.0	49.0	48.0		3129,1908,2511,1308,2511	1.2	0.9	2	dbSNP_120	48	2008,6592	348.4+/-327.0	244,1520,2536	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,,,,	286,2004,4213	AA,AG,GG		23.3488,12.8915,19.8062	,,,,	1043/3178,636/1037,837/1238,436/2571,837/2972	238283605	2576,10430	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon8			AGGGAAGCCGCTC	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.3129C>T	2.37:g.238283605G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.795;A|0.205	0.205	strong		0.587	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
ENTHD2	146705	hgsc.bcm.edu	37	17	79202956	79202956	+	Silent	SNP	T	T	C	rs2048057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	93	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	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	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970993	45970993	+	Missense_Mutation	SNP	C	C	G	rs233239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45970993C>G	ENST00000391621.1	-	1	395	c.349G>C	c.(349-351)Gct>Cct	p.A117P	TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	117	22 X 5 AA repeats of C-C-X(3).		A -> P (in dbSNP:rs233239). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CATGAAGAAGCCCCACAGCAG	0.647													c|||	1141	0.227835	0.2209	0.1585	5008	,	,		21182	0.3651		0.2048	False		,,,				2504	0.1687				p.A117P		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.G349C						PASS	.	G	PRO/ALA,	1007,3399	361.1+/-315.5	113,781,1309	113.0	118.0	116.0		349,	0.1	0.0	21	dbSNP_79	116	1685,6915	305.2+/-307.3	158,1369,2773	no	missense,intron	TSPEAR,KRTAP10-2	NM_198693.2,NM_144991.2	27,	271,2150,4082	GG,GC,CC		19.593,22.8552,20.6981	possibly-damaging,	117/256,	45970993	2692,10314	2203	4300	6503	SO:0001583	missense	386679	exon1			AAGAAGCCCCACA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.349G>C	21.37:g.45970993C>G	ENSP00000375479:p.Ala117Pro	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	320	144	0.45	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	560	0.2564102564102564	111	0.22560975609756098	63	0.17403314917127072	215	0.3758741258741259	171	0.22559366754617413	c	2.552	-0.303826	0.05495	0.228552	0.19593	ENSG00000205445	ENST00000391621	T	0.00686	5.85	3.22	0.117	0.14652	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.47106	0.89	B	0.39185	0.293	T	0.03017	-1.1082	8	0.02654	T	1	.	6.221	0.20681	0.0:0.3402:0.5229:0.1369	rs233239;rs478904;rs905517	117	P60368	KR102_HUMAN	P	117	ENSP00000375479:A117P	ENSP00000375479:A117P	A	-	1	0	KRTAP10-2	44795421	0.009000	0.17119	0.000000	0.03702	0.007000	0.05969	0.105000	0.15333	0.092000	0.17331	-0.394000	0.06481	GCT	C|0.702;G|0.298	0.298	strong		0.647	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
MUC4	4585	hgsc.bcm.edu	37	3	195506258	195506258	+	Missense_Mutation	SNP	G	G	T	rs547058291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195506258G>T	ENST00000463781.3	-	2	12652	c.12193C>A	c.(12193-12195)Ctt>Att	p.L4065I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L4065I	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)		GTGACATGAAGAGGGGTGGCG	0.582													.|||	325	0.0648962	0.1581	0.0202	5008	,	,		10872	0.0089		0.0378	False		,,,				2504	0.0562				p.L4065I		Atlas-SNP	.											.	MUC4	1505	.	0			c.C12193A						PASS	.						31.0	17.0	22.0					3																	195506258		571	1292	1863	SO:0001583	missense	4585	exon2			CATGAAGAGGGGT	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.12193C>A	3.37:g.195506258G>T	ENSP00000417498:p.Leu4065Ile	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	279	270	0.967742	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	80	0.03663003663003663	56	0.11382113821138211	10	0.027624309392265192	1	0.0017482517482517483	13	0.017150395778364115	g	1.506	-0.550799	0.03996	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.39592	1.26;1.07	.	.	.	.	.	.	.	.	T	0.00384	0.0012	N	0.19112	0.55	0.09310	N	1	B	0.17667	0.023	B	0.11329	0.006	T	0.15235	-1.0444	7	.	.	.	.	2.1699	0.03846	0.0:0.3304:0.3416:0.328	.	3937	E7ESK3	.	I	4065	ENSP00000417498:L4065I;ENSP00000420243:L4065I	.	L	-	1	0	MUC4	196991037	0.001000	0.12720	0.001000	0.08648	0.065000	0.16274	-0.428000	0.06991	-0.812000	0.04363	0.064000	0.15345	CTT	G|0.963;T|0.037	0.037	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FCGRT	2217	hgsc.bcm.edu	37	19	50017724	50017724	+	Silent	SNP	C	C	T	rs2878342	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50017724C>T	ENST00000221466.5	+	4	1068	c.582C>T	c.(580-582)cgC>cgT	p.R194R	FCGRT_ENST00000594823.1_3'UTR|FCGRT_ENST00000599988.1_Intron|FCGRT_ENST00000426395.3_Silent_p.R194R|FCGRT_ENST00000596975.1_Intron	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	194	Alpha-2.				antigen processing and presentation (GO:0019882)|IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor (GO:0002416)|immune response (GO:0006955)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG binding (GO:0019864)			endometrium(3)|kidney(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	9		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;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		AGAGGGGCCGCGGAAACCTGG	0.662													C|||	735	0.146765	0.348	0.1023	5008	,	,		14689	0.0238		0.0855	False		,,,				2504	0.0961				p.R194R		Atlas-SNP	.											FCGRT,NS,carcinoma,0,1	FCGRT	23	1	0			c.C582T						PASS	.	C	,	1477,2929		246,985,972	19.0	22.0	21.0		582,582	-8.6	0.0	19	dbSNP_101	21	718,7874		30,658,3608	no	coding-synonymous,coding-synonymous	FCGRT	NM_001136019.2,NM_004107.4	,	276,1643,4580	TT,TC,CC		8.3566,33.5225,16.8872	,	194/366,194/366	50017724	2195,10803	2203	4296	6499	SO:0001819	synonymous_variant	2217	exon4			GGGCCGCGGAAAC	U12255	CCDS12770.1	19q13.3	2013-01-11				ENSG00000104870		"""Immunoglobulin superfamily / C1-set domain containing"""	3621	protein-coding gene	gene with protein product		601437				7964511, 8646894	Standard	NM_001136019		Approved	FCRN, alpha-chain	uc002pog.2	P55899		ENST00000221466.5:c.582C>T	19.37:g.50017724C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_001136019	Q5HYM5|Q9HBV7|Q9NZ19	Silent	SNP	ENST00000221466.5	37	CCDS12770.1	277	0.12683150183150182	165	0.3353658536585366	37	0.10220994475138122	17	0.02972027972027972	58	0.07651715039577836	C	5.219	0.225948	0.09916	0.335225	0.083566	ENSG00000104870	ENST00000415900	.	.	.	4.3	-8.6	0.00889	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.40526	P	0.01911099999999999	.	.	.	.	.	.	T	0.18461	-1.0336	4	0.87932	D	0	.	3.8572	0.08981	0.231:0.5127:0.1636:0.0928	rs2878342;rs2878342	.	.	.	V	140	.	ENSP00000391574:A140V	A	+	2	0	FCGRT	54709536	0.000000	0.05858	0.000000	0.03702	0.689000	0.40095	-4.406000	0.00239	-4.568000	0.00042	-1.203000	0.01651	GCG	C|0.846;T|0.154	0.154	strong		0.662	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1		
MUC4	4585	hgsc.bcm.edu	37	3	195513743	195513743	+	Missense_Mutation	SNP	G	G	T	rs59668135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513743G>T	ENST00000463781.3	-	2	5167	c.4708C>A	c.(4708-4710)Cct>Act	p.P1570T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1570T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)		CTGGTGACAGGAAGAGGGGTG	0.572																																					p.P1570T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C4708A						PASS	.						26.0	19.0	21.0					3																	195513743		687	1584	2271	SO:0001583	missense	4585	exon2			TGACAGGAAGAGG	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.4708C>A	3.37:g.195513743G>T	ENSP00000417498:p.Pro1570Thr	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	272	148	0.544118	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	.	.	.	.	.	.	.	.	.	.	-	8.497	0.863334	0.17250	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.55;1.54	.	.	.	.	.	.	.	.	T	0.19005	0.0456	N	0.08118	0	0.44323	P	0.0027930000000000454	P	0.48350	0.909	P	0.50440	0.641	T	0.23619	-1.0183	6	.	.	.	.	5.8679	0.18786	8.0E-4:0.0:0.9992:0.0	rs59668135	1570	E7ESK3	.	T	1570	ENSP00000417498:P1570T;ENSP00000420243:P1570T	.	P	-	1	0	MUC4	196998138	0.001000	0.12720	0.030000	0.17652	0.030000	0.12068	-0.064000	0.11636	0.088000	0.17205	0.089000	0.15464	CCT	G|0.944;T|0.055	0.055	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CDC42BPA	8476	hgsc.bcm.edu	37	1	227504745	227504745	+	Silent	SNP	A	A	G	rs144296174		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227504745A>G	ENST00000366769.3	-	1	1430	c.139T>C	c.(139-141)Ttg>Ctg	p.L47L	CDC42BPA_ENST00000334218.5_Silent_p.L47L|CDC42BPA_ENST00000535525.1_Silent_p.L47L|CDC42BPA_ENST00000366764.2_Silent_p.L47L|CDC42BPA_ENST00000366767.3_Silent_p.L47L|CDC42BPA_ENST00000366766.2_Silent_p.L47L|CDC42BPA_ENST00000366765.3_Silent_p.L47L	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TCTCTTCTCAATGGAGAATTA	0.378													a|||	1	0.000199681	0.0008	0.0	5008	,	,		18255	0.0		0.0	False		,,,				2504	0.0				p.L47L		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.T139C						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	102.0	96.0	98.0		139,139	-1.5	0.8	1	dbSNP_134	98	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CDC42BPA	NM_003607.3,NM_014826.4	,	0,5,6498	GG,GA,AA		0.0,0.1135,0.0384	,	47/1720,47/1639	227504745	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	8476	exon1			TTCTCAATGGAGA	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.139T>C	1.37:g.227504745A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	167	84	0.502994	NM_003607		Silent	SNP	ENST00000366769.3	37	CCDS1558.1																																																																																			A|1.000;G|0.000	0.000	strong		0.378	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
GUCA1C	9626	hgsc.bcm.edu	37	3	108639384	108639384	+	Missense_Mutation	SNP	T	T	C	rs6804162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108639384T>C	ENST00000261047.3	-	2	385	c.253A>G	c.(253-255)Atg>Gtg	p.M85V	GUCA1C_ENST00000393963.3_Missense_Mutation_p.M85V|GUCA1C_ENST00000471108.1_Missense_Mutation_p.M85V	NM_005459.3	NP_005450.3	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C	85	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		M -> V (in dbSNP:rs6804162).		phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(2)|large_intestine(1)|liver(1)|lung(8)|pancreas(1)|skin(1)	14						TTTTCTTGCATGATTAGATTT	0.289													C|||	1688	0.337061	0.438	0.2522	5008	,	,		18067	0.25		0.3807	False		,,,				2504	0.3057				p.M85V	NSCLC(157;1360 1999 30631 40189 44208)	Atlas-SNP	.											.	GUCA1C	39	.	0			c.A253G						PASS	.	C	VAL/MET	1844,2562	630.5+/-395.5	393,1058,752	77.0	74.0	75.0		253	3.1	0.0	3	dbSNP_116	75	3062,5534	657.8+/-401.5	548,1966,1784	yes	missense	GUCA1C	NM_005459.3	21	941,3024,2536	CC,CT,TT		35.6212,41.852,37.7327	benign	85/210	108639384	4906,8096	2203	4298	6501	SO:0001583	missense	9626	exon2			CTTGCATGATTAG	AF110002	CCDS2954.1	3q13.1	2013-01-10			ENSG00000138472	ENSG00000138472		"""EF-hand domain containing"""	4680	protein-coding gene	gene with protein product	"""guanylyl cyclase-activating protein 3"""	605128				10037746, 11860507	Standard	NM_005459		Approved	GCAP3	uc003dxj.2	O95843	OTTHUMG00000159204	ENST00000261047.3:c.253A>G	3.37:g.108639384T>C	ENSP00000261047:p.Met85Val	Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	302	302	1	NM_005459	O95844|Q9UNM0	Missense_Mutation	SNP	ENST00000261047.3	37	CCDS2954.1	741	0.3392857142857143	205	0.4166666666666667	93	0.2569060773480663	143	0.25	300	0.39577836411609496	C	6.052	0.377909	0.11466	0.41852	0.356212	ENSG00000138472	ENST00000393963;ENST00000261047;ENST00000471108	T;T;T	0.40476	1.03;1.03;1.03	5.17	3.1	0.35709	EF-hand-like domain (1);	0.215490	0.39909	N	0.001229	T	0.00012	0.0000	N	0.11255	0.115	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44757	-0.9307	9	0.06236	T	0.91	.	2.791	0.05388	0.2015:0.4347:0.0:0.3638	rs6804162;rs52828740;rs56507439;rs56791641;rs6804162	85;85	C9JNI2;O95843	.;GUC1C_HUMAN	V	85	ENSP00000377535:M85V;ENSP00000261047:M85V;ENSP00000417761:M85V	ENSP00000261047:M85V	M	-	1	0	GUCA1C	110122074	0.009000	0.17119	0.005000	0.12908	0.729000	0.41735	-0.034000	0.12225	0.598000	0.29829	-0.186000	0.12905	ATG	T|0.647;C|0.353	0.353	strong		0.289	GUCA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353819.1	NM_005459	
DIDO1	11083	hgsc.bcm.edu	37	20	61513649	61513649	+	Missense_Mutation	SNP	G	G	T	rs6011441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61513649G>T	ENST00000266070.4	-	16	3984	c.3659C>A	c.(3658-3660)cCg>cAg	p.P1220Q	DIDO1_ENST00000395343.1_Missense_Mutation_p.P1220Q	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1220			P -> Q (in dbSNP:rs6011441).		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)					CGCTTCTTCCGGTTGAAGTCG	0.512													g|||	915	0.182708	0.5295	0.0692	5008	,	,		14709	0.0238		0.0755	False		,,,				2504	0.0685				p.P1220Q	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1,NS,carcinoma,+1,1	DIDO1	321	1	0			c.C3659A						PASS	.	G	GLN/PRO,GLN/PRO	2121,2285	573.1+/-383.5	507,1107,589	95.0	103.0	100.0		3659,3659	-0.3	0.0	20	dbSNP_114	100	815,7785	188.1+/-235.2	49,717,3534	yes	missense,missense	DIDO1	NM_001193369.1,NM_033081.2	76,76	556,1824,4123	TT,TG,GG		9.4767,48.1389,22.5742	benign,benign	1220/2241,1220/2241	61513649	2936,10070	2203	4300	6503	SO:0001583	missense	11083	exon16			TCTTCCGGTTGAA	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.3659C>A	20.37:g.61513649G>T	ENSP00000266070:p.Pro1220Gln	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001193369	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	356	0.163003663003663	250	0.508130081300813	29	0.08011049723756906	13	0.022727272727272728	64	0.08443271767810026	g	5.265	0.234363	0.09969	0.481389	0.094767	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.07908	3.15;3.15	5.2	-0.263	0.12954	.	0.614591	0.13264	N	0.401065	T	0.00012	0.0000	N	0.00926	-1.1	0.50171	P	1.44000000000033E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.44034	-0.9354	9	0.06494	T	0.89	-5.6941	15.0221	0.71637	0.0:0.0:0.5494:0.4506	rs6011441;rs60572892;rs6011441	1220	Q9BTC0	DIDO1_HUMAN	Q	1220	ENSP00000266070:P1220Q;ENSP00000378752:P1220Q	ENSP00000266070:P1220Q	P	-	2	0	DIDO1	60984094	0.094000	0.21725	0.000000	0.03702	0.003000	0.03518	0.750000	0.26334	-0.261000	0.09405	-0.527000	0.04329	CCG	A|0.000;G|0.803;T|0.197	0.197	strong		0.512	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
PLEC	5339	hgsc.bcm.edu	37	8	145007409	145007409	+	Silent	SNP	G	G	A	rs115081018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145007409G>A	ENST00000322810.4	-	13	1954	c.1785C>T	c.(1783-1785)acC>acT	p.T595T	PLEC_ENST00000345136.3_Silent_p.T458T|PLEC_ENST00000398774.2_Silent_p.T426T|PLEC_ENST00000356346.3_Silent_p.T444T|PLEC_ENST00000527096.1_Silent_p.T481T|PLEC_ENST00000354589.3_Silent_p.T458T|PLEC_ENST00000357649.2_Silent_p.T462T|PLEC_ENST00000436759.2_Silent_p.T485T|PLEC_ENST00000354958.2_Silent_p.T436T	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	595	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CATCCTTGAGGGTCTGCACGT	0.677													G|||	83	0.0165735	0.059	0.0072	5008	,	,		16349	0.0		0.0	False		,,,				2504	0.0				p.T595T		Atlas-SNP	.											.	PLEC	1144	.	0			c.C1785T						PASS	.	G	,,,,,,,	160,3982		4,152,1915	63.0	72.0	69.0		1455,1332,1308,1785,1278,1374,1386,1374	1.0	1.0	8	dbSNP_132	69	4,8358		0,4,4177	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	,,,,,,,	4,156,6092	AA,AG,GG		0.0478,3.8629,1.3116	,,,,,,,	485/4575,444/4534,436/4526,595/4685,426/4516,458/4548,462/4552,458/4548	145007409	164,12340	2071	4181	6252	SO:0001819	synonymous_variant	5339	exon13			CTTGAGGGTCTGC	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.1785C>T	8.37:g.145007409G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.988;A|0.012	0.012	strong		0.677	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
HMMR	3161	hgsc.bcm.edu	37	5	162910165	162910165	+	Missense_Mutation	SNP	G	G	C	rs2230362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162910165G>C	ENST00000358715.3	+	14	1705	c.1669G>C	c.(1669-1671)Gat>Cat	p.D557H	HMMR_ENST00000432118.2_Missense_Mutation_p.D471H|HMMR_ENST00000393915.4_Missense_Mutation_p.D558H|RP11-80G7.1_ENST00000521666.1_RNA|RP11-80G7.1_ENST00000514724.2_RNA|HMMR_ENST00000353866.3_Missense_Mutation_p.D542H			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	557			D -> H (in dbSNP:rs2230362).		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)	ACAGCTGGAAGATGAAGAAGG	0.313													G|||	46	0.0091853	0.0287	0.0115	5008	,	,		17759	0.0		0.0	False		,,,				2504	0.0				p.D558H		Atlas-SNP	.											.	HMMR	64	.	0			c.G1672C						PASS	.	G	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	103,4303		1,101,2101	53.0	54.0	53.0		1672,1411,1669,1624	3.2	0.9	5	dbSNP_98	53	0,8598		0,0,4299	yes	missense,missense,missense,missense	HMMR	NM_001142556.1,NM_001142557.1,NM_012484.2,NM_012485.2	81,81,81,81	1,101,6400	CC,CG,GG		0.0,2.3377,0.7921	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	558/726,471/639,557/725,542/710	162910165	103,12901	2203	4299	6502	SO:0001583	missense	3161	exon14			CTGGAAGATGAAG	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.1669G>C	5.37:g.162910165G>C	ENSP00000351554:p.Asp557His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	119	48	0.403361	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	17	0.007783882783882784	12	0.024390243902439025	5	0.013812154696132596	0	0.0	0	0.0	G	9.635	1.137453	0.21123	0.023377	0.0	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.07800	3.16;3.16;3.16;3.16;3.16	5.03	3.24	0.37175	.	0.678925	0.15280	N	0.270748	T	0.02304	0.0071	N	0.08118	0	0.09310	N	1	P;P;P;P	0.44380	0.697;0.755;0.834;0.834	B;B;B;B	0.41036	0.332;0.346;0.319;0.319	T	0.36553	-0.9743	10	0.49607	T	0.09	-4.1167	11.5254	0.50576	0.1543:0.0:0.8457:0.0	rs2230362;rs2230362	471;558;542;557	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	H	443;542;558;534;471;557	ENSP00000400527:D443H;ENSP00000185942:D542H;ENSP00000377492:D558H;ENSP00000402673:D471H;ENSP00000351554:D557H	ENSP00000185942:D542H	D	+	1	0	HMMR	162842743	0.991000	0.36638	0.881000	0.34555	0.305000	0.27757	1.054000	0.30455	1.482000	0.48325	0.655000	0.94253	GAT	G|0.990;C|0.010	0.010	strong		0.313	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	
CPNE2	221184	hgsc.bcm.edu	37	16	57144689	57144689	+	Missense_Mutation	SNP	C	C	T	rs141954860		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57144689C>T	ENST00000535318.2	+	3	396	c.35C>T	c.(34-36)gCg>gTg	p.A12V	CPNE2_ENST00000290776.8_Missense_Mutation_p.A12V|CPNE2_ENST00000565874.1_Missense_Mutation_p.A12V|CPNE2_ENST00000537605.1_5'UTR			Q96FN4	CPNE2_HUMAN	copine II	12	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5)	21		all_neural(199;0.224)				GCCCCAGCAGCGGGGGCAGCC	0.642													c|||	1	0.000199681	0.0008	0.0	5008	,	,		13191	0.0		0.0	False		,,,				2504	0.0				p.A12V		Atlas-SNP	.											.	CPNE2	48	.	0			c.C35T						PASS	.	C	VAL/ALA	0,4394		0,0,2197	28.0	27.0	28.0		35	-2.0	0.0	16	dbSNP_134	28	6,8592		0,6,4293	no	missense	CPNE2	NM_152727.5	64	0,6,6490	TT,TC,CC		0.0698,0.0,0.0462	benign	12/549	57144689	6,12986	2197	4299	6496	SO:0001583	missense	221184	exon2			CAGCAGCGGGGGC		CCDS10774.1	16q13	2008-02-05			ENSG00000140848	ENSG00000140848			2315	protein-coding gene	gene with protein product		604206				9430674	Standard	NM_152727		Approved	CPN2	uc002eks.2	Q96FN4	OTTHUMG00000133471	ENST00000535318.2:c.35C>T	16.37:g.57144689C>T	ENSP00000439018:p.Ala12Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_152727	Q68D19|Q719H8|Q86XP9	Missense_Mutation	SNP	ENST00000535318.2	37	CCDS10774.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.381069	0.42207	0.0	6.98E-4	ENSG00000140848	ENST00000290776;ENST00000535318	T;T	0.05319	3.46;3.46	5.08	-1.97	0.07503	C2 calcium/lipid-binding domain, CaLB (1);	1.227400	0.05504	N	0.558977	T	0.04861	0.0131	N	0.24115	0.695	0.09310	N	0.999999	B;B	0.13145	0.007;0.001	B;B	0.04013	0.001;0.001	T	0.45056	-0.9287	10	0.33141	T	0.24	-14.5631	7.8677	0.29547	0.0:0.5348:0.2084:0.2568	.	12;12	A8K8A4;Q96FN4	.;CPNE2_HUMAN	V	12	ENSP00000290776:A12V;ENSP00000439018:A12V	ENSP00000290776:A12V	A	+	2	0	CPNE2	55702190	0.000000	0.05858	0.000000	0.03702	0.234000	0.25298	-0.045000	0.12003	-0.152000	0.11156	-0.201000	0.12746	GCG	C|0.999;T|0.001	0.001	strong		0.642	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727	
DNAH9	1770	hgsc.bcm.edu	37	17	11583192	11583192	+	Missense_Mutation	SNP	C	C	T	rs8070501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11583192C>T	ENST00000262442.4	+	18	3540	c.3472C>T	c.(3472-3474)Cgg>Tgg	p.R1158W	DNAH9_ENST00000454412.2_Missense_Mutation_p.R1158W	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1158	Stem. {ECO:0000250}.		R -> W (in dbSNP:rs8070501).		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)		TGTTAAAGAACGGCAGAGTAA	0.408													C|||	57	0.0113818	0.0408	0.0029	5008	,	,		18781	0.001		0.0	False		,,,				2504	0.0				p.R1158W		Atlas-SNP	.											DNAH9,rectum,carcinoma,0,1	DNAH9	695	1	0			c.C3472T						PASS	.	C	TRP/ARG	164,4242	111.6+/-149.8	6,152,2045	136.0	129.0	132.0		3472	2.5	0.9	17	dbSNP_116	132	2,8598	1.2+/-3.3	0,2,4298	yes	missense	DNAH9	NM_001372.3	101	6,154,6343	TT,TC,CC		0.0233,3.7222,1.2763	probably-damaging	1158/4487	11583192	166,12840	2203	4300	6503	SO:0001583	missense	1770	exon18			AAAGAACGGCAGA	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.3472C>T	17.37:g.11583192C>T	ENSP00000262442:p.Arg1158Trp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	C	14.02	2.409862	0.42715	0.037222	2.33E-4	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.25414	1.8;1.8	5.69	2.5	0.30297	.	0.257159	0.32343	N	0.006221	T	0.25717	0.0626	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.60865	-0.7178	10	0.87932	D	0	.	16.2874	0.82727	0.6259:0.3741:0.0:0.0	rs8070501;rs52812603;rs56633662;rs8070501	1158	Q9NYC9	DYH9_HUMAN	W	1158	ENSP00000262442:R1158W;ENSP00000414874:R1158W	ENSP00000262442:R1158W	R	+	1	2	DNAH9	11523917	0.585000	0.26774	0.926000	0.36857	0.245000	0.25701	0.963000	0.29293	0.294000	0.22547	0.650000	0.86243	CGG	C|0.988;T|0.012	0.012	strong		0.408	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20864356	20864356	+	Silent	SNP	C	C	T	rs7963279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:20864356C>T	ENST00000266509.2	+	5	809	c.441C>T	c.(439-441)tcC>tcT	p.S147S	SLCO1C1_ENST00000381552.1_Silent_p.S147S|SLCO1C1_ENST00000540354.1_Silent_p.S147S|SLCO1C1_ENST00000545102.1_Silent_p.S29S|SLCO1C1_ENST00000545604.1_Silent_p.S147S	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	147					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)	CCTCCAATTCCACTCTCAGCA	0.348													T|||	1210	0.241613	0.2799	0.2579	5008	,	,		19304	0.0516		0.3062	False		,,,				2504	0.3078				p.S147S		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C441T						PASS	.	T	,,,	1275,3131	701.1+/-406.7	186,903,1114	141.0	135.0	137.0		87,441,441,441	-3.3	0.3	12	dbSNP_116	137	2768,5832	679.2+/-403.5	438,1892,1970	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	,,,	624,2795,3084	TT,TC,CC		32.186,28.9378,31.0857	,,,	29/613,147/664,147/731,147/713	20864356	4043,8963	2203	4300	6503	SO:0001819	synonymous_variant	53919	exon5			CAATTCCACTCTC	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.441C>T	12.37:g.20864356C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Silent	SNP	ENST00000266509.2	37	CCDS8683.1																																																																																			C|0.727;T|0.273	0.273	strong		0.348	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
ZNF69	7620	hgsc.bcm.edu	37	19	11998777	11998777	+	Silent	SNP	C	C	T	rs3810314	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11998777C>T	ENST00000429654.2	+	1	179	c.39C>T	c.(37-39)ccC>ccT	p.P13P	ZNF69_ENST00000340180.5_Silent_p.P13P			Q9UC07	ZNF69_HUMAN	zinc finger protein 69	13					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|skin(2)	4				Lung(535;0.011)		GAGAGGACCCCGGGACATCTG	0.637													c|||	579	0.115615	0.3389	0.0432	5008	,	,		16314	0.0228		0.0239	False		,,,				2504	0.0552				p.P13P		Atlas-SNP	.											.	ZNF69	27	.	0			c.C39T						PASS	.	C		1247,3159	428.7+/-342.0	173,901,1129	77.0	66.0	70.0		39	-1.1	0.0	19	dbSNP_107	70	164,8436	76.9+/-139.5	1,162,4137	no	coding-synonymous	ZNF69	NM_021915.2		174,1063,5266	TT,TC,CC		1.907,28.3023,10.8488		13/150	11998777	1411,11595	2203	4300	6503	SO:0001819	synonymous_variant	7620	exon1			GGACCCCGGGACA	X60076	CCDS32914.1	19p13.2	2013-01-08	2006-05-12		ENSG00000198429	ENSG00000198429		"""Zinc fingers, C2H2-type"", ""-"""	13138	protein-coding gene	gene with protein product		194543	"""zinc finger protein 69 (Cos5)"""			1639391	Standard	NM_021915		Approved	Cos5	uc002mst.4	Q9UC07	OTTHUMG00000156526	ENST00000429654.2:c.39C>T	19.37:g.11998777C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	141	62	0.439716	NM_021915	Q86VA7	Silent	SNP	ENST00000429654.2	37																																																																																				C|0.897;T|0.103	0.103	strong		0.637	ZNF69-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000344082.1	NM_021915	
SGK223	157285	hgsc.bcm.edu	37	8	8234113	8234113	+	Silent	SNP	G	G	A	rs2921005	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8234113G>A	ENST00000520004.1	-	3	2070	c.1806C>T	c.(1804-1806)gtC>gtT	p.V602V	SGK223_ENST00000330777.4_Silent_p.V602V			Q86YV5	SG223_HUMAN		604							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CACTGATAGCGACACCGTTGG	0.662													G|||	500	0.0998403	0.1029	0.0519	5008	,	,		16608	0.0744		0.0616	False		,,,				2504	0.1953				p.V602V	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1806T						PASS	.	G		428,3548		19,390,1579	34.0	38.0	37.0		1806	-2.9	0.0	8	dbSNP_101	37	460,7890		10,440,3725	no	coding-synonymous	SGK223	NM_001080826.1		29,830,5304	AA,AG,GG		5.509,10.7646,7.2043		602/1403	8234113	888,11438	1988	4175	6163	SO:0001819	synonymous_variant	0	exon2			GATAGCGACACCG																												ENST00000520004.1:c.1806C>T	8.37:g.8234113G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			G|0.918;A|0.082	0.082	strong		0.662	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
SOAT1	6646	hgsc.bcm.edu	37	1	179310262	179310262	+	Silent	SNP	C	C	T	rs11576517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179310262C>T	ENST00000367619.3	+	7	740	c.597C>T	c.(595-597)ccC>ccT	p.P199P	SOAT1_ENST00000540564.1_Silent_p.P141P|SOAT1_ENST00000535686.1_5'UTR|SOAT1_ENST00000539888.1_Silent_p.P134P	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	199					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol storage (GO:0010878)|macrophage derived foam cell differentiation (GO:0010742)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|sterol O-acyltransferase activity (GO:0004772)	p.P199P(1)		central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20					Ezetimibe(DB00973)|Hesperetin(DB01094)	TTTCAGTTCCCTATTTTCTGT	0.453													C|||	1414	0.282348	0.1354	0.2406	5008	,	,		16077	0.4782		0.2406	False		,,,				2504	0.3517				p.P199P		Atlas-SNP	.											SOAT1,NS,carcinoma,0,1	SOAT1	53	1	1	Substitution - coding silent(1)	stomach(1)	c.C597T						PASS	.	C		596,3810	259.5+/-263.1	39,518,1646	204.0	187.0	193.0		597	-1.8	1.0	1	dbSNP_120	193	1822,6778	325.9+/-317.1	177,1468,2655	no	coding-synonymous	SOAT1	NM_003101.4		216,1986,4301	TT,TC,CC		21.186,13.527,18.5914		199/551	179310262	2418,10588	2203	4300	6503	SO:0001819	synonymous_variant	6646	exon7			AGTTCCCTATTTT	L21934	CCDS1330.1, CCDS58047.1, CCDS58048.1	1q25	2008-08-26	2008-08-26		ENSG00000057252	ENSG00000057252	2.3.1.26		11177	protein-coding gene	gene with protein product	"""acyl-Coenzyme A: cholesterol acyltransferase"""	102642	"""sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1"""	SOAT, STAT		8407899	Standard	NM_003101		Approved	ACAT	uc001gml.3	P35610	OTTHUMG00000035253	ENST00000367619.3:c.597C>T	1.37:g.179310262C>T		Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	228	109	0.47807	NM_003101	A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	Silent	SNP	ENST00000367619.3	37	CCDS1330.1																																																																																			C|0.773;T|0.227	0.227	strong		0.453	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	NM_003101	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110539175	110539175	+	Missense_Mutation	SNP	T	T	A	rs141977750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110539175T>A	ENST00000378402.5	+	77	12751	c.12647T>A	c.(12646-12648)aTt>aAt	p.I4216N		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4216					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)			ACTGTAGTAATTAGCTGTCTG	0.418										HNSCC(38;0.096)			T|||	46	0.0091853	0.0325	0.0043	5008	,	,		17708	0.0		0.0	False		,,,				2504	0.0				p.I4216N		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T12647A						PASS	.	T	ASN/ILE	77,3947		0,77,1935	93.0	98.0	96.0		12647	1.8	0.0	8	dbSNP_134	96	0,8418		0,0,4209	yes	missense	PKHD1L1	NM_177531.4	149	0,77,6144	AA,AT,TT		0.0,1.9135,0.6189	benign	4216/4244	110539175	77,12365	2012	4209	6221	SO:0001583	missense	93035	exon77			TAGTAATTAGCTG	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.12647T>A	8.37:g.110539175T>A	ENSP00000367655:p.Ile4216Asn	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	204	105	0.514706	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	T	7.650	0.682659	0.14907	0.019135	0.0	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.87412	-2.25;-2.08	5.64	1.83	0.25207	.	0.492124	0.18017	N	0.154354	T	0.52933	0.1765	N	0.24115	0.695	0.09310	N	1	B	0.34015	0.435	B	0.27170	0.077	T	0.58312	-0.7658	10	0.72032	D	0.01	.	7.5255	0.27653	0.0:0.253:0.0:0.747	.	4216	Q86WI1	PKHL1_HUMAN	N	4216;1144	ENSP00000367655:I4216N;ENSP00000437376:I1144N	ENSP00000367655:I4216N	I	+	2	0	PKHD1L1	110608351	0.002000	0.14202	0.001000	0.08648	0.122000	0.20287	0.151000	0.16283	0.068000	0.16574	0.528000	0.53228	ATT	T|0.993;A|0.007	0.007	strong		0.418	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
PIGR	5284	hgsc.bcm.edu	37	1	207110888	207110888	+	Silent	SNP	G	G	A	rs291097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207110888G>A	ENST00000356495.4	-	4	780	c.597C>T	c.(595-597)ggC>ggT	p.G199G		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	199	Ig-like V-type 2.				detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)	p.G199G(1)		central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACAGTAACTGGCCAGTACCCT	0.478													G|||	1162	0.232029	0.6921	0.1844	5008	,	,		23475	0.0546		0.0249	False		,,,				2504	0.0399				p.G199G		Atlas-SNP	.											PIGR,NS,carcinoma,0,1	PIGR	98	1	1	Substitution - coding silent(1)	stomach(1)	c.C597T						PASS	.	G		2629,1777	643.2+/-397.8	813,1003,387	80.0	73.0	75.0		597	-2.9	0.0	1	dbSNP_79	75	235,8365	94.2+/-156.2	5,225,4070	no	coding-synonymous	PIGR	NM_002644.3		818,1228,4457	AA,AG,GG		2.7326,40.3314,22.0206		199/765	207110888	2864,10142	2203	4300	6503	SO:0001819	synonymous_variant	5284	exon4			TAACTGGCCAGTA		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"""Immunoglobulin superfamily / V-set domain containing"""	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.597C>T	1.37:g.207110888G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	134	59	0.440298	NM_002644	Q68D81|Q8IZY7	Silent	SNP	ENST00000356495.4	37	CCDS1474.1																																																																																			G|0.779;A|0.221	0.221	strong		0.478	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644	
XPO4	64328	hgsc.bcm.edu	37	13	21374333	21374333	+	Silent	SNP	A	A	G	rs9579954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:21374333A>G	ENST00000255305.6	-	15	2180	c.2109T>C	c.(2107-2109)acT>acC	p.T703T	XPO4_ENST00000400602.2_Silent_p.T703T			Q9C0E2	XPO4_HUMAN	exportin 4	703					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)		GGAGCTGCACAGTGTCATTTG	0.458													A|||	309	0.0617013	0.0242	0.0403	5008	,	,		19337	0.0		0.1382	False		,,,				2504	0.1125				p.T703T		Atlas-SNP	.											.	XPO4	153	.	0			c.T2109C						PASS	.	A		171,3835		4,163,1836	111.0	108.0	109.0		2109	-3.1	0.9	13	dbSNP_119	109	1129,7213		71,987,3113	no	coding-synonymous	XPO4	NM_022459.4		75,1150,4949	GG,GA,AA		13.5339,4.2686,10.528		703/1152	21374333	1300,11048	2003	4171	6174	SO:0001819	synonymous_variant	64328	exon15			CTGCACAGTGTCA	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.2109T>C	13.37:g.21374333A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	175	89	0.508571	NM_022459	Q5VUZ5|Q8N3V6|Q9H934	Silent	SNP	ENST00000255305.6	37	CCDS41872.1																																																																																			A|0.912;G|0.088	0.088	strong		0.458	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459	
FZD5	7855	hgsc.bcm.edu	37	2	208632817	208632817	+	Missense_Mutation	SNP	G	G	A	rs35994626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:208632817G>A	ENST00000295417.3	-	2	1200	c.647C>T	c.(646-648)cCc>cTc	p.P216L		NM_003468.3	NP_003459.2	Q13467	FZD5_HUMAN	frizzled class receptor 5	216			P -> L (in dbSNP:rs35994626).		angiogenesis (GO:0001525)|anterior/posterior axis specification, embryo (GO:0008595)|apoptotic process (GO:0006915)|apoptotic process involved in morphogenesis (GO:0060561)|axonogenesis (GO:0007409)|brain development (GO:0007420)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)|cell maturation (GO:0048469)|cellular response to molecule of bacterial origin (GO:0071219)|chorionic trophoblast cell differentiation (GO:0060718)|embryonic axis specification (GO:0000578)|embryonic camera-type eye development (GO:0031076)|gonad development (GO:0008406)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|neuron differentiation (GO:0030182)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic camera-type eye development (GO:0031077)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of chorionic trophoblast cell proliferation (GO:1901382)|regulation of tight junction assembly (GO:2000810)|Spemann organizer formation (GO:0060061)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell differentiation in thymus (GO:0033077)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	cell projection (GO:0042995)|cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			NS(1)|kidney(1)|lung(1)|ovary(2)|prostate(1)|skin(1)	7				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.13)|Lung(261;0.134)		CGCGCAGTTGGGCACCTGGCC	0.647													G|||	124	0.0247604	0.0015	0.0346	5008	,	,		18142	0.0		0.0616	False		,,,				2504	0.0368				p.P216L		Atlas-SNP	.											.	FZD5	22	.	0			c.C647T						PASS	.	G	LEU/PRO	55,4351	50.9+/-86.3	0,55,2148	47.0	47.0	47.0		647	2.9	1.0	2	dbSNP_126	47	679,7921	166.8+/-218.7	26,627,3647	yes	missense	FZD5	NM_003468.3	98	26,682,5795	AA,AG,GG		7.8953,1.2483,5.6435	benign	216/586	208632817	734,12272	2203	4300	6503	SO:0001583	missense	7855	exon2			CAGTTGGGCACCT	U43318	CCDS33366.1	2q33.3	2014-01-29	2014-01-29		ENSG00000163251	ENSG00000163251		"""GPCR / Class F : Frizzled receptors"""	4043	protein-coding gene	gene with protein product		601723	"""frizzled (Drosophila) homolog 5"", ""chromosome 2 open reading frame 31"", ""frizzled homolog 5 (Drosophila)"", ""frizzled 5, seven transmembrane spanning receptor"", ""frizzled family receptor 5"""	C2orf31		8626800, 11408929	Standard	NM_003468		Approved	HFZ5, DKFZP434E2135	uc002vcj.3	Q13467	OTTHUMG00000154790	ENST00000295417.3:c.647C>T	2.37:g.208632817G>A	ENSP00000354607:p.Pro216Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_003468	A8K2X1|B2RCZ1|Q53R22	Missense_Mutation	SNP	ENST00000295417.3	37	CCDS33366.1	56	0.02564102564102564	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	42	0.055408970976253295	G	12.13	1.845603	0.32606	0.012483	0.078953	ENSG00000163251	ENST00000295417	T	0.79845	-1.31	5.05	2.94	0.34122	.	0.294105	0.32258	N	0.006352	T	0.08358	0.0208	L	0.28192	0.835	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.43972	-0.9358	10	0.41790	T	0.15	.	3.0492	0.06164	0.1303:0.1681:0.5291:0.1726	rs35994626;rs61752181	216	Q13467	FZD5_HUMAN	L	216	ENSP00000354607:P216L	ENSP00000354607:P216L	P	-	2	0	FZD5	208341062	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.812000	0.47994	2.355000	0.79922	0.561000	0.74099	CCC	G|0.953;A|0.047	0.047	strong		0.647	FZD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337060.1	NM_003468	
CEACAM6	4680	hgsc.bcm.edu	37	19	42260697	42260697	+	Missense_Mutation	SNP	G	G	A	rs61736638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42260697G>A	ENST00000199764.6	+	2	472	c.254G>A	c.(253-255)gGa>gAa	p.G85E	AC011513.4_ENST00000601409.1_RNA|CEA_ENST00000598976.1_Intron	NM_002483.4	NP_002474.3	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	85	Ig-like V-type.				cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|kidney(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.00575)|all cancers(3;0.0352)|Epithelial(262;0.0797)		TATGTAATAGGAACTCAACAA	0.498													g|||	146	0.0291534	0.1074	0.0043	5008	,	,		18669	0.0		0.001	False		,,,				2504	0.0				p.G85E		Atlas-SNP	.											.	CEACAM6	52	.	0			c.G254A						PASS	.	G	GLU/GLY	359,4047	184.3+/-211.7	13,333,1857	246.0	230.0	235.0		254	-3.8	0.0	19	dbSNP_129	235	7,8589	5.0+/-18.6	0,7,4291	no	missense	CEACAM6	NM_002483.4	98	13,340,6148	AA,AG,GG		0.0814,8.148,2.815	benign	85/345	42260697	366,12636	2203	4298	6501	SO:0001583	missense	4680	exon2			TAATAGGAACTCA	M29541	CCDS12585.1	19q13.1-q13.2	2013-01-29			ENSG00000086548	ENSG00000086548		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1818	protein-coding gene	gene with protein product		163980		NCA			Standard	NM_002483		Approved	CD66c	uc002orm.2	P40199	OTTHUMG00000151064	ENST00000199764.6:c.254G>A	19.37:g.42260697G>A	ENSP00000199764:p.Gly85Glu	Somatic	446	1	0.00224215		WXS	Illumina HiSeq	Phase_I	429	205	0.477855	NM_002483	Q13774|Q14920|Q53XP7	Missense_Mutation	SNP	ENST00000199764.6	37	CCDS12585.1	51	0.023351648351648352	47	0.09552845528455285	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	0.011	-1.703438	0.00719	0.08148	8.14E-4	ENSG00000086548	ENST00000199764	T	0.64085	-0.08	1.92	-3.84	0.04256	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01189	0.0039	N	0.16903	0.455	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.02333	-1.1175	9	0.54805	T	0.06	.	5.4199	0.16394	0.2722:0.4787:0.2491:0.0	rs61736638	85	P40199	CEAM6_HUMAN	E	85	ENSP00000199764:G85E	ENSP00000199764:G85E	G	+	2	0	CEACAM6	46952537	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.930000	0.00689	-3.925000	0.00091	-3.948000	0.00015	GGA	G|0.974;A|0.026	0.026	strong		0.498	CEACAM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321147.1		
TMEM63A	9725	hgsc.bcm.edu	37	1	226034913	226034913	+	Splice_Site	SNP	G	G	A	rs58852301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226034913G>A	ENST00000366835.3	-	24	2522	c.2252C>T	c.(2251-2253)cCc>cTc	p.P751L	RP11-285F7.2_ENST00000424332.1_RNA	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	751					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)					AGGCACGTAGGGCTGTCAGCA	0.592													G|||	193	0.0385383	0.1346	0.0202	5008	,	,		20323	0.0		0.0	False		,,,				2504	0.001				p.P751L		Atlas-SNP	.											TMEM63A,colon,carcinoma,+1,1	TMEM63A	75	1	0			c.C2252T						PASS	.	G	LEU/PRO	562,3838	234.2+/-247.1	35,492,1673	65.0	56.0	59.0		2252	3.1	1.0	1	dbSNP_129	59	0,8598		0,0,4299	yes	missense-near-splice	TMEM63A	NM_014698.2	98	35,492,5972	AA,AG,GG		0.0,12.7727,4.3237	benign	751/808	226034913	562,12436	2200	4299	6499	SO:0001630	splice_region_variant	9725	exon24			ACGTAGGGCTGTC		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.2251-1C>T	1.37:g.226034913G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	37	CCDS31042.1	78	0.03571428571428571	70	0.14227642276422764	8	0.022099447513812154	0	0.0	0	0.0	G	10.91	1.484973	0.26598	0.127727	0.0	ENSG00000196187	ENST00000366835	T	0.16597	2.33	4.11	3.1	0.35709	.	0.162225	0.53938	D	0.000053	T	0.00109	0.0003	L	0.57536	1.79	0.09310	P	0.99999999815609	B	0.06786	0.001	B	0.08055	0.003	T	0.05989	-1.0852	9	0.33940	T	0.23	-22.7721	5.9809	0.19407	0.1448:0.0:0.8552:0.0	rs58852301	751	O94886	TM63A_HUMAN	L	751	ENSP00000355800:P751L	ENSP00000355800:P751L	P	-	2	0	TMEM63A	224101536	1.000000	0.71417	0.999000	0.59377	0.909000	0.53808	1.585000	0.36600	2.146000	0.66826	0.448000	0.29417	CCC	G|0.956;A|0.044	0.044	strong		0.592	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	Missense_Mutation
RECQL	5965	hgsc.bcm.edu	37	12	21623969	21623969	+	Silent	SNP	A	A	G	rs6500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21623969A>G	ENST00000444129.2	-	14	2199	c.1731T>C	c.(1729-1731)aaT>aaC	p.N577N	RECQL_ENST00000421138.2_Silent_p.N577N	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	577					DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)	membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						TGTTCAGAAGATTAGCTTTAG	0.343								Other identified genes with known or suspected DNA repair function					A|||	758	0.151358	0.1483	0.1066	5008	,	,		14694	0.2946		0.0895	False		,,,				2504	0.1033				p.N577N		Atlas-SNP	.											.	RECQL	45	.	0			c.T1731C						PASS	.	A	,,	498,3908	230.7+/-244.8	31,436,1736	74.0	67.0	69.0		1731,,1731	3.3	0.9	12	dbSNP_52	69	789,7809	184.9+/-232.8	34,721,3544	no	coding-synonymous,utr-3,coding-synonymous	RECQL,PYROXD1	NM_002907.3,NM_024854.3,NM_032941.2	,,	65,1157,5280	GG,GA,AA		9.1766,11.3028,9.897	,,	577/650,,577/650	21623969	1287,11717	2203	4299	6502	SO:0001819	synonymous_variant	5965	exon15			CAGAAGATTAGCT	D37984	CCDS31756.1	12p12.1	2014-03-07	2014-03-07	2014-03-07	ENSG00000004700	ENSG00000004700			9948	protein-coding gene	gene with protein product	"""DNA helicase Q1-like"""	600537	"""RecQ protein-like (DNA helicase Q1-like)"""			7527136, 7961977	Standard	NM_002907		Approved	RecQ1, RecQL1	uc001rex.3	P46063	OTTHUMG00000169131	ENST00000444129.2:c.1731T>C	12.37:g.21623969A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	143	66	0.461538	NM_032941	A8K6G2	Silent	SNP	ENST00000444129.2	37	CCDS31756.1																																																																																			A|0.888;G|0.112	0.112	strong		0.343	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907	
SNAPC4	6621	hgsc.bcm.edu	37	9	139273402	139273402	+	Silent	SNP	C	C	T	rs3812567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139273402C>T	ENST00000298532.2	-	21	3245	c.2877G>A	c.(2875-2877)gcG>gcA	p.A959A		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GTTTGGCTGCCGCGGGGGCCC	0.662													T|||	3910	0.780751	0.9856	0.6455	5008	,	,		11872	0.8452		0.6909	False		,,,				2504	0.6258				p.A959A		Atlas-SNP	.											.	SNAPC4	82	.	0			c.G2877A						PASS	.	T		4127,257		1947,233,12	16.0	19.0	18.0		2877	-2.0	0.0	9	dbSNP_107	18	5890,2690		2015,1860,415	no	coding-synonymous	SNAPC4	NM_003086.2		3962,2093,427	TT,TC,CC		31.352,5.8622,22.7322		959/1470	139273402	10017,2947	2192	4290	6482	SO:0001819	synonymous_variant	6621	exon21			GGCTGCCGCGGGG	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.2877G>A	9.37:g.139273402C>T		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	258	257	0.996124	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			C|0.201;T|0.799	0.799	strong		0.662	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
HPS3	84343	hgsc.bcm.edu	37	3	148881673	148881673	+	Silent	SNP	C	C	T	rs3732557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148881673C>T	ENST00000296051.2	+	14	2666	c.2526C>T	c.(2524-2526)caC>caT	p.H842H	HPS3_ENST00000460120.1_Silent_p.H677H	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	842					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CATGGGTTCACGTCGTAATAT	0.279									Hermansky-Pudlak syndrome				C|||	778	0.155351	0.0136	0.1441	5008	,	,		17878	0.2738		0.1799	False		,,,				2504	0.2076				p.H842H		Atlas-SNP	.											.	HPS3	104	.	0			c.C2526T						PASS	.	C		201,4203	120.4+/-158.0	4,193,2005	79.0	78.0	78.0		2526	-2.1	0.1	3	dbSNP_107	78	1627,6969	298.1+/-303.7	162,1303,2833	no	coding-synonymous	HPS3	NM_032383.3		166,1496,4838	TT,TC,CC		18.9274,4.564,14.0615		842/1005	148881673	1828,11172	2202	4298	6500	SO:0001819	synonymous_variant	84343	exon14	Familial Cancer Database	HPS, HPS1-8	GGTTCACGTCGTA	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2526C>T	3.37:g.148881673C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Silent	SNP	ENST00000296051.2	37	CCDS3140.1																																																																																			C|0.849;T|0.151	0.151	strong		0.279	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919624	12919624	+	Missense_Mutation	SNP	C	C	G	rs80027487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919624C>G	ENST00000240189.2	+	3	451	c.364C>G	c.(364-366)Ctg>Gtg	p.L122V		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	122					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)		AGCCTGGGCCCTGTCCTGCTT	0.552													.|||	543	0.108427	0.1256	0.098	5008	,	,		21092	0.129		0.1064	False		,,,				2504	0.0736				p.L122V		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.C364G						PASS	.	C	VAL/LEU	199,4205		45,109,2048	144.0	165.0	158.0		364	-0.5	0.0	1	dbSNP_131	158	176,8418		41,94,4162	no	missense	PRAMEF2	NM_023014.1	32	86,203,6210	GG,GC,CC		2.0479,4.5186,2.8851	probably-damaging	122/475	12919624	375,12623	2202	4297	6499	SO:0001583	missense	65122	exon3			TGGGCCCTGTCCT		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.364C>G	1.37:g.12919624C>G	ENSP00000240189:p.Leu122Val	Somatic	343	1	0.00291545		WXS	Illumina HiSeq	Phase_I	326	153	0.469325	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	165	0.07554945054945054	31	0.06300813008130081	26	0.0718232044198895	52	0.09090909090909091	56	0.07387862796833773	C	1.694	-0.503174	0.04261	0.045186	0.020479	ENSG00000120952	ENST00000240189	T	0.16457	2.34	0.842	-0.531	0.11894	.	35.621100	0.00166	N	0.000000	T	0.00412	0.0013	L	0.27053	0.805	0.80722	P	0.0	P	0.44044	0.825	B	0.39562	0.303	T	0.13255	-1.0516	9	0.16896	T	0.51	.	4.3822	0.11299	0.0:0.5326:0.4674:0.0	.	122	O60811	PRAM2_HUMAN	V	122	ENSP00000240189:L122V	ENSP00000240189:L122V	L	+	1	2	PRAMEF2	12842211	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.385000	0.07379	-0.153000	0.11137	0.194000	0.17425	CTG	C|0.896;G|0.104	0.104	strong		0.552	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
FNDC1	84624	hgsc.bcm.edu	37	6	159654720	159654720	+	Missense_Mutation	SNP	G	G	C	rs115529940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159654720G>C	ENST00000297267.9	+	11	3376	c.3176G>C	c.(3175-3177)aGc>aCc	p.S1059T	FNDC1_ENST00000340366.6_Missense_Mutation_p.S996T	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1059					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)		TACACGGCGAGCTCCAGAGGG	0.701													G|||	62	0.0123802	0.0439	0.0058	5008	,	,		14068	0.0		0.0	False		,,,				2504	0.0				p.S1059T		Atlas-SNP	.											.	FNDC1	250	.	0			c.G3176C						PASS	.	G	THR/SER	102,3642		2,98,1772	9.0	12.0	11.0		3176	0.4	0.1	6	dbSNP_132	11	1,7791		0,1,3895	yes	missense	FNDC1	NM_032532.2	58	2,99,5667	CC,CG,GG		0.0128,2.7244,0.8929	benign	1059/1895	159654720	103,11433	1872	3896	5768	SO:0001583	missense	84624	exon11			CGGCGAGCTCCAG	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.3176G>C	6.37:g.159654720G>C	ENSP00000297267:p.Ser1059Thr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	9	0.2	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	25|25	0.011446886446886446|0.011446886446886446	23|23	0.046747967479674794|0.046747967479674794	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	12.73|12.73	2.026772|2.026772	0.35797|0.35797	0.027244|0.027244	1.28E-4|1.28E-4	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.09538	.|2.97;3.87	4.86|4.86	0.374|0.374	0.16183|0.16183	.|.	.|0.613338	.|0.15407	.|N	.|0.263994	T|T	0.01870|0.01870	0.0059|0.0059	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	.|P;P	.|0.40731	.|0.728;0.608	.|B;B	.|0.36092	.|0.217;0.115	T|T	0.42548|0.42548	-0.9445|-0.9445	5|10	.|0.51188	.|T	.|0.08	-5.582|-5.582	2.6419|2.6419	0.04973|0.04973	0.3758:0.0:0.4119:0.2123|0.3758:0.0:0.4119:0.2123	.|.	.|996;1059	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	D|T	954|1059;996	.|ENSP00000297267:S1059T;ENSP00000342460:S996T	.|ENSP00000297267:S1059T	E|S	+|+	3|2	2|0	FNDC1|FNDC1	159574710|159574710	0.096000|0.096000	0.21769|0.21769	0.052000|0.052000	0.19188|0.19188	0.053000|0.053000	0.15095|0.15095	0.113000|0.113000	0.15499|0.15499	0.445000|0.445000	0.26639|0.26639	0.561000|0.561000	0.74099|0.74099	GAG|AGC	G|0.986;C|0.014	0.014	strong		0.701	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
USP17L2	377630	hgsc.bcm.edu	37	8	11995004	11995004	+	Silent	SNP	C	C	T	rs186311075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11995004C>T	ENST00000333796.3	-	1	1582	c.1266G>A	c.(1264-1266)gaG>gaA	p.E422E	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	422	Mediates interaction with SUDS3.				apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						CCACCAAGCGCTCGTCCAACT	0.562													C|||	51	0.0101837	0.0363	0.0043	5008	,	,		20092	0.0		0.0	False		,,,				2504	0.0				p.E422E		Atlas-SNP	.											.	USP17L2	47	.	0			c.G1266A						PASS	.	C		58,3128		3,52,1538	59.0	65.0	63.0		1266	0.7	0.0	8		63	5,7101		1,3,3549	no	coding-synonymous	USP17L2	NM_201402.2		4,55,5087	TT,TC,CC		0.0704,1.8205,0.6121		422/531	11995004	63,10229	1593	3553	5146	SO:0001819	synonymous_variant	377630	exon1			CAAGCGCTCGTCC	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"""deubiquitinating enzyme 3"""	610186	"""ubiquitin specific peptidase 17-like 2"""				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.1266G>A	8.37:g.11995004C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	131	27	0.206107	NM_201402		Silent	SNP	ENST00000333796.3	37	CCDS43713.1																																																																																			C|0.992;T|0.008	0.008	strong		0.562	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402	
RPP38	10557	hgsc.bcm.edu	37	10	15145855	15145855	+	Missense_Mutation	SNP	C	C	G	rs15772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:15145855C>G	ENST00000378197.4	+	3	1056	c.542C>G	c.(541-543)gCg>gGg	p.A181G	RPP38_ENST00000378202.5_Missense_Mutation_p.A181G|RPP38_ENST00000451677.1_Intron|NMT2_ENST00000466201.1_Intron	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	181			A -> G (in dbSNP:rs15772). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		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						CTAGCCTTGGCGTTCAAAAAG	0.488													G|||	1813	0.362021	0.8699	0.2118	5008	,	,		19539	0.1131		0.2346	False		,,,				2504	0.1697				p.A181G	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.C542G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	3327,1079	390.3+/-327.6	1253,821,129	67.0	67.0	67.0		542,542,542	5.7	1.0	10	dbSNP_52	67	2031,6569	720.8+/-406.3	239,1553,2508	yes	missense,missense,missense	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	60,60,60	1492,2374,2637	GG,GC,CC		23.6163,24.4893,41.1964	benign,benign,benign	181/284,181/284,181/284	15145855	5358,7648	2203	4300	6503	SO:0001583	missense	10557	exon2			CCTTGGCGTTCAA	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.542C>G	10.37:g.15145855C>G	ENSP00000367439:p.Ala181Gly	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Missense_Mutation	SNP	ENST00000378197.4	37	CCDS7108.1	760	0.34798534798534797	430	0.8739837398373984	89	0.24585635359116023	63	0.11013986013986014	178	0.23482849604221637	G	3.216	-0.160663	0.06502	0.755107	0.236163	ENSG00000152464	ENST00000378203;ENST00000378202;ENST00000378197	T;T;T	0.53206	0.63;0.63;0.63	5.68	5.68	0.88126	Ribosomal protein L7Ae/L30e/S12e/Gadd45 (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00808	-1.17	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41822	-0.9487	9	0.02654	T	1	-20.1945	16.8756	0.86051	0.0:0.1285:0.8715:0.0	rs15772;rs1132102;rs3192597;rs52820525;rs58876686;rs15772	181	P78345	RPP38_HUMAN	G	181	ENSP00000367445:A181G;ENSP00000367444:A181G;ENSP00000367439:A181G	ENSP00000367439:A181G	A	+	2	0	RPP38	15185861	1.000000	0.71417	0.961000	0.40146	0.003000	0.03518	7.662000	0.83803	1.415000	0.47037	-0.187000	0.12897	GCG	C|0.612;G|0.388	0.388	strong		0.488	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414	
C19orf44	84167	hgsc.bcm.edu	37	19	16612011	16612011	+	Silent	SNP	T	T	C	rs728117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16612011T>C	ENST00000221671.3	+	2	564	c.408T>C	c.(406-408)tcT>tcC	p.S136S	CTD-3222D19.2_ENST00000409035.1_Intron|C19orf44_ENST00000594035.1_Silent_p.S136S	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	136										endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						GAATCCTCTCTGGGGGTGCAC	0.512													C|||	1835	0.366414	0.643	0.3415	5008	,	,		17337	0.1736		0.3221	False		,,,				2504	0.2546				p.S136S		Atlas-SNP	.											.	C19orf44	47	.	0			c.T408C						PASS	.	C		2698,1708	509.6+/-367.3	843,1012,348	55.0	61.0	59.0		408	-2.9	0.0	19	dbSNP_86	59	2642,5958	684.2+/-403.9	411,1820,2069	no	coding-synonymous	C19orf44	NM_032207.2		1254,2832,2417	CC,CT,TT		30.7209,38.7653,41.058		136/658	16612011	5340,7666	2203	4300	6503	SO:0001819	synonymous_variant	84167	exon2			CCTCTCTGGGGGT	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.408T>C	19.37:g.16612011T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	41	0.577465	NM_032207	Q8N6Y7	Silent	SNP	ENST00000221671.3	37	CCDS12345.1																																																																																			T|0.663;C|0.337	0.337	strong		0.512	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207	
DSPP	1834	hgsc.bcm.edu	37	4	88535869	88535869	+	Silent	SNP	C	C	T	rs200233307		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88535869C>T	ENST00000282478.7	+	4	2088	c.2055C>T	c.(2053-2055)aaC>aaT	p.N685N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.N685N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	685	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcaacagcagtgata	0.478																																					p.N685N		Atlas-SNP	.											DSPP,NS,carcinoma,0,2	DSPP	174	2	0			c.C2055T						PASS	.						116.0	132.0	126.0					4																	88535869		1685	3089	4774	SO:0001819	synonymous_variant	1834	exon5			CAGCAACAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2055C>T	4.37:g.88535869C>T		Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	346	58	0.16763	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.478	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
VDR	7421	hgsc.bcm.edu	37	12	48272895	48272895	+	Start_Codon_SNP	SNP	A	A	G	rs2228570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48272895A>G	ENST00000395324.2	-	3	270	c.2T>C	c.(1-3)aTg>aCg	p.M1T	VDR_ENST00000550325.1_Missense_Mutation_p.M51T|VDR_ENST00000549336.1_Start_Codon_SNP_p.M1T|VDR_ENST00000535672.1_5'UTR|VDR_ENST00000229022.3_Start_Codon_SNP_p.M1T			P11473	VDR_HUMAN	vitamin D (1,25- dihydroxyvitamin D3) receptor	1					bile acid signaling pathway (GO:0038183)|calcium ion transport (GO:0006816)|cell morphogenesis (GO:0000902)|cellular calcium ion homeostasis (GO:0006874)|decidualization (GO:0046697)|gene expression (GO:0010467)|intestinal absorption (GO:0050892)|lactation (GO:0007595)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|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 apoptotic process involved in mammary gland involution (GO:0060058)|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 vitamin D 24-hydroxylase activity (GO:0010980)|regulation of calcidiol 1-monooxygenase activity (GO:0060558)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin D receptor signaling pathway (GO:0070561)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcitriol binding (GO:1902098)|calcitriol receptor activity (GO:0008434)|DNA binding (GO:0003677)|lithocholic acid binding (GO:1902121)|lithocholic acid receptor activity (GO:0038186)|retinoid X receptor binding (GO:0046965)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(3)|skin(2)	22		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Alfacalcidol(DB01436)|Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	CATTGCCTCCATCCCTGTAAG	0.642													A|||	3363	0.671526	0.8109	0.5173	5008	,	,		12574	0.5823		0.6223	False		,,,				2504	0.7352				p.M51T		Atlas-SNP	.											.	VDR	47	.	0			c.T152C	GRCh37	CM972826	VDR	M	rs2228570	PASS	.	A	THR/MET,THR/MET,THR/MET	3474,932	736.5+/-410.8	1363,748,92	70.0	61.0	64.0		2,2,152	2.9	1.0	12	dbSNP_98	64	5281,3319	644.1+/-400.0	1644,1993,663	yes	missense,missense,missense	VDR	NM_000376.2,NM_001017535.1,NM_001017536.1	81,81,81	3007,2741,755	GG,GA,AA		38.593,21.153,32.6849	probably-damaging,probably-damaging,probably-damaging	1/428,1/428,51/478	48272895	8755,4251	2203	4300	6503	SO:0001582	initiator_codon_variant	7421	exon3			GCCTCCATCCCTG	J03258	CCDS8757.1, CCDS55820.1	12q12-q14	2014-06-13				ENSG00000111424		"""Nuclear hormone receptors"""	12679	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 163"""	601769				1662663	Standard	NM_001017536		Approved	NR1I1, PPP1R163	uc001rql.3	P11473		ENST00000395324.2:c.2T>C	12.37:g.48272895A>G	ENSP00000378734:p.Met1Thr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_001017536	B2R5Q1|G3V1V9|Q5PSV3	Missense_Mutation	SNP	ENST00000395324.2	37	CCDS8757.1	1427	0.6533882783882784	409	0.8313008130081301	208	0.574585635359116	353	0.6171328671328671	457	0.6029023746701847	A	17.39	3.376748	0.61735	0.78847	0.61407	ENSG00000111424	ENST00000395324;ENST00000229022;ENST00000549336;ENST00000550325;ENST00000546653;ENST00000550314;ENST00000548664	D;D;D;D;D;D;D	0.93953	-3.24;-3.24;-3.24;-3.12;-2.88;-3.32;-3.16	5.58	2.89	0.33648	.	0.149012	0.56097	D	0.000031	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B;D	0.63880	0.289;0.993	B;P	0.58928	0.275;0.848	T	0.45571	-0.9252	8	0.87932	D	0	.	9.9501	0.41634	0.8342:0.0:0.1658:0.0	rs2228570;rs8179174;rs10735810;rs17881966;rs52811041;rs56641119;rs57067622;rs10735810	1;51	P11473;G3V1V9	VDR_HUMAN;.	T	1;1;1;51;1;1;1	ENSP00000378734:M1T;ENSP00000229022:M1T;ENSP00000449573:M1T;ENSP00000447173:M51T;ENSP00000448659:M1T;ENSP00000449561:M1T;ENSP00000450105:M1T	ENSP00000229022:M1T	M	-	2	0	VDR	46559162	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.298000	0.59067	0.944000	0.37579	0.533000	0.62120	ATG	T|0.044;G|0.570;C|0.097;A|0.288	0.570	strong		0.642	VDR-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406433.1		Missense_Mutation
CNGA4	1262	hgsc.bcm.edu	37	11	6262909	6262909	+	Missense_Mutation	SNP	G	G	A	rs61745230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6262909G>A	ENST00000379936.2	+	5	1281	c.1166G>A	c.(1165-1167)cGa>cAa	p.R389Q	CNGA4_ENST00000533426.1_Missense_Mutation_p.R158Q	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	389					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 cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TACATCATCCGAGAGGGTCAA	0.532													G|||	143	0.0285543	0.0492	0.0317	5008	,	,		22525	0.0129		0.0308	False		,,,				2504	0.0123				p.R389Q		Atlas-SNP	.											.	CNGA4	96	.	0			c.G1166A						PASS	.	G	GLN/ARG	215,4187	131.0+/-167.6	5,205,1991	278.0	238.0	251.0		1166	5.0	1.0	11	dbSNP_129	251	193,8399	84.5+/-147.0	3,187,4106	yes	missense	CNGA4	NM_001037329.3	43	8,392,6097	AA,AG,GG		2.2463,4.8841,3.1399	probably-damaging	389/576	6262909	408,12586	2201	4296	6497	SO:0001583	missense	1262	exon5			TCATCCGAGAGGG	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2152	protein-coding gene	gene with protein product		609472	"""cyclic nucleotide gated channel beta 2"""	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.1166G>A	11.37:g.6262909G>A	ENSP00000369268:p.Arg389Gln	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	160	78	0.4875	NM_001037329		Missense_Mutation	SNP	ENST00000379936.2	37	CCDS31408.1	65	0.02976190476190476	27	0.054878048780487805	14	0.03867403314917127	6	0.01048951048951049	18	0.023746701846965697	G	17.57	3.422670	0.62733	0.048841	0.022463	ENSG00000132259	ENST00000533426;ENST00000379936	D;D	0.92299	-3.01;-3.01	5.0	5.0	0.66597	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.139396	0.49305	D	0.000150	T	0.50718	0.1632	N	0.20445	0.575	0.37153	D	0.90222	P;P;P	0.49961	0.806;0.93;0.803	B;B;B	0.39339	0.249;0.174;0.297	T	0.74134	-0.3763	10	0.24483	T	0.36	.	10.5989	0.45354	0.0881:0.0:0.9119:0.0	rs61745230	158;389;349	B4DYQ8;Q8IV77;Q8IV77-2	.;CNGA4_HUMAN;.	Q	158;389	ENSP00000433399:R158Q;ENSP00000369268:R389Q	ENSP00000369268:R389Q	R	+	2	0	CNGA4	6219485	0.642000	0.27260	0.957000	0.39632	0.974000	0.67602	1.297000	0.33400	2.588000	0.87417	0.655000	0.94253	CGA	G|0.966;A|0.034	0.034	strong		0.532	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329	
CCL24	6369	hgsc.bcm.edu	37	7	75442730	75442730	+	Missense_Mutation	SNP	T	T	G	rs2302006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75442730T>G	ENST00000416943.1	-	3	178	c.85A>C	c.(85-87)Atc>Ctc	p.I29L	CCL24_ENST00000222902.2_Missense_Mutation_p.I29L	NM_002991.2	NP_002982.2	O00175	CCL24_HUMAN	chemokine (C-C motif) ligand 24	29			I -> L (in dbSNP:rs2302006). {ECO:0000269|PubMed:14702039}.		cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of inflammatory response (GO:0050729)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(1)|lung(2)	3						GGAGAGGGGATGACCACAGAG	0.562													T|||	1733	0.346046	0.2685	0.4063	5008	,	,		17705	0.5595		0.1839	False		,,,				2504	0.3548				p.I29L		Atlas-SNP	.											.	CCL24	11	.	0			c.A85C						PASS	.	T	LEU/ILE	1230,3176		173,884,1146	69.0	72.0	71.0		85	-0.4	0.0	7	dbSNP_100	71	1725,6875		170,1385,2745	yes	missense	CCL24	NM_002991.2	5	343,2269,3891	GG,GT,TT		20.0581,27.9165,22.7203	benign	29/120	75442730	2955,10051	2203	4300	6503	SO:0001583	missense	6369	exon2			AGGGGATGACCAC	U85768	CCDS34670.1	7q11.23	2013-02-25	2002-08-22	2002-08-23	ENSG00000106178	ENSG00000106178		"""Chemokine ligands"", ""Endogenous ligands"""	10623	protein-coding gene	gene with protein product	"""CK-beta-6"", ""myeloid progenitor inhibitory factor 2"", ""eotaxin-2"""	602495	"""small inducible cytokine subfamily A (Cys-Cys), member 24"""	SCYA24		9104803, 9598329	Standard	NM_002991		Approved	Ckb-6, MPIF-2, eotaxin-2, MPIF2	uc011kga.2	O00175	OTTHUMG00000156635	ENST00000416943.1:c.85A>C	7.37:g.75442730T>G	ENSP00000400533:p.Ile29Leu	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	51	35	0.686275	NM_002991	B2R5K2	Missense_Mutation	SNP	ENST00000416943.1	37	CCDS34670.1	739	0.3383699633699634	141	0.2865853658536585	125	0.3453038674033149	325	0.5681818181818182	148	0.19525065963060687	.	6.304	0.424243	0.11928	0.279165	0.200581	ENSG00000106178	ENST00000222902;ENST00000416943	T;T	0.03689	3.84;3.84	3.61	-0.408	0.12381	Chemokine interleukin-8-like domain (1);	1.308000	0.05150	N	0.495911	T	0.00012	0.0000	L	0.37800	1.135	0.80722	P	0.0	B	0.11235	0.004	B	0.14023	0.01	T	0.35895	-0.9770	9	0.16420	T	0.52	.	9.5265	0.39167	0.0:0.0:0.5652:0.4348	rs2302006;rs11465292;rs60968338;rs2302006	29	O00175	CCL24_HUMAN	L	29	ENSP00000222902:I29L;ENSP00000400533:I29L	ENSP00000222902:I29L	I	-	1	0	CCL24	75280666	0.696000	0.27757	0.004000	0.12327	0.004000	0.04260	0.260000	0.18424	-0.058000	0.13177	-0.291000	0.09656	ATC	T|0.714;G|0.286	0.286	strong		0.562	CCL24-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344886.1	NM_002991	
OR6C74	254783	hgsc.bcm.edu	37	12	55641255	55641255	+	Nonsense_Mutation	SNP	C	C	T	rs4522268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	232	0	0		WXS	Illumina HiSeq	Phase_I	219	83	0.378995	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		
NT5C1B	93034	hgsc.bcm.edu	37	2	18766123	18766123	+	Missense_Mutation	SNP	C	C	T	rs61742608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:18766123C>T	ENST00000359846.2	-	5	637	c.560G>A	c.(559-561)cGg>cAg	p.R187Q	NT5C1B_ENST00000460052.1_5'Flank|NT5C1B_ENST00000304081.4_Missense_Mutation_p.R127Q|NT5C1B-RDH14_ENST00000532967.1_Missense_Mutation_p.R187Q|RNU6-1215P_ENST00000384441.1_RNA|NT5C1B_ENST00000600945.1_Missense_Mutation_p.R187Q	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	187	Pro-rich.				nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				GTCCAGCGACCGGGGCAGCTG	0.716													C|||	571	0.114018	0.267	0.1455	5008	,	,		12159	0.0615		0.0447	False		,,,				2504	0.0102				p.R204Q		Atlas-SNP	.											.	NT5C1B	72	.	0			c.G611A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1033,3319		132,769,1275	12.0	17.0	15.0		560,509,611,566,386,560,380	-3.9	0.0	2	dbSNP_129	15	397,8075		19,359,3858	no	missense,missense,missense,missense,missense,missense,missense	NT5C1B,NT5C1B-RDH14	NM_001002006.2,NM_001199086.1,NM_001199087.1,NM_001199088.1,NM_001199103.1,NM_001199104.1,NM_033253.3	43,43,43,43,43,43,43	151,1128,5133	TT,TC,CC		4.686,23.7362,11.151	benign,benign,benign,benign,benign,benign,benign	187/611,170/594,204/628,189/613,129/651,187/603,127/551	18766123	1430,11394	2176	4236	6412	SO:0001583	missense	93034	exon5			AGCGACCGGGGCA	AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.560G>A	2.37:g.18766123C>T	ENSP00000352904:p.Arg187Gln	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	20	17	0.85	NM_001199087	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Missense_Mutation	SNP	ENST00000359846.2	37	CCDS33150.1	223	0.1021062271062271	108	0.21951219512195122	38	0.10497237569060773	38	0.06643356643356643	39	0.051451187335092345	C	11.28	1.592744	0.28357	0.237362	0.04686	ENSG00000250741;ENSG00000250741;ENSG00000185013;ENSG00000185013;ENSG00000185013	ENST00000532967;ENST00000444297;ENST00000304081;ENST00000359846;ENST00000416783	D	0.88818	-2.43	2.12	-3.92	0.04155	.	1.469850	0.04541	N	0.388145	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;D;P;P;B;P;B;P	0.55172	0.429;0.97;0.696;0.604;0.043;0.512;0.074;0.68	B;B;B;B;B;B;B;B	0.30495	0.035;0.116;0.033;0.035;0.003;0.073;0.003;0.073	T	0.44345	-0.9334	9	0.12103	T	0.63	-17.3016	0.7244	0.00946	0.2453:0.2471:0.3271:0.1805	.	170;204;127;170;129;127;187;187	E7EXB7;B4DZ86;B4DXQ9;B4DXZ9;C9J2C7;Q96P26-2;Q96P26;Q96P26-4	.;.;.;.;.;.;5NT1B_HUMAN;.	Q	187;129;127;187;204	ENSP00000412639:R129Q	ENSP00000305979:R127Q	R	-	2	0	NT5C1B-RDH14;NT5C1B	18629604	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.170000	0.03118	-1.076000	0.03125	-0.309000	0.09137	CGG	C|0.899;T|0.101	0.101	strong		0.716	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1		
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692277	31692277	+	Missense_Mutation	SNP	G	G	T	rs3804007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31692277G>T	ENST00000360542.3	-	1	330	c.77C>A	c.(76-78)tCc>tAc	p.S26Y		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	26			S -> Y (in dbSNP:rs3804007).			intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GAGGTCGATGGAGGTGAGAGG	0.542													G|||	509	0.101637	0.2035	0.0893	5008	,	,		19648	0.0218		0.0527	False		,,,				2504	0.1053				p.S26Y		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.C77A						PASS	.	G	TYR/SER	806,3600	321.3+/-297.0	62,682,1459	66.0	68.0	67.0		77	4.9	0.0	21	dbSNP_107	67	512,8088	144.7+/-200.5	15,482,3803	yes	missense	KRTAP26-1	NM_203405.1	144	77,1164,5262	TT,TG,GG		5.9535,18.2932,10.1338	probably-damaging	26/211	31692277	1318,11688	2203	4300	6503	SO:0001583	missense	388818	exon1			TCGATGGAGGTGA	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"""Keratin associated proteins"""	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.77C>A	21.37:g.31692277G>T	ENSP00000353742:p.Ser26Tyr	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	208	107	0.514423	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	171	0.0782967032967033	94	0.1910569105691057	28	0.07734806629834254	9	0.015734265734265736	40	0.052770448548812667	G	12.75	2.031278	0.35797	0.182932	0.059535	ENSG00000197683	ENST00000360542	T	0.05925	3.37	4.95	4.95	0.65309	.	0.351539	0.25878	N	0.027710	T	0.00039	0.0001	M	0.78456	2.415	0.80722	P	0.0	D	0.89917	1.0	D	0.79108	0.992	T	0.01053	-1.1467	9	0.66056	D	0.02	-16.96	14.402	0.67053	0.0:0.0:1.0:0.0	rs3804007;rs52829761;rs3804007	26	Q6PEX3	KR261_HUMAN	Y	26	ENSP00000353742:S26Y	ENSP00000353742:S26Y	S	-	2	0	KRTAP26-1	30614148	0.035000	0.19736	0.040000	0.18447	0.060000	0.15804	1.639000	0.37176	2.664000	0.90586	0.655000	0.94253	TCC	G|0.909;T|0.091	0.091	strong		0.542	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405	
CELA2B	51032	hgsc.bcm.edu	37	1	15809876	15809876	+	Silent	SNP	G	G	A	rs10927792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:15809876G>A	ENST00000375910.3	+	5	499	c.474G>A	c.(472-474)acG>acA	p.T158T		NM_015849.2	NP_056933	P08218	CEL2B_HUMAN	chymotrypsin-like elastase family, member 2B	158	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8						GCTACGTCACGGGCTGGGGAA	0.642													G|||	1734	0.346246	0.348	0.3545	5008	,	,		19203	0.5694		0.2416	False		,,,				2504	0.2157				p.T158T		Atlas-SNP	.											.	CELA2B	37	.	0			c.G474A						PASS	.	G		1419,2987	463.6+/-353.6	220,979,1004	70.0	64.0	66.0		474	-7.6	0.2	1	dbSNP_120	66	2111,6483	361.5+/-332.4	270,1571,2456	no	coding-synonymous	CELA2B	NM_015849.2		490,2550,3460	AA,AG,GG		24.5636,32.2061,27.1538		158/270	15809876	3530,9470	2203	4297	6500	SO:0001819	synonymous_variant	51032	exon5			CGTCACGGGCTGG		CCDS30605.1	1p36.21	2009-07-09			ENSG00000215704	ENSG00000215704			29995	protein-coding gene	gene with protein product	"""pancreatic elastase IIB"""	609444				3646943, 16327289	Standard	NM_015849		Approved	RP11-265F14.2, ELA2B	uc001awl.3	P08218	OTTHUMG00000002259	ENST00000375910.3:c.474G>A	1.37:g.15809876G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	143	62	0.433566	NM_015849	Q14D16|Q6ISM5|Q96QV5	Silent	SNP	ENST00000375910.3	37	CCDS30605.1																																																																																			G|0.250;A|0.750	0.750	weak		0.642	CELA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006448.1	NM_015849	
ATOH1	474	hgsc.bcm.edu	37	4	94750650	94750650	+	Silent	SNP	C	C	T	rs34543561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:94750650C>T	ENST00000306011.3	+	1	609	c.573C>T	c.(571-573)aaC>aaT	p.N191N		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	191	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				auditory receptor cell fate determination (GO:0042668)|auditory receptor cell fate specification (GO:0042667)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|cerebral cortex development (GO:0021987)|inner ear morphogenesis (GO:0042472)|negative regulation of apoptotic process (GO:0043066)|neuron migration (GO:0001764)|positive regulation of auditory receptor cell differentiation (GO:0045609)|positive regulation of neuron differentiation (GO:0045666)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|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)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)		CGTTCAACAACGACAAGAAGC	0.582													C|||	29	0.00579073	0.0219	0.0	5008	,	,		17596	0.0		0.0	False		,,,				2504	0.0				p.N191N		Atlas-SNP	.											ATOH1,NS,carcinoma,+2,1	ATOH1	40	1	0			c.C573T						PASS	.	C		97,4309	77.8+/-116.1	2,93,2108	53.0	54.0	53.0		573	4.4	1.0	4	dbSNP_126	53	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ATOH1	NM_005172.1		2,95,6406	TT,TC,CC		0.0233,2.2015,0.7612		191/355	94750650	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	474	exon1			CAACAACGACAAG	U61148	CCDS3638.1	4q22	2013-05-21			ENSG00000172238	ENSG00000172238		"""Basic helix-loop-helix proteins"""	797	protein-coding gene	gene with protein product		601461				8872459	Standard	NM_005172		Approved	HATH1, MATH-1, Math1, bHLHa14	uc003hta.1	Q92858	OTTHUMG00000130972	ENST00000306011.3:c.573C>T	4.37:g.94750650C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	192	98	0.510417	NM_005172	Q14CT9	Silent	SNP	ENST00000306011.3	37	CCDS3638.1																																																																																			C|0.992;T|0.008	0.008	strong		0.582	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172	
ASPM	259266	hgsc.bcm.edu	37	1	197093361	197093361	+	Missense_Mutation	SNP	G	G	A	rs16841081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:197093361G>A	ENST00000367409.4	-	13	3525	c.3269C>T	c.(3268-3270)tCt>tTt	p.S1090F	ASPM_ENST00000367408.1_Missense_Mutation_p.S340F|ASPM_ENST00000294732.7_Missense_Mutation_p.S1090F	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1090			S -> F (in dbSNP:rs16841081). {ECO:0000269|PubMed:15489334}.		developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						AAGATCATCAGAATGGCATGA	0.303													G|||	224	0.0447284	0.1626	0.013	5008	,	,		15011	0.0		0.0	False		,,,				2504	0.0				p.S1090F		Atlas-SNP	.											.	ASPM	444	.	0			c.C3269T						PASS	.	G	PHE/SER,PHE/SER	634,3768	268.6+/-268.5	45,544,1612	93.0	95.0	94.0		3269,3269	3.6	0.0	1	dbSNP_123	94	2,8550	1.2+/-3.3	0,2,4274	yes	missense,missense	ASPM	NM_001206846.1,NM_018136.4	155,155	45,546,5886	AA,AG,GG		0.0234,14.4025,4.9097	probably-damaging,probably-damaging	1090/1893,1090/3478	197093361	636,12318	2201	4276	6477	SO:0001583	missense	259266	exon13			TCATCAGAATGGC	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.3269C>T	1.37:g.197093361G>A	ENSP00000356379:p.Ser1090Phe	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	284	138	0.485915	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	83	0.038003663003663	77	0.1565040650406504	6	0.016574585635359115	0	0.0	0	0.0	G	7.626	0.677857	0.14841	0.144025	2.34E-4	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408	T;T;T	0.59224	0.28;1.55;1.26	5.53	3.64	0.41730	Calponin homology domain (1);	0.608927	0.16421	N	0.215176	T	0.00271	0.0008	M	0.62723	1.935	0.80722	P	0.0	B;B	0.21520	0.006;0.057	B;B	0.15870	0.005;0.014	T	0.14117	-1.0484	9	0.66056	D	0.02	.	5.9506	0.19245	0.2999:0.0:0.7001:0.0	rs16841081;rs52835075;rs16841081	1090;1090	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	F	1090;1090;340	ENSP00000356379:S1090F;ENSP00000294732:S1090F;ENSP00000356378:S340F	ENSP00000294732:S1090F	S	-	2	0	ASPM	195359984	0.002000	0.14202	0.010000	0.14722	0.290000	0.27261	1.303000	0.33470	1.485000	0.48380	0.585000	0.79938	TCT	G|0.952;A|0.048	0.048	strong		0.303	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
POTEC	388468	hgsc.bcm.edu	37	18	14542654	14542654	+	Silent	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:14542654C>A	ENST00000358970.5	-	1	491	c.492G>T	c.(490-492)acG>acT	p.T164T	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	164								p.T164T(2)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TGTTCATGTCCGTGTCCCTGA	0.592																																					p.T164T		Atlas-SNP	.											POTEC,NS,carcinoma,-1,5	POTEC	129	5	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.G492T						scavenged	.						260.0	241.0	247.0					18																	14542654		692	1591	2283	SO:0001819	synonymous_variant	388468	exon1			CATGTCCGTGTCC	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.492G>T	18.37:g.14542654C>A		Somatic	816	4	0.00490196		WXS	Illumina HiSeq	Phase_I	927	15	0.0161812	NM_001137671		Silent	SNP	ENST00000358970.5	37	CCDS45835.1																																																																																			.	.	none		0.592	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
OR7A10	390892	hgsc.bcm.edu	37	19	14952238	14952238	+	Missense_Mutation	SNP	A	A	G	rs12972670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14952238A>G	ENST00000248058.1	-	1	451	c.452T>C	c.(451-453)aTg>aCg	p.M151T		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	151			M -> T (in dbSNP:rs12972670).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					CAGAACACTCATGATCCAGGA	0.453													.|||	617	0.123203	0.1422	0.1196	5008	,	,		21909	0.0903		0.1541	False		,,,				2504	0.1022				p.M151T		Atlas-SNP	.											OR7A10,colon,carcinoma,0,1	OR7A10	33	1	0			c.T452C						PASS	.	A	THR/MET	678,3728	286.0+/-278.5	58,562,1583	74.0	71.0	72.0		452	2.8	0.0	19	dbSNP_121	72	1457,7143	278.6+/-293.5	139,1179,2982	yes	missense	OR7A10	NM_001005190.1	81	197,1741,4565	GG,GA,AA		16.9419,15.3881,16.4155	benign	151/310	14952238	2135,10871	2203	4300	6503	SO:0001583	missense	390892	exon1			ACACTCATGATCC		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.452T>C	19.37:g.14952238A>G	ENSP00000248058:p.Met151Thr	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	164	91	0.554878	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	260	0.11904761904761904	69	0.1402439024390244	48	0.13259668508287292	27	0.0472027972027972	116	0.15303430079155672	a	0.596	-0.830989	0.02713	0.153881	0.169419	ENSG00000127515	ENST00000248058	T	0.00441	7.41	2.75	2.75	0.32379	GPCR, rhodopsin-like superfamily (1);	0.862066	0.09618	N	0.777980	T	0.00012	0.0000	N	0.21324	0.655	0.80722	P	0.0	B	0.10296	0.003	B	0.19666	0.026	T	0.19031	-1.0318	9	0.49607	T	0.09	.	9.0825	0.36561	1.0:0.0:0.0:0.0	rs12972670;rs16979967;rs58275244;rs12972670	151	O76100	OR7AA_HUMAN	T	151	ENSP00000248058:M151T	ENSP00000248058:M151T	M	-	2	0	OR7A10	14813238	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	-0.724000	0.04947	1.301000	0.44836	0.113000	0.15668	ATG	A|0.860;G|0.140	0.140	strong		0.453	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077904	19077904	+	Missense_Mutation	SNP	T	T	G	rs11024970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:19077904T>G	ENST00000329773.2	-	2	133	c.46A>C	c.(46-48)Aat>Cat	p.N16H		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	16			N -> H (in dbSNP:rs11024970). {ECO:0000269|PubMed:15862286}.		positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)			NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						TCATTTCCATTCACTGTTGTA	0.532													T|||	566	0.113019	0.1944	0.036	5008	,	,		18231	0.1468		0.0656	False		,,,				2504	0.0716				p.N16H	GBM(198;1966 2199 4849 37227 49954)	Atlas-SNP	.											.	MRGPRX2	42	.	0			c.A46C						PASS	.	T	HIS/ASN	702,3696		61,580,1558	192.0	208.0	203.0		46	3.9	0.0	11	dbSNP_120	203	428,8158		7,414,3872	yes	missense	MRGPRX2	NM_054030.2	68	68,994,5430	GG,GT,TT		4.9849,15.9618,8.703	probably-damaging	16/331	19077904	1130,11854	2199	4293	6492	SO:0001583	missense	117194	exon2			TTCCATTCACTGT		CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"""GPCR / Class A : Orphans"""	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.46A>C	11.37:g.19077904T>G	ENSP00000333800:p.Asn16His	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_054030	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Missense_Mutation	SNP	ENST00000329773.2	37	CCDS7847.1	219	0.10027472527472528	92	0.18699186991869918	14	0.03867403314917127	67	0.11713286713286714	46	0.06068601583113457	.	15.60	2.882651	0.51908	0.159618	0.049849	ENSG00000183695	ENST00000329773	T	0.06687	3.27	5.04	3.91	0.45181	.	1.260630	0.05164	N	0.498462	T	0.00039	0.0001	L	0.54323	1.7	0.80722	P	0.0	P	0.50617	0.937	P	0.58266	0.836	T	0.13150	-1.0520	9	0.72032	D	0.01	.	6.4342	0.21815	0.0:0.1872:0.0:0.8128	rs11024970;rs52815501;rs59607758;rs11024970	16	Q96LB1	MRGX2_HUMAN	H	16	ENSP00000333800:N16H	ENSP00000333800:N16H	N	-	1	0	MRGPRX2	19034480	0.000000	0.05858	0.048000	0.18961	0.032000	0.12392	0.063000	0.14410	1.052000	0.40392	0.533000	0.62120	AAT	T|0.899;G|0.101	0.101	strong		0.532	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030	
COL6A3	1293	hgsc.bcm.edu	37	2	238267717	238267717	+	Silent	SNP	C	C	T	rs2646254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238267717C>T	ENST00000295550.4	-	20	6821	c.6369G>A	c.(6367-6369)ttG>ttA	p.L2123L	COL6A3_ENST00000472056.1_Silent_p.L1516L|COL6A3_ENST00000409809.1_Silent_p.L1917L|COL6A3_ENST00000346358.4_Silent_p.L1923L|COL6A3_ENST00000347401.3_Silent_p.L1922L|COL6A3_ENST00000353578.4_Silent_p.L1917L	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2123	Collagen-like 2.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AAGAACCAGGCAATCCTTTGT	0.418													C|||	1657	0.330871	0.5416	0.2507	5008	,	,		19812	0.3522		0.1511	False		,,,				2504	0.2658				p.L2123L		Atlas-SNP	.											.	COL6A3	608	.	0			c.G6369A						PASS	.	C	,,	2073,2333	570.8+/-382.9	485,1103,615	208.0	226.0	220.0		6369,4548,5751	4.3	0.2	2	dbSNP_100	220	1168,7432	239.0+/-270.3	77,1014,3209	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	562,2117,3824	TT,TC,CC		13.5814,47.0495,24.9193	,,	2123/3178,1516/2571,1917/2972	238267717	3241,9765	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon20			ACCAGGCAATCCT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.6369G>A	2.37:g.238267717C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	222	98	0.441441	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.720;T|0.280	0.280	strong		0.418	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
FLG	2312	hgsc.bcm.edu	37	1	152277239	152277239	+	Missense_Mutation	SNP	G	G	A	rs111486002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152277239G>A	ENST00000368799.1	-	3	10158	c.10123C>T	c.(10123-10125)Cgg>Tgg	p.R3375W	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3375	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)			CCCCCTGACCGGTCACGTGCG	0.587									Ichthyosis				G|||	106	0.0211661	0.0756	0.0072	5008	,	,		19341	0.001		0.0	False		,,,				2504	0.0				p.R3375W		Atlas-SNP	.											.	FLG	900	.	0			c.C10123T						PASS	.	G	TRP/ARG	153,4253	93.4+/-132.2	4,145,2054	286.0	306.0	299.0		10123	1.8	0.0	1	dbSNP_132	299	2,8598	2.2+/-6.3	0,2,4298	no	missense	FLG	NM_002016.1	101	4,147,6352	AA,AG,GG		0.0233,3.4725,1.1918	probably-damaging	3375/4062	152277239	155,12851	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGACCGGTCACG	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.10123C>T	1.37:g.152277239G>A	ENSP00000357789:p.Arg3375Trp	Somatic	443	1	0.00225734		WXS	Illumina HiSeq	Phase_I	385	185	0.480519	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	G	9.323	1.058443	0.19987	0.034725	2.33E-4	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.00966	5.49	1.82	1.82	0.25136	.	.	.	.	.	T	0.01454	0.0047	M	0.63428	1.95	0.09310	N	1	D	0.89917	1.0	D	0.71414	0.973	T	0.51529	-0.8694	9	0.72032	D	0.01	.	7.1799	0.25765	0.0:0.0:1.0:0.0	.	3375	P20930	FILA_HUMAN	W	3375;313	ENSP00000357789:R3375W	ENSP00000357786:R313W	R	-	1	2	FLG	150543863	.	.	0.001000	0.08648	0.001000	0.01503	.	.	1.327000	0.45338	0.454000	0.30748	CGG	G|0.986;A|0.014	0.014	strong		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CELSR1	9620	hgsc.bcm.edu	37	22	46859701	46859701	+	Silent	SNP	C	C	T	rs140328042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46859701C>T	ENST00000262738.3	-	2	4085	c.4086G>A	c.(4084-4086)acG>acA	p.T1362T	CELSR1_ENST00000395964.1_Silent_p.T1362T	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1362					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)		GGTCGATCTCCGTCTCGCAGT	0.692													C|||	11	0.00219649	0.0083	0.0	5008	,	,		13548	0.0		0.0	False		,,,				2504	0.0				p.T1362T		Atlas-SNP	.											.	CELSR1	242	.	0			c.G4086A						PASS	.	C		37,4357		0,37,2160	33.0	33.0	33.0		4086	-9.5	0.7	22	dbSNP_134	33	0,8594		0,0,4297	no	coding-synonymous	CELSR1	NM_014246.1		0,37,6457	TT,TC,CC		0.0,0.8421,0.2849		1362/3015	46859701	37,12951	2197	4297	6494	SO:0001819	synonymous_variant	9620	exon2			GATCTCCGTCTCG	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.4086G>A	22.37:g.46859701C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	8.918	0.960317	0.18507	0.008421	0.0	ENSG00000075275	ENST00000454637	.	.	.	4.75	-9.49	0.00587	.	.	.	.	.	T	0.25232	0.0613	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37911	-0.9685	4	.	.	.	.	1.2491	0.01978	0.1999:0.3436:0.1613:0.2952	.	.	.	.	Q	737	.	.	R	-	2	0	CELSR1	45238365	0.000000	0.05858	0.651000	0.29564	0.922000	0.55478	-3.266000	0.00534	-2.191000	0.00756	-0.892000	0.02923	CGG	C|0.997;T|0.003	0.003	strong		0.692	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
ALCAM	214	hgsc.bcm.edu	37	3	105260518	105260518	+	Silent	SNP	G	G	A	rs579565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:105260518G>A	ENST00000306107.5	+	8	1400	c.900G>A	c.(898-900)ctG>ctA	p.L300L	ALCAM_ENST00000472644.2_Silent_p.L300L|ALCAM_ENST00000486979.2_Silent_p.L249L|ALCAM_ENST00000389927.4_Intron|ALCAM_ENST00000481337.1_3'UTR	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	300	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CTTACACACTGACGGATGTGA	0.423													G|||	1186	0.236821	0.3041	0.3084	5008	,	,		19891	0.1548		0.2366	False		,,,				2504	0.18				p.L300L		Atlas-SNP	.											.	ALCAM	71	.	0			c.G900A						PASS	.	G		1260,3146	428.7+/-342.0	184,892,1127	163.0	131.0	142.0		900	5.3	1.0	3	dbSNP_83	142	1903,6697	335.4+/-321.4	219,1465,2616	no	coding-synonymous	ALCAM	NM_001627.3		403,2357,3743	AA,AG,GG		22.1279,28.5974,24.3195		300/584	105260518	3163,9843	2203	4300	6503	SO:0001819	synonymous_variant	214	exon8			CACACTGACGGAT	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.900G>A	3.37:g.105260518G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Silent	SNP	ENST00000306107.5	37	CCDS33810.1																																																																																			G|0.759;A|0.241	0.241	strong		0.423	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
PARP4	143	hgsc.bcm.edu	37	13	25027745	25027745	+	Missense_Mutation	SNP	T	T	C	rs386769073|rs1130943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25027745T>C	ENST00000381989.3	-	23	2911	c.2806A>G	c.(2806-2808)Atg>Gtg	p.M936V	PARP4_ENST00000480576.1_5'Flank	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	936	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.			M -> A (in Ref. 2; AAC62491 and 3; BAA11494). {ECO:0000305}.|M -> T (in Ref. 1; AAD47250). {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)		TCTGCTGCCATGGTATTGCTT	0.478													N|||	352	0.0702875	0.2262	0.0216	5008	,	,		15989	0.0298		0.001	False		,,,				2504	0.0072				p.M936V		Atlas-SNP	.											PARP4,NS,carcinoma,+2,1	PARP4	142	1	0			c.A2806G						PASS	.	C	VAL/MET	795,3611	743.2+/-411.4	86,623,1494	277.0	217.0	237.0		2806	-3.9	0.0	13	dbSNP_86	237	14,8586	818.4+/-406.9	0,14,4286	yes	missense	PARP4	NM_006437.3	21	86,637,5780	CC,CT,TT		0.1628,18.0436,6.2202	benign	936/1725	25027745	809,12197	2203	4300	6503	SO:0001583	missense	143	exon23			CTGCCATGGTATT	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.2806A>G	13.37:g.25027745T>C	ENSP00000371419:p.Met936Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	191	95	0.497382	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	84	0.038461538461538464	71	0.1443089430894309	7	0.019337016574585635	6	0.01048951048951049	0	0.0	C	2.522	-0.310435	0.05458	0.180436	0.001628	ENSG00000102699	ENST00000381989	T	0.07567	3.18	4.29	-3.89	0.04193	von Willebrand factor, type A (3);	1.850880	0.02221	N	0.063999	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.41538	-0.9503	9	0.16896	T	0.51	0.2561	6.1523	0.20318	0.1226:0.3669:0.0:0.5105	rs1130943;rs3190390;rs12323011;rs17413359	936	Q9UKK3	PARP4_HUMAN	V	936	ENSP00000371419:M936V	ENSP00000371419:M936V	M	-	1	0	PARP4	23925745	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.131000	0.03238	-1.328000	0.02261	-0.273000	0.10243	ATG	T|0.949;C|0.051	0.051	strong		0.478	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
EMR1	2015	hgsc.bcm.edu	37	19	6904137	6904137	+	Missense_Mutation	SNP	C	C	T	rs370094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6904137C>T	ENST00000312053.4	+	8	930	c.893C>T	c.(892-894)gCa>gTa	p.A298V	EMR1_ENST00000250572.8_Missense_Mutation_p.A298V|EMR1_ENST00000381407.5_Missense_Mutation_p.A157V|EMR1_ENST00000450315.3_Intron|EMR1_ENST00000381404.4_Missense_Mutation_p.A246V	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	298	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		A -> V (in dbSNP:rs370094). {ECO:0000269|PubMed:7601460}.		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)					GGCTGCATTGCAGGCTTTCAT	0.473													C|||	2167	0.432708	0.6664	0.4193	5008	,	,		18598	0.4554		0.2396	False		,,,				2504	0.3016				p.A298V		Atlas-SNP	.											.	EMR1	153	.	0			c.C893T						PASS	.	C	VAL/ALA	2594,1812	639.8+/-397.2	780,1034,389	91.0	85.0	87.0		893	-7.8	0.0	19	dbSNP_80	87	2212,6388	375.7+/-337.9	291,1630,2379	yes	missense	EMR1	NM_001974.3	64	1071,2664,2768	TT,TC,CC		25.7209,41.1257,36.9522	benign	298/887	6904137	4806,8200	2203	4300	6503	SO:0001583	missense	2015	exon8			GCATTGCAGGCTT	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.893C>T	19.37:g.6904137C>T	ENSP00000311545:p.Ala298Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	113	58	0.513274	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	918	0.42032967032967034	318	0.6463414634146342	137	0.3784530386740331	283	0.49475524475524474	180	0.23746701846965698	C	2.567	-0.300602	0.05495	0.588743	0.257209	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407	D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01	3.89	-7.78	0.01223	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	N	0.20845	0.615	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.11329	0.0;0.002;0.002;0.006	T	0.15435	-1.0437	8	0.48119	T	0.1	.	3.6824	0.08316	0.1963:0.4428:0.0932:0.2678	rs370094;rs2229770;rs52795015;rs59154947;rs370094	157;298;246;298	B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;EMR1_HUMAN	V	298;298;246;298;157	ENSP00000311545:A298V;ENSP00000370811:A246V;ENSP00000250572:A298V;ENSP00000370814:A157V	ENSP00000250572:A298V	A	+	2	0	EMR1	6855137	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.439000	0.01016	-3.955000	0.00087	-2.282000	0.00269	GCA	C|0.602;T|0.398	0.398	strong		0.473	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197248	39197248	+	Silent	SNP	G	G	A	rs570985299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39197248G>A	ENST00000306271.4	-	1	465	c.402C>T	c.(400-402)tgC>tgT	p.C134C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	134						keratin filament (GO:0045095)		p.C134C(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCTCACCACGCAGCAGGGGG	0.672													a|||	3	0.000599042	0.0008	0.0	5008	,	,		16961	0.0		0.0	False		,,,				2504	0.002				p.C134C		Atlas-SNP	.											KRTAP1-1,NS,carcinoma,0,1	KRTAP1-1	23	1	1	Substitution - coding silent(1)	endometrium(1)	c.C402T						scavenged	.						24.0	29.0	27.0					17																	39197248		2078	4173	6251	SO:0001819	synonymous_variant	81851	exon1			CACCACGCAGCAG	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.402C>T	17.37:g.39197248G>A		Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	186	2	0.0107527	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			.	.	none		0.672	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
CAPN12	147968	hgsc.bcm.edu	37	19	39226163	39226163	+	Silent	SNP	G	G	A	rs141009431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39226163G>A	ENST00000328867.4	-	13	1913	c.1605C>T	c.(1603-1605)agC>agT	p.S535S	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Silent_p.S386S	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	535	Domain III.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GCAGGTCTGCGCTGATCACGT	0.647													G|||	11	0.00219649	0.0083	0.0	5008	,	,		8622	0.0		0.0	False		,,,				2504	0.0				p.S535S		Atlas-SNP	.											.	CAPN12	43	.	0			c.C1605T						PASS	.	G		27,4355	30.8+/-60.4	0,27,2164	38.0	37.0	37.0		1605	3.0	1.0	19	dbSNP_134	37	0,8590		0,0,4295	no	coding-synonymous	CAPN12	NM_144691.3		0,27,6459	AA,AG,GG		0.0,0.6162,0.2081		535/720	39226163	27,12945	2191	4295	6486	SO:0001819	synonymous_variant	147968	exon13			GTCTGCGCTGATC	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1605C>T	19.37:g.39226163G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			G|0.998;A|0.002	0.002	strong		0.647	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
CEACAM20	125931	hgsc.bcm.edu	37	19	45017301	45017301	+	RNA	SNP	T	T	C	rs34921521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45017301T>C	ENST00000454753.1	-	0	1635							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)				AGGATCCCGATGACAATACCA	0.567											OREG0025538	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	78	0.0155751	0.0575	0.0029	5008	,	,		15361	0.0		0.0	False		,,,				2504	0.0				p.I453V		Atlas-SNP	.											CEACAM20,NS,carcinoma,0,1	CEACAM20	31	1	0			c.A1357G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	166,3902		5,156,1873	76.0	76.0	76.0		1357,1078,1078,1357	-5.6	0.0	19	dbSNP_126	76	1,8347		0,1,4173	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	29,29,29,29	5,157,6046	CC,CT,TT		0.012,4.0806,1.345	benign,benign,benign,benign	453/597,360/492,360/504,453/585	45017301	167,12249	2034	4174	6208			125931	exon7			TCCCGATGACAAT	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.45017301T>C		Somatic	67	0	0	928	WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				T|0.986;C|0.014	0.014	strong		0.567	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
HSPA4	3308	hgsc.bcm.edu	37	5	132437531	132437531	+	Silent	SNP	C	C	T	rs1131809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132437531C>T	ENST00000304858.2	+	17	2407	c.2118C>T	c.(2116-2118)atC>atT	p.I706I		NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	706					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGAAACAGATCCAACAGTATA	0.289													C|||	837	0.167133	0.1664	0.1066	5008	,	,		18023	0.0913		0.2316	False		,,,				2504	0.2229				p.I706I	Colon(114;1299 1588 6063 12302 48757)	Atlas-SNP	.											.	HSPA4	68	.	0			c.C2118T						PASS	.	C		738,3668	300.1+/-286.2	67,604,1532	65.0	63.0	64.0		2118	1.3	1.0	5	dbSNP_86	64	2017,6583	347.9+/-326.8	228,1561,2511	no	coding-synonymous	HSPA4	NM_002154.3		295,2165,4043	TT,TC,CC		23.4535,16.7499,21.1825		706/841	132437531	2755,10251	2203	4300	6503	SO:0001819	synonymous_variant	3308	exon17			ACAGATCCAACAG	AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"""Heat shock proteins / HSP70"""	5237	protein-coding gene	gene with protein product	"""hsp70 RY"""	601113	"""heat shock 70kD protein 4"""			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.2118C>T	5.37:g.132437531C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	196	79	0.403061	NM_002154	O95756|Q2TAL4|Q9BUK9	Silent	SNP	ENST00000304858.2	37	CCDS4166.1																																																																																			C|0.802;T|0.198	0.198	strong		0.289	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431	
CUBN	8029	hgsc.bcm.edu	37	10	16932490	16932490	+	Missense_Mutation	SNP	G	G	T	rs1801238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:16932490G>T	ENST00000377833.4	-	55	8700	c.8635C>A	c.(8635-8637)Cta>Ata	p.L2879I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2879	CUB 21. {ECO:0000255|PROSITE- ProRule:PRU00059}.		L -> I (in dbSNP:rs45474496). {ECO:0000269|PubMed:10080186}.		cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CCAGTGGCTAGCAGGGCTTTG	0.522													G|||	70	0.0139776	0.0023	0.0144	5008	,	,		14824	0.0		0.0398	False		,,,				2504	0.0174				p.L2879I		Atlas-SNP	.											.	CUBN	515	.	0			c.C8635A						PASS	.	G	ILE/LEU	23,4383	29.9+/-59.1	0,23,2180	112.0	102.0	106.0		8635	-0.4	0.9	10	dbSNP_127	106	322,8278	113.9+/-173.9	7,308,3985	yes	missense	CUBN	NM_001081.3	5	7,331,6165	TT,TG,GG		3.7442,0.522,2.6526	probably-damaging	2879/3624	16932490	345,12661	2203	4300	6503	SO:0001583	missense	8029	exon55			TGGCTAGCAGGGC	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.8635C>A	10.37:g.16932490G>T	ENSP00000367064:p.Leu2879Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	30	0.013736263736263736	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	24	0.0316622691292876	G	14.23	2.473839	0.43942	0.00522	0.037442	ENSG00000107611	ENST00000377833	T	0.19250	2.16	5.78	-0.444	0.12245	CUB (5);	0.000000	0.36703	N	0.002460	T	0.09555	0.0235	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00891	-1.1525	10	0.72032	D	0.01	.	6.8581	0.24052	0.4405:0.0:0.4375:0.1221	rs45474496;rs52835348	2879	O60494	CUBN_HUMAN	I	2879	ENSP00000367064:L2879I	ENSP00000367064:L2879I	L	-	1	2	CUBN	16972496	0.986000	0.35501	0.875000	0.34327	0.192000	0.23643	0.421000	0.21280	-0.028000	0.13850	0.655000	0.94253	CTA	G|0.977;T|0.023	0.023	strong		0.522	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
HERC2	8924	hgsc.bcm.edu	37	15	28389880	28389880	+	Silent	SNP	G	G	A	rs1133496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:28389880G>A	ENST00000261609.7	-	72	11187	c.11079C>T	c.(11077-11079)agC>agT	p.S3693S		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)		CAGACCCATCGCTGATGAACT	0.592													G|||	434	0.0866613	0.3132	0.0274	5008	,	,		20257	0.0		0.001	False		,,,				2504	0.0				p.S3693S		Atlas-SNP	.											.	HERC2	501	.	0			c.C11079T						PASS	.	G		1171,3235	414.6+/-336.9	156,859,1188	106.0	86.0	93.0		11079	-2.7	1.0	15	dbSNP_86	93	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	HERC2	NM_004667.4		156,863,5484	AA,AG,GG		0.0465,26.5774,9.0343		3693/4835	28389880	1175,11831	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon72			CCCATCGCTGATG	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.11079C>T	15.37:g.28389880G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	145	73	0.503448	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.916;A|0.084	0.084	strong		0.592	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
CCDC154	645811	hgsc.bcm.edu	37	16	1484455	1484455	+	Missense_Mutation	SNP	T	T	C	rs61743495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	98	0	0		WXS	Illumina HiSeq	Phase_I	94	57	0.606383	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	
NTRK3	4916	hgsc.bcm.edu	37	15	88576215	88576215	+	Silent	SNP	G	G	A	rs2229909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:88576215G>A	ENST00000360948.2	-	13	1619	c.1458C>T	c.(1456-1458)caC>caT	p.H486H	NTRK3_ENST00000558676.1_Silent_p.H478H|NTRK3_ENST00000558306.1_5'UTR|NTRK3_ENST00000540489.2_Silent_p.H486H|NTRK3_ENST00000557856.1_Silent_p.H478H|NTRK3_ENST00000394480.2_Silent_p.H486H|NTRK3_ENST00000317501.3_Silent_p.H486H|NTRK3_ENST00000357724.2_Silent_p.H478H|NTRK3_ENST00000355254.2_Silent_p.H486H|NTRK3_ENST00000542733.2_Silent_p.H388H	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	486					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)		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)			TGGTGATGCCGTGGTTGATGT	0.607			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)			G|||	143	0.0285543	0.1051	0.0058	5008	,	,		10706	0.0		0.0	False		,,,				2504	0.0				p.H486H		Atlas-SNP	.		Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	NTRK3_ENST00000360948,NS,carcinoma,0,3	NTRK3	587	3	0			c.C1458T						PASS	.	G	,,	457,3945	216.4+/-235.1	27,403,1771	97.0	61.0	73.0		1458,1458,1458	-4.4	1.0	15	dbSNP_129	73	2,8596	3.0+/-9.4	0,2,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	NTRK3	NM_001007156.2,NM_001012338.2,NM_002530.3	,,	27,405,6068	AA,AG,GG		0.0233,10.3816,3.5308	,,	486/613,486/840,486/826	88576215	459,12541	2201	4299	6500	SO:0001819	synonymous_variant	4916	exon14			GATGCCGTGGTTG	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.1458C>T	15.37:g.88576215G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	ENST00000360948.2	37	CCDS32322.1																																																																																			G|0.962;A|0.038	0.038	strong		0.607	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
CAMKK1	84254	hgsc.bcm.edu	37	17	3786456	3786456	+	Silent	SNP	C	C	T	rs737362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3786456C>T	ENST00000348335.2	-	6	676	c.528G>A	c.(526-528)ccG>ccA	p.P176P	CAMKK1_ENST00000158166.5_Silent_p.P176P|CAMKK1_ENST00000381769.2_Silent_p.P203P|CAMKK1_ENST00000381771.2_Silent_p.P176P	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|RP domain.				synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	11				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		GGGACCCTCTCGGGGGAGGGC	0.627													C|||	289	0.0577077	0.2118	0.0101	5008	,	,		19719	0.0		0.002	False		,,,				2504	0.0				p.P176P		Atlas-SNP	.											.	CAMKK1	70	.	0			c.G528A						PASS	.	C	,,	836,3570	328.5+/-300.6	77,682,1444	61.0	60.0	60.0		528,528,528	-10.9	0.0	17	dbSNP_86	60	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous	CAMKK1	NM_032294.2,NM_172206.1,NM_172207.2	,,	77,691,5735	TT,TC,CC		0.1047,18.9741,6.497	,,	176/506,176/506,176/521	3786456	845,12161	2203	4300	6503	SO:0001819	synonymous_variant	84254	exon6			CCCTCTCGGGGGA	AL136576	CCDS11038.1, CCDS11039.1	17p13.3	2004-02-18			ENSG00000004660	ENSG00000004660			1469	protein-coding gene	gene with protein product		611411				11230166	Standard	NM_172207		Approved	DKFZp761M0423, CAMKKA, MGC34095	uc002fwt.3	Q8N5S9	OTTHUMG00000090725	ENST00000348335.2:c.528G>A	17.37:g.3786456C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_032294	Q9BQH3	Silent	SNP	ENST00000348335.2	37	CCDS11038.1																																																																																			C|0.934;T|0.066	0.066	strong		0.627	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207	
KCTD19	146212	hgsc.bcm.edu	37	16	67325711	67325711	+	Missense_Mutation	SNP	C	C	T	rs16957289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67325711C>T	ENST00000304372.5	-	13	2303	c.2248G>A	c.(2248-2250)Gag>Aag	p.E750K		NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	750			E -> K (in dbSNP:rs16957289).		protein homooligomerization (GO:0051260)					endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		TCACTGGCCTCGGGCAGAGGC	0.502													C|||	497	0.0992412	0.2564	0.0548	5008	,	,		18331	0.003		0.0388	False		,,,				2504	0.0798				p.E750K		Atlas-SNP	.											KCTD19,brain,glioma,0,1	KCTD19	82	1	0			c.G2248A						PASS	.	C	LYS/GLU	810,2984		91,628,1178	32.0	34.0	33.0		2248	2.9	0.8	16	dbSNP_123	33	331,7905		8,315,3795	yes	missense	KCTD19	NM_001100915.1	56	99,943,4973	TT,TC,CC		4.0189,21.3495,9.4846	benign	750/927	67325711	1141,10889	1897	4118	6015	SO:0001583	missense	146212	exon13			TGGCCTCGGGCAG	AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 19"""				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.2248G>A	16.37:g.67325711C>T	ENSP00000305702:p.Glu750Lys	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_001100915	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	37	CCDS42179.1	184	0.08424908424908426	132	0.2682926829268293	21	0.058011049723756904	2	0.0034965034965034965	29	0.03825857519788918	C	13.26	2.183236	0.38511	0.213495	0.040189	ENSG00000168676	ENST00000304372	T	0.60797	0.16	4.97	2.89	0.33648	.	0.536806	0.16994	N	0.191166	T	0.00012	0.0000	N	0.14661	0.345	0.48975	P	2.609999999999557E-4	B	0.23806	0.091	B	0.17098	0.017	T	0.13202	-1.0518	9	0.59425	D	0.04	-3.6579	5.2969	0.15756	0.0:0.6895:0.0:0.3105	rs16957289;rs52809534;rs16957289	750	Q17RG1	KCD19_HUMAN	K	750	ENSP00000305702:E750K	ENSP00000305702:E750K	E	-	1	0	KCTD19	65883212	0.979000	0.34478	0.827000	0.32855	0.436000	0.31835	1.058000	0.30504	0.558000	0.29135	0.462000	0.41574	GAG	C|0.929;T|0.071	0.071	strong		0.502	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367	
AKAP10	11216	hgsc.bcm.edu	37	17	19835185	19835185	+	Missense_Mutation	SNP	G	G	C	rs141355495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19835185G>C	ENST00000225737.6	-	10	1731	c.1574C>G	c.(1573-1575)aCt>aGt	p.T525S	AKAP10_ENST00000395536.3_Intron|RP11-209D14.4_ENST00000583067.1_RNA	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	525					blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					GCCAGGAGCAGTCAGCGACAC	0.488													G|||	3	0.000599042	0.0023	0.0	5008	,	,		14389	0.0		0.0	False		,,,				2504	0.0				p.T525S		Atlas-SNP	.											.	AKAP10	47	.	0			c.C1574G						PASS	.	G	SER/THR	6,4400	12.9+/-30.5	0,6,2197	85.0	83.0	84.0		1574	2.8	0.2	17	dbSNP_134	84	0,8600		0,0,4300	yes	missense	AKAP10	NM_007202.2	58	0,6,6497	CC,CG,GG		0.0,0.1362,0.0461	benign	525/663	19835185	6,13000	2203	4300	6503	SO:0001583	missense	11216	exon10			GGAGCAGTCAGCG	AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"""A-kinase anchor proteins"""	368	protein-coding gene	gene with protein product	"""dual-specificity A-kinase anchoring protein 2"", ""protein kinase A anchoring protein 10"", ""mitochondrial A kinase PPKA anchor protein 10"""	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.1574C>G	17.37:g.19835185G>C	ENSP00000225737:p.Thr525Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_007202	B2R650|Q96AJ7	Missense_Mutation	SNP	ENST00000225737.6	37	CCDS11214.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	5.299	0.240537	0.10023	0.001362	0.0	ENSG00000108599	ENST00000225737	T	0.28666	1.6	5.82	2.79	0.32731	.	0.783781	0.12491	N	0.464265	T	0.05914	0.0154	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33752	-0.9856	10	0.09084	T	0.74	0.4362	1.6078	0.02687	0.238:0.1522:0.4703:0.1395	.	525	O43572	AKA10_HUMAN	S	525	ENSP00000225737:T525S	ENSP00000225737:T525S	T	-	2	0	AKAP10	19775777	0.767000	0.28508	0.197000	0.23402	0.325000	0.28411	0.898000	0.28404	0.820000	0.34516	0.650000	0.86243	ACT	G|0.999;C|0.001	0.001	strong		0.488	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202	
AKAP6	9472	hgsc.bcm.edu	37	14	33014869	33014869	+	Missense_Mutation	SNP	C	C	T	rs3742926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:33014869C>T	ENST00000280979.4	+	4	1180	c.1010C>T	c.(1009-1011)gCt>gTt	p.A337V	AKAP6_ENST00000557354.1_Missense_Mutation_p.A337V|AKAP6_ENST00000557272.1_Missense_Mutation_p.A337V	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	337			A -> V (in dbSNP:rs3742926).		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)		ACAAATGCTGCTCAACCCTCC	0.493													T|||	881	0.175919	0.233	0.1859	5008	,	,		20444	0.1815		0.1004	False		,,,				2504	0.1636				p.A337V	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.C1010T						PASS	.	T	VAL/ALA	887,3519	741.1+/-411.2	78,731,1394	73.0	64.0	67.0		1010	-5.0	0.0	14	dbSNP_107	67	804,7796	781.9+/-407.6	37,730,3533	yes	missense	AKAP6	NM_004274.4	64	115,1461,4927	TT,TC,CC		9.3488,20.1316,13.0017	benign	337/2320	33014869	1691,11315	2203	4300	6503	SO:0001583	missense	9472	exon4			ATGCTGCTCAACC	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.1010C>T	14.37:g.33014869C>T	ENSP00000280979:p.Ala337Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	121	76	0.628099	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	367	0.16804029304029305	121	0.2459349593495935	62	0.1712707182320442	97	0.16958041958041958	87	0.11477572559366754	T	0.013	-1.629818	0.00813	0.201316	0.093488	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272;ENST00000553547	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.61	-4.96	0.03038	.	1.589520	0.03277	N	0.185626	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29458	-1.0011	9	0.16420	T	0.52	1.892	0.6198	0.00776	0.2906:0.2271:0.3018:0.1805	rs3742926;rs52801792;rs61666772;rs3742926	337;337	A7E242;Q13023	.;AKAP6_HUMAN	V	337;337;337;95	ENSP00000280979:A337V;ENSP00000450531:A337V;ENSP00000451247:A337V;ENSP00000451239:A95V	ENSP00000280979:A337V	A	+	2	0	AKAP6	32084620	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.734000	0.04893	-0.707000	0.05022	-0.254000	0.11334	GCT	C|0.859;T|0.141	0.141	strong		0.493	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
ARHGAP32	9743	hgsc.bcm.edu	37	11	128994781	128994781	+	Silent	SNP	G	G	A	rs114955890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:128994781G>A	ENST00000310343.9	-	3	233	c.234C>T	c.(232-234)ggC>ggT	p.G78G	ARHGAP32_ENST00000524655.1_Silent_p.G4G	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	78					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						GAACATCTGCGCCTCTTGCCT	0.333													G|||	6	0.00119808	0.0045	0.0	5008	,	,		15533	0.0		0.0	False		,,,				2504	0.0				p.G78G		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.C234T						PASS	.	G		17,3115		0,17,1549	108.0	98.0	101.0		234	2.2	1.0	11	dbSNP_132	101	0,7156		0,0,3578	no	coding-synonymous	ARHGAP32	NM_001142685.1		0,17,5127	AA,AG,GG		0.0,0.5428,0.1652		78/2088	128994781	17,10271	1566	3578	5144	SO:0001819	synonymous_variant	9743	exon3			ATCTGCGCCTCTT	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.234C>T	11.37:g.128994781G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	59	34	0.576271	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																			G|0.998;A|0.002	0.002	strong		0.333	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
QRFP	347148	hgsc.bcm.edu	37	9	133769169	133769169	+	Silent	SNP	G	G	A	rs3847193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	171	0	0		WXS	Illumina HiSeq	Phase_I	135	135	1	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	
ELK3	2004	hgsc.bcm.edu	37	12	96641344	96641344	+	Silent	SNP	G	G	A	rs115218295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:96641344G>A	ENST00000228741.3	+	3	1160	c.834G>A	c.(832-834)tcG>tcA	p.S278S	ELK3_ENST00000552142.1_Intron	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	278					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|wound healing (GO:0042060)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	purine-rich negative regulatory element binding (GO:0032422)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.S278S(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(5)|ovary(2)|prostate(1)|stomach(2)	20	all_cancers(2;0.00173)					ACCTGTCATCGGGCTCCAAGA	0.602													G|||	45	0.00898562	0.0333	0.0	5008	,	,		16138	0.0		0.001	False		,,,				2504	0.0				p.S278S		Atlas-SNP	.											.	ELK3	36	.	1	Substitution - coding silent(1)	lung(1)	c.G834A						PASS	.	G		125,4281	90.6+/-129.3	2,121,2080	67.0	75.0	72.0		834	-1.9	0.9	12	dbSNP_132	72	0,8600		0,0,4300	no	coding-synonymous	ELK3	NM_005230.2		2,121,6380	AA,AG,GG		0.0,2.837,0.9611		278/408	96641344	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	2004	exon3			GTCATCGGGCTCC	BC017371	CCDS9060.1	12q23	2006-12-30				ENSG00000111145			3325	protein-coding gene	gene with protein product		600247				7851904	Standard	NM_005230		Approved	ERP, NET, SAP2	uc001teo.1	P41970		ENST00000228741.3:c.834G>A	12.37:g.96641344G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_005230	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Silent	SNP	ENST00000228741.3	37	CCDS9060.1																																																																																			G|0.990;A|0.010	0.010	strong		0.602	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408694.1	NM_005230	
KRTAP21-2	337978	hgsc.bcm.edu	37	21	32119495	32119495	+	Missense_Mutation	SNP	C	C	G	rs12053674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:32119495C>G	ENST00000333892.2	-	1	56	c.26G>C	c.(25-27)tGc>tCc	p.C9S		NM_181617.1	NP_853648.1	Q3LI59	KR212_HUMAN	keratin associated protein 21-2	9				C -> S (in Ref. 1; BAE46374). {ECO:0000305}.		intermediate filament (GO:0005882)	structural constituent of cutaneous appendage (GO:0030281)			lung(4)|skin(2)|upper_aerodigestive_tract(1)	7						gccccCACAGCAGTTTCTGTA	0.493													G|||	1043	0.208267	0.385	0.0519	5008	,	,		20384	0.3571		0.0686	False		,,,				2504	0.0706				p.C9S		Atlas-SNP	.											.	KRTAP21-2	16	.	0			c.G26C						PASS	.	G	SER/CYS	1449,2957	682.0+/-404.1	230,989,984	152.0	153.0	153.0		26	-0.7	0.0	21	dbSNP_120	153	410,8190	801.0+/-407.4	12,386,3902	yes	missense	KRTAP21-2	NM_181617.1	112	242,1375,4886	GG,GC,CC		4.7674,32.887,14.2934	benign	9/84	32119495	1859,11147	2203	4300	6503	SO:0001583	missense	337978	exon1			CCACAGCAGTTTC	AP001709	CCDS13605.1	21q22.1	2006-03-13			ENSG00000187026	ENSG00000187026		"""Keratin associated proteins"""	18946	protein-coding gene	gene with protein product						12359730	Standard	NM_181617		Approved	KAP21.2	uc011adh.2	Q3LI59	OTTHUMG00000057769	ENST00000333892.2:c.26G>C	21.37:g.32119495C>G	ENSP00000334287:p.Cys9Ser	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	241	103	0.427386	NM_181617		Missense_Mutation	SNP	ENST00000333892.2	37	CCDS13605.1	443	0.20283882783882784	160	0.3252032520325203	17	0.04696132596685083	210	0.36713286713286714	56	0.07387862796833773	G	1.078	-0.667704	0.03428	0.32887	0.047674	ENSG00000187026	ENST00000333892	T	0.08634	3.07	4.81	-0.735	0.11137	.	0.422367	0.17443	N	0.174059	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43491	-0.9388	8	0.02654	T	1	-0.3615	3.4867	0.07622	0.0867:0.3986:0.2439:0.2709	rs12053674;rs52790703;rs12053674	9	Q3LI59	KR212_HUMAN	S	9	ENSP00000334287:C9S	ENSP00000334287:C9S	C	-	2	0	KRTAP21-2	31041366	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.538000	0.06120	-0.040000	0.13580	-0.371000	0.07208	TGC	C|0.840;G|0.160	0.160	strong		0.493	KRTAP21-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128221.2		
COG7	91949	hgsc.bcm.edu	37	16	23409440	23409440	+	Missense_Mutation	SNP	G	G	A	rs16940094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23409440G>A	ENST00000307149.5	-	14	1999	c.1814C>T	c.(1813-1815)aCg>aTg	p.T605M		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	605			T -> M (in dbSNP:rs16940094).		intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		GATGCCAGCCGTATTCCAGCT	0.532													G|||	441	0.0880591	0.1861	0.1239	5008	,	,		19099	0.0169		0.0258	False		,,,				2504	0.0675				p.T605M		Atlas-SNP	.											.	COG7	62	.	0			c.C1814T						PASS	.	G	MET/THR	681,3713	286.9+/-279.0	50,581,1566	122.0	98.0	106.0		1814	3.7	0.7	16	dbSNP_123	106	257,8343	101.4+/-162.7	4,249,4047	yes	missense	COG7	NM_153603.3	81	54,830,5613	AA,AG,GG		2.9884,15.4984,7.2187	possibly-damaging	605/771	23409440	938,12056	2197	4300	6497	SO:0001583	missense	91949	exon14			CCAGCCGTATTCC	AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"""Components of oligomeric golgi complex"""	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1814C>T	16.37:g.23409440G>A	ENSP00000305442:p.Thr605Met	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	150	87	0.58	NM_153603	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	37	CCDS10610.1	136	0.06227106227106227	79	0.16056910569105692	28	0.07734806629834254	11	0.019230769230769232	18	0.023746701846965697	G	13.05	2.121490	0.37436	0.154984	0.029884	ENSG00000168434	ENST00000307149	T	0.44881	0.91	5.6	3.67	0.42095	.	0.270197	0.42682	N	0.000671	T	0.00178	0.0005	N	0.24115	0.695	0.34894	P	0.254186	D	0.57571	0.98	P	0.52109	0.69	T	0.05632	-1.0873	9	0.42905	T	0.14	-15.5303	10.0248	0.42066	0.1547:0.0:0.8453:0.0	rs16940094;rs16940094	605	P83436	COG7_HUMAN	M	605	ENSP00000305442:T605M	ENSP00000305442:T605M	T	-	2	0	COG7	23316941	1.000000	0.71417	0.745000	0.31077	0.194000	0.23727	5.583000	0.67484	0.747000	0.32809	-0.742000	0.03525	ACG	G|0.931;A|0.069	0.069	strong		0.532	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1		
ADAMTS14	140766	hgsc.bcm.edu	37	10	72500863	72500863	+	Silent	SNP	C	C	G	rs10999500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72500863C>G	ENST00000373207.1	+	12	1869	c.1869C>G	c.(1867-1869)tcC>tcG	p.S623S	ADAMTS14_ENST00000373208.1_Silent_p.S626S	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	623	Cys-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						AGCGCAACTCCTACTATGTGC	0.612													C|||	3341	0.667133	0.6498	0.5663	5008	,	,		20631	0.8571		0.6113	False		,,,				2504	0.6237				p.S626S		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.C1878G						PASS	.	C	,	2866,1540	670.9+/-402.4	928,1010,265	75.0	64.0	68.0		1869,1878	3.4	1.0	10	dbSNP_120	68	5173,3427	638.3+/-399.3	1572,2029,699	no	coding-synonymous,coding-synonymous	ADAMTS14	NM_080722.3,NM_139155.2	,	2500,3039,964	GG,GC,CC		39.8488,34.9523,38.1901	,	623/1224,626/1227	72500863	8039,4967	2203	4300	6503	SO:0001819	synonymous_variant	140766	exon12			CAACTCCTACTAT	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1869C>G	10.37:g.72500863C>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	126	56	0.444444	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			C|0.339;G|0.661	0.661	strong		0.612	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
KRTAP17-1	83902	hgsc.bcm.edu	37	17	39471888	39471888	+	Silent	SNP	C	C	T	rs34354631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39471888C>T	ENST00000334202.3	-	1	59	c.15G>A	c.(13-15)ccG>ccA	p.P5P		NM_031964.1	NP_114170.1	Q9BYP8	KR171_HUMAN	keratin associated protein 17-1	5						intermediate filament (GO:0005882)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			AGCAGTCCCCCGGGCAGCACC	0.657													C|||	622	0.124201	0.3275	0.0548	5008	,	,		13406	0.0506		0.0795	False		,,,				2504	0.0204				p.P5P		Atlas-SNP	.											.	KRTAP17-1	14	.	0			c.G15A						PASS	.	C		1217,3171		178,861,1155	19.0	22.0	21.0		15	-6.7	1.0	17	dbSNP_126	21	693,7867		27,639,3614	no	coding-synonymous	KRTAP17-1	NM_031964.1		205,1500,4769	TT,TC,CC		8.0958,27.7347,14.7513		5/106	39471888	1910,11038	2194	4280	6474	SO:0001819	synonymous_variant	83902	exon1			GTCCCCCGGGCAG	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.15G>A	17.37:g.39471888C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	46	44	0.956522	NM_031964		Silent	SNP	ENST00000334202.3	37	CCDS11387.1																																																																																			C|0.866;T|0.134	0.134	strong		0.657	KRTAP17-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257296.1		
MEP1B	4225	hgsc.bcm.edu	37	18	29797921	29797921	+	Missense_Mutation	SNP	C	C	T	rs616114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:29797921C>T	ENST00000269202.6	+	14	2131	c.2084C>T	c.(2083-2085)cCg>cTg	p.P695L	MEP1B_ENST00000581447.1_Missense_Mutation_p.P695L	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	695			P -> L (in dbSNP:rs616114). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9288916}.		digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						AATTTGACTCCGCAAAATGTA	0.393													C|||	1782	0.355831	0.4251	0.2882	5008	,	,		22256	0.255		0.3648	False		,,,				2504	0.4049				p.P695L		Atlas-SNP	.											.	MEP1B	54	.	0			c.C2084T	GRCh37	CM065309	MEP1B	M	rs616114	PASS	.	C	LEU/PRO	1534,2324		321,892,716	103.0	101.0	101.0		2084	0.4	0.0	18	dbSNP_83	101	3220,5040		638,1944,1548	yes	missense	MEP1B	NM_005925.2	98	959,2836,2264	TT,TC,CC		38.9831,39.7615,39.2309	benign	695/702	29797921	4754,7364	1929	4130	6059	SO:0001583	missense	4225	exon14			TGACTCCGCAAAA	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.2084C>T	18.37:g.29797921C>T	ENSP00000269202:p.Pro695Leu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	187	106	0.566845	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	778	0.35622710622710624	225	0.4573170731707317	109	0.3011049723756906	160	0.27972027972027974	284	0.37467018469656993	C	0.016	-1.529447	0.00951	0.397615	0.389831	ENSG00000141434	ENST00000269202	T	0.17854	2.25	5.68	0.414	0.16406	.	2.205680	0.01512	N	0.017988	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	0.45512	-0.9256	9	0.02654	T	1	5.6145	9.8349	0.40963	0.0:0.3279:0.0:0.6721	rs616114;rs17663247;rs616114	695	Q16820	MEP1B_HUMAN	L	695	ENSP00000269202:P695L	ENSP00000269202:P695L	P	+	2	0	MEP1B	28051919	0.005000	0.15991	0.004000	0.12327	0.028000	0.11728	0.916000	0.28651	-0.149000	0.11215	-0.600000	0.04104	CCG	C|0.631;T|0.368	0.368	strong		0.393	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
TTLL11	158135	hgsc.bcm.edu	37	9	124855220	124855220	+	Missense_Mutation	SNP	G	G	A	rs61742325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124855220G>A	ENST00000373776.3	-	1	665	c.478C>T	c.(478-480)Ccc>Tcc	p.P160S	TTLL11_ENST00000474723.1_5'UTR|TTLL11_ENST00000321582.5_Missense_Mutation_p.P160S	NM_194252.2	NP_919228.2	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	160					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						GCCGCACTGGGCTGCGCCGGG	0.766													G|||	247	0.0493211	0.1808	0.0115	5008	,	,		11208	0.0		0.0	False		,,,				2504	0.0				p.P160S		Atlas-SNP	.											.	TTLL11	67	.	0			c.C478T						PASS	.	G	SER/PRO,SER/PRO	440,3254		12,416,1419	5.0	6.0	6.0		478,478	0.4	0.2	9	dbSNP_129	6	1,7393		0,1,3696	no	missense,missense	TTLL11	NM_001139442.1,NM_194252.2	74,74	12,417,5115	AA,AG,GG		0.0135,11.9112,3.9773	possibly-damaging,possibly-damaging	160/801,160/539	124855220	441,10647	1847	3697	5544	SO:0001583	missense	158135	exon1			CACTGGGCTGCGC	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"""Tubulin tyrosine ligase-like family"""	18113	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 20"""	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000373776.3:c.478C>T	9.37:g.124855220G>A	ENSP00000362881:p.Pro160Ser	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_001139442		Missense_Mutation	SNP	ENST00000373776.3	37	CCDS6834.2	98	0.04487179487179487	90	0.18292682926829268	8	0.022099447513812154	0	0.0	0	0.0	G	8.451	0.853131	0.17106	0.119112	1.35E-4	ENSG00000175764	ENST00000321582;ENST00000373776	T;T	0.08458	3.24;3.09	4.73	0.383	0.16239	.	8.202900	0.00520	U	0.000189	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.16396	0.017;0.01	B;B	0.10450	0.005;0.003	T	0.41360	-0.9513	8	.	.	.	.	3.3638	0.07196	0.0901:0.2587:0.426:0.2252	.	160;160	F8W6M1;Q8NHH1	.;TTL11_HUMAN	S	160	ENSP00000321346:P160S;ENSP00000362881:P160S	.	P	-	1	0	TTLL11	123895041	0.067000	0.21026	0.156000	0.22583	0.281000	0.26958	0.757000	0.26433	0.382000	0.24878	-0.379000	0.06801	CCC	G|0.955;A|0.045	0.045	strong		0.766	TTLL11-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053907.1	XM_088486	
UCK2	7371	hgsc.bcm.edu	37	1	165859482	165859482	+	Silent	SNP	T	T	C	rs145654595		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:165859482T>C	ENST00000367879.4	+	2	444	c.141T>C	c.(139-141)aaT>aaC	p.N47N	UCK2_ENST00000372212.4_Silent_p.N47N	NM_012474.4	NP_036606.2	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2	47					cellular response to oxygen levels (GO:0071453)|CTP salvage (GO:0044211)|feeding behavior (GO:0007631)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to axon injury (GO:0048678)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					TGGGGCAGAATGAGGTGGACT	0.557																																					p.N47N		Atlas-SNP	.											.	UCK2	31	.	0			c.T141C						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	138.0	120.0	126.0		141	-3.1	1.0	1	dbSNP_134	126	0,8600		0,0,4300	no	coding-synonymous	UCK2	NM_012474.4		0,2,6501	CC,CT,TT		0.0,0.0454,0.0154		47/262	165859482	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7371	exon2			GCAGAATGAGGTG	AF236637	CCDS1252.1	1p32	2012-10-02	2004-07-13	2004-07-14	ENSG00000143179	ENSG00000143179	2.7.1.48		12562	protein-coding gene	gene with protein product		609329	"""uridine monophosphate kinase"""	UMPK			Standard	NM_012474		Approved		uc001gdp.3	Q9BZX2	OTTHUMG00000040117	ENST00000367879.4:c.141T>C	1.37:g.165859482T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	243	118	0.485597	NM_012474	Q5VV91|Q7KZV3|Q92528|Q96KG5|Q9BU42	Silent	SNP	ENST00000367879.4	37	CCDS1252.1																																																																																			T|1.000;C|0.000	0.000	weak		0.557	UCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096753.1	NM_012474	
CRYBG3	131544	hgsc.bcm.edu	37	3	97607290	97607290	+	Silent	SNP	G	G	A	rs13065340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:97607290G>A	ENST00000182096.4	+	6	1615	c.1551G>A	c.(1549-1551)ccG>ccA	p.P517P		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2465							carbohydrate binding (GO:0030246)	p.P517P(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						CATTACATCCGCTTCAAATGG	0.368													G|||	1024	0.204473	0.112	0.317	5008	,	,		17657	0.1637		0.2833	False		,,,				2504	0.2106				p.P2465P		Atlas-SNP	.											CRYBG3,NS,carcinoma,0,1	CRYBG3	86	1	1	Substitution - coding silent(1)	stomach(1)	c.G7395A						PASS	.	G		455,3197		26,403,1397	48.0	43.0	45.0		7395	-1.9	1.0	3	dbSNP_121	45	2341,5823		348,1645,2089	no	coding-synonymous	CRYBG3	XM_003118522.2		374,2048,3486	AA,AG,GG		28.6747,12.4589,23.6628		2465/2971	97607290	2796,9020	1826	4082	5908	SO:0001819	synonymous_variant	131544	exon9			ACATCCGCTTCAA			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.1551G>A	3.37:g.97607290G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Silent	SNP	ENST00000182096.4	37																																																																																				G|0.786;A|0.214	0.214	strong		0.368	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605	
NLGN2	57555	hgsc.bcm.edu	37	17	7318396	7318396	+	Silent	SNP	C	C	T	rs2241233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7318396C>T	ENST00000302926.2	+	5	1039	c.966C>T	c.(964-966)agC>agT	p.S322S	NLGN2_ENST00000575301.1_Silent_p.S322S	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	322					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				GAGAGGACAGCGCTGAAGCTG	0.667													C|||	3851	0.76897	0.4909	0.8919	5008	,	,		18796	0.9534		0.8499	False		,,,				2504	0.7843				p.S322S		Atlas-SNP	.											.	NLGN2	61	.	0			c.C966T						PASS	.	C		2332,2074	598.1+/-389.0	605,1122,476	45.0	44.0	44.0		966	-3.1	0.7	17	dbSNP_98	44	7339,1261	752.3+/-407.4	3122,1095,83	no	coding-synonymous	NLGN2	NM_020795.2		3727,2217,559	TT,TC,CC		14.6628,47.0722,25.642		322/836	7318396	9671,3335	2203	4300	6503	SO:0001819	synonymous_variant	57555	exon5			GGACAGCGCTGAA	AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.966C>T	17.37:g.7318396C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	110	48	0.436364	NM_020795	Q9P2I1	Silent	SNP	ENST00000302926.2	37	CCDS11103.1																																																																																			C|0.234;T|0.766	0.766	strong		0.667	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795	
GRK5	2869	hgsc.bcm.edu	37	10	121086097	121086097	+	Missense_Mutation	SNP	A	A	T	rs2230345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:121086097A>T	ENST00000392870.2	+	2	451	c.122A>T	c.(121-123)cAg>cTg	p.Q41L		NM_005308.2	NP_005299.1	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5	41	N-terminal.		Q -> L (exerts a protective effect in heart failure and ischemia; dbSNP:rs17098707). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:18425130}.		adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|phospholipid binding (GO:0005543)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(5)|lung(15)|skin(3)|stomach(1)|urinary_tract(1)	27		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		CACATTAGCCAGTGTGAAGAC	0.552													A|||	532	0.10623	0.3003	0.0331	5008	,	,		18780	0.0188		0.0139	False		,,,				2504	0.0808				p.Q41L		Atlas-SNP	.											.	GRK5	58	.	0			c.A122T	GRCh37	CM082797	GRK5	M	rs17098707	PASS	.	A	LEU/GLN	1166,3240	411.3+/-335.7	162,842,1199	70.0	65.0	66.0		122	3.9	1.0	10	dbSNP_123	66	97,8503	53.1+/-113.8	0,97,4203	yes	missense	GRK5	NM_005308.2	113	162,939,5402	TT,TA,AA		1.1279,26.4639,9.7109	benign	41/591	121086097	1263,11743	2203	4300	6503	SO:0001583	missense	2869	exon2			TTAGCCAGTGTGA	L15388	CCDS7612.1	10q26.11	2013-09-19	2004-02-04	2004-02-06	ENSG00000198873	ENSG00000198873			4544	protein-coding gene	gene with protein product		600870		GPRK5		7685906	Standard	NM_005308		Approved		uc001led.3	P34947	OTTHUMG00000019149	ENST00000392870.2:c.122A>T	10.37:g.121086097A>T	ENSP00000376609:p.Gln41Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_005308	D3DRD0|Q5T059	Missense_Mutation	SNP	ENST00000392870.2	37	CCDS7612.1	192	0.08791208791208792	160	0.3252032520325203	15	0.04143646408839779	6	0.01048951048951049	11	0.014511873350923483	A	19.26	3.792917	0.70452	0.264639	0.011279	ENSG00000198873	ENST00000369106;ENST00000392870	T	0.02280	4.36	5.02	3.87	0.44632	Regulator of G protein signalling superfamily (1);	0.000000	0.49305	U	0.000157	T	0.00012	0.0000	L	0.28776	0.89	0.09310	P	0.9999999999999988	B	0.09022	0.002	B	0.04013	0.001	T	0.50215	-0.8854	9	0.56958	D	0.05	-14.9861	10.8419	0.46720	0.8506:0.0:0.0:0.1494	rs17098707;rs52829401;rs17098707	41	P34947	GRK5_HUMAN	L	41	ENSP00000376609:Q41L	ENSP00000358102:Q41L	Q	+	2	0	GRK5	121076087	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.862000	0.56009	0.833000	0.34828	0.533000	0.62120	CAG	A|0.905;T|0.095	0.095	strong		0.552	GRK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050652.2	NM_005308	
MSH3	4437	hgsc.bcm.edu	37	5	79974885	79974885	+	Missense_Mutation	SNP	C	C	T	rs35121792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79974885C>T	ENST00000265081.6	+	8	1393	c.1313C>T	c.(1312-1314)gCg>gTg	p.A438V		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	438					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CAAACAGAGGCGCTCATCCAC	0.473								Mismatch excision repair (MMR)					C|||	5	0.000998403	0.0015	0.0	5008	,	,		15950	0.0		0.0	False		,,,				2504	0.0031				p.A438V	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.C1313T						PASS	.	C	VAL/ALA	14,4392	21.2+/-45.6	0,14,2189	133.0	129.0	130.0		1313	-11.0	0.0	5	dbSNP_126	130	0,8600		0,0,4300	yes	missense	MSH3	NM_002439.3	64	0,14,6489	TT,TC,CC		0.0,0.3177,0.1076	benign	438/1138	79974885	14,12992	2203	4300	6503	SO:0001583	missense	4437	exon8			CAGAGGCGCTCAT	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.1313C>T	5.37:g.79974885C>T	ENSP00000265081:p.Ala438Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.513487	0.44660	0.003177	0.0	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.86562	-2.14	5.51	-11.0	0.00169	DNA mismatch repair protein MutS, connector (2);	1.009680	0.07961	N	0.982372	T	0.70185	0.3195	N	0.14661	0.345	0.09310	N	1	B	0.22800	0.075	B	0.21546	0.035	T	0.55780	-0.8087	9	.	.	.	4.4871	11.55	0.50715	0.1018:0.6438:0.1479:0.1066	rs35121792	438	P20585	MSH3_HUMAN	V	438;429	ENSP00000265081:A438V	.	A	+	2	0	MSH3	80010641	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.700000	0.01905	-2.495000	0.00514	-1.181000	0.01715	GCG	C|0.999;T|0.001	0.001	strong		0.473	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
TTN	7273	hgsc.bcm.edu	37	2	179447787	179447787	+	Missense_Mutation	SNP	G	G	T	rs62618736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179447787G>T	ENST00000591111.1	-	263	61044	c.60820C>A	c.(60820-60822)Cag>Aag	p.Q20274K	TTN_ENST00000589042.1_Missense_Mutation_p.Q21915K|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Q12850K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Q19347K|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Q12975K|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Q13042K|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20274	Ig-like 111.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGATTCCGCTGCATGGCCATC	0.458													G|||	80	0.0159744	0.0575	0.0058	5008	,	,		18275	0.0		0.0	False		,,,				2504	0.0				p.Q21915K		Atlas-SNP	.											.	TTN	18412	.	0			c.C65743A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN	187,3793		5,177,1808	81.0	78.0	79.0		39124,38923,58039,38548	-1.6	1.0	2	dbSNP_129	79	1,8339		0,1,4169	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	53,53,53,53	5,178,5977	TT,TG,GG		0.012,4.6985,1.526	benign,benign,benign,benign	13042/27119,12975/27052,19347/33424,12850/26927	179447787	188,12132	1990	4170	6160	SO:0001583	missense	7273	exon313			TCCGCTGCATGGC	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.60820C>A	2.37:g.179447787G>T	ENSP00000465570:p.Gln20274Lys	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	228	122	0.535088	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		42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	G	14.68	2.608015	0.46527	0.046985	1.2E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.82	-1.62	0.08372	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02970	0.0088	N	0.04132	-0.27	0.23946	N	0.99638	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	0.03898	-1.0994	9	0.87932	D	0	.	18.5575	0.91090	0.0:0.0:0.6894:0.3106	rs62618736	12850;12975;13042;20274	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	19347;12850;13042;12975;12848	ENSP00000343764:Q19347K;ENSP00000434586:Q12850K;ENSP00000340554:Q13042K;ENSP00000352154:Q12975K	ENSP00000340554:Q13042K	Q	-	1	0	TTN	179156033	0.009000	0.17119	0.957000	0.39632	0.907000	0.53573	0.075000	0.14686	-0.544000	0.06232	-0.274000	0.10170	CAG	G|0.985;T|0.015	0.015	strong		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SLC5A11	115584	hgsc.bcm.edu	37	16	24888593	24888593	+	Silent	SNP	A	A	G	rs8052587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24888593A>G	ENST00000347898.3	+	7	1114	c.492A>G	c.(490-492)gcA>gcG	p.A164A	SLC5A11_ENST00000569071.1_Silent_p.A100A|SLC5A11_ENST00000424767.2_Silent_p.A129A|SLC5A11_ENST00000568579.1_Silent_p.A94A|SLC5A11_ENST00000449109.2_Silent_p.A100A|SLC5A11_ENST00000565769.1_Silent_p.A100A|SLC5A11_ENST00000567758.1_Silent_p.A129A|SLC5A11_ENST00000545376.1_Silent_p.A94A|SLC5A11_ENST00000539472.1_Silent_p.A100A	NM_052944.3	NP_443176.2			solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		ACATGTATGCAGGTGCCATCT	0.488													A|||	695	0.138778	0.23	0.0965	5008	,	,		23254	0.0		0.1531	False		,,,				2504	0.1738				p.A164A		Atlas-SNP	.											.	SLC5A11	97	.	0			c.A492G						PASS	.	A		895,3499	347.5+/-309.5	92,711,1394	396.0	330.0	352.0		492	-3.7	0.9	16	dbSNP_116	352	1226,7374	247.4+/-275.4	86,1054,3160	no	coding-synonymous	SLC5A11	NM_052944.2		178,1765,4554	GG,GA,AA		14.2558,20.3687,16.3229		164/676	24888593	2121,10873	2197	4300	6497	SO:0001819	synonymous_variant	115584	exon7			GTATGCAGGTGCC	AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"""Solute carriers"""	23091	protein-coding gene	gene with protein product		610238	"""solute carrier family 5 (sodium/glucose cotransporter), member 11"""			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000347898.3:c.492A>G	16.37:g.24888593A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	239	115	0.481172	NM_052944		Silent	SNP	ENST00000347898.3	37	CCDS10625.1																																																																																			A|0.850;G|0.150	0.150	strong		0.488	SLC5A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214091.3	NM_052944	
ENGASE	64772	hgsc.bcm.edu	37	17	77082390	77082390	+	Missense_Mutation	SNP	G	G	A	rs11871357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77082390G>A	ENST00000579016.1	+	14	2191	c.2191G>A	c.(2191-2193)Gag>Aag	p.E731K		NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	731			E -> K (in dbSNP:rs11871357).			cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						ACCTCAGGCCGAGTGGGGCAG	0.652													G|||	226	0.0451278	0.1672	0.0072	5008	,	,		18045	0.0		0.0	False		,,,				2504	0.0				p.E731K		Atlas-SNP	.											ENGASE,NS,carcinoma,-1,1	ENGASE	55	1	0			c.G2191A						PASS	.	G	LYS/GLU	507,3419		28,451,1484	42.0	50.0	47.0		2191	3.7	0.9	17	dbSNP_120	47	12,8276		0,12,4132	yes	missense	ENGASE	NM_001042573.1	56	28,463,5616	AA,AG,GG		0.1448,12.9139,4.2492	possibly-damaging	731/744	77082390	519,11695	1963	4144	6107	SO:0001583	missense	64772	exon14			CAGGCCGAGTGGG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.2191G>A	17.37:g.77082390G>A	ENSP00000462333:p.Glu731Lys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	CCDS42394.1	62	0.028388278388278388	61	0.12398373983739837	1	0.0027624309392265192	0	0.0	0	0.0	G	9.605	1.129684	0.21041	0.129139	0.001448	ENSG00000167280	ENST00000545583	.	.	.	4.78	3.74	0.42951	.	0.425847	0.25291	N	0.031721	T	0.00328	0.0010	M	0.65975	2.015	0.42538	D	0.993067	P	0.45011	0.848	B	0.33960	0.173	T	0.06972	-1.0797	9	0.15066	T	0.55	-28.3266	3.1644	0.06530	0.0965:0.1746:0.5481:0.1808	rs11871357;rs11871357	731	Q8NFI3	ENASE_HUMAN	K	731	.	ENSP00000438577:E731K	E	+	1	0	ENGASE	74593985	0.563000	0.26594	0.919000	0.36401	0.056000	0.15407	1.450000	0.35134	2.193000	0.70182	0.591000	0.81541	GAG	G|0.965;A|0.035	0.035	strong		0.652	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
ZNF860	344787	hgsc.bcm.edu	37	3	32031643	32031643	+	Missense_Mutation	SNP	A	A	G	rs386659897|rs13065048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:32031643A>G	ENST00000360311.4	+	2	1621	c.1072A>G	c.(1072-1074)Aca>Gca	p.T358A		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	358					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						TTCACACCTCACACAACACAC	0.403													a|||	2357	0.470647	0.7988	0.3602	5008	,	,		21395	0.4534		0.1968	False		,,,				2504	0.4049				p.T358A		Atlas-SNP	.											.	ZNF860	96	.	0			c.A1072G						PASS	.	G	ALA/THR	933,451		325,283,84	48.0	50.0	49.0		1072	-0.7	0.0	3	dbSNP_121	49	608,2574		57,494,1040	no	missense	ZNF860	NM_001137674.2	58	382,777,1124	GG,GA,AA		19.1075,32.5867,33.7495	benign	358/633	32031643	1541,3025	692	1591	2283	SO:0001583	missense	344787	exon2			CACCTCACACAAC	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1072A>G	3.37:g.32031643A>G	ENSP00000373274:p.Thr358Ala	Somatic	392	0	0		WXS	Illumina HiSeq	Phase_I	329	134	0.407295	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	913	0.41804029304029305	385	0.782520325203252	126	0.34806629834254144	249	0.4353146853146853	153	0.20184696569920843	a	0.001	-2.874949	0.00062	0.674133	0.191075	ENSG00000197385	ENST00000360311	T	0.06849	3.25	0.345	-0.691	0.11305	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.22034	-1.0228	7	.	.	.	.	2.7881	0.05379	0.2503:0.0:0.5021:0.2476	rs13065048;rs52806446;rs60333482;rs13065048	358	A6NHJ4	ZN860_HUMAN	A	358	ENSP00000373274:T358A	.	T	+	1	0	ZNF860	32006647	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.246000	0.18160	-2.012000	0.00950	-2.005000	0.00442	ACA	A|0.615;G|0.385	0.385	strong		0.403	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
IFT140	9742	hgsc.bcm.edu	37	16	1618306	1618306	+	Missense_Mutation	SNP	C	C	T	rs8050974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1618306C>T	ENST00000426508.2	-	15	2045	c.1682G>A	c.(1681-1683)aGc>aAc	p.S561N	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	561			S -> N (in dbSNP:rs8050974).		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)				CTCCGCCAGGCTCCTGCAGCT	0.662													C|||	128	0.0255591	0.0953	0.0029	5008	,	,		18208	0.0		0.0	False		,,,				2504	0.0				p.S561N		Atlas-SNP	.											.	IFT140	128	.	0			c.G1682A						PASS	.	C	ASN/SER	393,4005	193.0+/-218.2	17,359,1823	71.0	51.0	58.0		1682	-4.9	0.9	16	dbSNP_116	58	2,8598	1.2+/-3.3	0,2,4298	yes	missense	IFT140	NM_014714.3	46	17,361,6121	TT,TC,CC		0.0233,8.9359,3.0389	benign	561/1463	1618306	395,12603	2199	4300	6499	SO:0001583	missense	9742	exon15			GCCAGGCTCCTGC	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.1682G>A	16.37:g.1618306C>T	ENSP00000406012:p.Ser561Asn	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	55	0.025183150183150184	54	0.10975609756097561	1	0.0027624309392265192	0	0.0	0	0.0	C	0.085	-1.177507	0.01633	0.089359	2.33E-4	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.70516	-0.49	5.79	-4.95	0.03048	.	0.370546	0.32357	N	0.006210	T	0.00724	0.0024	N	0.02854	-0.475	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07947	-1.0746	10	0.10902	T	0.67	.	10.6786	0.45799	0.0:0.453:0.0951:0.4519	rs8050974;rs8050974	561;286	Q96RY7;B4DR58	IF140_HUMAN;.	N	561	ENSP00000406012:S561N	ENSP00000380562:S561N	S	-	2	0	IFT140	1558307	0.997000	0.39634	0.855000	0.33649	0.090000	0.18270	0.272000	0.18644	-1.081000	0.03105	-1.110000	0.02074	AGC	C|0.964;T|0.036	0.036	strong		0.662	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
ABCA7	10347	hgsc.bcm.edu	37	19	1044712	1044712	+	Missense_Mutation	SNP	A	A	G	rs567222111|rs3764647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1044712A>G	ENST00000263094.6	+	11	1415	c.1184A>G	c.(1183-1185)cAc>cGc	p.H395R	ABCA7_ENST00000435683.2_Missense_Mutation_p.H257R|ABCA7_ENST00000433129.1_Missense_Mutation_p.H395R	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	395			H -> R (in dbSNP:rs3764647). {ECO:0000269|PubMed:12111378}.		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)		GATGTGGGGCACCTGGTGGGC	0.677													G|||	545	0.108826	0.2572	0.0259	5008	,	,		14078	0.0923		0.0358	False		,,,				2504	0.0593				p.H395R		Atlas-SNP	.											.	ABCA7	174	.	0			c.A1184G						PASS	.	G	ARG/HIS	1054,3344	689.3+/-405.1	126,802,1271	39.0	39.0	39.0		1184	-4.4	0.0	19	dbSNP_107	39	348,8248	775.2+/-407.7	4,340,3954	yes	missense	ABCA7	NM_019112.3	29	130,1142,5225	GG,GA,AA		4.0484,23.9654,10.7896	benign	395/2147	1044712	1402,11592	2199	4298	6497	SO:0001583	missense	10347	exon11			TGGGGCACCTGGT	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.1184A>G	19.37:g.1044712A>G	ENSP00000263094:p.His395Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	90	32	0.355556	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	212	0.09706959706959707	128	0.2601626016260163	10	0.027624309392265192	47	0.08216783216783216	27	0.03562005277044855	G	2.961	-0.214544	0.06101	0.239654	0.040484	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.85556	-2.0;-2.0	4.1	-4.44	0.03557	.	.	.	.	.	T	0.00012	0.0000	N	0.02751	-0.505	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.02431	-1.1160	8	0.07030	T	0.85	.	3.7456	0.08547	0.4253:0.0:0.1756:0.3991	rs3764647;rs3764647	257;395	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	R	395	ENSP00000263094:H395R;ENSP00000414062:H395R	ENSP00000263094:H395R	H	+	2	0	ABCA7	995712	0.000000	0.05858	0.000000	0.03702	0.177000	0.22998	-2.738000	0.00800	-1.146000	0.02854	-0.374000	0.07098	CAC	A|0.886;G|0.114	0.114	strong		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
TOP3A	7156	hgsc.bcm.edu	37	17	18217958	18217958	+	Silent	SNP	C	C	T	rs2230153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18217958C>T	ENST00000321105.5	-	1	349	c.135G>A	c.(133-135)gcG>gcA	p.A45A	SMCR8_ENST00000406438.3_5'Flank|TOP3A_ENST00000582230.1_5'UTR|TOP3A_ENST00000542570.1_5'UTR	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	45	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						TCCCCTTGGCCGCGTCGTTTT	0.657													C|||	231	0.0461262	0.1596	0.0259	5008	,	,		17522	0.0		0.002	False		,,,				2504	0.0				p.A45A		Atlas-SNP	.											.	TOP3A	85	.	0			c.G135A						PASS	.	C		552,3854	248.1+/-256.1	40,472,1691	55.0	43.0	47.0		135	1.0	1.0	17	dbSNP_116	47	48,8552	29.6+/-80.5	0,48,4252	no	coding-synonymous	TOP3A	NM_004618.3		40,520,5943	TT,TC,CC		0.5581,12.5284,4.6133		45/1002	18217958	600,12406	2203	4300	6503	SO:0001819	synonymous_variant	7156	exon1			CTTGGCCGCGTCG	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.135G>A	17.37:g.18217958C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	175	89	0.508571	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Silent	SNP	ENST00000321105.5	37	CCDS11194.1	90	0.04120879120879121	78	0.15853658536585366	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	C	14.01	2.407166	0.42715	0.125284	0.005581	ENSG00000177302	ENST00000412083	.	.	.	5.44	1.01	0.19927	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.9999999999999994	.	.	.	.	.	.	T	0.11012	-1.0605	3	.	.	.	-26.1119	6.8195	0.23849	0.4676:0.3924:0.0:0.14	rs7212337	.	.	.	S	25	.	.	G	-	1	0	TOP3A	18158683	0.002000	0.14202	1.000000	0.80357	0.984000	0.73092	-1.659000	0.01975	0.367000	0.24454	0.655000	0.94253	GGC	C|0.948;T|0.052	0.052	strong		0.657	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
KTN1	3895	hgsc.bcm.edu	37	14	56096731	56096731	+	Silent	SNP	A	A	G	rs2274075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:56096731A>G	ENST00000395314.3	+	7	1205	c.1137A>G	c.(1135-1137)cgA>cgG	p.R379R	KTN1_ENST00000395309.3_Silent_p.R379R|KTN1_ENST00000413890.2_Silent_p.R379R|KTN1_ENST00000395308.1_Silent_p.R379R|KTN1_ENST00000438792.2_Silent_p.R379R|KTN1_ENST00000395311.1_Silent_p.R379R|KTN1_ENST00000416613.1_Silent_p.R379R	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	379					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TGAAAGATCGAATTGGAACAT	0.289			T	RET	papillary thryoid								G|||	305	0.0609026	0.0484	0.072	5008	,	,		21066	0.0159		0.0626	False		,,,				2504	0.1145				p.R379R		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	KTN1_ENST00000416613,NS,carcinoma,+1,1	KTN1	147	1	0			c.A1137G						PASS	.	G	,,,	266,4140	800.9+/-415.6	8,250,1945	122.0	122.0	122.0		1137,1137,1137,1137	-0.8	1.0	14	dbSNP_100	122	845,7755	779.1+/-407.7	43,759,3498	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	,,,	51,1009,5443	GG,GA,AA		9.8256,6.0372,8.5422	,,,	379/1358,379/1307,379/1301,379/1358	56096731	1111,11895	2203	4300	6503	SO:0001819	synonymous_variant	3895	exon7			AGATCGAATTGGA		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.1137A>G	14.37:g.56096731A>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	159	63	0.396226	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																			A|0.925;G|0.075	0.075	strong		0.289	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
DOK3	79930	hgsc.bcm.edu	37	5	176936822	176936822	+	Missense_Mutation	SNP	G	G	A	rs371788222		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176936822G>A	ENST00000357198.4	-	1	36	c.32C>T	c.(31-33)gCg>gTg	p.A11V	DOK3_ENST00000501403.2_Intron|DOK3_ENST00000312943.6_Intron|DOK3_ENST00000377112.4_Intron	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3	11					Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|lung(7)	13	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	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)|Epithelial(233;0.191)			CTGGGCACGCGCGTCTGATCG	0.711																																					p.A11V		Atlas-SNP	.											DOK3,NS,carcinoma,-1,1	DOK3	41	1	0			c.C32T						PASS	.	G	,,VAL/ALA	1,4403	2.1+/-5.4	0,1,2201	52.0	52.0	52.0		,,32	2.3	0.0	5		52	0,8600		0,0,4300	no	intron,intron,missense	DOK3	NM_001144875.1,NM_001144876.1,NM_024872.2	,,64	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	,,benign	,,11/497	176936822	1,13003	2202	4300	6502	SO:0001583	missense	79930	exon1			GCACGCGCGTCTG	AK026223	CCDS4426.1, CCDS47349.1, CCDS47350.1	5q35	2008-02-05			ENSG00000146094	ENSG00000146094			24583	protein-coding gene	gene with protein product		611435				10733577, 12595900	Standard	NM_024872		Approved	FLJ22570	uc003mhk.3	Q7L591	OTTHUMG00000130850	ENST00000357198.4:c.32C>T	5.37:g.176936822G>A	ENSP00000349727:p.Ala11Val	Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	310	144	0.464516	NM_024872	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	Missense_Mutation	SNP	ENST00000357198.4	37	CCDS4426.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.161465	0.38119	2.27E-4	0.0	ENSG00000146094	ENST00000357198	T	0.20200	2.09	3.22	2.34	0.29019	.	1.986640	0.03416	U	0.205582	T	0.12263	0.0298	N	0.08118	0	0.20563	N	0.999886	B	0.25955	0.138	B	0.11329	0.006	T	0.21381	-1.0247	10	0.87932	D	0	-23.7375	6.3296	0.21262	0.1376:0.0:0.8624:0.0	.	11	Q7L591	DOK3_HUMAN	V	11	ENSP00000349727:A11V	ENSP00000349727:A11V	A	-	2	0	DOK3	176869428	.	.	0.005000	0.12908	0.011000	0.07611	.	.	0.915000	0.36847	0.491000	0.48974	GCG	.	.	weak		0.711	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872	
ITLN1	55600	hgsc.bcm.edu	37	1	160854620	160854620	+	Silent	SNP	T	T	C	rs35779394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160854620T>C	ENST00000326245.3	-	2	163	c.48A>G	c.(46-48)ggA>ggG	p.G16G		NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	16					positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			CTGTACTCCATCCTCTGGTGG	0.498													C|||	585	0.116813	0.2481	0.0303	5008	,	,		21689	0.0992		0.004	False		,,,				2504	0.135				p.G16G		Atlas-SNP	.											.	ITLN1	45	.	0			c.A48G						PASS	.	C		936,3470	737.1+/-410.8	95,746,1362	240.0	220.0	227.0		48	-1.5	0.0	1	dbSNP_126	227	64,8536	816.5+/-406.9	0,64,4236	no	coding-synonymous	ITLN1	NM_017625.2		95,810,5598	CC,CT,TT		0.7442,21.2438,7.6888		16/314	160854620	1000,12006	2203	4300	6503	SO:0001819	synonymous_variant	55600	exon2			ACTCCATCCTCTG	AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.48A>G	1.37:g.160854620T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Silent	SNP	ENST00000326245.3	37	CCDS1211.1																																																																																			T|0.921;C|0.079	0.079	strong		0.498	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625	
ZKSCAN8	7745	hgsc.bcm.edu	37	6	28120898	28120898	+	Silent	SNP	G	G	A	rs17774663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28120898G>A	ENST00000330236.6	+	6	1024	c.840G>A	c.(838-840)caG>caA	p.Q280Q	ZKSCAN8_ENST00000457389.2_Silent_p.Q280Q	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	280	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)										CTGGAATCCAGCCACATGGAG	0.468													a|||	1100	0.219649	0.2958	0.2608	5008	,	,		20259	0.1875		0.1968	False		,,,				2504	0.1442				p.Q280Q		Atlas-SNP	.											ZNF192,NS,carcinoma,+1,1	.	.	1	0			c.G840A						PASS	.	T		1223,3183	707.1+/-407.5	174,875,1154	83.0	84.0	83.0		840	-11.2	0.1	6	dbSNP_123	83	1897,6703	728.3+/-406.7	216,1465,2619	no	coding-synonymous	ZNF192	NM_006298.2		390,2340,3773	AA,AG,GG		22.0581,27.7576,23.9889		280/579	28120898	3120,9886	2203	4300	6503	SO:0001819	synonymous_variant	7745	exon6			AATCCAGCCACAT		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12983	protein-coding gene	gene with protein product		602240	"""zinc finger protein 192"""	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	ENST00000330236.6:c.840G>A	6.37:g.28120898G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	183	99	0.540984	NM_006298	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	Silent	SNP	ENST00000330236.6	37	CCDS4645.1																																																																																			G|0.765;A|0.235	0.235	strong		0.468	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2		
APLP1	333	hgsc.bcm.edu	37	19	36370011	36370011	+	Silent	SNP	G	G	A	rs2227909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36370011G>A	ENST00000221891.4	+	16	1941	c.1749G>A	c.(1747-1749)gtG>gtA	p.V583V	APLP1_ENST00000537454.2_Silent_p.V543V|RN7SL402P_ENST00000465059.1_RNA|APLP1_ENST00000586861.1_Silent_p.V576V	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	45	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	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	
NLRC5	84166	hgsc.bcm.edu	37	16	57101340	57101340	+	Missense_Mutation	SNP	T	T	C	rs7190199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57101340T>C	ENST00000262510.6	+	35	4589	c.4364T>C	c.(4363-4365)gTc>gCc	p.V1455A	NLRC5_ENST00000308149.7_Missense_Mutation_p.V1426A|NLRC5_ENST00000539144.1_Missense_Mutation_p.V1426A|NLRC5_ENST00000436936.1_Missense_Mutation_p.V1455A	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1455			V -> A (in dbSNP:rs7190199).		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)				AGCCTTCTTGTCGGGCAGCTG	0.567													T|||	450	0.0898562	0.146	0.0893	5008	,	,		19926	0.1181		0.0646	False		,,,				2504	0.0112				p.V1455A		Atlas-SNP	.											.	NLRC5	186	.	0			c.T4364C						PASS	.	T	ALA/VAL	562,3834	251.8+/-258.4	36,490,1672	126.0	117.0	120.0		4364	-2.2	0.0	16	dbSNP_116	120	445,8155	134.9+/-192.2	16,413,3871	yes	missense	NLRC5	NM_032206.3	64	52,903,5543	CC,CT,TT		5.1744,12.7843,7.7485	benign	1455/1867	57101340	1007,11989	2198	4300	6498	SO:0001583	missense	84166	exon34			TTCTTGTCGGGCA	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.4364T>C	16.37:g.57101340T>C	ENSP00000262510:p.Val1455Ala	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	216	104	0.481481	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	213	0.09752747252747253	56	0.11382113821138211	30	0.08287292817679558	80	0.13986013986013987	47	0.06200527704485488	T	6.600	0.478986	0.12581	0.127843	0.051744	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144	T;T;T;T	0.54479	2.14;2.14;0.57;2.14	4.64	-2.22	0.06952	.	.	.	.	.	T	0.00178	0.0005	N	0.03253	-0.375	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.07558	-1.0766	8	0.49607	T	0.09	.	4.5154	0.11932	0.154:0.3836:0.0:0.4624	rs7190199;rs7190199	1455	Q86WI3	NLRC5_HUMAN	A	1455;1426;1455;1426	ENSP00000262510:V1455A;ENSP00000308886:V1426A;ENSP00000389739:V1455A;ENSP00000441727:V1426A	ENSP00000262510:V1455A	V	+	2	0	NLRC5	55658841	0.000000	0.05858	0.000000	0.03702	0.258000	0.26162	-0.273000	0.08548	-0.545000	0.06224	0.450000	0.29827	GTC	T|0.912;C|0.088	0.088	strong		0.567	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
AKAP11	11215	hgsc.bcm.edu	37	13	42876996	42876996	+	Missense_Mutation	SNP	G	G	A	rs114980445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:42876996G>A	ENST00000025301.2	+	8	4289	c.4114G>A	c.(4114-4116)Gcc>Acc	p.A1372T		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1372					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)		CAATAGGCTTGCCTACCGATC	0.413													G|||	22	0.00439297	0.0144	0.0043	5008	,	,		21346	0.0		0.0	False		,,,				2504	0.0				p.A1372T		Atlas-SNP	.											.	AKAP11	146	.	0			c.G4114A						PASS	.	G	THR/ALA	79,4327	69.8+/-107.6	0,79,2124	88.0	82.0	84.0		4114	6.2	1.0	13	dbSNP_132	84	1,8599	1.2+/-3.3	0,1,4299	yes	missense	AKAP11	NM_016248.3	58	0,80,6423	AA,AG,GG		0.0116,1.793,0.6151	probably-damaging	1372/1902	42876996	80,12926	2203	4300	6503	SO:0001583	missense	11215	exon8			AGGCTTGCCTACC	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.4114G>A	13.37:g.42876996G>A	ENSP00000025301:p.Ala1372Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	G	28.1	4.892258	0.91889	0.01793	1.16E-4	ENSG00000023516	ENST00000025301	T	0.56444	0.46	6.16	6.16	0.99307	.	0.065315	0.64402	D	0.000013	T	0.60287	0.2257	M	0.71581	2.175	0.54753	D	0.999989	D	0.89917	1.0	D	0.72982	0.979	T	0.69194	-0.5209	10	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	1372	Q9UKA4	AKA11_HUMAN	T	1372	ENSP00000025301:A1372T	ENSP00000025301:A1372T	A	+	1	0	AKAP11	41774996	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.096000	0.94182	2.937000	0.99478	0.650000	0.86243	GCC	G|0.992;A|0.008	0.008	strong		0.413	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
MAP3K6	9064	hgsc.bcm.edu	37	1	27688633	27688633	+	Missense_Mutation	SNP	G	G	A	rs1138294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:27688633G>A	ENST00000493901.1	-	10	1603	c.1364C>T	c.(1363-1365)aCc>aTc	p.T455I	MAP3K6_ENST00000374040.3_Missense_Mutation_p.T447I|MAP3K6_ENST00000357582.2_Missense_Mutation_p.T455I	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	455			T -> I (in dbSNP:rs1138294). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17210579}.		activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		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;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CACCACCTGGGTGGGGTCATT	0.602													G|||	1555	0.310503	0.0983	0.2147	5008	,	,		20741	0.5397		0.3777	False		,,,				2504	0.3599				p.T455I		Atlas-SNP	.											.	MAP3K6	134	.	0			c.C1364T						PASS	.	G	ILE/THR	649,3757	269.2+/-268.9	44,561,1598	44.0	40.0	42.0		1364	-1.1	0.4	1	dbSNP_86	42	3016,5584	454.1+/-363.4	543,1930,1827	yes	missense	MAP3K6	NM_004672.3	89	587,2491,3425	AA,AG,GG		35.0698,14.7299,28.1793	benign	455/1289	27688633	3665,9341	2203	4300	6503	SO:0001583	missense	9064	exon9			ACCTGGGTGGGGT	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.1364C>T	1.37:g.27688633G>A	ENSP00000419591:p.Thr455Ile	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	303	146	0.481848	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	37	CCDS299.1	714|714	0.3269230769230769|0.3269230769230769	57|57	0.11585365853658537|0.11585365853658537	83|83	0.2292817679558011|0.2292817679558011	282|282	0.493006993006993|0.493006993006993	292|292	0.38522427440633245|0.38522427440633245	G|G	9.768|9.768	1.171945|1.171945	0.21704|0.21704	0.147299|0.147299	0.350698|0.350698	ENSG00000142733|ENSG00000142733	ENST00000472410|ENST00000374040;ENST00000493901;ENST00000545447;ENST00000357582	.|T;T;T	.|0.09630	.|2.96;2.96;2.96	4.93|4.93	-1.12|-1.12	0.09808|0.09808	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.20685|0.20685	0.6|0.6	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.0;0.001	T|T	0.45293|0.45293	-0.9271|-0.9271	4|8	.|0.39692	.|T	.|0.17	.|.	0.6264|0.6264	0.00786|0.00786	0.3861:0.1243:0.2381:0.2516|0.3861:0.1243:0.2381:0.2516	rs1138294;rs3202045;rs3813799;rs52827923;rs60875383;rs1138294|rs1138294;rs3202045;rs3813799;rs52827923;rs60875383;rs1138294	.|447;455	.|O95382-3;O95382	.|.;M3K6_HUMAN	S|I	179|447;455;178;455	.|ENSP00000363152:T447I;ENSP00000419591:T455I;ENSP00000350195:T455I	.|ENSP00000350195:T455I	P|T	-|-	1|2	0|0	MAP3K6|MAP3K6	27561220|27561220	0.000000|0.000000	0.05858|0.05858	0.395000|0.395000	0.26283|0.26283	0.995000|0.995000	0.86356|0.86356	-1.184000|-1.184000	0.03076|0.03076	-0.091000|-0.091000	0.12440|0.12440	0.650000|0.650000	0.86243|0.86243	CCC|ACC	G|0.712;A|0.288	0.288	strong		0.602	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672	
PPEF2	5470	hgsc.bcm.edu	37	4	76797551	76797551	+	Missense_Mutation	SNP	C	C	G	rs370312706		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:76797551C>G	ENST00000286719.7	-	11	1565	c.1209G>C	c.(1207-1209)caG>caC	p.Q403H		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	403	Catalytic.				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)			GGCCTGCTTGCTGCCGGCACC	0.677																																					p.Q403H	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.G1209C						PASS	.						29.0	32.0	31.0					4																	76797551		2203	4300	6503	SO:0001583	missense	5470	exon11			TGCTTGCTGCCGG	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.1209G>C	4.37:g.76797551C>G	ENSP00000286719:p.Gln403His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.738539	0.30774	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.41758	0.99	4.94	3.21	0.36854	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);Metallophosphoesterase domain (1);	1.466720	0.04609	N	0.399943	T	0.43100	0.1232	L	0.41236	1.265	0.25277	N	0.989465	P;P	0.41569	0.755;0.6	P;B	0.44946	0.465;0.382	T	0.29640	-1.0005	10	0.33940	T	0.23	0.0283	9.0738	0.36508	0.0:0.8174:0.0:0.1826	.	403;403	O14830-2;O14830	.;PPE2_HUMAN	H	403	ENSP00000286719:Q403H	ENSP00000286719:Q403H	Q	-	3	2	PPEF2	77016575	0.764000	0.28473	0.014000	0.15608	0.095000	0.18619	2.772000	0.47678	0.510000	0.28216	-0.339000	0.08088	CAG	.	.	alt		0.677	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239	
STARD7	56910	hgsc.bcm.edu	37	2	96861159	96861159	+	Missense_Mutation	SNP	C	C	G	rs2276650	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:96861159C>G	ENST00000337288.5	-	2	802	c.419G>C	c.(418-420)cGt>cCt	p.R140P	STARD7_ENST00000462501.1_5'UTR	NM_020151.3	NP_064536.2	Q9NQZ5	STAR7_HUMAN	StAR-related lipid transfer (START) domain containing 7	140	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.		R -> P (in dbSNP:rs2276650). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)	lipid binding (GO:0008289)	p.R65P(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|stomach(2)	14						CATTTCCCAACGTTGCTCTTT	0.498													N|||	660	0.131789	0.0454	0.134	5008	,	,		19125	0.124		0.17	False		,,,				2504	0.2157				p.R140P		Atlas-SNP	.											STARD7,NS,carcinoma,0,1	STARD7	49	1	1	Substitution - Missense(1)	stomach(1)	c.G419C						PASS	.	G	PRO/ARG	294,4112	797.8+/-415.4	10,274,1919	151.0	116.0	128.0		419	4.7	0.0	2	dbSNP_100	128	1418,7182	746.9+/-407.3	122,1174,3004	yes	missense	STARD7	NM_020151.3	103	132,1448,4923	GG,GC,CC		16.4884,6.6727,13.1632	benign	140/371	96861159	1712,11294	2203	4300	6503	SO:0001583	missense	56910	exon2			TCCCAACGTTGCT	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.419G>C	2.37:g.96861159C>G	ENSP00000338030:p.Arg140Pro	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	221	84	0.380091	NM_020151	D3DXG9|Q53T44|Q6GU43|Q969M6	Missense_Mutation	SNP	ENST00000337288.5	37	CCDS2017.2	266	0.12179487179487179	21	0.042682926829268296	46	0.1270718232044199	66	0.11538461538461539	133	0.17546174142480211	G	0.772	-0.765499	0.02996	0.066727	0.164884	ENSG00000084090	ENST00000337288;ENST00000443962	T;T	0.03094	4.05;4.05	5.62	4.73	0.59995	Lipid-binding START (3);START-like domain (1);	0.264075	0.36972	N	0.002307	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	0.48502	-0.9030	9	0.17832	T	0.49	-4.41	9.4979	0.38999	0.0:0.2954:0.5518:0.1529	rs2276650;rs17419527;rs17845138;rs17856446;rs17857941;rs17858069;rs52838299;rs2276650	140	Q9NQZ5	STAR7_HUMAN	P	140;39	ENSP00000338030:R140P;ENSP00000409410:R39P	ENSP00000338030:R140P	R	-	2	0	STARD7	96224886	0.927000	0.31430	0.014000	0.15608	0.676000	0.39594	2.586000	0.46119	0.708000	0.31955	-0.120000	0.15030	CGT	C|0.878;G|0.122	0.122	strong		0.498	STARD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252848.2		
ARL11	115761	hgsc.bcm.edu	37	13	50205025	50205025	+	Missense_Mutation	SNP	T	T	C	rs3803185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:50205025T>C	ENST00000282026.1	+	2	777	c.442T>C	c.(442-444)Tgc>Cgc	p.C148R	ARL11_ENST00000490932.1_Intron	NM_138450.5	NP_612459.1	Q969Q4	ARL11_HUMAN	ADP-ribosylation factor-like 11	148			C -> R (in dbSNP:rs3803185). {ECO:0000269|PubMed:15843669}.		hematopoietic progenitor cell differentiation (GO:0002244)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			kidney(1)|large_intestine(4)|ovary(1)	6		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00174)|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;0.119)|Kidney(9;0.169)	GBM - Glioblastoma multiforme(99;1.67e-09)		CCAGGACCACTGCTGGGAGCT	0.612													T|||	1271	0.253794	0.0666	0.4006	5008	,	,		16728	0.1865		0.496	False		,,,				2504	0.2229				p.C148R		Atlas-SNP	.											.	ARL11	26	.	0			c.T442C	GRCh37	CM062430	ARL11	M	rs3803185	PASS	.	T	ARG/CYS	643,3763	265.0+/-266.4	50,543,1610	36.0	35.0	36.0		442	-10.8	0.0	13	dbSNP_107	36	4418,4178	553.7+/-386.3	1153,2112,1033	yes	missense	ARL11	NM_138450.5	180	1203,2655,2643	CC,CT,TT		48.604,14.5937,38.9248	benign	148/197	50205025	5061,7941	2203	4298	6501	SO:0001583	missense	115761	exon2			GACCACTGCTGGG	AF441378	CCDS9419.1	13q14.12	2014-05-09			ENSG00000152213	ENSG00000152213		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	24046	protein-coding gene	gene with protein product		609351				12477932	Standard	NM_138450		Approved	ARLTS1, FLJ33930	uc001vdf.2	Q969Q4	OTTHUMG00000016919	ENST00000282026.1:c.442T>C	13.37:g.50205025T>C	ENSP00000282026:p.Cys148Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_138450		Missense_Mutation	SNP	ENST00000282026.1	37	CCDS9419.1	673	0.30815018315018317	36	0.07317073170731707	146	0.40331491712707185	97	0.16958041958041958	394	0.5197889182058048	T	0.113	-1.135197	0.01742	0.145937	0.51396	ENSG00000152213	ENST00000282026	T	0.81330	-1.48	5.42	-10.8	0.00216	.	0.790281	0.12116	N	0.498086	T	0.00012	0.0000	N	0.04724	-0.175	0.58432	P	4.000000000004E-6	B	0.06786	0.001	B	0.08055	0.003	T	0.16364	-1.0405	9	0.32370	T	0.25	-17.1507	5.6024	0.17361	0.4664:0.3524:0.0788:0.1023	rs3803185;rs3803185	148	Q969Q4	ARL11_HUMAN	R	148	ENSP00000282026:C148R	ENSP00000282026:C148R	C	+	1	0	ARL11	49103026	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.348000	0.02629	-2.504000	0.00508	-1.140000	0.01884	TGC	T|0.660;C|0.340	0.340	strong		0.612	ARL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044929.2	NM_138450	
THADA	63892	hgsc.bcm.edu	37	2	43819139	43819139	+	Silent	SNP	A	A	G	rs17031095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:43819139A>G	ENST00000405006.4	-	3	474	c.123T>C	c.(121-123)caT>caC	p.H41H	THADA_ENST00000403856.1_Silent_p.H41H|THADA_ENST00000405975.2_Silent_p.H41H|THADA_ENST00000404790.1_Silent_p.H41H|THADA_ENST00000402360.2_Silent_p.H41H|THADA_ENST00000415080.2_5'UTR	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	123	0	0		WXS	Illumina HiSeq	Phase_I	120	67	0.558333	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29912348	29912348	+	Missense_Mutation	SNP	A	A	G	rs1137078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29912348A>G	ENST00000396634.1	+	7	1308	c.967A>G	c.(967-969)Act>Gct	p.T323A	HLA-A_ENST00000376809.5_Missense_Mutation_p.T323A|HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376806.5_Missense_Mutation_p.T323A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	323					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						AGCTGTGATCACTGGAGCTGT	0.592									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|||	1292	0.257987	0.3994	0.2305	5008	,	,		19059	0.1984		0.1769	False		,,,				2504	0.2311				p.T323A		Atlas-SNP	.											.	HLA-A	89	.	0			c.A967G						PASS	.						111.0	106.0	108.0					6																	29912348		1511	2709	4220	SO:0001583	missense	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTGATCACTGGAG	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.967A>G	6.37:g.29912348A>G	ENSP00000379873:p.Thr323Ala	Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	522	179	0.342912	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	527	0.2413003663003663	198	0.4024390243902439	87	0.24033149171270718	121	0.21153846153846154	121	0.15963060686015831	.	3.109	-0.183024	0.06340	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809	T;T;T	0.00648	6.02;5.99;6.02	3.09	-6.18	0.02085	.	0.889866	0.09141	U	0.842941	T	0.00241	0.0007	L	0.43701	1.375	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.0;0.001;0.002;0.001;0.002	T	0.39231	-0.9624	9	0.87932	D	0	.	5.3051	0.15799	0.3194:0.2957:0.3849:0.0	rs1137078;rs2231112;rs3179280;rs9260189;rs17424431;rs17845173;rs17857981;rs41558515	202;323;323;323;323	B4DVB9;P16188;Q5SRN5;P30455;P04439	.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	A	323	ENSP00000379873:T323A;ENSP00000366002:T323A;ENSP00000366005:T323A	ENSP00000366002:T323A	T	+	1	0	HLA-A	30020327	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.200000	0.03029	-1.981000	0.00989	-1.713000	0.00713	ACT	A|0.761;G|0.239	0.239	strong		0.592	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
POFUT1	23509	hgsc.bcm.edu	37	20	30822455	30822455	+	Silent	SNP	C	C	T	rs7263390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:30822455C>T	ENST00000375749.3	+	7	1220	c.1158C>T	c.(1156-1158)gaC>gaT	p.D386D	POFUT1_ENST00000539210.1_Silent_p.D175D	NM_015352.1	NP_056167.1	Q9H488	OFUT1_HUMAN	protein O-fucosyltransferase 1	386					angiogenesis (GO:0001525)|embryo development (GO:0009790)|fucose metabolic process (GO:0006004)|heart development (GO:0007507)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|O-glycan processing (GO:0016266)|protein O-linked fucosylation (GO:0036066)|protein O-linked glycosylation (GO:0006493)|regulation of transcription, DNA-templated (GO:0006355)|somitogenesis (GO:0001756)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	6			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			AGCTGCGGGACGAGTTCTGAT	0.632													C|||	92	0.0183706	0.0651	0.0086	5008	,	,		18001	0.0		0.0	False		,,,				2504	0.0				p.D386D		Atlas-SNP	.											.	POFUT1	52	.	0			c.C1158T						PASS	.	C		233,4173	136.1+/-172.1	8,217,1978	54.0	54.0	54.0		1158	-3.8	1.0	20	dbSNP_116	54	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	POFUT1	NM_015352.1		8,224,6271	TT,TC,CC		0.0814,5.2882,1.8453		386/389	30822455	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	23509	exon7			GCGGGACGAGTTC	AF375884	CCDS13198.1, CCDS13199.1	20q11	2013-03-06			ENSG00000101346	ENSG00000101346	2.4.1.221	"""Fucosyltransferases"""	14988	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 1"""	607491				9023546, 9525914	Standard	NM_015352		Approved	O-FUT, O-Fuc-T, KIAA0180, FUT12	uc002wxp.3	Q9H488	OTTHUMG00000133268	ENST00000375749.3:c.1158C>T	20.37:g.30822455C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_015352	A8K4R8|E1P5M4|Q14685|Q5W185|Q9BW76	Silent	SNP	ENST00000375749.3	37	CCDS13198.1																																																																																			C|0.973;T|0.027	0.027	strong		0.632	POFUT1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078613.1	NM_015352	
WDR72	256764	hgsc.bcm.edu	37	15	53907679	53907679	+	Silent	SNP	T	T	C	rs16966318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:53907679T>C	ENST00000396328.1	-	15	2963	c.2724A>G	c.(2722-2724)ctA>ctG	p.L908L	WDR72_ENST00000557913.1_Silent_p.L905L|WDR72_ENST00000559418.1_Silent_p.L918L|WDR72_ENST00000360509.5_Silent_p.L908L	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	908										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)		TAACTAAAAATAGTCTGCTCA	0.338													T|||	666	0.132987	0.4289	0.0591	5008	,	,		16414	0.0		0.0408	False		,,,				2504	0.0174				p.L908L		Atlas-SNP	.											.	WDR72	177	.	0			c.A2724G						PASS	.	T		1507,2871		273,961,955	30.0	32.0	31.0		2724	-4.3	0.9	15	dbSNP_123	31	332,8242		5,322,3960	no	coding-synonymous	WDR72	NM_182758.2		278,1283,4915	CC,CT,TT		3.8722,34.4221,14.1986		908/1103	53907679	1839,11113	2189	4287	6476	SO:0001819	synonymous_variant	256764	exon15			TAAAAATAGTCTG	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.2724A>G	15.37:g.53907679T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	146	81	0.554795	NM_182758	Q7Z3I3|Q8N8X2	Silent	SNP	ENST00000396328.1	37	CCDS10151.1																																																																																			T|0.867;C|0.133	0.133	strong		0.338	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
RPS6KA1	6195	hgsc.bcm.edu	37	1	26887592	26887592	+	Silent	SNP	T	T	C	rs1064196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26887592T>C	ENST00000374168.2	+	16	1552	c.1398T>C	c.(1396-1398)taT>taC	p.Y466Y	RPS6KA1_ENST00000374166.4_Silent_p.Y455Y|RPS6KA1_ENST00000531382.1_Silent_p.Y475Y|RPS6KA1_ENST00000374162.2_Silent_p.Y374Y|RPS6KA1_ENST00000530003.1_Silent_p.Y450Y|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	128	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	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	
EXOSC9	5393	hgsc.bcm.edu	37	4	122737965	122737965	+	Missense_Mutation	SNP	G	G	C	rs1051881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:122737965G>C	ENST00000243498.5	+	12	1382	c.1274G>C	c.(1273-1275)aGt>aCt	p.S425T	EXOSC9_ENST00000379663.3_Missense_Mutation_p.S442T|EXOSC9_ENST00000512454.1_Missense_Mutation_p.S409T|CCNA2_ENST00000274026.5_3'UTR	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	425			S -> T (in dbSNP:rs1051881).		exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|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)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						AAAGCACCAAGTAAAAAGCCA	0.299													G|||	650	0.129792	0.4266	0.0648	5008	,	,		16115	0.0179		0.0139	False		,,,				2504	0.0092				p.S442T		Atlas-SNP	.											.	EXOSC9	51	.	0			c.G1325C						PASS	.	G	,THR/SER,THR/SER	1647,2753		294,1059,847	33.0	34.0	33.0		,1274,1325	4.1	1.0	4	dbSNP_86	33	197,8397		2,193,4102	yes	utr-3,missense,missense	CCNA2,EXOSC9	NM_001237.3,NM_005033.2,NM_001034194.1	,58,58	296,1252,4949	CC,CG,GG		2.2923,37.4318,14.1912	,benign,benign	,425/440,442/457	122737965	1844,11150	2200	4297	6497	SO:0001583	missense	5393	exon13			CACCAAGTAAAAA	M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 1 (75kD)"""	606180	"""polymyositis/scleroderma autoantigen 1, 75kDa"""	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.1274G>C	4.37:g.122737965G>C	ENSP00000243498:p.Ser425Thr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	160	82	0.5125	NM_001034194	Q12883|Q4W5P5|Q86Y41|Q86Y48	Missense_Mutation	SNP	ENST00000243498.5	37	CCDS3722.2	227	0.10393772893772894	180	0.36585365853658536	30	0.08287292817679558	11	0.019230769230769232	6	0.0079155672823219	G	12.10	1.835842	0.32421	0.374318	0.022923	ENSG00000123737	ENST00000243498;ENST00000379663;ENST00000512454	T;T;T	0.25749	1.79;1.81;1.78	4.96	4.13	0.48395	.	0.331832	0.35585	N	0.003112	T	0.00012	0.0000	L	0.38175	1.15	0.09310	P	0.9999999999999557	B;B;B	0.29301	0.067;0.034;0.241	B;B;B	0.33042	0.032;0.032;0.157	T	0.44697	-0.9311	9	0.12430	T	0.62	-26.7721	10.9773	0.47473	0.0879:0.0:0.9121:0.0	rs1051881;rs1803182;rs3192269;rs52807748;rs1051881	409;425;442	D6RIY6;Q06265;Q06265-2	.;EXOS9_HUMAN;.	T	425;442;409	ENSP00000243498:S425T;ENSP00000368984:S442T;ENSP00000425782:S409T	ENSP00000243498:S425T	S	+	2	0	EXOSC9	122957415	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.232000	0.32636	1.462000	0.47948	-0.252000	0.11476	AGT	G|0.885;C|0.115	0.115	strong		0.299	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2	NM_005033	
INTS5	80789	hgsc.bcm.edu	37	11	62415285	62415285	+	Missense_Mutation	SNP	C	C	T	rs149821915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62415285C>T	ENST00000330574.2	-	2	2319	c.2267G>A	c.(2266-2268)cGt>cAt	p.R756H	GANAB_ENST00000356638.3_5'Flank|GANAB_ENST00000540933.1_5'Flank|GANAB_ENST00000534779.1_5'Flank|GANAB_ENST00000346178.4_5'Flank	NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	756					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(6)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	36						CTTTAAGCCACGGCCGATGAC	0.557																																					p.R756H		Atlas-SNP	.											.	INTS5	81	.	0			c.G2267A						PASS	.	C	HIS/ARG	6,4398	11.4+/-27.6	0,6,2196	51.0	57.0	55.0		2267	3.5	1.0	11	dbSNP_134	55	0,8598		0,0,4299	yes	missense	INTS5	NM_030628.1	29	0,6,6495	TT,TC,CC		0.0,0.1362,0.0461	benign	756/1020	62415285	6,12996	2202	4299	6501	SO:0001583	missense	80789	exon2			AAGCCACGGCCGA	AK123587	CCDS8027.1	11q12.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000185085	ENSG00000185085			29352	protein-coding gene	gene with protein product		611349	"""KIAA1698"""	KIAA1698		16239144	Standard	NM_030628		Approved	INT5	uc001nud.3	Q6P9B9	OTTHUMG00000167605	ENST00000330574.2:c.2267G>A	11.37:g.62415285C>T	ENSP00000327889:p.Arg756His	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	143	75	0.524476	NM_030628	Q8N6W5|Q9C0G5	Missense_Mutation	SNP	ENST00000330574.2	37	CCDS8027.1	.	.	.	.	.	.	.	.	.	.	C	7.215	0.596297	0.13875	0.001362	0.0	ENSG00000185085	ENST00000330574	.	.	.	5.43	3.53	0.40419	.	0.200939	0.45867	D	0.000336	T	0.29126	0.0724	L	0.28115	0.83	0.30938	N	0.726113	B	0.10296	0.003	B	0.04013	0.001	T	0.14282	-1.0478	9	0.25106	T	0.35	.	6.0709	0.19889	0.0:0.6759:0.1555:0.1686	.	756	Q6P9B9	INT5_HUMAN	H	756	.	ENSP00000327889:R756H	R	-	2	0	INTS5	62171861	0.146000	0.22672	1.000000	0.80357	0.864000	0.49448	0.847000	0.27696	1.530000	0.49136	-0.145000	0.13849	CGT	C|1.000;T|0.000	0.000	strong		0.557	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628	
C9orf156	51531	hgsc.bcm.edu	37	9	100672338	100672338	+	Missense_Mutation	SNP	C	C	T	rs2282192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100672338C>T	ENST00000375119.3	-	4	1046	c.970G>A	c.(970-972)Gtg>Atg	p.V324M	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	324			V -> M (in dbSNP:rs2282192).		viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				GCAGGAACCACGCTGCGGGGA	0.592													C|||	2951	0.589257	0.7935	0.4553	5008	,	,		19915	0.7788		0.2704	False		,,,				2504	0.5409				p.V324M		Atlas-SNP	.											C9orf156,NS,meningioma,0,1	C9orf156	35	1	0			c.G970A						PASS	.	C	MET/VAL	3121,1285	699.7+/-406.5	1113,895,195	58.0	53.0	54.0		970	-3.4	0.0	9	dbSNP_100	54	2332,6268	389.4+/-342.9	311,1710,2279	yes	missense	C9orf156	NM_016481.3	21	1424,2605,2474	TT,TC,CC		27.1163,29.1648,41.9268	benign	324/442	100672338	5453,7553	2203	4300	6503	SO:0001583	missense	51531	exon4			GAACCACGCTGCG	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"""Nef (lentivirus myristoylated factor) associated protein 1"""						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.970G>A	9.37:g.100672338C>T	ENSP00000364260:p.Val324Met	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	95	62	0.652632	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Missense_Mutation	SNP	ENST00000375119.3	37	CCDS6730.1	1203	0.5508241758241759	391	0.7947154471544715	152	0.4198895027624309	445	0.777972027972028	215	0.2836411609498681	C	10.47	1.360029	0.24598	0.708352	0.271163	ENSG00000136932	ENST00000375119;ENST00000375118	T;T	0.47528	0.84;0.84	5.03	-3.42	0.04825	Uncharacterised domain UPF0066, YaeB-like domain (1);	1.123640	0.06526	N	0.740603	T	0.00012	0.0000	L	0.38838	1.175	0.80722	P	0.0	B;B	0.18610	0.029;0.007	B;B	0.13407	0.009;0.001	T	0.39502	-0.9611	9	0.44086	T	0.13	-0.2542	1.5546	0.02582	0.1786:0.3526:0.102:0.3668	rs2282192;rs52801806;rs61011015;rs2282192	178;324	Q5T114;Q9BU70	.;NAP1_HUMAN	M	324;178	ENSP00000364260:V324M;ENSP00000364259:V178M	ENSP00000364259:V178M	V	-	1	0	C9orf156	99712159	0.000000	0.05858	0.001000	0.08648	0.222000	0.24845	-0.162000	0.10012	-0.506000	0.06558	-1.559000	0.00887	GTG	C|0.504;T|0.496	0.496	strong		0.592	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481	
ANKRD28	23243	hgsc.bcm.edu	37	3	15807763	15807763	+	Silent	SNP	G	G	A	rs185386403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:15807763G>A	ENST00000399451.2	-	3	535	c.168C>T	c.(166-168)atC>atT	p.I56I	ANKRD28_ENST00000497037.1_5'UTR|ANKRD28_ENST00000383777.1_Silent_p.I89I	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	56						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						GAAGTTCAATGATTTCTGCAT	0.328													G|||	13	0.00259585	0.0008	0.0058	5008	,	,		16531	0.0		0.005	False		,,,				2504	0.0031				p.I56I		Atlas-SNP	.											.	ANKRD28	121	.	0			c.C168T						PASS	.	G	,	4,3682		0,4,1839	71.0	70.0	70.0		,168	0.8	1.0	3		70	65,8087		1,63,4012	no	utr-5,coding-synonymous	ANKRD28	NM_001195098.1,NM_015199.3	,	1,67,5851	AA,AG,GG		0.7974,0.1085,0.5829	,	,56/1054	15807763	69,11769	1843	4076	5919	SO:0001819	synonymous_variant	23243	exon3			TTCAATGATTTCT	AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	29024	protein-coding gene	gene with protein product	"""phosphatase interactor targeting K protein"", ""protein phosphatase 6 ankyrin repeat subunit A"", ""protein phosphatase 1, regulatory subunit 65"""	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.168C>T	3.37:g.15807763G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_015199	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Silent	SNP	ENST00000399451.2	37	CCDS46769.1																																																																																			G|0.996;A|0.004	0.004	strong		0.328	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199	
PPEF2	5470	hgsc.bcm.edu	37	4	76811175	76811175	+	Missense_Mutation	SNP	G	G	T	rs28436183	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	241	0	0		WXS	Illumina HiSeq	Phase_I	269	126	0.468401	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	
UNC5B	219699	hgsc.bcm.edu	37	10	73057755	73057755	+	Silent	SNP	G	G	C	rs10823720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73057755G>C	ENST00000335350.6	+	16	2996	c.2580G>C	c.(2578-2580)ctG>ctC	p.L860L	UNC5B_ENST00000373192.4_Silent_p.L849L	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	860					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						AGATCCCACTGTCCATCCGCC	0.577													G|||	330	0.0658946	0.0492	0.0072	5008	,	,		21886	0.1786		0.0089	False		,,,				2504	0.0726				p.L860L		Atlas-SNP	.											.	UNC5B	123	.	0			c.G2580C						PASS	.	G		191,4215	122.5+/-159.9	5,181,2017	137.0	100.0	113.0		2580	0.5	0.4	10	dbSNP_120	113	177,8423	81.8+/-144.4	1,175,4124	no	coding-synonymous	UNC5B	NM_170744.4		6,356,6141	CC,CG,GG		2.0581,4.335,2.8295		860/946	73057755	368,12638	2203	4300	6503	SO:0001819	synonymous_variant	219699	exon16			CCCACTGTCCATC	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.2580G>C	10.37:g.73057755G>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	94	37	0.393617	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																			G|0.964;C|0.036	0.036	strong		0.577	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
DSC1	1823	hgsc.bcm.edu	37	18	28722039	28722039	+	Silent	SNP	G	G	A	rs2577075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28722039G>A	ENST00000257198.5	-	9	1444	c.1183C>T	c.(1183-1185)Cta>Tta	p.L395L	RP11-408H20.2_ENST00000581836.1_RNA|DSC1_ENST00000257197.3_Silent_p.L395L	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	395	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			TTTCCTTGTAGGATTTTGTAT	0.363													G|||	1726	0.344649	0.4085	0.3746	5008	,	,		16726	0.5655		0.2127	False		,,,				2504	0.1452				p.L395L		Atlas-SNP	.											.	DSC1	240	.	0			c.C1183T						PASS	.	G	,	1770,2636	524.7+/-371.4	357,1056,790	169.0	169.0	169.0		1183,1183	3.7	1.0	18	dbSNP_100	169	1610,6990	299.8+/-304.6	161,1288,2851	no	coding-synonymous,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	518,2344,3641	AA,AG,GG		18.7209,40.1725,25.988	,	395/841,395/895	28722039	3380,9626	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon9			CTTGTAGGATTTT	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1183C>T	18.37:g.28722039G>A		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	226	96	0.424779	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			G|0.696;A|0.304	0.304	strong		0.363	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
KRT33B	3884	hgsc.bcm.edu	37	17	39521726	39521726	+	Missense_Mutation	SNP	T	T	C	rs61741663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39521726T>C	ENST00000251646.3	-	4	717	c.668A>G	c.(667-669)cAg>cGg	p.Q223R		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	223	Coil 2.|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)				GTTCAGGACCTGGTTCAGGTC	0.577													T|||	85	0.0169728	0.0635	0.0014	5008	,	,		18746	0.0		0.0	False		,,,				2504	0.0				p.Q223R		Atlas-SNP	.											KRT33B,NS,carcinoma,0,1	KRT33B	46	1	0			c.A668G						PASS	.	T	ARG/GLN	260,4120		25,210,1955	77.0	73.0	75.0		668	1.7	0.0	17	dbSNP_129	75	0,8600		0,0,4300	no	missense	KRT33B	NM_002279.3	43	25,210,6255	CC,CT,TT		0.0,5.9361,2.0031	benign	223/405	39521726	260,12720	2190	4300	6490	SO:0001583	missense	3884	exon4			AGGACCTGGTTCA	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.668A>G	17.37:g.39521726T>C	ENSP00000251646:p.Gln223Arg	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	230	111	0.482609	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	37	CCDS11389.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	t	0.004	-2.255496	0.00265	0.059361	0.0	ENSG00000131738	ENST00000251646	D	0.88818	-2.43	4.78	1.66	0.24008	Filament (1);	0.334269	0.24422	N	0.038665	T	0.08403	0.0209	N	0.01289	-0.905	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.42531	-0.9446	10	0.02654	T	1	.	7.0528	0.25083	0.0:0.524:0.0:0.476	rs61741663	223	Q14525	KT33B_HUMAN	R	223	ENSP00000251646:Q223R	ENSP00000251646:Q223R	Q	-	2	0	KRT33B	36775252	0.042000	0.20092	0.037000	0.18230	0.025000	0.11179	0.380000	0.20602	0.300000	0.22699	-0.911000	0.02809	CAG	T|0.976;C|0.024	0.024	strong		0.577	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
TC2N	123036	hgsc.bcm.edu	37	14	92264736	92264736	+	Silent	SNP	A	A	G	rs147695092		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:92264736A>G	ENST00000435962.2	-	7	968	c.645T>C	c.(643-645)atT>atC	p.I215I	TC2N_ENST00000340892.5_Silent_p.I215I|TC2N_ENST00000556018.1_Silent_p.I215I|TC2N_ENST00000360594.5_Silent_p.I215I	NM_001128596.1	NP_001122068	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear	215					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(5)|skin(1)|upper_aerodigestive_tract(2)	18				COAD - Colon adenocarcinoma(157;0.218)		CTGATAGAGTAATTGTATCTG	0.328													A|||	1	0.000199681	0.0008	0.0	5008	,	,		15932	0.0		0.0	False		,,,				2504	0.0				p.I215I		Atlas-SNP	.											.	TC2N	49	.	0			c.T645C						PASS	.	A	,,	4,4392	8.1+/-20.4	0,4,2194	43.0	46.0	45.0		645,645,645	3.2	1.0	14	dbSNP_134	45	0,8570		0,0,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	TC2N	NM_001128595.1,NM_001128596.1,NM_152332.4	,,	0,4,6479	GG,GA,AA		0.0,0.091,0.0308	,,	215/491,215/491,215/491	92264736	4,12962	2198	4285	6483	SO:0001819	synonymous_variant	123036	exon7			TAGAGTAATTGTA	AA243837	CCDS9897.1, CCDS73679.1	14q32.12	2007-10-17	2007-08-17	2007-08-17		ENSG00000165929			19859	protein-coding gene	gene with protein product	"""C2 calcium-dependent domain containing 1"""		"""chromosome 14 open reading frame 47"", ""membrane targeting (tandem) C2 domain containing 1"""	C14orf47, MTAC2D1		11526914	Standard	NM_001128596		Approved	FLJ36557, Tac2-N, C2CD1	uc001xzt.4	Q8N9U0		ENST00000435962.2:c.645T>C	14.37:g.92264736A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	133	74	0.556391	NM_001128596		Silent	SNP	ENST00000435962.2	37	CCDS9897.1																																																																																			A|1.000;G|0.000	0.000	weak		0.328	TC2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411778.1	NM_152332	
TCF21	6943	hgsc.bcm.edu	37	6	134210600	134210600	+	Missense_Mutation	SNP	G	G	T	rs56412384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:134210600G>T	ENST00000367882.4	+	1	325	c.65G>T	c.(64-66)gGg>gTg	p.G22V	RP3-323P13.2_ENST00000607573.1_RNA|RP3-323P13.2_ENST00000607033.1_RNA|RP3-323P13.2_ENST00000606544.1_RNA|RP3-323P13.2_ENST00000607641.1_RNA|TCF21_ENST00000237316.3_Missense_Mutation_p.G22V	NM_003206.3	NP_003197.2	O43680	TCF21_HUMAN	transcription factor 21	22					branching involved in ureteric bud morphogenesis (GO:0001658)|branchiomeric skeletal muscle development (GO:0014707)|bronchiole development (GO:0060435)|diaphragm development (GO:0060539)|embryonic digestive tract morphogenesis (GO:0048557)|epithelial cell differentiation (GO:0030855)|gland development (GO:0048732)|glomerulus development (GO:0032835)|kidney development (GO:0001822)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lung vasculature development (GO:0060426)|metanephric glomerular capillary formation (GO:0072277)|metanephric mesenchymal cell differentiation (GO:0072162)|morphogenesis of a branching structure (GO:0001763)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|reproductive structure development (GO:0048608)|respiratory system development (GO:0060541)|Sertoli cell differentiation (GO:0060008)|sex determination (GO:0007530)|spleen development (GO:0048536)|ureteric bud development (GO:0001657)|vasculature development (GO:0001944)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|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)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	13	Colorectal(23;0.221)|Breast(56;0.247)			GBM - Glioblastoma multiforme(68;0.00518)|OV - Ovarian serous cystadenocarcinoma(155;0.00783)		GAATGTGACGGGTTGAAAATG	0.567													G|||	298	0.0595048	0.2057	0.0259	5008	,	,		17673	0.004		0.001	False		,,,				2504	0.0031				p.G22V		Atlas-SNP	.											TCF21,NS,carcinoma,+1,1	TCF21	30	1	0			c.G65T	GRCh37	HM050002	TCF21	M	rs56412384	scavenged	.	G	VAL/GLY,VAL/GLY	766,3640	311.6+/-292.2	84,598,1521	97.0	102.0	100.0		65,65	3.5	1.0	6	dbSNP_129	100	17,8583	11.9+/-42.8	0,17,4283	yes	missense,missense	TCF21	NM_003206.3,NM_198392.2	109,109	84,615,5804	TT,TG,GG		0.1977,17.3854,6.0203	benign,benign	22/180,22/180	134210600	783,12223	2203	4300	6503	SO:0001583	missense	6943	exon1			GTGACGGGTTGAA	AF047419	CCDS5167.1	6q23.2	2014-09-17			ENSG00000118526	ENSG00000118526		"""Basic helix-loop-helix proteins"""	11632	protein-coding gene	gene with protein product		603306				9507058	Standard	NM_198392		Approved	POD1, bHLHa23	uc003qei.4	O43680	OTTHUMG00000015608	ENST00000367882.4:c.65G>T	6.37:g.134210600G>T	ENSP00000356857:p.Gly22Val	Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_003206	E1P581|O43545|Q6ICV0|Q9BZ14	Missense_Mutation	SNP	ENST00000367882.4	37	CCDS5167.1	108	0.04945054945054945	94	0.1910569105691057	10	0.027624309392265192	3	0.005244755244755245	1	0.0013192612137203166	G	10.95	1.496669	0.26861	0.173854	0.001977	ENSG00000118526	ENST00000367882;ENST00000237316	D;D	0.96200	-3.94;-3.94	4.43	3.53	0.40419	.	0.306082	0.28566	N	0.014896	D	0.85660	0.5748	L	0.36672	1.1	0.09310	P	0.99999762263	B	0.13594	0.008	B	0.11329	0.006	T	0.76484	-0.2942	9	0.15952	T	0.53	-15.4673	12.9612	0.58460	0.0:0.1708:0.8291:0.0	rs56412384;rs61729590	22	O43680	TCF21_HUMAN	V	22	ENSP00000356857:G22V;ENSP00000237316:G22V	ENSP00000237316:G22V	G	+	2	0	TCF21	134252293	1.000000	0.71417	0.997000	0.53966	0.798000	0.45092	5.440000	0.66563	0.797000	0.33971	0.313000	0.20887	GGG	G|0.944;T|0.056	0.056	strong		0.567	TCF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042292.1	NM_198392	
OR13C5	138799	hgsc.bcm.edu	37	9	107361452	107361452	+	Silent	SNP	C	C	G	rs376107801|rs377523807|rs199665292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361452C>G	ENST00000374779.2	-	1	336	c.243G>C	c.(241-243)acG>acC	p.T81T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	81						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AGCTCACTAGCGTGGAGGGAA	0.512													G|||	1377	0.27496	0.3116	0.2133	5008	,	,		19807	0.4504		0.1163	False		,,,				2504	0.2515				p.T81T		Atlas-SNP	.											OR13C5,NS,carcinoma,-2,1	OR13C5	60	1	0			c.G243C						PASS	.						15.0	28.0	23.0					9																	107361452		2059	4256	6315	SO:0001819	synonymous_variant	138799	exon1			CACTAGCGTGGAG		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.243G>C	9.37:g.107361452C>G		Somatic	753	1	0.00132802		WXS	Illumina HiSeq	Phase_I	718	299	0.416435	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			.	.	weak		0.512	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
KTN1	3895	hgsc.bcm.edu	37	14	56146357	56146357	+	Silent	SNP	G	G	A	rs11546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:56146357G>A	ENST00000395314.3	+	43	4091	c.4023G>A	c.(4021-4023)gcG>gcA	p.A1341A	KTN1_ENST00000395309.3_Silent_p.A1341A|KTN1_ENST00000413890.2_Silent_p.A1290A|KTN1_ENST00000395308.1_Silent_p.A1290A|KTN1_ENST00000555573.1_Silent_p.A318A|KTN1_ENST00000438792.2_Silent_p.A1284A|KTN1_ENST00000395311.1_Silent_p.A1290A|KTN1_ENST00000416613.1_Silent_p.A1341A|KTN1_ENST00000554507.1_Silent_p.A579A	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	1341					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TGCTTCAGGCGGTAAACCAAC	0.408			T	RET	papillary thryoid								A|||	313	0.0625	0.053	0.0749	5008	,	,		20007	0.0159		0.0626	False		,,,				2504	0.1145				p.A1341A		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.G4023A						PASS	.	A	,,,	277,4129	800.7+/-415.6	8,261,1934	133.0	132.0	133.0		4023,3870,3852,4023	-2.3	0.0	14	dbSNP_52	133	845,7755	781.1+/-407.6	43,759,3498	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	,,,	51,1020,5432	AA,AG,GG		9.8256,6.2869,8.6268	,,,	1341/1358,1290/1307,1284/1301,1341/1358	56146357	1122,11884	2203	4300	6503	SO:0001819	synonymous_variant	3895	exon43			TCAGGCGGTAAAC		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.4023G>A	14.37:g.56146357G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_001079521	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1	113	0.051739926739926737	28	0.056910569105691054	27	0.07458563535911603	7	0.012237762237762238	51	0.06728232189973615	A	6.153	0.396415	0.11638	0.062869	0.098256	ENSG00000126777	ENST00000554294	.	.	.	6.17	-2.35	0.06684	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17258	-1.0375	4	.	.	.	3.4215	0.509	0.00592	0.3443:0.2056:0.2497:0.2004	rs11546;rs1051114;rs3191495;rs10147720;rs17354479;rs17685568	.	.	.	Q	112	.	.	R	+	2	0	KTN1	55216110	0.139000	0.22563	0.010000	0.14722	0.691000	0.40173	-0.219000	0.09228	-0.584000	0.05913	-0.254000	0.11334	CGG	G|0.923;A|0.077	0.077	strong		0.408	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
IFNL3	282617	hgsc.bcm.edu	37	19	39735535	39735535	+	Missense_Mutation	SNP	C	C	A	rs141536970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39735535C>A	ENST00000413851.2	-	1	111	c.73G>T	c.(73-75)Gcc>Tcc	p.A25S	IFNL4_ENST00000606380.1_RNA	NM_172139.2	NP_742151.2	Q8IZI9	IFNL3_HUMAN	interferon, lambda 3	25					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of viral genome replication (GO:0045071)|positive regulation of immune response (GO:0050778)	extracellular space (GO:0005615)											CGGAGCCTGGCGACAGGAACT	0.617													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		20221	0.0		0.0	False		,,,				2504	0.0				p.A25S		Atlas-SNP	.											.	.	.	.	0			c.G73T						PASS	.	C	SER/ALA	29,4377	34.3+/-65.2	0,29,2174	61.0	58.0	59.0		73	-4.4	0.0	19	dbSNP_134	59	0,8600		0,0,4300	no	missense	IL28B	NM_172139.2	99	0,29,6474	AA,AC,CC		0.0,0.6582,0.223	benign	25/197	39735535	29,12977	2203	4300	6503	SO:0001583	missense	282617	exon1			GCCTGGCGACAGG	AY129149	CCDS12530.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000197110	ENSG00000197110		"""Interferons"""	18365	protein-coding gene	gene with protein product		607402	"""interleukin 28B"", ""interleukin 28B (interferon, lambda 3)"""	IL28B			Standard	NM_172139		Approved	IL-28B, IL28C	uc010xut.2	Q8IZI9	OTTHUMG00000182805	ENST00000413851.2:c.73G>T	19.37:g.39735535C>A	ENSP00000409000:p.Ala25Ser	Somatic	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	322	171	0.531056	NM_172139	A2BDE1|Q6VN56|Q7Z4J3|Q8IWL6	Missense_Mutation	SNP	ENST00000413851.2	37	CCDS12530.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	8.463	0.855868	0.17106	0.006582	0.0	ENSG00000197110	ENST00000413851	T	0.13657	2.57	3.14	-4.41	0.03590	.	0.976044	0.08385	N	0.953834	T	0.01156	0.0038	N	0.00347	-1.61	0.09310	N	1	B	0.14438	0.01	B	0.17433	0.018	T	0.40757	-0.9546	10	0.30854	T	0.27	-2.8121	1.9017	0.03269	0.1148:0.1693:0.2396:0.4763	.	25	Q8IZI9	IL28B_HUMAN	S	25	ENSP00000409000:A25S	ENSP00000409000:A25S	A	-	1	0	IL28B	44427375	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.104000	0.10923	-0.417000	0.07461	-1.495000	0.00966	GCC	A|0.003;C|0.997	0.003	strong		0.617	IFNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463832.1	NM_172139	
MAN2B2	23324	hgsc.bcm.edu	37	4	6596360	6596360	+	Missense_Mutation	SNP	G	G	A	rs2301795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6596360G>A	ENST00000285599.3	+	7	994	c.958G>A	c.(958-960)Gtg>Atg	p.V320M	MAN2B2_ENST00000504248.1_Missense_Mutation_p.V269M	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	320			V -> M (in dbSNP:rs2301795). {ECO:0000269|PubMed:17974005}.		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						CGGTGTCTCGGTGCAGTATGC	0.602													G|||	2281	0.455471	0.4387	0.4755	5008	,	,		20498	0.3879		0.5388	False		,,,				2504	0.4479				p.V320M		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G958A						PASS	.	G	MET/VAL	1930,2476	549.9+/-377.9	431,1068,704	127.0	95.0	106.0		958	2.8	0.0	4	dbSNP_100	106	4455,4145	588.1+/-392.3	1138,2179,983	yes	missense	MAN2B2	NM_015274.1	21	1569,3247,1687	AA,AG,GG		48.1977,43.8039,49.0927	benign	320/1010	6596360	6385,6621	2203	4300	6503	SO:0001583	missense	23324	exon7			GTCTCGGTGCAGT	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.958G>A	4.37:g.6596360G>A	ENSP00000285599:p.Val320Met	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	1021	0.4674908424908425	233	0.4735772357723577	169	0.46685082872928174	216	0.3776223776223776	403	0.5316622691292876	G	6.829	0.522162	0.13066	0.438039	0.518023	ENSG00000013288	ENST00000285599;ENST00000504248	T;T	0.76709	-1.04;-1.04	4.52	2.76	0.32466	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.350241	0.28927	N	0.013700	T	0.00012	0.0000	L	0.53671	1.685	0.39621	P	0.029962000000000044	B;B;B	0.33299	0.37;0.126;0.407	B;B;B	0.40477	0.33;0.138;0.167	T	0.45833	-0.9234	9	0.40728	T	0.16	-6.2654	8.0974	0.30837	0.0849:0.0:0.7574:0.1577	rs2301795;rs17724940;rs60981402;rs2301795	269;320;320	E9PCD7;Q9Y2E5;Q9Y2E5-2	.;MA2B2_HUMAN;.	M	320;269	ENSP00000285599:V320M;ENSP00000423129:V269M	ENSP00000285599:V320M	V	+	1	0	MAN2B2	6647261	0.998000	0.40836	0.001000	0.08648	0.090000	0.18270	3.562000	0.53777	0.341000	0.23771	0.543000	0.68304	GTG	G|0.522;A|0.478	0.478	strong		0.602	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
ACSM4	341392	hgsc.bcm.edu	37	12	7477100	7477100	+	Missense_Mutation	SNP	G	G	A	rs61584783		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7477100G>A	ENST00000399422.4	+	11	1490	c.1442G>A	c.(1441-1443)cGt>cAt	p.R481H		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	481			R -> H (in dbSNP:rs61584783).		acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty-acyl-CoA synthase activity (GO:0004321)|metal ion binding (GO:0046872)			endometrium(6)|kidney(1)|lung(14)	21						TTCAGGTACCGTATTGGGCCA	0.463													G|||	155	0.0309505	0.1127	0.0086	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.R481H		Atlas-SNP	.											.	ACSM4	98	.	0			c.G1442A						PASS	.	G	HIS/ARG	395,3577		24,347,1615	139.0	128.0	132.0		1442	1.8	1.0	12	dbSNP_129	132	1,8369		0,1,4184	yes	missense	ACSM4	NM_001080454.1	29	24,348,5799	AA,AG,GG		0.0119,9.9446,3.2086	probably-damaging	481/581	7477100	396,11946	1986	4185	6171	SO:0001583	missense	341392	exon11			GGTACCGTATTGG		CCDS44825.1	12p13.31	2008-06-12			ENSG00000215009	ENSG00000215009		"""Acyl-CoA synthetase family"""	32016	protein-coding gene	gene with protein product	"""similar to olfactory specific medium-chain acyl CoA synthetase"""	614360				17762044	Standard	NM_001080454		Approved		uc001qsx.1	P0C7M7	OTTHUMG00000154975	ENST00000399422.4:c.1442G>A	12.37:g.7477100G>A	ENSP00000382349:p.Arg481His	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	157	76	0.484076	NM_001080454	A8MTI6	Missense_Mutation	SNP	ENST00000399422.4	37	CCDS44825.1	57	0.0260989010989011	54	0.10975609756097561	3	0.008287292817679558	0	0.0	0	0.0	G	17.40	3.379356	0.61845	0.099446	1.19E-4	ENSG00000215009	ENST00000399422	T	0.15256	2.44	2.74	1.84	0.25277	AMP-dependent synthetase/ligase (1);	0.000000	0.38959	U	0.001517	T	0.01061	0.0035	M	0.92122	3.275	0.40110	D	0.97647	D	0.89917	1.0	D	0.79108	0.992	T	0.00431	-1.1743	10	0.87932	D	0	-4.6674	7.7673	0.28986	0.1334:0.0:0.8666:0.0	rs61584783	481	P0C7M7	ACSM4_HUMAN	H	481	ENSP00000382349:R481H	ENSP00000382349:R481H	R	+	2	0	ACSM4	7368367	1.000000	0.71417	0.984000	0.44739	0.981000	0.71138	6.064000	0.71169	0.721000	0.32231	0.557000	0.71058	CGT	G|0.979;A|0.021	0.021	strong		0.463	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454	
FANCM	57697	hgsc.bcm.edu	37	14	45606287	45606287	+	Missense_Mutation	SNP	C	C	T	rs10138997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45606287C>T	ENST00000267430.5	+	2	609	c.524C>T	c.(523-525)tCc>tTc	p.S175F	FKBP3_ENST00000396062.3_5'Flank|FANCM_ENST00000542564.2_Missense_Mutation_p.S175F|FKBP3_ENST00000216330.3_5'Flank|FANCM_ENST00000556036.1_Missense_Mutation_p.S175F	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	175	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		S -> F (in dbSNP:rs10138997).		DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						ACACAAGCTTCCACCAGGAAG	0.378								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				T|||	1031	0.205871	0.4864	0.0879	5008	,	,		18628	0.121		0.0676	False		,,,				2504	0.1401				p.S175F		Atlas-SNP	.											FANCM,NS,carcinoma,+1,1	FANCM	225	1	0			c.C524T						PASS	.	T	PHE/SER	1741,2665	647.2+/-398.5	325,1091,787	96.0	99.0	98.0		524	4.2	0.7	14	dbSNP_119	98	475,8125	797.9+/-407.4	14,447,3839	yes	missense	FANCM	NM_020937.2	155	339,1538,4626	TT,TC,CC		5.5233,39.5143,17.0383	benign	175/2049	45606287	2216,10790	2203	4300	6503	SO:0001583	missense	57697	exon2	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAGCTTCCACCAG	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.524C>T	14.37:g.45606287C>T	ENSP00000267430:p.Ser175Phe	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	396	0.1813186813186813	233	0.4735772357723577	35	0.09668508287292818	69	0.12062937062937062	59	0.07783641160949868	T	10.68	1.417076	0.25552	0.395143	0.055233	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564	T;T;T	0.15834	2.39;2.39;2.39	5.39	4.21	0.49690	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.410133	0.27340	N	0.019809	T	0.00012	0.0000	L	0.55103	1.725	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.08055	0.002;0.001;0.003	T	0.46721	-0.9171	9	0.44086	T	0.13	.	1.3198	0.02114	0.1456:0.1596:0.1515:0.5432	rs10138997;rs52796356;rs58102728;rs10138997	175;175;175	B2RTQ9;Q8IYD8;Q8IYD8-2	.;FANCM_HUMAN;.	F	175	ENSP00000450596:S175F;ENSP00000267430:S175F;ENSP00000442493:S175F	ENSP00000267430:S175F	S	+	2	0	FANCM	44676037	0.000000	0.05858	0.686000	0.30086	0.962000	0.63368	0.043000	0.13971	0.329000	0.23460	-0.269000	0.10298	TCC	C|0.815;T|0.185	0.185	strong		0.378	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412260	105412260	+	Missense_Mutation	SNP	G	G	C	rs11160826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105412260G>C	ENST00000333244.5	-	7	9647	c.9528C>G	c.(9526-9528)gaC>gaG	p.D3176E	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3176			D -> E (in dbSNP:rs11160826).			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)			GGAGGCTCAGGTCGGCCTCCA	0.602																																					p.D3176E		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C9528G						PASS	.	G	GLU/ASP	1884,1948		634,616,666	148.0	117.0	128.0		9528	-5.5	0.0	14	dbSNP_120	128	572,6538		182,208,3165	no	missense	AHNAK2	NM_138420.2	45	816,824,3831	CC,CG,GG		8.045,49.1649,22.4456	possibly-damaging	3176/5796	105412260	2456,8486	1916	3555	5471	SO:0001583	missense	113146	exon7			GCTCAGGTCGGCC	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.9528C>G	14.37:g.105412260G>C	ENSP00000353114:p.Asp3176Glu	Somatic	391	0	0		WXS	Illumina HiSeq	Phase_I	393	382	0.97201	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	483	0.22115384615384615	203	0.41260162601626016	88	0.2430939226519337	155	0.270979020979021	37	0.048812664907651716	g	0.111	-1.138293	0.01742	0.491649	0.08045	ENSG00000185567	ENST00000333244	T	0.02050	4.48	2.74	-5.48	0.02592	.	.	.	.	.	T	0.00012	0.0000	L	0.39397	1.21	0.80722	P	0.0	P	0.40619	0.724	B	0.34452	0.183	T	0.29181	-1.0020	8	0.18276	T	0.48	.	7.5023	0.27524	0.1682:0.1939:0.5589:0.0791	rs11160826;rs58738060	3176	Q8IVF2	AHNK2_HUMAN	E	3176	ENSP00000353114:D3176E	ENSP00000353114:D3176E	D	-	3	2	AHNAK2	104483305	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-4.560000	0.00215	-2.504000	0.00508	-2.640000	0.00151	GAC	G|0.779;C|0.221	0.221	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
HLA-A	3105	hgsc.bcm.edu	37	6	29910660	29910660	+	Missense_Mutation	SNP	A	A	G	rs41559117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29910660A>G	ENST00000396634.1	+	4	541	c.200A>G	c.(199-201)cAg>cGg	p.Q67R	HLA-A_ENST00000376809.5_Missense_Mutation_p.Q67R|HLA-A_ENST00000376802.2_Missense_Mutation_p.Q67R|HLA-A_ENST00000376806.5_Missense_Mutation_p.Q67R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	67	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	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						GCCGCGAGCCAGAGGATGGAG	0.682									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|||	114	0.0227636	0.0575	0.0288	5008	,	,		14823	0.002		0.007	False		,,,				2504	0.0092				p.Q67R		Atlas-SNP	.											.	HLA-A	89	.	0			c.A200G						PASS	.	A	ARG/GLN	189,4215		2,185,2015	48.0	46.0	46.0		200	-0.8	0.2	6	dbSNP_127	46	76,8522		0,76,4223	no	missense	HLA-A	NM_002116.7	43	2,261,6238	GG,GA,AA		0.8839,4.2916,2.0381	possibly-damaging	67/366	29910660	265,12737	2202	4299	6501	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGAGCCAGAGGAT	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.200A>G	6.37:g.29910660A>G	ENSP00000379873:p.Gln67Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	219	54	0.246575	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	36	0.016483516483516484	22	0.044715447154471545	8	0.022099447513812154	2	0.0034965034965034965	4	0.005277044854881266	.	6.554	0.470589	0.12461	0.042916	0.008839	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00705	5.81;5.81;5.81;5.81	3.72	-0.813	0.10850	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	.	.	.	.	T	0.00580	0.0019	N	0.21545	0.675	0.09310	N	1	B;D;B;D;B	0.54772	0.0;0.968;0.001;0.968;0.0	B;D;B;D;B	0.75484	0.006;0.986;0.006;0.986;0.006	T	0.55673	-0.8104	9	0.49607	T	0.09	.	5.0607	0.14555	0.5529:0.3361:0.0:0.1109	rs41559117	67;67;67;67;67	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	R	67	ENSP00000379873:Q67R;ENSP00000366002:Q67R;ENSP00000366005:Q67R;ENSP00000365998:Q67R	ENSP00000348012:Q67R	Q	+	2	0	HLA-A	30018639	0.000000	0.05858	0.192000	0.23308	0.357000	0.29423	-1.236000	0.02925	0.031000	0.15407	-1.821000	0.00599	CAG	A|0.977;C|0.002;G|0.021	0.021	strong		0.682	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
WWP2	11060	hgsc.bcm.edu	37	16	69963355	69963355	+	Silent	SNP	G	G	A	rs1566452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69963355G>A	ENST00000359154.2	+	12	1340	c.1239G>A	c.(1237-1239)aaG>aaA	p.K413K	WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000568684.1_5'UTR|WWP2_ENST00000448661.1_Silent_p.K413K|WWP2_ENST00000356003.2_Silent_p.K413K|WWP2_ENST00000542271.1_Silent_p.K297K	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	413	WW 3. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|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 transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TGGCAGAGAAGAGACAGGACA	0.557													G|||	4282	0.855032	0.9455	0.7493	5008	,	,		17978	0.9683		0.7535	False		,,,				2504	0.7955				p.K413K		Atlas-SNP	.											.	WWP2	88	.	0			c.G1239A						PASS	.	G	,	3933,463	777.5+/-414.2	1759,415,24	51.0	47.0	49.0		1239,	4.3	1.0	16	dbSNP_88	49	6376,2224	703.7+/-405.4	2379,1618,303	no	coding-synonymous,utr-5	WWP2	NM_007014.3,NM_199424.1	,	4138,2033,327	AA,AG,GG		25.8605,10.5323,20.6756	,	413/871,	69963355	10309,2687	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon12			AGAGAAGAGACAG	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.1239G>A	16.37:g.69963355G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			A|0.812;C|0.000	0.812	strong		0.557	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
AGFG2	3268	hgsc.bcm.edu	37	7	100160264	100160264	+	Missense_Mutation	SNP	T	T	C	rs17855473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100160264T>C	ENST00000300176.4	+	8	1168	c.1046T>C	c.(1045-1047)aTg>aCg	p.M349T	AGFG2_ENST00000262935.4_3'UTR|AGFG2_ENST00000474713.1_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	349				M -> T (in Ref. 2; AAH17329). {ECO:0000305}.	regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCTGTCACGATGGGCGGCGGC	0.647													C|||	910	0.181709	0.3449	0.1455	5008	,	,		15023	0.0188		0.1869	False		,,,				2504	0.1493				p.M349T		Atlas-SNP	.											AGFG2,NS,carcinoma,0,1	AGFG2	44	1	0			c.T1046C						PASS	.	C	THR/MET	1380,3026	671.4+/-402.5	209,962,1032	31.0	32.0	32.0		1046	3.6	0.0	7	dbSNP_123	32	1612,6988	723.3+/-406.5	148,1316,2836	yes	missense	AGFG2	NM_006076.4	81	357,2278,3868	CC,CT,TT		18.7442,31.3209,23.0048	benign	349/482	100160264	2992,10014	2203	4300	6503	SO:0001583	missense	3268	exon8			TCACGATGGGCGG	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"""ADP-ribosylation factor GTPase activating proteins"""	5177	protein-coding gene	gene with protein product		604019	"""HIV-1 Rev binding protein-like"""	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1046T>C	7.37:g.100160264T>C	ENSP00000300176:p.Met349Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	110	54	0.490909	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	37	CCDS5697.1	365|365	0.1671245421245421|0.1671245421245421	170|170	0.34552845528455284|0.34552845528455284	52|52	0.143646408839779|0.143646408839779	2|2	0.0034965034965034965|0.0034965034965034965	141|141	0.18601583113456466|0.18601583113456466	C|C	0.029|0.029	-1.347421|-1.347421	0.01266|0.01266	0.313209|0.313209	0.187442|0.187442	ENSG00000106351|ENSG00000106351	ENST00000300176|ENST00000429987	T|.	0.20738|.	2.05|.	4.51|4.51	3.64|3.64	0.41730|0.41730	.|.	0.880910|.	0.10039|.	N|.	0.723737|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00308|0.00308	-1.67|-1.67	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.42396|0.42396	-0.9454|-0.9454	9|4	0.16896|.	T|.	0.51|.	-19.9228|-19.9228	8.6556|8.6556	0.34062|0.34062	0.0:0.854:0.0:0.146|0.0:0.854:0.0:0.146	rs17855473;rs17855473|rs17855473;rs17855473	349|.	O95081|.	AGFG2_HUMAN|.	T|R	349|91	ENSP00000300176:M349T|.	ENSP00000300176:M349T|.	M|W	+|+	2|1	0|0	AGFG2|AGFG2	99998200|99998200	0.002000|0.002000	0.14202|0.14202	0.001000|0.001000	0.08648|0.08648	0.006000|0.006000	0.05464|0.05464	0.912000|0.912000	0.28597|0.28597	0.524000|0.524000	0.28502|0.28502	-1.653000|-1.653000	0.00756|0.00756	ATG|TGG	T|0.797;C|0.203	0.203	strong		0.647	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076	
SPRR1A	6698	hgsc.bcm.edu	37	1	152957856	152957856	+	Missense_Mutation	SNP	C	C	G	rs143282605		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152957856C>G	ENST00000368762.1	+	1	150	c.150C>G	c.(148-150)caC>caG	p.H50Q	SPRR1A_ENST00000307122.2_Missense_Mutation_p.H50Q			P35321	SPR1A_HUMAN	small proline-rich protein 1A	50	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(2)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)	7	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCCCTGCCACCCCAAAGTGC	0.647																																					p.H50Q		Atlas-SNP	.											.	SPRR1A	17	.	0			c.C150G						PASS	.																																			SO:0001583	missense	6698	exon2			CTGCCACCCCAAA	L05187	CCDS1032.1	1q21-q22	2008-02-05			ENSG00000169474	ENSG00000169474			11259	protein-coding gene	gene with protein product		182265				8325635	Standard	NM_005987		Approved		uc001faw.3	P35321	OTTHUMG00000014404	ENST00000368762.1:c.150C>G	1.37:g.152957856C>G	ENSP00000357751:p.His50Gln	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	125	24	0.192	NM_001199828	B1AN47|D3DV31|Q2M303|Q9UDG4	Missense_Mutation	SNP	ENST00000368762.1	37	CCDS1032.1	.	.	.	.	.	.	.	.	.	.	C	3.605	-0.080674	0.07141	.	.	ENSG00000169474	ENST00000307122;ENST00000368762	T;T	0.11169	2.8;2.8	5.64	-8.48	0.00935	.	0.637243	0.13026	N	0.419668	T	0.01222	0.0040	.	.	.	0.09310	N	0.999997	B	0.30326	0.276	B	0.32393	0.145	T	0.37009	-0.9724	9	0.29301	T	0.29	-0.4448	1.0644	0.01608	0.3555:0.2828:0.17:0.1916	.	50	P35321	SPR1A_HUMAN	Q	50	ENSP00000307340:H50Q;ENSP00000357751:H50Q	ENSP00000307340:H50Q	H	+	3	2	SPRR1A	151224480	0.020000	0.18652	0.125000	0.21846	0.298000	0.27526	-1.221000	0.02968	-1.749000	0.01330	-0.300000	0.09419	CAC	.	.	weak		0.647	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987	
CES5A	221223	hgsc.bcm.edu	37	16	55880480	55880480	+	Missense_Mutation	SNP	A	A	C	rs11860456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:55880480A>C	ENST00000290567.9	-	13	1732	c.1611T>G	c.(1609-1611)gaT>gaG	p.D537E	CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000518005.1_Missense_Mutation_p.D431E|CES5A_ENST00000319165.9_Missense_Mutation_p.D487E|CES5A_ENST00000520435.1_Missense_Mutation_p.D507E|CES5A_ENST00000521992.1_Missense_Mutation_p.D566E	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	537			D -> E (in dbSNP:rs11860456). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						TGGTCCAAAAATCCACCCGCG	0.522													C|||	1624	0.324281	0.4977	0.1988	5008	,	,		16733	0.2817		0.2793	False		,,,				2504	0.2689				p.D566E		Atlas-SNP	.											.	CES5A	206	.	0			c.T1698G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP	2089,2307		490,1109,599	211.0	208.0	209.0		1611,1698,1461	2.6	0.2	16	dbSNP_120	209	2086,6514		265,1556,2479	yes	missense,missense,missense	CES5A	NM_001143685.1,NM_001190158.1,NM_145024.2	45,45,45	755,2665,3078	CC,CA,AA		24.2558,47.5205,32.1253	benign,benign,benign	537/576,566/605,487/526	55880480	4175,8821	2198	4300	6498	SO:0001583	missense	221223	exon14			CCAAAAATCCACC	AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"""Carboxylesterases"""	26459	protein-coding gene	gene with protein product			"""carboxylesterase 7"""	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1611T>G	16.37:g.55880480A>C	ENSP00000290567:p.Asp537Glu	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	200	119	0.595	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	695	0.3182234432234432	241	0.4898373983739837	84	0.23204419889502761	162	0.28321678321678323	208	0.27440633245382584	.	0.020	-1.432466	0.01108	0.475205	0.242558	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.61	2.58	0.30949	Carboxylesterase, type B (1);	1.217400	0.05929	N	0.634854	T	0.00012	0.0000	N	0.01809	-0.71	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.40979	-0.9534	9	0.19147	T	0.46	.	6.1655	0.20388	0.1316:0.6521:0.0:0.2163	rs11860456;rs12924366;rs16955806;rs52805099;rs58244961;rs11860456	537;487	Q6NT32;Q6NT32-2	EST5A_HUMAN;.	E	566;487;431;537;507;317	ENSP00000428864:D566E;ENSP00000324271:D487E;ENSP00000428571:D431E;ENSP00000290567:D537E;ENSP00000428887:D507E	ENSP00000290567:D537E	D	-	3	2	CES5A	54437981	0.000000	0.05858	0.183000	0.23137	0.011000	0.07611	-1.208000	0.03005	0.123000	0.18342	-0.121000	0.15023	GAT	A|0.672;C|0.328	0.328	strong		0.522	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	
AHNAK2	113146	hgsc.bcm.edu	37	14	105405599	105405599	+	Missense_Mutation	SNP	G	G	C	rs3742935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105405599G>C	ENST00000333244.5	-	7	16308	c.16189C>G	c.(16189-16191)Cct>Gct	p.P5397A	AHNAK2_ENST00000557457.1_Missense_Mutation_p.P395A	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5397			P -> A (in dbSNP:rs3742935). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			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)		p.P367A(2)|p.P5397A(1)		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)			CTGGGGGCAGGGAAGGAGAAC	0.483													G|||	2780	0.555112	0.6437	0.5115	5008	,	,		20937	0.4117		0.5338	False		,,,				2504	0.636				p.P5397A		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,3	AHNAK2	719	3	3	Substitution - Missense(3)	prostate(2)|stomach(1)	c.C16189G						PASS	.	G	ALA/PRO	2594,1260		879,836,212	66.0	69.0	68.0		16189	4.4	0.5	14	dbSNP_107	68	4503,3789		1234,2035,877	yes	missense	AHNAK2	NM_138420.2	27	2113,2871,1089	CC,CG,GG		45.6946,32.6933,41.5692	possibly-damaging	5397/5796	105405599	7097,5049	1927	4146	6073	SO:0001583	missense	113146	exon7			GGGCAGGGAAGGA	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.16189C>G	14.37:g.105405599G>C	ENSP00000353114:p.Pro5397Ala	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1147	0.5251831501831502	324	0.6585365853658537	199	0.5497237569060773	222	0.3881118881118881	402	0.5303430079155673	G	13.02	2.111375	0.37242	0.673067	0.543054	ENSG00000185567	ENST00000557457;ENST00000333244	T;T	0.02916	4.11;4.95	5.31	4.36	0.52297	.	0.486738	0.15250	U	0.272366	T	0.00012	0.0000	L	0.34521	1.04	0.41306	P	0.012923000000000018	D	0.56287	0.975	P	0.51516	0.672	T	0.00051	-1.2192	9	0.07990	T	0.79	.	11.0018	0.47611	0.0:0.0:0.7372:0.2627	rs3742935;rs17846446;rs17859495;rs52832784;rs60927454;rs3742935	5397	Q8IVF2	AHNK2_HUMAN	A	395;5397	ENSP00000450998:P395A;ENSP00000353114:P5397A	ENSP00000353114:P5397A	P	-	1	0	AHNAK2	104476644	0.905000	0.30787	0.474000	0.27266	0.832000	0.47134	1.290000	0.33319	2.663000	0.90544	0.491000	0.48974	CCT	G|0.480;C|0.520	0.520	strong		0.483	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OR4X1	390113	hgsc.bcm.edu	37	11	48286256	48286256	+	Missense_Mutation	SNP	C	C	T	rs10838852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48286256C>T	ENST00000320048.1	+	1	844	c.844C>T	c.(844-846)Cct>Tct	p.P282S		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	282			P -> S (in dbSNP:rs10838852).			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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						TCTCTTAAACCCTGTGATTTA	0.413													C|||	1924	0.384185	0.1641	0.5807	5008	,	,		22893	0.3829		0.5696	False		,,,				2504	0.3528				p.P282S		Atlas-SNP	.											.	OR4X1	75	.	0			c.C844T						PASS	.	C	SER/PRO	959,3443	361.6+/-315.8	97,765,1339	84.0	79.0	81.0		844	4.3	1.0	11	dbSNP_120	81	4869,3727	618.2+/-396.8	1377,2115,806	yes	missense	OR4X1	NM_001004726.1	74	1474,2880,2145	TT,TC,CC		43.3574,21.7856,44.8377	probably-damaging	282/306	48286256	5828,7170	2201	4298	6499	SO:0001583	missense	390113	exon1			TTAAACCCTGTGA	AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"""GPCR / Class A : Olfactory receptors"""	14854	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily X, member 1"""				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.844C>T	11.37:g.48286256C>T	ENSP00000321506:p.Pro282Ser	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	257	119	0.463035	NM_001004726	Q6IF74	Missense_Mutation	SNP	ENST00000320048.1	37	CCDS31487.1	1002	0.45879120879120877	101	0.20528455284552846	210	0.580110497237569	251	0.4388111888111888	440	0.5804749340369393	C	13.59	2.283838	0.40394	0.217856	0.566426	ENSG00000176567	ENST00000320048	T	0.63417	-0.04	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	H	0.98314	4.2	0.34700	P	0.27333700000000005	D	0.89917	1.0	D	0.91635	0.999	T	0.48927	-0.8991	8	0.87932	D	0	.	14.6159	0.68547	0.0:1.0:0.0:0.0	rs10838852;rs17728056;rs60486813;rs10838852	282	Q8NH49	OR4X1_HUMAN	S	282	ENSP00000321506:P282S	ENSP00000321506:P282S	P	+	1	0	OR4X1	48242832	0.999000	0.42202	0.985000	0.45067	0.098000	0.18820	4.351000	0.59398	2.368000	0.80403	0.563000	0.77884	CCT	C|0.567;N|0.000	.	strong		0.413	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726	
A2M	2	hgsc.bcm.edu	37	12	9251209	9251209	+	Silent	SNP	C	C	T	rs185750870		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9251209C>T	ENST00000318602.7	-	15	2152	c.1845G>A	c.(1843-1845)gcG>gcA	p.A615A		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	615					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)	TCACCGAGGACGCCGAGAGCT	0.572													C|||	18	0.00359425	0.0129	0.0014	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.A615A		Atlas-SNP	.											.	A2M	180	.	0			c.G1845A						PASS	.	C		41,4365		0,41,2162	28.0	28.0	28.0		1845	-11.1	0.0	12		28	1,8597		0,1,4298	no	coding-synonymous	A2M	NM_000014.4		0,42,6460	TT,TC,CC		0.0116,0.9305,0.323		615/1475	9251209	42,12962	2203	4299	6502	SO:0001819	synonymous_variant	2	exon15			CGAGGACGCCGAG	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.1845G>A	12.37:g.9251209C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Silent	SNP	ENST00000318602.7	37	CCDS44827.1																																																																																			C|0.998;T|0.002	0.002	strong		0.572	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	
XRCC4	7518	hgsc.bcm.edu	37	5	82648943	82648943	+	Splice_Site	SNP	G	G	A	rs1805377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82648943G>A	ENST00000511817.1	+	8	973		c.e8-1		XRCC4_ENST00000282268.3_Intron|XRCC4_ENST00000338635.6_Splice_Site|XRCC4_ENST00000396027.4_Intron			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4						cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		TTTCTTTTCAGTTCTAGGCCT	0.343								Non-homologous end-joining					A|||	1879	0.3752	0.4758	0.3329	5008	,	,		16220	0.7044		0.1402	False		,,,				2504	0.1718				.		Atlas-SNP	.											.	XRCC4	37	.	0			c.894-1G>A	GRCh37	CS075240	XRCC4	S	rs1805377	PASS	.	A	,,	1933,2469	591.6+/-387.6	422,1089,690	76.0	86.0	82.0		,,	-0.1	0.7	5	dbSNP_92	82	1052,7548	764.1+/-407.6	64,924,3312	yes	intron,splice-3,intron	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	,,	486,2013,4002	AA,AG,GG		12.2326,43.9119,22.958	,,	,,	82648943	2985,10017	2201	4300	6501	SO:0001630	splice_region_variant	7518	exon8			TTTTCAGTTCTAG	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.894-1G>A	5.37:g.82648943G>A		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	161	71	0.440994	NM_022406	A8K3X4|Q9BS72|Q9UP94	Splice_Site	SNP	ENST00000511817.1	37	CCDS4059.1	858	0.39285714285714285	239	0.48577235772357724	115	0.31767955801104975	394	0.6888111888111889	110	0.14511873350923482	A	0.718	-0.784496	0.02907	0.439119	0.122326	ENSG00000152422	ENST00000338635;ENST00000511817;ENST00000514538	.	.	.	5.51	-0.0652	0.13769	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.3151	0.07030	0.3839:0.0:0.2655:0.3506	rs1805377;rs3777014;rs61086000;rs1805377	.	.	.	.	-1	.	.	.	+	.	.	XRCC4	82684699	0.003000	0.15002	0.723000	0.30687	0.002000	0.02628	-0.958000	0.03857	-0.153000	0.11137	-2.023000	0.00429	.	G|0.679;A|0.321	0.321	strong		0.343	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	Intron
LRRFIP1	9208	hgsc.bcm.edu	37	2	238672253	238672253	+	Missense_Mutation	SNP	A	A	G	rs3739041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238672253A>G	ENST00000392000.4	+	11	2014	c.1897A>G	c.(1897-1899)Aaa>Gaa	p.K633E	LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000244815.5_Missense_Mutation_p.K609E|LRRFIP1_ENST00000289175.6_Missense_Mutation_p.K577E	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	633			K -> E (in dbSNP:rs3739041).		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)		TCCAAAACAGAAAATTGCAGC	0.393													A|||	536	0.107029	0.3192	0.0231	5008	,	,		20700	0.0794		0.005	False		,,,				2504	0.0133				p.K633E		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.A1897G						PASS	.	A	,,GLU/LYS,GLU/LYS,GLU/LYS	1285,3121	420.8+/-339.2	210,865,1128	65.0	67.0	67.0		,,1897,1729,1825	-8.1	0.0	2	dbSNP_107	67	34,8566	21.6+/-65.8	0,34,4266	no	intron,intron,missense,missense,missense	LRRFIP1	NM_001137550.1,NM_001137551.1,NM_001137552.1,NM_001137553.1,NM_004735.3	,,56,56,56	210,899,5394	GG,GA,AA		0.3953,29.1648,10.1415	,,benign,benign,benign	,,633/809,577/753,609/785	238672253	1319,11687	2203	4300	6503	SO:0001583	missense	9208	exon11			AAACAGAAAATTG	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.1897A>G	2.37:g.238672253A>G	ENSP00000375857:p.Lys633Glu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_001137552	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	37	CCDS46552.1	246	0.11263736263736264	176	0.35772357723577236	15	0.04143646408839779	53	0.09265734265734266	2	0.002638522427440633	A	6.998	0.554341	0.13374	0.291648	0.003953	ENSG00000124831	ENST00000289175;ENST00000244815;ENST00000392000	T;T;T	0.10005	2.93;2.92;2.94	5.71	-8.08	0.01094	.	2.288530	0.02094	N	0.053352	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.10450	0.005;0.001;0.005	T	0.33979	-0.9847	9	0.15499	T	0.54	1.0E-4	16.0385	0.80648	0.2426:0.0979:0.6595:0.0	rs3739041	577;633;609	Q32MZ4-3;Q32MZ4;Q32MZ4-2	.;LRRF1_HUMAN;.	E	577;609;633	ENSP00000289175:K577E;ENSP00000244815:K609E;ENSP00000375857:K633E	ENSP00000244815:K609E	K	+	1	0	LRRFIP1	238336992	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.699000	0.01906	-1.586000	0.01632	0.533000	0.62120	AAA	.	.	weak		0.393	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
CPAMD8	27151	hgsc.bcm.edu	37	19	17025292	17025292	+	Missense_Mutation	SNP	G	G	A	rs706761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17025292G>A	ENST00000443236.1	-	29	3975	c.3944C>T	c.(3943-3945)aCt>aTt	p.T1315I		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1268						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						CAGCGGGACAGTGCCGTGGAT	0.622													G|||	3222	0.643371	0.8419	0.4597	5008	,	,		17864	0.7073		0.5835	False		,,,				2504	0.501				p.T1315I		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C3944T						PASS	.	G	ILE/THR	3356,812		1370,616,98	71.0	75.0	74.0		3944	1.8	0.6	19	dbSNP_86	74	4606,3838		1251,2104,867	yes	missense	CPAMD8	NM_015692.2	89	2621,2720,965	AA,AG,GG		45.4524,19.4818,36.8696	possibly-damaging	1315/1933	17025292	7962,4650	2084	4222	6306	SO:0001583	missense	27151	exon29			GGGACAGTGCCGT	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.3944C>T	19.37:g.17025292G>A	ENSP00000402505:p.Thr1315Ile	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	1420	0.6501831501831502	406	0.8252032520325203	169	0.46685082872928174	400	0.6993006993006993	445	0.5870712401055409	G	9.429	1.085015	0.20390	0.805182	0.545476	ENSG00000160111	ENST00000291440	.	.	.	2.93	1.8	0.24995	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.142056	0.45867	U	0.000336	T	0.00012	0.0000	M	0.62088	1.915	0.09310	P	1.0	P	0.36874	0.572	B	0.38921	0.285	T	0.19451	-1.0305	8	0.38643	T	0.18	.	7.7179	0.28715	0.0:0.0:0.3572:0.6428	rs706761;rs58635731;rs706761	1268	Q8IZJ3	CPMD8_HUMAN	I	1315	.	ENSP00000291440:T1315I	T	-	2	0	CPAMD8	16886292	1.000000	0.71417	0.611000	0.29010	0.054000	0.15201	4.636000	0.61339	1.202000	0.43218	0.555000	0.69702	ACT	G|0.358;A|0.642	0.642	strong		0.622	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
APOBEC3B	9582	hgsc.bcm.edu	37	22	39387531	39387531	+	Silent	SNP	C	C	T	rs200377379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39387531C>T	ENST00000333467.3	+	6	963	c.918C>T	c.(916-918)cgC>cgT	p.R306R	APOBEC3B-AS1_ENST00000513758.2_RNA|APOBEC3B_ENST00000407298.3_Silent_p.R281R|APOBEC3B_ENST00000402182.3_Silent_p.R306R	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	306				R -> P (in Ref. 1; AAD00089). {ECO:0000305}.	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)					TGAGACTGCGCATCTTCGCTG	0.582													C|||	13	0.00259585	0.0061	0.0	5008	,	,		15612	0.001		0.0	False		,,,				2504	0.0041				p.R306R		Atlas-SNP	.											APOBEC3B,colon,carcinoma,+2,2	APOBEC3B	32	2	0			c.C918T						scavenged	.						145.0	145.0	145.0					22																	39387531		2198	4283	6481	SO:0001819	synonymous_variant	9582	exon6			ACTGCGCATCTTC	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.918C>T	22.37:g.39387531C>T		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	205	43	0.209756	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			.	.	weak		0.582	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
TPTE2	93492	hgsc.bcm.edu	37	13	20056679	20056679	+	Missense_Mutation	SNP	T	T	G	rs200244531		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:20056679T>G	ENST00000400230.2	-	4	172	c.128A>C	c.(127-129)gAa>gCa	p.E43A	TPTE2_ENST00000382975.4_Missense_Mutation_p.E43A|TPTE2_ENST00000382977.4_Missense_Mutation_p.E43A|TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000390680.2_Intron|TPTE2_ENST00000400103.2_Missense_Mutation_p.E43A|TPTE2_ENST00000382978.1_Missense_Mutation_p.E43A|TPTE2_ENST00000457266.2_Missense_Mutation_p.E43A			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	43					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.E43A(1)		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)		GGAAAGTCGTTCTAACATACT	0.313																																					p.E43A		Atlas-SNP	.											TPTE2_ENST00000400230,NS,carcinoma,0,1	TPTE2	225	1	1	Substitution - Missense(1)	kidney(1)	c.A128C						scavenged	.						52.0	51.0	51.0					13																	20056679		2201	4299	6500	SO:0001583	missense	93492	exon5			AGTCGTTCTAACA	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.128A>C	13.37:g.20056679T>G	ENSP00000383089:p.Glu43Ala	Somatic	362	2	0.00552486		WXS	Illumina HiSeq	Phase_I	377	4	0.0106101	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	T	2.387	-0.340821	0.05243	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548	D;D;D;D;D;D	0.94931	-3.56;-3.53;-3.47;-3.47;-3.56;-3.53	2.06	0.858	0.19030	.	0.878504	0.09602	U	0.780065	D	0.86159	0.5866	N	0.21448	0.665	0.09310	N	1	B;B	0.28850	0.225;0.0	B;B	0.19946	0.027;0.0	T	0.74598	-0.3612	9	.	.	.	-0.5937	3.8365	0.08896	0.0:0.192:0.0:0.808	.	43;43	A8MX64;Q6XPS3	.;TPTE2_HUMAN	A	43	ENSP00000372438:E43A;ENSP00000382974:E43A;ENSP00000383089:E43A;ENSP00000372437:E43A;ENSP00000372435:E43A;ENSP00000442218:E43A	.	E	-	2	0	TPTE2	18954679	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.422000	0.21296	0.241000	0.21283	0.383000	0.25322	GAA	.	.	weak		0.313	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
MURC	347273	hgsc.bcm.edu	37	9	103348634	103348634	+	Silent	SNP	G	G	A	rs2780956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:103348634G>A	ENST00000307584.5	+	2	1061	c.996G>A	c.(994-996)agG>agA	p.R332R		NM_001018116.1	NP_001018126.1	Q5BKX8	MURC_HUMAN	muscle-related coiled-coil protein	332					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Z disc (GO:0030018)				endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)	16		Acute lymphoblastic leukemia(62;0.0461)				ATGAAGGAAGGGAAATCCCCA	0.483													G|||	1469	0.293331	0.2405	0.4784	5008	,	,		15010	0.0804		0.4254	False		,,,				2504	0.317				p.R332R		Atlas-SNP	.											.	MURC	43	.	0			c.G996A						PASS	.	G		1353,3053	445.9+/-347.8	209,935,1059	48.0	51.0	50.0		996	3.4	0.2	9	dbSNP_100	50	3583,5017	516.7+/-378.9	729,2125,1446	no	coding-synonymous	MURC	NM_001018116.1		938,3060,2505	AA,AG,GG		41.6628,30.7081,37.9517		332/365	103348634	4936,8070	2203	4300	6503	SO:0001819	synonymous_variant	347273	exon2			AGGAAGGGAAATC	BC090888	CCDS35083.1	9q31.1	2014-09-17			ENSG00000170681	ENSG00000170681			33742	protein-coding gene	gene with protein product	"""muscle-restricted coiled-coil protein"""					18508909, 18332105	Standard	NM_001018116		Approved	cavin-4, CAVIN4	uc004bba.3	Q5BKX8	OTTHUMG00000020368	ENST00000307584.5:c.996G>A	9.37:g.103348634G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_001018116	B1PRL3|B4DT88	Silent	SNP	ENST00000307584.5	37	CCDS35083.1																																																																																			G|0.649;A|0.351	0.351	strong		0.483	MURC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053419.2	NM_001018116	
CNGB3	54714	hgsc.bcm.edu	37	8	87588198	87588198	+	Missense_Mutation	SNP	T	T	C	rs3735972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87588198T>C	ENST00000320005.5	-	18	2311	c.2264A>G	c.(2263-2265)gAa>gGa	p.E755G		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	755			E -> G (in dbSNP:rs3735972). {ECO:0000269|PubMed:10958649, ECO:0000269|PubMed:15712225}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						TGCTGTACATTCAGGTCTGTC	0.398													T|||	412	0.0822684	0.0696	0.085	5008	,	,		18346	0.1022		0.0885	False		,,,				2504	0.0706				p.E755G		Atlas-SNP	.											CNGB3,NS,carcinoma,-1,1	CNGB3	176	1	0			c.A2264G						PASS	.	T	GLY/GLU	310,4096	167.6+/-198.6	11,288,1904	242.0	243.0	243.0		2264	3.0	0.0	8	dbSNP_107	243	743,7857	179.5+/-228.6	32,679,3589	yes	missense	CNGB3	NM_019098.4	98	43,967,5493	CC,CT,TT		8.6395,7.0359,8.0963	benign	755/810	87588198	1053,11953	2203	4300	6503	SO:0001583	missense	54714	exon18			GTACATTCAGGTC	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2153	protein-coding gene	gene with protein product		605080	"""achromatopsia (rod monochromacy) 3"", ""achromatopsia (rod monochromacy) 1"""	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.2264A>G	8.37:g.87588198T>C	ENSP00000316605:p.Glu755Gly	Somatic	317	1	0.00315457		WXS	Illumina HiSeq	Phase_I	323	172	0.532508	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	177	0.08104395604395605	29	0.05894308943089431	33	0.09116022099447514	48	0.08391608391608392	67	0.08839050131926121	T	10.79	1.449535	0.26074	0.070359	0.086395	ENSG00000170289	ENST00000320005	D	0.97186	-4.28	5.37	2.97	0.34412	.	0.666605	0.14178	N	0.336259	T	0.38665	0.1049	N	0.14661	0.345	0.80722	P	0.0	B;B	0.27732	0.187;0.118	B;B	0.27500	0.08;0.037	T	0.73808	-0.3866	9	0.28530	T	0.3	.	6.4711	0.22009	0.0:0.0817:0.1575:0.7608	rs3735972;rs52818605;rs56540041;rs57600088;rs3735972	750;755	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	G	755	ENSP00000316605:E755G	ENSP00000316605:E755G	E	-	2	0	CNGB3	87657314	0.002000	0.14202	0.000000	0.03702	0.022000	0.10575	1.196000	0.32198	0.426000	0.26116	0.383000	0.25322	GAA	T|0.921;C|0.079	0.079	strong		0.398	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098	
MAP3K2	10746	hgsc.bcm.edu	37	2	128075319	128075319	+	Silent	SNP	C	C	T	rs11899533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128075319C>T	ENST00000409947.1	-	14	1494	c.1212G>A	c.(1210-1212)gaG>gaA	p.E404E	RNU6-1147P_ENST00000363380.1_RNA|MAP3K2_ENST00000344908.5_Silent_p.E404E			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	404	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	GAATTTCACACTCAAGTGCAT	0.358													C|||	83	0.0165735	0.059	0.0058	5008	,	,		15585	0.0		0.0	False		,,,				2504	0.001				p.E404E		Atlas-SNP	.											.	MAP3K2	78	.	0			c.G1212A						PASS	.	C		218,3466		6,206,1630	55.0	52.0	53.0		1212	-1.5	0.9	2	dbSNP_120	53	1,8183		0,1,4091	no	coding-synonymous	MAP3K2	NM_006609.4		6,207,5721	TT,TC,CC		0.0122,5.9175,1.8453		404/620	128075319	219,11649	1842	4092	5934	SO:0001819	synonymous_variant	10746	exon13			TTCACACTCAAGT	AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6854	protein-coding gene	gene with protein product	"""MAP/ERK kinase kinase 2"""	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.1212G>A	2.37:g.128075319C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_006609	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Silent	SNP	ENST00000409947.1	37	CCDS46404.1																																																																																			C|0.981;T|0.019	0.019	strong		0.358	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609	
TADA2A	6871	hgsc.bcm.edu	37	17	35830554	35830554	+	Missense_Mutation	SNP	A	A	C	rs142392695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:35830554A>C	ENST00000394395.2	+	13	1119	c.946A>C	c.(946-948)Aaa>Caa	p.K316Q	TADA2A_ENST00000591992.1_3'UTR|TADA2A_ENST00000225396.6_Missense_Mutation_p.K316Q	NM_001166105.1	NP_001159577.1	O75478	TAD2A_HUMAN	transcriptional adaptor 2A	316					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)|skin(1)	13						AGAGCGCCTTAAACGCACTAT	0.507													A|||	16	0.00319489	0.0121	0.0	5008	,	,		16970	0.0		0.0	False		,,,				2504	0.0				p.K316Q		Atlas-SNP	.											.	TADA2A	91	.	0			c.A946C						PASS	.	A	GLN/LYS,GLN/LYS	52,4354	52.9+/-88.7	0,52,2151	143.0	135.0	138.0		946,946	5.6	1.0	17	dbSNP_134	138	0,8600		0,0,4300	yes	missense,missense	TADA2A	NM_001166105.1,NM_001488.3	53,53	0,52,6451	CC,CA,AA		0.0,1.1802,0.3998	possibly-damaging,possibly-damaging	316/444,316/444	35830554	52,12954	2203	4300	6503	SO:0001583	missense	6871	exon13			CGCCTTAAACGCA	AK022767	CCDS11319.1, CCDS45656.1	17q12-q21	2014-04-10	2009-10-02	2009-10-02	ENSG00000108264	ENSG00000276234			11531	protein-coding gene	gene with protein product		602276	"""transcriptional adaptor 2 (ADA2 homolog, yeast)-like"""	TADA2L		8552087	Standard	XM_006722043		Approved	ADA2, hADA2, ADA2A	uc002hnt.3	O75478	OTTHUMG00000188469	ENST00000394395.2:c.946A>C	17.37:g.35830554A>C	ENSP00000377918:p.Lys316Gln	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_001488	A8MVD0|B3KMU9|Q9BVJ0|Q9UCW2|Q9UP49	Missense_Mutation	SNP	ENST00000394395.2	37	CCDS11319.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	A	25.5	4.644355	0.87859	0.011802	0.0	ENSG00000108264	ENST00000394395;ENST00000428846;ENST00000225396	T;T	0.43294	0.95;0.95	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.18299	0.0439	N	0.14661	0.345	0.80722	D	1	P	0.47409	0.895	B	0.38056	0.264	T	0.05194	-1.0900	10	0.16420	T	0.52	-20.0499	15.8074	0.78524	1.0:0.0:0.0:0.0	.	316	O75478	TAD2A_HUMAN	Q	316;215;316	ENSP00000377918:K316Q;ENSP00000225396:K316Q	ENSP00000225396:K316Q	K	+	1	0	TADA2A	32904667	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	8.946000	0.92992	2.127000	0.65507	0.533000	0.62120	AAA	A|0.996;C|0.004	0.004	strong		0.507	TADA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256677.3	NM_001488	
AHNAK2	113146	hgsc.bcm.edu	37	14	105408955	105408955	+	Missense_Mutation	SNP	A	A	G	rs2819422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105408955A>G	ENST00000333244.5	-	7	12952	c.12833T>C	c.(12832-12834)gTg>gCg	p.V4278A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4278			V -> A (in dbSNP:rs2819422).			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)			CTCCAGCCGCACACTGTCCAG	0.607													G|||	2908	0.580671	0.7375	0.5187	5008	,	,		19583	0.4127		0.5338	False		,,,				2504	0.6339				p.V4278A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T12833C						PASS	.	G	ALA/VAL	2954,1074		1076,802,136	151.0	168.0	162.0		12833	-0.3	0.0	14	dbSNP_100	162	4512,3804		1234,2044,880	no	missense	AHNAK2	NM_138420.2	64	2310,2846,1016	GG,GA,AA		45.7431,26.6634,39.5172	benign	4278/5796	105408955	7466,4878	2014	4158	6172	SO:0001583	missense	113146	exon7			AGCCGCACACTGT	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.12833T>C	14.37:g.105408955A>G	ENSP00000353114:p.Val4278Ala	Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	303	301	0.993399	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1193	0.5462454212454212	369	0.75	201	0.5552486187845304	221	0.38636363636363635	402	0.5303430079155673	a	0	-2.656781	0.00108	0.733366	0.542569	ENSG00000185567	ENST00000333244	T	0.01178	5.22	0.177	-0.353	0.12594	.	.	.	.	.	T	0.00012	0.0000	N	0.11023	0.085	0.80722	P	0.0	B	0.02656	0.0	B	0.11329	0.006	T	0.41752	-0.9491	7	0.07990	T	0.79	.	.	.	.	rs2819422;rs59931905;rs2819422	4278	Q8IVF2	AHNK2_HUMAN	A	4278	ENSP00000353114:V4278A	ENSP00000353114:V4278A	V	-	2	0	AHNAK2	104480000	0.705000	0.27846	0.005000	0.12908	0.001000	0.01503	1.298000	0.33412	-2.385000	0.00590	-2.426000	0.00216	GTG	A|0.462;G|0.538	0.538	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SELPLG	6404	hgsc.bcm.edu	37	12	109017672	109017672	+	Missense_Mutation	SNP	G	G	C	rs63748999|rs372173288|rs540144714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109017672G>C	ENST00000550948.1	-	2	636	c.412C>G	c.(412-414)Ccc>Gcc	p.P138A	SELPLG_ENST00000228463.6_Missense_Mutation_p.P154A|SELPLG_ENST00000388962.3_Intron			Q14242	SELPL_HUMAN	selectin P ligand	138	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GCCTCCGTGGGCACTGGTTGA	0.617													C|||	441	0.0880591	0.0272	0.0504	5008	,	,		19574	0.2034		0.0795	False		,,,				2504	0.0869				p.P154A		Atlas-SNP	.											SELPLG_ENST00000550948,NS,carcinoma,0,14	SELPLG	138	14	0			c.C460G						scavenged	.						160.0	124.0	137.0					12																	109017672		2199	4278	6477	SO:0001583	missense	6404	exon2			CCGTGGGCACTGG		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.412C>G	12.37:g.109017672G>C	ENSP00000447752:p.Pro138Ala	Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	250	77	0.308	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	C	0.375	-0.932076	0.02359	.	.	ENSG00000110876	ENST00000550948;ENST00000228463	T;T	0.27402	1.67;1.67	3.23	-6.47	0.01902	.	.	.	.	.	T	0.07188	0.0182	N	0.02539	-0.55	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24154	-1.0168	9	0.02654	T	1	-1.189	3.3056	0.06998	0.2007:0.2624:0.3957:0.1411	.	154;138	B7Z5C7;Q14242	.;SELPL_HUMAN	A	138;154	ENSP00000447752:P138A;ENSP00000228463:P154A	ENSP00000228463:P154A	P	-	1	0	SELPLG	107541801	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.940000	0.00329	-1.755000	0.01320	-0.339000	0.08088	CCC	.	.	none		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
LAMA2	3908	hgsc.bcm.edu	37	6	129824406	129824406	+	Missense_Mutation	SNP	A	A	G	rs73599293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:129824406A>G	ENST00000421865.2	+	60	8577	c.8528A>G	c.(8527-8529)aAt>aGt	p.N2843S		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2843	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ACCAAAATCAATGATGGCCAG	0.493													A|||	96	0.0191693	0.0673	0.0086	5008	,	,		20534	0.0		0.001	False		,,,				2504	0.0				p.N2843S		Atlas-SNP	.											.	LAMA2	481	.	0			c.A8528G						PASS	.	A	SER/ASN,SER/ASN	305,4101	166.2+/-197.5	11,283,1909	81.0	76.0	78.0		8528,8516	5.9	1.0	6	dbSNP_130	78	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	46,46	11,287,6205	GG,GA,AA		0.0465,6.9224,2.3758	probably-damaging,probably-damaging	2843/3123,2839/3119	129824406	309,12697	2203	4300	6503	SO:0001583	missense	3908	exon60			AAATCAATGATGG	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.8528A>G	6.37:g.129824406A>G	ENSP00000400365:p.Asn2843Ser	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	23	0.010531135531135532	19	0.03861788617886179	4	0.011049723756906077	0	0.0	0	0.0	A	14.58	2.577584	0.45902	0.069224	4.65E-4	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.71222	-0.55	5.86	5.86	0.93980	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.000000	0.85682	D	0.000000	T	0.76593	0.4009	L	0.54863	1.705	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.76329	-0.2999	9	.	.	.	.	16.2479	0.82454	1.0:0.0:0.0:0.0	.	2844;2843	A6NF00;P24043	.;LAMA2_HUMAN	S	2843;2842;2843;861	ENSP00000400365:N2843S	.	N	+	2	0	LAMA2	129866099	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.796000	0.85898	2.241000	0.73720	0.533000	0.62120	AAT	A|0.980;G|0.020	0.020	strong		0.493	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
OR5B12	390191	hgsc.bcm.edu	37	11	58207203	58207203	+	Missense_Mutation	SNP	C	C	T	rs11229457|rs386753911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	124	63	0.508065	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	
TTN	7273	hgsc.bcm.edu	37	2	179621353	179621353	+	Intron	SNP	G	G	A	rs57389274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179621353G>A	ENST00000591111.1	-	44	10528				TTN_ENST00000589042.1_Missense_Mutation_p.S3617F|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S3446F|TTN-AS1_ENST00000578746.1_RNA			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)			GGAACTTTGAGATACACTTTC	0.383													G|||	98	0.0195687	0.0726	0.0029	5008	,	,		22444	0.0		0.0	False		,,,				2504	0.0				p.S3617F		Atlas-SNP	.											.	TTN	18412	.	0			c.C10850T						PASS	.	G	,,,,PHE/SER	191,3647		6,179,1734	112.0	113.0	113.0		,,,,10337	3.3	0.8	2	dbSNP_129	113	6,8254		0,6,4124	yes	intron,intron,intron,intron,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,155	6,185,5858	AA,AG,GG		0.0726,4.9766,1.6284	,,,,	,,,,3446/27119	179621353	197,11901	1919	4130	6049	SO:0001627	intron_variant	7273	exon46			CTTTGAGATACAC	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.10303+2357C>T	2.37:g.179621353G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	135	58	0.42963	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		36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	G	12.02	1.813296	0.32053	0.049766	7.26E-4	ENSG00000155657	ENST00000342175	T	0.60672	0.17	6.17	3.3	0.37823	.	.	.	.	.	T	0.06735	0.0172	.	.	.	0.80722	D	1	B	0.24092	0.097	B	0.23150	0.044	T	0.08249	-1.0731	8	0.87932	D	0	.	12.2661	0.54679	0.0:0.1167:0.6404:0.2429	rs57389274	3446	E7ET18	.	F	3446	ENSP00000340554:S3446F	ENSP00000340554:S3446F	S	-	2	0	TTN	179329598	1.000000	0.71417	0.783000	0.31826	0.997000	0.91878	2.776000	0.47709	0.422000	0.26005	0.655000	0.94253	TCT	G|0.982;A|0.018	0.018	strong		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MASP1	5648	hgsc.bcm.edu	37	3	186954324	186954324	+	Intron	SNP	G	G	A	rs3774268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	95	0	0		WXS	Illumina HiSeq	Phase_I	131	56	0.427481	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	
LRRC36	55282	hgsc.bcm.edu	37	16	67418957	67418957	+	Missense_Mutation	SNP	A	A	G	rs16957415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67418957A>G	ENST00000329956.6	+	14	2249	c.2230A>G	c.(2230-2232)Agc>Ggc	p.S744G	LRRC36_ENST00000435835.3_Missense_Mutation_p.S519G|LRRC36_ENST00000563189.1_Missense_Mutation_p.S623G|LRRC36_ENST00000541146.1_Missense_Mutation_p.S216G|LRRC36_ENST00000290940.7_3'UTR	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36	744			S -> G (in dbSNP:rs16957415).							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)		TCTAATACAGAGCGTCTTGGA	0.542													A|||	440	0.0878594	0.2148	0.0476	5008	,	,		17925	0.003		0.0388	False		,,,				2504	0.0828				p.S744G		Atlas-SNP	.											LRRC36,NS,carcinoma,-2,1	LRRC36	68	1	0			c.A2230G						scavenged	.	A	GLY/SER,GLY/SER	784,3612	315.2+/-294.0	75,634,1489	99.0	87.0	91.0		1867,2230	4.6	0.9	16	dbSNP_123	91	353,8247	118.8+/-178.2	9,335,3956	yes	missense,missense	LRRC36	NM_001161575.1,NM_018296.5	56,56	84,969,5445	GG,GA,AA		4.1047,17.8344,8.7488	benign,benign	623/634,744/755	67418957	1137,11859	2198	4300	6498	SO:0001583	missense	55282	exon14			ATACAGAGCGTCT	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.2230A>G	16.37:g.67418957A>G	ENSP00000329943:p.Ser744Gly	Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	149	95	0.637584	NM_018296	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Missense_Mutation	SNP	ENST00000329956.6	37	CCDS32467.1	162	0.07417582417582418	110	0.22357723577235772	20	0.055248618784530384	2	0.0034965034965034965	30	0.0395778364116095	A	11.20	1.569672	0.28003	0.178344	0.041047	ENSG00000159708	ENST00000329956;ENST00000541146;ENST00000435835	T;T;T	0.54071	3.01;0.59;1.3	5.65	4.56	0.56223	.	0.412785	0.23642	N	0.046018	T	0.00039	0.0001	L	0.36672	1.1	0.38483	P	0.05221399999999998	B;B;B;B	0.10296	0.001;0.003;0.003;0.003	B;B;B;B	0.11329	0.004;0.006;0.006;0.004	T	0.05937	-1.0855	9	0.44086	T	0.13	-1.1703	8.3398	0.32237	0.9134:0.0:0.0866:0.0	rs16957415;rs52835857;rs16957415	216;519;623;744	B7Z4G3;B7Z7B3;Q1X8D7-2;Q1X8D7	.;.;.;LRC36_HUMAN	G	744;216;519	ENSP00000329943:S744G;ENSP00000445861:S216G;ENSP00000411122:S519G	ENSP00000329943:S744G	S	+	1	0	LRRC36	65976458	0.782000	0.28689	0.851000	0.33527	0.110000	0.19582	1.090000	0.30902	1.152000	0.42452	0.533000	0.62120	AGC	A|0.907;G|0.093	0.093	strong		0.542	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296	
NUP153	9972	hgsc.bcm.edu	37	6	17675553	17675553	+	Silent	SNP	T	T	C	rs61748704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	129	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	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		
DIRC1	116093	hgsc.bcm.edu	37	2	189599373	189599373	+	Missense_Mutation	SNP	A	A	G	rs58846152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:189599373A>G	ENST00000308100.4	-	2	545	c.275T>C	c.(274-276)tTg>tCg	p.L92S	AC079613.1_ENST00000431708.1_RNA	NM_052952.2	NP_443184.1	Q969H9	DIRC1_HUMAN	disrupted in renal carcinoma 1	92			L -> S (in dbSNP:rs58846152).							large_intestine(1)|lung(6)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00842)|Epithelial(96;0.102)			CCACCCCCTCAATGAGTTAAG	0.383													A|||	167	0.0333466	0.121	0.0086	5008	,	,		18397	0.0		0.001	False		,,,				2504	0.0				p.L92S		Atlas-SNP	.											.	DIRC1	13	.	0			c.T275C						PASS	.	A	SER/LEU	350,4056	180.8+/-209.0	13,324,1866	155.0	160.0	158.0		275	1.2	0.0	2	dbSNP_129	158	2,8598	1.2+/-3.3	0,2,4298	yes	missense	DIRC1	NM_052952.2	145	13,326,6164	GG,GA,AA		0.0233,7.9437,2.7064	benign	92/105	189599373	352,12654	2203	4300	6503	SO:0001583	missense	116093	exon2			CCCCTCAATGAGT	AY039011	CCDS2296.1	2q33	2008-05-22			ENSG00000174325	ENSG00000174325			15760	protein-coding gene	gene with protein product		606423				11587072	Standard	NM_052952		Approved		uc002uqi.1	Q969H9	OTTHUMG00000132646	ENST00000308100.4:c.275T>C	2.37:g.189599373A>G	ENSP00000307860:p.Leu92Ser	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	186	79	0.424731	NM_052952	Q08AK1	Missense_Mutation	SNP	ENST00000308100.4	37	CCDS2296.1	53	0.024267399267399268	49	0.09959349593495935	4	0.011049723756906077	0	0.0	0	0.0	A	1.548	-0.540046	0.04053	0.079437	2.33E-4	ENSG00000174325	ENST00000308100	T	0.42131	0.98	2.38	1.21	0.21127	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.11251	-1.0595	9	0.87932	D	0	.	4.1545	0.10254	0.8279:0.0:0.1721:0.0	rs58846152	92	Q969H9	DIRC1_HUMAN	S	92	ENSP00000307860:L92S	ENSP00000307860:L92S	L	-	2	0	DIRC1	189307618	0.031000	0.19500	0.003000	0.11579	0.015000	0.08874	0.917000	0.28665	0.329000	0.23460	0.533000	0.62120	TTG	A|0.976;G|0.024	0.024	strong		0.383	DIRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255897.2	NM_052952	
ARMC12	221481	hgsc.bcm.edu	37	6	35716613	35716613	+	Missense_Mutation	SNP	A	A	G	rs73729781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35716613A>G	ENST00000373866.3	+	6	1011	c.989A>G	c.(988-990)cAg>cGg	p.Q330R	ARMC12_ENST00000373869.3_Missense_Mutation_p.Q320R|ARMC12_ENST00000288065.2_Missense_Mutation_p.Q357R			Q5T9G4	ARM12_HUMAN	armadillo repeat containing 12	330						nucleus (GO:0005634)											TCCTCCTGCCAGCCCAGTCGT	0.488													A|||	26	0.00519169	0.0189	0.0014	5008	,	,		17917	0.0		0.0	False		,,,				2504	0.0				p.Q357R		Atlas-SNP	.											.	.	.	.	0			c.A1070G						PASS	.	A	ARG/GLN	63,4343	57.4+/-93.9	0,63,2140	44.0	47.0	46.0		1070	-9.5	0.0	6	dbSNP_130	46	0,8600		0,0,4300	yes	missense	C6orf81	NM_145028.3	43	0,63,6440	GG,GA,AA		0.0,1.4299,0.4844	benign	357/368	35716613	63,12943	2203	4300	6503	SO:0001583	missense	221481	exon6			CCTGCCAGCCCAG	AK058119	CCDS4809.1, CCDS69093.1, CCDS69094.1	6p21.31	2013-02-14	2011-12-14	2011-12-14	ENSG00000157343	ENSG00000157343		"""Armadillo repeat containing"""	21099	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 81"""	C6orf81			Standard	XM_005248920		Approved	FLJ25390	uc003ola.3	Q5T9G4	OTTHUMG00000014577	ENST00000373866.3:c.989A>G	6.37:g.35716613A>G	ENSP00000362973:p.Gln330Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	75	43	0.573333	NM_145028	Q8NEB2|Q96LL8	Missense_Mutation	SNP	ENST00000373866.3	37		10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	1.845	-0.466582	0.04476	0.014299	0.0	ENSG00000157343	ENST00000373869;ENST00000288065;ENST00000373866	T;T	0.39997	1.05;1.07	4.77	-9.54	0.00572	.	1.744990	0.03118	N	0.163415	T	0.02267	0.0070	N	0.01874	-0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07102	-1.0790	10	0.02654	T	1	.	1.28	0.02039	0.1771:0.3484:0.2459:0.2287	.	320;357	Q5T9G4-3;Q5T9G4-2	.;.	R	320;357;330	ENSP00000288065:Q357R;ENSP00000362973:Q330R	ENSP00000288065:Q357R	Q	+	2	0	C6orf81	35824591	0.000000	0.05858	0.001000	0.08648	0.269000	0.26545	-0.566000	0.05922	-1.836000	0.01190	-0.400000	0.06385	CAG	A|0.995;G|0.005	0.005	strong		0.488	ARMC12-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040311.2	NM_145028	
ZFPM2	23414	hgsc.bcm.edu	37	8	106813672	106813672	+	Silent	SNP	A	A	G	rs920628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:106813672A>G	ENST00000407775.2	+	8	1612	c.1362A>G	c.(1360-1362)ccA>ccG	p.P454P	ZFPM2_ENST00000520492.1_Silent_p.P322P|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000521622.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000509144.2_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000520433.1_RNA|ZFPM2_ENST00000517361.1_Silent_p.P322P|ZFPM2_ENST00000378472.4_Silent_p.P185P|RP11-152P17.2_ENST00000520594.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	454					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			ACCAGAGACCAGAGATACAGC	0.453													G|||	629	0.125599	0.3873	0.0533	5008	,	,		20947	0.0069		0.0288	False		,,,				2504	0.045				p.P454P		Atlas-SNP	.											ZFPM2,NS,carcinoma,+2,1	ZFPM2	219	1	0			c.A1362G						PASS	.	G		1161,2601		174,813,894	64.0	70.0	68.0		1362	-4.6	0.5	8	dbSNP_86	68	196,8020		4,188,3916	no	coding-synonymous	ZFPM2	NM_012082.3		178,1001,4810	GG,GA,AA		2.3856,30.8612,11.3291		454/1152	106813672	1357,10621	1881	4108	5989	SO:0001819	synonymous_variant	23414	exon8			GAGACCAGAGATA	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.1362A>G	8.37:g.106813672A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Silent	SNP	ENST00000407775.2	37	CCDS47908.1																																																																																			A|0.885;G|0.115	0.115	strong		0.453	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
BTN3A2	11118	hgsc.bcm.edu	37	6	26370833	26370833	+	Splice_Site	SNP	T	T	G	rs58367598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26370833T>G	ENST00000356386.2	+	5	903		c.e5+2		BTN3A2_ENST00000396934.3_Splice_Site|BTN3A2_ENST00000532994.1_Splice_Site|BTN3A2_ENST00000377708.2_Splice_Site|BTN3A2_ENST00000396948.1_Splice_Site|BTN3A2_ENST00000508906.2_Splice_Site|BTN3A2_ENST00000527422.1_Splice_Site	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2						interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						CCATCGCAGGTCAGTACCTGC	0.532													T|||	214	0.0427316	0.0802	0.0202	5008	,	,		18081	0.005		0.0447	False		,,,				2504	0.045				.		Atlas-SNP	.											.	BTN3A2	44	.	0			c.589+2T>G						PASS	.	T	,,,,	298,4108	161.4+/-193.6	6,286,1911	77.0	75.0	76.0		,,,,	2.2	0.5	6	dbSNP_129	76	388,8212	126.7+/-185.1	9,370,3921	no	splice-5,splice-5,splice-5,splice-5,splice-5	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	15,656,5832	GG,GT,TT		4.5116,6.7635,5.2745	,,,,	,,,,	26370833	686,12320	2203	4300	6503	SO:0001630	splice_region_variant	11118	exon4			CGCAGGTCAGTAC	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.715+2T>G	6.37:g.26370833T>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	135	81	0.6	NM_001197249	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Splice_Site	SNP	ENST00000356386.2	37	CCDS4605.1	81	0.03708791208791209	40	0.08130081300813008	7	0.019337016574585635	0	0.0	34	0.044854881266490766	T	10.98	1.505574	0.26949	0.067635	0.045116	ENSG00000186470	ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	.	.	.	2.16	2.16	0.27623	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.3209	0.21217	0.0:0.0:0.0:1.0	rs58367598	.	.	.	.	-1	.	.	.	+	.	.	BTN3A2	26478812	0.985000	0.35326	0.496000	0.27539	0.305000	0.27757	1.644000	0.37228	1.235000	0.43724	0.333000	0.21579	.	T|0.951;G|0.049	0.049	strong		0.532	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		Intron
ZNF770	54989	hgsc.bcm.edu	37	15	35273867	35273867	+	Missense_Mutation	SNP	C	C	A	rs141323293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:35273867C>A	ENST00000356321.4	-	3	2113	c.1769G>T	c.(1768-1770)gGt>gTt	p.G590V		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	590					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)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		CCCGGTGCTACCAGGAATAAA	0.438													C|||	3	0.000599042	0.0023	0.0	5008	,	,		19415	0.0		0.0	False		,,,				2504	0.0				p.G590V		Atlas-SNP	.											.	ZNF770	64	.	0			c.G1769T						PASS	.	C	VAL/GLY	45,4357	46.7+/-81.2	0,45,2156	117.0	119.0	118.0		1769	-0.4	0.0	15	dbSNP_134	118	0,8596		0,0,4298	no	missense	ZNF770	NM_014106.3	109	0,45,6454	AA,AC,CC		0.0,1.0223,0.3462	possibly-damaging	590/692	35273867	45,12953	2201	4298	6499	SO:0001583	missense	54989	exon3			GTGCTACCAGGAA	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"""Zinc fingers, C2H2-type"""	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.1769G>T	15.37:g.35273867C>A	ENSP00000348673:p.Gly590Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_014106	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	37	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	C	0.324	-0.960173	0.02267	0.010223	0.0	ENSG00000198146	ENST00000356321	T	0.10288	2.89	5.24	-0.357	0.12579	.	0.716901	0.12735	N	0.443539	T	0.03434	0.0099	N	0.14661	0.345	0.21020	N	0.999802	B	0.16396	0.017	B	0.15052	0.012	T	0.39014	-0.9634	10	0.33141	T	0.24	-0.2229	4.5334	0.12017	0.1656:0.3386:0.0:0.4958	.	590	Q6IQ21	ZN770_HUMAN	V	590	ENSP00000348673:G590V	ENSP00000348673:G590V	G	-	2	0	ZNF770	33061159	0.039000	0.19947	0.021000	0.16686	0.125000	0.20455	0.555000	0.23422	0.090000	0.17273	0.467000	0.42956	GGT	C|0.996;A|0.004	0.004	strong		0.438	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106	
MGAM	8972	hgsc.bcm.edu	37	7	141736732	141736732	+	Missense_Mutation	SNP	G	G	A	rs116034282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141736732G>A	ENST00000549489.2	+	18	2281	c.2186G>A	c.(2185-2187)cGt>cAt	p.R729H	MGAM_ENST00000475668.2_Missense_Mutation_p.R729H	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	729	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)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CTCTTCTTCCGTGCTCACAGC	0.493													G|||	56	0.0111821	0.0401	0.0043	5008	,	,		19313	0.0		0.0	False		,,,				2504	0.0				p.R729H		Atlas-SNP	.											.	MGAM	767	.	0			c.G2186A						PASS	.	G	HIS/ARG	129,3941		3,123,1909	199.0	203.0	202.0		2186	-1.0	0.0	7	dbSNP_132	202	0,8388		0,0,4194	yes	missense	MGAM	NM_004668.2	29	3,123,6103	AA,AG,GG		0.0,3.1695,1.0355	possibly-damaging	729/1858	141736732	129,12329	2035	4194	6229	SO:0001583	missense	8972	exon18			TCTTCCGTGCTCA	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.2186G>A	7.37:g.141736732G>A	ENSP00000447378:p.Arg729His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	28	0.01282051282051282	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	0	0.0	G	12.77	2.038656	0.35989	0.031695	0.0	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.91464	-2.85	5.81	-0.982	0.10266	Glycoside hydrolase, superfamily (1);	0.281671	0.23492	N	0.047582	T	0.44159	0.1280	N	0.20685	0.6	0.09310	N	1	B	0.30021	0.265	B	0.22753	0.041	T	0.54748	-0.8247	10	0.32370	T	0.25	.	11.754	0.51866	0.5808:0.0:0.4192:0.0	.	729	O43451	MGA_HUMAN	H	729;729;606	ENSP00000447378:R729H	ENSP00000316431:R606H	R	+	2	0	MGAM	141383201	0.034000	0.19679	0.000000	0.03702	0.991000	0.79684	0.534000	0.23098	-0.502000	0.06596	-0.145000	0.13849	CGT	G|0.986;A|0.014	0.014	strong		0.493	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
CYB5RL	606495	hgsc.bcm.edu	37	1	54661150	54661150	+	Missense_Mutation	SNP	C	C	T	rs946448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000419823.2_Missense_Mutation_p.R47K|CYB5RL_ENST00000287899.8_Missense_Mutation_p.R47K|MRPL37_ENST00000487096.1_Intron|CYB5RL_ENST00000497820.1_Missense_Mutation_p.R47K|CYB5RL_ENST00000542737.1_Missense_Mutation_p.R47K|RP11-446E24.4_ENST00000311841.7_Missense_Mutation_p.R47K|CYB5RL_ENST00000401046.3_5'UTR			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	50	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	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	
FCRL6	343413	hgsc.bcm.edu	37	1	159778983	159778983	+	Silent	SNP	T	T	C	rs12083967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159778983T>C	ENST00000368106.3	+	4	553	c.552T>C	c.(550-552)ccT>ccC	p.P184P	FCRL6_ENST00000392235.3_Intron|FCRL6_ENST00000339348.5_Silent_p.P184P|FCRL6_ENST00000321935.6_Silent_p.P191P	NM_001004310.2	NP_001004310.2	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6	184	Ig-like C2-type 2.					external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				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)					AGGTGGCCCCTGAGGGTGGCC	0.662													.|||	1360	0.271565	0.5265	0.2363	5008	,	,		18874	0.1855		0.1998	False		,,,				2504	0.1145				p.P184P		Atlas-SNP	.											.	FCRL6	61	.	0			c.T552C						PASS	.	T		2008,2396	508.6+/-367.0	478,1052,672	41.0	47.0	45.0		552	-2.9	0.0	1	dbSNP_120	45	1624,6976	284.4+/-296.6	161,1302,2837	no	coding-synonymous	FCRL6	NM_001004310.2		639,2354,3509	CC,CT,TT		18.8837,45.5949,27.9299		184/435	159778983	3632,9372	2202	4300	6502	SO:0001819	synonymous_variant	343413	exon4			GGCCCCTGAGGGT	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.552T>C	1.37:g.159778983T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_001004310	A1KXW6|A2A4D6|Q6DN73|Q6XRC3|Q6ZNI1	Silent	SNP	ENST00000368106.3	37	CCDS30912.1																																																																																			T|0.738;C|0.262	0.262	strong		0.662	FCRL6-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276853.1	NM_001004310	
SLC9C2	284525	hgsc.bcm.edu	37	1	173516915	173516915	+	Silent	SNP	G	G	A	rs114115413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173516915G>A	ENST00000367714.3	-	13	1892	c.1470C>T	c.(1468-1470)caC>caT	p.H490H	SLC9C2_ENST00000536496.1_Silent_p.H388H|SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	490					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TATGTGAAACGTGGGAAAACT	0.353													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		18017	0.0		0.0	False		,,,				2504	0.0				p.H490H		Atlas-SNP	.											.	.	.	.	0			c.C1470T						PASS	.	G		125,4281	92.0+/-130.7	3,119,2081	134.0	119.0	124.0		1470	-8.2	0.0	1	dbSNP_132	124	0,8600		0,0,4300	no	coding-synonymous	SLC9A11	NM_178527.3		3,119,6381	AA,AG,GG		0.0,2.837,0.9611		490/1125	173516915	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	284525	exon13			TGAAACGTGGGAA	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.1470C>T	1.37:g.173516915G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	37	CCDS1308.1																																																																																			G|0.989;A|0.011	0.011	strong		0.353	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
IFNA16	3449	hgsc.bcm.edu	37	9	21216864	21216864	+	Silent	SNP	A	A	G	rs28368164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21216864A>G	ENST00000380216.1	-	1	446	c.441T>C	c.(439-441)ttT>ttC	p.F147F		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	147					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		TGATTCTTTGAAAGTATTTCC	0.458													A|||	131	0.0261581	0.0499	0.0216	5008	,	,		18727	0.001		0.0427	False		,,,				2504	0.0061				p.F147F		Atlas-SNP	.											.	IFNA16	27	.	0			c.T441C						PASS	.	A		199,4207		5,189,2009	229.0	220.0	223.0		441	0.7	0.0	9	dbSNP_125	223	381,8219		7,367,3926	no	coding-synonymous	IFNA16	NM_002173.2		12,556,5935	GG,GA,AA		4.4302,4.5166,4.4595		147/190	21216864	580,12426	2203	4300	6503	SO:0001819	synonymous_variant	3449	exon1			TCTTTGAAAGTAT		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"""Interferons"""	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.441T>C	9.37:g.21216864A>G		Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	287	122	0.425087	NM_002173	Q5VV12	Silent	SNP	ENST00000380216.1	37	CCDS34996.1																																																																																			A|0.957;G|0.043	0.043	strong		0.458	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173	
TPGS1	91978	hgsc.bcm.edu	37	19	507560	507560	+	Silent	SNP	G	G	A	rs61746565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:507560G>A	ENST00000359315.5	+	1	262	c.54G>A	c.(52-54)acG>acA	p.T18T	AC005775.2_ENST00000592413.1_RNA	NM_033513.2	NP_277048.2	Q6ZTW0	TPGS1_HUMAN	tubulin polyglutamylase complex subunit 1	18					adult behavior (GO:0030534)|multicellular organismal development (GO:0007275)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|synaptic transmission (GO:0007268)|vesicle localization (GO:0051648)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)	tubulin-glutamic acid ligase activity (GO:0070740)										CCGGTTTCACGGACAGCGGCC	0.706													G|||	35	0.00698882	0.025	0.0029	5008	,	,		11141	0.0		0.0	False		,,,				2504	0.0				p.T18T		Atlas-SNP	.											.	.	.	.	0			c.G54A						PASS	.						3.0	5.0	5.0					19																	507560		1241	3077	4318	SO:0001819	synonymous_variant	91978	exon1			TTTCACGGACAGC	BC009520	CCDS42454.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000141933	ENSG00000141933			25058	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 20"""	C19orf20		11441184, 12972506	Standard	NM_033513		Approved	GTRGEO22, PGs1	uc002lou.3	Q6ZTW0		ENST00000359315.5:c.54G>A	19.37:g.507560G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	24	23	0.958333	NM_033513	Q96GE2	Silent	SNP	ENST00000359315.5	37	CCDS42454.1																																																																																			G|0.991;A|0.009	0.009	strong		0.706	TPGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451887.2	NM_033513	
MT-ND5	4540	hgsc.bcm.edu	37	M	13789	13789	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:13789T>C	ENST00000361567.2	+	1	1453	c.1453T>C	c.(1453-1455)Tac>Cac	p.Y485H	MT-TT_ENST00000387460.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	485					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CAATCCCCCTCTACCTAAAAC	0.463																																					p.Y485H		Atlas-SNP	.											.	.	.	.	0			c.T1453C						PASS	.																																			SO:0001583	missense	0	exon1			CCCCTCTACCTAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1453T>C	M.37:g.13789T>C	ENSP00000354813:p.Tyr485His	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.463	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
PSG5	5673	hgsc.bcm.edu	37	19	43680051	43680051	+	Missense_Mutation	SNP	C	C	T	rs1058285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43680051C>T	ENST00000366175.3	-	3	810	c.680G>A	c.(679-681)cGc>cAc	p.R227H	PSG5_ENST00000407568.1_Intron|PSG5_ENST00000599812.1_Missense_Mutation_p.R320H|PSG5_ENST00000407356.1_Missense_Mutation_p.R227H|PSG5_ENST00000342951.6_Missense_Mutation_p.R227H|PSG5_ENST00000404580.1_Missense_Mutation_p.R227H			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	227	Ig-like C2-type 1.		R -> H (in dbSNP:rs1058285). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1922019, ECO:0000269|PubMed:2735907, ECO:0000269|PubMed:2789512}.		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				TGGGTCACTGCGCATGCCACC	0.493													C|||	3818	0.76238	0.8245	0.5821	5008	,	,		20297	0.9851		0.6123	False		,,,				2504	0.7311				p.R227H		Atlas-SNP	.											PSG5,NS,carcinoma,+1,1	PSG5	58	1	0			c.G680A						PASS	.	C	HIS/ARG,HIS/ARG	3465,937	737.2+/-410.9	1384,697,120	163.0	157.0	159.0		680,680	-0.6	0.0	19	dbSNP_86	159	5169,3421	638.3+/-399.3	1609,1951,735	no	missense,missense	PSG5	NM_001130014.1,NM_002781.3	29,29	2993,2648,855	TT,TC,CC		39.8254,21.2858,33.5437	benign,benign	227/336,227/336	43680051	8634,4358	2201	4295	6496	SO:0001583	missense	5673	exon3			TCACTGCGCATGC		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.680G>A	19.37:g.43680051C>T	ENSP00000382334:p.Arg227His	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_002781	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	1650	0.7554945054945055	415	0.8434959349593496	207	0.5718232044198895	567	0.9912587412587412	461	0.6081794195250659	c	2.454	-0.325779	0.05350	0.787142	0.601746	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000342951;ENST00000404580	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	1.08	-0.623	0.11556	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.69823	2.125	0.80722	P	0.0	B	0.18610	0.029	B	0.25140	0.058	T	0.14868	-1.0457	8	0.42905	T	0.14	.	5.5781	0.17235	0.0:0.6701:0.3299:0.0	rs1058285;rs3179036;rs3198896;rs17845347;rs17858192;rs58622191;rs1058285	227	Q15238	PSG5_HUMAN	H	227	ENSP00000382334:R227H;ENSP00000386008:R227H;ENSP00000344413:R227H;ENSP00000385250:R227H	ENSP00000344413:R227H	R	-	2	0	PSG5	48371891	0.000000	0.05858	0.016000	0.15963	0.006000	0.05464	-0.267000	0.08619	-1.394000	0.02077	-1.271000	0.01417	CGC	C|0.311;T|0.689	0.689	strong		0.493	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
MYOM2	9172	hgsc.bcm.edu	37	8	2037833	2037833	+	Silent	SNP	G	G	C	rs2294061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2037833G>C	ENST00000262113.4	+	15	1788	c.1647G>C	c.(1645-1647)tcG>tcC	p.S549S	MYOM2_ENST00000523438.1_5'UTR	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	549	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		CTTTGTAGTCGGTGGTGGGGA	0.557													C|||	1122	0.224042	0.4244	0.1628	5008	,	,		18049	0.2083		0.162	False		,,,				2504	0.0767				p.S549S		Atlas-SNP	.											.	MYOM2	251	.	0			c.G1647C						PASS	.	C		1674,2732	650.5+/-399.1	321,1032,850	64.0	65.0	65.0		1647	-5.2	0.0	8	dbSNP_100	65	1257,7343	756.6+/-407.5	92,1073,3135	no	coding-synonymous	MYOM2	NM_003970.2		413,2105,3985	CC,CG,GG		14.6163,37.9936,22.5358		549/1466	2037833	2931,10075	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon15			GTAGTCGGTGGTG		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.1647G>C	8.37:g.2037833G>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	121	53	0.438017	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			G|0.783;C|0.217	0.217	strong		0.557	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
ARHGAP28	79822	hgsc.bcm.edu	37	18	6908976	6908976	+	Missense_Mutation	SNP	G	G	A	rs116232392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6908976G>A	ENST00000383472.4	+	17	2152	c.2048G>A	c.(2047-2049)tGt>tAt	p.C683Y	ARHGAP28_ENST00000419673.2_Missense_Mutation_p.C524Y|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.C524Y|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.C519Y			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	683					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)				TCATCAGAATGTATTAAGATT	0.284													G|||	125	0.0249601	0.0877	0.0115	5008	,	,		16064	0.0		0.001	False		,,,				2504	0.0				p.C524Y		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.G1571A						PASS	.	G	TYR/CYS	318,4064	152.9+/-186.6	7,304,1880	39.0	45.0	43.0		1571	3.0	0.9	18	dbSNP_132	43	8,8568	5.7+/-21.5	0,8,4280	yes	missense	ARHGAP28	NM_001010000.2	194	7,312,6160	AA,AG,GG		0.0933,7.257,2.5158	benign	524/571	6908976	326,12632	2191	4288	6479	SO:0001583	missense	79822	exon16			CAGAATGTATTAA	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.2048G>A	18.37:g.6908976G>A	ENSP00000372964:p.Cys683Tyr	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	141	54	0.382979	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	37		53	0.024267399267399268	51	0.10365853658536585	2	0.0055248618784530384	0	0.0	0	0.0	G	7.913	0.736819	0.15574	0.07257	9.33E-4	ENSG00000088756	ENST00000419673;ENST00000531294;ENST00000314319	T;T;T	0.07327	3.2;3.21;3.2	5.8	2.98	0.34508	.	.	.	.	.	T	0.00144	0.0004	N	0.14661	0.345	0.25779	P	0.9847541	B	0.19073	0.033	B	0.16722	0.016	T	0.41270	-0.9518	8	0.05833	T	0.94	.	5.225	0.15389	0.2961:0.1403:0.5637:0.0	.	683	Q9P2N2	RHG28_HUMAN	Y	524;519;524	ENSP00000392660:C524Y;ENSP00000437262:C519Y;ENSP00000313506:C524Y	ENSP00000313506:C524Y	C	+	2	0	ARHGAP28	6898976	0.061000	0.20836	0.902000	0.35471	0.988000	0.76386	1.237000	0.32695	0.343000	0.23821	0.650000	0.86243	TGT	G|0.979;A|0.021	0.021	strong		0.284	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
SVEP1	79987	hgsc.bcm.edu	37	9	113170323	113170323	+	Silent	SNP	G	G	A	rs111722103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113170323G>A	ENST00000401783.2	-	38	7893	c.7557C>T	c.(7555-7557)acC>acT	p.T2519T	SVEP1_ENST00000374469.1_Silent_p.T2496T|SVEP1_ENST00000297826.5_Silent_p.T445T	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2519	Sushi 19. {ECO:0000255|PROSITE- ProRule:PRU00302}.			T -> I (in Ref. 6; CAD97901). {ECO:0000305}.	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						AGTAGGTAACGGTCTGTCCAT	0.488													G|||	154	0.0307508	0.1097	0.013	5008	,	,		21854	0.0		0.0	False		,,,				2504	0.0				p.T2519T		Atlas-SNP	.											SVEP1,NS,carcinoma,0,1	SVEP1	326	1	0			c.C7557T						PASS	.	G		334,3532		13,308,1612	49.0	48.0	49.0		7557	-1.3	0.0	9	dbSNP_132	49	5,8261		0,5,4128	no	coding-synonymous	SVEP1	NM_153366.3		13,313,5740	AA,AG,GG		0.0605,8.6394,2.7943		2519/3572	113170323	339,11793	1933	4133	6066	SO:0001819	synonymous_variant	79987	exon38			GGTAACGGTCTGT	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.7557C>T	9.37:g.113170323G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	90	66	0.733333	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			G|0.977;A|0.023	0.023	strong		0.488	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
COL27A1	85301	hgsc.bcm.edu	37	9	116930013	116930013	+	Missense_Mutation	SNP	G	G	A	rs74339956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116930013G>A	ENST00000356083.3	+	3	569	c.178G>A	c.(178-180)Ggg>Agg	p.G60R		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	60					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						GACGAAGGCCGGGAGCCCTGC	0.677													G|||	70	0.0139776	0.0522	0.0014	5008	,	,		16813	0.0		0.0	False		,,,				2504	0.0				p.G60R		Atlas-SNP	.											.	COL27A1	200	.	0			c.G178A						PASS	.	G	ARG/GLY	211,4195	122.5+/-159.9	6,199,1998	71.0	84.0	80.0		178	2.3	1.0	9	dbSNP_131	80	0,8598		0,0,4299	yes	missense	COL27A1	NM_032888.2	125	6,199,6297	AA,AG,GG		0.0,4.7889,1.6226	benign	60/1861	116930013	211,12793	2203	4299	6502	SO:0001583	missense	85301	exon3			AAGGCCGGGAGCC	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.178G>A	9.37:g.116930013G>A	ENSP00000348385:p.Gly60Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	102	37	0.362745	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	9.795	1.179007	0.21787	0.047889	0.0	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	T;T	0.03242	4.0;4.0	5.32	2.3	0.28687	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	.	.	.	.	T	0.00300	0.0009	N	0.01576	-0.805	0.24118	N	0.995813	B	0.02656	0.0	B	0.01281	0.0	T	0.48885	-0.8995	9	0.32370	T	0.25	.	6.932	0.24447	0.0:0.5451:0.36:0.095	.	60	Q8IZC6	CORA1_HUMAN	R	60;60;7;7	ENSP00000348385:G60R;ENSP00000391328:G7R	ENSP00000348385:G60R	G	+	1	0	COL27A1	115969834	0.010000	0.17322	1.000000	0.80357	0.271000	0.26615	1.569000	0.36428	0.627000	0.30340	-0.516000	0.04426	GGG	G|0.985;A|0.015	0.015	strong		0.677	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
ATAD2B	54454	hgsc.bcm.edu	37	2	23980608	23980608	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:23980608G>A	ENST00000238789.5	-	25	4101	c.3758C>T	c.(3757-3759)cCg>cTg	p.P1253L	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	1253						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)	p.P1253Q(2)		central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTCTGCTCCGGGTTTAAGGA	0.438																																					p.P1253L		Atlas-SNP	.											ATAD2B_ENST00000238789,NS,carcinoma,+1,1	ATAD2B	110	1	2	Substitution - Missense(2)	lung(1)|kidney(1)	c.C3758T						scavenged	.						86.0	83.0	84.0					2																	23980608		1880	4100	5980	SO:0001583	missense	54454	exon25			TGCTCCGGGTTTA	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"""ATPases / AAA-type"""	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.3758C>T	2.37:g.23980608G>A	ENSP00000238789:p.Pro1253Leu	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	187	3	0.0160428	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.185|9.185	1.024551|1.024551	0.19433|0.19433	.|.	.|.	ENSG00000119778|ENSG00000119778	ENST00000238789;ENST00000546030|ENST00000381024	D|.	0.91295|.	-2.82|.	4.77|4.77	4.77|4.77	0.60923|0.60923	.|.	0.653298|.	0.15072|.	N|.	0.282139|.	T|T	0.25827|0.25827	0.0629|0.0629	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	0.999999|0.999999	B;B|.	0.29862|.	0.168;0.259|.	B;B|.	0.17098|.	0.008;0.017|.	T|T	0.11690|0.11690	-1.0577|-1.0577	10|5	0.40728|.	T|.	0.16|.	.|.	8.2424|8.2424	0.31669|0.31669	0.0806:0.0:0.7621:0.1572|0.0806:0.0:0.7621:0.1572	.|.	1253;1248|.	Q9ULI0;Q9ULI0-2|.	ATD2B_HUMAN;.|.	L|W	1253;421|529	ENSP00000238789:P1253L|.	ENSP00000238789:P1253L|.	P|R	-|-	2|1	0|2	ATAD2B|ATAD2B	23834112|23834112	0.998000|0.998000	0.40836|0.40836	0.612000|0.612000	0.29024|0.29024	0.459000|0.459000	0.32528|0.32528	3.389000|3.389000	0.52516|0.52516	2.566000|2.566000	0.86566|0.86566	0.563000|0.563000	0.77884|0.77884	CCG|CGG	.	.	none		0.438	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
LDLR	3949	hgsc.bcm.edu	37	19	11222300	11222300	+	Missense_Mutation	SNP	G	G	A	rs11669576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11222300G>A	ENST00000558518.1	+	8	1358	c.1171G>A	c.(1171-1173)Gcc>Acc	p.A391T	LDLR_ENST00000558013.1_Missense_Mutation_p.A391T|LDLR_ENST00000557933.1_Missense_Mutation_p.A391T|LDLR_ENST00000455727.2_Missense_Mutation_p.A223T|LDLR_ENST00000545707.1_Missense_Mutation_p.A264T|LDLR_ENST00000535915.1_Missense_Mutation_p.A350T	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	391	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		A -> T (in dbSNP:rs11669576).		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	CCACACGAAGGCCTGCAAGGC	0.642													G|||	339	0.0676917	0.202	0.0375	5008	,	,		16827	0.0		0.0437	False		,,,				2504	0.002				p.A391T	GBM(18;201 575 7820 21545)	Atlas-SNP	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.G1171A	GRCh37	CM014366	LDLR	M	rs11669576	PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	762,3644	304.6+/-288.6	78,606,1519	41.0	40.0	40.0		1171,1171,1048,667,808,790	-0.8	0.1	19	dbSNP_120	40	416,8184	127.8+/-186.1	15,386,3899	yes	missense,missense,missense,missense,missense,missense	LDLR	NM_000527.4,NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195802.1,NM_001195803.1	58,58,58,58,58,58	93,992,5418	AA,AG,GG		4.8372,17.2946,9.0574	benign,benign,benign,benign,benign,benign	391/861,391/859,350/820,223/693,270/740,264/683	11222300	1178,11828	2203	4300	6503	SO:0001583	missense	3949	exon8			ACGAAGGCCTGCA	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1171G>A	19.37:g.11222300G>A	ENSP00000454071:p.Ala391Thr	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	37	CCDS12254.1	165	0.07554945054945054	116	0.23577235772357724	15	0.04143646408839779	0	0.0	34	0.044854881266490766	G	0.031	-1.331617	0.01298	0.172946	0.048372	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000535915;ENST00000455727	D;D;D	0.91894	-2.93;-2.93;-2.93	5.56	-0.825	0.10809	Growth factor, receptor (1);EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.361880	0.23079	N	0.052177	T	0.00039	0.0001	N	0.00045	-2.45	0.48452	P	3.4599999999995745E-4	B;B;B;B;B;B	0.12013	0.005;0.002;0.005;0.003;0.005;0.005	B;B;B;B;B;B	0.21360	0.009;0.023;0.034;0.023;0.034;0.034	T	0.48305	-0.9047	9	0.05620	T	0.96	.	3.2134	0.06690	0.4419:0.0:0.2395:0.3186	rs11669576;rs11669576	223;264;270;350;403;391	B4DR00;B4DJZ8;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;.;LDLR_HUMAN	T	391;264;350;223	ENSP00000437639:A264T;ENSP00000440520:A350T;ENSP00000397829:A223T	ENSP00000252444:A391T	A	+	1	0	LDLR	11083300	0.000000	0.05858	0.134000	0.22075	0.182000	0.23217	-0.187000	0.09656	0.036000	0.15547	0.591000	0.81541	GCC	G|0.916;A|0.084	0.084	strong		0.642	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
HYDIN	54768	hgsc.bcm.edu	37	16	71009054	71009054	+	Missense_Mutation	SNP	C	C	T	rs201855097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71009054C>T	ENST00000393567.2	-	31	4907	c.4757G>A	c.(4756-4758)cGc>cAc	p.R1586H		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1586					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)				CAGTTTGCGGCGACTCCGATG	0.512													C|||	27	0.00539137	0.0144	0.0029	5008	,	,		20704	0.001		0.005	False		,,,				2504	0.0				p.R1586H		Atlas-SNP	.											LOC652153,NS,carcinoma,-1,2	HYDIN	788	2	0			c.G4757A						scavenged	.						2.0	2.0	2.0					16																	71009054		1187	2725	3912	SO:0001583	missense	54768	exon31			TTGCGGCGACTCC	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.4757G>A	16.37:g.71009054C>T	ENSP00000377197:p.Arg1586His	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	170	45	0.264706	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.388546	0.25118	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00966	5.49	4.61	-0.89	0.10577	.	0.499604	0.14321	U	0.326982	T	0.01189	0.0039	M	0.66939	2.045	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.42344	-0.9457	10	0.42905	T	0.14	.	3.7169	0.08441	0.1643:0.4632:0.0:0.3725	.	1585	F8WD23	.	H	1586;1585	ENSP00000377197:R1586H	ENSP00000313052:R1585H	R	-	2	0	HYDIN	69566555	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	0.261000	0.18442	-0.186000	0.10533	-0.444000	0.05651	CGC	C|0.999;T|0.001	0.001	weak		0.512	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
TAS2R20	259295	hgsc.bcm.edu	37	12	11149769	11149769	+	Missense_Mutation	SNP	T	T	C	rs10845281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11149769T>C	ENST00000538986.1	-	1	705	c.706A>G	c.(706-708)Ata>Gta	p.I236V	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	236			I -> V (in dbSNP:rs10845281). {ECO:0000269|PubMed:15496549}.		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)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						GCAAGTAATATGAGGAAGGAG	0.393													T|||	2118	0.422923	0.0651	0.3847	5008	,	,		20724	0.755		0.3817	False		,,,				2504	0.6339				p.I236V		Atlas-SNP	.											.	TAS2R20	17	.	0			c.A706G						PASS	.	T	VAL/ILE	442,3964	212.2+/-232.1	18,406,1779	154.0	152.0	152.0		706	-1.6	0.0	12	dbSNP_120	152	3016,5584	465.5+/-366.5	544,1928,1828	yes	missense	TAS2R20	NM_176889.2	29	562,2334,3607	CC,CT,TT		35.0698,10.0318,26.5877	benign	236/310	11149769	3458,9548	2203	4300	6503	SO:0001583	missense	259295	exon1			GTAATATGAGGAA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.706A>G	12.37:g.11149769T>C	ENSP00000441624:p.Ile236Val	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	202	84	0.415842	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	898	0.41117216117216115	33	0.06707317073170732	155	0.4281767955801105	426	0.7447552447552448	284	0.37467018469656993	T	4.775	0.144169	0.09134	0.100318	0.350698	ENSG00000255837	ENST00000538986	T	0.00864	5.6	2.66	-1.57	0.08506	.	1.555360	0.04751	U	0.424564	T	0.00012	0.0000	L	0.31476	0.935	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.08166	-1.0735	9	0.62326	D	0.03	.	0.4216	0.00457	0.3201:0.1817:0.1247:0.3734	rs10845281;rs52830191;rs10845281	236	P59543	T2R20_HUMAN	V	236	ENSP00000441624:I236V	ENSP00000441624:I236V	I	-	1	0	TAS2R20	11041036	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.139000	0.16036	-0.493000	0.06678	-2.198000	0.00308	ATA	T|0.675;C|0.325	0.325	strong		0.393	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
MGAT1	4245	hgsc.bcm.edu	37	5	180219838	180219838	+	Missense_Mutation	SNP	C	C	T	rs61743256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180219838C>T	ENST00000446023.2	-	3	884	c.134G>A	c.(133-135)gGc>gAc	p.G45D	MGAT1_ENST00000427865.2_Missense_Mutation_p.G45D|MGAT1_ENST00000307826.4_Missense_Mutation_p.G45D|MGAT1_ENST00000393340.3_Missense_Mutation_p.G45D|MGAT1_ENST00000333055.3_Missense_Mutation_p.G45D	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	45					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|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)			GGCGGGGTCGCCATCGAGAGC	0.677													T|||	81	0.0161741	0.0333	0.0029	5008	,	,		13792	0.001		0.0	False		,,,				2504	0.0348				p.G45D		Atlas-SNP	.											.	MGAT1	48	.	0			c.G134A						PASS	.	T	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	77,4251		0,77,2087	9.0	10.0	10.0		134,134,134,134,134	3.4	0.0	5	dbSNP_129	10	1,8491		0,1,4245	yes	missense,missense,missense,missense,missense	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	94,94,94,94,94	0,78,6332	TT,TC,CC		0.0118,1.7791,0.6084	benign,benign,benign,benign,benign	45/446,45/446,45/446,45/446,45/446	180219838	78,12742	2164	4246	6410	SO:0001583	missense	4245	exon3			GGGTCGCCATCGA	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.134G>A	5.37:g.180219838C>T	ENSP00000404718:p.Gly45Asp	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	0.001	-3.025352	0.00041	0.017791	1.18E-4	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865;ENST00000504671;ENST00000506889;ENST00000514283;ENST00000512695;ENST00000506269;ENST00000514438;ENST00000502678;ENST00000513431	D;D;D;D;D;D;D;D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63	4.71	3.41	0.39046	.	0.694372	0.14686	N	0.304491	T	0.44726	0.1307	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40346	-0.9568	10	0.08599	T	0.76	-8.3269	4.0209	0.09665	0.0:0.2398:0.1766:0.5835	.	45	P26572	MGAT1_HUMAN	D	45	ENSP00000332073:G45D;ENSP00000311888:G45D;ENSP00000404718:G45D;ENSP00000377010:G45D;ENSP00000402838:G45D;ENSP00000424891:G45D;ENSP00000425988:G45D;ENSP00000424382:G45D;ENSP00000427116:G45D;ENSP00000422906:G45D;ENSP00000421738:G45D;ENSP00000422588:G45D;ENSP00000423401:G45D	ENSP00000311888:G45D	G	-	2	0	MGAT1	180152444	0.000000	0.05858	0.020000	0.16555	0.026000	0.11368	0.260000	0.18424	0.282000	0.22254	-0.535000	0.04281	GGC	C|0.993;T|0.007	0.007	strong		0.677	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
DSPP	1834	hgsc.bcm.edu	37	4	88537243	88537243	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88537243C>A	ENST00000282478.7	+	4	3462	c.3429C>A	c.(3427-3429)gaC>gaA	p.D1143E	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1143E			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1143	Asp/Ser-rich.			D -> E (in Ref. 1; AAF42472). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D1143D(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgacagcagtgaca	0.562																																					p.D1143E		Atlas-SNP	.											DSPP,NS,carcinoma,0,6	DSPP	174	6	1	Substitution - coding silent(1)	stomach(1)	c.C3429A						scavenged	.						36.0	50.0	45.0					4																	88537243		1513	2785	4298	SO:0001583	missense	1834	exon5			CAGTGACAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3429C>A	4.37:g.88537243C>A	ENSP00000282478:p.Asp1143Glu	Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	237	26	0.109705	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	C	0.016	-1.530299	0.00951	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88201	-2.35;-2.35	1.37	-2.09	0.07232	.	0.760977	0.10684	N	0.646028	T	0.74313	0.3700	N	0.03608	-0.345	0.09310	N	1	D	0.58620	0.983	P	0.45406	0.479	T	0.68398	-0.5419	10	0.52906	T	0.07	-6.576	6.5853	0.22616	0.0:0.6688:0.0:0.3312	.	1143	Q9NZW4	DSPP_HUMAN	E	1143	ENSP00000382213:D1143E;ENSP00000282478:D1143E	ENSP00000282478:D1143E	D	+	3	2	DSPP	88756267	0.982000	0.34865	0.151000	0.22473	0.006000	0.05464	0.555000	0.23422	-0.845000	0.04179	-0.856000	0.03024	GAC	.	.	none		0.562	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ZNF469	84627	hgsc.bcm.edu	37	16	88500340	88500340	+	Silent	SNP	G	G	A	rs61472141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88500340G>A	ENST00000437464.1	+	2	6378	c.6378G>A	c.(6376-6378)ccG>ccA	p.P2126P	ZNF469_ENST00000565624.1_Silent_p.P2154P	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2126					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						CAGCATCTCCGTCCTGCAGGG	0.682													A|||	569	0.113618	0.3306	0.0432	5008	,	,		14726	0.0506		0.0318	False		,,,				2504	0.0194				p.P2126P		Atlas-SNP	.											.	ZNF469	121	.	0			c.G6378A						PASS	.						5.0	8.0	7.0					16																	88500340		669	1559	2228	SO:0001819	synonymous_variant	84627	exon2			ATCTCCGTCCTGC	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.6378G>A	16.37:g.88500340G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			G|0.896;A|0.104	0.104	strong		0.682	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
PCDHGB3	56102	hgsc.bcm.edu	37	5	140751128	140751128	+	Missense_Mutation	SNP	C	C	G	rs2240697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140751128C>G	ENST00000576222.1	+	1	1298	c.1167C>G	c.(1165-1167)aaC>aaG	p.N389K	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	389	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		N -> K (in dbSNP:rs2240697).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAAAAGGAAACTTCCCCTTTA	0.443													.|||	2801	0.559305	0.8994	0.6326	5008	,	,		21441	0.3274		0.4264	False		,,,				2504	0.4233				p.N389K		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.C1167G						PASS	.	G	,,,,,,,LYS/ASN,LYS/ASN	3221,629		1358,505,62	53.0	54.0	54.0		,,,,,,,1167,1167	-9.9	0.0	5	dbSNP_98	54	3580,4674		759,2062,1306	yes	intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032097.1	,,,,,,,94,94	2117,2567,1368	GG,GC,CC		43.3729,16.3377,43.812	,,,,,,,,	,,,,,,,389/930,389/815	140751128	6801,5303	1925	4127	6052	SO:0001583	missense	56102	exon1			AGGAAACTTCCCC	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1167C>G	5.37:g.140751128C>G	ENSP00000461862:p.Asn389Lys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_018924	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			C|0.477;G|0.523	0.523	strong		0.443	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
NOM1	64434	hgsc.bcm.edu	37	7	156754895	156754895	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:156754895C>T	ENST00000275820.3	+	5	1698	c.1683C>T	c.(1681-1683)cgC>cgT	p.R561R		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	561						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		ATGACATGCGCAAAATTCCAG	0.428																																					p.R561R		Atlas-SNP	.											NOM1,NS,carcinoma,+1,1	NOM1	73	1	0			c.C1683T						scavenged	.						205.0	203.0	204.0					7																	156754895		2203	4300	6503	SO:0001819	synonymous_variant	64434	exon5			CATGCGCAAAATT	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1683C>T	7.37:g.156754895C>T		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	220	4	0.0181818	NM_138400	Q96I08	Silent	SNP	ENST00000275820.3	37	CCDS34787.1																																																																																			.	.	none		0.428	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
ZSCAN31	64288	hgsc.bcm.edu	37	6	28297313	28297313	+	Missense_Mutation	SNP	T	T	A	rs853678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28297313T>A	ENST00000414429.1	-	6	1051	c.148A>T	c.(148-150)Act>Tct	p.T50S	ZSCAN31_ENST00000439158.1_Missense_Mutation_p.T50S|ZSCAN31_ENST00000396838.2_Missense_Mutation_p.T50S|ZSCAN31_ENST00000446474.1_Intron|ZSCAN31_ENST00000481934.1_5'Flank|ZSCAN31_ENST00000344279.6_Missense_Mutation_p.T50S			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	50	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.		T -> S (in dbSNP:rs853678).		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)										GGACCAGGAGTCTCTTGGTAA	0.522													T|||	901	0.179912	0.3585	0.1369	5008	,	,		16858	0.129		0.1193	False		,,,				2504	0.0838				p.T50S		Atlas-SNP	.											.	.	.	.	0			c.A148T						PASS	.	T	SER/THR,SER/THR,SER/THR,SER/THR	1478,2928	473.3+/-356.6	247,984,972	111.0	123.0	119.0		148,148,148,148	-1.0	0.4	6	dbSNP_86	119	1247,7353	249.2+/-276.5	92,1063,3145	yes	missense,missense,missense,missense	ZNF323	NM_001135215.1,NM_001135216.1,NM_030899.4,NM_145909.2	58,58,58,58	339,2047,4117	AA,AT,TT		14.5,33.5452,20.9519	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	50/407,50/407,50/407,50/407	28297313	2725,10281	2203	4300	6503	SO:0001583	missense	64288	exon2			CAGGAGTCTCTTG		CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"""-"", ""Zinc fingers, C2H2-type"""	14097	protein-coding gene	gene with protein product		610794	"""zinc finger protein 310 pseudogene"", ""zinc finger protein 323"""	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.148A>T	6.37:g.28297313T>A	ENSP00000390076:p.Thr50Ser	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	128	125	0.976562	NM_030899	Q6P178|Q8WWS5	Missense_Mutation	SNP	ENST00000414429.1	37	CCDS4649.1	377	0.17261904761904762	162	0.32926829268292684	50	0.13812154696132597	80	0.13986013986013987	85	0.11213720316622691	T	11.25	1.582386	0.28180	0.335452	0.145	ENSG00000235109	ENST00000396838;ENST00000439158;ENST00000414429;ENST00000344279;ENST00000453745;ENST00000439636;ENST00000447021;ENST00000426756;ENST00000446222;ENST00000434036	T;T;T;T;T;T;T;T;T;T	0.04083	3.71;3.71;3.71;3.71;3.71;3.71;3.71;3.71;3.71;3.71	4.56	-1.04	0.10068	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.00754	0.0025	N	0.20445	0.575	0.80722	P	0.0	B	0.20550	0.046	B	0.18263	0.021	T	0.48822	-0.9001	8	0.22109	T	0.4	.	0.5838	0.00716	0.261:0.1681:0.1338:0.437	rs853678;rs61109611;rs853678	50	Q96LW9	ZN323_HUMAN	S	50	ENSP00000380050:T50S;ENSP00000413705:T50S;ENSP00000390076:T50S;ENSP00000345339:T50S;ENSP00000389479:T50S;ENSP00000412519:T50S;ENSP00000416108:T50S;ENSP00000406376:T50S;ENSP00000411033:T50S;ENSP00000416225:T50S	ENSP00000345339:T50S	T	-	1	0	ZNF323	28405292	0.041000	0.20044	0.415000	0.26534	0.996000	0.88848	0.881000	0.28173	0.191000	0.20236	0.460000	0.39030	ACT	T|0.794;N|0.000	.	strong		0.522	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899	
ZNF106	64397	hgsc.bcm.edu	37	15	42742464	42742464	+	Missense_Mutation	SNP	A	A	G	rs12101559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42742464A>G	ENST00000263805.4	-	2	2263	c.1937T>C	c.(1936-1938)aTa>aCa	p.I646T	ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_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	646			I -> T (in dbSNP:rs12101559).		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)										CTGGCGAACTATGGGATTACA	0.458													G|||	1220	0.24361	0.4841	0.2824	5008	,	,		19882	0.1776		0.0229	False		,,,				2504	0.1861				p.I646T		Atlas-SNP	.											.	ZFP106	117	.	0			c.T1937C						PASS	.	G	THR/ILE	1748,2658	647.4+/-398.5	343,1062,798	173.0	181.0	178.0		1937	3.2	0.0	15	dbSNP_120	178	175,8423	811.3+/-407.1	2,171,4126	yes	missense	ZFP106	NM_022473.1	89	345,1233,4924	GG,GA,AA		2.0354,39.6732,14.7878	benign	646/1884	42742464	1923,11081	2203	4299	6502	SO:0001583	missense	64397	exon2			CGAACTATGGGAT	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.1937T>C	15.37:g.42742464A>G	ENSP00000263805:p.Ile646Thr	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	220	109	0.495455	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	396	0.1813186813186813	219	0.4451219512195122	74	0.20441988950276244	91	0.1590909090909091	12	0.0158311345646438	G	0	-2.595337	0.00125	0.396732	0.020354	ENSG00000103994	ENST00000263805	T	0.30981	1.51	5.14	3.25	0.37280	.	0.545725	0.18118	N	0.151131	T	0.00012	0.0000	N	0.00707	-1.245	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47886	-0.9082	9	0.02654	T	1	-0.1179	7.5802	0.27961	0.1429:0.0:0.7231:0.134	rs12101559;rs52834511;rs61504795;rs12101559	646	Q9H2Y7	ZF106_HUMAN	T	646	ENSP00000263805:I646T	ENSP00000263805:I646T	I	-	2	0	ZFP106	40529756	0.012000	0.17670	0.001000	0.08648	0.275000	0.26752	0.777000	0.26718	0.425000	0.26087	-0.128000	0.14901	ATA	A|0.833;G|0.167	0.167	strong		0.458	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
SSPO	23145	hgsc.bcm.edu	37	7	149486420	149486420	+	RNA	SNP	C	C	G	rs855693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149486420C>G	ENST00000378016.2	+	0	4396							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)			ACGCTGCCTGCCGCCGGCCCT	0.677													C|||	135	0.0269569	0.0976	0.0086	5008	,	,		16567	0.0		0.0	False		,,,				2504	0.0				p.P1466A		Atlas-SNP	.											.	.	.	.	0			c.C4396G						PASS	.	C		238,4158		9,220,1969	20.0	24.0	22.0		4400	4.6	1.0	7	dbSNP_86	22	4,8582		0,4,4289	yes	coding-notMod3	SSPO	NM_198455.2		9,224,6258	GG,GC,CC		0.0466,5.414,1.8641			149486420	242,12740	2198	4293	6491			23145	exon30			TGCCTGCCGCCGG	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.149486420C>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.979;G|0.021	0.021	strong		0.677	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
SMCO2	341346	hgsc.bcm.edu	37	12	27641465	27641465	+	Silent	SNP	A	A	G	rs76288777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27641465A>G	ENST00000535986.1	+	5	585	c.585A>G	c.(583-585)caA>caG	p.Q195Q	SMCO2_ENST00000538647.1_Intron|SMCO2_ENST00000298876.4_Silent_p.Q145Q|SMCO2_ENST00000416383.1_Silent_p.Q195Q			A6NFE2	SMCO2_HUMAN	single-pass membrane protein with coiled-coil domains 2	195						integral component of membrane (GO:0016021)											ACCTTGATCAAGGGACAAGCA	0.453													A|||	31	0.0061901	0.0219	0.0029	5008	,	,		16660	0.0		0.0	False		,,,				2504	0.0				p.Q195Q		Atlas-SNP	.											.	.	.	.	0			c.A585G						PASS	.	A		46,1338		0,46,646	59.0	59.0	59.0		585	1.9	0.0	12	dbSNP_132	59	1,3181		0,1,1590	no	coding-synonymous	C12orf70	NM_001145010.1		0,47,2236	GG,GA,AA		0.0314,3.3237,1.0293		195/344	27641465	47,4519	692	1591	2283	SO:0001819	synonymous_variant	0	exon6			TGATCAAGGGACA		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.585A>G	12.37:g.27641465A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_001145010		Silent	SNP	ENST00000535986.1	37	CCDS44852.1																																																																																			A|0.993;G|0.007	0.007	strong		0.453	SMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402867.1	NM_001145010	
LRP1	4035	hgsc.bcm.edu	37	12	57603647	57603647	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57603647C>T	ENST00000243077.3	+	80	12901	c.12435C>T	c.(12433-12435)ccC>ccT	p.P4145P		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4145					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)	p.P4145P(1)		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)	ACAAGCAGCCCGAAGGTGGGG	0.632																																					p.P4145P		Atlas-SNP	.											LRP1,bladder,carcinoma,0,1	LRP1	428	1	1	Substitution - coding silent(1)	urinary_tract(1)	c.C12435T						PASS	.						35.0	37.0	36.0					12																	57603647		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon80			GCAGCCCGAAGGT	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.12435C>T	12.37:g.57603647C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			.	.	none		0.632	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18955744	18955744	+	Silent	SNP	C	C	T	rs11599929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	159	101	0.63522	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	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5146395	5146395	+	Missense_Mutation	SNP	A	A	G	rs1863968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:5146395A>G	ENST00000274181.7	+	3	466	c.328A>G	c.(328-330)Atg>Gtg	p.M110V	ADAMTS16_ENST00000511368.1_Missense_Mutation_p.M110V|CTD-2297D10.1_ENST00000514848.1_RNA	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	110			M -> V (in dbSNP:rs1863968).		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						CGACTTCCACATGGATCTGAG	0.552													A|||	2418	0.482827	0.3525	0.4035	5008	,	,		17901	0.4286		0.6133	False		,,,				2504	0.637				p.M110V		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.A328G						PASS	.	A	VAL/MET	1651,2329		349,953,688	78.0	80.0	79.0		328	-11.5	0.5	5	dbSNP_92	79	5137,3181		1597,1943,619	yes	missense	ADAMTS16	NM_139056.2	21	1946,2896,1307	GG,GA,AA		38.2424,41.4824,44.804	benign	110/1225	5146395	6788,5510	1990	4159	6149	SO:0001583	missense	170690	exon3			TTCCACATGGATC	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.328A>G	5.37:g.5146395A>G	ENSP00000274181:p.Met110Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	1012	0.4633699633699634	168	0.34146341463414637	165	0.4558011049723757	226	0.3951048951048951	453	0.5976253298153035	A	9.286	1.049358	0.19827	0.414824	0.617576	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	T;T	0.05199	3.48;3.48	5.74	-11.5	0.00074	Peptidase M12B, propeptide (1);	0.379381	0.26955	N	0.021648	T	0.00012	0.0000	L	0.45137	1.4	0.46823	P	7.869999999999822E-4	B;B;B	0.12013	0.005;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.001	T	0.48559	-0.9025	9	0.66056	D	0.02	.	8.248	0.31700	0.1265:0.6005:0.1182:0.1548	rs1863968;rs16874855;rs52809911;rs59226841;rs1863968	110;110;110	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	V	110	ENSP00000274181:M110V;ENSP00000421631:M110V	ENSP00000274181:M110V	M	+	1	0	ADAMTS16	5199395	0.006000	0.16342	0.517000	0.27799	0.205000	0.24178	-1.137000	0.03219	-2.247000	0.00703	-0.400000	0.06385	ATG	G|0.499;N|0.001	0.499	strong		0.552	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
OR13D1	286365	hgsc.bcm.edu	37	9	107457275	107457275	+	Missense_Mutation	SNP	A	A	C	rs10820709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107457275A>C	ENST00000318763.5	+	1	616	c.573A>C	c.(571-573)caA>caC	p.Q191H		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	191			Q -> H (in dbSNP:rs10820709). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						CCCTATTGCAAACAGTTCTGA	0.428													A|||	2439	0.487021	0.6778	0.4827	5008	,	,		22591	0.505		0.3151	False		,,,				2504	0.3906				p.Q191H		Atlas-SNP	.											.	OR13D1	42	.	0			c.A573C						PASS	.	A	HIS/GLN	2788,1618	664.0+/-401.3	887,1014,302	164.0	147.0	153.0		573	-0.5	0.2	9	dbSNP_120	153	2602,5998	420.9+/-353.5	407,1788,2105	no	missense	OR13D1	NM_001004484.1	24	1294,2802,2407	CC,CA,AA		30.2558,36.7227,41.4424	probably-damaging	191/347	107457275	5390,7616	2203	4300	6503	SO:0001583	missense	286365	exon1			ATTGCAAACAGTT		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"""GPCR / Class A : Olfactory receptors"""	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.573A>C	9.37:g.107457275A>C	ENSP00000317357:p.Gln191His	Somatic	331	1	0.00302115		WXS	Illumina HiSeq	Phase_I	344	109	0.31686	NM_001004484	B9EIS1|Q6IFL1	Missense_Mutation	SNP	ENST00000318763.5	37	CCDS35094.1	1006	0.4606227106227106	313	0.6361788617886179	155	0.4281767955801105	289	0.5052447552447552	249	0.32849604221635886	A	2.797	-0.249970	0.05867	0.632773	0.302558	ENSG00000179055	ENST00000318763	T	0.00019	9.06	3.87	-0.483	0.12075	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000142	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.21147	0.052	B	0.27887	0.084	T	0.40346	-0.9568	9	0.35671	T	0.21	.	4.6636	0.12655	0.6395:0.162:0.1985:0.0	rs10820709;rs10820709	191	Q8NGV5	O13D1_HUMAN	H	191	ENSP00000317357:Q191H	ENSP00000317357:Q191H	Q	+	3	2	OR13D1	106497096	0.000000	0.05858	0.150000	0.22450	0.078000	0.17371	-0.772000	0.04694	0.074000	0.16767	0.418000	0.28097	CAA	A|0.560;C|0.440	0.440	strong		0.428	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
INTU	27152	hgsc.bcm.edu	37	4	128565000	128565000	+	Silent	SNP	A	A	G	rs3749507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:128565000A>G	ENST00000335251.6	+	2	574	c.471A>G	c.(469-471)cgA>cgG	p.R157R	INTU_ENST00000296461.5_Silent_p.R157R	NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	157					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						TCCAACAGCGATACAAAGATG	0.398													G|||	3087	0.616414	0.6725	0.5778	5008	,	,		21138	0.5506		0.5368	False		,,,				2504	0.7178				p.R157R		Atlas-SNP	.											INTU,NS,carcinoma,+1,1	INTU	92	1	0			c.A471G						PASS	.	G		2821,1585	492.4+/-362.4	897,1027,279	96.0	95.0	95.0		471	0.6	0.2	4	dbSNP_107	95	4515,4085	561.9+/-387.9	1189,2137,974	no	coding-synonymous	INTU	NM_015693.3		2086,3164,1253	GG,GA,AA		47.5,35.9737,43.5953		157/943	128565000	7336,5670	2203	4300	6503	SO:0001819	synonymous_variant	27152	exon2			ACAGCGATACAAA	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"""PDZ domain containing 6"", ""inturned planar cell polarity effector homolog (Drosophila)"""	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.471A>G	4.37:g.128565000A>G		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	295	150	0.508475	NM_015693	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Silent	SNP	ENST00000335251.6	37	CCDS34061.1																																																																																			A|0.427;G|0.573	0.573	strong		0.398	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707	
RBM19	9904	hgsc.bcm.edu	37	12	114377835	114377835	+	Missense_Mutation	SNP	A	A	G	rs2290788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114377835A>G	ENST00000545145.2	-	15	1946	c.1868T>C	c.(1867-1869)aTc>aCc	p.I623T	RBM19_ENST00000392561.3_Missense_Mutation_p.I623T|RBM19_ENST00000261741.5_Missense_Mutation_p.I623T|RP11-780K2.1_ENST00000550206.1_RNA	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	623	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.		I -> T (in dbSNP:rs2290788). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GATGGCAGTGATTCCGCCCTC	0.642													A|||	965	0.192692	0.3245	0.0735	5008	,	,		16454	0.1885		0.1133	False		,,,				2504	0.1851				p.I623T		Atlas-SNP	.											.	RBM19	117	.	0			c.T1868C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE	1342,3064	436.1+/-344.5	224,894,1085	54.0	60.0	58.0		1868,1868,1868	3.1	0.7	12	dbSNP_100	58	888,7712	196.3+/-241.3	39,810,3451	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	89,89,89	263,1704,4536	GG,GA,AA		10.3256,30.4585,17.1459	benign,benign,benign	623/961,623/961,623/961	114377835	2230,10776	2203	4300	6503	SO:0001583	missense	9904	exon15			GCAGTGATTCCGC	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1868T>C	12.37:g.114377835A>G	ENSP00000442053:p.Ile623Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	351	0.16071428571428573	137	0.2784552845528455	26	0.0718232044198895	102	0.17832167832167833	86	0.11345646437994723	A	12.45	1.941992	0.34283	0.304585	0.103256	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.06608	3.28;3.28;3.28	4.3	3.08	0.35506	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.262265	0.37219	N	0.002186	T	0.00012	0.0000	N	0.10645	0.015	0.21915	P	0.999477564	B	0.20261	0.043	B	0.36808	0.233	T	0.44390	-0.9331	9	0.02654	T	1	-12.7717	10.0478	0.42197	0.8499:0.0:0.0:0.1501	rs2290788;rs17849835;rs17857860;rs2290788	623	Q9Y4C8	RBM19_HUMAN	T	623	ENSP00000442053:I623T;ENSP00000376344:I623T;ENSP00000261741:I623T	ENSP00000261741:I623T	I	-	2	0	RBM19	112862218	1.000000	0.71417	0.693000	0.30195	0.561000	0.35649	8.500000	0.90498	1.600000	0.50102	0.459000	0.35465	ATC	A|0.832;G|0.168	0.168	strong		0.642	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
DNAH6	1768	hgsc.bcm.edu	37	2	84921433	84921433	+	Silent	SNP	A	A	G	rs1192295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:84921433A>G	ENST00000237449.6	+	45	7361	c.7353A>G	c.(7351-7353)acA>acG	p.T2451T	DNAH6_ENST00000602588.1_Silent_p.T423T|DNAH6_ENST00000398278.2_Silent_p.T2402T|DNAH6_ENST00000389394.3_Silent_p.T2451T			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2451	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TAGGAGGCACAGGAAAGCAGT	0.443													A|||	498	0.0994409	0.2602	0.0432	5008	,	,		21203	0.002		0.0646	False		,,,				2504	0.0583				p.T2451T		Atlas-SNP	.											.	DNAH6	194	.	0			c.A7353G						PASS	.	A		306,1078		31,244,417	153.0	136.0	141.0		7353	-6.6	0.9	2	dbSNP_87	141	173,3009		4,165,1422	no	coding-synonymous	DNAH6	NM_001370.1		35,409,1839	GG,GA,AA		5.4368,22.1098,10.4906		2451/4159	84921433	479,4087	692	1591	2283	SO:0001819	synonymous_variant	1768	exon46			AGGCACAGGAAAG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7353A>G	2.37:g.84921433A>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	176	78	0.443182	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			A|0.904;G|0.096	0.096	strong		0.443	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
IRF2	3660	hgsc.bcm.edu	37	4	185310218	185310218	+	Silent	SNP	C	C	T	rs1131553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:185310218C>T	ENST00000393593.3	-	9	951	c.744G>A	c.(742-744)ggG>ggA	p.G248G		NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	248					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G248G(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		AGTGTGGCCGCCCCTTTCAAG	0.498													C|||	2119	0.423123	0.3548	0.5245	5008	,	,		20139	0.4216		0.3598	False		,,,				2504	0.5102				p.G248G		Atlas-SNP	.											IRF2,NS,carcinoma,0,1	IRF2	53	1	1	Substitution - coding silent(1)	stomach(1)	c.G744A						PASS	.	C		1525,2881	483.3+/-359.7	262,1001,940	129.0	111.0	117.0		744	-4.0	0.9	4	dbSNP_107	117	3376,5224	500.1+/-375.1	677,2022,1601	no	coding-synonymous	IRF2	NM_002199.3		939,3023,2541	TT,TC,CC		39.2558,34.6119,37.6826		248/350	185310218	4901,8105	2203	4300	6503	SO:0001819	synonymous_variant	3660	exon9			TGGCCGCCCCTTT		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.744G>A	4.37:g.185310218C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	168	87	0.517857	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Silent	SNP	ENST00000393593.3	37	CCDS3835.1	869	0.39789377289377287	184	0.37398373983739835	192	0.5303867403314917	211	0.3688811188811189	282	0.3720316622691293	C	4.681	0.126624	0.08931	0.346119	0.392558	ENSG00000168310	ENST00000505067	.	.	.	5.31	-4.03	0.04021	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999610463	.	.	.	.	.	.	T	0.48151	-0.9060	3	.	.	.	.	1.1333	0.01749	0.3733:0.1003:0.2741:0.2523	rs3775543;rs17417214;rs3775543	.	.	.	T	182	.	.	A	-	1	0	IRF2	185547212	0.073000	0.21202	0.901000	0.35422	0.846000	0.48090	-1.266000	0.02842	-0.699000	0.05077	-0.324000	0.08512	GCG	C|0.617;T|0.383	0.383	strong		0.498	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1		
FREM2	341640	hgsc.bcm.edu	37	13	39343822	39343822	+	Missense_Mutation	SNP	C	C	T	rs9603422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39343822C>T	ENST00000280481.7	+	4	5734	c.5518C>T	c.(5518-5520)Cgg>Tgg	p.R1840W		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1840	Calx-beta 1.		R -> W (in dbSNP:rs9603422).		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)		ATGGCGAGTGCGGATCCTGAG	0.542													C|||	710	0.141773	0.2057	0.0591	5008	,	,		14813	0.1617		0.1143	False		,,,				2504	0.1217				p.R1840W		Atlas-SNP	.											.	FREM2	385	.	0			c.C5518T						PASS	.	C	TRP/ARG	949,3457	358.9+/-314.6	100,749,1354	131.0	108.0	116.0		5518	3.3	0.2	13	dbSNP_119	116	1040,7560	220.9+/-258.5	60,920,3320	yes	missense	FREM2	NM_207361.4	101	160,1669,4674	TT,TC,CC		12.093,21.5388,15.2929	probably-damaging	1840/3170	39343822	1989,11017	2203	4300	6503	SO:0001583	missense	341640	exon4			CGAGTGCGGATCC	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.5518C>T	13.37:g.39343822C>T	ENSP00000280481:p.Arg1840Trp	Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	256	107	0.417969	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	312	0.14285714285714285	112	0.22764227642276422	24	0.06629834254143646	84	0.14685314685314685	92	0.12137203166226913	C	11.76	1.735572	0.30774	0.215388	0.12093	ENSG00000150893	ENST00000280481	T	0.30981	1.51	5.01	3.29	0.37713	Na-Ca exchanger/integrin-beta4 (2);	0.065177	0.64402	D	0.000008	T	0.00039	0.0001	M	0.87180	2.865	0.19300	P	0.9999752728	D	0.89917	1.0	D	0.76575	0.988	T	0.04440	-1.0951	9	0.38643	T	0.18	.	8.4587	0.32915	0.2741:0.6538:0.0:0.0721	rs9603422;rs52793831;rs9603422	1840	Q5SZK8	FREM2_HUMAN	W	1840	ENSP00000280481:R1840W	ENSP00000280481:R1840W	R	+	1	2	FREM2	38241822	0.972000	0.33761	0.160000	0.22671	0.035000	0.12851	0.845000	0.27668	0.538000	0.28769	-0.942000	0.02676	CGG	C|0.848;T|0.152	0.152	strong		0.542	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
ABCG4	64137	hgsc.bcm.edu	37	11	119027691	119027691	+	Missense_Mutation	SNP	C	C	G	rs12271907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119027691C>G	ENST00000449422.2	+	9	1223	c.1035C>G	c.(1033-1035)aaC>aaG	p.N345K	ABCG4_ENST00000531739.1_Missense_Mutation_p.N345K|ABCG4_ENST00000307417.3_Missense_Mutation_p.N345K|AP002956.1_ENST00000599663.1_Intron	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	345					cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	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)		CTGAGAAGAACGAGGTCCCTG	0.607													C|||	379	0.0756789	0.2685	0.0331	5008	,	,		22013	0.0		0.001	False		,,,				2504	0.0				p.N345K		Atlas-SNP	.											.	ABCG4	77	.	0			c.C1035G						PASS	.	C	LYS/ASN,LYS/ASN	977,3423	367.3+/-318.2	117,743,1340	169.0	155.0	159.0		1035,1035	-11.3	0.0	11	dbSNP_120	159	7,8583	4.3+/-15.6	0,7,4288	yes	missense,missense	ABCG4	NM_001142505.1,NM_022169.4	94,94	117,750,5628	GG,GC,CC		0.0815,22.2045,7.5751	benign,benign	345/647,345/647	119027691	984,12006	2200	4295	6495	SO:0001583	missense	64137	exon9			GAAGAACGAGGTC	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1035C>G	11.37:g.119027691C>G	ENSP00000406874:p.Asn345Lys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	49	29	0.591837	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	37	CCDS8415.1	162	0.07417582417582418	154	0.3130081300813008	8	0.022099447513812154	0	0.0	0	0.0	C	9.694	1.152791	0.21371	0.222045	8.15E-4	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739;ENST00000534402	D;D;D;T	0.86562	-2.14;-2.14;-2.14;0.92	5.65	-11.3	0.00108	.	0.718923	0.14549	N	0.312774	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.22604	0.072	B	0.20577	0.03	T	0.08493	-1.0719	9	0.06365	T	0.9	-5.4059	11.0626	0.47957	0.0:0.2915:0.2915:0.4171	rs12271907;rs12271907	345	Q9H172	ABCG4_HUMAN	K	345;345;345;23	ENSP00000304111:N345K;ENSP00000406874:N345K;ENSP00000434318:N345K;ENSP00000434571:N23K	ENSP00000304111:N345K	N	+	3	2	ABCG4	118532901	0.002000	0.14202	0.001000	0.08648	0.350000	0.29205	-2.018000	0.01444	-3.564000	0.00140	-1.778000	0.00651	AAC	C|0.928;G|0.072;T|0.000	0.072	strong		0.607	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
ROGDI	79641	hgsc.bcm.edu	37	16	4847976	4847976	+	Missense_Mutation	SNP	C	C	T	rs546063670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4847976C>T	ENST00000322048.7	-	9	1036	c.658G>A	c.(658-660)Gct>Act	p.A220T	RP11-127I20.5_ENST00000592465.1_RNA|ROGDI_ENST00000586336.1_5'UTR	NM_024589.2	NP_078865.1	Q9GZN7	ROGDI_HUMAN	rogdi homolog (Drosophila)	220					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	intracellular (GO:0005622)|nucleus (GO:0005634)				endometrium(2)|lung(1)|ovary(1)|skin(1)	5						GCGCCCCCAGCTGGGCGGAAG	0.701													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17557	0.0		0.0	False		,,,				2504	0.0				p.A220T		Atlas-SNP	.											.	ROGDI	11	.	0			c.G658A						PASS	.						27.0	29.0	28.0					16																	4847976		2197	4299	6496	SO:0001583	missense	79641	exon9			CCCCAGCTGGGCG	AK026039	CCDS10523.1	16p13.3	2014-09-17			ENSG00000067836	ENSG00000067836			29478	protein-coding gene	gene with protein product		614574				11230166	Standard	NM_024589		Approved	FLJ22386	uc002cxv.4	Q9GZN7	OTTHUMG00000129479	ENST00000322048.7:c.658G>A	16.37:g.4847976C>T	ENSP00000322832:p.Ala220Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	148	87	0.587838	NM_024589	Q6IA00	Missense_Mutation	SNP	ENST00000322048.7	37	CCDS10523.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.396518	0.25205	.	.	ENSG00000067836	ENST00000322048	T	0.42900	0.96	5.11	0.509	0.16977	.	0.114933	0.64402	D	0.000019	T	0.23249	0.0562	N	0.22421	0.69	0.28464	N	0.915729	B	0.13145	0.007	B	0.19148	0.024	T	0.18555	-1.0333	10	0.18276	T	0.48	-10.8216	7.925	0.29870	0.5389:0.3846:0.0:0.0765	.	220	Q9GZN7	ROGDI_HUMAN	T	220	ENSP00000322832:A220T	ENSP00000322832:A220T	A	-	1	0	ROGDI	4787977	0.000000	0.05858	0.178000	0.23040	0.322000	0.28314	-0.231000	0.09069	0.147000	0.19030	0.561000	0.74099	GCT	.	.	none		0.701	ROGDI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251643.3	NM_024589	
OR2C3	81472	hgsc.bcm.edu	37	1	247695427	247695427	+	Missense_Mutation	SNP	C	C	G	rs34220133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247695427C>G	ENST00000366487.3	-	2	748	c.387G>C	c.(385-387)agG>agC	p.R129S	GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000531662.1_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000527084.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	129			R -> S (in dbSNP:rs34220133).			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)			AATGGAGTGGCCTGCAGATGG	0.592													C|||	346	0.0690895	0.0333	0.0504	5008	,	,		21239	0.002		0.1372	False		,,,				2504	0.1299				p.R129S		Atlas-SNP	.											OR2C3,NS,carcinoma,0,1	OR2C3	92	1	0			c.G387C						PASS	.	C	SER/ARG	219,4187	134.5+/-170.7	6,207,1990	66.0	68.0	67.0		387	2.0	0.9	1	dbSNP_126	67	1411,7189	271.1+/-289.3	117,1177,3006	yes	missense	OR2C3	NM_198074.4	110	123,1384,4996	GG,GC,CC		16.407,4.9705,12.5327	probably-damaging	129/321	247695427	1630,11376	2203	4300	6503	SO:0001583	missense	81472	exon2			GAGTGGCCTGCAG	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.387G>C	1.37:g.247695427C>G	ENSP00000355443:p.Arg129Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	116	46	0.396552	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Missense_Mutation	SNP	ENST00000366487.3	37	CCDS1634.2	143	0.06547619047619048	12	0.024390243902439025	25	0.06906077348066299	2	0.0034965034965034965	104	0.13720316622691292	C	17.27	3.347422	0.61183	0.049705	0.16407	ENSG00000196242	ENST00000366487	T	0.01304	5.03	3.89	2.0	0.26442	GPCR, rhodopsin-like superfamily (1);	0.430133	0.16469	U	0.213067	T	0.00012	0.0000	L	0.46157	1.445	0.42774	P	0.0061550000000000216	B	0.33694	0.421	B	0.28139	0.086	T	0.47394	-0.9121	9	0.87932	D	0	.	7.8991	0.29723	0.0:0.7916:0.0:0.2084	rs34220133	129	Q8N628	OR2C3_HUMAN	S	129	ENSP00000355443:R129S	ENSP00000355443:R129S	R	-	3	2	OR2C3	245762050	0.000000	0.05858	0.853000	0.33588	0.950000	0.60333	-2.208000	0.01229	0.418000	0.25898	0.650000	0.86243	AGG	C|0.891;G|0.109	0.109	strong		0.592	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074	
NDUFAF5	79133	hgsc.bcm.edu	37	20	13797179	13797179	+	Silent	SNP	G	G	A	rs34901599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:13797179G>A	ENST00000378106.5	+	9	968	c.849G>A	c.(847-849)gcG>gcA	p.A283A	NDUFAF5_ENST00000475968.1_3'UTR|NDUFAF5_ENST00000463598.1_Silent_p.A255A	NM_024120.4	NP_077025.2	Q5TEU4	NDUF5_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	283					mitochondrial respiratory chain complex I assembly (GO:0032981)	extrinsic component of mitochondrial inner membrane (GO:0031314)	methyltransferase activity (GO:0008168)										TGGCAGCTGCGGCAGTGTACA	0.493													G|||	228	0.0455272	0.1619	0.0101	5008	,	,		17420	0.0		0.007	False		,,,				2504	0.0				p.A283A		Atlas-SNP	.											.	.	.	.	0			c.G849A						PASS	.	G	,	560,3846	249.0+/-256.6	25,510,1668	114.0	98.0	104.0		765,849	-11.2	0.0	20	dbSNP_126	104	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous,coding-synonymous	C20orf7	NM_001039375.2,NM_024120.4	,	25,520,5958	AA,AG,GG		0.1163,12.7099,4.3826	,	255/318,283/346	13797179	570,12436	2203	4300	6503	SO:0001819	synonymous_variant	79133	exon9			AGCTGCGGCAGTG		CCDS13118.1, CCDS33441.1	20p12.1	2012-10-12	2012-05-08	2012-05-08	ENSG00000101247	ENSG00000101247		"""Mitochondrial respiratory chain complex assembly factors"""	15899	protein-coding gene	gene with protein product		612360	"""chromosome 20 open reading frame 7"""	C20orf7		18940309, 21607760	Standard	NM_024120		Approved	dJ842G6.1	uc002wom.3	Q5TEU4	OTTHUMG00000031909	ENST00000378106.5:c.849G>A	20.37:g.13797179G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_024120	A8K166|Q6GPH3|Q9H6F4	Silent	SNP	ENST00000378106.5	37	CCDS13118.1																																																																																			G|0.960;A|0.040	0.040	strong		0.493	NDUFAF5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078057.2	NM_001039375	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32714083	32714083	+	Missense_Mutation	SNP	T	T	C	rs9276436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32714083T>C	ENST00000374940.3	+	4	782	c.680T>C	c.(679-681)gTg>gCg	p.V227A		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	227			V -> A (in dbSNP:rs9276436). {ECO:0000269|PubMed:14574404}.		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)"""	GGGTTGTCTGTGGGCCTCATG	0.547													.|||	548	0.109425	0.2693	0.147	5008	,	,		21943	0.002		0.0815	False		,,,				2504	0.0061				p.V227A		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.T680C						PASS	.	C	ALA/VAL	724,2298		79,566,866	163.0	161.0	162.0		680	0.5	0.2	6	dbSNP_118	162	422,4996		14,394,2301	no	missense	HLA-DQA2	NM_020056.4	64	93,960,3167	CC,CT,TT		7.7889,23.9576,13.5782	benign	227/256	32714083	1146,7294	1511	2709	4220	SO:0001583	missense	3118	exon4			TGTCTGTGGGCCT		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.680T>C	6.37:g.32714083T>C	ENSP00000364076:p.Val227Ala	Somatic	611	0	0		WXS	Illumina HiSeq	Phase_I	690	306	0.443478	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	231	0.10576923076923077	128	0.2601626016260163	54	0.14917127071823205	2	0.0034965034965034965	47	0.06200527704485488	.	2.795	-0.250545	0.05867	0.239576	0.077889	ENSG00000237541	ENST00000374940	T	0.02140	4.43	3.06	0.523	0.17060	.	1.014970	0.07913	U	0.974554	T	0.01835	0.0058	M	0.88181	2.935	0.54753	P	1.2000000000012001E-5	B	0.12013	0.005	B	0.17979	0.02	T	0.27872	-1.0061	9	0.66056	D	0.02	.	6.2586	0.20887	0.0:0.1701:0.0:0.8299	rs9276436;rs17213358;rs17219757;rs9276436	227	P01906	DQA2_HUMAN	A	227	ENSP00000364076:V227A	ENSP00000364076:V227A	V	+	2	0	HLA-DQA2	32822061	0.686000	0.27661	0.177000	0.23020	0.027000	0.11550	0.916000	0.28651	-0.031000	0.13781	-3.317000	0.00044	GTG	T|0.882;C|0.118	0.118	strong		0.547	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
ZDHHC11	79844	hgsc.bcm.edu	37	5	825286	825286	+	Missense_Mutation	SNP	G	G	T	rs2335585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:825286G>T	ENST00000283441.8	-	8	1399	c.1016C>A	c.(1015-1017)aCg>aAg	p.T339K	ZDHHC11_ENST00000424784.2_Missense_Mutation_p.T339K|ZDHHC11_ENST00000503758.2_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	339						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			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)			TACCCGTGCCGTCGAATCCCC	0.547																																					p.T339K		Atlas-SNP	.											ZDHHC11_ENST00000424784,NS,carcinoma,0,2	ZDHHC11	97	2	0			c.C1016A						PASS	.	G	LYS/THR	49,4357		0,49,2154	175.0	127.0	143.0		1016	0.1	0.0	5	dbSNP_100	143	124,8468		2,120,4174	yes	missense	ZDHHC11	NM_024786.2	78	2,169,6328	TT,TG,GG		1.4432,1.1121,1.331	benign	339/413	825286	173,12825	2203	4296	6499	SO:0001583	missense	79844	exon8			CGTGCCGTCGAAT	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.1016C>A	5.37:g.825286G>T	ENSP00000283441:p.Thr339Lys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	226	41	0.181416	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	N	1.645	-0.515441	0.04200	0.011121	0.014432	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.27104	1.69;1.69	0.131	0.131	0.14755	.	.	.	.	.	T	0.06462	0.0166	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36841	-0.9731	8	0.06099	T	0.92	.	.	.	.	rs2335585;rs16900451;rs52807118;rs59749811;rs2335585	339	Q9H8X9	ZDH11_HUMAN	K	339	ENSP00000397719:T339K;ENSP00000283441:T339K	ENSP00000283441:T339K	T	-	2	0	ZDHHC11	878286	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	0.529000	0.23019	0.171000	0.19730	0.174000	0.16983	ACG	G|0.985;T|0.015	0.015	strong		0.547	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
CTSB	1508	hgsc.bcm.edu	37	8	11710174	11710174	+	Missense_Mutation	SNP	T	T	C	rs1803250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11710174T>C	ENST00000353047.6	-	3	410	c.157A>G	c.(157-159)Agc>Ggc	p.S53G	CTSB_ENST00000453527.2_Missense_Mutation_p.S53G|CTSB_ENST00000345125.3_Missense_Mutation_p.S53G|CTSB_ENST00000531089.1_Missense_Mutation_p.S53G|CTSB_ENST00000533455.1_Missense_Mutation_p.S53G|CTSB_ENST00000434271.1_Missense_Mutation_p.S53G|CTSB_ENST00000525076.1_5'UTR|CTSB_ENST00000415599.2_Missense_Mutation_p.S53G|CTSB_ENST00000534510.1_Missense_Mutation_p.S53G|CTSB_ENST00000530640.2_Missense_Mutation_p.S53G	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	53			S -> G (in dbSNP:rs1803250). {ECO:0000269|PubMed:15489334}.		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)			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)		TTCAAGTAGCTCATGTCCACG	0.612													T|||	288	0.057508	0.0325	0.0879	5008	,	,		17881	0.0		0.1511	False		,,,				2504	0.0327				p.S53G		Atlas-SNP	.											.	CTSB	24	.	0			c.A157G						PASS	.	T	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	219,4187	131.0+/-167.6	6,207,1990	139.0	106.0	117.0		157,157,157,157,157	5.8	1.0	8	dbSNP_89	117	1196,7404	242.5+/-272.5	87,1022,3191	yes	missense,missense,missense,missense,missense	CTSB	NM_001908.3,NM_147780.2,NM_147781.2,NM_147782.2,NM_147783.2	56,56,56,56,56	93,1229,5181	CC,CT,TT		13.907,4.9705,10.8796	benign,benign,benign,benign,benign	53/340,53/340,53/340,53/340,53/340	11710174	1415,11591	2203	4300	6503	SO:0001583	missense	1508	exon5			AGTAGCTCATGTC	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.157A>G	8.37:g.11710174T>C	ENSP00000345672:p.Ser53Gly	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_147780	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	176	0.08058608058608059	21	0.042682926829268296	36	0.09944751381215469	0	0.0	119	0.15699208443271767	T	13.56	2.272847	0.40194	0.049705	0.13907	ENSG00000164733	ENST00000434271;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000415599;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000534636;ENST00000533572;ENST00000530296;ENST00000526195;ENST00000527243;ENST00000534149;ENST00000526645;ENST00000530573;ENST00000505496;ENST00000524500;ENST00000531502;ENST00000527215;ENST00000532656;ENST00000534382;ENST00000528965	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34	5.85	5.85	0.93711	Peptidase C1A, propeptide (1);	0.071971	0.85682	D	0.000000	T	0.00144	0.0004	L	0.47190	1.495	0.22034	P	0.999404319	B	0.21753	0.06	B	0.15052	0.012	T	0.05666	-1.0871	9	0.38643	T	0.18	.	11.4166	0.49956	0.0:0.0:0.1508:0.8492	rs1803250;rs2230068;rs11548598;rs17757721;rs17855418;rs52837364;rs61727982	53	P07858	CATB_HUMAN	G	53	ENSP00000415889:S53G;ENSP00000345672:S53G;ENSP00000435105:S53G;ENSP00000433215:S53G;ENSP00000409917:S53G;ENSP00000411254:S53G;ENSP00000342070:S53G;ENSP00000432244:S53G;ENSP00000434217:S53G;ENSP00000436159:S53G;ENSP00000433995:S53G;ENSP00000435074:S53G;ENSP00000436627:S53G;ENSP00000434725:S53G;ENSP00000436122:S53G;ENSP00000431518:S53G;ENSP00000435650:S53G;ENSP00000436074:S53G;ENSP00000435886:S53G;ENSP00000431143:S53G;ENSP00000435260:S53G;ENSP00000433929:S53G	ENSP00000342070:S53G	S	-	1	0	CTSB	11747583	1.000000	0.71417	0.994000	0.49952	0.560000	0.35617	3.402000	0.52608	2.233000	0.73108	0.533000	0.62120	AGC	T|0.896;C|0.103;A|0.000	0.103	strong		0.612	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780	
SGIP1	84251	hgsc.bcm.edu	37	1	67105495	67105495	+	Silent	SNP	G	G	A	rs187876611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:67105495G>A	ENST00000371037.4	+	5	284	c.207G>A	c.(205-207)gcG>gcA	p.A69A	SGIP1_ENST00000371035.3_Intron|SGIP1_ENST00000371036.3_Silent_p.A44A|SGIP1_ENST00000468286.1_3'UTR|SGIP1_ENST00000237247.6_Silent_p.A73A|SGIP1_ENST00000371039.1_Silent_p.A45A	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	69					endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021)	AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	71						GATTTTATGCGGAAATTGATT	0.299													G|||	5	0.000998403	0.0	0.0	5008	,	,		19033	0.005		0.0	False		,,,				2504	0.0				p.A69A		Atlas-SNP	.											SGIP1_ENST00000371039,right_upper_lobe,carcinoma,+2,2	SGIP1	272	2	0			c.G207A						scavenged	.	G		0,4406		0,0,2203	92.0	93.0	93.0		207	-6.7	0.9	1		93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SGIP1	NM_032291.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		69/829	67105495	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	84251	exon5			TTATGCGGAAATT	AL136561	CCDS30744.1	1p31.3	2008-02-05			ENSG00000118473	ENSG00000118473			25412	protein-coding gene	gene with protein product		611540				11230166	Standard	NM_032291		Approved	DKFZp761D221	uc001dcr.3	Q9BQI5	OTTHUMG00000009161	ENST00000371037.4:c.207G>A	1.37:g.67105495G>A		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	274	4	0.0145985	NM_032291	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Silent	SNP	ENST00000371037.4	37	CCDS30744.1																																																																																			G|0.998;A|0.002	0.002	strong		0.299	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291	
TSHZ2	128553	hgsc.bcm.edu	37	20	51872038	51872038	+	Missense_Mutation	SNP	G	G	A	rs6097319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:51872038G>A	ENST00000371497.5	+	2	2928	c.2041G>A	c.(2041-2043)Gcc>Acc	p.A681T	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000603338.2_Missense_Mutation_p.A678T|TSHZ2_ENST00000329613.6_Missense_Mutation_p.A678T	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	681			A -> T (in dbSNP:rs6097319).		multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			CAATGGGTGCGCCCTCGCCAA	0.637													G|||	308	0.0615016	0.2231	0.013	5008	,	,		16470	0.0		0.004	False		,,,				2504	0.0				p.A681T		Atlas-SNP	.											.	TSHZ2	209	.	0			c.G2041A						PASS	.	G	THR/ALA,THR/ALA	827,3579	325.6+/-299.2	98,631,1474	50.0	46.0	48.0		2032,2041	-1.2	0.0	20	dbSNP_114	48	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	TSHZ2	NM_001193421.1,NM_173485.5	58,58	98,637,5768	AA,AG,GG		0.0698,18.7699,6.4047	benign,benign	678/1032,681/1035	51872038	833,12173	2203	4300	6503	SO:0001583	missense	128553	exon2			GGGTGCGCCCTCG	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2041G>A	20.37:g.51872038G>A	ENSP00000360552:p.Ala681Thr	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	28	0.583333	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	122	0.055860805860805864	118	0.23983739837398374	4	0.011049723756906077	0	0.0	0	0.0	G	2.194	-0.384541	0.04966	0.187699	6.98E-4	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.37752	1.18;1.18	5.53	-1.21	0.09524	.	0.276183	0.39020	N	0.001485	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.29579	-1.0007	9	0.10111	T	0.7	1.382	2.2477	0.04035	0.3252:0.1119:0.4479:0.115	rs6097319;rs6097319	681	Q9NRE2	TSH2_HUMAN	T	681;678;207	ENSP00000360552:A681T;ENSP00000333114:A678T	ENSP00000333114:A678T	A	+	1	0	TSHZ2	51305445	0.046000	0.20272	0.000000	0.03702	0.029000	0.11900	0.728000	0.26013	-0.174000	0.10743	0.643000	0.83706	GCC	G|0.935;A|0.065	0.065	strong		0.637	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
F9	2158	hgsc.bcm.edu	37	X	138643939	138643939	+	Silent	SNP	A	A	G	rs112057482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:138643939A>G	ENST00000218099.2	+	8	1102	c.1095A>G	c.(1093-1095)tcA>tcG	p.S365S	F9_ENST00000394090.2_Silent_p.S327S	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	365	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)	AAGGGAGATCAGCTTTAGTTC	0.438													A|||	42	0.0111258	0.0287	0.0058	3775	,	,		14652	0.0		0.0	False		,,,				2504	0.0				p.S365S		Atlas-SNP	.											.	F9	107	.	0			c.A1095G	GRCh37	CD010617	F9	D	rs112057482	PASS	.	A		127,3708		1,104,21,1527,550	141.0	117.0	125.0		1095	-9.5	0.0	X	dbSNP_132	125	1,6727		0,1,0,2427,1872	no	coding-synonymous	F9	NM_000133.3		1,105,21,3954,2422	GG,GA,G,AA,A		0.0149,3.3116,1.2118		365/462	138643939	128,10435	2203	4300	6503	SO:0001819	synonymous_variant	2158	exon8			GAGATCAGCTTTA	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.1095A>G	X.37:g.138643939A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	136	85	0.625	NM_000133	A8K9N4|F2RM36|Q5FBE1|Q5JYJ8	Silent	SNP	ENST00000218099.2	37	CCDS14666.1																																																																																			A|0.989;G|0.011	0.011	strong		0.438	F9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058557.1		
PALLD	23022	hgsc.bcm.edu	37	4	169432673	169432673	+	Silent	SNP	C	C	T	rs61051061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169432673C>T	ENST00000505667.1	+	2	191	c.18C>T	c.(16-18)tcC>tcT	p.S6S	PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000261509.6_Silent_p.S6S|PALLD_ENST00000333488.4_5'Flank			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	6					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)		GGACCTCCTCCCATGAGTCCT	0.483									Pancreatic Cancer, Familial Clustering of				C|||	926	0.184904	0.2292	0.1441	5008	,	,		17777	0.1925		0.1958	False		,,,				2504	0.135				p.S6S	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C18T						PASS	.	C	,	1033,3373	373.0+/-320.6	129,775,1299	67.0	67.0	67.0		18,18	2.9	0.9	4	dbSNP_129	67	1775,6825	309.3+/-309.3	184,1407,2709	yes	coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_016081.3	,	313,2182,4008	TT,TC,CC		20.6395,23.4453,21.59	,	6/1124,6/1107	169432673	2808,10198	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	CTCCTCCCATGAG	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.18C>T	4.37:g.169432673C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			C|0.791;T|0.209	0.209	strong		0.483	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
SIRPA	140885	hgsc.bcm.edu	37	20	1895963	1895963	+	Missense_Mutation	SNP	A	A	G	rs373583167|rs386811662|rs17855613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1895963A>G	ENST00000358771.4	+	2	450	c.298A>G	c.(298-300)Aac>Gac	p.N100D	SIRPA_ENST00000400068.3_Missense_Mutation_p.N100D|SIRPA_ENST00000356025.3_Missense_Mutation_p.N100D	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	100	Ig-like V-type.		N -> E (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CACAAAGAGAAACAACATGGA	0.522																																					p.N100D	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,brain,glioma,-2,4	SIRPA	83	4	0			c.A298G						scavenged	.																																			SO:0001583	missense	140885	exon3			AAGAGAAACAACA	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.298A>G	20.37:g.1895963A>G	ENSP00000351621:p.Asn100Asp	Somatic	558	1	0.00179211		WXS	Illumina HiSeq	Phase_I	361	24	0.066482	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	A	10.72	1.430951	0.25726	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02236	4.38;4.38;4.38	5.11	-5.69	0.02428	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.743450	0.02696	N	0.111247	T	0.03651	0.0104	L	0.55481	1.735	0.09310	N	1	B;B;B	0.17465	0.0;0.022;0.0	B;B;B	0.24701	0.004;0.055;0.007	T	0.41875	-0.9484	10	0.51188	T	0.08	.	10.2665	0.43457	0.2384:0.1377:0.6239:0.0	rs17855613	80;100;100	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	D	100	ENSP00000382941:N100D;ENSP00000348307:N100D;ENSP00000351621:N100D	ENSP00000348307:N100D	N	+	1	0	SIRPA	1843963	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.479000	0.02327	-1.294000	0.02360	-0.388000	0.06559	AAC	.	.	weak		0.522	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
CCDC40	55036	hgsc.bcm.edu	37	17	78069129	78069129	+	Missense_Mutation	SNP	G	G	T	rs61686936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78069129G>T	ENST00000397545.4	+	18	2927	c.2900G>T	c.(2899-2901)cGc>cTc	p.R967L		NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	967					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			GCGGTTGCCCGCAGAGAGACC	0.667													G|||	137	0.0273562	0.0991	0.0072	5008	,	,		16509	0.0		0.001	False		,,,				2504	0.0				p.R967L		Atlas-SNP	.											CCDC40,colon,carcinoma,0,1	CCDC40	198	1	0			c.G2900T						PASS	.	G	LEU/ARG	367,3957		14,339,1809	54.0	66.0	62.0		2900	-0.6	1.0	17	dbSNP_129	62	2,8516		0,2,4257	yes	missense	CCDC40	NM_017950.3	102	14,341,6066	TT,TG,GG		0.0235,8.4875,2.8734	possibly-damaging	967/1143	78069129	369,12473	2162	4259	6421	SO:0001583	missense	55036	exon18			TTGCCCGCAGAGA	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.2900G>T	17.37:g.78069129G>T	ENSP00000380679:p.Arg967Leu	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	250	126	0.504	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Missense_Mutation	SNP	ENST00000397545.4	37	CCDS42395.1	60	0.027472527472527472	58	0.11788617886178862	2	0.0055248618784530384	0	0.0	0	0.0	G	11.65	1.700481	0.30142	0.084875	2.35E-4	ENSG00000141519	ENST00000397545	T	0.57436	0.4	5.38	-0.582	0.11709	.	.	.	.	.	T	0.00666	0.0022	L	0.57536	1.79	0.09310	P	0.9999999999999583	P;B	0.40619	0.724;0.397	B;B	0.36289	0.202;0.221	T	0.06534	-1.0821	8	0.48119	T	0.1	-13.7927	6.9297	0.24434	0.3554:0.0:0.5288:0.1159	rs61686936;rs61749048	967;750	Q4G0X9;Q4G0X9-3	CCD40_HUMAN;.	L	967	ENSP00000380679:R967L	ENSP00000380679:R967L	R	+	2	0	CCDC40	75683724	0.797000	0.28877	0.997000	0.53966	0.125000	0.20455	0.916000	0.28651	0.263000	0.21812	0.563000	0.77884	CGC	A|0.000;G|0.981;T|0.019	0.019	strong		0.667	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082	
LAMB4	22798	hgsc.bcm.edu	37	7	107696289	107696289	+	Silent	SNP	C	C	T	rs17154865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107696289C>T	ENST00000388781.3	-	25	3626	c.3543G>A	c.(3541-3543)caG>caA	p.Q1181Q	LAMB4_ENST00000388780.3_Silent_p.Q1181Q|LAMB4_ENST00000205386.4_Silent_p.Q1181Q	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1181	Domain II.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						TGTGGTCCCACTGATCAAAGC	0.542													T|||	1003	0.20028	0.6906	0.0692	5008	,	,		19520	0.004		0.0149	False		,,,				2504	0.0235				p.Q1181Q		Atlas-SNP	.											.	LAMB4	253	.	0			c.G3543A						PASS	.	T		2505,1901	545.7+/-376.8	723,1059,421	94.0	91.0	92.0		3543	-10.3	0.0	7	dbSNP_123	92	112,8488	814.3+/-407.0	1,110,4189	no	coding-synonymous	LAMB4	NM_007356.2		724,1169,4610	TT,TC,CC		1.3023,43.1457,20.1215		1181/1762	107696289	2617,10389	2203	4300	6503	SO:0001819	synonymous_variant	22798	exon25			GTCCCACTGATCA	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.3543G>A	7.37:g.107696289C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	145	82	0.565517	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			C|0.806;T|0.194	0.194	strong		0.542	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
TRPV1	7442	hgsc.bcm.edu	37	17	3476990	3476990	+	Silent	SNP	G	G	A	rs17706245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3476990G>A	ENST00000571088.1	-	13	2253	c.2040C>T	c.(2038-2040)atC>atT	p.I680I	TRPV1_ENST00000174621.6_Silent_p.I678I|TRPV1_ENST00000310522.5_Silent_p.I620I|TRPV1_ENST00000576351.1_Silent_p.I670I|TRPV1_ENST00000399756.4_Silent_p.I680I|SHPK_ENST00000572705.1_Silent_p.I680I|TRPV1_ENST00000425167.2_Silent_p.I691I|TRPV1_ENST00000399759.3_Silent_p.I680I	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	680					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	CCATGAGGGCGATGAGCATGT	0.542													g|||	378	0.0754792	0.1558	0.0159	5008	,	,		14347	0.0417		0.0388	False		,,,				2504	0.0818				p.I680I	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.C2040T						PASS	.	A	,,,	660,3742	256.4+/-261.2	46,568,1587	135.0	133.0	133.0		2040,2040,2040,2040	-11.2	0.0	17	dbSNP_123	133	436,8164	131.3+/-189.1	13,410,3877	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	,,,	59,978,5464	AA,AG,GG		5.0698,14.9932,8.4295	,,,	680/840,680/840,680/840,680/840	3476990	1096,11906	2201	4300	6501	SO:0001819	synonymous_variant	7442	exon13			GAGGGCGATGAGC	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.2040C>T	17.37:g.3476990G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Silent	SNP	ENST00000571088.1	37	CCDS45576.1																																																																																			G|0.942;A|0.058	0.058	strong		0.542	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
RAET1L	154064	hgsc.bcm.edu	37	6	150346532	150346532	+	Missense_Mutation	SNP	T	T	C	rs1543547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:150346532T>C	ENST00000367341.1	-	1	75	c.76A>G	c.(76-78)Agg>Ggg	p.R26G	RAET1L_ENST00000286380.2_Missense_Mutation_p.R26G			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	26			R -> G (in dbSNP:rs1543547).		antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		CCGTCTCGCCTAGCCCGGGAC	0.647													C|||	2029	0.405152	0.4902	0.4035	5008	,	,		15138	0.245		0.4523	False		,,,				2504	0.408				p.R26G		Atlas-SNP	.											.	RAET1L	21	.	0			c.A76G						PASS	.	C	GLY/ARG	2088,2318	585.5+/-386.3	496,1096,611	43.0	45.0	44.0		76	0.4	0.0	6	dbSNP_88	44	3871,4729	592.4+/-393.0	874,2123,1303	no	missense	RAET1L	NM_130900.2	125	1370,3219,1914	CC,CT,TT		45.0116,47.3899,45.8173	benign	26/247	150346532	5959,7047	2203	4300	6503	SO:0001583	missense	154064	exon1			CTCGCCTAGCCCG	AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918			16798	protein-coding gene	gene with protein product		611047				11827464	Standard	NM_130900		Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.76A>G	6.37:g.150346532T>C	ENSP00000356310:p.Arg26Gly	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_130900	A3KME4|Q8TE74	Missense_Mutation	SNP	ENST00000367341.1	37	CCDS5224.1	873	0.39972527472527475	239	0.48577235772357724	166	0.4585635359116022	122	0.21328671328671328	346	0.45646437994722955	c	0.004	-2.352112	0.00217	0.473899	0.450116	ENSG00000155918	ENST00000367341;ENST00000286380	T;T	0.00730	5.77;5.77	0.428	0.428	0.16499	.	.	.	.	.	T	0.00109	0.0003	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.04509	-1.0946	7	0.23302	T	0.38	.	.	.	.	rs1543547;rs17431364;rs61168803	26	Q5VY80	RET1L_HUMAN	G	26	ENSP00000356310:R26G;ENSP00000286380:R26G	ENSP00000286380:R26G	R	-	1	2	RAET1L	150388225	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.048000	0.03517	-0.417000	0.07461	-0.971000	0.02607	AGG	C|0.440;N|0.000	0.440	strong		0.647	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042676.1	NM_130900	
SV2B	9899	hgsc.bcm.edu	37	15	91827264	91827264	+	Silent	SNP	C	C	T	rs2301664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91827264C>T	ENST00000394232.1	+	11	1991	c.1521C>T	c.(1519-1521)caC>caT	p.H507H	SV2B_ENST00000330276.4_Silent_p.H507H|SV2B_ENST00000545111.2_Silent_p.H356H	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	507					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			TCTACGAGCACAAGTTCATCA	0.522													T|||	642	0.128195	0.261	0.062	5008	,	,		19686	0.0506		0.0765	False		,,,				2504	0.1288				p.H507H		Atlas-SNP	.											.	SV2B	98	.	0			c.C1521T						PASS	.	T	,	1020,3376	726.5+/-409.7	111,798,1289	192.0	186.0	188.0		1068,1521	-2.2	0.4	15	dbSNP_100	188	682,7914	788.1+/-407.6	34,614,3650	no	coding-synonymous,coding-synonymous	SV2B	NM_001167580.1,NM_014848.4	,	145,1412,4939	TT,TC,CC		7.9339,23.2029,13.1004	,	356/533,507/684	91827264	1702,11290	2198	4298	6496	SO:0001819	synonymous_variant	9899	exon12			CGAGCACAAGTTC	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1521C>T	15.37:g.91827264C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	37	CCDS10370.1																																																																																			C|0.870;T|0.130	0.130	strong		0.522	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
ABTB2	25841	hgsc.bcm.edu	37	11	34378381	34378381	+	Missense_Mutation	SNP	G	G	C	rs1925368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34378381G>C	ENST00000435224.2	-	1	1174	c.750C>G	c.(748-750)caC>caG	p.H250Q	ABTB2_ENST00000298992.2_Missense_Mutation_p.H64Q	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	250			H -> Q (in dbSNP:rs1925368). {ECO:0000269|PubMed:14702039}.		cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				CATCAGGGCTGTGGCTGGCCA	0.667													C|||	896	0.178914	0.2859	0.0879	5008	,	,		16857	0.373		0.0626	False		,,,				2504	0.0184				p.H250Q		Atlas-SNP	.											.	ABTB2	101	.	0			c.C750G						PASS	.	C	GLN/HIS	1058,3346		127,804,1271	24.0	21.0	22.0		750	3.8	1.0	11	dbSNP_92	22	575,8019		12,551,3734	yes	missense	ABTB2	NM_145804.2	24	139,1355,5005	CC,CG,GG		6.6907,24.0236,12.5635	benign	250/1026	34378381	1633,11365	2202	4297	6499	SO:0001583	missense	25841	exon1			AGGGCTGTGGCTG	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.750C>G	11.37:g.34378381G>C	ENSP00000410157:p.His250Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Missense_Mutation	SNP	ENST00000435224.2	37	CCDS7890.2	438	0.20054945054945056	137	0.2784552845528455	36	0.09944751381215469	225	0.39335664335664333	40	0.052770448548812667	C	2.321	-0.355532	0.05138	0.240236	0.066907	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.57907	0.37;0.37	4.72	3.81	0.43845	Histone-fold (2);	0.145459	0.47093	N	0.000255	T	0.00012	0.0000	N	0.00436	-1.5	0.51233	P	8.60000000000305E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40794	-0.9544	9	0.11485	T	0.65	-9.1489	9.2476	0.37536	0.0:0.7737:0.1463:0.08	rs1925368;rs3740794;rs1925368	64	Q8N961	ABTB2_HUMAN	Q	250;64	ENSP00000410157:H250Q;ENSP00000298992:H64Q	ENSP00000298992:H64Q	H	-	3	2	ABTB2	34334957	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	2.560000	0.45896	0.437000	0.26423	-0.371000	0.07208	CAC	G|0.844;C|0.156	0.156	strong		0.667	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804	
DMRTC2	63946	hgsc.bcm.edu	37	19	42354629	42354629	+	Silent	SNP	T	T	C	rs2305809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42354629T>C	ENST00000269945.3	+	8	903	c.852T>C	c.(850-852)ggT>ggC	p.G284G	DMRTC2_ENST00000596827.1_Silent_p.G335G	NM_001040283.1	NP_001035373.1	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2	284	Pro-rich.				male meiosis I (GO:0007141)|positive regulation of histone H3-K9 dimethylation (GO:1900111)|positive regulation of histone H3-K9 trimethylation (GO:1900114)|sex differentiation (GO:0007548)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|XY body (GO:0001741)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	10						GGACATCTGGTCCCTCAGAGT	0.627													C|||	3047	0.608427	0.916	0.572	5008	,	,		16805	0.5258		0.4702	False		,,,				2504	0.4458				p.G284G		Atlas-SNP	.											.	DMRTC2	31	.	0			c.T852C						PASS	.	C		3676,730	288.4+/-279.8	1545,586,72	44.0	51.0	48.0		852	2.3	0.3	19	dbSNP_100	48	4114,4486	575.9+/-390.3	963,2188,1149	no	coding-synonymous	DMRTC2	NM_001040283.1		2508,2774,1221	CC,CT,TT		47.8372,16.5683,40.1046		284/368	42354629	7790,5216	2203	4300	6503	SO:0001819	synonymous_variant	63946	exon8			ATCTGGTCCCTCA	AJ291669	CCDS33034.1	19q13.2	2008-07-16				ENSG00000142025			13911	protein-coding gene	gene with protein product		614806				11863363	Standard	NM_001040283		Approved		uc002ors.3	Q8IXT2		ENST00000269945.3:c.852T>C	19.37:g.42354629T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001040283	Q8N6Q2|Q96M39|Q96SD4	Silent	SNP	ENST00000269945.3	37	CCDS33034.1																																																																																			T|0.398;C|0.602	0.602	strong		0.627	DMRTC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463045.1	NM_001040283	
TMC4	147798	hgsc.bcm.edu	37	19	54665970	54665970	+	Silent	SNP	C	C	T	rs36655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54665970C>T	ENST00000376591.4	-	11	1703	c.1572G>A	c.(1570-1572)caG>caA	p.Q524Q	TMC4_ENST00000416963.1_Silent_p.Q106Q|TMC4_ENST00000301187.4_Silent_p.Q518Q|LENG1_ENST00000222224.3_5'Flank|TMC4_ENST00000476013.2_5'Flank	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	524					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CCTGGAACTCCTGGGTCCCCG	0.687													C|||	1237	0.247005	0.1808	0.2464	5008	,	,		9717	0.1558		0.328	False		,,,				2504	0.3476				p.Q524Q		Atlas-SNP	.											.	TMC4	89	.	0			c.G1572A						PASS	.	C	,	898,3500		88,722,1389	28.0	30.0	29.0		1572,1554	4.7	1.0	19	dbSNP_76	29	2769,5831		434,1901,1965	no	coding-synonymous,coding-synonymous	TMC4	NM_001145303.1,NM_144686.2	,	522,2623,3354	TT,TC,CC		32.1977,20.4184,28.212	,	524/713,518/707	54665970	3667,9331	2199	4300	6499	SO:0001819	synonymous_variant	147798	exon11			GAACTCCTGGGTC	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.1572G>A	19.37:g.54665970C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Silent	SNP	ENST00000376591.4	37	CCDS46174.1																																																																																			C|0.743;T|0.257	0.257	strong		0.687	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
ZNF717	100131827	hgsc.bcm.edu	37	3	75786684	75786684	+	Missense_Mutation	SNP	G	G	T	rs201345045		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75786684G>T	ENST00000478296.1	-	4	2216	c.1940C>A	c.(1939-1941)aCa>aAa	p.T647K	ZNF717_ENST00000422325.1_Missense_Mutation_p.T697K|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.T690K|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	687					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TTTCCCCGGTGTGAGTTCTCT	0.403																																					p.T697K		Atlas-SNP	.											.	ZNF717	160	.	0			c.C2090A						PASS	.						4.0	4.0	4.0					3																	75786684		567	1412	1979	SO:0001583	missense	100131827	exon5			CCCGGTGTGAGTT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1940C>A	3.37:g.75786684G>T	ENSP00000419377:p.Thr647Lys	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	50	11	0.22	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		.	.	.	.	.	.	.	.	.	.	.	10.94	1.493736	0.26774	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.06218	3.33;3.49;3.49	1.63	0.715	0.18186	.	.	.	.	.	T	0.12774	0.0310	L	0.39397	1.21	0.39053	P	0.039634999999999976	D	0.76494	0.999	D	0.69654	0.965	T	0.18272	-1.0342	8	0.87932	D	0	.	6.1449	0.20280	0.186:0.0:0.814:0.0	.	697	C9JSV9	.	K	647;697;690	ENSP00000419377:T647K;ENSP00000409514:T697K;ENSP00000383643:T690K	ENSP00000383643:T690K	T	-	2	0	ZNF717	75869374	1.000000	0.71417	0.019000	0.16419	0.001000	0.01503	3.759000	0.55227	0.256000	0.21614	-0.268000	0.10319	ACA	.	.	weak		0.403	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
MTMR9	66036	hgsc.bcm.edu	37	8	11142529	11142529	+	Silent	SNP	T	T	C	rs61752023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11142529T>C	ENST00000221086.3	+	1	605	c.132T>C	c.(130-132)aaT>aaC	p.N44N	MTMR9_ENST00000526292.1_5'Flank	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	44						cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		GGCAGGACAATACGGAGGAGC	0.657													C|||	214	0.0427316	0.1573	0.0072	5008	,	,		12961	0.0		0.001	False		,,,				2504	0.0				p.N44N		Atlas-SNP	.											.	MTMR9	58	.	0			c.T132C						PASS	.	C		609,3797	765.8+/-413.4	36,537,1630	36.0	38.0	37.0		132	3.0	1.0	8	dbSNP_129	37	2,8598	817.5+/-406.9	0,2,4298	no	coding-synonymous	MTMR9	NM_015458.3		36,539,5928	CC,CT,TT		0.0233,13.8221,4.6978		44/550	11142529	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	66036	exon1			GGACAATACGGAG	AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	14596	protein-coding gene	gene with protein product		606260	"""myotubularin related protein 8"""	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.132T>C	8.37:g.11142529T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_015458	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Silent	SNP	ENST00000221086.3	37	CCDS5979.1																																																																																			T|0.958;C|0.042	0.042	strong		0.657	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458	
OR2A14	135941	hgsc.bcm.edu	37	7	143826603	143826603	+	Missense_Mutation	SNP	G	G	T	rs2961160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143826603G>T	ENST00000408899.2	+	1	453	c.398G>T	c.(397-399)aGc>aTc	p.S133I		NM_001001659.1	NP_001001659.1	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A, member 14	133			S -> I (in dbSNP:rs2961160). {ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:14983052}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(17)|skin(1)	22	Melanoma(164;0.0783)					CGTTACAATAGCCTCATGAGC	0.517													T|||	3305	0.659944	0.7579	0.7435	5008	,	,		21600	0.7371		0.4841	False		,,,				2504	0.5695				p.S133I		Atlas-SNP	.											OR2A14,NS,carcinoma,+1,1	OR2A14	66	1	0			c.G398T						PASS	.	T	ILE/SER	3225,1095		1205,815,140	191.0	198.0	196.0		398	3.0	0.4	7	dbSNP_101	196	4555,3971		1243,2069,951	yes	missense	OR2A14	NM_001001659.1	142	2448,2884,1091	TT,TG,GG		46.5752,25.3472,39.4364	benign	133/311	143826603	7780,5066	2160	4263	6423	SO:0001583	missense	135941	exon1			ACAATAGCCTCAT		CCDS43672.1	7q35	2013-09-20		2004-03-08	ENSG00000221938	ENSG00000221938		"""GPCR / Class A : Olfactory receptors"""	15084	protein-coding gene	gene with protein product				OR2A14P, OR2A6			Standard	NM_001001659		Approved	OST182	uc011kua.2	Q96R47	OTTHUMG00000158003	ENST00000408899.2:c.398G>T	7.37:g.143826603G>T	ENSP00000386137:p.Ser133Ile	Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	300	300	1	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		
SIDT2	51092	hgsc.bcm.edu	37	11	117063020	117063020	+	Silent	SNP	C	C	T	rs12285062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117063020C>T	ENST00000324225.4	+	20	2454	c.1923C>T	c.(1921-1923)caC>caT	p.H641H	SIDT2_ENST00000431081.2_Silent_p.H638H|SIDT2_ENST00000532062.1_5'Flank	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	641					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	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;0.000219)|all cancers(92;0.00144)		CCATCATTCACATCATCGCCA	0.632													C|||	40	0.00798722	0.0272	0.0058	5008	,	,		17690	0.0		0.0	False		,,,				2504	0.0				p.H641H		Atlas-SNP	.											.	SIDT2	82	.	0			c.C1923T						PASS	.	C		125,4277	92.0+/-130.7	2,121,2078	122.0	102.0	109.0		1923	0.0	1.0	11	dbSNP_120	109	2,8590	2.2+/-6.3	0,2,4294	no	coding-synonymous	SIDT2	NM_001040455.1		2,123,6372	TT,TC,CC		0.0233,2.8396,0.9774		641/833	117063020	127,12867	2201	4296	6497	SO:0001819	synonymous_variant	51092	exon20			CATTCACATCATC	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.1923C>T	11.37:g.117063020C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_001040455	Q8NBY7|Q9Y357	Silent	SNP	ENST00000324225.4	37	CCDS31682.1																																																																																			C|0.990;T|0.010	0.010	strong		0.632	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996	
FAN1	22909	hgsc.bcm.edu	37	15	31196984	31196984	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31196984G>A	ENST00000362065.4	+	2	409	c.118G>A	c.(118-120)Gct>Act	p.A40T	FAN1_ENST00000565466.1_Missense_Mutation_p.A40T|FAN1_ENST00000561594.1_Missense_Mutation_p.A40T|FAN1_ENST00000561607.1_Missense_Mutation_p.A40T	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	40					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						TGCACCACCTGCTAAACTTGC	0.398								Direct reversal of damage																													p.A40T		Atlas-SNP	.											.	FAN1	77	.	0			c.G118A						PASS	.						74.0	76.0	75.0					15																	31196984		2202	4300	6502	SO:0001583	missense	22909	exon2			CCACCTGCTAAAC		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"""KIAA1018"", ""myotubularin related protein 15"""	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.118G>A	15.37:g.31196984G>A	ENSP00000354497:p.Ala40Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	135	67	0.496296	NM_001146095	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	37	CCDS32186.1	.	.	.	.	.	.	.	.	.	.	g	21.9	4.222546	0.79464	.	.	ENSG00000198690	ENST00000362065	D	0.82711	-1.64	5.28	3.31	0.37934	.	0.247400	0.41097	D	0.000947	D	0.88749	0.6521	M	0.66939	2.045	0.39089	D	0.961052	D;D	0.89917	0.986;1.0	P;D	0.72982	0.738;0.979	D	0.89320	0.3639	10	0.72032	D	0.01	-9.7976	12.0726	0.53626	0.0:0.1314:0.7318:0.1368	.	40;40	Q9Y2M0;Q9Y2M0-2	FAN1_HUMAN;.	T	40	ENSP00000354497:A40T	ENSP00000354497:A40T	A	+	1	0	FAN1	28984276	0.538000	0.26394	0.288000	0.24862	0.886000	0.51366	2.025000	0.41059	0.662000	0.31006	0.555000	0.69702	GCT	.	.	none		0.398	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967	
BCAS1	8537	hgsc.bcm.edu	37	20	52611552	52611552	+	Splice_Site	SNP	G	G	A	rs60878965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52611552G>A	ENST00000395961.3	-	6	1092	c.926C>T	c.(925-927)aCg>aTg	p.T309M	BCAS1_ENST00000371435.2_Splice_Site_p.T309M|BCAS1_ENST00000434986.2_Splice_Site_p.T22M|BCAS1_ENST00000371440.3_Splice_Site_p.T309M	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	309						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				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)			ACTACCTACCGTGTCTTCTGG	0.343													G|||	449	0.0896565	0.3245	0.0274	5008	,	,		16173	0.0		0.001	False		,,,				2504	0.0				p.T309M		Atlas-SNP	.											.	BCAS1	77	.	0			c.C926T						PASS	.	G	MET/THR	1210,3196	421.1+/-339.2	174,862,1167	185.0	200.0	195.0		926	2.5	1.0	20	dbSNP_129	195	11,8589	8.4+/-32.0	0,11,4289	yes	missense-near-splice	BCAS1	NM_003657.2	81	174,873,5456	AA,AG,GG		0.1279,27.4626,9.388	possibly-damaging	309/585	52611552	1221,11785	2203	4300	6503	SO:0001630	splice_region_variant	8537	exon6			CCTACCGTGTCTT	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.927+1C>T	20.37:g.52611552G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	NM_003657	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	37	CCDS13444.1	163|163	0.07463369963369963|0.07463369963369963	155|155	0.3150406504065041|0.3150406504065041	8|8	0.022099447513812154|0.022099447513812154	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.69|16.69	3.194122|3.194122	0.58017|0.58017	0.274626|0.274626	0.001279|0.001279	ENSG00000064787|ENSG00000064787	ENST00000422805|ENST00000448484;ENST00000371440;ENST00000448710;ENST00000395961;ENST00000371435;ENST00000434986	.|T;T;T;T;T	.|0.08458	.|3.09;3.09;3.09;3.09;3.09	5.84|5.84	2.46|2.46	0.29980|0.29980	.|.	.|0.270974	.|0.35525	.|N	.|0.003141	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.61703|0.61703	1.905|1.905	0.09310|0.09310	P|P	0.9999999999996939|0.9999999999996939	.|D;P;D;P;D;D	.|0.89917	.|1.0;0.777;1.0;0.944;0.993;0.993	.|D;B;D;B;P;P	.|0.65773	.|0.938;0.1;0.938;0.332;0.596;0.596	T|T	0.40365|0.40365	-0.9567|-0.9567	4|9	.|0.54805	.|T	.|0.06	-4.1201|-4.1201	11.7384|11.7384	0.51778|0.51778	0.0:0.0:0.3884:0.6116|0.0:0.0:0.3884:0.6116	rs60878965;rs61731748|rs60878965;rs61731748	.|309;22;309;309;309;309	.|B2RCQ5;B4DFL4;O75363-2;G3XAF7;A0AVG7;O75363	.|.;.;.;.;.;BCAS1_HUMAN	W|M	28|171;309;187;309;309;22	.|ENSP00000396361:T171M;ENSP00000360495:T309M;ENSP00000379290:T309M;ENSP00000360490:T309M;ENSP00000409956:T22M	.|ENSP00000360490:T309M	R|T	-|-	1|2	2|0	BCAS1|BCAS1	52044959|52044959	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.929000|0.929000	0.56500|0.56500	1.044000|1.044000	0.30329|0.30329	0.727000|0.727000	0.32360|0.32360	0.655000|0.655000	0.94253|0.94253	CGG|ACG	G|0.916;A|0.084	0.084	strong		0.343	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657	Missense_Mutation
SEL1L	6400	hgsc.bcm.edu	37	14	81969158	81969158	+	Silent	SNP	A	A	G	rs35377988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:81969158A>G	ENST00000336735.4	-	6	800	c.684T>C	c.(682-684)gcT>gcC	p.A228A	SEL1L_ENST00000555824.1_Silent_p.A228A	NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	228	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		CAAATAAAAGAGCATATGACA	0.423													A|||	195	0.0389377	0.1437	0.0072	5008	,	,		1526	0.0		0.0	False		,,,				2504	0.0				p.A228A		Atlas-SNP	.											.	SEL1L	67	.	0			c.T684C						PASS	.	A		477,3929	224.6+/-240.7	21,435,1747	185.0	175.0	178.0		684	-1.6	1.0	14	dbSNP_126	178	0,8600		0,0,4300	no	coding-synonymous	SEL1L	NM_005065.4		21,435,6047	GG,GA,AA		0.0,10.8261,3.6675		228/795	81969158	477,12529	2203	4300	6503	SO:0001819	synonymous_variant	6400	exon6			TAAAAGAGCATAT		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"""sel-1 suppressor of lin-12-like 1 (C. elegans)"""	602329	"""sel-1 (suppressor of lin-12, C.elegans)-like"""			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.684T>C	14.37:g.81969158A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	94	35	0.37234	NM_001244984	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	37	CCDS9876.1																																																																																			A|0.957;G|0.043	0.043	strong		0.423	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065	
SALL4	57167	hgsc.bcm.edu	37	20	50408614	50408614	+	Silent	SNP	A	A	G	rs76870996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50408614A>G	ENST00000217086.4	-	2	519	c.408T>C	c.(406-408)aaT>aaC	p.N136N	SALL4_ENST00000483130.1_5'UTR|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Silent_p.N136N	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	136					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						AGCTGCCGCCATTCTCCCTGT	0.592													A|||	67	0.0133786	0.0469	0.0058	5008	,	,		16786	0.0		0.001	False		,,,				2504	0.0				p.N136N		Atlas-SNP	.											.	SALL4	168	.	0			c.T408C						PASS	.	A		172,4234	113.3+/-151.4	6,160,2037	128.0	134.0	132.0		408	-7.7	0.0	20	dbSNP_131	132	0,8600		0,0,4300	no	coding-synonymous	SALL4	NM_020436.3		6,160,6337	GG,GA,AA		0.0,3.9038,1.3225		136/1054	50408614	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			GCCGCCATTCTCC	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.408T>C	20.37:g.50408614A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			A|0.988;G|0.012	0.012	strong		0.592	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
KRT78	196374	hgsc.bcm.edu	37	12	53238387	53238387	+	Missense_Mutation	SNP	C	C	T	rs61764061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53238387C>T	ENST00000304620.4	-	5	940	c.877G>A	c.(877-879)Gcc>Acc	p.A293T	KRT78_ENST00000359499.4_Missense_Mutation_p.A183T	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	293	Coil 2.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						CTGCTCCGGGCGATCTCCTCG	0.622													C|||	615	0.122804	0.2239	0.0173	5008	,	,		19876	0.2282		0.0119	False		,,,				2504	0.0665				p.A293T		Atlas-SNP	.											.	KRT78	41	.	0			c.G877A						PASS	.	C	THR/ALA	944,3462	359.6+/-314.9	108,728,1367	122.0	91.0	101.0		877	1.2	0.0	12	dbSNP_129	101	98,8502	54.0+/-114.7	1,96,4203	yes	missense	KRT78	NM_173352.2	58	109,824,5570	TT,TC,CC		1.1395,21.4253,8.0117	benign	293/521	53238387	1042,11964	2203	4300	6503	SO:0001583	missense	196374	exon5			TCCGGGCGATCTC	AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.877G>A	12.37:g.53238387C>T	ENSP00000306261:p.Ala293Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	53	51	0.962264	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Missense_Mutation	SNP	ENST00000304620.4	37	CCDS8840.1	229	0.10485347985347986	100	0.2032520325203252	5	0.013812154696132596	115	0.20104895104895104	9	0.011873350923482849	C	20.5	4.000530	0.74818	0.214253	0.011395	ENSG00000170423	ENST00000359499;ENST00000304620;ENST00000539860	D;D	0.90620	-2.7;-2.7	5.07	1.16	0.20824	Filament (1);	.	.	.	.	T	0.00384	0.0012	M	0.72894	2.215	0.34272	P	0.31884199999999996	P	0.38597	0.639	B	0.33254	0.16	T	0.05338	-1.0891	8	0.72032	D	0.01	.	9.0529	0.36387	0.0:0.6929:0.0:0.3071	rs61764061	293	Q8N1N4	K2C78_HUMAN	T	183;293;64	ENSP00000352479:A183T;ENSP00000306261:A293T	ENSP00000306261:A293T	A	-	1	0	KRT78	51524654	0.672000	0.27530	0.005000	0.12908	0.003000	0.03518	1.364000	0.34171	0.006000	0.14734	0.563000	0.77884	GCC	C|0.918;T|0.082	0.082	strong		0.622	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352	
DSC1	1823	hgsc.bcm.edu	37	18	28710615	28710615	+	Silent	SNP	C	C	A	rs1816634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28710615C>A	ENST00000257198.5	-	16	2808	c.2547G>T	c.(2545-2547)tcG>tcT	p.S849S	RP11-408H20.2_ENST00000581836.1_RNA|DSC1_ENST00000257197.3_3'UTR|RP11-408H20.3_ENST00000582307.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	849					homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CATAGTTATACGAACAAACGT	0.418													C|||	465	0.0928514	0.2542	0.0533	5008	,	,		18467	0.0		0.0467	False		,,,				2504	0.046				p.S849S		Atlas-SNP	.											.	DSC1	240	.	0			c.G2547T						PASS	.	C	,	886,3520	344.1+/-307.9	88,710,1405	133.0	134.0	134.0		,2547	-12.3	0.0	18	dbSNP_92	134	344,8256	118.1+/-177.6	6,332,3962	no	utr-3,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	94,1042,5367	AA,AC,CC		4.0,20.1089,9.4572	,	,849/895	28710615	1230,11776	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon16			GTTATACGAACAA	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.2547G>T	18.37:g.28710615C>A		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	256	105	0.410156	NM_024421	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			C|0.914;A|0.086	0.086	strong		0.418	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
CD109	135228	hgsc.bcm.edu	37	6	74407182	74407182	+	Missense_Mutation	SNP	G	G	T	rs9446983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74407182G>T	ENST00000287097.5	+	2	246	c.134G>T	c.(133-135)gGg>gTg	p.G45V	CD109_ENST00000437994.2_Missense_Mutation_p.G45V|CD109_ENST00000422508.2_Missense_Mutation_p.G45V|RP11-553A21.3_ENST00000428865.2_RNA			Q6YHK3	CD109_HUMAN	CD109 molecule	45			G -> V (in dbSNP:rs9446983).		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						GTGACTATTGGGGTGGAGCTT	0.522													G|||	75	0.014976	0.056	0.0014	5008	,	,		18228	0.0		0.0	False		,,,				2504	0.0				p.G45V		Atlas-SNP	.											CD109,NS,carcinoma,-1,1	CD109	170	1	0			c.G134T						PASS	.	G	VAL/GLY,VAL/GLY,VAL/GLY	158,4248	106.9+/-145.3	1,156,2046	118.0	118.0	118.0		134,134,134	5.3	1.0	6	dbSNP_119	118	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	109,109,109	1,157,6345	TT,TG,GG		0.0116,3.586,1.2225	possibly-damaging,possibly-damaging,possibly-damaging	45/1429,45/1369,45/1446	74407182	159,12847	2203	4300	6503	SO:0001583	missense	135228	exon2			CTATTGGGGTGGA	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.134G>T	6.37:g.74407182G>T	ENSP00000287097:p.Gly45Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	93	51	0.548387	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	19.50	3.840234	0.71488	0.03586	1.16E-4	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.26810	1.98;1.71;1.98	5.31	5.31	0.75309	.	0.090017	0.44285	D	0.000473	T	0.26448	0.0646	N	0.19112	0.55	0.47778	D	0.99951	D;D;P;P	0.89917	1.0;0.999;0.508;0.938	D;D;B;P	0.97110	1.0;0.984;0.176;0.706	T	0.03077	-1.1075	10	0.38643	T	0.18	.	16.0095	0.80391	0.0:0.0:1.0:0.0	rs9446983;rs52825035;rs9446983	45;45;45;45	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	V	45	ENSP00000388062:G45V;ENSP00000404475:G45V;ENSP00000287097:G45V	ENSP00000287097:G45V	G	+	2	0	CD109	74463903	1.000000	0.71417	0.998000	0.56505	0.711000	0.40976	3.673000	0.54591	2.779000	0.95612	0.655000	0.94253	GGG	G|0.986;T|0.014	0.014	strong		0.522	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
SYNE2	23224	hgsc.bcm.edu	37	14	64688335	64688335	+	Silent	SNP	G	G	A	rs75079588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64688335G>A	ENST00000344113.4	+	111	20246	c.20034G>A	c.(20032-20034)gcG>gcA	p.A6678A	SYNE2_ENST00000554584.1_Silent_p.A6594A|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.A3335A|SYNE2_ENST00000358025.3_Silent_p.A6701A|SYNE2_ENST00000357395.3_Silent_p.A3063A|SYNE2_ENST00000394768.2_Silent_p.A3063A|SYNE2_ENST00000458046.2_Silent_p.A349A|SYNE2_ENST00000554805.1_Silent_p.A461A|SYNE2_ENST00000555022.1_Silent_p.A556A|SYNE2_ENST00000441438.2_Silent_p.A223A	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6678					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.A6701A(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)		TGTGGTTAGCGAGTGCCAAGA	0.547													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		18920	0.0		0.0	False		,,,				2504	0.0				p.A6701A		Atlas-SNP	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	1	1	Substitution - coding silent(1)	lung(1)	c.G20103A						PASS	.	G	,,,	88,4318	73.6+/-111.7	1,86,2116	179.0	174.0	175.0		20034,669,1047,20103	-9.2	0.0	14	dbSNP_131	175	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182910.2,NM_182913.2,NM_182914.2	,,,	1,87,6415	AA,AG,GG		0.0116,1.9973,0.6843	,,,	6678/6886,223/430,349/557,6701/6908	64688335	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon112			GTTAGCGAGTGCC	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.20034G>A	14.37:g.64688335G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	161	88	0.546584	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			G|0.994;A|0.006	0.006	strong		0.547	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
MICU1	10367	hgsc.bcm.edu	37	10	74183034	74183034	+	Silent	SNP	G	G	A	rs186054834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:74183034G>A	ENST00000361114.5	-	9	1125	c.1029C>T	c.(1027-1029)acC>acT	p.T343T	MICU1_ENST00000398763.4_Silent_p.T145T|MICU1_ENST00000418483.2_Silent_p.T145T|MICU1_ENST00000398761.4_Silent_p.T345T|MICU1_ENST00000401998.3_Silent_p.T343T	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	343					calcium ion import (GO:0070509)|calcium ion transmembrane import into mitochondrion (GO:0036444)|defense response (GO:0006952)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein homooligomerization (GO:0051260)	calcium channel complex (GO:0034704)|integral component of mitochondrial membrane (GO:0032592)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										TCTGCATGGCGGTCAGCTTCT	0.493													G|||	3	0.000599042	0.0023	0.0	5008	,	,		19951	0.0		0.0	False		,,,				2504	0.0				p.T343T		Atlas-SNP	.											.	.	.	.	0			c.C1029T						PASS	.	G	,,	5,3985		0,5,1990	106.0	100.0	102.0		1029,435,1035	-11.3	0.3	10		102	0,8342		0,0,4171	no	coding-synonymous,coding-synonymous,coding-synonymous	MICU1	NM_001195518.1,NM_001195519.1,NM_006077.3	,,	0,5,6161	AA,AG,GG		0.0,0.1253,0.0405	,,	343/477,145/279,345/479	74183034	5,12327	1995	4171	6166	SO:0001819	synonymous_variant	10367	exon9			CATGGCGGTCAGC	Y17711	CCDS55714.1, CCDS55715.1	10q22.1	2013-01-10	2011-06-23	2011-06-23	ENSG00000107745	ENSG00000107745		"""EF-hand domain containing"""	1530	protein-coding gene	gene with protein product		605084	"""calcium binding atopy-related autoantigen 1"""	CBARA1		9806765, 20693986	Standard	NM_006077		Approved	CALC, EFHA3, FLJ12684	uc001jtb.2	Q9BPX6	OTTHUMG00000018437	ENST00000361114.5:c.1029C>T	10.37:g.74183034G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	160	69	0.43125	NM_001195518	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Silent	SNP	ENST00000361114.5	37	CCDS55715.1																																																																																			G|0.999;A|0.001	0.001	strong		0.493	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161022247	161022247	+	Missense_Mutation	SNP	C	C	T	rs149524176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161022247C>T	ENST00000368013.3	-	8	1243	c.923G>A	c.(922-924)cGg>cAg	p.R308Q	ARHGAP30_ENST00000368016.3_Missense_Mutation_p.R308Q|ARHGAP30_ENST00000368015.1_Missense_Mutation_p.R131Q	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	308					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CTCAGCCCCCCGTGGAAGTTT	0.537													C|||	4	0.000798722	0.003	0.0	5008	,	,		16986	0.0		0.0	False		,,,				2504	0.0				p.R308Q		Atlas-SNP	.											LOC257106,NS,carcinoma,-1,2	ARHGAP30	105	2	0			c.G923A						PASS	.	C	GLN/ARG,GLN/ARG	5,4401	9.9+/-24.2	0,5,2198	198.0	211.0	207.0		923,923	3.8	0.5	1	dbSNP_134	207	0,8600		0,0,4300	no	missense,missense	ARHGAP30	NM_001025598.1,NM_181720.2	43,43	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	possibly-damaging,possibly-damaging	308/1102,308/891	161022247	5,13001	2203	4300	6503	SO:0001583	missense	257106	exon8			GCCCCCCGTGGAA	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.923G>A	1.37:g.161022247C>T	ENSP00000356992:p.Arg308Gln	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	89	35	0.393258	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	37	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.429037	0.43122	0.001135	0.0	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.38401	2.84;2.76;1.14	4.72	3.77	0.43336	.	0.396100	0.21881	N	0.067728	T	0.28333	0.0700	L	0.56199	1.76	0.09310	N	1	D;D	0.65815	0.995;0.989	P;P	0.56788	0.716;0.806	T	0.11665	-1.0578	10	0.66056	D	0.02	.	5.6555	0.17640	0.2053:0.6933:0.0:0.1014	.	308;308	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	Q	308;308;160;131	ENSP00000356995:R308Q;ENSP00000356992:R308Q;ENSP00000356994:R131Q	ENSP00000356992:R308Q	R	-	2	0	ARHGAP30	159288871	0.000000	0.05858	0.542000	0.28115	0.981000	0.71138	0.424000	0.21330	0.924000	0.37069	0.549000	0.68633	CGG	C|0.999;T|0.001	0.001	strong		0.537	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549563	32549563	+	Silent	SNP	G	G	A	rs77689370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32549563G>A	ENST00000360004.5	-	3	528	c.423C>T	c.(421-423)caC>caT	p.H141H		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	141	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						CCAGGAGGTTGTGGTGCTGCA	0.517										Multiple Myeloma(14;0.17)																											p.H141H		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C423T						PASS	.						92.0	112.0	105.0					6																	32549563		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon3			GAGGTTGTGGTGC	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.423C>T	6.37:g.32549563G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	243	80	0.329218	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			A|0.051;C|0.002;G|0.947	0.051	strong		0.517	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
GJB7	375519	hgsc.bcm.edu	37	6	87994101	87994101	+	Missense_Mutation	SNP	G	G	A	rs41273281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:87994101G>A	ENST00000525899.1	-	3	875	c.530C>T	c.(529-531)aCg>aTg	p.T177M	GJB7_ENST00000296882.3_Missense_Mutation_p.T177M	NM_198568.2	NP_940970.1	Q6PEY0	CXB7_HUMAN	gap junction protein, beta 7, 25kDa	177			T -> M (in dbSNP:rs41273281).		cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)	5		all_cancers(76;1.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;7.38e-10)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00323)		BRCA - Breast invasive adenocarcinoma(108;0.0167)		GATGAAGATCGTCTTCTCAGT	0.403													G|||	381	0.0760783	0.2088	0.0389	5008	,	,		21437	0.001		0.0467	False		,,,				2504	0.0307				p.T177M		Atlas-SNP	.											GJB7,NS,carcinoma,+1,2	GJB7	28	2	0			c.C530T						PASS	.	G	MET/THR	822,3584	328.0+/-300.3	83,656,1464	112.0	107.0	109.0		530	0.6	0.1	6	dbSNP_127	109	335,8265	116.3+/-176.0	5,325,3970	yes	missense	GJB7	NM_198568.2	81	88,981,5434	AA,AG,GG		3.8953,18.6564,8.8959	benign	177/224	87994101	1157,11849	2203	4300	6503	SO:0001583	missense	375519	exon3			AAGATCGTCTTCT	AJ414563	CCDS5008.1	6q15	2008-02-05	2007-11-06			ENSG00000164411		"""Ion channels / Gap junction proteins (connexins)"""	16690	protein-coding gene	gene with protein product	"""connexin 25"""	611921	"""gap junction protein, beta 7"""				Standard	NM_198568		Approved	CX25, bA136M9.1	uc003plo.2	Q6PEY0		ENST00000525899.1:c.530C>T	6.37:g.87994101G>A	ENSP00000435355:p.Thr177Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	107	41	0.383178	NM_198568	B3KXL0|Q96KP0	Missense_Mutation	SNP	ENST00000525899.1	37	CCDS5008.1	144	0.06593406593406594	98	0.1991869918699187	13	0.03591160220994475	0	0.0	33	0.04353562005277045	G	2.237	-0.374671	0.05034	0.186564	0.038953	ENSG00000164411	ENST00000525899;ENST00000296882	D;D	0.96365	-3.99;-3.99	5.12	0.601	0.17529	Gap junction protein, cysteine-rich domain (1);	0.153133	0.42548	U	0.000696	D	0.86581	0.5967	L	0.46670	1.46	0.58432	P	1.0000000000287557E-6	B	0.26975	0.165	B	0.20577	0.03	T	0.77153	-0.2692	9	0.56958	D	0.05	.	4.2044	0.10481	0.2451:0.0:0.2505:0.5043	rs41273281;rs57142874	177	Q6PEY0	CXB7_HUMAN	M	177	ENSP00000435355:T177M;ENSP00000296882:T177M	ENSP00000296882:T177M	T	-	2	0	GJB7	88050820	0.732000	0.28121	0.099000	0.21106	0.009000	0.06853	1.080000	0.30779	0.157000	0.19338	-0.899000	0.02877	ACG	G|0.918;A|0.082	0.082	strong		0.403	GJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394780.1		
SBNO1	55206	hgsc.bcm.edu	37	12	123799974	123799974	+	Silent	SNP	A	A	G	rs6488868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123799974A>G	ENST00000602398.1	-	23	3193	c.3066T>C	c.(3064-3066)ggT>ggC	p.G1022G	SBNO1_ENST00000420886.2_Silent_p.G1022G|SBNO1_ENST00000602750.1_Silent_p.G1021G|SBNO1_ENST00000267176.4_Silent_p.G1021G			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1022					regulation of transcription, DNA-templated (GO:0006355)					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)		CCCTTCTATCACCATGTGTAA	0.363													G|||	3431	0.685104	0.4523	0.6916	5008	,	,		19843	0.9544		0.7217	False		,,,				2504	0.68				p.G1022G		Atlas-SNP	.											.	SBNO1	138	.	0			c.T3066C						PASS	.	G	,	2141,2265	596.3+/-388.6	508,1125,570	142.0	134.0	137.0		3066,3063	-11.5	0.1	12	dbSNP_116	137	6423,2177	372.0+/-336.5	2408,1607,285	no	coding-synonymous,coding-synonymous	SBNO1	NM_001167856.1,NM_018183.3	,	2916,2732,855	GG,GA,AA		25.314,48.5928,34.1535	,	1022/1394,1021/1393	123799974	8564,4442	2203	4300	6503	SO:0001819	synonymous_variant	55206	exon22			TCTATCACCATGT	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.3066T>C	12.37:g.123799974A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	94	37	0.393617	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	37	CCDS53844.1																																																																																			A|0.316;G|0.684	0.684	strong		0.363	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
DOC2B	8447	hgsc.bcm.edu	37	17	31199	31199	+	Silent	SNP	G	G	A	rs551529924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:31199G>A	ENST00000343572.7	-	1	228	c.72C>T	c.(70-72)ccC>ccT	p.P24P	DOC2B_ENST00000609727.1_5'Flank|AC108004.2_ENST00000576171.1_lincRNA	NM_003585.3	NP_003576	Q14184	DOC2B_HUMAN	double C2-like domains, beta	24	Mediates interaction with DYNLT1.|Negatively regulates targeting to plasma membrane. {ECO:0000250}.				calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of insulin secretion (GO:0032024)|positive regulation of vesicle fusion (GO:0031340)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			endometrium(2)|ovary(1)	3						GGATGGGGCCGGGGCACACGT	0.751													G|||	8	0.00159744	0.0053	0.0014	5008	,	,		3708	0.0		0.0	False		,,,				2504	0.0				p.P24P		Atlas-SNP	.											.	DOC2B	6	.	0			c.C72T						PASS	.						3.0	3.0	3.0					17																	31199		571	1338	1909	SO:0001819	synonymous_variant	8447	exon1			GGGGCCGGGGCAC	D70830	CCDS73934.1	17p13.3	2014-07-16			ENSG00000272636	ENSG00000272636		"""Synaptotagmins"""	2986	protein-coding gene	gene with protein product		604568	"""double C2-like domains, beta-like"""	DOC2BL		7826360	Standard	NM_003585		Approved		uc010vpx.1	Q14184	OTTHUMG00000154415	ENST00000343572.7:c.72C>T	17.37:g.31199G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_003585		Silent	SNP	ENST00000343572.7	37																																																																																				.	.	none		0.751	DOC2B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335122.3	NM_003585	
TTC4	7268	hgsc.bcm.edu	37	1	55188437	55188437	+	Missense_Mutation	SNP	C	C	T	rs62000412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55188437C>T	ENST00000371281.3	+	5	646	c.559C>T	c.(559-561)Ctt>Ttt	p.L187F	MROH7-TTC4_ENST00000414150.2_3'UTR|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	187										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						AGAGAAGAAGCTTCTGGAAAT	0.463													C|||	65	0.0129792	0.0484	0.0014	5008	,	,		20967	0.0		0.0	False		,,,				2504	0.0				p.L187F		Atlas-SNP	.											.	TTC4	21	.	0			c.C559T						PASS	.	C	PHE/LEU	192,4214	121.7+/-159.2	4,184,2015	122.0	115.0	117.0		559	5.4	1.0	1	dbSNP_129	117	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TTC4	NM_004623.4	22	4,186,6313	TT,TC,CC		0.0233,4.3577,1.4916	probably-damaging	187/388	55188437	194,12812	2203	4300	6503	SO:0001583	missense	7268	exon5			AAGAAGCTTCTGG		CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"""Tetratricopeptide (TTC) repeat domain containing"""	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.559C>T	1.37:g.55188437C>T	ENSP00000360329:p.Leu187Phe	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Missense_Mutation	SNP	ENST00000371281.3	37	CCDS596.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	C	21.3	4.125911	0.77436	0.043577	2.33E-4	ENSG00000243725	ENST00000371281;ENST00000371284	T	0.20200	2.09	5.42	5.42	0.78866	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.13841	0.0335	M	0.82716	2.605	0.58432	D	0.999996	P;D	0.64830	0.908;0.994	P;P	0.51945	0.514;0.685	T	0.06320	-1.0833	9	0.48119	T	0.1	-11.5851	18.1602	0.89706	0.0:1.0:0.0:0.0	rs62000412	187;198	O95801;Q5TA95	TTC4_HUMAN;.	F	187;198	ENSP00000360329:L187F	ENSP00000360329:L187F	L	+	1	0	TTC4	54961025	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.354000	0.52254	2.703000	0.92315	0.460000	0.39030	CTT	C|0.986;T|0.014	0.014	strong		0.463	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623	
LILRB2	10288	hgsc.bcm.edu	37	19	54782165	54782165	+	Missense_Mutation	SNP	C	C	T	rs4993133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782165C>T	ENST00000391749.4	-	7	1478	c.1207G>A	c.(1207-1209)Gac>Aac	p.D403N	LILRB2_ENST00000391746.1_Missense_Mutation_p.D403N|LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000314446.5_Missense_Mutation_p.D403N|LILRB2_ENST00000434421.1_Missense_Mutation_p.D287N|LILRB2_ENST00000391748.1_Missense_Mutation_p.D403N	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	403	Ig-like C2-type 4.		D -> N (in dbSNP:rs4993133).		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)		AGGTAGGGGTCGGAGTTGAGT	0.592													.|||	31	0.0061901	0.0204	0.0014	5008	,	,		17568	0.0		0.002	False		,,,				2504	0.001				p.D403N		Atlas-SNP	.											.	LILRB2	94	.	0			c.G1207A						PASS	.	T	ASN/ASP,ASN/ASP	51,4355	821.0+/-416.4	1,49,2153	101.0	94.0	96.0		1207,1207	-2.2	0.0	19	dbSNP_113	96	5,8595	818.7+/-406.8	0,5,4295	no	missense,missense	LILRB2	NM_001080978.2,NM_005874.3	23,23	1,54,6448	TT,TC,CC		0.0581,1.1575,0.4306	benign,benign	403/598,403/599	54782165	56,12950	2203	4300	6503	SO:0001583	missense	10288	exon7			AGGGGTCGGAGTT	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.1207G>A	19.37:g.54782165C>T	ENSP00000375629:p.Asp403Asn	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	142	61	0.429577	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	9	0.004120879120879121	7	0.014227642276422764	0	0.0	0	0.0	2	0.002638522427440633	T	1.465	-0.561273	0.03939	0.011575	5.81E-4	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00717	5.79;5.79;5.79;5.79;5.79	1.88	-2.23	0.06930	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.810930	0.01046	N	0.004391	T	0.00300	0.0009	N	0.03294	-0.36	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.43653	-0.9378	10	0.06494	T	0.89	.	0.3448	0.00339	0.2691:0.185:0.1425:0.4034	rs4993133	403;420;403	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	N	403;403;403;403;287	ENSP00000375628:D403N;ENSP00000319960:D403N;ENSP00000375629:D403N;ENSP00000375626:D403N;ENSP00000410117:D287N	ENSP00000319960:D403N	D	-	1	0	LILRB2	59473977	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.319000	0.00514	-1.728000	0.01366	-2.542000	0.00179	GAC	C|0.995;T|0.005	0.005	strong		0.592	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
TTN	7273	hgsc.bcm.edu	37	2	179412452	179412452	+	Missense_Mutation	SNP	C	C	T	rs67665715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179412452C>T	ENST00000591111.1	-	289	89202	c.88978G>A	c.(88978-88980)Gtc>Atc	p.V29660I	TTN_ENST00000589042.1_Missense_Mutation_p.V31301I|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V22236I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V28733I|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V22361I|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V22428I|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29660	Ig-like 135.				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)			ACAACTGTGACGCTAAATGTT	0.478													C|||	180	0.0359425	0.1271	0.0159	5008	,	,		20351	0.0		0.001	False		,,,				2504	0.0				p.V31301I		Atlas-SNP	.											.	TTN	18412	.	0			c.G93901A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	395,3517		24,347,1585	139.0	130.0	133.0		67282,67081,86197,66706	-2.3	0.9	2	dbSNP_130	133	8,8316		0,8,4154	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	24,355,5739	TT,TC,CC		0.0961,10.0971,3.2936	benign,benign,benign,benign	22428/27119,22361/27052,28733/33424,22236/26927	179412452	403,11833	1956	4162	6118	SO:0001583	missense	7273	exon339			CTGTGACGCTAAA	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.88978G>A	2.37:g.179412452C>T	ENSP00000465570:p.Val29660Ile	Somatic	387	0	0		WXS	Illumina HiSeq	Phase_I	438	243	0.554795	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		86	0.039377289377289376	78	0.15853658536585366	8	0.022099447513812154	0	0.0	0	0.0	C	6.281	0.420045	0.11928	0.100971	9.61E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.92	-2.32	0.06745	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00271	0.0008	N	0.17631	0.505	0.30962	P	0.723517	B;B;B;B	0.09022	0.002;0.002;0.002;0.002	B;B;B;B	0.08055	0.002;0.002;0.003;0.003	T	0.09618	-1.0666	8	0.87932	D	0	.	13.3122	0.60386	0.0:0.727:0.0:0.273	.	22236;22361;22428;29660	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	28733;22236;22428;22361;22233	ENSP00000343764:V28733I;ENSP00000434586:V22236I;ENSP00000340554:V22428I;ENSP00000352154:V22361I	ENSP00000340554:V22428I	V	-	1	0	TTN	179120698	0.965000	0.33210	0.865000	0.33974	0.314000	0.28054	0.991000	0.29654	-0.306000	0.08818	-1.934000	0.00508	GTC	C|0.967;T|0.033	0.033	strong		0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CACNA1S	779	hgsc.bcm.edu	37	1	201012484	201012484	+	Missense_Mutation	SNP	C	C	T	rs13374149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201012484C>T	ENST00000362061.3	-	40	5199	c.4973G>A	c.(4972-4974)cGt>cAt	p.R1658H	RP11-168O16.2_ENST00000415359.1_RNA|CACNA1S_ENST00000367338.3_Missense_Mutation_p.R1639H	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1658			R -> H (in dbSNP:rs13374149).		axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GGTATTGGCACGAGCCAGGGG	0.547											OREG0014067	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	499	0.0996406	0.2867	0.0418	5008	,	,		19713	0.001		0.0577	False		,,,				2504	0.0327				p.R1658H		Atlas-SNP	.											.	CACNA1S	249	.	0			c.G4973A						PASS	.	C	HIS/ARG	1116,3290		137,842,1224	229.0	185.0	200.0		4973	1.6	1.0	1	dbSNP_121	200	456,8144		13,430,3857	yes	missense	CACNA1S	NM_000069.2	29	150,1272,5081	TT,TC,CC		5.3023,25.3291,12.0867	benign	1658/1874	201012484	1572,11434	2203	4300	6503	SO:0001583	missense	779	exon40			TTGGCACGAGCCA	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.4973G>A	1.37:g.201012484C>T	ENSP00000355192:p.Arg1658His	Somatic	186	0	0	2118	WXS	Illumina HiSeq	Phase_I	172	83	0.482558	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	195	0.08928571428571429	135	0.27439024390243905	16	0.04419889502762431	1	0.0017482517482517483	43	0.05672823218997362	.	10.82	1.457511	0.26161	0.253291	0.053023	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.96232	-3.95;-3.88	4.63	1.62	0.23740	.	464.918000	0.00166	U	0.000000	T	0.00144	0.0004	L	0.50333	1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.50030	-0.8875	9	0.26408	T	0.33	.	6.6767	0.23098	0.3124:0.6007:0.0:0.0869	rs13374149;rs52818718;rs13374149	1658	Q13698	CAC1S_HUMAN	H	1658;1639	ENSP00000355192:R1658H;ENSP00000356307:R1639H	ENSP00000355192:R1658H	R	-	2	0	CACNA1S	199279107	0.019000	0.18553	0.958000	0.39756	0.886000	0.51366	-0.316000	0.08071	0.166000	0.19597	0.544000	0.68410	CGT	C|0.890;T|0.110	0.110	strong		0.547	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
GREB1	9687	hgsc.bcm.edu	37	2	11755316	11755316	+	Silent	SNP	C	C	T	rs16857699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11755316C>T	ENST00000381486.2	+	20	3522	c.3222C>T	c.(3220-3222)aaC>aaT	p.N1074N	GREB1_ENST00000396123.1_Silent_p.N72N|GREB1_ENST00000234142.5_Silent_p.N1074N	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1074						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)		TTGTGAGCAACGAGGTTCCCT	0.562													C|||	318	0.0634984	0.23	0.0187	5008	,	,		21207	0.0		0.001	False		,,,				2504	0.0				p.N1074N	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.C3222T						PASS	.	C		736,3390		56,624,1383	85.0	87.0	86.0		3222	-3.1	0.1	2	dbSNP_123	86	9,8407		0,9,4199	no	coding-synonymous	GREB1	NM_014668.3		56,633,5582	TT,TC,CC		0.1069,17.8381,5.94		1074/1950	11755316	745,11797	2063	4208	6271	SO:0001819	synonymous_variant	9687	exon20			GAGCAACGAGGTT		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.3222C>T	2.37:g.11755316C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	159	159	1	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	CCDS42655.1																																																																																			C|0.946;T|0.054	0.054	strong		0.562	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
CYP24A1	1591	hgsc.bcm.edu	37	20	52786219	52786219	+	Silent	SNP	G	G	A	rs2296241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52786219G>A	ENST00000216862.3	-	4	945	c.552C>T	c.(550-552)gcC>gcT	p.A184A	CYP24A1_ENST00000395954.3_Silent_p.A42A|CYP24A1_ENST00000395955.3_Silent_p.A184A	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	184					osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin D receptor signaling pathway (GO:0070561)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity (GO:0030342)|25-hydroxycholecalciferol-24-hydroxylase activity (GO:0008403)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Corticotropin(DB01285)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	CCATAAAATCGGCCAAGACCT	0.408													A|||	2294	0.458067	0.4917	0.4222	5008	,	,		21649	0.4058		0.5328	False		,,,				2504	0.4151				p.A184A		Atlas-SNP	.											CYP24A1,trunk,malignant_melanoma,-1,1	CYP24A1	75	1	0			c.C552T						PASS	.	A	,	2184,2222	590.7+/-387.4	515,1154,534	106.0	92.0	97.0		552,552	-3.5	1.0	20	dbSNP_100	97	4635,3965	551.3+/-385.9	1236,2163,901	yes	coding-synonymous,coding-synonymous	CYP24A1	NM_000782.4,NM_001128915.1	,	1751,3317,1435	AA,AG,GG		46.1047,49.5688,47.5704	,	184/515,184/449	52786219	6819,6187	2203	4300	6503	SO:0001819	synonymous_variant	1591	exon4			AAAATCGGCCAAG	U60669	CCDS33491.1, CCDS46616.1	20q13.2-q13.3	2003-02-28	2003-02-14	2003-02-28	ENSG00000019186	ENSG00000019186		"""Cytochrome P450s"""	2602	protein-coding gene	gene with protein product		126065	"""cytochrome P450, subfamily XXIV (vitamin D 24-hydroxylase)"""	CYP24			Standard	NM_000782		Approved	CP24, P450-CC24	uc002xwv.2	Q07973	OTTHUMG00000032773	ENST00000216862.3:c.552C>T	20.37:g.52786219G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	124	59	0.475806	NM_000782	Q15807|Q32ML3|Q5I2W7	Silent	SNP	ENST00000216862.3	37	CCDS33491.1																																																																																			G|0.500;A|0.500	0.500	strong		0.408	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2		
PCDHB4	56131	hgsc.bcm.edu	37	5	140503017	140503017	+	Silent	SNP	G	G	A	rs144689137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140503017G>A	ENST00000194152.1	+	1	1437	c.1437G>A	c.(1435-1437)tcG>tcA	p.S479S	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	479	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACAGAGACTCGGGCACCAACG	0.667													g|||	133	0.0265575	0.0862	0.0159	5008	,	,		14724	0.0		0.008	False		,,,				2504	0.0				p.S479S		Atlas-SNP	.											PCDHB4,right_upper_lobe,carcinoma,+1,1	PCDHB4	177	1	0			c.G1437A						scavenged	.						42.0	48.0	46.0					5																	140503017		2202	4295	6497	SO:0001819	synonymous_variant	56131	exon1			AGACTCGGGCACC	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1437G>A	5.37:g.140503017G>A		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	237	23	0.0970464	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			G|0.216;A|0.784	0.784	strong		0.667	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
PASK	23178	hgsc.bcm.edu	37	2	242054403	242054403	+	Intron	SNP	G	G	A	rs3815305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242054403G>A	ENST00000405260.1	-	14	4032				PASK_ENST00000544142.1_Intron|PASK_ENST00000358649.4_Intron|PASK_ENST00000539818.1_Intron|PASK_ENST00000403638.3_Missense_Mutation_p.R1130W|PASK_ENST00000234040.4_Intron|PASK_ENST00000475666.1_5'Flank	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase						negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		TGCAGCCACCGGACCCAGGCA	0.547													G|||	1220	0.24361	0.3162	0.2291	5008	,	,		18665	0.4147		0.0974	False		,,,				2504	0.1299				p.R1130W		Atlas-SNP	.											.	PASK	230	.	0			c.C3388T						PASS	.																																			SO:0001627	intron_variant	23178	exon14			GCCACCGGACCCA	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.3333+54C>T	2.37:g.242054403G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_001252124	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	531	0.24313186813186813	146	0.2967479674796748	72	0.19889502762430938	237	0.4143356643356643	76	0.10026385224274406	G	10.73	1.432611	0.25813	.	.	ENSG00000115687	ENST00000403638	T	0.51817	0.69	3.78	-2.3	0.06785	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41680	-0.9495	7	0.87932	D	0	.	6.7909	0.23699	0.2611:0.1384:0.6005:0.0	rs3815305;rs61610946;rs3815305	1130	G5E9F1	.	W	1130	ENSP00000384438:R1130W	ENSP00000384438:R1130W	R	-	1	2	PASK	241703076	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.947000	0.03901	-0.677000	0.05231	-0.416000	0.06073	CGG	G|0.764;A|0.236	0.236	strong		0.547	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
MDC1	9656	hgsc.bcm.edu	37	6	30680608	30680608	+	Missense_Mutation	SNP	C	C	T	rs2075015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30680608C>T	ENST00000376406.3	-	5	1758	c.1111G>A	c.(1111-1113)Gag>Aag	p.E371K	MDC1_ENST00000494654.1_5'Flank|MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Missense_Mutation_p.E371K	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	371	Required for nuclear localization (NLS1).		E -> K (in dbSNP:rs2075015). {ECO:0000269|PubMed:16702430}.		DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						GCCTGGCTCTCCTGCAGATGG	0.542								Other conserved DNA damage response genes					C|||	317	0.0632987	0.1324	0.0504	5008	,	,		21001	0.0645		0.0189	False		,,,				2504	0.0235				p.E371K		Atlas-SNP	.											.	MDC1	218	.	0			c.G1111A						PASS	.	C	LYS/GLU	325,2695		22,281,1207	87.0	98.0	94.0		1111	2.3	0.1	6	dbSNP_96	94	91,5325		0,91,2617	yes	missense	MDC1	NM_014641.2	56	22,372,3824	TT,TC,CC		1.6802,10.7616,4.9312	possibly-damaging	371/2090	30680608	416,8020	1510	2708	4218	SO:0001583	missense	9656	exon5			GGCTCTCCTGCAG	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.1111G>A	6.37:g.30680608C>T	ENSP00000365588:p.Glu371Lys	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	147	75	0.510204	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	142	0.06501831501831502	63	0.12804878048780488	19	0.052486187845303865	49	0.08566433566433566	11	0.014511873350923483	C	15.37	2.813758	0.50527	0.107616	0.016802	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.03441	4.04;3.93	4.19	2.32	0.28847	.	0.419494	0.17581	N	0.169108	T	0.02533	0.0077	M	0.71581	2.175	0.47511	P	5.560000000000009E-4	P;P;P;B	0.43750	0.506;0.506;0.816;0.154	B;B;B;B	0.43809	0.319;0.203;0.432;0.048	T	0.35871	-0.9771	9	0.59425	D	0.04	-3.3359	6.0072	0.19553	0.0:0.7543:0.0:0.2457	rs2075015;rs2075015	371;243;371;371	Q14676-2;B4DYH4;Q14676;Q14676-4	.;.;MDC1_HUMAN;.	K	371;371;371;243	ENSP00000365588:E371K;ENSP00000365587:E371K	ENSP00000365587:E371K	E	-	1	0	MDC1	30788587	0.002000	0.14202	0.094000	0.20943	0.767000	0.43475	0.631000	0.24568	0.675000	0.31264	0.561000	0.74099	GAG	C|0.939;T|0.061	0.061	strong		0.542	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
MKRN3	7681	hgsc.bcm.edu	37	15	23811592	23811592	+	Silent	SNP	C	C	T	rs2239669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:23811592C>T	ENST00000314520.3	+	1	1139	c.663C>T	c.(661-663)ccC>ccT	p.P221P	MKRN3_ENST00000568252.1_Intron|RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000564592.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	221					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		CATCTGCCCCCGAGGCTCCTC	0.592													C|||	1051	0.209864	0.1596	0.1715	5008	,	,		17393	0.1875		0.3161	False		,,,				2504	0.2188				p.P221P		Atlas-SNP	.											.	MKRN3	155	.	0			c.C663T						PASS	.	C		794,3612	313.3+/-293.0	58,678,1467	47.0	52.0	50.0		663	-8.1	0.0	15	dbSNP_98	50	2651,5949	420.5+/-353.4	421,1809,2070	no	coding-synonymous	MKRN3	NM_005664.3		479,2487,3537	TT,TC,CC		30.8256,18.0209,26.4878		221/508	23811592	3445,9561	2203	4300	6503	SO:0001819	synonymous_variant	7681	exon1			TGCCCCCGAGGCT	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"""RING-type (C3HC4) zinc fingers"""	7114	protein-coding gene	gene with protein product	"""zinc finger protein 127"""	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.663C>T	15.37:g.23811592C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_005664		Silent	SNP	ENST00000314520.3	37	CCDS10013.1																																																																																			C|0.745;A|0.002	.	strong		0.592	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664	
CRACR2A	84766	hgsc.bcm.edu	37	12	3747496	3747496	+	Missense_Mutation	SNP	G	G	C	rs58583720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:3747496G>C	ENST00000440314.2	-	14	1869	c.1396C>G	c.(1396-1398)Cgg>Ggg	p.R466G		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)			CGGAGCGGCCGGGGGTACGGA	0.612													G|||	59	0.0117812	0.0416	0.0058	5008	,	,		14651	0.0		0.0	False		,,,				2504	0.0				p.R466G		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.C1396G						PASS	.	G	GLY/ARG	50,1334		1,48,643	20.0	24.0	23.0		1396	3.5	0.0	12	dbSNP_129	23	0,3182		0,0,1591	yes	missense	EFCAB4B	NM_001144958.1	125	1,48,2234	CC,CG,GG		0.0,3.6127,1.0951	benign	466/732	3747496	50,4516	692	1591	2283	SO:0001583	missense	84766	exon14			GCGGCCGGGGGTA																												ENST00000440314.2:c.1396C>G	12.37:g.3747496G>C	ENSP00000409382:p.Arg466Gly	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	46	0.567901	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000440314.2	37	CCDS44803.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.054114	0.36277	0.036127	0.0	ENSG00000130038	ENST00000440314	T	0.61274	0.12	4.4	3.51	0.40186	.	.	.	.	.	T	0.23926	0.0579	.	.	.	0.36197	D	0.85047	P	0.42620	0.785	P	0.45506	0.483	T	0.53479	-0.8433	8	0.45353	T	0.12	.	10.1568	0.42827	0.0984:0.0:0.9016:0.0	rs58583720	466	Q9BSW2-2	.	G	466	ENSP00000409382:R466G	ENSP00000409382:R466G	R	-	1	2	EFCAB4B	3617757	0.331000	0.24713	0.007000	0.13788	0.194000	0.23727	4.138000	0.58017	1.074000	0.40909	0.557000	0.71058	CGG	A|0.002;C|0.001;G|0.997	0.001	strong		0.612	EFCAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398640.2		
HEPH	9843	hgsc.bcm.edu	37	X	65427040	65427040	+	Silent	SNP	T	T	C	rs61746100|rs806607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:65427040T>C	ENST00000343002.2	+	13	2959	c.2295T>C	c.(2293-2295)taT>taC	p.Y765Y	HEPH_ENST00000441993.2_Silent_p.Y768Y|HEPH_ENST00000336279.5_Silent_p.Y498Y|HEPH_ENST00000519389.1_Silent_p.Y819Y|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	140	0	0		WXS	Illumina HiSeq	Phase_I	122	122	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	
KIF18B	146909	hgsc.bcm.edu	37	17	43010064	43010064	+	Silent	SNP	G	G	A	rs57250020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43010064G>A	ENST00000593135.1	-	9	1312	c.1215C>T	c.(1213-1215)ccC>ccT	p.P405P	KIF18B_ENST00000590129.1_Silent_p.P414P|KIF18B_ENST00000339151.4_Silent_p.P405P|KIF18B_ENST00000438933.2_Silent_p.P405P|KIF18B_ENST00000587309.1_Silent_p.P405P	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	414	Pro-rich.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				GTCCCGACTTGGGAGATCCTG	0.637													G|||	485	0.096845	0.2133	0.1037	5008	,	,		17275	0.0407		0.0278	False		,,,				2504	0.0634				p.P405P		Atlas-SNP	.											.	KIF18B	63	.	0			c.C1215T						PASS	.	G		647,3211		47,553,1329	107.0	121.0	116.0		1215	3.9	0.4	17	dbSNP_129	116	245,8003		10,225,3889	no	coding-synonymous	KIF18B	NM_001080443.1		57,778,5218	AA,AG,GG		2.9704,16.7703,7.3682		405/856	43010064	892,11214	1929	4124	6053	SO:0001819	synonymous_variant	146909	exon9			CGACTTGGGAGAT		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"""Kinesins"""	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.1215C>T	17.37:g.43010064G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	71	23	0.323944	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Silent	SNP	ENST00000593135.1	37	CCDS45709.2																																																																																			G|0.935;A|0.065	0.065	strong		0.637	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443	
MS4A7	58475	hgsc.bcm.edu	37	11	60154242	60154242	+	Missense_Mutation	SNP	C	C	A	rs2233249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60154242C>A	ENST00000300184.3	+	4	531	c.335C>A	c.(334-336)cCc>cAc	p.P112H	MS4A7_ENST00000358246.1_Missense_Mutation_p.P67H|MS4A7_ENST00000530234.2_Intron|MS4A7_ENST00000534016.1_Missense_Mutation_p.P67H|MS4A14_ENST00000531787.1_Intron	NM_021201.4|NM_206939.1	NP_067024.1|NP_996822.1	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member 7	112			P -> H (in dbSNP:rs2233249).			integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(8)|ovary(1)|skin(1)	20						TCAACTAAGCCCTTTGTAAGT	0.373													C|||	122	0.024361	0.0688	0.0058	5008	,	,		20741	0.001		0.0	False		,,,				2504	0.0266				p.P112H		Atlas-SNP	.											.	MS4A7	38	.	0			c.C335A						PASS	.	C	HIS/PRO,HIS/PRO,HIS/PRO,HIS/PRO	306,4100	166.5+/-197.7	9,288,1906	132.0	122.0	125.0		335,200,335,200	-0.3	0.0	11	dbSNP_98	125	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense,missense,missense	MS4A7	NM_021201.4,NM_206938.1,NM_206939.1,NM_206940.1	77,77,77,77	9,290,6204	AA,AC,CC		0.0233,6.9451,2.3681	probably-damaging,probably-damaging,probably-damaging,probably-damaging	112/241,67/196,112/241,67/196	60154242	308,12698	2203	4300	6503	SO:0001583	missense	58475	exon4			CTAAGCCCTTTGT	AB026043	CCDS7985.1, CCDS7986.1	11q12	2008-03-25				ENSG00000166927			13378	protein-coding gene	gene with protein product		606502				11245982, 11401424	Standard	NM_021201		Approved	CD20L4, CFFM4, MS4A8	uc001npf.3	Q9GZW8		ENST00000300184.3:c.335C>A	11.37:g.60154242C>A	ENSP00000300184:p.Pro112His	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_021201	A6NP53|Q6IAG8	Missense_Mutation	SNP	ENST00000300184.3	37	CCDS7985.1	34	0.015567765567765568	31	0.06300813008130081	3	0.008287292817679558	0	0.0	0	0.0	C	10.60	1.397107	0.25205	0.069451	2.33E-4	ENSG00000166927	ENST00000300184;ENST00000358246;ENST00000534016;ENST00000530614;ENST00000528215	T;T;T;T;T	0.68624	4.35;4.35;4.35;4.35;-0.34	3.81	-0.294	0.12831	.	2.546860	0.01657	N	0.024878	T	0.21387	0.0515	M	0.66939	2.045	0.09310	N	1	D;D;D	0.76494	0.992;0.99;0.999	P;P;D	0.65323	0.873;0.723;0.934	T	0.44174	-0.9345	10	0.18710	T	0.47	-25.1732	3.2297	0.06744	0.1847:0.5024:0.0:0.3128	rs2233249;rs52808452;rs60638376;rs2233249	67;67;112	E9PIV6;Q9GZW8-2;Q9GZW8	.;.;MS4A7_HUMAN	H	112;67;67;67;38	ENSP00000300184:P112H;ENSP00000350983:P67H;ENSP00000434637:P67H;ENSP00000433861:P67H;ENSP00000431408:P38H	ENSP00000300184:P112H	P	+	2	0	MS4A7	59910818	0.000000	0.05858	0.012000	0.15200	0.386000	0.30323	0.406000	0.21032	-0.149000	0.11215	-0.471000	0.05019	CCC	C|0.973;A|0.027	0.027	strong		0.373	MS4A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394299.1		
HTT	3064	hgsc.bcm.edu	37	4	3137674	3137674	+	Missense_Mutation	SNP	G	G	A	rs363075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:3137674G>A	ENST00000355072.5	+	20	2822	c.2677G>A	c.(2677-2679)Ggg>Agg	p.G893R		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	893			G -> R (in dbSNP:rs363075).		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)		CTTACACAGAGGGGCTCATCA	0.383													G|||	119	0.023762	0.003	0.0259	5008	,	,		17994	0.0		0.0736	False		,,,				2504	0.0235				p.G893R		Atlas-SNP	.											.	HTT	221	.	0			c.G2677A						PASS	.	G	ARG/GLY	49,3645		1,47,1799	155.0	142.0	146.0		2677	4.8	1.0	4	dbSNP_79	146	492,7702		6,480,3611	yes	missense	HTT	NM_002111.6	125	7,527,5410	AA,AG,GG		6.0044,1.3265,4.5508	probably-damaging	893/3143	3137674	541,11347	1847	4097	5944	SO:0001583	missense	3064	exon20			CACAGAGGGGCTC	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.2677G>A	4.37:g.3137674G>A	ENSP00000347184:p.Gly893Arg	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	271	134	0.494465	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	56	0.02564102564102564	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	46	0.06068601583113457	G	23.5	4.419932	0.83559	0.013265	0.060044	ENSG00000197386	ENST00000355072	T	0.05580	3.42	5.68	4.84	0.62591	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.02047	0.0064	L	0.49126	1.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00093	-1.2080	10	0.62326	D	0.03	.	14.9025	0.70689	0.069:0.0:0.931:0.0	rs363075;rs52792844;rs363075	893	P42858	HD_HUMAN	R	893	ENSP00000347184:G893R	ENSP00000347184:G893R	G	+	1	0	HTT	3107472	1.000000	0.71417	0.992000	0.48379	0.968000	0.65278	6.780000	0.75063	1.403000	0.46800	0.655000	0.94253	GGG	G|0.959;A|0.041	0.041	strong		0.383	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
COMT	1312	hgsc.bcm.edu	37	22	19950268	19950268	+	Silent	SNP	G	G	A	rs740602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19950268G>A	ENST00000361682.6	+	3	601	c.219G>A	c.(217-219)caG>caA	p.Q73Q	COMT_ENST00000403710.1_Silent_p.Q73Q|COMT_ENST00000406520.3_Silent_p.Q73Q|COMT_ENST00000407537.1_Silent_p.Q23Q|COMT_ENST00000449653.1_Silent_p.Q23Q|MIR4761_ENST00000585066.1_RNA|COMT_ENST00000403184.1_Silent_p.Q73Q	NM_000754.3	NP_000745.1	P21964	COMT_HUMAN	catechol-O-methyltransferase	73					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)			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)	GGAACGCACAGAGCGTGCTGG	0.622													G|||	300	0.0599042	0.2005	0.0202	5008	,	,		18048	0.0		0.0089	False		,,,				2504	0.0123				p.Q73Q		Atlas-SNP	.											.	COMT	10	.	0			c.G219A						PASS	.	G	,,,	790,3616	314.4+/-293.6	72,646,1485	80.0	75.0	77.0		219,219,219,69	2.2	1.0	22	dbSNP_86	77	39,8561	25.7+/-73.6	0,39,4261	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COMT	NM_000754.3,NM_001135161.1,NM_001135162.1,NM_007310.2	,,,	72,685,5746	AA,AG,GG		0.4535,17.9301,6.374	,,,	73/272,73/272,73/272,23/222	19950268	829,12177	2203	4300	6503	SO:0001819	synonymous_variant	1312	exon3			CGCACAGAGCGTG		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.219G>A	22.37:g.19950268G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_000754	A8MPV9|Q6IB07|Q6ICE6|Q9BWC7	Silent	SNP	ENST00000361682.6	37	CCDS13770.1																																																																																			A|0.059;C|0.007	0.059	strong		0.622	COMT-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318936.2	NM_000754	
CD44	960	hgsc.bcm.edu	37	11	35201842	35201842	+	Silent	SNP	C	C	T	rs1071695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:35201842C>T	ENST00000428726.2	+	3	378	c.255C>T	c.(253-255)caC>caT	p.H85H	CD44_ENST00000415148.2_Silent_p.H85H|CD44_ENST00000526669.2_Silent_p.H85H|CD44_ENST00000433354.2_Silent_p.H85H|CD44_ENST00000449691.2_Silent_p.H85H|CD44_ENST00000263398.6_Silent_p.H85H|CD44_ENST00000434472.2_Silent_p.H85H|CD44_ENST00000360158.4_Silent_p.H85H|CD44_ENST00000278386.6_Intron|CD44_ENST00000352818.4_Silent_p.H85H|CD44_ENST00000437706.2_Silent_p.H85H|CD44_ENST00000433892.2_Silent_p.H85H	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	85	Link. {ECO:0000255|PROSITE- ProRule:PRU00323}.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	TAGAAGGGCACGTGGTGATTC	0.438													C|||	698	0.139377	0.149	0.2205	5008	,	,		19558	0.0714		0.173	False		,,,				2504	0.1043				p.H85H		Atlas-SNP	.											CD44,colon,carcinoma,0,1	CD44	48	1	0			c.C255T	GRCh37	CM076085	CD44	M	rs1071695	PASS	.	C	,,,,,,,	712,3692	296.7+/-284.4	54,604,1544	168.0	140.0	150.0		255,255,255,255,,255,255,255	-8.2	0.3	11	dbSNP_86	150	1477,7119	280.8+/-294.7	123,1231,2944	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	CD44	NM_000610.3,NM_001001389.1,NM_001001390.1,NM_001001391.1,NM_001001392.1,NM_001202555.1,NM_001202556.1,NM_001202557.1	,,,,,,,	177,1835,4488	TT,TC,CC		17.1824,16.1671,16.8385	,,,,,,,	85/743,85/700,85/494,85/362,,85/430,85/341,85/295	35201842	2189,10811	2202	4298	6500	SO:0001819	synonymous_variant	960	exon3			AGGGCACGTGGTG	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.255C>T	11.37:g.35201842C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	231	114	0.493506	NM_001001391	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	37	CCDS7897.1	333|333	0.15247252747252749|0.15247252747252749	75|75	0.1524390243902439|0.1524390243902439	79|79	0.21823204419889503|0.21823204419889503	47|47	0.08216783216783216|0.08216783216783216	132|132	0.1741424802110818|0.1741424802110818	C|C	4.473|4.473	0.087625|0.087625	0.08583|0.08583	0.161671|0.161671	0.171824|0.171824	ENSG00000026508|ENSG00000026508	ENST00000442151;ENST00000528455|ENST00000527889;ENST00000531873	.|.	.|.	.|.	5.86|5.86	-8.16|-8.16	0.01061|0.01061	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999831683|0.999999831683	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.18366|0.18366	-1.0339|-1.0339	3|3	.|.	.|.	.|.	-5.8315|-5.8315	17.4346|17.4346	0.87548|0.87548	0.0:0.1989:0.0:0.8011|0.0:0.1989:0.0:0.8011	rs1071695;rs3198437;rs3198804;rs11542696;rs17423178;rs17849845;rs1071695|rs1071695;rs3198437;rs3198804;rs11542696;rs17423178;rs17849845;rs1071695	.|.	.|.	.|.	C|M	85;22|41;6	.|.	.|.	R|T	+|+	1|2	0|0	CD44|CD44	35158418|35158418	0.001000|0.001000	0.12720|0.12720	0.296000|0.296000	0.24974|0.24974	0.509000|0.509000	0.34042|0.34042	-3.037000|-3.037000	0.00634|0.00634	-1.565000|-1.565000	0.01676|0.01676	-0.806000|-0.806000	0.03193|0.03193	CGT|ACG	C|0.835;T|0.165	0.165	strong		0.438	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
ZNF439	90594	hgsc.bcm.edu	37	19	11978130	11978130	+	Silent	SNP	A	A	G	rs10417222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11978130A>G	ENST00000304030.2	+	3	446	c.246A>G	c.(244-246)acA>acG	p.T82T	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_5'UTR	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	82	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)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						GGAGTGTCACAGAAGAGAAAG	0.333													a|||	80	0.0159744	0.0582	0.0043	5008	,	,		19117	0.0		0.0	False		,,,				2504	0.0				p.T82T		Atlas-SNP	.											.	ZNF439	67	.	0			c.A246G						PASS	.	A		277,4117	141.9+/-177.2	9,259,1929	69.0	73.0	72.0		246	-1.1	0.0	19	dbSNP_119	72	5,8591	3.7+/-12.6	0,5,4293	no	coding-synonymous	ZNF439	NM_152262.2		9,264,6222	GG,GA,AA		0.0582,6.3041,2.1709		82/500	11978130	282,12708	2197	4298	6495	SO:0001819	synonymous_variant	90594	exon3			TGTCACAGAAGAG	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.246A>G	19.37:g.11978130A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_152262	Q8IYZ7|Q96SU1	Silent	SNP	ENST00000304030.2	37	CCDS12268.1																																																																																			A|0.978;G|0.022	0.022	strong		0.333	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1		
PPL	5493	hgsc.bcm.edu	37	16	4935257	4935257	+	Silent	SNP	G	G	A	rs571194570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4935257G>A	ENST00000345988.2	-	22	3488	c.3399C>T	c.(3397-3399)ctC>ctT	p.L1133L	PPL_ENST00000590782.2_Silent_p.L1131L	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1133					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						ATTGGCGGGTGAGATCGCTGA	0.627													G|||	13	0.00259585	0.0091	0.0014	5008	,	,		12926	0.0		0.0	False		,,,				2504	0.0				p.L1133L		Atlas-SNP	.											.	PPL	168	.	0			c.C3399T						PASS	.						79.0	71.0	74.0					16																	4935257		2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			GCGGGTGAGATCG	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3399C>T	16.37:g.4935257G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	135	48	0.355556	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			.	.	none		0.627	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
TYW1	55253	hgsc.bcm.edu	37	7	66660242	66660242	+	Missense_Mutation	SNP	A	A	G	rs2949097		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:66660242A>G	ENST00000359626.5	+	15	2059	c.1895A>G	c.(1894-1896)cAc>cGc	p.H632R		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	632			H -> R (in dbSNP:rs2949097). {ECO:0000269|PubMed:14702039}.		tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)	p.H632R(1)		breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				CAGTTTGTCCACGAGTTGGTG	0.473																																					p.H632R		Atlas-SNP	.											TYW1,NS,carcinoma,0,1	TYW1	71	1	1	Substitution - Missense(1)	stomach(1)	c.A1895G						PASS	.						143.0	147.0	146.0					7																	66660242		2201	4298	6499	SO:0001583	missense	55253	exon15			TTGTCCACGAGTT	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1895A>G	7.37:g.66660242A>G	ENSP00000352645:p.His632Arg	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	138	33	0.23913	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Missense_Mutation	SNP	ENST00000359626.5	37	CCDS5538.1	423	0.1936813186813187	166	0.33739837398373984	76	0.20994475138121546	42	0.07342657342657342	139	0.18337730870712401	G	0.041	-1.284326	0.01398	.	.	ENSG00000198874	ENST00000359626	T	0.39592	1.07	3.7	-1.73	0.08081	tRNA wybutosine-synthesis (1);	0.536026	0.18649	N	0.135065	T	0.00012	0.0000	N	0.00332	-1.63	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46176	-0.9210	9	0.22706	T	0.39	.	10.5776	0.45235	0.6569:0.0:0.3431:0.0	rs2949097;rs3210780	632	Q9NV66	TYW1_HUMAN	R	632	ENSP00000352645:H632R	ENSP00000352645:H632R	H	+	2	0	TYW1	66297677	0.000000	0.05858	0.006000	0.13384	0.030000	0.12068	0.026000	0.13599	-0.771000	0.04608	-1.185000	0.01705	CAC	A|0.500;G|0.500	0.500	weak		0.473	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
CEACAM21	90273	hgsc.bcm.edu	37	19	42092225	42092225	+	Splice_Site	SNP	G	G	A	rs62119455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42092225G>A	ENST00000401445.2	+	6	908		c.e6+1		CEACAM21_ENST00000482870.2_Intron|CEACAM21_ENST00000407170.2_Splice_Site|CEACAM21_ENST00000187608.9_Splice_Site			Q3KPI0	CEA21_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 21							integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	13						CATCTCCTAGGTAAGACTGTC	0.592													g|||	124	0.0247604	0.0825	0.0072	5008	,	,		17365	0.0		0.0099	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CEACAM21	52	.	0			c.882+1G>A						PASS	.	G	,	261,3973		8,245,1864	63.0	66.0	65.0		,	1.2	0.0	19	dbSNP_129	65	58,8460		1,56,4202	yes	splice-5,splice-5	CEACAM21	NM_001098506.1,NM_033543.3	,	9,301,6066	AA,AG,GG		0.6809,6.1644,2.5016	,	,	42092225	319,12433	2117	4259	6376	SO:0001630	splice_region_variant	90273	exon6			TCCTAGGTAAGAC	AK023602	CCDS46086.1, CCDS46087.1, CCDS74373.1	19q13.2	2013-01-29			ENSG00000007129	ENSG00000007129		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28834	protein-coding gene	gene with protein product						12477932	Standard	XM_005278397		Approved	R29124_1, FLJ13540	uc002ore.4	Q3KPI0	OTTHUMG00000151062	ENST00000401445.2:c.879+1G>A	19.37:g.42092225G>A		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	158	158	1	NM_001098506	B7WNQ6|O75296|Q6UY47|Q96ER7	Splice_Site	SNP	ENST00000401445.2	37	CCDS46086.1																																																																																			G|0.981;A|0.019	0.019	strong		0.592	CEACAM21-005	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321140.1	NM_033543	Intron
WDR55	54853	hgsc.bcm.edu	37	5	140048792	140048792	+	Silent	SNP	C	C	A	rs35080423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140048792C>A	ENST00000358337.5	+	6	1026	c.789C>A	c.(787-789)acC>acA	p.T263T	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	263					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCAGTCACCGAGAGTCTGC	0.547													C|||	51	0.0101837	0.0378	0.0014	5008	,	,		21176	0.0		0.0	False		,,,				2504	0.0				p.T263T		Atlas-SNP	.											WDR55,NS,carcinoma,+2,1	WDR55	27	1	0			c.C789A						scavenged	.	C		113,4293	88.2+/-126.9	3,107,2093	84.0	77.0	79.0		789	-10.2	0.1	5	dbSNP_126	79	0,8600		0,0,4300	no	coding-synonymous	WDR55	NM_017706.4		3,107,6393	AA,AC,CC		0.0,2.5647,0.8688		263/384	140048792	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	54853	exon6			AGTCACCGAGAGT	AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"""WD repeat domain containing"""	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.789C>A	5.37:g.140048792C>A		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_017706	Q9NXK4	Silent	SNP	ENST00000358337.5	37	CCDS4235.1																																																																																			C|0.991;A|0.009	0.009	strong		0.547	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706	
KIRREL2	84063	hgsc.bcm.edu	37	19	36351906	36351906	+	Silent	SNP	C	C	A	rs73928338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36351906C>A	ENST00000360202.5	+	8	1222	c.1024C>A	c.(1024-1026)Cgg>Agg	p.R342R	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Silent_p.R342R|KIRREL2_ENST00000347900.6_Silent_p.R292R|KIRREL2_ENST00000262625.7_Silent_p.R342R	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	342	Ig-like C2-type 4.				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)			CCCGCTTCCACGGGTAACCTG	0.662													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		13850	0.0		0.0	False		,,,				2504	0.0				p.R342R		Atlas-SNP	.											.	KIRREL2	170	.	0			c.C1024A						PASS	.	C	,,	76,4284		0,76,2104	11.0	13.0	12.0		1024,874,1024	4.5	1.0	19	dbSNP_130	12	1,8531		0,1,4265	no	coding-synonymous,coding-synonymous,coding-synonymous	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	,,	0,77,6369	AA,AC,CC		0.0117,1.7431,0.5973	,,	342/634,292/584,342/709	36351906	77,12815	2180	4266	6446	SO:0001819	synonymous_variant	84063	exon8			CTTCCACGGGTAA	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.1024C>A	19.37:g.36351906C>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	37	CCDS12481.1																																																																																			C|0.994;A|0.006	0.006	strong		0.662	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
CEP170	9859	hgsc.bcm.edu	37	1	243329093	243329093	+	Silent	SNP	G	G	C	rs2789194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:243329093G>C	ENST00000366542.1	-	13	2220	c.2169C>G	c.(2167-2169)ggC>ggG	p.G723G	CEP170_ENST00000366544.1_Silent_p.G625G|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000366543.1_Silent_p.G625G|CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000437499.1_RNA	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	723						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GAGCAGAGCTGCCTAAGTGAA	0.398													G|||	192	0.0383387	0.143	0.0043	5008	,	,		20676	0.0		0.0	False		,,,				2504	0.0				p.G723G		Atlas-SNP	.											.	CEP170	153	.	0			c.C2169G						PASS	.	G	,,	483,3189		39,405,1392	163.0	150.0	154.0		1875,1875,2169	1.0	0.0	1	dbSNP_100	154	3,8169		0,3,4083	no	coding-synonymous,coding-synonymous,coding-synonymous	CEP170	NM_001042404.1,NM_001042405.1,NM_014812.2	,,	39,408,5475	CC,CG,GG		0.0367,13.1536,4.1033	,,	625/1487,625/1461,723/1585	243329093	486,11358	1836	4086	5922	SO:0001819	synonymous_variant	9859	exon13			AGAGCTGCCTAAG	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2169C>G	1.37:g.243329093G>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	217	108	0.497696	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Silent	SNP	ENST00000366542.1	37	CCDS44339.1	64	0.029304029304029304	61	0.12398373983739837	3	0.008287292817679558	0	0.0	0	0.0	G	0.006	-2.025614	0.00414	0.131536	3.67E-4	ENSG00000143702	ENST00000336415	.	.	.	5.25	1.02	0.19986	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.15407	-1.0438	4	.	.	.	-3.8866	4.2033	0.10476	0.1806:0.0:0.4641:0.3553	rs2789194;rs2789194	.	.	.	G	687	.	.	A	-	2	0	CEP170	241395716	0.104000	0.21937	0.003000	0.11579	0.284000	0.27059	0.869000	0.27996	-0.080000	0.12685	-0.439000	0.05793	GCA	G|0.978;C|0.022	0.022	strong		0.398	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
KMT2E	55904	hgsc.bcm.edu	37	7	104717517	104717517	+	Silent	SNP	C	C	T	rs2240455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:104717517C>T	ENST00000311117.3	+	10	1421	c.876C>T	c.(874-876)taC>taT	p.Y292Y	KMT2E_ENST00000257745.4_Silent_p.Y292Y|KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000476671.1_Silent_p.Y292Y|KMT2E_ENST00000334877.4_Silent_p.Y292Y	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	292					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)										ACAACCAGTACAGTGAGGGTG	0.388													T|||	1919	0.383187	0.59	0.2435	5008	,	,		17085	0.6319		0.1342	False		,,,				2504	0.2025				p.Y292Y		Atlas-SNP	.											.	MLL5	173	.	0			c.C876T						PASS	.	T	,	2304,2102	574.8+/-383.8	606,1092,505	127.0	118.0	121.0		876,876	-2.9	1.0	7	dbSNP_98	121	1057,7543	770.7+/-407.7	69,919,3312	no	coding-synonymous,coding-synonymous	MLL5	NM_018682.3,NM_182931.2	,	675,2011,3817	TT,TC,CC		12.2907,47.7077,25.8419	,	292/1859,292/1859	104717517	3361,9645	2203	4300	6503	SO:0001819	synonymous_variant	55904	exon9			CCAGTACAGTGAG	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.876C>T	7.37:g.104717517C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	193	97	0.502591	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Silent	SNP	ENST00000311117.3	37	CCDS34723.1																																																																																			C|0.620;T|0.380	0.380	strong		0.388	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
TRIM45	80263	hgsc.bcm.edu	37	1	117659292	117659292	+	Missense_Mutation	SNP	C	C	T	rs76902778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117659292C>T	ENST00000256649.4	-	3	1824	c.1298G>A	c.(1297-1299)gGc>gAc	p.G433D	TRIM45_ENST00000369464.3_Missense_Mutation_p.G415D|TRIM45_ENST00000369461.3_Missense_Mutation_p.G376D	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	433					bone development (GO:0060348)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|prostate(1)	23	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		TCCTCCCCTGCCCATGATTTC	0.483													C|||	235	0.0469249	0.0272	0.0101	5008	,	,		19218	0.0774		0.0229	False		,,,				2504	0.093				p.G433D		Atlas-SNP	.											TRIM45,caecum,carcinoma,+1,1	TRIM45	55	1	0			c.G1298A						PASS	.	C	ASP/GLY,ASP/GLY	191,4215	121.3+/-158.8	3,185,2015	90.0	85.0	87.0		1244,1298	4.2	1.0	1	dbSNP_131	87	176,8424	80.6+/-143.3	1,174,4125	yes	missense,missense	TRIM45	NM_001145635.1,NM_025188.3	94,94	4,359,6140	TT,TC,CC		2.0465,4.335,2.8218	possibly-damaging,possibly-damaging	415/563,433/581	117659292	367,12639	2203	4300	6503	SO:0001583	missense	80263	exon3			CCCCTGCCCATGA		CCDS893.1, CCDS44200.1	1p13.1	2011-04-20	2011-01-25		ENSG00000134253	ENSG00000134253		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19018	protein-coding gene	gene with protein product		609318	"""tripartite motif-containing 45"""			15351693	Standard	NM_025188		Approved	FLJ13181, RNF99	uc001egz.2	Q9H8W5	OTTHUMG00000012119	ENST00000256649.4:c.1298G>A	1.37:g.117659292C>T	ENSP00000256649:p.Gly433Asp	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	96	35	0.364583	NM_025188	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	82	0.037545787545787544	11	0.022357723577235773	3	0.008287292817679558	49	0.08566433566433566	19	0.025065963060686015	C	10.14	1.268814	0.23136	0.04335	0.020465	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	D;D;D	0.84298	-1.83;-1.83;-1.83	5.09	4.18	0.49190	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.498732	0.21918	N	0.067214	T	0.77267	0.4105	M	0.80028	2.48	0.25612	P	0.9864925	P;P	0.40834	0.73;0.552	B;B	0.41412	0.283;0.356	T	0.74734	-0.3565	9	0.16420	T	0.52	-15.1848	10.8074	0.46527	0.0:0.9136:0.0:0.0864	.	415;433	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	D	433;415;376	ENSP00000256649:G433D;ENSP00000358476:G415D;ENSP00000358473:G376D	ENSP00000256649:G433D	G	-	2	0	TRIM45	117460815	1.000000	0.71417	1.000000	0.80357	0.668000	0.39293	2.912000	0.48782	1.378000	0.46305	0.563000	0.77884	GGC	C|0.971;T|0.029	0.029	strong		0.483	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188	
LILRA1	11024	hgsc.bcm.edu	37	19	55105727	55105727	+	Silent	SNP	A	A	G	rs28469702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55105727A>G	ENST00000251372.3	+	2	200	c.18A>G	c.(16-18)acA>acG	p.T6T	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Silent_p.T6T|LILRA1_ENST00000473156.1_Intron|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	6					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CCATCGTCACAGTCCTGATCT	0.582													N|||	1469	0.293331	0.5189	0.2723	5008	,	,		16772	0.2778		0.1034	False		,,,				2504	0.2147				p.T6T		Atlas-SNP	.											.	LILRA1	105	.	0			c.A18G						PASS	.	C		1332,3074		439,454,1310	86.0	108.0	101.0		18	-4.8	0.0	19	dbSNP_125	101	274,8326		47,180,4073	no	coding-synonymous	LILRA1	NM_006863.1		486,634,5383	GG,GA,AA		3.186,30.2315,12.3481		6/490	55105727	1606,11400	2203	4300	6503	SO:0001819	synonymous_variant	11024	exon2			CGTCACAGTCCTG	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.18A>G	19.37:g.55105727A>G		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_006863	O75018|Q3MJA6	Silent	SNP	ENST00000251372.3	37	CCDS12901.1																																																																																			A|0.789;G|0.211	0.211	strong		0.582	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
DNHD1	144132	hgsc.bcm.edu	37	11	6549779	6549779	+	Missense_Mutation	SNP	A	A	C	rs4633449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6549779A>C	ENST00000527990.2	+	9	1865	c.1865A>C	c.(1864-1866)gAc>gCc	p.D622A	DNHD1_ENST00000254579.6_Missense_Mutation_p.D622A			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	622					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)		GACTCAAAAGACGAATTTCTG	0.532													C|||	3656	0.730032	0.6944	0.6585	5008	,	,		19003	0.874		0.6302	False		,,,				2504	0.7832				p.D622A		Atlas-SNP	.											.	DNHD1	198	.	0			c.A1865C						PASS	.	C	ALA/ASP	954,430		326,302,64	94.0	85.0	88.0		1865	-2.8	0.0	11	dbSNP_111	88	2138,1044		723,692,176	yes	missense	DNHD1	NM_144666.2	126	1049,994,240	CC,CA,AA		32.8096,31.0694,32.2821	benign	622/4754	6549779	3092,1474	692	1591	2283	SO:0001583	missense	144132	exon11			CAAAAGACGAATT	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.1865A>C	11.37:g.6549779A>C	ENSP00000436180:p.Asp622Ala	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	1562	0.7152014652014652	353	0.717479674796748	236	0.6519337016574586	487	0.8513986013986014	486	0.6411609498680739	C	4.359	0.066121	0.08388	0.689306	0.671904	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.24151	1.87;1.87	4.47	-2.8	0.05823	.	.	.	.	.	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	0.25257	-1.0137	8	0.07175	T	0.84	.	3.7229	0.08463	0.408:0.2437:0.0:0.3484	rs4633449;rs61259590;rs4633449	622	Q96M86	DNHD1_HUMAN	A	622	ENSP00000254579:D622A;ENSP00000436180:D622A	ENSP00000254579:D622A	D	+	2	0	DNHD1	6506355	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.220000	0.02971	-1.046000	0.03246	-0.217000	0.12591	GAC	A|0.272;C|0.728	0.728	strong		0.532	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
C16orf62	57020	hgsc.bcm.edu	37	16	19590444	19590444	+	Silent	SNP	T	T	C	rs11866050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19590444T>C	ENST00000251143.5	+	6	516	c.504T>C	c.(502-504)ttT>ttC	p.F168F	C16orf62_ENST00000543152.1_5'UTR|C16orf62_ENST00000417362.2_Silent_p.F168F|C16orf62_ENST00000538853.1_3'UTR|C16orf62_ENST00000448695.1_Silent_p.F46F|C16orf62_ENST00000438132.3_Silent_p.F257F|C16orf62_ENST00000542263.1_Silent_p.F257F			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	168				F -> S (in Ref. 3; CAH10399). {ECO:0000305}.		integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						TGGATGACTTTGAGGAGGTGA	0.502													T|||	359	0.0716853	0.2057	0.0144	5008	,	,		18705	0.0337		0.0209	False		,,,				2504	0.0225				p.F257F		Atlas-SNP	.											.	C16orf62	164	.	0			c.T771C						PASS	.	T		633,3761	272.8+/-271.0	34,565,1598	94.0	83.0	87.0		771	-1.1	1.0	16	dbSNP_120	87	152,8448	72.3+/-134.9	0,152,4148	no	coding-synonymous	C16orf62	NM_020314.5		34,717,5746	CC,CT,TT		1.7674,14.406,6.0412		257/1053	19590444	785,12209	2197	4300	6497	SO:0001819	synonymous_variant	57020	exon6			TGACTTTGAGGAG		CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.504T>C	16.37:g.19590444T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	108	61	0.564815	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Silent	SNP	ENST00000251143.5	37																																																																																				T|0.937;C|0.063	0.063	strong		0.502	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314	
EGLN2	112398	hgsc.bcm.edu	37	19	41306771	41306771	+	Silent	SNP	G	G	A	rs143206553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41306771G>A	ENST00000593726.1	+	1	1322	c.294G>A	c.(292-294)gcG>gcA	p.A98A	CTC-490E21.12_ENST00000601627.1_5'Flank|EGLN2_ENST00000406058.2_Silent_p.A98A|EGLN2_ENST00000303961.4_Silent_p.A98A|EGLN2_ENST00000594140.1_5'Flank|RAB4B-EGLN2_ENST00000594136.1_3'UTR			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	98	Bipartite nuclear localization signal.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|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)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	GCGCTGCAGCGCTGGTCACCA	0.677													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		16000	0.0		0.0	False		,,,				2504	0.0				p.A98A		Atlas-SNP	.											.	EGLN2	31	.	0			c.G294A						PASS	.	G	,	77,4321		0,77,2122	14.0	16.0	15.0		294,294	-3.8	0.7	19	dbSNP_134	15	0,8582		0,0,4291	no	coding-synonymous,coding-synonymous	EGLN2	NM_053046.3,NM_080732.3	,	0,77,6413	AA,AG,GG		0.0,1.7508,0.5932	,	98/408,98/408	41306771	77,12903	2199	4291	6490	SO:0001819	synonymous_variant	112398	exon2			TGCAGCGCTGGTC	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"""HIF prolyl hydroxylase 1"""	606424	"""EGL nine (C.elegans) homolog 2"", ""egl nine homolog 2 (C. elegans)"""				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.294G>A	19.37:g.41306771G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Silent	SNP	ENST00000593726.1	37	CCDS12567.1																																																																																			G|0.993;A|0.007	0.007	strong		0.677	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1		
FEV	54738	hgsc.bcm.edu	37	2	219846749	219846749	+	Silent	SNP	G	G	A	rs860573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219846749G>A	ENST00000295727.1	-	3	938	c.357C>T	c.(355-357)ggC>ggT	p.G119G	LINC00608_ENST00000432733.1_lincRNA	NM_017521.2	NP_059991.1	Q99581	FEV_HUMAN	FEV (ETS oncogene family)	119					cell differentiation (GO:0030154)|neuron fate specification (GO:0048665)|neuron maturation (GO:0042551)|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)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|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 corepressor activity (GO:0003714)		EWSR1/FEV(11)|FUS/FEV(2)	large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	4		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CGTAGCGCTTGCCATGCACCT	0.677			T	"""EWSR1,  FUS"""	Ewing sarcoma								g|||	726	0.144968	0.2723	0.0432	5008	,	,		9822	0.1379		0.0219	False		,,,				2504	0.1789				p.G119G	NSCLC(198;941 2228 4658 24163 34665)	Atlas-SNP	.		Dom	yes		2	2q36	54738	FEV protein - (HSRNAFEV)		M	.	FEV	10	.	0			c.C357T						PASS	.			920,3486	349.5+/-310.4	92,736,1375	104.0	70.0	82.0		357	2.5	1.0	2	dbSNP_86	82	109,8491	57.2+/-118.5	1,107,4192	no	coding-synonymous	FEV	NM_017521.2		93,843,5567	AA,AG,GG		1.2674,20.8806,7.9117		119/239	219846749	1029,11977	2203	4300	6503	SO:0001819	synonymous_variant	54738	exon3			GCGCTTGCCATGC		CCDS2428.1	2q36	2008-02-05			ENSG00000163497	ENSG00000163497			18562	protein-coding gene	gene with protein product		607150	"""FEV (fifth Ewing variant)"""			9121764	Standard	NM_017521		Approved	Pet-1	uc002vji.1	Q99581	OTTHUMG00000133080	ENST00000295727.1:c.357C>T	2.37:g.219846749G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_017521		Silent	SNP	ENST00000295727.1	37	CCDS2428.1																																																																																			G|0.902;A|0.098	0.098	strong		0.677	FEV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256725.1		
OR4L1	122742	hgsc.bcm.edu	37	14	20528321	20528321	+	Missense_Mutation	SNP	A	A	G	rs1958716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20528321A>G	ENST00000315683.1	+	1	118	c.118A>G	c.(118-120)Atg>Gtg	p.M40V		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	40			M -> V (in dbSNP:rs1958716).			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(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		TGCTACTGTGATGGGAAACAT	0.393													N|||	2688	0.536741	0.4902	0.5562	5008	,	,		20619	0.5734		0.3857	False		,,,				2504	0.7035				p.M40V		Atlas-SNP	.											.	OR4L1	98	.	0			c.A118G						PASS	.		VAL/MET	2154,2252		521,1112,570	180.0	185.0	183.0		118	-5.8	0.0	14	dbSNP_92	183	3465,5135		729,2007,1564	yes	missense	OR4L1	NM_001004717.1	21	1250,3119,2134	GG,GA,AA		40.2907,48.8879,43.2031	benign	40/313	20528321	5619,7387	2203	4300	6503	SO:0001583	missense	122742	exon1			ACTGTGATGGGAA		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.118A>G	14.37:g.20528321A>G	ENSP00000319217:p.Met40Val	Somatic	342	1	0.00292398		WXS	Illumina HiSeq	Phase_I	345	154	0.446377	NM_001004717	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	1083	0.4958791208791209	255	0.5182926829268293	192	0.5303867403314917	320	0.5594405594405595	316	0.41688654353562005	.	5.342	0.248431	0.10130	0.488879	0.402907	ENSG00000176246	ENST00000315683	T	0.00448	7.38	3.84	-5.83	0.02325	.	1.004810	0.08017	N	0.991451	T	0.00012	0.0000	N	0.03238	-0.38	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06041	-1.0849	9	0.30854	T	0.27	.	0.3958	0.00418	0.3004:0.1965:0.13:0.3731	rs1958716;rs17126034;rs52817587;rs59618621;rs1958716	40	Q8NH43	OR4L1_HUMAN	V	40	ENSP00000319217:M40V	ENSP00000319217:M40V	M	+	1	0	OR4L1	19598161	0.000000	0.05858	0.001000	0.08648	0.960000	0.62799	-5.017000	0.00159	-1.322000	0.02278	-0.148000	0.13756	ATG	A|0.531;G|0.469	0.469	strong		0.393	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
TARBP1	6894	hgsc.bcm.edu	37	1	234595070	234595070	+	Missense_Mutation	SNP	T	T	C	rs35562024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:234595070T>C	ENST00000040877.1	-	8	1537	c.1538A>G	c.(1537-1539)gAt>gGt	p.D513G		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	513			D -> G (in dbSNP:rs35562024).		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)			ATGAATAACATCCCTGACATC	0.378													T|||	78	0.0155751	0.053	0.0072	5008	,	,		19358	0.0		0.003	False		,,,				2504	0.0				p.D513G		Atlas-SNP	.											.	TARBP1	111	.	0			c.A1538G						PASS	.	T	GLY/ASP	242,4164	141.1+/-176.5	14,214,1975	111.0	101.0	104.0		1538	2.0	0.4	1	dbSNP_126	104	55,8545	33.8+/-87.4	0,55,4245	yes	missense	TARBP1	NM_005646.3	94	14,269,6220	CC,CT,TT		0.6395,5.4925,2.2836	probably-damaging	513/1622	234595070	297,12709	2203	4300	6503	SO:0001583	missense	6894	exon8			ATAACATCCCTGA		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.1538A>G	1.37:g.234595070T>C	ENSP00000040877:p.Asp513Gly	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_005646	Q9H581	Missense_Mutation	SNP	ENST00000040877.1	37	CCDS1601.1	26	0.011904761904761904	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	T	11.32	1.603675	0.28534	0.054925	0.006395	ENSG00000059588	ENST00000040877	T	0.06371	3.31	5.67	2.0	0.26442	.	0.273360	0.41823	N	0.000805	T	0.01092	0.0036	M	0.65975	2.015	0.44000	D	0.996702	B	0.19200	0.034	B	0.15052	0.012	T	0.22800	-1.0206	10	0.66056	D	0.02	-15.9034	6.0978	0.20031	0.121:0.1334:0.0:0.7455	rs35562024	513	Q13395	TARB1_HUMAN	G	513	ENSP00000040877:D513G	ENSP00000040877:D513G	D	-	2	0	TARBP1	232661693	0.998000	0.40836	0.374000	0.26016	0.481000	0.33189	2.918000	0.48829	0.139000	0.18822	0.533000	0.62120	GAT	T|0.982;C|0.018	0.018	strong		0.378	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
PRB2	653247	hgsc.bcm.edu	37	12	11546742	11546742	+	Silent	SNP	T	T	C	rs201044388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11546742T>C	ENST00000389362.4	-	3	305	c.270A>G	c.(268-270)caA>caG	p.Q90Q	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	90	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GTGGGGGACCTTGAGGTTTGT	0.617																																					p.Q90Q		Atlas-SNP	.											PRB2_ENST00000389362,NS,carcinoma,0,2	PRB2	168	2	0			c.A270G						PASS	.						150.0	171.0	164.0					12																	11546742		2136	4199	6335	SO:0001819	synonymous_variant	653247	exon3			GGGACCTTGAGGT	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.270A>G	12.37:g.11546742T>C		Somatic	424	1	0.00235849		WXS	Illumina HiSeq	Phase_I	405	105	0.259259	NM_006248	O00599|P02811|P04281	Silent	SNP	ENST00000389362.4	37	CCDS41757.2																																																																																			T|0.776;C|0.224	0.224	strong		0.617	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
TET3	200424	hgsc.bcm.edu	37	2	74274812	74274812	+	Missense_Mutation	SNP	G	G	A	rs72816199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74274812G>A	ENST00000409262.3	+	1	1363	c.1363G>A	c.(1363-1365)Gtg>Atg	p.V455M		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	455					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGGAGGTCCCGTGGGAACGGA	0.612													G|||	80	0.0159744	0.0582	0.0	5008	,	,		16252	0.0		0.002	False		,,,				2504	0.001				p.V455M		Atlas-SNP	.											.	TET3	101	.	0			c.G1363A						PASS	.	G	MET/VAL	169,3733		4,161,1786	29.0	36.0	33.0		1363	-2.6	0.0	2	dbSNP_130	33	22,8214		0,22,4096	yes	missense	TET3	NM_144993.1	21	4,183,5882	AA,AG,GG		0.2671,4.3311,1.5736	benign	455/1661	74274812	191,11947	1951	4118	6069	SO:0001583	missense	200424	exon1			GGTCCCGTGGGAA		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"""tet oncogene family member 3"""			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.1363G>A	2.37:g.74274812G>A	ENSP00000386869:p.Val455Met	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	ENST00000409262.3	37	CCDS46339.1	35	0.016025641025641024	33	0.06707317073170732	0	0.0	0	0.0	2	0.002638522427440633	G	3.290	-0.145224	0.06627	0.043311	0.002671	ENSG00000187605	ENST00000305799;ENST00000409262;ENST00000233310	T;T	0.27557	1.66;2.47	5.02	-2.61	0.06171	.	.	.	.	.	T	0.00845	0.0028	N	0.12182	0.205	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.20806	-1.0264	9	0.45353	T	0.12	.	0.2235	0.00171	0.2976:0.2306:0.2467:0.2251	.	455	O43151	TET3_HUMAN	M	497;455;455	ENSP00000307803:V497M;ENSP00000386869:V455M	ENSP00000233310:V455M	V	+	1	0	TET3	74128320	0.000000	0.05858	0.001000	0.08648	0.417000	0.31264	-1.268000	0.02836	-0.836000	0.04229	0.591000	0.81541	GTG	G|0.986;A|0.014	0.014	strong		0.612	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4		
C17orf85	55421	hgsc.bcm.edu	37	17	3728315	3728315	+	Silent	SNP	C	C	T	rs218719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3728315C>T	ENST00000389005.4	-	7	744	c.717G>A	c.(715-717)gaG>gaA	p.E239E	C17orf85_ENST00000158149.3_5'UTR|C17orf85_ENST00000577169.1_5'UTR	NM_001114118.2	NP_001107590.1	Q53F19	CQ085_HUMAN	chromosome 17 open reading frame 85	239							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (3;0.0725)		TTAACAAAGACTCCTCTTCTA	0.308													C|||	249	0.0497204	0.1808	0.0115	5008	,	,		17016	0.001		0.0	False		,,,				2504	0.001				p.E239E		Atlas-SNP	.											.	C17orf85	66	.	0			c.G717A						PASS	.	C	,	179,1205		16,147,529	120.0	94.0	102.0		717,	-1.8	1.0	17	dbSNP_79	102	2,3172		0,2,1585	no	coding-synonymous,utr-5	C17orf85	NM_001114118.1,NM_018553.3	,	16,149,2114	TT,TC,CC		0.063,12.9335,3.971	,	239/621,	3728315	181,4377	692	1587	2279	SO:0001819	synonymous_variant	55421	exon7			CAAAGACTCCTCT		CCDS45578.1	17p13.2	2012-10-23			ENSG00000074356	ENSG00000074356			24612	protein-coding gene	gene with protein product	"""ELG protein"""					11412301	Standard	NM_001114118		Approved	HSA277841, ELG	uc010ckl.2	Q53F19	OTTHUMG00000177672	ENST00000389005.4:c.717G>A	17.37:g.3728315C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	27	11	0.407407	NM_001114118	B3KWG7|Q7L406|Q96FK1|Q9NXZ4	Silent	SNP	ENST00000389005.4	37	CCDS45578.1																																																																																			C|0.932;T|0.068	0.068	strong		0.308	C17orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438385.1	NM_018553	
LRRC16B	90668	hgsc.bcm.edu	37	14	24529209	24529209	+	Silent	SNP	C	C	T	rs61564890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24529209C>T	ENST00000342740.5	+	23	2053	c.1899C>T	c.(1897-1899)ccC>ccT	p.P633P	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	633						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)		TGTCCTTCCCCGTGAGCGACA	0.642													C|||	959	0.191494	0.0416	0.2104	5008	,	,		20833	0.4643		0.0616	False		,,,				2504	0.2331				p.P633P		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C1899T						PASS	.	C		199,4207	122.1+/-159.5	6,187,2010	154.0	131.0	139.0		1899	-9.1	0.2	14	dbSNP_129	139	474,8126	139.5+/-196.2	11,452,3837	no	coding-synonymous	LRRC16B	NM_138360.3		17,639,5847	TT,TC,CC		5.5116,4.5166,5.1745		633/1373	24529209	673,12333	2203	4300	6503	SO:0001819	synonymous_variant	90668	exon23			CTTCCCCGTGAGC	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.1899C>T	14.37:g.24529209C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																			C|0.908;T|0.092	0.092	strong		0.642	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
CUEDC1	404093	hgsc.bcm.edu	37	17	55950082	55950082	+	Silent	SNP	G	G	A	rs16942487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:55950082G>A	ENST00000577830.1	-	5	1139	c.726C>T	c.(724-726)aaC>aaT	p.N242N	CUEDC1_ENST00000407144.2_Silent_p.N242N|CUEDC1_ENST00000578357.1_5'Flank|CUEDC1_ENST00000360238.2_Silent_p.N242N|CUEDC1_ENST00000577840.1_Silent_p.N105N	NM_001271875.1	NP_001258804.1	Q9NWM3	CUED1_HUMAN	CUE domain containing 1	242										endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12						TGAACTCCTCGTTCTGCAGGA	0.632													G|||	182	0.0363419	0.1324	0.0101	5008	,	,		19386	0.0		0.0	False		,,,				2504	0.0				p.N242N		Atlas-SNP	.											.	CUEDC1	37	.	0			c.C726T						PASS	.	G		498,3908	230.1+/-244.4	30,438,1735	88.0	72.0	78.0		726	-2.5	1.0	17	dbSNP_123	78	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CUEDC1	NM_017949.1		30,440,6033	AA,AG,GG		0.0233,11.3028,3.8444		242/387	55950082	500,12506	2203	4300	6503	SO:0001819	synonymous_variant	404093	exon5			CTCCTCGTTCTGC	AK000746	CCDS11599.1	17q23.2	2004-03-16				ENSG00000180891			31350	protein-coding gene	gene with protein product							Standard	NM_001271875		Approved		uc002ive.2	Q9NWM3		ENST00000577830.1:c.726C>T	17.37:g.55950082G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_001271875	D3DTZ2|Q9NWD0	Silent	SNP	ENST00000577830.1	37	CCDS11599.1																																																																																			G|0.966;A|0.034	0.034	strong		0.632	CUEDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443305.1	NM_017949	
VAV2	7410	hgsc.bcm.edu	37	9	136640122	136640122	+	Silent	SNP	G	G	A	rs7875953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136640122G>A	ENST00000371850.3	-	25	2101	c.2070C>T	c.(2068-2070)caC>caT	p.H690H	VAV2_ENST00000371851.1_Silent_p.H680H|VAV2_ENST00000406606.3_Silent_p.H680H	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	690	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		TCCCGCTGGCGTGGGACTTGA	0.617													G|||	132	0.0263578	0.0923	0.0115	5008	,	,		18617	0.0		0.002	False		,,,				2504	0.0				p.H690H		Atlas-SNP	.											VAV2_ENST00000371850,colon,carcinoma,0,2	VAV2	165	2	0			c.C2070T						PASS	.	G	,	426,3980	207.2+/-228.6	26,374,1803	71.0	64.0	66.0		2070,2040	-3.2	1.0	9	dbSNP_116	66	5,8593	3.0+/-9.4	0,5,4294	no	coding-synonymous,coding-synonymous	VAV2	NM_001134398.1,NM_003371.3	,	26,379,6097	AA,AG,GG		0.0582,9.6686,3.3144	,	690/879,680/840	136640122	431,12573	2203	4299	6502	SO:0001819	synonymous_variant	7410	exon25			GCTGGCGTGGGAC		CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12658	protein-coding gene	gene with protein product		600428	"""vav 2 oncogene"""			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.2070C>T	9.37:g.136640122G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	135	86	0.637037	NM_001134398	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Silent	SNP	ENST00000371850.3	37	CCDS48053.1																																																																																			G|0.963;A|0.037	0.037	strong		0.617	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1		
INADL	10207	hgsc.bcm.edu	37	1	62579907	62579907	+	Silent	SNP	C	C	T	rs7418709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62579907C>T	ENST00000371158.2	+	35	4758	c.4644C>T	c.(4642-4644)atC>atT	p.I1548I	INADL_ENST00000545929.1_Silent_p.I193I|INADL_ENST00000316485.6_Silent_p.I1578I|INADL_ENST00000543708.1_Silent_p.I362I	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1548	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GCCTGAGCATCGTTGGGAAAC	0.512													C|||	1490	0.297524	0.2791	0.2291	5008	,	,		18642	0.7113		0.0696	False		,,,				2504	0.1789				p.I1548I		Atlas-SNP	.											.	INADL	179	.	0			c.C4644T						PASS	.	C		1137,3269	404.9+/-333.3	157,823,1223	54.0	58.0	56.0		4644	-0.8	0.9	1	dbSNP_116	56	762,7838	182.0+/-230.6	39,684,3577	no	coding-synonymous	INADL	NM_176877.2		196,1507,4800	TT,TC,CC		8.8605,25.8057,14.601		1548/1802	62579907	1899,11107	2203	4300	6503	SO:0001819	synonymous_variant	10207	exon35			GAGCATCGTTGGG	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.4644C>T	1.37:g.62579907C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	179	78	0.435754	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			C|0.784;T|0.216	0.216	strong		0.512	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
C20orf96	140680	hgsc.bcm.edu	37	20	259818	259818	+	Silent	SNP	G	G	A	rs6035541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:259818G>A	ENST00000360321.2	-	5	598	c.460C>T	c.(460-462)Ctg>Ttg	p.L154L	C20orf96_ENST00000382369.5_Silent_p.L119L|C20orf96_ENST00000400269.3_Silent_p.L96L	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	41	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	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	
SPINK2	6691	hgsc.bcm.edu	37	4	57687711	57687711	+	Intron	SNP	T	T	C	rs781543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57687711T>C	ENST00000248701.4	-	1	135				SPINK2_ENST00000506738.1_Missense_Mutation_p.T40A|SPINK2_ENST00000504762.1_Missense_Mutation_p.T40A	NM_021114.2	NP_066937.1	P20155	ISK2_HUMAN	serine peptidase inhibitor, Kazal type 2 (acrosin-trypsin inhibitor)						negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(1)|lung(2)	4	Glioma(25;0.08)|all_neural(26;0.181)					CCGCCGCCGGTCTGACTCCCA	0.716													C|||	1104	0.220447	0.5651	0.2421	5008	,	,		11426	0.0913		0.0616	False		,,,				2504	0.0358				p.T40A		Atlas-SNP	.											.	SPINK2	12	.	0			c.A118G						PASS	.						4.0	8.0	7.0					4																	57687711		611	1499	2110	SO:0001627	intron_variant	6691	exon1			CGCCGGTCTGACT	BC022514	CCDS3508.1, CCDS63971.1, CCDS63972.1, CCDS75128.1	4q12	2011-08-31	2005-08-17		ENSG00000128040	ENSG00000128040		"""Serine peptidase inhibitors, Kazal type"""	11245	protein-coding gene	gene with protein product		605753	"""serine protease inhibitor, Kazal type 2 (acrosin-trypsin inhibitor)"""			8428671	Standard	NM_001271718		Approved	HUSI-II	uc031sep.1	P20155	OTTHUMG00000128769	ENST00000248701.4:c.55+62A>G	4.37:g.57687711T>C		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	30	10	0.333333	NM_001271722	Q6FGH2	Missense_Mutation	SNP	ENST00000248701.4	37	CCDS3508.1	454	0.2078754578754579	259	0.5264227642276422	79	0.21823204419889503	66	0.11538461538461539	50	0.06596306068601583	C	12.00	1.807913	0.31961	.	.	ENSG00000128040	ENST00000506738;ENST00000504762	T;T	0.78924	-1.22;-1.18	2.14	-0.787	0.10943	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.39272	-0.9622	5	0.10636	T	0.68	.	3.3457	0.07134	0.0:0.3465:0.2146:0.439	rs781543	.	.	.	A	40	ENSP00000425961:T40A;ENSP00000423858:T40A	ENSP00000423858:T40A	T	-	1	0	SPINK2	57382468	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.241000	0.08940	-0.647000	0.05444	-0.642000	0.03964	ACC	T|0.791;C|0.209	0.209	strong		0.716	SPINK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250690.2	NM_021114	
NBEA	26960	hgsc.bcm.edu	37	13	35864573	35864573	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:35864573C>T	ENST00000400445.3	+	35	6358	c.5824C>T	c.(5824-5826)Ctg>Ttg	p.L1942L	NBEA_ENST00000540320.1_Silent_p.L1942L|NBEA_ENST00000310336.4_Silent_p.L1942L|NBEA_ENST00000379939.2_Silent_p.L1939L	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1942					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)		GCTTGTTATGCTGCTTTGTTC	0.323																																					p.L1942L		Atlas-SNP	.											NBEA,NS,carcinoma,-2,1	NBEA	340	1	0			c.C5824T						scavenged	.						292.0	274.0	280.0					13																	35864573		1857	4092	5949	SO:0001819	synonymous_variant	26960	exon35			GTTATGCTGCTTT	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.5824C>T	13.37:g.35864573C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	154	3	0.0194805	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	37	CCDS45026.1																																																																																			.	.	none		0.323	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
TGM6	343641	hgsc.bcm.edu	37	20	2377204	2377204	+	Silent	SNP	C	C	T	rs16984872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2377204C>T	ENST00000202625.2	+	4	538	c.477C>T	c.(475-477)agC>agT	p.S159S	TGM6_ENST00000477505.1_Intron|TGM6_ENST00000381423.1_Silent_p.S159S	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	159					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	ACGTGCTCAGCGACAGCGGCA	0.612													C|||	193	0.0385383	0.1225	0.0259	5008	,	,		19129	0.0		0.0099	False		,,,				2504	0.0031				p.S159S		Atlas-SNP	.											TGM6,NS,carcinoma,0,1	TGM6	126	1	0			c.C477T						PASS	.	C		447,3959	215.8+/-234.7	28,391,1784	96.0	85.0	89.0		477	-5.3	0.9	20	dbSNP_123	89	87,8513	49.4+/-109.1	0,87,4213	no	coding-synonymous	TGM6	NM_198994.2		28,478,5997	TT,TC,CC		1.0116,10.1453,4.1058		159/707	2377204	534,12472	2203	4300	6503	SO:0001819	synonymous_variant	343641	exon4			GCTCAGCGACAGC	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.477C>T	20.37:g.2377204C>T		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	266	124	0.466165	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	37	CCDS13025.1																																																																																			C|0.960;T|0.040	0.040	strong		0.612	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
IDH3A	3419	hgsc.bcm.edu	37	15	78458638	78458638	+	Silent	SNP	C	C	T	rs2304826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:78458638C>T	ENST00000299518.2	+	10	1094	c.1011C>T	c.(1009-1011)gaC>gaT	p.D337D	IDH3A_ENST00000561366.1_3'UTR|IDH3A_ENST00000558554.1_Silent_p.D302D|IDH3A_ENST00000441490.2_Silent_p.D228D|IDH3A_ENST00000558535.1_3'UTR|IDH3A_ENST00000559205.1_Silent_p.D58D	NM_005530.2	NP_005521.1	P50213	IDH3A_HUMAN	isocitrate dehydrogenase 3 (NAD+) alpha	337					carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	12						CAATTAAGGACGGAAAGGTAA	0.458													C|||	297	0.0593051	0.1286	0.0159	5008	,	,		22649	0.0685		0.0189	False		,,,				2504	0.0286				p.D337D		Atlas-SNP	.											.	IDH3A	24	.	0			c.C1011T						PASS	.	C		436,3956	211.2+/-231.4	20,396,1780	189.0	180.0	183.0		1011	-7.8	0.6	15	dbSNP_100	183	130,8456	67.3+/-129.8	1,128,4164	no	coding-synonymous	IDH3A	NM_005530.2		21,524,5944	TT,TC,CC		1.5141,9.9271,4.3612		337/367	78458638	566,12412	2196	4293	6489	SO:0001819	synonymous_variant	3419	exon10			TAAGGACGGAAAG		CCDS10297.1	15q25.1-q25.2	2008-07-18			ENSG00000166411	ENSG00000166411	1.1.1.41		5384	protein-coding gene	gene with protein product	"""H-IDH alpha"", ""isocitric dehydrogenase"", ""isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial"", ""NAD+-specific ICDH"", ""NAD(H)-specific isocitrate dehydrogenase alpha subunit"", ""isocitrate dehydrogenase (NAD+) alpha chain"""	601149				8833160	Standard	NM_005530		Approved		uc002bdd.3	P50213	OTTHUMG00000143732	ENST00000299518.2:c.1011C>T	15.37:g.78458638C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	143	79	0.552448	NM_005530	D3DW83|Q9H3X0	Silent	SNP	ENST00000299518.2	37	CCDS10297.1																																																																																			C|0.950;T|0.050	0.050	strong		0.458	IDH3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289799.4	NM_005530	
ADPRHL2	54936	hgsc.bcm.edu	37	1	36557619	36557619	+	Missense_Mutation	SNP	G	G	A	rs2236387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36557619G>A	ENST00000373178.4	+	4	655	c.625G>A	c.(625-627)Gag>Aag	p.E209K		NM_017825.2	NP_060295.1	Q9NX46	ARHL2_HUMAN	ADP-ribosylhydrolase like 2	209			E -> K (in dbSNP:rs2236387). {ECO:0000269|Ref.5}.			mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(ADP-ribose) glycohydrolase activity (GO:0004649)			cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|pancreas(1)	8		Myeloproliferative disorder(586;0.0393)				GTCTTCCAGCGAGCACTTTCT	0.627													G|||	872	0.174121	0.3018	0.2493	5008	,	,		18600	0.2431		0.008	False		,,,				2504	0.0481				p.E209K		Atlas-SNP	.											.	ADPRHL2	25	.	0			c.G625A						PASS	.	G	LYS/GLU	1070,3336	385.8+/-325.9	119,832,1252	90.0	87.0	88.0		625	3.6	0.6	1	dbSNP_98	88	46,8554	29.6+/-80.5	0,46,4254	yes	missense	ADPRHL2	NM_017825.2	56	119,878,5506	AA,AG,GG		0.5349,24.2851,8.5807	benign	209/364	36557619	1116,11890	2203	4300	6503	SO:0001583	missense	54936	exon4			TCCAGCGAGCACT	AJ427295	CCDS402.1	1p34.3	2008-02-05			ENSG00000116863	ENSG00000116863			21304	protein-coding gene	gene with protein product		610624				12070318, 16278211	Standard	NM_017825		Approved	ARH3, FLJ20446	uc001bzt.3	Q9NX46	OTTHUMG00000007628	ENST00000373178.4:c.625G>A	1.37:g.36557619G>A	ENSP00000362273:p.Glu209Lys	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	256	131	0.511719	NM_017825	Q53G94|Q6IAB8|Q9BY47	Missense_Mutation	SNP	ENST00000373178.4	37	CCDS402.1	392	0.1794871794871795	143	0.29065040650406504	84	0.23204419889502761	159	0.27797202797202797	6	0.0079155672823219	G	9.241	1.038237	0.19669	0.242851	0.005349	ENSG00000116863	ENST00000373178;ENST00000540867;ENST00000543954	T	0.34472	1.36	5.48	3.61	0.41365	.	0.266755	0.42821	N	0.000650	T	0.00012	0.0000	L	0.58510	1.815	0.30939	P	0.7259979999999999	B	0.02656	0.0	B	0.04013	0.001	T	0.19745	-1.0296	9	0.24483	T	0.36	-29.8068	16.3192	0.82939	0.0925:0.0:0.9075:0.0	rs2236387;rs52806607;rs56497330;rs57078360;rs2236387	209	Q9NX46	ARHL2_HUMAN	K	209;129;55	ENSP00000362273:E209K	ENSP00000362273:E209K	E	+	1	0	ADPRHL2	36330206	0.984000	0.35163	0.583000	0.28640	0.388000	0.30384	2.148000	0.42235	0.293000	0.22520	-1.736000	0.00690	GAG	G|0.871;A|0.129	0.129	strong		0.627	ADPRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020199.1	NM_017825	
BPIFB4	149954	hgsc.bcm.edu	37	20	31671663	31671663	+	Silent	SNP	T	T	C	rs2424945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31671663T>C	ENST00000375483.3	+	3	660	c.660T>C	c.(658-660)acT>acC	p.T220T		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	220	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCCTCAGCACTGTGCAAGGCA	0.637													C|||	1899	0.379193	0.6074	0.4035	5008	,	,		17966	0.1984		0.333	False		,,,				2504	0.2873				p.T220T		Atlas-SNP	.											.	.	.	.	0			c.T660C						PASS	.	C		2492,1892		751,990,451	33.0	38.0	36.0		660	-1.4	1.0	20	dbSNP_100	36	2915,5623		517,1881,1871	no	coding-synonymous	BPIFB4	NM_182519.2		1268,2871,2322	CC,CT,TT		34.1415,43.1569,41.8434		220/615	31671663	5407,7515	2192	4269	6461	SO:0001819	synonymous_variant	149954	exon3			CAGCACTGTGCAA	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.660T>C	20.37:g.31671663T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	37	CCDS13213.2																																																																																			T|0.623;C|0.377	0.377	strong		0.637	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
DDX60L	91351	hgsc.bcm.edu	37	4	169362557	169362557	+	Missense_Mutation	SNP	C	C	G	rs13151700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169362557C>G	ENST00000511577.1	-	10	1472	c.1225G>C	c.(1225-1227)Gtt>Ctt	p.V409L	DDX60L_ENST00000505890.1_Missense_Mutation_p.V409L|DDX60L_ENST00000260184.7_Missense_Mutation_p.V409L			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	409			V -> L (in dbSNP:rs13151700).				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)		GACTTTCCAACGTTAAATTCT	0.358													C|||	1674	0.334265	0.0469	0.5159	5008	,	,		17538	0.6141		0.3439	False		,,,				2504	0.2955				p.V409L		Atlas-SNP	.											.	DDX60L	116	.	0			c.G1225C						PASS	.	C	LEU/VAL	351,3307		31,289,1509	109.0	104.0	106.0		1225	3.1	0.8	4	dbSNP_121	106	2714,5446		435,1844,1801	yes	missense	DDX60L	NM_001012967.1	32	466,2133,3310	GG,GC,CC		33.2598,9.5954,25.935	benign	409/1707	169362557	3065,8753	1829	4080	5909	SO:0001583	missense	91351	exon10			TTCCAACGTTAAA	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.1225G>C	4.37:g.169362557C>G	ENSP00000422423:p.Val409Leu	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		817	0.3740842490842491	27	0.054878048780487805	171	0.4723756906077348	365	0.6381118881118881	254	0.33509234828496043	C	11.22	1.574833	0.28092	0.095954	0.332598	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.18502	2.22;2.22;2.21;2.86	3.1	3.1	0.35709	.	0.263396	0.19176	U	0.120809	T	0.00012	0.0000	M	0.65975	2.015	0.46631	P	8.650000000000047E-4	B;B;B	0.32620	0.378;0.336;0.378	B;B;B	0.25987	0.065;0.048;0.065	T	0.20974	-1.0259	9	0.09084	T	0.74	.	9.9765	0.41786	0.0:1.0:0.0:0.0	rs13151700;rs17706604;rs52823633;rs13151700	409;409;409	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	L	409;409;409;137	ENSP00000260184:V409L;ENSP00000422423:V409L;ENSP00000422202:V409L;ENSP00000421026:V137L	ENSP00000260184:V409L	V	-	1	0	DDX60L	169599132	0.993000	0.37304	0.808000	0.32385	0.024000	0.10985	3.471000	0.53107	1.411000	0.46957	0.313000	0.20887	GTT	C|0.615;G|0.385	0.385	strong		0.358	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
ZFP36L2	678	hgsc.bcm.edu	37	2	43452334	43452334	+	Silent	SNP	G	G	A	rs397823004|rs8098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:43452334G>A	ENST00000282388.3	-	2	902	c.609C>T	c.(607-609)atC>atT	p.I203I	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	203	RNA-binding.				cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				GGCAGAAGCCGATGGTATGAA	0.672													G|||	576	0.115016	0.2141	0.0519	5008	,	,		13494	0.003		0.0676	False		,,,				2504	0.1902				p.I203I		Atlas-SNP	.											.	ZFP36L2	56	.	0			c.C609T						PASS	.	G		842,3564	312.2+/-292.5	92,658,1453	31.0	29.0	30.0		609	0.6	1.0	2	dbSNP_52	30	618,7982	156.7+/-210.5	24,570,3706	no	coding-synonymous	ZFP36L2	NM_006887.4		116,1228,5159	AA,AG,GG		7.186,19.1103,11.2256		203/495	43452334	1460,11546	2203	4300	6503	SO:0001819	synonymous_variant	678	exon2			GAAGCCGATGGTA	X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"""RING-type (C3HC4) zinc fingers"""	1108	protein-coding gene	gene with protein product		612053	"""zinc finger protein 36, C3H type-like 1"", ""zinc finger protein 36, C3H type-like 2"""	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.609C>T	2.37:g.43452334G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_006887	Q53TB4|Q9BSJ3	Silent	SNP	ENST00000282388.3	37	CCDS1811.1																																																																																			G|0.886;A|0.114	0.114	strong		0.672	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887	
LUZP1	7798	hgsc.bcm.edu	37	1	23418576	23418576	+	Missense_Mutation	SNP	T	T	C	rs144862656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23418576T>C	ENST00000302291.4	-	4	2980	c.2179A>G	c.(2179-2181)Acc>Gcc	p.T727A	LUZP1_ENST00000374623.3_Missense_Mutation_p.T727A|LUZP1_ENST00000418342.1_Missense_Mutation_p.T727A|LUZP1_ENST00000314174.5_Missense_Mutation_p.T727A			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	727					artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		AGCTCCATGGTATTGGTGGAG	0.493													C|||	23	0.00459265	0.0159	0.0029	5008	,	,		20483	0.0		0.0	False		,,,				2504	0.0				p.T727A		Atlas-SNP	.											.	LUZP1	83	.	0			c.A2179G						PASS	.	C	ALA/THR,ALA/THR	41,4365	799.2+/-415.5	0,41,2162	182.0	199.0	193.0		2179,2179	3.8	0.4	1	dbSNP_134	193	1,8599	812.4+/-407.1	0,1,4299	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	58,58	0,42,6461	CC,CT,TT		0.0116,0.9305,0.3229	benign,benign	727/1077,727/1077	23418576	42,12964	2203	4300	6503	SO:0001583	missense	7798	exon4			CCATGGTATTGGT	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.2179A>G	1.37:g.23418576T>C	ENSP00000303758:p.Thr727Ala	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	C	0.005	-2.197318	0.00299	0.009305	1.16E-4	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.12039	2.94;2.94;2.94;2.72	4.74	3.81	0.43845	.	0.350958	0.20869	N	0.084207	T	0.01905	0.0060	N	0.00347	-1.61	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38628	-0.9652	10	0.23891	T	0.37	.	4.1464	0.10217	0.3497:0.476:0.0:0.1743	.	727;727	Q86V48-2;Q86V48	.;LUZP1_HUMAN	A	727	ENSP00000393460:T727A;ENSP00000363752:T727A;ENSP00000303758:T727A;ENSP00000313705:T727A	ENSP00000303758:T727A	T	-	1	0	LUZP1	23291163	0.087000	0.21565	0.421000	0.26609	0.137000	0.21094	0.043000	0.13971	0.605000	0.29947	-0.330000	0.08379	ACC	T|0.997;C|0.003	0.003	strong		0.493	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631	
TMCO3	55002	hgsc.bcm.edu	37	13	114175032	114175032	+	Missense_Mutation	SNP	G	G	A	rs2260335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114175032G>A	ENST00000434316.2	+	8	1686	c.1327G>A	c.(1327-1329)Gcc>Acc	p.A443T	TMCO3_ENST00000375391.1_Intron|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	443			A -> T (in dbSNP:rs2260335).			integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			ACAGGCGGGCGCCAGTGCATC	0.478													G|||	1020	0.203674	0.41	0.1369	5008	,	,		16153	0.1498		0.1282	False		,,,				2504	0.1053				p.A443T		Atlas-SNP	.											.	TMCO3	77	.	0			c.G1327A						PASS	.	G	THR/ALA	1517,2889	483.0+/-359.6	258,1001,944	79.0	72.0	74.0		1327	4.1	0.0	13	dbSNP_100	74	1079,7521	225.2+/-261.4	60,959,3281	yes	missense	TMCO3	NM_017905.4	58	318,1960,4225	AA,AG,GG		12.5465,34.4303,19.96	benign	443/678	114175032	2596,10410	2203	4300	6503	SO:0001583	missense	55002	exon8			GCGGGCGCCAGTG	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.1327G>A	13.37:g.114175032G>A	ENSP00000389399:p.Ala443Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Missense_Mutation	SNP	ENST00000434316.2	37	CCDS9537.1	430	0.19688644688644688	195	0.39634146341463417	51	0.1408839779005525	92	0.16083916083916083	92	0.12137203166226913	G	3.243	-0.154835	0.06544	0.344303	0.125465	ENSG00000150403	ENST00000434316	T	0.15834	2.39	4.94	4.09	0.47781	Cation/H+ exchanger (1);	0.309976	0.34110	N	0.004248	T	0.00012	0.0000	L	0.28274	0.84	0.18873	P	0.9999847456	B;B	0.24092	0.015;0.097	B;B	0.21151	0.021;0.033	T	0.48969	-0.8987	9	0.19590	T	0.45	-19.3477	13.1084	0.59259	0.0789:0.0:0.9211:0.0	rs2260335;rs57107498	443;443	Q6UWJ1;Q6UWJ1-2	TMCO3_HUMAN;.	T	443	ENSP00000389399:A443T	ENSP00000389399:A443T	A	+	1	0	TMCO3	113223033	0.972000	0.33761	0.012000	0.15200	0.017000	0.09413	2.740000	0.47418	1.083000	0.41159	0.495000	0.49567	GCC	G|0.805;A|0.195	0.195	strong		0.478	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
TUBB2B	347733	hgsc.bcm.edu	37	6	3225759	3225759	+	Silent	SNP	C	C	A	rs148302841		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:3225759C>A	ENST00000259818.7	-	4	755	c.564G>T	c.(562-564)tcG>tcT	p.S188S	TUBB2B_ENST00000473006.1_5'UTR	NM_178012.4	NP_821080.1	Q9BVA1	TBB2B_HUMAN	tubulin, beta 2B class IIb	188					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|neuron migration (GO:0001764)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			kidney(2)|large_intestine(5)|lung(1)|prostate(1)|skin(1)	10	Ovarian(93;0.0386)	all_hematologic(90;0.108)				GCTGGTGGACCGAGAGGGTGG	0.577																																					p.S188S		Atlas-SNP	.											TUBB2B,caecum,carcinoma,-1,1	TUBB2B	25	1	0			c.G564T						scavenged	.						32.0	31.0	31.0					6																	3225759		1633	3399	5032	SO:0001819	synonymous_variant	347733	exon4			GTGGACCGAGAGG	BC001352	CCDS4485.1	6p25.2	2011-10-10	2011-10-10		ENSG00000137285	ENSG00000137285		"""Tubulins"""	30829	protein-coding gene	gene with protein product	"""class IIb beta-tubulin"""	612850	"""tubulin, beta 2B"""			8619474, 9110174	Standard	NM_178012		Approved	MGC8685, DKFZp566F223, bA506K6.1	uc003mvg.3	Q9BVA1	OTTHUMG00000014143	ENST00000259818.7:c.564G>T	6.37:g.3225759C>A		Somatic	528	2	0.00378788		WXS	Illumina HiSeq	Phase_I	562	91	0.161922	NM_178012	A8K068	Silent	SNP	ENST00000259818.7	37	CCDS4485.1																																																																																			C|0.750;A|0.250	0.250	weak		0.577	TUBB2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039680.2	NM_178012	
DSG1	1828	hgsc.bcm.edu	37	18	28919779	28919779	+	Missense_Mutation	SNP	A	A	C	rs8091003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28919779A>C	ENST00000257192.4	+	11	1690	c.1478A>C	c.(1477-1479)aAt>aCt	p.N493T		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	493	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		N -> T (in dbSNP:rs8091003).		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)			GACAGGACTAATACAGAGCCG	0.348													A|||	1178	0.235224	0.556	0.1225	5008	,	,		16074	0.0645		0.0875	False		,,,				2504	0.2096				p.N493T		Atlas-SNP	.											.	DSG1	176	.	0			c.A1478C						PASS	.	A	THR/ASN	2024,2382	562.8+/-381.0	459,1106,638	93.0	94.0	93.0		1478	-9.5	0.0	18	dbSNP_116	93	622,7978	162.5+/-215.2	30,562,3708	yes	missense	DSG1	NM_001942.2	65	489,1668,4346	CC,CA,AA		7.2326,45.9374,20.3445	benign	493/1050	28919779	2646,10360	2203	4300	6503	SO:0001583	missense	1828	exon11			GGACTAATACAGA	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.1478A>C	18.37:g.28919779A>C	ENSP00000257192:p.Asn493Thr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	405	0.18543956043956045	268	0.5447154471544715	45	0.12430939226519337	34	0.05944055944055944	58	0.07651715039577836	A	2.735	-0.263516	0.05754	0.459374	0.072326	ENSG00000134760	ENST00000257192	T	0.55930	0.49	4.74	-9.48	0.00591	Cadherin (1);	1.368040	0.04512	N	0.383090	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	0.12785	-1.0534	9	0.21014	T	0.42	.	4.4894	0.11806	0.5194:0.2746:0.1138:0.0922	rs8091003;rs58228580;rs8091003	493	Q02413	DSG1_HUMAN	T	493	ENSP00000257192:N493T	ENSP00000257192:N493T	N	+	2	0	DSG1	27173777	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.021000	0.13489	-3.401000	0.00171	-1.337000	0.01257	AAT	A|0.796;C|0.204	0.204	strong		0.348	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
BTBD1	53339	hgsc.bcm.edu	37	15	83725291	83725291	+	Silent	SNP	T	T	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83725291T>A	ENST00000261721.4	-	2	610	c.408A>T	c.(406-408)ctA>ctT	p.L136L	BTBD1_ENST00000379403.2_Silent_p.L136L|RP11-382A20.7_ENST00000570202.1_RNA|RP11-382A20.5_ENST00000566841.1_RNA|RP11-382A20.6_ENST00000568441.1_RNA	NM_001011885.1|NM_025238.3	NP_001011885.1|NP_079514.1	Q9H0C5	BTBD1_HUMAN	BTB (POZ) domain containing 1	136	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)|regulation of protein binding (GO:0043393)	cytoplasmic mRNA processing body (GO:0000932)|protein complex (GO:0043234)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	10				all cancers(203;0.000186)		CATCTGAATATAGAAATCTGG	0.358																																					p.L136L		Atlas-SNP	.											BTBD1,NS,carcinoma,-2,1	BTBD1	32	1	0			c.A408T						PASS	.						87.0	83.0	84.0					15																	83725291		2203	4300	6503	SO:0001819	synonymous_variant	53339	exon2			TGAATATAGAAAT	AF355402	CCDS10322.1, CCDS32313.1	15q24	2013-01-08			ENSG00000064726	ENSG00000064726		"""BTB/POZ domain containing"""	1120	protein-coding gene	gene with protein product		608530					Standard	XM_006720573		Approved		uc002bjn.3	Q9H0C5	OTTHUMG00000147364	ENST00000261721.4:c.408A>T	15.37:g.83725291T>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	87	35	0.402299	NM_025238	A6NMI8|Q9BX71|Q9NWN4	Silent	SNP	ENST00000261721.4	37	CCDS10322.1																																																																																			.	.	none		0.358	BTBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304008.1		
MFGE8	4240	hgsc.bcm.edu	37	15	89450003	89450003	+	Silent	SNP	G	G	A	rs2271714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89450003G>A	ENST00000566497.1	-	4	455	c.394C>T	c.(394-396)Ctg>Ttg	p.L132L	MFGE8_ENST00000542878.1_Silent_p.L88L|MFGE8_ENST00000268150.8_Silent_p.L132L|MFGE8_ENST00000539437.1_Silent_p.L124L|MFGE8_ENST00000268151.7_Silent_p.L132L|MFGE8_ENST00000559997.1_5'UTR			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	132	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)	p.L132L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					CTCCGCAGCAGGTTCACCTGG	0.587													G|||	1047	0.209065	0.4002	0.1787	5008	,	,		18372	0.2798		0.0398	False		,,,				2504	0.0736				p.L132L		Atlas-SNP	.											MFGE8,NS,carcinoma,0,1	MFGE8	60	1	1	Substitution - coding silent(1)	stomach(1)	c.C394T						PASS	.	G	,	1517,2883	481.0+/-359.0	264,989,947	95.0	76.0	83.0		394,394	4.1	1.0	15	dbSNP_100	83	357,8241	119.2+/-178.6	9,339,3951	no	coding-synonymous,coding-synonymous	MFGE8	NM_001114614.1,NM_005928.2	,	273,1328,4898	AA,AG,GG		4.1521,34.4773,14.4176	,	132/336,132/388	89450003	1874,11124	2200	4299	6499	SO:0001819	synonymous_variant	4240	exon4			GCAGCAGGTTCAC	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"""sperm surface protein hP47"""	602281	"""sperm associated antigen 10"""	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.394C>T	15.37:g.89450003G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	114	65	0.570175	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Silent	SNP	ENST00000566497.1	37	CCDS10347.1																																																																																			G|0.826;A|0.174	0.174	strong		0.587	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928	
UGT3A1	133688	hgsc.bcm.edu	37	5	35957462	35957462	+	Silent	SNP	G	G	A	rs10428673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:35957462G>A	ENST00000274278.3	-	5	1260	c.903C>T	c.(901-903)ggC>ggT	p.G301G	UGT3A1_ENST00000507113.1_Silent_p.G267G|UGT3A1_ENST00000513233.1_5'UTR|UGT3A1_ENST00000503189.1_Silent_p.G301G	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	301						integral component of membrane (GO:0016021)|UDP-N-acetylglucosamine transferase complex (GO:0043541)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|skin(4)	46	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TCAACATGGAGCCAAAGGCCA	0.488													G|||	40	0.00798722	0.028	0.0043	5008	,	,		20323	0.0		0.0	False		,,,				2504	0.0				p.G301G		Atlas-SNP	.											.	UGT3A1	95	.	0			c.C903T						PASS	.	G		109,4297		1,107,2095	104.0	90.0	95.0		903	1.4	1.0	5	dbSNP_119	95	2,8598		0,2,4298	no	coding-synonymous	UGT3A1	NM_152404.3		1,109,6393	AA,AG,GG		0.0233,2.4739,0.8535		301/524	35957462	111,12895	2203	4300	6503	SO:0001819	synonymous_variant	133688	exon5			CATGGAGCCAAAG		CCDS3913.1, CCDS54841.1	5p13.2	2014-05-20			ENSG00000145626	ENSG00000145626		"""UDP glucuronosyltransferases"""	26625	protein-coding gene	gene with protein product							Standard	NM_152404		Approved	FLJ34658	uc003jjv.2	Q6NUS8	OTTHUMG00000131107	ENST00000274278.3:c.903C>T	5.37:g.35957462G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	135	69	0.511111	NM_152404	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Silent	SNP	ENST00000274278.3	37	CCDS3913.1																																																																																			G|0.991;A|0.009	0.009	strong		0.488	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404	
OR5V1	81696	hgsc.bcm.edu	37	6	29323905	29323905	+	Missense_Mutation	SNP	A	A	C	rs6930033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29323905A>C	ENST00000377154.1	-	4	367	c.68T>G	c.(67-69)tTg>tGg	p.L23W	OR5V1_ENST00000543825.1_Missense_Mutation_p.L23W			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	23			L -> W (in dbSNP:rs6930033). {ECO:0000269|PubMed:14574404, 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)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TAAAAACTGCAATTCATTTAG	0.373													A|||	1258	0.251198	0.1672	0.2478	5008	,	,		18385	0.4038		0.17	False		,,,				2504	0.2935				p.L23W	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											.	OR5V1	63	.	0			c.T68G						PASS	.	A	TRP/LEU	651,3745		51,549,1598	73.0	76.0	75.0		68	4.4	0.0	6	dbSNP_116	75	1376,7208		125,1126,3041	yes	missense	OR5V1	NM_030876.5	61	176,1675,4639	CC,CA,AA		16.0298,14.8089,15.6163	probably-damaging	23/322	29323905	2027,10953	2198	4292	6490	SO:0001583	missense	81696	exon1			AACTGCAATTCAT		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"""GPCR / Class A : Olfactory receptors"""	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.68T>G	6.37:g.29323905A>C	ENSP00000366359:p.Leu23Trp	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	37	CCDS4657.1	516	0.23626373626373626	76	0.15447154471544716	93	0.2569060773480663	231	0.40384615384615385	116	0.15303430079155672	A	15.56	2.868850	0.51588	0.148089	0.160298	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.05580	3.42;3.42	4.37	4.37	0.52481	.	0.341744	0.16651	N	0.205208	T	0.11879	0.0289	M	0.76170	2.325	0.80722	P	0.0	D	0.69078	0.997	P	0.57283	0.817	T	0.01951	-1.1241	9	0.56958	D	0.05	-14.7225	13.6641	0.62384	1.0:0.0:0.0:0.0	rs6930033;rs52796609;rs60291414;rs6930033	23	Q9UGF6	OR5V1_HUMAN	W	23	ENSP00000366359:L23W;ENSP00000443309:L23W	ENSP00000366356:L23W	L	-	2	0	OR5V1	29431884	0.000000	0.05858	0.004000	0.12327	0.852000	0.48524	1.174000	0.31932	1.953000	0.56701	0.438000	0.28831	TTG	A|0.805;C|0.195	0.195	strong		0.373	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3		
LRIG1	26018	hgsc.bcm.edu	37	3	66433458	66433458	+	Silent	SNP	G	G	A	rs34042409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:66433458G>A	ENST00000273261.3	-	15	2963	c.2439C>T	c.(2437-2439)tgC>tgT	p.C813C	LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000383703.3_Silent_p.C790C	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	813					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		GGTAGATGATGCACACCCAGA	0.577													G|||	261	0.0521166	0.1906	0.013	5008	,	,		19695	0.0		0.0	False		,,,				2504	0.0				p.C813C		Atlas-SNP	.											.	LRIG1	138	.	0			c.C2439T						PASS	.	G		705,3701	294.7+/-283.3	56,593,1554	115.0	90.0	99.0		2439	5.9	1.0	3	dbSNP_126	99	7,8593	5.7+/-21.5	0,7,4293	yes	coding-synonymous	LRIG1	NM_015541.2		56,600,5847	AA,AG,GG		0.0814,16.0009,5.4744		813/1094	66433458	712,12294	2203	4300	6503	SO:0001819	synonymous_variant	26018	exon15			GATGATGCACACC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.2439C>T	3.37:g.66433458G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			G|0.941;A|0.059	0.059	strong		0.577	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
THBS2	7058	hgsc.bcm.edu	37	6	169622490	169622490	+	Silent	SNP	G	G	A	rs9505895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:169622490G>A	ENST00000366787.3	-	20	3324	c.3075C>T	c.(3073-3075)gcC>gcT	p.A1025A	XXyac-YX65C7_A.2_ENST00000444188.1_RNA|THBS2_ENST00000488355.1_5'UTR	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	117	0	0		WXS	Illumina HiSeq	Phase_I	147	86	0.585034	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	
ZFP14	57677	hgsc.bcm.edu	37	19	36832427	36832427	+	Missense_Mutation	SNP	A	A	T	rs115297808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36832427A>T	ENST00000270001.7	-	5	416	c.301T>A	c.(301-303)Ttt>Att	p.F101I		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	101					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(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					TCCCACTGAAATGAATATATT	0.343													A|||	69	0.013778	0.0507	0.0029	5008	,	,		17204	0.0		0.0	False		,,,				2504	0.0				p.F101I		Atlas-SNP	.											.	ZFP14	68	.	0			c.T301A						PASS	.	A	ILE/PHE	147,4259	94.8+/-133.5	4,139,2060	52.0	54.0	53.0		301	2.0	0.5	19	dbSNP_132	53	2,8586	1.2+/-3.3	0,2,4292	yes	missense	ZFP14	NM_020917.2	21	4,141,6352	TT,TA,AA		0.0233,3.3364,1.1467	benign	101/534	36832427	149,12845	2203	4294	6497	SO:0001583	missense	57677	exon5			ACTGAAATGAATA	AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"""Zinc fingers, C2H2-type"", ""-"""	29312	protein-coding gene	gene with protein product			"""zinc finger protein 14 homolog (mouse)"""			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.301T>A	19.37:g.36832427A>T	ENSP00000270001:p.Phe101Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_020917	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	37	CCDS33002.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	a	3.299	-0.143207	0.06669	0.033364	2.33E-4	ENSG00000142065	ENST00000270001;ENST00000392172	T	0.06528	3.29	4.2	2.05	0.26809	.	0.326738	0.22483	N	0.059470	T	0.00666	0.0022	L	0.38175	1.15	0.19775	N	0.999956	B;B	0.16603	0.018;0.005	B;B	0.12837	0.008;0.008	T	0.44907	-0.9297	10	0.21014	T	0.42	.	4.3827	0.11302	0.691:0.2011:0.1079:0.0	.	101;101	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	I	101	ENSP00000270001:F101I	ENSP00000270001:F101I	F	-	1	0	ZFP14	41524267	0.005000	0.15991	0.453000	0.27007	0.613000	0.37349	1.042000	0.30303	0.240000	0.21263	0.523000	0.50628	TTT	A|0.990;T|0.010	0.010	strong		0.343	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917	
ZDHHC11	79844	hgsc.bcm.edu	37	5	825297	825297	+	Silent	SNP	A	A	G	rs1808545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:825297A>G	ENST00000283441.8	-	8	1388	c.1005T>C	c.(1003-1005)gaT>gaC	p.D335D	ZDHHC11_ENST00000424784.2_Silent_p.D335D|ZDHHC11_ENST00000503758.2_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	335						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			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)			TCGAATCCCCATCCTGGTTTA	0.547																																					p.D335D		Atlas-SNP	.											.	ZDHHC11	97	.	0			c.T1005C						PASS	.						191.0	137.0	155.0					5																	825297		2203	4296	6499	SO:0001819	synonymous_variant	79844	exon8			ATCCCCATCCTGG	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.1005T>C	5.37:g.825297A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	260	55	0.211538	NM_024786	Q6UWR9	Silent	SNP	ENST00000283441.8	37	CCDS3857.1																																																																																			A|0.977;G|0.023	0.023	strong		0.547	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
URB2	9816	hgsc.bcm.edu	37	1	229773441	229773441	+	Silent	SNP	C	C	T	rs3811475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229773441C>T	ENST00000258243.2	+	4	3217	c.3081C>T	c.(3079-3081)acC>acT	p.T1027T		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1027						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						GAAAAATCACCGCATTCCTCT	0.463													C|||	1027	0.205072	0.2156	0.2464	5008	,	,		20811	0.4315		0.0626	False		,,,				2504	0.0746				p.T1027T		Atlas-SNP	.											.	URB2	152	.	0			c.C3081T						PASS	.	C		932,3474	354.1+/-312.5	101,730,1372	67.0	69.0	68.0		3081	-6.6	0.0	1	dbSNP_107	68	555,8045	150.6+/-205.5	14,527,3759	no	coding-synonymous	URB2	NM_014777.2		115,1257,5131	TT,TC,CC		6.4535,21.153,11.4332		1027/1525	229773441	1487,11519	2203	4300	6503	SO:0001819	synonymous_variant	9816	exon4			AATCACCGCATTC	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.3081C>T	1.37:g.229773441C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	159	68	0.427673	NM_014777	Q5VYC9	Silent	SNP	ENST00000258243.2	37	CCDS31052.1																																																																																			C|0.857;T|0.143	0.143	strong		0.463	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
TRPM6	140803	hgsc.bcm.edu	37	9	77418802	77418802	+	Splice_Site	SNP	G	G	A	rs115354606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:77418802G>A	ENST00000360774.1	-	15	1876	c.1639C>T	c.(1639-1641)Cac>Tac	p.H547Y	TRPM6_ENST00000376864.4_Splice_Site_p.H547Y|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000361255.3_Splice_Site_p.H542Y|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000451710.3_Splice_Site_p.H547Y|TRPM6_ENST00000449912.2_Splice_Site_p.H542Y	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	547					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						TGTCTCTGGTGCTGGGAAAGG	0.388													G|||	164	0.0327476	0.1127	0.0187	5008	,	,		17133	0.0		0.002	False		,,,				2504	0.0				p.H547Y		Atlas-SNP	.											.	TRPM6	377	.	0			c.C1639T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	400,4006	201.1+/-224.2	18,364,1821	142.0	135.0	137.0		1624,1624,1639	2.7	0.7	9	dbSNP_132	137	9,8591	6.4+/-24.3	0,9,4291	yes	missense-near-splice,missense-near-splice,missense-near-splice	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	83,83,83	18,373,6112	AA,AG,GG		0.1047,9.0785,3.1447	benign,benign,benign	542/2018,542/2018,547/2023	77418802	409,12597	2203	4300	6503	SO:0001630	splice_region_variant	140803	exon15			TCTGGTGCTGGGA	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.1639-1C>T	9.37:g.77418802G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	61	0.693182	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	67	0.030677655677655676	58	0.11788617886178862	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	G	16.51	3.143177	0.57044	0.090785	0.001047	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76;-0.76	5.51	2.69	0.31865	.	0.768746	0.12808	N	0.437439	T	0.03390	0.0098	M	0.67953	2.075	0.36472	P	0.132695	D;B	0.54397	0.966;0.402	P;B	0.49421	0.61;0.196	T	0.47799	-0.9089	9	0.62326	D	0.03	.	6.3637	0.21443	0.2288:0.1334:0.6379:0.0	.	547;542	Q9BX84;Q9BX84-3	TRPM6_HUMAN;.	Y	547;547;542;542;547;210;210	ENSP00000354006:H547Y;ENSP00000407341:H547Y;ENSP00000396672:H542Y;ENSP00000354962:H542Y;ENSP00000366060:H547Y	ENSP00000309693:H210Y	H	-	1	0	TRPM6	76608622	0.107000	0.21998	0.717000	0.30585	0.861000	0.49209	0.067000	0.14510	0.302000	0.22762	0.563000	0.77884	CAC	G|0.969;A|0.031	0.031	strong		0.388	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	Missense_Mutation
PYCRL	65263	hgsc.bcm.edu	37	8	144688736	144688736	+	Missense_Mutation	SNP	C	C	G	rs2242090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144688736C>G	ENST00000220966.6	-	4	515	c.486G>C	c.(484-486)aaG>aaC	p.K162N	PYCRL_ENST00000377579.3_Missense_Mutation_p.K13N|PYCRL_ENST00000495276.1_5'UTR	NM_023078.3	NP_075566.2	Q53H96	P5CR3_HUMAN	pyrroline-5-carboxylate reductase-like	150					L-proline biosynthetic process (GO:0055129)		pyrroline-5-carboxylate reductase activity (GO:0004735)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	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;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)		L-Proline(DB00172)	GCTGCAGGAGCTTGGTCTCGC	0.667													C|||	1638	0.327077	0.0809	0.3977	5008	,	,		17053	0.3879		0.5239	False		,,,				2504	0.3446				p.K162N		Atlas-SNP	.											PYCRL,NS,carcinoma,0,2	PYCRL	14	2	0			c.G486C						PASS	.	C	ASN/LYS	604,3800	254.0+/-259.7	48,508,1646	46.0	36.0	40.0		486	0.5	0.2	8	dbSNP_98	40	4632,3966	585.0+/-391.8	1296,2040,963	no	missense	PYCRL	NM_023078.3	94	1344,2548,2609	GG,GC,CC		46.127,13.7148,40.2707	benign	162/287	144688736	5236,7766	2202	4299	6501	SO:0001583	missense	65263	exon4			CAGGAGCTTGGTC	AF086378	CCDS6407.2	8q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000104524	ENSG00000104524			25846	protein-coding gene	gene with protein product							Standard	NM_023078		Approved	FLJ13852	uc003yyy.3	Q53H96	OTTHUMG00000157010	ENST00000220966.6:c.486G>C	8.37:g.144688736C>G	ENSP00000220966:p.Lys162Asn	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	190	89	0.468421	NM_023078	B3KMB5|B4DVT6|H0Y6C3|Q8N3N9|Q96HX4|Q9H896	Missense_Mutation	SNP	ENST00000220966.6	37	CCDS6407.2	820	0.37545787545787546	53	0.10772357723577236	172	0.47513812154696133	198	0.34615384615384615	397	0.5237467018469657	C	8.270	0.813088	0.16537	0.137148	0.53873	ENSG00000104524	ENST00000220966;ENST00000377579;ENST00000433751	T;T;T	0.80123	-0.07;-1.34;-0.07	5.05	0.47	0.16747	.	0.767289	0.12455	N	0.467428	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.39542	-0.9609	6	0.39692	T	0.17	-0.0352	1.6791	0.02828	0.1426:0.42:0.1402:0.2972	rs2242090;rs17845144;rs17857947	.	.	.	N	162;13;137	ENSP00000220966:K162N;ENSP00000366802:K13N;ENSP00000404493:K137N	ENSP00000220966:K162N	K	-	3	2	PYCRL	144759879	0.000000	0.05858	0.207000	0.23584	0.583000	0.36354	-0.340000	0.07821	0.166000	0.19597	0.462000	0.41574	AAG	C|0.608;G|0.392	0.392	strong		0.667	PYCRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347081.2	NM_023078	
WDR64	128025	hgsc.bcm.edu	37	1	241951329	241951329	+	Missense_Mutation	SNP	C	C	T	rs12074374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241951329C>T	ENST00000366552.2	+	23	3061	c.2854C>T	c.(2854-2856)Cgg>Tgg	p.R952W	WDR64_ENST00000437684.2_Missense_Mutation_p.R785W	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	952			R -> W (in dbSNP:rs12074374).							breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GATATTTGACCGGGAAAAGTA	0.363													C|||	563	0.11242	0.2186	0.1254	5008	,	,		20463	0.005		0.16	False		,,,				2504	0.0215				p.R952W		Atlas-SNP	.											WDR64_ENST00000366552,NS,carcinoma,-1,2	WDR64	234	2	0			c.C2854T						PASS	.	C	TRP/ARG	944,3462	354.6+/-312.7	92,760,1351	53.0	53.0	53.0		2854	2.8	0.9	1	dbSNP_120	53	1450,7150	275.4+/-291.8	134,1182,2984	yes	missense	WDR64	NM_144625.4	101	226,1942,4335	TT,TC,CC		16.8605,21.4253,18.4069	probably-damaging	952/1082	241951329	2394,10612	2203	4300	6503	SO:0001583	missense	128025	exon23			TTTGACCGGGAAA	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"""WD repeat domain containing"""	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.2854C>T	1.37:g.241951329C>T	ENSP00000355510:p.Arg952Trp	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	84	51	0.607143	NM_144625	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	37		275	0.1259157509157509	104	0.21138211382113822	53	0.1464088397790055	2	0.0034965034965034965	116	0.15303430079155672	C	16.98	3.271363	0.59649	0.214253	0.168605	ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635	T;T;T	0.42131	1.17;0.98;0.99	5.69	2.8	0.32819	.	0.363501	0.23589	N	0.046575	T	0.00073	0.0002	L	0.60455	1.87	0.45791	P	0.0013250000000000206	D;D	0.89917	0.999;1.0	P;D	0.64687	0.874;0.928	T	0.05007	-1.0912	9	0.87932	D	0	-2.9469	9.3749	0.38277	0.417:0.4484:0.1345:0.0	rs12074374;rs52791125;rs56770384;rs12074374	952;505	B1ANS9;D1MPS4	WDR64_HUMAN;.	W	952;785;556	ENSP00000355510:R952W;ENSP00000402446:R785W;ENSP00000406656:R556W	ENSP00000355510:R952W	R	+	1	2	WDR64	240017952	0.148000	0.22702	0.856000	0.33681	0.989000	0.77384	0.373000	0.20484	0.339000	0.23719	-0.134000	0.14843	CGG	C|0.837;T|0.163	0.163	strong		0.363	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625	
RPAP3	79657	hgsc.bcm.edu	37	12	48075597	48075597	+	Silent	SNP	A	A	G	rs36123489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48075597A>G	ENST00000005386.3	-	10	1111	c.996T>C	c.(994-996)taT>taC	p.Y332Y	RPAP3_ENST00000380650.4_Silent_p.Y332Y|RPAP3_ENST00000432584.3_Silent_p.Y173Y	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	332										endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					CAGCTTCTTCATATCTATTGA	0.313													A|||	224	0.0447284	0.1566	0.0231	5008	,	,		18004	0.0		0.001	False		,,,				2504	0.0				p.Y332Y		Atlas-SNP	.											.	RPAP3	45	.	0			c.T996C						PASS	.	A	,,	647,3757	277.8+/-273.9	49,549,1604	61.0	59.0	59.0		996,519,996	1.9	1.0	12	dbSNP_126	59	12,8584	8.4+/-32.0	0,12,4286	no	coding-synonymous,coding-synonymous,coding-synonymous	RPAP3	NM_001146075.1,NM_001146076.1,NM_024604.2	,,	49,561,5890	GG,GA,AA		0.1396,14.6912,5.0692	,,	332/632,173/507,332/666	48075597	659,12341	2202	4298	6500	SO:0001819	synonymous_variant	79657	exon10			TTCTTCATATCTA	AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"""Tetratricopeptide (TTC) repeat domain containing"""	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.996T>C	12.37:g.48075597A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_024604	B4DRW9|Q6PHR5	Silent	SNP	ENST00000005386.3	37	CCDS8753.1																																																																																			A|0.952;G|0.048	0.048	strong		0.313	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604	
MASP2	10747	hgsc.bcm.edu	37	1	11103408	11103408	+	Silent	SNP	G	G	A	rs7536030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11103408G>A	ENST00000400897.3	-	5	744	c.729C>T	c.(727-729)taC>taT	p.Y243Y		NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	243	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)	p.Y243Y(1)		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)		TGAGAAAGTCGTAGGGACACA	0.587													G|||	367	0.0732827	0.2648	0.0187	5008	,	,		19805	0.0		0.0	False		,,,				2504	0.0041				p.Y243Y	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											MASP2,colon,carcinoma,0,1	MASP2	71	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C729T						PASS	.	G		1054,3346	365.4+/-317.4	125,804,1271	56.0	43.0	47.0		729	-1.1	1.0	1	dbSNP_116	47	21,8579	11.9+/-42.8	1,19,4280	no	coding-synonymous	MASP2	NM_006610.3		126,823,5551	AA,AG,GG		0.2442,23.9545,8.2692		243/687	11103408	1075,11925	2200	4300	6500	SO:0001819	synonymous_variant	10747	exon5			AAAGTCGTAGGGA	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.729C>T	1.37:g.11103408G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Silent	SNP	ENST00000400897.3	37	CCDS123.1																																																																																			G|0.904;A|0.096	0.096	strong		0.587	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610	
GPATCH4	54865	hgsc.bcm.edu	37	1	156567847	156567847	+	Missense_Mutation	SNP	G	G	C	rs141345590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156567847G>C	ENST00000438976.2	-	5	358	c.328C>G	c.(328-330)Ctg>Gtg	p.L110V	GPATCH4_ENST00000334588.7_Missense_Mutation_p.L59V|GPATCH4_ENST00000368232.4_Missense_Mutation_p.L105V|GPATCH4_ENST00000497287.1_5'UTR			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	105							poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(3)|stomach(1)	17	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTCTGATACAGCAAGTTGGGC	0.463													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		21358	0.0		0.0	False		,,,				2504	0.0				p.L110V		Atlas-SNP	.											.	GPATCH4	34	.	0			c.C328G						PASS	.	G	VAL/LEU,VAL/LEU	171,4235	115.0+/-153.0	4,163,2036	145.0	141.0	142.0		328,313	2.3	1.0	1	dbSNP_134	142	0,8600		0,0,4300	yes	missense,missense	GPATCH4	NM_015590.3,NM_182679.2	32,32	4,163,6336	CC,CG,GG		0.0,3.8811,1.3148	probably-damaging,probably-damaging	110/376,105/371	156567847	171,12835	2203	4300	6503	SO:0001583	missense	54865	exon5			GATACAGCAAGTT	BC056904	CCDS1146.1, CCDS44245.1	1q22	2013-01-28		2006-12-13	ENSG00000160818	ENSG00000160818		"""G patch domain containing"""	25982	protein-coding gene	gene with protein product				GPATC4		12477932	Standard	NM_015590		Approved	FLJ20249, DKFZP434F1735	uc001fpl.3	Q5T3I0	OTTHUMG00000033203	ENST00000438976.2:c.328C>G	1.37:g.156567847G>C	ENSP00000396441:p.Leu110Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	182	91	0.5	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Missense_Mutation	SNP	ENST00000438976.2	37	CCDS44245.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	G	16.61	3.172437	0.57584	0.038811	0.0	ENSG00000160818	ENST00000368232;ENST00000368229;ENST00000438976;ENST00000334588	.	.	.	5.47	2.33	0.28932	.	0.073719	0.53938	D	0.000052	T	0.36496	0.0969	L	0.57130	1.785	0.41650	D	0.989123	D;D	0.58268	0.982;0.982	P;P	0.51266	0.664;0.664	T	0.31696	-0.9934	9	0.42905	T	0.14	-1.1016	3.0104	0.06043	0.2718:0.0:0.5275:0.2007	.	110;105	E9PAV9;Q5T3I0	.;GPTC4_HUMAN	V	105;105;110;59	.	ENSP00000334793:L59V	L	-	1	2	GPATCH4	154834471	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	1.145000	0.31577	0.837000	0.34925	0.655000	0.94253	CTG	G|0.988;C|0.012	0.012	strong		0.463	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725	
MGA	23269	hgsc.bcm.edu	37	15	42019421	42019421	+	Silent	SNP	A	A	G	rs61736067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42019421A>G	ENST00000570161.1	+	9	3474	c.3474A>G	c.(3472-3474)ccA>ccG	p.P1158P	MGA_ENST00000389936.4_Silent_p.P1158P|MGA_ENST00000219905.7_Silent_p.P1158P|MGA_ENST00000545763.1_Silent_p.P1158P|MGA_ENST00000566586.1_Silent_p.P1158P			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)	GACATTACCCATTATGGGTAA	0.408													A|||	80	0.0159744	0.0582	0.0029	5008	,	,		18915	0.0		0.001	False		,,,				2504	0.0				p.P1158P		Atlas-SNP	.											.	MGA	264	.	0			c.A3474G						PASS	.	A	,	166,3584		7,152,1716	86.0	79.0	81.0		3474,3474	0.6	1.0	15	dbSNP_129	81	3,8199		0,3,4098	no	coding-synonymous,coding-synonymous	MGA	NM_001080541.2,NM_001164273.1	,	7,155,5814	GG,GA,AA		0.0366,4.4267,1.414	,	1158/2857,1158/3066	42019421	169,11783	1875	4101	5976	SO:0001819	synonymous_variant	23269	exon10			TTACCCATTATGG	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.3474A>G	15.37:g.42019421A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																			A|0.988;G|0.012	0.012	strong		0.408	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
TJP2	9414	hgsc.bcm.edu	37	9	71835842	71835842	+	Missense_Mutation	SNP	C	C	A	rs41305539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:71835842C>A	ENST00000377245.4	+	5	590	c.382C>A	c.(382-384)Cag>Aag	p.Q128K	TJP2_ENST00000539225.1_Missense_Mutation_p.Q159K|TJP2_ENST00000265384.7_Missense_Mutation_p.Q128K|TJP2_ENST00000535702.1_Missense_Mutation_p.Q132K|TJP2_ENST00000453658.2_Missense_Mutation_p.Q105K|TJP2_ENST00000348208.4_Missense_Mutation_p.Q128K	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	128					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GGCCGCACTTCAGGCCAGCCC	0.572													C|||	639	0.127596	0.3283	0.0331	5008	,	,		14868	0.0387		0.0368	False		,,,				2504	0.1084				p.Q159K		Atlas-SNP	.											.	TJP2	120	.	0			c.C475A						PASS	.	C	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN	1328,3076	421.7+/-339.5	210,908,1084	37.0	34.0	35.0		313,394,475,382,382,382	2.9	0.0	9	dbSNP_127	35	166,8428	72.9+/-135.5	2,162,4133	yes	missense,missense,missense,missense,missense,missense	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	53,53,53,53,53,53	212,1070,5217	AA,AC,CC		1.9316,30.1544,11.4941	benign,benign,benign,benign,benign,benign	105/1021,132/1158,159/1222,128/994,128/1191,128/1044	71835842	1494,11504	2202	4297	6499	SO:0001583	missense	9414	exon5			GCACTTCAGGCCA	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.382C>A	9.37:g.71835842C>A	ENSP00000366453:p.Gln128Lys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	93	54	0.580645	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	239	0.10943223443223443	171	0.3475609756097561	10	0.027624309392265192	23	0.04020979020979021	35	0.04617414248021108	C	0.375	-0.932100	0.02359	0.301544	0.019316	ENSG00000119139	ENST00000453658;ENST00000423935;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T;T	0.30182	3.18;1.54;3.18;3.18;3.17;3.18;3.23	6.03	2.89	0.33648	PDZ/DHR/GLGF (1);	0.573781	0.19319	N	0.117182	T	0.00012	0.0000	N	0.16368	0.405	0.80722	P	0.0	B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001	B;B;B;B;B	0.11329	0.004;0.006;0.002;0.003;0.004	T	0.37174	-0.9717	9	0.02654	T	1	.	12.0357	0.53423	0.3496:0.5619:0.0884:0.0	rs41305539	159;132;128;128;128	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	K	105;105;128;128;128;132;159	ENSP00000392178:Q105K;ENSP00000402941:Q105K;ENSP00000366453:Q128K;ENSP00000345893:Q128K;ENSP00000265384:Q128K;ENSP00000442090:Q132K;ENSP00000438262:Q159K	ENSP00000265384:Q128K	Q	+	1	0	TJP2	71025662	0.156000	0.22821	0.004000	0.12327	0.544000	0.35116	1.079000	0.30766	0.847000	0.35167	0.655000	0.94253	CAG	C|0.892;A|0.108	0.108	strong		0.572	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125855665	125855665	+	Missense_Mutation	SNP	T	T	G	rs9282691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125855665T>G	ENST00000393434.2	-	11	1635	c.1286A>C	c.(1285-1287)gAg>gCg	p.E429A	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.E429A|ALDH1L1_ENST00000393431.2_Missense_Mutation_p.E429A|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.E439A|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.E328A	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	429	Aldehyde dehydrogenase.		E -> A (in dbSNP:rs9282691).		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)	ATCCACGAACTCCCCCCCAAT	0.587													T|||	348	0.0694888	0.2368	0.0331	5008	,	,		19282	0.0		0.0	False		,,,				2504	0.0123				p.E439A		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.A1316C						PASS	.	T	ALA/GLU	884,3522	318.8+/-295.8	95,694,1414	99.0	89.0	92.0		1286	-6.2	0.0	3	dbSNP_126	92	5,8595	3.0+/-9.4	0,5,4295	yes	missense	ALDH1L1	NM_012190.2	107	95,699,5709	GG,GT,TT		0.0581,20.0635,6.8353	benign	429/903	125855665	889,12117	2203	4300	6503	SO:0001583	missense	10840	exon11			ACGAACTCCCCCC	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.1286A>C	3.37:g.125855665T>G	ENSP00000377083:p.Glu429Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	118	0.05402930402930403	104	0.21138211382113822	14	0.03867403314917127	0	0.0	0	0.0	T	4.666	0.123895	0.08931	0.200635	5.81E-4	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434;ENST00000393431	T;T;T;T;T	0.09445	2.98;2.98;2.98;2.98;3.08	3.67	-6.25	0.02039	Acyl carrier protein-like (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	2.485370	0.02081	N	0.052371	T	0.00012	0.0000	L	0.49126	1.545	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.35724	-0.9777	9	0.51188	T	0.08	.	3.3174	0.07038	0.1797:0.0968:0.1379:0.5855	rs9282691;rs52830184;rs60301528;rs9282691	328;481;429	E9PBX3;Q59G10;O75891	.;.;AL1L1_HUMAN	A	439;429;328;429;429	ENSP00000273450:E439A;ENSP00000420293:E429A;ENSP00000395881:E328A;ENSP00000377083:E429A;ENSP00000377081:E429A	ENSP00000273450:E439A	E	-	2	0	ALDH1L1	127338355	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.150000	0.16263	-1.451000	0.01933	-0.402000	0.06365	GAG	T|0.935;G|0.065	0.065	strong		0.587	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
PTPRN2	5799	hgsc.bcm.edu	37	7	157959888	157959888	+	Silent	SNP	G	G	A	rs73745197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157959888G>A	ENST00000389418.4	-	6	654	c.645C>T	c.(643-645)gaC>gaT	p.D215D	PTPRN2_ENST00000409483.1_Silent_p.D177D|PTPRN2_ENST00000389416.4_Silent_p.D198D|PTPRN2_ENST00000389413.3_Silent_p.D215D|PTPRN2_ENST00000404321.2_Silent_p.D238D	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	215					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCGGCAGGAGGTCCTCGCGGA	0.652													G|||	100	0.0199681	0.0688	0.0086	5008	,	,		15889	0.0		0.003	False		,,,				2504	0.0				p.D215D		Atlas-SNP	.											.	PTPRN2	243	.	0			c.C645T						PASS	.		,,	303,4101	159.2+/-191.8	12,279,1911	42.0	42.0	42.0		645,594,645	2.3	0.0	7	dbSNP_130	42	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	12,279,6211	AA,AG,GG		0.0,6.8801,2.3301	,,	215/1016,198/999,215/987	157959888	303,12701	2202	4300	6502	SO:0001819	synonymous_variant	5799	exon6			CAGGAGGTCCTCG	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.645C>T	7.37:g.157959888G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	70	40	0.571429	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			G|0.973;A|0.027	0.027	strong		0.652	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
PNMT	5409	hgsc.bcm.edu	37	17	37826249	37826249	+	Silent	SNP	A	A	G	rs5638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37826249A>G	ENST00000269582.2	+	3	774	c.456A>G	c.(454-456)aaA>aaG	p.K152K	PNMT_ENST00000394246.1_Silent_p.K54K|PNMT_ENST00000581428.1_3'UTR	NM_002686.3	NP_002677.1	P11086	PNMT_HUMAN	phenylethanolamine N-methyltransferase	152					catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|epinephrine biosynthetic process (GO:0042418)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phenylethanolamine N-methyltransferase activity (GO:0004603)			NS(1)|breast(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8	all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|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;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCAGGGTGAAACGGGTCCTGC	0.657													A|||	317	0.0632987	0.1725	0.0317	5008	,	,		16981	0.004		0.0129	False		,,,				2504	0.0511				p.K152K		Atlas-SNP	.											.	PNMT	17	.	0			c.A456G						PASS	.	A		640,3766	252.4+/-258.8	45,550,1608	41.0	44.0	43.0		456	4.0	1.0	17	dbSNP_52	43	169,8429	74.5+/-137.1	1,167,4131	no	coding-synonymous	PNMT	NM_002686.3		46,717,5739	GG,GA,AA		1.9656,14.5256,6.2212		152/283	37826249	809,12195	2203	4299	6502	SO:0001819	synonymous_variant	5409	exon3			GGTGAAACGGGTC		CCDS11343.1	17q	2010-04-16			ENSG00000141744	ENSG00000141744	2.1.1.28		9160	protein-coding gene	gene with protein product		171190		PENT		3372503	Standard	NM_002686		Approved		uc002hsi.2	P11086	OTTHUMG00000133209	ENST00000269582.2:c.456A>G	17.37:g.37826249A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_002686		Silent	SNP	ENST00000269582.2	37	CCDS11343.1																																																																																			A|0.933;G|0.067	0.067	strong		0.657	PNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256923.2	NM_002686	
SLC7A4	6545	hgsc.bcm.edu	37	22	21385427	21385427	+	Missense_Mutation	SNP	G	G	C	rs80061703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21385427G>C	ENST00000382932.2	-	2	742	c.675C>G	c.(673-675)gaC>gaG	p.D225E	AC002472.11_ENST00000450652.1_RNA|SLC7A4_ENST00000403586.1_Missense_Mutation_p.D225E	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	225					basic amino acid transport (GO:0015802)|cellular amino acid metabolic process (GO:0006520)|transport (GO:0006810)	integral component of membrane (GO:0016021)	basic amino acid transmembrane transporter activity (GO:0015174)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	AGCCGCCTTCGTCAGCGCTCC	0.597													G|||	150	0.0299521	0.1104	0.0058	5008	,	,		20919	0.0		0.0	False		,,,				2504	0.0				p.D225E		Atlas-SNP	.											.	SLC7A4	50	.	0			c.C675G						PASS	.	G	GLU/ASP	446,3960	209.5+/-230.2	21,404,1778	55.0	56.0	56.0		675	0.6	0.2	22	dbSNP_131	56	5,8595	4.3+/-15.6	0,5,4295	yes	missense	SLC7A4	NM_004173.2	45	21,409,6073	CC,CG,GG		0.0581,10.1226,3.4676	benign	225/636	21385427	451,12555	2203	4300	6503	SO:0001583	missense	6545	exon2			GCCTTCGTCAGCG	AJ000730	CCDS33608.1	22q11.21	2013-07-19	2013-07-19		ENSG00000099960	ENSG00000099960		"""Solute carriers"""	11062	protein-coding gene	gene with protein product		603752	"""solute carrier family 7 (cationic amino acid transporter, y+ system), member 4"", ""solute carrier family 7 (orphan transporter), member 4"""			9598310, 11665818	Standard	NM_004173		Approved	HCAT3, CAT-4, VH	uc002zud.3	O43246	OTTHUMG00000150896	ENST00000382932.2:c.675C>G	22.37:g.21385427G>C	ENSP00000372390:p.Asp225Glu	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	54	34	0.62963	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Missense_Mutation	SNP	ENST00000382932.2	37	CCDS33608.1	51	0.023351648351648352	47	0.09552845528455285	4	0.011049723756906077	0	0.0	0	0.0	G	0.007	-1.958563	0.00465	0.101226	5.81E-4	ENSG00000099960	ENST00000403586;ENST00000382932	D;D	0.89123	-2.47;-2.47	5.28	0.649	0.17806	Amino acid permease domain (1);	0.917457	0.09445	N	0.801263	T	0.03263	0.0095	N	0.00811	-1.165	0.20563	N	0.999887	B	0.02656	0.0	B	0.08055	0.003	T	0.40251	-0.9573	10	0.02654	T	1	.	2.2473	0.04034	0.1467:0.403:0.2873:0.1629	.	225	O43246	CTR4_HUMAN	E	225	ENSP00000384278:D225E;ENSP00000372390:D225E	ENSP00000372390:D225E	D	-	3	2	SLC7A4	19715427	0.085000	0.21516	0.212000	0.23672	0.016000	0.09150	0.308000	0.19314	0.022000	0.15160	-1.219000	0.01604	GAC	G|0.969;C|0.031	0.031	strong		0.597	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173	
HCN3	57657	hgsc.bcm.edu	37	1	155247408	155247408	+	Silent	SNP	G	G	T	rs184885598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155247408G>T	ENST00000368358.3	+	1	35	c.27G>T	c.(25-27)gcG>gcT	p.A9A	CLK2_ENST00000536801.1_5'UTR	NM_020897.2	NP_065948.1	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 3	9					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)	cAMP binding (GO:0030552)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	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)			GGCCGGCGGCGGGGGCCAGCG	0.726													G|||	109	0.0217652	0.0794	0.0058	5008	,	,		10168	0.0		0.0	False		,,,				2504	0.0				p.A9A		Atlas-SNP	.											.	HCN3	74	.	0			c.G27T						PASS	.			200,3496		3,194,1651	3.0	5.0	4.0		27	-1.1	0.0	1		4	0,7522		0,0,3761	no	coding-synonymous	HCN3	NM_020897.1		3,194,5412	TT,TG,GG		0.0,5.4113,1.7828		9/775	155247408	200,11018	1848	3761	5609	SO:0001819	synonymous_variant	57657	exon1			GGCGGCGGGGGCC	AB040968	CCDS1108.1	1q21.2	2011-07-05			ENSG00000143630	ENSG00000143630		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	19183	protein-coding gene	gene with protein product		609973				16382102	Standard	NM_020897		Approved	KIAA1535	uc001fjz.2	Q9P1Z3	OTTHUMG00000035872	ENST00000368358.3:c.27G>T	1.37:g.155247408G>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	13	8	0.615385	NM_020897	D3DV90|Q4VX12|Q8N6W6|Q9BWQ2	Silent	SNP	ENST00000368358.3	37	CCDS1108.1																																																																																			G|0.983;T|0.017	0.017	strong		0.726	HCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087388.1	NM_020897	
FCGR3A	2214	hgsc.bcm.edu	37	1	161599654	161599654	+	Intron	SNP	G	G	T	rs5030738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161599654G>T	ENST00000540048.1	-	2	94				FCGR3B_ENST00000531221.1_Missense_Mutation_p.A114D|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367962.4_Intron|FCGR3B_ENST00000367964.2_Missense_Mutation_p.A78D|FCGR2B_ENST00000367960.5_Intron|FCGR3B_ENST00000294800.3_Missense_Mutation_p.A78D|FCGR2B_ENST00000403078.3_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)	GACTGTGGCAGCGTCAATGAA	0.537													G|||	415	0.0828674	0.2194	0.0274	5008	,	,		9903	0.0		0.0149	False		,,,				2504	0.093				p.A114D		Atlas-SNP	.											FCGR3B,NS,carcinoma,-1,2	FCGR3B	35	2	0			c.C341A						PASS	.	G	ASP/ALA	839,3489		219,401,1544	89.0	99.0	95.0		233	-4.0	0.0	1	dbSNP_113	95	171,8427		6,159,4134	no	missense	FCGR3B	NM_000570.4	126	225,560,5678	TT,TG,GG		1.9888,19.3854,7.8137	benign	78/234	161599654	1010,11916	2164	4299	6463	SO:0001627	intron_variant	2215	exon3			GTGGCAGCGTCAA	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+503C>A	1.37:g.161599654G>T		Somatic	385	2	0.00519481		WXS	Illumina HiSeq	Phase_I	405	362	0.893827	NM_001244753	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	37		138	0.06318681318681318	114	0.23170731707317074	16	0.04419889502762431	0	0.0	8	0.010554089709762533	G	6.652	0.488714	0.12641	0.193854	0.019888	ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221;ENST00000534776	T;T;T;T	0.07216	3.21;3.21;3.21;3.21	2.79	-4.03	0.04021	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.831670	0.01069	N	0.004789	T	0.01124	0.0037	N	0.16567	0.415	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.43147	-0.9409	9	0.25751	T	0.34	.	1.0347	0.01546	0.1338:0.2589:0.2896:0.3177	rs5030738	78	O75015	FCG3B_HUMAN	D	78;78;114;61	ENSP00000356941:A78D;ENSP00000294800:A78D;ENSP00000433642:A114D;ENSP00000437084:A61D	ENSP00000294800:A78D	A	-	2	0	FCGR3B	159866278	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.311000	0.01128	-0.976000	0.03542	0.388000	0.25769	GCT	G|0.953;T|0.047	0.047	strong		0.537	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569	
LY75	4065	hgsc.bcm.edu	37	2	160690646	160690646	+	Silent	SNP	T	T	C	rs6722188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160690646T>C	ENST00000263636.4	-	27	3777	c.3750A>G	c.(3748-3750)ccA>ccG	p.P1250P	LY75-CD302_ENST00000505052.1_Silent_p.P1250P|LY75_ENST00000554112.1_Silent_p.P1250P|LY75-CD302_ENST00000504764.1_Silent_p.P1250P|LY75_ENST00000553424.1_Silent_p.P1250P	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1250					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)		AGTTCTGAAATGGTATCCACG	0.353													T|||	553	0.110423	0.4024	0.0288	5008	,	,		20151	0.0		0.001	False		,,,				2504	0.0				p.P1250P		Atlas-SNP	.											.	LY75	151	.	0			c.A3750G						PASS	.	T	,,	1532,2874	485.3+/-360.3	266,1000,937	145.0	134.0	138.0		3750,3750,3750	-4.4	1.0	2	dbSNP_116	138	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	266,1018,5219	CC,CT,TT		0.2093,34.7708,11.9176	,,	1250/1874,1250/1818,1250/1723	160690646	1550,11456	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon27			CTGAAATGGTATC	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.3750A>G	2.37:g.160690646T>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	150	86	0.573333	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			T|0.880;C|0.120	0.120	strong		0.353	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
COL1A1	1277	hgsc.bcm.edu	37	17	48264448	48264448	+	Silent	SNP	A	A	G	rs1800218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48264448A>G	ENST00000225964.5	-	47	3577	c.3459T>C	c.(3457-3459)gaT>gaC	p.D1153D		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	1153	Triple-helical region.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	CGTTGAGTCCATCTTTGCCAG	0.622			T	"""PDGFB, USP6"""	"""dermatofibrosarcoma protuberans, aneurysmal bone cyst """		Osteogenesis imperfecta						A|||	234	0.0467252	0.1626	0.0072	5008	,	,		18926	0.0		0.003	False		,,,				2504	0.0112				p.D1153D		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"""collagen, type I, alpha 1"""	yes	M	.	COL1A1	158	.	0			c.T3459C						PASS	.	A		653,3753	268.0+/-268.2	46,561,1596	34.0	37.0	36.0		3459	-3.3	1.0	17	dbSNP_89	36	11,8587	7.7+/-29.5	0,11,4288	no	coding-synonymous	COL1A1	NM_000088.3		46,572,5884	GG,GA,AA		0.1279,14.8207,5.1061		1153/1465	48264448	664,12340	2203	4299	6502	SO:0001819	synonymous_variant	1277	exon47			GAGTCCATCTTTG	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"""Collagens"""	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.3459T>C	17.37:g.48264448A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	37	CCDS11561.1																																																																																			A|0.952;G|0.048	0.048	strong		0.622	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2		
OSBPL1A	114876	hgsc.bcm.edu	37	18	21752366	21752366	+	Silent	SNP	A	A	G	rs2077984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:21752366A>G	ENST00000319481.3	-	22	2381	c.2175T>C	c.(2173-2175)taT>taC	p.Y725Y	OSBPL1A_ENST00000357041.4_Silent_p.Y343Y|RNA5SP452_ENST00000363004.1_RNA|OSBPL1A_ENST00000399443.3_Silent_p.Y212Y	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	725					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)					CCACATTGCCATACTGTTCGA	0.388													G|||	605	0.120807	0.3222	0.0317	5008	,	,		19396	0.0724		0.0169	False		,,,				2504	0.0685				p.Y725Y		Atlas-SNP	.											.	OSBPL1A	94	.	0			c.T2175C						PASS	.	G	,,	1165,3241	712.6+/-408.1	158,849,1196	204.0	178.0	187.0		1029,636,2175	-8.7	0.5	18	dbSNP_96	187	126,8474	813.9+/-407.0	0,126,4174	no	coding-synonymous,coding-synonymous,coding-synonymous	OSBPL1A	NM_001242508.1,NM_018030.4,NM_080597.3	,,	158,975,5370	GG,GA,AA		1.4651,26.4412,9.9262	,,	343/569,212/438,725/951	21752366	1291,11715	2203	4300	6503	SO:0001819	synonymous_variant	114876	exon22			ATTGCCATACTGT	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.2175T>C	18.37:g.21752366A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	124	52	0.419355	NM_080597	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	37	CCDS11884.1																																																																																			A|0.894;G|0.106	0.106	strong		0.388	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597	
QRICH2	84074	hgsc.bcm.edu	37	17	74288421	74288421	+	Missense_Mutation	SNP	A	A	G	rs6501878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74288421A>G	ENST00000262765.5	-	4	2068	c.1889T>C	c.(1888-1890)aTa>aCa	p.I630T		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	630	Gln-rich.		I -> T (in dbSNP:rs6501878).|I -> V (in dbSNP:rs6501879).					p.I630_G639delIVQRGLVQPG(3)		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						acgctgaactataccaggttg	0.537													a|||	2303	0.459864	0.6861	0.3084	5008	,	,		23715	0.5665		0.2734	False		,,,				2504	0.3436				p.I630T		Atlas-SNP	.											.	QRICH2	143	.	3	Deletion - In frame(3)	stomach(3)	c.T1889C						PASS	.	G	THR/ILE	1346,2454		623,100,1177	73.0	84.0	81.0		1889	-9.4	0.0	17	dbSNP_116	81	535,7851		209,117,3867	no	missense	QRICH2	NM_032134.1	89	832,217,5044	GG,GA,AA		6.3797,35.4211,15.4357	benign	630/1664	74288421	1881,10305	1900	4193	6093	SO:0001583	missense	84074	exon4			TGAACTATACCAG	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.1889T>C	17.37:g.74288421A>G	ENSP00000262765:p.Ile630Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	143	45	0.314685	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	713	0.32646520146520147	254	0.516260162601626	85	0.23480662983425415	267	0.46678321678321677	107	0.14116094986807387	a	4.894	0.166137	0.09339	0.354211	0.063797	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.21361	2.01	4.72	-9.44	0.00603	.	.	.	.	.	T	0.00012	0.0000	N	0.04636	-0.2	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41466	-0.9507	8	0.11794	T	0.64	0.5378	13.5155	0.61539	0.7104:0.0815:0.2081:0.0	rs6501878;rs6501878	630;630	B5MD94;Q9H0J4	.;QRIC2_HUMAN	T	630	ENSP00000262765:I630T	ENSP00000262765:I630T	I	-	2	0	QRICH2	71800016	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-8.857000	0.00016	-3.030000	0.00266	-2.691000	0.00139	ATA	A|0.636;G|0.364	0.364	strong		0.537	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
ZNF180	7733	hgsc.bcm.edu	37	19	44981516	44981516	+	Silent	SNP	C	C	T	rs16979130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44981516C>T	ENST00000221327.4	-	5	1463	c.1182G>A	c.(1180-1182)tcG>tcA	p.S394S	ZNF180_ENST00000592529.1_Silent_p.S367S|ZNF180_ENST00000585514.1_5'Flank|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000391956.4_Silent_p.S369S	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	394					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(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				AAACAAGGTGCGAGCTCCGGC	0.463													C|||	320	0.0638978	0.1362	0.0504	5008	,	,		18452	0.0794		0.005	False		,,,				2504	0.0204				p.S394S	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.G1182A						PASS	.	C		501,3905	232.0+/-245.7	24,453,1726	66.0	68.0	67.0		1182	-10.9	0.4	19	dbSNP_123	67	23,8577	16.0+/-53.3	0,23,4277	no	coding-synonymous	ZNF180	NM_013256.3		24,476,6003	TT,TC,CC		0.2674,11.3709,4.0289		394/693	44981516	524,12482	2203	4300	6503	SO:0001819	synonymous_variant	7733	exon5			AAGGTGCGAGCTC	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1182G>A	19.37:g.44981516C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																			C|0.953;T|0.047	0.047	strong		0.463	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
NCKAP1	10787	hgsc.bcm.edu	37	2	183817154	183817154	+	Silent	SNP	T	T	C	rs111993802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:183817154T>C	ENST00000361354.4	-	23	2952	c.2580A>G	c.(2578-2580)tcA>tcG	p.S860S	NCKAP1_ENST00000360982.2_Silent_p.S866S	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	860					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			CAACTTGTGATGAAATATGCC	0.313													t|||	50	0.00998403	0.0356	0.0043	5008	,	,		17373	0.0		0.0	False		,,,				2504	0.0				p.S866S		Atlas-SNP	.											.	NCKAP1	105	.	0			c.A2598G						PASS	.	C	,	133,4273	92.5+/-131.2	2,129,2072	68.0	73.0	71.0		2580,2598	3.2	1.0	2	dbSNP_132	71	6,8580	4.3+/-15.6	0,6,4287	no	coding-synonymous,coding-synonymous	NCKAP1	NM_013436.3,NM_205842.1	,	2,135,6359	CC,CT,TT		0.0699,3.0186,1.0699	,	860/1129,866/1135	183817154	139,12853	2203	4293	6496	SO:0001819	synonymous_variant	10787	exon24			TTGTGATGAAATA	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.2580A>G	2.37:g.183817154T>C		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	188	97	0.515957	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Silent	SNP	ENST00000361354.4	37	CCDS2287.1																																																																																			T|0.987;C|0.013	0.013	strong		0.313	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842	
KRT84	3890	hgsc.bcm.edu	37	12	52779244	52779244	+	Silent	SNP	A	A	G	rs1732304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52779244A>G	ENST00000257951.3	-	1	192	c.126T>C	c.(124-126)ccT>ccC	p.P42P	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	42	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CCCGGAATCCAGGCCCACTCC	0.582													G|||	1389	0.277356	0.4183	0.3112	5008	,	,		19985	0.1944		0.2008	False		,,,				2504	0.227				p.P42P		Atlas-SNP	.											.	KRT84	61	.	0			c.T126C						PASS	.	G		1658,2748	649.0+/-398.8	352,954,897	66.0	75.0	72.0		126	-3.5	0.0	12	dbSNP_89	72	1733,6867	731.2+/-406.8	170,1393,2737	no	coding-synonymous	KRT84	NM_033045.3		522,2347,3634	GG,GA,AA		20.1512,37.6305,26.0726		42/601	52779244	3391,9615	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon1			GAATCCAGGCCCA	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.126T>C	12.37:g.52779244A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.744;G|0.256	0.256	strong		0.582	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
COL1A2	1278	hgsc.bcm.edu	37	7	94030899	94030899	+	Silent	SNP	T	T	C	rs1800222|rs74315131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	114	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	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	
ITGAD	3681	hgsc.bcm.edu	37	16	31429479	31429479	+	Silent	SNP	T	T	C	rs78517822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31429479T>C	ENST00000389202.2	+	21	2632	c.2583T>C	c.(2581-2583)agT>agC	p.S861S		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	861					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GCCGCTGCAGTGTCAACCACC	0.572													c|||	265	0.0529153	0.1906	0.0173	5008	,	,		17653	0.0		0.001	False		,,,				2504	0.0				p.S861S		Atlas-SNP	.											.	ITGAD	154	.	0			c.T2583C						PASS	.	C		752,3642	754.3+/-412.4	67,618,1512	140.0	132.0	135.0		2583	4.1	0.8	16	dbSNP_132	135	12,8588	818.8+/-406.8	0,12,4288	no	coding-synonymous	ITGAD	NM_005353.2		67,630,5800	CC,CT,TT		0.1395,17.1142,5.8796		861/1162	31429479	764,12230	2197	4300	6497	SO:0001819	synonymous_variant	3681	exon21			CTGCAGTGTCAAC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.2583T>C	16.37:g.31429479T>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	205	96	0.468293	NM_005353	Q15575|Q15576	Silent	SNP	ENST00000389202.2	37	CCDS32438.1																																																																																			T|0.947;C|0.053	0.053	strong		0.572	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605266	32605266	+	Missense_Mutation	SNP	G	G	A	rs1047992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32605266G>A	ENST00000343139.5	+	1	133	c.31G>A	c.(31-33)Gcc>Acc	p.A11T	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.A11T|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.A11T	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	11			A -> T (in allele DQA1*05:05, allele DQA1*05:08 and allele DQA1*05:09; dbSNP:rs1047992).	A -> S (in Ref. 4; AAA59760). {ECO:0000305}.	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						GCTGCTGGGGGCCCTCGCTCT	0.517																																					p.A11T		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.G31A						PASS	.	G	THR/ALA	316,4090		43,230,1930	75.0	68.0	70.0		31	0.0	0.0	6	dbSNP_86	70	564,8036		60,444,3796	no	missense	HLA-DQA1	NM_002122.3	58	103,674,5726	AA,AG,GG		6.5581,7.172,6.7661	benign	11/256	32605266	880,12126	2203	4300	6503	SO:0001583	missense	3117	exon1			CTGGGGGCCCTCG		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.31G>A	6.37:g.32605266G>A	ENSP00000339398:p.Ala11Thr	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	87	24	0.275862	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	255	0.11675824175824176	72	0.14634146341463414	46	0.1270718232044199	54	0.0944055944055944	83	0.10949868073878628	.	3.358	-0.131142	0.06753	0.07172	0.065581	ENSG00000196735	ENST00000422863;ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949	T;T;T;T;T	0.24723	1.84;4.7;4.7;4.39;4.7	4.15	0.00859	0.14075	.	0.954045	0.08671	N	0.910981	T	0.04363	0.0120	N	0.17838	0.53	0.80722	P	0.0	B;B	0.25609	0.13;0.004	B;B	0.22152	0.038;0.019	T	0.43972	-0.9358	9	0.18276	T	0.48	.	6.123	0.20164	0.4943:0.0:0.5057:0.0	rs1047992;rs2308822;rs9469203;rs16868253;rs35899717	17;11	Q59F33;G4XQK2	.;.	T	11	ENSP00000405797:A11T;ENSP00000339398:A11T;ENSP00000378767:A11T;ENSP00000437302:A11T;ENSP00000364087:A11T	ENSP00000339398:A11T	A	+	1	0	HLA-DQA1	32713244	0.000000	0.05858	0.006000	0.13384	0.168000	0.22595	-0.452000	0.06787	0.098000	0.17522	-0.275000	0.10095	GCC	G|0.879;A|0.121	0.121	strong		0.517	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
FBXO18	84893	hgsc.bcm.edu	37	10	5979117	5979117	+	Silent	SNP	T	T	C	rs2274033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000379999.5_Silent_p.C1053C|FBXO18_ENST00000397269.3_Silent_p.C506C	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	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	213	106	0.497653	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	
MAP10	54627	hgsc.bcm.edu	37	1	232941215	232941215	+	Missense_Mutation	SNP	A	A	G	rs41271527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232941215A>G	ENST00000418460.1	+	1	573	c.446A>G	c.(445-447)gAg>gGg	p.E149G		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	7					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										TCGCTGTCCGAGCGGCTCTTC	0.677													A|||	315	0.0628994	0.0908	0.0432	5008	,	,		12965	0.0347		0.0517	False		,,,				2504	0.0798				p.E149G		Atlas-SNP	.											.	.	.	.	0			c.A446G						PASS	.	A	GLY/GLU	332,3612		14,304,1654	8.0	11.0	10.0		446	3.8	0.9	1	dbSNP_127	10	342,7942		9,324,3809	yes	missense	KIAA1383	NM_019090.2	98	23,628,5463	GG,GA,AA		4.1284,8.4178,5.5119	benign	149/1048	232941215	674,11554	1972	4142	6114	SO:0001583	missense	54627	exon1			TGTCCGAGCGGCT	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.446A>G	1.37:g.232941215A>G	ENSP00000403208:p.Glu149Gly	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	135	62	0.459259	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	107	0.04899267399267399	39	0.07926829268292683	17	0.04696132596685083	13	0.022727272727272728	38	0.05013192612137203	A	15.00	2.702542	0.48307	0.084178	0.041284	ENSG00000212916	ENST00000418460	.	.	.	4.94	3.77	0.43336	.	0.190060	0.24891	N	0.034776	T	0.05044	0.0135	M	0.63428	1.95	0.31196	N	0.700311	B	0.32800	0.385	B	0.39805	0.31	T	0.32719	-0.9896	9	0.51188	T	0.08	-4.86	9.5261	0.39165	0.9163:0.0:0.0837:0.0	rs41271527	7	Q9P2G4	K1383_HUMAN	G	149	.	ENSP00000403208:E149G	E	+	2	0	KIAA1383	231007838	1.000000	0.71417	0.898000	0.35279	0.054000	0.15201	2.070000	0.41491	0.783000	0.33636	0.260000	0.18958	GAG	A|0.951;G|0.049	0.049	strong		0.677	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
OR2G2	81470	hgsc.bcm.edu	37	1	247751936	247751936	+	Missense_Mutation	SNP	T	T	G	rs146039934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247751936T>G	ENST00000320065.1	+	1	275	c.275T>G	c.(274-276)aTg>aGg	p.M92R	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	92						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)			TGGGAACCCATGAAAACTATC	0.527													t|||	30	0.00599042	0.0219	0.0014	5008	,	,		21752	0.0		0.0	False		,,,				2504	0.0				p.M92R		Atlas-SNP	.											.	OR2G2	88	.	0			c.T275G						PASS	.	C	ARG/MET	98,4308	79.9+/-118.3	1,96,2106	185.0	152.0	163.0		275	-6.5	0.0	1	dbSNP_134	163	0,8600		0,0,4300	yes	missense	OR2G2	NM_001001915.1	91	1,96,6406	GG,GT,TT		0.0,2.2242,0.7535	benign	92/318	247751936	98,12908	2203	4300	6503	SO:0001583	missense	81470	exon1			AACCCATGAAAAC	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.275T>G	1.37:g.247751936T>G	ENSP00000326349:p.Met92Arg	Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	347	176	0.507205	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	t	2.892	-0.229477	0.06022	0.022242	0.0	ENSG00000177489	ENST00000320065	T	0.01347	4.99	4.29	-6.53	0.01866	GPCR, rhodopsin-like superfamily (1);	2.209360	0.02699	U	0.111542	T	0.00271	0.0008	N	0.00408	-1.53	0.09310	N	1	B	0.16396	0.017	B	0.22753	0.041	T	0.49934	-0.8886	10	0.30078	T	0.28	.	1.2983	0.02074	0.4808:0.1651:0.1223:0.2318	.	92	Q8NGZ5	OR2G2_HUMAN	R	92	ENSP00000326349:M92R	ENSP00000326349:M92R	M	+	2	0	OR2G2	245818559	0.000000	0.05858	0.000000	0.03702	0.145000	0.21501	-0.280000	0.08468	-0.902000	0.03886	-0.332000	0.08345	ATG	T|0.994;G|0.006	0.006	strong		0.527	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
DNAH9	1770	hgsc.bcm.edu	37	17	11532835	11532835	+	Silent	SNP	A	A	G	rs9895535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	93	0	0		WXS	Illumina HiSeq	Phase_I	117	117	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	
GPR113	165082	hgsc.bcm.edu	37	2	26540951	26540951	+	Silent	SNP	G	G	A	rs116141676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26540951G>A	ENST00000311519.1	-	2	218	c.219C>T	c.(217-219)agC>agT	p.S73S	GPR113_ENST00000541401.1_Intron|GPR113_ENST00000333478.6_Intron|GPR113_ENST00000459892.1_Intron|GPR113_ENST00000421160.2_Intron	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	73					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)					ATCGGCCAAAGCTAGAAGATA	0.582													G|||	83	0.0165735	0.0605	0.0043	5008	,	,		19300	0.0		0.0	False		,,,				2504	0.0				p.S73S		Atlas-SNP	.											.	GPR113	134	.	0			c.C219T						PASS	.	G	,,	66,1318		3,60,629	58.0	64.0	62.0		219,,	0.0	0.0	2	dbSNP_132	62	0,3182		0,0,1591	no	coding-synonymous,intron,intron	GPR113	NM_001145168.1,NM_001145169.1,NM_153835.3	,,	3,60,2220	AA,AG,GG		0.0,4.7688,1.4455	,,	73/1080,,	26540951	66,4500	692	1591	2283	SO:0001819	synonymous_variant	165082	exon2			GCCAAAGCTAGAA	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.219C>T	2.37:g.26540951G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	145	59	0.406897	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Silent	SNP	ENST00000311519.1	37	CCDS46239.1																																																																																			G|0.986;A|0.014	0.014	strong		0.582	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
CHTF18	63922	hgsc.bcm.edu	37	16	845819	845819	+	Silent	SNP	A	A	G	rs2294446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:845819A>G	ENST00000262315.9	+	17	2373	c.2310A>G	c.(2308-2310)gcA>gcG	p.A770A	CHTF18_ENST00000317063.6_Silent_p.A979A|CHTF18_ENST00000455171.2_Silent_p.A798A	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	770					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)				ACATTCTTGCACCCAAGCTCC	0.687													N|||	988	0.197284	0.357	0.0865	5008	,	,		11945	0.1012		0.0169	False		,,,				2504	0.3446				p.A770A		Atlas-SNP	.											.	CHTF18	52	.	0			c.A2310G						PASS	.			1164,3060		143,878,1091	18.0	26.0	24.0		2310	-8.4	0.0	16	dbSNP_100	24	179,8245		1,177,4034	yes	coding-synonymous	CHTF18	NM_022092.2		144,1055,5125	GG,GA,AA		2.1249,27.5568,10.6183		770/976	845819	1343,11305	2112	4212	6324	SO:0001819	synonymous_variant	63922	exon17			TCTTGCACCCAAG	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.2310A>G	16.37:g.845819A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	37	CCDS45371.1																																																																																			A|0.862;G|0.138	0.138	strong		0.687	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
ANKRD27	84079	hgsc.bcm.edu	37	19	33131227	33131227	+	Silent	SNP	C	C	T	rs10410241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33131227C>T	ENST00000306065.4	-	11	1127	c.969G>A	c.(967-969)acG>acA	p.T323T	ANKRD27_ENST00000587352.1_Silent_p.T323T	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	323	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					TAGGGATCTCCGTTTTCACAA	0.458													C|||	375	0.0748802	0.2738	0.0173	5008	,	,		20964	0.0		0.001	False		,,,				2504	0.0				p.T323T		Atlas-SNP	.											ANKRD27,colon,carcinoma,-1,1	ANKRD27	86	1	0			c.G969A						PASS	.	C		963,3443	364.9+/-317.2	123,717,1363	114.0	106.0	109.0		969	1.7	1.0	19	dbSNP_119	109	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	ANKRD27	NM_032139.2		123,720,5660	TT,TC,CC		0.0349,21.8566,7.4273		323/1051	33131227	966,12040	2203	4300	6503	SO:0001819	synonymous_variant	84079	exon11			GATCTCCGTTTTC	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.969G>A	19.37:g.33131227C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	209	91	0.435407	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	CCDS32986.1																																																																																			C|0.924;T|0.076	0.076	strong		0.458	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
PRAMEF4	400735	hgsc.bcm.edu	37	1	12943038	12943038	+	Missense_Mutation	SNP	A	A	C	rs3121081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12943038A>C	ENST00000235349.5	-	2	248	c.178T>G	c.(178-180)Tcc>Gcc	p.S60A		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	60					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)		AAGGGCCAGGACTGCACCATC	0.597													N|||	1312	0.261981	0.4304	0.2118	5008	,	,		15162	0.1627		0.2336	False		,,,				2504	0.2014				p.S60A		Atlas-SNP	.											PRAMEF4,caecum,carcinoma,+1,1	PRAMEF4	62	1	0			c.T178G						scavenged	.						49.0	57.0	55.0					1																	12943038		2188	4269	6457	SO:0001583	missense	400735	exon2			GCCAGGACTGCAC		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.178T>G	1.37:g.12943038A>C	ENSP00000235349:p.Ser60Ala	Somatic	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	134	130	0.970149	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	323	0.1478937728937729	91	0.18495934959349594	51	0.1408839779005525	63	0.11013986013986014	118	0.15567282321899736	N	0.017	-1.493857	0.01009	.	.	ENSG00000243073	ENST00000235349	T	0.12569	2.67	1.48	1.48	0.22813	.	0.898344	0.09686	N	0.769021	T	0.00012	0.0000	N	0.00047	-2.43	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43212	-0.9405	9	0.02654	T	1	.	5.0346	0.14428	0.3518:0.6482:0.0:0.0	rs3121081	60	O60810	PRAM4_HUMAN	A	60	ENSP00000235349:S60A	ENSP00000235349:S60A	S	-	1	0	PRAMEF4	12865625	0.752000	0.28338	0.624000	0.29186	0.029000	0.11900	0.312000	0.19397	0.205000	0.20568	-0.503000	0.04515	TCC	A|0.852;C|0.148	0.148	strong		0.597	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
MUC4	4585	hgsc.bcm.edu	37	3	195505812	195505812	+	Silent	SNP	G	G	A	rs544214064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195505812G>A	ENST00000463781.3	-	2	13098	c.12639C>T	c.(12637-12639)gaC>gaT	p.D4213D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D4213D	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)		CTGAGGAAGTGTCGGTGACAG	0.592													.|||	2	0.000399361	0.0	0.0	5008	,	,		14064	0.0		0.0	False		,,,				2504	0.002				p.D4213D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,5	MUC4	1505	5	0			c.C12639T						scavenged	.						26.0	23.0	24.0					3																	195505812		690	1578	2268	SO:0001819	synonymous_variant	4585	exon2			GGAAGTGTCGGTG	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.12639C>T	3.37:g.195505812G>A		Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	251	4	0.0159363	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																																																																																			.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
UPP2	151531	hgsc.bcm.edu	37	2	158971664	158971664	+	Missense_Mutation	SNP	A	A	C	rs7561584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:158971664A>C	ENST00000005756.4	+	3	426	c.232A>C	c.(232-234)Atg>Ctg	p.M78L	UPP2_ENST00000460456.1_Intron|UPP2_ENST00000409859.4_Missense_Mutation_p.M135L|UPP2_ENST00000605860.1_Missense_Mutation_p.M135L	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	78			M -> L (in dbSNP:rs7561584).		nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	TGCACTGTTTATGCACAAGGA	0.458													A|||	24	0.00479233	0.0166	0.0029	5008	,	,		14199	0.0		0.0	False		,,,				2504	0.0				p.M135L		Atlas-SNP	.											.	UPP2	60	.	0			c.A403C						PASS	.	A	LEU/MET,LEU/MET	83,4323	70.9+/-108.8	2,79,2122	104.0	104.0	104.0		232,403	4.5	0.9	2	dbSNP_116	104	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	UPP2	NM_173355.3,NM_001135098.1	15,15	2,82,6419	CC,CA,AA		0.0349,1.8838,0.6612	benign,benign	78/318,135/375	158971664	86,12920	2203	4300	6503	SO:0001583	missense	151531	exon5			CTGTTTATGCACA	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.232A>C	2.37:g.158971664A>C	ENSP00000005756:p.Met78Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	88	35	0.397727	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	37	CCDS2207.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	6.495	0.459468	0.12342	0.018838	3.49E-4	ENSG00000007001	ENST00000409859;ENST00000005756	T;T	0.35421	1.31;1.31	5.7	4.53	0.55603	Nucleoside phosphorylase domain (1);	0.153191	0.64402	D	0.000007	T	0.10294	0.0252	N	0.12961	0.28	0.46317	D	0.998983	B	0.06786	0.001	B	0.08055	0.003	T	0.04128	-1.0975	10	0.11794	T	0.64	.	11.9742	0.53081	0.8546:0.1454:0.0:0.0	rs7561584;rs7561584	78	O95045	UPP2_HUMAN	L	135;78	ENSP00000387230:M135L;ENSP00000005756:M78L	ENSP00000005756:M78L	M	+	1	0	UPP2	158679910	1.000000	0.71417	0.940000	0.37924	0.318000	0.28184	5.969000	0.70422	0.974000	0.38366	0.533000	0.62120	ATG	A|0.994;C|0.006	0.006	strong		0.458	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355	
BPIFB2	80341	hgsc.bcm.edu	37	20	31598909	31598909	+	Silent	SNP	G	G	A	rs61734339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31598909G>A	ENST00000170150.3	+	3	384	c.189G>A	c.(187-189)gcG>gcA	p.A63A		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	63			A -> V (in dbSNP:rs34128772).			extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										GTGGAGAGGCGCTTCAGCCCA	0.622													G|||	26	0.00519169	0.0159	0.0014	5008	,	,		18832	0.0		0.004	False		,,,				2504	0.0				p.A63A		Atlas-SNP	.											.	.	.	.	0			c.G189A						PASS	.	G		72,4334	65.3+/-102.7	1,70,2132	89.0	74.0	79.0		189	2.5	0.0	20	dbSNP_129	79	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	BPIFB2	NM_025227.1		1,75,6427	AA,AG,GG		0.0581,1.6341,0.592		63/459	31598909	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	80341	exon3			AGAGGCGCTTCAG	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"""BPI fold containing"""	16177	protein-coding gene	gene with protein product		614108	"""bactericidal/permeability-increasing protein-like 1"""	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.189G>A	20.37:g.31598909G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Silent	SNP	ENST00000170150.3	37	CCDS13210.1																																																																																			G|0.992;A|0.008	0.008	strong		0.622	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227	
PVRL1	5818	hgsc.bcm.edu	37	11	119509485	119509485	+	Missense_Mutation	SNP	G	G	A	rs73571271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119509485G>A	ENST00000341398.2	-	7	1182	c.1183C>T	c.(1183-1185)Cct>Tct	p.P395S	RP11-196E1.3_ENST00000601999.1_RNA|RP11-196E1.3_ENST00000532153.1_RNA	NM_203285.1	NP_976030.1	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	0					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		CTGGGAGAAGGCTCCGGCTTC	0.617													G|||	94	0.01877	0.0643	0.013	5008	,	,		19246	0.0		0.0	False		,,,				2504	0.0				p.P395S		Atlas-SNP	.											.	PVRL1	133	.	0			c.C1183T						PASS	.	G	SER/PRO	274,4124	154.0+/-187.5	4,266,1929	48.0	46.0	46.0		1183	1.5	0.0	11	dbSNP_130	46	1,8589	1.2+/-3.3	0,1,4294	yes	missense	PVRL1	NM_203285.1	74	4,267,6223	AA,AG,GG		0.0116,6.2301,2.1173		395/459	119509485	275,12713	2199	4295	6494	SO:0001583	missense	5818	exon7			GAGAAGGCTCCGG	X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9706	protein-coding gene	gene with protein product	"""nectin"""	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000341398.2:c.1183C>T	11.37:g.119509485G>A	ENSP00000344974:p.Pro395Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_203285	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Missense_Mutation	SNP	ENST00000341398.2	37	CCDS8425.1	41	0.018772893772893772	34	0.06910569105691057	7	0.019337016574585635	0	0.0	0	0.0	G	5.225	0.226965	0.09916	0.062301	1.16E-4	ENSG00000110400	ENST00000341398	T	0.77098	-1.07	3.39	1.49	0.22878	.	.	.	.	.	T	0.13072	0.0317	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14504	-1.0470	9	0.31617	T	0.26	.	5.6558	0.17642	0.257:0.0:0.743:0.0	.	395	Q15223-2	.	S	395	ENSP00000344974:P395S	ENSP00000344974:P395S	P	-	1	0	PVRL1	119014695	0.013000	0.17824	0.002000	0.10522	0.017000	0.09413	1.059000	0.30517	0.413000	0.25759	-0.448000	0.05591	CCT	G|0.978;A|0.022	0.022	strong		0.617	PVRL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388230.1		
FAM186B	84070	hgsc.bcm.edu	37	12	49994658	49994658	+	Missense_Mutation	SNP	C	C	G	rs74086906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49994658C>G	ENST00000257894.2	-	4	926	c.765G>C	c.(763-765)agG>agC	p.R255S	FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.R165S|PRPF40B_ENST00000508736.1_3'UTR	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	255						protein complex (GO:0043234)				breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCTCCAGGCTCCTGTTCTCCT	0.557													C|||	200	0.0399361	0.1445	0.0115	5008	,	,		20376	0.0		0.001	False		,,,				2504	0.0				p.R255S		Atlas-SNP	.											.	FAM186B	72	.	0			c.G765C						PASS	.	C	SER/ARG	471,3935	223.9+/-240.3	27,417,1759	118.0	107.0	111.0		765	-3.4	0.0	12	dbSNP_130	111	2,8598	1.2+/-3.3	0,2,4298	yes	missense	FAM186B	NM_032130.2	110	27,419,6057	GG,GC,CC		0.0233,10.69,3.6368	benign	255/894	49994658	473,12533	2203	4300	6503	SO:0001583	missense	84070	exon4			CAGGCTCCTGTTC	AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 25"""	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.765G>C	12.37:g.49994658C>G	ENSP00000257894:p.Arg255Ser	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	288	114	0.395833	NM_032130	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	37	CCDS8788.1	85	0.03891941391941392	77	0.1565040650406504	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	9.727	1.161124	0.21538	0.1069	2.33E-4	ENSG00000135436	ENST00000544141;ENST00000257894	T;T	0.13307	2.6;2.81	5.35	-3.38	0.04883	.	0.418099	0.20622	N	0.088744	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B;B	0.28783	0.222;0.024	B;B	0.20955	0.032;0.015	T	0.37619	-0.9698	8	.	.	.	-11.8042	1.6749	0.02820	0.1249:0.2948:0.1626:0.4177	.	165;255	B4DZ15;Q8IYM0	.;F186B_HUMAN	S	165;255	ENSP00000438569:R165S;ENSP00000257894:R255S	.	R	-	3	2	FAM186B	48280925	0.000000	0.05858	0.019000	0.16419	0.986000	0.74619	-0.460000	0.06720	-0.364000	0.08088	-0.157000	0.13467	AGG	C|0.964;G|0.036	0.036	strong		0.557	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130	
OBSCN	84033	hgsc.bcm.edu	37	1	228509324	228509324	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228509324C>T	ENST00000422127.1	+	55	14826	c.14782C>T	c.(14782-14784)Cga>Tga	p.R4928*	OBSCN_ENST00000284548.11_Nonsense_Mutation_p.R4928*|OBSCN_ENST00000570156.2_Nonsense_Mutation_p.R5885*|OBSCN_ENST00000366709.4_Nonsense_Mutation_p.R2047*|OBSCN_ENST00000366707.4_Nonsense_Mutation_p.R2562*	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4928	Ig-like 48.				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)				GGCAGATGTGCGAGCCCGCTG	0.637																																					p.R5885X		Atlas-SNP	.											OBSCN,NS,carcinoma,-1,1	OBSCN	2142	1	0			c.C17653T						scavenged	.						36.0	40.0	39.0					1																	228509324		2178	4270	6448	SO:0001587	stop_gained	84033	exon66			GATGTGCGAGCCC	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.14782C>T	1.37:g.228509324C>T	ENSP00000409493:p.Arg4928*	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	117	2	0.017094	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Nonsense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	63	75.133045	0.99993	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.	.	.	5.34	3.26	0.37387	.	0.379769	0.23334	N	0.049310	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	8.2366	0.31629	0.2663:0.6445:0.0:0.0891	.	.	.	.	X	4928;4928;2562;2047	.	ENSP00000284548:R4928X	R	+	1	2	OBSCN	226575947	0.759000	0.28416	0.148000	0.22405	0.153000	0.21895	1.280000	0.33202	1.265000	0.44215	-0.140000	0.14226	CGA	.	.	none		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33572355	33572355	+	Silent	SNP	C	C	G	rs200701439		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:33572355C>G	ENST00000290943.6	+	16	3129	c.3033C>G	c.(3031-3033)ctC>ctG	p.L1011L		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	1011										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						ACTTTCTTCTCTAGAATCCAC	0.328																																					p.L1010L		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.C3030G						PASS	.																																			SO:0001819	synonymous_variant	441459	exon16			TCTTCTCTAGAAT			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.3033C>G	9.37:g.33572355C>G		Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	350	14	0.04	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				C|0.998;G|0.002	0.002	weak		0.328	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
SORCS1	114815	hgsc.bcm.edu	37	10	108389111	108389111	+	Silent	SNP	A	A	G	rs3802553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:108389111A>G	ENST00000263054.6	-	19	2518	c.2511T>C	c.(2509-2511)ttT>ttC	p.F837F	SORCS1_ENST00000344440.6_Silent_p.F837F|SORCS1_ENST00000369698.1_Silent_p.F372F	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	837	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				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)		TACCATCGCCAAAGTCCACTT	0.512													A|||	1162	0.232029	0.2829	0.1052	5008	,	,		21478	0.3383		0.0815	False		,,,				2504	0.2986				p.F837F		Atlas-SNP	.											.	SORCS1	534	.	0			c.T2511C						PASS	.	A	,,,,,	1141,3265	404.6+/-333.2	146,849,1208	141.0	102.0	115.0		2511,2511,2511,2511,2511,2511	-9.0	0.1	10	dbSNP_107	115	637,7963	163.8+/-216.2	27,583,3690	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	,,,,,	173,1432,4898	GG,GA,AA		7.407,25.8965,13.6706	,,,,,	837/1199,837/1180,837/1131,837/1160,837/1180,837/1169	108389111	1778,11228	2203	4300	6503	SO:0001819	synonymous_variant	114815	exon19			ATCGCCAAAGTCC	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.2511T>C	10.37:g.108389111A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1																																																																																			A|0.841;G|0.159	0.159	strong		0.512	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
C18orf32	497661	hgsc.bcm.edu	37	18	47008736	47008736	+	Silent	SNP	G	G	A	rs148432146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47008736G>A	ENST00000318240.3	-	3	421	c.210C>T	c.(208-210)atC>atT	p.I70I	C18orf32_ENST00000582392.1_Silent_p.I70I|RPL17-C18orf32_ENST00000584895.1_3'UTR|C18orf32_ENST00000579820.1_Silent_p.I70I|RPL17-C18orf32_ENST00000332968.6_3'UTR|RP11-110H1.4_ENST00000580150.1_RNA	NM_001035005.3	NP_001030177.1	Q8TCD1	CR032_HUMAN	chromosome 18 open reading frame 32	70					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)		signal transducer activity (GO:0004871)			large_intestine(2)|lung(1)	3						TTTTATCACAGATTTCTGTTG	0.348													G|||	5	0.000998403	0.003	0.0014	5008	,	,		17984	0.0		0.0	False		,,,				2504	0.0				p.I70I		Atlas-SNP	.											.	C18orf32	8	.	0			c.C210T						PASS	.	G	,,,	21,4383	28.1+/-56.4	0,21,2181	112.0	118.0	116.0		210,210,,	2.8	0.8	18	dbSNP_134	116	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,utr-3,utr-3	C18orf32,RPL17-C18ORF32	NM_001035005.3,NM_001199346.1,NM_001199355.1,NM_001199356.1	,,,	0,21,6479	AA,AG,GG		0.0,0.4768,0.1615	,,,	70/77,70/77,,	47008736	21,12979	2202	4298	6500	SO:0001819	synonymous_variant	497661	exon3			ATCACAGATTTCT	AK027111	CCDS32831.1	18q21.1	2012-10-24			ENSG00000177576	ENSG00000177576			31690	protein-coding gene	gene with protein product							Standard	NM_001035005		Approved	FLJ23458	uc002ldl.3	Q8TCD1	OTTHUMG00000179688	ENST00000318240.3:c.210C>T	18.37:g.47008736G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	96	56	0.583333	NM_001199346		Silent	SNP	ENST00000318240.3	37	CCDS32831.1																																																																																			G|0.999;A|0.001	0.001	strong		0.348	C18orf32-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447656.1	NM_001035005	
FCRL5	83416	hgsc.bcm.edu	37	1	157497597	157497597	+	Silent	SNP	C	C	T	rs73011545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157497597C>T	ENST00000361835.3	-	9	1927	c.1770G>A	c.(1768-1770)ccG>ccA	p.P590P	FCRL5_ENST00000368191.3_Silent_p.P505P|FCRL5_ENST00000368190.3_Silent_p.P590P|FCRL5_ENST00000356953.4_Silent_p.P590P	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	590	Ig-like C2-type 6.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				GAGAGCCTCTCGGGGCCTCAC	0.597													N|||	210	0.0419329	0.0514	0.013	5008	,	,		17067	0.1141		0.0099	False		,,,				2504	0.0082				p.P590P		Atlas-SNP	.											FCRL5,NS,carcinoma,-1,1	FCRL5	177	1	0			c.G1770A						PASS	.	T	,	183,4223	115.9+/-153.8	3,177,2023	50.0	54.0	53.0		1770,1770	-4.0	0.0	1	dbSNP_130	53	65,8535	39.8+/-96.3	1,63,4236	no	coding-synonymous,coding-synonymous	FCRL5	NM_001195388.1,NM_031281.2	,	4,240,6259	TT,TC,CC		0.7558,4.1534,1.9068	,	590/999,590/978	157497597	248,12758	2203	4300	6503	SO:0001819	synonymous_variant	83416	exon9			GCCTCTCGGGGCC	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.1770G>A	1.37:g.157497597C>T		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	178	66	0.370787	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Silent	SNP	ENST00000361835.3	37	CCDS1165.1																																																																																			C|0.972;T|0.028	0.028	strong		0.597	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
CD8B	926	hgsc.bcm.edu	37	2	87073817	87073817	+	Missense_Mutation	SNP	G	G	C	rs1126874		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:87073817G>C	ENST00000390655.6	-	4	631	c.573C>G	c.(571-573)atC>atG	p.I191M	CD8B_ENST00000431506.2_Intron|CD8B_ENST00000331469.2_Missense_Mutation_p.I191M|CD8B_ENST00000393759.2_Missense_Mutation_p.I191M|CD8B_ENST00000349455.3_Intron|CD8B_ENST00000393761.2_Intron	NM_004931.4	NP_004922.1	P10966	CD8B_HUMAN	CD8b molecule	191					immune response (GO:0006955)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|MHC class I protein binding (GO:0042288)	p.I191M(2)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	13						AGCACAGGTGGATGGCCACTC	0.552																																					p.I191M		Atlas-SNP	.											CD8B_ENST00000393759,NS,carcinoma,0,2	CD8B	37	2	2	Substitution - Missense(2)	kidney(2)	c.C573G						scavenged	.																																			SO:0001583	missense	926	exon4			CAGGTGGATGGCC		CCDS1994.1, CCDS1995.1, CCDS42708.1, CCDS1997.1, CCDS54376.1	2p12	2013-01-11	2006-03-28	2006-03-09	ENSG00000172116	ENSG00000172116		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1707	protein-coding gene	gene with protein product		186730	"""CD8 antigen, beta polypeptide 1 (p37)"""	CD8B1		1541829	Standard	NM_172213		Approved		uc002srw.3	P10966	OTTHUMG00000130264	ENST00000390655.6:c.573C>G	2.37:g.87073817G>C	ENSP00000375070:p.Ile191Met	Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	413	29	0.0702179	NM_004931	P14860|P14861|Q15980|Q496E0|Q496E1|Q496E2|Q9UDB4|Q9UDB5|Q9UDB6|Q9UDB7|Q9UDB8|Q9UDB9|Q9UDC0|Q9UQ55	Missense_Mutation	SNP	ENST00000390655.6	37	CCDS1997.1	.	.	.	.	.	.	.	.	.	.	g	11.44	1.639958	0.29157	.	.	ENSG00000172116	ENST00000393759;ENST00000331469;ENST00000390655;ENST00000445248	.	.	.	4.91	0.92	0.19397	.	0.581228	0.17685	N	0.165462	T	0.30386	0.0763	.	.	.	0.09310	N	0.999999	B;B;B;B	0.33807	0.3;0.3;0.426;0.426	B;B;B;B	0.35278	0.098;0.098;0.199;0.199	T	0.17745	-1.0359	8	0.59425	D	0.04	-3.6541	5.5609	0.17144	0.1776:0.2773:0.545:0.0	.	191;191;191;191	Q53QL8;P10966;P10966-2;P10966-6	.;CD8B_HUMAN;.;.	M	191	.	ENSP00000331172:I191M	I	-	3	3	CD8B	86927328	0.916000	0.31088	0.002000	0.10522	0.678000	0.39670	0.548000	0.23314	0.063000	0.16370	0.655000	0.94253	ATC	.	.	weak		0.552	CD8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330402.1	NM_172099	
GPR37	2861	hgsc.bcm.edu	37	7	124404371	124404371	+	Silent	SNP	G	G	A	rs61744942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:124404371G>A	ENST00000303921.2	-	1	1310	c.660C>T	c.(658-660)gcC>gcT	p.A220A		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	220					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						ATCCATTCTGGGCCAGCGCCC	0.642													G|||	509	0.101637	0.2201	0.0591	5008	,	,		12246	0.0		0.0835	False		,,,				2504	0.0951				p.A220A		Atlas-SNP	.											GPR37,rectum,carcinoma,-1,1	GPR37	89	1	0			c.C660T						scavenged	.	G		826,3580	320.7+/-296.8	67,692,1444	36.0	40.0	39.0		660	-3.0	1.0	7	dbSNP_129	39	711,7889	172.0+/-222.8	29,653,3618	no	coding-synonymous	GPR37	NM_005302.2		96,1345,5062	AA,AG,GG		8.2674,18.7472,11.8176		220/614	124404371	1537,11469	2203	4300	6503	SO:0001819	synonymous_variant	2861	exon1			ATTCTGGGCCAGC		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"""GPCR / Class A : Orphans"""	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.660C>T	7.37:g.124404371G>A		Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Silent	SNP	ENST00000303921.2	37	CCDS5792.1																																																																																			G|0.889;A|0.111	0.111	strong		0.642	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302	
NUP50	10762	hgsc.bcm.edu	37	22	45577231	45577231	+	Silent	SNP	T	T	C	rs226524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45577231T>C	ENST00000347635.4	+	6	1534	c.1068T>C	c.(1066-1068)gaT>gaC	p.D356D	NUP50_ENST00000425733.2_Silent_p.D106D|NUP50_ENST00000407019.2_Silent_p.D328D|NUP50_ENST00000396096.2_Silent_p.D328D|CTA-268H5.12_ENST00000610217.1_RNA	NM_007172.3	NP_009103.2	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa	356	RanBD1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intracellular transport (GO:0046907)|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)	nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		AAGAAGAAGATGCTTTTTACT	0.423													T|||	1388	0.277157	0.2398	0.2349	5008	,	,		17451	0.5704		0.166	False		,,,				2504	0.1697				p.D356D		Atlas-SNP	.											.	NUP50	24	.	0			c.T1068C						PASS	.	T	,	1049,3357	385.8+/-325.9	111,827,1265	80.0	82.0	81.0		1068,984	0.1	1.0	22	dbSNP_79	81	1307,7293	256.6+/-281.0	111,1085,3104	no	coding-synonymous,coding-synonymous	NUP50	NM_007172.3,NM_153645.2	,	222,1912,4369	CC,CT,TT		15.1977,23.8084,18.1147	,	356/469,328/441	45577231	2356,10650	2203	4300	6503	SO:0001819	synonymous_variant	10762	exon6			AGAAGATGCTTTT	AF107840	CCDS14062.1, CCDS14063.1	22q13.3	2007-01-22	2002-08-29		ENSG00000093000	ENSG00000093000			8065	protein-coding gene	gene with protein product		604646	"""nucleoporin 50kD"""	NPAP60L		10449902	Standard	XM_005261312		Approved		uc003bfr.3	Q9UKX7	OTTHUMG00000151265	ENST00000347635.4:c.1068T>C	22.37:g.45577231T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_007172	B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5	Silent	SNP	ENST00000347635.4	37	CCDS14062.1																																																																																			T|0.772;C|0.228	0.228	strong		0.423	NUP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321993.2		
ATP10B	23120	hgsc.bcm.edu	37	5	160047491	160047491	+	Missense_Mutation	SNP	A	A	C	rs375262733		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:160047491A>C	ENST00000327245.5	-	15	3125	c.2279T>G	c.(2278-2280)cTc>cGc	p.L760R	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	760					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGTGCAGAGGAGGCTGAAGGT	0.597																																					p.L760R		Atlas-SNP	.											.	ATP10B	201	.	0			c.T2279G						PASS	.	A	ARG/LEU	1,4181		0,1,2090	38.0	40.0	39.0		2279	5.4	0.9	5		39	0,8452		0,0,4226	no	missense	ATP10B	NM_025153.2	102	0,1,6316	CC,CA,AA		0.0,0.0239,0.0079	probably-damaging	760/1462	160047491	1,12633	2091	4226	6317	SO:0001583	missense	23120	exon15			CAGAGGAGGCTGA	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.2279T>G	5.37:g.160047491A>C	ENSP00000313600:p.Leu760Arg	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	241	100	0.414938	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.448539	0.84101	2.39E-4	0.0	ENSG00000118322	ENST00000327245;ENST00000520108	T;T	0.79033	-1.23;-1.23	5.36	5.36	0.76844	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.403835	0.25230	N	0.032170	T	0.82144	0.4973	L	0.49455	1.56	0.38198	D	0.940098	P;P	0.51933	0.949;0.949	P;P	0.57846	0.745;0.828	T	0.83105	-0.0126	9	.	.	.	.	14.5725	0.68220	1.0:0.0:0.0:0.0	.	368;760	Q2YDW8;O94823	.;AT10B_HUMAN	R	760;368	ENSP00000313600:L760R;ENSP00000431081:L368R	.	L	-	2	0	ATP10B	159980069	1.000000	0.71417	0.919000	0.36401	0.912000	0.54170	9.159000	0.94728	2.042000	0.60477	0.533000	0.62120	CTC	.	.	weak		0.597	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153	
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802629	31802629	+	Silent	SNP	C	C	T	rs73356729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31802629C>T	ENST00000334068.2	+	1	58	c.36C>T	c.(34-36)tcC>tcT	p.S12S		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	12						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						ACTTCTCCTCCCGCTCCTTTG	0.547													-|||	220	0.0439297	0.1581	0.0144	5008	,	,		18637	0.0		0.001	False		,,,				2504	0.0				p.S12S	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.C36T						PASS	.	C		473,3933		25,423,1755	109.0	111.0	110.0		36	0.1	0.1	21	dbSNP_130	110	10,8590		0,10,4290	no	coding-synonymous	KRTAP13-4	NM_181600.1		25,433,6045	TT,TC,CC		0.1163,10.7354,3.7137		12/161	31802629	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	284827	exon1			CTCCTCCCGCTCC	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.36C>T	21.37:g.31802629C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	242	104	0.429752	NM_181600	A2RRL3	Silent	SNP	ENST00000334068.2	37	CCDS13592.1																																																																																			C|0.963;T|0.037	0.037	strong		0.547	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1		
FCGBP	8857	hgsc.bcm.edu	37	19	40373950	40373950	+	Missense_Mutation	SNP	G	G	T	rs200958848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40373950G>T	ENST00000221347.6	-	26	12135	c.12128C>A	c.(12127-12129)aCc>aAc	p.T4043N	FCGBP_ENST00000595713.1_5'Flank	NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4043	Cys-rich.			T -> N (in Ref. 1; BAA19526). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)		p.T4043N(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)			agcACCTTTGGTGACGCAGCT	0.637													g|||	355	0.0708866	0.0242	0.0159	5008	,	,		20309	0.244		0.0239	False		,,,				2504	0.0429				p.T4043N		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	lung(1)	c.C12128A						scavenged	.						41.0	42.0	41.0					19																	40373950		2124	4117	6241	SO:0001583	missense	8857	exon26			CCTTTGGTGACGC	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.12128C>A	19.37:g.40373950G>T	ENSP00000221347:p.Thr4043Asn	Somatic	808	1	0.00123762		WXS	Illumina HiSeq	Phase_I	223	39	0.174888	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	g	0.780	-0.762570	0.02996	.	.	ENSG00000090920	ENST00000221347	T	0.19532	2.14	2.82	-4.06	0.03986	von Willebrand factor, type C (1);	.	.	.	.	T	0.12433	0.0302	L	0.31664	0.95	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.41680	-0.9495	8	0.16896	T	0.51	.	10.7073	0.45962	0.0:0.0:0.3532:0.6468	.	4043	Q9Y6R7	FCGBP_HUMAN	N	4043	ENSP00000221347:T4043N	ENSP00000221347:T4043N	T	-	2	0	FCGBP	45065790	0.051000	0.20477	0.021000	0.16686	0.010000	0.07245	-0.835000	0.04386	-0.764000	0.04651	-0.677000	0.03784	ACC	G|0.750;T|0.250	0.250	weak		0.637	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF407	55628	hgsc.bcm.edu	37	18	72344202	72344202	+	Silent	SNP	T	T	C	rs374837339		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:72344202T>C	ENST00000299687.5	+	1	1227	c.1227T>C	c.(1225-1227)agT>agC	p.S409S	ZNF407_ENST00000309902.6_Silent_p.S409S|ZNF407_ENST00000577538.1_Silent_p.S409S|ZNF407_ENST00000582337.1_Silent_p.S409S	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	409					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		ACGGTAACAGTGTAACCTCGA	0.453																																					p.S409S		Atlas-SNP	.											.	ZNF407	231	.	0			c.T1227C						PASS	.	T	,,	1,3749		0,1,1874	57.0	59.0	58.0		1227,1227,1227	-3.8	0.0	18		58	0,8230		0,0,4115	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	0,1,5989	CC,CT,TT		0.0,0.0267,0.0083	,,	409/1816,409/1661,409/2249	72344202	1,11979	1875	4115	5990	SO:0001819	synonymous_variant	55628	exon1			TAACAGTGTAACC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1227T>C	18.37:g.72344202T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	119	66	0.554622	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			.	.	weak		0.453	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
SMAD3	4088	hgsc.bcm.edu	37	15	67457335	67457335	+	Silent	SNP	A	A	G	rs1065080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:67457335A>G	ENST00000327367.4	+	2	619	c.309A>G	c.(307-309)ctA>ctG	p.L103L	SMAD3_ENST00000439724.3_Silent_p.L59L|SMAD3_ENST00000537194.2_5'Flank|SMAD3_ENST00000559092.1_Missense_Mutation_p.Y85C|SMAD3_ENST00000540846.2_5'UTR	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	103	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				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)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|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 beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		ACCACGAGCTACGGGCCATGG	0.592													G|||	4177	0.834065	0.8669	0.9135	5008	,	,		16957	0.7619		0.8608	False		,,,				2504	0.7802				p.L103L		Atlas-SNP	.											.	SMAD3	119	.	0			c.A309G						PASS	.	G	,,	3842,560	250.6+/-257.6	1677,488,36	101.0	104.0	103.0		,177,309	2.4	1.0	15	dbSNP_86	103	7598,1000	215.0+/-254.5	3356,886,57	no	utr-5,coding-synonymous,coding-synonymous	SMAD3	NM_001145102.1,NM_001145103.1,NM_005902.3	,,	5033,1374,93	GG,GA,AA		11.6306,12.7215,12.0	,,	,59/382,103/426	67457335	11440,1560	2201	4299	6500	SO:0001819	synonymous_variant	4088	exon2			CGAGCTACGGGCC	BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"""SMADs"""	6769	protein-coding gene	gene with protein product		603109	"""MAD, mothers against decapentaplegic homolog 3 (Drosophila)"", ""SMAD, mothers against DPP homolog 3 (Drosophila)"""	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.309A>G	15.37:g.67457335A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_005902	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Silent	SNP	ENST00000327367.4	37	CCDS10222.1																																																																																			A|0.132;G|0.868	0.868	strong		0.592	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902	
IQCE	23288	hgsc.bcm.edu	37	7	2611908	2611908	+	Silent	SNP	G	G	C	rs147584030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2611908G>C	ENST00000402050.2	+	5	526	c.342G>C	c.(340-342)ctG>ctC	p.L114L	IQCE_ENST00000404984.1_Silent_p.L63L|IQCE_ENST00000438376.2_Silent_p.L98L|IQCE_ENST00000325979.7_Silent_p.L49L	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	114						mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		CTGACTGTCTGACAGACACCT	0.607													G|||	42	0.00838658	0.0303	0.0029	5008	,	,		18614	0.0		0.0	False		,,,				2504	0.0				p.L114L		Atlas-SNP	.											.	IQCE	66	.	0			c.G342C						PASS	.	G	,	116,3980		1,114,1933	51.0	55.0	54.0		294,342	3.3	0.0	7	dbSNP_134	54	4,8406		0,4,4201	no	coding-synonymous,coding-synonymous	IQCE	NM_001100390.1,NM_152558.3	,	1,118,6134	CC,CG,GG		0.0476,2.832,0.9595	,	98/680,114/696	2611908	120,12386	2048	4205	6253	SO:0001819	synonymous_variant	23288	exon5			CTGTCTGACAGAC	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.342G>C	7.37:g.2611908G>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	37	CCDS43542.1																																																																																			G|0.994;C|0.006	0.006	strong		0.607	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
OR52M1	119772	hgsc.bcm.edu	37	11	4566870	4566870	+	Silent	SNP	T	T	C	rs61747520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4566870T>C	ENST00000360213.1	+	1	450	c.450T>C	c.(448-450)tcT>tcC	p.S150S		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	150						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)		GGCTTGTTTCTCTCCTCCGGG	0.532													T|||	133	0.0265575	0.0303	0.0159	5008	,	,		18160	0.0337		0.0288	False		,,,				2504	0.0194				p.S150S		Atlas-SNP	.											OR52M1,right_upper_lobe,carcinoma,+1,1	OR52M1	53	1	0			c.T450C						PASS	.	T		133,4269	97.6+/-136.3	4,125,2072	102.0	101.0	101.0		450	1.1	0.3	11	dbSNP_129	101	272,8324	102.9+/-164.1	5,262,4031	no	coding-synonymous	OR52M1	NM_001004137.1		9,387,6103	CC,CT,TT		3.1643,3.0214,3.1159		150/318	4566870	405,12593	2201	4298	6499	SO:0001819	synonymous_variant	119772	exon1			TGTTTCTCTCCTC	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.450T>C	11.37:g.4566870T>C		Somatic	432	2	0.00462963		WXS	Illumina HiSeq	Phase_I	470	218	0.46383	NM_001004137		Silent	SNP	ENST00000360213.1	37	CCDS31353.1																																																																																			T|0.968;C|0.032	0.032	strong		0.532	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137	
FAT3	120114	hgsc.bcm.edu	37	11	92538422	92538422	+	Silent	SNP	C	C	T	rs59542280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92538422C>T	ENST00000298047.6	+	10	9017	c.9000C>T	c.(8998-9000)ctC>ctT	p.L3000L	FAT3_ENST00000525166.1_Silent_p.L2850L|FAT3_ENST00000409404.2_Silent_p.L3000L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3000	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)				TTTACTTTCTCAATATCACTG	0.488										TCGA Ovarian(4;0.039)			C|||	78	0.0155751	0.0567	0.0043	5008	,	,		16467	0.0		0.0	False		,,,				2504	0.0				p.L3000L		Atlas-SNP	.											.	FAT3	1822	.	0			c.C9000T						PASS	.	C		199,3665		5,189,1738	82.0	84.0	83.0		9000	4.2	1.0	11	dbSNP_129	83	0,8304		0,0,4152	no	coding-synonymous	FAT3	NM_001008781.2		5,189,5890	TT,TC,CC		0.0,5.1501,1.6354		3000/4558	92538422	199,11969	1932	4152	6084	SO:0001819	synonymous_variant	120114	exon10			CTTTCTCAATATC	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.9000C>T	11.37:g.92538422C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	140	65	0.464286	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.988;T|0.012	0.012	strong		0.488	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
ZNF616	90317	hgsc.bcm.edu	37	19	52619065	52619065	+	Missense_Mutation	SNP	T	T	C	rs3764537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52619065T>C	ENST00000600228.1	-	4	1613	c.1352A>G	c.(1351-1353)cAt>cGt	p.H451R	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	451			H -> R (in dbSNP:rs3764537).		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)		CACTGCAAGATGTGAATGCTT	0.398													C|||	1835	0.366414	0.7277	0.2579	5008	,	,		25460	0.2262		0.0954	False		,,,				2504	0.3783				p.H451R		Atlas-SNP	.											.	ZNF616	109	.	0			c.A1352G						PASS	.	C	ARG/HIS	2742,1664	506.9+/-366.5	852,1038,313	161.0	141.0	148.0		1352	-2.2	0.0	19	dbSNP_107	148	854,7746	780.9+/-407.6	48,758,3494	yes	missense	ZNF616	NM_178523.3	29	900,1796,3807	CC,CT,TT		9.9302,37.7667,27.6488	benign	451/782	52619065	3596,9410	2203	4300	6503	SO:0001583	missense	90317	exon4			GCAAGATGTGAAT	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.1352A>G	19.37:g.52619065T>C	ENSP00000471000:p.His451Arg	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	186	186	1	NM_178523	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	37	CCDS33090.1	632	0.2893772893772894	334	0.6788617886178862	99	0.27348066298342544	135	0.23601398601398602	64	0.08443271767810026	C	0.013	-1.640100	0.00799	0.622333	0.099302	ENSG00000204611	ENST00000330123	.	.	.	1.08	-2.15	0.07102	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.28458	0.855	0.80722	P	0.0	B	0.11235	0.004	B	0.10450	0.005	T	0.42865	-0.9426	7	0.19590	T	0.45	.	3.9491	0.09361	0.0:0.3831:0.1826:0.4343	rs3764537;rs52830804;rs59937016;rs3764537	451	Q08AN1	ZN616_HUMAN	R	451	.	ENSP00000328722:H451R	H	-	2	0	ZNF616	57310877	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-1.917000	0.01575	-2.083000	0.00867	-1.840000	0.00586	CAT	T|0.701;C|0.299	0.299	strong		0.398	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892	
KIF7	374654	hgsc.bcm.edu	37	15	90192363	90192363	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90192363G>A	ENST00000394412.3	-	4	841	c.765C>T	c.(763-765)ggC>ggT	p.G255G		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	255	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)			CCCTCTCTGAGCCCGCCAGGT	0.711																																					p.G255G		Atlas-SNP	.											.	KIF7	130	.	0			c.C765T						PASS	.						9.0	13.0	12.0					15																	90192363		684	1585	2269	SO:0001819	synonymous_variant	374654	exon4			CTCTGAGCCCGCC	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.765C>T	15.37:g.90192363G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Silent	SNP	ENST00000394412.3	37	CCDS32325.2																																																																																			.	.	none		0.711	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525	
CCDC109B	55013	hgsc.bcm.edu	37	4	110581363	110581363	+	Missense_Mutation	SNP	T	T	A	rs4698744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:110581363T>A	ENST00000394650.4	+	3	321	c.188T>A	c.(187-189)aTt>aAt	p.I63N	CCDC109B_ENST00000515114.1_3'UTR	NM_017918.4	NP_060388.2	Q9NWR8	MCUB_HUMAN	coiled-coil domain containing 109B	63			I -> N (in dbSNP:rs4698744).		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)		ATAACAGTTATTTATAGACAT	0.308													A|||	1477	0.294928	0.1346	0.3804	5008	,	,		15650	0.4802		0.3201	False		,,,				2504	0.2342				p.I63N		Atlas-SNP	.											.	CCDC109B	47	.	0			c.T188A						PASS	.	A	ASN/ILE	199,1185		15,169,508	74.0	57.0	62.0		188	-7.5	0.0	4	dbSNP_111	62	983,2199		156,671,764	yes	missense	CCDC109B	NM_017918.4	149	171,840,1272	AA,AT,TT		30.8925,14.3786,25.887	benign	63/337	110581363	1182,3384	692	1591	2283	SO:0001583	missense	55013	exon3			CAGTTATTTATAG	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.188T>A	4.37:g.110581363T>A	ENSP00000378145:p.Ile63Asn	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_017918	A8K4Y3|Q6IAC1	Missense_Mutation	SNP	ENST00000394650.4	37	CCDS3683.2	727	0.33287545787545786	80	0.16260162601626016	138	0.3812154696132597	270	0.47202797202797203	239	0.3153034300791557	A	6.289	0.421491	0.11928	0.143786	0.308925	ENSG00000005059	ENST00000394650;ENST00000452915	T;T	0.45276	0.9;0.9	5.28	-7.51	0.01346	.	0.868148	0.09770	N	0.758169	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37267	-0.9713	9	0.13470	T	0.59	-0.215	5.0765	0.14634	0.3719:0.1008:0.4294:0.0979	rs4698744;rs17619522;rs58266701;rs4698744	63;42	Q9NWR8;C9JTJ6	C109B_HUMAN;.	N	63;42	ENSP00000378145:I63N;ENSP00000414591:I42N	ENSP00000378145:I63N	I	+	2	0	CCDC109B	110800812	0.126000	0.22350	0.000000	0.03702	0.820000	0.46376	0.094000	0.15107	-2.463000	0.00535	-1.099000	0.02127	ATT	T|0.669;A|0.331	0.331	strong		0.308	CCDC109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254865.1	NM_017918	
ZSCAN2	54993	hgsc.bcm.edu	37	15	85164530	85164530	+	Silent	SNP	C	C	T	rs115131715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85164530C>T	ENST00000448803.2	+	3	1396	c.1104C>T	c.(1102-1104)ggC>ggT	p.G368G	ZSCAN2_ENST00000538076.1_Intron|ZSCAN2_ENST00000327179.6_Silent_p.G367G|ZSCAN2_ENST00000541040.1_Intron|ZSCAN2_ENST00000358472.3_Silent_p.G218G|ZSCAN2_ENST00000485222.2_Intron|ZSCAN2_ENST00000546148.1_Silent_p.G368G	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2	368					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|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)|kidney(2)|large_intestine(7)|liver(2)|lung(4)|ovary(1)|pancreas(1)	19				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		AAGAATGCGGCGAAAGCTTTA	0.502													C|||	49	0.00978435	0.0363	0.0014	5008	,	,		18077	0.0		0.0	False		,,,				2504	0.0				p.G368G		Atlas-SNP	.											.	ZSCAN2	43	.	0			c.C1104T						PASS	.	C		132,4274	96.2+/-134.9	3,126,2074	132.0	137.0	135.0		1104	-6.7	0.8	15	dbSNP_132	135	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ZSCAN2	NM_181877.3		3,127,6372	TT,TC,CC		0.0116,2.9959,1.0228		368/615	85164530	133,12871	2203	4299	6502	SO:0001819	synonymous_variant	54993	exon3			ATGCGGCGAAAGC	BC041620	CCDS10329.2, CCDS32315.1, CCDS32316.1	15q25.2	2013-01-08	2004-11-01	2004-11-02	ENSG00000176371	ENSG00000176371		"""-"", ""Zinc fingers, C2H2-type"""	20994	protein-coding gene	gene with protein product			"""zinc finger protein 29"""	ZFP29		1937051	Standard	NM_017894		Approved	FLJ20595, ZNF854	uc002bkr.3	Q7Z7L9	OTTHUMG00000074027	ENST00000448803.2:c.1104C>T	15.37:g.85164530C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	61	35	0.57377	NM_181877	A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Silent	SNP	ENST00000448803.2	37	CCDS10329.2																																																																																			C|0.988;T|0.012	0.012	strong		0.502	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894	
CLYBL	171425	hgsc.bcm.edu	37	13	100511247	100511247	+	Missense_Mutation	SNP	G	G	A	rs35680839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:100511247G>A	ENST00000376360.1	+	3	409	c.382G>A	c.(382-384)Gtc>Atc	p.V128I	CLYBL_ENST00000376355.3_Missense_Mutation_p.V128I|CLYBL_ENST00000444838.2_Missense_Mutation_p.V128I|CLYBL_ENST00000376354.1_Missense_Mutation_p.V128I|CLYBL_ENST00000339105.4_Missense_Mutation_p.V128I			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	128			V -> I (in dbSNP:rs35680839).			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)					GCAATCCCGGGTCCTTCCTTC	0.493													G|||	273	0.0545128	0.0	0.0764	5008	,	,		17544	0.1558		0.0487	False		,,,				2504	0.0143				p.V128I		Atlas-SNP	.											.	CLYBL	48	.	0			c.G382A						PASS	.	G	ILE/VAL	51,4355	50.9+/-86.3	0,51,2152	74.0	69.0	71.0		382	4.2	1.0	13	dbSNP_126	71	391,8209	124.4+/-183.2	15,361,3924	yes	missense	CLYBL	NM_206808.2	29	15,412,6076	AA,AG,GG		4.5465,1.1575,3.3984	benign	128/341	100511247	442,12564	2203	4300	6503	SO:0001583	missense	171425	exon3			TCCCGGGTCCTTC	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.382G>A	13.37:g.100511247G>A	ENSP00000365538:p.Val128Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_206808	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	37	CCDS32002.1	160	0.07326007326007326	0	0.0	26	0.0718232044198895	102	0.17832167832167833	32	0.04221635883905013	G	13.06	2.124978	0.37533	0.011575	0.045465	ENSG00000125246	ENST00000376355;ENST00000376360;ENST00000444838;ENST00000376354;ENST00000339105;ENST00000416504;ENST00000443887	T;T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;1.59;1.59	5.91	4.17	0.49024	Aldehyde-lyase domain (1);Pyruvate/Phosphoenolpyruvate kinase (2);	0.352028	0.32655	N	0.005815	T	0.00039	0.0001	L	0.40543	1.245	0.26918	P	0.9667446	B;B;B	0.20550	0.034;0.046;0.034	B;B;B	0.22152	0.029;0.017;0.038	T	0.15009	-1.0452	9	0.26408	T	0.33	-16.5761	10.1485	0.42778	0.2151:0.0:0.7849:0.0	rs35680839	128;128;128	B4DU60;Q8N0X4-2;Q8N0X4	.;.;CLYBL_HUMAN	I	128;128;128;128;128;45;45	ENSP00000365533:V128I;ENSP00000365538:V128I;ENSP00000404768:V128I;ENSP00000365532:V128I;ENSP00000342991:V128I;ENSP00000403408:V45I;ENSP00000401586:V45I	ENSP00000342991:V128I	V	+	1	0	CLYBL	99309248	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	3.470000	0.53100	1.503000	0.48686	0.655000	0.94253	GTC	G|0.956;A|0.044	0.044	strong		0.493	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1		
FSIP1	161835	hgsc.bcm.edu	37	15	39910431	39910431	+	Missense_Mutation	SNP	A	A	G	rs10152640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39910431A>G	ENST00000350221.3	-	11	1413	c.1204T>C	c.(1204-1206)Tgt>Cgt	p.C402R		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	402			C -> R (in dbSNP:rs10152640). {ECO:0000269|Ref.3}.					p.C402R(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCAGAGAGACATGATGTGGAC	0.318													G|||	2063	0.411941	0.7458	0.2594	5008	,	,		20215	0.3095		0.3072	False		,,,				2504	0.2822				p.C402R		Atlas-SNP	.											FSIP1,NS,carcinoma,0,2	FSIP1	53	2	1	Substitution - Missense(1)	stomach(1)	c.T1204C						PASS	.	G	ARG/CYS	2789,1577		917,955,311	44.0	48.0	47.0		1204	-0.4	0.1	15	dbSNP_119	47	2544,5964		382,1780,2092	yes	missense	FSIP1	NM_152597.4	180	1299,2735,2403	GG,GA,AA		29.9013,36.12,41.4246	benign	402/582	39910431	5333,7541	2183	4254	6437	SO:0001583	missense	161835	exon11			AGAGACATGATGT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1204T>C	15.37:g.39910431A>G	ENSP00000280236:p.Cys402Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	872	0.3992673992673993	346	0.7032520325203252	106	0.292817679558011	188	0.32867132867132864	232	0.30606860158311344	G	0.009	-1.857666	0.00558	0.6388	0.299013	ENSG00000150667	ENST00000350221	T	0.10668	2.85	5.06	-0.452	0.12205	.	0.738656	0.11694	N	0.538597	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	0.15723	-1.0427	8	.	.	.	8.7668	2.7672	0.05323	0.2845:0.4014:0.2062:0.1079	rs10152640;rs52803468;rs57454183;rs10152640	402	Q8NA03	FSIP1_HUMAN	R	402	ENSP00000280236:C402R	.	C	-	1	0	FSIP1	37697723	0.001000	0.12720	0.088000	0.20740	0.012000	0.07955	-0.124000	0.10595	-0.082000	0.12640	-0.726000	0.03593	TGT	A|0.599;G|0.401	0.401	strong		0.318	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
FRMD7	90167	hgsc.bcm.edu	37	X	131212487	131212487	+	Missense_Mutation	SNP	G	G	C	rs61742429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:131212487G>C	ENST00000298542.4	-	12	1733	c.1558C>G	c.(1558-1560)Cat>Gat	p.H520D	FRMD7_ENST00000370879.1_Missense_Mutation_p.H400D|FRMD7_ENST00000464296.1_Missense_Mutation_p.H505D	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	520					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					ACATAGCTATGTGGACTTGTC	0.493													C|||	35	0.00927152	0.0257	0.0014	3775	,	,		13862	0.0		0.0	False		,,,				2504	0.0				p.H520D		Atlas-SNP	.											.	FRMD7	69	.	0			c.C1558G						PASS	.	C	ASP/HIS	75,3760		0,62,13,1570,558	164.0	160.0	162.0		1558	3.6	0.4	X	dbSNP_129	162	0,6728		0,0,0,2428,1872	yes	missense	FRMD7	NM_194277.2	81	0,62,13,3998,2430	CC,CG,C,GG,G		0.0,1.9557,0.71	benign	520/715	131212487	75,10488	2203	4300	6503	SO:0001583	missense	90167	exon12			AGCTATGTGGACT	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1558C>G	X.37:g.131212487G>C	ENSP00000298542:p.His520Asp	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	215	84	0.390698	NM_194277	C0LLJ3|Q5JX99	Missense_Mutation	SNP	ENST00000298542.4	37	CCDS35397.1	3	0.0018083182640144665	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	0.001	-3.523968	0.00010	0.019557	0.0	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	D;D;D	0.84800	-1.9;-1.55;-1.67	4.55	3.59	0.41128	.	0.259811	0.32041	N	0.006663	T	0.37461	0.1004	N	0.01168	-0.975	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49244	-0.8960	10	0.02654	T	1	.	4.1382	0.10181	0.1501:0.4756:0.2878:0.0865	rs61742429	505;520	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	D	400;520;505	ENSP00000359916:H400D;ENSP00000298542:H520D;ENSP00000417996:H505D	ENSP00000298542:H520D	H	-	1	0	FRMD7	131040168	0.727000	0.28069	0.447000	0.26932	0.007000	0.05969	0.526000	0.22971	1.017000	0.39495	-0.170000	0.13304	CAT	G|0.982;C|0.018	0.018	strong		0.493	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277	
SNED1	25992	hgsc.bcm.edu	37	2	242012729	242012729	+	Missense_Mutation	SNP	G	G	A	rs6721345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242012729G>A	ENST00000310397.8	+	27	3866	c.3866G>A	c.(3865-3867)cGg>cAg	p.R1289Q	SNED1_ENST00000342631.6_Intron|SNED1_ENST00000401884.1_Missense_Mutation_p.R1289Q|SNED1_ENST00000405547.3_Intron|MTERFD2_ENST00000464344.2_5'UTR	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1289			R -> Q (in dbSNP:rs6721345).		cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GCCCCCAAGCGGGTCAGCCTG	0.637													A|||	170	0.0339457	0.1218	0.013	5008	,	,		18018	0.0		0.0	False		,,,				2504	0.0				p.R1289Q		Atlas-SNP	.											.	SNED1	76	.	0			c.G3866A						PASS	.	A	GLN/ARG	389,3689		21,347,1671	23.0	30.0	27.0		3866	-1.4	0.0	2	dbSNP_116	27	1,8307		0,1,4153	yes	missense	SNED1	NM_001080437.1	43	21,348,5824	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	0.012,9.539,3.1487	benign	1289/1414	242012729	390,11996	2039	4154	6193	SO:0001583	missense	25992	exon27			CCAAGCGGGTCAG	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.3866G>A	2.37:g.242012729G>A	ENSP00000308893:p.Arg1289Gln	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	161	72	0.447205	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	55	0.025183150183150184	50	0.1016260162601626	5	0.013812154696132596	0	0.0	0	0.0	A	1.776	-0.483082	0.04383	0.09539	1.2E-4	ENSG00000162804	ENST00000401884;ENST00000310397	D;D	0.82433	-1.61;-1.58	4.46	-1.35	0.09114	.	0.544077	0.15478	N	0.260251	T	0.01627	0.0052	N	0.00583	-1.355	0.09310	N	1	B;B	0.12630	0.006;0.002	B;B	0.06405	0.002;0.001	T	0.20207	-1.0282	10	0.10111	T	0.7	.	6.6262	0.22830	0.1901:0.5219:0.288:0.0	rs6721345;rs6721345	1289;1289	Q8TER0-5;Q8TER0	.;SNED1_HUMAN	Q	1289	ENSP00000384871:R1289Q;ENSP00000308893:R1289Q	ENSP00000308893:R1289Q	R	+	2	0	SNED1	241661402	0.000000	0.05858	0.018000	0.16275	0.715000	0.41141	0.261000	0.18442	-0.370000	0.08016	-0.381000	0.06696	CGG	G|0.966;A|0.034	0.034	strong		0.637	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
DNAH2	146754	hgsc.bcm.edu	37	17	7673928	7673928	+	Silent	SNP	C	C	G	rs9909288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7673928C>G	ENST00000572933.1	+	26	5612	c.4152C>G	c.(4150-4152)ccC>ccG	p.P1384P	DNAH2_ENST00000389173.2_Silent_p.P1384P			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1384	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)				ACATAGTACCCTACAAGGATA	0.542													C|||	1793	0.358027	0.3404	0.4424	5008	,	,		21160	0.374		0.2913	False		,,,				2504	0.3742				p.P1384P		Atlas-SNP	.											.	DNAH2	498	.	0			c.C4152G						PASS	.	C		1416,2990	461.9+/-353.1	225,966,1012	86.0	83.0	84.0		4152	5.6	1.0	17	dbSNP_119	84	2193,6407	374.2+/-337.3	278,1637,2385	no	coding-synonymous	DNAH2	NM_020877.2		503,2603,3397	GG,GC,CC		25.5,32.138,27.7487		1384/4428	7673928	3609,9397	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon25			AGTACCCTACAAG	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.4152C>G	17.37:g.7673928C>G		Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			C|0.704;G|0.296	0.296	strong		0.542	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
CFAP46	54777	hgsc.bcm.edu	37	10	134628208	134628208	+	Missense_Mutation	SNP	C	C	T	rs61733298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134628208C>T	ENST00000368586.5	-	52	7331	c.7231G>A	c.(7231-7233)Gac>Aac	p.D2411N	TTC40_ENST00000263170.5_Missense_Mutation_p.D572N	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TTGTCTGAGTCGACTATGATG	0.652													C|||	134	0.0267572	0.0923	0.013	5008	,	,		13521	0.0		0.001	False		,,,				2504	0.002				p.D2411N		Atlas-SNP	.											.	TTC40	100	.	0			c.G7231A						PASS	.	C	ASN/ASP	383,4021		14,355,1833	24.0	26.0	25.0		2167	4.3	0.0	10	dbSNP_129	25	8,8588		0,8,4290	yes	missense	C10orf92	NM_001200049.1	23	14,363,6123	TT,TC,CC		0.0931,8.6966,3.0077	probably-damaging	723/1028	134628208	391,12609	2202	4298	6500	SO:0001583	missense	54777	exon52			CTGAGTCGACTAT																												ENST00000368586.5:c.7231G>A	10.37:g.134628208C>T	ENSP00000357575:p.Asp2411Asn	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	40	0.018315018315018316	36	0.07317073170731707	4	0.011049723756906077	0	0.0	0	0.0	C	15.33	2.802406	0.50315	0.086966	9.31E-4	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.34275	1.37;1.37	4.32	4.32	0.51571	.	0.091107	0.39274	N	0.001412	T	0.01976	0.0062	L	0.51422	1.61	0.46336	D	0.998994	D	0.65815	0.995	P	0.52793	0.709	T	0.00115	-1.2039	10	0.33940	T	0.23	.	12.3296	0.55031	0.0:1.0:0.0:0.0	.	572	Q8IYW2	CJ092_HUMAN	N	2411;572	ENSP00000357575:D2411N;ENSP00000263170:D572N	ENSP00000263170:D572N	D	-	1	0	C10orf93	134478198	0.010000	0.17322	0.016000	0.15963	0.025000	0.11179	0.774000	0.26675	1.959000	0.56917	0.591000	0.81541	GAC	C|0.968;T|0.032	0.032	strong		0.652	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
AMDHD2	51005	hgsc.bcm.edu	37	16	2578131	2578131	+	Silent	SNP	C	C	G	rs35816046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2578131C>G	ENST00000293971.6	+	6	793	c.699C>G	c.(697-699)ctC>ctG	p.L233L	CEMP1_ENST00000382350.1_Intron|AMDHD2_ENST00000413459.3_Silent_p.L233L|AMDHD2_ENST00000565570.1_Intron|AMDHD2_ENST00000302956.4_Silent_p.L233L	NM_015944.3	NP_057028.2	Q9Y303	NAGA_HUMAN	amidohydrolase domain containing 2	233					carbohydrate metabolic process (GO:0005975)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylneuraminate catabolic process (GO:0019262)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-phosphate deacetylase activity (GO:0008448)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)|skin(2)|urinary_tract(2)	19						TCACCCACCTCTTCAACGCCA	0.667													C|||	109	0.0217652	0.0802	0.0043	5008	,	,		13645	0.0		0.0	False		,,,				2504	0.0				p.L233L		Atlas-SNP	.											.	AMDHD2	33	.	0			c.C699G						PASS	.	C	,	285,4111	155.5+/-188.7	9,267,1922	74.0	76.0	75.0		699,699	5.4	1.0	16	dbSNP_126	75	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	AMDHD2	NM_001145815.1,NM_015944.3	,	9,269,6220	GG,GC,CC		0.0233,6.4832,2.2084	,	233/595,233/440	2578131	287,12709	2198	4300	6498	SO:0001819	synonymous_variant	51005	exon6			CCACCTCTTCAAC	AF132948	CCDS10471.1, CCDS53984.1	16p13.3	2008-02-05			ENSG00000162066	ENSG00000162066			24262	protein-coding gene	gene with protein product						10810093	Standard	NM_001145815		Approved	CGI-14	uc010uwc.2	Q9Y303	OTTHUMG00000128866	ENST00000293971.6:c.699C>G	16.37:g.2578131C>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	98	37	0.377551	NM_001145815	B4DL77|Q8WV54	Silent	SNP	ENST00000293971.6	37																																																																																				G|0.019;C|0.981	0.019	strong		0.667	AMDHD2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000435652.1	NM_015944	
SMPDL3B	27293	hgsc.bcm.edu	37	1	28282292	28282292	+	Missense_Mutation	SNP	T	T	C	rs3813803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:28282292T>C	ENST00000373894.3	+	6	979	c.788T>C	c.(787-789)gTc>gCc	p.V263A	SMPDL3B_ENST00000373888.4_Missense_Mutation_p.V263A|RP11-460I13.2_ENST00000448015.1_RNA|SMPDL3B_ENST00000549094.1_Missense_Mutation_p.V215A	NM_014474.2	NP_055289.2	Q92485	ASM3B_HUMAN	sphingomyelin phosphodiesterase, acid-like 3B	263					sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	16		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)		CTGAAGGTGGTCCGGAAGCAT	0.542													T|||	933	0.186302	0.0703	0.255	5008	,	,		19887	0.2123		0.2684	False		,,,				2504	0.183				p.V263A		Atlas-SNP	.											.	SMPDL3B	54	.	0			c.T788C						PASS	.	T	ALA/VAL,ALA/VAL	464,3942	219.1+/-236.9	31,402,1770	105.0	92.0	97.0		788,788	5.3	0.8	1	dbSNP_107	97	2549,6051	416.1+/-352.0	389,1771,2140	yes	missense,missense	SMPDL3B	NM_001009568.1,NM_014474.2	64,64	420,2173,3910	CC,CT,TT		29.6395,10.5311,23.1662	possibly-damaging,possibly-damaging	263/374,263/456	28282292	3013,9993	2203	4300	6503	SO:0001583	missense	27293	exon6			AGGTGGTCCGGAA	Y08134	CCDS30655.1, CCDS30656.1	1p35.3	2008-02-05			ENSG00000130768	ENSG00000130768			21416	protein-coding gene	gene with protein product							Standard	NM_014474		Approved	ASML3B	uc001bpg.3	Q92485	OTTHUMG00000003910	ENST00000373894.3:c.788T>C	1.37:g.28282292T>C	ENSP00000363001:p.Val263Ala	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	131	73	0.557252	NM_001009568	B7ZB35|Q5T0Z0|Q96CB7	Missense_Mutation	SNP	ENST00000373894.3	37	CCDS30655.1	475	0.2174908424908425	37	0.07520325203252033	91	0.2513812154696133	138	0.24125874125874125	209	0.2757255936675462	T	17.52	3.409377	0.62399	0.105311	0.296395	ENSG00000130768	ENST00000373894;ENST00000373888;ENST00000549094;ENST00000412515	D;D;D	0.92752	-3.1;-3.1;-3.1	5.34	5.34	0.76211	Metallophosphoesterase domain (1);	0.184020	0.47455	D	0.000238	T	0.00039	0.0001	M	0.68952	2.095	0.32187	P	0.5795939999999999	D;D;D	0.63046	0.99;0.992;0.971	P;P;P	0.57152	0.716;0.814;0.716	T	0.00000	-1.5165	9	0.54805	T	0.06	-26.7775	15.2914	0.73868	0.0:0.0:0.0:1.0	rs3813803;rs52818124;rs56731368;rs3813803	215;263;263	F8VWW8;Q92485;Q92485-2	.;ASM3B_HUMAN;.	A	263;263;215;215	ENSP00000363001:V263A;ENSP00000362995:V263A;ENSP00000449450:V215A	ENSP00000362995:V263A	V	+	2	0	SMPDL3B	28154879	1.000000	0.71417	0.796000	0.32109	0.013000	0.08279	7.608000	0.82898	2.009000	0.58944	0.379000	0.24179	GTC	T|0.782;C|0.218	0.218	strong		0.542	SMPDL3B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011170.1	NM_014474	
TTC8	123016	hgsc.bcm.edu	37	14	89338786	89338786	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:89338786A>G	ENST00000345383.5	+	12	1391	c.1307A>G	c.(1306-1308)cAc>cGc	p.H436R	TTC8_ENST00000338104.6_Missense_Mutation_p.H462R|TTC8_ENST00000380656.2_Missense_Mutation_p.H446R|TTC8_ENST00000346301.4_Missense_Mutation_p.H406R|TTC8_ENST00000354441.6_Missense_Mutation_p.H181R|TTC8_ENST00000536576.1_Missense_Mutation_p.H207R|TTC8_ENST00000358622.5_Missense_Mutation_p.H248R	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	472					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						CGGAAGGGCCACGTTGAACAG	0.517																																					p.H446R		Atlas-SNP	.											.	TTC8	42	.	0			c.A1337G						PASS	.						131.0	110.0	117.0					14																	89338786		2203	4300	6503	SO:0001583	missense	123016	exon13			AGGGCCACGTTGA	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"""Tetratricopeptide (TTC) repeat domain containing"""	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.1307A>G	14.37:g.89338786A>G	ENSP00000339486:p.His436Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Missense_Mutation	SNP	ENST00000345383.5	37	CCDS9885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.85|11.85	1.761724|1.761724	0.31228|0.31228	.|.	.|.	ENSG00000165533|ENSG00000165533	ENST00000345383;ENST00000536576;ENST00000346301;ENST00000338104;ENST00000354441;ENST00000380656;ENST00000358622|ENST00000554686	T;T;T;T;T;T;T|.	0.58797|.	1.0;0.31;1.0;1.0;0.31;1.0;1.0|.	5.59|5.59	5.59|5.59	0.84812|0.84812	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.094735|.	0.64402|.	D|.	0.000001|.	T|T	0.30103|0.30103	0.0754|0.0754	N|N	0.02802|0.02802	-0.49|-0.49	0.49798|0.49798	D|D	0.999823|0.999823	B;B;B;B;B|.	0.12013|.	0.005;0.0;0.005;0.0;0.0|.	B;B;B;B;B|.	0.14578|.	0.004;0.004;0.011;0.002;0.002|.	T|T	0.27872|0.27872	-1.0061|-1.0061	10|5	0.27082|.	T|.	0.32|.	-24.1045|-24.1045	11.1717|11.1717	0.48575|0.48575	0.9283:0.0:0.0717:0.0|0.9283:0.0:0.0717:0.0	.|.	181;207;472;416;446|.	Q8TAM2-2;B3KSL8;Q8TAM2;Q8TAM2-3;Q8TAM2-4|.	.;.;TTC8_HUMAN;.;.|.	R|A	436;207;406;462;181;446;248|396	ENSP00000339486:H436R;ENSP00000445067:H207R;ENSP00000298324:H406R;ENSP00000337653:H462R;ENSP00000346427:H181R;ENSP00000370031:H446R;ENSP00000351439:H248R|.	ENSP00000337653:H462R|.	H|T	+|+	2|1	0|0	TTC8|TTC8	88408539|88408539	0.992000|0.992000	0.36948|0.36948	0.930000|0.930000	0.37139|0.37139	0.977000|0.977000	0.68977|0.68977	2.851000|2.851000	0.48302|0.48302	2.254000|2.254000	0.74563|0.74563	0.459000|0.459000	0.35465|0.35465	CAC|ACG	.	.	none		0.517	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596	
PRDM1	639	hgsc.bcm.edu	37	6	106536253	106536253	+	Missense_Mutation	SNP	G	G	A	rs2185379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:106536253G>A	ENST00000369096.4	+	2	454	c.220G>A	c.(220-222)Ggt>Agt	p.G74S	PRDM1_ENST00000369091.2_Missense_Mutation_p.G38S	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	74			G -> S (in dbSNP:rs2185379).		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)	p.?(1)		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)		TGCTGATGGCGGTACTTCGGT	0.488			"""D, N, Mis, F, S"""		DLBCL								G|||	295	0.0589058	0.0658	0.0476	5008	,	,		19692	0.0784		0.0318	False		,,,				2504	0.0654				p.G74S		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	.	PRDM1	195	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.G220A						PASS	.	G	SER/GLY	310,4096	167.3+/-198.3	10,290,1903	216.0	190.0	199.0		220	4.0	0.9	6	dbSNP_96	199	278,8322	104.8+/-165.8	7,264,4029	yes	missense	PRDM1	NM_001198.3	56	17,554,5932	AA,AG,GG		3.2326,7.0359,4.521	benign	74/826	106536253	588,12418	2203	4300	6503	SO:0001583	missense	639	exon2			GATGGCGGTACTT		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.220G>A	6.37:g.106536253G>A	ENSP00000358092:p.Gly74Ser	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	273	131	0.479853	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	126	0.057692307692307696	36	0.07317073170731707	18	0.049723756906077346	45	0.07867132867132867	27	0.03562005277044855	G	0.021	-1.425252	0.01126	0.070359	0.032326	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000424894	T;T;T	0.41758	3.33;3.25;0.99	5.8	4.01	0.46588	.	0.401077	0.28349	N	0.015662	T	0.13157	0.0319	L	0.46157	1.445	0.29381	N	0.863344	B	0.16166	0.016	B	0.09377	0.004	T	0.17228	-1.0376	10	0.11182	T	0.66	-12.5745	8.0928	0.30811	0.2895:0.0:0.7105:0.0	rs2185379;rs3747785;rs2185379	74	O75626	PRDM1_HUMAN	S	38;74;38;38	ENSP00000358087:G38S;ENSP00000358092:G74S;ENSP00000395566:G38S	ENSP00000358087:G38S	G	+	1	0	PRDM1	106642946	1.000000	0.71417	0.883000	0.34634	0.041000	0.13682	2.661000	0.46758	1.463000	0.47967	0.563000	0.77884	GGT	G|0.948;A|0.052	0.052	strong		0.488	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
AHNAK2	113146	hgsc.bcm.edu	37	14	105416959	105416959	+	Missense_Mutation	SNP	A	A	G	rs2013462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416959A>G	ENST00000333244.5	-	7	4948	c.4829T>C	c.(4828-4830)gTg>gCg	p.V1610A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1610						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)			TGTCACTTCCACCTTGGGGCC	0.597													.|||	2849	0.56889	0.6785	0.4914	5008	,	,		14812	0.3621		0.5964	False		,,,				2504	0.6605				p.V1610A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T4829C						PASS	.	G	ALA/VAL	2347,1261		910,527,367	86.0	103.0	98.0		4829	-7.7	0.0	14	dbSNP_92	98	4754,3292		1652,1450,921	no	missense	AHNAK2	NM_138420.2	64	2562,1977,1288	GG,GA,AA		40.9147,34.9501,39.0681	benign	1610/5796	105416959	7101,4553	1804	4023	5827	SO:0001583	missense	113146	exon7			ACTTCCACCTTGG	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.4829T>C	14.37:g.105416959A>G	ENSP00000353114:p.Val1610Ala	Somatic	379	3	0.00791557		WXS	Illumina HiSeq	Phase_I	286	286	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	915	0.41895604395604397	242	0.491869918699187	167	0.4613259668508287	140	0.24475524475524477	366	0.48284960422163586	N	5.418	0.262361	0.10294	0.650499	0.590853	ENSG00000185567	ENST00000333244	T	0.00912	5.55	3.83	-7.66	0.01277	.	.	.	.	.	T	0.00012	0.0000	N	0.17248	0.465	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.24012	-1.0172	8	0.12430	T	0.62	.	2.6755	0.05080	0.2901:0.1285:0.4119:0.1695	.	1610	Q8IVF2	AHNK2_HUMAN	A	1610	ENSP00000353114:V1610A	ENSP00000353114:V1610A	V	-	2	0	AHNAK2	104488004	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.010000	0.00314	-1.715000	0.01389	-0.665000	0.03846	GTG	A|0.579;G|0.421	0.421	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TTN	7273	hgsc.bcm.edu	37	2	179610477	179610477	+	Intron	SNP	A	A	G	rs16866488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179610477A>G	ENST00000591111.1	-	46	10585				TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Silent_p.D5550D|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000578746.1_RNA			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)			CTAATTTTCCATCTTTGTACC	0.418													A|||	51	0.0101837	0.0371	0.0029	5008	,	,		20781	0.0		0.0	False		,,,				2504	0.0				p.D5550D		Atlas-SNP	.											.	TTN	18412	.	0			c.T16650C						PASS	.	A	,,,,	123,4283	93.0+/-131.7	2,119,2082	118.0	118.0	118.0		,,16650,,	-0.3	1.0	2	dbSNP_123	118	4,8594	3.0+/-9.4	0,4,4295	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	2,123,6377	GG,GA,AA		0.0465,2.7916,0.9766	,,,,	,,5550/5605,,	179610477	127,12877	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			TTTTCCATCTTTG	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.10361-3829T>C	2.37:g.179610477A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	168	88	0.52381	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|0.987;G|0.013	0.013	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DMBT1	1755	hgsc.bcm.edu	37	10	124402677	124402677	+	Silent	SNP	A	A	G	rs1052715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:124402677A>G	ENST00000338354.3	+	53	7111	c.7005A>G	c.(7003-7005)ccA>ccG	p.P2335P	DMBT1_ENST00000344338.3_Silent_p.P2325P|DMBT1_ENST00000368909.3_Silent_p.P2335P|DMBT1_ENST00000368955.3_Silent_p.P2325P|DMBT1_ENST00000359586.6_Silent_p.P1055P|DMBT1_ENST00000330163.4_Silent_p.P1707P|DMBT1_ENST00000368956.2_Silent_p.P1707P			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	2335	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				ACTCCTCGCCATCTCTTCGCA	0.562													G|||	3224	0.64377	0.8767	0.5029	5008	,	,		18545	0.6687		0.4125	False		,,,				2504	0.6411				p.P2335P	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.A7005G						PASS	.	G	,,	3414,776		1430,554,111	122.0	133.0	130.0		5121,7005,6975	-10.6	0.0	10	dbSNP_86	130	3531,4913		739,2053,1430	no	coding-synonymous,coding-synonymous,coding-synonymous	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	,,	2169,2607,1541	GG,GA,AA		41.8167,18.5203,45.0293	,,	1707/1786,2335/2414,2325/2404	124402677	6945,5689	2095	4222	6317	SO:0001819	synonymous_variant	1755	exon53			CTCGCCATCTCTT		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.7005A>G	10.37:g.124402677A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																				A|0.423;G|0.577	0.577	strong		0.562	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
MRO	83876	hgsc.bcm.edu	37	18	48333203	48333203	+	Missense_Mutation	SNP	C	C	G	rs4940019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:48333203C>G	ENST00000428869.2	-	5	375	c.117G>C	c.(115-117)agG>agC	p.R39S	MRO_ENST00000588444.1_Missense_Mutation_p.R39S|MRO_ENST00000431965.2_Missense_Mutation_p.R53S|MRO_ENST00000587291.1_Intron|MRO_ENST00000256425.2_Missense_Mutation_p.R39S|MRO_ENST00000436348.2_Missense_Mutation_p.R53S|MRO_ENST00000398439.3_Missense_Mutation_p.R39S			Q9BYG7	MSTRO_HUMAN	maestro	39			R -> S (in dbSNP:rs4940019). {ECO:0000269|PubMed:14702039}.			nucleolus (GO:0005730)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|skin(2)	10		Colorectal(6;0.0596)		Colorectal(21;0.082)		GCTTCTGGAACCTCAGTTTCC	0.463													C|||	2319	0.463059	0.1929	0.6816	5008	,	,		19022	0.4673		0.496	False		,,,				2504	0.635				p.R53S		Atlas-SNP	.											.	MRO	36	.	0			c.G159C						PASS	.	C	SER/ARG,SER/ARG,SER/ARG,SER/ARG	1065,3341	387.7+/-326.6	111,843,1249	84.0	87.0	86.0		117,159,159,117	2.6	0.1	18	dbSNP_111	86	4146,4454	565.6+/-388.5	1008,2130,1162	yes	missense,missense,missense,missense	MRO	NM_001127174.1,NM_001127175.1,NM_001127176.1,NM_031939.3	110,110,110,110	1119,2973,2411	GG,GC,CC		48.2093,24.1716,40.0661	benign,benign,benign,benign	39/197,53/211,53/263,39/249	48333203	5211,7795	2203	4300	6503	SO:0001583	missense	83876	exon3			CTGGAACCTCAGT	AK054702	CCDS11947.1, CCDS45867.1, CCDS45868.1, CCDS45869.1	18q21	2012-12-19	2004-06-15		ENSG00000134042	ENSG00000134042		"""maestro heat-like repeat containing"""	24121	protein-coding gene	gene with protein product	"""B29 protein"", ""beside the Ma29 deletion"""	608080	"""chromosome 18 open reading frame 3"""	C18orf3		11401430	Standard	NM_031939		Approved	B29, FLJ30140	uc010dpa.3	Q9BYG7	OTTHUMG00000132692	ENST00000428869.2:c.117G>C	18.37:g.48333203C>G	ENSP00000409509:p.Arg39Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_001127175	B7Z2I5|B7Z3B2|E9PAT5|E9PBI3|K7EKJ8|Q8N6K5	Missense_Mutation	SNP	ENST00000428869.2	37	CCDS11947.1	980	0.44871794871794873	94	0.1910569105691057	230	0.6353591160220995	288	0.5034965034965035	368	0.48548812664907653	C	7.049	0.564038	0.13498	0.241716	0.482093	ENSG00000134042	ENST00000436348;ENST00000431965;ENST00000428869;ENST00000398439;ENST00000256425	T;T;T;T;T	0.31247	2.38;1.98;1.5;1.5;1.5	5.39	2.63	0.31362	Armadillo-type fold (1);	2.863360	0.00855	N	0.001864	T	0.00012	0.0000	M	0.72479	2.2	0.80722	P	0.0	B;P;B;B	0.35774	0.016;0.519;0.024;0.002	B;B;B;B	0.37480	0.006;0.251;0.02;0.007	T	0.47573	-0.9107	9	0.09590	T	0.72	-20.4336	5.1639	0.15075	0.1637:0.6627:0.0:0.1736	rs4940019;rs52818026;rs57216618;rs4940019	39;53;53;39	E9PFU2;E9PBI3;E9PAT5;Q9BYG7	.;.;.;MSTRO_HUMAN	S	53;53;39;39;39	ENSP00000397900:R53S;ENSP00000392614:R53S;ENSP00000409509:R39S;ENSP00000381465:R39S;ENSP00000256425:R39S	ENSP00000256425:R39S	R	-	3	2	MRO	46587201	0.019000	0.18553	0.094000	0.20943	0.732000	0.41865	0.590000	0.23954	0.271000	0.22005	-0.300000	0.09419	AGG	C|0.579;G|0.421	0.421	strong		0.463	MRO-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449478.2	NM_031939	
DDIAS	220042	hgsc.bcm.edu	37	11	82644059	82644059	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:82644059G>C	ENST00000533655.1	+	6	1891	c.1679G>C	c.(1678-1680)aGa>aCa	p.R560T	C11orf82_ENST00000329143.3_Missense_Mutation_p.R259T|C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000430323.2_Missense_Mutation_p.R560T|C11orf82_ENST00000525361.1_Intron	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		560					apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						AAGACTATCAGAATCTCACCA	0.333																																					p.R560T		Atlas-SNP	.											.	C11orf82	71	.	0			c.G1679C						PASS	.						39.0	40.0	40.0					11																	82644059		2203	4297	6500	SO:0001583	missense	220042	exon6			CTATCAGAATCTC																												ENST00000533655.1:c.1679G>C	11.37:g.82644059G>C	ENSP00000435421:p.Arg560Thr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	37	CCDS8263.1	.	.	.	.	.	.	.	.	.	.	G	3.431	-0.116076	0.06881	.	.	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	T;T;T	0.18338	2.48;2.48;2.22	5.73	0.776	0.18532	.	0.891385	0.09988	N	0.730156	T	0.20901	0.0503	L	0.57536	1.79	0.09310	N	1	D	0.56521	0.976	P	0.46685	0.524	T	0.17167	-1.0378	9	.	.	.	.	8.4326	0.32766	0.3684:0.0:0.6316:0.0	.	560	Q8IXT1	NOXIN_HUMAN	T	560;560;259	ENSP00000414687:R560T;ENSP00000435421:R560T;ENSP00000329930:R259T	.	R	+	2	0	C11orf82	82321707	0.000000	0.05858	0.001000	0.08648	0.144000	0.21451	-0.075000	0.11431	0.102000	0.17638	0.655000	0.94253	AGA	.	.	none		0.333	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1		
VPS25	84313	hgsc.bcm.edu	37	17	40926695	40926695	+	Silent	SNP	A	A	T	rs2305218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40926695A>T	ENST00000253794.2	+	3	271	c.231A>T	c.(229-231)gtA>gtT	p.V77V		NM_032353.2	NP_115729.1	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25 homolog (S. cerevisiae)	77					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 membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)	5		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		TCCAGATTGTATTAGAGGAAC	0.428													A|||	518	0.103435	0.1021	0.0418	5008	,	,		15999	0.1825		0.0318	False		,,,				2504	0.1411				p.V77V		Atlas-SNP	.											.	VPS25	11	.	0			c.A231T						PASS	.	A		421,3985	205.8+/-227.6	22,377,1804	122.0	118.0	119.0		231	-3.2	1.0	17	dbSNP_100	119	214,8386	90.4+/-152.6	0,214,4086	no	coding-synonymous	VPS25	NM_032353.2		22,591,5890	TT,TA,AA		2.4884,9.5552,4.8824		77/177	40926695	635,12371	2203	4300	6503	SO:0001819	synonymous_variant	84313	exon3			GATTGTATTAGAG	AB014763	CCDS11438.1	17q21.31	2014-02-12	2006-04-04		ENSG00000131475	ENSG00000131475			28122	protein-coding gene	gene with protein product		610907	"""vacuolar protein sorting 25 (yeast)"""			15511219	Standard	NM_032353		Approved	MGC10540, EAP20, DERP9	uc002ibi.3	Q9BRG1		ENST00000253794.2:c.231A>T	17.37:g.40926695A>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	165	80	0.484848	NM_032353	B2R581	Silent	SNP	ENST00000253794.2	37	CCDS11438.1																																																																																			A|0.936;T|0.064	0.064	strong		0.428	VPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452383.1	NM_032353	
NUP188	23511	hgsc.bcm.edu	37	9	131767668	131767668	+	Silent	SNP	A	A	C	rs2287363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131767668A>C	ENST00000372577.2	+	40	4617	c.4596A>C	c.(4594-4596)tcA>tcC	p.S1532S	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1532					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						CCTCCTCCTCAAAGCAGCCCG	0.597													C|||	2262	0.451677	0.4728	0.4957	5008	,	,		19526	0.4067		0.4672	False		,,,				2504	0.4223				p.S1532S		Atlas-SNP	.											.	NUP188	140	.	0			c.A4596C						PASS	.	C		2007,2399	582.1+/-385.5	439,1129,635	37.0	38.0	38.0		4596	2.0	1.0	9	dbSNP_100	38	3525,5075	607.7+/-395.3	739,2047,1514	no	coding-synonymous	NUP188	NM_015354.1		1178,3176,2149	CC,CA,AA		40.9884,45.5515,42.5342		1532/1750	131767668	5532,7474	2203	4300	6503	SO:0001819	synonymous_variant	23511	exon40			CTCCTCAAAGCAG	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.4596A>C	9.37:g.131767668A>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			A|0.553;C|0.447	0.447	strong		0.597	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
MUC4	4585	hgsc.bcm.edu	37	3	195505893	195505893	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195505893G>A	ENST00000463781.3	-	2	13017	c.12558C>T	c.(12556-12558)tcC>tcT	p.S4186S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S4186S	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)		TGTCACCTGTGGATGCTGAGG	0.592																																					p.S4186S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C12558T						PASS	.						19.0	13.0	15.0					3																	195505893		691	1574	2265	SO:0001819	synonymous_variant	4585	exon2			ACCTGTGGATGCT	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.12558C>T	3.37:g.195505893G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	240	14	0.0583333	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																																																																																			.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DAAM1	23002	hgsc.bcm.edu	37	14	59797235	59797235	+	Silent	SNP	A	A	G	rs941884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:59797235A>G	ENST00000395125.1	+	12	1412	c.1389A>G	c.(1387-1389)caA>caG	p.Q463Q	DAAM1_ENST00000360909.3_Silent_p.Q463Q|DAAM1_ENST00000351081.1_Silent_p.Q463Q	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	463					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)		ATGAGCTACAACAGAAACTGG	0.368													A|||	3284	0.655751	0.5166	0.6398	5008	,	,		22275	0.8383		0.661	False		,,,				2504	0.6616				p.Q463Q		Atlas-SNP	.											.	DAAM1	95	.	0			c.A1389G						PASS	.	A		2360,2046	607.9+/-391.1	639,1082,482	79.0	75.0	76.0		1389	-0.9	1.0	14	dbSNP_86	76	5560,3040	660.9+/-401.8	1807,1946,547	no	coding-synonymous	DAAM1	NM_014992.1		2446,3028,1029	GG,GA,AA		35.3488,46.4367,39.105		463/1079	59797235	7920,5086	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon13			GCTACAACAGAAA	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.1389A>G	14.37:g.59797235A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	149	82	0.550336	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			A|0.377;G|0.623	0.623	strong		0.368	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
FAM21A	387680	hgsc.bcm.edu	37	10	47909792	47909792	+	Missense_Mutation	SNP	C	C	T	rs201373575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:47909792C>T	ENST00000358474.5	+	11	889	c.889C>T	c.(889-891)Cgg>Tgg	p.R297W		NM_018232.1	NP_060702.1	Q5SNT6	FA21B_HUMAN		297					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)		p.R297W(2)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10						CCCCCAGGATCGGCAAGCTGG	0.498													C|||	1254	0.250399	0.1861	0.1513	5008	,	,		7006	0.4306		0.2028	False		,,,				2504	0.271				p.R297W		Atlas-SNP	.											FAM21B_ENST00000358474,NS,carcinoma,0,2	FAM21B	31	2	2	Substitution - Missense(2)	prostate(2)	c.C889T						scavenged	.						17.0	21.0	20.0					10																	47909792		589	2506	3095	SO:0001583	missense	55747	exon11			CAGGATCGGCAAG																												ENST00000358474.5:c.889C>T	10.37:g.47909792C>T	ENSP00000351259:p.Arg297Trp	Somatic	934	3	0.00321199		WXS	Illumina HiSeq	Phase_I	185	6	0.0324324	NM_018232		Missense_Mutation	SNP	ENST00000358474.5	37	CCDS44379.1	.	.	.	.	.	.	.	.	.	.	.	12.06	1.824831	0.32237	.	.	ENSG00000152726	ENST00000358474;ENST00000535219;ENST00000355876	.	.	.	2.3	1.19	0.21007	.	1.629960	0.03041	N	0.153324	T	0.31295	0.0792	M	0.68317	2.08	0.09310	N	1	P;B	0.39352	0.669;0.41	B;B	0.20577	0.03;0.021	T	0.44922	-0.9296	9	0.72032	D	0.01	0.1363	5.4742	0.16686	0.3296:0.6704:0.0:0.0	.	297;385	Q5SNT6;B7ZME8	FA21B_HUMAN;.	W	297;134;288	.	ENSP00000348138:R288W	R	+	1	2	FAM21B	47429798	0.000000	0.05858	0.005000	0.12908	0.138000	0.21146	0.358000	0.20216	1.299000	0.44798	0.152000	0.16155	CGG	C|0.949;T|0.051	0.051	strong		0.498	FAM21B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047871.2		
FLG	2312	hgsc.bcm.edu	37	1	152283811	152283811	+	Missense_Mutation	SNP	G	G	A	rs3120649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152283811G>A	ENST00000368799.1	-	3	3586	c.3551C>T	c.(3550-3552)tCg>tTg	p.S1184L	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1184	Ser-rich.		S -> L (in dbSNP:rs3120649).		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)			TCTATCTACCGATTGCTCATG	0.592									Ichthyosis				g|||	604	0.120607	0.4002	0.0303	5008	,	,		20335	0.0496		0.001	False		,,,				2504	0.0031				p.S1184L		Atlas-SNP	.											FLG,caecum,carcinoma,0,1	FLG	900	1	0			c.C3551T						PASS	.	A	LEU/SER	1450,2956	469.0+/-355.3	230,990,983	351.0	357.0	355.0		3551	-2.8	0.0	1	dbSNP_103	355	15,8585	10.5+/-38.8	0,15,4285	no	missense	FLG	NM_002016.1	145	230,1005,5268	AA,AG,GG		0.1744,32.9097,11.264	benign	1184/4062	152283811	1465,11541	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCTACCGATTGCT	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.3551C>T	1.37:g.152283811G>A	ENSP00000357789:p.Ser1184Leu	Somatic	387	1	0.00258398		WXS	Illumina HiSeq	Phase_I	387	384	0.992248	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	191	0.08745421245421245	175	0.3556910569105691	11	0.03038674033149171	5	0.008741258741258742	0	0.0	g	5.236	0.229052	0.09916	0.329097	0.001744	ENSG00000143631	ENST00000368799	T	0.03745	3.82	2.75	-2.77	0.05877	.	.	.	.	.	T	0.01254	0.0041	M	0.78637	2.42	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.45512	-0.9256	8	0.25751	T	0.34	.	1.3189	0.02112	0.1257:0.1832:0.3195:0.3716	rs3120649;rs52832198;rs3120649	1184	P20930	FILA_HUMAN	L	1184	ENSP00000357789:S1184L	ENSP00000357789:S1184L	S	-	2	0	FLG	150550435	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.791000	0.04599	-0.766000	0.04639	-1.172000	0.01736	TCG	G|0.881;A|0.119	0.119	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LYPD3	27076	hgsc.bcm.edu	37	19	43967423	43967423	+	Silent	SNP	G	G	A	rs79420167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43967423G>A	ENST00000244333.3	-	4	487	c.399C>T	c.(397-399)taC>taT	p.Y133Y		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	133					cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				CGTTGGGCGGGTATGCACTCT	0.647													G|||	52	0.0103834	0.0378	0.0029	5008	,	,		15418	0.0		0.0	False		,,,				2504	0.0				p.Y133Y		Atlas-SNP	.											.	LYPD3	24	.	0			c.C399T						PASS	.	G		130,4276	94.8+/-133.5	4,122,2077	49.0	46.0	47.0		399	-2.9	0.0	19	dbSNP_132	47	0,8600		0,0,4300	no	coding-synonymous	LYPD3	NM_014400.2		4,122,6377	AA,AG,GG		0.0,2.9505,0.9995		133/347	43967423	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	27076	exon4			GGGCGGGTATGCA	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.399C>T	19.37:g.43967423G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_014400	Q9UJ74	Silent	SNP	ENST00000244333.3	37	CCDS12620.1																																																																																			G|0.987;A|0.013	0.013	strong		0.647	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400	
APOB	338	hgsc.bcm.edu	37	2	21224843	21224843	+	Missense_Mutation	SNP	G	G	A	rs12713450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:21224843G>A	ENST00000233242.1	-	29	13578	c.13451C>T	c.(13450-13452)aCg>aTg	p.T4484M	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4484			T -> M (in dbSNP:rs12713450).		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)					TATTTTCTTCGTCGCAATGGC	0.378													G|||	192	0.0383387	0.1263	0.0259	5008	,	,		18757	0.0		0.006	False		,,,				2504	0.001				p.T4484M		Atlas-SNP	.											APOB,NS,carcinoma,+1,1	APOB	761	1	0			c.C13451T						scavenged	.	G	MET/THR	444,3962	204.8+/-226.9	20,404,1779	85.0	91.0	89.0		13451	2.2	0.0	2	dbSNP_126	89	43,8557	28.5+/-78.6	0,43,4257	yes	missense	APOB	NM_000384.2	81	20,447,6036	AA,AG,GG		0.5,10.0772,3.7444	benign	4484/4564	21224843	487,12519	2203	4300	6503	SO:0001583	missense	338	exon29			TTCTTCGTCGCAA	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.13451C>T	2.37:g.21224843G>A	ENSP00000233242:p.Thr4484Met	Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	72	0.03296703296703297	60	0.12195121951219512	8	0.022099447513812154	0	0.0	4	0.005277044854881266	G	0.008	-1.930298	0.00488	0.100772	0.005	ENSG00000084674	ENST00000233242	T	0.37915	1.17	5.9	2.22	0.28083	.	0.646971	0.15282	N	0.270656	T	0.00109	0.0003	N	0.00095	-2.16	0.22552	N	0.998995	B	0.06786	0.001	B	0.04013	0.001	T	0.33085	-0.9882	10	0.28530	T	0.3	.	6.3395	0.21314	0.4718:0.0:0.5282:0.0	rs12713450;rs17240965;rs52805962;rs60161843;rs12713450	4484	P04114	APOB_HUMAN	M	4484	ENSP00000233242:T4484M	ENSP00000233242:T4484M	T	-	2	0	APOB	21078348	0.907000	0.30839	0.005000	0.12908	0.008000	0.06430	1.767000	0.38501	0.490000	0.27771	-0.312000	0.09012	ACG	G|0.968;A|0.032	0.032	strong		0.378	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
ABCA13	154664	hgsc.bcm.edu	37	7	48506566	48506566	+	Missense_Mutation	SNP	A	A	G	rs4917152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	106	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	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	
CHAD	1101	hgsc.bcm.edu	37	17	48542690	48542690	+	Missense_Mutation	SNP	G	G	A	rs2231510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48542690G>A	ENST00000508540.1	-	3	1201	c.1049C>T	c.(1048-1050)aCc>aTc	p.T350I	ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000300441.4_Intron|ACSF2_ENST00000427954.2_Intron|ACSF2_ENST00000502667.1_Intron|CHAD_ENST00000258969.4_Missense_Mutation_p.T350I|ACSF2_ENST00000541920.1_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	350			T -> I (in dbSNP:rs2231510).		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)			GGACCTCTTGGTGGGGAACTT	0.597													G|||	100	0.0199681	0.0734	0.0043	5008	,	,		17381	0.0		0.0	False		,,,				2504	0.0				p.T350I		Atlas-SNP	.											.	CHAD	36	.	0			c.C1049T						PASS	.	G	ILE/THR,	338,4068	178.0+/-206.8	13,312,1878	56.0	52.0	53.0		1049,	5.1	1.0	17	dbSNP_98	53	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron	CHAD,ACSF2	NM_001267.2,NM_025149.4	89,	13,313,6177	AA,AG,GG		0.0116,7.6714,2.6065	benign,	350/360,	48542690	339,12667	2203	4300	6503	SO:0001583	missense	1101	exon3			CTCTTGGTGGGGA	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.1049C>T	17.37:g.48542690G>A	ENSP00000423812:p.Thr350Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_001267	A8K812|Q6GTU0|Q96RJ5	Missense_Mutation	SNP	ENST00000508540.1	37	CCDS11568.1	39|39	0.017857142857142856|0.017857142857142856	38|38	0.07723577235772358|0.07723577235772358	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	17.86|17.86	3.492361|3.492361	0.64074|0.64074	0.076714|0.076714	1.16E-4|1.16E-4	ENSG00000136457|ENSG00000136457	ENST00000506187|ENST00000508540;ENST00000258969	.|T;T	.|0.56275	.|0.47;0.47	5.12|5.12	5.12|5.12	0.69794|0.69794	.|.	.|0.056342	.|0.64402	.|D	.|0.000001	T|T	0.05960|0.05960	0.0155|0.0155	L|L	0.45352|0.45352	1.415|1.415	0.58432|0.58432	D|D	0.999997|0.999997	.|D	.|0.64830	.|0.994	.|P	.|0.50314	.|0.637	T|T	0.03413|0.03413	-1.1039|-1.1039	5|10	.|0.37606	.|T	.|0.19	.|.	18.5806|18.5806	0.91170|0.91170	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs2231510;rs2231510|rs2231510;rs2231510	.|350	.|O15335	.|CHAD_HUMAN	S|I	33|350	.|ENSP00000423812:T350I;ENSP00000258969:T350I	.|ENSP00000258969:T350I	P|T	-|-	1|2	0|0	CHAD|CHAD	45897689|45897689	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.971000|0.971000	0.66376|0.66376	8.496000|8.496000	0.90485|0.90485	2.380000|2.380000	0.81148|0.81148	0.655000|0.655000	0.94253|0.94253	CCA|ACC	G|0.966;A|0.034	0.034	strong		0.597	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267	
PKN2	5586	hgsc.bcm.edu	37	1	89273241	89273241	+	Missense_Mutation	SNP	A	A	G	rs12085658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89273241A>G	ENST00000370521.3	+	14	2323	c.1964A>G	c.(1963-1965)cAa>cGa	p.Q655R	PKN2_ENST00000370505.3_Missense_Mutation_p.Q498R|PKN2_ENST00000370513.5_Missense_Mutation_p.Q607R|PKN2_ENST00000544045.1_Missense_Mutation_p.Q329R	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	655			Q -> R (in dbSNP:rs12085658).		apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		TTTAATCTACAAGATTTCAGG	0.318													A|||	43	0.00858626	0.0295	0.0058	5008	,	,		16355	0.0		0.0	False		,,,				2504	0.0				p.Q655R		Atlas-SNP	.											.	PKN2	109	.	0			c.A1964G						PASS	.	A	ARG/GLN	90,3516		0,90,1713	150.0	145.0	146.0		1964	5.8	1.0	1	dbSNP_120	146	0,8134		0,0,4067	yes	missense	PKN2	NM_006256.2	43	0,90,5780	GG,GA,AA		0.0,2.4958,0.7666	benign	655/985	89273241	90,11650	1803	4067	5870	SO:0001583	missense	5586	exon14			ATCTACAAGATTT	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1964A>G	1.37:g.89273241A>G	ENSP00000359552:p.Gln655Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	37	CCDS714.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	A	15.07	2.724560	0.48833	0.024958	0.0	ENSG00000065243	ENST00000370521;ENST00000370505;ENST00000370513;ENST00000544045	T;T;T;T	0.24538	1.85;1.85;1.85;1.85	5.75	5.75	0.90469	Protein kinase-like domain (1);	0.162237	0.28612	U	0.014721	T	0.07728	0.0194	N	0.08118	0	0.36654	D	0.877588	B;B;B	0.22683	0.073;0.073;0.025	B;B;B	0.17098	0.017;0.017;0.013	T	0.09773	-1.0659	10	0.54805	T	0.06	.	16.0549	0.80794	1.0:0.0:0.0:0.0	rs12085658;rs52814429;rs12085658	639;607;655	B4DTP5;E7ESL7;Q16513	.;.;PKN2_HUMAN	R	655;498;607;329	ENSP00000359552:Q655R;ENSP00000359536:Q498R;ENSP00000359544:Q607R;ENSP00000439643:Q329R	ENSP00000359536:Q498R	Q	+	2	0	PKN2	89045829	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.711000	0.61881	2.193000	0.70182	0.477000	0.44152	CAA	A|0.992;G|0.008	0.008	strong		0.318	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256	
LRRC14B	389257	hgsc.bcm.edu	37	5	195318	195318	+	Silent	SNP	T	T	C	rs6886707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:195318T>C	ENST00000328278.3	+	2	1423	c.1395T>C	c.(1393-1395)gcT>gcC	p.A465A	CTD-2083E4.7_ENST00000563761.1_RNA	NM_001080478.1	NP_001073947.1	A6NHZ5	LR14B_HUMAN	leucine rich repeat containing 14B	465										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	10						TGCTGCGGGCTGACCGAGAGG	0.552													C|||	945	0.188698	0.4955	0.1354	5008	,	,		18137	0.005		0.1352	False		,,,				2504	0.0562				p.A465A		Atlas-SNP	.											.	LRRC14B	30	.	0			c.T1395C						PASS	.	C		1805,2549		382,1041,754	111.0	122.0	119.0		1395	-4.5	0.0	5	dbSNP_116	119	1015,7543		74,867,3338	no	coding-synonymous	LRRC14B	NM_001080478.1		456,1908,4092	CC,CT,TT		11.8602,41.4561,21.8401		465/515	195318	2820,10092	2177	4279	6456	SO:0001819	synonymous_variant	389257	exon2			GCGGGCTGACCGA		CCDS47184.1	5p15.33	2010-02-17			ENSG00000185028	ENSG00000185028			37268	protein-coding gene	gene with protein product							Standard	NM_001080478		Approved		uc003jal.1	A6NHZ5	OTTHUMG00000161578	ENST00000328278.3:c.1395T>C	5.37:g.195318T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_001080478		Silent	SNP	ENST00000328278.3	37	CCDS47184.1																																																																																			T|0.847;C|0.153	0.153	strong		0.552	LRRC14B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000365393.2	NM_001080478	
MUC17	140453	hgsc.bcm.edu	37	7	100677457	100677457	+	Silent	SNP	G	G	T	rs59155935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677457G>T	ENST00000306151.4	+	3	2824	c.2760G>T	c.(2758-2760)ggG>ggT	p.G920G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	920	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)					CAACTCCTGGGGAAGGAAGCA	0.517													T|||	68	0.0135783	0.0431	0.0043	5008	,	,		33068	0.002		0.002	False		,,,				2504	0.0041				p.G920G		Atlas-SNP	.											.	MUC17	804	.	0			c.G2760T						PASS	.	T		10,4396	823.5+/-416.5	0,10,2193	365.0	326.0	339.0		2760	-2.4	0.0	7	dbSNP_129	339	4,8596	818.2+/-406.9	0,4,4296	no	coding-synonymous	MUC17	NM_001040105.1		0,14,6489	TT,TG,GG		0.0465,0.227,0.1076		920/4494	100677457	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TCCTGGGGAAGGA	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.2760G>T	7.37:g.100677457G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	197	44	0.22335	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.951;T|0.049	0.049	strong		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CHRM4	1132	hgsc.bcm.edu	37	11	46406767	46406767	+	Silent	SNP	G	G	A	rs2067482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46406767G>A	ENST00000433765.2	-	1	1340	c.1341C>T	c.(1339-1341)acC>acT	p.T447T		NM_000741.2	NP_000732.2	P08173	ACM4_HUMAN	cholinergic receptor, muscarinic 4	447					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|regulation of locomotion (GO:0040012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			breast(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	20				GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CAGGGTTGATGGTGCTGTTGA	0.572													g|||	555	0.110823	0.1059	0.0807	5008	,	,		20073	0.0506		0.167	False		,,,				2504	0.1431				p.T447T	Esophageal Squamous(171;1020 1936 4566 30205 42542)	Atlas-SNP	.											.	CHRM4	47	.	0			c.C1341T						PASS	.			498,3906	225.6+/-241.4	27,444,1731	138.0	141.0	140.0		1341	3.7	1.0	11	dbSNP_96	140	1492,7106	281.7+/-295.2	121,1250,2928	no	coding-synonymous	CHRM4	NM_000741.2		148,1694,4659	AA,AG,GG		17.3529,11.3079,15.3053		447/480	46406767	1990,11012	2202	4299	6501	SO:0001819	synonymous_variant	1132	exon1			GTTGATGGTGCTG	M16405	CCDS44581.1	11p12-p11.2	2012-08-08			ENSG00000180720	ENSG00000180720		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1953	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 4"""	118495				1577490	Standard	NM_000741		Approved		uc001nct.1	P08173	OTTHUMG00000154371	ENST00000433765.2:c.1341C>T	11.37:g.46406767G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	201	93	0.462687	NM_000741	B2RPP4|Q0VD60|Q4VBK7	Silent	SNP	ENST00000433765.2	37	CCDS44581.1																																																																																			G|0.844;T|0.003	.	strong		0.572	CHRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334985.1	NM_000741	
KIAA1211	57482	hgsc.bcm.edu	37	4	57180546	57180546	+	Missense_Mutation	SNP	G	G	A	rs145781098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57180546G>A	ENST00000504228.1	+	6	983	c.878G>A	c.(877-879)cGg>cAg	p.R293Q	KIAA1211_ENST00000264229.6_Missense_Mutation_p.R293Q|KIAA1211_ENST00000541073.1_Missense_Mutation_p.R286Q			Q6ZU35	K1211_HUMAN	KIAA1211	293	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)					GAGCAGCAGCGGAGCCTGGAA	0.697													G|||	27	0.00539137	0.0197	0.0014	5008	,	,		13712	0.0		0.0	False		,,,				2504	0.0				p.R293Q		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G878A						PASS	.	G	GLN/ARG	46,3696		0,46,1825	5.0	8.0	7.0		878	-2.7	0.0	4	dbSNP_134	7	6,7630		0,6,3812	no	missense	KIAA1211	NM_020722.1	43	0,52,5637	AA,AG,GG		0.0786,1.2293,0.457	benign	293/1234	57180546	52,11326	1871	3818	5689	SO:0001583	missense	57482	exon8			AGCAGCGGAGCCT	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.878G>A	4.37:g.57180546G>A	ENSP00000423366:p.Arg293Gln	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	12.98	2.100302	0.37048	0.012293	7.86E-4	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.14391	2.51;2.51;2.52	4.88	-2.66	0.06077	.	.	.	.	.	T	0.00815	0.0027	N	0.00246	-1.78	0.09310	N	1	B;B;B	0.15930	0.015;0.015;0.015	B;B;B	0.11329	0.006;0.003;0.003	T	0.44159	-0.9346	9	0.11485	T	0.65	-0.6858	6.6117	0.22755	0.3545:0.2188:0.4268:0.0	.	286;286;293	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	Q	293;293;286;203	ENSP00000264229:R293Q;ENSP00000423366:R293Q;ENSP00000444006:R286Q	ENSP00000264229:R293Q	R	+	2	0	KIAA1211	56875303	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	-0.656000	0.05342	-0.778000	0.04566	0.462000	0.41574	CGG	G|0.994;A|0.006	0.006	strong		0.697	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
PM20D1	148811	hgsc.bcm.edu	37	1	205811828	205811828	+	Silent	SNP	A	A	T	rs4951025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:205811828A>T	ENST00000367136.4	-	7	923	c.879T>A	c.(877-879)acT>acA	p.T293T	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	293					negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)	p.T293T(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			GCTGCAATACAGTCACCACTG	0.443													C|||	1425	0.284545	0.4183	0.2421	5008	,	,		22567	0.2917		0.1352	False		,,,				2504	0.2802				p.T293T		Atlas-SNP	.											PM20D1,NS,carcinoma,0,1	PM20D1	56	1	1	Substitution - coding silent(1)	stomach(1)	c.T879A						PASS	.	C		1618,2788		313,992,898	129.0	118.0	122.0		879	-2.0	0.0	1	dbSNP_111	122	1150,7450		76,998,3226	no	coding-synonymous	PM20D1	NM_152491.4		389,1990,4124	TT,TA,AA		13.3721,36.7227,21.2825		293/503	205811828	2768,10238	2203	4300	6503	SO:0001819	synonymous_variant	148811	exon7			CAATACAGTCACC		CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.879T>A	1.37:g.205811828A>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	88	36	0.409091	NM_152491	Q6P4E3|Q96DM4	Silent	SNP	ENST00000367136.4	37	CCDS1460.1																																																																																			A|0.756;T|0.244	0.244	strong		0.443	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
OTOF	9381	hgsc.bcm.edu	37	2	26700700	26700700	+	Intron	SNP	G	G	A	rs4665855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26700700G>A	ENST00000272371.2	-	19	2341				OTOF_ENST00000339598.3_Intron|OTOF_ENST00000402415.3_Missense_Mutation_p.P21L|OTOF_ENST00000338581.6_Intron|OTOF_ENST00000403946.3_Intron	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin						membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTTGATCAGGGGAGTGAGGGA	0.572													G|||	3018	0.602636	0.4561	0.5994	5008	,	,		18953	0.9841		0.4414	False		,,,				2504	0.5757				p.P21L	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											OTOF_ENST00000402415,NS,carcinoma,0,2	OTOF	524	2	0			c.C62T						PASS	.	G	,,LEU/PRO,	1167,1487		265,637,425	46.0	53.0	50.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,62,	-0.6	0.0	2	dbSNP_111	50	1821,2795		348,1125,835	yes	intron,intron,missense,intron	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,98,	613,1762,1260	AA,AG,GG		39.4497,43.9714,41.1004	,,,	,,21/1308,	26700700	2988,4282	1327	2308	3635	SO:0001627	intron_variant	9381	exon1			ATCAGGGGAGTGA	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2215-83C>T	2.37:g.26700700G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	204	201	0.985294	NM_194322	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	1357	0.6213369963369964	231	0.4695121951219512	211	0.5828729281767956	561	0.9807692307692307	354	0.46701846965699206	G	2.955	-0.215799	0.06101	0.439714	0.394497	ENSG00000115155	ENST00000402415	T	0.76839	-1.05	3.62	-0.572	0.11745	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.29971	-0.9994	6	.	.	.	.	0.7994	0.01072	0.2277:0.1857:0.3963:0.1903	rs4665855;rs58375897;rs4665855	21	Q9HC10-3	.	L	21	ENSP00000383906:P21L	.	P	-	2	0	OTOF	26554204	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.242000	0.18087	-0.112000	0.11979	-1.581000	0.00855	CCC	G|0.410;A|0.590	0.590	strong		0.572	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
PRUNE2	158471	hgsc.bcm.edu	37	9	79319725	79319725	+	Missense_Mutation	SNP	T	T	C	rs375144440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79319725T>C	ENST00000376718.3	-	8	7588	c.7465A>G	c.(7465-7467)Aca>Gca	p.T2489A	PRUNE2_ENST00000428286.1_Missense_Mutation_p.T2130A	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2489					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GAATTATCTGTTTCTACTTCC	0.448											OREG0019258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2	0.000399361	0.0015	0.0	5008	,	,		20535	0.0		0.0	False		,,,				2504	0.0				p.T2489A		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A7465G						PASS	.	T	ALA/THR	5,3131		0,5,1563	72.0	60.0	64.0		7465	-1.6	0.2	9		64	0,7162		0,0,3581	no	missense	PRUNE2	NM_015225.2	58	0,5,5144	CC,CT,TT		0.0,0.1594,0.0486	benign	2489/3089	79319725	5,10293	1568	3581	5149	SO:0001583	missense	158471	exon8			TATCTGTTTCTAC	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.7465A>G	9.37:g.79319725T>C	ENSP00000365908:p.Thr2489Ala	Somatic	132	0	0	1190	WXS	Illumina HiSeq	Phase_I	149	104	0.697987	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.828|6.828	0.521980|0.521980	0.13005|0.13005	0.001594|0.001594	0.0|0.0	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376718;ENST00000428286;ENST00000422033	.|T;T	.|0.47869	.|0.83;0.83	5.66|5.66	-1.6|-1.6	0.08426|0.08426	.|.	.|0.512611	.|0.18219	.|N	.|0.147951	T|T	0.31295|0.31295	0.0792|0.0792	L|L	0.48362|0.48362	1.52|1.52	0.25662|0.25662	N|N	0.985999|0.985999	.|B	.|0.15141	.|0.012	.|B	.|0.11329	.|0.006	T|T	0.15235|0.15235	-1.0444|-1.0444	5|10	.|0.21540	.|T	.|0.41	-0.3544|-0.3544	4.9213|4.9213	0.13871|0.13871	0.3138:0.2585:0.0:0.4276|0.3138:0.2585:0.0:0.4276	.|.	.|2489	.|Q8WUY3	.|PRUN2_HUMAN	S|A	1810|2489;2130;2488	.|ENSP00000365908:T2489A;ENSP00000397425:T2130A	.|ENSP00000365908:T2489A	N|T	-|-	2|1	0|0	PRUNE2|PRUNE2	78509545|78509545	0.492000|0.492000	0.26027|0.26027	0.226000|0.226000	0.23910|0.23910	0.731000|0.731000	0.41821|0.41821	0.124000|0.124000	0.15728|0.15728	-0.097000|-0.097000	0.12307|0.12307	0.533000|0.533000	0.62120|0.62120	AAC|ACA	.	.	weak		0.448	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
PSG2	5670	hgsc.bcm.edu	37	19	43586664	43586664	+	Missense_Mutation	SNP	C	C	G	rs3887660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43586664C>G	ENST00000406487.1	-	1	156	c.58G>C	c.(58-60)Gtc>Ctc	p.V20L	PSG2_ENST00000491995.1_5'UTR	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	20			V -> L (in dbSNP:rs3887660). {ECO:0000269|PubMed:15489334}.		cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.V20L(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				TCACCTGTGACCAGGAGCCCC	0.557													G|||	2011	0.401558	0.6604	0.3847	5008	,	,		15645	0.1647		0.2763	False		,,,				2504	0.4366				p.V20L		Atlas-SNP	.											PSG2,NS,carcinoma,0,1	PSG2	84	1	1	Substitution - Missense(1)	stomach(1)	c.G58C						scavenged	.	G	LEU/VAL	2565,1837	516.5+/-369.2	800,965,436	73.0	84.0	80.0		58	0.9	0.0	19	dbSNP_108	80	2589,6005	677.6+/-403.4	408,1773,2116	no	missense	PSG2	NM_031246.3	32	1208,2738,2552	GG,GC,CC		30.1257,41.731,39.6584		20/336	43586664	5154,7842	2201	4297	6498	SO:0001583	missense	5670	exon1			CTGTGACCAGGAG		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.58G>C	19.37:g.43586664C>G	ENSP00000385706:p.Val20Leu	Somatic	35	1	0.0285714		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	631	0.2889194139194139	253	0.5142276422764228	119	0.3287292817679558	77	0.1346153846153846	182	0.24010554089709762	g	0.005	-2.197153	0.00299	0.58269	0.301257	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.20200	2.09	0.929	0.929	0.19449	.	.	.	.	.	T	0.00012	0.0000	N	0.00017	-2.825	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43310	-0.9399	8	0.02654	T	1	.	4.8558	0.13559	0.0:0.3956:0.6044:0.0	rs3887660;rs16976190;rs17405493;rs17856656;rs59584375	20;20	B5MCM8;P11465	.;PSG2_HUMAN	L	20	ENSP00000385706:V20L	ENSP00000332984:V20L	V	-	1	0	PSG2	48278504	0.355000	0.24921	0.006000	0.13384	0.012000	0.07955	-0.238000	0.08977	-0.027000	0.13873	-1.122000	0.02009	GTC	C|0.628;G|0.372	0.372	strong		0.557	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
CTNNA1	1495	hgsc.bcm.edu	37	5	138266546	138266546	+	Silent	SNP	G	G	A	rs1059110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:138266546G>A	ENST00000302763.7	+	16	2310	c.2220G>A	c.(2218-2220)tcG>tcA	p.S740S	CTNNA1_ENST00000540387.1_Silent_p.S370S|CTNNA1_ENST00000355078.5_Silent_p.S637S|CTNNA1_ENST00000518825.1_Silent_p.S740S	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	740					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAAATACATCGGATGTCATCA	0.463													A|||	1247	0.249002	0.4259	0.2695	5008	,	,		20368	0.0079		0.2714	False		,,,				2504	0.2209				p.S740S		Atlas-SNP	.											.	CTNNA1	114	.	0			c.G2220A						PASS	.	A		1797,2609	641.3+/-397.4	345,1107,751	85.0	87.0	86.0		2220	-2.0	1.0	5	dbSNP_86	86	2557,6043	691.9+/-404.5	371,1815,2114	no	coding-synonymous	CTNNA1	NM_001903.2		716,2922,2865	AA,AG,GG		29.7326,40.7853,33.4769		740/907	138266546	4354,8652	2203	4300	6503	SO:0001819	synonymous_variant	1495	exon16			TACATCGGATGTC	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"""catenin (cadherin-associated protein), alpha 1 (102kD)"""			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2220G>A	5.37:g.138266546G>A		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	226	101	0.446903	NM_001903	Q12795|Q8N1C0	Silent	SNP	ENST00000302763.7	37	CCDS34243.1																																																																																			G|0.693;A|0.307	0.307	strong		0.463	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656805	46656805	+	Silent	SNP	G	G	A	rs6519994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	161	0	0		WXS	Illumina HiSeq	Phase_I	169	81	0.47929	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	
BRWD1	54014	hgsc.bcm.edu	37	21	40570830	40570830	+	Missense_Mutation	SNP	G	G	C	rs2234547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:40570830G>C	ENST00000333229.2	-	40	5839	c.5512C>G	c.(5512-5514)Cat>Gat	p.H1838D	BRWD1_ENST00000342449.3_Missense_Mutation_p.H1838D|BRWD1_ENST00000380800.3_Missense_Mutation_p.H1838D	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1838					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)				TCCATTTTATGACATTTCCCA	0.373													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		19409	0.0		0.0	False		,,,				2504	0.0				p.H1838D	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.C5512G						PASS	.	G	ASP/HIS,ASP/HIS	15,4389	22.3+/-47.3	0,15,2187	134.0	133.0	133.0		5512,5512	3.2	0.2	21	dbSNP_98	133	0,8600		0,0,4300	yes	missense,missense	BRWD1	NM_018963.4,NM_033656.3	81,81	0,15,6487	CC,CG,GG		0.0,0.3406,0.1153	benign,benign	1838/2321,1838/2270	40570830	15,12989	2202	4300	6502	SO:0001583	missense	54014	exon40			TTTTATGACATTT	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.5512C>G	21.37:g.40570830G>C	ENSP00000330753:p.His1838Asp	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	172	84	0.488372	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	G	11.80	1.746199	0.30955	0.003406	0.0	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.44083	0.93;0.93;0.93	5.48	3.18	0.36537	.	0.908791	0.09391	N	0.808490	T	0.14098	0.0341	L	0.54323	1.7	0.09310	N	1	B;B	0.26775	0.095;0.159	B;B	0.24155	0.051;0.021	T	0.08534	-1.0717	10	0.35671	T	0.21	-2.3847	4.7666	0.13135	0.1553:0.4107:0.434:0.0	rs2234547;rs2234547	1838;1838	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	D	1838	ENSP00000330753:H1838D;ENSP00000344333:H1838D;ENSP00000370178:H1838D	ENSP00000330753:H1838D	H	-	1	0	BRWD1	39492700	0.000000	0.05858	0.203000	0.23512	0.374000	0.29953	0.674000	0.25218	2.576000	0.86940	0.655000	0.94253	CAT	G|0.997;C|0.003	0.003	strong		0.373	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
LRRN3	54674	hgsc.bcm.edu	37	7	110763563	110763563	+	Silent	SNP	T	T	C	rs214865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:110763563T>C	ENST00000422987.3	+	2	1566	c.735T>C	c.(733-735)gaT>gaC	p.D245D	IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000415362.1_Intron|LRRN3_ENST00000451085.1_Silent_p.D245D|IMMP2L_ENST00000489381.1_Intron|LRRN3_ENST00000308478.5_Silent_p.D245D|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000437687.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	245					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		CTTTTTACGATAACAGGCTTA	0.358													C|||	472	0.0942492	0.3011	0.0418	5008	,	,		18738	0.002		0.0298	False		,,,				2504	0.0133				p.D245D		Atlas-SNP	.											.	LRRN3	132	.	0			c.T735C						PASS	.	C	,,,	1203,3203	693.7+/-405.7	159,885,1159	55.0	59.0	57.0		735,735,735,	3.2	1.0	7	dbSNP_79	57	236,8360	793.0+/-407.5	3,230,4065	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	LRRN3,IMMP2L	NM_001099658.1,NM_001099660.1,NM_018334.4,NM_032549.3	,,,	162,1115,5224	CC,CT,TT		2.7455,27.3037,11.0675	,,,	245/709,245/709,245/709,	110763563	1439,11563	2203	4298	6501	SO:0001819	synonymous_variant	54674	exon2			TTACGATAACAGG	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17200	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 5"""					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.735T>C	7.37:g.110763563T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	144	75	0.520833	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	37	CCDS5754.1																																																																																			T|0.892;C|0.108	0.108	strong		0.358	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334	
FCN2	2220	hgsc.bcm.edu	37	9	137779026	137779026	+	Missense_Mutation	SNP	C	C	T	rs17549193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:137779026C>T	ENST00000291744.6	+	8	717	c.707C>T	c.(706-708)aCg>aTg	p.T236M	FCN2_ENST00000350339.2_Missense_Mutation_p.T198M	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	236	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		T -> M (in dbSNP:rs17549193).		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)		GATTCCCTGACGTTCCACAAC	0.468													C|||	1246	0.248802	0.3646	0.2493	5008	,	,		24104	0.0665		0.2753	False		,,,				2504	0.2526				p.T236M		Atlas-SNP	.											.	FCN2	55	.	0			c.C707T	GRCh37	CM051922	FCN2	M	rs17549193	PASS	.	C	MET/THR,MET/THR	1500,2906	479.0+/-358.4	252,996,955	161.0	141.0	148.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	707,593	2.1	0.0	9	dbSNP_123	148	2495,6105	409.4+/-349.8	363,1769,2168	yes	missense,missense	FCN2	NM_004108.2,NM_015837.2	81,81	615,2765,3123	TT,TC,CC		29.0116,34.0445,30.7166	benign,benign	236/314,198/276	137779026	3995,9011	2203	4300	6503	SO:0001583	missense	2220	exon8			CCCTGACGTTCCA	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.707C>T	9.37:g.137779026C>T	ENSP00000291744:p.Thr236Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	142	98	0.690141	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	528	0.24175824175824176	194	0.3943089430894309	93	0.2569060773480663	29	0.050699300699300696	212	0.2796833773087071	C	9.210	1.030738	0.19512	0.340445	0.290116	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.79247	-1.25;-1.25	4.05	2.06	0.26882	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.557101	0.14767	N	0.299635	T	0.00012	0.0000	M	0.75884	2.315	0.44395	P	0.0026960000000000317	P;P	0.44578	0.838;0.57	B;B	0.30855	0.121;0.1	T	0.11084	-1.0602	9	0.46703	T	0.11	.	6.6263	0.22830	0.1744:0.7225:0.0:0.1031	rs57863140	198;236	Q15485-2;Q15485	.;FCN2_HUMAN	M	198;236	ENSP00000291741:T198M;ENSP00000291744:T236M	ENSP00000291744:T236M	T	+	2	0	FCN2	136918847	0.011000	0.17503	0.023000	0.16930	0.042000	0.13812	0.771000	0.26633	0.628000	0.30357	0.563000	0.77884	ACG	C|0.716;T|0.284	0.284	strong		0.468	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	
ANKRD6	22881	hgsc.bcm.edu	37	6	90338863	90338863	+	Silent	SNP	C	C	T	rs9353687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90338863C>T	ENST00000522441.1	+	15	2159	c.1518C>T	c.(1516-1518)tgC>tgT	p.C506C	ANKRD6_ENST00000369408.5_Silent_p.C471C|ANKRD6_ENST00000447838.2_Silent_p.C506C|ANKRD6_ENST00000520793.1_Silent_p.C447C|ANKRD6_ENST00000339746.4_Silent_p.C506C|LYRM2_ENST00000520441.1_Intron	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	506					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		AAACCTGGTGCATGTTAAAGA	0.378													C|||	841	0.167931	0.1876	0.1398	5008	,	,		18179	0.2222		0.1809	False		,,,				2504	0.092				p.C506C		Atlas-SNP	.											.	ANKRD6	51	.	0			c.C1518T						PASS	.	C	,,,,	705,2943		73,559,1192	82.0	81.0	81.0		1518,1518,1413,1341,1518	4.0	1.0	6	dbSNP_119	81	1461,6697		132,1197,2750	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANKRD6	NM_001242809.1,NM_001242811.1,NM_001242813.1,NM_001242814.1,NM_014942.4	,,,,	205,1756,3942	TT,TC,CC		17.9088,19.3257,18.3466	,,,,	506/728,506/728,471/693,447/664,506/723	90338863	2166,9640	1824	4079	5903	SO:0001819	synonymous_variant	22881	exon15			CTGGTGCATGTTA	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"""Ankyrin repeat domain containing"""	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.1518C>T	6.37:g.90338863C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Silent	SNP	ENST00000522441.1	37	CCDS56441.1	419	0.19184981684981686	99	0.20121951219512196	46	0.1270718232044199	131	0.229020979020979	143	0.18865435356200527	C	9.377	1.071923	0.20147	0.193257	0.179088	ENSG00000135299	ENST00000492158	.	.	.	6.07	3.97	0.46021	.	.	.	.	.	T	0.53222	0.1783	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.56245	-0.8011	3	.	.	.	-6.6477	14.3358	0.66589	0.0:0.8596:0.0:0.1404	rs9353687	.	.	.	Y	80	.	.	H	+	1	0	ANKRD6	90395584	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.526000	0.45607	1.550000	0.49438	0.655000	0.94253	CAT	C|0.815;T|0.185	0.185	strong		0.378	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1		
CYB5R1	51706	hgsc.bcm.edu	37	1	202935911	202935911	+	Missense_Mutation	SNP	T	T	C	rs2232842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:202935911T>C	ENST00000367249.4	-	2	205	c.131A>G	c.(130-132)aAt>aGt	p.N44S	CYB5R1_ENST00000497655.1_5'Flank	NM_016243.2	NP_057327.2	Q9UHQ9	NB5R1_HUMAN	cytochrome b5 reductase 1	44	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.		N -> S (in dbSNP:rs2232842).		sterol biosynthetic process (GO:0016126)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			breast(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(75;0.141)		Flavin adenine dinucleotide(DB03147)	GTACTTTTCATTGGGGTCCAG	0.622													T|||	964	0.192492	0.1392	0.2161	5008	,	,		17434	0.4117		0.0278	False		,,,				2504	0.1912				p.N44S		Atlas-SNP	.											.	CYB5R1	25	.	0			c.A131G						PASS	.	T	SER/ASN	648,3758	274.6+/-272.0	49,550,1604	47.0	48.0	48.0		131	3.4	1.0	1	dbSNP_98	48	237,8363	95.6+/-157.4	3,231,4066	yes	missense	CYB5R1	NM_016243.2	46	52,781,5670	CC,CT,TT		2.7558,14.7072,6.8046	benign	44/306	202935911	885,12121	2203	4300	6503	SO:0001583	missense	51706	exon2			TTTTCATTGGGGT	AF169481	CCDS1431.1	1q32.1	2011-04-08		2005-07-13	ENSG00000159348	ENSG00000159348	1.6.2.2		13397	protein-coding gene	gene with protein product		608341	"""NAD(P)H:quinone oxidoreductase type 3, polypeptide A2"""	NQO3A2		12975309, 10611283	Standard	NM_016243		Approved	humb5R2	uc001gyt.2	Q9UHQ9	OTTHUMG00000041387	ENST00000367249.4:c.131A>G	1.37:g.202935911T>C	ENSP00000356218:p.Asn44Ser	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_016243	A0PK21|B2R8E0|O95329|Q53F73|Q8NCL5|Q9UHJ1	Missense_Mutation	SNP	ENST00000367249.4	37	CCDS1431.1	399	0.18269230769230768	66	0.13414634146341464	61	0.1685082872928177	251	0.4388111888111888	21	0.027704485488126648	T	11.08	1.533635	0.27387	0.147072	0.027558	ENSG00000159348	ENST00000367249	D	0.84370	-1.84	5.69	3.38	0.38709	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);	0.444378	0.24516	N	0.037841	T	0.00012	0.0000	N	0.25245	0.725	0.30890	P	0.730461	B	0.06786	0.001	B	0.04013	0.001	T	0.30446	-0.9978	9	0.21540	T	0.41	2.4602	8.5924	0.33695	0.0:0.1567:0.0:0.8433	rs2232842;rs57624406;rs2232842	44	Q9UHQ9	NB5R1_HUMAN	S	44	ENSP00000356218:N44S	ENSP00000356218:N44S	N	-	2	0	CYB5R1	201202534	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	1.265000	0.33027	0.440000	0.26502	-0.899000	0.02877	AAT	T|0.886;C|0.114	0.114	strong		0.622	CYB5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099155.1	NM_016243	
SLC9A9	285195	hgsc.bcm.edu	37	3	143185920	143185920	+	Silent	SNP	A	A	G	rs61734421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:143185920A>G	ENST00000316549.6	-	12	1636	c.1428T>C	c.(1426-1428)ttT>ttC	p.F476F		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	476					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)			breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						TTCCTCCTCCAAATACCCAGA	0.473													A|||	23	0.00459265	0.0166	0.0014	5008	,	,		19226	0.0		0.0	False		,,,				2504	0.0				p.F476F		Atlas-SNP	.											.	SLC9A9	117	.	0			c.T1428C						PASS	.	A		91,4315	75.2+/-113.4	1,89,2113	141.0	116.0	124.0		1428	-3.0	0.9	3	dbSNP_129	124	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC9A9	NM_173653.3		1,91,6411	GG,GA,AA		0.0233,2.0654,0.7151		476/646	143185920	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	285195	exon12			TCCTCCAAATACC	AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"""Solute carriers"""	20653	protein-coding gene	gene with protein product		608396	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 9"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 9"""			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.1428T>C	3.37:g.143185920A>G		Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	314	151	0.480892	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Silent	SNP	ENST00000316549.6	37	CCDS33872.1																																																																																			A|0.993;G|0.007	0.007	strong		0.473	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653	
OR2A5	393046	hgsc.bcm.edu	37	7	143748364	143748364	+	Silent	SNP	T	T	C	rs4407791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143748364T>C	ENST00000408906.2	+	1	904	c.870T>C	c.(868-870)taT>taC	p.Y290Y		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					CCTTGATCTATAGCCTGAGGA	0.517													.|||	3414	0.681709	0.8911	0.7522	5008	,	,		20215	0.6637		0.502	False		,,,				2504	0.5521				p.Y290Y		Atlas-SNP	.											.	OR2A5	78	.	0			c.T870C						PASS	.	C		3276,640		1372,532,54	108.0	105.0	106.0		870	3.4	1.0	7	dbSNP_111	106	4503,3841		1230,2043,899	no	coding-synonymous	OR2A5	NM_012365.1		2602,2575,953	CC,CT,TT		46.0331,16.3432,36.5498		290/312	143748364	7779,4481	1958	4172	6130	SO:0001819	synonymous_variant	393046	exon1			GATCTATAGCCTG	U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"""GPCR / Class A : Olfactory receptors"""	8232	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 5"""	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.870T>C	7.37:g.143748364T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	144	144	1	NM_012365	B9EGX2|O43885|O43888	Silent	SNP	ENST00000408906.2	37	CCDS43668.1																																																																																			T|0.357;C|0.643	0.643	strong		0.517	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1		
SMYD1	150572	hgsc.bcm.edu	37	2	88396174	88396174	+	Silent	SNP	T	T	C	rs2919881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:88396174T>C	ENST00000419482.2	+	6	844	c.759T>C	c.(757-759)atT>atC	p.I253I	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.I240I	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	253	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						TGTCCTATATTGACTTCCTCA	0.483													C|||	1572	0.313898	0.4244	0.2579	5008	,	,		22653	0.1627		0.3559	False		,,,				2504	0.317				p.I253I		Atlas-SNP	.											.	SMYD1	95	.	0			c.T759C						PASS	.	C		1789,2617	641.1+/-397.4	357,1075,771	111.0	105.0	107.0		759	-3.6	0.9	2	dbSNP_101	107	3139,5461	656.5+/-401.4	570,1999,1731	no	coding-synonymous	SMYD1	NM_198274.3		927,3074,2502	CC,CT,TT		36.5,40.6037,37.8902		253/491	88396174	4928,8078	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon6			CTATATTGACTTC	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.759T>C	2.37:g.88396174T>C		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	158	158	1	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			T|0.654;C|0.346	0.346	strong		0.483	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
OGFR	11054	hgsc.bcm.edu	37	20	61443871	61443871	+	Missense_Mutation	SNP	C	C	T	rs77478162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61443871C>T	ENST00000290291.6	+	7	929	c.904C>T	c.(904-906)Cat>Tat	p.H302Y	OGFR_ENST00000370461.1_Missense_Mutation_p.H250Y	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	302					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CTCTCTGCCCCATCCGCTCGA	0.682													C|||	91	0.0181709	0.0666	0.0043	5008	,	,		13687	0.0		0.0	False		,,,				2504	0.0				p.H302Y		Atlas-SNP	.											.	OGFR	63	.	0			c.C904T						PASS	.	C	TYR/HIS	186,4136		0,186,1975	8.0	8.0	8.0		904	-1.5	0.0	20	dbSNP_131	8	2,8478		0,2,4238	yes	missense	OGFR	NM_007346.2	83	0,188,6213	TT,TC,CC		0.0236,4.3036,1.4685	benign	302/678	61443871	188,12614	2161	4240	6401	SO:0001583	missense	11054	exon7			CTGCCCCATCCGC	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.904C>T	20.37:g.61443871C>T	ENSP00000290291:p.His302Tyr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	8.778	0.927439	0.18056	0.043036	2.36E-4	ENSG00000060491	ENST00000290291;ENST00000370468;ENST00000357163;ENST00000370469;ENST00000370461	T;T;T	0.43688	1.94;0.94;1.52	3.86	-1.55	0.08558	.	4.120900	0.01321	N	0.010938	T	0.02848	0.0085	N	0.22421	0.69	0.09310	N	1	B;B;B	0.24651	0.035;0.006;0.108	B;B;B	0.23018	0.031;0.001;0.043	T	0.06752	-1.0809	10	0.37606	T	0.19	0.1436	0.781	0.01041	0.2558:0.3046:0.1089:0.3306	.	302;285;302	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	Y	302;302;302;157;250	ENSP00000290291:H302Y;ENSP00000359499:H302Y;ENSP00000359491:H250Y	ENSP00000290291:H302Y	H	+	1	0	OGFR	60914316	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.754000	0.04787	-0.100000	0.12241	-0.254000	0.11334	CAT	C|0.984;T|0.016	0.016	strong		0.682	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
DUSP27	92235	hgsc.bcm.edu	37	1	167095765	167095765	+	Missense_Mutation	SNP	G	G	A	rs6668826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167095765G>A	ENST00000361200.2	+	6	1563	c.1397G>A	c.(1396-1398)cGc>cAc	p.R466H	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.R466H|DUSP27_ENST00000271385.5_Missense_Mutation_p.R466H			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	466			R -> H (in dbSNP:rs6668826).		protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GGCAGGAGGCGCCGCGCAGAC	0.657													G|||	1648	0.329073	0.2716	0.2003	5008	,	,		16759	0.7421		0.168	False		,,,				2504	0.2382				p.R466H		Atlas-SNP	.											.	DUSP27	235	.	0			c.G1397A						PASS	.	G	HIS/ARG	1134,3270		156,822,1224	20.0	20.0	20.0		1397	-0.1	0.2	1	dbSNP_116	20	1470,7130		121,1228,2951	yes	missense	DUSP27	NM_001080426.1	29	277,2050,4175	AA,AG,GG		17.093,25.7493,20.0246	benign	466/1159	167095765	2604,10400	2202	4300	6502	SO:0001583	missense	92235	exon5			GGAGGCGCCGCGC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1397G>A	1.37:g.167095765G>A	ENSP00000354483:p.Arg466His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	770	0.3525641025641026	138	0.2804878048780488	74	0.20441988950276244	435	0.7604895104895105	123	0.16226912928759896	G	9.024	0.985628	0.18889	0.257493	0.17093	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03152	4.03;4.03;4.03	5.17	-0.114	0.13564	.	0.885835	0.09670	N	0.771269	T	0.00724	0.0024	N	0.17674	0.51	0.80722	P	0.0	B	0.11235	0.004	B	0.01281	0.0	T	0.46527	-0.9185	9	0.23891	T	0.37	-1.7364	5.0653	0.14578	0.3141:0.1417:0.5442:0.0	rs6668826;rs60156845;rs6668826	466	Q5VZP5	DUS27_HUMAN	H	466	ENSP00000354483:R466H;ENSP00000271385:R466H;ENSP00000404874:R466H	ENSP00000271385:R466H	R	+	2	0	DUSP27	165362389	0.000000	0.05858	0.172000	0.22920	0.278000	0.26855	0.147000	0.16202	-0.028000	0.13850	0.643000	0.83706	CGC	G|0.731;A|0.269	0.269	strong		0.657	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048661	33048661	+	Missense_Mutation	SNP	A	A	G	rs386699871|rs1042151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33048661A>G	ENST00000418931.2	+	2	429	c.313A>G	c.(313-315)Atg>Gtg	p.M105V	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.M105V|HLA-DPA1_ENST00000419277.1_5'Flank	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	105	Beta-1.		M -> I (in allele DPB1*08:02, allele DPB1*09:02, allele DPB1*13:01, allele DPB1*13:02 and allele DPB1*19:01; dbSNP:rs1042153).|M -> V (in allele DPB1*01:01, allele DPB1*03:01, allele DPB1*05:02, allele DPB1*08:01, allele DPB1*09:01, allele DPB1*10:01, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*17:02, allele DPB1*21:02, allele DPB1*22:02, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*29:01, allele DPB1*35:01, allele DPB1*37:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*50:01, allele DPB1*52:01, allele DPB1*54:01, allele DPB1*56:01, allele DPB1*57:01, allele DPB1*65:01, allele DPB1*67:01, allele DPB1*68:01, allele DPB1*70:01, allele DPB1*73:01, allele DPB1*75:01, allele DPB1*76:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*84:01, allele DPB1*88:01, allele DPB1*90:01 and allele DPB1*92:01; dbSNP:rs1042151). {ECO:0000269|PubMed:6330724}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)	p.M105V(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GCCGGACAGGATGTGCAGACA	0.706													.|||	1264	0.252396	0.416	0.2133	5008	,	,		12428	0.1171		0.2068	False		,,,				2504	0.2454				p.M105V		Atlas-SNP	.											HLA-DPB1,NS,lymphoid_neoplasm,0,1	HLA-DPB1	28	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A313G						scavenged	.						29.0	31.0	31.0					6																	33048661		1510	2709	4219	SO:0001583	missense	3115	exon2			GACAGGATGTGCA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.313A>G	6.37:g.33048661A>G	ENSP00000408146:p.Met105Val	Somatic	33	9	0.272727		WXS	Illumina HiSeq	Phase_I	32	19	0.59375	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	505	0.23122710622710624	218	0.44308943089430897	66	0.18232044198895028	72	0.1258741258741259	149	0.19656992084432717	A	0.010	-1.789266	0.00623	.	.	ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835	T;T;T	0.00281	8.32;8.32;8.32	3.49	-6.98	0.01611	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	2.303120	0.02598	N	0.100781	T	0.00012	0.0000	N	0.00016	-2.855	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.40365	-0.9567	9	0.08837	T	0.75	.	3.2203	0.06713	0.5003:0.1109:0.2764:0.1123	rs1042151;rs3173291;rs11551417;rs17221143	71;115;105	A2ALJ6;Q59GY1;P04440	.;.;DPB1_HUMAN	V	105;105;105;82	ENSP00000408146:M105V;ENSP00000439674:M105V;ENSP00000412654:M82V	ENSP00000389210:M105V	M	+	1	0	HLA-DPB1	33156639	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.609000	0.00886	-1.748000	0.01332	-2.039000	0.00418	ATG	A|0.776;G|0.224	0.224	strong		0.706	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
BPIFA2	140683	hgsc.bcm.edu	37	20	31757078	31757078	+	Missense_Mutation	SNP	G	G	A	rs6059139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31757078G>A	ENST00000253362.2	+	2	273	c.127G>A	c.(127-129)Gga>Aga	p.G43R	BPIFA2_ENST00000354932.5_Missense_Mutation_p.G43R			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	43			G -> R (in dbSNP:rs6059139).			extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										TCTTCACGAGGGACTTGAGAC	0.463													G|||	141	0.028155	0.0998	0.0058	5008	,	,		20844	0.0		0.005	False		,,,				2504	0.0				p.G43R		Atlas-SNP	.											.	.	.	.	0			c.G127A						PASS	.	G	ARG/GLY	408,3998	201.8+/-224.7	16,376,1811	145.0	120.0	128.0		127	2.2	0.0	20	dbSNP_114	128	17,8583	12.6+/-44.7	0,17,4283	yes	missense	BPIFA2	NM_080574.2	125	16,393,6094	AA,AG,GG		0.1977,9.2601,3.2677	possibly-damaging	43/250	31757078	425,12581	2203	4300	6503	SO:0001583	missense	140683	exon2			CACGAGGGACTTG	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.127G>A	20.37:g.31757078G>A	ENSP00000253362:p.Gly43Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	95	31	0.326316	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	59	0.027014652014652016	52	0.10569105691056911	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	2.971	-0.212453	0.06140	0.092601	0.001977	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.13089	2.62;2.62	4.16	2.22	0.28083	.	0.708924	0.12096	N	0.499960	T	0.00241	0.0007	L	0.41824	1.3	0.80722	P	0.0	P	0.36010	0.532	B	0.36922	0.236	T	0.20075	-1.0286	9	0.51188	T	0.08	-10.3634	6.3866	0.21563	0.2201:0.0:0.7799:0.0	rs6059139;rs52815538;rs6059139	43	Q96DR5	BPIA2_HUMAN	R	43	ENSP00000253362:G43R;ENSP00000347012:G43R	ENSP00000253362:G43R	G	+	1	0	BPIFA2	31220739	0.001000	0.12720	0.002000	0.10522	0.009000	0.06853	0.736000	0.26130	0.707000	0.31934	0.655000	0.94253	GGA	G|0.962;A|0.038	0.038	strong		0.463	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	
OBSCN	84033	hgsc.bcm.edu	37	1	228476367	228476367	+	Missense_Mutation	SNP	A	A	T	rs386640016|rs3795790	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228476367A>T	ENST00000422127.1	+	38	10161	c.10117A>T	c.(10117-10119)Agc>Tgc	p.S3373C	OBSCN_ENST00000359599.6_Missense_Mutation_p.S2220C|OBSCN_ENST00000284548.11_Missense_Mutation_p.S3373C|OBSCN_ENST00000570156.2_Missense_Mutation_p.S3802C|OBSCN_ENST00000366709.4_Missense_Mutation_p.S492C|OBSCN_ENST00000366707.4_Missense_Mutation_p.S492C	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3373	Ig-like 34.		S -> C (in dbSNP:rs3795790).		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)				ACACCAAGAGAGCATAGAAGG	0.602													A|||	480	0.0958466	0.0514	0.0144	5008	,	,		20986	0.3165		0.0258	False		,,,				2504	0.0583				p.S3802C		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A11404T						PASS	.	A	CYS/SER,CYS/SER	182,3930		8,166,1882	72.0	77.0	75.0		10117,10117	-1.3	0.1	1	dbSNP_107	75	119,8285		0,119,4083	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	112,112	8,285,5965	TT,TA,AA		1.416,4.4261,2.4049	benign,benign	3373/7969,3373/6621	228476367	301,12215	2056	4202	6258	SO:0001583	missense	84033	exon43			CAAGAGAGCATAG	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.10117A>T	1.37:g.228476367A>T	ENSP00000409493:p.Ser3373Cys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	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	208	0.09523809523809523	17	0.034552845528455285	3	0.008287292817679558	167	0.291958041958042	21	0.027704485488126648	A	9.448	1.089846	0.20390	0.044261	0.01416	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23	0.666	-1.33	0.09172	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.536026	0.14449	U	0.318939	T	0.00012	0.0000	N	0.20483	0.58	0.49483	P	2.0699999999995722E-4	P;B	0.52170	0.951;0.002	P;B	0.59115	0.852;0.008	T	0.15009	-1.0452	8	0.34782	T	0.22	.	.	.	.	rs3795790;rs60799870;rs3795790	3373;3373	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	C	3373;3373;492;492;2220	ENSP00000284548:S3373C;ENSP00000409493:S3373C;ENSP00000355668:S492C;ENSP00000355670:S492C;ENSP00000352613:S2220C	ENSP00000284548:S3373C	S	+	1	0	OBSCN	226542990	0.124000	0.22315	0.095000	0.20976	0.198000	0.23893	0.791000	0.26915	-1.387000	0.02095	-0.608000	0.04076	AGC	A|0.887;T|0.113	0.113	strong		0.602	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
TRIM49	57093	hgsc.bcm.edu	37	11	89531780	89531780	+	Missense_Mutation	SNP	G	G	C	rs149578071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:89531780G>C	ENST00000329758.1	-	8	1205	c.877C>G	c.(877-879)Cat>Gat	p.H293D	TRIM49_ENST00000532501.2_Missense_Mutation_p.H216D	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	293	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			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)				GCTTCTTCATGATGCAGAGTA	0.313																																					p.H293D		Atlas-SNP	.											.	TRIM49	45	.	0			c.C877G						PASS	.						27.0	37.0	34.0					11																	89531780		2150	4292	6442	SO:0001583	missense	57093	exon8			CTTCATGATGCAG	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.877C>G	11.37:g.89531780G>C	ENSP00000327604:p.His293Asp	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_020358	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Missense_Mutation	SNP	ENST00000329758.1	37	CCDS8287.1	314	0.14377289377289376	57	0.11585365853658537	86	0.23756906077348067	96	0.16783216783216784	75	0.09894459102902374	G	1.031	-0.681762	0.03353	.	.	ENSG00000168930	ENST00000329758;ENST00000532501	T	0.60672	0.17	0.539	0.539	0.17156	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.14438	0.01	B	0.13407	0.009	T	0.13818	-1.0495	6	.	.	.	.	.	.	.	.	293	P0CI25	TRI49_HUMAN	D	293;216	ENSP00000327604:H293D	.	H	-	1	0	TRIM49	89171428	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.486000	0.02312	0.568000	0.29311	0.194000	0.17425	CAT	G|0.500;C|0.500	0.500	weak		0.313	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358	
CLASP2	23122	hgsc.bcm.edu	37	3	33759474	33759474	+	Silent	SNP	C	C	T	rs112019256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:33759474C>T	ENST00000468888.2	-	1	67	c.21G>A	c.(19-21)gaG>gaA	p.E7E	CLASP2_ENST00000399362.4_Silent_p.E7E|CLASP2_ENST00000359576.5_Silent_p.E7E|CLASP2_ENST00000307312.7_5'UTR			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	0					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						CGCAGAAGTACTCCATGCTGC	0.726													C|||	37	0.00738818	0.025	0.0014	5008	,	,		9762	0.002		0.0	False		,,,				2504	0.001				p.E7E		Atlas-SNP	.											.	CLASP2	138	.	0			c.G21A						PASS	.	C		54,3038		0,54,1492	3.0	4.0	3.0		21	1.0	1.0	3	dbSNP_132	3	2,7002		0,2,3500	no	coding-synonymous	CLASP2	NM_015097.2		0,56,4992	TT,TC,CC		0.0286,1.7464,0.5547		7/1516	33759474	56,10040	1546	3502	5048	SO:0001819	synonymous_variant	23122	exon1			GAAGTACTCCATG	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.21G>A	3.37:g.33759474C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	14	5	0.357143	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37																																																																																				C|0.333;T|0.667	0.667	weak		0.726	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	
SCN4A	6329	hgsc.bcm.edu	37	17	62018737	62018737	+	Silent	SNP	G	G	A	rs59081944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62018737G>A	ENST00000435607.1	-	24	4981	c.4905C>T	c.(4903-4905)atC>atT	p.I1635I	SCN4A_ENST00000578147.1_Silent_p.I1635I	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1635					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)	GGCTGTAGGCGATGAACTGGG	0.567													G|||	92	0.0183706	0.0681	0.0029	5008	,	,		18690	0.0		0.0	False		,,,				2504	0.0				p.I1635I		Atlas-SNP	.											.	SCN4A	205	.	0			c.C4905T						PASS	.	G		190,4046		4,182,1932	52.0	59.0	56.0		4905	-3.4	0.9	17	dbSNP_129	56	1,8481		0,1,4240	no	coding-synonymous	SCN4A	NM_000334.4		4,183,6172	AA,AG,GG		0.0118,4.4854,1.5018		1635/1837	62018737	191,12527	2118	4241	6359	SO:0001819	synonymous_variant	6329	exon24			GTAGGCGATGAAC	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.4905C>T	17.37:g.62018737G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	228	101	0.442982	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			G|0.983;A|0.017	0.017	strong		0.567	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
ZNF684	127396	hgsc.bcm.edu	37	1	41012847	41012847	+	Silent	SNP	A	A	G	rs41268081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:41012847A>G	ENST00000372699.3	+	5	1103	c.852A>G	c.(850-852)tcA>tcG	p.S284S	ZNF684_ENST00000493756.1_3'UTR	NM_152373.3	NP_689586.3	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	284					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(2)|kidney(2)|lung(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			GGTATAGTTCATCCCTTTATA	0.393													A|||	277	0.0553115	0.1498	0.0346	5008	,	,		21003	0.0		0.0447	False		,,,				2504	0.0102				p.S284S		Atlas-SNP	.											.	ZNF684	37	.	0			c.A852G						PASS	.	A		529,3877	242.5+/-252.5	33,463,1707	81.0	86.0	84.0		852	-2.3	1.0	1	dbSNP_127	84	391,8209	126.3+/-184.8	17,357,3926	no	coding-synonymous	ZNF684	NM_152373.3		50,820,5633	GG,GA,AA		4.5465,12.0064,7.0737		284/379	41012847	920,12086	2203	4300	6503	SO:0001819	synonymous_variant	127396	exon5			TAGTTCATCCCTT		CCDS454.1	1p34.2	2013-01-08			ENSG00000117010	ENSG00000117010		"""Zinc fingers, C2H2-type"", ""-"""	28418	protein-coding gene	gene with protein product	"""hypothetical protein MGC27466"""					12477932	Standard	NM_152373		Approved	MGC27466	uc001cft.2	Q5T5D7	OTTHUMG00000007359	ENST00000372699.3:c.852A>G	1.37:g.41012847A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	131	54	0.412214	NM_152373	Q2NKY4	Silent	SNP	ENST00000372699.3	37	CCDS454.1																																																																																			A|0.934;G|0.066	0.066	strong		0.393	ZNF684-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019260.3	NM_152373	
RPUSD3	285367	hgsc.bcm.edu	37	3	9881953	9881953	+	Silent	SNP	C	C	T	rs116550290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9881953C>T	ENST00000383820.5	-	7	640	c.639G>A	c.(637-639)ctG>ctA	p.L213L	RPUSD3_ENST00000485705.1_5'Flank|TTLL3_ENST00000455274.1_Intron|RPUSD3_ENST00000424438.1_Silent_p.L181L|RPUSD3_ENST00000433535.2_Silent_p.L198L	NM_173659.3	NP_775930.2	Q6P087	RUSD3_HUMAN	RNA pseudouridylate synthase domain containing 3	213					pseudouridine synthesis (GO:0001522)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			central_nervous_system(2)|endometrium(3)|lung(2)	7	Medulloblastoma(99;0.227)					TGACACCTTCCAGGATGTCCT	0.577													c|||	100	0.0199681	0.0719	0.0072	5008	,	,		18351	0.0		0.0	False		,,,				2504	0.0				p.L213L		Atlas-SNP	.											.	RPUSD3	19	.	0			c.G639A						PASS	.	C	,	279,4127	154.8+/-188.1	13,253,1937	126.0	120.0	122.0		594,639	0.2	1.0	3	dbSNP_132	122	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	RPUSD3	NM_001142547.1,NM_173659.3	,	13,254,6236	TT,TC,CC		0.0116,6.3323,2.1529	,	198/337,213/352	9881953	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	285367	exon7			ACCTTCCAGGATG	BC032135	CCDS2586.2, CCDS46744.1	3p25.3	2013-02-11			ENSG00000156990	ENSG00000156990		"""RNA pseudouridylate synthase domain containing"""	28437	protein-coding gene	gene with protein product						12477932	Standard	NM_173659		Approved	MGC29784	uc011atk.2	Q6P087	OTTHUMG00000128441	ENST00000383820.5:c.639G>A	3.37:g.9881953C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_173659	B4DS39|Q6P6A9|Q8N1B2|Q8NAV3	Silent	SNP	ENST00000383820.5	37	CCDS2586.2	34	0.015567765567765568	30	0.06097560975609756	4	0.011049723756906077	0	0.0	0	0.0	c	11.95	1.790450	0.31685	0.063323	1.16E-4	ENSG00000156990	ENST00000423108	.	.	.	4.32	0.221	0.15283	.	.	.	.	.	.	.	.	.	.	.	0.22096	N	0.999367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7934	0.29133	0.0:0.6051:0.0:0.3949	.	.	.	.	X	42	.	.	W	-	2	0	RPUSD3	9856953	0.096000	0.21769	0.976000	0.42696	0.910000	0.53928	0.097000	0.15168	0.088000	0.17205	-0.260000	0.10688	TGG	C|0.979;T|0.021	0.021	strong		0.577	RPUSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250238.1	NM_173659	
CEP89	84902	hgsc.bcm.edu	37	19	33450806	33450806	+	Splice_Site	SNP	C	C	T	rs73926195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33450806C>T	ENST00000305768.5	-	3	393	c.305G>A	c.(304-306)cGg>cAg	p.R102Q	CEP89_ENST00000590597.2_Splice_Site_p.R102Q	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	102					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.R102L(1)|p.R102Q(1)		breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						TGGTACCTACCGAGGCCTCAG	0.587													C|||	266	0.053115	0.1921	0.0173	5008	,	,		20668	0.0		0.0	False		,,,				2504	0.0				p.R102Q		Atlas-SNP	.											CEP89,colon,carcinoma,-1,4	CEP89	82	4	2	Substitution - Missense(2)	ovary(1)|prostate(1)	c.G305A						PASS	.	C	GLN/ARG	699,3707	291.5+/-281.6	54,591,1558	94.0	75.0	81.0		305	2.0	0.8	19	dbSNP_130	81	5,8595	3.7+/-12.6	0,5,4295	yes	missense-near-splice	CEP89	NM_032816.3	43	54,596,5853	TT,TC,CC		0.0581,15.8647,5.4129	benign	102/784	33450806	704,12302	2203	4300	6503	SO:0001630	splice_region_variant	84902	exon3			ACCTACCGAGGCC	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.305+1G>A	19.37:g.33450806C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	144	73	0.506944	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	83	0.038003663003663	75	0.1524390243902439	8	0.022099447513812154	0	0.0	0	0.0	C	8.786	0.929433	0.18131	0.158647	5.81E-4	ENSG00000121289	ENST00000305768	T	0.30182	1.54	5.48	2.01	0.26516	.	0.317619	0.28382	N	0.015556	T	0.00039	0.0001	N	0.04203	-0.255	0.31021	P	0.718148	B;B	0.25235	0.017;0.121	B;B	0.14023	0.008;0.01	T	0.33929	-0.9849	8	.	.	.	-1.7133	10.2426	0.43321	0.0:0.7433:0.0:0.2567	.	102;102	Q96ST8-3;Q96ST8	.;CEP89_HUMAN	Q	102	ENSP00000306105:R102Q	.	R	-	2	0	CEP89	38142646	0.975000	0.34042	0.770000	0.31555	0.026000	0.11368	0.915000	0.28638	0.162000	0.19483	0.655000	0.94253	CGG	C|0.944;T|0.056	0.056	strong		0.587	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	Missense_Mutation
SOX30	11063	hgsc.bcm.edu	37	5	157053365	157053365	+	Missense_Mutation	SNP	C	C	T	rs889057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:157053365C>T	ENST00000265007.6	-	5	2586	c.2245G>A	c.(2245-2247)Gtg>Atg	p.V749M	SOX30_ENST00000311371.5_3'UTR|SOX30_ENST00000519442.1_Missense_Mutation_p.V444M	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	749			V -> M (in dbSNP:rs889057).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCCCTGAGCACTTTTTCTTCT	0.373													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17935	0.0		0.0	False		,,,				2504	0.0				p.V749M	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.G2245A						PASS	.	C	,MET/VAL	17,4389	11.4+/-27.6	0,17,2186	57.0	61.0	60.0		,2245	5.4	1.0	5	dbSNP_86	60	0,8600		0,0,4300	yes	utr-3,missense	SOX30	NM_007017.2,NM_178424.1	,21	0,17,6486	TT,TC,CC		0.0,0.3858,0.1307	,probably-damaging	,749/754	157053365	17,12989	2203	4300	6503	SO:0001583	missense	11063	exon5			TGAGCACTTTTTC	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.2245G>A	5.37:g.157053365C>T	ENSP00000265007:p.Val749Met	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	17.31	3.357836	0.61403	0.003858	0.0	ENSG00000039600	ENST00000265007;ENST00000519442	D;D	0.98567	-4.82;-5.0	5.44	5.44	0.79542	.	0.000000	0.52532	D	0.000071	D	0.97676	0.9238	L	0.27053	0.805	0.37021	D	0.89618	D;D	0.76494	0.998;0.999	D;D	0.68765	0.915;0.96	D	0.99894	1.1141	10	0.87932	D	0	.	14.3095	0.66407	0.1478:0.8522:0.0:0.0	rs889057;rs52805214;rs889057	444;749	B4DXW7;O94993	.;SOX30_HUMAN	M	749;444	ENSP00000265007:V749M;ENSP00000427984:V444M	ENSP00000265007:V749M	V	-	1	0	SOX30	156985943	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.502000	0.53332	2.712000	0.92718	0.650000	0.86243	GTG	C|0.998;T|0.002	0.002	strong		0.373	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
FAM65C	140876	hgsc.bcm.edu	37	20	49214156	49214156	+	Missense_Mutation	SNP	A	A	G	rs6020624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:49214156A>G	ENST00000327979.2	-	14	2150	c.1739T>C	c.(1738-1740)cTg>cCg	p.L580P	FAM65C_ENST00000045083.2_Missense_Mutation_p.L580P|FAM65C_ENST00000535356.1_Missense_Mutation_p.L584P			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	580			L -> P (in dbSNP:rs6020624). {ECO:0000269|PubMed:14702039}.							endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CAGCTCATCCAGGGCGAAGTC	0.657													G|||	3497	0.698283	0.7337	0.6758	5008	,	,		15441	0.7034		0.7058	False		,,,				2504	0.6534				p.L580P		Atlas-SNP	.											.	FAM65C	87	.	0			c.T1739C						PASS	.	G	PRO/LEU	3234,1172	394.9+/-329.4	1205,824,174	63.0	53.0	56.0		1739	1.1	0.0	20	dbSNP_114	56	6081,2519	395.7+/-345.2	2140,1801,359	yes	missense	FAM65C	NM_080829.2	98	3345,2625,533	GG,GA,AA		29.2907,26.6001,28.3792	benign	580/947	49214156	9315,3691	2203	4300	6503	SO:0001583	missense	140876	exon14			TCATCCAGGGCGA	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 175"", ""chromosome 20 open reading frame 176"""	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.1739T>C	20.37:g.49214156A>G	ENSP00000332663:p.Leu580Pro	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	137	136	0.992701	NM_080829	Q5QPB6|Q9NQQ2	Missense_Mutation	SNP	ENST00000327979.2	37	CCDS13431.2	1541	0.7055860805860806	370	0.7520325203252033	239	0.6602209944751382	406	0.7097902097902098	526	0.6939313984168866	G	0.642	-0.813151	0.02798	0.733999	0.707093	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	T;T;T	0.13657	2.58;2.58;2.57	4.6	1.11	0.20524	.	0.737333	0.12258	N	0.485006	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12116	-1.0560	9	0.39692	T	0.17	-3.9663	4.9545	0.14033	0.0812:0.2788:0.5047:0.1352	rs6020624;rs8121333;rs17197759;rs57799996;rs6020624	584;580	F5H0X2;Q96MK2	.;FA65C_HUMAN	P	580;580;584	ENSP00000332663:L580P;ENSP00000045083:L580P;ENSP00000439802:L584P	ENSP00000045083:L580P	L	-	2	0	FAM65C	48647563	0.035000	0.19736	0.000000	0.03702	0.013000	0.08279	1.921000	0.40035	0.101000	0.17610	-0.215000	0.12644	CTG	A|0.279;G|0.721	0.721	strong		0.657	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1		
MACF1	23499	hgsc.bcm.edu	37	1	39907949	39907949	+	Missense_Mutation	SNP	A	A	G	rs682351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39907949A>G	ENST00000372915.3	+	75	18689	c.18602A>G	c.(18601-18603)aAa>aGa	p.K6201R	MACF1_ENST00000564288.1_Missense_Mutation_p.K6302R|MACF1_ENST00000361689.2_Missense_Mutation_p.K4243R|MACF1_ENST00000545844.1_Missense_Mutation_p.K4243R|MACF1_ENST00000539005.1_Missense_Mutation_p.K4113R|MACF1_ENST00000317713.7_Missense_Mutation_p.K4243R|MACF1_ENST00000567887.1_Missense_Mutation_p.K6339R|MACF1_ENST00000289893.4_Missense_Mutation_p.K4745R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6201			K -> R (in dbSNP:rs682351).		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)			ACAGAACTCAAACACCTCTGG	0.453													A|||	60	0.0119808	0.0431	0.0043	5008	,	,		19820	0.0		0.0	False		,,,				2504	0.0				p.K4243R		Atlas-SNP	.											.	MACF1	909	.	0			c.A12728G						PASS	.	A	ARG/LYS,ARG/LYS	177,4229	114.6+/-152.6	3,171,2029	54.0	55.0	54.0		14234,12728	6.0	1.0	1	dbSNP_83	54	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	MACF1	NM_033044.3,NM_012090.4	26,26	3,174,6326	GG,GA,AA		0.0349,4.0172,1.384	benign,benign	4745/5939,4243/5431	39907949	180,12826	2203	4300	6503	SO:0001583	missense	23499	exon73			AACTCAAACACCT	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.18602A>G	1.37:g.39907949A>G	ENSP00000362006:p.Lys6201Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	14.28	2.488881	0.44249	0.040172	3.49E-4	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000002	T	0.06781	0.0173	N	0.12637	0.245	0.80722	D	1	B;B	0.31413	0.003;0.322	B;B	0.33454	0.014;0.164	T	0.04128	-1.0975	10	0.38643	T	0.18	.	16.5582	0.84512	1.0:0.0:0.0:0.0	rs682351;rs52811310;rs682351	6201;4243	Q9UPN3;F8W8Q1	MACF1_HUMAN;.	R	4243;6201;4243;4243;4113;4745	ENSP00000439537:K4243R;ENSP00000362006:K6201R;ENSP00000354573:K4243R;ENSP00000313438:K4243R;ENSP00000444364:K4113R;ENSP00000289893:K4745R	ENSP00000289893:K4745R	K	+	2	0	MACF1	39680536	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.094000	0.57721	2.308000	0.77769	0.533000	0.62120	AAA	A|0.986;G|0.014	0.014	strong		0.453	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
FLG	2312	hgsc.bcm.edu	37	1	152284505	152284505	+	Missense_Mutation	SNP	C	C	G	rs201137357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284505C>G	ENST00000368799.1	-	3	2892	c.2857G>C	c.(2857-2859)Gag>Cag	p.E953Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_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						PASS	.	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	483	1	0.00207039		WXS	Illumina HiSeq	Phase_I	701	195	0.278174	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	
PLCE1	51196	hgsc.bcm.edu	37	10	96025697	96025697	+	Silent	SNP	G	G	A	rs41291134	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:96025697G>A	ENST00000371380.3	+	15	4498	c.4263G>A	c.(4261-4263)tcG>tcA	p.S1421S	PLCE1_ENST00000371385.3_Silent_p.S1113S|PLCE1_ENST00000371375.1_Silent_p.S1113S|PLCE1_ENST00000260766.3_Silent_p.S1421S			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1421	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				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)				GAGAATCCTCGGTAGAACTCT	0.433													G|||	327	0.0652955	0.1392	0.036	5008	,	,		16901	0.0327		0.0368	False		,,,				2504	0.0491				p.S1421S		Atlas-SNP	.											PLCE1_ENST00000371375,NS,carcinoma,+1,3	PLCE1	543	3	0			c.G4263A						PASS	.	G	,	426,3338		17,392,1473	89.0	88.0	88.0		3339,4263	-2.6	1.0	10	dbSNP_127	88	182,8042		3,176,3933	no	coding-synonymous,coding-synonymous	PLCE1	NM_001165979.1,NM_016341.3	,	20,568,5406	AA,AG,GG		2.213,11.3177,5.0717	,	1113/1995,1421/2303	96025697	608,11380	1882	4112	5994	SO:0001819	synonymous_variant	51196	exon16			ATCCTCGGTAGAA		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.4263G>A	10.37:g.96025697G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	159	78	0.490566	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	37	CCDS41552.1																																																																																			G|0.957;A|0.043	0.043	strong		0.433	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
GLO1	2739	hgsc.bcm.edu	37	6	38650588	38650588	+	Silent	SNP	T	T	A	rs1130534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:38650588T>A	ENST00000373365.4	-	4	458	c.372A>T	c.(370-372)ggA>ggT	p.G124G	GLO1_ENST00000470973.1_5'UTR	NM_006708.2	NP_006699.2	Q04760	LGUL_HUMAN	glyoxalase I	124					carbohydrate metabolic process (GO:0005975)|glutathione metabolic process (GO:0006749)|methylglyoxal metabolic process (GO:0009438)|negative regulation of apoptotic process (GO:0043066)|osteoclast differentiation (GO:0030316)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lactoylglutathione lyase activity (GO:0004462)|zinc ion binding (GO:0008270)			lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	6					Glutathione(DB00143)|Indomethacin(DB00328)	ACTTACCGAATCCTCGAGGGT	0.348													T|||	1176	0.234824	0.3525	0.1643	5008	,	,		16878	0.2312		0.1272	False		,,,				2504	0.2403				p.G124G		Atlas-SNP	.											.	GLO1	12	.	0			c.A372T						PASS	.	T		1334,3072	446.3+/-348.0	215,904,1084	142.0	119.0	127.0		372	1.9	1.0	6	dbSNP_86	127	1001,7599	215.6+/-254.9	61,879,3360	no	coding-synonymous	GLO1	NM_006708.2		276,1783,4444	AA,AT,TT		11.6395,30.2769,17.9533		124/185	38650588	2335,10671	2203	4300	6503	SO:0001819	synonymous_variant	2739	exon4			ACCGAATCCTCGA	L07837	CCDS4837.1	6p21.3-p21.1	2012-10-02			ENSG00000124767	ENSG00000124767	4.4.1.5		4323	protein-coding gene	gene with protein product	"""glyoxalase domain containing 1"""	138750				8449929, 7684374	Standard	NM_006708		Approved	GLOD1	uc003ooc.3	Q04760	OTTHUMG00000014636	ENST00000373365.4:c.372A>T	6.37:g.38650588T>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_006708	B2R6P7|B4DDV0|P78375|Q59EL0|Q5TZW3|Q96FC0|Q96J41	Silent	SNP	ENST00000373365.4	37	CCDS4837.1																																																																																			T|0.811;A|0.189	0.189	strong		0.348	GLO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040438.2	NM_006708	
GRHL3	57822	hgsc.bcm.edu	37	1	24658063	24658063	+	Missense_Mutation	SNP	C	C	G	rs2486668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24658063C>G	ENST00000350501.5	+	2	292	c.165C>G	c.(163-165)gaC>gaG	p.D55E	GRHL3_ENST00000342072.4_5'UTR|GRHL3_ENST00000361548.4_Missense_Mutation_p.D55E|GRHL3_ENST00000530984.1_3'UTR|GRHL3_ENST00000236255.4_Missense_Mutation_p.D60E|GRHL3_ENST00000356046.2_Missense_Mutation_p.D9E	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	55	Transcription activation.		D -> E (in dbSNP:rs2486668).		central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.D60E(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		GAGATGATGACAGTGTTGCGG	0.498													C|||	894	0.178514	0.2277	0.1311	5008	,	,		21488	0.1944		0.164	False		,,,				2504	0.1442				p.D60E		Atlas-SNP	.											GRHL3,NS,carcinoma,0,1	GRHL3	69	1	1	Substitution - Missense(1)	stomach(1)	c.C180G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	911,3495	350.5+/-310.9	79,753,1371	228.0	184.0	199.0		165,165,180,27	0.3	1.0	1	dbSNP_100	199	1414,7186	272.2+/-289.9	121,1172,3007	yes	missense,missense,missense,missense	GRHL3	NM_198174.2,NM_198173.2,NM_021180.3,NM_001195010.1	45,45,45,45	200,1925,4378	GG,GC,CC		16.4419,20.6764,17.8764	benign,benign,benign,benign	55/627,55/603,60/608,9/557	24658063	2325,10681	2203	4300	6503	SO:0001583	missense	57822	exon2			TGATGACAGTGTT	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"""transcription factor CP2-like 4"""	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.165C>G	1.37:g.24658063C>G	ENSP00000288955:p.Asp55Glu	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	195	195	1	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	
C1orf168	199920	hgsc.bcm.edu	37	1	57257817	57257817	+	Silent	SNP	T	T	C	rs2298130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57257817T>C	ENST00000343433.6	-	2	749	c.669A>G	c.(667-669)aaA>aaG	p.K223K	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	223										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						TTTCCCAGCTTTTTCTGATAT	0.522													C|||	1259	0.251398	0.3601	0.1599	5008	,	,		16319	0.3542		0.1431	False		,,,				2504	0.1748				p.K223K		Atlas-SNP	.											.	C1orf168	102	.	0			c.A669G						PASS	.	C		1414,2990	651.2+/-399.2	224,966,1012	69.0	77.0	74.0		669	2.8	0.0	1	dbSNP_100	74	1191,7409	754.7+/-407.5	105,981,3214	no	coding-synonymous	C1orf168	NM_001004303.4		329,1947,4226	CC,CT,TT		13.8488,32.1072,20.0323		223/729	57257817	2605,10399	2202	4300	6502	SO:0001819	synonymous_variant	199920	exon2			CCAGCTTTTTCTG	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.669A>G	1.37:g.57257817T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	127	64	0.503937	NM_001004303	Q63HM3|Q6ZUY6	Silent	SNP	ENST00000343433.6	37	CCDS30729.1																																																																																			T|0.778;C|0.222	0.222	strong		0.522	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303	
APBA3	9546	hgsc.bcm.edu	37	19	3759802	3759802	+	Missense_Mutation	SNP	C	C	A	rs35932323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3759802C>A	ENST00000316757.3	-	2	661	c.461G>T	c.(460-462)tGg>tTg	p.W154L	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	154			W -> L (in dbSNP:rs35932323).		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)		CCCCTCCACCCATTCTGGGGA	0.637													C|||	145	0.0289537	0.1067	0.0058	5008	,	,		15097	0.0		0.0	False		,,,				2504	0.0				p.W154L		Atlas-SNP	.											.	APBA3	28	.	0			c.G461T						PASS	.	C	LEU/TRP	361,4039		17,327,1856	22.0	26.0	25.0		461	2.4	0.2	19	dbSNP_126	25	4,8580		0,4,4288	yes	missense	APBA3	NM_004886.3	61	17,331,6144	AA,AC,CC		0.0466,8.2045,2.8112	possibly-damaging	154/576	3759802	365,12619	2200	4292	6492	SO:0001583	missense	9546	exon2			TCCACCCATTCTG	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.461G>T	19.37:g.3759802C>A	ENSP00000315136:p.Trp154Leu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	53	0.024267399267399268	50	0.1016260162601626	3	0.008287292817679558	0	0.0	0	0.0	C	8.915	0.959726	0.18507	0.082045	4.66E-4	ENSG00000011132	ENST00000316757	T	0.06849	3.25	4.67	2.42	0.29668	.	0.166985	0.29040	N	0.013333	T	0.00178	0.0005	L	0.27053	0.805	0.22213	N	0.999285	B	0.22003	0.063	B	0.19666	0.026	T	0.45906	-0.9229	10	0.22109	T	0.4	.	6.1778	0.20453	0.1873:0.7142:0.0:0.0985	rs35932323	154	O96018	APBA3_HUMAN	L	154	ENSP00000315136:W154L	ENSP00000315136:W154L	W	-	2	0	APBA3	3710802	0.002000	0.14202	0.211000	0.23655	0.049000	0.14656	0.219000	0.17641	1.041000	0.40125	0.561000	0.74099	TGG	C|0.975;A|0.025	0.025	strong		0.637	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
AJAP1	55966	hgsc.bcm.edu	37	1	4772716	4772716	+	Silent	SNP	C	C	T	rs78250331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:4772716C>T	ENST00000378191.4	+	2	1167	c.786C>T	c.(784-786)aaC>aaT	p.N262N	AJAP1_ENST00000378190.3_Silent_p.N262N	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	262					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)		CCAGCAACAACGGGGAAGTCA	0.602													C|||	299	0.0597045	0.0348	0.0187	5008	,	,		16261	0.1429		0.002	False		,,,				2504	0.0961				p.N262N		Atlas-SNP	.											.	AJAP1	68	.	0			c.C786T						PASS	.	C	,	139,4267	98.5+/-137.1	2,135,2066	71.0	78.0	76.0		786,786	-7.2	0.0	1	dbSNP_131	76	15,8585	10.5+/-38.8	0,15,4285	no	coding-synonymous,coding-synonymous	AJAP1	NM_001042478.1,NM_018836.3	,	2,150,6351	TT,TC,CC		0.1744,3.1548,1.1841	,	262/412,262/412	4772716	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	55966	exon2			CAACAACGGGGAA	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.786C>T	1.37:g.4772716C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_018836	Q9Y229	Silent	SNP	ENST00000378191.4	37	CCDS54.1																																																																																			C|0.978;T|0.022	0.022	strong		0.602	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836	
ABCC11	85320	hgsc.bcm.edu	37	16	48248918	48248918	+	Silent	SNP	T	T	C	rs8047091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48248918T>C	ENST00000394747.1	-	8	1471	c.1122A>G	c.(1120-1122)aaA>aaG	p.K374K	ABCC11_ENST00000537808.1_Silent_p.K374K|ABCC11_ENST00000356608.2_Silent_p.K374K|ABCC11_ENST00000353782.5_Silent_p.K374K|ABCC11_ENST00000394748.1_Silent_p.K374K	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	374	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|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)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	TCTCCAATAGTTTCCTTTCCT	0.463													T|||	851	0.169928	0.3623	0.1455	5008	,	,		19216	0.0446		0.167	False		,,,				2504	0.0593				p.K374K		Atlas-SNP	.											.	ABCC11	177	.	0			c.A1122G						PASS	.	T	,,	1400,3002	461.7+/-353.0	228,944,1029	102.0	98.0	100.0		1122,1122,1122	-1.1	0.0	16	dbSNP_116	100	1337,7263	260.9+/-283.5	112,1113,3075	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	340,2057,4104	CC,CT,TT		15.5465,31.8037,21.0506	,,	374/1383,374/1383,374/1345	48248918	2737,10265	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon8			CAATAGTTTCCTT	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.1122A>G	16.37:g.48248918T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	123	120	0.97561	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			T|0.806;C|0.194	0.194	strong		0.463	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
HRC	3270	hgsc.bcm.edu	37	19	49657754	49657754	+	Silent	SNP	G	G	A	rs567490515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657754G>A	ENST00000252825.4	-	1	927	c.741C>T	c.(739-741)gaC>gaT	p.D247D	HRC_ENST00000595625.1_Silent_p.D247D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	247	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Asp-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		catcatcatcgtcatcttctt	0.507													G|||	238	0.047524	0.053	0.0476	5008	,	,		25432	0.0169		0.0417	False		,,,				2504	0.0777				p.D247D	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.C741T						PASS	.						127.0	92.0	104.0					19																	49657754		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			ATCATCGTCATCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.741C>T	19.37:g.49657754G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	136	6	0.0441176	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			.	.	none		0.507	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
CD180	4064	hgsc.bcm.edu	37	5	66479383	66479383	+	Missense_Mutation	SNP	T	T	C	rs2230523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:66479383T>C	ENST00000256447.4	-	3	1445	c.1288A>G	c.(1288-1290)Acc>Gcc	p.T430A	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	430			T -> A (in dbSNP:rs2230523).		B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		TGTAAGCGGGTAAATGCCAAA	0.458													T|||	93	0.0185703	0.0681	0.0043	5008	,	,		21421	0.0		0.0	False		,,,				2504	0.0				p.T430A		Atlas-SNP	.											CD180,NS,carcinoma,+1,2	CD180	78	2	0			c.A1288G						PASS	.	T	ALA/THR	254,4152	146.1+/-180.8	17,220,1966	175.0	181.0	179.0		1288	4.8	0.6	5	dbSNP_98	179	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CD180	NM_005582.2	58	17,221,6265	CC,CT,TT		0.0116,5.7649,1.9606	probably-damaging	430/662	66479383	255,12751	2203	4300	6503	SO:0001583	missense	4064	exon3			AGCGGGTAAATGC	D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"""CD molecules"""	6726	protein-coding gene	gene with protein product		602226	"""lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD"", ""CD180 antigen"""	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.1288A>G	5.37:g.66479383T>C	ENSP00000256447:p.Thr430Ala	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	146	66	0.452055	NM_005582	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	37	CCDS3992.1	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	T	12.29	1.894010	0.33442	0.057649	1.16E-4	ENSG00000134061	ENST00000256447	T	0.58060	0.36	4.81	4.81	0.61882	.	0.083576	0.50627	D	0.000118	T	0.14270	0.0345	M	0.83223	2.63	0.47441	D	0.99942	D	0.55605	0.972	P	0.46026	0.501	T	0.42599	-0.9442	10	0.33141	T	0.24	.	13.091	0.59167	0.0:0.0:0.0:1.0	rs2230523;rs52799097;rs2230523	430	Q99467	CD180_HUMAN	A	430	ENSP00000256447:T430A	ENSP00000256447:T430A	T	-	1	0	CD180	66515139	0.998000	0.40836	0.627000	0.29227	0.064000	0.16182	2.658000	0.46733	2.020000	0.59435	0.460000	0.39030	ACC	T|0.978;C|0.022	0.022	strong		0.458	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582	
SLC37A2	219855	hgsc.bcm.edu	37	11	124947149	124947149	+	Silent	SNP	G	G	A	rs12276567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124947149G>A	ENST00000403796.2	+	3	466	c.165G>A	c.(163-165)tcG>tcA	p.S55S	SLC37A2_ENST00000298280.5_Silent_p.S55S|SLC37A2_ENST00000407458.1_Silent_p.S55S|SLC37A2_ENST00000308074.4_Silent_p.S55S	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	55					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.S55S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		AGAACTGCTCGGAGCAGATCA	0.542													G|||	1687	0.336861	0.5242	0.2925	5008	,	,		21821	0.1419		0.2634	False		,,,				2504	0.3916				p.S55S	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											SLC37A2_ENST00000403796,NS,adenoma,0,3	SLC37A2	105	3	1	Substitution - coding silent(1)	prostate(1)	c.G165A						PASS	.	G	,	2062,2340	569.4+/-382.6	486,1090,625	186.0	182.0	183.0		165,165	-8.6	0.0	11	dbSNP_120	183	2197,6401	374.0+/-337.2	264,1669,2366	no	coding-synonymous,coding-synonymous	SLC37A2	NM_001145290.1,NM_198277.2	,	750,2759,2991	AA,AG,GG		25.5525,46.8423,32.7615	,	55/502,55/506	124947149	4259,8741	2201	4299	6500	SO:0001819	synonymous_variant	219855	exon3			CTGCTCGGAGCAG	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.165G>A	11.37:g.124947149G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Silent	SNP	ENST00000403796.2	37	CCDS44757.1																																																																																			G|0.679;A|0.321	0.321	strong		0.542	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
MORC1	27136	hgsc.bcm.edu	37	3	108719470	108719470	+	Silent	SNP	C	C	G	rs3762698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108719470C>G	ENST00000483760.1	-	20	2101	c.2058G>C	c.(2056-2058)ctG>ctC	p.L686L	MORC1_ENST00000232603.5_Silent_p.L707L					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						CTACAAAGTTCAGACTCTGCT	0.358													C|||	1038	0.207268	0.2693	0.2003	5008	,	,		18160	0.0278		0.2694	False		,,,				2504	0.2495				p.L707L		Atlas-SNP	.											.	MORC1	211	.	0			c.G2121C						PASS	.	C		1265,3141	432.0+/-343.1	188,889,1126	177.0	173.0	174.0		2121	-2.0	0.0	3	dbSNP_107	174	2422,6176	400.8+/-346.9	354,1714,2231	no	coding-synonymous	MORC1	NM_014429.3		542,2603,3357	GG,GC,CC		28.1693,28.7108,28.3528		707/985	108719470	3687,9317	2203	4299	6502	SO:0001819	synonymous_variant	27136	exon21			AAAGTTCAGACTC	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.2058G>C	3.37:g.108719470C>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_014429		Silent	SNP	ENST00000483760.1	37																																																																																				C|0.734;G|0.266	0.266	strong		0.358	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
CAMKK2	10645	hgsc.bcm.edu	37	12	121712077	121712077	+	Missense_Mutation	SNP	T	T	A	rs3817190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121712077T>A	ENST00000324774.5	-	2	1081	c.253A>T	c.(253-255)Acc>Tcc	p.T85S	CAMKK2_ENST00000404169.3_Missense_Mutation_p.T85S|CAMKK2_ENST00000347034.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000337174.3_Missense_Mutation_p.T85S|CAMKK2_ENST00000402834.4_Missense_Mutation_p.T85S|CAMKK2_ENST00000412367.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000538733.1_Missense_Mutation_p.T85S|CAMKK2_ENST00000446440.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000535524.1_5'UTR|CAMKK2_ENST00000392473.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000392474.2_Missense_Mutation_p.T85S	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	85			T -> S (in dbSNP:rs3817190). {ECO:0000269|PubMed:11395482, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9872452}.		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)					GACCCGGAGGTGTCAAGGGGG	0.692													T|||	2062	0.411741	0.6225	0.3084	5008	,	,		13569	0.2976		0.4076	False		,,,				2504	0.3221				p.T85S		Atlas-SNP	.											CAMKK2_ENST00000392473,NS,carcinoma,0,2	CAMKK2	87	2	0			c.A253T						PASS	.	T	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	2469,1931		700,1069,431	20.0	24.0	23.0		253,253,253,253,253,253,253	-0.6	0.0	12	dbSNP_107	23	3539,5057		752,2035,1511	no	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	58,58,58,58,58,58,58	1452,3104,1942	AA,AT,TT		41.1703,43.8864,46.2296	benign,benign,benign,benign,benign,benign,benign	85/589,85/542,85/499,85/534,85/491,85/546,85/542	121712077	6008,6988	2200	4298	6498	SO:0001583	missense	10645	exon2			CGGAGGTGTCAAG	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.253A>T	12.37:g.121712077T>A	ENSP00000312741:p.Thr85Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	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	936	0.42857142857142855	318	0.6463414634146342	121	0.3342541436464088	186	0.32517482517482516	311	0.4102902374670185	T	0.231	-1.020843	0.02061	0.561136	0.411703	ENSG00000110931	ENST00000392474;ENST00000347034;ENST00000538733;ENST00000337174;ENST00000324774;ENST00000412367;ENST00000404169;ENST00000360452;ENST00000446440;ENST00000392473;ENST00000543477;ENST00000544485	T;T;T;T;T;T;T;T;T;T;T	0.72167	-0.63;-0.6;-0.61;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;2.03;1.56	4.17	-0.591	0.11675	.	1.005170	0.08018	N	0.991504	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0;0.0;0.001	T	0.43734	-0.9373	9	0.10902	T	0.67	-0.6485	2.7347	0.05237	0.3091:0.4379:0.152:0.101	rs3817190;rs17852337;rs3817190	85;85;85;85;85;85;85	Q96RR4-6;Q96RR4-2;Q96RR4-7;Q96RR4-5;Q96RR4-4;Q96RR4;Q96RR4-3	.;.;.;.;.;KKCC2_HUMAN;.	S	85;85;85;85;85;85;85;68;85;85;85;85	ENSP00000376266:T85S;ENSP00000321230:T85S;ENSP00000445944:T85S;ENSP00000336634:T85S;ENSP00000312741:T85S;ENSP00000388368:T85S;ENSP00000384600:T85S;ENSP00000388273:T85S;ENSP00000376265:T85S;ENSP00000444894:T85S;ENSP00000445400:T85S	ENSP00000312741:T85S	T	-	1	0	CAMKK2	120196460	0.000000	0.05858	0.001000	0.08648	0.134000	0.20937	-0.775000	0.04679	0.061000	0.16311	-0.464000	0.05259	ACC	T|0.543;A|0.457	0.457	strong		0.692	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	
KIRREL2	84063	hgsc.bcm.edu	37	19	36351545	36351545	+	Missense_Mutation	SNP	C	C	A	rs73928337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36351545C>A	ENST00000360202.5	+	7	1102	c.904C>A	c.(904-906)Cgc>Agc	p.R302S	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Missense_Mutation_p.R302S|KIRREL2_ENST00000347900.6_Missense_Mutation_p.R252S|KIRREL2_ENST00000262625.7_Missense_Mutation_p.R302S	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	302	Ig-like C2-type 3.				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)			TAGCGCCAACCGCAGTACTGC	0.677													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		16057	0.0		0.0	False		,,,				2504	0.0				p.R302S		Atlas-SNP	.											KIRREL2_ENST00000262625,NS,carcinoma,-1,2	KIRREL2	170	2	0			c.C904A						PASS	.	C	SER/ARG,SER/ARG,SER/ARG	87,4319	72.0+/-110.0	0,87,2116	63.0	69.0	67.0		904,754,904	4.0	1.0	19	dbSNP_130	67	0,8600		0,0,4300	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	110,110,110	0,87,6416	AA,AC,CC		0.0,1.9746,0.6689	probably-damaging,probably-damaging,probably-damaging	302/634,252/584,302/709	36351545	87,12919	2203	4300	6503	SO:0001583	missense	84063	exon7			GCCAACCGCAGTA	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.904C>A	19.37:g.36351545C>A	ENSP00000353331:p.Arg302Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	12	0.005494505494505495	8	0.016260162601626018	4	0.011049723756906077	0	0.0	0	0.0	c	21.8	4.203992	0.79127	0.019746	0.0	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.14766	2.48;2.48;2.48	3.99	3.99	0.46301	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.42053	D	0.000769	T	0.10766	0.0263	N	0.22421	0.69	0.37484	D	0.916104	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.998;0.998	D;D;D;D;D	0.85130	0.993;0.988;0.997;0.994;0.994	T	0.04191	-1.0970	10	0.35671	T	0.21	-18.2581	11.8642	0.52484	0.0:1.0:0.0:0.0	.	302;282;302;252;302	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	S	302;252;302;282	ENSP00000262625:R302S;ENSP00000345067:R252S;ENSP00000353331:R302S	ENSP00000262625:R302S	R	+	1	0	KIRREL2	41043385	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	2.485000	0.45250	2.257000	0.74773	0.444000	0.29173	CGC	C|0.994;A|0.006	0.006	strong		0.677	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
SYVN1	84447	hgsc.bcm.edu	37	11	64898226	64898226	+	Silent	SNP	C	C	T	rs9971407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64898226C>T	ENST00000377190.3	-	11	1105	c.1011G>A	c.(1009-1011)tcG>tcA	p.S337S	SYVN1_ENST00000307289.6_Silent_p.S286S|SYVN1_ENST00000526060.1_Silent_p.S337S|SYVN1_ENST00000294256.8_Silent_p.S337S|SYVN1_ENST00000526121.1_5'UTR	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	337					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)	p.S337S(1)		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						GCGCTGGCAGCGATGCACGAA	0.692													c|||	657	0.13119	0.1051	0.1556	5008	,	,		10257	0.0615		0.2266	False		,,,				2504	0.1227				p.S337S		Atlas-SNP	.											SYVN1,NS,lymphoid_neoplasm,0,1	SYVN1	55	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1011A						PASS	.	C	,	524,3876		36,452,1712	21.0	25.0	24.0		1011,1011	-10.4	0.1	11	dbSNP_119	24	2025,6561		255,1515,2523	no	coding-synonymous,coding-synonymous	SYVN1	NM_032431.2,NM_172230.2	,	291,1967,4235	TT,TC,CC		23.5849,11.9091,19.6288	,	337/617,337/618	64898226	2549,10437	2200	4293	6493	SO:0001819	synonymous_variant	84447	exon11			TGGCAGCGATGCA	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.1011G>A	11.37:g.64898226C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_172230	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Silent	SNP	ENST00000377190.3	37	CCDS31605.1																																																																																			C|0.844;T|0.156	0.156	strong		0.692	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431	
NOTO	344022	hgsc.bcm.edu	37	2	73435601	73435601	+	Silent	SNP	T	T	C	rs17008862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73435601T>C	ENST00000398468.3	+	2	865	c.456T>C	c.(454-456)acT>acC	p.T152T		NM_001134462.1	NP_001127934.1	A8MTQ0	NOTO_HUMAN	notochord homeobox	152					cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|notochord development (GO:0030903)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)	2						TACAGGACACTGAGAGACAGC	0.537													T|||	461	0.0920527	0.1944	0.0259	5008	,	,		20189	0.0149		0.0686	False		,,,				2504	0.1043				p.T152T		Atlas-SNP	.											.	NOTO	20	.	0			c.T456C						PASS	.	T		216,1168		18,180,494	125.0	117.0	120.0		456	-3.5	0.0	2	dbSNP_123	120	211,2971		6,199,1386	no	coding-synonymous	NOTO	NM_001134462.1		24,379,1880	CC,CT,TT		6.631,15.6069,9.3517		152/252	73435601	427,4139	692	1591	2283	SO:0001819	synonymous_variant	344022	exon2			GGACACTGAGAGA		CCDS46335.1	2p13.2	2011-06-20	2007-02-15		ENSG00000214513	ENSG00000214513		"""Homeoboxes / ANTP class : NKL subclass"""	31839	protein-coding gene	gene with protein product			"""notochord homolog (Xenopus laevis)"""			15231714	Standard	NM_001134462		Approved		uc010yrd.2	A8MTQ0	OTTHUMG00000164128	ENST00000398468.3:c.456T>C	2.37:g.73435601T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_001134462	B4DJ59|B7ZAU5	Silent	SNP	ENST00000398468.3	37	CCDS46335.1																																																																																			T|0.920;C|0.080	0.080	strong		0.537	NOTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377385.2	XM_292889	
TNPO2	30000	hgsc.bcm.edu	37	19	12816559	12816559	+	Silent	SNP	G	G	T	rs7248726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12816559G>T	ENST00000592287.1	-	15	1800	c.1692C>A	c.(1690-1692)ccC>ccA	p.P564P	TNPO2_ENST00000588216.1_Silent_p.P564P|TNPO2_ENST00000441499.1_Silent_p.P564P|TNPO2_ENST00000425528.1_Silent_p.P564P|TNPO2_ENST00000356861.5_Silent_p.P564P|SNORD41_ENST00000386967.1_RNA|TNPO2_ENST00000450764.2_Silent_p.P564P	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	564					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GGATCAGTGGGGGCATCAGCT	0.597													G|||	739	0.147564	0.5272	0.0461	5008	,	,		18127	0.0		0.0099	False		,,,				2504	0.0				p.P564P		Atlas-SNP	.											.	TNPO2	108	.	0			c.C1692A						PASS	.	G	,,	1656,2570		326,1004,783	32.0	32.0	32.0		1692,1692,1692	-10.9	0.2	19	dbSNP_116	32	119,8253		2,115,4069	no	coding-synonymous,coding-synonymous,coding-synonymous	TNPO2	NM_001136195.1,NM_001136196.1,NM_013433.4	,,	328,1119,4852	TT,TG,GG		1.4214,39.186,14.0895	,,	564/888,564/898,564/888	12816559	1775,10823	2113	4186	6299	SO:0001819	synonymous_variant	30000	exon15			CAGTGGGGGCATC	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"""Importins"""	19998	protein-coding gene	gene with protein product	"""importin 3"", ""karyopherin beta 2b"""	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.1692C>A	19.37:g.12816559G>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_013433	O14655|Q6IN77	Silent	SNP	ENST00000592287.1	37	CCDS45991.1																																																																																			G|0.849;T|0.151	0.151	strong		0.597	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433	
CLUAP1	23059	hgsc.bcm.edu	37	16	3554799	3554799	+	Silent	SNP	T	T	C	rs34672214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3554799T>C	ENST00000576634.1	+	2	246	c.102T>C	c.(100-102)ctT>ctC	p.L34L	LA16c-306E5.3_ENST00000574423.2_RNA|CLUAP1_ENST00000341633.5_Silent_p.L34L|CLUAP1_ENST00000571025.1_Silent_p.L34L|CLUAP1_ENST00000417763.2_5'UTR	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	34					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						ATTTTGGACTTGTATCTGAAG	0.383													T|||	283	0.0565096	0.115	0.0331	5008	,	,		19316	0.0556		0.0159	False		,,,				2504	0.0368				p.L34L		Atlas-SNP	.											.	CLUAP1	32	.	0			c.T102C						PASS	.	T		427,3967	207.5+/-228.8	19,389,1789	111.0	109.0	110.0		102	3.1	1.0	16	dbSNP_126	110	138,8462	69.0+/-131.5	0,138,4162	no	coding-synonymous	CLUAP1	NM_015041.1		19,527,5951	CC,CT,TT		1.6047,9.7178,4.3482		34/414	3554799	565,12429	2197	4300	6497	SO:0001819	synonymous_variant	23059	exon2			TGGACTTGTATCT	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.102T>C	16.37:g.3554799T>C		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	192	84	0.4375	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	37	CCDS32381.1																																																																																			T|0.955;C|0.045	0.045	strong		0.383	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
SPEM1	374768	hgsc.bcm.edu	37	17	7324588	7324588	+	Silent	SNP	G	G	A	rs78583740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7324588G>A	ENST00000323675.3	+	3	619	c.594G>A	c.(592-594)ctG>ctA	p.L198L	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	198					sperm individualization (GO:0007291)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	12		Prostate(122;0.173)				GGTCCGAGCTGGGCCTAAGGG	0.632													G|||	241	0.048123	0.1762	0.0115	5008	,	,		17257	0.0		0.0	False		,,,				2504	0.0				p.L198L		Atlas-SNP	.											.	SPEM1	41	.	0			c.G594A						PASS	.	G		512,3372		36,440,1466	50.0	55.0	53.0		594	4.8	0.5	17	dbSNP_132	53	3,8221		0,3,4109	no	coding-synonymous	SPEM1	NM_199339.2		36,443,5575	AA,AG,GG		0.0365,13.1823,4.2534		198/310	7324588	515,11593	1942	4112	6054	SO:0001819	synonymous_variant	374768	exon3			CGAGCTGGGCCTA	AK097400	CCDS42254.1	17p13.1	2011-12-12	2008-02-04	2008-02-04	ENSG00000181323	ENSG00000181323			32429	protein-coding gene	gene with protein product		615116	"""chromosome 17 open reading frame 83"""	C17orf83		17426145, 20558241, 21184802	Standard	NM_199339		Approved	FLJ40081	uc002ggv.3	Q8N4L4		ENST00000323675.3:c.594G>A	17.37:g.7324588G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_199339		Silent	SNP	ENST00000323675.3	37	CCDS42254.1																																																																																			G|0.961;A|0.039	0.039	strong		0.632	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339	
TIPIN	54962	hgsc.bcm.edu	37	15	66641732	66641732	+	Missense_Mutation	SNP	G	G	C	rs2063690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:66641732G>C	ENST00000261881.4	-	5	417	c.332C>G	c.(331-333)gCa>gGa	p.A111G	SCARNA14_ENST00000516903.1_RNA|TIPIN_ENST00000367709.4_Missense_Mutation_p.A10G|Y_RNA_ENST00000411339.1_RNA	NM_017858.2	NP_060328	Q9BVW5	TIPIN_HUMAN	TIMELESS interacting protein	111	Interaction with TIMELESS.		A -> G (in dbSNP:rs2063690). {ECO:0000269|Ref.2}.		cell cycle phase transition (GO:0044770)|DNA replication checkpoint (GO:0000076)|intra-S DNA damage checkpoint (GO:0031573)|mitotic nuclear division (GO:0007067)|positive regulation of cell proliferation (GO:0008284)|regulation of nuclear cell cycle DNA replication (GO:0033262)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)				autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	7						TAGCCTATGTGCCCAGTGCTC	0.408													G|||	701	0.139976	0.0666	0.1297	5008	,	,		17463	0.3214		0.0855	False		,,,				2504	0.1155				p.A111G		Atlas-SNP	.											.	TIPIN	23	.	0			c.C332G						PASS	.	G	GLY/ALA	330,4072	171.9+/-202.1	9,312,1880	120.0	116.0	117.0		332	5.5	1.0	15	dbSNP_94	117	739,7859	176.8+/-226.5	28,683,3588	yes	missense	TIPIN	NM_017858.2	60	37,995,5468	CC,CG,GG		8.595,7.4966,8.2231	probably-damaging	111/302	66641732	1069,11931	2201	4299	6500	SO:0001583	missense	54962	exon5			CTATGTGCCCAGT	BK001386	CCDS10215.1	15q22.31	2012-03-02	2006-08-08		ENSG00000075131	ENSG00000075131			30750	protein-coding gene	gene with protein product	"""CSM3 homolog (S. cerevisiae)"""	610716				12875843, 17102137	Standard	NM_017858		Approved	FLJ20516	uc002apr.2	Q9BVW5	OTTHUMG00000133188	ENST00000261881.4:c.332C>G	15.37:g.66641732G>C	ENSP00000261881:p.Ala111Gly	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_017858	B2CW64|Q9NWZ6	Missense_Mutation	SNP	ENST00000261881.4	37	CCDS10215.1	362	0.16575091575091574	38	0.07723577235772358	37	0.10220994475138122	223	0.38986013986013984	64	0.08443271767810026	G	16.01	3.002140	0.54254	0.074966	0.08595	ENSG00000075131	ENST00000367709;ENST00000261881	T;T	0.49720	0.77;0.77	5.54	5.54	0.83059	Replication fork protection component Swi3 (2);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.37697	1.125	0.09310	P	0.9999999875026	P	0.37663	0.604	B	0.38954	0.286	T	0.42396	-0.9454	9	0.41790	T	0.15	-20.1045	18.0484	0.89340	0.0:0.0:1.0:0.0	rs2063690;rs17686704;rs2063690	111	Q9BVW5	TIPIN_HUMAN	G	10;111	ENSP00000356682:A10G;ENSP00000261881:A111G	ENSP00000261881:A111G	A	-	2	0	TIPIN	64428786	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.354000	0.97083	2.610000	0.88304	0.555000	0.69702	GCA	G|0.877;C|0.123	0.123	strong		0.408	TIPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256897.2	NM_017858	
ITGB3	3690	hgsc.bcm.edu	37	17	45368337	45368337	+	Silent	SNP	A	A	C	rs15908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45368337A>C	ENST00000559488.1	+	9	1159	c.1143A>C	c.(1141-1143)gtA>gtC	p.V381V	ITGB3_ENST00000560629.1_Silent_p.R370R|ITGB3_ENST00000435993.2_Silent_p.V334V|ITGB3_ENST00000571680.1_Silent_p.V381V	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	381					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)	GTTCTAAAGTAGAGCTGGAAG	0.488													C|||	2159	0.43111	0.4115	0.3602	5008	,	,		21527	0.5476		0.3678	False		,,,				2504	0.453				p.V381V		Atlas-SNP	.											.	ITGB3	157	.	0			c.A1143C						PASS	.	C		1856,2550	634.1+/-396.1	387,1082,734	138.0	124.0	128.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1143	-11.0	0.1	17	dbSNP_52	128	3152,5448	655.4+/-401.3	557,2038,1705	no	coding-synonymous	ITGB3	NM_000212.2		944,3120,2439	CC,CA,AA		36.6512,42.1244,38.5053		381/789	45368337	5008,7998	2203	4300	6503	SO:0001819	synonymous_variant	3690	exon9			TAAAGTAGAGCTG		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.1143A>C	17.37:g.45368337A>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	37	CCDS11511.1																																																																																			A|0.586;C|0.414	0.414	strong		0.488	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
SRP72	6731	hgsc.bcm.edu	37	4	57361553	57361553	+	Silent	SNP	A	A	G	rs34419325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57361553A>G	ENST00000342756.5	+	17	2392	c.1671A>G	c.(1669-1671)aaA>aaG	p.K557K	SRP72_ENST00000510663.1_Silent_p.K496K	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	557	Poly-Lys.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					AGAAAAAGAAAAAGAAGGGTA	0.269													A|||	583	0.116414	0.0598	0.0576	5008	,	,		15029	0.251		0.0954	False		,,,				2504	0.1176				p.K557K		Atlas-SNP	.											.	SRP72	59	.	0			c.A1671G						PASS	.	A		234,4076		6,222,1927	25.0	26.0	25.0		1671	4.7	1.0	4	dbSNP_126	25	597,7929		27,543,3693	no	coding-synonymous	SRP72	NM_006947.3		33,765,5620	GG,GA,AA		7.0021,5.4292,6.474		557/672	57361553	831,12005	2155	4263	6418	SO:0001819	synonymous_variant	6731	exon17			AAAGAAAAAGAAG	AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"""Tetratricopeptide (TTC) repeat domain containing"""	11303	protein-coding gene	gene with protein product		602122	"""signal recognition particle 72kD"""			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.1671A>G	4.37:g.57361553A>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	215	121	0.562791	NM_006947	G5E9Z8|Q7Z3C0	Silent	SNP	ENST00000342756.5	37	CCDS3506.1																																																																																			A|0.915;G|0.085	0.085	strong		0.269	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7		
HLA-C	3107	hgsc.bcm.edu	37	6	31239116	31239116	+	Missense_Mutation	SNP	G	G	A	rs1131119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	64	3	0.046875		WXS	Illumina HiSeq	Phase_I	104	35	0.336538	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	
DUSP27	92235	hgsc.bcm.edu	37	1	167096770	167096770	+	Missense_Mutation	SNP	G	G	C	rs371850525		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167096770G>C	ENST00000361200.2	+	6	2568	c.2402G>C	c.(2401-2403)tGc>tCc	p.C801S	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.C801S|DUSP27_ENST00000271385.5_Missense_Mutation_p.C801S			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	801					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GTGCTGTCCTGCAACACCACA	0.567																																					p.C801S		Atlas-SNP	.											.	DUSP27	235	.	0			c.G2402C						PASS	.	G	SER/CYS	1,4405	2.1+/-5.4	0,1,2202	83.0	74.0	77.0		2402	3.2	0.9	1		77	0,8600		0,0,4300	no	missense	DUSP27	NM_001080426.1	112	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	benign	801/1159	167096770	1,13005	2203	4300	6503	SO:0001583	missense	92235	exon5			TGTCCTGCAACAC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2402G>C	1.37:g.167096770G>C	ENSP00000354483:p.Cys801Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.752901	0.00085	2.27E-4	0.0	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03035	4.07;4.07;4.07	5.17	3.24	0.37175	.	1.061880	0.07353	N	0.882768	T	0.00412	0.0013	N	0.01352	-0.895	0.18873	N	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.33033	-0.9884	10	0.05721	T	0.95	-3.5335	9.1613	0.37023	0.1176:0.3669:0.5156:0.0	.	801	Q5VZP5	DUS27_HUMAN	S	801	ENSP00000354483:C801S;ENSP00000271385:C801S;ENSP00000404874:C801S	ENSP00000271385:C801S	C	+	2	0	DUSP27	165363394	0.260000	0.24053	0.904000	0.35570	0.039000	0.13416	0.246000	0.18160	1.143000	0.42306	-0.371000	0.07208	TGC	.	.	none		0.567	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
GGTLC2	91227	hgsc.bcm.edu	37	22	22989237	22989237	+	Missense_Mutation	SNP	G	G	A	rs60008056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:22989237G>A	ENST00000480559.1	+	2	190	c.190G>A	c.(190-192)Gtc>Atc	p.V64I	GGTLC2_ENST00000448514.1_Missense_Mutation_p.V64I|POM121L1P_ENST00000402027.1_RNA	NM_199127.2	NP_954578.2	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase light chain 2	64					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)	gamma-glutamyltransferase activity (GO:0003840)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)		TGGCTCCAAGGTCCGCTCCCC	0.582													.|||	207	0.0413339	0.1369	0.0173	5008	,	,		9662	0.0		0.0119	False		,,,				2504	0.002				p.V64I		Atlas-SNP	.											.	GGTLC2	20	.	0			c.G190A						PASS	.	G	ILE/VAL	562,3844	247.5+/-255.7	40,482,1681	53.0	57.0	56.0		190		0.0	22	dbSNP_129	56	84,8510	47.6+/-106.9	1,82,4214	no	missense	GGTLC2	NM_199127.2	29	41,564,5895	AA,AG,GG		0.9774,12.7553,4.9692	possibly-damaging	64/219	22989237	646,12354	2203	4297	6500	SO:0001583	missense	91227	exon2			TCCAAGGTCCGCT	X98922	CCDS13802.2	22q11.21	2008-03-25	2008-03-10	2008-03-10	ENSG00000100121	ENSG00000100121		"""Gamma-glutamyltransferases"""	18596	protein-coding gene	gene with protein product		612339	"""gamma-glutamyltransferase-like 4"""	GGTL4		9074928, 18357469	Standard	NM_199127		Approved		uc010gtt.2	Q14390	OTTHUMG00000151177	ENST00000480559.1:c.190G>A	22.37:g.22989237G>A	ENSP00000419751:p.Val64Ile	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	262	122	0.465649	NM_199127	A1A516|A2VCM9|Q5NV76|Q6ISH0	Missense_Mutation	SNP	ENST00000480559.1	37	CCDS13802.2	101	0.04624542124542125	84	0.17073170731707318	6	0.016574585635359115	0	0.0	11	0.014511873350923483	g	8.048	0.765267	0.15914	0.127553	0.009774	ENSG00000100121	ENST00000480559;ENST00000448514	T;T	0.08282	3.11;3.11	.	.	.	.	0.210063	0.39615	N	0.001304	T	0.00039	0.0001	L	0.39326	1.205	0.31416	P	0.6748419999999999	B;B	0.27700	0.045;0.186	B;B	0.39935	0.104;0.314	T	0.41945	-0.9480	8	0.23891	T	0.37	-50.9151	5.8178	0.18506	0.001:0.0:0.999:0.0	rs60008056	64;64	Q14390;B7WND7	GGTL2_HUMAN;.	I	64	ENSP00000419751:V64I;ENSP00000415676:V64I	ENSP00000415676:V64I	V	+	1	0	GGTLC2	21319237	0.995000	0.38212	0.000000	0.03702	0.000000	0.00434	3.240000	0.51368	-0.000000	0.14550	0.000000	0.15137	GTC	G|0.952;A|0.048	0.048	strong		0.582	GGTLC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321662.1	NM_199127	
RUFY1	80230	hgsc.bcm.edu	37	5	179020622	179020622	+	Silent	SNP	T	T	C	rs4701135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179020622T>C	ENST00000319449.4	+	11	1401	c.1389T>C	c.(1387-1389)aaT>aaC	p.N463N	RUFY1_ENST00000437570.2_Silent_p.N355N|RP11-1379J22.2_ENST00000500262.1_RNA|RUFY1_ENST00000393438.2_Silent_p.N355N|RUFY1_ENST00000377001.2_3'UTR	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	463					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)			AAGCGATTAATTTACAGATGT	0.468										HNSCC(44;0.11)			T|||	369	0.0736821	0.0431	0.0793	5008	,	,		19915	0.0853		0.1054	False		,,,				2504	0.0665				p.N463N		Atlas-SNP	.											.	RUFY1	101	.	0			c.T1389C						PASS	.	T	,,	222,4184	133.7+/-170.0	7,208,1988	95.0	100.0	98.0		1065,1065,1389	-2.8	0.2	5	dbSNP_111	98	958,7642	208.3+/-249.8	60,838,3402	no	coding-synonymous,coding-synonymous,coding-synonymous	RUFY1	NM_001040451.1,NM_001040452.1,NM_025158.3	,,	67,1046,5390	CC,CT,TT		11.1395,5.0386,9.0727	,,	355/601,355/601,463/709	179020622	1180,11826	2203	4300	6503	SO:0001819	synonymous_variant	80230	exon11			GATTAATTTACAG	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.1389T>C	5.37:g.179020622T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	139	67	0.482014	NM_025158	Q59FF3|Q71S93|Q9H6I3	Silent	SNP	ENST00000319449.4	37	CCDS4445.2	176|176	0.08058608058608059|0.08058608058608059	24|24	0.04878048780487805|0.04878048780487805	30|30	0.08287292817679558|0.08287292817679558	47|47	0.08216783216783216|0.08216783216783216	75|75	0.09894459102902374|0.09894459102902374	T|T	0.692|0.692	-0.794213|-0.794213	0.02862|0.02862	0.050386|0.050386	0.111395|0.111395	ENSG00000176783|ENSG00000176783	ENST00000502434|ENST00000508609	.|.	.|.	.|.	5.1|5.1	-2.79|-2.79	0.05841|0.05841	.|.	.|.	.|.	.|.	.|.	T|T	0.01387|0.01387	0.0045|0.0045	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999357027|0.9999999999357027	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.41787|0.41787	-0.9489|-0.9489	3|3	.|.	.|.	.|.	-12.0535|-12.0535	13.6985|13.6985	0.62593|0.62593	0.0:0.6314:0.0:0.3686|0.0:0.6314:0.0:0.3686	rs4701135;rs4701135|rs4701135;rs4701135	.|.	.|.	.|.	L|T	141|252	.|.	.|.	F|I	+|+	1|2	0|0	RUFY1|RUFY1	178953228|178953228	0.004000|0.004000	0.15560|0.15560	0.243000|0.243000	0.24186|0.24186	0.022000|0.022000	0.10575|0.10575	-0.566000|-0.566000	0.05922|0.05922	-0.427000|-0.427000	0.07350|0.07350	0.459000|0.459000	0.35465|0.35465	TTT|ATT	T|0.912;C|0.088	0.088	strong		0.468	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451	
ULK4	54986	hgsc.bcm.edu	37	3	41831203	41831203	+	Missense_Mutation	SNP	C	C	T	rs17215589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:41831203C>T	ENST00000301831.4	-	21	2605	c.2143G>A	c.(2143-2145)Gct>Act	p.A715T		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	715			A -> T (in dbSNP:rs17215589).		cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		AACATGGCAGCGAATAAGGTC	0.393													T|||	408	0.0814696	0.0552	0.0879	5008	,	,		19692	0.002		0.166	False		,,,				2504	0.1074				p.A715T		Atlas-SNP	.											.	ULK4	150	.	0			c.G2143A						PASS	.	T	THR/ALA	254,3610		9,236,1687	112.0	109.0	110.0		2143	2.3	0.0	3	dbSNP_123	110	1240,7006		90,1060,2973	yes	missense	ULK4	NM_017886.2	58	99,1296,4660	TT,TC,CC		15.0376,6.5735,12.3369	benign	715/1276	41831203	1494,10616	1932	4123	6055	SO:0001583	missense	54986	exon21			TGGCAGCGAATAA	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2143G>A	3.37:g.41831203C>T	ENSP00000301831:p.Ala715Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	194	0.08882783882783883	29	0.05894308943089431	30	0.08287292817679558	2	0.0034965034965034965	133	0.17546174142480211	T	2.507	-0.313897	0.05422	0.065735	0.150376	ENSG00000168038	ENST00000301831	T	0.66099	-0.19	5.91	2.31	0.28768	Armadillo-like helical (1);Armadillo-type fold (2);	0.222920	0.38272	N	0.001755	T	0.00039	0.0001	N	0.02802	-0.49	0.09310	P	0.999999898638	B	0.06786	0.001	B	0.06405	0.002	T	0.12066	-1.0562	9	0.02654	T	1	.	4.5461	0.12081	0.2099:0.287:0.0:0.5031	rs17215589;rs17215589	715	Q96C45	ULK4_HUMAN	T	715	ENSP00000301831:A715T	ENSP00000301831:A715T	A	-	1	0	ULK4	41806207	0.719000	0.27986	0.028000	0.17463	0.890000	0.51754	-0.189000	0.09629	-0.047000	0.13423	-0.254000	0.11334	GCT	C|0.898;T|0.102	0.102	strong		0.393	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
PIK3CD	5293	hgsc.bcm.edu	37	1	9784423	9784423	+	Silent	SNP	C	C	T	rs11121484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	140	0	0		WXS	Illumina HiSeq	Phase_I	143	73	0.51049	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	
LEPR	3953	hgsc.bcm.edu	37	1	66075952	66075952	+	Missense_Mutation	SNP	G	G	C	rs1805094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:66075952G>C	ENST00000349533.6	+	14	2153	c.1968G>C	c.(1966-1968)aaG>aaC	p.K656N	LEPR_ENST00000406510.3_Intron|LEPR_ENST00000371058.1_Missense_Mutation_p.K656N|LEPR_ENST00000371060.3_Missense_Mutation_p.K656N|LEPR_ENST00000371059.3_Missense_Mutation_p.K656N|LEPR_ENST00000344610.8_Missense_Mutation_p.K656N	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		CTATGAAAAAGGAGAAAAATG	0.269													G|||	713	0.142372	0.1997	0.1888	5008	,	,		18092	0.0585		0.1511	False		,,,				2504	0.1094				p.K656N		Atlas-SNP	.											.	LEPR	284	.	0			c.G1968C	GRCh37	CM025915	LEPR	M	rs8179183	PASS	.	G	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	828,3574	303.5+/-288.0	71,686,1444	53.0	55.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1968,1968,1968,1968,1968,1968	-2.9	0.0	1	dbSNP_117	54	1467,7121	271.3+/-289.5	134,1199,2961	yes	missense,missense,missense,missense,missense,missense	LEPR	NM_001003679.3,NM_001003680.3,NM_001198687.1,NM_001198688.1,NM_001198689.1,NM_002303.5	94,94,94,94,94,94	205,1885,4405	CC,CG,GG		17.082,18.8096,17.6674	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	656/897,656/959,656/959,656/907,656/897,656/1166	66075952	2295,10695	2201	4294	6495	SO:0001583	missense	3953	exon14			GAAAAAGGAGAAA	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.1968G>C	1.37:g.66075952G>C	ENSP00000330393:p.Lys656Asn	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	154	64	0.415584	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	317	0.14514652014652016	87	0.17682926829268292	68	0.1878453038674033	38	0.06643356643356643	124	0.16358839050131926	G	8.525	0.869742	0.17322	0.188096	0.17082	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.57273	0.43;0.42;0.43;0.41;0.43	5.33	-2.91	0.05631	Fibronectin, type III (2);	0.254500	0.43260	D	0.000596	T	0.27313	0.0670	L	0.47190	1.495	0.25609	P	0.9865115	P;P;P	0.51351	0.696;0.798;0.944	B;B;P	0.48552	0.232;0.409;0.581	T	0.28427	-1.0044	9	0.23891	T	0.37	-8.3309	9.1333	0.36859	0.3785:0.0:0.5107:0.1108	rs8179183;rs17127774;rs52811589;rs8179183	656;656;656	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	N	656	ENSP00000340884:K656N;ENSP00000330393:K656N;ENSP00000360099:K656N;ENSP00000360098:K656N;ENSP00000360097:K656N	ENSP00000340884:K656N	K	+	3	2	LEPR	65848540	0.102000	0.21896	0.045000	0.18777	0.677000	0.39632	-0.497000	0.06428	-0.833000	0.04245	-1.000000	0.02509	AAG	G|0.841;C|0.159	0.159	strong		0.269	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
SEC14L5	9717	hgsc.bcm.edu	37	16	5061191	5061191	+	Silent	SNP	C	C	T	rs8055468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5061191C>T	ENST00000251170.7	+	15	2076	c.1896C>T	c.(1894-1896)gaC>gaT	p.D632D	RP11-165E7.1_ENST00000588778.1_RNA	NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	632	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						CGGGTGTGGACGATGTCCTGA	0.652													C|||	159	0.0317492	0.1135	0.0115	5008	,	,		16324	0.001		0.0	False		,,,				2504	0.0				p.D632D		Atlas-SNP	.											.	SEC14L5	79	.	0			c.C1896T						PASS	.	C		368,3642		19,330,1656	25.0	29.0	28.0		1896	-5.6	0.0	16	dbSNP_116	28	7,8319		0,7,4156	no	coding-synonymous	SEC14L5	NM_014692.1		19,337,5812	TT,TC,CC		0.0841,9.1771,3.0399		632/697	5061191	375,11961	2005	4163	6168	SO:0001819	synonymous_variant	9717	exon15			TGTGGACGATGTC	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.1896C>T	16.37:g.5061191C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	146	69	0.472603	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			C|0.968;T|0.032	0.032	strong		0.652	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
WWP2	11060	hgsc.bcm.edu	37	16	69973825	69973825	+	Silent	SNP	G	G	A	rs3748389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69973825G>A	ENST00000359154.2	+	24	2696	c.2595G>A	c.(2593-2595)gaG>gaA	p.E865E	WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000568684.1_Silent_p.E426E|WWP2_ENST00000448661.1_Silent_p.E865E|WWP2_ENST00000356003.2_Silent_p.E865E|WWP2_ENST00000542271.1_Silent_p.E749E	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	865	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|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 transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						AGGAGACCGAGGGCTTTGGAC	0.612													G|||	2646	0.528355	0.3994	0.3862	5008	,	,		17241	0.8819		0.3449	False		,,,				2504	0.6278				p.E865E		Atlas-SNP	.											WWP2,NS,carcinoma,0,1	WWP2	88	1	0			c.G2595A						PASS	.	G	,	1633,2763	497.4+/-363.8	305,1023,870	84.0	63.0	70.0		2595,1278	3.4	1.0	16	dbSNP_107	70	3045,5555	462.0+/-365.6	554,1937,1809	no	coding-synonymous,coding-synonymous	WWP2	NM_007014.3,NM_199424.1	,	859,2960,2679	AA,AG,GG		35.407,37.1474,35.9957	,	865/871,426/432	69973825	4678,8318	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon24			GACCGAGGGCTTT	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.2595G>A	16.37:g.69973825G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			G|0.572;A|0.428	0.428	strong		0.612	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
MYOM1	8736	hgsc.bcm.edu	37	18	3126811	3126811	+	Missense_Mutation	SNP	A	A	G	rs1071600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3126811A>G	ENST00000356443.4	-	19	3212	c.2879T>C	c.(2878-2880)aTt>aCt	p.I960T	MYOM1_ENST00000582016.1_5'UTR|MYOM1_ENST00000261606.7_Missense_Mutation_p.I864T|MYOM1_ENST00000400569.3_Missense_Mutation_p.I960T	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	960	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> T (in dbSNP:rs1071600). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7505783, ECO:0000269|Ref.1}.		muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.I960T(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TGCCCCTCCAATCTTATCTGG	0.453													A|||	1274	0.254393	0.3177	0.1988	5008	,	,		20132	0.3204		0.1571	False		,,,				2504	0.2403				p.I960T		Atlas-SNP	.											MYOM1,NS,carcinoma,0,1	MYOM1	192	1	1	Substitution - Missense(1)	stomach(1)	c.T2879C						PASS	.	A	THR/ILE,THR/ILE	1017,2887		125,767,1060	98.0	89.0	92.0		2879,2591	1.4	1.0	18	dbSNP_86	92	1175,7127		78,1019,3054	yes	missense,missense	MYOM1	NM_003803.3,NM_019856.1	89,89	203,1786,4114	GG,GA,AA		14.1532,26.0502,17.9584	benign,benign	960/1686,864/1590	3126811	2192,10014	1952	4151	6103	SO:0001583	missense	8736	exon19			CCTCCAATCTTAT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2879T>C	18.37:g.3126811A>G	ENSP00000348821:p.Ile960Thr	Somatic	339	0	0		WXS	Illumina HiSeq	Phase_I	364	165	0.453297	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	562	0.2573260073260073	169	0.3434959349593496	65	0.17955801104972377	207	0.3618881118881119	121	0.15963060686015831	A	0.202	-1.044108	0.01997	0.260502	0.141532	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.54479	0.57;0.57;0.57	5.46	1.43	0.22495	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.317474	0.37857	N	0.001914	T	0.00012	0.0000	N	0.01086	-1.025	0.51767	P	6.700000000003925E-5	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.41858	-0.9485	9	0.12103	T	0.63	.	7.3969	0.26942	0.1872:0.3443:0.4685:0.0	rs1071600;rs52834060;rs60947648;rs1071600	864;960	P52179-2;P52179	.;MYOM1_HUMAN	T	960;960;864	ENSP00000348821:I960T;ENSP00000383413:I960T;ENSP00000261606:I864T	ENSP00000261606:I864T	I	-	2	0	MYOM1	3116811	0.006000	0.16342	0.972000	0.41901	0.926000	0.56050	0.450000	0.21762	-0.028000	0.13850	-0.242000	0.12053	ATT	A|0.744;G|0.256	0.256	strong		0.453	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
MACF1	23499	hgsc.bcm.edu	37	1	39908506	39908506	+	Missense_Mutation	SNP	G	G	A	rs587404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000539005.1_Missense_Mutation_p.A4220T|MACF1_ENST00000317713.7_Missense_Mutation_p.A4350T|MACF1_ENST00000567887.1_Missense_Mutation_p.A6446T|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	130	0	0		WXS	Illumina HiSeq	Phase_I	124	71	0.572581	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	
TBC1D5	9779	hgsc.bcm.edu	37	3	17208267	17208267	+	Missense_Mutation	SNP	T	T	C	rs1138454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:17208267T>C	ENST00000253692.7	-	21	3750	c.2086A>G	c.(2086-2088)Att>Gtt	p.I696V	TBC1D5_ENST00000446818.2_Missense_Mutation_p.I718V|TBC1D5_ENST00000414318.2_5'UTR|TBC1D5_ENST00000429383.4_Missense_Mutation_p.I696V	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	696			I -> V (in dbSNP:rs1138454).			retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						ACCTGTTTAATGGCCCCTGAC	0.488													T|||	1341	0.267772	0.2103	0.3112	5008	,	,		17861	0.0794		0.3936	False		,,,				2504	0.3793				p.I718V		Atlas-SNP	.											.	TBC1D5	69	.	0			c.A2152G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	1030,3376	379.9+/-323.5	108,814,1281	112.0	101.0	105.0		2086,2152,2086	-9.4	0.0	3	dbSNP_86	105	3447,5153	507.0+/-376.7	698,2051,1551	yes	missense,missense,missense	TBC1D5	NM_001134380.1,NM_001134381.1,NM_014744.2	29,29,29	806,2865,2832	CC,CT,TT		40.0814,23.3772,34.4226	benign,benign,benign	696/796,718/818,696/796	17208267	4477,8529	2203	4300	6503	SO:0001583	missense	9779	exon23			GTTTAATGGCCCC	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.2086A>G	3.37:g.17208267T>C	ENSP00000253692:p.Ile696Val	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_001134381	A6NP25|C9JP52	Missense_Mutation	SNP	ENST00000253692.7	37	CCDS33714.1	575	0.2632783882783883	123	0.25	116	0.32044198895027626	37	0.06468531468531469	299	0.3944591029023747	T	6.504	0.461153	0.12342	0.233772	0.400814	ENSG00000131374	ENST00000253692;ENST00000429383;ENST00000446818	T;T;T	0.28666	1.61;1.61;1.6	4.7	-9.41	0.00613	.	1.736360	0.02827	N	0.126339	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	0.26710	-1.0095	9	0.14252	T	0.57	4.8919	4.3982	0.11374	0.0993:0.4419:0.2011:0.2577	rs3202373	718;696;696	C9JP52;B9A6K1;Q92609	.;.;TBCD5_HUMAN	V	696;696;718	ENSP00000253692:I696V;ENSP00000398127:I696V;ENSP00000402935:I718V	ENSP00000253692:I696V	I	-	1	0	TBC1D5	17183271	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.064000	0.01387	-2.129000	0.00817	-0.375000	0.07067	ATT	T|0.701;C|0.299	0.299	strong		0.488	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744	
KIF1C	10749	hgsc.bcm.edu	37	17	4925674	4925674	+	Silent	SNP	C	C	T	rs73345356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4925674C>T	ENST00000320785.5	+	22	2655	c.2298C>T	c.(2296-2298)caC>caT	p.H766H	AC109333.10_ENST00000438266.1_RNA	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	766					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						ACTTCCGCCACGGGCGGGCTG	0.677													C|||	167	0.0333466	0.1188	0.0115	5008	,	,		17324	0.0		0.002	False		,,,				2504	0.0				p.H766H	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											KIF1C,colon,carcinoma,0,1	KIF1C	70	1	0			c.C2298T						PASS	.	C		432,3962		26,380,1791	19.0	18.0	19.0		2298	-1.4	1.0	17	dbSNP_130	19	16,8566		0,16,4275	no	coding-synonymous	KIF1C	NM_006612.5		26,396,6066	TT,TC,CC		0.1864,9.8316,3.4525		766/1104	4925674	448,12528	2197	4291	6488	SO:0001819	synonymous_variant	10749	exon22			CCGCCACGGGCGG	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.2298C>T	17.37:g.4925674C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																			C|0.964;T|0.036	0.036	strong		0.677	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
ALK	238	hgsc.bcm.edu	37	2	29416481	29416481	+	Missense_Mutation	SNP	T	T	C	rs1881420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	353	0	0		WXS	Illumina HiSeq	Phase_I	344	161	0.468023	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	
CCDC88C	440193	hgsc.bcm.edu	37	14	91805804	91805804	+	Silent	SNP	C	C	T	rs61220159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91805804C>T	ENST00000389857.6	-	8	713	c.627G>A	c.(625-627)ctG>ctA	p.L209L		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	209					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GGTCCACGATCAGCTGCAGCC	0.602													C|||	166	0.033147	0.1188	0.013	5008	,	,		17173	0.0		0.0	False		,,,				2504	0.0				p.L209L		Atlas-SNP	.											.	CCDC88C	192	.	0			c.G627A						PASS	.	C		438,3852		17,404,1724	41.0	50.0	47.0		627	-0.9	1.0	14	dbSNP_129	47	4,8512		0,4,4254	yes	coding-synonymous	CCDC88C	NM_001080414.3		17,408,5978	TT,TC,CC		0.047,10.2098,3.4515		209/2029	91805804	442,12364	2145	4258	6403	SO:0001819	synonymous_variant	440193	exon8			CACGATCAGCTGC		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.627G>A	14.37:g.91805804C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	230	124	0.53913	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			C|0.968;T|0.032	0.032	strong		0.602	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
SCUBE2	57758	hgsc.bcm.edu	37	11	9051475	9051475	+	Missense_Mutation	SNP	G	G	C	rs3751057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9051475G>C	ENST00000309263.3	-	18	2444	c.2372C>G	c.(2371-2373)aCt>aGt	p.T791S	RP11-467K18.2_ENST00000531592.1_RNA|SCUBE2_ENST00000450649.2_Missense_Mutation_p.T665S|SCUBE2_ENST00000520467.1_Missense_Mutation_p.T763S|SCUBE2_ENST00000457346.2_Missense_Mutation_p.T820S			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	791			T -> S (in dbSNP:rs3751057).			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)		GTCAGTCGTAGTATTTCCTGG	0.433													G|||	475	0.0948482	0.1097	0.0519	5008	,	,		20560	0.121		0.0676	False		,,,				2504	0.1063				p.T763S		Atlas-SNP	.											.	SCUBE2	102	.	0			c.C2288G						PASS	.	G	SER/THR,SER/THR	476,3926	226.2+/-241.8	20,436,1745	208.0	202.0	204.0		1994,2288	5.2	1.0	11	dbSNP_107	204	703,7889	173.2+/-223.7	27,649,3620	yes	missense,missense	SCUBE2	NM_001170690.1,NM_020974.2	58,58	47,1085,5365	CC,CG,GG		8.182,10.8133,9.0734	probably-damaging,probably-damaging	665/808,763/972	9051475	1179,11815	2201	4296	6497	SO:0001583	missense	57758	exon18			GTCGTAGTATTTC	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.2372C>G	11.37:g.9051475G>C	ENSP00000310658:p.Thr791Ser	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	269	123	0.457249	NM_020974	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		176	0.08058608058608059	57	0.11585365853658537	17	0.04696132596685083	53	0.09265734265734266	49	0.06464379947229551	G	26.1	4.705731	0.89018	0.108133	0.08182	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	5.19	5.19	0.71726	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	T	0.06050	0.0157	M	0.84585	2.705	0.09310	P	0.9999999293489	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.91635	0.994;0.999;0.999	T	0.55127	-0.8189	9	0.62326	D	0.03	.	18.7036	0.91630	0.0:0.0:1.0:0.0	rs3751057;rs52803158;rs56444362;rs3751057	665;763;791	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	S	820;791;665;763	ENSP00000390481:T820S;ENSP00000310658:T791S;ENSP00000415187:T665S;ENSP00000429969:T763S	ENSP00000310658:T791S	T	-	2	0	SCUBE2	9008051	1.000000	0.71417	0.964000	0.40570	0.981000	0.71138	7.879000	0.87236	2.415000	0.81967	0.491000	0.48974	ACT	G|0.908;C|0.092	0.092	strong		0.433	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974	
SORD	6652	hgsc.bcm.edu	37	15	45353365	45353365	+	Silent	SNP	G	G	A	rs11542063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45353365G>A	ENST00000267814.9	+	4	546	c.366G>A	c.(364-366)acG>acA	p.T122T	SORD_ENST00000558580.1_Silent_p.T101T|RP11-109D20.1_ENST00000560324.1_RNA	NM_003104.5	NP_003095.2	Q00796	DHSO_HUMAN	sorbitol dehydrogenase	122					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)		TCTGTGCCACGCCCCCCGATG	0.527													.|||	42	0.00838658	0.0136	0.0115	5008	,	,		19314	0.0		0.0139	False		,,,				2504	0.002				p.T122T		Atlas-SNP	.											SORD,caecum,carcinoma,0,2	SORD	24	2	0			c.G366A						scavenged	.	A		45,4351	820.2+/-416.4	0,45,2153	120.0	100.0	106.0		366	-8.4	0.4	15	dbSNP_120	106	189,8407	810.8+/-407.1	3,183,4112	no	coding-synonymous	SORD	NM_003104.5		3,228,6265	AA,AG,GG		2.1987,1.0237,1.8011		122/358	45353365	234,12758	2198	4298	6496	SO:0001819	synonymous_variant	6652	exon4			TGCCACGCCCCCC		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.366G>A	15.37:g.45353365G>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	337	8	0.0237389	NM_003104	B2R655|B7Z3A6|J3JZZ5|Q16682|Q9UMD6	Silent	SNP	ENST00000267814.9	37	CCDS10116.1																																																																																			G|0.984;A|0.016	0.016	strong		0.527	SORD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254033.3		
CDNF	441549	hgsc.bcm.edu	37	10	14862140	14862140	+	Missense_Mutation	SNP	C	C	A	rs61740068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:14862140C>A	ENST00000378442.1	-	6	600	c.97G>T	c.(97-99)Gca>Tca	p.A33S	CDNF_ENST00000378441.2_5'UTR			Q49AH0	CDNF_HUMAN	cerebral dopamine neurotrophic factor	135						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(1)	5						TCAACTGATGCCAAGTCCAGT	0.418													C|||	76	0.0151757	0.0522	0.0072	5008	,	,		19434	0.0		0.0	False		,,,				2504	0.002				p.A135S		Atlas-SNP	.											.	CDNF	19	.	0			c.G403T						PASS	.	C	SER/ALA	205,4201	127.4+/-164.3	3,199,2001	96.0	98.0	97.0		403	5.9	1.0	10	dbSNP_129	97	0,8600		0,0,4300	yes	missense	CDNF	NM_001029954.2	99	3,199,6301	AA,AC,CC		0.0,4.6527,1.5762	benign	135/188	14862140	205,12801	2203	4300	6503	SO:0001583	missense	441549	exon4			CTGATGCCAAGTC	BC037872	CCDS31148.1	10p13	2009-06-04	2009-06-04	2009-06-04	ENSG00000185267	ENSG00000185267			24913	protein-coding gene	gene with protein product	"""conserved dopamine neurotrophic factor"""	611233	"""arginine-rich, mutated in early stage tumors-like 1"""	ARMETL1		17611540	Standard	NM_001029954		Approved		uc001inb.1	Q49AH0	OTTHUMG00000017713	ENST00000378442.1:c.97G>T	10.37:g.14862140C>A	ENSP00000367703:p.Ala33Ser	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	NM_001029954	A2RUU0|B4DVW3	Missense_Mutation	SNP	ENST00000378442.1	37		27	0.012362637362637362	24	0.04878048780487805	3	0.008287292817679558	0	0.0	0	0.0	C	3.967	-0.009097	0.07727	0.046527	0.0	ENSG00000185267	ENST00000378442;ENST00000465530	.	.	.	5.9	5.9	0.94986	.	0.284770	0.36519	N	0.002549	T	0.03783	0.0107	N	0.04994	-0.135	0.34379	D	0.692882	B	0.22983	0.078	B	0.21360	0.034	T	0.09185	-1.0686	9	0.02654	T	1	-13.8964	13.0686	0.59048	0.0:0.9231:0.0:0.0769	.	135	Q49AH0	CDNF_HUMAN	S	33;135	.	ENSP00000367703:A33S	A	-	1	0	CDNF	14902146	1.000000	0.71417	0.997000	0.53966	0.555000	0.35460	3.795000	0.55499	2.806000	0.96561	0.655000	0.94253	GCA	C|0.985;A|0.015	0.015	strong		0.418	CDNF-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000046919.1	NM_001029954	
NCOR2	9612	hgsc.bcm.edu	37	12	124841276	124841276	+	Silent	SNP	G	G	A	rs200441401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124841276G>A	ENST00000405201.1	-	23	3153	c.3153C>T	c.(3151-3153)tcC>tcT	p.S1051S	NCOR2_ENST00000429285.2_Silent_p.S1041S|NCOR2_ENST00000356219.3_Silent_p.S1058S|NCOR2_ENST00000397355.1_Silent_p.S1042S|NCOR2_ENST00000404621.1_Silent_p.S1041S|NCOR2_ENST00000404121.2_Silent_p.S612S			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1059					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)		AGGGCAGGCCGGAAGTCCAGC	0.677													G|||	5	0.000998403	0.003	0.0	5008	,	,		14484	0.0		0.0	False		,,,				2504	0.001				p.S1051S		Atlas-SNP	.											.	NCOR2	475	.	0			c.C3153T						PASS	.	G	,,	10,3816		0,10,1903	12.0	17.0	15.0		3123,3123,3153	-4.4	0.3	12		15	1,8229		0,1,4114	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	0,11,6017	AA,AG,GG		0.0122,0.2614,0.0912	,,	1041/2459,1041/2505,1051/2515	124841276	11,12045	1913	4115	6028	SO:0001819	synonymous_variant	9612	exon25			CAGGCCGGAAGTC	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.3153C>T	12.37:g.124841276G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	192	94	0.489583	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			G|1.000;A|0.000	0.000	strong		0.677	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
TLDC1	57707	hgsc.bcm.edu	37	16	84520496	84520496	+	Missense_Mutation	SNP	C	C	G	rs34244563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84520496C>G	ENST00000343629.6	-	5	881	c.699G>C	c.(697-699)gaG>gaC	p.E233D	TLDC1_ENST00000561807.1_5'Flank|TLDC1_ENST00000535580.1_Missense_Mutation_p.E206D	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	233			E -> D (in dbSNP:rs34244563).			lysosomal membrane (GO:0005765)											CCACTTGACGCTCAGGGACCA	0.572													C|||	55	0.0109824	0.0401	0.0014	5008	,	,		21248	0.0		0.001	False		,,,				2504	0.0				p.E233D		Atlas-SNP	.											.	KIAA1609	39	.	0			c.G699C						PASS	.	C	ASP/GLU	128,4272	91.6+/-130.3	3,122,2075	45.0	44.0	44.0		699	5.0	0.4	16	dbSNP_126	44	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KIAA1609	NM_020947.3	45	3,125,6372	GG,GC,CC		0.0349,2.9091,1.0077	possibly-damaging	233/457	84520496	131,12869	2200	4300	6500	SO:0001583	missense	57707	exon5			TTGACGCTCAGGG	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"""TLD domain containing 1"""		"""KIAA1609"""	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.699G>C	16.37:g.84520496C>G	ENSP00000343635:p.Glu233Asp	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	145	72	0.496552	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	37	CCDS32498.1	27	0.012362637362637362	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.308	1.054856	0.19907	0.029091	3.49E-4	ENSG00000140950	ENST00000343629;ENST00000535580	T;T	0.10668	3.03;2.85	4.98	4.98	0.66077	.	0.749691	0.13046	N	0.418157	T	0.01905	0.0060	M	0.67953	2.075	0.25363	N	0.988763	P;B	0.51933	0.949;0.251	B;B	0.43301	0.415;0.051	T	0.19128	-1.0315	10	0.22706	T	0.39	-28.8132	7.464	0.27312	0.0:0.725:0.1841:0.0909	rs34244563	206;233	F5GWS3;Q6P9B6	.;K1609_HUMAN	D	233;206	ENSP00000343635:E233D;ENSP00000441997:E206D	ENSP00000343635:E233D	E	-	3	2	KIAA1609	83077997	0.971000	0.33674	0.403000	0.26384	0.015000	0.08874	1.112000	0.31172	2.295000	0.77249	0.563000	0.77884	GAG	C|0.989;G|0.011	0.011	strong		0.572	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947	
MUC4	4585	hgsc.bcm.edu	37	3	195509606	195509606	+	Missense_Mutation	SNP	C	C	T	rs200244334		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509606C>T	ENST00000463781.3	-	2	9304	c.8845G>A	c.(8845-8847)Gac>Aac	p.D2949N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D2949N	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)		GAGGAAGTGTCGGTGACAGGA	0.592																																					p.D2949N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G8845A						scavenged	.						10.0	8.0	9.0					3																	195509606		648	1501	2149	SO:0001583	missense	4585	exon2			AAGTGTCGGTGAC	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.8845G>A	3.37:g.195509606C>T	ENSP00000417498:p.Asp2949Asn	Somatic	295	7	0.0237288		WXS	Illumina HiSeq	Phase_I	203	28	0.137931	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	7.799	0.713161	0.15306	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.54;1.54	.	.	.	.	.	.	.	.	T	0.11281	0.0275	N	0.19112	0.55	0.09310	N	1	P	0.50710	0.938	B	0.29663	0.105	T	0.19484	-1.0304	7	.	.	.	.	3.2503	0.06812	0.0:0.638:0.0:0.362	.	2821	E7ESK3	.	N	2949	ENSP00000417498:D2949N;ENSP00000420243:D2949N	.	D	-	1	0	MUC4	196994385	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.907000	0.04067	-0.000000	0.14550	0.000000	0.15137	GAC	C|0.625;T|0.375	0.375	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SVEP1	79987	hgsc.bcm.edu	37	9	113233738	113233738	+	Silent	SNP	T	T	C	rs61732942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113233738T>C	ENST00000401783.2	-	16	3240	c.2904A>G	c.(2902-2904)gcA>gcG	p.A968A	SVEP1_ENST00000374469.1_Silent_p.A945A|SVEP1_ENST00000302728.8_Silent_p.A968A|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	968					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						GTATTTCTGATGCAAGCTGAA	0.428													T|||	210	0.0419329	0.1513	0.0144	5008	,	,		16743	0.0		0.0	False		,,,				2504	0.0				p.A968A		Atlas-SNP	.											.	SVEP1	326	.	0			c.A2904G						PASS	.	T		458,3258		27,404,1427	122.0	112.0	115.0		2904	-11.0	0.2	9	dbSNP_129	115	5,8209		0,5,4102	no	coding-synonymous	SVEP1	NM_153366.3		27,409,5529	CC,CT,TT		0.0609,12.3251,3.881		968/3572	113233738	463,11467	1858	4107	5965	SO:0001819	synonymous_variant	79987	exon16			TTCTGATGCAAGC	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.2904A>G	9.37:g.113233738T>C		Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	267	181	0.677903	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			T|0.963;C|0.037	0.037	strong		0.428	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
LILRB3	11025	hgsc.bcm.edu	37	19	54720967	54720967	+	Missense_Mutation	SNP	G	G	A	rs114510580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54720967G>A	ENST00000391750.1	-	14	2027	c.1891C>T	c.(1891-1893)Cac>Tac	p.H631Y	LILRB3_ENST00000245620.9_Missense_Mutation_p.H632Y|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.H648Y|LILRB3_ENST00000346401.6_Missense_Mutation_p.H643Y|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000440558.2_Missense_Mutation_p.H631Y|LILRA6_ENST00000270464.5_Missense_Mutation_p.H632Y|LILRA6_ENST00000419410.2_Missense_Mutation_p.H632Y|LILRB3_ENST00000424807.1_Missense_Mutation_p.H631Y			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	631					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCGGGCTAGTGGATGGCCAGA	0.627													.|||	171	0.0341454	0.1271	0.0043	5008	,	,		17170	0.0		0.0	False		,,,				2504	0.0				p.H632Y		Atlas-SNP	.											.	LILRB3	67	.	0			c.C1894T						PASS	.	G	TYR/HIS,TYR/HIS	442,3964	213.5+/-233.1	18,406,1779	90.0	84.0	86.0		1894,1891	0.7	0.0	19	dbSNP_132	86	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	83,83	18,409,6076	AA,AG,GG		0.0349,10.0318,3.4215	probably-damaging,probably-damaging	632/633,631/632	54720967	445,12561	2203	4300	6503	SO:0001583	missense	11025	exon13			GCTAGTGGATGGC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1891C>T	19.37:g.54720967G>A	ENSP00000375630:p.His631Tyr	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	333	140	0.42042	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	60	0.027472527472527472	57	0.11585365853658537	1	0.0027624309392265192	2	0.0034965034965034965	0	0.0	G	13.16	2.154570	0.38021	0.100318	3.49E-4	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00630	6.11;6.11;6.17;6.13;6.16;6.1;6.11;6.14	2.92	0.672	0.17935	.	.	.	.	.	T	0.00039	0.0001	M	0.73598	2.24	0.09310	N	1	D;P;B;P;P;P;P	0.71674	0.998;0.644;0.226;0.956;0.791;0.721;0.849	D;B;B;P;B;B;P	0.79784	0.993;0.425;0.064;0.61;0.324;0.056;0.555	T	0.52845	-0.8521	9	0.87932	D	0	.	2.9682	0.05915	0.1554:0.0:0.5739:0.2707	.	648;631;632;643;648;631;632	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	Y	631;631;643;632;648;631;632;632	ENSP00000375630:H631Y;ENSP00000412771:H631Y;ENSP00000345184:H643Y;ENSP00000245620:H632Y;ENSP00000384274:H648Y;ENSP00000390120:H631Y;ENSP00000270464:H632Y;ENSP00000411227:H632Y	ENSP00000270464:H632Y	H	-	1	0	LILRB3;LILRA6	59412779	0.015000	0.18098	0.004000	0.12327	0.059000	0.15707	2.746000	0.47467	0.274000	0.22072	0.472000	0.43445	CAC	G|0.962;A|0.038	0.038	strong		0.627	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
TTC21B	79809	hgsc.bcm.edu	37	2	166773971	166773971	+	Silent	SNP	G	G	A	rs6750044	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166773971G>A	ENST00000243344.7	-	14	1832	c.1695C>T	c.(1693-1695)taC>taT	p.Y565Y		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	565					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						TTATCAAATGGTATAAAGGAT	0.313													A|||	1461	0.291733	0.3094	0.2291	5008	,	,		17512	0.2014		0.3668	False		,,,				2504	0.3282				p.Y565Y		Atlas-SNP	.											.	TTC21B	130	.	0			c.C1695T						PASS	.	A		1353,3053	688.4+/-405.0	210,933,1060	125.0	120.0	121.0		1695	3.5	1.0	2	dbSNP_116	121	3345,5253	642.6+/-399.8	636,2073,1590	no	coding-synonymous	TTC21B	NM_024753.3		846,3006,2650	AA,AG,GG		38.9044,30.7081,36.1273		565/1317	166773971	4698,8306	2203	4299	6502	SO:0001819	synonymous_variant	79809	exon14			CAAATGGTATAAA	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.1695C>T	2.37:g.166773971G>A		Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	149	85	0.57047	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Silent	SNP	ENST00000243344.7	37	CCDS33315.1																																																																																			G|0.668;A|0.332	0.332	strong		0.313	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	
DNAH17	8632	hgsc.bcm.edu	37	17	76482435	76482435	+	Silent	SNP	C	C	T	rs61743860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76482435C>T	ENST00000585328.1	-	45	7081	c.6957G>A	c.(6955-6957)acG>acA	p.T2319T	RP11-559N14.5_ENST00000588565.1_RNA|DNAH17_ENST00000389840.5_Silent_p.T2310T|RP11-559N14.5_ENST00000585969.1_RNA|DNAH17_ENST00000586052.1_5'UTR	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	134	0	0		WXS	Illumina HiSeq	Phase_I	171	95	0.555556	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	
TBC1D10C	374403	hgsc.bcm.edu	37	11	67176898	67176898	+	Silent	SNP	A	A	G	rs11227788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67176898A>G	ENST00000542590.1	+	9	1028	c.1014A>G	c.(1012-1014)tcA>tcG	p.S338S	TBC1D10C_ENST00000312390.5_Silent_p.S338S|TBC1D10C_ENST00000526387.1_Missense_Mutation_p.R274G			Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	338					retrograde transport, endosome to Golgi (GO:0042147)	filopodium membrane (GO:0031527)|membrane (GO:0016020)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			TGGTGCTGTCAGAGCGGGACC	0.706													G|||	1769	0.353235	0.829	0.4063	5008	,	,		15246	0.2579		0.0835	False		,,,				2504	0.0481				p.R274G		Atlas-SNP	.											.	TBC1D10C	42	.	0			c.A820G						PASS	.	G		1874,1720		484,906,407	4.0	5.0	5.0		1014	-10.1	0.0	11	dbSNP_120	5	442,6982		21,400,3291	no	coding-synonymous	TBC1D10C	NM_198517.2		505,1306,3698	GG,GA,AA		5.9537,47.8575,21.0201		338/447	67176898	2316,8702	1797	3712	5509	SO:0001819	synonymous_variant	374403	exon9			GCTGTCAGAGCGG	BC035630	CCDS8162.1, CCDS58150.1	11q13.1	2013-07-09			ENSG00000175463	ENSG00000175463			24702	protein-coding gene	gene with protein product		610831				17230191, 20404108	Standard	NM_001256508		Approved	FLJ00332, Carabin, EPI64C	uc001ola.4	Q8IV04	OTTHUMG00000167139	ENST00000542590.1:c.1014A>G	11.37:g.67176898A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_001256508	G3V1D6	Missense_Mutation	SNP	ENST00000542590.1	37	CCDS8162.1	739	0.3383699633699634	403	0.8191056910569106	117	0.32320441988950277	150	0.26223776223776224	69	0.09102902374670185	G	4.738	0.137218	0.09032	0.521425	0.059537	ENSG00000175463	ENST00000526387	.	.	.	5.05	-10.1	0.00402	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999260067	B	0.02656	0.0	B	0.01281	0.0	T	0.36744	-0.9735	6	0.62326	D	0.03	.	3.0224	0.06079	0.3073:0.0692:0.3588:0.2647	rs11227788;rs59198381	274	G3V1D6	.	G	274	.	ENSP00000435543:R274G	R	+	1	2	TBC1D10C	66933474	0.000000	0.05858	0.013000	0.15412	0.052000	0.14988	-7.640000	0.00032	-5.141000	0.00021	-3.964000	0.00015	AGA	A|0.659;G|0.341	0.341	strong		0.706	TBC1D10C-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395492.2	NM_198517	
IGF2R	3482	hgsc.bcm.edu	37	6	160453978	160453978	+	Silent	SNP	A	A	G	rs1570070	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	72	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	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	
MAML3	55534	hgsc.bcm.edu	37	4	140811131	140811131	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:140811131G>T	ENST00000509479.2	-	2	2315	c.1459C>A	c.(1459-1461)Caa>Aaa	p.Q487K	MAML3_ENST00000398940.1_Missense_Mutation_p.Q26K|MAML3_ENST00000327122.5_Missense_Mutation_p.Q331K	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					tgttgctgttgctgtttctgc	0.557																																					p.Q487K		Atlas-SNP	.											.	MAML3	192	.	0			c.C1459A						PASS	.						19.0	21.0	20.0					4																	140811131		2198	4294	6492	SO:0001583	missense	55534	exon2			GCTGTTGCTGTTT	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1459C>A	4.37:g.140811131G>T	ENSP00000421180:p.Gln487Lys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	93	7	0.0752688	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	G	1.344	-0.593356	0.03771	.	.	ENSG00000196782	ENST00000509479;ENST00000327122;ENST00000398940	T;T	0.66460	0.85;-0.21	4.28	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.40570	0.1122	N	0.08118	0	0.46499	D	0.999073	B	0.19200	0.034	B	0.18871	0.023	T	0.36359	-0.9751	10	0.02654	T	1	.	12.5248	0.56079	0.0:0.0:1.0:0.0	.	487	Q96JK9	MAML3_HUMAN	K	487;331;26	ENSP00000421180:Q487K;ENSP00000313316:Q331K	ENSP00000313316:Q331K	Q	-	1	0	MAML3	141030581	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	6.453000	0.73488	2.671000	0.90904	0.650000	0.86243	CAA	.	.	none		0.557	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
MCF2L2	23101	hgsc.bcm.edu	37	3	183027542	183027542	+	Missense_Mutation	SNP	T	T	G	rs7639705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183027542T>G	ENST00000328913.3	-	10	1372	c.1075A>C	c.(1075-1077)Att>Ctt	p.I359L	MCF2L2_ENST00000447025.2_Missense_Mutation_p.I359L|MCF2L2_ENST00000414362.2_Missense_Mutation_p.I359L|MCF2L2_ENST00000473233.1_Missense_Mutation_p.I359L	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	359			I -> L (in dbSNP:rs7639705). {ECO:0000269|PubMed:14702039}.				Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I359L(1)		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)			TCCTTAAGAATCTGCTCCACG	0.448													G|||	1675	0.334465	0.4244	0.2363	5008	,	,		17356	0.3562		0.2167	False		,,,				2504	0.3814				p.I359L		Atlas-SNP	.											MCF2L2,NS,carcinoma,0,1	MCF2L2	164	1	1	Substitution - Missense(1)	stomach(1)	c.A1075C						scavenged	.	G	LEU/ILE	1762,2644	645.6+/-398.2	377,1008,818	160.0	148.0	152.0		1075	3.8	0.0	3	dbSNP_116	152	1689,6911	738.6+/-407.1	170,1349,2781	yes	missense	MCF2L2	NM_015078.2	5	547,2357,3599	GG,GT,TT		19.6395,39.9909,26.5339	benign	359/1115	183027542	3451,9555	2203	4300	6503	SO:0001583	missense	23101	exon10			TAAGAATCTGCTC	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.1075A>C	3.37:g.183027542T>G	ENSP00000328118:p.Ile359Leu	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	126	74	0.587302	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	637	0.2916666666666667	181	0.3678861788617886	96	0.26519337016574585	192	0.3356643356643357	168	0.22163588390501318	G	0.349	-0.945787	0.02304	0.399909	0.196395	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000414362	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	4.73	3.84	0.44239	.	0.066665	0.64402	N	0.000009	T	0.00012	0.0000	N	0.00456	-1.48	0.49483	P	2.0600000000003948E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44862	-0.9300	9	0.02654	T	1	.	14.0032	0.64446	0.0:0.0:0.7235:0.2765	rs7639705;rs17749805;rs52825331;rs61011857;rs7639705	359;359	Q86YR7-2;Q86YR7	.;MF2L2_HUMAN	L	359	ENSP00000328118:I359L;ENSP00000420070:I359L;ENSP00000388190:I359L;ENSP00000414131:I359L	ENSP00000328118:I359L	I	-	1	0	MCF2L2	184510236	1.000000	0.71417	0.037000	0.18230	0.074000	0.17049	3.804000	0.55568	0.706000	0.31912	-0.121000	0.15023	ATT	T|0.718;G|0.282	0.282	strong		0.448	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
CACNA1I	8911	hgsc.bcm.edu	37	22	39966856	39966856	+	Silent	SNP	C	C	T	rs3747178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39966856C>T	ENST00000402142.3	+	1	99	c.99C>T	c.(97-99)tcC>tcT	p.S33S	CACNA1I_ENST00000407673.1_Silent_p.S33S|CACNA1I_ENST00000401624.1_Silent_p.S33S|CACNA1I_ENST00000400164.3_Silent_p.S33S|CACNA1I_ENST00000404898.1_Silent_p.S33S|CACNA1I_ENST00000336649.4_Silent_p.S33S	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	33					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	GCCCCCCATCCTCCCCGCCAG	0.677													C|||	1647	0.328874	0.0545	0.33	5008	,	,		14247	0.7272		0.3429	False		,,,				2504	0.274				p.S33S		Atlas-SNP	.											.	CACNA1I	264	.	0			c.C99T						PASS	.	C	,	351,3691		14,323,1684	27.0	33.0	31.0		99,99	-6.7	0.3	22	dbSNP_107	31	2504,5828		402,1700,2064	no	coding-synonymous,coding-synonymous	CACNA1I	NM_001003406.1,NM_021096.3	,	416,2023,3748	TT,TC,CC		30.0528,8.6838,23.0726	,	33/2189,33/2224	39966856	2855,9519	2021	4166	6187	SO:0001819	synonymous_variant	8911	exon1			CCCATCCTCCCCG	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.99C>T	22.37:g.39966856C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_001003406	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Silent	SNP	ENST00000402142.3	37	CCDS46710.1																																																																																			C|0.650;T|0.350	0.350	strong		0.677	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
TBX15	6913	hgsc.bcm.edu	37	1	119427937	119427937	+	Silent	SNP	G	G	A	rs145938710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:119427937G>A	ENST00000369429.3	-	8	1236	c.1227C>T	c.(1225-1227)gcC>gcT	p.A409A	TBX15_ENST00000207157.3_Silent_p.A303A			Q96SF7	TBX15_HUMAN	T-box 15	409					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)		AGCTCTGCAAGGCAGCCATGT	0.542													G|||	8	0.00159744	0.0061	0.0	5008	,	,		20115	0.0		0.0	False		,,,				2504	0.0				p.A303A		Atlas-SNP	.											.	TBX15	95	.	0			c.C909T						PASS	.	G		18,4388	23.3+/-48.9	0,18,2185	47.0	45.0	46.0		909	2.3	1.0	1	dbSNP_134	46	0,8600		0,0,4300	no	coding-synonymous	TBX15	NM_152380.2		0,18,6485	AA,AG,GG		0.0,0.4085,0.1384		303/497	119427937	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	6913	exon8			CTGCAAGGCAGCC	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.1227C>T	1.37:g.119427937G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_152380	Q08E76|Q5JT54|Q5T9S7	Silent	SNP	ENST00000369429.3	37																																																																																				G|0.998;A|0.002	0.002	strong		0.542	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380	
WNK2	65268	hgsc.bcm.edu	37	9	96026243	96026243	+	Silent	SNP	G	G	A	rs55981123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:96026243G>A	ENST00000297954.4	+	15	3624	c.3624G>A	c.(3622-3624)acG>acA	p.T1208T	WNK2_ENST00000349097.3_Silent_p.T820T|WNK2_ENST00000395477.2_Silent_p.T1208T|WNK2_ENST00000427277.2_Silent_p.T820T|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000356055.3_5'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1208					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						AGCTGGAGACGCACAACCACA	0.607													G|||	514	0.102636	0.1762	0.1124	5008	,	,		10483	0.001		0.1431	False		,,,				2504	0.0593				p.T1208T		Atlas-SNP	.											WNK2_ENST00000297954,caecum,carcinoma,0,4	WNK2	277	4	0			c.G3624A						PASS	.	G		726,3680	298.1+/-285.1	58,610,1535	132.0	96.0	108.0		3624	-10.3	0.4	9	dbSNP_129	108	1025,7575	218.4+/-256.8	66,893,3341	no	coding-synonymous	WNK2	NM_006648.3		124,1503,4876	AA,AG,GG		11.9186,16.4775,13.463		1208/2218	96026243	1751,11255	2203	4300	6503	SO:0001819	synonymous_variant	65268	exon15			GGAGACGCACAAC	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.3624G>A	9.37:g.96026243G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		242|242	0.1108058608058608|0.1108058608058608	90|90	0.18292682926829268|0.18292682926829268	45|45	0.12430939226519337|0.12430939226519337	1|1	0.0017482517482517483|0.0017482517482517483	106|106	0.13984168865435356|0.13984168865435356	G|G	9.325|9.325	1.058954|1.058954	0.19987|0.19987	0.164775|0.164775	0.119186|0.119186	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730;ENST00000448251	.|.	.|.	.|.	5.15|5.15	-10.3|-10.3	0.00346|0.00346	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999997|0.9999999999999997	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.08086|0.08086	-1.0739|-1.0739	3|3	.|.	.|.	.|.	.|.	4.5012|4.5012	0.11865|0.11865	0.5339:0.2285:0.0848:0.1528|0.5339:0.2285:0.0848:0.1528	rs55981123|rs55981123	.|.	.|.	.|.	T|H	812|1204;5	.|.	.|.	A|R	+|+	1|2	0|0	WNK2|WNK2	95066064|95066064	0.000000|0.000000	0.05858|0.05858	0.410000|0.410000	0.26471|0.26471	0.988000|0.988000	0.76386|0.76386	-1.789000|-1.789000	0.01761|0.01761	-2.243000|-2.243000	0.00707|0.00707	-0.251000|-0.251000	0.11542|0.11542	GCA|CGC	G|0.870;A|0.130	0.130	strong		0.607	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
FLG	2312	hgsc.bcm.edu	37	1	152276474	152276474	+	Missense_Mutation	SNP	G	G	A	rs76019722		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276474G>A	ENST00000368799.1	-	3	10923	c.10888C>T	c.(10888-10890)Cac>Tac	p.H3630Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3630	Ser-rich.		H -> Y (in dbSNP:rs9436065).		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)			GACTGCTGGTGGTGGGATCCA	0.542									Ichthyosis																												p.H3630Y		Atlas-SNP	.											.	FLG	900	.	0			c.C10888T						PASS	.	G	TYR/HIS	1203,3199		0,1203,998	203.0	163.0	176.0		10888	2.2	0.0	1	dbSNP_131	176	14,8576		0,14,4281	no	missense	FLG	NM_002016.1	83	0,1217,5279	AA,AG,GG		0.163,27.3285,9.3673	probably-damaging	3630/4062	152276474	1217,11775	2201	4295	6496	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTGGTGGTGGGA	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.10888C>T	1.37:g.152276474G>A	ENSP00000357789:p.His3630Tyr	Somatic	367	0	0		WXS	Illumina HiSeq	Phase_I	572	364	0.636364	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	157	0.07188644688644688	146	0.2967479674796748	11	0.03038674033149171	0	0.0	0	0.0	G	9.840	1.190882	0.21954	0.273285	0.00163	ENSG00000143631	ENST00000368799	T	0.01665	4.7	4.11	2.18	0.27775	.	.	.	.	.	T	0.01627	0.0052	M	0.63428	1.95	0.09310	N	1	D	0.67145	0.996	D	0.75020	0.985	T	0.24728	-1.0152	9	0.02654	T	1	.	6.2399	0.20785	0.2304:0.0:0.7696:0.0	rs9436065;rs52822444;rs9436065	3630	P20930	FILA_HUMAN	Y	3630	ENSP00000357789:H3630Y	ENSP00000357789:H3630Y	H	-	1	0	FLG	150543098	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	0.464000	0.21988	1.051000	0.40369	0.502000	0.49764	CAC	G|0.997;A|0.003	0.003	weak		0.542	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
GAA	2548	hgsc.bcm.edu	37	17	78092081	78092081	+	Silent	SNP	G	G	T	rs17853996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78092081G>T	ENST00000302262.3	+	18	2790	c.2571G>T	c.(2569-2571)ctG>ctT	p.L857L	GAA_ENST00000390015.3_Silent_p.L857L	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	857					cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	GAGGGGAGCTGTTCTGGGACG	0.657													G|||	11	0.00219649	0.0083	0.0	5008	,	,		17228	0.0		0.0	False		,,,				2504	0.0				p.L857L		Atlas-SNP	.											.	GAA	66	.	0			c.G2571T						PASS	.	G	,,	48,4358	50.2+/-85.5	0,48,2155	65.0	74.0	71.0		2571,2571,2571	-1.4	1.0	17	dbSNP_123	71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	GAA	NM_000152.3,NM_001079803.1,NM_001079804.1	,,	0,48,6455	TT,TG,GG		0.0,1.0894,0.3691	,,	857/953,857/953,857/953	78092081	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	2548	exon19			GGAGCTGTTCTGG		CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"""Pompe disease"", ""glycogen storage disease type II"""	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.2571G>T	17.37:g.78092081G>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Silent	SNP	ENST00000302262.3	37	CCDS32760.1																																																																																			G|0.997;T|0.003	0.003	strong		0.657	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		
COL5A3	50509	hgsc.bcm.edu	37	19	10088271	10088271	+	Splice_Site	SNP	C	C	G	rs2161468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10088271C>G	ENST00000264828.3	-	42	3210	c.3125G>C	c.(3124-3126)cGg>cCg	p.R1042P		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1042	Triple-helical region.		R -> P (in dbSNP:rs2161468).		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)			GTCACTTACCCGGGACCCCTT	0.642													G|||	1754	0.35024	0.3389	0.2522	5008	,	,		13859	0.3313		0.3946	False		,,,				2504	0.409				p.R1042P		Atlas-SNP	.											.	COL5A3	243	.	0			c.G3125C						PASS	.	G	PRO/ARG	1597,2809	652.3+/-399.4	286,1025,892	40.0	39.0	40.0		3125	2.7	1.0	19	dbSNP_96	40	3474,5126	618.5+/-396.8	688,2098,1514	yes	missense-near-splice	COL5A3	NM_015719.3	103	974,3123,2406	GG,GC,CC		40.3953,36.246,38.9897	benign	1042/1746	10088271	5071,7935	2203	4300	6503	SO:0001630	splice_region_variant	50509	exon42			CTTACCCGGGACC	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.3126+1G>C	19.37:g.10088271C>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	781	0.3576007326007326	182	0.3699186991869919	99	0.27348066298342544	205	0.3583916083916084	295	0.3891820580474934	G	0.033	-1.324178	0.01309	0.36246	0.403953	ENSG00000080573	ENST00000264828	D	0.90069	-2.61	4.84	2.68	0.31781	.	0.160820	0.41396	N	0.000888	T	0.00012	0.0000	N	0.02876	-0.465	0.49915	P	1.6199999999999548E-4	B	0.16603	0.018	B	0.04013	0.001	T	0.14504	-1.0470	9	0.02654	T	1	.	6.5611	0.22487	0.1698:0.1493:0.6809:0.0	rs2161468;rs52800016;rs2161468	1042	P25940	CO5A3_HUMAN	P	1042	ENSP00000264828:R1042P	ENSP00000264828:R1042P	R	-	2	0	COL5A3	9949271	1.000000	0.71417	0.998000	0.56505	0.114000	0.19823	4.928000	0.63447	0.256000	0.21614	-0.120000	0.15030	CGG	C|0.631;G|0.369	0.369	strong		0.642	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	Missense_Mutation
IL1RL2	8808	hgsc.bcm.edu	37	2	102851708	102851708	+	Missense_Mutation	SNP	T	T	C	rs2302612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102851708T>C	ENST00000264257.2	+	11	1775	c.1649T>C	c.(1648-1650)cTg>cCg	p.L550P	IL1RL2_ENST00000539491.1_Missense_Mutation_p.L550P|IL1RL2_ENST00000481806.1_3'UTR|IL1RL2_ENST00000441515.2_Missense_Mutation_p.L432P	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	97	0	0	1369	WXS	Illumina HiSeq	Phase_I	111	111	1	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	
DACT2	168002	hgsc.bcm.edu	37	6	168708751	168708751	+	Silent	SNP	A	A	G	rs10945499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:168708751A>G	ENST00000366795.3	-	4	1774	c.1686T>C	c.(1684-1686)tcT>tcC	p.S562S	DACT2_ENST00000610183.1_Silent_p.S392S|DACT2_ENST00000366796.3_Intron|DACT2_ENST00000607983.1_Silent_p.S154S	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	562					epithelial cell morphogenesis (GO:0003382)|hematopoietic progenitor cell differentiation (GO:0002244)|inner medullary collecting duct development (GO:0072061)|negative regulation of cell adhesion (GO:0007162)|negative regulation of nodal signaling pathway (GO:1900108)|skin development (GO:0043588)	mitochondrion (GO:0005739)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)|transcription factor binding (GO:0008134)			endometrium(1)	1		Breast(66;1.46e-05)|Ovarian(120;0.0728)		OV - Ovarian serous cystadenocarcinoma(33;5.33e-21)|BRCA - Breast invasive adenocarcinoma(81;1.18e-06)|GBM - Glioblastoma multiforme(31;0.000957)		GGGTGGACTCAGAACAGGAGC	0.706													G|||	2547	0.508586	0.8056	0.4107	5008	,	,		11419	0.3244		0.3688	False		,,,				2504	0.5102				p.S562S		Atlas-SNP	.											DACT2_ENST00000366795,NS,carcinoma,0,2	DACT2	46	2	0			c.T1686C						PASS	.	G		1006,378		366,274,52	29.0	39.0	36.0		1686	-8.6	0.7	6	dbSNP_120	36	1150,2032		213,724,654	no	coding-synonymous	DACT2	NM_214462.3		579,998,706	GG,GA,AA		36.1408,27.3121,47.2186		562/775	168708751	2156,2410	692	1591	2283	SO:0001819	synonymous_variant	168002	exon4			GGACTCAGAACAG	AF318336	CCDS47519.1, CCDS69241.1, CCDS75554.1	6q27	2013-05-15	2013-05-15	2003-09-17	ENSG00000164488	ENSG00000164488			21231	protein-coding gene	gene with protein product		608966	"""chromosome 6 open reading frame 116"", ""dapper homolog 2, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 2 (Xenopus laevis)"""	C6orf116			Standard	NM_001286351		Approved	bA503C24.7, DAPPER2	uc003qwq.3	Q5SW24	OTTHUMG00000016046	ENST00000366795.3:c.1686T>C	6.37:g.168708751A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Silent	SNP	ENST00000366795.3	37	CCDS47519.1																																																																																			A|0.525;G|0.475	0.475	strong		0.706	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
SMCO2	341346	hgsc.bcm.edu	37	12	27641473	27641473	+	Missense_Mutation	SNP	G	G	A	rs412978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27641473G>A	ENST00000535986.1	+	5	593	c.593G>A	c.(592-594)aGc>aAc	p.S198N	SMCO2_ENST00000538647.1_Intron|SMCO2_ENST00000298876.4_Missense_Mutation_p.S148N|SMCO2_ENST00000416383.1_Missense_Mutation_p.S198N			A6NFE2	SMCO2_HUMAN	single-pass membrane protein with coiled-coil domains 2	198				ST -> CA (in Ref. 2; DY654457). {ECO:0000305}.		integral component of membrane (GO:0016021)											CAAGGGACAAGCACTGAGGTA	0.443													A|||	1622	0.323882	0.5794	0.1974	5008	,	,		16884	0.371		0.0706	False		,,,				2504	0.2802				p.S198N		Atlas-SNP	.											.	.	.	.	0			c.G593A						PASS	.	A	ASN/SER	695,689		175,345,172	56.0	57.0	57.0		593	1.6	0.0	12	dbSNP_80	57	225,2957		13,199,1379	yes	missense	C12orf70	NM_001145010.1	46	188,544,1551	AA,AG,GG		7.071,49.7832,20.1489	benign	198/344	27641473	920,3646	692	1591	2283	SO:0001583	missense	0	exon6			GGACAAGCACTGA		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.593G>A	12.37:g.27641473G>A	ENSP00000441688:p.Ser198Asn	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_001145010		Missense_Mutation	SNP	ENST00000535986.1	37	CCDS44852.1	610	0.2793040293040293	267	0.5426829268292683	70	0.19337016574585636	219	0.38286713286713286	54	0.0712401055408971	A	0.001	-3.455855	0.00012	0.502168	0.07071	ENSG00000165935	ENST00000298876;ENST00000416383;ENST00000535986	.	.	.	2.81	1.62	0.23740	.	0.219013	0.23252	N	0.050238	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	0.44498	-0.9324	8	0.02654	T	1	-3.3301	2.4017	0.04403	0.6236:0.0:0.1387:0.2377	rs412978;rs52797881;rs61528370;rs412978	198	A6NFE2	CL070_HUMAN	N	148;198;198	.	ENSP00000298876:S148N	S	+	2	0	C12orf70	27532740	0.013000	0.17824	0.007000	0.13788	0.001000	0.01503	0.529000	0.23019	0.057000	0.16193	-1.978000	0.00458	AGC	G|0.691;A|0.309	0.309	strong		0.443	SMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402867.1	NM_001145010	
OR2A5	393046	hgsc.bcm.edu	37	7	143747796	143747796	+	Missense_Mutation	SNP	C	C	A	rs61741408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143747796C>A	ENST00000408906.2	+	1	336	c.302C>A	c.(301-303)aCc>aAc	p.T101N		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	101						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L103fs*14(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)					ACAATGCAGACCTTTTTATAC	0.428													C|||	16	0.00319489	0.0121	0.0	5008	,	,		24203	0.0		0.0	False		,,,				2504	0.0				p.T101N		Atlas-SNP	.											OR2A5,colon,carcinoma,+1,5	OR2A5	78	5	1	Deletion - Frameshift(1)	lung(1)	c.C302A						PASS	.	C	ASN/THR	58,4162		0,58,2052	151.0	149.0	150.0		302	4.5	1.0	7	dbSNP_129	150	1,8505		0,1,4252	yes	missense	OR2A5	NM_012365.1	65	0,59,6304	AA,AC,CC		0.0118,1.3744,0.4636	benign	101/312	143747796	59,12667	2110	4253	6363	SO:0001583	missense	393046	exon1			TGCAGACCTTTTT	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.302C>A	7.37:g.143747796C>A	ENSP00000386208:p.Thr101Asn	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	165	85	0.515152	NM_012365	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	10.44	1.350249	0.24512	0.013744	1.18E-4	ENSG00000221836	ENST00000408906	T	0.02974	4.09	5.37	4.47	0.54385	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.03390	0.0098	M	0.71036	2.16	0.31492	N	0.665835	B	0.27932	0.194	B	0.27262	0.078	T	0.00896	-1.1523	9	0.66056	D	0.02	.	8.4796	0.33034	0.0:0.8307:0.0:0.1693	rs61741408	101	Q96R48	OR2A5_HUMAN	N	101	ENSP00000386208:T101N	ENSP00000386208:T101N	T	+	2	0	OR2A5	143378729	0.000000	0.05858	0.994000	0.49952	0.301000	0.27625	0.546000	0.23284	2.797000	0.96272	0.650000	0.86243	ACC	C|0.997;A|0.003	0.003	strong		0.428	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1		
FMN2	56776	hgsc.bcm.edu	37	1	240371085	240371085	+	Silent	SNP	A	A	T	rs71646826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	126	4	0.031746		WXS	Illumina HiSeq	Phase_I	210	31	0.147619	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	
RIN2	54453	hgsc.bcm.edu	37	20	19870235	19870235	+	Missense_Mutation	SNP	C	C	T	rs56311184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:19870235C>T	ENST00000255006.6	+	2	286	c.137C>T	c.(136-138)tCg>tTg	p.S46L	RIN2_ENST00000440354.2_5'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	0					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						AGTGGAGCCTCGCTGGGGGAA	0.517													C|||	152	0.0303514	0.1135	0.0029	5008	,	,		17379	0.0		0.0	False		,,,				2504	0.0				p.S46L		Atlas-SNP	.											.	RIN2	126	.	0			c.C137T						PASS	.	C	LEU/SER,	279,3423		9,261,1581	18.0	22.0	21.0		137,	-2.0	0.4	20	dbSNP_129	21	9,8079		0,9,4035	no	missense,utr-5	RIN2	NM_001242581.1,NM_018993.3	145,	9,270,5616	TT,TC,CC		0.1113,7.5365,2.4427	,	46/945,	19870235	288,11502	1851	4044	5895	SO:0001583	missense	54453	exon2			GAGCCTCGCTGGG	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.137C>T	20.37:g.19870235C>T	ENSP00000255006:p.Ser46Leu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	37	CCDS56182.1	49	0.022435897435897436	49	0.09959349593495935	0	0.0	0	0.0	0	0.0	C	10.87	1.472553	0.26423	0.075365	0.001113	ENSG00000132669	ENST00000255006	T	0.07567	3.18	6.08	-1.98	0.07480	.	0.420043	0.17780	N	0.162278	T	0.00109	0.0003	N	0.08118	0	0.29121	N	0.880245	.	.	.	.	.	.	T	0.46484	-0.9188	7	.	.	.	-6.4224	7.2284	0.26028	0.0:0.2563:0.1453:0.5984	rs56311184	.	.	.	L	46	ENSP00000255006:S46L	.	S	+	2	0	RIN2	19818235	0.000000	0.05858	0.361000	0.25849	0.847000	0.48162	-0.597000	0.05713	-0.023000	0.13963	0.655000	0.94253	TCG	C|0.977;T|0.023	0.023	strong		0.517	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
NLRP4	147945	hgsc.bcm.edu	37	19	56369314	56369314	+	Silent	SNP	G	G	A	rs16986718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56369314G>A	ENST00000301295.6	+	3	977	c.555G>A	c.(553-555)acG>acA	p.T185T	NLRP4_ENST00000587891.1_Silent_p.T110T|NLRP4_ENST00000346986.5_Silent_p.T185T	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	185	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TCCTGTACACGTTCTATTTCT	0.498													A|||	1229	0.245407	0.3222	0.2651	5008	,	,		19870	0.2391		0.2575	False		,,,				2504	0.1217				p.T185T		Atlas-SNP	.											NLRP4_ENST00000301295,colon,carcinoma,0,1	NLRP4	331	1	0			c.G555A						PASS	.	A		1434,2972	466.4+/-354.5	233,968,1002	109.0	108.0	108.0		555	-8.5	0.0	19	dbSNP_123	108	2243,6357	380.1+/-339.5	291,1661,2348	yes	coding-synonymous	NLRP4	NM_134444.4		524,2629,3350	AA,AG,GG		26.0814,32.5465,28.2716		185/995	56369314	3677,9329	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			GTACACGTTCTAT	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.555G>A	19.37:g.56369314G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	182	82	0.450549	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			G|0.718;A|0.281	0.281	strong		0.498	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
MKI67	4288	hgsc.bcm.edu	37	10	129901825	129901825	+	Missense_Mutation	SNP	T	T	C	rs10082391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129901825T>C	ENST00000368654.3	-	13	8654	c.8279A>G	c.(8278-8280)gAt>gGt	p.D2760G	MKI67_ENST00000368653.3_Missense_Mutation_p.D2400G	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2760	16 X 122 AA approximate repeats.		D -> G (in dbSNP:rs10082391).		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)				GATGCCTTTATCTTCACCTGC	0.498													T|||	1162	0.232029	0.3404	0.2277	5008	,	,		21174	0.2599		0.1571	False		,,,				2504	0.137				p.D2760G		Atlas-SNP	.											.	MKI67	363	.	0			c.A8279G						PASS	.	T	GLY/ASP,GLY/ASP	1359,3047	452.0+/-349.9	207,945,1051	169.0	150.0	157.0		7199,8279	-2.4	0.0	10	dbSNP_119	157	1493,7107	283.5+/-296.1	137,1219,2944	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	94,94	344,2164,3995	CC,CT,TT		17.3605,30.8443,21.9283	possibly-damaging,possibly-damaging	2400/2897,2760/3257	129901825	2852,10154	2203	4300	6503	SO:0001583	missense	4288	exon13			CCTTTATCTTCAC	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.8279A>G	10.37:g.129901825T>C	ENSP00000357643:p.Asp2760Gly	Somatic	347	1	0.00288184		WXS	Illumina HiSeq	Phase_I	380	190	0.5	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	488	0.22344322344322345	147	0.29878048780487804	68	0.1878453038674033	150	0.26223776223776224	123	0.16226912928759896	T	12.16	1.856009	0.32791	0.308443	0.173605	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02103	4.45;4.45	3.34	-2.42	0.06542	.	.	.	.	.	T	0.00012	0.0000	N	0.10874	0.06	0.80722	P	0.0	P;D;P	0.61697	0.928;0.99;0.845	P;P;P	0.53102	0.588;0.718;0.58	T	0.48547	-0.9026	8	0.27082	T	0.32	.	4.821	0.13390	0.0:0.5127:0.2059:0.2814	rs10082391;rs52833203;rs60789844;rs10082391	2759;2400;2760	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	G	2760;2400;2759	ENSP00000357643:D2760G;ENSP00000357642:D2400G	ENSP00000357642:D2400G	D	-	2	0	MKI67	129791815	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.206000	0.17375	-0.615000	0.05679	-0.256000	0.11100	GAT	A|0.005;C|0.218	0.218	strong		0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
ZFYVE9	9372	hgsc.bcm.edu	37	1	52705174	52705174	+	Silent	SNP	A	A	G	rs34437486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:52705174A>G	ENST00000371591.1	+	3	2216	c.2085A>G	c.(2083-2085)gtA>gtG	p.V695V	ZFYVE9_ENST00000287727.3_Silent_p.V695V|ZFYVE9_ENST00000357206.2_Silent_p.V695V	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	695					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						TGGCTCCAGTATGGGTACCGG	0.478													A|||	30	0.00599042	0.0227	0.0	5008	,	,		18368	0.0		0.0	False		,,,				2504	0.0				p.V695V		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.A2085G						PASS	.	A	,,	126,4280	93.0+/-131.7	1,124,2078	71.0	69.0	70.0		2085,2085,2085	-7.1	0.7	1	dbSNP_126	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ZFYVE9	NM_004799.2,NM_007323.1,NM_007324.2	,,	1,125,6377	GG,GA,AA		0.0116,2.8597,0.9765	,,	695/1426,695/763,695/1367	52705174	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	9372	exon4			TCCAGTATGGGTA	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.2085A>G	1.37:g.52705174A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	154	70	0.454545	NM_007323	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Silent	SNP	ENST00000371591.1	37	CCDS563.1																																																																																			A|0.991;G|0.009	0.009	strong		0.478	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	
SEMA7A	8482	hgsc.bcm.edu	37	15	74706943	74706943	+	Silent	SNP	G	G	A	rs1046146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:74706943G>A	ENST00000261918.4	-	10	1787	c.1239C>T	c.(1237-1239)gtC>gtT	p.V413V	SEMA7A_ENST00000543145.2_Silent_p.V399V|SEMA7A_ENST00000542748.1_Silent_p.V248V	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	413	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						GCATGCGGTGGACGGCCACTT	0.572													G|||	922	0.184105	0.3986	0.036	5008	,	,		17268	0.1915		0.0467	False		,,,				2504	0.1329				p.V413V		Atlas-SNP	.											.	SEMA7A	58	.	0			c.C1239T						PASS	.	G	,,	1418,2976	463.0+/-353.4	231,956,1010	98.0	103.0	101.0		1197,744,1239	-6.2	0.7	15	dbSNP_86	101	392,8200	125.5+/-184.1	13,366,3917	no	coding-synonymous,coding-synonymous,coding-synonymous	SEMA7A	NM_001146029.1,NM_001146030.1,NM_003612.3	,,	244,1322,4927	AA,AG,GG		4.5624,32.2713,13.9381	,,	399/653,248/502,413/667	74706943	1810,11176	2197	4296	6493	SO:0001819	synonymous_variant	8482	exon10			GCGGTGGACGGCC	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"""Semaphorins"", ""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10741	protein-coding gene	gene with protein product	"""John Milton Hagen blood group"", ""H-Sema K1"""	607961	"""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A"", ""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"""	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1239C>T	15.37:g.74706943G>A		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	215	95	0.44186	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Silent	SNP	ENST00000261918.4	37	CCDS10262.1																																																																																			G|0.846;A|0.154	0.154	strong		0.572	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350778	50350778	+	Missense_Mutation	SNP	T	T	G	rs112781654		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:50350778T>G	ENST00000289292.7	-	6	3647	c.3364A>C	c.(3364-3366)Aag>Cag	p.K1122Q	SHROOM4_ENST00000460112.3_Missense_Mutation_p.K1006Q|SHROOM4_ENST00000376020.2_Missense_Mutation_p.K1122Q			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1122	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)					tgttgctgcttctgctgctgG	0.582																																					p.K1122Q		Atlas-SNP	.											.	SHROOM4	171	.	0			c.A3364C						PASS	.						22.0	20.0	21.0					X																	50350778		2201	4295	6496	SO:0001583	missense	57477	exon6			GCTGCTTCTGCTG	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.3364A>C	X.37:g.50350778T>G	ENSP00000289292:p.Lys1122Gln	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	95	8	0.0842105	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	T	1.804	-0.476250	0.04414	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.09073	3.02;3.02;3.02	4.36	1.23	0.21249	.	0.932286	0.08995	N	0.863864	T	0.02304	0.0071	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45071	-0.9286	10	0.06099	T	0.92	.	5.8974	0.18947	0.0:0.1611:0.3673:0.4717	.	1122	Q9ULL8	SHRM4_HUMAN	Q	1122;1122;1006	ENSP00000289292:K1122Q;ENSP00000365188:K1122Q;ENSP00000421450:K1006Q	ENSP00000289292:K1122Q	K	-	1	0	SHROOM4	50367518	0.007000	0.16637	0.012000	0.15200	0.528000	0.34623	0.084000	0.14891	0.088000	0.17205	0.417000	0.27973	AAG	T|0.500;G|0.500	0.500	weak		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
MUC4	4585	hgsc.bcm.edu	37	3	195509036	195509036	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509036C>G	ENST00000463781.3	-	2	9874	c.9415G>C	c.(9415-9417)Gtc>Ctc	p.V3139L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3139L	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)		GTGCTGGTGACAGGAAGAGCG	0.592																																					p.V3139L		Atlas-SNP	.											.	MUC4	1505	.	0			c.G9415C						PASS	.						23.0	11.0	15.0					3																	195509036		660	1552	2212	SO:0001583	missense	4585	exon2			TGGTGACAGGAAG	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.9415G>C	3.37:g.195509036C>G	ENSP00000417498:p.Val3139Leu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	256	98	0.382812	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	0.928	-0.713736	0.03206	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34072	1.38;1.42	.	.	.	.	.	.	.	.	T	0.16428	0.0395	N	0.19112	0.55	0.09310	N	1	B	0.33494	0.414	B	0.22386	0.039	T	0.15607	-1.0431	7	.	.	.	.	4.5444	0.12074	0.0:0.5833:0.4166:0.0	.	3011	E7ESK3	.	L	3139	ENSP00000417498:V3139L;ENSP00000420243:V3139L	.	V	-	1	0	MUC4	196993815	0.675000	0.27558	0.000000	0.03702	0.000000	0.00434	2.005000	0.40864	-0.000000	0.14550	0.000000	0.15137	GTC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC2	4583	hgsc.bcm.edu	37	11	1075920	1075920	+	Splice_Site	SNP	G	G	A	rs11825977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1075920G>A	ENST00000441003.2	+	2	373	c.346G>A	c.(346-348)Gtg>Atg	p.V116M	MUC2_ENST00000359061.5_Splice_Site_p.V116M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	116	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.		V -> M (in dbSNP:rs11825977).		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)	TAACGGGGCCGTGTGAGTGTG	0.632													A|||	578	0.115415	0.2148	0.0821	5008	,	,		17247	0.001		0.2078	False		,,,				2504	0.0276				p.V116M		Atlas-SNP	.											.	MUC2	614	.	0			c.G346A						PASS	.	A	MET/VAL	826,3184		103,620,1282	18.0	20.0	19.0		346	-7.6	0.6	11	dbSNP_120	19	1757,6545		199,1359,2593	yes	missense-near-splice	MUC2	NM_002457.2	21	302,1979,3875	AA,AG,GG		21.1636,20.5985,20.9795	possibly-damaging	116/2813	1075920	2583,9729	2005	4151	6156	SO:0001630	splice_region_variant	4583	exon2			GGGGCCGTGTGAG	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.347+1G>A	11.37:g.1075920G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		313	0.1433150183150183	102	0.2073170731707317	39	0.10773480662983426	1	0.0017482517482517483	171	0.22559366754617413	A	1.513	-0.548989	0.04024	0.205985	0.211636	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.59772	0.24;0.24	3.78	-7.56	0.01322	.	1.101460	0.07009	N	0.824818	T	0.00012	0.0000	N	0.11131	0.1	0.80722	P	0.0	B	0.31413	0.322	B	0.21708	0.036	T	0.04165	-1.0972	9	0.33141	T	0.24	.	2.0602	0.03590	0.3385:0.3431:0.2074:0.111	rs11825977;rs59632081;rs11825977	116	E7EUV1	.	M	116	ENSP00000415183:V116M;ENSP00000351956:V116M	ENSP00000351956:V116M	V	+	1	0	MUC2	1065920	0.020000	0.18652	0.582000	0.28627	0.104000	0.19210	-0.102000	0.10956	-2.618000	0.00441	-2.870000	0.00099	GTG	G|0.851;A|0.149	0.149	strong		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	Missense_Mutation
OR51M1	390059	hgsc.bcm.edu	37	11	5411398	5411398	+	Missense_Mutation	SNP	T	T	G	rs2736531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5411398T>G	ENST00000328611.3	+	1	792	c.770T>G	c.(769-771)cTc>cGc	p.L257R	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001004756.2	NP_001004756.2	Q9H341	O51M1_HUMAN	olfactory receptor, family 51, subfamily M, member 1	257			L -> R (in dbSNP:rs2736531). {ECO:0000269|PubMed:11121057}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|upper_aerodigestive_tract(1)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.98e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCGCTCCTCTCTGTGCTGTG	0.562													T|||	1805	0.360423	0.3419	0.3228	5008	,	,		20493	0.3145		0.3767	False		,,,				2504	0.4427				p.L257R		Atlas-SNP	.											.	OR51M1	60	.	0			c.T770G						PASS	.	T	ARG/LEU	1355,2769		217,921,924	99.0	92.0	94.0		770	5.2	1.0	11	dbSNP_100	94	3136,5260		601,1934,1663	yes	missense	OR51M1	NM_001004756.2	102	818,2855,2587	GG,GT,TT		37.3511,32.8565,35.8706	benign	257/327	5411398	4491,8029	2062	4198	6260	SO:0001583	missense	390059	exon1			CTCCTCTCTGTGC	BK004382	CCDS53596.1	11p15.4	2012-08-09			ENSG00000184698	ENSG00000184698		"""GPCR / Class A : Olfactory receptors"""	14847	protein-coding gene	gene with protein product							Standard	NM_001004756		Approved		uc010qzc.2	Q9H341	OTTHUMG00000066680	ENST00000328611.3:c.770T>G	11.37:g.5411398T>G	ENSP00000333196:p.Leu257Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_001004756	Q6IF80	Missense_Mutation	SNP	ENST00000328611.3	37	CCDS53596.1	721	0.3301282051282051	157	0.31910569105691056	127	0.35082872928176795	174	0.3041958041958042	263	0.3469656992084433	T	18.57	3.653476	0.67472	0.328565	0.373511	ENSG00000184698	ENST00000328611	T	0.51325	0.71	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.288076	0.18688	U	0.133956	T	0.00012	0.0000	M	0.68952	2.095	0.27897	P	0.939105	P	0.49307	0.922	P	0.59948	0.866	T	0.21314	-1.0249	9	0.87932	D	0	.	14.0973	0.65032	0.0:0.0:0.0:1.0	rs2736531;rs52814371;rs2736531	246	Q9H341	O51M1_HUMAN	R	257	ENSP00000333196:L257R	ENSP00000333196:L257R	L	+	2	0	OR51M1	5367974	0.569000	0.26643	1.000000	0.80357	0.790000	0.44656	4.461000	0.60115	2.207000	0.71202	0.533000	0.62120	CTC	T|0.663;G|0.337	0.337	strong		0.562	OR51M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142981.1	NM_001004756	
IRAK4	51135	hgsc.bcm.edu	37	12	44180295	44180295	+	Missense_Mutation	SNP	G	G	A	rs4251545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:44180295G>A	ENST00000448290.2	+	11	1353	c.1282G>A	c.(1282-1284)Gct>Act	p.A428T	IRAK4_ENST00000431837.1_Missense_Mutation_p.A304T|IRAK4_ENST00000551736.1_Missense_Mutation_p.A428T|IRAK4_ENST00000440781.2_Missense_Mutation_p.A304T	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	428	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in dbSNP:rs4251545). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.5}.		cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		TTCAGTTGAAGCTATGTACTC	0.284													g|||	854	0.170527	0.3169	0.1455	5008	,	,		13391	0.127		0.0865	False		,,,				2504	0.1217				p.A428T		Atlas-SNP	.											.	IRAK4	77	.	0			c.G1282A						PASS	.	A	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	1200,3206	407.8+/-334.4	154,892,1157	68.0	79.0	75.0		1282,910,910,910,1282	-0.3	0.1	12	dbSNP_111	75	847,7743	190.8+/-237.2	35,777,3483	yes	missense,missense,missense,missense,missense	IRAK4	NM_001114182.2,NM_001145256.1,NM_001145257.1,NM_001145258.1,NM_016123.3	58,58,58,58,58	189,1669,4640	AA,AG,GG		9.8603,27.2356,15.751	benign,benign,benign,benign,benign	428/461,304/337,304/337,304/337,428/461	44180295	2047,10949	2203	4295	6498	SO:0001583	missense	51135	exon11			GTTGAAGCTATGT	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		ENST00000448290.2:c.1282G>A	12.37:g.44180295G>A	ENSP00000390651:p.Ala428Thr	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	132	78	0.590909	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	37	CCDS8744.1	328	0.15018315018315018	160	0.3252032520325203	51	0.1408839779005525	55	0.09615384615384616	62	0.08179419525065963	g	8.196	0.797029	0.16327	0.272356	0.098603	ENSG00000198001	ENST00000440781;ENST00000431837;ENST00000448290;ENST00000551736	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	6.02	-0.286	0.12862	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.615280	0.18370	N	0.143300	T	0.00012	0.0000	L	0.37630	1.12	0.54753	P	1.2000000000012001E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.24333	-1.0163	9	0.35671	T	0.21	-0.8847	7.4103	0.27014	0.6553:0.1054:0.2393:0.0	rs4251545;rs52833385;rs57239220;rs4251545	428	Q9NWZ3	IRAK4_HUMAN	T	304;304;428;428	ENSP00000408734:A304T;ENSP00000390327:A304T;ENSP00000390651:A428T;ENSP00000446490:A428T	ENSP00000390327:A304T	A	+	1	0	IRAK4	42466562	0.972000	0.33761	0.062000	0.19696	0.991000	0.79684	0.757000	0.26433	-0.274000	0.09232	-0.127000	0.14921	GCT	G|0.843;A|0.157	0.157	strong		0.284	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1		
MC1R	4157	hgsc.bcm.edu	37	16	89986566	89986566	+	Silent	SNP	C	C	T	rs3212367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89986566C>T	ENST00000555147.1	+	1	2280	c.900C>T	c.(898-900)ttC>ttT	p.F300F	MC1R_ENST00000555427.1_Silent_p.F300F|RP11-566K11.4_ENST00000554623.1_RNA|RP11-566K11.7_ENST00000570217.1_RNA|TUBB3_ENST00000556922.1_Silent_p.F300F|TUBB3_ENST00000554444.1_5'Flank	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	300					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)		TCTACGCCTTCCACAGCCAGG	0.612									Melanoma, Familial Clustering of				C|||	98	0.0195687	0.0711	0.0058	5008	,	,		20124	0.0		0.0	False		,,,				2504	0.0				p.F300F		Atlas-SNP	.											.	MC1R	20	.	0			c.C900T						PASS	.	C		201,3963		2,197,1883	62.0	66.0	64.0		900	3.3	1.0	16	dbSNP_106	64	5,8459		0,5,4227	no	coding-synonymous	MC1R	NM_002386.3		2,202,6110	TT,TC,CC		0.0591,4.8271,1.6313		300/318	89986566	206,12422	2082	4232	6314	SO:0001819	synonymous_variant	4157	exon1	Familial Cancer Database		CGCCTTCCACAGC		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.900C>T	16.37:g.89986566C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	162	75	0.462963	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Silent	SNP	ENST00000555147.1	37	CCDS56011.1																																																																																			C|0.978;T|0.022	0.022	strong		0.612	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
ABCC10	89845	hgsc.bcm.edu	37	6	43413669	43413669	+	Silent	SNP	G	G	A	rs112977568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43413669G>A	ENST00000372530.4	+	15	3578	c.3363G>A	c.(3361-3363)ggG>ggA	p.G1121G	ABCC10_ENST00000244533.3_Silent_p.G1093G	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	1121	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	GGGCCACAGGGGCCACCTACA	0.622													G|||	37	0.00738818	0.0272	0.0	5008	,	,		18669	0.0		0.001	False		,,,				2504	0.0				p.G1121G		Atlas-SNP	.											.	ABCC10	118	.	0			c.G3363A						PASS	.	G	,	106,4248		1,104,2072	21.0	23.0	22.0		3363,3279	3.4	1.0	6	dbSNP_132	22	0,8536		0,0,4268	no	coding-synonymous,coding-synonymous	ABCC10	NM_001198934.1,NM_033450.2	,	1,104,6340	AA,AG,GG		0.0,2.4345,0.8223	,	1121/1493,1093/1465	43413669	106,12784	2177	4268	6445	SO:0001819	synonymous_variant	89845	exon15			CACAGGGGCCACC	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.3363G>A	6.37:g.43413669G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	37	CCDS56430.1																																																																																			G|0.992;A|0.008	0.008	strong		0.622	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
FRAS1	80144	hgsc.bcm.edu	37	4	79432455	79432455	+	Silent	SNP	A	A	C	rs3749488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79432455A>C	ENST00000264895.6	+	64	10248	c.9808A>C	c.(9808-9810)Agg>Cgg	p.R3270R		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3266					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						CTTCAGCCGGAGGTTCCATGT	0.488													A|||	2026	0.404553	0.4455	0.2925	5008	,	,		20972	0.4554		0.2674	False		,,,				2504	0.5174				p.R3270R		Atlas-SNP	.											.	FRAS1	779	.	0			c.A9808C						PASS	.	A		1642,2560		339,964,798	127.0	126.0	126.0		9808	-0.3	1.0	4	dbSNP_107	126	2109,6351		266,1577,2387	no	coding-synonymous	FRAS1	NM_025074.6		605,2541,3185	CC,CA,AA		24.9291,39.0766,29.6241		3270/4013	79432455	3751,8911	2101	4230	6331	SO:0001819	synonymous_variant	80144	exon64			AGCCGGAGGTTCC	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.9808A>C	4.37:g.79432455A>C		Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	313	146	0.466454	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	805	0.3685897435897436	219	0.4451219512195122	99	0.27348066298342544	277	0.48426573426573427	210	0.2770448548812665	A	10.70	1.425249	0.25639	0.390766	0.249291	ENSG00000138759	ENST00000512123	.	.	.	5.7	-0.309	0.12769	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.50566	-0.8813	3	.	.	.	.	15.3355	0.74250	0.3525:0.6475:0.0:0.0	rs3749488;rs60064328;rs3749488	.	.	.	A	1498	.	.	E	+	2	0	FRAS1	79651479	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.791000	0.38744	0.387000	0.25024	0.383000	0.25322	GAG	A|0.628;C|0.372	0.372	strong		0.488	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
UMPS	7372	hgsc.bcm.edu	37	3	124456742	124456742	+	Missense_Mutation	SNP	G	G	C	rs1801019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124456742G>C	ENST00000232607.2	+	3	744	c.638G>C	c.(637-639)gGt>gCt	p.G213A	UMPS_ENST00000498715.1_3'UTR|UMPS_ENST00000538242.1_Missense_Mutation_p.G35A|UMPS_ENST00000536109.1_Missense_Mutation_p.G121A|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	73	0	0		WXS	Illumina HiSeq	Phase_I	96	42	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	
TMEM176A	55365	hgsc.bcm.edu	37	7	150498773	150498773	+	Silent	SNP	C	C	T	rs10239586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150498773C>T	ENST00000484928.1	+	2	716	c.135C>T	c.(133-135)acC>acT	p.T45T	TMEM176B_ENST00000434545.1_5'Flank|TMEM176A_ENST00000004103.3_Silent_p.T45T|TMEM176B_ENST00000447204.2_5'Flank|TMEM176B_ENST00000450753.2_5'Flank|TMEM176B_ENST00000492607.1_5'Flank|TMEM176B_ENST00000326442.5_5'Flank|TMEM176A_ENST00000461345.1_Intron			Q96HP8	T176A_HUMAN	transmembrane protein 176A	45					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCCGGGCCACCCAGGCCAGGG	0.711													C|||	33	0.00658946	0.025	0.0	5008	,	,		12886	0.0		0.0	False		,,,				2504	0.0				p.T45T		Atlas-SNP	.											.	TMEM176A	35	.	0			c.C135T						PASS	.	C		60,4254		0,60,2097	8.0	9.0	8.0		135	3.0	0.0	7	dbSNP_119	8	0,8462		0,0,4231	no	coding-synonymous	TMEM176A	NM_018487.2		0,60,6328	TT,TC,CC		0.0,1.3908,0.4696		45/236	150498773	60,12716	2157	4231	6388	SO:0001819	synonymous_variant	55365	exon2			GGCCACCCAGGCC	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.135C>T	7.37:g.150498773C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	30	17	0.566667	NM_018487	D3DX00|Q9NYC7	Silent	SNP	ENST00000484928.1	37	CCDS5909.1																																																																																			C|0.993;T|0.007	0.007	strong		0.711	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037557	33037557	+	Silent	SNP	C	C	T	rs1042177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33037557C>T	ENST00000419277.1	-	3	336	c.207G>A	c.(205-207)aaG>aaA	p.K69K	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Silent_p.K69K	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	69	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CGGTCTCCTTCTTGTCCAGAT	0.453													.|||	1181	0.235823	0.3775	0.2363	5008	,	,		19499	0.1022		0.1551	False		,,,				2504	0.2648				p.K69K		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G207A						PASS	.	C	,,	807,2215		129,549,833	69.0	91.0	83.0		207,207,207	3.0	0.8	6	dbSNP_86	83	718,4700		45,628,2036	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	174,1177,2869	TT,TC,CC		13.2521,26.7042,18.0687	,,	69/261,69/261,69/261	33037557	1525,6915	1511	2709	4220	SO:0001819	synonymous_variant	3113	exon2			CTCCTTCTTGTCC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.207G>A	6.37:g.33037557C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	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	
SERPINA5	5104	hgsc.bcm.edu	37	14	95053863	95053863	+	Missense_Mutation	SNP	C	C	T	rs6118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95053863C>T	ENST00000554866.1	+	2	278	c.164C>T	c.(163-165)gCc>gTc	p.A55V	SERPINA5_ENST00000553780.1_Missense_Mutation_p.A55V|SERPINA5_ENST00000554276.1_Missense_Mutation_p.A55V|SERPINA5_ENST00000329597.7_Missense_Mutation_p.A55V			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	55			A -> V (in allele PCI*B; dbSNP:rs6118). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:8713781, ECO:0000269|Ref.6}.		fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CTCTACAGGGCCTTGGCTTCC	0.617													C|||	1382	0.275958	0.6157	0.1196	5008	,	,		18490	0.2758		0.0905	False		,,,				2504	0.1186				p.A55V		Atlas-SNP	.											.	SERPINA5	69	.	0			c.C164T						PASS	.	C	VAL/ALA	2242,2164	582.4+/-385.6	573,1096,534	42.0	40.0	41.0		164	0.8	1.0	14	dbSNP_52	41	818,7782	188.4+/-235.4	41,736,3523	yes	missense	SERPINA5	NM_000624.4	64	614,1832,4057	TT,TC,CC		9.5116,49.1148,23.5276	possibly-damaging	55/407	95053863	3060,9946	2203	4300	6503	SO:0001583	missense	5104	exon3			ACAGGGCCTTGGC	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.164C>T	14.37:g.95053863C>T	ENSP00000451126:p.Ala55Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_000624	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	37	CCDS9928.1	551	0.2522893772893773	291	0.5914634146341463	48	0.13259668508287292	142	0.24825174825174826	70	0.09234828496042216	C	2.095	-0.407466	0.04832	0.508852	0.095116	ENSG00000188488	ENST00000554220;ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000553511;ENST00000554633;ENST00000555681;ENST00000554276;ENST00000557598	D;D;D;D;D;D;D;D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97	4.11	0.813	0.18749	Serpin domain (3);	0.357145	0.22789	N	0.055621	T	0.00012	0.0000	L	0.42686	1.345	0.80722	P	0.0	P;P	0.43885	0.784;0.82	B;B	0.33339	0.153;0.162	T	0.48547	-0.9026	9	0.40728	T	0.16	.	6.2696	0.20947	0.343:0.3768:0.2802:0.0	rs6118;rs933176;rs60797362;rs6118	55;55	G3V5Q9;P05154	.;IPSP_HUMAN	V	55	ENSP00000450484:A55V;ENSP00000450837:A55V;ENSP00000452469:A55V;ENSP00000451126:A55V;ENSP00000333203:A55V;ENSP00000450745:A55V;ENSP00000451215:A55V;ENSP00000451697:A55V;ENSP00000451650:A55V;ENSP00000451610:A55V;ENSP00000450485:A55V	ENSP00000333203:A55V	A	+	2	0	SERPINA5	94123616	0.000000	0.05858	0.996000	0.52242	0.121000	0.20230	0.741000	0.26202	0.442000	0.26555	0.561000	0.74099	GCC	C|0.764;T|0.236	0.236	strong		0.617	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
NPY4R	5540	hgsc.bcm.edu	37	10	47086915	47086915	+	Silent	SNP	C	C	T	rs59974223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:47086915C>T	ENST00000395716.1	+	2	217	c.132C>T	c.(130-132)atC>atT	p.I44I	NPY4R_ENST00000374312.1_Silent_p.I44I			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	44					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										TGGTCTTCATCGTCACTTCCT	0.522																																					p.I44I		Atlas-SNP	.											.	PPYR1	54	.	0			c.C132T						PASS	.	C		589,3817		0,589,1614	238.0	209.0	219.0		132	0.5	0.5	10	dbSNP_129	219	922,7678		0,922,3378	no	coding-synonymous	PPYR1	NM_005972.4		0,1511,4992	TT,TC,CC		10.7209,13.3681,11.6177		44/376	47086915	1511,11495	2203	4300	6503	SO:0001819	synonymous_variant	5540	exon3			CTTCATCGTCACT		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"""GPCR / Class A : Neuropeptide receptors : Y"""	9329	protein-coding gene	gene with protein product		601790	"""pancreatic polypeptide receptor 1"""	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.132C>T	10.37:g.47086915C>T		Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	428	114	0.266355	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Silent	SNP	ENST00000395716.1	37	CCDS31193.1																																																																																			C|0.835;T|0.165	0.165	strong		0.522	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
SMCHD1	23347	hgsc.bcm.edu	37	18	2740798	2740798	+	Silent	SNP	A	A	T	rs115632137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2740798A>T	ENST00000320876.6	+	28	3950	c.3612A>T	c.(3610-3612)tcA>tcT	p.S1204S	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Silent_p.S1204S	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1204					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						TTGATAGCTCAAATTTGAAAA	0.313													A|||	154	0.0307508	0.1104	0.0101	5008	,	,		14819	0.0		0.001	False		,,,				2504	0.0				p.S1204S		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A3612T						PASS	.	A		399,3233		26,347,1443	108.0	110.0	109.0		3612	-0.6	1.0	18	dbSNP_132	109	7,8115		0,7,4054	no	coding-synonymous	SMCHD1	NM_015295.2		26,354,5497	TT,TA,AA		0.0862,10.9857,3.4541		1204/2006	2740798	406,11348	1816	4061	5877	SO:0001819	synonymous_variant	23347	exon28			TAGCTCAAATTTG	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.3612A>T	18.37:g.2740798A>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	129	74	0.573643	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			A|0.973;T|0.027	0.027	strong		0.313	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
MBTPS1	8720	hgsc.bcm.edu	37	16	84115393	84115393	+	Silent	SNP	G	G	A	rs12933523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84115393G>A	ENST00000343411.3	-	11	1902	c.1407C>T	c.(1405-1407)ctC>ctT	p.L469L	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	469	Peptidase S8.				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)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GATAGGCTCTGAGCAGATCGA	0.592													G|||	471	0.0940495	0.0287	0.1153	5008	,	,		14673	0.1131		0.1779	False		,,,				2504	0.0613				p.L469L		Atlas-SNP	.											.	MBTPS1	85	.	0			c.C1407T						PASS	.	G		245,4155	143.1+/-178.2	4,237,1959	100.0	94.0	96.0		1407	-3.9	0.0	16	dbSNP_121	96	1554,7046	291.7+/-300.5	130,1294,2876	no	coding-synonymous	MBTPS1	NM_003791.2		134,1531,4835	AA,AG,GG		18.0698,5.5682,13.8385		469/1053	84115393	1799,11201	2200	4300	6500	SO:0001819	synonymous_variant	8720	exon11			GGCTCTGAGCAGA	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"""membrane-bound transcription factor protease, site 1"""			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.1407C>T	16.37:g.84115393G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	48	28	0.583333	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	37	CCDS10941.1																																																																																			G|0.869;A|0.131	0.131	strong		0.592	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791	
SPINK14	408187	hgsc.bcm.edu	37	5	147553829	147553829	+	Silent	SNP	C	C	T	rs79779038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147553829C>T	ENST00000356972.1	+	3	144	c.144C>T	c.(142-144)agC>agT	p.S48S	SPINK14_ENST00000562793.1_Intron	NM_001001325.1	NP_001001325.1	Q6IE38	ISK14_HUMAN	serine peptidase inhibitor, Kazal type 14 (putative)	48	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|large_intestine(1)|lung(1)	3						TAAACTTGAGCTGGTACAATG	0.413													T|||	536	0.107029	0.388	0.0303	5008	,	,		9611	0.001		0.001	False		,,,				2504	0.0				p.S48S		Atlas-SNP	.											.	SPINK14	9	.	0			c.C144T						PASS	.	T		841,2147		340,161,993	107.0	107.0	107.0		144	0.1	1.0	5	dbSNP_131	107	13,6231		1,11,3110	no	coding-synonymous	SPINK14	NM_001001325.1		341,172,4103	TT,TC,CC		0.2082,28.1459,9.2504		48/98	147553829	854,8378	1494	3122	4616	SO:0001819	synonymous_variant	408187	exon3			CTTGAGCTGGTAC		CCDS4288.1	5q32	2011-08-31			ENSG00000196800	ENSG00000196800		"""Serine peptidase inhibitors, Kazal type"""	33825	protein-coding gene	gene with protein product							Standard	NM_001001325		Approved	SPINK5L2	uc031sls.1	Q6IE38	OTTHUMG00000129732	ENST00000356972.1:c.144C>T	5.37:g.147553829C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001001325		Silent	SNP	ENST00000356972.1	37	CCDS4288.1																																																																																			C|0.919;T|0.081	0.081	strong		0.413	SPINK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251943.2	NM_001001325	
GRIPAP1	56850	hgsc.bcm.edu	37	X	48847444	48847444	+	Missense_Mutation	SNP	G	G	A	rs61735977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48847444G>A	ENST00000376441.1	-	7	570	c.536C>T	c.(535-537)cCg>cTg	p.P179L	GRIPAP1_ENST00000376425.3_Missense_Mutation_p.P179L|GRIPAP1_ENST00000376444.3_Missense_Mutation_p.P134L|GRIPAP1_ENST00000376423.4_Missense_Mutation_p.P126L|GRIPAP1_ENST00000473581.1_5'UTR	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	179						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						GGTGGGGGCCGGGCCCCCTGG	0.607													g|||	210	0.0556291	0.1536	0.0101	3775	,	,		13683	0.0		0.0	False		,,,				2504	0.0				p.P179L		Atlas-SNP	.											.	GRIPAP1	128	.	0			c.C536T						PASS	.	G	LEU/PRO,LEU/PRO	586,3247		42,415,87,1174,484	39.0	39.0	39.0		536,377	-3.4	0.0	X	dbSNP_129	39	3,6720		1,0,1,2425,1870	yes	missense,missense	GRIPAP1	NM_020137.3,NM_207672.1	98,98	43,415,88,3599,2354	AA,AG,A,GG,G		0.0446,15.2883,5.5798	benign,benign	179/842,126/626	48847444	589,9967	2202	4297	6499	SO:0001583	missense	56850	exon7			GGGGCCGGGCCCC	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.536C>T	X.37:g.48847444G>A	ENSP00000365624:p.Pro179Leu	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	274	144	0.525547	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	37	CCDS35248.1	68	0.040988547317661245	42	0.09375	4	0.011049723756906077	0	0.0	0	0.0	G	5.167	0.216332	0.09810	0.152883	4.46E-4	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291;ENST00000376423	.	.	.	4.93	-3.43	0.04810	.	0.972273	0.08459	N	0.942672	T	0.00109	0.0003	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.0;0.002;0.0	T	0.24657	-1.0154	8	0.25751	T	0.34	0.5395	1.8839	0.03234	0.123:0.1269:0.4976:0.2524	.	126;69;179	Q4V328-2;Q4V328-3;Q4V328	.;.;GRAP1_HUMAN	L	179;134;179;179;126	.	ENSP00000365606:P126L	P	-	2	0	GRIPAP1	48732388	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.152000	0.10159	-0.872000	0.04037	-1.012000	0.02466	CCG	G|0.945;A|0.055	0.055	strong		0.607	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
CCDC157	550631	hgsc.bcm.edu	37	22	30761995	30761995	+	Silent	SNP	G	G	A	rs61732271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30761995G>A	ENST00000405659.1	+	3	715	c.6G>A	c.(4-6)gcG>gcA	p.A2A	CCDC157_ENST00000338306.3_Silent_p.A2A|CCDC157_ENST00000399824.2_Silent_p.A2A			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	2										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						TGAGGATGGCGCACCTGCTGG	0.657													G|||	89	0.0177716	0.0651	0.0029	5008	,	,		18741	0.0		0.001	False		,,,				2504	0.0				p.A2A		Atlas-SNP	.											.	CCDC157	86	.	0			c.G6A						PASS	.	G		69,1315		1,67,624	21.0	27.0	25.0		6	-10.5	0.8	22	dbSNP_129	25	0,3182		0,0,1591	no	coding-synonymous	CCDC157	NM_001017437.2		1,67,2215	AA,AG,GG		0.0,4.9855,1.5112		2/753	30761995	69,4497	692	1591	2283	SO:0001819	synonymous_variant	550631	exon3			GATGGCGCACCTG	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.6G>A	22.37:g.30761995G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	20	5	0.25	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			G|0.990;A|0.010	0.010	strong		0.657	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
NEIL3	55247	hgsc.bcm.edu	37	4	178231219	178231219	+	Missense_Mutation	SNP	C	C	T	rs34007209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:178231219C>T	ENST00000264596.3	+	1	230	c.112C>T	c.(112-114)Cgc>Tgc	p.R38C		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	38			R -> C (in dbSNP:rs34007209). {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)		TCTGCAGGGCCGCGCCTTGCG	0.652								Base excision repair (BER), DNA glycosylases					C|||	530	0.105831	0.3623	0.0447	5008	,	,		12349	0.0		0.0149	False		,,,				2504	0.0051				p.R38C		Atlas-SNP	.											NEIL3,NS,carcinoma,0,2	NEIL3	89	2	0			c.C112T						PASS	.	C	CYS/ARG	1374,3022		237,900,1061	14.0	16.0	15.0		112	-0.4	0.0	4	dbSNP_126	15	159,8417		4,151,4133	no	missense	NEIL3	NM_018248.2	180	241,1051,5194	TT,TC,CC		1.854,31.2557,11.8178	possibly-damaging	38/606	178231219	1533,11439	2198	4288	6486	SO:0001583	missense	55247	exon1			CAGGGCCGCGCCT	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.112C>T	4.37:g.178231219C>T	ENSP00000264596:p.Arg38Cys	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	57	33	0.578947	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	198	0.09065934065934066	170	0.34552845528455284	16	0.04419889502762431	0	0.0	12	0.0158311345646438	C	13.86	2.362325	0.41902	0.312557	0.01854	ENSG00000109674	ENST00000264596	T	0.23552	1.9	4.59	-0.355	0.12587	DNA glycosylase/AP lyase, catalytic domain (1);	1.002150	0.08041	N	0.995170	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.48640	0.913	B	0.35312	0.2	T	0.41893	-0.9483	9	0.59425	D	0.04	-0.0398	4.619	0.12440	0.0:0.4873:0.155:0.3576	rs34007209	38	Q8TAT5	NEIL3_HUMAN	C	38	ENSP00000264596:R38C	ENSP00000264596:R38C	R	+	1	0	NEIL3	178468213	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-0.600000	0.05693	-0.228000	0.09869	0.561000	0.74099	CGC	C|0.884;T|0.116	0.116	strong		0.652	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
HNRNPA2B1	3181	hgsc.bcm.edu	37	7	26236235	26236235	+	Silent	SNP	T	T	C	rs34317198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:26236235T>C	ENST00000354667.4	-	6	723	c.555A>G	c.(553-555)agA>agG	p.R185R	HNRNPA2B1_ENST00000356674.7_Silent_p.R173R	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	185	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|RNA binding (GO:0003723)|single-stranded telomeric DNA binding (GO:0043047)		HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22						ACAAAGCCTTTCTTACTTCTG	0.323			T	ETV1	prostate								T|||	259	0.0517173	0.1861	0.0173	5008	,	,		19739	0.0		0.001	False		,,,				2504	0.0				p.R185R		Atlas-SNP	.		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	.	HNRNPA2B1	70	.	0			c.A555G						PASS	.	T	,	677,3729	285.5+/-278.2	40,597,1566	168.0	179.0	176.0		519,555	4.9	1.0	7	dbSNP_126	176	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	HNRNPA2B1	NM_002137.3,NM_031243.2	,	40,603,5860	CC,CT,TT		0.0698,15.3654,5.2514	,	173/342,185/354	26236235	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	3181	exon6			AGCCTTTCTTACT	D28877	CCDS5397.1, CCDS43557.1	7p15	2013-02-12		2007-08-16	ENSG00000122566	ENSG00000122566		"""RNA binding motif (RRM) containing"""	5033	protein-coding gene	gene with protein product		600124		HNRPA2B1		8029005	Standard	NM_002137		Approved		uc003sxr.4	P22626	OTTHUMG00000023471	ENST00000354667.4:c.555A>G	7.37:g.26236235T>C		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	170	78	0.458824	NM_031243	A8K064|P22627|Q9UC98|Q9UDJ2	Silent	SNP	ENST00000354667.4	37	CCDS43557.1																																																																																			T|0.935;C|0.065	0.065	strong		0.323	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137	
MFSD6L	162387	hgsc.bcm.edu	37	17	8701701	8701701	+	Silent	SNP	A	A	G	rs16957601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8701701A>G	ENST00000329805.4	-	1	966	c.738T>C	c.(736-738)ttT>ttC	p.F246F		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	246						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						AGGAGAGGATAAAAGTCCGCC	0.582													G|||	141	0.028155	0.1021	0.0072	5008	,	,		17572	0.0		0.001	False		,,,				2504	0.0				p.F246F		Atlas-SNP	.											.	MFSD6L	46	.	0			c.T738C						PASS	.	G		349,4057	788.5+/-414.9	14,321,1868	56.0	63.0	60.0		738	2.8	1.0	17	dbSNP_123	60	2,8598	812.0+/-407.1	0,2,4298	no	coding-synonymous	MFSD6L	NM_152599.3		14,323,6166	GG,GA,AA		0.0233,7.921,2.6988		246/587	8701701	351,12655	2203	4300	6503	SO:0001819	synonymous_variant	162387	exon1			GAGGATAAAAGTC	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.738T>C	17.37:g.8701701A>G		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	12	9	0.75	NM_152599	Q6YL34|Q8NA76	Silent	SNP	ENST00000329805.4	37	CCDS11146.1																																																																																			A|0.974;G|0.026	0.026	strong		0.582	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1	NM_152599	
BAI1	575	hgsc.bcm.edu	37	8	143599594	143599594	+	Silent	SNP	C	C	T	rs75573695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143599594C>T	ENST00000517894.1	+	19	3807	c.2913C>T	c.(2911-2913)tcC>tcT	p.S971S	BAI1_ENST00000323289.5_Silent_p.S971S			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	971					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					TCTACGTGTCCGTGTGGAGGT	0.632													C|||	247	0.0493211	0.1142	0.0187	5008	,	,		14503	0.0258		0.002	False		,,,				2504	0.0562				p.S971S		Atlas-SNP	.											.	BAI1	146	.	0			c.C2913T						PASS	.	C		384,4012	181.2+/-209.3	15,354,1829	148.0	152.0	151.0		2913	-3.8	1.0	8	dbSNP_132	151	9,8573	6.4+/-24.3	0,9,4282	no	coding-synonymous	BAI1	NM_001702.2		15,363,6111	TT,TC,CC		0.1049,8.7352,3.0282		971/1585	143599594	393,12585	2198	4291	6489	SO:0001819	synonymous_variant	575	exon18			CGTGTCCGTGTGG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"""-"", ""GPCR / Class B : Orphans"""	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.2913C>T	8.37:g.143599594C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	145	67	0.462069	NM_001702		Silent	SNP	ENST00000517894.1	37																																																																																				C|0.964;T|0.036	0.036	strong		0.632	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702	
GPC2	221914	hgsc.bcm.edu	37	7	99773879	99773879	+	Silent	SNP	G	G	A	rs74662631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99773879G>A	ENST00000292377.2	-	2	443	c.276C>T	c.(274-276)agC>agT	p.S92S	GPC2_ENST00000471050.1_5'Flank|STAG3_ENST00000317296.5_5'Flank|STAG3_ENST00000426455.1_5'Flank|STAG3_ENST00000394018.2_5'Flank	NM_152742.1	NP_689955.1	Q8N158	GPC2_HUMAN	glypican 2	92					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)|neuron differentiation (GO:0030182)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	anchored component of membrane (GO:0031225)|endoplasmic reticulum (GO:0005783)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(3)	18	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GAAAGGAGCCGCTGTCCTCCA	0.587													G|||	87	0.0173722	0.0628	0.0058	5008	,	,		14063	0.0		0.0	False		,,,				2504	0.0				p.S92S		Atlas-SNP	.											.	GPC2	49	.	0			c.C276T						PASS	.	G		233,4173	138.4+/-174.2	6,221,1976	54.0	45.0	48.0		276	-4.0	0.4	7	dbSNP_132	48	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPC2	NM_152742.1		6,222,6275	AA,AG,GG		0.0116,5.2882,1.7992		92/580	99773879	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	221914	exon2			GGAGCCGCTGTCC	BX375153	CCDS5689.1	7q22.1	2007-02-16	2007-02-15		ENSG00000213420	ENSG00000213420		"""Proteoglycans / Cell Surface : Glypicans"""	4450	protein-coding gene	gene with protein product	"""glypican proteoglycan 2, cerebroglycan proteoglycan"""		"""glypican 2 (cerebroglycan)"""			8294498	Standard	NM_152742		Approved	cerebroglycan, FLJ38962, DKFZp547M109	uc003utv.3	Q8N158	OTTHUMG00000154894	ENST00000292377.2:c.276C>T	7.37:g.99773879G>A		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	276	136	0.492754	NM_152742	A4D2A7	Silent	SNP	ENST00000292377.2	37	CCDS5689.1																																																																																			G|0.985;A|0.015	0.015	strong		0.587	GPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337556.1	NM_152742	
TAS2R30	259293	hgsc.bcm.edu	37	12	11286214	11286214	+	Missense_Mutation	SNP	C	C	G	rs200082783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11286214C>G	ENST00000539585.1	-	1	1029	c.630G>C	c.(628-630)caG>caC	p.Q210H	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	210					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						TGCCATGGAGCTGCATCTTCT	0.428																																					p.Q210H		Atlas-SNP	.											TAS2R30,NS,carcinoma,0,1	TAS2R30	28	1	0			c.G630C						scavenged	.						214.0	229.0	224.0					12																	11286214		2203	4300	6503	SO:0001583	missense	259293	exon1			ATGGAGCTGCATC	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19112	protein-coding gene	gene with protein product		613963	"""taste receptor, type 2, member 47"""	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.630G>C	12.37:g.11286214C>G	ENSP00000444736:p.Gln210His	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	283	25	0.0883392	NM_001097643	Q645X7	Missense_Mutation	SNP	ENST00000539585.1	37	CCDS53750.1	.	.	.	.	.	.	.	.	.	.	-	5.367	0.253041	0.10185	.	.	ENSG00000256188	ENST00000539585	T	0.00966	5.49	2.6	-0.678	0.11353	.	.	.	.	.	T	0.02012	0.0063	M	0.84846	2.72	0.09310	N	1	B	0.20887	0.049	B	0.33254	0.16	T	0.41305	-0.9516	9	0.66056	D	0.02	.	2.6486	0.04992	0.2226:0.4927:0.0:0.2847	.	210	P59541	T2R30_HUMAN	H	210	ENSP00000444736:Q210H	ENSP00000444736:Q210H	Q	-	3	2	TAS2R30	11177481	0.000000	0.05858	0.002000	0.10522	0.021000	0.10359	-1.414000	0.02471	-0.324000	0.08589	-0.823000	0.03104	CAG	C|0.944;G|0.055	0.055	strong		0.428	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643	
BRAT1	221927	hgsc.bcm.edu	37	7	2578181	2578181	+	Missense_Mutation	SNP	C	C	T	rs61627394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2578181C>T	ENST00000340611.4	-	14	2244	c.1988G>A	c.(1987-1989)gGc>gAc	p.G663D	BRAT1_ENST00000473879.1_5'UTR	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	663					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						CAAAGTCTGGCCCAGGAACAC	0.711													C|||	584	0.116613	0.0877	0.0591	5008	,	,		14377	0.2748		0.0199	False		,,,				2504	0.1329				p.G663D		Atlas-SNP	.											.	BRAT1	57	.	0			c.G1988A						PASS	.	C	ASP/GLY	280,4114		10,260,1927	13.0	16.0	15.0		1988	-8.4	0.0	7	dbSNP_129	15	88,8492		0,88,4202	yes	missense	BRAT1	NM_152743.3	94	10,348,6129	TT,TC,CC		1.0256,6.3723,2.8364	benign	663/822	2578181	368,12606	2197	4290	6487	SO:0001583	missense	221927	exon14			GTCTGGCCCAGGA	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.1988G>A	7.37:g.2578181C>T	ENSP00000339637:p.Gly663Asp	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	220	0.10073260073260074	38	0.07723577235772358	11	0.03038674033149171	156	0.2727272727272727	15	0.01978891820580475	C	1.011	-0.687781	0.03328	0.063723	0.010256	ENSG00000106009	ENST00000340611	T	0.68765	-0.35	5.33	-8.42	0.00957	Armadillo-like helical (1);	0.814283	0.11368	N	0.571237	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.16802	0.019	B	0.11329	0.006	T	0.13764	-1.0497	9	0.12103	T	0.63	-0.4834	1.5988	0.02669	0.3633:0.0785:0.2464:0.3118	rs61627394;rs61745778	663	Q6PJG6	BRAT1_HUMAN	D	663	ENSP00000339637:G663D	ENSP00000339637:G663D	G	-	2	0	BRAT1	2544707	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-2.036000	0.01421	-1.585000	0.01634	0.561000	0.74099	GGC	C|0.936;T|0.064	0.064	strong		0.711	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
EHMT1	79813	hgsc.bcm.edu	37	9	140707590	140707590	+	Silent	SNP	C	C	T	rs35943616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140707590C>T	ENST00000460843.1	+	20	3027	c.3000C>T	c.(2998-3000)ccC>ccT	p.P1000P		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1000					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		ACTCGGCCCCCGACAGGCCCA	0.622													C|||	555	0.110823	0.4017	0.0274	5008	,	,		17819	0.005		0.0	False		,,,				2504	0.0				p.P1000P		Atlas-SNP	.											.	EHMT1	196	.	0			c.C3000T						PASS	.	C		1428,2978	446.9+/-348.2	236,956,1011	34.0	40.0	38.0		3000	-9.4	0.0	9	dbSNP_126	38	12,8588	7.7+/-29.5	1,10,4289	no	coding-synonymous	EHMT1	NM_024757.4		237,966,5300	TT,TC,CC		0.1395,32.4103,11.0718		1000/1299	140707590	1440,11566	2203	4300	6503	SO:0001819	synonymous_variant	79813	exon20			GGCCCCCGACAGG	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.3000C>T	9.37:g.140707590C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_024757	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			C|0.899;T|0.101	0.101	strong		0.622	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
CCDC66	285331	hgsc.bcm.edu	37	3	56650054	56650054	+	Missense_Mutation	SNP	T	T	C	rs112267342|rs111934125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	86	0	0		WXS	Illumina HiSeq	Phase_I	84	8	0.0952381	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	
CBFB	865	hgsc.bcm.edu	37	16	67116169	67116169	+	Silent	SNP	C	C	T	rs78053453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67116169C>T	ENST00000290858.6	+	5	714	c.453C>T	c.(451-453)cgC>cgT	p.R151R	CBFB_ENST00000561924.2_Silent_p.R51R|CBFB_ENST00000412916.2_Silent_p.R151R	NM_001755.2|NM_022845.2	NP_001746.1|NP_074036.1	Q13951	PEBB_HUMAN	core-binding factor, beta subunit	151					cell maturation (GO:0048469)|definitive hemopoiesis (GO:0060216)|lymphocyte differentiation (GO:0030098)|myeloid cell differentiation (GO:0030099)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|large_intestine(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)		GAAGGACACGCGAATTTGAAG	0.433			T	MYH11	AML								C|||	358	0.0714856	0.1853	0.0115	5008	,	,		12709	0.0377		0.002	False		,,,				2504	0.0665				p.R151R		Atlas-SNP	.		Dom	yes		16	16q22	865	"""core-binding factor, beta subunit"""		L	CBFB_ENST00000412916,NS,carcinoma,+1,2	CBFB	52	2	0			c.C453T						PASS	.	C	,	664,3736	281.9+/-276.2	46,572,1582	98.0	90.0	93.0		453,453	0.1	1.0	16	dbSNP_132	93	10,8590	5.7+/-21.5	0,10,4290	no	coding-synonymous,coding-synonymous	CBFB	NM_001755.2,NM_022845.2	,	46,582,5872	TT,TC,CC		0.1163,15.0909,5.1846	,	151/183,151/188	67116169	674,12326	2200	4300	6500	SO:0001819	synonymous_variant	865	exon5			GACACGCGAATTT	BC018509	CCDS10827.1, CCDS45508.1	16q22.1	2008-02-05			ENSG00000067955	ENSG00000067955			1539	protein-coding gene	gene with protein product		121360				8351518, 7587111	Standard	NM_001755		Approved	PEBP2B	uc002erb.3	Q13951	OTTHUMG00000137520	ENST00000290858.6:c.453C>T	16.37:g.67116169C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_022845	A8K347|Q13124|Q9HCT2	Silent	SNP	ENST00000290858.6	37	CCDS10827.1																																																																																			C|0.951;T|0.049	0.049	strong		0.433	CBFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268843.2	NM_001755	
TACC3	10460	hgsc.bcm.edu	37	4	1737502	1737502	+	Silent	SNP	C	C	T	rs11248073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1737502C>T	ENST00000313288.4	+	8	1795	c.1689C>T	c.(1687-1689)ttC>ttT	p.F563F		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	563					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			ACCTCAAGTTCGACCCCCTCC	0.592													.|||	1954	0.390176	0.1263	0.3732	5008	,	,		17029	0.6935		0.3429	False		,,,				2504	0.4949				p.F563F	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.C1689T						PASS	.			790,3616	319.6+/-296.2	91,608,1504	137.0	110.0	119.0		1689	-7.1	0.0	4	dbSNP_120	119	3020,5580	465.7+/-366.6	533,1954,1813	no	coding-synonymous	TACC3	NM_006342.1		624,2562,3317	TT,TC,CC		35.1163,17.9301,29.2942		563/839	1737502	3810,9196	2203	4300	6503	SO:0001819	synonymous_variant	10460	exon8			CAAGTTCGACCCC	AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.1689C>T	4.37:g.1737502C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Silent	SNP	ENST00000313288.4	37	CCDS3352.1	861	0.3942307692307692	65	0.13211382113821138	132	0.36464088397790057	394	0.6888111888111889	270	0.3562005277044855	c	0.648	-0.810689	0.02798	0.179301	0.351163	ENSG00000013810	ENST00000470136	.	.	.	5.27	-7.14	0.01527	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999983626	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.2683	16.5141	0.84294	0.0:0.1984:0.0:0.8016	rs11248073;rs11248073	.	.	.	X	200	.	.	R	+	1	2	TACC3	1707300	0.989000	0.36119	0.004000	0.12327	0.015000	0.08874	0.174000	0.16743	-1.407000	0.02043	-0.792000	0.03331	CGA	C|0.661;T|0.339	0.339	strong		0.592	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
LNX2	222484	hgsc.bcm.edu	37	13	28130473	28130473	+	Silent	SNP	G	G	A	rs115119970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:28130473G>A	ENST00000316334.3	-	7	1575	c.1446C>T	c.(1444-1446)acC>acT	p.T482T		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	482	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		CCCCAGCAACGGTCATGCCAA	0.468													G|||	67	0.0133786	0.0446	0.0043	5008	,	,		15881	0.0		0.005	False		,,,				2504	0.0				p.T482T		Atlas-SNP	.											.	LNX2	70	.	0			c.C1446T						PASS	.	G		138,4268	98.9+/-137.6	0,138,2065	114.0	100.0	105.0		1446	-5.4	0.7	13	dbSNP_132	105	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	LNX2	NM_153371.3		0,146,6357	AA,AG,GG		0.093,3.1321,1.1226		482/691	28130473	146,12860	2203	4300	6503	SO:0001819	synonymous_variant	222484	exon7			AGCAACGGTCATG	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.1446C>T	13.37:g.28130473G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	29	0.341176	NM_153371	Q5W0P0|Q6ZMH2|Q96SH4	Silent	SNP	ENST00000316334.3	37	CCDS9323.1																																																																																			G|0.988;A|0.012	0.012	strong		0.468	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2		
FBF1	85302	hgsc.bcm.edu	37	17	73929118	73929118	+	Missense_Mutation	SNP	G	G	A	rs149283443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73929118G>A	ENST00000586717.1	-	4	356	c.83C>T	c.(82-84)aCa>aTa	p.T28I	FBF1_ENST00000319129.5_Missense_Mutation_p.T28I|FBF1_ENST00000389570.4_Missense_Mutation_p.T28I			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	28					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						AGATACACCTGTGGTGTCTCT	0.448													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17472	0.0		0.0	False		,,,				2504	0.0				p.T28I		Atlas-SNP	.											.	FBF1	48	.	0			c.C83T						PASS	.	G	ILE/THR	33,3797		0,33,1882	71.0	69.0	70.0		83	0.6	0.0	17	dbSNP_134	70	1,8275		0,1,4137	yes	missense	FBF1	NM_001080542.1	89	0,34,6019	AA,AG,GG		0.0121,0.8616,0.2809	benign	28/1134	73929118	34,12072	1915	4138	6053	SO:0001583	missense	85302	exon4			ACACCTGTGGTGT	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.83C>T	17.37:g.73929118G>A	ENSP00000465132:p.Thr28Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	35	0.636364	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	10.15	1.271825	0.23221	0.008616	1.21E-4	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.20332	2.08;2.08	3.74	0.562	0.17290	.	.	.	.	.	T	0.09512	0.0234	L	0.36672	1.1	0.09310	N	1	B;B;B	0.33583	0.418;0.418;0.418	B;B;B	0.31101	0.124;0.058;0.058	T	0.21655	-1.0239	9	0.59425	D	0.04	6.5178	3.4486	0.07490	0.2201:0.0:0.5802:0.1997	.	42;28;28	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	I	28;28;28;41	ENSP00000374221:T28I;ENSP00000324292:T28I	ENSP00000324292:T28I	T	-	2	0	FBF1	71440713	0.000000	0.05858	0.000000	0.03702	0.167000	0.22549	0.333000	0.19768	0.162000	0.19483	0.557000	0.71058	ACA	G|0.997;A|0.003	0.003	strong		0.448	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
ABCC4	10257	hgsc.bcm.edu	37	13	95696540	95696540	+	Silent	SNP	C	C	T	rs11568695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:95696540C>T	ENST00000376887.4	-	28	3723	c.3609G>A	c.(3607-3609)gcG>gcA	p.A1203A	ABCC4_ENST00000412704.1_Silent_p.A1156A	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1203	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	CATTTGCCGTCGCTTCATCAA	0.398													C|||	225	0.0449281	0.1604	0.013	5008	,	,		19815	0.001		0.002	False		,,,				2504	0.001				p.A1203A		Atlas-SNP	.											ABCC4_ENST00000376887,colon,carcinoma,-1,2	ABCC4	248	2	0			c.G3609A						PASS	.	C		644,3762	270.4+/-269.6	52,540,1611	72.0	64.0	66.0		3609	-6.7	0.9	13	dbSNP_126	66	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	ABCC4	NM_005845.3		52,550,5901	TT,TC,CC		0.1163,14.6164,5.0284		1203/1326	95696540	654,12352	2203	4300	6503	SO:0001819	synonymous_variant	10257	exon28			TGCCGTCGCTTCA	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.3609G>A	13.37:g.95696540C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	37	CCDS9474.1																																																																																			C|0.950;T|0.050	0.050	strong		0.398	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
ITPR2	3709	hgsc.bcm.edu	37	12	26834833	26834833	+	Silent	SNP	G	G	A	rs35412320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26834833G>A	ENST00000381340.3	-	13	1799	c.1383C>T	c.(1381-1383)aaC>aaT	p.N461N		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	461					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)	TTATTGTGCCGTTTTCTAGCT	0.378													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		19655	0.0		0.0	False		,,,				2504	0.0				p.N461N		Atlas-SNP	.											ITPR2,colon,carcinoma,-2,1	ITPR2	270	1	0			c.C1383T						PASS	.	G		94,3584		1,92,1746	196.0	185.0	189.0		1383	-10.2	0.4	12	dbSNP_126	189	1,8193		0,1,4096	no	coding-synonymous	ITPR2	NM_002223.2		1,93,5842	AA,AG,GG		0.0122,2.5557,0.8002		461/2702	26834833	95,11777	1839	4097	5936	SO:0001819	synonymous_variant	3709	exon13			TGTGCCGTTTTCT	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.1383C>T	12.37:g.26834833G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	119	44	0.369748	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.991;A|0.009	0.009	strong		0.378	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
CALM3	808	hgsc.bcm.edu	37	19	47112207	47112207	+	Silent	SNP	C	C	T	rs35617141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47112207C>T	ENST00000291295.9	+	5	589	c.390C>T	c.(388-390)gaC>gaT	p.D130D	CALM3_ENST00000599839.1_Silent_p.D94D|CALM3_ENST00000596362.1_Silent_p.D130D|CTB-12A17.3_ENST00000597609.1_RNA|CALM3_ENST00000594523.1_Silent_p.D94D|CALM3_ENST00000477244.1_3'UTR|CALM3_ENST00000391918.2_Silent_p.D94D|CALM3_ENST00000598871.1_Silent_p.D94D|CALM3_ENST00000597743.1_Silent_p.D64D	NM_005184.2	NP_005175.2	P62158	CALM_HUMAN	calmodulin 3 (phosphorylase kinase, delta)	130	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|detection of calcium ion (GO:0005513)|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)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide metabolic process (GO:0046209)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cyclic nucleotide metabolic process (GO:0030801)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cytokinesis (GO:0032465)|regulation of heart rate (GO:0002027)|regulation of high voltage-gated calcium channel activity (GO:1901841)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcomere (GO:0030017)|spindle microtubule (GO:0005876)|spindle pole (GO:0000922)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|N-terminal myristoylation domain binding (GO:0031997)|nitric-oxide synthase regulator activity (GO:0030235)|phospholipase binding (GO:0043274)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|protein phosphatase activator activity (GO:0072542)|protein serine/threonine kinase activator activity (GO:0043539)|thioesterase binding (GO:0031996)|titin binding (GO:0031432)			breast(1)|cervix(2)|endometrium(1)|lung(1)|ovary(1)	6		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000683)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0341)	Aprindine(DB01429)|Bepridil(DB01244)|Chlorpromazine(DB00477)|Cinchocaine(DB00527)|Felodipine(DB01023)|Flunarizine(DB04841)|Fluphenazine(DB00623)|Isoflurane(DB00753)|Loperamide(DB00836)|Melatonin(DB01065)|Nicardipine(DB00622)|Nifedipine(DB01115)|Perphenazine(DB00850)|Phenoxybenzamine(DB00925)|Pimozide(DB01100)|Promethazine(DB01069)|Trifluoperazine(DB00831)	GGGAGGCTGACATCGATGGAG	0.542													C|||	37	0.00738818	0.0265	0.0029	5008	,	,		21757	0.0		0.0	False		,,,				2504	0.0				p.D130D		Atlas-SNP	.											.	CALM3	9	.	0			c.C390T						PASS	.	C		98,4308	79.9+/-118.3	0,98,2105	93.0	71.0	79.0		390	4.8	1.0	19	dbSNP_126	79	0,8600		0,0,4300	no	coding-synonymous	CALM3	NM_005184.2		0,98,6405	TT,TC,CC		0.0,2.2242,0.7535		130/150	47112207	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	808	exon5			GGCTGACATCGAT		CCDS33061.1	19q13.2-q13.3	2013-02-25			ENSG00000160014	ENSG00000160014		"""EF-hand domain containing"", ""Endogenous ligands"""	1449	protein-coding gene	gene with protein product	"""prepro-calmodulin 3"""	114183					Standard	NM_005184		Approved	PHKD	uc002pew.3	P62158	OTTHUMG00000133517	ENST00000291295.9:c.390C>T	19.37:g.47112207C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	83	47	0.566265	NM_005184	P02593|P70667|P99014|Q13942|Q53S29|Q61379|Q61380|Q96HK3	Silent	SNP	ENST00000291295.9	37	CCDS33061.1																																																																																			C|0.990;T|0.010	0.010	strong		0.542	CALM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257483.2		
OR4D2	124538	hgsc.bcm.edu	37	17	56247794	56247794	+	Missense_Mutation	SNP	C	C	T	rs148697791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56247794C>T	ENST00000545221.1	+	1	778	c.778C>T	c.(778-780)Cgg>Tgg	p.R260W		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	260						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						CCTCTATGCCCGGCCCTTCAC	0.542													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		21719	0.0		0.0	False		,,,				2504	0.0				p.R260W		Atlas-SNP	.											.	OR4D2	48	.	0			c.C778T						PASS	.	C	TRP/ARG	59,4347	57.4+/-93.9	0,59,2144	167.0	129.0	142.0		778	5.7	1.0	17	dbSNP_134	142	0,8600		0,0,4300	yes	missense	OR4D2	NM_001004707.3	101	0,59,6444	TT,TC,CC		0.0,1.3391,0.4536	benign	260/308	56247794	59,12947	2203	4300	6503	SO:0001583	missense	124538	exon1			TATGCCCGGCCCT		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.778C>T	17.37:g.56247794C>T	ENSP00000441354:p.Arg260Trp	Somatic	361	1	0.00277008		WXS	Illumina HiSeq	Phase_I	362	191	0.527624	NM_001004707	Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	37	CCDS32688.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	12.16	1.854682	0.32791	0.013391	0.0	ENSG00000255713	ENST00000545221	T	0.37915	1.17	5.71	5.71	0.89125	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000115	T	0.25082	0.0609	M	0.81341	2.54	0.30651	N	0.755458	B	0.33345	0.409	B	0.34931	0.192	T	0.40887	-0.9539	10	0.30854	T	0.27	-13.8261	11.0572	0.47925	0.0:0.9155:0.0:0.0845	.	260	P58180	OR4D2_HUMAN	W	260	ENSP00000441354:R260W	ENSP00000441354:R260W	R	+	1	2	OR4D2	53602793	0.003000	0.15002	0.994000	0.49952	0.678000	0.39670	1.764000	0.38471	2.860000	0.98153	0.609000	0.83330	CGG	C|0.995;T|0.005	0.005	strong		0.542	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1		
RINT1	60561	hgsc.bcm.edu	37	7	105182995	105182995	+	Silent	SNP	G	G	A	rs7805216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:105182995G>A	ENST00000257700.2	+	4	645	c.414G>A	c.(412-414)gcG>gcA	p.A138A	RINT1_ENST00000477285.1_3'UTR	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	138					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TGCTGACTGCGCAACCTTGGA	0.403													G|||	307	0.0613019	0.2209	0.0187	5008	,	,		16144	0.0		0.002	False		,,,				2504	0.0				p.A138A		Atlas-SNP	.											.	RINT1	65	.	0			c.G414A						PASS	.	G		770,3636	312.7+/-292.7	65,640,1498	120.0	112.0	115.0		414	-10.0	0.1	7	dbSNP_116	115	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	RINT1	NM_021930.4		65,646,5792	AA,AG,GG		0.0698,17.4762,5.9665		138/793	105182995	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	60561	exon4			GACTGCGCAACCT	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.414G>A	7.37:g.105182995G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	218	106	0.486239	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Silent	SNP	ENST00000257700.2	37	CCDS34726.1																																																																																			G|0.939;A|0.061	0.061	strong		0.403	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930	
HAPLN3	145864	hgsc.bcm.edu	37	15	89421327	89421327	+	Silent	SNP	A	A	G	rs2280463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89421327A>G	ENST00000359595.3	-	5	1171	c.957T>C	c.(955-957)ggT>ggC	p.G319G	HAPLN3_ENST00000562889.1_Silent_p.G381G	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	319	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	AGCGGACGCTACCATCTGCCA	0.647													G|||	2193	0.437899	0.8139	0.3228	5008	,	,		14462	0.256		0.2932	False		,,,				2504	0.3476				p.G319G		Atlas-SNP	.											.	HAPLN3	43	.	0			c.T957C						PASS	.	G		3289,1111	398.5+/-330.9	1243,803,154	94.0	93.0	93.0		957	2.5	1.0	15	dbSNP_100	93	2665,5933	684.5+/-404.0	393,1879,2027	no	coding-synonymous	HAPLN3	NM_178232.2		1636,2682,2181	GG,GA,AA		30.9956,25.25,45.807		319/361	89421327	5954,7044	2200	4299	6499	SO:0001819	synonymous_variant	145864	exon5			GACGCTACCATCT	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"""Immunoglobulin superfamily / V-set domain containing"""	21446	protein-coding gene	gene with protein product			"""extracellular link domain containing, 1"""	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.957T>C	15.37:g.89421327A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_178232	A8K7P0	Silent	SNP	ENST00000359595.3	37	CCDS10346.1																																																																																			A|0.561;G|0.439	0.439	strong		0.647	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
RNASE4	6038	hgsc.bcm.edu	37	14	21167837	21167837	+	Missense_Mutation	SNP	G	G	A	rs59543367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21167837G>A	ENST00000555835.1	+	2	983	c.307G>A	c.(307-309)Gta>Ata	p.V103I	RNASE4_ENST00000304704.4_Missense_Mutation_p.V103I|RP11-903H12.3_ENST00000554286.1_RNA|AL163636.6_ENST00000553909.1_3'UTR|RNASE4_ENST00000397995.2_Missense_Mutation_p.V103I|RNASE4_ENST00000555597.1_Missense_Mutation_p.V103I	NM_002937.3	NP_002928.1	P34096	RNAS4_HUMAN	ribonuclease, RNase A family, 4	103					cellular response to starvation (GO:0009267)|mRNA cleavage (GO:0006379)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_cancers(95;0.00304)		Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	GBM - Glioblastoma multiforme(265;0.0133)		CCATGAGGGTGTAGTGAAGGT	0.493													G|||	22	0.00439297	0.0151	0.0029	5008	,	,		22587	0.0		0.0	False		,,,				2504	0.0				p.V103I	Esophageal Squamous(59;1059 1362 26290 51151)	Atlas-SNP	.											.	RNASE4	18	.	0			c.G307A						PASS	.	G	ILE/VAL,ILE/VAL	58,4348	57.4+/-93.9	0,58,2145	154.0	127.0	136.0		307,307	2.9	1.0	14	dbSNP_129	136	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	RNASE4	NM_002937.3,NM_194431.1	29,29	0,61,6442	AA,AG,GG		0.0349,1.3164,0.469	benign,benign	103/148,103/148	21167837	61,12945	2203	4300	6503	SO:0001583	missense	6038	exon2			GAGGGTGTAGTGA	U36775	CCDS9555.1	14q11	2014-07-16			ENSG00000258818	ENSG00000258818		"""Ribonucleases, RNase A"""	10047	protein-coding gene	gene with protein product		601030				7501448	Standard	NM_002937		Approved		uc001vxy.4	P34096	OTTHUMG00000029575	ENST00000555835.1:c.307G>A	14.37:g.21167837G>A	ENSP00000452245:p.Val103Ile	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	30	22	0.733333	NM_002937		Missense_Mutation	SNP	ENST00000555835.1	37	CCDS9555.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	15.78	2.935052	0.52866	0.013164	3.49E-4	ENSG00000258818;ENSG00000258818;ENSG00000258818;ENSG00000181784;ENSG00000181784;ENSG00000181784	ENST00000555835;ENST00000397995;ENST00000555597;ENST00000398001;ENST00000304704;ENST00000397999	T;T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67;-0.67;-0.67	5.8	2.92	0.33932	Ribonuclease A, domain (4);	0.325719	0.26453	N	0.024288	T	0.39572	0.1083	L	0.29908	0.895	0.28449	N	0.916432	B	0.06786	0.001	B	0.11329	0.006	T	0.47711	-0.9096	10	0.52906	T	0.07	-2.5954	8.6786	0.34194	0.2536:0.0:0.7464:0.0	rs59543367	103	P34096	RNAS4_HUMAN	I	103	ENSP00000452245:V103I;ENSP00000381081:V103I;ENSP00000451624:V103I;ENSP00000381087:V103I;ENSP00000307096:V103I;ENSP00000381085:V103I	ENSP00000307096:V103I	V	+	1	0	AL163636.2;RNASE4	20237677	0.769000	0.28531	0.998000	0.56505	0.957000	0.61999	1.259000	0.32956	0.886000	0.36113	0.650000	0.86243	GTA	G|0.994;A|0.006	0.006	strong		0.493	RNASE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073729.3		
LRCH4	4034	hgsc.bcm.edu	37	7	100175853	100175853	+	Silent	SNP	G	G	T	rs187288824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100175853G>T	ENST00000310300.6	-	7	929	c.877C>A	c.(877-879)Cgg>Agg	p.R293R	LRCH4_ENST00000497245.1_5'UTR	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	293					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)					CCATCGTACCGATGTCCCGGA	0.592																																					p.R293R		Atlas-SNP	.											LRCH4,NS,carcinoma,0,1	LRCH4	53	1	0			c.C877A						scavenged	.						114.0	91.0	99.0					7																	100175853		2203	4300	6503	SO:0001819	synonymous_variant	4034	exon7			CGTACCGATGTCC	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.877C>A	7.37:g.100175853G>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	129	3	0.0232558	NM_002319	A4D2D5|Q8WV85|Q96ID0	Silent	SNP	ENST00000310300.6	37	CCDS34706.1																																																																																			G|0.999;A|0.001	.	alt		0.592	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319	
UBXN11	91544	hgsc.bcm.edu	37	1	26612460	26612460	+	Silent	SNP	G	G	A	rs11247900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26612460G>A	ENST00000374222.1	-	10	1092	c.628C>T	c.(628-630)Ctg>Ttg	p.L210L	UBXN11_ENST00000357089.4_Silent_p.L177L|UBXN11_ENST00000436301.2_Silent_p.L135L|UBXN11_ENST00000374217.2_Silent_p.L177L|UBXN11_ENST00000535108.1_Silent_p.L52L|UBXN11_ENST00000374221.3_Silent_p.L210L|UBXN11_ENST00000314675.7_Silent_p.L90L|UBXN11_ENST00000374223.1_5'UTR			Q5T124	UBX11_HUMAN	UBX domain protein 11	210						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						TCTACCACCAGCTCACTAAGA	0.632											OREG0013265	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	646	0.128994	0.202	0.1066	5008	,	,		17288	0.0228		0.1909	False		,,,				2504	0.092				p.L210L		Atlas-SNP	.											.	UBXN11	54	.	0			c.C628T						PASS	.	G	,,	591,3317		48,495,1411	38.0	41.0	40.0		268,529,628	2.9	1.0	1	dbSNP_120	40	1366,6934		103,1160,2887	no	coding-synonymous,coding-synonymous,coding-synonymous	UBXN11	NM_001077262.1,NM_145345.2,NM_183008.2	,,	151,1655,4298	AA,AG,GG		16.4578,15.1228,16.0305	,,	90/401,177/488,210/521	26612460	1957,10251	1954	4150	6104	SO:0001819	synonymous_variant	91544	exon10			CCACCAGCTCACT	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.628C>T	1.37:g.26612460G>A		Somatic	136	0	0	788	WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			G|0.862;A|0.138	0.138	strong		0.632	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
SECTM1	6398	hgsc.bcm.edu	37	17	80285085	80285085	+	Missense_Mutation	SNP	T	T	G	rs73999869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80285085T>G	ENST00000269389.3	-	2	382	c.32A>C	c.(31-33)cAc>cCc	p.H11P	SECTM1_ENST00000580437.1_Missense_Mutation_p.H11P	NM_003004.2	NP_002995.1	Q8WVN6	SCTM1_HUMAN	secreted and transmembrane 1	11					immune response (GO:0006955)|mesoderm development (GO:0007498)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine activity (GO:0005125)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(2)|lung(1)	4	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00928)|BRCA - Breast invasive adenocarcinoma(99;0.0833)			CTGGGAAACGTGGCCAGGGAA	0.622													G|||	238	0.047524	0.1097	0.0533	5008	,	,		15772	0.0		0.0398	False		,,,				2504	0.0164				p.H11P		Atlas-SNP	.											.	SECTM1	14	.	0			c.A32C						PASS	.	G	PRO/HIS	391,4009	747.9+/-411.9	24,343,1833	53.0	43.0	46.0		32	-4.2	0.0	17	dbSNP_130	46	356,8244	778.2+/-407.7	11,334,3955	yes	missense	SECTM1	NM_003004.2	77	35,677,5788	GG,GT,TT		4.1395,8.8864,5.7462	benign	11/249	80285085	747,12253	2200	4300	6500	SO:0001583	missense	6398	exon2			GAAACGTGGCCAG	U77643	CCDS11808.1	17q25	2008-07-18				ENSG00000141574			10707	protein-coding gene	gene with protein product	"""K12 protein"", ""type 1a transmembrane protein"""	602602				9480746	Standard	NM_003004		Approved	K12	uc002keo.3	Q8WVN6		ENST00000269389.3:c.32A>C	17.37:g.80285085T>G	ENSP00000269389:p.His11Pro	Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	221	90	0.40724	NM_003004	B2R7H0|O00466	Missense_Mutation	SNP	ENST00000269389.3	37	CCDS11808.1	111	0.050824175824175824	59	0.11991869918699187	20	0.055248618784530384	0	0.0	32	0.04221635883905013	G	2.949	-0.217084	0.06101	0.088864	0.041395	ENSG00000141574	ENST00000269389	.	.	.	2.11	-4.22	0.03800	.	.	.	.	.	T	0.00109	0.0003	N	0.01048	-1.04	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.24799	-1.0150	7	0.52906	T	0.07	.	1.072	0.01623	0.4537:0.16:0.2249:0.1615	.	11;11;11	Q53G27;Q8WVN6;A8K3U3	.;SCTM1_HUMAN;.	P	11	.	ENSP00000269389:H11P	H	-	2	0	SECTM1	77878374	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.650000	0.00858	-1.735000	0.01353	-0.478000	0.04885	CAC	T|0.943;G|0.057	0.057	strong		0.622	SECTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442856.1	NM_003004	
AKAP8L	26993	hgsc.bcm.edu	37	19	15512393	15512393	+	Silent	SNP	G	G	A	rs61739315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15512393G>A	ENST00000397410.5	-	5	514	c.384C>T	c.(382-384)tgC>tgT	p.C128C	AKAP8L_ENST00000595465.2_Silent_p.C67C|AKAP8L_ENST00000595879.1_5'Flank	NM_014371.2	NP_055186.2	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like	128						cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(4)|kidney(2)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	11						CCCTCGAGTCGCAGGACTCAT	0.597													G|||	43	0.00858626	0.0295	0.0058	5008	,	,		17723	0.0		0.0	False		,,,				2504	0.0				p.C128C		Atlas-SNP	.											.	AKAP8L	64	.	0			c.C384T						PASS	.	G		118,4112		2,114,1999	29.0	28.0	29.0		384	2.4	1.0	19	dbSNP_129	29	2,8440		0,2,4219	no	coding-synonymous	AKAP8L	NM_014371.2		2,116,6218	AA,AG,GG		0.0237,2.7896,0.947		128/647	15512393	120,12552	2115	4221	6336	SO:0001819	synonymous_variant	26993	exon5			CGAGTCGCAGGAC	BC000713	CCDS46005.1	19p13.12	2013-10-16			ENSG00000011243	ENSG00000011243			29857	protein-coding gene	gene with protein product	"""neighbor of A kinase anchoring protein 95"""	609475				10748171, 10761695	Standard	XM_005259854		Approved	NAKAP95, HAP95	uc002naw.1	Q9ULX6	OTTHUMG00000182446	ENST00000397410.5:c.384C>T	19.37:g.15512393G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_014371	B4DJ74|B5BU90|O94792|Q96J58|Q9NRQ0|Q9UGM0	Silent	SNP	ENST00000397410.5	37	CCDS46005.1																																																																																			G|0.991;A|0.009	0.009	strong		0.597	AKAP8L-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461301.2	NM_014371	
HRC	3270	hgsc.bcm.edu	37	19	49658084	49658084	+	Silent	SNP	G	G	A	rs57897109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49658084G>A	ENST00000252825.4	-	1	597	c.411C>T	c.(409-411)caC>caT	p.H137H	TRPM4_ENST00000427978.2_5'Flank|TRPM4_ENST00000252826.5_5'Flank|HRC_ENST00000595625.1_Silent_p.H137H	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	137	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		CTTCACTCCCGTGGCCTCTGT	0.602													A|||	515	0.102835	0.2905	0.0461	5008	,	,		18391	0.0179		0.0427	False		,,,				2504	0.0389				p.H137H	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.C411T						PASS	.	A		1012,3394	729.3+/-410.0	118,776,1309	165.0	122.0	137.0		411	-3.3	0.0	19	dbSNP_129	137	304,8296	805.8+/-407.3	6,292,4002	no	coding-synonymous	HRC	NM_002152.2		124,1068,5311	AA,AG,GG		3.5349,22.9687,10.1184		137/700	49658084	1316,11690	2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			ACTCCCGTGGCCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.411C>T	19.37:g.49658084G>A		Somatic	308	1	0.00324675		WXS	Illumina HiSeq	Phase_I	352	185	0.525568	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			G|0.903;A|0.097	0.097	strong		0.602	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642823	1642823	+	Silent	SNP	G	G	A	rs529692233|rs374921824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1642823G>A	ENST00000399682.1	-	1	545	c.501C>T	c.(499-501)tcC>tcT	p.S167S		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CACAACCTGAGGAGGAGCAGC	0.617													g|||	139	0.0277556	0.0522	0.0159	5008	,	,		14834	0.0179		0.0229	False		,,,				2504	0.0184				p.S167S		Atlas-SNP	.											KRTAP5-4,colon,carcinoma,0,1	KRTAP5-4	78	1	0			c.C501T						scavenged	.						22.0	34.0	30.0					11																	1642823		692	1590	2282	SO:0001819	synonymous_variant	387267	exon1			ACCTGAGGAGGAG	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.501C>T	11.37:g.1642823G>A		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	201	10	0.0497512	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.617	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
PMS2	5395	hgsc.bcm.edu	37	7	6026959	6026959	+	Missense_Mutation	SNP	G	G	C	rs63750685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6026959G>C	ENST00000265849.7	-	11	1542	c.1437C>G	c.(1435-1437)caC>caG	p.H479Q	PMS2_ENST00000441476.2_Missense_Mutation_p.H373Q|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Missense_Mutation_p.H479Q|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	479			H -> Q. {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)			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)		CACTGGGTCCGTGACTGGAAC	0.577			"""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				C|||	14	0.00279553	0.0053	0.0029	5008	,	,		16803	0.0		0.003	False		,,,				2504	0.002				p.H479Q		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.C1437G						PASS	.	C	GLN/HIS	43,4363	37.6+/-69.7	0,43,2160	100.0	97.0	98.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1437	2.2	0.0	7	dbSNP_130	98	24,8576	14.0+/-48.4	0,24,4276	no	missense	PMS2	NM_000535.5	24	0,67,6436	CC,CG,GG		0.2791,0.9759,0.5151	benign	479/863	6026959	67,12939	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	GGGTCCGTGACTG		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.1437C>G	7.37:g.6026959G>C	ENSP00000265849:p.His479Gln	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	.	.	.	.	.	.	.	.	.	.	g	5.130	0.209574	0.09757	0.009759	0.002791	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;D	0.85339	1.14;1.14;-1.97	5.48	2.17	0.27698	.	3.116210	0.00714	N	0.000858	T	0.55049	0.1896	N	0.01352	-0.895	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	0.59016	-0.7533	10	0.13108	T	0.6	0.0332	4.2932	0.10888	0.1392:0.478:0.2756:0.1072	rs63750685	479;479;373	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	Q	479;432;373;479	ENSP00000265849:H479Q;ENSP00000392843:H373Q;ENSP00000384308:H479Q	ENSP00000265849:H479Q	H	-	3	2	PMS2	5993485	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.182000	0.16900	0.282000	0.22254	-0.126000	0.14955	CAC	G|0.994;C|0.006	0.006	strong		0.577	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
GPNMB	10457	hgsc.bcm.edu	37	7	23300352	23300352	+	Silent	SNP	G	G	T	rs35115002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:23300352G>T	ENST00000381990.2	+	6	1139	c.978G>T	c.(976-978)ccG>ccT	p.P326P	GPNMB_ENST00000539136.1_Silent_p.P227P|GPNMB_ENST00000258733.4_Silent_p.P326P|GPNMB_ENST00000453162.2_Silent_p.P268P	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	326	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.|Poly-Pro.				bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			GTCCGCCACCGCCACCACCAC	0.493													G|||	11	0.00219649	0.0083	0.0	5008	,	,		18491	0.0		0.0	False		,,,				2504	0.0				p.P326P		Atlas-SNP	.											.	GPNMB	88	.	0			c.G978T						PASS	.	G	,	58,4348	56.2+/-92.4	0,58,2145	119.0	128.0	125.0		978,978	-0.3	0.0	7	dbSNP_126	125	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GPNMB	NM_001005340.1,NM_002510.2	,	0,58,6445	TT,TG,GG		0.0,1.3164,0.4459	,	326/573,326/561	23300352	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	10457	exon6			GCCACCGCCACCA	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.978G>T	7.37:g.23300352G>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_002510	A4D155|Q6UVX1|Q8N1A1	Silent	SNP	ENST00000381990.2	37	CCDS34610.1																																																																																			G|0.995;T|0.005	0.005	strong		0.493	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340	
ZNF446	55663	hgsc.bcm.edu	37	19	58991075	58991075	+	Silent	SNP	C	C	T	rs140158663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58991075C>T	ENST00000594369.1	+	5	1074	c.693C>T	c.(691-693)taC>taT	p.Y231Y	ZNF446_ENST00000335841.4_Intron|ZNF446_ENST00000596341.1_Silent_p.Y231Y	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	231	KRAB.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		TGGAGAAGTACGGCACAGTGG	0.667													C|||	8	0.00159744	0.0061	0.0	5008	,	,		13917	0.0		0.0	False		,,,				2504	0.0				p.Y231Y		Atlas-SNP	.											.	ZNF446	22	.	0			c.C693T						PASS	.	C		19,4387	25.3+/-52.1	0,19,2184	106.0	93.0	97.0		693	-0.8	0.5	19	dbSNP_134	97	0,8600		0,0,4300	no	coding-synonymous	ZNF446	NM_017908.2		0,19,6484	TT,TC,CC		0.0,0.4312,0.1461		231/451	58991075	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	55663	exon5			GAAGTACGGCACA		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.693C>T	19.37:g.58991075C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_017908		Silent	SNP	ENST00000594369.1	37	CCDS12982.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	18.25	3.582969	0.65992	0.004312	0.0	ENSG00000083838	ENST00000391694	.	.	.	4.99	-0.83	0.10792	.	.	.	.	.	T	0.24122	0.0584	.	.	.	0.21675	N	0.999593	.	.	.	.	.	.	T	0.37126	-0.9719	5	0.87932	D	0	-20.9173	7.3852	0.26878	0.0:0.4473:0.0:0.5527	.	.	.	.	M	61	.	ENSP00000375576:T61M	T	+	2	0	ZNF446	63682887	0.000000	0.05858	0.518000	0.27811	0.871000	0.50021	-0.566000	0.05922	0.062000	0.16340	0.655000	0.94253	ACG	C|0.998;T|0.002	0.002	strong		0.667	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908	
HHLA1	10086	hgsc.bcm.edu	37	8	133092138	133092138	+	Missense_Mutation	SNP	G	G	A	rs2403730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133092138G>A	ENST00000414222.1	-	10	751	c.752C>T	c.(751-753)cCc>cTc	p.P251L	HHLA1_ENST00000434736.2_Missense_Mutation_p.P287L|OC90_ENST00000262283.5_Intron	NM_001145095.1	NP_001138567.1	C9JL84	HHLA1_HUMAN	HERV-H LTR-associating 1	251						extracellular region (GO:0005576)		p.P251L(1)		endometrium(6)|kidney(1)|lung(2)|skin(1)|stomach(2)	12						CCAGTGTCCGGGGCTTGTACT	0.552													G|||	1284	0.25639	0.1672	0.389	5008	,	,		18254	0.1984		0.3032	False		,,,				2504	0.2945				p.P251L		Atlas-SNP	.											HHLA1,NS,carcinoma,0,1	HHLA1	35	1	1	Substitution - Missense(1)	stomach(1)	c.C752T						PASS	.	G	LEU/PRO	285,1099		31,223,438	108.0	83.0	90.0		752	-0.7	0.0	8	dbSNP_100	90	1033,2149		152,729,710	yes	missense	HHLA1	NM_001145095.1	98	183,952,1148	AA,AG,GG		32.4639,20.5925,28.8655	benign	251/532	133092138	1318,3248	692	1591	2283	SO:0001583	missense	10086	exon10			TGTCCGGGGCTTG	AF110315		8q24	2011-03-01			ENSG00000132297	ENSG00000132297			4904	protein-coding gene	gene with protein product		604109		PLA2L		10329003	Standard	NM_001145095		Approved		uc011liy.1	C9JL84	OTTHUMG00000140390	ENST00000414222.1:c.752C>T	8.37:g.133092138G>A	ENSP00000388322:p.Pro251Leu	Somatic	412	0	0		WXS	Illumina HiSeq	Phase_I	421	200	0.475059	NM_001145095		Missense_Mutation	SNP	ENST00000414222.1	37		551	0.2522893772893773	69	0.1402439024390244	135	0.3729281767955801	125	0.21853146853146854	222	0.2928759894459103	G	10.85	1.468091	0.26335	0.205925	0.324639	ENSG00000132297	ENST00000414222;ENST00000434736	.	.	.	4.82	-0.714	0.11219	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.10450	0.001;0.005	T	0.45026	-0.9289	7	0.26408	T	0.33	.	0.6554	0.00834	0.3373:0.1655:0.3274:0.1697	rs2403730;rs3739279;rs17571473;rs52807392;rs56513099;rs59545753;rs2403730	251;108	C9JL84;C9JL84-2	HHLA1_HUMAN;.	L	251;287	.	ENSP00000388322:P251L	P	-	2	0	HHLA1	133161320	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.195000	0.09546	-0.034000	0.13713	-0.142000	0.14014	CCC	G|0.754;A|0.246	0.246	strong		0.552	HHLA1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XR_017860	
ZC3H6	376940	hgsc.bcm.edu	37	2	113089267	113089267	+	Silent	SNP	T	T	C	rs7601200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113089267T>C	ENST00000409871.1	+	12	3173	c.2772T>C	c.(2770-2772)aaT>aaC	p.N924N	AC115115.2_ENST00000607612.1_RNA|ZC3H6_ENST00000343936.4_Silent_p.N924N	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	924							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						TTCATCAAAATACAGTGTCCA	0.398													C|||	3634	0.725639	0.9728	0.6455	5008	,	,		20981	0.7421		0.5477	False		,,,				2504	0.6145				p.N924N		Atlas-SNP	.											.	ZC3H6	93	.	0			c.T2772C						PASS	.	C		3350,364		1515,320,22	72.0	66.0	67.0		2772	0.1	0.0	2	dbSNP_116	67	4229,3971		1073,2083,944	no	coding-synonymous	ZC3H6	NM_198581.2		2588,2403,966	CC,CT,TT		48.4268,9.8008,36.3858		924/1190	113089267	7579,4335	1857	4100	5957	SO:0001819	synonymous_variant	376940	exon12			TCAAAATACAGTG	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.2772T>C	2.37:g.113089267T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_198581	A9JR71|Q6ZW96	Silent	SNP	ENST00000409871.1	37	CCDS46393.1																																																																																			T|0.273;C|0.727	0.727	strong		0.398	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581	
ZSCAN25	221785	hgsc.bcm.edu	37	7	99227027	99227027	+	Missense_Mutation	SNP	C	C	T	rs142120776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99227027C>T	ENST00000394152.2	+	8	1346	c.1019C>T	c.(1018-1020)aCc>aTc	p.T340I	ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.T340I|ZSCAN25_ENST00000262941.6_Missense_Mutation_p.T268I	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	340					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)										GAAGTCAAAACCCACAGCTCC	0.617													C|||	14	0.00279553	0.0106	0.0	5008	,	,		18729	0.0		0.0	False		,,,				2504	0.0				p.T340I		Atlas-SNP	.											.	.	.	.	0			c.C1019T						PASS	.	C	ILE/THR	48,4358	47.5+/-82.1	0,48,2155	57.0	50.0	52.0		1019	3.9	0.0	7	dbSNP_134	52	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF498	NM_145115.2	89	0,49,6454	TT,TC,CC		0.0116,1.0894,0.3767	possibly-damaging	340/545	99227027	49,12957	2203	4300	6503	SO:0001583	missense	221785	exon8			TCAAAACCCACAG	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"""-"", ""Zinc fingers, C2H2-type"""	21961	protein-coding gene	gene with protein product			"""zinc finger protein 498"""	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.1019C>T	7.37:g.99227027C>T	ENSP00000377708:p.Thr340Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	8.033	0.762232	0.15914	0.010894	1.16E-4	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.09073	3.03;3.03;3.02	3.89	3.89	0.44902	.	0.669254	0.13160	N	0.409125	T	0.03520	0.0101	N	0.11364	0.135	0.09310	N	1	B;B	0.26195	0.144;0.089	B;B	0.21546	0.025;0.035	T	0.35724	-0.9777	10	0.23891	T	0.37	-2.1444	14.1776	0.65552	0.0:1.0:0.0:0.0	.	268;340	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	I	340;340;268	ENSP00000377708:T340I;ENSP00000334800:T340I;ENSP00000262941:T268I	ENSP00000262941:T268I	T	+	2	0	ZNF498	99064963	0.017000	0.18338	0.018000	0.16275	0.514000	0.34195	1.627000	0.37050	2.454000	0.82982	0.561000	0.74099	ACC	C|0.998;T|0.002	0.002	strong		0.617	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115	
OR2AE1	81392	hgsc.bcm.edu	37	7	99473858	99473858	+	Missense_Mutation	SNP	G	G	C	rs17161997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99473858G>C	ENST00000316368.2	-	1	822	c.799C>G	c.(799-801)Cta>Gta	p.L267V		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	267			L -> V (in dbSNP:rs17161997).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					TTCTGCAATAGAGTGCACTGG	0.468													G|||	654	0.130591	0.3986	0.0591	5008	,	,		21809	0.001		0.0577	False		,,,				2504	0.0276				p.L267V		Atlas-SNP	.											.	OR2AE1	32	.	0			c.C799G						PASS	.	G	VAL/LEU	1449,2957	468.5+/-355.1	226,997,980	91.0	95.0	94.0		799	2.0	0.0	7	dbSNP_123	94	422,8178	130.8+/-188.7	15,392,3893	yes	missense	OR2AE1	NM_001005276.1	32	241,1389,4873	CC,CG,GG		4.907,32.887,14.3857	benign	267/324	99473858	1871,11135	2203	4300	6503	SO:0001583	missense	81392	exon1			GCAATAGAGTGCA	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"""GPCR / Class A : Olfactory receptors"""	15087	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily AE, member 2"""	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.799C>G	7.37:g.99473858G>C	ENSP00000313936:p.Leu267Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	108	46	0.425926	NM_001005276	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	274	0.12545787545787546	206	0.4186991869918699	25	0.06906077348066299	1	0.0017482517482517483	42	0.055408970976253295	G	1.212	-0.629361	0.03610	0.32887	0.04907	ENSG00000244623	ENST00000316368	T	0.00091	8.74	3.84	1.97	0.26223	GPCR, rhodopsin-like superfamily (1);	0.202882	0.24674	N	0.036535	T	0.00012	0.0000	N	0.16862	0.45	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.09729	-1.0661	9	0.66056	D	0.02	.	11.9505	0.52952	0.0:0.3361:0.6639:0.0	rs17161997;rs17161997	267	Q8NHA4	O2AE1_HUMAN	V	267	ENSP00000313936:L267V	ENSP00000313936:L267V	L	-	1	2	OR2AE1	99311794	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.452000	0.21795	0.563000	0.29222	0.494000	0.49563	CTA	G|0.862;C|0.138	0.138	strong		0.468	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1		
TTN	7273	hgsc.bcm.edu	37	2	179414318	179414318	+	Missense_Mutation	SNP	C	C	T	rs747122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179414318C>T	ENST00000591111.1	-	288	87432	c.87208G>A	c.(87208-87210)Gtg>Atg	p.V29070M	TTN_ENST00000589042.1_Missense_Mutation_p.V30711M|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V21646M|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V28143M|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V21771M|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V21838M|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29070	Fibronectin type-III 111. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> M. {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)			TGAGCAACCACTGGATCAGAA	0.373													C|||	752	0.15016	0.2731	0.1787	5008	,	,		21696	0.0248		0.0487	False		,,,				2504	0.1973				p.V30711M		Atlas-SNP	.											.	TTN	18412	.	0			c.G92131A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL	971,2753		131,709,1022	112.0	111.0	111.0		64936,84427,65311,65512	5.7	1.0	2	dbSNP_86	111	252,7938		8,236,3851	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	21,21,21,21	139,945,4873	TT,TC,CC		3.0769,26.0741,10.2652	probably-damaging,probably-damaging,probably-damaging,probably-damaging	21646/26927,28143/33424,21771/27052,21838/27119	179414318	1223,10691	1862	4095	5957	SO:0001583	missense	7273	exon338			CAACCACTGGATC	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.87208G>A	2.37:g.179414318C>T	ENSP00000465570:p.Val29070Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	102	58	0.568627	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		246	0.11263736263736264	150	0.3048780487804878	58	0.16022099447513813	5	0.008741258741258742	33	0.04353562005277045	C	15.04	2.715720	0.48622	0.260741	0.030769	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	5.74	5.74	0.90152	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.66378	2.025	0.23773	P	0.99688228	D;D;D;D	0.54397	0.966;0.966;0.966;0.966	P;P;P;P	0.52159	0.618;0.618;0.618;0.691	T	0.01848	-1.1261	8	0.87932	D	0	.	15.8576	0.78994	0.1362:0.8638:0.0:0.0	rs747122;rs61267780;rs747122	21646;21771;21838;29070	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	28143;21646;21838;21771;21643	ENSP00000343764:V28143M;ENSP00000434586:V21646M;ENSP00000340554:V21838M;ENSP00000352154:V21771M	ENSP00000340554:V21838M	V	-	1	0	TTN	179122564	0.993000	0.37304	1.000000	0.80357	0.961000	0.63080	1.240000	0.32731	2.873000	0.98535	0.563000	0.77884	GTG	C|0.882;T|0.118	0.118	strong		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FCGBP	8857	hgsc.bcm.edu	37	19	40368520	40368520	+	Silent	SNP	G	G	C	rs36079378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40368520G>C	ENST00000221347.6	-	28	12835	c.12828C>G	c.(12826-12828)ggC>ggG	p.G4276G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4276	VWFD 10. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.G4276G(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGAAGCCAGGGCCCTCGTACT	0.652													G|||	2378	0.47484	0.5643	0.3026	5008	,	,		15152	0.5853		0.3698	False		,,,				2504	0.4703				p.G4276G		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - coding silent(1)	stomach(1)	c.C12828G						scavenged	.						49.0	51.0	51.0					19																	40368520		2203	4295	6498	SO:0001819	synonymous_variant	8857	exon28			GCCAGGGCCCTCG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12828C>G	19.37:g.40368520G>C		Somatic	167	2	0.011976		WXS	Illumina HiSeq	Phase_I	185	130	0.702703	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.500;C|0.500	0.500	strong		0.652	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
HDAC9	9734	hgsc.bcm.edu	37	7	18914209	18914209	+	Silent	SNP	G	G	T	rs17140166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:18914209G>T	ENST00000432645.2	+	21	2784	c.2784G>T	c.(2782-2784)gtG>gtT	p.V928V	HDAC9_ENST00000441542.2_Silent_p.V931V|HDAC9_ENST00000406451.4_Silent_p.V928V|HDAC9_ENST00000401921.1_Silent_p.V887V	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	928	Histone deacetylase.				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)	GGTACAAAGTGACGGCAAAAT	0.443													G|||	94	0.01877	0.0681	0.0029	5008	,	,		18680	0.0		0.002	False		,,,				2504	0.0				p.V931V		Atlas-SNP	.											.	HDAC9	560	.	0			c.G2793T						PASS	.	G	,,	258,3528		7,244,1642	67.0	62.0	64.0		2784,2784,2793	1.4	1.0	7	dbSNP_123	64	4,8238		0,4,4117	no	coding-synonymous,coding-synonymous,coding-synonymous	HDAC9	NM_058176.2,NM_178423.1,NM_178425.2	,,	7,248,5759	TT,TG,GG		0.0485,6.8146,2.1783	,,	928/1012,928/1067,931/1070	18914209	262,11766	1893	4121	6014	SO:0001819	synonymous_variant	9734	exon21			CAAAGTGACGGCA	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.2784G>T	7.37:g.18914209G>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			G|0.975;T|0.025	0.025	strong		0.443	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
KIF2B	84643	hgsc.bcm.edu	37	17	51900836	51900836	+	Missense_Mutation	SNP	C	C	T	rs59657238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:51900836C>T	ENST00000268919.4	+	1	598	c.442C>T	c.(442-444)Ccc>Tcc	p.P148S		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	148			P -> S (in dbSNP:rs59657238).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GAAAAAGTCTCCCTGCCTCTG	0.567													C|||	293	0.0585064	0.1483	0.0259	5008	,	,		17038	0.001		0.0626	False		,,,				2504	0.0153				p.P148S		Atlas-SNP	.											.	KIF2B	254	.	0			c.C442T						PASS	.	C	SER/PRO	497,3909	211.5+/-231.7	22,453,1728	53.0	57.0	55.0		442	0.3	0.3	17	dbSNP_129	55	446,8154	126.7+/-185.1	12,422,3866	yes	missense	KIF2B	NM_032559.4	74	34,875,5594	TT,TC,CC		5.186,11.2801,7.2505	benign	148/674	51900836	943,12063	2203	4300	6503	SO:0001583	missense	84643	exon1			AAGTCTCCCTGCC	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.442C>T	17.37:g.51900836C>T	ENSP00000268919:p.Pro148Ser	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	144	0.06593406593406594	83	0.16869918699186992	13	0.03591160220994475	0	0.0	48	0.0633245382585752	C	0.971	-0.700139	0.03279	0.112801	0.05186	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.72725	-0.68	4.99	0.323	0.15893	.	0.317263	0.22194	N	0.063336	T	0.00144	0.0004	N	0.11927	0.2	0.36768	P	0.11636500000000005	B	0.20887	0.049	B	0.16722	0.016	T	0.03112	-1.1071	9	0.07482	T	0.82	.	3.98	0.09490	0.2754:0.4093:0.2414:0.0739	rs59657238;rs62069524	148	Q8N4N8	KIF2B_HUMAN	S	148;71	ENSP00000268919:P148S	ENSP00000268919:P148S	P	+	1	0	KIF2B	49255835	0.000000	0.05858	0.291000	0.24904	0.377000	0.30045	0.255000	0.18333	0.023000	0.15187	-0.136000	0.14681	CCC	C|0.931;T|0.069	0.069	strong		0.567	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
MC1R	4157	hgsc.bcm.edu	37	16	89986608	89986608	+	Silent	SNP	A	A	G	rs2228478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89986608A>G	ENST00000555147.1	+	1	2322	c.942A>G	c.(940-942)acA>acG	p.T314T	MC1R_ENST00000555427.1_Silent_p.T314T|RP11-566K11.4_ENST00000554623.1_RNA|RP11-566K11.7_ENST00000570217.1_RNA|TUBB3_ENST00000556922.1_Silent_p.T314T|TUBB3_ENST00000554444.1_5'Flank	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	314					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		AGGTGCTGACATGCTCCTGGT	0.592									Melanoma, Familial Clustering of				G|||	1297	0.258986	0.4871	0.0836	5008	,	,		19553	0.2927		0.0924	False		,,,				2504	0.2117				p.T314T		Atlas-SNP	.											.	MC1R	20	.	0			c.A942G						PASS	.	G		1731,2511		347,1037,737	67.0	66.0	66.0		942	0.6	0.8	16	dbSNP_98	66	914,7554		55,804,3375	no	coding-synonymous	MC1R	NM_002386.3		402,1841,4112	GG,GA,AA		10.7936,40.8062,20.8104		314/318	89986608	2645,10065	2121	4234	6355	SO:0001819	synonymous_variant	4157	exon1	Familial Cancer Database		GCTGACATGCTCC		CCDS56011.1	16q24.3	2012-10-05			ENSG00000258839	ENSG00000258839		"""GPCR / Class A : Melanocortin receptors"""	6929	protein-coding gene	gene with protein product		155555				8458079	Standard	NM_002386		Approved	MSH-R		Q01726		ENST00000555147.1:c.942A>G	16.37:g.89986608A>G		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	212	104	0.490566	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Silent	SNP	ENST00000555147.1	37	CCDS56011.1																																																																																			A|0.821;G|0.179	0.179	strong		0.592	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
THRSP	7069	hgsc.bcm.edu	37	11	77775157	77775157	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77775157G>A	ENST00000281030.2	+	1	251	c.230G>A	c.(229-231)cGg>cAg	p.R77Q	NDUFC2-KCTD14_ENST00000530054.1_Intron|NDUFC2-KCTD14_ENST00000528251.1_Intron	NM_003251.3	NP_003242.1	Q92748	THRSP_HUMAN	thyroid hormone responsive	77					lipid metabolic process (GO:0006629)|regulation of lipid biosynthetic process (GO:0046890)|regulation of transcription, DNA-templated (GO:0006355)|regulation of triglyceride biosynthetic process (GO:0010866)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7	all_cancers(14;2.23e-19)|all_epithelial(13;7.49e-22)|Breast(9;6.38e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;2.15e-25)			CTGCTGCCGCGGGAGGAGTGG	0.632																																					p.R77Q		Atlas-SNP	.											.	THRSP	18	.	0			c.G230A						PASS	.						66.0	70.0	68.0					11																	77775157		2200	4292	6492	SO:0001583	missense	7069	exon1			TGCCGCGGGAGGA	Y08409	CCDS8256.1	11q14.1	2012-06-19	2010-06-25		ENSG00000151365	ENSG00000151365			11800	protein-coding gene	gene with protein product	"""SPOT14 homolog (rat)"""	601926	"""thyroid hormone responsive SPOT14 (rat) homolog"", ""lipogenic protein 1"""	LPGP1		9003802	Standard	NM_003251		Approved	SPOT14, Lpgp, S14, THRP	uc001oyx.3	Q92748	OTTHUMG00000166632	ENST00000281030.2:c.230G>A	11.37:g.77775157G>A	ENSP00000281030:p.Arg77Gln	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_003251	B2R4W7	Missense_Mutation	SNP	ENST00000281030.2	37	CCDS8256.1	.	.	.	.	.	.	.	.	.	.	G	9.274	1.046346	0.19748	.	.	ENSG00000151365	ENST00000281030	.	.	.	4.96	1.88	0.25563	.	0.320599	0.29328	N	0.012474	T	0.18045	0.0433	.	.	.	0.09310	N	1	B	0.25169	0.119	B	0.17722	0.019	T	0.09684	-1.0663	8	0.26408	T	0.33	-4.5778	3.7206	0.08454	0.3124:0.1858:0.5018:0.0	.	77	Q92748	THRSP_HUMAN	Q	77	.	ENSP00000281030:R77Q	R	+	2	0	THRSP	77452805	0.582000	0.26749	0.195000	0.23364	0.730000	0.41778	0.188000	0.17018	0.700000	0.31782	0.561000	0.74099	CGG	.	.	none		0.632	THRSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390939.1	NM_003251	
LY6G6C	80740	hgsc.bcm.edu	37	6	31692558	31692558	+	5'Flank	SNP	C	C	T	rs34741956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31692558C>T	ENST00000375819.2	-	0	0				C6orf25_ENST00000375805.2_Silent_p.T162T|C6orf25_ENST00000480039.1_Silent_p.T186T|C6orf25_ENST00000375810.4_Nonsense_Mutation_p.R193*|DDAH2_ENST00000480913.1_5'Flank|C6orf25_ENST00000375809.3_Nonsense_Mutation_p.R193*	NM_025261.2	NP_079537.1	O95867	LY66C_HUMAN	lymphocyte antigen 6 complex, locus G6C							anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(1)|large_intestine(1)|lung(1)|skin(1)	4						TTGTGAAAACCGAGCCCCAGA	0.572													C|||	8	0.00159744	0.0061	0.0	5008	,	,		16458	0.0		0.0	False		,,,				2504	0.0				p.R193X		Atlas-SNP	.											.	C6orf25	52	.	0			c.C577T						PASS	.	C	stop/ARG,,,stop/ARG,,stop/ARG	11,4395	19.1+/-41.9	0,11,2192	55.0	50.0	52.0		577,558,486,445,426,577	-8.9	0.0	6	dbSNP_126	52	0,8600		0,0,4300	yes	stop-gained,coding-synonymous,coding-synonymous,stop-gained,coding-synonymous,stop-gained	C6orf25	NM_025260.3,NM_138272.2,NM_138273.2,NM_138274.2,NM_138275.2,NM_138277.2	,,,,,	0,11,6492	TT,TC,CC		0.0,0.2497,0.0846	,,,,,	193/238,186/242,162/218,149/194,142/198,193/223	31692558	11,12995	2203	4300	6503	SO:0001631	upstream_gene_variant	80739	exon5			GAAAACCGAGCCC		CCDS4714.1	6p21	2008-08-29	2002-07-29	2002-08-01	ENSG00000204421	ENSG00000204421			13936	protein-coding gene	gene with protein product		610435	"""chromosome 6 open reading frame 24"""	C6orf24		10384126, 12079290	Standard	NM_025261		Approved	G6c, NG24	uc003nwh.3	O95867	OTTHUMG00000031251		6.37:g.31692558C>T	Exception_encountered	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	152	77	0.506579	NM_138277	Q5SRS8|Q8IY94	Nonsense_Mutation	SNP	ENST00000375819.2	37	CCDS4714.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	6.984	0.551598	0.13374	0.002497	0.0	ENSG00000204420	ENST00000375810;ENST00000375809;ENST00000375804	.	.	.	4.71	-8.89	0.00785	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.2739	0.9778	0.01429	0.2001:0.1463:0.3061:0.3475	rs34741956	.	.	.	X	193;193;149	.	ENSP00000364962:R149X	R	+	1	2	C6orf25	31800537	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.465000	0.00995	-1.689000	0.01434	0.591000	0.81541	CGA	C|0.997;T|0.003	0.003	strong		0.572	LY6G6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076530.2		
CD164L2	388611	hgsc.bcm.edu	37	1	27709020	27709020	+	Missense_Mutation	SNP	T	T	C	rs2504779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:27709020T>C	ENST00000374030.1	-	2	366	c.226A>G	c.(226-228)Atg>Gtg	p.M76V	CD164L2_ENST00000374025.3_Missense_Mutation_p.M76V|CD164L2_ENST00000374027.3_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	78	0	0		WXS	Illumina HiSeq	Phase_I	91	50	0.549451	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	
CELSR1	9620	hgsc.bcm.edu	37	22	46763671	46763671	+	Silent	SNP	A	A	G	rs7285515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46763671A>G	ENST00000262738.3	-	28	8033	c.8034T>C	c.(8032-8034)gaT>gaC	p.D2678D		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2678					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)		AGCTCAGTGCATCGCGGTTCA	0.652											OREG0026655	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	1122	0.224042	0.6664	0.1167	5008	,	,		18026	0.002		0.1292	False		,,,				2504	0.0286				p.D2678D		Atlas-SNP	.											.	CELSR1	242	.	0			c.T8034C						PASS	.			2540,1854		724,1092,381	41.0	36.0	38.0		8034	1.5	0.2	22	dbSNP_116	38	1049,7547		62,925,3311	no	coding-synonymous	CELSR1	NM_014246.1		786,2017,3692	GG,GA,AA		12.2034,42.1939,27.6289		2678/3015	46763671	3589,9401	2197	4298	6495	SO:0001819	synonymous_variant	9620	exon28			CAGTGCATCGCGG	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.8034T>C	22.37:g.46763671A>G		Somatic	207	0	0	941	WXS	Illumina HiSeq	Phase_I	195	195	1	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			A|0.740;G|0.260	0.260	strong		0.652	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183708	11183708	+	Missense_Mutation	SNP	T	T	C	rs80125932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11183708T>C	ENST00000390675.2	-	1	298	c.227A>G	c.(226-228)tAt>tGt	p.Y76C	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	76					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						TTCTACACTATAAAAAGCTGG	0.408																																					p.Y76C		Atlas-SNP	.											.	TAS2R31	24	.	0			c.A227G						PASS	.	T	CYS/TYR	98,4028		0,98,1965	81.0	95.0	91.0		227	1.1	0.0	12	dbSNP_131	91	880,7650		0,880,3385	no	missense	TAS2R31	NM_176885.2	194	0,978,5350	CC,CT,TT		10.3165,2.3752,7.7276	benign	76/310	11183708	978,11678	2063	4265	6328	SO:0001583	missense	259290	exon1			ACACTATAAAAAG	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.227A>G	12.37:g.11183708T>C	ENSP00000375093:p.Tyr76Cys	Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	344	54	0.156977	NM_176885	P59547|Q17R84|Q645X5	Missense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	.	.	.	.	.	.	.	.	.	.	T	5.935	0.356563	0.11239	0.023752	0.103165	ENSG00000256436	ENST00000390675	T	0.38240	1.15	2.45	1.15	0.20763	.	.	.	.	.	T	0.01061	0.0035	M	0.75777	2.31	0.09310	N	1	B	0.18863	0.031	B	0.27262	0.078	T	0.16541	-1.0399	9	0.54805	T	0.06	.	5.2988	0.15766	0.0:0.0:0.2988:0.7012	.	76	P59538	T2R31_HUMAN	C	76	ENSP00000375093:Y76C	ENSP00000375093:Y76C	Y	-	2	0	TAS2R31	11074975	0.001000	0.12720	0.005000	0.12908	0.116000	0.19942	0.134000	0.15932	0.151000	0.19162	0.163000	0.16589	TAT	T|0.871;C|0.129	0.129	strong		0.408	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
CBLN3	643866	hgsc.bcm.edu	37	14	24898135	24898135	+	Silent	SNP	C	C	T	rs57646536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24898135C>T	ENST00000267406.6	-	1	596	c.126G>A	c.(124-126)gaG>gaA	p.E42E	CBLN3_ENST00000555436.1_Intron|KHNYN_ENST00000556842.1_5'Flank|KHNYN_ENST00000553935.1_5'Flank|KHNYN_ENST00000251343.5_5'Flank	NM_001039771.2	NP_001034860.1	Q6UW01	CBLN3_HUMAN	cerebellin 3 precursor	42						cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				central_nervous_system(1)|lung(3)	4				GBM - Glioblastoma multiforme(265;0.00159)		GGCACTCCCCCTCCAGCAGGA	0.716													C|||	296	0.0591054	0.2088	0.0274	5008	,	,		13699	0.0		0.001	False		,,,				2504	0.0				p.E42E		Atlas-SNP	.											.	CBLN3	21	.	0			c.G126A						PASS	.	C		554,3752		31,492,1630	9.0	11.0	10.0		126	1.0	1.0	14	dbSNP_129	10	5,8401		0,5,4198	no	coding-synonymous	CBLN3	NM_001039771.2		31,497,5828	TT,TC,CC		0.0595,12.8658,4.3974		42/206	24898135	559,12153	2153	4203	6356	SO:0001819	synonymous_variant	643866	exon1			CTCCCCCTCCAGC	AY359070	CCDS32057.1	14q12	2006-12-13				ENSG00000139899			20146	protein-coding gene	gene with protein product		612978				12975309	Standard	NM_001039771		Approved		uc001wpg.4	Q6UW01		ENST00000267406.6:c.126G>A	14.37:g.24898135C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_001039771		Silent	SNP	ENST00000267406.6	37	CCDS32057.1																																																																																			C|0.963;T|0.037	0.037	strong		0.716	CBLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412943.1	XM_115232	
RGAG4	340526	hgsc.bcm.edu	37	X	71350294	71350294	+	Missense_Mutation	SNP	A	A	G	rs146618350		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:71350294A>G	ENST00000545866.1	-	1	1464	c.1097T>C	c.(1096-1098)aTg>aCg	p.M366T	RGAG4_ENST00000609883.1_Missense_Mutation_p.M366T|NHSL2_ENST00000540800.1_Intron	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	366										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					AAAAGCCCTCATGCGCTTCCT	0.498													A|||	19	0.00503311	0.0144	0.0	3775	,	,		14735	0.0		0.0	False		,,,				2504	0.0				p.M366T		Atlas-SNP	.											.	RGAG4	63	.	0			c.T1097C						PASS	.	A	,THR/MET	57,3395		0,49,8,1392,562	43.0	36.0	39.0		,1097	2.9	0.0	X	dbSNP_134	39	0,6522		0,0,0,2358,1806	yes	intron,missense	RGAG4,NHSL2	NM_001013627.2,NM_001024455.3	,81	0,49,8,3750,2368	GG,GA,G,AA,A		0.0,1.6512,0.5715	,benign	,366/570	71350294	57,9917	2011	4164	6175	SO:0001583	missense	340526	exon1			GCCCTCATGCGCT	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.1097T>C	X.37:g.71350294A>G	ENSP00000441366:p.Met366Thr	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	238	237	0.995798	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	37	CCDS55446.1	10	0.006027727546714889	7	0.01440329218106996	0	0.0	0	0.0	0	0.0	A	9.812	1.183556	0.21870	0.016512	0.0	ENSG00000242732	ENST00000545866;ENST00000479991	T;T	0.12984	2.63;2.63	4.13	2.94	0.34122	.	.	.	.	.	T	0.03305	0.0096	N	0.14661	0.345	0.09310	N	1	B	0.22276	0.067	B	0.15052	0.012	T	0.39742	-0.9599	8	.	.	.	-2.2205	8.3218	0.32134	0.8026:0.1974:0.0:0.0	.	366	Q5HYW3	RGAG4_HUMAN	T	366	ENSP00000441366:M366T;ENSP00000418667:M366T	.	M	-	2	0	RGAG4	71267019	0.000000	0.05858	0.001000	0.08648	0.122000	0.20287	0.748000	0.26305	0.701000	0.31803	0.486000	0.48141	ATG	A|0.994;G|0.006	0.006	strong		0.498	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455	
ANKRD36B	57730	hgsc.bcm.edu	37	2	98201527	98201527	+	RNA	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98201527G>A	ENST00000443455.1	-	0	508							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		TATTTGGATCGGCGCCATTTT	0.413																																					p.A110A		Atlas-SNP	.											.	.	.	.	0			c.C330T						PASS	.						22.0	18.0	19.0					2																	98201527		692	1578	2270			57730	exon3			TGGATCGGCGCCA	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98201527G>A		Somatic	1252	1	0.000798722		WXS	Illumina HiSeq	Phase_I	1172	406	0.346416	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Silent	SNP	ENST00000443455.1	37																																																																																				.	.	none		0.413	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
MUC17	140453	hgsc.bcm.edu	37	7	100678568	100678568	+	Missense_Mutation	SNP	A	A	T	rs75492258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678568A>T	ENST00000306151.4	+	3	3935	c.3871A>T	c.(3871-3873)Acc>Tcc	p.T1291S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1291	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)					CACGCTGGTGACCAGTCCTGA	0.478																																					p.T1291S		Atlas-SNP	.											MUC17,adrenal_gland,adrenal_cortical_adenoma,0,1	MUC17	804	1	0			c.A3871T						PASS	.	G	SER/THR	962,3444		0,962,1241	269.0	257.0	261.0		3871	-0.9	0.0	7	dbSNP_131	261	807,7793		0,807,3493	no	missense	MUC17	NM_001040105.1	58	0,1769,4734	TT,TA,AA		9.3837,21.8339,13.6014	benign	1291/4494	100678568	1769,11237	2203	4300	6503	SO:0001583	missense	140453	exon3			CTGGTGACCAGTC	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.3871A>T	7.37:g.100678568A>T	ENSP00000302716:p.Thr1291Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	145	31	0.213793	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.027	-1.364480	0.01235	0.218339	0.093837	ENSG00000169876	ENST00000306151	T	0.02323	4.34	0.471	-0.942	0.10398	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.44314	-0.9336	8	0.14656	T	0.56	.	.	.	.	.	1291	Q685J3	MUC17_HUMAN	S	1291	ENSP00000302716:T1291S	ENSP00000302716:T1291S	T	+	1	0	MUC17	100465288	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.016000	0.01446	-3.635000	0.00129	-3.626000	0.00027	ACC	A|0.934;T|0.066	0.066	strong		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MS4A15	219995	hgsc.bcm.edu	37	11	60531264	60531264	+	Missense_Mutation	SNP	A	A	G	rs12363342	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60531264A>G	ENST00000405633.3	+	2	137	c.58A>G	c.(58-60)Agt>Ggt	p.S20G	MS4A15_ENST00000337911.4_Intron|MS4A15_ENST00000528170.1_Missense_Mutation_p.S20G	NM_001098835.1	NP_001092305.1	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member 15	20			S -> G (in dbSNP:rs12363342).			integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(3)	6						AAACAACGCCAGTGGCCTCTG	0.572													A|||	1321	0.263778	0.2398	0.2853	5008	,	,		20159	0.2123		0.3588	False		,,,				2504	0.2362				p.S20G		Atlas-SNP	.											.	MS4A15	37	.	0			c.A58G						PASS	.	A	GLY/SER,	1092,2998		168,756,1121	102.0	102.0	102.0		58,	4.1	1.0	11	dbSNP_120	102	3246,5118		639,1968,1575	yes	missense,intron	MS4A15	NM_001098835.1,NM_152717.2	56,	807,2724,2696	GG,GA,AA		38.8092,26.6993,34.8322	probably-damaging,	20/241,	60531264	4338,8116	2045	4182	6227	SO:0001583	missense	219995	exon2			AACGCCAGTGGCC	AY584608	CCDS7991.1, CCDS44617.1, CCDS60802.1	11q12.2	2008-03-25							28573	protein-coding gene	gene with protein product							Standard	NM_001098835		Approved		uc009ynf.1	Q8N5U1		ENST00000405633.3:c.58A>G	11.37:g.60531264A>G	ENSP00000386022:p.Ser20Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_001098835	A9UJY6|A9UJY7|F2Z2J5	Missense_Mutation	SNP	ENST00000405633.3	37	CCDS44617.1	593	0.2715201465201465	108	0.21951219512195122	117	0.32320441988950277	99	0.17307692307692307	269	0.3548812664907652	A	13.46	2.242511	0.39598	0.266993	0.388092	ENSG00000166961	ENST00000528170;ENST00000405633	T;T	0.17213	2.29;2.87	5.21	4.07	0.47477	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.40139	P	0.02318600000000004	D;D	0.63880	0.993;0.982	P;D	0.67548	0.842;0.952	T	0.46062	-0.9218	8	0.51188	T	0.08	-21.4375	7.8754	0.29590	0.9042:0.0:0.0958:0.0	rs12363342	20;20	F2Z2J5;Q8N5U1	.;M4A15_HUMAN	G	20	ENSP00000434165:S20G;ENSP00000386022:S20G	ENSP00000386022:S20G	S	+	1	0	MS4A15	60287840	0.267000	0.24122	0.968000	0.41197	0.097000	0.18754	0.111000	0.15458	0.797000	0.33971	0.379000	0.24179	AGT	A|0.709;G|0.291	0.291	strong		0.572	MS4A15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395618.1		
DHRS4	10901	hgsc.bcm.edu	37	14	24424367	24424367	+	Silent	SNP	G	G	A	rs12147221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24424367G>A	ENST00000313250.5	+	2	455	c.252G>A	c.(250-252)acG>acA	p.T84T	DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000397075.3_Silent_p.T84T|DHRS4_ENST00000397073.2_Silent_p.T66T|DHRS4_ENST00000382761.3_Silent_p.T66T|DHRS4_ENST00000397074.3_Silent_p.T84T|DHRS4_ENST00000559632.1_Silent_p.T84T|DHRS4_ENST00000543741.2_Silent_p.T84T|DHRS4_ENST00000308178.8_Silent_p.T66T|DHRS4_ENST00000558263.1_Silent_p.T84T|DHRS4_ENST00000421831.1_Silent_p.T66T|DHRS4_ENST00000558581.1_Silent_p.T84T	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	244	0	0		WXS	Illumina HiSeq	Phase_I	321	157	0.489097	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		
PRSS36	146547	hgsc.bcm.edu	37	16	31151927	31151927	+	Silent	SNP	G	G	A	rs61976958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31151927G>A	ENST00000268281.4	-	13	2111	c.2053C>T	c.(2053-2055)Ctg>Ttg	p.L685L	PRSS36_ENST00000418068.2_Intron|PRSS36_ENST00000569305.1_Silent_p.L680L	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	685	Peptidase S1 3. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						CGGGAGCTCAGCTCCAGGAGG	0.706													G|||	78	0.0155751	0.0545	0.0086	5008	,	,		15742	0.0		0.0	False		,,,				2504	0.0				p.L685L		Atlas-SNP	.											.	PRSS36	50	.	0			c.C2053T						PASS	.	G		227,4155		8,211,1972	14.0	19.0	17.0		2053	2.7	1.0	16	dbSNP_129	17	1,8573		0,1,4286	no	coding-synonymous	PRSS36	NM_173502.3		8,212,6258	AA,AG,GG		0.0117,5.1803,1.7598		685/856	31151927	228,12728	2191	4287	6478	SO:0001819	synonymous_variant	146547	exon13			AGCTCAGCTCCAG	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"""Serine peptidases / Serine peptidases"""	26906	protein-coding gene	gene with protein product	"""polyserase 2"""	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.2053C>T	16.37:g.31151927G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_173502	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Silent	SNP	ENST00000268281.4	37	CCDS32436.1																																																																																			G|0.983;A|0.017	0.017	strong		0.706	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502	
ROBO4	54538	hgsc.bcm.edu	37	11	124764176	124764176	+	Silent	SNP	T	T	C	rs11820142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124764176T>C	ENST00000306534.3	-	8	1724	c.1239A>G	c.(1237-1239)ccA>ccG	p.P413P	ROBO4_ENST00000533054.1_Silent_p.P268P|ROBO4_ENST00000526899.1_5'Flank	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	413	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		AGTAGGAGCCTGGCATATGGG	0.597													T|||	125	0.0249601	0.0893	0.0086	5008	,	,		3618	0.0		0.001	False		,,,				2504	0.0				p.P413P		Atlas-SNP	.											.	ROBO4	130	.	0			c.A1239G						PASS	.	T		344,4058	179.4+/-207.9	9,326,1866	111.0	87.0	95.0		1239	1.1	1.0	11	dbSNP_120	95	2,8596	1.2+/-3.3	0,2,4297	no	coding-synonymous	ROBO4	NM_019055.5		9,328,6163	CC,CT,TT		0.0233,7.8146,2.6615		413/1008	124764176	346,12654	2201	4299	6500	SO:0001819	synonymous_variant	54538	exon8			GGAGCCTGGCATA	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.1239A>G	11.37:g.124764176T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			T|0.971;C|0.029	0.029	strong		0.597	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
NRIP1	8204	hgsc.bcm.edu	37	21	16340289	16340289	+	Silent	SNP	C	C	T	rs2229741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:16340289C>T	ENST00000400202.1	-	3	937	c.225G>A	c.(223-225)ggG>ggA	p.G75G	NRIP1_ENST00000400199.1_Silent_p.G75G|NRIP1_ENST00000318948.4_Silent_p.G75G			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	75	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)	p.G75G(1)		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)		GCATGCCAGACCCCTGATATG	0.443													T|||	3002	0.599441	0.7829	0.549	5008	,	,		22522	0.7738		0.4026	False		,,,				2504	0.41				p.G75G		Atlas-SNP	.											NRIP1,NS,carcinoma,0,1	NRIP1	103	1	1	Substitution - coding silent(1)	prostate(1)	c.G225A						PASS	.	T		3170,1236	426.6+/-341.2	1153,864,186	62.0	56.0	58.0	http://www.ncbi.nlm.nih.gov/pubmed?term	225	3.3	1.0	21	dbSNP_98	58	3594,5006	626.6+/-397.9	736,2122,1442	yes	coding-synonymous	NRIP1	NM_003489.3		1889,2986,1628	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	41.7907,28.0527,47.9932		75/1159	16340289	6764,6242	2203	4300	6503	SO:0001819	synonymous_variant	8204	exon4			GCCAGACCCCTGA	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.225G>A	21.37:g.16340289C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	119	64	0.537815	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	37	CCDS13568.1																																																																																			C|0.443;T|0.557	0.557	strong		0.443	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
ROR2	4920	hgsc.bcm.edu	37	9	94499797	94499797	+	Silent	SNP	A	A	G	rs16907720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:94499797A>G	ENST00000375708.3	-	5	696	c.498T>C	c.(496-498)gaT>gaC	p.D166D	ROR2_ENST00000375715.1_Silent_p.D26D|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	166					cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CGTGGTAATCATCCCTGGTAA	0.512													A|||	361	0.0720847	0.1959	0.0504	5008	,	,		16550	0.0		0.0537	False		,,,				2504	0.0133				p.D166D		Atlas-SNP	.											.	ROR2	167	.	0			c.T498C						PASS	.	A		757,3649	309.1+/-290.9	63,631,1509	80.0	73.0	75.0		498	-4.9	0.8	9	dbSNP_123	75	573,8027	153.7+/-208.1	19,535,3746	no	coding-synonymous	ROR2	NM_004560.3		82,1166,5255	GG,GA,AA		6.6628,17.1811,10.226		166/944	94499797	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	4920	exon5			GTAATCATCCCTG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.498T>C	9.37:g.94499797A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	38	26	0.684211	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	37	CCDS6691.1																																																																																			A|0.902;G|0.098	0.098	strong		0.512	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
BEST1	7439	hgsc.bcm.edu	37	11	61730427	61730427	+	Intron	SNP	G	G	T	rs115979721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61730427G>T	ENST00000378043.4	+	10	2382				FTH1_ENST00000529631.1_Intron|BEST1_ENST00000378042.3_Intron|BEST1_ENST00000449131.2_Missense_Mutation_p.A541S|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000301774.9_Missense_Mutation_p.A229S	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						AGCTTCCCTTGCTCTGAGCCT	0.562													G|||	107	0.0213658	0.0764	0.0086	5008	,	,		19855	0.0		0.0	False		,,,				2504	0.0				p.A541S		Atlas-SNP	.											.	BEST1	85	.	0			c.G1621T						PASS	.	G	SER/ALA,	74,1310		2,70,620	123.0	114.0	116.0		1621,	-5.3	0.0	11	dbSNP_132	116	0,3182		0,0,1591	yes	missense,intron	BEST1	NM_001139443.1,NM_004183.3	99,	2,70,2211	TT,TG,GG		0.0,5.3468,1.6207	,	541/605,	61730427	74,4492	692	1591	2283	SO:0001627	intron_variant	7439	exon9			TCCCTTGCTCTGA	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1739+62G>T	11.37:g.61730427G>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	165	81	0.490909	NM_001139443	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Missense_Mutation	SNP	ENST00000378043.4	37	CCDS31580.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	G	12.96	2.094835	0.36952	0.053468	0.0	ENSG00000167995	ENST00000301774;ENST00000449131	T;D	0.97089	-0.32;-4.24	4.13	-5.35	0.02697	.	.	.	.	.	T	0.35098	0.0920	N	0.08118	0	0.09310	N	0.999995	B	0.17268	0.021	B	0.14023	0.01	T	0.73116	-0.4084	8	.	.	.	.	0.3641	0.00369	0.2188:0.2264:0.2454:0.3094	.	541	O76090-3	.	S	229;541	ENSP00000301774:A229S;ENSP00000399709:A541S	.	A	+	1	0	BEST1	61487003	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.419000	0.07071	-1.297000	0.02351	-0.311000	0.09066	GCT	G|0.977;T|0.023	0.023	strong		0.562	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
POTEG	404785	hgsc.bcm.edu	37	14	19563532	19563532	+	Missense_Mutation	SNP	A	A	G	rs199732644		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:19563532A>G	ENST00000409832.3	+	5	1098	c.1046A>G	c.(1045-1047)cAt>cGt	p.H349R	RNU6-1239P_ENST00000391310.1_RNA|CTD-2311B13.5_ENST00000548748.1_lincRNA	NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	349				H -> R (in Ref. 1; AAS58868/AAS58871). {ECO:0000305}.						cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						GTTTCTAGTCATCATAATGTG	0.353																																					p.H349R		Atlas-SNP	.											POTEG,NS,carcinoma,-1,2	POTEG	118	2	0			c.A1046G						scavenged	.	A	ARG/HIS	52,2240		0,52,1094	61.0	98.0	86.0		1046	-1.0	0.0	14	dbSNP_134	86	3,4981		0,3,2489	no	missense	POTEG	NM_001005356.2	29	0,55,3583	GG,GA,AA		0.0602,2.2688,0.7559	benign	349/509	19563532	55,7221	1146	2492	3638	SO:0001583	missense	404785	exon5			CTAGTCATCATAA		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.1046A>G	14.37:g.19563532A>G	ENSP00000386971:p.His349Arg	Somatic	293	1	0.00341297		WXS	Illumina HiSeq	Phase_I	320	10	0.03125	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	37	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	N	0.424	-0.906853	0.02434	0.022688	6.02E-4	ENSG00000222036	ENST00000409832	T	0.62941	-0.01	1.09	-1.03	0.10102	Ankyrin repeat-containing domain (4);	3.636160	0.02887	N	0.133696	T	0.28928	0.0718	N	0.17248	0.465	0.80722	P	0.0	B	0.16802	0.019	B	0.20955	0.032	T	0.16217	-1.0410	9	0.34782	T	0.22	.	5.8199	0.18522	0.235:0.0:0.765:0.0	.	349	Q6S5H5	POTEG_HUMAN	R	349	ENSP00000386971:H349R	ENSP00000386971:H349R	H	+	2	0	POTEG	18633532	0.001000	0.12720	0.000000	0.03702	0.044000	0.14063	0.831000	0.27476	-0.390000	0.07774	-1.412000	0.01120	CAT	A|0.250;G|0.750	0.750	weak		0.353	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
ANKUB1	389161	hgsc.bcm.edu	37	3	149485581	149485581	+	Missense_Mutation	SNP	C	C	T	rs75855073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:149485581C>T	ENST00000383050.3	-	5	1324	c.868G>A	c.(868-870)Gta>Ata	p.V290I	ANKUB1_ENST00000462519.2_Missense_Mutation_p.V290I|ANKUB1_ENST00000446160.1_Missense_Mutation_p.V290I			A6NFN9	ANKUB_HUMAN	ankyrin repeat and ubiquitin domain containing 1	290										breast(1)|kidney(1)|lung(1)|skin(1)	4						AAATATAATACACAGTCTTTA	0.388													C|||	112	0.0223642	0.0794	0.0101	5008	,	,		21007	0.0		0.0	False		,,,				2504	0.0				p.V290I		Atlas-SNP	.											.	ANKUB1	27	.	0			c.G868A						PASS	.	C	ILE/VAL	73,1311		1,71,620	89.0	74.0	79.0		868	5.2	0.3	3	dbSNP_132	79	0,3182		0,0,1591	yes	missense	ANKUB1	NM_001144960.1	29	1,71,2211	TT,TC,CC		0.0,5.2746,1.5988	benign	290/545	149485581	73,4493	692	1591	2283	SO:0001583	missense	389161	exon5			ATAATACACAGTC	AK027233		3q25.1	2013-01-11	2011-05-10	2011-05-10	ENSG00000206199	ENSG00000206199		"""Ankyrin repeat domain containing"""	29642	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 16"""	C3orf16			Standard	NM_001144960		Approved		uc003exl.3	A6NFN9	OTTHUMG00000159615	ENST00000383050.3:c.868G>A	3.37:g.149485581C>T	ENSP00000372522:p.Val290Ile	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_001144960	B4E2N8	Missense_Mutation	SNP	ENST00000383050.3	37		49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	C	15.33	2.800905	0.50315	0.052746	0.0	ENSG00000206199	ENST00000446160;ENST00000383050;ENST00000462519	T;T;T	0.71698	-0.59;-0.59;-0.59	5.16	5.16	0.70880	Ankyrin repeat-containing domain (3);	.	.	.	.	T	0.12135	0.0295	L	0.35723	1.085	0.26889	N	0.967365	D;D	0.61697	0.99;0.979	P;P	0.60789	0.879;0.879	T	0.42327	-0.9458	9	0.44086	T	0.13	.	17.4257	0.87525	0.0:1.0:0.0:0.0	.	290;290	A6NFN9;E9PHT4	ANKUB_HUMAN;.	I	290	ENSP00000387907:V290I;ENSP00000372522:V290I;ENSP00000417635:V290I	ENSP00000372522:V290I	V	-	1	0	ANKUB1	150968271	0.977000	0.34250	0.346000	0.25655	0.995000	0.86356	3.945000	0.56637	2.401000	0.81631	0.591000	0.81541	GTA	C|0.974;T|0.026	0.026	strong		0.388	ANKUB1-201	KNOWN	basic	protein_coding	protein_coding		NM_001144960	
MED13	9969	hgsc.bcm.edu	37	17	60087932	60087932	+	Missense_Mutation	SNP	T	T	C	rs114223275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60087932T>C	ENST00000397786.2	-	9	2022	c.1946A>G	c.(1945-1947)gAa>gGa	p.E649G		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	649					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|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)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	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 coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TGTTACACTTTCCTGTCCAAA	0.333													T|||	7	0.00139776	0.0053	0.0	5008	,	,		20038	0.0		0.0	False		,,,				2504	0.0				p.E649G		Atlas-SNP	.											.	MED13	181	.	0			c.A1946G						PASS	.	T	GLY/GLU	11,3675		0,11,1832	67.0	60.0	62.0		1946	5.6	1.0	17	dbSNP_132	62	0,8172		0,0,4086	yes	missense	MED13	NM_005121.2	98	0,11,5918	CC,CT,TT		0.0,0.2984,0.0928	probably-damaging	649/2175	60087932	11,11847	1843	4086	5929	SO:0001583	missense	9969	exon9			ACACTTTCCTGTC	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.1946A>G	17.37:g.60087932T>C	ENSP00000380888:p.Glu649Gly	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	12.76	2.033391	0.35893	0.002984	0.0	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.75367	-0.93	5.62	5.62	0.85841	.	0.156711	0.44483	D	0.000448	T	0.74604	0.3738	L	0.46157	1.445	0.58432	D	0.999998	P;B	0.44139	0.827;0.181	P;B	0.46758	0.526;0.014	T	0.75639	-0.3248	10	0.46703	T	0.11	-17.8348	15.804	0.78477	0.0:0.0:0.0:1.0	.	162;649	Q9P0Q5;Q9UHV7	.;MED13_HUMAN	G	649;648	ENSP00000380888:E649G	ENSP00000262436:E648G	E	-	2	0	MED13	57442714	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.998000	0.63927	2.131000	0.65755	0.477000	0.44152	GAA	T|0.999;C|0.001	0.001	strong		0.333	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
COPE	11316	hgsc.bcm.edu	37	19	19030120	19030120	+	Missense_Mutation	SNP	G	G	C	rs2231987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19030120G>C	ENST00000262812.4	-	1	86	c.38C>G	c.(37-39)tCc>tGc	p.S13C	DDX49_ENST00000247003.4_5'Flank|COPE_ENST00000351079.4_Missense_Mutation_p.S13C|COPE_ENST00000600932.1_Missense_Mutation_p.S13C|AC002985.3_ENST00000596918.1_Intron|DDX49_ENST00000438170.2_5'Flank|COPE_ENST00000349893.4_Missense_Mutation_p.S13C	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	13			S -> C (in dbSNP:rs2231987).		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						TACCTCCCCGGAGCCGCCGGA	0.652													G|||	357	0.0712859	0.2526	0.0259	5008	,	,		12900	0.0		0.005	False		,,,				2504	0.0				p.S13C		Atlas-SNP	.											.	COPE	26	.	0			c.C38G						PASS	.	G	CYS/SER,CYS/SER,CYS/SER	1007,3399	349.3+/-310.3	111,785,1307	34.0	38.0	37.0		38,38,38	5.7	1.0	19	dbSNP_98	37	16,8584	11.2+/-40.8	0,16,4284	yes	missense,missense,missense	COPE	NM_007263.3,NM_199442.1,NM_199444.1	112,112,112	111,801,5591	CC,CG,GG		0.186,22.8552,7.8656	possibly-damaging,possibly-damaging,possibly-damaging	13/309,13/258,13/257	19030120	1023,11983	2203	4300	6503	SO:0001583	missense	11316	exon1			TCCCCGGAGCCGC	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.38C>G	19.37:g.19030120G>C	ENSP00000262812:p.Ser13Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_007263	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	Missense_Mutation	SNP	ENST00000262812.4	37	CCDS12387.1	140	0.0641025641025641	131	0.266260162601626	7	0.019337016574585635	0	0.0	2	0.002638522427440633	G	18.45	3.626301	0.66901	0.228552	0.00186	ENSG00000105669	ENST00000262812;ENST00000351079;ENST00000349893;ENST00000538245	T;T;T	0.48201	1.4;0.82;1.42	5.66	5.66	0.87406	.	0.314966	0.32002	N	0.006726	T	0.00012	0.0000	N	0.08118	0	0.32799	P	0.500166	P;P;P;P	0.51653	0.947;0.454;0.454;0.876	B;B;B;B	0.43916	0.436;0.319;0.319;0.319	T	0.16660	-1.0395	9	0.54805	T	0.06	-26.4078	18.3234	0.90246	0.0:0.0:1.0:0.0	rs2231987	13;13;13;13	Q53HJ6;A6NE29;A6NKA3;O14579	.;.;.;COPE_HUMAN	C	13;13;13;12	ENSP00000262812:S13C;ENSP00000345674:S13C;ENSP00000343134:S13C	ENSP00000262812:S13C	S	-	2	0	COPE	18891120	1.000000	0.71417	0.999000	0.59377	0.716000	0.41182	5.416000	0.66417	2.679000	0.91253	0.563000	0.77884	TCC	G|0.928;C|0.072	0.072	strong		0.652	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464801.1	NM_007263	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377120	49377120	+	Silent	SNP	C	C	T	rs34899467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49377120C>T	ENST00000200453.5	+	2	899	c.630C>T	c.(628-630)gcC>gcT	p.A210A		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	210	Glu-rich.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CTACTTCTGCCTTGTCTCCAG	0.512													C|||	82	0.0163738	0.0545	0.0014	5008	,	,		18999	0.002		0.0	False		,,,				2504	0.0072				p.A210A		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.C630T						PASS	.	C		201,4205	124.9+/-162.1	2,197,2004	128.0	141.0	137.0		630	-0.7	0.0	19	dbSNP_126	137	0,8600		0,0,4300	no	coding-synonymous	PPP1R15A	NM_014330.3		2,197,6304	TT,TC,CC		0.0,4.562,1.5454		210/675	49377120	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon2			TTCTGCCTTGTCT	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.630C>T	19.37:g.49377120C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			C|0.984;T|0.016	0.016	strong		0.512	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
MAP10	54627	hgsc.bcm.edu	37	1	232942276	232942276	+	Missense_Mutation	SNP	G	G	A	rs61735495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232942276G>A	ENST00000418460.1	+	1	1634	c.1507G>A	c.(1507-1509)Gaa>Aaa	p.E503K		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	361					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										TGCAGCACACGAACATCCTCC	0.403													G|||	107	0.0213658	0.0794	0.0029	5008	,	,		20484	0.0		0.0	False		,,,				2504	0.0				p.E503K		Atlas-SNP	.											.	.	.	.	0			c.G1507A						PASS	.	G	LYS/GLU	242,3624		6,230,1697	71.0	69.0	70.0		1507	2.5	0.0	1	dbSNP_129	70	0,8278		0,0,4139	yes	missense	KIAA1383	NM_019090.2	56	6,230,5836	AA,AG,GG		0.0,6.2597,1.9928	possibly-damaging	503/1048	232942276	242,11902	1933	4139	6072	SO:0001583	missense	54627	exon1			GCACACGAACATC	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.1507G>A	1.37:g.232942276G>A	ENSP00000403208:p.Glu503Lys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	G	17.33	3.362324	0.61403	0.062597	0.0	ENSG00000212916	ENST00000418460	.	.	.	4.69	2.48	0.30137	.	.	.	.	.	T	0.04679	0.0127	M	0.67953	2.075	0.09310	N	1	P	0.49559	0.925	B	0.43052	0.406	T	0.02774	-1.1112	8	0.37606	T	0.19	-11.7864	6.2799	0.21001	0.1287:0.1763:0.695:0.0	rs61735495	361	Q9P2G4	K1383_HUMAN	K	503	.	ENSP00000403208:E503K	E	+	1	0	KIAA1383	231008899	0.003000	0.15002	0.008000	0.14137	0.002000	0.02628	0.383000	0.20651	0.673000	0.31224	0.655000	0.94253	GAA	G|0.988;A|0.012	0.012	strong		0.403	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464736	39464736	+	Missense_Mutation	SNP	C	C	G	rs2074284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	140	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	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	
URI1	8725	hgsc.bcm.edu	37	19	30500195	30500195	+	Missense_Mutation	SNP	G	G	C	rs151025990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:30500195G>C	ENST00000542441.2	+	8	1267	c.970G>C	c.(970-972)Gct>Cct	p.A324P	URI1_ENST00000312051.6_Missense_Mutation_p.A284P|URI1_ENST00000360605.4_Missense_Mutation_p.A306P|URI1_ENST00000392271.1_Missense_Mutation_p.A248P			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	324					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)										cgaCCATGAGGCTTTAGGGGT	0.378													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21705	0.0		0.0	False		,,,				2504	0.0				p.A324P		Atlas-SNP	.											.	.	.	.	0			c.G970C						PASS	.	G	PRO/ALA,PRO/ALA	13,4393	20.2+/-43.8	0,13,2190	95.0	82.0	86.0		970,850	-3.2	0.0	19	dbSNP_134	86	0,8600		0,0,4300	yes	missense,missense	C19orf2	NM_003796.2,NM_134447.1	27,27	0,13,6490	CC,CG,GG		0.0,0.2951,0.1	benign,benign	324/536,284/496	30500195	13,12993	2203	4300	6503	SO:0001583	missense	8725	exon8			CATGAGGCTTTAG	AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	13236	protein-coding gene	gene with protein product	"""unconventional prefoldin RPB5 interactor"", ""RPB5-mediating protein"", ""protein phosphatase 1, regulatory subunit 19"""	603494	"""chromosome 19 open reading frame 2"""	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.970G>C	19.37:g.30500195G>C	ENSP00000442436:p.Ala324Pro	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_003796	A8K805|H7BY42|Q8TC23|Q9UNU3	Missense_Mutation	SNP	ENST00000542441.2	37	CCDS12420.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.04	2.714683	0.48622	0.002951	0.0	ENSG00000105176	ENST00000360605;ENST00000392271;ENST00000542441;ENST00000312051	T	0.50001	0.76	5.03	-3.22	0.05125	.	1.234740	0.05290	N	0.520817	T	0.22003	0.0530	N	0.08118	0	0.09310	N	1	P;B;P	0.38642	0.545;0.41;0.641	B;B;B	0.32864	0.147;0.11;0.154	T	0.13019	-1.0525	10	0.37606	T	0.19	-1.217	5.6351	0.17532	0.3821:0.0:0.4983:0.1197	.	284;324;321	F8W9T0;O94763;Q8TC23	.;RMP_HUMAN;.	P	322;248;324;284	ENSP00000442436:A324P	ENSP00000312530:A284P	A	+	1	0	C19orf2	35192035	0.042000	0.20092	0.000000	0.03702	0.248000	0.25809	0.075000	0.14686	-0.488000	0.06726	0.491000	0.48974	GCT	G|0.998;C|0.002	0.002	strong		0.378	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447	
NLRP7	199713	hgsc.bcm.edu	37	19	55450727	55450727	+	Missense_Mutation	SNP	C	C	T	rs775881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55450727C>T	ENST00000590030.1	-	3	1500	c.1460G>A	c.(1459-1461)gGg>gAg	p.G487E	NLRP7_ENST00000340844.2_Missense_Mutation_p.G487E|NLRP7_ENST00000448121.2_Missense_Mutation_p.G487E|NLRP7_ENST00000446217.1_Missense_Mutation_p.G515E|NLRP7_ENST00000328092.5_Missense_Mutation_p.G487E|NLRP7_ENST00000588756.1_Missense_Mutation_p.G487E|NLRP7_ENST00000592784.1_Missense_Mutation_p.G487E			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	487	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		G -> E (in dbSNP:rs775881).				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)		CCTGTCCTCCCCCTCCTCCTT	0.582													.|||	629	0.125599	0.3888	0.0634	5008	,	,		18526	0.003		0.0477	False		,,,				2504	0.0204				p.G487E		Atlas-SNP	.											.	NLRP7	411	.	0			c.G1460A						PASS	.	T	GLU/GLY,GLU/GLY,GLU/GLY	1593,2813	662.7+/-401.1	277,1039,887	56.0	54.0	55.0		1460,1460,1460	-0.8	0.0	19	dbSNP_86	55	251,8349	808.2+/-407.2	4,243,4053	no	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	98,98,98	281,1282,4940	TT,TC,CC		2.9186,36.1552,14.1781	benign,benign,benign	487/1038,487/1010,487/981	55450727	1844,11162	2203	4300	6503	SO:0001583	missense	199713	exon4			TCCTCCCCCTCCT	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.1460G>A	19.37:g.55450727C>T	ENSP00000465520:p.Gly487Glu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	251	0.11492673992673992	193	0.39227642276422764	29	0.08011049723756906	0	0.0	29	0.03825857519788918	T	0.020	-1.447617	0.01089	0.361552	0.029186	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.73897	-0.74;-0.74;-0.79;-0.77	1.56	-0.809	0.10864	.	.	.	.	.	T	0.00012	0.0000	N	0.01761	-0.735	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;0.001	T	0.10291	-1.0636	8	0.02654	T	1	.	2.9693	0.05918	0.0:0.3758:0.2638:0.3604	rs775881;rs56740557	515;487;487;487	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	E	487;487;487;515;254	ENSP00000329568:G487E;ENSP00000409137:G487E;ENSP00000339491:G487E;ENSP00000414273:G515E	ENSP00000329568:G487E	G	-	2	0	NLRP7	60142539	0.000000	0.05858	0.000000	0.03702	0.474000	0.32979	0.249000	0.18216	-0.813000	0.04357	-0.931000	0.02705	GGG	C|0.869;T|0.131	0.131	strong		0.582	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
COL27A1	85301	hgsc.bcm.edu	37	9	117051020	117051020	+	Silent	SNP	A	A	G	rs1687410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117051020A>G	ENST00000356083.3	+	43	4474	c.4083A>G	c.(4081-4083)ggA>ggG	p.G1361G		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1361	Collagen-like 12.|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						GGGAACCGGGAGACCCTGGGT	0.577													G|||	1173	0.234225	0.3631	0.1988	5008	,	,		15830	0.2827		0.1372	False		,,,				2504	0.135				p.G1361G		Atlas-SNP	.											.	COL27A1	200	.	0			c.A4083G						PASS	.	G		1440,2966	676.4+/-403.2	249,942,1012	59.0	64.0	62.0		4083	2.8	1.0	9	dbSNP_89	62	1142,7458	764.3+/-407.6	75,992,3233	no	coding-synonymous	COL27A1	NM_032888.2		324,1934,4245	GG,GA,AA		13.2791,32.6827,19.8524		1361/1861	117051020	2582,10424	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon43			ACCGGGAGACCCT	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.4083A>G	9.37:g.117051020A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	100	69	0.69	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			A|0.790;G|0.210	0.210	strong		0.577	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
MUC2	4583	hgsc.bcm.edu	37	11	1092841	1092841	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1092841G>A	ENST00000441003.2	+	30	4687	c.4660G>A	c.(4660-4662)Ggc>Agc	p.G1554S	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.G1555S|MUC2_ENST00000333592.6_5'Flank	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	0.632																																					p.G1554S		Atlas-SNP	.											MUC2_ENST00000441003,trunk,malignant_melanoma,-1,2	MUC2	614	2	0			c.G4660A						scavenged	.						79.0	103.0	94.0					11																	1092841		1868	3445	5313	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.4660G>A	11.37:g.1092841G>A	ENSP00000415183:p.Gly1554Ser	Somatic	124	26	0.209677		WXS	Illumina HiSeq	Phase_I	130	37	0.284615	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	G	3.185	-0.167089	0.06461	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11821	2.74;2.98	1.33	-2.66	0.06077	.	0.401141	0.15760	U	0.245987	T	0.03827	0.0108	.	.	.	0.09310	N	1	B	0.16802	0.019	B	0.01281	0.0	T	0.39921	-0.9590	9	0.07175	T	0.84	.	2.8157	0.05455	0.4548:0.0:0.3399:0.2053	.	1554	E7EUV1	.	S	1554;1555	ENSP00000415183:G1554S;ENSP00000351956:G1555S	ENSP00000351956:G1555S	G	+	1	0	MUC2	1082841	0.000000	0.05858	0.001000	0.08648	0.338000	0.28826	-2.797000	0.00763	-0.263000	0.09378	0.109000	0.15622	GGC	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ZBTB4	57659	hgsc.bcm.edu	37	17	7365289	7365289	+	Silent	SNP	A	A	T	rs114898274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7365289A>T	ENST00000311403.4	-	4	3351	c.3012T>A	c.(3010-3012)gtT>gtA	p.V1004V	ZBTB4_ENST00000380599.4_Silent_p.V1004V	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	1004					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		GGGTTCTCTCAACCCCTGCCC	0.617													A|||	41	0.0081869	0.0287	0.0043	5008	,	,		14891	0.0		0.0	False		,,,				2504	0.0				p.V1004V		Atlas-SNP	.											.	ZBTB4	163	.	0			c.T3012A						PASS	.	A	,	88,4318	74.1+/-112.3	1,86,2116	58.0	64.0	62.0		3012,3012	0.3	1.0	17	dbSNP_132	62	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	ZBTB4	NM_001128833.1,NM_020899.3	,	1,92,6410	TT,TA,AA		0.0698,1.9973,0.7227	,	1004/1014,1004/1014	7365289	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	57659	exon4			TCTCTCAACCCCT	AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.3012T>A	17.37:g.7365289A>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Silent	SNP	ENST00000311403.4	37	CCDS11107.1																																																																																			A|0.992;T|0.008	0.008	strong		0.617	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899	
TACC2	10579	hgsc.bcm.edu	37	10	123970513	123970513	+	Silent	SNP	G	G	A	rs35913854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123970513G>A	ENST00000369005.1	+	9	6913	c.6573G>A	c.(6571-6573)acG>acA	p.T2191T	TACC2_ENST00000515273.1_Silent_p.T2195T|TACC2_ENST00000515603.1_Silent_p.T2146T|TACC2_ENST00000453444.2_Silent_p.T2195T|TACC2_ENST00000358010.1_Silent_p.T337T|TACC2_ENST00000360561.3_Silent_p.T269T|TACC2_ENST00000368999.1_Silent_p.T269T|TACC2_ENST00000334433.3_Silent_p.T2191T|TACC2_ENST00000369004.3_Silent_p.T269T|TACC2_ENST00000260733.3_Silent_p.T269T|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000513429.1_Silent_p.T337T|TACC2_ENST00000369000.1_5'UTR	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2191					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGGAGGAGACGCCCCTTGAGC	0.597													G|||	369	0.0736821	0.2648	0.0259	5008	,	,		15618	0.0		0.001	False		,,,				2504	0.0				p.T2191T		Atlas-SNP	.											.	TACC2	271	.	0			c.G6573A						PASS	.	G	,,,	913,3491	324.5+/-298.6	109,695,1398	54.0	66.0	62.0		807,807,1011,6573	-11.1	0.0	10	dbSNP_126	62	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	,,,	109,709,5684	AA,AG,GG		0.1628,20.7312,7.1286	,,,	269/1027,269/997,337/1095,2191/2949	123970513	927,12077	2202	4300	6502	SO:0001819	synonymous_variant	10579	exon9			GGAGACGCCCCTT	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.6573G>A	10.37:g.123970513G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			G|0.936;A|0.064	0.064	strong		0.597	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
PCDHB8	56128	hgsc.bcm.edu	37	5	140559350	140559350	+	Missense_Mutation	SNP	C	C	T	rs111768595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140559350C>T	ENST00000239444.2	+	1	1980	c.1735C>T	c.(1735-1737)Cgg>Tgg	p.R579W	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	579	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			GCTGGTGCCCCGGGCGGCCGA	0.706													C|||	658	0.13139	0.2398	0.1585	5008	,	,		17380	0.0407		0.1103	False		,,,				2504	0.0808				p.R579W		Atlas-SNP	.											PCDHB8,NS,carcinoma,-1,1	PCDHB8	199	1	0			c.C1735T						scavenged	.						7.0	15.0	13.0					5																	140559350		2054	4075	6129	SO:0001583	missense	56128	exon1			GTGCCCCGGGCGG	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.1735C>T	5.37:g.140559350C>T	ENSP00000239444:p.Arg579Trp	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	11	2	0.181818	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	282	0.12912087912087913	112	0.22764227642276422	56	0.15469613259668508	26	0.045454545454545456	88	0.11609498680738786	C	16.86	3.238758	0.58995	.	.	ENSG00000120322	ENST00000239444	T	0.68479	-0.33	4.22	-1.7	0.08159	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.00073	0.0002	M	0.92691	3.335	0.43317	P	0.004662999999999973	P	0.36587	0.559	P	0.47981	0.563	T	0.40213	-0.9575	8	0.87932	D	0	.	4.9982	0.14251	0.2904:0.5137:0.0772:0.1187	.	579	Q9UN66	PCDB8_HUMAN	W	579	ENSP00000239444:R579W	ENSP00000239444:R579W	R	+	1	2	PCDHB8	140539534	0.000000	0.05858	0.989000	0.46669	0.830000	0.47004	-1.199000	0.03032	-0.636000	0.05524	0.298000	0.19748	CGG	.	.	weak		0.706	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
SCN7A	6332	hgsc.bcm.edu	37	2	167301338	167301338	+	Silent	SNP	A	A	G	rs35213258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:167301338A>G	ENST00000409855.1	-	12	1686	c.1560T>C	c.(1558-1560)tgT>tgC	p.C520C		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	520					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)	AGGTCAGAAAACATACGTTTA	0.333													A|||	124	0.0247604	0.0272	0.0173	5008	,	,		17057	0.0		0.0577	False		,,,				2504	0.0184				p.C520C		Atlas-SNP	.											.	SCN7A	410	.	0			c.T1560C						PASS	.	A		113,3533		2,109,1712	49.0	48.0	48.0		1560	-2.8	0.1	2	dbSNP_126	48	285,7873		8,269,3802	no	coding-synonymous	SCN7A	NM_002976.3		10,378,5514	GG,GA,AA		3.4935,3.0993,3.3717		520/1683	167301338	398,11406	1823	4079	5902	SO:0001819	synonymous_variant	6332	exon12			CAGAAAACATACG	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.1560T>C	2.37:g.167301338A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	145	59	0.406897	NM_002976		Silent	SNP	ENST00000409855.1	37	CCDS46442.1																																																																																			A|0.967;G|0.033	0.033	strong		0.333	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
OPRL1	4987	hgsc.bcm.edu	37	20	62729272	62729272	+	Silent	SNP	G	G	A	rs61742883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62729272G>A	ENST00000349451.3	+	5	763	c.351G>A	c.(349-351)ccG>ccA	p.P117P	OPRL1_ENST00000355631.4_Silent_p.P117P|OPRL1_ENST00000336866.2_Silent_p.P117P	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	117					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavior (GO:0007610)|opioid receptor signaling pathway (GO:0038003)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|nociceptin receptor activity (GO:0001626)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					GCTTCTGGCCGTTTGGGAATG	0.542													G|||	95	0.0189696	0.062	0.0159	5008	,	,		21303	0.0		0.002	False		,,,				2504	0.0				p.P117P		Atlas-SNP	.											.	OPRL1	47	.	0			c.G351A						PASS	.	G	,,	215,4191	129.8+/-166.5	5,205,1993	173.0	152.0	159.0		351,351,351	-9.5	0.8	20	dbSNP_129	159	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	OPRL1	NM_000913.4,NM_001200019.1,NM_182647.2	,,	5,212,6286	AA,AG,GG		0.0814,4.8797,1.7069	,,	117/371,117/371,117/371	62729272	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	4987	exon3			CTGGCCGTTTGGG		CCDS13556.1	20q13.33	2012-08-08			ENSG00000125510	ENSG00000125510		"""GPCR / Class A : Opioid receptors"""	8155	protein-coding gene	gene with protein product	"""LC132 receptor-like"", ""orphanin FQ receptor"", ""kappa3-related opioid receptor"""	602548				8137918	Standard	NM_000913		Approved	NOCIR, ORL1, OOR, KOR-3	uc021wgs.1	P41146	OTTHUMG00000033027	ENST00000349451.3:c.351G>A	20.37:g.62729272G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	192	94	0.489583	NM_000913	Q8TD34|Q8WYH9|Q9H4K4	Silent	SNP	ENST00000349451.3	37	CCDS13556.1																																																																																			G|0.982;A|0.018	0.018	strong		0.542	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647	
NOS2	4843	hgsc.bcm.edu	37	17	26085931	26085931	+	Silent	SNP	G	G	A	rs3729662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26085931G>A	ENST00000313735.6	-	26	3563	c.3330C>T	c.(3328-3330)gtC>gtT	p.V1110V		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	1110					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	AATAGTCCTCGACCTGCTCCT	0.607													.|||	73	0.0145767	0.0537	0.0029	5008	,	,		20547	0.0		0.0	False		,,,				2504	0.0				p.V1110V		Atlas-SNP	.											.	NOS2	113	.	0			c.C3330T						PASS	.	G		158,4248	102.5+/-141.1	1,156,2046	30.0	28.0	29.0		3330	-9.7	0.2	17	dbSNP_107	29	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	NOS2	NM_000625.4		1,157,6341	AA,AG,GG		0.0116,3.586,1.2233		1110/1154	26085931	159,12839	2203	4296	6499	SO:0001819	synonymous_variant	4843	exon26			GTCCTCGACCTGC	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.3330C>T	17.37:g.26085931G>A		Somatic	422	0	0		WXS	Illumina HiSeq	Phase_I	451	212	0.470067	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																			.	.	weak		0.607	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
INPP5J	27124	hgsc.bcm.edu	37	22	31529463	31529463	+	Silent	SNP	C	C	A	rs35342535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31529463C>A	ENST00000331075.5	+	11	2452	c.2403C>A	c.(2401-2403)acC>acA	p.T801T	INPP5J_ENST00000404390.3_Silent_p.T433T|INPP5J_ENST00000404453.1_Silent_p.T166T|INPP5J_ENST00000405300.1_Silent_p.T434T|INPP5J_ENST00000401755.1_Silent_p.T166T|INPP5J_ENST00000402238.1_Intron|INPP5J_ENST00000412277.2_Silent_p.T734T|INPP5J_ENST00000400294.2_Silent_p.T434T	NM_001284285.1	NP_001271214.1	Q15735	PI5PA_HUMAN	inositol polyphosphate-5-phosphatase J	801	Required for ruffle localization. {ECO:0000250}.				inositol phosphate metabolic process (GO:0043647)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						ATGGGAATACCTACCAGGTAC	0.537													C|||	1301	0.259784	0.1906	0.281	5008	,	,		19967	0.0208		0.3877	False		,,,				2504	0.453				p.T433T		Atlas-SNP	.											.	INPP5J	94	.	0			c.C1299A						PASS	.	C		834,3112		86,662,1225	97.0	95.0	95.0		1299	2.3	1.0	22	dbSNP_126	95	3215,5099		632,1951,1574	no	coding-synonymous	INPP5J	NM_001002837.1		718,2613,2799	AA,AC,CC		38.6697,21.1353,33.0261		433/639	31529463	4049,8211	1973	4157	6130	SO:0001819	synonymous_variant	27124	exon11			GAATACCTACCAG	U45975	CCDS46687.1, CCDS63453.1, CCDS63454.1, CCDS63455.1, CCDS74847.1	22q12.2	2008-09-09	2008-09-09	2008-09-09	ENSG00000185133	ENSG00000185133			8956	protein-coding gene	gene with protein product		606481	"""phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A"""	PIB5PA		10591208	Standard	NM_001284287		Approved	INPP5	uc003aju.4	Q15735	OTTHUMG00000151206	ENST00000331075.5:c.2403C>A	22.37:g.31529463C>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_001002837	B3KS54|Q32M61|Q6ZTH6|Q8N902|Q9UDT9	Silent	SNP	ENST00000331075.5	37																																																																																				C|0.726;A|0.274	0.274	strong		0.537	INPP5J-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000321784.1	NM_001002837	
ARHGEF4	50649	hgsc.bcm.edu	37	2	131803624	131803624	+	Silent	SNP	C	C	T	rs114004756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131803624C>T	ENST00000326016.5	+	14	2454	c.1935C>T	c.(1933-1935)ccC>ccT	p.P645P	ARHGEF4_ENST00000409303.1_Silent_p.P585P|ARHGEF4_ENST00000428230.2_Silent_p.P147P|ARHGEF4_ENST00000392953.3_3'UTR|ARHGEF4_ENST00000525839.1_3'UTR|ARHGEF4_ENST00000355771.3_Silent_p.P574P	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	645					apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		TTGGCCGGCCCTGCTACCTGA	0.677													C|||	20	0.00399361	0.0151	0.0	5008	,	,		16752	0.0		0.0	False		,,,				2504	0.0				p.P645P		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.C1935T						PASS	.	C	,	66,4340	61.1+/-98.1	3,60,2140	61.0	72.0	68.0		1935,	-1.7	1.0	2	dbSNP_132	68	0,8600		0,0,4300	no	coding-synonymous,utr-3	ARHGEF4	NM_015320.2,NM_032995.1	,	3,60,6440	TT,TC,CC		0.0,1.498,0.5075	,	645/691,	131803624	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	50649	exon14			CCGGCCCTGCTAC	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1935C>T	2.37:g.131803624C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	180	73	0.405556	NM_015320	Q9HDC6|Q9UPP0	Silent	SNP	ENST00000326016.5	37	CCDS2165.1																																																																																			C|0.996;T|0.004	0.004	strong		0.677	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4		
PNKD	25953	hgsc.bcm.edu	37	2	219205471	219205471	+	Silent	SNP	G	G	A	rs34014804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219205471G>A	ENST00000273077.4	+	5	537	c.486G>A	c.(484-486)ggG>ggA	p.G162G	PNKD_ENST00000258362.3_Silent_p.G138G|AC021016.8_ENST00000411433.1_RNA|PNKD_ENST00000436005.2_Silent_p.G102G	NM_015488.4	NP_056303.3	Q8N490	PNKD_HUMAN	paroxysmal nonkinesigenic dyskinesia	162					glutathione biosynthetic process (GO:0006750)|neuromuscular process controlling posture (GO:0050884)|regulation of dopamine metabolic process (GO:0042053)|regulation of synaptic transmission, dopaminergic (GO:0032225)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10		Renal(207;0.0474)		Epithelial(149;7.33e-07)|all cancers(144;0.000133)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AAAAGGAAGGGGTCACCTTGG	0.602													G|||	257	0.0513179	0.0968	0.0591	5008	,	,		18777	0.005		0.0606	False		,,,				2504	0.0225				p.G162G		Atlas-SNP	.											.	PNKD	58	.	0			c.G486A						PASS	.	G	,	433,3973	209.5+/-230.2	20,393,1790	129.0	114.0	119.0		486,414	-10.2	0.0	2	dbSNP_126	119	423,8177	132.5+/-190.1	9,405,3886	no	coding-synonymous,coding-synonymous	PNKD	NM_015488.4,NM_022572.4	,	29,798,5676	AA,AG,GG		4.9186,9.8275,6.5816	,	162/386,138/362	219205471	856,12150	2203	4300	6503	SO:0001819	synonymous_variant	25953	exon5			GGAAGGGGTCACC		CCDS2411.1, CCDS2413.1, CCDS42816.1	2q35	2011-01-21	2007-07-12		ENSG00000127838	ENSG00000127838			9153	protein-coding gene	gene with protein product	"""myofibrillogenesis regulator 1"""	609023	"""paroxysmal nonkinesiogenic dyskinesia"""			8659518	Standard	NM_015488		Approved	DYT8, PDC, DKFZp564N1362, FPD1, MR-1, BRP17, FKSG19, TAHCCP2, KIAA1184, KIPP1184, MGC31943, PKND1	uc002vhn.3	Q8N490	OTTHUMG00000133110	ENST00000273077.4:c.486G>A	2.37:g.219205471G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_015488	A8K1F2|Q96A48|Q9BU26|Q9NSX4|Q9ULN6|Q9Y4T1	Silent	SNP	ENST00000273077.4	37	CCDS2411.1																																																																																			G|0.939;A|0.061	0.061	strong		0.602	PNKD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256775.2		
CHRNA4	1137	hgsc.bcm.edu	37	20	61990939	61990939	+	Silent	SNP	G	G	A	rs2273506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61990939G>A	ENST00000370263.4	-	2	410	c.189C>T	c.(187-189)ctC>ctT	p.L63L	RP11-261N11.8_ENST00000370257.1_RNA|CHRNA4_ENST00000463705.1_Intron	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	63					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	CGAAGCGGACGAGGACCACGT	0.637													G|||	571	0.114018	0.1354	0.0634	5008	,	,		16883	0.0992		0.0646	False		,,,				2504	0.1871				p.L63L		Atlas-SNP	.											.	CHRNA4	98	.	0			c.C189T						PASS	.	G		600,3794	258.6+/-262.5	43,514,1640	124.0	101.0	109.0		189	-8.5	0.5	20	dbSNP_100	109	602,7982	158.3+/-211.8	24,554,3714	yes	coding-synonymous	CHRNA4	NM_000744.5		67,1068,5354	AA,AG,GG		7.013,13.655,9.2618		63/628	61990939	1202,11776	2197	4292	6489	SO:0001819	synonymous_variant	1137	exon2			GCGGACGAGGACC		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1958	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 4 (neuronal)"""	118504	"""cholinergic receptor, nicotinic, alpha polypeptide 4"""	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.189C>T	20.37:g.61990939G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Silent	SNP	ENST00000370263.4	37	CCDS13517.1																																																																																			G|0.910;A|0.090	0.090	strong		0.637	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3		
HIST1H2BD	3017	hgsc.bcm.edu	37	6	26158456	26158456	+	Missense_Mutation	SNP	C	C	T	rs62623440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26158456C>T	ENST00000289316.2	+	1	83	c.59C>T	c.(58-60)aCt>aTt	p.T20I	HIST1H2BD_ENST00000377777.4_Missense_Mutation_p.T20I	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	20					chromatin organization (GO:0006325)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	24						AAGGCGGTGACTAAGGCTCAG	0.527													C|||	47	0.00938498	0.0348	0.0014	5008	,	,		19251	0.0		0.0	False		,,,				2504	0.0				p.T20I		Atlas-SNP	.											.	HIST1H2BD	45	.	0			c.C59T						PASS	.	C	ILE/THR,ILE/THR	128,4278		1,126,2076	126.0	124.0	124.0		59,59	4.1	1.0	6	dbSNP_129	124	1,8599		0,1,4299	yes	missense,missense	HIST1H2BD	NM_021063.3,NM_138720.2	89,89	1,127,6375	TT,TC,CC		0.0116,2.9051,0.9918	probably-damaging,probably-damaging	20/127,20/127	26158456	129,12877	2203	4300	6503	SO:0001583	missense	3017	exon1			CGGTGACTAAGGC	M60751	CCDS4587.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158373	ENSG00000158373		"""Histones / Replication-dependent"""	4747	protein-coding gene	gene with protein product		602799	"""H2B histone family, member B"", ""histone 1, H2bd"""	H2BFB		1916825, 12408966	Standard	NM_021063		Approved	H2B/b	uc003ngr.3	P58876	OTTHUMG00000014426	ENST00000289316.2:c.59C>T	6.37:g.26158456C>T	ENSP00000289316:p.Thr20Ile	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	145	61	0.42069	NM_021063		Missense_Mutation	SNP	ENST00000289316.2	37	CCDS4587.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	.	15.37	2.814326	0.50527	0.029051	1.16E-4	ENSG00000158373	ENST00000377777;ENST00000289316	T;T	0.23754	1.89;1.89	4.95	4.07	0.47477	Histone-fold (2);	0.000000	0.42821	D	0.000655	T	0.19604	0.0471	M	0.79805	2.47	0.36491	D	0.868429	P	0.39216	0.664	B	0.39935	0.314	T	0.08554	-1.0716	10	0.72032	D	0.01	.	9.0973	0.36647	0.0:0.7713:0.147:0.0817	rs62623440	20	P58876	H2B1D_HUMAN	I	20	ENSP00000367008:T20I;ENSP00000289316:T20I	ENSP00000289316:T20I	T	+	2	0	HIST1H2BD	26266435	1.000000	0.71417	1.000000	0.80357	0.480000	0.33159	3.805000	0.55575	1.392000	0.46585	0.644000	0.83932	ACT	C|0.990;T|0.010	0.010	strong		0.527	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063	
COL11A2	1302	hgsc.bcm.edu	37	6	33153528	33153528	+	Missense_Mutation	SNP	C	C	T	rs9277934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33153528C>T	ENST00000341947.2	-	6	1053	c.826G>A	c.(826-828)Gag>Aag	p.E276K	COL11A2_ENST00000361917.1_Intron|COL11A2_ENST00000374713.1_Intron|COL11A2_ENST00000395197.1_Missense_Mutation_p.E276K|COL11A2_ENST00000357486.1_Missense_Mutation_p.E276K|COL11A2_ENST00000374714.1_Intron|COL11A2_ENST00000374708.4_Intron|COL11A2_ENST00000374712.1_Missense_Mutation_p.E276K	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	88	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	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			
PSG3	5671	hgsc.bcm.edu	37	19	43237080	43237080	+	Missense_Mutation	SNP	T	T	C	rs76931703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43237080T>C	ENST00000327495.5	-	3	749	c.565A>G	c.(565-567)Atg>Gtg	p.M189V	PSG3_ENST00000595140.1_Missense_Mutation_p.M189V|PSG3_ENST00000490592.1_5'Flank	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	189	Ig-like C2-type 1.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				CTGTGAGTCATAGGGAGGCTC	0.498													.|||	53	0.0105831	0.0378	0.0043	5008	,	,		20000	0.0		0.0	False		,,,				2504	0.0				p.M189V		Atlas-SNP	.											.	PSG3	82	.	0			c.A565G						PASS	.	T	VAL/MET	167,4239		4,159,2040	240.0	239.0	239.0		565	-1.4	0.0	19	dbSNP_131	239	1,8599		0,1,4299	yes	missense	PSG3	NM_021016.3	21	4,160,6339	CC,CT,TT		0.0116,3.7903,1.2917	benign	189/429	43237080	168,12838	2203	4300	6503	SO:0001583	missense	5671	exon3			GAGTCATAGGGAG		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.565A>G	19.37:g.43237080T>C	ENSP00000332215:p.Met189Val	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	235	116	0.493617	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	37	CCDS12611.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	-	0.003	-2.475018	0.00167	0.037903	1.16E-4	ENSG00000221826	ENST00000327495	T	0.08458	3.09	1.59	-1.36	0.09085	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00524	0.0017	N	0.02275	-0.615	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.41752	-0.9491	9	0.02654	T	1	.	4.1694	0.10322	0.0:0.5437:0.0:0.4563	.	167;189	Q08266;Q16557	.;PSG3_HUMAN	V	189	ENSP00000332215:M189V	ENSP00000332215:M189V	M	-	1	0	PSG3	47928920	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.084000	0.03393	-0.464000	0.06963	-0.562000	0.04174	ATG	T|0.988;C|0.012	0.012	strong		0.498	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016	
MAP10	54627	hgsc.bcm.edu	37	1	232941677	232941677	+	Missense_Mutation	SNP	G	G	T	rs3766497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232941677G>T	ENST00000418460.1	+	1	1035	c.908G>T	c.(907-909)cGt>cTt	p.R303L		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	161					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										CACCGGGGACGTTTCCCCCTG	0.687													G|||	673	0.134385	0.2504	0.085	5008	,	,		14586	0.1369		0.0517	False		,,,				2504	0.0951				p.R303L		Atlas-SNP	.											.	.	.	.	0			c.G908T						PASS	.	G	LEU/ARG	828,3246		78,672,1287	12.0	15.0	14.0		908	0.4	0.0	1	dbSNP_107	14	365,7975		12,341,3817	yes	missense	KIAA1383	NM_019090.2	102	90,1013,5104	TT,TG,GG		4.3765,20.324,9.6101	benign	303/1048	232941677	1193,11221	2037	4170	6207	SO:0001583	missense	54627	exon1			GGGGACGTTTCCC	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.908G>T	1.37:g.232941677G>T	ENSP00000403208:p.Arg303Leu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	143	140	0.979021	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	238	0.10897435897435898	101	0.20528455284552846	30	0.08287292817679558	69	0.12062937062937062	38	0.05013192612137203	G	12.69	2.012307	0.35511	0.20324	0.043765	ENSG00000212916	ENST00000418460	.	.	.	4.94	0.452	0.16634	.	1.175810	0.06895	U	0.804872	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.14805	0.011	B	0.11329	0.006	T	0.26883	-1.0090	8	0.27082	T	0.32	-0.0895	4.2395	0.10642	0.0776:0.1603:0.5018:0.2602	rs3766497;rs3766497	161	Q9P2G4	K1383_HUMAN	L	303	.	ENSP00000403208:R303L	R	+	2	0	KIAA1383	231008300	0.000000	0.05858	0.000000	0.03702	0.185000	0.23345	-0.256000	0.08757	0.288000	0.22398	-0.263000	0.10527	CGT	G|0.897;T|0.103	0.103	strong		0.687	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
MYH8	4626	hgsc.bcm.edu	37	17	10297658	10297658	+	Missense_Mutation	SNP	A	A	G	rs8069834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10297658A>G	ENST00000403437.2	-	35	5168	c.5074T>C	c.(5074-5076)Tgg>Cgg	p.W1692R	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1692			W -> R (in dbSNP:rs8069834).		ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						AGAGTGGCCCACAGCTCCTCG	0.607									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				G|||	2431	0.485423	0.7595	0.4856	5008	,	,		16128	0.124		0.6322	False		,,,				2504	0.3364				p.W1692R		Atlas-SNP	.											.	MYH8	346	.	0			c.T5074C						PASS	.	G	ARG/TRP	3176,1230	425.7+/-340.9	1139,898,166	108.0	99.0	102.0		5074	1.8	1.0	17	dbSNP_116	102	5013,3585	519.7+/-379.5	1473,2067,759	no	missense	MYH8	NM_002472.2	101	2612,2965,925	GG,GA,AA		41.6957,27.9165,37.0271	benign	1692/1938	10297658	8189,4815	2203	4299	6502	SO:0001583	missense	4626	exon35	Familial Cancer Database	Carney Complex Variant	TGGCCCACAGCTC		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.5074T>C	17.37:g.10297658A>G	ENSP00000384330:p.Trp1692Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	129	60	0.465116	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	1082	0.49542124542124544	369	0.75	176	0.4861878453038674	66	0.11538461538461539	471	0.6213720316622692	G	1.894	-0.454810	0.04540	0.720835	0.583043	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.74209	-0.82	5.06	1.84	0.25277	Myosin tail (1);	0.000000	0.37623	N	0.002002	T	0.00012	0.0000	N	0.00001	-3.88	0.51767	P	6.499999999998174E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.49597	-0.8923	9	0.02654	T	1	.	8.832	0.35089	0.068:0.0:0.4266:0.5054	rs8069834;rs8069834	1692	P13535	MYH8_HUMAN	R	1692	ENSP00000384330:W1692R	ENSP00000252173:W1692R	W	-	1	0	MYH8	10238383	0.997000	0.39634	0.998000	0.56505	0.990000	0.78478	0.948000	0.29096	0.017000	0.15025	-0.128000	0.14901	TGG	A|0.408;G|0.592	0.592	strong		0.607	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
PI4K2A	55361	hgsc.bcm.edu	37	10	99410790	99410790	+	Silent	SNP	T	T	C	rs7915721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99410790T>C	ENST00000370631.3	+	2	585	c.528T>C	c.(526-528)ccT>ccC	p.P176P	PI4K2A_ENST00000555577.1_Silent_p.P146P|PI4K2A_ENST00000370649.3_Silent_p.P146P	NM_018425.2	NP_060895.1	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	176	PI3K/PI4K.				basophil degranulation (GO:0002561)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endosome (GO:0005768)|exocytic vesicle (GO:0070382)|Golgi apparatus (GO:0005794)|growing cell tip (GO:0035838)|host cell presynaptic membrane (GO:0044231)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|AP-3 adaptor complex binding (GO:0035651)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)	p.P176P(2)|p.P146P(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		TGTGCTGTCCTTGCTGCTTTG	0.517													C|||	1715	0.342452	0.6233	0.2666	5008	,	,		20300	0.3006		0.2028	False		,,,				2504	0.2035				p.P176P		Atlas-SNP	.											PI4K2A_ENST00000555577,NS,carcinoma,0,2	PI4K2A	57	2	3	Substitution - coding silent(3)	prostate(3)	c.T528C						scavenged	.	C		2425,1981	556.8+/-379.6	676,1073,454	92.0	79.0	83.0		528	3.1	1.0	10	dbSNP_116	83	1911,6689	726.6+/-406.6	192,1527,2581	no	coding-synonymous	PI4K2A	NM_018425.2		868,2600,3035	CC,CT,TT		22.2209,44.9614,33.3385		176/480	99410790	4336,8670	2203	4300	6503	SO:0001819	synonymous_variant	55361	exon2			CTGTCCTTGCTGC	AF070611	CCDS7469.1	10q24	2011-02-09			ENSG00000155252	ENSG00000155252			30031	protein-coding gene	gene with protein product		609763				11244087, 11279162	Standard	NM_018425		Approved	PI4KII, DKFZP761G1923, PIK42A	uc001kog.1	Q9BTU6	OTTHUMG00000018863	ENST00000370631.3:c.528T>C	10.37:g.99410790T>C		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	130	65	0.5	NM_018425	D3DR59|Q9NSG8	Silent	SNP	ENST00000370631.3	37	CCDS7469.1																																																																																			T|0.663;C|0.337	0.337	strong		0.517	PI4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049735.1	NM_018425	
ROBO4	54538	hgsc.bcm.edu	37	11	124766128	124766128	+	Silent	SNP	A	A	G	rs4078313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124766128A>G	ENST00000306534.3	-	4	1130	c.645T>C	c.(643-645)caT>caC	p.H215H	ROBO4_ENST00000533054.1_Silent_p.H70H|ROBO4_ENST00000526899.1_5'UTR	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	215	Ig-like C2-type 2.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GGCTCTCCCTATGTCCTGCGC	0.627													G|||	2483	0.495807	0.8162	0.2853	5008	,	,		16460	0.4534		0.334	False		,,,				2504	0.4223				p.H215H		Atlas-SNP	.											.	ROBO4	130	.	0			c.T645C						PASS	.	G		3161,1241	427.4+/-341.5	1151,859,191	85.0	84.0	84.0		645	0.2	0.0	11	dbSNP_108	84	2684,5914	684.3+/-404.0	433,1818,2048	no	coding-synonymous	ROBO4	NM_019055.5		1584,2677,2239	GG,GA,AA		31.2166,28.1917,44.9615		215/1008	124766128	5845,7155	2201	4299	6500	SO:0001819	synonymous_variant	54538	exon4			CTCCCTATGTCCT	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.645T>C	11.37:g.124766128A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	125	45	0.36	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	
TENM2	57451	hgsc.bcm.edu	37	5	167674370	167674370	+	Silent	SNP	C	C	T	rs3733988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:167674370C>T	ENST00000518659.1	+	27	6465	c.6426C>T	c.(6424-6426)atC>atT	p.I2142I	TENM2_ENST00000403607.2_Silent_p.I1966I|TENM2_ENST00000545108.1_Silent_p.I2141I|TENM2_ENST00000519204.1_Silent_p.I2021I|TENM2_ENST00000520394.1_Silent_p.I1903I	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2142					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.I1975I(1)									TCAACCAGATCATCACCACTG	0.502													T|||	2181	0.435503	0.4418	0.4496	5008	,	,		22119	0.1726		0.5408	False		,,,				2504	0.5798				p.I2133I		Atlas-SNP	.											ODZ2,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C6399T						PASS	.	T		1689,2371		343,1003,684	131.0	128.0	129.0		6399	4.7	1.0	5	dbSNP_107	129	4405,3949		1191,2023,963	no	coding-synonymous	ODZ2	NM_001122679.1		1534,3026,1647	TT,TC,CC		47.2708,41.601,49.0897		2133/2766	167674370	6094,6320	2030	4177	6207	SO:0001819	synonymous_variant	57451	exon27			CCAGATCATCACC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.6426C>T	5.37:g.167674370C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				C|0.592;T|0.408	0.408	strong		0.502	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
FCRL6	343413	hgsc.bcm.edu	37	1	159785370	159785370	+	Silent	SNP	T	T	C	rs4301626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159785370T>C	ENST00000368106.3	+	10	1225	c.1224T>C	c.(1222-1224)agT>agC	p.S408S	FCRL6_ENST00000392235.3_Nonstop_Mutation_p.*312R|FCRL6_ENST00000339348.5_Nonstop_Mutation_p.*398R|FCRL6_ENST00000321935.6_Nonstop_Mutation_p.*414R	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	156	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	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	
EMR1	2015	hgsc.bcm.edu	37	19	6903920	6903920	+	Missense_Mutation	SNP	A	A	G	rs443658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6903920A>G	ENST00000312053.4	+	7	798	c.761A>G	c.(760-762)aAt>aGt	p.N254S	EMR1_ENST00000250572.8_Missense_Mutation_p.N254S|EMR1_ENST00000381407.5_Missense_Mutation_p.N113S|EMR1_ENST00000450315.3_Intron|EMR1_ENST00000381404.4_Missense_Mutation_p.N202S	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	254	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		N -> S (in dbSNP:rs443658). {ECO:0000269|PubMed:7601460}.		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)					GCACCAAGCAATGGACAGTTG	0.458													A|||	2167	0.432708	0.6664	0.4193	5008	,	,		23379	0.4554		0.2396	False		,,,				2504	0.3016				p.N254S		Atlas-SNP	.											EMR1,NS,carcinoma,+1,1	EMR1	153	1	0			c.A761G						PASS	.	A	SER/ASN	2594,1812	639.9+/-397.2	780,1034,389	99.0	98.0	98.0		761	-0.2	0.0	19	dbSNP_80	98	2211,6389	375.7+/-337.9	290,1631,2379	yes	missense	EMR1	NM_001974.3	46	1070,2665,2768	GG,GA,AA		25.7093,41.1257,36.9445	benign	254/887	6903920	4805,8201	2203	4300	6503	SO:0001583	missense	2015	exon7			CAAGCAATGGACA	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.761A>G	19.37:g.6903920A>G	ENSP00000311545:p.Asn254Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	918	0.42032967032967034	318	0.6463414634146342	137	0.3784530386740331	283	0.49475524475524474	180	0.23746701846965698	A	1.890	-0.455654	0.04540	0.588743	0.257093	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407	D;D;D;D	0.92647	-3.08;-2.22;-3.08;-2.22	3.35	-0.148	0.13424	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	L	0.28776	0.89	0.54753	P	1.799999999996249E-5	B;D;P;P	0.71674	0.304;0.998;0.555;0.832	B;D;B;P	0.80764	0.068;0.994;0.159;0.519	T	0.48547	-0.9026	8	0.02654	T	1	.	5.7979	0.18397	0.5085:0.0:0.4915:0.0	rs443658;rs2228534;rs52792901;rs59336086;rs443658	113;254;202;254	B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;EMR1_HUMAN	S	254;254;202;254;113	ENSP00000311545:N254S;ENSP00000370811:N202S;ENSP00000250572:N254S;ENSP00000370814:N113S	ENSP00000250572:N254S	N	+	2	0	EMR1	6854920	0.000000	0.05858	0.041000	0.18516	0.229000	0.25112	-0.193000	0.09573	0.024000	0.15214	-0.408000	0.06270	AAT	T|0.001;G|0.397	0.397	strong		0.458	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
CLEC2D	29121	hgsc.bcm.edu	37	12	9833524	9833524	+	Missense_Mutation	SNP	C	C	G	rs3764022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9833524C>G	ENST00000290855.6	+	2	89	c.67C>G	c.(67-69)Ctg>Gtg	p.L23V	CLEC2D_ENST00000545918.1_Intron|CLEC2D_ENST00000261339.6_Intron|CLEC2D_ENST00000543300.1_Missense_Mutation_p.L23V|CLEC2D_ENST00000487752.1_3'UTR|CLEC2D_ENST00000261340.7_Missense_Mutation_p.L23V	NM_013269.5	NP_037401.1	Q9UHP7	CLC2D_HUMAN	C-type lectin domain family 2, member D	23			L -> V (in dbSNP:rs3764022). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20843815}.		cell surface receptor signaling pathway (GO:0007166)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|stomach(1)	9						TCCAGGTTGTCTGCATTCAAA	0.289													C|||	1464	0.292332	0.1006	0.281	5008	,	,		-128	0.3641		0.338	False		,,,				2504	0.4387				p.L23V		Atlas-SNP	.											.	CLEC2D	54	.	0			c.C67G						PASS	.	C	VAL/LEU,,VAL/LEU,,VAL/LEU	652,3752	279.3+/-274.7	45,562,1595	109.0	105.0	106.0		67,,67,,67	0.4	0.0	12	dbSNP_107	106	2788,5810	440.8+/-359.6	436,1916,1947	yes	missense,intron,missense,intron,missense	CLEC2D	NM_001004419.3,NM_001197317.1,NM_001197318.1,NM_001197319.1,NM_013269.4	32,,32,,32	481,2478,3542	GG,GC,CC		32.4261,14.8047,26.4575	probably-damaging,,probably-damaging,,probably-damaging	23/195,,23/133,,23/192	9833524	3440,9562	2202	4299	6501	SO:0001583	missense	29121	exon2			GGTTGTCTGCATT	AF133299	CCDS8602.1, CCDS31741.1, CCDS55800.1, CCDS55801.1, CCDS55802.1	12p13.31	2011-05-24	2005-09-29		ENSG00000069493	ENSG00000069493		"""C-type lectin domain containing"""	14351	protein-coding gene	gene with protein product	"""C-type lectin related f"", ""lectin-like transcript 1"""	605659	"""C-type lectin superfamily 2, member D"""				Standard	NM_013269		Approved	LLT1, CLAX, OCIL	uc001qwf.3	Q9UHP7	OTTHUMG00000168369	ENST00000290855.6:c.67C>G	12.37:g.9833524C>G	ENSP00000290855:p.Leu23Val	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_001004419	D6CI39|D6CI40|D6CI41|Q6YID5|Q8WUP7|Q9HD37|Q9HD38	Missense_Mutation	SNP	ENST00000290855.6	37	CCDS8602.1	626	0.2866300366300366	50	0.1016260162601626	120	0.3314917127071823	196	0.34265734265734266	260	0.34300791556728233	C	3.592	-0.083370	0.07141	0.148047	0.324261	ENSG00000069493	ENST00000261340;ENST00000290855;ENST00000543300;ENST00000430909	T;T;T;T	0.11930	4.42;4.58;2.73;4.21	1.31	0.395	0.16304	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.24092	0.017;0.097	B;B	0.13407	0.004;0.009	T	0.49263	-0.8958	7	.	.	.	-0.0039	3.5716	0.07920	0.0:0.7377:0.0:0.2623	rs3764022;rs17806644;rs17858519;rs52825100;rs58083171;rs3764022	23;23	Q9UHP7;Q9UHP7-3	CLC2D_HUMAN;.	V	23;23;23;2	ENSP00000261340:L23V;ENSP00000290855:L23V;ENSP00000443065:L23V;ENSP00000413045:L2V	.	L	+	1	2	CLEC2D	9724791	0.000000	0.05858	0.004000	0.12327	0.078000	0.17371	-0.327000	0.07955	0.141000	0.18875	0.436000	0.28706	CTG	C|0.732;G|0.268	0.268	strong		0.289	CLEC2D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000335424.2	NM_013269	
RAB40AL	282808	hgsc.bcm.edu	37	X	102192328	102192328	+	Missense_Mutation	SNP	A	A	G	rs386826706|rs61745026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192328A>G	ENST00000218249.5	+	1	129	c.82A>G	c.(82-84)Agt>Ggt	p.S28G	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	28					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						CGTAGGCAAGAGTGAGATCCT	0.672													.|||	989	0.261987	0.4085	0.0677	3775	,	,		9977	0.1171		0.005	False		,,,				2504	0.2853				p.S28G		Atlas-SNP	.											.	RAB40AL	33	.	0			c.A82G						PASS	.	G	GLY/SER	1332,2501		326,411,269,895,300	55.0	74.0	67.0		82	1.0	0.3	X	dbSNP_129	67	24,6704		0,17,7,2411,1865	no	missense	RAB40AL	NM_001031834.1	56	326,428,276,3306,2165	GG,GA,G,AA,A		0.3567,34.7508,12.8397	benign	28/279	102192328	1356,9205	2201	4300	6501	SO:0001583	missense	282808	exon1			GGCAAGAGTGAGA	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"""Ras like GTPase"""	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.82A>G	X.37:g.102192328A>G	ENSP00000218249:p.Ser28Gly	Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	280	279	0.996429	NM_001031834	Q495H3	Missense_Mutation	SNP	ENST00000218249.5	37	CCDS35353.1	264	0.15913200723327306	133	0.35561497326203206	11	0.03089887640449438	40	0.0749063670411985	3	0.00395778364116095	.	0.956	-0.704854	0.03255	0.347508	0.003567	ENSG00000102128	ENST00000218249	D	0.86497	-2.13	0.99	0.99	0.19807	Small GTP-binding protein domain (1);	0.000000	0.47852	N	0.000202	T	0.00012	0.0000	M	0.85542	2.76	0.51482	P	7.299999999998974E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.21827	-1.0234	9	0.16896	T	0.51	.	5.2814	0.15678	0.2323:0.0:0.7677:0.0	rs61745026	28	P0C0E4	RB40L_HUMAN	G	28	ENSP00000218249:S28G	ENSP00000218249:S28G	S	+	1	0	RAB40AL	102078984	1.000000	0.71417	0.324000	0.25361	0.013000	0.08279	3.381000	0.52455	-0.028000	0.13850	-0.354000	0.07668	AGT	A|0.823;G|0.177	0.177	strong		0.672	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834	
CXCR6	10663	hgsc.bcm.edu	37	3	45987980	45987980	+	Missense_Mutation	SNP	G	G	A	rs2234355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:45987980G>A	ENST00000458629.1	+	1	1470	c.7G>A	c.(7-9)Gag>Aag	p.E3K	CXCR6_ENST00000304552.4_Missense_Mutation_p.E3K|CXCR6_ENST00000438735.1_Missense_Mutation_p.E3K|FYCO1_ENST00000438446.1_Intron|FYCO1_ENST00000296137.2_Intron|CXCR6_ENST00000457814.1_Missense_Mutation_p.E3K|FYCO1_ENST00000535325.1_Intron			O00574	CXCR6_HUMAN	chemokine (C-X-C motif) receptor 6	3			E -> K (in dbSNP:rs2234355). {ECO:0000269|Ref.4}.		chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|viral genome replication (GO:0019079)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(3)|lung(1)|prostate(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CACCATGGCAGAGCATGATTA	0.483													G|||	702	0.140176	0.4909	0.0677	5008	,	,		22359	0.0		0.005	False		,,,				2504	0.001				p.E3K	Esophageal Squamous(63;1005 1117 15521 45762 47089)	Atlas-SNP	.											.	CXCR6	17	.	0			c.G7A						PASS	.	G	LYS/GLU,	1842,2564	534.4+/-373.9	402,1038,763	139.0	141.0	140.0		7,	3.8	0.2	3	dbSNP_98	140	23,8577	16.0+/-53.3	0,23,4277	yes	missense,intron	CXCR6,FYCO1	NM_006564.1,NM_024513.2	56,	402,1061,5040	AA,AG,GG		0.2674,41.8066,14.3395	benign,	3/343,	45987980	1865,11141	2203	4300	6503	SO:0001583	missense	10663	exon2			ATGGCAGAGCATG	AF007545	CCDS2735.1	3p21	2012-08-08			ENSG00000172215	ENSG00000172215		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	16647	protein-coding gene	gene with protein product		605163				9166430, 9230441	Standard	XM_005264809		Approved	TYMSTR, STRL33, BONZO, CD186	uc003cpc.1	O00574	OTTHUMG00000133448	ENST00000458629.1:c.7G>A	3.37:g.45987980G>A	ENSP00000395704:p.Glu3Lys	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_006564	O00575|Q9HCA5	Missense_Mutation	SNP	ENST00000458629.1	37	CCDS2735.1	255	0.11675824175824176	230	0.46747967479674796	24	0.06629834254143646	0	0.0	1	0.0013192612137203166	G	17.55	3.418151	0.62622	0.418066	0.002674	ENSG00000172215	ENST00000438735;ENST00000304552;ENST00000458629;ENST00000457814	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.57	3.8	0.43715	.	3.673050	0.00622	N	0.000453	T	0.00012	0.0000	N	0.19112	0.55	0.35184	P	0.227213	P	0.39665	0.682	B	0.30401	0.115	T	0.29882	-0.9997	9	0.46703	T	0.11	.	9.5395	0.39242	0.1649:0.0:0.8351:0.0	rs2234355;rs52808267;rs56447809;rs2234355	3	O00574	CXCR6_HUMAN	K	3	ENSP00000396218:E3K;ENSP00000304414:E3K;ENSP00000395704:E3K;ENSP00000396886:E3K	ENSP00000304414:E3K	E	+	1	0	CXCR6	45962984	0.000000	0.05858	0.206000	0.23566	0.198000	0.23893	0.391000	0.20784	0.729000	0.32403	0.655000	0.94253	GAG	G|0.857;A|0.143	0.143	strong		0.483	CXCR6-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344395.1		
OR4E2	26686	hgsc.bcm.edu	37	14	22134018	22134018	+	Missense_Mutation	SNP	C	C	T	rs61732411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:22134018C>T	ENST00000408935.1	+	1	722	c.722C>T	c.(721-723)tCg>tTg	p.S241L		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		TCTACCTGCTCGGCCCACTTC	0.527													C|||	699	0.139577	0.2526	0.1628	5008	,	,		21318	0.005		0.2038	False		,,,				2504	0.0429				p.S241L		Atlas-SNP	.											OR4E2,NS,carcinoma,-1,1	OR4E2	44	1	0			c.C722T						scavenged	.	C	LEU/SER	921,2999		109,703,1148	96.0	93.0	94.0		722	4.8	1.0	14	dbSNP_129	94	1719,6581		190,1339,2621	yes	missense	OR4E2	NM_001001912.1	145	299,2042,3769	TT,TC,CC		20.7108,23.4949,21.6039	benign	241/314	22134018	2640,9580	1960	4150	6110	SO:0001583	missense	26686	exon1			CCTGCTCGGCCCA		CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"""GPCR / Class A : Olfactory receptors"""	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.722C>T	14.37:g.22134018C>T	ENSP00000386195:p.Ser241Leu	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	232	109	0.469828	NM_001001912	Q6IET6|Q96R62	Missense_Mutation	SNP	ENST00000408935.1	37	CCDS41916.1	311	0.1423992673992674	106	0.21544715447154472	59	0.16298342541436464	2	0.0034965034965034965	144	0.18997361477572558	C	12.41	1.928415	0.34002	0.234949	0.207108	ENSG00000221977	ENST00000408935	T	0.35789	1.29	5.68	4.79	0.61399	GPCR, rhodopsin-like superfamily (1);	0.255127	0.19259	U	0.118721	T	0.00012	0.0000	L	0.59967	1.855	0.39721	P	0.02852600000000005	P	0.35363	0.497	B	0.33254	0.16	T	0.10474	-1.0628	9	0.54805	T	0.06	.	13.0304	0.58839	0.0:0.9212:0.0:0.0788	rs61732411	241	Q8NGC2	OR4E2_HUMAN	L	241	ENSP00000386195:S241L	ENSP00000386195:S241L	S	+	2	0	OR4E2	21203858	0.000000	0.05858	0.997000	0.53966	0.487000	0.33371	0.099000	0.15210	1.534000	0.49203	0.655000	0.94253	TCG	C|0.830;T|0.170	0.170	strong		0.527	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1		
GNA12	2768	hgsc.bcm.edu	37	7	2834754	2834754	+	Silent	SNP	T	T	C	rs2230877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2834754T>C	ENST00000275364.3	-	2	495	c.333A>G	c.(331-333)gcA>gcG	p.A111A	GNA12_ENST00000544127.1_Silent_p.A35A|GNA12_ENST00000407904.3_Silent_p.A52A	NM_007353.2	NP_031379.2	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein) alpha 12	111					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic digit morphogenesis (GO:0042733)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|platelet activation (GO:0030168)|regulation of cell shape (GO:0008360)|regulation of fibroblast migration (GO:0010762)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)|response to drug (GO:0042493)|Rho protein signal transduction (GO:0007266)	brush border membrane (GO:0031526)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		GCTTATCTCGTGCATCAACAA	0.468													T|||	99	0.0197684	0.0514	0.0101	5008	,	,		21010	0.0		0.0159	False		,,,				2504	0.0082				p.A111A		Atlas-SNP	.											.	GNA12	35	.	0			c.A333G						PASS	.	T		207,4199	127.8+/-164.7	6,195,2002	131.0	128.0	129.0		333	-11.2	0.5	7	dbSNP_123	129	77,8523	45.8+/-104.6	1,75,4224	no	coding-synonymous	GNA12	NM_007353.2		7,270,6226	CC,CT,TT		0.8953,4.6981,2.1836		111/382	2834754	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	2768	exon2			ATCTCGTGCATCA	L01694	CCDS5335.1, CCDS64584.1, CCDS64583.1	7p22.3	2006-07-08			ENSG00000146535	ENSG00000146535			4380	protein-coding gene	gene with protein product		604394				8423800, 16247467	Standard	NM_007353		Approved	gep	uc003smu.3	Q03113	OTTHUMG00000023064	ENST00000275364.3:c.333A>G	7.37:g.2834754T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_007353	A4D204|B3KXS2|B7Z3F7|Q2T9L1|Q5PPR5|Q86UM8|Q8TD71|Q9UDU9	Silent	SNP	ENST00000275364.3	37	CCDS5335.1																																																																																			T|0.980;C|0.020	0.020	strong		0.468	GNA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241608.1	NM_007353	
DMGDH	29958	hgsc.bcm.edu	37	5	78326750	78326750	+	Missense_Mutation	SNP	G	G	C	rs1805073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:78326750G>C	ENST00000255189.3	-	10	1617	c.1589C>G	c.(1588-1590)gCg>gGg	p.A530G	DMGDH_ENST00000380311.4_Missense_Mutation_p.A329G|DMGDH_ENST00000540686.1_Missense_Mutation_p.A150G	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	530			A -> G (in dbSNP:rs1805073). {ECO:0000269|PubMed:11231903}.		amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		GTCAGTTACCGCTACTCTTTG	0.418													C|||	1532	0.305911	0.4985	0.1974	5008	,	,		16959	0.1399		0.2962	False		,,,				2504	0.3037				p.A530G		Atlas-SNP	.											DMGDH,colon,adenoma,+1,1	DMGDH	88	1	0			c.C1589G						PASS	.	C	GLY/ALA	2049,2357	608.8+/-391.2	469,1111,623	132.0	123.0	126.0		1589	5.9	1.0	5	dbSNP_89	126	2467,6133	696.2+/-404.9	378,1711,2211	yes	missense	DMGDH	NM_013391.2	60	847,2822,2834	CC,CG,GG		28.686,46.5048,34.7224	benign	530/867	78326750	4516,8490	2203	4300	6503	SO:0001583	missense	29958	exon10			GTTACCGCTACTC	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.1589C>G	5.37:g.78326750G>C	ENSP00000255189:p.Ala530Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_013391	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	651	0.2980769230769231	266	0.540650406504065	72	0.19889502762430938	90	0.15734265734265734	223	0.2941952506596306	C	8.492	0.862213	0.17178	0.465048	0.28686	ENSG00000132837	ENST00000255189;ENST00000523732;ENST00000380311;ENST00000540686;ENST00000539598	T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34	5.86	5.86	0.93980	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00808	-1.17	0.39246	P	0.03604700000000005	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.35649	-0.9780	9	0.02654	T	1	.	17.248	0.87033	0.0:0.8743:0.1257:0.0	rs1805073;rs52829837;rs59861506;rs1805073	150;329;380;530	B4E1J9;F8W6P8;F5H1C7;Q9UI17	.;.;.;M2GD_HUMAN	G	530;369;329;150;380	ENSP00000255189:A530G;ENSP00000430972:A369G;ENSP00000369667:A329G;ENSP00000439478:A150G	ENSP00000255189:A530G	A	-	2	0	DMGDH	78362506	1.000000	0.71417	1.000000	0.80357	0.675000	0.39556	6.012000	0.70767	1.498000	0.48600	-0.215000	0.12644	GCG	G|0.677;C|0.323	0.323	strong		0.418	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
XRCC4	7518	hgsc.bcm.edu	37	5	82400773	82400773	+	Missense_Mutation	SNP	C	C	G	rs28383138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82400773C>G	ENST00000511817.1	+	2	115	c.35C>G	c.(34-36)tCt>tGt	p.S12C	XRCC4_ENST00000282268.3_Missense_Mutation_p.S12C|XRCC4_ENST00000338635.6_Missense_Mutation_p.S12C|XRCC4_ENST00000396027.4_Missense_Mutation_p.S12C|XRCC4_ENST00000509268.1_3'UTR			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	12			S -> C (in dbSNP:rs28383138). {ECO:0000269|Ref.6}.		cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		CACCTTGTTTCTGAACCCAGT	0.333								Non-homologous end-joining					C|||	39	0.00778754	0.0287	0.0014	5008	,	,		14902	0.0		0.0	False		,,,				2504	0.0				p.S12C		Atlas-SNP	.											.	XRCC4	37	.	0			c.C35G						PASS	.	C	CYS/SER,CYS/SER,CYS/SER	104,4302	81.9+/-120.4	4,96,2103	90.0	94.0	93.0		35,35,35	4.8	1.0	5	dbSNP_125	93	0,8596		0,0,4298	yes	missense,missense,missense	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	112,112,112	4,96,6401	GG,GC,CC		0.0,2.3604,0.7999	probably-damaging,probably-damaging,probably-damaging	12/335,12/337,12/335	82400773	104,12898	2203	4298	6501	SO:0001583	missense	7518	exon2			TTGTTTCTGAACC	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.35C>G	5.37:g.82400773C>G	ENSP00000421491:p.Ser12Cys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	144	69	0.479167	NM_003401	A8K3X4|Q9BS72|Q9UP94	Missense_Mutation	SNP	ENST00000511817.1	37	CCDS4059.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	14.29	2.491902	0.44352	0.023604	0.0	ENSG00000152422	ENST00000282268;ENST00000338635;ENST00000396027;ENST00000511817	T;T;T;T	0.21031	2.03;2.03;2.03;2.03	5.67	4.8	0.61643	DNA double-strand break repair and VJ recombination XRCC4, N-terminal (2);	0.132928	0.51477	D	0.000085	T	0.23330	0.0564	M	0.74258	2.255	0.49687	D	0.99981	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.34378	-0.9831	10	0.87932	D	0	-5.2753	14.8049	0.69945	0.0:0.9305:0.0:0.0695	rs28383138	12;12;12	Q13426-2;Q13426;Q13426-3	.;XRCC4_HUMAN;.	C	12	ENSP00000282268:S12C;ENSP00000342011:S12C;ENSP00000379344:S12C;ENSP00000421491:S12C	ENSP00000282268:S12C	S	+	2	0	XRCC4	82436529	1.000000	0.71417	0.994000	0.49952	0.199000	0.23934	3.483000	0.53194	1.524000	0.49035	0.591000	0.81541	TCT	C|0.993;G|0.007	0.007	strong		0.333	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	
MUC4	4585	hgsc.bcm.edu	37	3	195512412	195512412	+	Missense_Mutation	SNP	C	C	G	rs529970030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512412C>G	ENST00000463781.3	-	2	6498	c.6039G>C	c.(6037-6039)caG>caC	p.Q2013H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.Q2013H	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)		GAGGGGTGGCCTGTCCTGTAG	0.592													.|||	40	0.00798722	0.0287	0.0014	5008	,	,		29205	0.0		0.001	False		,,,				2504	0.0				p.Q2013H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	0			c.G6039C						scavenged	.						34.0	36.0	35.0					3																	195512412		667	1580	2247	SO:0001583	missense	4585	exon2			GGTGGCCTGTCCT	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.6039G>C	3.37:g.195512412C>G	ENSP00000417498:p.Gln2013His	Somatic	343	5	0.0145773		WXS	Illumina HiSeq	Phase_I	115	15	0.130435	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	0.775	-0.764279	0.02996	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37411	1.3;1.2	.	.	.	.	.	.	.	.	T	0.09024	0.0223	N	0.02539	-0.55	0.80722	P	0.0	B	0.26876	0.162	B	0.08055	0.003	T	0.16778	-1.0391	5	.	.	.	.	.	.	.	.	2013	E7ESK3	.	H	2013	ENSP00000417498:Q2013H;ENSP00000420243:Q2013H	.	Q	-	3	2	MUC4	196996807	0.001000	0.12720	0.001000	0.08648	0.007000	0.05969	0.489000	0.22387	-2.075000	0.00876	-2.332000	0.00249	CAG	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SGK223	157285	hgsc.bcm.edu	37	8	8234219	8234219	+	Missense_Mutation	SNP	G	G	A	rs4840955|rs373458829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8234219G>A	ENST00000520004.1	-	3	1964	c.1700C>T	c.(1699-1701)cCg>cTg	p.P567L	SGK223_ENST00000330777.4_Missense_Mutation_p.P567L			Q86YV5	SG223_HUMAN		569							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GTCAGCCAGCGGTGACACTGG	0.657													G|||	2270	0.453275	0.388	0.4323	5008	,	,		16798	0.6409		0.3002	False		,,,				2504	0.5204				p.P567L	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1700T						PASS	.	G	LEU/PRO	1293,2749		229,835,957	24.0	29.0	27.0		1700	4.9	0.0	8	dbSNP_111	27	2275,6025		338,1599,2213	yes	missense	SGK223	NM_001080826.1	98	567,2434,3170	AA,AG,GG		27.4096,31.9891,28.9094	probably-damaging	567/1403	8234219	3568,8774	2021	4150	6171	SO:0001583	missense	0	exon2			GCCAGCGGTGACA																												ENST00000520004.1:c.1700C>T	8.37:g.8234219G>A	ENSP00000428054:p.Pro567Leu	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	906	0.41483516483516486	193	0.39227642276422764	131	0.36187845303867405	367	0.6416083916083916	215	0.2836411609498681	G	14.12	2.440334	0.43326	0.319891	0.274096	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.59906	0.23;0.23	4.91	4.91	0.64330	.	0.000000	0.64402	D	0.000003	T	0.00012	0.0000	M	0.62723	1.935	0.32196	P	0.578445	B	0.25312	0.123	B	0.18871	0.023	T	0.48969	-0.8987	9	0.56958	D	0.05	.	7.8195	0.29280	0.0832:0.0:0.7549:0.1619	rs4840955;rs61637687	567	Q86YV5	SG223_HUMAN	L	567	ENSP00000330930:P567L;ENSP00000428054:P567L	ENSP00000330930:P567L	P	-	2	0	AC068353.1	8271629	1.000000	0.71417	0.040000	0.18447	0.002000	0.02628	4.250000	0.58772	2.446000	0.82766	0.563000	0.77884	CCG	G|0.631;A|0.369	0.369	strong		0.657	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
EP400	57634	hgsc.bcm.edu	37	12	132549300	132549300	+	Missense_Mutation	SNP	A	A	G	rs7136109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132549300A>G	ENST00000333577.4	+	49	8639	c.8530A>G	c.(8530-8532)Aca>Gca	p.T2844A	EP400_ENST00000389561.2_Missense_Mutation_p.T2808A|EP400_ENST00000389562.2_Missense_Mutation_p.T2807A|EP400_ENST00000330386.6_Missense_Mutation_p.T2727A|EP400_ENST00000332482.4_Missense_Mutation_p.T2771A			Q96L91	EP400_HUMAN	E1A binding protein p400	2844				T -> A (in Ref. 1; AAK97789 and 7; AAB91441). {ECO:0000305}.	chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCCGCAGCCAACAGCCCAAGT	0.652													A|||	758	0.151358	0.5545	0.0303	5008	,	,		12499	0.0		0.004	False		,,,				2504	0.0				p.T2808A		Atlas-SNP	.											.	EP400	370	.	0			c.A8422G						PASS	.	A	ALA/THR	1958,2442	493.8+/-362.8	442,1074,684	29.0	44.0	39.0		8422	-2.0	0.0	12	dbSNP_116	39	24,8572	16.0+/-53.3	0,24,4274	yes	missense	EP400	NM_015409.4	58	442,1098,4958	GG,GA,AA		0.2792,44.5,15.2508	benign	2808/3124	132549300	1982,11014	2200	4298	6498	SO:0001583	missense	57634	exon48			CAGCCAACAGCCC	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8530A>G	12.37:g.132549300A>G	ENSP00000333602:p.Thr2844Ala	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	56	28	0.5	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		257	0.11767399267399267	242	0.491869918699187	13	0.03591160220994475	0	0.0	2	0.002638522427440633	A	4.805	0.149598	0.09185	0.445	0.002792	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.89681	-2.49;-2.49;-2.53;-2.52;-2.55	4.97	-1.96	0.07525	.	0.381428	0.28360	N	0.015636	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B	0.23316	0.05;0.083;0.043;0.0	B;B;B;B	0.23419	0.04;0.046;0.046;0.0	T	0.17806	-1.0357	9	0.08179	T	0.78	.	8.3027	0.32023	0.2929:0.2481:0.4589:0.0	rs7136109	2844;2808;2727;2807	Q96L91;Q96L91-2;Q96L91-4;Q96L91-5	EP400_HUMAN;.;.;.	A	2844;2808;2807;2771;2727;2808	ENSP00000333602:T2844A;ENSP00000374212:T2808A;ENSP00000374213:T2807A;ENSP00000331737:T2771A;ENSP00000330620:T2727A	ENSP00000330620:T2727A	T	+	1	0	EP400	131115253	0.000000	0.05858	0.000000	0.03702	0.496000	0.33645	-0.458000	0.06737	-0.616000	0.05671	-0.589000	0.04120	ACA	A|0.883;G|0.117	0.117	strong		0.652	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
ITGA11	22801	hgsc.bcm.edu	37	15	68612556	68612556	+	Silent	SNP	T	T	C	rs2271724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68612556T>C	ENST00000315757.7	-	20	2669	c.2583A>G	c.(2581-2583)tcA>tcG	p.S861S	ITGA11_ENST00000423218.2_Silent_p.S861S	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	861					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)			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						GCAGGTTTGCTGACTGCGAGA	0.582													T|||	997	0.199081	0.084	0.1441	5008	,	,		17219	0.5595		0.0308	False		,,,				2504	0.1953				p.S861S		Atlas-SNP	.											.	ITGA11	110	.	0			c.A2583G						PASS	.	T		293,3843		8,277,1783	58.0	59.0	59.0		2583	-10.8	0.1	15	dbSNP_100	59	242,8168		0,242,3963	no	coding-synonymous	ITGA11	NM_001004439.1		8,519,5746	CC,CT,TT		2.8775,7.0841,4.2643		861/1189	68612556	535,12011	2068	4205	6273	SO:0001819	synonymous_variant	22801	exon20			GTTTGCTGACTGC	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.2583A>G	15.37:g.68612556T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			T|0.827;C|0.173	0.173	strong		0.582	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
LAMA1	284217	hgsc.bcm.edu	37	18	6958609	6958609	+	Missense_Mutation	SNP	T	T	C	rs543355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6958609T>C	ENST00000389658.3	-	55	7924	c.7831A>G	c.(7831-7833)Aca>Gca	p.T2611A	RP11-781P6.1_ENST00000584722.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2611	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		T -> A (in dbSNP:rs543355).		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)				TCTACTAATGTGCCCAACTTC	0.408													C|||	728	0.145367	0.4917	0.0663	5008	,	,		19526	0.001		0.0298	False		,,,				2504	0.001				p.T2611A		Atlas-SNP	.											LAMA1,colon,carcinoma,0,1	LAMA1	458	1	0			c.A7831G						PASS	.	C	ALA/THR	1940,2466	622.2+/-393.9	445,1050,708	119.0	97.0	104.0		7831	-1.2	0.0	18	dbSNP_83	104	238,8362	808.8+/-407.2	4,230,4066	yes	missense	LAMA1	NM_005559.3	58	449,1280,4774	CC,CT,TT		2.7674,44.0309,16.7461	benign	2611/3076	6958609	2178,10828	2203	4300	6503	SO:0001583	missense	284217	exon55			CTAATGTGCCCAA	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.7831A>G	18.37:g.6958609T>C	ENSP00000374309:p.Thr2611Ala	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	187	76	0.406417	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	272	0.12454212454212454	229	0.4654471544715447	20	0.055248618784530384	0	0.0	23	0.030343007915567283	C	1.449	-0.565554	0.03939	0.440309	0.027674	ENSG00000101680	ENST00000389658;ENST00000344342	T	0.79141	-1.24	5.48	-1.21	0.09524	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.839609	0.10473	N	0.670527	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	0.37776	-0.9691	9	0.28530	T	0.3	.	2.0424	0.03553	0.1834:0.2819:0.3444:0.1904	rs543355;rs52796151;rs60897184;rs543355	2611	P25391	LAMA1_HUMAN	A	2611;64	ENSP00000374309:T2611A	ENSP00000341000:T64A	T	-	1	0	LAMA1	6948609	0.253000	0.23982	0.001000	0.08648	0.087000	0.18053	0.198000	0.17217	-0.379000	0.07906	-0.719000	0.03609	ACA	C|0.157;G|0.000;T|0.843	0.157	strong		0.408	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
OBSCN	84033	hgsc.bcm.edu	37	1	228469870	228469870	+	Missense_Mutation	SNP	C	C	T	rs3795785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228469870C>T	ENST00000422127.1	+	31	8478	c.8434C>T	c.(8434-8436)Cgg>Tgg	p.R2812W	OBSCN_ENST00000359599.6_Missense_Mutation_p.R1659W|OBSCN_ENST00000284548.11_Missense_Mutation_p.R2812W|OBSCN_ENST00000570156.2_Missense_Mutation_p.R3241W|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2812	Ig-like 27.		R -> W (in dbSNP:rs3795785).		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)				CTTCTCTGTGCGGGGCCTCAC	0.652													C|||	437	0.0872604	0.0439	0.013	5008	,	,		16137	0.2808		0.0249	False		,,,				2504	0.0634				p.R3241W		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C9721T						PASS	.	C	TRP/ARG,TRP/ARG	187,3787		6,175,1806	31.0	36.0	35.0		8434,8434	-0.2	0.0	1	dbSNP_107	35	148,8144		0,148,3998	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	101,101	6,323,5804	TT,TC,CC		1.7849,4.7056,2.7311	benign,benign	2812/7969,2812/6621	228469870	335,11931	1987	4146	6133	SO:0001583	missense	84033	exon36			TCTGTGCGGGGCC	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.8434C>T	1.37:g.228469870C>T	ENSP00000409493:p.Arg2812Trp	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	226	88	0.389381	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	217	0.09935897435897435	18	0.036585365853658534	5	0.013812154696132596	170	0.2972027972027972	24	0.0316622691292876	C	9.047	0.991227	0.18966	0.047056	0.017849	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599;ENST00000366706;ENST00000366704	T;T;T	0.41400	1.0;1.0;1.0	4.21	-0.154	0.13399	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	1.005240	0.08013	N	0.990625	T	0.00012	0.0000	M	0.70275	2.135	0.28160	P	0.9290387	B;B;B	0.21606	0.058;0.035;0.048	B;B;B	0.20577	0.011;0.001;0.03	T	0.25467	-1.0131	9	0.66056	D	0.02	.	10.1616	0.42855	0.0:0.5157:0.4097:0.0746	rs3795785;rs61099141;rs3795785	2812;2812;2812	Q5VST9;Q5VST9-2;Q5VST9-3	OBSCN_HUMAN;.;.	W	2812;2812;1659;511;218	ENSP00000284548:R2812W;ENSP00000409493:R2812W;ENSP00000352613:R1659W	ENSP00000284548:R2812W	R	+	1	2	OBSCN	226536493	0.004000	0.15560	0.026000	0.17262	0.140000	0.21249	0.994000	0.29693	-0.239000	0.09710	-1.520000	0.00934	CGG	C|0.882;T|0.118	0.118	strong		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
VPS13A	23230	hgsc.bcm.edu	37	9	79875104	79875104	+	Silent	SNP	A	A	G	rs73466058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79875104A>G	ENST00000360280.3	+	23	2651	c.2391A>G	c.(2389-2391)ccA>ccG	p.P797P	VPS13A_ENST00000376634.4_Silent_p.P797P|VPS13A_ENST00000357409.5_Silent_p.P797P|VPS13A_ENST00000376636.3_Silent_p.P797P	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	797					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						AACCTGAACCAGTAACTGAAG	0.313													A|||	72	0.014377	0.0537	0.0014	5008	,	,		13428	0.0		0.0	False		,,,				2504	0.0				p.P797P		Atlas-SNP	.											.	VPS13A	735	.	0			c.A2391G						PASS	.	A	,,,	182,4224	118.0+/-155.7	3,176,2024	72.0	73.0	73.0		2391,2391,2391,2391	1.9	0.0	9	dbSNP_130	73	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	3,177,6322	GG,GA,AA		0.0116,4.1307,1.4073	,,,	797/3136,797/3070,797/3096,797/3175	79875104	183,12821	2203	4299	6502	SO:0001819	synonymous_variant	23230	exon23			TGAACCAGTAACT	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.2391A>G	9.37:g.79875104A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	150	93	0.62	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			A|0.987;G|0.013	0.013	strong		0.313	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
GCAT	23464	hgsc.bcm.edu	37	22	38205989	38205989	+	Intron	SNP	T	T	C	rs2285178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38205989T>C	ENST00000248924.6	+	2	252				GCAT_ENST00000323205.6_Missense_Mutation_p.L77S|GCAT_ENST00000415371.1_Intron	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase						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)	GGCCTGCCCTTGCCCCACCTG	0.557													.|||	1380	0.275559	0.1014	0.3098	5008	,	,		18233	0.3135		0.332	False		,,,				2504	0.3896				p.L77S		Atlas-SNP	.											.	GCAT	27	.	0			c.T230C						PASS	.	T	SER/LEU,	618,3788	253.4+/-259.3	47,524,1632	66.0	43.0	51.0		230,	0.0	0.0	22	dbSNP_100	51	2672,5926	399.5+/-346.5	383,1906,2010	yes	missense,intron	GCAT	NM_001171690.1,NM_014291.3	145,	430,2430,3642	CC,CT,TT		31.077,14.0263,25.2999	,	77/446,	38205989	3290,9714	2203	4299	6502	SO:0001627	intron_variant	23464	exon2			TGCCCTTGCCCCA	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.197-45T>C	22.37:g.38205989T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	173	83	0.479769	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Missense_Mutation	SNP	ENST00000248924.6	37	CCDS13957.1	614	0.28113553113553114	54	0.10975609756097561	114	0.3149171270718232	195	0.3409090909090909	251	0.3311345646437995	t	5.786	0.329321	0.10956	0.140263	0.31077	ENSG00000100116	ENST00000323205;ENST00000445195;ENST00000394944	D;D	0.94793	-3.52;-1.86	3.68	0.00572	0.14064	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	B	0.19583	0.037	B	0.13407	0.009	T	0.09378	-1.0677	7	0.87932	D	0	.	4.1025	0.10020	0.3637:0.0:0.1877:0.4486	rs2285178;rs59294489;rs2285178	77	E2QC23	.	S	77	ENSP00000371110:L77S;ENSP00000406719:L77S	ENSP00000371110:L77S	L	+	2	0	GCAT	36535935	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	0.213000	0.17521	-0.072000	0.12864	0.402000	0.26972	TTG	T|0.723;C|0.277	0.277	strong		0.557	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2	
ITIH6	347365	hgsc.bcm.edu	37	X	54783952	54783952	+	Missense_Mutation	SNP	A	A	G	rs150850201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54783952A>G	ENST00000218436.6	-	8	2584	c.2555T>C	c.(2554-2556)aTc>aCc	p.I852T		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	852	Pro-rich.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										AGATAATAAGATTTTAGGGGT	0.507													A|||	43	0.0113907	0.0303	0.0043	3775	,	,		13466	0.0		0.0	False		,,,				2504	0.0				p.I852T		Atlas-SNP	.											.	.	.	.	0			c.T2555C						PASS	.	-	THR/ILE	166,3669		3,134,26,1495,545	74.0	71.0	72.0		2555	1.4	0.0	X	dbSNP_134	72	2,6726		0,1,1,2427,1871	yes	missense	ITIH5L	NM_198510.2	89	3,135,27,3922,2416	GG,GA,G,AA,A		0.0297,4.3286,1.5905	possibly-damaging	852/1314	54783952	168,10395	2203	4300	6503	SO:0001583	missense	347365	exon8			AATAAGATTTTAG	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.2555T>C	X.37:g.54783952A>G	ENSP00000218436:p.Ile852Thr	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	227	115	0.506608	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	20	0.012055455093429777	8	0.01694915254237288	0	0.0	0	0.0	0	0.0	A	9.484	1.098979	0.20552	0.043286	2.97E-4	ENSG00000102313	ENST00000218436	T	0.02863	4.13	3.91	1.43	0.22495	.	14.783200	0.01116	U	0.005696	T	0.00608	0.0020	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.42032	-0.9475	9	0.72032	D	0.01	.	5.1877	0.15193	0.4176:0.0:0.5824:0.0	.	852	Q6UXX5	ITH5L_HUMAN	T	852	ENSP00000218436:I852T	ENSP00000218436:I852T	I	-	2	0	ITIH5L	54800677	0.003000	0.15002	0.007000	0.13788	0.008000	0.06430	0.571000	0.23669	0.275000	0.22094	0.380000	0.24917	ATC	A|0.982;G|0.018	0.018	strong		0.507	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
UGGT1	56886	hgsc.bcm.edu	37	2	128939817	128939817	+	Silent	SNP	G	G	A	rs1699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	178	178	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	
ARHGAP4	393	hgsc.bcm.edu	37	X	153176254	153176254	+	Silent	SNP	A	A	G	rs2070097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153176254A>G	ENST00000350060.5	-	15	1757	c.1716T>C	c.(1714-1716)caT>caC	p.H572H	ARHGAP4_ENST00000370016.1_Silent_p.H551H|ARHGAP4_ENST00000467421.1_5'UTR|ARHGAP4_ENST00000537206.1_Silent_p.H549H|ARHGAP4_ENST00000393721.1_Silent_p.H394H|ARHGAP4_ENST00000370028.3_Silent_p.H612H	NM_001666.4	NP_001657.3	P98171	RHG04_HUMAN	Rho GTPase activating protein 4	572	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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)					AGTCCAGGTCATGGGCAGTGC	0.682											OREG0003617	type=REGULATORY REGION|Gene=ARHGAP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	2661	0.704901	0.6914	0.4928	3775	,	,		6158	0.5437		0.3062	False		,,,				2504	0.5613				p.H612H		Atlas-SNP	.											.	ARHGAP4	103	.	0			c.T1836C						PASS	.	G	,	3240,563		1191,370,488,60,73	13.0	15.0	15.0		1836,1716	-6.9	0.0	X	dbSNP_96	15	2616,4076		384,1102,746,931,1112	no	coding-synonymous,coding-synonymous	ARHGAP4	NM_001164741.1,NM_001666.4	,	1575,1472,1234,991,1185	GG,GA,G,AA,A		39.0915,14.8041,44.202	,	612/987,572/947	153176254	5856,4639	2182	4275	6457	SO:0001819	synonymous_variant	393	exon16			CAGGTCATGGGCA	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.1716T>C	X.37:g.153176254A>G		Somatic	82	0	0	1753	WXS	Illumina HiSeq	Phase_I	97	35	0.360825	NM_001164741	Q14144|Q86UY3	Silent	SNP	ENST00000350060.5	37	CCDS14736.1	1043	0.6286919831223629	234	0.7959183673469388	118	0.44696969696969696	218	0.5828877005347594	163	0.26547231270358307	a	0.105	-1.146679	0.01714	0.851959	0.390915	ENSG00000089820	ENST00000454164;ENST00000442172	.	.	.	4.61	-6.94	0.01633	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.24137	P	0.99574145	.	.	.	.	.	.	T	0.07009	-1.0795	3	.	.	.	.	7.0917	0.25287	0.6809:0.0919:0.1343:0.0929	rs2070097;rs17846493;rs17859557;rs61248836;rs2070097	.	.	.	T	72;61	.	.	M	-	2	0	ARHGAP4	152829448	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.160000	0.03147	-2.323000	0.00639	-2.187000	0.00313	ATG	A|0.354;G|0.646	0.646	strong		0.682	ARHGAP4-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061119.1	NM_001666	
CPNE7	27132	hgsc.bcm.edu	37	16	89645360	89645360	+	Silent	SNP	G	G	A	rs149812493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89645360G>A	ENST00000268720.5	+	3	583	c.453G>A	c.(451-453)acG>acA	p.T151T	CPNE7_ENST00000319518.8_Intron	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	151					lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		TGTGCTGCACGGAATCCTCAC	0.542													G|||	42	0.00838658	0.031	0.0014	5008	,	,		16677	0.0		0.0	False		,,,				2504	0.0				p.T151T		Atlas-SNP	.											.	CPNE7	56	.	0			c.G453A						PASS	.	G	,	132,4264	95.3+/-134.0	2,128,2068	115.0	98.0	104.0		453,	-0.3	0.0	16	dbSNP_134	104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron	CPNE7	NM_014427.4,NM_153636.2	,	2,129,6367	AA,AG,GG		0.0116,3.0027,1.0234	,	151/634,	89645360	133,12863	2198	4300	6498	SO:0001819	synonymous_variant	27132	exon3			CTGCACGGAATCC	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.453G>A	16.37:g.89645360G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_014427		Silent	SNP	ENST00000268720.5	37	CCDS10980.1																																																																																			G|0.988;A|0.012	0.012	strong		0.542	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
OR10C1	442194	hgsc.bcm.edu	37	6	29408476	29408476	+	Silent	SNP	A	A	G	rs2074465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29408476A>G	ENST00000444197.2	+	1	1394	c.684A>G	c.(682-684)ccA>ccG	p.P228P	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	228						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)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TCCGGATCCCATCTGTTGCGG	0.572													A|||	316	0.063099	0.152	0.0562	5008	,	,		18057	0.0456		0.0159	False		,,,				2504	0.0143				p.P228P		Atlas-SNP	.											.	OR10C1	58	.	0			c.A684G						PASS	.	A		340,2682		23,294,1194	216.0	239.0	230.0		684	-3.1	0.3	6	dbSNP_96	230	93,5325		2,89,2618	no	coding-synonymous	OR10C1	NM_013941.3		25,383,3812	GG,GA,AA		1.7165,11.2508,5.1303		228/313	29408476	433,8007	1511	2709	4220	SO:0001819	synonymous_variant	442194	exon1			GATCCCATCTGTT		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.684A>G	6.37:g.29408476A>G		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	195	80	0.410256	NM_013941	Q5SUN7|Q96R18	Silent	SNP	ENST00000444197.2	37	CCDS34364.1																																																																																			A|0.939;G|0.061	0.061	strong		0.572	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2		
HEXIM2	124790	hgsc.bcm.edu	37	17	43246456	43246456	+	Silent	SNP	G	G	A	rs34207107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43246456G>A	ENST00000307275.3	+	4	577	c.141G>A	c.(139-141)ccG>ccA	p.P47P	HEXIM2_ENST00000591576.1_Silent_p.P47P|RP13-890H12.2_ENST00000589451.1_RNA|HEXIM2_ENST00000592695.1_Silent_p.P47P|RP13-890H12.2_ENST00000589796.1_RNA	NM_144608.1	NP_653209.1	Q96MH2	HEXI2_HUMAN	hexamethylene bis-acetamide inducible 2	47					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)			endometrium(1)|large_intestine(3)|lung(1)	5						CCCTGACACCGCGGATGGAGA	0.642													G|||	209	0.0417332	0.143	0.0159	5008	,	,		15993	0.0		0.003	False		,,,				2504	0.0061				p.P47P		Atlas-SNP	.											.	HEXIM2	19	.	0			c.G141A						PASS	.	G		546,3860	240.6+/-251.3	31,484,1688	110.0	125.0	120.0		141	-7.9	0.0	17	dbSNP_126	120	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous	HEXIM2	NM_144608.1		31,516,5956	AA,AG,GG		0.3721,12.3922,4.4441		47/287	43246456	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	124790	exon4			GACACCGCGGATG	AK056946	CCDS11496.1	17q21.31	2011-07-29	2011-07-29			ENSG00000168517			28591	protein-coding gene	gene with protein product		615695				12832472	Standard	NM_144608		Approved	FLJ32384	uc002iih.1	Q96MH2		ENST00000307275.3:c.141G>A	17.37:g.43246456G>A		Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_144608	D3DX66	Silent	SNP	ENST00000307275.3	37	CCDS11496.1																																																																																			G|0.962;A|0.038	0.038	strong		0.642	HEXIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450181.1	NM_144608	
SLC39A13	91252	hgsc.bcm.edu	37	11	47431703	47431703	+	Missense_Mutation	SNP	A	A	G	rs61897432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:47431703A>G	ENST00000362021.4	+	2	100	c.58A>G	c.(58-60)Act>Gct	p.T20A	RP11-750H9.5_ENST00000532943.1_RNA|SLC39A13_ENST00000524928.1_Missense_Mutation_p.T20A|SLC39A13_ENST00000531974.1_Missense_Mutation_p.T20A|SLC39A13_ENST00000354884.4_Missense_Mutation_p.T20A|SLC39A13_ENST00000533076.1_Missense_Mutation_p.T20A|RP11-750H9.5_ENST00000532340.1_RNA	NM_001128225.2	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter), member 13	20					cellular zinc ion homeostasis (GO:0006882)|connective tissue development (GO:0061448)|zinc ion transmembrane transport (GO:0071577)	Golgi apparatus (GO:0005794)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|kidney(1)|lung(1)|prostate(1)	4				Lung(87;0.0936)		CCTCTTCCTCACTGCCCTTGC	0.627													A|||	383	0.0764776	0.0628	0.098	5008	,	,		3883	0.0466		0.1491	False		,,,				2504	0.0358				p.T20A		Atlas-SNP	.											.	SLC39A13	18	.	0			c.A58G						PASS	.	A	ALA/THR,ALA/THR	370,4020		15,340,1840	53.0	60.0	58.0		58,58	-1.2	0.1	11	dbSNP_129	58	1191,7375		97,997,3189	yes	missense,missense	SLC39A13	NM_001128225.2,NM_152264.4	58,58	112,1337,5029	GG,GA,AA		13.9038,8.4282,12.0485	benign,benign	20/372,20/365	47431703	1561,11395	2195	4283	6478	SO:0001583	missense	91252	exon2			TTCCTCACTGCCC		CCDS7934.1, CCDS44592.1	11p11.2	2013-05-22			ENSG00000165915	ENSG00000165915		"""Solute carriers"""	20859	protein-coding gene	gene with protein product		608735	"""solute carrier family 39 (metal ion transporter), member 13"""			12659941	Standard	NM_001128225		Approved	FLJ25785	uc009ylq.3	Q96H72	OTTHUMG00000166890	ENST00000362021.4:c.58A>G	11.37:g.47431703A>G	ENSP00000354689:p.Thr20Ala	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_152264	D3DQR6|D3DQR7|E9PLY1|E9PQV3|Q659D9|Q8N7C9|Q8WV10	Missense_Mutation	SNP	ENST00000362021.4	37	CCDS44592.1	212	0.09706959706959707	42	0.08536585365853659	40	0.11049723756906077	18	0.03146853146853147	112	0.14775725593667546	A	10.11	1.260164	0.23051	0.084282	0.139038	ENSG00000165915	ENST00000533076;ENST00000531974;ENST00000531419;ENST00000531865;ENST00000362021;ENST00000354884;ENST00000526614;ENST00000527091;ENST00000524928	T;T;T;T;T;T;T;T;T	0.70282	-0.47;1.01;1.03;-0.44;-0.33;-0.13;0.02;1.01;0.96	5.4	-1.24	0.09435	.	0.820829	0.10843	N	0.627968	T	0.00241	0.0007	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.09022	0.0;0.001;0.002	B;B;B	0.12156	0.002;0.001;0.007	T	0.06862	-1.0803	9	0.08381	T	0.77	-2.3508	5.0379	0.14443	0.3836:0.0:0.4545:0.1619	rs61897432	20;20;20	Q96H72;Q96H72-2;E9PNE7	S39AD_HUMAN;.;.	A	20	ENSP00000434290:T20A;ENSP00000435845:T20A;ENSP00000432302:T20A;ENSP00000434684:T20A;ENSP00000354689:T20A;ENSP00000346956:T20A;ENSP00000432499:T20A;ENSP00000435076:T20A;ENSP00000437186:T20A	ENSP00000346956:T20A	T	+	1	0	SLC39A13	47388279	0.000000	0.05858	0.100000	0.21137	0.592000	0.36648	-0.111000	0.10807	0.052000	0.16007	0.459000	0.35465	ACT	A|0.882;G|0.118	0.118	strong		0.627	SLC39A13-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395652.1	NM_152264	
VPS39	23339	hgsc.bcm.edu	37	15	42459034	42459034	+	Silent	SNP	T	T	C	rs1619030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42459034T>C	ENST00000348544.4	-	15	1487	c.1488A>G	c.(1486-1488)ctA>ctG	p.L496L	VPS39_ENST00000318006.5_Silent_p.L485L			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	496					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		GAGCCTTCTTTAGCACGTGCT	0.547													C|||	1995	0.398363	0.739	0.4942	5008	,	,		20631	0.1815		0.1332	False		,,,				2504	0.3661				p.L485L		Atlas-SNP	.											.	VPS39	53	.	0			c.A1455G						PASS	.	C		2756,1650	505.1+/-366.0	893,970,340	145.0	128.0	134.0		1455	4.9	1.0	15	dbSNP_89	134	1201,7397	762.9+/-407.6	97,1007,3195	no	coding-synonymous	VPS39	NM_015289.2		990,1977,3535	CC,CT,TT		13.9684,37.4489,30.4291		485/876	42459034	3957,9047	2203	4299	6502	SO:0001819	synonymous_variant	23339	exon14			CTTCTTTAGCACG	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"""vacuolar protein sorting 39 (yeast)"""			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.1488A>G	15.37:g.42459034T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	165	164	0.993939	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Silent	SNP	ENST00000348544.4	37	CCDS10083.1																																																																																			T|0.694;C|0.306	0.306	strong		0.547	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289	
PSG2	5670	hgsc.bcm.edu	37	19	43575928	43575928	+	Silent	SNP	G	G	A	rs1064935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43575928G>A	ENST00000406487.1	-	4	986	c.888C>T	c.(886-888)agC>agT	p.S296S		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	296	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.S296S(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				CATAGAGCCCGCTATGCTTTG	0.468													G|||	223	0.0445288	0.0522	0.0043	5008	,	,		19689	0.0952		0.0	False		,,,				2504	0.0562				p.S296S		Atlas-SNP	.											PSG2,NS,carcinoma,0,1	PSG2	84	1	1	Substitution - coding silent(1)	stomach(1)	c.C888T						PASS	.	G		210,4194	129.8+/-166.5	13,184,2005	176.0	183.0	180.0		888	-0.1	0.0	19	dbSNP_86	180	18,8580	11.9+/-42.8	0,18,4281	no	coding-synonymous	PSG2	NM_031246.3		13,202,6286	AA,AG,GG		0.2094,4.7684,1.7536		296/336	43575928	228,12774	2202	4299	6501	SO:0001819	synonymous_variant	5670	exon4			GAGCCCGCTATGC		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.888C>T	19.37:g.43575928G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	211	89	0.421801	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			T|0.002;G|0.976;A|0.023	0.023	strong		0.468	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
GOT2	2806	hgsc.bcm.edu	37	16	58757668	58757668	+	Silent	SNP	A	A	C	rs14221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58757668A>C	ENST00000245206.5	-	2	356	c.228T>G	c.(226-228)gtT>gtG	p.V76V	GOT2_ENST00000434819.2_Silent_p.V76V|GOT2_ENST00000564400.1_5'UTR	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	76					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)	CGCTAGGCAGAACGTAAGGCT	0.493													C|||	3547	0.708267	0.8676	0.7608	5008	,	,		20232	0.6339		0.662	False		,,,				2504	0.5798				p.V76V		Atlas-SNP	.											.	GOT2	42	.	0			c.T228G						PASS	.	C		3631,765	310.5+/-291.6	1493,645,60	201.0	205.0	203.0		228	3.2	1.0	16	dbSNP_52	203	5581,3019	465.9+/-366.6	1809,1963,528	no	coding-synonymous	GOT2	NM_002080.2		3302,2608,588	CC,CA,AA		35.1047,17.4022,29.1167		76/431	58757668	9212,3784	2198	4300	6498	SO:0001819	synonymous_variant	2806	exon2			AGGCAGAACGTAA		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.228T>G	16.37:g.58757668A>C		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	183	77	0.420765	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Silent	SNP	ENST00000245206.5	37	CCDS10801.1																																																																																			A|0.293;C|0.707;G|0.000	0.707	strong		0.493	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
GRID2	2895	hgsc.bcm.edu	37	4	94344042	94344042	+	Missense_Mutation	SNP	G	G	A	rs10034345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	121	0	0		WXS	Illumina HiSeq	Phase_I	134	58	0.432836	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		
KRT32	3882	hgsc.bcm.edu	37	17	39623496	39623496	+	Missense_Mutation	SNP	C	C	T	rs115680799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39623496C>T	ENST00000225899.3	-	1	185	c.82G>A	c.(82-84)Ggc>Agc	p.G28S	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	28	Head.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				CAGTTCACGCCGCTGGAACAG	0.637													C|||	89	0.0177716	0.0658	0.0029	5008	,	,		17468	0.0		0.0	False		,,,				2504	0.0				p.G28S		Atlas-SNP	.											.	KRT32	57	.	0			c.G82A						PASS	.	C	SER/GLY	211,4193		4,203,1995	31.0	34.0	33.0		82	-0.2	0.0	17	dbSNP_132	33	6,8594		0,6,4294	yes	missense	KRT32	NM_002278.3	56	4,209,6289	TT,TC,CC		0.0698,4.7911,1.6687	benign	28/449	39623496	217,12787	2202	4300	6502	SO:0001583	missense	3882	exon1			TCACGCCGCTGGA	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.82G>A	17.37:g.39623496C>T	ENSP00000225899:p.Gly28Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	0.012	-1.657918	0.00779	0.047911	6.98E-4	ENSG00000108759	ENST00000225899	D	0.86164	-2.08	5.16	-0.18	0.13295	.	0.662243	0.13290	N	0.399058	T	0.14917	0.0360	N	0.01874	-0.695	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.35599	-0.9782	10	0.10377	T	0.69	.	2.9903	0.05981	0.3289:0.3218:0.0:0.3493	.	28	Q14532	K1H2_HUMAN	S	28	ENSP00000225899:G28S	ENSP00000225899:G28S	G	-	1	0	KRT32	36877022	0.000000	0.05858	0.020000	0.16555	0.005000	0.04900	-0.360000	0.07622	0.060000	0.16281	-0.339000	0.08088	GGC	C|0.981;T|0.019	0.019	strong		0.637	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
APOBEC4	403314	hgsc.bcm.edu	37	1	183617094	183617094	+	Missense_Mutation	SNP	G	G	A	rs10911391|rs386637462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:183617094G>A	ENST00000308641.4	-	2	1094	c.823C>T	c.(823-825)Ccg>Tcg	p.P275S	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)	275			P -> S (in dbSNP:rs10911391).		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						TGTCCACTCGGCATTTGAAAA	0.478													G|||	473	0.0944489	0.18	0.036	5008	,	,		20202	0.1091		0.0318	False		,,,				2504	0.0695				p.P275S		Atlas-SNP	.											.	APOBEC4	45	.	0			c.C823T						PASS	.	G	,SER/PRO	668,3738	282.8+/-276.7	46,576,1581	88.0	91.0	90.0		,823	0.9	0.0	1	dbSNP_120	90	242,8358	96.1+/-157.9	1,240,4059	yes	intron,missense	RGL1,APOBEC4	NM_015149.3,NM_203454.2	,74	47,816,5640	AA,AG,GG		2.814,15.1611,6.9968	,benign	,275/368	183617094	910,12096	2203	4300	6503	SO:0001583	missense	403314	exon2			CACTCGGCATTTG	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.823C>T	1.37:g.183617094G>A	ENSP00000310622:p.Pro275Ser	Somatic	386	0	0		WXS	Illumina HiSeq	Phase_I	395	202	0.511392	NM_203454	Q8N7F6	Missense_Mutation	SNP	ENST00000308641.4	37	CCDS1358.1	155	0.07097069597069597	73	0.1483739837398374	16	0.04419889502762431	43	0.07517482517482517	23	0.030343007915567283	G	0.023	-1.403808	0.01165	0.151611	0.02814	ENSG00000173627	ENST00000308641	T	0.11063	2.81	4.78	0.865	0.19074	.	0.826979	0.10237	N	0.698973	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46484	-0.9188	9	0.10111	T	0.7	.	2.2323	0.04000	0.154:0.0888:0.1613:0.5959	rs10911391	275	Q8WW27	ABEC4_HUMAN	S	275	ENSP00000310622:P275S	ENSP00000310622:P275S	P	-	1	0	APOBEC4	181883717	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	-0.117000	0.10708	0.197000	0.20387	-0.264000	0.10439	CCG	G|0.933;A|0.067	0.067	strong		0.478	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454	
TSPEAR	54084	hgsc.bcm.edu	37	21	45953576	45953576	+	Silent	SNP	C	C	T	rs148713881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45953576C>T	ENST00000323084.4	-	3	599	c.534G>A	c.(532-534)ccG>ccA	p.P178P	TSPEAR_ENST00000397916.1_Silent_p.P110P	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	178	Laminin G-like.				sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						ACATGTCCACCGGGAGGCCGC	0.677													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		13631	0.0		0.0	False		,,,				2504	0.0				p.P178P		Atlas-SNP	.											TSPEAR,caecum,carcinoma,0,1	TSPEAR	110	1	0			c.G534A						PASS	.	C		104,4254		5,94,2080	19.0	19.0	19.0		534	-0.2	0.7	21	dbSNP_134	19	0,8526		0,0,4263	no	coding-synonymous	TSPEAR	NM_144991.2		5,94,6343	TT,TC,CC		0.0,2.3864,0.8072		178/670	45953576	104,12780	2179	4263	6442	SO:0001819	synonymous_variant	54084	exon3			GTCCACCGGGAGG	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"""chromosome 21 open reading frame 29"", ""deafness, autosomal recessive 98"""	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.534G>A	21.37:g.45953576C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			C|0.990;T|0.010	0.010	strong		0.677	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991	
OBSL1	23363	hgsc.bcm.edu	37	2	220427395	220427395	+	Splice_Site	SNP	G	G	A	rs3183099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220427395G>A	ENST00000404537.1	-	8	2738	c.2682C>T	c.(2680-2682)gaC>gaT	p.D894D	OBSL1_ENST00000373876.1_Splice_Site_p.D894D|OBSL1_ENST00000373873.4_Splice_Site_p.D894D|OBSL1_ENST00000265318.4_Splice_Site_p.D894D|OBSL1_ENST00000289656.3_Splice_Site_p.D481D|OBSL1_ENST00000603926.1_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	56	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	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
PRSS50	29122	hgsc.bcm.edu	37	3	46784467	46784467	+	Intron	SNP	G	G	A	rs58943210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46784467G>A	ENST00000460241.1	-	4	1129				PRSS45_ENST00000442359.2_Missense_Mutation_p.P130L			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						GGGGACAACTGGGGGGAAGAA	0.527													G|||	1317	0.262979	0.528	0.1844	5008	,	,		20178	0.121		0.1441	False		,,,				2504	0.229				p.P130L	Pancreas(41;915 1239 11561 17469)	Atlas-SNP	.											.	PRSS45	12	.	0			c.C389T						PASS	.	G	LEU/PRO	1684,2364		355,974,695	67.0	73.0	71.0		389	-4.4	0.0	3	dbSNP_129	71	1204,7184		79,1046,3069	yes	missense	PRSS45	NM_199183.2	98	434,2020,3764	AA,AG,GG		14.3538,41.6008,23.2229	benign	130/229	46784467	2888,9548	2024	4194	6218	SO:0001627	intron_variant	377047	exon3			ACAACTGGGGGGA	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+5647C>T	3.37:g.46784467G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	116	62	0.534483	NM_199183		Missense_Mutation	SNP	ENST00000460241.1	37	CCDS2745.1	468	0.21428571428571427	231	0.4695121951219512	58	0.16022099447513813	65	0.11363636363636363	114	0.1503957783641161	G	8.503	0.864696	0.17250	0.416008	0.143538	ENSG00000188086	ENST00000331814;ENST00000442359	D	0.89415	-2.51	4.82	-4.4	0.03600	.	2.033210	0.02114	N	0.055041	T	0.00012	0.0000	.	.	.	0.58432	P	9.99999999995449E-6	B	0.06786	0.001	B	0.09377	0.004	T	0.15809	-1.0424	8	0.30854	T	0.27	.	6.0784	0.19928	0.0:0.2292:0.2548:0.5161	rs58943210	130	Q7RTY3-2	.	L	162;130	ENSP00000401932:P130L	ENSP00000330940:P162L	P	-	2	0	PRSS45	46759471	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.748000	0.01826	-1.107000	0.03004	-0.147000	0.13772	CCA	G|0.801;A|0.199	0.199	strong		0.527	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1		
PENK	5179	hgsc.bcm.edu	37	8	57354380	57354380	+	Silent	SNP	T	T	C	rs76702938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:57354380T>C	ENST00000314922.3	-	2	331	c.255A>G	c.(253-255)agA>agG	p.R85R	PENK_ENST00000451791.2_Silent_p.R85R|PENK_ENST00000523274.1_5'UTR	NM_006211.3	NP_006202.1	P01210	PENK_HUMAN	proenkephalin	85					aggressive behavior (GO:0002118)|behavioral fear response (GO:0001662)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|startle response (GO:0001964)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	21		all_lung(136;0.229)	Epithelial(17;0.000873)|all cancers(17;0.0069)			TGCTATTTTCTCTGAGGGTGC	0.468													T|||	12	0.00239617	0.0091	0.0	5008	,	,		17675	0.0		0.0	False		,,,				2504	0.0				p.R85R		Atlas-SNP	.											.	PENK	59	.	0			c.A255G						PASS	.	T	,	15,4391	21.2+/-45.6	0,15,2188	98.0	100.0	99.0		255,255	1.5	0.0	8	dbSNP_132	99	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PENK	NM_001135690.1,NM_006211.3	,	0,15,6488	CC,CT,TT		0.0,0.3404,0.1153	,	85/268,85/268	57354380	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	5179	exon4			ATTTTCTCTGAGG		CCDS6168.1	8q23-q24	2013-02-26				ENSG00000181195		"""Endogenous ligands"""	8831	protein-coding gene	gene with protein product	"""preproenkephalin"""	131330				6281660	Standard	NM_006211		Approved		uc003xsz.2	P01210		ENST00000314922.3:c.255A>G	8.37:g.57354380T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	107	58	0.542056	NM_001135690	B2RC23|Q6FHC6|Q6FHE6	Silent	SNP	ENST00000314922.3	37	CCDS6168.1																																																																																			T|0.999;C|0.001	0.001	strong		0.468	PENK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378645.1		
BPIFB1	92747	hgsc.bcm.edu	37	20	31890175	31890175	+	Missense_Mutation	SNP	G	G	T	rs6120222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31890175G>T	ENST00000253354.1	+	10	1099	c.938G>T	c.(937-939)aGt>aTt	p.S313I	BPIFB1_ENST00000464032.1_3'UTR	NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	313			S -> I (in dbSNP:rs6120222).		innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										CTTCCTGAGAGTGCCCATCGG	0.577													T|||	593	0.118411	0.4319	0.0245	5008	,	,		19315	0.0		0.005	False		,,,				2504	0.0				p.S313I		Atlas-SNP	.											.	.	.	.	0			c.G938T						PASS	.	T	ILE/SER	1560,2846	668.3+/-402.0	260,1040,903	210.0	181.0	191.0		938	3.3	0.0	20	dbSNP_114	191	26,8574	818.1+/-406.9	0,26,4274	yes	missense	BPIFB1	NM_033197.2	142	260,1066,5177	TT,TG,GG		0.3023,35.4063,12.1944	benign	313/485	31890175	1586,11420	2203	4300	6503	SO:0001583	missense	92747	exon10			CTGAGAGTGCCCA	BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"""BPI fold containing"""	16108	protein-coding gene	gene with protein product	"""von Ebner minor salivary gland protein"""		"""chromosome 20 open reading frame 114"""	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.938G>T	20.37:g.31890175G>T	ENSP00000253354:p.Ser313Ile	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	161	74	0.459627	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	37	CCDS13218.1	215	0.09844322344322344	201	0.40853658536585363	10	0.027624309392265192	0	0.0	4	0.005277044854881266	T	1.380	-0.583585	0.03827	0.354063	0.003023	ENSG00000125999	ENST00000253354;ENST00000375378	T	0.07444	3.19	4.4	3.27	0.37495	.	1.095670	0.07173	N	0.852655	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	0.46693	-0.9173	9	0.37606	T	0.19	0.4692	4.8873	0.13710	0.0:0.0993:0.1871:0.7136	rs6120222;rs6120222	313	Q8TDL5	BPIB1_HUMAN	I	313;144	ENSP00000253354:S313I	ENSP00000253354:S313I	S	+	2	0	BPIFB1	31353836	0.026000	0.19158	0.042000	0.18584	0.008000	0.06430	1.275000	0.33144	0.296000	0.22592	-0.525000	0.04345	AGT	G|0.875;T|0.125	0.125	strong		0.577	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197	
CASKIN2	57513	hgsc.bcm.edu	37	17	73498483	73498483	+	Missense_Mutation	SNP	T	T	C	rs7503373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73498483T>C	ENST00000321617.3	-	18	3258	c.2672A>G	c.(2671-2673)gAg>gGg	p.E891G	CASKIN2_ENST00000433559.2_Missense_Mutation_p.E809G	NM_020753.3	NP_065804.2	Q8WXE0	CSKI2_HUMAN	CASK interacting protein 2	891	Pro-rich.		E -> G (in dbSNP:rs7503373). {ECO:0000269|PubMed:10574461, ECO:0000269|PubMed:12040031, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18669648}.			cytoplasm (GO:0005737)				endometrium(1)|kidney(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	18	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)			CCCTGGGCTCTCATCTAGTGG	0.736													C|||	3994	0.797524	0.9894	0.6556	5008	,	,		8267	0.5159		0.8996	False		,,,				2504	0.8241				p.E891G		Atlas-SNP	.											.	CASKIN2	66	.	0			c.A2672G						PASS	.	C	GLY/GLU,GLY/GLU	3686,98		1798,90,4	4.0	5.0	4.0		2426,2672	0.6	0.0	17	dbSNP_116	4	7033,535		3265,503,16	yes	missense,missense	CASKIN2	NM_001142643.1,NM_020753.3	98,98	5063,593,20	CC,CT,TT		7.0692,2.5899,5.5761	benign,benign	809/1121,891/1203	73498483	10719,633	1892	3784	5676	SO:0001583	missense	57513	exon18			GGGCTCTCATCTA	AB032965	CCDS11723.1, CCDS45775.1	17q25.1	2014-09-04			ENSG00000177303	ENSG00000177303		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	18200	protein-coding gene	gene with protein product		612185				12040031	Standard	NM_020753		Approved	KIAA1139, FLJ21609, ANKS5B	uc002joc.4	Q8WXE0	OTTHUMG00000179683	ENST00000321617.3:c.2672A>G	17.37:g.73498483T>C	ENSP00000325355:p.Glu891Gly	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	29	28	0.965517	NM_020753	B4DTT3|B7Z9H1|Q7LG69|Q9ULT1	Missense_Mutation	SNP	ENST00000321617.3	37	CCDS11723.1	1693	0.7751831501831502	484	0.983739837398374	264	0.7292817679558011	266	0.46503496503496505	679	0.895778364116095	C	1.131	-0.652527	0.03480	0.974101	0.929308	ENSG00000177303	ENST00000321617;ENST00000433559	T;T	0.56103	0.48;0.48	4.87	0.576	0.17380	.	0.150547	0.30890	N	0.008672	T	0.00012	0.0000	N	0.00926	-1.1	0.44207	P	0.0029679999999999707	B	0.02656	0.0	B	0.01281	0.0	T	0.24012	-1.0172	9	0.15499	T	0.54	.	2.1311	0.03750	0.1241:0.3434:0.1218:0.4107	rs7503373	891	Q8WXE0	CSKI2_HUMAN	G	891;809	ENSP00000325355:E891G;ENSP00000406963:E809G	ENSP00000325355:E891G	E	-	2	0	CASKIN2	71010078	0.000000	0.05858	0.001000	0.08648	0.206000	0.24218	-0.889000	0.04144	-0.210000	0.10140	-0.320000	0.08662	GAG	T|0.224;C|0.776	0.776	strong		0.736	CASKIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447609.1	NM_020753	
RUFY4	285180	hgsc.bcm.edu	37	2	218954716	218954716	+	Missense_Mutation	SNP	A	A	G	rs116710266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218954716A>G	ENST00000344321.7	+	13	2173	c.1655A>G	c.(1654-1656)tAc>tGc	p.Y552C	RUFY4_ENST00000441828.2_3'UTR|RUFY4_ENST00000374155.3_3'UTR	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	552							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)		TCCATGGATTACAAGAAGAGA	0.632													A|||	70	0.0139776	0.0499	0.0058	5008	,	,		17641	0.0		0.0	False		,,,				2504	0.0				p.Y552C		Atlas-SNP	.											.	RUFY4	59	.	0			c.A1655G						PASS	.	A	CYS/TYR	158,3840		3,152,1844	37.0	44.0	42.0		1655	0.7	0.7	2	dbSNP_132	42	0,8322		0,0,4161	yes	missense	RUFY4	NM_198483.3	194	3,152,6005	GG,GA,AA		0.0,3.952,1.2825	probably-damaging	552/572	218954716	158,12162	1999	4161	6160	SO:0001583	missense	285180	exon13			TGGATTACAAGAA	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.1655A>G	2.37:g.218954716A>G	ENSP00000345900:p.Tyr552Cys	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	280	153	0.546429	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	37		35	0.016025641025641024	31	0.06300813008130081	4	0.011049723756906077	0	0.0	0	0.0	A	11.43	1.636570	0.29068	0.03952	0.0	ENSG00000188282	ENST00000344321	T	0.76709	-1.04	4.6	0.663	0.17885	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	.	.	.	.	T	0.17238	0.0414	M	0.68952	2.095	0.80722	D	1	P	0.46784	0.884	B	0.32342	0.144	T	0.47182	-0.9137	9	0.59425	D	0.04	.	1.8069	0.03082	0.5702:0.1707:0.0947:0.1644	.	552	Q6ZNE9	RUFY4_HUMAN	C	552	ENSP00000345900:Y552C	ENSP00000345900:Y552C	Y	+	2	0	RUFY4	218662961	0.997000	0.39634	0.740000	0.30986	0.070000	0.16714	0.369000	0.20416	0.249000	0.21456	-0.488000	0.04728	TAC	A|0.982;G|0.018	0.018	strong		0.632	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483	
MUC1	4582	hgsc.bcm.edu	37	1	155161714	155161714	+	Missense_Mutation	SNP	G	G	A	rs544579074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155161714G>A	ENST00000368395.1	-	2	490	c.419C>T	c.(418-420)tCg>tTg	p.S140L	MUC1_ENST00000368396.4_Intron|MUC1_ENST00000343256.5_Intron|MUC1_ENST00000368398.3_Intron|MUC1_ENST00000368393.3_Intron|MUC1_ENST00000342482.4_Intron|MUC1_ENST00000457295.2_Intron|MUC1_ENST00000368392.3_Intron|RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000337604.5_Intron|MUC1_ENST00000438413.1_Intron|MUC1_ENST00000462215.1_Intron|MUC1_ENST00000368389.2_Intron|MUC1_ENST00000368390.3_Intron|MUC1_ENST00000338684.5_Intron	NM_001204285.1|NM_001204286.1	NP_001191214.1|NP_001191215.1	P15941	MUC1_HUMAN	mucin 1, cell surface associated	920	42 X 20 AA approximate tandem repeats of P-A-P-G-S-T-A-P-P-A-H-G-V-T-S-A-P-D-T-R.				cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription by competitive promoter binding (GO:0010944)|O-glycan processing (GO:0016266)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|post-translational protein modification (GO:0043687)|regulation of transcription from RNA polymerase II promoter in response to stress (GO:0043618)|response to hypoxia (GO:0001666)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|nuclear chromatin (GO:0000790)|vesicle (GO:0031982)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|skin(2)	10	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GTCCGGGGCCGAGGTGACACC	0.776			T	IGH@	B-NHL								G|||	100	0.0199681	0.0726	0.0058	5008	,	,		6075	0.0		0.0	False		,,,				2504	0.0				p.S149L		Atlas-SNP	.		Dom	yes		1	1q21	4582	"""mucin 1, transmembrane"""		L	.	MUC1	94	.	0			c.C446T						PASS	.																																			SO:0001583	missense	4582	exon2			GGGGCCGAGGTGA	J05581	CCDS1098.1, CCDS30882.1, CCDS30883.1, CCDS41408.1, CCDS41409.1, CCDS55640.1, CCDS55641.1, CCDS55642.1, CCDS55640.2, CCDS72933.1, CCDS72934.1, CCDS72935.1, CCDS72936.1	1q22	2014-01-31	2006-03-14		ENSG00000185499	ENSG00000185499		"""CD molecules"", ""Mucins"""	7508	protein-coding gene	gene with protein product		158340	"""mucin 1, transmembrane"", ""medullary cystic kidney disease 1 (autosomal dominant)"""	PUM, MCKD1		1697589, 23396133	Standard	NM_002456		Approved	CD227, PEM, ADMCKD, ADMCKD1, MCKD, MCD	uc031ppv.1	P15941	OTTHUMG00000035681	ENST00000368395.1:c.419C>T	1.37:g.155161714G>A	ENSP00000357380:p.Ser140Leu	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	6	4	0.666667	NM_001204286	A5YRV1|A6ZID9|A6ZIE0|B1AVQ8|B1AVR0|B6ECA1|E7ESE5|E7EUG9|P13931|P15942|P17626|Q0VAP5|Q0VAP6|Q14128|Q14876|Q16437|Q16442|Q16615|Q6S4Y3|Q7Z547|Q7Z548|Q7Z550|Q7Z552|Q9BXA4|Q9UE75|Q9UE76|Q9UQL1|Q9Y4J2	Missense_Mutation	SNP	ENST00000368395.1	37	CCDS55640.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.880738	0.51801	.	.	ENSG00000185499	ENST00000368395	T	0.50277	0.75	2.94	2.94	0.34122	.	1.042050	0.07734	N	0.945652	T	0.46756	0.1409	L	0.41492	1.28	0.44261	D	0.997118	D	0.61697	0.99	D	0.63957	0.92	T	0.45585	-0.9251	10	0.37606	T	0.19	0.7388	12.1668	0.54135	0.0:0.0:1.0:0.0	.	140	P15941	MUC1_HUMAN	L	140	ENSP00000357380:S140L	ENSP00000357380:S140L	S	-	2	0	MUC1	153428338	0.000000	0.05858	0.015000	0.15790	0.005000	0.04900	0.439000	0.21575	1.981000	0.57761	0.485000	0.47835	TCG	.	.	none		0.776	MUC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086735.1	NM_002456	
SIDT2	51092	hgsc.bcm.edu	37	11	117050007	117050007	+	Missense_Mutation	SNP	G	G	A	rs61729992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117050007G>A	ENST00000324225.4	+	1	559	c.28G>A	c.(28-30)Gtg>Atg	p.V10M	SIDT2_ENST00000431081.2_Missense_Mutation_p.V10M	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	10					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	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;0.000219)|all cancers(92;0.00144)		GCCCTTCTTGGTGCTCTTGGT	0.677													G|||	43	0.00858626	0.0303	0.0029	5008	,	,		11337	0.0		0.001	False		,,,				2504	0.0				p.V10M		Atlas-SNP	.											.	SIDT2	82	.	0			c.G28A						PASS	.	G	MET/VAL	83,4319	70.3+/-108.2	0,83,2118	72.0	66.0	68.0		28	2.3	0.1	11	dbSNP_129	68	0,8592		0,0,4296	yes	missense	SIDT2	NM_001040455.1	21	0,83,6414	AA,AG,GG		0.0,1.8855,0.6388	benign	10/833	117050007	83,12911	2201	4296	6497	SO:0001583	missense	51092	exon1			TTCTTGGTGCTCT	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.28G>A	11.37:g.117050007G>A	ENSP00000314023:p.Val10Met	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	44	15	0.340909	NM_001040455	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	37	CCDS31682.1	19	0.0086996336996337	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	11.97	1.798338	0.31777	0.018855	0.0	ENSG00000149577	ENST00000324225;ENST00000532960;ENST00000525347;ENST00000278951;ENST00000431081;ENST00000392956	T;T;T;T	0.50548	2.12;0.74;2.1;2.12	4.19	2.28	0.28536	.	1.095770	0.07106	N	0.841382	T	0.19644	0.0472	L	0.44542	1.39	0.25313	N	0.989181	B;P;P;B	0.43701	0.126;0.815;0.718;0.232	B;B;B;B	0.43251	0.206;0.413;0.235;0.07	T	0.17806	-1.0357	10	0.62326	D	0.03	-4.7017	5.5137	0.16894	0.1108:0.2032:0.6859:0.0	rs61729992	10;10;10;10	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	M	10	ENSP00000314023:V10M;ENSP00000431176:V10M;ENSP00000278951:V10M;ENSP00000399635:V10M	ENSP00000278951:V10M	V	+	1	0	SIDT2	116555217	1.000000	0.71417	0.081000	0.20488	0.384000	0.30261	3.334000	0.52097	0.393000	0.25203	0.561000	0.74099	GTG	G|0.991;A|0.009	0.009	strong		0.677	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996	
CPA5	93979	hgsc.bcm.edu	37	7	130007388	130007388	+	Missense_Mutation	SNP	G	G	T	rs17854248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:130007388G>T	ENST00000485477.1	+	10	2143	c.1014G>T	c.(1012-1014)gaG>gaT	p.E338D	CPA5_ENST00000355388.3_Missense_Mutation_p.E338D|CPA5_ENST00000461828.1_Missense_Mutation_p.E338D|CPA5_ENST00000466363.2_Missense_Mutation_p.E338D|CPA5_ENST00000393213.3_Missense_Mutation_p.E338D|CPA5_ENST00000474905.1_Missense_Mutation_p.E338D|CPA5_ENST00000431780.2_Missense_Mutation_p.E338D			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	338			E -> D (in dbSNP:rs17854248). {ECO:0000269|PubMed:11920156, ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					GATTGCTGGAGCCCGTTTCAA	0.517													G|||	670	0.133786	0.208	0.0908	5008	,	,		18238	0.003		0.1958	False		,,,				2504	0.135				p.E338D		Atlas-SNP	.											.	CPA5	61	.	0			c.G1014T						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU	929,3477	356.1+/-313.4	105,719,1379	116.0	112.0	114.0		1014,1014,1014	3.8	1.0	7	dbSNP_123	114	1797,6803	324.6+/-316.5	188,1421,2691	yes	missense,missense,missense	CPA5	NM_001127441.1,NM_001127442.1,NM_080385.4	45,45,45	293,2140,4070	TT,TG,GG		20.8953,21.0849,20.9596	benign,benign,benign	338/437,338/404,338/437	130007388	2726,10280	2203	4300	6503	SO:0001583	missense	93979	exon11			GCTGGAGCCCGTT	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.1014G>T	7.37:g.130007388G>T	ENSP00000420237:p.Glu338Asp	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	310	138	0.445161	NM_080385	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	37	CCDS5819.1	306	0.1401098901098901	111	0.22560975609756098	38	0.10497237569060773	1	0.0017482517482517483	156	0.20580474934036938	G	8.114	0.779385	0.16120	0.210849	0.208953	ENSG00000158525	ENST00000355388;ENST00000461828;ENST00000466363;ENST00000485477;ENST00000431780;ENST00000474905;ENST00000393213	T;T;T;T;T;T;T	0.11063	2.81;2.81;2.81;2.81;2.81;2.81;2.81	5.61	3.81	0.43845	Peptidase M14, carboxypeptidase A (2);	0.096048	0.45606	D	0.000349	T	0.00012	0.0000	L	0.32530	0.975	0.45733	P	0.0013640000000000319	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.45086	-0.9285	8	.	.	.	.	8.5473	0.33429	0.3033:0.0:0.6967:0.0	rs17854248;rs60477216	338;338	G3V0G8;Q8WXQ8	.;CBPA5_HUMAN	D	338	ENSP00000347549:E338D;ENSP00000418183:E338D;ENSP00000419025:E338D;ENSP00000420237:E338D;ENSP00000393045:E338D;ENSP00000417314:E338D;ENSP00000376907:E338D	.	E	+	3	2	CPA5	129794624	0.000000	0.05858	0.995000	0.50966	0.168000	0.22595	-0.706000	0.05047	0.732000	0.32470	0.462000	0.41574	GAG	G|0.810;T|0.190	0.190	strong		0.517	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441	
TRAF3	7187	hgsc.bcm.edu	37	14	103342049	103342049	+	Missense_Mutation	SNP	T	T	C	rs1131877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103342049T>C	ENST00000560371.1	+	4	603	c.386T>C	c.(385-387)aTg>aCg	p.M129T	TRAF3_ENST00000392745.2_Missense_Mutation_p.M129T|TRAF3_ENST00000351691.5_Missense_Mutation_p.M129T|TRAF3_ENST00000539721.1_Missense_Mutation_p.M129T|TRAF3_ENST00000347662.4_Missense_Mutation_p.M129T	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	129			M -> T (in dbSNP:rs1131877). {ECO:0000269|PubMed:7530216, ECO:0000269|PubMed:7533327}.		apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|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)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		GAGCAGTTAATGCTGGGACAT	0.438													C|||	2353	0.469848	0.9062	0.4856	5008	,	,		18243	0.3978		0.2475	False		,,,				2504	0.1718				p.M129T		Atlas-SNP	.											.	TRAF3	60	.	0			c.T386C						PASS	.	C	THR/MET,THR/MET,THR/MET,THR/MET	3603,803	322.9+/-297.8	1488,627,88	132.0	125.0	127.0		386,386,386,386	3.6	0.0	14	dbSNP_86	127	2000,6600	722.8+/-406.4	217,1566,2517	yes	missense,missense,missense,missense	TRAF3	NM_001199427.1,NM_003300.3,NM_145725.2,NM_145726.2	81,81,81,81	1705,2193,2605	CC,CT,TT		23.2558,18.2251,43.0801	benign,benign,benign,benign	129/486,129/569,129/569,129/544	103342049	5603,7403	2203	4300	6503	SO:0001583	missense	7187	exon5			AGTTAATGCTGGG	U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.386T>C	14.37:g.103342049T>C	ENSP00000454207:p.Met129Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_145726	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Missense_Mutation	SNP	ENST00000560371.1	37	CCDS9975.1	1021	0.4674908424908425	445	0.9044715447154471	160	0.4419889502762431	221	0.38636363636363635	195	0.25725593667546176	C	0.018	-1.475064	0.01035	0.817749	0.232558	ENSG00000131323	ENST00000392745;ENST00000347662;ENST00000351691;ENST00000539721	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	5.51	3.64	0.41730	TRAF-like (1);Seven In Absentia Homolog-type (1);	0.656589	0.16982	N	0.191649	T	0.00012	0.0000	N	0.01122	-1.005	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.21449	-1.0245	9	0.13108	T	0.6	-2.886	8.278	0.31883	0.1279:0.7379:0.0:0.1342	rs1131877;rs2180394;rs2229853;rs3192127;rs17817905;rs52830086;rs57223463;rs1131877	129;129;129	Q13114-2;A6NHG8;Q13114	.;.;TRAF3_HUMAN	T	129	ENSP00000376500:M129T;ENSP00000328003:M129T;ENSP00000332468:M129T;ENSP00000445998:M129T	ENSP00000328003:M129T	M	+	2	0	TRAF3	102411802	0.030000	0.19436	0.000000	0.03702	0.304000	0.27724	2.369000	0.44231	0.354000	0.24105	-0.119000	0.15052	ATG	T|0.550;C|0.450	0.450	strong		0.438	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	
RAB19	401409	hgsc.bcm.edu	37	7	140125878	140125878	+	Silent	SNP	C	C	T	rs4585665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140125878C>T	ENST00000356407.3	+	3	650	c.582C>T	c.(580-582)aaC>aaT	p.N194N	RAB19_ENST00000275874.5_Silent_p.N241N|RAB19_ENST00000537763.1_Silent_p.N194N			A4D1S5	RAB19_HUMAN	RAB19, member RAS oncogene family	194					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(3)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	9	Melanoma(164;0.0142)					GTGCCCTGAACGGCCTCCCCC	0.562													C|||	61	0.0121805	0.0439	0.0043	5008	,	,		18656	0.0		0.0	False		,,,				2504	0.0				p.N194N		Atlas-SNP	.											.	RAB19	21	.	0			c.C582T						PASS	.	C		126,4280	93.0+/-131.7	2,122,2079	77.0	72.0	74.0		582	0.4	0.0	7	dbSNP_111	74	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	RAB19	NM_001008749.2		2,124,6377	TT,TC,CC		0.0233,2.8597,0.9842		194/218	140125878	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	401409	exon4			CCTGAACGGCCTC		CCDS34762.1, CCDS34762.2	7q34	2014-05-09			ENSG00000146955	ENSG00000146955		"""RAB, member RAS oncogene"""	19982	protein-coding gene	gene with protein product							Standard	NM_001008749		Approved	RAB19B	uc010lni.2	A4D1S5	OTTHUMG00000157410	ENST00000356407.3:c.582C>T	7.37:g.140125878C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001008749	A4D1S6|B2RTS6|B5MDR2|Q9UL27	Silent	SNP	ENST00000356407.3	37	CCDS34762.2																																																																																			C|0.989;T|0.011	0.011	strong		0.562	RAB19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348740.1		
FBN3	84467	hgsc.bcm.edu	37	19	8176919	8176919	+	Silent	SNP	C	C	T	rs4804264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	175	0	0		WXS	Illumina HiSeq	Phase_I	185	80	0.432432	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29912087	29912087	+	Missense_Mutation	SNP	G	G	T	rs1059632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29912087G>T	ENST00000396634.1	+	6	1149	c.808G>T	c.(808-810)Gct>Tct	p.A270S	HLA-A_ENST00000376809.5_Missense_Mutation_p.A270S|HLA-A_ENST00000376802.2_Missense_Mutation_p.A270S|HLA-A_ENST00000376806.5_Missense_Mutation_p.A270S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	270	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						GAAGTGGGCGGCTGTGGTGGT	0.627									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.A270S		Atlas-SNP	.											.	HLA-A	89	.	0			c.G808T						PASS	.						31.0	31.0	31.0					6																	29912087		1510	2705	4215	SO:0001583	missense	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TGGGCGGCTGTGG	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.808G>T	6.37:g.29912087G>T	ENSP00000379873:p.Ala270Ser	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	377	118	0.312997	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	8.494	0.862723	0.17178	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000536480;ENST00000376809;ENST00000376802	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	3.69	2.8	0.32819	Immunoglobulin-like (4);Immunoglobulin C1-set (8);Immunoglobulin-like fold (4);	0.636476	0.12630	U	0.452285	T	0.17280	0.0415	L	0.55481	1.735	0.58432	P	1.999999999946489E-6	P;B;D;B;D;B;B	0.62365	0.823;0.0;0.991;0.0;0.991;0.0;0.0	D;B;D;B;D;B;B	0.91635	0.973;0.038;0.999;0.038;0.999;0.038;0.038	T	0.03157	-1.1066	9	0.49607	T	0.09	.	8.6885	0.34251	0.0:0.0:0.7739:0.2261	rs2231093;rs17840079	149;270;270;270;270;270;270	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	S	270;270;58;270;270	ENSP00000379873:A270S;ENSP00000366002:A270S;ENSP00000366005:A270S;ENSP00000365998:A270S	ENSP00000365998:A270S	A	+	1	0	HLA-A	30020066	0.000000	0.05858	0.652000	0.29579	0.832000	0.47134	0.401000	0.20948	0.870000	0.35726	0.485000	0.47835	GCT	G|0.860;T|0.140	0.140	strong		0.627	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
RNF123	63891	hgsc.bcm.edu	37	3	49743010	49743010	+	Silent	SNP	C	C	G	rs76989089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49743010C>G	ENST00000327697.6	+	24	2346	c.2202C>G	c.(2200-2202)ccC>ccG	p.P734P	RNF123_ENST00000432042.1_Silent_p.P588P	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	734					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		TGGGGCGGCCCCCCGAGGAGC	0.647													C|||	93	0.0185703	0.0015	0.0274	5008	,	,		16085	0.0		0.0477	False		,,,				2504	0.0245				p.P734P		Atlas-SNP	.											.	RNF123	100	.	0			c.C2202G						PASS	.	C		28,4378	32.6+/-62.9	0,28,2175	36.0	39.0	38.0		2202	0.3	1.0	3	dbSNP_133	38	319,8281	109.0+/-169.6	10,299,3991	no	coding-synonymous	RNF123	NM_022064.2		10,327,6166	GG,GC,CC		3.7093,0.6355,2.668		734/1315	49743010	347,12659	2203	4300	6503	SO:0001819	synonymous_variant	63891	exon24			GCGGCCCCCCGAG	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.2202C>G	3.37:g.49743010C>G		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	209	103	0.492823	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	37	CCDS33758.1																																																																																			C|0.974;G|0.026	0.026	strong		0.647	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
OR10G8	219869	hgsc.bcm.edu	37	11	123900694	123900694	+	Missense_Mutation	SNP	A	A	G	rs75994039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123900694A>G	ENST00000431524.1	+	1	398	c.365A>G	c.(364-366)tAc>tGc	p.Y122C		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y122C(1)		breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		TGTGATCGCTACCTGGCCATC	0.557													A|||	357	0.0712859	0.0514	0.1427	5008	,	,		21158	0.1448		0.007	False		,,,				2504	0.0378				p.Y122C		Atlas-SNP	.											OR10G8,NS,carcinoma,0,1	OR10G8	132	1	1	Substitution - Missense(1)	stomach(1)	c.A365G						PASS	.	A	CYS/TYR	192,4210	123.3+/-160.7	4,184,2013	155.0	145.0	148.0		365	1.8	1.0	11	dbSNP_131	148	24,8574	16.6+/-54.9	0,24,4275	yes	missense	OR10G8	NM_001004464.1	194	4,208,6288	GG,GA,AA		0.2791,4.3617,1.6615	probably-damaging	122/312	123900694	216,12784	2201	4299	6500	SO:0001583	missense	219869	exon1			ATCGCTACCTGGC	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"""GPCR / Class A : Olfactory receptors"""	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.365A>G	11.37:g.123900694A>G	ENSP00000389072:p.Tyr122Cys	Somatic	641	0	0		WXS	Illumina HiSeq	Phase_I	571	308	0.539405	NM_001004464	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	174	0.07967032967032966	25	0.0508130081300813	60	0.16574585635359115	83	0.1451048951048951	6	0.0079155672823219	A	15.67	2.902071	0.52227	0.043617	0.002791	ENSG00000234560	ENST00000431524	T	0.56444	0.46	3.04	1.84	0.25277	GPCR, rhodopsin-like superfamily (1);	0.168879	0.28301	N	0.015846	T	0.00412	0.0013	M	0.84585	2.705	0.28590	P	0.9097025	D	0.71674	0.998	D	0.67231	0.95	T	0.25012	-1.0144	9	0.72032	D	0.01	.	7.5222	0.27635	0.8073:0.0:0.0:0.1927	.	122	Q8NGN5	O10G8_HUMAN	C	122	ENSP00000389072:Y122C	ENSP00000389072:Y122C	Y	+	2	0	OR10G8	123405904	0.780000	0.28664	0.999000	0.59377	0.896000	0.52359	1.683000	0.37638	0.340000	0.23745	0.528000	0.53228	TAC	A|0.966;G|0.034	0.034	strong		0.557	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464	
ABCA1	19	hgsc.bcm.edu	37	9	107586753	107586753	+	Missense_Mutation	SNP	T	T	C	rs2066714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107586753T>C	ENST00000374736.3	-	18	3043	c.2649A>G	c.(2647-2649)atA>atG	p.I883M	ABCA1_ENST00000494467.1_5'Flank	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	883			I -> M (associated with higher plasma cholesterol; dbSNP:rs2066714). {ECO:0000269|PubMed:10431237, ECO:0000269|PubMed:10938021, ECO:0000269|PubMed:11238261, ECO:0000269|PubMed:11257261, ECO:0000269|PubMed:12709788, ECO:0000269|PubMed:12966036, ECO:0000269|PubMed:15520867}.		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)	TACTTTCTGATATTCTCTTCT	0.493													C|||	1787	0.356829	0.5083	0.2233	5008	,	,		20805	0.6865		0.1352	False		,,,				2504	0.135				p.I883M		Atlas-SNP	.											ABCA1,NS,adenoma,0,1	ABCA1	244	1	0			c.A2649G	GRCh37	CM990005	ABCA1	M	rs2066714	scavenged	.	C	MET/ILE	2045,2361	609.1+/-391.3	497,1051,655	118.0	103.0	108.0		2649	0.2	0.1	9	dbSNP_94	108	1154,7446	766.1+/-407.6	72,1010,3218	yes	missense	ABCA1	NM_005502.3	10	569,2061,3873	CC,CT,TT		13.4186,46.414,24.5963	benign	883/2262	107586753	3199,9807	2203	4300	6503	SO:0001583	missense	19	exon18			TTCTGATATTCTC	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.2649A>G	9.37:g.107586753T>C	ENSP00000363868:p.Ile883Met	Somatic	211	2	0.00947867		WXS	Illumina HiSeq	Phase_I	229	156	0.681223	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	799	0.3658424908424908	244	0.4959349593495935	77	0.212707182320442	387	0.6765734265734266	91	0.12005277044854881	C	2.696	-0.272003	0.05716	0.46414	0.134186	ENSG00000165029	ENST00000374736	D	0.88586	-2.4	5.71	0.162	0.14981	.	2.186690	0.01451	N	0.015505	T	0.00012	0.0000	N	0.22421	0.69	0.36654	P	0.12242900000000001	B	0.09022	0.002	B	0.06405	0.002	T	0.46484	-0.9188	9	0.45353	T	0.12	.	3.2794	0.06909	0.133:0.2132:0.0845:0.5693	rs2066714;rs2853570;rs4149313;rs58387182;rs4149313	883	O95477	ABCA1_HUMAN	M	883	ENSP00000363868:I883M	ENSP00000363868:I883M	I	-	3	3	ABCA1	106626574	0.000000	0.05858	0.065000	0.19835	0.016000	0.09150	-1.119000	0.03276	-0.081000	0.12662	-1.212000	0.01626	ATA	T|0.686;C|0.314	0.314	strong		0.493	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274212	39274212	+	Missense_Mutation	SNP	C	C	T	rs187464255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39274212C>T	ENST00000391413.2	-	1	394	c.356G>A	c.(355-357)tGc>tAc	p.C119Y		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	119	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gggtctgcagcagctggacac	0.652													c|||	125	0.0249601	0.0923	0.0029	5008	,	,		17401	0.0		0.001	False		,,,				2504	0.0				p.C119Y		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.G356A						PASS	.						4.0	8.0	7.0					17																	39274212		643	1521	2164	SO:0001583	missense	653240	exon1			CTGCAGCAGCTGG	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.356G>A	17.37:g.39274212C>T	ENSP00000375232:p.Cys119Tyr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	37	0.313559	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	39	0.017857142857142856	36	0.07317073170731707	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	.	13.97	2.395614	0.42512	.	.	ENSG00000212721	ENST00000391413	T	0.03717	3.83	3.63	3.63	0.41609	.	.	.	.	.	T	0.01489	0.0048	H	0.95365	3.66	0.34837	D	0.740315	P	0.46395	0.877	P	0.54544	0.755	T	0.19063	-1.0317	9	0.72032	D	0.01	.	13.1597	0.59537	0.0:1.0:0.0:0.0	.	119	Q9BYQ6	KR411_HUMAN	Y	119	ENSP00000375232:C119Y	ENSP00000375232:C119Y	C	-	2	0	KRTAP4-11	36527738	0.060000	0.20803	0.929000	0.37066	0.073000	0.16967	0.773000	0.26661	1.757000	0.51966	0.514000	0.50259	TGC	C|0.982;T|0.018	0.018	strong		0.652	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
ANKRD33	341405	hgsc.bcm.edu	37	12	52282060	52282060	+	5'UTR	SNP	C	C	T	rs697634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52282060C>T	ENST00000340970.4	+	0	60				ANKRD33_ENST00000301190.6_Silent_p.R30R|ANKRD33_ENST00000538991.1_5'UTR|ANKRD33_ENST00000547119.1_3'UTR			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33						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)		TTGTGCTCCGCGGAGCCTGGG	0.567													C|||	1661	0.331669	0.149	0.451	5008	,	,		16569	0.4117		0.2952	False		,,,				2504	0.4489				p.R30R		Atlas-SNP	.											.	ANKRD33	33	.	0			c.C90T						PASS	.	C	,	681,3725	287.2+/-279.2	55,571,1577	101.0	93.0	95.0		,90	-4.7	0.0	12	dbSNP_86	95	2676,5924	429.8+/-356.3	396,1884,2020	no	utr-5,coding-synonymous	ANKRD33	NM_001130015.1,NM_182608.3	,	451,2455,3597	TT,TC,CC		31.1163,15.4562,25.8112	,	,30/453	52282060	3357,9649	2203	4300	6503	SO:0001623	5_prime_UTR_variant	341405	exon1			GCTCCGCGGAGCC		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.-312C>T	12.37:g.52282060C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	133	71	0.533835	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Silent	SNP	ENST00000340970.4	37	CCDS44892.1																																																																																			C|0.719;T|0.281	0.281	strong		0.567	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
CCDC150	284992	hgsc.bcm.edu	37	2	197521750	197521750	+	Missense_Mutation	SNP	G	G	A	rs34133636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:197521750G>A	ENST00000389175.4	+	4	601	c.466G>A	c.(466-468)Gaa>Aaa	p.E156K	CCDC150_ENST00000472405.2_Missense_Mutation_p.E53K|CCDC150_ENST00000423093.2_Intron|CCDC150_ENST00000272831.7_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	156			E -> K (in dbSNP:rs34133636).					p.E156K(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						GTTGCATCTCGAAGTTATGAA	0.478													G|||	528	0.105431	0.1929	0.0634	5008	,	,		21617	0.0238		0.0596	False		,,,				2504	0.1483				p.E156K		Atlas-SNP	.											CCDC150,NS,carcinoma,0,1	CCDC150	96	1	1	Substitution - Missense(1)	stomach(1)	c.G466A						PASS	.	G	LYS/GLU	629,3301		53,523,1389	75.0	76.0	76.0		466	3.9	1.0	2	dbSNP_126	76	443,7867		15,413,3727	yes	missense	CCDC150	NM_001080539.1	56	68,936,5116	AA,AG,GG		5.3309,16.0051,8.7582	probably-damaging	156/1102	197521750	1072,11168	1965	4155	6120	SO:0001583	missense	284992	exon4			CATCTCGAAGTTA		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.466G>A	2.37:g.197521750G>A	ENSP00000373827:p.Glu156Lys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	133	71	0.533835	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Missense_Mutation	SNP	ENST00000389175.4	37	CCDS46478.1	164	0.07509157509157509	73	0.1483739837398374	27	0.07458563535911603	18	0.03146853146853147	46	0.06068601583113457	G	13.24	2.178777	0.38511	0.160051	0.053309	ENSG00000144395	ENST00000389175;ENST00000536389;ENST00000472405	T;T	0.30182	1.54;1.54	4.78	3.88	0.44766	.	0.000000	0.64402	D	0.000002	T	0.00241	0.0007	M	0.62723	1.935	0.09310	P	0.9999999999999987	D;D	0.89917	0.975;1.0	P;D	0.80764	0.557;0.994	T	0.04752	-1.0929	9	0.22109	T	0.4	-6.3836	12.594	0.56459	0.0:0.1684:0.8315:0.0	rs34133636;rs60151852	156;156	Q8NCX0;F5H6M2	CC150_HUMAN;.	K	156;156;53	ENSP00000373827:E156K;ENSP00000441149:E53K	ENSP00000373827:E156K	E	+	1	0	CCDC150	197229995	1.000000	0.71417	0.964000	0.40570	0.014000	0.08584	4.205000	0.58466	1.199000	0.43173	0.655000	0.94253	GAA	G|0.924;A|0.076	0.076	strong		0.478	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539	
ZNF213	7760	hgsc.bcm.edu	37	16	3188789	3188789	+	Silent	SNP	G	G	A	rs35931391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3188789G>A	ENST00000396878.3	+	4	1042	c.567G>A	c.(565-567)acG>acA	p.T189T	ZNF213_ENST00000574902.1_Silent_p.T189T|ZNF213_ENST00000416391.2_Intron|ZNF213_ENST00000576416.1_Silent_p.T189T	NM_001134655.1|NM_004220.2	NP_001128127.1|NP_004211.1	O14771	ZN213_HUMAN	zinc finger protein 213	189					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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	16						CCGGAGAGACGACGGACACCT	0.542													G|||	274	0.0547125	0.2012	0.0101	5008	,	,		19201	0.0		0.001	False		,,,				2504	0.0				p.T189T		Atlas-SNP	.											.	ZNF213	36	.	0			c.G567A						PASS	.	G	,	709,3685	297.6+/-284.8	61,587,1549	66.0	63.0	64.0		567,567	-10.3	0.0	16	dbSNP_126	64	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous	ZNF213	NM_001134655.1,NM_004220.2	,	61,596,5840	AA,AG,GG		0.1047,16.1356,5.5256	,	189/460,189/460	3188789	718,12276	2197	4300	6497	SO:0001819	synonymous_variant	7760	exon4			AGAGACGACGGAC	AF017433	CCDS10495.1	16p13.3	2014-05-13	2007-02-20	2007-02-20	ENSG00000085644	ENSG00000085644		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13005	protein-coding gene	gene with protein product		608387				9653642, 10023065	Standard	NM_004220		Approved	CR53, ZKSCAN21, ZSCAN53	uc010uws.2	O14771	OTTHUMG00000177519	ENST00000396878.3:c.567G>A	16.37:g.3188789G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	112	62	0.553571	NM_004220	A8K1B9|B4DMG6|Q96IS1	Silent	SNP	ENST00000396878.3	37	CCDS10495.1																																																																																			G|0.949;A|0.051	0.051	strong		0.542	ZNF213-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437334.1	NM_004220	
DNAH14	127602	hgsc.bcm.edu	37	1	225339732	225339732	+	Missense_Mutation	SNP	C	C	T	rs115743416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225339732C>T	ENST00000445597.2	+	19	3685	c.3685C>T	c.(3685-3687)Cgt>Tgt	p.R1229C	DNAH14_ENST00000430092.1_Missense_Mutation_p.R1639C|DNAH14_ENST00000439375.2_Missense_Mutation_p.R1639C			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1229					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AAAAGAAATTCGTATCAATAT	0.333													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		21528	0.0		0.0	False		,,,				2504	0.0				p.R1639C		Atlas-SNP	.											DNAH14_ENST00000430092,colon,carcinoma,-1,2	DNAH14	300	2	0			c.C4915T						PASS	.	C	CYS/ARG	41,1343		0,41,651	279.0	248.0	257.0		4915	5.1	1.0	1	dbSNP_132	257	0,3182		0,0,1591	no	missense	DNAH14	NM_001373.1	180	0,41,2242	TT,TC,CC		0.0,2.9624,0.8979	probably-damaging	1639/4516	225339732	41,4525	692	1591	2283	SO:0001583	missense	127602	exon31			GAAATTCGTATCA	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.3685C>T	1.37:g.225339732C>T	ENSP00000409472:p.Arg1229Cys	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	19.94	3.920296	0.73098	0.029624	0.0	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375;ENST00000328556	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	6.03	5.13	0.70059	.	0.110231	0.34460	U	0.003951	T	0.14527	0.0351	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.03034	-1.1080	10	0.59425	D	0.04	.	14.0411	0.64676	0.0:0.9269:0.0:0.0731	.	1639	Q0VDD8-4	.	C	1229;1639;1639;736	ENSP00000409472:R1229C;ENSP00000414402:R1639C;ENSP00000392061:R1639C;ENSP00000332424:R736C	ENSP00000332424:R736C	R	+	1	0	DNAH14	223406355	0.000000	0.05858	0.998000	0.56505	0.924000	0.55760	0.521000	0.22893	1.568000	0.49683	0.603000	0.83216	CGT	C|0.993;T|0.007	0.007	strong		0.333	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
OR13C5	138799	hgsc.bcm.edu	37	9	107361449	107361449	+	Silent	SNP	T	T	C	rs146576115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361449T>C	ENST00000374779.2	-	1	339	c.246A>G	c.(244-246)ctA>ctG	p.L82L		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						GGAAGCTCACTAGCGTGGAGG	0.517													C|||	3407	0.680312	0.761	0.5937	5008	,	,		20749	0.9573		0.4225	False		,,,				2504	0.6125				p.L82L		Atlas-SNP	.											.	OR13C5	60	.	0			c.A246G						PASS	.						17.0	31.0	26.0					9																	107361449		2130	4279	6409	SO:0001819	synonymous_variant	138799	exon1			GCTCACTAGCGTG		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.246A>G	9.37:g.107361449T>C		Somatic	752	2	0.00265957		WXS	Illumina HiSeq	Phase_I	705	293	0.415603	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			.	.	weak		0.517	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
ELMO2	63916	hgsc.bcm.edu	37	20	45014804	45014804	+	Silent	SNP	G	G	A	rs201990540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:45014804G>A	ENST00000290246.6	-	9	830	c.636C>T	c.(634-636)gcC>gcT	p.A212A	ELMO2_ENST00000352077.2_Silent_p.A210A|ELMO2_ENST00000445496.2_Silent_p.A29A|ELMO2_ENST00000396391.1_Silent_p.A212A|ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000439931.2_Silent_p.A212A|ELMO2_ENST00000372176.1_Silent_p.A124A	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	212					apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				TGATTTCCTCGGCTATCTTCT	0.527													g|||	3	0.000599042	0.0015	0.0014	5008	,	,		19968	0.0		0.0	False		,,,				2504	0.0				p.A212A		Atlas-SNP	.											ELMO2,NS,carcinoma,-1,1	ELMO2	51	1	0			c.C636T						scavenged	.						135.0	124.0	128.0					20																	45014804		2203	4300	6503	SO:0001819	synonymous_variant	63916	exon8			TTCCTCGGCTATC	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.636C>T	20.37:g.45014804G>A		Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	111	5	0.045045	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Silent	SNP	ENST00000290246.6	37	CCDS13398.1																																																																																			G|0.998;A|0.002	0.002	strong		0.527	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086	
TEAD2	8463	hgsc.bcm.edu	37	19	49852070	49852070	+	Missense_Mutation	SNP	G	G	A	rs201393859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49852070G>A	ENST00000311227.2	-	8	715	c.625C>T	c.(625-627)Ccc>Tcc	p.P209S	TEAD2_ENST00000377214.4_Missense_Mutation_p.P212S|TEAD2_ENST00000539846.1_Missense_Mutation_p.P81S|TEAD2_ENST00000601519.1_Missense_Mutation_p.P212S|TEAD2_ENST00000593945.1_Missense_Mutation_p.P213S|TEAD2_ENST00000598810.1_Missense_Mutation_p.P213S|TEAD2_ENST00000598397.1_5'UTR	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	209	Pro-rich.|Transcriptional activation. {ECO:0000255}.				gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		GTAGGTGGGGGCAGGGGTGAG	0.577													G|||	35	0.00698882	0.0265	0.0	5008	,	,		9950	0.0		0.0	False		,,,				2504	0.0				p.P213S		Atlas-SNP	.											.	TEAD2	70	.	0			c.C637T						PASS	.	G	SER/PRO	94,4128		2,90,2019	11.0	14.0	13.0		625	3.6	1.0	19		13	2,8324		0,2,4161	yes	missense	TEAD2	NM_003598.1	74	2,92,6180	AA,AG,GG		0.024,2.2264,0.7651	benign	209/448	49852070	96,12452	2111	4163	6274	SO:0001583	missense	8463	exon9			GTGGGGGCAGGGG	X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.625C>T	19.37:g.49852070G>A	ENSP00000310701:p.Pro209Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	127	57	0.448819	NM_001256660	B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Missense_Mutation	SNP	ENST00000311227.2	37	CCDS12761.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	5.217	0.225622	0.09916	0.022264	2.4E-4	ENSG00000074219	ENST00000311227;ENST00000377214;ENST00000539846	T;T;T	0.34275	1.37;1.37;1.37	5.73	3.58	0.41010	.	0.229512	0.31031	N	0.008399	T	0.08980	0.0222	N	0.04148	-0.265	0.48975	D	0.999734	B;B;B	0.16166	0.01;0.016;0.006	B;B;B	0.22753	0.018;0.041;0.018	T	0.04930	-1.0917	10	0.30854	T	0.27	-21.1627	11.4865	0.50356	0.1569:0.0:0.8431:0.0	.	81;209;212	B4DTJ6;Q15562;Q8NA25	.;TEAD2_HUMAN;.	S	209;212;81	ENSP00000310701:P209S;ENSP00000366419:P212S;ENSP00000437928:P81S	ENSP00000310701:P209S	P	-	1	0	TEAD2	54543882	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	5.441000	0.66569	1.577000	0.49804	-0.150000	0.13652	CCC	G|0.995;A|0.005	0.005	strong		0.577	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465465.1	NM_003598	
GPRIN3	285513	hgsc.bcm.edu	37	4	90168945	90168945	+	Missense_Mutation	SNP	A	A	C	rs34322172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:90168945A>C	ENST00000609438.1	-	2	2835	c.2317T>G	c.(2317-2319)Tct>Gct	p.S773A	GPRIN3_ENST00000333209.4_Missense_Mutation_p.S773A	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	773										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		TCTAACACAGAAGACGGGGCA	0.463													A|||	34	0.00678914	0.025	0.0014	5008	,	,		17083	0.0		0.0	False		,,,				2504	0.0				p.S773A		Atlas-SNP	.											.	GPRIN3	90	.	0			c.T2317G						PASS	.	A	ALA/SER	121,4285	90.2+/-128.9	3,115,2085	91.0	97.0	95.0		2317	4.2	0.0	4	dbSNP_126	95	0,8600		0,0,4300	yes	missense	GPRIN3	NM_198281.2	99	3,115,6385	CC,CA,AA		0.0,2.7463,0.9303	probably-damaging	773/777	90168945	121,12885	2203	4300	6503	SO:0001583	missense	285513	exon2			ACACAGAAGACGG	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.2317T>G	4.37:g.90168945A>C	ENSP00000476603:p.Ser773Ala	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	183	93	0.508197	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	A	7.014	0.557400	0.13436	0.027463	0.0	ENSG00000185477	ENST00000333209	T	0.15256	2.44	5.45	4.24	0.50183	.	0.261257	0.20448	N	0.092147	T	0.04543	0.0124	N	0.22421	0.69	0.31631	N	0.649051	B	0.27997	0.197	B	0.31812	0.136	T	0.05616	-1.0874	10	0.87932	D	0	-8.6401	11.9204	0.52789	0.7247:0.2753:0.0:0.0	rs34322172	773	Q6ZVF9	GRIN3_HUMAN	A	773	ENSP00000328672:S773A	ENSP00000328672:S773A	S	-	1	0	GPRIN3	90387968	1.000000	0.71417	0.032000	0.17829	0.031000	0.12232	4.535000	0.60629	1.051000	0.40369	0.533000	0.62120	TCT	A|0.992;C|0.008	0.008	strong		0.463	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
MLKL	197259	hgsc.bcm.edu	37	16	74709233	74709233	+	Missense_Mutation	SNP	C	C	A	rs144526386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:74709233C>A	ENST00000306247.7	-	4	944	c.605G>T	c.(604-606)gGc>gTc	p.G202V	MLKL_ENST00000308807.7_Intron	NM_001142497.1	NP_001135969.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						ACTGGCTGAGCCAGTCTTCAC	0.493													C|||	51	0.0101837	0.0023	0.0144	5008	,	,		19105	0.0		0.0209	False		,,,				2504	0.0174				p.G202V		Atlas-SNP	.											.	MLKL	51	.	0			c.G605T						PASS	.	C	VAL/GLY,	17,4379	23.3+/-48.9	0,17,2181	113.0	108.0	110.0		605,	-1.0	0.0	16	dbSNP_134	110	162,8438	76.3+/-139.0	2,158,4140	yes	missense,intron	MLKL	NM_001142497.1,NM_152649.2	109,	2,175,6321	AA,AC,CC		1.8837,0.3867,1.3773	,	202/264,	74709233	179,12817	2198	4300	6498	SO:0001583	missense	197259	exon4			GCTGAGCCAGTCT	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000306247.7:c.605G>T	16.37:g.74709233C>A	ENSP00000303118:p.Gly202Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_001142497		Missense_Mutation	SNP	ENST00000306247.7	37	CCDS45528.1	23	0.010531135531135532	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	8.923	0.961462	0.18583	0.003867	0.018837	ENSG00000168404	ENST00000306247	T	0.12147	2.71	4.96	-1.05	0.10036	.	.	.	.	.	T	0.14313	0.0346	.	.	.	0.09310	N	1	D	0.67145	0.996	D	0.65573	0.936	T	0.07501	-1.0769	8	0.48119	T	0.1	.	8.2986	0.32001	0.0:0.4852:0.0:0.5148	.	202	Q8NB16-2	.	V	202	ENSP00000303118:G202V	ENSP00000303118:G202V	G	-	2	0	MLKL	73266734	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.620000	0.05565	-0.228000	0.09869	-0.374000	0.07098	GGC	C|0.986;A|0.014	0.014	strong		0.493	MLKL-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436402.1	NM_152649	
TMEM201	199953	hgsc.bcm.edu	37	1	9671935	9671935	+	Silent	SNP	C	C	T	rs4073292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9671935C>T	ENST00000340381.6	+	10	1899	c.1890C>T	c.(1888-1890)gcC>gcT	p.A630A	TMEM201_ENST00000377376.4_Silent_p.A606A	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	630					fibroblast migration (GO:0010761)|nuclear migration (GO:0007097)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				lung(3)|upper_aerodigestive_tract(1)	4	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)		CGGAGGAGGCCGCCACCTGGA	0.642													C|||	355	0.0708866	0.2564	0.0202	5008	,	,		15597	0.0		0.002	False		,,,				2504	0.0				p.A630A		Atlas-SNP	.											.	TMEM201	63	.	0			c.C1890T						PASS	.	C		298,1086		35,228,429	21.0	21.0	21.0		1890	-2.5	0.0	1	dbSNP_108	21	4,3178		0,4,1587	no	coding-synonymous	TMEM201	NM_001130924.2		35,232,2016	TT,TC,CC		0.1257,21.5318,6.6141		630/667	9671935	302,4264	692	1591	2283	SO:0001819	synonymous_variant	199953	exon10			GGAGGCCGCCACC		CCDS30579.1, CCDS44055.1, CCDS44055.2	1p36.22	2009-11-06			ENSG00000188807	ENSG00000188807			33719	protein-coding gene	gene with protein product							Standard	NM_001130924		Approved	RP13-15M17.2, NET5	uc021ofy.1	Q5SNT2	OTTHUMG00000057457	ENST00000340381.6:c.1890C>T	1.37:g.9671935C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_001130924	B9EH90|Q5SNT3	Silent	SNP	ENST00000340381.6	37	CCDS44055.2	154	0.07051282051282051	145	0.29471544715447157	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	C	0.113	-1.136063	0.01742	0.215318	0.001257	ENSG00000188807	ENST00000416541	.	.	.	5.28	-2.46	0.06461	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.34304	-0.9834	3	.	.	.	-6.4317	7.9697	0.30119	0.0:0.4376:0.1547:0.4077	rs4073292;rs17034220;rs4073292	.	.	.	C	516	.	.	R	+	1	0	TMEM201	9594522	0.000000	0.05858	0.011000	0.14972	0.058000	0.15608	-0.270000	0.08584	-0.319000	0.08652	-1.134000	0.01955	CGC	C|0.934;T|0.066	0.066	strong		0.642	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866	
LRRC4C	57689	hgsc.bcm.edu	37	11	40137543	40137543	+	Silent	SNP	T	T	C	rs2953310	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:40137543T>C	ENST00000278198.2	-	2	2263	c.300A>G	c.(298-300)agA>agG	p.R100R	LRRC4C_ENST00000528697.1_Silent_p.R100R|LRRC4C_ENST00000530763.1_Silent_p.R100R|LRRC4C_ENST00000527150.1_Silent_p.R100R			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	100					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)		p.R100R(1)		NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TTTCCAAGTGTCTCAAGTGCT	0.473													C|||	2501	0.499401	0.7027	0.5058	5008	,	,		19910	0.6052		0.3728	False		,,,				2504	0.2413				p.R100R		Atlas-SNP	.											LRRC4C,NS,carcinoma,0,1	LRRC4C	190	1	1	Substitution - coding silent(1)	stomach(1)	c.A300G						scavenged	.	C		2917,1489	477.0+/-357.8	981,955,267	96.0	90.0	92.0		300	3.9	1.0	11	dbSNP_101	92	3562,5038	629.9+/-398.3	730,2102,1468	no	coding-synonymous	LRRC4C	NM_020929.1		1711,3057,1735	CC,CT,TT		41.4186,33.7948,49.8155		100/641	40137543	6479,6527	2203	4300	6503	SO:0001819	synonymous_variant	57689	exon7			CAAGTGTCTCAAG	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.300A>G	11.37:g.40137543T>C		Somatic	167	1	0.00598802		WXS	Illumina HiSeq	Phase_I	161	81	0.503106	NM_001258419	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	37	CCDS31464.1																																																																																			T|0.478;C|0.522	0.522	strong		0.473	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
SLC7A4	6545	hgsc.bcm.edu	37	22	21386019	21386019	+	Missense_Mutation	SNP	G	G	A	rs2072550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21386019G>A	ENST00000382932.2	-	2	150	c.83C>T	c.(82-84)aCc>aTc	p.T28I	AC002472.11_ENST00000450652.1_RNA|MIR649_ENST00000384843.1_RNA|SLC7A4_ENST00000403586.1_Missense_Mutation_p.T28I	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	28			T -> I (in dbSNP:rs2072550). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.		basic amino acid transport (GO:0015802)|cellular amino acid metabolic process (GO:0006520)|transport (GO:0006810)	integral component of membrane (GO:0016021)	basic amino acid transmembrane transporter activity (GO:0015174)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CGTCTCCATGGTGGAGTCCTC	0.657													G|||	1653	0.330072	0.3396	0.2507	5008	,	,		16256	0.5446		0.1093	False		,,,				2504	0.3793				p.T28I		Atlas-SNP	.											SLC7A4,NS,carcinoma,0,1	SLC7A4	50	1	0			c.C83T						PASS	.	G	ILE/THR	1310,3096	425.9+/-341.0	193,924,1086	40.0	42.0	41.0		83	-2.4	0.0	22	dbSNP_96	41	877,7723	196.6+/-241.5	54,769,3477	yes	missense	SLC7A4	NM_004173.2	89	247,1693,4563	AA,AG,GG		10.1977,29.7322,16.8153	benign	28/636	21386019	2187,10819	2203	4300	6503	SO:0001583	missense	6545	exon2			TCCATGGTGGAGT	AJ000730	CCDS33608.1	22q11.21	2013-07-19	2013-07-19		ENSG00000099960	ENSG00000099960		"""Solute carriers"""	11062	protein-coding gene	gene with protein product		603752	"""solute carrier family 7 (cationic amino acid transporter, y+ system), member 4"", ""solute carrier family 7 (orphan transporter), member 4"""			9598310, 11665818	Standard	NM_004173		Approved	HCAT3, CAT-4, VH	uc002zud.3	O43246	OTTHUMG00000150896	ENST00000382932.2:c.83C>T	22.37:g.21386019G>A	ENSP00000372390:p.Thr28Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Missense_Mutation	SNP	ENST00000382932.2	37	CCDS33608.1	589	0.2696886446886447	149	0.30284552845528456	80	0.22099447513812154	285	0.4982517482517482	75	0.09894459102902374	G	10.19	1.282348	0.23392	0.297322	0.101977	ENSG00000099960	ENST00000403586;ENST00000382932;ENST00000426145	D;D;T	0.85955	-2.05;-2.05;1.5	5.37	-2.36	0.06663	.	0.511281	0.22093	N	0.064732	T	0.00012	0.0000	M	0.74258	2.255	0.80722	P	0.0	B	0.22683	0.073	B	0.23018	0.043	T	0.40831	-0.9542	9	0.38643	T	0.18	.	11.613	0.51072	0.1239:0.6088:0.2673:0.0	rs2072550;rs61412131;rs2072550	28	O43246	CTR4_HUMAN	I	28	ENSP00000384278:T28I;ENSP00000372390:T28I;ENSP00000408727:T28I	ENSP00000372390:T28I	T	-	2	0	SLC7A4	19716019	1.000000	0.71417	0.006000	0.13384	0.685000	0.39939	2.623000	0.46435	-0.167000	0.10871	-0.479000	0.04858	ACC	G|0.786;A|0.214	0.214	strong		0.657	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173	
CNDP1	84735	hgsc.bcm.edu	37	18	72226578	72226578	+	Silent	SNP	C	C	A	rs9807352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:72226578C>A	ENST00000358821.3	+	3	402	c.174C>A	c.(172-174)gcC>gcA	p.A58A	CNDP1_ENST00000585136.1_3'UTR|RP11-231E4.3_ENST00000583702.1_RNA|CNDP1_ENST00000582365.1_Silent_p.A15A	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	58						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)		AGTGGGTGGCCATCGAGAGCG	0.637													C|||	344	0.0686901	0.1649	0.0216	5008	,	,		16230	0.0635		0.0278	False		,,,				2504	0.0194				p.A58A	Melanoma(32;1029 1042 25286 38395 44237)	Atlas-SNP	.											.	CNDP1	98	.	0			c.C174A						PASS	.	C		608,3798	266.8+/-267.5	43,522,1638	97.0	82.0	87.0		174	-2.8	0.0	18	dbSNP_119	87	190,8410	83.1+/-145.7	2,186,4112	no	coding-synonymous	CNDP1	NM_032649.5		45,708,5750	AA,AC,CC		2.2093,13.7994,6.1356		58/508	72226578	798,12208	2203	4300	6503	SO:0001819	synonymous_variant	84735	exon3			GGTGGCCATCGAG		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.174C>A	18.37:g.72226578C>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	41	0.621212	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Silent	SNP	ENST00000358821.3	37	CCDS12007.1																																																																																			C|0.934;A|0.066	0.066	strong		0.637	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
ZNF195	7748	hgsc.bcm.edu	37	11	3383015	3383015	+	Missense_Mutation	SNP	G	G	A	rs7125523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:3383015G>A	ENST00000399602.4	-	4	457	c.331C>T	c.(331-333)Cgt>Tgt	p.R111C	ZNF195_ENST00000354599.6_Intron|ZNF195_ENST00000438262.2_Intron|ZNF195_ENST00000005082.9_Missense_Mutation_p.R111C|ZNF195_ENST00000526601.1_Missense_Mutation_p.R115C|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000429541.2_Intron|ZNF195_ENST00000343338.7_Intron	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	111	Spacer.				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(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		ggctgggcacggtggttcaca	0.502													g|||	110	0.0219649	0.0794	0.0072	5008	,	,		18477	0.0		0.0	False		,,,				2504	0.0				p.R115C		Atlas-SNP	.											.	ZNF195	77	.	0			c.C343T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,,,	87,1297		0,87,605	184.0	176.0	179.0		331,331,343,,,	-0.4	0.0	11	dbSNP_116	179	4,3178		0,4,1587	yes	missense,missense,missense,intron,intron,intron	ZNF195	NM_001130519.2,NM_001130520.2,NM_001242841.1,NM_001242842.1,NM_001242843.1,NM_007152.4	180,180,180,,,	0,91,2192	AA,AG,GG		0.1257,6.2861,1.993	possibly-damaging,possibly-damaging,possibly-damaging,,,	111/607,111/630,115/611,,,	3383015	91,4475	692	1591	2283	SO:0001583	missense	7748	exon5			GGGCACGGTGGTT		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"""Zinc fingers, C2H2-type"", ""-"""	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.331C>T	11.37:g.3383015G>A	ENSP00000382511:p.Arg111Cys	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_001242841	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Missense_Mutation	SNP	ENST00000399602.4	37	CCDS44522.1	43	0.019688644688644688	39	0.07926829268292683	4	0.011049723756906077	0	0.0	0	0.0	g	0.950	-0.706656	0.03230	0.062861	0.001257	ENSG00000005801	ENST00000399602;ENST00000005082;ENST00000526601;ENST00000533036;ENST00000534569	T;T;T;T;T	0.14766	5.12;5.12;5.12;5.12;2.48	0.225	-0.451	0.12214	.	.	.	.	.	T	0.00271	0.0008	N	0.25992	0.78	0.09310	N	1	B;B;P	0.50710	0.0;0.0;0.938	B;B;B	0.22753	0.0;0.0;0.041	T	0.33727	-0.9857	8	0.56958	D	0.05	.	.	.	.	rs7125523	115;111;111	O14628-6;O14628-5;O14628	.;.;ZN195_HUMAN	C	111;111;115;130;115	ENSP00000382511:R111C;ENSP00000005082:R111C;ENSP00000435828:R115C;ENSP00000433911:R130C;ENSP00000437265:R115C	ENSP00000005082:R111C	R	-	1	0	ZNF195	3339591	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-0.653000	0.05360	-1.864000	0.01148	-1.842000	0.00583	CGT	G|0.980;A|0.020	0.020	strong		0.502	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2		
IFI16	3428	hgsc.bcm.edu	37	1	159024668	159024668	+	Missense_Mutation	SNP	A	A	T	rs6940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159024668A>T	ENST00000295809.7	+	12	2590	c.2335A>T	c.(2335-2337)Act>Tct	p.T779S	IFI16_ENST00000340979.6_Missense_Mutation_p.T667S|IFI16_ENST00000448393.2_Missense_Mutation_p.T667S|IFI16_ENST00000430894.2_Missense_Mutation_p.T727S|IFI16_ENST00000368131.4_Missense_Mutation_p.T723S|IFI16_ENST00000359709.3_Missense_Mutation_p.T723S|IFI16_ENST00000368132.3_Missense_Mutation_p.T723S			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	779			T -> S (in dbSNP:rs6940).		activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					AAGTATGGAAACTTCACCAGA	0.363													A|||	1131	0.225839	0.2595	0.062	5008	,	,		18370	0.3482		0.1193	False		,,,				2504	0.2802				p.T723S		Atlas-SNP	.											.	IFI16	111	.	0			c.A2167T						PASS	.	A	SER/THR,SER/THR	1018,3388	359.6+/-314.9	138,742,1323	105.0	98.0	100.0		2167,2167	3.5	0.0	1	dbSNP_52	100	1136,7464	226.1+/-261.9	71,994,3235	yes	missense,missense	IFI16	NM_001206567.1,NM_005531.2	58,58	209,1736,4558	TT,TA,AA		13.2093,23.1049,16.5616	possibly-damaging,possibly-damaging	723/730,723/730	159024668	2154,10852	2203	4300	6503	SO:0001583	missense	3428	exon11			ATGGAAACTTCAC	M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.2335A>T	1.37:g.159024668A>T	ENSP00000295809:p.Thr779Ser	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	298	297	0.996644	NM_001206567	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Missense_Mutation	SNP	ENST00000295809.7	37		403|403	0.18452380952380953|0.18452380952380953	146|146	0.2967479674796748|0.2967479674796748	21|21	0.058011049723756904|0.058011049723756904	150|150	0.26223776223776224|0.26223776223776224	86|86	0.11345646437994723|0.11345646437994723	A|A	15.88|15.88	2.964063|2.964063	0.53507|0.53507	0.231049|0.231049	0.132093|0.132093	ENSG00000163565|ENSG00000163565	ENST00000448393|ENST00000359709;ENST00000295809;ENST00000340979;ENST00000368131;ENST00000368132;ENST00000430894	.|T;T;T;T;T	.|0.04406	.|3.63;3.65;3.65;3.65;3.64	3.51|3.51	3.51|3.51	0.40186|0.40186	.|.	.|.	.|.	.|.	.|.	T|T	0.03695|0.03695	0.0105|0.0105	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	P|P	0.0|0.0	.|D;D;D	.|0.89917	.|0.958;1.0;1.0	.|P;D;D	.|0.83275	.|0.622;0.996;0.996	T|T	0.48614|0.48614	-0.9020|-0.9020	4|8	.|0.15066	.|T	.|0.55	.|.	8.7275|8.7275	0.34478|0.34478	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs6940;rs1057076;rs2070268;rs3197685;rs3737524;rs52792467;rs6940|rs6940;rs1057076;rs2070268;rs3197685;rs3737524;rs52792467;rs6940	.|727;667;723	.|E7EPR3;Q16666-3;Q16666-2	.|.;.;.	N|S	487|408;779;667;723;723;727	.|ENSP00000295809:T779S;ENSP00000342741:T667S;ENSP00000357113:T723S;ENSP00000357114:T723S;ENSP00000394935:T727S	.|ENSP00000295809:T779S	K|T	+|+	3|1	2|0	IFI16|IFI16	157291292|157291292	0.055000|0.055000	0.20627|0.20627	0.036000|0.036000	0.18154|0.18154	0.059000|0.059000	0.15707|0.15707	1.085000|1.085000	0.30840|0.30840	1.815000|1.815000	0.52974|0.52974	0.459000|0.459000	0.35465|0.35465	AAA|ACT	A|0.827;T|0.173	0.173	strong		0.363	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1	NM_005531	
RAB11FIP5	26056	hgsc.bcm.edu	37	2	73339675	73339675	+	Silent	SNP	C	C	T	rs143108301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73339675C>T	ENST00000258098.6	-	1	471	c.231G>A	c.(229-231)ctG>ctA	p.L77L	RP11-44N22.3_ENST00000608612.1_RNA	NM_015470.2	NP_056285.1	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	77	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cellular response to acidic pH (GO:0071468)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|regulation of protein localization to cell surface (GO:2000008)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)			biliary_tract(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	23						CCCCCGGCGGCAGCTCGAAGG	0.736													C|||	2	0.000399361	0.0008	0.0	5008	,	,		10052	0.001		0.0	False		,,,				2504	0.0				p.L77L		Atlas-SNP	.											.	RAB11FIP5	66	.	0			c.G231A						PASS	.	C		4,4354		0,4,2175	11.0	10.0	10.0		231	1.9	1.0	2	dbSNP_134	10	0,8504		0,0,4252	no	coding-synonymous	RAB11FIP5	NM_015470.2		0,4,6427	TT,TC,CC		0.0,0.0918,0.0311		77/654	73339675	4,12858	2179	4252	6431	SO:0001819	synonymous_variant	26056	exon1			CGGCGGCAGCTCG	AF334812	CCDS1923.1	2p13	2008-02-05			ENSG00000135631	ENSG00000135631			24845	protein-coding gene	gene with protein product		605536				10048485, 11163216	Standard	NM_015470		Approved	GAF1, KIAA0857, RIP11, pp75	uc002sis.4	Q9BXF6	OTTHUMG00000129779	ENST00000258098.6:c.231G>A	2.37:g.73339675C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_015470	O94939|Q9P0M1	Silent	SNP	ENST00000258098.6	37	CCDS1923.1																																																																																			C|1.000;T|0.000	0.000	weak		0.736	RAB11FIP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251995.1	NM_015470	
AOC1	26	hgsc.bcm.edu	37	7	150553605	150553605	+	Missense_Mutation	SNP	C	C	T	rs10156191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150553605C>T	ENST00000493429.1	+	4	631	c.47C>T	c.(46-48)aCg>aTg	p.T16M	AOC1_ENST00000360937.4_Missense_Mutation_p.T16M|AOC1_ENST00000416793.2_Missense_Mutation_p.T16M|AOC1_ENST00000467291.1_Missense_Mutation_p.T16M			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	16			T -> M (in dbSNP:rs10156191). {ECO:0000269|Ref.4}.		amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	ATGCTGCAGACGGCCATGGCG	0.602													T|||	1567	0.312899	0.5613	0.2464	5008	,	,		18928	0.122		0.2654	False		,,,				2504	0.2699				p.T16M		Atlas-SNP	.											.	ABP1	92	.	0			c.C47T						PASS	.	T	MET/THR	1966,1902		502,962,470	31.0	33.0	32.0		47	-0.6	0.0	7	dbSNP_119	32	2203,6057		270,1663,2197	yes	missense	ABP1	NM_001091.2	81	772,2625,2667	TT,TC,CC		26.6707,49.1727,34.375	benign	16/752	150553605	4169,7959	1934	4130	6064	SO:0001583	missense	26	exon2			TGCAGACGGCCAT	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.47C>T	7.37:g.150553605C>T	ENSP00000418614:p.Thr16Met	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	37	CCDS43679.1	627	0.28708791208791207	274	0.556910569105691	91	0.2513812154696133	67	0.11713286713286714	195	0.25725593667546176	T	9.043	0.990180	0.18966	0.508273	0.266707	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000460213;ENST00000360937;ENST00000416793;ENST00000483043	T;T;T;T;T;T	0.11821	4.4;4.4;2.74;4.4;4.4;3.39	4.84	-0.636	0.11508	Copper amine oxidase, N2/N3-terminal (1);	1.880150	0.03074	N	0.157613	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.47114	-0.9142	9	0.32370	T	0.25	1.8438	10.1427	0.42744	0.0:0.501:0.0:0.499	rs10156191;rs10278856;rs10156191	16;16	C9J690;P19801	.;ABP1_HUMAN	M	16	ENSP00000418614:T16M;ENSP00000418328:T16M;ENSP00000418557:T16M;ENSP00000354193:T16M;ENSP00000411613:T16M;ENSP00000417392:T16M	ENSP00000354193:T16M	T	+	2	0	ABP1	150184538	0.007000	0.16637	0.000000	0.03702	0.019000	0.09904	0.182000	0.16900	-0.572000	0.06006	-1.062000	0.02293	ACG	C|0.708;T|0.292	0.292	strong		0.602	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
PLIN4	729359	hgsc.bcm.edu	37	19	4508960	4508960	+	Silent	SNP	C	C	T	rs112037560	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4508960C>T	ENST00000301286.3	-	4	3479	c.3480G>A	c.(3478-3480)ctG>ctA	p.L1160L		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1160						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						GGGAGGCAGCCAGCTGAGCTG	0.642													C|||	207	0.0413339	0.1021	0.0159	5008	,	,		16148	0.0		0.0129	False		,,,				2504	0.0491				p.L1160L		Atlas-SNP	.											.	PLIN4	191	.	0			c.G3480A						PASS	.	C		356,3550		17,322,1614	26.0	30.0	29.0		3480	2.9	1.0	19	dbSNP_132	29	122,8142		1,120,4011	no	coding-synonymous	PLIN4	NM_001080400.1		18,442,5625	TT,TC,CC		1.4763,9.1142,3.9277		1160/1358	4508960	478,11692	1953	4132	6085	SO:0001819	synonymous_variant	729359	exon4			GGCAGCCAGCTGA	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.3480G>A	19.37:g.4508960C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	43	26	0.604651	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			C|0.974;T|0.026	0.026	strong		0.642	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
TF	7018	hgsc.bcm.edu	37	3	133487000	133487000	+	Silent	SNP	C	C	T	rs8177286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133487000C>T	ENST00000402696.3	+	13	2099	c.1614C>T	c.(1612-1614)ggC>ggT	p.G538G	TF_ENST00000264998.3_Silent_p.G411G	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	538	Transferrin-like 2. {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)	GCTACACAGGCGCTTTCAGGT	0.433													C|||	66	0.0131789	0.0461	0.0043	5008	,	,		19064	0.002		0.0	False		,,,				2504	0.0				p.G538G		Atlas-SNP	.											.	TF	116	.	0			c.C1614T						PASS	.	C		168,4238	111.6+/-149.8	3,162,2038	69.0	72.0	71.0		1614	-3.7	0.6	3	dbSNP_117	71	0,8600		0,0,4300	no	coding-synonymous	TF	NM_001063.3		3,162,6338	TT,TC,CC		0.0,3.813,1.2917		538/699	133487000	168,12838	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon13			CACAGGCGCTTTC		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.1614C>T	3.37:g.133487000C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			C|0.987;T|0.013	0.013	strong		0.433	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
PKHD1	5314	hgsc.bcm.edu	37	6	51720838	51720838	+	Silent	SNP	T	T	C	rs9349603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:51720838T>C	ENST00000371117.3	-	49	8039	c.7764A>G	c.(7762-7764)ttA>ttG	p.L2588L	PKHD1_ENST00000340994.4_Silent_p.L2588L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2588					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)					CAGTCATGGTTAAATCATAAG	0.383													T|||	2699	0.538938	0.4523	0.5634	5008	,	,		20327	0.8383		0.3191	False		,,,				2504	0.5562				p.L2588L		Atlas-SNP	.											.	PKHD1	927	.	0			c.A7764G						PASS	.	T	,	1903,2503	545.2+/-376.7	428,1047,728	142.0	147.0	146.0		7764,7764	3.8	1.0	6	dbSNP_119	146	2709,5891	433.8+/-357.5	466,1777,2057	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	894,2824,2785	CC,CT,TT		31.5,43.1911,35.4606	,	2588/4075,2588/3397	51720838	4612,8394	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon49			CATGGTTAAATCA	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.7764A>G	6.37:g.51720838T>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	166	74	0.445783	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			T|0.577;C|0.423	0.423	strong		0.383	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
FNDC1	84624	hgsc.bcm.edu	37	6	159654408	159654408	+	Missense_Mutation	SNP	G	G	A	rs73799344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159654408G>A	ENST00000297267.9	+	11	3064	c.2864G>A	c.(2863-2865)aGc>aAc	p.S955N	FNDC1_ENST00000340366.6_Missense_Mutation_p.S892N	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	955					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)		GTTCAACAGAGCACAGACGCG	0.617													G|||	259	0.0517173	0.1846	0.0216	5008	,	,		18211	0.0		0.0	False		,,,				2504	0.0				p.S955N		Atlas-SNP	.											.	FNDC1	250	.	0			c.G2864A						PASS	.	G	ASN/SER	784,3552		68,648,1452	57.0	68.0	64.0		2864	3.8	0.1	6	dbSNP_130	64	8,8520		0,8,4256	yes	missense	FNDC1	NM_032532.2	46	68,656,5708	AA,AG,GG		0.0938,18.0812,6.1567	benign	955/1895	159654408	792,12072	2168	4264	6432	SO:0001583	missense	84624	exon11			AACAGAGCACAGA	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.2864G>A	6.37:g.159654408G>A	ENSP00000297267:p.Ser955Asn	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	107	0.04899267399267399	99	0.20121951219512196	8	0.022099447513812154	0	0.0	0	0.0	G	16.37	3.104157	0.56291	0.180812	9.38E-4	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.10005	2.92;3.77	3.81	3.81	0.43845	.	0.352689	0.24945	N	0.034358	T	0.06735	0.0172	L	0.29908	0.895	0.58432	P	1.999999999946489E-6	D;P	0.57257	0.979;0.734	P;B	0.56563	0.801;0.398	T	0.27839	-1.0062	9	0.13108	T	0.6	-19.0686	11.4852	0.50350	0.0:0.0:1.0:0.0	.	892;955	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	N	955;892	ENSP00000297267:S955N;ENSP00000342460:S892N	ENSP00000297267:S955N	S	+	2	0	FNDC1	159574398	0.523000	0.26274	0.140000	0.22221	0.635000	0.38103	1.701000	0.37825	2.423000	0.82170	0.561000	0.74099	AGC	G|0.959;A|0.041	0.041	strong		0.617	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
MRPL9	65005	hgsc.bcm.edu	37	1	151733335	151733335	+	Missense_Mutation	SNP	T	T	G	rs8480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151733335T>G	ENST00000368830.3	-	6	713	c.629A>C	c.(628-630)gAa>gCa	p.E210A	OAZ3_ENST00000479764.1_5'Flank|MRPL9_ENST00000368829.3_Missense_Mutation_p.E176A|MRPL9_ENST00000467306.1_5'UTR|RP11-98D18.15_ENST00000601684.1_RNA|OAZ3_ENST00000315067.8_5'Flank|OAZ3_ENST00000453029.2_5'Flank|RP11-98D18.3_ENST00000512280.1_RNA|OAZ3_ENST00000321531.5_5'Flank	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	210			E -> A (in dbSNP:rs8480). {ECO:0000269|PubMed:11279069}.		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)			GATAGGCTCTTCTGGTAACTT	0.393													T|||	2564	0.511981	0.6936	0.5951	5008	,	,		14847	0.4365		0.4642	False		,,,				2504	0.3344				p.E210A		Atlas-SNP	.											.	MRPL9	21	.	0			c.A629C						PASS	.	T	ALA/GLU	2777,1629	660.1+/-400.7	871,1035,297	94.0	88.0	90.0		629	5.3	1.0	1	dbSNP_52	90	4111,4489	564.0+/-388.2	970,2171,1159	yes	missense	MRPL9	NM_031420.2	107	1841,3206,1456	GG,GT,TT		47.8023,36.9723,47.0398	probably-damaging	210/268	151733335	6888,6118	2203	4300	6503	SO:0001583	missense	65005	exon6			GGCTCTTCTGGTA	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.629A>C	1.37:g.151733335T>G	ENSP00000357823:p.Glu210Ala	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	25	14	0.56	NM_031420	B2RD99|Q5SZR2|Q9BSW8	Missense_Mutation	SNP	ENST00000368830.3	37	CCDS1003.1	1138	0.5210622710622711	347	0.7052845528455285	211	0.5828729281767956	231	0.40384615384615385	349	0.4604221635883905	T	18.44	3.625299	0.66901	0.630277	0.478023	ENSG00000143436	ENST00000368830;ENST00000368829	T;T	0.36520	1.25;1.41	5.27	5.27	0.74061	.	0.198238	0.36234	N	0.002702	T	0.31827	0.0809	M	0.70275	2.135	0.25674	P	0.9858646	D	0.54772	0.968	P	0.48552	0.581	T	0.32428	-0.9907	9	0.40728	T	0.16	-16.0534	11.5085	0.50481	0.0:0.0:0.0:1.0	rs8480;rs1046989;rs16939319;rs52833399;rs59220170;rs8480	210	Q9BYD2	RM09_HUMAN	A	210;176	ENSP00000357823:E210A;ENSP00000357822:E176A	ENSP00000357822:E176A	E	-	2	0	MRPL9	149999959	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.818000	0.62657	2.198000	0.70561	0.533000	0.62120	GAA	T|0.485;G|0.515	0.515	strong		0.393	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2	NM_031420	
OR5D14	219436	hgsc.bcm.edu	37	11	55563602	55563602	+	Missense_Mutation	SNP	G	G	A	rs68042892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55563602G>A	ENST00000335605.1	+	1	571	c.571G>A	c.(571-573)Ggc>Agc	p.G191S		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G191S(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)				CTCTGTGTCTGGCTCTGATAT	0.438													N|||	525	0.104832	0.1884	0.0461	5008	,	,		20460	0.0813		0.0924	False		,,,				2504	0.0706				p.G191S		Atlas-SNP	.											OR5D14,NS,carcinoma,0,1	OR5D14	116	1	1	Substitution - Missense(1)	stomach(1)	c.G571A						PASS	.	A	SER/GLY	670,3730	763.2+/-413.2	63,544,1593	213.0	207.0	209.0		571	-1.0	0.0	11	dbSNP_130	209	727,7865	786.0+/-407.6	32,663,3601	yes	missense	OR5D14	NM_001004735.1	56	95,1207,5194	AA,AG,GG		8.4614,15.2273,10.7528	benign	191/315	55563602	1397,11595	2200	4296	6496	SO:0001583	missense	219436	exon1			GTGTCTGGCTCTG	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.571G>A	11.37:g.55563602G>A	ENSP00000334456:p.Gly191Ser	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	315	157	0.498413	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	213	0.09752747252747253	92	0.18699186991869918	21	0.058011049723756904	35	0.06118881118881119	65	0.08575197889182058	a	6.430	0.447491	0.12223	0.152273	0.084614	ENSG00000186113	ENST00000335605	T	0.00048	8.82	5.08	-0.978	0.10279	GPCR, rhodopsin-like superfamily (1);	0.566189	0.16176	N	0.226056	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	0.05115	-1.0905	9	0.59425	D	0.04	-3.1471	7.6783	0.28499	0.2259:0.0:0.0843:0.6898	.	191	Q8NGL3	OR5DE_HUMAN	S	191	ENSP00000334456:G191S	ENSP00000334456:G191S	G	+	1	0	OR5D14	55320178	0.021000	0.18746	0.000000	0.03702	0.000000	0.00434	0.417000	0.21214	-0.350000	0.08262	-1.237000	0.01550	GGC	G|0.896;A|0.104	0.104	strong		0.438	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735	
DNAH6	1768	hgsc.bcm.edu	37	2	84816015	84816015	+	Silent	SNP	A	A	G	rs1006244	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:84816015A>G	ENST00000237449.6	+	15	2555	c.2547A>G	c.(2545-2547)caA>caG	p.Q849Q	DNAH6_ENST00000398278.2_Silent_p.Q849Q|DNAH6_ENST00000389394.3_Silent_p.Q849Q			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	849	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						ATAATCTGCAATCTGTTCTGG	0.348													A|||	544	0.108626	0.3169	0.0548	5008	,	,		16616	0.0109		0.0209	False		,,,				2504	0.0562				p.Q849Q		Atlas-SNP	.											.	DNAH6	194	.	0			c.A2547G						PASS	.	A		399,985		49,301,342	140.0	120.0	126.0		2547	-7.0	0.0	2	dbSNP_86	126	84,3096		0,84,1506	no	coding-synonymous	DNAH6	NM_001370.1		49,385,1848	GG,GA,AA		2.6415,28.8295,10.5828		849/4159	84816015	483,4081	692	1590	2282	SO:0001819	synonymous_variant	1768	exon16			TCTGCAATCTGTT	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.2547A>G	2.37:g.84816015A>G		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	310	144	0.464516	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			A|0.901;G|0.099	0.099	strong		0.348	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
SLC14A1	6563	hgsc.bcm.edu	37	18	43319519	43319519	+	Missense_Mutation	SNP	G	G	A	rs1058396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:43319519G>A	ENST00000321925.4	+	8	1070	c.838G>A	c.(838-840)Gac>Aac	p.D280N	RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000436407.3_Missense_Mutation_p.D336N|RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000415427.3_Missense_Mutation_p.D336N|SLC14A1_ENST00000402943.2_Missense_Mutation_p.D175N|SLC14A1_ENST00000502059.2_Missense_Mutation_p.D172N|SLC14A1_ENST00000535474.1_Missense_Mutation_p.D148N|SLC14A1_ENST00000586142.1_Missense_Mutation_p.D280N|SLC14A1_ENST00000589700.1_Silent_p.R230R|SLC14A1_ENST00000591541.1_5'UTR	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	280			D -> N (in Jk(b); dbSNP:rs1058396). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9215669, ECO:0000269|Ref.6, ECO:0000269|Ref.8}.		transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						CCCATTTGAGGACATCTACTT	0.522													G|||	2058	0.410942	0.2277	0.5187	5008	,	,		21202	0.5258		0.501	False		,,,				2504	0.3712				p.D336N		Atlas-SNP	.											.	SLC14A1	84	.	0			c.G1006A	GRCh37	CM973381	SLC14A1	M	rs1058396	PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	1169,3237	411.5+/-335.8	166,837,1200	117.0	101.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1006,838,1006,838	-7.6	0.2	18	dbSNP_86	107	4177,4423	567.8+/-388.9	1013,2151,1136	yes	missense,missense,missense,missense	SLC14A1	NM_001128588.3,NM_001146036.2,NM_001146037.1,NM_015865.6	23,23,23,23	1179,2988,2336	AA,AG,GG		48.5698,26.532,41.1041	benign,benign,benign,benign	336/446,280/390,336/446,280/390	43319519	5346,7660	2203	4300	6503	SO:0001583	missense	6563	exon7			TTTGAGGACATCT	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"""Blood group antigens"", ""Solute carriers"""	10918	protein-coding gene	gene with protein product		613868	"""Kidd blood group"", ""solute carrier family 14 (urea transporter), member 1"""	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.838G>A	18.37:g.43319519G>A	ENSP00000318546:p.Asp280Asn	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	165	164	0.993939	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Missense_Mutation	SNP	ENST00000321925.4	37	CCDS11925.1	983	0.4500915750915751	123	0.25	185	0.511049723756906	297	0.5192307692307693	378	0.49868073878627966	G	8.967	0.971992	0.18736	0.26532	0.485698	ENSG00000141469	ENST00000321925;ENST00000415427;ENST00000502059;ENST00000402943;ENST00000535474;ENST00000436407	T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74	5.62	-7.56	0.01322	.	0.406612	0.26106	N	0.026306	T	0.00012	0.0000	N	0.16201	0.385	0.25146	P	0.99046678	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.12837	0.002;0.008;0.008	T	0.41448	-0.9508	9	0.17369	T	0.5	-2.2595	13.0875	0.59149	0.7465:0.1444:0.1091:0.0	rs1058396;rs1802856;rs3199014;rs17748015;rs17846462;rs17847469;rs17859515;rs56527960;rs56745862;rs1058396	336;172;280	Q13336-2;B3KXJ3;Q13336	.;.;UT1_HUMAN	N	280;336;172;175;148;336	ENSP00000318546:D280N;ENSP00000412309:D336N;ENSP00000442180:D172N;ENSP00000385320:D175N;ENSP00000441998:D148N;ENSP00000390637:D336N	ENSP00000318546:D280N	D	+	1	0	SLC14A1	41573517	0.104000	0.21937	0.182000	0.23118	0.859000	0.49053	0.700000	0.25601	-1.283000	0.02393	0.591000	0.81541	GAC	G|0.587;A|0.413	0.413	strong		0.522	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865	
VIT	5212	hgsc.bcm.edu	37	2	37041439	37041439	+	Missense_Mutation	SNP	C	C	T	rs11901202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37041439C>T	ENST00000389975.3	+	15	2274	c.1972C>T	c.(1972-1974)Cat>Tat	p.H658Y	VIT_ENST00000497382.1_Missense_Mutation_p.H327Y|VIT_ENST00000379241.3_Missense_Mutation_p.H636Y|VIT_ENST00000401530.1_Missense_Mutation_p.H637Y|VIT_ENST00000404084.1_Missense_Mutation_p.H610Y|VIT_ENST00000379242.3_Missense_Mutation_p.H673Y	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	658	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.		H -> Y (in dbSNP:rs11901202). {ECO:0000269|PubMed:15489334}.		extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)	p.H673N(1)		autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				TGACAACCTCCATCAGTATGT	0.532													T|||	595	0.11881	0.1558	0.0403	5008	,	,		20134	0.1806		0.0139	False		,,,				2504	0.1687				p.H673Y		Atlas-SNP	.											VIT,mouth,carcinoma,0,1	VIT	138	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C2017T						PASS	.	T	TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS	616,3790	769.0+/-413.6	33,550,1620	129.0	111.0	117.0		1972,1909,1906,2017	4.3	1.0	2	dbSNP_120	117	18,8582	818.5+/-406.9	0,18,4282	yes	missense,missense,missense,missense	VIT	NM_001177969.1,NM_001177970.1,NM_001177971.1,NM_053276.3	83,83,83,83	33,568,5902	TT,TC,CC		0.2093,13.9809,4.8747	benign,benign,benign,benign	658/679,637/658,636/657,673/694	37041439	634,12372	2203	4300	6503	SO:0001583	missense	5212	exon16			AACCTCCATCAGT	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.1972C>T	2.37:g.37041439C>T	ENSP00000374625:p.His658Tyr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_053276	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	37	CCDS54347.1	170	0.07783882783882784	63	0.12804878048780488	4	0.011049723756906077	95	0.1660839160839161	8	0.010554089709762533	T	3.916	-0.019047	0.07634	0.139809	0.002093	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000497382;ENST00000404084;ENST00000379241;ENST00000401530	T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	5.41	4.26	0.50523	von Willebrand factor, type A (3);	0.120226	0.64402	N	0.000017	T	0.00241	0.0007	N	0.08118	0	0.54753	P	1.8999999999991246E-5	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	0.05451	-1.0884	9	0.56958	D	0.05	-11.8809	5.7221	0.17992	0.0:0.145:0.1421:0.7129	rs11901202;rs56608660;rs11901202	637;636;658;673	E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4	.;.;VITRN_HUMAN;.	Y	673;658;327;610;636;637	ENSP00000368544:H673Y;ENSP00000374625:H658Y;ENSP00000417874:H327Y;ENSP00000384154:H610Y;ENSP00000368543:H636Y;ENSP00000385658:H637Y	ENSP00000368543:H636Y	H	+	1	0	VIT	36894943	1.000000	0.71417	0.976000	0.42696	0.960000	0.62799	2.303000	0.43646	0.377000	0.24735	-0.254000	0.11334	CAT	C|0.932;T|0.068	0.068	strong		0.532	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			
CXCR2	3579	hgsc.bcm.edu	37	2	219000193	219000193	+	Silent	SNP	A	A	G	rs2228414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219000193A>G	ENST00000318507.2	+	3	1096	c.669A>G	c.(667-669)ccA>ccG	p.P223P		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	223					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						TCATCGTGCCACTGCTGATCA	0.562													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		21834	0.0		0.0	False		,,,				2504	0.0				p.P223P		Atlas-SNP	.											.	CXCR2	54	.	0			c.A669G						PASS	.	G	,	167,4239	111.2+/-149.4	3,161,2039	174.0	159.0	164.0		669,669	-10.8	0.0	2	dbSNP_98	164	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CXCR2	NM_001168298.1,NM_001557.3	,	3,161,6339	GG,GA,AA		0.0,3.7903,1.284	,	223/361,223/361	219000193	167,12839	2203	4300	6503	SO:0001819	synonymous_variant	3579	exon4			CGTGCCACTGCTG	U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"", ""Interleukins and interleukin receptors"""	6027	protein-coding gene	gene with protein product		146928	"""interleukin 8 receptor, beta"""	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.669A>G	2.37:g.219000193A>G		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	214	124	0.579439	NM_001168298	Q8IUZ1|Q9P2T6|Q9P2T7	Silent	SNP	ENST00000318507.2	37	CCDS2408.1																																																																																			A|0.985;G|0.015	0.015	strong		0.562	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2	NM_001557	
MT-ND3	4537	hgsc.bcm.edu	37	M	10321	10321	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10321T>C	ENST00000361227.2	+	1	263	c.263T>C	c.(262-264)gTt>gCt	p.V88A	MT-TS1_ENST00000387416.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03897	NU3M_HUMAN	mitochondrially encoded NADH dehydrogenase 3	88					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)										GCCACTAATAGTTATGTCATC	0.373																																					p.V88A		Atlas-SNP	.											.	.	.	.	0			c.T263C						PASS	.																																			SO:0001583	missense	0	exon1			TAATAGTTATGTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198840	ENSG00000198840	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7458	protein-coding gene	gene with protein product	"""complex I ND3 subunit"", ""NADH-ubiquinone oxidoreductase chain 3"""	516002	"""NADH dehydrogenase 3"""	MTND3			Standard			Approved	ND3, NAD3		P03897		ENST00000361227.2:c.263T>C	M.37:g.10321T>C	ENSP00000355206:p.Val88Ala	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	ENST00000361227		Missense_Mutation	SNP	ENST00000361227.2	37																																																																																				.	.	none		0.373	MT-ND3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024033	
NLRP10	338322	hgsc.bcm.edu	37	11	7982432	7982432	+	Missense_Mutation	SNP	G	G	A	rs59039403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7982432G>A	ENST00000328600.2	-	2	888	c.727C>T	c.(727-729)Cgg>Tgg	p.R243W		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	243	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AACAGGAGCCGCTCTGGCTGC	0.552													G|||	163	0.0325479	0.0446	0.0014	5008	,	,		17215	0.1002		0.001	False		,,,				2504	0.001				p.R243W		Atlas-SNP	.											.	NLRP10	146	.	0			c.C727T						PASS	.	G	TRP/ARG	169,4233	108.6+/-147.0	7,155,2039	41.0	43.0	42.0		727	0.1	1.0	11	dbSNP_129	42	3,8589	3.0+/-9.4	0,3,4293	yes	missense	NLRP10	NM_176821.3	101	7,158,6332	AA,AG,GG		0.0349,3.8392,1.3237	probably-damaging	243/656	7982432	172,12822	2201	4296	6497	SO:0001583	missense	338322	exon2			GGAGCCGCTCTGG	AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"""Nucleotide-binding domain and leucine rich repeat containing"""	21464	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"""	609662	"""NACHT, leucine rich repeat and PYD containing 10"""	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.727C>T	11.37:g.7982432G>A	ENSP00000327763:p.Arg243Trp	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_176821	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	37	CCDS7784.1	92	0.04212454212454213	22	0.044715447154471545	1	0.0027624309392265192	68	0.11888111888111888	1	0.0013192612137203166	G	15.04	2.715929	0.48622	0.038392	3.49E-4	ENSG00000182261	ENST00000328600	D	0.83914	-1.78	4.85	0.12	0.14691	NACHT nucleoside triphosphatase (1);	0.000000	0.35207	N	0.003364	T	0.15349	0.0370	M	0.92833	3.35	0.38979	P	0.041081000000000034	D	0.89917	1.0	D	0.97110	1.0	T	0.68394	-0.5420	9	0.87932	D	0	.	5.8866	0.18884	0.0987:0.0:0.4385:0.4628	rs59039403	243	Q86W26	NAL10_HUMAN	W	243	ENSP00000327763:R243W	ENSP00000327763:R243W	R	-	1	2	NLRP10	7939008	0.000000	0.05858	0.994000	0.49952	0.475000	0.33008	0.234000	0.17930	0.136000	0.18733	0.655000	0.94253	CGG	G|0.976;A|0.024	0.024	strong		0.552	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821	
FAM83D	81610	hgsc.bcm.edu	37	20	37555116	37555116	+	Missense_Mutation	SNP	G	G	C	rs3752290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:37555116G>C	ENST00000217429.4	+	1	162	c.121G>C	c.(121-123)Gtg>Ctg	p.V41L		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	11					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				CCTGGACGAGGTGCCCGCCGC	0.701													C|||	2010	0.401358	0.5076	0.3847	5008	,	,		10968	0.4157		0.3429	False		,,,				2504	0.3149				p.V41L		Atlas-SNP	.											FAM83D,NS,carcinoma,0,2	FAM83D	60	2	0			c.G121C						scavenged	.	C	LEU/VAL	1601,2097		394,813,642	8.0	11.0	10.0		121	3.4	0.9	20	dbSNP_107	10	2399,5669		370,1659,2005	no	missense	FAM83D	NM_030919.2	32	764,2472,2647	CC,CG,GG		29.7348,43.2937,33.9963	benign	41/616	37555116	4000,7766	1849	4034	5883	SO:0001583	missense	81610	exon1			GACGAGGTGCCCG	AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 129"""	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.121G>C	20.37:g.37555116G>C	ENSP00000217429:p.Val41Leu	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	12	2	0.166667	NM_030919	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Missense_Mutation	SNP	ENST00000217429.4	37	CCDS42872.1	870	0.3983516483516483	269	0.5467479674796748	136	0.3756906077348066	202	0.3531468531468531	263	0.3469656992084433	C	0.704	-0.789777	0.02884	0.432937	0.297348	ENSG00000101447	ENST00000217429;ENST00000424027	T	0.10477	2.87	5.48	3.44	0.39384	.	0.490125	0.16258	N	0.222396	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38757	-0.9646	9	0.06891	T	0.86	.	7.0157	0.24887	0.0:0.4204:0.417:0.1626	rs3752290;rs17846649;rs17859744;rs3752290	11;11	Q9H4H8;Q9H4H8-2	FA83D_HUMAN;.	L	41;11	ENSP00000217429:V41L	ENSP00000217429:V41L	V	+	1	0	FAM83D	36988530	0.003000	0.15002	0.905000	0.35620	0.017000	0.09413	0.278000	0.18753	0.696000	0.31696	-0.120000	0.15030	GTG	G|0.618;C|0.382	0.382	strong		0.701	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1		
RETSAT	54884	hgsc.bcm.edu	37	2	85570857	85570857	+	Missense_Mutation	SNP	G	G	A	rs4832169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85570857G>A	ENST00000295802.4	-	10	1710	c.1598C>T	c.(1597-1599)gCc>gTc	p.A533V	RETSAT_ENST00000263854.6_Silent_p.C477C|RETSAT_ENST00000457495.2_Missense_Mutation_p.A472V|RETSAT_ENST00000475624.2_5'UTR	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	533			A -> V (in dbSNP:rs4832169).		oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	CCCGTAGCAGGCACCTCGGGG	0.612																																					p.A533V		Atlas-SNP	.											.	RETSAT	56	.	0			c.C1598T						PASS	.						45.0	47.0	46.0					2																	85570857		2203	4300	6503	SO:0001583	missense	54884	exon10			TAGCAGGCACCTC	AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	1.3.99.23		25991	protein-coding gene	gene with protein product						12975309, 15358783	Standard	NM_017750		Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.1598C>T	2.37:g.85570857G>A	ENSP00000295802:p.Ala533Val	Somatic	545	0	0		WXS	Illumina HiSeq	Phase_I	426	47	0.110329	NM_017750	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Missense_Mutation	SNP	ENST00000295802.4	37	CCDS1972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.31|18.31	3.596672|3.596672	0.66332|0.66332	.|.	.|.	ENSG00000042445|ENSG00000042445	ENST00000295802;ENST00000457495|ENST00000449375	T;T|.	0.25250|.	1.84;1.81|.	5.02|5.02	4.0|4.0	0.46444|0.46444	.|.	0.122893|.	0.52532|.	D|.	0.000064|.	T|T	0.60971|0.60971	0.2310|0.2310	M|M	0.71581|0.71581	2.175|2.175	0.09310|0.09310	P|P	1.0|1.0	P;P;P|.	0.44659|.	0.534;0.534;0.84|.	B;B;B|.	0.41374|.	0.355;0.355;0.288|.	T|T	0.70081|0.70081	-0.4970|-0.4970	9|4	0.49607|.	T|.	0.09|.	-11.1835|-11.1835	9.7757|9.7757	0.40618|0.40618	0.0:0.0:0.6602:0.3397|0.0:0.0:0.6602:0.3397	rs4832169;rs12988064;rs4832169|rs4832169;rs12988064;rs4832169	472;472;533|.	G5E9N3;B4DKE1;Q6NUM9|.	.;.;RETST_HUMAN|.	V|S	533;472|322	ENSP00000295802:A533V;ENSP00000405040:A472V|.	ENSP00000295802:A533V|.	A|P	-|-	2|1	0|0	RETSAT|RETSAT	85424368|85424368	1.000000|1.000000	0.71417|0.71417	0.913000|0.913000	0.36048|0.36048	0.496000|0.496000	0.33645|0.33645	4.580000|4.580000	0.60942|0.60942	2.492000|2.492000	0.84095|0.84095	0.561000|0.561000	0.74099|0.74099	GCC|CCT	G|0.786;A|0.214	0.214	strong		0.612	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750	
FMO2	2327	hgsc.bcm.edu	37	1	171168584	171168584	+	Missense_Mutation	SNP	C	C	T	rs386636736|rs2020862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171168584C>T	ENST00000209929.7	+	5	742	c.584C>T	c.(583-585)tCa>tTa	p.S195L	RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000529935.1_Intron|FMO2_ENST00000441535.1_Missense_Mutation_p.S195L|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	195					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.S195L(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					ATGGGAAACTCAGGCTCAGAT	0.488													C|||	2368	0.472843	0.5265	0.4827	5008	,	,		19421	0.5456		0.2962	False		,,,				2504	0.5				p.S195L		Atlas-SNP	.											FMO2,NS,carcinoma,-1,2	FMO2	66	2	1	Substitution - Missense(1)	stomach(1)	c.C584T	GRCh37	CM033900	FMO2	M	rs2020862	PASS	.	C	LEU/SER	2174,2232	585.1+/-386.2	561,1052,590	134.0	140.0	138.0		584	6.2	1.0	1	dbSNP_98	138	2753,5847	439.1+/-359.1	448,1857,1995	yes	missense	FMO2	NM_001460.2	145	1009,2909,2585	TT,TC,CC		32.0116,49.3418,37.8825	probably-damaging	195/472	171168584	4927,8079	2203	4300	6503	SO:0001583	missense	2327	exon5			GAAACTCAGGCTC	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.584C>T	1.37:g.171168584C>T	ENSP00000209929:p.Ser195Leu	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	232	124	0.534483	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	788	0.3608058608058608	190	0.3861788617886179	136	0.3756906077348066	272	0.4755244755244755	190	0.25065963060686014	C	22.4	4.283324	0.80803	0.493418	0.320116	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.60548	0.18;0.18	6.17	6.17	0.99709	.	0.056199	0.85682	D	0.000000	T	0.80824	0.4697	H	0.99689	4.705	0.09310	P	0.9999999445746	B	0.29232	0.238	B	0.41764	0.366	T	0.82810	-0.0273	9	0.87932	D	0	-3.8921	19.6509	0.95805	0.0:1.0:0.0:0.0	rs2020862;rs2266706;rs58871762;rs2020862	195	Q99518	FMO2_HUMAN	L	195	ENSP00000209929:S195L;ENSP00000405905:S195L	ENSP00000209929:S195L	S	+	2	0	FMO2	169435208	1.000000	0.71417	0.969000	0.41365	0.124000	0.20399	5.980000	0.70516	2.941000	0.99782	0.655000	0.94253	TCA	C|0.606;T|0.394	0.394	strong		0.488	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
KCNH5	27133	hgsc.bcm.edu	37	14	63269180	63269180	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:63269180C>T	ENST00000322893.7	-	9	1957	c.1689G>A	c.(1687-1689)gcG>gcA	p.A563A	KCNH5_ENST00000420622.2_Silent_p.A563A|KCNH5_ENST00000394968.1_Silent_p.A505A	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	563					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GGAACTCTACCGCCAAGGCGC	0.507																																					p.A563A		Atlas-SNP	.											KCNH5_ENST00000394968,caecum,carcinoma,0,3	KCNH5	320	3	0			c.G1689A						scavenged	.						89.0	82.0	84.0					14																	63269180		2203	4300	6503	SO:0001819	synonymous_variant	27133	exon9			CTCTACCGCCAAG	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.1689G>A	14.37:g.63269180C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	144	3	0.0208333	NM_172375	C9JP98	Silent	SNP	ENST00000322893.7	37	CCDS9756.1																																																																																			.	.	none		0.507	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
ZNF99	7652	hgsc.bcm.edu	37	19	22941938	22941938	+	Missense_Mutation	SNP	T	T	G	rs6511379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22941938T>G	ENST00000596209.1	-	4	863	c.773A>C	c.(772-774)aAa>aCa	p.K258T	ZNF99_ENST00000397104.3_Intron	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	258					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTCTTCACATTTGCAGGGTTT	0.328													T|||	616	0.123003	0.3366	0.0432	5008	,	,		18580	0.0813		0.0427	False		,,,				2504	0.0164				p.K258T		Atlas-SNP	.											.	ZNF99	273	.	0			c.A773C						PASS	.	T		589,1693		75,439,627	8.0	8.0	8.0			-1.1	0.0	19	dbSNP_116	8	128,4274		4,120,2077	no	intron	ZNF99	NM_001080409.2		79,559,2704	GG,GT,TT		2.9078,25.8107,10.7271			22941938	717,5967	1141	2201	3342	SO:0001583	missense	7652	exon4			TCACATTTGCAGG	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.773A>C	19.37:g.22941938T>G	ENSP00000472969:p.Lys258Thr	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	25	24	0.96	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1																																																																																			T|0.901;G|0.099	0.099	strong		0.328	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
C1orf64	149563	hgsc.bcm.edu	37	1	16332679	16332679	+	Silent	SNP	T	T	C	rs3738646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16332679T>C	ENST00000329454.2	+	2	416	c.348T>C	c.(346-348)tcT>tcC	p.S116S	RP11-5P18.5_ENST00000437156.1_RNA	NM_178840.2	NP_849162.1	Q8NEQ6	CA064_HUMAN	chromosome 1 open reading frame 64	116										breast(2)|endometrium(1)|lung(3)	6		Colorectal(325;0.000435)|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;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;2.08e-05)|BRCA - Breast invasive adenocarcinoma(304;9.19e-05)|Kidney(64;0.000165)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0114)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGAGGGTCTGTGGCCTCAG	0.647													T|||	455	0.0908546	0.0129	0.1455	5008	,	,		18258	0.2113		0.0835	False		,,,				2504	0.0409				p.S116S		Atlas-SNP	.											.	C1orf64	16	.	0			c.T348C						PASS	.	T		138,4268	96.7+/-135.4	2,134,2067	44.0	47.0	46.0		348	-4.8	0.0	1	dbSNP_107	46	743,7857	178.3+/-227.7	32,679,3589	no	coding-synonymous	C1orf64	NM_178840.2		34,813,5656	CC,CT,TT		8.6395,3.1321,6.7738		116/170	16332679	881,12125	2203	4300	6503	SO:0001819	synonymous_variant	149563	exon2			AGGGTCTGTGGCC	AK127425	CCDS166.1	1p36.13	2013-10-11			ENSG00000183888	ENSG00000183888			28339	protein-coding gene	gene with protein product	"""ER-related factor"""					22341523	Standard	NM_178840		Approved	MGC24047, ERRF	uc001axn.3	Q8NEQ6	OTTHUMG00000009523	ENST00000329454.2:c.348T>C	1.37:g.16332679T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_178840	B3KXI9	Silent	SNP	ENST00000329454.2	37	CCDS166.1																																																																																			T|0.916;C|0.084	0.084	strong		0.647	C1orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026317.1	NM_178840	
SLC35B3	51000	hgsc.bcm.edu	37	6	8413890	8413890	+	Silent	SNP	A	A	G	rs3757099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:8413890A>G	ENST00000379660.4	-	11	1547	c.1098T>C	c.(1096-1098)ctT>ctC	p.L366L		NM_001142540.1|NM_001142541.1|NM_015948.3	NP_001136012.1|NP_001136013.1|NP_057032.2	Q9H1N7	S35B3_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B3	366					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)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(1)|prostate(1)	15	Ovarian(93;0.0569)					TGTAAACATTAAGAAATATAC	0.299													G|||	1792	0.357827	0.6974	0.2421	5008	,	,		16596	0.125		0.2296	False		,,,				2504	0.3528				p.L366L	Melanoma(83;700 1353 9357 11478 30548)	Atlas-SNP	.											.	SLC35B3	38	.	0			c.T1098C						PASS	.	G	,,	2887,1517	451.0+/-349.5	963,961,278	54.0	47.0	49.0		1098,1098,1098	3.1	1.0	6	dbSNP_107	49	2071,6525	685.2+/-404.0	226,1619,2453	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC35B3	NM_001142540.1,NM_001142541.1,NM_015948.3	,,	1189,2580,2731	GG,GA,AA		24.0926,34.446,38.1385	,,	366/402,366/402,366/402	8413890	4958,8042	2202	4298	6500	SO:0001819	synonymous_variant	51000	exon11			AACATTAAGAAAT	AF132953	CCDS4508.1	6p24.3	2013-07-17	2013-07-17	2003-09-10	ENSG00000124786	ENSG00000124786		"""Solute carriers"""	21601	protein-coding gene	gene with protein product	"""3' phosphoadenosine 5' phosphosulfate transporter 2"""	610845	"""chromosome 6 open reading frame 196"", ""solute carrier family 35, member B3"""	C6orf196		10810093	Standard	XM_005249156		Approved	CGI-19, dJ453H5.1, PAPST2	uc010joe.3	Q9H1N7	OTTHUMG00000014224	ENST00000379660.4:c.1098T>C	6.37:g.8413890A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	46	29	0.630435	NM_001142540	A6NKX9|Q1XH11|Q6MZJ0|Q7Z662|Q9Y308	Silent	SNP	ENST00000379660.4	37	CCDS4508.1																																																																																			A|0.639;G|0.360	0.360	strong		0.299	SLC35B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039802.1	NM_015948	
CEP85L	387119	hgsc.bcm.edu	37	6	118803091	118803091	+	Missense_Mutation	SNP	C	C	G	rs9489410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118803091C>G	ENST00000368491.3	-	8	2217	c.1596G>C	c.(1594-1596)caG>caC	p.Q532H	CEP85L_ENST00000368488.5_Missense_Mutation_p.Q535H	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	532			Q -> H (in dbSNP:rs9489410).			centrosome (GO:0005813)|cytoplasm (GO:0005737)											CTTCCAGAATCTGCAGCTAAG	0.318													C|||	166	0.033147	0.059	0.0173	5008	,	,		11959	0.0		0.0189	False		,,,				2504	0.0583				p.Q535H		Atlas-SNP	.											.	CEP85L	26	.	0			c.G1605C						PASS	.	C	HIS/GLN,HIS/GLN	194,3380		4,186,1597	67.0	57.0	60.0		1596,1605	2.3	1.0	6	dbSNP_119	60	164,7956		1,162,3897	yes	missense,missense	C6orf204	NM_001042475.2,NM_001178035.1	24,24	5,348,5494	GG,GC,CC		2.0197,5.4281,3.0614	probably-damaging,probably-damaging	532/806,535/809	118803091	358,11336	1787	4060	5847	SO:0001583	missense	387119	exon9			CAGAATCTGCAGC	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.1596G>C	6.37:g.118803091C>G	ENSP00000357477:p.Gln532His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	46	0.021062271062271064	26	0.052845528455284556	6	0.016574585635359115	0	0.0	14	0.018469656992084433	C	16.03	3.005806	0.54254	0.054281	0.020197	ENSG00000111860	ENST00000368491;ENST00000368488;ENST00000434604	T;T;T	0.11821	2.74;2.74;2.74	5.24	2.29	0.28610	.	0.061562	0.64402	D	0.000004	T	0.16642	0.0400	L	0.56769	1.78	0.34826	D	0.73918	D;D	0.76494	0.999;0.999	D;D	0.69479	0.964;0.964	T	0.02588	-1.1137	10	0.72032	D	0.01	-5.1646	9.1618	0.37028	0.0:0.6637:0.0:0.3363	rs9489410;rs52802289;rs9489410	535;532	F8W6J2;Q5SZL2	.;CF204_HUMAN	H	532;535;535	ENSP00000357477:Q532H;ENSP00000357474:Q535H;ENSP00000392131:Q535H	ENSP00000357474:Q535H	Q	-	3	2	C6orf204	118909784	1.000000	0.71417	0.999000	0.59377	0.937000	0.57800	0.983000	0.29552	0.219000	0.20840	0.561000	0.74099	CAG	C|0.982;G|0.018	0.018	strong		0.318	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
LIPI	149998	hgsc.bcm.edu	37	21	15516948	15516948	+	Missense_Mutation	SNP	C	C	T	rs2822432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:15516948C>T	ENST00000536861.1	-	9	1290	c.1291G>A	c.(1291-1293)Gaa>Aaa	p.E431K	AP001347.6_ENST00000432621.1_RNA|AP001347.6_ENST00000428809.1_RNA|LIPI_ENST00000344577.2_Missense_Mutation_p.E452K			Q6XZB0	LIPI_HUMAN	lipase, member I	431			E -> K (in dbSNP:rs2822432). {ECO:0000269|PubMed:12719377}.		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		TCTTACCTTTCTGGGTATGTA	0.294													C|||	1589	0.317292	0.5537	0.4006	5008	,	,		15349	0.0526		0.33	False		,,,				2504	0.1984				p.E452K		Atlas-SNP	.											.	LIPI	95	.	0			c.G1354A						PASS	.	C	LYS/GLU	2345,2055	557.1+/-379.7	637,1071,492	56.0	60.0	59.0		1354	5.3	1.0	21	dbSNP_100	59	2904,5690	428.6+/-355.9	490,1924,1883	yes	missense	LIPI	NM_198996.2	56	1127,2995,2375	TT,TC,CC		33.791,46.7045,40.3956	benign	452/482	15516948	5249,7745	2200	4297	6497	SO:0001583	missense	149998	exon9			ACCTTTCTGGGTA	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"""membrane-associated phospholipase A1 beta"", ""cancer/testis antigen 17"""	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.1291G>A	21.37:g.15516948C>T	ENSP00000440381:p.Glu431Lys	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	132	51	0.386364	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	37		697	0.3191391941391941	265	0.5386178861788617	144	0.39779005524861877	33	0.057692307692307696	255	0.33641160949868076	C	23.2	4.387982	0.82902	0.532955	0.33791	ENSG00000188992	ENST00000344577;ENST00000536861	D;D	0.88975	-2.45;-2.44	5.34	5.34	0.76211	.	0.684752	0.12545	U	0.459591	T	0.00012	0.0000	L	0.61218	1.895	0.37979	P	0.06645599999999996	B	0.31274	0.317	B	0.36666	0.23	T	0.35325	-0.9793	9	0.13470	T	0.59	.	14.9043	0.70706	0.0:1.0:0.0:0.0	rs2822432;rs60846610;rs2822432	452	Q6XZB0-2	.	K	452;431	ENSP00000343331:E452K;ENSP00000440381:E431K	ENSP00000343331:E452K	E	-	1	0	LIPI	14438819	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.230000	0.32612	2.654000	0.90174	0.650000	0.86243	GAA	C|0.629;T|0.371	0.371	strong		0.294	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996	
TRIM3	10612	hgsc.bcm.edu	37	11	6478619	6478619	+	Silent	SNP	G	G	A	rs16913748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6478619G>A	ENST00000525074.1	-	5	997	c.603C>T	c.(601-603)atC>atT	p.I201I	TRIM3_ENST00000537602.1_Silent_p.I201I|TRIM3_ENST00000345851.3_Silent_p.I201I|TRIM3_ENST00000536344.1_Silent_p.I82I|TRIM3_ENST00000359518.3_Silent_p.I201I|TRIM3_ENST00000529058.1_5'UTR	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	201					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACGCTGCACTGATCTGGGCCA	0.617													G|||	938	0.1873	0.2973	0.1772	5008	,	,		20774	0.0188		0.1849	False		,,,				2504	0.2219				p.I201I	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.C603T						PASS	.	G	,	1271,3131	434.1+/-343.8	178,915,1108	95.0	87.0	90.0		603,603	2.1	1.0	11	dbSNP_123	90	1764,6828	318.4+/-313.7	189,1386,2721	no	coding-synonymous,coding-synonymous	TRIM3	NM_006458.2,NM_033278.2	,	367,2301,3829	AA,AG,GG		20.5307,28.8732,23.3569	,	201/745,201/745	6478619	3035,9959	2201	4296	6497	SO:0001819	synonymous_variant	10612	exon5			TGCACTGATCTGG	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.603C>T	11.37:g.6478619G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																			G|0.791;A|0.209	0.209	strong		0.617	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
PCDHB11	56125	hgsc.bcm.edu	37	5	140579358	140579358	+	Missense_Mutation	SNP	A	A	G	rs3756323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140579358A>G	ENST00000354757.3	+	1	11	c.11A>G	c.(10-12)cAa>cGa	p.Q4R	PCDHB11_ENST00000536699.1_5'UTR	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	4			Q -> R (in dbSNP:rs3756323).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATGGAGAACCAAGGGACACGC	0.502													G|||	764	0.152556	0.2579	0.1902	5008	,	,		21054	0.0407		0.1581	False		,,,				2504	0.093				p.Q4R		Atlas-SNP	.											.	PCDHB11	162	.	0			c.A11G						PASS	.	G	ARG/GLN	1043,3363	725.1+/-409.6	115,813,1275	79.0	74.0	76.0		11	0.2	0.0	5	dbSNP_107	76	1473,7127	749.9+/-407.4	137,1199,2964	yes	missense	PCDHB11	NM_018931.2	43	252,2012,4239	GG,GA,AA		17.1279,23.6723,19.3449	benign	4/798	140579358	2516,10490	2203	4300	6503	SO:0001583	missense	56125	exon1			AGAACCAAGGGAC	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.11A>G	5.37:g.140579358A>G	ENSP00000346802:p.Gln4Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	70	44	0.628571	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	333	0.15247252747252749	122	0.24796747967479674	63	0.17403314917127072	26	0.045454545454545456	122	0.16094986807387862	G	2.426	-0.331889	0.05314	0.236723	0.171279	ENSG00000197479	ENST00000354757	T	0.46063	0.88	2.69	0.238	0.15480	.	.	.	.	.	T	0.00012	0.0000	N	0.01482	-0.84	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39375	-0.9617	8	0.09843	T	0.71	.	7.8071	0.29209	0.1035:0.3818:0.5147:0.0	rs3756323;rs52814876;rs58371514;rs3756323	4	Q9Y5F2	PCDBB_HUMAN	R	4	ENSP00000346802:Q4R	ENSP00000346802:Q4R	Q	+	2	0	PCDHB11	140559542	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.201000	0.09464	-0.041000	0.13558	-0.368000	0.07277	CAA	A|0.818;G|0.182	0.182	strong		0.502	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
ARHGEF5	7984	hgsc.bcm.edu	37	7	144060802	144060802	+	Missense_Mutation	SNP	C	C	T	rs3823677		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:144060802C>T	ENST00000056217.5	+	2	1214	c.1040C>T	c.(1039-1041)aCc>aTc	p.T347I	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	347					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					AAGAGTCAAACCTTTTTGGGA	0.527																																					p.T347I		Atlas-SNP	.											ARHGEF5,colon,carcinoma,+1,1	ARHGEF5	73	1	0			c.C1040T						scavenged	.						62.0	56.0	58.0					7																	144060802		2079	3981	6060	SO:0001583	missense	7984	exon2			GTCAAACCTTTTT	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.1040C>T	7.37:g.144060802C>T	ENSP00000056217:p.Thr347Ile	Somatic	1118	0	0		WXS	Illumina HiSeq	Phase_I	878	396	0.451025	NM_005435	A6NNJ2|Q6ZML7	Missense_Mutation	SNP	ENST00000056217.5	37	CCDS34771.1	764	0.3498168498168498	142	0.2886178861788618	126	0.34806629834254144	284	0.4965034965034965	212	0.2796833773087071	c	8.471	0.857559	0.17106	.	.	ENSG00000050327	ENST00000056217	T	0.73047	-0.71	3.54	-2.18	0.07037	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.44802	-0.9304	7	.	.	.	-0.3178	0.5401	0.00644	0.2016:0.2872:0.2203:0.2909	.	347	Q12774	ARHG5_HUMAN	I	347	ENSP00000056217:T347I	.	T	+	2	0	ARHGEF5	143691735	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.478000	0.06575	-0.083000	0.12618	-0.235000	0.12190	ACC	.	.	weak		0.527	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
PPP1R26	9858	hgsc.bcm.edu	37	9	138379608	138379608	+	Silent	SNP	C	C	T	rs139160467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138379608C>T	ENST00000356818.2	+	4	3801	c.3252C>T	c.(3250-3252)acC>acT	p.T1084T	PPP1R26_ENST00000605660.1_Silent_p.T1084T|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000401470.3_Silent_p.T1084T|PPP1R26_ENST00000605286.1_Silent_p.T1084T|PPP1R26_ENST00000604351.1_Silent_p.T1084T	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	1084					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TGCTGTCCACCCAGCTCTTCC	0.726													C|||	57	0.0113818	0.0424	0.0014	5008	,	,		14055	0.0		0.0	False		,,,				2504	0.0				p.T1084T		Atlas-SNP	.											.	.	.	.	0			c.C3252T						PASS	.	C		72,3236		0,72,1582	4.0	5.0	5.0		3252	-7.1	0.1	9	dbSNP_134	5	2,7236		0,2,3617	no	coding-synonymous	KIAA0649	NM_014811.3		0,74,5199	TT,TC,CC		0.0276,2.1765,0.7017		1084/1210	138379608	74,10472	1654	3619	5273	SO:0001819	synonymous_variant	9858	exon4			GTCCACCCAGCTC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.3252C>T	9.37:g.138379608C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	22	8	0.363636	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																			C|0.989;T|0.011	0.011	strong		0.726	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
LILRB5	10990	hgsc.bcm.edu	37	19	54754778	54754778	+	Missense_Mutation	SNP	G	G	A	rs150660840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54754778G>A	ENST00000316219.5	-	13	1752	c.1645C>T	c.(1645-1647)Ccc>Tcc	p.P549S	LILRB5_ENST00000345866.6_Missense_Mutation_p.P450S|LILRB5_ENST00000449561.2_Missense_Mutation_p.P550S|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000450632.1_Silent_p.P619P	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	549					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACATCCTGGGGGGCTTCAGAT	0.632																																					p.P550S		Atlas-SNP	.											LILRB5,NS,carcinoid-endocrine_tumour,+1,1	LILRB5	176	1	0			c.C1648T						scavenged	.	G	SER/PRO,SER/PRO,SER/PRO	50,4356	36.8+/-68.6	2,46,2155	38.0	43.0	42.0		1648,1348,1645	0.3	0.0	19	dbSNP_134	42	5,8587	3.7+/-12.6	0,5,4291	no	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	74,74,74	2,51,6446	AA,AG,GG		0.0582,1.1348,0.4231	benign,benign,benign	550/592,450/492,549/591	54754778	55,12943	2203	4296	6499	SO:0001583	missense	10990	exon13			CCTGGGGGGCTTC	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1645C>T	19.37:g.54754778G>A	ENSP00000320390:p.Pro549Ser	Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	220	14	0.0636364	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559321	0.27827	0.011348	5.82E-4	ENSG00000105609	ENST00000316219;ENST00000449561;ENST00000345866	T;T;T	0.00543	6.77;6.74;6.68	2.75	0.32	0.15878	.	.	.	.	.	T	0.00496	0.0016	M	0.72894	2.215	0.09310	N	0.999999	B;B;P	0.43169	0.235;0.041;0.8	B;B;B	0.41036	0.202;0.054;0.346	T	0.46596	-0.9180	9	0.59425	D	0.04	.	3.188	0.06607	0.1533:0.0:0.5888:0.2579	.	450;550;549	O75023-2;O75023-3;O75023	.;.;LIRB5_HUMAN	S	549;550;450	ENSP00000320390:P549S;ENSP00000406478:P550S;ENSP00000263430:P450S	ENSP00000320390:P549S	P	-	1	0	LILRB5	59446590	0.000000	0.05858	0.034000	0.17996	0.619000	0.37552	-0.640000	0.05440	0.033000	0.15463	0.585000	0.79938	CCC	G|0.994;A|0.006	0.006	strong		0.632	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
PLG	5340	hgsc.bcm.edu	37	6	161152240	161152240	+	Missense_Mutation	SNP	G	G	A	rs4252125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:161152240G>A	ENST00000308192.9	+	11	1477	c.1414G>A	c.(1414-1416)Gat>Aat	p.D472N		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	472			D -> N (in dbSNP:rs4252125). {ECO:0000269|PubMed:2318848, ECO:0000269|Ref.4, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CCTGCTTCCAGATGTAGAGAC	0.502													A|||	700	0.139776	0.152	0.1787	5008	,	,		19629	0.0		0.2962	False		,,,				2504	0.0787				p.D472N		Atlas-SNP	.											.	PLG	150	.	0			c.G1414A	GRCh37	CM043559	PLG	M	rs4252125	PASS	.	A	ASN/ASP	804,3602	749.7+/-412.0	66,672,1465	95.0	87.0	90.0		1414	2.1	0.0	6	dbSNP_111	90	2604,5996	688.3+/-404.3	368,1868,2064	yes	missense	PLG	NM_000301.3	23	434,2540,3529	AA,AG,GG		30.2791,18.2478,26.2033	benign	472/811	161152240	3408,9598	2203	4300	6503	SO:0001583	missense	5340	exon11			CTTCCAGATGTAG	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1414G>A	6.37:g.161152240G>A	ENSP00000308938:p.Asp472Asn	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_000301	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	ENST00000308192.9	37	CCDS5279.1	354	0.1620879120879121	69	0.1402439024390244	73	0.20165745856353592	0	0.0	212	0.2796833773087071	A	4.858	0.159413	0.09236	0.182478	0.302791	ENSG00000122194	ENST00000308192	T	0.62105	0.05	4.5	2.08	0.27032	.	0.677337	0.12596	N	0.455126	T	0.18593	0.0446	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.03993	-1.0986	9	0.34782	T	0.22	.	8.3175	0.32108	0.7311:0.0:0.2689:0.0	rs4252125;rs17639358;rs52806400;rs60784473;rs4252125	472	P00747	PLMN_HUMAN	N	472	ENSP00000308938:D472N	ENSP00000308938:D472N	D	+	1	0	PLG	161072230	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.058000	0.14301	-0.295000	0.08960	-2.697000	0.00138	GAT	G|0.784;A|0.216	0.216	strong		0.502	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
FBXO33	254170	hgsc.bcm.edu	37	14	39871017	39871017	+	Silent	SNP	T	T	C	rs7156962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:39871017T>C	ENST00000298097.7	-	3	1096	c.759A>G	c.(757-759)aaA>aaG	p.K253K	FBXO33_ENST00000554190.1_Intron	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	253					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		AGGACAGCCATTTCAGTTGCC	0.413													T|||	885	0.176717	0.3457	0.0879	5008	,	,		19732	0.0724		0.1213	False		,,,				2504	0.1759				p.K253K		Atlas-SNP	.											.	FBXO33	21	.	0			c.A759G						PASS	.	T		1470,2936	470.9+/-355.9	217,1036,950	70.0	72.0	71.0		759	-0.3	1.0	14	dbSNP_116	71	884,7716	197.5+/-242.1	42,800,3458	no	coding-synonymous	FBXO33	NM_203301.3		259,1836,4408	CC,CT,TT		10.2791,33.3636,18.0993		253/556	39871017	2354,10652	2203	4300	6503	SO:0001819	synonymous_variant	254170	exon3			CAGCCATTTCAGT	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"""F-boxes /  ""other"""""	19833	protein-coding gene	gene with protein product		609103	"""F-box only protein 33"""				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.759A>G	14.37:g.39871017T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Silent	SNP	ENST00000298097.7	37	CCDS9677.1																																																																																			T|0.825;C|0.175	0.175	strong		0.413	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2		
OR3A1	4994	hgsc.bcm.edu	37	17	3195603	3195603	+	Nonsense_Mutation	SNP	T	T	A	rs7218125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3195603T>A	ENST00000323404.1	-	1	273	c.274A>T	c.(274-276)Aag>Tag	p.K92*	RP11-64J4.2_ENST00000573491.1_RNA	NM_002550.2	NP_002541.2	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A, member 1	92					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	20						ACTGCACGCTTGCGGGACAGG	0.567													.|||	111	0.0221645	0.0779	0.0101	5008	,	,		18657	0.0		0.001	False		,,,				2504	0.0				p.K92X	GBM(20;287 516 18743 28660 36594)	Atlas-SNP	.											.	OR3A1	46	.	0			c.A274T						PASS	.	T	stop/LYS	278,4128	155.5+/-188.7	10,258,1935	82.0	67.0	72.0		274	3.0	0.1	17	dbSNP_116	72	3,8597	2.2+/-6.3	0,3,4297	yes	stop-gained	OR3A1	NM_002550.2		10,261,6232	AA,AT,TT		0.0349,6.3096,2.1605		92/316	3195603	281,12725	2203	4300	6503	SO:0001587	stop_gained	4994	exon1			CACGCTTGCGGGA	X80391	CCDS11023.1	17p13.3	2012-08-09			ENSG00000180090	ENSG00000180090		"""GPCR / Class A : Olfactory receptors"""	8282	protein-coding gene	gene with protein product						8921386, 8647456	Standard	NM_002550		Approved	OLFRA03, OR40, OR17-40	uc002fvh.1	P47881	OTTHUMG00000090642	ENST00000323404.1:c.274A>T	17.37:g.3195603T>A	ENSP00000313803:p.Lys92*	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	277	148	0.534296	NM_002550	Q4VB06|Q6IFM4	Nonsense_Mutation	SNP	ENST00000323404.1	37	CCDS11023.1	37	0.01694139194139194	31	0.06300813008130081	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	10.77	1.444920	0.25987	0.063096	3.49E-4	ENSG00000180090	ENST00000323404	.	.	.	5.31	3.01	0.34805	.	0.663946	0.13864	N	0.357451	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6046	7.6409	0.28292	0.0:0.0758:0.1405:0.7836	rs7218125;rs16952824;rs7218125	.	.	.	X	92	.	ENSP00000313803:K92X	K	-	1	0	OR3A1	3142353	0.000000	0.05858	0.097000	0.21041	0.002000	0.02628	0.063000	0.14410	1.003000	0.39130	0.528000	0.53228	AAG	T|0.972;A|0.028	0.028	strong		0.567	OR3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207302.2		
KLHL30	377007	hgsc.bcm.edu	37	2	239059610	239059610	+	Silent	SNP	C	C	T	rs61736173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	169	0	0		WXS	Illumina HiSeq	Phase_I	172	95	0.552326	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	
CYBA	1535	hgsc.bcm.edu	37	16	88713213	88713213	+	Silent	SNP	C	C	G	rs2228472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88713213C>G	ENST00000261623.3	-	4	375	c.237G>C	c.(235-237)ctG>ctC	p.L79L	CYBA_ENST00000567174.1_Silent_p.L79L|CYBA_ENST00000569359.1_Silent_p.L79L|CYBA_ENST00000561972.1_5'Flank	NM_000101.3	NP_000092.2	P13498	CY24A_HUMAN	cytochrome b-245, alpha polypeptide	79					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)|cellular response to amino acid stimulus (GO:0071230)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|cytochrome complex assembly (GO:0017004)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|negative regulation of glomerular filtration by angiotensin (GO:0003106)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of cell growth (GO:0030307)|positive regulation of endothelial cell proliferation (GO:0001938)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|response to nutrient levels (GO:0031667)|smooth muscle hypertrophy (GO:0014895)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|secretory granule (GO:0030141)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)			endometrium(1)|liver(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0478)	Dextromethorphan(DB00514)	AGGGCCCGAACAGCTTCACCA	0.652													C|||	227	0.0453275	0.1672	0.0086	5008	,	,		15785	0.0		0.0	False		,,,				2504	0.0				p.L79L		Atlas-SNP	.											.	CYBA	12	.	0			c.G237C						PASS	.	C		627,3769	269.8+/-269.2	48,531,1619	81.0	91.0	87.0		237	0.7	0.3	16	dbSNP_98	87	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	CYBA	NM_000101.2		48,536,5914	GG,GC,CC		0.0581,14.263,4.863		79/196	88713213	632,12364	2198	4300	6498	SO:0001819	synonymous_variant	1535	exon4			CCCGAACAGCTTC		CCDS32504.1	16q24	2014-09-17				ENSG00000051523		"""Cytochrome b genes"""	2577	protein-coding gene	gene with protein product	"""flavocytochrome b-558 alpha polypeptide"""	608508				2243141	Standard	NM_000101		Approved	p22-PHOX	uc002flb.4	P13498		ENST00000261623.3:c.237G>C	16.37:g.88713213C>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_000101	Q14090|Q9BR72	Silent	SNP	ENST00000261623.3	37	CCDS32504.1																																																																																			C|0.949;G|0.051	0.051	strong		0.652	CYBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422765.1	NM_000101	
IFNA10	3446	hgsc.bcm.edu	37	9	21206724	21206724	+	Nonsense_Mutation	SNP	G	G	A	rs145785282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21206724G>A	ENST00000357374.2	-	1	418	c.373C>T	c.(373-375)Cag>Tag	p.Q125*		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	125					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		CCAACCTCCTGTATCACACAT	0.463													g|||	48	0.00958466	0.0325	0.0043	5008	,	,		19993	0.0		0.002	False		,,,				2504	0.0				p.Q125X		Atlas-SNP	.											.	IFNA10	29	.	0			c.C373T						PASS	.	G	stop/GLN	104,4300		2,100,2100	69.0	76.0	73.0		373	0.4	0.0	9	dbSNP_134	73	4,8556		0,4,4276	no	stop-gained	IFNA10	NM_002171.1		2,104,6376	AA,AG,GG		0.0467,2.3615,0.8331		125/190	21206724	108,12856	2202	4280	6482	SO:0001587	stop_gained	3446	exon1			CCTCCTGTATCAC		CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"""Interferons"""	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.373C>T	9.37:g.21206724G>A	ENSP00000369566:p.Gln125*	Somatic	599	0	0		WXS	Illumina HiSeq	Phase_I	702	210	0.299145	NM_002171	Q5VV13	Nonsense_Mutation	SNP	ENST00000357374.2	37	CCDS6499.1	.	.	.	.	.	.	.	.	.	.	-	12.34	1.908152	0.33721	0.023615	4.67E-4	ENSG00000186803	ENST00000357374	.	.	.	3.75	0.383	0.16239	.	0.485956	0.22193	N	0.063355	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	7.857	0.29489	0.0:0.3253:0.508:0.1667	.	.	.	.	X	125	.	ENSP00000369566:Q125X	Q	-	1	0	IFNA10	21196724	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.002000	0.13061	0.171000	0.19730	-0.667000	0.03836	CAG	G|0.996;A|0.004	0.004	strong		0.463	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171	
OR1J2	26740	hgsc.bcm.edu	37	9	125273435	125273435	+	Missense_Mutation	SNP	G	G	A	rs41277120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125273435G>A	ENST00000335302.5	+	1	355	c.355G>A	c.(355-357)Gca>Aca	p.A119T		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	119			A -> T (in dbSNP:rs41277120).			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)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						TACATCAATGGCATATGACCG	0.408													G|||	483	0.0964457	0.0734	0.0187	5008	,	,		24802	0.2817		0.0149	False		,,,				2504	0.0757				p.A119T		Atlas-SNP	.											.	OR1J2	64	.	0			c.G355A						PASS	.	G	THR/ALA	273,4133	152.9+/-186.6	8,257,1938	162.0	136.0	145.0		355	4.1	0.6	9	dbSNP_127	145	122,8478	63.5+/-125.6	3,116,4181	yes	missense	OR1J2	NM_054107.1	58	11,373,6119	AA,AG,GG		1.4186,6.1961,3.0371	probably-damaging	119/314	125273435	395,12611	2203	4300	6503	SO:0001583	missense	26740	exon1			TCAATGGCATATG		CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"""GPCR / Class A : Olfactory receptors"""	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.355G>A	9.37:g.125273435G>A	ENSP00000335575:p.Ala119Thr	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	250	77	0.308	NM_054107	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Missense_Mutation	SNP	ENST00000335302.5	37	CCDS35121.1	243	0.11126373626373626	32	0.06504065040650407	7	0.019337016574585635	195	0.3409090909090909	9	0.011873350923482849	G	15.03	2.710987	0.48517	0.061961	0.014186	ENSG00000197233	ENST00000335302;ENST00000444856	T	0.54071	0.59	5.02	4.11	0.48088	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39615	U	0.001302	T	0.00012	0.0000	H	0.97635	4.045	0.38813	P	0.044537999999999967	D	0.89917	1.0	D	0.97110	1.0	T	0.25398	-1.0133	9	0.87932	D	0	.	5.6578	0.17652	0.0953:0.0:0.6023:0.3024	rs41277120	119	Q8NGS2	OR1J2_HUMAN	T	119	ENSP00000335575:A119T	ENSP00000335575:A119T	A	+	1	0	OR1J2	124313256	1.000000	0.71417	0.570000	0.28473	0.034000	0.12701	1.969000	0.40510	1.339000	0.45563	0.650000	0.86243	GCA	G|0.948;A|0.052	0.052	strong		0.408	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1		
DIRAS3	9077	hgsc.bcm.edu	37	1	68512441	68512441	+	Silent	SNP	A	A	G	rs61736596	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:68512441A>G	ENST00000370981.1	-	4	1176	c.540T>C	c.(538-540)atT>atC	p.I180I	GNG12-AS1_ENST00000420587.1_RNA|DIRAS3_ENST00000395201.1_Silent_p.I180I|GNG12-AS1_ENST00000413628.1_RNA			O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	180					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of gene expression by genetic imprinting (GO:0006349)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TCTTGGCTGAAATCTCCATGA	0.547													G|||	464	0.0926518	0.2829	0.0548	5008	,	,		19228	0.0		0.0388	False		,,,				2504	0.0133				p.I180I		Atlas-SNP	.											.	DIRAS3	31	.	0			c.T540C						PASS	.	G		1086,3320	720.9+/-409.1	134,818,1251	124.0	121.0	122.0		540	2.8	0.3	1	dbSNP_129	122	266,8334	807.6+/-407.2	4,258,4038	no	coding-synonymous	DIRAS3	NM_004675.2		138,1076,5289	GG,GA,AA		3.093,24.6482,10.3952		180/230	68512441	1352,11654	2203	4300	6503	SO:0001819	synonymous_variant	9077	exon2			GGCTGAAATCTCC	U96750	CCDS641.1	1p31	2014-05-09		2005-01-27	ENSG00000162595	ENSG00000162595			687	protein-coding gene	gene with protein product		605193	"""ras homolog gene family, member I"""	ARHI		9874798	Standard	XM_006711027		Approved	NOEY2	uc001ded.3	O95661	OTTHUMG00000009544	ENST00000370981.1:c.540T>C	1.37:g.68512441A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	171	91	0.532164	NM_004675	B3KMP3	Silent	SNP	ENST00000370981.1	37	CCDS641.1																																																																																			A|0.900;G|0.100	0.100	strong		0.547	DIRAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026354.2	NM_004675	
GPR98	84059	hgsc.bcm.edu	37	5	90103487	90103487	+	Missense_Mutation	SNP	T	T	C	rs7729495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:90103487T>C	ENST00000405460.2	+	73	15001	c.14905T>C	c.(14905-14907)Tgg>Cgg	p.W4969R	GPR98_ENST00000425867.2_Missense_Mutation_p.W630R	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4969					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)		TAGCCCTGGTTGGCCAGAGGC	0.493													C|||	274	0.0547125	0.1967	0.0187	5008	,	,		17141	0.0		0.001	False		,,,				2504	0.0				p.W4969R		Atlas-SNP	.											.	GPR98	605	.	0			c.T14905C						PASS	.	C	ARG/TRP	619,3067		59,501,1283	64.0	62.0	63.0		14905	4.8	0.0	5	dbSNP_116	63	5,8173		0,5,4084	yes	missense	GPR98	NM_032119.3	101	59,506,5367	CC,CT,TT		0.0611,16.7933,5.2596	benign	4969/6307	90103487	624,11240	1843	4089	5932	SO:0001583	missense	84059	exon73			CCTGGTTGGCCAG	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.14905T>C	5.37:g.90103487T>C	ENSP00000384582:p.Trp4969Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	124	0.056776556776556776	116	0.23577235772357724	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	0.009	-1.821869	0.00589	0.167933	6.11E-4	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.25579	1.91;1.79	5.76	4.84	0.62591	.	0.605769	0.17932	N	0.157144	T	0.00012	0.0000	N	0.00210	-1.845	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	0.31586	-0.9938	8	.	.	.	.	9.4256	0.38578	0.2064:0.7169:0.0:0.0767	rs7729495;rs52807777;rs7729495	630;4969;630	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	R	4969;4969;630	ENSP00000384582:W4969R;ENSP00000392618:W630R	.	W	+	1	0	GPR98	90139243	0.000000	0.05858	0.007000	0.13788	0.040000	0.13550	0.823000	0.27366	1.454000	0.47793	-0.119000	0.15052	TGG	T|0.926;C|0.074	0.074	strong		0.493	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
MUC4	4585	hgsc.bcm.edu	37	3	195507227	195507227	+	Missense_Mutation	SNP	C	C	T	rs569772156|rs74187968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507227C>T	ENST00000463781.3	-	2	11683	c.11224G>A	c.(11224-11226)Gtc>Atc	p.V3742I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3742I	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)		AGAGGGGTGACGTGACCTGTG	0.582													.|||	4	0.000798722	0.0015	0.0	5008	,	,		9263	0.001		0.0	False		,,,				2504	0.001				p.V3742I		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.G11224A						PASS	.						26.0	26.0	26.0					3																	195507227		670	1583	2253	SO:0001583	missense	4585	exon2			GGGTGACGTGACC	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.11224G>A	3.37:g.195507227C>T	ENSP00000417498:p.Val3742Ile	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	70	46	0.657143	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	2.258	-0.369947	0.05069	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.43294	1.2;0.95	0.885	-1.77	0.07982	.	0.000000	0.25514	U	0.030158	T	0.16041	0.0386	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.01281	0.0	T	0.10753	-1.0616	9	.	.	.	.	0.1331	0.00076	0.2533:0.2479:0.2524:0.2464	.	3614	E7ESK3	.	I	3742	ENSP00000417498:V3742I;ENSP00000420243:V3742I	.	V	-	1	0	MUC4	196992006	0.000000	0.05858	0.023000	0.16930	0.045000	0.14185	-2.139000	0.01302	-0.948000	0.03668	0.064000	0.15345	GTC	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PNPLA1	285848	hgsc.bcm.edu	37	6	36269946	36269946	+	Missense_Mutation	SNP	A	A	G	rs145856102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36269946A>G	ENST00000394571.2	+	6	1084	c.1084A>G	c.(1084-1086)Act>Gct	p.T362A	PNPLA1_ENST00000388715.3_Missense_Mutation_p.T267A|PNPLA1_ENST00000312917.5_Missense_Mutation_p.T276A	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	362	Pro-rich.				lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						GGCCTCTTCAACTCCACTTTC	0.562											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T362A		Atlas-SNP	.											.	PNPLA1	92	.	0			c.A1084G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	18,4388	25.3+/-52.1	0,18,2185	130.0	125.0	127.0		826,1084,799	0.2	0.0	6	dbSNP_134	127	0,8600		0,0,4300	yes	missense,missense,missense	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	58,58,58	0,18,6485	GG,GA,AA		0.0,0.4085,0.1384	benign,benign,benign	276/447,362/533,267/438	36269946	18,12988	2203	4300	6503	SO:0001583	missense	285848	exon6			TCTTCAACTCCAC		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.1084A>G	6.37:g.36269946A>G	ENSP00000378072:p.Thr362Ala	Somatic	132	0	0	861	WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	.	.	.	.	.	.	.	.	.	.	A	0.635	-0.815820	0.02776	0.004085	0.0	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.27256	1.91;1.91;1.68;1.68	5.4	0.208	0.15221	.	2.180320	0.02285	N	0.069728	T	0.03136	0.0092	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	0.25641	-1.0126	10	0.18710	T	0.47	0.729	2.0907	0.03656	0.1506:0.4124:0.2712:0.1658	.	362;276	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	A	267;276;363;362	ENSP00000373367:T267A;ENSP00000321116:T276A;ENSP00000391868:T363A;ENSP00000378072:T362A	ENSP00000321116:T276A	T	+	1	0	PNPLA1	36377924	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.120000	0.15647	0.002000	0.14630	-1.513000	0.00942	ACT	A|0.998;G|0.002	0.002	strong		0.562	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
FAM118A	55007	hgsc.bcm.edu	37	22	45728370	45728370	+	Missense_Mutation	SNP	G	G	A	rs6007594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45728370G>A	ENST00000216214.3	+	7	1550	c.716G>A	c.(715-717)cGt>cAt	p.R239H	FAM118A_ENST00000441876.2_Missense_Mutation_p.R239H|FAM118A_ENST00000405548.3_Missense_Mutation_p.R57H	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	239			R -> H (in dbSNP:rs6007594). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)		p.R239H(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		GAGACCCTTCGTGATCAGATA	0.458													G|||	2632	0.525559	0.8411	0.3905	5008	,	,		20074	0.5218		0.2724	False		,,,				2504	0.4591				p.R239H		Atlas-SNP	.											FAM118A,NS,carcinoma,0,1	FAM118A	32	1	1	Substitution - Missense(1)	stomach(1)	c.G716A						scavenged	.	G	HIS/ARG,HIS/ARG	3274,1132	714.4+/-408.4	1225,824,154	129.0	138.0	135.0		716,716	5.8	0.2	22	dbSNP_114	135	2331,6269	391.1+/-343.5	318,1695,2287	yes	missense,missense	FAM118A	NM_001104595.1,NM_017911.2	29,29	1543,2519,2441	AA,AG,GG		27.1047,25.6922,43.0955	probably-damaging,probably-damaging	239/358,239/358	45728370	5605,7401	2203	4300	6503	SO:0001583	missense	55007	exon6			CCCTTCGTGATCA	BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 8"""	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.716G>A	22.37:g.45728370G>A	ENSP00000216214:p.Arg239His	Somatic	260	2	0.00769231		WXS	Illumina HiSeq	Phase_I	223	107	0.479821	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Missense_Mutation	SNP	ENST00000216214.3	37	CCDS14065.1	1048	0.47985347985347987	406	0.8252032520325203	149	0.4116022099447514	295	0.5157342657342657	198	0.2612137203166227	G	20.4	3.981425	0.74474	0.743078	0.271047	ENSG00000100376	ENST00000216214;ENST00000441876;ENST00000405548	T;T;T	0.29142	1.58;1.58;1.58	5.8	5.8	0.92144	.	0.132445	0.52532	D	0.000067	T	0.00012	0.0000	N	0.25647	0.755	0.24306	P	0.99510402	D	0.76494	0.999	D	0.65323	0.934	T	0.02852	-1.1102	9	0.46703	T	0.11	-4.8413	12.9483	0.58386	0.0748:0.0:0.9252:0.0	rs6007594;rs6519925;rs17845391;rs17858248;rs52828151;rs60885839;rs6007594	239	Q9NWS6	F118A_HUMAN	H	239;239;57	ENSP00000216214:R239H;ENSP00000395892:R239H;ENSP00000384836:R57H	ENSP00000216214:R239H	R	+	2	0	FAM118A	44107034	1.000000	0.71417	0.243000	0.24186	0.953000	0.61014	5.769000	0.68865	2.743000	0.94032	0.655000	0.94253	CGT	G|0.536;A|0.464	0.464	strong		0.458	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
PRSS50	29122	hgsc.bcm.edu	37	3	46783959	46783959	+	Intron	SNP	T	T	C	rs58830807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46783959T>C	ENST00000460241.1	-	4	1129				PRSS45_ENST00000442359.2_Missense_Mutation_p.I190V			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						TATTTGGTGATGCGGGTGTAC	0.547													C|||	1317	0.262979	0.528	0.1844	5008	,	,		20274	0.121		0.1441	False		,,,				2504	0.229				p.I190V	Pancreas(41;915 1239 11561 17469)	Atlas-SNP	.											.	PRSS45	12	.	0			c.A568G						PASS	.	C	VAL/ILE	1731,2457		367,997,730	214.0	267.0	249.0		568	-0.1	0.0	3	dbSNP_129	249	1221,7235		80,1061,3087	yes	missense	PRSS45	NM_199183.2	29	447,2058,3817	CC,CT,TT		14.4395,41.3324,23.347	benign	190/229	46783959	2952,9692	2094	4228	6322	SO:0001627	intron_variant	377047	exon4			TGGTGATGCGGGT	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+6155A>G	3.37:g.46783959T>C		Somatic	446	0	0		WXS	Illumina HiSeq	Phase_I	440	214	0.486364	NM_199183		Missense_Mutation	SNP	ENST00000460241.1	37	CCDS2745.1	468	0.21428571428571427	231	0.4695121951219512	58	0.16022099447513813	65	0.11363636363636363	114	0.1503957783641161	C	0.008	-1.920869	0.00498	0.413324	0.144395	ENSG00000188086	ENST00000331814;ENST00000442359	D	0.87650	-2.28	5.65	-0.106	0.13596	.	0.432871	0.20158	N	0.098016	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.14587	-1.0467	8	0.02654	T	1	.	9.715	0.40270	0.0:0.4503:0.0:0.5497	rs58830807;rs62246245	190	Q7RTY3-2	.	V	222;190	ENSP00000401932:I190V	ENSP00000330940:I222V	I	-	1	0	PRSS45	46758963	0.000000	0.05858	0.010000	0.14722	0.254000	0.26022	-0.998000	0.03701	-0.453000	0.07076	-0.726000	0.03593	ATC	T|0.801;C|0.199	0.199	strong		0.547	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1		
FMO2	2327	hgsc.bcm.edu	37	1	171168585	171168585	+	Silent	SNP	A	A	G	rs2020861|rs386636736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171168585A>G	ENST00000209929.7	+	5	743	c.585A>G	c.(583-585)tcA>tcG	p.S195S	RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000529935.1_Intron|FMO2_ENST00000441535.1_Silent_p.S195S|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	195					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.S195S(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGGGAAACTCAGGCTCAGATA	0.488													G|||	2951	0.589257	0.7209	0.6167	5008	,	,		19431	0.6032		0.3877	False		,,,				2504	0.5849				p.S195S		Atlas-SNP	.											FMO2,NS,carcinoma,0,2	FMO2	66	2	1	Substitution - coding silent(1)	stomach(1)	c.A585G						PASS	.	G		2951,1455	468.5+/-355.1	983,985,235	135.0	140.0	139.0		585	-12.3	0.0	1	dbSNP_98	139	3589,5011	627.2+/-397.9	765,2059,1476	no	coding-synonymous	FMO2	NM_001460.2		1748,3044,1711	GG,GA,AA		41.7326,33.0232,49.7155		195/472	171168585	6540,6466	2203	4300	6503	SO:0001819	synonymous_variant	2327	exon5			AAACTCAGGCTCA	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.585A>G	1.37:g.171168585A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	236	124	0.525424	NM_001460	Q53XR0	Silent	SNP	ENST00000209929.7	37	CCDS1293.1																																																																																			A|0.536;G|0.464	0.464	strong		0.488	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
MCC	4163	hgsc.bcm.edu	37	5	112437438	112437438	+	Silent	SNP	T	T	G	rs62374708	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112437438T>G	ENST00000302475.4	-	6	1389	c.826A>C	c.(826-828)Agg>Cgg	p.R276R	MCC_ENST00000515367.2_Silent_p.R213R|MCC_ENST00000408903.3_Silent_p.R466R|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	276					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ATGCTCACCCTCCTCCGGAGC	0.587													T|||	378	0.0754792	0.2315	0.0144	5008	,	,		16935	0.0417		0.0119	False		,,,				2504	0.0082				p.R466R		Atlas-SNP	.											MCC_ENST00000408903,NS,carcinoma,+1,2	MCC	234	2	0			c.A1396C						PASS	.	T	,	852,3552	334.4+/-303.4	86,680,1436	95.0	90.0	92.0		1396,826	0.2	1.0	5	dbSNP_129	92	93,8507	51.1+/-111.2	1,91,4208	no	coding-synonymous,coding-synonymous	MCC	NM_001085377.1,NM_002387.2	,	87,771,5644	GG,GT,TT		1.0814,19.346,7.267	,	466/1020,276/830	112437438	945,12059	2202	4300	6502	SO:0001819	synonymous_variant	4163	exon8			TCACCCTCCTCCG		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.826A>C	5.37:g.112437438T>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_001085377	D3DT05|Q6ZR04	Silent	SNP	ENST00000302475.4	37	CCDS4111.1																																																																																			T|0.933;G|0.067	0.067	strong		0.587	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
DNAH17	8632	hgsc.bcm.edu	37	17	76547634	76547634	+	Missense_Mutation	SNP	T	T	C	rs16971526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76547634T>C	ENST00000585328.1	-	16	2498	c.2374A>G	c.(2374-2376)Att>Gtt	p.I792V	DNAH17_ENST00000389840.5_Missense_Mutation_p.I792V	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	792	Stem. {ECO:0000250}.		I -> V (in dbSNP:rs16971526).		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)			GCCTGGGAAATTCCTTCTATA	0.498													T|||	496	0.0990415	0.0265	0.1167	5008	,	,		19070	0.1032		0.1034	False		,,,				2504	0.1759				p.I792V		Atlas-SNP	.											.	DNAH17	347	.	0			c.A2374G						PASS	.	T	VAL/ILE	186,4220	118.8+/-156.5	5,176,2022	160.0	128.0	139.0		2374	2.4	0.0	17	dbSNP_123	139	1147,7453	236.2+/-268.5	81,985,3234	yes	missense	DNAH17	NM_173628.3	29	86,1161,5256	CC,CT,TT		13.3372,4.2215,10.2491	possibly-damaging	792/4463	76547634	1333,11673	2203	4300	6503	SO:0001583	missense	8632	exon16			GGGAAATTCCTTC	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.2374A>G	17.37:g.76547634T>C	ENSP00000465516:p.Ile792Val	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	153	64	0.418301	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		193	0.08836996336996338	19	0.03861788617886179	49	0.13535911602209943	49	0.08566433566433566	76	0.10026385224274406	T	2.588	-0.295801	0.05532	0.042215	0.133372	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.26957	1.7	4.6	2.37	0.29283	.	.	.	.	.	T	0.00300	0.0009	M	0.72576	2.205	0.80722	P	0.0	P	0.45240	0.854	P	0.51266	0.664	T	0.04115	-1.0976	8	0.54805	T	0.06	.	7.479	0.27393	0.0:0.1769:0.0:0.8231	rs16971526;rs52814830;rs16971526	494	Q9UFH2-4	.	V	792	ENSP00000374490:I792V	ENSP00000300671:I792V	I	-	1	0	DNAH17	74059229	0.898000	0.30612	0.009000	0.14445	0.015000	0.08874	1.822000	0.39052	0.239000	0.21243	0.379000	0.24179	ATT	T|0.904;C|0.096	0.096	strong		0.498	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
MIA2	117153	hgsc.bcm.edu	37	14	39703324	39703324	+	Silent	SNP	A	A	G	rs7141840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:39703324A>G	ENST00000280082.3	+	1	205	c.6A>G	c.(4-6)gcA>gcG	p.A2A	MIA2_ENST00000556784.1_Silent_p.A2A|RP11-407N17.3_ENST00000553728.1_Silent_p.A2A	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	2					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		TTAGCATGGCAAAATTTGGCG	0.423													G|||	3004	0.59984	0.8616	0.5029	5008	,	,		16921	0.6548		0.4742	False		,,,				2504	0.3875				p.A2A		Atlas-SNP	.											.	MIA2	82	.	0			c.A6G						PASS	.	G		3614,792	317.2+/-295.0	1495,624,84	94.0	89.0	91.0		6	3.3	0.4	14	dbSNP_116	91	4174,4426	586.5+/-392.1	1019,2136,1145	no	coding-synonymous	MIA2	NM_054024.3		2514,2760,1229	GG,GA,AA		48.5349,17.9755,40.1199		2/655	39703324	7788,5218	2203	4300	6503	SO:0001819	synonymous_variant	117153	exon1			CATGGCAAAATTT	BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.6A>G	14.37:g.39703324A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_054024	A1L4H0|Q9H6C1	Silent	SNP	ENST00000280082.3	37	CCDS9672.1																																																																																			A|0.389;G|0.611	0.611	strong		0.423	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024	
BRAF	673	hgsc.bcm.edu	37	7	140481425	140481425	+	Silent	SNP	T	T	C	rs56216404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140481425T>C	ENST00000288602.6	-	11	1443	c.1383A>G	c.(1381-1383)caA>caG	p.Q461Q		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	461	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)	ATCCAATTCTTTGTCCCACTG	0.393		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				T|||	27	0.00539137	0.0204	0.0	5008	,	,		15131	0.0		0.0	False		,,,				2504	0.0				p.Q461Q	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.A1383G						PASS	.	T		41,4365	43.1+/-76.7	0,41,2162	170.0	145.0	154.0		1383	-3.9	1.0	7	dbSNP_129	154	0,8596		0,0,4298	no	coding-synonymous	BRAF	NM_004333.4		0,41,6460	CC,CT,TT		0.0,0.9305,0.3153		461/767	140481425	41,12961	2203	4298	6501	SO:0001819	synonymous_variant	673	exon11	Familial Cancer Database	CFC, CFCS	AATTCTTTGTCCC	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.1383A>G	7.37:g.140481425T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	T	9.986	1.229394	0.22542	0.009305	0.0	ENSG00000157764	ENST00000496384	.	.	.	5.62	-3.94	0.04130	.	.	.	.	.	T	0.26593	0.0650	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40887	-0.9539	4	.	.	.	.	7.9193	0.29837	0.1332:0.5351:0.0:0.3317	rs56216404;rs61730028	.	.	.	R	69	.	.	K	-	2	0	BRAF	140127894	0.871000	0.30034	0.970000	0.41538	0.993000	0.82548	-0.010000	0.12743	-0.751000	0.04734	-0.481000	0.04817	AAA	T|0.995;C|0.005	0.005	strong		0.393	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201866	32201866	+	RNA	SNP	A	A	G	rs9982755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:32201866A>G	ENST00000452750.1	-	0	212							Q8IUC3	KRA71_HUMAN	keratin associated protein 7-1 (gene/pseudogene)							intermediate filament (GO:0005882)											TAGCCCAGGGAGCTGTAGCCA	0.567													A|||	2557	0.510583	0.4266	0.6614	5008	,	,		18117	0.4454		0.5278	False		,,,				2504	0.5665				p.S51P		Atlas-SNP	.											.	.	.	.	0			c.T151C						PASS	.						53.0	59.0	57.0					21																	32201866		692	1591	2283			337878	exon2			CCAGGGAGCTGTA	AJ457063	CCDS74780.1	21q22.1	2014-04-10	2010-03-12		ENSG00000184586	ENSG00000274749		"""Keratin associated proteins"""	18934	protein-coding gene	gene with protein product			"""keratin associated protein 7-1"""			12359730	Standard	NM_181606		Approved	KAP7.1	uc011adj.2	Q8IUC3	OTTHUMG00000188305		21.37:g.32201866A>G		Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	248	117	0.471774	NM_181606	Q3LI56	Missense_Mutation	SNP	ENST00000452750.1	37																																																																																				A|0.480;G|0.520	0.520	strong		0.567	KRTAP7-1-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000128248.3	NM_181606	
NPL	80896	hgsc.bcm.edu	37	1	182787797	182787797	+	Silent	SNP	G	G	A	rs58343016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182787797G>A	ENST00000367553.1	+	8	623	c.579G>A	c.(577-579)caG>caA	p.Q193Q	NPL_ENST00000258317.2_Silent_p.Q193Q|NPL_ENST00000367555.1_Silent_p.Q193Q|NPL_ENST00000367552.2_Silent_p.Q193Q|NPL_ENST00000367554.3_Silent_p.Q174Q|NPL_ENST00000463899.1_3'UTR	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	193					carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)			breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						GCCAGCAACAGTTTGCTTTCC	0.458													G|||	83	0.0165735	0.0605	0.0043	5008	,	,		20020	0.0		0.0	False		,,,				2504	0.0				p.Q193Q		Atlas-SNP	.											.	NPL	55	.	0			c.G579A						PASS	.	G	,,,,	222,4184	133.7+/-170.0	5,212,1986	73.0	73.0	73.0		522,579,579,579,579	-0.5	1.0	1	dbSNP_129	73	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPL	NM_001200050.1,NM_001200051.1,NM_001200052.1,NM_001200056.1,NM_030769.2	,,,,	5,212,6286	AA,AG,GG		0.0,5.0386,1.7069	,,,,	174/302,193/241,193/231,193/285,193/321	182787797	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	80896	exon9			GCAACAGTTTGCT	AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"""dihydrodipicolinate synthetase homolog 1 (E. coli)"""	611412	"""chromosome 1 open reading frame 13"""	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.579G>A	1.37:g.182787797G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_001200052	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Silent	SNP	ENST00000367553.1	37	CCDS1350.1																																																																																			G|0.983;A|0.017	0.017	strong		0.458	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769	
DGUOK	1716	hgsc.bcm.edu	37	2	74174013	74174013	+	Silent	SNP	G	G	A	rs1804599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74174013G>A	ENST00000264093.4	+	3	508	c.423G>A	c.(421-423)gaG>gaA	p.E141E	DGUOK_ENST00000348222.1_Silent_p.E141E|DGUOK_ENST00000356837.6_Silent_p.E119E|DGUOK_ENST00000462685.1_3'UTR|DGUOK-AS1_ENST00000453103.1_RNA	NM_080916.2	NP_550438.1	Q16854	DGUOK_HUMAN	deoxyguanosine kinase	141					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|dGTP metabolic process (GO:0046070)|guanosine metabolic process (GO:0008617)|negative regulation of neuron projection development (GO:0010977)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein phosphorylation (GO:0006468)|purine deoxyribonucleoside metabolic process (GO:0046122)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxyguanosine kinase activity (GO:0004138)|nucleoside kinase activity (GO:0019206)			endometrium(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	8					Nelarabine(DB01280)	AGATCTTTGAGAGGTCTGTGT	0.507													G|||	89	0.0177716	0.0613	0.0115	5008	,	,		17020	0.0		0.0	False		,,,				2504	0.0				p.E141E		Atlas-SNP	.											.	DGUOK	16	.	0			c.G423A						PASS	.	G	,	197,4209	124.1+/-161.4	6,185,2012	49.0	43.0	45.0		423,423	4.8	1.0	2	dbSNP_89	45	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	DGUOK	NM_080916.1,NM_080918.1	,	6,187,6310	AA,AG,GG		0.0233,4.4712,1.5301	,	141/278,141/190	74174013	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	1716	exon3			CTTTGAGAGGTCT	U41668	CCDS1931.1, CCDS1932.1	2p13	2008-02-05			ENSG00000114956	ENSG00000114956	2.7.1.113		2858	protein-coding gene	gene with protein product		601465					Standard	NM_080916		Approved	dGK	uc002sjx.3	Q16854	OTTHUMG00000129819	ENST00000264093.4:c.423G>A	2.37:g.74174013G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_080918	P78532|Q16759|Q4ZG09|Q7L1W9|Q96BC1	Silent	SNP	ENST00000264093.4	37	CCDS1931.1																																																																																			G|0.986;A|0.014	0.014	strong		0.507	DGUOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252050.1		
PRMT9	90826	hgsc.bcm.edu	37	4	148594177	148594177	+	Missense_Mutation	SNP	C	C	T	rs73853975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:148594177C>T	ENST00000322396.6	-	4	918	c.676G>A	c.(676-678)Gaa>Aaa	p.E226K	PRMT10_ENST00000541232.1_Missense_Mutation_p.E113K	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		226	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						ATCCCTGCTTCCATCTTGTTT	0.388													C|||	229	0.0457268	0.1702	0.0058	5008	,	,		14532	0.0		0.0	False		,,,				2504	0.0				p.E226K		Atlas-SNP	.											.	PRMT10	68	.	0			c.G676A						PASS	.	C	LYS/GLU	610,3796	267.1+/-267.6	41,528,1634	160.0	150.0	154.0		676	4.6	1.0	4	dbSNP_130	154	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PRMT10	NM_138364.2	56	41,531,5931	TT,TC,CC		0.0349,13.8448,4.7132	benign	226/846	148594177	613,12393	2203	4300	6503	SO:0001583	missense	90826	exon4			CTGCTTCCATCTT																												ENST00000322396.6:c.676G>A	4.37:g.148594177C>T	ENSP00000314396:p.Glu226Lys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	151	77	0.509934	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	106	0.048534798534798536	105	0.21341463414634146	1	0.0027624309392265192	0	0.0	0	0.0	C	18.24	3.579466	0.65878	0.138448	3.49E-4	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.23348	1.91;1.91	5.44	4.58	0.56647	.	0.210963	0.49305	D	0.000159	T	0.00012	0.0000	L	0.38733	1.17	0.24656	P	0.99349699	B	0.24675	0.109	B	0.30943	0.122	T	0.21211	-1.0252	9	0.41790	T	0.15	-7.5111	10.3867	0.44145	0.0:0.791:0.1363:0.0727	.	226	Q6P2P2	ANM10_HUMAN	K	226;113	ENSP00000314396:E226K;ENSP00000439508:E113K	ENSP00000314396:E226K	E	-	1	0	PRMT10	148813627	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	3.053000	0.49901	1.242000	0.43836	0.655000	0.94253	GAA	C|0.946;T|0.054	0.054	strong		0.388	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
ARMC2	84071	hgsc.bcm.edu	37	6	109274527	109274527	+	Missense_Mutation	SNP	A	A	G	rs113651966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:109274527A>G	ENST00000392644.4	+	13	2056	c.1888A>G	c.(1888-1890)Ata>Gta	p.I630V	ARMC2_ENST00000368972.3_Missense_Mutation_p.I465V	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	630										endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)	24		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		CAACCCGGGGATAGTGGGCCT	0.647													A|||	185	0.0369409	0.1354	0.0086	5008	,	,		15139	0.0		0.0	False		,,,				2504	0.0				p.I630V		Atlas-SNP	.											.	ARMC2	56	.	0			c.A1888G						PASS	.	A	VAL/ILE	364,4034		19,326,1854	19.0	22.0	21.0		1888	0.2	0.0	6	dbSNP_132	21	4,8582		0,4,4289	yes	missense	ARMC2	NM_032131.4	29	19,330,6143	GG,GA,AA		0.0466,8.2765,2.8343	benign	630/868	109274527	368,12616	2199	4293	6492	SO:0001583	missense	84071	exon13			CCGGGGATAGTGG	BC030603	CCDS5069.2, CCDS69168.1	6q21	2013-02-14			ENSG00000118690	ENSG00000118690		"""Armadillo repeat containing"""	23045	protein-coding gene	gene with protein product							Standard	XM_005267154		Approved	DKFZp434P0714, bA787I22.1	uc003pss.4	Q8NEN0	OTTHUMG00000015335	ENST00000392644.4:c.1888A>G	6.37:g.109274527A>G	ENSP00000376417:p.Ile630Val	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_032131	A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	Missense_Mutation	SNP	ENST00000392644.4	37	CCDS5069.2	54	0.024725274725274724	52	0.10569105691056911	2	0.0055248618784530384	0	0.0	0	0.0	A	0.641	-0.813501	0.02798	0.082765	4.66E-4	ENSG00000118690	ENST00000368972;ENST00000392644	T;T	0.45276	0.9;0.9	5.77	0.178	0.15058	Armadillo-like helical (1);Armadillo-type fold (1);	0.543484	0.20833	N	0.084855	T	0.02807	0.0084	N	0.01705	-0.755	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.36504	-0.9745	10	0.06891	T	0.86	.	1.986	0.03436	0.4394:0.1382:0.2977:0.1247	.	630	Q8NEN0	ARMC2_HUMAN	V	465;630	ENSP00000357968:I465V;ENSP00000376417:I630V	ENSP00000357968:I465V	I	+	1	0	ARMC2	109381220	0.002000	0.14202	0.000000	0.03702	0.027000	0.11550	0.009000	0.13219	-0.042000	0.13535	-0.249000	0.11873	ATA	A|0.969;G|0.031	0.031	strong		0.647	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041732.2	NM_032131	
MUC4	4585	hgsc.bcm.edu	37	3	195511690	195511690	+	Missense_Mutation	SNP	G	G	C	rs199920095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511690G>C	ENST00000463781.3	-	2	7220	c.6761C>G	c.(6760-6762)aCc>aGc	p.T2254S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2254S	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)		AAGAGGGGTGGTGTCACCTGT	0.582													.|||	270	0.0539137	0.0809	0.0447	5008	,	,		11644	0.0		0.0984	False		,,,				2504	0.0337				p.T2254S		Atlas-SNP	.											MUC4_ENST00000463781,NS,haematopoietic_neoplasm,0,1	MUC4	1505	1	0			c.C6761G						PASS	.						31.0	28.0	29.0					3																	195511690		686	1583	2269	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.6761C>G	3.37:g.195511690G>C	ENSP00000417498:p.Thr2254Ser	Somatic	536	0	0		WXS	Illumina HiSeq	Phase_I	242	100	0.413223	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	2.943	-0.218414	0.06101	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.49;1.53	.	.	.	.	.	.	.	.	T	0.17534	0.0421	N	0.19112	0.55	0.09310	N	1	P	0.42584	0.784	B	0.39706	0.307	T	0.11641	-1.0579	6	.	.	.	.	.	.	.	.	2254	E7ESK3	.	S	2254	ENSP00000417498:T2254S;ENSP00000420243:T2254S	.	T	-	2	0	MUC4	196996085	0.002000	0.14202	0.012000	0.15200	0.106000	0.19336	0.449000	0.21744	0.488000	0.27723	0.064000	0.15345	ACC	G|0.945;C|0.055	0.055	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
AGAP7P	653268	hgsc.bcm.edu	37	10	51465429	51465429	+	Missense_Mutation	SNP	C	C	T	rs183573385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:51465429C>T	ENST00000374095.5	-	7	1152	c.1027G>A	c.(1027-1029)Gac>Aac	p.D343N		NM_001077685.1	NP_001071153.1	Q5VUJ5	AGAP7_HUMAN		343	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	11						GTGTCCATGTCCTTGGATAGG	0.562													-|||	17	0.00339457	0.0	0.0043	5008	,	,		17858	0.0		0.0139	False		,,,				2504	0.0				p.D343N		Atlas-SNP	.											.	AGAP7	33	.	0			c.G1027A						PASS	.	C	ASN/ASP	8,4396		0,8,2194	116.0	137.0	130.0		1027		0.0	10		130	44,8556		0,44,4256	no	missense	AGAP7	NM_001077685.1	23	0,52,6450	TT,TC,CC		0.5116,0.1817,0.3999	benign	343/664	51465429	52,12952	2202	4300	6502	SO:0001583	missense	653268	exon7			CCATGTCCTTGGA																												ENST00000374095.5:c.1027G>A	10.37:g.51465429C>T	ENSP00000363208:p.Asp343Asn	Somatic	591	0	0		WXS	Illumina HiSeq	Phase_I	650	348	0.535385	NM_001077685	A6NGH4	Missense_Mutation	SNP	ENST00000374095.5	37	CCDS41524.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	.	4.603	0.112029	0.08831	0.001817	0.005116	ENSG00000204169	ENST00000374095	T	0.56103	0.48	.	.	.	Pleckstrin homology domain (3);	0.720818	0.12823	N	0.436252	T	0.35393	0.0930	M	0.74647	2.275	0.25300	N	0.98928	B	0.06786	0.001	B	0.15052	0.012	T	0.30937	-0.9961	9	0.27082	T	0.32	.	4.5676	0.12195	0.0:0.6819:0.0:0.3181	.	343	Q5VUJ5	AGAP7_HUMAN	N	343	ENSP00000363208:D343N	ENSP00000363208:D343N	D	-	1	0	AGAP7	51135435	0.999000	0.42202	0.016000	0.15963	0.016000	0.09150	2.917000	0.48821	-1.351000	0.02197	-1.360000	0.01215	GAC	C|0.996;T|0.004	0.004	strong		0.562	AGAP7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048033.1		
FOXD4	2298	hgsc.bcm.edu	37	9	117877	117877	+	Silent	SNP	C	C	T	rs7022056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117877C>T	ENST00000382500.2	-	1	540	c.243G>A	c.(241-243)gaG>gaA	p.E81E		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	81					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)		CGGTGCCAAACTCTGAGGGGT	0.711													C|||	1209	0.241414	0.4198	0.2594	5008	,	,		13926	0.0496		0.2296	False		,,,				2504	0.1973				p.E81E		Atlas-SNP	.											.	FOXD4	75	.	0			c.G243A						PASS	.	C		1567,2821		218,1131,845	37.0	62.0	53.0		243	0.3	0.0	9	dbSNP_116	53	2002,6582		167,1668,2457	no	coding-synonymous	FOXD4	NM_207305.3		385,2799,3302	TT,TC,CC		23.3225,35.711,27.5131		81/440	117877	3569,9403	2194	4292	6486	SO:0001819	synonymous_variant	2298	exon1			GCCAAACTCTGAG	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.243G>A	9.37:g.117877C>T		Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	349	170	0.487106	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Silent	SNP	ENST00000382500.2	37	CCDS34975.1																																																																																			C|0.500;T|0.500	0.500	weak		0.711	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
CARD14	79092	hgsc.bcm.edu	37	17	78177668	78177668	+	Missense_Mutation	SNP	G	G	A	rs34822755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78177668G>A	ENST00000573882.1	+	18	2803	c.2267G>A	c.(2266-2268)tGc>tAc	p.C756Y	RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000576824.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|RP11-334C17.5_ENST00000573935.1_RNA|CARD14_ENST00000392434.2_3'UTR|CARD14_ENST00000344227.2_Missense_Mutation_p.C756Y			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	756					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			ACTCAGCAGTGCACCGTGACC	0.672													G|||	38	0.00758786	0.0272	0.0029	5008	,	,		16016	0.0		0.0	False		,,,				2504	0.0				p.C756Y		Atlas-SNP	.											.	CARD14	98	.	0			c.G2267A						PASS	.	G	TYR/CYS	127,4273		2,123,2075	27.0	24.0	25.0		2267	3.1	0.2	17	dbSNP_126	25	4,8592		0,4,4294	yes	missense	CARD14	NM_024110.3	194	2,127,6369	AA,AG,GG		0.0465,2.8864,1.008	benign	756/1005	78177668	131,12865	2200	4298	6498	SO:0001583	missense	79092	exon16			AGCAGTGCACCGT	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2267G>A	17.37:g.78177668G>A	ENSP00000458715:p.Cys756Tyr	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	283	139	0.491166	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	7.289	0.610773	0.14066	0.028864	4.65E-4	ENSG00000141527	ENST00000344227	T	0.05258	3.47	4.12	3.12	0.35913	.	0.712962	0.13426	N	0.388808	T	0.01320	0.0043	N	0.14661	0.345	0.33297	D	0.5643	B	0.15141	0.012	B	0.18871	0.023	T	0.17837	-1.0356	10	0.59425	D	0.04	-4.1501	6.7425	0.23443	0.1003:0.1828:0.7169:0.0	rs34822755	756	Q9BXL6	CAR14_HUMAN	Y	756	ENSP00000344549:C756Y	ENSP00000344549:C756Y	C	+	2	0	CARD14	75792263	0.870000	0.30015	0.159000	0.22649	0.311000	0.27955	1.320000	0.33666	0.706000	0.31912	0.485000	0.47835	TGC	G|0.991;A|0.009	0.009	strong		0.672	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
SH2D4A	63898	hgsc.bcm.edu	37	8	19192332	19192332	+	Silent	SNP	G	G	T	rs56005620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:19192332G>T	ENST00000265807.3	+	4	888	c.477G>T	c.(475-477)tcG>tcT	p.S159S	SH2D4A_ENST00000519207.1_Silent_p.S159S|SH2D4A_ENST00000518040.1_Silent_p.S114S	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						PASS	.	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	74	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	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	
GRIK1	2897	hgsc.bcm.edu	37	21	30925928	30925928	+	Missense_Mutation	SNP	A	A	G	rs363504	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:30925928A>G	ENST00000399907.1	-	17	3116	c.2705T>C	c.(2704-2706)tTa>tCa	p.L902S	GRIK1_ENST00000535441.1_Intron|GRIK1_ENST00000389125.3_Intron|GRIK1_ENST00000399913.1_Intron|GRIK1_ENST00000399909.1_Missense_Mutation_p.L887S|GRIK1_ENST00000327783.4_Intron|GRIK1_ENST00000389124.2_Intron|GRIK1_ENST00000309434.7_Missense_Mutation_p.L904S|GRIK1_ENST00000399914.1_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	85	0	0		WXS	Illumina HiSeq	Phase_I	105	59	0.561905	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		
USP24	23358	hgsc.bcm.edu	37	1	55545240	55545240	+	Missense_Mutation	SNP	T	T	C	rs116203669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55545240T>C	ENST00000294383.6	-	60	7170	c.7171A>G	c.(7171-7173)Atg>Gtg	p.M2391V	USP24_ENST00000407756.1_Missense_Mutation_p.M2231V	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	2391					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						CCTTCAGACATGAACAACAAG	0.433													T|||	23	0.00459265	0.0174	0.0	5008	,	,		20623	0.0		0.0	False		,,,				2504	0.0				p.M2391V		Atlas-SNP	.											.	USP24	323	.	0			c.A7171G						PASS	.	T	VAL/MET	33,3727		0,33,1847	159.0	154.0	156.0		7171	-2.0	1.0	1	dbSNP_132	156	0,8242		0,0,4121	yes	missense	USP24	NM_015306.2	21	0,33,5968	CC,CT,TT		0.0,0.8777,0.275	benign	2391/2621	55545240	33,11969	1880	4121	6001	SO:0001583	missense	23358	exon60			CAGACATGAACAA	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.7171A>G	1.37:g.55545240T>C	ENSP00000294383:p.Met2391Val	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	0.334	-0.954398	0.02285	0.008777	0.0	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.01887	4.58;4.58	4.8	-1.97	0.07503	.	0.295167	0.28544	N	0.014980	T	0.00468	0.0015	N	0.02539	-0.55	0.20764	N	0.999858	B	0.02656	0.0	B	0.01281	0.0	T	0.46707	-0.9172	10	0.28530	T	0.3	.	5.8291	0.18570	0.3638:0.0:0.4105:0.2258	.	2231	B7WPF4	.	V	2391;2231	ENSP00000294383:M2391V;ENSP00000385700:M2231V	ENSP00000294383:M2391V	M	-	1	0	USP24	55317828	0.985000	0.35326	0.995000	0.50966	0.984000	0.73092	0.139000	0.16036	-0.284000	0.09102	-0.691000	0.03719	ATG	T|0.996;C|0.004	0.004	strong		0.433	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
MUC16	94025	hgsc.bcm.edu	37	19	9071916	9071916	+	Missense_Mutation	SNP	G	G	A	rs35346115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9071916G>A	ENST00000397910.4	-	3	15733	c.15530C>T	c.(15529-15531)aCt>aTt	p.T5177I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5179	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AATGTTTGTAGTCTCAGAGGA	0.478													G|||	49	0.00978435	0.0008	0.0216	5008	,	,		20472	0.001		0.0268	False		,,,				2504	0.0051				p.T5177I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C15530T						PASS	.	G	ILE/THR	17,3971		0,17,1977	283.0	266.0	272.0		15530	0.6	0.0	19	dbSNP_126	272	253,8085		5,243,3921	yes	missense	MUC16	NM_024690.2	89	5,260,5898	AA,AG,GG		3.0343,0.4263,2.1905	probably-damaging	5177/14508	9071916	270,12056	1994	4169	6163	SO:0001583	missense	94025	exon3			TTTGTAGTCTCAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15530C>T	19.37:g.9071916G>A	ENSP00000381008:p.Thr5177Ile	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	169	85	0.502959	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	28	0.01282051282051282	0	0.0	6	0.016574585635359115	1	0.0017482517482517483	21	0.027704485488126648	g	2.171	-0.389853	0.04932	0.004263	0.030343	ENSG00000181143	ENST00000397910	T	0.23147	1.92	1.65	0.563	0.17296	.	.	.	.	.	T	0.11281	0.0275	L	0.55481	1.735	.	.	.	D	0.65815	0.995	P	0.51945	0.685	T	0.24621	-1.0155	8	0.87932	D	0	.	4.0586	0.09827	0.2293:0.0:0.7707:0.0	rs35346115	5177	B5ME49	.	I	5177	ENSP00000381008:T5177I	ENSP00000381008:T5177I	T	-	2	0	MUC16	8932916	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.111000	0.03303	0.269000	0.21961	0.121000	0.15741	ACT	G|0.980;A|0.020	0.020	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GEMIN4	50628	hgsc.bcm.edu	37	17	650371	650371	+	Silent	SNP	C	C	T	rs61735317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:650371C>T	ENST00000319004.5	-	2	1030	c.912G>A	c.(910-912)tcG>tcA	p.S304S	GEMIN4_ENST00000437269.1_3'UTR|GEMIN4_ENST00000576778.1_Silent_p.S293S	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	304					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GTTTGGCCAGCGAGGTCAGGC	0.627													C|||	116	0.0231629	0.0832	0.0058	5008	,	,		20285	0.0		0.002	False		,,,				2504	0.0				p.S304S		Atlas-SNP	.											.	GEMIN4	116	.	0			c.G912A						PASS	.	C		280,3980		7,266,1857	116.0	127.0	124.0		912	-11.3	0.1	17	dbSNP_129	124	4,8464		0,4,4230	no	coding-synonymous	GEMIN4	NM_015721.2		7,270,6087	TT,TC,CC		0.0472,6.5728,2.2313		304/1059	650371	284,12444	2130	4234	6364	SO:0001819	synonymous_variant	50628	exon2			GGCCAGCGAGGTC	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.912G>A	17.37:g.650371C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	118	66	0.559322	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			C|0.978;T|0.022	0.022	strong		0.627	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
C1orf61	10485	hgsc.bcm.edu	37	1	156377720	156377720	+	Silent	SNP	G	G	A	rs141938076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156377720G>A	ENST00000368243.1	-	5	335	c.219C>T	c.(217-219)tcC>tcT	p.S73S	C1orf61_ENST00000488498.2_5'UTR	NM_006365.1	NP_006356.1	Q13536	CROC4_HUMAN	chromosome 1 open reading frame 61	73						nucleus (GO:0005634)				large_intestine(2)|lung(2)|skin(1)	5	Hepatocellular(266;0.158)					TACACCTGGTGGAGATTCCAC	0.582													G|||	12	0.00239617	0.0083	0.0014	5008	,	,		19992	0.0		0.0	False		,,,				2504	0.0				p.S73S		Atlas-SNP	.											.	C1orf61	15	.	0			c.C219T						PASS	.	G		24,4382		0,24,2179	114.0	86.0	96.0		219	-0.4	0.0	1	dbSNP_134	96	0,8594		0,0,4297	no	coding-synonymous	C1orf61	NM_006365.1		0,24,6476	AA,AG,GG		0.0,0.5447,0.1846		73/157	156377720	24,12976	2203	4297	6500	SO:0001819	synonymous_variant	10485	exon5			CCTGGTGGAGATT		CCDS1142.1	1q22	2014-03-17			ENSG00000125462	ENSG00000125462			30780	protein-coding gene	gene with protein product	"""contingent replication of cDNA-4"", ""transcriptional activator of the c fos promoter"""					10995546, 23012322	Standard	XM_005244832		Approved	CROC4	uc001fou.1	Q13536	OTTHUMG00000031022	ENST00000368243.1:c.219C>T	1.37:g.156377720G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_006365	B1ALL5|B1ALL8	Silent	SNP	ENST00000368243.1	37	CCDS1142.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	3.575	-0.086754	0.07097	0.005447	0.0	ENSG00000125462	ENST00000368242	.	.	.	3.36	-0.454	0.12197	.	.	.	.	.	T	0.12305	0.0299	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32719	-0.9896	4	.	.	.	.	5.8054	0.18438	0.5029:0.0:0.4971:0.0	.	.	.	.	L	105	.	.	P	-	2	0	C1orf61	154644344	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.003000	0.13083	-0.069000	0.12931	0.542000	0.68232	CCA	G|0.998;A|0.002	0.002	strong		0.582	C1orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075988.1	NM_006365	
ABCA12	26154	hgsc.bcm.edu	37	2	215851303	215851303	+	Silent	SNP	A	A	G	rs34351934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	85	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	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	
MSLN	10232	hgsc.bcm.edu	37	16	814058	814058	+	Missense_Mutation	SNP	C	C	T	rs9927389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:814058C>T	ENST00000382862.3	+	5	310	c.215C>T	c.(214-216)gCg>gTg	p.A72V	MSLN_ENST00000566549.1_Missense_Mutation_p.A72V|MSLN_ENST00000545450.2_Missense_Mutation_p.A72V|MSLN_ENST00000563941.1_Missense_Mutation_p.A72V	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	72			A -> V (in dbSNP:rs9927389).		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)				TTCCCGTGTGCGGAGGTGTCC	0.647													C|||	464	0.0926518	0.1422	0.0375	5008	,	,		13653	0.0367		0.0179	False		,,,				2504	0.1994				p.A72V		Atlas-SNP	.											MSLN_ENST00000446427,NS,carcinoma,0,2	MSLN	109	2	0			c.C215T						scavenged	.	C	VAL/ALA,VAL/ALA,VAL/ALA	498,3886	224.9+/-240.9	25,448,1719	53.0	43.0	46.0		215,215,215	-1.8	0.0	16	dbSNP_119	46	177,8401	79.8+/-142.4	3,171,4115	yes	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	64,64,64	28,619,5834	TT,TC,CC		2.0634,11.3595,5.2075	benign,benign,benign	72/623,72/623,72/631	814058	675,12287	2192	4289	6481	SO:0001583	missense	10232	exon6			CGTGTGCGGAGGT	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.215C>T	16.37:g.814058C>T	ENSP00000372313:p.Ala72Val	Somatic	50	1	0.02		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	108	0.04945054945054945	59	0.11991869918699187	14	0.03867403314917127	24	0.04195804195804196	11	0.014511873350923483	C	4.746	0.138663	0.09083	0.113595	0.020634	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.12569	2.67;2.67	2.72	-1.81	0.07882	.	2.331450	0.02832	N	0.126889	T	0.00109	0.0003	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.17465	0.007;0.015;0.022;0.007	B;B;B;B	0.11329	0.003;0.006;0.003;0.003	T	0.33137	-0.9880	10	0.31617	T	0.26	0.2519	5.264	0.15589	0.4048:0.4736:0.0:0.1216	rs9927389;rs9927389	71;72;72;72	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	V	72	ENSP00000442965:A72V;ENSP00000372313:A72V	ENSP00000372313:A72V	A	+	2	0	MSLN	754059	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.582000	0.00905	-1.484000	0.01856	-2.388000	0.00228	GCG	C|0.941;T|0.059	0.059	strong		0.647	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
LSM4	25804	hgsc.bcm.edu	37	19	18420501	18420501	+	Silent	SNP	G	G	A	rs148380214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18420501G>A	ENST00000593829.1	-	4	568	c.315C>T	c.(313-315)ggC>ggT	p.G105G	LSM4_ENST00000252816.6_Silent_p.G91G	NM_001252129.1|NM_012321.4	NP_001239058.1|NP_036453.1	Q9Y4Z0	LSM4_HUMAN	LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)	105					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U6 snRNP (GO:0005688)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|lung(3)	6						GGCCAGCGCCGCCCATGCCGC	0.682													g|||	9	0.00179712	0.0068	0.0	5008	,	,		16325	0.0		0.0	False		,,,				2504	0.0				p.G105G		Atlas-SNP	.											.	LSM4	15	.	0			c.C315T						PASS	.			37,4365		0,37,2164	29.0	28.0	28.0		315	-3.1	1.0	19	dbSNP_134	28	0,8596		0,0,4298	no	coding-synonymous	LSM4	NM_012321.3		0,37,6462	AA,AG,GG		0.0,0.8405,0.2847		105/140	18420501	37,12961	2201	4298	6499	SO:0001819	synonymous_variant	25804	exon4			AGCGCCGCCCATG	AF117235	CCDS12374.1, CCDS62601.1	19p13.1	2008-02-05				ENSG00000130520			17259	protein-coding gene	gene with protein product		607284				10369684, 10523320	Standard	NM_012321		Approved	YER112W	uc002niq.3	Q9Y4Z0		ENST00000593829.1:c.315C>T	19.37:g.18420501G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	35	26	0.742857	NM_012321		Silent	SNP	ENST00000593829.1	37	CCDS12374.1																																																																																			G|0.997;A|0.003	0.003	strong		0.682	LSM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466321.1		
ZNF610	162963	hgsc.bcm.edu	37	19	52869278	52869278	+	Missense_Mutation	SNP	G	G	C	rs321937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52869278G>C	ENST00000403906.3	+	6	1103	c.647G>C	c.(646-648)cGt>cCt	p.R216P	ZNF610_ENST00000321287.8_Missense_Mutation_p.R216P|ZNF610_ENST00000601151.1_Missense_Mutation_p.R173P|ZNF610_ENST00000327920.8_Missense_Mutation_p.R216P	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	216			R -> P (in dbSNP:rs321937). {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)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		TTTAGAGTCCGTGCAAGCCTT	0.378													C|||	4062	0.811102	0.82	0.7954	5008	,	,		19235	0.6419		0.9006	False		,,,				2504	0.8926				p.R216P		Atlas-SNP	.											.	ZNF610	84	.	0			c.G647C						PASS	.	C	PRO/ARG,PRO/ARG,PRO/ARG,PRO/ARG	3621,785	311.9+/-292.3	1488,645,70	72.0	72.0	72.0		647,647,518,647	-1.6	0.0	19	dbSNP_79	72	7532,1068	223.3+/-260.1	3298,936,66	yes	missense,missense,missense,missense	ZNF610	NM_001161425.1,NM_001161426.1,NM_001161427.1,NM_173530.2	103,103,103,103	4786,1581,136	CC,CG,GG		12.4186,17.8166,14.2473	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	216/463,216/463,173/420,216/463	52869278	11153,1853	2203	4300	6503	SO:0001583	missense	162963	exon6			GAGTCCGTGCAAG	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"""Zinc fingers, C2H2-type"", ""-"""	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.647G>C	19.37:g.52869278G>C	ENSP00000383922:p.Arg216Pro	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	134	133	0.992537	NM_001161426	A8K4C3|Q86YH8|Q8NDS9	Missense_Mutation	SNP	ENST00000403906.3	37	CCDS12851.1	1724	0.7893772893772893	397	0.806910569105691	300	0.8287292817679558	348	0.6083916083916084	679	0.895778364116095	C	4.044	0.005798	0.07866	0.821834	0.875814	ENSG00000167554	ENST00000403906;ENST00000321287;ENST00000327920	T;T	0.02446	4.29;4.29	1.64	-1.62	0.08372	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	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	0.05178	-1.0901	8	0.34782	T	0.22	.	7.3999	0.26958	0.1307:0.1787:0.6906:0.0	rs321937;rs17836040;rs17846268;rs17859290;rs52805135;rs56553672;rs59534436;rs321937	173;216	Q8N9Z0-2;Q8N9Z0	.;ZN610_HUMAN	P	216;173;216	ENSP00000383922:R216P;ENSP00000327597:R216P	ENSP00000324441:R173P	R	+	2	0	ZNF610	57561090	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-1.124000	0.03260	-1.309000	0.02315	-1.474000	0.01003	CGT	G|0.176;C|0.824	0.824	strong		0.378	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530	
RFWD3	55159	hgsc.bcm.edu	37	16	74664698	74664698	+	Silent	SNP	A	A	G	rs78796563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:74664698A>G	ENST00000361070.4	-	10	1832	c.1735T>C	c.(1735-1737)Tta>Cta	p.L579L	RFWD3_ENST00000571750.1_Silent_p.L579L	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	579					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L579L(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						TGAGCTACTAACTCCTGCACA	0.473													A|||	67	0.0133786	0.0023	0.0259	5008	,	,		18719	0.0		0.0288	False		,,,				2504	0.0174				p.L579L		Atlas-SNP	.											RFWD3,NS,carcinoma,0,1	RFWD3	49	1	1	Substitution - coding silent(1)	lung(1)	c.T1735C						scavenged	.	A		28,4368	32.6+/-62.9	1,26,2171	94.0	70.0	78.0		1735	3.5	0.3	16	dbSNP_132	78	267,8333	102.3+/-163.5	4,259,4037	no	coding-synonymous	RFWD3	NM_018124.3		5,285,6208	GG,GA,AA		3.1047,0.6369,2.2699		579/775	74664698	295,12701	2198	4300	6498	SO:0001819	synonymous_variant	55159	exon10			CTACTAACTCCTG	AK001382	CCDS32486.1	16q22.3	2013-01-09						"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.1735T>C	16.37:g.74664698A>G		Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	75	44	0.586667	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Silent	SNP	ENST00000361070.4	37	CCDS32486.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124	
SENP7	57337	hgsc.bcm.edu	37	3	101090924	101090924	+	Missense_Mutation	SNP	T	T	A	rs116197973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101090924T>A	ENST00000394095.2	-	7	777	c.724A>T	c.(724-726)Act>Tct	p.T242S	SENP7_ENST00000314261.7_Missense_Mutation_p.T176S|SENP7_ENST00000394091.1_Missense_Mutation_p.T78S|SENP7_ENST00000348610.3_Missense_Mutation_p.T209S|SENP7_ENST00000358203.3_Missense_Mutation_p.T78S|SENP7_ENST00000394094.2_Missense_Mutation_p.T177S	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	242						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			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						TTGTGCGCAGTCTGCTTTGCA	0.368													C|||	50	0.00998403	0.0371	0.0014	5008	,	,		13274	0.0		0.0	False		,,,				2504	0.0				p.T242S		Atlas-SNP	.											.	SENP7	170	.	0			c.A724T						PASS	.	C	SER/THR,SER/THR	156,4250		4,148,2051	135.0	126.0	129.0		529,724	1.3	0.0	3	dbSNP_132	129	0,8600		0,0,4300	yes	missense,missense	SENP7	NM_001077203.1,NM_020654.3	58,58	4,148,6351	AA,AT,TT		0.0,3.5406,1.1994	benign,benign	177/986,242/1051	101090924	156,12850	2203	4300	6503	SO:0001583	missense	57337	exon7			GCGCAGTCTGCTT		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.724A>T	3.37:g.101090924T>A	ENSP00000377655:p.Thr242Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	3.708	-0.060054	0.07317	0.035406	0.0	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.16743	2.32;2.33;2.32;2.32;2.32;2.32	5.1	1.33	0.21861	.	1.879190	0.02560	N	0.096662	T	0.01940	0.0061	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.29792	-1.0000	10	0.32370	T	0.25	-0.178	7.9128	0.29800	0.0:0.565:0.0:0.435	.	78;176;209;242	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	S	242;177;176;78;78;209	ENSP00000377655:T242S;ENSP00000377654:T177S;ENSP00000313624:T176S;ENSP00000377651:T78S;ENSP00000350936:T78S;ENSP00000342159:T209S	ENSP00000313624:T176S	T	-	1	0	SENP7	102573614	0.029000	0.19370	0.027000	0.17364	0.001000	0.01503	-0.162000	0.10012	-0.170000	0.10816	-0.927000	0.02713	ACT	T|0.988;A|0.012	0.012	strong		0.368	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
PRSS38	339501	hgsc.bcm.edu	37	1	228003879	228003879	+	Silent	SNP	C	C	T	rs112241411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228003879C>T	ENST00000366757.3	+	2	261	c.237C>T	c.(235-237)taC>taT	p.Y79Y		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	79	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						GCGTGCACTACGCAGGCCTCC	0.662													C|||	73	0.0145767	0.0537	0.0029	5008	,	,		13078	0.0		0.0	False		,,,				2504	0.0				p.Y79Y		Atlas-SNP	.											PRSS38,colon,carcinoma,0,1	PRSS38	55	1	0			c.C237T						PASS	.	C		279,4127	150.3+/-184.3	4,271,1928	60.0	68.0	65.0		237	-0.7	0.0	1	dbSNP_132	65	1,8597		0,1,4298	no	coding-synonymous	PRSS38	NM_183062.2		4,272,6226	TT,TC,CC		0.0116,6.3323,2.1532		79/327	228003879	280,12724	2203	4299	6502	SO:0001819	synonymous_variant	339501	exon2			GCACTACGCAGGC		CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"""Serine peptidases / Serine peptidases"""	29625	protein-coding gene	gene with protein product	"""marapsin 2"""					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.237C>T	1.37:g.228003879C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	254	131	0.515748	NM_183062	Q7RTY6	Silent	SNP	ENST00000366757.3	37	CCDS1563.1																																																																																			C|0.982;T|0.018	0.018	strong		0.662	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062	
CRYBB2	1415	hgsc.bcm.edu	37	22	25627604	25627604	+	Silent	SNP	G	G	A	rs8140949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25627604G>A	ENST00000398215.2	+	6	654	c.483G>A	c.(481-483)ggG>ggA	p.G161G		NM_000496.2	NP_000487.1	P43320	CRBB2_HUMAN	crystallin, beta B2	161	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|response to stimulus (GO:0050896)|visual perception (GO:0007601)		identical protein binding (GO:0042802)|structural constituent of eye lens (GO:0005212)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)	10						GCTACCGTGGGCTGCAGTACC	0.632													G|||	1654	0.330272	0.2784	0.2839	5008	,	,		17136	0.4325		0.2058	False		,,,				2504	0.456				p.G161G		Atlas-SNP	.											.	CRYBB2	18	.	0			c.G483A						PASS	.	G		1214,3192	421.5+/-339.4	180,854,1169	98.0	91.0	94.0		483	0.6	1.0	22	dbSNP_116	94	1820,6780	326.6+/-317.4	202,1416,2682	no	coding-synonymous	CRYBB2	NM_000496.2		382,2270,3851	AA,AG,GG		21.1628,27.5533,23.3277		161/206	25627604	3034,9972	2203	4300	6503	SO:0001819	synonymous_variant	1415	exon6			CCGTGGGCTGCAG		CCDS13831.1	22q11.23	2008-06-10			ENSG00000244752	ENSG00000244752			2398	protein-coding gene	gene with protein product		123620		CCA2, CRYB2A, CRYB2		9158139, 8224918	Standard	XM_006724141		Approved		uc003abp.1	P43320	OTTHUMG00000150905	ENST00000398215.2:c.483G>A	22.37:g.25627604G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	179	95	0.530726	NM_000496	Q9UCM8	Silent	SNP	ENST00000398215.2	37	CCDS13831.1																																																																																			G|0.756;A|0.244	0.244	strong		0.632	CRYBB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320350.1	NM_000496	
NLRP11	204801	hgsc.bcm.edu	37	19	56321517	56321517	+	Silent	SNP	T	T	C	rs7249635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56321517T>C	ENST00000589093.1	-	3	552	c.459A>G	c.(457-459)ggA>ggG	p.G153G	NLRP11_ENST00000360133.3_Silent_p.G153G|NLRP11_ENST00000589824.2_Silent_p.G153G|NLRP11_ENST00000443188.1_Silent_p.G153G|NLRP11_ENST00000592953.1_Silent_p.G54G			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	153	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		ATGCTCTCTCTCCCATCAGGA	0.413													T|||	878	0.175319	0.3366	0.0519	5008	,	,		20720	0.2351		0.0517	False		,,,				2504	0.1104				p.G153G		Atlas-SNP	.											.	NLRP11	139	.	0			c.A459G						PASS	.	T		1215,3191	406.6+/-333.9	172,871,1160	81.0	75.0	77.0		459	2.2	0.0	19	dbSNP_116	77	424,8176	125.1+/-183.8	9,406,3885	no	coding-synonymous	NLRP11	NM_145007.3		181,1277,5045	CC,CT,TT		4.9302,27.576,12.6019		153/1034	56321517	1639,11367	2203	4300	6503	SO:0001819	synonymous_variant	204801	exon5			TCTCTCTCCCATC	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.459A>G	19.37:g.56321517T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Silent	SNP	ENST00000589093.1	37	CCDS12935.1																																																																																			T|0.849;C|0.151	0.151	strong		0.413	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
CFAP74	85452	hgsc.bcm.edu	37	1	1896440	1896440	+	IGR	SNP	G	G	A	rs16824585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1896440G>A								TMEM52 (45728 upstream) : C1orf222 (23122 downstream)																							GTGCGCTCCAGGATGTCCTTG	0.647													g|||	1085	0.216653	0.2489	0.2032	5008	,	,		16690	0.2718		0.2276	False		,,,				2504	0.1145				p.L488L		Atlas-SNP	.											.	KIAA1751	92	.	0			c.C1462T						PASS	.			949,3145		126,697,1224	40.0	44.0	43.0		1462	2.2	1.0	1	dbSNP_123	43	2052,6326		258,1536,2395	no	coding-synonymous	KIAA1751	NM_001080484.1		384,2233,3619	AA,AG,GG		24.4927,23.1803,24.0619		488/763	1896440	3001,9471	2047	4189	6236	SO:0001628	intergenic_variant	85452	exon13			GCTCCAGGATGTC																													1.37:g.1896440G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	129	60	0.465116	NM_001080484		Silent	SNP		37																																																																																				G|0.764;A|0.236	0.236	strong	0	0.647								
KHDC1	80759	hgsc.bcm.edu	37	6	74019376	74019376	+	Missense_Mutation	SNP	T	T	C	rs16883573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74019376T>C	ENST00000370384.3	-	1	562	c.62A>G	c.(61-63)tAc>tGc	p.Y21C	KHDC1_ENST00000484801.1_5'UTR	NM_001251874.1	NP_001238803.1	Q4VXA5	KHDC1_HUMAN	KH homology domain containing 1	21						integral component of membrane (GO:0016021)	RNA binding (GO:0003723)			large_intestine(1)|lung(4)|skin(1)	6						CAGGACTCCGTATTCTGAGAC	0.507											OREG0017531	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	822	0.164137	0.3026	0.1182	5008	,	,		19925	0.1419		0.0984	False		,,,				2504	0.1002				p.Y21C		Atlas-SNP	.											.	KHDC1	10	.	0			c.A62G						PASS	.																																			SO:0001583	missense	80759	exon1			ACTCCGTATTCTG		CCDS43480.1, CCDS59027.1	6q13	2014-05-15	2007-11-13	2007-11-13	ENSG00000135314	ENSG00000135314			21366	protein-coding gene	gene with protein product		611688	"""chromosome 6 open reading frame 148"""	C6orf148		17913455	Standard	NM_030568		Approved	MGC10818, bA257K9.4, NDG1	uc003pgn.4	Q4VXA5	OTTHUMG00000015030	ENST00000370384.3:c.62A>G	6.37:g.74019376T>C	ENSP00000359411:p.Tyr21Cys	Somatic	78	0	0	1149	WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_001251874	Q5JSQ7|Q8WTV2|Q96NQ5	Missense_Mutation	SNP	ENST00000370384.3	37	CCDS59027.1	327	0.14972527472527472	144	0.2926829268292683	36	0.09944751381215469	70	0.12237762237762238	77	0.10158311345646438	C	0.007	-1.934343	0.00488	.	.	ENSG00000135314	ENST00000370384	T	0.31769	1.48	1.93	0.0809	0.14422	.	.	.	.	.	T	0.07638	0.0192	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24693	-1.0153	7	0.51188	T	0.08	.	5.045	0.14479	0.0:0.485:0.0:0.515	rs16883573;rs52824993;rs60891542;rs16883573	21	Q4VXA5	KHDC1_HUMAN	C	21	ENSP00000359411:Y21C	ENSP00000359411:Y21C	Y	-	2	0	KHDC1	74076097	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.075000	0.14686	-0.296000	0.08947	-0.479000	0.04858	TAC	T|0.846;C|0.154	0.154	strong		0.507	KHDC1-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000148103.2	NM_030568	
TMEM232	642987	hgsc.bcm.edu	37	5	109960989	109960989	+	Silent	SNP	A	A	G	rs61730920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:109960989A>G	ENST00000455884.2	-	7	797	c.747T>C	c.(745-747)taT>taC	p.Y249Y	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Silent_p.Y249Y			C9JQI7	TM232_HUMAN	transmembrane protein 232	249						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						CTGTGTTCTCATATCTTTTCT	0.363													A|||	798	0.159345	0.3457	0.1354	5008	,	,		17424	0.0833		0.0905	False		,,,				2504	0.0736				p.Y249Y		Atlas-SNP	.											.	TMEM232	57	.	0			c.T747C						PASS	.	A		427,957		71,285,336	262.0	227.0	238.0		747	3.3	0.0	5	dbSNP_129	238	293,2889		14,265,1312	no	coding-synonymous	TMEM232	NM_001039763.3		85,550,1648	GG,GA,AA		9.208,30.8526,15.7687		249/658	109960989	720,3846	692	1591	2283	SO:0001819	synonymous_variant	642987	exon7			GTTCTCATATCTT	AK125070	CCDS47253.1, CCDS47253.2	5q22.1	2014-02-12	2009-10-02		ENSG00000186952	ENSG00000186952			37270	protein-coding gene	gene with protein product							Standard	NM_001039763		Approved	FLJ43080	uc011cvh.2	C9JQI7	OTTHUMG00000163297	ENST00000455884.2:c.747T>C	5.37:g.109960989A>G		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	259	259	1	NM_001039763	B4DKF4	Silent	SNP	ENST00000455884.2	37	CCDS47253.2																																																																																			A|0.859;G|0.141	0.141	strong		0.363	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
DSG1	1828	hgsc.bcm.edu	37	18	28908178	28908178	+	Missense_Mutation	SNP	G	G	C	rs74368609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28908178G>C	ENST00000257192.4	+	4	455	c.243G>C	c.(241-243)caG>caC	p.Q81H		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	81	Cadherin 1. {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)			CTGCAAACCAGCAAGTTACAT	0.368													G|||	26	0.00519169	0.0189	0.0014	5008	,	,		19822	0.0		0.0	False		,,,				2504	0.0				p.Q81H		Atlas-SNP	.											.	DSG1	176	.	0			c.G243C						PASS	.	G	HIS/GLN	97,4309	78.8+/-117.2	0,97,2106	92.0	89.0	90.0		243	2.8	1.0	18	dbSNP_131	90	0,8598		0,0,4299	yes	missense	DSG1	NM_001942.2	24	0,97,6405	CC,CG,GG		0.0,2.2015,0.7459	probably-damaging	81/1050	28908178	97,12907	2203	4299	6502	SO:0001583	missense	1828	exon4			AAACCAGCAAGTT	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.243G>C	18.37:g.28908178G>C	ENSP00000257192:p.Gln81His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	17.26	3.343886	0.61073	0.022015	0.0	ENSG00000134760	ENST00000257192	T	0.61158	0.13	5.59	2.78	0.32641	Cadherin (4);Cadherin-like (1);	0.315599	0.27526	N	0.018975	T	0.47021	0.1423	L	0.59436	1.845	0.80722	D	1	D	0.60575	0.988	D	0.66196	0.942	T	0.54275	-0.8318	10	0.26408	T	0.33	.	4.6815	0.12738	0.3769:0.0:0.4739:0.1491	.	81	Q02413	DSG1_HUMAN	H	81	ENSP00000257192:Q81H	ENSP00000257192:Q81H	Q	+	3	2	DSG1	27162176	0.896000	0.30565	1.000000	0.80357	0.992000	0.81027	0.009000	0.13219	0.705000	0.31890	0.563000	0.77884	CAG	G|0.992;C|0.008	0.008	strong		0.368	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
KRTAP4-2	85291	hgsc.bcm.edu	37	17	39334314	39334314	+	Missense_Mutation	SNP	A	A	T	rs200720939		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39334314A>T	ENST00000377726.2	-	1	146	c.103T>A	c.(103-105)Tgc>Agc	p.C35S		NM_033062.3	NP_149051	Q9BYR5	KRA42_HUMAN	keratin associated protein 4-2	35	20 X 5 AA repeats OF C-C-[GRQVS]-[SPT]- [VSTQ].					keratin filament (GO:0045095)				kidney(2)|lung(4)|upper_aerodigestive_tract(1)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GGGCGGCAGCAGGTGGTCCTG	0.657																																					p.C35S		Atlas-SNP	.											KRTAP4-2_ENST00000458321,NS,haematopoietic_neoplasm,0,4	KRTAP4-2	93	4	0			c.T103A						scavenged	.						48.0	52.0	50.0					17																	39334314		2199	4289	6488	SO:0001583	missense	85291	exon1			GGCAGCAGGTGGT	AJ406934	CCDS11384.1	17q21.2	2013-06-25			ENSG00000244537	ENSG00000244537		"""Keratin associated proteins"""	18900	protein-coding gene	gene with protein product						11279113	Standard	NM_033062		Approved	KAP4.2	uc002hwd.3	Q9BYR5	OTTHUMG00000133437	ENST00000377726.2:c.103T>A	17.37:g.39334314A>T	ENSP00000366955:p.Cys35Ser	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	246	26	0.105691	NM_033062	A0JP64	Missense_Mutation	SNP	ENST00000377726.2	37	CCDS11384.1	.	.	.	.	.	.	.	.	.	.	.	9.002	0.980423	0.18812	.	.	ENSG00000244537	ENST00000377726;ENST00000458321	T	0.02085	4.46	4.24	4.24	0.50183	.	0.212644	0.23275	U	0.049980	T	0.10035	0.0246	H	0.95402	3.665	0.32423	N	0.54916	B	0.33883	0.43	B	0.40602	0.334	T	0.00912	-1.1517	10	0.49607	T	0.09	.	11.5905	0.50943	1.0:0.0:0.0:0.0	.	35	Q9BYR5	KRA42_HUMAN	S	35;152	ENSP00000366955:C35S	ENSP00000366955:C35S	C	-	1	0	KRTAP4-2	36587840	0.997000	0.39634	0.987000	0.45799	0.045000	0.14185	4.092000	0.57707	1.667000	0.50832	0.421000	0.28195	TGC	.	.	weak		0.657	KRTAP4-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257305.1		
PRR22	163154	hgsc.bcm.edu	37	19	5783712	5783712	+	Silent	SNP	C	C	T	rs2446211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5783712C>T	ENST00000419421.2	-	3	650	c.546G>A	c.(544-546)ccG>ccA	p.P182P		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	182	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GGGGTGGCAGCGGGGCCGGGC	0.716													c|||	1687	0.336861	0.4228	0.1931	5008	,	,		8488	0.5456		0.165	False		,,,				2504	0.2843				p.P182P		Atlas-SNP	.											PRR22_ENST00000419421,NS,carcinoma,0,2	PRR22	25	2	0			c.G546A						PASS	.	T		1038,2702		151,736,983	3.0	5.0	4.0		546	-5.2	0.0	19	dbSNP_100	4	1020,6676		80,860,2908	no	coding-synonymous	PRR22	NM_001134316.1		231,1596,3891	TT,TC,CC		13.2536,27.754,17.9958		182/423	5783712	2058,9378	1870	3848	5718	SO:0001819	synonymous_variant	163154	exon3			TGGCAGCGGGGCC	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.546G>A	19.37:g.5783712C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_001134316	E9PB31	Silent	SNP	ENST00000419421.2	37	CCDS45933.1																																																																																			C|0.689;T|0.311	0.311	strong		0.716	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
ZNF587	84914	hgsc.bcm.edu	37	19	58371136	58371136	+	Silent	SNP	G	G	C	rs10405648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58371136G>C	ENST00000339656.5	+	3	1538	c.1356G>C	c.(1354-1356)ctG>ctC	p.L452L	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597652.1_5'Flank|ZNF587_ENST00000419854.1_Silent_p.L409L|ZNF814_ENST00000597342.1_Intron|ZNF587_ENST00000423137.1_Silent_p.L451L|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	452					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		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;0.0264)		ATCATCTTCTGGTTCATGAGA	0.433																																					p.L452L	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.G1356C						PASS	.	C	,	1481,2925		369,743,1091	125.0	154.0	144.0		1353,1356	-3.5	0.0	19	dbSNP_119	144	556,8044		36,484,3780	no	coding-synonymous,coding-synonymous	ZNF587	NM_001204817.1,NM_032828.3	,	405,1227,4871	CC,CG,GG		6.4651,33.6133,15.662	,	451/575,452/576	58371136	2037,10969	2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			TCTTCTGGTTCAT	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1356G>C	19.37:g.58371136G>C		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	193	80	0.414508	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			G|0.742;C|0.258	0.258	strong		0.433	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049916	69049916	+	Missense_Mutation	SNP	G	G	A	rs61734450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69049916G>A	ENST00000295381.3	+	10	2061	c.1642G>A	c.(1642-1644)Gag>Aag	p.E548K	ARHGAP25_ENST00000409202.3_Missense_Mutation_p.E549K|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.E542K|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.E242K|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.E509K|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.E541K	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	548					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CTCTGGAGAAGAGGAAATTGA	0.443													G|||	9	0.00179712	0.0068	0.0	5008	,	,		20738	0.0		0.0	False		,,,				2504	0.0				p.E549K		Atlas-SNP	.											ARHGAP25,NS,carcinoma,0,1	ARHGAP25	175	1	0			c.G1645A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	15,4389	21.2+/-45.6	0,15,2187	70.0	79.0	76.0		1645,1624,1525,1621	4.5	1.0	2	dbSNP_129	76	0,8598		0,0,4299	yes	missense,missense,missense,missense	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	56,56,56,56	0,15,6486	AA,AG,GG		0.0,0.3406,0.1154	benign,benign,benign,benign	549/647,542/640,509/607,541/639	69049916	15,12987	2202	4299	6501	SO:0001583	missense	9938	exon10			GGAGAAGAGGAAA	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1642G>A	2.37:g.69049916G>A	ENSP00000295381:p.Glu548Lys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.43	1.637568	0.29157	0.003406	0.0	ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000543533;ENST00000479844	T;T;T;T;T;T	0.41400	2.82;2.82;2.56;1.0;1.0;1.0	5.42	4.53	0.55603	.	0.709828	0.14852	N	0.294619	T	0.26412	0.0645	N	0.19112	0.55	0.80722	D	1	B;P;P;B;B	0.39480	0.361;0.675;0.675;0.355;0.015	B;B;B;B;B	0.36666	0.054;0.154;0.23;0.165;0.011	T	0.02728	-1.1118	10	0.08381	T	0.77	.	13.8458	0.63466	0.0:0.153:0.847:0.0	rs61734450	509;549;542;541;548	E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331	.;.;.;.;RHG25_HUMAN	K	548;549;509;541;542;542;533;242	ENSP00000295381:E548K;ENSP00000386911:E549K;ENSP00000420583:E509K;ENSP00000386863:E541K;ENSP00000386241:E542K;ENSP00000417467:E242K	ENSP00000295381:E548K	E	+	1	0	ARHGAP25	68903420	0.641000	0.27251	0.975000	0.42487	0.790000	0.44656	1.904000	0.39868	1.399000	0.46721	0.557000	0.71058	GAG	G|0.998;A|0.002	0.002	strong		0.443	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552942	43552942	+	Silent	SNP	G	G	A	rs71373588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43552942G>A	ENST00000430334.3	-	4	580	c.447C>T	c.(445-447)taC>taT	p.Y149Y	PLEKHM1_ENST00000421073.2_Silent_p.Y60Y	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	149	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CGGTGGGCTGGTAGTACTCAT	0.637													G|||	20	0.00399361	0.0136	0.0029	5008	,	,		18295	0.0		0.0	False		,,,				2504	0.0				p.Y149Y		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.C447T						PASS	.	G		76,4328	63.5+/-100.7	2,72,2128	41.0	39.0	40.0		447	-2.8	1.0	17	dbSNP_130	40	0,8600		0,0,4300	no	coding-synonymous	PLEKHM1	NM_014798.2		2,72,6428	AA,AG,GG		0.0,1.7257,0.5844		149/1057	43552942	76,12928	2202	4300	6502	SO:0001819	synonymous_variant	9842	exon4			GGGCTGGTAGTAC	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.447C>T	17.37:g.43552942G>A		Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	281	131	0.466192	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			G|0.993;A|0.007	0.007	strong		0.637	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
KIAA1456	57604	hgsc.bcm.edu	37	8	12879198	12879198	+	Missense_Mutation	SNP	A	A	T	rs34995506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:12879198A>T	ENST00000524591.2	+	5	1499	c.1010A>T	c.(1009-1011)cAt>cTt	p.H337L	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	337			H -> L (in dbSNP:rs34995506).				methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						AATGGAGACCATCAAGGGGAA	0.433													A|||	978	0.195288	0.2436	0.1585	5008	,	,		19756	0.1885		0.1183	False		,,,				2504	0.2423				p.H337L		Atlas-SNP	.											.	KIAA1456	20	.	0			c.A1010T						PASS	.	A	LEU/HIS,LEU/HIS	829,2877		97,635,1121	71.0	70.0	70.0		632,1010	-2.3	0.0	8	dbSNP_126	70	1122,7074		80,962,3056	yes	missense,missense	KIAA1456	NM_001099677.1,NM_020844.2	99,99	177,1597,4177	TT,TA,AA		13.6896,22.3691,16.3922	benign,benign	211/329,337/455	12879198	1951,9951	1853	4098	5951	SO:0001583	missense	57604	exon5			GAGACCATCAAGG	BC035082	CCDS47808.1	8p22	2013-10-04	2011-02-23	2011-02-23	ENSG00000250305	ENSG00000250305			26725	protein-coding gene	gene with protein product		615666	"""chromosome 8 open reading frame 79"""	C8orf79		23381944	Standard	NM_020844		Approved	FLJ36980	uc010lsq.3	Q8N9K7	OTTHUMG00000165477	ENST00000524591.2:c.1010A>T	8.37:g.12879198A>T	ENSP00000432695:p.His337Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_020844	Q96AW6	Missense_Mutation	SNP	ENST00000524591.2	37	CCDS47808.1	378	0.17307692307692307	113	0.22967479674796748	64	0.17679558011049723	112	0.1958041958041958	89	0.11741424802110818	A	4.289	0.052782	0.08291	0.223691	0.136896	ENSG00000250305	ENST00000524591;ENST00000529978	T	0.09445	2.98	4.38	-2.34	0.06704	.	2.018840	0.01919	N	0.040416	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.26400	0.148	B	0.17433	0.018	T	0.39881	-0.9592	9	0.22109	T	0.4	1.2381	0.3267	0.00312	0.3156:0.2675:0.1572:0.2598	rs34995506;rs62486881	337	Q9P272	K1456_HUMAN	L	337;250	ENSP00000432695:H337L	ENSP00000432695:H337L	H	+	2	0	AC135352.2	12923569	0.000000	0.05858	0.001000	0.08648	0.143000	0.21401	0.072000	0.14617	-0.507000	0.06549	-0.496000	0.04628	CAT	A|0.832;T|0.168	0.168	strong		0.433	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677	
C20orf27	54976	hgsc.bcm.edu	37	20	3736160	3736160	+	Missense_Mutation	SNP	G	G	A	rs140915844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3736160G>A	ENST00000379772.3	-	4	1067	c.257C>T	c.(256-258)cCc>cTc	p.P86L	C20orf27_ENST00000217195.8_Missense_Mutation_p.P111L	NM_001258429.1	NP_001245358.1	Q9GZN8	CT027_HUMAN	chromosome 20 open reading frame 27	86										central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)|urinary_tract(1)	7						GTGCAGGCTGGGGACAGGTGC	0.617													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20807	0.0		0.0	False		,,,				2504	0.0				p.P111L		Atlas-SNP	.											.	C20orf27	17	.	0			c.C332T						PASS	.	G	LEU/PRO	20,4386	27.2+/-55.0	0,20,2183	80.0	64.0	69.0		332	3.2	1.0	20	dbSNP_134	69	0,8600		0,0,4300	yes	missense	C20orf27	NM_001039140.1	98	0,20,6483	AA,AG,GG		0.0,0.4539,0.1538	benign	111/200	3736160	20,12986	2203	4300	6503	SO:0001583	missense	54976	exon4			AGGCTGGGGACAG	AK000557	CCDS33436.1, CCDS58763.1	20p13	2011-01-25			ENSG00000101220	ENSG00000101220			15873	protein-coding gene	gene with protein product	"""hypothetical protein LOC54976"""					11780052	Standard	NM_001258429		Approved	FLJ20550	uc002wjh.2	Q9GZN8	OTTHUMG00000031753	ENST00000379772.3:c.257C>T	20.37:g.3736160G>A	ENSP00000369097:p.Pro86Leu	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_001039140	A8K4J0|D3DVX8|Q5JX81|Q9NWX3	Missense_Mutation	SNP	ENST00000379772.3	37	CCDS58763.1	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	16.38|16.38	3.108437|3.108437	0.56291|0.56291	0.004539|0.004539	0.0|0.0	ENSG00000101220|ENSG00000101220	ENST00000379772;ENST00000217195;ENST00000399672;ENST00000379765|ENST00000399683	.|.	.|.	.|.	4.15|4.15	3.17|3.17	0.36434|0.36434	.|.	0.139643|0.139643	0.48286|0.48286	U|N	0.000198|0.000198	T|T	0.67915|0.67915	0.2944|0.2944	M|M	0.74881|0.74881	2.28|2.28	0.80722|0.80722	D|D	1|1	B;B;D|.	0.57257|.	0.001;0.435;0.979|.	B;B;P|.	0.59487|.	0.003;0.215;0.858|.	T|T	0.64179|0.64179	-0.6468|-0.6468	9|7	0.72032|0.19147	D|T	0.01|0.46	-3.9217|-3.9217	11.1696|11.1696	0.48563|0.48563	0.0:0.0:0.8075:0.1925|0.0:0.0:0.8075:0.1925	.|.	86;111;86|.	Q9GZN8;Q9GZN8-2;E9PAL2|.	CT027_HUMAN;.;.|.	L|S	86;111;86;86|80	.|.	ENSP00000217195:P111L|ENSP00000382591:P80S	P|P	-|-	2|1	0|0	C20orf27|C20orf27	3684160|3684160	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	4.963000|4.963000	0.63694|0.63694	1.297000|1.297000	0.44761|0.44761	0.561000|0.561000	0.74099|0.74099	CCC|CCA	G|0.999;A|0.001	0.001	strong		0.617	C20orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077750.2	NM_001039140	
MAATS1	89876	hgsc.bcm.edu	37	3	119466025	119466025	+	Missense_Mutation	SNP	G	G	A	rs9853426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119466025G>A	ENST00000273390.5	+	15	2043	c.1966G>A	c.(1966-1968)Gcg>Acg	p.A656T	RP11-169N13.4_ENST00000489428.2_RNA	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	492						mitochondrion (GO:0005739)											GAATACCGAAGCGAATACTGC	0.388													G|||	71	0.0141773	0.0522	0.0014	5008	,	,		20049	0.0		0.0	False		,,,				2504	0.001				p.A656T		Atlas-SNP	.											.	.	.	.	0			c.G1966A						PASS	.	G	THR/ALA	210,4196	129.8+/-166.5	3,204,1996	112.0	105.0	107.0		1966	5.5	1.0	3	dbSNP_119	107	4,8596	1.2+/-3.3	1,2,4297	yes	missense	C3orf15	NM_033364.3	58	4,206,6293	AA,AG,GG		0.0465,4.7662,1.6454	benign	656/768	119466025	214,12792	2203	4300	6503	SO:0001583	missense	89876	exon15			ACCGAAGCGAATA	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.1966G>A	3.37:g.119466025G>A	ENSP00000273390:p.Ala656Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	146	75	0.513699	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	G	14.23	2.472805	0.43942	0.047662	4.65E-4	ENSG00000183833	ENST00000273390	T	0.22743	1.94	5.47	5.47	0.80525	.	0.170071	0.51477	D	0.000100	T	0.03136	0.0092	L	0.29908	0.895	0.80722	D	1	B;B;B	0.23990	0.095;0.055;0.095	B;B;B	0.26416	0.051;0.048;0.069	T	0.02519	-1.1147	10	0.42905	T	0.14	-11.3258	19.3267	0.94265	0.0:0.0:1.0:0.0	rs9853426;rs52829415;rs9853426	492;594;656	Q7Z4T9;Q7Z4T9-3;Q7Z4T9-7	AAT1_HUMAN;.;.	T	656	ENSP00000273390:A656T	ENSP00000273390:A656T	A	+	1	0	C3orf15	120948715	1.000000	0.71417	0.999000	0.59377	0.271000	0.26615	7.014000	0.76380	2.565000	0.86533	0.591000	0.81541	GCG	G|0.983;A|0.017	0.017	strong		0.388	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72517830	72517830	+	Missense_Mutation	SNP	G	G	A	rs10999516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72517830G>A	ENST00000373207.1	+	20	3050	c.3050G>A	c.(3049-3051)aGc>aAc	p.S1017N	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.S1020N	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1017	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.		S -> N (in dbSNP:rs10999516).		collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CAGGTCTGCAGCCTGCCCGCC	0.622													G|||	1069	0.213458	0.1543	0.2262	5008	,	,		18477	0.37		0.1849	False		,,,				2504	0.1524				p.S1020N		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.G3059A						PASS	.	G	ASN/SER,ASN/SER	769,3637	307.5+/-290.0	67,635,1501	40.0	38.0	38.0		3050,3059	3.4	1.0	10	dbSNP_120	38	1384,7216	264.8+/-285.7	113,1158,3029	yes	missense,missense	ADAMTS14	NM_080722.3,NM_139155.2	46,46	180,1793,4530	AA,AG,GG		16.093,17.4535,16.5539	benign,benign	1017/1224,1020/1227	72517830	2153,10853	2203	4300	6503	SO:0001583	missense	140766	exon20			TCTGCAGCCTGCC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.3050G>A	10.37:g.72517830G>A	ENSP00000362303:p.Ser1017Asn	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	30	0.352941	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	500	0.22893772893772893	75	0.1524390243902439	69	0.19060773480662985	213	0.3723776223776224	143	0.18865435356200527	G	11.65	1.702981	0.30232	0.174535	0.16093	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.52754	0.65;0.65	4.34	3.39	0.38822	.	0.482320	0.22699	N	0.056718	T	0.00012	0.0000	N	0.01640	-0.785	0.38674	P	0.047624	B;P	0.34699	0.019;0.464	B;B	0.39027	0.044;0.288	T	0.35773	-0.9775	9	0.10111	T	0.7	.	5.8642	0.18765	0.1314:0.0:0.6843:0.1842	rs10999516;rs57370271	1017;1020	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	N	1020;1017	ENSP00000362304:S1020N;ENSP00000362303:S1017N	ENSP00000362303:S1017N	S	+	2	0	ADAMTS14	72187836	0.998000	0.40836	1.000000	0.80357	0.945000	0.59286	2.373000	0.44266	2.250000	0.74265	0.561000	0.74099	AGC	G|0.824;A|0.176	0.176	strong		0.622	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
PLD2	5338	hgsc.bcm.edu	37	17	4721376	4721376	+	Missense_Mutation	SNP	A	A	G	rs17854914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	90	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	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	
REST	5978	hgsc.bcm.edu	37	4	57797414	57797414	+	Missense_Mutation	SNP	C	C	T	rs3796529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57797414C>T	ENST00000309042.7	+	4	2704	c.2390C>T	c.(2389-2391)cCa>cTa	p.P797L		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	797	Pro-rich.		P -> L (in dbSNP:rs3796529). {ECO:0000269|PubMed:8568247}.		cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P797L(2)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CAGAGGGAGCCACCTCCTCCC	0.532													C|||	1306	0.260783	0.2738	0.2248	5008	,	,		18741	0.377		0.1849	False		,,,				2504	0.227				p.P797L		Atlas-SNP	.											REST,NS,carcinoma,0,1	REST	104	1	2	Substitution - Missense(2)	prostate(2)	c.C2390T						PASS	.	C	LEU/PRO,LEU/PRO	1121,3285	398.3+/-330.8	125,871,1207	108.0	120.0	116.0		2390,2390	0.4	0.0	4	dbSNP_107	116	1636,6964	302.2+/-305.8	141,1354,2805	yes	missense,missense	REST	NM_001193508.1,NM_005612.4	98,98	266,2225,4012	TT,TC,CC		19.0233,25.4426,21.1979	probably-damaging,probably-damaging	797/1098,797/1098	57797414	2757,10249	2203	4300	6503	SO:0001583	missense	5978	exon4			GGGAGCCACCTCC	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.2390C>T	4.37:g.57797414C>T	ENSP00000311816:p.Pro797Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	CCDS3509.1	544	0.2490842490842491	123	0.25	71	0.19613259668508287	208	0.36363636363636365	142	0.18733509234828497	C	12.13	1.845760	0.32606	0.254426	0.190233	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.06218	3.33	3.08	0.384	0.16244	.	1.097820	0.07026	N	0.827581	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.11235	0.004;0.001	B;B	0.09377	0.004;0.001	T	0.48007	-0.9072	9	0.42905	T	0.14	-0.8172	5.4341	0.16472	0.0:0.6053:0.0:0.3947	rs3796529;rs57306785;rs3796529	774;797	F8WAN5;Q13127	.;REST_HUMAN	L	797;774	ENSP00000311816:P797L	ENSP00000311816:P797L	P	+	2	0	REST	57492171	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-1.057000	0.03486	0.027000	0.15297	-0.192000	0.12808	CCA	C|0.784;T|0.216	0.216	strong		0.532	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
MFSD8	256471	hgsc.bcm.edu	37	4	128842761	128842761	+	Missense_Mutation	SNP	G	G	A	rs3733319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:128842761G>A	ENST00000296468.3	-	12	1395	c.1268C>T	c.(1267-1269)gCt>gTt	p.A423V	MFSD8_ENST00000515130.1_5'UTR|MFSD8_ENST00000513559.1_Missense_Mutation_p.A378V	NM_152778.2	NP_689991.1	Q8NHS3	MFSD8_HUMAN	major facilitator superfamily domain containing 8	423			A -> V (in dbSNP:rs3733319). {ECO:0000269|PubMed:14702039}.		cell death (GO:0008219)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)				cervix(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)	23						TATTAGCACAGCTGATGTAAG	0.453													A|||	615	0.122804	0.1815	0.1023	5008	,	,		16924	0.2649		0.0209	False		,,,				2504	0.0164				p.A423V		Atlas-SNP	.											.	MFSD8	46	.	0			c.C1268T						PASS	.	A	VAL/ALA	798,3608	751.5+/-412.2	80,638,1485	107.0	111.0	109.0		1268	0.1	0.0	4	dbSNP_107	109	120,8480	814.0+/-407.0	0,120,4180	yes	missense	MFSD8	NM_152778.2	64	80,758,5665	AA,AG,GG		1.3953,18.1117,7.0583	benign	423/519	128842761	918,12088	2203	4300	6503	SO:0001583	missense	256471	exon12			AGCACAGCTGATG	AK074564	CCDS3736.1	4q28.2	2014-09-17			ENSG00000164073	ENSG00000164073			28486	protein-coding gene	gene with protein product		611124	"""ceroid-lipofuscinosis, neuronal 7, late infantile, variant"""	CLN7		17564970	Standard	NM_152778		Approved	MGC33302	uc003ifp.3	Q8NHS3	OTTHUMG00000133303	ENST00000296468.3:c.1268C>T	4.37:g.128842761G>A	ENSP00000296468:p.Ala423Val	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	221	110	0.497738	NM_152778	B2RDM1|B7Z205|Q8N2P3	Missense_Mutation	SNP	ENST00000296468.3	37	CCDS3736.1	306	0.1401098901098901	81	0.16463414634146342	36	0.09944751381215469	169	0.29545454545454547	20	0.026385224274406333	A	9.089	1.001328	0.19121	0.181117	0.013953	ENSG00000164073	ENST00000296468;ENST00000513559	T;T	0.74947	-0.89;-0.89	5.17	0.137	0.14787	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.428219	0.25227	N	0.032194	T	0.00012	0.0000	L	0.37630	1.12	0.23198	P	0.9981352	B	0.02656	0.0	B	0.04013	0.001	T	0.12268	-1.0554	9	0.17369	T	0.5	0.0037	1.9931	0.03451	0.3111:0.0917:0.4196:0.1776	rs3733319;rs52801898;rs3733319	423	Q8NHS3	MFSD8_HUMAN	V	423;378	ENSP00000296468:A423V;ENSP00000425000:A378V	ENSP00000296468:A423V	A	-	2	0	MFSD8	129062211	0.981000	0.34729	0.000000	0.03702	0.872000	0.50106	1.508000	0.35769	-0.468000	0.06922	-1.322000	0.01289	GCT	G|0.894;A|0.106	0.106	strong		0.453	MFSD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257097.1	NM_152778	
KIAA0319L	79932	hgsc.bcm.edu	37	1	35919979	35919979	+	Silent	SNP	A	A	G	rs10796920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35919979A>G	ENST00000325722.3	-	11	1998	c.1764T>C	c.(1762-1764)acT>acC	p.T588T	KIAA0319L_ENST00000485551.1_5'UTR|KIAA0319L_ENST00000373266.4_Silent_p.T25T	NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	588	PKD 3. {ECO:0000255|PROSITE- ProRule:PRU00151}.					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)				GCACAATAACAGTCACTTGAG	0.498													A|||	386	0.0770767	0.0348	0.1052	5008	,	,		22059	0.2371		0.003	False		,,,				2504	0.0256				p.T588T		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.T1764C						PASS	.	A		147,4259	103.4+/-141.9	3,141,2059	190.0	153.0	165.0		1764	-0.6	1.0	1	dbSNP_120	165	25,8575	18.5+/-59.3	0,25,4275	no	coding-synonymous	KIAA0319L	NM_024874.4		3,166,6334	GG,GA,AA		0.2907,3.3364,1.3225		588/1050	35919979	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	79932	exon11			AATAACAGTCACT	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.1764T>C	1.37:g.35919979A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	165	80	0.484848	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Silent	SNP	ENST00000325722.3	37	CCDS390.1																																																																																			A|0.959;G|0.041	0.041	strong		0.498	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874	
TEX13A	56157	hgsc.bcm.edu	37	X	104464674	104464674	+	Silent	SNP	G	G	A	rs183606927		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:104464674G>A	ENST00000413579.1	-	2	519	c.408C>T	c.(406-408)ctC>ctT	p.L136L	TEX13A_ENST00000372575.1_Silent_p.L136L|IL1RAPL2_ENST00000344799.4_Intron|TEX13A_ENST00000372578.3_Silent_p.L136L|IL1RAPL2_ENST00000372582.1_Intron			Q9BXU3	TX13A_HUMAN	testis expressed 13A	136							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						GCACCTCCACGAGGCTGGTCT	0.607													G|||	61	0.0161589	0.0363	0.0072	3775	,	,		11953	0.0		0.003	False		,,,				2504	0.0051				p.L136L		Atlas-SNP	.											.	TEX13A	55	.	0			c.C408T						PASS	.	G	,	245,3427		5,188,47,1358,523	36.0	36.0	36.0		,408	-0.1	0.0	X		36	4,6586		0,1,3,2385,1815	no	intron,coding-synonymous	IL1RAPL2,TEX13A	NM_017416.1,NM_031274.3	,	5,189,50,3743,2338	AA,AG,A,GG,G		0.0607,6.6721,2.4264	,	,136/410	104464674	249,10013	2121	4204	6325	SO:0001819	synonymous_variant	56157	exon2			CTCCACGAGGCTG	AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.408C>T	X.37:g.104464674G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	25	0.3125	NM_031274	B1B1G8|Q32NB6	Silent	SNP	ENST00000413579.1	37																																																																																				G|0.992;A|0.008	0.008	strong		0.607	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274	
C5orf52	100190949	hgsc.bcm.edu	37	5	157098756	157098756	+	Missense_Mutation	SNP	G	G	T	rs11740603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:157098756G>T	ENST00000409999.3	+	1	196	c.134G>T	c.(133-135)cGc>cTc	p.R45L	SOX30_ENST00000519442.1_5'Flank	NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	45										endometrium(2)|lung(1)	3						CTCGGCCGCCGCCCAGAAATC	0.697													.|||	838	0.167332	0.2943	0.1326	5008	,	,		12484	0.0734		0.1581	False		,,,				2504	0.1268				p.R45L		Atlas-SNP	.											.	C5orf52	17	.	0			c.G134T						PASS	.						7.0	12.0	10.0					5																	157098756		682	1560	2242	SO:0001583	missense	100190949	exon1			GCCGCCGCCCAGA	BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.134G>T	5.37:g.157098756G>T	ENSP00000387027:p.Arg45Leu	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	212	209	0.985849	NM_001145132		Missense_Mutation	SNP	ENST00000409999.3	37	CCDS47329.1	367	0.16804029304029305	142	0.2886178861788618	56	0.15469613259668508	49	0.08566433566433566	120	0.158311345646438	G	12.96	2.095218	0.36952	.	.	ENSG00000187658	ENST00000409999	.	.	.	0.946	0.946	0.19549	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P	0.47841	0.901	P	0.45276	0.475	T	0.34079	-0.9843	7	0.49607	T	0.09	-2.3101	5.1825	0.15167	0.0:0.0:1.0:0.0	rs11740603;rs58072612;rs11740603	45	A6NGY3	CE052_HUMAN	L	45	.	ENSP00000387027:R45L	R	+	2	0	C5orf52	157031334	0.005000	0.15991	0.005000	0.12908	0.012000	0.07955	-0.028000	0.12350	0.780000	0.33566	0.313000	0.20887	CGC	G|0.814;T|0.186	0.186	strong		0.697	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335664.1	NM_001145132	
PIF1	80119	hgsc.bcm.edu	37	15	65112116	65112116	+	Silent	SNP	C	C	T	rs145376177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65112116C>T	ENST00000268043.4	-	8	1357	c.1263G>A	c.(1261-1263)gtG>gtA	p.V421V	PIF1_ENST00000333425.6_Silent_p.V421V|PIF1_ENST00000559239.1_Silent_p.V421V					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						GCCTCGTGGCCACAATCCCAT	0.652													C|||	2	0.000399361	0.0	0.0	5008	,	,		18557	0.002		0.0	False		,,,				2504	0.0				p.V421V		Atlas-SNP	.											.	PIF1	43	.	0			c.G1263A						PASS	.	C		1,4403	2.1+/-5.4	0,1,2201	81.0	72.0	75.0		1263	4.7	1.0	15	dbSNP_134	75	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PIF1	NM_025049.2		0,2,6499	TT,TC,CC		0.0116,0.0227,0.0154		421/642	65112116	2,13000	2202	4299	6501	SO:0001819	synonymous_variant	80119	exon8			CGTGGCCACAATC	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.1263G>A	15.37:g.65112116C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_025049		Silent	SNP	ENST00000268043.4	37	CCDS10195.2																																																																																			C|1.000;T|0.000	0.000	weak		0.652	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049	
IGFALS	3483	hgsc.bcm.edu	37	16	1842454	1842454	+	Intron	SNP	G	G	A	rs34680334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1842454G>A	ENST00000215539.3	-	2	127				IGFALS_ENST00000568221.1_Intron|IGFALS_ENST00000415638.3_Missense_Mutation_p.H27Y			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						CTGCCCGAGTGAGCCTGATAC	0.701													G|||	347	0.0692891	0.2511	0.0187	5008	,	,		12605	0.0		0.002	False		,,,				2504	0.0				p.H27Y		Atlas-SNP	.											.	IGFALS	29	.	0			c.C79T						PASS	.	G	,TYR/HIS	325,1837		9,307,765	2.0	4.0	3.0		,79	-1.3	0.0	16	dbSNP_126	3	3,3869		0,3,1933	yes	intron,missense	IGFALS	NM_004970.2,NM_001146006.1	,83	9,310,2698	AA,AG,GG		0.0775,15.0324,5.4359	,benign	,27/644	1842454	328,5706	1081	1936	3017	SO:0001627	intron_variant	3483	exon2			CCGAGTGAGCCTG	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.17-52C>T	16.37:g.1842454G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	13	9	0.692308	NM_001146006	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	114	0.0521978021978022	105	0.21341463414634146	7	0.019337016574585635	2	0.0034965034965034965	0	0.0	G	8.995	0.978678	0.18812	0.150324	7.75E-4	ENSG00000099769	ENST00000415638	T	0.54071	0.59	1.11	-1.27	0.09347	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.33266	0.404	B	0.18263	0.021	T	0.11717	-1.0576	8	0.66056	D	0.02	.	1.1011	0.01684	0.1624:0.2175:0.4:0.22	rs34680334	27	E9PGU3	.	Y	27	ENSP00000416683:H27Y	ENSP00000416683:H27Y	H	-	1	0	IGFALS	1782455	0.002000	0.14202	0.000000	0.03702	0.043000	0.13939	0.803000	0.27083	-0.428000	0.07339	0.549000	0.68633	CAC	G|0.947;A|0.053	0.053	strong		0.701	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
EYS	346007	hgsc.bcm.edu	37	6	65622463	65622463	+	Missense_Mutation	SNP	A	A	G	rs9294631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:65622463A>G	ENST00000370621.3	-	16	3081	c.2555T>C	c.(2554-2556)cTt>cCt	p.L852P	EYS_ENST00000503581.1_Missense_Mutation_p.L852P|EYS_ENST00000370616.2_Missense_Mutation_p.L852P			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	852	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.		L -> P (in dbSNP:rs9294631).		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						TAGGTCACAAAGGTTATAGCG	0.408													G|||	3237	0.646366	0.9274	0.6239	5008	,	,		15500	0.4177		0.5835	False		,,,				2504	0.5828				p.L852P		Atlas-SNP	.											.	EYS	527	.	0			c.T2555C						PASS	.	G	PRO/LEU	1215,169		535,145,12	178.0	149.0	157.0		2555	3.1	0.6	6	dbSNP_119	157	1831,1351		525,781,285	yes	missense	EYS	NM_001142800.1	98	1060,926,297	GG,GA,AA		42.4576,12.211,33.2895	probably-damaging	852/3145	65622463	3046,1520	692	1591	2283	SO:0001583	missense	346007	exon16			TCACAAAGGTTAT		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.2555T>C	6.37:g.65622463A>G	ENSP00000359655:p.Leu852Pro	Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	283	283	1	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		1335	0.6112637362637363	454	0.9227642276422764	214	0.5911602209944752	232	0.40559440559440557	435	0.5738786279683378	G	0.115	-1.133005	0.01756	0.87789	0.575424	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.71698	-0.59;-0.59;-0.59	5.0	3.08	0.35506	.	0.870241	0.09380	N	0.810023	T	0.14787	0.0357	N	0.01624	-0.795	0.09310	P	0.9999999999999973	B	0.02656	0.0	B	0.01281	0.0	T	0.10019	-1.0648	9	0.07482	T	0.82	.	5.6412	0.17565	0.185:0.1583:0.6567:0.0	rs9294631;rs59157154;rs9294631	852	Q5T1H1-1	.	P	852	ENSP00000424243:L852P;ENSP00000359655:L852P;ENSP00000359650:L852P	ENSP00000359650:L852P	L	-	2	0	EYS	65679184	1.000000	0.71417	0.640000	0.29408	0.410000	0.31052	3.908000	0.56355	0.094000	0.17404	-0.215000	0.12644	CTT	A|0.375;G|0.625	0.625	strong		0.408	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
AES	166	hgsc.bcm.edu	37	19	3062857	3062857	+	5'Flank	SNP	T	T	C	rs11539938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3062857T>C	ENST00000327141.4	-	0	0				AES_ENST00000586839.1_5'Flank|AES_ENST00000592330.1_5'Flank|AES_ENST00000221561.8_Silent_p.L23L	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	56	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	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	
C5AR2	27202	hgsc.bcm.edu	37	19	47844899	47844899	+	Silent	SNP	C	C	T	rs34085015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47844899C>T	ENST00000595464.1	+	2	1061	c.843C>T	c.(841-843)ctC>ctT	p.L281L	C5AR2_ENST00000257267.2_Silent_p.L281L|C5AR2_ENST00000600626.1_Silent_p.L281L	NM_001271749.1	NP_001258678.1	Q9P296	C5AR2_HUMAN	complement component 5a receptor 2	281					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)										GCCTTGCCCTCGCTCACAGCT	0.667													C|||	27	0.00539137	0.0174	0.0043	5008	,	,		16697	0.0		0.001	False		,,,				2504	0.0				p.L281L		Atlas-SNP	.											.	.	.	.	0			c.C843T						PASS	.	C		92,4314	75.2+/-113.4	1,90,2112	59.0	59.0	59.0		843	-7.9	0.0	19	dbSNP_126	59	0,8600		0,0,4300	no	coding-synonymous	GPR77	NM_018485.1		1,90,6412	TT,TC,CC		0.0,2.0881,0.7074		281/338	47844899	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	27202	exon2			TGCCCTCGCTCAC	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.843C>T	19.37:g.47844899C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	86	48	0.55814	NM_001271750	B2RA09	Silent	SNP	ENST00000595464.1	37	CCDS12699.1																																																																																			C|0.992;T|0.008	0.008	strong		0.667	C5AR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466926.1	NM_018485	
MST1L	11223	hgsc.bcm.edu	37	1	17087474	17087474	+	RNA	SNP	C	C	T	rs60783416		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17087474C>T	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GGGCCCACAGCGACCAGCACA	0.632																																					p.R64H		Atlas-SNP	.											.	.	.	.	0			c.G191A						PASS	.																																					11223	exon2			CCACAGCGACCAG	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.17087474C>T		Somatic	684	0	0		WXS	Illumina HiSeq	Phase_I	868	93	0.107143	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	6.967	0.548403	0.13312	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	0.849673	0.09888	N	0.742825	T	0.33089	0.0851	.	.	.	.	.	.	B	0.19706	0.038	B	0.15870	0.014	T	0.32534	-0.9903	5	0.56958	D	0.05	.	.	.	.	rs60783416	64	Q2TV78-2	.	H	34;64;64	.	ENSP00000439273:R64H	R	-	2	0	MST1P9	16960061	0.458000	0.25760	0.000000	0.03702	0.000000	0.00434	-0.046000	0.11983	-0.000000	0.14550	0.000000	0.15137	CGC	C|0.500;T|0.500	0.500	weak		0.632	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249471	71249471	+	Missense_Mutation	SNP	A	A	T	rs112605265		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249471A>T	ENST00000398534.3	+	1	401	c.370A>T	c.(370-372)Agc>Tgc	p.S124C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	124	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)	p.S124C(1)		cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						TAAGCCCTGCAGCTGCTCTTC	0.602																																					p.S124C		Atlas-SNP	.											KRTAP5-8,extremity,malignant_melanoma,0,1	KRTAP5-8	28	1	1	Substitution - Missense(1)	skin(1)	c.A370T						scavenged	.						172.0	182.0	179.0					11																	71249471		2200	4294	6494	SO:0001583	missense	57830	exon1			CCCTGCAGCTGCT	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.370A>T	11.37:g.71249471A>T	ENSP00000420723:p.Ser124Cys	Somatic	173	2	0.0115607		WXS	Illumina HiSeq	Phase_I	241	12	0.0497925	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	37	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	-	0.003	-2.403875	0.00195	.	.	ENSG00000241233	ENST00000398534	T	0.01234	5.13	0.978	-1.96	0.07525	.	.	.	.	.	T	0.00241	0.0007	N	0.00009	-3.06	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45249	-0.9274	9	0.02654	T	1	.	4.0663	0.09862	0.6007:0.0:0.0:0.3993	.	124	O75690	KRA58_HUMAN	C	124	ENSP00000420723:S124C	ENSP00000420723:S124C	S	+	1	0	KRTAP5-8	70927119	0.038000	0.19896	0.000000	0.03702	0.000000	0.00434	0.224000	0.17738	-0.699000	0.05077	-2.447000	0.00209	AGC	A|0.500;T|0.500	0.500	weak		0.602	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
KRT31	3881	hgsc.bcm.edu	37	17	39551533	39551533	+	Silent	SNP	G	G	A	rs6503626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39551533G>A	ENST00000251645.2	-	5	892	c.840C>T	c.(838-840)aaC>aaT	p.N280N		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	280	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				TCTCCAGGGCGTTGACTGTGC	0.597													G|||	67	0.0133786	0.0469	0.0	5008	,	,		20660	0.0		0.0	False		,,,				2504	0.0051				p.N280N		Atlas-SNP	.											.	KRT31	158	.	0			c.C840T						PASS	.	G		123,4283	80.9+/-119.3	6,111,2086	98.0	90.0	93.0		840	-4.3	0.9	17	dbSNP_116	93	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	KRT31	NM_002277.2		6,113,6384	AA,AG,GG		0.0233,2.7916,0.9611		280/417	39551533	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	3881	exon5			CAGGGCGTTGACT	X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6448	protein-coding gene	gene with protein product	"""hard keratin type I 1"""	601077	"""keratin, hair, acidic, 1"""	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.840C>T	17.37:g.39551533G>A		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	210	101	0.480952	NM_002277	Q9UE12	Silent	SNP	ENST00000251645.2	37	CCDS11391.1																																																																																			G|0.988;A|0.012	0.012	strong		0.597	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277	
FAM135A	57579	hgsc.bcm.edu	37	6	71235647	71235647	+	Missense_Mutation	SNP	C	C	T	rs16869301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71235647C>T	ENST00000418814.2	+	15	3474	c.2860C>T	c.(2860-2862)Cct>Tct	p.P954S	FAM135A_ENST00000457062.2_Missense_Mutation_p.P741S|FAM135A_ENST00000361499.3_Missense_Mutation_p.P758S|FAM135A_ENST00000370479.3_Missense_Mutation_p.P741S|FAM135A_ENST00000505769.1_Missense_Mutation_p.P534S|FAM135A_ENST00000505868.1_Missense_Mutation_p.P954S	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	954			P -> S (in dbSNP:rs16869301).							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						CTTCCAGAGTCCTGATAAATC	0.353													C|||	102	0.0203674	0.0726	0.0058	5008	,	,		19255	0.0		0.002	False		,,,				2504	0.0				p.P954S		Atlas-SNP	.											.	FAM135A	181	.	0			c.C2860T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	296,4110	158.9+/-191.5	7,282,1914	52.0	55.0	54.0		2272,2860,2221	0.9	1.0	6	dbSNP_123	54	4,8590	3.7+/-12.6	0,4,4293	yes	missense,missense,missense	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	74,74,74	7,286,6207	TT,TC,CC		0.0465,6.7181,2.3077	benign,benign,benign	758/1320,954/1516,741/1303	71235647	300,12700	2203	4297	6500	SO:0001583	missense	57579	exon13			CAGAGTCCTGATA	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.2860C>T	6.37:g.71235647C>T	ENSP00000410768:p.Pro954Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	C	0.006	-2.070499	0.00379	0.067181	4.65E-4	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.21031	2.35;2.35;2.03;2.35;2.34;2.34	5.96	0.852	0.18995	.	0.426506	0.24048	N	0.042035	T	0.04907	0.0132	L	0.38531	1.155	0.20703	N	0.999861	B;B;B;B	0.21821	0.061;0.002;0.003;0.009	B;B;B;B	0.16289	0.015;0.004;0.011;0.01	T	0.35624	-0.9781	10	0.36615	T	0.2	.	7.0338	0.24983	0.0:0.5415:0.2138:0.2447	rs16869301;rs52792378;rs16869301	954;954;758;741	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	S	954;741;534;741;758;954	ENSP00000410768:P954S;ENSP00000359510:P741S;ENSP00000423785:P534S;ENSP00000409201:P741S;ENSP00000354913:P758S;ENSP00000423307:P954S	ENSP00000354913:P758S	P	+	1	0	FAM135A	71292368	0.903000	0.30736	0.997000	0.53966	0.055000	0.15305	0.715000	0.25822	0.405000	0.25532	-0.136000	0.14681	CCT	C|0.974;T|0.026	0.026	strong		0.353	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
C9	735	hgsc.bcm.edu	37	5	39364554	39364554	+	Missense_Mutation	SNP	G	G	A	rs700233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:39364554G>A	ENST00000263408.4	-	1	108	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	C9_ENST00000509186.1_Intron	NM_001737.3	NP_001728.1	P02748	CO9_HUMAN	complement component 9	5			R -> W (in dbSNP:rs700233).		complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|hemolysis by symbiont of host erythrocytes (GO:0019836)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane attack complex (GO:0005579)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)			GCAAAGCTCCGGCAGGCTGAC	0.517													G|||	1433	0.286142	0.2413	0.3718	5008	,	,		18252	0.0714		0.4235	False		,,,				2504	0.3661				p.R5W		Atlas-SNP	.											.	C9	116	.	0			c.C13T						PASS	.	G	TRP/ARG	1121,3285	402.6+/-332.4	158,805,1240	82.0	71.0	75.0		13	-8.7	0.0	5	dbSNP_86	75	3563,5037	515.9+/-378.7	730,2103,1467	yes	missense	C9	NM_001737.3	101	888,2908,2707	AA,AG,GG		41.4302,25.4426,36.0141	benign	5/560	39364554	4684,8322	2203	4300	6503	SO:0001583	missense	735	exon1			AGCTCCGGCAGGC		CCDS3929.1	5p14-p12	2014-09-17			ENSG00000113600	ENSG00000113600		"""Complement system"""	1358	protein-coding gene	gene with protein product		120940					Standard	NM_001737		Approved		uc003jlv.4	P02748	OTTHUMG00000094767	ENST00000263408.4:c.13C>T	5.37:g.39364554G>A	ENSP00000263408:p.Arg5Trp	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	NM_001737		Missense_Mutation	SNP	ENST00000263408.4	37	CCDS3929.1	644	0.2948717948717949	129	0.2621951219512195	143	0.39502762430939226	46	0.08041958041958042	326	0.43007915567282323	G	10.63	1.405274	0.25378	0.254426	0.414302	ENSG00000113600	ENST00000263408	T	0.34072	1.38	4.45	-8.66	0.00866	.	3.427000	0.00687	N	0.000708	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26224	-1.0109	9	0.37606	T	0.19	5.1937	0.3149	0.00294	0.2623:0.2207:0.2768:0.2401	rs700233;rs1631129;rs3854893;rs17385752;rs58690123;rs700233	5	P02748	CO9_HUMAN	W	5	ENSP00000263408:R5W	ENSP00000263408:R5W	R	-	1	2	C9	39400311	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	-2.551000	0.00928	-1.634000	0.01537	-1.233000	0.01565	CGG	G|0.675;A|0.325	0.325	strong		0.517	C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211576.3		
TPSD1	23430	hgsc.bcm.edu	37	16	1306671	1306671	+	Silent	SNP	G	G	A	rs1141966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1306671G>A	ENST00000211076.3	+	2	385	c.237G>A	c.(235-237)gcG>gcA	p.A79A	TPSD1_ENST00000397534.2_Silent_p.A72A|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	79	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TGCTAACCGCGGCGCACTGCG	0.701													-|||	2225	0.444289	0.3351	0.3012	5008	,	,		17135	0.7946		0.3211	False		,,,				2504	0.4591				p.A79A		Atlas-SNP	.											.	TPSD1	47	.	0			c.G237A						PASS	.	G		1420,2978		209,1002,988	43.0	52.0	49.0		237	-6.0	0.0	16	dbSNP_86	49	2535,6061		359,1817,2122	no	coding-synonymous	TPSD1	NM_012217.2		568,2819,3110	AA,AG,GG		29.4905,32.2874,30.4371		79/243	1306671	3955,9039	2199	4298	6497	SO:0001819	synonymous_variant	23430	exon2			AACCGCGGCGCAC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.237G>A	16.37:g.1306671G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	181	97	0.535912	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			G|1.000;|0.000	.	weak		0.701	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
ZNF577	84765	hgsc.bcm.edu	37	19	52376226	52376226	+	Silent	SNP	C	C	T	rs9807840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52376226C>T	ENST00000301399.5	-	7	1382	c.1017G>A	c.(1015-1017)tcG>tcA	p.S339S	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Silent_p.S280S|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000451628.2_Silent_p.S280S	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GAATGAGCTTCGACTTGCTTC	0.438													C|||	853	0.170327	0.2943	0.1427	5008	,	,		22276	0.0427		0.0358	False		,,,				2504	0.2924				p.S339S		Atlas-SNP	.											.	ZNF577	63	.	0			c.G1017A						PASS	.	C	,	1178,3228		167,844,1192	71.0	66.0	68.0		840,1017	-0.7	0.0	19	dbSNP_119	68	164,8436		1,162,4137	no	coding-synonymous,coding-synonymous	ZNF577	NM_001135590.1,NM_032679.2	,	168,1006,5329	TT,TC,CC		1.907,26.7363,10.3183	,	280/427,339/486	52376226	1342,11664	2203	4300	6503	SO:0001819	synonymous_variant	84765	exon7			GAGCTTCGACTTG	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1017G>A	19.37:g.52376226C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			C|0.891;T|0.109	0.109	strong		0.438	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
BAD	572	hgsc.bcm.edu	37	11	64051853	64051853	+	5'UTR	SNP	G	G	A	rs75052600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64051853G>A	ENST00000394532.3	-	0	258				BAD_ENST00000544785.1_5'Flank|BAD_ENST00000309032.3_Intron|GPR137_ENST00000313074.3_5'Flank|GPR137_ENST00000411458.1_Silent_p.V5V|GPR137_ENST00000539851.1_5'Flank|BAD_ENST00000394531.3_Intron|GPR137_ENST00000377702.4_5'Flank|GPR137_ENST00000438980.2_5'Flank	NM_004322.3	NP_004313.1	Q92934	BAD_HUMAN	BCL2-associated agonist of cell death						activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ADP metabolic process (GO:0046031)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|ATP metabolic process (GO:0046034)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to chromate (GO:0071247)|cellular response to hypoxia (GO:0071456)|cellular response to lipid (GO:0071396)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose catabolic process (GO:0006007)|glucose homeostasis (GO:0042593)|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)|pore complex assembly (GO:0046931)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of autophagy (GO:0010508)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane potential (GO:0010918)|positive regulation of neuron death (GO:1901216)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of mitochondrial membrane permeability (GO:0046902)|release of cytochrome c from mitochondria (GO:0001836)|response to amino acid (GO:0043200)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to oleic acid (GO:0034201)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|suppression by virus of host apoptotic process (GO:0019050)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|lipid binding (GO:0008289)|phospholipid binding (GO:0005543)|protein kinase binding (GO:0019901)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4						TCTGGGCTGTGAGGACAAGAT	0.647													G|||	95	0.0189696	0.0658	0.0101	5008	,	,		18548	0.0		0.001	False		,,,				2504	0.0				p.V5V		Atlas-SNP	.											.	GPR137	52	.	0			c.G15A						PASS	.	G	,,	193,4209	120.8+/-158.4	8,177,2016	59.0	64.0	62.0		15,,	0.8	0.0	11	dbSNP_131	62	3,8591	3.0+/-9.4	0,3,4294	no	coding-synonymous,utr-5,intron	BAD,GPR137	NM_001170726.1,NM_004322.3,NM_032989.2	,,	8,180,6310	AA,AG,GG		0.0349,4.3844,1.5082	,,	5/476,,	64051853	196,12800	2201	4297	6498	SO:0001623	5_prime_UTR_variant	56834	exon1			GGCTGTGAGGACA	AF021792	CCDS8065.1	11q13.1	2014-03-07	2008-08-19		ENSG00000002330	ENSG00000002330			936	protein-coding gene	gene with protein product		603167				8929532	Standard	NM_004322		Approved	BCL2L8, BBC2	uc001nzd.3	Q92934	OTTHUMG00000134302	ENST00000394532.3:c.-13C>T	11.37:g.64051853G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_001170726	O14803|Q6FH21	Silent	SNP	ENST00000394532.3	37	CCDS8065.1																																																																																			G|0.986;A|0.014	0.014	strong		0.647	BAD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259180.2	NM_032989	
FAM159A	348378	hgsc.bcm.edu	37	1	53099242	53099242	+	Missense_Mutation	SNP	G	G	A	rs182623287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53099242G>A	ENST00000517870.1	+	1	227	c.77G>A	c.(76-78)gGc>gAc	p.G26D	FAM159A_ENST00000401050.3_3'UTR	NM_001042693.1	NP_001036158.1	Q6UWV7	F159A_HUMAN	family with sequence similarity 159, member A	26						integral component of membrane (GO:0016021)				endometrium(3)|lung(6)|upper_aerodigestive_tract(1)	10						cggccggggggcgaggcggcc	0.716													G|||	5	0.000998403	0.0008	0.0058	5008	,	,		9747	0.0		0.0	False		,,,				2504	0.0				p.G26D		Atlas-SNP	.											.	FAM159A	22	.	0			c.G77A						PASS	.						14.0	16.0	16.0					1																	53099242		1869	4059	5928	SO:0001583	missense	348378	exon1			CGGGGGGCGAGGC		CCDS41336.1	1p32.3	2008-08-08			ENSG00000182183	ENSG00000182183			28757	protein-coding gene	gene with protein product						12477932	Standard	NM_001042693		Approved	MGC52498	uc001cuf.3	Q6UWV7	OTTHUMG00000008330	ENST00000517870.1:c.77G>A	1.37:g.53099242G>A	ENSP00000429726:p.Gly26Asp	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_001042693	Q6ZRG4	Missense_Mutation	SNP	ENST00000517870.1	37	CCDS41336.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	12.99	2.103714	0.37145	.	.	ENSG00000182183	ENST00000517870	.	.	.	3.44	3.44	0.39384	.	0.253016	0.29876	U	0.010972	T	0.22666	0.0547	N	0.03608	-0.345	0.36963	D	0.893453	P	0.34639	0.461	B	0.39562	0.303	T	0.23511	-1.0186	9	0.06625	T	0.88	.	15.773	0.78187	0.0:0.0:1.0:0.0	.	26	Q6UWV7	F159A_HUMAN	D	26	.	ENSP00000429726:G26D	G	+	2	0	FAM159A	52871830	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.263000	0.43293	1.860000	0.53959	0.455000	0.32223	GGC	G|0.999;A|0.001	0.001	strong		0.716	FAM159A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022934.2	NM_001042693	
ITGA6	3655	hgsc.bcm.edu	37	2	173339808	173339808	+	Missense_Mutation	SNP	G	G	A	rs11895564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:173339808G>A	ENST00000264106.6	+	8	1458	c.1255G>A	c.(1255-1257)Gca>Aca	p.A419T	ITGA6_ENST00000409080.1_Missense_Mutation_p.A380T|ITGA6_ENST00000343713.4_Missense_Mutation_p.A375T|ITGA6_ENST00000375221.2_Missense_Mutation_p.A419T|ITGA6_ENST00000409532.1_Missense_Mutation_p.A261T|ITGA6_ENST00000264107.7_Missense_Mutation_p.A380T			P23229	ITA6_HUMAN	integrin, alpha 6	419				A -> T (in Ref. 4; BAG59130 and 7; AAI36456/AAI36457). {ECO:0000305}.	amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			GTTTGGCATTGCAGTAAAAAA	0.333													G|||	1260	0.251597	0.3253	0.2248	5008	,	,		18864	0.0933		0.2793	False		,,,				2504	0.3057				p.A380T		Atlas-SNP	.											ITGA6,NS,NS,-1,1	ITGA6	171	1	0			c.G1138A						PASS	.	G	THR/ALA,THR/ALA	1505,2901	477.4+/-357.9	250,1005,948	78.0	79.0	78.0		1138,1138	4.5	1.0	2	dbSNP_120	78	2560,6040	415.9+/-351.9	370,1820,2110	yes	missense,missense	ITGA6	NM_000210.2,NM_001079818.1	58,58	620,2825,3058	AA,AG,GG		29.7674,34.158,31.2548	benign,benign	380/1074,380/1092	173339808	4065,8941	2203	4300	6503	SO:0001583	missense	3655	exon7			GGCATTGCAGTAA		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"""CD molecules"", ""Integrins"""	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.1255G>A	2.37:g.173339808G>A	ENSP00000264106:p.Ala419Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_001079818	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	37		524	0.23992673992673993	164	0.3333333333333333	97	0.26795580110497236	53	0.09265734265734266	210	0.2770448548812665	G	20.9	4.068903	0.76301	0.34158	0.297674	ENSG00000091409	ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358	T;T;T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	5.35	4.46	0.54185	.	0.160749	0.56097	D	0.000036	T	0.00012	0.0000	L	0.56396	1.775	0.19775	P	0.9999532777	P;B;P;P	0.45428	0.571;0.042;0.858;0.858	B;B;P;P	0.58172	0.389;0.133;0.834;0.746	T	0.01413	-1.1361	8	.	.	.	.	13.3506	0.60599	0.0:0.0:0.7145:0.2855	rs11895564;rs52804239;rs61334157;rs11895564	375;419;380;380	P23229-4;P23229-9;G5E9H1;P23229-2	.;.;.;.	T	261;380;419;419;375;380;419;375	ENSP00000386614:A261T;ENSP00000264107:A380T;ENSP00000264106:A419T;ENSP00000364369:A419T;ENSP00000341078:A375T;ENSP00000386896:A380T;ENSP00000406694:A419T;ENSP00000394169:A375T	.	A	+	1	0	ITGA6	173048054	1.000000	0.71417	0.967000	0.41034	0.946000	0.59487	3.120000	0.50430	1.225000	0.43566	0.650000	0.86243	GCA	G|0.714;A|0.286	0.286	strong		0.333	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
DNAH8	1769	hgsc.bcm.edu	37	6	38825329	38825329	+	Silent	SNP	C	C	T	rs2061907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:38825329C>T	ENST00000359357.3	+	40	5372	c.5118C>T	c.(5116-5118)caC>caT	p.H1706H	DNAH8_ENST00000441566.1_Silent_p.H1706H|DNAH8_ENST00000449981.2_Silent_p.H1923H			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1706					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						TGTGGACACACGATTCAGAAG	0.338													C|||	2425	0.484225	0.3555	0.6037	5008	,	,		19122	0.6944		0.3767	False		,,,				2504	0.4673				p.H1923H		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,0,4	DNAH8	1239	4	0			c.C5769T						scavenged	.	C		1571,2835	489.9+/-361.6	290,991,922	99.0	98.0	98.0		5769	-0.6	1.0	6	dbSNP_94	98	3671,4929	525.5+/-380.8	786,2099,1415	no	coding-synonymous	DNAH8	NM_001206927.1		1076,3090,2337	TT,TC,CC		42.686,35.6559,40.3045		1923/4708	38825329	5242,7764	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon42			GACACACGATTCA	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.5118C>T	6.37:g.38825329C>T		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	165	75	0.454545	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				C|0.559;T|0.441	0.441	strong		0.338	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
HK2	3099	hgsc.bcm.edu	37	2	75101454	75101454	+	Silent	SNP	T	T	C	rs2229622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	301	300	0.996678	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	
GPR146	115330	hgsc.bcm.edu	37	7	1097394	1097394	+	Silent	SNP	T	T	C	rs11767527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1097394T>C	ENST00000397095.1	+	2	466	c.243T>C	c.(241-243)ccT>ccC	p.P81P	C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000397098.3_Intron|GPR146_ENST00000297468.3_Silent_p.P81P|C7orf50_ENST00000397100.2_Intron|RP11-449P15.1_ENST00000549241.1_RNA			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	81						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P81P(2)		autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		CCCTGGCCCCTGTGCACCTGC	0.652													t|||	345	0.0688898	0.0204	0.0821	5008	,	,		18317	0.0		0.1262	False		,,,				2504	0.137				p.P81P		Atlas-SNP	.											GPR146,NS,carcinoma,0,3	GPR146	20	3	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.T243C						PASS	.		,,,	200,4200	116.3+/-154.2	3,194,2003	34.0	31.0	32.0		,,,243	-7.6	0.0	7	dbSNP_120	32	1339,7259	240.0+/-270.9	102,1135,3062	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	105,1329,5065	CC,CT,TT		15.5734,4.5455,11.8403	,,,	,,,81/334	1097394	1539,11459	2200	4299	6499	SO:0001819	synonymous_variant	115330	exon1			GGCCCCTGTGCAC	BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"""GPCR / Class A : Orphans"""	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.243T>C	7.37:g.1097394T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	48	16	0.333333	NM_138445	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																			T|0.898;C|0.102	0.102	strong		0.652	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
C15orf40	123207	hgsc.bcm.edu	37	15	83673653	83673653	+	3'UTR	SNP	A	A	C	rs74028206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83673653A>C	ENST00000513601.2	-	0	1165				C15orf40_ENST00000451195.3_Intron|C15orf40_ENST00000538348.2_Intron|C15orf40_ENST00000304177.5_3'UTR|RP11-382A20.5_ENST00000566841.1_RNA			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40											large_intestine(3)|lung(2)|skin(1)	6						AACTGCATTCAACAAGTagtc	0.393													A|||	66	0.0131789	0.0386	0.0173	5008	,	,		15049	0.0		0.003	False		,,,				2504	0.0				p.V146V		Atlas-SNP	.											.	C15orf40	18	.	0			c.T438G						PASS	.	A	,,,	38,1346		1,36,655	112.0	100.0	104.0		438,,,	1.1	0.0	15	dbSNP_130	104	0,3182		0,0,1591	no	coding-synonymous,intron,intron,utr-3	C15orf40	NM_001160114.1,NM_001160115.1,NM_001160116.1,NM_144597.2	,,,	1,36,2246	CC,CA,AA		0.0,2.7457,0.8322	,,,	146/154,,,	83673653	38,4528	692	1591	2283	SO:0001624	3_prime_UTR_variant	123207	exon4			GCATTCAACAAGT	BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.*696T>G	15.37:g.83673653A>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_001160114	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Silent	SNP	ENST00000513601.2	37	CCDS32312.2																																																																																			A|0.985;C|0.015	0.015	strong		0.393	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597	
SNX21	90203	hgsc.bcm.edu	37	20	44469290	44469290	+	Missense_Mutation	SNP	G	G	A	rs4638862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44469290G>A	ENST00000491381.1	+	4	528	c.460G>A	c.(460-462)Gcc>Acc	p.A154T	SNX21_ENST00000372542.1_Missense_Mutation_p.A145T|SNX21_ENST00000462307.1_Silent_p.S157S|SNX21_ENST00000372541.1_Silent_p.S148S|SNX21_ENST00000342644.5_Missense_Mutation_p.A154T|SNX21_ENST00000344780.4_3'UTR			Q969T3	SNX21_HUMAN	sorting nexin family member 21	154	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.		A -> T (in dbSNP:rs4638862). {ECO:0000269|PubMed:15489334}.		protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				CTACACCCTCGCCGTGATCGG	0.642													G|||	1754	0.35024	0.0658	0.5202	5008	,	,		14028	0.4276		0.5298	False		,,,				2504	0.3497				p.A154T		Atlas-SNP	.											.	SNX21	23	.	0			c.G460A						PASS	.	G	,,THR/ALA,THR/ALA	692,3714	286.0+/-278.5	64,564,1575	84.0	87.0	86.0		453,471,460,460	2.4	1.0	20	dbSNP_111	86	4586,4014	591.5+/-392.8	1222,2142,936	yes	coding-synonymous,coding-synonymous,missense,missense	SNX21	NM_001042632.1,NM_001042633.1,NM_033421.2,NM_152897.1	,,58,58	1286,2706,2511	AA,AG,GG		46.6744,15.7059,40.5813	,,probably-damaging,probably-damaging	151/153,157/159,154/374,154/200	44469290	5278,7728	2203	4300	6503	SO:0001583	missense	90203	exon4			ACCCTCGCCGTGA	AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"""Sorting nexins"", ""Tetratricopeptide (TTC) repeat domain containing"""	16154	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 161"""	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.460G>A	20.37:g.44469290G>A	ENSP00000418593:p.Ala154Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_033421	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Missense_Mutation	SNP	ENST00000491381.1	37	CCDS13377.1	873	0.39972527472527475	34	0.06910569105691057	172	0.47513812154696133	252	0.4405594405594406	415	0.5474934036939314	G	8.862	0.947087	0.18356	0.157059	0.533256	ENSG00000124104	ENST00000491381;ENST00000342644;ENST00000372542	T;T;T	0.27720	1.65;1.65;1.65	4.34	2.39	0.29439	Phox homologous domain (4);	0.416437	0.25869	N	0.027770	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999974067	B;B;B	0.20988	0.004;0.007;0.05	B;B;B	0.15484	0.005;0.005;0.013	T	0.45644	-0.9247	8	0.22706	T	0.39	-4.6567	3.9307	0.09283	0.1956:0.0:0.5137:0.2907	rs4638862;rs17851752;rs52829951;rs58614376;rs4638862	145;154;154	Q5JZH3;Q969T3;Q5JZH5	.;SNX21_HUMAN;.	T	154;154;145	ENSP00000418593:A154T;ENSP00000344586:A154T;ENSP00000361620:A145T	ENSP00000344586:A154T	A	+	1	0	SNX21	43902697	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	1.246000	0.32803	0.473000	0.27368	0.462000	0.41574	GCC	G|0.611;A|0.389	0.389	strong		0.642	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421	
KRT33B	3884	hgsc.bcm.edu	37	17	39521752	39521752	+	Silent	SNP	G	G	A	rs61741664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39521752G>A	ENST00000251646.3	-	4	691	c.642C>T	c.(640-642)gaC>gaT	p.D214D		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	214	Linker 12.|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)				CGGGAGCAGCGTCCACCTCCA	0.542													G|||	72	0.014377	0.0537	0.0014	5008	,	,		19114	0.0		0.0	False		,,,				2504	0.0				p.D214D		Atlas-SNP	.											.	KRT33B	46	.	0			c.C642T						PASS	.	G		204,4178		19,166,2006	66.0	64.0	64.0		642	-4.8	0.7	17	dbSNP_129	64	1,8599		0,1,4299	no	coding-synonymous	KRT33B	NM_002279.3		19,167,6305	AA,AG,GG		0.0116,4.6554,1.5791		214/405	39521752	205,12777	2191	4300	6491	SO:0001819	synonymous_variant	3884	exon4			AGCAGCGTCCACC	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.642C>T	17.37:g.39521752G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	200	100	0.5	NM_002279	O76010	Silent	SNP	ENST00000251646.3	37	CCDS11389.1																																																																																			G|0.981;A|0.019	0.019	strong		0.542	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
SPATA16	83893	hgsc.bcm.edu	37	3	172766822	172766822	+	Silent	SNP	G	G	A	rs508508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:172766822G>A	ENST00000351008.3	-	3	858	c.675C>T	c.(673-675)agC>agT	p.S225S		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	225					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			AACTTGCCACGCTTGCTATAT	0.383													G|||	859	0.171526	0.2231	0.1801	5008	,	,		17129	0.1379		0.1511	False		,,,				2504	0.1513				p.S225S		Atlas-SNP	.											SPATA16,NS,haematopoietic_neoplasm,-1,2	SPATA16	111	2	0			c.C675T						PASS	.	G		1031,3375	380.2+/-323.6	131,769,1303	104.0	92.0	96.0		675	-2.7	1.0	3	dbSNP_83	96	1243,7357	249.3+/-276.6	92,1059,3149	no	coding-synonymous	SPATA16	NM_031955.5		223,1828,4452	AA,AG,GG		14.4535,23.3999,17.4842		225/570	172766822	2274,10732	2203	4300	6503	SO:0001819	synonymous_variant	83893	exon3			TGCCACGCTTGCT	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.675C>T	3.37:g.172766822G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	119	70	0.588235	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Silent	SNP	ENST00000351008.3	37	CCDS3221.1																																																																																			G|0.824;A|0.176	0.176	strong		0.383	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955	
TMEM255B	348013	hgsc.bcm.edu	37	13	114507956	114507956	+	Silent	SNP	G	G	A	rs56032548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114507956G>A	ENST00000375353.3	+	8	795	c.768G>A	c.(766-768)acG>acA	p.T256T	TMEM255B_ENST00000467169.1_3'UTR	NM_182614.2	NP_872420.1	Q8WV15	T255B_HUMAN	transmembrane protein 255B	256						integral component of membrane (GO:0016021)											TCCGCCTGACGCCCGAGCCCG	0.672													G|||	355	0.0708866	0.2534	0.0288	5008	,	,		14726	0.0		0.0	False		,,,				2504	0.0				p.T256T		Atlas-SNP	.											.	.	.	.	0			c.G768A						PASS	.	G		962,3442	354.4+/-312.6	113,736,1353	62.0	60.0	60.0		768	-5.7	0.0	13	dbSNP_129	60	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	FAM70B	NM_182614.2		113,753,5636	AA,AG,GG		0.1977,21.8438,7.5285		256/327	114507956	979,12025	2202	4300	6502	SO:0001819	synonymous_variant	348013	exon8			CCTGACGCCCGAG	BC018995	CCDS45071.1	13q34	2012-11-30	2012-11-30	2012-11-30	ENSG00000184497	ENSG00000184497			28297	protein-coding gene	gene with protein product			"""family with sequence similarity 70, member B"""	FAM70B		12477932	Standard	NM_182614		Approved	MGC20579	uc001vuh.3	Q8WV15	OTTHUMG00000017398	ENST00000375353.3:c.768G>A	13.37:g.114507956G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_182614		Silent	SNP	ENST00000375353.3	37	CCDS45071.1																																																																																			G|0.922;A|0.078	0.078	strong		0.672	TMEM255B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045953.4	NM_182614	
FLG	2312	hgsc.bcm.edu	37	1	152282113	152282113	+	Missense_Mutation	SNP	G	G	A	rs3120647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152282113G>A	ENST00000368799.1	-	3	5284	c.5249C>T	c.(5248-5250)tCc>tTc	p.S1750F	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1750	Ser-rich.		S -> F (in dbSNP:rs3120647).		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)			GCCACGTGTGGACTCTTGGTG	0.602									Ichthyosis				G|||	548	0.109425	0.3979	0.0303	5008	,	,		19409	0.0		0.001	False		,,,				2504	0.0				p.S1750F		Atlas-SNP	.											.	FLG	900	.	0			c.C5249T						PASS	.	G	PHE/SER	1445,2961	467.0+/-354.7	227,991,985	201.0	207.0	205.0		5249	3.9	0.0	1	dbSNP_103	205	14,8586	9.8+/-36.6	0,14,4286	no	missense	FLG	NM_002016.1	155	227,1005,5271	AA,AG,GG		0.1628,32.7962,11.2179	probably-damaging	1750/4062	152282113	1459,11547	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGTGTGGACTCTT	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.5249C>T	1.37:g.152282113G>A	ENSP00000357789:p.Ser1750Phe	Somatic	464	3	0.00646552		WXS	Illumina HiSeq	Phase_I	467	464	0.993576	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	184	0.08424908424908426	173	0.3516260162601626	11	0.03038674033149171	0	0.0	0	0.0	G	11.13	1.546902	0.27652	0.327962	0.001628	ENSG00000143631	ENST00000368799	T	0.02421	4.3	3.93	3.93	0.45458	.	.	.	.	.	T	0.08582	0.0213	M	0.82323	2.585	0.80722	P	0.0	D	0.61697	0.99	D	0.71656	0.974	T	0.01504	-1.1338	8	0.54805	T	0.06	1.0E-4	11.86	0.52461	0.0:0.0:1.0:0.0	rs57870089	1750	P20930	FILA_HUMAN	F	1750	ENSP00000357789:S1750F	ENSP00000357789:S1750F	S	-	2	0	FLG	150548737	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.005000	0.13129	1.891000	0.54761	0.461000	0.40582	TCC	G|0.884;A|0.116	0.116	strong		0.602	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
HUS1	3364	hgsc.bcm.edu	37	7	48008869	48008869	+	Missense_Mutation	SNP	G	G	C	rs138848570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:48008869G>C	ENST00000258774.5	-	6	610	c.587C>G	c.(586-588)aCt>aGt	p.T196S	HUS1_ENST00000432325.1_Missense_Mutation_p.T175S	NM_004507.3	NP_004498.1	O60921	HUS1_HUMAN	HUS1 checkpoint homolog (S. pombe)	196					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)				TACTAATTCAGTTTCTATTTT	0.294								Direct reversal of damage;Other conserved DNA damage response genes			OREG0018063	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	21	0.00419329	0.0159	0.0	5008	,	,		20315	0.0		0.0	False		,,,				2504	0.0				p.T196S	Ovarian(103;466 1517 21788 34610 43890)	Atlas-SNP	.											.	HUS1	36	.	0			c.C587G						PASS	.	G	SER/THR	20,4378	28.1+/-56.4	1,18,2180	95.0	99.0	98.0		587	5.2	1.0	7	dbSNP_134	98	0,8600		0,0,4300	yes	missense	HUS1	NM_004507.3	58	1,18,6480	CC,CG,GG		0.0,0.4548,0.1539	benign	196/281	48008869	20,12978	2199	4300	6499	SO:0001583	missense	3364	exon6			AATTCAGTTTCTA	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.587C>G	7.37:g.48008869G>C	ENSP00000258774:p.Thr196Ser	Somatic	51	0	0	951	WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_004507	B4DFI9	Missense_Mutation	SNP	ENST00000258774.5	37	CCDS34635.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	G	16.67	3.187502	0.57909	0.004548	0.0	ENSG00000136273	ENST00000258774;ENST00000432325;ENST00000432627	T;T;T	0.13196	2.61;2.61;2.61	5.19	5.19	0.71726	.	0.052227	0.85682	N	0.000000	T	0.02888	0.0086	L	0.46567	1.45	0.54753	D	0.999987	B	0.30033	0.266	B	0.40228	0.323	T	0.07829	-1.0752	10	0.22109	T	0.4	-12.6777	16.5638	0.84573	0.0:0.0:1.0:0.0	.	196	O60921	HUS1_HUMAN	S	196;175;175	ENSP00000258774:T196S;ENSP00000416588:T175S;ENSP00000404855:T175S	ENSP00000258774:T196S	T	-	2	0	HUS1	47975394	1.000000	0.71417	0.951000	0.38953	0.999000	0.98932	7.975000	0.88055	2.563000	0.86464	0.655000	0.94253	ACT	G|0.996;C|0.004	0.004	strong		0.294	HUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340952.1	NM_004507	
IGSF11	152404	hgsc.bcm.edu	37	3	118621664	118621664	+	Missense_Mutation	SNP	C	C	A	rs36052974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:118621664C>A	ENST00000393775.2	-	7	1304	c.999G>T	c.(997-999)gaG>gaT	p.E333D	IGSF11_ENST00000354673.2_Missense_Mutation_p.E332D|IGSF11_ENST00000425327.2_Missense_Mutation_p.E332D|IGSF11_ENST00000489689.1_Missense_Mutation_p.E309D|IGSF11_ENST00000441144.2_Missense_Mutation_p.E308D|IGSF11_ENST00000491903.1_Missense_Mutation_p.E305D	NM_001015887.1	NP_001015887.1	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11	333			E -> D (in dbSNP:rs36052974). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16108831}.		cell adhesion (GO:0007155)|regulation of growth (GO:0040008)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GGCTGACTGACTCTGTGTTTC	0.468													C|||	1319	0.263379	0.3775	0.317	5008	,	,		20723	0.1319		0.1292	False		,,,				2504	0.3446				p.E333D		Atlas-SNP	.											.	IGSF11	122	.	0			c.G999T						PASS	.	C	ASP/GLU,ASP/GLU	1610,2796	498.1+/-364.0	298,1014,891	146.0	151.0	149.0		999,996	3.5	0.3	3	dbSNP_126	149	1287,7313	254.7+/-279.9	93,1101,3106	yes	missense,missense	IGSF11	NM_001015887.1,NM_152538.2	45,45	391,2115,3997	AA,AC,CC		14.9651,36.5411,22.2743	benign,benign	333/432,332/431	118621664	2897,10109	2203	4300	6503	SO:0001583	missense	152404	exon7			GACTGACTCTGTG	AB079879	CCDS2983.1, CCDS46891.1	3q21.2	2013-01-11			ENSG00000144847	ENSG00000144847		"""Immunoglobulin superfamily / I-set domain containing"""	16669	protein-coding gene	gene with protein product	"""cancer/testis antigen 119"""	608351				12207903	Standard	XM_006713516		Approved	BT-IgSF, MGC35227, Igsf13, VSIG3, CT119	uc003ebw.3	Q5DX21	OTTHUMG00000159387	ENST00000393775.2:c.999G>T	3.37:g.118621664C>A	ENSP00000377370:p.Glu333Asp	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	195	95	0.487179	NM_001015887	C9JZN0|Q8N4F1|Q8N7T8|Q8NDD2	Missense_Mutation	SNP	ENST00000393775.2	37	CCDS46891.1	483	0.22115384615384615	196	0.3983739837398374	110	0.30386740331491713	83	0.1451048951048951	94	0.12401055408970976	C	7.735	0.700035	0.15106	0.365411	0.149651	ENSG00000144847	ENST00000425327;ENST00000393775;ENST00000489689;ENST00000354673;ENST00000441144;ENST00000491903	T;T;D;T;D;D	0.83506	-0.87;-1.09;-1.73;-0.87;-1.67;-1.56	5.28	3.46	0.39613	.	0.591478	0.15720	N	0.247925	T	0.00012	0.0000	N	0.12182	0.205	0.36515	P	0.13019099999999995	B;B;B;B;B	0.09022	0.001;0.002;0.002;0.001;0.001	B;B;B;B;B	0.11329	0.003;0.006;0.006;0.003;0.003	T	0.18524	-1.0334	9	0.13853	T	0.58	.	8.8141	0.34985	0.0:0.4972:0.4201:0.0827	rs36052974	305;308;332;309;333	C9JBA5;Q5DX21-3;Q5DX21-2;C9JMW0;Q5DX21	.;.;.;.;IGS11_HUMAN	D	332;333;309;332;308;305	ENSP00000406092:E332D;ENSP00000377370:E333D;ENSP00000420486:E309D;ENSP00000346700:E332D;ENSP00000401240:E308D;ENSP00000417413:E305D	ENSP00000346700:E332D	E	-	3	2	IGSF11	120104354	1.000000	0.71417	0.273000	0.24645	0.925000	0.55904	3.961000	0.56759	0.787000	0.33731	-0.136000	0.14681	GAG	C|0.777;A|0.223	0.223	strong		0.468	IGSF11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355075.2		
OR5D18	219438	hgsc.bcm.edu	37	11	55587591	55587591	+	Silent	SNP	C	C	T	rs142792552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55587591C>T	ENST00000333976.4	+	1	506	c.486C>T	c.(484-486)tgC>tgT	p.C162C		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				AACTGACGTGCTCTGCTTTAA	0.453													N|||	7	0.00139776	0.0053	0.0	5008	,	,		18790	0.0		0.0	False		,,,				2504	0.0				p.C162C		Atlas-SNP	.											.	OR5D18	121	.	0			c.C486T						PASS	.	C		43,4357		0,43,2157	203.0	189.0	193.0		486	-0.8	0.2	11	dbSNP_134	193	0,8592		0,0,4296	no	coding-synonymous	OR5D18	NM_001001952.1		0,43,6453	TT,TC,CC		0.0,0.9773,0.331		162/314	55587591	43,12949	2200	4296	6496	SO:0001819	synonymous_variant	219438	exon1			GACGTGCTCTGCT	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.486C>T	11.37:g.55587591C>T		Somatic	309	1	0.00323625		WXS	Illumina HiSeq	Phase_I	345	163	0.472464	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Silent	SNP	ENST00000333976.4	37	CCDS31510.1																																																																																			C|0.997;T|0.003	0.003	strong		0.453	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952	
ACSBG1	23205	hgsc.bcm.edu	37	15	78466006	78466006	+	Missense_Mutation	SNP	G	G	A	rs11072735	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:78466006G>A	ENST00000258873.4	-	13	2223	c.2018C>T	c.(2017-2019)gCg>gTg	p.A673V	ACSBG1_ENST00000560817.1_Missense_Mutation_p.A431V|ACSBG1_ENST00000541759.1_Missense_Mutation_p.A431V	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	673			A -> V (in dbSNP:rs11072735). {ECO:0000269|PubMed:14702039}.		long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						GGGCCGGGCCGCCGCGTTCAT	0.567													G|||	306	0.0611022	0.1354	0.0159	5008	,	,		18635	0.0685		0.0189	False		,,,				2504	0.0286				p.A673V		Atlas-SNP	.											ACSBG1,mouth,carcinoma,+1,1	ACSBG1	79	1	0			c.C2018T						scavenged	.	G	VAL/ALA,VAL/ALA	471,3921	223.3+/-239.8	25,421,1750	91.0	75.0	80.0		2006,2018	4.4	0.0	15	dbSNP_120	80	129,8457	67.0+/-129.4	1,127,4165	yes	missense,missense	ACSBG1	NM_001199377.1,NM_015162.4	64,64	26,548,5915	AA,AG,GG		1.5024,10.724,4.6232	benign,benign	669/721,673/725	78466006	600,12378	2196	4293	6489	SO:0001583	missense	23205	exon13			CGGGCCGCCGCGT	AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"""Acyl-CoA synthetase family"""	29567	protein-coding gene	gene with protein product	"""bubblegum"", ""very long-chain acyl-CoA synthetase"", ""lipidosin"""	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.2018C>T	15.37:g.78466006G>A	ENSP00000258873:p.Ala673Val	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_015162	B2RB61|O75126|Q76N27|Q9HC26	Missense_Mutation	SNP	ENST00000258873.4	37	CCDS10298.1	119	0.05448717948717949	58	0.11788617886178862	9	0.024861878453038673	38	0.06643356643356643	14	0.018469656992084433	G	4.942	0.174970	0.09391	0.10724	0.015024	ENSG00000103740	ENST00000258873;ENST00000541759	T;T	0.03831	3.79;3.79	5.35	4.43	0.53597	.	0.224065	0.37437	N	0.002091	T	0.00039	0.0001	N	0.01482	-0.84	0.09310	N	1	B;B	0.19706	0.038;0.011	B;B	0.12156	0.007;0.005	T	0.48210	-0.9055	10	0.02654	T	1	-9.3878	9.6131	0.39674	0.1571:0.0:0.8429:0.0	rs11072735;rs11072735	669;673	B7Z2Y6;Q96GR2	.;ACBG1_HUMAN	V	673;431	ENSP00000258873:A673V;ENSP00000439955:A431V	ENSP00000258873:A673V	A	-	2	0	ACSBG1	76253061	0.997000	0.39634	0.019000	0.16419	0.090000	0.18270	5.564000	0.67359	1.491000	0.48482	0.591000	0.81541	GCG	G|0.954;A|0.046	0.046	strong		0.567	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162	
VPS33B	26276	hgsc.bcm.edu	37	15	91550232	91550232	+	Silent	SNP	G	G	A	rs59648701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91550232G>A	ENST00000333371.3	-	9	1001	c.648C>T	c.(646-648)ggC>ggT	p.G216G	VPS33B_ENST00000535906.1_Silent_p.G189G|VPS33B_ENST00000535843.1_Silent_p.G125G	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	216					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|membrane fusion (GO:0061025)|platelet alpha granule organization (GO:0070889)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule (GO:0031091)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|stomach(2)	16	Lung NSC(78;0.0987)|all_lung(78;0.175)					CCTTGGTTTCGCCATCCTCCT	0.527													G|||	120	0.0239617	0.0809	0.0144	5008	,	,		19376	0.0		0.003	False		,,,				2504	0.0				p.G216G		Atlas-SNP	.											.	VPS33B	42	.	0			c.C648T						PASS	.	G		294,4102	161.4+/-193.6	7,280,1911	114.0	118.0	117.0		648	-1.7	1.0	15	dbSNP_129	117	8,8588	7.1+/-27.0	0,8,4290	no	coding-synonymous	VPS33B	NM_018668.3		7,288,6201	AA,AG,GG		0.0931,6.6879,2.3245		216/618	91550232	302,12690	2198	4298	6496	SO:0001819	synonymous_variant	26276	exon9			GGTTTCGCCATCC	AF201694	CCDS10369.1, CCDS73783.1	15q26.1	2006-12-19	2006-12-19		ENSG00000184056	ENSG00000184056			12712	protein-coding gene	gene with protein product		608552	"""vacuolar protein sorting 33B (yeast homolog)"""			8996080	Standard	XM_005254887		Approved	FLJ14848	uc002bqp.1	Q9H267	OTTHUMG00000149835	ENST00000333371.3:c.648C>T	15.37:g.91550232G>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	33	32	0.969697	NM_018668	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Silent	SNP	ENST00000333371.3	37	CCDS10369.1																																																																																			G|0.978;A|0.022	0.022	strong		0.527	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668	
PAPSS1	9061	hgsc.bcm.edu	37	4	108574677	108574677	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:108574677G>T	ENST00000265174.4	-	9	1479	c.1207C>A	c.(1207-1209)Cta>Ata	p.L403I	PAPSS1_ENST00000511304.1_5'UTR	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	403					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)		TTCTGCTTTAGCTCAGTAGGA	0.393																																					p.L403I		Atlas-SNP	.											PAPSS1,NS,carcinoma,+1,1	PAPSS1	57	1	0			c.C1207A						scavenged	.						140.0	131.0	134.0					4																	108574677		2203	4300	6503	SO:0001583	missense	9061	exon9			GCTTTAGCTCAGT	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.1207C>A	4.37:g.108574677G>T	ENSP00000265174:p.Leu403Ile	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	207	4	0.0193237	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Missense_Mutation	SNP	ENST00000265174.4	37	CCDS3676.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.581299	0.86748	.	.	ENSG00000138801	ENST00000265174	T	0.31510	1.49	5.47	5.47	0.80525	Sulphate adenylyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.53094	0.1775	L	0.55481	1.735	0.80722	D	1	P	0.48834	0.916	D	0.71656	0.974	T	0.43376	-0.9395	10	0.42905	T	0.14	-15.3606	19.3341	0.94307	0.0:0.0:1.0:0.0	.	403	O43252	PAPS1_HUMAN	I	403	ENSP00000265174:L403I	ENSP00000265174:L403I	L	-	1	2	PAPSS1	108794126	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.436000	0.80404	2.558000	0.86282	0.557000	0.71058	CTA	.	.	none		0.393	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2		
MYBPC1	4604	hgsc.bcm.edu	37	12	102036305	102036305	+	Silent	SNP	C	C	T	rs2293468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:102036305C>T	ENST00000550270.1	+	9	699	c.699C>T	c.(697-699)gaC>gaT	p.D233D	MYBPC1_ENST00000536007.1_Silent_p.D214D|MYBPC1_ENST00000441232.1_Silent_p.D233D|MYBPC1_ENST00000541119.1_Silent_p.D221D|MYBPC1_ENST00000360610.2_Silent_p.D233D|MYBPC1_ENST00000551300.1_Silent_p.D134D|MYBPC1_ENST00000547405.1_Silent_p.D207D|MYBPC1_ENST00000361685.2_Silent_p.D258D|MYBPC1_ENST00000553190.1_Silent_p.D233D|MYBPC1_ENST00000452455.2_Silent_p.D233D|MYBPC1_ENST00000547509.1_Silent_p.D219D|MYBPC1_ENST00000545503.2_Silent_p.D233D|MYBPC1_ENST00000392934.3_Silent_p.D220D|MYBPC1_ENST00000549145.1_Silent_p.D246D|MYBPC1_ENST00000361466.2_Silent_p.D258D|MYBPC1_ENST00000550501.1_Intron			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	233				GITDLR -> ESPTCS (in Ref. 1; CAA46987). {ECO:0000305}.	cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						GAATCACCGACCTGCGCGGCA	0.627													C|||	1474	0.294329	0.289	0.2493	5008	,	,		19254	0.3879		0.2823	False		,,,				2504	0.2495				p.D258D		Atlas-SNP	.											.	MYBPC1	235	.	0			c.C774T						PASS	.	C	,,,	1283,3123	433.3+/-343.5	197,889,1117	88.0	71.0	76.0		774,774,699,699	3.4	1.0	12	dbSNP_100	76	2466,6134	403.5+/-347.8	343,1780,2177	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYBPC1	NM_002465.2,NM_206819.1,NM_206820.1,NM_206821.1	,,,	540,2669,3294	TT,TC,CC		28.6744,29.1194,28.8252	,,,	258/1172,258/1149,233/1142,233/1124	102036305	3749,9257	2203	4300	6503	SO:0001819	synonymous_variant	4604	exon11			CACCGACCTGCGC		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7549	protein-coding gene	gene with protein product		160794	"""myosin-binding protein C, slow-type"""			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.699C>T	12.37:g.102036305C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Silent	SNP	ENST00000550270.1	37	CCDS9085.1																																																																																			C|0.704;T|0.296	0.296	strong		0.627	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
LRIG1	26018	hgsc.bcm.edu	37	3	66431280	66431280	+	Missense_Mutation	SNP	C	C	T	rs9877201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:66431280C>T	ENST00000273261.3	-	18	3300	c.2776G>A	c.(2776-2778)Ggt>Agt	p.G926S	LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.G903S	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	926			G -> S (in dbSNP:rs9877201).		innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		ACCCGGCCACCGTGTTCTGAA	0.597													C|||	554	0.110623	0.3873	0.0346	5008	,	,		18811	0.0		0.0179	False		,,,				2504	0.0				p.G926S		Atlas-SNP	.											LRIG1,NS,carcinoma,0,1	LRIG1	138	1	0			c.G2776A						PASS	.	C	SER/GLY	1492,2914	473.5+/-356.7	259,974,970	49.0	52.0	51.0		2776	-3.4	0.0	3	dbSNP_119	51	84,8516	48.9+/-108.6	1,82,4217	yes	missense	LRIG1	NM_015541.2	56	260,1056,5187	TT,TC,CC		0.9767,33.8629,12.1175	benign	926/1094	66431280	1576,11430	2203	4300	6503	SO:0001583	missense	26018	exon18			GGCCACCGTGTTC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.2776G>A	3.37:g.66431280C>T	ENSP00000273261:p.Gly926Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	210	0.09615384615384616	187	0.3800813008130081	8	0.022099447513812154	0	0.0	15	0.01978891820580475	C	10.82	1.457361	0.26161	0.338629	0.009767	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.69040	-0.18;-0.37	5.34	-3.41	0.04839	.	0.402609	0.28016	N	0.016939	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B;B;B	0.24651	0.012;0.108;0.007	B;B;B	0.15870	0.014;0.014;0.002	T	0.38908	-0.9639	9	0.18710	T	0.47	.	8.9885	0.36008	0.145:0.5962:0.0:0.2587	rs9877201;rs52813156;rs59347115;rs9877201	903;926;926	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	S	926;903;829	ENSP00000273261:G926S;ENSP00000373208:G903S	ENSP00000273261:G926S	G	-	1	0	LRIG1	66513970	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.284000	0.08422	-0.442000	0.07190	-0.794000	0.03295	GGT	C|0.879;T|0.121	0.121	strong		0.597	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
KIAA1328	57536	hgsc.bcm.edu	37	18	34647176	34647176	+	Silent	SNP	T	T	C	rs3747895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:34647176T>C	ENST00000280020.5	+	7	922	c.900T>C	c.(898-900)ccT>ccC	p.P300P	KIAA1328_ENST00000586501.1_Silent_p.P16P|KIAA1328_ENST00000591619.1_Silent_p.P296P|KIAA1328_ENST00000543923.1_Silent_p.P192P|KIAA1328_ENST00000435985.2_Silent_p.P16P|KIAA1328_ENST00000586135.1_Silent_p.P16P	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	300										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		ATCTTAAGCCTACTCCTAGTC	0.443													T|||	1297	0.258986	0.643	0.1311	5008	,	,		21398	0.1101		0.1292	False		,,,				2504	0.1176				p.P300P		Atlas-SNP	.											.	KIAA1328	39	.	0			c.T900C						PASS	.	T		2272,1844		625,1022,411	104.0	98.0	100.0		900	0.1	0.0	18	dbSNP_107	100	1148,7264		78,992,3136	no	coding-synonymous	KIAA1328	NM_020776.1		703,2014,3547	CC,CT,TT		13.6472,44.8008,27.2989		300/578	34647176	3420,9108	2058	4206	6264	SO:0001819	synonymous_variant	57536	exon7			TAAGCCTACTCCT	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.900T>C	18.37:g.34647176T>C		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	174	173	0.994253	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Silent	SNP	ENST00000280020.5	37	CCDS45855.1																																																																																			T|0.749;C|0.251	0.251	strong		0.443	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776	
OR5L1	219437	hgsc.bcm.edu	37	11	55578987	55578987	+	Silent	SNP	T	T	C	rs386753698|rs67727364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55578987T>C	ENST00000333973.2	+	1	134	c.45T>C	c.(43-45)ctT>ctC	p.L15L		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	15						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L15L(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TCATTCTCCTTGGACTATCAG	0.433													N|||	525	0.104832	0.1884	0.0461	5008	,	,		18304	0.0813		0.0924	False		,,,				2504	0.0706				p.L15L		Atlas-SNP	.											OR5L1,NS,carcinoma,0,1	OR5L1	145	1	1	Substitution - coding silent(1)	stomach(1)	c.T45C						scavenged	.	C		670,3730		63,544,1593	201.0	191.0	194.0		45	-2.8	0.0	11	dbSNP_130	194	724,7862		32,660,3601	no	coding-synonymous	OR5L1	NM_001004738.1		95,1204,5194	CC,CT,TT		8.4323,15.2273,10.7346		15/312	55578987	1394,11592	2200	4293	6493	SO:0001819	synonymous_variant	219437	exon1			TCTCCTTGGACTA	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.45T>C	11.37:g.55578987T>C		Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	113	63	0.557522	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			T|0.898;C|0.102	0.102	strong		0.433	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
NEB	4703	hgsc.bcm.edu	37	2	152476028	152476028	+	Missense_Mutation	SNP	C	C	G	rs10172023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152476028C>G	ENST00000172853.10	-	69	10227	c.10080G>C	c.(10078-10080)tgG>tgC	p.W3360C	NEB_ENST00000603639.1_Missense_Mutation_p.W3603C|NEB_ENST00000409198.1_Missense_Mutation_p.W3360C|NEB_ENST00000604864.1_Missense_Mutation_p.W3603C|NEB_ENST00000397345.3_Missense_Mutation_p.W3603C|NEB_ENST00000427231.2_Missense_Mutation_p.W3603C			P20929	NEBU_HUMAN	nebulin	3360			W -> C (in dbSNP:rs10172023). {ECO:0000269|PubMed:7739042}.		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)		GCAGGCAGATCCATTCATGCA	0.483													C|||	1101	0.219848	0.1316	0.2478	5008	,	,		21041	0.244		0.3062	False		,,,				2504	0.2055				p.W3603C		Atlas-SNP	.											.	NEB	1697	.	0			c.G10809C						PASS	.	C	CYS/TRP,CYS/TRP,CYS/TRP	564,3494		42,480,1507	158.0	151.0	153.0		10809,10809,10080	5.6	1.0	2	dbSNP_119	153	2784,5616		483,1818,1899	yes	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	215,215,215	525,2298,3406	GG,GC,CC		33.1429,13.8985,26.8743	probably-damaging,probably-damaging,probably-damaging	3603/8526,3603/8526,3360/6670	152476028	3348,9110	2029	4200	6229	SO:0001583	missense	4703	exon73			GCAGATCCATTCA	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.10080G>C	2.37:g.152476028C>G	ENSP00000172853:p.Trp3360Cys	Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	154	90	0.584416	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		547	0.25045787545787546	71	0.1443089430894309	85	0.23480662983425415	145	0.2534965034965035	246	0.3245382585751979	C	13.94	2.387416	0.42308	0.138985	0.331429	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	5.61	5.61	0.85477	.	0.067367	0.64402	D	0.000005	T	0.00012	0.0000	M	0.87456	2.885	0.09310	P	1.0	D	0.89917	1.0	D	0.81914	0.995	T	0.03945	-1.0990	9	0.52906	T	0.07	.	16.2703	0.82612	0.0:0.8676:0.1324:0.0	rs10172023;rs10172023	3360	P20929	NEBU_HUMAN	C	3360;3603;3603;3360	ENSP00000386259:W3360C;ENSP00000380505:W3603C;ENSP00000416578:W3603C;ENSP00000172853:W3360C	ENSP00000172853:W3360C	W	-	3	0	NEB	152184274	1.000000	0.71417	0.999000	0.59377	0.325000	0.28411	1.494000	0.35616	2.793000	0.96121	0.655000	0.94253	TGG	C|0.769;G|0.231	0.231	strong		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
LY6G5B	58496	hgsc.bcm.edu	37	6	31639845	31639845	+	Missense_Mutation	SNP	C	C	A	rs11758242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31639845C>A	ENST00000375864.4	+	3	1176	c.392C>A	c.(391-393)tCc>tAc	p.S131Y	CSNK2B-LY6G5B-1181_ENST00000375880.2_3'UTR|LY6G5B_ENST00000409525.1_Missense_Mutation_p.S76Y	NM_021221.2	NP_067044.2	Q8NDX9	LY65B_HUMAN	lymphocyte antigen 6 complex, locus G5B	131			S -> Y (in dbSNP:rs11758242).			extracellular region (GO:0005576)				lung(4)	4						CTGTCTGACTCCCAGATTCAG	0.607													C|||	286	0.0571086	0.1316	0.0764	5008	,	,		16595	0.0179		0.0258	False		,,,				2504	0.0153				p.S131Y		Atlas-SNP	.											LY6G5B,NS,carcinoma,0,1	LY6G5B	8	1	0			c.C392A						PASS	.	C	TYR/SER	334,2688		18,298,1195	53.0	50.0	51.0		392	-0.4	0.0	6	dbSNP_120	51	152,5264		1,150,2557	yes	missense	LY6G5B	NM_021221.2	144	19,448,3752	AA,AC,CC		2.8065,11.0523,5.7597	benign	131/202	31639845	486,7952	1511	2708	4219	SO:0001583	missense	58496	exon3			CTGACTCCCAGAT	AF129756	CCDS34400.1	6p21.3	2008-08-01	2002-07-29	2002-08-01	ENSG00000240053	ENSG00000240053			13931	protein-coding gene	gene with protein product		610433	"""chromosome 6 open reading frame 19"""	C6orf19		8812450, 12079290, 17008713	Standard	NM_021221		Approved	G5b		Q8NDX9	OTTHUMG00000031227	ENST00000375864.4:c.392C>A	6.37:g.31639845C>A	ENSP00000365024:p.Ser131Tyr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	137	57	0.416058	NM_021221	B0UXB2|B0UZ65|B0UZP8|B7ZCA3|Q5SQ62|Q5SST3|Q9UKT0|Q9UMQ0	Missense_Mutation	SNP	ENST00000375864.4	37	CCDS34400.1	139	0.06364468864468864	74	0.15040650406504066	29	0.08011049723756906	16	0.027972027972027972	20	0.026385224274406333	C	0.580	-0.837366	0.02692	0.110523	0.028065	ENSG00000240053	ENST00000409691;ENST00000375864;ENST00000409525	T;T	0.26067	1.76;1.76	3.68	-0.402	0.12404	.	.	.	.	.	T	0.05731	0.0150	L	0.29908	0.895	.	.	.	B	0.28324	0.207	B	0.27715	0.082	T	0.31586	-0.9938	8	0.62326	D	0.03	-0.2784	3.6555	0.08220	0.0:0.4487:0.1881:0.3632	rs11758242;rs52832321;rs11758242	131	Q8NDX9	LY65B_HUMAN	Y	128;131;76	ENSP00000365024:S131Y;ENSP00000386365:S76Y	ENSP00000365024:S131Y	S	+	2	0	LY6G5B	31747824	0.023000	0.18921	0.003000	0.11579	0.123000	0.20343	0.107000	0.15375	-0.100000	0.12241	-0.467000	0.05162	TCC	C|0.932;A|0.068	0.068	strong		0.607	LY6G5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000124389.4		
CDH13	1012	hgsc.bcm.edu	37	16	83378487	83378487	+	Silent	SNP	T	T	C	rs145120824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:83378487T>C	ENST00000566620.1	+	6	947	c.657T>C	c.(655-657)gaT>gaC	p.D219D	CDH13_ENST00000268613.10_Silent_p.D266D|CDH13_ENST00000428848.3_Silent_p.D180D|CDH13_ENST00000569454.1_3'UTR	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	219	Cadherin 1. {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)		AGACCACTGATGTCAATGGCA	0.438													T|||	21	0.00419329	0.0144	0.0029	5008	,	,		19418	0.0		0.0	False		,,,				2504	0.0				p.D266D		Atlas-SNP	.											.	CDH13	97	.	0			c.T798C						PASS	.	T	,,,	47,3655		0,47,1804	78.0	80.0	79.0		798,540,,657	3.5	0.8	16	dbSNP_134	79	0,8178		0,0,4089	no	coding-synonymous,coding-synonymous,utr-5,coding-synonymous	CDH13	NM_001220488.1,NM_001220489.1,NM_001220490.1,NM_001257.4	,,,	0,47,5893	CC,CT,TT		0.0,1.2696,0.3956	,,,	266/761,180/675,,219/714	83378487	47,11833	1851	4089	5940	SO:0001819	synonymous_variant	1012	exon7			CACTGATGTCAAT	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.657T>C	16.37:g.83378487T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	120	48	0.4	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	37	CCDS58486.1																																																																																			T|0.996;C|0.004	0.004	strong		0.438	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257	
ANKRD18A	253650	hgsc.bcm.edu	37	9	38595886	38595886	+	Missense_Mutation	SNP	T	T	C	rs2996347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:38595886T>C	ENST00000399703.5	-	9	1825	c.1451A>G	c.(1450-1452)aAt>aGt	p.N484S		NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	484			N -> S (in dbSNP:rs2996347).					p.N484S(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						TTTTAAGGTATTGAACTTCAC	0.413													.|||	1662	0.331869	0.4826	0.317	5008	,	,		20583	0.4603		0.2187	False		,,,				2504	0.1227				p.N484S		Atlas-SNP	.											ANKRD18A,NS,carcinoma,0,1	ANKRD18A	49	1	1	Substitution - Missense(1)	stomach(1)	c.A1451G						PASS	.	T	SER/ASN	628,756		136,356,200	95.0	67.0	75.0		1451	1.4	0.0	9	dbSNP_101	75	651,2529		66,519,1005	no	missense	ANKRD18A	NM_147195.2	46	202,875,1205	CC,CT,TT		20.4717,45.3757,28.0237	possibly-damaging	484/993	38595886	1279,3285	692	1590	2282	SO:0001583	missense	253650	exon9			AAGGTATTGAACT	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.1451A>G	9.37:g.38595886T>C	ENSP00000382610:p.Asn484Ser	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	187	89	0.475936	NM_147195	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	Missense_Mutation	SNP	ENST00000399703.5	37	CCDS55311.1	745	0.3411172161172161	249	0.5060975609756098	99	0.27348066298342544	224	0.3916083916083916	173	0.22823218997361477	T	5.964	0.361918	0.11296	0.453757	0.204717	ENSG00000180071	ENST00000399703	T	0.17370	2.28	1.35	1.35	0.21983	.	.	.	.	.	T	0.00012	0.0000	N	0.25286	0.73	0.29173	P	0.877008	B	0.12013	0.005	B	0.01281	0.0	T	0.44314	-0.9336	8	0.35671	T	0.21	.	6.8814	0.24174	0.0:0.0:0.0:1.0	rs2996347;rs7036857;rs59857660;rs2996347	484	Q8IVF6	AN18A_HUMAN	S	484	ENSP00000382610:N484S	ENSP00000382610:N484S	N	-	2	0	ANKRD18A	38585886	0.234000	0.23783	0.009000	0.14445	0.065000	0.16274	0.494000	0.22467	0.892000	0.36259	0.113000	0.15668	AAT	T|0.680;C|0.320	0.320	strong		0.413	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052506.3		
TFDP1	7027	hgsc.bcm.edu	37	13	114265331	114265331	+	Silent	SNP	C	C	T	rs4150731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114265331C>T	ENST00000375370.5	+	3	245	c.33C>T	c.(31-33)aaC>aaT	p.N11N	TFDP1_ENST00000538138.1_5'UTR|TFDP1_ENST00000465174.1_3'UTR|TFDP1_ENST00000544902.1_5'UTR	NM_007111.4	NP_009042.1	Q14186	TFDP1_HUMAN	transcription factor Dp-1	11					anoikis (GO:0043276)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|epidermis development (GO:0008544)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA biosynthetic process (GO:2000278)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)			TTGAAGCCAACGGAGAACTCA	0.453										TSP Lung(29;0.18)			C|||	121	0.0241613	0.0552	0.0014	5008	,	,		20846	0.0456		0.0	False		,,,				2504	0.001				p.N11N		Atlas-SNP	.											.	TFDP1	70	.	0			c.C33T						PASS	.	C		261,4145	148.0+/-182.4	6,249,1948	190.0	181.0	184.0		33	-1.2	1.0	13	dbSNP_110	184	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TFDP1	NM_007111.4		6,251,6246	TT,TC,CC		0.0233,5.9237,2.0221		11/411	114265331	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	7027	exon3			AGCCAACGGAGAA	BC011685	CCDS9538.1	13q34	2008-07-18			ENSG00000198176	ENSG00000198176			11749	protein-coding gene	gene with protein product		189902				8413592, 9027491	Standard	NM_007111		Approved	Dp-1, DRTF1, DP1	uc001vtw.3	Q14186	OTTHUMG00000017388	ENST00000375370.5:c.33C>T	13.37:g.114265331C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	189	94	0.497355	NM_007111	B4DLQ9|Q5JSB4|Q8IZL5	Silent	SNP	ENST00000375370.5	37	CCDS9538.1																																																																																			C|0.975;T|0.025	0.025	strong		0.453	TFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045918.3	NM_007111	
PSG3	5671	hgsc.bcm.edu	37	19	43243217	43243217	+	Missense_Mutation	SNP	A	A	G	rs34721205|rs12185496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43243217A>G	ENST00000327495.5	-	2	273	c.89T>C	c.(88-90)tTg>tCg	p.L30S	PSG3_ENST00000595140.1_Missense_Mutation_p.L30S|PSG3_ENST00000490592.1_5'UTR	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	30			L -> P (in dbSNP:rs12185496). {ECO:0000269|PubMed:2302228, ECO:0000269|PubMed:2341148, ECO:0000269|PubMed:2350345, ECO:0000269|PubMed:3265688}.|L -> S (in dbSNP:rs12185496).		defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				AGTGGTAGGCAAGTTCCAGAA	0.483													.|||	3288	0.65655	0.8903	0.6571	5008	,	,		17929	0.4772		0.5507	False		,,,				2504	0.6339				p.L30S		Atlas-SNP	.											PSG3,NS,carcinoma,-1,1	PSG3	82	1	0			c.T89C						PASS	.	G	SER/LEU	3437,967		1552,333,317	108.0	141.0	130.0		89	-1.2	0.0	19	dbSNP_120	130	3680,4920		1246,1188,1866	yes	missense	PSG3	NM_021016.3	145	2798,1521,2183	GG,GA,AA		42.7907,21.9573,45.2707	benign	30/429	43243217	7117,5887	2202	4300	6502	SO:0001583	missense	5671	exon2			GTAGGCAAGTTCC		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.89T>C	19.37:g.43243217A>G	ENSP00000332215:p.Leu30Ser	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	217	214	0.986175	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	37	CCDS12611.1	1098	0.5027472527472527	344	0.6991869918699187	199	0.5497237569060773	212	0.3706293706293706	343	0.4525065963060686	N	3.073	-0.190683	0.06299	0.780427	0.427907	ENSG00000221826	ENST00000327495	T	0.20332	2.08	1.39	-1.17	0.09648	.	.	.	.	.	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B	0.06786	0.001	B	0.13407	0.009	T	0.18085	-1.0348	8	0.36615	T	0.2	.	5.7905	0.18357	0.3984:0.0:0.6016:0.0	rs12185496;rs58971165	30	Q16557	PSG3_HUMAN	S	30	ENSP00000332215:L30S	ENSP00000332215:L30S	L	-	2	0	PSG3	47935057	0.000000	0.05858	0.009000	0.14445	0.008000	0.06430	-2.830000	0.00744	-0.710000	0.05001	-2.222000	0.00295	TTG	.	.	alt		0.483	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016	
VASN	114990	hgsc.bcm.edu	37	16	4431880	4431880	+	Silent	SNP	C	C	T	rs13333950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4431880C>T	ENST00000304735.3	+	2	1157	c.1002C>T	c.(1000-1002)aaC>aaT	p.N334N	CORO7_ENST00000574025.1_Intron|CORO7_ENST00000537233.2_Intron|CORO7_ENST00000251166.4_Intron|CORO7_ENST00000539968.1_Intron|CORO7_ENST00000423908.2_Intron|CORO7-PAM16_ENST00000572467.1_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	334	LRRCT.				cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						CGCCCAAGAACGCTGGCCGGC	0.692													C|||	177	0.0353435	0.1309	0.0058	5008	,	,		14062	0.0		0.0	False		,,,				2504	0.0				p.N334N		Atlas-SNP	.											.	VASN	21	.	0			c.C1002T						PASS	.	C	,,,,	532,3842		38,456,1693	19.0	22.0	21.0		,,,,1002	-11.3	0.1	16	dbSNP_121	21	1,8583		0,1,4291	no	intron,intron,intron,intron,coding-synonymous	CORO7,VASN,CORO7-PAM16	NM_001201472.1,NM_001201473.1,NM_001201479.1,NM_024535.4,NM_138440.2	,,,,	38,457,5984	TT,TC,CC		0.0116,12.1628,4.1133	,,,,	,,,,334/674	4431880	533,12425	2187	4292	6479	SO:0001819	synonymous_variant	114990	exon2			CAAGAACGCTGGC	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"""slit-like 2 (Drosophila)"""	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.1002C>T	16.37:g.4431880C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Silent	SNP	ENST00000304735.3	37	CCDS10514.1																																																																																			C|0.962;T|0.038	0.038	strong		0.692	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440	
MEGF6	1953	hgsc.bcm.edu	37	1	3421897	3421897	+	Missense_Mutation	SNP	A	A	G	rs2821008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3421897A>G	ENST00000356575.4	-	17	2289	c.2063T>C	c.(2062-2064)cTg>cCg	p.L688P	MEGF6_ENST00000294599.4_Missense_Mutation_p.L583P	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	688			L -> P (in dbSNP:rs2821008).			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)		AAAGTAGCCCAGCTCACACTC	0.697													G|||	1298	0.259185	0.4251	0.2277	5008	,	,		14841	0.2331		0.1799	False		,,,				2504	0.1656				p.L688P	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.T2063C						PASS	.	G	PRO/LEU	1392,2658		266,860,899	14.0	19.0	17.0		2063	2.5	0.0	1	dbSNP_100	17	1381,6983		125,1131,2926	yes	missense	MEGF6	NM_001409.3	98	391,1991,3825	GG,GA,AA		16.5112,34.3704,22.3377	benign	688/1542	3421897	2773,9641	2025	4182	6207	SO:0001583	missense	1953	exon17			TAGCCCAGCTCAC	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.2063T>C	1.37:g.3421897A>G	ENSP00000348982:p.Leu688Pro	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	502	0.22985347985347984	177	0.3597560975609756	83	0.2292817679558011	113	0.19755244755244755	129	0.17018469656992086	G	0.004	-2.349863	0.00219	0.343704	0.165112	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.13657	2.57;2.57	4.43	2.53	0.30540	EGF-like, laminin (1);	0.623994	0.15945	N	0.237012	T	0.00012	0.0000	N	0.00358	-1.6	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45264	-0.9273	9	0.25106	T	0.35	-1.8612	8.0441	0.30538	0.3309:0.0:0.6691:0.0	rs2821008;rs2821008	688;583	O75095;O75095-2	MEGF6_HUMAN;.	P	583;688	ENSP00000294599:L583P;ENSP00000348982:L688P	ENSP00000294599:L583P	L	-	2	0	MEGF6	3411757	0.003000	0.15002	0.027000	0.17364	0.337000	0.28794	1.318000	0.33643	0.094000	0.17404	-0.355000	0.07637	CTG	A|0.775;G|0.225	0.225	strong		0.697	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
GPR179	440435	hgsc.bcm.edu	37	17	36486004	36486004	+	Missense_Mutation	SNP	T	T	C	rs55727040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36486004T>C	ENST00000342292.4	-	11	3468	c.3448A>G	c.(3448-3450)Aag>Gag	p.K1150E	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1150			K -> E (in dbSNP:rs55727040).		visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				AGGGACTCCTTGTCATCGGAG	0.622													C|||	805	0.160743	0.4887	0.0994	5008	,	,		18575	0.0		0.0746	False		,,,				2504	0.0153				p.K1150E		Atlas-SNP	.											.	GPR179	170	.	0			c.A3448G						PASS	.	C	GLU/LYS	1575,2633		286,1003,815	147.0	149.0	148.0		3448	5.1	0.8	17	dbSNP_129	148	437,8025		10,417,3804	yes	missense	GPR179	NM_001004334.2	56	296,1420,4619	CC,CT,TT		5.1643,37.4287,15.88	benign	1150/2368	36486004	2012,10658	2104	4231	6335	SO:0001583	missense	440435	exon11			ACTCCTTGTCATC		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.3448A>G	17.37:g.36486004T>C	ENSP00000345060:p.Lys1150Glu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	288	0.13186813186813187	206	0.4186991869918699	38	0.10497237569060773	0	0.0	44	0.05804749340369393	C	0.135	-1.109424	0.01813	0.374287	0.051643	ENSG00000188888	ENST00000342292	T	0.37058	1.22	5.09	5.09	0.68999	.	0.000000	0.51477	N	0.000097	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39583	-0.9607	9	0.02654	T	1	-12.5624	11.095	0.48139	0.0:0.9133:0.0:0.0867	rs55727040	1150	Q6PRD1	GP179_HUMAN	E	1150	ENSP00000345060:K1150E	ENSP00000345060:K1150E	K	-	1	0	GPR179	33739530	0.000000	0.05858	0.837000	0.33122	0.087000	0.18053	0.195000	0.17155	1.380000	0.46344	-0.355000	0.07637	AAG	T|0.897;C|0.103	0.103	strong		0.622	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
MKI67	4288	hgsc.bcm.edu	37	10	129906364	129906364	+	Missense_Mutation	SNP	G	G	A	rs4750685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129906364G>A	ENST00000368654.3	-	13	4115	c.3740C>T	c.(3739-3741)aCt>aTt	p.T1247I	MKI67_ENST00000368653.3_Missense_Mutation_p.T887I	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1247	16 X 122 AA approximate repeats.		T -> I (in dbSNP:rs4750685).		cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.T1247I(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGGTATTTTAGTGGTTTTACC	0.512													G|||	515	0.102835	0.0666	0.1556	5008	,	,		18082	0.1359		0.0785	False		,,,				2504	0.1053				p.T1247I		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - Missense(1)	stomach(1)	c.C3740T						scavenged	.	G	ILE/THR,ILE/THR	295,4111	161.4+/-193.6	11,273,1919	105.0	108.0	107.0		2660,3740	1.0	0.0	10	dbSNP_111	107	771,7829	183.5+/-231.7	39,693,3568	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	89,89	50,966,5487	AA,AG,GG		8.9651,6.6954,8.1962	possibly-damaging,possibly-damaging	887/2897,1247/3257	129906364	1066,11940	2203	4300	6503	SO:0001583	missense	4288	exon13			ATTTTAGTGGTTT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.3740C>T	10.37:g.129906364G>A	ENSP00000357643:p.Thr1247Ile	Somatic	289	2	0.00692042		WXS	Illumina HiSeq	Phase_I	272	121	0.444853	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	209	0.09569597069597069	33	0.06707317073170732	39	0.10773480662983426	79	0.1381118881118881	58	0.07651715039577836	G	12.96	2.093039	0.36952	0.066954	0.089651	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.03242	4.0;4.0	3.0	1.05	0.20165	.	0.914623	0.08986	N	0.865071	T	0.00073	0.0002	M	0.65975	2.015	0.80722	P	0.0	P;D;D	0.89917	0.936;1.0;0.997	P;D;D	0.79108	0.559;0.992;0.939	T	0.31280	-0.9949	9	0.32370	T	0.25	.	4.5988	0.12343	0.4006:0.0:0.5994:0.0	rs4750685;rs52820823;rs57830646;rs4750685	1246;887;1247	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	I	1247;887;1246	ENSP00000357643:T1247I;ENSP00000357642:T887I	ENSP00000357642:T887I	T	-	2	0	MKI67	129796354	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	0.535000	0.23114	0.583000	0.29574	0.456000	0.33151	ACT	G|0.915;A|0.085	0.085	strong		0.512	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
UQCRH	7388	hgsc.bcm.edu	37	1	46775856	46775856	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46775856C>A	ENST00000311672.5	+	3	247	c.111C>A	c.(109-111)tgC>tgA	p.C37*		NM_001089591.1|NM_006004.2	NP_001083060.1|NP_005995.2	P07919	QCR6_HUMAN	ubiquinol-cytochrome c reductase hinge protein	37					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|protein heterooligomerization (GO:0051291)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	4	Acute lymphoblastic leukemia(166;0.155)					GAGAGCAATGCGAGCAGTTGG	0.468																																					p.C37X		Atlas-SNP	.											.	UQCRH	4	.	0			c.C111A						PASS	.						84.0	85.0	85.0					1																	46775856		2203	4300	6503	SO:0001587	stop_gained	7388	exon3			GCAATGCGAGCAG	BC001934	CCDS30704.1	1p34.1	2011-07-04			ENSG00000173660	ENSG00000173660	1.10.2.2	"""Mitochondrial respiratory chain complex / Complex III"""	12590	protein-coding gene	gene with protein product	"""ubiquinol-cytochrome c reductase, complex III subunit VIII"""	613844				2826252	Standard	XM_005271167		Approved	QCR6, UQCR8	uc001cpp.3	P07919	OTTHUMG00000007813	ENST00000311672.5:c.111C>A	1.37:g.46775856C>A	ENSP00000309565:p.Cys37*	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	193	100	0.518135	NM_006004	B2R4V9|D3DQ18|Q5TDF6|Q6LDB8|Q9BQ91	Nonsense_Mutation	SNP	ENST00000311672.5	37	CCDS30704.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.424984	0.83667	.	.	ENSG00000173660	ENST00000311672	.	.	.	5.23	0.0755	0.14399	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1407	9.4087	0.38477	0.0:0.3877:0.0:0.6123	.	.	.	.	X	37	.	ENSP00000309565:C37X	C	+	3	2	UQCRH	46548443	0.816000	0.29132	0.998000	0.56505	0.997000	0.91878	-0.075000	0.11431	0.135000	0.18707	0.655000	0.94253	TGC	.	.	none		0.468	UQCRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021451.1	NM_006004	
PON1	5444	hgsc.bcm.edu	37	7	94937446	94937446	+	Missense_Mutation	SNP	T	T	C	rs662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:94937446T>C	ENST00000222381.3	-	6	806	c.575A>G	c.(574-576)cAa>cGa	p.Q192R	PON1_ENST00000542556.1_Missense_Mutation_p.Q192R	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	192			Q -> R (polymorphism important for activity; dbSNP:rs662). {ECO:0000269|PubMed:1657140, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:7916578, ECO:0000269|PubMed:8098250, ECO:0000269|PubMed:8393742, ECO:0000269|PubMed:8393745, ECO:0000269|Ref.8}.		aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)	p.Q192R(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	CTCCCAGGATTGTAAGTAGGG	0.398													C|||	2719	0.542931	0.7526	0.4986	5008	,	,		16184	0.6657		0.2903	False		,,,				2504	0.4243				p.Q192R	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											PON1,NS,carcinoma,0,1	PON1	55	1	1	Substitution - Missense(1)	stomach(1)	c.A575G	GRCh37	CM930596	PON1	M	rs662	PASS	.	C	ARG/GLN	2910,1496	475.5+/-357.3	958,994,251	130.0	108.0	116.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	575	-1.0	0.0	7	dbSNP_36	116	2451,6149	698.1+/-405.0	360,1731,2209	yes	missense	PON1	NM_000446.5	43	1318,2725,2460	CC,CT,TT		28.5,33.9537,41.2194	benign	192/356	94937446	5361,7645	2203	4300	6503	SO:0001583	missense	5444	exon6			CAGGATTGTAAGT	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.575A>G	7.37:g.94937446T>C	ENSP00000222381:p.Gln192Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	1127	0.5160256410256411	368	0.7479674796747967	172	0.47513812154696133	367	0.6416083916083916	220	0.29023746701846964	C	0.090	-1.168995	0.01660	0.660463	0.285	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.45276	0.9;0.9	5.04	-1.02	0.10135	Six-bladed beta-propeller, TolB-like (1);	0.663414	0.14660	N	0.306026	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	0.33189	-0.9878	9	0.09084	T	0.74	-0.0356	8.8215	0.35030	0.1205:0.2374:0.0:0.6421	rs662;rs11567868;rs13306697;rs17773773;rs60480675;rs662	192;192	F5H4W9;P27169	.;PON1_HUMAN	R	192	ENSP00000222381:Q192R;ENSP00000444854:Q192R	ENSP00000222381:Q192R	Q	-	2	0	PON1	94775382	0.000000	0.05858	0.001000	0.08648	0.185000	0.23345	-1.304000	0.02741	-0.587000	0.05890	-0.215000	0.12644	CAA	T|0.544;C|0.456	0.456	strong		0.398	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
C6orf223	221416	hgsc.bcm.edu	37	6	43970602	43970602	+	Silent	SNP	G	G	C	rs117880737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43970602G>C	ENST00000336600.5	+	4	488	c.468G>C	c.(466-468)ccG>ccC	p.P156P	C6orf223_ENST00000448947.2_3'UTR|RP5-1120P11.1_ENST00000422059.1_RNA|C6orf223_ENST00000439969.2_3'UTR|RP5-1120P11.1_ENST00000607590.1_RNA|C6orf223_ENST00000442114.2_Silent_p.P136P	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	156										central_nervous_system(1)|lung(2)|pancreas(1)|prostate(1)|urinary_tract(1)	6	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)			CGAGGAGCCCGGGACAGGTGA	0.791													G|||	208	0.0415335	0.053	0.0303	5008	,	,		8130	0.0466		0.0427	False		,,,				2504	0.0276				p.P156P		Atlas-SNP	.											.	C6orf223	14	.	0			c.G468C						PASS	.	G	,	100,3698		0,100,1799	4.0	5.0	5.0		,468	-7.6	0.0	6	dbSNP_132	5	119,7499		2,115,3692	no	utr-3,coding-synonymous	C6orf223	NM_001171992.1,NM_153246.4	,	2,215,5491	CC,CG,GG		1.5621,2.633,1.9184	,	,156/243	43970602	219,11197	1899	3809	5708	SO:0001819	synonymous_variant	221416	exon4			GAGCCCGGGACAG	BC032706	CCDS34459.1, CCDS55016.1	6p21.1	2012-09-05			ENSG00000181577	ENSG00000181577			28692	protein-coding gene	gene with protein product						12477932	Standard	NM_153246		Approved	MGC45491	uc003own.3	Q8N319	OTTHUMG00000014753	ENST00000336600.5:c.468G>C	6.37:g.43970602G>C		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_153246	E9PB59|Q8N575	Silent	SNP	ENST00000336600.5	37	CCDS34459.1																																																																																			G|0.957;C|0.043	0.043	strong		0.791	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246	
MUC2	4583	hgsc.bcm.edu	37	11	1092890	1092890	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1092890C>T	ENST00000441003.2	+	30	4736	c.4709C>T	c.(4708-4710)aCc>aTc	p.T1570I	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1571I|MUC2_ENST00000333592.6_5'Flank	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	159	2	0.0125786		WXS	Illumina HiSeq	Phase_I	163	8	0.0490798	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	
SSPO	23145	hgsc.bcm.edu	37	7	149509419	149509419	+	RNA	SNP	C	C	T	rs740109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149509419C>T	ENST00000378016.2	+	0	9817							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)			GGGAGGCCTGCGGAGCCGGAC	0.726													C|||	1248	0.249201	0.41	0.1628	5008	,	,		13006	0.255		0.1511	False		,,,				2504	0.1881				p.R3273W		Atlas-SNP	.											.	.	.	.	0			c.C9817T						PASS	.	C		1050,2336		171,708,814	6.0	7.0	7.0		9827	1.5	0.9	7	dbSNP_96	7	1112,6548		106,900,2824	no	coding-notMod3	SSPO	NM_198455.2		277,1608,3638	TT,TC,CC		14.517,31.01,19.5727			149509419	2162,8884	1693	3830	5523			23145	exon69			GGCCTGCGGAGCC	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.149509419C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	25	10	0.4	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.776;T|0.224	0.224	strong		0.726	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808292	18808292	+	Missense_Mutation	SNP	C	C	A	rs372156529|rs2992753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:18808292C>A	ENST00000400664.1	+	1	869	c.817C>A	c.(817-819)Cat>Aat	p.H273N		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	273			H -> N (in dbSNP:rs2992753). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AATGGAGGAGCATTTCATACA	0.592													A|||	3370	0.672923	0.6604	0.7277	5008	,	,		19405	0.8958		0.6113	False		,,,				2504	0.4847				p.H273N		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C817A						PASS	.	A	ASN/HIS	2930,1476	471.8+/-356.2	967,996,240	79.0	82.0	81.0		817	4.9	0.6	1	dbSNP_101	81	5407,3193	479.0+/-370.0	1697,2013,590	yes	missense	KLHDC7A	NM_152375.2	68	2664,3009,830	AA,AC,CC		37.1279,33.4998,35.8988	benign	273/778	18808292	8337,4669	2203	4300	6503	SO:0001583	missense	127707	exon1			GAGGAGCATTTCA	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.817C>A	1.37:g.18808292C>A	ENSP00000383505:p.His273Asn	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	1574	0.7206959706959707	330	0.6707317073170732	254	0.7016574585635359	523	0.9143356643356644	467	0.6160949868073878	A	0.017	-1.498345	0.01001	0.665002	0.628721	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.68181	-0.31	4.92	4.92	0.64577	.	0.547006	0.17223	N	0.182256	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	0.41893	-0.9483	9	0.02654	T	1	.	10.5437	0.45047	0.6915:0.3085:0.0:0.0	rs2992753;rs58143972;rs2992753	273	Q5VTJ3	KLD7A_HUMAN	N	273;210	ENSP00000383505:H273N	ENSP00000383505:H273N	H	+	1	0	KLHDC7A	18680879	0.998000	0.40836	0.650000	0.29550	0.277000	0.26821	2.560000	0.45896	0.717000	0.32145	-0.824000	0.03097	CAT	C|0.325;A|0.675	0.675	strong		0.592	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
HMOX1	3162	hgsc.bcm.edu	37	22	35777185	35777185	+	Missense_Mutation	SNP	G	G	C	rs2071747	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:35777185G>C	ENST00000216117.8	+	1	358	c.19G>C	c.(19-21)Gac>Cac	p.D7H		NM_002133.2	NP_002124.1	P09601	HMOX1_HUMAN	heme oxygenase (decycling) 1	7			D -> H (in dbSNP:rs2071747). {ECO:0000269|Ref.3}.		angiogenesis (GO:0001525)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to cadmium ion (GO:0071276)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient (GO:0031670)|endothelial cell proliferation (GO:0001935)|erythrocyte homeostasis (GO:0034101)|excretion (GO:0007588)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|iron ion homeostasis (GO:0055072)|low-density lipoprotein particle clearance (GO:0034383)|negative regulation of DNA binding (GO:0043392)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smooth muscle cell proliferation (GO:0048662)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|protein homooligomerization (GO:0051260)|regulation of angiogenesis (GO:0045765)|regulation of blood pressure (GO:0008217)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to estrogen (GO:0043627)|response to hydrogen peroxide (GO:0042542)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|smooth muscle hyperplasia (GO:0014806)|transmembrane transport (GO:0055085)|wound healing involved in inflammatory response (GO:0002246)	caveola (GO:0005901)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)|phospholipase D activity (GO:0004630)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16					Vitamin E(DB00163)	TCCGCAACCCGACAGGCAAGC	0.721													G|||	182	0.0363419	0.0287	0.0216	5008	,	,		11362	0.0536		0.0586	False		,,,				2504	0.0164				p.D7H		Atlas-SNP	.											.	HMOX1	32	.	0			c.G19C						PASS	.	G	HIS/ASP	60,3634		1,58,1788	4.0	5.0	5.0		19	2.4	1.0	22	dbSNP_96	5	276,7250		2,272,3489	no	missense	HMOX1	NM_002133.2	81	3,330,5277	CC,CG,GG		3.6673,1.6243,2.9947	benign	7/289	35777185	336,10884	1847	3763	5610	SO:0001583	missense	3162	exon1			CAACCCGACAGGC		CCDS13914.1	22q12	2003-10-13			ENSG00000100292	ENSG00000100292	1.14.99.3		5013	protein-coding gene	gene with protein product		141250				10591208	Standard	NM_002133		Approved	bK286B10, HO-1	uc003ant.2	P09601	OTTHUMG00000150960	ENST00000216117.8:c.19G>C	22.37:g.35777185G>C	ENSP00000216117:p.Asp7His	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	19	8	0.421053	NM_002133		Missense_Mutation	SNP	ENST00000216117.8	37	CCDS13914.1	110	0.05036630036630037	22	0.044715447154471545	8	0.022099447513812154	36	0.06293706293706294	44	0.05804749340369393	G	10.07	1.249851	0.22880	0.016243	0.036673	ENSG00000100292	ENST00000412893;ENST00000216117	T;T	0.18502	2.21;2.26	3.44	2.43	0.29744	Haem oxygenase-like, multi-helical (1);	1.539270	0.03633	N	0.238258	T	0.01029	0.0034	N	0.08118	0	0.29095	N	0.88183	B	0.06786	0.001	B	0.04013	0.001	T	0.18366	-1.0339	10	0.62326	D	0.03	-14.9887	6.7633	0.23552	0.1276:0.0:0.8724:0.0	rs2071747;rs11555831;rs17879005;rs2071747	7	P09601	HMOX1_HUMAN	H	7	ENSP00000413316:D7H;ENSP00000216117:D7H	ENSP00000216117:D7H	D	+	1	0	HMOX1	34107185	0.604000	0.26932	0.996000	0.52242	0.335000	0.28730	0.359000	0.20233	1.033000	0.39918	0.650000	0.86243	GAC	G|0.952;C|0.048	0.048	strong		0.721	HMOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320657.1		
KIF13A	63971	hgsc.bcm.edu	37	6	17764731	17764731	+	Silent	SNP	G	G	C	rs6459569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:17764731G>C	ENST00000259711.6	-	39	5133	c.5028C>G	c.(5026-5028)gcC>gcG	p.A1676A	KIF13A_ENST00000378814.5_Silent_p.A1628A|KIF13A_ENST00000378816.5_Silent_p.A1641A|KIF13A_ENST00000378826.2_Silent_p.A1641A|KIF13A_ENST00000378843.2_Silent_p.A1628A	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1676					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)			GGCTCCCTTTGGCTAAGGCAC	0.468													G|||	830	0.165735	0.3979	0.098	5008	,	,		19998	0.0635		0.0696	False		,,,				2504	0.1043				p.A1676A		Atlas-SNP	.											.	KIF13A	276	.	0			c.C5028G						PASS	.	G	,,,	1359,2639		247,865,887	108.0	105.0	106.0		4923,4884,4884,5028	4.6	1.0	6	dbSNP_116	106	695,7643		31,633,3505	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	278,1498,4392	CC,CG,GG		8.3353,33.992,16.6505	,,,	1641/1771,1628/1758,1628/1750,1676/1806	17764731	2054,10282	1999	4169	6168	SO:0001819	synonymous_variant	63971	exon39			CCCTTTGGCTAAG	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.5028C>G	6.37:g.17764731G>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			G|0.857;C|0.143	0.143	strong		0.468	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
ARL5C	390790	hgsc.bcm.edu	37	17	37319103	37319103	+	Missense_Mutation	SNP	T	T	C	rs657723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37319103T>C	ENST00000269586.7	-	3	115	c.116A>G	c.(115-117)aAt>aGt	p.N39S	ARL5C_ENST00000583123.1_5'Flank|ARL5C_ENST00000444555.1_Missense_Mutation_p.N39S	NM_001143968.1	NP_001137440.1	A6NH57	ARL5C_HUMAN	ADP-ribosylation factor-like 5C	39					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)										GACCACCTCATTGGTCAAGCT	0.542													T|||	1668	0.333067	0.6657	0.219	5008	,	,		18627	0.256		0.2386	False		,,,				2504	0.1411				p.N39S		Atlas-SNP	.											.	ARL5C	3	.	0			c.A116G						PASS	.	T	SER/ASN	842,542		257,328,107	63.0	50.0	54.0		116	3.2	0.2	17	dbSNP_83	54	622,2560		55,512,1024	yes	missense	ARL5C	NM_001143968.1	46	312,840,1131	CC,CT,TT		19.5475,39.1618,32.0631	benign	39/180	37319103	1464,3102	692	1591	2283	SO:0001583	missense	390790	exon3			ACCTCATTGGTCA		CCDS45664.1	17q12	2014-05-09	2005-11-08	2005-11-08	ENSG00000141748	ENSG00000141748		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	31111	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 12"""	ARL12			Standard	NM_001143968		Approved		uc010wea.2	A6NH57		ENST00000269586.7:c.116A>G	17.37:g.37319103T>C	ENSP00000269586:p.Asn39Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_001143968		Missense_Mutation	SNP	ENST00000269586.7	37	CCDS45664.1	731	0.3347069597069597	330	0.6707317073170732	87	0.24033149171270718	137	0.2395104895104895	177	0.23350923482849603	T	8.077	0.771602	0.16051	0.608382	0.195475	ENSG00000141748	ENST00000444555;ENST00000269586	T;T	0.63417	-0.04;-0.04	4.28	3.2	0.36748	Small GTP-binding protein domain (1);	0.179653	0.46442	D	0.000285	T	0.00012	0.0000	L	0.49640	1.575	0.28672	P	0.9055534	B	0.12630	0.006	B	0.13407	0.009	T	0.40213	-0.9575	9	0.87932	D	0	-3.7022	8.0005	0.30293	0.0:0.0985:0.0:0.9015	rs657723;rs801251;rs52813513;rs61534829;rs657723	39	A6NH57	ARL5C_HUMAN	S	39	ENSP00000387615:N39S;ENSP00000269586:N39S	ENSP00000269586:N39S	N	-	2	0	ARL5C	34572629	1.000000	0.71417	0.204000	0.23530	0.001000	0.01503	5.360000	0.66086	0.800000	0.34041	-0.250000	0.11733	AAT	T|0.644;C|0.356	0.356	strong		0.542	ARL5C-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444566.1	NM_001143968	
GGTLC1	92086	hgsc.bcm.edu	37	20	23966316	23966316	+	Silent	SNP	T	T	C	rs111546926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23966316T>C	ENST00000335694.4	-	5	723	c.519A>G	c.(517-519)agA>agG	p.R173R	GGTLC1_ENST00000278765.4_Silent_p.R173R|GGTLC1_ENST00000286890.4_Silent_p.R173R	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	173					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						GGTCAATGTTTCTCTCCACTG	0.597													.|||	337	0.0672923	0.2239	0.0274	5008	,	,		16839	0.002		0.0089	False		,,,				2504	0.0112				p.R173R		Atlas-SNP	.											.	GGTLC1	37	.	0			c.A519G						PASS	.	T	,	856,3550	316.3+/-294.6	75,706,1422	52.0	54.0	53.0		519,519	0.8	0.4	20	dbSNP_132	53	103,8489	51.9+/-112.3	1,101,4194	no	coding-synonymous,coding-synonymous	GGTLC1	NM_178311.2,NM_178312.2	,	76,807,5616	CC,CT,TT		1.1988,19.4281,7.3781	,	173/226,173/226	23966316	959,12039	2203	4296	6499	SO:0001819	synonymous_variant	92086	exon5			AATGTTTCTCTCC	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"""Gamma-glutamyltransferases"""	16437	protein-coding gene	gene with protein product		612338	"""gamma-glutamyltransferase-like activity 4"", ""gamma-glutamyltransferase-like activity 3"""	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.519A>G	20.37:g.23966316T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_178311	D3DW43|Q08246	Silent	SNP	ENST00000335694.4	37	CCDS13163.1																																																																																			T|0.937;C|0.063	0.063	strong		0.597	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2	
GIMAP8	155038	hgsc.bcm.edu	37	7	150164189	150164189	+	Silent	SNP	C	C	A	rs143212982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150164189C>A	ENST00000307271.3	+	2	977	c.403C>A	c.(403-405)Cgg>Agg	p.R135R		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	135	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)		TGTCTTCACTCGGAAGGATGA	0.463																																					p.R135R		Atlas-SNP	.											GIMAP8,NS,carcinoma,-1,1	GIMAP8	136	1	0			c.C403A						PASS	.	C		37,4369	41.6+/-74.8	0,37,2166	79.0	75.0	76.0		403	-4.4	0.0	7	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	GIMAP8	NM_175571.2		0,38,6465	AA,AC,CC		0.0116,0.8398,0.2922		135/666	150164189	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	155038	exon2			TTCACTCGGAAGG	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.403C>A	7.37:g.150164189C>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	201	104	0.517413	NM_175571		Silent	SNP	ENST00000307271.3	37	CCDS34777.1																																																																																			A|0.002;C|0.998;G|0.001	0.002	strong		0.463	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
BACE1	23621	hgsc.bcm.edu	37	11	117163824	117163824	+	Silent	SNP	C	C	G	rs638405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117163824C>G	ENST00000313005.6	-	5	1246	c.786G>C	c.(784-786)gtG>gtC	p.V262V	BACE1_ENST00000528053.1_Silent_p.V262V|BACE1_ENST00000510630.1_Silent_p.V137V|BACE1_ENST00000428381.2_Silent_p.V193V|BACE1_ENST00000445823.2_Silent_p.V218V|BACE1_ENST00000513780.1_Silent_p.V237V|BACE1_ENST00000514464.1_5'Flank|BACE1_ENST00000392937.6_Silent_p.V162V	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	262					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		GCACAATGATCACCTCATAAT	0.507													C|||	2772	0.553514	0.5363	0.549	5008	,	,		17135	0.6498		0.4076	False		,,,				2504	0.6309				p.V262V		Atlas-SNP	.											.	BACE1	33	.	0			c.G786C						PASS	.	C	,,,,,	2289,2113	601.2+/-389.7	589,1111,501	250.0	238.0	242.0		486,411,786,654,711,579	0.6	1.0	11	dbSNP_83	242	3400,5192	502.6+/-375.7	683,2034,1579	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BACE1	NM_001207048.1,NM_001207049.1,NM_012104.4,NM_138971.3,NM_138972.3,NM_138973.3	,,,,,	1272,3145,2080	GG,GC,CC		39.5717,48.0009,43.7817	,,,,,	162/402,137/377,262/502,218/458,237/477,193/433	117163824	5689,7305	2201	4296	6497	SO:0001819	synonymous_variant	23621	exon5			AATGATCACCTCA	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"""beta-site APP-cleaving enzyme"""	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.786G>C	11.37:g.117163824C>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	114	66	0.578947	NM_012104	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Silent	SNP	ENST00000313005.6	37	CCDS8383.1	1119	0.5123626373626373	278	0.5650406504065041	190	0.5248618784530387	354	0.6188811188811189	297	0.391820580474934	C	10.34	1.322171	0.23994	0.519991	0.395717	ENSG00000186318	ENST00000530844;ENST00000504995	.	.	.	6.07	0.58	0.17402	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40553	-0.9557	3	.	.	.	.	1.3856	0.02240	0.1254:0.3307:0.2724:0.2714	rs638405;rs60889749;rs638405	.	.	.	H	132;192	.	.	D	-	1	0	BACE1	116669034	0.957000	0.32711	1.000000	0.80357	0.977000	0.68977	0.011000	0.13264	0.414000	0.25790	-0.768000	0.03414	GAT	C|0.533;G|0.467	0.467	strong		0.507	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1		
TRPV2	51393	hgsc.bcm.edu	37	17	16336992	16336992	+	Silent	SNP	C	C	G	rs14039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16336992C>G	ENST00000338560.7	+	13	2493	c.2094C>G	c.(2092-2094)ccC>ccG	p.P698P	TRPV2_ENST00000577397.1_Silent_p.P268P	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	698					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.P698P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		ATGGCAGCCCCGATGAGCGCT	0.627													C|||	1443	0.288139	0.3124	0.3401	5008	,	,		20447	0.2232		0.3579	False		,,,				2504	0.2137				p.P698P		Atlas-SNP	.											TRPV2,NS,carcinoma,0,1	TRPV2	74	1	1	Substitution - coding silent(1)	stomach(1)	c.C2094G						PASS	.	C		1464,2942	469.4+/-355.4	260,944,999	111.0	97.0	102.0		2094	-5.2	0.1	17	dbSNP_52	102	3244,5356	485.9+/-371.7	609,2026,1665	no	coding-synonymous	TRPV2	NM_016113.4		869,2970,2664	GG,GC,CC		37.7209,33.2274,36.1987		698/765	16336992	4708,8298	2203	4300	6503	SO:0001819	synonymous_variant	51393	exon13			CAGCCCCGATGAG	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.2094C>G	17.37:g.16336992C>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_016113	A6NML2|A8K0Z0|Q9Y670	Silent	SNP	ENST00000338560.7	37	CCDS32576.1																																																																																			T|0.000;G|0.355;C|0.645	0.355	strong		0.627	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
PCNT	5116	hgsc.bcm.edu	37	21	47766113	47766113	+	Missense_Mutation	SNP	T	T	G	rs34500739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47766113T>G	ENST00000359568.5	+	4	818	c.711T>G	c.(709-711)caT>caG	p.H237Q	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	237	Glu-rich.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CTGGCCTGCATCAGAGTCAGG	0.602													G|||	128	0.0255591	0.028	0.0303	5008	,	,		16755	0.001		0.0646	False		,,,				2504	0.0041				p.H237Q		Atlas-SNP	.											.	PCNT	283	.	0			c.T711G						PASS	.	G	GLN/HIS	192,4214	807.9+/-415.9	5,182,2016	83.0	74.0	77.0		711	3.3	1.0	21	dbSNP_126	77	528,8072	795.4+/-407.5	11,506,3783	yes	missense	PCNT	NM_006031.5	24	16,688,5799	GG,GT,TT		6.1395,4.3577,5.5359	benign	237/3337	47766113	720,12286	2203	4300	6503	SO:0001583	missense	5116	exon4			CCTGCATCAGAGT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.711T>G	21.37:g.47766113T>G	ENSP00000352572:p.His237Gln	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	129	71	0.550388	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	92	0.04212454212454213	21	0.042682926829268296	16	0.04419889502762431	1	0.0017482517482517483	54	0.0712401055408971	G	2.436	-0.329782	0.05314	0.043577	0.061395	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01279	5.06	3.27	3.27	0.37495	.	.	.	.	.	T	0.00073	0.0002	N	0.00926	-1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45145	-0.9281	9	0.09084	T	0.74	.	8.0049	0.30319	0.0:0.0:0.7564:0.2436	rs34500739	119;237	O95613-2;O95613	.;PCNT_HUMAN	Q	237;224	ENSP00000352572:H237Q	ENSP00000338675:H224Q	H	+	3	2	PCNT	46590541	0.057000	0.20700	0.965000	0.40720	0.171000	0.22731	0.660000	0.25009	0.988000	0.38734	-0.648000	0.03929	CAT	T|0.949;G|0.051	0.051	strong		0.602	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
GCN1L1	10985	hgsc.bcm.edu	37	12	120589064	120589064	+	Silent	SNP	G	G	C	rs2286045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:120589064G>C	ENST00000300648.6	-	34	4206	c.4194C>G	c.(4192-4194)gcC>gcG	p.A1398A		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1398					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)					CCAGGCCATAGGCGGCCCCTT	0.587													C|||	1915	0.382388	0.6573	0.17	5008	,	,		17533	0.5427		0.1561	False		,,,				2504	0.229				p.A1398A		Atlas-SNP	.											GCN1L1,colon,carcinoma,0,1	GCN1L1	207	1	0			c.C4194G						PASS	.	C		2419,1901		682,1055,423	48.0	54.0	52.0		4194	-10.6	0.0	12	dbSNP_100	52	1304,7214		126,1052,3081	no	coding-synonymous	GCN1L1	NM_006836.1		808,2107,3504	CC,CG,GG		15.3088,44.0046,28.9998		1398/2672	120589064	3723,9115	2160	4259	6419	SO:0001819	synonymous_variant	10985	exon34			GCCATAGGCGGCC	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.4194C>G	12.37:g.120589064G>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	109	54	0.495413	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																			G|0.685;C|0.315	0.315	strong		0.587	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
LRP2	4036	hgsc.bcm.edu	37	2	170070348	170070348	+	Silent	SNP	T	T	C	rs11886219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170070348T>C	ENST00000263816.3	-	36	6144	c.5859A>G	c.(5857-5859)cgA>cgG	p.R1953R		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1953					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)"""	CCAGGATCATTCGATCTGTTC	0.368													T|||	806	0.160942	0.4947	0.0965	5008	,	,		19502	0.0		0.0527	False		,,,				2504	0.0327				p.R1953R		Atlas-SNP	.											.	LRP2	751	.	0			c.A5859G						PASS	.	T		1814,2592	527.0+/-372.0	381,1052,770	76.0	74.0	75.0		5859	-2.4	1.0	2	dbSNP_120	75	485,8115	138.4+/-195.2	21,443,3836	no	coding-synonymous	LRP2	NM_004525.2		402,1495,4606	CC,CT,TT		5.6395,41.1711,17.6765		1953/4656	170070348	2299,10707	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon36			GATCATTCGATCT		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.5859A>G	2.37:g.170070348T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	139	67	0.482014	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			T|0.827;C|0.173	0.173	strong		0.368	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125826003	125826003	+	Missense_Mutation	SNP	T	T	C	rs4646750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125826003T>C	ENST00000393434.2	-	21	2783	c.2434A>G	c.(2434-2436)Atc>Gtc	p.I812V	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.I812V|ALDH1L1-AS1_ENST00000512384.1_RNA|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.I711V|ALDH1L1_ENST00000393431.2_3'UTR|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.I822V	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	812	Aldehyde dehydrogenase.		I -> V (in dbSNP:rs4646750).		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)	AACCGAGAGATGATCATGACA	0.517													T|||	324	0.0646965	0.112	0.0692	5008	,	,		20531	0.0308		0.0646	False		,,,				2504	0.0327				p.I822V		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.A2464G						PASS	.	T	VAL/ILE	510,3896	235.5+/-248.0	23,464,1716	173.0	150.0	157.0		2434	2.8	1.0	3	dbSNP_111	157	652,7948	165.7+/-217.8	25,602,3673	yes	missense	ALDH1L1	NM_012190.2	29	48,1066,5389	CC,CT,TT		7.5814,11.5751,8.9343	benign	812/903	125826003	1162,11844	2203	4300	6503	SO:0001583	missense	10840	exon21			GAGAGATGATCAT	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.2434A>G	3.37:g.125826003T>C	ENSP00000377083:p.Ile812Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	150	0.06868131868131869	55	0.11178861788617886	26	0.0718232044198895	18	0.03146853146853147	51	0.06728232189973615	T	8.039	0.763418	0.15914	0.115751	0.075814	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.05319	3.46;3.46;3.46;3.46	3.98	2.83	0.33086	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.143965	0.44902	N	0.000405	T	0.00073	0.0002	N	0.11064	0.09	0.09310	P	0.9999999999999973	B;B;B	0.28026	0.151;0.198;0.039	B;B;B	0.31016	0.123;0.103;0.069	T	0.41574	-0.9501	9	0.40728	T	0.16	.	7.2766	0.26288	0.0:0.109:0.0:0.891	rs4646750;rs56475654;rs59802481;rs4646750	711;347;812	E9PBX3;Q6ZV71;O75891	.;.;AL1L1_HUMAN	V	822;812;711;812	ENSP00000273450:I822V;ENSP00000420293:I812V;ENSP00000395881:I711V;ENSP00000377083:I812V	ENSP00000273450:I822V	I	-	1	0	ALDH1L1	127308693	1.000000	0.71417	1.000000	0.80357	0.595000	0.36748	1.912000	0.39946	0.606000	0.29965	0.260000	0.18958	ATC	T|0.919;C|0.081	0.081	strong		0.517	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
PPP3CA	5530	hgsc.bcm.edu	37	4	102117083	102117083	+	Silent	SNP	C	C	T	rs3730251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:102117083C>T	ENST00000394854.3	-	2	932	c.249G>A	c.(247-249)gcG>gcA	p.A83A	PPP3CA_ENST00000323055.6_Silent_p.A83A|PPP3CA_ENST00000512215.1_Silent_p.A83A|PPP3CA_ENST00000394853.4_Silent_p.A83A|PPP3CA_ENST00000523694.2_Intron|PPP3CA_ENST00000507176.1_Intron	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	83	Catalytic.				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)		CAGTGACTGGCGCATCAATAT	0.418													C|||	348	0.0694888	0.2133	0.0115	5008	,	,		17748	0.0446		0.001	False		,,,				2504	0.0123				p.A83A		Atlas-SNP	.											PPP3CA,NS,carcinoma,-1,1	PPP3CA	51	1	0			c.G249A						PASS	.	C	,,	911,3495	347.7+/-309.6	98,715,1390	83.0	84.0	83.0		249,249,249	-11.9	0.1	4	dbSNP_107	83	29,8571	20.4+/-63.3	0,29,4271	no	coding-synonymous,coding-synonymous,coding-synonymous	PPP3CA	NM_000944.4,NM_001130691.1,NM_001130692.1	,,	98,744,5661	TT,TC,CC		0.3372,20.6764,7.2274	,,	83/522,83/512,83/470	102117083	940,12066	2203	4300	6503	SO:0001819	synonymous_variant	5530	exon2			GACTGGCGCATCA		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.249G>A	4.37:g.102117083C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_000944	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Silent	SNP	ENST00000394854.3	37	CCDS34037.1																																																																																			C|0.936;T|0.064	0.064	strong		0.418	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944	
KRTAP19-4	337971	hgsc.bcm.edu	37	21	31869286	31869286	+	Missense_Mutation	SNP	T	T	C	rs2298437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31869286T>C	ENST00000334058.2	-	1	165	c.143A>G	c.(142-144)tAc>tGc	p.Y48C		NM_181610.1	NP_853641.1	Q3LI73	KR194_HUMAN	keratin associated protein 19-4	48			Y -> C (in dbSNP:rs2298437). {ECO:0000269|PubMed:15489334}.			intermediate filament (GO:0005882)				central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TGGGCGGCAGTAGCCATATCC	0.493													C|||	3076	0.614217	0.82	0.6571	5008	,	,		17328	0.3194		0.5606	False		,,,				2504	0.6646				p.Y48C		Atlas-SNP	.											KRTAP19-4,uveal_tract,malignant_melanoma,+1,1	KRTAP19-4	22	1	0			c.A143G						PASS	.	C	CYS/TYR	3296,1110	395.8+/-329.8	1230,836,137	119.0	125.0	123.0		143	-4.2	0.0	21	dbSNP_100	123	4972,3628	521.3+/-379.9	1440,2092,768	yes	missense	KRTAP19-4	NM_181610.1	194	2670,2928,905	CC,CT,TT		42.186,25.1929,36.4293	benign	48/85	31869286	8268,4738	2203	4300	6503	SO:0001583	missense	337971	exon1			CGGCAGTAGCCAT	AP001708	CCDS33534.1	21q22.1	2011-02-10			ENSG00000186967	ENSG00000186967		"""Keratin associated proteins"""	18939	protein-coding gene	gene with protein product						12359730	Standard	NM_181610		Approved	KAP19.4	uc011acz.2	Q3LI73	OTTHUMG00000057767	ENST00000334058.2:c.143A>G	21.37:g.31869286T>C	ENSP00000335567:p.Tyr48Cys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_181610	Q17RT4|Q17RT6	Missense_Mutation	SNP	ENST00000334058.2	37	CCDS33534.1	1247	0.5709706959706959	411	0.8353658536585366	243	0.6712707182320442	186	0.32517482517482516	407	0.5369393139841688	C	7.165	0.586432	0.13749	0.748071	0.57814	ENSG00000186967	ENST00000334058	T	0.07444	3.19	4.03	-4.2	0.03823	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.17837	-1.0356	7	0.87932	D	0	.	4.8584	0.13571	0.258:0.2009:0.0:0.5411	rs2298437;rs52825099;rs2298437	48	Q3LI73	KR194_HUMAN	C	48	ENSP00000335567:Y48C	ENSP00000335567:Y48C	Y	-	2	0	KRTAP19-4	30791157	0.000000	0.05858	0.002000	0.10522	0.143000	0.21401	-1.290000	0.02777	-1.323000	0.02275	-0.186000	0.12905	TAC	T|0.392;C|0.608	0.608	strong		0.493	KRTAP19-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128219.2		
MUC4	4585	hgsc.bcm.edu	37	3	195508692	195508692	+	Missense_Mutation	SNP	G	G	C	rs528841424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508692G>C	ENST00000463781.3	-	2	10218	c.9759C>G	c.(9757-9759)gaC>gaG	p.D3253E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3253E	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)		CTGAGGAAGTGTCGGTGACAG	0.562													.|||	426	0.0850639	0.3109	0.0216	5008	,	,		10371	0.0		0.0	False		,,,				2504	0.0				p.D3253E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C9759G						scavenged	.						3.0	2.0	3.0					3																	195508692		528	1216	1744	SO:0001583	missense	4585	exon2			GGAAGTGTCGGTG	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.9759C>G	3.37:g.195508692G>C	ENSP00000417498:p.Asp3253Glu	Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	115	74	0.643478	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	7.901	0.734401	0.15574	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29142	1.58;1.58	1.03	-1.18	0.09617	.	.	.	.	.	T	0.26268	0.0641	N	0.08118	0	0.09310	N	1	D	0.61080	0.989	D	0.71656	0.974	T	0.26052	-1.0114	8	.	.	.	.	5.5419	0.17043	0.0:0.0:0.6865:0.3135	.	3125	E7ESK3	.	E	3253	ENSP00000417498:D3253E;ENSP00000420243:D3253E	.	D	-	3	2	MUC4	196993471	0.000000	0.05858	0.014000	0.15608	0.048000	0.14542	-0.521000	0.06245	0.494000	0.27859	0.089000	0.15464	GAC	.	.	none		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
STK10	6793	hgsc.bcm.edu	37	5	171533629	171533629	+	Silent	SNP	A	A	G	rs2306963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:171533629A>G	ENST00000176763.5	-	6	1126	c.783T>C	c.(781-783)tcT>tcC	p.S261S		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTCACCACTTAGAGGGCGTGA	0.662													A|||	3801	0.758986	0.677	0.768	5008	,	,		13410	0.8542		0.7435	False		,,,				2504	0.7812				p.S261S		Atlas-SNP	.											.	STK10	100	.	0			c.T783C						PASS	.	A		3019,1387	682.9+/-404.2	1056,907,240	62.0	58.0	59.0		783	-5.2	0.2	5	dbSNP_100	59	6124,2476	694.2+/-404.7	2177,1770,353	no	coding-synonymous	STK10	NM_005990.3		3233,2677,593	GG,GA,AA		28.7907,31.4798,29.7017		261/969	171533629	9143,3863	2203	4300	6503	SO:0001819	synonymous_variant	6793	exon6			CCACTTAGAGGGC	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.783T>C	5.37:g.171533629A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	122	66	0.540984	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	37	CCDS34290.1																																																																																			A|0.272;G|0.728	0.728	strong		0.662	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38652993	38652993	+	Silent	SNP	C	C	T	rs332864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38652993C>T	ENST00000222345.6	+	14	4271	c.3762C>T	c.(3760-3762)tcC>tcT	p.S1254S		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1254					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)			GCAAAGATTCCCCCAACAGGC	0.632													C|||	1454	0.290335	0.0915	0.2968	5008	,	,		19272	0.2381		0.4682	False		,,,				2504	0.4254				p.S1254S		Atlas-SNP	.											SIPA1L3,NS,adenoma,0,1	SIPA1L3	150	1	0			c.C3762T						scavenged	.	C		611,3795	265.9+/-266.9	50,511,1642	96.0	75.0	82.0		3762	2.3	1.0	19	dbSNP_79	82	3808,4792	537.5+/-383.2	806,2196,1298	no	coding-synonymous	SIPA1L3	NM_015073.1		856,2707,2940	TT,TC,CC		44.2791,13.8675,33.9766		1254/1782	38652993	4419,8587	2203	4300	6503	SO:0001819	synonymous_variant	23094	exon14			AGATTCCCCCAAC	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.3762C>T	19.37:g.38652993C>T		Somatic	233	2	0.00858369		WXS	Illumina HiSeq	Phase_I	217	115	0.529954	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	37	CCDS33007.1																																																																																			C|0.679;T|0.321	0.321	strong		0.632	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
LILRA6	79168	hgsc.bcm.edu	37	19	54744777	54744777	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54744777C>T	ENST00000396365.2	-	5	924	c.885G>A	c.(883-885)agG>agA	p.R295R	LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Silent_p.R295R|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000419410.2_Silent_p.R295R|LILRA6_ENST00000245621.5_Silent_p.R295R	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	295	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CACCATAGCACCTGTACTGGC	0.677																																					p.R295R		Atlas-SNP	.											.	LILRA6	75	.	0			c.G885A						PASS	.						57.0	71.0	66.0					19																	54744777		2203	4300	6503	SO:0001819	synonymous_variant	79168	exon5			ATAGCACCTGTAC	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.885G>A	19.37:g.54744777C>T		Somatic	396	0	0		WXS	Illumina HiSeq	Phase_I	477	65	0.136268	NM_024318		Silent	SNP	ENST00000396365.2	37	CCDS42610.1																																																																																			.	.	weak		0.677	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
TRERF1	55809	hgsc.bcm.edu	37	6	42232475	42232475	+	Silent	SNP	G	G	A	rs2295274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42232475G>A	ENST00000372922.4	-	7	2164	c.1602C>T	c.(1600-1602)caC>caT	p.H534H	TRERF1_ENST00000354325.2_Silent_p.H534H|TRERF1_ENST00000541110.1_Silent_p.H534H|TRERF1_ENST00000372917.4_Silent_p.H534H|TRERF1_ENST00000340840.2_Silent_p.H534H	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	534	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCATTCCCCCGTGGGACCGCA	0.572													G|||	754	0.150559	0.1362	0.1066	5008	,	,		19343	0.122		0.169	False		,,,				2504	0.2117				p.H534H		Atlas-SNP	.											.	TRERF1	124	.	0			c.C1602T						PASS	.	G		677,3729	286.9+/-279.0	49,579,1575	99.0	87.0	91.0		1602	-3.5	0.9	6	dbSNP_100	91	1413,7187	272.3+/-290.0	117,1179,3004	no	coding-synonymous	TRERF1	NM_033502.2		166,1758,4579	AA,AG,GG		16.4302,15.3654,16.0695		534/1201	42232475	2090,10916	2203	4300	6503	SO:0001819	synonymous_variant	55809	exon7			TCCCCCGTGGGAC	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1602C>T	6.37:g.42232475G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	37	CCDS4867.1																																																																																			G|0.848;A|0.152	0.152	strong		0.572	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
HHLA3	11147	hgsc.bcm.edu	37	1	70820802	70820802	+	Silent	SNP	G	G	A	rs17131261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:70820802G>A	ENST00000359875.5	+	1	308	c.168G>A	c.(166-168)aaG>aaA	p.K56K	ANKRD13C_ENST00000262346.6_5'Flank|HHLA3_ENST00000486110.1_3'UTR|HHLA3_ENST00000531950.1_Silent_p.K56K|ANKRD13C_ENST00000370944.4_5'Flank|HHLA3_ENST00000361764.4_Intron|HHLA3_ENST00000370940.5_Intron|HHLA3_ENST00000432224.1_Silent_p.K56K	NM_001036645.1	NP_001031722.1	Q9XRX5	HHLA3_HUMAN	HERV-H LTR-associating 3	56										large_intestine(3)|lung(1)	4						tatgtacgaagctagcaaata	0.502													G|||	134	0.0267572	0.0938	0.0144	5008	,	,		20899	0.0		0.0	False		,,,				2504	0.0				p.K56K		Atlas-SNP	.											.	HHLA3	11	.	0			c.G168A						PASS	.	G	,,	319,4087	170.1+/-200.6	8,303,1892	92.0	72.0	79.0		,168,	2.6	0.0	1	dbSNP_123	79	5,8595	3.7+/-12.6	0,5,4295	no	intron,coding-synonymous,intron	HHLA3	NM_001031693.2,NM_001036645.1,NM_001036646.1	,,	8,308,6187	AA,AG,GG		0.0581,7.2401,2.4912	,,	,56/115,	70820802	324,12682	2203	4300	6503	SO:0001819	synonymous_variant	11147	exon1			TACGAAGCTAGCA	AF126164	CCDS649.1, CCDS30752.1, CCDS30753.1	1p31.1	2008-02-05			ENSG00000197568	ENSG00000197568			4906	protein-coding gene	gene with protein product		604372				10444326	Standard	NR_027404		Approved		uc001dfa.3	Q9XRX5	OTTHUMG00000009346	ENST00000359875.5:c.168G>A	1.37:g.70820802G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_001036645	D3DQ74|Q5VZP2|Q96FH5|Q9XRX4	Silent	SNP	ENST00000359875.5	37	CCDS30753.1																																																																																			G|0.971;A|0.029	0.029	strong		0.502	HHLA3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025911.2	NM_007071	
AKNAD1	254268	hgsc.bcm.edu	37	1	109377070	109377070	+	Splice_Site	SNP	C	C	A	rs12060255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109377070C>A	ENST00000370001.3	-	9	2013	c.1745G>T	c.(1744-1746)gGg>gTg	p.G582V	AKNAD1_ENST00000369995.3_Splice_Site_p.G582V|AKNAD1_ENST00000369994.1_Splice_Site_p.G552V|AKNAD1_ENST00000357393.4_Splice_Site_p.G289V	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	582			G -> V (in dbSNP:rs12060255).			cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						GGACATTACCCCAGAGTTAGA	0.443													C|||	666	0.132987	0.2095	0.0951	5008	,	,		18089	0.12		0.1133	False		,,,				2504	0.09				p.G582V		Atlas-SNP	.											.	AKNAD1	83	.	0			c.G1745T						PASS	.	C	VAL/GLY	821,3585	301.8+/-287.1	84,653,1466	63.0	56.0	59.0		1745	-0.0	0.0	1	dbSNP_120	59	972,7628	196.2+/-241.2	54,864,3382	yes	missense-near-splice	AKNAD1	NM_152763.3	109	138,1517,4848	AA,AC,CC		11.3023,18.6337,13.7859	possibly-damaging	582/837	109377070	1793,11213	2203	4300	6503	SO:0001630	splice_region_variant	254268	exon9			ATTACCCCAGAGT	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.1746+1G>T	1.37:g.109377070C>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	37	CCDS791.2	300	0.13736263736263737	114	0.23170731707317074	37	0.10220994475138122	66	0.11538461538461539	83	0.10949868073878628	C	8.353	0.831248	0.16820	0.186337	0.113023	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	T;T;T;T	0.15834	3.17;2.39;3.08;3.15	3.31	-0.038	0.13881	.	.	.	.	.	T	0.02727	0.0082	L	0.29908	0.895	0.58432	P	1.0000000000287557E-6	B;P	0.37864	0.396;0.61	B;B	0.30029	0.1;0.11	T	0.40079	-0.9582	8	0.42905	T	0.14	5.4051	2.5826	0.04822	0.2287:0.5013:0.0:0.2699	rs12060255	289;582	B4DET8;Q5T1N1	.;AKND1_HUMAN	V	582;289;552;582	ENSP00000359018:G582V;ENSP00000349968:G289V;ENSP00000359011:G552V;ENSP00000359012:G582V	ENSP00000349968:G289V	G	-	2	0	AKNAD1	109178593	0.007000	0.16637	0.001000	0.08648	0.052000	0.14988	0.598000	0.24074	0.207000	0.20607	0.462000	0.41574	GGG	C|0.870;A|0.130	0.130	strong		0.443	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	Missense_Mutation
PSG2	5670	hgsc.bcm.edu	37	19	43576029	43576029	+	Missense_Mutation	SNP	C	C	T	rs112235686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43576029C>T	ENST00000406487.1	-	4	885	c.787G>A	c.(787-789)Gcg>Acg	p.A263T		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	263	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				TTAGAGTTCGCGAAGCAAGAC	0.438													C|||	8	0.00159744	0.0061	0.0	5008	,	,		20011	0.0		0.0	False		,,,				2504	0.0				p.A263T		Atlas-SNP	.											PSG2,colon,carcinoma,+1,2	PSG2	84	2	0			c.G787A						PASS	.	C	THR/ALA	27,4377	33.5+/-64.1	2,23,2177	180.0	191.0	187.0		787	-0.0	0.0	19	dbSNP_132	187	10,8588	7.7+/-29.5	0,10,4289	yes	missense	PSG2	NM_031246.3	58	2,33,6466	TT,TC,CC		0.1163,0.6131,0.2846		263/336	43576029	37,12965	2202	4299	6501	SO:0001583	missense	5670	exon4			AGTTCGCGAAGCA		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.787G>A	19.37:g.43576029C>T	ENSP00000385706:p.Ala263Thr	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	195	89	0.45641	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	c	1.983	-0.433771	0.04669	0.006131	0.001163	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.15603	2.41	1.26	-0.0241	0.13940	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.10981	0.0268	M	0.73372	2.23	0.09310	N	1	B;B	0.22414	0.069;0.003	B;B	0.20767	0.031;0.022	T	0.35400	-0.9790	9	0.20519	T	0.43	.	3.758	0.08593	0.0:0.7179:0.0:0.2821	.	263;263	B5MCM8;P11465	.;PSG2_HUMAN	T	263	ENSP00000385706:A263T	ENSP00000332984:A263T	A	-	1	0	PSG2	48267869	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.248000	0.08854	-0.149000	0.11215	0.398000	0.26397	GCG	C|0.998;T|0.002	0.002	strong		0.438	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
MUC17	140453	hgsc.bcm.edu	37	7	100678527	100678527	+	Missense_Mutation	SNP	G	G	T	rs73402889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678527G>T	ENST00000306151.4	+	3	3894	c.3830G>T	c.(3829-3831)aGt>aTt	p.S1277I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1277	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)					AGTGAAGGAAGTACTCTATTA	0.498																																					p.S1277I		Atlas-SNP	.											MUC17,adrenal_gland,adrenal_cortical_adenoma,0,1	MUC17	804	1	0			c.G3830T						PASS	.	G	ILE/SER	508,3898		0,508,1695	279.0	268.0	272.0		3830	0.4	0.0	7	dbSNP_131	272	744,7856		0,744,3556	yes	missense	MUC17	NM_001040105.1	142	0,1252,5251	TT,TG,GG		8.6512,11.5297,9.6263	possibly-damaging	1277/4494	100678527	1252,11754	2203	4300	6503	SO:0001583	missense	140453	exon3			AAGGAAGTACTCT	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.3830G>T	7.37:g.100678527G>T	ENSP00000302716:p.Ser1277Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	153	36	0.235294	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	209	0.09569597069597069	65	0.13211382113821138	35	0.09668508287292818	26	0.045454545454545456	83	0.10949868073878628	g	0.856	-0.736924	0.03111	0.115297	0.086512	ENSG00000169876	ENST00000306151	T	0.02631	4.22	0.373	0.373	0.16178	.	.	.	.	.	T	0.00039	0.0001	L	0.29908	0.895	0.09310	N	1	P	0.47604	0.898	B	0.36885	0.235	T	0.55224	-0.8174	8	0.42905	T	0.14	.	.	.	.	.	1277	Q685J3	MUC17_HUMAN	I	1277	ENSP00000302716:S1277I	ENSP00000302716:S1277I	S	+	2	0	MUC17	100465247	0.000000	0.05858	0.010000	0.14722	0.017000	0.09413	-1.635000	0.02018	0.472000	0.27344	0.134000	0.15878	AGT	G|0.918;T|0.082	0.082	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MUC6	4588	hgsc.bcm.edu	37	11	1016960	1016960	+	Silent	SNP	G	G	T	rs113980831		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1016960G>T	ENST00000421673.2	-	31	5891	c.5841C>A	c.(5839-5841)acC>acA	p.T1947T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1947	Approximate repeats.|Thr-rich.			NITPKHTSTGTRTPV -> KITTNPTSIGSSTPM (in Ref. 5; AAA35866). {ECO:0000305}.	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)		CAGGGGTTCTGGTGCCTGTAC	0.572																																					p.T1947T		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	0			c.C5841A						scavenged	.						516.0	536.0	529.0					11																	1016960		2200	4292	6492	SO:0001819	synonymous_variant	4588	exon31			GGTTCTGGTGCCT	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.5841C>A	11.37:g.1016960G>T		Somatic	918	5	0.00544662		WXS	Illumina HiSeq	Phase_I	1031	130	0.126091	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			G|0.500;T|0.500	0.500	weak		0.572	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
TRPC4	7223	hgsc.bcm.edu	37	13	38211046	38211046	+	Silent	SNP	T	T	C	rs731860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:38211046T>C	ENST00000379705.3	-	11	3785	c.2928A>G	c.(2926-2928)agA>agG	p.R976R	TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000379681.3_Silent_p.R981R|TRPC4_ENST00000379679.1_Silent_p.R803R|TRPC4_ENST00000338947.5_Silent_p.R803R|TRPC4_ENST00000358477.2_Silent_p.R892R|TRPC4_ENST00000355779.2_Silent_p.R835R|TRPC4_ENST00000379673.2_Silent_p.R827R|TRPC4_ENST00000447043.1_Silent_p.R835R			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	976	Binds to ITPR1, ITPR2 and ITPR3.|PDZ-binding domain.				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)		AGTATCACAATCTTGTGGTCA	0.403													T|||	154	0.0307508	0.1112	0.0086	5008	,	,		19821	0.0		0.001	False		,,,				2504	0.0				p.R981R		Atlas-SNP	.											.	TRPC4	389	.	0			c.A2943G						PASS	.	T	,,,,,	428,3978	208.5+/-229.5	24,380,1799	118.0	111.0	114.0		2676,2481,2505,2409,2943,2928	-1.3	0.2	13	dbSNP_86	114	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	,,,,,	24,387,6092	CC,CT,TT		0.0814,9.714,3.3446	,,,,,	892/894,827/829,835/837,803/805,981/983,976/978	38211046	435,12571	2203	4300	6503	SO:0001819	synonymous_variant	7223	exon11			TCACAATCTTGTG	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.2928A>G	13.37:g.38211046T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	112	63	0.5625	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																			T|0.959;C|0.041	0.041	strong		0.403	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84581889	84581889	+	Silent	SNP	G	G	A	rs12439867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	144	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	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	
TEX33	339669	hgsc.bcm.edu	37	22	37397876	37397876	+	Splice_Site	SNP	A	A	G	rs148258673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37397876A>G	ENST00000405091.2	-	4	741		c.e4+1		TEX33_ENST00000402860.3_Splice_Site|TEX33_ENST00000381821.1_Splice_Site			O43247	TEX33_HUMAN	testis expressed 33																		CTGCTATGACACCTGCTCCTC	0.493													A|||	11	0.00219649	0.0076	0.0014	5008	,	,		21381	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	TEX33	25	.	0			c.489+2T>C						PASS	.	A	,	62,4344		0,62,2141	86.0	58.0	68.0		,	4.6	1.0	22	dbSNP_134	68	0,8600		0,0,4300	yes	splice-5,splice-5	C22orf33	NM_001163857.1,NM_178552.3	,	0,62,6441	GG,GA,AA		0.0,1.4072,0.4767	,	,	37397876	62,12944	2203	4300	6503	SO:0001630	splice_region_variant	339669	exon4			TATGACACCTGCT	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.489+1T>C	22.37:g.37397876A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_001163857	B1AH46|Q6ICF2|Q8IVQ2|Q9Y4V8	Splice_Site	SNP	ENST00000405091.2	37	CCDS54524.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	15.90	2.968886	0.53614	0.014072	0.0	ENSG00000185264	ENST00000402860;ENST00000405091;ENST00000381821	.	.	.	5.68	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.1587	0.37009	0.9146:0.0:0.0854:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C22orf33	35727822	0.995000	0.38212	0.992000	0.48379	0.817000	0.46193	3.503000	0.53340	2.159000	0.67721	0.533000	0.62120	.	A|0.997;G|0.003	0.003	strong		0.493	TEX33-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318778.2	NM_178552	Intron
KIAA0368	23392	hgsc.bcm.edu	37	9	114182353	114182353	+	Silent	SNP	C	C	T	rs16916080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114182353C>T	ENST00000338205.5	-	15	1722	c.1503G>A	c.(1501-1503)gtG>gtA	p.V501V	KIAA0368_ENST00000259335.4_Silent_p.V679V			Q5VYK3	ECM29_HUMAN	KIAA0368	507					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)		p.V679V(1)		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						CTGAGGGAAACACCGTACTGG	0.398													C|||	479	0.095647	0.1868	0.0187	5008	,	,		13432	0.1627		0.0109	False		,,,				2504	0.045				p.V679V		Atlas-SNP	.											KIAA0368,NS,carcinoma,0,1	KIAA0368	144	1	1	Substitution - coding silent(1)	stomach(1)	c.G2037A						PASS	.	C		553,3213		43,467,1373	101.0	99.0	99.0		2037	5.4	1.0	9	dbSNP_123	99	114,8106		0,114,3996	no	coding-synonymous	KIAA0368	NM_001080398.1		43,581,5369	TT,TC,CC		1.3869,14.684,5.5648		679/2018	114182353	667,11319	1883	4110	5993	SO:0001819	synonymous_variant	23392	exon17			GGGAAACACCGTA	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.1503G>A	9.37:g.114182353C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	58	36	0.62069	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				C|0.908;T|0.092	0.092	strong		0.398	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
MRPS11	64963	hgsc.bcm.edu	37	15	89011226	89011226	+	Missense_Mutation	SNP	G	G	C	rs16941907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89011226G>C	ENST00000325844.4	+	2	418	c.153G>C	c.(151-153)caG>caC	p.Q51H	MRPL46_ENST00000312475.4_5'Flank|MRPS11_ENST00000557974.1_3'UTR|MRPS11_ENST00000353598.6_Missense_Mutation_p.Q51H	NM_022839.3	NP_073750.2	P82912	RT11_HUMAN	mitochondrial ribosomal protein S11	51			Q -> H (in dbSNP:rs16941907).		DNA damage response, detection of DNA damage (GO:0042769)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(3)	3	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			AAGTTGAACAGAACGCGGCTC	0.632													G|||	111	0.0221645	0.0658	0.0014	5008	,	,		16046	0.006		0.0	False		,,,				2504	0.0174				p.Q51H		Atlas-SNP	.											.	MRPS11	14	.	0			c.G153C						PASS	.	G	HIS/GLN,HIS/GLN	311,4085		17,277,1904	26.0	25.0	26.0		153,153	3.3	0.0	15	dbSNP_123	26	7,8589		0,7,4291	yes	missense,missense	MRPS11	NM_022839.3,NM_176805.2	24,24	17,284,6195	CC,CG,GG		0.0814,7.0746,2.4477	benign,benign	51/195,51/162	89011226	318,12674	2198	4298	6496	SO:0001583	missense	64963	exon2			TGAACAGAACGCG	AB051349	CCDS10342.1, CCDS10343.1	15q25	2012-09-13			ENSG00000181991	ENSG00000181991		"""Mitochondrial ribosomal proteins / small subunits"""	14050	protein-coding gene	gene with protein product	"""cervical cancer proto-oncogene 2"""	611977				11402041	Standard	NM_022839		Approved	FLJ23406, HCC-2, FLJ22512	uc002bml.3	P82912	OTTHUMG00000148678	ENST00000325844.4:c.153G>C	15.37:g.89011226G>C	ENSP00000317376:p.Gln51His	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	173	79	0.456647	NM_176805	B2RD52|Q969D7|Q96GI3|Q9BYC3	Missense_Mutation	SNP	ENST00000325844.4	37	CCDS10342.1	36	0.016483516483516484	33	0.06707317073170732	1	0.0027624309392265192	2	0.0034965034965034965	0	0.0	G	13.70	2.314655	0.40996	0.070746	8.14E-4	ENSG00000181991	ENST00000325844;ENST00000353598	T;T	0.31510	1.49;1.51	4.25	3.33	0.38152	.	1.112800	0.06892	N	0.804449	T	0.01592	0.0051	N	0.14661	0.345	0.09310	N	1	B;B;B	0.26935	0.164;0.071;0.102	B;B;B	0.30401	0.115;0.06;0.054	T	0.20371	-1.0277	10	0.72032	D	0.01	-0.1994	8.3162	0.32102	0.1088:0.0:0.8912:0.0	rs16941907;rs16941907	50;51;51	P82912-2;P82912-3;P82912	.;.;RT11_HUMAN	H	51	ENSP00000317376:Q51H;ENSP00000318054:Q51H	ENSP00000317376:Q51H	Q	+	3	2	MRPS11	86812230	0.004000	0.15560	0.001000	0.08648	0.010000	0.07245	1.495000	0.35627	1.131000	0.42111	0.655000	0.94253	CAG	G|0.980;C|0.020	0.020	strong		0.632	MRPS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309067.2	NM_022839	
WDR93	56964	hgsc.bcm.edu	37	15	90281381	90281381	+	Silent	SNP	T	T	C	rs35017767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90281381T>C	ENST00000268130.7	+	16	1976	c.1875T>C	c.(1873-1875)tgT>tgC	p.C625C	WDR93_ENST00000560294.1_Silent_p.C597C|WDR93_ENST00000444934.2_Silent_p.C342C	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	625					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			CAAAAAATTGTACCATTCCTC	0.453													C|||	235	0.0469249	0.1755	0.0043	5008	,	,		17775	0.0		0.0	False		,,,				2504	0.0				p.C625C		Atlas-SNP	.											.	WDR93	63	.	0			c.T1875C						PASS	.	C		662,3738	763.7+/-413.2	44,574,1582	232.0	238.0	236.0		1875	-1.2	0.0	15	dbSNP_126	236	6,8592	818.8+/-406.8	0,6,4293	no	coding-synonymous	WDR93	NM_020212.1		44,580,5875	CC,CT,TT		0.0698,15.0455,5.1393		625/687	90281381	668,12330	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon16			AAATTGTACCATT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1875T>C	15.37:g.90281381T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	153	90	0.588235	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			T|0.955;C|0.045	0.045	strong		0.453	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
MT-ND6	4541	hgsc.bcm.edu	37	M	14178	14178	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:14178T>C	ENST00000361681.2	-	1	495	c.496A>G	c.(496-498)Att>Gtt	p.I166V	MT-TT_ENST00000387460.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	166					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						CTCAATTACAATATATACACC	0.413																																					p.I166V		Atlas-SNP	.											.	.	.	.	0			c.A496G						PASS	.																																			SO:0001583	missense	0	exon1			TTACAATATATAC			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.496A>G	M.37:g.14178T>C	ENSP00000354665:p.Ile166Val	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	ENST00000361681	Q34774|Q8HG30	Missense_Mutation	SNP	ENST00000361681.2	37																																																																																				.	.	none		0.413	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
KRBA2	124751	hgsc.bcm.edu	37	17	8273654	8273654	+	Missense_Mutation	SNP	G	G	A	rs74532943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8273654G>A	ENST00000331336.2	-	2	282	c.277C>T	c.(277-279)Cct>Tct	p.P93S	RP11-849F2.5_ENST00000583963.1_RNA|RP11-849F2.5_ENST00000580537.1_RNA|RP11-849F2.7_ENST00000582471.1_3'UTR|KRBA2_ENST00000396267.1_Missense_Mutation_p.P11S	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	93	KRAB.				DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)			endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						GAAACCCCAGGTGGATCATTT	0.383													G|||	198	0.0395367	0.1407	0.013	5008	,	,		19763	0.0		0.001	False		,,,				2504	0.002				p.P93S		Atlas-SNP	.											.	KRBA2	34	.	0			c.C277T						PASS	.	G	SER/PRO	443,3963	192.6+/-218.0	21,401,1781	89.0	92.0	91.0		277	-2.6	0.0	17	dbSNP_131	91	7,8589	5.0+/-18.6	0,7,4291	yes	missense	KRBA2	NM_213597.2	74	21,408,6072	AA,AG,GG		0.0814,10.0545,3.461	benign	93/493	8273654	450,12552	2203	4298	6501	SO:0001583	missense	124751	exon2			CCCCAGGTGGATC	BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"""-"""	26989	protein-coding gene	gene with protein product			"""KRAB A domain containing 2"""			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.277C>T	17.37:g.8273654G>A	ENSP00000328017:p.Pro93Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_213597	Q8IYY0	Missense_Mutation	SNP	ENST00000331336.2	37	CCDS11141.1	81	0.03708791208791209	75	0.1524390243902439	6	0.016574585635359115	0	0.0	0	0.0	G	0.116	-1.132002	0.01756	0.100545	8.14E-4	ENSG00000184619	ENST00000396267;ENST00000331336	T;T	0.23754	1.98;1.89	2.42	-2.57	0.06248	Krueppel-associated box (1);	.	.	.	.	T	0.00073	0.0002	L	0.31476	0.935	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.35425	-0.9789	8	0.22109	T	0.4	.	2.9115	0.05738	0.5175:0.0:0.2709:0.2117	.	93	Q6ZNG9	KRBA2_HUMAN	S	11;93	ENSP00000379565:P11S;ENSP00000328017:P93S	ENSP00000328017:P93S	P	-	1	0	KRBA2	8214379	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-1.059000	0.03479	-0.614000	0.05687	0.555000	0.69702	CCT	G|0.969;A|0.031	0.031	strong		0.383	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597	
PALLD	23022	hgsc.bcm.edu	37	4	169433333	169433333	+	Silent	SNP	C	C	T	rs7673220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169433333C>T	ENST00000505667.1	+	2	851	c.678C>T	c.(676-678)gaC>gaT	p.D226D	PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000261509.6_Silent_p.D226D|PALLD_ENST00000333488.4_Silent_p.D103D			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	226					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)		CTATGGAAGACCAAGGGGAGA	0.582									Pancreatic Cancer, Familial Clustering of				C|||	1200	0.239617	0.2368	0.1844	5008	,	,		17119	0.1935		0.33	False		,,,				2504	0.2372				p.D226D	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C678T						PASS	.	C	,	1117,3289	398.5+/-330.9	151,815,1237	101.0	104.0	103.0		678,678	-5.9	0.0	4	dbSNP_116	103	2811,5789	444.9+/-360.8	461,1889,1950	no	coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_016081.3	,	612,2704,3187	TT,TC,CC		32.686,25.3518,30.2014	,	226/1124,226/1107	169433333	3928,9078	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	GGAAGACCAAGGG	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.678C>T	4.37:g.169433333C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			C|0.724;T|0.276	0.276	strong		0.582	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
HRASLS5	117245	hgsc.bcm.edu	37	11	63256441	63256441	+	Missense_Mutation	SNP	C	C	G	rs940611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:63256441C>G	ENST00000301790.4	-	3	436	c.277G>C	c.(277-279)Gct>Cct	p.A93P	HRASLS5_ENST00000540857.1_Missense_Mutation_p.A83P|HRASLS5_ENST00000539221.1_Missense_Mutation_p.A93P			Q96KN8	HRSL5_HUMAN	HRAS-like suppressor family, member 5	93			A -> P (in dbSNP:rs940611).				transferase activity, transferring acyl groups (GO:0016746)			endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	14						CTAACTACAGCCTTCTCCCTA	0.373													G|||	1156	0.230831	0.652	0.0893	5008	,	,		16993	0.1478		0.0487	False		,,,				2504	0.0348				p.A93P		Atlas-SNP	.											.	HRASLS5	28	.	0			c.G277C						PASS	.	G	PRO/ALA,PRO/ALA,PRO/ALA	2309,2093	565.1+/-381.6	603,1103,495	158.0	155.0	156.0		277,247,277	-1.0	0.0	11	dbSNP_86	156	402,8194	801.0+/-407.4	12,378,3908	yes	missense,missense,missense	HRASLS5	NM_001146728.1,NM_001146729.1,NM_054108.3	27,27,27	615,1481,4403	GG,GC,CC		4.6766,47.5466,20.8571	benign,benign,benign	93/254,83/270,93/280	63256441	2711,10287	2201	4298	6499	SO:0001583	missense	117245	exon3			CTACAGCCTTCTC	AJ416558	CCDS8044.1, CCDS53646.1, CCDS53647.1	11q13.2	2006-08-16			ENSG00000168004	ENSG00000168004			24978	protein-coding gene	gene with protein product		611474					Standard	NM_001146729		Approved	HRLP5	uc001nwy.2	Q96KN8	OTTHUMG00000167806	ENST00000301790.4:c.277G>C	11.37:g.63256441C>G	ENSP00000301790:p.Ala93Pro	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	175	89	0.508571	NM_001146728	B7X6T1|F5GZ87|F5H4Y9	Missense_Mutation	SNP	ENST00000301790.4	37	CCDS8044.1	450	0.20604395604395603	300	0.6097560975609756	30	0.08287292817679558	85	0.1486013986013986	35	0.04617414248021108	G	0.008	-1.880860	0.00532	0.524534	0.046766	ENSG00000168004	ENST00000540857;ENST00000539221;ENST00000301790	T;T;T	0.25250	1.81;2.31;1.85	3.25	-1.03	0.10102	.	3.853830	0.00877	N	0.002097	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42207	-0.9465	9	0.02654	T	1	-5.2561	5.7094	0.17927	0.2081:0.486:0.3059:0.0	rs940611;rs52822334;rs60572363;rs940611	93;83;93	F5GZ87;F5H4Y9;Q96KN8	.;.;HRSL5_HUMAN	P	83;93;93	ENSP00000444809:A83P;ENSP00000443873:A93P;ENSP00000301790:A93P	ENSP00000301790:A93P	A	-	1	0	HRASLS5	63013017	0.005000	0.15991	0.017000	0.16124	0.001000	0.01503	-0.444000	0.06854	-0.480000	0.06803	-1.255000	0.01485	GCT	C|0.786;G|0.214	0.214	strong		0.373	HRASLS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396375.1	NM_054108	
SPATA6L	55064	hgsc.bcm.edu	37	9	4625546	4625546	+	Silent	SNP	C	C	T	rs12338523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:4625546C>T	ENST00000454239.2	-	7	695	c.450G>A	c.(448-450)cgG>cgA	p.R150R	SPATA6L_ENST00000381895.5_Silent_p.R27R|SPATA6L_ENST00000475086.1_Silent_p.R92R|SPATA6L_ENST00000223517.5_5'UTR|SPATA6L_ENST00000381890.5_Silent_p.R164R			Q8N4H0	SPA6L_HUMAN	spermatogenesis associated 6-like	150																	ATAAAGGCCTCCGTGACTCAT	0.294													T|||	73	0.0145767	0.0499	0.0101	5008	,	,		15547	0.0		0.0	False		,,,				2504	0.0				p.R92R		Atlas-SNP	.											.	SPATA6L	3	.	0			c.G276A						PASS	.	T		130,3480		1,128,1676	62.0	63.0	63.0		276	-1.8	0.0	9	dbSNP_120	63	2,8128		0,2,4063	no	coding-synonymous	C9orf68	NM_001039395.3		1,130,5739	TT,TC,CC		0.0246,3.6011,1.1244		92/335	4625546	132,11608	1805	4065	5870	SO:0001819	synonymous_variant	55064	exon5			AGGCCTCCGTGAC	AK000920	CCDS43785.1, CCDS43785.2	9p24.2	2012-03-15	2012-03-15	2012-03-15	ENSG00000106686	ENSG00000106686			25472	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 68"""	C9orf68			Standard	NM_001039395		Approved	FLJ10058	uc011llz.2	Q8N4H0	OTTHUMG00000019469	ENST00000454239.2:c.450G>A	9.37:g.4625546C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001039395	B4DIY4|Q5JVJ5|Q8IY90	Silent	SNP	ENST00000454239.2	37																																																																																				C|0.994;T|0.006	0.006	strong		0.294	SPATA6L-202	KNOWN	basic	protein_coding	protein_coding		NM_017985	
FAM186B	84070	hgsc.bcm.edu	37	12	49993766	49993766	+	Missense_Mutation	SNP	C	C	G	rs12299908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49993766C>G	ENST00000257894.2	-	4	1818	c.1657G>C	c.(1657-1659)Gag>Cag	p.E553Q	FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.E463Q|PRPF40B_ENST00000508736.1_3'UTR	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	553			E -> Q (in dbSNP:rs12299908).			protein complex (GO:0043234)				breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCCACATCCTCCCCTAGCTGC	0.592													C|||	464	0.0926518	0.3169	0.0202	5008	,	,		18890	0.001		0.0169	False		,,,				2504	0.0133				p.E553Q		Atlas-SNP	.											.	FAM186B	72	.	0			c.G1657C						PASS	.	C	GLN/GLU	1166,3240	410.4+/-335.4	148,870,1185	95.0	86.0	89.0		1657	0.1	0.0	12	dbSNP_120	89	175,8425	79.5+/-142.1	2,171,4127	yes	missense	FAM186B	NM_032130.2	29	150,1041,5312	GG,GC,CC		2.0349,26.4639,10.3106	possibly-damaging	553/894	49993766	1341,11665	2203	4300	6503	SO:0001583	missense	84070	exon4			CATCCTCCCCTAG	AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 25"""	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.1657G>C	12.37:g.49993766C>G	ENSP00000257894:p.Glu553Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_032130	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	37	CCDS8788.1	145	0.06639194139194139	124	0.25203252032520324	6	0.016574585635359115	1	0.0017482517482517483	14	0.018469656992084433	C	13.34	2.209076	0.39003	0.264639	0.020349	ENSG00000135436	ENST00000544141;ENST00000532262;ENST00000257894	T;T;T	0.11169	2.8;2.8;3.0	4.41	0.105	0.14535	.	0.175215	0.27613	N	0.018599	T	0.00012	0.0000	M	0.64997	1.995	0.80722	P	0.0	B;B	0.23937	0.094;0.094	B;B	0.23275	0.045;0.045	T	0.39272	-0.9622	8	.	.	.	-8.9157	4.2987	0.10915	0.0:0.4093:0.3723:0.2185	rs12299908;rs12299908	463;553	B4DZ15;Q8IYM0	.;F186B_HUMAN	Q	463;166;553	ENSP00000438569:E463Q;ENSP00000436995:E166Q;ENSP00000257894:E553Q	.	E	-	1	0	FAM186B	48280033	0.000000	0.05858	0.003000	0.11579	0.022000	0.10575	0.032000	0.13732	0.396000	0.25283	0.563000	0.77884	GAG	C|0.909;G|0.091	0.091	strong		0.592	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130	
ULK4	54986	hgsc.bcm.edu	37	3	41877414	41877414	+	Missense_Mutation	SNP	T	T	C	rs3774372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:41877414T>C	ENST00000301831.4	-	18	2168	c.1706A>G	c.(1705-1707)aAa>aGa	p.K569R		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	569			K -> R (in dbSNP:rs3774372).	AIVLLTELIRENFRNSKLKQCLLPTLGE -> TTSSIGIGI LNCLVQHSTPVPRQCLVYV (in Ref. 3; AAH14794). {ECO:0000305}.	cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CTGTTTTAATTTGCTGTTCCT	0.363													T|||	865	0.172724	0.1974	0.1369	5008	,	,		14471	0.1458		0.1849	False		,,,				2504	0.18				p.K569R		Atlas-SNP	.											.	ULK4	150	.	0			c.A1706G						PASS	.	T	ARG/LYS	766,2902		74,618,1142	135.0	134.0	135.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1706	5.5	1.0	3	dbSNP_107	135	1373,6785		118,1137,2824	yes	missense	ULK4	NM_017886.2	26	192,1755,3966	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	16.8301,20.8833,18.0873	possibly-damaging	569/1276	41877414	2139,9687	1834	4079	5913	SO:0001583	missense	54986	exon18			TTTAATTTGCTGT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1706A>G	3.37:g.41877414T>C	ENSP00000301831:p.Lys569Arg	Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	221	120	0.542986	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	392	0.1794871794871795	105	0.21341463414634146	51	0.1408839779005525	88	0.15384615384615385	148	0.19525065963060687	T	13.98	2.400184	0.42613	0.208833	0.168301	ENSG00000168038	ENST00000301831	T	0.64438	-0.1	5.48	5.48	0.80851	Armadillo-like helical (1);Armadillo-type fold (2);	0.057123	0.64402	U	0.000002	T	0.00039	0.0001	L	0.33485	1.01	0.09310	P	1.0	P	0.42456	0.78	B	0.39027	0.288	T	0.09100	-1.0690	9	0.14252	T	0.57	.	14.0999	0.65049	0.0:0.0:0.0:1.0	rs3774372;rs17216668;rs56443480;rs3774372	569	Q96C45	ULK4_HUMAN	R	569	ENSP00000301831:K569R	ENSP00000301831:K569R	K	-	2	0	ULK4	41852418	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.095000	0.57728	2.204000	0.70986	0.528000	0.53228	AAA	T|0.818;C|0.182	0.182	strong		0.363	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
DOCK8	81704	hgsc.bcm.edu	37	9	328144	328144	+	Silent	SNP	G	G	A	rs35746964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:328144G>A	ENST00000453981.1	+	9	1129	c.1017G>A	c.(1015-1017)ccG>ccA	p.P339P	DOCK8_ENST00000469391.1_Silent_p.P271P|DOCK8_ENST00000432829.2_Silent_p.P271P			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	339					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)		TCACCTACCCGTCCTCAGACA	0.493													G|||	11	0.00219649	0.0083	0.0	5008	,	,		20591	0.0		0.0	False		,,,				2504	0.0				p.P339P		Atlas-SNP	.											DOCK8_ENST00000453981,colon,carcinoma,0,2	DOCK8	401	2	0			c.G1017A						PASS	.	G	,,	41,4365	44.6+/-78.6	0,41,2162	100.0	82.0	88.0		813,813,1017	-8.7	0.6	9	dbSNP_126	88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	0,42,6461	AA,AG,GG		0.0116,0.9305,0.3229	,,	271/2000,271/2032,339/2100	328144	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon9			CTACCCGTCCTCA	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.1017G>A	9.37:g.328144G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	146	80	0.547945	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			G|0.996;A|0.004	0.004	strong		0.493	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
CD1B	910	hgsc.bcm.edu	37	1	158299299	158299299	+	Silent	SNP	C	C	T	rs11806249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158299299C>T	ENST00000368168.3	-	4	854	c.747G>A	c.(745-747)caG>caA	p.Q249Q		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	249	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					TGTCCCCTAGCTGAGTGCCCT	0.612													.|||	67	0.0133786	0.0499	0.0014	5008	,	,		18986	0.0		0.0	False		,,,				2504	0.0				p.Q249Q		Atlas-SNP	.											.	CD1B	78	.	0			c.G747A						PASS	.	C		188,4218	120.0+/-157.7	5,178,2020	140.0	124.0	129.0		747	2.3	0.0	1	dbSNP_120	129	0,8600		0,0,4300	no	coding-synonymous	CD1B	NM_001764.2		5,178,6320	TT,TC,CC		0.0,4.2669,1.4455		249/334	158299299	188,12818	2203	4300	6503	SO:0001819	synonymous_variant	910	exon4			CCCTAGCTGAGTG	M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1635	protein-coding gene	gene with protein product		188360	"""CD1B antigen, b polypeptide"", ""CD1b antigen"""	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.747G>A	1.37:g.158299299C>T		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	325	151	0.464615	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Silent	SNP	ENST00000368168.3	37	CCDS1176.1																																																																																			C|0.984;T|0.016	0.016	strong		0.612	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764	
KRTAP25-1	100131902	hgsc.bcm.edu	37	21	31661653	31661653	+	Silent	SNP	A	A	G	rs2832759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31661653A>G	ENST00000416044.1	-	1	179	c.156T>C	c.(154-156)ggT>ggC	p.G52G		NM_001128598.1	NP_001122070.1	Q3LHN0	KR251_HUMAN	keratin associated protein 25-1	52						intermediate filament (GO:0005882)				breast(1)	1						TAGTTTGATTACCATAGGAGA	0.408													A|||	863	0.172324	0.3041	0.1412	5008	,	,		19219	0.0903		0.1382	False		,,,				2504	0.136				p.G52G		Atlas-SNP	.											.	KRTAP25-1	13	.	0			c.T156C						PASS	.						103.0	100.0	101.0					21																	31661653		692	1590	2282	SO:0001819	synonymous_variant	100131902	exon1			TTGATTACCATAG		CCDS46640.1	21q22.1	2010-10-18	2008-02-26	2008-04-22	ENSG00000232263	ENSG00000232263		"""Keratin associated proteins"""	34003	protein-coding gene	gene with protein product							Standard	NM_001128598		Approved	KAP25.1	uc010glr.1	Q3LHN0	OTTHUMG00000125482	ENST00000416044.1:c.156T>C	21.37:g.31661653A>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	247	98	0.396761	NM_001128598		Silent	SNP	ENST00000416044.1	37	CCDS46640.1																																																																																			A|0.846;G|0.154	0.154	strong		0.408	KRTAP25-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246805.1	NM_001128598	
ZFYVE19	84936	hgsc.bcm.edu	37	15	41105979	41105979	+	Silent	SNP	C	C	G	rs116749518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41105979C>G	ENST00000355341.4	+	9	1680	c.1179C>G	c.(1177-1179)ccC>ccG	p.P393P	ZFYVE19_ENST00000336455.5_Silent_p.P383P|ZFYVE19_ENST00000564258.1_Silent_p.P218P|ZFYVE19_ENST00000570108.1_Silent_p.P370P|ZFYVE19_ENST00000299173.10_Silent_p.P325P	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	393					abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CTTCTCGACCCTGGACGCAAC	0.612													C|||	18	0.00359425	0.0136	0.0	5008	,	,		18843	0.0		0.0	False		,,,				2504	0.0				p.P393P		Atlas-SNP	.											.	ZFYVE19	31	.	0			c.C1179G						PASS	.	C		33,3971		1,31,1970	49.0	54.0	52.0		1179	1.1	0.0	15	dbSNP_132	52	1,8315		0,1,4157	no	coding-synonymous	ZFYVE19	NM_001077268.1		1,32,6127	GG,GC,CC		0.012,0.8242,0.276		393/472	41105979	34,12286	2002	4158	6160	SO:0001819	synonymous_variant	84936	exon9			TCGACCCTGGACG	AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"""Zinc fingers, FYVE domain containing"""	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.1179C>G	15.37:g.41105979C>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_001077268	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Silent	SNP	ENST00000355341.4	37	CCDS42025.1																																																																																			C|0.997;G|0.003	0.003	strong		0.612	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850	
BBS9	27241	hgsc.bcm.edu	37	7	33545253	33545253	+	Missense_Mutation	SNP	A	A	G	rs140882212		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:33545253A>G	ENST00000242067.6	+	20	2815	c.2294A>G	c.(2293-2295)gAa>gGa	p.E765G	BBS9_ENST00000354265.4_Missense_Mutation_p.E730G|BBS9_ENST00000396127.2_Missense_Mutation_p.E730G|BBS9_ENST00000355070.2_Missense_Mutation_p.E760G|BBS9_ENST00000350941.3_Missense_Mutation_p.E725G	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	765	Interaction with LZTL1.				cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			GACACTCAAGAATTGGTAAGG	0.468									Bardet-Biedl syndrome				A|||	1	0.000199681	0.0008	0.0	5008	,	,		17434	0.0		0.0	False		,,,				2504	0.0				p.E765G		Atlas-SNP	.											.	BBS9	194	.	0			c.A2294G						PASS	.	A	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	4,4402	6.2+/-15.9	0,4,2199	38.0	38.0	38.0		2189,2279,2174,2294	5.6	1.0	7	dbSNP_134	38	0,8600		0,0,4300	yes	missense,missense,missense,missense	BBS9	NM_001033604.1,NM_001033605.1,NM_014451.3,NM_198428.2	98,98,98,98	0,4,6499	GG,GA,AA		0.0,0.0908,0.0308	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	730/853,760/883,725/848,765/888	33545253	4,13002	2203	4300	6503	SO:0001583	missense	27241	exon20	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CTCAAGAATTGGT		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"""parathyroid hormone responsive B1 gene"""	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.2294A>G	7.37:g.33545253A>G	ENSP00000242067:p.Glu765Gly	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	59	34	0.576271	NM_198428	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Missense_Mutation	SNP	ENST00000242067.6	37	CCDS43566.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	16.89	3.246980	0.59103	9.08E-4	0.0	ENSG00000122507	ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132	T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38	5.61	5.61	0.85477	.	0.060219	0.64402	D	0.000004	T	0.24198	0.0586	L	0.46741	1.465	0.80722	D	1	P;P;D;P;P	0.54601	0.877;0.929;0.967;0.929;0.923	P;P;P;P;P	0.49252	0.501;0.501;0.604;0.501;0.501	T	0.00684	-1.1611	10	0.45353	T	0.12	-25.845	15.0016	0.71476	1.0:0.0:0.0:0.0	.	765;725;760;730;765	Q3SYG4-3;Q3SYG4-2;E9PDC9;Q3SYG4-4;Q3SYG4	.;.;.;.;PTHB1_HUMAN	G	765;725;730;760;730;765	ENSP00000242067:E765G;ENSP00000313122:E725G;ENSP00000379433:E730G;ENSP00000347182:E760G;ENSP00000346214:E730G	ENSP00000242067:E765G	E	+	2	0	BBS9	33511778	1.000000	0.71417	0.990000	0.47175	0.956000	0.61745	7.327000	0.79147	2.146000	0.66826	0.459000	0.35465	GAA	A|1.000;G|0.000	0.000	strong		0.468	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1		
CPT1B	1375	hgsc.bcm.edu	37	22	51009953	51009953	+	Missense_Mutation	SNP	C	C	T	rs470117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:51009953C>T	ENST00000360719.2	-	14	1728	c.1591G>A	c.(1591-1593)Gag>Aag	p.E531K	CPT1B_ENST00000440709.1_Missense_Mutation_p.E450K|CPT1B_ENST00000405237.3_Missense_Mutation_p.E531K|CPT1B_ENST00000312108.7_Missense_Mutation_p.E531K|CPT1B_ENST00000457250.1_Missense_Mutation_p.E497K|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000395650.2_Missense_Mutation_p.E531K|CPT1B_ENST00000434492.2_Missense_Mutation_p.E326K	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	531			E -> K (in dbSNP:rs470117). {ECO:0000269|PubMed:11258795, ECO:0000269|PubMed:14702039}.		carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		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)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		TAGGAACTCTCGATGACCGCC	0.577													C|||	1677	0.334864	0.0915	0.4352	5008	,	,		19631	0.4593		0.4602	False		,,,				2504	0.3354				p.E531K	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.G1591A	GRCh37	CM070885	CPT1B	M	rs470117	PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	689,3717	287.5+/-279.3	60,569,1574	109.0	95.0	100.0		1489,1591,1348,1591,1591,1591,1591	5.3	1.0	22	dbSNP_80	100	3935,4665	546.8+/-385.0	919,2097,1284	yes	missense,missense,missense,missense,missense,missense,missense	CPT1B	NM_001145134.1,NM_001145135.1,NM_001145136.1,NM_001145137.1,NM_004377.3,NM_152245.2,NM_152246.2	56,56,56,56,56,56,56	979,2666,2858	TT,TC,CC		45.7558,15.6378,35.5528	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	497/739,531/773,450/692,531/773,531/773,531/773,531/773	51009953	4624,8382	2203	4300	6503	SO:0001583	missense	1375	exon14			AACTCTCGATGAC	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.1591G>A	22.37:g.51009953C>T	ENSP00000353945:p.Glu531Lys	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	37	CCDS14098.1	821	0.3759157509157509	60	0.12195121951219512	154	0.425414364640884	267	0.46678321678321677	340	0.44854881266490765	C	17.42	3.385632	0.61956	0.156378	0.457558	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000440709;ENST00000434492;ENST00000395650	D;D;D;D;D;D;D	0.89050	-2.46;-2.46;-2.46;-2.46;-2.46;-2.46;-2.46	5.31	5.31	0.75309	.	0.048276	0.85682	D	0.000000	T	0.00012	0.0000	M	0.70903	2.155	0.09310	P	0.999999999303188	D;B;P	0.54397	0.966;0.159;0.683	P;B;B	0.46076	0.503;0.094;0.311	T	0.02301	-1.1180	9	0.41790	T	0.15	-28.5847	16.511	0.84284	0.0:1.0:0.0:0.0	rs470117;rs17848465;rs60919458;rs470117	450;497;531	E9PCP2;B7Z4U4;Q92523	.;.;CPT1B_HUMAN	K	531;531;531;497;450;326;531	ENSP00000385486:E531K;ENSP00000312189:E531K;ENSP00000353945:E531K;ENSP00000409342:E497K;ENSP00000414713:E450K;ENSP00000410966:E326K;ENSP00000379011:E531K	ENSP00000312189:E531K	E	-	1	0	CPT1B	49356819	1.000000	0.71417	0.993000	0.49108	0.408000	0.30992	2.827000	0.48112	2.768000	0.95171	0.561000	0.74099	GAG	C|0.649;T|0.351	0.351	strong		0.577	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246	
XYLT2	64132	hgsc.bcm.edu	37	17	48434008	48434008	+	Missense_Mutation	SNP	C	C	T	rs151294421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48434008C>T	ENST00000017003.2	+	8	1668	c.1619C>T	c.(1618-1620)aCc>aTc	p.T540I	XYLT2_ENST00000507602.1_Missense_Mutation_p.T540I	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	540					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)					TGGGAGAACACCTACGACGCG	0.627													C|||	21	0.00419329	0.0129	0.0043	5008	,	,		16601	0.0		0.0	False		,,,				2504	0.001				p.T540I		Atlas-SNP	.											.	XYLT2	51	.	0			c.C1619T						PASS	.	C	ILE/THR	52,4354	51.6+/-87.1	0,52,2151	67.0	71.0	70.0		1619	-0.0	0.6	17	dbSNP_134	70	0,8600		0,0,4300	yes	missense	XYLT2	NM_022167.2	89	0,52,6451	TT,TC,CC		0.0,1.1802,0.3998	benign	540/866	48434008	52,12954	2203	4300	6503	SO:0001583	missense	64132	exon8			AGAACACCTACGA	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.1619C>T	17.37:g.48434008C>T	ENSP00000017003:p.Thr540Ile	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	21	9	0.428571	NM_022167	Q6UY41|Q86V00	Missense_Mutation	SNP	ENST00000017003.2	37	CCDS11563.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	1.807	-0.475727	0.04414	0.011802	0.0	ENSG00000015532	ENST00000017003;ENST00000507602	T;T	0.38077	1.16;1.16	4.89	-0.0431	0.13861	.	0.659654	0.15078	N	0.281852	T	0.09730	0.0239	N	0.03608	-0.345	0.24112	N	0.995837	B	0.02656	0.0	B	0.04013	0.001	T	0.29792	-1.0000	10	0.15952	T	0.53	-8.2731	9.014	0.36159	0.0:0.3312:0.0:0.6688	.	540	Q9H1B5	XYLT2_HUMAN	I	540	ENSP00000017003:T540I;ENSP00000426501:T540I	ENSP00000017003:T540I	T	+	2	0	XYLT2	45789007	0.101000	0.21875	0.586000	0.28679	0.021000	0.10359	1.227000	0.32576	0.116000	0.18110	-0.253000	0.11424	ACC	C|0.996;T|0.004	0.004	strong		0.627	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19126578	19126578	+	Silent	SNP	T	T	C	rs114869688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19126578T>C	ENST00000381440.3	+	1	1325	c.795T>C	c.(793-795)acT>acC	p.T265T	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	265						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						CCTTGGCCACTGTGCGTTACA	0.642											OREG0023657	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	16	0.00319489	0.0121	0.0	5008	,	,		17325	0.0		0.0	False		,,,				2504	0.0				p.T265T		Atlas-SNP	.											ITPRIPL2,colon,carcinoma,+1,1	ITPRIPL2	40	1	0			c.T795C						PASS	.	T		72,4322	63.5+/-100.7	0,72,2125	94.0	95.0	95.0		795	-9.6	0.3	16	dbSNP_132	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITPRIPL2	NM_001034841.3		0,73,6424	CC,CT,TT		0.0116,1.6386,0.5618		265/536	19126578	73,12921	2197	4300	6497	SO:0001819	synonymous_variant	162073	exon1			GGCCACTGTGCGT		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"""inositol 1,4,5-triphosphate receptor interacting protein-like 2"""				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.795T>C	16.37:g.19126578T>C		Somatic	106	0	0	730	WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_001034841		Silent	SNP	ENST00000381440.3	37	CCDS32395.1																																																																																			T|0.995;C|0.005	0.005	strong		0.642	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	NM_001034841	
KRT14	3861	hgsc.bcm.edu	37	17	39742807	39742807	+	Missense_Mutation	SNP	C	C	T	rs3826550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39742807C>T	ENST00000167586.6	-	1	366	c.280G>A	c.(280-282)Gct>Act	p.A94T		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	94	Head.		A -> T (in dbSNP:rs3826550). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9989794, ECO:0000269|Ref.3}.		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)				cccaagccagcaccaaggcca	0.632													C|||	1456	0.290735	0.4153	0.2709	5008	,	,		15358	0.0575		0.4145	False		,,,				2504	0.2495				p.A94T		Atlas-SNP	.											.	KRT14	65	.	0			c.G280A						PASS	.						125.0	126.0	126.0					17																	39742807		2203	4300	6503	SO:0001583	missense	3861	exon1			AGCCAGCACCAAG	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.280G>A	17.37:g.39742807C>T	ENSP00000167586:p.Ala94Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Missense_Mutation	SNP	ENST00000167586.6	37	CCDS11400.1	654	0.29945054945054944	202	0.4105691056910569	110	0.30386740331491713	27	0.0472027972027972	315	0.4155672823218997	C	6.698	0.497409	0.12762	.	.	ENSG00000186847	ENST00000167586	D	0.89415	-2.51	5.11	5.11	0.69529	.	0.845655	0.10115	N	0.714173	T	0.00012	0.0000	L	0.58101	1.795	0.46654	P	8.550000000000502E-4	B	0.20780	0.048	B	0.27500	0.08	T	0.08289	-1.0729	9	0.22706	T	0.39	.	14.2293	0.65879	0.0:0.9257:0.0:0.0743	rs3826550;rs17497944;rs17855365;rs17855479;rs3826550	94	P02533	K1C14_HUMAN	T	94	ENSP00000167586:A94T	ENSP00000167586:A94T	A	-	1	0	KRT14	36996333	0.000000	0.05858	0.725000	0.30721	0.013000	0.08279	0.065000	0.14466	2.541000	0.85698	0.549000	0.68633	GCT	C|0.705;T|0.295	0.295	strong		0.632	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
VRK2	7444	hgsc.bcm.edu	37	2	58350340	58350340	+	Silent	SNP	T	T	C	rs17049354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:58350340T>C	ENST00000435505.2	+	11	1393	c.648T>C	c.(646-648)ttT>ttC	p.F216F	VRK2_ENST00000417641.2_Silent_p.F216F|VRK2_ENST00000412104.2_Silent_p.F216F|VRK2_ENST00000440705.2_Silent_p.F193F|VRK2_ENST00000340157.4_Silent_p.F216F			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	216	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						CAATAGAGTTTACCAGCTTGG	0.388													T|||	210	0.0419329	0.152	0.0115	5008	,	,		18926	0.0		0.001	False		,,,				2504	0.0				p.F216F		Atlas-SNP	.											.	VRK2	46	.	0			c.T648C						PASS	.	T	,,,,	501,3905	232.3+/-245.9	34,433,1736	108.0	105.0	106.0		648,648,579,648,648	1.8	1.0	2	dbSNP_123	106	8,8592	4.3+/-15.6	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VRK2	NM_001130480.2,NM_001130481.2,NM_001130482.2,NM_001130483.2,NM_006296.5	,,,,	34,441,6028	CC,CT,TT		0.093,11.3709,3.9136	,,,,	216/509,216/509,193/486,216/397,216/509	58350340	509,12497	2203	4300	6503	SO:0001819	synonymous_variant	7444	exon8			AGAGTTTACCAGC	AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.648T>C	2.37:g.58350340T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_001130480	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Silent	SNP	ENST00000435505.2	37	CCDS1859.1																																																																																			T|0.962;C|0.038	0.038	strong		0.388	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296	
OR5B3	441608	hgsc.bcm.edu	37	11	58170143	58170143	+	Missense_Mutation	SNP	C	C	G	rs11229409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58170143C>G	ENST00000309403.2	-	1	739	c.740G>C	c.(739-741)gGc>gCc	p.G247A		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	247			G -> A (in dbSNP:rs11229409).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G247A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ATAGAAGATGCCGACTGCAAT	0.428													G|||	1453	0.290136	0.3533	0.2695	5008	,	,		22285	0.1448		0.3628	False		,,,				2504	0.2945				p.G247A		Atlas-SNP	.											OR5B3,colon,carcinoma,-1,2	OR5B3	65	2	1	Substitution - Missense(1)	stomach(1)	c.G740C						scavenged	.	G	ALA/GLY	1442,2960	681.5+/-404.0	229,984,988	88.0	88.0	88.0		740	4.1	0.8	11	dbSNP_120	88	3093,5497	658.3+/-401.6	549,1995,1751	yes	missense	OR5B3	NM_001005469.1	60	778,2979,2739	GG,GC,CC		36.007,32.7578,34.9061	benign	247/315	58170143	4535,8457	2201	4295	6496	SO:0001583	missense	441608	exon1			AAGATGCCGACTG	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.740G>C	11.37:g.58170143C>G	ENSP00000308270:p.Gly247Ala	Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	655	0.2999084249084249	195	0.39634146341463417	89	0.24585635359116023	95	0.1660839160839161	276	0.3641160949868074	g	4.175	0.031006	0.08101	0.327578	0.36007	ENSG00000172769	ENST00000309403	T	0.35789	1.29	4.05	4.05	0.47172	GPCR, rhodopsin-like superfamily (1);	0.290390	0.25050	N	0.033521	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	0.44892	-0.9298	9	0.33141	T	0.24	-22.6339	6.9802	0.24698	0.096:0.1787:0.7253:0.0	rs11229409;rs52829287;rs60600384;rs11229409	247	Q8NH48	OR5B3_HUMAN	A	247	ENSP00000308270:G247A	ENSP00000308270:G247A	G	-	2	0	OR5B3	57926719	0.000000	0.05858	0.764000	0.31436	0.106000	0.19336	0.063000	0.14410	1.070000	0.40811	-0.127000	0.14921	GGC	C|0.674;G|0.326	0.326	strong		0.428	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
DCPS	28960	hgsc.bcm.edu	37	11	126174164	126174164	+	Silent	SNP	C	C	T	rs695029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:126174164C>T	ENST00000263579.4	+	1	518	c.189C>T	c.(187-189)ttC>ttT	p.F63F	RP11-712L6.5_ENST00000524964.1_5'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	63					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)		AAATCATTTTCCTACACGGGA	0.547													C|||	1531	0.305711	0.0749	0.3905	5008	,	,		17744	0.624		0.2008	False		,,,				2504	0.3374				p.F63F		Atlas-SNP	.											DCPS,NS,carcinoma,+2,1	DCPS	33	1	0			c.C189T						PASS	.	C		466,3936	218.1+/-236.3	26,414,1761	72.0	71.0	71.0		189	3.8	0.9	11	dbSNP_83	71	1723,6873	311.4+/-310.3	160,1403,2735	no	coding-synonymous	DCPS	NM_014026.3		186,1817,4496	TT,TC,CC		20.0442,10.5861,16.8411		63/338	126174164	2189,10809	2201	4298	6499	SO:0001819	synonymous_variant	28960	exon1			CATTTTCCTACAC	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.189C>T	11.37:g.126174164C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	53	0.540816	NM_014026	Q8NHL8|Q9Y2S5	Silent	SNP	ENST00000263579.4	37	CCDS8473.1																																																																																			C|0.772;T|0.228	0.228	strong		0.547	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
FGF12	2257	hgsc.bcm.edu	37	3	192078253	192078253	+	Missense_Mutation	SNP	T	T	C	rs142373936		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:192078253T>C	ENST00000454309.2	-	2	1099	c.274A>G	c.(274-276)Acc>Gcc	p.T92A	FGF12_ENST00000264730.3_Missense_Mutation_p.T30A|FGF12_ENST00000445105.2_Missense_Mutation_p.T30A|FGF12_ENST00000430714.1_Intron|FGF12_ENST00000450716.1_Missense_Mutation_p.T30A	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12	92					adult locomotory behavior (GO:0008344)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell-cell signaling (GO:0007267)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|JNK cascade (GO:0007254)|negative regulation of cation channel activity (GO:2001258)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|regulation of membrane depolarization (GO:0003254)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)			endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		CCATCAATGGTACCATCTGGG	0.408													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19416	0.0		0.0	False		,,,				2504	0.0				p.T92A		Atlas-SNP	.											.	FGF12	88	.	0			c.A274G						PASS	.	T	ALA/THR,ALA/THR	1,4405	2.1+/-5.4	0,1,2202	176.0	150.0	159.0		88,274	3.0	1.0	3	dbSNP_134	159	0,8600		0,0,4300	no	missense,missense	FGF12	NM_004113.5,NM_021032.4	58,58	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign	30/182,92/244	192078253	1,13005	2203	4300	6503	SO:0001583	missense	2257	exon2			CAATGGTACCATC	U66197	CCDS3301.1, CCDS46983.1	3q28	2008-07-18			ENSG00000114279	ENSG00000114279			3668	protein-coding gene	gene with protein product	"""fibroblast growth factor 12B"", ""fibroblast growth factor homologous factor 1"", ""myocyte-activating factor"", ""fibroblast growth factor FGF-12b"""	601513		FGF12B		8790420, 9345906	Standard	NM_021032		Approved	FHF1	uc003fsx.3	P61328	OTTHUMG00000156132	ENST00000454309.2:c.274A>G	3.37:g.192078253T>C	ENSP00000413496:p.Thr92Ala	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	213	92	0.431925	NM_021032	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Missense_Mutation	SNP	ENST00000454309.2	37	CCDS3301.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	13.05	2.121112	0.37436	2.27E-4	0.0	ENSG00000114279	ENST00000264730;ENST00000392454;ENST00000445105;ENST00000454309;ENST00000450716;ENST00000448795;ENST00000418610	D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	5.53	3.03	0.35002	.	0.136032	0.64402	N	0.000002	T	0.70657	0.3249	L	0.48935	1.535	0.47441	D	0.999428	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.64846	-0.6311	10	0.42905	T	0.14	.	6.4797	0.22055	0.1389:0.0758:0.0:0.7853	.	30;92	P61328-2;P61328	.;FGF12_HUMAN	A	30;30;30;92;30;6;30	ENSP00000264730:T30A;ENSP00000393686:T30A;ENSP00000413496:T92A;ENSP00000397635:T30A;ENSP00000412904:T6A;ENSP00000395517:T30A	ENSP00000264730:T30A	T	-	1	0	FGF12	193560947	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.860000	0.39428	0.953000	0.37825	0.482000	0.46254	ACC	T|1.000;C|0.000	0.000	strong		0.408	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032	
C17orf97	400566	hgsc.bcm.edu	37	17	263657	263657	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:263657C>T	ENST00000360127.6	+	2	1039	c.1023C>T	c.(1021-1023)gcC>gcT	p.A341A	C17orf97_ENST00000571106.1_Intron|AC108004.3_ENST00000466740.2_RNA	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	371	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.							p.A341A(2)		breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						ACCCCGAGGCCCTCAAGGGCT	0.697																																					p.A341A		Atlas-SNP	.											C17orf97_ENST00000360127,NS,carcinoma,0,2	C17orf97	76	2	2	Substitution - coding silent(2)	lung(2)	c.C1023T						scavenged	.						10.0	16.0	14.0					17																	263657		1853	3854	5707	SO:0001819	synonymous_variant	400566	exon2			CGAGGCCCTCAAG	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.1023C>T	17.37:g.263657C>T		Somatic	309	2	0.00647249		WXS	Illumina HiSeq	Phase_I	329	4	0.0121581	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Silent	SNP	ENST00000360127.6	37	CCDS32519.2																																																																																			.	.	none		0.697	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
C2orf54	79919	hgsc.bcm.edu	37	2	241828012	241828012	+	Silent	SNP	T	T	C	rs6708304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	97	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	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	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48601454	48601454	+	Silent	SNP	T	T	C	rs251684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48601454T>C	ENST00000599921.1	-	6	867	c.510A>G	c.(508-510)ccA>ccG	p.P170P	PLA2G4C_ENST00000413144.2_Silent_p.P170P|PLA2G4C_ENST00000599111.1_Silent_p.P180P|PLA2G4C_ENST00000354276.3_Silent_p.P170P			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	170	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				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)		CTGCAAATATTGGGTAGGGTA	0.517													C|||	3325	0.663938	0.7179	0.6441	5008	,	,		20639	0.7411		0.6083	False		,,,				2504	0.5828				p.P180P		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.A540G						PASS	.	C	,,	3063,1343	450.4+/-349.3	1063,937,203	150.0	123.0	132.0		540,510,510	-5.8	0.9	19	dbSNP_79	132	5410,3190	483.4+/-371.1	1704,2002,594	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	,,	2767,2939,797	CC,CT,TT		37.093,30.4812,34.8531	,,	180/552,170/528,170/542	48601454	8473,4533	2203	4300	6503	SO:0001819	synonymous_variant	8605	exon6			AAATATTGGGTAG	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.510A>G	19.37:g.48601454T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	181	85	0.469613	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Silent	SNP	ENST00000599921.1	37	CCDS12710.1																																																																																			T|0.337;C|0.663	0.663	strong		0.517	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110491801	110491801	+	Silent	SNP	T	T	C	rs116618272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110491801T>C	ENST00000378402.5	+	54	9215	c.9111T>C	c.(9109-9111)ttT>ttC	p.F3037F		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3037	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ATGATTCTTTTTGGCAATCAT	0.328										HNSCC(38;0.096)			T|||	39	0.00778754	0.0287	0.0014	5008	,	,		20916	0.0		0.0	False		,,,				2504	0.0				p.F3037F		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T9111C						PASS	.	T		56,3594		1,54,1770	127.0	111.0	116.0		9111	-2.1	1.0	8	dbSNP_132	116	0,8152		0,0,4076	no	coding-synonymous	PKHD1L1	NM_177531.4		1,54,5846	CC,CT,TT		0.0,1.5342,0.4745		3037/4244	110491801	56,11746	1825	4076	5901	SO:0001819	synonymous_variant	93035	exon54			TTCTTTTTGGCAA	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.9111T>C	8.37:g.110491801T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			T|0.993;C|0.007	0.007	strong		0.328	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383351	39383351	+	Missense_Mutation	SNP	T	T	C	rs146532415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39383351T>C	ENST00000377721.3	+	1	452	c.445T>C	c.(445-447)Tgc>Cgc	p.C149R	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.C133R	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	149	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CCGCCCAGCCTGCTGTGAGAC	0.607													.|||	58	0.0115815	0.0424	0.0029	5008	,	,		19288	0.0		0.0	False		,,,				2504	0.0				p.C149R		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.T445C						PASS	.	T	ARG/CYS	126,4166		3,120,2023	19.0	21.0	20.0		445	1.8	0.0	17	dbSNP_134	20	0,8406		0,0,4203	no	missense	KRTAP9-2	NM_031961.2	180	3,120,6226	CC,CT,TT		0.0,2.9357,0.9923	probably-damaging	149/175	39383351	126,12572	2146	4203	6349	SO:0001583	missense	83899	exon1			CCAGCCTGCTGTG	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.445T>C	17.37:g.39383351T>C	ENSP00000366950:p.Cys149Arg	Somatic	336	1	0.00297619		WXS	Illumina HiSeq	Phase_I	400	149	0.3725	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	19.02	3.746233	0.69418	0.029357	0.0	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.05139	4.92;3.49	2.89	1.78	0.24846	.	.	.	.	.	T	0.02649	0.0080	M	0.74389	2.26	0.52501	D	0.999959	B	0.25904	0.137	B	0.23852	0.049	T	0.08806	-1.0704	9	0.87932	D	0	.	6.5335	0.22339	0.0:0.1318:0.0:0.8682	.	149	Q9BYQ4	KRA92_HUMAN	R	149;133	ENSP00000366950:C149R;ENSP00000398325:C133R	ENSP00000366950:C149R	C	+	1	0	KRTAP9-2	36636877	0.403000	0.25319	0.010000	0.14722	0.911000	0.54048	0.513000	0.22770	0.325000	0.23359	0.248000	0.18094	TGC	T|0.993;C|0.007	0.007	strong		0.607	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
AADAC	13	hgsc.bcm.edu	37	3	151545601	151545601	+	Missense_Mutation	SNP	G	G	A	rs1803155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151545601G>A	ENST00000232892.7	+	5	967	c.841G>A	c.(841-843)Gtt>Att	p.V281I	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	281			V -> I (in alleles AADAC*2 and AADAC*3; mildly decreased enzyme activity; dbSNP:rs1803155). {ECO:0000269|PubMed:12721789, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:22415931, ECO:0000269|PubMed:8063807, ECO:0000269|Ref.4}.		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)			CTTCAAATTTGTTAATTGGAG	0.378													G|||	3678	0.734425	0.7731	0.7522	5008	,	,		18459	0.5774		0.7674	False		,,,				2504	0.7975				p.V281I	Ovarian(30;839 841 2699 32801 46334)	Atlas-SNP	.											.	AADAC	49	.	0			c.G841A						PASS	.	G	ILE/VAL	3367,1039	706.3+/-407.4	1274,819,110	57.0	60.0	59.0		841	3.9	0.9	3	dbSNP_89	59	6750,1846	716.5+/-406.1	2657,1436,205	yes	missense	AADAC	NM_001086.2	29	3931,2255,315	AA,AG,GG		21.4751,23.5815,22.1889	possibly-damaging	281/400	151545601	10117,2885	2203	4298	6501	SO:0001583	missense	13	exon5			AAATTTGTTAATT	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.841G>A	3.37:g.151545601G>A	ENSP00000232892:p.Val281Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_001086	A8K3L3|D3DNJ6|Q8N1A9	Missense_Mutation	SNP	ENST00000232892.7	37	CCDS33877.1	1548	0.7087912087912088	380	0.7723577235772358	259	0.7154696132596685	322	0.5629370629370629	587	0.7744063324538258	G	16.66	3.183921	0.57800	0.764185	0.785249	ENSG00000114771	ENST00000232892	T	0.58210	0.35	4.81	3.94	0.45596	.	0.057250	0.64402	N	0.000002	T	0.00012	0.0000	L	0.60957	1.885	0.09310	P	1.0	P	0.40553	0.721	B	0.37144	0.242	T	0.17107	-1.0380	9	0.35671	T	0.21	-7.2416	12.9254	0.58257	0.0794:0.0:0.9206:0.0	rs1803155;rs3732547;rs52798024;rs56910669;rs1803155	281	P22760	AAAD_HUMAN	I	281	ENSP00000232892:V281I	ENSP00000232892:V281I	V	+	1	0	AADAC	153028291	1.000000	0.71417	0.856000	0.33681	0.995000	0.86356	3.772000	0.55325	1.006000	0.39211	0.591000	0.81541	GTT	G|0.250;A|0.750	0.750	strong		0.378	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086	
IFNAR1	3454	hgsc.bcm.edu	37	21	34715699	34715699	+	Missense_Mutation	SNP	G	G	C	rs2257167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:34715699G>C	ENST00000270139.3	+	4	654	c.502G>C	c.(502-504)Gtt>Ctt	p.V168L	IFNAR1_ENST00000442357.2_Missense_Mutation_p.V168L|IFNAR1_ENST00000416947.2_Missense_Mutation_p.V99L	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	168	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> L (in dbSNP:rs2257167). {ECO:0000269|PubMed:1370833, ECO:0000269|PubMed:2153461, ECO:0000269|Ref.4}.		cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""""""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)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	ATATAGCTTAGTTATCTGGAA	0.338													G|||	1146	0.228834	0.1626	0.2233	5008	,	,		18559	0.377		0.1292	False		,,,				2504	0.272				p.V168L	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											.	IFNAR1	44	.	0			c.G502C	GRCh37	CM035835	IFNAR1	M	rs2257167	PASS	.	G	LEU/VAL	701,3705	291.0+/-281.2	61,579,1563	140.0	149.0	146.0		502	0.8	0.0	21	dbSNP_100	146	1159,7441	237.1+/-269.0	61,1037,3202	yes	missense	IFNAR1	NM_000629.2	32	122,1616,4765	CC,CG,GG		13.4767,15.9101,14.3011	benign	168/558	34715699	1860,11146	2203	4300	6503	SO:0001583	missense	3454	exon4			AGCTTAGTTATCT		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"""Interferons"""	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.502G>C	21.37:g.34715699G>C	ENSP00000270139:p.Val168Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Missense_Mutation	SNP	ENST00000270139.3	37	CCDS13624.1	455	0.20833333333333334	71	0.1443089430894309	84	0.23204419889502761	202	0.3531468531468531	98	0.12928759894459102	G	15.93	2.977718	0.53720	0.159101	0.134767	ENSG00000142166	ENST00000416947;ENST00000270139;ENST00000442357	T;T;T	0.28666	1.6;1.6;1.6	5.86	0.838	0.18902	Fibronectin, type III (2);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	1.095030	0.06767	N	0.782750	T	0.00012	0.0000	L	0.46741	1.465	0.80722	P	0.0	P	0.41748	0.761	P	0.45474	0.482	T	0.28459	-1.0043	9	0.08381	T	0.77	-3.6636	4.8545	0.13552	0.3252:0.16:0.5148:0.0	rs2257167;rs17875817;rs52830923;rs2257167	168	P17181	INAR1_HUMAN	L	99;168;168	ENSP00000395606:V99L;ENSP00000270139:V168L;ENSP00000407406:V168L	ENSP00000270139:V168L	V	+	1	0	IFNAR1	33637569	0.000000	0.05858	0.000000	0.03702	0.374000	0.29953	0.111000	0.15458	0.360000	0.24265	0.650000	0.86243	GTT	G|0.831;C|0.169	0.169	strong		0.338	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		
COL5A3	50509	hgsc.bcm.edu	37	19	10071347	10071347	+	Missense_Mutation	SNP	C	C	T	rs2277969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10071347C>T	ENST00000264828.3	-	66	5156	c.5071G>A	c.(5071-5073)Gtc>Atc	p.V1691I		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1691	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.		V -> I (in dbSNP:rs2277969).		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)			TCCTGGGGGACGCTGACAGTG	0.627													C|||	1267	0.252995	0.385	0.2853	5008	,	,		17190	0.1091		0.1889	False		,,,				2504	0.2658				p.V1691I		Atlas-SNP	.											.	COL5A3	243	.	0			c.G5071A						PASS	.	C	ILE/VAL	1505,2901	476.6+/-357.7	230,1045,928	64.0	65.0	65.0		5071	1.8	0.4	19	dbSNP_100	65	1632,6968	300.4+/-304.9	139,1354,2807	yes	missense	COL5A3	NM_015719.3	29	369,2399,3735	TT,TC,CC		18.9767,34.158,24.1196	benign	1691/1746	10071347	3137,9869	2203	4300	6503	SO:0001583	missense	50509	exon66			GGGGGACGCTGAC	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.5071G>A	19.37:g.10071347C>T	ENSP00000264828:p.Val1691Ile	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	469	0.21474358974358973	176	0.35772357723577236	89	0.24585635359116023	59	0.10314685314685315	145	0.19129287598944592	C	10.12	1.262374	0.23051	0.34158	0.189767	ENSG00000080573	ENST00000264828	T	0.75704	-0.96	4.03	1.81	0.25067	Fibrillar collagen, C-terminal (4);	0.297436	0.26213	U	0.025666	T	0.00012	0.0000	L	0.46157	1.445	0.52501	P	4.300000000001525E-5	B	0.15930	0.015	B	0.10450	0.005	T	0.17684	-1.0361	9	0.41790	T	0.15	.	8.4159	0.32670	0.0:0.7959:0.0:0.2041	rs2277969;rs3207622;rs59814308;rs2277969	1691	P25940	CO5A3_HUMAN	I	1691	ENSP00000264828:V1691I	ENSP00000264828:V1691I	V	-	1	0	COL5A3	9932347	0.747000	0.28283	0.354000	0.25760	0.078000	0.17371	1.637000	0.37155	0.917000	0.36895	0.462000	0.41574	GTC	C|0.770;T|0.230	0.230	strong		0.627	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
CSF2RB	1439	hgsc.bcm.edu	37	22	37326443	37326443	+	Missense_Mutation	SNP	G	G	C	rs16845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37326443G>C	ENST00000403662.3	+	7	967	c.745G>C	c.(745-747)Gag>Cag	p.E249Q	CSF2RB_ENST00000262825.5_Missense_Mutation_p.E249Q|CSF2RB_ENST00000406230.1_Missense_Mutation_p.E249Q|CSF2RB_ENST00000536485.1_Missense_Mutation_p.E190Q			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	249			E -> Q (in dbSNP:rs16845).		cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	CCAGAACCTGGAGTGCTTCTT	0.622													C|||	521	0.104034	0.2148	0.0476	5008	,	,		18469	0.004		0.0477	False		,,,				2504	0.1554				p.E249Q		Atlas-SNP	.											.	CSF2RB	104	.	0			c.G745C						PASS	.	C	GLN/GLU	934,3472	735.2+/-410.7	93,748,1362	106.0	106.0	106.0		745	5.0	1.0	22	dbSNP_60	106	468,8132	797.6+/-407.4	7,454,3839	yes	missense	CSF2RB	NM_000395.2	29	100,1202,5201	CC,CG,GG		5.4419,21.1984,10.7796	benign	249/898	37326443	1402,11604	2203	4300	6503	SO:0001583	missense	1439	exon7			AACCTGGAGTGCT	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.745G>C	22.37:g.37326443G>C	ENSP00000384053:p.Glu249Gln	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	37	CCDS13936.1	177	0.08104395604395605	120	0.24390243902439024	18	0.049723756906077346	4	0.006993006993006993	35	0.04617414248021108	C	6.917	0.538836	0.13250	0.211984	0.054419	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000421539;ENST00000536485	T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07	5.04	5.04	0.67666	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.174780	0.28360	N	0.015633	T	0.00012	0.0000	N	0.00063	-2.32	0.52501	P	4.999999999999449E-5	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.22695	-1.0209	9	0.02654	T	1	-18.811	13.2198	0.59881	0.0:0.8396:0.1604:0.0	rs16845;rs2228091;rs17402640;rs16845	249;249	P32927-2;P32927	.;IL3RB_HUMAN	Q	249;249;249;249;169;190	ENSP00000384053:E249Q;ENSP00000262825:E249Q;ENSP00000385271:E249Q;ENSP00000393585:E169Q;ENSP00000440003:E190Q	ENSP00000262825:E249Q	E	+	1	0	CSF2RB	35656389	0.905000	0.30787	0.986000	0.45419	0.953000	0.61014	1.340000	0.33896	1.255000	0.44051	-0.322000	0.08575	GAG	G|0.901;C|0.099	0.099	strong		0.622	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
EPHA10	284656	hgsc.bcm.edu	37	1	38186189	38186189	+	Missense_Mutation	SNP	C	C	T	rs6671088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38186189C>T	ENST00000373048.4	-	13	2245	c.2246G>A	c.(2245-2247)gGg>gAg	p.G749E	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000427468.2_Missense_Mutation_p.G749E|EPHA10_ENST00000330210.7_Missense_Mutation_p.G244E|EPHA10_ENST00000540011.1_3'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	749	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		G -> E (in dbSNP:rs6671088).		ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGGCAGCAACCCCATCAGTTG	0.632													C|||	561	0.112021	0.1785	0.0879	5008	,	,		17125	0.001		0.1551	False		,,,				2504	0.1094				p.G749E		Atlas-SNP	.											EPHA10,NS,carcinoma,0,2	EPHA10	120	2	0			c.G2246A						PASS	.	C	GLU/GLY	729,3437		60,609,1414	20.0	25.0	23.0		2246	4.0	1.0	1	dbSNP_116	23	1367,7027		112,1143,2942	yes	missense	EPHA10	NM_001099439.1	98	172,1752,4356	TT,TC,CC		16.2854,17.4988,16.6879	probably-damaging	749/1009	38186189	2096,10464	2083	4197	6280	SO:0001583	missense	284656	exon13			AGCAACCCCATCA	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2246G>A	1.37:g.38186189C>T	ENSP00000362139:p.Gly749Glu	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	257	109	0.424125	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	238	0.10897435897435898	88	0.17886178861788618	36	0.09944751381215469	0	0.0	114	0.1503957783641161	C	20.3	3.971582	0.74246	0.174988	0.162854	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000373048	D;D;D	0.81739	-1.53;-1.53;-1.53	4.93	4.0	0.46444	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38111	N	0.001809	T	0.00300	0.0009	N	0.20530	0.585	0.09310	P	0.9999999999999999	P	0.46277	0.875	B	0.40477	0.33	T	0.30592	-0.9973	9	0.87932	D	0	.	14.3163	0.66452	0.0:0.7191:0.2809:0.0	rs6671088;rs59740185;rs6671088	749	Q5JZY3	EPHAA_HUMAN	E	244;749;749	ENSP00000330379:G244E;ENSP00000397746:G749E;ENSP00000362139:G749E	ENSP00000330379:G244E	G	-	2	0	EPHA10	37958776	0.964000	0.33143	0.990000	0.47175	0.974000	0.67602	2.038000	0.41184	1.059000	0.40554	0.467000	0.42956	GGG	C|0.875;T|0.125	0.125	strong		0.632	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
CATSPER1	117144	hgsc.bcm.edu	37	11	65787666	65787666	+	Silent	SNP	G	G	A	rs34769321|rs3829937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65787666G>A	ENST00000312106.5	-	9	2207	c.2070C>T	c.(2068-2070)gcC>gcT	p.A690A		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	690					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						GGATCCGGGCGGCCCTCTGGG	0.662													G|||	814	0.16254	0.2065	0.1254	5008	,	,		15119	0.1181		0.16	False		,,,				2504	0.1779				p.A690A		Atlas-SNP	.											.	CATSPER1	101	.	0			c.C2070T						PASS	.	G		904,3498	344.9+/-308.3	95,714,1392	43.0	45.0	44.0		2070	-9.2	0.0	11	dbSNP_107	44	1331,7261	257.5+/-281.5	102,1127,3067	no	coding-synonymous	CATSPER1	NM_053054.3		197,1841,4459	AA,AG,GG		15.4912,20.5361,17.2002		690/781	65787666	2235,10759	2201	4296	6497	SO:0001819	synonymous_variant	117144	exon9			CCGGGCGGCCCTC	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.2070C>T	11.37:g.65787666G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	144	58	0.402778	NM_053054	Q96P76	Silent	SNP	ENST00000312106.5	37	CCDS8127.1																																																																																			G|0.834;A|0.166	0.166	strong		0.662	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
RBM19	9904	hgsc.bcm.edu	37	12	114377877	114377877	+	Missense_Mutation	SNP	T	T	C	rs2290789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114377877T>C	ENST00000545145.2	-	15	1904	c.1826A>G	c.(1825-1827)cAt>cGt	p.H609R	RBM19_ENST00000392561.3_Missense_Mutation_p.H609R|RBM19_ENST00000261741.5_Missense_Mutation_p.H609R|RP11-780K2.1_ENST00000550206.1_RNA	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	609	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.		H -> R (in dbSNP:rs2290789). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GCTGCCAAAATGGCCGAAGGT	0.642													C|||	996	0.198882	0.3464	0.0764	5008	,	,		17496	0.1885		0.1133	False		,,,				2504	0.1851				p.H609R		Atlas-SNP	.											.	RBM19	117	.	0			c.A1826G						PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS	1442,2964	676.6+/-403.3	255,932,1016	63.0	69.0	67.0		1826,1826,1826	0.2	0.0	12	dbSNP_100	67	886,7714	776.2+/-407.7	38,810,3452	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	29,29,29	293,1742,4468	CC,CT,TT		10.3023,32.7281,17.8994	benign,benign,benign	609/961,609/961,609/961	114377877	2328,10678	2203	4300	6503	SO:0001583	missense	9904	exon15			CCAAAATGGCCGA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1826A>G	12.37:g.114377877T>C	ENSP00000442053:p.His609Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	362	0.16575091575091574	147	0.29878048780487804	27	0.07458563535911603	102	0.17832167832167833	86	0.11345646437994723	C	0	-2.782507	0.00079	0.327281	0.103023	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05319	3.46;3.46;3.46	4.29	0.25	0.15535	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.381500	0.26387	N	0.024675	T	0.00012	0.0000	N	0.00280	-1.71	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40961	-0.9535	9	0.05833	T	0.94	-0.08	6.9575	0.24580	0.0:0.4211:0.1156:0.4633	rs2290789;rs17856105;rs17856174;rs2290789	609	Q9Y4C8	RBM19_HUMAN	R	609	ENSP00000442053:H609R;ENSP00000376344:H609R;ENSP00000261741:H609R	ENSP00000261741:H609R	H	-	2	0	RBM19	112862260	0.437000	0.25593	0.025000	0.17156	0.040000	0.13550	0.866000	0.27954	-0.236000	0.09753	-1.007000	0.02485	CAT	T|0.830;C|0.170	0.170	strong		0.642	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
CRYZ	1429	hgsc.bcm.edu	37	1	75175865	75175865	+	Missense_Mutation	SNP	C	C	T	rs17095822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:75175865C>T	ENST00000340866.5	-	6	634	c.547G>A	c.(547-549)Gag>Aag	p.E183K	CRYZ_ENST00000492102.1_5'Flank|CRYZ_ENST00000370871.3_Missense_Mutation_p.E183K|CRYZ_ENST00000370872.3_Missense_Mutation_p.E46K|CRYZ_ENST00000417775.1_Missense_Mutation_p.E183K	NM_001889.3	NP_001880.2	Q08257	QOR_HUMAN	crystallin, zeta (quinone reductase)	183			E -> K (in dbSNP:rs17095822).		protein homotetramerization (GO:0051289)|visual perception (GO:0007601)|xenobiotic catabolic process (GO:0042178)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	mRNA 3'-UTR binding (GO:0003730)|NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)	10					Dicoumarol(DB00266)	TGTCCTTCCTCAGTACCAGCA	0.353													C|||	105	0.0209665	0.0756	0.0043	5008	,	,		15672	0.001		0.0	False		,,,				2504	0.001				p.E183K		Atlas-SNP	.											.	CRYZ	28	.	0			c.G547A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	244,4162	141.9+/-177.2	7,230,1966	78.0	79.0	79.0		547,547,136,547	4.6	1.0	1	dbSNP_123	79	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	CRYZ	NM_001130042.1,NM_001130043.1,NM_001134759.1,NM_001889.3	56,56,56,56	7,233,6263	TT,TC,CC		0.0349,5.5379,1.8991	benign,benign,benign,benign	183/330,183/296,46/193,183/330	75175865	247,12759	2203	4300	6503	SO:0001583	missense	1429	exon6			CTTCCTCAGTACC		CCDS665.1, CCDS44162.1, CCDS44163.1	1p31.1	2013-02-14			ENSG00000116791	ENSG00000116791			2419	protein-coding gene	gene with protein product		123691					Standard	NM_001889		Approved		uc001dgj.3	Q08257	OTTHUMG00000009620	ENST00000340866.5:c.547G>A	1.37:g.75175865C>T	ENSP00000339399:p.Glu183Lys	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	303	145	0.478548	NM_001130043	A6NN60|D3DQ76|Q53FT0|Q59EU7|Q5HYE7|Q6NSK9	Missense_Mutation	SNP	ENST00000340866.5	37	CCDS665.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	C	7.833	0.720290	0.15372	0.055379	3.49E-4	ENSG00000116791	ENST00000340866;ENST00000370872;ENST00000417775;ENST00000370871;ENST00000370870;ENST00000441120	T;T;T;T;T;T	0.32272	3.43;3.43;3.43;1.46;3.43;3.43	5.54	4.63	0.57726	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.170547	0.48767	D	0.000162	T	0.18173	0.0436	L	0.54863	1.705	0.42476	D	0.992842	B;B;B	0.27068	0.141;0.167;0.029	B;B;B	0.35114	0.051;0.196;0.027	T	0.05084	-1.0907	10	0.39692	T	0.17	.	9.917	0.41442	0.0:0.7871:0.1388:0.074	rs17095822;rs56573849;rs17095822	46;183;183	Q5HYE7;A6NN60;Q08257	.;.;QOR_HUMAN	K	183;46;183;183;183;183	ENSP00000339399:E183K;ENSP00000359909:E46K;ENSP00000399805:E183K;ENSP00000359908:E183K;ENSP00000359907:E183K;ENSP00000404289:E183K	ENSP00000339399:E183K	E	-	1	0	CRYZ	74948453	0.995000	0.38212	0.965000	0.40720	0.170000	0.22686	2.685000	0.46959	1.464000	0.47987	0.563000	0.77884	GAG	C|0.979;T|0.021	0.021	strong		0.353	CRYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026514.1		
SPTA1	6708	hgsc.bcm.edu	37	1	158626378	158626378	+	Silent	SNP	C	C	T	rs857691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158626378C>T	ENST00000368147.4	-	20	3054	c.2874G>A	c.(2872-2874)ctG>ctA	p.L958L		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	958					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CCTGATTCCGCAGAGCTTTCA	0.398													T|||	2121	0.423522	0.7935	0.3588	5008	,	,		16600	0.4087		0.2495	False		,,,				2504	0.1636				p.L958L		Atlas-SNP	.											.	SPTA1	720	.	0			c.G2874A						PASS	.	T		2587,1125		905,777,174	167.0	171.0	170.0		2874	-9.1	0.0	1	dbSNP_86	170	2017,6169		273,1471,2349	no	coding-synonymous	SPTA1	NM_003126.2		1178,2248,2523	TT,TC,CC		24.6396,30.3071,38.6956		958/2420	158626378	4604,7294	1856	4093	5949	SO:0001819	synonymous_variant	6708	exon20			ATTCCGCAGAGCT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2874G>A	1.37:g.158626378C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			C|0.581;T|0.419	0.419	strong		0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
CYP4F12	66002	hgsc.bcm.edu	37	19	15794411	15794411	+	Silent	SNP	C	C	T	rs61731191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794411C>T	ENST00000550308.1	+	7	1136	c.756C>T	c.(754-756)gaC>gaT	p.D252D	CYP4F12_ENST00000324632.10_Silent_p.D252D	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	252					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	TCTCCCATGACGGGCGGCGCT	0.557													.|||	88	0.0175719	0.0635	0.0043	5008	,	,		21374	0.0		0.001	False		,,,				2504	0.0				p.D252D		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C756T						PASS	.	C		286,4104		0,286,1909	76.0	78.0	77.0		756	-4.9	0.0	19	dbSNP_129	77	4,8584		0,4,4290	yes	coding-synonymous	CYP4F12	NM_023944.3		0,290,6199	TT,TC,CC		0.0466,6.5148,2.2346		252/525	15794411	290,12688	2195	4294	6489	SO:0001819	synonymous_variant	66002	exon7			CCATGACGGGCGG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.756C>T	19.37:g.15794411C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	210	58	0.27619	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			C|0.985;T|0.015	0.015	strong		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
FN1	2335	hgsc.bcm.edu	37	2	216298084	216298084	+	Silent	SNP	G	G	A	rs2289202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:216298084G>A	ENST00000359671.1	-	3	643	c.378C>T	c.(376-378)atC>atT	p.I126I	FN1_ENST00000336916.4_Silent_p.I126I|FN1_ENST00000432072.2_Silent_p.I126I|FN1_ENST00000354785.4_Silent_p.I126I|FN1_ENST00000421182.1_Silent_p.I126I|FN1_ENST00000357009.2_Silent_p.I126I|AC012462.1_ENST00000412951.1_RNA|FN1_ENST00000345488.5_Silent_p.I126I|FN1_ENST00000323926.6_Silent_p.I126I|FN1_ENST00000346544.3_Silent_p.I126I|FN1_ENST00000426059.1_Silent_p.I126I|FN1_ENST00000356005.4_Silent_p.I126I|FN1_ENST00000446046.1_Silent_p.I126I|FN1_ENST00000357867.4_Silent_p.I126I|FN1_ENST00000443816.1_Silent_p.I126I			P02751	FINC_HUMAN	fibronectin 1	126	Fibrin- and heparin-binding 1.|Fibronectin type-I 2. {ECO:0000255|PROSITE-ProRule:PRU00478}.			I -> V (in Ref. 5; CAH18136). {ECO:0000305}.	acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	GCCCAGCCCCGATGCAGGTAC	0.448													G|||	722	0.144169	0.2549	0.1427	5008	,	,		21425	0.001		0.2445	False		,,,				2504	0.0399				p.I126I		Atlas-SNP	.											FN1,NS,carcinoma,-2,1	FN1	521	1	0			c.C378T						PASS	.	G	,,,,,	1058,3348	387.0+/-326.3	123,812,1268	159.0	144.0	149.0		378,378,378,378,378,378	-5.8	0.8	2	dbSNP_100	149	2099,6501	363.0+/-333.0	266,1567,2467	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FN1	NM_002026.2,NM_054034.2,NM_212474.1,NM_212476.1,NM_212478.1,NM_212482.1	,,,,,	389,2379,3735	AA,AG,GG		24.407,24.0127,24.2734	,,,,,	126/2356,126/658,126/2177,126/2297,126/2331,126/2478	216298084	3157,9849	2203	4300	6503	SO:0001819	synonymous_variant	2335	exon3			AGCCCCGATGCAG		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.378C>T	2.37:g.216298084G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	142	57	0.401408	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	37																																																																																				G|0.783;A|0.217	0.217	strong		0.448	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21945530	21945530	+	Silent	SNP	C	C	T	rs77539762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21945530C>T	ENST00000374765.4	-	5	254	c.54G>A	c.(52-54)ccG>ccA	p.P18P	RAP1GAP_ENST00000374761.2_Silent_p.P49P|RAP1GAP_ENST00000374757.3_5'UTR|RAP1GAP_ENST00000374763.2_Silent_p.P18P|RAP1GAP_ENST00000542643.2_Silent_p.P18P|RAP1GAP_ENST00000290101.4_Silent_p.P82P	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	18					GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		TGAGGGGCGGCGGGAAGGAGC	0.647													c|||	270	0.0539137	0.1452	0.0303	5008	,	,		15468	0.0		0.0378	False		,,,				2504	0.0194				p.P82P		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.G246A						PASS	.	T	,,	538,3864		31,476,1694	79.0	59.0	66.0		54,246,54	-7.2	0.8	1	dbSNP_131	66	295,8301		4,287,4007	no	coding-synonymous,coding-synonymous,coding-synonymous	RAP1GAP	NM_001145657.1,NM_001145658.1,NM_002885.2	,,	35,763,5701	TT,TC,CC		3.4318,12.2217,6.4087	,,	18/682,82/728,18/664	21945530	833,12165	2201	4298	6499	SO:0001819	synonymous_variant	5909	exon5			GGGCGGCGGGAAG	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.54G>A	1.37:g.21945530C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			C|0.939;T|0.061	0.061	strong		0.647	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
SEL1L3	23231	hgsc.bcm.edu	37	4	25849329	25849329	+	Missense_Mutation	SNP	T	T	C	rs16877661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:25849329T>C	ENST00000399878.3	-	2	442	c.320A>G	c.(319-321)cAg>cGg	p.Q107R	SEL1L3_ENST00000513364.1_Intron|SEL1L3_ENST00000502949.1_5'UTR|SEL1L3_ENST00000264868.5_Missense_Mutation_p.Q72R	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	107			Q -> R (in dbSNP:rs16877661).			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						AACACAAGGCTGAGAGCATAA	0.408													T|||	106	0.0211661	0.0779	0.0043	5008	,	,		20619	0.0		0.0	False		,,,				2504	0.0				p.Q107R		Atlas-SNP	.											.	SEL1L3	62	.	0			c.A320G						PASS	.	T	ARG/GLN	216,3516		6,204,1656	116.0	105.0	108.0		320	5.2	1.0	4	dbSNP_123	108	2,8224		0,2,4111	yes	missense	SEL1L3	NM_015187.3	43	6,206,5767	CC,CT,TT		0.0243,5.7878,1.823	benign	107/1133	25849329	218,11740	1866	4113	5979	SO:0001583	missense	23231	exon2			CAAGGCTGAGAGC	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.320A>G	4.37:g.25849329T>C	ENSP00000382767:p.Gln107Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	T	12.92	2.082924	0.36758	0.057878	2.43E-4	ENSG00000091490	ENST00000399878;ENST00000264868	T;T	0.11712	2.75;2.76	5.25	5.25	0.73442	.	0.355245	0.29980	N	0.010710	T	0.00666	0.0022	L	0.38531	1.155	0.80722	D	1	B	0.16396	0.017	B	0.15870	0.014	T	0.18745	-1.0327	10	0.59425	D	0.04	-16.01	9.7021	0.40194	0.0:0.0776:0.0:0.9224	rs16877661;rs52796481;rs16877661	107	Q68CR1	SE1L3_HUMAN	R	107;72	ENSP00000382767:Q107R;ENSP00000264868:Q72R	ENSP00000264868:Q72R	Q	-	2	0	SEL1L3	25458427	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.246000	0.51414	1.995000	0.58328	0.449000	0.29647	CAG	T|0.984;C|0.016	0.016	strong		0.408	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
HELT	391723	hgsc.bcm.edu	37	4	185940196	185940196	+	Intron	SNP	A	A	T	rs370662812		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:185940196A>T	ENST00000515777.1	+	1	115				HELT_ENST00000505610.1_Intron|HELT_ENST00000338875.4_Silent_p.A38A			A6NFD8	HELT_HUMAN	helt bHLH transcription factor						central nervous system development (GO:0007417)|GABAergic neuron differentiation in basal ganglia (GO:0021858)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	14		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;8.92e-26)|Epithelial(43;3.02e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-11)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		GACCGATGGCAGGGAAGTGCC	0.602																																					p.A38A		Atlas-SNP	.											.	HELT	34	.	0			c.A114T						PASS	.	A		0,4406		0,0,2203	75.0	70.0	72.0		114	-2.8	0.0	4		72	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	HELT	NM_001029887.1		0,1,6502	TT,TA,AA		0.0116,0.0,0.0077		38/328	185940196	1,13005	2203	4300	6503	SO:0001627	intron_variant	391723	exon1			GATGGCAGGGAAG	BC144567	CCDS75214.1, CCDS75215.1	4q35.1	2014-07-17	2011-09-12		ENSG00000187821	ENSG00000187821		"""Basic helix-loop-helix proteins"""	33783	protein-coding gene	gene with protein product	"""megane bHLH factor"", ""HES-like"""		"""Hey-like transcription factor (zebrafish)"", ""HES/HEY-like transcription factor"""			14764602, 17611227	Standard	XM_005262989		Approved	HESL, HCM1228, Mgn, bHLHb44, MEGANE	uc011ckq.2	A6NFD8	OTTHUMG00000160484	ENST00000515777.1:c.27+87A>T	4.37:g.185940196A>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_001029887	B2RTS5|B7ZMI7|B7ZMI8	Silent	SNP	ENST00000515777.1	37																																																																																				.	.	weak		0.602	HELT-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000360792.1	NM_001300781	
MPZL3	196264	hgsc.bcm.edu	37	11	118100634	118100634	+	Splice_Site	SNP	T	T	A	rs7105729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118100634T>A	ENST00000278949.4	-	6	738	c.683A>T	c.(682-684)gAt>gTt	p.D228V	MPZL3_ENST00000525386.1_Splice_Site_p.I47F|MPZL3_ENST00000527472.1_Splice_Site_p.D216V			Q6UWV2	MPZL3_HUMAN	myelin protein zero-like 3	228			D -> V (in dbSNP:rs7105729).		cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|hair cycle (GO:0042633)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.046)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		ATAGTCTGAATCCTGGAGGGA	0.453													T|||	223	0.0445288	0.1528	0.0274	5008	,	,		19501	0.0		0.002	False		,,,				2504	0.0				p.D228V		Atlas-SNP	.											.	MPZL3	22	.	0			c.A683T						PASS	.	T	VAL/ASP	613,3787	268.6+/-268.5	54,505,1641	101.0	93.0	96.0		683	5.8	1.0	11	dbSNP_116	96	7,8585	6.4+/-24.3	0,7,4289	yes	missense-near-splice	MPZL3	NM_198275.1	152	54,512,5930	AA,AT,TT		0.0815,13.9318,4.7722	benign	228/236	118100634	620,12372	2200	4296	6496	SO:0001630	splice_region_variant	196264	exon6			TCTGAATCCTGGA	AK095399	CCDS8392.1, CCDS66241.1	11q23.3	2013-01-11			ENSG00000160588	ENSG00000160588		"""Immunoglobulin superfamily / V-set domain containing"""	27279	protein-coding gene	gene with protein product		611707				17273165	Standard	NM_198275		Approved		uc001psm.3	Q6UWV2	OTTHUMG00000166966	ENST00000278949.4:c.682-1A>T	11.37:g.118100634T>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	49	0.662162	NM_198275	A8K025|B4DLD5|B4E2I8	Missense_Mutation	SNP	ENST00000278949.4	37	CCDS8392.1	92|92	0.04212454212454213|0.04212454212454213	81|81	0.16463414634146342|0.16463414634146342	11|11	0.03038674033149171|0.03038674033149171	0|0	0.0|0.0	0|0	0.0|0.0	T|T	19.48|19.48	3.834812|3.834812	0.71373|0.71373	0.139318|0.139318	8.15E-4|8.15E-4	ENSG00000160588|ENSG00000160588	ENST00000278949;ENST00000527472|ENST00000525386	D;D|.	0.96651|.	-3.93;-4.08|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00271|0.00271	0.0008|0.0008	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	P|P	0.9999999999999915|0.9999999999999915	P;P|.	0.47191|.	0.693;0.891|.	P;P|.	0.45681|.	0.49;0.49|.	T|T	0.11792|0.11792	-1.0573|-1.0573	9|5	0.87932|0.41790	D|T	0|0.15	.|.	12.5017|12.5017	0.55960|0.55960	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs7105729;rs52792812;rs7105729|rs7105729;rs52792812;rs7105729	216;228|.	B4E2I8;Q6UWV2|.	.;MPZL3_HUMAN|.	V|F	228;216|47	ENSP00000278949:D228V;ENSP00000432106:D216V|.	ENSP00000278949:D228V|ENSP00000434636:I47F	D|I	-|-	2|1	0|0	MPZL3|MPZL3	117605844|117605844	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.873000|0.873000	0.50193|0.50193	4.093000|4.093000	0.57714|0.57714	2.215000|2.215000	0.71742|0.71742	0.460000|0.460000	0.39030|0.39030	GAT|ATT	T|0.954;A|0.046	0.046	strong		0.453	MPZL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392109.1	NM_198275	Missense_Mutation
NCOR1	9611	hgsc.bcm.edu	37	17	15968887	15968887	+	Silent	SNP	T	T	C	rs7210057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15968887T>C	ENST00000268712.3	-	33	5120	c.4863A>G	c.(4861-4863)caA>caG	p.Q1621Q	NCOR1_ENST00000395857.3_Silent_p.Q205Q|NCOR1_ENST00000395851.1_Silent_p.Q1637Q	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1621	Interaction with C1D. {ECO:0000250}.|Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CTTGCATCTGTTGTGAGGTAA	0.483													T|||	96	0.0191693	0.0666	0.0115	5008	,	,		19833	0.0		0.0	False		,,,				2504	0.0				p.Q1637Q		Atlas-SNP	.											.	NCOR1	240	.	0			c.A4911G						PASS	.	T	,	229,4177	137.3+/-173.1	5,219,1979	192.0	167.0	175.0		4911,4863	0.8	1.0	17	dbSNP_116	175	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	NCOR1	NM_001190440.1,NM_006311.3	,	5,222,6276	CC,CT,TT		0.0349,5.1975,1.7838	,	1637/2338,1621/2441	15968887	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	9611	exon32			CATCTGTTGTGAG	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.4863A>G	17.37:g.15968887T>C		Somatic	299	1	0.00334448		WXS	Illumina HiSeq	Phase_I	314	150	0.477707	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	37	CCDS11175.1																																																																																			T|0.979;C|0.021	0.021	strong		0.483	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
C5orf47	133491	hgsc.bcm.edu	37	5	173416508	173416508	+	Missense_Mutation	SNP	C	C	T	rs115473626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:173416508C>T	ENST00000340147.6	+	1	347	c.242C>T	c.(241-243)cCt>cTt	p.P81L	C5orf47_ENST00000522195.1_Intron	NM_001144954.1	NP_001138426.1	Q569G3	CE047_HUMAN	chromosome 5 open reading frame 47	81										kidney(1)|prostate(1)	2						CCCACGACCCCTGGTGTGGAG	0.706													C|||	30	0.00599042	0.0144	0.0058	5008	,	,		10710	0.0		0.007	False		,,,				2504	0.0				p.P81L		Atlas-SNP	.											.	C5orf47	14	.	0			c.C242T						PASS	.						9.0	15.0	13.0					5																	173416508		686	1587	2273	SO:0001583	missense	133491	exon1			CGACCCCTGGTGT		CCDS47343.1	5q35.2	2012-02-24			ENSG00000185056	ENSG00000185056			27026	protein-coding gene	gene with protein product						12477932	Standard	NM_001144954		Approved	LOC133491	uc003mcw.4	Q569G3	OTTHUMG00000163349	ENST00000340147.6:c.242C>T	5.37:g.173416508C>T	ENSP00000340887:p.Pro81Leu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_001144954	Q8IYU7	Missense_Mutation	SNP	ENST00000340147.6	37	CCDS47343.1	37	0.01694139194139194	18	0.036585365853658534	3	0.008287292817679558	0	0.0	16	0.021108179419525065	C	0.329	-0.957101	0.02267	.	.	ENSG00000185056	ENST00000340147	.	.	.	1.16	0.0674	0.14366	.	.	.	.	.	T	0.05227	0.0139	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22243	-1.0222	8	0.14252	T	0.57	-0.6825	6.6571	0.22994	0.0:0.778:0.0:0.222	.	81	Q569G3	CE047_HUMAN	L	81	.	ENSP00000340887:P81L	P	+	2	0	C5orf47	173349114	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.573000	0.05874	-1.553000	0.01702	-1.786000	0.00637	CCT	C|0.984;T|0.016	0.016	strong		0.706	C5orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372926.1	NM_001144954	
C10orf95	79946	hgsc.bcm.edu	37	10	104210861	104210861	+	Missense_Mutation	SNP	C	C	A	rs73349055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:104210861C>A	ENST00000239125.1	-	2	201	c.127G>T	c.(127-129)Ggg>Tgg	p.G43W	RP11-18I14.10_ENST00000596045.1_RNA|RP11-18I14.10_ENST00000473970.2_RNA|RP11-18I14.10_ENST00000594818.1_RNA|RP11-18I14.10_ENST00000596366.1_RNA|RP11-18I14.10_ENST00000492465.2_RNA|RP11-18I14.10_ENST00000494270.2_RNA	NM_024886.1	NP_079162.1	Q9H7T3	CJ095_HUMAN	chromosome 10 open reading frame 95	43										liver(1)	1		Colorectal(252;0.207)		Epithelial(162;8.34e-09)|all cancers(201;1.95e-07)|BRCA - Breast invasive adenocarcinoma(275;0.213)		GGTCGGCCCCCCAGGCGGCTG	0.657													C|||	318	0.0634984	0.2315	0.0144	5008	,	,		11331	0.0		0.002	False		,,,				2504	0.0				p.G43W		Atlas-SNP	.											.	C10orf95	5	.	0			c.G127T						PASS	.	C	TRP/GLY	452,2752		21,410,1171	9.0	11.0	10.0		127	-0.7	0.0	10	dbSNP_130	10	11,6951		0,11,3470	yes	missense	C10orf95	NM_024886.1	184	21,421,4641	AA,AC,CC		0.158,14.1074,4.5544	probably-damaging	43/258	104210861	463,9703	1602	3481	5083	SO:0001583	missense	79946	exon2			GGCCCCCCAGGCG	AK024342	CCDS7534.1	10q24.32	2014-02-19	2014-02-19	2014-02-19	ENSG00000120055	ENSG00000120055			25880	protein-coding gene	gene with protein product							Standard	NM_024886		Approved	FLJ14280	uc001kvo.1	Q9H7T3	OTTHUMG00000018959	ENST00000239125.1:c.127G>T	10.37:g.104210861C>A	ENSP00000239125:p.Gly43Trp	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	16	7	0.4375	NM_024886	A0AVQ7	Missense_Mutation	SNP	ENST00000239125.1	37	CCDS7534.1	121	0.0554029304029304	115	0.23373983739837398	6	0.016574585635359115	0	0.0	0	0.0	C	12.67	2.007558	0.35415	0.141074	0.00158	ENSG00000120055	ENST00000239125	.	.	.	4.67	-0.695	0.11291	.	1.984030	0.02659	N	0.107299	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.63046	0.992	P	0.56751	0.805	T	0.04281	-1.0963	8	0.87932	D	0	-26.9089	1.7389	0.02948	0.1583:0.0984:0.3263:0.417	.	43	Q9H7T3	CJ095_HUMAN	W	43	.	ENSP00000239125:G43W	G	-	1	0	C10orf95	104200851	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.146000	0.16180	-0.211000	0.10124	-0.350000	0.07774	GGG	C|0.954;A|0.046	0.046	strong		0.657	C10orf95-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050065.1	NM_024886	
NPL	80896	hgsc.bcm.edu	37	1	182785865	182785865	+	Silent	SNP	C	C	T	rs1128759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182785865C>T	ENST00000367553.1	+	7	425	c.381C>T	c.(379-381)ttC>ttT	p.F127F	NPL_ENST00000258317.2_Silent_p.F127F|NPL_ENST00000367555.1_Silent_p.F127F|NPL_ENST00000367552.2_Silent_p.F127F|NPL_ENST00000367554.3_Silent_p.F108F|NPL_ENST00000463899.1_3'UTR	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	127					carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)			breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						TGATTAATTTCCTAAAGGAAG	0.423													C|||	464	0.0926518	0.2723	0.036	5008	,	,		18121	0.0089		0.0119	False		,,,				2504	0.0593				p.F127F		Atlas-SNP	.											.	NPL	55	.	0			c.C381T						PASS	.	C	,,,,	1070,3336	383.5+/-324.9	137,796,1270	75.0	66.0	69.0		324,381,381,381,381	-0.1	1.0	1	dbSNP_86	69	79,8521	44.9+/-103.4	0,79,4221	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPL	NM_001200050.1,NM_001200051.1,NM_001200052.1,NM_001200056.1,NM_030769.2	,,,,	137,875,5491	TT,TC,CC		0.9186,24.2851,8.8344	,,,,	108/302,127/241,127/231,127/285,127/321	182785865	1149,11857	2203	4300	6503	SO:0001819	synonymous_variant	80896	exon8			TAATTTCCTAAAG	AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"""dihydrodipicolinate synthetase homolog 1 (E. coli)"""	611412	"""chromosome 1 open reading frame 13"""	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.381C>T	1.37:g.182785865C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_001200052	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Silent	SNP	ENST00000367553.1	37	CCDS1350.1																																																																																			C|0.921;T|0.079	0.079	strong		0.423	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769	
LAMA1	284217	hgsc.bcm.edu	37	18	6961950	6961950	+	Silent	SNP	T	T	C	rs145257845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6961950T>C	ENST00000389658.3	-	52	7539	c.7446A>G	c.(7444-7446)ttA>ttG	p.L2482L		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2482					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)				CTACCTCCAGTAAACAGCCTT	0.378													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		20021	0.0		0.0	False		,,,				2504	0.0				p.L2482L		Atlas-SNP	.											.	LAMA1	458	.	0			c.A7446G						PASS	.	T		15,4391	22.3+/-47.3	0,15,2188	130.0	131.0	131.0		7446	-9.1	0.0	18	dbSNP_134	131	0,8600		0,0,4300	no	coding-synonymous	LAMA1	NM_005559.3		0,15,6488	CC,CT,TT		0.0,0.3404,0.1153		2482/3076	6961950	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon52			CTCCAGTAAACAG	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.7446A>G	18.37:g.6961950T>C		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	300	163	0.543333	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			T|0.998;C|0.002	0.002	strong		0.378	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
MUC2	4583	hgsc.bcm.edu	37	11	1093600	1093600	+	Missense_Mutation	SNP	G	G	A	rs74193969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1093600G>A	ENST00000441003.2	+	30	5446	c.5419G>A	c.(5419-5421)Ggc>Agc	p.G1807S	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.G1763S|MUC2_ENST00000333592.6_Missense_Mutation_p.G95S	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)				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	0.607													N|||	721	0.14397	0.0189	0.1398	5008	,	,		19218	0.4117		0.0358	False		,,,				2504	0.1513				p.G1807S		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.G5419A						scavenged	.	G	SER/GLY	136,4252		1,134,2059	104.0	140.0	128.0		5416	0.5	0.0	11	dbSNP_130	128	224,8326		2,220,4053	yes	missense	MUC2	NM_002457.2	56	3,354,6112	AA,AG,GG		2.6199,3.0994,2.7825	benign	1806/2813	1093600	360,12578	2194	4275	6469	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.5419G>A	11.37:g.1093600G>A	ENSP00000415183:p.Gly1807Ser	Somatic	127	2	0.015748		WXS	Illumina HiSeq	Phase_I	141	55	0.390071	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	G	2.204	-0.382251	0.04966	0.030994	0.026199	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.17370	3.2;3.45;2.28	1.71	0.462	0.16695	.	0.254805	0.16288	U	0.221059	T	0.01976	0.0062	.	.	.	0.50313	P	1.3900000000000023E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.39961	-0.9588	8	0.09590	T	0.72	.	5.0135	0.14324	0.8191:0.0:0.1809:0.0	.	1807	E7EUV1	.	S	1807;1763;95	ENSP00000415183:G1807S;ENSP00000351956:G1763S;ENSP00000331373:G95S	ENSP00000331373:G95S	G	+	1	0	MUC2	1083600	0.000000	0.05858	0.003000	0.11579	0.041000	0.13682	-0.389000	0.07342	-0.046000	0.13446	-1.373000	0.01185	GGC	G|0.965;A|0.036	0.036	strong		0.607	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
IL16	3603	hgsc.bcm.edu	37	15	81592384	81592384	+	Missense_Mutation	SNP	C	C	T	rs17875513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81592384C>T	ENST00000302987.4	+	13	2717	c.2717C>T	c.(2716-2718)tCg>tTg	p.S906L	IL16_ENST00000394660.2_Missense_Mutation_p.S906L|IL16_ENST00000560230.1_3'UTR|IL16_ENST00000394652.2_Missense_Mutation_p.S205L			Q14005	IL16_HUMAN	interleukin 16	906			S -> L (in dbSNP:rs17875513). {ECO:0000269|Ref.8}.		immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GTACTGTCCTCGGGGTCCCCT	0.642													C|||	215	0.0429313	0.1536	0.0115	5008	,	,		11772	0.0		0.004	False		,,,				2504	0.0				p.S906L		Atlas-SNP	.											.	IL16	254	.	0			c.C2717T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER	558,3836		38,482,1677	44.0	49.0	47.0		2717,614,2717	-9.7	0.0	15	dbSNP_124	47	28,8572		0,28,4272	yes	missense,missense,missense	IL16	NM_001172128.1,NM_004513.5,NM_172217.3	145,145,145	38,510,5949	TT,TC,CC		0.3256,12.6991,4.5098	benign,benign,benign	906/1332,205/632,906/1333	81592384	586,12408	2197	4300	6497	SO:0001583	missense	3603	exon14			TGTCCTCGGGGTC	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.2717C>T	15.37:g.81592384C>T	ENSP00000302935:p.Ser906Leu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	82	0.037545787545787544	76	0.15447154471544716	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	8.558	0.877168	0.17395	0.126991	0.003256	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653;ENST00000394652;ENST00000394656	T;T;T	0.10763	2.84;2.84;3.43	4.85	-9.71	0.00518	.	1.594110	0.03725	N	0.252561	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B;B;B	0.14438	0.001;0.01;0.0;0.001;0.0;0.001	B;B;B;B;B;B	0.04013	0.001;0.001;0.0;0.001;0.001;0.001	T	0.30208	-0.9986	9	0.30078	T	0.28	.	8.1212	0.30971	0.0709:0.1747:0.5288:0.2256	rs17875513	738;399;443;296;906;906	F8W7Z5;Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;.;IL16_HUMAN;.	L	906;738;906;443;296;205;205	ENSP00000378155:S906L;ENSP00000302935:S906L;ENSP00000378147:S205L	ENSP00000302935:S906L	S	+	2	0	IL16	79379439	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.830000	0.00744	-1.944000	0.01038	-1.710000	0.00715	TCG	C|0.955;T|0.045	0.045	strong		0.642	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
CDC27	996	hgsc.bcm.edu	37	17	45234727	45234727	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45234727T>A	ENST00000066544.3	-	6	592	c.499A>T	c.(499-501)Aca>Tca	p.T167S	CDC27_ENST00000531206.1_Missense_Mutation_p.T167S|CDC27_ENST00000527547.1_Missense_Mutation_p.T167S|CDC27_ENST00000446365.2_Missense_Mutation_p.T106S|CDC27_ENST00000528748.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	167					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						AATTTAAATGTTTGGTCAGGA	0.368																																					p.T167S		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,+2,10	CDC27	337	10	0			c.A499T						scavenged	.						73.0	73.0	73.0					17																	45234727		2203	4300	6503	SO:0001583	missense	996	exon6			TAAATGTTTGGTC	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.499A>T	17.37:g.45234727T>A	ENSP00000066544:p.Thr167Ser	Somatic	191	5	0.026178		WXS	Illumina HiSeq	Phase_I	164	6	0.0365854	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.623232	0.46840	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.67171	-0.25;-0.25;0.04;-0.25;0.89	5.39	5.39	0.77823	.	0.119985	0.64402	D	0.000020	T	0.47192	0.1432	N	0.08118	0	0.39122	D	0.961682	P;P;P;B	0.38677	0.475;0.528;0.642;0.211	B;B;B;B	0.36092	0.049;0.217;0.204;0.067	T	0.59762	-0.7393	10	0.72032	D	0.01	-19.1215	13.3763	0.60741	0.0:0.0:0.0:1.0	.	106;167;167;167	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	S	167;167;106;167;167	ENSP00000066544:T167S;ENSP00000434614:T167S;ENSP00000392802:T106S;ENSP00000437339:T167S;ENSP00000432105:T167S	ENSP00000066544:T167S	T	-	1	0	CDC27	42589726	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.374000	0.66167	2.053000	0.61076	0.528000	0.53228	ACA	.	.	none		0.368	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
ZNF638	27332	hgsc.bcm.edu	37	2	71654450	71654450	+	Silent	SNP	A	A	G	rs60163900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71654450A>G	ENST00000409544.1	+	24	6081	c.5451A>G	c.(5449-5451)aaA>aaG	p.K1817K	ZNF638_ENST00000264447.4_Silent_p.K1817K|ZNF638_ENST00000409407.1_Silent_p.K757K|ZNF638_ENST00000355812.3_3'UTR	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	59	58	0.983051	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	
PTH1R	5745	hgsc.bcm.edu	37	3	46945000	46945000	+	Missense_Mutation	SNP	G	G	A	rs77048718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46945000G>A	ENST00000313049.5	+	14	1839	c.1636G>A	c.(1636-1638)Gag>Aag	p.E546K	PTH1R_ENST00000430002.2_Missense_Mutation_p.E546K|PTH1R_ENST00000449590.1_Missense_Mutation_p.E546K|PTH1R_ENST00000418619.1_Missense_Mutation_p.E546K			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor	546					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|bone mineralization (GO:0030282)|bone resorption (GO:0045453)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|osteoblast development (GO:0002076)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|skeletal system development (GO:0001501)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	parathyroid hormone receptor activity (GO:0004991)|peptide hormone binding (GO:0017046)|protein self-association (GO:0043621)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(2)|stomach(1)|urinary_tract(2)	19					Preotact(DB05829)|Teriparatide(DB06285)	CCCAGCCCTGGAGACCCTCGA	0.692													G|||	43	0.00858626	0.0015	0.013	5008	,	,		14428	0.0		0.0278	False		,,,				2504	0.0041				p.E546K		Atlas-SNP	.											.	PTH1R	49	.	0			c.G1636A						PASS	.	G	LYS/GLU,LYS/GLU	18,4388	25.3+/-52.1	0,18,2185	70.0	69.0	69.0		1636,1636	1.8	0.1	3	dbSNP_131	69	219,8381	91.4+/-153.5	6,207,4087	yes	missense,missense	PTH1R	NM_000316.2,NM_001184744.1	56,56	6,225,6272	AA,AG,GG		2.5465,0.4085,1.8222	benign,benign	546/594,546/594	46945000	237,12769	2203	4300	6503	SO:0001583	missense	5745	exon15			GCCCTGGAGACCC		CCDS2747.1	3p22-p21.1	2012-08-10	2008-11-18	2008-11-18	ENSG00000160801	ENSG00000160801		"""GPCR / Class B : Parathyroid hormone receptors"""	9608	protein-coding gene	gene with protein product		168468	"""parathyroid hormone receptor 1"""	PTHR, PTHR1		8020952	Standard	NM_001184744		Approved		uc021wxg.1	Q03431	OTTHUMG00000133515	ENST00000313049.5:c.1636G>A	3.37:g.46945000G>A	ENSP00000321999:p.Glu546Lys	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	162	80	0.493827	NM_001184744	Q2M1U3	Missense_Mutation	SNP	ENST00000313049.5	37	CCDS2747.1	24	0.01098901098901099	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	20	0.026385224274406333	G	11.78	1.741593	0.30865	0.004085	0.025465	ENSG00000160801	ENST00000449590;ENST00000418619;ENST00000430002;ENST00000313049;ENST00000313063;ENST00000422115	T;T;T;T;T	0.77750	0.67;0.67;0.67;0.67;-1.12	1.79	1.79	0.24919	.	.	.	.	.	T	0.33789	0.0875	L	0.34521	1.04	0.25845	N	0.984009	B	0.22480	0.07	B	0.16722	0.016	T	0.32613	-0.9900	9	0.07030	T	0.85	.	3.7227	0.08463	0.2428:0.0:0.7572:0.0	.	546	Q03431	PTH1R_HUMAN	K	546;546;546;546;851;135	ENSP00000402723:E546K;ENSP00000411424:E546K;ENSP00000413774:E546K;ENSP00000321999:E546K;ENSP00000396176:E135K	ENSP00000321999:E546K	E	+	1	0	PTH1R	46920004	0.325000	0.24660	0.056000	0.19401	0.951000	0.60555	1.840000	0.39230	1.319000	0.45190	0.563000	0.77884	GAG	A|0.019;C|0.000;G|0.981	0.019	strong		0.692	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316	
MKI67	4288	hgsc.bcm.edu	37	10	129921195	129921195	+	Silent	SNP	A	A	T	rs1063536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129921195A>T	ENST00000368654.3	-	4	612	c.237T>A	c.(235-237)ccT>ccA	p.P79P	MKI67_ENST00000368653.3_Silent_p.P79P	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	79					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.P79P(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTAGCCGTACAGGCTCATCAA	0.353													A|||	619	0.123602	0.1641	0.1441	5008	,	,		20270	0.122		0.0875	False		,,,				2504	0.093				p.P79P		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - coding silent(1)	stomach(1)	c.T237A						PASS	.	A	,	647,3759	277.2+/-273.6	42,563,1598	144.0	135.0	138.0		237,237	-5.6	0.0	10	dbSNP_86	138	669,7931	169.3+/-220.7	28,613,3659	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	70,1176,5257	TT,TA,AA		7.7791,14.6845,10.1184	,	79/2897,79/3257	129921195	1316,11690	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon4			CCGTACAGGCTCA	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.237T>A	10.37:g.129921195A>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	161	80	0.496894	NM_001145966	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			A|0.894;T|0.106	0.106	strong		0.353	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
TINAG	27283	hgsc.bcm.edu	37	6	54254589	54254589	+	Splice_Site	SNP	A	A	C	rs3736352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:54254589A>C	ENST00000259782.4	+	11	1393	c.1297A>C	c.(1297-1299)Att>Ctt	p.I433L		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	433			I -> L (in dbSNP:rs3736352).		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)			TTTTCTGCAGATTGCTGCCAA	0.363													A|||	561	0.112021	0.0998	0.0259	5008	,	,		18323	0.3145		0.0467	False		,,,				2504	0.0481				p.I433L		Atlas-SNP	.											.	TINAG	102	.	0			c.A1297C						PASS	.	A	LEU/ILE	359,4047	183.3+/-210.9	14,331,1858	107.0	105.0	106.0		1297	0.5	1.0	6	dbSNP_107	106	283,8317	106.2+/-167.1	8,267,4025	yes	missense-near-splice	TINAG	NM_014464.3	5	22,598,5883	CC,CA,AA		3.2907,8.148,4.9362	benign	433/477	54254589	642,12364	2203	4300	6503	SO:0001630	splice_region_variant	27283	exon11			CTGCAGATTGCTG	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.1297-1A>C	6.37:g.54254589A>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_014464	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	37	CCDS4955.1	260	0.11904761904761904	49	0.09959349593495935	11	0.03038674033149171	167	0.291958041958042	33	0.04353562005277045	A	10.87	1.473884	0.26423	0.08148	0.032907	ENSG00000137251	ENST00000339741;ENST00000259782;ENST00000370865	D	0.88201	-2.35	5.89	0.524	0.17066	Peptidase C1A, papain C-terminal (2);	0.339136	0.28946	N	0.013634	T	0.57080	0.2029	N	0.10733	0.035	0.09310	P	0.9999999999999842	P	0.35192	0.489	B	0.34590	0.186	T	0.48559	-0.9025	8	.	.	.	.	7.9067	0.29765	0.6357:0.0:0.3643:0.0	rs3736352;rs52789794;rs3736352	433	Q9UJW2	TINAG_HUMAN	L	292;433;112	ENSP00000259782:I433L	.	I	+	1	0	TINAG	54362548	1.000000	0.71417	0.999000	0.59377	0.723000	0.41478	1.757000	0.38400	0.086000	0.17137	-0.346000	0.07831	ATT	A|0.919;C|0.081	0.081	strong		0.363	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464	Missense_Mutation
ZYG11B	79699	hgsc.bcm.edu	37	1	53262456	53262456	+	Splice_Site	SNP	G	G	A	rs11206020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53262456G>A	ENST00000294353.6	+	8	1630	c.1485G>A	c.(1483-1485)agG>agA	p.R495R	ZYG11B_ENST00000443756.2_Splice_Site_p.R495R|ZYG11B_ENST00000545132.1_Splice_Site_p.R495R	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	495										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						TCATTGTCAGGGTAAGTCTAT	0.328													G|||	201	0.0401358	0.1452	0.0115	5008	,	,		10687	0.0		0.001	False		,,,				2504	0.0				p.R495R		Atlas-SNP	.											.	ZYG11B	61	.	0			c.G1485A						PASS	.	G		532,3874	238.7+/-250.0	28,476,1699	136.0	126.0	130.0		1485	2.2	1.0	1	dbSNP_120	130	6,8594	3.7+/-12.6	0,6,4294	yes	coding-synonymous-near-splice	ZYG11B	NM_024646.2		28,482,5993	AA,AG,GG		0.0698,12.0744,4.1366		495/745	53262456	538,12468	2203	4300	6503	SO:0001630	splice_region_variant	79699	exon8			TGTCAGGGTAAGT	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"""ZYG11 cell cycle regulator family"""	25820	protein-coding gene	gene with protein product			"""zyg-11 homolog (C. elegans)"", ""zyg-11 homolog B (C. elegans)"""	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.1485+1G>A	1.37:g.53262456G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	NM_024646	Q8N2X3|Q9H8L8	Silent	SNP	ENST00000294353.6	37	CCDS30717.1																																																																																			G|0.962;A|0.038	0.038	strong		0.328	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646	Silent
CLTCL1	8218	hgsc.bcm.edu	37	22	19196449	19196449	+	Missense_Mutation	SNP	T	T	C	rs182543131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19196449T>C	ENST00000263200.10	-	21	3497	c.3425A>G	c.(3424-3426)cAg>cGg	p.Q1142R	CLTCL1_ENST00000353891.5_Missense_Mutation_p.Q1142R|CLTCL1_ENST00000427926.1_Missense_Mutation_p.Q1142R|CLTCL1_ENST00000442042.2_5'Flank	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1142	Heavy chain arm.|Proximal segment.				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)					GCTGGCTGACTGAACAACTTC	0.517			T	?	ALCL								T|||	3	0.000599042	0.0023	0.0	5008	,	,		19417	0.0		0.0	False		,,,				2504	0.0				p.Q1142R		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.A3425G						PASS	.	T	ARG/GLN,ARG/GLN	5,3951		0,5,1973	58.0	59.0	59.0		3425,3425	2.8	1.0	22		59	0,8310		0,0,4155	yes	missense,missense	CLTCL1	NM_001835.3,NM_007098.3	43,43	0,5,6128	CC,CT,TT		0.0,0.1264,0.0408	benign,benign	1142/1584,1142/1641	19196449	5,12261	1978	4155	6133	SO:0001583	missense	8218	exon21			GCTGACTGAACAA		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.3425A>G	22.37:g.19196449T>C	ENSP00000445677:p.Gln1142Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	12.81	2.050304	0.36181	0.001264	0.0	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.19532	2.14;2.14;2.14	3.85	2.82	0.32997	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.229394	0.37577	N	0.002026	T	0.15565	0.0375	N	0.26042	0.785	0.35290	D	0.782104	B;B	0.22541	0.003;0.071	B;B	0.31390	0.02;0.129	T	0.13899	-1.0492	10	0.39692	T	0.17	-8.2343	8.8849	0.35398	0.0:0.0903:0.0:0.9097	.	1142;1142	P53675-2;P53675	.;CLH2_HUMAN	R	1142	ENSP00000439662:Q1142R;ENSP00000445677:Q1142R;ENSP00000441158:Q1142R	ENSP00000445677:Q1142R	Q	-	2	0	CLTCL1	17576449	1.000000	0.71417	0.975000	0.42487	0.916000	0.54674	5.366000	0.66122	0.537000	0.28751	0.533000	0.62120	CAG	T|0.999;C|0.001	0.001	strong		0.517	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
BCO2	83875	hgsc.bcm.edu	37	11	112071464	112071464	+	Missense_Mutation	SNP	C	C	T	rs115780398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:112071464C>T	ENST00000357685.5	+	7	1129	c.994C>T	c.(994-996)Cgg>Tgg	p.R332W	BCO2_ENST00000393032.2_Missense_Mutation_p.R298W|BCO2_ENST00000526088.1_Missense_Mutation_p.R298W|BCO2_ENST00000438022.1_Missense_Mutation_p.R298W|BCO2_ENST00000532593.1_Missense_Mutation_p.R227W|BCO2_ENST00000531169.1_Missense_Mutation_p.R298W|BCO2_ENST00000361053.4_Missense_Mutation_p.R259W			Q9BYV7	BCDO2_HUMAN	beta-carotene oxygenase 2	332					carotene catabolic process (GO:0016121)|carotene metabolic process (GO:0016119)|carotenoid metabolic process (GO:0016116)|oxidation-reduction process (GO:0055114)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			NS(1)|breast(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)	16						GTGTAATACGCGGTTTCATGT	0.398													C|||	31	0.0061901	0.0212	0.0014	5008	,	,		18093	0.002		0.0	False		,,,				2504	0.0				p.R332W	GBM(177;1916 2099 21049 29541 39946)	Atlas-SNP	.											BCO2,colon,carcinoma,0,1	BCO2	44	1	0			c.C994T						PASS	.	C	TRP/ARG,TRP/ARG	81,4321	69.8+/-107.6	0,81,2120	120.0	123.0	122.0		892,994	0.0	0.0	11	dbSNP_132	122	1,8593	1.2+/-3.3	0,1,4296	yes	missense,missense	BCO2	NM_001037290.1,NM_031938.4	101,101	0,82,6416	TT,TC,CC		0.0116,1.8401,0.631	probably-damaging,probably-damaging	298/546,332/580	112071464	82,12914	2201	4297	6498	SO:0001583	missense	83875	exon7			AATACGCGGTTTC	AJ290393	CCDS8358.2, CCDS41716.1, CCDS58181.1, CCDS58182.1, CCDS58183.1	11q23.1	2014-05-12	2008-04-15	2008-04-15	ENSG00000197580	ENSG00000197580	1.13.11.71		18503	protein-coding gene	gene with protein product	"""beta-carotene 9',10' oxygenase"", ""carotenoid-9',10'-cleaving dioxygenase"""	611740	"""beta-carotene dioxygenase 2"""	BCDO2		11278918, 15983114, 15949678	Standard	NM_031938		Approved	FLJ34464, B-DIOX-II	uc001pnf.3	Q9BYV7	OTTHUMG00000167155	ENST00000357685.5:c.994C>T	11.37:g.112071464C>T	ENSP00000350314:p.Arg332Trp	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_031938	B0YIX5|B4DNC3|E9PBI8|E9PJJ1|Q8IUS0|Q96JC8|Q96JY5	Missense_Mutation	SNP	ENST00000357685.5	37	CCDS8358.2	16	0.007326007326007326	13	0.026422764227642278	1	0.0027624309392265192	2	0.0034965034965034965	0	0.0	C	5.058	0.196301	0.09599	0.018401	1.16E-4	ENSG00000197580	ENST00000357685;ENST00000393032;ENST00000361053;ENST00000438022;ENST00000526088;ENST00000532593;ENST00000531169	D;D;D;D;D;D;D	0.95885	-3.84;-3.84;-3.84;-3.84;-3.84;-3.84;-3.84	5.45	0.0177	0.14113	.	0.629740	0.16560	N	0.209094	D	0.85120	0.5624	L	0.39566	1.225	0.09310	N	1	D;D;D;D	0.63046	0.965;0.99;0.965;0.992	P;P;P;P	0.58970	0.788;0.659;0.788;0.849	T	0.81052	-0.1107	10	0.37606	T	0.19	-11.5438	1.2953	0.02068	0.2227:0.4126:0.1085:0.2562	.	309;259;332;159	C9JEZ9;E9PBI8;Q9BYV7;Q8NAZ7	.;.;BCDO2_HUMAN;.	W	332;298;259;298;298;227;298	ENSP00000350314:R332W;ENSP00000376752:R298W;ENSP00000354338:R259W;ENSP00000414843:R298W;ENSP00000436615:R298W;ENSP00000431802:R227W;ENSP00000437053:R298W	ENSP00000350314:R332W	R	+	1	2	BCO2	111576674	0.000000	0.05858	0.010000	0.14722	0.089000	0.18198	0.047000	0.14056	0.024000	0.15214	-0.203000	0.12734	CGG	C|0.994;T|0.006	0.006	strong		0.398	BCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256570.3	NM_001037290	
DPAGT1	1798	hgsc.bcm.edu	37	11	118967758	118967758	+	Missense_Mutation	SNP	T	T	C	rs643788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118967758T>C	ENST00000409993.2	-	11	2728	c.1177A>G	c.(1177-1179)Atc>Gtc	p.I393V	DPAGT1_ENST00000432443.2_Missense_Mutation_p.I312V|H2AFX_ENST00000530167.1_5'Flank|DPAGT1_ENST00000354202.4_Missense_Mutation_p.I393V			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	393			I -> V (in dbSNP:rs643788). {ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		GAGAAGGTGATGGCACTGCCC	0.488													T|||	2170	0.433307	0.2844	0.2983	5008	,	,		23742	0.631		0.4563	False		,,,				2504	0.5031				p.I393V		Atlas-SNP	.											.	DPAGT1	43	.	0			c.A1177G						PASS	.	T	VAL/ILE	1307,3093	441.0+/-346.2	199,909,1092	146.0	131.0	136.0		1177	-4.2	0.0	11	dbSNP_83	136	3723,4867	530.4+/-381.8	811,2101,1383	yes	missense	DPAGT1	NM_001382.3	29	1010,3010,2475	CC,CT,TT		43.3411,29.7045,38.7221	benign	393/409	118967758	5030,7960	2200	4295	6495	SO:0001583	missense	1798	exon9			AGGTGATGGCACT	Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.1177A>G	11.37:g.118967758T>C	ENSP00000386597:p.Ile393Val	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	144	59	0.409722	NM_001382	O15216|Q86WV9|Q9BWE6	Missense_Mutation	SNP	ENST00000409993.2	37	CCDS8411.1	938	0.42948717948717946	120	0.24390243902439024	127	0.35082872928176795	357	0.6241258741258742	334	0.44063324538258575	T	0.012	-1.647350	0.00792	0.297045	0.433411	ENSG00000172269	ENST00000409993;ENST00000354202;ENST00000432443	D;D;D	0.91068	-2.78;-2.78;-2.63	5.38	-4.23	0.03789	.	0.950055	0.08878	N	0.880464	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.36016	-0.9765	9	0.12766	T	0.61	-29.2396	2.1096	0.03699	0.2219:0.1524:0.1217:0.504	rs643788;rs3186349;rs17259019;rs17854515;rs58852432;rs643788	312;393	E7EW40;Q9H3H5	.;GPT_HUMAN	V	393;393;312	ENSP00000386597:I393V;ENSP00000346142:I393V;ENSP00000404036:I312V	ENSP00000346142:I393V	I	-	1	0	DPAGT1	118472968	0.000000	0.05858	0.037000	0.18230	0.231000	0.25187	-0.320000	0.08028	-0.993000	0.03467	-3.207000	0.00054	ATC	A|0.003;C|0.413	0.413	strong		0.488	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382	
STRC	161497	hgsc.bcm.edu	37	15	43897499	43897499	+	Missense_Mutation	SNP	T	T	C	rs2920780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43897499T>C	ENST00000450892.2	-	19	3970	c.3893A>G	c.(3892-3894)cAc>cGc	p.H1298R	RNU6-554P_ENST00000410466.1_RNA|STRC_ENST00000541030.1_Missense_Mutation_p.H525R	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	1298					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		GGCTGCCTGGTGGAGGGGGGT	0.542													T|||	1457	0.290935	0.5446	0.2003	5008	,	,		18193	0.2728		0.1014	False		,,,				2504	0.226				p.H1298R		Atlas-SNP	.											.	STRC	58	.	0			c.A3893G						PASS	.	T	ARG/HIS	1981,2409		455,1071,669	15.0	14.0	14.0		3893	2.9	1.0	15	dbSNP_101	14	836,7712		49,738,3487	no	missense	STRC	NM_153700.2	29	504,1809,4156	CC,CT,TT		9.7801,45.1253,21.7731	benign	1298/1776	43897499	2817,10121	2195	4274	6469	SO:0001583	missense	161497	exon19			GCCTGGTGGAGGG	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.3893A>G	15.37:g.43897499T>C	ENSP00000401513:p.His1298Arg	Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	358	128	0.357542	NM_153700		Missense_Mutation	SNP	ENST00000450892.2	37	CCDS10098.1	590	0.27014652014652013	266	0.540650406504065	74	0.20441988950276244	180	0.3146853146853147	70	0.09234828496042216	T	12.77	2.038989	0.35989	0.451253	0.097801	ENSG00000242866	ENST00000450892;ENST00000299992;ENST00000541030	T;T	0.76186	-1.0;-1.0	5.46	2.86	0.33363	.	0.509337	0.18353	N	0.143832	T	0.00012	0.0000	N	0.12182	0.205	0.34793	P	0.26405100000000004	B;B	0.18310	0.027;0.0	B;B	0.11329	0.006;0.002	T	0.45101	-0.9284	9	0.12766	T	0.61	-5.1913	6.9989	0.24799	0.0:0.23:0.0:0.77	rs2920780;rs58216659	525;1298	F5GXA4;Q7RTU9	.;STRC_HUMAN	R	1298;1298;525	ENSP00000401513:H1298R;ENSP00000440413:H525R	ENSP00000299992:H1298R	H	-	2	0	STRC	41684791	1.000000	0.71417	0.982000	0.44146	0.621000	0.37620	1.762000	0.38451	1.024000	0.39682	0.454000	0.30748	CAC	.	.	weak		0.542	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
KNDC1	85442	hgsc.bcm.edu	37	10	135012583	135012583	+	Missense_Mutation	SNP	C	C	A	rs111276772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135012583C>A	ENST00000304613.3	+	14	2592	c.2571C>A	c.(2569-2571)gaC>gaA	p.D857E	KNDC1_ENST00000368571.2_Missense_Mutation_p.D792E|KNDC1_ENST00000368572.2_Missense_Mutation_p.D857E			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	857	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)		AACGTGATGACCAGAGTCCAG	0.741													C|||	102	0.0203674	0.0749	0.0029	5008	,	,		10501	0.0		0.001	False		,,,				2504	0.0				p.D857E		Atlas-SNP	.											.	KNDC1	155	.	0			c.C2571A						PASS	.		GLU/ASP	232,4062		3,226,1918	10.0	12.0	11.0		2571	-3.8	0.0	10	dbSNP_132	11	5,8501		0,5,4248	yes	missense	KNDC1	NM_152643.6	45	3,231,6166	AA,AC,CC		0.0588,5.4029,1.8516	benign	857/1750	135012583	237,12563	2147	4253	6400	SO:0001583	missense	85442	exon14			TGATGACCAGAGT	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.2571C>A	10.37:g.135012583C>A	ENSP00000304437:p.Asp857Glu	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	C	7.348	0.622286	0.14193	0.054029	5.88E-4	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.18502	2.69;2.69;2.21	1.93	-3.85	0.04243	.	13.355300	0.01309	U	0.010560	T	0.00552	0.0018	N	0.08118	0	0.09310	N	1	B;B;B	0.26195	0.144;0.002;0.106	B;B;B	0.19666	0.026;0.003;0.018	T	0.19614	-1.0300	10	0.22109	T	0.4	.	6.2917	0.21063	0.192:0.2336:0.5744:0.0	.	857;792;857	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	E	857;857;792	ENSP00000304437:D857E;ENSP00000357561:D857E;ENSP00000357560:D792E	ENSP00000304437:D857E	D	+	3	2	KNDC1	134862573	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.062000	0.14389	-0.906000	0.03866	-0.828000	0.03084	GAC	C|0.983;A|0.017	0.017	strong		0.741	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
VCAN	1462	hgsc.bcm.edu	37	5	82786194	82786194	+	Silent	SNP	T	T	C	rs12332199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82786194T>C	ENST00000265077.3	+	3	913	c.348T>C	c.(346-348)acT>acC	p.T116T	VCAN_ENST00000513984.1_Silent_p.T116T|VCAN_ENST00000343200.5_Silent_p.T116T|VCAN_ENST00000502527.2_Silent_p.T116T|VCAN_ENST00000342785.4_Silent_p.T116T|VCAN_ENST00000512590.2_Silent_p.T68T	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	116	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CCTCCCTCACTGTGGTCAAGC	0.532													C|||	1714	0.342252	0.5	0.3775	5008	,	,		19796	0.2034		0.3936	False		,,,				2504	0.1943				p.T116T		Atlas-SNP	.											.	VCAN	498	.	0			c.T348C						PASS	.	C	,,,	2057,2349	608.2+/-391.1	468,1121,614	146.0	137.0	140.0		348,348,348,348	0.9	0.1	5	dbSNP_120	140	3247,5353	649.2+/-400.6	601,2045,1654	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	1069,3166,2268	CC,CT,TT		37.7558,46.6863,40.7812	,,,	116/656,116/2410,116/1643,116/3397	82786194	5304,7702	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon3			CCTCACTGTGGTC	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.348T>C	5.37:g.82786194T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			T|0.613;C|0.387	0.387	strong		0.532	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
PCDHGA3	56112	hgsc.bcm.edu	37	5	140725828	140725828	+	Missense_Mutation	SNP	C	C	T	rs7736541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140725828C>T	ENST00000253812.6	+	1	2228	c.2228C>T	c.(2227-2229)gCg>gTg	p.A743V	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	743			A -> V (in dbSNP:rs7736541).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTGTGGGCGCGGACGGGGTT	0.667													.|||	2709	0.540935	0.8495	0.6297	5008	,	,		13856	0.3264		0.4274	False		,,,				2504	0.3988				p.A743V		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.C2228T						PASS	.	T	,,VAL/ALA,VAL/ALA	3497,909		1397,703,103	49.0	60.0	56.0		,,2228,2228	4.1	1.0	5	dbSNP_116	56	3761,4839		808,2145,1347	no	intron,intron,missense,missense	PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_032011.1	,,64,64	2205,2848,1450	TT,TC,CC		43.7326,20.631,44.195	,,,	,,743/933,743/830	140725828	7258,5748	2203	4300	6503	SO:0001583	missense	56112	exon1			TGGGCGCGGACGG	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.2228C>T	5.37:g.140725828C>T	ENSP00000253812:p.Ala743Val	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	206	202	0.980583	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	1148	0.5256410256410257	394	0.8008130081300813	220	0.6077348066298343	193	0.3374125874125874	341	0.449868073878628	.	4.381	0.070226	0.08436	0.79369	0.437326	ENSG00000254245	ENST00000253812	T	0.41400	1.0	5.33	4.14	0.48551	.	0.467918	0.13384	N	0.391917	T	0.00012	0.0000	N	0.00006	-3.215	0.48762	P	2.9599999999996296E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.42498	-0.9448	9	0.02654	T	1	.	5.5632	0.17157	0.2648:0.0722:0.0:0.663	rs7736541;rs59073584	743;743	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	V	743	ENSP00000253812:A743V	ENSP00000253812:A743V	A	+	2	0	PCDHGA3	140706012	0.003000	0.15002	0.983000	0.44433	0.605000	0.37080	0.472000	0.22116	0.399000	0.25367	-0.360000	0.07572	GCG	C|0.492;T|0.508	0.508	strong		0.667	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
KLHL38	340359	hgsc.bcm.edu	37	8	124658203	124658203	+	Missense_Mutation	SNP	T	T	C	rs72711231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124658203T>C	ENST00000325995.7	-	3	1545	c.1522A>G	c.(1522-1524)Aaa>Gaa	p.K508E	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	508										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						CTCCGGTCTTTCATGTCCGCA	0.522													T|||	563	0.11242	0.0477	0.0692	5008	,	,		20602	0.2143		0.0348	False		,,,				2504	0.2055				p.K508E		Atlas-SNP	.											.	KLHL38	81	.	0			c.A1522G						PASS	.	T	GLU/LYS	171,4011		4,163,1924	83.0	91.0	88.0		1522	5.2	1.0	8	dbSNP_130	88	320,8144		8,304,3920	yes	missense	KLHL38	NM_001081675.2	56	12,467,5844	CC,CT,TT		3.7807,4.089,3.8827	possibly-damaging	508/582	124658203	491,12155	2091	4232	6323	SO:0001583	missense	340359	exon3			GGTCTTTCATGTC		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.1522A>G	8.37:g.124658203T>C	ENSP00000321475:p.Lys508Glu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	196	95	0.484694	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	37	CCDS43766.1	204	0.09340659340659341	29	0.05894308943089431	21	0.058011049723756904	126	0.2202797202797203	28	0.036939313984168866	T	15.81	2.943702	0.53079	0.04089	0.037807	ENSG00000175946	ENST00000325995	T	0.66280	-0.2	5.18	5.18	0.71444	Kelch-type beta propeller (1);	0.137965	0.64402	D	0.000005	T	0.00039	0.0001	L	0.60455	1.87	0.21355	P	0.999710004	P	0.36789	0.57	B	0.35114	0.196	T	0.06162	-1.0842	9	0.23891	T	0.37	.	15.0289	0.71691	0.0:0.0:0.0:1.0	.	508	Q2WGJ6	KLH38_HUMAN	E	508	ENSP00000321475:K508E	ENSP00000321475:K508E	K	-	1	0	KLHL38	124727384	1.000000	0.71417	0.992000	0.48379	0.814000	0.46013	6.186000	0.72026	1.963000	0.57068	0.374000	0.22700	AAA	T|0.924;C|0.076	0.076	strong		0.522	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
POR	5447	hgsc.bcm.edu	37	7	75615006	75615006	+	Missense_Mutation	SNP	C	C	T	rs1057868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75615006C>T	ENST00000461988.1	+	13	1613	c.1508C>T	c.(1507-1509)gCc>gTc	p.A503V	POR_ENST00000419840.1_Missense_Mutation_p.A317V|POR_ENST00000394893.1_Missense_Mutation_p.A503V|POR_ENST00000439269.1_Missense_Mutation_p.A241V|POR_ENST00000545601.1_Missense_Mutation_p.A311V|POR_ENST00000450476.1_Missense_Mutation_p.A402V|TMEM120A_ENST00000338761.4_RNA|TMEM120A_ENST00000493111.2_RNA	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	500	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)	AAGGAGCCTGCCGGGGAGAAC	0.657													C|||	1433	0.286142	0.1702	0.2795	5008	,	,		15499	0.374		0.2952	False		,,,				2504	0.3476				p.A503V		Atlas-SNP	.											.	POR	46	.	0			c.C1508T	GRCh37	CM057356	POR	M	rs1057868	PASS	.	C	VAL/ALA	698,3446		75,548,1449	12.0	16.0	14.0		1508	3.5	0.0	7	dbSNP_86	14	2247,6049		309,1629,2210	yes	missense	POR	NM_000941.2	64	384,2177,3659	TT,TC,CC		27.0853,16.8436,23.6736	benign	503/681	75615006	2945,9495	2072	4148	6220	SO:0001583	missense	5447	exon13			AGCCTGCCGGGGA	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.1508C>T	7.37:g.75615006C>T	ENSP00000419970:p.Ala503Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	93	52	0.55914	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Missense_Mutation	SNP	ENST00000461988.1	37	CCDS5579.1	628	0.2875457875457875	68	0.13821138211382114	106	0.292817679558011	223	0.38986013986013984	231	0.30474934036939316	C	7.739	0.700936	0.15172	0.168436	0.270853	ENSG00000127948	ENST00000461988;ENST00000419840;ENST00000394893;ENST00000545601;ENST00000450476;ENST00000439269	D;D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64;-1.64	4.4	3.51	0.40186	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);	0.267846	0.35903	N	0.002907	T	0.00012	0.0000	N	0.13235	0.315	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	0.17167	-1.0378	9	0.29301	T	0.29	-1.5153	8.3965	0.32559	0.0:0.8905:0.0:0.1095	rs1057868;rs3198400;rs17840495;rs17846082;rs17859083;rs57699079	500;402;311;509	P16435;E7EVY7;F5H468;Q59ED7	NCPR_HUMAN;.;.;.	V	503;317;503;311;402;241	ENSP00000419970:A503V;ENSP00000414244:A317V;ENSP00000378355:A503V;ENSP00000446149:A311V;ENSP00000416572:A402V;ENSP00000412490:A241V	ENSP00000378355:A503V	A	+	2	0	POR	75452942	0.033000	0.19621	0.003000	0.11579	0.158000	0.22134	0.907000	0.28531	1.188000	0.43014	0.561000	0.74099	GCC	C|0.723;T|0.277	0.277	strong		0.657	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941	
SCN9A	6335	hgsc.bcm.edu	37	2	167145106	167145106	+	Silent	SNP	C	C	A	rs58465962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:167145106C>A	ENST00000409435.1	-	9	1154	c.1155G>T	c.(1153-1155)gtG>gtT	p.V385V	SCN9A_ENST00000303354.6_Silent_p.V386V|SCN9A_ENST00000409672.1_Silent_p.V385V|SCN9A_ENST00000375387.4_Silent_p.V386V|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	385					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCAGGAAAATCACTACGACAA	0.383													C|||	229	0.0457268	0.1551	0.0187	5008	,	,		15943	0.0		0.003	False		,,,				2504	0.0082				p.V385V		Atlas-SNP	.											.	SCN9A	296	.	0			c.G1155T						PASS	.	C		457,3229		28,401,1414	79.0	76.0	77.0		1155	1.8	1.0	2	dbSNP_129	77	45,8183		3,39,4072	no	coding-synonymous	SCN9A	NM_002977.3		31,440,5486	AA,AC,CC		0.5469,12.3983,4.2135		385/1978	167145106	502,11412	1843	4114	5957	SO:0001819	synonymous_variant	6335	exon10			GAAAATCACTACG	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1155G>T	2.37:g.167145106C>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			C|0.964;A|0.036	0.036	strong		0.383	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
SPAG17	200162	hgsc.bcm.edu	37	1	118644430	118644430	+	Silent	SNP	A	A	G	rs10754367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118644430A>G	ENST00000336338.5	-	5	632	c.567T>C	c.(565-567)aaT>aaC	p.N189N		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	189	Lys-rich.					cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TCACTGGTGCATTTGCCTCAG	0.498													G|||	2824	0.563898	0.6906	0.5072	5008	,	,		18672	0.4534		0.5477	False		,,,				2504	0.5634				p.N189N		Atlas-SNP	.											.	SPAG17	263	.	0			c.T567C						PASS	.	G		3023,1383	456.9+/-351.5	1051,921,231	312.0	267.0	282.0		567	-0.1	0.0	1	dbSNP_120	282	4844,3756	534.2+/-382.6	1369,2106,825	yes	coding-synonymous	SPAG17	NM_206996.2		2420,3027,1056	GG,GA,AA		43.6744,31.389,39.5125		189/2224	118644430	7867,5139	2203	4300	6503	SO:0001819	synonymous_variant	200162	exon5			TGGTGCATTTGCC		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.567T>C	1.37:g.118644430A>G		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	209	99	0.473684	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			A|0.430;G|0.570	0.570	strong		0.498	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
NOTCH2	4853	hgsc.bcm.edu	37	1	120480583	120480583	+	Silent	SNP	G	G	A	rs7543643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120480583G>A	ENST00000256646.2	-	20	3453	c.3234C>T	c.(3232-3234)tgC>tgT	p.C1078C		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1078	EGF-like 28. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTTCTGAACGCAAGTACCTT	0.468			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome				G|||	356	0.0710863	0.2458	0.0202	5008	,	,		18636	0.002		0.001	False		,,,				2504	0.0143				p.C1078C		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C3234T						PASS	.	G	,	906,3500	350.5+/-310.9	88,730,1385	133.0	122.0	125.0		3234,3234	-1.8	0.0	1	dbSNP_116	125	24,8576	16.6+/-54.9	0,24,4276	yes	coding-synonymous,coding-synonymous	NOTCH2	NM_001200001.1,NM_024408.3	,	88,754,5661	AA,AG,GG		0.2791,20.5629,7.1505	,	1078/1236,1078/2472	120480583	930,12076	2203	4300	6503	SO:0001819	synonymous_variant	4853	exon20	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CTGAACGCAAGTA	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.3234C>T	1.37:g.120480583G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_001200001	Q5T3X7|Q99734|Q9H240	Silent	SNP	ENST00000256646.2	37	CCDS908.1																																																																																			G|0.925;A|0.075	0.075	strong		0.468	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
CNGA2	1260	hgsc.bcm.edu	37	X	150912171	150912171	+	Missense_Mutation	SNP	G	G	A	rs150539917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:150912171G>A	ENST00000329903.4	+	6	1229	c.1196G>A	c.(1195-1197)cGa>cAa	p.R399Q		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	399			R -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)	p.R399Q(1)		breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					ATGCAGTTCCGAAAGGTCAGC	0.493													G|||	104	0.0275497	0.0726	0.0072	3775	,	,		18285	0.0		0.003	False		,,,				2504	0.0				p.R399Q		Atlas-SNP	.											.	CNGA2	136	.	1	Substitution - Missense(1)	breast(1)	c.G1196A						PASS	.	G	GLN/ARG	355,3480		19,261,56,1352,515	93.0	82.0	86.0		1196	3.2	1.0	X	dbSNP_134	86	2,6726		0,1,1,2427,1871	yes	missense	CNGA2	NM_005140.1	43	19,262,57,3779,2386	AA,AG,A,GG,G		0.0297,9.2568,3.3797	probably-damaging	399/665	150912171	357,10206	2203	4300	6503	SO:0001583	missense	1260	exon7			AGTTCCGAAAGGT	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.1196G>A	X.37:g.150912171G>A	ENSP00000328478:p.Arg399Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_005140	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	48	0.028933092224231464	33	0.07051282051282051	2	0.005555555555555556	0	0.0	1	0.0013192612137203166	G	15.92	2.975018	0.53720	0.092568	2.97E-4	ENSG00000183862	ENST00000329903	D	0.97066	-4.23	4.96	3.18	0.36537	Cyclic nucleotide-binding-like (1);	0.057024	0.64402	D	0.000001	T	0.77745	0.4176	M	0.88450	2.955	0.20764	P	0.999856176	D	0.89917	1.0	D	0.79108	0.992	T	0.79874	-0.1619	9	0.46703	T	0.11	.	9.1566	0.36996	0.1872:0.0:0.8128:0.0	.	399	Q16280	CNGA2_HUMAN	Q	399	ENSP00000328478:R399Q	ENSP00000328478:R399Q	R	+	2	0	CNGA2	150662827	1.000000	0.71417	0.996000	0.52242	0.974000	0.67602	5.415000	0.66411	0.437000	0.26423	-0.344000	0.07964	CGA	G|0.964;A|0.036	0.036	strong		0.493	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140	
NLRP7	199713	hgsc.bcm.edu	37	19	55450696	55450696	+	Silent	SNP	G	G	A	rs775880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55450696G>A	ENST00000590030.1	-	3	1531	c.1491C>T	c.(1489-1491)atC>atT	p.I497I	NLRP7_ENST00000340844.2_Silent_p.I497I|NLRP7_ENST00000448121.2_Silent_p.I497I|NLRP7_ENST00000446217.1_Silent_p.I525I|NLRP7_ENST00000328092.5_Silent_p.I497I|NLRP7_ENST00000588756.1_Silent_p.I497I|NLRP7_ENST00000592784.1_Silent_p.I497I			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	497							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)		GTACGTCCCCGATGTCCCAGG	0.562													.|||	447	0.0892572	0.2368	0.0562	5008	,	,		18553	0.003		0.0706	False		,,,				2504	0.0215				p.I497I		Atlas-SNP	.											.	NLRP7	411	.	0			c.C1491T						PASS	.	A	,,	922,3484	736.7+/-410.8	100,722,1381	72.0	69.0	70.0		1491,1491,1491	-1.5	0.0	19	dbSNP_86	70	314,8286	801.4+/-407.4	3,308,3989	no	coding-synonymous,coding-synonymous,coding-synonymous	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	,,	103,1030,5370	AA,AG,GG		3.6512,20.926,9.5033	,,	497/1038,497/1010,497/981	55450696	1236,11770	2203	4300	6503	SO:0001819	synonymous_variant	199713	exon4			GTCCCCGATGTCC	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.1491C>T	19.37:g.55450696G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			G|0.908;A|0.092	0.092	strong		0.562	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
MUC6	4588	hgsc.bcm.edu	37	11	1017566	1017566	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017566G>A	ENST00000421673.2	-	31	5285	c.5235C>T	c.(5233-5235)acC>acT	p.T1745T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1745	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			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)		GGGATGTAGAGGTTTTGGCCG	0.547																																					p.T1745T		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,-2,2	MUC6	408	2	0			c.C5235T						scavenged	.						769.0	740.0	750.0					11																	1017566		2199	4287	6486	SO:0001819	synonymous_variant	4588	exon31			TGTAGAGGTTTTG	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.5235C>T	11.37:g.1017566G>A		Somatic	1007	23	0.0228401		WXS	Illumina HiSeq	Phase_I	1214	88	0.0724876	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	none		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
MICA	100507436	hgsc.bcm.edu	37	6	31378425	31378425	+	Missense_Mutation	SNP	A	A	G	rs1051786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31378425A>G	ENST00000449934.2	+	2	230	c.176A>G	c.(175-177)tAt>tGt	p.Y59C	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)				TTCCTGCGCTATGACAGGCAG	0.542													g|||	1827	0.364816	0.4788	0.4078	5008	,	,		19566	0.3006		0.3141	False		,,,				2504	0.2986				p.Y59C		Atlas-SNP	.											.	MICA	21	.	0			c.A176G						PASS	.	G	CYS/TYR	579,805		132,315,245	40.0	44.0	43.0		176	-5.5	0.0	6	dbSNP_86	43	919,2263		126,667,798	no	missense	MICA	NM_001177519.1	194	258,982,1043	GG,GA,AA		28.8812,41.8353,32.8077	benign	59/333	31378425	1498,3068	692	1591	2283	SO:0001583	missense	100507436	exon2			TGCGCTATGACAG	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.176A>G	6.37:g.31378425A>G	ENSP00000413079:p.Tyr59Cys	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	184	184	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	799	0.3658424908424908	227	0.4613821138211382	169	0.46685082872928174	160	0.27972027972027974	243	0.32058047493403696	N	4.126	0.021662	0.08006	0.418353	0.288812	ENSG00000204520	ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.03635	3.86;3.86	2.89	-5.5	0.02576	.	0.906056	0.08949	N	0.870393	T	0.00695	0.0023	.	.	.	0.80722	P	0.0	B	0.22983	0.078	B	0.24541	0.054	T	0.44922	-0.9296	8	0.34782	T	0.22	.	3.6542	0.08214	0.5494:0.0:0.1662:0.2844	rs1051786;rs3192167;rs16899591;rs17200165;rs17845517;rs17858407;rs17879747;rs58269144	59	Q96QC4	.	C	59;59;59;46	ENSP00000413079:Y59C;ENSP00000402410:Y46C	ENSP00000365394:Y59C	Y	+	2	0	MICA	31486404	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.180000	0.00569	-2.184000	0.00762	-2.615000	0.00158	TAT	A|0.641;G|0.359	0.359	strong		0.542	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
CYP4F12	66002	hgsc.bcm.edu	37	19	15791074	15791074	+	Missense_Mutation	SNP	A	A	G	rs114254919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791074A>G	ENST00000550308.1	+	4	744	c.364A>G	c.(364-366)Aat>Gat	p.N122D	CYP4F12_ENST00000324632.10_Missense_Mutation_p.N122D	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	122					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	ACCCAAGGATAATCTCTTCAT	0.567													.|||	103	0.0205671	0.0734	0.0072	5008	,	,		20731	0.0		0.001	False		,,,				2504	0.0				p.N122D		Atlas-SNP	.											CYP4F12,colon,carcinoma,-1,1	CYP4F12	89	1	0			c.A364G						PASS	.	G	ASP/ASN	190,4188		1,188,2000	139.0	143.0	142.0		364	-5.8	0.0	19	dbSNP_132	142	3,8585		0,3,4291	yes	missense	CYP4F12	NM_023944.3	23	1,191,6291	GG,GA,AA		0.0349,4.3399,1.4885	benign	122/525	15791074	193,12773	2189	4294	6483	SO:0001583	missense	66002	exon4			AAGGATAATCTCT	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.364A>G	19.37:g.15791074A>G	ENSP00000448998:p.Asn122Asp	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	372	95	0.255376	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	38	0.0173992673992674	35	0.07113821138211382	3	0.008287292817679558	0	0.0	0	0.0	.	1.398	-0.578943	0.03854	0.043399	3.49E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.78707	-1.2;-1.2	2.92	-5.84	0.02318	.	1.494030	0.04917	N	0.454288	T	0.07458	0.0188	N	0.16567	0.415	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	0.22836	-1.0205	10	0.11794	T	0.64	.	1.4308	0.02333	0.4684:0.1455:0.2397:0.1465	.	122;122;122	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	D	122	ENSP00000448998:N122D;ENSP00000321821:N122D	ENSP00000321821:N122D	N	+	1	0	CYP4F12	15652074	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.894000	0.00707	-2.136000	0.00810	-1.140000	0.01884	AAT	A|0.989;G|0.011	0.011	strong		0.567	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
CNGB1	1258	hgsc.bcm.edu	37	16	57935443	57935443	+	Missense_Mutation	SNP	C	C	A	rs16942445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57935443C>A	ENST00000251102.8	-	28	2941	c.2881G>T	c.(2881-2883)Gca>Tca	p.A961S	CNGB1_ENST00000564448.1_Missense_Mutation_p.A955S	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	961			A -> S (in dbSNP:rs16942445).		cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						TGAAAGAGTGCGACTTTGCTA	0.537													C|||	193	0.0385383	0.1384	0.0086	5008	,	,		22586	0.0		0.004	False		,,,				2504	0.0				p.A961S	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.G2881T						PASS	.	C	SER/ALA	387,3743		19,349,1697	111.0	114.0	113.0		2881	3.9	1.0	16	dbSNP_123	113	5,8409		0,5,4202	yes	missense	CNGB1	NM_001297.4	99	19,354,5899	AA,AC,CC		0.0594,9.3705,3.125	benign	961/1252	57935443	392,12152	2065	4207	6272	SO:0001583	missense	1258	exon28			AGAGTGCGACTTT	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2881G>T	16.37:g.57935443C>A	ENSP00000251102:p.Ala961Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	37	CCDS42169.1	63	0.028846153846153848	59	0.11991869918699187	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	8.424	0.846959	0.17034	0.093705	5.94E-4	ENSG00000070729	ENST00000251102	D	0.96427	-4.01	4.8	3.86	0.44501	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.070612	0.56097	D	0.000026	T	0.17450	0.0419	L	0.28556	0.865	0.80722	D	1	B;B	0.23540	0.087;0.082	B;B	0.28784	0.041;0.094	T	0.62955	-0.6744	10	0.14252	T	0.57	.	8.8322	0.35091	0.0:0.8291:0.0:0.1709	rs16942445;rs52812859;rs16942445	333;961	Q14028-2;Q14028	.;CNGB1_HUMAN	S	961	ENSP00000251102:A961S	ENSP00000251102:A961S	A	-	1	0	CNGB1	56492944	1.000000	0.71417	0.996000	0.52242	0.031000	0.12232	2.124000	0.42006	1.028000	0.39785	-0.215000	0.12644	GCA	C|0.957;A|0.043	0.043	strong		0.537	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
SSPO	23145	hgsc.bcm.edu	37	7	149489037	149489037	+	RNA	SNP	T	T	C	rs1635802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149489037T>C	ENST00000378016.2	+	0	5378							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)			CCCGGAGGCCTGCACAGCACC	0.652													C|||	202	0.0403355	0.1029	0.0144	5008	,	,		16636	0.004		0.003	False		,,,				2504	0.0501				p.L1793P		Atlas-SNP	.											.	.	.	.	0			c.T5378C						PASS	.	C		308,3816		12,284,1766	25.0	30.0	28.0		5382	3.9	0.0	7	dbSNP_89	28	19,8349		0,19,4165	no	coding-notMod3	SSPO	NM_198455.2		12,303,5931	CC,CT,TT		0.2271,7.4685,2.6177			149489037	327,12165	2062	4184	6246			23145	exon35			GAGGCCTGCACAG	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.149489037T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.977;C|0.023	0.023	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
MT-ND4	4538	hgsc.bcm.edu	37	M	12049	12049	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:12049C>T	ENST00000361381.2	+	1	1290	c.1290C>T	c.(1288-1290)ttC>ttT	p.F430F	MT-TS2_ENST00000387449.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	430					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						AAACCCTCATTCACACGAGAA	0.448																																					p.F430F		Atlas-SNP	.											.	.	.	.	0			c.C1290T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CTCATTCACACGA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1290C>T	M.37:g.12049C>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.448	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
TMEM199	147007	hgsc.bcm.edu	37	17	26691321	26691321	+	IGR	SNP	A	A	G	rs9910163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26691321A>G	ENST00000292114.3	+	0	3148				VTN_ENST00000536498.1_Missense_Mutation_p.L206S|TMEM199_ENST00000509083.1_Intron|VTN_ENST00000438614.1_Missense_Mutation_p.L206S|CTB-96E2.2_ENST00000555059.2_3'UTR|VTN_ENST00000431468.1_Missense_Mutation_p.L207S|CTB-96E2.7_ENST00000577850.1_RNA|CTB-96E2.3_ENST00000591482.1_RNA	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		GACAATGGCCAAGGCATAGAT	0.577													G|||	4403	0.879193	0.9887	0.7651	5008	,	,		19616	0.9921		0.7584	False		,,,				2504	0.82				p.L207S		Atlas-SNP	.											.	SEBOX	20	.	0			c.T620C						PASS	.	G	SER/LEU	4023,173		1932,159,7	27.0	31.0	29.0		620	2.1	0.1	17	dbSNP_119	29	6566,1888		2540,1486,201	yes	missense	SEBOX	NM_001080837.2	145	4472,1645,208	GG,GA,AA		22.3326,4.123,16.2925	benign	207/217	26691321	10589,2061	2098	4227	6325	SO:0001628	intergenic_variant	645832	exon3			ATGGCCAAGGCAT	AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 32"""	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498		17.37:g.26691321A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_001080837		Missense_Mutation	SNP	ENST00000292114.3	37	CCDS11228.1	1900	0.86996336996337	483	0.9817073170731707	285	0.787292817679558	569	0.9947552447552448	563	0.7427440633245382	G	0.012	-1.684992	0.00745	0.95877	0.776674	ENSG00000109072;ENSG00000109072;ENSG00000109072;ENSG00000109072;ENSG00000258852	ENST00000431468;ENST00000536498;ENST00000438614;ENST00000247029;ENST00000555059	D;D;D	0.91180	-2.72;-2.8;-2.8	5.21	2.09	0.27110	.	0.331751	0.22185	N	0.063460	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.45963	-0.9225	9	0.05959	T	0.93	.	12.9531	0.58411	0.0717:0.0:0.8187:0.1096	rs9910163;rs60945713;rs9910163	207;206	Q9HB31;C9JDG5	SEBOX_HUMAN;.	S	207;206;206;211;232	ENSP00000416240:L207S;ENSP00000444503:L206S;ENSP00000395142:L206S	ENSP00000247029:L211S	L	-	2	0	VTN;CTB-96E2.2	23715448	0.981000	0.34729	0.147000	0.22382	0.188000	0.23474	1.886000	0.39688	0.080000	0.16959	-1.964000	0.00472	TTG	A|0.120;G|0.880	0.880	strong		0.577	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464	
PREP	5550	hgsc.bcm.edu	37	6	105776792	105776792	+	Silent	SNP	G	G	A	rs6902415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:105776792G>A	ENST00000369110.3	-	9	1317	c.1125C>T	c.(1123-1125)ttC>ttT	p.F375F		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	375					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	CATCGAGCGGGAAGGTCTTAA	0.463													G|||	1158	0.23123	0.6241	0.0735	5008	,	,		17509	0.0704		0.0676	False		,,,				2504	0.1462				p.F375F		Atlas-SNP	.											.	PREP	65	.	0			c.C1125T						PASS	.	G		2312,2094	604.8+/-390.4	618,1076,509	128.0	126.0	127.0		1125	1.6	1.0	6	dbSNP_116	127	540,8060	149.1+/-204.2	20,500,3780	no	coding-synonymous	PREP	NM_002726.4		638,1576,4289	AA,AG,GG		6.2791,47.5261,21.9283		375/711	105776792	2852,10154	2203	4300	6503	SO:0001819	synonymous_variant	5550	exon9			GAGCGGGAAGGTC		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.1125C>T	6.37:g.105776792G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_002726	Q8N6D4	Silent	SNP	ENST00000369110.3	37	CCDS5053.1																																																																																			G|0.789;A|0.211	0.211	strong		0.463	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
ZNF362	149076	hgsc.bcm.edu	37	1	33745781	33745781	+	Missense_Mutation	SNP	G	G	A	rs143005937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:33745781G>A	ENST00000539719.1	+	5	576	c.406G>A	c.(406-408)Gcg>Acg	p.A136T	ZNF362_ENST00000373428.5_Missense_Mutation_p.A136T	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	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)			endometrium(3)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				AAGCGCGGGCGCGGGCACGGG	0.697													G|||	40	0.00798722	0.0272	0.0058	5008	,	,		11977	0.0		0.0	False		,,,				2504	0.0				p.A136T	Pancreas(162;1431 2676 35353 38425)	Atlas-SNP	.											.	ZNF362	31	.	0			c.G406A						PASS	.	G	THR/ALA	138,4266	98.5+/-137.1	6,126,2070	53.0	59.0	57.0		406	1.2	0.0	1	dbSNP_134	57	0,8596		0,0,4298	yes	missense	ZNF362	NM_152493.2	58	6,126,6368	AA,AG,GG		0.0,3.1335,1.0615	benign	136/421	33745781	138,12862	2202	4298	6500	SO:0001583	missense	149076	exon5			GCGGGCGCGGGCA		CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"""Zinc fingers, C2H2-type"""	18079	protein-coding gene	gene with protein product	"""rotund homolog (Drosophila)"""						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.406G>A	1.37:g.33745781G>A	ENSP00000446335:p.Ala136Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	137	81	0.591241	NM_152493	Q8WYU4	Missense_Mutation	SNP	ENST00000539719.1	37	CCDS377.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	0.389	-0.924363	0.02377	0.031335	0.0	ENSG00000160094	ENST00000483388;ENST00000539719;ENST00000373428	T;T	0.07567	3.18;3.18	2.39	1.17	0.20885	.	1.192330	0.06286	N	0.698320	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.45687	-0.9244	10	0.12766	T	0.61	.	4.807	0.13325	0.8237:0.0:0.1763:0.0	.	136	Q5T0B9	ZN362_HUMAN	T	123;136;136	ENSP00000446335:A136T;ENSP00000362527:A136T	ENSP00000362527:A136T	A	+	1	0	ZNF362	33518368	0.998000	0.40836	0.007000	0.13788	0.438000	0.31896	0.857000	0.27831	0.111000	0.17947	-0.839000	0.03059	GCG	G|0.989;A|0.011	0.011	strong		0.697	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011857.2	NM_152493	
MYO5B	4645	hgsc.bcm.edu	37	18	47506874	47506874	+	Silent	SNP	G	G	T	rs16951352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47506874G>T	ENST00000285039.7	-	9	1295	c.996C>A	c.(994-996)atC>atA	p.I332I		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	332	Myosin motor.				endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		CAAGGTGCAAGATAGAAGCAA	0.418													G|||	61	0.0121805	0.0431	0.0043	5008	,	,		18907	0.0		0.001	False		,,,				2504	0.0				p.I332I		Atlas-SNP	.											.	MYO5B	178	.	0			c.C996A						PASS	.	G		125,3877		0,125,1876	117.0	113.0	114.0		996	4.3	1.0	18	dbSNP_123	114	11,8301		0,11,4145	no	coding-synonymous	MYO5B	NM_001080467.2		0,136,6021	TT,TG,GG		0.1323,3.1234,1.1044		332/1849	47506874	136,12178	2001	4156	6157	SO:0001819	synonymous_variant	4645	exon9			GTGCAAGATAGAA	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.996C>A	18.37:g.47506874G>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			G|0.993;T|0.007	0.007	strong		0.418	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
IDS	3423	hgsc.bcm.edu	37	X	148582549	148582549	+	Silent	SNP	G	G	A	rs1141608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:148582549G>A	ENST00000340855.6	-	4	647	c.438C>T	c.(436-438)acC>acT	p.T146T	IDS_ENST00000422081.2_5'UTR|IDS_ENST00000541269.1_5'UTR|IDS_ENST00000370441.4_Silent_p.T146T|IDS_ENST00000370443.4_Silent_p.T146T|IDS_ENST00000427113.2_5'Flank|IDS_ENST00000490775.1_5'UTR	NM_000202.5|NM_001166550.1	NP_000193.1|NP_001160022.1	P22304	IDS_HUMAN	iduronate 2-sulfatase	146					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	lysosomal lumen (GO:0043202)	iduronate-2-sulfatase activity (GO:0004423)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(5)|large_intestine(2)|lung(8)|prostate(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					GAGAATCATCGGTATGGTTAG	0.378													G|||	727	0.192583	0.1989	0.1369	3775	,	,		14561	0.002		0.3161	False		,,,				2504	0.0501				p.T146T		Atlas-SNP	.											.	IDS	46	.	0			c.C438T						PASS	.	G	,,	968,2867		117,600,134,915,437	120.0	110.0	114.0		438,168,438	1.1	1.0	X	dbSNP_86	114	2656,4072		401,1104,750,923,1122	no	coding-synonymous,coding-synonymous,coding-synonymous	IDS	NM_000202.5,NM_001166550.1,NM_006123.4	,,	518,1704,884,1838,1559	AA,AG,A,GG,G		39.4768,25.2412,34.3084	,,	146/551,56/461,146/344	148582549	3624,6939	2203	4300	6503	SO:0001819	synonymous_variant	3423	exon4			ATCATCGGTATGG	M58342	CCDS14685.1, CCDS14686.1	Xq27.3-q28	2012-10-02	2008-08-01		ENSG00000010404	ENSG00000010404	3.1.6.13		5389	protein-coding gene	gene with protein product	"""Hunter syndrome"""	300823		SIDS			Standard	NM_006123		Approved		uc011mxe.2	P22304	OTTHUMG00000022615	ENST00000340855.6:c.438C>T	X.37:g.148582549G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	74	26	0.351351	NM_006123	D3DWT4|Q14604|Q9BRM3	Silent	SNP	ENST00000340855.6	37	CCDS14685.1																																																																																			G|0.703;0|0.015	.	strong		0.378	IDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058677.3		
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117553	46117553	+	Missense_Mutation	SNP	C	C	A	rs35076450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46117553C>A	ENST00000400365.3	+	1	467	c.437C>A	c.(436-438)cCg>cAg	p.P146Q	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	146	19 X 5 AA repeats of C-C-X(3).		P -> Q (in dbSNP:rs35076450).			keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						ATCTCCTCCCCGTGTCAACAG	0.612													C|||	19	0.00379393	0.0136	0.0014	5008	,	,		19291	0.0		0.0	False		,,,				2504	0.0				p.P146Q		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.C437A						PASS	.	C	GLN/PRO,	66,4340	61.7+/-98.7	1,64,2138	161.0	165.0	164.0		437,	0.9	0.1	21	dbSNP_126	164	0,8600		0,0,4300	no	missense,intron	TSPEAR,KRTAP10-12	NM_198699.1,NM_144991.2	76,	1,64,6438	AA,AC,CC		0.0,1.498,0.5075	possibly-damaging,	146/246,	46117553	66,12940	2203	4300	6503	SO:0001583	missense	386685	exon1			CCTCCCCGTGTCA	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"""Keratin associated proteins"""	20533	protein-coding gene	gene with protein product			"""keratin associated protein 18-12"""	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.437C>A	21.37:g.46117553C>A	ENSP00000383216:p.Pro146Gln	Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	265	136	0.513208	NM_198699	B2RPA3	Missense_Mutation	SNP	ENST00000400365.3	37	CCDS42967.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	c	0.797	-0.756781	0.03019	0.01498	0.0	ENSG00000189169	ENST00000400365;ENST00000452870	T	0.00644	6.01	2.19	0.906	0.19314	.	.	.	.	.	T	0.00552	0.0018	L	0.56280	1.765	0.09310	N	1	P	0.36660	0.564	B	0.32149	0.141	T	0.48536	-0.9027	9	0.54805	T	0.06	.	5.9287	0.19126	0.0:0.5224:0.4776:0.0	rs35076450	146	P60413	KR10C_HUMAN	Q	146;54	ENSP00000383216:P146Q	ENSP00000383216:P146Q	P	+	2	0	KRTAP10-12	44941981	0.001000	0.12720	0.088000	0.20740	0.003000	0.03518	0.160000	0.16462	0.881000	0.35993	0.305000	0.20034	CCG	C|0.995;A|0.005	0.005	strong		0.612	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699	
RP1L1	94137	hgsc.bcm.edu	37	8	10464755	10464755	+	Missense_Mutation	SNP	C	C	T	rs55642448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10464755C>T	ENST00000382483.3	-	4	7076	c.6853G>A	c.(6853-6855)Gga>Aga	p.G2285R		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2365	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.G2285R(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GGAGTGTCTCCACCTGGGGAA	0.597													C|||	2364	0.472045	0.3464	0.5317	5008	,	,		17514	0.5516		0.3976	False		,,,				2504	0.5941				p.G2285R		Atlas-SNP	.											RP1L1,NS,carcinoma,0,2	RP1L1	453	2	1	Substitution - Missense(1)	prostate(1)	c.G6853A						PASS	.	C	ARG/GLY	1376,2534		259,858,838	130.0	135.0	134.0		6853	3.3	0.0	8	dbSNP_129	134	3221,5071		630,1961,1555	yes	missense	RP1L1	NM_178857.5	125	889,2819,2393	TT,TC,CC		38.8447,35.1918,37.6742	possibly-damaging	2285/2401	10464755	4597,7605	1955	4146	6101	SO:0001583	missense	94137	exon4			TGTCTCCACCTGG	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.6853G>A	8.37:g.10464755C>T	ENSP00000371923:p.Gly2285Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	974	0.445970695970696	161	0.32723577235772355	172	0.47513812154696133	331	0.5786713286713286	310	0.40897097625329815	C	12.65	2.000991	0.35320	0.351918	0.388447	ENSG00000183638	ENST00000382483	T	0.07327	3.2	4.23	3.35	0.38373	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.36010	0.532	B	0.32342	0.144	T	0.06698	-1.0812	8	0.39692	T	0.17	-4.8465	7.615	0.28152	0.0:0.7443:0.1654:0.0904	rs55642448;rs62490853	2285	A6NKC6	.	R	2285	ENSP00000371923:G2285R	ENSP00000371923:G2285R	G	-	1	0	RP1L1	10502165	0.000000	0.05858	0.001000	0.08648	0.105000	0.19272	0.102000	0.15272	1.141000	0.42275	0.505000	0.49811	GGA	C|0.574;T|0.426	0.426	strong		0.597	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
SEC31B	25956	hgsc.bcm.edu	37	10	102269085	102269085	+	Missense_Mutation	SNP	C	C	A	rs3793706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102269085C>A	ENST00000370345.3	-	4	484	c.387G>T	c.(385-387)ttG>ttT	p.L129F	SEC31B_ENST00000535773.1_Intron|NDUFB8_ENST00000557395.1_Intron|NDUFB8_ENST00000531258.1_Intron|SEC31B_ENST00000370329.5_Missense_Mutation_p.L129F|SEC31B_ENST00000451524.1_Missense_Mutation_p.L129F	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	132	0	0	1365	WXS	Illumina HiSeq	Phase_I	127	61	0.480315	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	
ITGA7	3679	hgsc.bcm.edu	37	12	56089357	56089357	+	Missense_Mutation	SNP	C	C	T	rs1800974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56089357C>T	ENST00000555728.1	-	15	2112	c.2084G>A	c.(2083-2085)cGc>cAc	p.R695H	ITGA7_ENST00000394230.2_Missense_Mutation_p.R655H|ITGA7_ENST00000347027.6_Missense_Mutation_p.R645H|ITGA7_ENST00000257879.6_Missense_Mutation_p.R651H|ITGA7_ENST00000394229.2_Missense_Mutation_p.R651H|ITGA7_ENST00000257880.7_Missense_Mutation_p.R695H|ITGA7_ENST00000553804.1_Missense_Mutation_p.R655H|ITGA7_ENST00000452168.2_Missense_Mutation_p.R558H			Q13683	ITA7_HUMAN	integrin, alpha 7	695			R -> H (in dbSNP:rs1800974). {ECO:0000269|PubMed:10403775, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9473524, ECO:0000269|PubMed:9590299, ECO:0000269|Ref.3}.		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)			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						GAAGCGGGCGCGGACCAGCTG	0.597													C|||	3002	0.599441	0.3094	0.621	5008	,	,		18591	0.9306		0.495	False		,,,				2504	0.7423				p.R655H		Atlas-SNP	.											.	ITGA7	194	.	0			c.G1964A	GRCh37	CM067685	ITGA7	M	rs1800974	PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	1497,2909	479.4+/-358.5	250,997,956	78.0	74.0	75.0		1964,1673,1952	-0.7	0.1	12	dbSNP_89	75	4373,4227	583.1+/-391.5	1143,2087,1070	yes	missense,missense,missense	ITGA7	NM_001144996.1,NM_001144997.1,NM_002206.2	29,29,29	1393,3084,2026	TT,TC,CC		49.1512,33.9764,45.133	benign,benign,benign	655/1142,558/1045,651/1138	56089357	5870,7136	2203	4300	6503	SO:0001583	missense	3679	exon14			CGGGCGCGGACCA		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.2084G>A	12.37:g.56089357C>T	ENSP00000452387:p.Arg695His	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	221	109	0.493213	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Missense_Mutation	SNP	ENST00000555728.1	37		1284	0.5879120879120879	162	0.32926829268292684	209	0.5773480662983426	528	0.9230769230769231	385	0.5079155672823219	C	9.646	1.140294	0.21205	0.339764	0.508488	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000555728	T;T;T;T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84	4.84	-0.706	0.11249	Integrin alpha-2 (1);	0.821367	0.11353	N	0.572722	T	0.00012	0.0000	N	0.16656	0.425	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.06405	0.001;0.0;0.001;0.002	T	0.29088	-1.0023	9	0.15952	T	0.53	.	9.2195	0.37368	0.0:0.3884:0.0:0.6116	rs1800974;rs17434612;rs17855683;rs61528939;rs1800974	558;695;655;714	Q13683-13;Q13683;Q13683-3;Q4LE35	.;ITA7_HUMAN;.;.	H	655;651;645;558;695;655;651;695	ENSP00000452120:R655H;ENSP00000257879:R651H;ENSP00000343009:R645H;ENSP00000393844:R558H;ENSP00000257880:R695H;ENSP00000377777:R655H;ENSP00000377776:R651H;ENSP00000452387:R695H	ENSP00000257879:R651H	R	-	2	0	ITGA7	54375624	0.001000	0.12720	0.079000	0.20413	0.953000	0.61014	0.204000	0.17335	-0.033000	0.13736	0.561000	0.74099	CGC	C|0.489;T|0.511	0.511	strong		0.597	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	
POLRMT	5442	hgsc.bcm.edu	37	19	617573	617573	+	Missense_Mutation	SNP	G	G	A	rs142850300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:617573G>A	ENST00000588649.2	-	19	3662	c.3578C>T	c.(3577-3579)tCt>tTt	p.S1193F	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	1193	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)			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)		GCCTTACTCAGAGCAGAACCG	0.637													g|||	29	0.00579073	0.0197	0.0043	5008	,	,		11732	0.0		0.0	False		,,,				2504	0.0				p.S1193F		Atlas-SNP	.											.	POLRMT	91	.	0			c.C3578T						PASS	.	G	PHE/SER	73,4333		1,71,2131	42.0	41.0	41.0		3578	2.1	0.0	19	dbSNP_134	41	0,8600		0,0,4300	yes	missense	POLRMT	NM_005035.3	155	1,71,6431	AA,AG,GG		0.0,1.6568,0.5613	benign	1193/1231	617573	73,12933	2203	4300	6503	SO:0001583	missense	5442	exon19			TACTCAGAGCAGA		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.3578C>T	19.37:g.617573G>A	ENSP00000465759:p.Ser1193Phe	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	25	0.657895	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	.	0.192	-1.052853	0.01965	0.016568	0.0	ENSG00000099821	ENST00000215591	T	0.47528	0.84	3.21	2.12	0.27331	.	1.125910	0.06566	N	0.747594	T	0.31638	0.0803	M	0.68317	2.08	0.09310	N	1	B	0.14805	0.011	B	0.26310	0.068	T	0.36529	-0.9744	10	0.37606	T	0.19	.	7.4584	0.27280	0.0:0.0:0.7418:0.2582	.	1193	O00411	RPOM_HUMAN	F	1193	ENSP00000215591:S1193F	ENSP00000215591:S1193F	S	-	2	0	POLRMT	568573	0.086000	0.21541	0.007000	0.13788	0.002000	0.02628	1.811000	0.38942	0.645000	0.30675	0.431000	0.28591	TCT	G|0.995;A|0.005	0.005	strong		0.637	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
C2orf43	60526	hgsc.bcm.edu	37	2	20886706	20886706	+	Missense_Mutation	SNP	T	T	C	rs147773589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20886706T>C	ENST00000237822.3	-	7	1014	c.935A>G	c.(934-936)gAc>gGc	p.D312G	C2orf43_ENST00000403006.2_Missense_Mutation_p.D182G|C2orf43_ENST00000541941.1_Missense_Mutation_p.D182G|C2orf43_ENST00000440866.2_3'UTR|C2orf43_ENST00000381090.3_Missense_Mutation_p.D312G|C2orf43_ENST00000435420.2_Missense_Mutation_p.D264G	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	312										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCAATCATGTCTGCCATTTC	0.433													T|||	7	0.00139776	0.0053	0.0	5008	,	,		18458	0.0		0.0	False		,,,				2504	0.0				p.D312G		Atlas-SNP	.											.	C2orf43	28	.	0			c.A935G						PASS	.	T	GLY/ASP	30,4376	37.6+/-69.7	0,30,2173	159.0	141.0	147.0		935	-4.0	0.0	2	dbSNP_134	147	0,8600		0,0,4300	yes	missense	C2orf43	NM_021925.2	94	0,30,6473	CC,CT,TT		0.0,0.6809,0.2307	benign	312/326	20886706	30,12976	2203	4300	6503	SO:0001583	missense	60526	exon7			ATCATGTCTGCCA	AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961			26145	protein-coding gene	gene with protein product		613570				17135363, 24357060	Standard	NM_001282723		Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000237822.3:c.935A>G	2.37:g.20886706T>C	ENSP00000237822:p.Asp312Gly	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	167	89	0.532934	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Missense_Mutation	SNP	ENST00000237822.3	37	CCDS1702.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	4.392	0.072364	0.08436	0.006809	0.0	ENSG00000118961	ENST00000403006;ENST00000381090;ENST00000237822;ENST00000435420;ENST00000541941	T;T;T	0.46063	0.88;1.49;0.88	5.93	-4.01	0.04045	.	2.110680	0.01630	N	0.023469	T	0.20740	0.0499	L	0.28274	0.84	0.09310	N	1	B;B;B;B	0.11235	0.001;0.001;0.002;0.004	B;B;B;B	0.09377	0.001;0.001;0.003;0.004	T	0.12451	-1.0547	10	0.24483	T	0.36	0.2807	7.2059	0.25907	0.0808:0.0673:0.4763:0.3756	.	270;264;312;312	B4DS38;B7ZAJ5;Q9H6V9;B5MDU6	.;.;CB043_HUMAN;.	G	182;312;312;264;182	ENSP00000384267:D182G;ENSP00000388635:D264G;ENSP00000440570:D182G	ENSP00000237822:D312G	D	-	2	0	C2orf43	20750187	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-0.087000	0.11215	-0.401000	0.07644	0.533000	0.62120	GAC	T|0.998;C|0.002	0.002	strong		0.433	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925	
KIF1C	10749	hgsc.bcm.edu	37	17	4918122	4918122	+	Silent	SNP	A	A	G	rs57144955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4918122A>G	ENST00000320785.5	+	18	2013	c.1656A>G	c.(1654-1656)ccA>ccG	p.P552P	KIF1C_ENST00000573815.1_3'UTR	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	552	FHA.				ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						TCCCCCAGCCAGATGGAGAAG	0.587													A|||	170	0.0339457	0.1225	0.0101	5008	,	,		19813	0.0		0.001	False		,,,				2504	0.0				p.P552P	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											.	KIF1C	70	.	0			c.A1656G						PASS	.	A		454,3952		26,402,1775	41.0	29.0	33.0		1656	-9.6	0.1	17	dbSNP_129	33	4,8594		0,4,4295	no	coding-synonymous	KIF1C	NM_006612.5		26,406,6070	GG,GA,AA		0.0465,10.3041,3.522		552/1104	4918122	458,12546	2203	4299	6502	SO:0001819	synonymous_variant	10749	exon18			CCAGCCAGATGGA	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.1656A>G	17.37:g.4918122A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																			A|0.964;G|0.036	0.036	strong		0.587	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
PDE4DIP	9659	hgsc.bcm.edu	37	1	144852477	144852477	+	Missense_Mutation	SNP	G	G	A	rs148370554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144852477G>A	ENST00000369354.3	-	44	7211	c.7022C>T	c.(7021-7023)cCa>cTa	p.P2341L	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.P2426L|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.P2477L|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.P2235L			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2341					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)		TGGAGTACATGGCAGAGCCCT	0.512			T	PDGFRB	MPD								.|||	165	0.0329473	0.1203	0.0072	5008	,	,		45392	0.0		0.001	False		,,,				2504	0.0				p.P2341L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C7022T						PASS	.						50.0	49.0	49.0					1																	144852477		2203	4293	6496	SO:0001583	missense	9659	exon44			GTACATGGCAGAG	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.7022C>T	1.37:g.144852477G>A	ENSP00000358360:p.Pro2341Leu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	118	6	0.0508475	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	.	4.717	0.133299	0.09032	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000530740;ENST00000369359	T;T;T;T	0.01787	4.64;4.74;4.74;4.75	4.47	0.476	0.16779	.	.	.	.	.	T	0.00845	0.0028	M	0.64404	1.975	0.09310	N	1	B;B	0.12630	0.0;0.006	B;B	0.08055	0.0;0.003	T	0.40961	-0.9535	9	0.54805	T	0.06	.	7.4413	0.27185	0.3516:0.0:0.6483:0.0	.	2235;2341	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	L	2235;2341;2426;2477	ENSP00000327209:P2235L;ENSP00000358360:P2341L;ENSP00000435654:P2426L;ENSP00000358366:P2477L	ENSP00000327209:P2235L	P	-	2	0	PDE4DIP	143563834	0.000000	0.05858	0.001000	0.08648	0.174000	0.22865	0.216000	0.17585	-0.094000	0.12374	-0.274000	0.10170	CCA	.	.	weak		0.512	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
OR10G9	219870	hgsc.bcm.edu	37	11	123893904	123893904	+	Missense_Mutation	SNP	C	C	T	rs144495400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123893904C>T	ENST00000375024.1	+	1	185	c.185C>T	c.(184-186)aCc>aTc	p.T62I		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T62I(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)		TACTTCCTCACCAACCTGTCC	0.552													C|||	395	0.0788738	0.0787	0.147	5008	,	,		21277	0.1448		0.007	False		,,,				2504	0.0368				p.T62I		Atlas-SNP	.											OR10G9,NS,carcinoma,0,1	OR10G9	80	1	1	Substitution - Missense(1)	stomach(1)	c.C185T						scavenged	.	C	ILE/THR	273,4127	141.1+/-176.5	8,257,1935	43.0	42.0	42.0		185	1.3	1.0	11	dbSNP_134	42	24,8530	14.6+/-50.1	0,24,4253	no	missense	OR10G9	NM_001001953.1	89	8,281,6188	TT,TC,CC		0.2806,6.2045,2.2927	benign	62/312	123893904	297,12657	2200	4277	6477	SO:0001583	missense	219870	exon1			TCCTCACCAACCT	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.185C>T	11.37:g.123893904C>T	ENSP00000364164:p.Thr62Ile	Somatic	708	2	0.00282486		WXS	Illumina HiSeq	Phase_I	685	327	0.477372	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	196	0.08974358974358974	45	0.09146341463414634	62	0.1712707182320442	83	0.1451048951048951	6	0.0079155672823219	C	10.75	1.439666	0.25900	0.062045	0.002806	ENSG00000236981	ENST00000375024	T	0.01092	5.35	3.33	1.28	0.21552	GPCR, rhodopsin-like superfamily (1);	0.649434	0.13528	N	0.381190	T	0.00012	0.0000	L	0.33339	1.005	0.36500	P	0.131035	B	0.02656	0.0	B	0.13407	0.009	T	0.40156	-0.9578	9	0.72032	D	0.01	.	9.0	0.36077	0.0:0.2886:0.6123:0.099	.	62	Q8NGN4	O10G9_HUMAN	I	62	ENSP00000364164:T62I	ENSP00000364164:T62I	T	+	2	0	OR10G9	123399114	0.000000	0.05858	0.983000	0.44433	0.981000	0.71138	-0.275000	0.08525	0.188000	0.20168	0.655000	0.94253	ACC	T|1.000;|0.000	1.000	weak		0.552	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
SHROOM3	57619	hgsc.bcm.edu	37	4	77476809	77476809	+	Silent	SNP	T	T	C	rs75039400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77476809T>C	ENST00000296043.6	+	2	1169	c.216T>C	c.(214-216)gcT>gcC	p.A72A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	72	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			AACTGCAGGCTGGGGATGAGG	0.577													C|||	84	0.0167732	0.0628	0.0014	5008	,	,		18555	0.0		0.0	False		,,,				2504	0.0				p.A72A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T216C						PASS	.	C		219,4187	806.1+/-415.8	4,211,1988	110.0	105.0	107.0		216	-7.1	0.0	4	dbSNP_131	107	3,8597	819.2+/-406.8	0,3,4297	no	coding-synonymous	SHROOM3	NM_020859.3		4,214,6285	CC,CT,TT		0.0349,4.9705,1.7069		72/1997	77476809	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	57619	exon2			GCAGGCTGGGGAT	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.216T>C	4.37:g.77476809T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	CCDS3579.2																																																																																			T|0.980;C|0.020	0.020	strong		0.577	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
ECHDC3	79746	hgsc.bcm.edu	37	10	11805249	11805249	+	Silent	SNP	T	T	C	rs61739577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:11805249T>C	ENST00000379215.4	+	5	829	c.618T>C	c.(616-618)ggT>ggC	p.G206G	ECHDC3_ENST00000496136.1_3'UTR	NM_024693.4	NP_078969	Q96DC8	ECHD3_HUMAN	enoyl CoA hydratase domain containing 3	206						mitochondrion (GO:0005739)	catalytic activity (GO:0003824)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)	4						TCTTTACTGGTGAGCCCATTT	0.642													C|||	734	0.146565	0.1831	0.1556	5008	,	,		18562	0.0139		0.2256	False		,,,				2504	0.1462				p.G206G		Atlas-SNP	.											.	ECHDC3	12	.	0			c.T618C						PASS	.	C		834,3572	746.1+/-411.7	80,674,1449	75.0	60.0	65.0		618	2.6	1.0	10	dbSNP_129	65	2084,6516	716.1+/-406.1	280,1524,2496	no	coding-synonymous	ECHDC3	NM_024693.4		360,2198,3945	CC,CT,TT		24.2326,18.9287,22.4358		206/304	11805249	2918,10088	2203	4300	6503	SO:0001819	synonymous_variant	79746	exon5			TACTGGTGAGCCC	AF275677	CCDS7084.1	10p14	2010-04-30	2010-04-30		ENSG00000134463	ENSG00000134463			23489	protein-coding gene	gene with protein product			"""enoyl Coenzyme A hydratase domain containing 3"""			12477932	Standard	NM_024693		Approved	FLJ20909	uc001ikw.4	Q96DC8	OTTHUMG00000017675	ENST00000379215.4:c.618T>C	10.37:g.11805249T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_024693	Q53HR9|Q5W0J7|Q8WYY8|Q9BVL8|Q9H7G4	Silent	SNP	ENST00000379215.4	37	CCDS7084.1																																																																																			T|0.807;C|0.193	0.193	strong		0.642	ECHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046771.1	NM_024693	
IL31	386653	hgsc.bcm.edu	37	12	122658492	122658492	+	Silent	SNP	G	G	A	rs56719421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122658492G>A	ENST00000377035.1	-	2	90	c.64C>T	c.(64-66)Ctg>Ttg	p.L22L		NM_001014336.1	NP_001014358.1	Q6EBC2	IL31_HUMAN	interleukin 31	22					immune system process (GO:0002376)	extracellular space (GO:0005615)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;6.93e-05)|Breast(359;0.0544)		OV - Ovarian serous cystadenocarcinoma(86;3.27e-29)|Epithelial(86;4.86e-27)|BRCA - Breast invasive adenocarcinoma(302;0.223)		TGGGAGGCCAGCCAGCCTCCC	0.547													G|||	365	0.0728834	0.2035	0.0331	5008	,	,		19213	0.006		0.0219	False		,,,				2504	0.046				p.L22L		Atlas-SNP	.											IL31,colon,carcinoma,+1,1	IL31	23	1	0			c.C64T						PASS	.	G	,	730,3676	300.4+/-286.3	65,600,1538	81.0	77.0	78.0		64,	1.8	0.0	12	dbSNP_129	78	232,8368	95.0+/-156.8	1,230,4069	no	coding-synonymous,intron	LRRC43,IL31	NM_001014336.1,NM_152759.4	,	66,830,5607	AA,AG,GG		2.6977,16.5683,7.3966	,	22/165,	122658492	962,12044	2203	4300	6503	SO:0001819	synonymous_variant	386653	exon2			AGGCCAGCCAGCC	AY499343	CCDS31919.1	12q24.31	2011-07-21			ENSG00000204671	ENSG00000204671		"""Interleukins and interleukin receptors"""	19372	protein-coding gene	gene with protein product		609509				15184896	Standard	NM_001014336		Approved	IL-31	uc001ubv.3	Q6EBC2	OTTHUMG00000168916	ENST00000377035.1:c.64C>T	12.37:g.122658492G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	146	76	0.520548	NM_001014336	A2RUQ1	Silent	SNP	ENST00000377035.1	37	CCDS31919.1																																																																																			G|0.928;A|0.072	0.072	strong		0.547	IL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401594.1	NM_001014336	
ADD2	119	hgsc.bcm.edu	37	2	70933494	70933494	+	Missense_Mutation	SNP	T	T	C	rs201443444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70933494T>C	ENST00000264436.4	-	3	491	c.47A>G	c.(46-48)cAg>cGg	p.Q16R	ADD2_ENST00000430656.1_Missense_Mutation_p.Q32R|ADD2_ENST00000355733.3_Missense_Mutation_p.Q16R|ADD2_ENST00000413157.2_Missense_Mutation_p.Q16R|ADD2_ENST00000407644.2_Missense_Mutation_p.Q16R|ADD2_ENST00000473232.1_5'Flank	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	16					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						AGGCTGCCCCTGCGGGGGCGG	0.642													T|||	73	0.0145767	0.0204	0.0144	5008	,	,		17067	0.0169		0.0189	False		,,,				2504	0.0				p.Q32R		Atlas-SNP	.											.	ADD2	261	.	0			c.A95G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	67,4337	58.1+/-94.6	1,65,2136	43.0	48.0	46.0		47,95,47,47,47	5.1	1.0	2	dbSNP_134	46	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	ADD2	NM_001185054.1,NM_001185055.1,NM_001617.3,NM_017482.3,NM_017488.3	43,43,43,43,43	1,65,6436	CC,CT,TT		0.0,1.5213,0.5152	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	16/727,32/576,16/727,16/560,16/644	70933494	67,12937	2202	4300	6502	SO:0001583	missense	119	exon2			TGCCCCTGCGGGG	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.47A>G	2.37:g.70933494T>C	ENSP00000264436:p.Gln16Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	37	CCDS1906.1	48	0.02197802197802198	27	0.054878048780487805	6	0.016574585635359115	6	0.01048951048951049	9	0.011873350923482849	T	13.89	2.372523	0.42003	0.015213	0.0	ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000456320;ENST00000355733;ENST00000522886;ENST00000264439;ENST00000356565;ENST00000517596;ENST00000413157;ENST00000430656;ENST00000415348;ENST00000425976;ENST00000447731	T;T;T;T;T;T;T;T	0.30448	1.58;1.58;1.58;1.58;1.58;1.53;1.58;1.58	5.11	5.11	0.69529	.	0.367672	0.26875	N	0.022043	T	0.03520	0.0101	L	0.29908	0.895	0.32494	N	0.539867	B;B;D;B;B;P	0.55385	0.138;0.058;0.971;0.215;0.18;0.867	B;B;B;B;B;B	0.39217	0.065;0.098;0.294;0.065;0.109;0.269	T	0.09400	-1.0676	10	0.52906	T	0.07	-11.8187	13.1749	0.59621	0.0:0.0:0.0:1.0	.	32;16;16;16;16;16	B4DM17;P35612-4;E9PAN1;Q05DK5;P35612;P35612-3	.;.;.;.;ADDB_HUMAN;.	R	16;16;16;16;16;16;16;16;16;32;16;16;16	ENSP00000264436:Q16R;ENSP00000384677:Q16R;ENSP00000347972:Q16R;ENSP00000430243:Q16R;ENSP00000388072:Q16R;ENSP00000398112:Q32R;ENSP00000412357:Q16R;ENSP00000412681:Q16R	ENSP00000264436:Q16R	Q	-	2	0	ADD2	70787002	0.024000	0.19004	0.998000	0.56505	0.919000	0.55068	0.633000	0.24598	2.265000	0.75225	0.482000	0.46254	CAG	T|0.978;C|0.022	0.022	strong		0.642	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617	
NLRP6	171389	hgsc.bcm.edu	37	11	284477	284477	+	Missense_Mutation	SNP	T	T	C	rs74044411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:284477T>C	ENST00000312165.5	+	7	2375	c.2375T>C	c.(2374-2376)gTa>gCa	p.V792A	NLRP6_ENST00000534750.1_Missense_Mutation_p.V791A|RP11-326C3.2_ENST00000533924.1_RNA	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	792					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	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;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCCCACAGGGTACAGCTGCCT	0.697													T|||	324	0.0646965	0.2337	0.0202	5008	,	,		14829	0.0		0.001	False		,,,				2504	0.0				p.V792A		Atlas-SNP	.											.	NLRP6	4	.	0			c.T2375C						PASS	.	T	ALA/VAL	832,3574	301.5+/-286.9	87,658,1458	26.0	28.0	27.0		2375	1.9	0.1	11	dbSNP_130	27	11,8589	7.1+/-27.0	0,11,4289	yes	missense	NLRP6	NM_138329.1	64	87,669,5747	CC,CT,TT		0.1279,18.8833,6.4816	benign	792/893	284477	843,12163	2203	4300	6503	SO:0001583	missense	171389	exon7			ACAGGGTACAGCT	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.2375T>C	11.37:g.284477T>C	ENSP00000309767:p.Val792Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	79	30	0.379747	NM_138329	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	37	CCDS7693.1	99	0.04532967032967033	90	0.18292682926829268	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	T	10.94	1.491727	0.26774	0.188833	0.001279	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.54675	0.56;0.56	3.06	1.93	0.25924	.	1.705140	0.04569	U	0.393007	T	0.00073	0.0002	L	0.40543	1.245	0.09310	N	1	B;B	0.29037	0.006;0.231	B;B	0.22386	0.008;0.039	T	0.07927	-1.0747	10	0.87932	D	0	.	6.1513	0.20313	0.0:0.1362:0.0:0.8638	.	791;792	E9PJZ8;P59044	.;NALP6_HUMAN	A	791;792	ENSP00000433617:V791A;ENSP00000309767:V792A	ENSP00000309767:V792A	V	+	2	0	NLRP6	274477	0.524000	0.26282	0.112000	0.21494	0.161000	0.22273	1.453000	0.35167	1.414000	0.47017	0.374000	0.22700	GTA	T|0.940;C|0.060	0.060	strong		0.697	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
TMEFF2	23671	hgsc.bcm.edu	37	2	192922499	192922499	+	Missense_Mutation	SNP	G	G	A	rs61744272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:192922499G>A	ENST00000272771.5	-	5	1626	c.442C>T	c.(442-444)Cat>Tat	p.H148Y	TMEFF2_ENST00000392314.1_Missense_Mutation_p.H148Y	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2	148						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(12)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			GAGCCTTCATGGACTGTAGGA	0.403													G|||	92	0.0183706	0.0635	0.0086	5008	,	,		18753	0.0		0.002	False		,,,				2504	0.0				p.H148Y	Pancreas(50;1277 1381 28487 47072)	Atlas-SNP	.											.	TMEFF2	54	.	0			c.C442T						PASS	.	G	TYR/HIS	282,4124	158.5+/-191.2	10,262,1931	95.0	86.0	89.0		442	4.0	0.9	2	dbSNP_129	89	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMEFF2	NM_016192.2	83	10,264,6229	AA,AG,GG		0.0233,6.4004,2.1836	possibly-damaging	148/375	192922499	284,12722	2203	4300	6503	SO:0001583	missense	23671	exon5			CTTCATGGACTGT	AB017269	CCDS2314.1	2q32.3	2010-05-04			ENSG00000144339	ENSG00000144339			11867	protein-coding gene	gene with protein product	"""transmembrane protein TENB2"", ""tomoregulin"", ""cancer/testis antigen family 120, member 2"""	605734				10903839	Standard	NM_016192		Approved	TENB2, HPP1, TR, TPEF, CT120.2	uc002utc.3	Q9UIK5	OTTHUMG00000132723	ENST00000272771.5:c.442C>T	2.37:g.192922499G>A	ENSP00000272771:p.His148Tyr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	128	68	0.53125	NM_016192	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Missense_Mutation	SNP	ENST00000272771.5	37	CCDS2314.1	31	0.014194139194139194	27	0.054878048780487805	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	1.594	-0.528334	0.04112	0.064004	2.33E-4	ENSG00000144339	ENST00000392314;ENST00000272771	T;T	0.58797	0.31;0.31	4.93	3.99	0.46301	.	0.338199	0.31335	N	0.007834	T	0.03827	0.0108	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.03043	-1.1079	10	0.15499	T	0.54	-18.1134	13.1246	0.59346	0.0:0.0:0.78:0.2199	.	148	Q9UIK5	TEFF2_HUMAN	Y	148	ENSP00000376128:H148Y;ENSP00000272771:H148Y	ENSP00000272771:H148Y	H	-	1	0	TMEFF2	192630744	1.000000	0.71417	0.949000	0.38748	0.824000	0.46624	3.823000	0.55715	2.713000	0.92767	0.655000	0.94253	CAT	G|0.982;A|0.018	0.018	strong		0.403	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057343	46057343	+	Silent	SNP	C	C	A	rs76468958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057343C>A	ENST00000380095.1	+	1	71	c.9C>A	c.(7-9)gcC>gcA	p.A3A	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	3						keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						GCATGGCCGCCTCCACCATGT	0.647													A|||	197	0.0393371	0.1362	0.0043	5008	,	,		18834	0.002		0.001	False		,,,				2504	0.0112				p.A3A		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C9A						PASS	.	A	,	601,3805	770.0+/-413.7	46,509,1648	107.0	115.0	112.0		,9	-4.6	0.0	21	dbSNP_131	112	5,8595	818.7+/-406.8	0,5,4295	no	intron,coding-synonymous	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,	46,514,5943	AA,AC,CC		0.0581,13.6405,4.6594	,	,3/252	46057343	606,12400	2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			GGCCGCCTCCACC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.9C>A	21.37:g.46057343C>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	219	103	0.47032	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.960;A|0.040	0.040	strong		0.647	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
OR4C15	81309	hgsc.bcm.edu	37	11	55322211	55322211	+	Silent	SNP	A	A	G	rs9804659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55322211A>G	ENST00000314644.2	+	1	429	c.429A>G	c.(427-429)aaA>aaG	p.K143K		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	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(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						ATGTGACAAAAACCATCTCTT	0.478										HNSCC(20;0.049)			a|||	1265	0.252596	0.1014	0.3242	5008	,	,		19759	0.3919		0.2833	False		,,,				2504	0.2311				p.K143K		Atlas-SNP	.											.	OR4C15	145	.	0			c.A429G						PASS	.	A		561,3841	252.1+/-258.6	27,507,1667	159.0	140.0	146.0		429	2.8	1.0	11	dbSNP_119	146	2288,6304	385.5+/-341.5	329,1630,2337	no	coding-synonymous	OR4C15	NM_001001920.1		356,2137,4004	GG,GA,AA		26.6294,12.7442,21.9255		143/371	55322211	2849,10145	2201	4296	6497	SO:0001819	synonymous_variant	81309	exon1			GACAAAAACCATC	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.429A>G	11.37:g.55322211A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_001001920	Q6IFE2	Silent	SNP	ENST00000314644.2	37	CCDS31501.1																																																																																			A|0.760;G|0.240	0.240	strong		0.478	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920	
TLR8	51311	hgsc.bcm.edu	37	X	12924826	12924826	+	Start_Codon_SNP	SNP	A	A	G	rs3764880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:12924826A>G	ENST00000218032.6	+	1	88	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	TLR8-AS1_ENST00000451564.1_RNA|TLR8_ENST00000311912.5_5'UTR	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	1					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CAACAGAAACATGGTAAGCCA	0.453													G|||	1751	0.463841	0.2201	0.317	3775	,	,		14224	0.6121		0.2048	False		,,,				2504	0.4264				p.M1V		Atlas-SNP	.											.	TLR8	134	.	0			c.A1G	GRCh37	CM083186	TLR8	M	rs3764880	PASS	.	G	VAL/MET	1013,2822		133,601,146,898,425	67.0	58.0	61.0		1	-3.6	0.0	X	dbSNP_107	61	1664,5064		141,936,446,1351,1426	yes	missense	TLR8	NM_138636.4	21	274,1537,592,2249,1851	GG,GA,G,AA,A		24.7325,26.4146,25.3432	benign	1/1042	12924826	2677,7886	2203	4300	6503	SO:0001582	initiator_codon_variant	51311	exon1			AGAAACATGGTAA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1A>G	X.37:g.12924826A>G	ENSP00000218032:p.Met1Val	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	289	133	0.460208	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	728	0.4388185654008439	85	0.1985981308411215	77	0.2711267605633803	221	0.65	100	0.1557632398753894	G	0.369	-0.934864	0.02340	0.264146	0.247325	ENSG00000101916	ENST00000218032	T	0.27890	1.64	4.56	-3.64	0.04515	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46798	P	7.909999999999862E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.43278	-0.9401	7	0.87932	D	0	.	1.7067	0.02883	0.3541:0.2228:0.3092:0.1138	rs3764880;rs52808745;rs58935011;rs3764880	1	Q9NR97	TLR8_HUMAN	V	1	ENSP00000218032:M1V	ENSP00000218032:M1V	M	+	1	0	TLR8	12834747	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.626000	0.05527	-1.451000	0.01933	-3.568000	0.00029	ATG	A|0.639;0|0.017	.	strong		0.453	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	Missense_Mutation
PARP15	165631	hgsc.bcm.edu	37	3	122354796	122354796	+	Missense_Mutation	SNP	G	G	C	rs145474072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122354796G>C	ENST00000464300.2	+	12	1952	c.1886G>C	c.(1885-1887)cGt>cCt	p.R629P	PARP15_ENST00000310366.4_Missense_Mutation_p.R395P|PARP15_ENST00000483793.1_Missense_Mutation_p.R434P|PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000493645.1_Missense_Mutation_p.R326P	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	629	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		ACAAAGGGACGTGCAGGATTA	0.478													G|||	29	0.00579073	0.0219	0.0	5008	,	,		19916	0.0		0.0	False		,,,				2504	0.0				p.R629P		Atlas-SNP	.											.	PARP15	115	.	0			c.G1886C						PASS	.	G	PRO/ARG,PRO/ARG	66,4340	62.3+/-99.4	2,62,2139	162.0	132.0	142.0		1184,1886	-4.6	0.0	3	dbSNP_134	142	0,8600		0,0,4300	yes	missense,missense	PARP15	NM_152615.1,NM_001113523.1	103,103	2,62,6439	CC,CG,GG		0.0,1.498,0.5075	benign,benign	395/445,629/679	122354796	66,12940	2203	4300	6503	SO:0001583	missense	165631	exon12			AGGGACGTGCAGG	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1886G>C	3.37:g.122354796G>C	ENSP00000417214:p.Arg629Pro	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	8.506	0.865423	0.17250	0.01498	0.0	ENSG00000173200	ENST00000464300;ENST00000483793;ENST00000542823;ENST00000310366;ENST00000493645	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	3.99	-4.55	0.03441	Poly(ADP-ribose) polymerase, catalytic domain (2);	.	.	.	.	T	0.05686	0.0149	N	0.26162	0.8	0.09310	N	1	P;B;B;D;B	0.56521	0.566;0.246;0.427;0.976;0.124	B;B;B;B;B	0.43386	0.348;0.222;0.119;0.418;0.162	T	0.14504	-1.0470	9	0.45353	T	0.12	.	5.9187	0.19070	0.3756:0.2583:0.3661:0.0	.	326;395;376;434;607	B7ZL48;Q460N3-2;F5H8I1;C9J7L3;Q460N3	.;.;.;.;PAR15_HUMAN	P	629;434;376;395;326	ENSP00000417214:R629P;ENSP00000417785:R434P;ENSP00000308436:R395P;ENSP00000419488:R326P	ENSP00000308436:R395P	R	+	2	0	PARP15	123837486	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.511000	0.06321	-1.056000	0.03205	-1.043000	0.02367	CGT	G|0.995;C|0.005	0.005	strong		0.478	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
GIMAP5	55340	hgsc.bcm.edu	37	7	150439500	150439500	+	Silent	SNP	C	C	T	rs759011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150439500C>T	ENST00000358647.3	+	3	640	c.273C>T	c.(271-273)gcC>gcT	p.A91A	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	91	AIG1-type G.				myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGTCACAGGCCGATACCCAAG	0.597													T|||	1953	0.389976	0.5696	0.2651	5008	,	,		18052	0.3006		0.3082	False		,,,				2504	0.4121				p.A295A		Atlas-SNP	.											GIMAP5,NS,carcinoma,0,1	.	.	1	0			c.C885T						PASS	.	T	,	2405,2001	560.3+/-380.4	672,1061,470	111.0	99.0	103.0		885,273	1.4	0.0	7	dbSNP_86	103	2642,5958	686.6+/-404.1	390,1862,2048	no	coding-synonymous,coding-synonymous	GIMAP5,GIMAP1-GIMAP5	NM_001199577.1,NM_018384.4	,	1062,2923,2518	TT,TC,CC		30.7209,45.4153,38.8052	,	295/512,91/308	150439500	5047,7959	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			ACAGGCCGATACC	AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"""GTPases, IMAP"""	18005	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 5"""	608086	"""immune associated nucleotide 4 like 1 (mouse)"""	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.273C>T	7.37:g.150439500C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001199577	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Silent	SNP	ENST00000358647.3	37	CCDS5907.1																																																																																			T|0.385;G|0.004	0.385	strong		0.597	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384	
QRFPR	84109	hgsc.bcm.edu	37	4	122254014	122254014	+	Silent	SNP	A	A	G	rs55975435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:122254014A>G	ENST00000394427.2	-	4	1170	c.759T>C	c.(757-759)ctT>ctC	p.L253L	QRFPR_ENST00000334383.5_Intron	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	253				VILFLLPLMVMLILYSKIGYELWIKKRVGDGSVLRTIHGKE MSKIAR -> SSSSSCLLW (in Ref. 1; AAL26488). {ECO:0000305}.	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)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						GAATAGTTCGAAGCACTGAAC	0.353													A|||	478	0.0954473	0.1021	0.0749	5008	,	,		14558	0.1151		0.1044	False		,,,				2504	0.0716				p.L253L		Atlas-SNP	.											.	QRFPR	65	.	0			c.T759C						PASS	.	A		361,4045	184.0+/-211.4	13,335,1855	90.0	86.0	87.0		759	-0.6	0.8	4	dbSNP_129	87	875,7725	196.3+/-241.3	49,777,3474	no	coding-synonymous	QRFPR	NM_198179.2		62,1112,5329	GG,GA,AA		10.1744,8.1934,9.5033		253/432	122254014	1236,11770	2203	4300	6503	SO:0001819	synonymous_variant	84109	exon4			AGTTCGAAGCACT	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.759T>C	4.37:g.122254014A>G		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	252	114	0.452381	NM_198179		Silent	SNP	ENST00000394427.2	37	CCDS3719.1																																																																																			A|0.909;G|0.091	0.091	strong		0.353	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
TTC23	64927	hgsc.bcm.edu	37	15	99678257	99678257	+	Silent	SNP	G	G	A	rs28617660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:99678257G>A	ENST00000394132.2	-	14	2119	c.1302C>T	c.(1300-1302)gaC>gaT	p.D434D	TTC23_ENST00000262074.4_Silent_p.D434D|TTC23_ENST00000558663.1_Silent_p.D434D|TTC23_ENST00000558613.1_Silent_p.D434D|TTC23_ENST00000394136.1_Silent_p.D434D|TTC23_ENST00000394135.3_Silent_p.D434D|RP11-6O2.3_ENST00000564527.1_RNA			Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23	434										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)			CCAGCAGGGTGTCCTGAGGGA	0.607													G|||	724	0.144569	0.348	0.0677	5008	,	,		16457	0.0486		0.0805	False		,,,				2504	0.089				p.D434D		Atlas-SNP	.											.	TTC23	33	.	0			c.C1302T						PASS	.	G	,,,,,,	1150,2786		185,780,1003	45.0	51.0	49.0		1302,1302,1302,1302,1302,1302,1302	2.9	0.0	15	dbSNP_125	49	645,7625		23,599,3513	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTC23	NM_001040655.1,NM_001040656.1,NM_001040657.1,NM_001040658.1,NM_001040659.1,NM_001040660.1,NM_022905.4	,,,,,,	208,1379,4516	AA,AG,GG		7.7993,29.2175,14.7059	,,,,,,	434/448,434/448,434/448,434/448,434/448,434/448,434/448	99678257	1795,10411	1968	4135	6103	SO:0001819	synonymous_variant	64927	exon12			CAGGGTGTCCTGA		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.1302C>T	15.37:g.99678257G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_001040657	A8K6M5|Q53HK0|Q96BC9|Q9H8W9|Q9H9S7	Silent	SNP	ENST00000394132.2	37	CCDS10379.2	281	0.12866300366300365	164	0.3333333333333333	23	0.06353591160220995	28	0.04895104895104895	66	0.0870712401055409	G	6.755	0.508122	0.12883	0.292175	0.077993	ENSG00000103852	ENST00000434594	.	.	.	4.77	2.89	0.33648	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.35450	-0.9788	3	.	.	.	0.0	7.4339	0.27143	0.2032:0.0:0.7968:0.0	rs28617660	.	.	.	I	245	.	.	T	-	2	0	TTC23	97495780	0.010000	0.17322	0.000000	0.03702	0.033000	0.12548	1.861000	0.39438	0.540000	0.28808	-0.251000	0.11542	ACA	G|0.888;A|0.112	0.112	strong		0.607	TTC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303953.2	NM_022905	
CUL5	8065	hgsc.bcm.edu	37	11	107943124	107943124	+	Silent	SNP	T	T	C	rs111339569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:107943124T>C	ENST00000393094.2	+	9	1556	c.940T>C	c.(940-942)Ttg>Ctg	p.L314L		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	314					calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|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)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		GTTGAAAGACTTGGAGGAACA	0.348													T|||	72	0.014377	0.053	0.0029	5008	,	,		19109	0.0		0.0	False		,,,				2504	0.0				p.L314L		Atlas-SNP	.											.	CUL5	71	.	0			c.T940C						PASS	.	T		204,4198	127.0+/-164.0	4,196,2001	113.0	111.0	112.0		940	3.9	1.0	11	dbSNP_132	112	1,8595		0,1,4297	no	coding-synonymous	CUL5	NM_003478.3		4,197,6298	CC,CT,TT		0.0116,4.6343,1.5772		314/781	107943124	205,12793	2201	4298	6499	SO:0001819	synonymous_variant	8065	exon9			AAAGACTTGGAGG	X81882	CCDS31668.1	11q22.3	2011-05-24			ENSG00000166266	ENSG00000166266			2556	protein-coding gene	gene with protein product		601741				8681378, 9037604	Standard	XM_005271682		Approved	VACM-1	uc001pjv.3	Q93034	OTTHUMG00000166369	ENST00000393094.2:c.940T>C	11.37:g.107943124T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_003478	A8K960|O14766|Q9BZC6	Silent	SNP	ENST00000393094.2	37	CCDS31668.1																																																																																			T|0.987;C|0.013	0.013	strong		0.348	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1		
UNC5D	137970	hgsc.bcm.edu	37	8	35606168	35606168	+	Silent	SNP	T	T	C	rs1436615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:35606168T>C	ENST00000404895.2	+	12	2218	c.1890T>C	c.(1888-1890)caT>caC	p.H630H	UNC5D_ENST00000287272.2_Silent_p.H561H|UNC5D_ENST00000420357.1_Silent_p.H563H|UNC5D_ENST00000416672.1_Silent_p.H635H|UNC5D_ENST00000453357.2_Silent_p.H625H|UNC5D_ENST00000449677.1_Silent_p.H206H	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	630	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		GTTCTGAGCATTGGAATATCC	0.488													C|||	480	0.0958466	0.2995	0.0331	5008	,	,		17501	0.0		0.0089	False		,,,				2504	0.0532				p.H630H		Atlas-SNP	.											UNC5D_ENST00000404895,caecum,carcinoma,-2,3	UNC5D	393	3	0			c.T1890C						scavenged	.	C		1067,3339	723.2+/-409.4	146,775,1282	153.0	136.0	142.0		1890	5.2	1.0	8	dbSNP_88	142	121,8479	814.0+/-407.0	2,117,4181	no	coding-synonymous	UNC5D	NM_080872.2		148,892,5463	CC,CT,TT		1.407,24.217,9.1342		630/954	35606168	1188,11818	2203	4300	6503	SO:0001819	synonymous_variant	137970	exon12			TGAGCATTGGAAT	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"""Immunoglobulin superfamily / I-set domain containing"""	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.1890T>C	8.37:g.35606168T>C		Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	146	63	0.431507	NM_080872	Q8WYP7	Silent	SNP	ENST00000404895.2	37	CCDS6093.2																																																																																			T|0.896;C|0.104	0.104	strong		0.488	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2		
PROSER1	80209	hgsc.bcm.edu	37	13	39587865	39587865	+	Silent	SNP	A	A	C	rs3751378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39587865A>C	ENST00000352251.3	-	11	2357	c.1524T>G	c.(1522-1524)tcT>tcG	p.S508S	PROSER1_ENST00000350125.3_Silent_p.S486S|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	508	Ser-rich.																CAGAAGAGTCAGAGTTCTGAA	0.512													A|||	1117	0.223043	0.2458	0.1599	5008	,	,		20185	0.2183		0.162	False		,,,				2504	0.3047				p.S508S		Atlas-SNP	.											C13orf23,NS,carcinoma,-1,1	.	.	1	0			c.T1524G						PASS	.	A	,	1073,3333	389.8+/-327.4	114,845,1244	79.0	77.0	78.0		1524,1458	-10.2	0.0	13	dbSNP_107	78	1209,7391	244.9+/-273.9	91,1027,3182	no	coding-synonymous,coding-synonymous	PROSER1	NM_025138.3,NM_170719.2	,	205,1872,4426	CC,CA,AA		14.0581,24.3532,17.5457	,	508/945,486/923	39587865	2282,10724	2203	4300	6503	SO:0001819	synonymous_variant	80209	exon11			AGAGTCAGAGTTC	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.1524T>G	13.37:g.39587865A>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																			A|0.810;C|0.190	0.190	strong		0.512	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
OR5AK2	390181	hgsc.bcm.edu	37	11	56756565	56756565	+	Silent	SNP	G	G	A	rs62001001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56756565G>A	ENST00000326855.2	+	1	219	c.177G>A	c.(175-177)acG>acA	p.T59T		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	59						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T59T(1)		breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						AAACACTCACGTACTTTTTTC	0.363													.|||	58	0.0115815	0.0431	0.0014	5008	,	,		21424	0.0		0.0	False		,,,				2504	0.0				p.T59T		Atlas-SNP	.											OR5AK2,NS,carcinoma,0,1	OR5AK2	45	1	1	Substitution - coding silent(1)	prostate(1)	c.G177A						PASS	.	G		174,4228	113.8+/-151.8	2,170,2029	118.0	104.0	109.0		177	0.4	0.9	11	dbSNP_129	109	3,8589	2.2+/-6.3	0,3,4293	no	coding-synonymous	OR5AK2	NM_001005323.1		2,173,6322	AA,AG,GG		0.0349,3.9527,1.3622		59/310	56756565	177,12817	2201	4296	6497	SO:0001819	synonymous_variant	390181	exon1			ACTCACGTACTTT	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.177G>A	11.37:g.56756565G>A		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	251	116	0.462151	NM_001005323	B2RNZ9	Silent	SNP	ENST00000326855.2	37	CCDS31538.1																																																																																			G|0.987;A|0.013	0.013	strong		0.363	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323	
SPEG	10290	hgsc.bcm.edu	37	2	220347907	220347907	+	Missense_Mutation	SNP	A	A	G	rs200747365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220347907A>G	ENST00000312358.7	+	30	5854	c.5722A>G	c.(5722-5724)Atg>Gtg	p.M1908V	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1908					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)		GTGGGTGACCATGCCCAGAAG	0.672													A|||	9	0.00179712	0.0053	0.0029	5008	,	,		14834	0.0		0.0	False		,,,				2504	0.0				p.M1908V		Atlas-SNP	.											.	SPEG	272	.	0			c.A5722G						PASS	.	A	VAL/MET	26,3634		0,26,1804	8.0	10.0	9.0		5722	2.7	1.0	2		9	0,8058		0,0,4029	no	missense	SPEG	NM_005876.4	21	0,26,5833	GG,GA,AA		0.0,0.7104,0.2219	benign	1908/3268	220347907	26,11692	1830	4029	5859	SO:0001583	missense	10290	exon30			GTGACCATGCCCA	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.5722A>G	2.37:g.220347907A>G	ENSP00000311684:p.Met1908Val	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	8.935	0.964345	0.18583	0.007104	0.0	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.59772	0.24	4.75	2.74	0.32292	Protein kinase-like domain (1);	0.410582	0.17489	N	0.172415	T	0.11367	0.0277	N	0.00377	-1.585	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26018	-1.0115	10	0.02654	T	1	.	5.4349	0.16476	0.3428:0.0:0.6572:0.0	.	1908	Q15772	SPEG_HUMAN	V	1908	ENSP00000311684:M1908V	ENSP00000265327:M1908V	M	+	1	0	SPEG	220056151	0.991000	0.36638	0.999000	0.59377	0.966000	0.64601	2.141000	0.42168	0.456000	0.26937	0.374000	0.22700	ATG	A|1.000;G|0.000	0.000	strong		0.672	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
C21orf2	755	hgsc.bcm.edu	37	21	45755646	45755646	+	Silent	SNP	C	C	T	rs146104157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45755646C>T	ENST00000339818.4	-	3	345	c.138G>A	c.(136-138)acG>acA	p.T46T	C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000325223.7_Silent_p.T46T|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000397956.3_Silent_p.T46T	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	46					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)		GGTACCTGAGCGTGATCACCT	0.607													C|||	13	0.00259585	0.0091	0.0	5008	,	,		20080	0.0		0.0	False		,,,				2504	0.001				p.T46T		Atlas-SNP	.											.	C21orf2	10	.	0			c.G138A						PASS	.	C		35,4369		0,35,2167	65.0	42.0	50.0		138	-3.1	1.0	21	dbSNP_134	50	1,8587		0,1,4293	no	coding-synonymous	C21orf2	NM_004928.2		0,36,6460	TT,TC,CC		0.0116,0.7947,0.2771		46/257	45755646	36,12956	2202	4294	6496	SO:0001819	synonymous_variant	755	exon3			CCTGAGCGTGATC	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.138G>A	21.37:g.45755646C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	178	79	0.44382	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Silent	SNP	ENST00000339818.4	37	CCDS13709.1																																																																																			C|0.997;T|0.003	0.003	strong		0.607	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
ZMIZ2	83637	hgsc.bcm.edu	37	7	44804989	44804989	+	Missense_Mutation	SNP	G	G	A	rs114574038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44804989G>A	ENST00000309315.4	+	16	2176	c.2053G>A	c.(2053-2055)Gtg>Atg	p.V685M	ZMIZ2_ENST00000433667.1_Missense_Mutation_p.V653M|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.V659M|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.V627M|ZMIZ2_ENST00000441627.1_Missense_Mutation_p.V685M	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	685					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						GCCAGTGCCCGTGAAGCCTGA	0.637													G|||	47	0.00938498	0.0333	0.0043	5008	,	,		15398	0.0		0.0	False		,,,				2504	0.0				p.V685M	NSCLC(20;604 852 1948 16908 50522)	Atlas-SNP	.											.	ZMIZ2	82	.	0			c.G2053A						PASS	.	G	MET/VAL,MET/VAL	122,4158		1,120,2019	37.0	40.0	39.0		2053,1975	3.2	0.9	7	dbSNP_132	39	2,8500		0,2,4249	yes	missense,missense	ZMIZ2	NM_031449.3,NM_174929.2	21,21	1,122,6268	AA,AG,GG		0.0235,2.8505,0.9701	possibly-damaging,possibly-damaging	685/921,659/895	44804989	124,12658	2140	4251	6391	SO:0001583	missense	83637	exon16			GTGCCCGTGAAGC	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.2053G>A	7.37:g.44804989G>A	ENSP00000311778:p.Val685Met	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	37	CCDS43576.1	20	0.009157509157509158	16	0.032520325203252036	2	0.0055248618784530384	2	0.0034965034965034965	0	0.0	G	19.81	3.896626	0.72639	0.028505	2.35E-4	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.32753	1.44;1.45;1.45;1.45;1.44	5.14	3.18	0.36537	.	0.277121	0.24642	N	0.036798	T	0.19446	0.0467	M	0.73598	2.24	0.52501	D	0.999953	P;P;P	0.50156	0.932;0.888;0.932	P;P;P	0.54100	0.656;0.557;0.742	T	0.06463	-1.0825	10	0.45353	T	0.12	-7.8333	7.1482	0.25595	0.284:0.0:0.716:0.0	.	659;685;627	Q8NF64-2;Q8NF64;Q8NF64-3	.;ZMIZ2_HUMAN;.	M	627;685;685;653;659;688	ENSP00000409648:V627M;ENSP00000311778:V685M;ENSP00000414723:V685M;ENSP00000396601:V653M;ENSP00000265346:V659M	ENSP00000265346:V659M	V	+	1	0	ZMIZ2	44771514	0.800000	0.28916	0.881000	0.34555	0.984000	0.73092	1.202000	0.32271	1.398000	0.46701	0.561000	0.74099	GTG	G|0.990;A|0.010	0.010	strong		0.637	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643066	1643066	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1643066A>G	ENST00000399682.1	-	1	302	c.258T>C	c.(256-258)ggT>ggC	p.G86G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.G86G(1)		NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCCTTGGAACCCCCACAAG	0.667																																					p.G86G		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,3	KRTAP5-4	78	3	1	Substitution - coding silent(1)	endometrium(1)	c.T258C						scavenged	.						9.0	15.0	13.0					11																	1643066		683	1577	2260	SO:0001819	synonymous_variant	387267	exon1			CTTGGAACCCCCA	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.258T>C	11.37:g.1643066A>G		Somatic	227	14	0.061674		WXS	Illumina HiSeq	Phase_I	295	35	0.118644	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.667	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
ADAD2	161931	hgsc.bcm.edu	37	16	84228770	84228770	+	Missense_Mutation	SNP	G	G	C	rs11149631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84228770G>C	ENST00000315906.5	+	4	755	c.703G>C	c.(703-705)Ggg>Cgg	p.G235R	RP11-486L19.2_ENST00000561900.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.G307R|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	235			G -> R (in dbSNP:rs11149631).		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						GGCCTGTAAGGGGACTGTGGC	0.667													G|||	1383	0.276158	0.4463	0.2363	5008	,	,		16039	0.1964		0.3101	False		,,,				2504	0.1217				p.G307R		Atlas-SNP	.											.	ADAD2	46	.	0			c.G919C						PASS	.	G	ARG/GLY,ARG/GLY	1854,2546	504.4+/-365.8	394,1066,740	28.0	30.0	29.0		703,919	2.8	1.0	16	dbSNP_120	29	2543,6053	385.8+/-341.6	380,1783,2135	yes	missense,missense	ADAD2	NM_001145400.1,NM_139174.3	125,125	774,2849,2875	CC,CG,GG		29.5835,42.1364,33.8335	possibly-damaging,possibly-damaging	235/584,307/666	84228770	4397,8599	2200	4298	6498	SO:0001583	missense	161931	exon5			TGTAAGGGGACTG	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.703G>C	16.37:g.84228770G>C	ENSP00000325153:p.Gly235Arg	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	37	CCDS45536.1	666	0.30494505494505497	231	0.4695121951219512	95	0.26243093922651933	105	0.18356643356643357	235	0.3100263852242744	G	11.12	1.544385	0.27563	0.421364	0.295835	ENSG00000140955	ENST00000315906;ENST00000268624	T;T	0.17054	2.3;2.3	4.9	2.82	0.32997	.	0.266470	0.29383	N	0.012303	T	0.00012	0.0000	L	0.35854	1.095	0.35317	P	0.21559300000000003	B;B	0.33755	0.037;0.424	B;B	0.37692	0.03;0.256	T	0.49560	-0.8927	9	0.35671	T	0.21	-21.8216	5.6378	0.17546	0.1068:0.2017:0.6915:0.0	rs11149631;rs60033045;rs11149631	235;307	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	R	235;307	ENSP00000325153:G235R;ENSP00000268624:G307R	ENSP00000268624:G307R	G	+	1	0	ADAD2	82786271	0.994000	0.37717	1.000000	0.80357	0.671000	0.39405	1.829000	0.39121	2.419000	0.82065	0.650000	0.86243	GGG	G|0.680;C|0.320	0.320	strong		0.667	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
KRT23	25984	hgsc.bcm.edu	37	17	39084504	39084504	+	Missense_Mutation	SNP	T	T	C	rs9257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39084504T>C	ENST00000209718.3	-	6	1331	c.907A>G	c.(907-909)Aca>Gca	p.T303A	AC004231.2_ENST00000418393.1_RNA|KRT23_ENST00000436344.3_Missense_Mutation_p.T166A	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)	303	Coil 2.|Rod.		T -> A (in dbSNP:rs9257). {ECO:0000269|PubMed:14702039}.			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000301)|Ovarian(249;0.15)				CTGTACTGTGTCTGCAGGTCA	0.577													C|||	2921	0.583267	0.6029	0.6081	5008	,	,		20442	0.7083		0.4076	False		,,,				2504	0.591				p.T303A		Atlas-SNP	.											.	KRT23	59	.	0			c.A907G						PASS	.	C	ALA/THR	2468,1938	552.1+/-378.4	695,1078,430	290.0	246.0	261.0		907	-1.5	0.4	17	dbSNP_52	261	3385,5215	641.6+/-399.7	689,2007,1604	yes	missense	KRT23	NM_015515.3	58	1384,3085,2034	CC,CT,TT		39.3605,43.9855,45.0023	benign	303/423	39084504	5853,7153	2203	4300	6503	SO:0001583	missense	25984	exon6			ACTGTGTCTGCAG	AF102848	CCDS11380.1, CCDS62182.1	17q21.2	2013-01-16			ENSG00000108244	ENSG00000108244		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6438	protein-coding gene	gene with protein product		606194				11135429, 16831889	Standard	NM_015515		Approved	K23, DKFZP434G032, HAIK1, CK23, MGC26158	uc002hvm.1	Q9C075	OTTHUMG00000133376	ENST00000209718.3:c.907A>G	17.37:g.39084504T>C	ENSP00000209718:p.Thr303Ala	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	191	189	0.989529	NM_015515	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Missense_Mutation	SNP	ENST00000209718.3	37	CCDS11380.1	1224	0.5604395604395604	290	0.5894308943089431	204	0.56353591160221	425	0.743006993006993	305	0.4023746701846966	C	7.644	0.681559	0.14907	0.560145	0.393605	ENSG00000108244	ENST00000209718;ENST00000436344	D;D	0.87887	-2.31;-2.31	5.79	-1.48	0.08745	Filament (1);	0.259681	0.27388	N	0.019584	T	0.00012	0.0000	N	0.00980	-1.08	0.54753	P	1.399999999995849E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.37502	-0.9703	9	0.07030	T	0.85	.	8.4899	0.33093	0.0999:0.3939:0.0:0.5062	rs9257;rs1127662;rs2285818;rs3183856;rs11545730;rs17342108;rs17349802;rs52825935;rs56695583;rs9257	303	Q9C075	K1C23_HUMAN	A	303;166	ENSP00000209718:T303A;ENSP00000414056:T166A	ENSP00000209718:T303A	T	-	1	0	KRT23	36338030	0.800000	0.28916	0.368000	0.25939	0.605000	0.37080	0.423000	0.21313	-0.303000	0.08856	-0.726000	0.03593	ACA	T|0.485;C|0.515	0.515	strong		0.577	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1		
ARHGEF2	9181	hgsc.bcm.edu	37	1	155935158	155935158	+	Silent	SNP	T	T	C	rs149517516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155935158T>C	ENST00000361247.4	-	6	615	c.516A>G	c.(514-516)tcA>tcG	p.S172S	ARHGEF2_ENST00000462460.2_Silent_p.S217S|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000313667.4_Silent_p.S172S|ARHGEF2_ENST00000368316.1_Silent_p.S145S|ARHGEF2_ENST00000313695.7_Silent_p.S145S|ARHGEF2_ENST00000368315.4_Silent_p.S173S	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	172					actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CTGTGGACTGTGAGAGGATCC	0.587													T|||	17	0.00339457	0.0129	0.0	5008	,	,		19917	0.0		0.0	False		,,,				2504	0.0				p.S172S	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.A516G						PASS	.	T	,,	90,4316	73.6+/-111.7	1,88,2114	72.0	72.0	72.0		516,516,435	-11.3	0.3	1	dbSNP_134	72	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF2	NM_001162383.1,NM_001162384.1,NM_004723.3	,,	1,88,6414	CC,CT,TT		0.0,2.0427,0.692	,,	172/987,172/986,145/959	155935158	90,12916	2203	4300	6503	SO:0001819	synonymous_variant	9181	exon6			GGACTGTGAGAGG	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	682	protein-coding gene	gene with protein product		607560	"""rho/rac guanine nucleotide exchange factor (GEF) 2"""			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.516A>G	1.37:g.155935158T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	170	87	0.511765	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Silent	SNP	ENST00000361247.4	37	CCDS53376.1																																																																																			T|0.995;C|0.005	0.005	strong		0.587	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723	
TSTD2	158427	hgsc.bcm.edu	37	9	100388119	100388119	+	Missense_Mutation	SNP	G	G	T	rs10817858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	159	0	0		WXS	Illumina HiSeq	Phase_I	140	85	0.607143	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	
ATG4B	23192	hgsc.bcm.edu	37	2	242610172	242610172	+	Missense_Mutation	SNP	A	A	G	rs138274580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242610172A>G	ENST00000404914.3	+	11	1092	c.989A>G	c.(988-990)aAt>aGt	p.N330S	ATG4B_ENST00000474739.2_Missense_Mutation_p.N316S|ATG4B_ENST00000402096.1_Missense_Mutation_p.N256S|ATG4B_ENST00000396411.3_Missense_Mutation_p.N256S|ATG4B_ENST00000405546.3_Missense_Mutation_p.N330S	NM_013325.4|NM_178326.2	NP_037457.3|NP_847896.1	Q9Y4P1	ATG4B_HUMAN	autophagy related 4B, cysteine peptidase	330					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|positive regulation of autophagy (GO:0010508)|positive regulation of protein catabolic process (GO:0045732)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)			breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		GATGACTTCAATGATTGGTGC	0.557													a|||	391	0.0780751	0.1536	0.0259	5008	,	,		19379	0.0675		0.0099	False		,,,				2504	0.0941				p.N330S	Melanoma(78;458 1323 6342 12171 39523)	Atlas-SNP	.											.	ATG4B	35	.	0			c.A989G						PASS	.	G	SER/ASN,SER/ASN	525,3375		25,475,1450	74.0	74.0	74.0		989,989	3.3	0.0	2	dbSNP_134	74	112,8138		3,106,4016	yes	missense,missense	ATG4B	NM_013325.4,NM_178326.2	46,46	28,581,5466	GG,GA,AA		1.3576,13.4615,5.2428	benign,benign	330/394,330/381	242610172	637,11513	1950	4125	6075	SO:0001583	missense	23192	exon11			ACTTCAATGATTG	AB023160	CCDS46564.1, CCDS46565.1	2q37.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000168397	ENSG00000168397			20790	protein-coding gene	gene with protein product		611338	"""APG4 autophagy 4 homolog B (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog B (S. cerevisiae)"""	APG4B		12446702	Standard	NM_013325		Approved	Apg4B, KIAA0943, DKFZp586D1822, AUTL1	uc002wbv.3	Q9Y4P1	OTTHUMG00000151514	ENST00000404914.3:c.989A>G	2.37:g.242610172A>G	ENSP00000384259:p.Asn330Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_178326	B7WNK2|Q53NU4|Q6ZUV8|Q8WYM9|Q96K07|Q96K96|Q96SZ1|Q9Y2F2	Missense_Mutation	SNP	ENST00000404914.3	37	CCDS46564.1	120	0.054945054945054944	70	0.14227642276422764	9	0.024861878453038673	36	0.06293706293706294	5	0.006596306068601583	a	11.78	1.739671	0.30774	0.134615	0.013576	ENSG00000168397	ENST00000405546;ENST00000337606;ENST00000402096;ENST00000404914;ENST00000474739;ENST00000396411;ENST00000428861	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	5.66	3.29	0.37713	.	0.261099	0.44902	N	0.000402	T	0.00300	0.0009	L	0.56769	1.78	0.80722	P	0.0	B;B;B;B;B;B	0.32031	0.082;0.061;0.352;0.171;0.002;0.024	B;B;B;B;B;B	0.28916	0.043;0.063;0.061;0.096;0.027;0.026	T	0.05869	-1.0859	9	0.33940	T	0.23	-12.2164	10.7049	0.45950	0.882:0.0:0.118:0.0	.	316;447;83;418;330;256	F5H7P2;B4DZK0;B3KVU2;Q9Y4P1-2;Q9Y4P1;Q9Y4P1-4	.;.;.;.;ATG4B_HUMAN;.	S	330;447;256;330;316;256;167	ENSP00000383964:N330S;ENSP00000384661:N256S;ENSP00000384259:N330S;ENSP00000442378:N316S;ENSP00000379692:N256S;ENSP00000404783:N167S	ENSP00000336547:N447S	N	+	2	0	ATG4B	242258845	0.788000	0.28762	0.004000	0.12327	0.974000	0.67602	2.999000	0.49473	0.425000	0.26087	-1.050000	0.02344	AAT	A|0.945;G|0.055	0.055	strong		0.557	ATG4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322967.3	NM_013325	
STK32C	282974	hgsc.bcm.edu	37	10	134038817	134038817	+	Missense_Mutation	SNP	C	C	T	rs148669059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134038817C>T	ENST00000368622.1	-	7	826	c.445G>A	c.(445-447)Gtc>Atc	p.V149I	STK32C_ENST00000368625.4_Missense_Mutation_p.V279I					serine/threonine kinase 32C											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|ovary(2)|skin(1)	23		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		CCGCCGTTGACAAAAGAGTGG	0.627													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		18797	0.0		0.0	False		,,,				2504	0.0				p.V266I		Atlas-SNP	.											.	STK32C	61	.	0			c.G796A						PASS	.	C	ILE/VAL	38,4360	40.8+/-73.8	0,38,2161	27.0	30.0	29.0		796	4.5	1.0	10	dbSNP_134	29	2,8592	2.2+/-6.3	0,2,4295	yes	missense	STK32C	NM_173575.2	29	0,40,6456	TT,TC,CC		0.0233,0.864,0.3079	benign	266/487	134038817	40,12952	2199	4297	6496	SO:0001583	missense	282974	exon7			CGTTGACAAAAGA	AK057849	CCDS7666.1	10q26.3	2004-07-22			ENSG00000165752	ENSG00000165752			21332	protein-coding gene	gene with protein product							Standard	NM_173575		Approved	PKE, MGC23665, YANK3	uc001lle.1	Q86UX6	OTTHUMG00000019285	ENST00000368622.1:c.445G>A	10.37:g.134038817C>T	ENSP00000357611:p.Val149Ile	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	102	54	0.529412	NM_173575		Missense_Mutation	SNP	ENST00000368622.1	37		.	.	.	.	.	.	.	.	.	.	C	18.26	3.583708	0.65992	0.00864	2.33E-4	ENSG00000165752	ENST00000368622;ENST00000298630;ENST00000368625	T;T;T	0.62364	0.03;0.03;0.03	4.49	4.49	0.54785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.264823	0.24443	N	0.038493	T	0.47655	0.1457	N	0.14661	0.345	0.42125	D	0.991448	P;P;P	0.39376	0.67;0.629;0.577	P;B;B	0.50537	0.643;0.439;0.179	T	0.56962	-0.7892	10	0.46703	T	0.11	.	11.5206	0.50549	0.0:0.7538:0.2461:0.0	.	279;266;149	B7Z7J1;Q86UX6;Q86UX6-2	.;ST32C_HUMAN;.	I	149;266;279	ENSP00000357611:V149I;ENSP00000298630:V266I;ENSP00000357614:V279I	ENSP00000298630:V266I	V	-	1	0	STK32C	133888807	0.991000	0.36638	0.998000	0.56505	0.753000	0.42808	2.948000	0.49066	2.059000	0.61396	0.585000	0.79938	GTC	C|0.996;T|0.004	0.004	strong		0.627	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575	
ACACB	32	hgsc.bcm.edu	37	12	109629457	109629457	+	Silent	SNP	C	C	T	rs7135947	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109629457C>T	ENST00000338432.7	+	14	2303	c.2184C>T	c.(2182-2184)ggC>ggT	p.G728G	ACACB_ENST00000377848.3_Silent_p.G728G|ACACB_ENST00000377854.5_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	278	0	0		WXS	Illumina HiSeq	Phase_I	268	141	0.526119	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	
CST4	1472	hgsc.bcm.edu	37	20	23669598	23669598	+	Silent	SNP	C	C	T	rs73902132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23669598C>T	ENST00000217423.3	-	1	79	c.9G>A	c.(7-9)cgG>cgA	p.R3R		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	3					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					TACACAGAGGCCGGGCCATGG	0.617													.|||	170	0.0339457	0.1225	0.0115	5008	,	,		15350	0.0		0.0	False		,,,				2504	0.0				p.R3R		Atlas-SNP	.											.	CST4	37	.	0			c.G9A						PASS	.	C		418,3988	202.5+/-225.2	18,382,1803	44.0	44.0	44.0		9	-0.2	0.0	20	dbSNP_130	44	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	CST4	NM_001899.2		18,385,6100	TT,TC,CC		0.0349,9.4871,3.237		3/142	23669598	421,12585	2203	4300	6503	SO:0001819	synonymous_variant	1472	exon1			CAGAGGCCGGGCC		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.9G>A	20.37:g.23669598C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	109	40	0.366972	NM_001899	Q9UBI5|Q9UCS9	Silent	SNP	ENST00000217423.3	37	CCDS13159.1																																																																																			C|0.964;T|0.036	0.036	strong		0.617	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899	
MTPN	136319	hgsc.bcm.edu	37	7	135612057	135612057	+	3'UTR	SNP	G	G	C	rs78834486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:135612057G>C	ENST00000393085.3	-	0	3189				AC015987.1_ENST00000419211.1_RNA|AC015987.2_ENST00000416501.1_5'UTR|LUZP6_ENST00000589735.1_Missense_Mutation_p.P48A	NM_001128619.2|NM_145808.3	NP_001122091.2|NP_665807.1	P58546	MTPN_HUMAN	myotrophin						catecholamine metabolic process (GO:0006584)|cell growth (GO:0016049)|cerebellar granule cell differentiation (GO:0021707)|neuron differentiation (GO:0030182)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell growth (GO:0030307)|positive regulation of macromolecule biosynthetic process (GO:0010557)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein metabolic process (GO:0051247)|regulation of barbed-end actin filament capping (GO:2000812)|regulation of striated muscle tissue development (GO:0016202)|regulation of translation (GO:0006417)|skeletal muscle tissue regeneration (GO:0043403)|striated muscle cell differentiation (GO:0051146)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|nucleus (GO:0005634)				endometrium(1)|lung(4)|prostate(1)	6						GAACTACTTGGGATATTCAAG	0.418													G|||	27	0.00539137	0.0197	0.0014	5008	,	,		19246	0.0		0.0	False		,,,				2504	0.0				p.P48A		Atlas-SNP	.											.	.	.	.	0			c.C142G						PASS	.	G	ALA/PRO,	20,1364		0,20,672	172.0	145.0	153.0		142,	-2.5	0.0	7	dbSNP_132	153	0,3182		0,0,1591	no	missense,utr-3	MTPN,LUZP6	NM_001128619.1,NM_145808.3	27,	0,20,2263	CC,CG,GG		0.0,1.4451,0.438	,	48/59,	135612057	20,4546	692	1591	2283	SO:0001624	3_prime_UTR_variant	767558	exon4			TACTTGGGATATT	AC015987	CCDS5842.1	7q33-q35	2013-01-10			ENSG00000105887	ENSG00000105887		"""Ankyrin repeat domain containing"""	15667	protein-coding gene	gene with protein product	"""granule cell differentiation protein"""	606484				11474205	Standard	NM_145808		Approved	MYOTROPHIN, GCDP, V-1		P58546	OTTHUMG00000155627	ENST00000393085.3:c.*2617C>G	7.37:g.135612057G>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_001128619		Missense_Mutation	SNP	ENST00000393085.3	37	CCDS5842.1																																																																																			G|0.993;C|0.007	0.007	strong		0.418	MTPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340921.1	NM_145808	
ZNF93	81931	hgsc.bcm.edu	37	19	20044886	20044886	+	Silent	SNP	T	T	C	rs10401345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:20044886T>C	ENST00000343769.5	+	4	1150	c.1122T>C	c.(1120-1122)tgT>tgC	p.C374C	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	374					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)	p.C374C(1)		endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						GTGAAGAATGTGGCAAAGCCT	0.388													t|||	601	0.120008	0.2534	0.0447	5008	,	,		22657	0.0506		0.0437	False		,,,				2504	0.1431				p.C374C		Atlas-SNP	.											ZNF93,NS,carcinoma,0,1	ZNF93	81	1	1	Substitution - coding silent(1)	stomach(1)	c.T1122C						PASS	.	T		928,3478	355.1+/-312.9	98,732,1373	89.0	89.0	89.0		1122	0.9	0.5	19	dbSNP_119	89	281,8319	105.4+/-166.3	2,277,4021	no	coding-synonymous	ZNF93	NM_031218.3		100,1009,5394	CC,CT,TT		3.2674,21.0622,9.2957		374/621	20044886	1209,11797	2203	4300	6503	SO:0001819	synonymous_variant	81931	exon4			AGAATGTGGCAAA	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.1122T>C	19.37:g.20044886T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Silent	SNP	ENST00000343769.5	37	CCDS32973.1																																																																																			T|0.908;C|0.092	0.092	strong		0.388	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218	
FAM151A	338094	hgsc.bcm.edu	37	1	55075452	55075452	+	Missense_Mutation	SNP	G	G	A	rs1368883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55075452G>A	ENST00000302250.2	-	8	1407	c.1247C>T	c.(1246-1248)gCg>gTg	p.A416V	ACOT11_ENST00000343744.2_3'UTR|ACOT11_ENST00000481208.1_3'UTR|FAM151A_ENST00000371304.2_Intron|ACOT11_ENST00000371316.3_Intron	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	416			A -> V (in dbSNP:rs1368883). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						TGCGGGCTCCGCTATTTGCAA	0.617													G|||	1514	0.302316	0.1959	0.3588	5008	,	,		18263	0.1815		0.5388	False		,,,				2504	0.2873				p.A416V		Atlas-SNP	.											.	FAM151A	58	.	0			c.C1247T						PASS	.	G	,,VAL/ALA	1097,3309	395.4+/-329.6	137,823,1243	43.0	46.0	45.0		,,1247	2.3	0.0	1	dbSNP_88	45	4479,4121	588.7+/-392.4	1148,2183,969	yes	intron,utr-3,missense	ACOT11,FAM151A	NM_015547.3,NM_147161.3,NM_176782.2	,,64	1285,3006,2212	AA,AG,GG		47.9186,24.8979,42.8725	,,benign	,,416/586	55075452	5576,7430	2203	4300	6503	SO:0001583	missense	338094	exon8			GGCTCCGCTATTT	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.1247C>T	1.37:g.55075452G>A	ENSP00000306888:p.Ala416Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Missense_Mutation	SNP	ENST00000302250.2	37	CCDS594.1	720	0.32967032967032966	82	0.16666666666666666	147	0.40607734806629836	91	0.1590909090909091	400	0.5277044854881267	G	1.583	-0.531093	0.04112	0.248979	0.520814	ENSG00000162391	ENST00000302250	T	0.11385	2.78	4.17	2.26	0.28386	.	0.606935	0.15337	N	0.267684	T	0.00012	0.0000	L	0.31294	0.92	0.80722	P	0.0	B	0.25206	0.12	B	0.23275	0.045	T	0.39251	-0.9623	9	0.56958	D	0.05	-1.9697	7.2099	0.25927	0.1908:0.0:0.8092:0.0	rs1368883;rs1622365;rs12729963;rs17855486;rs1368883	416	Q8WW52	F151A_HUMAN	V	416	ENSP00000306888:A416V	ENSP00000306888:A416V	A	-	2	0	FAM151A	54848040	0.001000	0.12720	0.002000	0.10522	0.034000	0.12701	0.284000	0.18864	0.682000	0.31407	0.655000	0.94253	GCG	G|0.630;A|0.370	0.370	strong		0.617	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782	
ITGB3	3690	hgsc.bcm.edu	37	17	45369789	45369789	+	Silent	SNP	G	G	A	rs4634|rs397843979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45369789G>A	ENST00000559488.1	+	10	1561	c.1545G>A	c.(1543-1545)cgG>cgA	p.R515R	ITGB3_ENST00000560629.1_Missense_Mutation_p.G504R|ITGB3_ENST00000435993.2_Silent_p.R468R	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	515	Cysteine-rich tandem repeats.		R -> Q (in alloantigen CA(+)/TU(+); dbSNP:rs13306487). {ECO:0000269|PubMed:7694683}.		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)	GCAGCCCCCGGGAGGGTCAGC	0.627													G|||	1439	0.28734	0.2564	0.268	5008	,	,		17711	0.3313		0.2903	False		,,,				2504	0.2945				p.R515R		Atlas-SNP	.											ITGB3_ENST00000435993,colon,carcinoma,0,2	ITGB3	157	2	0			c.G1545A						PASS	.	G		1187,3219	415.0+/-337.0	156,875,1172	79.0	73.0	75.0		1545	2.0	1.0	17	dbSNP_52	75	2505,6095	410.5+/-350.2	355,1795,2150	no	coding-synonymous	ITGB3	NM_000212.2		511,2670,3322	AA,AG,GG		29.1279,26.9405,28.3869		515/789	45369789	3692,9314	2203	4300	6503	SO:0001819	synonymous_variant	3690	exon10			CCCCCGGGAGGGT		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.1545G>A	17.37:g.45369789G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	37	CCDS11511.1																																																																																			G|0.717;A|0.283	0.283	strong		0.627	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
NCKAP5L	57701	hgsc.bcm.edu	37	12	50190653	50190653	+	Silent	SNP	C	C	T	rs3741555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50190653C>T	ENST00000335999.6	-	8	1191	c.990G>A	c.(988-990)caG>caA	p.Q330Q		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	326	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CCTCAAGGAGCTGGCCCAGGT	0.652													C|||	1382	0.275958	0.23	0.3847	5008	,	,		16740	0.5466		0.0537	False		,,,				2504	0.2106				p.Q330Q		Atlas-SNP	.											NCKAP5L_ENST00000335999,rectum,carcinoma,0,2	NCKAP5L	142	2	0			c.G990A						PASS	.	C		818,3146		97,624,1261	16.0	19.0	18.0		990	2.2	1.0	12	dbSNP_107	18	394,7876		9,376,3750	no	coding-synonymous	NCKAP5L	NM_001037806.3		106,1000,5011	TT,TC,CC		4.7642,20.6357,9.9068		330/1335	50190653	1212,11022	1982	4135	6117	SO:0001819	synonymous_variant	57701	exon8			AAGGAGCTGGCCC	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.990G>A	12.37:g.50190653C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	37	CCDS41781.2	602	0.27564102564102566	118	0.23983739837398374	126	0.34806629834254144	319	0.5576923076923077	39	0.051451187335092345	C	8.398	0.841268	0.16891	0.206357	0.047642	ENSG00000167566	ENST00000433948	.	.	.	4.12	2.21	0.28008	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999738904	.	.	.	.	.	.	T	0.48007	-0.9072	3	.	.	.	-6.4151	7.0432	0.25031	0.0:0.6158:0.0:0.3842	rs3741555;rs58965238;rs3741555	.	.	.	T	45	.	.	A	-	1	0	NCKAP5L	48476920	0.992000	0.36948	0.993000	0.49108	0.963000	0.63663	0.922000	0.28734	0.299000	0.22661	0.462000	0.41574	GCT	C|0.733;T|0.267	0.267	strong		0.652	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497	
SLC33A1	9197	hgsc.bcm.edu	37	3	155571275	155571275	+	Missense_Mutation	SNP	T	T	C	rs3804769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:155571275T>C	ENST00000392845.3	-	1	892	c.512A>G	c.(511-513)gAc>gGc	p.D171G	SLC33A1_ENST00000359479.3_Missense_Mutation_p.D171G|SLC33A1_ENST00000460729.1_5'Flank			O00400	ACATN_HUMAN	solute carrier family 33 (acetyl-CoA transporter), member 1	171			D -> G (in dbSNP:rs3804769).		acetyl-CoA transport (GO:0015876)|cell death (GO:0008219)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	acetyl-CoA transporter activity (GO:0008521)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	22			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GGGTGTTCTGTCATCGGTATT	0.488													C|||	618	0.123403	0.1271	0.0749	5008	,	,		17837	0.1587		0.0636	False		,,,				2504	0.1779				p.D171G		Atlas-SNP	.											.	SLC33A1	57	.	0			c.A512G						PASS	.	C	GLY/ASP,GLY/ASP	441,3965	785.4+/-414.7	26,389,1788	67.0	70.0	69.0		512,512	5.4	0.8	3	dbSNP_107	69	440,8160	799.5+/-407.4	8,424,3868	yes	missense,missense	SLC33A1	NM_001190992.1,NM_004733.3	94,94	34,813,5656	CC,CT,TT		5.1163,10.0091,6.7738	benign,benign	171/550,171/550	155571275	881,12125	2203	4300	6503	SO:0001583	missense	9197	exon1			GTTCTGTCATCGG	D88152	CCDS3173.1	3q25.31	2013-05-22		2002-12-06	ENSG00000169359	ENSG00000169359		"""Solute carriers"""	95	protein-coding gene	gene with protein product		603690	"""acetyl-Coenzyme A transporter"", ""spastic paraplegia 42 (autosomal dominant)"""	ACATN, SPG42		9096318, 19061983	Standard	NM_004733		Approved	AT-1, AT1	uc003fao.2	O00400	OTTHUMG00000158481	ENST00000392845.3:c.512A>G	3.37:g.155571275T>C	ENSP00000376587:p.Asp171Gly	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_004733	B2R5Q2|D3DNK4	Missense_Mutation	SNP	ENST00000392845.3	37	CCDS3173.1	210|210	0.09615384615384616|0.09615384615384616	47|47	0.09552845528455285|0.09552845528455285	30|30	0.08287292817679558|0.08287292817679558	85|85	0.1486013986013986|0.1486013986013986	48|48	0.0633245382585752|0.0633245382585752	C|C	9.091|9.091	1.001647|1.001647	0.19121|0.19121	0.100091|0.100091	0.051163|0.051163	ENSG00000169359|ENSG00000169359	ENST00000392845;ENST00000359479|ENST00000475842	T;T|.	0.71934|.	-0.61;-0.61|.	5.42|5.42	5.42|5.42	0.78866|0.78866	Major facilitator superfamily domain, general substrate transporter (1);|.	0.155351|.	0.46145|.	N|.	0.000312|.	T|.	0.00241|.	0.0007|.	N|N	0.11131|0.11131	0.1|0.1	0.34001|0.34001	P|P	0.349685|0.349685	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|.	0.12656|.	-1.0539|.	9|.	0.11794|.	T|.	0.64|.	-6.2744|-6.2744	14.7771|14.7771	0.69738|0.69738	0.0:0.9305:0.0:0.0695|0.0:0.9305:0.0:0.0695	rs3804769;rs52811474;rs3804769|rs3804769;rs52811474;rs3804769	171|.	O00400|.	ACATN_HUMAN|.	G|W	171|2	ENSP00000376587:D171G;ENSP00000352456:D171G|.	ENSP00000352456:D171G|.	D|X	-|-	2|3	0|0	SLC33A1|SLC33A1	157053969|157053969	1.000000|1.000000	0.71417|0.71417	0.763000|0.763000	0.31416|0.31416	0.808000|0.808000	0.45660|0.45660	3.586000|3.586000	0.53950|0.53950	1.449000|1.449000	0.47699|0.47699	-0.124000|-0.124000	0.14976|0.14976	GAC|TGA	T|0.919;C|0.081	0.081	strong		0.488	SLC33A1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351130.3	NM_004733	
VWA8	23078	hgsc.bcm.edu	37	13	42442546	42442546	+	Missense_Mutation	SNP	A	A	G	rs3742262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:42442546A>G	ENST00000379310.3	-	10	1216	c.1148T>C	c.(1147-1149)aTg>aCg	p.M383T	VWA8_ENST00000281496.6_Missense_Mutation_p.M383T	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	383			M -> T (in dbSNP:rs3742262). {ECO:0000269|PubMed:17974005}.			extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										ATGGTTTTCCATCATCTTCTC	0.358													A|||	1113	0.222244	0.056	0.3026	5008	,	,		17551	0.1895		0.3231	False		,,,				2504	0.32				p.M383T		Atlas-SNP	.											.	.	.	.	0			c.T1148C						PASS	.	A	THR/MET,THR/MET	381,4025	191.2+/-216.9	10,361,1832	145.0	130.0	135.0		1148,1148	0.9	0.0	13	dbSNP_107	135	2773,5827	440.8+/-359.6	453,1867,1980	yes	missense,missense	KIAA0564	NM_001009814.1,NM_015058.1	81,81	463,2228,3812	GG,GA,AA		32.2442,8.6473,24.2503	benign,benign	383/1040,383/1906	42442546	3154,9852	2203	4300	6503	SO:0001583	missense	23078	exon10			TTTTCCATCATCT	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"""KIAA0564"""	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.1148T>C	13.37:g.42442546A>G	ENSP00000368612:p.Met383Thr	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	181	95	0.524862	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	523	0.23946886446886448	32	0.06504065040650407	116	0.32044198895027626	121	0.21153846153846154	254	0.33509234828496043	A	0.004	-2.267391	0.00259	0.086473	0.322442	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496;ENST00000398857	T;T	0.10192	3.09;2.9	4.63	0.953	0.19590	.	0.927533	0.09044	N	0.856935	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	0.47611	-0.9104	9	0.13853	T	0.58	.	5.1762	0.15137	0.2184:0.0:0.4149:0.3667	rs3742262;rs17534800;rs60079135;rs3742262	383	A3KMH1	K0564_HUMAN	T	287;383;383;383	ENSP00000368612:M383T;ENSP00000281496:M383T	ENSP00000251030:M287T	M	-	2	0	KIAA0564	41340546	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	0.140000	0.16056	0.025000	0.15241	-0.147000	0.13772	ATG	A|0.760;G|0.240	0.240	strong		0.358	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
CEP68	23177	hgsc.bcm.edu	37	2	65298657	65298657	+	Missense_Mutation	SNP	A	A	G	rs13389745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:65298657A>G	ENST00000377990.2	+	3	630	c.427A>G	c.(427-429)Att>Gtt	p.I143V	CEP68_ENST00000546106.1_Missense_Mutation_p.I143V|CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000260569.4_Missense_Mutation_p.I143V|CEP68_ENST00000497039.1_3'UTR|RAB1A_ENST00000494188.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	143					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						AACAACAACTATTTGCTCAGG	0.517													A|||	358	0.0714856	0.261	0.0187	5008	,	,		22452	0.0		0.0	False		,,,				2504	0.0				p.I143V		Atlas-SNP	.											.	CEP68	69	.	0			c.A427G						PASS	.	A	VAL/ILE	853,3553	336.3+/-304.3	84,685,1434	104.0	99.0	101.0		427	-0.6	0.0	2	dbSNP_121	101	3,8597	3.7+/-12.6	0,3,4297	yes	missense	CEP68	NM_015147.2	29	84,688,5731	GG,GA,AA		0.0349,19.36,6.5816	benign	143/758	65298657	856,12150	2203	4300	6503	SO:0001583	missense	23177	exon3			ACAACTATTTGCT	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.427A>G	2.37:g.65298657A>G	ENSP00000367229:p.Ile143Val	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	202	101	0.5	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	148	0.06776556776556776	143	0.29065040650406504	5	0.013812154696132596	0	0.0	0	0.0	A	5.245	0.230663	0.09969	0.1936	3.49E-4	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.28255	1.62;1.62;1.62	6.07	-0.64	0.11493	.	0.631703	0.14683	N	0.304637	T	0.00012	0.0000	N	0.04508	-0.205	0.58432	P	1.0000000000287557E-6	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	0.42015	-0.9476	9	0.02654	T	1	-1.7066	11.1914	0.48687	0.317:0.2513:0.4316:0.0	rs13389745;rs52830313;rs57922580;rs13389745	131;143;143;143;143	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	V	143;143;143;131	ENSP00000367229:I143V;ENSP00000438306:I143V;ENSP00000260569:I143V	ENSP00000260569:I143V	I	+	1	0	CEP68	65152161	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	-0.938000	0.03938	-0.309000	0.08779	-1.959000	0.00480	ATT	A|0.929;G|0.071	0.071	strong		0.517	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
ZNF587	84914	hgsc.bcm.edu	37	19	58371274	58371274	+	Silent	SNP	G	G	T	rs10405892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58371274G>T	ENST00000339656.5	+	3	1676	c.1494G>T	c.(1492-1494)ggG>ggT	p.G498G	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597652.1_5'Flank|ZNF587_ENST00000419854.1_Silent_p.G455G|ZNF814_ENST00000597342.1_Intron|ZNF587_ENST00000423137.1_Silent_p.G497G|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	498					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(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		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;0.0264)		GTGAATGTGGGAAATCATTTC	0.408																																					p.G498G	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											ZNF587,NS,carcinoma,+2,1	ZNF587	53	1	0			c.G1494T						PASS	.						132.0	136.0	134.0					19																	58371274		2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			ATGTGGGAAATCA	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1494G>T	19.37:g.58371274G>T		Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	338	155	0.45858	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			G|0.822;T|0.178	0.178	strong		0.408	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
CTNND1	1500	hgsc.bcm.edu	37	11	57563991	57563991	+	Silent	SNP	C	C	T	rs10896644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57563991C>T	ENST00000399050.4	+	6	1019	c.483C>T	c.(481-483)gaC>gaT	p.D161D	CTNND1_ENST00000534579.1_Silent_p.D107D|CTNND1_ENST00000361796.4_Silent_p.D161D|CTNND1_ENST00000532787.1_Silent_p.D60D|CTNND1_ENST00000415361.2_Silent_p.D60D|CTNND1_ENST00000360682.6_Silent_p.D161D|CTNND1_ENST00000529873.1_Silent_p.D107D|CTNND1_ENST00000428599.2_Silent_p.D161D|CTNND1_ENST00000528621.1_Silent_p.D107D|CTNND1_ENST00000528232.1_Silent_p.D60D|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000399039.4_Silent_p.D161D|CTNND1_ENST00000526938.1_Silent_p.D161D|CTNND1_ENST00000426142.2_Silent_p.D60D|CTNND1_ENST00000531014.1_Intron|CTNND1_ENST00000529526.1_Silent_p.D107D|CTNND1_ENST00000532463.1_Silent_p.D60D|CTNND1_ENST00000530748.1_Silent_p.D107D|CTNND1_ENST00000361391.6_Silent_p.D161D|CTNND1_ENST00000532245.1_Silent_p.D60D|CTNND1_ENST00000361332.4_Silent_p.D161D|CTNND1_ENST00000527467.1_Intron|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000529919.1_Silent_p.D161D|CTNND1_ENST00000532649.1_Silent_p.D107D|CTNND1_ENST00000530094.1_Silent_p.D60D|CTNND1_ENST00000532844.1_Silent_p.D107D|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000358694.6_Silent_p.D161D|CTNND1_ENST00000526357.1_Silent_p.D107D|CTNND1_ENST00000529986.1_Silent_p.D60D|CTNND1_ENST00000524630.1_Silent_p.D161D	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	161					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				TGGGACCAGACGGGTTGCCTG	0.463													C|||	1359	0.271366	0.1762	0.3314	5008	,	,		20175	0.1012		0.4284	False		,,,				2504	0.3712				p.D161D		Atlas-SNP	.											.	CTNND1	203	.	0			c.C483T						PASS	.	C	,,,,,,,,,,,,,,,,,,,,,	893,3063		116,661,1201	82.0	86.0	85.0		483,483,483,483,483,180,180,180,180,180,180,180,321,321,483,321,321,321,321,180,321,483	-5.8	0.8	11	dbSNP_120	85	3413,4933		696,2021,1456	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	CTNND1	NM_001085458.1,NM_001085459.1,NM_001085460.1,NM_001085461.1,NM_001085462.1,NM_001085463.1,NM_001085464.1,NM_001085465.1,NM_001085466.1,NM_001085467.1,NM_001085468.1,NM_001085469.1,NM_001206883.1,NM_001206884.1,NM_001206885.1,NM_001206886.1,NM_001206887.1,NM_001206888.1,NM_001206889.1,NM_001206890.1,NM_001206891.1,NM_001331.2	,,,,,,,,,,,,,,,,,,,,,	812,2682,2657	TT,TC,CC		40.8938,22.5733,35.0024	,,,,,,,,,,,,,,,,,,,,,	161/969,161/963,161/934,161/934,161/934,60/868,60/862,60/841,60/839,60/833,60/833,60/833,107/915,107/886,161/940,107/909,107/888,107/880,107/880,60/833,107/880,161/942	57563991	4306,7996	1978	4173	6151	SO:0001819	synonymous_variant	1500	exon6			ACCAGACGGGTTG	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"""Armadillo repeat containing"""	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.483C>T	11.37:g.57563991C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	116	61	0.525862	NM_001085461	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Silent	SNP	ENST00000399050.4	37	CCDS44604.1																																																																																			C|0.728;T|0.272	0.272	strong		0.463	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331	
APBA2	321	hgsc.bcm.edu	37	15	29398914	29398914	+	Silent	SNP	C	C	T	rs8032178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:29398914C>T	ENST00000558402.1	+	13	2408	c.1809C>T	c.(1807-1809)ggC>ggT	p.G603G	APBA2_ENST00000558259.1_Silent_p.G603G|APBA2_ENST00000411764.1_Silent_p.G591G|APBA2_ENST00000558330.1_Silent_p.G591G|APBA2_ENST00000561069.1_Silent_p.G603G			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	603	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		TGATGAATGGCGGCCCGGCTG	0.662													C|||	295	0.0589058	0.2118	0.0202	5008	,	,		13171	0.001		0.0	False		,,,				2504	0.0				p.G603G		Atlas-SNP	.											.	APBA2	132	.	0			c.C1809T						PASS	.	C	,	801,3605	312.2+/-292.5	71,659,1473	48.0	49.0	49.0		1773,1809	-8.4	0.4	15	dbSNP_116	49	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous,coding-synonymous	APBA2	NM_001130414.1,NM_005503.3	,	71,662,5768	TT,TC,CC		0.0349,18.1798,6.1837	,	591/738,603/750	29398914	804,12198	2203	4298	6501	SO:0001819	synonymous_variant	321	exon11			GAATGGCGGCCCG	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1809C>T	15.37:g.29398914C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	222	107	0.481982	NM_005503	E9PGI4|O60571|Q5XKC0	Silent	SNP	ENST00000558402.1	37	CCDS10022.1																																																																																			C|0.932;T|0.068	0.068	strong		0.662	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
ABHD12	26090	hgsc.bcm.edu	37	20	25319977	25319977	+	Missense_Mutation	SNP	C	C	T	rs11904930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:25319977C>T	ENST00000339157.5	-	2	474	c.202G>A	c.(202-204)Gtg>Atg	p.V68M	ABHD12_ENST00000376542.3_Missense_Mutation_p.V68M	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	68					adult walking behavior (GO:0007628)|phosphatidylserine catabolic process (GO:0006660)|response to auditory stimulus (GO:0010996)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)	acylglycerol lipase activity (GO:0047372)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	12						CGCAACCACACGCCCTTTCGC	0.423													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		17996	0.0		0.0	False		,,,				2504	0.0				p.V68M		Atlas-SNP	.											.	ABHD12	46	.	0			c.G202A						PASS	.	C	MET/VAL,MET/VAL	88,4318	74.1+/-112.3	1,86,2116	102.0	92.0	95.0		202,202	2.1	1.0	20	dbSNP_120	95	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ABHD12	NM_001042472.2,NM_015600.4	21,21	1,88,6414	TT,TC,CC		0.0233,1.9973,0.692	benign,benign	68/399,68/405	25319977	90,12916	2203	4300	6503	SO:0001583	missense	26090	exon2			ACCACACGCCCTT	AL117442	CCDS13172.1, CCDS42857.1	20p11.21	2007-04-24	2006-03-10	2006-03-10	ENSG00000100997	ENSG00000100997		"""Abhydrolase domain containing"""	15868	protein-coding gene	gene with protein product		613599	"""chromosome 20 open reading frame 22"""	C20orf22			Standard	NM_015600		Approved	DKFZP434P106, dJ965G21.2, BEM46L2, ABHD12A	uc002wuq.3	Q8N2K0	OTTHUMG00000032121	ENST00000339157.5:c.202G>A	20.37:g.25319977C>T	ENSP00000341408:p.Val68Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Missense_Mutation	SNP	ENST00000339157.5	37	CCDS42857.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	10.04	1.241327	0.22711	0.019973	2.33E-4	ENSG00000100997	ENST00000376542;ENST00000339157;ENST00000526543;ENST00000450393	T;T;T	0.25749	1.78;1.78;1.78	5.51	2.13	0.27403	.	0.327344	0.28409	N	0.015448	T	0.04452	0.0122	N	0.08118	0	0.19300	N	0.999971	B;B;B	0.12013	0.001;0.001;0.005	B;B;B	0.06405	0.002;0.001;0.002	T	0.15464	-1.0436	10	0.44086	T	0.13	0.0354	1.0324	0.01541	0.1484:0.1871:0.2866:0.378	rs11904930	23;68;68	Q5T712;Q8N2K0;Q8N2K0-2	.;ABD12_HUMAN;.	M	68;68;30;23	ENSP00000365725:V68M;ENSP00000341408:V68M;ENSP00000413311:V23M	ENSP00000341408:V68M	V	-	1	0	ABHD12	25267977	0.214000	0.23563	0.996000	0.52242	0.608000	0.37181	0.149000	0.16243	0.676000	0.31285	-0.226000	0.12346	GTG	C|0.993;T|0.007	0.007	strong		0.423	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600	
PLXNA2	5362	hgsc.bcm.edu	37	1	208207839	208207839	+	Splice_Site	SNP	G	G	A	rs3736963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:208207839G>A	ENST00000367033.3	-	27	5620	c.4863C>T	c.(4861-4863)taC>taT	p.Y1621Y		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1621					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)		GGTTCTCACCGTATCTGCTGA	0.602													G|||	2217	0.442692	0.5401	0.4539	5008	,	,		19932	0.2579		0.6203	False		,,,				2504	0.3108				p.Y1621Y		Atlas-SNP	.											.	PLXNA2	178	.	0			c.C4863T						PASS	.	G		2430,1976	619.1+/-393.3	653,1124,426	92.0	82.0	85.0		4863	-3.5	0.9	1	dbSNP_107	85	4941,3659	622.5+/-397.3	1414,2113,773	yes	coding-synonymous-near-splice	PLXNA2	NM_025179.3		2067,3237,1199	AA,AG,GG		42.5465,44.8479,43.3262		1621/1895	208207839	7371,5635	2203	4300	6503	SO:0001630	splice_region_variant	5362	exon27			CTCACCGTATCTG	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.4864+1C>T	1.37:g.208207839G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			G|0.471;A|0.529	0.529	strong		0.602	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	Silent
EVPL	2125	hgsc.bcm.edu	37	17	74006079	74006079	+	Silent	SNP	G	G	A	rs79450818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74006079G>A	ENST00000301607.3	-	22	3460	c.3207C>T	c.(3205-3207)gaC>gaT	p.D1069D	EVPL_ENST00000586740.1_Silent_p.D1091D	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1069	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TCTCCTTCACGTCCACCTCCC	0.592													G|||	58	0.0115815	0.0431	0.0014	5008	,	,		21848	0.0		0.0	False		,,,				2504	0.0				p.D1069D		Atlas-SNP	.											.	EVPL	155	.	0			c.C3207T						PASS	.	G		141,4265	101.2+/-139.8	2,137,2064	149.0	140.0	143.0		3207	-3.6	0.0	17	dbSNP_132	143	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EVPL	NM_001988.2		2,138,6363	AA,AG,GG		0.0116,3.2002,1.0918		1069/2034	74006079	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	2125	exon22			CTTCACGTCCACC	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.3207C>T	17.37:g.74006079G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	70	0.608696	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																			G|0.987;A|0.013	0.013	strong		0.592	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
THOC6	79228	hgsc.bcm.edu	37	16	3076393	3076393	+	Silent	SNP	C	C	T	rs8057262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3076393C>T	ENST00000326266.8	+	6	686	c.390C>T	c.(388-390)aaC>aaT	p.N130N	THOC6_ENST00000574549.1_Silent_p.N106N|HCFC1R1_ENST00000574151.1_5'Flank|THOC6_ENST00000253952.9_Silent_p.N130N|HCFC1R1_ENST00000574980.1_5'Flank|HCFC1R1_ENST00000248089.3_5'Flank|HCFC1R1_ENST00000572355.1_5'Flank|HCFC1R1_ENST00000354679.3_5'Flank|THOC6_ENST00000575576.1_Silent_p.N106N|HCFC1R1_ENST00000396916.1_5'Flank	NM_024339.3	NP_077315.2	Q86W42	THOC6_HUMAN	THO complex 6 homolog (Drosophila)	130					apoptotic process (GO:0006915)|central nervous system development (GO:0007417)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	13						CTGAGATCAACGCTTTGCTGC	0.542													c|||	216	0.043131	0.1589	0.0072	5008	,	,		22149	0.0		0.001	False		,,,				2504	0.0				p.N130N		Atlas-SNP	.											.	THOC6	40	.	0			c.C390T						PASS	.	C	,	548,3848	248.4+/-256.2	32,484,1682	120.0	102.0	108.0		390,390	-3.4	0.9	16	dbSNP_116	108	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	THOC6	NM_001142350.1,NM_024339.3	,	32,488,5978	TT,TC,CC		0.0465,12.4659,4.2475	,	130/297,130/342	3076393	552,12444	2198	4300	6498	SO:0001819	synonymous_variant	79228	exon6			GATCAACGCTTTG	BC050674	CCDS10491.1, CCDS45392.1	16p13.3	2013-02-11	2006-03-02	2006-03-02		ENSG00000131652		"""WD repeat domain containing"", ""THO complex subunits"""	28369	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 35"""	615403	"""WD repeat domain 58"""	WDR58		12477932	Standard	NM_024339		Approved	MGC2655, fSAP35	uc002ctb.2	Q86W42		ENST00000326266.8:c.390C>T	16.37:g.3076393C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_001142350	B2RA85|Q8NBR1|Q9BTV9	Silent	SNP	ENST00000326266.8	37	CCDS10491.1																																																																																			C|0.955;T|0.045	0.045	strong		0.542	THOC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436981.1	NM_024339	
TENM3	55714	hgsc.bcm.edu	37	4	183720831	183720831	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:183720831G>A	ENST00000511685.1	+	28	7550	c.7427G>A	c.(7426-7428)aGc>aAc	p.S2476N	TENM3_ENST00000406950.2_Missense_Mutation_p.S2476N			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2476					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTGCAGGTGAgccggcgccgg	0.697																																					p.S2476N		Atlas-SNP	.											.	.	.	.	0			c.G7427A						PASS	.						5.0	7.0	7.0					4																	183720831		1716	3423	5139	SO:0001583	missense	55714	exon27			AGGTGAGCCGGCG	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.7427G>A	4.37:g.183720831G>A	ENSP00000424226:p.Ser2476Asn	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	10	8	0.8	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.054373	0.36277	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86627	-2.15;-2.15	4.79	3.94	0.45596	.	.	.	.	.	T	0.79505	0.4457	L	0.32530	0.975	0.53005	D	0.999968	B	0.27498	0.18	B	0.18871	0.023	T	0.74352	-0.3693	9	0.18276	T	0.48	.	15.4632	0.75377	0.0:0.1392:0.8608:0.0	.	2476	Q9P273	TEN3_HUMAN	N	2476	ENSP00000424226:S2476N;ENSP00000385276:S2476N	ENSP00000385276:S2476N	S	+	2	0	ODZ3	183957825	1.000000	0.71417	0.997000	0.53966	0.764000	0.43329	6.546000	0.73887	1.357000	0.45904	0.557000	0.71058	AGC	.	.	none		0.697	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
INTS4	92105	hgsc.bcm.edu	37	11	77635882	77635882	+	Silent	SNP	A	A	C	rs7119720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77635882A>C	ENST00000534064.1	-	12	1462	c.1428T>G	c.(1426-1428)gtT>gtG	p.V476V	INTS4_ENST00000529807.1_Silent_p.V476V|INTS4_ENST00000525931.1_5'UTR	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	476					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			CTTTGGTTGAAACATTAGTAC	0.353													A|||	871	0.173922	0.1687	0.1427	5008	,	,		20915	0.1478		0.2068	False		,,,				2504	0.1963				p.V476V		Atlas-SNP	.											.	INTS4	89	.	0			c.T1428G						PASS	.	A		763,3625		57,649,1488	25.0	25.0	25.0		1428	0.7	1.0	11	dbSNP_116	25	1735,6825		166,1403,2711	no	coding-synonymous	INTS4	NM_033547.3		223,2052,4199	CC,CA,AA		20.2687,17.3883,19.2926		476/964	77635882	2498,10450	2194	4280	6474	SO:0001819	synonymous_variant	92105	exon12			GGTTGAAACATTA	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.1428T>G	11.37:g.77635882A>C		Somatic	372	1	0.00268817		WXS	Illumina HiSeq	Phase_I	401	168	0.418953	NM_033547	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Silent	SNP	ENST00000534064.1	37	CCDS31644.1																																																																																			A|0.818;C|0.182	0.182	strong		0.353	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547	
PCNT	5116	hgsc.bcm.edu	37	21	47863757	47863757	+	Missense_Mutation	SNP	A	A	C	rs2073380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47863757A>C	ENST00000359568.5	+	45	9842	c.9735A>C	c.(9733-9735)agA>agC	p.R3245S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	3245	Interaction with NEK2.		R -> S (in dbSNP:rs2073380).		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)					CTCCACCCAGAACCAGAGAGT	0.582													A|||	1033	0.20627	0.056	0.1354	5008	,	,		14631	0.4117		0.2157	False		,,,				2504	0.2382				p.R3245S		Atlas-SNP	.											.	PCNT	283	.	0			c.A9735C						PASS	.	A	SER/ARG	356,4050	179.0+/-207.6	16,324,1863	56.0	67.0	63.0		9735	-3.0	0.0	21	dbSNP_96	63	1849,6751	321.6+/-315.2	193,1463,2644	yes	missense	PCNT	NM_006031.5	110	209,1787,4507	CC,CA,AA		21.5,8.0799,16.9537	benign	3245/3337	47863757	2205,10801	2203	4300	6503	SO:0001583	missense	5116	exon45			ACCCAGAACCAGA	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.9735A>C	21.37:g.47863757A>C	ENSP00000352572:p.Arg3245Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	513	0.2348901098901099	31	0.06300813008130081	60	0.16574585635359115	257	0.4493006993006993	165	0.21767810026385223	A	6.196	0.404264	0.11754	0.080799	0.215	ENSG00000160299	ENST00000359568	T	0.01414	4.92	5.0	-2.95	0.05564	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.14438	0.006;0.01	B;B	0.13407	0.009;0.004	T	0.35574	-0.9783	8	0.08381	T	0.77	.	1.0943	0.01670	0.2612:0.3348:0.2529:0.1511	rs2073380;rs52807129;rs2073380	3048;3245	O95613-2;O95613	.;PCNT_HUMAN	S	3245	ENSP00000352572:R3245S	ENSP00000352572:R3245S	R	+	3	2	PCNT	46688185	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.016000	0.12613	-0.225000	0.09913	0.533000	0.62120	AGA	A|0.810;C|0.190	0.190	strong		0.582	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
GPR98	84059	hgsc.bcm.edu	37	5	90016763	90016763	+	Missense_Mutation	SNP	T	T	C	rs199833843		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:90016763T>C	ENST00000405460.2	+	45	9731	c.9635T>C	c.(9634-9636)aTa>aCa	p.I3212T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3212					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)		GCCACCTCCATAGACATCGAA	0.363													T|||	1	0.000199681	0.0008	0.0	5008	,	,		14469	0.0		0.0	False		,,,				2504	0.0				p.I3212T		Atlas-SNP	.											.	GPR98	605	.	0			c.T9635C						PASS	.	T	THR/ILE	6,3780		0,6,1887	164.0	164.0	164.0		9635	5.8	0.0	5		164	0,8246		0,0,4123	yes	missense	GPR98	NM_032119.3	89	0,6,6010	CC,CT,TT		0.0,0.1585,0.0499	benign	3212/6307	90016763	6,12026	1893	4123	6016	SO:0001583	missense	84059	exon45			CCTCCATAGACAT	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.9635T>C	5.37:g.90016763T>C	ENSP00000384582:p.Ile3212Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.64|12.64	1.999550|1.999550	0.35320|0.35320	0.001585|0.001585	0.0|0.0	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.32023|.	1.47|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	0.571652|.	0.20166|.	N|.	0.097852|.	T|.	0.63426|.	0.2510|.	L|L	0.46157|0.46157	1.445|1.445	0.80722|0.80722	D|D	1|1	B;B|.	0.28820|.	0.224;0.094|.	B;B|.	0.21360|.	0.034;0.016|.	T|.	0.60188|.	-0.7312|.	10|.	0.66056|.	D|.	0.02|.	.|.	16.0796|16.0796	0.80995|0.80995	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	3212;3212|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	T|Q	3212|778	ENSP00000384582:I3212T|.	ENSP00000296619:I3212T|.	I|X	+|+	2|1	0|0	GPR98|GPR98	90052519|90052519	0.221000|0.221000	0.23642|0.23642	0.005000|0.005000	0.12908|0.12908	0.200000|0.200000	0.23975|0.23975	3.355000|3.355000	0.52262|0.52262	2.195000|2.195000	0.70347|0.70347	0.528000|0.528000	0.53228|0.53228	ATA|TAG	.	.	weak		0.363	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
SLC2A7	155184	hgsc.bcm.edu	37	1	9083094	9083094	+	Missense_Mutation	SNP	G	G	T	rs61744620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9083094G>T	ENST00000400906.1	-	3	193	c.194C>A	c.(193-195)gCa>gAa	p.A65E		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	65					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			NS(1)|breast(1)|endometrium(4)|large_intestine(10)|lung(4)|prostate(2)|skin(2)	24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		CATGAATGTTGCGTGTCGCTC	0.502													G|||	118	0.0235623	0.0847	0.0086	5008	,	,		20374	0.0		0.0	False		,,,				2504	0.0				p.A65E		Atlas-SNP	.											SLC2A7,rectum,carcinoma,-1,2	SLC2A7	56	2	0			c.C194A						PASS	.	G	GLU/ALA	324,4082	172.3+/-202.3	18,288,1897	171.0	158.0	162.0		194	1.6	0.0	1	dbSNP_129	162	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC2A7	NM_207420.2	107	18,289,6196	TT,TG,GG		0.0116,7.3536,2.4988	benign	65/513	9083094	325,12681	2203	4300	6503	SO:0001583	missense	155184	exon3			AATGTTGCGTGTC	AL356306	CCDS98.2	1p36.2	2013-05-22			ENSG00000197241	ENSG00000197241		"""Solute carriers"""	13445	protein-coding gene	gene with protein product	"""intestinal facilitative glucose transporter 7"""	610371				11780753	Standard	NM_207420		Approved	GLUT7	uc009vmo.1	Q6PXP3	OTTHUMG00000057499	ENST00000400906.1:c.194C>A	1.37:g.9083094G>T	ENSP00000383698:p.Ala65Glu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_207420	A2A333	Missense_Mutation	SNP	ENST00000400906.1	37	CCDS98.2	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	13.62	2.292105	0.40594	0.073536	1.16E-4	ENSG00000197241	ENST00000400906	T	0.73047	-0.71	4.68	1.57	0.23409	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.305652	0.30210	N	0.010158	T	0.01287	0.0042	N	0.04994	-0.135	0.09310	N	1	B	0.10296	0.003	B	0.14578	0.011	T	0.03086	-1.1074	10	0.44086	T	0.13	.	15.0439	0.71813	0.0:0.5434:0.4566:0.0	.	65	Q6PXP3	GTR7_HUMAN	E	65	ENSP00000383698:A65E	ENSP00000383698:A65E	A	-	2	0	SLC2A7	9005681	0.000000	0.05858	0.002000	0.10522	0.305000	0.27757	1.115000	0.31209	0.567000	0.29293	0.556000	0.70494	GCA	G|0.974;T|0.026	0.026	strong		0.502	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519158	48519158	+	Missense_Mutation	SNP	C	C	T	rs34129198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48519158C>T	ENST00000339841.2	+	4	395	c.217C>T	c.(217-219)Cgc>Tgc	p.R73C	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	73	Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		AGATTACCCACGCTGTATCTT	0.463													c|||	810	0.161741	0.2103	0.1254	5008	,	,		20377	0.0724		0.1531	False		,,,				2504	0.2229				p.R73C		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.C217T						PASS	.	C	CYS/ARG	884,3522	343.3+/-307.6	86,712,1405	106.0	83.0	91.0		217	2.2	0.9	19	dbSNP_126	91	1294,7306	256.1+/-280.7	91,1112,3097	yes	missense	ELSPBP1	NM_022142.4	180	177,1824,4502	TT,TC,CC		15.0465,20.0635,16.7461	probably-damaging	73/224	48519158	2178,10828	2203	4300	6503	SO:0001583	missense	64100	exon4			TACCCACGCTGTA	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.217C>T	19.37:g.48519158C>T	ENSP00000340660:p.Arg73Cys	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	325	0.1488095238095238	107	0.21747967479674796	59	0.16298342541436464	47	0.08216783216783216	112	0.14775725593667546	C	9.088	1.000976	0.19121	0.200635	0.150465	ENSG00000169393	ENST00000339841	T	0.10005	2.92	3.4	2.21	0.28008	Fibronectin, type II, collagen-binding (3);Kringle-like fold (1);	0.186449	0.24554	N	0.037536	T	0.00012	0.0000	L	0.35414	1.06	0.40606	P	0.018378000000000005	P	0.35226	0.491	B	0.27608	0.081	T	0.45425	-0.9262	9	0.38643	T	0.18	.	7.0708	0.25177	0.2693:0.7306:0.0:0.0	rs34129198	73	Q96BH3	ESPB1_HUMAN	C	73	ENSP00000340660:R73C	ENSP00000340660:R73C	R	+	1	0	ELSPBP1	53210970	0.868000	0.29978	0.938000	0.37757	0.306000	0.27790	1.077000	0.30741	1.817000	0.53016	0.543000	0.68304	CGC	C|0.837;T|0.163	0.163	strong		0.463	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
GABRG3	2567	hgsc.bcm.edu	37	15	27777751	27777751	+	Silent	SNP	T	T	C	rs16950126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:27777751T>C	ENST00000333743.6	+	10	1382	c.1128T>C	c.(1126-1128)taT>taC	p.Y376Y	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	376					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)	TGCAGAACTATTCCCTCCTGG	0.423													T|||	316	0.063099	0.2216	0.0274	5008	,	,		19532	0.0		0.004	False		,,,				2504	0.0				p.Y376Y	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.T1128C						PASS	.	T		648,3304		48,552,1376	91.0	88.0	89.0		1128	-7.8	0.7	15	dbSNP_123	89	8,8332		0,8,4162	no	coding-synonymous	GABRG3	NM_033223.4		48,560,5538	CC,CT,TT		0.0959,16.3968,5.3368		376/468	27777751	656,11636	1976	4170	6146	SO:0001819	synonymous_variant	2567	exon10			GAACTATTCCCTC		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.1128T>C	15.37:g.27777751T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	147	75	0.510204	NM_033223	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1																																																																																			T|0.932;C|0.068	0.068	strong		0.423	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
SNTG2	54221	hgsc.bcm.edu	37	2	1204796	1204796	+	Missense_Mutation	SNP	C	C	T	rs6751090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1204796C>T	ENST00000308624.5	+	9	728	c.599C>T	c.(598-600)tCg>tTg	p.S200L	SNTG2_ENST00000407292.1_Missense_Mutation_p.S73L|SNTG2_ENST00000467759.1_3'UTR	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	200			S -> L (in dbSNP:rs6751090).		central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)	p.S200L(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		CAGGCCCCATCGTCACCTTCC	0.567													C|||	1031	0.205871	0.4766	0.0749	5008	,	,		17247	0.0972		0.0646	False		,,,				2504	0.1902				p.S200L		Atlas-SNP	.											SNTG2,colon,carcinoma,0,4	SNTG2	125	4	2	Substitution - Missense(2)	stomach(1)|breast(1)	c.C599T						PASS	.	C	LEU/SER	1628,2566		312,1004,781	66.0	72.0	70.0		599	4.0	1.0	2	dbSNP_116	70	583,7891		24,535,3678	yes	missense	SNTG2	NM_018968.3	145	336,1539,4459	TT,TC,CC		6.8799,38.8174,17.4534	benign	200/540	1204796	2211,10457	2097	4237	6334	SO:0001583	missense	54221	exon9			CCCCATCGTCACC	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.599C>T	2.37:g.1204796C>T	ENSP00000311837:p.Ser200Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	73	43	0.589041	NM_018968	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	37	CCDS46220.1	350	0.16025641025641027	229	0.4654471544715447	27	0.07458563535911603	50	0.08741258741258741	44	0.05804749340369393	C	13.95	2.390441	0.42410	0.388174	0.068799	ENSG00000172554	ENST00000308624;ENST00000407292	T;T	0.57436	0.4;0.4	4.03	4.03	0.46877	.	0.223972	0.40064	N	0.001200	T	0.00012	0.0000	M	0.79475	2.455	0.20074	P	0.9999380064	D;D	0.60160	0.987;0.987	P;P	0.47891	0.56;0.537	T	0.48352	-0.9043	9	0.09843	T	0.71	.	16.1279	0.81406	0.0:1.0:0.0:0.0	rs6751090;rs59130779;rs6751090	73;200	Q9NY99-2;Q9NY99	.;SNTG2_HUMAN	L	200;73	ENSP00000311837:S200L;ENSP00000385020:S73L	ENSP00000311837:S200L	S	+	2	0	SNTG2	1194796	1.000000	0.71417	0.976000	0.42696	0.541000	0.35023	5.411000	0.66386	1.931000	0.55961	0.453000	0.30009	TCG	C|0.811;T|0.189	0.189	strong		0.567	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968	
OR10H4	126541	hgsc.bcm.edu	37	19	16060248	16060248	+	Missense_Mutation	SNP	A	A	G	rs16980822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16060248A>G	ENST00000322107.1	+	1	431	c.431A>G	c.(430-432)cAt>cGt	p.H144R		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	144			H -> R (in dbSNP:rs16980822).			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(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						GACTGTGCCCATCTTGTGGCC	0.537													.|||	1211	0.241813	0.4622	0.1772	5008	,	,		23626	0.0546		0.2644	False		,,,				2504	0.1595				p.H144R		Atlas-SNP	.											OR10H4,NS,carcinoma,+1,1	OR10H4	48	1	0			c.A431G						PASS	.	G	ARG/HIS	1849,2557		384,1081,738	183.0	157.0	166.0		431	0.4	0.0	19	dbSNP_123	166	2049,6551		235,1579,2486	yes	missense	OR10H4	NM_001004465.1	29	619,2660,3224	GG,GA,AA		23.8256,41.9655,29.9708	benign	144/317	16060248	3898,9108	2203	4300	6503	SO:0001583	missense	126541	exon1			GTGCCCATCTTGT	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"""GPCR / Class A : Olfactory receptors"""	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.431A>G	19.37:g.16060248A>G	ENSP00000318834:p.His144Arg	Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	274	273	0.99635	NM_001004465	Q6IFJ2|Q96R57	Missense_Mutation	SNP	ENST00000322107.1	37	CCDS32941.1	549	0.25137362637362637	237	0.4817073170731707	82	0.2265193370165746	40	0.06993006993006994	190	0.25065963060686014	N	0.676	-0.799908	0.02841	0.419655	0.238256	ENSG00000176231	ENST00000322107	T	0.35789	1.29	1.53	0.441	0.16577	GPCR, rhodopsin-like superfamily (1);	0.568736	0.13060	N	0.416993	T	0.00012	0.0000	N	0.02842	-0.48	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47849	-0.9085	9	0.18710	T	0.47	.	4.571	0.12210	0.6061:0.0:0.3939:0.0	rs16980822;rs52815203;rs59896686;rs16980822	144	Q8NGA5	O10H4_HUMAN	R	144	ENSP00000318834:H144R	ENSP00000318834:H144R	H	+	2	0	OR10H4	15921248	0.000000	0.05858	0.001000	0.08648	0.069000	0.16628	-2.003000	0.01463	-0.004000	0.14419	-0.392000	0.06488	CAT	A|0.724;G|0.276	0.276	strong		0.537	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1		
MUC4	4585	hgsc.bcm.edu	37	3	195509611	195509611	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509611A>T	ENST00000463781.3	-	2	9299	c.8840T>A	c.(8839-8841)gTc>gAc	p.V2947D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V2947D	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.V2947D(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)		AGTGTCGGTGACAGGAAGAGG	0.592																																					p.V2947D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	skin(2)|endometrium(1)	c.T8840A						scavenged	.						10.0	8.0	9.0					3																	195509611		654	1505	2159	SO:0001583	missense	4585	exon2			TCGGTGACAGGAA	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.8840T>A	3.37:g.195509611A>T	ENSP00000417498:p.Val2947Asp	Somatic	292	2	0.00684932		WXS	Illumina HiSeq	Phase_I	211	3	0.014218	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	4.900	0.167345	0.09339	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.5;1.49	.	.	.	.	.	.	.	.	T	0.24509	0.0594	N	0.08118	0	0.09310	N	1	D	0.65815	0.995	D	0.68483	0.958	T	0.10154	-1.0642	7	.	.	.	.	1.3928	0.02254	0.3276:0.0:0.3249:0.3475	.	2819	E7ESK3	.	D	2947	ENSP00000417498:V2947D;ENSP00000420243:V2947D	.	V	-	2	0	MUC4	196994390	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.286000	0.08399	-0.000000	0.14550	0.000000	0.15137	GTC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CHRM1	1128	hgsc.bcm.edu	37	11	62677529	62677529	+	Silent	SNP	C	C	T	rs2067478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62677529C>T	ENST00000306960.3	-	2	1585	c.1044G>A	c.(1042-1044)caG>caA	p.Q348Q	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	348					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	GCTTGGCCAGCTGCTCCTTTC	0.612													C|||	293	0.0585064	0.1286	0.0231	5008	,	,		19135	0.0169		0.0258	False		,,,				2504	0.0654				p.Q348Q		Atlas-SNP	.											.	CHRM1	29	.	0			c.G1044A						PASS	.	C		496,3906	230.7+/-244.8	25,446,1730	50.0	49.0	49.0		1044	1.5	1.0	11	dbSNP_96	49	307,8289	110.8+/-171.2	7,293,3998	no	coding-synonymous	CHRM1	NM_000738.2		32,739,5728	TT,TC,CC		3.5714,11.2676,6.1779		348/461	62677529	803,12195	2201	4298	6499	SO:0001819	synonymous_variant	1128	exon2			GGCCAGCTGCTCC	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1950	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 1"""	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1044G>A	11.37:g.62677529C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_000738	Q96RH1	Silent	SNP	ENST00000306960.3	37	CCDS8040.1																																																																																			C|0.938;T|0.062	0.062	strong		0.612	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738	
FAM90A1	55138	hgsc.bcm.edu	37	12	8375112	8375112	+	Missense_Mutation	SNP	G	G	T	rs9668582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:8375112G>T	ENST00000538603.1	-	7	1259	c.701C>A	c.(700-702)gCg>gAg	p.A234E	FAM90A1_ENST00000307435.6_Missense_Mutation_p.A234E	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	234			A -> E (in dbSNP:rs9668582). {ECO:0000269|PubMed:15489334}.				nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		ACAGCCACCCGCAGGGCTGCT	0.657																																					p.A234E		Atlas-SNP	.											.	FAM90A1	68	.	0			c.C701A						PASS	.						39.0	63.0	55.0					12																	8375112		2070	4218	6288	SO:0001583	missense	55138	exon7			CCACCCGCAGGGC	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.701C>A	12.37:g.8375112G>T	ENSP00000445418:p.Ala234Glu	Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	302	302	1	NM_018088	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	454	0.2078754578754579	85	0.17276422764227642	67	0.1850828729281768	197	0.34440559440559443	105	0.13852242744063326	.	0.004	-2.244152	0.00271	.	.	ENSG00000171847	ENST00000307435;ENST00000538603	T;T	0.06608	3.28;3.28	0.713	-1.43	0.08884	.	.	.	.	.	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34204	-0.9838	7	0.02654	T	1	7.4118	.	.	.	rs9668582;rs17857268	234	Q86YD7	F90A1_HUMAN	E	234	ENSP00000307798:A234E;ENSP00000445418:A234E	ENSP00000307798:A234E	A	-	2	0	FAM90A1	8266379	0.005000	0.15991	0.000000	0.03702	0.014000	0.08584	-0.767000	0.04720	-1.652000	0.01502	-1.448000	0.01049	GCG	G|0.793;T|0.207	0.207	strong		0.657	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
OBSL1	23363	hgsc.bcm.edu	37	2	220421417	220421417	+	Missense_Mutation	SNP	C	C	G	rs1983210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220421417C>G	ENST00000404537.1	-	13	4151	c.4095G>C	c.(4093-4095)gaG>gaC	p.E1365D	OBSL1_ENST00000373876.1_Missense_Mutation_p.E1273D|OBSL1_ENST00000265318.4_Missense_Mutation_p.E1273D|OBSL1_ENST00000603926.1_Missense_Mutation_p.E1365D|OBSL1_ENST00000265317.5_Missense_Mutation_p.E264D|RP11-256I23.2_ENST00000597192.1_RNA	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1365	Ig-like 12.			E -> D (in Ref. 4; BAA31632). {ECO:0000305}.	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)		GTGGTGTCAGCTCCGAGACCA	0.597													C|||	3629	0.724641	0.6036	0.6873	5008	,	,		20402	0.7163		0.7366	False		,,,				2504	0.911				p.E1365D		Atlas-SNP	.											OBSL1_ENST00000404537,NS,carcinoma,0,1	OBSL1	120	1	0			c.G4095C						PASS	.	C	ASP/GLU,ASP/GLU	2769,1573		911,947,313	37.0	41.0	39.0		4095,4095	2.1	1.0	2	dbSNP_92	39	6240,2266		2298,1644,311	yes	missense,missense	OBSL1	NM_001173431.1,NM_015311.2	45,45	3209,2591,624	GG,GC,CC		26.64,36.2275,29.8801	possibly-damaging,possibly-damaging	1365/1544,1365/1897	220421417	9009,3839	2171	4253	6424	SO:0001583	missense	23363	exon13			TGTCAGCTCCGAG	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.4095G>C	2.37:g.220421417C>G	ENSP00000385636:p.Glu1365Asp	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	276	146	0.528986	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	37	CCDS46520.1	1520|1520	0.6959706959706959|0.6959706959706959	307|307	0.6239837398373984|0.6239837398373984	255|255	0.7044198895027625|0.7044198895027625	401|401	0.701048951048951|0.701048951048951	557|557	0.7348284960422163|0.7348284960422163	C|C	11.98|11.98	1.801775|1.801775	0.31869|0.31869	0.637725|0.637725	0.7336|0.7336	ENSG00000124006|ENSG00000124006	ENST00000265318;ENST00000404537;ENST00000373876;ENST00000265317|ENST00000456147	T;T;T;T|.	0.71934|.	-0.61;-0.61;-0.61;-0.61|.	4.16|4.16	2.11|2.11	0.27256|0.27256	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.72894|0.72894	2.215|2.215	0.31591|0.31591	P|P	0.653918|0.653918	P;P;B|.	0.44946|.	0.592;0.846;0.071|.	B;P;B|.	0.54706|.	0.418;0.759;0.075|.	T|T	0.38156|0.38156	-0.9674|-0.9674	8|4	0.23302|.	T|.	0.38|.	.|.	10.1036|10.1036	0.42519|0.42519	0.0:0.7993:0.0:0.2007|0.0:0.7993:0.0:0.2007	rs1983210;rs56494775;rs56756988;rs1983210|rs1983210;rs56494775;rs56756988;rs1983210	1366;1365;264|.	A4KVA4;O75147;E7ER99|.	.;OBSL1_HUMAN;.|.	D|T	1273;1365;1273;264|267	ENSP00000265318:E1273D;ENSP00000385636:E1365D;ENSP00000362983:E1273D;ENSP00000265317:E264D|.	ENSP00000265317:E264D|.	E|S	-|-	3|2	2|0	OBSL1|OBSL1	220129661|220129661	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.248000|0.248000	0.25809|0.25809	0.902000|0.902000	0.28459|0.28459	0.954000|0.954000	0.37851|0.37851	0.306000|0.306000	0.20318|0.20318	GAG|AGC	C|0.289;G|0.711	0.711	strong		0.597	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
OR13C5	138799	hgsc.bcm.edu	37	9	107361642	107361642	+	Missense_Mutation	SNP	G	G	A	rs1851722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361642G>A	ENST00000374779.2	-	1	146	c.53C>T	c.(52-54)tCt>tTt	p.S18F		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	18			S -> F (in dbSNP:rs1851722).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						TGGGTGACCAGAAAGTCCCTT	0.388													G|||	1205	0.240615	0.0998	0.366	5008	,	,		20151	0.38		0.2445	False		,,,				2504	0.1943				p.S18F		Atlas-SNP	.											.	OR13C5	60	.	0			c.C53T						PASS	.						49.0	52.0	51.0					9																	107361642		2201	4294	6495	SO:0001583	missense	138799	exon1			TGACCAGAAAGTC		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.53C>T	9.37:g.107361642G>A	ENSP00000363911:p.Ser18Phe	Somatic	478	1	0.00209205		WXS	Illumina HiSeq	Phase_I	489	234	0.478528	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	599	0.2742673992673993	53	0.10772357723577236	127	0.35082872928176795	218	0.3811188811188811	201	0.26517150395778366	G	15.10	2.732376	0.48939	.	.	ENSG00000255800	ENST00000374779	T	0.00441	7.41	3.84	2.91	0.33838	.	0.000000	0.36932	U	0.002336	T	0.00012	0.0000	M	0.76170	2.325	0.80722	P	0.0	D	0.60575	0.988	P	0.54924	0.764	T	0.49143	-0.8970	9	0.87932	D	0	.	10.221	0.43196	0.0:0.0:0.8:0.2	rs1851722;rs35304986;rs57432004;rs1851722	18	Q8NGS8	O13C5_HUMAN	F	18	ENSP00000363911:S18F	ENSP00000363911:S18F	S	-	2	0	OR13C5	106401463	0.025000	0.19082	0.002000	0.10522	0.240000	0.25518	2.042000	0.41222	0.777000	0.33496	0.531000	0.56144	TCT	G|1.000;|0.000	.	weak		0.388	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
CPAMD8	27151	hgsc.bcm.edu	37	19	17091368	17091368	+	Silent	SNP	T	T	G	rs8103646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17091368T>G	ENST00000443236.1	-	14	1696	c.1665A>C	c.(1663-1665)cgA>cgC	p.R555R	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	508						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						CCCGCTTGCTTCGCTGCTGGG	0.587													T|||	2373	0.473842	0.6475	0.3559	5008	,	,		17983	0.5506		0.3509	False		,,,				2504	0.3701				p.R555R		Atlas-SNP	.											CPAMD8,NS,carcinoma,-1,1	CPAMD8	192	1	0			c.A1665C						PASS	.	T		2244,1706		634,976,365	58.0	65.0	63.0		1665	0.6	1.0	19	dbSNP_116	63	2636,5682		401,1834,1924	no	coding-synonymous	CPAMD8	NM_015692.2		1035,2810,2289	GG,GT,TT		31.6903,43.1899,39.7783		555/1933	17091368	4880,7388	1975	4159	6134	SO:0001819	synonymous_variant	27151	exon14			CTTGCTTCGCTGC	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.1665A>C	19.37:g.17091368T>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	1035	0.4739010989010989	317	0.6443089430894309	133	0.3674033149171271	312	0.5454545454545454	273	0.36015831134564646	T	7.048	0.563842	0.13498	0.568101	0.316903	ENSG00000160111	ENST00000443236	.	.	.	2.9	0.633	0.17712	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999769414	.	.	.	.	.	.	T	0.43572	-0.9383	3	.	.	.	.	7.1737	0.25732	0.0:0.4272:0.0:0.5728	rs8103646	.	.	.	A	566	.	.	E	-	2	0	CPAMD8	16952368	0.968000	0.33430	0.972000	0.41901	0.565000	0.35776	-0.114000	0.10757	0.105000	0.17753	0.383000	0.25322	GAA	T|0.601;G|0.399	0.399	strong		0.587	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
IPO13	9670	hgsc.bcm.edu	37	1	44433055	44433055	+	Silent	SNP	G	G	A	rs34392712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44433055G>A	ENST00000372343.3	+	19	3344	c.2682G>A	c.(2680-2682)aaG>aaA	p.K894K	IPO13_ENST00000372339.3_Silent_p.K112K|DPH2_ENST00000412950.2_5'Flank|DPH2_ENST00000396758.2_5'Flank|DPH2_ENST00000255108.3_5'Flank	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	894					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)				CCCTGAACAAGCACTGCTTCA	0.617													g|||	67	0.0133786	0.0499	0.0014	5008	,	,		18701	0.0		0.0	False		,,,				2504	0.0				p.K894K		Atlas-SNP	.											.	IPO13	86	.	0			c.G2682A						PASS	.			173,4233	110.4+/-148.6	3,167,2033	72.0	70.0	71.0		2682	-0.2	1.0	1	dbSNP_126	71	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	IPO13	NM_014652.3		3,168,6332	AA,AG,GG		0.0116,3.9265,1.3378		894/964	44433055	174,12832	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon19			GAACAAGCACTGC	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.2682G>A	1.37:g.44433055G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	117	59	0.504274	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			G|0.989;A|0.011	0.011	strong		0.617	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411096	105411096	+	Missense_Mutation	SNP	T	T	G	rs146355838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105411096T>G	ENST00000333244.5	-	7	10811	c.10692A>C	c.(10690-10692)ttA>ttC	p.L3564F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3564						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)			TGGGCGTCTTTAAACTGGGCA	0.612													.|||	364	0.0726837	0.2648	0.0173	5008	,	,		17395	0.0		0.002	False		,,,				2504	0.0				p.L3564F		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A10692C						PASS	.	T	PHE/LEU	745,2943		103,539,1202	98.0	113.0	108.0		10692	-0.5	0.1	14	dbSNP_134	108	9,8157		0,9,4074	no	missense	AHNAK2	NM_138420.2	22	103,548,5276	GG,GT,TT		0.1102,20.2007,6.3607	possibly-damaging	3564/5796	105411096	754,11100	1844	4083	5927	SO:0001583	missense	113146	exon7			CGTCTTTAAACTG	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.10692A>C	14.37:g.105411096T>G	ENSP00000353114:p.Leu3564Phe	Somatic	238	2	0.00840336		WXS	Illumina HiSeq	Phase_I	254	252	0.992126	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	79	0.036172161172161175	74	0.15040650406504066	5	0.013812154696132596	0	0.0	0	0.0	t	0.125	-1.120104	0.01785	0.202007	0.001102	ENSG00000185567	ENST00000333244	T	0.01034	5.42	3.75	-0.46	0.12175	.	.	.	.	.	T	0.00012	0.0000	N	0.01086	-1.025	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.38373	-0.9664	8	0.39692	T	0.17	.	3.0553	0.06182	0.0902:0.143:0.3249:0.4419	.	3564	Q8IVF2	AHNK2_HUMAN	F	3564	ENSP00000353114:L3564F	ENSP00000353114:L3564F	L	-	3	2	AHNAK2	104482141	0.002000	0.14202	0.063000	0.19743	0.003000	0.03518	-0.991000	0.03728	-0.179000	0.10654	-3.555000	0.00030	TTA	T|0.971;G|0.029	0.029	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MUC4	4585	hgsc.bcm.edu	37	3	195511781	195511781	+	Missense_Mutation	SNP	G	G	A	rs71291863		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511781G>A	ENST00000463781.3	-	2	7129	c.6670C>T	c.(6670-6672)Cct>Tct	p.P2224S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2224S	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)		ACAAGAAGAGGGATGGCGTGA	0.597																																					p.P2224S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,3	MUC4	1505	3	0			c.C6670T						PASS	.						34.0	32.0	33.0					3																	195511781		653	1583	2236	SO:0001583	missense	4585	exon2			GAAGAGGGATGGC	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.6670C>T	3.37:g.195511781G>A	ENSP00000417498:p.Pro2224Ser	Somatic	404	1	0.00247525		WXS	Illumina HiSeq	Phase_I	187	47	0.251337	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	4.909	0.168944	0.09339	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28255	1.76;1.62	.	.	.	.	.	.	.	.	T	0.13030	0.0316	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.24440	-1.0160	6	.	.	.	.	.	.	.	.	2224	E7ESK3	.	S	2224	ENSP00000417498:P2224S;ENSP00000420243:P2224S	.	P	-	1	0	MUC4	196996176	0.235000	0.23794	0.000000	0.03702	0.001000	0.01503	1.269000	0.33074	-1.833000	0.01195	-2.092000	0.00371	CCT	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC22A24	283238	hgsc.bcm.edu	37	11	62886706	62886706	+	Missense_Mutation	SNP	C	C	T	rs116063135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62886706C>T	ENST00000417740.1	-	3	1049	c.608G>A	c.(607-609)cGc>cAc	p.R203H	SLC22A24_ENST00000326192.5_Missense_Mutation_p.R203H	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	203					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						TGCCAAGAAGCGCAGTATGCA	0.438													C|||	58	0.0115815	0.0439	0.0	5008	,	,		21113	0.0		0.0	False		,,,				2504	0.0				p.R203H		Atlas-SNP	.											.	SLC22A24	31	.	0			c.G608A						PASS	.	C	HIS/ARG	59,1325		0,59,633	136.0	120.0	125.0		608	1.8	0.0	11	dbSNP_132	125	1,3181		0,1,1590	yes	missense	SLC22A24	NM_001136506.2	29	0,60,2223	TT,TC,CC		0.0314,4.263,1.3141	probably-damaging	203/553	62886706	60,4506	692	1591	2283	SO:0001583	missense	283238	exon3			AAGAAGCGCAGTA		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.608G>A	11.37:g.62886706C>T	ENSP00000396586:p.Arg203His	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	162	84	0.518519	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	37		23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	19.33	3.807587	0.70797	0.04263	3.14E-4	ENSG00000197658	ENST00000417740;ENST00000531535;ENST00000326192	D;T	0.90197	-2.63;-0.51	3.77	1.79	0.24919	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	U	0.000000	D	0.83353	0.5236	H	0.96365	3.81	0.09310	N	1	D;D	0.76494	0.999;0.995	D;P	0.66602	0.945;0.843	T	0.80094	-0.1526	10	0.87932	D	0	.	8.3277	0.32167	0.0:0.7891:0.0:0.2109	.	203;203	Q8N4F4;C9JC66	S22AO_HUMAN;.	H	203	ENSP00000396586:R203H;ENSP00000321549:R203H	ENSP00000321549:R203H	R	-	2	0	SLC22A24	62643282	0.007000	0.16637	0.002000	0.10522	0.505000	0.33919	1.812000	0.38952	0.801000	0.34066	0.501000	0.49751	CGC	C|0.988;T|0.012	0.012	strong		0.438	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
PAK2	5062	hgsc.bcm.edu	37	3	196529982	196529982	+	Missense_Mutation	SNP	A	A	G	rs78043821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196529982A>G	ENST00000327134.3	+	4	705	c.383A>G	c.(382-384)aAg>aGg	p.K128R		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	128	Autoregulatory region. {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)		GATGTCCTAAAGTTCTACGAC	0.463																																					p.K128R		Atlas-SNP	.											PAK2_ENST00000327134,NS,lymphoid_neoplasm,0,2	PAK2	113	2	0			c.A383G						scavenged	.						107.0	95.0	99.0					3																	196529982		2203	4300	6503	SO:0001583	missense	5062	exon4			TCCTAAAGTTCTA	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.383A>G	3.37:g.196529982A>G	ENSP00000314067:p.Lys128Arg	Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	156	13	0.0833333	NM_002577	Q13154|Q6ISC3	Missense_Mutation	SNP	ENST00000327134.3	37	CCDS3321.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.176399	0.78564	.	.	ENSG00000180370	ENST00000327134	D	0.86230	-2.09	5.27	5.27	0.74061	PAK-box/P21-Rho-binding (1);	0.000000	0.85682	D	0.000000	D	0.86990	0.6066	L	0.55743	1.74	0.80722	D	1	P	0.37015	0.578	B	0.43155	0.41	D	0.86926	0.2070	10	0.48119	T	0.1	.	14.3609	0.66771	1.0:0.0:0.0:0.0	.	128	Q13177	PAK2_HUMAN	R	128	ENSP00000314067:K128R	ENSP00000314067:K128R	K	+	2	0	PAK2	198014379	1.000000	0.71417	0.990000	0.47175	0.859000	0.49053	6.986000	0.76200	2.002000	0.58637	0.460000	0.39030	AAG	A|0.915;G|0.084	0.084	strong		0.463	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
XKR3	150165	hgsc.bcm.edu	37	22	17280822	17280822	+	Missense_Mutation	SNP	G	G	A	rs5748648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17280822G>A	ENST00000331428.5	-	3	530	c.428C>T	c.(427-429)aCg>aTg	p.T143M		NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN	XK, Kell blood group complex subunit-related family, member 3	143			T -> M (in dbSNP:rs5748648).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				TTCCAGCATCGTGTTTCTCTT	0.403													.|||	715	0.142772	0.2458	0.121	5008	,	,		18015	0.0952		0.0656	False		,,,				2504	0.1472				p.T143M		Atlas-SNP	.											.	XKR3	51	.	0			c.C428T						PASS	.	G	MET/THR	742,3042		77,588,1227	224.0	201.0	208.0		428	-1.5	0.0	22	dbSNP_114	208	470,7794		17,436,3679	yes	missense	XKR3	NM_175878.3	81	94,1024,4906	AA,AG,GG		5.6873,19.6089,10.0598	probably-damaging	143/460	17280822	1212,10836	1892	4132	6024	SO:0001583	missense	150165	exon3			AGCATCGTGTTTC	AY989815	CCDS42975.1	22q11.1	2007-01-16	2006-01-12		ENSG00000172967	ENSG00000172967			28778	protein-coding gene	gene with protein product		611674	"""X Kell blood group precursor-related family, member 3"""			16431037	Standard	NM_175878		Approved	MGC57211, XTES	uc002zlv.3	Q5GH77	OTTHUMG00000143726	ENST00000331428.5:c.428C>T	22.37:g.17280822G>A	ENSP00000331704:p.Thr143Met	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	340	159	0.467647	NM_175878	B2RPN1|Q52PG8|Q8N7E1	Missense_Mutation	SNP	ENST00000331428.5	37	CCDS42975.1	264	0.12087912087912088	112	0.22764227642276422	42	0.11602209944751381	59	0.10314685314685315	51	0.06728232189973615	.	6.601	0.479201	0.12581	0.196089	0.056873	ENSG00000172967	ENST00000331428	T	0.59906	0.23	0.762	-1.52	0.08637	.	2.055320	0.04189	N	0.327994	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.17268	0.021	B	0.06405	0.002	T	0.04153	-1.0973	9	0.40728	T	0.16	.	2.1147	0.03711	0.3174:0.0:0.2134:0.4692	rs5748648;rs52798570;rs58098509;rs5748648	143	Q5GH77	XKR3_HUMAN	M	143	ENSP00000331704:T143M	ENSP00000331704:T143M	T	-	2	0	XKR3	15660822	0.988000	0.35896	0.001000	0.08648	0.016000	0.09150	0.275000	0.18698	-1.384000	0.02103	-1.082000	0.02213	ACG	G|0.881;A|0.119	0.119	strong		0.403	XKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289789.1	NM_175878	
NEIL3	55247	hgsc.bcm.edu	37	4	178257364	178257364	+	Missense_Mutation	SNP	G	G	C	rs17064658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:178257364G>C	ENST00000264596.3	+	4	634	c.516G>C	c.(514-516)caG>caC	p.Q172H		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	172			Q -> H (in dbSNP:rs17064658). {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)		TTAAAAAACAGAAAGGCCGGA	0.398								Base excision repair (BER), DNA glycosylases					G|||	123	0.0245607	0.0741	0.0144	5008	,	,		16964	0.0		0.0099	False		,,,				2504	0.0051				p.Q172H		Atlas-SNP	.											.	NEIL3	89	.	0			c.G516C						PASS	.	G	HIS/GLN	255,4151	147.3+/-181.8	12,231,1960	138.0	142.0	141.0		516	2.3	0.7	4	dbSNP_123	141	99,8501	54.0+/-114.7	1,97,4202	yes	missense	NEIL3	NM_018248.2	24	13,328,6162	CC,CG,GG		1.1512,5.7876,2.7218	possibly-damaging	172/606	178257364	354,12652	2203	4300	6503	SO:0001583	missense	55247	exon4			AAAACAGAAAGGC	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.516G>C	4.37:g.178257364G>C	ENSP00000264596:p.Gln172His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	44	0.020146520146520148	29	0.05894308943089431	7	0.019337016574585635	0	0.0	8	0.010554089709762533	G	11.19	1.566029	0.27915	0.057876	0.011512	ENSG00000109674	ENST00000264596	T	0.14516	2.5	4.93	2.28	0.28536	DNA glycosylase/AP lyase, H2TH DNA-binding (1);Ribosomal protein S13-like, H2TH (1);	0.118971	0.64402	D	0.000017	T	0.01454	0.0047	L	0.31207	0.915	0.40999	D	0.984912	D	0.53312	0.959	P	0.53760	0.734	T	0.07195	-1.0785	10	0.37606	T	0.19	-13.2033	7.8072	0.29209	0.3219:0.0:0.6781:0.0	rs17064658;rs52811923;rs17064658	172	Q8TAT5	NEIL3_HUMAN	H	172	ENSP00000264596:Q172H	ENSP00000264596:Q172H	Q	+	3	2	NEIL3	178494358	0.987000	0.35691	0.674000	0.29902	0.558000	0.35554	1.962000	0.40442	0.367000	0.24454	0.655000	0.94253	CAG	G|0.975;C|0.025	0.025	strong		0.398	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
IRF2BP1	26145	hgsc.bcm.edu	37	19	46387344	46387344	+	Silent	SNP	G	G	A	rs11550348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46387344G>A	ENST00000302165.3	-	1	2032	c.1689C>T	c.(1687-1689)ttC>ttT	p.F563F		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	563					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		CGCCCTGCATGAAGGCCCAGG	0.652											OREG0025563	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	684	0.136581	0.3185	0.1023	5008	,	,		14190	0.001		0.1034	False		,,,				2504	0.089				p.F563F		Atlas-SNP	.											.	IRF2BP1	23	.	0			c.C1689T						PASS	.	G		1262,3144	427.0+/-341.4	202,858,1143	57.0	52.0	54.0		1689	1.2	1.0	19	dbSNP_120	54	1115,7485	229.1+/-263.9	85,945,3270	no	coding-synonymous	IRF2BP1	NM_015649.1		287,1803,4413	AA,AG,GG		12.9651,28.6428,18.2762		563/585	46387344	2377,10629	2203	4300	6503	SO:0001819	synonymous_variant	26145	exon1			CTGCATGAAGGCC	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.1689C>T	19.37:g.46387344G>A		Somatic	71	0	0	938	WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_015649	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Silent	SNP	ENST00000302165.3	37	CCDS12678.1																																																																																			G|0.836;A|0.164	0.164	strong		0.652	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649	
DNMT3B	1789	hgsc.bcm.edu	37	20	31388080	31388080	+	Silent	SNP	C	C	T	rs17123657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31388080C>T	ENST00000328111.2	+	17	2202	c.1881C>T	c.(1879-1881)gaC>gaT	p.D627D	DNMT3B_ENST00000456297.2_Silent_p.D531D|DNMT3B_ENST00000375623.4_3'UTR|DNMT3B_ENST00000201963.3_Silent_p.D619D|DNMT3B_ENST00000344505.4_Silent_p.D607D|DNMT3B_ENST00000353855.2_Silent_p.D607D|DNMT3B_ENST00000348286.2_Silent_p.D607D|DNMT3B_ENST00000443239.3_Silent_p.D565D	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	627	S-adenosyl-L-methionine binding. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ACGTGAACGACGTGAGGAACA	0.498													C|||	277	0.0553115	0.1944	0.0144	5008	,	,		21823	0.0		0.007	False		,,,				2504	0.0031				p.D627D		Atlas-SNP	.											DNMT3B_ENST00000201963,NS,carcinoma,+2,4	DNMT3B	196	4	0			c.C1881T						PASS	.	C	,,,,,	762,3644	312.7+/-292.7	71,620,1512	198.0	170.0	180.0		1695,1593,1881,1821,1821,1857	-1.8	0.9	20	dbSNP_123	180	30,8570	21.0+/-64.5	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DNMT3B	NM_001207055.1,NM_001207056.1,NM_006892.3,NM_175848.1,NM_175849.1,NM_175850.2	,,,,,	71,650,5782	TT,TC,CC		0.3488,17.2946,6.0895	,,,,,	565/729,531/695,627/854,607/834,607/771,619/846	31388080	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	1789	exon17			GAACGACGTGAGG		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.1881C>T	20.37:g.31388080C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_006892	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Silent	SNP	ENST00000328111.2	37	CCDS13205.1																																																																																			C|0.944;T|0.056	0.056	strong		0.498	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892	
TNFRSF25	8718	hgsc.bcm.edu	37	1	6525257	6525257	+	Silent	SNP	C	C	T	rs45438594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6525257C>T	ENST00000356876.3	-	3	273	c.186G>A	c.(184-186)acG>acA	p.T62T	TNFRSF25_ENST00000351959.5_Silent_p.T62T|TNFRSF25_ENST00000348333.3_Intron|TNFRSF25_ENST00000461703.2_5'UTR|TNFRSF25_ENST00000377782.3_Silent_p.T62T|TNFRSF25_ENST00000351748.3_Intron	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	62					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|central_nervous_system(2)|endometrium(1)|lung(4)|prostate(1)|stomach(1)	10	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		CGCAGGGCTCCGTGCAAGGGG	0.647													c|||	186	0.0371406	0.1135	0.0115	5008	,	,		16887	0.0		0.004	False		,,,				2504	0.0245				p.T62T		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.G186A						PASS	.		,,,,,	397,4009	194.0+/-219.0	16,365,1822	45.0	43.0	44.0		186,186,186,186,,	-3.9	0.5	1	dbSNP_127	44	11,8589	7.1+/-27.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron	TNFRSF25	NM_001039664.1,NM_003790.2,NM_148965.1,NM_148966.1,NM_148967.1,NM_148970.1	,,,,,	16,376,6111	TT,TC,CC		0.1279,9.0104,3.137	,,,,,	62/182,62/418,62/427,62/381,,	6525257	408,12598	2203	4300	6503	SO:0001819	synonymous_variant	8718	exon3			GGGCTCCGTGCAA	U72763	CCDS71.1, CCDS72.1, CCDS73.1, CCDS74.1, CCDS75.1	1p36.2	2008-02-05	2002-12-20	2002-12-20	ENSG00000215788	ENSG00000215788		"""Tumor necrosis factor receptor superfamily"""	11910	protein-coding gene	gene with protein product		603366	"""tumor necrosis factor receptor superfamily, member 12 (translocating chain-association membrane protein)"""	TNFRSF12		9052839, 8934525	Standard	NM_003790		Approved	DR3, TRAMP, WSL-1, LARD, WSL-LR, DDR3, TR3, APO-3	uc001anh.3	Q93038	OTTHUMG00000000831	ENST00000356876.3:c.186G>A	1.37:g.6525257C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_148966	B1ALX2|B1ALX3|B7ZLL7|O00275|O00276|O00277|O00278|O00279|O00280|O14865|O14866|P78507|P78515|Q17RU4|Q92983|Q93036|Q93037|Q99722|Q99830|Q99831|Q9BY86|Q9UME0|Q9UME1|Q9UME5	Silent	SNP	ENST00000356876.3	37	CCDS71.1																																																																																			C|0.965;T|0.035	0.035	strong		0.647	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965	
SEC16B	89866	hgsc.bcm.edu	37	1	177902388	177902388	+	Silent	SNP	G	G	A	rs3813647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:177902388G>A	ENST00000308284.6	-	22	2873	c.2784C>T	c.(2782-2784)ccC>ccT	p.P928P	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)	928					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						CGTCTCCAGCGGGGGATGCGT	0.592													G|||	464	0.0926518	0.093	0.111	5008	,	,		17865	0.0268		0.172	False		,,,				2504	0.0654				p.P928P		Atlas-SNP	.											.	SEC16B	92	.	0			c.C2784T						PASS	.	G		434,3510		25,384,1563	29.0	36.0	34.0		2784	1.8	0.2	1	dbSNP_107	34	1498,6858		129,1240,2809	no	coding-synonymous	SEC16B	NM_033127.2		154,1624,4372	AA,AG,GG		17.9272,11.0041,15.7073		928/1061	177902388	1932,10368	1972	4178	6150	SO:0001819	synonymous_variant	89866	exon22			TCCAGCGGGGGAT	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.2784C>T	1.37:g.177902388G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	111	109	0.981982	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			G|0.878;A|0.122	0.122	strong		0.592	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
SLMAP	7871	hgsc.bcm.edu	37	3	57743531	57743531	+	Silent	SNP	A	A	G	rs147270008		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:57743531A>G	ENST00000428312.1	+	1	247	c.153A>G	c.(151-153)ctA>ctG	p.L51L	SLMAP_ENST00000449503.2_Silent_p.L51L|SLMAP_ENST00000295951.3_Silent_p.L51L|SLMAP_ENST00000416870.1_5'UTR|SLMAP_ENST00000295952.3_Silent_p.L51L|SLMAP_ENST00000383718.3_Silent_p.L51L			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	51	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.|Necessary for targeting to centrosomes. {ECO:0000250}.				muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)				endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		GCAAAGTGCTATCAAGGAACC	0.498																																					p.L51L		Atlas-SNP	.											.	SLMAP	46	.	0			c.A153G						PASS	.	A		1,4405		0,1,2202	78.0	70.0	73.0		153	1.8	1.0	3	dbSNP_134	73	0,8600		0,0,4300	no	coding-synonymous	SLMAP	NM_007159.2		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		51/812	57743531	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7871	exon1			AGTGCTATCAAGG	AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"""Sarcolemmal-associated protein"""	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.153A>G	3.37:g.57743531A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	223	106	0.475336	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Silent	SNP	ENST00000428312.1	37																																																																																				A|1.000;G|0.000	0.000	weak		0.498	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159	
NCAPD2	9918	hgsc.bcm.edu	37	12	6639981	6639981	+	Missense_Mutation	SNP	C	C	G	rs2240871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6639981C>G	ENST00000315579.5	+	30	4761	c.3962C>G	c.(3961-3963)aCt>aGt	p.T1321S	RP5-940J5.3_ENST00000537921.1_RNA|NCAPD2_ENST00000545962.1_Missense_Mutation_p.T1276S	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1321			T -> S (in dbSNP:rs2240871). {ECO:0000269|PubMed:15489334}.		mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						AAACCATCCACTGGTACGTAA	0.522													C|||	920	0.183706	0.0658	0.1988	5008	,	,		18395	0.3671		0.1829	False		,,,				2504	0.1442				p.T1321S		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C3962G						PASS	.	C	SER/THR	330,4076	173.4+/-203.2	13,304,1886	62.0	64.0	63.0		3962	2.4	0.0	12	dbSNP_98	63	1523,7077	283.6+/-296.2	135,1253,2912	yes	missense	NCAPD2	NM_014865.3	58	148,1557,4798	GG,GC,CC		17.7093,7.4898,14.2473	benign	1321/1402	6639981	1853,11153	2203	4300	6503	SO:0001583	missense	9918	exon30			CATCCACTGGTAC	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"""chromosome condensation related SMC associated protein 1"""	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.3962C>G	12.37:g.6639981C>G	ENSP00000325017:p.Thr1321Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	77	28	0.363636	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	37	CCDS8548.1	459	0.21016483516483517	33	0.06707317073170732	73	0.20165745856353592	214	0.3741258741258741	139	0.18337730870712401	C	1.095	-0.662912	0.03454	0.074898	0.177093	ENSG00000010292	ENST00000315579;ENST00000545962	T;T	0.16897	2.58;2.31	5.42	2.4	0.29515	.	1.768640	0.02053	N	0.050195	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.43212	-0.9405	9	0.15066	T	0.55	1.0634	8.1283	0.31012	0.0:0.6505:0.1269:0.2226	rs2240871;rs11545059;rs17852509;rs2240871	1276;1321	F5GZJ1;Q15021	.;CND1_HUMAN	S	1321;1276	ENSP00000325017:T1321S;ENSP00000444417:T1276S	ENSP00000325017:T1321S	T	+	2	0	NCAPD2	6510242	0.000000	0.05858	0.001000	0.08648	0.066000	0.16364	0.129000	0.15830	0.664000	0.31047	0.561000	0.74099	ACT	C|0.834;G|0.166	0.166	strong		0.522	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
AURKC	6795	hgsc.bcm.edu	37	19	57743518	57743518	+	Silent	SNP	C	C	T	rs142351971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57743518C>T	ENST00000302804.7	+	3	408	c.222C>T	c.(220-222)ctC>ctT	p.L74L	AURKC_ENST00000599062.1_Silent_p.L71L|AURKC_ENST00000415300.2_Silent_p.L55L|AURKC_ENST00000598785.1_Silent_p.L40L|AURKC_ENST00000448930.1_Silent_p.L40L	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	74	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		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;0.0122)		TGAAGGTTCTCTTCAAGTCGC	0.517													c|||	7	0.00139776	0.0053	0.0	5008	,	,		18570	0.0		0.0	False		,,,				2504	0.0				p.L74L		Atlas-SNP	.											AURKC_ENST00000302804,colon,carcinoma,+2,2	AURKC	97	2	0			c.C222T						PASS	.	C	,,	20,4386	28.1+/-56.4	1,18,2184	61.0	52.0	55.0		222,165,120	-4.8	1.0	19	dbSNP_134	55	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	AURKC	NM_001015878.1,NM_001015879.1,NM_003160.2	,,	1,18,6484	TT,TC,CC		0.0,0.4539,0.1538	,,	74/310,55/291,40/276	57743518	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	6795	exon3			GGTTCTCTTCAAG		CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"""serine/threonine kinase 13 (aurora/IPL1-like)"""	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.222C>T	19.37:g.57743518C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	66	19	0.287879	NM_001015878	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Silent	SNP	ENST00000302804.7	37	CCDS33128.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160	
ACACB	32	hgsc.bcm.edu	37	12	109693982	109693982	+	Silent	SNP	C	C	T	rs3742023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109693982C>T	ENST00000338432.7	+	45	6323	c.6204C>T	c.(6202-6204)caC>caT	p.H2068H	ACACB_ENST00000377848.3_Silent_p.H2068H|ACACB_ENST00000377854.5_Silent_p.H1998H|ACACB_ENST00000543201.1_Silent_p.H734H			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2068	Carboxyltransferase.				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)	TCTTTGACCACGGCAGTTTCA	0.607													C|||	1278	0.255192	0.1241	0.2709	5008	,	,		17499	0.2817		0.3777	False		,,,				2504	0.2679				p.H2068H		Atlas-SNP	.											.	ACACB	330	.	0			c.C6204T						PASS	.	C		675,3731	284.9+/-277.9	58,559,1586	72.0	66.0	68.0		6204	-3.5	0.9	12	dbSNP_107	68	3088,5512	473.1+/-368.5	550,1988,1762	no	coding-synonymous	ACACB	NM_001093.3		608,2547,3348	TT,TC,CC		35.907,15.32,28.9328		2068/2459	109693982	3763,9243	2203	4300	6503	SO:0001819	synonymous_variant	32	exon44			TGACCACGGCAGT	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.6204C>T	12.37:g.109693982C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	176	90	0.511364	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.719;T|0.281	0.281	strong		0.607	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
KIAA1755	85449	hgsc.bcm.edu	37	20	36841536	36841536	+	Missense_Mutation	SNP	G	G	A	rs142596886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36841536G>A	ENST00000279024.4	-	14	3782	c.3511C>T	c.(3511-3513)Cgc>Tgc	p.R1171C		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1171										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)				CCAGTGAGGCGAGGGACCTGG	0.637													G|||	6	0.00119808	0.0045	0.0	5008	,	,		17653	0.0		0.0	False		,,,				2504	0.0				p.R1171C		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C3511T						PASS	.	G	CYS/ARG	23,4383	30.8+/-60.4	0,23,2180	38.0	40.0	40.0		3511	2.9	0.1	20	dbSNP_134	40	0,8600		0,0,4300	yes	missense	KIAA1755	NM_001029864.1	180	0,23,6480	AA,AG,GG		0.0,0.522,0.1768	possibly-damaging	1171/1201	36841536	23,12983	2203	4300	6503	SO:0001583	missense	85449	exon14			TGAGGCGAGGGAC	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.3511C>T	20.37:g.36841536G>A	ENSP00000279024:p.Arg1171Cys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	10.17	1.275548	0.23307	0.00522	0.0	ENSG00000149633	ENST00000279024	T	0.05855	3.38	4.88	2.94	0.34122	.	1.496300	0.03995	N	0.295521	T	0.04227	0.0117	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	10	0.72032	D	0.01	.	6.9683	0.24635	0.2031:0.0:0.7969:0.0	.	1171	Q5JYT7	K1755_HUMAN	C	1171	ENSP00000279024:R1171C	ENSP00000279024:R1171C	R	-	1	0	KIAA1755	36274950	0.139000	0.22563	0.060000	0.19600	0.030000	0.12068	1.048000	0.30379	0.660000	0.30964	0.561000	0.74099	CGC	G|0.999;A|0.001	0.001	strong		0.637	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
HELZ2	85441	hgsc.bcm.edu	37	20	62200738	62200738	+	Missense_Mutation	SNP	G	G	A	rs6089924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62200738G>A	ENST00000467148.1	-	4	920	c.851C>T	c.(850-852)gCg>gTg	p.A284V	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	284					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)										GTGGCCGAGCGCCAGATTCCT	0.692													G|||	922	0.184105	0.4228	0.1369	5008	,	,		15348	0.0317		0.0676	False		,,,				2504	0.1718				p.A284V		Atlas-SNP	.											.	.	.	.	0			c.C851T						PASS	.	G	VAL/ALA	1573,2809		289,995,907	19.0	22.0	21.0		851	-7.4	0.0	20	dbSNP_114	21	636,7956		18,600,3678	yes	missense	PRIC285	NM_001037335.2	64	307,1595,4585	AA,AG,GG		7.4022,35.8969,17.0264	benign	284/2650	62200738	2209,10765	2191	4296	6487	SO:0001583	missense	85441	exon5			CCGAGCGCCAGAT	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.851C>T	20.37:g.62200738G>A	ENSP00000417401:p.Ala284Val	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	56	35	0.625	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	329	0.15064102564102563	207	0.42073170731707316	46	0.1270718232044199	26	0.045454545454545456	50	0.06596306068601583	G	0.636	-0.815403	0.02776	0.358969	0.074022	ENSG00000130589	ENST00000467148	T	0.21543	2.0	3.69	-7.38	0.01407	.	1.940130	0.02154	N	0.058273	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.37478	-0.9704	9	0.35671	T	0.21	-4.376	0.3965	0.00419	0.1827:0.2367:0.3342:0.2464	rs6089924	284	Q9BYK8	PR285_HUMAN	V	284	ENSP00000417401:A284V	ENSP00000417401:A284V	A	-	2	0	RP4-697K14.7	61671182	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.034000	0.03567	-1.757000	0.01316	-0.440000	0.05779	GCG	G|0.836;A|0.164	0.164	strong		0.692	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
ZNF22	7570	hgsc.bcm.edu	37	10	45499272	45499272	+	Silent	SNP	C	C	G	rs3740092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:45499272C>G	ENST00000298299.3	+	2	1049	c.456C>G	c.(454-456)tcC>tcG	p.S152S	C10orf25_ENST00000298298.1_5'Flank|CEP164P1_ENST00000456938.2_RNA	NM_006963.4	NP_008894.2	P17026	ZNF22_HUMAN	zinc finger protein 22	152					odontogenesis (GO:0042476)|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)|breast(2)|endometrium(1)|kidney(2)|lung(2)	8		Prostate(175;0.0352)|all_neural(218;0.202)				GCCAGAGCTCCCACCTTATTC	0.483													C|||	187	0.0373403	0.0151	0.0101	5008	,	,		17093	0.0893		0.0427	False		,,,				2504	0.0276				p.S152S		Atlas-SNP	.											ZNF22,colon,carcinoma,0,1	ZNF22	28	1	0			c.C456G						PASS	.	C		63,4343	60.5+/-97.4	0,63,2140	92.0	98.0	96.0		456	1.7	1.0	10	dbSNP_107	96	417,8183	131.3+/-189.1	6,405,3889	no	coding-synonymous	ZNF22	NM_006963.4		6,468,6029	GG,GC,CC		4.8488,1.4299,3.6906		152/225	45499272	480,12526	2203	4300	6503	SO:0001819	synonymous_variant	7570	exon2			GAGCTCCCACCTT	BC041139	CCDS7211.1	10q11	2013-01-08	2012-07-12		ENSG00000165512	ENSG00000165512		"""Zinc fingers, C2H2-type"""	13012	protein-coding gene	gene with protein product		194529					Standard	NM_006963		Approved	KOX15, HKR-T1, ZNF422, Zfp422	uc001jbw.3	P17026	OTTHUMG00000018064	ENST00000298299.3:c.456C>G	10.37:g.45499272C>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_006963	Q5T741|Q96FM4	Silent	SNP	ENST00000298299.3	37	CCDS7211.1																																																																																			C|0.960;G|0.040	0.040	strong		0.483	ZNF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047761.1	NM_006963	
CSMD3	114788	hgsc.bcm.edu	37	8	114186003	114186003	+	Missense_Mutation	SNP	T	T	C	rs2219898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:114186003T>C	ENST00000297405.5	-	4	901	c.657A>G	c.(655-657)atA>atG	p.I219M	CSMD3_ENST00000352409.3_Missense_Mutation_p.I219M|CSMD3_ENST00000455883.2_Missense_Mutation_p.I219M|CSMD3_ENST00000519485.1_5'UTR|CSMD3_ENST00000343508.3_Missense_Mutation_p.I179M	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	219	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.		I -> M (in dbSNP:rs2219898). {ECO:0000269|PubMed:12943675}.			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						CTGAATTGGCTATGCAGGTGA	0.428										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			T|||	2334	0.466054	0.4365	0.611	5008	,	,		17045	0.6766		0.2674	False		,,,				2504	0.3906				p.I219M		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A657G						PASS	.	T	MET/ILE,MET/ILE,MET/ILE	1761,2645	524.6+/-371.4	368,1025,810	134.0	125.0	128.0		657,657,537	1.1	1.0	8	dbSNP_96	128	2303,6297	387.9+/-342.4	309,1685,2306	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	10,10,10	677,2710,3116	CC,CT,TT		26.7791,39.9682,31.2471	possibly-damaging,possibly-damaging,possibly-damaging	219/3539,219/3708,179/3668	114186003	4064,8942	2203	4300	6503	SO:0001583	missense	114788	exon4			ATTGGCTATGCAG	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.657A>G	8.37:g.114186003T>C	ENSP00000297405:p.Ile219Met	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	160	61	0.38125	NM_052900	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	1012	0.4633699633699634	229	0.4654471544715447	195	0.5386740331491713	395	0.6905594405594405	193	0.2546174142480211	T	7.868	0.727602	0.15439	0.399682	0.267791	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	5.09	1.06	0.20224	Complement control module (2);Sushi/SCR/CCP (3);	0.186890	0.33631	N	0.004715	T	0.00012	0.0000	N	0.25245	0.725	0.44643	P	0.0023729999999999585	P;P;P;P	0.51653	0.828;0.571;0.947;0.708	B;B;P;P	0.52159	0.392;0.168;0.691;0.622	T	0.25745	-1.0123	9	0.37606	T	0.19	.	7.6324	0.28247	0.1313:0.0:0.2743:0.5944	rs2219898;rs52789540;rs58255477;rs2219898	219;219;219;179	Q7Z407-3;Q7Z407-4;Q7Z407;Q7Z407-2	.;.;CSMD3_HUMAN;.	M	179;219;219;219	ENSP00000345799:I179M;ENSP00000297405:I219M;ENSP00000412263:I219M;ENSP00000343124:I219M	ENSP00000297405:I219M	I	-	3	3	CSMD3	114255179	0.994000	0.37717	0.999000	0.59377	0.996000	0.88848	0.054000	0.14205	0.003000	0.14656	0.528000	0.53228	ATA	T|0.622;C|0.378	0.378	strong		0.428	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
MYCBP2	23077	hgsc.bcm.edu	37	13	77738664	77738664	+	Silent	SNP	A	A	G	rs2274547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:77738664A>G	ENST00000544440.2	-	43	6375	c.6358T>C	c.(6358-6360)Ttg>Ctg	p.L2120L	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Silent_p.L2120L|MYCBP2_ENST00000407578.2_Silent_p.L2158L					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TCTTTTTCCAATTGGATGACT	0.368													A|||	1153	0.230232	0.093	0.0965	5008	,	,		19334	0.3661		0.169	False		,,,				2504	0.4335				p.L2158L		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.T6472C						PASS	.	A		520,3886	235.5+/-248.0	28,464,1711	90.0	84.0	86.0		6472	0.5	1.0	13	dbSNP_100	86	1459,7141	277.8+/-293.0	105,1249,2946	no	coding-synonymous	MYCBP2	NM_015057.4		133,1713,4657	GG,GA,AA		16.9651,11.8021,15.2161		2158/4679	77738664	1979,11027	2203	4300	6503	SO:0001819	synonymous_variant	23077	exon43			TTTCCAATTGGAT	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.6358T>C	13.37:g.77738664A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_015057		Silent	SNP	ENST00000544440.2	37																																																																																				A|0.832;G|0.168	0.168	strong		0.368	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
FANCA	2175	hgsc.bcm.edu	37	16	89839752	89839752	+	Silent	SNP	C	C	T	rs17232917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89839752C>T	ENST00000389301.3	-	22	1971	c.1941G>A	c.(1939-1941)gaG>gaA	p.E647E	FANCA_ENST00000567284.2_5'UTR|FANCA_ENST00000568369.1_Silent_p.E647E	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	647					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)		CCAGGGGCTCCTCAGCAGAGT	0.562			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	191	0.038139	0.1407	0.0072	5008	,	,		17401	0.0		0.0	False		,,,				2504	0.0				p.E647E		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.G1941A						PASS	.	C		425,3647		19,387,1630	32.0	27.0	29.0		1941	-9.1	0.0	16	dbSNP_123	29	1,7893		0,1,3946	no	coding-synonymous	FANCA	NM_000135.2		19,388,5576	TT,TC,CC		0.0127,10.4371,3.5601		647/1456	89839752	426,11540	2036	3947	5983	SO:0001819	synonymous_variant	2175	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGGCTCCTCAGCA	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.1941G>A	16.37:g.89839752C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	52	0.553191	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			C|0.960;T|0.040	0.040	strong		0.562	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
ATXN1	6310	hgsc.bcm.edu	37	6	16327918	16327918	+	Missense_Mutation	SNP	C	C	A	rs28555263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.						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	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	65	7	0.107692	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	
EFCAB13	124989	hgsc.bcm.edu	37	17	45471443	45471443	+	Silent	SNP	G	G	A	rs7217678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45471443G>A	ENST00000331493.2	+	16	2190	c.1779G>A	c.(1777-1779)acG>acA	p.T593T	EFCAB13_ENST00000517484.1_Silent_p.T497T	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	593						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TGAGCAACACGGAATGCTTCT	0.299													g|||	87	0.0173722	0.0628	0.0029	5008	,	,		14107	0.0		0.002	False		,,,				2504	0.0				p.T593T		Atlas-SNP	.											C17orf57,NS,carcinoma,+1,1	.	.	1	0			c.G1779A						PASS	.	G	,	238,4168	138.0+/-173.8	7,224,1972	106.0	119.0	114.0		1491,1779	-2.9	0.2	17	dbSNP_116	114	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	C17orf57	NM_001195192.1,NM_152347.4	,	7,228,6268	AA,AG,GG		0.0465,5.4017,1.8607	,	497/785,593/974	45471443	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	124989	exon16			CAACACGGAATGC	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.1779G>A	17.37:g.45471443G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	159	68	0.427673	NM_152347	G3V128|Q49AG9	Silent	SNP	ENST00000331493.2	37	CCDS11512.1																																																																																			G|0.977;A|0.023	0.023	strong		0.299	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
ZC3H4	23211	hgsc.bcm.edu	37	19	47575291	47575291	+	Silent	SNP	A	A	G	rs144210335|rs79459609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47575291A>G	ENST00000253048.5	-	13	1927	c.1890T>C	c.(1888-1890)ccT>ccC	p.P630P	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	630	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		ggtgcatgtcaggatgcatTG	0.647													A|||	130	0.0259585	0.0908	0.0115	5008	,	,		17612	0.0		0.002	False		,,,				2504	0.0				p.P630P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.T1890C						PASS	.	A		211,3961		8,195,1883	29.0	34.0	32.0		1890	-9.0	0.7	19	dbSNP_131	32	18,8402		0,18,4192	no	coding-synonymous	ZC3H4	NM_015168.1		8,213,6075	GG,GA,AA		0.2138,5.0575,1.8186		630/1304	47575291	229,12363	2086	4210	6296	SO:0001819	synonymous_variant	23211	exon13			CATGTCAGGATGC	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1890T>C	19.37:g.47575291A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			A|0.983;G|0.017	0.017	strong		0.647	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
RAD21	5885	hgsc.bcm.edu	37	8	117864867	117864867	+	Missense_Mutation	SNP	A	A	C	rs75160167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:117864867A>C	ENST00000297338.2	-	10	1529	c.1242T>G	c.(1240-1242)gaT>gaG	p.D414E	RAD21_ENST00000518055.1_5'Flank|RAD21_ENST00000523986.1_5'Flank	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	414					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TGAGGAATTCATCCAAATTAT	0.403													A|||	36	0.0071885	0.0265	0.0014	5008	,	,		15827	0.0		0.0	False		,,,				2504	0.0				p.D414E		Atlas-SNP	.											.	RAD21	95	.	0			c.T1242G						PASS	.	A	GLU/ASP	88,4318	74.1+/-112.3	0,88,2115	115.0	112.0	113.0		1242	5.5	1.0	8	dbSNP_131	113	0,8600		0,0,4300	yes	missense	RAD21	NM_006265.2	45	0,88,6415	CC,CA,AA		0.0,1.9973,0.6766	benign	414/632	117864867	88,12918	2203	4300	6503	SO:0001583	missense	5885	exon10			GAATTCATCCAAA	BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"""sister chromatid cohesion 1"""	606462	"""RAD21 (S. pombe) homolog"""			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.1242T>G	8.37:g.117864867A>C	ENSP00000297338:p.Asp414Glu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	203	86	0.423645	NM_006265	A8K0E0|Q15001|Q99568	Missense_Mutation	SNP	ENST00000297338.2	37	CCDS6321.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	A	13.90	2.373790	0.42105	0.019973	0.0	ENSG00000164754	ENST00000297338	T	0.50277	0.75	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.18341	0.0440	L	0.32530	0.975	0.80722	D	1	B	0.28900	0.227	B	0.21360	0.034	T	0.12967	-1.0527	10	0.02654	T	1	-14.1824	15.669	0.77258	1.0:0.0:0.0:0.0	.	414	O60216	RAD21_HUMAN	E	414	ENSP00000297338:D414E	ENSP00000297338:D414E	D	-	3	2	RAD21	117934048	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.009000	0.57110	2.092000	0.63282	0.460000	0.39030	GAT	A|0.992;C|0.008	0.008	strong		0.403	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265	
CXXC1	30827	hgsc.bcm.edu	37	18	47809710	47809710	+	Silent	SNP	A	A	G	rs150530383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47809710A>G	ENST00000285106.6	-	13	2310	c.1596T>C	c.(1594-1596)gaT>gaC	p.D532D	MBD1_ENST00000436910.1_5'Flank|MBD1_ENST00000585672.1_5'Flank|CXXC1_ENST00000589940.1_Intron|MBD1_ENST00000585595.1_5'Flank|MBD1_ENST00000587605.1_5'Flank|MBD1_ENST00000590208.1_5'Flank|MBD1_ENST00000398493.1_5'Flank|MBD1_ENST00000347968.3_5'Flank|MBD1_ENST00000591416.1_5'Flank|CXXC1_ENST00000412036.2_Silent_p.D536D|MBD1_ENST00000269471.5_5'Flank|MBD1_ENST00000269468.5_5'Flank|MBD1_ENST00000349085.2_5'Flank|MBD1_ENST00000339998.6_5'Flank|MBD1_ENST00000353909.3_5'Flank|CXXC1_ENST00000587396.1_5'Flank|MBD1_ENST00000382948.5_5'Flank|MBD1_ENST00000457839.2_5'Flank|MBD1_ENST00000424334.2_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	532					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						GATTATACACATCACAGAAGA	0.572													A|||	11	0.00219649	0.0083	0.0	5008	,	,		18925	0.0		0.0	False		,,,				2504	0.0				p.D536D		Atlas-SNP	.											.	CXXC1	50	.	0			c.T1608C						PASS	.	A	,	12,4394	19.1+/-41.9	0,12,2191	133.0	139.0	137.0		1608,1596	1.9	1.0	18	dbSNP_134	137	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CXXC1	NM_001101654.1,NM_014593.3	,	0,12,6491	GG,GA,AA		0.0,0.2724,0.0923	,	536/661,532/657	47809710	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	30827	exon13			ATACACATCACAG	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.1596T>C	18.37:g.47809710A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Silent	SNP	ENST00000285106.6	37	CCDS11945.1																																																																																			A|0.999;G|0.001	0.001	strong		0.572	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593	
UBXN4	23190	hgsc.bcm.edu	37	2	136511817	136511817	+	Silent	SNP	A	A	G	rs1050115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:136511817A>G	ENST00000272638.9	+	4	614	c.303A>G	c.(301-303)gaA>gaG	p.E101E	UBXN4_ENST00000490163.1_3'UTR	NM_014607.3	NP_055422.1	Q92575	UBXN4_HUMAN	UBX domain protein 4	101					response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)		p.E101E(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	24						CTGCAGATGAACTTGTTACAA	0.393													A|||	1009	0.201478	0.174	0.2061	5008	,	,		20902	0.1935		0.2137	False		,,,				2504	0.2311				p.E101E		Atlas-SNP	.											UBXN4,NS,carcinoma,0,1	UBXN4	54	1	1	Substitution - coding silent(1)	prostate(1)	c.A303G						PASS	.	A		515,3291		22,471,1410	170.0	158.0	162.0		303	0.7	1.0	2	dbSNP_86	162	1398,6856		147,1104,2876	no	coding-synonymous	UBXN4	NM_014607.3		169,1575,4286	GG,GA,AA		16.9372,13.5313,15.8624		101/509	136511817	1913,10147	1903	4127	6030	SO:0001819	synonymous_variant	23190	exon4			AGATGAACTTGTT	D87684	CCDS42761.1	2q21.3-q22.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000144224	ENSG00000144224		"""UBX domain containing"""	14860	protein-coding gene	gene with protein product	"""erasin"""	611216	"""UBX domain-containing 2"", ""UBX domain containing 2"""	UBXDC1, UBXD2		16968747	Standard	NM_014607		Approved	KIAA0242	uc002tur.3	Q92575	OTTHUMG00000153577	ENST00000272638.9:c.303A>G	2.37:g.136511817A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	111	63	0.567568	NM_014607	A8K9W4|Q4ZG56|Q8IYM5	Silent	SNP	ENST00000272638.9	37	CCDS42761.1																																																																																			A|0.774;G|0.226	0.226	strong		0.393	UBXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331696.1	NM_014607	
ZNF263	10127	hgsc.bcm.edu	37	16	3339435	3339435	+	Missense_Mutation	SNP	G	G	C	rs220379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3339435G>C	ENST00000219069.5	+	6	1805	c.929G>C	c.(928-930)tGc>tCc	p.C310S	ZNF263_ENST00000574253.1_Missense_Mutation_p.A144P|ZNF263_ENST00000538765.1_5'UTR	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	310			C -> S (in dbSNP:rs220379).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|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)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						CCGTCTGTATGCTCTGAGAAC	0.522													C|||	1363	0.272165	0.5378	0.3545	5008	,	,		18726	0.0357		0.2634	False		,,,				2504	0.1074				p.C310S		Atlas-SNP	.											.	ZNF263	58	.	0			c.G929C						PASS	.	C	SER/CYS	2258,2136	573.1+/-383.5	601,1056,540	85.0	95.0	92.0		929	-0.9	0.0	16	dbSNP_79	92	2111,6489	709.8+/-405.7	253,1605,2442	yes	missense	ZNF263	NM_005741.4	112	854,2661,2982	CC,CG,GG		24.5465,48.6117,33.6232	benign	310/684	3339435	4369,8625	2197	4300	6497	SO:0001583	missense	10127	exon6			CTGTATGCTCTGA	AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.929G>C	16.37:g.3339435G>C	ENSP00000219069:p.Cys310Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_005741	B2R634|O43387|Q96H95	Missense_Mutation	SNP	ENST00000219069.5	37	CCDS10499.1	588	0.2692307692307692	244	0.4959349593495935	131	0.36187845303867405	21	0.03671328671328671	192	0.2532981530343008	C	2.814	-0.246389	0.05867	0.513883	0.245465	ENSG00000006194	ENST00000219069	T	0.04654	3.58	5.49	-0.916	0.10489	.	0.709753	0.12876	N	0.431863	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	0.38757	-0.9646	9	0.05525	T	0.97	.	2.0718	0.03615	0.1501:0.2518:0.3966:0.2015	rs220379;rs220379	310	O14978	ZN263_HUMAN	S	310	ENSP00000219069:C310S	ENSP00000219069:C310S	C	+	2	0	ZNF263	3279436	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.858000	0.04281	-0.156000	0.11079	-0.120000	0.15030	TGC	G|0.701;C|0.299	0.299	strong		0.522	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2		
ARHGAP20	57569	hgsc.bcm.edu	37	11	110451470	110451470	+	Missense_Mutation	SNP	T	T	C	rs151169911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:110451470T>C	ENST00000260283.4	-	16	2484	c.2200A>G	c.(2200-2202)Att>Gtt	p.I734V	ARHGAP20_ENST00000528829.1_Missense_Mutation_p.I698V|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.I708V|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.I698V|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.I711V|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.I277V|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.I708V	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	734					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)|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)		TGAGAAAGAATTGCATCACAG	0.448													T|||	3	0.000599042	0.0023	0.0	5008	,	,		21606	0.0		0.0	False		,,,				2504	0.0				p.I734V		Atlas-SNP	.											.	ARHGAP20	150	.	0			c.A2200G						PASS	.	T	VAL/ILE	10,4392	15.5+/-35.6	0,10,2191	66.0	69.0	68.0		2200	-1.6	0.0	11	dbSNP_134	68	0,8596		0,0,4298	yes	missense	ARHGAP20	NM_020809.2	29	0,10,6489	CC,CT,TT		0.0,0.2272,0.0769	benign	734/1192	110451470	10,12988	2201	4298	6499	SO:0001583	missense	57569	exon16			AAAGAATTGCATC	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.2200A>G	11.37:g.110451470T>C	ENSP00000260283:p.Ile734Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	4.295	0.054024	0.08291	0.002272	0.0	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.07908	3.15;3.15;3.18;3.15;3.15;3.15;3.15	5.93	-1.65	0.08291	.	0.430046	0.22922	N	0.054011	T	0.03220	0.0094	N	0.25647	0.755	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	0.44205	-0.9343	10	0.06365	T	0.9	.	13.7174	0.62705	0.0:0.7298:0.0:0.2702	.	708;734;711	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	V	734;708;277;711;698;708;698	ENSP00000260283:I734V;ENSP00000349660:I708V;ENSP00000437905:I277V;ENSP00000432076:I711V;ENSP00000436319:I698V;ENSP00000436522:I708V;ENSP00000431399:I698V	ENSP00000260283:I734V	I	-	1	0	ARHGAP20	109956680	0.028000	0.19301	0.033000	0.17914	0.860000	0.49131	0.237000	0.17985	-0.263000	0.09378	-0.408000	0.06270	ATT	T|0.999;C|0.001	0.001	strong		0.448	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809	
OTOF	9381	hgsc.bcm.edu	37	2	26699033	26699033	+	Silent	SNP	G	G	A	rs73920285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26699033G>A	ENST00000272371.2	-	23	2955	c.2829C>T	c.(2827-2829)ggC>ggT	p.G943G	OTOF_ENST00000339598.3_Silent_p.G196G|OTOF_ENST00000402415.3_Silent_p.G253G|OTOF_ENST00000338581.6_Silent_p.G196G|OTOF_ENST00000403946.3_Silent_p.G943G	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	943					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGCATGCAGGCCCAGGCCCT	0.667													G|||	218	0.0435304	0.1566	0.013	5008	,	,		13310	0.0		0.002	False		,,,				2504	0.0				p.G943G	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											OTOF_ENST00000402415,NS,carcinoma,0,3	OTOF	524	3	0			c.C2829T						PASS	.	G	,,,	542,3860	235.2+/-247.8	27,488,1686	34.0	35.0	35.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	588,2829,759,588	3.6	1.0	2	dbSNP_130	35	3,8593	2.2+/-6.3	0,3,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	27,491,5981	AA,AG,GG		0.0349,12.3126,4.193	,,,	196/1231,943/1998,253/1308,196/1231	26699033	545,12453	2201	4298	6499	SO:0001819	synonymous_variant	9381	exon23			ATGCAGGCCCAGG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2829C>T	2.37:g.26699033G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			G|0.953;A|0.047	0.047	strong		0.667	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
CASP5	838	hgsc.bcm.edu	37	11	104871193	104871193	+	Silent	SNP	A	A	G	rs45501691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:104871193A>G	ENST00000260315.3	-	6	746	c.747T>C	c.(745-747)gcT>gcC	p.A249A	CASP5_ENST00000444749.2_Silent_p.A191A|CASP5_ENST00000531367.1_Silent_p.A107A|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000418434.1_Silent_p.A107A|CASP5_ENST00000526056.1_Silent_p.A262A|CASP5_ENST00000393141.2_Silent_p.A262A			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	249					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		CTGGTCTGGCAGCAAATGCCC	0.448													A|||	212	0.0423323	0.1543	0.0115	5008	,	,		17767	0.0		0.0	False		,,,				2504	0.0				p.A262A		Atlas-SNP	.											.	CASP5	213	.	0			c.T786C						PASS	.	A	,,,	601,3803		51,499,1652	98.0	89.0	92.0		573,321,786,747	1.9	0.2	11	dbSNP_127	92	5,8593		0,5,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASP5	NM_001136109.1,NM_001136110.1,NM_001136112.1,NM_004347.3	,,,	51,504,5946	GG,GA,AA		0.0582,13.6467,4.6608	,,,	191/377,107/293,262/448,249/435	104871193	606,12396	2202	4299	6501	SO:0001819	synonymous_variant	838	exon6			TCTGGCAGCAAAT		CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"""Caspases"""	1506	protein-coding gene	gene with protein product		602665	"""caspase 5, apoptosis-related cysteine protease"""			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.747T>C	11.37:g.104871193A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	118	68	0.576271	NM_001136112	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Silent	SNP	ENST00000260315.3	37	CCDS8328.2																																																																																			A|0.954;G|0.046	0.046	strong		0.448	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347	
NLRC5	84166	hgsc.bcm.edu	37	16	57060136	57060136	+	Missense_Mutation	SNP	G	G	T	rs149735722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57060136G>T	ENST00000262510.6	+	6	1506	c.1281G>T	c.(1279-1281)caG>caT	p.Q427H	NLRC5_ENST00000308149.7_Missense_Mutation_p.Q427H|NLRC5_ENST00000539144.1_Missense_Mutation_p.Q427H|NLRC5_ENST00000436936.1_Missense_Mutation_p.Q427H	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	427	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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)				CCCCAGGCCAGTCTGTGGCCC	0.632													G|||	13	0.00259585	0.0098	0.0	5008	,	,		19350	0.0		0.0	False		,,,				2504	0.0				p.Q427H		Atlas-SNP	.											NLRC5,NS,carcinoma,+1,1	NLRC5	186	1	0			c.G1281T						scavenged	.	G	HIS/GLN	16,4380	22.3+/-47.3	0,16,2182	67.0	67.0	67.0		1281	1.6	0.8	16	dbSNP_134	67	0,8600		0,0,4300	yes	missense	NLRC5	NM_032206.3	24	0,16,6482	TT,TG,GG		0.0,0.364,0.1231	probably-damaging	427/1867	57060136	16,12980	2198	4300	6498	SO:0001583	missense	84166	exon5			AGGCCAGTCTGTG	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.1281G>T	16.37:g.57060136G>T	ENSP00000262510:p.Gln427His	Somatic	44	1	0.0227273		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	3|3	0.0013736263736263737|0.0013736263736263737	3|3	0.006097560975609756|0.006097560975609756	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	8.532|8.532	0.871284|0.871284	0.17322|0.17322	0.00364|0.00364	0.0|0.0	ENSG00000140853|ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144|ENST00000538805	T;T;T;T|.	0.75477|.	-0.75;-0.77;-0.94;-0.77|.	5.21|5.21	1.62|1.62	0.23740|0.23740	.|.	0.000000|.	0.32819|.	N|.	0.005615|.	T|T	0.42832|0.42832	0.1220|0.1220	L|L	0.60455|0.60455	1.87|1.87	0.09310|0.09310	N|N	1|1	P;B;B;B|.	0.42518|.	0.782;0.204;0.191;0.157|.	B;B;B;B|.	0.39339|.	0.297;0.056;0.112;0.122|.	T|T	0.37686|0.37686	-0.9695|-0.9695	10|5	0.44086|.	T|.	0.13|.	.|.	11.318|11.318	0.49403|0.49403	0.2425:0.0:0.7575:0.0|0.2425:0.0:0.7575:0.0	.|.	427;427;427;427|.	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3|.	.;.;.;NLRC5_HUMAN|.	H|F	427|180	ENSP00000262510:Q427H;ENSP00000308886:Q427H;ENSP00000389739:Q427H;ENSP00000441727:Q427H|.	ENSP00000262510:Q427H|.	Q|V	+|+	3|1	2|0	NLRC5|NLRC5	55617637|55617637	0.142000|0.142000	0.22610|0.22610	0.826000|0.826000	0.32828|0.32828	0.189000|0.189000	0.23516|0.23516	0.756000|0.756000	0.26419|0.26419	0.568000|0.568000	0.29311|0.29311	0.561000|0.561000	0.74099|0.74099	CAG|GTC	G|0.998;T|0.002	0.002	strong		0.632	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
MAT1A	4143	hgsc.bcm.edu	37	10	82034842	82034842	+	Silent	SNP	A	A	G	rs10887711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:82034842A>G	ENST00000372213.3	-	7	1142	c.882T>C	c.(880-882)gcT>gcC	p.A294A	MAT1A_ENST00000485270.1_5'UTR	NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	294					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	CAGCATATGCAGCTGAGCGGT	0.607													G|||	4209	0.840455	0.9266	0.7781	5008	,	,		16178	0.9712		0.6412	False		,,,				2504	0.8384				p.A294A		Atlas-SNP	.											MAT1A,NS,carcinoma,0,1	MAT1A	52	1	0			c.T882C						PASS	.	G		3831,573		1675,481,46	33.0	34.0	34.0		882	-10.0	0.0	10	dbSNP_120	34	5359,3235		1696,1967,634	no	coding-synonymous	MAT1A	NM_000429.2		3371,2448,680	GG,GA,AA		37.6425,13.0109,29.2968		294/396	82034842	9190,3808	2202	4297	6499	SO:0001819	synonymous_variant	4143	exon7			ATATGCAGCTGAG		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"""S-adenosylmethionine synthetase"""	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.882T>C	10.37:g.82034842A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_000429	D3DWD5|Q5QP09	Silent	SNP	ENST00000372213.3	37	CCDS7365.1																																																																																			A|0.229;G|0.771	0.771	strong		0.607	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429	
ZNF559	84527	hgsc.bcm.edu	37	19	9453160	9453160	+	Nonsense_Mutation	SNP	C	C	T	rs150358404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9453160C>T	ENST00000393883.2	+	6	1681	c.1033C>T	c.(1033-1035)Cga>Tga	p.R345*	ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000538743.1_Nonsense_Mutation_p.R265*|ZNF559_ENST00000603380.1_Nonsense_Mutation_p.R345*|ZNF177_ENST00000605471.1_Intron|ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000587557.1_Nonsense_Mutation_p.R409*|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF559_ENST00000586255.1_Intron|ZNF559_ENST00000317221.7_3'UTR|ZNF177_ENST00000446085.4_Intron|ZNF177_ENST00000602856.1_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	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)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						AAAACACAGGCGAACTCACAC	0.408													C|||	5	0.000998403	0.0038	0.0	5008	,	,		20978	0.0		0.0	False		,,,				2504	0.0				p.R409X		Atlas-SNP	.											ZNF559,NS,carcinoma,-1,4	ZNF559	77	4	0			c.C1225T						PASS	.	C	,stop/ARG,stop/ARG,,,,,,,stop/ARG	9,4397	15.5+/-35.6	0,9,2194	62.0	58.0	60.0		,1225,907,,,,,,,1033	-3.7	0.0	19	dbSNP_134	60	2,8598	2.2+/-6.3	0,2,4298	yes	intron,stop-gained,stop-gained,utr-3,utr-3,utr-3,utr-3,utr-3,intron,stop-gained	ZNF559,ZNF559-ZNF177	NM_001172650.2,NM_001202406.1,NM_001202407.1,NM_001202408.1,NM_001202409.1,NM_001202410.1,NM_001202411.1,NM_001202412.1,NM_001202425.1,NM_032497.2	,,,,,,,,,	0,11,6492	TT,TC,CC		0.0233,0.2043,0.0846	,,,,,,,,,	,409/603,303/497,,,,,,,345/539	9453160	11,12995	2203	4300	6503	SO:0001587	stop_gained	84527	exon6			CACAGGCGAACTC	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"""Zinc fingers, C2H2-type"", ""-"""	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.1033C>T	19.37:g.9453160C>T	ENSP00000377461:p.Arg345*	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_001202406	K7EMG6	Nonsense_Mutation	SNP	ENST00000393883.2	37	CCDS12211.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	24.8	4.571286	0.86542	0.002043	2.33E-4	ENSG00000188321	ENST00000317221;ENST00000538743;ENST00000393883	.	.	.	1.87	-3.74	0.04385	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.8332	0.18593	0.3663:0.5052:0.1284:0.0	.	.	.	.	X	345;265;345	.	ENSP00000325393:R345X	R	+	1	2	ZNF559	9314160	0.000000	0.05858	0.000000	0.03702	0.493000	0.33554	-2.312000	0.01127	-1.360000	0.02172	0.313000	0.20887	CGA	C|0.999;T|0.001	0.001	strong		0.408	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497	
ZNF330	27309	hgsc.bcm.edu	37	4	142155072	142155072	+	Missense_Mutation	SNP	T	T	A	rs34631212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:142155072T>A	ENST00000262990.4	+	10	1120	c.892T>A	c.(892-894)Ttg>Atg	p.L298M	ZNF330_ENST00000421169.2_Missense_Mutation_p.L238M	NM_014487.4	NP_055302.1	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330	298			L -> M (in dbSNP:rs34631212).			chromosome, centromeric region (GO:0000775)|midbody (GO:0030496)|nucleolus (GO:0005730)	metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	14	all_hematologic(180;0.162)					GTCATCAGATTTGTTTACTAA	0.453													T|||	199	0.0397364	0.1437	0.0115	5008	,	,		20408	0.0		0.001	False		,,,				2504	0.0				p.L298M		Atlas-SNP	.											.	ZNF330	31	.	0			c.T892A						PASS	.	T	MET/LEU	459,3947	218.4+/-236.5	16,427,1760	127.0	133.0	131.0		892	2.1	1.0	4	dbSNP_126	131	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ZNF330	NM_014487.4	15	16,430,6057	AA,AT,TT		0.0349,10.4176,3.5522	benign	298/321	142155072	462,12544	2203	4300	6503	SO:0001583	missense	27309	exon10			TCAGATTTGTTTA	AJ006591	CCDS3754.1	4q31.21	2008-05-15			ENSG00000109445	ENSG00000109445		"""Zinc fingers, C2H2-type"""	15462	protein-coding gene	gene with protein product		609550				11528117, 10593942	Standard	NM_001292002		Approved	NOA36, HSA6591	uc003iiq.4	Q9Y3S2	OTTHUMG00000133413	ENST00000262990.4:c.892T>A	4.37:g.142155072T>A	ENSP00000262990:p.Leu298Met	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	164	74	0.451219	NM_014487	B2RDA3	Missense_Mutation	SNP	ENST00000262990.4	37	CCDS3754.1	73	0.033424908424908424	68	0.13821138211382114	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	T	13.71	2.318489	0.40996	0.104176	3.49E-4	ENSG00000109445	ENST00000262990;ENST00000421169	T;T	0.31510	1.49;1.49	6.17	2.08	0.27032	.	0.358122	0.29212	N	0.012804	T	0.00144	0.0004	N	0.14661	0.345	0.28660	N	0.906172	B;B	0.29716	0.255;0.225	B;B	0.39771	0.146;0.309	T	0.15378	-1.0439	10	0.36615	T	0.2	-31.7734	6.1183	0.20139	0.0:0.456:0.2274:0.3166	rs34631212;rs57194793	238;298	E9PDK6;Q9Y3S2	.;ZN330_HUMAN	M	298;238	ENSP00000262990:L298M;ENSP00000397397:L238M	ENSP00000262990:L298M	L	+	1	2	ZNF330	142374522	0.504000	0.26123	1.000000	0.80357	0.990000	0.78478	0.442000	0.21628	0.416000	0.25844	0.533000	0.62120	TTG	T|0.968;A|0.032	0.032	strong		0.453	ZNF330-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257271.2	NM_014487	
AHNAK2	113146	hgsc.bcm.edu	37	14	105409959	105409959	+	Silent	SNP	G	G	T	rs10152073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105409959G>T	ENST00000333244.5	-	7	11948	c.11829C>A	c.(11827-11829)gcC>gcA	p.A3943A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3943						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)			CATCCAGCTTGGCTCCTGGGG	0.607													.|||	2776	0.554313	0.6369	0.5144	5008	,	,		19904	0.4117		0.5358	False		,,,				2504	0.637				p.A3943A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C11829A						PASS	.	G		2672,1306		899,874,216	166.0	178.0	174.0		11829	-0.5	0.1	14	dbSNP_119	174	4511,3785		1241,2029,878	no	coding-synonymous	AHNAK2	NM_138420.2		2140,2903,1094	TT,TG,GG		45.6244,32.8306,41.4779		3943/5796	105409959	7183,5091	1989	4148	6137	SO:0001819	synonymous_variant	113146	exon7			CAGCTTGGCTCCT	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.11829C>A	14.37:g.105409959G>T		Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	318	317	0.996855	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.467;T|0.533	0.533	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ABCB7	22	hgsc.bcm.edu	37	X	74284996	74284996	+	Silent	SNP	T	T	C	rs1340990|rs386825773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:74284996T>C	ENST00000373394.3	-	13	1747	c.1740A>G	c.(1738-1740)gcA>gcG	p.A580A	ABCB7_ENST00000339447.4_Silent_p.A540A|ABCB7_ENST00000253577.3_Silent_p.A581A|ABCB7_ENST00000534570.1_5'Flank			O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 7	580	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.		A -> V (in dbSNP:rs1340989).		cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)			breast(1)|endometrium(5)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)	20						ATTTTGCCACTGCATACACTT	0.418													N|||	445	0.117881	0.3192	0.0331	3775	,	,		13377	0.0		0.0	False		,,,				2504	0.0				p.A581A		Atlas-SNP	.											.	ABCB7	69	.	0			c.A1743G						PASS	.			1422,2413		238,743,203,651,368	123.0	93.0	103.0		1743	-3.6	0.6	X	dbSNP_88	103	8,6720		0,7,1,2421,1871	no	coding-synonymous	ABCB7	NM_004299.3		238,750,204,3072,2239	CC,CT,C,TT,T		0.1189,37.0795,13.5378		581/754	74284996	1430,9133	2203	4300	6503	SO:0001819	synonymous_variant	22	exon13			TGCCACTGCATAC	AF038950	CCDS14428.1, CCDS65290.1, CCDS65291.1, CCDS75994.1	Xq13.3	2012-03-14			ENSG00000131269	ENSG00000131269		"""ATP binding cassette transporters / subfamily B"""	48	protein-coding gene	gene with protein product		300135		ABC7		9143506	Standard	NM_004299		Approved	EST140535, Atm1p, ASAT	uc004ebz.4	O75027	OTTHUMG00000021862	ENST00000373394.3:c.1740A>G	X.37:g.74284996T>C		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	250	121	0.484	NM_004299	G3XAC4|O75345|Q5VWY7|Q5VWY8|Q9BRE1|Q9UND1|Q9UP01	Silent	SNP	ENST00000373394.3	37																																																																																				T|0.867;0|0.003	.	strong		0.418	ABCB7-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000057274.1	NM_004299	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21358933	21358933	+	Missense_Mutation	SNP	G	G	C	rs59502379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21358933G>C	ENST00000256958.2	+	11	1559	c.1463G>C	c.(1462-1464)gGt>gCt	p.G488A		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	488	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.		G -> A (in dbSNP:rs59502379). {ECO:0000269|PubMed:11477075}.		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	TGTCTAGCAGGTTGCAAATCT	0.363													G|||	56	0.0111821	0.0408	0.0029	5008	,	,		17184	0.0		0.0	False		,,,				2504	0.0				p.G488A		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.G1463C	GRCh37	CM016147	SLCO1B1	M	rs59502379	PASS	.	G	ALA/GLY	155,4251	104.3+/-142.8	3,149,2051	127.0	125.0	126.0		1463	4.1	1.0	12	dbSNP_129	126	1,8597	1.2+/-3.3	0,1,4298	yes	missense	SLCO1B1	NM_006446.4	60	3,150,6349	CC,CG,GG		0.0116,3.5179,1.1996	probably-damaging	488/692	21358933	156,12848	2203	4299	6502	SO:0001583	missense	10599	exon11			TAGCAGGTTGCAA		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1463G>C	12.37:g.21358933G>C	ENSP00000256958:p.Gly488Ala	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	150	55	0.366667	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	G	14.57	2.574305	0.45902	0.035179	1.16E-4	ENSG00000134538	ENST00000256958	T	0.04862	3.54	4.06	4.06	0.47325	Proteinase inhibitor I1, Kazal (1);Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Protease inhibitor, Kazal-type (1);	0.000000	0.85682	D	0.000000	T	0.11067	0.0270	H	0.96805	3.885	0.48632	D	0.999686	D	0.89917	1.0	D	0.97110	1.0	T	0.44421	-0.9329	10	0.87932	D	0	.	13.1306	0.59380	0.0:0.0:1.0:0.0	rs59502379	488	Q9Y6L6	SO1B1_HUMAN	A	488	ENSP00000256958:G488A	ENSP00000256958:G488A	G	+	2	0	SLCO1B1	21250200	1.000000	0.71417	1.000000	0.80357	0.335000	0.28730	7.474000	0.81024	1.783000	0.52377	0.484000	0.47621	GGT	G|0.988;C|0.012	0.012	strong		0.363	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
PLCB1	23236	hgsc.bcm.edu	37	20	8770822	8770822	+	Splice_Site	SNP	C	C	T	rs2294597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:8770822C>T	ENST00000338037.6	+	31	3364	c.3337C>T	c.(3337-3339)Cta>Tta	p.L1113L	PLCB1_ENST00000378641.3_Splice_Site_p.L1113L|PLCB1_ENST00000378637.2_Splice_Site_p.L1113L	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	1113					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						TTTCTTATAGCTAGAAGAAGC	0.368													C|||	1145	0.228634	0.1263	0.2219	5008	,	,		19106	0.1329		0.3022	False		,,,				2504	0.3947				p.G1113X		Atlas-SNP	.											.	PLCB1	394	.	0			c.G3337T						PASS	.	C	,	622,3784	259.2+/-262.9	54,514,1635	47.0	47.0	47.0		3337,3337	3.3	1.0	20	dbSNP_100	47	2673,5927	408.4+/-349.5	451,1771,2078	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	PLCB1	NM_015192.2,NM_182734.1	,	505,2285,3713	TT,TC,CC		31.0814,14.1171,25.3345	,	1113/1217,1113/1174	8770822	3295,9711	2203	4300	6503	SO:0001630	splice_region_variant	23236	exon31			TTATAGCTAGAAG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.3337-1C>T	20.37:g.8770822C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_182734	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Nonsense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																			C|0.774;T|0.226	0.226	strong		0.368	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		Silent
ZNF880	400713	hgsc.bcm.edu	37	19	52887282	52887282	+	Missense_Mutation	SNP	A	A	G	rs324125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	146	0	0		WXS	Illumina HiSeq	Phase_I	163	88	0.539877	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	
TMEM176B	28959	hgsc.bcm.edu	37	7	150490376	150490376	+	Missense_Mutation	SNP	C	C	T	rs2072443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150490376C>T	ENST00000447204.2	-	5	772	c.400G>A	c.(400-402)Gca>Aca	p.A134T	TMEM176B_ENST00000429904.2_Missense_Mutation_p.A134T|TMEM176B_ENST00000434545.1_Missense_Mutation_p.A134T|TMEM176B_ENST00000450753.2_Missense_Mutation_p.A97T|TMEM176B_ENST00000492607.1_Missense_Mutation_p.A134T|TMEM176B_ENST00000326442.5_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	69	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	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	
PAG1	55824	hgsc.bcm.edu	37	8	81905397	81905397	+	Silent	SNP	A	A	G	rs2016465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:81905397A>G	ENST00000220597.4	-	4	776	c.66T>C	c.(64-66)gcT>gcC	p.A22A		NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	22					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			TGGCGACAGCAGCCAGACTTC	0.567													G|||	2624	0.523962	0.8487	0.3156	5008	,	,		18022	0.5268		0.326	False		,,,				2504	0.4335				p.A22A		Atlas-SNP	.											.	PAG1	39	.	0			c.T66C						PASS	.	G		3250,1156	410.4+/-335.4	1214,822,167	81.0	75.0	77.0		66	-10.7	0.0	8	dbSNP_92	77	2778,5822	678.6+/-403.5	439,1900,1961	no	coding-synonymous	PAG1	NM_018440.3		1653,2722,2128	GG,GA,AA		32.3023,26.2369,46.3478		22/433	81905397	6028,6978	2203	4300	6503	SO:0001819	synonymous_variant	55824	exon4			GACAGCAGCCAGA	AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"""Csk-binding protein"", ""transmembrane adaptor protein PAG"""	605767	"""phosphoprotein associated with glycosphingolipid microdomains 1"""			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.66T>C	8.37:g.81905397A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_018440	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Silent	SNP	ENST00000220597.4	37	CCDS6227.1																																																																																			A|0.513;G|0.487	0.487	strong		0.567	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440	
F5	2153	hgsc.bcm.edu	37	1	169519112	169519112	+	Missense_Mutation	SNP	C	C	T	rs6020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169519112C>T	ENST00000367797.3	-	10	1739	c.1538G>A	c.(1537-1539)aGa>aAa	p.R513K	F5_ENST00000367796.3_Missense_Mutation_p.R513K|F5_ENST00000546081.1_3'UTR	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	513	F5/8 type A 2.|Plastocyanin-like 3.		R -> K (in dbSNP:rs6020). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9454741, 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)	GGCGATGTCTCTCATGATGTC	0.423													C|||	1320	0.263578	0.3238	0.1052	5008	,	,		15771	0.627		0.0239	False		,,,				2504	0.1667				p.R513K		Atlas-SNP	.											.	F5	301	.	0			c.G1538A	GRCh37	CM980660	F5	M	rs6020	PASS	.	C	LYS/ARG	1183,3223	414.6+/-336.9	189,805,1209	200.0	180.0	187.0		1538	5.7	1.0	1	dbSNP_52	187	93,8507	52.3+/-112.8	2,89,4209	yes	missense	F5	NM_000130.4	26	191,894,5418	TT,TC,CC		1.0814,26.8498,9.8109	benign	513/2225	169519112	1276,11730	2203	4300	6503	SO:0001583	missense	2153	exon10			ATGTCTCTCATGA	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.1538G>A	1.37:g.169519112C>T	ENSP00000356771:p.Arg513Lys	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	192	88	0.458333	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	577	0.2641941391941392	142	0.2886178861788618	31	0.0856353591160221	384	0.6713286713286714	20	0.026385224274406333	C	20.2	3.942248	0.73672	0.268498	0.010814	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.98914	-5.23;-5.23	5.71	5.71	0.89125	Cupredoxin (2);	0.053031	0.85682	D	0.000000	D	0.94915	0.8356	L	0.31845	0.965	0.38750	P	0.04590799999999995	P	0.48503	0.911	B	0.42282	0.382	D	0.94162	0.7415	9	0.27082	T	0.32	-13.5561	13.0952	0.59188	0.0:0.9267:0.0:0.0733	rs6020;rs56575896;rs6020	513	P12259	FA5_HUMAN	K	513	ENSP00000356771:R513K;ENSP00000356770:R513K	ENSP00000356770:R513K	R	-	2	0	F5	167785736	0.958000	0.32768	0.976000	0.42696	0.943000	0.58893	3.068000	0.50018	2.697000	0.92050	0.655000	0.94253	AGA	C|0.805;T|0.195	0.195	strong		0.423	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
KITLG	4254	hgsc.bcm.edu	37	12	88912624	88912624	+	Silent	SNP	G	G	A	rs17015782	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:88912624G>A	ENST00000228280.5	-	4	395	c.213C>T	c.(211-213)agC>agT	p.S71S	KITLG_ENST00000347404.5_Silent_p.S71S|KITLG_ENST00000378535.4_5'UTR|KITLG_ENST00000357116.4_Intron	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand	71					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|negative regulation of mast cell apoptotic process (GO:0033026)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of myeloid leukocyte differentiation (GO:0002763)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	stem cell factor receptor binding (GO:0005173)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)	9						CTACCATCTCGCTTATCCAAC	0.353									Testicular Cancer, Familial Clustering of				G|||	52	0.0103834	0.0378	0.0029	5008	,	,		20000	0.0		0.0	False		,,,				2504	0.0				p.S71S		Atlas-SNP	.											.	KITLG	26	.	0			c.C213T						PASS	.	G	,	154,4252	106.0+/-144.5	2,150,2051	76.0	74.0	75.0		213,213	-10.1	0.0	12	dbSNP_123	75	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KITLG	NM_000899.4,NM_003994.5	,	2,150,6351	AA,AG,GG		0.0,3.4952,1.1841	,	71/274,71/246	88912624	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	4254	exon4	Familial Cancer Database		CATCTCGCTTATC	M59964	CCDS31867.1, CCDS31868.1	12q22	2010-11-23			ENSG00000049130	ENSG00000049130			6343	protein-coding gene	gene with protein product	"""mast cell growth factor"", ""stem cell factor"", ""steel factor"", ""familial progressive hyperpigmentation 2"""	184745		MGF		2208279, 1707188, 19375057	Standard	NM_003994		Approved	SCF, SF, Kitl, KL-1, FPH2	uc001tav.3	P21583	OTTHUMG00000169888	ENST00000228280.5:c.213C>T	12.37:g.88912624G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_003994	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Silent	SNP	ENST00000228280.5	37	CCDS31868.1																																																																																			G|0.988;A|0.012	0.012	strong		0.353	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406424.2	NM_003994	
MUC4	4585	hgsc.bcm.edu	37	3	195515093	195515093	+	Missense_Mutation	SNP	G	G	T	rs11916899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515093G>T	ENST00000463781.3	-	2	3817	c.3358C>A	c.(3358-3360)Cct>Act	p.P1120T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1120T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	559					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)		ACAGGAAGAGGGGTGGTGTGA	0.572													.|||	93	0.0185703	0.0333	0.0115	5008	,	,		18503	0.002		0.0159	False		,,,				2504	0.0235				p.P1120T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C3358A						PASS	.						14.0	8.0	10.0					3																	195515093		671	1548	2219	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGT	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.3358C>A	3.37:g.195515093G>T	ENSP00000417498:p.Pro1120Thr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	367	129	0.351499	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	.	.	.	.	.	.	.	.	.	.	-	3.123	-0.180056	0.06380	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33654	1.4;1.4	0.814	-1.63	0.08345	.	.	.	.	.	T	0.18635	0.0447	N	0.19112	0.55	0.09310	N	1	B	0.23735	0.09	B	0.28465	0.09	T	0.25328	-1.0135	8	.	.	.	.	2.4115	0.04426	0.2913:0.0:0.3067:0.4019	rs11916899	1120	E7ESK3	.	T	1120	ENSP00000417498:P1120T;ENSP00000420243:P1120T	.	P	-	1	0	MUC4	196999488	0.000000	0.05858	0.000000	0.03702	0.134000	0.20937	-1.465000	0.02357	-1.645000	0.01515	0.064000	0.15345	CCT	A|0.002;G|0.995;T|0.004	0.004	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HGF	3082	hgsc.bcm.edu	37	7	81388042	81388042	+	Silent	SNP	T	T	C	rs5745635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:81388042T>C	ENST00000222390.5	-	3	559	c.333A>G	c.(331-333)gaA>gaG	p.E111E	HGF_ENST00000453018.1_Silent_p.E8E|HGF_ENST00000453411.1_Silent_p.E111E|HGF_ENST00000423064.2_Silent_p.E111E|HGF_ENST00000457544.2_Silent_p.E111E|HGF_ENST00000354224.6_Silent_p.E111E|HGF_ENST00000444829.2_Silent_p.E111E	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	111	PAN. {ECO:0000255|PROSITE- ProRule:PRU00315}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|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 via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						CATGGCCAAATTCTTTTTTCA	0.313													C|||	518	0.103435	0.3139	0.0317	5008	,	,		14939	0.0079		0.006	False		,,,				2504	0.0685				p.E111E		Atlas-SNP	.											HGF,spleen,lymphoid_neoplasm,-2,1	HGF	171	1	0			c.A333G						PASS	.	C	,,,,	1261,3145	702.0+/-406.8	174,913,1116	108.0	107.0	107.0		333,333,333,333,333	-3.0	0.1	7	dbSNP_114	107	92,8504	814.1+/-407.0	1,90,4207	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HGF	NM_000601.4,NM_001010931.1,NM_001010932.1,NM_001010933.1,NM_001010934.1	,,,,	175,1003,5323	CC,CT,TT		1.0703,28.6201,10.4061	,,,,	111/729,111/291,111/724,111/286,111/211	81388042	1353,11649	2203	4298	6501	SO:0001819	synonymous_variant	3082	exon3			GCCAAATTCTTTT		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"""hepatopoietin A"", ""fibroblast-derived tumor cytotoxic factor"", ""scatter factor"", ""lung fibroblast-derived mitogen"""	142409	"""deafness, autosomal recessive 39"""	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.333A>G	7.37:g.81388042T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Silent	SNP	ENST00000222390.5	37	CCDS5597.1																																																																																			T|0.896;C|0.104	0.104	strong		0.313	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601	
RAPSN	5913	hgsc.bcm.edu	37	11	47463220	47463220	+	Silent	SNP	C	C	T	rs45603036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:47463220C>T	ENST00000298854.2	-	5	1068	c.855G>A	c.(853-855)caG>caA	p.Q285Q	RAPSN_ENST00000524487.1_Silent_p.Q232Q|RAPSN_ENST00000352508.3_Intron|RNU6-1302P_ENST00000516518.1_RNA|RAPSN_ENST00000528356.1_5'UTR|RAPSN_ENST00000529341.1_Intron	NM_005055.4	NP_005046.2	Q13702	RAPSN_HUMAN	receptor-associated protein of the synapse	285					positive regulation of neuron apoptotic process (GO:0043525)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)	acetylcholine receptor binding (GO:0033130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(6)|ovary(2)	12						GCGCCTGCACCTGCCCCAGGC	0.647													C|||	358	0.0714856	0.0446	0.0951	5008	,	,		13668	0.0466		0.1501	False		,,,				2504	0.0358				p.Q285Q		Atlas-SNP	.											.	RAPSN	27	.	0			c.G855A						PASS	.	C	,	294,4108	152.2+/-185.9	7,280,1914	32.0	32.0	32.0		855,	2.8	1.0	11	dbSNP_127	32	1229,7367	238.2+/-269.8	97,1035,3166	no	coding-synonymous,intron	RAPSN	NM_005055.4,NM_032645.4	,	104,1315,5080	TT,TC,CC		14.2973,6.6788,11.7172	,	285/413,	47463220	1523,11475	2201	4298	6499	SO:0001819	synonymous_variant	5913	exon5			CTGCACCTGCCCC		CCDS7936.1, CCDS7937.1	11p11.2	2009-04-28	2007-02-23		ENSG00000165917	ENSG00000165917		"""RING-type (C3HC4) zinc fingers"""	9863	protein-coding gene	gene with protein product	"""rapsyn"""	601592	"""receptor-associated protein of the synapse, 43kD"""			8812503	Standard	NM_005055		Approved	RNF205, CMS1D, CMS1E	uc001nfi.2	Q13702	OTTHUMG00000166891	ENST00000298854.2:c.855G>A	11.37:g.47463220C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	242	118	0.487603	NM_005055	Q8TDF3|Q9BTD9	Silent	SNP	ENST00000298854.2	37	CCDS7936.1																																																																																			C|0.891;T|0.109	0.109	strong		0.647	RAPSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391726.1		
GJA4	2701	hgsc.bcm.edu	37	1	35259946	35259946	+	Silent	SNP	G	G	A	rs1764389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	189	0	0		WXS	Illumina HiSeq	Phase_I	162	162	1	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	
MUC4	4585	hgsc.bcm.edu	37	3	195511310	195511310	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511310G>C	ENST00000463781.3	-	2	7600	c.7141C>G	c.(7141-7143)Cac>Gac	p.H2381D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H2381D	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.H2381D(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)		GGGGTGGTGTGACCTGAGGAT	0.592																																					p.H2381D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	kidney(2)|endometrium(1)	c.C7141G						PASS	.																																			SO:0001583	missense	4585	exon2			TGGTGTGACCTGA	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.7141C>G	3.37:g.195511310G>C	ENSP00000417498:p.His2381Asp	Somatic	517	1	0.00193424		WXS	Illumina HiSeq	Phase_I	131	29	0.221374	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	1.138	-0.650349	0.03506	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29397	1.57;1.57	.	.	.	.	.	.	.	.	T	0.13243	0.0321	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.18650	-1.0330	7	.	.	.	.	3.5687	0.07909	0.0:0.2526:0.4955:0.2518	.	2381	E7ESK3	.	D	2381	ENSP00000417498:H2381D;ENSP00000420243:H2381D	.	H	-	1	0	MUC4	196995705	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-3.920000	0.00334	-2.619000	0.00441	-2.366000	0.00237	CAC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HSD17B11	51170	hgsc.bcm.edu	37	4	88278484	88278484	+	Silent	SNP	T	T	G	rs34025653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88278484T>G	ENST00000358290.4	-	5	957	c.642A>C	c.(640-642)acA>acC	p.T214T	HSD17B11_ENST00000507286.1_Silent_p.T170T|HSD17B11_ENST00000507518.1_5'UTR	NM_016245.3	NP_057329.2	Q8NBQ5	DHB11_HUMAN	hydroxysteroid (17-beta) dehydrogenase 11	214					androgen catabolic process (GO:0006710)|steroid biosynthetic process (GO:0006694)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|lipid particle (GO:0005811)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|steroid dehydrogenase activity (GO:0016229)			cervix(1)|endometrium(4)|kidney(2)|lung(2)|ovary(2)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000339)		GACACAGACATGTTGTTTTGA	0.368													T|||	288	0.057508	0.2095	0.0159	5008	,	,		19416	0.0		0.0	False		,,,				2504	0.0				p.T214T		Atlas-SNP	.											.	HSD17B11	28	.	0			c.A642C						PASS	.	T		732,3672	301.5+/-286.9	69,594,1539	134.0	115.0	122.0		642	-11.3	0.6	4	dbSNP_126	122	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	HSD17B11	NM_016245.3		69,601,5832	GG,GT,TT		0.0814,16.6213,5.6829		214/301	88278484	739,12265	2202	4300	6502	SO:0001819	synonymous_variant	51170	exon5			CAGACATGTTGTT	AF126780	CCDS3619.1	4q22.1	2011-09-20	2006-11-22	2006-11-22	ENSG00000198189	ENSG00000198189	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	22960	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 2"", ""short chain dehydrogenase/reductase family 16C, member 2"""	612831	"""dehydrogenase/reductase (SDR family) member 8"""	DHRS8		11165019, 12697717, 19027726	Standard	XM_006714232		Approved	RetSDR2, 17-BETA-HSD11, 17-BETA-HSDXI, PAN1B, SDR16C2	uc003hqp.2	Q8NBQ5	OTTHUMG00000130594	ENST00000358290.4:c.642A>C	4.37:g.88278484T>G		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	176	68	0.386364	NM_016245	Q96HF6|Q9UKU4	Silent	SNP	ENST00000358290.4	37	CCDS3619.1																																																																																			T|0.938;G|0.062	0.062	strong		0.368	HSD17B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253041.1	NM_016245	
APOA4	337	hgsc.bcm.edu	37	11	116692558	116692558	+	Silent	SNP	G	G	A	rs5101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:116692558G>A	ENST00000357780.3	-	3	330	c.216C>T	c.(214-216)taC>taT	p.Y72Y		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	72	13 X 22 AA approximate tandem repeats.				cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		ggtcacctgcgtAAGTGTTCA	0.547													G|||	488	0.0974441	0.3517	0.0317	5008	,	,		21530	0.0		0.001	False		,,,				2504	0.0				p.Y72Y		Atlas-SNP	.											.	APOA4	51	.	0			c.C216T						PASS	.	G		1211,3191	420.6+/-339.1	162,887,1152	126.0	117.0	120.0		216	0.6	0.0	11	dbSNP_52	120	9,8583	5.7+/-21.5	0,9,4287	no	coding-synonymous	APOA4	NM_000482.3		162,896,5439	AA,AG,GG		0.1047,27.5102,9.3889		72/397	116692558	1220,11774	2201	4296	6497	SO:0001819	synonymous_variant	337	exon3			ACCTGCGTAAGTG		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"""Apolipoproteins"""	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.216C>T	11.37:g.116692558G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	31	0.364706	NM_000482	A8MSL6|Q14CW8|Q6Q787	Silent	SNP	ENST00000357780.3	37	CCDS31681.1																																																																																			G|0.883;A|0.117	0.117	strong		0.547	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482	
SMTNL2	342527	hgsc.bcm.edu	37	17	4497137	4497137	+	Missense_Mutation	SNP	T	T	C	rs9916524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4497137T>C	ENST00000389313.4	+	4	818	c.751T>C	c.(751-753)Tgg>Cgg	p.W251R	SMTNL2_ENST00000338859.4_Missense_Mutation_p.W107R	NM_001114974.1	NP_001108446.1	Q2TAL5	SMTL2_HUMAN	smoothelin-like 2	251			W -> R (in dbSNP:rs9916524).							breast(1)|endometrium(9)|kidney(1)|lung(1)|skin(1)	13				READ - Rectum adenocarcinoma(115;0.0325)		CTCTTTCACGTGGTCTGTGCC	0.592													C|||	229	0.0457268	0.1399	0.0159	5008	,	,		18798	0.0		0.008	False		,,,				2504	0.0256				p.W251R		Atlas-SNP	.											.	SMTNL2	57	.	0			c.T751C						PASS	.	C	ARG/TRP,ARG/TRP	520,3886	776.1+/-414.1	26,468,1709	76.0	69.0	72.0		751,319	-0.1	0.0	17	dbSNP_119	72	10,8590	818.7+/-406.8	0,10,4290	yes	missense,missense	SMTNL2	NM_001114974.1,NM_198501.2	101,101	26,478,5999	CC,CT,TT		0.1163,11.8021,4.075	benign,benign	251/462,107/318	4497137	530,12476	2203	4300	6503	SO:0001583	missense	342527	exon4			TTCACGTGGTCTG	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.751T>C	17.37:g.4497137T>C	ENSP00000373964:p.Trp251Arg	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	118	45	0.381356	NM_001114974	Q6ZVK6	Missense_Mutation	SNP	ENST00000389313.4	37	CCDS45583.1	93	0.042582417582417584	84	0.17073170731707318	4	0.011049723756906077	0	0.0	5	0.006596306068601583	C	0.021	-1.428801	0.01117	0.118021	0.001163	ENSG00000188176	ENST00000338859;ENST00000389313	T;T	0.80994	-1.41;-1.44	4.45	-0.126	0.13515	.	.	.	.	.	T	0.00178	0.0005	N	0.02142	-0.665	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.01814	-1.1268	9	0.02654	T	1	-20.7736	3.6672	0.08260	0.4915:0.3015:0.0:0.207	rs9916524;rs52797495;rs56667747;rs9916524	251	Q2TAL5	SMTL2_HUMAN	R	107;251	ENSP00000345143:W107R;ENSP00000373964:W251R	ENSP00000345143:W107R	W	+	1	0	SMTNL2	4443886	0.000000	0.05858	0.018000	0.16275	0.001000	0.01503	-2.881000	0.00715	-0.161000	0.10983	-1.043000	0.02367	TGG	T|0.951;C|0.049	0.049	strong		0.592	SMTNL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439129.1	NM_198501	
LANCL2	55915	hgsc.bcm.edu	37	7	55433884	55433884	+	Missense_Mutation	SNP	A	A	C	rs2272263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:55433884A>C	ENST00000254770.2	+	1	744	c.166A>C	c.(166-168)Acg>Ccg	p.T56P		NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	56			T -> P (in dbSNP:rs2272263). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.7}.		negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			CCCGGCGACCACGGATGAGCC	0.731													A|||	1029	0.205471	0.1437	0.1787	5008	,	,		12935	0.1567		0.325	False		,,,				2504	0.2352				p.T56P		Atlas-SNP	.											.	LANCL2	54	.	0			c.A166C						PASS	.	A	PRO/THR	674,3684		58,558,1563	8.0	11.0	10.0		166	-7.8	0.0	7	dbSNP_100	10	2547,5989		420,1707,2141	yes	missense	LANCL2	NM_018697.3	38	478,2265,3704	CC,CA,AA		29.8383,15.4658,24.9806	benign	56/451	55433884	3221,9673	2179	4268	6447	SO:0001583	missense	55915	exon1			GCGACCACGGATG	AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434			6509	protein-coding gene	gene with protein product	"""testis-specific adriamycin sensitivity protein"", ""G protein-coupled receptor 69B"""	612919	"""LanC (bacterial lantibiotic synthetase component C)-like 2"""	GPR69B		11762191	Standard	NM_018697		Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.166A>C	7.37:g.55433884A>C	ENSP00000254770:p.Thr56Pro	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	39	9	0.230769	NM_018697	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Missense_Mutation	SNP	ENST00000254770.2	37	CCDS5517.1	513	0.2348901098901099	70	0.14227642276422764	74	0.20441988950276244	110	0.19230769230769232	259	0.341688654353562	A	12.05	1.821845	0.32237	0.154658	0.298383	ENSG00000132434	ENST00000254770	T	0.31510	1.49	4.28	-7.8	0.01214	.	1.067980	0.07294	N	0.872988	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	0.43782	-0.9370	9	0.30854	T	0.27	.	10.0708	0.42332	0.1673:0.297:0.5357:0.0	rs2272263;rs11546653	56	Q9NS86	LANC2_HUMAN	P	56	ENSP00000254770:T56P	ENSP00000254770:T56P	T	+	1	0	LANCL2	55401378	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	-1.546000	0.02188	-1.519000	0.01775	-0.379000	0.06801	ACG	A|0.758;C|0.242	0.242	strong		0.731	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697	
LDB3	11155	hgsc.bcm.edu	37	10	88476458	88476458	+	Missense_Mutation	SNP	G	G	A	rs113817827		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:88476458G>A	ENST00000361373.4	+	9	1627	c.1606G>A	c.(1606-1608)Gtc>Atc	p.V536I	LDB3_ENST00000352360.5_Missense_Mutation_p.V279I|LDB3_ENST00000429277.2_Missense_Mutation_p.V541I|LDB3_ENST00000263066.6_Missense_Mutation_p.V426I|LDB3_ENST00000458213.2_Missense_Mutation_p.V426I	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						CAGGGGGACCGTCCAGAGGGC	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		13034	0.001		0.0	False		,,,				2504	0.0				p.V541I		Atlas-SNP	.											.	LDB3	164	.	0			c.G1621A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	33.0	33.0	33.0		1276,1621,1606	-0.3	0.9	10	dbSNP_132	33	0,8600		0,0,4300	no	missense,missense,missense	LDB3	NM_001080114.1,NM_001171610.1,NM_007078.2	29,29,29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign,benign,benign	426/618,541/733,536/728	88476458	2,13004	2203	4300	6503	SO:0001583	missense	11155	exon10			GGGACCGTCCAGA	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.1606G>A	10.37:g.88476458G>A	ENSP00000355296:p.Val536Ile	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	235	105	0.446809	NM_001171610		Missense_Mutation	SNP	ENST00000361373.4	37	CCDS7377.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	13.41	2.227523	0.39399	4.54E-4	0.0	ENSG00000122367	ENST00000539402;ENST00000429277;ENST00000458213;ENST00000352360;ENST00000263066;ENST00000361373	T;T;T;T;T	0.54279	0.82;0.67;0.61;0.67;0.58	4.85	-0.331	0.12679	.	0.302757	0.18155	N	0.149948	T	0.21509	0.0518	N	0.05124	-0.11	0.80722	D	1	B;B;B;P;B	0.38729	0.001;0.003;0.0;0.644;0.0	B;B;B;B;B	0.32805	0.001;0.004;0.001;0.153;0.0	T	0.02852	-1.1102	10	0.35671	T	0.21	.	4.289	0.10869	0.1864:0.0:0.2957:0.5179	.	541;457;279;536;426	B4E3K3;F5H0C2;O75112-3;O75112;O75112-2	.;.;.;LDB3_HUMAN;.	I	457;541;426;279;426;536	ENSP00000401437:V541I;ENSP00000409148:V426I;ENSP00000263067:V279I;ENSP00000263066:V426I;ENSP00000355296:V536I	ENSP00000263066:V426I	V	+	1	0	LDB3	88466438	0.975000	0.34042	0.879000	0.34478	0.874000	0.50279	1.816000	0.38992	0.095000	0.17434	0.555000	0.69702	GTC	G|0.998;A|0.002	0.002	strong		0.667	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2		
KIAA0368	23392	hgsc.bcm.edu	37	9	114184477	114184477	+	Silent	SNP	C	C	T	rs868405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114184477C>T	ENST00000338205.5	-	13	1488	c.1269G>A	c.(1267-1269)cgG>cgA	p.R423R	KIAA0368_ENST00000259335.4_Silent_p.R601R			Q5VYK3	ECM29_HUMAN	KIAA0368	429					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)		p.R601R(1)		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						AATGTGGCATCCGACTGCAAA	0.358													T|||	479	0.095647	0.1861	0.0187	5008	,	,		19517	0.1617		0.0109	False		,,,				2504	0.047				p.R601R		Atlas-SNP	.											KIAA0368,NS,carcinoma,0,1	KIAA0368	144	1	1	Substitution - coding silent(1)	stomach(1)	c.G1803A						scavenged	.	T		546,3132		43,460,1336	69.0	67.0	68.0		1803	2.6	1.0	9	dbSNP_86	68	113,8081		0,113,3984	no	coding-synonymous	KIAA0368	NM_001080398.1		43,573,5320	TT,TC,CC		1.3791,14.845,5.5509		601/2018	114184477	659,11213	1839	4097	5936	SO:0001819	synonymous_variant	23392	exon15			TGGCATCCGACTG	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.1269G>A	9.37:g.114184477C>T		Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	92	52	0.565217	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				C|0.909;T|0.091	0.091	strong		0.358	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
B4GALNT4	338707	hgsc.bcm.edu	37	11	380390	380390	+	Silent	SNP	C	C	T	rs115057328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:380390C>T	ENST00000329962.6	+	18	2814	c.2814C>T	c.(2812-2814)gcC>gcT	p.A938A		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	938					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)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		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)		GCAGGCTGGCCTTCGCGCCCG	0.682													.|||	22	0.00439297	0.0151	0.0029	5008	,	,		13932	0.0		0.0	False		,,,				2504	0.0				p.A938A		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.C2814T						PASS	.	C		57,4349	51.6+/-87.1	0,57,2146	60.0	43.0	49.0		2814	3.8	1.0	11	dbSNP_132	49	0,8598		0,0,4299	no	coding-synonymous	B4GALNT4	NM_178537.4		0,57,6445	TT,TC,CC		0.0,1.2937,0.4383		938/1040	380390	57,12947	2203	4299	6502	SO:0001819	synonymous_variant	338707	exon18			GCTGGCCTTCGCG	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2814C>T	11.37:g.380390C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	104	64	0.615385	NM_178537	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																			C|0.995;T|0.005	0.005	strong		0.682	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
NSUN2	54888	hgsc.bcm.edu	37	5	6622139	6622139	+	Silent	SNP	G	G	T	rs148924682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:6622139G>T	ENST00000264670.6	-	6	923	c.612C>A	c.(610-612)gtC>gtA	p.V204V	NSUN2_ENST00000505264.1_Intron|NSUN2_ENST00000539938.1_Intron|NSUN2_ENST00000506139.1_Silent_p.V169V	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	204					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						CTGGAAAGGGGACATTCATGT	0.408													G|||	51	0.0101837	0.0348	0.0058	5008	,	,		18768	0.0		0.001	False		,,,				2504	0.0				p.V204V		Atlas-SNP	.											NSUN2,NS,carcinoma,-1,1	NSUN2	82	1	0			c.C612A						PASS	.	G	,	150,4256	103.8+/-142.4	3,144,2056	180.0	150.0	161.0		507,612	-1.7	0.3	5	dbSNP_134	161	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	NSUN2	NM_001193455.1,NM_017755.5	,	3,144,6356	TT,TG,GG		0.0,3.4044,1.1533	,	169/733,204/768	6622139	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	54888	exon6			AAAGGGGACATTC	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.612C>A	5.37:g.6622139G>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	109	48	0.440367	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	37	CCDS3869.1																																																																																			G|0.990;T|0.010	0.010	strong		0.408	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
ZNF98	148198	hgsc.bcm.edu	37	19	22574357	22574357	+	Missense_Mutation	SNP	C	C	G	rs200702907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	762	2	0.00262467		WXS	Illumina HiSeq	Phase_I	901	370	0.410655	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	
DEPDC4	120863	hgsc.bcm.edu	37	12	100657464	100657464	+	Missense_Mutation	SNP	T	T	C	rs7307415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:100657464T>C	ENST00000416321.1	-	2	367	c.365A>G	c.(364-366)cAt>cGt	p.H122R		NM_152317.2	NP_689530.1	Q8N2C3	DEPD4_HUMAN	DEP domain containing 4	122	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.		H -> R (in dbSNP:rs7307415).		intracellular signal transduction (GO:0035556)					NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)|urinary_tract(1)	15						TTGGCAAAGATGAACCCCTTT	0.363													T|||	465	0.0928514	0.2579	0.0692	5008	,	,		19287	0.0		0.0686	False		,,,				2504	0.0072				p.H122R		Atlas-SNP	.											.	DEPDC4	34	.	0			c.A365G						PASS	.	T	ARG/HIS	1074,3332	392.1+/-328.4	143,788,1272	126.0	116.0	119.0		365	-4.8	0.1	12	dbSNP_116	119	586,8014	157.3+/-211.0	27,532,3741	yes	missense	DEPDC4	NM_152317.2	29	170,1320,5013	CC,CT,TT		6.814,24.3759,12.7633	benign	122/295	100657464	1660,11346	2203	4300	6503	SO:0001583	missense	120863	exon2			CAAAGATGAACCC	AK090824	CCDS9075.1	12q23	2006-03-30				ENSG00000166153			22952	protein-coding gene	gene with protein product						12477932	Standard	XM_005268628		Approved	DEP.4, FLJ33505	uc001thi.3	Q8N2C3		ENST00000416321.1:c.365A>G	12.37:g.100657464T>C	ENSP00000396234:p.His122Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	99	53	0.535354	NM_152317	Q496C8|Q96BW0	Missense_Mutation	SNP	ENST00000416321.1	37	CCDS9075.1	200	0.09157509157509157	124	0.25203252032520324	27	0.07458563535911603	0	0.0	49	0.06464379947229551	T	0.009	-1.824954	0.00589	0.243759	0.06814	ENSG00000166153	ENST00000422147;ENST00000378250;ENST00000416321;ENST00000550587;ENST00000549249;ENST00000551642	T;T;T;T	0.21031	2.03;2.03;2.03;2.03	4.93	-4.79	0.03200	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.390052	0.26019	N	0.026833	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	0.13495	-1.0507	9	0.02654	T	1	.	11.9547	0.52974	0.0:0.3463:0.0:0.6537	rs7307415;rs52830271;rs59614867;rs7307415	122;55;122	E9PGM3;Q3ZCN8;Q8N2C3	.;.;DEPD4_HUMAN	R	122;55;122;122;55;115	ENSP00000396234:H122R;ENSP00000448385:H122R;ENSP00000448338:H55R;ENSP00000449590:H115R	ENSP00000367490:H122R	H	-	2	0	DEPDC4	99181595	0.132000	0.22450	0.059000	0.19551	0.405000	0.30901	0.320000	0.19540	-1.661000	0.01484	-1.032000	0.02404	CAT	T|0.876;C|0.124	0.124	strong		0.363	DEPDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408482.1	NM_152317	
SVIL	6840	hgsc.bcm.edu	37	10	29840164	29840164	+	Silent	SNP	A	A	G	rs3740002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	53	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	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		
UPK3A	7380	hgsc.bcm.edu	37	22	45683309	45683309	+	Silent	SNP	C	C	T	rs62001037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45683309C>T	ENST00000216211.4	+	3	497	c.465C>T	c.(463-465)ccC>ccT	p.P155P	UPK3A_ENST00000396082.2_Intron	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	155					cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		GTAACGCACCCCTGTCGGCAG	0.607													C|||	116	0.0231629	0.084	0.0058	5008	,	,		16168	0.0		0.001	False		,,,				2504	0.0				p.P155P		Atlas-SNP	.											.	UPK3A	14	.	0			c.C465T						PASS	.	C	,	338,4066		14,310,1878	28.0	27.0	28.0		,465	0.4	1.0	22	dbSNP_129	28	1,8599		0,1,4299	no	intron,coding-synonymous	UPK3A	NM_001167574.1,NM_006953.3	,	14,311,6177	TT,TC,CC		0.0116,7.6748,2.6069	,	,155/288	45683309	339,12665	2202	4300	6502	SO:0001819	synonymous_variant	7380	exon3			CGCACCCCTGTCG	AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"""uroplakin 3"""	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.465C>T	22.37:g.45683309C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Silent	SNP	ENST00000216211.4	37	CCDS14064.1																																																																																			C|0.973;T|0.027	0.027	strong		0.607	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953	
TRPM1	4308	hgsc.bcm.edu	37	15	31330280	31330280	+	Silent	SNP	A	A	G	rs2288242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31330280A>G	ENST00000256552.6	-	19	2553	c.2406T>C	c.(2404-2406)aaT>aaC	p.N802N	RP11-348B17.1_ENST00000561299.1_RNA|RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000542188.1_Silent_p.N819N|TRPM1_ENST00000397795.2_Silent_p.N780N	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)		TGCCATCCTCATTTTCCTTGG	0.383													G|||	3803	0.759385	0.5749	0.8689	5008	,	,		19421	0.9524		0.8469	False		,,,				2504	0.6421				p.N819N		Atlas-SNP	.											.	TRPM1	183	.	0			c.T2457C						PASS	.	G		2395,1335		772,851,242	120.0	108.0	112.0		2340	-10.7	0.2	15	dbSNP_100	112	6825,1363		2847,1131,116	no	coding-synonymous	TRPM1	NM_002420.4		3619,1982,358	GG,GA,AA		16.6463,35.7909,22.638		780/1604	31330280	9220,2698	1865	4094	5959	SO:0001819	synonymous_variant	4308	exon18			ATCCTCATTTTCC	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.2406T>C	15.37:g.31330280A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			A|0.207;G|0.793	0.793	strong		0.383	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
MED24	9862	hgsc.bcm.edu	37	17	38175866	38175866	+	Silent	SNP	G	G	A	rs11555254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38175866G>A	ENST00000394128.2	-	26	2967	c.2886C>T	c.(2884-2886)tcC>tcT	p.S962S	MED24_ENST00000501516.3_Silent_p.S981S|MED24_ENST00000356271.3_Silent_p.S949S|MED24_ENST00000394127.2_Silent_p.S949S|MED24_ENST00000394126.1_Silent_p.S987S	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	962					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)					CCTTGGGGCTGGACATGGCTG	0.647													G|||	557	0.111222	0.1762	0.1225	5008	,	,		17624	0.006		0.162	False		,,,				2504	0.0716				p.S962S		Atlas-SNP	.											.	MED24	89	.	0			c.C2886T						PASS	.	G	,	798,3608	316.9+/-294.8	72,654,1477	71.0	61.0	64.0		2847,2886	4.1	1.0	17	dbSNP_120	64	1405,7195	268.7+/-288.0	114,1177,3009	no	coding-synonymous,coding-synonymous	MED24	NM_001079518.1,NM_014815.3	,	186,1831,4486	AA,AG,GG		16.3372,18.1117,16.9383	,	949/977,962/990	38175866	2203,10803	2203	4300	6503	SO:0001819	synonymous_variant	9862	exon26			GGGGCTGGACATG	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.2886C>T	17.37:g.38175866G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	133	66	0.496241	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1	272	0.12454212454212454	91	0.18495934959349594	48	0.13259668508287292	3	0.005244755244755245	130	0.17150395778364116	G	10.91	1.484460	0.26598	0.181117	0.163372	ENSG00000008838	ENST00000422942	.	.	.	5.08	4.09	0.47781	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.2844	14.4219	0.67190	0.0753:0.0:0.9247:0.0	rs11555254;rs17850738;rs11555254	.	.	.	X	260	.	.	Q	-	1	0	MED24	35429392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.006000	0.49529	2.506000	0.84524	0.650000	0.86243	CAG	G|0.850;A|0.150	0.150	strong		0.647	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
LRRC24	441381	hgsc.bcm.edu	37	8	145748075	145748075	+	Silent	SNP	T	T	G	rs112652028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145748075T>G	ENST00000529415.2	-	5	1443	c.1326A>C	c.(1324-1326)ggA>ggC	p.G442G	LRRC14_ENST00000292524.1_3'UTR|LRRC14_ENST00000528528.1_3'UTR|LRRC24_ENST00000533758.1_Silent_p.G439G			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	442						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-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;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CGAACAGCGCTCCCTCCCCCG	0.682													G|||	75	0.014976	0.0522	0.0072	5008	,	,		9844	0.0		0.0	False		,,,				2504	0.001				p.G442G		Atlas-SNP	.											.	LRRC24	11	.	0			c.A1326C						PASS	.	G	,	155,4189		3,149,2020	13.0	14.0	14.0		1326,	3.1	1.0	8	dbSNP_132	14	2,8570		0,2,4284	no	coding-synonymous,utr-3	LRRC14,LRRC24	NM_001024678.3,NM_014665.2	,	3,151,6304	GG,GT,TT		0.0233,3.5681,1.2155	,	442/514,	145748075	157,12759	2172	4286	6458	SO:0001819	synonymous_variant	441381	exon5			CAGCGCTCCCTCC	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"""Immunoglobulin superfamily / I-set domain containing"""	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.1326A>C	8.37:g.145748075T>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_001024678		Silent	SNP	ENST00000529415.2	37	CCDS34969.1																																																																																			T|0.986;G|0.014	0.014	strong		0.682	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678	
OR2K2	26248	hgsc.bcm.edu	37	9	114090277	114090277	+	Missense_Mutation	SNP	G	G	A	rs73656223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114090277G>A	ENST00000374428.1	-	1	523	c.524C>T	c.(523-525)aCg>aTg	p.T175M	OR2K2_ENST00000302681.1_Missense_Mutation_p.T146M			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						CCAGGAGACCGTAGCCATCCG	0.547													G|||	74	0.0147764	0.053	0.0058	5008	,	,		21286	0.0		0.0	False		,,,				2504	0.0				p.T146M		Atlas-SNP	.											.	OR2K2	77	.	0			c.C437T						PASS	.	G	MET/THR	226,4180	116.7+/-154.6	5,216,1982	99.0	80.0	86.0		437	1.1	0.0	9	dbSNP_130	86	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR2K2	NM_205859.1	81	5,217,6281	AA,AG,GG		0.0116,5.1294,1.7453	benign	146/317	114090277	227,12779	2203	4300	6503	SO:0001583	missense	26248	exon1			GAGACCGTAGCCA	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.524C>T	9.37:g.114090277G>A	ENSP00000363550:p.Thr175Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Missense_Mutation	SNP	ENST00000374428.1	37		25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	4.460	0.085171	0.08583	0.051294	1.16E-4	ENSG00000171133	ENST00000302681;ENST00000374428	T;T	0.37752	1.18;1.18	4.92	1.09	0.20402	GPCR, rhodopsin-like superfamily (1);	1.107710	0.07088	U	0.838300	T	0.04092	0.0114	N	0.20986	0.625	0.09310	N	1	B	0.18461	0.028	B	0.14578	0.011	T	0.20371	-1.0277	10	0.72032	D	0.01	.	6.3971	0.21618	0.1168:0.2929:0.5903:0.0	.	175	Q8NGT1	OR2K2_HUMAN	M	146;175	ENSP00000305055:T146M;ENSP00000363550:T175M	ENSP00000305055:T146M	T	-	2	0	OR2K2	113130098	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	0.116000	0.15561	0.150000	0.19136	-0.423000	0.05987	ACG	G|0.982;A|0.018	0.018	strong		0.547	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859	
ZNF676	163223	hgsc.bcm.edu	37	19	22375868	22375868	+	Missense_Mutation	SNP	C	C	T	rs8104929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22375868C>T	ENST00000397121.2	-	2	397	c.80G>A	c.(79-81)gGa>gAa	p.G27E		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	27	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		G -> E (in dbSNP:rs8104929).		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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				GGGCTCTTTTCCTTGCTCCAG	0.408													C|||	2210	0.441294	0.6331	0.3689	5008	,	,		15924	0.3393		0.3459	False		,,,				2504	0.4366				p.G27E		Atlas-SNP	.											.	ZNF676	146	.	0			c.G80A						PASS	.	C	GLU/GLY	1715,1307		496,723,292	99.0	119.0	112.0		80	0.8	0.7	19	dbSNP_116	112	1902,3516		346,1210,1153	no	missense	ZNF676	NM_001001411.2	98	842,1933,1445	TT,TC,CC		35.1052,43.2495,42.8555	benign	27/589	22375868	3617,4823	1511	2709	4220	SO:0001583	missense	163223	exon2			TCTTTTCCTTGCT	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.80G>A	19.37:g.22375868C>T	ENSP00000380310:p.Gly27Glu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	37	CCDS42539.1	874	0.4001831501831502	310	0.6300813008130082	127	0.35082872928176795	181	0.31643356643356646	256	0.33773087071240104	.	6.915	0.538495	0.13250	0.567505	0.351052	ENSG00000196109	ENST00000397121	T	0.00892	5.57	0.784	0.784	0.18578	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	L	0.45228	1.405	0.44611	P	0.0024159999999999737	D	0.76494	0.999	D	0.71184	0.972	T	0.10753	-1.0616	8	0.25106	T	0.35	.	4.7436	0.13026	0.0:1.0:0.0:0.0	rs8104929;rs57089838	27	Q8N7Q3	ZN676_HUMAN	E	27	ENSP00000380310:G27E	ENSP00000380310:G27E	G	-	2	0	ZNF676	22167708	0.703000	0.27826	0.667000	0.29798	0.670000	0.39368	0.737000	0.26144	0.181000	0.19994	0.184000	0.17185	GGA	C|0.616;T|0.384	0.384	strong		0.408	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
OR13C5	138799	hgsc.bcm.edu	37	9	107361439	107361439	+	Missense_Mutation	SNP	G	G	C	rs4629933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361439G>C	ENST00000374779.2	-	1	349	c.256C>G	c.(256-258)Ctt>Gtt	p.L86V		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	86			L -> V (in dbSNP:rs4629933).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CTTTCTGAAAGGAAGCTCACT	0.527													G|||	3389	0.676717	0.7504	0.5937	5008	,	,		20678	0.9573		0.4225	False		,,,				2504	0.6084				p.L86V		Atlas-SNP	.											.	OR13C5	60	.	0			c.C256G						PASS	.						27.0	42.0	37.0					9																	107361439		2189	4294	6483	SO:0001583	missense	138799	exon1			CTGAAAGGAAGCT		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.256C>G	9.37:g.107361439G>C	ENSP00000363911:p.Leu86Val	Somatic	693	1	0.001443		WXS	Illumina HiSeq	Phase_I	666	298	0.447447	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	1384	0.6336996336996337	336	0.6829268292682927	201	0.5552486187845304	521	0.9108391608391608	326	0.43007915567282323	G	14.72	2.618900	0.46736	.	.	ENSG00000255800	ENST00000374779	T	0.01369	4.97	4.03	-8.0	0.01126	GPCR, rhodopsin-like superfamily (1);	0.289560	0.17451	U	0.173772	T	0.00012	0.0000	L	0.48877	1.53	0.80722	P	0.0	P	0.51791	0.948	B	0.42555	0.391	T	0.48570	-0.9024	9	0.32370	T	0.25	.	1.5125	0.02499	0.1543:0.3065:0.2305:0.3087	rs4629933;rs7025562	86	Q8NGS8	O13C5_HUMAN	V	86	ENSP00000363911:L86V	ENSP00000363911:L86V	L	-	1	0	OR13C5	106401260	0.000000	0.05858	0.000000	0.03702	0.515000	0.34225	-1.382000	0.02546	-1.158000	0.02811	0.531000	0.56144	CTT	G|0.308;C|0.692	0.692	strong		0.527	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
USP6	9098	hgsc.bcm.edu	37	17	5042715	5042715	+	Missense_Mutation	SNP	G	G	A	rs61740308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5042715G>A	ENST00000574788.1	+	22	3474	c.1244G>A	c.(1243-1245)tGt>tAt	p.C415Y	USP6_ENST00000304328.5_Missense_Mutation_p.C98Y|USP6_ENST00000250066.6_Missense_Mutation_p.C415Y|USP6_ENST00000332776.4_Missense_Mutation_p.C415Y			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	415					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						TCCACGCCCTGTCCTGGTGGG	0.652			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								G|||	509	0.101637	0.1982	0.0375	5008	,	,		17890	0.0784		0.1153	False		,,,				2504	0.0266				p.C415Y		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.G1244A						PASS	.	G	TYR/CYS	709,3697	291.3+/-281.4	61,587,1555	45.0	49.0	48.0		1244	0.1	0.1	17	dbSNP_129	48	951,7649	207.3+/-249.1	52,847,3401	yes	missense	USP6	NM_004505.2	194	113,1434,4956	AA,AG,GG		11.0581,16.0917,12.7633	possibly-damaging	415/1407	5042715	1660,11346	2203	4300	6503	SO:0001583	missense	9098	exon14			CGCCCTGTCCTGG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.1244G>A	17.37:g.5042715G>A	ENSP00000460380:p.Cys415Tyr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	48	0.564706	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	250	0.11446886446886446	97	0.19715447154471544	16	0.04419889502762431	52	0.09090909090909091	85	0.11213720316622691	G	9.321	1.058159	0.19987	0.160917	0.110581	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.27402	2.42;2.91;1.67	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	P;P	0.42518	0.782;0.676	P;B	0.48738	0.588;0.384	T	0.24368	-1.0162	7	0.72032	D	0.01	.	.	.	.	rs61740308	98;415	P35125-2;P35125	.;UBP6_HUMAN	Y	415;415;98	ENSP00000328010:C415Y;ENSP00000250066:C415Y;ENSP00000305473:C98Y	ENSP00000250066:C415Y	C	+	2	0	USP6	4983439	0.003000	0.15002	0.063000	0.19743	0.063000	0.16089	-0.046000	0.11983	0.132000	0.18615	0.134000	0.15878	TGT	G|0.881;A|0.119	0.119	strong		0.652	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
FREM1	158326	hgsc.bcm.edu	37	9	14801687	14801687	+	Silent	SNP	T	T	C	rs10738380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14801687T>C	ENST00000380880.3	-	20	4440	c.3657A>G	c.(3655-3657)gcA>gcG	p.A1219A	FREM1_ENST00000380881.4_Silent_p.A1220A|FREM1_ENST00000422223.2_Silent_p.A1219A			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1219					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)		TGTGAACAGGTGCATGTTTCT	0.443													T|||	886	0.176917	0.0325	0.1945	5008	,	,		19888	0.2312		0.2336	False		,,,				2504	0.2454				p.A1219A		Atlas-SNP	.											.	FREM1	261	.	0			c.A3657G						PASS	.	T		241,3679		4,233,1723	130.0	129.0	129.0		3657	0.3	0.0	9	dbSNP_120	129	1933,6383		235,1463,2460	no	coding-synonymous	FREM1	NM_144966.5		239,1696,4183	CC,CT,TT		23.2443,6.148,17.7672		1219/2180	14801687	2174,10062	1960	4158	6118	SO:0001819	synonymous_variant	158326	exon21			AACAGGTGCATGT	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.3657A>G	9.37:g.14801687T>C		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	322	135	0.419255	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			T|0.834;C|0.166	0.166	strong		0.443	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
ZNF462	58499	hgsc.bcm.edu	37	9	109687288	109687288	+	Silent	SNP	T	T	C	rs1000152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:109687288T>C	ENST00000277225.5	+	3	1384	c.1095T>C	c.(1093-1095)taT>taC	p.Y365Y	ZNF462_ENST00000441147.2_5'Flank|ZNF462_ENST00000457913.1_Silent_p.Y365Y			Q96JM2	ZN462_HUMAN	zinc finger protein 462	365					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GATCCCGTTATGGAATGACTG	0.418													T|||	988	0.197284	0.4297	0.17	5008	,	,		23464	0.129		0.0895	False		,,,				2504	0.0838				p.Y365Y		Atlas-SNP	.											ZNF462,colon,carcinoma,0,1	ZNF462	322	1	0			c.T1095C						PASS	.	T		1634,2772	503.5+/-365.6	291,1052,860	73.0	69.0	70.0		1095	-6.4	0.9	9	dbSNP_86	70	806,7794	188.7+/-235.6	50,706,3544	no	coding-synonymous	ZNF462	NM_021224.4		341,1758,4404	CC,CT,TT		9.3721,37.0858,18.7606		365/2507	109687288	2440,10566	2203	4300	6503	SO:0001819	synonymous_variant	58499	exon3			CCGTTATGGAATG	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.1095T>C	9.37:g.109687288T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	81	18	0.222222	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			T|0.801;C|0.199	0.199	strong		0.418	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
PAPL	390928	hgsc.bcm.edu	37	19	39575987	39575987	+	Silent	SNP	G	G	A	rs544041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39575987G>A	ENST00000331256.5	+	2	352	c.78G>A	c.(76-78)ggG>ggA	p.G26G	PAPL_ENST00000594229.1_Silent_p.G26G	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		26						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										GGTCCCTGGGGGCTCCCAGCG	0.592													g|||	691	0.137979	0.4962	0.0447	5008	,	,		19220	0.0		0.004	False		,,,				2504	0.0				p.G26G		Atlas-SNP	.											.	.	.	.	0			c.G78A						PASS	.	G		1854,2552	538.2+/-374.9	377,1100,726	124.0	113.0	117.0		78	-0.7	0.0	19	dbSNP_83	117	29,8571	19.8+/-62.0	0,29,4271	no	coding-synonymous	PAPL	NM_001004318.2		377,1129,4997	AA,AG,GG		0.3372,42.079,14.4779		26/439	39575987	1883,11123	2203	4300	6503	SO:0001819	synonymous_variant	0	exon2			CCTGGGGGCTCCC																												ENST00000331256.5:c.78G>A	19.37:g.39575987G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_001004318	B2RN68	Silent	SNP	ENST00000331256.5	37	CCDS33018.1																																																																																			G|0.870;A|0.130	0.130	strong		0.592	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		
ETV7	51513	hgsc.bcm.edu	37	6	36343802	36343802	+	Silent	SNP	G	G	A	rs2234074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36343802G>A	ENST00000340181.4	-	3	394	c.153C>T	c.(151-153)ccC>ccT	p.P51P	ETV7_ENST00000373737.4_Silent_p.P51P|ETV7_ENST00000538992.1_Intron|ETV7_ENST00000373738.1_Intron|ETV7_ENST00000339796.5_Silent_p.P51P	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	51	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				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						TCCACAGTGCGGGCTGGATGC	0.632													G|||	50	0.00998403	0.0378	0.0	5008	,	,		18446	0.0		0.0	False		,,,				2504	0.0				p.P51P		Atlas-SNP	.											.	ETV7	31	.	0			c.C153T						PASS	.	G	,,,,,,,	141,4265	99.8+/-138.5	0,141,2062	58.0	49.0	52.0		153,,,153,,,,153	-2.2	0.8	6	dbSNP_98	52	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,utr-5,coding-synonymous,intron,utr-5,intron,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	,,,,,,,	0,142,6361	AA,AG,GG		0.0116,3.2002,1.0918	,,,,,,,	51/318,,,51/265,,,,51/342	36343802	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	51513	exon3			CAGTGCGGGCTGG	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.153C>T	6.37:g.36343802G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	23	9	0.391304	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Silent	SNP	ENST00000340181.4	37	CCDS4819.1																																																																																			G|0.987;A|0.013	0.013	strong		0.632	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135	
FLG	2312	hgsc.bcm.edu	37	1	152281008	152281008	+	Silent	SNP	A	A	G	rs7512554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281008A>G	ENST00000368799.1	-	3	6389	c.6354T>C	c.(6352-6354)caT>caC	p.H2118H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	480	2	0.00416667		WXS	Illumina HiSeq	Phase_I	969	500	0.515996	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	
GMPPA	29926	hgsc.bcm.edu	37	2	220370746	220370746	+	Silent	SNP	G	G	A	rs13428617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220370746G>A	ENST00000358215.3	+	11	1314	c.945G>A	c.(943-945)gaG>gaA	p.E315E	AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373908.1_Silent_p.E315E|GMPPA_ENST00000373917.3_Silent_p.E368E|GMPPA_ENST00000313597.5_Silent_p.E315E|GMPPA_ENST00000341142.3_Silent_p.E315E	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	315					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		CCGTGGGTGAGGGTGTGCGGC	0.622													G|||	101	0.0201677	0.0726	0.0058	5008	,	,		17609	0.001		0.0	False		,,,				2504	0.0				p.E315E		Atlas-SNP	.											.	GMPPA	50	.	0			c.G945A						PASS	.	G	,	286,4116		10,266,1925	40.0	33.0	36.0		945,945	3.0	1.0	2	dbSNP_121	36	3,8591		0,3,4294	no	coding-synonymous,coding-synonymous	GMPPA	NM_013335.3,NM_205847.2	,	10,269,6219	AA,AG,GG		0.0349,6.497,2.2238	,	315/421,315/421	220370746	289,12707	2201	4297	6498	SO:0001819	synonymous_variant	29926	exon11			GGGTGAGGGTGTG	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.945G>A	2.37:g.220370746G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Silent	SNP	ENST00000358215.3	37	CCDS2441.1																																																																																			G|0.979;A|0.021	0.021	strong		0.622	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335	
FAM90A1	55138	hgsc.bcm.edu	37	12	8374812	8374812	+	Missense_Mutation	SNP	G	G	A	rs17855656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:8374812G>A	ENST00000538603.1	-	7	1559	c.1001C>T	c.(1000-1002)cCg>cTg	p.P334L	FAM90A1_ENST00000307435.6_Missense_Mutation_p.P334L	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	334			P -> L (in dbSNP:rs17855656). {ECO:0000269|PubMed:15489334}.				nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TGCGGCTGGCGGAGGTTGGAG	0.652													.|||	1132	0.226038	0.0983	0.1801	5008	,	,		14308	0.4087		0.1829	False		,,,				2504	0.2873				p.P334L		Atlas-SNP	.											FAM90A1,caecum,carcinoma,0,1	FAM90A1	68	1	0			c.C1001T						scavenged	.	G	LEU/PRO	380,3994		13,354,1820	17.0	17.0	17.0		1001	-1.4	0.0	12	dbSNP_123	17	1279,7285		88,1103,3091	no	missense	FAM90A1	NM_018088.3	98	101,1457,4911	AA,AG,GG		14.9346,8.6877,12.8227	benign	334/465	8374812	1659,11279	2187	4282	6469	SO:0001583	missense	55138	exon7			GCTGGCGGAGGTT	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.1001C>T	12.37:g.8374812G>A	ENSP00000445418:p.Pro334Leu	Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	270	181	0.67037	NM_018088	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	457	0.20924908424908426	44	0.08943089430894309	68	0.1878453038674033	217	0.3793706293706294	128	0.16886543535620052	.	0.006	-2.030824	0.00410	0.086877	0.149346	ENSG00000171847	ENST00000307435;ENST00000538603	T;T	0.15372	2.43;2.43	1.02	-1.44	0.08856	.	.	.	.	.	T	0.00012	0.0000	L	0.31476	0.935	0.80722	P	0.0	B	0.17667	0.023	B	0.15870	0.014	T	0.47699	-0.9097	8	0.34782	T	0.22	1.633	4.0479	0.09781	0.4969:0.0:0.5031:0.0	rs17855656	334	Q86YD7	F90A1_HUMAN	L	334	ENSP00000307798:P334L;ENSP00000445418:P334L	ENSP00000307798:P334L	P	-	2	0	FAM90A1	8266079	0.004000	0.15560	0.006000	0.13384	0.073000	0.16967	-0.651000	0.05372	-0.509000	0.06532	0.194000	0.17425	CCG	G|0.833;A|0.167	0.167	strong		0.652	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
KANK3	256949	hgsc.bcm.edu	37	19	8389405	8389405	+	Silent	SNP	G	G	A	rs12981073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8389405G>A	ENST00000593649.1	-	10	2375	c.2310C>T	c.(2308-2310)gcC>gcT	p.A770A	KANK3_ENST00000330915.3_Silent_p.A770A			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	770										breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						CAGCCTCCAGGGCGATGGCCA	0.632													G|||	769	0.153554	0.295	0.1383	5008	,	,		18814	0.0655		0.1223	False		,,,				2504	0.0961				p.A770A		Atlas-SNP	.											.	KANK3	35	.	0			c.C2310T						PASS	.	G		1101,3305	379.2+/-323.2	134,833,1236	26.0	26.0	26.0		2310	1.2	1.0	19	dbSNP_121	26	1053,7547	214.2+/-253.9	70,913,3317	no	coding-synonymous	KANK3	NM_198471.2		204,1746,4553	AA,AG,GG		12.2442,24.9887,16.5616		770/822	8389405	2154,10852	2203	4300	6503	SO:0001819	synonymous_variant	256949	exon10			CTCCAGGGCGATG	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.2310C>T	19.37:g.8389405G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	152	74	0.486842	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	Silent	SNP	ENST00000593649.1	37																																																																																				G|0.840;A|0.159	0.159	strong		0.632	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471	
OR6N2	81442	hgsc.bcm.edu	37	1	158746678	158746678	+	Missense_Mutation	SNP	T	T	C	rs41273541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158746678T>C	ENST00000339258.1	-	1	747	c.748A>G	c.(748-750)Atc>Gtc	p.I250V		NM_001005278.1	NP_001005278.1	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N, member 2	250			I -> V (in dbSNP:rs41273541).			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(6)|lung(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(112;0.0378)					CCAAAGAAGATGAGGACCACA	0.453													C|||	879	0.175519	0.2345	0.0288	5008	,	,		22440	0.1925		0.0437	False		,,,				2504	0.318				p.I250V		Atlas-SNP	.											.	OR6N2	78	.	0			c.A748G						PASS	.	C	VAL/ILE	824,3582	748.0+/-411.9	72,680,1451	85.0	84.0	85.0		748	1.2	1.0	1	dbSNP_127	85	401,8199	801.3+/-407.4	11,379,3910	yes	missense	OR6N2	NM_001005278.1	29	83,1059,5361	CC,CT,TT		4.6628,18.7018,9.4187	benign	250/318	158746678	1225,11781	2203	4300	6503	SO:0001583	missense	81442	exon1			AGAAGATGAGGAC	BK004200	CCDS30906.1	1q23.1	2012-08-09			ENSG00000188340	ENSG00000188340		"""GPCR / Class A : Olfactory receptors"""	15035	protein-coding gene	gene with protein product							Standard	NM_001005278		Approved		uc010pir.2	Q8NGY6	OTTHUMG00000022775	ENST00000339258.1:c.748A>G	1.37:g.158746678T>C	ENSP00000344101:p.Ile250Val	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	164	160	0.97561	NM_001005278	Q6IFR2	Missense_Mutation	SNP	ENST00000339258.1	37	CCDS30906.1	251	0.11492673992673992	104	0.21138211382113822	14	0.03867403314917127	101	0.17657342657342656	32	0.04221635883905013	C	2.754	-0.259368	0.05791	0.187018	0.046628	ENSG00000188340	ENST00000339258	T	0.00107	8.72	4.84	1.22	0.21188	GPCR, rhodopsin-like superfamily (1);	0.415403	0.17630	N	0.167403	T	0.00039	0.0001	L	0.41632	1.29	0.80722	P	0.0	B	0.11235	0.004	B	0.15870	0.014	T	0.08617	-1.0713	9	0.45353	T	0.12	-6.3668	9.9249	0.41485	0.0:0.232:0.0:0.768	rs41273541	250	Q8NGY6	OR6N2_HUMAN	V	250	ENSP00000344101:I250V	ENSP00000344101:I250V	I	-	1	0	OR6N2	157013302	0.000000	0.05858	0.972000	0.41901	0.304000	0.27724	-3.517000	0.00444	-0.189000	0.10482	-2.069000	0.00389	ATC	T|0.900;C|0.100	0.100	strong		0.453	OR6N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059068.1		
C21orf2	755	hgsc.bcm.edu	37	21	45750713	45750713	+	Missense_Mutation	SNP	C	C	T	rs62000360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45750713C>T	ENST00000339818.4	-	6	842	c.635G>A	c.(634-636)aGg>aAg	p.R212K	C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000325223.7_Missense_Mutation_p.R211K|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000397956.3_Missense_Mutation_p.R211K|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	212					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)		CACCCTGCCCCTGTGGCTGCT	0.697													C|||	126	0.0251597	0.0855	0.0159	5008	,	,		13869	0.0		0.002	False		,,,				2504	0.0				p.R212K		Atlas-SNP	.											.	C21orf2	10	.	0			c.G635A						PASS	.	C	LYS/ARG	228,4128		4,220,1954	11.0	13.0	12.0		635	-5.5	0.0	21	dbSNP_129	12	0,8504		0,0,4252	yes	missense	C21orf2	NM_004928.2	26	4,220,6206	TT,TC,CC		0.0,5.2342,1.7729	benign	212/257	45750713	228,12632	2178	4252	6430	SO:0001583	missense	755	exon6			CTGCCCCTGTGGC	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.635G>A	21.37:g.45750713C>T	ENSP00000344566:p.Arg212Lys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	155	80	0.516129	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	39	0.017857142857142856	34	0.06910569105691057	5	0.013812154696132596	0	0.0	0	0.0	C	1.956	-0.440014	0.04636	0.052342	0.0	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.30448	1.65;1.53;1.61	4.25	-5.48	0.02592	.	0.521247	0.22438	N	0.060048	T	0.00608	0.0020	N	0.08118	0	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	0.17410	-1.0370	10	0.02654	T	1	-26.1772	5.5943	0.17319	0.0:0.3756:0.2867:0.3377	.	211;211;212;171	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	K	212;211;211	ENSP00000344566:R212K;ENSP00000381047:R211K;ENSP00000317302:R211K	ENSP00000317302:R211K	R	-	2	0	C21orf2	44575141	0.000000	0.05858	0.029000	0.17559	0.002000	0.02628	-1.437000	0.02419	-1.158000	0.02811	-0.768000	0.03414	AGG	C|0.976;T|0.024	0.024	strong		0.697	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
TRPM2	7226	hgsc.bcm.edu	37	21	45821582	45821582	+	Missense_Mutation	SNP	T	T	G	rs9974927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45821582T>G	ENST00000397928.1	+	16	2785	c.2340T>G	c.(2338-2340)gaT>gaG	p.D780E	TRPM2_ENST00000300482.5_Missense_Mutation_p.D780E|TRPM2_ENST00000397932.2_Missense_Mutation_p.D780E|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000300481.9_Missense_Mutation_p.D760E	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	780			D -> E (in dbSNP:rs9974927). {ECO:0000269|Ref.6}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GGCTGCAGGATGTGGGCACCC	0.657													G|||	260	0.0519169	0.1407	0.062	5008	,	,		16222	0.0298		0.001	False		,,,				2504	0.0				p.D780E		Atlas-SNP	.											.	TRPM2	196	.	0			c.T2340G						PASS	.	G	GLU/ASP	485,3921	777.7+/-414.2	25,435,1743	88.0	71.0	77.0		2340	-8.6	0.0	21	dbSNP_119	77	7,8593	815.9+/-406.9	0,7,4293	yes	missense	TRPM2	NM_003307.3	45	25,442,6036	GG,GT,TT		0.0814,11.0077,3.7829	benign	780/1504	45821582	492,12514	2203	4300	6503	SO:0001583	missense	7226	exon16			GCAGGATGTGGGC	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2340T>G	21.37:g.45821582T>G	ENSP00000381023:p.Asp780Glu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	105	0.04807692307692308	72	0.14634146341463414	14	0.03867403314917127	19	0.033216783216783216	0	0.0	G	0.854	-0.737676	0.03111	0.110077	8.14E-4	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.51574	0.81;0.81;0.83;0.7	4.32	-8.64	0.00874	.	.	.	.	.	T	0.00073	0.0002	N	0.04508	-0.205	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	0.06058	-1.0848	9	0.05436	T	0.98	-0.4174	1.6889	0.02848	0.3751:0.1488:0.2961:0.18	rs9974927;rs57610450;rs9974927	780;566;780	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	E	780;780;760;780	ENSP00000300482:D780E;ENSP00000381023:D780E;ENSP00000300481:D760E;ENSP00000381026:D780E	ENSP00000300481:D760E	D	+	3	2	TRPM2	44646010	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.862000	0.00176	-2.458000	0.00538	-1.418000	0.01112	GAT	T|0.948;G|0.052	0.052	strong		0.657	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
GRIN2B	2904	hgsc.bcm.edu	37	12	13715975	13715975	+	Silent	SNP	A	A	G	rs1805247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:13715975A>G	ENST00000609686.1	-	13	4406	c.4197T>C	c.(4195-4197)caT>caC	p.H1399H		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	1399					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ATTTGCTGCCATGGAGCAAGC	0.632													A|||	1088	0.217252	0.3805	0.1196	5008	,	,		17467	0.1835		0.0815	False		,,,				2504	0.2403				p.H1399H		Atlas-SNP	.											GRIN2B,NS,carcinoma,-2,1	GRIN2B	303	1	0			c.T4197C						PASS	.	A		1406,3000	459.6+/-352.3	225,956,1022	43.0	42.0	43.0		4197	-0.3	1.0	12	dbSNP_92	43	755,7845	181.3+/-230.0	29,697,3574	no	coding-synonymous	GRIN2B	NM_000834.3		254,1653,4596	GG,GA,AA		8.7791,31.911,16.6154		1399/1485	13715975	2161,10845	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon13			GCTGCCATGGAGC		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.4197T>C	12.37:g.13715975A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			A|0.815;G|0.185	0.185	strong		0.632	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
PRR25	388199	hgsc.bcm.edu	37	16	863336	863336	+	Silent	SNP	T	T	C	rs11860086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	34	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	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	
PYROXD2	84795	hgsc.bcm.edu	37	10	100167396	100167396	+	Silent	SNP	G	G	A	rs12763326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	62	0	0		WXS	Illumina HiSeq	Phase_I	56	28	0.5	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	
POFUT2	23275	hgsc.bcm.edu	37	21	46685550	46685550	+	Splice_Site	SNP	C	C	T	rs112907087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46685550C>T	ENST00000349485.5	-	9	1163	c.1137G>A	c.(1135-1137)agG>agA	p.R379R	POFUT2_ENST00000331343.7_3'UTR|POFUT2_ENST00000471540.1_5'UTR	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	379					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)		CAATAAAAAACCTGCAAAGGA	0.493													C|||	27	0.00539137	0.0204	0.0	5008	,	,		16487	0.0		0.0	False		,,,				2504	0.0				p.R379R		Atlas-SNP	.											.	POFUT2	77	.	0			c.G1137A						PASS	.	C	,	86,4320	74.1+/-112.3	1,84,2118	52.0	57.0	56.0		,1137	3.9	1.0	21	dbSNP_132	56	0,8600		0,0,4300	yes	utr-3,coding-synonymous-near-splice	POFUT2	NM_015227.4,NM_133635.4	,	1,84,6418	TT,TC,CC		0.0,1.9519,0.6612	,	,379/430	46685550	86,12920	2203	4300	6503	SO:0001630	splice_region_variant	23275	exon9			AAAAAACCTGCAA	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.1137-1G>A	21.37:g.46685550C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_133635	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Silent	SNP	ENST00000349485.5	37	CCDS13719.1																																																																																			C|0.992;T|0.008	0.008	strong		0.493	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227	Silent
ALOX15B	247	hgsc.bcm.edu	37	17	7948175	7948175	+	Silent	SNP	C	C	T	rs6503070	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7948175C>T	ENST00000380183.4	+	6	844	c.705C>T	c.(703-705)gaC>gaT	p.D235D	ALOX15B_ENST00000573359.1_Silent_p.D235D|ALOX15B_ENST00000572022.1_Silent_p.D235D|ALOX15B_ENST00000380173.2_Silent_p.D235D	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	235	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)	p.D235D(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						GGCAGGAGGACGCCTTCTTCG	0.617													T|||	2991	0.597244	0.8699	0.5403	5008	,	,		12415	0.4087		0.4404	False		,,,				2504	0.6247				p.D235D		Atlas-SNP	.											ALOX15B,NS,carcinoma,0,1	ALOX15B	66	1	1	Substitution - coding silent(1)	stomach(1)	c.C705T						PASS	.	T	,,	3486,920	351.6+/-311.3	1380,726,97	94.0	63.0	73.0		705,705,705	-4.8	0.2	17	dbSNP_116	73	3723,4877	616.5+/-396.5	817,2089,1394	no	coding-synonymous,coding-synonymous,coding-synonymous	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	,,	2197,2815,1491	TT,TC,CC		43.2907,20.8806,44.5717	,,	235/648,235/603,235/677	7948175	7209,5797	2203	4300	6503	SO:0001819	synonymous_variant	247	exon6			GGAGGACGCCTTC	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.705C>T	17.37:g.7948175C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	188	186	0.989362	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Silent	SNP	ENST00000380183.4	37	CCDS11128.1																																																																																			A|0.000;C|0.449;T|0.551	0.551	strong		0.617	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
NANOG	79923	hgsc.bcm.edu	37	12	7945757	7945757	+	Silent	SNP	C	C	T	rs4438116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7945757C>T	ENST00000229307.4	+	2	582	c.363C>T	c.(361-363)agC>agT	p.S121S	NANOG_ENST00000526286.1_Silent_p.S121S	NM_024865.2	NP_079141.2	Q9H9S0	NANOG_HUMAN	Nanog homeobox	121					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|embryo development (GO:0009790)|embryonic pattern specification (GO:0009880)|endodermal cell fate specification (GO:0001714)|gonad development (GO:0008406)|mesodermal cell fate commitment (GO:0001710)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|response to retinoic acid (GO:0032526)|somatic stem cell maintenance (GO:0035019)|stem cell division (GO:0017145)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	14				Kidney(36;0.0872)		AATACCTCAGCCTCCAGCAGA	0.438													C|||	804	0.160543	0.1384	0.1787	5008	,	,		-128	0.006		0.3151	False		,,,				2504	0.1779				p.S121S		Atlas-SNP	.											.	NANOG	30	.	0			c.C363T						PASS	.	C		705,3665		61,583,1541	26.0	24.0	24.0		363	-1.3	1.0	12	dbSNP_111	24	2295,6121		325,1645,2238	no	coding-synonymous	NANOG	NM_024865.2		386,2228,3779	TT,TC,CC		27.2695,16.1327,23.4632		121/306	7945757	3000,9786	2185	4208	6393	SO:0001819	synonymous_variant	79923	exon2			CCTCAGCCTCCAG	AB093576	CCDS31736.1, CCDS73436.1	12p13.31	2011-06-20			ENSG00000111704	ENSG00000111704		"""Homeoboxes / ANTP class : NKL subclass"""	20857	protein-coding gene	gene with protein product		607937				12787505, 12787504	Standard	XM_005253484		Approved	FLJ12581, FLJ40451	uc009zfy.1	Q9H9S0		ENST00000229307.4:c.363C>T	12.37:g.7945757C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	175	77	0.44	NM_024865	D3DUU4|Q2TTG0|Q6JZS5	Silent	SNP	ENST00000229307.4	37	CCDS31736.1																																																																																			.	.	weak		0.438	NANOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387480.2	NM_024865	
LTF	4057	hgsc.bcm.edu	37	3	46501268	46501268	+	Missense_Mutation	SNP	C	C	T	rs1126477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46501268C>T	ENST00000231751.4	-	2	380	c.85G>A	c.(85-87)Gcc>Acc	p.A29T	LTF_ENST00000426532.2_5'UTR|LTF_ENST00000417439.1_Missense_Mutation_p.A29T	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	29	Bactericidal and antifungal activity.|Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.		A -> T (in dbSNP:rs1126477). {ECO:0000269|PubMed:11702692, ECO:0000269|PubMed:14573629, ECO:0000269|PubMed:22900286, ECO:0000269|PubMed:9873069, ECO:0000269|Ref.11, ECO:0000269|Ref.8, 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)		TGGGATACGGCGCACCACTGA	0.567													T|||	2352	0.469649	0.7693	0.4207	5008	,	,		17311	0.4167		0.2614	False		,,,				2504	0.3681				p.A29T		Atlas-SNP	.											LTF,NS,carcinoma,+2,1	LTF	98	1	0			c.G85A						scavenged	.	T	,THR/ALA	3066,1340	448.5+/-348.7	1065,936,202	106.0	87.0	93.0		,85	-3.6	0.0	3	dbSNP_86	93	2095,6505	717.1+/-406.1	255,1585,2460	yes	utr-5,missense	LTF	NM_001199149.1,NM_002343.3	,58	1320,2521,2662	TT,TC,CC		24.3605,30.4131,39.6817	,benign	,29/711	46501268	5161,7845	2203	4300	6503	SO:0001583	missense	4057	exon2			ATACGGCGCACCA		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.85G>A	3.37:g.46501268C>T	ENSP00000231751:p.Ala29Thr	Somatic	189	2	0.010582		WXS	Illumina HiSeq	Phase_I	205	107	0.521951	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	938	0.42948717948717946	363	0.7378048780487805	149	0.4116022099447514	229	0.40034965034965037	197	0.2598944591029024	T	0.357	-0.941430	0.02322	0.695869	0.243605	ENSG00000012223	ENST00000231751;ENST00000417439;ENST00000443496;ENST00000443743;ENST00000431944	T;T;T;T	0.34072	2.51;2.51;2.51;1.38	4.32	-3.58	0.04597	.	0.666605	0.15394	N	0.264678	T	0.00012	0.0000	N	0.04880	-0.145	0.58432	P	1.999999999946489E-6	B;B;B	0.16396	0.004;0.017;0.004	B;B;B	0.14023	0.006;0.01;0.006	T	0.34601	-0.9822	9	0.02654	T	1	-2.9129	12.8044	0.57605	0.0:0.4849:0.0:0.5151	rs1126477;rs3181524;rs4683233;rs11556844;rs17413032;rs52792663;rs57054226;rs1126477	29;16;29	E7ER44;E7EQB2;P02788	.;.;TRFL_HUMAN	T	29;29;16;29;40	ENSP00000231751:A29T;ENSP00000405546:A29T;ENSP00000397427:A16T;ENSP00000395234:A40T	ENSP00000231751:A29T	A	-	1	0	LTF	46476272	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.679000	0.01940	-1.497000	0.01826	-3.360000	0.00041	GCC	C|0.578;T|0.421	0.421	strong		0.567	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
KIAA1683	80726	hgsc.bcm.edu	37	19	18368524	18368524	+	Silent	SNP	C	C	T	rs61740686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18368524C>T	ENST00000600328.3	-	4	3202	c.3009G>A	c.(3007-3009)acG>acA	p.T1003T	KIAA1683_ENST00000600359.3_Silent_p.T957T|PDE4C_ENST00000596647.1_5'Flank|KIAA1683_ENST00000392413.4_Silent_p.T1190T|PDE4C_ENST00000355502.3_5'Flank			Q9H0B3	K1683_HUMAN	KIAA1683	1003						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GCTCCACCCACGTGACGGGGT	0.662													C|||	170	0.0339457	0.1248	0.0072	5008	,	,		15480	0.0		0.0	False		,,,				2504	0.0				p.T1190T		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G3570A						PASS	.	C	,,	427,3903		12,403,1750	23.0	30.0	28.0		3570,2871,3009	-2.8	0.0	19	dbSNP_129	28	0,8468		0,0,4234	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	12,403,5984	TT,TC,CC		0.0,9.8614,3.3365	,,	1190/1368,957/1135,1003/1181	18368524	427,12371	2165	4234	6399	SO:0001819	synonymous_variant	80726	exon4			CACCCACGTGACG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.3009G>A	19.37:g.18368524C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			C|0.964;T|0.036	0.036	strong		0.662	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
DNAJC21	134218	hgsc.bcm.edu	37	5	34937649	34937649	+	Silent	SNP	G	G	A	rs77480286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34937649G>A	ENST00000342382.4	+	5	884	c.657G>A	c.(655-657)gcG>gcA	p.A219A	DNAJC21_ENST00000303525.7_Silent_p.A219A|DNAJC21_ENST00000382021.2_Silent_p.A219A			Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21	219					protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A219A(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			GAGTGCAGGCGCATCGAAAAC	0.478													G|||	41	0.0081869	0.0303	0.0014	5008	,	,		18843	0.0		0.0	False		,,,				2504	0.0				p.A219A		Atlas-SNP	.											DNAJC21,caecum,carcinoma,0,1	DNAJC21	54	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G657A						PASS	.	G	,	68,4338	61.1+/-98.1	1,66,2136	77.0	85.0	82.0		657,657	-11.1	0.0	5	dbSNP_132	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	DNAJC21	NM_001012339.2,NM_194283.3	,	1,68,6434	AA,AG,GG		0.0233,1.5433,0.5382	,	219/532,219/577	34937649	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	134218	exon5			GCAGGCGCATCGA		CCDS3907.2, CCDS34144.1	5p13-p12	2012-10-05			ENSG00000168724	ENSG00000168724		"""Heat shock proteins / DNAJ (HSP40)"""	27030	protein-coding gene	gene with protein product	"""JJJ1 DnaJ domain protein homolog (S. cerevisiae)"""					15067379	Standard	XM_005248250		Approved	GS3, DNAJA5, JJJ1	uc003jjc.3	Q5F1R6	OTTHUMG00000074103	ENST00000342382.4:c.657G>A	5.37:g.34937649G>A		Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	228	108	0.473684	NM_001012339	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	Silent	SNP	ENST00000342382.4	37	CCDS34144.1																																																																																			G|0.992;A|0.008	0.008	strong		0.478	DNAJC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157337.1	NM_194283	
MROH9	80133	hgsc.bcm.edu	37	1	170965681	170965681	+	Silent	SNP	T	T	C	rs9427213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:170965681T>C	ENST00000367758.3	+	14	1470	c.1371T>C	c.(1369-1371)aaT>aaC	p.N457N	MROH9_ENST00000367759.4_Silent_p.N457N	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	457																	TTCTGCTGAATTGTTCTGGAC	0.413													T|||	626	0.125	0.2405	0.1369	5008	,	,		18557	0.0		0.1382	False		,,,				2504	0.0757				p.N457N		Atlas-SNP	.											.	.	.	.	0			c.T1371C						PASS	.	T	,	764,2988		86,592,1198	153.0	147.0	149.0		1371,1371	-0.6	0.9	1	dbSNP_119	149	951,7273		57,837,3218	no	coding-synonymous,coding-synonymous	C1orf129	NM_001163629.1,NM_025063.2	,	143,1429,4416	CC,CT,TT		11.5637,20.3625,14.3203	,	457/862,457/574	170965681	1715,10261	1876	4112	5988	SO:0001819	synonymous_variant	80133	exon14			GCTGAATTGTTCT	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.1371T>C	1.37:g.170965681T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	233	110	0.472103	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Silent	SNP	ENST00000367758.3	37	CCDS41436.1																																																																																			T|0.882;C|0.118	0.118	strong		0.413	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
CTRL	1506	hgsc.bcm.edu	37	16	67964203	67964203	+	Missense_Mutation	SNP	T	T	C	rs1134760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67964203T>C	ENST00000574481.1	-	6	1079	c.518A>G	c.(517-519)cAt>cGt	p.H173R	CTRL_ENST00000576408.1_5'Flank	NM_001907.2	NP_001898.1	P40313	CTRL_HUMAN	chymotrypsin-like	173	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		H -> R (in dbSNP:rs1134760).		digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|urinary_tract(1)	4		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		CTGCTGCAGATGTGCTGGTGT	0.612													C|||	1331	0.265775	0.4962	0.2277	5008	,	,		18645	0.0972		0.1829	False		,,,				2504	0.2403				p.H173R		Atlas-SNP	.											.	CTRL	11	.	0			c.A518G						PASS	.	C	ARG/HIS	2040,2356	605.6+/-390.6	476,1088,634	53.0	50.0	51.0		518	-1.8	0.0	16	dbSNP_86	51	1517,7083	742.6+/-407.2	165,1187,2948	yes	missense	CTRL	NM_001907.2	29	641,2275,3582	CC,CT,TT		17.6395,46.4058,27.37	benign	173/265	67964203	3557,9439	2198	4300	6498	SO:0001583	missense	1506	exon6			TGCAGATGTGCTG		CCDS10852.1	16q22.1	2008-02-05			ENSG00000141086	ENSG00000141086			2524	protein-coding gene	gene with protein product		118888				8268911	Standard	NM_001907		Approved		uc002euw.3	P40313	OTTHUMG00000137552	ENST00000574481.1:c.518A>G	16.37:g.67964203T>C	ENSP00000458537:p.His173Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_001907		Missense_Mutation	SNP	ENST00000574481.1	37	CCDS10852.1	546	0.25	255	0.5182926829268293	85	0.23480662983425415	69	0.12062937062937062	137	0.18073878627968337	C	15.21	2.766588	0.49574	0.464058	0.176395	ENSG00000141086	ENST00000319955	.	.	.	5.77	-1.81	0.07882	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.533087	0.20532	N	0.090498	T	0.00012	0.0000	N	0.04787	-0.16	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45745	-0.9240	8	0.19147	T	0.46	-7.6426	0.634	0.00799	0.202:0.2804:0.2516:0.266	rs1134760;rs2301246;rs3178755;rs3197102;rs11552952;rs16957618;rs16957622;rs61279753;rs1134760	173	P40313	CTRL_HUMAN	R	173	.	ENSP00000322629:H173R	H	-	2	0	CTRL	66521704	0.000000	0.05858	0.000000	0.03702	0.939000	0.58152	-1.500000	0.02283	-0.128000	0.11641	-0.186000	0.12905	CAT	T|0.738;C|0.262	0.262	strong		0.612	CTRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268886.3		
ADARB1	104	hgsc.bcm.edu	37	21	46641968	46641968	+	Silent	SNP	G	G	A	rs1051367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46641968G>A	ENST00000360697.3	+	10	2097	c.2082G>A	c.(2080-2082)aaG>aaA	p.K694K	ADARB1_ENST00000389863.4_Silent_p.K694K|ADARB1_ENST00000437626.1_3'UTR|ADARB1_ENST00000348831.4_Silent_p.K654K|ADARB1_ENST00000539173.1_Silent_p.K694K			P78563	RED1_HUMAN	adenosine deaminase, RNA-specific, B1	694	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|positive regulation of viral genome replication (GO:0045070)|regulation of cell cycle (GO:0051726)|RNA processing (GO:0006396)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA adenosine deaminase activity (GO:0003726)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(1)	17				Colorectal(79;0.115)		AGATTACCAAGCCCAACGTGT	0.527													G|||	2474	0.49401	0.3979	0.464	5008	,	,		18691	0.5595		0.5606	False		,,,				2504	0.5092				p.K694K		Atlas-SNP	.											.	ADARB1	81	.	0			c.G2082A						PASS	.	G	,,,	1879,2527	538.1+/-374.9	411,1057,735	67.0	60.0	62.0		1962,1962,2082,2082	-2.6	0.4	21	dbSNP_86	62	4583,4015	597.1+/-393.7	1271,2041,987	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADARB1	NM_001112.3,NM_001160230.1,NM_015833.3,NM_015834.3	,,,	1682,3098,1722	AA,AG,GG		46.6969,42.6464,49.6924	,,,	654/702,654/675,694/742,694/715	46641968	6462,6542	2203	4299	6502	SO:0001819	synonymous_variant	104	exon12			TACCAAGCCCAAC	U76420	CCDS33589.1, CCDS33590.1, CCDS42970.1	21q22.3	2012-03-22	2010-06-24		ENSG00000197381	ENSG00000197381	3.5.-.-		226	protein-coding gene	gene with protein product	"""RED1 homolog (rat)"""	601218	"""adenosine deaminase, RNA-specific, B1 (homolog of rat RED1)"""			9143496, 14759252	Standard	NR_027672		Approved	ADAR2, DRADA2, ADAR2g, DRABA2, RED1, hRED1, ADAR2a-L1, ADAR2a-L2, ADAR2a-L3, ADAR2a, ADAR2b, ADAR2c, ADAR2d	uc002zgy.2	P78563	OTTHUMG00000090295	ENST00000360697.3:c.2082G>A	21.37:g.46641968G>A		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	268	129	0.481343	NM_015834	A6NFK8|A6NJ84|C3TTQ1|C3TTQ2|C9JUP4|G5E9B4|O00395|O00465|O00691|O00692|P78555|Q4AE79|Q6P0M9|Q8NFD1	Silent	SNP	ENST00000360697.3	37	CCDS33589.1	1164	0.532967032967033	211	0.42886178861788615	173	0.47790055248618785	334	0.583916083916084	446	0.5883905013192612	G	3.092	-0.186757	0.06340	0.426464	0.533031	ENSG00000197381	ENST00000539917	.	.	.	5.05	-2.64	0.06114	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999990447	.	.	.	.	.	.	T	0.42582	-0.9443	4	0.26408	T	0.33	-38.1517	11.1863	0.48657	0.6426:0.0:0.3574:0.0	rs1051367;rs2228610;rs3191756;rs10451782;rs17417312;rs58045464;rs10451782	.	.	.	T	694	.	ENSP00000445318:A694T	A	+	1	0	ADARB1	45466396	1.000000	0.71417	0.362000	0.25862	0.336000	0.28762	0.686000	0.25392	-0.532000	0.06332	-0.768000	0.03414	GCC	G|0.494;A|0.506	0.506	strong		0.527	ADARB1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206648.2	NM_015833	
GPR182	11318	hgsc.bcm.edu	37	12	57389536	57389536	+	Silent	SNP	G	G	A	rs61740222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57389536G>A	ENST00000300098.1	+	2	762	c.543G>A	c.(541-543)tcG>tcA	p.S181S	HBCBP_ENST00000600202.1_5'Flank|RP11-474N8.5_ENST00000556850.1_RNA	NM_007264.3	NP_009195.1	O15218	GP182_HUMAN	G protein-coupled receptor 182	181					cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	15						GGGTCCTCTCGGCCATCATCC	0.642													G|||	65	0.0129792	0.0492	0.0	5008	,	,		19981	0.0		0.0	False		,,,				2504	0.0				p.S181S		Atlas-SNP	.											.	GPR182	35	.	0			c.G543A						PASS	.	G		158,4248	106.5+/-144.9	2,154,2047	61.0	53.0	56.0		543	-8.9	0.1	12	dbSNP_129	56	2,8598		0,2,4298	no	coding-synonymous	GPR182	NM_007264.3		2,156,6345	AA,AG,GG		0.0233,3.586,1.2302		181/405	57389536	160,12846	2203	4300	6503	SO:0001819	synonymous_variant	11318	exon2			CCTCTCGGCCATC	Y13583	CCDS8927.1	12q13.3	2012-08-21	2007-09-24	2007-09-24		ENSG00000166856		"""GPCR / Class A : Orphans"""	13708	protein-coding gene	gene with protein product		605307	"""adrenomedullin receptor"""	ADMR		9367907, 9535752	Standard	NM_007264		Approved	hrhAMR, G10D, AM-R	uc001smk.3	O15218		ENST00000300098.1:c.543G>A	12.37:g.57389536G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_007264		Silent	SNP	ENST00000300098.1	37	CCDS8927.1																																																																																			G|0.987;A|0.013	0.013	strong		0.642	GPR182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411212.1	NM_007264	
FNDC3B	64778	hgsc.bcm.edu	37	3	171969312	171969312	+	Silent	SNP	G	G	C	rs34553291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:171969312G>C	ENST00000336824.4	+	6	870	c.771G>C	c.(769-771)tcG>tcC	p.S257S	FNDC3B_ENST00000416957.1_Silent_p.S257S|FNDC3B_ENST00000415807.2_Silent_p.S257S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	257					cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		GCCCAAAGTCGAATGATTCAG	0.468													G|||	28	0.00559105	0.0212	0.0	5008	,	,		17937	0.0		0.0	False		,,,				2504	0.0				p.S257S		Atlas-SNP	.											FNDC3B,rectum,carcinoma,+1,1	FNDC3B	118	1	0			c.G771C						PASS	.	G	,	92,4314	75.7+/-113.9	0,92,2111	69.0	71.0	70.0		771,771	-7.6	0.1	3	dbSNP_126	70	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FNDC3B	NM_001135095.1,NM_022763.3	,	0,92,6411	CC,CG,GG		0.0,2.0881,0.7074	,	257/1205,257/1205	171969312	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	64778	exon6			AAAGTCGAATGAT	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.771G>C	3.37:g.171969312G>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																			G|0.993;C|0.007	0.007	strong		0.468	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
INSL4	3641	hgsc.bcm.edu	37	9	5233664	5233664	+	Silent	SNP	A	A	G	rs7030463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5233664A>G	ENST00000239316.4	+	2	312	c.207A>G	c.(205-207)tcA>tcG	p.S69S		NM_002195.1	NP_002186.1	Q14641	INSL4_HUMAN	insulin-like 4 (placenta)	69					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)		AAATGGTGTCAACCTCCAACA	0.398													A|||	163	0.0325479	0.121	0.0043	5008	,	,		21594	0.0		0.0	False		,,,				2504	0.0				p.S69S		Atlas-SNP	.											INSL4,right_upper_lobe,carcinoma,+2,1	INSL4	20	1	0			c.A207G						PASS	.	A		394,4012	197.4+/-221.5	15,364,1824	62.0	58.0	59.0		207	1.8	0.3	9	dbSNP_116	59	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	INSL4	NM_002195.1		15,366,6122	GG,GA,AA		0.0233,8.9424,3.0447		69/140	5233664	396,12610	2203	4300	6503	SO:0001819	synonymous_variant	3641	exon2			GGTGTCAACCTCC		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.207A>G	9.37:g.5233664A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_002195	A8K678|Q5W127	Silent	SNP	ENST00000239316.4	37	CCDS6459.1																																																																																			A|0.967;G|0.033	0.033	strong		0.398	INSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051616.2	NM_002195	
NXN	64359	hgsc.bcm.edu	37	17	706933	706933	+	Missense_Mutation	SNP	C	C	T	rs61731770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:706933C>T	ENST00000336868.3	-	7	1205	c.1114G>A	c.(1114-1116)Gta>Ata	p.V372I	NXN_ENST00000538650.1_Missense_Mutation_p.V63I|NXN_ENST00000575801.1_Missense_Mutation_p.V264I|NXN_ENST00000537628.2_Missense_Mutation_p.V123I	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	372				V -> I (in Ref. 4; AAH73845). {ECO:0000305}.	cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		TCCCCGGCTACGAAGAACAGA	0.602													c|||	110	0.0219649	0.0787	0.0043	5008	,	,		17906	0.0		0.003	False		,,,				2504	0.0				p.V372I		Atlas-SNP	.											.	NXN	32	.	0			c.G1114A						PASS	.	C	ILE/VAL,ILE/VAL	328,4078	173.4+/-203.2	20,288,1895	102.0	100.0	101.0		790,1114	5.3	1.0	17	dbSNP_129	101	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	NXN	NM_001205319.1,NM_022463.4	29,29	20,299,6184	TT,TC,CC		0.1279,7.4444,2.6065	benign,benign	264/328,372/436	706933	339,12667	2203	4300	6503	SO:0001583	missense	64359	exon7			CGGCTACGAAGAA		CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693			18008	protein-coding gene	gene with protein product		612895					Standard	NM_022463		Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.1114G>A	17.37:g.706933C>T	ENSP00000337443:p.Val372Ile	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	88	52	0.590909	NM_022463	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	Missense_Mutation	SNP	ENST00000336868.3	37	CCDS10998.1	42	0.019230769230769232	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	13.45	2.239485	0.39598	0.074444	0.001279	ENSG00000167693	ENST00000336868;ENST00000538650;ENST00000537628	T;T	0.28454	1.61;2.57	5.26	5.26	0.73747	Thioredoxin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.02727	0.0082	L	0.28274	0.84	0.58432	D	0.999996	D;D;D	0.76494	0.999;0.981;0.992	D;P;P	0.74674	0.984;0.899;0.834	T	0.00883	-1.1528	10	0.15952	T	0.53	-19.0247	17.8205	0.88649	0.0:1.0:0.0:0.0	.	264;63;372	B4DXQ0;B4DNN6;Q6DKJ4	.;.;NXN_HUMAN	I	372;63;264	ENSP00000337443:V372I;ENSP00000445087:V63I	ENSP00000337443:V372I	V	-	1	0	NXN	653683	1.000000	0.71417	0.983000	0.44433	0.246000	0.25737	4.470000	0.60175	2.635000	0.89317	0.655000	0.94253	GTA	C|0.977;T|0.023	0.023	strong		0.602	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206669.1		
VSIG10	54621	hgsc.bcm.edu	37	12	118520170	118520170	+	Silent	SNP	G	G	A	rs7488309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:118520170G>A	ENST00000359236.5	-	3	702	c.426C>T	c.(424-426)taC>taT	p.Y142Y	VSIG10_ENST00000536905.1_5'UTR	NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	142	Ig-like C2-type 2.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						CCCTGGCTGCGTAGAGGGTGC	0.607													G|||	2320	0.463259	0.4705	0.5908	5008	,	,		15185	0.5903		0.4115	False		,,,				2504	0.2853				p.Y142Y		Atlas-SNP	.											VSIG10,colon,carcinoma,0,1	VSIG10	41	1	0			c.C426T						PASS	.	G		1665,2219		373,919,650	66.0	72.0	70.0		426	-4.7	0.0	12	dbSNP_116	70	3382,4882		685,2012,1435	no	coding-synonymous	VSIG10	NM_019086.5		1058,2931,2085	AA,AG,GG		40.9245,42.8682,41.5459		142/541	118520170	5047,7101	1942	4132	6074	SO:0001819	synonymous_variant	54621	exon3			GGCTGCGTAGAGG		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.426C>T	12.37:g.118520170G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	163	59	0.361963	NM_019086	Q9NWQ7	Silent	SNP	ENST00000359236.5	37	CCDS44992.1																																																																																			G|0.506;A|0.494	0.494	strong		0.607	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
PTX4	390667	hgsc.bcm.edu	37	16	1536357	1536357	+	Silent	SNP	G	G	A	rs112226694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536357G>A	ENST00000447419.2	-	3	1045	c.1020C>T	c.(1018-1020)ttC>ttT	p.F340F	PTX4_ENST00000293922.1_Silent_p.F335F|PTX4_ENST00000440447.2_Missense_Mutation_p.S192L			Q96A99	PTX4_HUMAN	pentraxin 4, long	340	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						CCCCGATCACGAAGTGGATGG	0.662													G|||	88	0.0175719	0.0651	0.0029	5008	,	,		16575	0.0		0.0	False		,,,				2504	0.0				p.F335F		Atlas-SNP	.											.	PTX4	46	.	0			c.C1005T						PASS	.	G		251,4147	138.8+/-174.5	4,243,1952	42.0	50.0	47.0		1005	-11.2	0.2	16	dbSNP_132	47	0,8600		0,0,4300	no	coding-synonymous	PTX4	NM_001013658.1		4,243,6252	AA,AG,GG		0.0,5.7071,1.9311		335/474	1536357	251,12747	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GATCACGAAGTGG		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.1020C>T	16.37:g.1536357G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				G|0.979;A|0.021	0.021	strong		0.662	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
CALHM2	51063	hgsc.bcm.edu	37	10	105207176	105207176	+	Silent	SNP	G	G	A	rs2232663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105207176G>A	ENST00000260743.5	-	4	1228	c.705C>T	c.(703-705)gcC>gcT	p.A235A	CALHM2_ENST00000369788.3_Silent_p.A235A|CALHM2_ENST00000494180.1_5'Flank|RP11-225H22.7_ENST00000608063.1_RNA	NM_015916.4	NP_057000.2	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	235					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|skin(1)	11						AGTGCACCTCGGCCGTGCGCT	0.597													G|||	370	0.0738818	0.2663	0.0216	5008	,	,		20251	0.0		0.003	False		,,,				2504	0.0				p.A235A		Atlas-SNP	.											.	CALHM2	30	.	0			c.C705T						PASS	.	G		896,3510	345.7+/-308.6	84,728,1391	67.0	61.0	63.0		705	-8.1	0.7	10	dbSNP_98	63	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	CALHM2	NM_015916.4		84,755,5664	AA,AG,GG		0.314,20.3359,7.0967		235/324	105207176	923,12083	2203	4300	6503	SO:0001819	synonymous_variant	51063	exon4			CACCTCGGCCGTG	BC000039	CCDS7549.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000138172	ENSG00000138172			23493	protein-coding gene	gene with protein product		612235	"""family with sequence similarity 26, member B"""	FAM26B		18585350	Standard	NM_015916		Approved		uc001kxa.3	Q9HA72	OTTHUMG00000018990	ENST00000260743.5:c.705C>T	10.37:g.105207176G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_015916	D3DR94|O95893|Q6ZUV9	Silent	SNP	ENST00000260743.5	37	CCDS7549.1																																																																																			G|0.925;A|0.075	0.075	strong		0.597	CALHM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050159.1	NM_015916	
NUMA1	4926	hgsc.bcm.edu	37	11	71725612	71725612	+	Silent	SNP	A	A	G	rs142372284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71725612A>G	ENST00000393695.3	-	15	3268	c.2937T>C	c.(2935-2937)aaT>aaC	p.N979N	NUMA1_ENST00000358965.6_Silent_p.N979N|RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000351960.6_Intron	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						GTTCCAGCTCATTGCCCATCT	0.672			T	RARA	APL								A|||	14	0.00279553	0.0106	0.0	5008	,	,		17846	0.0		0.0	False		,,,				2504	0.0				p.N979N		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.T2937C						PASS	.	A		71,4329	59.3+/-96.0	1,69,2130	66.0	73.0	71.0		2937	-6.0	0.9	11	dbSNP_134	71	0,8586		0,0,4293	no	coding-synonymous	NUMA1	NM_006185.2		1,69,6423	GG,GA,AA		0.0,1.6136,0.5467		979/2116	71725612	71,12915	2200	4293	6493	SO:0001819	synonymous_variant	4926	exon15			CAGCTCATTGCCC	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.2937T>C	11.37:g.71725612A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																			A|0.995;G|0.005	0.005	strong		0.672	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
SERPINB12	89777	hgsc.bcm.edu	37	18	61234091	61234091	+	Silent	SNP	C	C	T	rs35623491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61234091C>T	ENST00000269491.1	+	7	1065	c.1065C>T	c.(1063-1065)aaC>aaT	p.N355N	SERPINB12_ENST00000382768.1_Silent_p.N375N	NM_080474.1	NP_536722.1	Q96P63	SPB12_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 12	355					hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of protein catabolic process (GO:0042177)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(5)|lung(19)|skin(1)	26						TGGATGAAAACGGTACCCAGG	0.453													C|||	184	0.0367412	0.1316	0.0101	5008	,	,		20333	0.0		0.003	False		,,,				2504	0.0				p.N355N		Atlas-SNP	.											.	SERPINB12	55	.	0			c.C1065T						PASS	.	C		482,3924	226.2+/-241.8	30,422,1751	78.0	82.0	80.0		1065	-4.4	0.1	18	dbSNP_126	80	1,8599		0,1,4299	no	coding-synonymous	SERPINB12	NM_080474.1		30,423,6050	TT,TC,CC		0.0116,10.9396,3.7137		355/406	61234091	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	89777	exon7			TGAAAACGGTACC	AF411191	CCDS11984.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166634	ENSG00000166634		"""Serine (or cysteine) peptidase inhibitors"""	14220	protein-coding gene	gene with protein product		615662	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 12"""			24172014	Standard	NM_080474		Approved	YUKOPIN	uc010xen.2	Q96P63	OTTHUMG00000132789	ENST00000269491.1:c.1065C>T	18.37:g.61234091C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_080474	Q3SYB4	Silent	SNP	ENST00000269491.1	37	CCDS11984.1																																																																																			C|0.962;T|0.038	0.038	strong		0.453	SERPINB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256197.1	NM_080474	
DNAH2	146754	hgsc.bcm.edu	37	17	7722048	7722048	+	Missense_Mutation	SNP	G	G	A	rs61743907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7722048G>A	ENST00000572933.1	+	70	12084	c.10624G>A	c.(10624-10626)Gcg>Acg	p.A3542T	DNAH2_ENST00000389173.2_Missense_Mutation_p.A3542T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3542	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(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)				CATCAACATCGCGGCTGGTAA	0.642													G|||	52	0.0103834	0.0363	0.0058	5008	,	,		20147	0.0		0.0	False		,,,				2504	0.0				p.A3542T		Atlas-SNP	.											.	DNAH2	498	.	0			c.G10624A						PASS	.	G	THR/ALA	146,4260	102.5+/-141.1	2,142,2059	119.0	107.0	111.0		10624	3.4	0.1	17	dbSNP_129	111	0,8600		0,0,4300	yes	missense	DNAH2	NM_020877.2	58	2,142,6359	AA,AG,GG		0.0,3.3137,1.1226	probably-damaging	3542/4428	7722048	146,12860	2203	4300	6503	SO:0001583	missense	146754	exon69			AACATCGCGGCTG	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.10624G>A	17.37:g.7722048G>A	ENSP00000458355:p.Ala3542Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	21.0	4.082529	0.76528	0.033137	0.0	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.22134	1.97	4.34	3.38	0.38709	.	0.000000	0.85682	D	0.000000	T	0.09468	0.0233	M	0.65498	2.005	0.80722	D	1	P;P	0.42735	0.749;0.788	B;P	0.44422	0.321;0.449	T	0.01702	-1.1292	10	0.22706	T	0.39	.	11.1468	0.48434	0.0914:0.0:0.9086:0.0	rs61743907	3503;3542	Q9P225-2;Q9P225	.;DYH2_HUMAN	T	3503;3542	ENSP00000373825:A3542T	ENSP00000353818:A3503T	A	+	1	0	DNAH2	7662773	1.000000	0.71417	0.117000	0.21633	0.933000	0.57130	5.115000	0.64655	1.045000	0.40225	0.563000	0.77884	GCG	G|0.989;A|0.011	0.011	strong		0.642	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
ZACN	353174	hgsc.bcm.edu	37	17	74076504	74076504	+	Splice_Site	SNP	G	G	A	rs8066946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74076504G>A	ENST00000334586.5	+	5	626	c.543G>A	c.(541-543)acG>acA	p.T181T	EXOC7_ENST00000591724.1_5'Flank|ZACN_ENST00000392503.2_Intron	NM_180990.3	NP_851321.2	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel	181					ion transmembrane transport (GO:0034220)|response to zinc ion (GO:0010043)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)|ligand-gated ion channel activity (GO:0015276)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	11						TCAGCAACACGGGTGCTGACA	0.657													G|||	424	0.0846645	0.3033	0.0331	5008	,	,		16820	0.0		0.0	False		,,,				2504	0.0				p.T181T		Atlas-SNP	.											.	ZACN	29	.	0			c.G543A						PASS	.	G		1144,3262	398.3+/-330.8	151,842,1210	61.0	56.0	58.0		543	-5.2	0.9	17	dbSNP_116	58	20,8580	11.9+/-42.8	0,20,4280	yes	coding-synonymous-near-splice	ZACN	NM_180990.3		151,862,5490	AA,AG,GG		0.2326,25.9646,8.9497		181/413	74076504	1164,11842	2203	4300	6503	SO:0001630	splice_region_variant	353174	exon5			CAACACGGGTGCT	AK122638	CCDS11740.2	17q25.3	2012-01-18	2008-04-17	2008-04-17	ENSG00000186919	ENSG00000186919		"""Ligand-gated ion channels / Zinc activated channels"""	29504	protein-coding gene	gene with protein product		610935	"""ligand-gated ion channel, zinc activated 1"""	LGICZ1		12381728, 16083862	Standard	NM_180990		Approved	LGICZ, L2, ZAC, ZAC1	uc002jqn.2	Q401N2	OTTHUMG00000157186	ENST00000334586.5:c.544+1G>A	17.37:g.74076504G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	79	45	0.56962	NM_180990	Q2TB29|Q6ZWK3|Q86YW4	Silent	SNP	ENST00000334586.5	37	CCDS11740.2																																																																																			G|0.913;A|0.087	0.087	strong		0.657	ZACN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347827.2	NM_180990	Silent
CENPL	91687	hgsc.bcm.edu	37	1	173772506	173772506	+	Silent	SNP	T	T	G	rs16846420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173772506T>G	ENST00000345664.6	-	4	771	c.558A>C	c.(556-558)gcA>gcC	p.A186A	CENPL_ENST00000367710.3_Silent_p.A186A|CENPL_ENST00000356198.2_Silent_p.A232A	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	186					mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(3)	11						CTGCTCCATTTGCAAGGAATA	0.408													T|||	564	0.11262	0.4032	0.0346	5008	,	,		19168	0.0		0.007	False		,,,				2504	0.0				p.A232A		Atlas-SNP	.											.	CENPL	26	.	0			c.A696C						PASS	.	T	,,	1339,3067	438.4+/-345.3	198,943,1062	104.0	114.0	111.0		696,558,558	5.0	1.0	1	dbSNP_123	111	31,8569	18.5+/-59.3	0,31,4269	no	coding-synonymous,coding-synonymous,coding-synonymous	CENPL	NM_001127181.2,NM_001171182.1,NM_033319.3	,,	198,974,5331	GG,GT,TT		0.3605,30.3904,10.5336	,,	232/391,186/345,186/345	173772506	1370,11636	2203	4300	6503	SO:0001819	synonymous_variant	91687	exon6			TCCATTTGCAAGG	BC033154, BC019022, AK055606	CCDS30938.1, CCDS44277.1	1q25.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000120334	ENSG00000120334			17879	protein-coding gene	gene with protein product		611503	"""chromosome 1 open reading frame 155"""	C1orf155		16622420, 16622419	Standard	NM_033319		Approved	dJ383J4.3, FLJ31044	uc001gje.4	Q8N0S6	OTTHUMG00000034802	ENST00000345664.6:c.558A>C	1.37:g.173772506T>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	171	85	0.497076	NM_001127181	Q5TEL5|Q96ND4	Silent	SNP	ENST00000345664.6	37	CCDS30938.1																																																																																			T|0.876;G|0.124	0.124	strong		0.408	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319	
OR5W2	390148	hgsc.bcm.edu	37	11	55681566	55681566	+	Missense_Mutation	SNP	G	G	A	rs61749302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55681566G>A	ENST00000344514.1	-	1	492	c.493C>T	c.(493-495)Cgc>Tgc	p.R165C		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	165						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R165C(1)		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						AAGCATAGGCGGAAGGCCAGT	0.428													G|||	469	0.0936502	0.1392	0.0403	5008	,	,		21011	0.0903		0.0944	False		,,,				2504	0.0726				p.R165C	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											OR5W2,NS,carcinoma,+1,5	OR5W2	112	5	1	Substitution - Missense(1)	large_intestine(1)	c.C493T						PASS	.	G	CYS/ARG	556,3846	246.5+/-255.1	41,474,1686	87.0	77.0	80.0		493	1.5	0.0	11	dbSNP_129	80	722,7870	174.6+/-224.8	31,660,3605	yes	missense	OR5W2	NM_001001960.1	180	72,1134,5291	AA,AG,GG		8.4032,12.6306,9.8353	benign	165/311	55681566	1278,11716	2201	4296	6497	SO:0001583	missense	390148	exon1			ATAGGCGGAAGGC	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.493C>T	11.37:g.55681566G>A	ENSP00000342448:p.Arg165Cys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	210	0.09615384615384616	81	0.16463414634146342	18	0.049723756906077346	44	0.07692307692307693	67	0.08839050131926121	G	4.463	0.085831	0.08583	0.126306	0.084032	ENSG00000187612	ENST00000344514	T	0.00188	8.59	4.77	1.45	0.22620	GPCR, rhodopsin-like superfamily (1);	0.602095	0.13398	N	0.390838	T	0.00012	0.0000	L	0.58510	1.815	0.80722	P	0.0	B	0.19583	0.037	B	0.24848	0.056	T	0.15492	-1.0435	9	0.59425	D	0.04	.	5.7223	0.17995	0.1028:0.0:0.3813:0.5159	.	165	Q8NH69	OR5W2_HUMAN	C	165	ENSP00000342448:R165C	ENSP00000342448:R165C	R	-	1	0	OR5W2	55438142	0.000000	0.05858	0.033000	0.17914	0.046000	0.14306	-1.143000	0.03200	0.425000	0.26087	0.549000	0.68633	CGC	G|0.903;A|0.097	0.097	strong		0.428	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
TRMT6	51605	hgsc.bcm.edu	37	20	5923204	5923204	+	Missense_Mutation	SNP	T	T	C	rs451571|rs35671838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5923204T>C	ENST00000203001.2	-	7	1026	c.896A>G	c.(895-897)gAa>gGa	p.E299G	TRMT6_ENST00000473131.1_5'UTR|TRMT6_ENST00000453074.2_Missense_Mutation_p.E129G	NM_015939.3	NP_057023.2	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6 homolog (S. cerevisiae)	299			E -> G (in dbSNP:rs451571). {ECO:0000269|PubMed:10810093, ECO:0000269|PubMed:14702039}.		regulation of translational initiation (GO:0006446)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	15						ATTCTCTTGTTCAGAAGCCTG	0.448													T|||	1480	0.295527	0.5628	0.245	5008	,	,		20723	0.1994		0.1074	False		,,,				2504	0.2628				p.E299G		Atlas-SNP	.											.	TRMT6	28	.	0			c.A896G						PASS	.	T	GLY/GLU	2123,2283		531,1061,611	154.0	149.0	151.0		896	2.7	0.0	20	dbSNP_80	151	901,7699		55,791,3454	yes	missense	TRMT6	NM_015939.3	98	586,1852,4065	CC,CT,TT		10.4767,48.1843,23.2508	benign	299/498	5923204	3024,9982	2203	4300	6503	SO:0001583	missense	51605	exon7			TCTTGTTCAGAAG	AK000613	CCDS13093.1, CCDS63225.1	20p12.3	2009-01-12			ENSG00000089195	ENSG00000089195			20900	protein-coding gene	gene with protein product						16043508	Standard	NM_001281467		Approved	GCD10, MGC5029, Gcd10p, CGI-09	uc002wmh.1	Q9UJA5	OTTHUMG00000031816	ENST00000203001.2:c.896A>G	20.37:g.5923204T>C	ENSP00000203001:p.Glu299Gly	Somatic	360	2	0.00555556		WXS	Illumina HiSeq	Phase_I	342	341	0.997076	NM_015939	B4DUV6|Q76P92|Q9BQV5|Q9ULR7|Q9Y2Z8	Missense_Mutation	SNP	ENST00000203001.2	37	CCDS13093.1	414	0.18956043956043955	195	0.39634146341463417	69	0.19060773480662985	87	0.1520979020979021	63	0.08311345646437995	T	11.54	1.669608	0.29693	0.481843	0.104767	ENSG00000089195	ENST00000203001;ENST00000453074	T;T	0.25749	1.81;1.78	6.17	2.66	0.31614	.	0.698218	0.14363	N	0.324302	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.47433	-0.9118	9	0.25106	T	0.35	-21.1694	2.6528	0.05003	0.1871:0.0736:0.1922:0.5471	rs451571;rs57013611;rs451571	129;299	B4DUV6;Q9UJA5	.;TRM6_HUMAN	G	299;129	ENSP00000203001:E299G;ENSP00000392070:E129G	ENSP00000203001:E299G	E	-	2	0	TRMT6	5871204	0.005000	0.15991	0.016000	0.15963	0.980000	0.70556	1.292000	0.33342	1.152000	0.42452	0.533000	0.62120	GAA	T|0.756;C|0.244	0.244	strong		0.448	TRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077889.2		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110413806	110413806	+	Silent	SNP	G	G	A	rs200316129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110413806G>A	ENST00000378402.5	+	14	1466	c.1362G>A	c.(1360-1362)caG>caA	p.Q454Q		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	454					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.Q456Q(1)		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)			TTCATCTGCAGAAAGGAAAAG	0.313										HNSCC(38;0.096)			G|||	2	0.000399361	0.0015	0.0	5008	,	,		13925	0.0		0.0	False		,,,				2504	0.0				p.Q454Q		Atlas-SNP	.											PKHD1L1,NS,carcinoma,0,1	PKHD1L1	522	1	1	Substitution - coding silent(1)	breast(1)	c.G1362A						PASS	.	G		2,3624		0,2,1811	76.0	69.0	71.0		1362	3.4	1.0	8		71	0,8154		0,0,4077	no	coding-synonymous	PKHD1L1	NM_177531.4		0,2,5888	AA,AG,GG		0.0,0.0552,0.017		454/4244	110413806	2,11778	1813	4077	5890	SO:0001819	synonymous_variant	93035	exon14			TCTGCAGAAAGGA	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.1362G>A	8.37:g.110413806G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			G|1.000;A|0.000	0.000	strong		0.313	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
TSEN2	80746	hgsc.bcm.edu	37	3	12531421	12531421	+	Missense_Mutation	SNP	G	G	A	rs12495784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:12531421G>A	ENST00000284995.6	+	2	509	c.122G>A	c.(121-123)cGt>cAt	p.R41H	TSEN2_ENST00000402228.3_Missense_Mutation_p.R41H|TSEN2_ENST00000314571.7_Missense_Mutation_p.R41H|TSEN2_ENST00000444864.1_Missense_Mutation_p.R41H|TSEN2_ENST00000383797.5_Missense_Mutation_p.R41H|TSEN2_ENST00000454502.2_Missense_Mutation_p.R41H|TSEN2_ENST00000415684.1_Missense_Mutation_p.R41H	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	41			R -> H (in dbSNP:rs12495784).		mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						AAGATATTCCGTGCTGAAATG	0.443													G|||	470	0.0938498	0.2118	0.0865	5008	,	,		21589	0.0298		0.0239	False		,,,				2504	0.0777				p.R41H		Atlas-SNP	.											.	TSEN2	46	.	0			c.G122A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	699,3707		41,617,1545	122.0	115.0	117.0		122,122,122,122,122	-1.6	0.0	3	dbSNP_120	117	120,8480		3,114,4183	yes	missense,missense,missense,missense,missense	TSEN2	NM_001145392.1,NM_001145393.1,NM_001145394.1,NM_001145395.1,NM_025265.3	29,29,29,29,29	44,731,5728	AA,AG,GG		1.3953,15.8647,6.2971	benign,benign,benign,benign,benign	41/466,41/440,41/407,41/403,41/466	12531421	819,12187	2203	4300	6503	SO:0001583	missense	80746	exon2			TATTCCGTGCTGA	BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"""tRNA splicing endonuclease subunits"""	28422	protein-coding gene	gene with protein product		608753	"""tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)"", ""tRNA splicing endonuclease 2 homolog (S. cerevisiae)"""			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.122G>A	3.37:g.12531421G>A	ENSP00000284995:p.Arg41His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_001145394	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Missense_Mutation	SNP	ENST00000284995.6	37	CCDS2611.1	158	0.07234432234432235	106	0.21544715447154472	25	0.06906077348066299	12	0.02097902097902098	15	0.01978891820580475	.	5.732	0.319584	0.10845	0.158647	0.013953	ENSG00000154743	ENST00000446004;ENST00000314571;ENST00000454502;ENST00000383797;ENST00000402228;ENST00000284995;ENST00000444864;ENST00000537959;ENST00000415684	T;T;T;T;T;T;T;T	0.58060	0.36;0.37;0.4;0.4;0.4;0.4;0.36;0.37	5.7	-1.6	0.08426	.	0.475201	0.21511	N	0.073377	T	0.00012	0.0000	N	0.20986	0.625	0.58432	P	2.9999999999752447E-6	B;B;B;B	0.28820	0.224;0.033;0.074;0.019	B;B;B;B	0.28305	0.088;0.013;0.054;0.007	T	0.17137	-1.0379	9	0.27785	T	0.31	-1.3989	7.2163	0.25961	0.5134:0.1249:0.3617:0.0	rs12495784;rs12495784	41;41;41;41	G5E9Q3;Q8NCE0;Q8NCE0-3;C9IZI7	.;SEN2_HUMAN;.;.	H	41	ENSP00000406238:R41H;ENSP00000323188:R41H;ENSP00000392029:R41H;ENSP00000373307:R41H;ENSP00000385976:R41H;ENSP00000284995:R41H;ENSP00000407974:R41H;ENSP00000416510:R41H	ENSP00000284995:R41H	R	+	2	0	TSEN2	12506421	0.003000	0.15002	0.005000	0.12908	0.030000	0.12068	-0.176000	0.09811	-0.377000	0.07930	-1.769000	0.00663	CGT	A|0.068;G|0.932	0.068	strong		0.443	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1	NM_025265	
VCAN	1462	hgsc.bcm.edu	37	5	82833369	82833369	+	Missense_Mutation	SNP	A	A	G	rs309559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82833369A>G	ENST00000265077.3	+	8	5112	c.4547A>G	c.(4546-4548)aAa>aGa	p.K1516R	VCAN_ENST00000343200.5_Missense_Mutation_p.K529R|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1516	GAG-beta.		K -> R (in dbSNP:rs309559).		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)	GGAACAGCCAAAAAAGGGGCA	0.448													A|||	2359	0.471046	0.5113	0.5274	5008	,	,		21484	0.3919		0.5258	False		,,,				2504	0.4018				p.K1516R		Atlas-SNP	.											.	VCAN	498	.	0			c.A4547G						PASS	.	A	,ARG/LYS,,ARG/LYS	2227,2179	587.0+/-386.6	557,1113,533	70.0	69.0	69.0		,1586,,4547	2.8	0.0	5	dbSNP_79	69	4258,4342	568.8+/-389.1	1064,2130,1106	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,26,,26	1621,3243,1639	GG,GA,AA		49.5116,49.4553,49.8616	,benign,,benign	,529/2410,,1516/3397	82833369	6485,6521	2203	4300	6503	SO:0001583	missense	1462	exon8			CAGCCAAAAAAGG	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.4547A>G	5.37:g.82833369A>G	ENSP00000265077:p.Lys1516Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	1060	0.48534798534798534	236	0.4796747967479675	192	0.5303867403314917	239	0.4178321678321678	393	0.5184696569920845	A	0.215	-1.033169	0.02029	0.505447	0.495116	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.84873	-1.89;-1.91;3.24	5.96	2.79	0.32731	.	0.512905	0.19591	N	0.110638	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.16802	0.019;0.011	B;B	0.19666	0.026;0.012	T	0.44452	-0.9327	9	0.29301	T	0.29	.	9.2557	0.37581	0.114:0.6976:0.0:0.1884	rs309559;rs310476;rs560411;rs3734012;rs3909225;rs16900527;rs17284461;rs59004049;rs309559	529;1516	P13611-2;P13611	.;CSPG2_HUMAN	R	1516;529;529	ENSP00000265077:K1516R;ENSP00000340062:K529R;ENSP00000426251:K529R	ENSP00000265077:K1516R	K	+	2	0	VCAN	82869125	0.002000	0.14202	0.002000	0.10522	0.000000	0.00434	0.289000	0.18957	0.852000	0.35287	-1.027000	0.02421	AAA	T|0.003;G|0.491	0.491	strong		0.448	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
MKI67	4288	hgsc.bcm.edu	37	10	129910475	129910475	+	Missense_Mutation	SNP	T	T	G	rs997983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129910475T>G	ENST00000368654.3	-	9	2266	c.1891A>C	c.(1891-1893)Atc>Ctc	p.I631L	MKI67_ENST00000484853.1_5'UTR|MKI67_ENST00000368653.3_Missense_Mutation_p.I271L	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	631			I -> L (in dbSNP:rs997983).		cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.I631V(1)|p.I631L(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTTCGGCTGATAGACACTCTC	0.443													T|||	553	0.110423	0.093	0.1585	5008	,	,		20495	0.1359		0.0795	False		,,,				2504	0.1053				p.I631L		Atlas-SNP	.											MKI67,rectum,carcinoma,0,2	MKI67	363	2	2	Substitution - Missense(2)	large_intestine(1)|stomach(1)	c.A1891C						PASS	.	T	LEU/ILE,LEU/ILE	412,3994	203.5+/-225.9	22,368,1813	112.0	100.0	104.0		811,1891	-8.1	0.0	10	dbSNP_86	104	777,7823	184.6+/-232.5	39,699,3562	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	5,5	61,1067,5375	GG,GT,TT		9.0349,9.3509,9.1419	benign,benign	271/2897,631/3257	129910475	1189,11817	2203	4300	6503	SO:0001583	missense	4288	exon9			GGCTGATAGACAC	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.1891A>C	10.37:g.129910475T>G	ENSP00000357643:p.Ile631Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	220	0.10073260073260074	43	0.08739837398373984	40	0.11049723756906077	79	0.1381118881118881	58	0.07651715039577836	T	7.470	0.646557	0.14451	0.093509	0.090349	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01246	5.14;5.11	4.03	-8.06	0.01102	.	0.788319	0.11269	N	0.581682	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B;B;B	0.11235	0.004;0.002;0.001	B;B;B	0.11329	0.006;0.004;0.002	T	0.44726	-0.9309	9	0.25106	T	0.35	.	1.3818	0.02232	0.1695:0.3373:0.2008:0.2923	rs997983;rs17731527;rs52826393;rs58983470;rs997983	630;271;631	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	L	631;271;630;206	ENSP00000357643:I631L;ENSP00000357642:I271L	ENSP00000357641:I206L	I	-	1	0	MKI67	129800465	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.743000	0.04845	-2.155000	0.00791	-0.291000	0.09656	ATC	T|0.906;G|0.094	0.094	strong		0.443	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
PDE6A	5145	hgsc.bcm.edu	37	5	149323781	149323781	+	Silent	SNP	G	G	A	rs149256612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149323781G>A	ENST00000255266.5	-	1	575	c.456C>T	c.(454-456)aaC>aaT	p.N152N		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	152	GAF 1.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	TGTTGGGGACGTTAGCAATCT	0.562																																					p.N152N		Atlas-SNP	.											.	PDE6A	98	.	0			c.C456T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	160.0	137.0	144.0		456	2.4	1.0	5	dbSNP_134	144	0,8600		0,0,4300	no	coding-synonymous	PDE6A	NM_000440.2		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		152/861	149323781	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			GGGGACGTTAGCA		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.456C>T	5.37:g.149323781G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	66	24	0.363636	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|1.000;A|0.000	0.000	strong		0.562	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
MEGF8	1954	hgsc.bcm.edu	37	19	42874900	42874900	+	Silent	SNP	C	C	T	rs28483598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42874900C>T	ENST00000251268.6	+	40	7053	c.7053C>T	c.(7051-7053)tgC>tgT	p.C2351C	MEGF8_ENST00000378073.4_5'UTR|MEGF8_ENST00000334370.4_Silent_p.C2284C	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2351					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				AGGCCGTGTGCGTGAACTGCC	0.562													C|||	92	0.0183706	0.0635	0.0072	5008	,	,		10552	0.001		0.002	False		,,,				2504	0.0				p.C2351C		Atlas-SNP	.											.	MEGF8	358	.	0			c.C7053T						PASS	.	C		213,4191		7,199,1996	65.0	56.0	59.0		6852	-2.4	1.0	19	dbSNP_125	59	10,8586		0,10,4288	no	coding-synonymous	MEGF8	NM_001410.2		7,209,6284	TT,TC,CC		0.1163,4.8365,1.7154		2284/2779	42874900	223,12777	2202	4298	6500	SO:0001819	synonymous_variant	1954	exon40			CGTGTGCGTGAAC	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.7053C>T	19.37:g.42874900C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	144	82	0.569444	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																				C|0.981;T|0.019	0.019	strong		0.562	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
ZNF697	90874	hgsc.bcm.edu	37	1	120165412	120165412	+	Silent	SNP	G	G	A	rs61734323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120165412G>A	ENST00000421812.2	-	3	1673	c.1554C>T	c.(1552-1554)aaC>aaT	p.N518N		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	518					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(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		TGTGCGGCTTGTTGCCCGTGT	0.642													G|||	60	0.0119808	0.0431	0.0029	5008	,	,		16736	0.0		0.001	False		,,,				2504	0.0				p.N518N		Atlas-SNP	.											.	ZNF697	26	.	0			c.C1554T						PASS	.	G		129,4179		2,125,2027	12.0	17.0	15.0		1554	4.1	1.0	1	dbSNP_129	15	1,8545		0,1,4272	no	coding-synonymous	ZNF697	NM_001080470.1		2,126,6299	AA,AG,GG		0.0117,2.9944,1.0114		518/546	120165412	130,12724	2154	4273	6427	SO:0001819	synonymous_variant	90874	exon3			CGGCTTGTTGCCC	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"""Zinc fingers, C2H2-type"""	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.1554C>T	1.37:g.120165412G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_001080470	Q96IT2	Silent	SNP	ENST00000421812.2	37	CCDS44202.1																																																																																			G|0.994;A|0.006	0.006	strong		0.642	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286	
FBXO16	157574	hgsc.bcm.edu	37	8	28321153	28321153	+	Silent	SNP	A	A	G	rs7822086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:28321153A>G	ENST00000380254.2	-	4	466	c.318T>C	c.(316-318)ccT>ccC	p.P106P	FBXO16_ENST00000518734.1_Silent_p.P94P|FBXO16_ENST00000517436.1_5'UTR|FBXO16_ENST00000346498.2_Silent_p.P94P	NM_001258211.1|NM_172366.3	NP_001245140.1|NP_758954.1	Q8IX29	FBX16_HUMAN	F-box protein 16	106	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.									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)		AAAGGCTCCGAGGGTCCAGGA	0.443													G|||	308	0.0615016	0.2194	0.0101	5008	,	,		20959	0.005		0.001	False		,,,				2504	0.0051				p.P106P		Atlas-SNP	.											.	FBXO16	29	.	0			c.T318C						PASS	.	G		735,3671	720.3+/-409.0	73,589,1541	55.0	53.0	54.0		318	2.7	1.0	8	dbSNP_116	54	8,8592	818.7+/-406.8	0,8,4292	no	coding-synonymous	FBXO16	NM_172366.2		73,597,5833	GG,GA,AA		0.093,16.6818,5.7127		106/293	28321153	743,12263	2203	4300	6503	SO:0001819	synonymous_variant	157574	exon4			GCTCCGAGGGTCC	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.318T>C	8.37:g.28321153A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	133	58	0.43609	NM_172366	Q3T1B2|Q3T1B3|Q3T1B4	Silent	SNP	ENST00000380254.2	37	CCDS6068.1																																																																																			A|0.932;G|0.068	0.068	strong		0.443	FBXO16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219988.2	NM_172366	
VGLL2	245806	hgsc.bcm.edu	37	6	117591755	117591755	+	Silent	SNP	T	T	C	rs13194610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	24	0	0		WXS	Illumina HiSeq	Phase_I	33	7	0.212121	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	
CELA2B	51032	hgsc.bcm.edu	37	1	15808872	15808872	+	Missense_Mutation	SNP	G	G	A	rs3766160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:15808872G>A	ENST00000375910.3	+	4	365	c.340G>A	c.(340-342)Gac>Aac	p.D114N	CELA2B_ENST00000494280.1_3'UTR	NM_015849.2	NP_056933	P08218	CEL2B_HUMAN	chymotrypsin-like elastase family, member 2B	114	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		D -> N (in dbSNP:rs3766160). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3646943}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8						CTGGAACTCCGACCAGGTCTC	0.572													G|||	1578	0.315096	0.2769	0.2896	5008	,	,		16447	0.5575		0.2376	False		,,,				2504	0.2147				p.D114N		Atlas-SNP	.											.	CELA2B	37	.	0			c.G340A						PASS	.	G	ASN/ASP	1151,3255	409.7+/-335.1	143,865,1195	117.0	114.0	115.0		340	0.5	0.1	1	dbSNP_107	115	2111,6489	363.7+/-333.3	269,1573,2458	yes	missense	CELA2B	NM_015849.2	23	412,2438,3653	AA,AG,GG		24.5465,26.1235,25.0807	benign	114/270	15808872	3262,9744	2203	4300	6503	SO:0001583	missense	51032	exon4			AACTCCGACCAGG		CCDS30605.1	1p36.21	2009-07-09			ENSG00000215704	ENSG00000215704			29995	protein-coding gene	gene with protein product	"""pancreatic elastase IIB"""	609444				3646943, 16327289	Standard	NM_015849		Approved	RP11-265F14.2, ELA2B	uc001awl.3	P08218	OTTHUMG00000002259	ENST00000375910.3:c.340G>A	1.37:g.15808872G>A	ENSP00000365075:p.Asp114Asn	Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	192	96	0.5	NM_015849	Q14D16|Q6ISM5|Q96QV5	Missense_Mutation	SNP	ENST00000375910.3	37	CCDS30605.1	701	0.320970695970696	118	0.23983739837398374	85	0.23480662983425415	305	0.5332167832167832	193	0.2546174142480211	G	0.134	-1.110469	0.01813	0.261235	0.245465	ENSG00000215704	ENST00000375910	D	0.88818	-2.43	3.01	0.469	0.16741	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.623510	0.03801	N	0.264463	T	0.00012	0.0000	N	0.04959	-0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.32981	-0.9886	9	0.02654	T	1	.	3.9956	0.09556	0.6422:0.2254:0.1324:0.0	rs3766160;rs52831934;rs61093493;rs3766160	114	P08218	CEL2B_HUMAN	N	114	ENSP00000365075:D114N	ENSP00000365075:D114N	D	+	1	0	CELA2B	15681459	0.000000	0.05858	0.073000	0.20177	0.080000	0.17528	0.067000	0.14510	-0.020000	0.14032	-0.532000	0.04303	GAC	G|0.715;A|0.285	0.285	strong		0.572	CELA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006448.1	NM_015849	
CLEC1A	51267	hgsc.bcm.edu	37	12	10224073	10224073	+	Missense_Mutation	SNP	T	T	G	rs77910243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:10224073T>G	ENST00000315330.4	-	6	764	c.702A>C	c.(700-702)agA>agC	p.R234S	CLEC1A_ENST00000457018.2_Missense_Mutation_p.R201S|CLEC1A_ENST00000420265.2_Missense_Mutation_p.R142S	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	234	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						CCACACAGTCTCTGCTTCTTG	0.378													T|||	51	0.0101837	0.0182	0.0115	5008	,	,		19919	0.0		0.0179	False		,,,				2504	0.001				p.R234S		Atlas-SNP	.											.	CLEC1A	48	.	0			c.A702C						PASS	.	T	SER/ARG	96,4310	77.8+/-116.1	1,94,2108	175.0	162.0	166.0		702	3.6	1.0	12	dbSNP_131	166	154,8446	74.2+/-136.8	2,150,4148	yes	missense	CLEC1A	NM_016511.2	110	3,244,6256	GG,GT,TT		1.7907,2.1788,1.9222	probably-damaging	234/281	10224073	250,12756	2203	4300	6503	SO:0001583	missense	51267	exon6			ACAGTCTCTGCTT	AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"""C-type lectin domain containing"""	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.702A>C	12.37:g.10224073T>G	ENSP00000326407:p.Arg234Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	95	31	0.326316	NM_016511	Q8IUW7|Q9NZH3	Missense_Mutation	SNP	ENST00000315330.4	37	CCDS8612.1	30	0.013736263736263736	7	0.014227642276422764	4	0.011049723756906077	0	0.0	19	0.025065963060686015	T	15.20	2.763480	0.49574	0.021788	0.017907	ENSG00000150048	ENST00000315330;ENST00000457018;ENST00000420265	T;T;T	0.16324	2.35;2.35;2.35	5.42	3.59	0.41128	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.229300	0.30999	N	0.008449	T	0.10680	0.0261	M	0.66939	2.045	0.33199	D	0.551847	P;D;B	0.55385	0.476;0.971;0.166	B;P;B	0.58210	0.159;0.835;0.112	T	0.22836	-1.0205	10	0.19590	T	0.45	.	7.779	0.29054	0.0:0.8032:0.0:0.1968	.	142;201;234	E7ESV9;E9PFB4;Q8NC01	.;.;CLC1A_HUMAN	S	234;201;142	ENSP00000326407:R234S;ENSP00000415048:R201S;ENSP00000417010:R142S	ENSP00000326407:R234S	R	-	3	2	CLEC1A	10115340	0.972000	0.33761	0.987000	0.45799	0.587000	0.36485	0.261000	0.18442	0.639000	0.30564	-0.468000	0.05107	AGA	T|0.983;G|0.017	0.017	strong		0.378	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511	
ZNF684	127396	hgsc.bcm.edu	37	1	41006341	41006341	+	Silent	SNP	T	T	C	rs74575870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:41006341T>C	ENST00000372699.3	+	3	350	c.99T>C	c.(97-99)taT>taC	p.Y33Y	ZNF684_ENST00000372696.3_Silent_p.Y33Y|ZNF684_ENST00000493756.1_Intron|ZNF684_ENST00000372697.3_Silent_p.Y33Y	NM_152373.3	NP_689586.3	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	33	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(2)|lung(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			GAACCCTGTATTGGGATGTGA	0.433													T|||	176	0.0351438	0.1278	0.0086	5008	,	,		18203	0.0		0.001	False		,,,				2504	0.0				p.Y33Y		Atlas-SNP	.											.	ZNF684	37	.	0			c.T99C						PASS	.	T		384,4022	194.3+/-219.2	13,358,1832	198.0	172.0	181.0		99	2.7	1.0	1	dbSNP_132	181	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	ZNF684	NM_152373.3		13,365,6125	CC,CT,TT		0.0814,8.7154,3.0063		33/379	41006341	391,12615	2203	4300	6503	SO:0001819	synonymous_variant	127396	exon3			CCTGTATTGGGAT		CCDS454.1	1p34.2	2013-01-08			ENSG00000117010	ENSG00000117010		"""Zinc fingers, C2H2-type"", ""-"""	28418	protein-coding gene	gene with protein product	"""hypothetical protein MGC27466"""					12477932	Standard	NM_152373		Approved	MGC27466	uc001cft.2	Q5T5D7	OTTHUMG00000007359	ENST00000372699.3:c.99T>C	1.37:g.41006341T>C		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	311	133	0.427653	NM_152373	Q2NKY4	Silent	SNP	ENST00000372699.3	37	CCDS454.1																																																																																			T|0.973;C|0.027	0.027	strong		0.433	ZNF684-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019260.3	NM_152373	
CHSY3	337876	hgsc.bcm.edu	37	5	129520932	129520932	+	Silent	SNP	T	T	G	rs73788438	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:129520932T>G	ENST00000305031.4	+	3	2455	c.2097T>G	c.(2095-2097)ctT>ctG	p.L699L		NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	699					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)	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)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		CCAGAGGTCTTGGTCTTGAAA	0.433													T|||	191	0.038139	0.1271	0.0245	5008	,	,		20200	0.0		0.001	False		,,,				2504	0.0051				p.L699L		Atlas-SNP	.											CHSY3,colon,carcinoma,+2,2	CHSY3	92	2	0			c.T2097G						PASS	.	T		466,3940	217.1+/-235.6	21,424,1758	88.0	83.0	85.0		2097	-1.4	1.0	5	dbSNP_130	85	13,8587	10.5+/-38.8	0,13,4287	no	coding-synonymous	CHSY3	NM_175856.4		21,437,6045	GG,GT,TT		0.1512,10.5765,3.6829		699/883	129520932	479,12527	2203	4300	6503	SO:0001819	synonymous_variant	337876	exon3			AGGTCTTGGTCTT	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.2097T>G	5.37:g.129520932T>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_175856	B2RP97|Q76L22|Q86Y52	Silent	SNP	ENST00000305031.4	37	CCDS34223.1																																																																																			T|0.966;G|0.034	0.034	strong		0.433	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856	
COMMD2	51122	hgsc.bcm.edu	37	3	149459413	149459413	+	Silent	SNP	C	C	T	rs11549572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:149459413C>T	ENST00000473414.1	-	5	549	c.495G>A	c.(493-495)ctG>ctA	p.L165L		NM_016094.3	NP_057178.2	Q86X83	COMD2_HUMAN	COMM domain containing 2	165	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.									NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			GGTCTGTCTGCAGAACTTTGG	0.428													T|||	1404	0.280351	0.6097	0.1354	5008	,	,		13701	0.2609		0.0785	False		,,,				2504	0.1656				p.L165L		Atlas-SNP	.											.	COMMD2	21	.	0			c.G495A						PASS	.	T		2304,2102	573.3+/-383.5	611,1082,510	228.0	236.0	234.0		495	3.0	0.9	3	dbSNP_120	234	693,7907	788.1+/-407.6	32,629,3639	yes	coding-synonymous	COMMD2	NM_016094.3		643,1711,4149	TT,TC,CC		8.0581,47.7077,23.0432		165/200	149459413	2997,10009	2203	4300	6503	SO:0001819	synonymous_variant	51122	exon5			TGTCTGCAGAACT	AY542158	CCDS3145.1	3q25.1	2004-02-20			ENSG00000114744	ENSG00000114744			24993	protein-coding gene	gene with protein product						15799966	Standard	NM_016094		Approved	HSPC042	uc003exj.2	Q86X83	OTTHUMG00000159616	ENST00000473414.1:c.495G>A	3.37:g.149459413C>T		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	284	147	0.517606	NM_016094	Q561V4|Q9H3L5|Q9Y5V1	Silent	SNP	ENST00000473414.1	37	CCDS3145.1																																																																																			C|0.755;T|0.245	0.245	strong		0.428	COMMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356515.1	NM_016094	
C11orf85	283129	hgsc.bcm.edu	37	11	64714908	64714908	+	Silent	SNP	A	A	G	rs75184517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64714908A>G	ENST00000301896.5	-	8	484	c.411T>C	c.(409-411)gcT>gcC	p.A137A	C11orf85_ENST00000536065.1_Silent_p.A31A|C11orf85_ENST00000432175.1_Silent_p.A137A|C11orf85_ENST00000530444.1_Silent_p.A59A	NM_001037225.1	NP_001032302.1	Q3KP22	CK085_HUMAN	chromosome 11 open reading frame 85	137										breast(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	7						TCCTCATCACAGCTCCTACTG	0.567													A|||	92	0.0183706	0.0643	0.0072	5008	,	,		19731	0.0		0.002	False		,,,				2504	0.0				p.A137A		Atlas-SNP	.											.	C11orf85	20	.	0			c.T411C						PASS	.	A		261,4141	148.8+/-183.1	10,241,1950	153.0	128.0	137.0		411	-1.4	0.0	11	dbSNP_132	137	0,8594		0,0,4297	no	coding-synonymous	C11orf85	NM_001037225.1		10,241,6247	GG,GA,AA		0.0,5.9291,2.0083		137/217	64714908	261,12735	2201	4297	6498	SO:0001819	synonymous_variant	283129	exon7			CATCACAGCTCCT	AK093130, BC033501	CCDS31603.1, CCDS73316.1	11q13.1	2012-08-10			ENSG00000168070	ENSG00000168070			27441	protein-coding gene	gene with protein product						14702039	Standard	XM_005273918		Approved		uc001ocb.1	Q3KP22		ENST00000301896.5:c.411T>C	11.37:g.64714908A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_001037225	B3KS99	Silent	SNP	ENST00000301896.5	37	CCDS31603.1																																																																																			A|0.982;G|0.018	0.018	strong		0.567	C11orf85-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385477.1	NM_001037225	
ARFGEF2	10564	hgsc.bcm.edu	37	20	47588949	47588949	+	Silent	SNP	G	G	A	rs116550473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47588949G>A	ENST00000371917.4	+	11	1512	c.1512G>A	c.(1510-1512)acG>acA	p.T504T		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	504					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			AGACTCTGACGAGGATCTGTG	0.408													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		20979	0.0		0.0	False		,,,				2504	0.0				p.T504T	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.G1512A						PASS	.	G		56,4350	56.2+/-92.4	0,56,2147	84.0	81.0	82.0		1512	-6.9	0.9	20	dbSNP_132	82	0,8600		0,0,4300	no	coding-synonymous	ARFGEF2	NM_006420.2		0,56,6447	AA,AG,GG		0.0,1.271,0.4306		504/1786	47588949	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	10564	exon11			TCTGACGAGGATC	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1512G>A	20.37:g.47588949G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																			G|0.996;A|0.004	0.004	strong		0.408	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420	
PRKAG2	51422	hgsc.bcm.edu	37	7	151257665	151257665	+	Silent	SNP	A	A	G	rs28763998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151257665A>G	ENST00000287878.4	-	15	2127	c.1623T>C	c.(1621-1623)atT>atC	p.I541I	PRKAG2_ENST00000392801.2_Silent_p.I497I|PRKAG2_ENST00000418337.2_Silent_p.I300I|PRKAG2_ENST00000492843.1_Silent_p.I417I|PRKAG2_ENST00000433631.2_Silent_p.I416I	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	541	CBS 4. {ECO:0000255|PROSITE- ProRule:PRU00703}.				ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	TAATACCCACAATACTATCTG	0.448													A|||	220	0.0439297	0.1596	0.013	5008	,	,		18994	0.0		0.0	False		,,,				2504	0.0				p.I541I		Atlas-SNP	.											.	PRKAG2	86	.	0			c.T1623C						PASS	.	A	,,	526,3880	242.1+/-252.3	28,470,1705	126.0	122.0	123.0		1491,1623,900	-5.7	0.2	7	dbSNP_125	123	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous,coding-synonymous,coding-synonymous	PRKAG2	NM_001040633.1,NM_016203.3,NM_024429.1	,,	28,472,6003	GG,GA,AA		0.0233,11.9383,4.0597	,,	497/526,541/570,300/329	151257665	528,12478	2203	4300	6503	SO:0001819	synonymous_variant	51422	exon15			ACCCACAATACTA	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"""AMPK gamma2"""	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.1623T>C	7.37:g.151257665A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Silent	SNP	ENST00000287878.4	37	CCDS5928.1																																																																																			A|0.955;G|0.045	0.045	strong		0.448	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203	
NBPF7	343505	hgsc.bcm.edu	37	1	120384162	120384162	+	IGR	SNP	G	G	A	rs78204967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120384162G>A								REG4 (29879 upstream) : ADAM30 (51993 downstream)																							CTCCCTTCCCGTAACTTCTCC	0.493													g|||	119	0.023762	0.0802	0.0115	5008	,	,		21233	0.0		0.004	False		,,,				2504	0.001				p.R134W		Atlas-SNP	.											NBPF7,NS,carcinoma,0,1	NBPF7	46	1	0			c.C400T						scavenged	.	G	TRP/ARG	282,4124	147.6+/-182.1	8,266,1929	137.0	154.0	148.0		400	-0.1	0.0	1	dbSNP_131	148	49,8551	29.6+/-80.5	1,47,4252	no	missense	NBPF7	NM_001047980.1	101	9,313,6181	AA,AG,GG		0.5698,6.4004,2.545	probably-damaging	134/422	120384162	331,12675	2203	4300	6503	SO:0001628	intergenic_variant	343505	exon3			CTTCCCGTAACTT																													1.37:g.120384162G>A		Somatic	245	2	0.00816326		WXS	Illumina HiSeq	Phase_I	204	99	0.485294	NM_001047980		Missense_Mutation	SNP		37																																																																																				G|0.983;A|0.017	0.017	strong	0	0.493								
CD180	4064	hgsc.bcm.edu	37	5	66479189	66479189	+	Silent	SNP	G	G	A	rs3733910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:66479189G>A	ENST00000256447.4	-	3	1639	c.1482C>T	c.(1480-1482)acC>acT	p.T494T	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	494					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		AGCTGCCCACGGTCTGAAGTA	0.468													G|||	441	0.0880591	0.2716	0.0231	5008	,	,		20929	0.0218		0.0209	False		,,,				2504	0.0235				p.T494T		Atlas-SNP	.											.	CD180	78	.	0			c.C1482T						PASS	.	G		1037,3369	380.6+/-323.8	134,769,1300	67.0	68.0	68.0		1482	-9.7	0.0	5	dbSNP_107	68	69,8531	40.8+/-97.7	3,63,4234	no	coding-synonymous	CD180	NM_005582.2		137,832,5534	AA,AG,GG		0.8023,23.5361,8.5038		494/662	66479189	1106,11900	2203	4300	6503	SO:0001819	synonymous_variant	4064	exon3			GCCCACGGTCTGA	D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"""CD molecules"""	6726	protein-coding gene	gene with protein product		602226	"""lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD"", ""CD180 antigen"""	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.1482C>T	5.37:g.66479189G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_005582	B2R7Z7|Q32MM5	Silent	SNP	ENST00000256447.4	37	CCDS3992.1																																																																																			G|0.912;A|0.088	0.088	strong		0.468	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582	
OR2H1	26716	hgsc.bcm.edu	37	6	29430356	29430356	+	Missense_Mutation	SNP	G	G	C	rs371076908|rs148433584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29430356G>C	ENST00000377136.1	+	4	1275	c.810G>C	c.(808-810)aaG>aaC	p.K270N	OR2H1_ENST00000442615.1_Missense_Mutation_p.K270N|OR2H1_ENST00000377132.1_Missense_Mutation_p.K270N|OR2H1_ENST00000396792.2_Missense_Mutation_p.K270N|OR2H1_ENST00000377133.1_Missense_Mutation_p.K270N|OR2H1_ENST00000473369.1_3'UTR			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	270						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						GGAGGGGCAAGTTCTTTGGTC	0.522													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		21364	0.0		0.0	False		,,,				2504	0.0				p.K270N		Atlas-SNP	.											.	OR2H1	38	.	0			c.G810C						PASS	.	G	ASN/LYS	42,2980		0,42,1469	113.0	115.0	114.0		810	2.2	0.9	6	dbSNP_134	114	0,5418		0,0,2709	no	missense	OR2H1	NM_030883.3	94	0,42,4178	CC,CG,GG		0.0,1.3898,0.4976	probably-damaging	270/317	29430356	42,8398	1511	2709	4220	SO:0001583	missense	26716	exon3			GGGCAAGTTCTTT	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.810G>C	6.37:g.29430356G>C	ENSP00000366340:p.Lys270Asn	Somatic	464	0	0		WXS	Illumina HiSeq	Phase_I	453	227	0.501104	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	10.39	1.335640	0.24253	0.013898	0.0	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.00207	8.55;8.55;8.55;8.55;8.55	3.09	2.22	0.28083	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42682	D	0.000675	T	0.00241	0.0007	M	0.87617	2.895	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.32824	-0.9892	10	0.87932	D	0	.	6.4805	0.22060	0.322:0.0:0.678:0.0	.	270	Q9GZK4	OR2H1_HUMAN	N	270	ENSP00000366340:K270N;ENSP00000366337:K270N;ENSP00000393254:K270N;ENSP00000366336:K270N;ENSP00000380010:K270N	ENSP00000366336:K270N	K	+	3	2	OR2H1	29538335	0.000000	0.05858	0.935000	0.37517	0.315000	0.28087	-1.183000	0.03079	0.870000	0.35726	-0.199000	0.12753	AAG	G|0.995;C|0.005	0.005	strong		0.522	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
HSPD1	3329	hgsc.bcm.edu	37	2	198363534	198363534	+	Silent	SNP	C	C	T	rs565153254		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:198363534C>T	ENST00000388968.3	-	2	306	c.39G>A	c.(37-39)ccG>ccA	p.P13P	HSPE1_ENST00000233893.5_5'Flank|HSPE1_ENST00000409729.1_5'Flank|HSPD1_ENST00000345042.2_Silent_p.P13P|HSPE1-MOB4_ENST00000604458.1_5'Flank|HSPD1_ENST00000544407.1_Silent_p.P13P|HSPE1_ENST00000409468.1_5'Flank	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	13					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)	p.P13P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			CCCTGGACACCGGTCTCATCT	0.502																																					p.P13P		Atlas-SNP	.											HSPD1_ENST00000426480,NS,haematopoietic_neoplasm,0,3	HSPD1	68	3	1	Substitution - coding silent(1)	breast(1)	c.G39A						scavenged	.						52.0	49.0	50.0					2																	198363534		2203	4300	6503	SO:0001819	synonymous_variant	3329	exon2			GGACACCGGTCTC	M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"""Heat Shock Proteins / Chaperonins"""	5261	protein-coding gene	gene with protein product		118190	"""heat shock 60kD protein 1 (chaperonin)"", ""spastic paraplegia 13 (autosomal dominant)"""	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.39G>A	2.37:g.198363534C>T		Somatic	310	4	0.0129032		WXS	Illumina HiSeq	Phase_I	352	6	0.0170455	NM_002156	B2R5M6|B7Z712|Q38L19|Q9UCR6	Silent	SNP	ENST00000388968.3	37	CCDS33357.1																																																																																			.	.	none		0.502	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156	
PCDHB2	56133	hgsc.bcm.edu	37	5	140475763	140475763	+	Silent	SNP	C	C	G	rs142417694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140475763C>G	ENST00000194155.4	+	1	1537	c.1389C>G	c.(1387-1389)cgC>cgG	p.R463R		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	463	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGTTCGTCCGCGAGAACAACA	0.637																																					p.R463R		Atlas-SNP	.											PCDHB2,NS,carcinoma,+2,2	PCDHB2	163	2	0			c.C1389G						scavenged	.						78.0	79.0	79.0					5																	140475763		2203	4296	6499	SO:0001819	synonymous_variant	56133	exon1			CGTCCGCGAGAAC	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1389C>G	5.37:g.140475763C>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	196	14	0.0714286	NM_018936	Q4KMU1	Silent	SNP	ENST00000194155.4	37	CCDS4244.1																																																																																			C|0.029;G|0.971	0.971	strong		0.637	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
HYDIN	54768	hgsc.bcm.edu	37	16	71101206	71101206	+	Silent	SNP	A	A	G	rs11866903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71101206A>G	ENST00000393567.2	-	15	2212	c.2062T>C	c.(2062-2064)Tta>Cta	p.L688L	HYDIN_ENST00000543639.1_5'Flank|HYDIN_ENST00000448089.2_Silent_p.L688L|HYDIN_ENST00000393550.2_Silent_p.L703L|HYDIN_ENST00000541601.1_Silent_p.L705L|HYDIN_ENST00000448691.1_Silent_p.L688L|HYDIN_ENST00000538248.1_Silent_p.L715L|HYDIN_ENST00000288168.10_Silent_p.L705L|HYDIN_ENST00000321489.5_Silent_p.L688L	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	688					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)				GCTGTAATTAAGAGCGCCAGC	0.562													A|||	378	0.0754792	0.2769	0.013	5008	,	,		18119	0.001		0.001	False		,,,				2504	0.001				p.L715L		Atlas-SNP	.											.	HYDIN	788	.	0			c.T2143C						PASS	.	A	,,,	969,3427	361.6+/-315.8	118,733,1347	68.0	59.0	62.0		2143,2113,2062,2062	-0.0	1.0	16	dbSNP_120	62	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HYDIN	NM_001198542.1,NM_001198543.1,NM_017558.3,NM_032821.2	,,,	118,737,5643	GG,GA,AA		0.0465,22.0428,7.4869	,,,	715/951,705/941,688/1018,688/5121	71101206	973,12023	2198	4300	6498	SO:0001819	synonymous_variant	54768	exon15			TAATTAAGAGCGC	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.2062T>C	16.37:g.71101206A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_001198542	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			A|0.919;G|0.081	0.081	strong		0.562	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
LILRB5	10990	hgsc.bcm.edu	37	19	54755923	54755923	+	Silent	SNP	A	A	G	rs34889610|rs12976868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54755923A>G	ENST00000316219.5	-	12	1727	c.1620T>C	c.(1618-1620)gaT>gaC	p.D540D	LILRB5_ENST00000345866.6_Silent_p.D441D|LILRB5_ENST00000449561.2_Silent_p.D541D|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000450632.1_Silent_p.D532D	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	540					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TCACCCGAGCATCCATCTCCA	0.632													.|||	1056	0.210863	0.2284	0.1556	5008	,	,		14747	0.0992		0.2525	False		,,,				2504	0.2986				p.D541D		Atlas-SNP	.											.	LILRB5	176	.	0			c.T1623C						PASS	.	G	,,	853,3553		78,697,1428	112.0	110.0	111.0		1623,1323,1620	0.5	0.0	19	dbSNP_121	111	1842,6758		243,1356,2701	no	coding-synonymous,coding-synonymous,coding-synonymous	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	,,	321,2053,4129	GG,GA,AA		21.4186,19.36,20.7212	,,	541/592,441/492,540/591	54755923	2695,10311	2203	4300	6503	SO:0001819	synonymous_variant	10990	exon12			CCGAGCATCCATC	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1620T>C	19.37:g.54755923A>G		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	214	110	0.514019	NM_001081442	Q8N760	Silent	SNP	ENST00000316219.5	37	CCDS12885.1																																																																																			A|0.786;G|0.214	0.214	strong		0.632	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
ARHGEF4	50649	hgsc.bcm.edu	37	2	131802045	131802045	+	Silent	SNP	C	C	T	rs10928515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131802045C>T	ENST00000326016.5	+	12	2292	c.1773C>T	c.(1771-1773)ccC>ccT	p.P591P	ARHGEF4_ENST00000409303.1_Silent_p.P531P|ARHGEF4_ENST00000428230.2_Intron|ARHGEF4_ENST00000392953.3_Silent_p.P591P|ARHGEF4_ENST00000525839.1_Silent_p.P591P|ARHGEF4_ENST00000355771.3_Silent_p.P520P	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	591	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		CCAGGAAGCCCGAGCAGAAGC	0.657													C|||	923	0.184305	0.2791	0.1196	5008	,	,		18450	0.1329		0.1074	False		,,,				2504	0.2342				p.P591P		Atlas-SNP	.											ARHGEF4,NS,carcinoma,0,1	ARHGEF4	89	1	0			c.C1773T						PASS	.	C	,	1042,3272		130,782,1245	41.0	35.0	37.0		1773,1773	-10.4	0.6	2	dbSNP_120	37	946,7552		57,832,3360	no	coding-synonymous,coding-synonymous	ARHGEF4	NM_015320.2,NM_032995.1	,	187,1614,4605	TT,TC,CC		11.132,24.1539,15.5167	,	591/691,591/671	131802045	1988,10824	2157	4249	6406	SO:0001819	synonymous_variant	50649	exon12			GAAGCCCGAGCAG	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1773C>T	2.37:g.131802045C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_032995	Q9HDC6|Q9UPP0	Silent	SNP	ENST00000326016.5	37	CCDS2165.1	328	0.15018315018315018	125	0.2540650406504065	43	0.11878453038674033	80	0.13986013986013987	80	0.10554089709762533	C	8.628	0.893035	0.17613	0.241539	0.11132	ENSG00000136002	ENST00000532720	.	.	.	5.19	-10.4	0.00318	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999999796378	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.449	0.00498	0.3745:0.1766:0.1526:0.2963	rs10928515;rs61026863	.	.	.	X	208	.	.	R	+	1	2	ARHGEF4	131518515	0.000000	0.05858	0.570000	0.28473	0.980000	0.70556	-4.997000	0.00161	-3.160000	0.00228	-1.319000	0.01295	CGA	A|0.000;C|0.838;G|0.000;T|0.161	0.161	strong		0.657	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4		
APOBEC3A	200315	hgsc.bcm.edu	37	22	39357581	39357581	+	Silent	SNP	C	C	T	rs35994173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39357581C>T	ENST00000402255.1	+	4	568	c.364C>T	c.(364-366)Ctg>Ttg	p.L122L	APOBEC3A_ENST00000249116.2_Silent_p.L122L			P31941	ABC3A_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A	122					cellular response to xenobiotic stimulus (GO:0071466)|clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine (GO:0044356)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(2)|ovary(1)|skin(1)	5	Melanoma(58;0.04)					ACACGTGAGACTGCGTATCTT	0.567													C|||	1231	0.245807	0.2436	0.1527	5008	,	,		10317	0.3046		0.162	False		,,,				2504	0.3405				p.L122L		Atlas-SNP	.											.	APOBEC3A	20	.	0			c.C364T						PASS	.	C		1060,3198		275,510,1344	99.0	97.0	97.0		364	1.5	0.0	22	dbSNP_130	97	1500,6648		389,722,2963	no	coding-synonymous	APOBEC3A	NM_145699.3		664,1232,4307	TT,TC,CC		18.4094,24.8943,20.6352		122/200	39357581	2560,9846	2129	4074	6203	SO:0001819	synonymous_variant	200315	exon3			GTGAGACTGCGTA	U03891	CCDS13981.1	22q13.1-q13.2	2014-01-28			ENSG00000128383	ENSG00000128383		"""Apolipoprotein B mRNA editing enzymes"""	17343	protein-coding gene	gene with protein product	"""phorbolin I"""	607109				11863358, 10469298	Standard	NM_145699		Approved	ARP3, PHRBN		P31941	OTTHUMG00000151004	ENST00000402255.1:c.364C>T	22.37:g.39357581C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	144	67	0.465278	NM_145699	A0AVM1|Q12807|Q5JZ93|Q9UH18	Silent	SNP	ENST00000402255.1	37	CCDS13981.1																																																																																			C|0.803;T|0.197	0.197	strong		0.567	APOBEC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320915.2	NM_145699	
C8orf44	56260	hgsc.bcm.edu	37	8	67592152	67592152	+	Missense_Mutation	SNP	T	T	C	rs1057463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:67592152T>C	ENST00000519561.1	+	3	594	c.443T>C	c.(442-444)tTc>tCc	p.F148S	C8orf44_ENST00000390159.3_Missense_Mutation_p.F148S|C8orf44-SGK3_ENST00000520044.1_3'UTR|C8orf44_ENST00000518860.1_3'UTR|C8orf44-SGK3_ENST00000519289.1_5'UTR	NM_019607.2	NP_062553.1	Q96CB5	CH044_HUMAN	chromosome 8 open reading frame 44	148			F -> S (in dbSNP:rs1057463). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)				endometrium(1)|kidney(1)|lung(2)	4	Breast(64;0.186)		Epithelial(68;0.000959)|OV - Ovarian serous cystadenocarcinoma(28;0.00318)|all cancers(69;0.00363)|BRCA - Breast invasive adenocarcinoma(89;0.149)			TCCAAAGGCTTCTGGAGTCTT	0.463													T|||	1094	0.21845	0.0514	0.2291	5008	,	,		17882	0.2401		0.2922	False		,,,				2504	0.3384				p.F148S		Atlas-SNP	.											.	C8orf44	18	.	0			c.T443C						PASS	.	T	SER/PHE,	403,4003	194.0+/-219.0	25,353,1825	47.0	50.0	49.0		443,	2.8	0.0	8	dbSNP_86	49	2536,6064	411.1+/-350.4	388,1760,2152	yes	missense,utr-5	C8orf44,C8orf44-SGK3	NM_019607.2,NM_001204173.1	155,	413,2113,3977	CC,CT,TT		29.4884,9.1466,22.5973	possibly-damaging,	148/160,	67592152	2939,10067	2203	4300	6503	SO:0001583	missense	56260	exon3			AAGGCTTCTGGAG	AK002129	CCDS6193.1	8q13.1	2012-05-16		2005-08-09	ENSG00000213865	ENSG00000213865			25646	protein-coding gene	gene with protein product						12477932	Standard	NM_019607		Approved	FLJ11267	uc003xwo.2	Q96CB5	OTTHUMG00000164562	ENST00000519561.1:c.443T>C	8.37:g.67592152T>C	ENSP00000428002:p.Phe148Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	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	
CACNA2D3	55799	hgsc.bcm.edu	37	3	55108188	55108188	+	Silent	SNP	A	A	G	rs35471424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:55108188A>G	ENST00000474759.1	+	38	3279	c.3231A>G	c.(3229-3231)acA>acG	p.T1077T	CACNA2D3_ENST00000490478.1_Silent_p.T983T|CACNA2D3_ENST00000478261.1_3'UTR|CACNA2D3_ENST00000415676.2_Silent_p.T1077T|CACNA2D3_ENST00000288197.5_Silent_p.T1077T	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	1077						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)	AAGCCCAGACAGTCCTCCTTC	0.517													A|||	439	0.0876597	0.115	0.1037	5008	,	,		19185	0.0		0.159	False		,,,				2504	0.0562				p.T1077T		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.A3231G						PASS	.	A		495,3737		35,425,1656	179.0	175.0	177.0		3231	-0.4	0.0	3	dbSNP_126	177	1325,7107		105,1115,2996	no	coding-synonymous	CACNA2D3	NM_018398.2		140,1540,4652	GG,GA,AA		15.7139,11.6966,14.3714		1077/1092	55108188	1820,10844	2116	4216	6332	SO:0001819	synonymous_variant	55799	exon38			CCAGACAGTCCTC	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.3231A>G	3.37:g.55108188A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	121	62	0.512397	NM_018398	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	37	CCDS54598.1																																																																																			A|0.903;G|0.097	0.097	strong		0.517	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		
DNAH10	196385	hgsc.bcm.edu	37	12	124265687	124265687	+	Missense_Mutation	SNP	T	T	C	rs11057353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	153	0	0		WXS	Illumina HiSeq	Phase_I	152	74	0.486842	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		
SERPINI2	5276	hgsc.bcm.edu	37	3	167167186	167167186	+	Silent	SNP	T	T	A	rs6770577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:167167186T>A	ENST00000476257.1	-	8	1267	c.969A>T	c.(967-969)tcA>tcT	p.S323S	SERPINI2_ENST00000471111.1_Silent_p.S323S|SERPINI2_ENST00000461846.1_Silent_p.S323S|SERPINI2_ENST00000264677.4_Silent_p.S323S			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	323					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						ACACTTCAGATGAATCTGGTT	0.294													T|||	1857	0.370807	0.3026	0.3761	5008	,	,		16258	0.3859		0.4095	False		,,,				2504	0.4039				p.S333S		Atlas-SNP	.											.	SERPINI2	85	.	0			c.A999T						PASS	.	T		1372,3034	450.2+/-349.3	218,936,1049	59.0	55.0	56.0		969	-2.9	0.9	3	dbSNP_116	56	3353,5247	492.8+/-373.4	672,2009,1619	no	coding-synonymous	SERPINI2	NM_006217.3		890,2945,2668	AA,AT,TT		38.9884,31.1394,36.3294		323/406	167167186	4725,8281	2203	4300	6503	SO:0001819	synonymous_variant	5276	exon8			TTCAGATGAATCT	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.969A>T	3.37:g.167167186T>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_001012303		Silent	SNP	ENST00000476257.1	37	CCDS3200.1																																																																																			T|0.632;A|0.368	0.368	strong		0.294	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
SSFA2	6744	hgsc.bcm.edu	37	2	182780817	182780817	+	Missense_Mutation	SNP	C	C	T	rs16867510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:182780817C>T	ENST00000431877.2	+	11	2629	c.2450C>T	c.(2449-2451)gCg>gTg	p.A817V	SSFA2_ENST00000409001.1_Missense_Mutation_p.A817V|SSFA2_ENST00000320370.7_Missense_Mutation_p.A817V|SSFA2_ENST00000428267.2_Missense_Mutation_p.A664V|SSFA2_ENST00000409136.1_Missense_Mutation_p.A326V	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	817			A -> V (in dbSNP:rs16867510).			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)			CAGAGTGAGGCGCCGCGGGTG	0.507													C|||	172	0.034345	0.1263	0.0072	5008	,	,		20029	0.0		0.0	False		,,,				2504	0.0				p.A817V		Atlas-SNP	.											SSFA2,colon,carcinoma,0,1	SSFA2	130	1	0			c.C2450T						scavenged	.	C	VAL/ALA,VAL/ALA	438,3968	210.2+/-230.7	29,380,1794	66.0	73.0	71.0		2450,2450	-9.2	0.0	2	dbSNP_123	71	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense	SSFA2	NM_001130445.1,NM_006751.5	64,64	29,387,6087	TT,TC,CC		0.0814,9.941,3.4215	benign,benign	817/1260,817/1257	182780817	445,12561	2203	4300	6503	SO:0001583	missense	6744	exon11			GTGAGGCGCCGCG	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.2450C>T	2.37:g.182780817C>T	ENSP00000388731:p.Ala817Val	Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	188	92	0.489362	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	52	0.023809523809523808	51	0.10365853658536585	1	0.0027624309392265192	0	0.0	0	0.0	C	2.957	-0.215497	0.06101	0.09941	8.14E-4	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136	T;T;T;T;T	0.14391	2.74;2.51;2.74;2.73;2.52	5.95	-9.19	0.00685	.	1.558920	0.02820	N	0.125417	T	0.00144	0.0004	N	0.03115	-0.41	0.80722	P	0.0	B;B;B;B;B	0.13594	0.003;0.008;0.002;0.002;0.002	B;B;B;B;B	0.06405	0.002;0.001;0.0;0.0;0.0	T	0.27123	-1.0083	9	0.20046	T	0.44	3.6137	7.4998	0.27511	0.0819:0.4875:0.2579:0.1727	rs16867510	664;326;817;817;817	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	V	817;817;817;664;326	ENSP00000388731:A817V;ENSP00000314669:A817V;ENSP00000387319:A817V;ENSP00000409867:A664V;ENSP00000386916:A326V	ENSP00000314669:A817V	A	+	2	0	SSFA2	182489062	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.387000	0.02535	-1.938000	0.01046	-0.793000	0.03317	GCG	C|0.965;T|0.035	0.035	strong		0.507	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751	
PRAME	23532	hgsc.bcm.edu	37	22	22899234	22899234	+	Missense_Mutation	SNP	A	A	G	rs1129172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:22899234A>G	ENST00000398741.1	-	3	325	c.19T>C	c.(19-21)Tgg>Cgg	p.W7R	PRAME_ENST00000405655.3_Missense_Mutation_p.W7R|PRAME_ENST00000406503.1_Missense_Mutation_p.W7R|PRAME_ENST00000539862.1_5'Flank|PRAME_ENST00000543184.1_Missense_Mutation_p.W7R|PRAME_ENST00000424204.2_5'Flank|PRAME_ENST00000402697.1_Missense_Mutation_p.W7R|PRAME_ENST00000485532.1_5'Flank|LL22NC03-63E9.3_ENST00000407120.1_5'Flank|PRAME_ENST00000398743.2_Missense_Mutation_p.W7R	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	7			W -> R (in dbSNP:rs2266988). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|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)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)	p.W7R(2)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CTTCTTACCCACAAACGCCTT	0.562													G|||	3537	0.70627	0.7564	0.6931	5008	,	,		14575	0.752		0.5944	False		,,,				2504	0.7157				p.W7R	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											PRAME,NS,carcinoma,0,4	PRAME	78	4	2	Substitution - Missense(2)	prostate(1)|central_nervous_system(1)	c.T19C						PASS	.	G	ARG/TRP,ARG/TRP,ARG/TRP,ARG/TRP,ARG/TRP	3252,1154	408.6+/-334.7	1206,840,157	186.0	164.0	171.0		19,19,19,19,19	2.8	0.4	22	dbSNP_100	171	4922,3678	523.7+/-380.4	1402,2118,780	yes	missense,missense,missense,missense,missense	PRAME	NM_006115.3,NM_206953.1,NM_206954.1,NM_206955.1,NM_206956.1	101,101,101,101,101	2608,2958,937	GG,GA,AA		42.7674,26.1916,37.1521	benign,benign,benign,benign,benign	7/510,7/510,7/510,7/510,7/510	22899234	8174,4832	2203	4300	6503	SO:0001583	missense	23532	exon3			TTACCCACAAACG	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.19T>C	22.37:g.22899234A>G	ENSP00000381726:p.Trp7Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_206954	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	37	CCDS13801.1	1490	0.6822344322344323	378	0.7682926829268293	235	0.649171270718232	422	0.7377622377622378	455	0.600263852242744	g	0.393	-0.922440	0.02396	0.738084	0.572326	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000402697;ENST00000439106;ENST00000420709;ENST00000406503;ENST00000403441	T;T;T;T;T;T;T;T;T	0.10477	2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87	2.78	2.78	0.32641	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.33482	P	0.41245699999999996	B	0.02656	0.0	B	0.01281	0.0	T	0.34054	-0.9844	8	0.02654	T	1	.	5.8996	0.18960	0.1457:0.0:0.8543:0.0	rs2266988;rs17497986;rs57013465	7	P78395	PRAME_HUMAN	R	7	ENSP00000381728:W7R;ENSP00000445675:W7R;ENSP00000381726:W7R;ENSP00000384343:W7R;ENSP00000385198:W7R;ENSP00000407320:W7R;ENSP00000412318:W7R;ENSP00000384058:W7R;ENSP00000385091:W7R	ENSP00000381726:W7R	W	-	1	0	PRAME	21229234	0.547000	0.26465	0.392000	0.26245	0.002000	0.02628	0.671000	0.25172	0.765000	0.33221	-0.213000	0.12676	TGG	G|0.653;N|0.000	0.653	strong		0.562	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953	
ADCY3	109	hgsc.bcm.edu	37	2	25046090	25046090	+	Silent	SNP	T	T	C	rs1127568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:25046090T>C	ENST00000260600.5	-	17	3722	c.2871A>G	c.(2869-2871)tcA>tcG	p.S957S	RP11-443B20.1_ENST00000606114.1_RNA|ADCY3_ENST00000405392.1_Silent_p.S544S	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	957					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					AGTCAAAATCTGAGATGATTT	0.502													C|||	3462	0.691294	0.5295	0.7695	5008	,	,		20373	0.879		0.668	False		,,,				2504	0.6851				p.S957S		Atlas-SNP	.											.	ADCY3	114	.	0			c.A2871G						PASS	.	C		2405,2001	561.5+/-380.7	642,1121,440	102.0	87.0	92.0		2871	-8.2	0.7	2	dbSNP_86	92	5729,2871	450.6+/-362.4	1927,1875,498	no	coding-synonymous	ADCY3	NM_004036.3		2569,2996,938	CC,CT,TT		33.3837,45.4153,37.4596		957/1145	25046090	8134,4872	2203	4300	6503	SO:0001819	synonymous_variant	109	exon17			AAAATCTGAGATG	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.2871A>G	2.37:g.25046090T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	47	0.54023	NM_004036	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	37	CCDS1715.1																																																																																			T|0.344;C|0.656	0.656	strong		0.502	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
TCEB3B	51224	hgsc.bcm.edu	37	18	44559578	44559578	+	Silent	SNP	G	G	A	rs149717505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44559578G>A	ENST00000332567.4	-	1	2410	c.2058C>T	c.(2056-2058)tcC>tcT	p.S686S	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	686					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						tgctCTGGCTGGAGGGAGTGT	0.627													G|||	9	0.00179712	0.0053	0.0029	5008	,	,		14981	0.0		0.0	False		,,,				2504	0.0				p.S686S		Atlas-SNP	.											.	TCEB3B	141	.	0			c.C2058T						PASS	.	G	,	25,4377		0,25,2176	38.0	43.0	41.0		2058,	1.1	0.0	18	dbSNP_134	41	0,8598		0,0,4299	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	0,25,6475	AA,AG,GG		0.0,0.5679,0.1923	,	686/754,	44559578	25,12975	2201	4299	6500	SO:0001819	synonymous_variant	51224	exon1			CTGGCTGGAGGGA	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.2058C>T	18.37:g.44559578G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	154	77	0.5	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			G|0.998;A|0.002	0.002	strong		0.627	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
TTC21A	199223	hgsc.bcm.edu	37	3	39180100	39180100	+	Missense_Mutation	SNP	G	G	A	rs80238762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39180100G>A	ENST00000431162.2	+	28	4005	c.3871G>A	c.(3871-3873)Gaa>Aaa	p.E1291K	TTC21A_ENST00000301819.6_Missense_Mutation_p.E1292K|TTC21A_ENST00000440121.1_Missense_Mutation_p.E1243K|TTC21A_ENST00000493856.1_3'UTR			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	1291				E -> K (in Ref. 2; BAG63755). {ECO:0000305}.						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)		GGAGGCCATTGAAATCTGCAA	0.522													G|||	29	0.00579073	0.0008	0.0173	5008	,	,		20962	0.0		0.0159	False		,,,				2504	0.0				p.E1291K		Atlas-SNP	.											.	TTC21A	96	.	0			c.G3871A						PASS	.	G	LYS/GLU,LYS/GLU	8,3990		0,8,1991	113.0	110.0	111.0		3727,3871	5.1	0.9	3	dbSNP_132	111	91,8241		1,89,4076	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	56,56	1,97,6067	AA,AG,GG		1.0922,0.2001,0.8029	possibly-damaging,possibly-damaging	1243/1273,1291/1321	39180100	99,12231	1999	4166	6165	SO:0001583	missense	199223	exon28			GCCATTGAAATCT	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.3871G>A	3.37:g.39180100G>A	ENSP00000398211:p.Glu1291Lys	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	236	111	0.470339	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	15	0.006868131868131868	0	0.0	7	0.019337016574585635	0	0.0	8	0.010554089709762533	G	22.7	4.325101	0.81580	0.002001	0.010922	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.78481	-1.18;-1.18;-1.18	5.14	5.14	0.70334	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.151938	0.42682	D	0.000679	T	0.72486	0.3466	M	0.64170	1.965	0.58432	D	0.999999	P;D;P	0.55605	0.921;0.972;0.953	P;P;P	0.53912	0.497;0.737;0.551	T	0.78620	-0.2133	10	0.41790	T	0.15	-2.9838	17.3579	0.87342	0.0:0.0:1.0:0.0	.	1243;1292;1291	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	K	1292;1274;1291;1243	ENSP00000301819:E1292K;ENSP00000398211:E1291K;ENSP00000410882:E1243K	ENSP00000301819:E1292K	E	+	1	0	TTC21A	39155104	1.000000	0.71417	0.918000	0.36340	0.278000	0.26855	7.431000	0.80335	2.377000	0.81083	0.561000	0.74099	GAA	G|0.989;A|0.011	0.011	strong		0.522	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
AKR1B15	441282	hgsc.bcm.edu	37	7	134264286	134264286	+	Silent	SNP	C	C	T	rs6467538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:134264286C>T	ENST00000457545.2	+	12	1280	c.1020C>T	c.(1018-1020)ttC>ttT	p.F340F	AKR1B15_ENST00000423958.1_Silent_p.F312F	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	340							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						ACTTTCCCTTCGATGCAGAAT	0.408													C|||	1681	0.335663	0.559	0.3084	5008	,	,		20009	0.1438		0.339	False		,,,				2504	0.2474				p.F340F		Atlas-SNP	.											.	AKR1B15	105	.	0			c.C1020T						PASS	.	C		2235,2169	554.5+/-379.0	576,1083,543	87.0	88.0	87.0		1020	-1.6	0.0	7	dbSNP_116	87	2959,5641	449.5+/-362.1	520,1919,1861	no	coding-synonymous	AKR1B15	NM_001080538.2		1096,3002,2404	TT,TC,CC		34.407,49.2507,39.9416		340/345	134264286	5194,7810	2202	4300	6502	SO:0001819	synonymous_variant	441282	exon12			TCCCTTCGATGCA		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"""Aldo-keto reductases"""	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.1020C>T	7.37:g.134264286C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	110	65	0.590909	NM_001080538	C9J3V2	Silent	SNP	ENST00000457545.2	37	CCDS47715.2																																																																																			C|0.651;T|0.349	0.349	strong		0.408	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2		
ARFGEF2	10564	hgsc.bcm.edu	37	20	47626847	47626847	+	Silent	SNP	T	T	C	rs2295580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47626847T>C	ENST00000371917.4	+	27	3663	c.3663T>C	c.(3661-3663)ggT>ggC	p.G1221G		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1221					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TCCGCTCAGGTTGGAAGAACA	0.567													C|||	1774	0.354233	0.5976	0.2752	5008	,	,		21249	0.1905		0.3171	False		,,,				2504	0.2883				p.G1221G	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											ARFGEF2,colon,carcinoma,0,1	ARFGEF2	160	1	0			c.T3663C						PASS	.	C		2283,2123	577.7+/-384.5	594,1095,514	139.0	109.0	119.0		3663	0.6	1.0	20	dbSNP_100	119	2970,5630	666.7+/-402.4	496,1978,1826	no	coding-synonymous	ARFGEF2	NM_006420.2		1090,3073,2340	CC,CT,TT		34.5349,48.1843,40.3891		1221/1786	47626847	5253,7753	2203	4300	6503	SO:0001819	synonymous_variant	10564	exon27			CTCAGGTTGGAAG	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.3663T>C	20.37:g.47626847T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																			A|0.003;C|0.372;G|0.003;T|0.622	0.372	strong		0.567	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420	
ARVCF	421	hgsc.bcm.edu	37	22	19960666	19960666	+	Missense_Mutation	SNP	G	G	A	rs115736959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19960666G>A	ENST00000263207.3	-	14	2705	c.2414C>T	c.(2413-2415)gCg>gTg	p.A805V	ARVCF_ENST00000401994.1_Missense_Mutation_p.A742V|ARVCF_ENST00000344269.3_Missense_Mutation_p.A742V|ARVCF_ENST00000406259.1_Missense_Mutation_p.A799V|ARVCF_ENST00000406522.1_Missense_Mutation_p.A736V	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	805					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)					AGCCACCAACGCTGGCACCCC	0.711													G|||	64	0.0127796	0.0446	0.0072	5008	,	,		10944	0.0		0.0	False		,,,				2504	0.0				p.A805V		Atlas-SNP	.											.	ARVCF	54	.	0			c.C2414T						PASS	.	G	VAL/ALA	188,4196		0,188,2004	19.0	18.0	18.0		2414	3.2	0.1	22	dbSNP_132	18	2,8574		0,2,4286	yes	missense	ARVCF	NM_001670.2	64	0,190,6290	AA,AG,GG		0.0233,4.2883,1.466	benign	805/963	19960666	190,12770	2192	4288	6480	SO:0001583	missense	421	exon14			ACCAACGCTGGCA		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.2414C>T	22.37:g.19960666G>A	ENSP00000263207:p.Ala805Val	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	15.10	2.734386	0.48939	0.042883	2.33E-4	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	4.34	3.24	0.37175	Armadillo-like helical (1);Armadillo-type fold (1);	0.113654	0.56097	D	0.000025	T	0.06325	0.0163	N	0.22421	0.69	0.36590	D	0.874035	P;D	0.54601	0.782;0.967	B;B	0.34779	0.189;0.163	T	0.07986	-1.0744	9	.	.	.	-12.0845	9.633	0.39791	0.0:0.0:0.6411:0.3589	.	805;321	O00192;E7EV58	ARVC_HUMAN;.	V	805;742;742;736;799	ENSP00000263207:A805V;ENSP00000342042:A742V;ENSP00000384341:A742V;ENSP00000384732:A736V;ENSP00000385444:A799V	.	A	-	2	0	ARVCF	18340666	0.895000	0.30542	0.102000	0.21198	0.078000	0.17371	3.057000	0.49931	2.416000	0.81992	0.561000	0.74099	GCG	G|0.985;A|0.015	0.015	strong		0.711	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558528	140558528	+	Missense_Mutation	SNP	A	A	G	rs3733694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140558528A>G	ENST00000239444.2	+	1	1158	c.913A>G	c.(913-915)Aag>Gag	p.K305E	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	305	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		K -> E (in dbSNP:rs3733694).		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)			AATTCGACTAAAGAAACAACT	0.393													A|||	644	0.128594	0.177	0.1787	5008	,	,		31989	0.0407		0.1531	False		,,,				2504	0.093				p.K305E		Atlas-SNP	.											.	PCDHB8	199	.	0			c.A913G						PASS	.	A	GLU/LYS	773,3633	308.8+/-290.8	70,633,1500	119.0	176.0	156.0		913	4.2	0.0	5	dbSNP_107	156	1246,7354	238.5+/-269.9	123,1000,3177	yes	missense	PCDHB8	NM_019120.3	56	193,1633,4677	GG,GA,AA		14.4884,17.5443,15.5236	benign	305/802	140558528	2019,10987	2203	4300	6503	SO:0001583	missense	56128	exon1			CGACTAAAGAAAC	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.913A>G	5.37:g.140558528A>G	ENSP00000239444:p.Lys305Glu	Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	151	74	0.490066	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	292	0.1336996336996337	92	0.18699186991869918	57	0.1574585635359116	26	0.045454545454545456	117	0.15435356200527706	A	2.278	-0.365459	0.05069	0.175443	0.144884	ENSG00000120322	ENST00000239444	T	0.01725	4.67	4.25	4.25	0.50352	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	M	0.72479	2.2	0.80722	P	0.0	B	0.33904	0.431	B	0.39971	0.315	T	0.42015	-0.9476	8	0.15952	T	0.53	.	9.2083	0.37302	0.8378:0.0:0.0:0.1622	rs3733694;rs17096956;rs17844492;rs3733694	305	Q9UN66	PCDB8_HUMAN	E	305	ENSP00000239444:K305E	ENSP00000239444:K305E	K	+	1	0	PCDHB8	140538712	0.000000	0.05858	0.017000	0.16124	0.014000	0.08584	-0.201000	0.09464	1.558000	0.49541	0.477000	0.44152	AAG	G|0.146;N|0.001	0.146	strong		0.393	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
GSG2	83903	hgsc.bcm.edu	37	17	3627619	3627619	+	Silent	SNP	C	C	T	rs1185511	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3627619C>T	ENST00000325418.4	+	1	409	c.390C>T	c.(388-390)tgC>tgT	p.C130C	ITGAE_ENST00000571185.1_5'UTR|ITGAE_ENST00000263087.4_Intron|CTD-3195I5.3_ENST00000571741.1_RNA	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	130					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)										GCACACCCTGCGGCCCGCTCC	0.731													C|||	804	0.160543	0.587	0.0403	5008	,	,		12752	0.0		0.0	False		,,,				2504	0.0				p.C130C		Atlas-SNP	.											.	GSG2	48	.	0			c.C390T						PASS	.	C	,	1822,2460		390,1042,709	6.0	8.0	8.0		,390	4.4	0.7	17	dbSNP_87	8	25,8313		0,25,4144	no	intron,coding-synonymous	ITGAE,GSG2	NM_002208.4,NM_031965.2	,	390,1067,4853	TT,TC,CC		0.2998,42.5502,14.6355	,	,130/799	3627619	1847,10773	2141	4169	6310	SO:0001819	synonymous_variant	83903	exon1			ACCCTGCGGCCCG	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.390C>T	17.37:g.3627619C>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	7	5	0.714286	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Silent	SNP	ENST00000325418.4	37	CCDS11036.1																																																																																			C|0.779;T|0.221	0.221	strong		0.731	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
PRDM6	93166	hgsc.bcm.edu	37	5	122515924	122515924	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:122515924G>A	ENST00000407847.4	+	7	1994	c.1580G>A	c.(1579-1581)cGg>cAg	p.R527Q		NM_001136239.1	NP_001129711.1	Q9NQX0	PRDM6_HUMAN	PR domain containing 6	527					negative regulation of smooth muscle cell differentiation (GO:0051151)|negative regulation of transcription, DNA-templated (GO:0045892)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	7						TCTAGTGACCGGCCTTTCAAG	0.542																																					p.R527Q		Atlas-SNP	.											PRDM6,colon,carcinoma,+1,1	PRDM6	26	1	0			c.G1580A						scavenged	.						71.0	80.0	77.0					5																	122515924		692	1591	2283	SO:0001583	missense	93166	exon7			GTGACCGGCCTTT	AF272898	CCDS47259.1	5q21-q23	2013-01-08			ENSG00000061455	ENSG00000061455		"""Zinc fingers, C2H2-type"""	9350	protein-coding gene	gene with protein product							Standard	NM_001136239		Approved		uc003kti.3	Q9NQX0	OTTHUMG00000150469	ENST00000407847.4:c.1580G>A	5.37:g.122515924G>A	ENSP00000384725:p.Arg527Gln	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	142	4	0.028169	NM_001136239	B5MCJ4|Q9NQW9	Missense_Mutation	SNP	ENST00000407847.4	37	CCDS47259.1	.	.	.	.	.	.	.	.	.	.	G	36	5.702179	0.96812	.	.	ENSG00000061455	ENST00000407847	T	0.16457	2.34	6.07	5.2	0.72013	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.20170	0.0485	L	0.41573	1.285	0.49213	D	0.999767	D	0.59357	0.985	P	0.45794	0.493	T	0.01130	-1.1442	10	0.87932	D	0	-33.2212	15.1361	0.72566	0.0673:0.0:0.9327:0.0	.	527	Q9NQX0	PRDM6_HUMAN	Q	527	ENSP00000384725:R527Q	ENSP00000384725:R527Q	R	+	2	0	PRDM6	122543823	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.009000	0.88606	1.571000	0.49722	0.655000	0.94253	CGG	.	.	none		0.542	PRDM6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318226.2	XM_049619	
BTNL9	153579	hgsc.bcm.edu	37	5	180485374	180485374	+	Silent	SNP	T	T	C	rs60738644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180485374T>C	ENST00000327705.9	+	10	1209	c.978T>C	c.(976-978)taT>taC	p.Y326Y	BTNL9_ENST00000376842.3_Silent_p.Y327Y	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	326	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCAAAAATATGCAGGTAACT	0.443													T|||	146	0.0291534	0.1044	0.0101	5008	,	,		19672	0.0		0.001	False		,,,				2504	0.0				p.Y326Y		Atlas-SNP	.											.	BTNL9	58	.	0			c.T978C						PASS	.	T		409,3997	201.1+/-224.2	21,367,1815	206.0	195.0	199.0		978	-0.5	0.8	5	dbSNP_129	199	3,8597	3.7+/-12.6	0,3,4297	no	coding-synonymous	BTNL9	NM_152547.4		21,370,6112	CC,CT,TT		0.0349,9.2828,3.1678		326/536	180485374	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	153579	exon10			AAAATATGCAGGT	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.978T>C	5.37:g.180485374T>C		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	303	141	0.465347	NM_152547	A6NL42|Q6P660|Q96DM5	Silent	SNP	ENST00000327705.9	37	CCDS4460.2																																																																																			T|0.963;C|0.037	0.037	strong		0.443	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547	
TMEM64	169200	hgsc.bcm.edu	37	8	91637929	91637929	+	Silent	SNP	T	T	C	rs75193995	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:91637929T>C	ENST00000458549.2	-	3	1290	c.1113A>G	c.(1111-1113)acA>acG	p.T371T	TMEM64_ENST00000519519.1_Silent_p.T110T|TMEM64_ENST00000418210.2_Silent_p.T319T	NM_001008495.3	NP_001008495.2	Q6YI46	TMM64_HUMAN	transmembrane protein 64	371					cytosolic calcium ion homeostasis (GO:0051480)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of ATPase activity (GO:0043462)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)	2			BRCA - Breast invasive adenocarcinoma(11;0.0598)			CTCCAGAAAATGTTAGGGTCC	0.408													T|||	27	0.00539137	0.0197	0.0014	5008	,	,		16021	0.0		0.0	False		,,,				2504	0.0				p.T371T		Atlas-SNP	.											.	TMEM64	31	.	0			c.A1113G						PASS	.	T	,	60,4346	57.4+/-93.9	2,56,2145	101.0	92.0	95.0		1113,957	-2.3	1.0	8	dbSNP_132	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TMEM64	NM_001008495.3,NM_001146273.1	,	2,57,6444	CC,CT,TT		0.0116,1.3618,0.469	,	371/381,319/329	91637929	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	169200	exon3			AGAAAATGTTAGG	AL834364	CCDS34920.2, CCDS55260.1	8q21.3	2005-08-09			ENSG00000180694	ENSG00000180694			25441	protein-coding gene	gene with protein product							Standard	NM_001008495		Approved	DKFZp762C1112	uc003yen.2	Q6YI46	OTTHUMG00000157185	ENST00000458549.2:c.1113A>G	8.37:g.91637929T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	174	77	0.442529	NM_001008495	B4DUC0|F5GXM4|Q2HIZ7|Q8N3G6	Silent	SNP	ENST00000458549.2	37	CCDS34920.2																																																																																			T|0.995;C|0.005	0.005	strong		0.408	TMEM64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347825.1	NM_001008495	
ZNFX1	57169	hgsc.bcm.edu	37	20	47874005	47874005	+	Silent	SNP	A	A	G	rs3021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47874005A>G	ENST00000396105.1	-	8	2859	c.2613T>C	c.(2611-2613)caT>caC	p.H871H	ZNFX1_ENST00000371752.1_Silent_p.H871H|ZNFX1_ENST00000371754.4_Silent_p.H871H	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	871							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CAGTGCCACAATGGTCTAGCC	0.567													A|||	691	0.137979	0.1921	0.17	5008	,	,		18090	0.0427		0.2018	False		,,,				2504	0.0746				p.H871H		Atlas-SNP	.											.	ZNFX1	194	.	0			c.T2613C						PASS	.	A		782,3624	316.9+/-294.8	64,654,1485	134.0	120.0	125.0		2613	-1.1	0.0	20	dbSNP_36	125	1928,6672	341.6+/-324.1	202,1524,2574	no	coding-synonymous	ZNFX1	NM_021035.2		266,2178,4059	GG,GA,AA		22.4186,17.7485,20.8365		871/1919	47874005	2710,10296	2203	4300	6503	SO:0001819	synonymous_variant	57169	exon8			GCCACAATGGTCT	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.2613T>C	20.37:g.47874005A>G		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	177	79	0.446328	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Silent	SNP	ENST00000396105.1	37	CCDS13417.1																																																																																			A|0.821;G|0.179;T|0.000	0.179	strong		0.567	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035	
SEZ6L	23544	hgsc.bcm.edu	37	22	26688401	26688401	+	Silent	SNP	T	T	C	rs16981666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26688401T>C	ENST00000248933.6	+	2	219	c.124T>C	c.(124-126)Ttg>Ctg	p.L42L	SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000403121.1_5'UTR|SEZ6L_ENST00000343706.4_Silent_p.L42L|SEZ6L_ENST00000360929.3_Silent_p.L42L|SEZ6L_ENST00000404234.3_Silent_p.L42L|SEZ6L_ENST00000529632.2_Silent_p.L42L			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	42					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						TGCTAGCCCTTTGGGTCCTTA	0.562													T|||	452	0.0902556	0.2322	0.0216	5008	,	,		18973	0.1012		0.0	False		,,,				2504	0.0286				p.L42L		Atlas-SNP	.											.	SEZ6L	174	.	0			c.T124C						PASS	.	T	,,,,,	955,3451	354.1+/-312.5	100,755,1348	47.0	39.0	42.0		124,124,124,124,124,124	-1.8	0.0	22	dbSNP_123	42	7,8593	5.0+/-18.6	0,7,4293	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	,,,,,	100,762,5641	CC,CT,TT		0.0814,21.675,7.3966	,,,,,	42/1024,42/1014,42/1012,42/950,42/949,42/1025	26688401	962,12044	2203	4300	6503	SO:0001819	synonymous_variant	23544	exon2			AGCCCTTTGGGTC	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.124T>C	22.37:g.26688401T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																			T|0.927;C|0.073	0.073	strong		0.562	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
PTBP1	5725	hgsc.bcm.edu	37	19	804327	804327	+	Silent	SNP	C	C	T	rs10420953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:804327C>T	ENST00000349038.4	+	5	397	c.324C>T	c.(322-324)aaC>aaT	p.N108N	PTBP1_ENST00000356948.6_Silent_p.N108N|MIR4745_ENST00000577608.1_RNA|PTBP1_ENST00000394601.4_Silent_p.N108N|PTBP1_ENST00000350092.4_Intron	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	108	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		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;0.000172)|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)		AGGCTGCCAACACCATGGTGA	0.627													C|||	448	0.0894569	0.0772	0.1527	5008	,	,		15416	0.0377		0.0934	False		,,,				2504	0.1104				p.N108N		Atlas-SNP	.											.	PTBP1	43	.	0			c.C324T						PASS	.	C	,,,	373,4033	187.4+/-214.1	21,331,1851	83.0	72.0	76.0		324,324,324,	4.6	1.0	19	dbSNP_119	76	791,7809	186.7+/-234.1	24,743,3533	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	45,1074,5384	TT,TC,CC		9.1977,8.4657,8.9497	,,,	108/558,108/551,108/532,	804327	1164,11842	2203	4300	6503	SO:0001819	synonymous_variant	5725	exon5			TGCCAACACCATG	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.324C>T	19.37:g.804327C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_031990	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.916;T|0.084	0.084	strong		0.627	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
FPR1	2357	hgsc.bcm.edu	37	19	52250216	52250216	+	Missense_Mutation	SNP	A	A	G	rs5030878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52250216A>G	ENST00000595042.1	-	3	173	c.32T>C	c.(31-33)aTc>aCc	p.I11T	FPR1_ENST00000304748.4_Missense_Mutation_p.I11T	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	11			I -> T (in dbSNP:rs5030878). {ECO:0000269|Ref.7}.		activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	CCCTCCAGAGATGTTCGTGGG	0.502													A|||	4177	0.834065	0.7852	0.7896	5008	,	,		20800	0.9613		0.7684	False		,,,				2504	0.8681				p.I11T		Atlas-SNP	.											.	FPR1	64	.	0			c.T32C	GRCh37	CM074875	FPR1	M	rs5030878	PASS	.	A	THR/ILE,THR/ILE	3488,918		1370,748,85	58.0	56.0	57.0		32,32	-6.9	0.0	19	dbSNP_113	57	6559,2041		2506,1547,247	yes	missense,missense	FPR1	NM_001193306.1,NM_002029.3	89,89	3876,2295,332	GG,GA,AA		23.7326,20.8352,22.751	benign,benign	11/351,11/351	52250216	10047,2959	2203	4300	6503	SO:0001583	missense	2357	exon3			CCAGAGATGTTCG	M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"""GPCR / Class A : Formyl peptide receptors"""	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.32T>C	19.37:g.52250216A>G	ENSP00000471493:p.Ile11Thr	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	227	117	0.515419	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	37	CCDS12839.1	1805	0.8264652014652014	377	0.766260162601626	290	0.8011049723756906	549	0.9597902097902098	589	0.7770448548812665	.	5.381	0.255528	0.10185	0.791648	0.762674	ENSG00000171051	ENST00000304748	T	0.37752	1.18	3.62	-6.88	0.01665	.	2.217780	0.02646	N	0.105855	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.13594	0.008	B	0.15484	0.013	T	0.28364	-1.0046	9	0.14252	T	0.57	.	0.3369	0.00327	0.245:0.2994:0.1958:0.2598	rs5030878;rs5030878	11	P21462	FPR1_HUMAN	T	11	ENSP00000302707:I11T	ENSP00000302707:I11T	I	-	2	0	FPR1	56942028	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.070000	0.01380	-1.802000	0.01244	0.533000	0.62120	ATC	A|0.201;G|0.799	0.799	strong		0.502	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029	
OR52E6	390078	hgsc.bcm.edu	37	11	5862845	5862845	+	Missense_Mutation	SNP	A	A	G	rs4592451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	135	0	0		WXS	Illumina HiSeq	Phase_I	145	74	0.510345	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	
FAM66D	100132923	hgsc.bcm.edu	37	8	11991328	11991328	+	RNA	SNP	G	G	A	rs144333235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11991328G>A	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		CTTCTCCCTGGGAGCAAGCTG	0.537													G|||	105	0.0209665	0.0749	0.0072	5008	,	,		22364	0.0		0.001	False		,,,				2504	0.0				p.P64L		Atlas-SNP	.											.	.	.	.	0			c.C191T						PASS	.																																					392197	exon1			TCCCTGGGAGCAA			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11991328G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	65	18	0.276923	NM_001256869		Missense_Mutation	SNP	ENST00000434078.2	37																																																																																				G|0.983;A|0.017	0.017	strong		0.537	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
B9D2	80776	hgsc.bcm.edu	37	19	41869392	41869392	+	Missense_Mutation	SNP	T	T	C	rs2241714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000539627.1_Intron|B9D2_ENST00000601597.1_5'UTR|TMEM91_ENST00000604123.1_Intron	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	117	0	0		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	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	
UGGT2	55757	hgsc.bcm.edu	37	13	96648384	96648384	+	Missense_Mutation	SNP	T	T	C	rs73562939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:96648384T>C	ENST00000376747.3	-	7	833	c.763A>G	c.(763-765)Act>Gct	p.T255A	UGGT2_ENST00000467305.1_5'UTR|UGGT2_ENST00000376714.3_Missense_Mutation_p.T255A|UGGT2_ENST00000397618.3_Missense_Mutation_p.T255A|UGGT2_ENST00000376712.4_Missense_Mutation_p.T255A	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	255					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						GTAGTATTAGTCACAGCTACA	0.328													T|||	102	0.0203674	0.0749	0.0029	5008	,	,		18668	0.0		0.001	False		,,,				2504	0.0				p.T255A		Atlas-SNP	.											.	UGGT2	127	.	0			c.A763G						PASS	.	T	ALA/THR	288,4116	158.1+/-190.9	10,268,1924	117.0	127.0	124.0		763	5.8	0.9	13	dbSNP_130	124	0,8598		0,0,4299	yes	missense	UGGT2	NM_020121.3	58	10,268,6223	CC,CT,TT		0.0,6.5395,2.215	benign	255/1517	96648384	288,12714	2202	4299	6501	SO:0001583	missense	55757	exon7			TATTAGTCACAGC	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.763A>G	13.37:g.96648384T>C	ENSP00000365938:p.Thr255Ala	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	215	98	0.455814	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	T	13.13	2.145554	0.37923	0.065395	0.0	ENSG00000102595	ENST00000376747;ENST00000376714;ENST00000397618;ENST00000376712	T;T	0.29397	1.57;1.57	5.84	5.84	0.93424	.	0.872316	0.10306	N	0.690619	T	0.02970	0.0088	L	0.60845	1.875	0.31130	N	0.707877	P;P;B	0.42692	0.787;0.787;0.004	B;B;B	0.36567	0.228;0.228;0.004	T	0.11966	-1.0566	10	0.87932	D	0	-2.0224	15.19	0.73035	0.0:0.0:0.0:1.0	.	255;255;255	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	A	255	ENSP00000365938:T255A;ENSP00000380743:T255A	ENSP00000365902:T255A	T	-	1	0	UGGT2	95446385	0.651000	0.27340	0.866000	0.34008	0.846000	0.48090	2.811000	0.47986	2.231000	0.72958	0.397000	0.26171	ACT	T|0.976;C|0.024	0.024	strong		0.328	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
SLC12A7	10723	hgsc.bcm.edu	37	5	1057738	1057738	+	Silent	SNP	G	G	A	rs60281693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:1057738G>A	ENST00000264930.5	-	22	2917	c.2874C>T	c.(2872-2874)acC>acT	p.T958T		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	958					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	TGTGGGACGCGGTGTTCCTGT	0.662													G|||	361	0.0720847	0.2564	0.0245	5008	,	,		12701	0.0		0.005	False		,,,				2504	0.0				p.T958T		Atlas-SNP	.											.	SLC12A7	97	.	0			c.C2874T						PASS	.	G		937,3469	355.1+/-312.9	103,731,1369	87.0	88.0	88.0		2874	-6.4	0.0	5	dbSNP_129	88	44,8554	27.9+/-77.7	1,42,4256	no	coding-synonymous	SLC12A7	NM_006598.2		104,773,5625	AA,AG,GG		0.5117,21.2665,7.5438		958/1084	1057738	981,12023	2203	4299	6502	SO:0001819	synonymous_variant	10723	exon22			GGACGCGGTGTTC	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2874C>T	5.37:g.1057738G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1	120	0.054945054945054944	110	0.22357723577235772	7	0.019337016574585635	1	0.0017482517482517483	2	0.002638522427440633	G	0.017	-1.499986	0.01001	0.212665	0.005117	ENSG00000113504	ENST00000513223	.	.	.	3.23	-6.45	0.01914	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.23036	P	0.99839583	.	.	.	.	.	.	T	0.20940	-1.0260	3	.	.	.	.	1.5148	0.02503	0.2916:0.095:0.3474:0.2659	rs60281693	.	.	.	C	316	.	.	R	-	1	0	SLC12A7	1110738	0.000000	0.05858	0.006000	0.13384	0.010000	0.07245	-6.333000	0.00070	-2.446000	0.00546	-1.786000	0.00637	CGC	G|0.931;A|0.069	0.069	strong		0.662	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
ITGB5	3693	hgsc.bcm.edu	37	3	124515509	124515509	+	Silent	SNP	G	G	A	rs2291088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	128	0	0		WXS	Illumina HiSeq	Phase_I	126	67	0.531746	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	
PRSS1	5644	hgsc.bcm.edu	37	7	142460744	142460744	+	Missense_Mutation	SNP	G	G	C	rs150930992		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142460744G>C	ENST00000311737.7	+	5	623	c.617G>C	c.(616-618)tGc>tCc	p.C206S	PRSS1_ENST00000486171.1_Missense_Mutation_p.C220S	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	206	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	CCTGTGGTCTGCAATGGACAG	0.493																																					p.C206S		Atlas-SNP	.											PRSS1,NS,carcinoma,0,1	PRSS1	68	1	0			c.G617C						scavenged	.						81.0	82.0	81.0					7																	142460744		2203	4300	6503	SO:0001583	missense	5644	exon5			TGGTCTGCAATGG	M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.617G>C	7.37:g.142460744G>C	ENSP00000308720:p.Cys206Ser	Somatic	382	2	0.0052356		WXS	Illumina HiSeq	Phase_I	420	10	0.0238095	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Missense_Mutation	SNP	ENST00000311737.7	37	CCDS5872.1	914	0.4184981684981685	216	0.43902439024390244	160	0.4419889502762431	196	0.34265734265734266	342	0.45118733509234826	G	11.31	1.601257	0.28534	.	.	ENSG00000204983	ENST00000486171;ENST00000311737;ENST00000529243	D;D	0.93712	-3.27;-3.27	3.18	2.29	0.28610	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.82630	2.6	0.58432	D	0.999991	B;B	0.27679	0.185;0.059	D;P	0.64595	0.927;0.814	T	0.00740	-1.1586	10	0.66056	D	0.02	.	9.9377	0.41561	0.1097:0.0:0.8903:0.0	.	220;206	E7EQ64;P07477	.;TRY1_HUMAN	S	220;206;196	ENSP00000417854:C220S;ENSP00000308720:C206S	ENSP00000308720:C206S	C	+	2	0	PRSS1	142140318	1.000000	0.71417	0.979000	0.43373	0.003000	0.03518	5.470000	0.66756	0.628000	0.30357	-1.112000	0.02068	TGC	G|0.582;C|0.418	0.418	strong		0.493	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		
WDR66	144406	hgsc.bcm.edu	37	12	122392038	122392038	+	Missense_Mutation	SNP	C	C	T	rs11043265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122392038C>T	ENST00000288912.4	+	10	2187	c.1333C>T	c.(1333-1335)Ctt>Ttt	p.L445F	WDR66_ENST00000397454.2_Missense_Mutation_p.L445F	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	445			L -> F (in dbSNP:rs11043265).				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)		CTTCAACAAGCTTGTGGGAAA	0.368													C|||	1555	0.310503	0.6309	0.0749	5008	,	,		16777	0.2937		0.0527	False		,,,				2504	0.3272				p.L445F	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C1333T						PASS	.	C	PHE/LEU,PHE/LEU	1972,1772		543,886,443	81.0	77.0	78.0		1333,1333	3.5	1.0	12	dbSNP_120	78	372,7830		7,358,3736	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	22,22	550,1244,4179	TT,TC,CC		4.5355,47.3291,19.6216	possibly-damaging,possibly-damaging	445/942,445/1150	122392038	2344,9602	1872	4101	5973	SO:0001583	missense	144406	exon10			AACAAGCTTGTGG	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.1333C>T	12.37:g.122392038C>T	ENSP00000288912:p.Leu445Phe	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	527	0.2413003663003663	304	0.6178861788617886	32	0.08839779005524862	149	0.26048951048951047	42	0.055408970976253295	C	11.39	1.624335	0.28889	0.526709	0.045355	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.53640	0.61;0.61	5.57	3.52	0.40303	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.877793	0.10201	N	0.703403	T	0.00012	0.0000	L	0.50333	1.59	0.47698	P	5.060000000000064E-4	B	0.33755	0.424	B	0.36378	0.223	T	0.40739	-0.9547	9	0.11485	T	0.65	.	9.323	0.37975	0.3608:0.5301:0.1091:0.0	rs11043265;rs52815107;rs58579724;rs11043265	445	Q8TBY9	WDR66_HUMAN	F	445	ENSP00000288912:L445F;ENSP00000380595:L445F	ENSP00000288912:L445F	L	+	1	0	WDR66	120876421	0.026000	0.19158	0.979000	0.43373	0.990000	0.78478	0.184000	0.16939	1.295000	0.44724	0.491000	0.48974	CTT	C|0.752;T|0.248	0.248	strong		0.368	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
NYNRIN	57523	hgsc.bcm.edu	37	14	24877699	24877699	+	Missense_Mutation	SNP	A	A	G	rs74036628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24877699A>G	ENST00000382554.3	+	3	1141	c.823A>G	c.(823-825)Agc>Ggc	p.S275G		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	275					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						CACAGCCCAGAGCACACCGCA	0.557													A|||	428	0.0854633	0.1377	0.036	5008	,	,		17776	0.1429		0.002	False		,,,				2504	0.0767				p.S275G		Atlas-SNP	.											.	NYNRIN	120	.	0			c.A823G						PASS	.	A	GLY/SER	401,3803		17,367,1718	16.0	18.0	17.0		823	3.8	0.0	14	dbSNP_130	17	13,8425		0,13,4206	yes	missense	NYNRIN	NM_025081.2	56	17,380,5924	GG,GA,AA		0.1541,9.5385,3.2748	benign	275/1899	24877699	414,12228	2102	4219	6321	SO:0001583	missense	57523	exon3			GCCCAGAGCACAC	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.823A>G	14.37:g.24877699A>G	ENSP00000371994:p.Ser275Gly	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	140	0.0641025641025641	61	0.12398373983739837	9	0.024861878453038673	68	0.11888111888111888	2	0.002638522427440633	A	3.063	-0.192825	0.06259	0.095385	0.001541	ENSG00000205978	ENST00000382554	T	0.11495	2.77	4.96	3.82	0.43975	.	3.272380	0.00664	N	0.000601	T	0.00109	0.0003	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30179	-0.9987	9	0.26408	T	0.33	.	7.2075	0.25915	0.9008:0.0:0.0992:0.0	.	275	Q9P2P1	NYNRI_HUMAN	G	275	ENSP00000371994:S275G	ENSP00000371994:S275G	S	+	1	0	NYNRIN	23947539	0.001000	0.12720	0.036000	0.18154	0.099000	0.18886	0.882000	0.28186	0.909000	0.36697	0.459000	0.35465	AGC	A|0.934;G|0.066	0.066	strong		0.557	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1		
GGH	8836	hgsc.bcm.edu	37	8	63938764	63938764	+	Missense_Mutation	SNP	G	G	A	rs11545078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:63938764G>A	ENST00000260118.6	-	5	854	c.452C>T	c.(451-453)aCt>aTt	p.T151I	RP11-659E9.4_ENST00000521556.1_RNA|GGH_ENST00000518113.1_5'UTR	NM_003878.2	NP_003869.1	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase)	151	Gamma-glutamyl hydrolase. {ECO:0000255|PROSITE-ProRule:PRU00607}.		T -> I (in dbSNP:rs11545078).		glutamine metabolic process (GO:0006541)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	exopeptidase activity (GO:0008238)|gamma-glutamyl-peptidase activity (GO:0034722)|omega peptidase activity (GO:0008242)	p.T151I(1)		breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(6)|stomach(1)	11	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|Methotrexate(DB00563)	ATCTGTGGCAGTTAATAAGCA	0.433													G|||	428	0.0854633	0.056	0.0403	5008	,	,		17363	0.0873		0.0924	False		,,,				2504	0.1483				p.T151I		Atlas-SNP	.											GGH,NS,carcinoma,0,1	GGH	32	1	1	Substitution - Missense(1)	stomach(1)	c.C452T	GRCh37	CM042063	GGH	M	rs11545078	PASS	.	G	ILE/THR	265,4141	150.3+/-184.3	3,259,1941	127.0	112.0	117.0		452	5.9	0.9	8	dbSNP_120	117	826,7774	190.3+/-236.8	38,750,3512	yes	missense	GGH	NM_003878.2	89	41,1009,5453	AA,AG,GG		9.6047,6.0145,8.3884	possibly-damaging	151/319	63938764	1091,11915	2203	4300	6503	SO:0001583	missense	8836	exon5			GTGGCAGTTAATA	U55206	CCDS6177.1	8q12.3	2008-02-05			ENSG00000137563	ENSG00000137563	3.4.19.9		4248	protein-coding gene	gene with protein product		601509				8816764, 10570974	Standard	NM_003878		Approved		uc003xuw.3	Q92820	OTTHUMG00000164365	ENST00000260118.6:c.452C>T	8.37:g.63938764G>A	ENSP00000260118:p.Thr151Ile	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	119	58	0.487395	NM_003878		Missense_Mutation	SNP	ENST00000260118.6	37	CCDS6177.1	156	0.07142857142857142	25	0.0508130081300813	15	0.04143646408839779	46	0.08041958041958042	70	0.09234828496042216	G	17.79	3.475038	0.63737	0.060145	0.096047	ENSG00000137563	ENST00000260118;ENST00000517622	T	0.44482	0.92	5.93	5.93	0.95920	.	0.135994	0.64402	D	0.000004	T	0.01287	0.0042	L	0.60845	1.875	0.09310	P	0.99999826864	P	0.38395	0.629	B	0.32928	0.155	T	0.03148	-1.1067	9	0.38643	T	0.18	-19.5529	19.1049	0.93290	0.0:0.0:1.0:0.0	rs11545078;rs61629507	151	Q92820	GGH_HUMAN	I	151;112	ENSP00000260118:T151I	ENSP00000260118:T151I	T	-	2	0	GGH	64101318	0.987000	0.35691	0.896000	0.35187	0.027000	0.11550	4.169000	0.58223	2.818000	0.97014	0.591000	0.81541	ACT	G|0.919;A|0.081	0.081	strong		0.433	GGH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378453.1		
ORM2	5005	hgsc.bcm.edu	37	9	117094119	117094119	+	Silent	SNP	G	G	A	rs148394636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117094119G>A	ENST00000431067.2	+	5	486	c.450G>A	c.(448-450)gaG>gaA	p.E150E	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	150					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	ACAAGCCAGAGACGACCAAGG	0.602													G|||	399	0.0796725	0.2943	0.0144	5008	,	,		17341	0.0		0.0	False		,,,				2504	0.0				p.E150E	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G450A						PASS	.	G		955,3451	347.2+/-309.4	112,731,1360	59.0	63.0	62.0		450	-2.4	0.0	9	dbSNP_134	62	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	ORM2	NM_000608.2		112,732,5656	AA,AG,GG		0.0116,21.675,7.3538		150/202	117094119	956,12044	2203	4297	6500	SO:0001819	synonymous_variant	5005	exon5			GCCAGAGACGACC		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.450G>A	9.37:g.117094119G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	182	46	0.252747	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Silent	SNP	ENST00000431067.2	37	CCDS6804.1																																																																																			G|0.931;A|0.069	0.069	strong		0.602	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
OAS2	4939	hgsc.bcm.edu	37	12	113435450	113435450	+	Silent	SNP	A	A	T	rs1293755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113435450A>T	ENST00000342315.4	+	4	967	c.753A>T	c.(751-753)gtA>gtT	p.V251V	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Silent_p.V251V	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	251	OAS domain 1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						TCAGAACCGTACTGGAGCTGA	0.512													T|||	4395	0.877596	0.9887	0.7997	5008	,	,		22556	1.0		0.6819	False		,,,				2504	0.8579				p.V251V	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.A753T						PASS	.	T	,	4143,263	149.5+/-183.7	1945,253,5	125.0	109.0	114.0		753,753	-3.0	0.0	12	dbSNP_87	114	5905,2695	431.6+/-356.9	2039,1827,434	no	coding-synonymous,coding-synonymous	OAS2	NM_002535.2,NM_016817.2	,	3984,2080,439	TT,TA,AA		31.3372,5.9691,22.7433	,	251/688,251/720	113435450	10048,2958	2203	4300	6503	SO:0001819	synonymous_variant	4939	exon4			AACCGTACTGGAG	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.753A>T	12.37:g.113435450A>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Silent	SNP	ENST00000342315.4	37	CCDS31906.1																																																																																			A|0.208;T|0.792	0.792	strong		0.512	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1		
TTC3	7267	hgsc.bcm.edu	37	21	38568308	38568308	+	Silent	SNP	C	C	T	rs6579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38568308C>T	ENST00000399017.2	+	42	8297	c.5550C>T	c.(5548-5550)caC>caT	p.H1850H	TTC3_ENST00000355666.1_Silent_p.H1850H|TTC3-AS1_ENST00000424733.1_RNA|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Silent_p.H1850H	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1850					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TTATTGAGCACCTGTCAGTGG	0.443													C|||	2965	0.592053	0.6445	0.6282	5008	,	,		19670	0.6032		0.4642	False		,,,				2504	0.6155				p.H1850H	Ovarian(38;194 1649 35661)	Atlas-SNP	.											TTC3,NS,carcinoma,+1,1	TTC3	182	1	0			c.C5550T						PASS	.	C	,	2767,1637	635.0+/-396.3	869,1029,304	46.0	56.0	53.0		5550,5550	1.3	0.6	21	dbSNP_52	53	3845,4755	518.9+/-379.4	898,2049,1353	no	coding-synonymous,coding-synonymous	TTC3	NM_001001894.1,NM_003316.3	,	1767,3078,1657	TT,TC,CC		44.7093,37.1708,49.1541	,	1850/2026,1850/2026	38568308	6612,6392	2202	4300	6502	SO:0001819	synonymous_variant	7267	exon42			TGAGCACCTGTCA	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5550C>T	21.37:g.38568308C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1	1238	0.5668498168498168	315	0.6402439024390244	219	0.6049723756906077	357	0.6241258741258742	347	0.4577836411609499	C	8.684	0.905837	0.17760	0.628292	0.447093	ENSG00000182670	ENST00000428693	.	.	.	4.34	1.26	0.21427	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999727439	.	.	.	.	.	.	T	0.42766	-0.9432	3	.	.	.	-3.1681	5.8525	0.18701	0.0:0.5031:0.3875:0.1093	rs6579;rs762138;rs1053981;rs3194540;rs59448802;rs6579	.	.	.	S	142	.	.	P	+	1	0	TTC3	37490178	0.995000	0.38212	0.614000	0.29051	0.859000	0.49053	0.114000	0.15520	0.337000	0.23665	0.467000	0.42956	CCT	C|0.476;T|0.524	0.524	strong		0.443	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
RUFY1	80230	hgsc.bcm.edu	37	5	179025789	179025789	+	Silent	SNP	G	G	A	rs72824522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179025789G>A	ENST00000319449.4	+	14	1740	c.1728G>A	c.(1726-1728)agG>agA	p.R576R	RUFY1_ENST00000437570.2_Silent_p.R468R|RP11-1379J22.2_ENST00000500262.1_RNA|RUFY1_ENST00000393438.2_Silent_p.R468R|RUFY1_ENST00000377001.2_3'UTR	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	576					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)			CTCTACTCAGGATGGAGCTGC	0.522										HNSCC(44;0.11)			G|||	361	0.0720847	0.0378	0.0764	5008	,	,		19945	0.0853		0.1064	False		,,,				2504	0.0665				p.R576R		Atlas-SNP	.											.	RUFY1	101	.	0			c.G1728A						PASS	.	G	,,	194,4212	122.9+/-160.3	6,182,2015	113.0	110.0	111.0		1404,1404,1728	-2.1	0.0	5	dbSNP_130	111	956,7644	208.4+/-249.9	60,836,3404	no	coding-synonymous,coding-synonymous,coding-synonymous	RUFY1	NM_001040451.1,NM_001040452.1,NM_025158.3	,,	66,1018,5419	AA,AG,GG		11.1163,4.4031,8.8421	,,	468/601,468/601,576/709	179025789	1150,11856	2203	4300	6503	SO:0001819	synonymous_variant	80230	exon14			ACTCAGGATGGAG	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.1728G>A	5.37:g.179025789G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	219	95	0.43379	NM_025158	Q59FF3|Q71S93|Q9H6I3	Silent	SNP	ENST00000319449.4	37	CCDS4445.2	173	0.07921245421245421	23	0.046747967479674794	28	0.07734806629834254	47	0.08216783216783216	75	0.09894459102902374	G	0.032	-1.325400	0.01309	0.044031	0.111163	ENSG00000176783	ENST00000502434	.	.	.	4.98	-2.1	0.07210	.	.	.	.	.	T	0.00608	0.0020	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.21143	-1.0254	3	.	.	.	-1.642	6.3823	0.21542	0.4772:0.1314:0.3914:0.0	.	.	.	.	N	254	.	.	D	+	1	0	RUFY1	178958395	0.235000	0.23794	0.001000	0.08648	0.019000	0.09904	0.424000	0.21330	-0.693000	0.05121	-0.459000	0.05422	GAT	G|0.912;A|0.088	0.088	strong		0.522	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451	
EIF4G2	1982	hgsc.bcm.edu	37	11	10821185	10821185	+	Silent	SNP	G	G	A	rs11542384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:10821185G>A	ENST00000526148.1	-	19	2748	c.2238C>T	c.(2236-2238)tcC>tcT	p.S746S	EIF4G2_ENST00000396525.2_Silent_p.S708S|SNORD97_ENST00000459187.1_RNA|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000339995.5_Silent_p.S746S|EIF4G2_ENST00000525681.1_Silent_p.S746S	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TGGTTTGAGGGGATGGATCCA	0.378													G|||	614	0.122604	0.4342	0.0504	5008	,	,		20172	0.0		0.005	False		,,,				2504	0.0				p.S746S		Atlas-SNP	.											.	EIF4G2	89	.	0			c.C2238T						PASS	.	G	,,	1686,2716	512.4+/-368.1	337,1012,852	148.0	145.0	146.0		2124,2238,2238	4.6	1.0	11	dbSNP_120	146	27,8561	17.3+/-56.4	0,27,4267	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF4G2	NM_001042559.2,NM_001172705.1,NM_001418.3	,,	337,1039,5119	AA,AG,GG		0.3144,38.3008,13.1871	,,	708/870,746/908,746/908	10821185	1713,11277	2201	4294	6495	SO:0001819	synonymous_variant	1982	exon19			TTGAGGGGATGGA	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.2238C>T	11.37:g.10821185G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	198	86	0.434343	NM_001172705		Silent	SNP	ENST00000526148.1	37	CCDS31428.1																																																																																			T|0.000;G|0.885;C|0.000;A|0.115	0.115	strong		0.378	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418	
KDM1B	221656	hgsc.bcm.edu	37	6	18213988	18213988	+	Silent	SNP	C	C	T	rs6903583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:18213988C>T	ENST00000297792.5	+	15	1566	c.1389C>T	c.(1387-1389)gcC>gcT	p.A463A	KDM1B_ENST00000397244.1_Silent_p.A464A|KDM1B_ENST00000388870.2_Silent_p.A696A|KDM1B_ENST00000546309.2_Intron			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	695					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						GGCTTTTTGCCGTGTTCTATG	0.423													C|||	701	0.139976	0.2118	0.1715	5008	,	,		19432	0.005		0.2107	False		,,,				2504	0.0869				p.A463A		Atlas-SNP	.											.	KDM1B	58	.	0			c.C1389T						PASS	.	C		912,3494	352.1+/-311.5	106,700,1397	170.0	164.0	166.0		1389	-1.9	0.9	6	dbSNP_116	166	1918,6682	340.5+/-323.6	226,1466,2608	no	coding-synonymous	KDM1B	NM_153042.3		332,2166,4005	TT,TC,CC		22.3023,20.699,21.7592		463/591	18213988	2830,10176	2203	4300	6503	SO:0001819	synonymous_variant	221656	exon15			TTTTGCCGTGTTC	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"""Chromatin-modifying enzymes / K-demethylases"""	21577	protein-coding gene	gene with protein product		613081	"""amine oxidase, flavin containing 1"", ""chromosome 6 open reading frame 193"", ""amine oxidase (flavin containing) domain 1"""	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.1389C>T	6.37:g.18213988C>T		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	242	107	0.442149	NM_153042	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Silent	SNP	ENST00000297792.5	37	CCDS34343.1	348	0.15934065934065933	101	0.20528455284552846	72	0.19889502762430938	2	0.0034965034965034965	173	0.22823218997361477	C	11.72	1.721985	0.30503	0.20699	0.223023	ENSG00000165097	ENST00000449850	.	.	.	5.88	-1.92	0.07618	.	.	.	.	.	T	0.19327	0.0464	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.19063	-1.0317	3	.	.	.	-23.6373	7.6149	0.28152	0.0:0.4205:0.126:0.4534	rs6903583;rs6903583	.	.	.	L	513	.	.	P	+	2	0	KDM1B	18321967	0.306000	0.24490	0.946000	0.38457	0.991000	0.79684	-0.426000	0.07008	-0.302000	0.08869	-0.238000	0.12139	CCG	C|0.808;T|0.192	0.192	strong		0.423	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042	
DMXL2	23312	hgsc.bcm.edu	37	15	51783820	51783820	+	Silent	SNP	T	T	C	rs10851500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51783820T>C	ENST00000251076.5	-	20	5195	c.4908A>G	c.(4906-4908)ggA>ggG	p.G1636G	DMXL2_ENST00000449909.3_Silent_p.G1000G|DMXL2_ENST00000543779.2_Silent_p.G1636G|RP11-707P17.1_ENST00000561007.1_RNA	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	87	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	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	
COL24A1	255631	hgsc.bcm.edu	37	1	86591141	86591141	+	Missense_Mutation	SNP	A	A	G	rs17128866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:86591141A>G	ENST00000370571.2	-	3	1244	c.878T>C	c.(877-879)aTc>aCc	p.I293T	COL24A1_ENST00000436319.1_Missense_Mutation_p.I293T	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	293			I -> T (in dbSNP:rs17128866).		extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		ATTTTTTATGATATTTGGAAT	0.383													A|||	321	0.0640974	0.0227	0.0375	5008	,	,		19786	0.1538		0.0616	False		,,,				2504	0.0491				p.I293T		Atlas-SNP	.											COL24A1,NS,carcinoma,+1,2	COL24A1	202	2	0			c.T878C						PASS	.	A	THR/ILE	93,3577		5,83,1747	111.0	104.0	106.0		878	-0.7	0.0	1	dbSNP_123	106	637,7565		24,589,3488	yes	missense	COL24A1	NM_152890.5	89	29,672,5235	GG,GA,AA		7.7664,2.5341,6.1489	benign	293/1715	86591141	730,11142	1835	4101	5936	SO:0001583	missense	255631	exon3			TTTATGATATTTG	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.878T>C	1.37:g.86591141A>G	ENSP00000359603:p.Ile293Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	117	64	0.547009	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	183	0.08379120879120878	19	0.03861788617886179	19	0.052486187845303865	94	0.16433566433566432	51	0.06728232189973615	A	0.024	-1.391107	0.01185	0.025341	0.077664	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.95412	-3.7;-3.7	5.27	-0.689	0.11313	.	1.491040	0.04786	N	0.430736	T	0.74382	0.3709	N	0.08118	0	0.80722	P	0.0	B;B	0.24426	0.103;0.012	B;B	0.21917	0.037;0.007	T	0.71981	-0.4428	9	0.19590	T	0.45	.	2.514	0.04663	0.52:0.2221:0.1493:0.1086	rs17128866;rs52821261;rs17128866	293;293	F8WDM8;Q17RW2	.;COOA1_HUMAN	T	293	ENSP00000359603:I293T;ENSP00000392531:I293T	ENSP00000359603:I293T	I	-	2	0	COL24A1	86363729	0.000000	0.05858	0.000000	0.03702	0.148000	0.21650	-0.015000	0.12634	-0.024000	0.13941	0.460000	0.39030	ATC	A|0.915;G|0.085	0.085	strong		0.383	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
PVR	5817	hgsc.bcm.edu	37	19	45150763	45150763	+	Silent	SNP	G	G	A	rs10421291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45150763G>A	ENST00000425690.3	+	2	647	c.348G>A	c.(346-348)gaG>gaA	p.E116E	PVR_ENST00000406449.4_Silent_p.E116E|PVR_ENST00000344956.4_Silent_p.E116E|PVR_ENST00000403059.4_Silent_p.E116E|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	116	Ig-like V-type.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		TGCGCGTAGAGGATGAAGGCA	0.617													G|||	250	0.0499201	0.1755	0.0259	5008	,	,		10654	0.0		0.0	False		,,,				2504	0.0				p.E116E		Atlas-SNP	.											.	PVR	23	.	0			c.G348A						PASS	.	G	,,,	658,3748	275.2+/-272.4	60,538,1605	59.0	53.0	55.0		348,348,348,348	-5.9	0.0	19	dbSNP_119	55	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	,,,	60,544,5899	AA,AG,GG		0.0698,14.9342,5.1053	,,,	116/373,116/365,116/393,116/418	45150763	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	5817	exon2			CGTAGAGGATGAA	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9705	protein-coding gene	gene with protein product	"""nectin-like 5"""	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.348G>A	19.37:g.45150763G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Silent	SNP	ENST00000425690.3	37	CCDS12640.1																																																																																			G|0.937;A|0.063	0.063	strong		0.617	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51917735	51917735	+	Silent	SNP	G	G	A	rs1974821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51917735G>A	ENST00000339313.5	-	9	1766	c.1650C>T	c.(1648-1650)aaC>aaT	p.N550N	SIGLEC10_ENST00000432469.2_Silent_p.N372N|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000439889.2_Silent_p.N492N|SIGLEC10_ENST00000353836.5_Silent_p.N455N|SIGLEC10_ENST00000441969.3_Silent_p.N397N|SIGLEC10_ENST00000525998.1_Silent_p.N365N|SIGLEC10_ENST00000436984.2_Silent_p.N407N|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.N550N|SIGLEC10_ENST00000442846.3_Silent_p.N307N|CTD-2616J11.2_ENST00000526996.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	550					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.N492N(1)|p.N550N(1)		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)		GAAACGCTCCGTTGGAGAATG	0.587													g|||	1142	0.228035	0.3404	0.1816	5008	,	,		18581	0.2113		0.1451	False		,,,				2504	0.2117				p.N550N		Atlas-SNP	.											SIGLEC12_ENST00000439889,NS,carcinoma,0,2	SIGLEC10	112	2	2	Substitution - coding silent(2)	stomach(2)	c.C1650T						scavenged	.	G	,,,,,,	1407,2999		211,985,1007	99.0	88.0	92.0		1476,1365,1221,1191,1116,921,1650	-9.1	0.0	19	dbSNP_92	92	1207,7393		84,1039,3177	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	,,,,,,	295,2024,4184	AA,AG,GG		14.0349,31.9337,20.0984	,,,,,,	492/640,455/603,407/555,397/545,372/520,307/455,550/698	51917735	2614,10392	2203	4300	6503	SO:0001819	synonymous_variant	89790	exon9			CGCTCCGTTGGAG	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.1650C>T	19.37:g.51917735G>A		Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	98	66	0.673469	NM_033130	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			G|0.795;A|0.205	0.205	strong		0.587	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769276	43769276	+	Silent	SNP	T	T	C	rs10880473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:43769276T>C	ENST00000389420.3	-	36	5351	c.5352A>G	c.(5350-5352)agA>agG	p.R1784R		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1784	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		AGTCTTCCCTTCTACTCCCAT	0.348													C|||	1121	0.223842	0.4266	0.1239	5008	,	,		18065	0.1002		0.1998	False		,,,				2504	0.1728				p.R1784R		Atlas-SNP	.											ADAMTS20_ENST00000389420,neck,malignant_melanoma,-2,1	ADAMTS20	635	1	0			c.A5352G						PASS	.	C		1647,2759	659.9+/-400.6	316,1015,872	156.0	153.0	154.0		5352	2.0	1.0	12	dbSNP_120	154	1768,6832	734.1+/-406.9	182,1404,2714	no	coding-synonymous	ADAMTS20	NM_025003.3		498,2419,3586	CC,CT,TT		20.5581,37.3808,26.2571		1784/1911	43769276	3415,9591	2203	4300	6503	SO:0001819	synonymous_variant	80070	exon36			TTCCCTTCTACTC	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.5352A>G	12.37:g.43769276T>C		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	131	75	0.572519	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	CCDS31778.2																																																																																			T|0.747;C|0.253	0.253	strong		0.348	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
TTC21A	199223	hgsc.bcm.edu	37	3	39180099	39180099	+	Silent	SNP	T	T	C	rs784498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39180099T>C	ENST00000431162.2	+	28	4004	c.3870T>C	c.(3868-3870)atT>atC	p.I1290I	TTC21A_ENST00000301819.6_Silent_p.I1291I|TTC21A_ENST00000440121.1_Silent_p.I1242I|TTC21A_ENST00000493856.1_3'UTR			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	1290										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)		TGGAGGCCATTGAAATCTGCA	0.527													C|||	3540	0.706869	0.5189	0.7435	5008	,	,		21037	0.7669		0.7654	False		,,,				2504	0.8129				p.I1290I		Atlas-SNP	.											.	TTC21A	96	.	0			c.T3870C						PASS	.	C	,	2435,1579		739,957,311	112.0	110.0	110.0		3726,3870	-10.3	0.5	3	dbSNP_86	110	6255,2071		2385,1485,293	no	coding-synonymous,coding-synonymous	TTC21A	NM_001105513.2,NM_145755.2	,	3124,2442,604	CC,CT,TT		24.8739,39.3373,29.5786	,	1242/1273,1290/1321	39180099	8690,3650	2007	4163	6170	SO:0001819	synonymous_variant	199223	exon28			GGCCATTGAAATC	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.3870T>C	3.37:g.39180099T>C		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	229	229	1	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Silent	SNP	ENST00000431162.2	37	CCDS46800.1																																																																																			T|0.306;C|0.694	0.694	strong		0.527	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
CYLD	1540	hgsc.bcm.edu	37	16	50783696	50783696	+	Silent	SNP	C	C	T	rs34564491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50783696C>T	ENST00000427738.3	+	2	292	c.87C>T	c.(85-87)agC>agT	p.S29S	CYLD_ENST00000311559.9_Silent_p.S29S|CYLD_ENST00000540145.1_Silent_p.S29S|CYLD_ENST00000568704.2_Silent_p.S29S|CYLD_ENST00000566206.1_Silent_p.S29S|CYLD_ENST00000569418.1_Silent_p.S29S|CYLD_ENST00000398568.2_Silent_p.S29S|CYLD_ENST00000564326.1_Silent_p.S29S			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	29					cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				AAGAATGCAGCGTTACAGACA	0.408			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis				C|||	63	0.0125799	0.0446	0.0058	5008	,	,		18761	0.0		0.0	False		,,,				2504	0.0				p.S29S		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.C87T						PASS	.	C	,,	145,3565		2,141,1712	83.0	79.0	80.0		87,87,87	2.0	1.0	16	dbSNP_126	80	1,8179		0,1,4089	no	coding-synonymous,coding-synonymous,coding-synonymous	CYLD	NM_001042355.1,NM_001042412.1,NM_015247.2	,,	2,142,5801	TT,TC,CC		0.0122,3.9084,1.2279	,,	29/954,29/954,29/957	50783696	146,11744	1855	4090	5945	SO:0001819	synonymous_variant	1540	exon3	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	ATGCAGCGTTACA	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.87C>T	16.37:g.50783696C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_001042355	O94934|Q7L3N6|Q96EH0|Q9NZX9	Silent	SNP	ENST00000427738.3	37	CCDS45482.1																																																																																			C|0.991;T|0.009	0.009	strong		0.408	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
VCAN	1462	hgsc.bcm.edu	37	5	82835852	82835852	+	Missense_Mutation	SNP	C	C	T	rs61733401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82835852C>T	ENST00000265077.3	+	8	7595	c.7030C>T	c.(7030-7032)Ccc>Tcc	p.P2344S	VCAN_ENST00000343200.5_Missense_Mutation_p.P1357S|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2344	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AGCAGAAGGACCCACGGTGGC	0.468													C|||	165	0.0329473	0.1172	0.0101	5008	,	,		19057	0.0		0.003	False		,,,				2504	0.0				p.P2344S		Atlas-SNP	.											.	VCAN	498	.	0			c.C7030T						PASS	.	C	,SER/PRO,,SER/PRO	417,3989	203.8+/-226.2	21,375,1807	90.0	85.0	87.0		,4069,,7030	2.0	0.0	5	dbSNP_129	87	4,8596	3.7+/-12.6	0,4,4296	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,74,,74	21,379,6103	TT,TC,CC		0.0465,9.4644,3.237	,benign,,benign	,1357/2410,,2344/3397	82835852	421,12585	2203	4300	6503	SO:0001583	missense	1462	exon8			GAAGGACCCACGG	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.7030C>T	5.37:g.82835852C>T	ENSP00000265077:p.Pro2344Ser	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	175	80	0.457143	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	64	0.029304029304029304	61	0.12398373983739837	3	0.008287292817679558	0	0.0	0	0.0	C	2.456	-0.325144	0.05350	0.094644	4.65E-4	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.37235	1.21;1.21	6.07	2.02	0.26589	.	0.557747	0.17822	N	0.160824	T	0.00271	0.0008	L	0.41824	1.3	0.09310	N	1	P;P	0.38597	0.639;0.506	B;B	0.30029	0.11;0.051	T	0.07539	-1.0767	10	0.09843	T	0.71	.	6.8445	0.23980	0.3387:0.5251:0.0:0.1362	rs61733401	1357;2344	P13611-2;P13611	.;CSPG2_HUMAN	S	2344;1357	ENSP00000265077:P2344S;ENSP00000340062:P1357S	ENSP00000265077:P2344S	P	+	1	0	VCAN	82871608	0.000000	0.05858	0.007000	0.13788	0.153000	0.21895	-0.086000	0.11233	0.839000	0.34971	0.650000	0.86243	CCC	C|0.965;T|0.035	0.035	strong		0.468	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
DSPP	1834	hgsc.bcm.edu	37	4	88537306	88537306	+	Silent	SNP	T	T	C	rs537399785|rs374381786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88537306T>C	ENST00000282478.7	+	4	3525	c.3492T>C	c.(3490-3492)gaT>gaC	p.D1164D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1164D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1164	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgatagcagcgaca	0.557																																					p.D1164D		Atlas-SNP	.											DSPP,rectum,carcinoma,0,2	DSPP	174	2	0			c.T3492C						scavenged	.						42.0	57.0	52.0					4																	88537306		1574	2772	4346	SO:0001819	synonymous_variant	1834	exon5			CAGCGATAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3492T>C	4.37:g.88537306T>C		Somatic	183	3	0.0163934		WXS	Illumina HiSeq	Phase_I	402	36	0.0895522	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.557	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ITGA9	3680	hgsc.bcm.edu	37	3	37536020	37536020	+	Silent	SNP	C	C	T	rs62001860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37536020C>T	ENST00000264741.5	+	5	829	c.573C>T	c.(571-573)caC>caT	p.H191H	ITGA9_ENST00000422441.1_Silent_p.H191H	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	191					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GAGAGGAACACGGCTCCTGCC	0.532													C|||	36	0.0071885	0.0272	0.0	5008	,	,		20312	0.0		0.0	False		,,,				2504	0.0				p.H191H		Atlas-SNP	.											.	ITGA9	98	.	0			c.C573T						PASS	.	C		68,4338	64.1+/-101.4	0,68,2135	152.0	152.0	152.0		573	-0.1	1.0	3	dbSNP_129	152	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITGA9	NM_002207.2		0,69,6434	TT,TC,CC		0.0116,1.5433,0.5305		191/1036	37536020	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	3680	exon5			GGAACACGGCTCC	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.573C>T	3.37:g.37536020C>T		Somatic	326	1	0.00306748		WXS	Illumina HiSeq	Phase_I	312	150	0.480769	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																			C|0.994;T|0.006	0.006	strong		0.532	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
RREB1	6239	hgsc.bcm.edu	37	6	7229346	7229346	+	Silent	SNP	T	T	C	rs2714315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	96	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	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		
GPSM2	29899	hgsc.bcm.edu	37	1	109465084	109465084	+	Missense_Mutation	SNP	T	T	A	rs61758992		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109465084T>A	ENST00000406462.2	+	14	2259	c.1486T>A	c.(1486-1488)Tta>Ata	p.L496I	AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_Missense_Mutation_p.L496I			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	496	GoLoco 1. {ECO:0000255|PROSITE- ProRule:PRU00097}.				establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		CTTTGACTTATTAAGCCGATT	0.353													T|||	1	0.000199681	0.0008	0.0	5008	,	,		17405	0.0		0.0	False		,,,				2504	0.0				p.L496I		Atlas-SNP	.											.	GPSM2	56	.	0			c.T1486A						PASS	.	T	ILE/LEU	6,4400	9.9+/-24.2	0,6,2197	124.0	124.0	124.0		1486	-3.6	0.0	1	dbSNP_129	124	0,8600		0,0,4300	yes	missense	GPSM2	NM_013296.4	5	0,6,6497	AA,AT,TT		0.0,0.1362,0.0461	possibly-damaging	496/685	109465084	6,13000	2203	4300	6503	SO:0001583	missense	29899	exon13			GACTTATTAAGCC	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"""Tetratricopeptide (TTC) repeat domain containing"""	29501	protein-coding gene	gene with protein product		609245	"""G-protein signalling modulator 2 (AGS3-like, C. elegans)"", ""deafness, autosomal recessive 82"""	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.1486T>A	1.37:g.109465084T>A	ENSP00000385510:p.Leu496Ile	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	178	78	0.438202	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	37	CCDS792.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.6|21.6	4.170507|4.170507	0.78452|0.78452	0.001362|0.001362	0.0|0.0	ENSG00000121957|ENSG00000121957	ENST00000406462;ENST00000264126|ENST00000441735	D;D|.	0.97941|.	-4.62;-4.62|.	6.17|6.17	-3.58|-3.58	0.04597|0.04597	GoLoco motif (3);|.	0.076404|.	0.53938|.	D|.	0.000049|.	T|.	0.26846|.	0.0657|.	L|L	0.53249|0.53249	1.67|1.67	0.25458|0.25458	N|N	0.987941|0.987941	B|.	0.22276|.	0.067|.	B|.	0.25291|.	0.059|.	T|.	0.40794|.	-0.9544|.	10|.	0.54805|.	T|.	0.06|.	-5.8623|-5.8623	11.0483|11.0483	0.47872|0.47872	0.0:0.5338:0.1124:0.3538|0.0:0.5338:0.1124:0.3538	rs61758992|rs61758992	496|.	P81274|.	GPSM2_HUMAN|.	I|X	496|85	ENSP00000385510:L496I;ENSP00000264126:L496I|.	ENSP00000264126:L496I|.	L|Y	+|+	1|3	2|2	GPSM2|GPSM2	109266607|109266607	0.073000|0.073000	0.21202|0.21202	0.000000|0.000000	0.03702|0.03702	0.983000|0.983000	0.72400|0.72400	0.418000|0.418000	0.21230|0.21230	-0.938000|-0.938000	0.03714|0.03714	0.533000|0.533000	0.62120|0.62120	TTA|TAT	T|1.000;A|0.000	0.000	weak		0.353	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296	
WFIKKN2	124857	hgsc.bcm.edu	37	17	48913352	48913352	+	Silent	SNP	G	G	A	rs117494161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48913352G>A	ENST00000311378.4	+	1	582	c.54G>A	c.(52-54)gcG>gcA	p.A18A	WFIKKN2_ENST00000426127.1_Intron	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	18					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)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			AGGTGGCAGCgctgctgctgc	0.682													G|||	94	0.01877	0.0477	0.0101	5008	,	,		18532	0.0218		0.0	False		,,,				2504	0.002				p.A18A		Atlas-SNP	.											.	WFIKKN2	69	.	0			c.G54A						PASS	.	G		190,4206		4,182,2012	14.0	14.0	14.0		54	0.4	1.0	17	dbSNP_132	14	8,8576		0,8,4284	no	coding-synonymous	WFIKKN2	NM_175575.5		4,190,6296	AA,AG,GG		0.0932,4.3221,1.5254		18/577	48913352	198,12782	2198	4292	6490	SO:0001819	synonymous_variant	124857	exon1			GGCAGCGCTGCTG	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30916	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20B"""	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.54G>A	17.37:g.48913352G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	107	63	0.588785	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			G|0.982;A|0.018	0.018	strong		0.682	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
LMF1	64788	hgsc.bcm.edu	37	16	961051	961051	+	Silent	SNP	C	C	T	rs2277893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:961051C>T	ENST00000262301.11	-	4	561	c.543G>A	c.(541-543)ggG>ggA	p.G181G	LMF1_ENST00000543238.1_Intron|LMF1_ENST00000539379.1_3'UTR|LMF1_ENST00000568897.1_5'UTR|LMF1_ENST00000399843.2_Silent_p.G181G	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	181					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)		p.G181G(1)		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)				TCCCCAGGAACCCCGTCTCCA	0.532													C|||	1913	0.381989	0.5613	0.3631	5008	,	,		16735	0.3056		0.1769	False		,,,				2504	0.4427				p.G181G		Atlas-SNP	.											LMF1,NS,carcinoma,0,1	LMF1	42	1	1	Substitution - coding silent(1)	stomach(1)	c.G543A						PASS	.	C		1896,2084		473,950,567	46.0	52.0	50.0		543	-9.1	0.5	16	dbSNP_100	50	1512,6772		140,1232,2770	no	coding-synonymous	LMF1	NM_022773.2		613,2182,3337	TT,TC,CC		18.2521,47.6382,27.7886		181/568	961051	3408,8856	1990	4142	6132	SO:0001819	synonymous_variant	64788	exon4			CAGGAACCCCGTC	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.543G>A	16.37:g.961051C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			C|0.748;T|0.252	0.252	strong		0.532	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
NOTCH4	4855	hgsc.bcm.edu	37	6	32184785	32184785	+	Missense_Mutation	SNP	C	C	G	rs11963697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32184785C>G	ENST00000375023.3	-	11	1936	c.1798G>C	c.(1798-1800)Gtt>Ctt	p.V600L	NOTCH4_ENST00000465528.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	600	EGF-like 15; calcium-binding. {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						CTGGCTCCAACGGGACATGGG	0.567													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		19616	0.0		0.0	False		,,,				2504	0.0				p.V600L		Atlas-SNP	.											.	NOTCH4	201	.	0			c.G1798C						PASS	.	C	LEU/VAL	14,3008		0,14,1497	120.0	92.0	102.0		1798	-7.7	0.0	6	dbSNP_120	102	0,5418		0,0,2709	yes	missense	NOTCH4	NM_004557.3	32	0,14,4206	GG,GC,CC		0.0,0.4633,0.1659	benign	600/2004	32184785	14,8426	1511	2709	4220	SO:0001583	missense	4855	exon11			CTCCAACGGGACA		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.1798G>C	6.37:g.32184785C>G	ENSP00000364163:p.Val600Leu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	210	95	0.452381	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	5.110	0.205944	0.09704	0.004633	0.0	ENSG00000204301	ENST00000375023	D	0.92299	-3.01	4.07	-7.74	0.01241	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	1.351570	0.05567	N	0.570461	T	0.75324	0.3834	L	0.29908	0.895	0.09310	N	1	B;B	0.21606	0.058;0.006	B;B	0.31191	0.125;0.003	T	0.72168	-0.4372	10	0.72032	D	0.01	.	7.0248	0.24934	0.0:0.3431:0.3629:0.294	rs11963697;rs11963697	600;600	Q6P3V5;Q99466	.;NOTC4_HUMAN	L	600	ENSP00000364163:V600L	ENSP00000364163:V600L	V	-	1	0	NOTCH4	32292763	0.000000	0.05858	0.001000	0.08648	0.070000	0.16714	-2.805000	0.00758	-1.167000	0.02779	-0.251000	0.11542	GTT	C|0.989;G|0.011;T|0.000	0.011	strong		0.567	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
PREB	10113	hgsc.bcm.edu	37	2	27354306	27354306	+	Silent	SNP	C	C	T	rs61276776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27354306C>T	ENST00000260643.2	-	9	1483	c.1230G>A	c.(1228-1230)caG>caA	p.Q410Q	PREB_ENST00000416802.1_5'Flank|PREB_ENST00000406567.3_Silent_p.Q352Q	NM_013388.4	NP_037520.1	Q9HCU5	PREB_HUMAN	prolactin regulatory element binding	410					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAAGGCACTCTGGAGCAGCA	0.577													C|||	48	0.00958466	0.0325	0.0072	5008	,	,		19726	0.0		0.0	False		,,,				2504	0.0				p.Q410Q		Atlas-SNP	.											.	PREB	37	.	0			c.G1230A						PASS	.	C		113,4285		3,107,2089	61.0	57.0	58.0		1230	5.1	1.0	2	dbSNP_129	58	1,8563		0,1,4281	no	coding-synonymous	PREB	NM_013388.4		3,108,6370	TT,TC,CC		0.0117,2.5693,0.8795		410/418	27354306	114,12848	2199	4282	6481	SO:0001819	synonymous_variant	10113	exon9			GGCACTCTGGAGC		CCDS1738.1	2p23	2013-01-10			ENSG00000138073	ENSG00000138073		"""WD repeat domain containing"""	9356	protein-coding gene	gene with protein product		606395				10194769, 12735795	Standard	NM_013388		Approved	SEC12	uc002rix.1	Q9HCU5	OTTHUMG00000097076	ENST00000260643.2:c.1230G>A	2.37:g.27354306C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_013388	Q53SZ8|Q9UH94	Silent	SNP	ENST00000260643.2	37	CCDS1738.1	17	0.007783882783882784	13	0.026422764227642278	4	0.011049723756906077	0	0.0	0	0.0	C	14.76	2.630999	0.46944	0.025693	1.17E-4	ENSG00000138073	ENST00000456259	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	T	0.45796	0.1360	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58521	-0.7622	4	.	.	.	-19.6044	13.7879	0.63121	0.0:1.0:0.0:0.0	rs61276776	.	.	.	K	153	.	.	R	-	2	0	PREB	27207810	0.977000	0.34250	1.000000	0.80357	0.997000	0.91878	1.333000	0.33816	2.611000	0.88343	0.655000	0.94253	AGA	C|0.989;T|0.011	0.011	strong		0.577	PREB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214195.1	NM_013388	
DCAF15	90379	hgsc.bcm.edu	37	19	14066772	14066772	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14066772T>C	ENST00000254337.6	+	4	436	c.415T>C	c.(415-417)Tac>Cac	p.Y139H	PODNL1_ENST00000588317.1_5'Flank|PODNL1_ENST00000538371.2_5'Flank|PODNL1_ENST00000538517.2_5'Flank	NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15	139					protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						CAGCGACCTGTACCTGACCGT	0.642																																					p.Y139H		Atlas-SNP	.											.	DCAF15	30	.	0			c.T415C						PASS	.						110.0	101.0	104.0					19																	14066772		2203	4300	6503	SO:0001583	missense	90379	exon4			GACCTGTACCTGA	BC002926	CCDS32926.1	19p13.12	2009-07-17	2009-07-17	2009-07-17	ENSG00000132017	ENSG00000132017		"""DDB1 and CUL4 associated factors"""	25095	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 72"""	C19orf72			Standard	NM_138353		Approved	MGC99481	uc002mxt.3	Q66K64		ENST00000254337.6:c.415T>C	19.37:g.14066772T>C	ENSP00000254337:p.Tyr139His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	113	5	0.0442478	NM_138353	B3KS86|Q96DW0|Q9BU31	Missense_Mutation	SNP	ENST00000254337.6	37	CCDS32926.1	.	.	.	.	.	.	.	.	.	.	t	13.68	2.309631	0.40895	.	.	ENSG00000132017	ENST00000254337	.	.	.	4.02	4.02	0.46733	.	0.000000	0.64402	D	0.000006	T	0.40247	0.1109	L	0.43152	1.355	0.47276	D	0.999373	P	0.42456	0.78	B	0.35353	0.201	T	0.28522	-1.0041	9	0.28530	T	0.3	-18.254	12.2557	0.54623	0.0:0.0:0.0:1.0	.	139	Q66K64	DCA15_HUMAN	H	139	.	ENSP00000254337:Y139H	Y	+	1	0	DCAF15	13927772	1.000000	0.71417	1.000000	0.80357	0.385000	0.30292	7.528000	0.81941	1.610000	0.50200	0.459000	0.35465	TAC	.	.	none		0.642	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353	
VTN	7448	hgsc.bcm.edu	37	17	26694861	26694861	+	Missense_Mutation	SNP	G	G	A	rs704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26694861G>A	ENST00000226218.4	-	7	1817	c.1199C>T	c.(1198-1200)aCg>aTg	p.T400M	VTN_ENST00000536498.1_De_novo_Start_OutOfFrame|TMEM199_ENST00000509083.1_Intron|VTN_ENST00000438614.1_De_novo_Start_OutOfFrame|SARM1_ENST00000379061.4_Intron|CTB-96E2.2_ENST00000555059.2_Missense_Mutation_p.T58M|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	84	0	0		WXS	Illumina HiSeq	Phase_I	83	47	0.566265	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	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276909	71276909	+	Silent	SNP	G	G	A	rs71272260|rs12289712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.						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	149	0	0		WXS	Illumina HiSeq	Phase_I	177	34	0.19209	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		
CNTN5	53942	hgsc.bcm.edu	37	11	100226883	100226883	+	Missense_Mutation	SNP	T	T	A	rs1216183	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:100226883T>A	ENST00000524871.1	+	25	3525	c.3235T>A	c.(3235-3237)Tct>Act	p.S1079T	CNTN5_ENST00000279463.3_Missense_Mutation_p.S1079T|CNTN5_ENST00000528682.1_Missense_Mutation_p.S1079T|CNTN5_ENST00000524560.1_3'UTR|CNTN5_ENST00000418526.2_Missense_Mutation_p.S1005T	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	1079			S -> T (in dbSNP:rs1216183). {ECO:0000269|PubMed:15489334}.		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)		GACCCTTCACTCTCTCTCCAC	0.413													A|||	1638	0.327077	0.531	0.2896	5008	,	,		19676	0.3313		0.1193	False		,,,				2504	0.2873				p.S1079T		Atlas-SNP	.											CNTN5_ENST00000524871,colon,carcinoma,-2,2	CNTN5	324	2	0			c.T3235A						PASS	.	A	THR/SER,THR/SER	1708,2280		366,976,652	137.0	133.0	134.0		3235,3013	1.5	0.1	11	dbSNP_87	134	886,7448		52,782,3333	yes	missense,missense	CNTN5	NM_014361.3,NM_175566.2	58,58	418,1758,3985	AA,AT,TT		10.6311,42.8285,21.0518	benign,benign	1079/1101,1005/1027	100226883	2594,9728	1994	4167	6161	SO:0001583	missense	53942	exon24			CTTCACTCTCTCT	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.3235T>A	11.37:g.100226883T>A	ENSP00000435637:p.Ser1079Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	95	54	0.568421	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	636	0.29120879120879123	254	0.516260162601626	95	0.26243093922651933	193	0.3374125874125874	94	0.12401055408970976	A	0.081	-1.183514	0.01620	0.428285	0.106311	ENSG00000149972	ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T	0.54479	0.58;0.58;0.57;0.58	5.4	1.5	0.22942	.	0.581661	0.18924	N	0.127412	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	0.46748	-0.9169	8	.	.	.	.	0.953	0.01379	0.3979:0.1191:0.1366:0.3463	rs1216183;rs17094898;rs52792685;rs1216183	1005;1079	O94779-2;O94779	.;CNTN5_HUMAN	T	1079;1079;1005;1079	ENSP00000436185:S1079T;ENSP00000435637:S1079T;ENSP00000393229:S1005T;ENSP00000279463:S1079T	.	S	+	1	0	CNTN5	99732093	0.000000	0.05858	0.057000	0.19452	0.209000	0.24338	-0.013000	0.12678	-0.254000	0.09500	-0.364000	0.07487	TCT	T|0.706;A|0.294	0.294	strong		0.413	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
HBS1L	10767	hgsc.bcm.edu	37	6	135359073	135359073	+	Intron	SNP	G	G	A	rs115458424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135359073G>A	ENST00000367837.5	-	4	637				HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000525067.1_Missense_Mutation_p.P112L|HBS1L_ENST00000367822.5_Silent_p.P174P|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000314674.3_Silent_p.P174P	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		CAAAATCAAAGGGTTTGCTAC	0.343													G|||	91	0.0181709	0.0628	0.0072	5008	,	,		21502	0.0		0.001	False		,,,				2504	0.002				p.P174P		Atlas-SNP	.											.	HBS1L	75	.	0			c.C522T						PASS	.						100.0	73.0	81.0					6																	135359073		692	1590	2282	SO:0001627	intron_variant	10767	exon5			ATCAAAGGGTTTG	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+1637C>T	6.37:g.135359073G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	126	70	0.555556	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1	38	0.0173992673992674	33	0.06707317073170732	5	0.013812154696132596	0	0.0	0	0.0	G	1.871	-0.460307	0.04508	.	.	ENSG00000112339	ENST00000525067	.	.	.	5.23	-0.875	0.10628	.	.	.	.	.	T	0.18257	0.0438	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.33059	-0.9883	5	0.87932	D	0	.	3.928	0.09272	0.3333:0.0:0.2811:0.3855	.	.	.	.	L	112	.	ENSP00000435608:P112L	P	-	2	0	HBS1L	135400766	0.568000	0.26635	0.283000	0.24790	0.501000	0.33797	0.566000	0.23593	-0.076000	0.12775	0.650000	0.86243	CCT	G|0.979;A|0.021	0.021	strong		0.343	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
ST6GAL2	84620	hgsc.bcm.edu	37	2	107450525	107450525	+	Missense_Mutation	SNP	T	T	C	rs12615112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:107450525T>C	ENST00000409382.3	-	3	1631	c.1021A>G	c.(1021-1023)Ata>Gta	p.I341V	ST6GAL2_ENST00000361686.4_Missense_Mutation_p.I341V|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000409087.3_Missense_Mutation_p.I341V	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	341			I -> V (in dbSNP:rs12615112).		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)	p.I341V(1)		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						ATGATGCGTATGGTGGTTTTA	0.398													C|||	1280	0.255591	0.2436	0.1542	5008	,	,		16802	0.4921		0.0775	False		,,,				2504	0.2832				p.I341V		Atlas-SNP	.											ST6GAL2,NS,carcinoma,0,1	ST6GAL2	159	1	1	Substitution - Missense(1)	stomach(1)	c.A1021G						scavenged	.	C	VAL/ILE,VAL/ILE,VAL/ILE	998,3408	730.9+/-410.2	110,778,1315	223.0	212.0	216.0		1021,1021,1021	-7.7	0.0	2	dbSNP_120	216	778,7822	783.8+/-407.6	23,732,3545	yes	missense,missense,missense	ST6GAL2	NM_001142351.1,NM_001142352.1,NM_032528.2	29,29,29	133,1510,4860	CC,CT,TT		9.0465,22.6509,13.6552	benign,benign,benign	341/530,341/467,341/530	107450525	1776,11230	2203	4300	6503	SO:0001583	missense	84620	exon3			TGCGTATGGTGGT	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.1021A>G	2.37:g.107450525T>C	ENSP00000386942:p.Ile341Val	Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	200	89	0.445	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	37	CCDS2073.1	502	0.22985347985347984	125	0.2540650406504065	57	0.1574585635359116	263	0.4597902097902098	57	0.07519788918205805	C	6.374	0.437102	0.12104	0.226509	0.090465	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.72282	-0.64;-0.64;-0.64	6.03	-7.68	0.01268	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);	0.574537	0.19688	N	0.108354	T	0.00012	0.0000	N	0.25957	0.775	0.80722	P	0.0	B;B	0.13145	0.007;0.003	B;B	0.20577	0.009;0.03	T	0.26292	-1.0107	9	0.23891	T	0.37	-7.2185	6.4229	0.21754	0.0829:0.0973:0.2465:0.5733	rs12615112;rs60735160;rs12615112	341;341	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	V	341	ENSP00000355273:I341V;ENSP00000386942:I341V;ENSP00000387332:I341V	ENSP00000355273:I341V	I	-	1	0	ST6GAL2	106816957	0.004000	0.15560	0.015000	0.15790	0.734000	0.41952	-0.133000	0.10451	-1.546000	0.01717	-1.767000	0.00664	ATA	T|0.811;C|0.189	0.189	strong		0.398	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43650915	43650915	+	Silent	SNP	C	C	T	rs41298781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:43650915C>T	ENST00000374466.3	+	2	653	c.318C>T	c.(316-318)ggC>ggT	p.G106G	CSGALNACT2_ENST00000374464.1_Silent_p.G106G	NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	106					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)			endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GGGCTAATGGCATAGGCTATC	0.423													C|||	189	0.0377396	0.0121	0.0317	5008	,	,		20405	0.0		0.0636	False		,,,				2504	0.089				p.G106G		Atlas-SNP	.											CSGALNACT2,NS,carcinoma,+2,1	CSGALNACT2	67	1	0			c.C318T						PASS	.	C		112,4294	87.3+/-125.9	3,106,2094	77.0	65.0	69.0		318	3.7	1.0	10	dbSNP_127	69	511,8089	145.9+/-201.5	22,467,3811	no	coding-synonymous	CSGALNACT2	NM_018590.3		25,573,5905	TT,TC,CC		5.9419,2.542,4.7901		106/543	43650915	623,12383	2203	4300	6503	SO:0001819	synonymous_variant	55454	exon2			TAATGGCATAGGC	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"""Beta 4-glycosyltransferases"""	24292	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"""					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.318C>T	10.37:g.43650915C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_018590	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Silent	SNP	ENST00000374466.3	37	CCDS7201.1																																																																																			C|0.955;T|0.045	0.045	strong		0.423	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047322	46047322	+	Silent	SNP	G	G	A	rs62220925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46047322G>A	ENST00000397911.3	+	1	283	c.234G>A	c.(232-234)tcG>tcA	p.S78S	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	78	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						GCACGCCCTCGTGCTGCCAGC	0.677													G|||	719	0.14357	0.3495	0.0706	5008	,	,		18721	0.0109		0.0666	False		,,,				2504	0.1329				p.S78S		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.G234A						PASS	.	G	,	1407,2987		231,945,1021	55.0	69.0	64.0		,234	-6.7	0.0	21	dbSNP_129	64	509,8071		15,479,3796	no	intron,coding-synonymous	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,	246,1424,4817	AA,AG,GG		5.9324,32.0209,14.768	,	,78/293	46047322	1916,11058	2197	4290	6487	SO:0001819	synonymous_variant	386676	exon1			GCCCTCGTGCTGC	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.234G>A	21.37:g.46047322G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	168	76	0.452381	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Silent	SNP	ENST00000397911.3	37	CCDS42961.1																																																																																			.	.	weak		0.677	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
CLEC10A	10462	hgsc.bcm.edu	37	17	6981353	6981353	+	Silent	SNP	G	G	C	rs732828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:6981353G>C	ENST00000254868.4	-	3	475	c.147C>G	c.(145-147)ctC>ctG	p.L49L	CLEC10A_ENST00000571664.1_Silent_p.L49L|CLEC10A_ENST00000416562.2_Silent_p.L49L|CLEC10A_ENST00000576617.1_Silent_p.L49L	NM_182906.2	NP_878910.1	Q8IUN9	CLC10_HUMAN	C-type lectin domain family 10, member A	49					endocytosis (GO:0006897)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						CCAGCAGCAGGAGGCCGAGGC	0.567													G|||	2065	0.41234	0.792	0.2882	5008	,	,		17759	0.2669		0.2903	False		,,,				2504	0.2628				p.L49L		Atlas-SNP	.											.	CLEC10A	40	.	0			c.C147G						PASS	.	G	,	3092,1314	697.1+/-406.2	1095,902,206	163.0	174.0	170.0		147,147	0.2	0.9	17	dbSNP_86	170	2445,6155	404.5+/-348.2	365,1715,2220	no	coding-synonymous,coding-synonymous	CLEC10A	NM_006344.2,NM_182906.2	,	1460,2617,2426	CC,CG,GG		28.4302,29.823,42.5727	,	49/293,49/317	6981353	5537,7469	2203	4300	6503	SO:0001819	synonymous_variant	10462	exon3			CAGCAGGAGGCCG	D50532	CCDS11087.1, CCDS45597.1	17p13.2	2014-05-20	2005-02-09	2005-02-11		ENSG00000132514		"""C-type lectin domain containing"", ""CD molecules"""	16916	protein-coding gene	gene with protein product	"""macrophage lectin 2 (calcium dependent)"""	605999	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 14 (macrophage-derived)"""	CLECSF13, CLECSF14		8598452	Standard	XM_005256411		Approved	HML2, HML, CD301	uc002gej.3	Q8IUN9		ENST00000254868.4:c.147C>G	17.37:g.6981353G>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	171	80	0.467836	NM_182906	A8K8J8|Q14538|Q6PIW3	Silent	SNP	ENST00000254868.4	37	CCDS11087.1																																																																																			G|0.584;C|0.416	0.416	strong		0.567	CLEC10A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439837.2	NM_006344	
PCNT	5116	hgsc.bcm.edu	37	21	47754576	47754576	+	Missense_Mutation	SNP	A	A	C	rs200285580		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47754576A>C	ENST00000359568.5	+	3	640	c.533A>C	c.(532-534)cAa>cCa	p.Q178P	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	178					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)					AGTGACCACCAACCGGAACAG	0.537																																					p.Q178P		Atlas-SNP	.											.	PCNT	283	.	0			c.A533C						PASS	.						205.0	139.0	161.0					21																	47754576		2203	4300	6503	SO:0001583	missense	5116	exon3			ACCACCAACCGGA	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.533A>C	21.37:g.47754576A>C	ENSP00000352572:p.Gln178Pro	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	333	48	0.144144	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	C	3.018	-0.202461	0.06219	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01258	5.09	0.235	0.235	0.15431	.	.	.	.	.	T	0.00754	0.0025	N	0.03608	-0.345	0.09310	N	1	B;B	0.20368	0.044;0.026	B;B	0.13407	0.009;0.004	T	0.47849	-0.9085	8	0.30854	T	0.27	.	.	.	.	.	60;178	O95613-2;O95613	.;PCNT_HUMAN	P	178;165	ENSP00000352572:Q178P	ENSP00000338675:Q165P	Q	+	2	0	PCNT	46579004	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-2.630000	0.00871	0.263000	0.21812	0.260000	0.18958	CAA	A|0.999;G|0.001	.	alt		0.537	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
GPR150	285601	hgsc.bcm.edu	37	5	94957071	94957071	+	Silent	SNP	A	A	T	rs375018988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:94957071A>T	ENST00000380007.2	+	1	1290	c.1092A>T	c.(1090-1092)cgA>cgT	p.R364R		NM_199243.1	NP_954713.1	Q8NGU9	GP150_HUMAN	G protein-coupled receptor 150	364						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(2)	2		all_cancers(142;0.000462)|all_epithelial(76;2.44e-06)|all_lung(232;0.0318)|Lung NSC(167;0.041)|Ovarian(225;0.051)		all cancers(79;1.82e-16)		GGCTCCGGCGACAGCTGCGGA	0.726													A|||	3	0.000599042	0.0023	0.0	5008	,	,		12900	0.0		0.0	False		,,,				2504	0.0				p.R364R		Atlas-SNP	.											.	GPR150	7	.	0			c.A1092T						PASS	.	A		12,3928		0,12,1958	4.0	6.0	5.0		1092	2.7	0.3	5		5	0,7982		0,0,3991	no	coding-synonymous	GPR150	NM_199243.1		0,12,5949	TT,TA,AA		0.0,0.3046,0.1007		364/435	94957071	12,11910	1970	3991	5961	SO:0001819	synonymous_variant	285601	exon1			CCGGCGACAGCTG	BC030197	CCDS4074.1	5q15	2012-08-21			ENSG00000178015	ENSG00000178015		"""GPCR / Class A : Orphans"""	23628	protein-coding gene	gene with protein product						12679517	Standard	NM_199243		Approved	PGR11	uc003kle.1	Q8NGU9	OTTHUMG00000121170	ENST00000380007.2:c.1092A>T	5.37:g.94957071A>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	21	14	0.666667	NM_199243		Silent	SNP	ENST00000380007.2	37	CCDS4074.1																																																																																			.	.	weak		0.726	GPR150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241657.2		
AGO1	26523	hgsc.bcm.edu	37	1	36359669	36359669	+	Silent	SNP	A	A	G	rs2296470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36359669A>G	ENST00000373204.4	+	6	894	c.681A>G	c.(679-681)ccA>ccG	p.P227P	AGO1_ENST00000373206.1_Silent_p.P152P	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	227	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				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)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										AGGCACAGCCAGTGATTGAGT	0.517													A|||	1536	0.306709	0.3994	0.3314	5008	,	,		20705	0.6558		0.0129	False		,,,				2504	0.1063				p.P227P		Atlas-SNP	.											.	.	.	.	0			c.A681G						PASS	.	A		1544,2862	486.5+/-360.6	272,1000,931	95.0	92.0	93.0		681	-4.1	1.0	1	dbSNP_100	93	75,8525	44.9+/-103.4	0,75,4225	no	coding-synonymous	EIF2C1	NM_012199.2		272,1075,5156	GG,GA,AA		0.8721,35.0431,12.4481		227/858	36359669	1619,11387	2203	4300	6503	SO:0001819	synonymous_variant	26523	exon6			ACAGCCAGTGATT	AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"""Argonaute/PIWI family"""	3262	protein-coding gene	gene with protein product	"""argonaute 1"""	606228	"""eukaryotic translation initiation factor 2C, 1"""	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.681A>G	1.37:g.36359669A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_012199	Q5TA57|Q6P4S0	Silent	SNP	ENST00000373204.4	37	CCDS398.1																																																																																			A|0.788;G|0.212	0.212	strong		0.517	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3		
PLA1A	51365	hgsc.bcm.edu	37	3	119327653	119327653	+	Silent	SNP	T	T	C	rs1723969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119327653T>C	ENST00000273371.4	+	3	384	c.312T>C	c.(310-312)ttT>ttC	p.F104F	PLA1A_ENST00000494440.1_Silent_p.F88F|PLA1A_ENST00000488919.1_5'UTR|PLA1A_ENST00000495992.1_Silent_p.F104F	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	104					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTGACACATTTATTAGAACCC	0.418													C|||	1706	0.340655	0.4985	0.1859	5008	,	,		21163	0.4504		0.1839	False		,,,				2504	0.2853				p.F104F		Atlas-SNP	.											.	PLA1A	65	.	0			c.T312C						PASS	.	C	,,	2034,2372	611.8+/-391.8	475,1084,644	170.0	171.0	171.0		312,,312	2.3	0.0	3	dbSNP_89	171	1713,6887	738.1+/-407.0	177,1359,2764	no	coding-synonymous,utr-5,coding-synonymous	PLA1A	NM_001206960.1,NM_001206961.1,NM_015900.3	,,	652,2443,3408	CC,CT,TT		19.9186,46.1643,28.8098	,,	104/441,,104/457	119327653	3747,9259	2203	4300	6503	SO:0001819	synonymous_variant	51365	exon3			CACATTTATTAGA	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.312T>C	3.37:g.119327653T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	193	193	1	NM_001206960	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Silent	SNP	ENST00000273371.4	37	CCDS2991.1																																																																																			T|0.678;C|0.322	0.322	strong		0.418	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2		
TECTA	7007	hgsc.bcm.edu	37	11	120989335	120989335	+	Missense_Mutation	SNP	A	A	G	rs612969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:120989335A>G	ENST00000392793.1	+	7	1382	c.1111A>G	c.(1111-1113)Aga>Gga	p.R371G	TECTA_ENST00000264037.2_Missense_Mutation_p.R371G			O75443	TECTA_HUMAN	tectorin alpha	371	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.		R -> G (in dbSNP:rs612969). {ECO:0000269|PubMed:10987647, ECO:0000269|PubMed:9590290}.		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)		TGAACACCGCAGAGGTTCAGC	0.547													G|||	2220	0.443291	0.7428	0.3818	5008	,	,		19359	0.246		0.4314	False		,,,				2504	0.2975				p.R371G		Atlas-SNP	.											.	TECTA	329	.	0			c.A1111G						PASS	.	G	GLY/ARG	2922,1484	474.6+/-357.0	963,996,244	93.0	93.0	93.0		1111	3.9	0.0	11	dbSNP_83	93	3545,5053	629.9+/-398.3	740,2065,1494	yes	missense	TECTA	NM_005422.2	125	1703,3061,1738	GG,GA,AA		41.2305,33.6813,49.7309	benign	371/2156	120989335	6467,6537	2203	4299	6502	SO:0001583	missense	7007	exon6			CACCGCAGAGGTT	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.1111A>G	11.37:g.120989335A>G	ENSP00000376543:p.Arg371Gly	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	1008	0.46153846153846156	356	0.7235772357723578	147	0.40607734806629836	170	0.2972027972027972	335	0.4419525065963061	G	3.893	-0.023615	0.07634	0.663187	0.412305	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.58060	0.36;0.36	5.72	3.86	0.44501	von Willebrand factor, type D domain (3);	0.115400	0.64402	N	0.000018	T	0.00012	0.0000	N	0.00223	-1.815	0.50632	P	1.1899999999998023E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.47799	-0.9089	9	0.02654	T	1	.	11.7181	0.51666	0.1898:0.0:0.8102:0.0	rs612969;rs58667510;rs612969	371	O75443	TECTA_HUMAN	G	371	ENSP00000376543:R371G;ENSP00000264037:R371G	ENSP00000264037:R371G	R	+	1	2	TECTA	120494545	1.000000	0.71417	0.003000	0.11579	0.877000	0.50540	4.856000	0.62932	0.364000	0.24374	-0.213000	0.12676	AGA	A|0.525;G|0.475	0.475	strong		0.547	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
ZNF831	128611	hgsc.bcm.edu	37	20	57829301	57829301	+	Missense_Mutation	SNP	T	T	C	rs259956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:57829301T>C	ENST00000371030.2	+	5	4537	c.4537T>C	c.(4537-4539)Tca>Cca	p.S1513P		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1513			S -> P (in dbSNP:rs259956).				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CAGTGCTGAATCACGAGACCA	0.527													C|||	3096	0.618211	0.3116	0.6081	5008	,	,		18876	0.9107		0.5606	False		,,,				2504	0.7975				p.S1513P		Atlas-SNP	.											ZNF831,caecum,carcinoma,0,1	ZNF831	287	1	0			c.T4537C						scavenged	.	C	PRO/SER	1427,2813		252,923,945	48.0	52.0	51.0		4537	-3.0	0.0	20	dbSNP_79	51	4568,3926		1251,2066,930	yes	missense	ZNF831	NM_178457.1	74	1503,2989,1875	CC,CT,TT		46.2209,33.6557,47.0787	benign	1513/1678	57829301	5995,6739	2120	4247	6367	SO:0001583	missense	128611	exon5			GCTGAATCACGAG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.4537T>C	20.37:g.57829301T>C	ENSP00000360069:p.Ser1513Pro	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	136	66	0.485294	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	1304	0.5970695970695971	149	0.30284552845528456	206	0.569060773480663	518	0.9055944055944056	431	0.5686015831134564	C	1.351	-0.591513	0.03799	0.336557	0.537791	ENSG00000124203	ENST00000371030	T	0.04917	3.53	5.6	-2.98	0.05513	.	0.971967	0.08452	N	0.943747	T	0.00012	0.0000	N	0.01003	-1.06	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	9	0.02654	T	1	0.0796	1.5739	0.02621	0.1233:0.2135:0.3263:0.3369	rs259956;rs17829996;rs52820703;rs61110182;rs259956	1513	Q5JPB2	ZN831_HUMAN	P	1513	ENSP00000360069:S1513P	ENSP00000360069:S1513P	S	+	1	0	ZNF831	57262696	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.381000	0.07417	-0.195000	0.10382	-0.197000	0.12766	TCA	T|0.411;C|0.589	0.589	strong		0.527	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
GFRA2	2675	hgsc.bcm.edu	37	8	21608105	21608105	+	Silent	SNP	C	C	G	rs2229903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:21608105C>G	ENST00000524240.1	-	4	1439	c.789G>C	c.(787-789)ctG>ctC	p.L263L	GFRA2_ENST00000517328.1_Silent_p.L263L|GFRA2_ENST00000518077.1_Silent_p.L130L|GFRA2_ENST00000400782.4_Silent_p.L158L	NM_001495.4	NP_001486.4	O00451	GFRA2_HUMAN	GDNF family receptor alpha 2	263					negative regulation of protein autophosphorylation (GO:0031953)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|prostate(1)|skin(1)	7				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		CTCACCGACACAGGTGGTCAG	0.632													C|||	380	0.0758786	0.1505	0.0187	5008	,	,		15635	0.1181		0.004	False		,,,				2504	0.046				p.L263L		Atlas-SNP	.											.	GFRA2	23	.	0			c.G789C						PASS	.	C	,,	498,3808		19,460,1674	18.0	20.0	19.0		474,390,789	2.8	1.0	8	dbSNP_131	19	59,8421		0,59,4181	no	coding-synonymous,coding-synonymous,coding-synonymous	GFRA2	NM_001165038.1,NM_001165039.1,NM_001495.4	,,	19,519,5855	GG,GC,CC		0.6958,11.5653,4.3563	,,	158/360,130/332,263/465	21608105	557,12229	2153	4240	6393	SO:0001819	synonymous_variant	2675	exon4			CCGACACAGGTGG	AF002700	CCDS47816.1, CCDS55207.1	8p21.3	2008-05-02			ENSG00000168546	ENSG00000168546			4244	protein-coding gene	gene with protein product		601956				9177201	Standard	NM_001165038		Approved	RETL2, GDNFRB, NTNRA, TRNR2	uc003wzu.1	O00451	OTTHUMG00000163897	ENST00000524240.1:c.789G>C	8.37:g.21608105C>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	149	81	0.543624	NM_001495	E9PD47|O15316|O15328|Q58J92|Q6GTR9|Q7Z5C2	Silent	SNP	ENST00000524240.1	37	CCDS47816.1																																																																																			C|0.935;G|0.065	0.065	strong		0.632	GFRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376254.3	NM_001495	
IQUB	154865	hgsc.bcm.edu	37	7	123152019	123152019	+	Missense_Mutation	SNP	C	C	T	rs10255061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:123152019C>T	ENST00000466202.1	-	2	952	c.376G>A	c.(376-378)Gtg>Atg	p.V126M	IQUB_ENST00000434450.1_Missense_Mutation_p.V126M|IQUB_ENST00000488987.1_Intron|IQUB_ENST00000324698.6_Missense_Mutation_p.V126M	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	126			V -> M (in dbSNP:rs10255061). {ECO:0000269|PubMed:15489334}.		cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)		p.V126M(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						GAATCTTCCACTGATTCTTGC	0.353													T|||	1342	0.267971	0.2194	0.2637	5008	,	,		19187	0.369		0.2863	False		,,,				2504	0.2137				p.V126M		Atlas-SNP	.											IQUB,NS,adenoma,0,2	IQUB	117	2	1	Substitution - Missense(1)	stomach(1)	c.G376A						PASS	.	T	MET/VAL	1048,3356	723.4+/-409.4	131,786,1285	64.0	64.0	64.0		376	-4.5	0.0	7	dbSNP_119	64	2296,6304	703.7+/-405.4	298,1700,2302	yes	missense	IQUB	NM_178827.4	21	429,2486,3587	TT,TC,CC		26.6977,23.7965,25.7152	benign	126/792	123152019	3344,9660	2202	4300	6502	SO:0001583	missense	154865	exon2			CTTCCACTGATTC	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.376G>A	7.37:g.123152019C>T	ENSP00000417769:p.Val126Met	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	37	CCDS5787.1	634	0.2902930402930403	104	0.21138211382113822	109	0.3011049723756906	202	0.3531468531468531	219	0.28891820580474936	T	7.972	0.749246	0.15710	0.237965	0.266977	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	T;T;T	0.42513	0.97;0.97;0.97	5.41	-4.47	0.03525	.	1.448530	0.04416	N	0.366878	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.09022	0.0;0.002;0.001	B;B;B	0.08055	0.001;0.003;0.001	T	0.33752	-0.9856	9	0.14252	T	0.57	.	11.0952	0.48141	0.1213:0.676:0.0:0.2027	rs10255061;rs56649278;rs59485939;rs10255061	126;126;126	A1A4Z1;Q8NA54-2;Q8NA54	.;.;IQUB_HUMAN	M	126	ENSP00000417769:V126M;ENSP00000324882:V126M;ENSP00000388498:V126M	ENSP00000324882:V126M	V	-	1	0	IQUB	122939255	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.742000	0.01835	-1.087000	0.03081	-0.254000	0.11334	GTG	C|0.741;T|0.259	0.259	strong		0.353	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
RHBG	57127	hgsc.bcm.edu	37	1	156351699	156351699	+	Missense_Mutation	SNP	G	G	A	rs3748569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156351699G>A	ENST00000368249.1	+	6	981	c.943G>A	c.(943-945)Ggg>Agg	p.G315R	RHBG_ENST00000537040.1_Missense_Mutation_p.G153R|RHBG_ENST00000451864.2_Intron|RHBG_ENST00000368246.2_Missense_Mutation_p.G315R|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	268	0	0		WXS	Illumina HiSeq	Phase_I	296	137	0.462838	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	
GCAT	23464	hgsc.bcm.edu	37	22	38211728	38211728	+	Silent	SNP	A	A	G	rs34340481	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38211728A>G	ENST00000248924.6	+	7	929	c.873A>G	c.(871-873)ccA>ccG	p.P291P	GCAT_ENST00000323205.6_Silent_p.P317P	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	291					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)	GCGCCCGGCCATACCTCTTCT	0.642													A|||	228	0.0455272	0.1649	0.0115	5008	,	,		17865	0.0		0.002	False		,,,				2504	0.0				p.P317P		Atlas-SNP	.											.	GCAT	27	.	0			c.A951G						PASS	.	A	,	584,3822	255.5+/-260.7	37,510,1656	88.0	97.0	94.0		951,873	-0.2	1.0	22	dbSNP_126	94	24,8576	15.3+/-51.7	0,24,4276	no	coding-synonymous,coding-synonymous	GCAT	NM_001171690.1,NM_014291.3	,	37,534,5932	GG,GA,AA		0.2791,13.2547,4.6748	,	317/446,291/420	38211728	608,12398	2203	4300	6503	SO:0001819	synonymous_variant	23464	exon7			CCGGCCATACCTC	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.873A>G	22.37:g.38211728A>G		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	263	119	0.452471	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Silent	SNP	ENST00000248924.6	37	CCDS13957.1																																																																																			A|0.958;G|0.042	0.042	strong		0.642	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2	
ARSF	416	hgsc.bcm.edu	37	X	3028260	3028260	+	Silent	SNP	C	C	T	rs17051478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:3028260C>T	ENST00000381127.1	+	10	1578	c.1357C>T	c.(1357-1359)Ctg>Ttg	p.L453L	ARSF_ENST00000537104.1_Silent_p.L453L|ARSF_ENST00000359361.2_Silent_p.L453L	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	453					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		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)				TGGCTCCTACCTGCACGCCGT	0.587													c|||	389	0.103046	0.1732	0.1225	3775	,	,		14845	0.0		0.0666	False		,,,				2504	0.0082				p.L453L		Atlas-SNP	.											.	ARSF	97	.	0			c.C1357T						PASS	.	C	,,	796,3039		69,541,117,1022,454	120.0	88.0	99.0		1357,1357,1357	0.7	0.0	X	dbSNP_123	99	507,6221		16,335,140,2077,1732	no	coding-synonymous,coding-synonymous,coding-synonymous	ARSF	NM_001201538.1,NM_001201539.1,NM_004042.4	,,	85,876,257,3099,2186	TT,TC,T,CC,C		7.5357,20.7562,12.3355	,,	453/591,453/591,453/591	3028260	1303,9260	2203	4300	6503	SO:0001819	synonymous_variant	416	exon10			TCCTACCTGCACG	X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"""Arylsulfatase family"""	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.1357C>T	X.37:g.3028260C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	201	110	0.547264	NM_004042	Q8TCC5	Silent	SNP	ENST00000381127.1	37	CCDS14123.1																																																																																			C|0.873;0|0.002	.	strong		0.587	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1		
LY75	4065	hgsc.bcm.edu	37	2	160738803	160738803	+	Missense_Mutation	SNP	G	G	A	rs35675007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160738803G>A	ENST00000263636.4	-	7	1105	c.1078C>T	c.(1078-1080)Cgc>Tgc	p.R360C	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.R360C|LY75_ENST00000554112.1_Missense_Mutation_p.R360C|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.R360C|LY75_ENST00000553424.1_Missense_Mutation_p.R360C	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	360					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)		GCATCACAGCGGGTATCTGAG	0.398													G|||	19	0.00379393	0.0121	0.0	5008	,	,		22106	0.001		0.0	False		,,,				2504	0.002				p.R360C		Atlas-SNP	.											LY75,NS,carcinoma,+1,1	LY75	151	1	0			c.C1078T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	44,4362	48.2+/-83.0	0,44,2159	114.0	111.0	112.0		1078,1078,1078	5.6	0.9	2	dbSNP_126	112	16,8584	11.9+/-42.8	0,16,4284	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	180,180,180	0,60,6443	AA,AG,GG		0.186,0.9986,0.4613	possibly-damaging,possibly-damaging,possibly-damaging	360/1874,360/1818,360/1723	160738803	60,12946	2203	4300	6503	SO:0001583	missense	4065	exon7			CACAGCGGGTATC	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.1078C>T	2.37:g.160738803G>A	ENSP00000263636:p.Arg360Cys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	77	27	0.350649	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	17.54	3.416115	0.62511	0.009986	0.00186	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.07444	3.19;3.19;3.19;3.19;3.19	5.57	5.57	0.84162	C-type lectin-like (1);	1.087950	0.07314	U	0.876324	T	0.14399	0.0348	L	0.43152	1.355	0.19300	N	0.99998	B;D;D	0.76494	0.272;0.999;0.999	B;P;P	0.56278	0.072;0.724;0.795	T	0.29912	-0.9996	10	0.54805	T	0.06	0.0491	14.2185	0.65809	0.0:0.2692:0.7308:0.0	rs35675007	360;360;360	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	C	360	ENSP00000451511:R360C;ENSP00000451446:R360C;ENSP00000263636:R360C;ENSP00000423463:R360C;ENSP00000421035:R360C	ENSP00000423463:R360C	R	-	1	0	LY75;LY75-CD302	160447049	0.995000	0.38212	0.857000	0.33713	0.986000	0.74619	2.505000	0.45424	2.632000	0.89209	0.650000	0.86243	CGC	G|0.996;A|0.004	0.004	strong		0.398	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
CCRL2	9034	hgsc.bcm.edu	37	3	46449864	46449864	+	Silent	SNP	G	G	T	rs6808835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46449864G>T	ENST00000399036.3	+	2	646	c.294G>T	c.(292-294)ggG>ggT	p.G98G	CCRL2_ENST00000400880.3_Silent_p.G98G|CCRL2_ENST00000357392.4_Silent_p.G110G|CCRL2_ENST00000400882.2_Silent_p.G98G|RP11-24F11.2_ENST00000451485.1_RNA	NM_003965.4	NP_003956.2	O00421	CCRL2_HUMAN	chemokine (C-C motif) receptor-like 2	98					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)		CTCATGCTGGGGGCGATCCCA	0.438													T|||	754	0.150559	0.3865	0.1354	5008	,	,		22724	0.0		0.1362	False		,,,				2504	0.0123				p.G110G		Atlas-SNP	.											.	CCRL2	23	.	0			c.G330T						PASS	.	T	,	1287,2727		204,879,924	86.0	85.0	86.0		330,294	-10.1	0.0	3	dbSNP_116	86	1248,7066		92,1064,3001	no	coding-synonymous,coding-synonymous	CCRL2	NM_001130910.1,NM_003965.4	,	296,1943,3925	TT,TG,GG		15.0108,32.0628,20.5629	,	110/357,98/345	46449864	2535,9793	2007	4157	6164	SO:0001819	synonymous_variant	9034	exon2			TGCTGGGGGCGAT	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.294G>T	3.37:g.46449864G>T		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	247	131	0.530364	NM_001130910	B4DKQ8|O75307|Q4VBB0|Q6IPX0|Q7KYQ9|Q96KP5|Q9UPG0	Silent	SNP	ENST00000399036.3	37	CCDS43079.1																																																																																			G|0.831;T|0.169	0.169	strong		0.438	CCRL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343909.2		
PPARGC1B	133522	hgsc.bcm.edu	37	5	149200008	149200008	+	Missense_Mutation	SNP	G	G	A	rs45518035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149200008G>A	ENST00000309241.5	+	2	123	c.91G>A	c.(91-93)Ggg>Agg	p.G31R	PPARGC1B_ENST00000394320.3_Missense_Mutation_p.G31R|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.G6R|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.G31R	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	31	Abolishes DNA transcriptional activity when missing.				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)			TGGAGGGTCCGGGGAGGAGCA	0.572													G|||	41	0.0081869	0.0295	0.0029	5008	,	,		17247	0.0		0.0	False		,,,				2504	0.0				p.G31R		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.G91A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY	96,4310	78.3+/-116.7	3,90,2110	83.0	90.0	88.0		91,16,91	5.8	0.9	5	dbSNP_127	88	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense,missense	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	125,125,125	3,92,6408	AA,AG,GG		0.0233,2.1788,0.7535	probably-damaging,probably-damaging,probably-damaging	31/985,6/960,31/1024	149200008	98,12908	2203	4300	6503	SO:0001583	missense	133522	exon2			GGGTCCGGGGAGG	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.91G>A	5.37:g.149200008G>A	ENSP00000312649:p.Gly31Arg	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	45	28	0.622222	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	g	22.2	4.254416	0.80135	0.021788	2.33E-4	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.16073	2.37;2.46;2.49;2.75	5.76	5.76	0.90799	.	0.096989	0.64402	D	0.000001	T	0.27594	0.0678	M	0.73217	2.22	0.50632	D	0.999885	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.987;0.999	P;P;P;P;D	0.67548	0.875;0.905;0.875;0.558;0.952	T	0.07888	-1.0749	10	0.87932	D	0	-33.0089	19.9678	0.97275	0.0:0.0:1.0:0.0	rs45518035	10;10;31;31;31	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	R	31;31;31;6	ENSP00000353638:G31R;ENSP00000377855:G31R;ENSP00000312649:G31R;ENSP00000384403:G6R	ENSP00000312649:G31R	G	+	1	0	PPARGC1B	149180201	1.000000	0.71417	0.930000	0.37139	0.301000	0.27625	7.339000	0.79282	2.724000	0.93272	0.651000	0.88453	GGG	G|0.994;A|0.006	0.006	strong		0.572	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
PTPRF	5792	hgsc.bcm.edu	37	1	44084739	44084739	+	Silent	SNP	C	C	T	rs1143701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44084739C>T	ENST00000359947.4	+	27	4852	c.4512C>T	c.(4510-4512)cgC>cgT	p.R1504R	PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000438120.1_Silent_p.R1495R|PTPRF_ENST00000372414.3_Silent_p.R1504R|PTPRF_ENST00000422171.2_Silent_p.R863R|PTPRF_ENST00000372413.3_Silent_p.R1495R	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1504	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)				GTGAGAAGCGCGAGCTGCGTC	0.582													T|||	3693	0.73742	0.9455	0.5764	5008	,	,		16146	0.7649		0.7167	False		,,,				2504	0.5634				p.R1504R		Atlas-SNP	.											.	PTPRF	172	.	0			c.C4512T						PASS	.	T	,	4040,366	186.7+/-213.5	1857,326,20	75.0	69.0	71.0		4512,4485	0.9	1.0	1	dbSNP_86	71	6431,2169	370.9+/-336.0	2440,1551,309	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	4297,1877,329	TT,TC,CC		25.2209,8.3069,19.491	,	1504/1908,1495/1899	44084739	10471,2535	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon27			GAAGCGCGAGCTG	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.4512C>T	1.37:g.44084739C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	120	116	0.966667	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	1672|1672	0.7655677655677655|0.7655677655677655	459|459	0.9329268292682927|0.9329268292682927	238|238	0.6574585635359116|0.6574585635359116	425|425	0.743006993006993|0.743006993006993	550|550	0.7255936675461742|0.7255936675461742	T|T	7.282|7.282	0.609324|0.609324	0.14066|0.14066	0.916931|0.916931	0.747791|0.747791	ENSG00000142949|ENSG00000142949	ENST00000429895|ENST00000412568;ENST00000414879	.|.	.|.	.|.	5.34|5.34	0.888|0.888	0.19206|0.19206	.|.	.|0.000000	.|0.33023	.|N	.|0.005372	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.40136|.	-0.9579|.	3|.	.|0.02654	.|T	.|1	.|.	3.3878|3.3878	0.07278|0.07278	0.0853:0.1957:0.3769:0.3421|0.0853:0.1957:0.3769:0.3421	rs1143701;rs1274775;rs17849117|rs1143701;rs1274775;rs17849117	.|.	.|.	.|.	V|X	1150|888;929	.|.	.|ENSP00000361484:R838X	A|R	+|+	2|1	0|2	PTPRF|PTPRF	43857326|43857326	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.942000|0.942000	0.58702|0.58702	0.863000|0.863000	0.27913|0.27913	-0.265000|-0.265000	0.09352|0.09352	-1.214000|-1.214000	0.01621|0.01621	GCG|CGA	A|0.000;C|0.209;T|0.790	0.790	strong		0.582	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
ERBB2	2064	hgsc.bcm.edu	37	17	37863268	37863268	+	Silent	SNP	G	G	A	rs4252610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37863268G>A	ENST00000269571.5	+	2	258	c.99G>A	c.(97-99)ctG>ctA	p.L33L	ERBB2_ENST00000578199.1_Silent_p.L3L|ERBB2_ENST00000540147.1_Silent_p.L3L|ERBB2_ENST00000406381.2_Silent_p.L3L|ERBB2_ENST00000445658.2_Intron|ERBB2_ENST00000540042.1_Silent_p.L3L|ERBB2_ENST00000584601.1_Silent_p.L3L|ERBB2_ENST00000541774.1_Silent_p.L18L|ERBB2_ENST00000584450.1_Silent_p.L33L			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	33					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	ACATGAAGCTGCGGCTCCCTG	0.637		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)			G|||	90	0.0179712	0.0673	0.0014	5008	,	,		17261	0.0		0.0	False		,,,				2504	0.0				p.L33L		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	ERBB2	429	.	0			c.G99A						PASS	.	G	,	206,4192		5,196,1998	40.0	35.0	37.0		9,99	2.0	1.0	17	dbSNP_111	37	0,8584		0,0,4292	no	coding-synonymous,coding-synonymous	ERBB2	NM_001005862.1,NM_004448.2	,	5,196,6290	AA,AG,GG		0.0,4.6839,1.5868	,	3/1226,33/1256	37863268	206,12776	2199	4292	6491	SO:0001819	synonymous_variant	2064	exon2			GAAGCTGCGGCTC	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.99G>A	17.37:g.37863268G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	137	63	0.459854	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent	SNP	ENST00000269571.5	37	CCDS32642.1																																																																																			G|0.982;A|0.018	0.018	strong		0.637	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346670	140346670	+	Silent	SNP	C	C	A	rs155809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140346670C>A	ENST00000289269.5	+	1	851	c.319C>A	c.(319-321)Cgg>Agg	p.R107R	PCDHA12_ENST00000398631.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHAC1_ENST00000253807.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	107	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCATTGATCGGGAGGCGCT	0.642													C|||	79	0.0157748	0.0567	0.0058	5008	,	,		18549	0.0		0.0	False		,,,				2504	0.0				p.R107R	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.C319A						PASS	.	C	,,,,,,,,,,,,,,,,,,	252,4154	137.7+/-173.5	5,242,1956	34.0	35.0	35.0		,319,,,,,,,,,,,,,,,,,319	5.7	1.0	5	dbSNP_79	35	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	5,243,6255	AA,AC,CC		0.0116,5.7195,1.9453	,,,,,,,,,,,,,,,,,,	,107/1008,,,,,,,,,,,,,,,,,107/885	140346670	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			ATTGATCGGGAGG	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.319C>A	5.37:g.140346670C>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	28	11	0.392857	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			C|0.979;A|0.021	0.021	strong		0.642	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
GOT2	2806	hgsc.bcm.edu	37	16	58750604	58750604	+	Silent	SNP	G	G	A	rs1058192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58750604G>A	ENST00000245206.5	-	7	944	c.816C>T	c.(814-816)tgC>tgT	p.C272C	GOT2_ENST00000434819.2_Silent_p.C229C|GOT2_ENST00000564400.1_Intron	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	272					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)	p.C272C(1)		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)	ATTGGCAGAGGCAAACATTAA	0.502													A|||	3607	0.720248	0.8896	0.7738	5008	,	,		20689	0.6478		0.67	False		,,,				2504	0.5798				p.C272C		Atlas-SNP	.											GOT2,NS,carcinoma,0,1	GOT2	42	1	1	Substitution - coding silent(1)	prostate(1)	c.C816T						PASS	.	A		3702,694	289.8+/-280.6	1553,596,49	73.0	60.0	65.0		816	0.8	1.0	16	dbSNP_86	65	5574,3026	466.3+/-366.7	1803,1968,529	no	coding-synonymous	GOT2	NM_002080.2		3356,2564,578	AA,AG,GG		35.186,15.7871,28.6242		272/431	58750604	9276,3720	2198	4300	6498	SO:0001819	synonymous_variant	2806	exon7			GCAGAGGCAAACA		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.816C>T	16.37:g.58750604G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Silent	SNP	ENST00000245206.5	37	CCDS10801.1																																																																																			G|0.286;A|0.714	0.714	strong		0.502	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
OAS2	4939	hgsc.bcm.edu	37	12	113444285	113444285	+	Silent	SNP	C	C	T	rs16942424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113444285C>T	ENST00000342315.4	+	8	1750	c.1536C>T	c.(1534-1536)tcC>tcT	p.S512S	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Silent_p.S512S	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	512	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						TGTATAAATCCTCGGACCTCC	0.522													C|||	172	0.034345	0.1203	0.0173	5008	,	,		16629	0.0		0.001	False		,,,				2504	0.0				p.S512S	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.C1536T						PASS	.	C	,	399,4007		18,363,1822	88.0	88.0	88.0		1536,1536	-0.6	0.0	12	dbSNP_123	88	19,8581		0,19,4281	no	coding-synonymous,coding-synonymous	OAS2	NM_002535.2,NM_016817.2	,	18,382,6103	TT,TC,CC		0.2209,9.0558,3.2139	,	512/688,512/720	113444285	418,12588	2203	4300	6503	SO:0001819	synonymous_variant	4939	exon8			TAAATCCTCGGAC	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.1536C>T	12.37:g.113444285C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Silent	SNP	ENST00000342315.4	37	CCDS31906.1																																																																																			C|0.957;T|0.043	0.043	strong		0.522	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1		
MT-ND4	4538	hgsc.bcm.edu	37	M	11252	11252	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11252A>G	ENST00000361381.2	+	1	493	c.493A>G	c.(493-495)Att>Gtt	p.I165V	MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	165					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						TCATCGCACTAATTTACACTC	0.473																																					p.I165V		Atlas-SNP	.											.	.	.	.	0			c.A493G						PASS	.																																			SO:0001583	missense	0	exon1			GCACTAATTTACA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.493A>G	M.37:g.11252A>G	ENSP00000354961:p.Ile165Val	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	37																																																																																				A|0.936;G|0.064	0.064	strong		0.473	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
APOBEC4	403314	hgsc.bcm.edu	37	1	183617413	183617413	+	Silent	SNP	T	T	C	rs12045762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:183617413T>C	ENST00000308641.4	-	2	775	c.504A>G	c.(502-504)gcA>gcG	p.A168A	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)	168					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						CGCGGTTCCATGCTGAGGCAG	0.463													T|||	473	0.0944489	0.18	0.036	5008	,	,		21034	0.1091		0.0318	False		,,,				2504	0.0695				p.A168A		Atlas-SNP	.											.	APOBEC4	45	.	0			c.A504G						PASS	.	T	,	667,3739	278.7+/-274.4	46,575,1582	60.0	65.0	63.0		,504	-10.0	0.0	1	dbSNP_120	63	242,8358	95.9+/-157.7	1,240,4059	no	intron,coding-synonymous	RGL1,APOBEC4	NM_015149.3,NM_203454.2	,	47,815,5641	CC,CT,TT		2.814,15.1384,6.9891	,	,168/368	183617413	909,12097	2203	4300	6503	SO:0001819	synonymous_variant	403314	exon2			GTTCCATGCTGAG	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.504A>G	1.37:g.183617413T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	70	26	0.371429	NM_203454	Q8N7F6	Silent	SNP	ENST00000308641.4	37	CCDS1358.1																																																																																			T|0.934;C|0.066	0.066	strong		0.463	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454	
ATP9B	374868	hgsc.bcm.edu	37	18	76870397	76870397	+	Silent	SNP	G	G	A	rs492657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:76870397G>A	ENST00000426216.2	+	3	353	c.336G>A	c.(334-336)gaG>gaA	p.E112E	ATP9B_ENST00000307671.7_Silent_p.E112E|ATP9B_ENST00000586722.1_Silent_p.E112E|ATP9B_ENST00000458297.2_Silent_p.E60E|ATP9B_ENST00000591464.1_Intron	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	112					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|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)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		GAAAGAAAGAGCTGAAAGCTC	0.318													A|||	578	0.115415	0.2882	0.0749	5008	,	,		18999	0.0228		0.1034	False		,,,				2504	0.0184				p.E112E		Atlas-SNP	.											.	ATP9B	96	.	0			c.G336A						PASS	.	A		1196,3210	705.1+/-407.2	143,910,1150	70.0	76.0	74.0		336	-1.9	0.9	18	dbSNP_83	74	809,7791	781.8+/-407.6	43,723,3534	no	coding-synonymous	ATP9B	NM_198531.3		186,1633,4684	AA,AG,GG		9.407,27.1448,15.416		112/1148	76870397	2005,11001	2203	4300	6503	SO:0001819	synonymous_variant	374868	exon3			GAAAGAGCTGAAA	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.336G>A	18.37:g.76870397G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_198531	O60872|Q08AD8|Q08AD9	Silent	SNP	ENST00000426216.2	37	CCDS12014.1																																																																																			G|0.862;A|0.138	0.138	strong		0.318	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
ESPNL	339768	hgsc.bcm.edu	37	2	239039779	239039779	+	Silent	SNP	G	G	A	rs73102306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239039779G>A	ENST00000343063.3	+	9	2687	c.2424G>A	c.(2422-2424)ctG>ctA	p.L808L	ESPNL_ENST00000409506.1_Silent_p.L440L|ESPNL_ENST00000409169.1_Silent_p.L764L|ESPNL_ENST00000477241.1_3'UTR	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	808										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		CCCACCTGCTGGGCAACTGGA	0.756													G|||	435	0.086861	0.0968	0.0634	5008	,	,		12580	0.0536		0.0915	False		,,,				2504	0.1196				p.L808L		Atlas-SNP	.											.	ESPNL	63	.	0			c.G2424A						PASS	.	G		281,3529		10,261,1634	3.0	3.0	3.0		2424	2.7	1.0	2	dbSNP_130	3	539,6963		9,521,3221	no	coding-synonymous	ESPNL	NM_194312.2		19,782,4855	AA,AG,GG		7.1848,7.3753,7.2489		808/1006	239039779	820,10492	1905	3751	5656	SO:0001819	synonymous_variant	339768	exon9			CCTGCTGGGCAAC	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2424G>A	2.37:g.239039779G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			G|0.922;A|0.078	0.078	strong		0.756	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
CDH13	1012	hgsc.bcm.edu	37	16	82892037	82892037	+	Missense_Mutation	SNP	A	A	G	rs72807847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:82892037A>G	ENST00000566620.1	+	2	406	c.116A>G	c.(115-117)aAt>aGt	p.N39S	CDH13_ENST00000268613.10_Missense_Mutation_p.N86S|CDH13_ENST00000431540.3_Missense_Mutation_p.N39S|CDH13_ENST00000428848.3_Missense_Mutation_p.N39S|CDH13_ENST00000446376.2_Missense_Mutation_p.N39S|CDH13_ENST00000567445.1_Missense_Mutation_p.N39S|CDH13_ENST00000565636.1_Missense_Mutation_p.N39S	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	39					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)		TTCCATATCAATCAGCCAGCT	0.378													A|||	219	0.04373	0.0446	0.0029	5008	,	,		19142	0.0595		0.007	False		,,,				2504	0.093				p.N86S		Atlas-SNP	.											.	CDH13	97	.	0			c.A257G						PASS	.	A	SER/ASN,SER/ASN,,SER/ASN,SER/ASN,SER/ASN	118,3660		3,112,1774	91.0	87.0	88.0		257,116,,116,116,116	3.6	0.0	16	dbSNP_130	88	61,8161		0,61,4050	yes	missense,missense,utr-5,missense,missense,missense	CDH13	NM_001220488.1,NM_001220489.1,NM_001220490.1,NM_001220491.1,NM_001220492.1,NM_001257.4	46,46,,46,46,46	3,173,5824	GG,GA,AA		0.7419,3.1233,1.4917	benign,benign,,benign,benign,benign	86/761,39/675,,39/191,39/176,39/714	82892037	179,11821	1889	4111	6000	SO:0001583	missense	1012	exon3			ATATCAATCAGCC	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.116A>G	16.37:g.82892037A>G	ENSP00000454435:p.Asn39Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	177	64	0.361582	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	37	CCDS58486.1	68	0.031135531135531136	27	0.054878048780487805	2	0.0055248618784530384	36	0.06293706293706294	3	0.00395778364116095	A	3.901	-0.022010	0.07634	0.031233	0.007419	ENSG00000140945	ENST00000268613;ENST00000428848;ENST00000536143;ENST00000539548;ENST00000431540;ENST00000446376	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	5.95	3.61	0.41365	Cadherin prodomain-like (1);Cadherin-like (1);	.	.	.	.	T	0.02304	0.0071	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.12156	0.004;0.007;0.003;0.001	T	0.15925	-1.0420	9	0.08179	T	0.78	.	7.9329	0.29912	0.7918:0.1373:0.0709:0.0	.	39;86;39;39	B7Z590;B7Z9B1;A8W477;P55290	.;.;.;CAD13_HUMAN	S	86;39;39;39;39;39	ENSP00000268613:N86S;ENSP00000394557:N39S;ENSP00000442225:N39S;ENSP00000408632:N39S;ENSP00000388804:N39S	ENSP00000268613:N86S	N	+	2	0	CDH13	81449538	0.146000	0.22672	0.043000	0.18650	0.992000	0.81027	2.525000	0.45598	1.082000	0.41137	-0.263000	0.10527	AAT	A|0.972;G|0.028	0.028	strong		0.378	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257	
ZFP36L1	677	hgsc.bcm.edu	37	14	69259662	69259662	+	5'UTR	SNP	C	C	A	rs1051533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:69259662C>A	ENST00000439696.2	-	0	295				ZFP36L1_ENST00000555997.1_5'Flank|ZFP36L1_ENST00000336440.3_5'UTR	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1						gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TCATCCTGTGCGTTCGCGCGA	0.602													C|||	1019	0.203474	0.3888	0.1513	5008	,	,		11682	0.0089		0.2127	False		,,,				2504	0.181				p.T67T		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.G201T						PASS	.	C		1583,2823	494.3+/-362.9	296,991,916	121.0	117.0	118.0			1.4	1.0	14	dbSNP_86	118	1916,6684	340.3+/-323.5	215,1486,2599	no	utr-5	ZFP36L1	NM_004926.3		511,2477,3515	AA,AC,CC		22.2791,35.9283,26.903			69259662	3499,9507	2203	4300	6503	SO:0001623	5_prime_UTR_variant	677	exon2			CCTGTGCGTTCGC	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"""RING-type (C3HC4) zinc fingers"""	1107	protein-coding gene	gene with protein product		601064	"""zinc finger protein, C3H type, 36-like 1"", ""zinc finger protein 36, C3H type-like 1"""	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.-7G>T	14.37:g.69259662C>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_001244701	Q13851	Silent	SNP	ENST00000439696.2	37	CCDS9791.1																																																																																			C|0.791;A|0.209	0.209	strong		0.602	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		
CENPE	1062	hgsc.bcm.edu	37	4	104117191	104117191	+	Silent	SNP	A	A	G	rs2290943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:104117191A>G	ENST00000265148.3	-	4	332	c.243T>C	c.(241-243)acT>acC	p.T81T	CENPE_ENST00000380026.3_Silent_p.T81T	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	81	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)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.T81T(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		AGGCAAATATAGTACCTGCAA	0.378													A|||	600	0.119808	0.0552	0.1153	5008	,	,		19569	0.1429		0.2207	False		,,,				2504	0.0828				p.T81T		Atlas-SNP	.											CENPE,NS,carcinoma,0,1	CENPE	253	1	1	Substitution - coding silent(1)	stomach(1)	c.T243C						PASS	.	A		252,4154	146.5+/-181.1	8,236,1959	95.0	88.0	91.0		243	-8.4	0.9	4	dbSNP_100	91	1775,6825	319.7+/-314.3	196,1383,2721	no	coding-synonymous	CENPE	NM_001813.2		204,1619,4680	GG,GA,AA		20.6395,5.7195,15.5851		81/2702	104117191	2027,10979	2203	4300	6503	SO:0001819	synonymous_variant	1062	exon4			AAATATAGTACCT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.243T>C	4.37:g.104117191A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_001813	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	37	CCDS34042.1																																																																																			A|0.848;G|0.152	0.152	strong		0.378	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SBNO2	22904	hgsc.bcm.edu	37	19	1110829	1110829	+	Silent	SNP	G	G	A	rs2302109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1110829G>A	ENST00000361757.3	-	26	3180	c.2943C>T	c.(2941-2943)aaC>aaT	p.N981N	SBNO2_ENST00000438103.2_Silent_p.N924N|SBNO2_ENST00000587024.1_Silent_p.N971N	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	208	0	0		WXS	Illumina HiSeq	Phase_I	194	194	1	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	
SLC25A37	51312	hgsc.bcm.edu	37	8	23429093	23429093	+	Missense_Mutation	SNP	G	G	T	rs116050502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:23429093G>T	ENST00000519973.1	+	4	940	c.742G>T	c.(742-744)Gcc>Tcc	p.A248S	FP15737_ENST00000399967.3_5'Flank	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	248					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)		CGGGGCCCTCGCCGCGGCCGC	0.662													G|||	33	0.00658946	0.025	0.0	5008	,	,		12709	0.0		0.0	False		,,,				2504	0.0				p.A248S		Atlas-SNP	.											.	SLC25A37	27	.	0			c.G742T						PASS	.	G	SER/ALA	93,3715		1,91,1812	22.0	26.0	25.0		742	5.8	0.2	8	dbSNP_132	25	1,8197		0,1,4098	yes	missense	SLC25A37	NM_016612.2	99	1,92,5910	TT,TG,GG		0.0122,2.4422,0.7829	possibly-damaging	248/339	23429093	94,11912	1904	4099	6003	SO:0001583	missense	51312	exon4			GCCCTCGCCGCGG	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.742G>T	8.37:g.23429093G>T	ENSP00000429200:p.Ala248Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	65	40	0.615385	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Missense_Mutation	SNP	ENST00000519973.1	37	CCDS47828.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	20.5	3.994188	0.74703	0.024422	1.22E-4	ENSG00000147454	ENST00000519973	T	0.79653	-1.29	5.8	5.8	0.92144	Mitochondrial carrier domain (2);	0.049561	0.85682	D	0.000000	T	0.80149	0.4570	L	0.54965	1.715	0.58432	D	0.999999	D	0.58970	0.984	D	0.69479	0.964	D	0.84394	0.0556	10	0.66056	D	0.02	-8.3551	18.6148	0.91299	0.0:0.0:1.0:0.0	.	248	Q9NYZ2	MFRN1_HUMAN	S	248	ENSP00000429200:A248S	ENSP00000429200:A248S	A	+	1	0	SLC25A37	23485038	1.000000	0.71417	0.214000	0.23707	0.949000	0.60115	5.096000	0.64535	2.740000	0.93945	0.650000	0.86243	GCC	G|0.994;T|0.006	0.006	strong		0.662	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612	
HDHD1	8226	hgsc.bcm.edu	37	X	6995438	6995438	+	Silent	SNP	C	C	T	rs1803675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:6995438C>T	ENST00000381077.5	-	3	409	c.333G>A	c.(331-333)ctG>ctA	p.L111L	HDHD1_ENST00000540122.1_Silent_p.L111L|HDHD1_ENST00000424830.2_Silent_p.L134L|HDHD1_ENST00000412827.2_Silent_p.L68L	NM_001178136.1|NM_012080.4	NP_001171607.1|NP_036212.3	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain containing 1	111					nucleotide metabolic process (GO:0009117)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)			breast(2)|large_intestine(1)|lung(3)	6						AGCTGGTGGCCAGTGCAAAGG	0.597													C|||	1051	0.278411	0.1074	0.3473	3775	,	,		12574	0.2153		0.1909	False		,,,				2504	0.2648				p.L134L		Atlas-SNP	.											.	HDHD1	21	.	0			c.G402A						PASS	.	C	,,,	645,2938		57,424,107,1025,464	51.0	51.0	51.0		402,333,204,333	-7.8	0.0	X	dbSNP_89	51	1700,4864		172,894,462,1310,1350	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HDHD1	NM_001135565.1,NM_001178135.1,NM_001178136.1,NM_012080.4	,,,	229,1318,569,2335,1814	TT,TC,T,CC,C		25.8988,18.0017,23.1103	,,,	134/252,111/209,68/186,111/229	6995438	2345,7802	2077	4188	6265	SO:0001819	synonymous_variant	8226	exon4			GGTGGCCAGTGCA	M86934	CCDS48075.1, CCDS48076.1, CCDS55366.1, CCDS55367.1	Xp22.32	2010-07-21	2010-07-21	2010-07-21	ENSG00000130021	ENSG00000130021			16818	protein-coding gene	gene with protein product		306480	"""family with sequence similarity 16, member A, X-linked"", ""haloacid dehalogenase-like hydrolase domain containing 1A"""	FAM16AX, HDHD1A		1734713, 1284467	Standard	NM_012080		Approved	DXF68S1E, GS1	uc011mhm.1	Q08623	OTTHUMG00000021101	ENST00000381077.5:c.333G>A	X.37:g.6995438C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	172	91	0.52907	NM_001135565	B2R7X6|B4DV93|B7Z6Q3|E9PAV8|F5GWZ2|Q53F84|Q96EB8	Silent	SNP	ENST00000381077.5	37	CCDS48075.1																																																																																			C|0.723;T|0.277	0.277	strong		0.597	HDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055683.2	NM_012080	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048663	33048663	+	Missense_Mutation	SNP	G	G	A	rs1042153|rs386699871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33048663G>A	ENST00000418931.2	+	2	431	c.315G>A	c.(313-315)atG>atA	p.M105I	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.M105I|HLA-DPA1_ENST00000419277.1_5'Flank	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	105	Beta-1.		M -> I (in allele DPB1*08:02, allele DPB1*09:02, allele DPB1*13:01, allele DPB1*13:02 and allele DPB1*19:01; dbSNP:rs1042153).|M -> V (in allele DPB1*01:01, allele DPB1*03:01, allele DPB1*05:02, allele DPB1*08:01, allele DPB1*09:01, allele DPB1*10:01, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*17:02, allele DPB1*21:02, allele DPB1*22:02, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*29:01, allele DPB1*35:01, allele DPB1*37:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*50:01, allele DPB1*52:01, allele DPB1*54:01, allele DPB1*56:01, allele DPB1*57:01, allele DPB1*65:01, allele DPB1*67:01, allele DPB1*68:01, allele DPB1*70:01, allele DPB1*73:01, allele DPB1*75:01, allele DPB1*76:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*84:01, allele DPB1*88:01, allele DPB1*90:01 and allele DPB1*92:01; dbSNP:rs1042151). {ECO:0000269|PubMed:6330724}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CGGACAGGATGTGCAGACACA	0.701													.|||	1549	0.309305	0.4607	0.2507	5008	,	,		12515	0.2123		0.2296	False		,,,				2504	0.3282				p.M105I		Atlas-SNP	.											HLA-DPB1,NS,lymphoid_neoplasm,+2,1	HLA-DPB1	28	1	0			c.G315A						scavenged	.						29.0	30.0	30.0					6																	33048663		1510	2709	4219	SO:0001583	missense	3115	exon2			CAGGATGTGCAGA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.315G>A	6.37:g.33048663G>A	ENSP00000408146:p.Met105Ile	Somatic	33	9	0.272727		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	602|602	0.27564102564102566|0.27564102564102566	239|239	0.48577235772357724|0.48577235772357724	82|82	0.2265193370165746|0.2265193370165746	116|116	0.20279720279720279|0.20279720279720279	165|165	0.21767810026385223|0.21767810026385223	G|G	11.30|11.30	1.597043|1.597043	0.28445|0.28445	.|.	.|.	ENSG00000223865|ENSG00000223865	ENST00000416804|ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835	.|T;T;T	.|0.00311	.|8.15;8.15;8.15	4.02|4.02	0.0296|0.0296	0.14163|0.14163	.|MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	.|2.303120	.|0.02598	.|U	.|0.100781	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.02181|0.02181	-0.65|-0.65	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.10450	.|0.001;0.004;0.005	T|T	0.28396|0.28396	-1.0045|-1.0045	4|9	.|0.52906	.|T	.|0.07	.|.	5.9122|5.9122	0.19035|0.19035	0.1929:0.4754:0.3317:0.0|0.1929:0.4754:0.3317:0.0	rs1042153;rs3173290;rs17214748;rs17420330;rs17851009|rs1042153;rs3173290;rs17214748;rs17420330;rs17851009	.|71;115;105	.|A2ALJ6;Q59GY1;P04440	.|.;.;DPB1_HUMAN	Y|I	72|105;105;105;82	.|ENSP00000408146:M105I;ENSP00000439674:M105I;ENSP00000412654:M82I	.|ENSP00000389210:M105I	C|M	+|+	2|3	0|0	HLA-DPB1|HLA-DPB1	33156641|33156641	0.030000|0.030000	0.19436|0.19436	0.450000|0.450000	0.26969|0.26969	0.008000|0.008000	0.06430|0.06430	0.177000|0.177000	0.16801|0.16801	0.105000|0.105000	0.17753|0.17753	-0.134000|-0.134000	0.14843|0.14843	TGT|ATG	G|0.755;A|0.245	0.245	strong		0.701	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
MTO1	25821	hgsc.bcm.edu	37	6	74190448	74190448	+	Silent	SNP	T	T	C	rs2036039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74190448T>C	ENST00000370300.4	+	8	1345	c.1255T>C	c.(1255-1257)Ttg>Ctg	p.L419L	MTO1_ENST00000370305.1_Silent_p.L345L|MTO1_ENST00000415954.2_Silent_p.L394L|MTO1_ENST00000498286.1_Silent_p.L394L	NM_012123.3|NM_133645.2	NP_036255.2|NP_598400.1	Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	419					mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)	p.L419L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						CACCCCTTCCTTGGAGACTCA	0.418													C|||	1042	0.208067	0.2693	0.1758	5008	,	,		19156	0.2123		0.1849	False		,,,				2504	0.1677				p.L419L		Atlas-SNP	.											MTO1,NS,carcinoma,0,1	MTO1	59	1	1	Substitution - coding silent(1)	stomach(1)	c.T1255C						PASS	.	C	,,	1141,3265	715.4+/-408.5	149,843,1211	183.0	165.0	171.0		1180,1180,1255	5.2	0.7	6	dbSNP_94	171	1541,7059	746.9+/-407.3	136,1269,2895	no	coding-synonymous,coding-synonymous,coding-synonymous	MTO1	NM_001123226.1,NM_012123.3,NM_133645.2	,,	285,2112,4106	CC,CT,TT		17.9186,25.8965,20.6213	,,	394/733,394/693,419/718	74190448	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	25821	exon8			CCTTCCTTGGAGA	AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297			19261	protein-coding gene	gene with protein product		614667	"""mitochondrial translation optimization 1 homolog (S. cerevisiae)"""			12011058, 22608499	Standard	NM_012123		Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000370300.4:c.1255T>C	6.37:g.74190448T>C		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	186	99	0.532258	NM_133645	B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	Silent	SNP	ENST00000370300.4	37	CCDS4979.1																																																																																			T|0.668;G|0.032;C|0.170;N|0.000;A|0.130	0.170	strong		0.418	MTO1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041215.2	NM_012123	
SP100	6672	hgsc.bcm.edu	37	2	231380146	231380146	+	Missense_Mutation	SNP	G	G	A	rs61733089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231380146G>A	ENST00000264052.5	+	25	2786	c.2431G>A	c.(2431-2433)Gct>Act	p.A811T	SP100_ENST00000340126.4_Intron	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	811					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)		GAATAACACCGCTGCAGCTGA	0.433													G|||	41	0.0081869	0.0287	0.0043	5008	,	,		19980	0.0		0.0	False		,,,				2504	0.0				p.A811T		Atlas-SNP	.											.	SP100	167	.	0			c.G2431A						PASS	.	G	,THR/ALA	125,4281	89.2+/-127.9	1,123,2079	47.0	49.0	49.0		,2431	0.2	0.1	2	dbSNP_129	49	0,8600		0,0,4300	yes	intron,missense	SP100	NM_001080391.1,NM_003113.3	,58	1,123,6379	AA,AG,GG		0.0,2.837,0.9611	,	,811/880	231380146	125,12881	2203	4300	6503	SO:0001583	missense	6672	exon25			AACACCGCTGCAG	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.2431G>A	2.37:g.231380146G>A	ENSP00000264052:p.Ala811Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_003113	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	ENST00000264052.5	37	CCDS2477.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	G	9.783	1.175944	0.21704	0.02837	0.0	ENSG00000067066	ENST00000264052	D	0.93189	-3.18	0.158	0.158	0.14942	High mobility group, HMG1/HMG2, subgroup (1);High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.	.	.	.	T	0.69949	0.3168	L	0.33485	1.01	0.43347	D	0.995409	P	0.42078	0.77	B	0.34346	0.18	T	0.73636	-0.3920	9	0.87932	D	0	.	6.0348	0.19702	5.0E-4:0.0:0.9995:0.0	rs61733089	811	P23497	SP100_HUMAN	T	811	ENSP00000264052:A811T	ENSP00000264052:A811T	A	+	1	0	SP100	231088390	0.000000	0.05858	0.057000	0.19452	0.058000	0.15608	-0.122000	0.10627	0.202000	0.20498	0.205000	0.17691	GCT	G|0.991;A|0.009	0.009	strong		0.433	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
TSPAN8	7103	hgsc.bcm.edu	37	12	71523134	71523134	+	Missense_Mutation	SNP	A	A	C	rs1051334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:71523134A>C	ENST00000393330.2	-	11	1189	c.637T>G	c.(637-639)Tca>Gca	p.S213A	TSPAN8_ENST00000247829.3_Missense_Mutation_p.S213A|TSPAN8_ENST00000546561.1_Missense_Mutation_p.S213A|TSPAN8_ENST00000552128.1_Missense_Mutation_p.S130A			P19075	TSN8_HUMAN	tetraspanin 8	213			S -> A (in dbSNP:rs1051334).		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)			AGTCCAAATGATATTCCAATA	0.279													C|||	1256	0.250799	0.1203	0.2291	5008	,	,		15575	0.2877		0.3986	False		,,,				2504	0.2526				p.S213A		Atlas-SNP	.											.	TSPAN8	30	.	0			c.T637G						PASS	.	C	ALA/SER	832,3562	728.1+/-409.9	78,676,1443	52.0	54.0	53.0		637	4.9	1.0	12	dbSNP_86	53	3526,5070	622.4+/-397.3	732,2062,1504	yes	missense	TSPAN8	NM_004616.2	99	810,2738,2947	CC,CA,AA		41.0191,18.9349,33.5489	benign	213/238	71523134	4358,8632	2197	4298	6495	SO:0001583	missense	7103	exon8			CAAATGATATTCC	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.637T>G	12.37:g.71523134A>C	ENSP00000377003:p.Ser213Ala	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	154	76	0.493506	NM_004616	B2R7T7|Q9BS78	Missense_Mutation	SNP	ENST00000393330.2	37	CCDS8999.1	623	0.28525641025641024	55	0.11178861788617886	94	0.2596685082872928	179	0.3129370629370629	295	0.3891820580474934	C	4.019	0.001031	0.07819	0.189349	0.410191	ENSG00000127324	ENST00000393330;ENST00000247829;ENST00000546561;ENST00000552128	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	5.77	4.88	0.63580	.	0.103092	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00013	-2.935	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40251	-0.9573	9	0.02654	T	1	.	12.0304	0.53394	0.315:0.685:0.0:0.0	rs1051334;rs3168483;rs17413936;rs17845049;rs17857828;rs61360808;rs1051334	213	P19075	TSN8_HUMAN	A	213;213;213;130	ENSP00000377003:S213A;ENSP00000247829:S213A;ENSP00000447160:S213A;ENSP00000449820:S130A	ENSP00000247829:S213A	S	-	1	0	TSPAN8	69809401	0.994000	0.37717	0.992000	0.48379	0.964000	0.63967	1.278000	0.33179	0.895000	0.36342	-0.121000	0.15023	TCA	A|0.689;C|0.311	0.311	strong		0.279	TSPAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404737.1	NM_004616	
OR6B3	150681	hgsc.bcm.edu	37	2	240984833	240984833	+	Silent	SNP	C	C	G	rs13389099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240984833C>G	ENST00000319423.4	-	1	656	c.657G>C	c.(655-657)gcG>gcC	p.A219A	PRR21_ENST00000408934.1_5'Flank	NM_173351.1	NP_775486.1	Q8NGW1	OR6B3_HUMAN	olfactory receptor, family 6, subfamily B, member 3	219						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)		GGGTGATGTGCGCATATGACA	0.592													t|||	1218	0.243211	0.2912	0.1744	5008	,	,		20769	0.2054		0.2614	False		,,,				2504	0.2474				p.A219A		Atlas-SNP	.											.	OR6B3	37	.	0			c.G657C						PASS	.	T		1287,3011		197,893,1059	62.0	67.0	65.0		657	-8.2	0.0	2	dbSNP_121	65	2297,6203		310,1677,2263	no	coding-synonymous	OR6B3	NM_173351.1		507,2570,3322	GG,GC,CC		27.0235,29.9442,28.0044		219/332	240984833	3584,9214	2149	4250	6399	SO:0001819	synonymous_variant	150681	exon1			GATGTGCGCATAT		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.657G>C	2.37:g.240984833C>G		Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	405	220	0.54321	NM_173351	Q6IFH3	Silent	SNP	ENST00000319423.4	37	CCDS42837.1																																																																																			C|0.751;G|0.249	0.249	strong		0.592	OR6B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326078.1		
RELN	5649	hgsc.bcm.edu	37	7	103205949	103205949	+	Silent	SNP	G	G	C	rs78221963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103205949G>C	ENST00000428762.1	-	34	5145	c.4986C>G	c.(4984-4986)acC>acG	p.T1662T	RELN_ENST00000343529.5_Silent_p.T1662T|RELN_ENST00000424685.2_Silent_p.T1662T	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1662					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)		ACTGCAAAAAGGTAGATGCTG	0.423													G|||	41	0.0081869	0.0303	0.0014	5008	,	,		18251	0.0		0.0	False		,,,				2504	0.0				p.T1662T	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C4986G						PASS	.	G	,	65,4341	59.9+/-96.7	0,65,2138	77.0	70.0	72.0		4986,4986	4.0	1.0	7	dbSNP_132	72	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	0,66,6437	CC,CG,GG		0.0116,1.4753,0.5075	,	1662/3461,1662/3459	103205949	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon34			CAAAAAGGTAGAT		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.4986C>G	7.37:g.103205949G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			G|0.993;C|0.007	0.007	strong		0.423	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
PTX4	390667	hgsc.bcm.edu	37	16	1537693	1537693	+	Missense_Mutation	SNP	C	C	A	rs61734779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1537693C>A	ENST00000447419.2	-	2	445	c.420G>T	c.(418-420)agG>agT	p.R140S	PTX4_ENST00000293922.1_Missense_Mutation_p.R135S|PTX4_ENST00000440447.2_Intron			Q96A99	PTX4_HUMAN	pentraxin 4, long	140						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						TGTGTGCCTTCCTTTCCCGGG	0.711													C|||	649	0.129593	0.2935	0.072	5008	,	,		14870	0.002		0.1074	False		,,,				2504	0.1033				p.R135S		Atlas-SNP	.											.	PTX4	46	.	0			c.G405T						PASS	.	C	SER/ARG	1165,3227		158,849,1189	26.0	32.0	30.0		405	-2.4	0.0	16	dbSNP_129	30	716,7862		30,656,3603	yes	missense	PTX4	NM_001013658.1	110	188,1505,4792	AA,AC,CC		8.3469,26.5255,14.5027	benign	135/474	1537693	1881,11089	2196	4289	6485	SO:0001583	missense	390667	exon2			TGCCTTCCTTTCC		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.420G>T	16.37:g.1537693C>A	ENSP00000445277:p.Arg140Ser	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		277	0.12683150183150182	164	0.3333333333333333	27	0.07458563535911603	0	0.0	86	0.11345646437994723	C	4.397	0.073239	0.08485	0.265255	0.083469	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.04917	3.68;3.53	4.99	-2.42	0.06542	.	1.741290	0.03367	N	0.198355	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.12013	0.005	B	0.10450	0.005	T	0.48234	-0.9053	9	0.18710	T	0.47	.	2.2588	0.04061	0.1171:0.4328:0.229:0.2212	.	135	Q96A99-2	.	S	140;135	ENSP00000445277:R140S;ENSP00000293922:R135S	ENSP00000293922:R135S	R	-	3	2	PTX4	1477694	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.284000	0.08422	-0.365000	0.08076	-0.258000	0.10820	AGG	C|0.868;A|0.132	0.132	strong		0.711	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
WFS1	7466	hgsc.bcm.edu	37	4	6303354	6303354	+	Missense_Mutation	SNP	G	G	A	rs734312	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6303354G>A	ENST00000226760.1	+	8	2002	c.1832G>A	c.(1831-1833)cGc>cAc	p.R611H	WFS1_ENST00000503569.1_Missense_Mutation_p.R611H	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	611			R -> H (in dbSNP:rs734312). {ECO:0000269|PubMed:10521293, ECO:0000269|PubMed:10624825, ECO:0000269|PubMed:10679252, ECO:0000269|PubMed:10760554, ECO:0000269|PubMed:11295831, ECO:0000269|PubMed:11709538, ECO:0000269|PubMed:15605410, ECO:0000269|PubMed:18688868, ECO:0000269|PubMed:9771706, ECO:0000269|Ref.5}.		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)	p.R611H(1)		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)		CTGCTGTTGCGCTGGTGGACC	0.637													G|||	2350	0.469249	0.0318	0.5476	5008	,	,		20311	0.8105		0.5626	False		,,,				2504	0.5573				p.R611H		Atlas-SNP	.											WFS1,NS,carcinoma,+1,2	WFS1	71	2	1	Substitution - Missense(1)	stomach(1)	c.G1832A	GRCh37	CM000447	WFS1	M	rs734312	PASS	.	G	HIS/ARG,HIS/ARG	515,3891	237.1+/-249.0	40,435,1728	199.0	184.0	189.0		1832,1832	4.6	1.0	4	dbSNP_86	189	4703,3897	606.5+/-395.1	1267,2169,864	yes	missense,missense	WFS1	NM_001145853.1,NM_006005.3	29,29	1307,2604,2592	AA,AG,GG		45.314,11.6886,40.1199	probably-damaging,probably-damaging	611/891,611/891	6303354	5218,7788	2203	4300	6503	SO:0001583	missense	7466	exon8			TGTTGCGCTGGTG	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.1832G>A	4.37:g.6303354G>A	ENSP00000226760:p.Arg611His	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	189	98	0.518519	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Missense_Mutation	SNP	ENST00000226760.1	37	CCDS3386.1	1136	0.5201465201465202	31	0.06300813008130081	202	0.5580110497237569	480	0.8391608391608392	423	0.558047493403694	G	7.640	0.680750	0.14907	0.116886	0.54686	ENSG00000109501	ENST00000503569;ENST00000226760	D;D	0.93604	-3.25;-3.25	5.41	4.57	0.56435	.	0.111903	0.64402	N	0.000013	T	0.00012	0.0000	M	0.80982	2.52	0.22142	P	0.999335408	B	0.26318	0.146	B	0.22601	0.04	T	0.47368	-0.9123	9	0.48119	T	0.1	-38.9527	13.2566	0.60083	0.0769:0.0:0.9231:0.0	rs734312;rs1046313;rs3733193;rs17719619;rs58910458;rs734312	611	O76024	WFS1_HUMAN	H	611	ENSP00000423337:R611H;ENSP00000226760:R611H	ENSP00000226760:R611H	R	+	2	0	WFS1	6354255	1.000000	0.71417	0.983000	0.44433	0.153000	0.21895	4.704000	0.61831	1.295000	0.44724	-0.258000	0.10820	CGC	G|0.550;A|0.450	0.450	strong		0.637	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
CLUAP1	23059	hgsc.bcm.edu	37	16	3576475	3576475	+	Missense_Mutation	SNP	A	A	C	rs35603863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3576475A>C	ENST00000576634.1	+	9	1063	c.919A>C	c.(919-921)Aag>Cag	p.K307Q	CLUAP1_ENST00000341633.5_Missense_Mutation_p.K307Q|CLUAP1_ENST00000572600.1_Missense_Mutation_p.K141Q|CLUAP1_ENST00000445795.2_Missense_Mutation_p.K66Q|CLUAP1_ENST00000571025.1_Missense_Mutation_p.K307Q|CLUAP1_ENST00000417763.2_Missense_Mutation_p.K141Q	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	307					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						GCGCCTGCTCAAGAGTGGAAG	0.418													A|||	78	0.0155751	0.056	0.0058	5008	,	,		15679	0.0		0.0	False		,,,				2504	0.0				p.K307Q		Atlas-SNP	.											.	CLUAP1	32	.	0			c.A919C						PASS	.	A	GLN/LYS,GLN/LYS	223,4171	127.0+/-164.0	5,213,1979	53.0	52.0	52.0		919,421	4.3	1.0	16	dbSNP_126	52	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	CLUAP1	NM_015041.1,NM_024793.1	53,53	5,214,6278	CC,CA,AA		0.0116,5.0751,1.7239	benign,benign	307/414,141/248	3576475	224,12770	2197	4300	6497	SO:0001583	missense	23059	exon9			CTGCTCAAGAGTG	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.919A>C	16.37:g.3576475A>C	ENSP00000460850:p.Lys307Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	A	11.85	1.761898	0.31228	0.050751	1.16E-4	ENSG00000103351	ENST00000341633;ENST00000417763;ENST00000445795	T;T;T	0.47869	1.55;0.83;0.84	5.41	4.3	0.51218	.	0.180820	0.64402	D	0.000017	T	0.09905	0.0243	M	0.64997	1.995	0.42629	D	0.993376	P;P;P	0.46706	0.813;0.498;0.883	B;B;B	0.41860	0.368;0.202;0.255	T	0.05683	-1.0870	10	0.14252	T	0.57	-26.918	10.7228	0.46050	0.8398:0.1602:0.0:0.0	rs35603863	141;307;66	Q96AJ1-2;Q96AJ1;B4DFY1	.;CLUA1_HUMAN;.	Q	307;141;66	ENSP00000344392:K307Q;ENSP00000388642:K141Q;ENSP00000397710:K66Q	ENSP00000344392:K307Q	K	+	1	0	CLUAP1	3516476	1.000000	0.71417	0.972000	0.41901	0.260000	0.26232	5.607000	0.67648	0.877000	0.35895	0.523000	0.50628	AAG	A|0.981;C|0.019	0.019	strong		0.418	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
WHSC1L1	54904	hgsc.bcm.edu	37	8	38205133	38205133	+	Missense_Mutation	SNP	G	G	A	rs13034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:38205133G>A	ENST00000317025.8	-	2	1074	c.557C>T	c.(556-558)aCg>aTg	p.T186M	WHSC1L1_ENST00000316985.3_Missense_Mutation_p.T186M|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.T186M|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.T186M	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	186			T -> M (in dbSNP:rs13034).		histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			CTTTGATTTCGTGTGCTCACT	0.373			T	NUP98	AML								G|||	74	0.0147764	0.0552	0.0014	5008	,	,		19666	0.0		0.0	False		,,,				2504	0.0				p.T186M		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.C557T						PASS	.	G	MET/THR,MET/THR	236,4170	139.6+/-175.2	5,226,1972	179.0	163.0	168.0		557,557	3.0	1.0	8	dbSNP_52	168	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	WHSC1L1	NM_017778.2,NM_023034.1	81,81	5,228,6270	AA,AG,GG		0.0233,5.3563,1.8299	benign,benign	186/646,186/1438	38205133	238,12768	2203	4300	6503	SO:0001583	missense	54904	exon2			GATTTCGTGTGCT	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.557C>T	8.37:g.38205133G>A	ENSP00000313983:p.Thr186Met	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	189	86	0.455026	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	37	CCDS43729.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	G	10.27	1.303287	0.23736	0.053563	2.33E-4	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985;ENST00000529223	D;D;D;T;T	0.95238	-3.64;-3.65;-3.65;-0.15;0.87	5.7	2.96	0.34315	.	0.453371	0.17834	U	0.160431	T	0.65719	0.2718	L	0.29908	0.895	0.33540	D	0.594756	B;B;B;B	0.25390	0.125;0.079;0.078;0.06	B;B;B;B	0.18561	0.008;0.009;0.022;0.005	T	0.79662	-0.1710	10	0.66056	D	0.02	.	11.7413	0.51794	0.1932:0.0:0.8068:0.0	rs13034	186;186;186;186	B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95	.;.;.;NSD3_HUMAN	M	186;186;123;186;186;186	ENSP00000393284:T186M;ENSP00000313983:T186M;ENSP00000434730:T186M;ENSP00000313410:T186M;ENSP00000435422:T186M	ENSP00000313410:T186M	T	-	2	0	WHSC1L1	38324290	0.999000	0.42202	0.997000	0.53966	0.896000	0.52359	1.040000	0.30278	0.348000	0.23949	-0.916000	0.02749	ACG	G|0.983;A|0.017	0.017	strong		0.373	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	
RGPD3	653489	hgsc.bcm.edu	37	2	107084716	107084716	+	Missense_Mutation	SNP	C	C	T	rs190902687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:107084716C>T	ENST00000409886.3	-	1	116	c.29G>A	c.(28-30)cGg>cAg	p.R10Q	RGPD3_ENST00000304514.7_Missense_Mutation_p.R10Q	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	10					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						GGCGACGTACCGCTCCCCGTA	0.692													.|||	45	0.00898562	0.0318	0.0043	5008	,	,		11990	0.0		0.0	False		,,,				2504	0.0				p.R10Q		Atlas-SNP	.											.	RGPD3	316	.	0			c.G29A						PASS	.	C	GLN/ARG	26,1358		0,26,666	63.0	92.0	84.0		29	1.8	1.0	2		84	0,3182		0,0,1591	no	missense	RGPD3	NM_001144013.1	43	0,26,2257	TT,TC,CC		0.0,1.8786,0.5694	probably-damaging	10/1759	107084716	26,4540	692	1591	2283	SO:0001583	missense	653489	exon1			ACGTACCGCTCCC		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.29G>A	2.37:g.107084716C>T	ENSP00000386588:p.Arg10Gln	Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	437	193	0.441648	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	.	12.78	2.039118	0.35989	0.018786	0.0	ENSG00000153165	ENST00000409886;ENST00000304514	T;T	0.53857	0.6;0.6	1.8	1.8	0.24995	.	.	.	.	.	T	0.27313	0.0670	L	0.54323	1.7	0.23685	N	0.997116	D	0.58620	0.983	P	0.49192	0.602	T	0.18429	-1.0337	9	0.59425	D	0.04	-11.0149	7.0248	0.24934	0.0:1.0:0.0:0.0	.	10	A6NKT7	RGPD3_HUMAN	Q	10	ENSP00000386588:R10Q;ENSP00000303659:R10Q	ENSP00000303659:R10Q	R	-	2	0	RGPD3	106451148	1.000000	0.71417	0.989000	0.46669	0.038000	0.13279	3.375000	0.52410	0.984000	0.38629	0.186000	0.17326	CGG	C|0.992;T|0.008	0.008	strong		0.692	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
ITGAD	3681	hgsc.bcm.edu	37	16	31422531	31422531	+	Silent	SNP	T	T	C	rs368058587		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31422531T>C	ENST00000389202.2	+	13	1540	c.1491T>C	c.(1489-1491)ccT>ccC	p.P497P		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	497					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GTCCCTTGCCTAGGGGGGTGA	0.627													t|||	1	0.000199681	0.0008	0.0	5008	,	,		15986	0.0		0.0	False		,,,				2504	0.0				p.P497P		Atlas-SNP	.											.	ITGAD	154	.	0			c.T1491C						PASS	.	T		2,4392	4.2+/-10.8	0,2,2195	82.0	79.0	80.0		1491	0.8	0.1	16		80	0,8600		0,0,4300	no	coding-synonymous	ITGAD	NM_005353.2		0,2,6495	CC,CT,TT		0.0,0.0455,0.0154		497/1162	31422531	2,12992	2197	4300	6497	SO:0001819	synonymous_variant	3681	exon13			CTTGCCTAGGGGG	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.1491T>C	16.37:g.31422531T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	229	104	0.454148	NM_005353	Q15575|Q15576	Silent	SNP	ENST00000389202.2	37	CCDS32438.1																																																																																			.	.	weak		0.627	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
SSPO	23145	hgsc.bcm.edu	37	7	149522163	149522163	+	RNA	SNP	C	C	G	rs73727642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149522163C>G	ENST00000378016.2	+	0	13950							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)			GAGGAGGCTGCCGGGAGCCAT	0.652													C|||	192	0.0383387	0.1354	0.0187	5008	,	,		15887	0.0		0.0	False		,,,				2504	0.0				p.C4650W		Atlas-SNP	.											.	.	.	.	0			c.C13950G						PASS	.	C		374,3424		21,332,1546	19.0	25.0	23.0		13964	3.5	0.4	7	dbSNP_130	23	7,8195		0,7,4094	yes	coding-notMod3	SSPO	NM_198455.2		21,339,5640	GG,GC,CC		0.0853,9.8473,3.175			149522163	381,11619	1899	4101	6000			23145	exon96			AGGCTGCCGGGAG	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.149522163C>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	23	0.348485	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.974;G|0.026	0.026	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
JPH2	57158	hgsc.bcm.edu	37	20	42744587	42744587	+	Silent	SNP	G	G	C	rs74352869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42744587G>C	ENST00000372980.3	-	4	2600	c.1728C>G	c.(1726-1728)ccC>ccG	p.P576P		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	576	Pro-rich.				calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			GTGGGGGCTCGGGCGGCGTGG	0.746													G|||	766	0.152955	0.2345	0.1254	5008	,	,		10507	0.0804		0.2247	False		,,,				2504	0.0634				p.P576P		Atlas-SNP	.											JPH2,NS,carcinoma,0,1	JPH2	86	1	0			c.C1728G						PASS	.	G		672,2910		75,522,1194	4.0	5.0	5.0		1728	1.3	0.9	20	dbSNP_131	5	1430,6150		154,1122,2514	no	coding-synonymous	JPH2	NM_020433.4		229,1644,3708	CC,CG,GG		18.8654,18.7605,18.8318		576/697	42744587	2102,9060	1791	3790	5581	SO:0001819	synonymous_variant	57158	exon4			GGGCTCGGGCGGC	AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.1728C>G	20.37:g.42744587G>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_020433	E1P5X1|O95913|Q5JY74|Q9UJN4	Silent	SNP	ENST00000372980.3	37	CCDS13325.1																																																																																			G|0.824;C|0.176	0.176	strong		0.746	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1		
SYCE1	93426	hgsc.bcm.edu	37	10	135370639	135370639	+	Missense_Mutation	SNP	C	C	A	rs8181357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135370639C>A	ENST00000343131.5	-	7	500	c.396G>T	c.(394-396)gaG>gaT	p.E132D	SYCE1_ENST00000432597.2_Missense_Mutation_p.E96D|SYCE1_ENST00000368517.3_Missense_Mutation_p.E96D|SPRN_ENST00000541506.1_Intron	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	132			E -> D (in dbSNP:rs8181357). {ECO:0000269|PubMed:15489334}.		synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.E96D(1)|p.E132D(1)		breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TCTCCTTGCACTCCTGCAACA	0.552													C|||	775	0.154752	0.0454	0.1715	5008	,	,		21943	0.2698		0.1093	False		,,,				2504	0.2188				p.E132D		Atlas-SNP	.											SYCE1_ENST00000343131,NS,carcinoma,0,2	SYCE1	81	2	2	Substitution - Missense(2)	stomach(2)	c.G396T						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	274,4132	151.4+/-185.3	6,262,1935	253.0	239.0	244.0		396,396,288	0.2	0.9	10	dbSNP_117	244	822,7778	189.1+/-236.0	45,732,3523	yes	missense,missense,missense	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	45,45,45	51,994,5458	AA,AC,CC		9.5581,6.2188,8.4269	probably-damaging,probably-damaging,probably-damaging	132/319,132/352,96/283	135370639	1096,11910	2203	4300	6503	SO:0001583	missense	93426	exon7			CTTGCACTCCTGC	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.396G>T	10.37:g.135370639C>A	ENSP00000341282:p.Glu132Asp	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	37	CCDS44501.1	329	0.15064102564102563	24	0.04878048780487805	62	0.1712707182320442	153	0.2674825174825175	90	0.11873350923482849	C	12.63	1.996834	0.35226	0.062188	0.095581	ENSG00000171772	ENST00000303903;ENST00000432597;ENST00000368517;ENST00000343131	T;T;T;T	0.32272	1.46;3.12;3.12;3.12	4.3	0.217	0.15264	.	0.389128	0.24176	N	0.040858	T	0.00012	0.0000	L	0.44542	1.39	0.42354	P	0.00761400000000001	B;B;B	0.15930	0.015;0.015;0.015	B;B;B	0.19946	0.016;0.027;0.016	T	0.30822	-0.9965	9	0.38643	T	0.18	-1.8451	5.4635	0.16630	0.0:0.5252:0.306:0.1688	rs8181357;rs11537981;rs17857024;rs52803233;rs8181357	4;132;96	Q8N0S2-3;Q8N0S2;Q8N0S2-2	.;SYCE1_HUMAN;.	D	132;96;96;132	ENSP00000303978:E132D;ENSP00000411779:E96D;ENSP00000357503:E96D;ENSP00000341282:E132D	ENSP00000303978:E132D	E	-	3	2	SYCE1	135220629	0.154000	0.22792	0.912000	0.35992	0.873000	0.50193	-0.666000	0.05280	0.050000	0.15949	0.655000	0.94253	GAG	C|0.892;A|0.108	0.108	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
CEP162	22832	hgsc.bcm.edu	37	6	84925636	84925636	+	Silent	SNP	A	A	C	rs9449840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84925636A>C	ENST00000403245.3	-	4	291	c.177T>G	c.(175-177)ctT>ctG	p.L59L	KIAA1009_ENST00000257766.4_5'UTR	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TTGTTCCAAGAAGTCCTAGGT	0.328													C|||	366	0.0730831	0.2602	0.0245	5008	,	,		16242	0.002		0.001	False		,,,				2504	0.002				p.L59L		Atlas-SNP	.											.	KIAA1009	119	.	0			c.T177G						PASS	.	C		1020,3368		119,782,1293	37.0	36.0	36.0		177	-3.0	0.0	6	dbSNP_119	36	6,8568		0,6,4281	no	coding-synonymous	KIAA1009	NM_014895.2		119,788,5574	CC,CA,AA		0.07,23.2452,7.9154		59/1404	84925636	1026,11936	2194	4287	6481	SO:0001819	synonymous_variant	22832	exon4			TCCAAGAAGTCCT																												ENST00000403245.3:c.177T>G	6.37:g.84925636A>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_014895		Silent	SNP	ENST00000403245.3	37	CCDS34494.2																																																																																			A|0.936;C|0.064	0.064	strong		0.328	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
SIPA1	6494	hgsc.bcm.edu	37	11	65418048	65418048	+	Silent	SNP	G	G	A	rs76089059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65418048G>A	ENST00000394224.3	+	16	3287	c.2991G>A	c.(2989-2991)gcG>gcA	p.A997A	MIR4489_ENST00000578869.1_RNA|SIPA1_ENST00000534313.1_Silent_p.A997A|SIPA1_ENST00000394227.3_Silent_p.A895A|SIPA1_ENST00000527525.1_Silent_p.A895A	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	997					cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582)			cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	10						AGGAGAAGGCGGACAGGGCGG	0.692													G|||	134	0.0267572	0.0968	0.0058	5008	,	,		14580	0.0		0.002	False		,,,				2504	0.0				p.A997A		Atlas-SNP	.											SIPA1,colon,carcinoma,+1,1	SIPA1	45	1	0			c.G2991A						PASS	.	G	,	448,3942		20,408,1767	24.0	29.0	27.0		2991,2991	-7.9	0.9	11	dbSNP_131	27	7,8561		0,7,4277	no	coding-synonymous,coding-synonymous	SIPA1	NM_006747.3,NM_153253.29	,	20,415,6044	AA,AG,GG		0.0817,10.205,3.5113	,	997/1043,997/1043	65418048	455,12503	2195	4284	6479	SO:0001819	synonymous_variant	6494	exon16			GAAGGCGGACAGG	AH006363, BC010492, BM677738	CCDS8108.1	11q13.3	2008-09-12	2008-09-12		ENSG00000213445	ENSG00000213445			10885	protein-coding gene	gene with protein product		602180				9027487	Standard	NM_006747		Approved	SPA1	uc001ofb.2	Q96FS4	OTTHUMG00000166541	ENST00000394224.3:c.2991G>A	11.37:g.65418048G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	241	105	0.435685	NM_006747	O14518|O60484|O60618|Q2YD83	Silent	SNP	ENST00000394224.3	37	CCDS8108.1																																																																																			G|0.964;A|0.036	0.036	strong		0.692	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747	
SLC24A4	123041	hgsc.bcm.edu	37	14	92922900	92922900	+	Silent	SNP	G	G	A	rs77671856	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000556739.1_3'UTR|SLC24A4_ENST00000393265.2_Silent_p.P337P|SLC24A4_ENST00000531433.1_Silent_p.P382P			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						scavenged	.	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	69	1	0.0144928	1293	WXS	Illumina HiSeq	Phase_I	70	34	0.485714	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	
MUC17	140453	hgsc.bcm.edu	37	7	100678372	100678372	+	Silent	SNP	T	T	G	rs11769823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678372T>G	ENST00000306151.4	+	3	3739	c.3675T>G	c.(3673-3675)ccT>ccG	p.P1225P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1225	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)					CAAGTATGCCTGTCAGACACA	0.517																																					p.P1225P		Atlas-SNP	.											.	MUC17	804	.	0			c.T3675G						PASS	.	T		615,3791		0,615,1588	312.0	292.0	299.0		3675	-1.5	0.0	7	dbSNP_120	299	777,7823		0,777,3523	no	coding-synonymous	MUC17	NM_001040105.1		0,1392,5111	GG,GT,TT		9.0349,13.9582,10.7028		1225/4494	100678372	1392,11614	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TATGCCTGTCAGA	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.3675T>G	7.37:g.100678372T>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	186	39	0.209677	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.914;G|0.086	0.086	strong		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CSMD1	64478	hgsc.bcm.edu	37	8	2820043	2820043	+	Silent	SNP	G	G	T	rs4876056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2820043G>T	ENST00000520002.1	-	62	10131	c.9576C>A	c.(9574-9576)tcC>tcA	p.S3192S	CSMD1_ENST00000542608.1_Silent_p.S3014S|CSMD1_ENST00000602557.1_Silent_p.S3192S|CSMD1_ENST00000602723.1_Silent_p.S3015S|CSMD1_ENST00000537824.1_Silent_p.S3191S|CSMD1_ENST00000400186.3_Silent_p.S3015S			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3192	Sushi 26. {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)		AGACTCTTCTGGAGGATCCCA	0.498													T|||	638	0.127396	0.3336	0.0836	5008	,	,		16851	0.1081		0.0229	False		,,,				2504	0.0072				p.S3191S		Atlas-SNP	.											CSMD1_ENST00000318252,NS,carcinoma,-1,1	CSMD1	1469	1	0			c.C9573A						PASS	.	T		1080,2772		146,788,992	65.0	64.0	64.0		9573	-11.2	0.0	8	dbSNP_111	64	236,8022		1,234,3894	no	coding-synonymous	CSMD1	NM_033225.5		147,1022,4886	TT,TG,GG		2.8578,28.0374,10.8671		3191/3565	2820043	1316,10794	1926	4129	6055	SO:0001819	synonymous_variant	64478	exon61			TCTTCTGGAGGAT			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.9576C>A	8.37:g.2820043G>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	86	49	0.569767	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		266	0.12179487179487179	169	0.3434959349593496	24	0.06629834254143646	60	0.1048951048951049	13	0.017150395778364115	T	0.437	-0.900256	0.02472	0.280374	0.028578	ENSG00000183117	ENST00000335551	.	.	.	5.6	-11.2	0.00127	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22903	P	0.99858238	.	.	.	.	.	.	T	0.24584	-1.0156	3	.	.	.	.	11.6209	0.51117	0.0:0.2273:0.1926:0.5801	rs4876056;rs4876056	.	.	.	K	2609	.	.	Q	-	1	0	CSMD1	2807450	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-2.681000	0.00837	-4.931000	0.00027	-0.256000	0.11100	CAG	G|0.871;T|0.129	0.129	strong		0.498	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
C2orf43	60526	hgsc.bcm.edu	37	2	21001192	21001192	+	Missense_Mutation	SNP	A	A	G	rs139472393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:21001192A>G	ENST00000237822.3	-	2	111	c.32T>C	c.(31-33)gTg>gCg	p.V11A	C2orf43_ENST00000403006.2_Intron|C2orf43_ENST00000541941.1_Intron|C2orf43_ENST00000419825.2_Missense_Mutation_p.V11A|C2orf43_ENST00000440866.2_Missense_Mutation_p.V11A|C2orf43_ENST00000381090.3_Missense_Mutation_p.V11A|C2orf43_ENST00000435420.2_Missense_Mutation_p.V11A	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	11										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCCTCATGCACAGGAATTTC	0.408													A|||	7	0.00139776	0.0053	0.0	5008	,	,		17655	0.0		0.0	False		,,,				2504	0.0				p.V11A		Atlas-SNP	.											.	C2orf43	28	.	0			c.T32C						PASS	.	A	ALA/VAL	21,4385	29.0+/-57.7	0,21,2182	82.0	84.0	84.0		32	5.9	1.0	2	dbSNP_134	84	0,8600		0,0,4300	yes	missense	C2orf43	NM_021925.2	64	0,21,6482	GG,GA,AA		0.0,0.4766,0.1615	possibly-damaging	11/326	21001192	21,12985	2203	4300	6503	SO:0001583	missense	60526	exon2			TCATGCACAGGAA	AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961			26145	protein-coding gene	gene with protein product		613570				17135363, 24357060	Standard	NM_001282723		Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000237822.3:c.32T>C	2.37:g.21001192A>G	ENSP00000237822:p.Val11Ala	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	91	34	0.373626	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Missense_Mutation	SNP	ENST00000237822.3	37	CCDS1702.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	16.00	2.998870	0.54147	0.004766	0.0	ENSG00000118961	ENST00000381090;ENST00000237822;ENST00000435420;ENST00000440866;ENST00000412261;ENST00000402479;ENST00000419825	.	.	.	5.94	5.94	0.96194	.	0.514514	0.19627	N	0.109780	T	0.50497	0.1619	L	0.44542	1.39	0.32473	N	0.54249	B;P;P;D;P;P	0.60575	0.349;0.852;0.952;0.988;0.852;0.852	B;B;P;P;B;B	0.49085	0.091;0.177;0.452;0.6;0.177;0.177	T	0.63567	-0.6608	9	0.62326	D	0.03	-8.1279	15.3805	0.74651	1.0:0.0:0.0:0.0	.	11;11;11;11;11;11	B4DS38;B4DRG3;B7ZAJ5;B4DWE2;Q9H6V9;B5MDU6	.;.;.;.;CB043_HUMAN;.	A	11	.	ENSP00000237822:V11A	V	-	2	0	C2orf43	20864673	0.996000	0.38824	0.992000	0.48379	0.114000	0.19823	5.670000	0.68088	2.279000	0.76181	0.459000	0.35465	GTG	A|0.999;G|0.001	0.001	strong		0.408	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925	
GPR85	54329	hgsc.bcm.edu	37	7	112724147	112724147	+	Silent	SNP	G	G	A	rs28392728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:112724147G>A	ENST00000297146.3	-	3	1233	c.630C>T	c.(628-630)caC>caT	p.H210H	GPR85_ENST00000449591.1_Silent_p.H210H|GPR85_ENST00000501255.2_Silent_p.H210H|GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000424100.1_Silent_p.H210H	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	210					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						TTCTTCGATCGTGGACGAAAA	0.498													G|||	97	0.019369	0.0703	0.0058	5008	,	,		19678	0.0		0.0	False		,,,				2504	0.0				p.H210H		Atlas-SNP	.											.	GPR85	49	.	0			c.C630T						PASS	.	G	,,,	296,4110	162.2+/-194.2	11,274,1918	56.0	55.0	55.0		630,630,630,630	-1.6	0.9	7	dbSNP_125	55	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPR85	NM_001146265.1,NM_001146266.1,NM_001146267.1,NM_018970.6	,,,	11,277,6215	AA,AG,GG		0.0349,6.7181,2.2989	,,,	210/371,210/371,210/371,210/371	112724147	299,12707	2203	4300	6503	SO:0001819	synonymous_variant	54329	exon3			TCGATCGTGGACG	AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604		"""GPCR / Class A : Orphans"""	4536	protein-coding gene	gene with protein product		605188				10978537, 10833454	Standard	NM_018970		Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.630C>T	7.37:g.112724147G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	94	39	0.414894	NM_001146265	Q9JHI6|Q9NPD1	Silent	SNP	ENST00000297146.3	37	CCDS5758.1																																																																																			G|0.978;A|0.022	0.022	strong		0.498	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2		
SLC39A4	55630	hgsc.bcm.edu	37	8	145639681	145639681	+	Missense_Mutation	SNP	G	G	C	rs1871534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145639681G>C	ENST00000301305.3	-	6	1219	c.1114C>G	c.(1114-1116)Ctc>Gtc	p.L372V	SLC39A4_ENST00000276833.5_Missense_Mutation_p.L347V|SLC39A4_ENST00000531013.1_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	372			L -> P (in AEZ). {ECO:0000269|PubMed:12032886}.|L -> V (in dbSNP:rs1871534).		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)			TCCCCAGTGAGTGCACCCACT	0.667													G|||	1268	0.253195	0.9145	0.0735	5008	,	,		15930	0.0		0.007	False		,,,				2504	0.001				p.L372V		Atlas-SNP	.											.	SLC39A4	54	.	0			c.C1114G						PASS	.	G	VAL/LEU,VAL/LEU	3399,989		1341,717,136	55.0	50.0	51.0		1039,1114	4.1	0.2	8	dbSNP_92	51	53,8541		0,53,4244	yes	missense,missense	SLC39A4	NM_017767.2,NM_130849.2	32,32	1341,770,4380	CC,CG,GG		0.6167,22.5387,26.5907	probably-damaging,probably-damaging	347/623,372/648	145639681	3452,9530	2194	4297	6491	SO:0001583	missense	55630	exon6			CAGTGAGTGCACC	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.1114C>G	8.37:g.145639681G>C	ENSP00000301305:p.Leu372Val	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	315	136	0.431746	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	467	0.21382783882783882	436	0.8861788617886179	29	0.08011049723756906	0	0.0	2	0.002638522427440633	G	17.34	3.364066	0.61513	0.774613	0.006167	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.61510	0.1;0.1	5.03	4.12	0.48240	.	0.164767	0.38720	N	0.001590	T	0.00012	0.0000	M	0.91612	3.225	0.22446	P	0.999095413	D;D	0.89917	0.991;1.0	P;D	0.85130	0.883;0.997	T	0.15492	-1.0435	9	0.87932	D	0	-23.7231	12.8953	0.58095	0.0:0.1654:0.8346:0.0	rs1871534;rs2928379;rs1871534	372;347	Q6P5W5;A6NDY5	S39A4_HUMAN;.	V	347;372	ENSP00000276833:L347V;ENSP00000301305:L372V	ENSP00000276833:L347V	L	-	1	0	SLC39A4	145610489	1.000000	0.71417	0.172000	0.22920	0.396000	0.30629	6.389000	0.73199	1.087000	0.41251	0.573000	0.79308	CTC	G|0.744;C|0.256	0.256	strong		0.667	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
ZNF567	163081	hgsc.bcm.edu	37	19	37210529	37210529	+	Silent	SNP	A	A	G	rs3108200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37210529A>G	ENST00000536254.2	+	6	1125	c.903A>G	c.(901-903)agA>agG	p.R301R	ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000392163.2_Silent_p.R270R|ZNF567_ENST00000585696.1_Silent_p.R270R|ZNF567_ENST00000360729.4_Silent_p.R270R|ZNF567_ENST00000588311.1_Silent_p.R270R			Q8N184	ZN567_HUMAN	zinc finger protein 567	301					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)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATCATCAGAGAACTCACACAG	0.423													A|||	1345	0.26857	0.3654	0.2032	5008	,	,		20404	0.2113		0.2942	False		,,,				2504	0.2168				p.R270R		Atlas-SNP	.											.	ZNF567	61	.	0			c.A810G						PASS	.	A		1515,2891	478.1+/-358.1	242,1031,930	50.0	52.0	52.0		810	1.5	1.0	19	dbSNP_103	52	2553,6047	414.9+/-351.6	383,1787,2130	no	coding-synonymous	ZNF567	NM_152603.2		625,2818,3060	GG,GA,AA		29.686,34.3849,31.2779		270/617	37210529	4068,8938	2203	4300	6503	SO:0001819	synonymous_variant	163081	exon4			TCAGAGAACTCAC	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"""Zinc fingers, C2H2-type"", ""-"""	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.903A>G	19.37:g.37210529A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	184	184	1	NM_152603	B3KX49|Q6N044	Silent	SNP	ENST00000536254.2	37																																																																																				A|0.701;G|0.299	0.299	strong		0.423	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603	
HAS1	3036	hgsc.bcm.edu	37	19	52223026	52223026	+	Silent	SNP	C	C	A	rs61736497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52223026C>A	ENST00000222115.1	-	2	169	c.135G>T	c.(133-135)ccG>ccT	p.P45P	HAS1_ENST00000594621.1_5'Flank|HAS1_ENST00000601714.1_Silent_p.P52P|HAS1_ENST00000540069.2_Silent_p.P44P	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	45					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		CGGAGGCCAGCGGCACCCCGG	0.711													c|||	271	0.0541134	0.1891	0.0202	5008	,	,		12432	0.0		0.003	False		,,,				2504	0.0041				p.P45P	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.G135T						PASS	.	C		634,3594		36,562,1516	5.0	7.0	6.0		135	-6.3	1.0	19	dbSNP_129	6	8,8282		0,8,4137	no	coding-synonymous	HAS1	NM_001523.2		36,570,5653	AA,AC,CC		0.0965,14.9953,5.1286		45/579	52223026	642,11876	2114	4145	6259	SO:0001819	synonymous_variant	3036	exon2			GGCCAGCGGCACC	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.135G>T	19.37:g.52223026C>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	27	16	0.592593	NM_001523	Q14470|Q9NS49	Silent	SNP	ENST00000222115.1	37	CCDS12838.1																																																																																			C|0.947;A|0.053	0.053	strong		0.711	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
UBE4B	10277	hgsc.bcm.edu	37	1	10211588	10211588	+	Silent	SNP	G	G	A	rs149899336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:10211588G>A	ENST00000253251.8	+	20	3347	c.2508G>A	c.(2506-2508)ttG>ttA	p.L836L	UBE4B_ENST00000377157.3_Silent_p.L720L|UBE4B_ENST00000343090.6_Silent_p.L965L					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-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;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CCACCAAGTTGTTGGTACCTT	0.453													G|||	3	0.000599042	0.0023	0.0	5008	,	,		22768	0.0		0.0	False		,,,				2504	0.0				p.L965L		Atlas-SNP	.											.	UBE4B	233	.	0			c.G2895A						PASS	.	G	,	15,4391	22.3+/-47.3	0,15,2188	166.0	152.0	157.0		2895,2508	4.2	0.9	1	dbSNP_134	157	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	UBE4B	NM_001105562.2,NM_006048.4	,	0,15,6488	AA,AG,GG		0.0,0.3404,0.1153	,	965/1303,836/1174	10211588	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	10277	exon21			CAAGTTGTTGGTA	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2508G>A	1.37:g.10211588G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	179	86	0.480447	NM_001105562		Silent	SNP	ENST00000253251.8	37	CCDS110.1																																																																																			G|0.999;A|0.001	0.001	strong		0.453	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048	
FNDC3A	22862	hgsc.bcm.edu	37	13	49775997	49775997	+	Missense_Mutation	SNP	A	A	G	rs45604939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:49775997A>G	ENST00000492622.2	+	24	3354	c.3049A>G	c.(3049-3051)Aca>Gca	p.T1017A	FNDC3A_ENST00000398316.3_Missense_Mutation_p.T961A|FNDC3A_ENST00000541916.1_Missense_Mutation_p.T1017A	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1017	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)		TAATGAGTCAACATCCTATAA	0.368													A|||	127	0.0253594	0.0008	0.0476	5008	,	,		15155	0.0		0.0676	False		,,,				2504	0.0256				p.T1017A		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3049G						PASS	.	A	ALA/THR,ALA/THR	52,4354	50.9+/-86.3	0,52,2151	94.0	95.0	94.0		3049,2881	3.7	1.0	13	dbSNP_127	94	602,7996	158.2+/-211.7	19,564,3716	yes	missense,missense	FNDC3A	NM_001079673.1,NM_014923.3	58,58	19,616,5867	GG,GA,AA		7.0016,1.1802,5.0292	possibly-damaging,possibly-damaging	1017/1199,961/1143	49775997	654,12350	2203	4299	6502	SO:0001583	missense	22862	exon24			GAGTCAACATCCT	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.3049A>G	13.37:g.49775997A>G	ENSP00000417257:p.Thr1017Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	149	77	0.516779	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	CCDS41886.1	68	0.031135531135531136	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	49	0.06464379947229551	A	22.8	4.334633	0.81801	0.011802	0.070016	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.61627	0.09;0.09;0.09	6.16	3.66	0.41972	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.079122	0.52532	D	0.000074	T	0.21509	0.0518	M	0.87547	2.89	0.80722	D	1	D;P	0.64830	0.994;0.597	D;P	0.68765	0.96;0.531	T	0.54794	-0.8240	10	0.48119	T	0.1	-24.27	9.0647	0.36455	0.7455:0.1304:0.0:0.1241	rs45604939	961;1017	Q9Y2H6-2;Q9Y2H6	.;FND3A_HUMAN	A	1017;953;1017;961	ENSP00000417257:T1017A;ENSP00000441831:T1017A;ENSP00000381362:T961A	ENSP00000338579:T953A	T	+	1	0	FNDC3A	48673998	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.904000	0.92590	0.515000	0.28320	0.528000	0.53228	ACA	A|0.954;G|0.046	0.046	strong		0.368	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923	
WFS1	7466	hgsc.bcm.edu	37	4	6302707	6302707	+	Silent	SNP	C	C	T	rs1801206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6302707C>T	ENST00000226760.1	+	8	1355	c.1185C>T	c.(1183-1185)gtC>gtT	p.V395V	WFS1_ENST00000503569.1_Silent_p.V395V	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	395					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)		AGGCCGAGGTCAACTTCGGCT	0.597													c|||	3213	0.641573	0.4455	0.6715	5008	,	,		22107	0.9038		0.6213	False		,,,				2504	0.636				p.V395V		Atlas-SNP	.											.	WFS1	71	.	0			c.C1185T	GRCh37	CM021362	WFS1	M	rs1801206	PASS	.		,	2048,2358	566.4+/-381.9	457,1134,612	194.0	188.0	190.0		1185,1185	-5.0	0.9	4	dbSNP_89	190	5145,3455	635.8+/-399.0	1524,2097,679	no	coding-synonymous,coding-synonymous	WFS1	NM_001145853.1,NM_006005.3	,	1981,3231,1291	TT,TC,CC		40.1744,46.4821,44.6948	,	395/891,395/891	6302707	7193,5813	2203	4300	6503	SO:0001819	synonymous_variant	7466	exon8			CGAGGTCAACTTC	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.1185C>T	4.37:g.6302707C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	207	207	1	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	37	CCDS3386.1																																																																																			C|0.405;T|0.595	0.595	strong		0.597	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
PPL	5493	hgsc.bcm.edu	37	16	4935258	4935258	+	Missense_Mutation	SNP	A	A	T	rs145318499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4935258A>T	ENST00000345988.2	-	22	3487	c.3398T>A	c.(3397-3399)cTc>cAc	p.L1133H	PPL_ENST00000590782.2_Missense_Mutation_p.L1131H	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1133					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						TTGGCGGGTGAGATCGCTGAC	0.627													A|||	13	0.00259585	0.0091	0.0014	5008	,	,		12714	0.0		0.0	False		,,,				2504	0.0				p.L1133H		Atlas-SNP	.											.	PPL	168	.	0			c.T3398A						PASS	.						79.0	71.0	74.0					16																	4935258		2197	4300	6497	SO:0001583	missense	5493	exon22			CGGGTGAGATCGC	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3398T>A	16.37:g.4935258A>T	ENSP00000340510:p.Leu1133His	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	149	54	0.362416	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	.	.	.	.	.	.	.	.	.	.	A	15.98	2.992856	0.54041	.	.	ENSG00000118898	ENST00000345988	T	0.43688	0.94	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000001	T	0.66626	0.2808	M	0.80746	2.51	0.49130	D	0.99975	D	0.89917	1.0	D	0.91635	0.999	T	0.72327	-0.4327	10	0.87932	D	0	.	15.0069	0.71519	1.0:0.0:0.0:0.0	.	1133	O60437	PEPL_HUMAN	H	1133	ENSP00000340510:L1133H	ENSP00000340510:L1133H	L	-	2	0	PPL	4875259	1.000000	0.71417	0.064000	0.19789	0.868000	0.49771	9.292000	0.96076	1.967000	0.57214	0.459000	0.35465	CTC	.	.	weak		0.627	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
CIZ1	25792	hgsc.bcm.edu	37	9	130938650	130938650	+	Silent	SNP	G	G	A	rs45475893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130938650G>A	ENST00000393608.1	-	11	2125	c.1923C>T	c.(1921-1923)gaC>gaT	p.D641D	CIZ1_ENST00000538431.1_Silent_p.D641D|CIZ1_ENST00000325721.8_Silent_p.D612D|CIZ1_ENST00000372948.3_Silent_p.D585D|CIZ1_ENST00000372954.1_Silent_p.D561D|CIZ1_ENST00000541172.1_Silent_p.D540D|CIZ1_ENST00000277465.4_Silent_p.D613D|CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000372938.5_Silent_p.D641D|CIZ1_ENST00000357558.5_Silent_p.D613D	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	641					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						TCTCCAGGACGTCCCGGGGCA	0.637													G|||	22	0.00439297	0.0151	0.0029	5008	,	,		19335	0.0		0.0	False		,,,				2504	0.0				p.D671D		Atlas-SNP	.											.	CIZ1	75	.	0			c.C2013T						PASS	.	G	,,,,	75,4331	67.0+/-104.6	0,75,2128	98.0	103.0	101.0		1755,1923,1740,1683,1923	-8.3	0.0	9	dbSNP_127	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	,,,,	0,76,6427	AA,AG,GG		0.0116,1.7022,0.5843	,,,,	585/843,641/899,580/838,561/819,641/899	130938650	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	25792	exon11			CAGGACGTCCCGG	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.1923C>T	9.37:g.130938650G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	119	86	0.722689	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	37	CCDS6894.1																																																																																			G|0.994;A|0.006	0.006	strong		0.637	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127	
OR51S1	119692	hgsc.bcm.edu	37	11	4869792	4869792	+	Missense_Mutation	SNP	A	A	G	rs57238061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4869792A>G	ENST00000322101.2	-	1	722	c.647T>C	c.(646-648)tTg>tCg	p.L216S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	216						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGGGGGTCCAAACCCATGGC	0.527													A|||	307	0.0613019	0.2209	0.0202	5008	,	,		18029	0.0		0.001	False		,,,				2504	0.0				p.L216S		Atlas-SNP	.											.	OR51S1	83	.	0			c.T647C						PASS	.	A	SER/LEU	791,3611	318.8+/-295.8	72,647,1482	78.0	82.0	80.0		647	4.1	1.0	11	dbSNP_129	80	11,8585	8.4+/-32.0	0,11,4287	yes	missense	OR51S1	NM_001004758.1	145	72,658,5769	GG,GA,AA		0.128,17.9691,6.1702	probably-damaging	216/324	4869792	802,12196	2201	4298	6499	SO:0001583	missense	119692	exon1			GGGTCCAAACCCA	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"""GPCR / Class A : Olfactory receptors"""	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.647T>C	11.37:g.4869792A>G	ENSP00000322754:p.Leu216Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	113	0.051739926739926737	105	0.21341463414634146	8	0.022099447513812154	0	0.0	0	0.0	A	16.28	3.079144	0.55753	0.179691	0.00128	ENSG00000176922	ENST00000322101	T	0.44482	0.92	5.25	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36002	N	0.002844	T	0.00039	0.0001	L	0.43923	1.385	0.54753	P	1.799999999996249E-5	P	0.39535	0.677	B	0.39419	0.299	T	0.11567	-1.0582	9	0.51188	T	0.08	-6.8936	10.3194	0.43756	0.9202:0.0:0.0798:0.0	rs57238061;rs61746907	216	Q8NGJ8	O51S1_HUMAN	S	216	ENSP00000322754:L216S	ENSP00000322754:L216S	L	-	2	0	OR51S1	4826368	0.007000	0.16637	0.966000	0.40874	0.681000	0.39784	2.118000	0.41949	2.203000	0.70933	0.533000	0.62120	TTG	A|0.944;G|0.056	0.056	strong		0.527	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
OR8U1	219417	hgsc.bcm.edu	37	11	56143113	56143113	+	Missense_Mutation	SNP	A	A	G	rs116344671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56143113A>G	ENST00000302270.1	+	1	14	c.14A>G	c.(13-15)aAt>aGt	p.N5S		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	5						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)					GCTCACATCAATTGCACCCAG	0.403													A|||	234	0.0467252	0.1649	0.0216	5008	,	,		15937	0.0		0.001	False		,,,				2504	0.0				p.N5S		Atlas-SNP	.											.	OR8U1	59	.	0			c.A14G						PASS	.	A	SER/ASN	496,3212		36,424,1394	93.0	85.0	88.0		14	5.9	0.4	11	dbSNP_132	88	8,8180		0,8,4086	yes	missense	OR8U1	NM_001005204.1	46	36,432,5480	GG,GA,AA		0.0977,13.3765,4.2367	probably-damaging	5/310	56143113	504,11392	1854	4094	5948	SO:0001583	missense	219417	exon1			ACATCAATTGCAC	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.14A>G	11.37:g.56143113A>G	ENSP00000304188:p.Asn5Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	197	99	0.502538	NM_001005204		Missense_Mutation	SNP	ENST00000302270.1	37	CCDS41647.1	89	0.04075091575091575	79	0.16056910569105692	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	A	8.024	0.760291	0.15914	0.133765	9.77E-4	ENSG00000172199	ENST00000302270	T	0.14640	2.49	5.87	5.87	0.94306	.	0.000000	0.51477	D	0.000094	T	0.00109	0.0003	M	0.87269	2.87	0.50632	P	1.1200000000000099E-4	B	0.32051	0.354	B	0.35114	0.196	T	0.11792	-1.0573	9	0.87932	D	0	.	8.66	0.34086	0.8549:0.0:0.1451:0.0	.	5	Q8NH10	OR8U1_HUMAN	S	5	ENSP00000304188:N5S	ENSP00000304188:N5S	N	+	2	0	OR8U1	55899689	0.994000	0.37717	0.396000	0.26296	0.042000	0.13812	3.480000	0.53172	2.247000	0.74100	0.523000	0.50628	AAT	A|0.974;G|0.026	0.026	strong		0.403	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
VPS13C	54832	hgsc.bcm.edu	37	15	62259637	62259637	+	Missense_Mutation	SNP	C	C	T	rs3784634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:62259637C>T	ENST00000261517.5	-	29	2994	c.2921G>A	c.(2920-2922)aGg>aAg	p.R974K	VPS13C_ENST00000395898.3_Missense_Mutation_p.R931K|VPS13C_ENST00000395896.4_Missense_Mutation_p.R974K|VPS13C_ENST00000249837.3_Missense_Mutation_p.R931K	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	136	0	0		WXS	Illumina HiSeq	Phase_I	120	120	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	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808526	18808526	+	Missense_Mutation	SNP	A	A	C	rs2992752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:18808526A>C	ENST00000400664.1	+	1	1103	c.1051A>C	c.(1051-1053)Aca>Cca	p.T351P		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	351			T -> P (in dbSNP:rs2992752). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CTCCCCGCAGACAGGGCCGTG	0.677													C|||	3369	0.672724	0.6611	0.7277	5008	,	,		15380	0.8948		0.6113	False		,,,				2504	0.4836				p.T351P		Atlas-SNP	.											KLHDC7A,NS,carcinoma,0,1	KLHDC7A	60	1	0			c.A1051C						scavenged	.	C	PRO/THR	2798,1418		971,856,281	12.0	16.0	15.0		1051	0.7	0.0	1	dbSNP_101	15	5294,3114		1724,1846,634	yes	missense	KLHDC7A	NM_152375.2	38	2695,2702,915	CC,CA,AA		37.0362,33.6338,35.8999	benign	351/778	18808526	8092,4532	2108	4204	6312	SO:0001583	missense	127707	exon1			CCGCAGACAGGGC	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.1051A>C	1.37:g.18808526A>C	ENSP00000383505:p.Thr351Pro	Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	1574	0.7206959706959707	330	0.6707317073170732	254	0.7016574585635359	523	0.9143356643356644	467	0.6160949868073878	C	0.317	-0.963986	0.02249	0.663662	0.629638	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.71461	-0.57	5.01	0.69	0.18039	.	1.313680	0.05153	N	0.496434	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37776	-0.9691	9	0.02654	T	1	.	3.8663	0.09018	0.4101:0.3546:0.0:0.2353	rs2992752;rs58275241	351	Q5VTJ3	KLD7A_HUMAN	P	351;288	ENSP00000383505:T351P	ENSP00000383505:T351P	T	+	1	0	KLHDC7A	18681113	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.198000	0.03035	-0.075000	0.12798	-1.961000	0.00478	ACA	A|0.310;C|0.690	0.690	strong		0.677	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
MUC17	140453	hgsc.bcm.edu	37	7	100677405	100677405	+	Missense_Mutation	SNP	G	G	A	rs141963257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677405G>A	ENST00000306151.4	+	3	2772	c.2708G>A	c.(2707-2709)cGt>cAt	p.R903H		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	903	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)					ACTGAAGCCCGTTCGTCTCCT	0.527													g|||	903	0.180312	0.2413	0.0836	5008	,	,		32677	0.1944		0.0964	False		,,,				2504	0.2382				p.R903H		Atlas-SNP	.											.	MUC17	804	.	0			c.G2708A						PASS	.						318.0	302.0	307.0					7																	100677405		2203	4300	6503	SO:0001583	missense	140453	exon3			AAGCCCGTTCGTC	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.2708G>A	7.37:g.100677405G>A	ENSP00000302716:p.Arg903His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	161	34	0.21118	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	0.072	-1.199648	0.01581	.	.	ENSG00000169876	ENST00000306151	T	0.02890	4.12	0.579	-1.16	0.09678	.	.	.	.	.	T	0.01592	0.0051	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45041	-0.9288	9	0.40728	T	0.16	.	4.33	0.11059	0.2123:0.3746:0.4131:0.0	.	903	Q685J3	MUC17_HUMAN	H	903	ENSP00000302716:R903H	ENSP00000302716:R903H	R	+	2	0	MUC17	100464125	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.209000	0.01228	-3.371000	0.00177	-3.222000	0.00052	CGT	.	.	weak		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
DMP1	1758	hgsc.bcm.edu	37	4	88584160	88584160	+	Silent	SNP	G	G	A	rs2615497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88584160G>A	ENST00000339673.6	+	6	1329	c.1230G>A	c.(1228-1230)gaG>gaA	p.E410E	DMP1_ENST00000282479.7_Silent_p.E394E|RP11-742B18.1_ENST00000506480.1_RNA|RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000507894.1_RNA	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	410					biomineral tissue development (GO:0031214)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|positive regulation of cell-substrate adhesion (GO:0010811)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1)	32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		AATCCAGTGAGAGCCTCAACT	0.567													G|||	1609	0.321286	0.4652	0.2061	5008	,	,		20365	0.2589		0.2366	False		,,,				2504	0.3599				p.E410E		Atlas-SNP	.											DMP1,caecum,carcinoma,0,1	DMP1	72	1	0			c.G1230A						PASS	.	G	,	1752,2654	521.9+/-370.6	343,1066,794	77.0	82.0	80.0		1182,1230	3.4	0.9	4	dbSNP_100	80	1930,6670	340.7+/-323.7	209,1512,2579	no	coding-synonymous,coding-synonymous	DMP1	NM_001079911.2,NM_004407.3	,	552,2578,3373	AA,AG,GG		22.4419,39.764,28.31	,	394/498,410/514	88584160	3682,9324	2203	4300	6503	SO:0001819	synonymous_variant	1758	exon6			CAGTGAGAGCCTC	U34037	CCDS3623.1, CCDS43249.1	4q21	2008-08-29	2008-08-29		ENSG00000152592	ENSG00000152592			2932	protein-coding gene	gene with protein product		600980	"""dentin matrix acidic phosphoprotein"""			8586437, 9177774	Standard	NM_001079911		Approved		uc003hqv.3	Q13316	OTTHUMG00000130598	ENST00000339673.6:c.1230G>A	4.37:g.88584160G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_004407	A1L4L3|O43265	Silent	SNP	ENST00000339673.6	37	CCDS3623.1																																																																																			G|0.715;A|0.285	0.285	strong		0.567	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1		
PIN4	5303	hgsc.bcm.edu	37	X	71416721	71416721	+	Silent	SNP	C	C	T	rs11415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:71416721C>T	ENST00000373669.2	+	3	311	c.279C>T	c.(277-279)gcC>gcT	p.A93A	RN7SL388P_ENST00000498736.2_RNA|PIN4_ENST00000423432.2_Silent_p.A93A|PIN4_ENST00000218432.5_Silent_p.A93A	NM_006223.3	NP_006214.2	Q9Y237	PIN4_HUMAN	protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)	68	PpiC. {ECO:0000255|PROSITE- ProRule:PRU00278}.				protein folding (GO:0006457)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome (GO:0030684)|spindle (GO:0005819)	bent DNA binding (GO:0003681)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(2)	3	Renal(35;0.156)					ATGAAGTGGCCGCACAGTATA	0.363													C|||	982	0.260132	0.2428	0.1354	3775	,	,		13353	0.3542		0.0199	False		,,,				2504	0.1943				p.A93A		Atlas-SNP	.											.	PIN4	8	.	0			c.C279T						PASS	.	C	,	1124,2711		135,677,177,820,394	87.0	88.0	87.0		279,279	-3.5	0.0	X	dbSNP_52	87	205,6523		2,150,51,2276,1821	no	coding-synonymous,coding-synonymous	PIN4	NM_001170747.1,NM_006223.3	,	137,827,228,3096,2215	TT,TC,T,CC,C		3.047,29.309,12.5817	,	93/134,93/157	71416721	1329,9234	2203	4300	6503	SO:0001819	synonymous_variant	5303	exon3			AGTGGCCGCACAG	AB009690	CCDS14417.1, CCDS55447.1	Xq13.1	2008-02-05	2006-01-12		ENSG00000102309	ENSG00000102309			8992	protein-coding gene	gene with protein product		300252	"""protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)"""			16522211, 17875217	Standard	NM_006223		Approved	PAR14, PAR17, EPVH	uc004eam.3	Q9Y237	OTTHUMG00000021811	ENST00000373669.2:c.279C>T	X.37:g.71416721C>T		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	236	234	0.991525	NM_001170747	A8E0G6|B3KXM0|F5H1P5|Q0D2H3|Q3MHV0|Q52M21|Q5HYW6|Q6IRW4	Silent	SNP	ENST00000373669.2	37	CCDS14417.1	364	0.21940928270042195	80	0.19047619047619047	28	0.08383233532934131	127	0.28475336322869954	11	0.014705882352941176	C	5.608	0.296938	0.10622	0.29309	0.03047	ENSG00000102309	ENST00000446576	.	.	.	5.55	-3.48	0.04739	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999503957	.	.	.	.	.	.	T	0.30765	-0.9967	3	.	.	.	-10.4394	7.603	0.28087	0.1089:0.3364:0.0:0.5547	rs11415;rs1044546;rs3184345;rs16991466;rs11415	.	.	.	L	98	.	.	P	+	2	0	PIN4	71333446	0.000000	0.05858	0.006000	0.13384	0.765000	0.43378	-1.269000	0.02834	-0.891000	0.03940	-0.354000	0.07668	CCG	C|0.810;0|0.003	.	strong		0.363	PIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057175.2	NM_006223	
ZNF292	23036	hgsc.bcm.edu	37	6	87969480	87969480	+	Missense_Mutation	SNP	G	G	A	rs6910541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:87969480G>A	ENST00000369577.3	+	8	6176	c.6133G>A	c.(6133-6135)Gta>Ata	p.V2045I	ZNF292_ENST00000339907.4_Missense_Mutation_p.V2040I	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2045			V -> I (in dbSNP:rs6910541). {ECO:0000269|PubMed:9628581}.			nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AAAACAACTTGTAGAAAAAAA	0.358													G|||	563	0.11242	0.1112	0.1527	5008	,	,		18764	0.0972		0.1064	False		,,,				2504	0.1074				p.V2045I		Atlas-SNP	.											.	ZNF292	479	.	0			c.G6133A						PASS	.	G	ILE/VAL	437,3161		24,389,1386	28.0	25.0	26.0		6133	-9.9	0.0	6	dbSNP_116	26	846,7270		37,772,3249	yes	missense	ZNF292	NM_015021.1	29	61,1161,4635	AA,AG,GG		10.4239,12.1456,10.9527	benign	2045/2724	87969480	1283,10431	1799	4058	5857	SO:0001583	missense	23036	exon8			CAACTTGTAGAAA	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.6133G>A	6.37:g.87969480G>A	ENSP00000358590:p.Val2045Ile	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	192	93	0.484375	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	275	0.1259157509157509	71	0.1443089430894309	61	0.1685082872928177	63	0.11013986013986014	80	0.10554089709762533	G	4.208	0.037399	0.08148	0.121456	0.104239	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.07114	3.22;3.23	5.87	-9.85	0.00476	.	1.934300	0.01884	N	0.038072	T	0.00608	0.0020	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40627	-0.9553	9	0.19147	T	0.46	.	6.9653	0.24619	0.1398:0.3551:0.4245:0.0806	rs6910541;rs52830459;rs61648684;rs6910541	2045	O60281	ZN292_HUMAN	I	2045;2040	ENSP00000358590:V2045I;ENSP00000342847:V2040I	ENSP00000342847:V2040I	V	+	1	0	ZNF292	88026199	0.000000	0.05858	0.000000	0.03702	0.445000	0.32107	-0.649000	0.05384	-1.686000	0.01439	-0.345000	0.07892	GTA	G|0.875;A|0.125	0.125	strong		0.358	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
MOB3A	126308	hgsc.bcm.edu	37	19	2078424	2078424	+	Silent	SNP	G	G	T	rs34059622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2078424G>T	ENST00000357066.3	-	3	515	c.136C>A	c.(136-138)Cgg>Agg	p.R46R	MOB3A_ENST00000592280.1_Silent_p.R46R|MOB3A_ENST00000592143.1_Intron	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	46						intracellular (GO:0005622)	metal ion binding (GO:0046872)										ACGGCCAGCCGCAGGTCCAGC	0.637													G|||	64	0.0127796	0.0461	0.0043	5008	,	,		15140	0.0		0.0	False		,,,				2504	0.0				p.R46R		Atlas-SNP	.											.	.	.	.	0			c.C136A						PASS	.	G		170,4236	112.5+/-150.6	4,162,2037	51.0	54.0	53.0		136	-2.5	0.3	19	dbSNP_126	53	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	MOB3A	NM_130807.2		4,164,6334	TT,TG,GG		0.0233,3.8584,1.3227		46/218	2078424	172,12832	2203	4299	6502	SO:0001819	synonymous_variant	126308	exon3			CCAGCCGCAGGTC	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.136C>A	19.37:g.2078424G>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			G|0.982;T|0.018	0.018	strong		0.637	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
TTN	7273	hgsc.bcm.edu	37	2	179611680	179611680	+	Intron	SNP	G	G	A	rs72648911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179611680G>A	ENST00000591111.1	-	46	10585				TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Silent_p.Y5149Y|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000578746.1_RNA			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)			CTGTAGGTGTGTAGAAATGCT	0.413													A|||	235	0.0469249	0.1725	0.0101	5008	,	,		19409	0.0		0.0	False		,,,				2504	0.0				p.Y5149Y		Atlas-SNP	.											.	TTN	18412	.	0			c.C15447T						PASS	.	A	,,,,	667,3739	763.1+/-413.2	50,567,1586	138.0	134.0	135.0		,,15447,,	-2.6	0.9	2	dbSNP_130	135	8,8590	818.5+/-406.9	0,8,4291	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	50,575,5877	AA,AG,GG		0.093,15.1384,5.1907	,,,,	,,5149/5605,,	179611680	675,12329	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			AGGTGTGTAGAAA	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.10361-5032C>T	2.37:g.179611680G>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	190	99	0.521053	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																																																																																				G|0.954;A|0.046	0.046	strong		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
GAPDH	2597	hgsc.bcm.edu	37	12	6646320	6646320	+	Silent	SNP	T	T	C	rs1065691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	32	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	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	
MT-CYB	4519	hgsc.bcm.edu	37	M	14766	14766	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:14766C>T	ENST00000361789.2	+	1	20	c.20C>T	c.(19-21)aCt>aTt	p.T7I	MT-TT_ENST00000387460.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	7			T -> I (in dbSNP:rs3135031). {ECO:0000269|PubMed:10453733, ECO:0000269|PubMed:11130070, ECO:0000269|PubMed:11553319, ECO:0000269|PubMed:12022039, ECO:0000269|PubMed:1757091, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:7530363, ECO:0000269|PubMed:7623448}.		cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						AATACGCAAAATTAACCCCCT	0.433																																					p.T7I		Atlas-SNP	.											.	.	.	.	0			c.C20T						PASS	.																																			SO:0001583	missense	0	exon1			GCAAAACTAACCC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.20C>T	M.37:g.14766C>T	ENSP00000354554:p.Thr7Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.433	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921110	12921110	+	Missense_Mutation	SNP	A	A	G	rs12139546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12921110A>G	ENST00000240189.2	+	4	988	c.901A>G	c.(901-903)Act>Gct	p.T301A		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	301			T -> A (in dbSNP:rs12139546).		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)		CTTGGAATTAACTTGTGGCAA	0.483													.|||	544	0.108626	0.1271	0.098	5008	,	,		22266	0.128		0.1074	False		,,,				2504	0.0726				p.T301A		Atlas-SNP	.											PRAMEF2,lymph_node,lymphoid_neoplasm,0,1	PRAMEF2	85	1	0			c.A901G						PASS	.	A	ALA/THR	621,3781	261.3+/-264.2	70,481,1650	106.0	109.0	108.0		901	0.8	0.0	1	dbSNP_120	108	968,7624	204.4+/-247.1	75,818,3403	yes	missense	PRAMEF2	NM_023014.1	58	145,1299,5053	GG,GA,AA		11.2663,14.1072,12.2287	possibly-damaging	301/475	12921110	1589,11405	2201	4296	6497	SO:0001583	missense	65122	exon4			GAATTAACTTGTG		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.901A>G	1.37:g.12921110A>G	ENSP00000240189:p.Thr301Ala	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	206	82	0.398058	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	232	0.10622710622710622	45	0.09146341463414634	36	0.09944751381215469	62	0.10839160839160839	89	0.11741424802110818	A	10.84	1.463907	0.26335	0.141072	0.112663	ENSG00000120952	ENST00000240189	T	0.51817	0.69	0.824	0.824	0.18818	.	0.135173	0.49916	D	0.000126	T	0.00440	0.0014	M	0.76727	2.345	0.80722	P	0.0	P	0.42337	0.776	P	0.46659	0.523	T	0.03576	-1.1023	9	0.46703	T	0.11	.	3.9396	0.09321	1.0:0.0:0.0:0.0	rs12139546	301	O60811	PRAM2_HUMAN	A	301	ENSP00000240189:T301A	ENSP00000240189:T301A	T	+	1	0	PRAMEF2	12843697	0.001000	0.12720	0.002000	0.10522	0.052000	0.14988	0.189000	0.17037	0.624000	0.30286	0.145000	0.16022	ACT	A|0.887;G|0.113	0.113	strong		0.483	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
CAPN9	10753	hgsc.bcm.edu	37	1	230910339	230910339	+	Silent	SNP	G	G	A	rs7517389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230910339G>A	ENST00000271971.2	+	8	1028	c.915G>A	c.(913-915)aaG>aaA	p.K305K	CAPN9_ENST00000354537.1_Intron|CAPN9_ENST00000366666.2_Silent_p.K242K|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000452640.1_RNA|RP11-99J16__A.2_ENST00000412344.1_RNA	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	305	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				CTGAGCAGAAGCGTCTGTGTC	0.517													G|||	473	0.0944489	0.1006	0.1081	5008	,	,		18139	0.0804		0.0457	False		,,,				2504	0.1411				p.K305K		Atlas-SNP	.											.	CAPN9	116	.	0			c.G915A						PASS	.	G	,	418,3988	205.8+/-227.6	12,394,1797	241.0	195.0	211.0		915,	-1.2	0.2	1	dbSNP_116	211	383,8217	124.3+/-183.0	10,363,3927	no	coding-synonymous,intron	CAPN9	NM_006615.2,NM_016452.1	,	22,757,5724	AA,AG,GG		4.4535,9.4871,6.1587	,	305/691,	230910339	801,12205	2203	4300	6503	SO:0001819	synonymous_variant	10753	exon8			GCAGAAGCGTCTG	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.915G>A	1.37:g.230910339G>A		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	300	157	0.523333	NM_006615	B1APS1|B1AQI0|Q9NS74	Silent	SNP	ENST00000271971.2	37	CCDS1586.1																																																																																			G|0.936;A|0.064	0.064	strong		0.517	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
OBP2B	29989	hgsc.bcm.edu	37	9	136083580	136083580	+	Silent	SNP	T	T	G	rs2073870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136083580T>G	ENST00000372034.3	-	3	258	c.217A>C	c.(217-219)Agg>Cgg	p.R73R	OBP2B_ENST00000461961.1_5'UTR|OBP2B_ENST00000372032.2_Splice_Site	NM_014581.2	NP_055396.1	Q9NPH6	OBP2B_HUMAN	odorant binding protein 2B	73					chemosensory behavior (GO:0007635)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			central_nervous_system(2)|large_intestine(1)|lung(3)|skin(1)	7				OV - Ovarian serous cystadenocarcinoma(145;3.41e-06)|Epithelial(140;1.88e-05)		TGGATGCACCTATCCTCCCTC	0.647													G|||	3692	0.73722	0.7481	0.8429	5008	,	,		10803	0.6607		0.837	False		,,,				2504	0.6237				p.R73R		Atlas-SNP	.											.	OBP2B	20	.	0			c.A217C						PASS	.	G		3363,1043	382.5+/-324.5	1273,817,113	56.0	58.0	58.0		217	0.9	0.0	9	dbSNP_96	58	7188,1410	268.2+/-287.7	2990,1208,101	no	coding-synonymous	OBP2B	NM_014581.2		4263,2025,214	GG,GT,TT		16.3992,23.6723,18.8634		73/171	136083580	10551,2453	2203	4299	6502	SO:0001819	synonymous_variant	29989	exon3			TGCACCTATCCTC	AJ251026	CCDS6961.1	9q34	2014-01-22			ENSG00000171102	ENSG00000171102		"""Lipocalins"""	23381	protein-coding gene	gene with protein product		604606					Standard	NM_001288987		Approved	hOBPIIb, LCN14	uc004ccz.3	Q9NPH6	OTTHUMG00000020860	ENST00000372034.3:c.217A>C	9.37:g.136083580T>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_014581	Q5VSP6|Q9NY51|Q9NY52	Silent	SNP	ENST00000372034.3	37	CCDS6961.1	1529	0.700091575091575	292	0.5934959349593496	293	0.8093922651933702	348	0.6083916083916084	596	0.7862796833773087	G	2.664	-0.279128	0.05642	0.763277	0.836008	ENSG00000171102	ENST00000372032	.	.	.	1.91	0.93	0.19454	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.1884	0.20510	0.0:0.0:0.4618:0.5382	rs2073870;rs2073870	.	.	.	.	-1	.	.	.	-	.	.	OBP2B	135073401	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.862000	0.04263	-0.059000	0.13154	-1.114000	0.02060	.	T|0.223;G|0.777	0.777	strong		0.647	OBP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054851.1	NM_014581	
PKD1L1	168507	hgsc.bcm.edu	37	7	47955167	47955167	+	Silent	SNP	A	A	G	rs17131941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47955167A>G	ENST00000289672.2	-	8	1140	c.1090T>C	c.(1090-1092)Ttg>Ctg	p.L364L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	364					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						GACATAtccaactgaaaatgt	0.323													A|||	90	0.0179712	0.0658	0.0043	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.L364L		Atlas-SNP	.											.	PKD1L1	328	.	0			c.T1090C						PASS	.	A		173,4233	113.3+/-151.4	3,167,2033	78.0	76.0	77.0		1090	0.4	0.0	7	dbSNP_123	77	0,8600		0,0,4300	no	coding-synonymous	PKD1L1	NM_138295.3		3,167,6333	GG,GA,AA		0.0,3.9265,1.3302		364/2850	47955167	173,12833	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon8			TATCCAACTGAAA	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.1090T>C	7.37:g.47955167A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			A|0.981;G|0.019	0.019	strong		0.323	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
NCOA7	135112	hgsc.bcm.edu	37	6	126249914	126249914	+	Missense_Mutation	SNP	T	T	G	rs1567|rs386705611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:126249914T>G	ENST00000368357.3	+	17	3178	c.2826T>G	c.(2824-2826)gaT>gaG	p.D942E	NCOA7_ENST00000229634.9_Missense_Mutation_p.D827E|NCOA7_ENST00000392477.2_Missense_Mutation_p.D942E	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	942	TLD.		D -> E (in dbSNP:rs1567).		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)		GGGCATTTGATTGAAATTCAG	0.433													G|||	827	0.165136	0.2617	0.0764	5008	,	,		16628	0.2401		0.1153	False		,,,				2504	0.0716				p.D942E		Atlas-SNP	.											.	NCOA7	92	.	0			c.T2826G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	1109,3297	715.1+/-408.4	152,805,1246	76.0	78.0	77.0		2793,2826,2826,2481,657,2826	4.1	1.0	6	dbSNP_36	77	1106,7494	768.0+/-407.6	64,978,3258	yes	missense,missense,missense,missense,missense,missense	NCOA7	NM_001122842.2,NM_001199619.1,NM_001199620.1,NM_001199621.1,NM_001199622.1,NM_181782.4	45,45,45,45,45,45	216,1783,4504	GG,GT,TT		12.8605,25.1702,17.0306	benign,benign,benign,benign,benign,benign	931/932,942/943,942/943,827/828,219/220,942/943	126249914	2215,10791	2203	4300	6503	SO:0001583	missense	135112	exon17			ATTTGATTGAAAT	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.2826T>G	6.37:g.126249914T>G	ENSP00000357341:p.Asp942Glu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	343|343	0.15705128205128205|0.15705128205128205	116|116	0.23577235772357724|0.23577235772357724	24|24	0.06629834254143646|0.06629834254143646	115|115	0.20104895104895104|0.20104895104895104	88|88	0.11609498680738786|0.11609498680738786	G|G	1.772|1.772	-0.484123|-0.484123	0.04383|0.04383	0.251702|0.251702	0.128605|0.128605	ENSG00000111912|ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634|ENST00000438495	T;T;T|.	0.06933|.	3.26;3.26;3.24|.	6.17|6.17	4.1|4.1	0.47936|0.47936	TLDc (1);|.	0.000000|.	0.85682|.	N|.	0.000000|.	T|T	0.03305|0.03305	0.0096|0.0096	N|N	0.01202|0.01202	-0.96|-0.96	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.0;0.001;0.0;0.0|.	T|T	0.38265|0.38265	-0.9669|-0.9669	9|4	0.02654|.	T|.	1|.	.|.	6.2777|6.2777	0.20989|0.20989	0.2432:0.0:0.6121:0.1447|0.2432:0.0:0.6121:0.1447	rs1567;rs52814580;rs59469171;rs1567|rs1567;rs52814580;rs59469171;rs1567	931;236;931;942|.	B3KXK4;Q5JVL0;Q8NI08-2;Q8NI08|.	.;.;.;NCOA7_HUMAN|.	E|V	942;942;827|237	ENSP00000357341:D942E;ENSP00000376269:D942E;ENSP00000229634:D827E|.	ENSP00000229634:D827E|.	D|L	+|+	3|1	2|2	NCOA7|NCOA7	126291607|126291607	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.734000|0.734000	0.41952|0.41952	1.200000|1.200000	0.32247|0.32247	0.952000|0.952000	0.37798|0.37798	-0.121000|-0.121000	0.15023|0.15023	GAT|TTG	T|0.829;G|0.171	0.171	strong		0.433	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748	
HIP1	3092	hgsc.bcm.edu	37	7	75221693	75221693	+	Silent	SNP	C	C	T	rs144446822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75221693C>T	ENST00000336926.6	-	3	350	c.324G>A	c.(322-324)ccG>ccA	p.P108P	HIP1_ENST00000434438.2_Silent_p.P108P	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	108	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						AACTCACGTTCGGGTGTCCAT	0.597			T	PDGFRB	CMML								C|||	6	0.00119808	0.0045	0.0	5008	,	,		20231	0.0		0.0	False		,,,				2504	0.0				p.P108P		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.G324A						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	59.0	50.0	53.0		324	-11.6	0.0	7	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous	HIP1	NM_005338.5		0,15,6488	TT,TC,CC		0.0,0.3404,0.1153		108/1038	75221693	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	3092	exon3			CACGTTCGGGTGT	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.324G>A	7.37:g.75221693C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	35	0.648148	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			C|0.999;T|0.001	0.001	strong		0.597	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
CAV3	859	hgsc.bcm.edu	37	3	8787220	8787220	+	Silent	SNP	T	T	C	rs13087941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:8787220T>C	ENST00000343849.2	+	2	200	c.123T>C	c.(121-123)ttT>ttC	p.F41F	CAV3_ENST00000397368.2_Silent_p.F41F|SSUH2_ENST00000478513.1_5'Flank|CAV3_ENST00000472766.1_Intron	NM_001234.4|NM_033337.2	NP_001225.1|NP_203123.1	P56539	CAV3_HUMAN	caveolin 3	41					actin filament organization (GO:0007015)|cardiac muscle cell development (GO:0055013)|caveola assembly (GO:0070836)|cell differentiation (GO:0030154)|cell growth (GO:0016049)|cholesterol homeostasis (GO:0042632)|cytoplasmic microtubule organization (GO:0031122)|endocytosis (GO:0006897)|establishment of protein localization to plasma membrane (GO:0090002)|glucose homeostasis (GO:0042593)|heart trabecula formation (GO:0060347)|membrane raft organization (GO:0031579)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of cell size (GO:0045792)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sarcomere organization (GO:0060299)|nucleus localization (GO:0051647)|plasma membrane organization (GO:0007009)|plasma membrane repair (GO:0001778)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein localization (GO:0008104)|protein localization to plasma membrane (GO:0072659)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of calcium ion import (GO:0090279)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart contraction (GO:0008016)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of nerve growth factor receptor activity (GO:0051394)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase B signaling (GO:0051896)|regulation of signal transduction by receptor internalization (GO:0038009)|regulation of skeletal muscle contraction (GO:0014819)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|T-tubule organization (GO:0033292)|triglyceride metabolic process (GO:0006641)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|dystrophin-associated glycoprotein complex (GO:0016010)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|connexin binding (GO:0071253)|ion channel binding (GO:0044325)|potassium channel inhibitor activity (GO:0019870)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein complex scaffold (GO:0032947)|sodium channel regulator activity (GO:0017080)	p.F41F(1)		breast(1)|kidney(2)|large_intestine(4)|lung(3)|prostate(1)	11						AGGTGGATTTTGAAGACGTGA	0.562													C|||	766	0.152955	0.2837	0.1311	5008	,	,		18630	0.0139		0.2326	False		,,,				2504	0.0532				p.F41F		Atlas-SNP	.											CAV3,NS,carcinoma,0,1	CAV3	20	1	1	Substitution - coding silent(1)	prostate(1)	c.T123C						PASS	.	C	,	1251,3155	704.6+/-407.1	175,901,1127	60.0	53.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	123,123	-7.3	0.6	3	dbSNP_121	56	2073,6527	716.8+/-406.1	242,1589,2469	no	coding-synonymous,coding-synonymous	CAV3	NM_001234.3,NM_033337.2	,	417,2490,3596	CC,CT,TT		24.1047,28.3931,25.5574	,	41/152,41/152	8787220	3324,9682	2203	4300	6503	SO:0001819	synonymous_variant	859	exon2			GGATTTTGAAGAC	AF043101	CCDS2569.1	3p25	2014-09-17			ENSG00000182533	ENSG00000182533			1529	protein-coding gene	gene with protein product	"""M-caveolin"""	601253				9536092, 9537420	Standard	NM_033337		Approved	VIP-21, LGMD1C, VIP21, LQT9	uc003brb.3	P56539	OTTHUMG00000090519	ENST00000343849.2:c.123T>C	3.37:g.8787220T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_033337	A8K777|Q3T1A4	Silent	SNP	ENST00000343849.2	37	CCDS2569.1																																																																																			T|0.791;C|0.209	0.209	strong		0.562	CAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207008.2	NM_033337	
CROCC	9696	hgsc.bcm.edu	37	1	17270751	17270751	+	Silent	SNP	G	G	A	rs12025984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17270751G>A	ENST00000375541.5	+	14	2034	c.1965G>A	c.(1963-1965)gcG>gcA	p.A655A	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)		AGGATGGCGCGCGGGTGCGCC	0.711													g|||	1190	0.23762	0.0182	0.3242	5008	,	,		21546	0.4643		0.2495	False		,,,				2504	0.227				p.A655A		Atlas-SNP	.											.	CROCC	185	.	0			c.G1965A						PASS	.						8.0	6.0	7.0					1																	17270751		2084	4087	6171	SO:0001819	synonymous_variant	9696	exon14			TGGCGCGCGGGTG	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.1965G>A	1.37:g.17270751G>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	18	5	0.277778	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			G|0.762;A|0.238	0.238	strong		0.711	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
OR2T6	254879	hgsc.bcm.edu	37	1	248551636	248551636	+	Missense_Mutation	SNP	T	T	G	rs954475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248551636T>G	ENST00000355728.2	+	1	727	c.727T>G	c.(727-729)Tca>Gca	p.S243A		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	243			S -> A (in dbSNP:rs954475).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACCTGCTCTTCACACATGAT	0.507													t|||	1851	0.369609	0.4962	0.3127	5008	,	,		22655	0.4365		0.1769	False		,,,				2504	0.3681				p.S243A		Atlas-SNP	.											.	OR2T6	101	.	0			c.T727G						PASS	.	T	ALA/SER	1921,2485	548.5+/-377.6	423,1075,705	259.0	220.0	234.0		727	2.8	0.0	1	dbSNP_86	234	1297,7303	256.6+/-281.0	92,1113,3095	yes	missense	OR2T6	NM_001005471.1	99	515,2188,3800	GG,GT,TT		15.0814,43.5996,24.7424	probably-damaging	243/309	248551636	3218,9788	2203	4300	6503	SO:0001583	missense	254879	exon1			TGCTCTTCACACA	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"""GPCR / Class A : Olfactory receptors"""	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.727T>G	1.37:g.248551636T>G	ENSP00000347965:p.Ser243Ala	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	239	123	0.514644	NM_001005471	A6NE36	Missense_Mutation	SNP	ENST00000355728.2	37	CCDS31114.1	720	0.32967032967032966	241	0.4898373983739837	94	0.2596685082872928	242	0.4230769230769231	143	0.18865435356200527	T	11.11	1.542475	0.27563	0.435996	0.150814	ENSG00000198104	ENST00000355728	T	0.38887	1.11	4.02	2.85	0.33270	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37219	N	0.002182	T	0.00012	0.0000	M	0.76938	2.355	0.50632	P	1.1300000000002974E-4	D	0.89917	1.0	D	0.97110	1.0	T	0.45381	-0.9265	9	0.87932	D	0	.	6.292	0.21065	0.0:0.089:0.1626:0.7484	rs954475;rs52796985;rs954475	243	Q8NHC8	OR2T6_HUMAN	A	243	ENSP00000347965:S243A	ENSP00000347965:S243A	S	+	1	0	OR2T6	246618259	0.237000	0.23815	0.048000	0.18961	0.377000	0.30045	0.605000	0.24179	0.673000	0.31224	0.523000	0.50628	TCA	T|0.707;G|0.293	0.293	strong		0.507	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471	
PNPLA5	150379	hgsc.bcm.edu	37	22	44287062	44287062	+	Silent	SNP	A	A	G	rs2071884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44287062A>G	ENST00000597664.1	-	2	435	c.306T>C	c.(304-306)gaT>gaC	p.D102D	PNPLA5_ENST00000381198.2_Intron|PNPLA5_ENST00000593866.1_Intron|PNPLA5_ENST00000216177.4_Silent_p.D102D			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						PASS	.	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	165	0	0		WXS	Illumina HiSeq	Phase_I	214	109	0.509346	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	
TMEM41B	440026	hgsc.bcm.edu	37	11	9305136	9305136	+	Silent	SNP	G	G	A	rs77349011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9305136G>A	ENST00000528080.1	-	7	1049	c.711C>T	c.(709-711)gtC>gtT	p.V237V	TMEM41B_ENST00000527813.1_Missense_Mutation_p.S191L	NM_015012.3	NP_055827.1	Q5BJD5	TM41B_HUMAN	transmembrane protein 41B	237					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(2)	7				all cancers(16;9.96e-08)|Epithelial(150;4.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0972)		AAGGAGGTGCGACACCTGAAA	0.333													G|||	356	0.0710863	0.2557	0.0231	5008	,	,		14041	0.0		0.002	False		,,,				2504	0.0				p.V237V		Atlas-SNP	.											TMEM41B,NS,haematopoietic_neoplasm,0,1	TMEM41B	22	1	0			c.C711T						PASS	.	G		876,3526	335.5+/-303.9	87,702,1412	45.0	43.0	44.0		711	0.6	1.0	11	dbSNP_131	44	9,8583	7.1+/-27.0	0,9,4287	no	coding-synonymous	TMEM41B	NM_015012.3		87,711,5699	AA,AG,GG		0.1047,19.9,6.8108		237/292	9305136	885,12109	2201	4296	6497	SO:0001819	synonymous_variant	440026	exon7			AGGTGCGACACCT	D26067	CCDS31424.1, CCDS53600.1	11p15.3	2008-02-05			ENSG00000166471	ENSG00000166471			28948	protein-coding gene	gene with protein product						7584026, 7584028	Standard	NM_015012		Approved	KIAA0033	uc001mhn.2	Q5BJD5	OTTHUMG00000165719	ENST00000528080.1:c.711C>T	11.37:g.9305136G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_015012	D3DQU9|E9PP29|Q15055|Q4G0P0	Silent	SNP	ENST00000528080.1	37	CCDS31424.1	109	0.04990842490842491	102	0.2073170731707317	7	0.019337016574585635	0	0.0	0	0.0	G	11.73	1.724415	0.30593	0.199	0.001047	ENSG00000166471	ENST00000527813	.	.	.	5.55	0.652	0.17823	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17137	-1.0379	4	0.59425	D	0.04	-12.5515	1.822	0.03112	0.415:0.2125:0.2657:0.1069	.	.	.	.	L	191	.	ENSP00000435685:S191L	S	-	2	0	TMEM41B	9261712	0.806000	0.28996	0.997000	0.53966	0.830000	0.47004	0.020000	0.13466	-0.132000	0.11557	-1.004000	0.02495	TCG	G|0.941;A|0.059	0.059	strong		0.333	TMEM41B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385940.2		
CASP4	837	hgsc.bcm.edu	37	11	104825597	104825597	+	Missense_Mutation	SNP	C	C	T	rs56226603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:104825597C>T	ENST00000444739.2	-	2	1049	c.139G>A	c.(139-141)Gat>Aat	p.D47N	CASP4_ENST00000531333.1_5'UTR|CASP4_ENST00000393150.3_5'UTR	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	47	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		D -> N (in dbSNP:rs56226603).		apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		GTTTTAGCATCGTAATATTTC	0.398													C|||	136	0.0271565	0.0946	0.0159	5008	,	,		19636	0.0		0.0	False		,,,				2504	0.0				p.D47N		Atlas-SNP	.											.	CASP4	57	.	0			c.G139A						PASS	.	C	ASN/ASP,	361,4043	185.0+/-212.2	22,317,1863	226.0	209.0	215.0		139,	0.0	0.0	11	dbSNP_129	215	1,8597	1.2+/-3.3	0,1,4298	yes	missense,utr-5	CASP4	NM_001225.3,NM_033306.2	23,	22,318,6161	TT,TC,CC		0.0116,8.1971,2.7842	benign,	47/378,	104825597	362,12640	2202	4299	6501	SO:0001583	missense	837	exon2			TAGCATCGTAATA	U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"""Caspases"""	1505	protein-coding gene	gene with protein product		602664	"""caspase 4, apoptosis-related cysteine protease"""			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.139G>A	11.37:g.104825597C>T	ENSP00000388566:p.Asp47Asn	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	180	60	0.333333	NM_001225	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	37	CCDS8327.1	65	0.02976190476190476	57	0.11585365853658537	8	0.022099447513812154	0	0.0	0	0.0	C	0.022	-1.408830	0.01155	0.081971	1.16E-4	ENSG00000196954	ENST00000444739;ENST00000417440	T;T	0.19394	2.15;2.15	3.04	0.0232	0.14136	DEATH-like (2);Caspase Recruitment (3);	0.704837	0.13761	N	0.364575	T	0.00073	0.0002	N	0.02357	-0.585	0.09310	N	0.999999	B;B;B	0.33288	0.406;0.007;0.002	B;B;B	0.26969	0.075;0.006;0.006	T	0.27123	-1.0083	10	0.02654	T	1	.	6.0472	0.19766	0.0:0.469:0.0:0.531	rs56226603;rs61751520	47;47;47	B4DJH5;B4E2D2;P49662	.;.;CASP4_HUMAN	N	47	ENSP00000388566:D47N;ENSP00000401673:D47N	ENSP00000401673:D47N	D	-	1	0	CASP4	104330807	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.945000	0.03909	0.002000	0.14630	-0.140000	0.14226	GAT	C|0.969;T|0.031	0.031	strong		0.398	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225	
TNXB	7148	hgsc.bcm.edu	37	6	32032756	32032756	+	Missense_Mutation	SNP	A	A	T	rs3749960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32032756A>T	ENST00000375244.3	-	19	6884	c.6683T>A	c.(6682-6684)tTt>tAt	p.F2228Y	TNXB_ENST00000375247.2_Missense_Mutation_p.F2228Y			P22105	TENX_HUMAN	tenascin XB	2300	Fibronectin type-III 14. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCCATTCTTAAACTGGACCAA	0.607													T|||	87	0.0173722	0.0136	0.0187	5008	,	,		17768	0.0556		0.0	False		,,,				2504	0.0				p.F2228Y		Atlas-SNP	.											.	TNXB	553	.	0			c.T6683A						PASS	.	T	TYR/PHE	12,2476		0,12,1232	27.0	31.0	30.0		6683	4.8	1.0	6	dbSNP_107	30	0,5060		0,0,2530	yes	missense	TNXB	NM_019105.6	22	0,12,3762	TT,TA,AA		0.0,0.4823,0.159	benign	2228/4243	32032756	12,7536	1244	2530	3774	SO:0001583	missense	7148	exon19			TTCTTAAACTGGA	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.6683T>A	6.37:g.32032756A>T	ENSP00000364393:p.Phe2228Tyr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		45	0.020604395604395604	10	0.02032520325203252	6	0.016574585635359115	29	0.050699300699300696	0	0.0	T	5.909	0.351823	0.11182	0.004823	0.0	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.48522	0.81;0.81	4.82	4.82	0.62117	.	0.000000	0.37715	N	0.001962	T	0.02083	0.0065	N	0.00033	-2.575	0.21579	N	0.99964	B	0.02656	0.0	B	0.04013	0.001	T	0.44019	-0.9355	10	0.02654	T	1	.	8.8957	0.35463	0.1666:0.0:0.0:0.8334	rs3749960;rs3749960	2228	P22105-3	.	Y	2228	ENSP00000364393:F2228Y;ENSP00000364396:F2228Y	ENSP00000364393:F2228Y	F	-	2	0	TNXB	32140734	1.000000	0.71417	0.999000	0.59377	0.693000	0.40251	3.024000	0.49674	0.860000	0.35481	-0.336000	0.08194	TTT	A|0.947;T|0.053	0.053	strong		0.607	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
DRD5	1816	hgsc.bcm.edu	37	4	9784642	9784642	+	Missense_Mutation	SNP	C	C	A	rs1800762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:9784642C>A	ENST00000304374.2	+	1	1385	c.989C>A	c.(988-990)cCg>cAg	p.P330Q		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	330			P -> Q (in dbSNP:rs1800762). {ECO:0000269|PubMed:7633397}.		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.P330Q(1)		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)	GAAGGCCCTCCGGCCGGCTTC	0.597													C|||	162	0.0323482	0.0234	0.0072	5008	,	,		19310	0.0863		0.0	False		,,,				2504	0.0399				p.P330Q		Atlas-SNP	.											DRD5,NS,carcinoma,0,1	DRD5	119	1	1	Substitution - Missense(1)	stomach(1)	c.C989A						PASS	.	C	GLN/PRO	114,4292	86.3+/-125.0	3,108,2092	89.0	90.0	90.0		989	-2.2	0.0	4	dbSNP_89	90	4,8596	3.7+/-12.6	0,4,4296	no	missense	DRD5	NM_000798.4	76	3,112,6388	AA,AC,CC		0.0465,2.5874,0.9073	benign	330/478	9784642	118,12888	2203	4300	6503	SO:0001583	missense	1816	exon1			GCCCTCCGGCCGG	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.989C>A	4.37:g.9784642C>A	ENSP00000306129:p.Pro330Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	104	61	0.586538	NM_000798	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	CCDS3405.1	56	0.02564102564102564	8	0.016260162601626018	3	0.008287292817679558	45	0.07867132867132867	0	0.0	c	0.290	-0.980733	0.02197	0.025874	4.65E-4	ENSG00000169676	ENST00000304374	T	0.68331	-0.32	4.48	-2.16	0.07080	GPCR, rhodopsin-like superfamily (1);	2.094460	0.02189	N	0.061125	T	0.03520	0.0101	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.05146	-1.0903	10	0.27082	T	0.32	.	6.2235	0.20695	0.435:0.2531:0.3119:0.0	rs1800762;rs61023474	330	P21918	DRD5_HUMAN	Q	330	ENSP00000306129:P330Q	ENSP00000306129:P330Q	P	+	2	0	DRD5	9393740	0.000000	0.05858	0.000000	0.03702	0.198000	0.23893	-0.462000	0.06704	-0.357000	0.08175	-0.515000	0.04445	CCG	C|0.986;A|0.014	0.014	strong		0.597	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
GRB10	2887	hgsc.bcm.edu	37	7	50742326	50742326	+	Missense_Mutation	SNP	T	T	C	rs185094083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:50742326T>C	ENST00000401949.1	-	6	638	c.169A>G	c.(169-171)Aac>Gac	p.N57D	GRB10_ENST00000357271.5_Missense_Mutation_p.N57D|GRB10_ENST00000398812.2_Missense_Mutation_p.N57D|GRB10_ENST00000398810.2_5'UTR|GRB10_ENST00000335866.3_5'UTR|GRB10_ENST00000402578.1_5'UTR|GRB10_ENST00000403097.1_Missense_Mutation_p.N51D|GRB10_ENST00000439599.1_Missense_Mutation_p.N51D|GRB10_ENST00000407526.1_5'UTR|GRB10_ENST00000402497.1_5'UTR|GRB10_ENST00000406641.1_5'UTR			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	57					insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					TTCATATCGTTCACCAGGGCT	0.522									Russell-Silver syndrome				T|||	14	0.00279553	0.0106	0.0	5008	,	,		21544	0.0		0.0	False		,,,				2504	0.0				p.N57D		Atlas-SNP	.											.	GRB10	155	.	0			c.A169G						PASS	.	T	ASP/ASN,,,ASP/ASN	21,4061		0,21,2020	57.0	59.0	59.0		169,,,169	4.5	1.0	7		59	1,8411		0,1,4205	yes	missense,utr-5,utr-5,missense	GRB10	NM_001001549.2,NM_001001550.2,NM_001001555.2,NM_005311.4	23,,,23	0,22,6225	CC,CT,TT		0.0119,0.5145,0.1761	probably-damaging,,,probably-damaging	57/549,,,57/595	50742326	22,12472	2041	4206	6247	SO:0001583	missense	2887	exon3	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	TATCGTTCACCAG		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.169A>G	7.37:g.50742326T>C	ENSP00000385770:p.Asn57Asp	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_005311	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Missense_Mutation	SNP	ENST00000401949.1	37	CCDS43582.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	25.0	4.597321	0.87055	0.005145	1.19E-4	ENSG00000106070	ENST00000398812;ENST00000439599;ENST00000403097;ENST00000357271;ENST00000401949;ENST00000439044	D;D;D;D;D;T	0.87571	-1.97;-1.97;-1.97;-2.27;-1.97;-1.14	5.67	4.53	0.55603	.	0.083534	0.85682	N	0.000000	T	0.78194	0.4245	L	0.55481	1.735	0.80722	D	1	B;B;B	0.28933	0.228;0.027;0.074	B;B;B	0.24006	0.05;0.024;0.025	T	0.76653	-0.2880	10	0.37606	T	0.19	-25.4018	11.6266	0.51149	0.0:0.0693:0.0:0.9307	.	51;57;57	Q13322-4;Q13322-2;Q13322	.;.;GRB10_HUMAN	D	57;51;51;57;57;51	ENSP00000381793:N57D;ENSP00000406716:N51D;ENSP00000385544:N51D;ENSP00000349818:N57D;ENSP00000385770:N57D;ENSP00000413023:N51D	ENSP00000349818:N57D	N	-	1	0	GRB10	50709820	1.000000	0.71417	0.990000	0.47175	0.689000	0.40095	5.866000	0.69590	1.097000	0.41459	0.533000	0.62120	AAC	T|0.999;C|0.001	0.001	strong		0.522	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1		
TMEM45B	120224	hgsc.bcm.edu	37	11	129722512	129722512	+	Silent	SNP	C	C	T	rs115605173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:129722512C>T	ENST00000524567.1	+	2	416	c.135C>T	c.(133-135)ctC>ctT	p.L45L	TMEM45B_ENST00000281441.3_Silent_p.L45L			Q96B21	TM45B_HUMAN	transmembrane protein 45B	45						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)		ATCAGCGTCTCGAGATCGTCG	0.483													C|||	40	0.00798722	0.0272	0.0058	5008	,	,		19521	0.0		0.0	False		,,,				2504	0.0				p.L45L		Atlas-SNP	.											.	TMEM45B	25	.	0			c.C135T						PASS	.	C		118,4284	89.2+/-127.9	1,116,2084	144.0	133.0	136.0		135	-11.3	0.0	11	dbSNP_132	136	10,8584	7.1+/-27.0	0,10,4287	no	coding-synonymous	TMEM45B	NM_138788.3		1,126,6371	TT,TC,CC		0.1164,2.6806,0.9849		45/276	129722512	128,12868	2201	4297	6498	SO:0001819	synonymous_variant	120224	exon2			GCGTCTCGAGATC	AK098106	CCDS8482.1	11q24.3	2008-02-05				ENSG00000151715			25194	protein-coding gene	gene with protein product						12477932	Standard	NM_138788		Approved	BC016153, FLJ40787	uc001qfe.1	Q96B21		ENST00000524567.1:c.135C>T	11.37:g.129722512C>T		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	248	132	0.532258	NM_138788	A8K2L8	Silent	SNP	ENST00000524567.1	37	CCDS8482.1																																																																																			C|0.991;T|0.009	0.009	strong		0.483	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1	NM_138788	
BST1	683	hgsc.bcm.edu	37	4	15713446	15713446	+	Silent	SNP	C	C	T	rs2302463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	137	0	0		WXS	Illumina HiSeq	Phase_I	153	76	0.496732	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	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37462885	37462885	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37462885C>T	ENST00000346753.3	-	17	2374	c.2258G>A	c.(2257-2259)gGc>gAc	p.G753D	TMPRSS6_ENST00000406856.1_Missense_Mutation_p.G766D|TMPRSS6_ENST00000381792.2_Missense_Mutation_p.G766D|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.G744D	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	753	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)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						ATCCTTCTTGCCCTTGCGGTA	0.607																																					p.G753D		Atlas-SNP	.											TMPRSS6,NS,neuroblastoma,+1,1	TMPRSS6	99	1	0			c.G2258A						scavenged	.						114.0	86.0	96.0					22																	37462885		2203	4300	6503	SO:0001583	missense	164656	exon17			TTCTTGCCCTTGC	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.2258G>A	22.37:g.37462885C>T	ENSP00000334962:p.Gly753Asp	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	191	3	0.0157068	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	37	CCDS13941.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892985	0.91889	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856	D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58	4.72	4.72	0.59763	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.134612	0.49305	D	0.000159	D	0.94991	0.8379	M	0.84433	2.695	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.95900	0.8914	10	0.87932	D	0	.	17.6779	0.88235	0.0:1.0:0.0:0.0	.	766;753	Q8IU80-5;Q8IU80	.;TMPS6_HUMAN	D	766;753;744;766	ENSP00000371211:G766D;ENSP00000334962:G753D;ENSP00000385453:G744D;ENSP00000384964:G766D	ENSP00000334962:G753D	G	-	2	0	TMPRSS6	35792831	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.582000	0.82546	2.151000	0.67156	0.591000	0.81541	GGC	.	.	none		0.607	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
GTPBP2	54676	hgsc.bcm.edu	37	6	43590408	43590408	+	Silent	SNP	G	G	A	rs16896609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43590408G>A	ENST00000307126.5	-	10	1428	c.1429C>T	c.(1429-1431)Ctg>Ttg	p.L477L	GTPBP2_ENST00000476510.1_5'UTR|GTPBP2_ENST00000307114.7_Silent_p.L389L	NM_019096.3	NP_061969.3			GTP binding protein 2											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			CCAAGCGCCAGTGTAGCAGCC	0.612													A|||	1036	0.206869	0.5643	0.0793	5008	,	,		21625	0.0357		0.0646	False		,,,				2504	0.137				p.L477L	GBM(116;405 1620 28302 32150 44768)	Atlas-SNP	.											.	GTPBP2	39	.	0			c.C1429T						PASS	.	A		2194,2212	588.7+/-387.0	561,1072,570	138.0	129.0	132.0		1429	-5.8	0.0	6	dbSNP_123	132	558,8042	792.9+/-407.5	13,532,3755	no	coding-synonymous	GTPBP2	NM_019096.3		574,1604,4325	AA,AG,GG		6.4884,49.7957,21.1595		477/603	43590408	2752,10254	2203	4300	6503	SO:0001819	synonymous_variant	54676	exon10			GCGCCAGTGTAGC	AB024574	CCDS4903.1, CCDS69124.1	6p21	2008-07-28			ENSG00000172432	ENSG00000172432			4670	protein-coding gene	gene with protein product		607434				10833435, 11054535	Standard	NM_019096		Approved		uc003ovs.3	Q9BX10	OTTHUMG00000014744	ENST00000307126.5:c.1429C>T	6.37:g.43590408G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_019096		Silent	SNP	ENST00000307126.5	37	CCDS4903.1	366	0.16758241758241757	268	0.5447154471544715	28	0.07734806629834254	25	0.043706293706293704	45	0.059366754617414245	A	7.485	0.649547	0.14516	0.497957	0.064884	ENSG00000172432	ENST00000419497;ENST00000432918	.	.	.	5.37	-5.75	0.02384	.	.	.	.	.	T	0.71668	0.3367	.	.	.	0.09310	P	0.9999999999685968	.	.	.	.	.	.	T	0.75712	-0.3222	4	0.62326	D	0.03	-9.6506	23.5311	0.99983	0.1559:0.0:0.8441:0.0	rs16896609;rs16896609	.	.	.	I	45	.	ENSP00000392944:T45I	T	-	2	0	GTPBP2	43698386	0.002000	0.14202	0.001000	0.08648	0.896000	0.52359	-0.001000	0.12947	-2.204000	0.00743	-1.396000	0.01147	ACT	G|0.812;A|0.188	0.188	strong		0.612	GTPBP2-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040679.1		
ANK1	286	hgsc.bcm.edu	37	8	41552840	41552840	+	Silent	SNP	G	G	A	rs34969689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:41552840G>A	ENST00000347528.4	-	27	3053	c.2970C>T	c.(2968-2970)atC>atT	p.I990I	ANK1_ENST00000379758.2_Silent_p.I990I|ANK1_ENST00000265709.8_Silent_p.I1031I|ANK1_ENST00000352337.4_Silent_p.I990I|ANK1_ENST00000289734.7_Silent_p.I990I|ANK1_ENST00000396945.1_Silent_p.I990I|ANK1_ENST00000396942.1_Silent_p.I990I	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	990	ZU5 1. {ECO:0000255|PROSITE- ProRule:PRU00485}.				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)			GGATCTCCACGATTACAGGGC	0.642													G|||	71	0.0141773	0.0522	0.0014	5008	,	,		20368	0.0		0.0	False		,,,				2504	0.001				p.I1031I		Atlas-SNP	.											.	ANK1	497	.	0			c.C3093T						PASS	.	G	,,,,	167,4239	109.9+/-148.2	2,163,2038	94.0	79.0	84.0		2970,3093,2970,2970,2970	-4.0	1.0	8	dbSNP_126	84	3,8597	2.2+/-6.3	0,3,4297	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	,,,,	2,166,6335	AA,AG,GG		0.0349,3.7903,1.3071	,,,,	990/1881,1031/1898,990/1857,990/1882,990/1720	41552840	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	286	exon28			CTCCACGATTACA	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.2970C>T	8.37:g.41552840G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	180	85	0.472222	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	22	0.010073260073260074	21	0.042682926829268296	1	0.0027624309392265192	0	0.0	0	0.0	G	8.916	0.959980	0.18507	0.037903	3.49E-4	ENSG00000029534	ENST00000520299	.	.	.	4.99	-4.02	0.04034	.	.	.	.	.	T	0.21674	0.0522	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43734	-0.9373	4	.	.	.	.	9.6086	0.39648	0.649:0.1048:0.2461:0.0	rs34969689	.	.	.	C	312	.	.	R	-	1	0	ANK1	41671997	0.000000	0.05858	0.956000	0.39512	0.803000	0.45373	-2.206000	0.01231	-0.779000	0.04560	-0.251000	0.11542	CGT	G|0.987;A|0.013	0.013	strong		0.642	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
ZNF217	7764	hgsc.bcm.edu	37	20	52198619	52198619	+	Silent	SNP	C	C	A	rs78786003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52198619C>A	ENST00000371471.2	-	2	1172	c.747G>T	c.(745-747)gcG>gcT	p.A249A	ZNF217_ENST00000302342.3_Silent_p.A249A|ZNF217_ENST00000540425.1_5'Flank			O75362	ZN217_HUMAN	zinc finger protein 217	249					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)			AGTCTGTCTGCGCGCTGCTGG	0.488													C|||	50	0.00998403	0.0348	0.0058	5008	,	,		21092	0.0		0.0	False		,,,				2504	0.0				p.A249A		Atlas-SNP	.											.	ZNF217	227	.	0			c.G747T						PASS	.	C		187,4219	118.4+/-156.1	1,185,2017	101.0	98.0	99.0		747	-8.0	0.0	20	dbSNP_131	99	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF217	NM_006526.2		1,187,6315	AA,AC,CC		0.0233,4.2442,1.4532		249/1049	52198619	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	7764	exon1			TGTCTGCGCGCTG	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.747G>T	20.37:g.52198619C>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																			C|0.985;A|0.015	0.015	strong		0.488	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
MGAT4A	11320	hgsc.bcm.edu	37	2	99256447	99256447	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99256447T>A	ENST00000264968.3	-	11	1509	c.1146A>T	c.(1144-1146)aaA>aaT	p.K382N	MGAT4A_ENST00000409391.1_Missense_Mutation_p.K382N|MGAT4A_ENST00000393487.1_Missense_Mutation_p.K382N|MGAT4A_ENST00000414521.2_Missense_Mutation_p.K254N			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	382					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						GAAGTAATGGTTTCATATAAT	0.343																																					p.K382N		Atlas-SNP	.											.	MGAT4A	51	.	0			c.A1146T						PASS	.						63.0	67.0	66.0					2																	99256447		2203	4300	6503	SO:0001583	missense	11320	exon12			TAATGGTTTCATA	AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	2.4.1.145	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7047	protein-coding gene	gene with protein product		604623	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A"""			10024668	Standard	NM_001160154		Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.1146A>T	2.37:g.99256447T>A	ENSP00000264968:p.Lys382Asn	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_012214	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Missense_Mutation	SNP	ENST00000264968.3	37	CCDS2036.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.462708	0.63513	.	.	ENSG00000071073	ENST00000393487;ENST00000414521;ENST00000264968;ENST00000409391	T;T;T;T	0.26957	1.7;1.75;1.7;1.7	5.64	1.45	0.22620	.	0.000000	0.85682	D	0.000000	T	0.49762	0.1576	M	0.85777	2.775	0.54753	D	0.999987	D;D	0.76494	0.988;0.999	P;D	0.78314	0.815;0.991	T	0.50792	-0.8786	10	0.52906	T	0.07	-5.7696	10.1002	0.42499	0.0:0.2309:0.0:0.7691	.	254;382	E9PEN2;Q9UM21	.;MGT4A_HUMAN	N	382;254;382;382	ENSP00000377127:K382N;ENSP00000404889:K254N;ENSP00000264968:K382N;ENSP00000386841:K382N	ENSP00000264968:K382N	K	-	3	2	MGAT4A	98622879	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	0.644000	0.24766	0.394000	0.25230	0.455000	0.32223	AAA	.	.	none		0.343	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214	
USP40	55230	hgsc.bcm.edu	37	2	234394569	234394569	+	Silent	SNP	A	A	G	rs386656355|rs2603547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234394569A>G	ENST00000427112.2	-	28	3284	c.3249T>C	c.(3247-3249)taT>taC	p.Y1083Y	USP40_ENST00000450966.1_Silent_p.Y1095Y|USP40_ENST00000251722.6_Silent_p.Y1083Y|USP40_ENST00000496298.1_5'UTR			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1083					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		GGGCAGGGGCATAGGTCCTCT	0.597													G|||	1286	0.256789	0.5053	0.1542	5008	,	,		16483	0.1458		0.2455	False		,,,				2504	0.1196				p.Y1095Y		Atlas-SNP	.											.	USP40	174	.	0			c.T3285C						PASS	.	G		1637,2333		357,923,705	14.0	16.0	15.0		3285	2.0	0.0	2	dbSNP_100	15	1735,6567		188,1359,2604	no	coding-synonymous	USP40	NM_018218.2		545,2282,3309	GG,GA,AA		20.8986,41.2343,27.4772		1095/1248	234394569	3372,8900	1985	4151	6136	SO:0001819	synonymous_variant	55230	exon28			AGGGGCATAGGTC	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3249T>C	2.37:g.234394569A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_018218	Q6NX38|Q70EL0	Silent	SNP	ENST00000427112.2	37	CCDS46547.1	520	0.23809523809523808	222	0.45121951219512196	56	0.15469613259668508	67	0.11713286713286714	175	0.23087071240105542	G	0.033	-1.324183	0.01309	0.412343	0.208986	ENSG00000085982	ENST00000454354	.	.	.	5.75	2.03	0.26663	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25277	P	0.9894669	.	.	.	.	.	.	T	0.46176	-0.9210	3	.	.	.	.	10.1403	0.42732	0.4526:0.0:0.5474:0.0	rs2603547;rs3738932;rs17668948;rs56738620;rs2603547	.	.	.	T	51	.	.	M	-	2	0	USP40	234059308	0.026000	0.19158	0.004000	0.12327	0.003000	0.03518	0.191000	0.17076	-0.094000	0.12374	-1.702000	0.00720	ATG	A|0.749;G|0.251	0.251	strong		0.597	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
MUC16	94025	hgsc.bcm.edu	37	19	9080462	9080462	+	Missense_Mutation	SNP	C	C	G	rs2547065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	71	0	0		WXS	Illumina HiSeq	Phase_I	101	42	0.415842	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	
HDC	3067	hgsc.bcm.edu	37	15	50534789	50534789	+	Missense_Mutation	SNP	A	A	G	rs16963486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:50534789A>G	ENST00000267845.3	-	12	2059	c.1657T>C	c.(1657-1659)Ttt>Ctt	p.F553L	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Missense_Mutation_p.F520L	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		TCTTCTGAAAAGCAGTCATCA	0.537													A|||	105	0.0209665	0.0764	0.0058	5008	,	,		20285	0.0		0.0	False		,,,				2504	0.0				p.F553L	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.T1657C						PASS	.	A	LEU/PHE	319,4073	168.3+/-199.2	11,297,1888	87.0	88.0	88.0		1657	5.7	1.0	15	dbSNP_123	88	1,8589	1.2+/-3.3	0,1,4294	yes	missense	HDC	NM_002112.3	22	11,298,6182	GG,GA,AA		0.0116,7.2632,2.465	probably-damaging	553/663	50534789	320,12662	2196	4295	6491	SO:0001583	missense	3067	exon12			CTGAAAAGCAGTC		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1657T>C	15.37:g.50534789A>G	ENSP00000267845:p.Phe553Leu	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	123	65	0.528455	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	A	17.30	3.353885	0.61293	0.072632	1.16E-4	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.14144	2.92;2.53	5.73	5.73	0.89815	.	0.365309	0.23805	N	0.044383	T	0.01061	0.0035	L	0.34521	1.04	0.43444	D	0.99562	D;D	0.67145	0.996;0.976	P;B	0.54759	0.76;0.446	T	0.00294	-1.1840	10	0.54805	T	0.06	-19.7657	16.0115	0.80406	1.0:0.0:0.0:0.0	rs16963486;rs52824591;rs16963486	520;553	B7ZM01;P19113	.;DCHS_HUMAN	L	553;520	ENSP00000267845:F553L;ENSP00000440252:F520L	ENSP00000267845:F553L	F	-	1	0	HDC	48322081	1.000000	0.71417	0.999000	0.59377	0.039000	0.13416	6.778000	0.75043	2.187000	0.69744	0.460000	0.39030	TTT	A|0.975;G|0.025	0.025	strong		0.537	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1		
MDH2	4191	hgsc.bcm.edu	37	7	75684273	75684273	+	Silent	SNP	G	G	A	rs77424348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75684273G>A	ENST00000315758.5	+	2	286	c.192G>A	c.(190-192)gtG>gtA	p.V64V	MDH2_ENST00000490105.1_3'UTR|MDH2_ENST00000443006.1_Intron|MDH2_ENST00000432020.2_Silent_p.V64V	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	64					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						CACCCGGAGTGGCCGCAGATC	0.612													g|||	28	0.00559105	0.0204	0.0014	5008	,	,		14182	0.0		0.0	False		,,,				2504	0.0				p.V64V		Atlas-SNP	.											.	MDH2	35	.	0			c.G192A						PASS	.	G		112,4294	86.8+/-125.4	3,106,2094	77.0	78.0	78.0		192	2.3	1.0	7	dbSNP_132	78	1,8599		0,1,4299	no	coding-synonymous	MDH2	NM_005918.2		3,107,6393	AA,AG,GG		0.0116,2.542,0.8688		64/339	75684273	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	4191	exon2			CGGAGTGGCCGCA		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.192G>A	7.37:g.75684273G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	77	54	0.701299	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Silent	SNP	ENST00000315758.5	37	CCDS5581.1																																																																																			G|0.984;A|0.016	0.016	strong		0.612	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1		
SF3B3	23450	hgsc.bcm.edu	37	16	70602221	70602221	+	Silent	SNP	C	C	T	rs12909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70602221C>T	ENST00000302516.5	+	22	3199	c.2988C>T	c.(2986-2988)atC>atT	p.I996I		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	996					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)	p.I996I(1)		breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				TCCAGACTATCGGACATAGGG	0.418													T|||	2538	0.506789	0.4175	0.4193	5008	,	,		21558	0.5804		0.4155	False		,,,				2504	0.7076				p.I996I		Atlas-SNP	.											SF3B3,NS,carcinoma,0,1	SF3B3	99	1	1	Substitution - coding silent(1)	stomach(1)	c.C2988T						PASS	.	T		1727,2669	649.6+/-398.9	328,1071,799	126.0	121.0	123.0		2988	3.6	1.0	16	dbSNP_52	123	3642,4958	624.6+/-397.6	785,2072,1443	no	coding-synonymous	SF3B3	NM_012426.4		1113,3143,2242	TT,TC,CC		42.3488,39.2857,41.3127		996/1218	70602221	5369,7627	2198	4300	6498	SO:0001819	synonymous_variant	23450	exon22			GACTATCGGACAT	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"""splicing factor 3b, subunit 3, 130kD"""			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.2988C>T	16.37:g.70602221C>T		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	220	220	1	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Silent	SNP	ENST00000302516.5	37	CCDS10894.1																																																																																			C|0.569;T|0.431	0.431	strong		0.418	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426	
FAT1	2195	hgsc.bcm.edu	37	4	187524176	187524176	+	Missense_Mutation	SNP	G	G	A	rs200262460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187524176G>A	ENST00000441802.2	-	20	11572	c.11363C>T	c.(11362-11364)cCa>cTa	p.P3788L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3788					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						GTGGACAGGTGGGCACCTTCC	0.493										HNSCC(5;0.00058)			G|||	4	0.000798722	0.003	0.0	5008	,	,		18565	0.0		0.0	False		,,,				2504	0.0				p.P3788L	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C11363T						PASS	.	G	LEU/PRO	4,3954		0,4,1975	88.0	88.0	88.0		11363	5.3	1.0	4	dbSNP_134	88	0,8326		0,0,4163	yes	missense	FAT1	NM_005245.3	98	0,4,6138	AA,AG,GG		0.0,0.1011,0.0326	benign	3788/4589	187524176	4,12280	1979	4163	6142	SO:0001583	missense	2195	exon20			ACAGGTGGGCACC	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.11363C>T	4.37:g.187524176G>A	ENSP00000406229:p.Pro3788Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	123	71	0.577236	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	13.22	2.170718	0.38315	0.001011	0.0	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.32023	1.47	5.26	5.26	0.73747	.	0.056195	0.64402	D	0.000001	T	0.32823	0.0842	L	0.58428	1.81	0.80722	D	1	B	0.30686	0.29	B	0.25759	0.063	T	0.07252	-1.0782	10	0.32370	T	0.25	.	19.2203	0.93793	0.0:0.0:1.0:0.0	.	3788	Q14517	FAT1_HUMAN	L	3788;3790	ENSP00000406229:P3788L	ENSP00000260147:P3790L	P	-	2	0	FAT1	187761170	1.000000	0.71417	0.956000	0.39512	0.080000	0.17528	9.111000	0.94308	2.614000	0.88457	0.557000	0.71058	CCA	G|1.000;A|0.000	0.000	strong		0.493	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
PCDHB12	56124	hgsc.bcm.edu	37	5	140589334	140589334	+	Silent	SNP	A	A	G	rs149716951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140589334A>G	ENST00000239450.2	+	1	1044	c.855A>G	c.(853-855)tcA>tcG	p.S285S	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	285	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(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)			CCCATGCCTCAGAAGATATTC	0.403													A|||	27	0.00539137	0.0204	0.0	5008	,	,		20813	0.0		0.0	False		,,,				2504	0.0				p.S285S		Atlas-SNP	.											.	PCDHB12	179	.	0			c.A855G						PASS	.	A		70,4336	63.5+/-100.7	1,68,2134	99.0	105.0	103.0		855	-4.1	1.0	5	dbSNP_134	103	0,8600		0,0,4300	no	coding-synonymous	PCDHB12	NM_018932.3		1,68,6434	GG,GA,AA		0.0,1.5887,0.5382		285/796	140589334	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	56124	exon1			TGCCTCAGAAGAT	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.855A>G	5.37:g.140589334A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_018932	B4DDU1	Silent	SNP	ENST00000239450.2	37	CCDS4254.1																																																																																			A|0.994;G|0.006	0.006	strong		0.403	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
ATP2A3	489	hgsc.bcm.edu	37	17	3850910	3850910	+	Silent	SNP	A	A	G	rs55837933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3850910A>G	ENST00000352011.3	-	8	924	c.870T>C	c.(868-870)cgT>cgC	p.R290R	ATP2A3_ENST00000397041.3_Silent_p.R290R|ATP2A3_ENST00000397043.3_Silent_p.R290R|ATP2A3_ENST00000309890.7_Silent_p.R290R|ATP2A3_ENST00000397035.3_Silent_p.R290R|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000359983.3_Silent_p.R290R			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	290					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		AGACAGCGCCACGCAGCCAGG	0.677													G|||	356	0.0710863	0.2564	0.0245	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.R290R	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T870C						PASS	.	G	,,,,,,	1054,3350		133,788,1281	28.0	31.0	30.0		870,870,870,870,870,870,870	-7.5	0.1	17	dbSNP_129	30	5,8591		0,5,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	133,793,5574	GG,GA,AA		0.0582,23.9328,8.1462	,,,,,,	290/1000,290/1053,290/1045,290/1044,290/1030,290/999,290/1030	3850910	1059,11941	2202	4298	6500	SO:0001819	synonymous_variant	489	exon8			AGCGCCACGCAGC		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.870T>C	17.37:g.3850910A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	43	26	0.604651	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			A|0.928;G|0.072	0.072	strong		0.677	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
HSD3B1	3283	hgsc.bcm.edu	37	1	120054215	120054215	+	Missense_Mutation	SNP	A	A	G	rs6201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120054215A>G	ENST00000369413.3	+	3	380	c.235A>G	c.(235-237)Atc>Gtc	p.I79V	HSD3B1_ENST00000235547.6_Missense_Mutation_p.I81V|HSD3B1_ENST00000528909.1_Missense_Mutation_p.I79V			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	79			I -> V (in dbSNP:rs6201). {ECO:0000269|PubMed:10391209}.		androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	CGTCTCGGTCATCATCCACAC	0.502													A|||	684	0.136581	0.385	0.0706	5008	,	,		20637	0.0546		0.005	False		,,,				2504	0.0675				p.I79V		Atlas-SNP	.											.	HSD3B1	53	.	0			c.A235G						PASS	.	A	VAL/ILE	1391,3015	452.2+/-349.9	229,933,1041	111.0	106.0	107.0		235	0.2	0.1	1	dbSNP_52	107	29,8571	20.4+/-63.3	0,29,4271	no	missense	HSD3B1	NM_000862.2	29	229,962,5312	GG,GA,AA		0.3372,31.5706,10.918	benign	79/374	120054215	1420,11586	2203	4300	6503	SO:0001583	missense	3283	exon3			TCGGTCATCATCC	S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5217	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 1"""	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.235A>G	1.37:g.120054215A>G	ENSP00000358421:p.Ile79Val	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	203	103	0.507389	NM_000862	A8K691|Q14545|Q8IV65	Missense_Mutation	SNP	ENST00000369413.3	37	CCDS903.1	203	0.09294871794871795	161	0.32723577235772355	22	0.06077348066298342	19	0.033216783216783216	1	0.0013192612137203166	A	0	-2.693868	0.00098	0.315706	0.003372	ENSG00000203857	ENST00000531340;ENST00000369413;ENST00000235547;ENST00000528909	T;D;D;D	0.82344	-1.46;-1.6;-1.6;-1.6	3.27	0.153	0.14897	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.063362	0.64402	N	0.000007	T	0.18964	0.0455	N	0.00277	-1.72	0.51767	P	6.700000000003925E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30297	-0.9983	9	0.02654	T	1	-8.2843	7.3042	0.26438	0.342:0.0:0.658:0.0	rs6201;rs60400881	81;79	Q5TDG2;P14060	.;3BHS1_HUMAN	V	79;79;81;79	ENSP00000435999:I79V;ENSP00000358421:I79V;ENSP00000235547:I81V;ENSP00000432268:I79V	ENSP00000235547:I81V	I	+	1	0	HSD3B1	119855738	0.996000	0.38824	0.124000	0.21820	0.006000	0.05464	2.367000	0.44213	0.119000	0.18210	-0.374000	0.07098	ATC	A|0.902;G|0.098	0.098	strong		0.502	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862	
AHCTF1	25909	hgsc.bcm.edu	37	1	247013733	247013733	+	Missense_Mutation	SNP	T	T	C	rs139763225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247013733T>C	ENST00000391829.2	-	33	5698	c.5575A>G	c.(5575-5577)Aaa>Gaa	p.K1859E	AHCTF1_ENST00000326225.3_Missense_Mutation_p.K1868E|AHCTF1_ENST00000366508.1_Missense_Mutation_p.K1894E|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1859	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				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)			ACTTCTTTTTTAGTAGTTTCT	0.328													T|||	222	0.0443291	0.1657	0.0043	5008	,	,		19442	0.0		0.0	False		,,,				2504	0.0				p.K1868E	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.A5602G						PASS	.	T	GLU/LYS	482,3810		21,440,1685	23.0	25.0	24.0		5602	5.2	0.4	1	dbSNP_134	24	6,8524		0,6,4259	no	missense	AHCTF1	NM_015446.4	56	21,446,5944	CC,CT,TT		0.0703,11.2302,3.806	benign	1868/2276	247013733	488,12334	2146	4265	6411	SO:0001583	missense	25909	exon33			CTTTTTTAGTAGT		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.5575A>G	1.37:g.247013733T>C	ENSP00000375705:p.Lys1859Glu	Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	408	167	0.409314	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		75	0.034340659340659344	74	0.15040650406504066	1	0.0027624309392265192	0	0.0	0	0.0	T	0	-2.799134	0.00076	0.112302	7.03E-4	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.29917	1.55;1.55;1.55	5.15	5.15	0.70609	.	2.053990	0.02125	N	0.055937	T	0.00109	0.0003	N	0.22421	0.69	0.09310	N	1	B;B;B	0.17667	0.014;0.016;0.023	B;B;B	0.14023	0.004;0.01;0.007	T	0.37979	-0.9682	10	0.05959	T	0.93	-0.8216	4.3077	0.10955	0.1767:0.097:0.0:0.7263	.	720;1894;1859	B3KTD2;Q8WYP5-2;Q8WYP5	.;.;ELYS_HUMAN	E	1894;1868;1859	ENSP00000355464:K1894E;ENSP00000355465:K1868E;ENSP00000375705:K1859E	ENSP00000355465:K1868E	K	-	1	0	AHCTF1	245080356	0.010000	0.17322	0.450000	0.26969	0.205000	0.24178	1.124000	0.31320	1.927000	0.55829	0.533000	0.62120	AAA	.	.	weak		0.328	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
PASK	23178	hgsc.bcm.edu	37	2	242063448	242063448	+	Silent	SNP	G	G	A	rs2302052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242063448G>A	ENST00000405260.1	-	11	3518	c.2820C>T	c.(2818-2820)gcC>gcT	p.A940A	PASK_ENST00000544142.1_Silent_p.A754A|PASK_ENST00000358649.4_Silent_p.A940A|PASK_ENST00000539818.1_Silent_p.A724A|PASK_ENST00000403638.3_Silent_p.A940A|PASK_ENST00000234040.4_Silent_p.A940A	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	940					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GGGTCCTGGCGGCTGAGTCGC	0.632													G|||	474	0.0946486	0.1369	0.0951	5008	,	,		11317	0.131		0.0606	False		,,,				2504	0.0348				p.A940A		Atlas-SNP	.											.	PASK	230	.	0			c.C2820T						PASS	.	G		627,3779	269.2+/-268.9	51,525,1627	45.0	48.0	47.0		2820	0.3	0.0	2	dbSNP_100	47	566,8034	151.9+/-206.6	18,530,3752	no	coding-synonymous	PASK	NM_015148.2		69,1055,5379	AA,AG,GG		6.5814,14.2306,9.1727		940/1324	242063448	1193,11813	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon11			CCTGGCGGCTGAG	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2820C>T	2.37:g.242063448G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			G|0.898;A|0.102	0.102	strong		0.632	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
SLC22A5	6584	hgsc.bcm.edu	37	5	131705949	131705949	+	Silent	SNP	T	T	C	rs2631365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:131705949T>C	ENST00000245407.3	+	1	506	c.285T>C	c.(283-285)ctT>ctC	p.L95L	SLC22A5_ENST00000435065.2_Silent_p.L95L|AC034220.3_ENST00000417795.1_RNA|AC034220.3_ENST00000457998.2_RNA	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	95					carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	TCTCGGCGCTTGGGCTGGAGC	0.692											OREG0003451	type=REGULATORY REGION|Gene=BC043424|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2435	0.486222	0.3434	0.3285	5008	,	,		11579	0.6736		0.4165	False		,,,				2504	0.6697				p.L95L		Atlas-SNP	.											.	SLC22A5	34	.	0			c.T285C						PASS	.	C		1347,2899		253,841,1029	9.0	11.0	10.0		285	-0.6	1.0	5	dbSNP_100	10	3097,5365		647,1803,1781	no	coding-synonymous	SLC22A5	NM_003060.3		900,2644,2810	CC,CT,TT		36.5989,31.724,34.9701		95/558	131705949	4444,8264	2123	4231	6354	SO:0001819	synonymous_variant	6584	exon1			GGCGCTTGGGCTG	AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"""Solute carriers"""	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.285T>C	5.37:g.131705949T>C		Somatic	108	0	0	1589	WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_003060	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Silent	SNP	ENST00000245407.3	37	CCDS4154.1																																																																																			T|0.732;C|0.268	0.268	strong		0.692	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060	
UPK3A	7380	hgsc.bcm.edu	37	22	45691594	45691594	+	Silent	SNP	A	A	G	rs1057356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45691594A>G	ENST00000216211.4	+	6	890	c.858A>G	c.(856-858)caA>caG	p.Q286Q	UPK3A_ENST00000396082.2_Silent_p.Q165Q	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	286					cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		GCAAGCTCCAAGACTGAGCCC	0.647													G|||	3146	0.628195	0.8843	0.4841	5008	,	,		17593	0.6508		0.3598	False		,,,				2504	0.637				p.Q286Q		Atlas-SNP	.											.	UPK3A	14	.	0			c.A858G						PASS	.	G	,	3524,882	328.3+/-300.5	1414,696,93	35.0	33.0	34.0		495,858	3.0	1.0	22	dbSNP_86	34	2982,5618	641.4+/-399.7	519,1944,1837	no	coding-synonymous,coding-synonymous	UPK3A	NM_001167574.1,NM_006953.3	,	1933,2640,1930	GG,GA,AA		34.6744,20.0182,49.9769	,	165/167,286/288	45691594	6506,6500	2203	4300	6503	SO:0001819	synonymous_variant	7380	exon6			GCTCCAAGACTGA	AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"""uroplakin 3"""	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.858A>G	22.37:g.45691594A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Silent	SNP	ENST00000216211.4	37	CCDS14064.1																																																																																			A|0.474;G|0.526	0.526	strong		0.647	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953	
CEACAM1	634	hgsc.bcm.edu	37	19	43031514	43031514	+	Missense_Mutation	SNP	G	G	T	rs8111171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43031514G>T	ENST00000161559.6	-	2	237	c.103C>A	c.(103-105)Cag>Aag	p.Q35K	CEACAM1_ENST00000358394.3_Missense_Mutation_p.Q35K|CEACAM1_ENST00000308072.4_5'UTR|CEACAM1_ENST00000599389.1_Missense_Mutation_p.Q35K|CEACAM1_ENST00000403444.3_Missense_Mutation_p.Q35K|CEACAM1_ENST00000352591.5_Missense_Mutation_p.Q35K|CEACAM1_ENST00000351134.3_Missense_Mutation_p.Q35K|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000403461.1_Missense_Mutation_p.Q35K|LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000594688.1_RNA	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	35	Ig-like V-type.		Q -> K (in dbSNP:rs8111171). {ECO:0000269|Ref.9}.		angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	GTAGTGAGCTGGGCAGTGGTG	0.502													g|||	596	0.11901	0.4228	0.0461	5008	,	,		19075	0.0		0.005	False		,,,				2504	0.0				p.Q35K		Atlas-SNP	.											.	CEACAM1	43	.	0			c.C103A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN	1556,2850	488.5+/-361.2	290,976,937	140.0	134.0	136.0		103,103,103,103,103,103	-0.2	0.0	19	dbSNP_116	136	22,8578	12.6+/-44.7	0,22,4278	yes	missense,missense,missense,missense,missense,missense	CEACAM1	NM_001024912.2,NM_001184813.1,NM_001184815.1,NM_001184816.1,NM_001205344.1,NM_001712.4	53,53,53,53,53,53	290,998,5215	TT,TG,GG		0.2558,35.3155,12.1329	benign,benign,benign,benign,benign,benign	35/465,35/431,35/462,35/369,35/469,35/527	43031514	1578,11428	2203	4300	6503	SO:0001583	missense	634	exon2			TGAGCTGGGCAGT	M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.103C>A	19.37:g.43031514G>T	ENSP00000161559:p.Gln35Lys	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	219	124	0.56621	NM_001184816	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	220	0.10073260073260074	196	0.3983739837398374	19	0.052486187845303865	0	0.0	5	0.006596306068601583	g	11.90	1.776621	0.31411	0.353155	0.002558	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000351134;ENST00000446434;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T	0.01647	4.71;4.71;4.71;4.71;4.71;4.71	3.6	-0.184	0.13280	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.49778	1.585	0.58432	P	2.9999999999752447E-6	B;B;B;B;B;B;B;B;B;B	0.22983	0.004;0.009;0.001;0.001;0.002;0.001;0.039;0.009;0.078;0.047	B;B;B;B;B;B;B;B;B;B	0.20184	0.006;0.003;0.005;0.003;0.002;0.004;0.028;0.008;0.015;0.027	T	0.36065	-0.9763	8	0.38643	T	0.18	.	6.2066	0.20606	0.0:0.3764:0.4131:0.2105	rs8111171;rs59246809	35;35;35;35;35;35;35;35;35;35	P13688-7;P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;.;CEAM1_HUMAN	K	35;35;35;62;35;35;35;35;35;35	ENSP00000161559:Q35K;ENSP00000351165:Q35K;ENSP00000325946:Q35K;ENSP00000244291:Q35K;ENSP00000384709:Q35K;ENSP00000384083:Q35K	ENSP00000161559:Q35K	Q	-	1	0	CEACAM1	47723354	0.691000	0.27709	0.001000	0.08648	0.306000	0.27790	0.186000	0.16978	0.061000	0.16311	0.491000	0.48974	CAG	G|0.888;T|0.112	0.112	strong		0.502	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712	
SACS	26278	hgsc.bcm.edu	37	13	23915089	23915089	+	Missense_Mutation	SNP	G	G	T	rs139993038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23915089G>T	ENST00000382292.3	-	9	3199	c.2926C>A	c.(2926-2928)Cgt>Agt	p.R976S	SACS_ENST00000402364.1_Missense_Mutation_p.R226S|SACS_ENST00000382298.3_Missense_Mutation_p.R976S			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	976					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TTTGCCAGACGAATAGTAGCT	0.348													G|||	8	0.00159744	0.0061	0.0	5008	,	,		20828	0.0		0.0	False		,,,				2504	0.0				p.R976S		Atlas-SNP	.											SACS_ENST00000382298,NS,carcinoma,0,2	SACS	871	2	0			c.C2926A						scavenged	.	G	SER/ARG	27,4379	33.5+/-64.1	0,27,2176	71.0	70.0	71.0		2926	6.1	1.0	13	dbSNP_134	71	0,8600		0,0,4300	no	missense	SACS	NM_014363.4	110	0,27,6476	TT,TG,GG		0.0,0.6128,0.2076	probably-damaging	976/4580	23915089	27,12979	2203	4300	6503	SO:0001583	missense	26278	exon10			CCAGACGAATAGT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.2926C>A	13.37:g.23915089G>T	ENSP00000371729:p.Arg976Ser	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	183	71	0.387978	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	32	5.112212	0.94339	0.006128	0.0	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87809	-2.14;-2.3;-2.14	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	D	0.82486	0.5047	L	0.34521	1.04	0.80722	D	1	D	0.53312	0.959	P	0.47528	0.549	D	0.85013	0.0907	10	0.56958	D	0.05	.	20.6013	0.99457	0.0:0.0:1.0:0.0	.	976	Q9NZJ4	SACS_HUMAN	S	976;226;976	ENSP00000371729:R976S;ENSP00000385844:R226S;ENSP00000371735:R976S	ENSP00000371729:R976S	R	-	1	0	SACS	22813089	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.476000	0.97823	2.878000	0.98634	0.650000	0.86243	CGT	A|0.000;G|0.999;T|0.001	0.001	strong		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
LRFN2	57497	hgsc.bcm.edu	37	6	40400823	40400823	+	Silent	SNP	C	C	T	rs61731039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:40400823C>T	ENST00000338305.6	-	2	572	c.30G>A	c.(28-30)gcG>gcA	p.A10A		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	10						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					CCATGCCAAACGCTAGCAGGC	0.597													c|||	248	0.0495208	0.1785	0.0144	5008	,	,		18737	0.0		0.002	False		,,,				2504	0.0				p.A10A		Atlas-SNP	.											LRFN2,NS,carcinoma,-1,1	LRFN2	133	1	0			c.G30A						PASS	.	T		702,3704	266.8+/-267.5	63,576,1564	36.0	38.0	37.0		30	-1.2	1.0	6	dbSNP_129	37	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous	LRFN2	NM_020737.1		63,589,5851	TT,TC,CC		0.1512,15.9328,5.4975		10/790	40400823	715,12291	2203	4300	6503	SO:0001819	synonymous_variant	57497	exon2			GCCAAACGCTAGC	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	21226	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 2"""	612808	"""KIAA1246"""	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.30G>A	6.37:g.40400823C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_020737	A5PKU3|Q5SYP9	Silent	SNP	ENST00000338305.6	37	CCDS34443.1																																																																																			C|0.950;T|0.050	0.050	strong		0.597	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372	
SP140L	93349	hgsc.bcm.edu	37	2	231248261	231248261	+	Missense_Mutation	SNP	C	C	T	rs28497362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231248261C>T	ENST00000415673.2	+	8	760	c.674C>T	c.(673-675)aCg>aTg	p.T225M	SP140L_ENST00000396563.4_Missense_Mutation_p.T225M|SP140L_ENST00000243810.6_Missense_Mutation_p.T225M|SP140L_ENST00000444636.1_Missense_Mutation_p.T225M	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	225			T -> M (in dbSNP:rs28497362).			nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						AGAATGGGAACGAGAACGCAG	0.368													C|||	1153	0.230232	0.1868	0.1599	5008	,	,		20124	0.1448		0.1551	False		,,,				2504	0.5041				p.T225M		Atlas-SNP	.											.	SP140L	68	.	0			c.C674T						PASS	.	C	MET/THR	609,3149		50,509,1320	99.0	106.0	104.0		674	-3.2	0.0	2	dbSNP_125	104	1213,7005		88,1037,2984	yes	missense	SP140L	NM_138402.4	81	138,1546,4304	TT,TC,CC		14.7603,16.2054,15.2138	benign	225/581	231248261	1822,10154	1879	4109	5988	SO:0001583	missense	93349	exon8			TGGGAACGAGAAC	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.674C>T	2.37:g.231248261C>T	ENSP00000397911:p.Thr225Met	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	271	132	0.487085	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	348	0.15934065934065933	87	0.17682926829268292	54	0.14917127071823205	94	0.16433566433566432	113	0.14907651715039577	C	1.288	-0.608551	0.03717	0.162054	0.147603	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	D;T;D;D	0.83163	-1.56;-1.21;-1.56;-1.69	2.4	-3.15	0.05233	.	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.25772	0.134;0.112	B;B	0.21546	0.035;0.013	T	0.03463	-1.1034	8	0.44086	T	0.13	.	1.0792	0.01639	0.2154:0.3363:0.2813:0.1669	rs28497362;rs28497362	225;225	Q9H930-2;Q9H930-4	.;.	M	225	ENSP00000395195:T225M;ENSP00000397911:T225M;ENSP00000243810:T225M;ENSP00000379811:T225M	ENSP00000243810:T225M	T	+	2	0	SP140L	230956505	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.927000	0.01561	-0.989000	0.03485	-0.893000	0.02921	ACG	C|0.819;T|0.181	0.181	strong		0.368	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
S100A5	6276	hgsc.bcm.edu	37	1	153509892	153509892	+	Silent	SNP	A	A	G	rs2248745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153509892A>G	ENST00000368718.1	-	4	440	c.159T>C	c.(157-159)gaT>gaC	p.D53D	BX470102.3_ENST00000420695.1_RNA|S100A5_ENST00000368717.2_Silent_p.D53D|S100A6_ENST00000368719.4_5'Flank|S100A6_ENST00000368720.2_5'Flank|S100A6_ENST00000496817.1_5'Flank|S100A5_ENST00000359215.1_Silent_p.D71D	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	150	0	0		WXS	Illumina HiSeq	Phase_I	176	81	0.460227	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	
SERPINF2	5345	hgsc.bcm.edu	37	17	1648502	1648502	+	Missense_Mutation	SNP	C	C	T	rs2070863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1648502C>T	ENST00000324015.3	+	3	174	c.97C>T	c.(97-99)Cgg>Tgg	p.R33W	SERPINF2_ENST00000450523.2_Missense_Mutation_p.R33W|SERPINF2_ENST00000382061.4_Missense_Mutation_p.R33W	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	33			R -> W (in dbSNP:rs2070863). {ECO:0000269|PubMed:10583218}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of proteolysis (GO:0030162)|response to organic substance (GO:0010033)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Ocriplasmin(DB08888)	GCCCTTGGGCCGGCAGGTACT	0.672													C|||	1197	0.239018	0.2201	0.2089	5008	,	,		9905	0.1855		0.1988	False		,,,				2504	0.3824				p.R33W		Atlas-SNP	.											.	SERPINF2	33	.	0			c.C97T	GRCh37	CM073337	SERPINF2	M	rs2070863	PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	894,3468		90,714,1377	23.0	18.0	20.0		97,97,97	3.0	0.0	17	dbSNP_96	20	1705,6805		177,1351,2727	yes	missense,missense,missense	SERPINF2	NM_000934.3,NM_001165920.1,NM_001165921.1	101,101,101	267,2065,4104	TT,TC,CC		20.0353,20.4952,20.1911	probably-damaging,probably-damaging,probably-damaging	33/492,33/492,33/428	1648502	2599,10273	2181	4255	6436	SO:0001583	missense	5345	exon3			TTGGGCCGGCAGG	D00174	CCDS11011.1, CCDS54064.1	17p13.3	2014-02-18	2005-08-18		ENSG00000167711	ENSG00000167711		"""Serine (or cysteine) peptidase inhibitors"""	9075	protein-coding gene	gene with protein product	"""alpha-2-plasmin inhibitor"", ""alpha-2-antiplasmin"""	613168	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2"""	PLI		3416655, 24172014	Standard	NM_000934		Approved	API, ALPHA-2-PI, A2AP, AAP	uc002ftk.1	P08697	OTTHUMG00000090552	ENST00000324015.3:c.97C>T	17.37:g.1648502C>T	ENSP00000321853:p.Arg33Trp	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_000934	B4E1B7|Q8N5U7|Q9UCG2|Q9UCG3	Missense_Mutation	SNP	ENST00000324015.3	37	CCDS11011.1	419	0.19184981684981686	99	0.20121951219512196	71	0.19613259668508287	103	0.18006993006993008	146	0.19261213720316622	C	11.31	1.601548	0.28534	0.204952	0.200353	ENSG00000167711	ENST00000453066;ENST00000324015;ENST00000450523;ENST00000423861;ENST00000453723;ENST00000382061	D;D;D;D;D	0.87809	-2.3;-1.97;-2.03;-1.72;-1.97	4.98	2.96	0.34315	.	1.515610	0.03304	N	0.189536	T	0.00356	0.0011	L	0.29908	0.895	0.80722	P	0.0	D;P	0.55172	0.97;0.946	B;B	0.42087	0.375;0.12	T	0.32295	-0.9912	9	0.52906	T	0.07	.	10.6516	0.45651	0.0:0.8237:0.0:0.1763	rs2070863;rs2234833;rs61057008;rs2070863	33;33	B4E1B7;P08697	.;A2AP_HUMAN	W	33	ENSP00000402286:R33W;ENSP00000321853:R33W;ENSP00000403877:R33W;ENSP00000402056:R33W;ENSP00000371493:R33W	ENSP00000321853:R33W	R	+	1	2	SERPINF2	1595252	0.001000	0.12720	0.003000	0.11579	0.006000	0.05464	0.793000	0.26944	0.235000	0.21160	-1.626000	0.00786	CGG	C|0.794;T|0.206	0.206	strong		0.672	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207078.3	NM_000934	
OAS1	4938	hgsc.bcm.edu	37	12	113357193	113357193	+	Splice_Site	SNP	G	G	A	rs10774671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113357193G>A	ENST00000202917.5	+	6	1301		c.e6-1		RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Intron|OAS1_ENST00000551241.1_Intron	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa						cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						CACCCTTTCAGGCTGAAAGCA	0.478													G|||	3077	0.614417	0.3601	0.7262	5008	,	,		25437	0.745		0.6481	False		,,,				2504	0.7096				.		Atlas-SNP	.											.	OAS1	128	.	0			c.1039-1G>A	GRCh37	CS051261	OAS1	S	rs10774671	PASS	.	G	,	1917,2489	547.6+/-377.3	420,1077,706	78.0	78.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,	2.9	0.1	12	dbSNP_120	78	5490,3110	657.0+/-401.4	1766,1958,576	yes	intron,splice-3	OAS1	NM_001032409.1,NM_016816.2	,	2186,3035,1282	AA,AG,GG		36.1628,43.5089,43.0494	,	,	113357193	7407,5599	2203	4300	6503	SO:0001630	splice_region_variant	4938	exon6			CTTTCAGGCTGAA	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"""2',5'-oligoadenylate synthetase 1 (40-46 kD)"""	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.1039-1G>A	12.37:g.113357193G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_016816	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Splice_Site	SNP	ENST00000202917.5	37	CCDS41838.1	1398	0.6401098901098901	203	0.41260162601626016	253	0.6988950276243094	447	0.7814685314685315	495	0.6530343007915568	G	5.040	0.193020	0.09599	0.435089	0.638372	ENSG00000089127	ENST00000202917	.	.	.	2.89	2.89	0.33648	.	.	.	.	.	.	.	.	.	.	.	0.31976	P	0.606467	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.4607	0.38783	0.0:0.0:1.0:0.0	rs10774671;rs57204057;rs10774671	.	.	.	.	-1	.	.	.	+	.	.	OAS1	111841576	0.004000	0.15560	0.099000	0.21106	0.019000	0.09904	0.497000	0.22514	1.927000	0.55829	0.557000	0.71058	.	G|0.396;A|0.604	0.604	strong		0.478	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2		Intron
MAP1B	4131	hgsc.bcm.edu	37	5	71495320	71495320	+	Silent	SNP	G	G	A	rs115914542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71495320G>A	ENST00000296755.7	+	5	6436	c.6138G>A	c.(6136-6138)gaG>gaA	p.E2046E		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2046					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.E2046D(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		AGACTGCAGAGAAAATCACTA	0.458													G|||	7	0.00139776	0.0053	0.0	5008	,	,		19505	0.0		0.0	False		,,,				2504	0.0				p.E2046E	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											MAP1B,rectum,carcinoma,0,2	MAP1B	243	2	2	Substitution - Missense(2)	large_intestine(2)	c.G6138A						PASS	.	G		10,4396	15.5+/-35.6	0,10,2193	117.0	129.0	125.0		6138	3.9	0.9	5	dbSNP_133	125	0,8600		0,0,4300	no	coding-synonymous	MAP1B	NM_005909.3		0,10,6493	AA,AG,GG		0.0,0.227,0.0769		2046/2469	71495320	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			TGCAGAGAAAATC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.6138G>A	5.37:g.71495320G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	163	87	0.533742	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																			G|0.999;A|0.001	0.001	strong		0.458	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
PLB1	151056	hgsc.bcm.edu	37	2	28855840	28855840	+	Silent	SNP	C	C	T	rs3752902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:28855840C>T	ENST00000327757.5	+	56	4076	c.4032C>T	c.(4030-4032)tcC>tcT	p.S1344S	AC074011.2_ENST00000431376.1_RNA|PLB1_ENST00000541605.1_Silent_p.S309S|PLB1_ENST00000422425.2_Silent_p.S1333S	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1344	4 X 308-326 AA approximate repeats.				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)					CCTTCTTCTCCGAGGACTGTT	0.582													C|||	628	0.125399	0.3646	0.0504	5008	,	,		17064	0.0516		0.0417	False		,,,				2504	0.0174				p.S1344S		Atlas-SNP	.											PLB1_ENST00000422425,NS,carcinoma,+1,2	PLB1	255	2	0			c.C4032T						PASS	.	C	,	1376,3030	457.5+/-351.6	200,976,1027	160.0	150.0	154.0		3999,4032	-6.1	0.8	2	dbSNP_107	154	171,8429	78.4+/-141.0	3,165,4132	no	coding-synonymous,coding-synonymous	PLB1	NM_001170585.1,NM_153021.4	,	203,1141,5159	TT,TC,CC		1.9884,31.2301,11.8945	,	1333/1448,1344/1459	28855840	1547,11459	2203	4300	6503	SO:0001819	synonymous_variant	151056	exon56			CTTCTCCGAGGAC		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.4032C>T	2.37:g.28855840C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	37	CCDS33168.1	232|232	0.10622710622710622|0.10622710622710622	161|161	0.32723577235772355|0.32723577235772355	18|18	0.049723756906077346|0.049723756906077346	34|34	0.05944055944055944|0.05944055944055944	19|19	0.025065963060686015|0.025065963060686015	C|C	10.40|10.40	1.338375|1.338375	0.24253|0.24253	0.312301|0.312301	0.019884|0.019884	ENSG00000163803|ENSG00000163803	ENST00000404858|ENST00000436775	.|.	.|.	.|.	5.77|5.77	-6.11|-6.11	0.02131|0.02131	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999999772039|0.999999999772039	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.42849|.	-0.9427|.	3|.	.|.	.|.	.|.	-24.6435|-24.6435	1.4277|1.4277	0.02327|0.02327	0.2139:0.1088:0.231:0.4463|0.2139:0.1088:0.231:0.4463	rs3752902;rs3752902|rs3752902;rs3752902	.|.	.|.	.|.	L|X	1332|72	.|.	.|.	P|R	+|+	2|1	0|2	PLB1|PLB1	28709344|28709344	0.003000|0.003000	0.15002|0.15002	0.797000|0.797000	0.32132|0.32132	0.951000|0.951000	0.60555|0.60555	-2.494000|-2.494000	0.00972|0.00972	-0.937000|-0.937000	0.03719|0.03719	-0.224000|-0.224000	0.12420|0.12420	CCG|CGA	C|0.881;T|0.119	0.119	strong		0.582	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
CRELD2	79174	hgsc.bcm.edu	37	22	50315363	50315363	+	Missense_Mutation	SNP	C	C	A	rs8139422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50315363C>A	ENST00000328268.4	+	5	620	c.546C>A	c.(544-546)gaC>gaA	p.D182E	CRELD2_ENST00000403427.3_Missense_Mutation_p.D182E|CRELD2_ENST00000404488.3_Missense_Mutation_p.D182E|CRELD2_ENST00000444954.1_3'UTR|CRELD2_ENST00000407217.3_Missense_Mutation_p.D182E	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	182			D -> E (in dbSNP:rs8139422).			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)		ACTGCATGGACGGCTACTTCA	0.677													C|||	1012	0.202077	0.5545	0.0634	5008	,	,		18641	0.0744		0.0288	False		,,,				2504	0.1339				p.D182E		Atlas-SNP	.											CRELD2_ENST00000404488,NS,lymphoid_neoplasm,+2,6	CRELD2	57	6	0			c.C546A						PASS	.	C	GLU/ASP,GLU/ASP	2180,2226	580.3+/-385.1	539,1102,562	84.0	87.0	86.0		546,546	-8.2	0.0	22	dbSNP_116	86	271,8329	102.7+/-163.9	3,265,4032	yes	missense,missense	CRELD2	NM_001135101.1,NM_024324.3	45,45	542,1367,4594	AA,AC,CC		3.1512,49.478,18.8451	possibly-damaging,possibly-damaging	182/403,182/354	50315363	2451,10555	2203	4300	6503	SO:0001583	missense	79174	exon5			CATGGACGGCTAC	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.546C>A	22.37:g.50315363C>A	ENSP00000332223:p.Asp182Glu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_024324	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Missense_Mutation	SNP	ENST00000328268.4	37	CCDS14082.1	360	0.16483516483516483	279	0.5670731707317073	23	0.06353591160220995	39	0.06818181818181818	19	0.025065963060686015	C	5.672	0.308604	0.10733	0.49478	0.031512	ENSG00000184164	ENST00000450207;ENST00000404488;ENST00000328268;ENST00000407217;ENST00000403427	D;T;D;D;D	0.97553	-4.43;0.65;-2.26;-2.26;-2.26	4.12	-8.23	0.01033	EGF-like, laminin (1);Growth factor, receptor (1);	0.282585	0.37053	N	0.002272	T	0.00012	0.0000	L	0.41632	1.29	0.44771	P	0.0022259999999999502	P;P;P;P;P;P	0.51933	0.949;0.79;0.902;0.794;0.816;0.87	P;P;P;B;B;B	0.50162	0.601;0.633;0.447;0.234;0.18;0.357	T	0.48525	-0.9028	9	0.06236	T	0.91	.	15.8268	0.78711	0.0:0.1287:0.0874:0.7838	rs8139422;rs8139422	182;182;182;182;182;182	Q6UXH1-2;Q6UXH1-5;Q6UXH1-4;A5GZA6;Q6UXH1;Q6UXH1-3	.;.;.;.;CREL2_HUMAN;.	E	182	ENSP00000387769:D182E;ENSP00000383938:D182E;ENSP00000332223:D182E;ENSP00000386034:D182E;ENSP00000384111:D182E	ENSP00000332223:D182E	D	+	3	2	CRELD2	48701367	0.000000	0.05858	0.001000	0.08648	0.607000	0.37147	-2.992000	0.00657	-3.063000	0.00256	-1.648000	0.00760	GAC	C|0.811;A|0.189	0.189	strong		0.677	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
HSD3B2	3284	hgsc.bcm.edu	37	1	119962118	119962118	+	Missense_Mutation	SNP	G	G	A	rs4986954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:119962118G>A	ENST00000543831.1	+	3	469	c.220G>A	c.(220-222)Gac>Aac	p.D74N	HSD3B2_ENST00000471656.1_3'UTR|HSD3B2_ENST00000369416.3_Missense_Mutation_p.D74N	NM_001166120.1	NP_001159592.1	P26439	3BHS2_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	74			D -> N (in dbSNP:rs4986954).		androgen biosynthetic process (GO:0006702)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(19)|ovary(2)|skin(1)	27	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	Corticotropin(DB01285)|Medroxyprogesterone Acetate(DB00603)|Trilostane(DB01108)	AGCCTGCCAGGACGTCTCGGT	0.498													G|||	15	0.00299521	0.0113	0.0	5008	,	,		20071	0.0		0.0	False		,,,				2504	0.0				p.D74N		Atlas-SNP	.											.	HSD3B2	48	.	0			c.G220A						PASS	.	G	ASN/ASP,ASN/ASP	39,4367		1,37,2165	112.0	89.0	97.0		220,220	3.9	0.9	1	dbSNP_111	97	0,8600		0,0,4300	no	missense,missense	HSD3B2	NM_000198.3,NM_001166120.1	23,23	1,37,6465	AA,AG,GG		0.0,0.8852,0.2999	benign,benign	74/373,74/373	119962118	39,12967	2203	4300	6503	SO:0001583	missense	3284	exon3			TGCCAGGACGTCT	BC038419	CCDS902.1	1p12	2014-06-03			ENSG00000203859	ENSG00000203859	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5218	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 2"""	613890				1363812, 19027726	Standard	NM_000198		Approved	SDR11E2	uc001eht.3	P26439	OTTHUMG00000012526	ENST00000543831.1:c.220G>A	1.37:g.119962118G>A	ENSP00000445122:p.Asp74Asn	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	196	88	0.44898	NM_001166120	A2RRA5|Q16010|Q53GD4|Q6AI10|Q6LDB9|Q99890|Q9UD08	Missense_Mutation	SNP	ENST00000543831.1	37	CCDS902.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	-	14.37	2.514988	0.44763	0.008852	0.0	ENSG00000203859	ENST00000543831;ENST00000433745;ENST00000369416	D;D;D	0.88509	-2.39;-2.39;-2.39	3.93	3.93	0.45458	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.054278	0.64402	D	0.000001	T	0.81969	0.4935	L	0.41906	1.305	0.30554	N	0.765177	P;P	0.36874	0.572;0.464	B;P	0.45913	0.173;0.497	T	0.77305	-0.2637	9	.	.	.	-17.182	13.5239	0.61584	0.0:0.0:1.0:0.0	rs4986954;rs52821087;rs4986954	74;74	P26439-2;P26439	.;3BHS2_HUMAN	N	74	ENSP00000445122:D74N;ENSP00000388292:D74N;ENSP00000358424:D74N	.	D	+	1	0	HSD3B2	119763641	1.000000	0.71417	0.934000	0.37439	0.009000	0.06853	7.003000	0.76310	1.943000	0.56356	0.298000	0.19748	GAC	G|0.996;A|0.004	0.004	strong		0.498	HSD3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034994.1	NM_000198	
COG5	10466	hgsc.bcm.edu	37	7	107002806	107002806	+	Missense_Mutation	SNP	A	A	G	rs2269970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107002806A>G	ENST00000347053.3	-	9	1038	c.988T>C	c.(988-990)Ttc>Ctc	p.F330L	COG5_ENST00000297135.3_Missense_Mutation_p.F330L|COG5_ENST00000393603.2_Missense_Mutation_p.F330L	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	330			F -> L (in dbSNP:rs2269970). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9792665}.		intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.F330L(1)		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						TTGGTCCAGAATGAGGCACGC	0.393													G|||	3247	0.648363	0.9803	0.5058	5008	,	,		16792	0.6429		0.5417	False		,,,				2504	0.4162				p.F330L		Atlas-SNP	.											COG5,NS,carcinoma,0,1	COG5	78	1	1	Substitution - Missense(1)	stomach(1)	c.T988C						PASS	.	G	LEU/PHE,LEU/PHE,LEU/PHE	3973,433	211.8+/-231.9	1784,405,14	83.0	82.0	82.0		988,988,988	4.8	0.7	7	dbSNP_100	82	4542,4058	559.6+/-387.4	1211,2120,969	yes	missense,missense,missense	COG5	NM_001161520.1,NM_006348.3,NM_181733.2	22,22,22	2995,2525,983	GG,GA,AA		47.186,9.8275,34.5302	benign,benign,benign	330/824,330/861,330/840	107002806	8515,4491	2203	4300	6503	SO:0001583	missense	10466	exon9			TCCAGAATGAGGC	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.988T>C	7.37:g.107002806A>G	ENSP00000334703:p.Phe330Leu	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	239	238	0.995816	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	1465	0.6707875457875457	478	0.9715447154471545	195	0.5386740331491713	370	0.6468531468531469	422	0.5567282321899736	G	7.813	0.716216	0.15306	0.901725	0.52814	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.27402	1.67;1.67;1.67	5.69	4.8	0.61643	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00013	-2.945	0.43471	P	0.0043159999999999865	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40869	-0.9540	9	0.02654	T	1	-5.2259	13.0763	0.59089	0.1317:0.0:0.8683:0.0	rs2269970;rs10377771;rs17351107;rs52812313;rs59416115;rs2269970	330;330	Q9UP83;Q9UP83-2	COG5_HUMAN;.	L	330	ENSP00000334703:F330L;ENSP00000297135:F330L;ENSP00000377228:F330L	ENSP00000297135:F330L	F	-	1	0	COG5	106790042	1.000000	0.71417	0.729000	0.30791	0.445000	0.32107	6.030000	0.70903	0.865000	0.35603	-0.119000	0.15052	TTC	A|0.339;G|0.661	0.661	strong		0.393	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
DRC7	84229	hgsc.bcm.edu	37	16	57732012	57732012	+	Missense_Mutation	SNP	G	G	A	rs55645458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57732012G>A	ENST00000360716.3	+	3	372	c.151G>A	c.(151-153)Gac>Aac	p.D51N	RP11-405F3.4_ENST00000563062.1_RNA|CCDC135_ENST00000394337.4_Missense_Mutation_p.D51N|CCDC135_ENST00000336825.8_Missense_Mutation_p.D51N			Q8IY82	CC135_HUMAN		51			D -> N (in dbSNP:rs55645458).		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						GACGCTCAGAGACCTGGAGAA	0.607													g|||	54	0.0107827	0.0	0.0072	5008	,	,		18158	0.0		0.0398	False		,,,				2504	0.0092				p.D51N		Atlas-SNP	.											.	CCDC135	97	.	0			c.G151A						PASS	.	G	ASN/ASP	47,4349	50.2+/-85.5	0,47,2151	100.0	91.0	94.0		151	4.2	1.0	16	dbSNP_129	94	422,8178	130.8+/-188.7	10,402,3888	yes	missense	CCDC135	NM_032269.5	23	10,449,6039	AA,AG,GG		4.907,1.0692,3.6088	possibly-damaging	51/875	57732012	469,12527	2198	4300	6498	SO:0001583	missense	84229	exon2			CTCAGAGACCTGG																												ENST00000360716.3:c.151G>A	16.37:g.57732012G>A	ENSP00000353942:p.Asp51Asn	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	35	0.016025641025641024	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	32	0.04221635883905013	G	15.87	2.961520	0.53400	0.010692	0.04907	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.10573	3.1;2.86;3.1	4.18	4.18	0.49190	.	0.477501	0.21157	N	0.079231	T	0.03434	0.0099	M	0.63843	1.955	0.32197	N	0.578329	D;D	0.59357	0.985;0.967	P;P	0.54270	0.747;0.718	T	0.00899	-1.1522	10	0.62326	D	0.03	-34.8223	12.3248	0.55005	0.0:0.0:1.0:0.0	rs55645458	51;51	Q8IY82-2;Q8IY82	.;CC135_HUMAN	N	51	ENSP00000377869:D51N;ENSP00000338938:D51N;ENSP00000353942:D51N	ENSP00000338938:D51N	D	+	1	0	CCDC135	56289513	0.994000	0.37717	0.997000	0.53966	0.030000	0.12068	2.049000	0.41288	2.613000	0.88420	0.549000	0.68633	GAC	G|0.971;A|0.029	0.029	strong		0.607	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
PROKR2	128674	hgsc.bcm.edu	37	20	5283051	5283051	+	Missense_Mutation	SNP	G	G	A	rs148868355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5283051G>A	ENST00000217270.3	-	2	789	c.790C>T	c.(790-792)Cgc>Tgc	p.R264C	PROKR2_ENST00000546004.1_Missense_Mutation_p.R264C	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	264					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						AGCCGCTTGCGAATCTGCTCC	0.612										HNSCC(71;0.22)			G|||	4	0.000798722	0.003	0.0	5008	,	,		20081	0.0		0.0	False		,,,				2504	0.0				p.R264C		Atlas-SNP	.											.	PROKR2	90	.	0			c.C790T						PASS	.	G	CYS/ARG	8,4398	14.3+/-33.2	0,8,2195	53.0	49.0	50.0		790	5.1	1.0	20	dbSNP_134	50	0,8600		0,0,4300	yes	missense	PROKR2	NM_144773.2	180	0,8,6495	AA,AG,GG		0.0,0.1816,0.0615	probably-damaging	264/385	5283051	8,12998	2203	4300	6503	SO:0001583	missense	128674	exon2			GCTTGCGAATCTG	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.790C>T	20.37:g.5283051G>A	ENSP00000217270:p.Arg264Cys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_144773	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Missense_Mutation	SNP	ENST00000217270.3	37	CCDS13089.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.99	3.522846	0.64747	0.001816	0.0	ENSG00000101292	ENST00000546004;ENST00000217270	T;T	0.38401	1.14;1.14	5.05	5.05	0.67936	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.64713	0.2623	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71069	-0.4699	10	0.72032	D	0.01	.	15.9064	0.79433	0.0:0.0:1.0:0.0	.	264	Q8NFJ6	PKR2_HUMAN	C	264	ENSP00000440790:R264C;ENSP00000217270:R264C	ENSP00000217270:R264C	R	-	1	0	PROKR2	5231051	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	2.754000	0.47532	2.370000	0.80446	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.612	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773	
MYO16	23026	hgsc.bcm.edu	37	13	109661359	109661359	+	Missense_Mutation	SNP	C	C	G	rs3825491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	65	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	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	
KCNK10	54207	hgsc.bcm.edu	37	14	88693725	88693725	+	Silent	SNP	G	G	C	rs2277524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:88693725G>C	ENST00000340700.5	-	4	1111	c.660C>G	c.(658-660)gtC>gtG	p.V220V	KCNK10_ENST00000319231.5_Silent_p.V225V|KCNK10_ENST00000312350.5_Silent_p.V225V	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	220					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	47						TCACTCGAAAGACCTTCTCCA	0.448													G|||	1713	0.342053	0.4501	0.2032	5008	,	,		18025	0.4405		0.2187	False		,,,				2504	0.32				p.V225V		Atlas-SNP	.											.	KCNK10	273	.	0			c.C675G						PASS	.	G	,,	1783,2623	526.8+/-372.0	353,1077,773	118.0	114.0	115.0		660,675,675	3.3	1.0	14	dbSNP_100	115	2049,6551	356.4+/-330.3	254,1541,2505	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNK10	NM_021161.4,NM_138317.2,NM_138318.2	,,	607,2618,3278	CC,CG,GG		23.8256,40.4675,29.4633	,,	220/539,225/544,225/544	88693725	3832,9174	2203	4300	6503	SO:0001819	synonymous_variant	54207	exon4			TCGAAAGACCTTC	AF279890	CCDS9880.1, CCDS9881.1, CCDS9882.1	14q31	2014-06-12						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6273	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 97"""	605873				10880510, 16382106	Standard	NM_021161		Approved	K2p10.1, TREK-2, TREK2, PPP1R97	uc001xwn.3	P57789		ENST00000340700.5:c.660C>G	14.37:g.88693725G>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Silent	SNP	ENST00000340700.5	37	CCDS9880.1																																																																																			G|0.690;C|0.310	0.310	strong		0.448	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161	
AKR1C2	1646	hgsc.bcm.edu	37	10	5043749	5043749	+	Missense_Mutation	SNP	G	G	A	rs147648222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5043749G>A	ENST00000380753.4	-	2	396	c.209C>T	c.(208-210)gCa>gTa	p.A70V	AKR1C2_ENST00000407674.1_Missense_Mutation_p.A70V|AKR1C2_ENST00000455190.1_Missense_Mutation_p.A70V|AKR1C2_ENST00000421196.3_Missense_Mutation_p.A70V	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	70					cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	ACTGCCATCTGCAATCTTGCT	0.443													G|||	17	0.00339457	0.0121	0.0	5008	,	,		21154	0.0		0.001	False		,,,				2504	0.0				p.A70V		Atlas-SNP	.											.	AKR1C2	68	.	0			c.C209T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	44,4362	48.2+/-83.0	1,42,2160	132.0	114.0	120.0		209,209,209	-1.2	0.9	10	dbSNP_134	120	0,8596		0,0,4298	no	missense,missense,missense	AKR1C2	NM_001135241.1,NM_001354.4,NM_205845.1	64,64,64	1,42,6458	AA,AG,GG		0.0,0.9986,0.3384	benign,benign,benign	70/140,70/324,70/324	5043749	44,12958	2203	4298	6501	SO:0001583	missense	1646	exon4			CCATCTGCAATCT	L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1.3.1.20, 1.1.1.213	"""Aldo-keto reductases"""	385	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III"""	600450	"""aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)"", ""testicular 17,20-desmolase deficiency"""	DDH2, TDD		9716498, 21802064	Standard	NM_001354		Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.209C>T	10.37:g.5043749G>A	ENSP00000370129:p.Ala70Val	Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	328	172	0.52439	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Missense_Mutation	SNP	ENST00000380753.4	37	CCDS7062.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	8.905	0.957221	0.18507	0.009986	0.0	ENSG00000151632	ENST00000380753;ENST00000421196;ENST00000407674;ENST00000455190	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	2.35	-1.18	0.09617	NADP-dependent oxidoreductase domain (3);	0.225703	0.28730	N	0.014335	T	0.33177	0.0854	M	0.65498	2.005	0.20821	N	0.999846	B;B;B	0.30526	0.283;0.128;0.063	B;B;B	0.30646	0.118;0.071;0.057	T	0.36744	-0.9735	10	0.62326	D	0.03	.	9.2164	0.37351	0.0:0.0:0.4586:0.5414	.	70;70;70	B4DKR9;B4DK69;P52895	.;.;AK1C2_HUMAN	V	70	ENSP00000370129:A70V;ENSP00000392694:A70V;ENSP00000385221:A70V;ENSP00000408440:A70V	ENSP00000370129:A70V	A	-	2	0	AKR1C2	5033749	0.876000	0.30132	0.896000	0.35187	0.326000	0.28443	3.023000	0.49666	-0.272000	0.09259	0.205000	0.17691	GCA	G|0.998;A|0.002	0.002	strong		0.443	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354	
HIP1R	9026	hgsc.bcm.edu	37	12	123341199	123341199	+	Missense_Mutation	SNP	A	A	C	rs7972242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123341199A>C	ENST00000253083.4	+	17	1671	c.1546A>C	c.(1546-1548)Aag>Cag	p.K516Q		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	516			K -> Q (in dbSNP:rs7972242).		receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		CCAGCTGGAGAAGCTCAAGAG	0.662													A|||	203	0.0405351	0.146	0.013	5008	,	,		15928	0.0		0.001	False		,,,				2504	0.0				p.K516Q		Atlas-SNP	.											.	HIP1R	68	.	0			c.A1546C						PASS	.	A	GLN/LYS	542,3854		30,482,1686	29.0	33.0	32.0		1546	2.2	1.0	12	dbSNP_116	32	7,8587		0,7,4290	yes	missense	HIP1R	NM_003959.1	53	30,489,5976	CC,CA,AA		0.0815,12.3294,4.2263	benign	516/1069	123341199	549,12441	2198	4297	6495	SO:0001583	missense	9026	exon17			CTGGAGAAGCTCA	AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.1546A>C	12.37:g.123341199A>C	ENSP00000253083:p.Lys516Gln	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	A	9.125	1.009956	0.19277	0.123294	8.15E-4	ENSG00000130787	ENST00000253083	T	0.14766	2.48	4.77	2.24	0.28232	.	0.103731	0.64402	D	0.000003	T	0.00073	0.0002	N	0.20483	0.58	0.32676	P	0.516181	B;B;B	0.14012	0.0;0.0;0.009	B;B;B	0.09377	0.001;0.004;0.004	T	0.38436	-0.9661	9	0.16420	T	0.52	-44.0738	5.6228	0.17467	0.5893:0.3098:0.101:0.0	rs7972242;rs7972242	516;516;504	O75146;Q6NXG8;B3KQW8	HIP1R_HUMAN;.;.	Q	516	ENSP00000253083:K516Q	ENSP00000253083:K516Q	K	+	1	0	HIP1R	121907152	0.990000	0.36364	0.998000	0.56505	0.681000	0.39784	0.484000	0.22308	0.682000	0.31407	0.459000	0.35465	AAG	A|0.954;C|0.046	0.046	strong		0.662	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959	
PCDHB12	56124	hgsc.bcm.edu	37	5	140590766	140590766	+	Missense_Mutation	SNP	A	A	G	rs2910006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140590766A>G	ENST00000239450.2	+	1	2476	c.2287A>G	c.(2287-2289)Aag>Gag	p.K763E	PCDHB13_ENST00000341948.4_5'Flank|PCDHB12_ENST00000541609.1_Missense_Mutation_p.K426E	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	763			K -> E (in dbSNP:rs2910006).		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)			CAGGTCAAATAAGTTCAAATT	0.502													G|||	1949	0.389177	0.7511	0.3386	5008	,	,		16246	0.1339		0.3211	False		,,,				2504	0.2689				p.K763E		Atlas-SNP	.											PCDHB12,tonsil,carcinoma,0,1	PCDHB12	179	1	0			c.A2287G						PASS	.	G	GLU/LYS	3093,1313	441.4+/-346.4	1082,929,192	74.0	75.0	75.0		2287	3.1	0.0	5	dbSNP_101	75	3042,5558	661.9+/-401.9	540,1962,1798	yes	missense	PCDHB12	NM_018932.3	56	1622,2891,1990	GG,GA,AA		35.3721,29.8003,47.1705	benign	763/796	140590766	6135,6871	2203	4300	6503	SO:0001583	missense	56124	exon1			TCAAATAAGTTCA	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.2287A>G	5.37:g.140590766A>G	ENSP00000239450:p.Lys763Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	828	0.3791208791208791	375	0.7621951219512195	124	0.3425414364640884	78	0.13636363636363635	251	0.3311345646437995	G	3.390	-0.124597	0.06795	0.701997	0.353721	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.12039	2.72;2.72	3.13	3.13	0.36017	.	.	.	.	.	T	0.00012	0.0000	N	0.00000	-4.025	0.46678	P	8.479999999999599E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.41251	-0.9519	8	0.02654	T	1	.	9.4973	0.38995	0.1133:0.0:0.8867:0.0	rs2910006;rs3776095;rs17844605;rs60542532;rs2910006	763	Q9Y5F1	PCDBC_HUMAN	E	426;763;383	ENSP00000440199:K426E;ENSP00000239450:K763E	ENSP00000239450:K763E	K	+	1	0	PCDHB12	140570950	1.000000	0.71417	0.002000	0.10522	0.009000	0.06853	6.496000	0.73670	0.422000	0.26005	-0.684000	0.03749	AAG	A|0.559;G|0.441	0.441	strong		0.502	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
PABPC1	26986	hgsc.bcm.edu	37	8	101727766	101727766	+	Silent	SNP	T	T	C	rs201406152		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101727766T>C	ENST00000318607.5	-	4	1695	c.567A>G	c.(565-567)gaA>gaG	p.E189E	PABPC1_ENST00000519004.1_Silent_p.E144E|PABPC1_ENST00000522387.1_Silent_p.E157E|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	189	CSDE1-binding.				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.E189E(5)		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)			CATTGGTGAATTCTTTTGCCC	0.343																																					p.E189E		Atlas-SNP	.											PABPC1,colon,carcinoma,-2,6	PABPC1	76	6	5	Substitution - coding silent(5)	kidney(5)	c.A567G						scavenged	.						98.0	87.0	91.0					8																	101727766		2203	4300	6503	SO:0001819	synonymous_variant	26986	exon4			GGTGAATTCTTTT	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.567A>G	8.37:g.101727766T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	138	6	0.0434783	NM_002568	Q15097|Q93004	Silent	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.36|10.36	1.329390|1.329390	0.24167|0.24167	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519596;ENST00000523555|ENST00000519100	.|.	.|.	.|.	5.03|5.03	-2.16|-2.16	0.07080|0.07080	.|.	.|.	.|.	.|.	.|.	T|T	0.55737|0.55737	0.1939|0.1939	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.53620|0.53620	-0.8413|-0.8413	4|4	.|.	.|.	.|.	.|.	10.9103|10.9103	0.47106|0.47106	0.0:0.219:0.0:0.781|0.0:0.219:0.0:0.781	.|.	.|.	.|.	.|.	V|S	22;136|61	.|.	.|.	I|N	-|-	1|2	0|0	PABPC1|PABPC1	101796942|101796942	0.676000|0.676000	0.27567|0.27567	0.993000|0.993000	0.49108|0.49108	0.994000|0.994000	0.84299|0.84299	-0.104000|-0.104000	0.10923|0.10923	-0.219000|-0.219000	0.10003|0.10003	-0.292000|-0.292000	0.09595|0.09595	ATT|AAT	T|0.998;C|0.002	0.002	weak		0.343	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
METTL21B	25895	hgsc.bcm.edu	37	12	58174306	58174306	+	Silent	SNP	T	T	C	rs923829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:58174306T>C	ENST00000300209.8	+	3	683	c.558T>C	c.(556-558)caT>caC	p.H186H	TSFM_ENST00000550559.1_5'Flank|TSFM_ENST00000543727.1_5'Flank|TSFM_ENST00000350762.5_5'Flank|TSFM_ENST00000548851.1_5'Flank|METTL21B_ENST00000551420.1_Silent_p.H5H|RP11-571M6.15_ENST00000553083.1_Intron|TSFM_ENST00000454289.3_5'Flank|TSFM_ENST00000540550.1_5'Flank|TSFM_ENST00000323833.8_5'Flank|RP11-571M6.15_ENST00000471530.1_Intron|METTL21B_ENST00000333012.5_3'UTR	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B	186						cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						GAAAGGAGCATGGGACAGAGA	0.567													t|||	2024	0.404153	0.2141	0.2767	5008	,	,		21672	0.6468		0.3191	False		,,,				2504	0.589				p.H186H		Atlas-SNP	.											.	METTL21B	16	.	0			c.T558C						PASS	.	T	,	1018,3388	377.5+/-322.5	116,786,1301	69.0	60.0	63.0		558,	-2.5	1.0	12	dbSNP_86	63	2755,5845	438.5+/-358.9	456,1843,2001	no	coding-synonymous,utr-3	METTL21B	NM_015433.2,NM_206914.1	,	572,2629,3302	CC,CT,TT		32.0349,23.1049,29.0097	,	186/227,	58174306	3773,9233	2203	4300	6503	SO:0001819	synonymous_variant	25895	exon3			GGAGCATGGGACA	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"""family with sequence similarity 119, member B"""	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459	ENST00000300209.8:c.558T>C	12.37:g.58174306T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_015433	Q9H749|Q9Y3W2	Silent	SNP	ENST00000300209.8	37	CCDS8957.1																																																																																			T|0.672;C|0.328	0.328	strong		0.567	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433	
TRIO	7204	hgsc.bcm.edu	37	5	14316642	14316642	+	Silent	SNP	G	G	A	rs55920001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:14316642G>A	ENST00000344204.4	+	9	1545	c.1521G>A	c.(1519-1521)tcG>tcA	p.S507S	TRIO_ENST00000509967.2_Silent_p.S458S|TRIO_ENST00000537187.1_Silent_p.S507S	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	507					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)					ATGGGAAGTCGCTCCTTGACA	0.557													G|||	182	0.0363419	0.0484	0.036	5008	,	,		19551	0.0278		0.0388	False		,,,				2504	0.0266				p.S507S		Atlas-SNP	.											.	TRIO	305	.	0			c.G1521A						PASS	.	G		241,4165	141.5+/-176.9	10,221,1972	69.0	61.0	64.0		1521	-10.8	0.3	5	dbSNP_129	64	354,8246	119.7+/-179.0	7,340,3953	no	coding-synonymous	TRIO	NM_007118.2		17,561,5925	AA,AG,GG		4.1163,5.4698,4.5748		507/3098	14316642	595,12411	2203	4300	6503	SO:0001819	synonymous_variant	7204	exon9			GAAGTCGCTCCTT	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.1521G>A	5.37:g.14316642G>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	250	116	0.464	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																			G|0.957;A|0.043	0.043	strong		0.557	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
FILIP1	27145	hgsc.bcm.edu	37	6	76022541	76022541	+	Missense_Mutation	SNP	G	G	A	rs34807169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:76022541G>A	ENST00000237172.7	-	5	3337	c.3007C>T	c.(3007-3009)Ccc>Tcc	p.P1003S	FILIP1_ENST00000393004.2_Missense_Mutation_p.P1003S|FILIP1_ENST00000370020.1_Missense_Mutation_p.P904S|FILIP1_ENST00000498523.1_5'UTR	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1003			P -> S (in dbSNP:rs34807169).							breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GGGGATGTGGGCCTGTCTGCA	0.502													G|||	151	0.0301518	0.1112	0.0058	5008	,	,		19431	0.0		0.0	False		,,,				2504	0.0				p.P1003S		Atlas-SNP	.											.	FILIP1	173	.	0			c.C3007T						PASS	.	G	SER/PRO	365,4041	187.1+/-213.8	15,335,1853	117.0	111.0	113.0		3007	5.1	1.0	6	dbSNP_126	113	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FILIP1	NM_015687.2	74	15,340,6148	AA,AG,GG		0.0581,8.2842,2.8448	probably-damaging	1003/1214	76022541	370,12636	2203	4300	6503	SO:0001583	missense	27145	exon5			ATGTGGGCCTGTC	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.3007C>T	6.37:g.76022541G>A	ENSP00000237172:p.Pro1003Ser	Somatic	241	1	0.00414938		WXS	Illumina HiSeq	Phase_I	237	109	0.459916	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	60	0.027472527472527472	57	0.11585365853658537	3	0.008287292817679558	0	0.0	0	0.0	G	15.74	2.922149	0.52653	0.082842	5.81E-4	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.19532	2.14;2.14;2.15	6.03	5.14	0.70334	.	0.273243	0.42548	D	0.000686	T	0.11452	0.0279	L	0.53249	1.67	0.53688	D	0.999977	B;B;B	0.31680	0.335;0.073;0.12	B;B;B	0.32624	0.058;0.103;0.149	T	0.05115	-1.0905	10	0.16420	T	0.52	-8.9487	17.2101	0.86928	0.0:0.1259:0.8741:0.0	rs34807169	1003;1003;1003	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	S	1003;1003;904	ENSP00000376728:P1003S;ENSP00000237172:P1003S;ENSP00000359037:P904S	ENSP00000237172:P1003S	P	-	1	0	FILIP1	76079261	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.086000	0.57664	1.518000	0.48934	0.655000	0.94253	CCC	G|0.973;A|0.027	0.027	strong		0.502	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179	
GNG8	94235	hgsc.bcm.edu	37	19	47137459	47137459	+	Silent	SNP	C	C	T	rs12974613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	84	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	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		
KIAA1024	23251	hgsc.bcm.edu	37	15	79748603	79748603	+	Silent	SNP	C	C	T	rs7183867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	143	0	0		WXS	Illumina HiSeq	Phase_I	144	142	0.986111	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	
FAM186B	84070	hgsc.bcm.edu	37	12	49993678	49993678	+	Missense_Mutation	SNP	C	C	T	rs52824916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49993678C>T	ENST00000257894.2	-	4	1906	c.1745G>A	c.(1744-1746)cGg>cAg	p.R582Q	FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.R492Q|PRPF40B_ENST00000508736.1_3'UTR	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	582						protein complex (GO:0043234)				breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AGATTGGGTCCGGCTTGGGGC	0.577													C|||	567	0.113219	0.2012	0.0922	5008	,	,		18406	0.0823		0.0885	False		,,,				2504	0.0665				p.R582Q		Atlas-SNP	.											.	FAM186B	72	.	0			c.G1745A						PASS	.	C	GLN/ARG	765,3641	313.0+/-292.9	62,641,1500	92.0	83.0	86.0		1745	1.5	0.0	12	dbSNP_128	86	721,7879	175.8+/-225.7	30,661,3609	yes	missense	FAM186B	NM_032130.2	43	92,1302,5109	TT,TC,CC		8.3837,17.3627,11.4255	possibly-damaging	582/894	49993678	1486,11520	2203	4300	6503	SO:0001583	missense	84070	exon4			TGGGTCCGGCTTG	AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 25"""	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.1745G>A	12.37:g.49993678C>T	ENSP00000257894:p.Arg582Gln	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	149	64	0.42953	NM_032130	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	37	CCDS8788.1	250	0.11446886446886446	103	0.20934959349593496	44	0.12154696132596685	35	0.06118881118881119	68	0.08970976253298153	C	10.34	1.324055	0.24080	0.173627	0.083837	ENSG00000135436	ENST00000544141;ENST00000532262;ENST00000257894	T;T;T	0.13089	2.63;2.62;2.85	4.33	1.51	0.23008	.	0.417675	0.17762	N	0.162860	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B;B	0.31318	0.319;0.168	B;B	0.25405	0.06;0.048	T	0.30327	-0.9982	8	.	.	.	-12.2787	6.0347	0.19699	0.0:0.6777:0.0:0.3223	rs52824916	492;582	B4DZ15;Q8IYM0	.;F186B_HUMAN	Q	492;195;582	ENSP00000438569:R492Q;ENSP00000436995:R195Q;ENSP00000257894:R582Q	.	R	-	2	0	FAM186B	48279945	0.000000	0.05858	0.026000	0.17262	0.074000	0.17049	0.139000	0.16036	0.577000	0.29470	0.563000	0.77884	CGG	C|0.886;T|0.114	0.114	strong		0.577	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130	
PROSER1	80209	hgsc.bcm.edu	37	13	39587889	39587889	+	Silent	SNP	T	T	C	rs3751377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39587889T>C	ENST00000352251.3	-	11	2333	c.1500A>G	c.(1498-1500)ctA>ctG	p.L500L	PROSER1_ENST00000350125.3_Silent_p.L478L|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	500	Ser-rich.																TAAGAGAAGATAGTGAAGCCA	0.473													T|||	1117	0.223043	0.2458	0.1599	5008	,	,		21247	0.2183		0.162	False		,,,				2504	0.3047				p.L500L		Atlas-SNP	.											.	.	.	.	0			c.A1500G						PASS	.	T	,	1076,3330	390.5+/-327.7	117,842,1244	86.0	83.0	84.0		1500,1434	-10.5	0.0	13	dbSNP_107	84	1205,7395	244.4+/-273.7	90,1025,3185	no	coding-synonymous,coding-synonymous	PROSER1	NM_025138.3,NM_170719.2	,	207,1867,4429	CC,CT,TT		14.0116,24.4212,17.5381	,	500/945,478/923	39587889	2281,10725	2203	4300	6503	SO:0001819	synonymous_variant	80209	exon11			AGAAGATAGTGAA	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.1500A>G	13.37:g.39587889T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																			T|0.809;C|0.191	0.191	strong		0.473	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
TMCC3	57458	hgsc.bcm.edu	37	12	94976159	94976159	+	Silent	SNP	T	T	C	rs3747551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:94976159T>C	ENST00000261226.4	-	2	365	c.234A>G	c.(232-234)gtA>gtG	p.V78V	TMCC3_ENST00000551457.1_Silent_p.V47V	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	78						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						TCTGCTCTGTTACCTTTAGAA	0.478													T|||	1634	0.326278	0.2421	0.4092	5008	,	,		19343	0.3522		0.3231	False		,,,				2504	0.3579				p.V78V		Atlas-SNP	.											.	TMCC3	63	.	0			c.A234G						PASS	.	T		1146,3260	408.6+/-334.7	161,824,1218	191.0	184.0	186.0		234	-10.6	0.3	12	dbSNP_107	186	2938,5662	458.6+/-364.7	515,1908,1877	no	coding-synonymous	TMCC3	NM_020698.2		676,2732,3095	CC,CT,TT		34.1628,26.01,31.4009		78/478	94976159	4084,8922	2203	4300	6503	SO:0001819	synonymous_variant	57458	exon2			CTCTGTTACCTTT	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"""Transmembrane and coiled-coil domain containing"""	29199	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 3"""			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.234A>G	12.37:g.94976159T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	121	68	0.561983	NM_020698	Q8IWB2	Silent	SNP	ENST00000261226.4	37	CCDS31877.1																																																																																			T|0.673;C|0.327	0.327	strong		0.478	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
NID2	22795	hgsc.bcm.edu	37	14	52486850	52486850	+	Silent	SNP	G	G	A	rs8007166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:52486850G>A	ENST00000216286.5	-	13	2720	c.2721C>T	c.(2719-2721)tgC>tgT	p.C907C	NID2_ENST00000541773.1_Silent_p.C806C	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	907	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			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)					GAGTATTGTAGCAGGTAGCTG	0.463													g|||	144	0.028754	0.1051	0.0072	5008	,	,		18243	0.0		0.0	False		,,,				2504	0.0				p.C907C		Atlas-SNP	.											.	NID2	201	.	0			c.C2721T						PASS	.	G		345,4061	181.2+/-209.3	15,315,1873	127.0	110.0	115.0		2721	4.6	1.0	14	dbSNP_116	115	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	NID2	NM_007361.3		15,321,6167	AA,AG,GG		0.0698,7.8302,2.6988		907/1376	52486850	351,12655	2203	4300	6503	SO:0001819	synonymous_variant	22795	exon13			ATTGTAGCAGGTA	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.2721C>T	14.37:g.52486850G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	37	CCDS9706.1																																																																																			G|0.971;A|0.029	0.029	strong		0.463	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110492328	110492328	+	Missense_Mutation	SNP	A	A	C	rs140472257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110492328A>C	ENST00000378402.5	+	55	9391	c.9287A>C	c.(9286-9288)tAc>tCc	p.Y3096S		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3096	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GAATCTTCTTACAGAGAAGTT	0.348										HNSCC(38;0.096)			A|||	43	0.00858626	0.0303	0.0043	5008	,	,		17254	0.0		0.0	False		,,,				2504	0.0				p.Y3096S		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A9287C						PASS	.	A	SER/TYR	59,3605		0,59,1773	51.0	52.0	52.0		9287	3.8	0.2	8	dbSNP_134	52	0,8158		0,0,4079	yes	missense	PKHD1L1	NM_177531.4	144	0,59,5852	CC,CA,AA		0.0,1.6103,0.4991	benign	3096/4244	110492328	59,11763	1832	4079	5911	SO:0001583	missense	93035	exon55			CTTCTTACAGAGA	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.9287A>C	8.37:g.110492328A>C	ENSP00000367655:p.Tyr3096Ser	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	138	58	0.42029	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	A	8.551	0.875589	0.17395	0.016103	0.0	ENSG00000205038	ENST00000378402	D	0.85411	-1.98	5.01	3.83	0.44106	G8 domain (2);	0.589185	0.17371	N	0.176674	T	0.69557	0.3124	M	0.76574	2.34	0.22213	N	0.999281	B	0.20164	0.042	B	0.32022	0.139	T	0.69176	-0.5214	10	0.36615	T	0.2	.	10.3982	0.44214	0.8352:0.1648:0.0:0.0	.	3096	Q86WI1	PKHL1_HUMAN	S	3096	ENSP00000367655:Y3096S	ENSP00000367655:Y3096S	Y	+	2	0	PKHD1L1	110561504	0.951000	0.32395	0.236000	0.24074	0.176000	0.22953	3.178000	0.50879	0.840000	0.34995	-0.323000	0.08544	TAC	A|0.993;C|0.007	0.007	strong		0.348	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
N4BP2L2	10443	hgsc.bcm.edu	37	13	33110831	33110831	+	Missense_Mutation	SNP	C	C	T	rs149614093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33110831C>T	ENST00000267068.3	-	2	498	c.334G>A	c.(334-336)Gca>Aca	p.A112T	N4BP2L2_ENST00000399396.3_Intron|N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.A112T	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	112					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TCATCGTCTGCGGATACTAAT	0.413													T|||	8	0.00159744	0.0053	0.0014	5008	,	,		19703	0.0		0.0	False		,,,				2504	0.0				p.A112T		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.G334A						PASS	.	T	THR/ALA,	35,4371	822.9+/-416.5	0,35,2168	194.0	193.0	193.0		334,	-0.4	0.0	13	dbSNP_134	193	0,8600		0,0,4300	yes	missense,intron	N4BP2L2	NM_014887.2,NM_033111.3	58,	0,35,6468	TT,TC,CC		0.0,0.7944,0.2691	,	112/584,	33110831	35,12971	2203	4300	6503	SO:0001583	missense	10443	exon2			CGTCTGCGGATAC	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"""phosphonoformate immuno-associated protein 5"""	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.334G>A	13.37:g.33110831C>T	ENSP00000267068:p.Ala112Thr	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	192	85	0.442708	NM_014887	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	37	CCDS9346.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	0.982	-0.696861	0.03279	0.007944	0.0	ENSG00000244754	ENST00000446957;ENST00000505213;ENST00000267068	T;T;T	0.41400	1.0;1.0;1.0	5.09	-0.355	0.12587	.	.	.	.	.	T	0.07818	0.0196	N	0.00707	-1.245	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30297	-0.9983	9	0.15499	T	0.54	-16.1287	5.0255	0.14383	0.1598:0.4478:0.0:0.3924	.	112;112	D6R968;Q92802	.;N42L2_HUMAN	T	112	ENSP00000394239:A112T;ENSP00000423362:A112T;ENSP00000267068:A112T	ENSP00000267068:A112T	A	-	1	0	N4BP2L2	32008831	0.005000	0.15991	0.000000	0.03702	0.071000	0.16799	-0.142000	0.10311	-0.249000	0.09569	-0.360000	0.07572	GCA	C|0.998;T|0.002	0.002	strong		0.413	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887	
AHNAK2	113146	hgsc.bcm.edu	37	14	105413790	105413790	+	Silent	SNP	G	G	A	rs11848564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105413790G>A	ENST00000333244.5	-	7	8117	c.7998C>T	c.(7996-7998)tcC>tcT	p.S2666S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2666						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)			ACGCCTCGATGGACTCGCCTG	0.557													.|||	1755	0.350439	0.4584	0.3314	5008	,	,		19053	0.0804		0.4841	False		,,,				2504	0.3589				p.S2666S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C7998T						PASS	.	G		1906,2152		482,942,605	192.0	211.0	205.0		7998	-2.7	0.0	14	dbSNP_120	205	4098,4278		1012,2074,1102	no	coding-synonymous	AHNAK2	NM_138420.2		1494,3016,1707	AA,AG,GG		48.9255,46.969,48.287		2666/5796	105413790	6004,6430	2029	4188	6217	SO:0001819	synonymous_variant	113146	exon7			CTCGATGGACTCG	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.7998C>T	14.37:g.105413790G>A		Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	392	391	0.997449	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.610;A|0.390	0.390	strong		0.557	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
IFT140	9742	hgsc.bcm.edu	37	16	1614097	1614097	+	Silent	SNP	A	A	G	rs8048410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1614097A>G	ENST00000426508.2	-	17	2331	c.1968T>C	c.(1966-1968)agT>agC	p.S656S	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	656					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)				GCCGGGGCTCACTCTGGTCCC	0.592													G|||	2530	0.505192	0.7179	0.3934	5008	,	,		14960	0.5675		0.2982	False		,,,				2504	0.4458				p.S656S		Atlas-SNP	.											.	IFT140	128	.	0			c.T1968C						PASS	.	G		2832,1566	488.1+/-361.1	911,1010,278	53.0	62.0	59.0		1968	-6.0	0.4	16	dbSNP_116	59	2666,5934	684.2+/-403.9	413,1840,2047	no	coding-synonymous	IFT140	NM_014714.3		1324,2850,2325	GG,GA,AA		31.0,35.6071,42.2988		656/1463	1614097	5498,7500	2199	4300	6499	SO:0001819	synonymous_variant	9742	exon17			GGGCTCACTCTGG	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.1968T>C	16.37:g.1614097A>G		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	245	115	0.469388	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																			A|0.566;G|0.434	0.434	strong		0.592	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
KIAA1024	23251	hgsc.bcm.edu	37	15	79755604	79755604	+	Missense_Mutation	SNP	A	A	G	rs2297773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:79755604A>G	ENST00000305428.3	+	3	2569	c.2494A>G	c.(2494-2496)Att>Gtt	p.I832V		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	832			I -> V (in dbSNP:rs2297773).			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						TTCTTGGACCATTGAGGAGTA	0.627													A|||	1277	0.254992	0.4962	0.1282	5008	,	,		19903	0.1478		0.2107	False		,,,				2504	0.1748				p.I832V		Atlas-SNP	.											.	KIAA1024	146	.	0			c.A2494G						PASS	.	A	VAL/ILE	1877,2515	541.1+/-375.7	410,1057,729	107.0	96.0	100.0		2494	-10.6	0.0	15	dbSNP_100	100	1699,6887	311.7+/-310.5	164,1371,2758	yes	missense	KIAA1024	NM_015206.2	29	574,2428,3487	GG,GA,AA		19.788,42.7368,27.5543	benign	832/917	79755604	3576,9402	2196	4293	6489	SO:0001583	missense	23251	exon3			TGGACCATTGAGG	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.2494A>G	15.37:g.79755604A>G	ENSP00000307461:p.Ile832Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	546	0.25	238	0.483739837398374	63	0.17403314917127072	82	0.14335664335664336	163	0.21503957783641162	A	7.689	0.690574	0.15039	0.427368	0.19788	ENSG00000169330	ENST00000305428	T	0.40225	1.04	5.32	-10.6	0.00265	.	0.655502	0.15131	N	0.278850	T	0.00012	0.0000	L	0.28344	0.845	0.39727	P	0.028442999999999996	B	0.02656	0.0	B	0.06405	0.002	T	0.31420	-0.9944	8	.	.	.	.	9.3297	0.38014	0.2438:0.4982:0.258:0.0	rs2297773;rs60393750;rs2297773	832	Q9UPX6	K1024_HUMAN	V	832	ENSP00000307461:I832V	.	I	+	1	0	KIAA1024	77542659	1.000000	0.71417	0.001000	0.08648	0.849000	0.48306	1.624000	0.37018	-2.170000	0.00776	-0.313000	0.08912	ATT	A|0.733;G|0.267	0.267	strong		0.627	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
MUC17	140453	hgsc.bcm.edu	37	7	100677995	100677995	+	Missense_Mutation	SNP	A	A	G	rs149287079		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677995A>G	ENST00000306151.4	+	3	3362	c.3298A>G	c.(3298-3300)Agc>Ggc	p.S1100G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1100	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)					TAGTGAAGGAAGCACTCCACT	0.517																																					p.S1100G		Atlas-SNP	.											.	MUC17	804	.	0			c.A3298G						PASS	.						490.0	389.0	423.0					7																	100677995		2203	4300	6503	SO:0001583	missense	140453	exon3			GAAGGAAGCACTC	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.3298A>G	7.37:g.100677995A>G	ENSP00000302716:p.Ser1100Gly	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	385	54	0.14026	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	0.119	-1.127913	0.01770	.	.	ENSG00000169876	ENST00000306151	T	0.02552	4.25	0.693	-1.39	0.08997	.	.	.	.	.	T	0.01870	0.0059	L	0.29908	0.895	0.09310	N	1	B	0.27192	0.171	B	0.14023	0.01	T	0.46721	-0.9171	9	0.25751	T	0.34	.	2.8064	0.05429	0.5265:0.2609:0.2126:0.0	.	1100	Q685J3	MUC17_HUMAN	G	1100	ENSP00000302716:S1100G	ENSP00000302716:S1100G	S	+	1	0	MUC17	100464715	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-1.232000	0.02936	-1.186000	0.02713	-1.357000	0.01221	AGC	.	.	weak		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SYNE2	23224	hgsc.bcm.edu	37	14	64612845	64612845	+	Silent	SNP	C	C	T	rs11629287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64612845C>T	ENST00000344113.4	+	84	15755	c.15543C>T	c.(15541-15543)atC>atT	p.I5181I	SYNE2_ENST00000554584.1_Silent_p.I5098I|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.I1815I|SYNE2_ENST00000358025.3_Silent_p.I5181I|SYNE2_ENST00000357395.3_Silent_p.I1566I|SYNE2_ENST00000394768.2_Silent_p.I1566I	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						PASS	.	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	184	0	0		WXS	Illumina HiSeq	Phase_I	191	90	0.471204	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	
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959279	45959279	+	Missense_Mutation	SNP	C	C	T	rs28644341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45959279C>T	ENST00000400375.1	-	1	799	c.755G>A	c.(754-756)tGt>tAt	p.C252Y	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	252	24 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(3)|prostate(4)|skin(1)	11						GGCAGGGGCACAGCAGGAGGA	0.726													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		14804	0.0		0.0	False		,,,				2504	0.0				p.C252Y		Atlas-SNP	.											.	KRTAP10-1	34	.	0			c.G755A						PASS	.	C	TYR/CYS,	119,4287	82.4+/-120.9	6,107,2090	43.0	50.0	48.0		755,	2.0	0.0	21	dbSNP_125	48	0,8600		0,0,4300	no	missense,intron	TSPEAR,KRTAP10-1	NM_198691.2,NM_144991.2	194,	6,107,6390	TT,TC,CC		0.0,2.7009,0.915	probably-damaging,	252/283,	45959279	119,12887	2203	4300	6503	SO:0001583	missense	386677	exon1			GGGGCACAGCAGG	AJ566380	CCDS42954.1	21q22.3	2007-10-05			ENSG00000215455	ENSG00000215455		"""Keratin associated proteins"""	22966	protein-coding gene	gene with protein product				KRTAP18-1			Standard	NM_198691		Approved	KAP10.1, KAP18.1	uc002zfh.1	P60331	OTTHUMG00000057627	ENST00000400375.1:c.755G>A	21.37:g.45959279C>T	ENSP00000383226:p.Cys252Tyr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_198691	Q0VAR0|Q0VAR1	Missense_Mutation	SNP	ENST00000400375.1	37	CCDS42954.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	c	0.012	-1.682141	0.00745	0.027009	0.0	ENSG00000215455	ENST00000400375	T	0.02345	4.33	2.93	2.0	0.26442	.	.	.	.	.	T	0.05090	0.0136	M	0.90922	3.16	0.09310	N	1	D	0.59357	0.985	D	0.63488	0.915	T	0.02313	-1.1178	9	0.46703	T	0.11	.	8.9015	0.35497	0.0:0.5471:0.4529:0.0	rs28644341	252	P60331	KR101_HUMAN	Y	252	ENSP00000383226:C252Y	ENSP00000383226:C252Y	C	-	2	0	KRTAP10-1	44783707	0.050000	0.20438	0.003000	0.11579	0.018000	0.09664	0.887000	0.28254	0.532000	0.28657	-0.499000	0.04595	TGT	C|0.991;T|0.009	0.009	strong		0.726	KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1		
BACH2	60468	hgsc.bcm.edu	37	6	90660319	90660319	+	Silent	SNP	T	T	C	rs9451298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90660319T>C	ENST00000257749.4	-	7	2213	c.1506A>G	c.(1504-1506)gtA>gtG	p.V502V	RP3-512E2.2_ENST00000413986.1_RNA|RP3-512E2.2_ENST00000445838.1_RNA|BACH2_ENST00000537989.1_Silent_p.V502V|BACH2_ENST00000343122.3_Silent_p.V502V	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	502						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)	p.V502V(1)		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)		CTTTGATTGGTACCGGGCAGC	0.662													C|||	1555	0.310503	0.4251	0.1931	5008	,	,		17279	0.2361		0.2773	False		,,,				2504	0.3497				p.V502V		Atlas-SNP	.											BACH2_ENST00000257749,NS,carcinoma,0,3	BACH2	224	3	1	Substitution - coding silent(1)	stomach(1)	c.A1506G						PASS	.	C	,	1636,2770	644.3+/-398.0	306,1024,873	51.0	59.0	56.0		1506,1506	5.3	1.0	6	dbSNP_119	56	2434,6166	683.4+/-403.9	355,1724,2221	no	coding-synonymous,coding-synonymous	BACH2	NM_001170794.1,NM_021813.2	,	661,2748,3094	CC,CT,TT		28.3023,37.1312,31.2932	,	502/842,502/842	90660319	4070,8936	2203	4300	6503	SO:0001819	synonymous_variant	60468	exon5			GATTGGTACCGGG	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.1506A>G	6.37:g.90660319T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Silent	SNP	ENST00000257749.4	37	CCDS5026.1																																																																																			T|0.695;C|0.305	0.305	strong		0.662	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813	
INTS1	26173	hgsc.bcm.edu	37	7	1542814	1542814	+	Silent	SNP	T	T	C	rs3752715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1542814T>C	ENST00000404767.3	-	3	157	c.72A>G	c.(70-72)ccA>ccG	p.P24P	INTS1_ENST00000389470.4_Silent_p.P152P|INTS1_ENST00000493531.1_5'Flank	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	24					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		TGAAGTCTCCTGGGGGAGGGT	0.557													C|||	2928	0.584665	0.7746	0.4179	5008	,	,		18049	0.7063		0.4642	False		,,,				2504	0.4448				p.P24P		Atlas-SNP	.											INTS1,colon,carcinoma,-1,1	INTS1	145	1	0			c.A72G						PASS	.			2592,1218		883,826,196	44.0	49.0	48.0		72	-9.5	0.0	7	dbSNP_107	48	3412,4838		681,2050,1394	no	coding-synonymous	INTS1	NM_001080453.2		1564,2876,1590	CC,CT,TT		41.3576,31.9685,49.7844		24/2191	1542814	6004,6056	1905	4125	6030	SO:0001819	synonymous_variant	26173	exon3			GTCTCCTGGGGGA	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.72A>G	7.37:g.1542814T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	137	136	0.992701	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																			T|0.412;C|0.588	0.588	strong		0.557	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
DSCR3	10311	hgsc.bcm.edu	37	21	38605694	38605694	+	Missense_Mutation	SNP	G	G	A	rs145630556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38605694G>A	ENST00000309117.6	-	4	638	c.401C>T	c.(400-402)aCa>aTa	p.T134I	AP001432.14_ENST00000440629.1_lincRNA|DSCR3_ENST00000288304.5_Missense_Mutation_p.T92I|DSCR3_ENST00000476950.1_Intron|DSCR3_ENST00000399000.3_5'UTR|DSCR3_ENST00000398998.1_Missense_Mutation_p.T86I|DSCR3_ENST00000399001.1_Intron|DSCR3_ENST00000539844.1_Intron	NM_006052.1	NP_006043.1	O14972	DSCR3_HUMAN	Down syndrome critical region gene 3	134						nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9						ACAGGTCTTTGTCAAGTCCTT	0.463													G|||	11	0.00219649	0.0083	0.0	5008	,	,		17905	0.0		0.0	False		,,,				2504	0.0				p.T134I		Atlas-SNP	.											.	DSCR3	21	.	0			c.C401T						PASS	.	G	ILE/THR	26,4380	31.7+/-61.6	0,26,2177	112.0	98.0	103.0		401	5.0	0.9	21	dbSNP_134	103	0,8600		0,0,4300	yes	missense	DSCR3	NM_006052.1	89	0,26,6477	AA,AG,GG		0.0,0.5901,0.1999	benign	134/298	38605694	26,12980	2203	4300	6503	SO:0001583	missense	10311	exon4			GTCTTTGTCAAGT	D87343	CCDS33553.1	21q22.2	2008-05-22			ENSG00000157538	ENSG00000157538			3044	protein-coding gene	gene with protein product		605298				9399594	Standard	NM_006052		Approved	DCRA	uc002ywf.1	O14972	OTTHUMG00000086659	ENST00000309117.6:c.401C>T	21.37:g.38605694G>A	ENSP00000311399:p.Thr134Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_006052	B2R6T8|B7Z6B1|D3DSH4|Q2TAY6	Missense_Mutation	SNP	ENST00000309117.6	37	CCDS33553.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	17.52	3.411061	0.62399	0.005901	0.0	ENSG00000157538	ENST00000309117;ENST00000288304;ENST00000398998	T	0.06933	3.24	5.0	5.0	0.66597	.	0.051278	0.85682	D	0.000000	T	0.11707	0.0285	M	0.72894	2.215	0.48288	D	0.99962	P	0.40834	0.73	B	0.42361	0.385	T	0.01504	-1.1338	10	0.38643	T	0.18	-0.2541	18.6523	0.91435	0.0:0.0:1.0:0.0	.	134	O14972	DSCR3_HUMAN	I	134;92;86	ENSP00000311399:T134I	ENSP00000288304:T92I	T	-	2	0	DSCR3	37527564	1.000000	0.71417	0.939000	0.37840	0.996000	0.88848	5.652000	0.67959	2.462000	0.83206	0.455000	0.32223	ACA	G|0.998;A|0.002	0.002	strong		0.463	DSCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194807.1		
PPP1R12C	54776	hgsc.bcm.edu	37	19	55606944	55606944	+	Missense_Mutation	SNP	G	G	A	rs35849605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55606944G>A	ENST00000263433.3	-	10	1270	c.1255C>T	c.(1255-1257)Cgc>Tgc	p.R419C	PPP1R12C_ENST00000435544.2_Missense_Mutation_p.R345C|PPP1R12C_ENST00000376393.2_Missense_Mutation_p.R419C	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)		AGGCCAAAGCGCCTGGAGAAG	0.627													G|||	126	0.0251597	0.0923	0.0058	5008	,	,		14816	0.0		0.0	False		,,,				2504	0.0				p.R419C		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.C1255T						PASS	.	G	CYS/ARG	353,4039		9,335,1852	10.0	12.0	11.0		1255	2.9	1.0	19	dbSNP_126	11	3,8557		0,3,4277	yes	missense	PPP1R12C	NM_017607.2	180	9,338,6129	AA,AG,GG		0.035,8.0373,2.7486	probably-damaging	419/783	55606944	356,12596	2196	4280	6476	SO:0001583	missense	54776	exon10			CAAAGCGCCTGGA	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.1255C>T	19.37:g.55606944G>A	ENSP00000263433:p.Arg419Cys	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_017607		Missense_Mutation	SNP	ENST00000263433.3	37	CCDS12916.1	51	0.023351648351648352	49	0.09959349593495935	2	0.0055248618784530384	0	0.0	0	0.0	G	18.24	3.580072	0.65992	0.080373	3.5E-4	ENSG00000125503	ENST00000263433;ENST00000376393;ENST00000435544	T;T;T	0.70045	-0.3;-0.32;-0.45	3.95	2.91	0.33838	.	0.302492	0.23868	N	0.043762	T	0.05044	0.0135	M	0.72353	2.195	0.43703	D	0.99616	D;D;D	0.61697	0.99;0.987;0.978	P;P;P	0.50896	0.556;0.653;0.451	T	0.36672	-0.9738	10	0.87932	D	0	.	6.5557	0.22460	0.1281:0.0:0.8719:0.0	rs35849605	345;418;419	B4DME2;Q9BZL4-3;Q9BZL4	.;.;PP12C_HUMAN	C	419;419;345	ENSP00000263433:R419C;ENSP00000365573:R419C;ENSP00000387833:R345C	ENSP00000263433:R419C	R	-	1	0	PPP1R12C	60298756	0.719000	0.27986	0.986000	0.45419	0.973000	0.67179	0.866000	0.27954	2.147000	0.66899	0.549000	0.68633	CGC	G|0.958;A|0.042	0.042	strong		0.627	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
NAPRT	93100	hgsc.bcm.edu	37	8	144658711	144658711	+	Silent	SNP	G	G	A	rs872935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144658711G>A	ENST00000449291.2	-	7	1207	c.913C>T	c.(913-915)Ctg>Ttg	p.L305L	NAPRT1_ENST00000435154.3_Silent_p.L305L|NAPRT1_ENST00000276844.7_Silent_p.L305L|RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000460623.1_5'Flank|NAPRT1_ENST00000426292.3_Silent_p.L305L																endometrium(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	6	all_cancers(97;6.49e-11)|all_epithelial(106;4.73e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.014)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CCCAGGGCCAGGGCGACTGCT	0.627													G|||	1990	0.397364	0.1672	0.4611	5008	,	,		17958	0.3938		0.6262	False		,,,				2504	0.4315				p.L305L		Atlas-SNP	.											.	NAPRT1	47	.	0			c.C913T						PASS	.	G		1024,3376	356.4+/-313.5	121,782,1297	27.0	27.0	27.0		913	1.4	0.7	8	dbSNP_86	27	5389,3211	629.3+/-398.2	1704,1981,615	no	coding-synonymous	NAPRT1	NM_145201.4		1825,2763,1912	AA,AG,GG		37.3372,23.2727,49.3308		305/539	144658711	6413,6587	2200	4300	6500	SO:0001819	synonymous_variant	93100	exon7			GGGCCAGGGCGAC																												ENST00000449291.2:c.913C>T	8.37:g.144658711G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_145201		Silent	SNP	ENST00000449291.2	37	CCDS6403.2																																																																																			G|0.525;C|0.000;A|0.475	0.475	strong		0.627	NAPRT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346708.3		
PTPRZ1	5803	hgsc.bcm.edu	37	7	121652964	121652964	+	Silent	SNP	T	T	C	rs139671030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:121652964T>C	ENST00000393386.2	+	12	4275	c.3864T>C	c.(3862-3864)agT>agC	p.S1288S	PTPRZ1_ENST00000483028.1_3'UTR|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1288					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						CTTTGTACAGTAATGATGAGT	0.398													T|||	22	0.00439297	0.0166	0.0	5008	,	,		20087	0.0		0.0	False		,,,				2504	0.0				p.S1288S		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T3864C						PASS	.	T	,,	46,4360	45.3+/-79.5	0,46,2157	74.0	69.0	70.0		,,3864	-1.6	0.0	7	dbSNP_134	70	0,8600		0,0,4300	yes	intron,intron,coding-synonymous	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,	0,46,6457	CC,CT,TT		0.0,1.044,0.3537	,,	,,1288/2316	121652964	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			GTACAGTAATGAT	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.3864T>C	7.37:g.121652964T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			T|0.997;C|0.003	0.003	strong		0.398	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
METTL15	196074	hgsc.bcm.edu	37	11	28351963	28351963	+	Missense_Mutation	SNP	A	A	T	rs11030280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:28351963A>T	ENST00000407364.3	+	7	1151	c.799A>T	c.(799-801)Att>Ttt	p.I267F	METTL15_ENST00000303459.6_3'UTR|METTL15_ENST00000342303.5_3'UTR|METTL15_ENST00000406787.3_Missense_Mutation_p.Y252F			A6NJ78	MET15_HUMAN	methyltransferase like 15	267			I -> F (in dbSNP:rs11030280).				methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						TCCCTCTGCTATTTATACACG	0.368													a|||	66	0.0131789	0.0484	0.0029	5008	,	,		18196	0.0		0.0	False		,,,				2504	0.0				p.I267F		Atlas-SNP	.											.	METTL15	63	.	0			c.A799T						PASS	.						26.0	20.0	22.0					11																	28351963		692	1591	2283	SO:0001583	missense	196074	exon7			TCTGCTATTTATA	AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519			26606	protein-coding gene	gene with protein product			"""methyltransferase 5 domain containing 1"""	METT5D1		12477932	Standard	NM_152636		Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.799A>T	11.37:g.28351963A>T	ENSP00000384369:p.Ile267Phe	Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	242	117	0.483471	NM_001113528	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	Missense_Mutation	SNP	ENST00000407364.3	37	CCDS44559.1	16|16	0.007326007326007326|0.007326007326007326	16|16	0.032520325203252036|0.032520325203252036	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	a|a	6.700|6.700	0.497771|0.497771	0.12762|0.12762	.|.	.|.	ENSG00000169519|ENSG00000169519	ENST00000407364|ENST00000406787	T|T	0.22743|0.42513	1.94|0.97	5.32|5.32	-8.55|-8.55	0.00908|0.00908	S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain (2);|.	1.236540|.	0.05563|.	N|.	0.569607|.	T|T	0.04497|0.04497	0.0123|0.0123	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.999999|0.999999	B|B	0.15473|0.02656	0.013|0.0	B|B	0.17979|0.04013	0.02|0.001	T|T	0.14227|0.14227	-1.0480|-1.0480	9|8	.|.	.|.	.|.	.|.	1.7987|1.7987	0.03067|0.03067	0.2726:0.3206:0.2653:0.1414|0.2726:0.3206:0.2653:0.1414	rs11030280|rs11030280	267|252	A6NJ78|A6NJ78-4	MET15_HUMAN|.	F|F	267|252	ENSP00000384369:I267F|ENSP00000385507:Y252F	.|.	I|Y	+|+	1|2	0|0	METTL15|METTL15	28308539|28308539	0.002000|0.002000	0.14202|0.14202	0.010000|0.010000	0.14722|0.14722	0.688000|0.688000	0.40055|0.40055	-0.377000|-0.377000	0.07456|0.07456	-0.966000|-0.966000	0.03587|0.03587	-1.125000|-1.125000	0.01998|0.01998	ATT|TAT	A|0.993;T|0.007	0.007	strong		0.368	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318135.2	NM_152636	
KRIT1	889	hgsc.bcm.edu	37	7	91842554	91842554	+	Silent	SNP	T	T	C	rs11542682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:91842554T>C	ENST00000340022.2	-	17	2998	c.1980A>G	c.(1978-1980)gtA>gtG	p.V660V	KRIT1_ENST00000394507.1_Silent_p.V660V|KRIT1_ENST00000412043.2_Silent_p.V660V|KRIT1_ENST00000394505.2_Silent_p.V660V|KRIT1_ENST00000394503.2_Silent_p.V612V	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	660	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				angiogenesis (GO:0001525)|cell redox homeostasis (GO:0045454)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|positive regulation of protein binding (GO:0032092)|regulation of catalytic activity (GO:0050790)|regulation of establishment of cell polarity (GO:2000114)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)|small GTPase regulator activity (GO:0005083)	p.V660V(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(2)|stomach(1)	22	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TATTCACTCCTACATACACAG	0.363													t|||	904	0.180511	0.1589	0.1239	5008	,	,		18715	0.3403		0.0825	False		,,,				2504	0.1861				p.V660V		Atlas-SNP	.											KRIT1,NS,carcinoma,0,1	KRIT1	66	1	1	Substitution - coding silent(1)	stomach(1)	c.A1980G						PASS	.	G	,,,,	536,3870	243.4+/-253.1	40,456,1707	159.0	149.0	152.0		1836,1980,1980,1980,1980	-0.2	1.0	7	dbSNP_120	152	795,7805	186.0+/-233.6	39,717,3544	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KRIT1	NM_001013406.1,NM_004912.3,NM_194454.1,NM_194455.1,NM_194456.1	,,,,	79,1173,5251	CC,CT,TT		9.2442,12.1652,10.2337	,,,,	612/689,660/737,660/737,660/737,660/737	91842554	1331,11675	2203	4300	6503	SO:0001819	synonymous_variant	889	exon18			CACTCCTACATAC	AJ294850	CCDS5624.1, CCDS34679.1	7q21.2	2014-09-17	2005-03-15	2005-03-17	ENSG00000001631	ENSG00000001631		"""Ankyrin repeat domain containing"""	1573	protein-coding gene	gene with protein product		604214	"""cerebral cavernous malformations 1"""	CCM1		7604043, 11342228	Standard	NM_194455		Approved	CAM	uc003ulu.1	O00522	OTTHUMG00000131187	ENST00000340022.2:c.1980A>G	7.37:g.91842554T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_194456	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Silent	SNP	ENST00000340022.2	37	CCDS5624.1																																																																																			T|0.867;C|0.133	0.133	strong		0.363	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1		
FAM26F	441168	hgsc.bcm.edu	37	6	116783585	116783585	+	Missense_Mutation	SNP	G	G	C	rs76716752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116783585G>C	ENST00000368605.1	+	2	588	c.493G>C	c.(493-495)Gac>Cac	p.D165H	FAM26F_ENST00000368606.3_Intron|RP1-93H18.6_ENST00000476099.1_RNA	NM_001010919.1	NP_001010919.1	Q5R3K3	FA26F_HUMAN	family with sequence similarity 26, member F	165					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(1)	3				GBM - Glioblastoma multiforme(226;0.0402)|all cancers(137;0.0627)|OV - Ovarian serous cystadenocarcinoma(136;0.0655)|Epithelial(106;0.231)		GGACGTGCAGGACCTCCTGAA	0.716													G|||	243	0.0485224	0.1747	0.0086	5008	,	,		12495	0.0		0.006	False		,,,				2504	0.0				p.S165P		Atlas-SNP	.											.	FAM26F	12	.	0			c.T493C						PASS	.	G	HIS/ASP	207,1869		8,191,839	3.0	2.0	2.0		493	0.7	0.0	6	dbSNP_131	2	9,2855		0,9,1423	yes	missense	FAM26F	NM_001010919.1	81	8,200,2262	CC,CG,GG		0.3142,9.9711,4.3725	possibly-damaging	165/316	116783585	216,4724	1038	1432	2470	SO:0001583	missense	441168	exon2			GTGCAGGACCTCC	AF086130	CCDS34519.1, CCDS64506.1	6q22.1	2007-06-20			ENSG00000188820	ENSG00000188820			33391	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 187"""	C6orf187			Standard	NM_001010919		Approved	RP1-93H18.5, OTTHUMP00000017061, OTTHUMP00000017062, dJ93H18.5	uc003pwv.4	Q5R3K3	OTTHUMG00000015438	ENST00000368605.1:c.493G>C	6.37:g.116783585G>C	ENSP00000357594:p.Asp165His	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_001010919	B9EJB0|Q5R3K4	Missense_Mutation	SNP	ENST00000368605.1	37	CCDS34519.1	91	0.041666666666666664	84	0.17073170731707318	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	22.3	4.278004	0.80692	0.099711	0.003142	ENSG00000188820	ENST00000368605	T	0.17528	2.27	4.82	0.664	0.17890	.	1.210450	0.05680	N	0.590259	T	0.09598	0.0236	L	0.46157	1.445	0.09310	N	1	D	0.57257	0.979	P	0.47915	0.561	T	0.33189	-0.9878	10	0.48119	T	0.1	-3.4085	9.6311	0.39780	0.4247:0.0:0.5753:0.0	.	165	Q5R3K3	FA26F_HUMAN	H	165	ENSP00000357594:D165H	ENSP00000357594:D165H	D	+	1	0	FAM26F	116890278	0.017000	0.18338	0.001000	0.08648	0.784000	0.44337	1.686000	0.37669	-0.058000	0.13177	0.313000	0.20887	GAC	G|0.954;C|0.046	0.046	strong		0.716	FAM26F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041946.1	NM_001010919	
PALLD	23022	hgsc.bcm.edu	37	4	169433326	169433326	+	Missense_Mutation	SNP	T	T	C	rs397718410|rs7655494|rs373066707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169433326T>C	ENST00000505667.1	+	2	844	c.671T>C	c.(670-672)aTg>aCg	p.M224T	PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000261509.6_Missense_Mutation_p.M224T|PALLD_ENST00000333488.4_Missense_Mutation_p.M101T			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	224			M -> I (in dbSNP:rs7671781).|M -> T (in dbSNP:rs7655494). {ECO:0000269|PubMed:14702039}.		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)		CAGAGCCCTATGGAAGACCAA	0.577									Pancreatic Cancer, Familial Clustering of				C|||	1200	0.239617	0.2368	0.1844	5008	,	,		17132	0.1935		0.33	False		,,,				2504	0.2372				p.M224T	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.T671C						PASS	.	C	THR/MET,THR/MET	1068,3338		151,766,1286	101.0	106.0	104.0		671,671	3.7	0.1	4	dbSNP_116	104	2621,5979		461,1699,2140	yes	missense,missense	PALLD	NM_001166108.1,NM_016081.3	81,81	612,2465,3426	CC,CT,TT		30.4767,24.2397,28.3638	benign,benign	224/1124,224/1107	169433326	3689,9317	2203	4300	6503	SO:0001583	missense	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GCCCTATGGAAGA	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.671T>C	4.37:g.169433326T>C	ENSP00000425556:p.Met224Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	447	0.20467032967032966	90	0.18292682926829268	68	0.1878453038674033	84	0.14685314685314685	205	0.2704485488126649	C	0.001	-2.912011	0.00056	0.242397	0.304767	ENSG00000129116	ENST00000261509;ENST00000505667;ENST00000508898;ENST00000333488	T;T;T;T	0.62364	0.14;0.41;0.03;0.11	5.41	3.67	0.42095	.	0.307711	0.17926	N	0.157333	T	0.00012	0.0000	N	0.01048	-1.04	0.52099	P	5.8000000000002494E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24905	-1.0147	9	0.06365	T	0.9	.	1.7516	0.02973	0.1746:0.4889:0.1151:0.2214	rs7655494;rs7655494	224;224	B7ZMM5;B2RTX2	.;.	T	224;224;203;101	ENSP00000261509:M224T;ENSP00000425556:M224T;ENSP00000423063:M203T;ENSP00000328945:M101T	ENSP00000261509:M224T	M	+	2	0	PALLD	169669901	0.008000	0.16893	0.120000	0.21714	0.007000	0.05969	0.369000	0.20416	0.273000	0.22049	-0.880000	0.02959	ATG	T|0.732;C|0.268	0.268	strong		0.577	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
MUC17	140453	hgsc.bcm.edu	37	7	100679390	100679390	+	Missense_Mutation	SNP	A	A	G	rs150982179		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100679390A>G	ENST00000306151.4	+	3	4757	c.4693A>G	c.(4693-4695)Acc>Gcc	p.T1565A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1565	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)					CAGCATGCAAACCTCAACTTA	0.488																																					p.T1565A		Atlas-SNP	.											MUC17,NS,carcinoma,-2,1	MUC17	804	1	0			c.A4693G						scavenged	.						265.0	248.0	254.0					7																	100679390		2203	4300	6503	SO:0001583	missense	140453	exon3			ATGCAAACCTCAA	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.4693A>G	7.37:g.100679390A>G	ENSP00000302716:p.Thr1565Ala	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	189	13	0.0687831	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	1.177	-0.639202	0.03557	.	.	ENSG00000169876	ENST00000306151	T	0.01887	4.58	0.364	0.364	0.16124	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B	0.16802	0.019	B	0.06405	0.002	T	0.47586	-0.9106	8	0.06236	T	0.91	.	.	.	.	.	1565	Q685J3	MUC17_HUMAN	A	1565	ENSP00000302716:T1565A	ENSP00000302716:T1565A	T	+	1	0	MUC17	100466110	0.012000	0.17670	0.001000	0.08648	0.002000	0.02628	1.128000	0.31369	0.391000	0.25143	0.102000	0.15555	ACC	.	.	weak		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FCRL6	343413	hgsc.bcm.edu	37	1	159778910	159778910	+	Missense_Mutation	SNP	G	G	A	rs72700615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159778910G>A	ENST00000368106.3	+	4	480	c.479G>A	c.(478-480)gGc>gAc	p.G160D	FCRL6_ENST00000392235.3_Intron|FCRL6_ENST00000339348.5_Missense_Mutation_p.G160D|FCRL6_ENST00000321935.6_Missense_Mutation_p.G167D	NM_001004310.2	NP_001004310.2	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6	160	Ig-like C2-type 2.					external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				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)					CAGGACAGGGGCCCTCACCCA	0.617													G|||	322	0.0642971	0.0371	0.085	5008	,	,		17807	0.0149		0.1392	False		,,,				2504	0.0603				p.G160D		Atlas-SNP	.											.	FCRL6	61	.	0			c.G479A						PASS	.	G	ASP/GLY	259,4147	149.5+/-183.7	3,253,1947	59.0	61.0	61.0		479	-0.5	0.0	1	dbSNP_130	61	1116,7484	231.5+/-265.5	85,946,3269	no	missense	FCRL6	NM_001004310.2	94	88,1199,5216	AA,AG,GG		12.9767,5.8783,10.572	benign	160/435	159778910	1375,11631	2203	4300	6503	SO:0001583	missense	343413	exon4			ACAGGGGCCCTCA	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.479G>A	1.37:g.159778910G>A	ENSP00000357086:p.Gly160Asp	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	207	113	0.545894	NM_001004310	A1KXW6|A2A4D6|Q6DN73|Q6XRC3|Q6ZNI1	Missense_Mutation	SNP	ENST00000368106.3	37	CCDS30912.1	179	0.08195970695970696	19	0.03861788617886179	46	0.1270718232044199	7	0.012237762237762238	107	0.14116094986807387	G	10.69	1.420661	0.25639	0.058783	0.129767	ENSG00000181036	ENST00000321935;ENST00000339348;ENST00000368106	T;T;T	0.03468	3.92;3.92;3.92	4.64	-0.505	0.11993	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.988811	0.08200	N	0.982432	T	0.00815	0.0027	N	0.17723	0.515	0.80722	P	0.0	B;B;B	0.19331	0.005;0.035;0.023	B;B;B	0.20184	0.006;0.028;0.025	T	0.47873	-0.9083	9	0.45353	T	0.12	.	3.8829	0.09086	0.2746:0.3861:0.3393:0.0	.	160;160;167	Q6DN72-3;Q6DN72;Q6DN72-2	.;FCRL6_HUMAN;.	D	167;160;160	ENSP00000320625:G167D;ENSP00000340949:G160D;ENSP00000357086:G160D	ENSP00000320625:G167D	G	+	2	0	FCRL6	158045534	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.052000	0.14163	0.353000	0.24079	0.585000	0.79938	GGC	G|0.901;A|0.099	0.099	strong		0.617	FCRL6-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276853.1	NM_001004310	
TMEM131	23505	hgsc.bcm.edu	37	2	98611994	98611994	+	Silent	SNP	G	G	T	rs2279824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98611994G>T	ENST00000186436.5	-	1	360	c.132C>A	c.(130-132)ggC>ggA	p.G44G	TMEM131_ENST00000425805.2_5'UTR	NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	44						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						GGTGCAGCGCGCCTAGGAggc	0.791													T|||	2965	0.592053	0.9138	0.5591	5008	,	,		7336	0.2867		0.7793	False		,,,				2504	0.3027				p.G44G		Atlas-SNP	.											.	TMEM131	258	.	0			c.C132A						PASS	.						1.0	1.0	1.0					2																	98611994		856	2126	2982	SO:0001819	synonymous_variant	23505	exon1			CAGCGCGCCTAGG	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.132C>A	2.37:g.98611994G>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_015348		Silent	SNP	ENST00000186436.5	37	CCDS46368.1																																																																																			G|0.352;T|0.648	0.648	strong		0.791	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542	
PREX2	80243	hgsc.bcm.edu	37	8	68968171	68968171	+	Silent	SNP	G	G	A	rs1434775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:68968171G>A	ENST00000288368.4	+	10	1477	c.1200G>A	c.(1198-1200)aaG>aaA	p.K400K	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	400	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AAGACCGAAAGAGAAAACTGA	0.403													A|||	2813	0.561701	0.8865	0.4755	5008	,	,		18889	0.2688		0.5239	False		,,,				2504	0.5245				p.K400K		Atlas-SNP	.											.	PREX2	614	.	0			c.G1200A						PASS	.	A	,	3619,787	315.8+/-294.3	1498,623,82	119.0	130.0	126.0		1200,1200	3.0	1.0	8	dbSNP_88	126	4215,4385	583.0+/-391.5	1038,2139,1123	no	coding-synonymous,coding-synonymous	PREX2	NM_024870.2,NM_025170.4	,	2536,2762,1205	AA,AG,GG		49.0116,17.862,39.7663	,	400/1607,400/980	68968171	7834,5172	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon10			CCGAAAGAGAAAA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1200G>A	8.37:g.68968171G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	25	0.308642	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			G|0.421;A|0.579	0.579	strong		0.403	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68934515	68934515	+	Silent	SNP	A	A	G	rs35687346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:68934515A>G	ENST00000356291.2	-	7	635	c.576T>C	c.(574-576)tcT>tcC	p.S192S	UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	192						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						GCATGTTTGAAGATGTCATCC	0.423													A|||	232	0.0463259	0.1619	0.0216	5008	,	,		21406	0.0		0.003	False		,,,				2504	0.0				p.S192S		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.T576C						PASS	.	A		551,3855	245.3+/-254.3	37,477,1689	88.0	83.0	85.0		576	-1.1	1.0	4	dbSNP_126	85	39,8561	25.1+/-72.6	0,39,4261	no	coding-synonymous	TMPRSS11F	NM_207407.2		37,516,5950	GG,GA,AA		0.4535,12.5057,4.5364		192/439	68934515	590,12416	2203	4300	6503	SO:0001819	synonymous_variant	389208	exon7			GTTTGAAGATGTC	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.576T>C	4.37:g.68934515A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	132	61	0.462121	NM_207407	A8MXX2	Silent	SNP	ENST00000356291.2	37	CCDS3520.1																																																																																			A|0.955;G|0.045	0.045	strong		0.423	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	
PLG	5340	hgsc.bcm.edu	37	6	161132146	161132146	+	Silent	SNP	C	C	T	rs4757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:161132146C>T	ENST00000308192.9	+	4	393	c.330C>T	c.(328-330)aaC>aaT	p.N110N	PLG_ENST00000462918.1_3'UTR|PLG_ENST00000366924.2_Silent_p.N110N	NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	110	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	ATGGAAAGAACTACAGAGGGA	0.453													C|||	1249	0.249401	0.5083	0.2248	5008	,	,		21058	0.001		0.3012	False		,,,				2504	0.1196				p.N110N		Atlas-SNP	.											.	PLG	150	.	0			c.C330T						PASS	.	C	,	2084,2322	573.3+/-383.5	478,1128,597	111.0	98.0	103.0		330,330	1.2	0.9	6	dbSNP_52	103	2713,5883	434.7+/-357.8	407,1899,1992	no	coding-synonymous,coding-synonymous	PLG	NM_000301.3,NM_001168338.1	,	885,3027,2589	TT,TC,CC		31.5612,47.2991,36.8943	,	110/811,110/137	161132146	4797,8205	2203	4298	6501	SO:0001819	synonymous_variant	5340	exon4			AAAGAACTACAGA	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.330C>T	6.37:g.161132146C>T		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	268	265	0.988806	NM_001168338	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			C|0.671;T|0.329	0.329	strong		0.453	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
ZC3H3	23144	hgsc.bcm.edu	37	8	144522388	144522388	+	Missense_Mutation	SNP	A	A	T	rs2272753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144522388A>T	ENST00000262577.5	-	11	2669	c.2638T>A	c.(2638-2640)Tca>Aca	p.S880T		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	880	Poly-Ser.				mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			ggaggggatgaggaggaggag	0.652													A|||	560	0.111821	0.0363	0.1167	5008	,	,		16934	0.2431		0.1461	False		,,,				2504	0.0399				p.S880T		Atlas-SNP	.											.	ZC3H3	75	.	0			c.T2638A						PASS	.	A	THR/SER	208,4198		8,192,2003	29.0	28.0	29.0		2638	-8.5	0.0	8	dbSNP_100	29	945,7653		118,709,3472	no	missense	ZC3H3	NM_015117.2	58	126,901,5475	TT,TA,AA		10.9909,4.7208,8.8665	possibly-damaging	880/949	144522388	1153,11851	2203	4299	6502	SO:0001583	missense	23144	exon11			GGGATGAGGAGGA	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"""Zinc fingers, CCCH-type domain containing"""	28972	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 3"""	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.2638T>A	8.37:g.144522388A>T	ENSP00000262577:p.Ser880Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	108	62	0.574074	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	273	0.125	24	0.04878048780487805	42	0.11602209944751381	124	0.21678321678321677	83	0.10949868073878628	A	10.21	1.288569	0.23478	0.047208	0.109909	ENSG00000014164	ENST00000262577	T	0.44083	0.93	4.25	-8.5	0.00927	.	2.759650	0.01499	N	0.017425	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.23650	0.089	B	0.18263	0.021	T	0.07927	-1.0747	9	0.11794	T	0.64	2.0487	4.56	0.12156	0.1813:0.3576:0.3664:0.0948	rs2272753	880	Q8IXZ2	ZC3H3_HUMAN	T	880	ENSP00000262577:S880T	ENSP00000262577:S880T	S	-	1	0	ZC3H3	144593531	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-4.369000	0.00245	-2.892000	0.00315	-0.605000	0.04089	TCA	A|0.879;T|0.121	0.121	strong		0.652	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
BCL9L	283149	hgsc.bcm.edu	37	11	118770054	118770054	+	Silent	SNP	G	G	A	rs12277303	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118770054G>A	ENST00000334801.3	-	8	4534	c.3570C>T	c.(3568-3570)aaC>aaT	p.N1190N	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1190	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		TCCCCTGTGCGTTGGGATGCA	0.692													G|||	262	0.0523163	0.1921	0.0101	5008	,	,		11201	0.0		0.001	False		,,,				2504	0.0				p.N1190N		Atlas-SNP	.											.	BCL9L	254	.	0			c.C3570T						PASS	.	G		401,3799		5,391,1704	5.0	6.0	6.0		3570	-0.1	0.9	11	dbSNP_120	6	6,8276		0,6,4135	no	coding-synonymous	BCL9L	NM_182557.2		5,397,5839	AA,AG,GG		0.0724,9.5476,3.2607		1190/1500	118770054	407,12075	2100	4141	6241	SO:0001819	synonymous_variant	283149	exon8			CTGTGCGTTGGGA	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.3570C>T	11.37:g.118770054G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	95	55	0.578947	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																			G|0.948;A|0.052	0.052	strong		0.692	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
ZNF540	163255	hgsc.bcm.edu	37	19	38102955	38102955	+	Silent	SNP	T	T	C	rs115588579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38102955T>C	ENST00000592533.1	+	5	1106	c.774T>C	c.(772-774)ctT>ctC	p.L258L	ZNF540_ENST00000589117.1_Silent_p.L226L|ZNF540_ENST00000316433.4_Silent_p.L258L|ZNF540_ENST00000343599.5_Silent_p.L258L	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	258					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACCCACAACTTAATCGACATC	0.343													T|||	33	0.00658946	0.0227	0.0043	5008	,	,		18475	0.0		0.0	False		,,,				2504	0.0				p.L258L		Atlas-SNP	.											.	ZNF540	75	.	0			c.T774C						PASS	.	T	,,	77,4329	64.7+/-102.0	1,75,2127	33.0	35.0	35.0		774,678,774	1.3	0.0	19	dbSNP_132	35	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF540	NM_001172225.1,NM_001172226.1,NM_152606.3	,,	1,76,6424	CC,CT,TT		0.0116,1.7476,0.5999	,,	258/661,226/629,258/661	38102955	78,12924	2203	4298	6501	SO:0001819	synonymous_variant	163255	exon5			ACAACTTAATCGA	AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"""Zinc fingers, C2H2-type"", ""-"""	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.774T>C	19.37:g.38102955T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_152606	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Silent	SNP	ENST00000592533.1	37	CCDS12506.1																																																																																			T|0.992;C|0.008	0.008	strong		0.343	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606	
CHD3	1107	hgsc.bcm.edu	37	17	7792326	7792326	+	Missense_Mutation	SNP	C	C	T	rs931543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7792326C>T	ENST00000330494.7	+	1	158	c.8C>T	c.(7-9)gCg>gTg	p.A3V	CHD3_ENST00000380358.4_Intron|CHD3_ENST00000358181.4_Missense_Mutation_p.A3V	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	3			A -> V (in dbSNP:rs931543).		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)				GTGATGAAGGCGGCAGACACT	0.468													T|||	392	0.0782748	0.2179	0.062	5008	,	,		18301	0.0278		0.0239	False		,,,				2504	0.0092				p.A3V		Atlas-SNP	.											.	CHD3	169	.	0			c.C8T						PASS	.	T	,VAL/ALA,VAL/ALA	865,3541		76,713,1414	151.0	155.0	154.0		,8,8	1.3	0.4	17	dbSNP_86	154	223,8377		4,215,4081	yes	intron,missense,missense	CHD3	NM_001005271.2,NM_001005273.2,NM_005852.3	,64,64	80,928,5495	TT,TC,CC		2.593,19.6323,8.3654	,,	,3/2001,3/1967	7792326	1088,11918	2203	4300	6503	SO:0001583	missense	1107	exon1			TGAAGGCGGCAGA	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.8C>T	17.37:g.7792326C>T	ENSP00000332628:p.Ala3Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_001005273	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	167	0.07646520146520147	105	0.21341463414634146	21	0.058011049723756904	23	0.04020979020979021	18	0.023746701846965697	N	14.54	2.564799	0.45694	0.196323	0.02593	ENSG00000170004	ENST00000358181;ENST00000330494	D;D	0.89552	-2.53;-2.53	3.7	1.29	0.21616	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.03394	-1.1041	8	0.16896	T	0.51	.	5.2159	0.15342	0.3615:0.5187:0.1197:0.0	rs931543;rs58342197;rs931543	3;3	Q12873-2;Q12873	.;CHD3_HUMAN	V	3	ENSP00000350907:A3V;ENSP00000332628:A3V	ENSP00000332628:A3V	A	+	2	0	CHD3	7733051	0.033000	0.19621	0.446000	0.26920	0.797000	0.45037	0.104000	0.15313	0.096000	0.17463	-0.398000	0.06409	GCG	C|0.915;T|0.085	0.085	strong		0.468	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	
ICAM3	3385	hgsc.bcm.edu	37	19	10446568	10446568	+	Missense_Mutation	SNP	T	T	C	rs2304237	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10446568T>C	ENST00000160262.5	-	3	636	c.428A>G	c.(427-429)gAt>gGt	p.D143G	RAVER1_ENST00000293677.6_5'Flank|ICAM3_ENST00000589261.1_Missense_Mutation_p.D66G	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	143	Ig-like C2-type 2.		D -> G (in dbSNP:rs2304237). {ECO:0000269|PubMed:1448173, ECO:0000269|PubMed:1448174, ECO:0000269|PubMed:8459213}.		extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			GGGCGACCCATCCTCCACTTG	0.697													C|||	899	0.179513	0.1407	0.1744	5008	,	,		15342	0.1131		0.2336	False		,,,				2504	0.2485				p.D143G		Atlas-SNP	.											.	ICAM3	29	.	0			c.A428G						PASS	.	C	GLY/ASP	721,3681		55,611,1535	15.0	16.0	15.0		428	5.0	0.0	19	dbSNP_100	15	1901,6689		230,1441,2624	yes	missense	ICAM3	NM_002162.3	94	285,2052,4159	CC,CT,TT		22.1304,16.3789,20.1817	benign	143/548	10446568	2622,10370	2201	4295	6496	SO:0001583	missense	3385	exon3			GACCCATCCTCCA		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.428A>G	19.37:g.10446568T>C	ENSP00000160262:p.Asp143Gly	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_002162	Q6PD68	Missense_Mutation	SNP	ENST00000160262.5	37	CCDS12235.1	383	0.17536630036630035	61	0.12398373983739837	70	0.19337016574585636	68	0.11888111888111888	184	0.24274406332453827	C	3.139	-0.176746	0.06380	0.163789	0.221304	ENSG00000076662	ENST00000160262	T	0.04083	3.71	4.98	4.98	0.66077	Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.240354	0.35739	N	0.003008	T	0.00012	0.0000	N	0.00023	-2.72	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35847	-0.9772	9	0.02654	T	1	-18.3636	9.9304	0.41519	0.0:0.9044:0.0:0.0956	rs2304237;rs59711512;rs2304237	66;143	B7Z6W6;P32942	.;ICAM3_HUMAN	G	143	ENSP00000160262:D143G	ENSP00000160262:D143G	D	-	2	0	ICAM3	10307568	0.005000	0.15991	0.026000	0.17262	0.003000	0.03518	0.596000	0.24044	1.249000	0.43950	-0.227000	0.12334	GAT	T|0.817;C|0.183	0.183	strong		0.697	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		
DDX20	11218	hgsc.bcm.edu	37	1	112308953	112308953	+	Missense_Mutation	SNP	T	T	C	rs197412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:112308953T>C	ENST00000369702.4	+	11	2527	c.1907T>C	c.(1906-1908)aTt>aCt	p.I636T	DDX20_ENST00000475700.1_Missense_Mutation_p.I244T	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	636			I -> T (in dbSNP:rs197412). {ECO:0000269|PubMed:15489334}.		ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATAAAGTTATTGAACAGAGA	0.453													C|||	2376	0.474441	0.7247	0.5072	5008	,	,		19469	0.3403		0.4185	False		,,,				2504	0.3088				p.I636T		Atlas-SNP	.											DDX20,NS,carcinoma,+1,1	DDX20	50	1	0			c.T1907C						PASS	.	C	THR/ILE	2950,1456	465.7+/-354.3	991,968,244	49.0	49.0	49.0		1907	3.9	0.3	1	dbSNP_79	49	3345,5255	640.4+/-399.6	669,2007,1624	yes	missense	DDX20	NM_007204.4	89	1660,2975,1868	CC,CT,TT		38.8953,33.0458,48.4007	benign	636/825	112308953	6295,6711	2203	4300	6503	SO:0001583	missense	11218	exon11			AAGTTATTGAACA	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.1907T>C	1.37:g.112308953T>C	ENSP00000358716:p.Ile636Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	1038	0.47527472527472525	360	0.7317073170731707	162	0.44751381215469616	198	0.34615384615384615	318	0.41952506596306066	C	0.006	-2.070387	0.00379	0.669542	0.388953	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.32023	1.47;1.98	5.72	3.86	0.44501	.	2.200060	0.01328	N	0.011173	T	0.02929	0.0087	N	0.00926	-1.1	0.44899	P	0.0020820000000000283	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33828	-0.9853	8	.	.	.	0.4742	5.1813	0.15161	0.1427:0.6287:0.0:0.2286	rs197412;rs482352;rs17569500;rs17845940;rs17856358;rs17857030;rs17858920;rs52814398;rs60229681;rs197412	244;636	E9PJ60;Q9UHI6	.;DDX20_HUMAN	T	636;244	ENSP00000358716:I636T;ENSP00000435660:I244T	.	I	+	2	0	DDX20	112110476	0.906000	0.30813	0.331000	0.25455	0.101000	0.19017	2.183000	0.42565	0.463000	0.27118	-0.766000	0.03442	ATT	C|0.483;N|0.000	0.483	strong		0.453	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
DNAJB13	374407	hgsc.bcm.edu	37	11	73670645	73670645	+	Silent	SNP	T	T	C	rs653263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	99	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	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	
LAMA3	3909	hgsc.bcm.edu	37	18	21447864	21447864	+	Nonsense_Mutation	SNP	C	C	T	rs552326056		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:21447864C>T	ENST00000313654.9	+	37	4991	c.4750C>T	c.(4750-4752)Cga>Tga	p.R1584*	LAMA3_ENST00000399516.3_Nonsense_Mutation_p.R1584*	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1584	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				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)					GCATCATGGACGAGTGCACGT	0.428													C|||	1	0.000199681	0.0	0.0	5008	,	,		15269	0.001		0.0	False		,,,				2504	0.0				p.R1584X		Atlas-SNP	.											LAMA3,NS,carcinoma,-1,2	LAMA3	397	2	0			c.C4750T						scavenged	.						134.0	139.0	137.0					18																	21447864		1997	4175	6172	SO:0001587	stop_gained	3909	exon37			CATGGACGAGTGC	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.4750C>T	18.37:g.21447864C>T	ENSP00000324532:p.Arg1584*	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	2	0.0186916	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Nonsense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	42	9.415914	0.99164	.	.	ENSG00000053747	ENST00000313654;ENST00000399516	.	.	.	5.45	2.5	0.30297	.	.	.	.	.	.	.	.	.	.	.	0.25940	N	0.982889	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.926	0.35641	0.3872:0.5452:0.0:0.0676	.	.	.	.	X	1584	.	ENSP00000324532:R1584X	R	+	1	2	LAMA3	19701862	0.615000	0.27026	0.014000	0.15608	0.309000	0.27889	1.093000	0.30939	0.281000	0.22233	0.655000	0.94253	CGA	.	.	none		0.428	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
FAM131C	348487	hgsc.bcm.edu	37	1	16386065	16386065	+	Silent	SNP	T	T	A	rs61769893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16386065T>A	ENST00000375662.4	-	6	669	c.486A>T	c.(484-486)acA>acT	p.T162T	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	162								p.T162T(1)		large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		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;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		AAGCGCTCAGTGTGGCCTCTG	0.662																																					p.T162T		Atlas-SNP	.											FAM131C,caecum,carcinoma,0,1	FAM131C	21	1	1	Substitution - coding silent(1)	large_intestine(1)	c.A486T						PASS	.						24.0	23.0	24.0					1																	16386065		1844	4061	5905	SO:0001819	synonymous_variant	348487	exon6			GCTCAGTGTGGCC		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.486A>T	1.37:g.16386065T>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	456	89	0.195175	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			T|0.958;A|0.042	0.042	strong		0.662	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
GPR26	2849	hgsc.bcm.edu	37	10	125447511	125447511	+	Silent	SNP	G	G	A	rs62640899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:125447511G>A	ENST00000284674.1	+	3	902	c.849G>A	c.(847-849)gcG>gcA	p.A283A		NM_153442.3	NP_703143.1	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	283					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	20		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)				AGTGCTTGGCGTACAGCAAGG	0.577													G|||	139	0.0277556	0.1006	0.0072	5008	,	,		17997	0.0		0.001	False		,,,				2504	0.0				p.A283A		Atlas-SNP	.											.	GPR26	47	.	0			c.G849A						PASS	.	G		363,4043	186.4+/-213.3	16,331,1856	91.0	80.0	84.0		849	2.3	1.0	10	dbSNP_129	84	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	GPR26	NM_153442.3		16,338,6149	AA,AG,GG		0.0814,8.2388,2.8448		283/338	125447511	370,12636	2203	4300	6503	SO:0001819	synonymous_variant	2849	exon3			CTTGGCGTACAGC		CCDS7636.1	10q26.2-q26.3	2012-08-21			ENSG00000154478	ENSG00000154478		"""GPCR / Class A : Orphans"""	4481	protein-coding gene	gene with protein product		604847					Standard	NM_153442		Approved		uc001lhh.3	Q8NDV2	OTTHUMG00000019204	ENST00000284674.1:c.849G>A	10.37:g.125447511G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_153442	Q2M2E2	Silent	SNP	ENST00000284674.1	37	CCDS7636.1																																																																																			G|0.970;A|0.030	0.030	strong		0.577	GPR26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050850.1		
SLC2A9	56606	hgsc.bcm.edu	37	4	9987324	9987324	+	Silent	SNP	G	G	A	rs3733589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:9987324G>A	ENST00000264784.3	-	4	557	c.504C>T	c.(502-504)atC>atT	p.I168I	SLC2A9_ENST00000309065.3_Silent_p.I139I|SLC2A9_ENST00000506583.1_Silent_p.I139I	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	168					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	AGCGTCCCACGATGAGCATTT	0.512													G|||	782	0.15615	0.09	0.1455	5008	,	,		23244	0.3919		0.0447	False		,,,				2504	0.1247				p.I168I		Atlas-SNP	.											.	SLC2A9	158	.	0			c.C504T						PASS	.	G	,	476,3930	225.2+/-241.2	28,420,1755	85.0	81.0	82.0		417,504	0.4	0.3	4	dbSNP_107	82	293,8307	108.2+/-168.9	4,285,4011	no	coding-synonymous,coding-synonymous	SLC2A9	NM_001001290.1,NM_020041.2	,	32,705,5766	AA,AG,GG		3.407,10.8034,5.9127	,	139/512,168/541	9987324	769,12237	2203	4300	6503	SO:0001819	synonymous_variant	56606	exon4			TCCCACGATGAGC	AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"""Solute carriers"""	13446	protein-coding gene	gene with protein product	"""urate voltage-driven efflux transporter 1"""	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.504C>T	4.37:g.9987324G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	210	103	0.490476	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Silent	SNP	ENST00000264784.3	37	CCDS3407.1																																																																																			G|0.895;A|0.105	0.105	strong		0.512	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1		
PFAS	5198	hgsc.bcm.edu	37	17	8172141	8172141	+	Missense_Mutation	SNP	G	G	A	rs73975814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8172141G>A	ENST00000314666.6	+	27	3806	c.3673G>A	c.(3673-3675)Gcc>Acc	p.A1225T	PFAS_ENST00000545834.1_Missense_Mutation_p.A801T	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1225	Glutamine amidotransferase type-1.				'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)	GATGGAGGGCGCCGTGCTGCC	0.697													G|||	46	0.0091853	0.0333	0.0	5008	,	,		14129	0.001		0.0	False		,,,				2504	0.001				p.A1225T		Atlas-SNP	.											.	PFAS	91	.	0			c.G3673A						PASS	.	G	THR/ALA	73,4329		0,73,2128	33.0	37.0	36.0		3673	4.4	0.0	17	dbSNP_130	36	0,8592		0,0,4296	no	missense	PFAS	NM_012393.2	58	0,73,6424	AA,AG,GG		0.0,1.6583,0.5618	benign	1225/1339	8172141	73,12921	2201	4296	6497	SO:0001583	missense	5198	exon27			GAGGGCGCCGTGC	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.3673G>A	17.37:g.8172141G>A	ENSP00000313490:p.Ala1225Thr	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	18	10	0.555556	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	13.30	2.195407	0.38806	0.016583	0.0	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.29397	1.57;2.3	5.41	4.41	0.53225	Glutamine amidotransferase type 1 (1);	0.192639	0.45606	D	0.000358	T	0.08670	0.0215	N	0.10685	0.025	0.09310	N	1	B;B	0.30439	0.279;0.279	B;B	0.31390	0.129;0.129	T	0.14504	-1.0470	10	0.87932	D	0	-12.0495	10.9394	0.47264	0.0:0.0:0.6471:0.3529	.	1225;1225	A8K8N7;O15067	.;PUR4_HUMAN	T	801;1225;634	ENSP00000441706:A801T;ENSP00000313490:A1225T	ENSP00000313490:A1225T	A	+	1	0	PFAS	8112866	0.998000	0.40836	0.033000	0.17914	0.848000	0.48234	3.977000	0.56874	1.220000	0.43490	0.563000	0.77884	GCC	G|0.994;A|0.006	0.006	strong		0.697	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
HECW2	57520	hgsc.bcm.edu	37	2	197208397	197208397	+	Silent	SNP	C	C	T	rs61741962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	117	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	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	
METTL4	64863	hgsc.bcm.edu	37	18	2554807	2554807	+	Missense_Mutation	SNP	T	T	G	rs34143130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2554807T>G	ENST00000574538.1	-	4	1465	c.690A>C	c.(688-690)gaA>gaC	p.E230D	snoU109_ENST00000459316.1_RNA|METTL4_ENST00000319888.6_Missense_Mutation_p.E230D	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	230			E -> D (in dbSNP:rs34143130).		nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						ATAAATCCTGTTCTGTAACAG	0.363													T|||	613	0.122404	0.264	0.0994	5008	,	,		19448	0.1329		0.0457	False		,,,				2504	0.0153				p.E230D		Atlas-SNP	.											.	METTL4	40	.	0			c.A690C						PASS	.	T	ASP/GLU	1019,3387	369.8+/-319.3	116,787,1300	62.0	56.0	58.0		690	1.3	1.0	18	dbSNP_126	58	380,8220	122.7+/-181.7	11,358,3931	yes	missense	METTL4	NM_022840.3	45	127,1145,5231	GG,GT,TT		4.4186,23.1276,10.7566	benign	230/473	2554807	1399,11607	2203	4300	6503	SO:0001583	missense	64863	exon4			ATCCTGTTCTGTA		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.690A>C	18.37:g.2554807T>G	ENSP00000458290:p.Glu230Asp	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Missense_Mutation	SNP	ENST00000574538.1	37	CCDS11826.1	267	0.12225274725274725	144	0.2926829268292683	25	0.06906077348066299	68	0.11888111888111888	30	0.0395778364116095	T	11.59	1.683554	0.29872	0.231276	0.044186	ENSG00000101574	ENST00000319888	T	0.23754	1.89	5.85	1.29	0.21616	.	0.222920	0.45361	N	0.000376	T	0.00012	0.0000	M	0.68317	2.08	0.35762	P	0.17974100000000004	B;B	0.23990	0.095;0.037	B;B	0.21360	0.034;0.012	T	0.28332	-1.0047	9	0.38643	T	0.18	-14.2895	6.1917	0.20528	0.0:0.4218:0.2324:0.3459	rs34143130	230;230	A8K1T6;Q8N3J2	.;METL4_HUMAN	D	230	ENSP00000320349:E230D	ENSP00000320349:E230D	E	-	3	2	METTL4	2544807	0.991000	0.36638	0.999000	0.59377	0.738000	0.42128	0.141000	0.16076	0.302000	0.22762	-0.242000	0.12053	GAA	T|0.889;G|0.111	0.111	strong		0.363	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840	
SPATA22	84690	hgsc.bcm.edu	37	17	3352331	3352331	+	Missense_Mutation	SNP	C	C	T	rs1488690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3352331C>T	ENST00000573128.1	-	6	925	c.442G>A	c.(442-444)Gtg>Atg	p.V148M	SPATA22_ENST00000575375.1_Missense_Mutation_p.V148M|SPATA22_ENST00000355380.4_Missense_Mutation_p.V105M|SPATA22_ENST00000541913.1_Missense_Mutation_p.V132M|SPATA22_ENST00000268981.5_Missense_Mutation_p.V148M|SPATA22_ENST00000572969.1_Missense_Mutation_p.V148M|SPATA22_ENST00000397168.3_Missense_Mutation_p.V148M			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	148			V -> M (in dbSNP:rs1488690). {ECO:0000269|PubMed:15489334}.		fertilization (GO:0009566)|gamete generation (GO:0007276)|meiotic DNA repair synthesis (GO:0000711)|regulation of meiotic cell cycle (GO:0051445)|reproductive system development (GO:0061458)|synapsis (GO:0007129)	chromosome (GO:0005694)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)	19						CCCGAACTCACTGGACAAGAA	0.353													c|||	1337	0.266973	0.2209	0.3501	5008	,	,		15865	0.4187		0.1809	False		,,,				2504	0.2025				p.V148M		Atlas-SNP	.											.	SPATA22	49	.	0			c.G442A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1087,3319	392.8+/-328.6	136,815,1252	216.0	208.0	211.0		442,313,442,442,442,442	-9.6	0.0	17	dbSNP_88	211	1585,7015	296.6+/-303.0	144,1297,2859	yes	missense,missense,missense,missense,missense,missense	SPATA22	NM_001170695.1,NM_001170696.1,NM_001170697.1,NM_001170698.1,NM_001170699.1,NM_032598.4	21,21,21,21,21,21	280,2112,4111	TT,TC,CC		18.4302,24.6709,20.5444	benign,benign,benign,benign,benign,benign	148/364,105/321,148/364,148/364,148/270,148/364	3352331	2672,10334	2203	4300	6503	SO:0001583	missense	84690	exon6			AACTCACTGGACA	AY035868	CCDS11027.1, CCDS54066.1, CCDS54067.1	17p13.3	2005-12-19							30705	protein-coding gene	gene with protein product						12477932	Standard	NM_001170696		Approved	NYD-SP20	uc002fvn.3	Q8NHS9		ENST00000573128.1:c.442G>A	17.37:g.3352331C>T	ENSP00000459580:p.Val148Met	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	231	108	0.467532	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Missense_Mutation	SNP	ENST00000573128.1	37	CCDS11027.1	593	0.2715201465201465	108	0.21951219512195122	127	0.35082872928176795	219	0.38286713286713286	139	0.18337730870712401	c	4.615	0.114227	0.08831	0.246709	0.184302	ENSG00000141255	ENST00000355380;ENST00000397168;ENST00000268981;ENST00000541913	T;T;T;T	0.18960	2.19;2.2;2.18;2.19	5.07	-9.61	0.00550	.	1.064140	0.07349	N	0.882007	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B	0.12013	0.002;0.001;0.005;0.001	B;B;B;B	0.10450	0.005;0.003;0.005;0.002	T	0.36768	-0.9734	9	0.26408	T	0.33	-26.657	15.7227	0.77724	0.0:0.2877:0.0:0.7123	rs1488690;rs17822669;rs17852662;rs52823975;rs57028597;rs1488690	132;148;105;148	F5GWB9;B4DXB1;Q8NHS9-2;Q8NHS9	.;.;.;SPT22_HUMAN	M	105;148;148;132	ENSP00000347541:V105M;ENSP00000380354:V148M;ENSP00000268981:V148M;ENSP00000441920:V132M	ENSP00000268981:V148M	V	-	1	0	SPATA22	3299081	0.002000	0.14202	0.019000	0.16419	0.059000	0.15707	-1.651000	0.01989	-1.929000	0.01057	-0.417000	0.06048	GTG	C|0.767;T|0.233	0.233	strong		0.353	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262091	39262091	+	Missense_Mutation	SNP	C	C	T	rs571292694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39262091C>T	ENST00000391415.1	+	1	508	c.451C>T	c.(451-453)Cgc>Tgc	p.R151C		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	151	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						caactgctgccgccccagctg	0.662													C|||	26	0.00519169	0.0197	0.0	5008	,	,		18753	0.0		0.0	False		,,,				2504	0.0				p.R151C		Atlas-SNP	.											.	KRTAP4-9	110	.	0			c.C451T						PASS	.						5.0	8.0	7.0					17																	39262091		667	1548	2215	SO:0001583	missense	100132386	exon1			TGCTGCCGCCCCA	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.451C>T	17.37:g.39262091C>T	ENSP00000375234:p.Arg151Cys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	186	64	0.344086	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	11.75	1.733214	0.30684	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00609	6.24	3.18	-6.36	0.01969	.	1.407670	0.05656	U	0.586011	T	0.00695	0.0023	M	0.69358	2.11	0.09310	N	0.999995	B	0.13594	0.008	B	0.06405	0.002	T	0.37033	-0.9723	10	0.54805	T	0.06	.	3.1538	0.06497	0.4027:0.2953:0.2179:0.0841	.	151	Q9BYQ8	KRA49_HUMAN	C	139;151;142	ENSP00000375234:R151C	ENSP00000334461:R142C	R	+	1	0	KRTAP4-9	36515617	0.000000	0.05858	0.000000	0.03702	0.674000	0.39518	-0.828000	0.04419	-3.015000	0.00271	-0.443000	0.05667	CGC	.	.	none		0.662	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329890	24329890	+	IGR	SNP	G	G	C	rs386824350|rs150066125		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24329890G>C								AC096509.1 (25096 upstream) : AC004552.1 (37035 downstream)																							gctaaagcaggagcagcagca	0.632													G|||	348	0.0921854	0.23	0.0447	3775	,	,		10384	0.001		0.0099	False		,,,				2504	0.002				p.P515A		Atlas-SNP	.											.	.	.	.	0			c.C1543G						PASS	.						10.0	9.0	9.0					X																	24329890		686	1583	2269	SO:0001628	intergenic_variant	170067	exon1			AAGCAGGAGCAGC																													X.37:g.24329890G>C		Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	280	138	0.492857	NM_001136233		Missense_Mutation	SNP		37																																																																																				G|0.925;C|0.075	0.075	strong	0	0.632								
CMYA5	202333	hgsc.bcm.edu	37	5	79026360	79026360	+	Missense_Mutation	SNP	G	G	A	rs16877124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79026360G>A	ENST00000446378.2	+	2	1803	c.1772G>A	c.(1771-1773)gGt>gAt	p.G591D		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	591	Glu-rich.		G -> D (in dbSNP:rs16877124).		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)		p.G591D(1)		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)		GTTTCTACTGGTTCTGCTTTT	0.408													A|||	1364	0.272364	0.5787	0.0821	5008	,	,		21788	0.3621		0.0815	False		,,,				2504	0.0971				p.G591D		Atlas-SNP	.											CMYA5,NS,carcinoma,0,1	CMYA5	643	1	1	Substitution - Missense(1)	stomach(1)	c.G1772A						PASS	.	A	ASP/GLY	1864,1958		458,948,505	238.0	234.0	235.0		1772	5.8	1.0	5	dbSNP_123	235	710,7574		39,632,3471	yes	missense	CMYA5	NM_153610.3	94	497,1580,3976	AA,AG,GG		8.5707,48.7703,21.2622	benign	591/4070	79026360	2574,9532	1911	4142	6053	SO:0001583	missense	202333	exon2			CTACTGGTTCTGC	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.1772G>A	5.37:g.79026360G>A	ENSP00000394770:p.Gly591Asp	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	176	176	1	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	622	0.2847985347985348	301	0.6117886178861789	30	0.08287292817679558	232	0.40559440559440557	59	0.07783641160949868	A	3.649	-0.071966	0.07228	0.487703	0.085707	ENSG00000164309	ENST00000446378	T	0.20463	2.07	5.8	5.8	0.92144	.	0.263939	0.27284	N	0.020071	T	0.00012	0.0000	N	0.00926	-1.1	0.47214	P	6.439999999999779E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.42899	-0.9424	9	0.02654	T	1	.	8.4593	0.32919	0.8479:0.0:0.1521:0.0	rs16877124;rs16877124	591	Q8N3K9	CMYA5_HUMAN	D	591	ENSP00000394770:G591D	ENSP00000394770:G591D	G	+	2	0	CMYA5	79062116	0.985000	0.35326	0.995000	0.50966	0.933000	0.57130	1.390000	0.34464	1.039000	0.40074	-0.360000	0.07572	GGT	G|0.704;A|0.296	0.296	strong		0.408	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
SORD	6652	hgsc.bcm.edu	37	15	45361180	45361180	+	Missense_Mutation	SNP	A	A	T	rs55739437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	291	0	0		WXS	Illumina HiSeq	Phase_I	307	305	0.993485	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		
XDH	7498	hgsc.bcm.edu	37	2	31610701	31610701	+	Silent	SNP	C	C	T	rs45575032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31610701C>T	ENST00000379416.3	-	8	675	c.627G>A	c.(625-627)gaG>gaA	p.E209E	XDH_ENST00000491727.1_5'UTR	NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	209					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)	GAAAAATGGGCTCCTGGGTTG	0.527													C|||	202	0.0403355	0.0151	0.0245	5008	,	,		18325	0.0575		0.0348	False		,,,				2504	0.0736				p.E209E	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.G627A						PASS	.	C		73,4331		1,71,2130	33.0	31.0	31.0		627	0.7	1.0	2	dbSNP_127	31	211,8385		1,209,4088	no	coding-synonymous	XDH	NM_000379.3		2,280,6218	TT,TC,CC		2.4546,1.6576,2.1846		209/1334	31610701	284,12716	2202	4298	6500	SO:0001819	synonymous_variant	7498	exon8			AATGGGCTCCTGG	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.627G>A	2.37:g.31610701C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	42	15	0.357143	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			C|0.972;T|0.028	0.028	strong		0.527	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
MAATS1	89876	hgsc.bcm.edu	37	3	119449159	119449159	+	Missense_Mutation	SNP	G	G	A	rs61742290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119449159G>A	ENST00000273390.5	+	8	1030	c.953G>A	c.(952-954)cGg>cAg	p.R318Q		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	318						mitochondrion (GO:0005739)											TTGAATGCCCGGTGGTCTAAA	0.438													G|||	23	0.00459265	0.0151	0.0043	5008	,	,		19286	0.0		0.0	False		,,,				2504	0.0				p.R318Q		Atlas-SNP	.											C3orf15,NS,carcinoma,+1,2	.	.	2	0			c.G953A						PASS	.	G	GLN/ARG	62,4344	58.7+/-95.3	0,62,2141	193.0	196.0	195.0		953	1.5	1.0	3	dbSNP_129	195	0,8600		0,0,4300	yes	missense	C3orf15	NM_033364.3	43	0,62,6441	AA,AG,GG		0.0,1.4072,0.4767	benign	318/768	119449159	62,12944	2203	4300	6503	SO:0001583	missense	89876	exon8			ATGCCCGGTGGTC	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.953G>A	3.37:g.119449159G>A	ENSP00000273390:p.Arg318Gln	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	131	69	0.526718	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	G	6.250	0.414169	0.11870	0.014072	0.0	ENSG00000183833	ENST00000273390	T	0.21734	1.99	5.2	1.55	0.23275	.	0.711873	0.14769	N	0.299528	T	0.05410	0.0143	N	0.04636	-0.2	0.80722	D	1	B;B;B;B;B	0.19935	0.008;0.04;0.012;0.019;0.005	B;B;B;B;B	0.12156	0.004;0.003;0.007;0.005;0.003	T	0.27297	-1.0078	10	0.12430	T	0.62	-20.1193	8.0697	0.30682	0.6841:0.0:0.3159:0.0	rs61742290	318;79;256;318;318	Q7Z4T9;Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	AAT1_HUMAN;.;.;.;.	Q	318	ENSP00000273390:R318Q	ENSP00000273390:R318Q	R	+	2	0	C3orf15	120931849	0.005000	0.15991	0.967000	0.41034	0.762000	0.43233	0.707000	0.25704	0.382000	0.24878	-0.484000	0.04775	CGG	G|0.995;A|0.005	0.005	strong		0.438	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
WDR90	197335	hgsc.bcm.edu	37	16	717523	717523	+	Silent	SNP	G	G	T	rs3752493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	78	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	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	
CDAN1	146059	hgsc.bcm.edu	37	15	43020983	43020983	+	Missense_Mutation	SNP	G	G	A	rs8023524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43020983G>A	ENST00000356231.3	-	20	2694	c.2671C>T	c.(2671-2673)Cgc>Tgc	p.R891C		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	891			R -> C (in dbSNP:rs8023524).		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)		TCTGCCTGGCGCACCAGATCT	0.567													G|||	1317	0.262979	0.4924	0.1282	5008	,	,		16633	0.0496		0.1859	False		,,,				2504	0.3476				p.R891C		Atlas-SNP	.											.	CDAN1	70	.	0			c.C2671T						PASS	.	G	CYS/ARG	1886,2520	539.6+/-375.3	396,1094,713	59.0	47.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2671	3.8	1.0	15	dbSNP_116	51	1620,6978	299.4+/-304.4	158,1304,2837	yes	missense	CDAN1	NM_138477.2	180	554,2398,3550	AA,AG,GG		18.8416,42.8053,26.9609	probably-damaging	891/1228	43020983	3506,9498	2203	4299	6502	SO:0001583	missense	146059	exon20			CCTGGCGCACCAG	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.2671C>T	15.37:g.43020983G>A	ENSP00000348564:p.Arg891Cys	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	187	87	0.465241	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	461	0.21108058608058608	219	0.4451219512195122	50	0.13812154696132597	37	0.06468531468531469	155	0.20448548812664907	G	18.56	3.650453	0.67472	0.428053	0.188416	ENSG00000140326	ENST00000356231;ENST00000267892	T	0.77877	-1.13	5.77	3.79	0.43588	.	0.789671	0.12571	N	0.457342	T	0.00012	0.0000	L	0.44542	1.39	0.29758	P	0.835791	D;D	0.63880	0.987;0.993	B;P	0.45712	0.409;0.491	T	0.31251	-0.9950	9	0.56958	D	0.05	-0.5786	8.3908	0.32526	0.0729:0.0:0.6087:0.3184	rs8023524;rs52797272;rs8023524	891;889	Q8IWY9;C9K0H8	CDAN1_HUMAN;.	C	891;889	ENSP00000348564:R891C	ENSP00000267892:R889C	R	-	1	0	CDAN1	40808275	0.697000	0.27767	0.961000	0.40146	0.994000	0.84299	0.862000	0.27899	1.447000	0.47661	0.561000	0.74099	CGC	G|0.749;A|0.251	0.251	strong		0.567	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
HSPA1L	3305	hgsc.bcm.edu	37	6	31778529	31778529	+	Silent	SNP	C	C	T	rs2075799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31778529C>T	ENST00000375654.4	-	2	1410	c.1221G>A	c.(1219-1221)acG>acA	p.T407T	HSPA1L_ENST00000417199.3_Silent_p.T407T	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	407					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						CGCCCCCAGCCGTCTCCAGCC	0.612													C|||	769	0.153554	0.233	0.1513	5008	,	,		17495	0.1845		0.0875	False		,,,				2504	0.0838				p.T407T		Atlas-SNP	.											HSPA1L,caecum,carcinoma,0,1	HSPA1L	185	1	0			c.G1221A						PASS	.	C		940,3466	358.1+/-314.2	90,760,1353	75.0	71.0	72.0		1221	-10.4	0.0	6	dbSNP_96	72	675,7925	168.8+/-220.3	36,603,3661	yes	coding-synonymous	HSPA1L	NM_005527.3		126,1363,5014	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	7.8488,21.3345,12.4173		407/642	31778529	1615,11391	2203	4300	6503	SO:0001819	synonymous_variant	3305	exon2			CCCAGCCGTCTCC	D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"""Heat shock proteins / HSP70"""	5234	protein-coding gene	gene with protein product		140559	"""heat shock 70kD protein-like 1"""			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.1221G>A	6.37:g.31778529C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	166	81	0.487952	NM_005527	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Silent	SNP	ENST00000375654.4	37	CCDS34413.1																																																																																			C|0.854;T|0.146	0.146	strong		0.612	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2		
RTN4IP1	84816	hgsc.bcm.edu	37	6	107076783	107076783	+	Silent	SNP	A	A	T	rs1987623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:107076783A>T	ENST00000369063.3	-	1	579	c.114T>A	c.(112-114)ccT>ccA	p.P38P	QRSL1_ENST00000369046.4_5'Flank|QRSL1_ENST00000369044.1_5'Flank|RTN4IP1_ENST00000539449.1_Silent_p.P38P	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	38						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		CAGTGCTCCTAGGAGAGGTAG	0.423													T|||	2340	0.467252	0.6074	0.5029	5008	,	,		19829	0.622		0.3181	False		,,,				2504	0.2464				p.P38P		Atlas-SNP	.											.	RTN4IP1	31	.	0			c.T114A						PASS	.	T		2533,1873	539.8+/-375.3	731,1071,401	126.0	116.0	119.0		114	-5.1	0.9	6	dbSNP_92	119	2365,6235	701.5+/-405.2	313,1739,2248	no	coding-synonymous	RTN4IP1	NM_032730.4		1044,2810,2649	TT,TA,AA		27.5,42.5102,37.6595		38/397	107076783	4898,8108	2203	4300	6503	SO:0001819	synonymous_variant	84816	exon1			GCTCCTAGGAGAG	AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.114T>A	6.37:g.107076783A>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	132	53	0.401515	NM_032730	Q8N9B3|Q8WZ66|Q9BRA4	Silent	SNP	ENST00000369063.3	37	CCDS5056.1																																																																																			A|0.608;T|0.392	0.392	strong		0.423	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1		
IL4R	3566	hgsc.bcm.edu	37	16	27374400	27374400	+	Missense_Mutation	SNP	A	A	G	rs1801275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27374400A>G	ENST00000395762.2	+	11	1986	c.1727A>G	c.(1726-1728)cAg>cGg	p.Q576R	IL4R_ENST00000170630.2_Missense_Mutation_p.Q576R|IL4R_ENST00000543915.2_Missense_Mutation_p.Q576R|IL4R_ENST00000380922.3_Missense_Mutation_p.Q561R	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	576	Required for IL4-induced gene expression.		Q -> R (associated with atopic dermatitis; lowered total IgE concentration; no effect on IL4-induced signal transduction; dbSNP:rs1801275). {ECO:0000269|PubMed:10233717, ECO:0000269|PubMed:10809862, ECO:0000269|PubMed:11285129, ECO:0000269|PubMed:9392697, 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						AGTGGCTATCAGGAGTTTGTA	0.647													G|||	1880	0.375399	0.792	0.3213	5008	,	,		17561	0.1657		0.2078	False		,,,				2504	0.2393				p.Q576R		Atlas-SNP	.											.	IL4R	70	.	0			c.A1727G	GRCh37	CM970783	IL4R	M	rs1801275	PASS	.	G	ARG/GLN	2963,1431		1034,895,268	26.0	33.0	31.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1727	2.8	0.5	16	dbSNP_89	31	1753,6847		173,1407,2720	yes	missense	IL4R	NM_000418.2	43	1207,2302,2988	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	20.3837,32.5671,36.2937	benign	576/826	27374400	4716,8278	2197	4300	6497	SO:0001583	missense	3566	exon11			GCTATCAGGAGTT	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.1727A>G	16.37:g.27374400A>G	ENSP00000379111:p.Gln576Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	68	43	0.632353	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	754	0.34523809523809523	400	0.8130081300813008	108	0.2983425414364641	82	0.14335664335664336	164	0.21635883905013192	G	0.768	-0.766897	0.02974	0.674329	0.203837	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.08984	3.04;3.04;3.03;3.04	4.81	2.8	0.32819	.	2.483730	0.02371	N	0.077918	T	0.00012	0.0000	N	0.00801	-1.175	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.33343	-0.9872	9	0.02654	T	1	-28.5034	6.9231	0.24399	0.3112:0.0:0.6888:0.0	rs1801275;rs52820812;rs61543625;rs1801275	561;576;576	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	R	576;576;561;576	ENSP00000379111:Q576R;ENSP00000441667:Q576R;ENSP00000370309:Q561R;ENSP00000170630:Q576R	ENSP00000170630:Q576R	Q	+	2	0	IL4R	27281901	0.995000	0.38212	0.512000	0.27736	0.660000	0.38997	1.015000	0.29963	0.463000	0.27118	-0.222000	0.12452	CAG	A|0.641;G|0.358	0.358	strong		0.647	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
PDZD2	23037	hgsc.bcm.edu	37	5	32077653	32077653	+	Missense_Mutation	SNP	G	G	A	rs61745726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32077653G>A	ENST00000438447.1	+	19	4011	c.3623G>A	c.(3622-3624)aGc>aAc	p.S1208N	PDZD2_ENST00000282493.3_Missense_Mutation_p.S1208N			O15018	PDZD2_HUMAN	PDZ domain containing 2	1208					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CTGGATGCCAGCCACCTCACA	0.498													G|||	454	0.090655	0.3298	0.0231	5008	,	,		18720	0.0		0.002	False		,,,				2504	0.0				p.S1208N		Atlas-SNP	.											.	PDZD2	306	.	0			c.G3623A						PASS	.	G	ASN/SER	1252,3154	430.6+/-342.6	174,904,1125	105.0	101.0	102.0		3623	4.1	0.0	5	dbSNP_129	102	4,8596	3.7+/-12.6	0,4,4296	yes	missense	PDZD2	NM_178140.2	46	174,908,5421	AA,AG,GG		0.0465,28.4158,9.6571	benign	1208/2840	32077653	1256,11750	2203	4300	6503	SO:0001583	missense	23037	exon18			ATGCCAGCCACCT	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3623G>A	5.37:g.32077653G>A	ENSP00000402033:p.Ser1208Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	178	0.0815018315018315	172	0.34959349593495936	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	G	5.804	0.332658	0.10956	0.284158	4.65E-4	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.06449	3.3;3.3	4.98	4.08	0.47627	.	0.800186	0.10630	N	0.652231	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B;B	0.24823	0.112;0.063	B;B	0.22386	0.026;0.039	T	0.41161	-0.9524	9	0.10636	T	0.68	.	10.343	0.43891	0.1022:0.0:0.8977:0.0	rs61745726	1034;1208	B4E3P2;O15018	.;PDZD2_HUMAN	N	1208;1013;1208	ENSP00000402033:S1208N;ENSP00000282493:S1208N	ENSP00000282493:S1208N	S	+	2	0	PDZD2	32113410	0.543000	0.26434	0.014000	0.15608	0.054000	0.15201	3.444000	0.52914	1.049000	0.40321	0.563000	0.77884	AGC	G|0.913;A|0.087	0.087	strong		0.498	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
PDE9A	5152	hgsc.bcm.edu	37	21	44179112	44179112	+	Missense_Mutation	SNP	C	C	G	rs146382324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44179112C>G	ENST00000291539.6	+	11	874	c.814C>G	c.(814-816)Ctg>Gtg	p.L272V	PDE9A_ENST00000398236.3_Missense_Mutation_p.L186V|PDE9A_ENST00000335440.6_Missense_Mutation_p.L170V|PDE9A_ENST00000335512.4_Missense_Mutation_p.L212V|PDE9A_ENST00000539837.1_Missense_Mutation_p.L144V|PDE9A_ENST00000398229.3_Missense_Mutation_p.L138V|PDE9A_ENST00000328862.6_Missense_Mutation_p.L246V|PDE9A_ENST00000398225.3_Missense_Mutation_p.L231V|PDE9A_ENST00000398224.3_Missense_Mutation_p.L145V|PDE9A_ENST00000398234.3_Missense_Mutation_p.L171V|PDE9A_ENST00000398227.3_Missense_Mutation_p.L112V|PDE9A_ENST00000380328.2_Missense_Mutation_p.L219V|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000349112.3_Missense_Mutation_p.L144V|PDE9A_ENST00000398232.3_Missense_Mutation_p.L205V	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	272					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	CCCACAGATGCTGAGCTGCCT	0.637													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19507	0.0		0.0	False		,,,				2504	0.0				p.L272V		Atlas-SNP	.											.	PDE9A	69	.	0			c.C814G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	11,4395	17.9+/-39.9	0,11,2192	81.0	65.0	71.0		634,433,430,655,511,193,193,556,334,163,412,508,193,163,613,691,736,193,193,814	5.1	1.0	21	dbSNP_134	71	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32	0,11,6492	GG,GC,CC		0.0,0.2497,0.0846	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	212/534,145/467,144/466,219/541,171/493,65/387,65/387,186/508,112/434,55/377,138/460,170/492,65/387,55/377,205/527,231/553,246/568,65/387,65/387,272/594	44179112	11,12995	2203	4300	6503	SO:0001583	missense	5152	exon11			CAGATGCTGAGCT	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.814C>G	21.37:g.44179112C>G	ENSP00000291539:p.Leu272Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	133	71	0.533835	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	18.52	3.641532	0.67244	0.002497	0.0	ENSG00000160191	ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000328862;ENST00000335440;ENST00000398225;ENST00000398229;ENST00000398227;ENST00000349112;ENST00000398224	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98	5.1	5.1	0.69264	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	T	0.79387	0.4437	L	0.53780	1.695	0.52099	D	0.999942	B;B;B;B;B;B;P;B;B;B;B;B;P;B;B;B	0.38597	0.079;0.101;0.101;0.237;0.101;0.161;0.639;0.237;0.101;0.101;0.237;0.11;0.579;0.441;0.101;0.027	B;B;B;B;B;B;P;B;B;B;B;B;B;B;B;B	0.48030	0.092;0.064;0.102;0.092;0.162;0.319;0.564;0.216;0.064;0.064;0.092;0.158;0.442;0.216;0.102;0.048	T	0.81147	-0.1065	10	0.66056	D	0.02	.	18.5908	0.91212	0.0:1.0:0.0:0.0	.	144;205;186;171;246;231;164;212;55;112;138;144;170;219;145;272	F5GWD0;O76083-13;O76083-8;O76083-6;O76083-15;O76083-14;O76083-16;O76083-2;O76083-10;O76083-9;O76083-11;O76083-4;O76083-12;O76083-5;O76083-3;O76083	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;PDE9A_HUMAN	V	212;144;272;219;205;171;186;246;170;231;138;112;144;145	ENSP00000335242:L212V;ENSP00000441899:L144V;ENSP00000291539:L272V;ENSP00000369685:L219V;ENSP00000381287:L205V;ENSP00000381289:L171V;ENSP00000381291:L186V;ENSP00000328699:L246V;ENSP00000335365:L170V;ENSP00000381281:L231V;ENSP00000381285:L138V;ENSP00000381283:L112V;ENSP00000344730:L144V;ENSP00000381280:L145V	ENSP00000291539:L272V	L	+	1	2	PDE9A	43052181	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.526000	0.60566	2.388000	0.81334	0.650000	0.86243	CTG	C|0.999;G|0.001	0.001	strong		0.637	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
TRPC5	7224	hgsc.bcm.edu	37	X	111020096	111020096	+	Silent	SNP	C	C	A	rs141761268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:111020096C>A	ENST00000262839.2	-	11	3285	c.2367G>T	c.(2365-2367)ggG>ggT	p.G789G		NM_012471.2	NP_036603.1	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel, subfamily C, member 5	789					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|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)			biliary_tract(1)|breast(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(38)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TGGCCCGAGCCCCACCACTGC	0.478													C|||	5	0.0013245	0.0038	0.0	3775	,	,		12501	0.0		0.0	False		,,,				2504	0.0				p.G789G		Atlas-SNP	.											.	TRPC5	142	.	0			c.G2367T						PASS	.	C		13,3822		0,9,4,1623,567	137.0	143.0	141.0		2367	2.8	1.0	X	dbSNP_134	141	0,6728		0,0,0,2428,1872	no	coding-synonymous	TRPC5	NM_012471.2		0,9,4,4051,2439	AA,AC,A,CC,C		0.0,0.339,0.1231		789/974	111020096	13,10550	2203	4300	6503	SO:0001819	synonymous_variant	7224	exon11			CCGAGCCCCACCA	AF054568	CCDS14561.1	Xq23	2014-06-13			ENSG00000072315	ENSG00000072315		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12337	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 159"""	300334				10493832, 16382100	Standard	NM_012471		Approved	PPP1R159	uc004epl.1	Q9UL62	OTTHUMG00000022212	ENST00000262839.2:c.2367G>T	X.37:g.111020096C>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	160	101	0.63125	NM_012471	B2RP53|O75233|Q5JXY8|Q9Y514	Silent	SNP	ENST00000262839.2	37	CCDS14561.1																																																																																			C|0.998;A|0.002	0.002	strong		0.478	TRPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057945.1	NM_012471	
SNX30	401548	hgsc.bcm.edu	37	9	115567184	115567184	+	Silent	SNP	T	T	C	rs1891402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:115567184T>C	ENST00000374232.3	+	2	449	c.285T>C	c.(283-285)gtT>gtC	p.V95V		NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	95	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						TCGTTATAGTTGATGATCCCA	0.438													C|||	4802	0.958866	0.9796	0.9654	5008	,	,		17614	0.999		0.9095	False		,,,				2504	0.9356				p.V95V		Atlas-SNP	.											.	SNX30	32	.	0			c.T285C						PASS	.	C		3818,114		1853,112,1	218.0	195.0	202.0		285	-0.1	1.0	9	dbSNP_92	202	7600,732		3467,666,33	no	coding-synonymous	SNX30	NM_001012994.1		5320,778,34	CC,CT,TT		8.7854,2.8993,6.8982		95/438	115567184	11418,846	1966	4166	6132	SO:0001819	synonymous_variant	401548	exon2			TATAGTTGATGAT	AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158		"""Sorting nexins"""	23685	protein-coding gene	gene with protein product							Standard	NM_001012994		Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.285T>C	9.37:g.115567184T>C		Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	176	175	0.994318	NM_001012994		Silent	SNP	ENST00000374232.3	37	CCDS43865.1																																																																																			T|0.054;C|0.946	0.946	strong		0.438	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053700.1		
GPR68	8111	hgsc.bcm.edu	37	14	91700846	91700846	+	Silent	SNP	G	G	A	rs2540862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91700846G>A	ENST00000531499.2	-	2	888	c.549C>T	c.(547-549)cgC>cgT	p.R183R	GPR68_ENST00000238699.3_Silent_p.R193R|GPR68_ENST00000529300.1_5'Flank|GPR68_ENST00000535815.1_Silent_p.R183R			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	183					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		AGTTGATGGCGCGCTGCCATG	0.632													G|||	767	0.153155	0.3366	0.0519	5008	,	,		19727	0.1677		0.004	False		,,,				2504	0.1155				p.R183R		Atlas-SNP	.											GPR68,colon,carcinoma,-2,1	GPR68	32	1	0			c.C549T						PASS	.	G	,	1280,3126	433.1+/-343.5	188,904,1111	69.0	51.0	57.0		549,549	-4.2	0.0	14	dbSNP_100	57	80,8520	46.3+/-105.2	0,80,4220	no	coding-synonymous,coding-synonymous	GPR68	NM_001177676.1,NM_003485.3	,	188,984,5331	AA,AG,GG		0.9302,29.0513,10.4567	,	183/366,183/366	91700846	1360,11646	2203	4300	6503	SO:0001819	synonymous_variant	8111	exon2			GATGGCGCGCTGC	U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"""GPCR / Class A : Orphans"""	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.549C>T	14.37:g.91700846G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	99	39	0.393939	NM_001177676	Q13334|Q4VBB4|Q6IX34	Silent	SNP	ENST00000531499.2	37	CCDS9894.2																																																																																			G|0.874;A|0.126	0.126	strong		0.632	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2		
TNRC18	84629	hgsc.bcm.edu	37	7	5417093	5417093	+	Silent	SNP	G	G	T	rs60530083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5417093G>T	ENST00000430969.1	-	7	2718	c.2370C>A	c.(2368-2370)cgC>cgA	p.R790R	TNRC18_ENST00000399537.4_Silent_p.R790R	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	790							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)		CGGCAGACCAGCGACCTGAGC	0.701													G|||	138	0.0275559	0.0514	0.0058	5008	,	,		11884	0.0139		0.002	False		,,,				2504	0.0511				p.R790R		Atlas-SNP	.											.	TNRC18	311	.	0			c.C2370A						PASS	.	G		181,3615		4,173,1721	8.0	11.0	10.0		2370	-0.9	0.9	7	dbSNP_129	10	21,8133		0,21,4056	no	coding-synonymous	TNRC18	NM_001080495.2		4,194,5777	TT,TG,GG		0.2575,4.7682,1.6904		790/2969	5417093	202,11748	1898	4077	5975	SO:0001819	synonymous_variant	84629	exon7			AGACCAGCGACCT	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.2370C>A	7.37:g.5417093G>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	53	32	0.603774	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.985;T|0.015	0.015	strong		0.701	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
TMEM232	642987	hgsc.bcm.edu	37	5	109941887	109941887	+	Missense_Mutation	SNP	C	C	T	rs73224392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:109941887C>T	ENST00000455884.2	-	9	1054	c.1004G>A	c.(1003-1005)aGc>aAc	p.S335N	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Missense_Mutation_p.S335N			C9JQI7	TM232_HUMAN	transmembrane protein 232	335						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						AGACATAATGCTTGAAACAAA	0.353													C|||	234	0.0467252	0.1694	0.0101	5008	,	,		12131	0.0		0.003	False		,,,				2504	0.0				p.S335N		Atlas-SNP	.											.	TMEM232	57	.	0			c.G1004A						PASS	.	C	ASN/SER	195,1189		17,161,514	70.0	59.0	62.0		1004	-2.9	0.3	5	dbSNP_130	62	5,3177		0,5,1586	yes	missense	TMEM232	NM_001039763.3	46	17,166,2100	TT,TC,CC		0.1571,14.0896,4.3802	benign	335/658	109941887	200,4366	692	1591	2283	SO:0001583	missense	642987	exon9			ATAATGCTTGAAA	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.1004G>A	5.37:g.109941887C>T	ENSP00000401477:p.Ser335Asn	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	217	98	0.451613	NM_001039763	B4DKF4	Missense_Mutation	SNP	ENST00000455884.2	37	CCDS47253.2	91	0.041666666666666664	86	0.17479674796747968	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.441	1.088145	0.20390	0.140896	0.001571	ENSG00000186952	ENST00000429839;ENST00000455884	.	.	.	5.45	-2.92	0.05615	.	0.756414	0.13148	N	0.410099	T	0.00073	0.0002	L	0.27053	0.805	0.80722	P	0.0	B;B;B	0.24186	0.099;0.004;0.037	B;B;B	0.19148	0.024;0.009;0.024	T	0.21724	-1.0237	7	.	.	.	-1.5952	5.9581	0.19286	0.0:0.3106:0.3588:0.3306	.	335;335;217	C9JQI7;C9JQI7-2;E9PFK0	TM232_HUMAN;.;.	N	335	.	.	S	-	2	0	TMEM232	109969786	0.000000	0.05858	0.319000	0.25293	0.578000	0.36192	-0.228000	0.09114	-0.134000	0.11516	-0.315000	0.08773	AGC	C|0.965;T|0.035	0.035	strong		0.353	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
ALPK1	80216	hgsc.bcm.edu	37	4	113352628	113352628	+	Missense_Mutation	SNP	A	A	G	rs13148353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:113352628A>G	ENST00000458497.1	+	11	2204	c.1925A>G	c.(1924-1926)cAt>cGt	p.H642R	ALPK1_ENST00000177648.9_Missense_Mutation_p.H642R|ALPK1_ENST00000504176.2_Missense_Mutation_p.H564R	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	642			H -> R (in dbSNP:rs13148353). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.5}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CATTCATTGCATTCACAGCTT	0.483													G|||	3298	0.658546	0.7481	0.5807	5008	,	,		21516	0.7014		0.6511	False		,,,				2504	0.5562				p.H642R		Atlas-SNP	.											.	ALPK1	125	.	0			c.A1925G						PASS	.	G	ARG/HIS,ARG/HIS	3196,1210	420.8+/-339.2	1158,880,165	94.0	88.0	90.0		1925,1925	2.5	0.0	4	dbSNP_121	90	5651,2949	458.8+/-364.7	1854,1943,503	yes	missense,missense	ALPK1	NM_001102406.1,NM_025144.3	29,29	3012,2823,668	GG,GA,AA		34.2907,27.4626,31.9775	benign,benign	642/1245,642/1245	113352628	8847,4159	2203	4300	6503	SO:0001583	missense	80216	exon11			CATTGCATTCACA	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.1925A>G	4.37:g.113352628A>G	ENSP00000398048:p.His642Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	1474	0.674908424908425	354	0.7195121951219512	209	0.5773480662983426	415	0.7255244755244755	496	0.6543535620052771	G	8.574	0.880768	0.17467	0.725374	0.657093	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.02323	4.41;4.41;4.34	5.2	2.53	0.30540	.	0.366946	0.31507	N	0.007528	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	0.04650	-1.0936	9	0.20046	T	0.44	1.0739	3.9921	0.09541	0.2619:0.5053:0.1536:0.0792	rs13148353;rs52817326;rs58328079;rs13148353	564;642	F5H138;Q96QP1	.;ALPK1_HUMAN	R	642;642;564	ENSP00000398048:H642R;ENSP00000177648:H642R;ENSP00000426044:H564R	ENSP00000177648:H642R	H	+	2	0	ALPK1	113572077	0.002000	0.14202	0.006000	0.13384	0.003000	0.03518	0.246000	0.18160	-0.030000	0.13804	-0.726000	0.03593	CAT	A|0.320;G|0.679	0.679	strong		0.483	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
BRD1	23774	hgsc.bcm.edu	37	22	50217387	50217387	+	Silent	SNP	G	G	A	rs11912787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50217387G>A	ENST00000216267.8	-	1	1065	c.579C>T	c.(577-579)ttC>ttT	p.F193F	BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000404034.1_Silent_p.F193F|BRD1_ENST00000404760.1_Silent_p.F193F|BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000457780.2_Silent_p.F193F|BRD1_ENST00000459821.1_5'Flank	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	105	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	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	
OR10K1	391109	hgsc.bcm.edu	37	1	158436201	158436201	+	Silent	SNP	T	T	C	rs76117330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158436201T>C	ENST00000289451.2	+	1	930	c.850T>C	c.(850-852)Ttg>Ctg	p.L284L		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, 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)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					CCTTACCCCATTGTTCAATCC	0.388													T|||	189	0.0377396	0.1354	0.013	5008	,	,		21238	0.0		0.001	False		,,,				2504	0.0				p.L284L		Atlas-SNP	.											.	OR10K1	80	.	0			c.T850C						PASS	.	T		513,3893	235.2+/-247.8	29,455,1719	146.0	140.0	142.0		850	-7.0	0.0	1	dbSNP_131	142	8,8592	7.1+/-27.0	0,8,4292	no	coding-synonymous	OR10K1	NM_001004473.1		29,463,6011	CC,CT,TT		0.093,11.6432,4.0058		284/314	158436201	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	391109	exon1			ACCCCATTGTTCA	AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"""GPCR / Class A : Olfactory receptors"""	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.850T>C	1.37:g.158436201T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_001004473	Q6IFS2	Silent	SNP	ENST00000289451.2	37	CCDS30897.1																																																																																			T|0.963;C|0.037	0.037	strong		0.388	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1		
PLOD2	5352	hgsc.bcm.edu	37	3	145809622	145809622	+	Missense_Mutation	SNP	A	A	G	rs138948307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:145809622A>G	ENST00000360060.3	-	8	1021	c.844T>C	c.(844-846)Tgt>Cgt	p.C282R	PLOD2_ENST00000494950.1_Missense_Mutation_p.C227R|RP11-274H2.2_ENST00000480247.1_RNA|PLOD2_ENST00000282903.5_Missense_Mutation_p.C282R	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	282					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|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)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	TCGAATTCACAAAGAGTGCAG	0.343													A|||	3	0.000599042	0.0015	0.0014	5008	,	,		17493	0.0		0.0	False		,,,				2504	0.0				p.C282R		Atlas-SNP	.											.	PLOD2	81	.	0			c.T844C						PASS	.	A	ARG/CYS,ARG/CYS	9,4397	15.5+/-35.6	0,9,2194	104.0	92.0	96.0		844,844	6.1	0.7	3	dbSNP_134	96	0,8600		0,0,4300	yes	missense,missense	PLOD2	NM_000935.2,NM_182943.2	180,180	0,9,6494	GG,GA,AA		0.0,0.2043,0.0692	probably-damaging,probably-damaging	282/738,282/759	145809622	9,12997	2203	4300	6503	SO:0001583	missense	5352	exon8			ATTCACAAAGAGT	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"""lysyl hydroxlase 2"""	601865	"""procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"""			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.844T>C	3.37:g.145809622A>G	ENSP00000353170:p.Cys282Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	136	53	0.389706	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	37	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172440	0.78452	0.002043	0.0	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000494950	T;T;T	0.69306	-0.39;-0.37;-0.35	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.84651	0.5519	M	0.89353	3.025	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.996	D;D;P	0.91635	0.997;0.999;0.903	D	0.87463	0.2409	10	0.87932	D	0	-32.5497	15.6071	0.76682	1.0:0.0:0.0:0.0	.	227;282;282	E7ETU9;O00469;O00469-2	.;PLOD2_HUMAN;.	R	282;282;227	ENSP00000282903:C282R;ENSP00000353170:C282R;ENSP00000420094:C227R	ENSP00000282903:C282R	C	-	1	0	PLOD2	147292312	1.000000	0.71417	0.726000	0.30738	0.917000	0.54804	7.900000	0.87376	2.323000	0.78572	0.528000	0.53228	TGT	A|0.999;G|0.001	0.001	strong		0.343	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
SSPN	8082	hgsc.bcm.edu	37	12	26383959	26383959	+	Missense_Mutation	SNP	G	G	A	rs12313736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26383959G>A	ENST00000242729.2	+	3	859	c.682G>A	c.(682-684)Gtc>Atc	p.V228I	RP11-283G6.5_ENST00000537525.1_RNA|RP11-283G6.5_ENST00000540625.1_RNA|SSPN_ENST00000535504.1_Intron|SSPN_ENST00000540266.1_Missense_Mutation_p.V125I|SSPN_ENST00000422622.2_Missense_Mutation_p.V125I|RP11-283G6.5_ENST00000541940.1_RNA|RP11-283G6.4_ENST00000540392.1_RNA	NM_005086.4	NP_005077.2	Q14714	SSPN_HUMAN	sarcospan	228			V -> I (in dbSNP:rs12313736).		cell adhesion (GO:0007155)|muscle contraction (GO:0006936)	cell junction (GO:0030054)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)				kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10	Colorectal(261;0.0847)					CTATGTGGGTGTCAGGATATG	0.483													G|||	457	0.091254	0.2821	0.0605	5008	,	,		17485	0.0		0.0258	False		,,,				2504	0.0164				p.V228I		Atlas-SNP	.											.	SSPN	19	.	0			c.G682A						PASS	.	G	ILE/VAL,ILE/VAL	993,3413	370.5+/-319.6	128,737,1338	107.0	103.0	104.0		373,682	3.9	0.9	12	dbSNP_120	104	302,8298	109.8+/-170.3	6,290,4004	yes	missense,missense	SSPN	NM_001135823.1,NM_005086.4	29,29	134,1027,5342	AA,AG,GG		3.5116,22.5374,9.9569	benign,benign	125/141,228/244	26383959	1295,11711	2203	4300	6503	SO:0001583	missense	8082	exon3			GTGGGTGTCAGGA	AF016028	CCDS8707.1, CCDS44850.1	12p11.2	2014-09-17	2012-03-14			ENSG00000123096			11322	protein-coding gene	gene with protein product		601599	"""Kras oncogene-associated gene"""	KRAG		9395445, 8661122	Standard	NM_005086		Approved	SPN1, SPN2	uc001rhe.3	Q14714		ENST00000242729.2:c.682G>A	12.37:g.26383959G>A	ENSP00000242729:p.Val228Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_005086	B3KS67	Missense_Mutation	SNP	ENST00000242729.2	37	CCDS8707.1	141	0.06456043956043957	104	0.21138211382113822	17	0.04696132596685083	0	0.0	20	0.026385224274406333	G	14.98	2.697051	0.48202	0.225374	0.035116	ENSG00000123096	ENST00000540266;ENST00000422622;ENST00000242729;ENST00000441067	T;T;T	0.33865	1.47;1.47;1.39	4.81	3.9	0.45041	.	0.202595	0.42821	D	0.000653	T	0.00012	0.0000	L	0.57536	1.79	0.22050	P	0.999396981	B	0.11235	0.004	B	0.06405	0.002	T	0.08764	-1.0706	8	.	.	.	-8.9216	7.5114	0.27575	0.1437:0.148:0.7083:0.0	rs12313736;rs52831951;rs12313736	228	Q14714	SSPN_HUMAN	I	125;125;228;202	ENSP00000442893:V125I;ENSP00000396087:V125I;ENSP00000242729:V228I	.	V	+	1	0	SSPN	26275226	0.003000	0.15002	0.919000	0.36401	0.943000	0.58893	1.274000	0.33132	2.396000	0.81511	0.563000	0.77884	GTC	G|0.913;A|0.087	0.087	strong		0.483	SSPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402654.2	NM_005086	
POTEE	445582	hgsc.bcm.edu	37	2	132021684	132021684	+	Missense_Mutation	SNP	C	C	A	rs2672150		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:132021684C>A	ENST00000356920.5	+	15	2750	c.2656C>A	c.(2656-2658)Cct>Act	p.P886T	POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	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	575	5	0.00869565		WXS	Illumina HiSeq	Phase_I	520	16	0.0307692	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	
KIAA0141	9812	hgsc.bcm.edu	37	5	141313888	141313888	+	Silent	SNP	A	A	C	rs115183657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141313888A>C	ENST00000432126.2	+	9	1115	c.981A>C	c.(979-981)ccA>ccC	p.P327P	KIAA0141_ENST00000194118.4_Silent_p.P327P	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	327					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACGAGACCCAGCCTCTTCGT	0.597													A|||	44	0.00878594	0.0318	0.0029	5008	,	,		14901	0.0		0.0	False		,,,				2504	0.0				p.P327P		Atlas-SNP	.											.	KIAA0141	44	.	0			c.A981C						PASS	.	A	,	104,4302	79.9+/-118.3	0,104,2099	49.0	47.0	48.0		981,981	-7.0	0.0	5	dbSNP_132	48	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KIAA0141	NM_001142603.1,NM_014773.3	,	0,104,6399	CC,CA,AA		0.0,2.3604,0.7996	,	327/516,327/516	141313888	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	9812	exon9			AGACCCAGCCTCT	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.981A>C	5.37:g.141313888A>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	NM_001142603	Q969R4|Q96EU9	Silent	SNP	ENST00000432126.2	37	CCDS4268.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	A	0.525	-0.860231	0.02610	0.023604	0.0	ENSG00000081791	ENST00000507481	.	.	.	5.55	-6.96	0.01622	.	.	.	.	.	T	0.06371	0.0164	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.24657	-1.0154	4	.	.	.	-1.6157	4.7459	0.13036	0.1625:0.5451:0.1777:0.1147	.	.	.	.	P	29	.	.	Q	+	2	0	KIAA0141	141294072	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.619000	0.05572	-1.086000	0.03084	-0.290000	0.09829	CAG	A|0.991;C|0.009	0.009	strong		0.597	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
MAP3K19	80122	hgsc.bcm.edu	37	2	135745722	135745722	+	Silent	SNP	A	A	G	rs10928526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:135745722A>G	ENST00000375845.3	-	7	750	c.720T>C	c.(718-720)agT>agC	p.S240S	MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392915.1_Silent_p.S257S|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Silent_p.S127S|MAP3K19_ENST00000392918.3_Intron	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	240							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										AAGATGTGAGACTTGGAATGT	0.478													G|||	1817	0.362819	0.3306	0.232	5008	,	,		19049	0.5417		0.2704	False		,,,				2504	0.41				p.S240S		Atlas-SNP	.											.	.	.	.	0			c.T720C						PASS	.	G	,	1393,3013	685.6+/-404.6	222,949,1032	97.0	108.0	105.0		,720	-0.5	0.0	2	dbSNP_120	105	1980,6620	721.7+/-406.4	259,1462,2579	no	intron,coding-synonymous	YSK4	NM_001018046.1,NM_025052.3	,	481,2411,3611	GG,GA,AA		23.0233,31.616,25.9342	,	,240/1329	135745722	3373,9633	2203	4300	6503	SO:0001819	synonymous_variant	80122	exon7			TGTGAGACTTGGA	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.720T>C	2.37:g.135745722A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	51	18	0.352941	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Silent	SNP	ENST00000375845.3	37	CCDS2176.2																																																																																			A|0.687;G|0.313	0.313	strong		0.478	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
PEX16	9409	hgsc.bcm.edu	37	11	45932458	45932458	+	Silent	SNP	G	G	A	rs150774189	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:45932458G>A	ENST00000378750.5	-	10	1186	c.943C>T	c.(943-945)Ctg>Ttg	p.L315L	PEX16_ENST00000532681.1_Silent_p.L220L|PEX16_ENST00000241041.3_Silent_p.L315L			Q9Y5Y5	PEX16_HUMAN	peroxisomal biogenesis factor 16	315	Interaction with PEX19.				ER-dependent peroxisome organization (GO:0032581)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)|protein localization to endoplasmic reticulum (GO:0070972)|protein targeting to peroxisome (GO:0006625)|protein to membrane docking (GO:0022615)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)			large_intestine(2)|lung(2)|ovary(2)|skin(1)	7				GBM - Glioblastoma multiforme(35;0.223)		CTTGTGACCAGGCCAACGCCA	0.597													G|||	19	0.00379393	0.0136	0.0014	5008	,	,		18792	0.0		0.0	False		,,,				2504	0.0				p.L315L		Atlas-SNP	.											.	PEX16	24	.	0			c.C943T						PASS	.	G	,	68,4338	62.3+/-99.4	2,64,2137	118.0	102.0	108.0		943,943	3.4	1.0	11	dbSNP_134	108	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	PEX16	NM_004813.2,NM_057174.2	,	2,64,6436	AA,AG,GG		0.0,1.5433,0.5229	,	315/337,315/347	45932458	68,12936	2203	4299	6502	SO:0001819	synonymous_variant	9409	exon10			TGACCAGGCCAAC	AF118240	CCDS7917.1, CCDS31472.1	11p	2007-12-14			ENSG00000121680	ENSG00000121680			8857	protein-coding gene	gene with protein product		603360				9922452	Standard	NM_057174		Approved		uc001nbt.3	Q9Y5Y5	OTTHUMG00000167005	ENST00000378750.5:c.943C>T	11.37:g.45932458G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_004813	Q9BWB9	Silent	SNP	ENST00000378750.5	37	CCDS31472.1																																																																																			G|0.995;A|0.005	0.005	strong		0.597	PEX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392398.1	NM_057174	
DIDO1	11083	hgsc.bcm.edu	37	20	61528074	61528074	+	Silent	SNP	T	T	C	rs910149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61528074T>C	ENST00000266070.4	-	7	2188	c.1863A>G	c.(1861-1863)gcA>gcG	p.A621A	DIDO1_ENST00000395340.1_Silent_p.A621A|DIDO1_ENST00000395335.2_Silent_p.A621A|DIDO1_ENST00000395343.1_Silent_p.A621A	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	621					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)					AGGCAGCCGTTGCCGCTGCAG	0.642													C|||	3375	0.673922	0.9433	0.5836	5008	,	,		16230	0.6577		0.4801	False		,,,				2504	0.59				p.A621A	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.A1863G						PASS	.	C	,,,	3793,613	253.0+/-259.1	1633,527,43	46.0	51.0	50.0		1863,1863,1863,1863	-1.0	0.0	20	dbSNP_86	50	4434,4166	543.3+/-384.4	1151,2132,1017	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_001193370.1,NM_033081.2,NM_080797.3	,,,	2784,2659,1060	CC,CT,TT		48.4419,13.9128,36.7446	,,,	621/2241,621/1190,621/2241,621/1190	61528074	8227,4779	2203	4300	6503	SO:0001819	synonymous_variant	11083	exon7			AGCCGTTGCCGCT	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.1863A>G	20.37:g.61528074T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			T|0.366;C|0.634	0.634	strong		0.642	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
MUC5B	727897	hgsc.bcm.edu	37	11	1255773	1255773	+	Silent	SNP	C	C	T	rs7116614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	186	0	0		WXS	Illumina HiSeq	Phase_I	186	87	0.467742	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	
ERN1	2081	hgsc.bcm.edu	37	17	62149423	62149423	+	Silent	SNP	G	G	A	rs374999844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62149423G>A	ENST00000433197.3	-	6	491	c.396C>T	c.(394-396)acC>acT	p.T132T	ERN1_ENST00000577567.1_5'UTR	NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						GCTTCTCTCCGGTCAGGAGGT	0.448													G|||	2	0.000399361	0.0015	0.0	5008	,	,		20164	0.0		0.0	False		,,,				2504	0.0				p.T132T		Atlas-SNP	.											.	ERN1	102	.	0			c.C396T						PASS	.	G		5,3827		0,5,1911	51.0	50.0	51.0		396	-2.8	1.0	17		51	1,8269		0,1,4134	no	coding-synonymous	ERN1	NM_001433.3		0,6,6045	AA,AG,GG		0.0121,0.1305,0.0496		132/978	62149423	6,12096	1916	4135	6051	SO:0001819	synonymous_variant	2081	exon6			CTCTCCGGTCAGG	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"""inositol-requiring enzyme 1"""	604033	"""ER to nucleus signalling 1"""			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.396C>T	17.37:g.62149423G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_001433		Silent	SNP	ENST00000433197.3	37	CCDS45762.1																																																																																			.	.	weak		0.448	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433	
HCST	10870	hgsc.bcm.edu	37	19	36394272	36394272	+	Silent	SNP	T	T	C	rs33964243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36394272T>C	ENST00000246551.4	+	2	177	c.63T>C	c.(61-63)acT>acC	p.T21T	NFKBID_ENST00000396901.1_5'Flank|NFKBID_ENST00000352614.2_5'Flank|NFKBID_ENST00000606253.1_5'Flank|HCST_ENST00000437550.2_Silent_p.T21T			Q9UBK5	HCST_HUMAN	hematopoietic cell signal transducer	21					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)			CTCAGACGACTCCAGGAGAGA	0.562													C|||	759	0.151558	0.4266	0.0548	5008	,	,		19857	0.1002		0.0099	False		,,,				2504	0.047				p.T21T		Atlas-SNP	.											.	HCST	10	.	0			c.T63C						PASS	.	C	,	1636,2770	659.8+/-400.6	306,1024,873	113.0	100.0	105.0		63,63	1.4	0.1	19	dbSNP_126	105	127,8473	813.8+/-407.0	1,125,4174	no	coding-synonymous,coding-synonymous	HCST	NM_001007469.1,NM_014266.3	,	307,1149,5047	CC,CT,TT		1.4767,37.1312,13.5553	,	21/93,21/94	36394272	1763,11243	2203	4300	6503	SO:0001819	synonymous_variant	10870	exon2			GACGACTCCAGGA	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.63T>C	19.37:g.36394272T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001007469	Q9UBS1|Q9Y3Y0	Silent	SNP	ENST00000246551.4	37	CCDS32998.1																																																																																			T|0.876;C|0.124	0.124	strong		0.562	HCST-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109520.3	NM_014266	
LILRA2	11027	hgsc.bcm.edu	37	19	55098736	55098736	+	Missense_Mutation	SNP	G	G	C	rs73939007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55098736G>C	ENST00000251377.3	+	9	1508	c.1375G>C	c.(1375-1377)Gtc>Ctc	p.V459L	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA2_ENST00000391738.3_Missense_Mutation_p.V459L|CTB-83J4.2_ENST00000596330.1_lincRNA|LILRA2_ENST00000391737.1_Missense_Mutation_p.V430L|LILRA2_ENST00000251376.3_Missense_Mutation_p.V442L|LILRB1_ENST00000418536.2_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	459					defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		GGCTGGCTTGGTCCTGGTGGT	0.567													g|||	51	0.0101837	0.0378	0.0014	5008	,	,		17382	0.0		0.0	False		,,,				2504	0.0				p.V459L		Atlas-SNP	.											.	LILRA2	99	.	0			c.G1375C						PASS	.	G	LEU/VAL,LEU/VAL	100,4306	79.3+/-117.8	0,100,2103	111.0	96.0	101.0		1375,1324	-5.5	0.0	19	dbSNP_130	101	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	LILRA2	NM_001130917.1,NM_006866.2	32,32	0,102,6401	CC,CG,GG		0.0233,2.2696,0.7843	,	459/484,442/467	55098736	102,12904	2203	4300	6503	SO:0001583	missense	11027	exon8			GGCTTGGTCCTGG	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.1375G>C	19.37:g.55098736G>C	ENSP00000251377:p.Val459Leu	Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	257	115	0.447471	NM_001130917	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	9.895	1.205412	0.22205	0.022696	2.33E-4	ENSG00000239998	ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T	0.00617	6.41;6.41;6.35;6.19	2.74	-5.49	0.02584	.	30.411000	0.00832	N	0.001664	T	0.00241	0.0007	L	0.43923	1.385	0.09310	N	0.999998	B;B;B	0.24258	0.098;0.1;0.024	B;B;B	0.25614	0.051;0.062;0.028	T	0.42965	-0.9420	10	0.49607	T	0.09	.	7.5721	0.27913	0.1909:0.1704:0.6387:0.0	.	430;459;442	A8MZH0;Q8N149;Q8N149-2	.;LIRA2_HUMAN;.	L	459;459;442;430	ENSP00000251377:V459L;ENSP00000375618:V459L;ENSP00000251376:V442L;ENSP00000375617:V430L	ENSP00000251376:V442L	V	+	1	0	LILRA2	59790548	0.005000	0.15991	0.002000	0.10522	0.162000	0.22319	-0.202000	0.09451	-1.128000	0.02922	-0.320000	0.08662	GTC	G|0.991;C|0.009	0.009	strong		0.567	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2		
MYOM3	127294	hgsc.bcm.edu	37	1	24421474	24421474	+	Missense_Mutation	SNP	G	G	A	rs6678540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24421474G>A	ENST00000374434.3	-	9	959	c.797C>T	c.(796-798)aCg>aTg	p.T266M	MYOM3_ENST00000330966.7_Missense_Mutation_p.T267M|MYOM3_ENST00000475306.1_5'UTR|MYOM3_ENST00000329601.7_Missense_Mutation_p.T266M	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	266			T -> M (in dbSNP:rs6678540). {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)		GGGGCCAAACGTCGATCCTGG	0.532													A|||	1602	0.319888	0.2746	0.2911	5008	,	,		18851	0.3383		0.4771	False		,,,				2504	0.2209				p.T266M		Atlas-SNP	.											.	MYOM3	131	.	0			c.C797T						PASS	.	A	MET/THR	1045,2801		156,733,1034	45.0	46.0	45.0		797	4.1	0.7	1	dbSNP_116	45	3747,4489		855,2037,1226	yes	missense	MYOM3	NM_152372.3	81	1011,2770,2260	AA,AG,GG		45.4954,27.1711,39.6623	benign	266/1438	24421474	4792,7290	1923	4118	6041	SO:0001583	missense	127294	exon9			CCAAACGTCGATC	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.797C>T	1.37:g.24421474G>A	ENSP00000363557:p.Thr266Met	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	120	66	0.55	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	820	0.37545787545787546	141	0.2865853658536585	116	0.32044198895027626	179	0.3129370629370629	384	0.5065963060686016	A	7.540	0.660523	0.14645	0.271711	0.454954	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.55930	0.53;0.53;0.49	5.18	4.06	0.47325	.	0.579783	0.19017	N	0.124919	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.09377	0.004;0.0	T	0.46484	-0.9188	9	0.12430	T	0.62	.	7.2915	0.26368	0.8218:0.0:0.1782:0.0	rs6678540;rs17184616;rs52794525;rs58002450;rs6678540	266;266	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	M	266;267;266	ENSP00000363557:T266M;ENSP00000332670:T267M;ENSP00000328415:T266M	ENSP00000328415:T266M	T	-	2	0	MYOM3	24294061	0.108000	0.22018	0.674000	0.29902	0.591000	0.36615	2.024000	0.41049	0.810000	0.34279	-0.381000	0.06696	ACG	G|0.633;A|0.367	0.367	strong		0.532	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
TENM4	26011	hgsc.bcm.edu	37	11	78399121	78399121	+	Silent	SNP	G	G	A	rs1792148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:78399121G>A	ENST00000278550.7	-	29	5700	c.5238C>T	c.(5236-5238)ggC>ggT	p.G1746G		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1746					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										TGTAGAAGGCGCCTGAGGCAG	0.542													A|||	662	0.132188	0.3222	0.1023	5008	,	,		18874	0.002		0.1342	False		,,,				2504	0.0286				p.G1746G		Atlas-SNP	.											ODZ4_ENST00000278550,colon,carcinoma,-2,1	.	.	1	0			c.C5238T						PASS	.	A		1085,3021		145,795,1113	159.0	163.0	162.0		5238	2.5	1.0	11	dbSNP_89	162	889,7415		45,799,3308	no	coding-synonymous	ODZ4	NM_001098816.2		190,1594,4421	AA,AG,GG		10.7057,26.4247,15.9065		1746/2770	78399121	1974,10436	2053	4152	6205	SO:0001819	synonymous_variant	26011	exon29			GAAGGCGCCTGAG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5238C>T	11.37:g.78399121G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			G|0.864;A|0.136	0.136	strong		0.542	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
STAB2	55576	hgsc.bcm.edu	37	12	104014294	104014294	+	Missense_Mutation	SNP	C	C	T	rs150189813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:104014294C>T	ENST00000388887.2	+	4	584	c.380C>T	c.(379-381)gCt>gTt	p.A127V		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						GGCAGTTGTGCTGAAGGCATG	0.493													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		19345	0.0		0.0	False		,,,				2504	0.0				p.A127V		Atlas-SNP	.											.	STAB2	370	.	0			c.C380T						PASS	.	C	VAL/ALA	5,4399		0,5,2197	115.0	93.0	100.0		380	1.8	0.1	12	dbSNP_134	100	0,8594		0,0,4297	yes	missense	STAB2	NM_017564.9	64	0,5,6494	TT,TC,CC		0.0,0.1135,0.0385	possibly-damaging	127/2552	104014294	5,12993	2202	4297	6499	SO:0001583	missense	55576	exon4			GTTGTGCTGAAGG	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.380C>T	12.37:g.104014294C>T	ENSP00000373539:p.Ala127Val	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	209	107	0.511962	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.25	2.179669	0.38511	0.001135	0.0	ENSG00000136011	ENST00000388887	D	0.83673	-1.75	4.98	1.84	0.25277	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.200082	0.43919	D	0.000512	T	0.71221	0.3314	L	0.33485	1.01	0.18873	N	0.999987	P	0.41041	0.736	B	0.38803	0.282	T	0.59762	-0.7393	10	0.18710	T	0.47	.	11.2145	0.48819	0.5338:0.4662:0.0:0.0	.	127	Q8WWQ8	STAB2_HUMAN	V	127	ENSP00000373539:A127V	ENSP00000373539:A127V	A	+	2	0	STAB2	102538424	0.227000	0.23707	0.136000	0.22124	0.997000	0.91878	0.357000	0.20199	0.122000	0.18314	0.549000	0.68633	GCT	C|1.000;T|0.000	0.000	strong		0.493	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
FUCA2	2519	hgsc.bcm.edu	37	6	143816859	143816859	+	Silent	SNP	C	C	T	rs8161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:143816859C>T	ENST00000002165.6	-	7	1444	c.1389G>A	c.(1387-1389)ctG>ctA	p.L463L	RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	463					fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)	p.L463L(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		TCACATTAGTCAGGGCTAGAG	0.448													T|||	2116	0.422524	0.4796	0.438	5008	,	,		18597	0.4821		0.339	False		,,,				2504	0.3589				p.L463L		Atlas-SNP	.											FUCA2,NS,carcinoma,0,1	FUCA2	28	1	1	Substitution - coding silent(1)	stomach(1)	c.G1389A						PASS	.	T		2070,2336	605.8+/-390.6	486,1098,619	88.0	74.0	79.0		1389	-1.4	0.0	6	dbSNP_52	79	2938,5662	668.3+/-402.5	523,1892,1885	yes	coding-synonymous	FUCA2	NM_032020.4		1009,2990,2504	TT,TC,CC		34.1628,46.9814,38.5053		463/468	143816859	5008,7998	2203	4300	6503	SO:0001819	synonymous_variant	2519	exon7			ATTAGTCAGGGCT	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1389G>A	6.37:g.143816859C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Silent	SNP	ENST00000002165.6	37	CCDS5200.1																																																																																			C|0.585;T|0.415	0.415	strong		0.448	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
SVIL	6840	hgsc.bcm.edu	37	10	29839787	29839787	+	Missense_Mutation	SNP	A	A	G	rs10160013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	88	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	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		
SEPT8	23176	hgsc.bcm.edu	37	5	132099999	132099999	+	Silent	SNP	A	A	G	rs30507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132099999A>G	ENST00000378719.2	-	3	501	c.264T>C	c.(262-264)taT>taC	p.Y88Y	SEPT8_ENST00000378721.4_Silent_p.Y88Y|SEPT8_ENST00000378706.1_Silent_p.Y88Y|SEPT8_ENST00000296873.7_Silent_p.Y88Y|SEPT8_ENST00000378701.1_Silent_p.Y88Y|SEPT8_ENST00000458488.2_Silent_p.Y88Y|SEPT8_ENST00000378699.2_Silent_p.Y28Y|SEPT8_ENST00000448933.1_Silent_p.Y28Y	NM_001098811.1	NP_001092281.1	Q92599	SEPT8_HUMAN	septin 8	88	Septin-type G.				cell cycle (GO:0007049)	septin complex (GO:0031105)	GTP binding (GO:0005525)		SEPT8/AFF4(2)	kidney(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCTGGAGGTCATAGGTCTGGG	0.562													G|||	2508	0.500799	0.9221	0.3199	5008	,	,		18143	0.747		0.1441	False		,,,				2504	0.1728				p.Y88Y		Atlas-SNP	.											.	SEPT8	28	.	0			c.T264C						PASS	.	G	,,,	3329,985		1313,703,141	95.0	102.0	100.0		264,264,84,264	-6.2	0.3	5	dbSNP_76	100	1016,7524		52,912,3306	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEPT8	NM_001098811.1,NM_001098812.1,NM_001098813.1,NM_015146.1	,,,	1365,1615,3447	GG,GA,AA		11.897,22.8326,33.8027	,,,	88/484,88/443,28/370,88/430	132099999	4345,8509	2157	4270	6427	SO:0001819	synonymous_variant	23176	exon3			GAGGTCATAGGTC	AF179995	CCDS43358.1, CCDS43359.1, CCDS43360.1, CCDS47262.1, CCDS75298.1	5q31	2013-01-21			ENSG00000164402	ENSG00000164402		"""Septins"""	16511	protein-coding gene	gene with protein product		608418				9039502, 9149945	Standard	NM_001098812		Approved	KIAA0202, SEP2	uc003kxr.2	Q92599	OTTHUMG00000059735	ENST00000378719.2:c.264T>C	5.37:g.132099999A>G		Somatic	231	2	0.00865801		WXS	Illumina HiSeq	Phase_I	259	256	0.988417	NM_015146	A6NC65|A6NKP6|F6W7K9|Q8IX36|Q8IX37|Q9BVB3	Silent	SNP	ENST00000378719.2	37	CCDS43358.1																																																																																			G|0.438;N|0.000	0.438	strong		0.562	SEPT8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132827.2	XM_034872	
FBN3	84467	hgsc.bcm.edu	37	19	8150428	8150428	+	Silent	SNP	G	G	A	rs34514496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8150428G>A	ENST00000600128.1	-	56	7320	c.6906C>T	c.(6904-6906)gcC>gcT	p.A2302A	FBN3_ENST00000601739.1_Silent_p.A2302A|FBN3_ENST00000270509.2_Silent_p.A2302A			Q75N90	FBN3_HUMAN	fibrillin 3	2302	TB 9.					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						GCAGCACCTCGGCAAAGCAGG	0.647													G|||	228	0.0455272	0.1619	0.0202	5008	,	,		15702	0.0		0.0	False		,,,				2504	0.0				p.A2302A		Atlas-SNP	.											.	FBN3	300	.	0			c.C6906T						PASS	.	G		536,3858		22,492,1683	11.0	12.0	12.0		6906	-6.9	0.9	19	dbSNP_126	12	13,8555		0,13,4271	no	coding-synonymous	FBN3	NM_032447.3		22,505,5954	AA,AG,GG		0.1517,12.1985,4.2355		2302/2810	8150428	549,12413	2197	4284	6481	SO:0001819	synonymous_variant	84467	exon55			CACCTCGGCAAAG		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.6906C>T	19.37:g.8150428G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.956;A|0.044	0.044	strong		0.647	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
MMP17	4326	hgsc.bcm.edu	37	12	132326298	132326298	+	Missense_Mutation	SNP	G	G	A	rs35466884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132326298G>A	ENST00000360564.1	+	5	938	c.836G>A	c.(835-837)cGc>cAc	p.R279H	MMP17_ENST00000535291.1_Missense_Mutation_p.R195H|MMP17_ENST00000535182.1_3'UTR	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	279					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	GACCCGCTGCGCTACGGGCTC	0.647													G|||	1264	0.252396	0.3177	0.1599	5008	,	,		16971	0.1657		0.1869	False		,,,				2504	0.3865				p.R279H		Atlas-SNP	.											.	MMP17	77	.	0			c.G836A						PASS	.	G	HIS/ARG	1424,2982	453.2+/-350.3	234,956,1013	53.0	45.0	48.0		836	-1.4	1.0	12	dbSNP_126	48	1431,7169	267.9+/-287.5	125,1181,2994	yes	missense	MMP17	NM_016155.4	29	359,2137,4007	AA,AG,GG		16.6395,32.3196,21.9514	benign	279/604	132326298	2855,10151	2203	4300	6503	SO:0001583	missense	4326	exon5			CGCTGCGCTACGG	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.836G>A	12.37:g.132326298G>A	ENSP00000353767:p.Arg279His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	97	40	0.412371	NM_016155	Q14850	Missense_Mutation	SNP	ENST00000360564.1	37	CCDS31927.1	439	0.20100732600732601	165	0.3353658536585366	45	0.12430939226519337	96	0.16783216783216784	133	0.17546174142480211	G	9.571	1.121060	0.20877	0.323196	0.166395	ENSG00000198598	ENST00000360564;ENST00000535291;ENST00000534865	T;T;T	0.17054	2.3;2.3;2.51	4.15	-1.36	0.09085	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.933443	0.08804	N	0.891295	T	0.00012	0.0000	N	0.11892	0.195	0.09310	P	0.99999999683036	B	0.11235	0.004	B	0.09377	0.004	T	0.47586	-0.9106	9	0.51188	T	0.08	.	5.4444	0.16527	0.6075:0.1672:0.2252:0.0	rs35466884;rs61942396	279	Q9ULZ9	MMP17_HUMAN	H	279;195;120	ENSP00000353767:R279H;ENSP00000441106:R195H;ENSP00000442104:R120H	ENSP00000353767:R279H	R	+	2	0	MMP17	130892251	1.000000	0.71417	0.989000	0.46669	0.024000	0.10985	2.944000	0.49034	-0.146000	0.11274	-0.233000	0.12211	CGC	G|0.780;A|0.220	0.220	strong		0.647	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
C10orf71	118461	hgsc.bcm.edu	37	10	50531907	50531907	+	Silent	SNP	C	C	T	rs74528495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50531907C>T	ENST00000374144.3	+	3	1605	c.1317C>T	c.(1315-1317)ccC>ccT	p.P439P	C10orf71_ENST00000323868.4_Silent_p.P439P			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	439										endometrium(1)	1						ATTATGATCCCCCCTTTAACA	0.522													C|||	27	0.00539137	0.0182	0.0043	5008	,	,		17686	0.0		0.0	False		,,,				2504	0.0				p.P439P		Atlas-SNP	.											.	C10orf71	179	.	0			c.C1317T						PASS	.	C	,	53,3975		0,53,1961	84.0	88.0	87.0		1317,1317	-2.9	0.4	10	dbSNP_133	87	1,8371		0,1,4185	no	coding-synonymous,coding-synonymous	C10orf71	NM_001135196.1,NM_199459.3	,	0,54,6146	TT,TC,CC		0.0119,1.3158,0.4355	,	439/1436,439/720	50531907	54,12346	2014	4186	6200	SO:0001819	synonymous_variant	118461	exon3			TGATCCCCCCTTT	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.1317C>T	10.37:g.50531907C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			C|0.994;T|0.006	0.006	strong		0.522	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
VARS	7407	hgsc.bcm.edu	37	6	31747833	31747833	+	Missense_Mutation	SNP	G	G	A	rs1076827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31747833G>A	ENST00000375663.3	-	26	3463	c.3023C>T	c.(3022-3024)cCg>cTg	p.P1008L	VARS_ENST00000482996.1_5'Flank|VWA7_ENST00000375688.4_5'Flank|VWA7_ENST00000375686.3_5'Flank|VWA7_ENST00000447450.1_5'Flank|VWA7_ENST00000467576.1_5'Flank|Y_RNA_ENST00000364685.1_RNA	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	1008			P -> L (in dbSNP:rs1076827).		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	GGTGACGGCCGGGAAGTCGTA	0.627													G|||	95	0.0189696	0.0658	0.0101	5008	,	,		17107	0.0		0.0	False		,,,				2504	0.001				p.P1008L		Atlas-SNP	.											.	VARS	76	.	0			c.C3023T						PASS	.	G	LEU/PRO	261,4145	150.3+/-184.3	5,251,1947	59.0	61.0	61.0		3023	5.2	1.0	6	dbSNP_86	61	5,8595	4.3+/-15.6	0,5,4295	yes	missense	VARS	NM_006295.2	98	5,256,6242	AA,AG,GG		0.0581,5.9237,2.0452	possibly-damaging	1008/1265	31747833	266,12740	2203	4300	6503	SO:0001583	missense	7407	exon26			ACGGCCGGGAAGT	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	12651	protein-coding gene	gene with protein product	"""valine tRNA ligase 1, cytoplasmic"""	192150	"""valyl-tRNA synthetase 2"""	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.3023C>T	6.37:g.31747833G>A	ENSP00000364815:p.Pro1008Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Missense_Mutation	SNP	ENST00000375663.3	37	CCDS34412.1	43	0.019688644688644688	40	0.08130081300813008	3	0.008287292817679558	0	0.0	0	0.0	G	12.66	2.003411	0.35320	0.059237	5.81E-4	ENSG00000204394	ENST00000375663	T	0.13420	2.59	5.23	5.23	0.72850	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class I, anticodon-binding (1);Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.000000	0.85682	D	0.000000	T	0.14270	0.0345	L	0.48260	1.515	0.80722	D	1	D	0.58268	0.982	P	0.55667	0.781	T	0.05178	-1.0901	10	0.21014	T	0.42	-11.0663	16.2949	0.82765	0.0:0.0:1.0:0.0	rs1076827;rs4368836;rs16867555;rs1076827	1008	P26640	SYVC_HUMAN	L	1008	ENSP00000364815:P1008L	ENSP00000364815:P1008L	P	-	2	0	VARS	31855812	1.000000	0.71417	0.975000	0.42487	0.423000	0.31445	5.547000	0.67249	2.445000	0.82738	0.650000	0.86243	CCG	G|0.978;A|0.022	0.022	strong		0.627	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295	
SSUH2	51066	hgsc.bcm.edu	37	3	8675539	8675539	+	Missense_Mutation	SNP	G	G	A	rs2276800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:8675539G>A	ENST00000317371.4	-	11	1311	c.86C>T	c.(85-87)cCg>cTg	p.P29L	SSUH2_ENST00000341795.3_Missense_Mutation_p.P29L|SSUH2_ENST00000544814.1_Intron|SSUH2_ENST00000415132.1_Missense_Mutation_p.P29L			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	29			P -> L (in dbSNP:rs2276800).			cytoplasm (GO:0005737)											GGACTCACGCGGGCCAGCCAG	0.657													A|||	1671	0.333666	0.6838	0.2651	5008	,	,		10609	0.1984		0.1829	False		,,,				2504	0.2035				p.P29L		Atlas-SNP	.											C3orf32,NS,carcinoma,0,2	.	.	2	0			c.C86T						PASS	.	A	LEU/PRO	2615,1791	503.9+/-365.7	793,1029,381	27.0	30.0	29.0		86	-4.0	0.0	3	dbSNP_100	29	1528,7072	728.5+/-406.7	120,1288,2892	yes	missense	C3orf32	NM_015931.1	98	913,2317,3273	AA,AG,GG		17.7674,40.6491,31.8545	probably-damaging	29/354	8675539	4143,8863	2203	4300	6503	SO:0001583	missense	51066	exon4			TCACGCGGGCCAG	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.86C>T	3.37:g.8675539G>A	ENSP00000324551:p.Pro29Leu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	97	93	0.958763	NM_015931	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	37	CCDS2568.1	636	0.29120879120879123	323	0.6565040650406504	89	0.24585635359116023	86	0.15034965034965034	138	0.1820580474934037	A	6.834	0.522996	0.13066	0.593509	0.177674	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132	T;T;T	0.51817	0.74;0.74;0.69	3.97	-4.02	0.04034	.	0.656465	0.14884	N	0.292819	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33085	-0.9882	9	0.07813	T	0.8	0.3753	6.2471	0.20825	0.3373:0.0:0.5156:0.147	rs2276800;rs57482921;rs2276800	29	Q9Y2M2	CC032_HUMAN	L	29	ENSP00000339150:P29L;ENSP00000324551:P29L;ENSP00000410757:P29L	ENSP00000324551:P29L	P	-	2	0	C3orf32	8650539	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.643000	0.05421	-1.368000	0.02149	-0.893000	0.02921	CCG	G|0.689;A|0.311	0.311	strong		0.657	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931	
TAS2R16	50833	hgsc.bcm.edu	37	7	122635389	122635389	+	Silent	SNP	G	G	A	rs2233988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:122635389G>A	ENST00000249284.2	-	1	365	c.300C>T	c.(298-300)acC>acT	p.T100T		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	100					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	bitter taste receptor activity (GO:0033038)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGTAGAACACGGTAAGCAAGC	0.373													G|||	442	0.0882588	0.3222	0.0216	5008	,	,		20838	0.0		0.0	False		,,,				2504	0.001				p.T100T		Atlas-SNP	.											.	TAS2R16	57	.	0			c.C300T						PASS	.	G		1009,3397		167,675,1361	75.0	74.0	75.0		300	1.6	0.1	7	dbSNP_98	75	7,8593		0,7,4293	no	coding-synonymous	TAS2R16	NM_016945.2		167,682,5654	AA,AG,GG		0.0814,22.9006,7.8118		100/292	122635389	1016,11990	2203	4300	6503	SO:0001819	synonymous_variant	50833	exon1			GAACACGGTAAGC	AF227139	CCDS5785.1	7q31.1-q31.3	2012-08-22			ENSG00000128519	ENSG00000128519		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14921	protein-coding gene	gene with protein product		604867				10761934	Standard	NM_016945		Approved	T2R16	uc003vkl.1	Q9NYV7	OTTHUMG00000157090	ENST00000249284.2:c.300C>T	7.37:g.122635389G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	53	0.410853	NM_016945	A4D0X2|Q502V3|Q549U8|Q645W1	Silent	SNP	ENST00000249284.2	37	CCDS5785.1																																																																																			G|0.917;A|0.083	0.083	strong		0.373	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945	
NOM1	64434	hgsc.bcm.edu	37	7	156745224	156745224	+	Silent	SNP	G	G	A	rs59371845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:156745224G>A	ENST00000275820.3	+	2	1059	c.1044G>A	c.(1042-1044)gaG>gaA	p.E348E		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	348						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		AAGCTGAGGAGACAGTGGACT	0.393													G|||	267	0.0533147	0.1906	0.0202	5008	,	,		21925	0.0		0.001	False		,,,				2504	0.0				p.E348E		Atlas-SNP	.											.	NOM1	73	.	0			c.G1044A						PASS	.	G		715,3691	298.1+/-285.1	53,609,1541	104.0	94.0	98.0		1044	1.0	0.0	7	dbSNP_129	98	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	NOM1	NM_138400.1		53,613,5837	AA,AG,GG		0.0465,16.2279,5.5282		348/861	156745224	719,12287	2203	4300	6503	SO:0001819	synonymous_variant	64434	exon2			TGAGGAGACAGTG	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1044G>A	7.37:g.156745224G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	166	81	0.487952	NM_138400	Q96I08	Silent	SNP	ENST00000275820.3	37	CCDS34787.1																																																																																			G|0.950;A|0.050	0.050	strong		0.393	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
ARID3C	138715	hgsc.bcm.edu	37	9	34625800	34625800	+	Silent	SNP	G	G	A	rs144207435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:34625800G>A	ENST00000378909.2	-	2	422	c.330C>T	c.(328-330)ctC>ctT	p.L110L		NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	110					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		GGTCTGCATCGAGCTCATACA	0.547													G|||	12	0.00239617	0.0083	0.0	5008	,	,		17241	0.0		0.001	False		,,,				2504	0.0				p.L110L		Atlas-SNP	.											ARID3C,NS,carcinoma,0,2	ARID3C	33	2	0			c.C330T						PASS	.	G		40,4366	44.6+/-78.6	0,40,2163	175.0	136.0	149.0		330	-2.9	1.0	9	dbSNP_134	149	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	ARID3C	NM_001017363.1		0,50,6453	AA,AG,GG		0.1163,0.9079,0.3844		110/413	34625800	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	138715	exon2			TGCATCGAGCTCA		CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"""-"""	21209	protein-coding gene	gene with protein product			"""AT rich interactive domain 3C (BRIGHT- like)"""				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.330C>T	9.37:g.34625800G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	146	80	0.547945	NM_001017363		Silent	SNP	ENST00000378909.2	37	CCDS35006.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061	
LZTR1	8216	hgsc.bcm.edu	37	22	21348914	21348914	+	Silent	SNP	C	C	T	rs4822790	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21348914C>T	ENST00000215739.8	+	15	2042	c.1683C>T	c.(1681-1683)cgC>cgT	p.R561R	LZTR1_ENST00000479606.1_3'UTR|LZTR1_ENST00000389355.3_Silent_p.R542R	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	561					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)			AGTTGTGCCGCCTGGAGCAGC	0.627													C|||	846	0.16893	0.1997	0.1124	5008	,	,		16176	0.2262		0.1352	False		,,,				2504	0.1431				p.R561R		Atlas-SNP	.											.	LZTR1	99	.	0			c.C1683T						PASS	.	C		791,3613	314.1+/-293.5	65,661,1476	63.0	49.0	54.0		1683	3.7	1.0	22	dbSNP_111	54	1023,7577	218.3+/-256.7	54,915,3331	no	coding-synonymous	LZTR1	NM_006767.3		119,1576,4807	TT,TC,CC		11.8953,17.9609,13.9496		561/841	21348914	1814,11190	2202	4300	6502	SO:0001819	synonymous_variant	8216	exon15			GTGCCGCCTGGAG	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.1683C>T	22.37:g.21348914C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	85	0.977012	NM_006767	Q14776|Q20WK0	Silent	SNP	ENST00000215739.8	37	CCDS33606.1																																																																																			C|0.855;T|0.145	0.145	strong		0.627	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767	
SRMS	6725	hgsc.bcm.edu	37	20	62173927	62173927	+	Missense_Mutation	SNP	G	G	A	rs378483|rs386816161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	136	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	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	
ZNF236	7776	hgsc.bcm.edu	37	18	74640002	74640002	+	Missense_Mutation	SNP	G	G	A	rs76679748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:74640002G>A	ENST00000253159.8	+	25	4726	c.4528G>A	c.(4528-4530)Gct>Act	p.A1510T	ZNF236_ENST00000320610.9_Missense_Mutation_p.A1512T	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1510					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		GGCACAGGCCGCTGGGCCCAC	0.542													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		13599	0.0		0.0	False		,,,				2504	0.0				p.A1510T		Atlas-SNP	.											.	ZNF236	325	.	0			c.G4528A						PASS	.	G	THR/ALA	32,3768		0,32,1868	45.0	49.0	48.0		4528	2.3	0.0	18	dbSNP_131	48	0,8234		0,0,4117	yes	missense	ZNF236	NM_007345.3	58	0,32,5985	AA,AG,GG		0.0,0.8421,0.2659	benign	1510/1846	74640002	32,12002	1900	4117	6017	SO:0001583	missense	7776	exon25			CAGGCCGCTGGGC	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.4528G>A	18.37:g.74640002G>A	ENSP00000253159:p.Ala1510Thr	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	200	99	0.495	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	0.098	-1.156936	0.01686	0.008421	0.0	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.10192	2.9;3.06	5.07	2.3	0.28687	.	0.166139	0.45126	D	0.000391	T	0.02688	0.0081	N	0.04880	-0.145	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.39461	-0.9613	10	0.25751	T	0.34	.	4.3857	0.11316	0.298:0.0:0.4852:0.2168	.	1510	Q9UL36	ZN236_HUMAN	T	1510	ENSP00000253159:A1510T;ENSP00000444524:A1510T	ENSP00000253159:A1510T	A	+	1	0	ZNF236	72768990	0.088000	0.21588	0.015000	0.15790	0.230000	0.25150	0.368000	0.20399	0.660000	0.30964	-1.276000	0.01395	GCT	G|0.996;A|0.004	0.004	strong		0.542	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
MYH7B	57644	hgsc.bcm.edu	37	20	33574784	33574784	+	Missense_Mutation	SNP	G	G	A	rs115275866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33574784G>A	ENST00000262873.7	+	13	1218	c.1126G>A	c.(1126-1128)Gcc>Acc	p.A376T		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	334	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GGAGCTCATCGCCACCGACGT	0.607													G|||	16	0.00319489	0.0121	0.0	5008	,	,		18635	0.0		0.0	False		,,,				2504	0.0				p.A376T		Atlas-SNP	.											MYH7B,colon,carcinoma,0,1	MYH7B	145	1	0			c.G1126A						PASS	.	G	THR/ALA	57,4197		0,57,2070	77.0	76.0	76.0		1126	3.7	1.0	20	dbSNP_132	76	1,8471		0,1,4235	yes	missense	MYH7B	NM_020884.3	58	0,58,6305	AA,AG,GG		0.0118,1.3399,0.4558	possibly-damaging	376/1984	33574784	58,12668	2127	4236	6363	SO:0001583	missense	57644	exon15			CTCATCGCCACCG	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.1126G>A	20.37:g.33574784G>A	ENSP00000262873:p.Ala376Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	19.22	3.786240	0.70337	0.013399	1.18E-4	ENSG00000078814	ENST00000262873	D	0.87491	-2.26	3.66	3.66	0.41972	Myosin head, motor domain (2);	0.000000	0.35708	N	0.003040	T	0.81612	0.4859	M	0.80847	2.515	0.39394	D	0.966466	P	0.51240	0.943	P	0.47299	0.543	D	0.87287	0.2296	10	0.72032	D	0.01	.	12.3325	0.55048	0.0878:0.0:0.9122:0.0	.	334	A7E2Y1	MYH7B_HUMAN	T	376	ENSP00000262873:A376T	ENSP00000262873:A376T	A	+	1	0	MYH7B	33038445	0.861000	0.29849	1.000000	0.80357	0.538000	0.34931	2.633000	0.46519	2.356000	0.79943	0.655000	0.94253	GCC	G|0.993;A|0.007	0.007	strong		0.607	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
KLHL2	11275	hgsc.bcm.edu	37	4	166149999	166149999	+	Missense_Mutation	SNP	A	A	G	rs80341433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:166149999A>G	ENST00000226725.6	+	3	452	c.193A>G	c.(193-195)Atg>Gtg	p.M65V	KLHL2_ENST00000421009.2_Silent_p.T8T|KLHL2_ENST00000514860.1_Missense_Mutation_p.M69V|KLHL2_ENST00000538127.1_Intron	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	65	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		GGCAGAAGACATGGAAATTTC	0.348													A|||	32	0.00638978	0.0234	0.0014	5008	,	,		20934	0.0		0.0	False		,,,				2504	0.0				p.M69V		Atlas-SNP	.											.	KLHL2	42	.	0			c.A205G						PASS	.	A	VAL/MET,,VAL/MET	77,4329	65.3+/-102.7	1,75,2127	68.0	65.0	66.0		205,,193	4.2	1.0	4	dbSNP_131	66	1,8599		0,1,4299	no	missense,intron,missense	KLHL2	NM_001161521.1,NM_001161522.1,NM_007246.3	21,,21	1,76,6426	GG,GA,AA		0.0116,1.7476,0.5997	benign,,benign	69/598,,65/594	166149999	78,12928	2203	4300	6503	SO:0001583	missense	11275	exon3			GAAGACATGGAAA	AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"""Kelch-like"", ""BTB/POZ domain containing"""	6353	protein-coding gene	gene with protein product	"""mayven"""	605774	"""kelch (Drosophila)-like 2 (Mayven)"", ""kelch-like 2, Mayven (Drosophila)"""			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.193A>G	4.37:g.166149999A>G	ENSP00000226725:p.Met65Val	Somatic	736	0	0		WXS	Illumina HiSeq	Phase_I	576	285	0.494792	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Missense_Mutation	SNP	ENST00000226725.6	37	CCDS34094.1	.	.	.	.	.	.	.	.	.	.	A	8.320	0.824018	0.16678	0.017476	1.16E-4	ENSG00000109466	ENST00000226725;ENST00000511305;ENST00000509704;ENST00000514860	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	4.16	4.16	0.48862	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.104953	0.64402	D	0.000003	T	0.10121	0.0248	N	0.00157	-1.96	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.10847	-1.0612	10	0.13470	T	0.59	.	8.1516	0.31143	0.9087:0.0:0.0913:0.0	.	69;65	B4DFH7;O95198	.;KLHL2_HUMAN	V	65;105;27;69	ENSP00000226725:M65V;ENSP00000422113:M105V;ENSP00000421324:M27V;ENSP00000424198:M69V	ENSP00000226725:M65V	M	+	1	0	KLHL2	166369449	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.885000	0.63142	1.750000	0.51863	0.383000	0.25322	ATG	A|0.994;G|0.006	0.006	strong		0.348	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1		
CACNA1G	8913	hgsc.bcm.edu	37	17	48701800	48701800	+	Silent	SNP	C	C	T	rs2301835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48701800C>T	ENST00000359106.5	+	37	6309	c.6309C>T	c.(6307-6309)ctC>ctT	p.L2103L	CACNA1G_ENST00000513689.2_Silent_p.L2013L|CACNA1G_ENST00000429973.2_Silent_p.L1992L|CACNA1G_ENST00000514181.1_Silent_p.L1985L|CACNA1G_ENST00000502264.1_Silent_p.L2032L|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000503485.1_Silent_p.L1976L|CACNA1G_ENST00000513964.1_Silent_p.L1965L|CACNA1G_ENST00000507510.2_Silent_p.L2058L|CACNA1G_ENST00000515165.1_Silent_p.L2010L|CACNA1G_ENST00000515765.1_Silent_p.L2047L|CACNA1G_ENST00000515411.1_Silent_p.L2040L|CACNA1G_ENST00000442258.2_Silent_p.L1969L|CACNA1G_ENST00000514079.1_Silent_p.L2017L|CACNA1G_ENST00000505165.1_Silent_p.L2010L|CACNA1G_ENST00000510115.1_Silent_p.L2024L|CACNA1G_ENST00000507896.1_Silent_p.L1999L|CACNA1G_ENST00000510366.1_Silent_p.L1958L|CACNA1G_ENST00000512389.1_Silent_p.L1999L|CACNA1G_ENST00000354983.4_Silent_p.L2069L|CACNA1G_ENST00000360761.4_Silent_p.L1987L|CACNA1G_ENST00000352832.5_Silent_p.L1976L|CACNA1G_ENST00000507336.1_Silent_p.L2092L|CACNA1G_ENST00000514717.1_Silent_p.L1953L|CACNA1G_ENST00000507609.1_Silent_p.L2003L|CACNA1G_ENST00000358244.5_Silent_p.L1976L	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2103					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CTCATCTGCTCCAGCCCCACA	0.637													C|||	580	0.115815	0.1884	0.0533	5008	,	,		14461	0.0982		0.0885	False		,,,				2504	0.1084				p.L2103L		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C6309T						PASS	.	C	,,,,,,,,,,,,,	588,3444		33,522,1461	30.0	31.0	31.0		6309,5928,6240,5997,6072,6141,5961,6096,6030,6174,5976,5928,5907,6207	1.0	1.0	17	dbSNP_100	31	629,7751		24,581,3585	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1G	NM_018896.3,NM_198376.1,NM_198377.1,NM_198378.1,NM_198379.1,NM_198380.1,NM_198382.1,NM_198383.1,NM_198384.1,NM_198385.1,NM_198386.1,NM_198387.1,NM_198388.1,NM_198396.1	,,,,,,,,,,,,,	57,1103,5046	TT,TC,CC		7.506,14.5833,9.805	,,,,,,,,,,,,,	2103/2378,1976/2172,2080/2355,1999/2274,2024/2299,2047/2322,1987/2262,2032/2307,2010/2285,2058/2333,1992/2267,1976/2251,1969/2244,2069/2344	48701800	1217,11195	2016	4190	6206	SO:0001819	synonymous_variant	8913	exon37			TCTGCTCCAGCCC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.6309C>T	17.37:g.48701800C>T		Somatic	345	0	0		WXS	Illumina HiSeq	Phase_I	340	174	0.511765	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	CCDS45730.1																																																																																			C|0.878;T|0.122	0.122	strong		0.637	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
C14orf159	80017	hgsc.bcm.edu	37	14	91666248	91666248	+	Splice_Site	SNP	T	T	C	rs28715808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91666248T>C	ENST00000523771.1	+	11	2031	c.1428T>C	c.(1426-1428)acT>acC	p.T476T	C14orf159_ENST00000518868.1_Splice_Site_p.T481T|C14orf159_ENST00000256324.10_Splice_Site_p.T481T|C14orf159_ENST00000412671.2_Splice_Site_p.T481T|C14orf159_ENST00000522322.1_Splice_Site_p.T476T|C14orf159_ENST00000523816.1_Splice_Site_p.T476T|C14orf159_ENST00000520328.1_Splice_Site_p.T464T|C14orf159_ENST00000428926.2_Splice_Site_p.T476T|C14orf159_ENST00000521077.2_Splice_Site_p.T481T|C14orf159_ENST00000525393.2_Splice_Site_p.T352T			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	135	0	0		WXS	Illumina HiSeq	Phase_I	155	86	0.554839	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
PROSER1	80209	hgsc.bcm.edu	37	13	39587677	39587677	+	Missense_Mutation	SNP	A	A	G	rs3751379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39587677A>G	ENST00000352251.3	-	11	2545	c.1712T>C	c.(1711-1713)gTg>gCg	p.V571A	PROSER1_ENST00000350125.3_Missense_Mutation_p.V549A|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	571	Ser-rich.		V -> A (in dbSNP:rs3751379). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.														GCTAACTGGCACTGACGTGGA	0.562													G|||	1407	0.28095	0.4463	0.1801	5008	,	,		21158	0.2183		0.17	False		,,,				2504	0.3078				p.V571A		Atlas-SNP	.											.	.	.	.	0			c.T1712C						PASS	.	G	ALA/VAL,ALA/VAL	1902,2504	627.4+/-394.9	393,1116,694	88.0	92.0	90.0		1712,1646	-1.6	0.0	13	dbSNP_107	90	1282,7318	759.3+/-407.5	103,1076,3121	yes	missense,missense	PROSER1	NM_025138.3,NM_170719.2	64,64	496,2192,3815	GG,GA,AA		14.907,43.1684,24.481	benign,benign	571/945,549/923	39587677	3184,9822	2203	4300	6503	SO:0001583	missense	80209	exon11			ACTGGCACTGACG	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.1712T>C	13.37:g.39587677A>G	ENSP00000332034:p.Val571Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	99	55	0.555556	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	37	CCDS9368.2	551	0.2522893772893773	222	0.45121951219512196	72	0.19889502762430938	127	0.22202797202797203	130	0.17150395778364116	G	2.517	-0.311523	0.05422	0.431684	0.14907	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.32515	1.45;1.46	5.05	-1.6	0.08426	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.49153	-0.8969	7	.	.	.	0.7186	6.6741	0.23083	0.5677:0.2225:0.2098:0.0	rs3751379;rs17846511;rs17859582;rs60335909;rs3751379	549;571	A6NJ97;Q86XN7	.;PRSR1_HUMAN	A	571;549	ENSP00000332034:V571A;ENSP00000339123:V549A	.	V	-	2	0	PROSER1	38485677	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	0.098000	0.15189	-0.788000	0.04504	-1.163000	0.01768	GTG	G|0.254;N|0.000	0.254	strong		0.562	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414312	105414312	+	Silent	SNP	T	T	C	rs79130434	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105414312T>C	ENST00000333244.5	-	7	7595	c.7476A>G	c.(7474-7476)tcA>tcG	p.S2492S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2492						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)			ACACCCCGAATGACGGCATCT	0.612													.|||	273	0.0545128	0.1097	0.134	5008	,	,		18153	0.0198		0.002	False		,,,				2504	0.0133				p.S2492S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A7476G						PASS	.	C		346,3674		28,290,1692	174.0	202.0	193.0		7476	-2.7	0.0	14	dbSNP_131	193	20,8322		0,20,4151	no	coding-synonymous	AHNAK2	NM_138420.2		28,310,5843	CC,CT,TT		0.2398,8.607,2.9607		2492/5796	105414312	366,11996	2010	4171	6181	SO:0001819	synonymous_variant	113146	exon7			CCCGAATGACGGC	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.7476A>G	14.37:g.105414312T>C		Somatic	298	1	0.0033557		WXS	Illumina HiSeq	Phase_I	260	126	0.484615	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			T|0.964;C|0.036	0.036	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
PELP1	27043	hgsc.bcm.edu	37	17	4576620	4576620	+	Silent	SNP	C	C	T	rs55677157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4576620C>T	ENST00000574876.1	-	15	1787	c.1770G>A	c.(1768-1770)ccG>ccA	p.P590P	PELP1_ENST00000572293.1_Silent_p.P640P|PELP1_ENST00000269230.7_Intron|PELP1_ENST00000436683.2_Silent_p.P443P|PELP1_ENST00000301396.4_Silent_p.P734P|AC091153.4_ENST00000441700.2_RNA			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	590					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						AGCGAGGAGACGGGGCCAGCA	0.652													C|||	425	0.0848642	0.0484	0.1282	5008	,	,		16334	0.003		0.2117	False		,,,				2504	0.0573				p.P590P		Atlas-SNP	.											.	PELP1	102	.	0			c.G1770A						PASS	.	C		292,4018		12,268,1875	19.0	30.0	27.0		1770	-3.2	0.9	17	dbSNP_129	27	1899,6647		204,1491,2578	no	coding-synonymous	PELP1	NM_014389.2		216,1759,4453	TT,TC,CC		22.2209,6.7749,17.0426		590/1131	4576620	2191,10665	2155	4273	6428	SO:0001819	synonymous_variant	27043	exon15			AGGAGACGGGGCC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.1770G>A	17.37:g.4576620C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	188	94	0.5	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	
NAT8	9027	hgsc.bcm.edu	37	2	73868446	73868446	+	Missense_Mutation	SNP	C	C	T	rs13424561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73868446C>T	ENST00000272425.3	-	2	459	c.310G>A	c.(310-312)Gag>Aag	p.E104K		NM_003960.3|NM_016347.2	NP_003951.3|NP_057431.2			N-acetyltransferase 8 (GCN5-related, putative)											breast(1)|endometrium(2)|kidney(2)|lung(2)|ovary(1)|prostate(1)	9						GAGCCACGCTCACTCAGGTAG	0.537													.|||	179	0.0357428	0.1286	0.013	5008	,	,		22094	0.0		0.0	False		,,,				2504	0.0				p.E104K		Atlas-SNP	.											.	NAT8	26	.	0			c.G310A						PASS	.	C	LYS/GLU	505,3901	235.2+/-247.8	38,429,1736	118.0	112.0	114.0		310	-0.2	0.0	2	dbSNP_121	114	3,8597	3.7+/-12.6	0,3,4297	yes	missense	NAT8	NM_003960.3	56	38,432,6033	TT,TC,CC		0.0349,11.4616,3.9059	possibly-damaging	104/228	73868446	508,12498	2203	4300	6503	SO:0001583	missense	9027	exon2			CACGCTCACTCAG	AB013094	CCDS1926.1	2p13.2	2012-03-20	2008-09-24		ENSG00000144035	ENSG00000144035			18069	protein-coding gene	gene with protein product		606716	"""N-acetyltransferase 8"""			11397015, 9852678, 19011241	Standard	NM_003960		Approved	Hcml1, TSC501, GLA, ATase2	uc002sji.1	Q9UHE5	OTTHUMG00000129818	ENST00000272425.3:c.310G>A	2.37:g.73868446C>T	ENSP00000272425:p.Glu104Lys	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	164	83	0.506098	NM_003960		Missense_Mutation	SNP	ENST00000272425.3	37	CCDS1926.1	75	0.034340659340659344	71	0.1443089430894309	4	0.011049723756906077	0	0.0	0	0.0	C	2.671	-0.277447	0.05679	0.114616	3.49E-4	ENSG00000144035	ENST00000272425	T	0.29397	1.57	3.86	-0.22	0.13130	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	1.343440	0.05236	N	0.511242	T	0.00144	0.0004	L	0.31752	0.955	0.80722	P	0.0	B	0.24426	0.103	B	0.17722	0.019	T	0.20739	-1.0266	9	0.08179	T	0.78	-1.1728	7.9371	0.29935	0.0:0.5069:0.0:0.4931	rs13424561;rs13424561	104	Q9UHE5	NAT8_HUMAN	K	104	ENSP00000272425:E104K	ENSP00000272425:E104K	E	-	1	0	NAT8	73721954	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.648000	0.05391	-0.174000	0.10743	-0.151000	0.13558	GAG	C|0.956;T|0.044	0.044	strong		0.537	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	NM_003960	
NELL1	4745	hgsc.bcm.edu	37	11	21581805	21581805	+	Silent	SNP	C	C	T	rs8176789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:21581805C>T	ENST00000357134.5	+	17	2009	c.1857C>T	c.(1855-1857)ggC>ggT	p.G619G	NELL1_ENST00000532434.1_Silent_p.G572G|NELL1_ENST00000298925.5_Silent_p.G647G|NELL1_ENST00000325319.5_Silent_p.G562G|NELL1_ENST00000529218.1_Intron	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	619	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						TGGCAGGGGGCTTTGACTGTC	0.522													C|||	2720	0.543131	0.2481	0.634	5008	,	,		20084	0.5774		0.8101	False		,,,				2504	0.5675				p.G619G		Atlas-SNP	.											.	NELL1	179	.	0			c.C1857T						PASS	.	C	,	1630,2776	501.0+/-364.9	307,1016,880	134.0	118.0	123.0		1857,1716	3.7	1.0	11	dbSNP_117	123	7040,1560	745.5+/-407.3	2899,1242,159	no	coding-synonymous,coding-synonymous	NELL1	NM_006157.3,NM_201551.1	,	3206,2258,1039	TT,TC,CC		18.1395,36.995,33.3385	,	619/811,572/764	21581805	8670,4336	2203	4300	6503	SO:0001819	synonymous_variant	4745	exon17			AGGGGGCTTTGAC	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.1857C>T	11.37:g.21581805C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	185	83	0.448649	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	37	CCDS7855.1																																																																																			C|0.342;T|0.658	0.658	strong		0.522	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
FAM162B	221303	hgsc.bcm.edu	37	6	117086378	117086378	+	Missense_Mutation	SNP	C	C	A	rs654128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	44	0	0		WXS	Illumina HiSeq	Phase_I	37	21	0.567568	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	
AOAH	313	hgsc.bcm.edu	37	7	36763688	36763688	+	Silent	SNP	C	C	T	rs2228411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:36763688C>T	ENST00000258749.5	-	1	465	c.66G>A	c.(64-66)tcG>tcA	p.S22S	AOAH_ENST00000535891.1_Silent_p.S22S|AOAH_ENST00000431169.1_Silent_p.S22S	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	22					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)	p.S22S(1)		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						CTGGAGAGGCCGAGGACTGAA	0.512													C|||	1894	0.378195	0.553	0.2867	5008	,	,		16715	0.4177		0.325	False		,,,				2504	0.2209				p.S22S		Atlas-SNP	.											AOAH,NS,carcinoma,0,2	AOAH	79	2	1	Substitution - coding silent(1)	stomach(1)	c.G66A						PASS	.	C	,,	2299,2107	602.4+/-389.9	610,1079,514	57.0	63.0	61.0		66,66,66	-2.8	0.0	7	dbSNP_98	61	3052,5548	469.0+/-367.5	554,1944,1802	no	coding-synonymous,coding-synonymous,coding-synonymous	AOAH	NM_001177506.1,NM_001177507.1,NM_001637.3	,,	1164,3023,2316	TT,TC,CC		35.4884,47.8212,41.1425	,,	22/689,22/544,22/576	36763688	5351,7655	2203	4300	6503	SO:0001819	synonymous_variant	313	exon1			AGAGGCCGAGGAC	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.66G>A	7.37:g.36763688C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001177507	A4D1Y5|B7Z490|Q53F13	Silent	SNP	ENST00000258749.5	37	CCDS5448.1																																																																																			C|0.590;T|0.410	0.410	strong		0.512	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	
SERPINB3	6317	hgsc.bcm.edu	37	18	61322998	61322998	+	Missense_Mutation	SNP	G	G	A	rs73962331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61322998G>A	ENST00000283752.5	-	8	1209	c.1066C>T	c.(1066-1068)Cct>Tct	p.P356S	SERPINB3_ENST00000332821.8_Missense_Mutation_p.P304S|SERPINB11_ENST00000489748.1_RNA	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	356					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						GTTGAAGTAGGTGATGATCCG	0.463													G|||	286	0.0571086	0.205	0.0144	5008	,	,		20255	0.0		0.004	False		,,,				2504	0.001				p.P356S		Atlas-SNP	.											.	SERPINB3	90	.	0			c.C1066T						PASS	.	G	SER/PRO	674,3732	277.2+/-273.6	53,568,1582	145.0	147.0	147.0		1066	0.5	0.0	18	dbSNP_130	147	15,8585	9.8+/-36.6	0,15,4285	yes	missense	SERPINB3	NM_006919.2	74	53,583,5867	AA,AG,GG		0.1744,15.2973,5.2976	benign	356/391	61322998	689,12317	2203	4300	6503	SO:0001583	missense	6317	exon8			AAGTAGGTGATGA	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1066C>T	18.37:g.61322998G>A	ENSP00000283752:p.Pro356Ser	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	203	71	0.349754	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	99	0.04532967032967033	91	0.18495934959349594	6	0.016574585635359115	0	0.0	2	0.002638522427440633	G	1.994	-0.431080	0.04669	0.152973	0.001744	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.83673	-1.75;-1.75	2.96	0.496	0.16896	Serpin domain (3);	3.431400	0.01103	N	0.005437	T	0.00178	0.0005	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	0.45483	-0.9258	9	0.02654	T	1	.	2.8087	0.05435	0.6154:0.1428:0.1014:0.1403	.	304;356	P29508-2;P29508	.;SPB3_HUMAN	S	356;304	ENSP00000283752:P356S;ENSP00000329498:P304S	ENSP00000283752:P356S	P	-	1	0	SERPINB3	59473978	0.018000	0.18449	0.004000	0.12327	0.000000	0.00434	0.503000	0.22610	0.107000	0.17824	-1.316000	0.01300	CCT	G|0.948;A|0.052	0.052	strong		0.463	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
GPR146	115330	hgsc.bcm.edu	37	7	1097895	1097895	+	Silent	SNP	A	A	G	rs61910751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1097895A>G	ENST00000397095.1	+	2	967	c.744A>G	c.(742-744)ccA>ccG	p.P248P	C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000397098.3_Intron|GPR146_ENST00000297468.3_Silent_p.P248P|C7orf50_ENST00000397100.2_Intron|RP11-449P15.1_ENST00000549241.1_RNA			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		TCTGGACGCCACACTATCTGA	0.647													G|||	345	0.0688898	0.0204	0.0821	5008	,	,		17834	0.0		0.1262	False		,,,				2504	0.137				p.P248P		Atlas-SNP	.											.	GPR146	20	.	0			c.A744G						PASS	.		,,,	206,4198	800.2+/-415.6	2,202,1998	59.0	48.0	52.0		,,,744	-10.2	0.0	7	dbSNP_129	52	1354,7244	751.8+/-407.4	106,1142,3051	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	108,1344,5049	GG,GA,AA		15.7478,4.6776,11.9982	,,,	,,,248/334	1097895	1560,11442	2202	4299	6501	SO:0001819	synonymous_variant	115330	exon1			GACGCCACACTAT	BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"""GPCR / Class A : Orphans"""	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.744A>G	7.37:g.1097895A>G		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_138445	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																			A|0.893;G|0.106;T|0.000	0.106	strong		0.647	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
DNAH5	1767	hgsc.bcm.edu	37	5	13931340	13931340	+	Missense_Mutation	SNP	C	C	T	rs1530496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13931340C>T	ENST00000265104.4	-	2	175	c.71G>A	c.(70-72)gGa>gAa	p.G24E		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	24	Stem. {ECO:0000250}.		G -> E (in dbSNP:rs1530496).		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)					TTCCTTCTCTCCCTTCAGTCT	0.378									Kartagener syndrome				T|||	2507	0.500599	0.6112	0.4669	5008	,	,		19739	0.7014		0.2833	False		,,,				2504	0.3916				p.G24E		Atlas-SNP	.											.	DNAH5	868	.	0			c.G71A						PASS	.	T	GLU/GLY	2480,1926	546.3+/-377.0	708,1064,431	87.0	88.0	88.0		71	5.6	1.0	5	dbSNP_88	88	2599,6001	687.2+/-404.2	407,1785,2108	yes	missense	DNAH5	NM_001369.2	98	1115,2849,2539	TT,TC,CC		30.2209,43.7131,39.0512	benign	24/4625	13931340	5079,7927	2203	4300	6503	SO:0001583	missense	1767	exon2	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TTCTCTCCCTTCA	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.71G>A	5.37:g.13931340C>T	ENSP00000265104:p.Gly24Glu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	1057	0.483974358974359	286	0.5813008130081301	162	0.44751381215469616	389	0.6800699300699301	220	0.29023746701846964	T	6.293	0.422151	0.11928	0.562869	0.302209	ENSG00000039139	ENST00000265104	T	0.19938	2.11	5.6	5.6	0.85130	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00044	-2.455	0.44825	P	0.0021660000000000013	B	0.02656	0.0	B	0.01281	0.0	T	0.42865	-0.9426	9	0.02654	T	1	.	11.6651	0.51368	0.0:0.0702:0.0:0.9298	rs1530496;rs52796631;rs59635012;rs1530496	24	Q8TE73	DYH5_HUMAN	E	24	ENSP00000265104:G24E	ENSP00000265104:G24E	G	-	2	0	DNAH5	13984340	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.349000	0.66010	1.060000	0.40578	-0.269000	0.10298	GGA	C|0.571;T|0.429	0.429	strong		0.378	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
COG5	10466	hgsc.bcm.edu	37	7	107204371	107204371	+	Missense_Mutation	SNP	C	C	T	rs73419464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107204371C>T	ENST00000347053.3	-	1	114	c.64G>A	c.(64-66)Gct>Act	p.A22T	DUS4L_ENST00000402620.1_5'Flank|DUS4L_ENST00000498786.1_Intron|DUS4L_ENST00000265720.3_5'Flank|COG5_ENST00000297135.3_Missense_Mutation_p.A22T|COG5_ENST00000393603.2_Missense_Mutation_p.A22T	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	22					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						ATGTCGTCAGCAGCAGAACGG	0.697													C|||	152	0.0303514	0.1089	0.0101	5008	,	,		12302	0.0		0.0	False		,,,				2504	0.001				p.A22T		Atlas-SNP	.											.	COG5	78	.	0			c.G64A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	347,4057		15,317,1870	18.0	18.0	18.0		64,64,64	1.7	0.4	7	dbSNP_130	18	7,8587		0,7,4290	yes	missense,missense,missense	COG5	NM_181733.2,NM_006348.3,NM_001161520.1	58,58,58	15,324,6160	TT,TC,CC		0.0815,7.8792,2.7235	benign,benign,benign	22/840,22/861,22/824	107204371	354,12644	2202	4297	6499	SO:0001583	missense	10466	exon1			CGTCAGCAGCAGA	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.64G>A	7.37:g.107204371C>T	ENSP00000334703:p.Ala22Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	112	64	0.571429	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	62	0.028388278388278388	57	0.11585365853658537	5	0.013812154696132596	0	0.0	0	0.0	C	14.15	2.449883	0.43531	0.078792	8.15E-4	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.18502	2.22;2.21;2.21	4.76	1.72	0.24424	.	0.904518	0.09273	N	0.824937	T	0.00144	0.0004	N	0.08118	0	0.21355	N	0.999718	B;B	0.21905	0.037;0.062	B;B	0.20184	0.013;0.028	T	0.38067	-0.9678	10	0.28530	T	0.3	-1.6692	12.2534	0.54611	0.0:0.4485:0.5515:0.0	.	22;22	Q9UP83;Q9UP83-2	COG5_HUMAN;.	T	22	ENSP00000334703:A22T;ENSP00000297135:A22T;ENSP00000377228:A22T	ENSP00000297135:A22T	A	-	1	0	COG5	106991607	0.002000	0.14202	0.354000	0.25760	0.206000	0.24218	0.304000	0.19228	0.574000	0.29417	0.591000	0.81541	GCT	C|0.970;T|0.030	0.030	strong		0.697	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
LRRC23	10233	hgsc.bcm.edu	37	12	7015707	7015707	+	Missense_Mutation	SNP	G	G	T	rs2071073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7015707G>T	ENST00000007969.8	+	4	591	c.371G>T	c.(370-372)cGg>cTg	p.R124L	LRRC23_ENST00000429740.1_Missense_Mutation_p.R124L|LRRC23_ENST00000323702.5_Missense_Mutation_p.R124L|LRRC23_ENST00000436789.1_Missense_Mutation_p.R124L|LRRC23_ENST00000443597.2_Missense_Mutation_p.R124L|LRRC23_ENST00000433346.1_Missense_Mutation_p.R124L	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	124			R -> L (in dbSNP:rs2071073). {ECO:0000269|PubMed:15489334}.					p.R124L(2)		NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						GATGGCAATCGGCTGCGAAGT	0.498													G|||	540	0.107827	0.1498	0.0865	5008	,	,		-128	0.2589		0.001	False		,,,				2504	0.0204				p.R124L		Atlas-SNP	.											LRRC23,NS,carcinoma,0,2	LRRC23	46	2	2	Substitution - Missense(2)	stomach(2)	c.G371T						PASS	.	G	LEU/ARG,LEU/ARG,LEU/ARG	600,3806	262.5+/-264.9	42,516,1645	316.0	308.0	310.0		371,371,371	-0.1	0.4	12	dbSNP_96	310	36,8564	24.0+/-70.4	1,34,4265	yes	missense,missense,missense	LRRC23	NM_001135217.1,NM_006992.3,NM_201650.2	102,102,102	43,550,5910	TT,TG,GG		0.4186,13.6178,4.8901	benign,benign,benign	124/344,124/313,124/344	7015707	636,12370	2203	4300	6503	SO:0001583	missense	10233	exon4			GCAATCGGCTGCG	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.371G>T	12.37:g.7015707G>T	ENSP00000007969:p.Arg124Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	128	69	0.539062	NM_001135217	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Missense_Mutation	SNP	ENST00000007969.8	37	CCDS8569.1	242	0.1108058608058608	80	0.16260162601626016	24	0.06629834254143646	138	0.24125874125874125	0	0.0	G	10.23	1.291792	0.23564	0.136178	0.004186	ENSG00000010626	ENST00000433346;ENST00000007969;ENST00000323702;ENST00000443597;ENST00000436789;ENST00000429740	T;T;T;T;T;T	0.31510	1.98;1.83;2.22;1.83;2.21;1.49	5.93	-0.0597	0.13792	.	.	.	.	.	T	0.00012	0.0000	N	0.16478	0.41	0.42570	P	0.006821999999999995	B;B;B;B;B;B	0.18610	0.029;0.001;0.001;0.014;0.006;0.018	B;B;B;B;B;B	0.22386	0.039;0.004;0.001;0.004;0.003;0.003	T	0.39820	-0.9595	8	0.30854	T	0.27	-2.06	7.7197	0.28725	0.6306:0.0:0.2452:0.1243	rs2071073;rs17198095;rs17852710;rs2071073	124;124;124;124;124;124	E9PDZ4;C9JEW3;A8K8K2;Q53EV4-2;Q53EV4;C9JKE8	.;.;.;.;LRC23_HUMAN;.	L	124	ENSP00000402554:R124L;ENSP00000007969:R124L;ENSP00000317464:R124L;ENSP00000390932:R124L;ENSP00000396049:R124L;ENSP00000397192:R124L	ENSP00000007969:R124L	R	+	2	0	LRRC23	6885968	0.853000	0.29707	0.362000	0.25862	0.922000	0.55478	-0.019000	0.12546	-0.315000	0.08703	0.561000	0.74099	CGG	G|0.920;N|0.000	.	strong		0.498	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992	
MMP17	4326	hgsc.bcm.edu	37	12	132329666	132329666	+	Silent	SNP	C	C	T	rs36031288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132329666C>T	ENST00000360564.1	+	7	1074	c.972C>T	c.(970-972)ccC>ccT	p.P324P	MMP17_ENST00000535004.1_5'Flank|MMP17_ENST00000535291.1_Silent_p.P240P|MMP17_ENST00000535182.1_3'UTR	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	324					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	CCTGCAGGCCCAGGAAGGACG	0.667													C|||	191	0.038139	0.1377	0.0101	5008	,	,		15735	0.0		0.002	False		,,,				2504	0.0				p.P324P		Atlas-SNP	.											.	MMP17	77	.	0			c.C972T						PASS	.	C		485,3921	225.9+/-241.6	31,423,1749	73.0	70.0	71.0		972	-2.7	0.1	12	dbSNP_126	71	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	MMP17	NM_016155.4		31,429,6043	TT,TC,CC		0.0698,11.0077,3.7752		324/604	132329666	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	4326	exon7			CAGGCCCAGGAAG	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.972C>T	12.37:g.132329666C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_016155	Q14850	Silent	SNP	ENST00000360564.1	37	CCDS31927.1																																																																																			C|0.961;T|0.039	0.039	strong		0.667	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
EYA2	2139	hgsc.bcm.edu	37	20	45816757	45816757	+	Silent	SNP	C	C	T	rs3818015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:45816757C>T	ENST00000327619.5	+	16	1967	c.1593C>T	c.(1591-1593)caC>caT	p.H531H	EYA2_ENST00000317304.6_Silent_p.H501H|EYA2_ENST00000357410.3_Silent_p.H452H	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	EYA transcriptional coactivator and phosphatase 2	531					DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|histone dephosphorylation (GO:0016576)|mesodermal cell fate specification (GO:0007501)|mitochondrial outer membrane permeabilization (GO:0097345)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of transcription, DNA-templated (GO:0006355)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0241)				CACTGAGGCACGCCCTGGAGC	0.602													C|||	680	0.135783	0.2776	0.0259	5008	,	,		17715	0.2024		0.004	False		,,,				2504	0.089				p.H531H	Pancreas(120;56 1725 18501 25218 43520)	Atlas-SNP	.											.	EYA2	85	.	0			c.C1593T						PASS	.	C	,	958,3444		94,770,1337	88.0	59.0	69.0		1593,1356	2.2	1.0	20	dbSNP_107	69	38,8554		1,36,4259	no	coding-synonymous,coding-synonymous	EYA2	NM_005244.4,NM_172110.3	,	95,806,5596	TT,TC,CC		0.4423,21.7628,7.6651	,	531/539,452/460	45816757	996,11998	2201	4296	6497	SO:0001819	synonymous_variant	2139	exon16			GAGGCACGCCCTG		CCDS13403.1, CCDS54471.1	20q13.1	2014-06-19	2014-06-19		ENSG00000064655	ENSG00000064655		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3520	protein-coding gene	gene with protein product		601654	"""eyes absent (Drosophila) homolog 2"", ""eyes absent homolog 2 (Drosophila)"""			9020840	Standard	NM_005244		Approved	EAB1	uc002xsm.3	O00167	OTTHUMG00000033041	ENST00000327619.5:c.1593C>T	20.37:g.45816757C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_005244	Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7	Silent	SNP	ENST00000327619.5	37	CCDS13403.1																																																																																			C|0.904;T|0.096	0.096	strong		0.602	EYA2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080326.2	NM_005244	
CD44	960	hgsc.bcm.edu	37	11	35223303	35223303	+	Silent	SNP	G	G	A	rs11033026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:35223303G>A	ENST00000428726.2	+	9	1245	c.1122G>A	c.(1120-1122)gaG>gaA	p.E374E	CD44_ENST00000415148.2_Silent_p.E331E|CD44_ENST00000526669.2_Intron|CD44_ENST00000433354.2_Silent_p.E375E|CD44_ENST00000449691.2_Silent_p.E374E|CD44_ENST00000263398.6_Intron|CD44_ENST00000434472.2_Intron|CD44_ENST00000360158.4_Intron|CD44_ENST00000278386.6_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000437706.2_Silent_p.E374E|CD44_ENST00000433892.2_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	374	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	AGCATCATGAGGAAGAAGAGA	0.473													G|||	473	0.0944489	0.3449	0.0245	5008	,	,		18781	0.0		0.0	False		,,,				2504	0.0				p.E374E		Atlas-SNP	.											.	CD44	48	.	0			c.G1122A						PASS	.	G	,,,,,,,	1185,3219	417.2+/-337.8	174,837,1191	153.0	129.0	137.0		1122,993,,,,,,	-10.3	0.1	11	dbSNP_120	137	12,8584	5.7+/-21.5	0,12,4286	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron,intron	CD44	NM_000610.3,NM_001001389.1,NM_001001390.1,NM_001001391.1,NM_001001392.1,NM_001202555.1,NM_001202556.1,NM_001202557.1	,,,,,,,	174,849,5477	AA,AG,GG		0.1396,26.9074,9.2077	,,,,,,,	374/743,331/700,,,,,,	35223303	1197,11803	2202	4298	6500	SO:0001819	synonymous_variant	960	exon9			TCATGAGGAAGAA	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.1122G>A	11.37:g.35223303G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	37	CCDS7897.1	176	0.08058608058608059	170	0.34552845528455284	6	0.016574585635359115	0	0.0	0	0.0	G	0.022	-1.413724	0.01145	0.269074	0.001396	ENSG00000026508	ENST00000528455	.	.	.	5.14	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.35450	-0.9788	3	.	.	.	-9.2826	1.2309	0.01943	0.2577:0.2623:0.3217:0.1583	rs11033026;rs11033026	.	.	.	R	226	.	.	G	+	1	0	CD44	35179879	0.000000	0.05858	0.068000	0.19968	0.002000	0.02628	-2.933000	0.00687	-1.585000	0.01634	-1.108000	0.02087	GGA	G|0.883;A|0.117	0.117	strong		0.473	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
FAM178B	51252	hgsc.bcm.edu	37	2	97559759	97559759	+	Silent	SNP	G	G	A	rs11677797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:97559759G>A	ENST00000417561.3	-	18	2123	c.2124C>T	c.(2122-2124)ctC>ctT	p.L708L	FAM178B_ENST00000327896.3_Silent_p.L528L|FAM178B_ENST00000490605.2_Silent_p.L560L|FAM178B_ENST00000393526.2_5'UTR|FAM178B_ENST00000470789.1_5'UTR			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	708										large_intestine(1)|ovary(1)	2						ATGGCCTCATGAGGCCCAGGA	0.622													.|||	2146	0.428514	0.236	0.4424	5008	,	,		17897	0.6766		0.1491	False		,,,				2504	0.7106				p.L560L		Atlas-SNP	.											.	FAM178B	35	.	0			c.C1680T						PASS	.	G	,,	1122,3282	394.7+/-329.4	151,820,1231	65.0	59.0	61.0		1680,57,	2.6	1.0	2	dbSNP_120	61	1572,7024	290.9+/-300.1	138,1296,2864	no	coding-synonymous,coding-synonymous,utr-5	FAM178B	NM_001122646.2,NM_001172667.1,NM_016490.4	,,	289,2116,4095	AA,AG,GG		18.2876,25.4768,20.7231	,,	560/680,19/139,	97559759	2694,10306	2202	4298	6500	SO:0001819	synonymous_variant	51252	exon14			CCTCATGAGGCCC	AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.2124C>T	2.37:g.97559759G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Silent	SNP	ENST00000417561.3	37																																																																																				G|0.745;A|0.255	0.255	strong		0.622	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490	
SLC25A26	115286	hgsc.bcm.edu	37	3	66293688	66293688	+	Silent	SNP	A	A	G	rs3772197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:66293688A>G	ENST00000354883.6	+	4	980	c.252A>G	c.(250-252)tcA>tcG	p.S84S	SLC25A26_ENST00000536651.1_3'UTR|SLC25A26_ENST00000336733.6_5'UTR|SLC25A26_ENST00000413054.1_5'UTR			Q70HW3	SAMC_HUMAN	solute carrier family 25 (S-adenosylmethionine carrier), member 26	84					S-adenosyl-L-methionine transmembrane transport (GO:1901962)|S-adenosyl-L-methionine transport (GO:0015805)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	S-adenosyl-L-methionine transmembrane transporter activity (GO:0000095)	p.S84S(1)		endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)|stomach(2)|urinary_tract(1)	8		Lung NSC(201;0.00774)		BRCA - Breast invasive adenocarcinoma(55;0.00046)|KIRC - Kidney renal clear cell carcinoma(15;0.0515)|Kidney(15;0.0648)		ATTCATCTTCATATTTGACAC	0.343													A|||	287	0.0573083	0.0295	0.0548	5008	,	,		15466	0.0377		0.0746	False		,,,				2504	0.0992				p.S84S		Atlas-SNP	.											SLC25A26,NS,carcinoma,0,1	SLC25A26	12	1	1	Substitution - coding silent(1)	stomach(1)	c.A252G						PASS	.	A	,	181,4225	116.7+/-154.6	5,171,2027	160.0	159.0	159.0		,252	-9.6	0.1	3	dbSNP_107	159	619,7981	161.0+/-214.0	15,589,3696	no	utr-5,coding-synonymous	SLC25A26	NM_001164796.1,NM_173471.3	,	20,760,5723	GG,GA,AA		7.1977,4.108,6.151	,	,84/275	66293688	800,12206	2203	4300	6503	SO:0001819	synonymous_variant	115286	exon4			ATCTTCATATTTG	AJ580932	CCDS54604.1, CCDS2905.2	3p14.2	2013-05-22	2012-03-29		ENSG00000144741	ENSG00000144741		"""Solute carriers"""	20661	protein-coding gene	gene with protein product		611037	"""solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 26"""			14674884	Standard	NM_173471		Approved		uc011bfq.2	Q70HW3	OTTHUMG00000149917	ENST00000354883.6:c.252A>G	3.37:g.66293688A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_173471	A8K758|B3KRZ7|Q7Z786|Q96E68	Silent	SNP	ENST00000354883.6	37	CCDS2905.2	138	0.06318681318681318	23	0.046747967479674794	33	0.09116022099447514	30	0.05244755244755245	52	0.06860158311345646	A	5.590	0.293637	0.10567	0.04108	0.071977	ENSG00000144741	ENST00000413054	.	.	.	5.67	-9.63	0.00544	.	.	.	.	.	T	0.00580	0.0019	.	.	.	0.09310	P	0.9999999999221516	.	.	.	.	.	.	T	0.15867	-1.0422	3	.	.	.	-28.0729	4.8763	0.13658	0.1925:0.3735:0.3461:0.0879	rs3772197;rs17823209;rs56630729;rs3772197	.	.	.	R	21	.	.	H	+	2	0	SLC25A26	66376379	0.000000	0.05858	0.121000	0.21740	0.526000	0.34562	-1.203000	0.03019	-0.938000	0.03714	-0.441000	0.05720	CAT	A|0.941;G|0.059	0.059	strong		0.343	SLC25A26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313894.2	NM_173471	
ADTRP	84830	hgsc.bcm.edu	37	6	11723636	11723636	+	Missense_Mutation	SNP	C	C	T	rs2076185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:11723636C>T	ENST00000414691.3	-	5	1014	c.604G>A	c.(604-606)Gtc>Atc	p.V202I	ADTRP_ENST00000379413.2_Missense_Mutation_p.V202I|ADTRP_ENST00000229583.5_Missense_Mutation_p.V220I|ADTRP_ENST00000514824.1_5'UTR	NM_032744.3	NP_116133.1	Q96IZ2	ADTRP_HUMAN	androgen-dependent TFPI-regulating protein	202			V -> I (in dbSNP:rs2076185).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											GCGATGAAGACGTAGCTGAGA	0.493													C|||	789	0.157548	0.0741	0.0418	5008	,	,		19217	0.4812		0.0368	False		,,,				2504	0.1431				p.V220I		Atlas-SNP	.											.	ADTRP	3	.	0			c.G658A						PASS	.	C	ILE/VAL,ILE/VAL	330,4076	174.8+/-204.3	12,306,1885	200.0	199.0	199.0		658,604	-11.9	0.0	6	dbSNP_96	199	226,8374	93.8+/-155.7	2,222,4076	yes	missense,missense	C6orf105	NM_001143948.1,NM_032744.3	29,29	14,528,5961	TT,TC,CC		2.6279,7.4898,4.275	benign,benign	220/249,202/231	11723636	556,12450	2203	4300	6503	SO:0001583	missense	84830	exon6			TGAAGACGTAGCT	AJ420520	CCDS4521.1, CCDS47374.1	6p24.1	2012-01-30	2012-01-27	2012-01-27	ENSG00000111863	ENSG00000111863			21214	protein-coding gene	gene with protein product	"""androgen-induced 1-like"""	614348	"""chromosome 6 open reading frame 105"""	C6orf105		21868574	Standard	NM_032744		Approved	dJ413H6.1, AIG1L	uc011dip.2	Q96IZ2	OTTHUMG00000014260	ENST00000414691.3:c.604G>A	6.37:g.11723636C>T	ENSP00000404416:p.Val202Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_001143948	B2R7T9|B4DV39|Q5THW1	Missense_Mutation	SNP	ENST00000414691.3	37	CCDS4521.1	337	0.1543040293040293	30	0.06097560975609756	10	0.027624309392265192	264	0.46153846153846156	33	0.04353562005277045	C	4.836	0.155405	0.09236	0.074898	0.026279	ENSG00000111863	ENST00000414691;ENST00000229583;ENST00000503285;ENST00000379413	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.96	-11.9	0.00025	.	1.141520	0.06148	N	0.673551	T	0.01189	0.0039	N	0.00446	-1.495	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.34354	-0.9832	9	0.08381	T	0.77	-1.3615	5.177	0.15141	0.0967:0.3665:0.3859:0.151	rs2076185;rs52797021;rs56622535;rs59870797;rs2076185	220;202	Q96IZ2-2;Q96IZ2	.;ADTRP_HUMAN	I	202;220;63;202	ENSP00000404416:V202I;ENSP00000229583:V220I;ENSP00000426507:V63I;ENSP00000368723:V202I	ENSP00000229583:V220I	V	-	1	0	C6orf105	11831622	0.000000	0.05858	0.002000	0.10522	0.030000	0.12068	-1.876000	0.01633	-1.553000	0.01702	-0.238000	0.12139	GTC	C|0.890;T|0.110	0.110	strong		0.493	ADTRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039864.3	NM_032744	
SSTR1	6751	hgsc.bcm.edu	37	14	38679473	38679473	+	Silent	SNP	C	C	T	rs2228497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:38679473C>T	ENST00000267377.2	+	3	1496	c.879C>T	c.(877-879)gtC>gtT	p.V293V		NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	somatostatin receptor 1	293					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glutamate receptor signaling pathway (GO:0007215)|negative regulation of cell proliferation (GO:0008285)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)|Pasireotide(DB06663)	TGCAGCTGGTCAACGTGTTTG	0.562													C|||	1031	0.205871	0.115	0.2205	5008	,	,		20321	0.0685		0.3082	False		,,,				2504	0.3548				p.V293V		Atlas-SNP	.											.	SSTR1	66	.	0			c.C879T						PASS	.	C		596,3810	261.9+/-264.6	41,514,1648	140.0	120.0	127.0		879	0.5	1.0	14	dbSNP_98	127	2732,5868	435.9+/-358.1	435,1862,2003	no	coding-synonymous	SSTR1	NM_001049.2		476,2376,3651	TT,TC,CC		31.7674,13.527,25.5882		293/392	38679473	3328,9678	2203	4300	6503	SO:0001819	synonymous_variant	6751	exon3			GCTGGTCAACGTG		CCDS9666.1	14q13	2012-08-08			ENSG00000139874	ENSG00000139874		"""GPCR / Class A : Somatostatin receptors"""	11330	protein-coding gene	gene with protein product		182451				8449518	Standard	NM_001049		Approved		uc001wul.1	P30872	OTTHUMG00000140249	ENST00000267377.2:c.879C>T	14.37:g.38679473C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_001049		Silent	SNP	ENST00000267377.2	37	CCDS9666.1																																																																																			C|0.772;T|0.228	0.228	strong		0.562	SSTR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409930.2		
KALRN	8997	hgsc.bcm.edu	37	3	124436234	124436234	+	Splice_Site	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124436234T>C	ENST00000291478.5	+	26	3487		c.e26+2		KALRN_ENST00000360013.3_Splice_Site|KALRN_ENST00000428018.2_Splice_Site	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase						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						GACATAAAGGTAATAAGAAGT	0.512																																					.		Atlas-SNP	.											TRAD,colon,carcinoma,0,2	KALRN	556	2	0			c.8415+2T>C						scavenged	.						55.0	53.0	54.0					3																	124436234		2203	4300	6503	SO:0001630	splice_region_variant	8997	exon59			TAAAGGTAATAAG	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	ENST00000291478.5:c.3324+2T>C	3.37:g.124436234T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	79	2	0.0253165	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Splice_Site	SNP	ENST00000291478.5	37	CCDS3028.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.973084	0.74246	.	.	ENSG00000160145	ENST00000360013;ENST00000354186;ENST00000291478;ENST00000428018	.	.	.	4.86	4.86	0.63082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6175	0.68560	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	KALRN	125918924	1.000000	0.71417	0.934000	0.37439	0.741000	0.42261	7.864000	0.87037	2.032000	0.59987	0.455000	0.32223	.	.	.	none		0.512	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947	Intron
PMS2	5395	hgsc.bcm.edu	37	7	6026864	6026864	+	Missense_Mutation	SNP	G	G	A	rs74902811|rs267608164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6026864G>A	ENST00000265849.7	-	11	1637	c.1532C>T	c.(1531-1533)aCg>aTg	p.T511M	PMS2_ENST00000441476.2_Missense_Mutation_p.T405M|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Missense_Mutation_p.T511M|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	511			T -> A (in dbSNP:rs2228007). {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)			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)		GTGACTGCCCGTGTCTGGGAT	0.622			"""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|||	185	0.0369409	0.1067	0.0058	5008	,	,		15619	0.0387		0.0	False		,,,				2504	0.001				p.T511M		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.C1532T						PASS	.	G	MET/THR	341,4065	175.9+/-205.1	8,325,1870	55.0	58.0	57.0		1532	-3.2	0.0	7	dbSNP_131	57	3,8597	2.2+/-6.3	0,3,4297	no	missense	PMS2	NM_000535.5	81	8,328,6167	AA,AG,GG		0.0349,7.7394,2.6449	benign	511/863	6026864	344,12662	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	CTGCCCGTGTCTG		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.1532C>T	7.37:g.6026864G>A	ENSP00000265849:p.Thr511Met	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	76	0.0347985347985348	55	0.11178861788617886	1	0.0027624309392265192	20	0.03496503496503497	0	0.0	g	9.587	1.125179	0.20959	0.077394	3.49E-4	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;D	0.86030	1.06;1.06;-2.06	5.54	-3.23	0.05109	.	1.625120	0.02813	N	0.124576	T	0.04363	0.0120	L	0.34521	1.04	0.09310	N	1	B;B;B	0.29253	0.239;0.03;0.239	B;B;B	0.15870	0.009;0.004;0.014	T	0.39860	-0.9593	10	0.44086	T	0.13	-2.1695	1.6864	0.02842	0.4375:0.1024:0.2528:0.2072	.	511;511;405	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	M	511;464;405;511	ENSP00000265849:T511M;ENSP00000392843:T405M;ENSP00000384308:T511M	ENSP00000265849:T511M	T	-	2	0	PMS2	5993390	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.454000	0.06770	-0.103000	0.12175	0.650000	0.86243	ACG	G|0.973;A|0.026	0.026	strong		0.622	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
TTLL1	25809	hgsc.bcm.edu	37	22	43455432	43455432	+	Silent	SNP	G	G	A	rs5759125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:43455432G>A	ENST00000266254.7	-	8	1089	c.849C>T	c.(847-849)gaC>gaT	p.D283D	TTLL1_ENST00000331018.7_Silent_p.D283D	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	283	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		AGTGGATCTCGTCGAACAGCT	0.642													G|||	1998	0.398962	0.4977	0.3141	5008	,	,		16415	0.7173		0.1064	False		,,,				2504	0.2986				p.D283D		Atlas-SNP	.											TTLL1,NS,carcinoma,0,1	TTLL1	41	1	0			c.C849T						PASS	.	G		1891,2515	541.3+/-375.7	411,1069,723	99.0	80.0	86.0		849	-2.6	1.0	22	dbSNP_114	86	921,7679	205.1+/-247.6	50,821,3429	no	coding-synonymous	TTLL1	NM_012263.4		461,1890,4152	AA,AG,GG		10.7093,42.9187,21.6208		283/424	43455432	2812,10194	2203	4300	6503	SO:0001819	synonymous_variant	25809	exon8			GATCTCGTCGAAC	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"""Tubulin tyrosine ligase-like family"""	1312	protein-coding gene	gene with protein product		608955	"""tubulin tyrosine ligase-like 1"""	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.849C>T	22.37:g.43455432G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1	782	0.35805860805860806	218	0.44308943089430897	104	0.287292817679558	391	0.6835664335664335	69	0.09102902374670185	G	10.57	1.387949	0.25118	0.429187	0.107093	ENSG00000100271	ENST00000495814	.	.	.	5.48	-2.61	0.06171	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999984994	.	.	.	.	.	.	T	0.40194	-0.9576	3	.	.	.	.	5.4795	0.16715	0.5278:0.2927:0.1795:0.0	rs5759125;rs61106588;rs5759125	.	.	.	M	209	.	.	T	-	2	0	TTLL1	41785376	1.000000	0.71417	0.959000	0.39883	0.991000	0.79684	1.739000	0.38217	-0.226000	0.09899	0.561000	0.74099	ACG	G|0.704;A|0.296	0.296	strong		0.642	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263	
PASD1	139135	hgsc.bcm.edu	37	X	150840690	150840690	+	Missense_Mutation	SNP	G	G	T	rs370395923		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:150840690G>T	ENST00000370357.4	+	14	1718	c.1473G>T	c.(1471-1473)gaG>gaT	p.E491D		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	491						nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					acctgaaggagcagcagcggc	0.527													G|||	16	0.00423841	0.0121	0.0	3775	,	,		14023	0.0		0.0	False		,,,				2504	0.0				p.E491D		Atlas-SNP	.											.	PASD1	286	.	0			c.G1473T						PASS	.	G	ASP/GLU	35,3366		0,33,2,1472,389	10.0	10.0	10.0		1473	1.0	0.0	X		10	1,5850		0,0,1,2208,1434	yes	missense	PASD1	NM_173493.2	45	0,33,3,3680,1823	TT,TG,T,GG,G		0.0171,1.0291,0.3891	possibly-damaging	491/774	150840690	36,9216	1896	3643	5539	SO:0001583	missense	139135	exon14			GAAGGAGCAGCAG	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.1473G>T	X.37:g.150840690G>T	ENSP00000359382:p.Glu491Asp	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	G	9.223	1.033777	0.19590	0.010291	1.71E-4	ENSG00000166049	ENST00000370357	T	0.17691	2.26	2.03	1.04	0.20106	.	.	.	.	.	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	P	0.50710	0.938	B	0.37387	0.248	T	0.23904	-1.0175	9	0.15066	T	0.55	.	4.9456	0.13987	0.0:0.0:0.6449:0.355	.	491	Q8IV76	PASD1_HUMAN	D	491	ENSP00000359382:E491D	ENSP00000359382:E491D	E	+	3	2	PASD1	150591346	0.001000	0.12720	0.004000	0.12327	0.251000	0.25915	-0.444000	0.06854	0.252000	0.21531	0.462000	0.41574	GAG	.	.	weak		0.527	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493	
TIMP3	7078	hgsc.bcm.edu	37	22	33253280	33253280	+	Silent	SNP	T	T	C	rs9862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:33253280T>C	ENST00000266085.6	+	3	550	c.249T>C	c.(247-249)caT>caC	p.H83H	SYN3_ENST00000358763.2_Intron|SYN3_ENST00000332840.5_Intron	NM_000362.4	NP_000353.1	P35625	TIMP3_HUMAN	TIMP metallopeptidase inhibitor 3	83	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				cellular response to organic substance (GO:0071310)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(2)|large_intestine(3)|lung(1)|urinary_tract(1)	7						AGTACATCCATACGGAAGCTT	0.507													C|||	3260	0.650958	0.8835	0.696	5008	,	,		20747	0.6121		0.4821	False		,,,				2504	0.5184				p.H83H		Atlas-SNP	.											.	TIMP3	31	.	0			c.T249C						PASS	.	C	,,,	3637,769	312.7+/-292.7	1499,639,65	159.0	130.0	140.0		249,,,	5.6	1.0	22	dbSNP_52	140	4332,4268	575.9+/-390.3	1095,2142,1063	no	coding-synonymous,intron,intron,intron	TIMP3,SYN3	NM_000362.4,NM_001135774.1,NM_003490.3,NM_133633.2	,,,	2594,2781,1128	CC,CT,TT		49.6279,17.4535,38.7283	,,,	83/212,,,	33253280	7969,5037	2203	4300	6503	SO:0001819	synonymous_variant	7078	exon3			CATCCATACGGAA		CCDS13911.1	22q12.3	2013-01-08	2008-07-31		ENSG00000100234	ENSG00000100234			11822	protein-coding gene	gene with protein product		188826	"""tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory)"""	SFD		8188246, 12652295	Standard	NM_000362		Approved		uc003anb.3	P35625	OTTHUMG00000030784	ENST00000266085.6:c.249T>C	22.37:g.33253280T>C		Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	235	235	1	NM_000362	B2RBY9|Q5THV4|Q9UC74|Q9UGS2	Silent	SNP	ENST00000266085.6	37	CCDS13911.1																																																																																			T|0.372;C|0.628	0.628	strong		0.507	TIMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075672.2	NM_000362	
IL25	64806	hgsc.bcm.edu	37	14	23845061	23845061	+	Missense_Mutation	SNP	T	T	C	rs149802556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23845061T>C	ENST00000329715.2	+	2	764	c.506T>C	c.(505-507)gTg>gCg	p.V169A	IL25_ENST00000397242.2_Missense_Mutation_p.V153A|CMTM5_ENST00000555731.1_5'Flank|CMTM5_ENST00000342473.4_5'Flank|CMTM5_ENST00000359320.3_5'Flank|CMTM5_ENST00000339180.4_5'Flank|CMTM5_ENST00000397227.3_5'Flank|CMTM5_ENST00000382809.2_5'Flank	NM_022789.3	NP_073626.1	Q9H293	IL25_HUMAN	interleukin 25	169					eosinophil differentiation (GO:0030222)|inflammatory response to antigenic stimulus (GO:0002437)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to fungus (GO:0009620)|response to nematode (GO:0009624)	extracellular space (GO:0005615)	interleukin-17E receptor binding (GO:0030380)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9	all_cancers(95;2e-05)			GBM - Glioblastoma multiforme(265;0.00665)|READ - Rectum adenocarcinoma(4;0.0276)|Colorectal(4;0.0396)		TTAGCTTGTGTGTGTGTGCGG	0.607																																					p.V169A		Atlas-SNP	.											.	IL25	21	.	0			c.T506C						PASS	.	T	ALA/VAL,ALA/VAL	2,4404	4.2+/-10.8	0,2,2201	150.0	137.0	141.0		506,458	4.6	1.0	14	dbSNP_134	141	0,8600		0,0,4300	no	missense,missense	IL25	NM_022789.3,NM_172314.1	64,64	0,2,6501	CC,CT,TT		0.0,0.0454,0.0154	probably-damaging,probably-damaging	169/178,153/162	23845061	2,13004	2203	4300	6503	SO:0001583	missense	64806	exon2			CTTGTGTGTGTGT	AF305200	CCDS9597.1, CCDS45086.1	14q11.2	2008-01-07	2006-05-17	2006-05-17	ENSG00000166090	ENSG00000166090		"""Interleukins and interleukin receptors"""	13765	protein-coding gene	gene with protein product		605658	"""interleukin 17E"""	IL17E		11058597, 11754819	Standard	NM_172314		Approved	IL-25, IL-17E	uc001wjq.3	Q9H293	OTTHUMG00000028749	ENST00000329715.2:c.506T>C	14.37:g.23845061T>C	ENSP00000328111:p.Val169Ala	Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	262	105	0.400763	NM_022789	Q2M3F0|Q8IZV3|Q8WXB0	Missense_Mutation	SNP	ENST00000329715.2	37	CCDS9597.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.049273	0.75846	4.54E-4	0.0	ENSG00000166090	ENST00000397242;ENST00000329715	T;T	0.55234	0.53;0.53	4.58	4.58	0.56647	.	0.145674	0.33023	N	0.005361	T	0.57636	0.2067	L	0.44542	1.39	0.30135	N	0.804464	P;D	0.64830	0.64;0.994	B;P	0.59056	0.334;0.851	T	0.58634	-0.7602	10	0.48119	T	0.1	-26.6522	10.2614	0.43430	0.0:0.0:0.0:1.0	.	169;153	Q9H293;Q9H293-2	IL25_HUMAN;.	A	153;169	ENSP00000380417:V153A;ENSP00000328111:V169A	ENSP00000328111:V169A	V	+	2	0	IL25	22914901	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.712000	0.54875	1.947000	0.56498	0.459000	0.35465	GTG	T|1.000;C|0.000	0.000	strong		0.607	IL25-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071789.2		
EPHA4	2043	hgsc.bcm.edu	37	2	222308226	222308226	+	Silent	SNP	T	T	C	rs10498111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:222308226T>C	ENST00000281821.2	-	10	1916	c.1875A>G	c.(1873-1875)aaA>aaG	p.K625K	EPHA4_ENST00000409938.1_Silent_p.K625K|EPHA4_ENST00000392071.4_Silent_p.K574K|EPHA4_ENST00000409854.1_Silent_p.K625K	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	625	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		CTCCTATAACTTTTTCAATCT	0.403													T|||	448	0.0894569	0.1589	0.0879	5008	,	,		19302	0.0863		0.008	False		,,,				2504	0.0838				p.K625K		Atlas-SNP	.											.	EPHA4	263	.	0			c.A1875G						PASS	.	T		600,3806	257.4+/-261.8	40,520,1643	148.0	131.0	137.0		1875	4.8	1.0	2	dbSNP_119	137	60,8540	36.9+/-92.0	1,58,4241	no	coding-synonymous	EPHA4	NM_004438.3		41,578,5884	CC,CT,TT		0.6977,13.6178,5.0746		625/987	222308226	660,12346	2203	4300	6503	SO:0001819	synonymous_variant	2043	exon10			TATAACTTTTTCA	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3388	protein-coding gene	gene with protein product		602188	"""EphA4"""	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.1875A>G	2.37:g.222308226T>C		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	217	98	0.451613	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Silent	SNP	ENST00000281821.2	37	CCDS2447.1																																																																																			T|0.936;C|0.064	0.064	strong		0.403	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3		
TNN	63923	hgsc.bcm.edu	37	1	175049405	175049405	+	Silent	SNP	C	C	A	rs61742080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:175049405C>A	ENST00000239462.4	+	4	1004	c.891C>A	c.(889-891)ccC>ccA	p.P297P		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	297	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GCTACTACCCCCTGGGGAAGG	0.582													C|||	357	0.0712859	0.202	0.0317	5008	,	,		18435	0.004		0.0298	False		,,,				2504	0.0348				p.P297P		Atlas-SNP	.											.	TNN	297	.	0			c.C891A						PASS	.	C		743,3663	305.2+/-288.9	57,629,1517	80.0	79.0	80.0		891	-7.2	0.5	1	dbSNP_129	80	226,8374	93.1+/-155.1	4,218,4078	no	coding-synonymous	TNN	NM_022093.1		61,847,5595	AA,AC,CC		2.6279,16.8634,7.4504		297/1300	175049405	969,12037	2203	4300	6503	SO:0001819	synonymous_variant	63923	exon4			CTACCCCCTGGGG	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.891C>A	1.37:g.175049405C>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	137	57	0.416058	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	37	CCDS30943.1																																																																																			C|0.931;A|0.069	0.069	strong		0.582	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
PTCD2	79810	hgsc.bcm.edu	37	5	71618069	71618069	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71618069A>G	ENST00000380639.5	+	2	214	c.198A>G	c.(196-198)gcA>gcG	p.A66A	PTCD2_ENST00000543322.1_Silent_p.A66A|MRPS27_ENST00000515404.1_5'Flank|MRPS27_ENST00000522095.1_5'Flank|MRPS27_ENST00000457646.4_5'Flank|PTCD2_ENST00000503868.1_Silent_p.A66A|PTCD2_ENST00000536805.1_5'UTR|MRPS27_ENST00000513900.1_5'Flank|MRPS27_ENST00000261413.5_5'Flank	NM_024754.3	NP_079030.3	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	66					kidney development (GO:0001822)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|muscle fiber development (GO:0048747)|regulation of mRNA processing (GO:0050684)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(1)|skin(1)	11		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)		TGGCTGTTGCATGTAATCTTT	0.299																																					p.A66A		Atlas-SNP	.											.	PTCD2	31	.	0			c.A198G						PASS	.						107.0	119.0	115.0					5																	71618069		1815	4077	5892	SO:0001819	synonymous_variant	79810	exon2			TGTTGCATGTAAT	BC018720	CCDS4014.2, CCDS68891.1, CCDS68892.1, CCDS75258.1	5q13.2	2008-02-05			ENSG00000049883	ENSG00000049883			25734	protein-coding gene	gene with protein product		615484				12477932	Standard	XM_005248601		Approved	FLJ12598	uc003kcb.3	Q8WV60	OTTHUMG00000100953	ENST00000380639.5:c.198A>G	5.37:g.71618069A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	75	24	0.32	NM_024754	B7Z5D0|B7Z8L7|E9PFV7|Q6IA65|Q9H9R0	Silent	SNP	ENST00000380639.5	37	CCDS4014.2																																																																																			.	.	none		0.299	PTCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218562.6	NM_024754	
TRIOBP	11078	hgsc.bcm.edu	37	22	38130459	38130459	+	Missense_Mutation	SNP	G	G	T	rs8140207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38130459G>T	ENST00000406386.3	+	9	4371	c.4116G>T	c.(4114-4116)gaG>gaT	p.E1372D		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1372			E -> D (in dbSNP:rs8140207).		actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GCCAAGCAGAGCCCCCTCATC	0.652													G|||	1322	0.263978	0.0401	0.2968	5008	,	,		16877	0.3016		0.3241	False		,,,				2504	0.4427				p.E1372D		Atlas-SNP	.											.	TRIOBP	262	.	0			c.G4116T						PASS	.	G	ASP/GLU	295,3593		11,273,1660	31.0	35.0	34.0		4116	0.9	0.0	22	dbSNP_116	34	2442,5822		337,1768,2027	yes	missense	TRIOBP	NM_001039141.2	45	348,2041,3687	TT,TG,GG		29.5499,7.5874,22.523	benign	1372/2366	38130459	2737,9415	1944	4132	6076	SO:0001583	missense	11078	exon9			AGCAGAGCCCCCT	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.4116G>T	22.37:g.38130459G>T	ENSP00000384312:p.Glu1372Asp	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	174	85	0.488506	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	585	0.26785714285714285	25	0.0508130081300813	109	0.3011049723756906	201	0.3513986013986014	250	0.32981530343007914	G	10.95	1.496753	0.26861	0.075874	0.295499	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.28454	1.61	5.45	0.937	0.19494	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	1.999999999946489E-6	B	0.21071	0.051	B	0.17979	0.02	T	0.46789	-0.9166	8	0.22109	T	0.4	.	3.1706	0.06551	0.3631:0.0:0.4543:0.1825	rs8140207;rs8140207	1372	Q9H2D6	TARA_HUMAN	D	1372;1333	ENSP00000384312:E1372D	ENSP00000384312:E1372D	E	+	3	2	TRIOBP	36460405	0.008000	0.16893	0.010000	0.14722	0.219000	0.24729	-0.109000	0.10840	0.228000	0.21019	0.563000	0.77884	GAG	G|0.726;T|0.274	0.274	strong		0.652	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
SMYD1	150572	hgsc.bcm.edu	37	2	88407959	88407959	+	Silent	SNP	T	T	C	rs2970918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:88407959T>C	ENST00000419482.2	+	9	1300	c.1215T>C	c.(1213-1215)caT>caC	p.H405H	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.H392H	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	405					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						CCAACTGGCATGCTGGTAACA	0.552													t|||	1995	0.398363	0.525	0.1441	5008	,	,		18792	0.5278		0.1819	False		,,,				2504	0.4969				p.H405H		Atlas-SNP	.											.	SMYD1	95	.	0			c.T1215C						PASS	.			2016,2390	563.2+/-381.1	455,1106,642	144.0	108.0	120.0		1215	-7.4	0.8	2	dbSNP_101	120	1593,7007	295.8+/-302.6	148,1297,2855	no	coding-synonymous	SMYD1	NM_198274.3		603,2403,3497	CC,CT,TT		18.5233,45.7558,27.7487		405/491	88407959	3609,9397	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon9			CTGGCATGCTGGT	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.1215T>C	2.37:g.88407959T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			T|0.711;G|0.000;C|0.288;A|0.000	0.288	strong		0.552	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
FLG	2312	hgsc.bcm.edu	37	1	152283367	152283367	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152283367T>C	ENST00000368799.1	-	3	4030	c.3995A>G	c.(3994-3996)cAt>cGt	p.H1332R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1332	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)			CTCTGTGTGATGAGTGCCTGA	0.552									Ichthyosis																												p.H1332R		Atlas-SNP	.											.	FLG	900	.	0			c.A3995G						PASS	.						304.0	292.0	296.0					1																	152283367		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTGTGATGAGTGC	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.3995A>G	1.37:g.152283367T>C	ENSP00000357789:p.His1332Arg	Somatic	509	0	0		WXS	Illumina HiSeq	Phase_I	622	48	0.0771704	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	2.821	-0.244841	0.05906	.	.	ENSG00000143631	ENST00000368799	T	0.03951	3.75	2.24	-3.75	0.04372	.	.	.	.	.	T	0.00580	0.0019	N	0.05383	-0.06	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45673	-0.9245	9	0.11182	T	0.66	.	8.4062	0.32616	0.0:0.3846:0.0:0.6154	.	1332	P20930	FILA_HUMAN	R	1332	ENSP00000357789:H1332R	ENSP00000357789:H1332R	H	-	2	0	FLG	150549991	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.669000	0.00398	-1.560000	0.01686	-1.470000	0.01010	CAT	.	.	none		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TTN	7273	hgsc.bcm.edu	37	2	179398509	179398509	+	Missense_Mutation	SNP	C	C	A	rs3731752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179398509C>A	ENST00000591111.1	-	308	98134	c.97910G>T	c.(97909-97911)gGa>gTa	p.G32637V	TTN_ENST00000589042.1_Missense_Mutation_p.G34278V|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G25213V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G31710V|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G25338V|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G25405V|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32637	Ig-like 144.		G -> V. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATAGTTACTCCAAACCGGAC	0.423													C|||	391	0.0780751	0.0847	0.0403	5008	,	,		21817	0.1716		0.0318	False		,,,				2504	0.047				p.G34278V		Atlas-SNP	.											.	TTN	18412	.	0			c.G102833T						PASS	.	C	VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY	245,3561		8,229,1666	97.0	89.0	92.0		75638,95129,76013,76214	5.6	1.0	2	dbSNP_107	92	163,8059		4,155,3952	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	109,109,109,109	12,384,5618	AA,AC,CC		1.9825,6.4372,3.3921	probably-damaging,probably-damaging,probably-damaging,probably-damaging	25213/26927,31710/33424,25338/27052,25405/27119	179398509	408,11620	1903	4111	6014	SO:0001583	missense	7273	exon358			GTTACTCCAAACC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.97910G>T	2.37:g.179398509C>A	ENSP00000465570:p.Gly32637Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		175	0.08012820512820513	38	0.07723577235772358	15	0.04143646408839779	100	0.17482517482517482	22	0.029023746701846966	C	15.09	2.730452	0.48939	0.064372	0.019825	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.6	5.6	0.85130	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Protein kinase-like domain (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.00300	0.0009	N	0.01874	-0.695	0.09310	P	0.9999999839552	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.73380	0.98;0.98;0.98;0.98	T	0.51647	-0.8679	8	0.87932	D	0	.	13.8517	0.63501	0.0:0.9246:0.0:0.0754	rs3731752;rs52831571;rs57847880;rs3731752	25213;25338;25405;32637	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	31710;25213;25405;25338;25210	ENSP00000343764:G31710V;ENSP00000434586:G25213V;ENSP00000340554:G25405V;ENSP00000352154:G25338V	ENSP00000340554:G25405V	G	-	2	0	TTN	179106755	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.794000	0.85869	2.641000	0.89580	0.491000	0.48974	GGA	C|0.922;A|0.078	0.078	strong		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
LARS2	23395	hgsc.bcm.edu	37	3	45459030	45459030	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:45459030C>T	ENST00000415258.1	+	4	561	c.420C>T	c.(418-420)gtC>gtT	p.V140V	LARS2_ENST00000265537.3_Silent_p.V140V|LARS2_ENST00000414984.1_Silent_p.V97V			Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	140					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	ATGCCGCAGTCGAGAGGAATC	0.398																																					p.V140V		Atlas-SNP	.											.	LARS2	48	.	0			c.C420T						PASS	.						123.0	116.0	118.0					3																	45459030		2203	4300	6503	SO:0001819	synonymous_variant	23395	exon5			CGCAGTCGAGAGG	AJ312685	CCDS2728.1	3p21.3	2012-10-26			ENSG00000011376	ENSG00000011376	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	17095	protein-coding gene	gene with protein product	"""leucine tRNA ligase 2, mitochondrial"""	604544				20194621, 15123417	Standard	NM_015340		Approved	KIAA0028, LEURS, MGC26121	uc003cop.1	Q15031	OTTHUMG00000133177	ENST00000415258.1:c.420C>T	3.37:g.45459030C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	100	29	0.29	NM_015340		Silent	SNP	ENST00000415258.1	37	CCDS2728.1																																																																																			.	.	none		0.398	LARS2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345001.1	NM_015340	
AP5M1	55745	hgsc.bcm.edu	37	14	57741550	57741550	+	Silent	SNP	A	A	G	rs1189899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:57741550A>G	ENST00000261558.3	+	2	1069	c.663A>G	c.(661-663)caA>caG	p.Q221Q	AP5M1_ENST00000431972.2_Silent_p.Q235Q	NM_018229.3	NP_060699.3	Q9H0R1	AP5M1_HUMAN	adaptor-related protein complex 5, mu 1 subunit	221	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytosol (GO:0005829)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)											AATCCATGCAATATGATAAAC	0.388													A|||	1364	0.272364	0.8321	0.0879	5008	,	,		17872	0.0655		0.0567	False		,,,				2504	0.0818				p.Q221Q		Atlas-SNP	.											.	.	.	.	0			c.A663G						PASS	.	A		2847,1505		956,935,285	85.0	94.0	91.0		663	-2.3	1.0	14	dbSNP_87	91	486,8090		12,462,3814	no	coding-synonymous	MUDENG	NM_018229.3		968,1397,4099	GG,GA,AA		5.667,34.5818,25.7812		221/491	57741550	3333,9595	2176	4288	6464	SO:0001819	synonymous_variant	55745	exon2			CATGCAATATGAT	AF094583	CCDS9729.1	14q22.2	2012-03-20	2012-03-20	2012-03-20	ENSG00000053770	ENSG00000053770			20192	protein-coding gene	gene with protein product	"""Mu-2 related death-inducing gene"""	614368	"""chromosome 14 open reading frame 108"", ""MU-2/AP1M2 domain containing, death-inducing"""	C14orf108, MUDENG		18395520	Standard	NM_018229		Approved	FLJ10813, MuD, mu5	uc001xcv.3	Q9H0R1	OTTHUMG00000140318	ENST00000261558.3:c.663A>G	14.37:g.57741550A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_018229	O95354|Q6ZMD7|Q96DX3|Q9NVC5	Silent	SNP	ENST00000261558.3	37	CCDS9729.1																																																																																			A|0.764;G|0.236	0.236	strong		0.388	AP5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276922.1	NM_018229	
TTN	7273	hgsc.bcm.edu	37	2	179441917	179441917	+	Missense_Mutation	SNP	T	T	C	rs72646881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179441917T>C	ENST00000591111.1	-	274	64446	c.64222A>G	c.(64222-64224)Atc>Gtc	p.I21408V	TTN_ENST00000589042.1_Missense_Mutation_p.I23049V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I13984V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I20481V|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I14109V|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I14176V|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	21408	Fibronectin type-III 55. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACATTACTGATTTCAACAGGA	0.448													T|||	182	0.0363419	0.1278	0.0173	5008	,	,		21850	0.0		0.001	False		,,,				2504	0.0				p.I23049V		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,+2,5	TTN	18412	5	0			c.A69145G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	402,3490		24,354,1568	60.0	59.0	59.0		42526,42325,61441,41950	3.2	1.0	2	dbSNP_130	59	8,8272		0,8,4132	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	24,362,5700	CC,CT,TT		0.0966,10.3289,3.3684	benign,benign,benign,benign	14176/27119,14109/27052,20481/33424,13984/26927	179441917	410,11762	1946	4140	6086	SO:0001583	missense	7273	exon324			TACTGATTTCAAC	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.64222A>G	2.37:g.179441917T>C	ENSP00000465570:p.Ile21408Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	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		86	0.039377289377289376	78	0.15853658536585366	8	0.022099447513812154	0	0.0	0	0.0	T	10.04	1.241565	0.22711	0.103289	9.66E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	5.62	3.18	0.36537	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00073	0.0002	N	0.02368	-0.58	0.40312	P	0.02127100000000004	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.07616	-1.0763	8	0.87932	D	0	.	4.7345	0.12981	0.129:0.2044:0.0:0.6665	.	13984;14109;14176;21408	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	20481;13984;14176;14109;13982	ENSP00000343764:I20481V;ENSP00000434586:I13984V;ENSP00000340554:I14176V;ENSP00000352154:I14109V	ENSP00000340554:I14176V	I	-	1	0	TTN	179150163	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.225000	0.32551	0.466000	0.27193	0.533000	0.62120	ATC	T|0.967;C|0.033	0.033	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84639350	84639350	+	Missense_Mutation	SNP	C	C	T	rs2277849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:84639350C>T	ENST00000286744.5	+	20	2829	c.2605C>T	c.(2605-2607)Ctc>Ttc	p.L869F	ADAMTSL3_ENST00000567716.1_3'UTR|ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.L869F	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	869	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.		L -> F (in dbSNP:rs2277849). {ECO:0000269|PubMed:15489334}.			proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.L869F(1)		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)			TCTACCAGGGCTCCCTCTTGT	0.522													C|||	1304	0.260383	0.3714	0.1571	5008	,	,		20793	0.3442		0.2714	False		,,,				2504	0.0859				p.L869F		Atlas-SNP	.											ADAMTSL3,NS,carcinoma,0,1	ADAMTSL3	290	1	1	Substitution - Missense(1)	stomach(1)	c.C2605T						PASS	.	C	PHE/LEU	1537,2869	486.2+/-360.5	252,1033,918	184.0	161.0	169.0		2605	2.4	0.1	15	dbSNP_100	169	2269,6331	383.0+/-340.6	291,1687,2322	yes	missense	ADAMTSL3	NM_207517.2	22	543,2720,3240	TT,TC,CC		26.3837,34.8842,29.2634	possibly-damaging	869/1692	84639350	3806,9200	2203	4300	6503	SO:0001583	missense	57188	exon20			CCAGGGCTCCCTC	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.2605C>T	15.37:g.84639350C>T	ENSP00000286744:p.Leu869Phe	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	638	0.29212454212454214	158	0.32113821138211385	64	0.17679558011049723	199	0.3479020979020979	217	0.2862796833773087	C	19.35	3.810236	0.70797	0.348842	0.263837	ENSG00000156218	ENST00000286744	T	0.62232	0.04	4.39	2.38	0.29361	.	0.810196	0.10421	N	0.676704	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	P;P	0.42941	0.606;0.794	B;P	0.45998	0.435;0.5	T	0.17501	-1.0367	9	0.54805	T	0.06	.	8.0735	0.30704	0.0:0.6773:0.1475:0.1752	rs2277849;rs17370789;rs52816289;rs61270368;rs2277849	869;869	P82987-2;P82987	.;ATL3_HUMAN	F	869	ENSP00000286744:L869F	ENSP00000286744:L869F	L	+	1	0	ADAMTSL3	82430354	0.428000	0.25522	0.121000	0.21740	0.978000	0.69477	1.014000	0.29950	1.043000	0.40175	0.650000	0.86243	CTC	C|0.712;T|0.288	0.288	strong		0.522	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
CSH2	1443	hgsc.bcm.edu	37	17	61950694	61950694	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61950694G>A	ENST00000392886.2	-	2	167	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	CSH2_ENST00000345366.7_Missense_Mutation_p.R6W|CSH2_ENST00000560142.1_Missense_Mutation_p.R6W|CSH2_ENST00000336844.5_Missense_Mutation_p.R6W	NM_020991.3	NP_066271.1	P0DML3	CSH2_HUMAN	chorionic somatomammotropin hormone 2	6						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			endometrium(2)|large_intestine(1)|lung(3)	6						AGGGACGTCCGGGAGCCTGGG	0.607																																					p.R6W		Atlas-SNP	.											.	CSH2	37	.	0			c.C16T						PASS	.						12.0	12.0	12.0					17																	61950694		2179	4248	6427	SO:0001583	missense	1443	exon2			ACGTCCGGGAGCC	V00573	CCDS11646.1, CCDS42368.1, CCDS42369.1	17q22-q24	2012-10-02							2441	protein-coding gene	gene with protein product	"""placental lactogen"", ""chorionic somatomammotropin B"""	118820				593368, 6208192	Standard	NM_020991		Approved	hCS-B, CSB, CS-2	uc002jch.3	P0DML3		ENST00000392886.2:c.16C>T	17.37:g.61950694G>A	ENSP00000376623:p.Arg6Trp	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	235	55	0.234043	NM_022645	P01243|Q0VDB1|Q14407	Missense_Mutation	SNP	ENST00000392886.2	37	CCDS42369.1	.	.	.	.	.	.	.	.	.	.	g	9.767	1.171702	0.21704	.	.	ENSG00000213218	ENST00000345366;ENST00000336844;ENST00000392886	D;D;D	0.91407	-2.84;-2.17;-2.36	4.1	3.12	0.35913	.	0.628574	0.16367	N	0.217506	D	0.83175	0.5197	L	0.39397	1.21	0.09310	N	1	D;B;D;B	0.54397	0.966;0.035;0.966;0.003	B;B;B;B	0.39660	0.306;0.006;0.306;0.005	T	0.72577	-0.4251	10	0.27082	T	0.32	.	7.9049	0.29757	0.1194:0.0:0.8806:0.0	.	6;6;6;6	P01243;A6NIT4;A8K6C2;B1A4H9	CSH_HUMAN;.;.;.	W	6	ENSP00000308396:R6W;ENSP00000338816:R6W;ENSP00000376623:R6W	ENSP00000338816:R6W	R	-	1	2	CSH2	59304426	0.001000	0.12720	0.003000	0.11579	0.011000	0.07611	0.623000	0.24447	0.839000	0.34971	0.561000	0.74099	CGG	G|0.980;A|0.020	0.020	strong		0.607	CSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417657.1	NM_020991	
ZNF879	345462	hgsc.bcm.edu	37	5	178459426	178459426	+	Missense_Mutation	SNP	A	A	C	rs17078991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:178459426A>C	ENST00000444149.2	+	5	665	c.477A>C	c.(475-477)gaA>gaC	p.E159D		NM_001136116.1	NP_001129588.1	B4DU55	ZN879_HUMAN	zinc finger protein 879	159					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.E159D(1)		endometrium(3)|kidney(2)|pancreas(1)|stomach(1)	7						AAGGTGTTGAATTTGGGAAAA	0.373													A|||	1824	0.364217	0.5182	0.255	5008	,	,		19198	0.4276		0.2237	False		,,,				2504	0.3129				p.E159D		Atlas-SNP	.											ZNF879,NS,carcinoma,0,2	ZNF879	41	2	1	Substitution - Missense(1)	stomach(1)	c.A477C						scavenged	.	A	ASP/GLU	618,766		138,342,212	91.0	77.0	81.0		477	-1.2	0.3	5	dbSNP_123	81	706,2476		75,556,960	yes	missense	ZNF879	NM_001136116.1	45	213,898,1172	CC,CA,AA		22.1873,44.6532,28.9969	benign	159/564	178459426	1324,3242	692	1591	2283	SO:0001583	missense	345462	exon5			TGTTGAATTTGGG	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.477A>C	5.37:g.178459426A>C	ENSP00000414887:p.Glu159Asp	Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_001136116		Missense_Mutation	SNP	ENST00000444149.2	37	CCDS47352.1	770	0.3525641025641026	243	0.49390243902439024	100	0.27624309392265195	244	0.42657342657342656	183	0.24142480211081793	A	9.372	1.070780	0.20147	0.446532	0.221873	ENSG00000234284	ENST00000444149	T	0.06933	3.24	4.45	-1.18	0.09617	.	.	.	.	.	T	0.00012	0.0000	L	0.37850	1.14	0.34582	P	0.28547900000000004	B	0.02656	0.0	B	0.04013	0.001	T	0.42120	-0.9470	8	0.42905	T	0.14	-4.0842	4.6168	0.12430	0.4554:0.3309:0.2137:0.0	rs17078991;rs52798739;rs17078991	159	B4DU55	ZN879_HUMAN	D	159	ENSP00000414887:E159D	ENSP00000414887:E159D	E	+	3	2	ZNF879	178392032	0.000000	0.05858	0.286000	0.24833	0.782000	0.44232	-0.068000	0.11561	-0.283000	0.09115	0.482000	0.46254	GAA	A|0.634;C|0.366	0.366	strong		0.373	ZNF879-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374447.1	NM_001136116	
CYP2A7	1549	hgsc.bcm.edu	37	19	41386033	41386033	+	Missense_Mutation	SNP	T	T	C	rs73032311	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41386033T>C	ENST00000301146.4	-	4	1151	c.610A>G	c.(610-612)Atg>Gtg	p.M204V	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.M153V	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	200	0	0		WXS	Illumina HiSeq	Phase_I	237	116	0.489451	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	
KIAA0895L	653319	hgsc.bcm.edu	37	16	67214346	67214346	+	Silent	SNP	C	C	T	rs7186508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67214346C>T	ENST00000290881.7	-	3	1094	c.168G>A	c.(166-168)gcG>gcA	p.A56A	KIAA0895L_ENST00000563831.2_Intron|KIAA0895L_ENST00000561621.1_Silent_p.A56A|KIAA0895L_ENST00000563902.1_Silent_p.A56A			Q68EN5	K895L_HUMAN	KIAA0895-like	56	Pro-rich.									breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1)	17						GGGGCTGCAGCGCTGGGGGGA	0.642													T|||	1003	0.20028	0.5129	0.0735	5008	,	,		15749	0.0248		0.0686	False		,,,				2504	0.184				p.A56A		Atlas-SNP	.											.	KIAA0895L	32	.	0			c.G168A						PASS	.	T		1443,2569		246,951,809	10.0	15.0	13.0		168	-5.4	0.1	16	dbSNP_116	13	510,7778		21,468,3655	no	coding-synonymous	KIAA0895L	NM_001040715.1		267,1419,4464	TT,TC,CC		6.1535,35.9671,15.878		56/472	67214346	1953,10347	2006	4144	6150	SO:0001819	synonymous_variant	653319	exon2			CTGCAGCGCTGGG	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.168G>A	16.37:g.67214346C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_001040715	A2VCS8|Q8N3H9|Q8NAQ5|Q96IE5	Silent	SNP	ENST00000290881.7	37	CCDS42177.1																																																																																			C|0.864;T|0.136	0.136	strong		0.642	KIAA0895L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421193.4	NM_001040715	
GRIK4	2900	hgsc.bcm.edu	37	11	120811161	120811161	+	Missense_Mutation	SNP	G	G	A	rs2230298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:120811161G>A	ENST00000527524.2	+	14	1869	c.1582G>A	c.(1582-1584)Gtt>Att	p.V528I	GRIK4_ENST00000438375.2_Missense_Mutation_p.V528I	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	528			V -> I (in dbSNP:rs35599906). {ECO:0000269|PubMed:8263508}.		glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		TCTTTACCGCGTTCATATGGT	0.388													G|||	151	0.0301518	0.1104	0.0072	5008	,	,		22695	0.0		0.0	False		,,,				2504	0.0				p.V528I		Atlas-SNP	.											.	GRIK4	149	.	0			c.G1582A						PASS	.	G	ILE/VAL	396,4010	195.7+/-220.2	25,346,1832	82.0	84.0	83.0		1582	5.5	1.0	11	dbSNP_126	83	7,8591	6.4+/-24.3	0,7,4292	yes	missense	GRIK4	NM_014619.2	29	25,353,6124	AA,AG,GG		0.0814,8.9877,3.099	probably-damaging	528/957	120811161	403,12601	2203	4299	6502	SO:0001583	missense	2900	exon12			TACCGCGTTCATA	S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1582G>A	11.37:g.120811161G>A	ENSP00000435648:p.Val528Ile	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	37	CCDS8433.1	61	0.027930402930402932	59	0.11991869918699187	2	0.0055248618784530384	0	0.0	0	0.0	G	21.3	4.125095	0.77436	0.089877	8.14E-4	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.11385	2.78;2.78	5.47	5.47	0.80525	Ionotropic glutamate receptor (1);	0.121890	0.56097	D	0.000035	T	0.00356	0.0011	L	0.39147	1.195	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.68353	0.957;0.871	T	0.00812	-1.1556	10	0.34782	T	0.22	.	18.9072	0.92467	0.0:0.0:1.0:0.0	rs35599906	528;528	A6H8K8;Q16099	.;GRIK4_HUMAN	I	528	ENSP00000435648:V528I;ENSP00000404063:V528I	ENSP00000404063:V528I	V	+	1	0	GRIK4	120316371	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.384000	0.97219	2.579000	0.87056	0.591000	0.81541	GTT	G|0.964;A|0.036	0.036	strong		0.388	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619	
MUC4	4585	hgsc.bcm.edu	37	3	195511889	195511889	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511889C>T	ENST00000463781.3	-	2	7021	c.6562G>A	c.(6562-6564)Ggt>Agt	p.G2188S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G2188S	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)		GTGGCGTGACCTGTGGATGCT	0.597																																					p.G2188S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	0			c.G6562A						scavenged	.						10.0	14.0	13.0					3																	195511889		621	1531	2152	SO:0001583	missense	4585	exon2			CGTGACCTGTGGA	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.6562G>A	3.37:g.195511889C>T	ENSP00000417498:p.Gly2188Ser	Somatic	489	2	0.00408998		WXS	Illumina HiSeq	Phase_I	411	11	0.026764	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	5.644	0.303428	0.10678	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28255	1.62;1.62	.	.	.	.	.	.	.	.	T	0.24774	0.0601	N	0.19112	0.55	0.09310	N	1	P	0.51449	0.945	P	0.53062	0.717	T	0.08911	-1.0699	7	.	.	.	.	3.4513	0.07499	0.4478:0.552:1.0E-4:1.0E-4	.	2188	E7ESK3	.	S	2188	ENSP00000417498:G2188S;ENSP00000420243:G2188S	.	G	-	1	0	MUC4	196996284	0.005000	0.15991	0.002000	0.10522	0.111000	0.19643	1.352000	0.34033	0.488000	0.27723	0.064000	0.15345	GGT	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TNR	7143	hgsc.bcm.edu	37	1	175335162	175335162	+	Silent	SNP	T	T	C	rs7516376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:175335162T>C	ENST00000367674.2	-	11	2874	c.2166A>G	c.(2164-2166)ccA>ccG	p.P722P	TNR_ENST00000263525.2_Silent_p.P722P			Q92752	TENR_HUMAN	tenascin R	722	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TCCCAGAGGATGGGGTAAAGG	0.552													T|||	277	0.0553115	0.1989	0.0202	5008	,	,		21185	0.0		0.0	False		,,,				2504	0.0				p.P722P		Atlas-SNP	.											TNR,NS,carcinoma,-1,2	TNR	399	2	0			c.A2166G						PASS	.	T		774,3632	314.1+/-293.5	71,632,1500	169.0	158.0	162.0		2166	-11.8	0.2	1	dbSNP_116	162	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	TNR	NM_003285.2		71,637,5795	CC,CT,TT		0.0581,17.567,5.9895		722/1359	175335162	779,12227	2203	4300	6503	SO:0001819	synonymous_variant	7143	exon11			AGAGGATGGGGTA	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.2166A>G	1.37:g.175335162T>C		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	241	114	0.473029	NM_003285	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																			T|0.929;C|0.071	0.071	strong		0.552	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
SRGAP2	23380	hgsc.bcm.edu	37	1	206566947	206566947	+	Missense_Mutation	SNP	C	C	T	rs375845037		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206566947C>T	ENST00000414007.1	+	3	328	c.328C>T	c.(328-330)Cgg>Tgg	p.R110W	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	250	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)					CATCAAAGCCCGGAATGAGTA	0.428																																					p.Q97X		Atlas-SNP	.											.	.	.	.	0			c.C289T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	13,3921		0,13,1954	127.0	110.0	115.0		491,491,491	5.7	1.0	1		115	0,8334		0,0,4167	yes	missense,missense,missense	SRGAP2	NM_001042758.1,NM_001170637.1,NM_015326.2	101,101,101	0,13,6121	TT,TC,CC		0.0,0.3305,0.106	probably-damaging,probably-damaging,probably-damaging	250/837,250/1071,250/1072	206566947	13,12255	1967	4167	6134	SO:0001583	missense	100996712	exon3			AAAGCCCGGAATG	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.328C>T	1.37:g.206566947C>T	ENSP00000390898:p.Arg110Trp	Somatic	553	0	0		WXS	Illumina HiSeq	Phase_I	647	99	0.153014	NM_001271887		Nonsense_Mutation	SNP	ENST00000414007.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.139626|4.139626	0.77775|0.77775	0.003305|0.003305	0.0|0.0	ENSG00000163486|ENSG00000163486	ENST00000295713|ENST00000414359;ENST00000414007	.|T	.|0.16457	.|2.34	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.42899|0.42899	0.1223|0.1223	.|.	.|.	.|.	.|0.30974	.|N	.|0.7227589999999999	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.998;0.999;0.999	T|T	0.48927|0.48927	-0.8991|-0.8991	3|8	.|0.87932	.|D	.|0	.|.	14.6067|14.6067	0.68483|0.68483	0.1807:0.8193:0.0:0.0|0.1807:0.8193:0.0:0.0	.|.	.|97;250;250	.|B4DDU0;O75044;B7Z3G4	.|.;FNBP2_HUMAN;.	L|W	163|164;110	.|ENSP00000390898:R110W	.|ENSP00000390898:R110W	P|R	+|+	2|1	0|2	SRGAP2|SRGAP2	204633570|204633570	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.909000|2.909000	0.48758|0.48758	2.705000|2.705000	0.92388|0.92388	0.555000|0.555000	0.69702|0.69702	CCG|CGG	.	.	none		0.428	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326	
TACR2	6865	hgsc.bcm.edu	37	10	71167027	71167027	+	Missense_Mutation	SNP	T	T	C	rs142415572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:71167027T>C	ENST00000373306.4	-	4	1294	c.751A>G	c.(751-753)Acc>Gcc	p.T251A	TACR2_ENST00000373307.1_Missense_Mutation_p.T39A	NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	251					excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						AGCACCATGGTCTTCACAAAC	0.587													T|||	81	0.0161741	0.0567	0.0086	5008	,	,		17645	0.0		0.0	False		,,,				2504	0.0				p.T251A		Atlas-SNP	.											.	TACR2	37	.	0			c.A751G						PASS	.	T	ALA/THR	263,4143	150.7+/-184.7	8,247,1948	152.0	129.0	137.0		751	3.6	1.0	10	dbSNP_134	137	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TACR2	NM_001057.2	58	8,248,6247	CC,CT,TT		0.0116,5.9691,2.0298	benign	251/399	71167027	264,12742	2203	4300	6503	SO:0001583	missense	6865	exon4			CCATGGTCTTCAC		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"""GPCR / Class A : Tachykinin receptors"""	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.751A>G	10.37:g.71167027T>C	ENSP00000362403:p.Thr251Ala	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	170	87	0.511765	NM_001057	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Missense_Mutation	SNP	ENST00000373306.4	37	CCDS7293.1	25	0.011446886446886446	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	0	0.0	T	15.05	2.719253	0.48728	0.059691	1.16E-4	ENSG00000075073	ENST00000373307;ENST00000373306	T;T	0.38722	1.12;1.12	5.11	3.64	0.41730	GPCR, rhodopsin-like superfamily (1);	0.240149	0.42964	N	0.000624	T	0.06005	0.0156	M	0.65677	2.01	0.29494	N	0.855447	B	0.10296	0.003	B	0.15484	0.013	T	0.12967	-1.0527	10	0.56958	D	0.05	.	9.0838	0.36567	0.0:0.1185:0.0:0.8815	.	251	P21452	NK2R_HUMAN	A	39;251	ENSP00000362404:T39A;ENSP00000362403:T251A	ENSP00000362403:T251A	T	-	1	0	TACR2	70837033	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.251000	0.72441	0.541000	0.28827	0.454000	0.30748	ACC	T|0.979;C|0.021	0.021	strong		0.587	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1		
INADL	10207	hgsc.bcm.edu	37	1	62288730	62288730	+	Missense_Mutation	SNP	G	G	C	rs1286812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62288730G>C	ENST00000371158.2	+	15	1911	c.1797G>C	c.(1795-1797)caG>caC	p.Q599H	INADL_ENST00000316485.6_Missense_Mutation_p.Q599H	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	599	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.		Q -> H (in dbSNP:rs1286812).		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						GTCTCCTACAGCCAGAAGATG	0.428													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		18625	0.0		0.0	False		,,,				2504	0.0				p.Q599H		Atlas-SNP	.											.	INADL	179	.	0			c.G1797C						PASS	.	G	HIS/GLN	95,4311	76.8+/-115.0	0,95,2108	154.0	140.0	145.0		1797	4.0	1.0	1	dbSNP_87	145	0,8600		0,0,4300	yes	missense	INADL	NM_176877.2	24	0,95,6408	CC,CG,GG		0.0,2.1562,0.7304	possibly-damaging	599/1802	62288730	95,12911	2203	4300	6503	SO:0001583	missense	10207	exon15			CCTACAGCCAGAA	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.1797G>C	1.37:g.62288730G>C	ENSP00000360200:p.Gln599His	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	219	111	0.506849	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	G	12.64	1.998539	0.35226	0.021562	0.0	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.27720	1.65;1.65	4.99	4.02	0.46733	PDZ/DHR/GLGF (4);	0.205916	0.32868	N	0.005548	T	0.16041	0.0386	L	0.35644	1.08	0.80722	D	1	D;D;P	0.65815	0.995;0.995;0.808	P;D;B	0.66716	0.894;0.946;0.442	T	0.01496	-1.1340	10	0.39692	T	0.17	.	6.7972	0.23732	0.1259:0.1743:0.6997:0.0	rs1286812;rs1286812	599;599;599	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	H	599	ENSP00000360200:Q599H;ENSP00000326199:Q599H	ENSP00000255202:Q599H	Q	+	3	2	INADL	62061318	0.999000	0.42202	1.000000	0.80357	0.416000	0.31233	0.561000	0.23515	2.322000	0.78497	0.561000	0.74099	CAG	G|0.992;C|0.008	0.008	strong		0.428	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
PRSS21	10942	hgsc.bcm.edu	37	16	2868783	2868783	+	Silent	SNP	A	A	G	rs2074906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2868783A>G	ENST00000005995.3	+	4	405	c.363A>G	c.(361-363)gtA>gtG	p.V121V	PRSS21_ENST00000455114.1_Silent_p.V119V|PRSS21_ENST00000450020.3_Silent_p.V121V			Q9Y6M0	TEST_HUMAN	protease, serine, 21 (testisin)	121	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	15						GTTACTTCGTATCGAATATCT	0.532													N|||	307	0.0613019	0.1452	0.0663	5008	,	,		20699	0.0585		0.002	False		,,,				2504	0.0082				p.V121V		Atlas-SNP	.											PRSS21,NS,carcinoma,+1,1	PRSS21	32	1	0			c.A363G						PASS	.	G	,,	522,3874	777.5+/-414.2	22,478,1698	185.0	148.0	160.0		363,357,363	0.0	0.0	16	dbSNP_96	160	37,8563	817.8+/-406.9	0,37,4263	no	coding-synonymous,coding-synonymous,coding-synonymous	PRSS21	NM_006799.2,NM_144956.1,NM_144957.1	,,	22,515,5961	GG,GA,AA		0.4302,11.8744,4.3013	,,	121/315,119/313,121/301	2868783	559,12437	2198	4300	6498	SO:0001819	synonymous_variant	10942	exon4			CTTCGTATCGAAT	AF058300	CCDS10478.1, CCDS45388.1	16p13.3	2010-05-07			ENSG00000007038	ENSG00000007038		"""Serine peptidases / Serine peptidases"""	9485	protein-coding gene	gene with protein product		608159				10397266, 9826525	Standard	NM_006799		Approved	ESP-1, TEST1, TESTISIN	uc002crt.4	Q9Y6M0	OTTHUMG00000128931	ENST00000005995.3:c.363A>G	16.37:g.2868783A>G		Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	186	185	0.994624	NM_144957	Q9NS34|Q9P2V6	Silent	SNP	ENST00000005995.3	37	CCDS10478.1																																																																																			A|0.944;G|0.056	0.056	strong		0.532	PRSS21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250910.1	NM_006799	
KRBA2	124751	hgsc.bcm.edu	37	17	8273246	8273246	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8273246C>T	ENST00000331336.2	-	2	690	c.685G>A	c.(685-687)Gtc>Atc	p.V229I	RP11-849F2.5_ENST00000583963.1_RNA|RP11-849F2.5_ENST00000580537.1_RNA|RP11-849F2.7_ENST00000582471.1_3'UTR|KRBA2_ENST00000396267.1_Missense_Mutation_p.V147I	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	229					DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)			endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						AGATATAAGACAATAACTTCT	0.453																																					p.V229I		Atlas-SNP	.											.	KRBA2	34	.	0			c.G685A						PASS	.						126.0	121.0	123.0					17																	8273246		2203	4300	6503	SO:0001583	missense	124751	exon2			ATAAGACAATAAC	BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"""-"""	26989	protein-coding gene	gene with protein product			"""KRAB A domain containing 2"""			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.685G>A	17.37:g.8273246C>T	ENSP00000328017:p.Val229Ile	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	225	61	0.271111	NM_213597	Q8IYY0	Missense_Mutation	SNP	ENST00000331336.2	37	CCDS11141.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.926066	0.34002	.	.	ENSG00000184619	ENST00000396267;ENST00000331336	T;T	0.23348	1.93;1.91	2.64	2.64	0.31445	.	.	.	.	.	T	0.13329	0.0323	N	0.08118	0	0.22982	N	0.998471	B	0.23490	0.086	B	0.22601	0.04	T	0.15350	-1.0440	9	0.48119	T	0.1	.	8.9489	0.35776	0.0:1.0:0.0:0.0	.	229	Q6ZNG9	KRBA2_HUMAN	I	147;229	ENSP00000379565:V147I;ENSP00000328017:V229I	ENSP00000328017:V229I	V	-	1	0	KRBA2	8213971	0.997000	0.39634	1.000000	0.80357	0.992000	0.81027	1.587000	0.36622	1.804000	0.52760	0.650000	0.86243	GTC	.	.	none		0.453	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253819	39253819	+	Missense_Mutation	SNP	G	G	C	rs201814486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39253819G>C	ENST00000333822.4	-	1	574	c.518C>G	c.(517-519)aCc>aGc	p.T173S		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	173					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						GCGGGGGCAGGTGGAGATGAC	0.632													G|||	264	0.0527157	0.1778	0.0231	5008	,	,		16542	0.0099		0.001	False		,,,				2504	0.002				p.T173S		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C518G						PASS	.						53.0	64.0	61.0					17																	39253819		691	1591	2282	SO:0001583	missense	728224	exon1			GGGCAGGTGGAGA	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.518C>G	17.37:g.39253819G>C	ENSP00000328444:p.Thr173Ser	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	167	46	0.275449	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	5.072	0.198925	0.09652	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.00590	6.36	3.73	2.73	0.32206	.	0.227898	0.21667	U	0.070931	T	0.00815	0.0027	L	0.35854	1.095	0.26449	N	0.975649	D	0.63046	0.992	P	0.57244	0.816	T	0.49597	-0.8923	10	0.07813	T	0.8	.	6.5126	0.22230	0.1366:0.0:0.8634:0.0	.	173	Q9BYQ9	KRA48_HUMAN	S	173;143	ENSP00000328444:T173S	ENSP00000414561:T143S	T	-	2	0	KRTAP4-8	36507345	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	2.706000	0.47135	1.794000	0.52575	0.449000	0.29647	ACC	.	.	weak		0.632	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
PABPC1	26986	hgsc.bcm.edu	37	8	101721899	101721899	+	Nonsense_Mutation	SNP	C	C	A	rs142985461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721899C>A	ENST00000318607.5	-	8	2161	c.1033G>T	c.(1033-1035)Gaa>Taa	p.E345*	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519004.1_Nonsense_Mutation_p.E300*|PABPC1_ENST00000522387.1_Nonsense_Mutation_p.E313*|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	345	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)			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)			TTAGTGGCTTCTTCTGGGGAG	0.423																																					p.E345X		Atlas-SNP	.											PABPC1,colon,carcinoma,+2,1	PABPC1	76	1	0			c.G1033T						scavenged	.						74.0	69.0	71.0					8																	101721899		2203	4298	6501	SO:0001587	stop_gained	26986	exon8			TGGCTTCTTCTGG	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.1033G>T	8.37:g.101721899C>A	ENSP00000313007:p.Glu345*	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	246	59	0.239837	NM_002568	Q15097|Q93004	Nonsense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	41|41|41	8.575894|8.575894|8.575894	0.98870|0.98870|0.98870	.|.|.	.|.|.	ENSG00000070756|ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387|ENST00000519100|ENST00000519596	.|.|.	.|.|.	.|.|.	4.92|4.92|4.92	4.92|4.92|4.92	0.64577|0.64577|0.64577	.|.|.	0.000000|.|.	0.64402|.|.	D|.|.	0.000008|.|.	.|T|T	.|0.74412|0.74412	.|0.3713|0.3713	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.73987|0.73987	.|-0.3809|-0.3809	.|3|3	0.87932|.|.	D|.|.	0|.|.	.|.|.	18.4911|18.4911|18.4911	0.90848|0.90848|0.90848	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|N|I	345;345;300;313|213|177	.|.|.	ENSP00000313007:E345X|.|.	E|K|R	-|-|-	1|3|2	0|2|0	PABPC1|PABPC1|PABPC1	101791075|101791075|101791075	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	7.748000|7.748000|7.748000	0.85085|0.85085|0.85085	2.426000|2.426000|2.426000	0.82243|0.82243|0.82243	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAA|AAG|AGA	C|0.842;A|0.159	0.159	strong		0.423	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
RBM11	54033	hgsc.bcm.edu	37	21	15591968	15591968	+	Missense_Mutation	SNP	G	G	A	rs141942958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:15591968G>A	ENST00000400577.3	+	2	190	c.181G>A	c.(181-183)Gaa>Aaa	p.E61K	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	61	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(U) RNA binding (GO:0008266)|protein homodimerization activity (GO:0042803)			endometrium(3)|kidney(3)|lung(7)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		TAAACACCCAGAATCGGTGTC	0.398													.|||	17	0.00339457	0.0106	0.0043	5008	,	,		16689	0.0		0.0	False		,,,				2504	0.0				p.E61K		Atlas-SNP	.											RBM11,NS,neuroblastoma,-1,1	RBM11	41	1	0			c.G181A						PASS	.	G	LYS/GLU	44,3092		0,44,1524	86.0	80.0	82.0		181	5.3	1.0	21	dbSNP_134	82	0,7162		0,0,3581	yes	missense	RBM11	NM_144770.3	56	0,44,5105	AA,AG,GG		0.0,1.4031,0.4273	possibly-damaging	61/282	15591968	44,10254	1568	3581	5149	SO:0001583	missense	54033	exon2			CACCCAGAATCGG	AF130358	CCDS46635.1	21q11	2013-02-12			ENSG00000185272	ENSG00000185272		"""RNA binding motif (RRM) containing"""	9897	protein-coding gene	gene with protein product						12036298	Standard	NM_144770		Approved		uc002yjo.4	P57052	OTTHUMG00000074263	ENST00000400577.3:c.181G>A	21.37:g.15591968G>A	ENSP00000383421:p.Glu61Lys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	146	88	0.60274	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	G	29.4	5.004735	0.93287	0.014031	0.0	ENSG00000185272	ENST00000400577	T	0.78364	-1.17	5.29	5.29	0.74685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.64402	D	0.000009	T	0.72220	0.3433	M	0.66378	2.025	0.58432	D	0.999994	P	0.41420	0.749	P	0.48189	0.57	T	0.78703	-0.2101	10	0.48119	T	0.1	-20.9416	18.9174	0.92512	0.0:0.0:1.0:0.0	.	61	P57052	RBM11_HUMAN	K	61	ENSP00000383421:E61K	ENSP00000383421:E61K	E	+	1	0	RBM11	14513839	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.772000	0.85439	2.661000	0.90470	0.655000	0.94253	GAA	G|0.995;A|0.005	0.005	strong		0.398	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770	
RPS26	6231	hgsc.bcm.edu	37	12	56437917	56437917	+	Silent	SNP	T	T	A	rs56696262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56437917T>A	ENST00000356464.5	+	4	641	c.327T>A	c.(325-327)cgT>cgA	p.R109R	RPS26_ENST00000552361.1_Silent_p.R109R|RP11-603J24.4_ENST00000551846.1_RNA			P62854	RS26_HUMAN	ribosomal protein S26	109				R -> A (in Ref. 1; CAA49345). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of RNA splicing (GO:0033119)|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 small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|small ribosomal subunit (GO:0015935)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	7			OV - Ovarian serous cystadenocarcinoma(18;0.123)			CTGCCCCACGTCCCCCACCAA	0.428													T|||	459	0.0916534	0.3328	0.0259	5008	,	,		17245	0.0		0.001	False		,,,				2504	0.0				p.R109R		Atlas-SNP	.											.	RPS26	9	.	0			c.T327A						PASS	.	T		1110,3296	399.0+/-331.0	134,842,1227	194.0	199.0	197.0		327	-3.5	1.0	12	dbSNP_129	197	12,8588	9.8+/-36.6	0,12,4288	no	coding-synonymous	RPS26	NM_001029.3		134,854,5515	AA,AT,TT		0.1395,25.1929,8.6268		109/116	56437917	1122,11884	2203	4300	6503	SO:0001819	synonymous_variant	6231	exon4			CCCACGTCCCCCA	AB007160	CCDS31832.1	12q13	2011-04-06				ENSG00000197728		"""S ribosomal proteins"""	10414	protein-coding gene	gene with protein product	"""40S ribosomal protein S26"""	603701				9582194, 8670309	Standard	NM_001029		Approved	S26	uc001sjf.3	P62854	OTTHUMG00000170139	ENST00000356464.5:c.327T>A	12.37:g.56437917T>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_001029	P02383|P70394|Q06722|Q3MHD8|Q6IRY4	Silent	SNP	ENST00000356464.5	37	CCDS31832.1																																																																																			T|0.925;A|0.075	0.075	strong		0.428	RPS26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407616.1	NM_001029	
OAS3	4940	hgsc.bcm.edu	37	12	113403684	113403684	+	Silent	SNP	C	C	T	rs2240188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113403684C>T	ENST00000228928.7	+	12	2718	c.2539C>T	c.(2539-2541)Ctg>Ttg	p.L847L	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	847	OAS domain 3.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						CCGAGCCCAGCTGGAGGCATG	0.582													C|||	1423	0.284145	0.4221	0.3775	5008	,	,		21311	0.1558		0.2604	False		,,,				2504	0.1881				p.L847L		Atlas-SNP	.											.	OAS3	63	.	0			c.C2539T						PASS	.	C		1461,2543		252,957,793	34.0	38.0	37.0		2539	2.5	1.0	12	dbSNP_98	37	2231,6139		305,1621,2259	no	coding-synonymous	OAS3	NM_006187.2		557,2578,3052	TT,TC,CC		26.6547,36.4885,29.8368		847/1088	113403684	3692,8682	2002	4185	6187	SO:0001819	synonymous_variant	4940	exon12			GCCCAGCTGGAGG	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.2539C>T	12.37:g.113403684C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_006187	Q2HJ14|Q9H3P5	Silent	SNP	ENST00000228928.7	37	CCDS44981.1																																																																																			C|0.728;T|0.272	0.272	strong		0.582	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
SMG8	55181	hgsc.bcm.edu	37	17	57288251	57288251	+	Missense_Mutation	SNP	C	C	T	rs8068240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:57288251C>T	ENST00000543872.2	+	2	1103	c.839C>T	c.(838-840)cCt>cTt	p.P280L	SMG8_ENST00000580498.1_Intron|SMG8_ENST00000300917.5_Missense_Mutation_p.P280L|SMG8_ENST00000578922.1_Missense_Mutation_p.P280L|CTD-2510F5.6_ENST00000577660.1_Intron			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	280			P -> L (in dbSNP:rs8068240).		gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						GTAGAACCTCCTCGGAACCAA	0.517													C|||	134	0.0267572	0.093	0.0159	5008	,	,		20461	0.0		0.0	False		,,,				2504	0.0				p.P280L		Atlas-SNP	.											.	SMG8	79	.	0			c.C839T						PASS	.	C	LEU/PRO	414,3992	199.4+/-223.0	25,364,1814	69.0	77.0	74.0		839	5.9	1.0	17	dbSNP_116	74	9,8591	7.1+/-27.0	0,9,4291	yes	missense	SMG8	NM_018149.6	98	25,373,6105	TT,TC,CC		0.1047,9.3963,3.2523	benign	280/992	57288251	423,12583	2203	4300	6503	SO:0001583	missense	55181	exon1			AACCTCCTCGGAA	AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"""chromosome 17 open reading frame 71"", ""smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.839C>T	17.37:g.57288251C>T	ENSP00000438748:p.Pro280Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	37	CCDS11615.1	45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	C	11.98	1.801825	0.31869	0.093963	0.001047	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.44881	0.91;0.91	5.88	5.88	0.94601	.	0.385695	0.31210	N	0.008044	T	0.01029	0.0034	N	0.14661	0.345	0.41054	D	0.985328	B	0.09022	0.002	B	0.12156	0.007	T	0.01235	-1.1410	10	0.66056	D	0.02	-9.762	12.6648	0.56835	0.0:0.9223:0.0:0.0777	rs8068240;rs52805280;rs56931279;rs8068240	280	Q8ND04	SMG8_HUMAN	L	280	ENSP00000300917:P280L;ENSP00000438748:P280L	ENSP00000300917:P280L	P	+	2	0	SMG8	54643033	0.003000	0.15002	1.000000	0.80357	0.939000	0.58152	0.955000	0.29188	2.769000	0.95229	0.655000	0.94253	CCT	C|0.967;T|0.033	0.033	strong		0.517	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149	
SRL	6345	hgsc.bcm.edu	37	16	4245656	4245656	+	Silent	SNP	G	G	A	rs76988584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4245656G>A	ENST00000399609.3	-	5	520	c.508C>T	c.(508-510)Cta>Tta	p.L170L	SRL_ENST00000537996.1_Silent_p.L128L	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	629	Acidic domain, probably binds calcium. {ECO:0000250}.					sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						AGCTTCTCTAGGAAATTCTGG	0.522													G|||	95	0.0189696	0.0703	0.0029	5008	,	,		18443	0.0		0.0	False		,,,				2504	0.0				p.L170L		Atlas-SNP	.											.	SRL	56	.	0			c.C508T						PASS	.	G		177,3613		5,167,1723	102.0	102.0	102.0		508	4.1	1.0	16	dbSNP_131	102	1,8253		0,1,4126	no	coding-synonymous	SRL	NM_001098814.1		5,168,5849	AA,AG,GG		0.0121,4.6702,1.4779		170/474	4245656	178,11866	1895	4127	6022	SO:0001819	synonymous_variant	6345	exon5			TCTCTAGGAAATT	AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739			11295	protein-coding gene	gene with protein product		604992				2762314	Standard	NM_001098814		Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.508C>T	16.37:g.4245656G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	248	118	0.475806	NM_001098814		Silent	SNP	ENST00000399609.3	37	CCDS42113.1																																																																																			G|0.992;A|0.008	0.008	strong		0.522	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152	
DDX20	11218	hgsc.bcm.edu	37	1	112309331	112309331	+	Missense_Mutation	SNP	T	T	C	rs85276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:112309331T>C	ENST00000369702.4	+	11	2905	c.2285T>C	c.(2284-2286)aTa>aCa	p.I762T	DDX20_ENST00000475700.1_Missense_Mutation_p.I370T	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	762			I -> T (in dbSNP:rs85276).		ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CATAGGGAAATACGTCTGAGT	0.463													C|||	831	0.165935	0.4274	0.0965	5008	,	,		20780	0.003		0.1252	False		,,,				2504	0.0716				p.I762T		Atlas-SNP	.											.	DDX20	50	.	0			c.T2285C						PASS	.	C	THR/ILE	1628,2778	660.4+/-400.7	296,1036,871	104.0	103.0	103.0		2285	4.8	0.0	1	dbSNP_79	103	1099,7501	768.2+/-407.6	69,961,3270	yes	missense	DDX20	NM_007204.4	89	365,1997,4141	CC,CT,TT		12.7791,36.9496,20.9672	benign	762/825	112309331	2727,10279	2203	4300	6503	SO:0001583	missense	11218	exon11			GGGAAATACGTCT	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2285T>C	1.37:g.112309331T>C	ENSP00000358716:p.Ile762Thr	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	338	0.15476190476190477	213	0.4329268292682927	30	0.08287292817679558	0	0.0	95	0.12532981530343007	C	0.007	-1.996505	0.00435	0.369496	0.127791	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.30714	1.52;2.08	5.82	4.85	0.62838	.	1.043140	0.07424	N	0.894524	T	0.02304	0.0071	N	0.00237	-1.79	0.51482	P	7.100000000004325E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41052	-0.9530	8	.	.	.	-0.4366	8.6229	0.33872	0.1785:0.7366:0.0:0.0849	rs85276;rs697388;rs742793;rs52833651;rs58747656;rs85276	370;762	E9PJ60;Q9UHI6	.;DDX20_HUMAN	T	762;370	ENSP00000358716:I762T;ENSP00000435660:I370T	.	I	+	2	0	DDX20	112110854	0.002000	0.14202	0.002000	0.10522	0.074000	0.17049	0.737000	0.26144	1.489000	0.48450	-0.119000	0.15052	ATA	A|0.004;C|0.196	0.196	strong		0.463	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253797	39253797	+	Silent	SNP	G	G	A	rs142150852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39253797G>A	ENST00000333822.4	-	1	596	c.540C>T	c.(538-540)tgC>tgT	p.C180C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	180					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						AAGAGGAGGCGCAGCACACGG	0.602													g|||	249	0.0497204	0.1778	0.0159	5008	,	,		17550	0.002		0.001	False		,,,				2504	0.0				p.C180C		Atlas-SNP	.											KRTAP4-8,colon,carcinoma,-2,1	KRTAP4-8	57	1	0			c.C540T						PASS	.						69.0	80.0	76.0					17																	39253797		692	1591	2283	SO:0001819	synonymous_variant	728224	exon1			GGAGGCGCAGCAC	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.540C>T	17.37:g.39253797G>A		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	227	81	0.356828	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
C5AR2	27202	hgsc.bcm.edu	37	19	47844653	47844653	+	Silent	SNP	G	G	A	rs36046934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47844653G>A	ENST00000595464.1	+	2	815	c.597G>A	c.(595-597)gcG>gcA	p.A199A	C5AR2_ENST00000257267.2_Silent_p.A199A|C5AR2_ENST00000600626.1_Silent_p.A199A	NM_001271749.1	NP_001258678.1	Q9P296	C5AR2_HUMAN	complement component 5a receptor 2	199					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)										CCGAGAATGCGGTGACTGCCA	0.692													A|||	86	0.0171725	0.0197	0.0202	5008	,	,		12978	0.0		0.0258	False		,,,				2504	0.0204				p.A199A		Atlas-SNP	.											GPR77,NS,carcinoma,+1,1	.	.	1	0			c.G597A						PASS	.	A		102,4304	816.1+/-416.2	1,100,2102	62.0	69.0	67.0		597	-4.5	0.0	19	dbSNP_126	67	153,8447	812.3+/-407.1	2,149,4149	no	coding-synonymous	GPR77	NM_018485.1		3,249,6251	AA,AG,GG		1.7791,2.315,1.9606		199/338	47844653	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	27202	exon2			GAATGCGGTGACT	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.597G>A	19.37:g.47844653G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	160	72	0.45	NM_001271750	B2RA09	Silent	SNP	ENST00000595464.1	37	CCDS12699.1																																																																																			G|0.979;A|0.021	0.021	strong		0.692	C5AR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466926.1	NM_018485	
TEAD3	7005	hgsc.bcm.edu	37	6	35452346	35452346	+	Silent	SNP	C	C	T	rs11756089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35452346C>T	ENST00000338863.7	-	3	485	c.258G>A	c.(256-258)acG>acA	p.T86T	TEAD3_ENST00000402886.3_Intron	NM_003214.3	NP_003205	Q99594	TEAD3_HUMAN	TEA domain family member 3	86					female pregnancy (GO:0007565)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	10						CCTGTTTTCTCGTCCGAGTCT	0.557													C|||	642	0.128195	0.3048	0.1369	5008	,	,		16018	0.0565		0.0537	False		,,,				2504	0.0337				p.T86T		Atlas-SNP	.											.	TEAD3	52	.	0			c.G258A						PASS	.	C		1079,3087		133,813,1137	111.0	122.0	118.0		258	-2.5	1.0	6	dbSNP_120	118	578,7808		32,514,3647	no	coding-synonymous	TEAD3	NM_003214.3		165,1327,4784	TT,TC,CC		6.8924,25.9001,13.2011		86/436	35452346	1657,10895	2083	4193	6276	SO:0001819	synonymous_variant	7005	exon3			TTTTCTCGTCCGA	X94439	CCDS47414.1	6p21.2	2008-07-28			ENSG00000007866	ENSG00000007866			11716	protein-coding gene	gene with protein product		603170		TEAD5		9889009, 9148898	Standard	NM_003214		Approved	TEF-5, ETFR-1	uc003oku.4	Q99594	OTTHUMG00000014571	ENST00000338863.7:c.258G>A	6.37:g.35452346C>T		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	220	112	0.509091	NM_003214	O95910|Q5BJG7|Q8N6Y4	Silent	SNP	ENST00000338863.7	37	CCDS47414.1																																																																																			C|0.863;T|0.137	0.137	strong		0.557	TEAD3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040298.2		
DEFB110	245913	hgsc.bcm.edu	37	6	49989622	49989622	+	Silent	SNP	A	A	G	rs9473719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49989622A>G	ENST00000371148.2	-	1	72	c.27T>C	c.(25-27)atT>atC	p.I9I	DEFB110_ENST00000393660.2_Silent_p.I9I	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	9					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					AAAAGTGCAGAATAAAGAAAA	0.313													A|||	75	0.014976	0.056	0.0014	5008	,	,		16040	0.0		0.0	False		,,,				2504	0.0				p.I9I		Atlas-SNP	.											.	DEFB110	5	.	0			c.T27C						PASS	.	A	,	200,4202	113.8+/-151.8	5,190,2006	32.0	36.0	35.0		27,27	3.5	1.0	6	dbSNP_119	35	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous,coding-synonymous	DEFB110	NM_001037497.1,NM_001037728.2	,	5,191,6301	GG,GA,AA		0.0116,4.5434,1.5469	,	9/68,9/63	49989622	201,12793	2201	4296	6497	SO:0001819	synonymous_variant	245913	exon1			GTGCAGAATAAAG	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"""Defensins, beta"""	18091	protein-coding gene	gene with protein product			"""defensin, beta 110"""			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.27T>C	6.37:g.49989622A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_001037728	Q30KR0	Silent	SNP	ENST00000371148.2	37	CCDS34475.1																																																																																			A|0.986;G|0.014	0.014	strong		0.313	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728	
ATP9B	374868	hgsc.bcm.edu	37	18	77097360	77097360	+	Missense_Mutation	SNP	A	A	T	rs585033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:77097360A>T	ENST00000426216.2	+	19	2211	c.2194A>T	c.(2194-2196)Atg>Ttg	p.M732L	RP11-800A18.4_ENST00000592906.1_RNA|ATP9B_ENST00000307671.7_Missense_Mutation_p.M732L|ATP9B_ENST00000543761.1_Missense_Mutation_p.M53L	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	732			M -> L (in dbSNP:rs585033).		establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|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)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		GGAGAGGGAGATGGAACTGCT	0.652													A|||	162	0.0323482	0.003	0.0562	5008	,	,		20784	0.001		0.1024	False		,,,				2504	0.0153				p.M732L		Atlas-SNP	.											.	ATP9B	96	.	0			c.A2194T						PASS	.	A	LEU/MET	99,4307	77.8+/-116.1	2,95,2106	120.0	100.0	107.0		2194	4.2	1.0	18	dbSNP_83	107	777,7823	184.2+/-232.2	44,689,3567	yes	missense	ATP9B	NM_198531.3	15	46,784,5673	TT,TA,AA		9.0349,2.2469,6.7354	benign	732/1148	77097360	876,12130	2203	4300	6503	SO:0001583	missense	374868	exon19			AGGGAGATGGAAC	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.2194A>T	18.37:g.77097360A>T	ENSP00000398076:p.Met732Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_198531	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	37	CCDS12014.1	97	0.044413919413919416	1	0.0020325203252032522	21	0.058011049723756904	1	0.0017482517482517483	74	0.09762532981530343	A	8.343	0.829243	0.16749	0.022469	0.090349	ENSG00000166377	ENST00000426216;ENST00000307671;ENST00000543761	T;T;D	0.98835	0.15;0.15;-5.17	5.36	4.18	0.49190	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.039059	0.85682	N	0.000000	T	0.37404	0.1002	N	0.03281	-0.365	0.54753	D	0.999984	B;B;B	0.16396	0.002;0.017;0.014	B;B;B	0.23716	0.012;0.048;0.028	T	0.77667	-0.2502	10	0.02654	T	1	.	11.587	0.50925	0.8662:0.0:0.0:0.1338	rs585033;rs585033	53;732;732	F5H8J1;O43861;O43861-2	.;ATP9B_HUMAN;.	L	732;732;53	ENSP00000398076:M732L;ENSP00000304500:M732L;ENSP00000442015:M53L	ENSP00000304500:M732L	M	+	1	0	ATP9B	75198348	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.809000	0.75211	0.850000	0.35239	0.533000	0.62120	ATG	A|0.943;T|0.057	0.057	strong		0.652	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
CDON	50937	hgsc.bcm.edu	37	11	125889526	125889526	+	Missense_Mutation	SNP	C	C	T	rs3740909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	79	0	0		WXS	Illumina HiSeq	Phase_I	122	70	0.57377	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	
RFPL4A	342931	hgsc.bcm.edu	37	19	56273285	56273285	+	Missense_Mutation	SNP	A	A	G	rs200422093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56273285A>G	ENST00000434937.2	+	2	290	c.119A>G	c.(118-120)aAg>aGg	p.K40R		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	40							zinc ion binding (GO:0008270)	p.K40R(1)		haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						TCACTCCAGAAGGAGCCCGAT	0.502																																					p.K40R		Atlas-SNP	.											ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	1	Substitution - Missense(1)	stomach(1)	c.A119G						scavenged	.						3.0	2.0	2.0					19																	56273285		554	1274	1828	SO:0001583	missense	342931	exon2			TCCAGAAGGAGCC		CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638		"""RING-type (C3HC4) zinc fingers"""	16449	protein-coding gene	gene with protein product		612601	"""ret finger protein-like 4"""	RFPL4		11850190	Standard	NM_001145014		Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.119A>G	19.37:g.56273285A>G	ENSP00000392936:p.Lys40Arg	Somatic	809	4	0.00494438		WXS	Illumina HiSeq	Phase_I	914	113	0.123632	NM_001145014		Missense_Mutation	SNP	ENST00000434937.2	37	CCDS46201.1	.	.	.	.	.	.	.	.	.	.	A	8.702	0.909908	0.17833	.	.	ENSG00000223638	ENST00000434937	T	0.10005	2.92	3.31	-0.759	0.11045	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);RDM domain, Ret finger protein-like (1);	.	.	.	.	T	0.12305	0.0299	M	0.72118	2.19	0.09310	N	1	B	0.32467	0.372	B	0.39531	0.302	T	0.35748	-0.9776	9	0.32370	T	0.25	-37.9873	0.4858	0.00555	0.4389:0.2097:0.1467:0.2047	.	40	A6NLU0	RFPLA_HUMAN	R	40	ENSP00000392936:K40R	ENSP00000392936:K40R	K	+	2	0	RFPL4A	60965097	0.000000	0.05858	0.000000	0.03702	0.144000	0.21451	-0.924000	0.03996	-0.357000	0.08175	0.383000	0.25322	AAG	.	.	weak		0.502	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384184.1	XM_292796	
JAG2	3714	hgsc.bcm.edu	37	14	105609161	105609161	+	Silent	SNP	G	G	A	rs61750260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105609161G>A	ENST00000331782.3	-	26	3991	c.3588C>T	c.(3586-3588)ttC>ttT	p.F1196F	JAG2_ENST00000347004.2_Silent_p.F1158F	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	1196					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)		TGTGTGAGAGGAACTTCTCCG	0.692													G|||	210	0.0419329	0.1498	0.0144	5008	,	,		10476	0.0		0.002	False		,,,				2504	0.0				p.F1196F		Atlas-SNP	.											.	JAG2	69	.	0			c.C3588T						PASS	.	G	,	476,3928	189.9+/-215.9	34,408,1760	28.0	27.0	27.0		3588,3474	4.0	1.0	14	dbSNP_129	27	8,8590	3.7+/-12.6	0,8,4291	no	coding-synonymous,coding-synonymous	JAG2	NM_002226.3,NM_145159.1	,	34,416,6051	AA,AG,GG		0.093,10.8084,3.7225	,	1196/1239,1158/1201	105609161	484,12518	2202	4299	6501	SO:0001819	synonymous_variant	3714	exon26			TGAGAGGAACTTC	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.3588C>T	14.37:g.105609161G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	CCDS9998.1																																																																																			G|0.961;A|0.039	0.039	strong		0.692	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
SAMD11	148398	hgsc.bcm.edu	37	1	871215	871215	+	Silent	SNP	C	C	G	rs28419423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:871215C>G	ENST00000342066.3	+	5	452	c.369C>G	c.(367-369)ccC>ccG	p.P123P		NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	123					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		TCGTTATGCCCGAGCATCAGA	0.672													t|||	268	0.0535144	0.0197	0.0937	5008	,	,		15217	0.1438		0.004	False		,,,				2504	0.0286				p.P123P		Atlas-SNP	.											.	SAMD11	34	.	0			c.C369G						PASS	.	T		115,4291	85.8+/-124.5	4,107,2092	84.0	79.0	81.0		369	-6.4	0.9	1	dbSNP_125	81	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	SAMD11	NM_152486.2		4,127,6372	GG,GC,CC		0.2326,2.6101,1.038		123/682	871215	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	148398	exon5			TATGCCCGAGCAT	BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"""Sterile alpha motif (SAM) domain containing"""	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.369C>G	1.37:g.871215C>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	189	108	0.571429	NM_152486	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	Silent	SNP	ENST00000342066.3	37	CCDS2.2	138	0.06318681318681318	14	0.028455284552845527	28	0.07734806629834254	94	0.16433566433566432	2	0.002638522427440633	c	3.143	-0.175812	0.06421	0.026101	0.002326	ENSG00000187634	ENST00000341065	.	.	.	3.9	-6.39	0.01951	.	0.000000	0.64402	D	0.000003	T	0.00144	0.0004	.	.	.	0.09310	P	0.9999999999932871	.	.	.	.	.	.	T	0.08330	-1.0727	5	0.87932	D	0	-20.2514	3.3004	0.06980	0.1265:0.1727:0.1253:0.5756	rs28419423	.	.	.	R	47	.	ENSP00000349216:P47R	P	+	2	0	SAMD11	861078	0.023000	0.18921	0.926000	0.36857	0.856000	0.48823	-1.339000	0.02652	-1.310000	0.02312	-2.077000	0.00380	CCG	C|0.975;G|0.025	0.025	strong		0.672	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276866.2	NM_152486	
C1orf174	339448	hgsc.bcm.edu	37	1	3807388	3807388	+	Silent	SNP	G	G	A	rs4131373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3807388G>A	ENST00000361605.3	-	3	461	c.363C>T	c.(361-363)ctC>ctT	p.L121L	C1orf174_ENST00000486765.1_5'UTR	NM_207356.2	NP_997239.2	Q8IYL3	CA174_HUMAN	chromosome 1 open reading frame 174	121						nucleus (GO:0005634)				endometrium(1)|large_intestine(5)|lung(4)|prostate(1)	11	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)		TGCAGCCACCGAGAGGAAGAC	0.562													G|||	732	0.146166	0.2458	0.1239	5008	,	,		19489	0.0129		0.1829	False		,,,				2504	0.1268				p.L121L		Atlas-SNP	.											.	C1orf174	20	.	0			c.C363T						PASS	.	G		1059,3347	387.5+/-326.5	123,813,1267	60.0	56.0	57.0		363	-8.1	0.0	1	dbSNP_108	57	1527,7073	287.0+/-298.0	140,1247,2913	no	coding-synonymous	C1orf174	NM_207356.2		263,2060,4180	AA,AG,GG		17.7558,24.0354,19.8831		121/244	3807388	2586,10420	2203	4300	6503	SO:0001819	synonymous_variant	339448	exon3			GCCACCGAGAGGA	BC035643	CCDS53.1	1p36.32	2012-07-25			ENSG00000198912	ENSG00000198912			27915	protein-coding gene	gene with protein product						12477932	Standard	NM_207356		Approved	RP13-531C17.2	uc001alf.3	Q8IYL3	OTTHUMG00000003739	ENST00000361605.3:c.363C>T	1.37:g.3807388G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	123	69	0.560976	NM_207356	A8K0C8|A8MUG9|Q5SR20|Q6NX36	Silent	SNP	ENST00000361605.3	37	CCDS53.1																																																																																			G|0.835;A|0.165	0.165	strong		0.562	C1orf174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010539.1	NM_207356	
TOP2B	7155	hgsc.bcm.edu	37	3	25639849	25639849	+	Silent	SNP	A	A	G	rs11548723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000540199.1_Silent_p.F462F|TOP2B_ENST00000542520.1_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	137	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	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			
DLG5	9231	hgsc.bcm.edu	37	10	79603423	79603423	+	Silent	SNP	C	C	T	rs12257229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79603423C>T	ENST00000372391.2	-	6	911	c.906G>A	c.(904-906)ctG>ctA	p.L302L	DLG5_ENST00000372388.2_Silent_p.L302L	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	302					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)			CCGTGTCATACAGTTTGTTGA	0.532													C|||	497	0.0992412	0.3593	0.0274	5008	,	,		21222	0.0		0.003	False		,,,				2504	0.0				p.L302L		Atlas-SNP	.											.	DLG5	154	.	0			c.G906A						PASS	.	C		1351,3055	449.4+/-349.0	200,951,1052	180.0	162.0	168.0		906	2.6	1.0	10	dbSNP_120	168	21,8579	14.0+/-48.4	0,21,4279	no	coding-synonymous	DLG5	NM_004747.3		200,972,5331	TT,TC,CC		0.2442,30.6627,10.549		302/1920	79603423	1372,11634	2203	4300	6503	SO:0001819	synonymous_variant	9231	exon6			GTCATACAGTTTG	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.906G>A	10.37:g.79603423C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	201	94	0.467662	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			C|0.888;T|0.112	0.112	strong		0.532	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
PLA1A	51365	hgsc.bcm.edu	37	3	119336962	119336962	+	Missense_Mutation	SNP	G	G	A	rs2692622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119336962G>A	ENST00000273371.4	+	7	923	c.851G>A	c.(850-852)aGc>aAc	p.S284N	PLA1A_ENST00000494440.1_Missense_Mutation_p.S268N|PLA1A_ENST00000488919.1_Missense_Mutation_p.S111N|PLA1A_ENST00000495992.1_Missense_Mutation_p.S268N	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	284			S -> N (in dbSNP:rs2692622).		lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CCCTGTGCCAGCTACAAGGCC	0.502													G|||	238	0.047524	0.1725	0.0144	5008	,	,		20613	0.0		0.0	False		,,,				2504	0.0				p.S284N		Atlas-SNP	.											.	PLA1A	65	.	0			c.G851A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	611,3795	267.1+/-267.6	36,539,1628	323.0	307.0	313.0		803,332,851	0.3	0.7	3	dbSNP_100	313	6,8594	4.3+/-15.6	0,6,4294	yes	missense,missense,missense	PLA1A	NM_001206960.1,NM_001206961.1,NM_015900.3	46,46,46	36,545,5922	AA,AG,GG		0.0698,13.8675,4.744	benign,benign,benign	268/441,111/284,284/457	119336962	617,12389	2203	4300	6503	SO:0001583	missense	51365	exon7			GTGCCAGCTACAA	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.851G>A	3.37:g.119336962G>A	ENSP00000273371:p.Ser284Asn	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	239	132	0.552301	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	37	CCDS2991.1	71	0.03250915750915751	68	0.13821138211382114	3	0.008287292817679558	0	0.0	0	0.0	G	11.49	1.653192	0.29425	0.138675	6.98E-4	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440;ENST00000475963	D;D;D;D;D	0.93247	-3.19;-3.19;-3.19;-3.19;-3.19	5.26	0.275	0.15659	Lipase, N-terminal (1);	0.427416	0.31268	N	0.007943	T	0.04679	0.0127	L	0.41492	1.28	0.46011	P	0.0011889999999999956	B;B	0.18013	0.005;0.025	B;B	0.20184	0.009;0.028	T	0.55611	-0.8114	9	0.56958	D	0.05	-5.9575	5.7584	0.18186	0.2197:0.2586:0.5217:0.0	rs2692622;rs52825291;rs2692622	268;284	Q53H76-3;Q53H76	.;PLA1A_HUMAN	N	284;111;268;268;150	ENSP00000273371:S284N;ENSP00000420625:S111N;ENSP00000417326:S268N;ENSP00000418793:S268N;ENSP00000417295:S150N	ENSP00000273371:S284N	S	+	2	0	PLA1A	120819652	0.995000	0.38212	0.688000	0.30117	0.454000	0.32378	0.833000	0.27504	-0.255000	0.09486	0.555000	0.69702	AGC	G|0.946;A|0.054	0.054	strong		0.502	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2		
SCN1A	6323	hgsc.bcm.edu	37	2	166868775	166868775	+	Silent	SNP	A	A	G	rs36031496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166868775A>G	ENST00000303395.4	-	19	3722	c.3723T>C	c.(3721-3723)taT>taC	p.Y1241Y	AC010127.3_ENST00000597623.1_RNA|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Silent_p.Y1213Y|SCN1A_ENST00000423058.2_Silent_p.Y1241Y|SCN1A_ENST00000375405.3_Silent_p.Y1230Y			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1241					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GCTGATCAATATATATATCTT	0.284													A|||	179	0.0357428	0.1316	0.0072	5008	,	,		18217	0.0		0.0	False		,,,				2504	0.0				p.Y1241Y		Atlas-SNP	.											.	SCN1A	641	.	0			c.T3723C						PASS	.	A	,,,	554,3852	240.3+/-251.1	48,458,1697	51.0	49.0	50.0		3723,3639,3723,3690	3.2	1.0	2	dbSNP_126	50	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	,,,	48,458,5995	GG,GA,AA		0.0,12.5738,4.2609	,,,	1241/2010,1213/1982,1241/2010,1230/1999	166868775	554,12448	2203	4298	6501	SO:0001819	synonymous_variant	6323	exon19			ATCAATATATATA	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3723T>C	2.37:g.166868775A>G		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	190	119	0.626316	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																			.	.	none		0.284	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
ATP13A1	57130	hgsc.bcm.edu	37	19	19766365	19766365	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19766365G>A	ENST00000357324.6	-	10	1394	c.1368C>T	c.(1366-1368)atC>atT	p.I456I	ATP13A1_ENST00000291503.5_Silent_p.I338I|ATP13A1_ENST00000496082.1_5'UTR	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	456	Poly-Ala.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CAGCTGCAGCGATGGCAAACA	0.607																																					p.I456I	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.C1368T						PASS	.						75.0	68.0	70.0					19																	19766365		2203	4300	6503	SO:0001819	synonymous_variant	57130	exon10			TGCAGCGATGGCA	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"""ATPases / P-type"""	24215	protein-coding gene	gene with protein product	"""cation transporting ATPase"""		"""ATPase type 13A"""	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.1368C>T	19.37:g.19766365G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	147	79	0.537415	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Silent	SNP	ENST00000357324.6	37	CCDS32970.2																																																																																			.	.	none		0.607	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410	
SSPO	23145	hgsc.bcm.edu	37	7	149477544	149477544	+	RNA	SNP	G	G	A	rs855677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149477544G>A	ENST00000378016.2	+	0	1615							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)			CGGTGACACCGTGCGCCAGCT	0.642													G|||	121	0.0241613	0.0893	0.0043	5008	,	,		19178	0.0		0.0	False		,,,				2504	0.0				p.V539M		Atlas-SNP	.											.	.	.	.	0			c.G1615A						PASS	.	G		253,4041		9,235,1903	31.0	38.0	36.0		1617	3.1	0.0	7	dbSNP_86	36	3,8479		0,3,4238	no	coding-notMod3	SSPO	NM_198455.2		9,238,6141	AA,AG,GG		0.0354,5.8919,2.0038			149477544	256,12520	2147	4241	6388			23145	exon12			GACACCGTGCGCC	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.149477544G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	121	53	0.438017	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.955;T|0.023	.	strong		0.642	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487169	32487169	+	Silent	SNP	C	C	T	rs143127183	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32487169C>T	ENST00000374975.3	-	3	692	c.630G>A	c.(628-630)acG>acA	p.T210T		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						TGAGAGGGCTCGTCACGCTTG	0.493													C|||	233	0.0465256	0.059	0.0389	5008	,	,		12789	0.0685		0.0368	False		,,,				2504	0.0225				p.T210T		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	0			c.G630A						scavenged	.						73.0	83.0	80.0					6																	32487169		1886	3734	5620	SO:0001819	synonymous_variant	3127	exon3			AGGGCTCGTCACG		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.630G>A	6.37:g.32487169C>T		Somatic	50	6	0.12		WXS	Illumina HiSeq	Phase_I	75	11	0.146667	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			C|0.100;T|0.900	0.900	weak		0.493	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
H2AFY	9555	hgsc.bcm.edu	37	5	134670765	134670765	+	Silent	SNP	A	A	G	rs3210047	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134670765A>G	ENST00000511689.1	-	9	1613	c.1020T>C	c.(1018-1020)tcT>tcC	p.S340S	H2AFY_ENST00000512507.1_5'UTR|H2AFY_ENST00000510038.1_Silent_p.S340S|H2AFY_ENST00000312469.4_Silent_p.S337S|H2AFY_ENST00000304332.4_Silent_p.S339S|H2AFY_ENST00000423969.2_Silent_p.S168S|CTC-349C3.1_ENST00000432382.3_Intron	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	340	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGGACATTGTAGACACGAAGT	0.488													G|||	598	0.119409	0.2753	0.0562	5008	,	,		22435	0.0556		0.0626	False		,,,				2504	0.0777				p.S340S		Atlas-SNP	.											.	H2AFY	61	.	0			c.T1020C						PASS	.	G	,,,	1176,3230	711.7+/-408.0	169,838,1196	137.0	125.0	129.0		1017,1017,1011,1020	-2.1	0.8	5	dbSNP_105	129	624,7976	791.2+/-407.6	24,576,3700	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	H2AFY	NM_001040158.1,NM_004893.2,NM_138609.2,NM_138610.2	,,,	193,1414,4896	GG,GA,AA		7.2558,26.6909,13.8398	,,,	339/372,339/372,337/370,340/373	134670765	1800,11206	2203	4300	6503	SO:0001819	synonymous_variant	9555	exon9			CATTGTAGACACG	AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"""Histones / Replication-independent"""	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.1020T>C	5.37:g.134670765A>G		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	250	126	0.504	NM_138610	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Silent	SNP	ENST00000511689.1	37	CCDS4185.1																																																																																			A|0.875;G|0.125	0.125	strong		0.488	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893	
UBXN11	91544	hgsc.bcm.edu	37	1	26608883	26608883	+	Silent	SNP	A	A	G	rs1134580|rs140364749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26608883A>G	ENST00000374222.1	-	16	1934	c.1470T>C	c.(1468-1470)ggT>ggC	p.G490G	UBXN11_ENST00000357089.4_Silent_p.G457G|UBXN11_ENST00000374217.2_Silent_p.G457G|UBXN11_ENST00000374221.3_Silent_p.G490G|UBXN11_ENST00000314675.7_Silent_p.G370G|UBXN11_ENST00000374223.1_Silent_p.G247G			Q5T124	UBX11_HUMAN	UBX domain protein 11	490	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						tggggccgggaccgggaccgg	0.711																																					p.G490G		Atlas-SNP	.											UBXN11,NS,carcinoma,-2,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.T1470C						PASS	.						33.0	42.0	39.0					1																	26608883		1797	4025	5822	SO:0001819	synonymous_variant	91544	exon16			GCCGGGACCGGGA	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1470T>C	1.37:g.26608883A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	43	14	0.325581	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			A|0.773;G|0.227	0.227	strong		0.711	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
MRPS18B	28973	hgsc.bcm.edu	37	6	30596135	30596135	+	IGR	SNP	A	A	G	rs6904236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30596135A>G	ENST00000259873.4	+	0	1532				ATAT1_ENST00000376483.4_Silent_p.A155A|ATAT1_ENST00000468713.1_3'UTR|ATAT1_ENST00000329992.8_Silent_p.A155A|ATAT1_ENST00000318999.7_Silent_p.A155A|ATAT1_ENST00000376485.4_Silent_p.A155A|ATAT1_ENST00000376478.2_Silent_p.A155A|ATAT1_ENST00000319027.5_Silent_p.A155A|ATAT1_ENST00000330083.5_Silent_p.A143A	NM_014046.3	NP_054765.1	Q9Y676	RT18B_HUMAN	mitochondrial ribosomal protein S18B						translation (GO:0006412)	cell junction (GO:0030054)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(2)	13						ACCAACTGGCAATTGACCGAC	0.517													G|||	231	0.0461262	0.1157	0.0346	5008	,	,		17429	0.0258		0.0199	False		,,,				2504	0.0082				p.A155A		Atlas-SNP	.											.	ATAT1	30	.	0			c.A465G						PASS	.	G	,,	308,2714		15,278,1218	91.0	83.0	86.0		429,429,465	1.9	1.0	6	dbSNP_116	86	111,5307		1,109,2599	yes	coding-synonymous,coding-synonymous,coding-synonymous	ATAT1	NM_001031722.2,NM_001190724.1,NM_024909.2	,,	16,387,3817	GG,GA,AA		2.0487,10.1919,4.9645	,,	143/410,143/289,155/334	30596135	419,8021	1511	2709	4220	SO:0001628	intergenic_variant	79969	exon6			ACTGGCAATTGAC	AF100761	CCDS4682.1	6p21	2012-09-13			ENSG00000204568	ENSG00000204568		"""Mitochondrial ribosomal proteins / small subunits"""	14516	protein-coding gene	gene with protein product		611982				11279123	Standard	NM_014046		Approved	MRPS18-2, PTD017, C6orf14, HSPC183	uc003nqo.2	Q9Y676	OTTHUMG00000031268		6.37:g.30596135A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	155	72	0.464516	NM_001254952	A6NDQ0|Q659G4|Q9BS27	Silent	SNP	ENST00000259873.4	37	CCDS4682.1																																																																																			A|0.957;G|0.043	0.043	strong		0.517	MRPS18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076584.2		
HPSE	10855	hgsc.bcm.edu	37	4	84222208	84222208	+	Silent	SNP	A	A	G	rs11031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84222208A>G	ENST00000405413.2	-	12	1513	c.1377T>C	c.(1375-1377)aaT>aaC	p.N459N	HPSE_ENST00000512196.1_Silent_p.N385N|HPSE_ENST00000311412.5_Silent_p.N459N|HPSE_ENST00000513463.1_Silent_p.N401N	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	459					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	ACTTGGTGACATTATGGAGGT	0.353													A|||	426	0.0850639	0.3064	0.0259	5008	,	,		18825	0.0		0.003	False		,,,				2504	0.0				p.N459N		Atlas-SNP	.											.	HPSE	55	.	0			c.T1377C						PASS	.	A	,,,	1123,3283	402.2+/-332.3	156,811,1236	119.0	126.0	123.0		1377,1155,1203,1377	-3.8	1.0	4	dbSNP_52	123	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HPSE	NM_001098540.2,NM_001166498.2,NM_001199830.1,NM_006665.5	,,,	156,829,5518	GG,GA,AA		0.2093,25.488,8.7729	,,,	459/544,385/470,401/486,459/544	84222208	1141,11865	2203	4300	6503	SO:0001819	synonymous_variant	10855	exon11			GGTGACATTATGG	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1377T>C	4.37:g.84222208A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Silent	SNP	ENST00000405413.2	37	CCDS3602.1																																																																																			A|0.911;G|0.089	0.089	strong		0.353	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665	
OR5R1	219479	hgsc.bcm.edu	37	11	56185327	56185327	+	Missense_Mutation	SNP	T	T	C	rs7933772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	33	0	0		WXS	Illumina HiSeq	Phase_I	43	28	0.651163	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	
OR10G7	390265	hgsc.bcm.edu	37	11	123909627	123909627	+	Missense_Mutation	SNP	T	T	C	rs11219420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909627T>C	ENST00000330487.5	-	1	90	c.82A>G	c.(82-84)Atc>Gtc	p.I28V		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	28			I -> V (in dbSNP:rs11219420).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I28V(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		ACCAGGAAGATTCCAAAGAGG	0.572													t|||	1598	0.319089	0.174	0.4568	5008	,	,		16316	0.3254		0.4294	False		,,,				2504	0.2975				p.I28V		Atlas-SNP	.											OR10G7,NS,carcinoma,0,1	OR10G7	103	1	1	Substitution - Missense(1)	stomach(1)	c.A82G						PASS	.						89.0	85.0	86.0					11																	123909627		2200	4298	6498	SO:0001583	missense	390265	exon1			GGAAGATTCCAAA	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.82A>G	11.37:g.123909627T>C	ENSP00000329689:p.Ile28Val	Somatic	419	0	0		WXS	Illumina HiSeq	Phase_I	224	110	0.491071	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	714	0.3269230769230769	74	0.15040650406504066	161	0.4447513812154696	202	0.3531468531468531	277	0.3654353562005277	C	2.011	-0.427174	0.04701	.	.	ENSG00000182634	ENST00000330487	T	0.03035	4.07	3.38	-6.76	0.01732	.	0.824866	0.10366	N	0.683403	T	0.00012	0.0000	N	0.01473	-0.845	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.36187	-0.9758	9	0.07990	T	0.79	.	3.721	0.08456	0.0824:0.3449:0.213:0.3597	rs11219420;rs57896133	28	Q8NGN6	O10G7_HUMAN	V	28	ENSP00000329689:I28V	ENSP00000329689:I28V	I	-	1	0	OR10G7	123414837	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-6.859000	0.00051	-3.501000	0.00151	-2.770000	0.00120	ATC	T|0.681;C|0.319	0.319	strong		0.572	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
VWDE	221806	hgsc.bcm.edu	37	7	12381687	12381687	+	Missense_Mutation	SNP	G	G	A	rs116125922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12381687G>A	ENST00000275358.3	-	23	4456	c.4268C>T	c.(4267-4269)aCa>aTa	p.T1423I		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1423	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						AATTTTACCTGTACTACAGGT	0.403													G|||	69	0.013778	0.0492	0.0014	5008	,	,		17679	0.0		0.0	False		,,,				2504	0.0031				p.T1423I		Atlas-SNP	.											.	VWDE	123	.	0			c.C4268T						PASS	.	G	ILE/THR	56,1328		1,54,637	83.0	76.0	78.0		4268	2.4	1.0	7	dbSNP_132	78	1,3181		0,1,1590	yes	missense	VWDE	NM_001135924.1	89	1,55,2227	AA,AG,GG		0.0314,4.0462,1.2484	possibly-damaging	1423/1591	12381687	57,4509	692	1591	2283	SO:0001583	missense	221806	exon23			TTACCTGTACTAC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.4268C>T	7.37:g.12381687G>A	ENSP00000275358:p.Thr1423Ile	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	G	16.79	3.220210	0.58560	0.040462	3.14E-4	ENSG00000146530	ENST00000275358;ENST00000536307	T	0.42131	0.98	4.38	2.42	0.29668	Epidermal growth factor-like, type 3 (1);	0.445804	0.23112	N	0.051794	T	0.15825	0.0381	L	0.35414	1.06	0.25456	N	0.987962	D	0.89917	1.0	D	0.69307	0.963	T	0.04915	-1.0918	10	0.23302	T	0.38	.	9.3739	0.38270	0.0799:0.0:0.7769:0.1432	.	1423	Q8N2E2	VWDE_HUMAN	I	1423;877	ENSP00000275358:T1423I	ENSP00000275358:T1423I	T	-	2	0	VWDE	12348212	1.000000	0.71417	0.996000	0.52242	0.638000	0.38207	4.130000	0.57964	1.193000	0.43086	0.650000	0.86243	ACA	G|0.990;A|0.010	0.010	strong		0.403	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
RNF213	57674	hgsc.bcm.edu	37	17	78262161	78262161	+	Splice_Site	SNP	T	T	C	rs17857135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78262161T>C	ENST00000582970.1	+	4	952	c.809T>C	c.(808-810)aTg>aCg	p.M270T	RNF213_ENST00000319921.4_Splice_Site_p.M270T|RNF213_ENST00000456466.1_Splice_Site_p.M270T|RNF213_ENST00000508628.2_Splice_Site_p.M319T	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	270				M -> T (in Ref. 4; AAH36891/AAH40341). {ECO:0000305}.	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)			TCAGCCTCTATGGTGAGTCAT	0.657													C|||	1059	0.211462	0.4516	0.1153	5008	,	,		16204	0.0655		0.1402	False		,,,				2504	0.1789				p.M270T		Atlas-SNP	.											RNF213_ENST00000456466,NS,carcinoma,0,6	RNF213	766	6	0			c.T809C						PASS	.	C	THR/MET,THR/MET	1594,2772		309,976,898	25.0	30.0	28.0		956,809	-1.3	0.0	17	dbSNP_123	28	1293,7185		117,1059,3063	yes	missense-near-splice,missense-near-splice	RNF213	NM_020914.4,NM_020954.2	81,81	426,2035,3961	CC,CT,TT		15.2512,36.5094,22.4774	benign,benign	319/5257,270/1064	78262161	2887,9957	2183	4239	6422	SO:0001630	splice_region_variant	57674	exon4			CCTCTATGGTGAG	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.810+1T>C	17.37:g.78262161T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	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	407	0.18635531135531136	212	0.43089430894308944	42	0.11602209944751381	37	0.06468531468531469	116	0.15303430079155672	C	4.576	0.107008	0.08780	0.365094	0.152512	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.40225	1.04;1.04	4.19	-1.33	0.09172	.	2.237800	0.02216	N	0.063634	T	0.00012	0.0000	N	0.08118	0	0.28504	P	0.9138847999999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41124	-0.9526	9	0.15952	T	0.53	-2.9558	1.0092	0.01493	0.4316:0.1641:0.244:0.1603	rs17857135;rs17857217;rs56981151	270;270	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	T	270;319;270;270	ENSP00000392123:M270T;ENSP00000324392:M270T	ENSP00000324392:M270T	M	+	2	0	RNF213	75876756	0.000000	0.05858	0.023000	0.16930	0.004000	0.04260	-0.744000	0.04839	-0.415000	0.07484	-0.762000	0.03455	ATG	T|0.785;C|0.215	0.215	strong		0.657	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	Missense_Mutation
OR10S1	219873	hgsc.bcm.edu	37	11	123848121	123848121	+	Missense_Mutation	SNP	T	T	C	rs17686210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123848121T>C	ENST00000531945.1	-	1	367	c.278A>G	c.(277-279)aAg>aGg	p.K93R		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	93			K -> R (in dbSNP:rs17686210).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		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)		TGCCATGACCTTGGGCACTGT	0.552													T|||	902	0.180112	0.1558	0.2161	5008	,	,		23775	0.1171		0.2903	False		,,,				2504	0.1391				p.K93R		Atlas-SNP	.											.	OR10S1	78	.	0			c.A278G						PASS	.	T	ARG/LYS	739,3665	302.4+/-287.4	65,609,1528	84.0	67.0	73.0		278	3.7	1.0	11	dbSNP_123	73	2217,6381	373.0+/-336.8	297,1623,2379	yes	missense	OR10S1	NM_001004474.1	26	362,2232,3907	CC,CT,TT		25.7851,16.7802,22.735	benign	93/332	123848121	2956,10046	2202	4299	6501	SO:0001583	missense	219873	exon1			ATGACCTTGGGCA	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"""GPCR / Class A : Olfactory receptors"""	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.278A>G	11.37:g.123848121T>C	ENSP00000431914:p.Lys93Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	88	29	0.329545	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	37	CCDS31701.1	449	0.20558608058608058	81	0.16463414634146342	87	0.24033149171270718	73	0.12762237762237763	208	0.27440633245382584	T	11.00	1.511627	0.27036	0.167802	0.257851	ENSG00000196248	ENST00000531945	T	0.06768	3.26	4.84	3.69	0.42338	GPCR, rhodopsin-like superfamily (1);	0.195670	0.24750	U	0.035919	T	0.00012	0.0000	L	0.28458	0.855	0.44373	P	0.00273000000000001	D	0.60575	0.988	P	0.51657	0.676	T	0.50734	-0.8793	9	0.48119	T	0.1	-9.7909	11.6588	0.51334	0.0:0.0:0.1488:0.8512	rs17686210;rs52830816;rs17686210	93	Q8NGN2	O10S1_HUMAN	R	93	ENSP00000431914:K93R	ENSP00000431914:K93R	K	-	2	0	OR10S1	123353331	0.335000	0.24748	1.000000	0.80357	0.953000	0.61014	0.933000	0.28897	0.877000	0.35895	-0.340000	0.08031	AAG	T|0.785;C|0.215	0.215	strong		0.552	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474	
RRM2B	50484	hgsc.bcm.edu	37	8	103251034	103251034	+	Intron	SNP	A	A	C	rs72554092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103251034A>C	ENST00000251810.3	-	1	292				RRM2B_ENST00000395912.2_Intron|RRM2B_ENST00000519317.1_Intron|KB-431C1.4_ENST00000520820.1_RNA|RRM2B_ENST00000519962.1_Intron	NM_001172478.1|NM_015713.4	NP_001165949.1|NP_056528.2	Q7LG56	RIR2B_HUMAN	ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process (GO:0009186)|deoxyribonucleoside triphosphate metabolic process (GO:0009200)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA repair (GO:0006281)|kidney development (GO:0001822)|mitochondrial DNA replication (GO:0006264)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|renal system process (GO:0003014)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	9	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000728)		Cladribine(DB00242)	GTGAGGGGGAAGACGCAACAG	0.637								Modulation of nucleotide pools					A|||	104	0.0207668	0.0764	0.0029	5008	,	,		13321	0.0		0.0	False		,,,				2504	0.001				p.L6R		Atlas-SNP	.											.	RRM2B	31	.	0			c.T17G						PASS	.	A	ARG/LEU,,	414,3992	200.4+/-223.7	20,374,1809	63.0	62.0	62.0		17,,	-4.6	0.0	8	dbSNP_130	62	2,8598	2.2+/-6.3	0,2,4298	yes	missense,intron,intron	RRM2B	NM_001172477.1,NM_001172478.1,NM_015713.4	102,,	20,376,6107	CC,CA,AA		0.0233,9.3963,3.1985	,,	6/424,,	103251034	416,12590	2203	4300	6503	SO:0001627	intron_variant	50484	exon1			GGGGGAAGACGCA	AB036532	CCDS34932.1, CCDS55267.1	8q23.1	2014-09-17			ENSG00000048392	ENSG00000048392			17296	protein-coding gene	gene with protein product		604712				10716435, 10980602, 17486094	Standard	NM_015713		Approved	p53R2	uc022azl.1	Q7LG56	OTTHUMG00000164776	ENST00000251810.3:c.48+20T>G	8.37:g.103251034A>C		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	26	15	0.576923	NM_001172477	B4E2N4|Q17R22|Q75PQ6|Q75PQ7|Q75PY8|Q75PY9|Q86YE3|Q9NPD6|Q9NTD8|Q9NUW3	Missense_Mutation	SNP	ENST00000251810.3	37	CCDS34932.1																																																																																			A|0.975;C|0.025	0.025	strong		0.637	RRM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380191.3		
ENG	2022	hgsc.bcm.edu	37	9	130616621	130616621	+	Missense_Mutation	SNP	G	G	A	rs35400405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130616621G>A	ENST00000373203.4	-	1	414	c.14C>T	c.(13-15)aCg>aTg	p.T5M	ENG_ENST00000344849.3_Missense_Mutation_p.T5M	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	5			T -> M (in dbSNP:rs35400405). {ECO:0000269|PubMed:9245986}.		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						CAGAGGGAGCGTGCCGCGGTC	0.721									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia				g|||	204	0.0407348	0.1256	0.0231	5008	,	,		13491	0.0		0.0199	False		,,,				2504	0.002				p.T5M		Atlas-SNP	.											.	ENG	44	.	0			c.C14T	GRCh37	CM004889	ENG	M	rs35400405	PASS	.		MET/THR,MET/THR	445,3945		20,405,1770	33.0	35.0	34.0		14,14	0.1	0.0	9	dbSNP_126	34	196,8378		4,188,4095	yes	missense,missense	ENG	NM_000118.2,NM_001114753.1	81,81	24,593,5865	AA,AG,GG		2.286,10.1367,4.9445	possibly-damaging,possibly-damaging	5/626,5/659	130616621	641,12323	2195	4287	6482	SO:0001583	missense	2022	exon1	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	GGGAGCGTGCCGC	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.14C>T	9.37:g.130616621G>A	ENSP00000362299:p.Thr5Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	129	86	0.666667	NM_001114753	Q14248|Q14926|Q5T9C0	Missense_Mutation	SNP	ENST00000373203.4	37	CCDS48029.1	91	0.041666666666666664	66	0.13414634146341464	10	0.027624309392265192	0	0.0	15	0.01978891820580475	G	3.401	-0.122326	0.06795	0.101367	0.02286	ENSG00000106991	ENST00000373203;ENST00000344849;ENST00000545345	T;T	0.42900	0.96;1.54	5.27	0.0968	0.14491	.	1.824350	0.02663	N	0.107751	T	0.00271	0.0008	N	0.08118	0	0.58432	P	4.000000000004E-6	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.11324	-1.0592	9	0.39692	T	0.17	-15.5952	8.2349	0.31620	0.4735:0.0:0.5265:0.0	rs35400405	5;5	Q5T9B9;P17813	.;EGLN_HUMAN	M	5	ENSP00000362299:T5M;ENSP00000341917:T5M	ENSP00000341917:T5M	T	-	2	0	ENG	129656442	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.362000	0.07602	0.037000	0.15575	-0.265000	0.10407	ACG	G|0.950;A|0.050	0.050	strong		0.721	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1		
MED14	9282	hgsc.bcm.edu	37	X	40573157	40573157	+	Silent	SNP	G	G	A	rs6520683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40573157G>A	ENST00000324817.1	-	5	643	c.525C>T	c.(523-525)gaC>gaT	p.D175D		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	175					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|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)|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)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	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 coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GAATAATTTTGTCCTGCAAAA	0.338													A|||	1136	0.300927	0.4584	0.1124	3775	,	,		12488	0.1538		0.1352	False		,,,				2504	0.1646				p.D175D		Atlas-SNP	.											.	MED14	108	.	0			c.C525T						PASS	.	A		1994,1841		442,809,301,381,270	122.0	122.0	122.0		525	3.2	1.0	X	dbSNP_116	122	1203,5525		74,735,320,1619,1552	no	coding-synonymous	MED14	NM_004229.3		516,1544,621,2000,1822	AA,AG,A,GG,G		17.8805,48.0052,30.266		175/1455	40573157	3197,7366	2203	4300	6503	SO:0001819	synonymous_variant	9282	exon5			AATTTTGTCCTGC	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.525C>T	X.37:g.40573157G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	225	117	0.52	NM_004229	Q4KMR7|Q9UNB3	Silent	SNP	ENST00000324817.1	37	CCDS14254.1																																																																																			G|0.693;A|0.307	0.307	strong		0.338	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229	
CNKSR1	10256	hgsc.bcm.edu	37	1	26508997	26508997	+	Silent	SNP	C	C	T	rs2802347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26508997C>T	ENST00000374253.5	+	6	585	c.546C>T	c.(544-546)caC>caT	p.H182H	CNKSR1_ENST00000480348.2_3'UTR|CNKSR1_ENST00000361530.6_Silent_p.H182H|CNKSR1_ENST00000531191.1_5'UTR	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	182					Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|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;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		GGATCTGCCACAACATCCTGG	0.652													C|||	259	0.0517173	0.1846	0.0202	5008	,	,		17396	0.0		0.001	False		,,,				2504	0.0				p.H182H	NSCLC(180;1396 2109 28270 30756 34275)	Atlas-SNP	.											.	CNKSR1	66	.	0			c.C546T						PASS	.	C		702,3704	293.3+/-282.5	64,574,1565	65.0	65.0	65.0		546	2.4	1.0	1	dbSNP_100	65	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CNKSR1	NM_006314.2		64,578,5861	TT,TC,CC		0.0465,15.9328,5.4283		182/714	26508997	706,12300	2203	4300	6503	SO:0001819	synonymous_variant	10256	exon6			CTGCCACAACATC	AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.546C>T	1.37:g.26508997C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	182	93	0.510989	NM_006314	B1AMW9|O95381	Silent	SNP	ENST00000374253.5	37		108	0.04945054945054945	98	0.1991869918699187	10	0.027624309392265192	0	0.0	0	0.0	C	13.82	2.352119	0.41700	0.159328	4.65E-4	ENSG00000142675	ENST00000422547	.	.	.	4.47	2.37	0.29283	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999889351	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-2.2956	5.5452	0.17059	0.0:0.4831:0.4021:0.1148	rs2802347	.	.	.	X	170	.	ENSP00000390945:Q170X	Q	+	1	0	CNKSR1	26381584	0.230000	0.23740	0.998000	0.56505	0.271000	0.26615	0.419000	0.21247	1.068000	0.40764	0.650000	0.86243	CAA	C|0.940;T|0.060	0.060	strong		0.652	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314	
SPINT1	6692	hgsc.bcm.edu	37	15	41146880	41146880	+	Silent	SNP	T	T	C	rs8028552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41146880T>C	ENST00000344051.4	+	8	1392	c.1158T>C	c.(1156-1158)agT>agC	p.S386S	SPINT1_ENST00000431806.1_Silent_p.S370S|SPINT1_ENST00000562057.1_Silent_p.S370S			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	386					branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		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;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		ATTTCCCCAGTGACAAAGGTG	0.592													T|||	1396	0.278754	0.5787	0.1614	5008	,	,		19474	0.1706		0.1889	False		,,,				2504	0.1605				p.S386S		Atlas-SNP	.											.	SPINT1	28	.	0			c.T1158C						PASS	.	T	,,	2219,2187	590.3+/-387.3	558,1103,542	114.0	107.0	109.0		1110,1110,1158	1.5	1.0	15	dbSNP_116	109	1728,6872	315.8+/-312.4	175,1378,2747	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINT1	NM_001032367.1,NM_003710.3,NM_181642.2	,,	733,2481,3289	CC,CT,TT		20.093,49.6369,30.3475	,,	370/514,370/514,386/530	41146880	3947,9059	2203	4300	6503	SO:0001819	synonymous_variant	6692	exon8			CCCCAGTGACAAA		CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"""serine protease inhibitor, Kunitz type 1"""				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.1158T>C	15.37:g.41146880T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_181642	Q7Z7D2	Silent	SNP	ENST00000344051.4	37	CCDS10067.1																																																																																			C|0.286;N|0.000	0.286	strong		0.592	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710	
USP31	57478	hgsc.bcm.edu	37	16	23080634	23080634	+	Missense_Mutation	SNP	C	C	A	rs10083789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23080634C>A	ENST00000219689.7	-	16	2791	c.2792G>T	c.(2791-2793)cGc>cTc	p.R931L	USP31_ENST00000567975.1_Missense_Mutation_p.R224L	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		GTGCTCACGGCGACTATGACT	0.547													C|||	729	0.145567	0.1157	0.1873	5008	,	,		18828	0.0546		0.3042	False		,,,				2504	0.0869				p.R931L		Atlas-SNP	.											.	USP31	122	.	0			c.G2792T						PASS	.	C	LEU/ARG	674,3720	286.3+/-278.7	54,566,1577	74.0	75.0	75.0		2792	5.1	0.2	16	dbSNP_119	75	2656,5944	427.5+/-355.6	416,1824,2060	yes	missense	USP31	NM_020718.3	102	470,2390,3637	AA,AC,CC		30.8837,15.3391,25.6272	probably-damaging	931/1353	23080634	3330,9664	2197	4300	6497	SO:0001583	missense	57478	exon16			TCACGGCGACTAT	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2792G>T	16.37:g.23080634C>A	ENSP00000219689:p.Arg931Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	399	0.18269230769230768	61	0.12398373983739837	78	0.2154696132596685	32	0.055944055944055944	228	0.3007915567282322	C	15.34	2.805061	0.50315	0.153391	0.308837	ENSG00000103404	ENST00000219689;ENST00000381162	T	0.09723	2.95	6.02	5.07	0.68467	.	0.425160	0.19991	N	0.101577	T	0.00012	0.0000	L	0.50333	1.59	0.51233	P	8.799999999997699E-5	D;D	0.58268	0.977;0.982	P;P	0.52159	0.691;0.518	T	0.54443	-0.8293	9	0.22706	T	0.39	-6.8887	14.4891	0.67639	0.0:0.93:0.0:0.07	rs10083789;rs17345123;rs17796446;rs61275052;rs10083789	234;931	Q70CQ4-2;Q70CQ4	.;UBP31_HUMAN	L	931;234	ENSP00000219689:R931L	ENSP00000219689:R931L	R	-	2	0	USP31	22988135	0.918000	0.31147	0.173000	0.22940	0.975000	0.68041	1.836000	0.39191	1.557000	0.49525	0.650000	0.86243	CGC	C|0.785;A|0.215	0.215	strong		0.547	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
NLRC4	58484	hgsc.bcm.edu	37	2	32476390	32476390	+	Silent	SNP	T	T	G	rs408813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32476390T>G	ENST00000404025.2	-	5	1031	c.543A>C	c.(541-543)cgA>cgC	p.R181R	NLRC4_ENST00000360906.5_Silent_p.R181R|NLRC4_ENST00000342905.6_Intron|NLRC4_ENST00000402280.1_Silent_p.R181R			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	181	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.|Nucleotide-binding domain (NBD). {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)	p.R181R(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GCATGGCAATTCGCTGCAGCA	0.562													T|||	2582	0.515575	0.6067	0.5922	5008	,	,		18573	0.3562		0.6074	False		,,,				2504	0.408				p.R181R		Atlas-SNP	.											NLRC4_ENST00000404025,NS,carcinoma,-1,4	NLRC4	165	4	1	Substitution - coding silent(1)	stomach(1)	c.A543C						PASS	.	T	,,	2537,1869	631.1+/-395.6	736,1065,402	70.0	70.0	70.0		543,543,543	2.1	1.0	2	dbSNP_80	70	5106,3494	634.0+/-398.8	1519,2068,713	no	coding-synonymous,coding-synonymous,coding-synonymous	NLRC4	NM_001199138.1,NM_001199139.1,NM_021209.4	,,	2255,3133,1115	GG,GT,TT		40.6279,42.4194,41.2348	,,	181/1025,181/1025,181/1025	32476390	7643,5363	2203	4300	6503	SO:0001819	synonymous_variant	58484	exon4			GGCAATTCGCTGC	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"""Nucleotide-binding domain and leucine rich repeat containing"""	16412	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4"", ""NOD-like receptor C4"""	606831	"""caspase recruitment domain family, member 12"""	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.543A>C	2.37:g.32476390T>G		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	196	195	0.994898	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Silent	SNP	ENST00000404025.2	37	CCDS33174.1																																																																																			T|0.422;G|0.578	0.578	strong		0.562	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209	
ST6GAL2	84620	hgsc.bcm.edu	37	2	107450589	107450589	+	Silent	SNP	C	C	T	rs3796111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:107450589C>T	ENST00000409382.3	-	3	1567	c.957G>A	c.(955-957)gcG>gcA	p.A319A	ST6GAL2_ENST00000361686.4_Silent_p.A319A|AC016994.2_ENST00000425419.1_RNA|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	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	157	157	1	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	
RHBG	57127	hgsc.bcm.edu	37	1	156347834	156347834	+	Missense_Mutation	SNP	T	T	A	rs11586833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156347834T>A	ENST00000368249.1	+	3	466	c.428T>A	c.(427-429)gTc>gAc	p.V143D	RHBG_ENST00000537040.1_Intron|RHBG_ENST00000451864.2_Missense_Mutation_p.V74D|RHBG_ENST00000368246.2_Missense_Mutation_p.V143D|RHBG_ENST00000255013.3_Missense_Mutation_p.V74D|RHBG_ENST00000400992.2_Missense_Mutation_p.V74D	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	143			V -> D (in dbSNP:rs11586833). {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)	p.V143D(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					TTTGGTGCCGTCCTGGGCAAG	0.602													T|||	1334	0.266374	0.1558	0.3588	5008	,	,		13610	0.3472		0.2584	False		,,,				2504	0.2751				p.V143D		Atlas-SNP	.											RHBG,NS,carcinoma,0,1	RHBG	133	1	1	Substitution - Missense(1)	stomach(1)	c.T428A						scavenged	.	T	ASP/VAL	670,3528		45,580,1474	67.0	71.0	70.0		428	4.9	0.0	1	dbSNP_120	70	1969,6473		233,1503,2485	yes	missense	RHBG	NM_020407.3	152	278,2083,3959	AA,AT,TT		23.3239,15.96,20.8782	probably-damaging	143/459	156347834	2639,10001	2099	4221	6320	SO:0001583	missense	57127	exon3			GTGCCGTCCTGGG	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.428T>A	1.37:g.156347834T>A	ENSP00000357232:p.Val143Asp	Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	190	94	0.494737	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		598	0.27380952380952384	74	0.15040650406504066	144	0.39779005524861877	196	0.34265734265734266	184	0.24274406332453827	T	20.7	4.036607	0.75617	0.1596	0.233239	ENSG00000132677	ENST00000368249;ENST00000368246;ENST00000400992;ENST00000255013;ENST00000451864	T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62	4.95	4.95	0.65309	Ammonium transporter AmtB-like (3);	0.257936	0.38005	N	0.001853	T	0.57770	0.2076	M	0.93420	3.415	0.18873	P	0.9999841511	D;B;D	0.89917	0.99;0.25;1.0	P;B;D	0.91635	0.845;0.159;0.999	T	0.71771	-0.4492	9	0.72032	D	0.01	-47.6869	13.5971	0.61996	0.0:0.0:0.0:1.0	rs11586833;rs17846689;rs17859789;rs52803169;rs60853732;rs11586833	143;74;180	Q9H310;Q9H310-3;Q5SZW5	RHBG_HUMAN;.;.	D	143;143;74;74;74	ENSP00000357232:V143D;ENSP00000357229:V143D;ENSP00000383777:V74D;ENSP00000255013:V74D;ENSP00000389836:V74D	ENSP00000255013:V74D	V	+	2	0	RHBG	154614458	0.958000	0.32768	0.016000	0.15963	0.980000	0.70556	7.399000	0.79935	2.084000	0.62774	0.459000	0.35465	GTC	T|0.733;A|0.267	0.267	strong		0.602	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
PSME4	23198	hgsc.bcm.edu	37	2	54120820	54120820	+	Silent	SNP	G	G	A	rs805412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:54120820G>A	ENST00000404125.1	-	35	4084	c.4029C>T	c.(4027-4029)tgC>tgT	p.C1343C	PSME4_ENST00000421748.2_Silent_p.C487C	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1343					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)			CCTTAAAGAGGCAAAAACGTC	0.294													A|||	2870	0.573083	0.5741	0.4553	5008	,	,		17845	0.7312		0.4374	False		,,,				2504	0.6319				p.C1343C		Atlas-SNP	.											.	PSME4	247	.	0			c.C4029T						PASS	.	A		2298,2106	563.4+/-381.2	607,1084,511	76.0	85.0	82.0		4029	4.5	1.0	2	dbSNP_86	82	3621,4971	618.1+/-396.7	762,2097,1437	no	coding-synonymous	PSME4	NM_014614.2		1369,3181,1948	AA,AG,GG		42.1439,47.8202,45.5448		1343/1844	54120820	5919,7077	2202	4296	6498	SO:0001819	synonymous_variant	23198	exon35			AAAGAGGCAAAAA	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.4029C>T	2.37:g.54120820G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	103	60	0.582524	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																			G|0.521;A|0.479	0.479	strong		0.294	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
GPR35	2859	hgsc.bcm.edu	37	2	241569535	241569535	+	Missense_Mutation	SNP	C	C	T	rs115880579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241569535C>T	ENST00000319838.5	+	6	1108	c.166C>T	c.(166-168)Cgc>Tgc	p.R56C	GPR35_ENST00000403859.1_Missense_Mutation_p.R56C|GPR35_ENST00000407714.1_Missense_Mutation_p.R56C|GPR35_ENST00000430267.1_Missense_Mutation_p.R56C|GPR35_ENST00000438013.2_Missense_Mutation_p.R87C	NM_001195381.1	NP_001182310.1	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35	56					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|cervix(1)|endometrium(1)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	17		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;5.29e-32)|all cancers(36;1.38e-29)|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;5.02e-06)|Lung(119;0.00163)|Colorectal(34;0.00463)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.031)		GACGGAGACCCGCATCTACAT	0.642													C|||	29	0.00579073	0.0204	0.0029	5008	,	,		18411	0.0		0.0	False		,,,				2504	0.0				p.R87C		Atlas-SNP	.											GPR35,NS,malignant_melanoma,-1,1	GPR35	43	1	0			c.C259T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	72,4334	65.3+/-102.7	1,70,2132	103.0	89.0	94.0		259,259,166	3.1	0.2	2	dbSNP_132	94	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	GPR35	NM_001195381.1,NM_001195382.1,NM_005301.3	180,180,180	1,74,6428	TT,TC,CC		0.0465,1.6341,0.5843	probably-damaging,probably-damaging,probably-damaging	87/341,87/341,56/310	241569535	76,12930	2203	4300	6503	SO:0001583	missense	2859	exon6			GAGACCCGCATCT		CCDS2541.1, CCDS56174.1	2q37.3	2012-08-21			ENSG00000178623	ENSG00000178623		"""GPCR / Class A : Orphans"""	4492	protein-coding gene	gene with protein product		602646				9479505	Standard	NM_005301		Approved		uc021vze.1	Q9HC97	OTTHUMG00000133356	ENST00000319838.5:c.166C>T	2.37:g.241569535C>T	ENSP00000322731:p.Arg56Cys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_001195382	J3KR30|O43495|Q17R58|Q4VBN5|Q4ZFV2|Q6FHI8|Q86UH4	Missense_Mutation	SNP	ENST00000319838.5	37	CCDS2541.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	C	15.47	2.843986	0.51164	0.016341	4.65E-4	ENSG00000178623	ENST00000319838;ENST00000403859;ENST00000438013;ENST00000407714;ENST00000430267	T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17	4.02	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.640810	0.14659	N	0.306078	T	0.33614	0.0869	M	0.79693	2.465	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.991;0.991	T	0.14980	-1.0453	10	0.54805	T	0.06	-20.0686	9.7984	0.40748	0.0:0.6693:0.3307:0.0	.	141;87;56	Q6ZMP9;A8K2J1;Q9HC97	.;.;GPR35_HUMAN	C	56;56;87;56;56	ENSP00000322731:R56C;ENSP00000385140:R56C;ENSP00000415890:R87C;ENSP00000384263:R56C;ENSP00000411788:R56C	ENSP00000322731:R56C	R	+	1	0	GPR35	241218208	0.000000	0.05858	0.235000	0.24058	0.783000	0.44284	-0.829000	0.04415	2.250000	0.74265	0.462000	0.41574	CGC	C|0.993;T|0.007	0.007	strong		0.642	GPR35-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325631.1	NM_001195382	
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743130	22743130	+	Silent	SNP	C	C	T	rs376169003		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:22743130C>T	ENST00000560659.2	+	8	1365	c.1365C>T	c.(1363-1365)caC>caT	p.H455H	GOLGA6L1_ENST00000316397.3_Silent_p.H505H			Q8N7Z2	GG6L1_HUMAN	golgin A6 family-like 1	499										NS(1)|breast(2)|endometrium(5)|large_intestine(1)|lung(1)|skin(1)	11						agaagatgcacgaccaggagg	0.557																																					p.H505H		Atlas-SNP	.											.	GOLGA6L1	20	.	0			c.C1515T						PASS	.						3.0	2.0	3.0					15																	22743130		901	1302	2203	SO:0001819	synonymous_variant	283767	exon8			GATGCACGACCAG	AK097517	CCDS73699.1	15q11.2	2012-10-05	2010-02-12		ENSG00000197414	ENSG00000277865			37444	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 1"""				Standard	NM_001001413		Approved		uc010tzx.1	Q8N7Z2	OTTHUMG00000171883	ENST00000560659.2:c.1365C>T	15.37:g.22743130C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	256	45	0.175781	NM_001001413		Silent	SNP	ENST00000560659.2	37																																																																																				.	.	weak		0.557	GOLGA6L1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000415616.2	NM_001001413	
PCDHGB2	56103	hgsc.bcm.edu	37	5	140739779	140739779	+	Missense_Mutation	SNP	C	C	G	rs17097231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140739779C>G	ENST00000522605.1	+	1	77	c.77C>G	c.(76-78)cCc>cGc	p.P26R	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	26			P -> R (in dbSNP:rs17097231).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTTGTTCCCCGGGGCTCTC	0.592											OREG0016857	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	653	0.130391	0.1573	0.1671	5008	,	,		14680	0.119		0.0706	False		,,,				2504	0.1411				p.P26R		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.C77G						PASS	.	C	,,,,,ARG/PRO,ARG/PRO	565,3303		41,483,1410	37.0	43.0	41.0		,,,,,77,77	2.5	0.3	5	dbSNP_123	41	742,7522		38,666,3428	yes	intron,intron,intron,intron,intron,missense,missense	PCDHGB2,PCDHGB1,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018922.2,NM_018923.2,NM_032096.1	,,,,,103,103	79,1149,4838	GG,GC,CC		8.9787,14.607,10.7732	,,,,,,	,,,,,26/932,26/812	140739779	1307,10825	1934	4132	6066	SO:0001583	missense	56103	exon1			TGTTCCCCGGGGC	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"""Cadherins / Protocadherins : Clustered"""	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.77C>G	5.37:g.140739779C>G	ENSP00000429018:p.Pro26Arg	Somatic	164	0	0	1658	WXS	Illumina HiSeq	Phase_I	191	75	0.39267	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	37	CCDS54924.1	254	0.1163003663003663	69	0.1402439024390244	55	0.15193370165745856	70	0.12237762237762238	60	0.079155672823219	.	0.087	-1.173915	0.01646	0.14607	0.089787	ENSG00000253910	ENST00000522605	T	0.49720	0.77	5.3	2.45	0.29901	Cadherin-like (1);	.	.	.	.	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	0.12293	-1.0553	8	0.24483	T	0.36	.	8.4831	0.33054	0.1542:0.1344:0.7114:0.0	rs17097231;rs52831211;rs58908268;rs17097231	26;26	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	R	26	ENSP00000429018:P26R	ENSP00000429018:P26R	P	+	2	0	PCDHGB2	140719963	0.001000	0.12720	0.286000	0.24833	0.249000	0.25844	0.942000	0.29017	0.694000	0.31654	-0.344000	0.07964	CCC	C|0.880;G|0.120	0.120	strong		0.592	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923	
CLSTN2	64084	hgsc.bcm.edu	37	3	140281768	140281768	+	Silent	SNP	G	G	A	rs35951028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:140281768G>A	ENST00000458420.3	+	14	2518	c.2328G>A	c.(2326-2328)ggG>ggA	p.G776G		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	776					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						AACTCAATGGGCGCTACACTA	0.542										HNSCC(16;0.037)			G|||	111	0.0221645	0.0779	0.0115	5008	,	,		21673	0.0		0.0	False		,,,				2504	0.0				p.G776G	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G2328A						PASS	.	G		331,4075	175.5+/-204.9	8,315,1880	60.0	58.0	59.0		2328	3.8	1.0	3	dbSNP_126	59	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CLSTN2	NM_022131.2		8,319,6176	AA,AG,GG		0.0465,7.5125,2.5757		776/956	140281768	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	64084	exon14			CAATGGGCGCTAC	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.2328G>A	3.37:g.140281768G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	ENST00000458420.3	37	CCDS3112.1																																																																																			G|0.973;A|0.027	0.027	strong		0.542	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
MACF1	23499	hgsc.bcm.edu	37	1	39853163	39853163	+	Silent	SNP	T	T	C	rs79901102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39853163T>C	ENST00000372915.3	+	57	14751	c.14664T>C	c.(14662-14664)caT>caC	p.H4888H	MACF1_ENST00000564288.1_Silent_p.H4883H|MACF1_ENST00000361689.2_Silent_p.H2821H|MACF1_ENST00000545844.1_Silent_p.H2821H|MACF1_ENST00000539005.1_Silent_p.H2800H|MACF1_ENST00000317713.7_Silent_p.H2821H|MACF1_ENST00000567887.1_Silent_p.H4920H|MACF1_ENST00000289893.4_Silent_p.H3323H			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4888					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)			TCAAAAACCATTGGGAAGAGC	0.438													T|||	125	0.0249601	0.0885	0.0086	5008	,	,		19483	0.0		0.001	False		,,,				2504	0.001				p.H2821H		Atlas-SNP	.											.	MACF1	909	.	0			c.T8463C						PASS	.	T	,	308,4096	161.1+/-193.3	8,292,1902	73.0	82.0	79.0		8463,9969	-12.3	0.0	1	dbSNP_131	79	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	MACF1	NM_012090.4,NM_033044.3	,	8,295,6199	CC,CT,TT		0.0349,6.9936,2.3916	,	2821/5431,3323/5939	39853163	311,12693	2202	4300	6502	SO:0001819	synonymous_variant	23499	exon54			AAACCATTGGGAA	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.14664T>C	1.37:g.39853163T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37																																																																																				T|0.975;C|0.025	0.025	strong		0.438	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
DNAH6	1768	hgsc.bcm.edu	37	2	84861723	84861723	+	Silent	SNP	C	C	T	rs7570005	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:84861723C>T	ENST00000237449.6	+	29	4619	c.4611C>T	c.(4609-4611)atC>atT	p.I1537I	DNAH6_ENST00000398278.2_Silent_p.I1537I|DNAH6_ENST00000389394.3_Silent_p.I1537I			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1537	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TGTCCGTCATCGCGCAGCAAC	0.468													T|||	867	0.173123	0.4622	0.0937	5008	,	,		18058	0.0129		0.0775	False		,,,				2504	0.1022				p.I1537I		Atlas-SNP	.											.	DNAH6	194	.	0			c.C4611T						PASS	.	T		600,784		116,368,208	76.0	67.0	70.0		4611	-5.5	0.7	2	dbSNP_116	70	251,2931		8,235,1348	no	coding-synonymous	DNAH6	NM_001370.1		124,603,1556	TT,TC,CC		7.8881,43.3526,18.6378		1537/4159	84861723	851,3715	692	1591	2283	SO:0001819	synonymous_variant	1768	exon30			CGTCATCGCGCAG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.4611C>T	2.37:g.84861723C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			C|0.843;T|0.157	0.157	strong		0.468	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
POLQ	10721	hgsc.bcm.edu	37	3	121154974	121154974	+	Missense_Mutation	SNP	T	T	C	rs1381057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121154974T>C	ENST00000264233.5	-	28	7666	c.7538A>G	c.(7537-7539)cAa>cGa	p.Q2513R		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2513				Q -> R (in Ref. 1; AAC33565 and 2; AAR08421). {ECO:0000305}.	ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CAAACCTGTTTGGTCACTTTG	0.368								DNA polymerases (catalytic subunits)					C|||	3732	0.745208	0.6309	0.6945	5008	,	,		20710	0.877		0.668	False		,,,				2504	0.8793				p.Q2513R	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A7538G						PASS	.	C	ARG/GLN	2840,1566	490.3+/-361.7	924,992,287	190.0	171.0	177.0		7538	-0.3	0.0	3	dbSNP_88	177	5869,2731	436.2+/-358.2	2002,1865,433	yes	missense	POLQ	NM_199420.3	43	2926,2857,720	CC,CT,TT		31.7558,35.5424,33.0386	benign	2513/2591	121154974	8709,4297	2203	4300	6503	SO:0001583	missense	10721	exon28			CCTGTTTGGTCAC	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.7538A>G	3.37:g.121154974T>C	ENSP00000264233:p.Gln2513Arg	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	225	115	0.511111	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	1562	0.7152014652014652	300	0.6097560975609756	250	0.6906077348066298	511	0.8933566433566433	501	0.6609498680738787	C	1.151	-0.646621	0.03531	0.644576	0.682442	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.47177	0.85	5.81	-0.307	0.12777	DNA-directed DNA polymerase, family A, palm domain (2);	0.799731	0.11667	N	0.541194	T	0.00012	0.0000	N	0.04959	-0.14	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.38607	-0.9653	9	0.02654	T	1	.	7.6272	0.28218	0.0:0.4356:0.1049:0.4595	rs1381057;rs17481360;rs52804123;rs1381057	2513;1685	O75417;O75417-2	DPOLQ_HUMAN;.	R	2136;2513;2649	ENSP00000264233:Q2513R	ENSP00000264233:Q2513R	Q	-	2	0	POLQ	122637664	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-0.473000	0.06615	-0.673000	0.05259	-0.941000	0.02677	CAA	T|0.298;C|0.702	0.702	strong		0.368	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
GABBR2	9568	hgsc.bcm.edu	37	9	101340316	101340316	+	Silent	SNP	T	T	C	rs3750344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101340316T>C	ENST00000259455.2	-	2	819	c.360A>G	c.(358-360)gcA>gcG	p.A120A		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	120					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	CGTATTTTATTGCATCGTAGA	0.493													t|||	807	0.161142	0.236	0.0908	5008	,	,		21374	0.1508		0.1799	False		,,,				2504	0.1012				p.A120A		Atlas-SNP	.											.	GABBR2	126	.	0			c.A360G						PASS	.			996,3410	373.0+/-320.6	113,770,1320	181.0	165.0	171.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	360	2.2	1.0	9	dbSNP_107	171	1435,7165	274.9+/-291.5	123,1189,2988	no	coding-synonymous	GABBR2	NM_005458.7		236,1959,4308	CC,CT,TT		16.686,22.6055,18.6914		120/942	101340316	2431,10575	2203	4300	6503	SO:0001819	synonymous_variant	9568	exon2			TTTTATTGCATCG	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.360A>G	9.37:g.101340316T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	102	30	0.294118	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Silent	SNP	ENST00000259455.2	37	CCDS6736.1																																																																																			T|0.809;C|0.191	0.191	strong		0.493	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
HEG1	57493	hgsc.bcm.edu	37	3	124732426	124732426	+	Missense_Mutation	SNP	G	G	A	rs113838848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124732426G>A	ENST00000311127.4	-	6	2064	c.1997C>T	c.(1996-1998)tCc>tTc	p.S666F	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	666	Ser-rich.				cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						agaagaggaggaggaggaaga	0.493													G|||	86	0.0171725	0.0598	0.0101	5008	,	,		20835	0.0		0.0	False		,,,				2504	0.0				p.S666F		Atlas-SNP	.											.	HEG1	109	.	0			c.C1997T						PASS	.	G	PHE/SER	183,4127		5,173,1977	55.0	61.0	59.0		1997	0.6	0.0	3	dbSNP_132	59	1,8509		0,1,4254	yes	missense	HEG1	NM_020733.1	155	5,174,6231	AA,AG,GG		0.0118,4.2459,1.4353	probably-damaging	666/1382	124732426	184,12636	2155	4255	6410	SO:0001583	missense	57493	exon6			GAGGAGGAGGAGG	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.1997C>T	3.37:g.124732426G>A	ENSP00000311502:p.Ser666Phe	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	130	72	0.553846	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	G	6.371	0.436495	0.12104	0.042459	1.18E-4	ENSG00000173706	ENST00000311127	D	0.89617	-2.54	0.635	0.635	0.17723	.	22.921900	0.01454	U	0.015599	T	0.57359	0.2048	N	0.08118	0	0.09310	N	1	D;D	0.58268	0.982;0.972	P;P	0.58013	0.452;0.831	T	0.72865	-0.4163	9	0.66056	D	0.02	.	.	.	.	.	666;666	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	F	666	ENSP00000311502:S666F	ENSP00000311502:S666F	S	-	2	0	HEG1	126215116	0.001000	0.12720	0.004000	0.12327	0.003000	0.03518	0.345000	0.19979	0.619000	0.30197	0.313000	0.20887	TCC	G|0.986;A|0.014	0.014	strong		0.493	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
ANKRD36B	57730	hgsc.bcm.edu	37	2	98206013	98206013	+	RNA	SNP	C	C	T	rs188661236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98206013C>T	ENST00000443455.1	-	0	314							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		CTCTTATTGGCGTCATAATAC	0.522													.|||	73	0.0145767	0.0469	0.0043	5008	,	,		11667	0.006		0.001	False		,,,				2504	0.001				p.A46T		Atlas-SNP	.											.	.	.	.	0			c.G136A						PASS	.	C	THR/ALA	41,1343		2,37,653	107.0	83.0	90.0		136	-1.5	0.0	2		90	0,3182		0,0,1591	no	missense	ANKRD36B	NM_025190.3	58	2,37,2244	TT,TC,CC		0.0,2.9624,0.8979	benign	46/1354	98206013	41,4525	692	1591	2283			57730	exon1			TATTGGCGTCATA	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98206013C>T		Somatic	295	1	0.00338983		WXS	Illumina HiSeq	Phase_I	262	127	0.484733	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				C|0.989;T|0.011	0.011	strong		0.522	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
MLPH	79083	hgsc.bcm.edu	37	2	238449007	238449007	+	Missense_Mutation	SNP	T	T	C	rs3817362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238449007T>C	ENST00000264605.3	+	10	1415	c.1121T>C	c.(1120-1122)gTg>gCg	p.V374A	MLPH_ENST00000445024.2_Missense_Mutation_p.V374A|MLPH_ENST00000338530.4_Missense_Mutation_p.V346A|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000410032.1_Missense_Mutation_p.V231A|MLPH_ENST00000409373.1_Missense_Mutation_p.V306A	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	374			V -> A (in dbSNP:rs3817362). {ECO:0000269|PubMed:14702039}.		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)		GGTGCTGGAGTGCGCACGGAG	0.622													T|||	2161	0.43151	0.8071	0.3026	5008	,	,		18892	0.3899		0.1193	False		,,,				2504	0.3793				p.V374A		Atlas-SNP	.											.	MLPH	41	.	0			c.T1121C						PASS	.	T	ALA/VAL,ALA/VAL	3125,1281	690.5+/-405.3	1116,893,194	64.0	61.0	62.0		1037,1121	0.1	0.0	2	dbSNP_107	62	1187,7413	240.1+/-271.0	73,1041,3186	yes	missense,missense	MLPH	NM_001042467.1,NM_024101.5	64,64	1189,1934,3380	CC,CT,TT		13.8023,29.074,33.1539	benign,benign	346/573,374/601	238449007	4312,8694	2203	4300	6503	SO:0001583	missense	79083	exon10			CTGGAGTGCGCAC	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.1121T>C	2.37:g.238449007T>C	ENSP00000264605:p.Val374Ala	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_024101	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	788|788	0.3608058608058608|0.3608058608058608	388|388	0.7886178861788617|0.7886178861788617	96|96	0.26519337016574585|0.26519337016574585	221|221	0.38636363636363635|0.38636363636363635	83|83	0.10949868073878628|0.10949868073878628	T|T	0.772|0.772	-0.765435|-0.765435	0.02996|0.02996	0.70926|0.70926	0.138023|0.138023	ENSG00000115648|ENSG00000115648	ENST00000436965|ENST00000410032;ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373;ENST00000437893	.|T;T;T;T;T;T	.|0.25250	.|2.05;2.17;2.05;2.02;1.81;1.93	4.66|4.66	0.0828|0.0828	0.14430|0.14430	.|.	.|6.460240	.|0.01732	.|N	.|0.028890	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B;B;B;B	.|0.17465	.|0.001;0.002;0.013;0.013;0.005;0.022;0.007;0.001	.|B;B;B;B;B;B;B;B	.|0.16289	.|0.001;0.001;0.01;0.007;0.002;0.015;0.002;0.001	T|T	0.39563|0.39563	-0.9608|-0.9608	4|9	.|0.08837	.|T	.|0.75	-8.0E-4|-8.0E-4	3.5252|3.5252	0.07757|0.07757	0.3479:0.3383:0.0:0.3138|0.3479:0.3383:0.0:0.3138	rs3817362;rs56654643;rs3817362|rs3817362;rs56654643;rs3817362	.|35;374;230;346;306;346;374;231	.|Q53QV8;B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36;G5E9G5	.|.;.;.;.;.;.;MELPH_HUMAN;.	R|A	95|231;374;374;346;306;134	.|ENSP00000386338:V231A;ENSP00000264605:V374A;ENSP00000414849:V374A;ENSP00000341845:V346A;ENSP00000386780:V306A;ENSP00000412438:V134A	.|ENSP00000264605:V374A	C|V	+|+	1|2	0|0	MLPH|MLPH	238113746|238113746	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-1.086000|-1.086000	0.03386|0.03386	-0.239000|-0.239000	0.09710|0.09710	-1.117000|-1.117000	0.02048|0.02048	TGC|GTG	T|0.643;C|0.357	0.357	strong		0.622	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
LRRC16A	55604	hgsc.bcm.edu	37	6	25606442	25606442	+	Missense_Mutation	SNP	A	A	G	rs201300946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:25606442A>G	ENST00000329474.6	+	35	4156	c.3788A>G	c.(3787-3789)aAa>aGa	p.K1263R		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1263					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						CAGTCCCCCAAACCCAGTCTG	0.582													A|||	5	0.000998403	0.0038	0.0	5008	,	,		16648	0.0		0.0	False		,,,				2504	0.0				p.K1263R		Atlas-SNP	.											.	LRRC16A	168	.	0			c.A3788G						PASS	.	A	ARG/LYS,ARG/LYS	10,3848		0,10,1919	42.0	50.0	47.0		3770,3788	5.8	1.0	6		47	0,8290		0,0,4145	yes	missense,missense	LRRC16A	NM_001173977.1,NM_017640.5	26,26	0,10,6064	GG,GA,AA		0.0,0.2592,0.0823	probably-damaging,probably-damaging	1257/1366,1263/1372	25606442	10,12138	1929	4145	6074	SO:0001583	missense	55604	exon35			CCCCCAAACCCAG	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.3788A>G	6.37:g.25606442A>G	ENSP00000331983:p.Lys1263Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_017640	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	37	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.846082	0.91277	0.002592	0.0	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.18657	2.2	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.35422	0.0931	M	0.65975	2.015	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.80764	0.993;0.993;0.994	T	0.05257	-1.0896	10	0.38643	T	0.18	-24.4349	16.2375	0.82384	1.0:0.0:0.0:0.0	.	1263;1257;1218	Q5VZK9;B2RTQ5;Q5VZK9-2	LR16A_HUMAN;.;.	R	1263;1218	ENSP00000331983:K1263R	ENSP00000331983:K1263R	K	+	2	0	LRRC16A	25714421	1.000000	0.71417	0.997000	0.53966	0.878000	0.50629	6.167000	0.71902	2.222000	0.72286	0.533000	0.62120	AAA	.	.	weak		0.582	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
CAPN11	11131	hgsc.bcm.edu	37	6	44151490	44151490	+	Missense_Mutation	SNP	G	G	A	rs7761137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	184	0	0		WXS	Illumina HiSeq	Phase_I	207	203	0.980676	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		
CTNNB1	1499	hgsc.bcm.edu	37	3	41266971	41266971	+	Silent	SNP	C	C	G	rs3856747	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:41266971C>G	ENST00000349496.5	+	5	922	c.642C>G	c.(640-642)acC>acG	p.T214T	CTNNB1_ENST00000453024.1_Silent_p.T207T|CTNNB1_ENST00000396185.3_Silent_p.T214T|CTNNB1_ENST00000405570.1_Silent_p.T214T|CTNNB1_ENST00000396183.3_Silent_p.T214T	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	214					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|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 cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|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)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T214T(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTCGTTGTACCGCTGGGACCT	0.478		15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of				C|||	5	0.000998403	0.0038	0.0	5008	,	,		21290	0.0		0.0	False		,,,				2504	0.0				p.T214T	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,colon,carcinoma,+2,2	CTNNB1	4904	2	1	Substitution - coding silent(1)	cervix(1)	c.C642G						PASS	.						104.0	99.0	101.0					3																	41266971		2203	4300	6503	SO:0001819	synonymous_variant	1499	exon5	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TTGTACCGCTGGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.642C>G	3.37:g.41266971C>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	201	110	0.547264	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	37	CCDS2694.1																																																																																			C|0.994;T|0.006	.	strong		0.478	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
SRMS	6725	hgsc.bcm.edu	37	20	62172269	62172269	+	Missense_Mutation	SNP	C	C	A	rs310654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	60	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	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	
NFU1	27247	hgsc.bcm.edu	37	2	69659126	69659126	+	Missense_Mutation	SNP	A	A	T	rs4453725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69659126A>T	ENST00000410022.2	-	2	279	c.74T>A	c.(73-75)aTg>aAg	p.M25K	NFU1_ENST00000303698.3_Start_Codon_SNP_p.M1K|NFU1_ENST00000471185.1_5'UTR|NFU1_ENST00000394305.1_5'UTR	NM_001002755.2	NP_001002755.1	Q9UMS0	NFU1_HUMAN	NFU1 iron-sulfur cluster scaffold	25			M -> K (in dbSNP:rs4453725). {ECO:0000269|PubMed:12915448, ECO:0000269|PubMed:14702039}.		iron-sulfur cluster assembly (GO:0016226)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron ion binding (GO:0005506)	p.M25K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	7						ATTCTTCAACATATGACAGAA	0.348													a|||	1588	0.317093	0.2526	0.3818	5008	,	,		16119	0.2103		0.4185	False		,,,				2504	0.364				p.M25K		Atlas-SNP	.											NFU1,NS,carcinoma,0,1	NFU1	19	1	1	Substitution - Missense(1)	prostate(1)	c.T74A						scavenged	.	A	LYS/MET,,,LYS/MET	1235,3171	425.5+/-340.8	158,919,1126	113.0	107.0	109.0		74,,,2	3.9	0.1	2	dbSNP_111	109	3671,4929	526.5+/-381.0	815,2041,1444	yes	missense,utr-5,utr-5,missense	NFU1	NM_001002755.1,NM_001002756.1,NM_001002757.1,NM_015700.2	95,,,95	973,2960,2570	TT,TA,AA		42.686,28.03,37.7211	benign,,,benign	25/255,,,1/231	69659126	4906,8100	2203	4300	6503	SO:0001583	missense	27247	exon2			TTCAACATATGAC	AJ132584	CCDS33217.1, CCDS42694.1, CCDS46315.1	2p15-p13	2014-07-03	2014-07-03	2006-10-24	ENSG00000169599	ENSG00000169599			16287	protein-coding gene	gene with protein product		608100	"""HIRA interacting protein 5"", ""NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae)"""	HIRIP5		11342215, 12886008	Standard	NR_045631		Approved	CGI-33, NifU, NIFUC	uc002sfk.3	Q9UMS0	OTTHUMG00000152668	ENST00000410022.2:c.74T>A	2.37:g.69659126A>T	ENSP00000387219:p.Met25Lys	Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001002755	B4DUL9|Q53QE5|Q6VNZ8|Q7Z5B1|Q7Z5B2|Q9Y322	Missense_Mutation	SNP	ENST00000410022.2	37	CCDS33217.1	676	0.30952380952380953	113	0.22967479674796748	138	0.3812154696132597	107	0.18706293706293706	318	0.41952506596306066	A	3.853	-0.031371	0.07543	0.2803	0.42686	ENSG00000169599	ENST00000410022;ENST00000303698	T;T	0.63096	-0.02;0.01	5.1	3.94	0.45596	.	1.058880	0.07247	N	0.865204	T	0.00012	0.0000	N	0.14661	0.345	0.53688	P	2.999999999997449E-5	B;B	0.19817	0.039;0.007	B;B	0.17722	0.019;0.008	T	0.33394	-0.9870	9	0.72032	D	0.01	-1.1234	6.8836	0.24187	0.8227:0.0:0.1773:0.0	rs4453725;rs4453725	1;25	Q9UMS0-3;Q9UMS0	.;NFU1_HUMAN	K	25;1	ENSP00000387219:M25K;ENSP00000306965:M1K	ENSP00000306965:M1K	M	-	2	0	NFU1	69512630	0.001000	0.12720	0.121000	0.21740	0.006000	0.05464	0.978000	0.29488	1.066000	0.40716	-0.261000	0.10672	ATG	A|0.636;T|0.364	0.364	strong		0.348	NFU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327279.3	NM_015700	
RGPD3	653489	hgsc.bcm.edu	37	2	107040985	107040985	+	Silent	SNP	T	T	C	rs140856347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:107040985T>C	ENST00000409886.3	-	20	3525	c.3438A>G	c.(3436-3438)cgA>cgG	p.R1146R	RGPD3_ENST00000304514.7_Silent_p.R1146R	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1146	RanBD1 1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				protein targeting to Golgi (GO:0000042)			p.R1146R(2)		breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TTGCTGCCAATCGCTCTAGTT	0.463													.|||	1440	0.28754	0.1868	0.2378	5008	,	,		15088	0.627		0.16	False		,,,				2504	0.2403				p.R1146R		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	2	2	Substitution - coding silent(2)	kidney(2)	c.A3438G						scavenged	.						17.0	13.0	14.0					2																	107040985		682	1556	2238	SO:0001819	synonymous_variant	653489	exon20			TGCCAATCGCTCT		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.3438A>G	2.37:g.107040985T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	15	14	0.933333	NM_001144013	B8ZZM4	Silent	SNP	ENST00000409886.3	37	CCDS46379.1																																																																																			.	.	weak		0.463	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
SALL3	27164	hgsc.bcm.edu	37	18	76753063	76753063	+	Silent	SNP	C	C	T	rs2472643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:76753063C>T	ENST00000537592.2	+	2	1072	c.1072C>T	c.(1072-1074)Ctg>Ttg	p.L358L	SALL3_ENST00000536229.3_Silent_p.L225L|SALL3_ENST00000575389.2_Silent_p.L358L	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	358					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.L358L(2)		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)		GGCGCCCGGCCTGCCAAGTCC	0.741													C|||	540	0.107827	0.1823	0.0533	5008	,	,		8166	0.0724		0.0666	False		,,,				2504	0.1247				p.L358L		Atlas-SNP	.											SALL3,NS,carcinoma,0,1	SALL3	162	1	2	Substitution - coding silent(2)	prostate(2)	c.C1072T						PASS	.	C		553,3761		41,471,1645	11.0	12.0	11.0		1072	4.4	1.0	18	dbSNP_100	11	622,7876		27,568,3654	no	coding-synonymous	SALL3	NM_171999.2		68,1039,5299	TT,TC,CC		7.3194,12.8187,9.1711		358/1301	76753063	1175,11637	2157	4249	6406	SO:0001819	synonymous_variant	27164	exon2			CCCGGCCTGCCAA	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.1072C>T	18.37:g.76753063C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	23	15	0.652174	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	37	CCDS12013.1																																																																																			C|0.915;T|0.085	0.085	strong		0.741	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
B3GNTL1	146712	hgsc.bcm.edu	37	17	80923536	80923536	+	Silent	SNP	C	C	T	rs4986144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80923536C>T	ENST00000320865.3	-	7	604	c.591G>A	c.(589-591)gaG>gaA	p.E197E	B3GNTL1_ENST00000571954.1_5'UTR|B3GNTL1_ENST00000576599.1_Silent_p.E86E	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	197							transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			CCTGACCTCCCTCGTTAAAGG	0.612													C|||	1117	0.223043	0.233	0.1974	5008	,	,		16277	0.3214		0.2336	False		,,,				2504	0.1155				p.E197E		Atlas-SNP	.											B3GNTL1,NS,malignant_melanoma,0,2	B3GNTL1	40	2	0			c.G591A						PASS	.	C		1013,3393	349.0+/-310.2	129,755,1319	37.0	34.0	35.0		591	2.8	1.0	17	dbSNP_111	35	2503,6095	374.9+/-337.6	338,1827,2134	no	coding-synonymous	B3GNTL1	NM_001009905.1		467,2582,3453	TT,TC,CC		29.1114,22.9914,27.0378		197/362	80923536	3516,9488	2203	4299	6502	SO:0001819	synonymous_variant	146712	exon7			ACCTCCCTCGTTA	AY634364	CCDS32778.1	17q25.3	2013-02-22	2004-01-13	2004-01-14	ENSG00000175711	ENSG00000175711		"""Glycosyltransferase family 2 domain containing"""	21727	protein-coding gene	gene with protein product		615337					Standard	NM_001009905		Approved	B3GNT8	uc002kgg.1	Q67FW5	OTTHUMG00000177788	ENST00000320865.3:c.591G>A	17.37:g.80923536C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	56	35	0.625	NM_001009905	Q6GV30|Q8WUT3	Silent	SNP	ENST00000320865.3	37	CCDS32778.1																																																																																			C|0.739;T|0.261	0.261	strong		0.612	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905	
COL6A2	1292	hgsc.bcm.edu	37	21	47535816	47535816	+	Missense_Mutation	SNP	G	G	A	rs61735835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47535816G>A	ENST00000300527.4	+	6	936	c.832G>A	c.(832-834)Gag>Aag	p.E278K	COL6A2_ENST00000357838.4_Missense_Mutation_p.E278K|COL6A2_ENST00000397763.1_Missense_Mutation_p.E278K|COL6A2_ENST00000310645.5_Missense_Mutation_p.E278K|COL6A2_ENST00000409416.1_Missense_Mutation_p.E278K	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	278	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)		TGAGCCGGGAGAGCCTGGCCA	0.657													G|||	41	0.0081869	0.028	0.0014	5008	,	,		15727	0.003		0.0	False		,,,				2504	0.0				p.E278K		Atlas-SNP	.											.	COL6A2	351	.	0			c.G832A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	105,4295	83.4+/-121.9	2,101,2097	63.0	57.0	59.0		832,832,832	4.0	1.0	21	dbSNP_129	59	2,8596	1.2+/-3.3	0,2,4297	yes	missense,missense,missense	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	56,56,56	2,103,6394	AA,AG,GG		0.0233,2.3864,0.8232	possibly-damaging,possibly-damaging,possibly-damaging	278/1020,278/919,278/829	47535816	107,12891	2200	4299	6499	SO:0001583	missense	1292	exon6			CCGGGAGAGCCTG	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.832G>A	21.37:g.47535816G>A	ENSP00000300527:p.Glu278Lys	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	G	12.81	2.050127	0.36181	0.023864	2.33E-4	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763	D;D;D;D;D	0.94184	-3.37;-3.37;-3.37;-3.37;-3.37	3.98	3.98	0.46160	.	1.534500	0.03661	N	0.242608	T	0.77418	0.4127	N	0.22421	0.69	0.25510	N	0.987462	P;P;P	0.49090	0.897;0.919;0.55	P;P;B	0.51615	0.675;0.514;0.198	T	0.78476	-0.2189	10	0.11485	T	0.65	-9.2802	11.7636	0.51918	0.0:0.0:0.7742:0.2258	rs61735835	278;278;278	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	K	278	ENSP00000300527:E278K;ENSP00000350497:E278K;ENSP00000312529:E278K;ENSP00000387115:E278K;ENSP00000380870:E278K	ENSP00000300527:E278K	E	+	1	0	COL6A2	46360244	0.075000	0.21258	1.000000	0.80357	0.787000	0.44495	0.977000	0.29475	1.956000	0.56807	0.555000	0.69702	GAG	G|0.991;A|0.009	0.009	strong		0.657	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
APEH	327	hgsc.bcm.edu	37	3	49721622	49721622	+	IGR	SNP	C	C	T	rs200268600		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49721622C>T	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Splice_Site_p.G673S|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCGTAGTCACCCTGGCAGGTA	0.567																																					p.G673S		Atlas-SNP	.											MST1,NS,carcinoma,0,2	MST1	84	2	0			c.G2017A						scavenged	.						19.0	19.0	19.0					3																	49721622		2202	4294	6496	SO:0001628	intergenic_variant	4485	exon18			AGTCACCCTGGCA	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49721622C>T		Somatic	501	22	0.0439122		WXS	Illumina HiSeq	Phase_I	556	34	0.0611511	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.4|26.4	4.733873|4.733873	0.89482|0.89482	.|.	.|.	ENSG00000173531|ENSG00000173531	ENST00000448220|ENST00000449682	.|D	.|0.97924	.|-4.61	5.59|5.59	5.59|5.59	0.84812|0.84812	.|.	0.000000|0.000000	0.43260|0.43260	D|D	0.000594|0.000594	D|D	0.98893|0.98893	0.9625|0.9625	M|M	0.86573|0.86573	2.825|2.825	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.77004	.|0.989	D|D	0.99593|0.99593	1.0976|1.0976	6|10	.|0.66056	.|D	.|0.02	.|.	19.5863|19.5863	0.95490|0.95490	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|673	.|G3XAK1	.|.	E|S	142|673	.|ENSP00000414287:G673S	.|ENSP00000414287:G673S	G|G	-|-	2|1	0|0	MST1|MST1	49696626|49696626	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	4.520000|4.520000	0.60524|0.60524	2.621000|2.621000	0.88768|0.88768	0.655000|0.655000	0.94253|0.94253	GGG|GGT	C|0.999;T|0.001	0.001	weak		0.567	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
MYBL2	4605	hgsc.bcm.edu	37	20	42310426	42310426	+	Silent	SNP	C	C	T	rs2227937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42310426C>T	ENST00000217026.4	+	3	244	c.117C>T	c.(115-117)gaC>gaT	p.D39D	MYBL2_ENST00000396863.4_Intron	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	39	HTH myb-type 1. {ECO:0000255|PROSITE- ProRule:PRU00625}.				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)			GTTGGCAGGACGAGCAGCTGA	0.587													C|||	166	0.033147	0.1188	0.013	5008	,	,		19096	0.0		0.0	False		,,,				2504	0.0				p.D39D		Atlas-SNP	.											.	MYBL2	82	.	0			c.C117T						PASS	.	C		478,3928	225.6+/-241.4	29,420,1754	79.0	69.0	72.0		117	-9.2	0.5	20	dbSNP_129	72	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	MYBL2	NM_002466.2		29,424,6050	TT,TC,CC		0.0465,10.8488,3.706		39/701	42310426	482,12524	2203	4300	6503	SO:0001819	synonymous_variant	4605	exon3			GCAGGACGAGCAG		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.117C>T	20.37:g.42310426C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Silent	SNP	ENST00000217026.4	37	CCDS13322.1																																																																																			C|0.967;T|0.033	0.033	strong		0.587	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
DTNBP1	84062	hgsc.bcm.edu	37	6	15523388	15523388	+	Missense_Mutation	SNP	T	T	C	rs73369534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:15523388T>C	ENST00000344537.5	-	10	1046	c.874A>G	c.(874-876)Aga>Gga	p.R292G	DTNBP1_ENST00000355917.3_Missense_Mutation_p.R293G|DTNBP1_ENST00000462989.2_Missense_Mutation_p.R136G	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	292	Dysbindin.				actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			GGCTTGGCTCTTAATTCTGAG	0.532									Hermansky-Pudlak syndrome				t|||	140	0.0279553	0.0998	0.0086	5008	,	,		19166	0.0		0.002	False		,,,				2504	0.0				p.R292G		Atlas-SNP	.											.	DTNBP1	56	.	0			c.A874G						PASS	.	T	GLY/ARG	400,4006	196.4+/-220.7	18,364,1821	154.0	163.0	160.0		874	2.4	0.0	6	dbSNP_130	160	5,8595	4.3+/-15.6	0,5,4295	yes	missense	DTNBP1	NM_032122.4	125	18,369,6116	CC,CT,TT		0.0581,9.0785,3.1139	possibly-damaging	292/352	15523388	405,12601	2203	4300	6503	SO:0001583	missense	84062	exon10	Familial Cancer Database	HPS, HPS1-8	TGGCTCTTAATTC	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17328	protein-coding gene	gene with protein product	"""dysbindin-1"", ""biogenesis of lysosomal organelles complex-1, subunit 8"""	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.874A>G	6.37:g.15523388T>C	ENSP00000341680:p.Arg292Gly	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	133	55	0.413534	NM_032122	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Missense_Mutation	SNP	ENST00000344537.5	37	CCDS4534.1	37	0.01694139194139194	33	0.06707317073170732	4	0.011049723756906077	0	0.0	0	0.0	t	12.91	2.078161	0.36662	0.090785	5.81E-4	ENSG00000047579	ENST00000344537;ENST00000462989;ENST00000355917;ENST00000397306;ENST00000509674	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.42	2.43	0.29744	.	1.442950	0.04672	N	0.410792	T	0.21387	0.0515	M	0.75447	2.3	0.09310	N	1	B	0.25390	0.125	B	0.31390	0.129	T	0.44081	-0.9351	10	0.49607	T	0.09	.	10.1887	0.43013	0.0:0.118:0.41:0.472	.	292	Q96EV8	DTBP1_HUMAN	G	292;136;293;211;109	ENSP00000341680:R292G;ENSP00000427239:R136G;ENSP00000348183:R293G;ENSP00000421797:R109G	ENSP00000341680:R292G	R	-	1	2	DTNBP1	15631367	0.149000	0.22717	0.000000	0.03702	0.104000	0.19210	2.937000	0.48979	0.621000	0.30232	-0.224000	0.12420	AGA	T|0.967;C|0.033	0.033	strong		0.532	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122	
KIAA2018	205717	hgsc.bcm.edu	37	3	113379720	113379720	+	Missense_Mutation	SNP	G	G	A	rs114838141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113379720G>A	ENST00000478658.1	-	5	826	c.809C>T	c.(808-810)tCt>tTt	p.S270F	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.S270F			Q68DE3	K2018_HUMAN	KIAA2018	270						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						TGTGTGCAAAGAATGATGTTG	0.413													G|||	22	0.00439297	0.0166	0.0	5008	,	,		22506	0.0		0.0	False		,,,				2504	0.0				p.S270F		Atlas-SNP	.											.	KIAA2018	180	.	0			c.C809T						PASS	.	G	PHE/SER	49,3769		0,49,1860	60.0	57.0	58.0		809	5.4	0.1	3	dbSNP_132	58	0,8260		0,0,4130	yes	missense	KIAA2018	NM_001009899.2	155	0,49,5990	AA,AG,GG		0.0,1.2834,0.4057	possibly-damaging	270/2246	113379720	49,12029	1909	4130	6039	SO:0001583	missense	205717	exon7			TGCAAAGAATGAT	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.809C>T	3.37:g.113379720G>A	ENSP00000420721:p.Ser270Phe	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	200	78	0.39	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	12.32	1.903297	0.33628	0.012834	0.0	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.17691	2.26;2.26	5.36	5.36	0.76844	.	0.360582	0.24061	N	0.041908	T	0.11281	0.0275	N	0.08118	0	0.30845	N	0.735209	D	0.76494	0.999	D	0.67231	0.95	T	0.04333	-1.0959	10	0.72032	D	0.01	-4.2876	14.9458	0.71029	0.0:0.0:0.8566:0.1433	.	270	Q68DE3	K2018_HUMAN	F	270	ENSP00000320794:S270F;ENSP00000420721:S270F	ENSP00000320794:S270F	S	-	2	0	KIAA2018	114862410	0.990000	0.36364	0.073000	0.20177	0.608000	0.37181	4.214000	0.58527	2.789000	0.95967	0.655000	0.94253	TCT	G|0.996;A|0.004	0.004	strong		0.413	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
OR10X1	128367	hgsc.bcm.edu	37	1	158549082	158549082	+	Missense_Mutation	SNP	A	A	T	rs61755876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158549082A>T	ENST00000368150.1	-	1	607	c.608T>A	c.(607-609)cTg>cAg	p.L203Q		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	203						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)					TATACAAGACAGCCTAATAAC	0.433													A|||	79	0.0157748	0.0582	0.0029	5008	,	,		22248	0.0		0.0	False		,,,				2504	0.0				p.L203Q		Atlas-SNP	.											.	OR10X1	96	.	0			c.T608A						PASS	.	A	GLN/LEU	227,4179	134.9+/-171.1	6,215,1982	85.0	85.0	85.0		608	4.8	0.0	1	dbSNP_129	85	3,8597	2.2+/-6.3	0,3,4297	yes	missense	OR10X1	NM_001004477.1	113	6,218,6279	TT,TA,AA		0.0349,5.1521,1.7684	probably-damaging	203/327	158549082	230,12776	2203	4300	6503	SO:0001583	missense	128367	exon1			CAAGACAGCCTAA	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.608T>A	1.37:g.158549082A>T	ENSP00000357132:p.Leu203Gln	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	207	100	0.483092	NM_001004477	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	37	CCDS30900.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	A	13.52	2.261476	0.39995	0.051521	3.49E-4	ENSG00000186400	ENST00000368150	T	0.00411	7.53	4.8	4.8	0.61643	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37393	N	0.002120	T	0.01124	0.0037	H	0.97390	3.995	0.22684	N	0.998857	D	0.89917	1.0	D	0.97110	1.0	T	0.29701	-1.0003	10	0.87932	D	0	.	13.4538	0.61187	1.0:0.0:0.0:0.0	rs61755876	203	Q8NGY0	O10X1_HUMAN	Q	203	ENSP00000357132:L203Q	ENSP00000357132:L203Q	L	-	2	0	OR10X1	156815706	0.944000	0.32072	0.042000	0.18584	0.176000	0.22953	8.331000	0.90022	1.998000	0.58463	0.455000	0.32223	CTG	A|0.972;T|0.028	0.028	strong		0.433	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477	
PRB2	653247	hgsc.bcm.edu	37	12	11546686	11546686	+	Missense_Mutation	SNP	C	C	T	rs76832300		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11546686C>T	ENST00000389362.4	-	3	361	c.326G>A	c.(325-327)cGa>cAa	p.R109Q	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	109	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			TCGGGGACTTCGGGACTTGTC	0.602																																					p.R109Q		Atlas-SNP	.											PRB2_ENST00000389362,bladder,carcinoma,0,2	PRB2	168	2	0			c.G326A						scavenged	.						324.0	347.0	339.0					12																	11546686		2203	4300	6503	SO:0001583	missense	653247	exon3			GGACTTCGGGACT	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.326G>A	12.37:g.11546686C>T	ENSP00000374013:p.Arg109Gln	Somatic	672	2	0.00297619		WXS	Illumina HiSeq	Phase_I	603	165	0.273632	NM_006248	O00599|P02811|P04281	Missense_Mutation	SNP	ENST00000389362.4	37	CCDS41757.2	.	.	.	.	.	.	.	.	.	.	.	0.127	-1.117972	0.01785	.	.	ENSG00000121335	ENST00000389362	T	0.04083	3.71	1.23	-2.46	0.06461	.	.	.	.	.	T	0.00936	0.0031	N	0.00227	-1.8	0.80722	P	0.0	B	0.23854	0.092	B	0.06405	0.002	T	0.36089	-0.9762	8	0.10902	T	0.67	.	2.7758	0.05347	0.2053:0.2954:0.0:0.4994	.	109	P02812	PRB2_HUMAN	Q	109	ENSP00000374013:R109Q	ENSP00000374013:R109Q	R	-	2	0	PRB2	11437953	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.294000	0.02767	-2.070000	0.00881	-1.096000	0.02151	CGA	.	.	weak		0.602	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
KIAA0754	643314	hgsc.bcm.edu	37	1	39879517	39879517	+	Missense_Mutation	SNP	G	G	A	rs587523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39879517G>A	ENST00000530275.1	+	1	3367	c.3172G>A	c.(3172-3174)Gaa>Aaa	p.E1058K	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000289893.4_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1058	Ala-rich.		E -> K (in dbSNP:rs587523).							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)			CACCCTGGAGGAACCCACTTC	0.637													N|||	206	0.0411342	0.1392	0.0187	5008	,	,		13391	0.002		0.004	False		,,,				2504	0.0031				p.E1194K		Atlas-SNP	.											.	KIAA0754	93	.	0			c.G3580A						PASS	.	G	,,LYS/GLU	469,3435		31,407,1514	18.0	21.0	20.0		,,3580	0.1	0.0	1	dbSNP_83	20	47,8247		0,47,4100	yes	intron,intron,missense	MACF1,KIAA0754	NM_012090.4,NM_033044.3,NM_015038.1	,,56	31,454,5614	AA,AG,GG		0.5667,12.0133,4.2302	,,benign	,,1194/1428	39879517	516,11682	1952	4147	6099	SO:0001583	missense	643314	exon1			CTGGAGGAACCCA			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.3172G>A	1.37:g.39879517G>A	ENSP00000431179:p.Glu1058Lys	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	191	96	0.502618	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		81	0.03708791208791209	73	0.1483739837398374	6	0.016574585635359115	0	0.0	2	0.002638522427440633	N	13.03	2.116599	0.37339	0.120133	0.005667	ENSG00000255103	ENST00000530275	T	0.26223	1.75	3.58	0.0671	0.14364	.	.	.	.	.	T	0.00073	0.0002	N	0.14661	0.345	0.09310	N	1	B	0.27351	0.176	B	0.17433	0.018	T	0.32929	-0.9888	9	0.28530	T	0.3	.	7.1222	0.25450	0.0:0.1645:0.4977:0.3378	rs587523;rs587523	1058	O94854	K0754_HUMAN	K	1058	ENSP00000431179:E1058K	ENSP00000431179:E1058K	E	+	1	0	RP4-562N20.1	39652104	0.089000	0.21612	0.001000	0.08648	0.083000	0.17756	2.290000	0.43531	0.013000	0.14918	0.205000	0.17691	GAA	G|0.932;A|0.068	0.068	strong		0.637	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
GIMAP6	474344	hgsc.bcm.edu	37	7	150325177	150325177	+	Missense_Mutation	SNP	C	C	T	rs11974345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150325177C>T	ENST00000328902.5	-	3	725	c.509G>A	c.(508-510)gGc>gAc	p.G170D	GIMAP6_ENST00000493969.1_3'UTR	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	170	AIG1-type G.		G -> D (in dbSNP:rs11974345).			cytosol (GO:0005829)	GTP binding (GO:0005525)			endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGGGAGCCGCCAGCCAGGTC	0.612													C|||	163	0.0325479	0.1203	0.0058	5008	,	,		16861	0.0		0.0	False		,,,				2504	0.0				p.G240D		Atlas-SNP	.											GIMAP6,NS,carcinoma,+1,1	GIMAP6	60	1	0			c.G719A						PASS	.	C	ASP/GLY	480,3926	224.6+/-240.7	28,424,1751	110.0	112.0	112.0		509	-1.6	0.0	7	dbSNP_120	112	4,8596	3.7+/-12.6	0,4,4296	yes	missense	GIMAP6	NM_024711.5	94	28,428,6047	TT,TC,CC		0.0465,10.8942,3.7214	benign	170/293	150325177	484,12522	2203	4300	6503	SO:0001583	missense	474344	exon3			GAGCCGCCAGCCA	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"""GTPases, IMAP"""	21918	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 6"""					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.509G>A	7.37:g.150325177C>T	ENSP00000330374:p.Gly170Asp	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	CCDS34778.1	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	C	10.17	1.277158	0.23307	0.108942	4.65E-4	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.32272	1.46	4.29	-1.56	0.08532	AIG1 (1);	0.323921	0.26719	N	0.022855	T	0.00241	0.0007	N	0.16708	0.43	0.09310	N	1	B;B	0.18863	0.003;0.031	B;B	0.17433	0.018;0.011	T	0.20240	-1.0281	10	0.12766	T	0.61	.	3.9744	0.09468	0.0:0.2878:0.3552:0.357	rs11974345;rs52826484;rs60915768;rs11974345	170;90	Q6P9H5;Q6P9H5-2	GIMA6_HUMAN;.	D	170;231	ENSP00000330374:G170D	ENSP00000330374:G170D	G	-	2	0	GIMAP6	149956110	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.081000	0.03403	-0.159000	0.11021	-0.304000	0.09214	GGC	C|0.960;T|0.040	0.040	strong		0.612	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711	
OR9Q2	219957	hgsc.bcm.edu	37	11	57958497	57958497	+	Missense_Mutation	SNP	T	T	C	rs34337292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57958497T>C	ENST00000311591.3	+	1	592	c.535T>C	c.(535-537)Tgt>Cgt	p.C179R		NM_001005283.2	NP_001005283.1	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q, member 2	179			C -> R (in dbSNP:rs34337292).			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)|large_intestine(3)|lung(24)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41		Breast(21;0.0589)				CTTCATTTTCTGTGACCTCCC	0.458													T|||	1021	0.203874	0.2806	0.2939	5008	,	,		22568	0.0734		0.2406	False		,,,				2504	0.1329				p.C179R		Atlas-SNP	.											OR9Q2,NS,carcinoma,-1,1	OR9Q2	78	1	0			c.T535C						scavenged	.	T	ARG/CYS	1245,3157	429.5+/-342.2	178,889,1134	112.0	108.0	109.0		535	5.1	1.0	11	dbSNP_126	109	2252,6340	380.7+/-339.8	303,1646,2347	yes	missense	OR9Q2	NM_001005283.2	180	481,2535,3481	CC,CT,TT		26.2104,28.2826,26.9124	probably-damaging	179/315	57958497	3497,9497	2201	4296	6497	SO:0001583	missense	219957	exon1			ATTTTCTGTGACC	AB065859	CCDS31544.1	11q12.1	2012-08-09		2004-03-10	ENSG00000186513	ENSG00000186513		"""GPCR / Class A : Olfactory receptors"""	15328	protein-coding gene	gene with protein product				OR9Q2P			Standard	NM_001005283		Approved		uc010rka.2	Q8NGE9	OTTHUMG00000167414	ENST00000311591.3:c.535T>C	11.37:g.57958497T>C	ENSP00000308714:p.Cys179Arg	Somatic	358	2	0.00558659		WXS	Illumina HiSeq	Phase_I	384	194	0.505208	NM_001005283		Missense_Mutation	SNP	ENST00000311591.3	37	CCDS31544.1	480	0.21978021978021978	139	0.28252032520325204	106	0.292817679558011	53	0.09265734265734266	182	0.24010554089709762	T	19.00	3.741288	0.69304	0.282826	0.262104	ENSG00000186513	ENST00000311591	T	0.62498	0.02	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000074	T	0.00039	0.0001	H	0.97611	4.04	0.09310	P	0.99999999660194	D	0.63880	0.993	D	0.65573	0.936	T	0.01393	-1.1366	9	0.87932	D	0	-13.7757	14.4675	0.67494	0.0:0.0:0.0:1.0	rs34337292	179	Q8NGE9	OR9Q2_HUMAN	R	179	ENSP00000308714:C179R	ENSP00000308714:C179R	C	+	1	0	OR9Q2	57715073	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	4.986000	0.63851	2.264000	0.75181	0.533000	0.62120	TGT	T|0.754;C|0.246	0.246	strong		0.458	OR9Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394540.1	NM_001005283	
RBM19	9904	hgsc.bcm.edu	37	12	114386723	114386723	+	Silent	SNP	G	G	A	rs7979406	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114386723G>A	ENST00000545145.2	-	10	1269	c.1191C>T	c.(1189-1191)gaC>gaT	p.D397D	RBM19_ENST00000392561.3_Silent_p.D397D|RBM19_ENST00000261741.5_Silent_p.D397D	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	397					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)					ATTCGGCCAGGTCCTCCTCCT	0.562													G|||	156	0.0311502	0.1104	0.013	5008	,	,		19228	0.0		0.001	False		,,,				2504	0.0				p.D397D		Atlas-SNP	.											.	RBM19	117	.	0			c.C1191T						PASS	.	G	,,	389,4017	194.0+/-219.0	16,357,1830	180.0	170.0	173.0		1191,1191,1191	4.3	1.0	12	dbSNP_116	173	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	16,360,6127	AA,AG,GG		0.0349,8.8289,3.014	,,	397/961,397/961,397/961	114386723	392,12614	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon10			GGCCAGGTCCTCC	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.1191C>T	12.37:g.114386723G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	247	121	0.489879	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			G|0.971;A|0.029	0.029	strong		0.562	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
OXNAD1	92106	hgsc.bcm.edu	37	3	16327909	16327909	+	Missense_Mutation	SNP	C	C	T	rs6777976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:16327909C>T	ENST00000285083.5	+	5	709	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C	OXNAD1_ENST00000544043.1_Missense_Mutation_p.R100C|OXNAD1_ENST00000435829.2_Missense_Mutation_p.R100C|OXNAD1_ENST00000605932.1_Missense_Mutation_p.R82C|OXNAD1_ENST00000606098.1_Missense_Mutation_p.R82C	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	82	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.		R -> C (in dbSNP:rs6777976). {ECO:0000269|Ref.3}.			mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						GAAGAGCCTCCGCTTGCTTGT	0.463													C|||	888	0.177316	0.2663	0.1081	5008	,	,		19351	0.1696		0.162	False		,,,				2504	0.1299				p.R82C		Atlas-SNP	.											OXNAD1,NS,carcinoma,-1,1	OXNAD1	31	1	0			c.C244T						PASS	.	C	CYS/ARG	1023,3383	378.0+/-322.7	105,813,1285	239.0	200.0	214.0		244	4.4	0.8	3	dbSNP_116	214	1220,7380	245.4+/-274.3	91,1038,3171	yes	missense	OXNAD1	NM_138381.3	180	196,1851,4456	TT,TC,CC		14.186,23.2183,17.2459	benign	82/313	16327909	2243,10763	2203	4300	6503	SO:0001583	missense	92106	exon5			AGCCTCCGCTTGC	AL832787	CCDS2630.1	3p25-p24	2010-03-19			ENSG00000154814	ENSG00000154814			25128	protein-coding gene	gene with protein product						12477932	Standard	NM_138381		Approved	MGC15763	uc003caw.3	Q96HP4	OTTHUMG00000129867	ENST00000285083.5:c.244C>T	3.37:g.16327909C>T	ENSP00000285083:p.Arg82Cys	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	221	105	0.475113	NM_138381	Q2HYC7|Q59FA4	Missense_Mutation	SNP	ENST00000285083.5	37	CCDS2630.1	401	0.18360805860805862	133	0.2703252032520325	40	0.11049723756906077	110	0.19230769230769232	118	0.15567282321899736	C	13.27	2.185915	0.38609	0.232183	0.14186	ENSG00000154814	ENST00000285083;ENST00000435829;ENST00000544043	T;T;T	0.15834	2.39;2.39;2.39	5.26	4.38	0.52667	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);	0.144057	0.64402	N	0.000009	T	0.00012	0.0000	M	0.83384	2.64	0.09310	P	0.999999804086	B;B	0.17038	0.02;0.006	B;B	0.14578	0.011;0.003	T	0.15378	-1.0439	9	0.39692	T	0.17	-8.4499	13.8797	0.63676	0.0:0.9255:0.0:0.0745	rs6777976;rs61694623;rs6777976	100;82	F5H620;Q96HP4	.;OXND1_HUMAN	C	82;82;100	ENSP00000285083:R82C;ENSP00000389872:R82C;ENSP00000437967:R100C	ENSP00000285083:R82C	R	+	1	0	OXNAD1	16302913	0.001000	0.12720	0.824000	0.32777	0.610000	0.37248	0.332000	0.19751	1.204000	0.43247	0.655000	0.94253	CGC	C|0.824;T|0.176	0.176	strong		0.463	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381	
WDSUB1	151525	hgsc.bcm.edu	37	2	160132089	160132089	+	Missense_Mutation	SNP	T	T	G	rs16843852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160132089T>G	ENST00000409990.3	-	4	900	c.644A>C	c.(643-645)aAa>aCa	p.K215T	WDSUB1_ENST00000409124.1_Missense_Mutation_p.K215T|WDSUB1_ENST00000358147.4_Missense_Mutation_p.K215T|WDSUB1_ENST00000359774.4_Missense_Mutation_p.K215T|WDSUB1_ENST00000392796.3_Missense_Mutation_p.K215T	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	215			K -> T (in dbSNP:rs16843852).				ubiquitin-protein transferase activity (GO:0004842)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|stomach(3)	16						AATCCAAATTTTGACTTGGCA	0.299													T|||	1023	0.204273	0.4372	0.0663	5008	,	,		15109	0.2252		0.0348	False		,,,				2504	0.1401				p.K215T		Atlas-SNP	.											.	WDSUB1	39	.	0			c.A644C						PASS	.	T	THR/LYS,THR/LYS,THR/LYS	1677,2729	507.9+/-366.8	328,1021,854	80.0	84.0	82.0		644,644,644	5.5	1.0	2	dbSNP_123	82	380,8218	123.6+/-182.4	6,368,3925	yes	missense,missense,missense	WDSUB1	NM_001128212.1,NM_001128213.1,NM_152528.2	78,78,78	334,1389,4779	GG,GT,TT		4.4196,38.0617,15.8182	probably-damaging,probably-damaging,probably-damaging	215/477,215/477,215/477	160132089	2057,10947	2203	4299	6502	SO:0001583	missense	151525	exon4			CAAATTTTGACTT	AK093494	CCDS2208.1	2q24.2	2013-01-28	2006-02-17	2005-03-25	ENSG00000196151	ENSG00000196151		"""WD repeat domain containing"", ""Sterile alpha motif (SAM) domain containing"", ""U-box domain containing"""	26697	protein-coding gene	gene with protein product			"""WD repeat and SAM domain containing 1"", ""WD repeat, SAM and U-box domain containing 1"""	WDSAM1		12477932	Standard	NM_152528		Approved	UBOX6, FLJ36175	uc002ual.4	Q8N9V3	OTTHUMG00000132028	ENST00000409990.3:c.644A>C	2.37:g.160132089T>G	ENSP00000387078:p.Lys215Thr	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	150	55	0.366667	NM_152528	Q53TI9|Q8N6N8	Missense_Mutation	SNP	ENST00000409990.3	37	CCDS2208.1	418	0.19139194139194138	218	0.44308943089430897	34	0.09392265193370165	137	0.2395104895104895	29	0.03825857519788918	T	19.79	3.892238	0.72524	0.380617	0.044196	ENSG00000196151	ENST00000359774;ENST00000358147;ENST00000392796;ENST00000409990;ENST00000409124	T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.043164	0.85682	D	0.000000	T	0.00012	0.0000	M	0.79123	2.44	0.21841	P	0.999517151	D;D;D	0.71674	0.997;0.998;0.975	P;P;P	0.61592	0.883;0.891;0.677	T	0.45175	-0.9279	9	0.42905	T	0.14	.	10.2792	0.43530	0.0:0.074:0.0:0.926	rs16843852;rs52823421;rs16843852	215;215;215	Q8N9V3-2;B8ZZF2;Q8N9V3	.;.;WSDU1_HUMAN	T	215	ENSP00000352820:K215T;ENSP00000350866:K215T;ENSP00000376545:K215T;ENSP00000387078:K215T;ENSP00000386891:K215T	ENSP00000350866:K215T	K	-	2	0	WDSUB1	159840335	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.292000	0.59031	2.209000	0.71365	0.533000	0.62120	AAA	G|0.185;N|0.000	0.185	strong		0.299	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528	
CLPB	81570	hgsc.bcm.edu	37	11	72040784	72040784	+	Silent	SNP	T	T	C	rs36049191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:72040784T>C	ENST00000294053.3	-	7	1103	c.930A>G	c.(928-930)gaA>gaG	p.E310E	CLPB_ENST00000437826.2_Silent_p.E265E|CLPB_ENST00000340729.5_Silent_p.E251E|CLPB_ENST00000538039.1_Silent_p.E280E|CLPB_ENST00000543042.1_Silent_p.E109E	NM_001258394.1|NM_030813.4	NP_001245323.1|NP_110440.1	Q9H078	CLPB_HUMAN	ClpB caseinolytic peptidase B homolog (E. coli)	310					cellular response to heat (GO:0034605)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	19						GCTTCATCACTTCCCCTTCTC	0.493													T|||	678	0.135383	0.27	0.0937	5008	,	,		19379	0.1577		0.0398	False		,,,				2504	0.0583				p.E310E		Atlas-SNP	.											.	CLPB	45	.	0			c.A930G						PASS	.	T		945,3455	360.9+/-315.4	94,757,1349	102.0	96.0	98.0		930	2.4	1.0	11	dbSNP_126	98	265,8321	102.9+/-164.1	2,261,4030	no	coding-synonymous	CLPB	NM_030813.3		96,1018,5379	CC,CT,TT		3.0864,21.4773,9.3177		310/708	72040784	1210,11776	2200	4293	6493	SO:0001819	synonymous_variant	81570	exon7			CATCACTTCCCCT	BC006404	CCDS8215.1, CCDS58152.1, CCDS58153.1, CCDS58154.1	11q13.4	2013-01-10			ENSG00000162129	ENSG00000162129		"""Ankyrin repeat domain containing"""	30664	protein-coding gene	gene with protein product	"""suppressor of potassium transport defect 3"""					11230166, 7835694	Standard	NM_030813		Approved	HSP78, SKD3, FLJ13152	uc010rqy.3	Q9H078	OTTHUMG00000167902	ENST00000294053.3:c.930A>G	11.37:g.72040784T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_030813	B4DXJ7|B4DXP7|E7EWN6|F8W7P6|Q8ND11|Q9H8Y0	Silent	SNP	ENST00000294053.3	37	CCDS8215.1	257	0.11767399267399267	116	0.23577235772357724	35	0.09668508287292818	79	0.1381118881118881	27	0.03562005277044855	T	1.116	-0.656719	0.03480	0.214773	0.030864	ENSG00000162129	ENST00000544382	.	.	.	5.43	2.39	0.29439	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999975282	.	.	.	.	.	.	T	0.10941	-1.0608	3	.	.	.	-22.2024	8.4064	0.32616	0.0:0.6921:0.0:0.3079	rs36049191;rs60307678	.	.	.	R	88	.	.	K	-	2	0	CLPB	71718432	0.974000	0.33945	1.000000	0.80357	0.105000	0.19272	0.048000	0.14078	0.195000	0.20347	-0.290000	0.09829	AAG	C|0.101;T|0.899	0.101	strong		0.493	CLPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396889.1	NM_030813	
OR5H1	26341	hgsc.bcm.edu	37	3	97851689	97851689	+	Missense_Mutation	SNP	T	T	C	rs201501927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:97851689T>C	ENST00000354565.2	+	1	148	c.148T>C	c.(148-150)Tgg>Cgg	p.W50R	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.W50R(4)		breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						TGCTGTCATCTGGAAAGACCC	0.418																																					p.W50R		Atlas-SNP	.											OR5H1,NS,carcinoma,0,4	OR5H1	71	4	4	Substitution - Missense(4)	endometrium(2)|kidney(2)	c.T148C						scavenged	.						56.0	59.0	58.0					3																	97851689		2193	4271	6464	SO:0001583	missense	26341	exon1			GTCATCTGGAAAG	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.148T>C	3.37:g.97851689T>C	ENSP00000346575:p.Trp50Arg	Somatic	913	5	0.00547645		WXS	Illumina HiSeq	Phase_I	1086	26	0.0239411	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	37	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	T	5.108	0.205565	0.09704	.	.	ENSG00000231192	ENST00000354565	T	0.03801	3.8	3.63	2.42	0.29668	GPCR, rhodopsin-like superfamily (1);	0.983509	0.08277	N	0.970503	T	0.05135	0.0137	N	0.04162	-0.26	0.22435	N	0.999102	D	0.56968	0.978	P	0.55871	0.786	T	0.50145	-0.8862	10	0.24483	T	0.36	.	8.0198	0.30402	0.0:0.0:0.2075:0.7924	.	50	A6NKK0	OR5H1_HUMAN	R	50	ENSP00000346575:W50R	ENSP00000346575:W50R	W	+	1	0	OR5H1	99334379	0.000000	0.05858	0.978000	0.43139	0.160000	0.22226	-0.055000	0.11807	0.438000	0.26450	0.164000	0.16699	TGG	T|0.796;C|0.204	0.204	strong		0.418	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338	
DHRS4	10901	hgsc.bcm.edu	37	14	24423090	24423090	+	Silent	SNP	A	A	G	rs2273944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24423090A>G	ENST00000313250.5	+	1	296	c.93A>G	c.(91-93)gcA>gcG	p.A31A	DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000397075.3_Silent_p.A31A|DHRS4_ENST00000397073.2_Silent_p.A13A|DHRS4_ENST00000382761.3_Silent_p.A13A|DHRS4_ENST00000397074.3_Silent_p.A31A|DHRS4_ENST00000559632.1_Silent_p.A31A|DHRS4_ENST00000543741.2_Silent_p.A31A|DHRS4_ENST00000308178.8_Silent_p.A13A|DHRS4_ENST00000558263.1_Silent_p.A31A|DHRS4_ENST00000421831.1_Silent_p.A13A|DHRS4_ENST00000558581.1_Silent_p.A31A	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	88	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	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		
AHNAK2	113146	hgsc.bcm.edu	37	14	105408811	105408811	+	Missense_Mutation	SNP	A	A	G	rs2819421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105408811A>G	ENST00000333244.5	-	7	13096	c.12977T>C	c.(12976-12978)cTg>cCg	p.L4326P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4326			L -> P (in dbSNP:rs2819421).			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)			CTCCACCTTCAGCGCAGACAC	0.597													G|||	2780	0.555112	0.6679	0.513	5008	,	,		19403	0.38		0.5338	False		,,,				2504	0.635				p.L4326P		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T12977C						PASS	.	G	PRO/LEU	2635,1275		874,887,194	157.0	171.0	166.0		12977	1.4	0.0	14	dbSNP_100	166	4459,3815		1220,2019,898	no	missense	AHNAK2	NM_138420.2	98	2094,2906,1092	GG,GA,AA		46.1083,32.6087,41.7761	benign	4326/5796	105408811	7094,5090	1955	4137	6092	SO:0001583	missense	113146	exon7			ACCTTCAGCGCAG	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.12977T>C	14.37:g.105408811A>G	ENSP00000353114:p.Leu4326Pro	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	238	108	0.453782	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1044	0.47802197802197804	310	0.6300813008130082	185	0.511049723756906	183	0.31993006993006995	366	0.48284960422163586	a	7.511	0.654684	0.14580	0.673913	0.538917	ENSG00000185567	ENST00000333244	T	0.00479	7.12	3.31	1.41	0.22369	.	0.000000	0.36200	N	0.002733	T	0.00012	0.0000	N	0.00007	-3.15	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17684	-1.0361	9	0.15952	T	0.53	.	8.0779	0.30726	0.2793:0.0:0.7207:0.0	rs2819421	4326	Q8IVF2	AHNK2_HUMAN	P	4326	ENSP00000353114:L4326P	ENSP00000353114:L4326P	L	-	2	0	AHNAK2	104479856	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.284000	0.18864	-0.311000	0.08754	-0.665000	0.03846	CTG	A|0.505;G|0.495	0.495	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
POLR3A	11128	hgsc.bcm.edu	37	10	79781326	79781326	+	Missense_Mutation	SNP	T	T	C	rs550436426		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79781326T>C	ENST00000372371.3	-	8	1300	c.1163A>G	c.(1162-1164)aAa>aGa	p.K388R	POLR3A_ENST00000484760.1_5'Flank	NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	388					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			AGTTAGAATTTTGGCCACATG	0.423													T|||	1	0.000199681	0.0008	0.0	5008	,	,		18712	0.0		0.0	False		,,,				2504	0.0				p.K388R		Atlas-SNP	.											.	POLR3A	104	.	0			c.A1163G						PASS	.						74.0	71.0	72.0					10																	79781326		2203	4300	6503	SO:0001583	missense	11128	exon8			AGAATTTTGGCCA	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"""RNA polymerase subunits"""	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.1163A>G	10.37:g.79781326T>C	ENSP00000361446:p.Lys388Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845255	0.91197	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.68331	-0.32	5.58	5.58	0.84498	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.62258	0.2413	L	0.41906	1.305	0.80722	D	1	P	0.46578	0.88	B	0.44133	0.442	T	0.61705	-0.7008	9	.	.	.	-24.6898	16.0507	0.80760	0.0:0.0:0.0:1.0	.	388	O14802	RPC1_HUMAN	R	388	ENSP00000361446:K388R	.	K	-	2	0	POLR3A	79451332	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.646000	0.83445	2.243000	0.73865	0.528000	0.53228	AAA	.	.	none		0.423	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055	
C5orf60	285679	hgsc.bcm.edu	37	5	179069413	179069413	+	Missense_Mutation	SNP	A	A	G	rs374415765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179069413A>G	ENST00000448248.2	-	5	786	c.761T>C	c.(760-762)aTa>aCa	p.I254T	C5orf60_ENST00000506142.1_5'Flank	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	143						integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						TTGGTGTCTTATGCGTCCAGC	0.562													a|||	117	0.0233626	0.0832	0.0072	5008	,	,		18498	0.0		0.002	False		,,,				2504	0.0				p.I254T		Atlas-SNP	.											.	C5orf60	24	.	0			c.T761C						PASS	.						200.0	171.0	180.0					5																	179069413		692	1591	2283	SO:0001583	missense	285679	exon5			TGTCTTATGCGTC	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.761T>C	5.37:g.179069413A>G	ENSP00000404583:p.Ile254Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	111	35	0.315315	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	37	CCDS47353.1	.	.	.	.	.	.	.	.	.	.	N	0.018	-1.471398	0.01044	.	.	ENSG00000204661	ENST00000448248	T	0.23147	1.92	0.226	0.226	0.15353	.	.	.	.	.	T	0.11580	0.0282	.	.	.	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36890	-0.9729	7	0.15499	T	0.54	.	.	.	.	.	258;254	A6NFR6-2;A6NFR6-4	.;.	T	254	ENSP00000404583:I254T	ENSP00000404583:I254T	I	-	2	0	C5orf60	179002019	0.079000	0.21365	0.036000	0.18154	0.053000	0.15095	-0.873000	0.04214	-0.682000	0.05197	-0.674000	0.03794	ATA	.	.	weak		0.562	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
LILRA4	23547	hgsc.bcm.edu	37	19	54848121	54848121	+	Missense_Mutation	SNP	C	C	T	rs141881690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54848121C>T	ENST00000291759.4	-	6	1302	c.1246G>A	c.(1246-1248)Gtg>Atg	p.V416M	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	416					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)		CCTGAGACCACGAGCTCCAGG	0.597													C|||	158	0.0315495	0.0613	0.0101	5008	,	,		18423	0.0		0.0109	False		,,,				2504	0.0603				p.V416M		Atlas-SNP	.											.	LILRA4	91	.	0			c.G1246A						PASS	.						80.0	67.0	71.0					19																	54848121		2203	4300	6503	SO:0001583	missense	23547	exon6			AGACCACGAGCTC	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.1246G>A	19.37:g.54848121C>T	ENSP00000291759:p.Val416Met	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	257	37	0.143969	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	6.736	0.504546	0.12822	.	.	ENSG00000239961	ENST00000291759	T	0.00848	5.62	2.4	-4.8	0.03190	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.277830	0.01713	N	0.027839	T	0.01489	0.0048	M	0.61703	1.905	0.09310	N	1	B	0.18166	0.026	B	0.17433	0.018	T	0.42816	-0.9429	10	0.33141	T	0.24	.	7.5849	0.27987	0.0:0.1789:0.6361:0.185	.	416	P59901	LIRA4_HUMAN	M	416	ENSP00000291759:V416M	ENSP00000291759:V416M	V	-	1	0	LILRA4	59539933	0.000000	0.05858	0.000000	0.03702	0.190000	0.23558	-4.042000	0.00307	-1.656000	0.01495	0.455000	0.32223	GTG	C|0.999;T|0.001	0.001	weak		0.597	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
TRPV4	59341	hgsc.bcm.edu	37	12	110238481	110238481	+	Silent	SNP	G	G	A	rs1344554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:110238481G>A	ENST00000418703.2	-	4	889	c.795C>T	c.(793-795)caC>caT	p.H265H	TRPV4_ENST00000536838.1_Silent_p.H231H|TRPV4_ENST00000544971.1_Intron|TRPV4_ENST00000346520.2_Silent_p.H265H|TRPV4_ENST00000261740.2_Silent_p.H265H|TRPV4_ENST00000537083.1_Silent_p.H265H|TRPV4_ENST00000392719.2_Intron|TRPV4_ENST00000541794.1_Intron	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	265					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						GGGCCTGGGCGTGGACATCAG	0.632													G|||	526	0.105032	0.1717	0.0764	5008	,	,		16886	0.0278		0.0447	False		,,,				2504	0.1769				p.H265H		Atlas-SNP	.											.	TRPV4	88	.	0			c.C795T						PASS	.	G	,,,,	677,3729	285.5+/-278.2	58,561,1584	75.0	61.0	66.0		,693,,795,795	-3.0	1.0	12	dbSNP_88	66	374,8226	123.2+/-182.1	6,362,3932	no	intron,coding-synonymous,intron,coding-synonymous,coding-synonymous	TRPV4	NM_001177428.1,NM_001177431.1,NM_001177433.1,NM_021625.4,NM_147204.2	,,,,	64,923,5516	AA,AG,GG		4.3488,15.3654,8.0809	,,,,	,231/838,,265/872,265/812	110238481	1051,11955	2203	4300	6503	SO:0001819	synonymous_variant	59341	exon4			CTGGGCGTGGACA	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18083	protein-coding gene	gene with protein product	"""osmosensitive transient receptor potential channel 4"""	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.795C>T	12.37:g.110238481G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_147204	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Silent	SNP	ENST00000418703.2	37	CCDS9134.1																																																																																			G|0.922;A|0.078	0.078	strong		0.632	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625	
C6orf118	168090	hgsc.bcm.edu	37	6	165715460	165715460	+	Silent	SNP	G	G	C	rs9459355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:165715460G>C	ENST00000230301.8	-	2	371	c.351C>G	c.(349-351)gcC>gcG	p.A117A	C6orf118_ENST00000543069.1_Silent_p.A13A	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	117										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)		TGGGGACCAGGGCCGTGTGGA	0.662													C|||	809	0.161542	0.357	0.1052	5008	,	,		16632	0.0129		0.1551	False		,,,				2504	0.0971				p.A117A		Atlas-SNP	.											.	C6orf118	116	.	0			c.C351G						PASS	.	C		1468,2938	677.8+/-403.4	254,960,989	65.0	69.0	68.0		351	-10.2	0.0	6	dbSNP_119	68	1227,7373	760.8+/-407.6	87,1053,3160	no	coding-synonymous	C6orf118	NM_144980.3		341,2013,4149	CC,CG,GG		14.2674,33.3182,20.7212		117/470	165715460	2695,10311	2203	4300	6503	SO:0001819	synonymous_variant	168090	exon2			GACCAGGGCCGTG		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.351C>G	6.37:g.165715460G>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_144980	Q8TC11	Silent	SNP	ENST00000230301.8	37	CCDS5288.1																																																																																			G|0.804;C|0.196	0.196	strong		0.662	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
SORCS2	57537	hgsc.bcm.edu	37	4	7741941	7741941	+	Missense_Mutation	SNP	G	G	A	rs189272447		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:7741941G>A	ENST00000507866.2	+	27	3539	c.3430G>A	c.(3430-3432)Gtg>Atg	p.V1144M	SORCS2_ENST00000329016.9_Missense_Mutation_p.V987M	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	1144					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						CCACTCAGGCGTGGTCCTGAG	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16669	0.0		0.0	False		,,,				2504	0.0				p.V1144M		Atlas-SNP	.											.	SORCS2	98	.	0			c.G3430A						PASS	.	G	MET/VAL	4,4138		0,4,2067	44.0	48.0	47.0		3430	3.8	0.9	4		47	1,8397		0,1,4198	yes	missense	SORCS2	NM_020777.2	21	0,5,6265	AA,AG,GG		0.0119,0.0966,0.0399	probably-damaging	1144/1160	7741941	5,12535	2071	4199	6270	SO:0001583	missense	57537	exon27			TCAGGCGTGGTCC	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.3430G>A	4.37:g.7741941G>A	ENSP00000422185:p.Val1144Met	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	19	8	0.421053	NM_020777	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	37	CCDS47008.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	21.3	4.122447	0.77436	9.66E-4	1.19E-4	ENSG00000184985	ENST00000507866;ENST00000329016;ENST00000505529	T;T	0.19394	2.17;2.15	3.78	3.78	0.43462	.	0.167836	0.25948	U	0.027280	T	0.38295	0.1035	L	0.60455	1.87	0.58432	D	0.999996	D;D	0.76494	0.999;0.958	P;B	0.58970	0.849;0.13	T	0.39375	-0.9617	10	0.87932	D	0	.	15.8127	0.78576	0.0:0.0:1.0:0.0	.	987;1144	B5MED8;Q96PQ0	.;SORC2_HUMAN	M	1144;987;86	ENSP00000422185:V1144M;ENSP00000329124:V987M	ENSP00000329124:V987M	V	+	1	0	SORCS2	7792841	1.000000	0.71417	0.893000	0.35052	0.845000	0.48019	7.974000	0.88039	1.935000	0.56089	0.561000	0.74099	GTG	G|0.999;A|0.001	0.001	strong		0.617	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	
CCS	9973	hgsc.bcm.edu	37	11	66366682	66366682	+	Missense_Mutation	SNP	G	G	A	rs61731812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:66366682G>A	ENST00000533244.1	+	3	649	c.208G>A	c.(208-210)Ggg>Agg	p.G70R	CCS_ENST00000310190.4_Missense_Mutation_p.G51R	NM_005125.1	NP_005116.1	O14618	CCS_HUMAN	copper chaperone for superoxide dismutase	70	HMA. {ECO:0000255|PROSITE- ProRule:PRU00280}.				copper ion transmembrane transport (GO:0035434)|intracellular copper ion transport (GO:0015680)|positive regulation of oxidoreductase activity (GO:0051353)|removal of superoxide radicals (GO:0019430)|superoxide metabolic process (GO:0006801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|protein disulfide oxidoreductase activity (GO:0015035)|superoxide dismutase activity (GO:0004784)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|large_intestine(2)|lung(3)|stomach(1)	9						GGAAGGCACGGGGCGGCAGGC	0.642													G|||	21	0.00419329	0.0144	0.0029	5008	,	,		18662	0.0		0.0	False		,,,				2504	0.0				p.G70R		Atlas-SNP	.											.	CCS	22	.	0			c.G208A						PASS	.	G	ARG/GLY	48,4352	50.9+/-86.3	0,48,2152	68.0	59.0	62.0		208	4.9	1.0	11	dbSNP_129	62	0,8590		0,0,4295	yes	missense	CCS	NM_005125.1	125	0,48,6447	AA,AG,GG		0.0,1.0909,0.3695	probably-damaging	70/275	66366682	48,12942	2200	4295	6495	SO:0001583	missense	9973	exon3			GGCACGGGGCGGC	AF002210	CCDS8146.1	11q13.2	2012-09-20			ENSG00000173992	ENSG00000173992			1613	protein-coding gene	gene with protein product		603864				9295278	Standard	NM_005125		Approved		uc001oir.3	O14618	OTTHUMG00000167238	ENST00000533244.1:c.208G>A	11.37:g.66366682G>A	ENSP00000436318:p.Gly70Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	57	0.626374	NM_005125	Q2M366|Q8NEV0	Missense_Mutation	SNP	ENST00000533244.1	37	CCDS8146.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	27.6	4.842813	0.91197	0.010909	0.0	ENSG00000173992	ENST00000533244;ENST00000310190	D;D	0.94092	-3.35;-2.58	4.87	4.87	0.63330	Heavy metal-associated domain, HMA (3);	0.000000	0.85682	D	0.000000	D	0.97417	0.9155	H	0.99261	4.49	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96137	0.9097	10	0.87932	D	0	.	13.3773	0.60747	0.0:0.0:1.0:0.0	rs61731812	70	O14618	CCS_HUMAN	R	70;51	ENSP00000436318:G70R;ENSP00000307870:G51R	ENSP00000307870:G51R	G	+	1	0	CCS	66123258	1.000000	0.71417	0.955000	0.39395	0.970000	0.65996	7.533000	0.81994	2.546000	0.85860	0.561000	0.74099	GGG	G|0.996;A|0.004	0.004	strong		0.642	CCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393826.1	NM_005125	
SMARCA2	6595	hgsc.bcm.edu	37	9	2116037	2116037	+	Silent	SNP	G	G	A	rs6601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2116037G>A	ENST00000382203.1	+	25	3881	c.3672G>A	c.(3670-3672)gaG>gaA	p.E1224E	SMARCA2_ENST00000349721.2_Silent_p.E1224E|SMARCA2_ENST00000357248.2_Silent_p.E1224E|SMARCA2_ENST00000382194.1_Silent_p.E1224E			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	1224					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|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)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		TGGAGCATGAGGAGGAAAATG	0.448											OREG0019074	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1179	0.235423	0.6838	0.1009	5008	,	,		17552	0.0188		0.1024	False		,,,				2504	0.0849				p.E1224E		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G3672A						PASS	.	A	,	2562,1844	529.7+/-372.7	765,1032,406	30.0	33.0	32.0		3672,3672	-6.9	0.2	9	dbSNP_52	32	924,7676	774.3+/-407.7	53,818,3429	no	coding-synonymous,coding-synonymous	SMARCA2	NM_003070.3,NM_139045.2	,	818,1850,3835	AA,AG,GG		10.7442,41.852,26.803	,	1224/1591,1224/1573	2116037	3486,9520	2203	4300	6503	SO:0001819	synonymous_variant	6595	exon25			GCATGAGGAGGAA	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.3672G>A	9.37:g.2116037G>A		Somatic	85	0	0	601	WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			A|0.255;G|0.745;T|0.000	0.255	strong		0.448	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
SNX4	8723	hgsc.bcm.edu	37	3	125179676	125179676	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125179676C>T	ENST00000251775.4	-	10	907	c.883G>A	c.(883-885)Gaa>Aaa	p.E295K	SNX4_ENST00000536067.1_Missense_Mutation_p.E150K	NM_003794.2	NP_003785.1	O95219	SNX4_HUMAN	sorting nexin 4	295					endocytic recycling (GO:0032456)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|early endosome membrane (GO:0031901)|membrane (GO:0016020)|protein complex (GO:0043234)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			breast(2)|central_nervous_system(1)|lung(6)|ovary(1)|skin(1)	11						TCTTCATCTTCCAAAATATCA	0.333																																					p.E295K		Atlas-SNP	.											.	SNX4	29	.	0			c.G883A						PASS	.						85.0	82.0	83.0					3																	125179676		2202	4298	6500	SO:0001583	missense	8723	exon10			CATCTTCCAAAAT	AF065485	CCDS3032.1	3q21.2	2014-02-12			ENSG00000114520	ENSG00000114520		"""Sorting nexins"""	11175	protein-coding gene	gene with protein product		605931				9819414	Standard	NM_003794		Approved	ATG24B	uc003eib.4	O95219	OTTHUMG00000159575	ENST00000251775.4:c.883G>A	3.37:g.125179676C>T	ENSP00000251775:p.Glu295Lys	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	196	94	0.479592	NM_003794	B3KMH0|B4DQV4|D3DNA3	Missense_Mutation	SNP	ENST00000251775.4	37	CCDS3032.1	.	.	.	.	.	.	.	.	.	.	C	30	5.053128	0.93793	.	.	ENSG00000114520	ENST00000251775;ENST00000536067	T;T	0.76578	-1.03;-1.03	5.34	5.34	0.76211	.	0.513245	0.21868	N	0.067933	D	0.86451	0.5936	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.68353	0.957	D	0.83631	0.0145	10	0.29301	T	0.29	-16.9581	17.4034	0.87467	0.0:1.0:0.0:0.0	.	295	O95219	SNX4_HUMAN	K	295;150	ENSP00000251775:E295K;ENSP00000440824:E150K	ENSP00000251775:E295K	E	-	1	0	SNX4	126662366	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.541000	0.73865	2.776000	0.95493	0.650000	0.86243	GAA	.	.	none		0.333	SNX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356299.1	NM_003794	
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1628965	1628965	+	Silent	SNP	G	G	A	rs57186801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1628965G>A	ENST00000399685.1	-	1	728	c.651C>T	c.(649-651)agC>agT	p.S217S		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	217	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)		GCTTgcagcagctggactggc	0.607													g|||	2317	0.46266	0.4962	0.4524	5008	,	,		18609	0.3889		0.5239	False		,,,				2504	0.4376				p.S217S		Atlas-SNP	.											.	KRTAP5-3	33	.	0			c.C651T						PASS	.	G		2171,2233	571.1+/-383.0	545,1081,576	142.0	148.0	146.0		651	1.2	1.0	11	dbSNP_129	146	4694,3904	603.4+/-394.7	1312,2070,917	no	coding-synonymous	KRTAP5-3	NM_001012708.2		1857,3151,1493	AA,AG,GG		45.4059,49.2961,47.2004		217/239	1628965	6865,6137	2202	4299	6501	SO:0001819	synonymous_variant	387266	exon1			GCAGCAGCTGGAC	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.651C>T	11.37:g.1628965G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	201	200	0.995025	NM_001012708	Q6PL44|Q701N3	Silent	SNP	ENST00000399685.1	37	CCDS41591.1																																																																																			G|0.525;A|0.475	0.475	strong		0.607	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1		
C11orf21	29125	hgsc.bcm.edu	37	11	2320884	2320884	+	Silent	SNP	A	A	G	rs1501466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2320884A>G	ENST00000381153.3	-	3	452	c.201T>C	c.(199-201)ggT>ggC	p.G67G	C11orf21_ENST00000470369.1_5'UTR|TSPAN32_ENST00000381121.3_5'Flank|TSPAN32_ENST00000182290.4_5'Flank			Q9P2W6	CK021_HUMAN	chromosome 11 open reading frame 21	67						cytoplasm (GO:0005737)											GAACAAGGGCACCATGGGCGG	0.627													G|||	1056	0.210863	0.3865	0.2262	5008	,	,		15372	0.0704		0.164	False		,,,				2504	0.1554				p.G113G		Atlas-SNP	.											C11orf21,NS,carcinoma,-2,1	C11orf21	11	1	0			c.T339C						scavenged	.	G		494,890		82,330,280	119.0	127.0	125.0		339	-0.2	0.0	11	dbSNP_88	125	538,2644		49,440,1102	no	coding-synonymous	C11orf21	NM_001142946.1		131,770,1382	GG,GA,AA		16.9076,35.6936,22.6018		113/179	2320884	1032,3534	692	1591	2283	SO:0001819	synonymous_variant	29125	exon4			AAGGGCACCATGG	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.201T>C	11.37:g.2320884A>G		Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	210	90	0.428571	NM_001142946		Silent	SNP	ENST00000381153.3	37																																																																																				A|0.799;G|0.201	0.201	strong		0.627	C11orf21-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000026908.2	NM_001142946	
OR4N2	390429	hgsc.bcm.edu	37	14	20295972	20295972	+	Missense_Mutation	SNP	G	G	A	rs76952476	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20295972G>A	ENST00000315947.1	+	1	365	c.365G>A	c.(364-366)cGc>cAc	p.R122H	OR4N2_ENST00000568211.1_Missense_Mutation_p.R122H	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|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)		GCCTTTGACCGCTACATCGCC	0.507													.|||	121	0.0241613	0.09	0.0029	5008	,	,		28676	0.0		0.0	False		,,,				2504	0.0				p.R122H		Atlas-SNP	.											OR4N2,NS,carcinoma,+1,5	OR4N2	125	5	0			c.G365A						PASS	.	G	HIS/ARG	333,4073		8,317,1878	158.0	168.0	165.0		365	4.5	1.0	14	dbSNP_131	165	3,8597		0,3,4297	no	missense	OR4N2	NM_001004723.1	29	8,320,6175	AA,AG,GG		0.0349,7.5579,2.5834	probably-damaging	122/308	20295972	336,12670	2203	4300	6503	SO:0001583	missense	390429	exon1			TTGACCGCTACAT		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.365G>A	14.37:g.20295972G>A	ENSP00000319601:p.Arg122His	Somatic	486	0	0		WXS	Illumina HiSeq	Phase_I	383	171	0.446475	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	.	18.31	3.594861	0.66219	0.075579	3.49E-4	ENSG00000176294	ENST00000557677;ENST00000315947	D;T	0.97161	-4.27;-1.1	4.53	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000113	T	0.66665	0.2812	M	0.90252	3.1	0.36488	D	0.868276	B	0.34103	0.437	B	0.30782	0.12	T	0.83054	-0.0151	10	0.72032	D	0.01	-14.9923	15.1112	0.72359	0.0:0.0:1.0:0.0	.	122	Q8NGD1	OR4N2_HUMAN	H	122	ENSP00000452022:R122H;ENSP00000319601:R122H	ENSP00000319601:R122H	R	+	2	0	OR4N2	19365812	0.992000	0.36948	1.000000	0.80357	0.999000	0.98932	5.956000	0.70315	2.488000	0.83962	0.591000	0.81541	CGC	G|0.977;A|0.023	0.023	strong		0.507	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
ROBO2	6092	hgsc.bcm.edu	37	3	77614215	77614215	+	Missense_Mutation	SNP	T	T	C	rs185792666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:77614215T>C	ENST00000461745.1	+	12	2693	c.1793T>C	c.(1792-1794)aTc>aCc	p.I598T	ROBO2_ENST00000487694.3_Missense_Mutation_p.I614T|ROBO2_ENST00000332191.8_Missense_Mutation_p.I598T	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	598	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GTCAGAGCGATCAACCCCCAA	0.498													T|||	10	0.00199681	0.0	0.0086	5008	,	,		17327	0.0		0.004	False		,,,				2504	0.0				p.I598T		Atlas-SNP	.											.	ROBO2	527	.	0			c.T1793C						PASS	.	T	THR/ILE,THR/ILE	2,3978		0,2,1988	131.0	129.0	130.0		1841,1793	6.0	1.0	3		130	43,8283		0,43,4120	yes	missense,missense	ROBO2	NM_001128929.2,NM_002942.4	89,89	0,45,6108	CC,CT,TT		0.5165,0.0503,0.3657	possibly-damaging,possibly-damaging	614/1395,598/1379	77614215	45,12261	1990	4163	6153	SO:0001583	missense	6092	exon12			GAGCGATCAACCC	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.1793T>C	3.37:g.77614215T>C	ENSP00000417164:p.Ile598Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	5	0.0022893772893772895	0	0.0	5	0.013812154696132596	0	0.0	0	0.0	T	17.82	3.482426	0.63962	5.03E-4	0.005165	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.57595	0.39;0.39;0.39	6.02	6.02	0.97574	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.46758	D	0.000269	T	0.47135	0.1429	N	0.25890	0.77	0.39849	D	0.973215	P;P;B	0.35411	0.486;0.5;0.296	P;P;P	0.50825	0.651;0.588;0.651	T	0.51340	-0.8718	9	0.20519	T	0.43	.	16.542	0.84395	0.0:0.0:0.0:1.0	.	614;598;598	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	T	614;614;618;598;598;319	ENSP00000417335:I614T;ENSP00000417164:I598T;ENSP00000327536:I598T	ENSP00000327536:I598T	I	+	2	0	ROBO2	77696905	1.000000	0.71417	0.995000	0.50966	0.962000	0.63368	5.141000	0.64814	2.304000	0.77564	0.528000	0.53228	ATC	T|0.996;C|0.004	0.004	strong		0.498	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246	
RPP40	10799	hgsc.bcm.edu	37	6	4996611	4996611	+	Missense_Mutation	SNP	T	T	G	rs61730291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4996611T>G	ENST00000380051.2	-	6	647	c.603A>C	c.(601-603)caA>caC	p.Q201H	RPP40_ENST00000464646.1_Missense_Mutation_p.Q141H|RPP40_ENST00000319533.5_Missense_Mutation_p.Q178H	NM_006638.2	NP_006629.2	O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	201					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			NS(1)|breast(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	14	Ovarian(93;0.11)	all_hematologic(90;0.0895)				GCTCCTGAATTTGGTACTTGG	0.473													T|||	158	0.0315495	0.115	0.0086	5008	,	,		19568	0.0		0.0	False		,,,				2504	0.0				p.Q201H		Atlas-SNP	.											.	RPP40	36	.	0			c.A603C						PASS	.	T	HIS/GLN	431,3975	209.8+/-230.5	23,385,1795	105.0	101.0	103.0		603	-5.1	0.6	6	dbSNP_129	103	0,8600		0,0,4300	yes	missense	RPP40	NM_006638.2	24	23,385,6095	GG,GT,TT		0.0,9.7821,3.3139	benign	201/364	4996611	431,12575	2203	4300	6503	SO:0001583	missense	10799	exon6			CTGAATTTGGTAC	U94317	CCDS34333.1, CCDS69040.1, CCDS75391.1	6p25.1	2012-05-21	2007-06-26	2004-03-19	ENSG00000124787	ENSG00000124787			20992	protein-coding gene	gene with protein product		606117	"""ribonuclease P1"", ""ribonuclease P 40kDa subunit"""	RNASEP1		9630247	Standard	NM_006638		Approved	bA428J1.3	uc003mwl.3	O75818	OTTHUMG00000014168	ENST00000380051.2:c.603A>C	6.37:g.4996611T>G	ENSP00000369391:p.Gln201His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_006638	Q5VX97|Q8WVK8	Missense_Mutation	SNP	ENST00000380051.2	37	CCDS34333.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	T	13.36	2.213743	0.39102	0.097821	0.0	ENSG00000124787	ENST00000380051;ENST00000319533;ENST00000464646	T;T;T	0.44083	0.93;0.93;0.93	5.23	-5.06	0.02946	.	0.748127	0.13823	N	0.360291	T	0.13841	0.0335	M	0.67953	2.075	0.29984	N	0.817458	B;B	0.09022	0.001;0.002	B;B	0.12156	0.003;0.007	T	0.12016	-1.0564	10	0.44086	T	0.13	-1.8359	2.4943	0.04618	0.1158:0.3526:0.2381:0.2936	.	178;201	O75818-2;O75818	.;RPP40_HUMAN	H	201;178;141	ENSP00000369391:Q201H;ENSP00000317998:Q178H;ENSP00000419431:Q141H	ENSP00000317998:Q178H	Q	-	3	2	RPP40	4941610	0.466000	0.25823	0.631000	0.29282	0.902000	0.53008	-0.492000	0.06467	-0.982000	0.03515	-0.321000	0.08615	CAA	T|0.971;G|0.029	0.029	strong		0.473	RPP40-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039733.2	NM_006638	
THEM5	284486	hgsc.bcm.edu	37	1	151820324	151820324	+	Missense_Mutation	SNP	T	T	C	rs6587625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151820324T>C	ENST00000368817.5	-	5	721	c.590A>G	c.(589-591)gAc>gGc	p.D197G	AL450992.2_ENST00000434182.1_RNA	NM_182578.3	NP_872384	Q8N1Q8	ACO15_HUMAN	thioesterase superfamily member 5	197			D -> G (in dbSNP:rs6587625).		cardiolipin acyl-chain remodeling (GO:0035965)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)	mitochondrial matrix (GO:0005759)	palmitoyl-CoA hydrolase activity (GO:0016290)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AACCAGAGAGTCCACGGGGAT	0.532													C|||	3896	0.777955	0.8752	0.8674	5008	,	,		15489	0.6815		0.833	False		,,,				2504	0.6258				p.D197G		Atlas-SNP	.											.	THEM5	41	.	0			c.A590G						PASS	.	C	GLY/ASP	3782,624	271.0+/-269.9	1625,532,46	94.0	89.0	91.0		590	4.2	1.0	1	dbSNP_116	91	6954,1646	304.6+/-307.0	2819,1316,165	yes	missense	THEM5	NM_182578.3	94	4444,1848,211	CC,CT,TT		19.1395,14.1625,17.4535	benign	197/248	151820324	10736,2270	2203	4300	6503	SO:0001583	missense	284486	exon5			AGAGAGTCCACGG	AK095283	CCDS1005.1	1q21.3	2008-02-05			ENSG00000196407	ENSG00000196407			26755	protein-coding gene	gene with protein product		615653					Standard	NM_182578		Approved	FLJ37964	uc021oyw.1	Q8N1Q8	OTTHUMG00000013070	ENST00000368817.5:c.590A>G	1.37:g.151820324T>C	ENSP00000357807:p.Asp197Gly	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_182578	Q5T1C3	Missense_Mutation	SNP	ENST00000368817.5	37	CCDS1005.1	1746|1746	0.7994505494505495|0.7994505494505495	426|426	0.8658536585365854|0.8658536585365854	309|309	0.8535911602209945|0.8535911602209945	379|379	0.6625874125874126|0.6625874125874126	632|632	0.8337730870712401|0.8337730870712401	C|C	0.017|0.017	-1.506755|-1.506755	0.00992|0.00992	0.858375|0.858375	0.808605|0.808605	ENSG00000196407|ENSG00000196407	ENST00000368817|ENST00000453881	T|.	0.12147|.	2.71|.	5.09|5.09	4.17|4.17	0.49024|0.49024	Thioesterase superfamily (1);|.	0.207171|.	0.40818|.	N|.	0.001017|.	T|T	0.02888|0.02888	0.0086|0.0086	N|N	0.00670|0.00670	-1.27|-1.27	0.51012|0.51012	P|P	9.40000000000385E-5|9.40000000000385E-5	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.38714|0.38714	-0.9648|-0.9648	9|4	0.02654|.	T|.	1|.	-13.1518|-13.1518	7.1408|7.1408	0.25554|0.25554	0.0:0.8002:0.0:0.1998|0.0:0.8002:0.0:0.1998	rs6587625;rs52794777;rs57310650;rs6587625|rs6587625;rs52794777;rs57310650;rs6587625	197|.	Q8N1Q8|.	THEM5_HUMAN|.	G|A	197|144	ENSP00000357807:D197G|.	ENSP00000357807:D197G|.	D|T	-|-	2|1	0|0	THEM5|THEM5	150086948|150086948	0.999000|0.999000	0.42202|0.42202	0.998000|0.998000	0.56505|0.56505	0.053000|0.053000	0.15095|0.15095	0.635000|0.635000	0.24629|0.24629	1.160000|1.160000	0.42584|0.42584	-0.119000|-0.119000	0.15052|0.15052	GAC|ACT	T|0.206;C|0.794	0.794	strong		0.532	THEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036678.2	NM_182578	
ACER1	125981	hgsc.bcm.edu	37	19	6333476	6333476	+	Silent	SNP	G	G	A	rs16993553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6333476G>A	ENST00000301452.4	-	1	164	c.87C>T	c.(85-87)taC>taT	p.Y29Y		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	29					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						TCACCGTGTTGTAGAACTCGG	0.572													G|||	451	0.0900559	0.0393	0.0634	5008	,	,		18511	0.0129		0.0855	False		,,,				2504	0.2618				p.Y29Y		Atlas-SNP	.											ACER1,NS,carcinoma,-2,1	ACER1	38	1	0			c.C87T						PASS	.	G		201,4203		4,193,2005	70.0	44.0	53.0		87	4.9	1.0	19	dbSNP_123	53	705,7893		37,631,3631	no	coding-synonymous	ACER1	NM_133492.2		41,824,5636	AA,AG,GG		8.1996,4.564,6.9682		29/265	6333476	906,12096	2202	4299	6501	SO:0001819	synonymous_variant	125981	exon1			CGTGTTGTAGAAC	AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"""Alkaline ceramidase"""	18356	protein-coding gene	gene with protein product		613491	"""N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"""	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.87C>T	19.37:g.6333476G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	NM_133492		Silent	SNP	ENST00000301452.4	37	CCDS12161.1																																																																																			G|0.938;A|0.062	0.062	strong		0.572	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492	
ADIPOR2	79602	hgsc.bcm.edu	37	12	1890199	1890199	+	Silent	SNP	G	G	A	rs16928751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:1890199G>A	ENST00000357103.4	+	6	1046	c.795G>A	c.(793-795)caG>caA	p.Q265Q		NM_024551.2	NP_078827.2	Q86V24	ADR2_HUMAN	adiponectin receptor 2	265					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|female pregnancy (GO:0007565)|heart development (GO:0007507)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of cell growth (GO:0030308)|positive regulation of glucose import (GO:0046326)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|receptor activity (GO:0004872)			endometrium(1)|large_intestine(3)|lung(7)|stomach(1)	12	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			TAGTCTCCCAGTGGGACATGT	0.438													G|||	532	0.10623	0.208	0.0663	5008	,	,		18929	0.0258		0.1252	False		,,,				2504	0.0603				p.Q265Q		Atlas-SNP	.											.	ADIPOR2	30	.	0			c.G795A						PASS	.	G		895,3511	345.1+/-308.4	98,699,1406	119.0	115.0	116.0		795	4.8	1.0	12	dbSNP_123	116	1048,7552	221.5+/-258.9	58,932,3310	no	coding-synonymous	ADIPOR2	NM_024551.2		156,1631,4716	AA,AG,GG		12.186,20.3132,14.9393		265/387	1890199	1943,11063	2203	4300	6503	SO:0001819	synonymous_variant	79602	exon6			CTCCCAGTGGGAC	AY424280	CCDS8511.1	12p13	2012-08-22			ENSG00000006831	ENSG00000006831		"""GPCR / Unclassified : Adiponectin receptors"""	24041	protein-coding gene	gene with protein product		607946				12802337	Standard	NM_024551		Approved	PAQR2, ACDCR2	uc001qjm.3	Q86V24	OTTHUMG00000130139	ENST00000357103.4:c.795G>A	12.37:g.1890199G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	195	84	0.430769	NM_024551	Q53YY5|Q9H737	Silent	SNP	ENST00000357103.4	37	CCDS8511.1																																																																																			G|0.876;A|0.124	0.124	strong		0.438	ADIPOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252447.2	NM_024551	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197638	39197638	+	Silent	SNP	A	A	G	rs112542604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39197638A>G	ENST00000306271.4	-	1	75	c.12T>C	c.(10-12)tgT>tgC	p.C4C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	4						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)			AGCTGGTCTGACAGCAGGCCA	0.562													a|||	527	0.105232	0.1899	0.1153	5008	,	,		16504	0.1597		0.0169	False		,,,				2504	0.0184				p.C4C		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.T12C						PASS	.	A		553,3361		37,479,1441	49.0	54.0	53.0		12	-3.9	0.0	17	dbSNP_132	53	124,8182		5,114,4034	no	coding-synonymous	KRTAP1-1	NM_030967.2		42,593,5475	GG,GA,AA		1.4929,14.1288,5.5401		4/178	39197638	677,11543	1957	4153	6110	SO:0001819	synonymous_variant	81851	exon1			GGTCTGACAGCAG	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.12T>C	17.37:g.39197638A>G		Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	284	114	0.401408	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			A|0.889;G|0.111	0.111	strong		0.562	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
HLA-C	3107	hgsc.bcm.edu	37	6	31239114	31239114	+	Missense_Mutation	SNP	G	G	T	rs1071649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	68	3	0.0441176		WXS	Illumina HiSeq	Phase_I	113	40	0.353982	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	
SERPINA5	5104	hgsc.bcm.edu	37	14	95058477	95058477	+	Silent	SNP	G	G	A	rs6117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95058477G>A	ENST00000554866.1	+	5	1236	c.1122G>A	c.(1120-1122)tcG>tcA	p.S374S	SERPINA5_ENST00000553780.1_Silent_p.S374S|SERPINA5_ENST00000554276.1_Silent_p.S374S|SERPINA5_ENST00000329597.7_Silent_p.S374S|RP11-986E7.7_ENST00000553947.1_Intron			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	374		Reactive bond.			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)	CTTTCAGGTCGGCCCGCCTGA	0.557													G|||	199	0.0397364	0.1399	0.0202	5008	,	,		18216	0.0		0.0	False		,,,				2504	0.0				p.S374S		Atlas-SNP	.											.	SERPINA5	69	.	0			c.G1122A						PASS	.	G		562,3844	251.8+/-258.4	41,480,1682	208.0	214.0	212.0		1122	-6.8	0.0	14	dbSNP_52	212	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	SERPINA5	NM_000624.4		41,487,5975	AA,AG,GG		0.0814,12.7553,4.3749		374/407	95058477	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	5104	exon6			CAGGTCGGCCCGC	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.1122G>A	14.37:g.95058477G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	124	77	0.620968	NM_000624	Q07616|Q9UG30	Silent	SNP	ENST00000554866.1	37	CCDS9928.1																																																																																			G|0.956;A|0.044	0.044	strong		0.557	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
CDC16	8881	hgsc.bcm.edu	37	13	115004935	115004935	+	Silent	SNP	T	T	C	rs2296970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:115004935T>C	ENST00000356221.3	+	5	459	c.351T>C	c.(349-351)ccT>ccC	p.P117P	CDC16_ENST00000375308.1_Silent_p.P23P|CDC16_ENST00000252457.5_Silent_p.P116P|CDC16_ENST00000375312.3_Silent_p.P23P|CDC16_ENST00000252458.6_Silent_p.P23P|CDC16_ENST00000375310.1_Silent_p.P23P|CDC16_ENST00000360383.3_Silent_p.P117P			Q13042	CDC16_HUMAN	cell division cycle 16	117					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			TCAAAGATCCTTCCAGCGACT	0.453													C|||	2212	0.441693	0.8366	0.3516	5008	,	,		17862	0.2024		0.3191	False		,,,				2504	0.3446				p.P117P		Atlas-SNP	.											.	CDC16	50	.	0			c.T351C						PASS	.	C	,	3269,1137	400.4+/-331.6	1229,811,163	43.0	48.0	46.0		351,351	2.6	1.0	13	dbSNP_100	46	2445,6155	694.4+/-404.7	368,1709,2223	no	coding-synonymous,coding-synonymous	CDC16	NM_001078645.1,NM_003903.3	,	1597,2520,2386	CC,CT,TT		28.4302,25.8057,43.9336	,	117/621,117/621	115004935	5714,7292	2203	4300	6503	SO:0001819	synonymous_variant	8881	exon5			AGATCCTTCCAGC	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.351T>C	13.37:g.115004935T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	91	35	0.384615	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																			T|0.563;C|0.437	0.437	strong		0.453	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	
CS	1431	hgsc.bcm.edu	37	12	56676279	56676279	+	Silent	SNP	A	A	G	rs528162217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56676279A>G	ENST00000351328.3	-	6	703	c.513T>C	c.(511-513)gcT>gcC	p.A171A	CS_ENST00000542324.2_Silent_p.A158A|CS_ENST00000548567.1_Silent_p.A105A	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	171					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)	p.A171A(1)		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)		GGGCTGTAACAGCTGCACTGA	0.527													A|||	44	0.00878594	0.0272	0.0014	5008	,	,		18707	0.003		0.003	False		,,,				2504	0.001				p.A171A		Atlas-SNP	.											CS,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CS	44	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.T513C						scavenged	.																																			SO:0001819	synonymous_variant	1431	exon6			TGTAACAGCTGCA		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.513T>C	12.37:g.56676279A>G		Somatic	341	1	0.00293255		WXS	Illumina HiSeq	Phase_I	294	35	0.119048	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Silent	SNP	ENST00000351328.3	37	CCDS8913.1																																																																																			.	.	none		0.527	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077	
DCXR	51181	hgsc.bcm.edu	37	17	79994600	79994600	+	Silent	SNP	C	C	T	rs61739740|rs9780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79994600C>T	ENST00000306869.2	-	4	394	c.345G>A	c.(343-345)tcG>tcA	p.S115S	RP13-650J16.1_ENST00000582558.1_RNA|DCXR_ENST00000584318.1_5'UTR|RP13-650J16.1_ENST00000584705.1_RNA	NM_001195218.1|NM_016286.3	NP_001182147.1|NP_057370.1	Q7Z4W1	DCXR_HUMAN	dicarbonyl/L-xylulose reductase	115					D-xylose metabolic process (GO:0042732)|glucose metabolic process (GO:0006006)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|xylulose metabolic process (GO:0005997)	brush border (GO:0005903)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)	L-xylulose reductase (NADP+) activity (GO:0050038)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)			kidney(1)|lung(3)	4	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			AGCTCACCTGCGACACCTGGA	0.607													T|||	1080	0.215655	0.6256	0.0908	5008	,	,		16475	0.0704		0.1014	False		,,,				2504	0.0174				p.S115S		Atlas-SNP	.											.	DCXR	10	.	0			c.G345A						PASS	.	T	,	2472,1934	549.6+/-377.8	696,1080,427	73.0	71.0	71.0		339,345	-9.0	0.2	17	dbSNP_129	71	1016,7584	771.5+/-407.7	63,890,3347	no	coding-synonymous,coding-synonymous	DCXR	NM_001195218.1,NM_016286.3	,	759,1970,3774	TT,TC,CC		11.814,43.8947,26.8184	,	113/243,115/245	79994600	3488,9518	2203	4300	6503	SO:0001819	synonymous_variant	51181	exon4			CACCTGCGACACC	AB013846	CCDS11799.1	17q25.3	2011-09-14				ENSG00000169738	1.1.1.10	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 20C, member 1"""	608347				11882650, 19027726	Standard	NM_016286		Approved	KIDCR, DCR, SDR20C1	uc002kdg.3	Q7Z4W1		ENST00000306869.2:c.345G>A	17.37:g.79994600C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_016286	Q9BTZ3|Q9UHY9	Silent	SNP	ENST00000306869.2	37	CCDS11799.1																																																																																			C|0.760;T|0.240	0.240	strong		0.607	DCXR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442153.2		
CLPTM1	1209	hgsc.bcm.edu	37	19	45490570	45490570	+	Silent	SNP	A	A	G	rs3786505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45490570A>G	ENST00000337392.5	+	8	1077	c.927A>G	c.(925-927)ccA>ccG	p.P309P	CLPTM1_ENST00000541297.2_Silent_p.P295P|CLPTM1_ENST00000589158.1_3'UTR|CLPTM1_ENST00000546079.1_Silent_p.P207P	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	309					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		CCTTCTGCCCACTCTCGCTTT	0.577													G|||	2137	0.426717	0.4788	0.4222	5008	,	,		19997	0.5288		0.341	False		,,,				2504	0.3425				p.P309P		Atlas-SNP	.											.	CLPTM1	109	.	0			c.A927G						PASS	.	G		2131,2275	598.7+/-389.1	502,1127,574	100.0	103.0	102.0		927	-9.3	0.7	19	dbSNP_107	102	2764,5836	678.7+/-403.5	456,1852,1992	no	coding-synonymous	CLPTM1	NM_001294.2		958,2979,2566	GG,GA,AA		32.1395,48.3659,37.6365		309/670	45490570	4895,8111	2203	4300	6503	SO:0001819	synonymous_variant	1209	exon8			CTGCCCACTCTCG	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.927A>G	19.37:g.45490570A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Silent	SNP	ENST00000337392.5	37	CCDS12651.1																																																																																			A|0.596;G|0.404	0.404	strong		0.577	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294	
ST6GAL2	84620	hgsc.bcm.edu	37	2	107459974	107459974	+	Missense_Mutation	SNP	C	C	T	rs3796110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:107459974C>T	ENST00000409382.3	-	2	1070	c.460G>A	c.(460-462)Ggg>Agg	p.G154R	ST6GAL2_ENST00000361686.4_Missense_Mutation_p.G154R|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000409087.3_Missense_Mutation_p.G154R	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	154			G -> R (in dbSNP:rs3796110).		growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						CCTGGCTCCCCGGGGGAAGGG	0.617													C|||	702	0.140176	0.1505	0.147	5008	,	,		14211	0.1369		0.1014	False		,,,				2504	0.1646				p.G154R		Atlas-SNP	.											ST6GAL2,NS,carcinoma,+1,1	ST6GAL2	159	1	0			c.G460A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY	655,3751	268.3+/-268.4	41,573,1589	82.0	99.0	93.0		460,460,460	-2.2	0.0	2	dbSNP_107	93	639,7961	160.4+/-213.5	20,599,3681	yes	missense,missense,missense	ST6GAL2	NM_001142351.1,NM_001142352.1,NM_032528.2	125,125,125	61,1172,5270	TT,TC,CC		7.4302,14.8661,9.9493	benign,benign,benign	154/530,154/467,154/530	107459974	1294,11712	2203	4300	6503	SO:0001583	missense	84620	exon2			GCTCCCCGGGGGA	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"""sialyltransferase 2 (monosialoganglioside sialyltransferase)"""	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.460G>A	2.37:g.107459974C>T	ENSP00000386942:p.Gly154Arg	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	122	64	0.52459	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	
TNS1	7145	hgsc.bcm.edu	37	2	218674697	218674697	+	Missense_Mutation	SNP	C	C	T	rs918949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218674697C>T	ENST00000171887.4	-	30	5262	c.4810G>A	c.(4810-4812)Gtc>Atc	p.V1604I	TNS1_ENST00000419504.1_Missense_Mutation_p.V1590I|TNS1_ENST00000430930.1_Missense_Mutation_p.V1583I	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1604			V -> I (in dbSNP:rs918949). {ECO:0000269|PubMed:11023826}.		cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		ACAGAGTTGACGAAGAGCACA	0.567													.|||	3056	0.610224	0.8071	0.5922	5008	,	,		20607	0.505		0.5865	False		,,,				2504	0.4898				p.V1604I		Atlas-SNP	.											.	TNS1	251	.	0			c.G4810A						PASS	.		ILE/VAL	3386,1020	727.3+/-409.8	1299,788,116	66.0	65.0	65.0		4810	-4.7	0.4	2	dbSNP_86	65	5251,3349	643.9+/-400.0	1619,2013,668	yes	missense	TNS1	NM_022648.4	29	2918,2801,784	TT,TC,CC		38.9419,23.1502,33.5922	benign	1604/1736	218674697	8637,4369	2203	4300	6503	SO:0001583	missense	7145	exon30			AGTTGACGAAGAG	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4810G>A	2.37:g.218674697C>T	ENSP00000171887:p.Val1604Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	1356	0.6208791208791209	391	0.7947154471544715	225	0.6215469613259669	285	0.4982517482517482	455	0.600263852242744	c	0.884	-0.727836	0.03158	0.768498	0.610581	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	4.44	-4.71	0.03279	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);Tensin phosphotyrosine-binding domain (1);	0.375075	0.25628	N	0.029377	T	0.00012	0.0000	N	0.00298	-1.69	0.09310	P	0.9999999999998628	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.003;0.002	T	0.44205	-0.9343	9	0.12430	T	0.62	.	15.3963	0.74798	0.0:0.2186:0.0:0.7814	rs918949;rs3853996;rs52826748;rs60183014;rs918949	1604;1583;1590	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	I	1604;742;1590;1583	ENSP00000171887:V1604I;ENSP00000394171:V742I;ENSP00000408724:V1590I;ENSP00000406016:V1583I	ENSP00000171887:V1604I	V	-	1	0	TNS1	218382942	1.000000	0.71417	0.368000	0.25939	0.728000	0.41692	0.655000	0.24933	-1.539000	0.01732	-0.401000	0.06369	GTC	C|0.354;T|0.646	0.646	strong		0.567	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
OBSCN	84033	hgsc.bcm.edu	37	1	228559225	228559225	+	Missense_Mutation	SNP	G	G	A	rs200269110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228559225G>A	ENST00000422127.1	+	94	20790	c.20746G>A	c.(20746-20748)Gag>Aag	p.E6916K	OBSCN_ENST00000570156.2_Missense_Mutation_p.E7873K|OBSCN_ENST00000366707.4_Missense_Mutation_p.E4550K	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6916					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)				AGGCCTGCGCGAGCCACTGAT	0.746													G|||	34	0.00678914	0.0257	0.0	5008	,	,		12917	0.0		0.0	False		,,,				2504	0.0				p.E7873K		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G23617A						PASS	.	G	LYS/GLU	70,3774		0,70,1852	5.0	9.0	8.0		20746	4.4	0.9	1		8	0,8116		0,0,4058	yes	missense	OBSCN	NM_001098623.1	56	0,70,5910	AA,AG,GG		0.0,1.821,0.5853	benign	6916/7969	228559225	70,11890	1922	4058	5980	SO:0001583	missense	84033	exon105			CTGCGCGAGCCAC	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.20746G>A	1.37:g.228559225G>A	ENSP00000409493:p.Glu6916Lys	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	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	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.35|17.35	3.368034|3.368034	0.61513|0.61513	0.01821|0.01821	0.0|0.0	ENSG00000154358|ENSG00000154358	ENST00000422127;ENST00000366707|ENST00000441106	T;T|T	0.65549|0.72394	-0.16;-0.1|-0.65	4.41|4.41	4.41|4.41	0.53225|0.53225	.|.	.|.	.|.	.|.	.|.	T|T	0.64068|0.64068	0.2565|0.2565	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|T	0.72301|0.72301	-0.4334|-0.4334	9|7	0.40728|0.41790	T|T	0.16|0.15	.|.	17.2084|17.2084	0.86924|0.86924	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	6916|.	Q5VST9|.	OBSCN_HUMAN|.	K|Q	6916;4550|1532	ENSP00000409493:E6916K;ENSP00000355668:E4550K|ENSP00000388554:R1532Q	ENSP00000355668:E4550K|ENSP00000388554:R1532Q	E|R	+|+	1|2	0|0	OBSCN|OBSCN	226625848|226625848	0.999000|0.999000	0.42202|0.42202	0.931000|0.931000	0.37212|0.37212	0.040000|0.040000	0.13550|0.13550	2.926000|2.926000	0.48892|0.48892	2.300000|2.300000	0.77407|0.77407	0.555000|0.555000	0.69702|0.69702	GAG|CGA	.	.	weak		0.746	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
RP1L1	94137	hgsc.bcm.edu	37	8	10467124	10467124	+	Missense_Mutation	SNP	G	G	C	rs4841399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10467124G>C	ENST00000382483.3	-	4	4707	c.4484C>G	c.(4483-4485)cCc>cGc	p.P1495R		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1575					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)		CCCCTGGGTGGGTTGGGCCTG	0.642													G|||	1411	0.281749	0.2511	0.353	5008	,	,		16131	0.3938		0.2555	False		,,,				2504	0.184				p.P1495R		Atlas-SNP	.											RP1L1,NS,carcinoma,0,1	RP1L1	453	1	0			c.C4484G						PASS	.	G	ARG/PRO	982,2946		128,726,1110	33.0	38.0	36.0		4484	-5.1	0.0	8	dbSNP_111	36	2003,6307		241,1521,2393	yes	missense	RP1L1	NM_178857.5	103	369,2247,3503	CC,CG,GG		24.1035,25.0,24.3912	possibly-damaging	1495/2401	10467124	2985,9253	1964	4155	6119	SO:0001583	missense	94137	exon4			TGGGTGGGTTGGG	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.4484C>G	8.37:g.10467124G>C	ENSP00000371923:p.Pro1495Arg	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	643	0.2944139194139194	100	0.2032520325203252	107	0.2955801104972376	242	0.4230769230769231	194	0.2559366754617414	G	9.308	1.054817	0.19907	0.25	0.241035	ENSG00000183638	ENST00000382483	T	0.04156	3.69	4.69	-5.06	0.02946	.	2.449500	0.02245	N	0.066177	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.45126	0.851	B	0.39935	0.314	T	0.37549	-0.9701	9	0.56958	D	0.05	3.2668	1.9854	0.03435	0.3306:0.2097:0.3541:0.1056	rs4841399	1495	A6NKC6	.	R	1495	ENSP00000371923:P1495R	ENSP00000371923:P1495R	P	-	2	0	RP1L1	10504534	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.416000	0.02467	-1.450000	0.01936	-0.339000	0.08088	CCC	G|0.722;C|0.278	0.278	strong		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
UBR4	23352	hgsc.bcm.edu	37	1	19471388	19471388	+	Silent	SNP	A	A	G	rs2274000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19471388A>G	ENST00000375254.3	-	54	7986	c.7959T>C	c.(7957-7959)atT>atC	p.I2653I	UBR4_ENST00000375226.2_Silent_p.I2664I|UBR4_ENST00000375267.2_Silent_p.I2653I|UBR4_ENST00000375217.2_Silent_p.I2681I	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2653					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.I2653I(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)		CAGTAGCTTCAATATGAGTTA	0.393													A|||	532	0.10623	0.2905	0.049	5008	,	,		19725	0.0704		0.0	False		,,,				2504	0.044				p.I2653I		Atlas-SNP	.											UBR4,NS,carcinoma,0,1	UBR4	415	1	1	Substitution - coding silent(1)	stomach(1)	c.T7959C						PASS	.	A		1132,3274	404.4+/-333.1	151,830,1222	138.0	120.0	126.0		7959	-0.4	1.0	1	dbSNP_100	126	28,8572	18.5+/-59.3	0,28,4272	no	coding-synonymous	UBR4	NM_020765.2		151,858,5494	GG,GA,AA		0.3256,25.6922,8.919		2653/5184	19471388	1160,11846	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon54			AGCTTCAATATGA	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.7959T>C	1.37:g.19471388A>G		Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	210	108	0.514286	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			A|0.904;G|0.096	0.096	strong		0.393	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
FLG	2312	hgsc.bcm.edu	37	1	152284854	152284854	+	Silent	SNP	A	A	G	rs3120653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284854A>G	ENST00000368799.1	-	3	2543	c.2508T>C	c.(2506-2508)gaT>gaC	p.D836D	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_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	470	2	0.00425532		WXS	Illumina HiSeq	Phase_I	522	517	0.990421	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	
ZFP62	643836	hgsc.bcm.edu	37	5	180278393	180278393	+	Missense_Mutation	SNP	C	C	G	rs705441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180278393C>G	ENST00000502412.1	-	2	159	c.102G>C	c.(100-102)atG>atC	p.M34I	ZFP62_ENST00000506377.1_5'UTR|ZFP62_ENST00000512132.1_Start_Codon_SNP_p.M1I|ZFP62_ENST00000359141.6_5'UTR	NM_001172638.1	NP_001166109.1	Q8NB50	ZFP62_HUMAN	ZFP62 zinc finger protein	34			M -> I (in dbSNP:rs705441). {ECO:0000269|PubMed:14702039}.		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)			NS(1)|endometrium(2)|pancreas(1)	4	all_cancers(89;4.01e-05)|all_epithelial(37;4.69e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00469)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TAGATTCAGGCATAGGATCCT	0.433													C|||	3574	0.713658	0.3722	0.8343	5008	,	,		22227	0.9603		0.7565	False		,,,				2504	0.7914				p.M34I		Atlas-SNP	.											.	ZFP62	33	.	0			c.G102C						PASS	.																																			SO:0001583	missense	643836	exon2			TTCAGGCATAGGA	AK002206	CCDS47357.1, CCDS47357.2, CCDS54955.1	5q35.3	2013-01-08	2012-11-27			ENSG00000196670		"""Zinc fingers, C2H2-type"""	23241	protein-coding gene	gene with protein product		610281	"""zinc finger protein 62 homolog (mouse)"", ""zinc finger protein 62"""			8808410	Standard	NM_152283		Approved	FLJ34231, ZET, ZNF755	uc011dhf.2	Q8NB50		ENST00000502412.1:c.102G>C	5.37:g.180278393C>G	ENSP00000423820:p.Met34Ile	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	292	133	0.455479	NM_001172638	B4DIP6|B4E0N3|B5MDX6|B7ZVZ2|B9EIP6|E9PFT8|J3QTA9	Missense_Mutation	SNP	ENST00000502412.1	37	CCDS54955.1	1614	0.739010989010989	188	0.3821138211382114	297	0.8204419889502762	552	0.965034965034965	577	0.7612137203166227	.	3.737	-0.054453	0.07362	.	.	ENSG00000196670	ENST00000512132;ENST00000502412;ENST00000504225;ENST00000506439;ENST00000509066	T;T;T;T;T	0.52526	3.26;3.25;3.22;0.76;0.66	3.83	0.886	0.19194	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.50313	P	1.40000000000029E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.12941	-1.0528	8	0.42905	T	0.14	.	2.8437	0.05537	0.1994:0.454:0.0:0.3466	rs705441;rs1301110;rs62407814	34	Q8NB50	ZFP62_HUMAN	I	1;34;1;1;1	ENSP00000426193:M1I;ENSP00000423820:M34I;ENSP00000422987:M1I;ENSP00000423709:M1I;ENSP00000424156:M1I	ENSP00000423820:M34I	M	-	3	0	ZFP62	180210999	0.000000	0.05858	0.028000	0.17463	0.006000	0.05464	-0.183000	0.09712	0.175000	0.19841	0.637000	0.83480	ATG	C|0.260;G|0.740	0.740	strong		0.433	ZFP62-002	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368386.2	NM_152283	
TRIM67	440730	hgsc.bcm.edu	37	1	231339713	231339713	+	Silent	SNP	C	C	T	rs11806609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:231339713C>T	ENST00000366653.5	+	6	1635	c.1635C>T	c.(1633-1635)gaC>gaT	p.D545D	TRIM67_ENST00000444294.3_Silent_p.D543D|TRIM67_ENST00000366652.2_Silent_p.D545D|TRIM67_ENST00000449018.3_Silent_p.D483D			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	545	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				GCCCCGTGGACGGCTACATCC	0.632													C|||	650	0.129792	0.1536	0.0389	5008	,	,		17177	0.2272		0.0358	False		,,,				2504	0.1585				p.D545D		Atlas-SNP	.											.	TRIM67	160	.	0			c.C1635T						PASS	.	C		560,3596		31,498,1549	49.0	63.0	58.0		1635	-7.7	0.6	1	dbSNP_120	58	302,8092		3,296,3898	no	coding-synonymous	TRIM67	NM_001004342.3		34,794,5447	TT,TC,CC		3.5978,13.4745,6.8685		545/784	231339713	862,11688	2078	4197	6275	SO:0001819	synonymous_variant	440730	exon6			CGTGGACGGCTAC	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"""Tripartite motif containing / Tripartite motif containing"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	31859	protein-coding gene	gene with protein product		610584	"""tripartite motif-containing 67"""				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.1635C>T	1.37:g.231339713C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	37	CCDS44333.1																																																																																			C|0.892;T|0.108	0.108	strong		0.632	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342	
TLR10	81793	hgsc.bcm.edu	37	4	38776107	38776107	+	Missense_Mutation	SNP	T	T	G	rs11096955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38776107T>G	ENST00000308973.4	-	4	1710	c.1105A>C	c.(1105-1107)Atc>Ctc	p.I369L	TLR10_ENST00000508334.1_Missense_Mutation_p.I369L|TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000506111.1_Missense_Mutation_p.I369L|TLR10_ENST00000361424.2_Missense_Mutation_p.I369L	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	369			I -> L (in dbSNP:rs11096955). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						GGCAGTTGGATAGTTCTTTTA	0.353													T|||	2502	0.499601	0.5469	0.4179	5008	,	,		20490	0.5546		0.3976	False		,,,				2504	0.5419				p.I369L		Atlas-SNP	.											TLR10,colon,carcinoma,0,1	TLR10	87	1	0			c.A1105C	GRCh37	CM057766	TLR10	M	rs11096955	PASS	.	T	LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE	2232,2174	586.9+/-386.6	551,1130,522	73.0	79.0	77.0		1105,1105,1105,1063,1105	1.2	0.2	4	dbSNP_120	77	2951,5649	455.3+/-363.7	525,1901,1874	yes	missense,missense,missense,missense,missense	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	5,5,5,5,5	1076,3031,2396	GG,GT,TT		34.314,49.3418,39.8508	benign,benign,benign,benign,benign	369/812,369/812,369/812,355/798,369/812	38776107	5183,7823	2203	4300	6503	SO:0001583	missense	81793	exon2			GTTGGATAGTTCT	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.1105A>C	4.37:g.38776107T>G	ENSP00000308925:p.Ile369Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	CCDS3445.1	1058	0.48443223443223443	271	0.5508130081300813	150	0.4143646408839779	353	0.6171328671328671	284	0.37467018469656993	T	4.611	0.113581	0.08831	0.506582	0.34314	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.23348	1.91;1.91;1.91;1.91	5.17	1.24	0.21308	.	0.844930	0.09983	N	0.730685	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.42068	-0.9473	9	0.26408	T	0.33	.	1.3343	0.02142	0.1332:0.2345:0.1548:0.4775	rs11096955;rs11096955	369	Q9BXR5	TLR10_HUMAN	L	369	ENSP00000308925:I369L;ENSP00000421483:I369L;ENSP00000354459:I369L;ENSP00000424923:I369L	ENSP00000308925:I369L	I	-	1	0	TLR10	38452502	0.000000	0.05858	0.198000	0.23420	0.683000	0.39861	-0.986000	0.03747	0.778000	0.33520	0.477000	0.44152	ATC	T|0.553;G|0.447	0.447	strong		0.353	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
LYPD4	147719	hgsc.bcm.edu	37	19	42343355	42343355	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42343355C>G	ENST00000330743.3	-	2	1216	c.5G>C	c.(4-6)gGa>gCa	p.G2A	LYPD4_ENST00000343055.4_Missense_Mutation_p.G2A|LYPD4_ENST00000601246.1_Missense_Mutation_p.G2A	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	2						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						ATGCTGGGGTCCCATGGCCCT	0.542																																					p.G2A		Atlas-SNP	.											.	LYPD4	30	.	0			c.G5C						PASS	.						123.0	117.0	119.0					19																	42343355		2203	4300	6503	SO:0001583	missense	147719	exon2			TGGGGTCCCATGG	AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.5G>C	19.37:g.42343355C>G	ENSP00000328737:p.Gly2Ala	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_173506	Q8IYW0	Missense_Mutation	SNP	ENST00000330743.3	37	CCDS12587.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.255112	0.39896	.	.	ENSG00000183103	ENST00000330743;ENST00000343055	T;T	0.13657	3.41;2.57	3.9	2.83	0.33086	.	0.430475	0.17224	N	0.182217	T	0.13030	0.0316	L	0.46157	1.445	0.23827	N	0.996738	P;P	0.49961	0.93;0.793	P;B	0.44477	0.451;0.264	T	0.12708	-1.0537	10	0.23302	T	0.38	-2.1155	8.5663	0.33543	0.241:0.759:0.0:0.0	.	2;2	Q6UWN0-2;Q6UWN0	.;LYPD4_HUMAN	A	2	ENSP00000328737:G2A;ENSP00000339568:G2A	ENSP00000328737:G2A	G	-	2	0	LYPD4	47035195	0.988000	0.35896	0.975000	0.42487	0.942000	0.58702	0.660000	0.25009	1.156000	0.42514	0.551000	0.68910	GGA	.	.	none		0.542	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1	NM_173506	
LAMA1	284217	hgsc.bcm.edu	37	18	7023371	7023371	+	Silent	SNP	A	A	G	rs684634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:7023371A>G	ENST00000389658.3	-	19	2586	c.2493T>C	c.(2491-2493)tgT>tgC	p.C831C		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	831	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AACCATCTGCACATCTGTATC	0.502													G|||	2190	0.4373	0.8533	0.389	5008	,	,		20795	0.1429		0.3807	False		,,,				2504	0.271				p.C831C		Atlas-SNP	.											LAMA1,NS,adenoma,0,1	LAMA1	458	1	0			c.T2493C						PASS	.	G		3319,1087	389.8+/-327.4	1257,805,141	77.0	75.0	75.0		2493	-6.0	0.9	18	dbSNP_83	75	3267,5333	645.7+/-400.2	603,2061,1636	no	coding-synonymous	LAMA1	NM_005559.3		1860,2866,1777	GG,GA,AA		37.9884,24.6709,49.3618		831/3076	7023371	6586,6420	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon19			ATCTGCACATCTG	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.2493T>C	18.37:g.7023371A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			A|0.524;G|0.476	0.476	strong		0.502	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
MICAL1	64780	hgsc.bcm.edu	37	6	109767931	109767931	+	Missense_Mutation	SNP	C	C	T	rs59056467|rs35260632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	263	133	0.505703	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	
GPN2	54707	hgsc.bcm.edu	37	1	27210721	27210721	+	Missense_Mutation	SNP	T	T	C	rs3170660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:27210721T>C	ENST00000374135.4	-	4	990	c.790A>G	c.(790-792)Aga>Gga	p.R264G	GPN2_ENST00000374133.3_Missense_Mutation_p.R85G|GPN2_ENST00000461282.1_5'Flank	NM_018066.3	NP_060536.3			GPN-loop GTPase 2											endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9						TCTTGGGCTCTGAAACAGTAT	0.532													C|||	4373	0.873203	0.9781	0.8256	5008	,	,		18986	0.997		0.6292	False		,,,				2504	0.8885				p.R264G		Atlas-SNP	.											.	GPN2	18	.	0			c.A790G						PASS	.	C	GLY/ARG	4040,366	185.7+/-212.7	1860,320,23	87.0	76.0	80.0		790	5.5	0.7	1	dbSNP_105	80	5388,3212	484.5+/-371.4	1683,2022,595	yes	missense	GPN2	NM_018066.3	125	3543,2342,618	CC,CT,TT		37.3488,8.3069,27.5104	benign	264/311	27210721	9428,3578	2203	4300	6503	SO:0001583	missense	54707	exon4			GGGCTCTGAAACA	AK001211	CCDS289.1	1p36.11	2008-04-30	2008-04-30	2008-04-30	ENSG00000142751	ENSG00000142751		"""GPN-loop GTPases"""	25513	protein-coding gene	gene with protein product			"""ATP binding domain 1 family, member B"""	ATPBD1B		12975309	Standard	NM_018066		Approved	FLJ10349	uc001bnd.1	Q9H9Y4	OTTHUMG00000004227	ENST00000374135.4:c.790A>G	1.37:g.27210721T>C	ENSP00000363250:p.Arg264Gly	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_018066		Missense_Mutation	SNP	ENST00000374135.4	37	CCDS289.1	1826	0.8360805860805861	481	0.9776422764227642	294	0.8121546961325967	572	1.0	479	0.6319261213720316	C	9.172	1.021476	0.19433	0.916931	0.626512	ENSG00000142751	ENST00000374135;ENST00000374133	T;T	0.19105	2.37;2.17	5.48	5.48	0.80851	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.08118	0	0.37519	P	0.08252999999999999	B	0.02656	0.0	B	0.01281	0.0	T	0.46289	-0.9202	9	0.02654	T	1	-10.032	14.1824	0.65583	0.0:0.9271:0.0:0.0729	rs3170660;rs17370367;rs17845131;rs17857934;rs17857983;rs52817375;rs56754148;rs3170660	264	Q9H9Y4	GPN2_HUMAN	G	264;85	ENSP00000363250:R264G;ENSP00000363248:R85G	ENSP00000363248:R85G	R	-	1	2	GPN2	27083308	1.000000	0.71417	0.712000	0.30502	0.826000	0.46750	5.788000	0.69020	1.329000	0.45376	-0.320000	0.08662	AGA	T|0.213;C|0.787	0.787	strong		0.532	GPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012175.2	NM_018066	
DBH	1621	hgsc.bcm.edu	37	9	136509370	136509370	+	Missense_Mutation	SNP	G	G	T	rs4531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136509370G>T	ENST00000393056.2	+	5	964	c.952G>T	c.(952-954)Gcc>Tcc	p.A318S		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	318			A -> S (in allele DBH-B; dbSNP:rs4531). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:10490716}.		behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	AGCCGGCCTTGCCTTCGGGGG	0.607													G|||	327	0.0652955	0.1316	0.0346	5008	,	,		18372	0.003		0.0716	False		,,,				2504	0.0552				p.A318S		Atlas-SNP	.											.	DBH	86	.	0			c.G952T						PASS	.	G	SER/ALA	530,3876	241.2+/-251.7	34,462,1707	99.0	94.0	96.0		952	-0.9	0.0	9	dbSNP_52	96	668,7932	167.5+/-219.3	26,616,3658	yes	missense	DBH	NM_000787.3	99	60,1078,5365	TT,TG,GG		7.7674,12.0291,9.2111	benign	318/618	136509370	1198,11808	2203	4300	6503	SO:0001583	missense	1621	exon5			GGCCTTGCCTTCG	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.952G>T	9.37:g.136509370G>T	ENSP00000376776:p.Ala318Ser	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	75	49	0.653333	NM_000787	Q5T381|Q96AG2	Missense_Mutation	SNP	ENST00000393056.2	37	CCDS6977.2	137	0.06272893772893773	66	0.13414634146341464	16	0.04419889502762431	1	0.0017482517482517483	54	0.0712401055408971	G	6.768	0.510628	0.12883	0.120291	0.077674	ENSG00000123454	ENST00000393056	T	0.28255	1.62	5.13	-0.852	0.10713	Copper type II, ascorbate-dependent monooxygenase, N-terminal (2);PHM/PNGase F domain (1);	0.296425	0.37012	N	0.002299	T	0.00271	0.0008	L	0.31752	0.955	0.58432	P	1.0000000000287557E-6	B	0.22276	0.067	B	0.32393	0.145	T	0.12811	-1.0533	9	0.25751	T	0.34	-27.7151	18.7539	0.91825	0.0:0.6379:0.3621:0.0	rs4531;rs4531	318	P09172	DOPO_HUMAN	S	318	ENSP00000376776:A318S	ENSP00000376776:A318S	A	+	1	0	DBH	135499191	0.697000	0.27767	0.000000	0.03702	0.003000	0.03518	0.926000	0.28804	-0.130000	0.11599	-0.311000	0.09066	GCC	G|0.913;T|0.087	0.087	strong		0.607	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
ANK2	287	hgsc.bcm.edu	37	4	114279770	114279770	+	Silent	SNP	T	T	C	rs145557320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:114279770T>C	ENST00000357077.4	+	38	10049	c.9996T>C	c.(9994-9996)agT>agC	p.S3332S	ANK2_ENST00000264366.6_Silent_p.S3299S|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3332					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TTCTATCCAGTGTAGATGAGG	0.443													T|||	39	0.00778754	0.0272	0.0029	5008	,	,		18580	0.0		0.001	False		,,,				2504	0.0				p.S3332S		Atlas-SNP	.											.	ANK2	576	.	0			c.T9996C						PASS	.	T	,,	114,4292	85.8+/-124.5	0,114,2089	110.0	113.0	112.0		,9996,	-2.8	0.2	4	dbSNP_134	112	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous,intron	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	,,	0,115,6388	CC,CT,TT		0.0116,2.5874,0.8842	,,	,3332/3958,	114279770	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	287	exon38			ATCCAGTGTAGAT	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.9996T>C	4.37:g.114279770T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1																																																																																			T|0.992;C|0.008	0.008	strong		0.443	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
UBR2	23304	hgsc.bcm.edu	37	6	42562027	42562027	+	Missense_Mutation	SNP	A	A	T	rs6905054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42562027A>T	ENST00000372899.1	+	4	774	c.516A>T	c.(514-516)gaA>gaT	p.E172D	UBR2_ENST00000372903.2_Missense_Mutation_p.E172D|UBR2_ENST00000372901.1_Missense_Mutation_p.E172D	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	172			E -> D (in dbSNP:rs6905054).		cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			ACACCTCTGAAATTGAGGAAG	0.363													A|||	166	0.033147	0.1089	0.0072	5008	,	,		17588	0.0099		0.0	False		,,,				2504	0.0072				p.E172D		Atlas-SNP	.											.	UBR2	134	.	0			c.A516T						PASS	.	A	ASP/GLU,ASP/GLU	360,4046	185.0+/-212.2	14,332,1857	113.0	110.0	111.0		516,516	5.2	1.0	6	dbSNP_116	111	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense	UBR2	NM_001184801.1,NM_015255.2	45,45	14,334,6155	TT,TA,AA		0.0233,8.1707,2.7833	benign,benign	172/440,172/1756	42562027	362,12644	2203	4300	6503	SO:0001583	missense	23304	exon4			CTCTGAAATTGAG	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.516A>T	6.37:g.42562027A>T	ENSP00000361990:p.Glu172Asp	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	66	22	0.333333	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	58	0.026556776556776556	50	0.1016260162601626	0	0.0	8	0.013986013986013986	0	0.0	A	11.03	1.518060	0.27211	0.081707	2.33E-4	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	T;T;T	0.73152	-0.72;0.27;0.27	5.17	5.17	0.71159	.	0.218116	0.47093	D	0.000242	T	0.34571	0.0902	N	0.22421	0.69	0.09310	P	0.9999999999999195	B;B	0.09022	0.001;0.002	B;B	0.12837	0.001;0.008	T	0.13415	-1.0510	9	0.11485	T	0.65	-28.0504	11.0648	0.47968	0.9248:0.0:0.0752:0.0	rs6905054;rs52816446;rs61683407;rs6905054	172;172	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	D	172	ENSP00000361994:E172D;ENSP00000361990:E172D;ENSP00000361992:E172D	ENSP00000361990:E172D	E	+	3	2	UBR2	42670005	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	1.373000	0.34272	1.953000	0.56701	0.459000	0.35465	GAA	A|0.966;T|0.034	0.034	strong		0.363	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
ASTN2	23245	hgsc.bcm.edu	37	9	119249690	119249690	+	Missense_Mutation	SNP	C	C	T	rs16933591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:119249690C>T	ENST00000313400.4	-	20	3545	c.3445G>A	c.(3445-3447)Gtc>Atc	p.V1149I	ASTN2_ENST00000341734.4_Missense_Mutation_p.V201I|ASTN2_ENST00000361209.2_Missense_Mutation_p.V1098I|ASTN2_ENST00000288520.5_Missense_Mutation_p.V250I|ASTN2_ENST00000361477.3_Missense_Mutation_p.V201I|ASTN2_ENST00000373996.3_Missense_Mutation_p.V1145I			O75129	ASTN2_HUMAN	astrotactin 2	1149	Fibronectin type-III.		V -> I (in dbSNP:rs16933591).		negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.V1098F(1)|p.V201F(1)		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						TAGATACTGACTTCAGGGACC	0.507													C|||	101	0.0201677	0.0741	0.0043	5008	,	,		17865	0.0		0.0	False		,,,				2504	0.0				p.V1098I		Atlas-SNP	.											ASTN2_ENST00000361477,NS,carcinoma,0,1	ASTN2	307	1	2	Substitution - Missense(2)	lung(2)	c.G3292A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	262,4144	150.7+/-184.7	5,252,1946	118.0	106.0	110.0		601,3292,748,601,601	3.6	1.0	9	dbSNP_123	110	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense,missense,missense,missense	ASTN2	NM_001184734.1,NM_014010.4,NM_198186.3,NM_198187.3,NM_198188.2	29,29,29,29,29	5,254,6244	TT,TC,CC		0.0233,5.9464,2.0298	benign,benign,benign,benign,benign	201/376,1098/1289,250/441,201/403,201/396	119249690	264,12742	2203	4300	6503	SO:0001583	missense	23245	exon19			TACTGACTTCAGG	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.3445G>A	9.37:g.119249690C>T	ENSP00000314038:p.Val1149Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	79	50	0.632911	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	C	12.97	2.096981	0.37048	0.059464	2.33E-4	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000288520;ENST00000341734;ENST00000373986;ENST00000361209;ENST00000361477	T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.49	3.6	0.41247	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.383922	0.28225	N	0.016137	T	0.01320	0.0043	N	0.08118	0	0.29275	N	0.870436	B;B;B;B;B;B;B	0.15473	0.013;0.0;0.006;0.0;0.01;0.0;0.0	B;B;B;B;B;B;B	0.11329	0.006;0.0;0.001;0.001;0.005;0.0;0.0	T	0.06338	-1.0832	10	0.20519	T	0.43	-28.4103	5.7264	0.18015	0.0:0.6328:0.0:0.3672	rs16933591;rs52796427;rs16933591	201;201;1098;1149;1145;201;250	B7ZKP4;B7ZKP5;O75129-2;O75129;O75129-3;O75129-6;O75129-4	.;.;.;ASTN2_HUMAN;.;.;.	I	1149;1145;250;201;872;1098;201	ENSP00000314038:V1149I;ENSP00000363108:V1145I;ENSP00000288520:V250I;ENSP00000339925:V201I;ENSP00000363098:V872I;ENSP00000354504:V1098I;ENSP00000355116:V201I	ENSP00000288520:V250I	V	-	1	0	ASTN2	118289511	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.748000	0.47483	1.436000	0.47453	0.655000	0.94253	GTC	C|0.979;T|0.021	0.021	strong		0.507	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
PLA1A	51365	hgsc.bcm.edu	37	3	119347623	119347623	+	Missense_Mutation	SNP	C	C	A	rs115172544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119347623C>A	ENST00000273371.4	+	10	1269	c.1197C>A	c.(1195-1197)ttC>ttA	p.F399L	PLA1A_ENST00000494440.1_Missense_Mutation_p.F383L|PLA1A_ENST00000488919.1_Missense_Mutation_p.F226L|PLA1A_ENST00000495992.1_Missense_Mutation_p.F383L	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	399	Involved in the recognition of diacyl- phospholipids.				lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AAGTGAAATTCAAGTTTCAGT	0.468													C|||	78	0.0155751	0.0545	0.0086	5008	,	,		21512	0.0		0.0	False		,,,				2504	0.0				p.F399L		Atlas-SNP	.											.	PLA1A	65	.	0			c.C1197A						PASS	.	C	LEU/PHE,LEU/PHE,LEU/PHE	161,4245	108.2+/-146.6	4,153,2046	141.0	134.0	136.0		1149,678,1197	2.2	0.9	3	dbSNP_132	136	0,8600		0,0,4300	yes	missense,missense,missense	PLA1A	NM_001206960.1,NM_001206961.1,NM_015900.3	22,22,22	4,153,6346	AA,AC,CC		0.0,3.6541,1.2379	benign,benign,benign	383/441,226/284,399/457	119347623	161,12845	2203	4300	6503	SO:0001583	missense	51365	exon10			GAAATTCAAGTTT	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.1197C>A	3.37:g.119347623C>A	ENSP00000273371:p.Phe399Leu	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	37	CCDS2991.1	26	0.011904761904761904	24	0.04878048780487805	2	0.0055248618784530384	0	0.0	0	0.0	C	0.008	-1.883913	0.00532	0.036541	0.0	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440	D;D;D;D	0.90004	-2.0;-2.6;-2.04;-2.12	5.29	2.23	0.28157	.	1.028510	0.07692	N	0.938840	T	0.34687	0.0906	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45234	-0.9275	10	0.02654	T	1	-0.7164	9.9541	0.41655	0.1251:0.5238:0.3511:0.0	.	383;399	Q53H76-3;Q53H76	.;PLA1A_HUMAN	L	399;226;383;383	ENSP00000273371:F399L;ENSP00000420625:F226L;ENSP00000417326:F383L;ENSP00000418793:F383L	ENSP00000273371:F399L	F	+	3	2	PLA1A	120830313	0.945000	0.32115	0.862000	0.33874	0.035000	0.12851	0.606000	0.24194	0.590000	0.29694	-0.304000	0.09214	TTC	C|0.984;A|0.016	0.016	strong		0.468	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2		
FXR1	8087	hgsc.bcm.edu	37	3	180630500	180630500	+	Silent	SNP	C	C	T	rs1805578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:180630500C>T	ENST00000357559.4	+	1	411	c.27C>T	c.(25-27)cgC>cgT	p.R9R	FXR1_ENST00000491674.1_Silent_p.R9R|FXR1_ENST00000491062.1_Silent_p.R9R|FXR1_ENST00000468861.1_5'UTR|FXR1_ENST00000445140.2_Silent_p.R9R|FXR1_ENST00000480918.1_5'Flank|FXR1_ENST00000305586.7_5'UTR	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	9	Agenet-like 1.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			TGGAGGTTCGCGGCTCTAACG	0.592											OREG0015934	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	179	0.0357428	0.1263	0.0159	5008	,	,		11846	0.0		0.001	False		,,,				2504	0.0				p.R9R		Atlas-SNP	.											.	FXR1	75	.	0			c.C27T						PASS	.	C	,,	444,3962	214.1+/-233.5	22,400,1781	146.0	145.0	145.0		27,,27	0.7	1.0	3	dbSNP_92	145	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,utr-5,coding-synonymous	FXR1	NM_001013438.2,NM_001013439.2,NM_005087.3	,,	22,405,6076	TT,TC,CC		0.0581,10.0772,3.4523	,,	9/540,,9/622	180630500	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	8087	exon1			GGTTCGCGGCTCT	M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.27C>T	3.37:g.180630500C>T		Somatic	312	1	0.00320513	1963	WXS	Illumina HiSeq	Phase_I	304	168	0.552632	NM_001013438	A8K9B8|Q7Z450|Q8N6R8	Silent	SNP	ENST00000357559.4	37	CCDS3238.1																																																																																			C|0.961;T|0.039	0.039	strong		0.592	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5		
FBN3	84467	hgsc.bcm.edu	37	19	8150353	8150353	+	Silent	SNP	C	C	T	rs61729617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8150353C>T	ENST00000600128.1	-	56	7395	c.6981G>A	c.(6979-6981)ggG>ggA	p.G2327G	FBN3_ENST00000601739.1_Silent_p.G2327G|FBN3_ENST00000270509.2_Silent_p.G2327G			Q75N90	FBN3_HUMAN	fibrillin 3	2327	TB 9.					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						CCCGGCCACCCCCACAGCAGC	0.692													C|||	204	0.0407348	0.1445	0.0187	5008	,	,		14856	0.0		0.0	False		,,,				2504	0.0				p.G2327G		Atlas-SNP	.											.	FBN3	300	.	0			c.G6981A						PASS	.	C		418,3948		15,388,1780	9.0	11.0	10.0		6981	3.6	0.8	19	dbSNP_129	10	8,8498		0,8,4245	no	coding-synonymous	FBN3	NM_032447.3		15,396,6025	TT,TC,CC		0.0941,9.574,3.3095		2327/2810	8150353	426,12446	2183	4253	6436	SO:0001819	synonymous_variant	84467	exon55			GCCACCCCCACAG		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.6981G>A	19.37:g.8150353C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			C|0.967;T|0.033	0.033	strong		0.692	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
FMN2	56776	hgsc.bcm.edu	37	1	240370629	240370629	+	Silent	SNP	C	C	G	rs10926166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:240370629C>G	ENST00000319653.9	+	5	2747	c.2517C>G	c.(2515-2517)acC>acG	p.T839T		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	839	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)			AGTTTCAAACCAGCCACGAAC	0.557													C|||	1439	0.28734	0.2617	0.2507	5008	,	,		15509	0.1032		0.4066	False		,,,				2504	0.4151				p.T839T		Atlas-SNP	.											.	FMN2	451	.	0			c.C2517G						PASS	.	C		1268,3138	432.0+/-343.1	184,900,1119	95.0	92.0	93.0		2517	3.2	1.0	1	dbSNP_120	93	3344,5256	494.2+/-373.8	636,2072,1592	no	coding-synonymous	FMN2	NM_020066.4		820,2972,2711	GG,GC,CC		38.8837,28.7789,35.4606		839/1723	240370629	4612,8394	2203	4300	6503	SO:0001819	synonymous_variant	56776	exon5			TCAAACCAGCCAC	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.2517C>G	1.37:g.240370629C>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	124	69	0.556452	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			C|0.679;G|0.321	0.321	strong		0.557	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
IFNA16	3449	hgsc.bcm.edu	37	9	21217022	21217022	+	Missense_Mutation	SNP	C	C	G	rs28368160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21217022C>G	ENST00000380216.1	-	1	288	c.283G>C	c.(283-285)Gat>Cat	p.D95H		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	95					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		GCAGATGAATCCTTTGTGCTG	0.493													C|||	130	0.0259585	0.0499	0.0216	5008	,	,		20197	0.0		0.0427	False		,,,				2504	0.0061				p.D95H		Atlas-SNP	.											.	IFNA16	27	.	0			c.G283C						PASS	.	C	HIS/ASP	208,4198		5,198,2000	129.0	125.0	126.0		283	-0.6	0.0	9	dbSNP_125	126	397,8203		7,383,3910	no	missense	IFNA16	NM_002173.2	81	12,581,5910	GG,GC,CC		4.6163,4.7208,4.6517	possibly-damaging	95/190	21217022	605,12401	2203	4300	6503	SO:0001583	missense	3449	exon1			ATGAATCCTTTGT		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"""Interferons"""	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.283G>C	9.37:g.21217022C>G	ENSP00000369564:p.Asp95His	Somatic	303	1	0.00330033		WXS	Illumina HiSeq	Phase_I	346	175	0.50578	NM_002173	Q5VV12	Missense_Mutation	SNP	ENST00000380216.1	37	CCDS34996.1	72	0.03296703296703297	27	0.054878048780487805	7	0.019337016574585635	0	0.0	38	0.05013192612137203	-	5.406	0.260048	0.10239	0.047208	0.046163	ENSG00000147885	ENST00000380216	T	0.03441	3.93	2.62	-0.618	0.11576	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	2.345320	0.01358	N	0.012141	T	0.01421	0.0046	L	0.47016	1.485	0.09310	N	1	P	0.47962	0.903	P	0.61275	0.886	T	0.17379	-1.0371	10	0.33940	T	0.23	.	3.9698	0.09447	0.0:0.3538:0.3876:0.2585	rs28368160	95	P05015	IFN16_HUMAN	H	95	ENSP00000369564:D95H	ENSP00000369564:D95H	D	-	1	0	IFNA16	21207022	0.000000	0.05858	0.000000	0.03702	0.107000	0.19398	-1.174000	0.03105	-0.295000	0.08960	0.184000	0.17185	GAT	C|0.957;G|0.043	0.043	strong		0.493	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173	
TRIP10	9322	hgsc.bcm.edu	37	19	6751103	6751103	+	Missense_Mutation	SNP	G	G	A	rs139253875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6751103G>A	ENST00000313244.9	+	15	1722	c.1687G>A	c.(1687-1689)Gag>Aag	p.E563K	CTD-3128G10.6_ENST00000594056.1_RNA|TRIP10_ENST00000600428.1_Missense_Mutation_p.E399K|TRIP10_ENST00000596758.1_Silent_p.P516P|TRIP10_ENST00000313285.8_Missense_Mutation_p.E507K			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	563	Interaction with ARHGAP17, DAAM1, DIAPH1 and DIAPH2.|Interaction with DNM1 and WASL.|Interaction with PDE6G. {ECO:0000250}.|Interaction with WAS.|Required for interaction with FASLG and localization to lysosomes.|Required for podosome formation.|SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.E507Q(1)|p.E563Q(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						CTCTATGGCCGAGGGTGAAGA	0.532													G|||	7	0.00139776	0.0053	0.0	5008	,	,		15820	0.0		0.0	False		,,,				2504	0.0				p.E507K		Atlas-SNP	.											TRIP10_ENST00000313244,NS,carcinoma,0,2	TRIP10	104	2	2	Substitution - Missense(2)	lung(2)	c.G1519A						PASS	.	G	LYS/GLU	13,4393	20.2+/-43.8	0,13,2190	52.0	59.0	57.0		1519	4.7	1.0	19	dbSNP_134	57	0,8600		0,0,4300	yes	missense	TRIP10	NM_004240.2	56	0,13,6490	AA,AG,GG		0.0,0.2951,0.1	possibly-damaging	507/546	6751103	13,12993	2203	4300	6503	SO:0001583	missense	9322	exon14			ATGGCCGAGGGTG	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"""Cdc42-interacting protein"""	604504	"""salt tolerator"""	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.1687G>A	19.37:g.6751103G>A	ENSP00000320117:p.Glu563Lys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Missense_Mutation	SNP	ENST00000313244.9	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	27.1	4.800102	0.90538	0.002951	0.0	ENSG00000125733	ENST00000313285;ENST00000313244	T;T	0.40756	1.02;1.02	4.66	4.66	0.58398	Src homology-3 domain (4);	0.349695	0.29822	N	0.011119	T	0.60894	0.2304	L	0.59912	1.85	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.85130	0.983;0.997	T	0.63739	-0.6569	10	0.87932	D	0	-32.2852	15.4165	0.74974	0.0:0.0:1.0:0.0	.	563;507	Q15642;Q15642-2	CIP4_HUMAN;.	K	507;563	ENSP00000320493:E507K;ENSP00000320117:E563K	ENSP00000320117:E563K	E	+	1	0	TRIP10	6702103	1.000000	0.71417	0.992000	0.48379	0.699000	0.40488	8.973000	0.93428	2.580000	0.87095	0.305000	0.20034	GAG	G|0.999;A|0.001	0.001	strong		0.532	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2		
TSPAN8	7103	hgsc.bcm.edu	37	12	71533534	71533534	+	Missense_Mutation	SNP	C	C	G	rs3763978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000552786.1_5'Flank|TSPAN8_ENST00000546561.1_Missense_Mutation_p.G73A|TSPAN8_ENST00000552128.1_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	94	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	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	
HDHD2	84064	hgsc.bcm.edu	37	18	44660923	44660923	+	Missense_Mutation	SNP	C	C	T	rs7230131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44660923C>T	ENST00000300605.6	-	3	406	c.254G>A	c.(253-255)cGg>cAg	p.R85Q	HDHD2_ENST00000587841.1_Intron	NM_032124.4	NP_115500.1	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain containing 2	85			R -> Q (in dbSNP:rs7230131).			extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(2)|lung(1)|skin(1)	6						GACTTGTTTCCGCTCTAGTAA	0.378													c|||	182	0.0363419	0.1293	0.0101	5008	,	,		18140	0.001		0.001	False		,,,				2504	0.002				p.R85Q		Atlas-SNP	.											.	HDHD2	12	.	0			c.G254A						PASS	.	C	GLN/ARG	435,3971	210.5+/-231.0	13,409,1781	110.0	108.0	109.0		254	3.6	1.0	18	dbSNP_116	109	4,8596	3.7+/-12.6	0,4,4296	yes	missense	HDHD2	NM_032124.4	43	13,413,6077	TT,TC,CC		0.0465,9.8729,3.3754	benign	85/260	44660923	439,12567	2203	4300	6503	SO:0001583	missense	84064	exon3			TGTTTCCGCTCTA	AL136681	CCDS32829.1	18q21.1	2008-02-05				ENSG00000167220			25364	protein-coding gene	gene with protein product						11230166	Standard	NM_032124		Approved	DKFZP564D1378	uc002lcs.3	Q9H0R4		ENST00000300605.6:c.254G>A	18.37:g.44660923C>T	ENSP00000300605:p.Arg85Gln	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_032124	A8K7T3|Q96NV4	Missense_Mutation	SNP	ENST00000300605.6	37	CCDS32829.1	55	0.025183150183150184	52	0.10569105691056911	3	0.008287292817679558	0	0.0	0	0.0	c	8.194	0.796607	0.16327	0.098729	4.65E-4	ENSG00000167220	ENST00000300605	T	0.29917	1.55	5.97	3.57	0.40892	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);	0.197776	0.44688	N	0.000433	T	0.00210	0.0006	N	0.02539	-0.55	0.26525	N	0.974354	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	10	0.02654	T	1	2.3857	10.9093	0.47099	0.0:0.1293:0.0:0.8707	rs7230131;rs52803001;rs7230131	85	Q9H0R4	HDHD2_HUMAN	Q	85	ENSP00000300605:R85Q	ENSP00000300605:R85Q	R	-	2	0	HDHD2	42914921	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	4.293000	0.59037	1.077000	0.40990	-0.285000	0.09966	CGG	C|0.966;T|0.034	0.034	strong		0.378	HDHD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450668.2	NM_032124	
MBOAT4	619373	hgsc.bcm.edu	37	8	29994923	29994923	+	Intron	SNP	G	G	A	rs77053651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:29994923G>A	ENST00000320542.3	-	2	429				LEPROTL1_ENST00000442880.2_3'UTR|LEPROTL1_ENST00000523116.1_Missense_Mutation_p.V139M	NM_001100916.1	NP_001094386.1	Q96T53	MBOA4_HUMAN	membrane bound O-acyltransferase domain containing 4						cellular protein metabolic process (GO:0044267)|peptidyl-serine octanoylation (GO:0018191)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	serine O-acyltransferase activity (GO:0016412)			endometrium(1)	1						CACTCAACCCGTGCTGAGGCT	0.562													G|||	82	0.0163738	0.056	0.0101	5008	,	,		19995	0.0		0.001	False		,,,				2504	0.0				p.V139M		Atlas-SNP	.											.	LEPROTL1	16	.	0			c.G415A						PASS	.	G	,MET/VAL	82,1302		3,76,613	51.0	44.0	46.0		,415	-1.1	0.0	8	dbSNP_132	46	1,3181		0,1,1590	yes	intron,missense	LEPROTL1,MBOAT4	NM_001100916.1,NM_001128208.1	,21	3,77,2203	AA,AG,GG		0.0314,5.9249,1.8178	,benign	,139/170	29994923	83,4483	692	1591	2283	SO:0001627	intron_variant	23484	exon4			CAACCCGTGCTGA	AF359269	CCDS47835.1	8p12	2008-08-04	2006-06-29	2006-06-29	ENSG00000177669	ENSG00000177669			32311	protein-coding gene	gene with protein product	"""ghrelin O-acyltransferase"""	611940	"""O-acyltransferase (membrane bound) domain containing 4"""	OACT4		18443287	Standard	NM_001100916		Approved	FKSG89, GOAT	uc010lvg.3	Q96T53	OTTHUMG00000163824	ENST00000320542.3:c.344+1124C>T	8.37:g.29994923G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	135	56	0.414815	NM_001128208	B1Q003	Missense_Mutation	SNP	ENST00000320542.3	37	CCDS47835.1	33	0.01510989010989011	29	0.05894308943089431	4	0.011049723756906077	0	0.0	0	0.0	G	13.55	2.271741	0.40194	0.059249	3.14E-4	ENSG00000104660	ENST00000523116	.	.	.	3.84	-1.13	0.09775	.	.	.	.	.	T	0.01523	0.0049	N	0.08118	0	0.09310	N	0.999999	B	0.16396	0.017	B	0.08055	0.003	T	0.23297	-1.0192	7	.	.	.	.	7.2794	0.26302	0.5248:0.0:0.4752:0.0	.	139	E9PHP8	.	M	139	.	.	V	+	1	0	LEPROTL1	30114465	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.030000	0.12308	-0.204000	0.10235	-0.469000	0.05056	GTG	G|0.984;A|0.016	0.016	strong		0.562	MBOAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375795.1		
WFIKKN2	124857	hgsc.bcm.edu	37	17	48917609	48917609	+	Silent	SNP	C	C	T	rs36031777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48917609C>T	ENST00000311378.4	+	2	1488	c.960C>T	c.(958-960)ggC>ggT	p.G320G	WFIKKN2_ENST00000426127.1_Silent_p.G227G|RP11-506D12.5_ENST00000572491.2_RNA	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	320					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)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			GCCCCAATGGCACGGCTTTCC	0.667													C|||	549	0.109625	0.1596	0.0274	5008	,	,		16399	0.0377		0.0278	False		,,,				2504	0.2587				p.G320G		Atlas-SNP	.											WFIKKN2,colon,carcinoma,0,1	WFIKKN2	69	1	0			c.C960T						PASS	.	C		597,3809	252.1+/-258.6	49,499,1655	50.0	45.0	46.0		960	4.4	1.0	17	dbSNP_126	46	237,8363	95.0+/-156.8	2,233,4065	no	coding-synonymous	WFIKKN2	NM_175575.5		51,732,5720	TT,TC,CC		2.7558,13.5497,6.4124		320/577	48917609	834,12172	2203	4300	6503	SO:0001819	synonymous_variant	124857	exon2			CAATGGCACGGCT	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30916	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20B"""	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.960C>T	17.37:g.48917609C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			C|0.933;T|0.067	0.067	strong		0.667	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
AMZ1	155185	hgsc.bcm.edu	37	7	2752026	2752026	+	Silent	SNP	G	G	A	rs61743920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2752026G>A	ENST00000312371.4	+	7	1379	c.1011G>A	c.(1009-1011)ccG>ccA	p.P337P	AMZ1_ENST00000489665.1_Intron|AMZ1_ENST00000407112.1_Missense_Mutation_p.V281I	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	337							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)		CGGGGGAGCCGTCAGTGTGGG	0.672													G|||	54	0.0107827	0.0386	0.0029	5008	,	,		15627	0.001		0.0	False		,,,				2504	0.0				p.P337P		Atlas-SNP	.											.	AMZ1	41	.	0			c.G1011A						PASS	.	G		160,4240	98.5+/-137.1	4,152,2044	23.0	28.0	26.0		1011	3.0	0.0	7	dbSNP_129	26	7,8591	5.7+/-21.5	0,7,4292	no	coding-synonymous	AMZ1	NM_133463.1		4,159,6336	AA,AG,GG		0.0814,3.6364,1.2848		337/499	2752026	167,12831	2200	4299	6499	SO:0001819	synonymous_variant	155185	exon7			GGAGCCGTCAGTG	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.1011G>A	7.37:g.2752026G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	37	CCDS34589.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	G	5.330	0.246159	0.10130	0.036364	8.14E-4	ENSG00000174945	ENST00000407112	T	0.35421	1.31	4.85	2.96	0.34315	.	.	.	.	.	T	0.05273	0.0140	.	.	.	0.09310	N	0.999999	B	0.20459	0.045	B	0.13407	0.009	T	0.16808	-1.0390	8	0.23302	T	0.38	-30.2079	7.4751	0.27371	0.0927:0.1681:0.7392:0.0	rs61743920	281	B3KRS0	.	I	281	ENSP00000386020:V281I	ENSP00000386020:V281I	V	+	1	0	AMZ1	2718552	0.000000	0.05858	0.027000	0.17364	0.064000	0.16182	-0.564000	0.05936	0.412000	0.25729	0.462000	0.41574	GTC	G|0.988;A|0.012	0.012	strong		0.672	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
ZNF93	81931	hgsc.bcm.edu	37	19	20044810	20044810	+	Missense_Mutation	SNP	C	C	T	rs75974774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:20044810C>T	ENST00000343769.5	+	4	1074	c.1046C>T	c.(1045-1047)gCc>gTc	p.A349V	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	349					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						TGTGGCAAAGCCTTTATTGCA	0.383													c|||	7	0.00139776	0.0053	0.0	5008	,	,		23005	0.0		0.0	False		,,,				2504	0.0				p.A349V		Atlas-SNP	.											.	ZNF93	81	.	0			c.C1046T						PASS	.	C	VAL/ALA	13,4393	20.2+/-43.8	0,13,2190	88.0	86.0	87.0		1046	0.9	0.8	19	dbSNP_131	87	0,8600		0,0,4300	yes	missense	ZNF93	NM_031218.3	64	0,13,6490	TT,TC,CC		0.0,0.2951,0.1	benign	349/621	20044810	13,12993	2203	4300	6503	SO:0001583	missense	81931	exon4			GCAAAGCCTTTAT	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.1046C>T	19.37:g.20044810C>T	ENSP00000342002:p.Ala349Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	92	47	0.51087	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Missense_Mutation	SNP	ENST00000343769.5	37	CCDS32973.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	c	16.93	3.258220	0.59321	0.002951	0.0	ENSG00000184635	ENST00000343769;ENST00000427325	T	0.13778	2.56	0.85	0.85	0.18980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12305	0.0299	L	0.28458	0.855	0.09310	N	0.999998	D	0.56035	0.974	P	0.60068	0.868	T	0.12760	-1.0535	9	0.52906	T	0.07	.	4.6298	0.12496	0.0:0.5889:0.4111:0.0	.	349	P35789	ZNF93_HUMAN	V	349	ENSP00000342002:A349V	ENSP00000342002:A349V	A	+	2	0	ZNF93	19905810	0.001000	0.12720	0.767000	0.31495	0.766000	0.43426	0.320000	0.19540	0.192000	0.20272	0.195000	0.17529	GCC	C|0.998;T|0.002	0.002	strong		0.383	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218	
IGSF9	57549	hgsc.bcm.edu	37	1	159898437	159898437	+	Missense_Mutation	SNP	G	G	A	rs35574000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159898437G>A	ENST00000368094.1	-	19	2938	c.2741C>T	c.(2740-2742)cCc>cTc	p.P914L	IGSF9_ENST00000361509.3_Missense_Mutation_p.P898L|IGSF9_ENST00000493195.1_5'UTR|TAGLN2_ENST00000368097.4_5'Flank	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	914	Pro-rich.		P -> L (in dbSNP:rs35574000).		dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			CAAGGGACTGGGTGGGGCTGC	0.657													G|||	74	0.0147764	0.0522	0.0072	5008	,	,		14684	0.0		0.0	False		,,,				2504	0.0				p.P914L		Atlas-SNP	.											.	IGSF9	123	.	0			c.C2741T						PASS	.	G	LEU/PRO,LEU/PRO	267,4113		7,253,1930	9.0	9.0	9.0		2741,2693	4.6	0.1	1	dbSNP_126	9	4,8536		0,4,4266	yes	missense,missense	IGSF9	NM_001135050.1,NM_020789.3	98,98	7,257,6196	AA,AG,GG		0.0468,6.0959,2.0975	probably-damaging,probably-damaging	914/1180,898/1164	159898437	271,12649	2190	4270	6460	SO:0001583	missense	57549	exon19			GGACTGGGTGGGG	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.2741C>T	1.37:g.159898437G>A	ENSP00000357073:p.Pro914Leu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	37	CCDS44254.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	G	14.74	2.625456	0.46840	0.060959	4.68E-4	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.66815	-0.23;-0.14	4.63	4.63	0.57726	.	0.000000	0.37906	N	0.001887	T	0.58694	0.2140	N	0.24115	0.695	0.21697	N	0.999586	D;B	0.89917	1.0;0.19	D;B	0.83275	0.996;0.081	T	0.53704	-0.8401	9	.	.	.	-10.2414	12.8357	0.57771	0.0:0.0:1.0:0.0	rs35574000	914;452	Q9P2J2;C9JI81	TUTLA_HUMAN;.	L	898;914;452	ENSP00000355049:P898L;ENSP00000357073:P914L	.	P	-	2	0	IGSF9	158165061	0.579000	0.26725	0.117000	0.21633	0.543000	0.35085	4.142000	0.58044	2.378000	0.81104	0.655000	0.94253	CCC	G|0.987;A|0.013	0.013	strong		0.657	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789	
KLHL32	114792	hgsc.bcm.edu	37	6	97533193	97533193	+	Silent	SNP	C	C	A	rs551403903		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:97533193C>A	ENST00000369261.4	+	6	966	c.603C>A	c.(601-603)tcC>tcA	p.S201S	KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000539200.1_Silent_p.S132S|KLHL32_ENST00000536676.1_Silent_p.S165S	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	201										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		GCCTGACCTCCCTGAGTGAAG	0.527																																					p.S201S		Atlas-SNP	.											KLHL32,mouth,carcinoma,+1,1	KLHL32	85	1	0			c.C603A						PASS	.						57.0	57.0	57.0					6																	97533193		2203	4300	6503	SO:0001819	synonymous_variant	114792	exon6			GACCTCCCTGAGT	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.603C>A	6.37:g.97533193C>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	83	4	0.0481928	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Silent	SNP	ENST00000369261.4	37	CCDS5038.1																																																																																			.	.	none		0.527	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904	
SUCO	51430	hgsc.bcm.edu	37	1	172547465	172547465	+	Silent	SNP	A	A	G	rs2285664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:172547465A>G	ENST00000263688.3	+	14	1587	c.1368A>G	c.(1366-1368)gaA>gaG	p.E456E	SUCO_ENST00000367723.4_Silent_p.E607E|SUCO_ENST00000610051.1_Silent_p.E419E|SUCO_ENST00000608151.1_Silent_p.E608E	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	456					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											TGGTGGAAGAATATGAAGAAA	0.358													A|||	1273	0.254193	0.2368	0.2089	5008	,	,		17330	0.2024		0.2296	False		,,,				2504	0.3885				p.E456E		Atlas-SNP	.											.	.	.	.	0			c.A1368G						PASS	.	A	,	1025,3381	378.3+/-322.8	111,803,1289	132.0	124.0	127.0		1368,1236	5.4	1.0	1	dbSNP_100	127	2069,6531	359.0+/-331.4	229,1611,2460	no	coding-synonymous,coding-synonymous	C1orf9	NM_014283.3,NM_016227.2	,	340,2414,3749	GG,GA,AA		24.0581,23.2637,23.789	,	456/1255,412/1211	172547465	3094,9912	2203	4300	6503	SO:0001819	synonymous_variant	51430	exon14			GGAAGAATATGAA	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1368A>G	1.37:g.172547465A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	166	83	0.5	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Silent	SNP	ENST00000263688.3	37	CCDS1303.1																																																																																			A|0.770;G|0.230	0.230	strong		0.358	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227	
ANKMY2	57037	hgsc.bcm.edu	37	7	16640491	16640491	+	Silent	SNP	G	G	A	rs541797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:16640491G>A	ENST00000306999.2	-	10	1464	c.1221C>T	c.(1219-1221)tcC>tcT	p.S407S		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	407						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)		CTTCAGGATTGGAATCCTTTT	0.443													G|||	901	0.179912	0.1967	0.3545	5008	,	,		20211	0.1012		0.166	False		,,,				2504	0.1288				p.S407S		Atlas-SNP	.											.	ANKMY2	46	.	0			c.C1221T						PASS	.	G		806,3600	321.0+/-296.9	74,658,1471	90.0	86.0	87.0		1221	0.7	0.0	7	dbSNP_83	87	1291,7309	255.2+/-280.2	91,1109,3100	yes	coding-synonymous	ANKMY2	NM_020319.2		165,1767,4571	AA,AG,GG		15.0116,18.2932,16.1233		407/442	16640491	2097,10909	2203	4300	6503	SO:0001819	synonymous_variant	57037	exon10			AGGATTGGAATCC	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.1221C>T	7.37:g.16640491G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	95	35	0.368421	NM_020319	A4D124|Q659G1|Q96BL3	Silent	SNP	ENST00000306999.2	37	CCDS5361.1																																																																																			G|0.835;A|0.165	0.165	strong		0.443	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319	
TMCO4	255104	hgsc.bcm.edu	37	1	20009837	20009837	+	Missense_Mutation	SNP	G	G	C	rs116650784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:20009837G>C	ENST00000294543.6	-	16	1842	c.1601C>G	c.(1600-1602)gCc>gGc	p.A534G	TMCO4_ENST00000375127.1_Missense_Mutation_p.A534G|TMCO4_ENST00000489814.1_5'UTR|TMCO4_ENST00000375122.2_Missense_Mutation_p.A494G	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	534						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)		GCAGCCTGGGGCCAGCAAGAG	0.672													G|||	115	0.0229633	0.0802	0.013	5008	,	,		16781	0.0		0.0	False		,,,				2504	0.0				p.A534G		Atlas-SNP	.											.	TMCO4	46	.	0			c.C1601G						PASS	.	G	GLY/ALA	310,4096	135.3+/-171.4	14,282,1907	30.0	33.0	32.0		1601	5.1	1.0	1	dbSNP_132	32	6,8594	5.0+/-18.6	0,6,4294	no	missense	TMCO4	NM_181719.4	60	14,288,6201	CC,CG,GG		0.0698,7.0359,2.4296	possibly-damaging	534/635	20009837	316,12690	2203	4300	6503	SO:0001583	missense	255104	exon16			CCTGGGGCCAGCA		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.1601C>G	1.37:g.20009837G>C	ENSP00000294543:p.Ala534Gly	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	201	95	0.472637	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Missense_Mutation	SNP	ENST00000294543.6	37	CCDS198.1	41	0.018772893772893772	36	0.07317073170731707	5	0.013812154696132596	0	0.0	0	0.0	G	14.56	2.573196	0.45902	0.070359	6.98E-4	ENSG00000162542	ENST00000294543;ENST00000375127;ENST00000375122	T;T;T	0.34275	1.39;1.41;1.37	5.11	5.11	0.69529	.	0.134780	0.33959	N	0.004400	T	0.02047	0.0064	L	0.32530	0.975	0.31140	N	0.706765	P;P;B	0.43231	0.473;0.801;0.42	B;B;B	0.35353	0.056;0.201;0.061	T	0.02070	-1.1219	10	0.39692	T	0.17	-0.7187	15.6348	0.76944	0.0:0.0:1.0:0.0	.	118;534;494	Q6ZSC6;Q5TGY1;Q5TGY1-2	.;TMCO4_HUMAN;.	G	534;534;494	ENSP00000294543:A534G;ENSP00000364269:A534G;ENSP00000364264:A494G	ENSP00000294543:A534G	A	-	2	0	TMCO4	19882424	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	2.016000	0.40971	2.532000	0.85374	0.563000	0.77884	GCC	G|0.975;C|0.025	0.025	strong		0.672	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719	
SIGLEC11	114132	hgsc.bcm.edu	37	19	50463670	50463670	+	Missense_Mutation	SNP	T	T	G	rs77553517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50463670T>G	ENST00000447370.2	-	3	559	c.469A>C	c.(469-471)Aag>Cag	p.K157Q	CTC-326K19.6_ENST00000451973.1_5'Flank|SIGLEC11_ENST00000426971.2_Missense_Mutation_p.K157Q	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	157					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		TCAGGCTTCTTAGTCAGGGCT	0.607																																					p.K157Q		Atlas-SNP	.											.	SIGLEC11	70	.	0			c.A469C						PASS	.	G	GLN/LYS,GLN/LYS	840,2990		167,506,1242	35.0	54.0	48.0		469,469	-0.6	0.0	19	dbSNP_131	48	1503,7087		54,1395,2846	yes	missense,missense	SIGLEC11	NM_001135163.1,NM_052884.2	53,53	221,1901,4088	GG,GT,TT		17.4971,21.9321,18.8647	benign,benign	157/603,157/699	50463670	2343,10077	1915	4295	6210	SO:0001583	missense	114132	exon3			GCTTCTTAGTCAG	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.469A>C	19.37:g.50463670T>G	ENSP00000412361:p.Lys157Gln	Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	73	71	0.972603	NM_052884		Missense_Mutation	SNP	ENST00000447370.2	37	CCDS12790.2	363	0.1662087912087912	102	0.2073170731707317	48	0.13259668508287292	112	0.1958041958041958	101	0.13324538258575197	G	0.021	-1.424972	0.01126	0.219321	0.174971	ENSG00000161640	ENST00000447370;ENST00000458019	T	0.03124	4.04	3.28	-0.577	0.11727	Immunoglobulin-like fold (1);	0.404011	0.21813	N	0.068733	T	0.00012	0.0000	N	0.00036	-2.54	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38950	-0.9637	9	0.16420	T	0.52	.	1.9279	0.03321	0.1102:0.1707:0.3701:0.349	.	157;157	Q96RL6-2;Q96RL6	.;SIG11_HUMAN	Q	157	ENSP00000412361:K157Q	ENSP00000412361:K157Q	K	-	1	0	SIGLEC11	55155482	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-0.174000	0.09839	-0.459000	0.07013	-0.217000	0.12591	AAG	T|0.840;G|0.160	0.160	strong		0.607	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884	
CNTROB	116840	hgsc.bcm.edu	37	17	7843053	7843053	+	Silent	SNP	C	C	T	rs11078719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7843053C>T	ENST00000563694.1	+	8	2075	c.1150C>T	c.(1150-1152)Ctg>Ttg	p.L384L	CNTROB_ENST00000380262.3_Silent_p.L384L|CNTROB_ENST00000565740.1_Silent_p.L384L|CNTROB_ENST00000380255.3_Silent_p.L384L	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	384	Required for centrosome localization.				centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				CCAGGCTCAGCTGGAAAGGGA	0.522													T|||	2979	0.594848	0.4433	0.6398	5008	,	,		20015	0.8016		0.4274	False		,,,				2504	0.727				p.L384L		Atlas-SNP	.											.	CNTROB	61	.	0			c.C1150T						PASS	.	T	,	2044,2362	578.7+/-384.7	482,1080,641	45.0	48.0	47.0		1150,1150	-6.8	0.2	17	dbSNP_120	47	3745,4853	586.7+/-392.1	829,2087,1383	no	coding-synonymous,coding-synonymous	CNTROB	NM_001037144.5,NM_053051.3	,	1311,3167,2024	TT,TC,CC		43.5566,46.3913,44.5171	,	384/926,384/904	7843053	5789,7215	2203	4299	6502	SO:0001819	synonymous_variant	116840	exon8			GCTCAGCTGGAAA	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.1150C>T	17.37:g.7843053C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Silent	SNP	ENST00000563694.1	37	CCDS11126.1																																																																																			C|0.506;T|0.494	0.494	strong		0.522	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	
MTCL1	23255	hgsc.bcm.edu	37	18	8825192	8825192	+	Silent	SNP	A	A	G	rs581894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:8825192A>G	ENST00000306329.11	+	13	4641	c.4641A>G	c.(4639-4641)ggA>ggG	p.G1547G	SOGA2_ENST00000518815.1_Silent_p.G553G|SOGA2_ENST00000359865.3_Silent_p.G1228G|SOGA2_ENST00000517570.1_Silent_p.G1187G|SOGA2_ENST00000400050.3_Silent_p.G1187G|SOGA2_ENST00000306285.7_Silent_p.G553G														p.G1229fs*52(1)									ACACCAAGGGAGGCCCTCCAG	0.687													G|||	2950	0.589058	0.7617	0.6441	5008	,	,		16650	0.4038		0.6342	False		,,,				2504	0.4611				p.G1228G		Atlas-SNP	.											CCDC165,NS,carcinoma,0,1	.	.	1	1	Deletion - Frameshift(1)	prostate(1)	c.A3684G						PASS	.	G		3180,1218		1179,822,198	18.0	21.0	20.0		3684	0.7	0.1	18	dbSNP_83	20	5108,3478		1604,1900,789	no	coding-synonymous	CCDC165	NM_015210.3		2783,2722,987	GG,GA,AA		40.5078,27.6944,36.1676		1228/1587	8825192	8288,4696	2199	4293	6492	SO:0001819	synonymous_variant	23255	exon15			CAAGGGAGGCCCT																												ENST00000306329.11:c.4641A>G	18.37:g.8825192A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_015210		Silent	SNP	ENST00000306329.11	37																																																																																				A|0.389;G|0.611	0.611	strong		0.687	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
IGF2R	3482	hgsc.bcm.edu	37	6	160469542	160469542	+	Silent	SNP	A	A	G	rs8191809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160469542A>G	ENST00000356956.1	+	18	2629	c.2481A>G	c.(2479-2481)gcA>gcG	p.A827A		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	827					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)	ACCGATATGCATCGGCTTGCC	0.493													A|||	48	0.00958466	0.0348	0.0029	5008	,	,		21284	0.0		0.0	False		,,,				2504	0.0				p.A827A		Atlas-SNP	.											.	IGF2R	251	.	0			c.A2481G						PASS	.	A		112,4294	85.8+/-124.5	0,112,2091	98.0	82.0	87.0		2481	-7.3	0.0	6	dbSNP_117	87	0,8600		0,0,4300	no	coding-synonymous	IGF2R	NM_000876.2		0,112,6391	GG,GA,AA		0.0,2.542,0.8611		827/2492	160469542	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	3482	exon18			ATATGCATCGGCT	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.2481A>G	6.37:g.160469542A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			A|0.988;G|0.012	0.012	strong		0.493	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
OR13C4	138804	hgsc.bcm.edu	37	9	107289352	107289352	+	Missense_Mutation	SNP	T	T	C	rs61738891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107289352T>C	ENST00000277216.3	-	1	138	c.139A>G	c.(139-141)Ata>Gta	p.I47V		NM_001001919.1	NP_001001919.1	Q8NGS5	O13C4_HUMAN	olfactory receptor, family 13, subfamily C, member 4	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(2)|lung(14)|skin(1)	18						ATGCTTGCTATGATCAGAACA	0.438													T|||	43	0.00858626	0.0318	0.0014	5008	,	,		22015	0.0		0.0	False		,,,				2504	0.0				p.I47V		Atlas-SNP	.											.	OR13C4	55	.	0			c.A139G						PASS	.	T	VAL/ILE	119,4287	89.2+/-127.9	1,117,2085	149.0	127.0	134.0		139	1.9	0.6	9	dbSNP_129	134	0,8600		0,0,4300	yes	missense	OR13C4	NM_001001919.1	29	1,117,6385	CC,CT,TT		0.0,2.7009,0.915	benign	47/319	107289352	119,12887	2203	4300	6503	SO:0001583	missense	138804	exon1			TTGCTATGATCAG		CCDS35088.1	9q31.1	2013-09-24			ENSG00000148136	ENSG00000148136		"""GPCR / Class A : Olfactory receptors"""	14722	protein-coding gene	gene with protein product							Standard	NM_001001919		Approved		uc011lvn.2	Q8NGS5	OTTHUMG00000020407	ENST00000277216.3:c.139A>G	9.37:g.107289352T>C	ENSP00000277216:p.Ile47Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	NM_001001919	Q6IF51|Q96R41	Missense_Mutation	SNP	ENST00000277216.3	37	CCDS35088.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	T	4.428	0.079162	0.08533	0.027009	0.0	ENSG00000148136	ENST00000277216;ENST00000545903	T	0.03889	3.77	4.45	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	0.410669	0.20335	U	0.094356	T	0.00815	0.0027	N	0.10782	0.045	0.09310	N	1	B	0.14805	0.011	B	0.15052	0.012	T	0.44772	-0.9306	10	0.40728	T	0.16	.	3.6631	0.08246	0.3365:0.0958:0.0:0.5676	.	47	Q8NGS5	O13C4_HUMAN	V	47;76	ENSP00000277216:I47V	ENSP00000277216:I47V	I	-	1	0	OR13C4	106329173	0.000000	0.05858	0.607000	0.28956	0.763000	0.43281	-0.351000	0.07711	0.256000	0.21614	0.482000	0.46254	ATA	T|0.992;C|0.008	0.008	strong		0.438	OR13C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053478.1		
INSR	3643	hgsc.bcm.edu	37	19	7267502	7267502	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7267502T>C	ENST00000302850.5	-	2	648	c.506A>G	c.(505-507)gAt>gGt	p.D169G	INSR_ENST00000341500.5_Missense_Mutation_p.D169G	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	169	Leu-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)"""	GATGTAATTATCCTCCACGGA	0.532																																					p.D169G		Atlas-SNP	.											INSR_ENST00000302850,NS,carcinoma,+1,2	INSR	265	2	0			c.A506G						scavenged	.						156.0	125.0	135.0					19																	7267502		2203	4300	6503	SO:0001583	missense	3643	exon2			TAATTATCCTCCA	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.506A>G	19.37:g.7267502T>C	ENSP00000303830:p.Asp169Gly	Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	239	3	0.0125523	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	37	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	T	12.39	1.922540	0.33908	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	D;D	0.82344	-1.6;-1.6	5.1	5.1	0.69264	.	0.000000	0.46442	U	0.000286	T	0.76898	0.4052	L	0.43923	1.385	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.10450	0.005;0.003;0.001	T	0.71803	-0.4482	10	0.31617	T	0.26	.	12.854	0.57873	0.0:0.0:0.0:1.0	.	160;169;169	Q86WY9;P06213-2;P06213	.;.;INSR_HUMAN	G	169	ENSP00000303830:D169G;ENSP00000342838:D169G	ENSP00000303830:D169G	D	-	2	0	INSR	7218502	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	7.623000	0.83113	1.916000	0.55485	0.460000	0.39030	GAT	.	.	none		0.532	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
CCDC125	202243	hgsc.bcm.edu	37	5	68588029	68588029	+	Missense_Mutation	SNP	T	T	C	rs112794294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68588029T>C	ENST00000396496.2	-	10	1192	c.1085A>G	c.(1084-1086)cAc>cGc	p.H362R	CCDC125_ENST00000396499.1_Missense_Mutation_p.H362R|CCDC125_ENST00000460090.1_Intron|CCDC125_ENST00000383374.2_Intron|CCDC125_ENST00000511257.1_Missense_Mutation_p.H237R			Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	362						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)		CTCTTTAAGGTGCTTCCAATT	0.318													T|||	58	0.0115815	0.0408	0.0058	5008	,	,		20797	0.0		0.0	False		,,,				2504	0.0				p.H362R		Atlas-SNP	.											.	CCDC125	41	.	0			c.A1085G						PASS	.	T	ARG/HIS	173,4231	113.3+/-151.4	1,171,2030	273.0	236.0	248.0		1085	-0.1	1.0	5	dbSNP_132	248	0,8600		0,0,4300	yes	missense	CCDC125	NM_176816.3	29	1,171,6330	CC,CT,TT		0.0,3.9282,1.3304	benign	362/512	68588029	173,12831	2202	4300	6502	SO:0001583	missense	202243	exon9			TTAAGGTGCTTCC	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.1085A>G	5.37:g.68588029T>C	ENSP00000379754:p.His362Arg	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	180	79	0.438889	NM_176816	Q86Z19	Missense_Mutation	SNP	ENST00000396496.2	37	CCDS4000.1	19	0.0086996336996337	15	0.03048780487804878	4	0.011049723756906077	0	0.0	0	0.0	T	0.922	-0.715564	0.03206	0.039282	0.0	ENSG00000183323	ENST00000396496;ENST00000396499;ENST00000511257	T;T;T	0.44482	0.92;0.92;0.92	4.28	-0.0527	0.13821	.	0.770151	0.12698	N	0.446592	T	0.06325	0.0163	L	0.41710	1.295	0.24112	N	0.995833	B	0.06786	0.001	B	0.09377	0.004	T	0.15206	-1.0445	10	0.17832	T	0.49	0.0174	2.3018	0.04164	0.1438:0.086:0.2964:0.4739	.	362	Q86Z20	CC125_HUMAN	R	362;362;237	ENSP00000379754:H362R;ENSP00000379756:H362R;ENSP00000426795:H237R	ENSP00000379754:H362R	H	-	2	0	CCDC125	68623785	0.832000	0.29368	0.951000	0.38953	0.996000	0.88848	0.157000	0.16402	-0.073000	0.12842	0.459000	0.35465	CAC	T|0.986;C|0.014	0.014	strong		0.318	CCDC125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254027.4	NM_176816	
AEBP1	165	hgsc.bcm.edu	37	7	44147485	44147485	+	Missense_Mutation	SNP	C	C	A	rs2537188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44147485C>A	ENST00000223357.3	+	5	1122	c.817C>A	c.(817-819)Ccc>Acc	p.P273T	MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_5'Flank	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	273	Pro-rich.		P -> T (in dbSNP:rs2537188).		cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						CTGGCCAGAGCCCCCTGAGGA	0.697													C|||	1790	0.357428	0.3684	0.2695	5008	,	,		13134	0.2738		0.3519	False		,,,				2504	0.4969				p.P273T		Atlas-SNP	.											AEBP1,NS,carcinoma,0,1	AEBP1	102	1	0			c.C817A						PASS	.	C	THR/PRO	1512,2824		285,942,941	10.0	13.0	12.0		817	1.4	0.1	7	dbSNP_100	12	3187,5327		639,1909,1709	no	missense	AEBP1	NM_001129.3	38	924,2851,2650	AA,AC,CC		37.4325,34.8708,36.5681	possibly-damaging	273/1159	44147485	4699,8151	2168	4257	6425	SO:0001583	missense	165	exon5			CCAGAGCCCCCTG	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"""aortic carboxypeptidase-like protein"", ""adipocyte enhancer binding protein 1"""	602981	"""AE-binding protein 1"""			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.817C>A	7.37:g.44147485C>A	ENSP00000223357:p.Pro273Thr	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	170	76	0.447059	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	CCDS5476.1	697	0.3191391941391941	148	0.3008130081300813	113	0.31215469613259667	155	0.270979020979021	281	0.370712401055409	C	8.109	0.778353	0.16120	0.348708	0.374325	ENSG00000106624	ENST00000223357	T	0.39997	1.05	4.54	1.41	0.22369	.	7.491200	0.00166	N	0.000008	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	9.000000000036756E-6	B	0.19817	0.039	B	0.14023	0.01	T	0.34950	-0.9808	9	0.48119	T	0.1	-0.4184	7.7789	0.29054	0.1715:0.4951:0.3335:0.0	rs2537188;rs60349212	273	Q8IUX7	AEBP1_HUMAN	T	273	ENSP00000223357:P273T	ENSP00000223357:P273T	P	+	1	0	AEBP1	44114010	0.001000	0.12720	0.074000	0.20217	0.361000	0.29550	0.387000	0.20718	0.318000	0.23185	0.491000	0.48974	CCC	C|0.678;A|0.322	0.322	strong		0.697	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129	
BDP1	55814	hgsc.bcm.edu	37	5	70818150	70818150	+	Missense_Mutation	SNP	C	C	G	rs12187098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70818150C>G	ENST00000358731.4	+	23	5289	c.5026C>G	c.(5026-5028)Caa>Gaa	p.Q1676E	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	1676			Q -> E (in dbSNP:rs12187098).		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)		TAGTTCAGCACAAATGACAAG	0.348													C|||	101	0.0201677	0.0454	0.013	5008	,	,		17087	0.0		0.0298	False		,,,				2504	0.002				p.Q1676E		Atlas-SNP	.											.	BDP1	204	.	0			c.C5026G						PASS	.	C	GLU/GLN	182,3514		3,176,1669	130.0	127.0	128.0		5026	4.5	0.1	5	dbSNP_120	128	196,7988		6,184,3902	yes	missense	BDP1	NM_018429.2	29	9,360,5571	GG,GC,CC		2.3949,4.9242,3.1818	possibly-damaging	1676/2625	70818150	378,11502	1848	4092	5940	SO:0001583	missense	55814	exon23			TCAGCACAAATGA	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.5026C>G	5.37:g.70818150C>G	ENSP00000351575:p.Gln1676Glu	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	173	76	0.439306	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	41	0.018772893772893772	19	0.03861788617886179	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	8.668	0.902198	0.17760	0.049242	0.023949	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.10477	2.87	5.35	4.48	0.54585	.	1.312210	0.05133	N	0.493011	T	0.01489	0.0048	L	0.47716	1.5	0.49687	D	0.999812	P;P	0.42871	0.557;0.792	B;B	0.37601	0.116;0.254	T	0.48514	-0.9029	10	0.02654	T	1	.	11.1063	0.48205	0.0:0.9126:0.0:0.0874	rs12187098;rs13169583;rs52833258;rs56647603;rs12187098	1676;1676	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	E	1676;1256	ENSP00000351575:Q1676E	ENSP00000351575:Q1676E	Q	+	1	0	BDP1	70853906	0.019000	0.18553	0.098000	0.21074	0.052000	0.14988	2.086000	0.41643	1.251000	0.43983	0.555000	0.69702	CAA	C|0.971;G|0.029	0.029	strong		0.348	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
SLC36A2	153201	hgsc.bcm.edu	37	5	150696447	150696447	+	Silent	SNP	C	C	T	rs369907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	136	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	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		
VPS54	51542	hgsc.bcm.edu	37	2	64160864	64160864	+	Missense_Mutation	SNP	G	G	C	rs34015596	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:64160864G>C	ENST00000272322.4	-	12	1836	c.1682C>G	c.(1681-1683)tCt>tGt	p.S561C	VPS54_ENST00000354504.3_Missense_Mutation_p.S408C|VPS54_ENST00000409558.4_Missense_Mutation_p.S549C			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	561			S -> C (in dbSNP:rs34015596).		growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						GCTGGATGAAGAATCAGTAGT	0.428													G|||	139	0.0277556	0.0998	0.0101	5008	,	,		17370	0.0		0.0	False		,,,				2504	0.0				p.S561C		Atlas-SNP	.											.	VPS54	57	.	0			c.C1682G						PASS	.	G	CYS/SER,CYS/SER	358,4048	185.0+/-212.2	14,330,1859	123.0	119.0	120.0		1646,1682	5.5	1.0	2	dbSNP_126	120	0,8600		0,0,4300	yes	missense,missense	VPS54	NM_001005739.1,NM_016516.2	112,112	14,330,6159	CC,CG,GG		0.0,8.1253,2.7526	probably-damaging,probably-damaging	549/966,561/978	64160864	358,12648	2203	4300	6503	SO:0001583	missense	51542	exon12			GATGAAGAATCAG	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 164"""	614633	"""vacuolar protein sorting 54 (yeast)"""			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.1682C>G	2.37:g.64160864G>C	ENSP00000272322:p.Ser561Cys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Missense_Mutation	SNP	ENST00000272322.4	37	CCDS33208.1	38	0.0173992673992674	34	0.06910569105691057	4	0.011049723756906077	0	0.0	0	0.0	G	22.3	4.266853	0.80469	0.081253	0.0	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	T;T;T	0.34859	1.34;1.37;1.37	5.47	5.47	0.80525	.	0.218968	0.49305	D	0.000159	T	0.03220	0.0094	N	0.22421	0.69	0.80722	D	1	D;D;D	0.63880	0.992;0.989;0.993	P;P;P	0.58660	0.794;0.701;0.843	T	0.01182	-1.1426	10	0.48119	T	0.1	.	19.3282	0.94273	0.0:0.0:1.0:0.0	rs34015596	408;561;549	Q9P1Q0-3;Q9P1Q0;Q9P1Q0-4	.;VPS54_HUMAN;.	C	408;561;549;549;561	ENSP00000346499:S408C;ENSP00000272322:S561C;ENSP00000386980:S549C	ENSP00000272322:S561C	S	-	2	0	VPS54	64014368	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.562000	0.82300	2.566000	0.86566	0.563000	0.77884	TCT	G|0.970;C|0.030	0.030	strong		0.428	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516	
LMNB1	4001	hgsc.bcm.edu	37	5	126140540	126140540	+	Silent	SNP	G	G	A	rs34224885	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:126140540G>A	ENST00000261366.5	+	2	793	c.432G>A	c.(430-432)tcG>tcA	p.S144S	LMNB1_ENST00000395354.1_Silent_p.S144S|LMNB1_ENST00000460265.1_3'UTR	NM_001198557.1|NM_005573.3	NP_001185486.1|NP_005564.1	P20700	LMNB1_HUMAN	lamin B1	144	Coil 1B.|Rod.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	lamin filament (GO:0005638)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		CACTGAATTCGAAAGATGCAG	0.428													G|||	113	0.0225639	0.0408	0.0331	5008	,	,		19240	0.0		0.0348	False		,,,				2504	0.001				p.S144S		Atlas-SNP	.											LMNB1,colon,carcinoma,+1,1	LMNB1	49	1	0			c.G432A						PASS	.	G	,	177,4229	116.7+/-154.6	3,171,2029	108.0	106.0	106.0		,432	-3.6	1.0	5	dbSNP_126	106	178,8422	82.0+/-144.6	3,172,4125	no	utr-5,coding-synonymous	LMNB1	NM_001198557.1,NM_005573.3	,	6,343,6154	AA,AG,GG		2.0698,4.0172,2.7295	,	,144/587	126140540	355,12651	2203	4300	6503	SO:0001819	synonymous_variant	4001	exon2			GAATTCGAAAGAT	L37737	CCDS4140.1	5q23.2	2013-01-16			ENSG00000113368	ENSG00000113368		"""Intermediate filaments type V, lamins"""	6637	protein-coding gene	gene with protein product		150340				7557986, 8838815	Standard	NM_005573		Approved		uc003kud.2	P20700	OTTHUMG00000128969	ENST00000261366.5:c.432G>A	5.37:g.126140540G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	114	49	0.429825	NM_005573	B2R6J6|Q3SYN7|Q96EI6	Silent	SNP	ENST00000261366.5	37	CCDS4140.1																																																																																			G|0.972;A|0.028	0.028	strong		0.428	LMNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250956.2	NM_005573	
TJP3	27134	hgsc.bcm.edu	37	19	3747890	3747890	+	Silent	SNP	C	C	T	rs10409928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3747890C>T	ENST00000541714.2	+	19	2883	c.2421C>T	c.(2419-2421)taC>taT	p.Y807Y	TJP3_ENST00000382008.3_Silent_p.Y821Y|TJP3_ENST00000539908.2_Silent_p.Y771Y|TJP3_ENST00000262968.9_Silent_p.Y840Y|TJP3_ENST00000587686.1_Silent_p.Y826Y|TJP3_ENST00000589378.1_Silent_p.Y816Y	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	807					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)		ACAGCGACTACGAGACGGACG	0.672													C|||	286	0.0571086	0.177	0.0187	5008	,	,		16934	0.0		0.0	False		,,,				2504	0.0399				p.Y816Y		Atlas-SNP	.											.	TJP3	79	.	0			c.C2448T						PASS	.	C		652,3752	261.0+/-264.0	45,562,1595	35.0	31.0	32.0		2520	-6.7	0.8	19	dbSNP_119	32	4,8592	3.0+/-9.4	0,4,4294	no	coding-synonymous	TJP3	NM_014428.1		45,566,5889	TT,TC,CC		0.0465,14.8047,5.0462		840/953	3747890	656,12344	2202	4298	6500	SO:0001819	synonymous_variant	27134	exon19			CGACTACGAGACG	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.2421C>T	19.37:g.3747890C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	132	76	0.575758	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			C|0.946;T|0.054	0.054	strong		0.672	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
USP17L2	377630	hgsc.bcm.edu	37	8	11996074	11996074	+	Missense_Mutation	SNP	T	T	C	rs142023572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11996074T>C	ENST00000333796.3	-	1	512	c.196A>G	c.(196-198)Aag>Gag	p.K66E	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	66				K -> E (in Ref. 1; AAR91701). {ECO:0000305}.	apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						GGAAGCTTCTTCCTGGGAGCA	0.577													t|||	237	0.0473243	0.1679	0.0173	5008	,	,		18470	0.0		0.001	False		,,,				2504	0.002				p.K66E		Atlas-SNP	.											USP17L2,bladder,carcinoma,+2,1	USP17L2	47	1	0			c.A196G						scavenged	.						43.0	58.0	53.0					8																	11996074		1243	2766	4009	SO:0001583	missense	377630	exon1			GCTTCTTCCTGGG	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"""deubiquitinating enzyme 3"""	610186	"""ubiquitin specific peptidase 17-like 2"""				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.196A>G	8.37:g.11996074T>C	ENSP00000333329:p.Lys66Glu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_201402		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	135	0.061813186813186816	73	0.1483739837398374	17	0.04696132596685083	21	0.03671328671328671	24	0.0316622691292876	t	4.441	0.081611	0.08533	.	.	ENSG00000223443	ENST00000333796	T	0.11169	2.8	0.36	0.36	0.16097	.	0.863387	0.09306	N	0.820218	T	0.00039	0.0001	.	.	.	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.41413	-0.9510	8	0.02654	T	1	.	2.3221	0.04213	0.0:0.39:0.3289:0.2811	.	66	Q6R6M4	U17L2_HUMAN	E	66	ENSP00000333329:K66E	ENSP00000333329:K66E	K	-	1	0	USP17L2	12033483	0.166000	0.22962	0.015000	0.15790	0.015000	0.08874	0.848000	0.27710	-0.366000	0.08064	-0.368000	0.07277	AAG	T|0.955;C|0.045	0.045	strong		0.577	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402	
CLCC1	23155	hgsc.bcm.edu	37	1	109479953	109479953	+	Missense_Mutation	SNP	G	G	A	rs150665002		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109479953G>A	ENST00000369971.2	-	10	1258	c.1129C>T	c.(1129-1131)Cgg>Tgg	p.R377W	CLCC1_ENST00000415331.1_Missense_Mutation_p.R327W|CLCC1_ENST00000369969.2_Missense_Mutation_p.R256W|CLCC1_ENST00000369970.3_Missense_Mutation_p.R327W|CLCC1_ENST00000369968.2_Missense_Mutation_p.R192W|CLCC1_ENST00000356970.2_Missense_Mutation_p.R377W|CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000302500.4_Missense_Mutation_p.R256W|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000369976.1_Intron|CLCC1_ENST00000348264.2_Missense_Mutation_p.R192W	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	377						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)		CTTCTATCCCGTGGCCGAAGT	0.517													g|||	1	0.000199681	0.0008	0.0	5008	,	,		15244	0.0		0.0	False		,,,				2504	0.0				p.R377W		Atlas-SNP	.											.	CLCC1	55	.	0			c.C1129T						PASS	.	A	TRP/ARG,TRP/ARG	7,4399	11.4+/-27.6	0,7,2196	67.0	69.0	68.0		1129,979	2.7	0.0	1	dbSNP_134	68	0,8600		0,0,4300	yes	missense,missense	CLCC1	NM_001048210.1,NM_015127.3	101,101	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	probably-damaging,probably-damaging	377/552,327/502	109479953	7,12999	2203	4300	6503	SO:0001583	missense	23155	exon10			TATCCCGTGGCCG	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.1129C>T	1.37:g.109479953G>A	ENSP00000358988:p.Arg377Trp	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_001048210	O94861|Q8WYP8|Q8WYP9|Q9BU25	Missense_Mutation	SNP	ENST00000369971.2	37	CCDS41362.1	.	.	.	.	.	.	.	.	.	.	g	6.512	0.462630	0.12402	0.001589	0.0	ENSG00000121940	ENST00000356970;ENST00000369971;ENST00000415331;ENST00000369969;ENST00000369968;ENST00000369970;ENST00000348264;ENST00000302500	T;T;T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77;0.77;0.77	5.57	2.72	0.32119	.	0.690178	0.15514	N	0.258371	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B;B;B;B	0.22851	0.008;0.076;0.008;0.0	B;B;B;B	0.17433	0.006;0.018;0.006;0.001	T	0.24261	-1.0165	10	0.36615	T	0.2	-3.3681	4.209	0.10502	0.2394:0.4109:0.2766:0.0731	.	192;256;327;377	Q96S66-4;Q96S66-3;Q96S66-2;Q96S66	.;.;.;CLCC1_HUMAN	W	377;377;327;256;192;327;192;256	ENSP00000349456:R377W;ENSP00000358988:R377W;ENSP00000411591:R327W;ENSP00000358986:R256W;ENSP00000358985:R192W;ENSP00000358987:R327W;ENSP00000337243:R192W;ENSP00000306552:R256W	ENSP00000306552:R256W	R	-	1	2	CLCC1	109281476	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.037000	0.13840	0.422000	0.26005	-0.820000	0.03113	CGG	G|1.000;A|0.000	0.000	strong		0.517	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127	
OR2AE1	81392	hgsc.bcm.edu	37	7	99474007	99474007	+	Missense_Mutation	SNP	T	T	C	rs60737583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99474007T>C	ENST00000316368.2	-	1	673	c.650A>G	c.(649-651)tAt>tGt	p.Y217C		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	217			Y -> C (in dbSNP:rs60737583).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GATGAAGACATAGGATGTAGA	0.488													T|||	372	0.0742812	0.2557	0.0288	5008	,	,		23905	0.001		0.002	False		,,,				2504	0.0112				p.Y217C		Atlas-SNP	.											.	OR2AE1	32	.	0			c.A650G						PASS	.	T	CYS/TYR	953,3453	361.1+/-315.5	103,747,1353	113.0	95.0	101.0		650	3.6	0.1	7	dbSNP_129	101	22,8578	14.0+/-48.4	0,22,4278	yes	missense	OR2AE1	NM_001005276.1	194	103,769,5631	CC,CT,TT		0.2558,21.6296,7.4965	probably-damaging	217/324	99474007	975,12031	2203	4300	6503	SO:0001583	missense	81392	exon1			AAGACATAGGATG	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"""GPCR / Class A : Olfactory receptors"""	15087	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily AE, member 2"""	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.650A>G	7.37:g.99474007T>C	ENSP00000313936:p.Tyr217Cys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_001005276	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	140	0.0641025641025641	127	0.258130081300813	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	T	13.17	2.158510	0.38119	0.216296	0.002558	ENSG00000244623	ENST00000316368	T	0.00520	6.85	3.62	3.62	0.41486	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36444	N	0.002597	T	0.00012	0.0000	H	0.95611	3.695	0.26077	P	0.9811449	D	0.89917	1.0	D	0.91635	0.999	T	0.23261	-1.0193	9	0.72032	D	0.01	.	10.8339	0.46675	0.0:0.0:0.0:1.0	rs60737583	217	Q8NHA4	O2AE1_HUMAN	C	217	ENSP00000313936:Y217C	ENSP00000313936:Y217C	Y	-	2	0	OR2AE1	99311943	1.000000	0.71417	0.058000	0.19502	0.189000	0.23516	5.082000	0.64450	1.877000	0.54381	0.405000	0.27470	TAT	T|0.932;C|0.068	0.068	strong		0.488	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1		
FSCN2	25794	hgsc.bcm.edu	37	17	79495890	79495890	+	Silent	SNP	C	C	T	rs117946784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79495890C>T	ENST00000417245.2	+	1	469	c.333C>T	c.(331-333)ttC>ttT	p.F111F	RP13-766D20.2_ENST00000430912.1_RNA|FSCN2_ENST00000334850.7_Silent_p.F111F|RP13-766D20.2_ENST00000442532.1_RNA	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	111					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|anatomical structure morphogenesis (GO:0009653)|eye photoreceptor cell development (GO:0042462)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|stereocilium (GO:0032420)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			endometrium(1)|lung(1)|prostate(1)|urinary_tract(1)	4	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GCCGCTTCTTCGGAGGCACCG	0.711													C|||	51	0.0101837	0.0023	0.0173	5008	,	,		15165	0.0		0.0209	False		,,,				2504	0.0153				p.F111F		Atlas-SNP	.											.	FSCN2	35	.	0			c.C333T						PASS	.	C	,	16,4090		0,16,2037	5.0	6.0	6.0		333,333	-1.7	0.9	17	dbSNP_132	6	130,8106		0,130,3988	no	coding-synonymous,coding-synonymous	FSCN2	NM_001077182.2,NM_012418.3	,	0,146,6025	TT,TC,CC		1.5784,0.3897,1.183	,	111/517,111/493	79495890	146,12196	2053	4118	6171	SO:0001819	synonymous_variant	25794	exon1			CTTCTTCGGAGGC	AF030165	CCDS45810.1, CCDS45811.1	17q25	2014-02-03	2014-02-03		ENSG00000186765	ENSG00000186765		"""Fascins"""	3960	protein-coding gene	gene with protein product		607643	"""fascin (Strongylocentrotus purpuratus) homolog 2 (actin-bundling protein, retinal)"", ""fascin homolog 2, actin-bundling protein, retinal (Strongylocentrotus purpuratus)"""			10234509	Standard	NM_012418		Approved	RP30, RFSN	uc010wuo.2	O14926	OTTHUMG00000167477	ENST00000417245.2:c.333C>T	17.37:g.79495890C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	10	5	0.5	NM_001077182	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	37	CCDS45811.1																																																																																			C|0.990;T|0.010	0.010	strong		0.711	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418	
MUC4	4585	hgsc.bcm.edu	37	3	195515435	195515435	+	Missense_Mutation	SNP	C	C	T	rs199540819	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515435C>T	ENST00000463781.3	-	2	3475	c.3016G>A	c.(3016-3018)Gcc>Acc	p.A1006T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1006T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	430	Repeat.|Ser-rich.				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.A1006T(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)		AGAGGGGTGGCGTGACCTGTG	0.582													.|||	29	0.00579073	0.0038	0.0202	5008	,	,		20547	0.002		0.006	False		,,,				2504	0.002				p.A1006T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	c.G3016A						scavenged	.						71.0	43.0	51.0					3																	195515435		692	1591	2283	SO:0001583	missense	4585	exon2			GGGTGGCGTGACC	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.3016G>A	3.37:g.195515435C>T	ENSP00000417498:p.Ala1006Thr	Somatic	218	5	0.0229358		WXS	Illumina HiSeq	Phase_I	580	21	0.0362069	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	9.628	1.135729	0.21123	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36699	1.25;1.24	1.24	-2.49	0.06403	.	.	.	.	.	T	0.15305	0.0369	N	0.14661	0.345	0.09310	N	1	B	0.14805	0.011	B	0.01281	0.0	T	0.23154	-1.0196	8	.	.	.	.	2.3206	0.04209	0.2815:0.1916:0.0:0.5269	.	1006	E7ESK3	.	T	1006	ENSP00000417498:A1006T;ENSP00000420243:A1006T	.	A	-	1	0	MUC4	196999830	.	.	0.001000	0.08648	0.173000	0.22820	.	.	-0.641000	0.05487	0.064000	0.15345	GCC	C|0.970;T|0.030	0.030	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TRERF1	55809	hgsc.bcm.edu	37	6	42233529	42233529	+	Silent	SNP	G	G	A	rs79466811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42233529G>A	ENST00000372922.4	-	6	2006	c.1444C>T	c.(1444-1446)Cta>Tta	p.L482L	TRERF1_ENST00000354325.2_Silent_p.L482L|TRERF1_ENST00000541110.1_Silent_p.L482L|TRERF1_ENST00000372917.4_Silent_p.L482L|TRERF1_ENST00000340840.2_Silent_p.L482L	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	482	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CCATCAGGTAGGTGCATCTAA	0.502													G|||	84	0.0167732	0.0605	0.0058	5008	,	,		18570	0.0		0.0	False		,,,				2504	0.0				p.L482L		Atlas-SNP	.											.	TRERF1	124	.	0			c.C1444T						PASS	.	G		239,4167	140.8+/-176.2	6,227,1970	56.0	54.0	55.0		1444	1.8	1.0	6	dbSNP_132	55	3,8597	3.7+/-12.6	0,3,4297	no	coding-synonymous	TRERF1	NM_033502.2		6,230,6267	AA,AG,GG		0.0349,5.4244,1.8607		482/1201	42233529	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	55809	exon6			CAGGTAGGTGCAT	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1444C>T	6.37:g.42233529G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	96	42	0.4375	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	37	CCDS4867.1																																																																																			G|0.981;A|0.019	0.019	strong		0.502	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
SLC16A5	9121	hgsc.bcm.edu	37	17	73096199	73096199	+	Silent	SNP	C	C	T	rs142993518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73096199C>T	ENST00000450736.2	+	4	856	c.441C>T	c.(439-441)ggC>ggT	p.G147G	SLC16A5_ENST00000580123.1_Silent_p.G147G|SLC16A5_ENST00000538213.2_Silent_p.G187G|SLC16A5_ENST00000329783.4_Silent_p.G147G			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	147					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	CCTCGATGGGCGTCTCCCTGG	0.642													C|||	6	0.00119808	0.0045	0.0	5008	,	,		16275	0.0		0.0	False		,,,				2504	0.0				p.G147G		Atlas-SNP	.											.	SLC16A5	80	.	0			c.C441T						PASS	.	C		24,4382	30.8+/-60.4	0,24,2179	41.0	39.0	40.0		441	-7.9	0.0	17	dbSNP_134	40	0,8600		0,0,4300	no	coding-synonymous	SLC16A5	NM_004695.2		0,24,6479	TT,TC,CC		0.0,0.5447,0.1845		147/506	73096199	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	9121	exon5			GATGGGCGTCTCC	U59299	CCDS11713.1	17q25.1	2013-07-18	2013-07-18		ENSG00000170190	ENSG00000170190		"""Solute carriers"""	10926	protein-coding gene	gene with protein product		603879	"""solute carrier family 16 (monocarboxylic acid transporters), member 5"", ""solute carrier family 16, member 5 (monocarboxylic acid transporter 6)"""			9425115	Standard	NM_004695		Approved	MCT5, MCT6	uc002jmr.4	O15375	OTTHUMG00000179277	ENST00000450736.2:c.441C>T	17.37:g.73096199C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_001271765	B4E288	Silent	SNP	ENST00000450736.2	37	CCDS11713.1																																																																																			C|0.998;T|0.002	0.002	strong		0.642	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695	
HLA-DOA	3111	hgsc.bcm.edu	37	6	32976013	32976013	+	Silent	SNP	G	G	A	rs78635760|rs41541116|rs538455361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32976013G>A	ENST00000229829.5	-	2	183	c.108C>T	c.(106-108)ccC>ccT	p.P36P	HLA-DOA_ENST00000495532.1_5'Flank|HLA-DOA_ENST00000450833.2_Silent_p.P6P	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	36	Alpha-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)|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						GGTAGAAGGCGGGTCCGTAGG	0.522													G|||	65	0.0129792	0.0454	0.0072	5008	,	,		19086	0.0		0.0	False		,,,				2504	0.0				p.P36P		Atlas-SNP	.											HLA-DOA,colon,carcinoma,0,1	HLA-DOA	22	1	0			c.C108T						PASS	.	G		140,2880		7,126,1377	47.0	49.0	48.0		108	0.4	1.0	6	dbSNP_131	48	3,5411		0,3,2704	no	coding-synonymous	HLA-DOA	NM_002119.3		7,129,4081	AA,AG,GG		0.0554,4.6358,1.6955		36/251	32976013	143,8291	1510	2707	4217	SO:0001819	synonymous_variant	3111	exon2			GAAGGCGGGTCCG	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.108C>T	6.37:g.32976013G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	89	60	0.674157	NM_002119	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Silent	SNP	ENST00000229829.5	37	CCDS4763.1	24	0.01098901098901099	21	0.042682926829268296	3	0.008287292817679558	0	0.0	0	0.0	G	11.11	1.541489	0.27563	0.046358	5.54E-4	ENSG00000204252	ENST00000432150	.	.	.	4.4	0.402	0.16344	.	0.265318	0.38720	N	0.001589	T	0.45577	0.1349	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48875	-0.8996	6	0.87932	D	0	.	5.2858	0.15700	0.0:0.0992:0.3715:0.5293	.	.	.	.	L	36	.	ENSP00000412819:P36L	P	-	2	0	HLA-DOA	33083991	0.970000	0.33590	0.999000	0.59377	0.977000	0.68977	-0.448000	0.06820	-0.008000	0.14320	-0.271000	0.10264	CCG	G|0.984;A|0.016	0.016	strong		0.522	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119	
MOGS	7841	hgsc.bcm.edu	37	2	74690039	74690039	+	Missense_Mutation	SNP	G	G	A	rs2268416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74690039G>A	ENST00000233616.4	-	4	1039	c.877C>T	c.(877-879)Ccc>Tcc	p.P293S	MOGS_ENST00000452063.2_Missense_Mutation_p.P187S|MOGS_ENST00000409065.1_3'UTR|MOGS_ENST00000535045.1_3'UTR|MOGS_ENST00000462443.1_5'UTR	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	293			P -> S (in dbSNP:rs2268416). {ECO:0000269|PubMed:7635146}.		cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						CGTTCAGGGGGGGCCCCTGGG	0.592													A|||	2698	0.538738	0.8714	0.3242	5008	,	,		18027	0.8214		0.159	False		,,,				2504	0.3405				p.P293S		Atlas-SNP	.											.	MOGS	58	.	0			c.C877T						PASS	.	A	SER/PRO,SER/PRO	2873,1041		1062,749,146	112.0	120.0	118.0		559,877	0.9	0.1	2	dbSNP_100	118	1202,7096		95,1012,3042	yes	missense,missense	MOGS	NM_001146158.1,NM_006302.2	74,74	1157,1761,3188	AA,AG,GG		14.4854,26.5968,33.3688	benign,benign	187/732,293/838	74690039	4075,8137	1957	4149	6106	SO:0001583	missense	7841	exon4			CAGGGGGGGCCCC	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"""glucosidase I"", ""processing A-glucosidase I"""	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.877C>T	2.37:g.74690039G>A	ENSP00000233616:p.Pro293Ser	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	37	CCDS42700.1	1100	0.5036630036630036	419	0.8516260162601627	97	0.26795580110497236	469	0.8199300699300699	115	0.1517150395778364	A	0.007	-1.939376	0.00484	0.734032	0.144854	ENSG00000115275	ENST00000233616;ENST00000452063;ENST00000448666	T;T;T	0.35973	1.28;1.28;1.28	4.85	0.945	0.19543	.	0.491884	0.22259	N	0.062440	T	0.00012	0.0000	N	0.01168	-0.975	0.09310	P	0.99999454037	B	0.02656	0.0	B	0.01281	0.0	T	0.33954	-0.9848	9	0.05721	T	0.95	-3.9946	1.0778	0.01636	0.5087:0.1551:0.1865:0.1497	rs2268416;rs58722329	293	Q13724	MOGS_HUMAN	S	293;187;187	ENSP00000233616:P293S;ENSP00000388201:P187S;ENSP00000410992:P187S	ENSP00000233616:P293S	P	-	1	0	MOGS	74543547	0.263000	0.24083	0.094000	0.20943	0.518000	0.34316	0.754000	0.26390	-0.235000	0.09767	-0.254000	0.11334	CCC	G|0.582;A|0.418	0.418	strong		0.592	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302	
PCDHGA10	56106	hgsc.bcm.edu	37	5	140793007	140793007	+	Missense_Mutation	SNP	A	A	G	rs4912751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140793007A>G	ENST00000398610.2	+	1	265	c.265A>G	c.(265-267)Atc>Gtc	p.I89V	PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	89	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> V (in dbSNP:rs4912751).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCAGCTTGATCACCGCGGG	0.617													N|||	2785	0.55611	0.8941	0.6239	5008	,	,		14913	0.3254		0.4245	False		,,,				2504	0.4243				p.I89V		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.A265G						PASS	.	G	,,VAL/ILE,,,,,,,,,,,,,,VAL/ILE	3572,716		1501,570,73	58.0	74.0	69.0		,,265,,,,,,,,,,,,,,265	2.8	1.0	5	dbSNP_111	69	3663,4883		792,2079,1402	no	intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032090.1	,,29,,,,,,,,,,,,,,29	2293,2649,1475	GG,GA,AA		42.8622,16.6978,43.6263	,,,,,,,,,,,,,,,,	,,89/937,,,,,,,,,,,,,,89/851	140793007	7235,5599	2144	4273	6417	SO:0001583	missense	56106	exon1			AGCTTGATCACCG		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"""Cadherins / Protocadherins : Clustered"""	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.265A>G	5.37:g.140793007A>G	ENSP00000381611:p.Ile89Val	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	37	CCDS47292.1	1169	0.5352564102564102	424	0.8617886178861789	217	0.5994475138121547	189	0.3304195804195804	339	0.4472295514511873	g	0.258	-1.001608	0.02128	0.833022	0.428622	ENSG00000253846	ENST00000398610	T	0.25749	1.78	5.89	2.76	0.32466	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00960	-1.095	0.49798	P	1.7800000000001148E-4	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.37197	-0.9716	8	0.02654	T	1	.	10.6926	0.45879	0.3043:0.0:0.6957:0.0	rs4912751;rs56999226;rs4912751	89;89	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	V	89	ENSP00000381611:I89V	ENSP00000381611:I89V	I	+	1	0	PCDHGA10	140773191	0.000000	0.05858	1.000000	0.80357	0.750000	0.42670	-2.080000	0.01368	0.352000	0.24053	-0.226000	0.12346	ATC	A|0.483;G|0.517	0.517	strong		0.617	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913	
STPG2	285555	hgsc.bcm.edu	37	4	99027184	99027184	+	Missense_Mutation	SNP	T	T	C	rs2903150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:99027184T>C	ENST00000295268.3	-	5	621	c.532A>G	c.(532-534)Atc>Gtc	p.I178V		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	178			I -> V (in dbSNP:rs2903150).														TCTCTCTTGATGTTAACATTT	0.254													t|||	1879	0.3752	0.4425	0.2882	5008	,	,		15525	0.2748		0.4026	False		,,,				2504	0.4213				p.I178V		Atlas-SNP	.											.	.	.	.	0			c.A532G						PASS	.	C	VAL/ILE	1967,2429	529.8+/-372.8	454,1059,685	81.0	83.0	82.0		532	2.6	1.0	4	dbSNP_101	82	3400,5194	487.8+/-372.2	692,2016,1589	yes	missense	C4orf37	NM_174952.2	29	1146,3075,2274	CC,CT,TT		39.5625,44.7452,41.3164	benign	178/460	99027184	5367,7623	2198	4297	6495	SO:0001583	missense	285555	exon5			TCTTGATGTTAAC	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.532A>G	4.37:g.99027184T>C	ENSP00000295268:p.Ile178Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	760	0.34798534798534797	193	0.39227642276422764	106	0.292817679558011	161	0.28146853146853146	300	0.39577836411609496	t	0.674	-0.800947	0.02841	0.447452	0.395625	ENSG00000163116	ENST00000295268	T	0.11385	2.78	5.04	2.61	0.31194	.	0.361157	0.28712	N	0.014387	T	0.00012	0.0000	L	0.52011	1.625	0.58432	P	8.000000000008E-6	B	0.22746	0.074	B	0.31614	0.133	T	0.46233	-0.9206	9	0.22109	T	0.4	-32.5742	6.054	0.19800	0.1206:0.1463:0.0:0.7331	rs2903150;rs52793168;rs61326598;rs2903150	178	Q8N412	CD037_HUMAN	V	178	ENSP00000295268:I178V	ENSP00000295268:I178V	I	-	1	0	C4orf37	99246207	1.000000	0.71417	0.997000	0.53966	0.048000	0.14542	0.706000	0.25690	0.089000	0.17243	-1.245000	0.01525	ATC	T|0.617;C|0.383	0.383	strong		0.254	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
ZAR1L	646799	hgsc.bcm.edu	37	13	32885654	32885654	+	Missense_Mutation	SNP	T	T	C	rs445909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:32885654T>C	ENST00000533490.2	-	3	827	c.409A>G	c.(409-411)Acc>Gcc	p.T137A	ZAR1L_ENST00000345108.6_Missense_Mutation_p.T137A			A6NP61	ZAR1L_HUMAN	zygote arrest 1-like	137						cytoplasm (GO:0005737)				NS(1)|kidney(1)	2						CTGCGGCCGGTGGCGGGCGAA	0.731													t|||	1963	0.391973	0.3313	0.4135	5008	,	,		13345	0.4851		0.3976	False		,,,				2504	0.3569				p.T137A		Atlas-SNP	.											ZAR1L,NS,meningioma,0,1	ZAR1L	17	1	0			c.A409G						PASS	.						2.0	3.0	3.0					13																	32885654		518	1327	1845	SO:0001583	missense	646799	exon1			GGCCGGTGGCGGG		CCDS45023.1	13q13.1	2014-02-20			ENSG00000189167	ENSG00000189167			37116	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 7"""					18442940	Standard	NM_001136571		Approved	Z3CXXC7	uc010abc.1	A6NP61	OTTHUMG00000016694	ENST00000533490.2:c.409A>G	13.37:g.32885654T>C	ENSP00000437289:p.Thr137Ala	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_001136571	B2RV03|B7ZBU2	Missense_Mutation	SNP	ENST00000533490.2	37	CCDS45023.1	879	0.4024725274725275	163	0.3313008130081301	139	0.3839779005524862	287	0.5017482517482518	290	0.38258575197889183	t	0.751	-0.772802	0.02951	.	.	ENSG00000189167	ENST00000345108	.	.	.	4.0	-6.3	0.02007	.	2.229460	0.02811	N	0.124375	T	0.00012	0.0000	N	0.03194	-0.395	0.80722	P	0.0	B	0.12013	0.005	B	0.10450	0.005	T	0.39014	-0.9634	8	0.05721	T	0.95	1.7448	7.7924	0.29127	0.0:0.3217:0.3846:0.2936	rs445909	137	A6NP61	ZAR1L_HUMAN	A	137	.	ENSP00000344616:T137A	T	-	1	0	ZAR1L	31783654	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.670000	0.05256	-0.840000	0.04206	-0.513000	0.04457	ACC	T|0.596;C|0.404	0.404	strong		0.731	ZAR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044403.5		
OR10G7	390265	hgsc.bcm.edu	37	11	123909441	123909441	+	Missense_Mutation	SNP	T	T	C	rs470208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909441T>C	ENST00000330487.5	-	1	276	c.268A>G	c.(268-270)Act>Gct	p.T90A		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	90			T -> A (in dbSNP:rs470208).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AAGGAGATAGTCCTGCCGCTT	0.517													t|||	92	0.0183706	0.0552	0.0086	5008	,	,		22993	0.0		0.0	False		,,,				2504	0.0133				p.T90A		Atlas-SNP	.											OR10G7,right_upper_lobe,carcinoma,+1,1	OR10G7	103	1	0			c.A268G						scavenged	.						220.0	235.0	230.0					11																	123909441		2200	4299	6499	SO:0001583	missense	390265	exon1			AGATAGTCCTGCC	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.268A>G	11.37:g.123909441T>C	ENSP00000329689:p.Thr90Ala	Somatic	843	18	0.0213523		WXS	Illumina HiSeq	Phase_I	630	107	0.169841	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	58	0.026556776556776556	25	0.0508130081300813	5	0.013812154696132596	6	0.01048951048951049	22	0.029023746701846966	C	0	-2.713855	0.00094	.	.	ENSG00000182634	ENST00000330487	T	0.00572	6.49	3.39	0.29	0.15728	GPCR, rhodopsin-like superfamily (1);	0.807151	0.10654	N	0.649576	T	0.00073	0.0002	N	0.11818	0.18	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34976	-0.9807	10	0.12430	T	0.62	.	5.2009	0.15264	0.0:0.2811:0.3445:0.3744	rs470208;rs666719;rs12363298;rs60309526	90	Q8NGN6	O10G7_HUMAN	A	90	ENSP00000329689:T90A	ENSP00000329689:T90A	T	-	1	0	OR10G7	123414651	0.000000	0.05858	0.001000	0.08648	0.144000	0.21451	-0.288000	0.08377	-0.300000	0.08895	-0.374000	0.07098	ACT	T|0.874;C|0.126	0.126	strong		0.517	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
KMT2C	58508	hgsc.bcm.edu	37	7	151859495	151859495	+	Missense_Mutation	SNP	C	C	G	rs115580901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151859495C>G	ENST00000262189.6	-	43	11385	c.11167G>C	c.(11167-11169)Gct>Cct	p.A3723P	KMT2C_ENST00000355193.2_Missense_Mutation_p.A3723P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3723					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)										TCTGTCTCAGCCTTTTCCAGT	0.478													C|||	9	0.00179712	0.0061	0.0014	5008	,	,		19613	0.0		0.0	False		,,,				2504	0.0				p.A3723P		Atlas-SNP	.											.	MLL3	1564	.	0			c.G11167C						PASS	.	C	PRO/ALA	19,4387	26.2+/-53.5	0,19,2184	177.0	181.0	180.0		11167	-2.0	0.0	7	dbSNP_133	180	0,8600		0,0,4300	yes	missense	MLL3	NM_170606.2	27	0,19,6484	GG,GC,CC		0.0,0.4312,0.1461	benign	3723/4912	151859495	19,12987	2203	4300	6503	SO:0001583	missense	58508	exon43			TCTCAGCCTTTTC	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.11167G>C	7.37:g.151859495C>G	ENSP00000262189:p.Ala3723Pro	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	176	93	0.528409	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	3|3	0.0013736263736263737|0.0013736263736263737	3|3	0.006097560975609756|0.006097560975609756	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	5.391|5.391	0.257270|0.257270	0.10239|0.10239	0.004312|0.004312	0.0|0.0	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	D;D;D|.	0.89415|.	-1.83;-1.81;-2.51|.	5.51|5.51	-2.01|-2.01	0.07410|0.07410	.|.	0.151901|.	0.29660|.	U|.	0.011527|.	T|T	0.18341|0.18341	0.0440|0.0440	L|L	0.29908|0.29908	0.895|0.895	0.29679|0.29679	N|N	0.841841|0.841841	B;B;B|.	0.10296|.	0.002;0.001;0.003|.	B;B;B|.	0.09377|.	0.003;0.003;0.004|.	T|T	0.24440|0.24440	-1.0160|-1.0160	10|5	0.37606|.	T|.	0.19|.	.|.	2.0729|2.0729	0.03618|0.03618	0.1792:0.4224:0.1773:0.2212|0.1792:0.4224:0.1773:0.2212	.|.	3723;2784;3723|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	P|A	3723;3723;309|1228	ENSP00000262189:A3723P;ENSP00000347325:A3723P;ENSP00000410411:A309P|.	ENSP00000262189:A3723P|.	A|G	-|-	1|2	0|0	MLL3|MLL3	151490428|151490428	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.471000|0.471000	0.32888|0.32888	-0.542000|-0.542000	0.06091|0.06091	-1.225000|-1.225000	0.02578|0.02578	-1.938000|-1.938000	0.00498|0.00498	GCT|GGC	C|0.998;G|0.002	0.002	strong		0.478	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
LPL	4023	hgsc.bcm.edu	37	8	19819724	19819724	+	Nonsense_Mutation	SNP	C	C	G	rs328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:19819724C>G	ENST00000311322.8	+	9	1891	c.1421C>G	c.(1420-1422)tCa>tGa	p.S474*		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	474					chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	AATAAGAAGTCAGGCTGGTGA	0.502													C|||	463	0.0924521	0.0613	0.0634	5008	,	,		19349	0.122		0.1302	False		,,,				2504	0.0859				p.S474X		Atlas-SNP	.											.	LPL	78	.	0			c.C1421G	GRCh37	CM900164	LPL	M	rs328	PASS	.	C	stop/SER	291,4115	159.2+/-191.8	7,277,1919	133.0	123.0	126.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1421	4.0	1.0	8	dbSNP_36	126	832,7768	191.4+/-237.6	45,742,3513	yes	stop-gained	LPL	NM_000237.2		52,1019,5432	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	9.6744,6.6046,8.6345		474/476	19819724	1123,11883	2203	4300	6503	SO:0001587	stop_gained	4023	exon9			AGAAGTCAGGCTG		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.1421C>G	8.37:g.19819724C>G	ENSP00000309757:p.Ser474*	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Nonsense_Mutation	SNP	ENST00000311322.8	37	CCDS6012.1	210	0.09615384615384616	26	0.052845528455284556	28	0.07734806629834254	63	0.11013986013986014	93	0.12269129287598944	C	42	9.203276	0.99099	0.066046	0.096744	ENSG00000175445	ENST00000311322;ENST00000535763	.	.	.	5.89	4.01	0.46588	.	1.169270	0.05850	N	0.621066	.	.	.	.	.	.	0.27649	P	0.947441	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.8612	7.5989	0.28065	0.2764:0.6427:0.0:0.0808	rs328;rs3735962;rs17482566;rs52834251;rs328	.	.	.	X	474;460	.	.	S	+	2	0	LPL	19864004	0.980000	0.34600	1.000000	0.80357	0.994000	0.84299	0.684000	0.25364	2.793000	0.96121	0.655000	0.94253	TCA	C|0.914;G|0.086	0.086	strong		0.502	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3		
DNHD1	144132	hgsc.bcm.edu	37	11	6585838	6585838	+	Silent	SNP	G	G	A	rs11825255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6585838G>A	ENST00000527990.2	+	30	10560	c.10560G>A	c.(10558-10560)caG>caA	p.Q3520Q	DNHD1_ENST00000254579.6_Silent_p.Q3520Q			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3520					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)		AATCGGAGCAGTACCAGTGGG	0.552													G|||	991	0.197883	0.5484	0.1254	5008	,	,		19760	0.0149		0.0417	False		,,,				2504	0.1247				p.Q3520Q		Atlas-SNP	.											.	DNHD1	198	.	0			c.G10560A						PASS	.	G		681,703		168,345,179	124.0	119.0	120.0		10560	4.7	0.9	11	dbSNP_120	120	153,3029		3,147,1441	no	coding-synonymous	DNHD1	NM_144666.2		171,492,1620	AA,AG,GG		4.8083,49.2052,18.2654		3520/4754	6585838	834,3732	692	1591	2283	SO:0001819	synonymous_variant	144132	exon32			GGAGCAGTACCAG	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.10560G>A	11.37:g.6585838G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.816;A|0.184	0.184	strong		0.552	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
CSMD2	114784	hgsc.bcm.edu	37	1	34112303	34112303	+	Silent	SNP	G	G	A	rs10798976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:34112303G>A	ENST00000373380.1	-	8	1558	c.1338C>T	c.(1336-1338)ctC>ctT	p.L446L	CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373381.4_Silent_p.L1573L			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1533	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TGCGGAAGGCGAGGAAGAGGC	0.557													G|||	535	0.106829	0.2716	0.0504	5008	,	,		17999	0.1181		0.004	False		,,,				2504	0.0184				p.L1533L		Atlas-SNP	.											.	CSMD2	946	.	0			c.C4599T						PASS	.	G		917,3489	355.6+/-313.1	89,739,1375	87.0	82.0	84.0		4599	-4.0	1.0	1	dbSNP_120	84	52,8548	33.3+/-86.6	0,52,4248	no	coding-synonymous	CSMD2	NM_052896.3		89,791,5623	AA,AG,GG		0.6047,20.8125,7.4504		1533/3488	34112303	969,12037	2203	4300	6503	SO:0001819	synonymous_variant	114784	exon29			GAAGGCGAGGAAG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.1338C>T	1.37:g.34112303G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	133	52	0.390977	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373380.1	37																																																																																				G|0.905;A|0.095	0.095	strong		0.557	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	
NSA2	10412	hgsc.bcm.edu	37	5	74069863	74069863	+	Silent	SNP	A	A	G	rs6874609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:74069863A>G	ENST00000296802.5	+	5	1062	c.693A>G	c.(691-693)acA>acG	p.T231T		NM_014886.3	NP_055701.1	O95478	NSA2_HUMAN	NSA2 ribosome biogenesis homolog (S. cerevisiae)	231					rRNA processing (GO:0006364)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|skin(1)	7						GCCTTGTGACACAAGGAGGCA	0.378													G|||	1907	0.380791	0.7481	0.3357	5008	,	,		16898	0.2063		0.2416	False		,,,				2504	0.2393				p.T231T		Atlas-SNP	.											NSA2,NS,carcinoma,+1,1	NSA2	18	1	0			c.A693G						PASS	.	G		2961,1445	466.6+/-354.6	1000,961,242	96.0	92.0	94.0		693	-3.0	1.0	5	dbSNP_116	94	1912,6688	726.4+/-406.6	204,1504,2592	yes	coding-synonymous	NSA2	NM_014886.3		1204,2465,2834	GG,GA,AA		22.2326,32.7962,37.4673		231/261	74069863	4873,8133	2203	4300	6503	SO:0001819	synonymous_variant	10412	exon5			TGTGACACAAGGA	AF077615	CCDS4025.1, CCDS75260.1	5q13.3	2010-01-18			ENSG00000164346	ENSG00000164346			30728	protein-coding gene	gene with protein product	"""hairy cell leukemia protein 1"", ""TGF beta-inducible nuclear protein 1"""	612497				11124703, 10486207	Standard	NM_014886		Approved	HUSSY-29, HCLG1, FLJ94393, TINP1	uc003kdk.2	O95478	OTTHUMG00000131273	ENST00000296802.5:c.693A>G	5.37:g.74069863A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_014886		Silent	SNP	ENST00000296802.5	37	CCDS4025.1																																																																																			A|0.624;G|0.376	0.376	strong		0.378	NSA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254041.3	NM_014886	
TMEM200B	399474	hgsc.bcm.edu	37	1	29447765	29447765	+	Silent	SNP	G	G	T	rs115927590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:29447765G>T	ENST00000420504.2	-	2	733	c.576C>A	c.(574-576)tcC>tcA	p.S192S	TMEM200B_ENST00000521452.1_Silent_p.S192S	NM_001171868.1	NP_001165339.1	Q69YZ2	T200B_HUMAN	transmembrane protein 200B	192	Pro-rich.					integral component of membrane (GO:0016021)				ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.00765)|Lung NSC(340;0.0153)|all_lung(284;0.0173)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;7.32e-08)|COAD - Colon adenocarcinoma(152;4.92e-06)|STAD - Stomach adenocarcinoma(196;0.00618)|BRCA - Breast invasive adenocarcinoma(304;0.0501)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.126)		CCCGACGCGGGGACGGGTCCC	0.692													G|||	46	0.0091853	0.0325	0.0043	5008	,	,		14044	0.0		0.0	False		,,,				2504	0.0				p.S192S		Atlas-SNP	.											.	TMEM200B	9	.	0			c.C576A						PASS	.	G	,	98,4306		2,94,2106	16.0	17.0	17.0		576,576	1.4	1.0	1	dbSNP_132	17	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	TMEM200B	NM_001003682.3,NM_001171868.1	,	2,94,6404	TT,TG,GG		0.0,2.2252,0.7538	,	192/308,192/308	29447765	98,12902	2202	4298	6500	SO:0001819	synonymous_variant	399474	exon2			ACGCGGGGACGGG		CCDS30658.1	1p35	2007-12-18			ENSG00000253304	ENSG00000253304			33785	protein-coding gene	gene with protein product						15722956	Standard	NM_001003682		Approved	TTMB	uc001brn.2	Q69YZ2	OTTHUMG00000003658	ENST00000420504.2:c.576C>A	1.37:g.29447765G>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_001171868	Q6P2G8|Q6P2Q5	Silent	SNP	ENST00000420504.2	37	CCDS30658.1																																																																																			G|0.990;T|0.010	0.010	strong		0.692	TMEM200B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010377.2	NM_001003682	
ZNF253	56242	hgsc.bcm.edu	37	19	20003109	20003109	+	Silent	SNP	A	A	G	rs8106559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:20003109A>G	ENST00000589717.1	+	4	1145	c.1053A>G	c.(1051-1053)ctA>ctG	p.L351L	CTC-559E9.8_ENST00000585571.1_RNA|ZNF253_ENST00000355650.4_Silent_p.L275L|AC011477.1_ENST00000578823.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	351				Missing (in Ref. 1; AAC26844). {ECO:0000305}.	negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCTTTCACCTATCCTCACACC	0.388													a|||	2422	0.483626	0.6762	0.379	5008	,	,		22620	0.6815		0.2376	False		,,,				2504	0.3466				p.L351L		Atlas-SNP	.											.	ZNF253	99	.	0			c.A1053G						PASS	.	A		2644,1696		840,964,366	46.0	50.0	49.0		1053	-1.8	0.0	19	dbSNP_116	49	2088,6472		252,1584,2444	no	coding-synonymous	ZNF253	NM_021047.2		1092,2548,2810	GG,GA,AA		24.3925,39.0783,36.6822		351/500	20003109	4732,8168	2170	4280	6450	SO:0001819	synonymous_variant	56242	exon4			TCACCTATCCTCA	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"""Zinc fingers, C2H2-type"", ""-"""	13497	protein-coding gene	gene with protein product		606954	"""zinc finger protein 411"""	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.1053A>G	19.37:g.20003109A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Silent	SNP	ENST00000589717.1	37	CCDS42532.1																																																																																			A|0.602;G|0.398	0.398	strong		0.388	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047	
PSMA4	5685	hgsc.bcm.edu	37	15	78841220	78841220	+	Silent	SNP	T	T	C	rs8053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:78841220T>C	ENST00000044462.7	+	9	870	c.720T>C	c.(718-720)caT>caC	p.H240H	PSMA4_ENST00000413382.2_Silent_p.H169H|PSMA4_ENST00000558341.1_Nonstop_Mutation_p.*126R|PSMA4_ENST00000558281.1_3'UTR|PSMA4_ENST00000559082.1_Silent_p.H240H|PSMA4_ENST00000558094.1_3'UTR|PSMA4_ENST00000560217.1_Silent_p.H209H	NM_002789.4	NP_002780.1	P25789	PSA4_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 4	240					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)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						TCAAAAAACATGAGGAAGAAG	0.353													C|||	3768	0.752396	0.8389	0.7781	5008	,	,		18985	0.8522		0.6282	False		,,,				2504	0.6421				p.H240H		Atlas-SNP	.											.	PSMA4	17	.	0			c.T720C						PASS	.	C	,,	3333,1059	387.5+/-326.5	1280,773,143	74.0	75.0	75.0		720,507,720	-7.6	0.5	15	dbSNP_52	75	5001,3585	518.6+/-379.3	1472,2057,764	no	coding-synonymous,coding-synonymous,coding-synonymous	PSMA4	NM_001102667.1,NM_001102668.1,NM_002789.4	,,	2752,2830,907	CC,CT,TT		41.754,24.112,35.7836	,,	240/262,169/191,240/262	78841220	8334,4644	2196	4293	6489	SO:0001819	synonymous_variant	5685	exon9			AAAACATGAGGAA	BC005361	CCDS10303.1, CCDS45319.1	15q24.1	2004-01-19			ENSG00000041357	ENSG00000041357		"""Proteasome (prosome, macropain) subunits"""	9533	protein-coding gene	gene with protein product		176846				2025653	Standard	NM_002789		Approved	HC9, HsT17706	uc010blf.3	P25789	OTTHUMG00000143859	ENST00000044462.7:c.720T>C	15.37:g.78841220T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_001102667	D3DW86|Q53XP2|Q567Q5|Q8TBD1	Silent	SNP	ENST00000044462.7	37	CCDS10303.1																																																																																			T|0.307;C|0.693	0.693	strong		0.353	PSMA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290107.5	NM_002789	
CKAP2L	150468	hgsc.bcm.edu	37	2	113514159	113514159	+	Missense_Mutation	SNP	T	T	A	rs17042341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113514159T>A	ENST00000302450.6	-	4	867	c.789A>T	c.(787-789)agA>agT	p.R263S	CKAP2L_ENST00000541405.1_Missense_Mutation_p.R98S|CKAP2L_ENST00000481732.1_5'Flank	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	263			R -> S (in dbSNP:rs17042341). {ECO:0000269|PubMed:15815621}.			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						GATCTGCTCCTCTAGAGAGTT	0.413													T|||	370	0.0738818	0.2073	0.0461	5008	,	,		20599	0.0		0.0497	False		,,,				2504	0.0143				p.R263S		Atlas-SNP	.											.	CKAP2L	54	.	0			c.A789T						PASS	.	T	SER/ARG	760,3646	309.7+/-291.2	60,640,1503	121.0	122.0	122.0		789	0.0	0.0	2	dbSNP_123	122	453,8147	135.6+/-192.8	15,423,3862	yes	missense	CKAP2L	NM_152515.3	110	75,1063,5365	AA,AT,TT		5.2674,17.2492,9.3265	possibly-damaging	263/746	113514159	1213,11793	2203	4300	6503	SO:0001583	missense	150468	exon4			TGCTCCTCTAGAG	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.789A>T	2.37:g.113514159T>A	ENSP00000305204:p.Arg263Ser	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Missense_Mutation	SNP	ENST00000302450.6	37	CCDS2100.1	138	0.06318681318681318	90	0.18292682926829268	15	0.04143646408839779	0	0.0	33	0.04353562005277045	T	12.82	2.052933	0.36181	0.172492	0.052674	ENSG00000169607	ENST00000541405;ENST00000302450	T;T	0.11495	2.77;3.42	5.35	0.0376	0.14197	.	0.522659	0.20267	N	0.095744	T	0.00039	0.0001	M	0.62723	1.935	0.80722	P	0.0	B	0.32829	0.386	B	0.34242	0.178	T	0.24476	-1.0159	9	0.46703	T	0.11	-11.3302	3.3236	0.07059	0.1664:0.2727:0.0:0.5609	rs17042341;rs52812224;rs17042341	263	Q8IYA6	CKP2L_HUMAN	S	98;263	ENSP00000438763:R98S;ENSP00000305204:R263S	ENSP00000305204:R263S	R	-	3	2	CKAP2L	113230630	0.001000	0.12720	0.009000	0.14445	0.631000	0.37964	0.626000	0.24492	0.193000	0.20303	-0.361000	0.07541	AGA	T|0.919;A|0.081	0.081	strong		0.413	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515	
ATP11A	23250	hgsc.bcm.edu	37	13	113479820	113479820	+	Missense_Mutation	SNP	A	A	G	rs368865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113479820A>G	ENST00000487903.1	+	11	1037	c.949A>G	c.(949-951)Atg>Gtg	p.M317V	ATP11A_ENST00000375645.3_Missense_Mutation_p.M317V|ATP11A_ENST00000283558.8_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	203	0	0		WXS	Illumina HiSeq	Phase_I	213	212	0.995305	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	
NOS3	4846	hgsc.bcm.edu	37	7	150710392	150710392	+	Silent	SNP	G	G	A	rs3730011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150710392G>A	ENST00000297494.3	+	25	3537	c.3180G>A	c.(3178-3180)gaG>gaA	p.E1060E	NOS3_ENST00000477227.1_3'UTR|ATG9B_ENST00000444312.1_3'UTR|NOS3_ENST00000461406.1_Silent_p.E854E|ATG9B_ENST00000377974.2_3'UTR|ATG9B_ENST00000494791.1_5'UTR|ATG9B_ENST00000605938.1_3'UTR	NM_000603.4	NP_000594.2	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					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)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACCGCGACGAGGTGCAGAACG	0.642											OREG0018443	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	18	0.00359425	0.0136	0.0	5008	,	,		13957	0.0		0.0	False		,,,				2504	0.0				p.E1060E		Atlas-SNP	.											NOS3,NS,carcinoma,+2,1	NOS3	131	1	0			c.G3180A						PASS	.	G	,	49,4357	50.2+/-85.5	1,47,2155	77.0	72.0	74.0		3180,	4.2	1.0	7	dbSNP_107	74	0,8600		0,0,4300	no	coding-synonymous,utr-3	NOS3,ATG9B	NM_000603.4,NM_173681.5	,	1,47,6455	AA,AG,GG		0.0,1.1121,0.3767	,	1060/1204,	150710392	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	4846	exon25			CGACGAGGTGCAG		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000297494.3:c.3180G>A	7.37:g.150710392G>A		Somatic	68	0	0	1734	WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_000603	Q495E5	Silent	SNP	ENST00000297494.3	37	CCDS5912.1																																																																																			G|0.995;A|0.005	0.005	strong		0.642	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603	
CACNA1S	779	hgsc.bcm.edu	37	1	201046164	201046164	+	Missense_Mutation	SNP	C	C	T	rs114191482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201046164C>T	ENST00000362061.3	-	12	1937	c.1711G>A	c.(1711-1713)Gtc>Atc	p.V571I	CACNA1S_ENST00000367338.3_Missense_Mutation_p.V571I	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	571					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)	GCGAAGATGACGATGAAGAGG	0.557													C|||	8	0.00159744	0.0053	0.0	5008	,	,		23357	0.001		0.0	False		,,,				2504	0.0				p.V571I		Atlas-SNP	.											.	CACNA1S	249	.	0			c.G1711A						PASS	.	C	ILE/VAL	29,4377	37.6+/-69.7	0,29,2174	152.0	135.0	141.0		1711	-2.8	1.0	1	dbSNP_132	141	0,8600		0,0,4300	yes	missense	CACNA1S	NM_000069.2	29	0,29,6474	TT,TC,CC		0.0,0.6582,0.223	benign	571/1874	201046164	29,12977	2203	4300	6503	SO:0001583	missense	779	exon12			AGATGACGATGAA	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.1711G>A	1.37:g.201046164C>T	ENSP00000355192:p.Val571Ile	Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	368	187	0.508152	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	4.708	0.131666	0.08981	0.006582	0.0	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.98381	-4.9;-4.9	4.45	-2.76	0.05896	Ion transport (1);	0.302241	0.36034	N	0.002837	D	0.87888	0.6291	N	0.11201	0.11	0.24428	N	0.994582	B	0.06786	0.001	B	0.08055	0.003	T	0.82733	-0.0311	10	0.02654	T	1	.	8.3162	0.32102	0.1089:0.1105:0.0:0.7805	.	571	Q13698	CAC1S_HUMAN	I	571	ENSP00000355192:V571I;ENSP00000356307:V571I	ENSP00000355192:V571I	V	-	1	0	CACNA1S	199312787	0.896000	0.30565	0.989000	0.46669	0.995000	0.86356	-0.005000	0.12855	-0.570000	0.06022	0.549000	0.68633	GTC	C|0.997;T|0.003	0.003	strong		0.557	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
OR11H1	81061	hgsc.bcm.edu	37	22	16449539	16449539	+	Missense_Mutation	SNP	A	A	G	rs199856986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	729	3	0.00411523		WXS	Illumina HiSeq	Phase_I	700	74	0.105714	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	
PCDHGA4	56111	hgsc.bcm.edu	37	5	140736814	140736814	+	Missense_Mutation	SNP	G	G	C	rs11575951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140736814G>C	ENST00000571252.1	+	1	2047	c.2047G>C	c.(2047-2049)Gac>Cac	p.D683H	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_5'Flank|PCDHGA2_ENST00000394576.2_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	683			D -> H (in dbSNP:rs11575951).		homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTTCAGCAGACCCAGACGA	0.622													.|||	254	0.0507188	0.1634	0.013	5008	,	,		19767	0.0		0.0258	False		,,,				2504	0.0031				p.D683H		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.G2047C						PASS	.	G	,,,HIS/ASP,,HIS/ASP	565,3811		40,485,1663	35.0	40.0	38.0		,,,2047,,2047	-4.2	0.0	5	dbSNP_120	38	150,8438		1,148,4145	yes	intron,intron,intron,missense,intron,missense	PCDHGB1,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018922.2,NM_032053.1	,,,81,,81	41,633,5808	CC,CG,GG		1.7466,12.9113,5.5153	,,,,,	,,,683/932,,683/821	140736814	715,12249	2188	4294	6482	SO:0001583	missense	56111	exon1			TCAGCAGACCCAG	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.2047G>C	5.37:g.140736814G>C	ENSP00000458570:p.Asp683His	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	160	80	0.5	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			G|0.957;C|0.043	0.043	strong		0.622	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
NLRC3	197358	hgsc.bcm.edu	37	16	3606947	3606947	+	RNA	SNP	G	G	T	rs116349864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3606947G>T	ENST00000301749.7	-	0	2553				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCTTCAAAGCGTCTGCCAGCG	0.582													g|||	78	0.0155751	0.056	0.0058	5008	,	,		18998	0.0		0.0	False		,,,				2504	0.0				p.D716E		Atlas-SNP	.											.	NLRC3	103	.	0			c.C2148A						PASS	.	A	GLU/ASP	187,3749		5,177,1786	78.0	87.0	84.0		2148	-7.0	0.6	16	dbSNP_132	84	1,8305		0,1,4152	yes	missense	NLRC3	NM_178844.2	45	5,178,5938	TT,TG,GG		0.012,4.751,1.5357	benign	716/1066	3606947	188,12054	1968	4153	6121			197358	exon8			CAAAGCGTCTGCC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3606947G>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	g	13.03	2.114951	0.37339	0.04751	1.2E-4	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.50548	0.74;0.74;0.74	5.37	-6.97	0.01616	.	0.127878	0.52532	N	0.000077	T	0.04318	0.0119	.	.	.	0.20563	N	0.999887	B	0.28026	0.198	B	0.34138	0.176	T	0.15780	-1.0425	9	0.18276	T	0.48	.	7.4907	0.27460	0.6283:0.0:0.1808:0.1909	.	763	C9JLH9	.	E	716;716;716;763	ENSP00000301749:D716E;ENSP00000352039:D716E;ENSP00000414415:D763E	ENSP00000301749:D716E	D	-	3	2	NLRC3	3546948	0.002000	0.14202	0.606000	0.28943	0.419000	0.31324	-1.356000	0.02609	-1.733000	0.01357	-2.239000	0.00288	GAC	G|0.985;T|0.015	0.015	strong		0.582	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
FAM83B	222584	hgsc.bcm.edu	37	6	54805688	54805688	+	Missense_Mutation	SNP	A	A	C	rs239798	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:54805688A>C	ENST00000306858.7	+	5	2035	c.1919A>C	c.(1918-1920)aAa>aCa	p.K640T	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	640			K -> T (in dbSNP:rs239798). {ECO:0000269|PubMed:15489334}.					p.K640T(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					TATATATATAAAACCTTGGGT	0.373													C|||	1450	0.289537	0.7065	0.1715	5008	,	,		17944	0.0337		0.1511	False		,,,				2504	0.2157				p.K640T		Atlas-SNP	.											FAM83B,NS,carcinoma,0,1	FAM83B	186	1	1	Substitution - Missense(1)	prostate(1)	c.A1919C						PASS	.	C	THR/LYS	2674,1722		823,1028,347	41.0	43.0	42.0		1919	4.7	0.1	6	dbSNP_79	42	1438,7156		105,1228,2964	yes	missense	FAM83B	NM_001010872.1	78	928,2256,3311	CC,CA,AA		16.7326,39.172,31.6551	benign	640/1012	54805688	4112,8878	2198	4297	6495	SO:0001583	missense	222584	exon5			TATATAAAACCTT	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.1919A>C	6.37:g.54805688A>C	ENSP00000304078:p.Lys640Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	548	0.2509157509157509	350	0.7113821138211383	73	0.20165745856353592	13	0.022727272727272728	112	0.14775725593667546	C	0.755	-0.771342	0.02951	0.60828	0.167326	ENSG00000168143	ENST00000306858	T	0.27557	1.66	5.55	4.66	0.58398	.	0.865524	0.10264	N	0.695617	T	0.02342	0.0072	N	0.00146	-1.995	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39683	-0.9602	9	0.09590	T	0.72	-7.5696	15.0301	0.71698	0.2604:0.7396:0.0:0.0	rs239798;rs52808658;rs57244784;rs239798	640	Q5T0W9	FA83B_HUMAN	T	640	ENSP00000304078:K640T	ENSP00000304078:K640T	K	+	2	0	FAM83B	54913647	0.528000	0.26314	0.067000	0.19924	0.901000	0.52897	4.107000	0.57811	0.801000	0.34066	-0.121000	0.15023	AAA	A|0.690;C|0.310	0.310	strong		0.373	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
VWA5B2	90113	hgsc.bcm.edu	37	3	183951135	183951135	+	Silent	SNP	C	C	T	rs729377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183951135C>T	ENST00000426955.2	+	3	580	c.480C>T	c.(478-480)gcC>gcT	p.A160A	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_5'Flank	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	160										breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						CCCCGCTggccccgccaggcc	0.701													C|||	1498	0.299121	0.3684	0.2608	5008	,	,		14658	0.3165		0.2783	False		,,,				2504	0.2362				p.A160A		Atlas-SNP	.											.	VWA5B2	47	.	0			c.C480T						PASS	.						11.0	15.0	14.0					3																	183951135		692	1591	2283	SO:0001819	synonymous_variant	90113	exon3			GCTGGCCCCGCCA		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.480C>T	3.37:g.183951135C>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_138345	B9EGN7	Silent	SNP	ENST00000426955.2	37	CCDS54686.1																																																																																			C|0.708;T|0.292	0.292	strong		0.701	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
CHST12	55501	hgsc.bcm.edu	37	7	2472599	2472599	+	Missense_Mutation	SNP	C	C	A	rs17132395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2472599C>A	ENST00000258711.6	+	2	460	c.325C>A	c.(325-327)Cgc>Agc	p.R109S		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	109			R -> S (in dbSNP:rs17132395).		carbohydrate biosynthetic process (GO:0016051)|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)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		CTGGTCCCCGCGCGACGCCCG	0.711													C|||	141	0.028155	0.0976	0.0159	5008	,	,		13900	0.0		0.001	False		,,,				2504	0.0				p.R109S		Atlas-SNP	.											.	CHST12	39	.	0			c.C325A						PASS	.	C	SER/ARG	357,4031		15,327,1852	19.0	25.0	23.0		325	5.0	0.0	7	dbSNP_123	23	2,8568		0,2,4283	no	missense	CHST12	NM_018641.4	110	15,329,6135	AA,AC,CC		0.0233,8.1358,2.7705	benign	109/415	2472599	359,12599	2194	4285	6479	SO:0001583	missense	55501	exon2			TCCCCGCGCGACG	AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.325C>A	7.37:g.2472599C>A	ENSP00000258711:p.Arg109Ser	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	10	8	0.8	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	C	4.045	0.006027	0.07866	0.081358	2.33E-4	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.61742	0.08;0.92	4.98	4.98	0.66077	.	0.798952	0.11372	N	0.570741	T	0.01029	0.0034	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.00870	-1.1533	10	0.08837	T	0.75	1.0898	13.2418	0.60002	0.1591:0.8409:0.0:0.0	rs17132395;rs17132395	109	Q9NRB3	CHSTC_HUMAN	S	109	ENSP00000258711:R109S;ENSP00000411207:R109S	ENSP00000258711:R109S	R	+	1	0	CHST12	2439125	0.002000	0.14202	0.022000	0.16811	0.456000	0.32438	1.538000	0.36094	2.304000	0.77564	0.561000	0.74099	CGC	C|0.976;A|0.024	0.024	strong		0.711	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641	
PTGFRN	5738	hgsc.bcm.edu	37	1	117452869	117452869	+	Missense_Mutation	SNP	C	C	G	rs77292583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117452869C>G	ENST00000393203.2	+	1	191	c.44C>G	c.(43-45)tCg>tGg	p.S15W	RP4-753F5.1_ENST00000610171.1_lincRNA	NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	15					lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		GCGCTCCTGTCGTTGGGTGAG	0.786													C|||	146	0.0291534	0.1074	0.0058	5008	,	,		7813	0.0		0.0	False		,,,				2504	0.0				p.S15W		Atlas-SNP	.											PTGFRN,NS,carcinoma,0,1	PTGFRN	91	1	0			c.C44G						PASS	.	C	TRP/SER	237,3861		2,233,1814	4.0	6.0	5.0		44	0.3	0.1	1	dbSNP_132	5	3,8095		0,3,4046	no	missense	PTGFRN	NM_020440.2	177	2,236,5860	GG,GC,CC		0.037,5.7833,1.9679	benign	15/880	117452869	240,11956	2049	4049	6098	SO:0001583	missense	5738	exon1			TCCTGTCGTTGGG	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9601	protein-coding gene	gene with protein product		601204	"""prostaglandin F2 receptor negative regulator"""			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.44C>G	1.37:g.117452869C>G	ENSP00000376899:p.Ser15Trp	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_020440	Q5VVU9|Q8N2K6	Missense_Mutation	SNP	ENST00000393203.2	37	CCDS890.1	47	0.02152014652014652	45	0.09146341463414634	2	0.0055248618784530384	0	0.0	0	0.0	C	5.911	0.352168	0.11182	0.057833	3.7E-4	ENSG00000134247	ENST00000393203	T	0.03982	3.74	3.41	0.296	0.15757	Immunoglobulin-like (1);	6.098340	0.00166	N	0.000011	T	0.01156	0.0038	N	0.14661	0.345	0.44214	D	0.997042	B	0.02656	0.0	B	0.01281	0.0	T	0.33394	-0.9870	10	0.66056	D	0.02	0.1948	3.6279	0.08120	0.0:0.498:0.2382:0.2638	.	15	Q9P2B2	FPRP_HUMAN	W	15	ENSP00000376899:S15W	ENSP00000376899:S15W	S	+	2	0	PTGFRN	117254392	0.444000	0.25649	0.089000	0.20774	0.001000	0.01503	-0.612000	0.05616	-0.140000	0.11394	-0.481000	0.04817	TCG	C|0.978;G|0.022	0.022	strong		0.786	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
F5	2153	hgsc.bcm.edu	37	1	169511755	169511755	+	Missense_Mutation	SNP	T	T	C	rs4524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	290	147	0.506897	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	
TMEM156	80008	hgsc.bcm.edu	37	4	39033851	39033851	+	Missense_Mutation	SNP	G	G	A	rs61732938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39033851G>A	ENST00000381938.3	-	1	190	c.83C>T	c.(82-84)cCg>cTg	p.P28L	TMEM156_ENST00000372489.2_5'UTR	NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156	28						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						CTCACCTTTCGGTGTCTTGAA	0.333													G|||	9	0.00179712	0.0061	0.0014	5008	,	,		16764	0.0		0.0	False		,,,				2504	0.0				p.P28L		Atlas-SNP	.											.	TMEM156	31	.	0			c.C83T						PASS	.	G	LEU/PRO	28,4376	31.7+/-61.6	0,28,2174	50.0	47.0	48.0		83	3.7	1.0	4	dbSNP_129	48	0,8600		0,0,4300	yes	missense	TMEM156	NM_024943.1	98	0,28,6474	AA,AG,GG		0.0,0.6358,0.2153	benign	28/297	39033851	28,12976	2202	4300	6502	SO:0001583	missense	80008	exon1			CCTTTCGGTGTCT	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.83C>T	4.37:g.39033851G>A	ENSP00000371364:p.Pro28Leu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_024943	Q9H5N9	Missense_Mutation	SNP	ENST00000381938.3	37	CCDS3448.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	0.012	-1.665798	0.00765	0.006358	0.0	ENSG00000121895	ENST00000381938;ENST00000344606	T;T	0.42513	1.98;0.97	5.39	3.65	0.41850	.	0.637311	0.14864	N	0.293940	T	0.19485	0.0468	L	0.34521	1.04	0.40731	D	0.982742	B	0.26902	0.163	B	0.22880	0.042	T	0.03384	-1.1042	10	0.09590	T	0.72	-3.7493	7.8212	0.29288	0.1868:0.0:0.8132:0.0	.	28	Q8N614	TM156_HUMAN	L	28	ENSP00000371364:P28L;ENSP00000343758:P28L	ENSP00000343758:P28L	P	-	2	0	TMEM156	38710246	0.962000	0.33011	0.992000	0.48379	0.081000	0.17604	1.670000	0.37502	1.404000	0.46819	-0.216000	0.12614	CCG	G|0.998;A|0.002	0.002	strong		0.333	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943	
OR4S2	219431	hgsc.bcm.edu	37	11	55419147	55419147	+	Silent	SNP	C	C	T	rs74538149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55419147C>T	ENST00000312422.2	+	1	768	c.768C>T	c.(766-768)taC>taT	p.Y256Y		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	256						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)				CTTTTATGTACATGCGCCCTG	0.463													c|||	56	0.0111821	0.0416	0.0014	5008	,	,		14395	0.0		0.0	False		,,,				2504	0.0				p.Y256Y		Atlas-SNP	.											.	OR4S2	89	.	0			c.C768T						PASS	.	C		169,4189		21,127,2031	161.0	136.0	145.0		768	0.1	1.0	11	dbSNP_132	145	3,8047		0,3,4022	yes	coding-synonymous	OR4S2	NM_001004059.2		21,130,6053	TT,TC,CC		0.0373,3.8779,1.3862		256/312	55419147	172,12236	2179	4025	6204	SO:0001819	synonymous_variant	219431	exon1			TATGTACATGCGC	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.768C>T	11.37:g.55419147C>T		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_001004059	Q6IF72	Silent	SNP	ENST00000312422.2	37	CCDS31505.1																																																																																			C|0.988;T|0.012	0.012	strong		0.463	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059	
ST3GAL4	6484	hgsc.bcm.edu	37	11	126277216	126277216	+	Silent	SNP	C	C	T	rs2230278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:126277216C>T	ENST00000526727.1	+	4	626	c.252C>T	c.(250-252)taC>taT	p.Y84Y	ST3GAL4_ENST00000526756.1_3'UTR|ST3GAL4_ENST00000392669.2_Silent_p.Y84Y|ST3GAL4_ENST00000449406.2_Silent_p.Y73Y|ST3GAL4_ENST00000534083.1_Silent_p.Y84Y|ST3GAL4_ENST00000356132.4_Silent_p.Y90Y|ST3GAL4_ENST00000227495.6_Silent_p.Y80Y|ST3GAL4_ENST00000534457.1_Silent_p.Y79Y|ST3GAL4_ENST00000530591.1_Silent_p.Y80Y|ST3GAL4_ENST00000444328.2_Silent_p.Y84Y|ST3GAL4_ENST00000532243.1_Silent_p.Y83Y			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	84					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)			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)		CATCTGCTTACGAGCTGCCCT	0.582													C|||	1734	0.346246	0.3646	0.3242	5008	,	,		15739	0.5099		0.3181	False		,,,				2504	0.1973				p.Y84Y		Atlas-SNP	.											.	ST3GAL4	25	.	0			c.C252T						PASS	.	C		1543,2859	486.0+/-360.5	274,995,932	122.0	116.0	118.0		240	-9.4	0.7	11	dbSNP_98	118	2608,5988	422.9+/-354.2	370,1868,2060	no	coding-synonymous	ST3GAL4	NM_006278.1		644,2863,2992	TT,TC,CC		30.3397,35.0522,31.9357		80/330	126277216	4151,8847	2201	4298	6499	SO:0001819	synonymous_variant	6484	exon5			TGCTTACGAGCTG	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.252C>T	11.37:g.126277216C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	117	68	0.581197	NM_001254757	A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	Silent	SNP	ENST00000526727.1	37	CCDS58193.1																																																																																			C|0.657;T|0.343	0.343	strong		0.582	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278	
MYO10	4651	hgsc.bcm.edu	37	5	16682062	16682062	+	Silent	SNP	C	C	T	rs16868979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16682062C>T	ENST00000513610.1	-	31	4561	c.4107G>A	c.(4105-4107)ccG>ccA	p.P1369P	MYO10_ENST00000274203.9_Silent_p.P726P|MYO10_ENST00000427430.2_Silent_p.P726P|MYO10_ENST00000505695.1_Silent_p.P708P|MYO10_ENST00000515803.1_Silent_p.P708P	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1369					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						GCATCTCCTCCGGCGTGTCGG	0.587													C|||	141	0.028155	0.0998	0.0058	5008	,	,		17271	0.0		0.0	False		,,,				2504	0.0051				p.P1369P		Atlas-SNP	.											MYO10,NS,carcinoma,0,1	MYO10	198	1	0			c.G4107A						PASS	.	C		367,3887		21,325,1781	112.0	113.0	113.0		4107	-11.6	0.4	5	dbSNP_123	113	2,8458		0,2,4228	no	coding-synonymous	MYO10	NM_012334.2		21,327,6009	TT,TC,CC		0.0236,8.6272,2.9023		1369/2059	16682062	369,12345	2127	4230	6357	SO:0001819	synonymous_variant	4651	exon31			CTCCTCCGGCGTG	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.4107G>A	5.37:g.16682062C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	127	64	0.503937	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			C|0.960;T|0.040	0.040	strong		0.587	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
SSPO	23145	hgsc.bcm.edu	37	7	149503843	149503843	+	RNA	SNP	T	T	G	rs10260959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149503843T>G	ENST00000378016.2	+	0	8671							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)			AGAGAACATGTTGTTCCGCTC	0.617													G|||	1858	0.371006	0.7995	0.2695	5008	,	,		18911	0.2004		0.162	False		,,,				2504	0.2546				p.L2891V		Atlas-SNP	.											.	.	.	.	0			c.T8671G						PASS	.	G		2602,1348		906,790,279	29.0	34.0	33.0		8675	3.2	1.0	7	dbSNP_119	33	1362,6786		137,1088,2849	yes	coding-notMod3	SSPO	NM_198455.2		1043,1878,3128	GG,GT,TT		16.7158,34.1266,32.7657			149503843	3964,8134	1975	4074	6049			23145	exon59			AACATGTTGTTCC	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.149503843T>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	200	200	1	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.674;G|0.326	0.326	strong		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CIZ1	25792	hgsc.bcm.edu	37	9	130948018	130948018	+	Silent	SNP	G	G	A	rs45545033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130948018G>A	ENST00000393608.1	-	5	598	c.396C>T	c.(394-396)ctC>ctT	p.L132L	CIZ1_ENST00000325721.8_Silent_p.L108L|CIZ1_ENST00000372948.3_Silent_p.L132L|CIZ1_ENST00000372954.1_Silent_p.L108L|CIZ1_ENST00000541172.1_Silent_p.L31L|CIZ1_ENST00000277465.4_Silent_p.L132L|CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000538431.1_Silent_p.L132L|CIZ1_ENST00000372938.5_Silent_p.L132L|CIZ1_ENST00000357558.5_Silent_p.L132L	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	132					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						TGGGGGCTGCGAGGCCTGGGG	0.602													G|||	162	0.0323482	0.1165	0.0115	5008	,	,		16972	0.0		0.0	False		,,,				2504	0.0				p.L162L		Atlas-SNP	.											.	CIZ1	75	.	0			c.C486T						PASS	.	G	,,,,	520,3886	238.4+/-249.8	36,448,1719	38.0	38.0	38.0		396,396,396,324,396	0.2	0.0	9	dbSNP_127	38	8,8592	3.7+/-12.6	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	,,,,	36,456,6011	AA,AG,GG		0.093,11.8021,4.0597	,,,,	132/843,132/899,132/838,108/819,132/899	130948018	528,12478	2203	4300	6503	SO:0001819	synonymous_variant	25792	exon5			GGCTGCGAGGCCT	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.396C>T	9.37:g.130948018G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	63	43	0.68254	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	37	CCDS6894.1																																																																																			G|0.962;A|0.038	0.038	strong		0.602	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127	
ZNF841	284371	hgsc.bcm.edu	37	19	52570714	52570714	+	Missense_Mutation	SNP	C	C	G	rs16983412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52570714C>G	ENST00000426391.2	-	5	624	c.73G>C	c.(73-75)Gtt>Ctt	p.V25L	ZNF841_ENST00000594295.1_Missense_Mutation_p.V141L|ZNF841_ENST00000359973.2_Missense_Mutation_p.V25L|ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000389534.4_Missense_Mutation_p.V141L			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	25					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(4)|kidney(3)|lung(3)	11						TGAAAGTCAACTTCCTGTAGA	0.373													G|||	986	0.196885	0.2254	0.1988	5008	,	,		15218	0.121		0.0994	False		,,,				2504	0.3354				p.V141L		Atlas-SNP	.											.	ZNF841	183	.	0			c.G421C						PASS	.	G	LEU/VAL	308,1076		28,252,412	99.0	75.0	82.0		421	-2.1	0.0	19	dbSNP_123	82	353,2829		20,313,1258	yes	missense	ZNF841	NM_001136499.1	32	48,565,1670	GG,GC,CC		11.0937,22.2543,14.4766	benign	141/925	52570714	661,3905	692	1591	2283	SO:0001583	missense	284371	exon7			AGTCAACTTCCTG	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.73G>C	19.37:g.52570714C>G	ENSP00000415453:p.Val25Leu	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	197	95	0.482233	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	37		332	0.152014652014652	110	0.22357723577235772	70	0.19337016574585636	78	0.13636363636363635	74	0.09762532981530343	G	0.013	-1.621716	0.00820	0.222543	0.110937	ENSG00000197608	ENST00000389534;ENST00000426391;ENST00000359973	T;T;T	0.06768	3.61;3.49;3.26	2.88	-2.09	0.07232	.	.	.	.	.	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	0.01281	0.0;0.0;0.0	T	0.47129	-0.9141	8	0.31617	T	0.26	.	5.1262	0.14886	0.3411:0.4249:0.234:0.0	rs16983412;rs52792279;rs16983412	141;25;25	Q6ZN19-3;Q6ZN19-2;Q6ZN19	.;.;ZN841_HUMAN	L	141;25;25	ENSP00000374185:V141L;ENSP00000415453:V25L;ENSP00000353060:V25L	ENSP00000353060:V25L	V	-	1	0	ZNF841	57262526	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	-0.719000	0.04974	-0.831000	0.04256	-0.647000	0.03941	GTT	C|0.844;G|0.156	0.156	strong		0.373	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155	
ACACB	32	hgsc.bcm.edu	37	12	109577465	109577465	+	Silent	SNP	C	C	T	rs11065655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109577465C>T	ENST00000338432.7	+	2	374	c.255C>T	c.(253-255)gcC>gcT	p.A85A	ACACB_ENST00000377848.3_Silent_p.A85A|ACACB_ENST00000377854.5_Silent_p.A85A			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	85					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)	CCAAAGATGCCGGTCGGCGGA	0.622													C|||	335	0.066893	0.233	0.0259	5008	,	,		14762	0.0		0.002	False		,,,				2504	0.0072				p.A85A		Atlas-SNP	.											.	ACACB	330	.	0			c.C255T						PASS	.	C		885,3521	338.4+/-305.3	86,713,1404	52.0	61.0	58.0		255	0.2	0.0	12	dbSNP_120	58	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	ACACB	NM_001093.3		86,720,5697	TT,TC,CC		0.0814,20.0862,6.8584		85/2459	109577465	892,12114	2203	4300	6503	SO:0001819	synonymous_variant	32	exon1			AGATGCCGGTCGG	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.255C>T	12.37:g.109577465C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	95	57	0.6	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.936;T|0.064	0.064	strong		0.622	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
SSPO	23145	hgsc.bcm.edu	37	7	149518148	149518148	+	RNA	SNP	A	A	G	rs10233245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149518148A>G	ENST00000378016.2	+	0	12491							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)			GCCTGGAGCCACTGGTCGGCC	0.677													G|||	2148	0.428914	0.6475	0.3646	5008	,	,		15805	0.4167		0.3062	False		,,,				2504	0.318				p.H4164R		Atlas-SNP	.											.	.	.	.	0			c.A12491G						PASS	.	G		2014,1864		612,790,537	4.0	7.0	6.0		12505	-1.9	1.0	7	dbSNP_119	6	2427,5615		449,1529,2043	no	coding-notMod3	SSPO	NM_198455.2		1061,2319,2580	GG,GA,AA		30.1791,48.066,37.2567			149518148	4441,7479	1939	4021	5960			23145	exon87			GGAGCCACTGGTC	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.149518148A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	43	26	0.604651	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				A|0.578;G|0.422	0.422	strong		0.677	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
ALDH8A1	64577	hgsc.bcm.edu	37	6	135271178	135271178	+	Missense_Mutation	SNP	T	T	C	rs56954234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135271178T>C	ENST00000265605.2	-	1	82	c.14A>G	c.(13-15)aAc>aGc	p.N5S	ALDH8A1_ENST00000367845.2_Missense_Mutation_p.N5S|ALDH8A1_ENST00000367847.2_Missense_Mutation_p.N5S	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	5					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		CAAAAGTGCGTTTGTTCCAGC	0.453													T|||	71	0.0141773	0.0514	0.0043	5008	,	,		19775	0.0		0.0	False		,,,				2504	0.0				p.N5S		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.A14G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	141,4265	98.9+/-137.6	3,135,2065	102.0	102.0	102.0		14,14,14	-1.8	0.0	6	dbSNP_129	102	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	ALDH8A1	NM_001193480.1,NM_022568.3,NM_170771.2	46,46,46	3,138,6362	CC,CT,TT		0.0349,3.2002,1.1072	benign,benign,benign	5/438,5/488,5/434	135271178	144,12862	2203	4300	6503	SO:0001583	missense	64577	exon1			AGTGCGTTTGTTC	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"""Aldehyde dehydrogenases"""	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.14A>G	6.37:g.135271178T>C	ENSP00000265605:p.Asn5Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	110	43	0.390909	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	33	0.01510989010989011	30	0.06097560975609756	3	0.008287292817679558	0	0.0	0	0.0	T	14.25	2.479974	0.44044	0.032002	3.49E-4	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	T;T;T	0.75154	-0.91;-0.88;-0.87	6.14	-1.83	0.07833	.	1.633190	0.02930	N	0.139121	T	0.28699	0.0711	N	0.11560	0.145	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.07121	-1.0789	10	0.21014	T	0.42	.	6.0545	0.19804	0.1131:0.3306:0.0:0.5563	rs56954234;rs61731728	5;5;5	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	S	5	ENSP00000265605:N5S;ENSP00000356819:N5S;ENSP00000356821:N5S	ENSP00000265605:N5S	N	-	2	0	ALDH8A1	135312871	0.000000	0.05858	0.000000	0.03702	0.932000	0.56968	0.157000	0.16402	-0.524000	0.06400	0.529000	0.55759	AAC	T|0.985;C|0.015	0.015	strong		0.453	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2		
KMT2D	8085	hgsc.bcm.edu	37	12	49446040	49446040	+	Missense_Mutation	SNP	C	C	T	rs1064210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49446040C>T	ENST00000301067.7	-	10	1425	c.1426G>A	c.(1426-1428)Gca>Aca	p.A476T		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	476	15 X 5 AA repeats of S/P-P-P-E/P-E/A.|Pro-rich.		A -> T (in dbSNP:rs1064210).		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)										AGTGGGGATGCGGGCAATTCC	0.647													C|||	443	0.0884585	0.3154	0.0202	5008	,	,		16514	0.0		0.001	False		,,,				2504	0.0112				p.A476T		Atlas-SNP	.											.	MLL2	1173	.	0			c.G1426A						PASS	.	C	THR/ALA	1173,3107		157,859,1124	94.0	105.0	101.0		1426	-0.8	0.0	12	dbSNP_86	101	14,8434		0,14,4210	yes	missense	MLL2	NM_003482.3	58	157,873,5334	TT,TC,CC		0.1657,27.4065,9.3259	benign	476/5538	49446040	1187,11541	2140	4224	6364	SO:0001583	missense	8085	exon10			GGGATGCGGGCAA	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.1426G>A	12.37:g.49446040C>T	ENSP00000301067:p.Ala476Thr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	159	0.07280219780219781	152	0.3089430894308943	6	0.016574585635359115	1	0.0017482517482517483	0	0.0	C	0.034	-1.318316	0.01320	0.274065	0.001657	ENSG00000167548	ENST00000301067	T	0.78816	-1.21	1.5	-0.819	0.10829	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15930	0.015	B	0.10450	0.005	T	0.12604	-1.0541	8	0.87932	D	0	.	0.5031	0.00583	0.2468:0.3228:0.2447:0.1857	rs1064210;rs1064210	476	O14686	MLL2_HUMAN	T	476	ENSP00000301067:A476T	ENSP00000301067:A476T	A	-	1	0	MLL2	47732307	0.000000	0.05858	0.003000	0.11579	0.064000	0.16182	-2.296000	0.01142	-0.247000	0.09597	0.313000	0.20887	GCA	C|0.937;T|0.063	0.063	strong		0.647	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
LIPE	3991	hgsc.bcm.edu	37	19	42906914	42906914	+	Missense_Mutation	SNP	G	G	T	rs7246232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42906914G>T	ENST00000244289.4	-	9	3088	c.2812C>A	c.(2812-2814)Cgt>Agt	p.R938S	LIPE-AS1_ENST00000593491.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000599276.1_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	938			R -> S (in dbSNP:rs7246232). {ECO:0000269|Ref.3}.		cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				AAGGCGGCACGGACGCCCAGG	0.602													G|||	101	0.0201677	0.0711	0.0072	5008	,	,		16054	0.0		0.002	False		,,,				2504	0.0				p.R938S		Atlas-SNP	.											.	LIPE	83	.	0			c.C2812A						PASS	.	G	SER/ARG	227,4179	135.7+/-171.8	6,215,1982	72.0	61.0	64.0		2812	-10.8	0.0	19	dbSNP_116	64	11,8589	8.4+/-32.0	0,11,4289	yes	missense	LIPE	NM_005357.2	110	6,226,6271	TT,TG,GG		0.1279,5.1521,1.8299	benign	938/1077	42906914	238,12768	2203	4300	6503	SO:0001583	missense	3991	exon9			CGGCACGGACGCC	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2812C>A	19.37:g.42906914G>T	ENSP00000244289:p.Arg938Ser	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_005357	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	49	0.022435897435897436	44	0.08943089430894309	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	6.053	0.378025	0.11466	0.051521	0.001279	ENSG00000079435	ENST00000244289	T	0.03272	3.99	5.38	-10.8	0.00216	.	1.425700	0.04445	N	0.371619	T	0.00109	0.0003	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.15870	0.014	T	0.33727	-0.9857	10	0.26408	T	0.33	5.9579	9.2186	0.37362	0.0796:0.1474:0.6138:0.1592	rs7246232;rs56962270;rs7246232	938	Q05469	LIPS_HUMAN	S	938	ENSP00000244289:R938S	ENSP00000244289:R938S	R	-	1	0	LIPE	47598754	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.465000	0.00995	-3.013000	0.00272	-1.669000	0.00746	CGT	G|0.970;T|0.030	0.030	strong		0.602	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357	
GPR144	347088	hgsc.bcm.edu	37	9	127220392	127220392	+	Splice_Site	SNP	G	G	C	rs58155983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127220392G>C	ENST00000334810.1	+	9	1562	c.1562G>C	c.(1561-1563)gGc>gCc	p.G521A				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	521					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						TCTCAGCCAGGCCTCTCTGGA	0.637													G|||	512	0.102236	0.1362	0.121	5008	,	,		19327	0.1935		0.0	False		,,,				2504	0.0542				p.G521A		Atlas-SNP	.											.	GPR144	33	.	0			c.G1562C						PASS	.	G	ALA/GLY	192,1192		13,166,513	50.0	50.0	50.0		1562	4.7	1.0	9	dbSNP_129	50	13,3169		0,13,1578	yes	missense-near-splice	GPR144	NM_001161808.1	60	13,179,2091	CC,CG,GG		0.4085,13.8728,4.4897	possibly-damaging	521/964	127220392	205,4361	692	1591	2283	SO:0001630	splice_region_variant	347088	exon9			AGCCAGGCCTCTC	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.1562-1G>C	9.37:g.127220392G>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	136	51	0.375	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	221	0.10119047619047619	66	0.13414634146341464	34	0.09392265193370165	121	0.21153846153846154	0	0.0	G	14.09	2.433146	0.43224	0.138728	0.004085	ENSG00000180264	ENST00000334810;ENST00000439837	T	0.51817	0.69	4.74	4.74	0.60224	.	.	.	.	.	T	0.00073	0.0002	M	0.61703	1.905	0.09310	P	1.0	D	0.63880	0.993	P	0.51777	0.679	T	0.03335	-1.1047	7	.	.	.	.	13.2255	0.59912	0.0:0.0:1.0:0.0	rs58155983	521	Q7Z7M1	GP144_HUMAN	A	521;252	ENSP00000335156:G521A	.	G	+	2	0	GPR144	126260213	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	2.383000	0.44354	2.169000	0.68431	0.561000	0.74099	GGC	G|0.898;C|0.102	0.102	strong		0.637	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	Missense_Mutation
FAM114A1	92689	hgsc.bcm.edu	37	4	38933869	38933869	+	Missense_Mutation	SNP	C	C	T	rs36058104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38933869C>T	ENST00000358869.2	+	12	1513	c.1337C>T	c.(1336-1338)tCg>tTg	p.S446L	FAM114A1_ENST00000515037.1_Missense_Mutation_p.S239L	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	446			S -> L (in dbSNP:rs36058104).			cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						GTATACATGTCGTCCATTGAA	0.368													T|||	146	0.0291534	0.0734	0.0058	5008	,	,		17511	0.005		0.002	False		,,,				2504	0.0389				p.S446L		Atlas-SNP	.											.	FAM114A1	42	.	0			c.C1337T						PASS	.	T	LEU/SER	267,4139	799.7+/-415.5	6,255,1942	63.0	62.0	62.0		1337	4.4	0.7	4	dbSNP_126	62	53,8547	816.7+/-406.9	2,49,4249	yes	missense	FAM114A1	NM_138389.2	145	8,304,6191	TT,TC,CC		0.6163,6.0599,2.4604	benign	446/564	38933869	320,12686	2203	4300	6503	SO:0001583	missense	92689	exon12			ACATGTCGTCCAT		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.1337C>T	4.37:g.38933869C>T	ENSP00000351740:p.Ser446Leu	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	261	106	0.40613	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	37	CCDS3447.1	27	0.012362637362637362	22	0.044715447154471545	2	0.0055248618784530384	2	0.0034965034965034965	1	0.0013192612137203166	T	0.057	-1.233148	0.01505	0.060599	0.006163	ENSG00000197712	ENST00000515037;ENST00000358869;ENST00000355404	T;T	0.22539	1.95;2.98	5.62	4.43	0.53597	.	0.312620	0.32231	N	0.006386	T	0.00468	0.0015	N	0.00446	-1.495	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36841	-0.9731	10	0.12103	T	0.63	-1.327	4.0001	0.09576	0.1273:0.068:0.1332:0.6715	rs36058104	239;446	Q6MZV4;Q8IWE2	.;NXP20_HUMAN	L	239;446;239	ENSP00000424115:S239L;ENSP00000351740:S446L	ENSP00000347569:S239L	S	+	2	0	FAM114A1	38610264	1.000000	0.71417	0.736000	0.30914	0.196000	0.23810	3.031000	0.49728	0.411000	0.25702	-0.516000	0.04426	TCG	C|0.979;T|0.021	0.021	strong		0.368	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	
CCDC15	80071	hgsc.bcm.edu	37	11	124857708	124857708	+	Missense_Mutation	SNP	G	G	A	rs4936966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124857708G>A	ENST00000344762.5	+	8	1845	c.1586G>A	c.(1585-1587)gGc>gAc	p.G529D	CCDC15_ENST00000529051.1_Missense_Mutation_p.G529D	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	529			G -> D (in dbSNP:rs4936966).			centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		AAATATCAAGGCCAGGATTTT	0.398													A|||	1437	0.286941	0.4705	0.1801	5008	,	,		18812	0.1935		0.1958	False		,,,				2504	0.3047				p.G529D		Atlas-SNP	.											CCDC15_ENST00000344762,colon,carcinoma,0,7	CCDC15	134	7	0			c.G1586A						PASS	.	A	ASP/GLY	1566,2052		356,854,599	175.0	168.0	170.0		1586	-3.0	0.0	11	dbSNP_111	170	1647,6511		173,1301,2605	yes	missense	CCDC15	NM_025004.2	94	529,2155,3204	AA,AG,GG		20.1888,43.2836,27.2843	benign	529/952	124857708	3213,8563	1809	4079	5888	SO:0001583	missense	80071	exon8			ATCAAGGCCAGGA	BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.1586G>A	11.37:g.124857708G>A	ENSP00000341684:p.Gly529Asp	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	101	35	0.346535	NM_025004	Q9H8U7	Missense_Mutation	SNP	ENST00000344762.5	37	CCDS44756.1	578	0.26465201465201466	242	0.491869918699187	71	0.19613259668508287	114	0.1993006993006993	151	0.19920844327176782	A	5.456	0.269138	0.10349	0.432836	0.201888	ENSG00000149548	ENST00000529051;ENST00000344762	T;T	0.28454	1.61;1.66	4.23	-2.98	0.05513	.	2.421730	0.01604	N	0.022219	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41538	-0.9503	9	0.06365	T	0.9	.	0.3885	0.00406	0.2229:0.2635:0.2557:0.2578	rs4936966;rs52818517;rs60858036;rs4936966	529	Q0P6D6	CCD15_HUMAN	D	529	ENSP00000435403:G529D;ENSP00000341684:G529D	ENSP00000341684:G529D	G	+	2	0	CCDC15	124362918	0.002000	0.14202	0.000000	0.03702	0.157000	0.22087	0.082000	0.14847	-0.801000	0.04427	-0.451000	0.05528	GGC	G|0.721;A|0.279	0.279	strong		0.398	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
OR5V1	81696	hgsc.bcm.edu	37	6	29323276	29323276	+	Missense_Mutation	SNP	C	C	T	rs61742983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29323276C>T	ENST00000377154.1	-	4	996	c.697G>A	c.(697-699)Gga>Aga	p.G233R	OR5V1_ENST00000543825.1_Missense_Mutation_p.G233R			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	233						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(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTTCGTCTTCCCTCTGAGGAC	0.468													C|||	277	0.0553115	0.1641	0.0375	5008	,	,		21777	0.0119		0.0189	False		,,,				2504	0.0031				p.G233R	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											.	OR5V1	63	.	0			c.G697A						PASS	.	C	ARG/GLY	704,3702	291.5+/-281.6	55,594,1554	91.0	81.0	85.0		697	3.2	0.2	6	dbSNP_129	85	123,8477	63.1+/-125.2	0,123,4177	yes	missense	OR5V1	NM_030876.5	125	55,717,5731	TT,TC,CC		1.4302,15.9782,6.3586	probably-damaging	233/322	29323276	827,12179	2203	4300	6503	SO:0001583	missense	81696	exon1			GTCTTCCCTCTGA		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"""GPCR / Class A : Olfactory receptors"""	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.697G>A	6.37:g.29323276C>T	ENSP00000366359:p.Gly233Arg	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	37	CCDS4657.1	132	0.06043956043956044	95	0.19308943089430894	15	0.04143646408839779	10	0.017482517482517484	12	0.0158311345646438	C	10.45	1.353760	0.24512	0.159782	0.014302	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.00295	8.25;8.25	5.01	3.19	0.36642	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00178	0.0005	M	0.89030	3	0.80722	P	0.0	P	0.34864	0.473	B	0.38712	0.28	T	0.05451	-1.0884	8	0.87932	D	0	-27.5218	9.027	0.36236	0.0:0.7655:0.0:0.2345	.	233	Q9UGF6	OR5V1_HUMAN	R	233	ENSP00000366359:G233R;ENSP00000443309:G233R	ENSP00000366356:G233R	G	-	1	0	OR5V1	29431255	0.000000	0.05858	0.184000	0.23157	0.400000	0.30750	-0.051000	0.11885	1.333000	0.45449	0.543000	0.68304	GGA	C|0.940;T|0.060	0.060	strong		0.468	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3		
SAP130	79595	hgsc.bcm.edu	37	2	128767929	128767929	+	Silent	SNP	A	A	G	rs35775122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128767929A>G	ENST00000259235.3	-	7	990	c.861T>C	c.(859-861)ccT>ccC	p.P287P	SAP130_ENST00000357702.5_Silent_p.P287P|SAP130_ENST00000259234.6_Silent_p.P261P	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	287					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		CTACCACAGCAGGAGGGATGG	0.463													A|||	146	0.0291534	0.1014	0.0144	5008	,	,		17514	0.0		0.002	False		,,,				2504	0.0				p.P287P		Atlas-SNP	.											.	SAP130	169	.	0			c.T861C						PASS	.	A	,	433,3973	209.5+/-230.2	23,387,1793	116.0	104.0	108.0		861,861	3.2	1.0	2	dbSNP_126	108	20,8580	13.3+/-46.6	0,20,4280	no	coding-synonymous,coding-synonymous	SAP130	NM_001145928.1,NM_024545.3	,	23,407,6073	GG,GA,AA		0.2326,9.8275,3.483	,	287/1084,287/1049	128767929	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	79595	exon7			CACAGCAGGAGGG	BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"""sin3A-associated protein, 130kDa"""			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.861T>C	2.37:g.128767929A>G		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Silent	SNP	ENST00000259235.3	37	CCDS2153.1																																																																																			A|0.972;G|0.028	0.028	strong		0.463	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545	
TTN	7273	hgsc.bcm.edu	37	2	179614059	179614059	+	Intron	SNP	T	T	C	rs16866490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179614059T>C	ENST00000591111.1	-	45	10585				TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Silent_p.Q4356Q|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000578746.1_RNA			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)			CAGCCTGACATTGTATGAATT	0.413													T|||	29	0.00579073	0.0204	0.0029	5008	,	,		18368	0.0		0.0	False		,,,				2504	0.0				p.Q4356Q		Atlas-SNP	.											.	TTN	18412	.	0			c.A13068G						PASS	.	T	,,,,	78,4328	62.9+/-100.1	0,78,2125	87.0	93.0	91.0		,,13068,,	-3.6	0.0	2	dbSNP_123	91	2,8594	1.2+/-3.3	0,2,4296	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	0,80,6421	CC,CT,TT		0.0233,1.7703,0.6153	,,,,	,,4356/5605,,	179614059	80,12922	2203	4298	6501	SO:0001627	intron_variant	7273	exon46			CTGACATTGTATG	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.10360+3791A>G	2.37:g.179614059T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	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|0.991;C|0.009	0.009	strong		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
WARS2	10352	hgsc.bcm.edu	37	1	119575818	119575818	+	Missense_Mutation	SNP	C	C	G	rs3790549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:119575818C>G	ENST00000235521.4	-	6	825	c.799G>C	c.(799-801)Gct>Cct	p.A267P	WARS2_ENST00000369426.5_3'UTR|WARS2_ENST00000537870.1_Missense_Mutation_p.A173P	NM_015836.3|NM_201263.2	NP_056651.1|NP_957715.1	Q9UGM6	SYWM_HUMAN	tryptophanyl tRNA synthetase 2, mitochondrial	267			A -> P (in dbSNP:rs3790549).		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)|vasculogenesis (GO:0001570)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(2)	15	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	GCGCGGCCAGCCGGGTCATAG	0.627													C|||	485	0.096845	0.1127	0.0331	5008	,	,		16387	0.2143		0.0437	False		,,,				2504	0.0542				p.A267P		Atlas-SNP	.											.	WARS2	69	.	0			c.G799C						PASS	.	C	PRO/ALA,	454,3952	214.1+/-233.5	19,416,1768	72.0	68.0	69.0		799,	4.9	0.0	1	dbSNP_107	69	371,8229	122.2+/-181.2	10,351,3939	yes	missense,utr-3	WARS2	NM_015836.3,NM_201263.2	27,	29,767,5707	GG,GC,CC		4.314,10.3041,6.3432	benign,	267/361,	119575818	825,12181	2203	4300	6503	SO:0001583	missense	10352	exon6			GGCCAGCCGGGTC	BC021722	CCDS900.1, CCDS30817.1	1p12	2011-07-01	2007-02-23		ENSG00000116874	ENSG00000116874	6.1.1.2	"""Aminoacyl tRNA synthetases / Class I"""	12730	protein-coding gene	gene with protein product	"""tryptophan tRNA ligase 2, mitochondrial"""	604733				10072595, 10828066	Standard	NM_201263		Approved	TrpRS	uc001ehn.3	Q9UGM6	OTTHUMG00000012335	ENST00000235521.4:c.799G>C	1.37:g.119575818C>G	ENSP00000235521:p.Ala267Pro	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	122	50	0.409836	NM_015836	B1ALR1|B2R9D4|Q53FT4|Q5VUD2|Q86TQ0	Missense_Mutation	SNP	ENST00000235521.4	37	CCDS900.1	210	0.09615384615384616	55	0.11178861788617886	20	0.055248618784530384	105	0.18356643356643357	30	0.0395778364116095	C	11.94	1.789287	0.31685	0.103041	0.04314	ENSG00000116874	ENST00000235521;ENST00000537870	T;T	0.51071	0.72;0.72	5.87	4.88	0.63580	.	0.532643	0.21702	N	0.070403	T	0.20170	0.0485	N	0.04655	-0.195	0.80722	P	0.0	B;P	0.35527	0.355;0.507	B;B	0.43838	0.433;0.393	T	0.15321	-1.0441	9	0.48119	T	0.1	-3.8674	11.814	0.52199	0.1895:0.741:0.0:0.0695	rs3790549;rs3790549	210;267	B7Z6G7;Q9UGM6	.;SYWM_HUMAN	P	267;173	ENSP00000235521:A267P;ENSP00000438807:A173P	ENSP00000235521:A267P	A	-	1	0	WARS2	119377341	0.036000	0.19791	0.008000	0.14137	0.448000	0.32197	2.312000	0.43726	2.785000	0.95823	0.655000	0.94253	GCT	C|0.914;G|0.086	0.086	strong		0.627	WARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034362.1	NM_015836	
DNAH9	1770	hgsc.bcm.edu	37	17	11532787	11532787	+	Silent	SNP	C	C	T	rs73290804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11532787C>T	ENST00000262442.4	+	7	1472	c.1404C>T	c.(1402-1404)agC>agT	p.S468S	DNAH9_ENST00000454412.2_Silent_p.S468S	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	468	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)		TGGAGTTCAGCGGCGTCAGAG	0.478													C|||	100	0.0199681	0.0726	0.0043	5008	,	,		15848	0.001		0.0	False		,,,				2504	0.0				p.S468S		Atlas-SNP	.											.	DNAH9	695	.	0			c.C1404T						PASS	.	C		272,4134	155.2+/-188.4	10,252,1941	100.0	98.0	99.0		1404	-0.7	1.0	17	dbSNP_130	99	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DNAH9	NM_001372.3		10,254,6239	TT,TC,CC		0.0233,6.1734,2.1067		468/4487	11532787	274,12732	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon7			GTTCAGCGGCGTC	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.1404C>T	17.37:g.11532787C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	159	78	0.490566	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.978;T|0.022	0.022	strong		0.478	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188392	140188392	+	Silent	SNP	C	C	G	rs7707144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140188392C>G	ENST00000530339.1	+	1	1620	c.1620C>G	c.(1618-1620)gcC>gcG	p.A540A	PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Silent_p.A540A|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.A540A|PCDHA1_ENST00000504120.2_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	540	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)			CTCGCGATGCCGGCGTGCCAC	0.657													.|||	286	0.0571086	0.208	0.013	5008	,	,		17478	0.001		0.001	False		,,,				2504	0.0				p.A540A		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,2	PCDHA4	419	2	0			c.C1620G						PASS	.	G	,,,,,	748,3658		64,620,1519	60.0	68.0	65.0		,,,1620,,1620	-0.6	1.0	5	dbSNP_116	65	2,8596		0,2,4297	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	,,,,,	64,622,5816	GG,GC,CC		0.0233,16.9768,5.7675	,,,,,	,,,540/948,,540/799	140188392	750,12254	2203	4299	6502	SO:0001819	synonymous_variant	56144	exon1			CGATGCCGGCGTG	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.1620C>G	5.37:g.140188392C>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	92	29	0.315217	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			C|0.937;G|0.063	0.063	strong		0.657	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
PTK7	5754	hgsc.bcm.edu	37	6	43109751	43109751	+	Silent	SNP	G	G	A	rs6905948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43109751G>A	ENST00000230419.4	+	12	2072	c.1851G>A	c.(1849-1851)ggG>ggA	p.G617G	PTK7_ENST00000481273.1_Silent_p.G625G|PTK7_ENST00000349241.2_Silent_p.G487G|PTK7_ENST00000352931.2_Silent_p.G617G|PTK7_ENST00000345201.2_Silent_p.G577G	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	617	Ig-like C2-type 7.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			AGGCCCAGGGGGACCCCAAGC	0.597													G|||	1693	0.338059	0.4781	0.4179	5008	,	,		17142	0.0972		0.3887	False		,,,				2504	0.2883				p.G625G		Atlas-SNP	.											PTK7,NS,carcinoma,+2,1	PTK7	101	1	0			c.G1875A						PASS	.	G	,,,	1975,2431	547.8+/-377.4	451,1073,679	54.0	58.0	57.0		1851,1731,1461,1851	-8.6	1.0	6	dbSNP_116	57	3262,5338	481.8+/-370.7	596,2070,1634	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK7	NM_002821.3,NM_152880.2,NM_152881.2,NM_152882.2	,,,	1047,3143,2313	AA,AG,GG		37.9302,44.8252,40.266	,,,	617/1071,577/1031,487/941,617/1015	43109751	5237,7769	2203	4300	6503	SO:0001819	synonymous_variant	5754	exon12			CCAGGGGGACCCC	AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9618	protein-coding gene	gene with protein product		601890	"""PTK7 protein tyrosine kinase 7"""			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.1851G>A	6.37:g.43109751G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_001270398	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Silent	SNP	ENST00000230419.4	37	CCDS4884.1																																																																																			G|0.619;A|0.381	0.381	strong		0.597	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2		
RGPD4	285190	hgsc.bcm.edu	37	2	108443511	108443511	+	Silent	SNP	C	C	G	rs7576738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:108443511C>G	ENST00000408999.3	+	1	119	c.42C>G	c.(40-42)tcC>tcG	p.S14S	AC096655.2_ENST00000457647.2_lincRNA|RGPD4_ENST00000354986.4_Silent_p.S14S	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	14					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						ACGTCGCCTCCGTGCAGGGCT	0.711													N|||	3138	0.626597	0.789	0.5144	5008	,	,		9949	0.3383		0.7028	False		,,,				2504	0.7055				p.S14S		Atlas-SNP	.											.	RGPD4	112	.	0			c.C42G						PASS	.						34.0	56.0	50.0					2																	108443511		692	1587	2279	SO:0001819	synonymous_variant	285190	exon1			CGCCTCCGTGCAG	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.42C>G	2.37:g.108443511C>G		Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	340	337	0.991176	NM_182588	B9A029	Silent	SNP	ENST00000408999.3	37	CCDS46381.1																																																																																			C|0.408;G|0.592	0.592	strong		0.711	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
WFS1	7466	hgsc.bcm.edu	37	4	6302519	6302519	+	Missense_Mutation	SNP	G	G	A	rs1801212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6302519G>A	ENST00000226760.1	+	8	1167	c.997G>A	c.(997-999)Gtc>Atc	p.V333I	WFS1_ENST00000503569.1_Missense_Mutation_p.V333I	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	333			V -> I (in dbSNP:rs1801212). {ECO:0000269|PubMed:10521293, ECO:0000269|PubMed:11295831, ECO:0000269|PubMed:11709537, ECO:0000269|PubMed:11709538, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15605410, ECO:0000269|PubMed:18688868, ECO:0000269|PubMed:9771706, ECO:0000269|PubMed:9817917}.		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)		CTTCTTCATCGTCAGCAACCT	0.542													a|||	4429	0.884385	0.9939	0.7767	5008	,	,		21069	0.995		0.7296	False		,,,				2504	0.8579				p.V333I		Atlas-SNP	.											.	WFS1	71	.	0			c.G997A						PASS	.		ILE/VAL,ILE/VAL	4172,234	137.3+/-173.1	1980,212,11	435.0	292.0	340.0		997,997	3.4	1.0	4	dbSNP_89	340	6224,2376	396.2+/-345.3	2242,1740,318	yes	missense,missense	WFS1	NM_001145853.1,NM_006005.3	29,29	4222,1952,329	AA,AG,GG		27.6279,5.3109,20.0677	benign,benign	333/891,333/891	6302519	10396,2610	2203	4300	6503	SO:0001583	missense	7466	exon8			TTCATCGTCAGCA	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.997G>A	4.37:g.6302519G>A	ENSP00000226760:p.Val333Ile	Somatic	458	0	0		WXS	Illumina HiSeq	Phase_I	480	476	0.991667	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Missense_Mutation	SNP	ENST00000226760.1	37	CCDS3386.1	1887	0.864010989010989	488	0.991869918699187	281	0.7762430939226519	572	1.0	546	0.7203166226912929	a	0.723	-0.782904	0.02907	0.946891	0.723721	ENSG00000109501	ENST00000503569;ENST00000226760	D;D	0.85411	-1.98;-1.98	4.6	3.4	0.38934	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00170	-1.935	0.50632	P	1.1499999999997623E-4	B	0.06786	0.001	B	0.01281	0.0	T	0.42224	-0.9464	9	0.06099	T	0.92	-32.8103	8.3817	0.32474	0.8357:0.0:0.1643:0.0	rs1801212;rs17719467;rs56429316;rs58906820;rs1801212	333	O76024	WFS1_HUMAN	I	333	ENSP00000423337:V333I;ENSP00000226760:V333I	ENSP00000226760:V333I	V	+	1	0	WFS1	6353420	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	3.738000	0.55067	0.169000	0.19679	-0.376000	0.06991	GTC	G|0.170;A|0.830	0.830	strong		0.542	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
ZNF276	92822	hgsc.bcm.edu	37	16	89790020	89790020	+	Silent	SNP	C	C	T	rs34629175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89790020C>T	ENST00000443381.2	+	4	1006	c.909C>T	c.(907-909)ccC>ccT	p.P303P	VPS9D1_ENST00000389386.3_5'Flank|ZNF276_ENST00000568064.1_Missense_Mutation_p.P222L|ZNF276_ENST00000446326.2_Missense_Mutation_p.P100L|ZNF276_ENST00000289816.5_Silent_p.P228P	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	303					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)		AGACCCTGCCCAGCACGGATG	0.697													C|||	131	0.0261581	0.0968	0.0043	5008	,	,		17634	0.0		0.0	False		,,,				2504	0.0				p.P303P		Atlas-SNP	.											.	ZNF276	70	.	0			c.C909T						PASS	.	C	,	354,4038		12,330,1854	30.0	37.0	34.0		909,684	2.4	0.1	16	dbSNP_126	34	1,8587		0,1,4293	no	coding-synonymous,coding-synonymous	ZNF276	NM_001113525.1,NM_152287.3	,	12,331,6147	TT,TC,CC		0.0116,8.0601,2.735	,	303/615,228/540	89790020	355,12625	2196	4294	6490	SO:0001819	synonymous_variant	92822	exon4			CCTGCCCAGCACG	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.909C>T	16.37:g.89790020C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Silent	SNP	ENST00000443381.2	37	CCDS45554.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	2.587	-0.296169	0.05532	0.080601	1.16E-4	ENSG00000158805	ENST00000446326	T	0.13307	2.6	5.66	2.44	0.29823	.	0.247400	0.40818	N	0.001014	T	0.00468	0.0015	.	.	.	0.24132	N	0.995761	B	0.11235	0.004	B	0.08055	0.003	T	0.30765	-0.9967	9	0.56958	D	0.05	-22.5813	5.0473	0.14490	0.0:0.5552:0.1597:0.2851	rs34629175	100	A8K186	.	L	100	ENSP00000415999:P100L	ENSP00000415999:P100L	P	+	2	0	ZNF276	88317521	0.001000	0.12720	0.110000	0.21437	0.015000	0.08874	0.109000	0.15417	0.240000	0.21263	-0.367000	0.07326	CCA	C|0.976;T|0.024	0.024	strong		0.697	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287	
PES1	23481	hgsc.bcm.edu	37	22	30977353	30977353	+	Missense_Mutation	SNP	T	T	A	rs42942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30977353T>A	ENST00000405677.1	-	10	1316	c.373A>T	c.(373-375)Acc>Tcc	p.T125S	PES1_ENST00000402281.1_Missense_Mutation_p.T125S|PES1_ENST00000402284.3_Missense_Mutation_p.T247S|PES1_ENST00000354694.7_Missense_Mutation_p.T264S|PES1_ENST00000335214.6_Missense_Mutation_p.T264S	NM_001282328.1	NP_001269257.1			pescadillo ribosomal biogenesis factor 1											breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	29						AACGCGTAGGTGCCCTCACCG	0.622													T|||	175	0.0349441	0.0908	0.0231	5008	,	,		15562	0.0		0.0268	False		,,,				2504	0.0123				p.T264S		Atlas-SNP	.											.	PES1	55	.	0			c.A790T						PASS	.	T	SER/THR	380,4026	190.5+/-216.4	16,348,1839	65.0	60.0	61.0		790	0.1	0.0	22	dbSNP_76	61	362,8238	120.6+/-179.8	5,352,3943	yes	missense	PES1	NM_014303.3	58	21,700,5782	AA,AT,TT		4.2093,8.6246,5.7051	benign	264/589	30977353	742,12264	2203	4300	6503	SO:0001583	missense	23481	exon8			CGTAGGTGCCCTC	U78310	CCDS13880.1, CCDS58802.1, CCDS74842.1	22q12.1	2012-02-23	2012-02-23		ENSG00000100029	ENSG00000100029			8848	protein-coding gene	gene with protein product		605819	"""pescadillo (zebrafish) homolog 1, containing BRCT domain"", ""pescadillo homolog 1, containing BRCT domain (zebrafish)"""			8985183, 10591208, 17353269	Standard	NM_014303		Approved	PES	uc003aij.2	O00541	OTTHUMG00000151077	ENST00000405677.1:c.373A>T	22.37:g.30977353T>A	ENSP00000385654:p.Thr125Ser	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_014303		Missense_Mutation	SNP	ENST00000405677.1	37		72	0.03296703296703297	40	0.08130081300813008	8	0.022099447513812154	0	0.0	24	0.0316622691292876	T	11.94	1.788469	0.31685	0.086246	0.042093	ENSG00000100029	ENST00000354694;ENST00000402281;ENST00000405677;ENST00000402284;ENST00000335214	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	5.29	0.0496	0.14290	.	0.696719	0.14653	N	0.306448	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B;B;B;B	0.21821	0.061;0.014;0.038;0.061	B;B;B;B	0.24394	0.053;0.033;0.023;0.053	T	0.14868	-1.0457	10	0.18710	T	0.47	-7.1103	9.8476	0.41037	0.0:0.4591:0.0:0.5409	rs42942;rs58665418;rs42942	264;247;264;264	B2RDF2;B5MCF9;O00541-2;O00541	.;.;.;PESC_HUMAN	S	264;125;125;247;264	ENSP00000346725:T264S;ENSP00000384366:T125S;ENSP00000385654:T125S;ENSP00000384252:T247S;ENSP00000334612:T264S	ENSP00000334612:T264S	T	-	1	0	PES1	29307353	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-0.359000	0.07632	0.038000	0.15604	0.459000	0.35465	ACC	T|0.948;A|0.052	0.052	strong		0.622	PES1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000321189.2	NM_014303	
ST7L	54879	hgsc.bcm.edu	37	1	113153536	113153536	+	Silent	SNP	T	T	C	rs35364712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113153536T>C	ENST00000358039.4	-	3	682	c.378A>G	c.(376-378)acA>acG	p.T126T	ST7L_ENST00000369669.1_5'UTR|ST7L_ENST00000369666.1_Silent_p.T109T|ST7L_ENST00000490067.1_Silent_p.T109T|ST7L_ENST00000538187.1_Silent_p.T70T|ST7L_ENST00000360743.4_Silent_p.T126T|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000369668.2_Silent_p.T126T|ST7L_ENST00000544629.1_Silent_p.T126T|ST7L_ENST00000543570.1_Silent_p.T109T|ST7L_ENST00000343210.7_Silent_p.T126T	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	126					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				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)		TGCTGCTCTCTGTTCCTCCCA	0.408													T|||	59	0.0117812	0.0431	0.0029	5008	,	,		21004	0.0		0.0	False		,,,				2504	0.0				p.T126T		Atlas-SNP	.											.	ST7L	31	.	0			c.A378G						PASS	.	T	,,,	197,4209	124.5+/-161.8	5,187,2011	156.0	150.0	152.0		378,327,378,378	4.9	1.0	1	dbSNP_126	152	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ST7L	NM_017744.4,NM_138727.3,NM_138728.2,NM_138729.3	,,,	5,188,6310	CC,CT,TT		0.0116,4.4712,1.5224	,,,	126/576,109/559,126/545,126/556	113153536	198,12808	2203	4300	6503	SO:0001819	synonymous_variant	54879	exon3			GCTCTCTGTTCCT	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.378A>G	1.37:g.113153536T>C		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	268	134	0.5	NM_138729	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Silent	SNP	ENST00000358039.4	37	CCDS848.1																																																																																			T|0.984;C|0.016	0.016	strong		0.408	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3		
ALS2	57679	hgsc.bcm.edu	37	2	202593280	202593280	+	Silent	SNP	G	G	A	rs3219161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:202593280G>A	ENST00000264276.6	-	15	3168	c.2796C>T	c.(2794-2796)tcC>tcT	p.S932S	ALS2_ENST00000457679.2_Silent_p.S244S	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	932	PH. {ECO:0000305}.				behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						ACCAATTCACGGAAAACCTCC	0.483													g|||	576	0.115016	0.0696	0.0418	5008	,	,		18748	0.2431		0.0656	False		,,,				2504	0.1472				p.S932S		Atlas-SNP	.											.	ALS2	172	.	0			c.C2796T						PASS	.	G		230,3604		7,216,1694	105.0	106.0	106.0		2796	0.7	1.0	2	dbSNP_106	106	695,7565		26,643,3461	no	coding-synonymous	ALS2	NM_020919.3		33,859,5155	AA,AG,GG		8.414,5.999,7.6484		932/1658	202593280	925,11169	1917	4130	6047	SO:0001819	synonymous_variant	57679	exon15			ATTCACGGAAAAC	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.2796C>T	2.37:g.202593280G>A		Somatic	386	0	0		WXS	Illumina HiSeq	Phase_I	430	208	0.483721	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Silent	SNP	ENST00000264276.6	37	CCDS42800.1																																																																																			G|0.900;A|0.100	0.100	strong		0.483	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919	
AXDND1	126859	hgsc.bcm.edu	37	1	179347832	179347832	+	Silent	SNP	T	T	C	rs10798674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179347832T>C	ENST00000367618.3	+	5	822	c.435T>C	c.(433-435)gtT>gtC	p.V145V	AXDND1_ENST00000461179.2_3'UTR|AXDND1_ENST00000457238.2_Silent_p.V145V	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	145										NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						AGAAGGCAGTTTGTCCCCCAC	0.363													T|||	2563	0.511781	0.2799	0.5274	5008	,	,		14205	0.6974		0.5159	False		,,,				2504	0.6186				p.V145V		Atlas-SNP	.											.	AXDND1	142	.	0			c.T435C						PASS	.	T		1413,2993	460.7+/-352.7	230,953,1020	128.0	105.0	113.0		435	-1.6	0.3	1	dbSNP_120	113	3991,4609	553.1+/-386.2	933,2125,1242	no	coding-synonymous	AXDND1	NM_144696.4		1163,3078,2262	CC,CT,TT		46.407,32.0699,41.5501		145/1013	179347832	5404,7602	2203	4300	6503	SO:0001819	synonymous_variant	126859	exon5			GGCAGTTTGTCCC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.435T>C	1.37:g.179347832T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Silent	SNP	ENST00000367618.3	37	CCDS30948.1																																																																																			T|0.546;C|0.454	0.454	strong		0.363	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	
DGKI	9162	hgsc.bcm.edu	37	7	137150665	137150665	+	Silent	SNP	T	T	C	rs35245703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:137150665T>C	ENST00000288490.5	-	27	2625	c.2625A>G	c.(2623-2625)gaA>gaG	p.E875E	DGKI_ENST00000446122.1_Silent_p.E857E|DGKI_ENST00000453654.2_Silent_p.E585E|DGKI_ENST00000424189.2_Silent_p.E888E	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	875					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						CCGAGGCTTGTTCCACCACCA	0.542													C|||	480	0.0958466	0.3555	0.013	5008	,	,		17525	0.0		0.001	False		,,,				2504	0.0				p.E875E		Atlas-SNP	.											.	DGKI	335	.	0			c.A2625G						PASS	.	C		1335,3071	695.8+/-406.0	210,915,1078	64.0	62.0	63.0		2625	2.9	1.0	7	dbSNP_126	63	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	DGKI	NM_004717.2		210,920,5373	CC,CT,TT		0.0581,30.2996,10.3029		875/1066	137150665	1340,11666	2203	4300	6503	SO:0001819	synonymous_variant	9162	exon27			GGCTTGTTCCACC	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2625A>G	7.37:g.137150665T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	76	28	0.368421	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	37	CCDS5845.1																																																																																			T|0.910;C|0.090	0.090	strong		0.542	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	
HAO1	54363	hgsc.bcm.edu	37	20	7920986	7920986	+	Silent	SNP	C	C	T	rs33931524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:7920986C>T	ENST00000378789.3	-	1	135	c.84G>A	c.(82-84)agG>agA	p.R28R		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	28	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				cellular nitrogen compound metabolic process (GO:0034641)|fatty acid alpha-oxidation (GO:0001561)|glycolate catabolic process (GO:0046296)|glyoxylate metabolic process (GO:0046487)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|glycolate oxidase activity (GO:0008891)|glyoxylate oxidase activity (GO:0047969)|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(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						TTGCCCCAGACCTGTAATAGT	0.318													C|||	161	0.0321486	0.1082	0.0187	5008	,	,		17203	0.0		0.003	False		,,,				2504	0.002				p.R28R		Atlas-SNP	.											.	HAO1	71	.	0			c.G84A						PASS	.	C		456,3950	215.1+/-234.2	17,422,1764	70.0	70.0	70.0		84	-3.4	0.8	20	dbSNP_126	70	41,8559	25.7+/-73.6	0,41,4259	no	coding-synonymous	HAO1	NM_017545.2		17,463,6023	TT,TC,CC		0.4767,10.3495,3.8213		28/371	7920986	497,12509	2203	4300	6503	SO:0001819	synonymous_variant	54363	exon1			CCCAGACCTGTAA	AL021879	CCDS13100.1	20p12	2005-01-10			ENSG00000101323	ENSG00000101323	1.1.3.15		4809	protein-coding gene	gene with protein product		605023		GOX1		9891009	Standard	NM_017545		Approved	GOX	uc002wmw.1	Q9UJM8	OTTHUMG00000031841	ENST00000378789.3:c.84G>A	20.37:g.7920986C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	98	53	0.540816	NM_017545	Q14CQ0|Q9UPZ0|Q9Y3I7	Silent	SNP	ENST00000378789.3	37	CCDS13100.1																																																																																			C|0.966;T|0.034	0.034	strong		0.318	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2		
DCAF8L2	347442	hgsc.bcm.edu	37	X	27765405	27765405	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:27765405G>A	ENST00000451261.2	+	5	792	c.393G>A	c.(391-393)gaG>gaA	p.E131E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	131	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aggaagaggaggaggaggagg	0.562																																					p.E131E		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G393A						PASS	.						20.0	18.0	18.0					X																	27765405		692	1587	2279	SO:0001819	synonymous_variant	347442	exon1			AGAGGAGGAGGAG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.393G>A	X.37:g.27765405G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	7	0.125	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			.	.	none		0.562	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
MECOM	2122	hgsc.bcm.edu	37	3	169098992	169098992	+	Missense_Mutation	SNP	G	G	A	rs7622799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:169098992G>A	ENST00000494292.1	-	2	455	c.358C>T	c.(358-360)Ccc>Tcc	p.P120S	MECOM_ENST00000485957.1_5'UTR	NM_004991.3	NP_004982.2	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	120			P -> S (in dbSNP:rs7622799).		regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P114S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CCATAACTGGGGTCTTTCAGG	0.408													G|||	766	0.152955	0.1362	0.3329	5008	,	,		20490	0.1558		0.1233	False		,,,				2504	0.0757				p.P120S		Atlas-SNP	.											MDS1,NS,carcinoma,0,1	MECOM	216	1	1	Substitution - Missense(1)	stomach(1)	c.C358T						PASS	.	G	,SER/PRO	483,3245		32,419,1413	90.0	87.0	88.0		,358	4.5	1.0	3	dbSNP_116	88	932,7278		53,826,3226	yes	intron,missense	MECOM	NM_001205194.1,NM_004991.3	,74	85,1245,4639	AA,AG,GG		11.352,12.956,11.8529	,possibly-damaging	,120/1240	169098992	1415,10523	1864	4105	5969	SO:0001583	missense	2122	exon2			AACTGGGGTCTTT	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000494292.1:c.358C>T	3.37:g.169098992G>A	ENSP00000417899:p.Pro120Ser	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	158	88	0.556962	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000494292.1	37		344	0.1575091575091575	59	0.11991869918699187	89	0.24585635359116023	94	0.16433566433566432	102	0.1345646437994723	G	1.493	-0.554124	0.03996	0.12956	0.11352	ENSG00000085276	ENST00000494292	T	0.71698	-0.59	5.4	4.52	0.55395	.	0.105398	0.42964	N	0.000640	T	0.00012	0.0000	N	0.12746	0.255	0.09310	P	1.0	B;B	0.30281	0.275;0.0	B;B	0.28916	0.096;0.002	T	0.06734	-1.0810	9	0.46703	T	0.11	.	13.2366	0.59972	0.0775:0.0:0.9225:0.0	rs7622799;rs52817261;rs59561788;rs7622799	120;120	Q13465;Q03112-3	MDS1_HUMAN;.	S	120	ENSP00000417899:P120S	ENSP00000417899:P120S	P	-	1	0	MECOM	170581686	1.000000	0.71417	0.974000	0.42286	0.381000	0.30169	2.496000	0.45346	1.252000	0.44001	0.650000	0.86243	CCC	G|0.861;A|0.139	0.139	strong		0.408	MECOM-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000351517.3	NM_005241, NM_004991	
GPI	2821	hgsc.bcm.edu	37	19	34872382	34872382	+	Silent	SNP	G	G	A	rs1864139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:34872382G>A	ENST00000356487.5	+	9	1003	c.762G>A	c.(760-762)aaG>aaA	p.K254K	GPI_ENST00000586425.1_Silent_p.K254K|GPI_ENST00000415930.3_Silent_p.K265K	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase	254					aldehyde catabolic process (GO:0046185)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|hemostasis (GO:0007599)|humoral immune response (GO:0006959)|learning or memory (GO:0007611)|methylglyoxal biosynthetic process (GO:0019242)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucose-6-phosphate isomerase activity (GO:0004347)|intramolecular transferase activity (GO:0016866)|monosaccharide binding (GO:0048029)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	25	Esophageal squamous(110;0.162)					CCAAAGTGAAGGAGTTTGGAA	0.468													G|||	601	0.120008	0.2443	0.0764	5008	,	,		21611	0.002		0.0507	False		,,,				2504	0.1759				p.K265K		Atlas-SNP	.											GPI,NS,carcinoma,+1,1	GPI	63	1	0			c.G795A						scavenged	.	G	,	907,3499	345.1+/-308.4	92,723,1388	165.0	166.0	165.0		762,795	1.7	1.0	19	dbSNP_92	165	441,8159	132.2+/-189.8	12,417,3871	no	coding-synonymous,coding-synonymous	GPI	NM_000175.3,NM_001184722.1	,	104,1140,5259	AA,AG,GG		5.1279,20.5856,10.3644	,	254/559,265/570	34872382	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	2821	exon9			AGTGAAGGAGTTT	M61214	CCDS12437.1, CCDS54246.1	19q13.1	2012-10-02	2010-05-11			ENSG00000105220	5.3.1.9		4458	protein-coding gene	gene with protein product		172400	"""glucose phosphate isomerase"""			2387591, 8575767	Standard	NM_001184722		Approved	AMF, NLK	uc002nvg.2	P06744		ENST00000356487.5:c.762G>A	19.37:g.34872382G>A		Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	135	80	0.592593	NM_001184722	B4DG39|Q9BRD3|Q9BSK5|Q9UHE6	Silent	SNP	ENST00000356487.5	37	CCDS12437.1																																																																																			G|0.897;A|0.103	0.103	strong		0.468	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451693.3		
DCAF16	54876	hgsc.bcm.edu	37	4	17805379	17805379	+	Missense_Mutation	SNP	G	G	A	rs7690457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:17805379G>A	ENST00000382247.1	-	3	1446	c.386C>T	c.(385-387)aCa>aTa	p.T129I	DCAF16_ENST00000507768.1_5'Flank|DCAF16_ENST00000536863.1_Missense_Mutation_p.T129I	NM_017741.3	NP_060211.3	Q9NXF7	DCA16_HUMAN	DDB1 and CUL4 associated factor 16	129			T -> I (in dbSNP:rs7690457).		protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				cervix(1)|endometrium(1)|lung(2)|ovary(1)	5						GCTGGGACTTGTAAGAGGCTT	0.507													G|||	580	0.115815	0.2648	0.0259	5008	,	,		17963	0.1002		0.0249	False		,,,				2504	0.0879				p.T129I		Atlas-SNP	.											.	DCAF16	19	.	0			c.C386T						PASS	.	G	ILE/THR	978,3428	366.6+/-317.9	109,760,1334	145.0	154.0	151.0		386	-7.8	0.0	4	dbSNP_116	151	251,8349	99.3+/-160.8	1,249,4050	yes	missense	DCAF16	NM_017741.3	89	110,1009,5384	AA,AG,GG		2.9186,22.197,9.4495	benign	129/217	17805379	1229,11777	2203	4300	6503	SO:0001583	missense	54876	exon3			GGACTTGTAAGAG	AK000287	CCDS3423.1	4p15.32	2009-07-17	2009-07-17	2009-07-17	ENSG00000163257	ENSG00000163257		"""DDB1 and CUL4 associated factors"""	25987	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 30"""	C4orf30		12477932	Standard	XM_005248169		Approved	FLJ20280	uc003gpn.3	Q9NXF7	OTTHUMG00000128536	ENST00000382247.1:c.386C>T	4.37:g.17805379G>A	ENSP00000371682:p.Thr129Ile	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	234	110	0.470085	NM_017741	B3KPB7	Missense_Mutation	SNP	ENST00000382247.1	37	CCDS3423.1	228	0.1043956043956044	140	0.2845528455284553	10	0.027624309392265192	57	0.09965034965034965	21	0.027704485488126648	G	10.28	1.307852	0.23821	0.22197	0.029186	ENSG00000163257	ENST00000382247;ENST00000536863	T;T	0.32272	1.46;1.46	3.91	-7.81	0.01210	.	.	.	.	.	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	0.38607	-0.9653	8	0.87932	D	0	5.3752	1.8409	0.03150	0.4934:0.1097:0.1651:0.2318	rs7690457;rs52827649;rs57652056;rs7690457	129	Q9NXF7	DCA16_HUMAN	I	129	ENSP00000371682:T129I;ENSP00000445736:T129I	ENSP00000371682:T129I	T	-	2	0	DCAF16	17414477	0.063000	0.20901	0.001000	0.08648	0.903000	0.53119	-1.319000	0.02702	-2.132000	0.00814	-0.367000	0.07326	ACA	G|0.893;A|0.107	0.107	strong		0.507	DCAF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250371.1	NM_017741	
EFCAB3	146779	hgsc.bcm.edu	37	17	60451185	60451185	+	Missense_Mutation	SNP	G	G	C	rs6504103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60451185G>C	ENST00000450662.2	+	2	116	c.45G>C	c.(43-45)aaG>aaC	p.K15N		NM_001144933.1	NP_001138405.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	0							calcium ion binding (GO:0005509)			cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			GAAATGGAAAGATTAATGTTA	0.254													G|||	123	0.0245607	0.0908	0.0029	5008	,	,		14237	0.0		0.001	False		,,,				2504	0.0				p.K15N		Atlas-SNP	.											.	EFCAB3	71	.	0			c.G45C						PASS	.						46.0	41.0	43.0					17																	60451185		692	1584	2276	SO:0001583	missense	146779	exon2			TGGAAAGATTAAT	AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"""EF-hand domain containing"""	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000450662.2:c.45G>C	17.37:g.60451185G>C	ENSP00000403932:p.Lys15Asn	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	145	71	0.489655	NM_001144933	J3KQM8	Missense_Mutation	SNP	ENST00000450662.2	37	CCDS45751.1	38	0.0173992673992674	37	0.07520325203252033	0	0.0	0	0.0	1	0.0013192612137203166	.	8.466	0.856348	0.17106	.	.	ENSG00000172421	ENST00000450662	T	0.10668	2.85	4.0	0.787	0.18596	.	.	.	.	.	T	0.00440	0.0014	.	.	.	0.18873	N	0.999986	.	.	.	.	.	.	T	0.42155	-0.9468	6	0.32370	T	0.25	.	5.523	0.16943	0.3862:0.0:0.6138:0.0	rs6504103;rs6504103	.	.	.	N	15	ENSP00000403932:K15N	ENSP00000403932:K15N	K	+	3	2	EFCAB3	57804917	0.869000	0.29996	0.031000	0.17742	0.003000	0.03518	0.480000	0.22244	0.396000	0.25283	0.591000	0.81541	AAG	G|0.983;C|0.017	0.017	strong		0.254	EFCAB3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379315.1	NM_173503	
THBS2	7058	hgsc.bcm.edu	37	6	169621536	169621536	+	Silent	SNP	A	A	G	rs1132742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:169621536A>G	ENST00000366787.3	-	21	3609	c.3360T>C	c.(3358-3360)acT>acC	p.T1120T	XXyac-YX65C7_A.2_ENST00000444188.1_RNA|THBS2_ENST00000488355.1_5'UTR	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	106	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	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	
FOXK1	221937	hgsc.bcm.edu	37	7	4802035	4802035	+	Silent	SNP	A	A	G	rs1053753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:4802035A>G	ENST00000328914.4	+	9	2142	c.2142A>G	c.(2140-2142)gtA>gtG	p.V714V	FOXK1_ENST00000446823.1_Silent_p.V551V	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GTGGTGCTGTAACCACACCGG	0.701													G|||	1465	0.292532	0.6785	0.121	5008	,	,		12597	0.0704		0.1471	False		,,,				2504	0.271				p.V714V		Atlas-SNP	.											.	FOXK1	64	.	0			c.A2142G						PASS	.	G		2104,2054		524,1056,499	12.0	14.0	14.0		2142	-5.3	0.0	7	dbSNP_86	14	1140,7002		97,946,3028	no	coding-synonymous	FOXK1	NM_001037165.1		621,2002,3527	GG,GA,AA		14.0015,49.3987,26.374		714/734	4802035	3244,9056	2079	4071	6150	SO:0001819	synonymous_variant	221937	exon9			TGCTGTAACCACA	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"""Forkhead boxes"""	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.2142A>G	7.37:g.4802035A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_001037165		Silent	SNP	ENST00000328914.4	37	CCDS34591.1																																																																																			A|0.728;G|0.272	0.272	strong		0.701	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
CYP51A1	1595	hgsc.bcm.edu	37	7	91743072	91743072	+	Silent	SNP	A	A	G	rs149576331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:91743072A>G	ENST00000003100.8	-	10	1602	c.1437T>C	c.(1435-1437)gaT>gaC	p.D479D	LRRD1_ENST00000422722.1_5'UTR|CYP51A1_ENST00000450723.1_Silent_p.D374D	NM_000786.3	NP_000777.1	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A, polypeptide 1	473					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via 24,25-dihydrolanosterol (GO:0033488)|demethylation (GO:0070988)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|sterol 14-demethylase activity (GO:0008398)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	10	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Itraconazole(DB01167)|Ketoconazole(DB01026)|Sertaconazole(DB01153)|Tioconazole(DB01007)	CATCAATGAGATCAAATTCAT	0.343													A|||	7	0.00139776	0.0053	0.0	5008	,	,		16883	0.0		0.0	False		,,,				2504	0.0				p.D479D	GBM(70;1100 1190 11592 25836 51397)	Atlas-SNP	.											.	CYP51A1	30	.	0			c.T1437C						PASS	.	A	,	6,4400	11.4+/-27.6	0,6,2197	109.0	107.0	108.0		1437,1122	4.0	1.0	7	dbSNP_134	108	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CYP51A1	NM_000786.3,NM_001146152.1	,	0,6,6497	GG,GA,AA		0.0,0.1362,0.0461	,	479/510,374/405	91743072	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	1595	exon10			AATGAGATCAAAT	U51685	CCDS5623.1, CCDS55123.1	7q21.2	2012-10-10	2003-02-14	2003-02-28	ENSG00000001630	ENSG00000001630		"""Cytochrome P450s"""	2649	protein-coding gene	gene with protein product		601637	"""cytochrome P450, 51 (lanosterol 14-alpha-demethylase)"""	CYP51		8975714	Standard	NM_000786		Approved	CP51, CYPL1, P450L1, LDM, P450-14DM	uc003ulm.4	Q16850	OTTHUMG00000131131	ENST00000003100.8:c.1437T>C	7.37:g.91743072A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	NM_000786	A4D1F8|B2RAI4|B4DJ55|O00770|O00772|Q16784|Q8N1A8|Q99868	Silent	SNP	ENST00000003100.8	37	CCDS5623.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	A	14.66	2.600307	0.46423	0.001362	0.0	ENSG00000001630	ENST00000422867	.	.	.	5.1	3.96	0.45880	.	.	.	.	.	T	0.39733	0.1089	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35748	-0.9776	4	.	.	.	.	3.9644	0.09424	0.6788:0.0:0.1664:0.1548	.	.	.	.	P	192	.	.	S	-	1	0	CYP51A1	91581008	0.988000	0.35896	1.000000	0.80357	0.998000	0.95712	0.350000	0.20079	0.977000	0.38444	0.482000	0.46254	TCT	A|0.999;G|0.001	0.001	strong		0.343	CYP51A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253812.4		
NMS	129521	hgsc.bcm.edu	37	2	101096960	101096960	+	Silent	SNP	C	C	T	rs1519654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	242	0	0		WXS	Illumina HiSeq	Phase_I	205	98	0.478049	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	
MYO7B	4648	hgsc.bcm.edu	37	2	128381861	128381861	+	Missense_Mutation	SNP	G	G	A	rs61743523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128381861G>A	ENST00000409816.2	+	28	3967	c.3935G>A	c.(3934-3936)cGa>cAa	p.R1312Q	RP11-286H15.1_ENST00000609697.1_RNA|MYO7B_ENST00000409090.1_Missense_Mutation_p.R165Q|MYO7B_ENST00000389524.4_Missense_Mutation_p.R1312Q|MYO7B_ENST00000428314.1_Missense_Mutation_p.R1312Q			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1312	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CAAGTCCTCCGAGGAGTCTGG	0.592													A|||	36	0.0071885	0.0234	0.0072	5008	,	,		19505	0.0		0.0	False		,,,				2504	0.0				p.R1312Q		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3935A						PASS	.	A	GLN/ARG	82,3886		2,78,1904	15.0	16.0	16.0		3935	-0.1	0.1	2	dbSNP_129	16	2,8290		0,2,4144	yes	missense	MYO7B	NM_001080527.1	43	2,80,6048	AA,AG,GG		0.0241,2.0665,0.6852	benign	1312/2117	128381861	84,12176	1984	4146	6130	SO:0001583	missense	4648	exon29			TCCTCCGAGGAGT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3935G>A	2.37:g.128381861G>A	ENSP00000386461:p.Arg1312Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	12	0.005494505494505495	9	0.018292682926829267	3	0.008287292817679558	0	0.0	0	0.0	.	13.32	2.200829	0.38905	0.020665	2.41E-4	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000437387;ENST00000409090	T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.6;-0.89	3.68	-0.0642	0.13773	FERM central domain (1);Band 4.1 domain (1);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.715826	0.13724	N	0.367181	T	0.49236	0.1545	M	0.79258	2.445	0.21579	N	0.999633	P	0.42337	0.776	B	0.32465	0.146	T	0.49995	-0.8879	10	0.38643	T	0.18	.	5.7748	0.18273	0.2859:0.0:0.5394:0.1747	rs61743523	1312	Q6PIF6	MYO7B_HUMAN	Q	1312;1312;165;1312;165;165	ENSP00000374175:R1312Q;ENSP00000415090:R1312Q;ENSP00000386461:R1312Q;ENSP00000404927:R165Q;ENSP00000386850:R165Q	ENSP00000272666:R165Q	R	+	2	0	MYO7B	128098331	0.985000	0.35326	0.083000	0.20561	0.098000	0.18820	2.232000	0.43018	-0.259000	0.09432	-0.361000	0.07541	CGA	G|0.993;A|0.007	0.007	strong		0.592	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
RPGR	6103	hgsc.bcm.edu	37	X	38156677	38156677	+	Missense_Mutation	SNP	C	C	T	rs1801687|rs281865303	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38156677C>T	ENST00000339363.3	-	11	1441	c.1274G>A	c.(1273-1275)aGg>aAg	p.R425K	TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Missense_Mutation_p.R425K|RPGR_ENST00000378505.2_Missense_Mutation_p.R425K|RPGR_ENST00000318842.7_Missense_Mutation_p.R425K|RPGR_ENST00000309513.3_Missense_Mutation_p.R363K|RPGR_ENST00000338898.3_Missense_Mutation_p.R425K			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	425			R -> K (in dbSNP:rs1801687). {ECO:0000269|PubMed:10480356, ECO:0000269|PubMed:10937588, ECO:0000269|PubMed:10980543, ECO:0000269|PubMed:9399904}.		cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						TAGTGTTCTCCTCATTGAAAA	0.358													T|||	488	0.129272	0.1271	0.1427	3775	,	,		12964	0.0516		0.0527	False		,,,				2504	0.1186				p.R425K		Atlas-SNP	.											.	RPGR	175	.	0			c.G1274A						PASS	.	T	LYS/ARG,LYS/ARG	591,3242		48,412,83,1171,488	61.0	53.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1274,1274	-5.9	0.0	X	dbSNP_89	56	344,6384		4,229,107,2195,1765	yes	missense,missense	RPGR	NM_000328.2,NM_001034853.1	26,26	52,641,190,3366,2253	TT,TC,T,CC,C		5.113,15.4187,8.8533	benign,benign	425/816,425/1153	38156677	935,9626	2202	4300	6502	SO:0001583	missense	6103	exon11			GTTCTCCTCATTG	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.1274G>A	X.37:g.38156677C>T	ENSP00000343671:p.Arg425Lys	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	194	92	0.474227	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		174	0.10488245931283906	34	0.0752212389380531	37	0.10818713450292397	23	0.04107142857142857	31	0.04234972677595628	T	0.356	-0.942055	0.02322	0.154187	0.05113	ENSG00000156313	ENST00000339363;ENST00000309513;ENST00000338898;ENST00000318842;ENST00000342811;ENST00000378505	T;T;T;T;T;T	0.47869	1.39;1.07;0.83;1.41;1.41;1.4	4.75	-5.87	0.02297	.	0.925114	0.09080	N	0.851441	T	0.00109	0.0003	N	0.08118	0	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.0	T	0.10660	-1.0620	9	0.41790	T	0.15	.	3.8908	0.09117	0.1485:0.118:0.4934:0.24	rs1801687;rs52835401	425;425	E9PE28;Q92834-2	.;.	K	425;363;425;425;425;425	ENSP00000343671:R425K;ENSP00000308783:R363K;ENSP00000340208:R425K;ENSP00000322219:R425K;ENSP00000339531:R425K;ENSP00000367766:R425K	ENSP00000308783:R363K	R	-	2	0	RPGR	38041621	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.250000	0.08830	-1.884000	0.01119	-4.401000	0.00006	AGG	C|0.904;T|0.096	0.096	strong		0.358	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548554	32548554	+	Silent	SNP	G	G	C	rs3830126		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32548554G>C	ENST00000360004.5	-	4	837	c.732C>G	c.(730-732)gcC>gcG	p.A244A		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	244					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						TGAACAGCCCGGCCCCAAGGA	0.557										Multiple Myeloma(14;0.17)																											p.A244A		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C732G						PASS	.						89.0	103.0	98.0					6																	32548554		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon4			CAGCCCGGCCCCA	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.732C>G	6.37:g.32548554G>C		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	483	36	0.0745342	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			.	.	alt		0.557	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
STK40	83931	hgsc.bcm.edu	37	1	36820015	36820015	+	Silent	SNP	T	T	C	rs115120808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36820015T>C	ENST00000373129.3	-	7	979	c.573A>G	c.(571-573)aaA>aaG	p.K191K	STK40_ENST00000373132.3_Silent_p.K191K|STK40_ENST00000373130.3_Silent_p.K196K|STK40_ENST00000482458.1_5'Flank|STK40_ENST00000359297.2_Silent_p.K191K	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	191	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			Missing (in Ref. 2; BAC11371). {ECO:0000305}.	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)				GCACGATATTTTTCTGTAAAA	0.527													T|||	55	0.0109824	0.0401	0.0029	5008	,	,		20477	0.0		0.0	False		,,,				2504	0.0				p.K191K		Atlas-SNP	.											.	STK40	53	.	0			c.A573G						PASS	.	T		162,4244	109.1+/-147.4	5,152,2046	189.0	177.0	181.0		573	3.0	1.0	1	dbSNP_132	181	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	STK40	NM_032017.1		5,153,6345	CC,CT,TT		0.0116,3.6768,1.2533		191/436	36820015	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	83931	exon7			GATATTTTTCTGT	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.573A>G	1.37:g.36820015T>C		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	173	81	0.468208	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Silent	SNP	ENST00000373129.3	37	CCDS407.1																																																																																			T|0.990;C|0.010	0.010	strong		0.527	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017	
MTUS1	57509	hgsc.bcm.edu	37	8	17612518	17612518	+	Missense_Mutation	SNP	A	A	G	rs61733696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17612518A>G	ENST00000262102.6	-	2	1023	c.799T>C	c.(799-801)Tct>Cct	p.S267P	MTUS1_ENST00000381862.3_Missense_Mutation_p.S267P|MTUS1_ENST00000519263.1_Missense_Mutation_p.S267P|MTUS1_ENST00000381869.3_Missense_Mutation_p.S267P	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	267					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)		TTTCCTGAAGAACATGCACAC	0.428													A|||	159	0.0317492	0.0	0.0144	5008	,	,		21815	0.0714		0.0288	False		,,,				2504	0.0491				p.S267P		Atlas-SNP	.											.	MTUS1	144	.	0			c.T799C						PASS	.	A	PRO/SER,PRO/SER	28,3874		0,28,1923	213.0	195.0	201.0		799,799	4.3	0.9	8	dbSNP_129	201	290,8006		4,282,3862	yes	missense,missense	MTUS1	NM_001001924.2,NM_001001925.2	74,74	4,310,5785	GG,GA,AA		3.4957,0.7176,2.607	probably-damaging,probably-damaging	267/1271,267/1217	17612518	318,11880	1951	4148	6099	SO:0001583	missense	57509	exon2			CTGAAGAACATGC	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.799T>C	8.37:g.17612518A>G	ENSP00000262102:p.Ser267Pro	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	60	0.027472527472527472	0	0.0	10	0.027624309392265192	26	0.045454545454545456	24	0.0316622691292876	A	12.91	2.078409	0.36662	0.007176	0.034957	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.30182	2.45;2.5;2.45;1.54	4.29	4.29	0.51040	.	0.100277	0.43260	D	0.000582	T	0.09379	0.0231	L	0.32530	0.975	0.33123	D	0.541998	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.996;0.996	T	0.35895	-0.9770	10	0.87932	D	0	-13.4164	10.1107	0.42561	1.0:0.0:0.0:0.0	rs61733696	267;267;267	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	P	267	ENSP00000371293:S267P;ENSP00000262102:S267P;ENSP00000430167:S267P;ENSP00000371286:S267P	ENSP00000262102:S267P	S	-	1	0	MTUS1	17656798	0.024000	0.19004	0.900000	0.35374	0.186000	0.23388	0.880000	0.28159	2.163000	0.67991	0.482000	0.46254	TCT	A|0.971;G|0.029	0.029	strong		0.428	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
SSBP4	170463	hgsc.bcm.edu	37	19	18542201	18542201	+	Silent	SNP	C	C	T	rs113198578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18542201C>T	ENST00000270061.7	+	6	702	c.408C>T	c.(406-408)aaC>aaT	p.N136N	SSBP4_ENST00000348495.6_Intron|SSBP4_ENST00000598159.2_Intron|SSBP4_ENST00000599699.2_5'Flank	NM_032627.4	NP_116016.1	Q9BWG4	SSBP4_HUMAN	single stranded DNA binding protein 4	136	Pro-rich.					nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|skin(1)	4						ACAACCCCAACGCCCCCATGA	0.697													C|||	148	0.0295527	0.0968	0.0159	5008	,	,		7118	0.0		0.0089	False		,,,				2504	0.0				p.N136N		Atlas-SNP	.											SSBP4,NS,neuroblastoma,0,1	SSBP4	19	1	0			c.C408T						PASS	.	C	,	349,3959		14,321,1819	10.0	10.0	10.0		,408	1.0	0.0	19	dbSNP_132	10	52,8436		0,52,4192	no	intron,coding-synonymous	SSBP4	NM_001009998.3,NM_032627.4	,	14,373,6011	TT,TC,CC		0.6126,8.1012,3.1338	,	,136/386	18542201	401,12395	2154	4244	6398	SO:0001819	synonymous_variant	170463	exon6			CCCCAACGCCCCC		CCDS12378.1, CCDS32960.1	19p13.1	2008-02-05				ENSG00000130511			15676	protein-coding gene	gene with protein product		607391				12079286	Standard	NM_032627		Approved		uc002niy.3	Q9BWG4		ENST00000270061.7:c.408C>T	19.37:g.18542201C>T		Somatic	367	0	0		WXS	Illumina HiSeq	Phase_I	425	236	0.555294	NM_032627	Q9BWW5	Silent	SNP	ENST00000270061.7	37	CCDS12378.1																																																																																			C|0.976;T|0.024	0.024	strong		0.697	SSBP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466348.3	NM_032627	
OR52E6	390078	hgsc.bcm.edu	37	11	5862780	5862780	+	Silent	SNP	T	T	C	rs4362172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	173	0	0		WXS	Illumina HiSeq	Phase_I	179	79	0.441341	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	
ATAD5	79915	hgsc.bcm.edu	37	17	29161202	29161202	+	Missense_Mutation	SNP	A	A	T	rs9910051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:29161202A>T	ENST00000321990.4	+	2	481	c.103A>T	c.(103-105)Acc>Tcc	p.T35S	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	35			T -> S (in dbSNP:rs9910051).		cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TGACACATCTACCTGCAAAAC	0.308													T|||	1442	0.287939	0.5681	0.2305	5008	,	,		17249	0.1359		0.1163	False		,,,				2504	0.2832				p.T35S		Atlas-SNP	.											.	ATAD5	150	.	0			c.A103T						PASS	.	T	SER/THR	2097,2303	549.6+/-377.8	501,1095,604	75.0	82.0	80.0		103	5.5	1.0	17	dbSNP_119	80	960,7638	761.2+/-407.6	45,870,3384	yes	missense	ATAD5	NM_024857.3	58	546,1965,3988	TT,TA,AA		11.1654,47.6591,23.519	benign	35/1845	29161202	3057,9941	2200	4299	6499	SO:0001583	missense	79915	exon2			ACATCTACCTGCA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.103A>T	17.37:g.29161202A>T	ENSP00000313171:p.Thr35Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	92	36	0.391304	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	518	0.23717948717948717	269	0.5467479674796748	81	0.22375690607734808	90	0.15734265734265734	78	0.10290237467018469	T	11.35	1.612102	0.28712	0.476591	0.111654	ENSG00000176208	ENST00000321990	T	0.05855	3.38	5.47	5.47	0.80525	.	0.556987	0.18338	N	0.144288	T	0.00012	0.0000	N	0.00112	-2.095	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40194	-0.9576	9	0.02654	T	1	.	6.5206	0.22272	0.1388:0.0722:0.0:0.789	rs9910051;rs52830976;rs9910051	35	Q96QE3	ATAD5_HUMAN	S	35	ENSP00000313171:T35S	ENSP00000313171:T35S	T	+	1	0	ATAD5	26185328	0.998000	0.40836	0.974000	0.42286	0.914000	0.54420	1.019000	0.30014	0.911000	0.36747	-0.257000	0.10917	ACC	A|0.786;N|0.000	.	strong		0.308	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
GLRA4	441509	hgsc.bcm.edu	37	X	102979184	102979184	+	Missense_Mutation	SNP	G	G	A	rs16984014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102979184G>A	ENST00000372617.4	-	4	736	c.316C>T	c.(316-318)Cgc>Tgc	p.R106C	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	106						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						TAGGACAGGCGTGGGTCATTC	0.542													G|||	280	0.0741722	0.2065	0.0101	3775	,	,		14747	0.0		0.0	False		,,,				2504	0.0				p.R106C		Atlas-SNP	.											.	GLRA4	86	.	0			c.C316T						PASS	.	G	CYS/ARG,CYS/ARG	690,2992		49,480,112,1027,458	109.0	107.0	108.0		316,316	5.4	1.0	X	dbSNP_123	108	4,6663		0,4,0,2404,1851	yes	missense,missense	GLRA4	NM_001024452.2,NM_001172285.1	180,180	49,484,112,3431,2309	AA,AG,A,GG,G		0.06,18.7398,6.706	probably-damaging,probably-damaging	106/418,106/343	102979184	694,9655	2126	4259	6385	SO:0001583	missense	441509	exon4			ACAGGCGTGGGTC	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.316C>T	X.37:g.102979184G>A	ENSP00000361700:p.Arg106Cys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	150	98	0.653333	NM_001024452		Missense_Mutation	SNP	ENST00000372617.4	37	CCDS43980.2	105	0.06329113924050633	66	0.15865384615384615	1	0.0027624309392265192	0	0.0	0	0.0	G	24.1	4.494287	0.85069	0.187398	6.0E-4	ENSG00000188828	ENST00000372617	D	0.82344	-1.6	5.37	5.37	0.77165	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.01905	0.0060	H	0.95917	3.74	0.09310	P	0.99999999821083	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.17349	-1.0372	9	0.87932	D	0	.	15.3872	0.74711	0.0:0.0:1.0:0.0	rs16984014;rs56514211;rs16984014	106;65	Q5JXX5;B9WSA6	GLRA4_HUMAN;.	C	106	ENSP00000361700:R106C	ENSP00000361700:R106C	R	-	1	0	GLRA4	102865840	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.903000	0.87398	2.224000	0.72417	0.513000	0.50165	CGC	0|0.009;A|0.067	0.067	strong		0.542	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452	
TAS2R20	259295	hgsc.bcm.edu	37	12	11150046	11150046	+	Missense_Mutation	SNP	G	G	T	rs12226920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11150046G>T	ENST00000538986.1	-	1	428	c.429C>A	c.(427-429)caC>caA	p.H143Q	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	143			H -> Q (in dbSNP:rs12226920).	VCH -> ICQ (in Ref. 3; AAU21140). {ECO:0000305}.	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)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						TCATCACAAGGTGACAAACCA	0.383													G|||	2119	0.423123	0.0651	0.3847	5008	,	,		20817	0.755		0.3827	False		,,,				2504	0.6339				p.H143Q		Atlas-SNP	.											.	TAS2R20	17	.	0			c.C429A						PASS	.	G	GLN/HIS	441,3965	211.2+/-231.4	18,405,1780	134.0	119.0	124.0		429	-4.8	0.0	12	dbSNP_120	124	3013,5587	463.2+/-365.9	544,1925,1831	yes	missense	TAS2R20	NM_176889.2	24	562,2330,3611	TT,TG,GG		35.0349,10.0091,26.557	benign	143/310	11150046	3454,9552	2203	4300	6503	SO:0001583	missense	259295	exon1			CACAAGGTGACAA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.429C>A	12.37:g.11150046G>T	ENSP00000441624:p.His143Gln	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	898	0.41117216117216115	33	0.06707317073170732	155	0.4281767955801105	426	0.7447552447552448	284	0.37467018469656993	G	4.234	0.042417	0.08196	0.100091	0.350349	ENSG00000255837	ENST00000538986	T	0.36520	1.25	2.93	-4.77	0.03219	.	1.298410	0.05758	N	0.604393	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.14805	0.011	B	0.22880	0.042	T	0.38329	-0.9666	9	0.27082	T	0.32	.	0.8786	0.01230	0.2054:0.1545:0.3359:0.3042	rs12226920;rs60423827;rs12226920	143	P59543	T2R20_HUMAN	Q	143	ENSP00000441624:H143Q	ENSP00000441624:H143Q	H	-	3	2	TAS2R20	11041313	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.459000	0.02370	-0.884000	0.03976	-0.312000	0.09012	CAC	G|0.671;T|0.329	0.329	strong		0.383	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
SALL4	57167	hgsc.bcm.edu	37	20	50406630	50406630	+	Missense_Mutation	SNP	T	T	G	rs6091375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50406630T>G	ENST00000217086.4	-	2	2503	c.2392A>C	c.(2392-2394)Atc>Ctc	p.I798L	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	798			I -> L (in dbSNP:rs6091375). {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						TTTGACTTGATGCTTTCGGCT	0.527													T|||	329	0.0656949	0.1619	0.049	5008	,	,		18816	0.0		0.0646	False		,,,				2504	0.0164				p.I798L		Atlas-SNP	.											.	SALL4	168	.	0			c.A2392C						PASS	.	T	LEU/ILE	696,3710	294.1+/-283.0	54,588,1561	81.0	78.0	79.0		2392	-5.1	0.2	20	dbSNP_114	79	498,8102	142.2+/-198.4	14,470,3816	yes	missense	SALL4	NM_020436.3	5	68,1058,5377	GG,GT,TT		5.7907,15.7966,9.1804	benign	798/1054	50406630	1194,11812	2203	4300	6503	SO:0001583	missense	57167	exon2			ACTTGATGCTTTC	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.2392A>C	20.37:g.50406630T>G	ENSP00000217086:p.Ile798Leu	Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	324	157	0.484568	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	159	0.07280219780219781	88	0.17886178861788618	22	0.06077348066298342	0	0.0	49	0.06464379947229551	T	4.686	0.127462	0.08981	0.157966	0.057907	ENSG00000101115	ENST00000217086	T	0.07800	3.16	5.67	-5.11	0.02901	.	0.990681	0.08190	N	0.984093	T	0.00012	0.0000	L	0.38175	1.15	0.20764	P	0.99985162	B	0.06786	0.001	B	0.06405	0.002	T	0.48258	-0.9051	9	0.10902	T	0.67	-18.3976	9.814	0.40840	0.0984:0.488:0.0:0.4137	rs6091375;rs52814636;rs56500327;rs6091375	798	Q9UJQ4	SALL4_HUMAN	L	798	ENSP00000217086:I798L	ENSP00000217086:I798L	I	-	1	0	SALL4	49840037	0.000000	0.05858	0.196000	0.23383	0.847000	0.48162	-1.163000	0.03138	-1.412000	0.02030	-0.408000	0.06270	ATC	T|0.917;G|0.083	0.083	strong		0.527	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
APEH	327	hgsc.bcm.edu	37	3	49721532	49721532	+	IGR	SNP	G	G	A	rs3197999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49721532G>A	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Missense_Mutation_p.R703C|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.R689C(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCTGGCCAGCGGGACCTTGCG	0.567													G|||	961	0.191893	0.2179	0.1686	5008	,	,		20686	0.0565		0.3131	False		,,,				2504	0.1881				p.R703C		Atlas-SNP	.											MST1,NS,carcinoma,0,1	MST1	84	1	1	Substitution - Missense(1)	stomach(1)	c.C2107T						PASS	.	G	CYS/ARG	1036,3370	380.4+/-323.7	120,796,1287	64.0	61.0	62.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2107	-2.8	0.1	3	dbSNP_105	62	2525,6075	411.6+/-350.5	385,1755,2160	yes	missense	MST1	NM_020998.3	180	505,2551,3447	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	29.3605,23.5134,27.3797	possibly-damaging	703/726	49721532	3561,9445	2203	4300	6503	SO:0001628	intergenic_variant	4485	exon18			GCCAGCGGGACCT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49721532G>A		Somatic	466	0	0		WXS	Illumina HiSeq	Phase_I	474	204	0.43038	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	472|472	0.21611721611721613|0.21611721611721613	119|119	0.241869918699187|0.241869918699187	81|81	0.22375690607734808|0.22375690607734808	37|37	0.06468531468531469|0.06468531468531469	235|235	0.3100263852242744|0.3100263852242744	G|G	17.19|17.19	3.327308|3.327308	0.60743|0.60743	0.235134|0.235134	0.293605|0.293605	ENSG00000173531|ENSG00000173531	ENST00000448220|ENST00000449682	.|D	.|0.89196	.|-2.48	5.59|5.59	-2.82|-2.82	0.05787|0.05787	.|.	.|0.559462	.|0.14941	.|N	.|0.289511	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.74389|0.74389	2.26|2.26	0.46298|0.46298	P|P	0.0010210000000000496|0.0010210000000000496	.|P	.|0.40681	.|0.727	.|B	.|0.40702	.|0.338	T|T	0.21280|0.21280	-1.0250|-1.0250	4|9	.|0.66056	.|D	.|0.02	.|.	12.6939|12.6939	0.56992|0.56992	0.07:0.7015:0.147:0.0815|0.07:0.7015:0.147:0.0815	rs3197999;rs52793577;rs60772290;rs3197999|rs3197999;rs52793577;rs60772290;rs3197999	.|703	.|G3XAK1	.|.	L|C	172|703	.|ENSP00000414287:R703C	.|ENSP00000414287:R703C	P|R	-|-	2|1	0|0	MST1|MST1	49696536|49696536	0.511000|0.511000	0.26179|0.26179	0.123000|0.123000	0.21794|0.21794	0.860000|0.860000	0.49131|0.49131	1.075000|1.075000	0.30716|0.30716	-0.545000|-0.545000	0.06224|0.06224	0.655000|0.655000	0.94253|0.94253	CCG|CGC	G|0.749;A|0.251	0.251	strong		0.567	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
ALMS1	7840	hgsc.bcm.edu	37	2	73716810	73716810	+	Missense_Mutation	SNP	G	G	A	rs3820700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73716810G>A	ENST00000264448.6	+	10	7832	c.7721G>A	c.(7720-7722)aGt>aAt	p.S2574N	ALMS1_ENST00000409009.1_Missense_Mutation_p.S2532N|AC096546.1_ENST00000408160.1_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2574			S -> N (in dbSNP:rs3820700). {ECO:0000269|PubMed:15489334}.		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						GCTGTATGTAGTCACATTATT	0.418													G|||	635	0.126797	0.087	0.0548	5008	,	,		18901	0.2014		0.1262	False		,,,				2504	0.1554				p.S2574N		Atlas-SNP	.											.	ALMS1	384	.	0			c.G7721A						PASS	.	G	ASN/SER	376,3454		17,342,1556	141.0	133.0	135.0		7721	4.4	1.0	2	dbSNP_107	135	1073,7159		68,937,3111	yes	missense	ALMS1	NM_015120.4	46	85,1279,4667	AA,AG,GG		13.0345,9.8172,12.0129	possibly-damaging	2574/4168	73716810	1449,10613	1915	4116	6031	SO:0001583	missense	7840	exon10			TATGTAGTCACAT	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.7721G>A	2.37:g.73716810G>A	ENSP00000264448:p.Ser2574Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	303	0.13873626373626374	45	0.09146341463414634	27	0.07458563535911603	131	0.229020979020979	100	0.13192612137203166	G	17.10	3.303631	0.60305	0.098172	0.130345	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.08896	3.04;3.04	4.45	4.45	0.53987	.	0.481828	0.19752	N	0.106868	T	0.00012	0.0000	L	0.46157	1.445	0.09310	P	1.0	D;D;D	0.67145	0.996;0.989;0.989	P;P;P	0.56563	0.801;0.801;0.801	T	0.38520	-0.9657	9	0.42905	T	0.14	.	12.9143	0.58197	0.0:0.0:1.0:0.0	rs3820700;rs17266475;rs59027531;rs3820700	2574;2532;2574	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	N	2532;2574	ENSP00000386627:S2532N;ENSP00000264448:S2574N	ENSP00000264448:S2574N	S	+	2	0	ALMS1	73570318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.331000	0.59273	2.748000	0.94277	0.650000	0.86243	AGT	G|0.855;A|0.145	0.145	strong		0.418	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2930339	2930339	+	Silent	SNP	G	G	A	rs4790115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2930339G>A	ENST00000254695.8	+	22	2172	c.2082G>A	c.(2080-2082)ccG>ccA	p.P694P	RAP1GAP2_ENST00000366401.4_Silent_p.P679P|RAP1GAP2_ENST00000540393.2_Silent_p.P675P|RAP1GAP2_ENST00000542807.1_Silent_p.P694P	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	694	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CTGCCACCCCGATCATCATGA	0.657													G|||	2140	0.427316	0.2428	0.4942	5008	,	,		17712	0.5486		0.4066	False		,,,				2504	0.5256				p.P694P		Atlas-SNP	.											RAP1GAP2_ENST00000254695,colon,carcinoma,0,2	RAP1GAP2	90	2	0			c.G2082A						PASS	.	G	,	1208,3184		180,848,1168	22.0	27.0	25.0		2037,2082	-1.5	1.0	17	dbSNP_111	25	3488,5074		722,2044,1515	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	902,2892,2683	AA,AG,GG		40.7381,27.5046,36.2514	,	679/716,694/731	2930339	4696,8258	2196	4281	6477	SO:0001819	synonymous_variant	23108	exon22			CACCCCGATCATC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.2082G>A	17.37:g.2930339G>A		Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	306	153	0.5	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			G|0.567;A|0.433	0.433	strong		0.657	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
LAMB1	3912	hgsc.bcm.edu	37	7	107591720	107591720	+	Silent	SNP	G	G	A	rs25660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107591720G>A	ENST00000222399.6	-	24	3572	c.3342C>T	c.(3340-3342)tgC>tgT	p.C1114C	LAMB1_ENST00000393561.1_Silent_p.C1138C	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1114	Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GGCACTCGCTGCAGGTGCGGC	0.607													G|||	229	0.0457268	0.1694	0.0043	5008	,	,		16184	0.0		0.002	False		,,,				2504	0.0				p.C1114C		Atlas-SNP	.											.	LAMB1	185	.	0			c.C3342T						PASS	.	G		632,3774	269.2+/-268.9	40,552,1611	54.0	50.0	51.0		3342	4.1	1.0	7	dbSNP_72	51	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	LAMB1	NM_002291.2		40,557,5906	AA,AG,GG		0.0581,14.3441,4.8977		1114/1787	107591720	637,12369	2203	4300	6503	SO:0001819	synonymous_variant	3912	exon24			CTCGCTGCAGGTG	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.3342C>T	7.37:g.107591720G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	150	150	1	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	37	CCDS5750.1																																																																																			G|0.957;A|0.043	0.043	strong		0.607	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
MYO18A	399687	hgsc.bcm.edu	37	17	27442710	27442710	+	Silent	SNP	G	G	C	rs28587908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27442710G>C	ENST00000527372.1	-	12	2379	c.2199C>G	c.(2197-2199)ccC>ccG	p.P733P	MYO18A_ENST00000531253.1_Silent_p.P733P|MYO18A_ENST00000533112.1_Silent_p.P733P|MYO18A_ENST00000354329.4_Silent_p.P733P	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	733	Myosin motor.				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)			CACTCTCCTCGGGGCCCTGGC	0.642													G|||	495	0.0988419	0.149	0.0562	5008	,	,		19160	0.0456		0.0497	False		,,,				2504	0.1667				p.P733P	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.C2199G						PASS	.	G	,	497,3575		26,445,1565	26.0	32.0	30.0		2199,2199	-10.9	0.4	17	dbSNP_125	30	355,8015		5,345,3835	no	coding-synonymous,coding-synonymous	MYO18A	NM_078471.3,NM_203318.1	,	31,790,5400	CC,CG,GG		4.2413,12.2053,6.8478	,	733/2055,733/2040	27442710	852,11590	2036	4185	6221	SO:0001819	synonymous_variant	399687	exon12			CTCCTCGGGGCCC	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.2199C>G	17.37:g.27442710G>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	37	CCDS45642.1																																																																																			G|0.893;C|0.107	0.107	strong		0.642	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
FAM214A	56204	hgsc.bcm.edu	37	15	52901284	52901284	+	Silent	SNP	T	T	C	rs58018557|rs386783993	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52901284T>C	ENST00000261844.7	-	6	1979	c.1827A>G	c.(1825-1827)tcA>tcG	p.S609S	FAM214A_ENST00000546305.2_Silent_p.S616S	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	609																	TTGAGGAAGTTGATAAACTAG	0.338													C|||	2472	0.49361	0.6233	0.317	5008	,	,		17171	0.8869		0.17	False		,,,				2504	0.3712				p.S609S		Atlas-SNP	.											.	.	.	.	0			c.A1827G						PASS	.	C		1897,1773		487,923,425	110.0	118.0	115.0		1827	-0.1	0.0	15	dbSNP_129	115	1271,6885		119,1033,2926	no	coding-synonymous	KIAA1370	NM_019600.2		606,1956,3351	CC,CT,TT		15.5836,48.3106,26.7884		609/1077	52901284	3168,8658	1835	4078	5913	SO:0001819	synonymous_variant	56204	exon6			GGAAGTTGATAAA	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.1827A>G	15.37:g.52901284T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	67	27	0.402985	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			T|0.652;C|0.348	0.348	strong		0.338	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
CRB2	286204	hgsc.bcm.edu	37	9	126133252	126133252	+	Silent	SNP	C	C	T	rs55965026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:126133252C>T	ENST00000373631.3	+	7	1921	c.1920C>T	c.(1918-1920)tgC>tgT	p.C640C	CRB2_ENST00000359999.3_Silent_p.C640C|CRB2_ENST00000373629.2_Silent_p.C308C	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	640	EGF-like 10. {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						GTCCCACGTGCGCTGATGGTG	0.617													C|||	160	0.0319489	0.0893	0.0159	5008	,	,		19920	0.0		0.0229	False		,,,				2504	0.0082				p.C640C		Atlas-SNP	.											.	CRB2	86	.	0			c.C1920T						PASS	.	C		332,4074	168.3+/-199.2	12,308,1883	56.0	61.0	59.0		1920	-3.2	0.1	9	dbSNP_129	59	257,8343	97.9+/-159.5	8,241,4051	no	coding-synonymous	CRB2	NM_173689.5		20,549,5934	TT,TC,CC		2.9884,7.5352,4.5287		640/1286	126133252	589,12417	2203	4300	6503	SO:0001819	synonymous_variant	286204	exon7			CACGTGCGCTGAT	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.1920C>T	9.37:g.126133252C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	51	33	0.647059	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			C|0.962;T|0.038	0.038	strong		0.617	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
OR10H5	284433	hgsc.bcm.edu	37	19	15905661	15905661	+	Missense_Mutation	SNP	C	C	A	rs67455341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15905661C>A	ENST00000308940.8	+	1	901	c.803C>A	c.(802-804)tCt>tAt	p.S268Y		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						GGTCCCCAGTCTCCGGAAGGA	0.577													.|||	1121	0.223842	0.3812	0.2565	5008	,	,		16995	0.002		0.2952	False		,,,				2504	0.1431				p.S268Y		Atlas-SNP	.											.	OR10H5	49	.	0			c.C803A						PASS	.	C	TYR/SER	1626,2780		303,1020,880	114.0	93.0	100.0		803	2.7	0.0	19	dbSNP_130	100	2161,6439		294,1573,2433	no	missense	OR10H5	NM_001004466.1	144	597,2593,3313	AA,AC,CC		25.1279,36.9042,29.1173	possibly-damaging	268/316	15905661	3787,9219	2203	4300	6503	SO:0001583	missense	284433	exon1			CCCAGTCTCCGGA	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.803C>A	19.37:g.15905661C>A	ENSP00000310704:p.Ser268Tyr	Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	217	124	0.571429	NM_001004466	Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	515	0.2358058608058608	177	0.3597560975609756	114	0.3149171270718232	1	0.0017482517482517483	223	0.2941952506596306	.	8.445	0.851648	0.17034	0.369042	0.251279	ENSG00000172519	ENST00000308940	T	0.00277	8.34	3.88	2.73	0.32206	GPCR, rhodopsin-like superfamily (1);	0.449535	0.18991	N	0.125583	T	0.00012	0.0000	M	0.85859	2.78	0.80722	P	0.0	D	0.53312	0.959	P	0.62649	0.905	T	0.36261	-0.9755	9	0.72032	D	0.01	.	9.6663	0.39986	0.0:0.6307:0.3693:0.0	.	268	Q8NGA6	O10H5_HUMAN	Y	268	ENSP00000310704:S268Y	ENSP00000310704:S268Y	S	+	2	0	OR10H5	15766661	0.000000	0.05858	0.019000	0.16419	0.035000	0.12851	0.184000	0.16939	1.878000	0.54408	0.585000	0.79938	TCT	C|0.733;A|0.267	0.267	strong		0.577	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
SYNE4	163183	hgsc.bcm.edu	37	19	36497747	36497747	+	Missense_Mutation	SNP	C	C	G	rs77925409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36497747C>G	ENST00000324444.3	-	4	634	c.523G>C	c.(523-525)Gcc>Ccc	p.A175P	ALKBH6_ENST00000495116.2_5'Flank|SYNE4_ENST00000340477.5_Intron|AC002116.8_ENST00000473572.2_RNA	NM_001039876.1	NP_001034965.1	Q8N205	SYNE4_HUMAN	spectrin repeat containing, nuclear envelope family member 4	175					establishment of epithelial cell apical/basal polarity (GO:0045198)	integral component of nuclear outer membrane (GO:0031309)											TGCTCCAGGGCTGCCCAGGCC	0.687													C|||	140	0.0279553	0.1006	0.0101	5008	,	,		14555	0.0		0.0	False		,,,				2504	0.0				p.A175P		Atlas-SNP	.											.	.	.	.	0			c.G523C						PASS	.	C	PRO/ALA	304,3792		11,282,1755	14.0	21.0	19.0		523	-1.4	0.0	19	dbSNP_131	19	6,8318		0,6,4156	yes	missense	C19orf46	NM_001039876.1	27	11,288,5911	GG,GC,CC		0.0721,7.4219,2.496	possibly-damaging	175/405	36497747	310,12110	2048	4162	6210	SO:0001583	missense	163183	exon4			CCAGGGCTGCCCA	BC038360	CCDS42553.1	19q13.12	2014-01-28	2012-05-31	2012-05-31	ENSG00000181392	ENSG00000181392			26703	protein-coding gene	gene with protein product		615535	"""chromosome 19 open reading frame 46"", ""deafness, autosomal recessive 76"""	C19orf46, DFNB76		23348741	Standard	XM_005258597		Approved	FLJ36445, Nesprin-4, Nesp4	uc002ocq.1	Q8N205	OTTHUMG00000048135	ENST00000324444.3:c.523G>C	19.37:g.36497747C>G	ENSP00000316130:p.Ala175Pro	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_001039876	A8MRS0|A8MYE3|Q7Z7L3	Missense_Mutation	SNP	ENST00000324444.3	37	CCDS42553.1	40	0.018315018315018316	34	0.06910569105691057	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	13.03	2.114112	0.37339	0.074219	7.21E-4	ENSG00000181392	ENST00000324444;ENST00000490730	T;T	0.53206	0.63;0.63	5.95	-1.44	0.08856	.	0.656922	0.16361	N	0.217750	T	0.02380	0.0073	L	0.40543	1.245	0.09310	N	1	B;B	0.21381	0.055;0.001	B;B	0.20577	0.03;0.002	T	0.07046	-1.0793	10	0.48119	T	0.1	-12.2768	2.0383	0.03545	0.2949:0.4044:0.1655:0.1353	.	175;175	D6RAE3;Q8N205	.;SYNE4_HUMAN	P	175	ENSP00000316130:A175P;ENSP00000422716:A175P	ENSP00000316130:A175P	A	-	1	0	C19orf46	41189587	0.002000	0.14202	0.030000	0.17652	0.956000	0.61745	-0.333000	0.07894	-0.067000	0.12976	-0.262000	0.10625	GCC	C|0.979;G|0.021	0.021	strong		0.687	SYNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109525.3	NM_001039876	
PSG4	5672	hgsc.bcm.edu	37	19	43709647	43709647	+	Silent	SNP	G	G	A	rs12985206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43709647G>A	ENST00000405312.3	-	1	279	c.42C>T	c.(40-42)acC>acT	p.T14T	PSG4_ENST00000244295.9_Silent_p.T14T|PSG4_ENST00000433626.2_Silent_p.T14T	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	14					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)				CCCCCTTCCAGGTGATGCGCT	0.597													G|||	3276	0.654153	0.6392	0.5274	5008	,	,		13710	0.7966		0.5865	False		,,,				2504	0.6871				p.P14P		Atlas-SNP	.											.	PSG4	129	.	0			c.C42T						PASS	.						62.0	61.0	61.0					19																	43709647		2186	4271	6457	SO:0001819	synonymous_variant	5672	exon1			CTTCCAGGTGATG		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.42C>T	19.37:g.43709647G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	29	21	0.724138	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Silent	SNP	ENST00000405312.3	37	CCDS46093.1																																																																																			G|0.536;A|0.464	0.464	strong		0.597	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
PCYOX1	51449	hgsc.bcm.edu	37	2	70503954	70503954	+	Silent	SNP	G	G	T	rs36012096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70503954G>T	ENST00000433351.2	+	6	976	c.948G>T	c.(946-948)ccG>ccT	p.P316P	PCYOX1_ENST00000545138.1_Silent_p.P238P|PCYOX1_ENST00000264441.5_Intron|PCYOX1_ENST00000505044.2_Silent_p.P239P	NM_016297.3	NP_057381.3	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1	316					prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)	15						TGGCCACTCCGTTGAATCGAA	0.368													G|||	464	0.0926518	0.3048	0.0187	5008	,	,		18461	0.001		0.003	False		,,,				2504	0.045				p.P316P		Atlas-SNP	.											.	PCYOX1	34	.	0			c.G948T						PASS	.	G		987,3419	365.1+/-317.3	112,763,1328	54.0	57.0	56.0		948	-5.4	0.9	2	dbSNP_126	56	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous	PCYOX1	NM_016297.3		112,788,5603	TT,TG,GG		0.2907,22.4013,7.781		316/506	70503954	1012,11994	2203	4300	6503	SO:0001819	synonymous_variant	51449	exon6			CACTCCGTTGAAT	AB020715	CCDS1902.1	2p13.3	2008-02-05			ENSG00000116005	ENSG00000116005	1.8.3.5		20588	protein-coding gene	gene with protein product		610995				10585463, 12186880	Standard	NM_016297		Approved	KIAA0908, PCL1	uc002sgn.4	Q9UHG3	OTTHUMG00000129671	ENST00000433351.2:c.948G>T	2.37:g.70503954G>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	199	89	0.447236	NM_016297	B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8	Silent	SNP	ENST00000433351.2	37	CCDS1902.1																																																																																			G|0.926;T|0.074	0.074	strong		0.368	PCYOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251872.3	NM_016297	
SDK1	221935	hgsc.bcm.edu	37	7	4308360	4308360	+	3'UTR	SNP	C	C	T	rs11981816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:4308360C>T	ENST00000404826.2	+	0	10125					NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1						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)		AGTGTGGCTCCCCGTGGGTCA	0.542													C|||	303	0.0605032	0.2201	0.0144	5008	,	,		17837	0.0		0.002	False		,,,				2504	0.0				p.P673L		Atlas-SNP	.											.	SDK1	361	.	0			c.C2018T						PASS	.	C		758,3648	299.3+/-285.7	79,600,1524	184.0	193.0	190.0			0.2	0.0	7	dbSNP_120	190	3,8591	2.2+/-6.3	0,3,4294	no	utr-3	SDK1	NM_152744.3		79,603,5818	TT,TC,CC		0.0349,17.2038,5.8538			4308360	761,12239	2203	4297	6500	SO:0001624	3_prime_UTR_variant	221935	exon20			TGGCTCCCCGTGG	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.*3344C>T	7.37:g.4308360C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	148	72	0.486486	NM_001079653	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			C|0.967;T|0.033	0.033	strong		0.542	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110408347	110408347	+	Silent	SNP	C	C	T	rs6469258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110408347C>T	ENST00000378402.5	+	11	1007	c.903C>T	c.(901-903)ccC>ccT	p.P301P		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	301	IPT/TIG 3.				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)			CAGATTTCCCCGTCAGAGTTC	0.393										HNSCC(38;0.096)			C|||	138	0.0275559	0.1006	0.0072	5008	,	,		17027	0.0		0.0	False		,,,				2504	0.0				p.P301P		Atlas-SNP	.											PKHD1L1,NS,carcinoma,+2,1	PKHD1L1	522	1	0			c.C903T						PASS	.	C		335,3603		16,303,1650	74.0	64.0	67.0		903	2.1	0.8	8	dbSNP_116	67	1,8335		0,1,4167	no	coding-synonymous	PKHD1L1	NM_177531.4		16,304,5817	TT,TC,CC		0.012,8.5069,2.7375		301/4244	110408347	336,11938	1969	4168	6137	SO:0001819	synonymous_variant	93035	exon11			TTTCCCCGTCAGA	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.903C>T	8.37:g.110408347C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			C|0.975;T|0.025	0.025	strong		0.393	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
KLHL38	340359	hgsc.bcm.edu	37	8	124663987	124663987	+	Missense_Mutation	SNP	C	C	G	rs16898691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124663987C>G	ENST00000325995.7	-	1	1203	c.1180G>C	c.(1180-1182)Ggg>Cgg	p.G394R	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	394			G -> R (in dbSNP:rs16898691).							breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						AGCTCCTGCCCTTCTCCAATC	0.602													C|||	583	0.116414	0.0461	0.0836	5008	,	,		21826	0.2192		0.0408	False		,,,				2504	0.2065				p.G394R		Atlas-SNP	.											.	KLHL38	81	.	0			c.G1180C						PASS	.	C	ARG/GLY	164,3860		4,156,1852	65.0	65.0	65.0		1180	3.2	0.8	8	dbSNP_123	65	370,7990		14,342,3824	yes	missense	KLHL38	NM_001081675.2	125	18,498,5676	GG,GC,CC		4.4258,4.0755,4.312	probably-damaging	394/582	124663987	534,11850	2012	4180	6192	SO:0001583	missense	340359	exon1			CCTGCCCTTCTCC		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.1180G>C	8.37:g.124663987C>G	ENSP00000321475:p.Gly394Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	37	CCDS43766.1	211	0.09661172161172162	25	0.0508130081300813	26	0.0718232044198895	128	0.22377622377622378	32	0.04221635883905013	C	10.04	1.240664	0.22711	0.040755	0.044258	ENSG00000175946	ENST00000325995	T	0.71103	-0.54	5.18	3.18	0.36537	Kelch-type beta propeller (1);	0.367273	0.33691	N	0.004655	T	0.00073	0.0002	L	0.49778	1.585	0.39734	P	0.02834700000000001	B	0.02656	0.0	B	0.06405	0.002	T	0.06935	-1.0799	9	0.72032	D	0.01	.	5.0825	0.14664	0.0:0.3131:0.0:0.6869	rs16898691;rs52812544;rs16898691	394	Q2WGJ6	KLH38_HUMAN	R	394	ENSP00000321475:G394R	ENSP00000321475:G394R	G	-	1	0	KLHL38	124733168	0.978000	0.34361	0.777000	0.31699	0.732000	0.41865	3.219000	0.51200	0.571000	0.29365	0.561000	0.74099	GGG	C|0.903;G|0.097	0.097	strong		0.602	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
PKD1L2	114780	hgsc.bcm.edu	37	16	81219187	81219187	+	RNA	SNP	C	C	T	rs13339342	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	71	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	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		
VPS13C	54832	hgsc.bcm.edu	37	15	62226423	62226423	+	Missense_Mutation	SNP	T	T	G	rs112236709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:62226423T>G	ENST00000261517.5	-	49	5936	c.5863A>C	c.(5863-5865)Aac>Cac	p.N1955H	VPS13C_ENST00000395898.3_Missense_Mutation_p.N1912H|VPS13C_ENST00000395896.4_Missense_Mutation_p.N1955H|VPS13C_ENST00000249837.3_Missense_Mutation_p.N1912H	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						CATACCTGGTTGATATCATTG	0.328													T|||	209	0.0417332	0.0408	0.0086	5008	,	,		12683	0.0605		0.0089	False		,,,				2504	0.0808				p.N1955H		Atlas-SNP	.											.	VPS13C	506	.	0			c.A5863C						PASS	.	T	HIS/ASN,HIS/ASN,HIS/ASN,HIS/ASN	128,4278	87.8+/-126.4	0,128,2075	97.0	107.0	103.0		5863,5734,5734,5863	1.5	0.0	15	dbSNP_132	103	68,8524	36.9+/-92.0	1,66,4229	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	68,68,68,68	1,194,6304	GG,GT,TT		0.7914,2.9051,1.5079	benign,benign,benign,benign	1955/3629,1912/3711,1912/3586,1955/3754	62226423	196,12802	2203	4296	6499	SO:0001583	missense	54832	exon49			CCTGGTTGATATC	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.5863A>C	15.37:g.62226423T>G	ENSP00000261517:p.Asn1955His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	63	0.028846153846153848	21	0.042682926829268296	4	0.011049723756906077	30	0.05244755244755245	8	0.010554089709762533	T	4.042	0.005477	0.07866	0.029051	0.007914	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.46063	0.88;0.88;1.06	5.19	1.47	0.22746	.	0.405845	0.28706	N	0.014407	T	0.04861	0.0131	L	0.43152	1.355	0.09310	N	1	B;B;B;B	0.10296	0.001;0.001;0.003;0.001	B;B;B;B	0.12156	0.007;0.007;0.005;0.002	T	0.10291	-1.0636	10	0.39692	T	0.17	.	2.3492	0.04279	0.125:0.1424:0.1302:0.6024	.	1912;1955;1912;1955	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	H	1912;1955;1955;1955	ENSP00000249837:N1912H;ENSP00000261517:N1955H;ENSP00000379233:N1955H	ENSP00000249837:N1912H	N	-	1	0	VPS13C	60013715	0.001000	0.12720	0.000000	0.03702	0.032000	0.12392	0.892000	0.28322	-0.021000	0.14009	0.528000	0.53228	AAC	T|0.980;G|0.020	0.020	strong		0.328	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
COL6A6	131873	hgsc.bcm.edu	37	3	130287096	130287096	+	Silent	SNP	C	C	T	rs61730501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130287096C>T	ENST00000358511.6	+	5	2080	c.2049C>T	c.(2047-2049)agC>agT	p.S683S	COL6A6_ENST00000453409.2_Silent_p.S683S	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	683	Nonhelical region.|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TGTCCCAAAGCGACATTTCAA	0.478													C|||	67	0.0133786	0.0477	0.0029	5008	,	,		20256	0.0		0.001	False		,,,				2504	0.001				p.S683S		Atlas-SNP	.											.	COL6A6	497	.	0			c.C2049T						PASS	.	C		128,3762		1,126,1818	153.0	152.0	152.0		2049	-11.5	0.0	3	dbSNP_129	152	1,8267		0,1,4133	no	coding-synonymous	COL6A6	NM_001102608.1		1,127,5951	TT,TC,CC		0.0121,3.2905,1.061		683/2264	130287096	129,12029	1945	4134	6079	SO:0001819	synonymous_variant	131873	exon5			CCAAAGCGACATT	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.2049C>T	3.37:g.130287096C>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	247	126	0.510121	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																			C|0.993;T|0.007	0.007	strong		0.478	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
TTN	7273	hgsc.bcm.edu	37	2	179401015	179401015	+	Missense_Mutation	SNP	G	G	A	rs72629779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179401015G>A	ENST00000591111.1	-	307	95760	c.95536C>T	c.(95536-95538)Ccc>Tcc	p.P31846S	TTN_ENST00000589042.1_Missense_Mutation_p.P33487S|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P24422S|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P30919S|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P24547S|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P24614S|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31846	Fibronectin type-III 131. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAGATTTGGGAGTGATGGGT	0.403													G|||	69	0.013778	0.0499	0.0043	5008	,	,		21952	0.0		0.0	False		,,,				2504	0.0				p.P33487S		Atlas-SNP	.											.	TTN	18412	.	0			c.C100459T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	127,3629		1,125,1752	87.0	80.0	83.0		73264,92755,73639,73840	5.8	1.0	2	dbSNP_130	83	2,8222		0,2,4110	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	74,74,74,74	1,127,5862	AA,AG,GG		0.0243,3.3813,1.0768	probably-damaging,probably-damaging,probably-damaging,probably-damaging	24422/26927,30919/33424,24547/27052,24614/27119	179401015	129,11851	1878	4112	5990	SO:0001583	missense	7273	exon357			ATTTGGGAGTGAT	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.95536C>T	2.37:g.179401015G>A	ENSP00000465570:p.Pro31846Ser	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	179	85	0.47486	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		22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	G	20.0	3.930466	0.73327	0.033813	2.43E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.76	5.76	0.90799	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46927	0.1418	M	0.80183	2.485	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.69327	-0.5174	9	0.87932	D	0	.	19.9595	0.97236	0.0:0.0:1.0:0.0	.	24422;24547;24614;31846	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	30919;24422;24614;24547;24419	ENSP00000343764:P30919S;ENSP00000434586:P24422S;ENSP00000340554:P24614S;ENSP00000352154:P24547S	ENSP00000340554:P24614S	P	-	1	0	TTN	179109261	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.997000	0.88414	2.706000	0.92434	0.563000	0.77884	CCC	G|0.990;A|0.010	0.010	strong		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PTX4	390667	hgsc.bcm.edu	37	16	1536047	1536047	+	Missense_Mutation	SNP	T	T	C	rs59554810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536047T>C	ENST00000447419.2	-	3	1355	c.1330A>G	c.(1330-1332)Atc>Gtc	p.I444V	PTX4_ENST00000293922.1_Missense_Mutation_p.I439V|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	444	Pentaxin.		I -> V (in dbSNP:rs59554810).			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						TCTTTCCCGATGGCAAGGTTT	0.632													T|||	277	0.0553115	0.1974	0.0231	5008	,	,		16980	0.0		0.0	False		,,,				2504	0.0				p.I439V		Atlas-SNP	.											.	PTX4	46	.	0			c.A1315G						PASS	.	T	VAL/ILE	834,3564	328.8+/-300.7	75,684,1440	69.0	68.0	68.0		1315	1.5	0.0	16	dbSNP_129	68	3,8597	2.2+/-6.3	0,3,4297	yes	missense	PTX4	NM_001013658.1	29	75,687,5737	CC,CT,TT		0.0349,18.9632,6.4395	benign	439/474	1536047	837,12161	2199	4300	6499	SO:0001583	missense	390667	exon3			TCCCGATGGCAAG		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.1330A>G	16.37:g.1536047T>C	ENSP00000445277:p.Ile444Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		110	0.05036630036630037	99	0.20121951219512196	11	0.03038674033149171	0	0.0	0	0.0	T	10.44	1.351103	0.24512	0.189632	3.49E-4	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.62788	0.0;0.0	5.21	1.54	0.23209	.	3.825800	0.00481	N	0.000131	T	0.00073	0.0002	N	0.22421	0.69	0.80722	P	0.0	B	0.17465	0.022	B	0.21917	0.037	T	0.03354	-1.1045	9	0.29301	T	0.29	.	2.6395	0.04967	0.1515:0.0841:0.1477:0.6167	rs59554810	439	Q96A99-2	.	V	444;439	ENSP00000445277:I444V;ENSP00000293922:I439V	ENSP00000293922:I439V	I	-	1	0	PTX4	1476048	0.001000	0.12720	0.002000	0.10522	0.006000	0.05464	0.387000	0.20718	-0.013000	0.14199	-0.376000	0.06991	ATC	T|0.942;C|0.058	0.058	strong		0.632	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
SLC27A3	11000	hgsc.bcm.edu	37	1	153750650	153750650	+	Missense_Mutation	SNP	G	G	A	rs35102232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153750650G>A	ENST00000368661.3	+	5	1381	c.1316G>A	c.(1315-1317)cGt>cAt	p.R439H	SLC27A3_ENST00000271857.2_Missense_Mutation_p.R520H|SLC27A3_ENST00000484014.1_3'UTR	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	439			R -> H (in dbSNP:rs35102232).		fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AAGGCAGAACGTGGCCATAAG	0.627													G|||	89	0.0177716	0.0628	0.0072	5008	,	,		17430	0.0		0.001	False		,,,				2504	0.0				p.R439H		Atlas-SNP	.											.	SLC27A3	42	.	0			c.G1316A						PASS	.	G	HIS/ARG	257,4147		5,247,1950	32.0	38.0	36.0		1316	-2.7	0.0	1	dbSNP_126	36	2,8598		0,2,4298	yes	missense	SLC27A3	NM_024330.1	29	5,249,6248	AA,AG,GG		0.0233,5.8356,1.9917	possibly-damaging	439/731	153750650	259,12745	2202	4300	6502	SO:0001583	missense	11000	exon5			CAGAACGTGGCCA	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.1316G>A	1.37:g.153750650G>A	ENSP00000357650:p.Arg439His	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	36	16	0.444444	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	37	CCDS1053.1	39|39	0.017857142857142856|0.017857142857142856	34|34	0.06910569105691057|0.06910569105691057	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	13.72|13.72	2.320062|2.320062	0.41096|0.41096	0.058356|0.058356	2.33E-4|2.33E-4	ENSG00000143554|ENSG00000143554	ENST00000271857;ENST00000368661|ENST00000458027	T;T|.	0.41758|.	0.99;0.99|.	5.03|5.03	-2.66|-2.66	0.06077|0.06077	AMP-dependent synthetase/ligase (1);|.	0.933680|.	0.09084|.	N|.	0.850843|.	T|T	0.37812|0.37812	0.1017|0.1017	M|M	0.83312|0.83312	2.635|2.635	0.09310|0.09310	N|N	1|1	B|.	0.19073|.	0.033|.	B|.	0.21546|.	0.035|.	T|T	0.49303|0.49303	-0.8954|-0.8954	10|5	0.42905|.	T|.	0.14|.	1.8444|1.8444	7.2084|7.2084	0.25919|0.25919	0.4489:0.1139:0.4372:0.0|0.4489:0.1139:0.4372:0.0	rs35102232|rs35102232	439|.	Q5K4L6|.	S27A3_HUMAN|.	H|M	520;439|144	ENSP00000271857:R520H;ENSP00000357650:R439H|.	ENSP00000271857:R520H|.	R|V	+|+	2|1	0|0	SLC27A3|SLC27A3	152017274|152017274	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.193000|0.193000	0.23685|0.23685	-1.444000|-1.444000	0.02403|0.02403	-0.720000|-0.720000	0.04935|0.04935	-0.605000|-0.605000	0.04089|0.04089	CGT|GTG	G|0.979;A|0.021	0.021	strong		0.627	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330	
SMTNL2	342527	hgsc.bcm.edu	37	17	4497160	4497160	+	Silent	SNP	T	T	C	rs8080130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4497160T>C	ENST00000389313.4	+	4	841	c.774T>C	c.(772-774)taT>taC	p.Y258Y	SMTNL2_ENST00000338859.4_Silent_p.Y114Y	NM_001114974.1	NP_001108446.1	Q2TAL5	SMTL2_HUMAN	smoothelin-like 2	258										breast(1)|endometrium(9)|kidney(1)|lung(1)|skin(1)	13				READ - Rectum adenocarcinoma(115;0.0325)		GCTCTGGCTATGGGGCAGTGA	0.582													C|||	3419	0.682708	0.5257	0.7709	5008	,	,		19667	0.8462		0.6441	False		,,,				2504	0.7035				p.Y258Y		Atlas-SNP	.											.	SMTNL2	57	.	0			c.T774C						PASS	.	C	,	2439,1967	552.7+/-378.6	668,1103,432	81.0	73.0	76.0		774,342	-5.6	0.2	17	dbSNP_116	76	5622,2978	461.5+/-365.4	1833,1956,511	no	coding-synonymous,coding-synonymous	SMTNL2	NM_001114974.1,NM_198501.2	,	2501,3059,943	CC,CT,TT		34.6279,44.6437,38.0209	,	258/462,114/318	4497160	8061,4945	2203	4300	6503	SO:0001819	synonymous_variant	342527	exon4			TGGCTATGGGGCA	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.774T>C	17.37:g.4497160T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_001114974	Q6ZVK6	Silent	SNP	ENST00000389313.4	37	CCDS45583.1																																																																																			T|0.350;C|0.650	0.650	strong		0.582	SMTNL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439129.1	NM_198501	
LYST	1130	hgsc.bcm.edu	37	1	235972435	235972435	+	Silent	SNP	T	T	C	rs3820553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235972435T>C	ENST00000389794.3	-	5	1857	c.1683A>G	c.(1681-1683)ctA>ctG	p.L561L	LYST_ENST00000389793.2_Silent_p.L561L|LYST_ENST00000536965.1_Silent_p.L561L			Q99698	LYST_HUMAN	lysosomal trafficking regulator	561					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)			AAGCCTGCTGTAGTAAGCGCA	0.448													T|||	1516	0.302716	0.4879	0.2983	5008	,	,		19124	0.0665		0.4235	False		,,,				2504	0.1748				p.L561L		Atlas-SNP	.											.	LYST	370	.	0			c.A1683G						PASS	.	T		2242,2164	591.9+/-387.7	572,1098,533	108.0	102.0	104.0		1683	-4.2	0.3	1	dbSNP_107	104	3437,5163	502.3+/-375.6	680,2077,1543	no	coding-synonymous	LYST	NM_000081.2		1252,3175,2076	CC,CT,TT		39.9651,49.1148,43.6645		561/3802	235972435	5679,7327	2203	4300	6503	SO:0001819	synonymous_variant	1130	exon5			CTGCTGTAGTAAG	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.1683A>G	1.37:g.235972435T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			T|0.616;C|0.384	0.384	strong		0.448	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
LYSMD4	145748	hgsc.bcm.edu	37	15	100269613	100269613	+	Silent	SNP	C	C	T	rs11852387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:100269613C>T	ENST00000409796.1	-	3	668	c.606G>A	c.(604-606)ccG>ccA	p.P202P	LYSMD4_ENST00000344791.2_Silent_p.P203P|LYSMD4_ENST00000604213.1_Intron|LYSMD4_ENST00000332728.4_Silent_p.P202P|LYSMD4_ENST00000545021.1_Silent_p.P76P	NM_001284417.1|NM_001284418.1|NM_001284420.1	NP_001271346.1|NP_001271347.1|NP_001271349.1	Q5XG99	LYSM4_HUMAN	LysM, putative peptidoglycan-binding, domain containing 4	202						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)	10	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)			TCGGAGGTGCCGGGAGCAGTG	0.483													C|||	448	0.0894569	0.2542	0.049	5008	,	,		20870	0.0228		0.0408	False		,,,				2504	0.0143				p.P203P		Atlas-SNP	.											.	LYSMD4	21	.	0			c.G609A						PASS	.	C		939,3467	359.9+/-315.0	98,743,1362	119.0	114.0	116.0		609	-9.2	0.0	15	dbSNP_120	116	333,8267	115.3+/-175.2	9,315,3976	no	coding-synonymous	LYSMD4	NM_152449.2		107,1058,5338	TT,TC,CC		3.8721,21.3118,9.7801		203/298	100269613	1272,11734	2203	4300	6503	SO:0001819	synonymous_variant	145748	exon6			AGGTGCCGGGAGC	BC041097	CCDS10381.1, CCDS66876.1, CCDS66877.1, CCDS73788.1	15q26.3	2005-10-24			ENSG00000183060	ENSG00000183060			26571	protein-coding gene	gene with protein product						12477932	Standard	NM_001284418		Approved	FLJ33008	uc002bvl.3	Q5XG99	OTTHUMG00000149853	ENST00000409796.1:c.606G>A	15.37:g.100269613C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_152449	A6NII6|A8K2N1|Q96LY7	Silent	SNP	ENST00000409796.1	37																																																																																				C|0.903;T|0.097	0.097	strong		0.483	LYSMD4-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335634.1	NM_152449	
LAMB3	3914	hgsc.bcm.edu	37	1	209788703	209788703	+	Silent	SNP	T	T	C	rs1049607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:209788703T>C	ENST00000356082.4	-	23	3566	c.3432A>G	c.(3430-3432)tcA>tcG	p.S1144S	LAMB3_ENST00000391911.1_Silent_p.S1144S|LAMB3_ENST00000367030.3_Silent_p.S1144S	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	1144	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		TCAGGTCCGCTGAGCGCAGCA	0.592													t|||	2320	0.463259	0.6694	0.3689	5008	,	,		19698	0.381		0.3648	False		,,,				2504	0.4376				p.S1144S		Atlas-SNP	.											.	LAMB3	136	.	0			c.A3432G						PASS	.	T	,,	2646,1760	646.2+/-398.3	791,1064,348	114.0	93.0	100.0		3432,3432,3432	-10.8	0.1	1	dbSNP_86	100	3088,5512	471.9+/-368.2	555,1978,1767	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	1346,3042,2115	CC,CT,TT		35.907,39.9455,44.0873	,,	1144/1173,1144/1173,1144/1173	209788703	5734,7272	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon23			GTCCGCTGAGCGC	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.3432A>G	1.37:g.209788703T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			T|0.560;C|0.440	0.440	strong		0.592	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
TMEM247	388946	hgsc.bcm.edu	37	2	46707886	46707886	+	Missense_Mutation	SNP	G	G	A	rs12612916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:46707886G>A	ENST00000434431.1	+	2	460	c.460G>A	c.(460-462)Gag>Aag	p.E154K		NM_001145051.2	NP_001138523.1	A6NEH6	TM247_HUMAN	transmembrane protein 247	154						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											GCTGCAGCAAGAGGCGGCGCC	0.687													G|||	972	0.194089	0.1225	0.1542	5008	,	,		15859	0.501		0.0398	False		,,,				2504	0.1616				p.E154K		Atlas-SNP	.											.	.	.	.	0			c.G460A						PASS	.						16.0	20.0	19.0					2																	46707886		690	1590	2280	SO:0001583	missense	388946	exon2			CAGCAAGAGGCGG		CCDS56117.1	2p21	2012-04-11			ENSG00000187600	ENSG00000187600			42967	protein-coding gene	gene with protein product							Standard	NM_001145051		Approved		uc010yod.3	A6NEH6	OTTHUMG00000153137	ENST00000434431.1:c.460G>A	2.37:g.46707886G>A	ENSP00000388684:p.Glu154Lys	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	126	56	0.444444	NM_001145051		Missense_Mutation	SNP	ENST00000434431.1	37	CCDS56117.1	423	0.1936813186813187	54	0.10975609756097561	48	0.13259668508287292	289	0.5052447552447552	32	0.04221635883905013	G	3.352	-0.132251	0.06753	.	.	ENSG00000187600	ENST00000434431	.	.	.	4.12	2.21	0.28008	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.12013	0.005	B	0.06405	0.002	T	0.46735	-0.9170	7	0.34782	T	0.22	.	7.083	0.25241	0.1786:0.4361:0.3853:0.0	rs12612916;rs57372875;rs12612916	154	A6NEH6	YB028_HUMAN	K	154	.	ENSP00000388684:E154K	E	+	1	0	AC018682.6	46561390	0.435000	0.25577	0.034000	0.17996	0.000000	0.00434	0.457000	0.21875	0.345000	0.23873	-0.344000	0.07964	GAG	G|0.798;A|0.202	0.202	strong		0.687	TMEM247-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329726.1	NM_001145051	
MAP2	4133	hgsc.bcm.edu	37	2	210557380	210557380	+	Silent	SNP	C	C	T	rs6720659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:210557380C>T	ENST00000360351.4	+	7	992	c.486C>T	c.(484-486)caC>caT	p.H162H	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000447185.1_Silent_p.H158H|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	162					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	TGGAGTTCCACGATCAACAGG	0.408													T|||	823	0.164337	0.2746	0.0692	5008	,	,		19732	0.1984		0.0765	False		,,,				2504	0.138				p.H162H	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.C486T						PASS	.	T	,,,	1102,3304	720.3+/-409.0	148,806,1249	66.0	62.0	63.0		,486,,	-3.4	0.0	2	dbSNP_116	63	605,7995	791.3+/-407.6	19,567,3714	no	intron,coding-synonymous,intron,intron	MAP2	NM_001039538.1,NM_002374.3,NM_031845.2,NM_031847.2	,,,	167,1373,4963	TT,TC,CC		7.0349,25.0113,13.1247	,,,	,162/1828,,	210557380	1707,11299	2203	4300	6503	SO:0001819	synonymous_variant	4133	exon7			GTTCCACGATCAA		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.486C>T	2.37:g.210557380C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	86	50	0.581395	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	37	CCDS2384.1																																																																																			C|0.852;T|0.148	0.148	strong		0.408	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
GRID2IP	392862	hgsc.bcm.edu	37	7	6591008	6591008	+	Silent	SNP	C	C	T	rs73059373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6591008C>T	ENST00000457091.2	-	1	59	c.60G>A	c.(58-60)cgG>cgA	p.R20R		NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	20	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.		R -> Q (in dbSNP:rs11761490).		long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						AGCCACCTAGCCGGAAGCCAA	0.652													C|||	778	0.155351	0.3812	0.1081	5008	,	,		11775	0.0526		0.0736	False		,,,				2504	0.0736				p.R20R		Atlas-SNP	.											GRID2IP_ENST00000457091,NS,carcinoma,0,2	GRID2IP	82	2	0			c.G60A						PASS	.						7.0	9.0	9.0					7																	6591008		687	1585	2272	SO:0001819	synonymous_variant	392862	exon1			ACCTAGCCGGAAG		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.60G>A	7.37:g.6591008C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	43	15	0.348837	NM_001145118		Silent	SNP	ENST00000457091.2	37	CCDS47537.1																																																																																			C|0.859;T|0.141	0.141	strong		0.652	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
ADPRH	141	hgsc.bcm.edu	37	3	119305169	119305169	+	Silent	SNP	G	G	A	rs20569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119305169G>A	ENST00000478399.1	+	3	1741	c.336G>A	c.(334-336)ccG>ccA	p.P112P	ADPRH_ENST00000357003.3_Silent_p.P112P|ADPRH_ENST00000465513.1_Silent_p.P112P|ADPRH_ENST00000471850.1_3'UTR|ADPRH_ENST00000478927.1_Silent_p.P112P			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	112					cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		AGCTGAAGCCGGGCAAGCCCA	0.602													G|||	996	0.198882	0.3222	0.1239	5008	,	,		17799	0.2292		0.1382	False		,,,				2504	0.1166				p.P112P	GBM(133;579 1804 5989 9967 40052)	Atlas-SNP	.											.	ADPRH	33	.	0			c.G336A						PASS	.	G		1271,3135	422.8+/-339.9	189,893,1121	87.0	95.0	92.0		336	-10.6	0.0	3	dbSNP_67	92	1219,7381	239.0+/-270.3	79,1061,3160	no	coding-synonymous	ADPRH	NM_001125.2		268,1954,4281	AA,AG,GG		14.1744,28.847,19.145		112/358	119305169	2490,10516	2203	4300	6503	SO:0001819	synonymous_variant	141	exon4			GAAGCCGGGCAAG	L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843			269	protein-coding gene	gene with protein product		603081				8349667, 12070318	Standard	NM_001125		Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.336G>A	3.37:g.119305169G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	134	69	0.514925	NM_001125	B2R8H1|D3DN83	Silent	SNP	ENST00000478399.1	37	CCDS2990.1																																																																																			G|0.802;A|0.198	0.198	strong		0.602	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355199.1	NM_001125	
POU6F2	11281	hgsc.bcm.edu	37	7	39379325	39379325	+	Missense_Mutation	SNP	C	C	T	rs2074936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:39379325C>T	ENST00000403058.1	+	6	750	c.596C>T	c.(595-597)cCg>cTg	p.P199L	POU6F2_ENST00000518318.2_Missense_Mutation_p.P199L|POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000559001.1_Missense_Mutation_p.P191L	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	199	Gln-rich.|Pro-rich.		P -> L (in dbSNP:rs2074936).		central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P199L(1)		NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						cagcCTCCCCCGTCAACCAAC	0.672													C|||	1354	0.270367	0.1921	0.1844	5008	,	,		12095	0.5833		0.159	False		,,,				2504	0.229				p.P199L		Atlas-SNP	.											POU6F2,NS,NS,0,1	POU6F2	117	1	1	Substitution - Missense(1)	NS(1)	c.C596T						PASS	.	C	LEU/PRO,LEU/PRO	799,3603		62,675,1464	16.0	20.0	19.0		596,596	2.7	0.2	7	dbSNP_96	19	1184,7406		98,988,3209	yes	missense,missense	POU6F2	NM_007252.3,NM_001166018.1	98,98	160,1663,4673	TT,TC,CC		13.7835,18.1508,15.2632	benign,benign	199/692,199/656	39379325	1983,11009	2201	4295	6496	SO:0001583	missense	11281	exon6			CTCCCCCGTCAAC	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"""Homeoboxes / POU class"""	21694	protein-coding gene	gene with protein product	"""Retina-derived POU-domain factor-1"""	609062	"""POU domain, class 6, transcription factor 2"""			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.596C>T	7.37:g.39379325C>T	ENSP00000384004:p.Pro199Leu	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	NM_007252	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Missense_Mutation	SNP	ENST00000403058.1	37	CCDS34620.2	634	0.2902930402930403	98	0.1991869918699187	75	0.20718232044198895	342	0.5979020979020979	119	0.15699208443271767	C	1.926	-0.447208	0.04572	0.181508	0.137835	ENSG00000106536	ENST00000403058;ENST00000518318	T;D	0.85411	1.06;-1.98	4.66	2.69	0.31865	.	2.961890	0.02261	U	0.067581	T	0.00012	0.0000	N	0.08118	0	0.40517	P	0.01920900000000003	P;B	0.43885	0.82;0.118	B;B	0.32928	0.155;0.016	T	0.38950	-0.9637	9	0.39692	T	0.17	.	12.6303	0.56653	0.4736:0.5264:0.0:0.0	rs2074936;rs10338353;rs52791432;rs2074936	199;199	P78424-2;P78424	.;PO6F2_HUMAN	L	199	ENSP00000384004:P199L;ENSP00000430514:P199L	ENSP00000384004:P199L	P	+	2	0	POU6F2	39345850	0.204000	0.23447	0.199000	0.23439	0.287000	0.27160	1.173000	0.31920	0.899000	0.36444	0.557000	0.71058	CCG	C|0.764;T|0.236	0.236	strong		0.672	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252	
ITGB5	3693	hgsc.bcm.edu	37	3	124492734	124492734	+	Silent	SNP	T	T	C	rs16835978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124492734T>C	ENST00000296181.4	-	11	2015	c.1719A>G	c.(1717-1719)gaA>gaG	p.E573E	ITGB5_ENST00000461306.1_5'UTR	NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	573	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)		GGCACTTGCATTCCCCGCAGT	0.557													T|||	247	0.0493211	0.1513	0.0317	5008	,	,		24075	0.001		0.0209	False		,,,				2504	0.0031				p.E573E		Atlas-SNP	.											ITGB5,mouth,carcinoma,-2,1	ITGB5	66	1	0			c.A1719G						PASS	.	T		571,3835	254.6+/-260.1	31,509,1663	88.0	71.0	77.0		1719	-0.9	1.0	3	dbSNP_123	77	207,8393	88.9+/-151.2	2,203,4095	no	coding-synonymous	ITGB5	NM_002213.3		33,712,5758	CC,CT,TT		2.407,12.9596,5.9819		573/800	124492734	778,12228	2203	4300	6503	SO:0001819	synonymous_variant	3693	exon11			CTTGCATTCCCCG	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.1719A>G	3.37:g.124492734T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_002213	B0LPF8|B2RD70	Silent	SNP	ENST00000296181.4	37	CCDS3030.1	83	0.038003663003663	60	0.12195121951219512	8	0.022099447513812154	0	0.0	15	0.01978891820580475	T	9.996	1.232276	0.22626	0.129596	0.02407	ENSG00000082781	ENST00000481591	.	.	.	5.19	-0.931	0.10438	.	.	.	.	.	T	0.00784	0.0026	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01488	-1.1342	4	.	.	.	.	9.0215	0.36202	0.1444:0.6796:0.0:0.176	rs16835978;rs16835978	.	.	.	S	263	.	.	N	-	2	0	ITGB5	125975424	0.277000	0.24220	0.991000	0.47740	0.995000	0.86356	-0.327000	0.07955	-0.395000	0.07715	-0.250000	0.11733	AAT	T|0.943;C|0.057	0.057	strong		0.557	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213	
CPAMD8	27151	hgsc.bcm.edu	37	19	17100552	17100552	+	Silent	SNP	A	A	G	rs1973093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17100552A>G	ENST00000443236.1	-	13	1468	c.1437T>C	c.(1435-1437)ccT>ccC	p.P479P	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	432						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						GAGCCCCCACAGGCTTCCCGT	0.607													G|||	3047	0.608427	0.8563	0.5043	5008	,	,		16498	0.629		0.5239	False		,,,				2504	0.4131				p.P479P		Atlas-SNP	.											CPAMD8,colon,carcinoma,-2,1	CPAMD8	192	1	0			c.T1437C						PASS	.	G		3096,828		1230,636,96	31.0	41.0	38.0		1437	-5.7	0.1	19	dbSNP_92	38	3989,4297		968,2053,1122	no	coding-synonymous	CPAMD8	NM_015692.2		2198,2689,1218	GG,GA,AA		48.1414,21.1009,41.9738		479/1933	17100552	7085,5125	1962	4143	6105	SO:0001819	synonymous_variant	27151	exon13			CCCCACAGGCTTC	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.1437T>C	19.37:g.17100552A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	1332	0.6098901098901099	417	0.8475609756097561	192	0.5303867403314917	347	0.6066433566433567	376	0.49604221635883905	G	0.021	-1.430601	0.01117	0.788991	0.481414	ENSG00000160111	ENST00000443236	.	.	.	2.87	-5.73	0.02398	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.23168	P	0.99818347	.	.	.	.	.	.	T	0.19289	-1.0310	3	.	.	.	.	3.5665	0.07901	0.5238:0.1882:0.1938:0.0942	rs1973093;rs59637240	.	.	.	P	490	.	.	L	-	2	0	CPAMD8	16961552	0.023000	0.18921	0.050000	0.19076	0.001000	0.01503	-1.443000	0.02405	-1.715000	0.01389	-2.582000	0.00168	CTG	A|0.428;G|0.572	0.572	strong		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
VN1R2	317701	hgsc.bcm.edu	37	19	53761740	53761740	+	Missense_Mutation	SNP	T	T	C	rs386810659|rs2965249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53761740T>C	ENST00000341702.3	+	1	196	c.112T>C	c.(112-114)Tgc>Cgc	p.C38R		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	38			C -> R (in dbSNP:rs2965249). {ECO:0000269|PubMed:12123587, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		taaatatcagtgcagcctggc	0.493													t|||	1575	0.314497	0.3321	0.2738	5008	,	,		17084	0.3671		0.2952	False		,,,				2504	0.2853				p.C38R		Atlas-SNP	.											.	VN1R2	71	.	0			c.T112C						PASS	.						11.0	12.0	12.0					19																	53761740		1888	3577	5465	SO:0001583	missense	317701	exon1			TATCAGTGCAGCC	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.112T>C	19.37:g.53761740T>C	ENSP00000351244:p.Cys38Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	95	33	0.347368	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	37	CCDS12862.1	696	0.31868131868131866	150	0.3048780487804878	117	0.32320441988950277	219	0.38286713286713286	210	0.2770448548812665	t	0.969	-0.700889	0.03255	.	.	ENSG00000196131	ENST00000341702	T	0.11604	2.76	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.399999999995849E-5	P	0.39520	0.676	B	0.42343	0.384	T	0.49263	-0.8958	6	0.87932	D	0	.	.	.	.	rs2965249	38	Q8NFZ6	VN1R2_HUMAN	R	38	ENSP00000351244:C38R	ENSP00000351244:C38R	C	+	1	0	VN1R2	58453552	0.173000	0.23056	0.192000	0.23308	0.193000	0.23685	0.000000	0.12993	0.064000	0.16427	0.063000	0.15292	TGC	T|0.678;C|0.322	0.322	strong		0.493	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856	
IGFALS	3483	hgsc.bcm.edu	37	16	1838050	1838050	+	IGR	SNP	A	A	G	rs57822546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1838050A>G	ENST00000215539.3	-	0	2116				NUBP2_ENST00000262302.9_Missense_Mutation_p.T200A|NUBP2_ENST00000565134.1_Missense_Mutation_p.T200A|NUBP2_ENST00000543305.1_Missense_Mutation_p.T59A|NUBP2_ENST00000565987.1_Missense_Mutation_p.T140A|NUBP2_ENST00000568706.1_Missense_Mutation_p.T59A			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						CCCACACTGCACGGTGAGTCC	0.662													A|||	461	0.0920527	0.3359	0.0216	5008	,	,		15389	0.0		0.002	False		,,,				2504	0.0				p.T200A		Atlas-SNP	.											.	NUBP2	25	.	0			c.A598G						PASS	.	G	ALA/THR	1287,3109	430.4+/-342.5	179,929,1090	64.0	66.0	65.0		598	-9.0	0.0	16	dbSNP_129	65	8,8592	5.7+/-21.5	0,8,4292	yes	missense	NUBP2	NM_012225.2	58	179,937,5382	GG,GA,AA		0.093,29.2766,9.9646	benign	200/272	1838050	1295,11701	2198	4300	6498	SO:0001628	intergenic_variant	10101	exon5			CACTGCACGGTGA	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.1838050A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_012225	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	165	0.07554945054945054	156	0.3170731707317073	9	0.024861878453038673	0	0.0	0	0.0	A	7.896	0.733364	0.15574	0.292766	9.3E-4	ENSG00000095906	ENST00000262302;ENST00000543305	T;T	0.40476	1.03;1.61	4.6	-9.03	0.00737	.	0.551776	0.20420	N	0.092691	T	0.00012	0.0000	N	0.03253	-0.375	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.22941	-1.0202	9	0.14252	T	0.57	-10.367	2.1262	0.03739	0.2373:0.079:0.3155:0.3683	rs57822546;rs61739604	200	Q9Y5Y2	NUBP2_HUMAN	A	200;59	ENSP00000262302:T200A;ENSP00000437763:T59A	ENSP00000262302:T200A	T	+	1	0	NUBP2	1778051	0.000000	0.05858	0.004000	0.12327	0.013000	0.08279	-0.292000	0.08332	-1.796000	0.01253	-2.629000	0.00154	ACG	A|0.895;G|0.105	0.105	strong		0.662	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
MUC17	140453	hgsc.bcm.edu	37	7	100677502	100677502	+	Silent	SNP	G	G	A	rs10267904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677502G>A	ENST00000306151.4	+	3	2869	c.2805G>A	c.(2803-2805)ccG>ccA	p.P935P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	935	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)					GCACCACGCCGGTAGTCAGTT	0.517																																					p.P935P		Atlas-SNP	.											MUC17,right_upper_lobe,carcinoma,+2,1	MUC17	804	1	0			c.G2805A						PASS	.	G		706,3700		0,706,1497	376.0	325.0	342.0		2805	-2.4	0.0	7	dbSNP_119	342	866,7734		0,866,3434	no	coding-synonymous	MUC17	NM_001040105.1		0,1572,4931	AA,AG,GG		10.0698,16.0236,12.0867		935/4494	100677502	1572,11434	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CACGCCGGTAGTC	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.2805G>A	7.37:g.100677502G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	242	55	0.227273	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.969;A|0.031	0.031	strong		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CDHR5	53841	hgsc.bcm.edu	37	11	621242	621242	+	Silent	SNP	C	C	T	rs112269777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:621242C>T	ENST00000358353.3	-	8	949	c.627G>A	c.(625-627)ccG>ccA	p.P209P	CDHR5_ENST00000529337.1_5'Flank|CDHR5_ENST00000397542.2_Silent_p.P209P|CDHR5_ENST00000349570.7_Silent_p.P209P			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	209	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043, ECO:0000305}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						CATTCTCCCCCGGAGTGTCCT	0.682													C|||	200	0.0399361	0.0772	0.036	5008	,	,		11793	0.001		0.0527	False		,,,				2504	0.0194				p.P209P		Atlas-SNP	.											.	CDHR5	77	.	0			c.G627A						PASS	.	C	,,	236,4170	137.3+/-173.1	8,220,1975	52.0	54.0	53.0		627,627,627	0.8	0.0	11	dbSNP_132	53	412,8186	127.8+/-186.1	14,384,3901	no	coding-synonymous,coding-synonymous,coding-synonymous	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	,,	22,604,5876	TT,TC,CC		4.7918,5.3563,4.9831	,,	209/840,209/846,209/652	621242	648,12356	2203	4299	6502	SO:0001819	synonymous_variant	53841	exon7			CTCCCCCGGAGTG	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.627G>A	11.37:g.621242C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	204	88	0.431373	NM_031264	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	37	CCDS7707.1	105	0.04807692307692308	49	0.09959349593495935	17	0.04696132596685083	0	0.0	39	0.051451187335092345	C	8.290	0.817618	0.16607	0.053563	0.047918	ENSG00000099834	ENST00000526077	T	0.50813	0.73	3.87	0.819	0.18785	.	.	.	.	.	T	0.01523	0.0049	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.05699	-1.0869	6	0.87932	D	0	0.1364	6.7107	0.23276	0.0:0.6467:0.0:0.3533	.	.	.	.	R	183	ENSP00000435082:G183R	ENSP00000435082:G183R	G	-	1	0	CDHR5	611242	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.268000	0.18571	0.264000	0.21851	-0.258000	0.10820	GGG	C|0.953;T|0.047	0.047	strong		0.682	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
NXPH4	11247	hgsc.bcm.edu	37	12	57619362	57619362	+	Silent	SNP	G	G	A	rs10783816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57619362G>A	ENST00000349394.5	+	2	934	c.759G>A	c.(757-759)ccG>ccA	p.P253P	Y_RNA_ENST00000365197.1_RNA	NM_007224.3	NP_009155.1	O95158	NXPH4_HUMAN	neurexophilin 4	253	V (Cys-rich).				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)		p.P253P(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)	10						TGTACGACCCGTCGCAGGTGT	0.592													A|||	1757	0.350839	0.3147	0.4337	5008	,	,		15675	0.4752		0.334	False		,,,				2504	0.2301				p.P253P		Atlas-SNP	.											NXPH4,NS,carcinoma,0,3	NXPH4	40	3	1	Substitution - coding silent(1)	stomach(1)	c.G759A						PASS	.	A		1390,3016	685.1+/-404.5	204,982,1017	48.0	50.0	49.0		759	-4.8	0.8	12	dbSNP_120	49	2836,5764	673.5+/-403.0	460,1916,1924	no	coding-synonymous	NXPH4	NM_007224.3		664,2898,2941	AA,AG,GG		32.9767,31.5479,32.4927		253/309	57619362	4226,8780	2203	4300	6503	SO:0001819	synonymous_variant	11247	exon2			CGACCCGTCGCAG	AF043469	CCDS8933.1	12q13.3	2014-09-04			ENSG00000182379	ENSG00000182379			8078	protein-coding gene	gene with protein product		604637				9570794	Standard	NM_007224		Approved	NPH4	uc009zpj.4	O95158	OTTHUMG00000171241	ENST00000349394.5:c.759G>A	12.37:g.57619362G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_007224	A8K4I4|Q7Z6L3|Q8N462	Silent	SNP	ENST00000349394.5	37	CCDS8933.1																																																																																			G|0.659;A|0.341	0.341	strong		0.592	NXPH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412474.1	NM_007224	
LCMT2	9836	hgsc.bcm.edu	37	15	43621947	43621947	+	Silent	SNP	A	A	G	rs3742969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43621947A>G	ENST00000305641.5	-	1	856	c.741T>C	c.(739-741)cgT>cgC	p.R247R	LCMT2_ENST00000567039.1_Intron|ADAL_ENST00000389651.4_5'Flank|ADAL_ENST00000428046.3_5'Flank|ADAL_ENST00000422466.2_5'Flank|LCMT2_ENST00000544735.1_Intron	NM_014793.4	NP_055608.2	O60294	TYW4_HUMAN	leucine carboxyl methyltransferase 2	247					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(1)|urinary_tract(1)	20		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)	CGTCAGGAAAACGCTCCAGGC	0.572													G|||	1983	0.395966	0.7322	0.2291	5008	,	,		17524	0.4683		0.1262	False		,,,				2504	0.2628				p.R247R		Atlas-SNP	.											.	LCMT2	48	.	0			c.T741C						PASS	.	G		2646,1756	502.0+/-365.1	803,1040,358	38.0	41.0	40.0		741	2.5	0.6	15	dbSNP_107	40	1093,7505	748.1+/-407.3	78,937,3284	no	coding-synonymous	LCMT2	NM_014793.4		881,1977,3642	GG,GA,AA		12.7123,39.891,28.7615		247/687	43621947	3739,9261	2201	4299	6500	SO:0001819	synonymous_variant	9836	exon1			AGGAAAACGCTCC	AF265443	CCDS10094.1	15q15.3	2007-01-26			ENSG00000168806	ENSG00000168806			17558	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 4"""	611246				9628581, 17150819	Standard	NM_014793		Approved	KIAA0547, MGC9534, TYW4, PPM2	uc001zrg.3	O60294	OTTHUMG00000130705	ENST00000305641.5:c.741T>C	15.37:g.43621947A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_014793	Q4JFT6|Q96B55|Q9NR10	Silent	SNP	ENST00000305641.5	37	CCDS10094.1																																																																																			A|0.668;G|0.332	0.332	strong		0.572	LCMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253205.1	NM_014793	
ADRA2A	150	hgsc.bcm.edu	37	10	112838135	112838135	+	Silent	SNP	C	C	G	rs142434876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:112838135C>G	ENST00000280155.2	+	1	1346	c.381C>G	c.(379-381)ctC>ctG	p.L127L		NM_000681.3	NP_000672.3	P08913	ADA2A_HUMAN	adrenoceptor alpha 2A	112					actin cytoskeleton organization (GO:0030036)|activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|acute inflammatory response (GO:0002526)|adenylate cyclase-inhibiting adrenergic receptor signaling pathway (GO:0071881)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|DNA replication (GO:0006260)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|fear response (GO:0042596)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intestinal absorption (GO:0050892)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of adrenergic receptor signaling pathway (GO:0071878)|negative regulation of calcium ion transmembrane transporter activity (GO:1901020)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of insulin secretion (GO:0046676)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|phospholipase C-activating adrenergic receptor signaling pathway (GO:0071882)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of vasodilation (GO:0045909)|positive regulation of wound healing (GO:0090303)|Ras protein signal transduction (GO:0007265)|regulation of insulin secretion (GO:0050796)|regulation of vasoconstriction (GO:0019229)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|thermoception (GO:0050955)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	alpha-1B adrenergic receptor binding (GO:0031692)|alpha-2C adrenergic receptor binding (GO:0031696)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|heterotrimeric G-protein binding (GO:0032795)|norepinephrine binding (GO:0051380)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			breast(1)|cervix(3)|endometrium(6)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(234;0.0735)|Lung NSC(174;0.238)		Epithelial(162;0.000316)|all cancers(201;0.00501)|BRCA - Breast invasive adenocarcinoma(275;0.118)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Dexmedetomidine(DB00633)|Dihydroergotamine(DB00320)|Dipivefrin(DB00449)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupirtine(DB06623)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Lofexidine(DB04948)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methyldopa(DB00968)|Mianserin(DB06148)|Mirtazapine(DB00370)|Naphazoline(DB06711)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phentolamine(DB00692)|Phenylpropanolamine(DB00397)|Pramipexole(DB00413)|Prazosin(DB00457)|Propericiazine(DB01608)|Pseudoephedrine(DB00852)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	ACCTGGCGCTCGACGTGCTCT	0.602													C|||	4	0.000798722	0.0023	0.0014	5008	,	,		15105	0.0		0.0	False		,,,				2504	0.0				p.L127L	Esophageal Squamous(173;605 2658 7278 49362)	Atlas-SNP	.											.	ADRA2A	38	.	0			c.C381G						PASS	.	C		32,4374	36.8+/-68.6	0,32,2171	94.0	75.0	82.0		381	2.3	1.0	10	dbSNP_134	82	0,8600		0,0,4300	no	coding-synonymous	ADRA2A	NM_000681.3		0,32,6471	GG,GC,CC		0.0,0.7263,0.246		127/466	112838135	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	150	exon1			GGCGCTCGACGTG	AF284095	CCDS7569.2	10q25.2	2012-08-08	2012-05-09		ENSG00000150594	ENSG00000150594		"""GPCR / Class A : Adrenoceptors : alpha"""	281	protein-coding gene	gene with protein product	"""alpha-2AAR subtype C10"", "" alpha-2A-adrenergic receptor"""	104210	"""adrenergic, alpha-2A-, receptor"""	ADRA2, ADRA2R			Standard	NM_000681		Approved	ADRAR	uc001kzo.3	P08913	OTTHUMG00000019050	ENST00000280155.2:c.381C>G	10.37:g.112838135C>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	172	97	0.563953	NM_000681	B0LPF6|Q2I8G2|Q2XN99|Q86TH8|Q9BZK1	Silent	SNP	ENST00000280155.2	37	CCDS7569.2																																																																																			C|0.998;G|0.002	0.002	strong		0.602	ADRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050372.2	NM_000681	
ESPNL	339768	hgsc.bcm.edu	37	2	239040218	239040218	+	Missense_Mutation	SNP	G	G	A	rs73102309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239040218G>A	ENST00000343063.3	+	9	3126	c.2863G>A	c.(2863-2865)Gcc>Acc	p.A955T	ESPNL_ENST00000409506.1_Missense_Mutation_p.A587T|ESPNL_ENST00000409169.1_Missense_Mutation_p.A911T|ESPNL_ENST00000477241.1_3'UTR	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	955				A -> T (in Ref. 1; BAC85884). {ECO:0000305}.						endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GCCTCACGCCGCCGTCCCCTG	0.687													G|||	670	0.133786	0.2368	0.0908	5008	,	,		14386	0.0546		0.1173	False		,,,				2504	0.1237				p.A955T		Atlas-SNP	.											.	ESPNL	63	.	0			c.G2863A						PASS	.	G	THR/ALA	921,3467		109,703,1382	16.0	18.0	17.0		2863	-8.3	0.0	2	dbSNP_130	17	1011,7585		55,901,3342	no	missense	ESPNL	NM_194312.2	58	164,1604,4724	AA,AG,GG		11.7613,20.9891,14.8799	benign	955/1006	239040218	1932,11052	2194	4298	6492	SO:0001583	missense	339768	exon9			CACGCCGCCGTCC	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.2863G>A	2.37:g.239040218G>A	ENSP00000339115:p.Ala955Thr	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	256	0.11721611721611722	95	0.19308943089430894	35	0.09668508287292818	41	0.07167832167832168	85	0.11213720316622691	G	5.082	0.200731	0.09652	0.209891	0.117613	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.63744	-0.06;1.04;0.64	4.16	-8.28	0.01013	.	0.795116	0.10989	N	0.611773	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.15549	-1.0433	9	0.15499	T	0.54	-0.9499	0.4266	0.00464	0.3016:0.1957:0.2867:0.216	.	911;955	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	T	955;911;587	ENSP00000339115:A955T;ENSP00000386577:A911T;ENSP00000386579:A587T	ENSP00000339115:A955T	A	+	1	0	ESPNL	238704957	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-1.492000	0.02300	-1.336000	0.02238	-0.378000	0.06908	GCC	G|0.865;A|0.135	0.135	strong		0.687	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
MAPKAP1	79109	hgsc.bcm.edu	37	9	128206855	128206855	+	Silent	SNP	C	C	T	rs35549826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:128206855C>T	ENST00000373498.1	-	10	1436	c.1368G>A	c.(1366-1368)acG>acA	p.T456T	MAPKAP1_ENST00000394063.1_Silent_p.T264T|MAPKAP1_ENST00000483937.1_5'UTR|MAPKAP1_ENST00000373497.5_Silent_p.T169T|MAPKAP1_ENST00000265960.3_Silent_p.T456T|MAPKAP1_ENST00000350766.3_Silent_p.T420T|MAPKAP1_ENST00000373511.2_Silent_p.T409T|MAPKAP1_ENST00000373503.3_Silent_p.T264T			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	456					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)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						TGCTTAGATACGTGAGTTTAA	0.453													c|||	29	0.00579073	0.0212	0.0014	5008	,	,		20762	0.0		0.0	False		,,,				2504	0.0				p.T456T		Atlas-SNP	.											MAPKAP1_ENST00000265960,NS,carcinoma,-1,4	MAPKAP1	68	4	0			c.G1368A						scavenged	.	T	,,,,	63,4343	59.9+/-96.7	1,61,2141	167.0	147.0	154.0		1368,1227,792,792,1260	-6.7	0.7	9	dbSNP_126	154	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPKAP1	NM_001006617.1,NM_001006619.1,NM_001006620.1,NM_001006621.1,NM_024117.3	,,,,	1,62,6440	TT,TC,CC		0.0116,1.4299,0.4921	,,,,	456/523,409/476,264/331,264/331,420/487	128206855	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	79109	exon11			TAGATACGTGAGT	M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487			18752	protein-coding gene	gene with protein product	"""stress-activated protein kinase-interacting 1"""	610558				15363842	Standard	NM_001006620		Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000373498.1:c.1368G>A	9.37:g.128206855C>T		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	166	67	0.403614	NM_001006617	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Silent	SNP	ENST00000373498.1	37	CCDS35140.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	c	4.720	0.133973	0.09032	0.014299	1.16E-4	ENSG00000119487	ENST00000444226	.	.	.	5.91	-6.66	0.01789	.	.	.	.	.	T	0.34948	0.0915	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53457	-0.8436	4	.	.	.	-6.8579	10.2871	0.43573	0.0:0.2969:0.167:0.5361	rs35549826	.	.	.	I	28	.	.	V	-	1	0	MAPKAP1	127246676	0.012000	0.17670	0.657000	0.29651	0.643000	0.38383	-1.022000	0.03611	-1.316000	0.02295	-4.302000	0.00007	GTA	C|0.994;T|0.006	0.006	strong		0.453	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1		
HKR1	284459	hgsc.bcm.edu	37	19	37854580	37854580	+	Missense_Mutation	SNP	C	C	T	rs3745764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37854580C>T	ENST00000324411.4	+	6	2152	c.1883C>T	c.(1882-1884)aCa>aTa	p.T628I	HKR1_ENST00000544914.1_Missense_Mutation_p.T355I|HKR1_ENST00000392153.3_Missense_Mutation_p.T609I|HKR1_ENST00000591134.1_Intron|HKR1_ENST00000591471.1_Missense_Mutation_p.T355I|HKR1_ENST00000589392.1_Missense_Mutation_p.T610I|HKR1_ENST00000541583.2_Missense_Mutation_p.T567I	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	114	0	0		WXS	Illumina HiSeq	Phase_I	177	82	0.463277	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	
CYP2A7	1549	hgsc.bcm.edu	37	19	41384702	41384702	+	Missense_Mutation	SNP	T	T	C	rs117539170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41384702T>C	ENST00000301146.4	-	5	1335	c.794A>G	c.(793-795)cAg>cGg	p.Q265R	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.Q214R	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	347	0	0		WXS	Illumina HiSeq	Phase_I	296	118	0.398649	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	
AIM1	202	hgsc.bcm.edu	37	6	106967778	106967778	+	Missense_Mutation	SNP	T	T	C	rs3747787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:106967778T>C	ENST00000369066.3	+	2	1958	c.1471T>C	c.(1471-1473)Tgc>Cgc	p.C491R		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		CAGTTTCCCATGCACTGATCT	0.458													T|||	872	0.174121	0.1808	0.1354	5008	,	,		22330	0.1161		0.2515	False		,,,				2504	0.1728				p.C491R		Atlas-SNP	.											.	AIM1	161	.	0			c.T1471C						PASS	.	T	ARG/CYS	733,3673	297.8+/-285.0	58,617,1528	83.0	89.0	87.0		1471	-5.8	0.0	6	dbSNP_107	87	2104,6496	356.3+/-330.2	259,1586,2455	yes	missense	AIM1	NM_001624.2	180	317,2203,3983	CC,CT,TT		24.4651,16.6364,21.813	benign	491/1724	106967778	2837,10169	2203	4300	6503	SO:0001583	missense	202	exon2			TTCCCATGCACTG	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1471T>C	6.37:g.106967778T>C	ENSP00000358062:p.Cys491Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	195	94	0.482051	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	390	0.17857142857142858	92	0.18699186991869918	57	0.1574585635359116	56	0.0979020979020979	185	0.24406332453825857	T	10.37	1.330824	0.24167	0.166364	0.244651	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.71341	-0.56	6.17	-5.75	0.02384	.	1.231230	0.05863	N	0.623317	T	0.23210	0.0561	N	0.20685	0.6	0.53005	P	3.500000000000725E-5	B	0.06786	0.001	B	0.06405	0.002	T	0.05131	-1.0904	9	0.23891	T	0.37	.	2.4107	0.04423	0.2004:0.1489:0.4535:0.1972	rs3747787;rs17495394;rs52819883;rs58298313;rs3747787	491	Q9Y4K1	AIM1_HUMAN	R	899;491	ENSP00000358062:C491R	ENSP00000285105:C899R	C	+	1	0	AIM1	107074471	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.826000	0.04429	-0.749000	0.04747	0.533000	0.62120	TGC	T|0.805;C|0.195	0.195	strong		0.458	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
IFNGR2	3460	hgsc.bcm.edu	37	21	34787312	34787312	+	Missense_Mutation	SNP	A	A	G	rs9808753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:34787312A>G	ENST00000290219.6	+	2	839	c.191A>G	c.(190-192)cAa>cGa	p.Q64R	IFNGR2_ENST00000381995.1_Missense_Mutation_p.Q83R|IFNGR2_ENST00000405436.1_5'UTR	NM_005534.3	NP_005525.2	P38484	INGR2_HUMAN	interferon gamma receptor 2 (interferon gamma transducer 1)	64	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Q -> R (in dbSNP:rs9808753). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8124716}.		cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	interferon-gamma receptor activity (GO:0004906)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	13					Interferon gamma-1b(DB00033)	GTTGTCTACCAAGTGCAGTTT	0.577													G|||	1362	0.271965	0.2489	0.196	5008	,	,		17759	0.4296		0.1431	False		,,,				2504	0.3272				p.Q64R		Atlas-SNP	.											.	IFNGR2	30	.	0			c.A191G						PASS	.	G	ARG/GLN	991,3415	731.6+/-410.3	106,779,1318	123.0	129.0	127.0		191	-1.3	0.1	21	dbSNP_119	127	1183,7417	764.3+/-407.6	89,1005,3206	yes	missense	IFNGR2	NM_005534.3	43	195,1784,4524	GG,GA,AA		13.7558,22.4921,16.7154	benign	64/338	34787312	2174,10832	2203	4300	6503	SO:0001583	missense	3460	exon2			TCTACCAAGTGCA		CCDS33544.1	21q22.1	2014-09-17			ENSG00000159128	ENSG00000159128		"""Interferons"", ""Fibronectin type III domain containing"""	5440	protein-coding gene	gene with protein product		147569		IFNGT1		3136170	Standard	NM_005534		Approved	AF-1	uc002yrp.4	P38484	OTTHUMG00000065188	ENST00000290219.6:c.191A>G	21.37:g.34787312A>G	ENSP00000290219:p.Gln64Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_005534	Q9BTL5	Missense_Mutation	SNP	ENST00000290219.6	37	CCDS33544.1	562	0.2573260073260073	109	0.22154471544715448	80	0.22099447513812154	255	0.4458041958041958	118	0.15567282321899736	G	0.005	-2.136795	0.00335	0.224921	0.137558	ENSG00000159128	ENST00000290219;ENST00000381995	T;T	0.73258	-0.73;-0.73	5.39	-1.31	0.09230	Fibronectin, type III (2);Immunoglobulin-like fold (1);	1.344440	0.05212	N	0.507005	T	0.00012	0.0000	N	0.21617	0.685	0.54753	P	1.399999999995849E-5	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.29549	-1.0008	8	.	.	.	-7.6724	7.2739	0.26273	0.6569:0.142:0.2011:0.0	rs9808753;rs17879493;rs52804646;rs61332453;rs9808753	83;64	E7EUY1;P38484	.;INGR2_HUMAN	R	64;83	ENSP00000290219:Q64R;ENSP00000371425:Q83R	.	Q	+	2	0	IFNGR2	33709182	0.198000	0.23374	0.107000	0.21349	0.006000	0.05464	0.163000	0.16520	-0.769000	0.04620	-1.557000	0.00889	CAA	A|0.793;G|0.207	0.207	strong		0.577	IFNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139916.1		
NOD1	10392	hgsc.bcm.edu	37	7	30492550	30492550	+	Silent	SNP	G	G	A	rs2235099|rs72551114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30492550G>A	ENST00000222823.4	-	6	1008	c.483C>T	c.(481-483)gaC>gaT	p.D161D	NOD1_ENST00000423334.2_Silent_p.D161D	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	161					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|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)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|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 cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|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 tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|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)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						CCATGATGGTGTCCATGTAGA	0.597													G|||	1693	0.338059	0.4024	0.1758	5008	,	,		19153	0.3869		0.2326	False		,,,				2504	0.4243				p.D161D		Atlas-SNP	.											.	NOD1	79	.	0			c.C483T						PASS	.	G		1679,2727	510.4+/-367.5	323,1033,847	119.0	99.0	106.0		483	2.5	1.0	7	dbSNP_98	106	2119,6481	365.1+/-333.8	281,1557,2462	no	coding-synonymous	NOD1	NM_006092.2		604,2590,3309	AA,AG,GG		24.6395,38.1071,29.2019		161/954	30492550	3798,9208	2203	4300	6503	SO:0001819	synonymous_variant	10392	exon6			GATGGTGTCCATG	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.483C>T	7.37:g.30492550G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	96	54	0.5625	NM_006092	B4DTU3|Q549U4|Q8IWF5	Silent	SNP	ENST00000222823.4	37	CCDS5427.1																																																																																			G|0.895;A|0.105	0.105	strong		0.597	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
SARDH	1757	hgsc.bcm.edu	37	9	136577770	136577770	+	Silent	SNP	C	C	T	rs147188337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136577770C>T	ENST00000371872.4	-	10	1556	c.1299G>A	c.(1297-1299)ccG>ccA	p.P433P	SARDH_ENST00000422262.2_Silent_p.P265P|SARDH_ENST00000439388.1_Silent_p.P433P	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	433					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		TGTCCTTCTCCGGGCGCCCAT	0.642													C|||	12	0.00239617	0.0091	0.0	5008	,	,		16347	0.0		0.0	False		,,,				2504	0.0				p.P433P		Atlas-SNP	.											.	SARDH	112	.	0			c.G1299A						PASS	.	C	,	54,4352	54.9+/-90.9	0,54,2149	69.0	68.0	69.0		1299,1299	-9.4	0.5	9	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	0,55,6448	TT,TC,CC		0.0116,1.2256,0.4229	,	433/919,433/919	136577770	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon10			CTTCTCCGGGCGC		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1299G>A	9.37:g.136577770C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	42	0.724138	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			C|0.996;T|0.004	0.004	strong		0.642	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
FAM83G	644815	hgsc.bcm.edu	37	17	18881225	18881225	+	Missense_Mutation	SNP	T	T	A	rs200348726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18881225T>A	ENST00000388995.6	-	5	1977	c.1754A>T	c.(1753-1755)gAc>gTc	p.D585V	SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|FAM83G_ENST00000585154.2_Missense_Mutation_p.D585V|FAM83G_ENST00000345041.4_Missense_Mutation_p.D585V|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395645.3_Intron|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395647.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	585	Poly-Asp.				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						TACGTAGTCGTCATCATCTTC	0.652													T|||	4	0.000798722	0.003	0.0	5008	,	,		16212	0.0		0.0	False		,,,				2504	0.0				p.D585V		Atlas-SNP	.											.	FAM83G	51	.	0			c.A1754T						PASS	.	T	VAL/ASP,,	12,4022		0,12,2005	45.0	52.0	50.0		1754,,	5.9	0.5	17		50	0,8316		0,0,4158	yes	missense,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	152,,	0,12,6163	AA,AT,TT		0.0,0.2975,0.0972	probably-damaging,,	585/824,,	18881225	12,12338	2017	4158	6175	SO:0001583	missense	644815	exon5			TAGTCGTCATCAT	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.1754A>T	17.37:g.18881225T>A	ENSP00000373647:p.Asp585Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	59	35	0.59322	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	20.7	4.038233	0.75617	0.002975	0.0	ENSG00000188522	ENST00000388995;ENST00000345041	T;T	0.15139	2.45;2.45	5.91	5.91	0.95273	.	0.446831	0.22573	N	0.058301	T	0.41119	0.1145	M	0.67953	2.075	0.80722	D	1	D	0.71674	0.998	D	0.68353	0.957	T	0.20974	-1.0259	10	0.87932	D	0	-28.3264	16.0171	0.80450	0.0:0.0:0.0:1.0	.	585	A6ND36	FA83G_HUMAN	V	585	ENSP00000373647:D585V;ENSP00000343279:D585V	ENSP00000343279:D585V	D	-	2	0	FAM83G	18821950	0.972000	0.33761	0.512000	0.27736	0.887000	0.51463	2.926000	0.48892	2.269000	0.75478	0.533000	0.62120	GAC	T|1.000;A|0.000	0.000	strong		0.652	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
PDHX	8050	hgsc.bcm.edu	37	11	34988343	34988343	+	Silent	SNP	T	T	C	rs61760973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34988343T>C	ENST00000227868.4	+	6	882	c.798T>C	c.(796-798)ccT>ccC	p.P266P	PDHX_ENST00000448838.3_Silent_p.P251P|PDHX_ENST00000430469.2_Intron			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	266					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)			TATCAACTCCTGGACAACCCA	0.493													T|||	586	0.117013	0.3177	0.062	5008	,	,		19415	0.0159		0.0318	False		,,,				2504	0.0767				p.P266P		Atlas-SNP	.											.	PDHX	40	.	0			c.T798C						PASS	.	T	,,	1204,3200	421.3+/-339.3	166,872,1164	97.0	94.0	95.0		753,,798	1.8	1.0	11	dbSNP_129	95	281,8315	104.6+/-165.6	5,271,4022	no	coding-synonymous,intron,coding-synonymous	PDHX	NM_001135024.1,NM_001166158.1,NM_003477.2	,,	171,1143,5186	CC,CT,TT		3.269,27.3388,11.4231	,,	251/487,,266/502	34988343	1485,11515	2202	4298	6500	SO:0001819	synonymous_variant	8050	exon6			AACTCCTGGACAA	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.798T>C	11.37:g.34988343T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Silent	SNP	ENST00000227868.4	37	CCDS7896.1																																																																																			T|0.897;C|0.103	0.103	strong		0.493	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
SLC18B1	116843	hgsc.bcm.edu	37	6	133105120	133105120	+	Missense_Mutation	SNP	C	C	T	rs6926101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133105120C>T	ENST00000275227.4	-	6	706	c.610G>A	c.(610-612)Gtc>Atc	p.V204I	SLC18B1_ENST00000538764.1_Missense_Mutation_p.V78I|SLC18B1_ENST00000367918.1_Intron	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	110	0	0		WXS	Illumina HiSeq	Phase_I	109	43	0.394495	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	
OR9K2	441639	hgsc.bcm.edu	37	12	55523860	55523860	+	Missense_Mutation	SNP	A	A	C	rs7305779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	67	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	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		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417738	105417738	+	Silent	SNP	G	G	C	rs536679222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417738G>C	ENST00000333244.5	-	7	4169	c.4050C>G	c.(4048-4050)tcC>tcG	p.S1350S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1350						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)			ACAGGTCCACGGAGGCCTCAA	0.592													.|||	371	0.0740815	0.0136	0.1398	5008	,	,		14224	0.0119		0.1571	False		,,,				2504	0.0879				p.S1350S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4050G						PASS	.						129.0	111.0	118.0					14																	105417738		1816	2913	4729	SO:0001819	synonymous_variant	113146	exon7			GTCCACGGAGGCC	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.4050C>G	14.37:g.105417738G>C		Somatic	371	0	0		WXS	Illumina HiSeq	Phase_I	265	107	0.403774	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.	.	none		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
C2orf83	56918	hgsc.bcm.edu	37	2	228476140	228476140	+	Nonsense_Mutation	SNP	C	C	T	rs2176186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	298	0	0		WXS	Illumina HiSeq	Phase_I	337	172	0.510386	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	
HIST1H2BH	8345	hgsc.bcm.edu	37	6	26252148	26252148	+	Silent	SNP	C	C	T	rs61746493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26252148C>T	ENST00000356350.2	+	1	270	c.270C>T	c.(268-270)atC>atT	p.I90I	HIST1H3F_ENST00000446824.2_5'Flank	NM_003524.2	NP_003515.1	Q93079	H2B1H_HUMAN	histone cluster 1, H2bh	90					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(3)|breast(2)|large_intestine(1)|lung(3)|ovary(3)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	17						GTTCGACCATCACCTCCAGGG	0.597													C|||	185	0.0369409	0.1309	0.0144	5008	,	,		18322	0.0		0.002	False		,,,				2504	0.0				p.I90I		Atlas-SNP	.											.	HIST1H2BH	36	.	0			c.C270T						PASS	.	C		426,3980		22,382,1799	85.0	89.0	88.0		270	3.7	1.0	6	dbSNP_129	88	27,8573		0,27,4273	no	coding-synonymous	HIST1H2BH	NM_003524.2		22,409,6072	TT,TC,CC		0.314,9.6686,3.483		90/127	26252148	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	8345	exon1			GACCATCACCTCC	Z80781	CCDS4601.1	6p21.3	2011-01-27	2006-10-11	2003-02-14	ENSG00000197459	ENSG00000275713		"""Histones / Replication-dependent"""	4755	protein-coding gene	gene with protein product		602806	"""H2B histone family, member J"", ""histone 1, H2bh"""	H2BFJ		9119399, 12408966	Standard	NM_003524		Approved	H2B/j	uc003nhh.3	Q93079	OTTHUMG00000014447	ENST00000356350.2:c.270C>T	6.37:g.26252148C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	171	91	0.532164	NM_003524	B2R541|Q4VB74	Silent	SNP	ENST00000356350.2	37	CCDS4601.1																																																																																			C|0.968;T|0.032	0.032	strong		0.597	HIST1H2BH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040110.1	NM_003524	
COX6B1	1340	hgsc.bcm.edu	37	19	36142187	36142187	+	Silent	SNP	C	C	T	rs7991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36142187C>T	ENST00000592141.1	+	2	307	c.42C>T	c.(40-42)acC>acT	p.T14T	COX6B1_ENST00000392201.1_Silent_p.T14T|COX6B1_ENST00000246554.3_Silent_p.T14T			P14854	CX6B1_HUMAN	cytochrome c oxidase subunit VIb polypeptide 1 (ubiquitous)	14					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)	p.T31T(1)|p.T14T(1)		lung(6)|prostate(1)|stomach(1)	8	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)			ACTACAAGACCGCCCCTTTTG	0.572													T|||	922	0.184105	0.2216	0.1441	5008	,	,		15726	0.2857		0.0755	False		,,,				2504	0.1687				p.T14T		Atlas-SNP	.											COX6B1_ENST00000392201,NS,carcinoma,0,2	COX6B1	20	2	2	Substitution - coding silent(2)	stomach(2)	c.C42T						PASS	.	T		903,3503	740.6+/-411.2	78,747,1378	99.0	83.0	88.0		42	-1.3	1.0	19	dbSNP_52	88	664,7936	789.4+/-407.6	27,610,3663	no	coding-synonymous	COX6B1	NM_001863.4		105,1357,5041	TT,TC,CC		7.7209,20.4948,12.0483		14/87	36142187	1567,11439	2203	4300	6503	SO:0001819	synonymous_variant	1340	exon2			CAAGACCGCCCCT	BC001015	CCDS12469.1	19q13.1	2011-07-04	2010-01-07	2004-08-12	ENSG00000126267	ENSG00000126267	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2280	protein-coding gene	gene with protein product		124089	"""cytochrome c oxidase subunit Vib"", ""cytochrome c oxidase subunit Vib polypeptide 1 (ubiquitous)"""	COX6B		1650756	Standard	NM_001863		Approved	COXG	uc002oav.3	P14854	OTTHUMG00000048112	ENST00000592141.1:c.42C>T	19.37:g.36142187C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001863	B2R5C9|Q6IBL4	Silent	SNP	ENST00000592141.1	37	CCDS12469.1																																																																																			C|0.859;T|0.141	0.141	strong		0.572	COX6B1-004	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459068.3	NM_001863	
FAM65B	9750	hgsc.bcm.edu	37	6	24828449	24828449	+	Missense_Mutation	SNP	C	C	T	rs61741706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24828449C>T	ENST00000259698.4	-	19	2819	c.2644G>A	c.(2644-2646)Gtc>Atc	p.V882I	FAM65B_ENST00000538035.1_Missense_Mutation_p.V861I	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	882					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						AAAACAGTGACGACTTCCGAG	0.537													C|||	114	0.0227636	0.0779	0.0072	5008	,	,		16614	0.0		0.006	False		,,,				2504	0.0				p.V882I		Atlas-SNP	.											.	FAM65B	134	.	0			c.G2644A						PASS	.	C	ILE/VAL	98,1286		2,94,596	66.0	59.0	61.0		2644	-2.8	0.9	6	dbSNP_129	61	7,3175		0,7,1584	yes	missense	FAM65B	NM_014722.2	29	2,101,2180	TT,TC,CC		0.22,7.0809,2.2996	benign	882/1069	24828449	105,4461	692	1591	2283	SO:0001583	missense	9750	exon19			CAGTGACGACTTC	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"""myogenesis-related and NCAM-associated protein homolog (chicken)"""	611410	"""chromosome 6 open reading frame 32"""	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.2644G>A	6.37:g.24828449C>T	ENSP00000259698:p.Val882Ile	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	50	12	0.24	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	43	0.019688644688644688	33	0.06707317073170732	4	0.011049723756906077	0	0.0	6	0.0079155672823219	C	6.371	0.436609	0.12104	0.070809	0.0022	ENSG00000111913	ENST00000259698;ENST00000538035	T;T	0.77620	-1.11;-1.11	5.92	-2.85	0.05734	.	0.352381	0.31566	N	0.007431	T	0.26195	0.0639	N	0.02539	-0.55	0.80722	D	1	B;B	0.12013	0.005;0.002	B;B	0.08055	0.003;0.003	T	0.09509	-1.0671	10	0.11485	T	0.65	-11.55	11.9871	0.53153	0.0:0.4035:0.0:0.5965	.	861;882	F5GX51;Q9Y4F9	.;FA65B_HUMAN	I	882;861	ENSP00000259698:V882I;ENSP00000441138:V861I	ENSP00000259698:V882I	V	-	1	0	FAM65B	24936428	0.979000	0.34478	0.945000	0.38365	0.944000	0.59088	0.090000	0.15025	-0.503000	0.06586	-0.136000	0.14681	GTC	C|0.984;T|0.016	0.016	strong		0.537	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
LRRC8A	56262	hgsc.bcm.edu	37	9	131670457	131670457	+	Silent	SNP	T	T	C	rs3750320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131670457T>C	ENST00000259324.5	+	3	1537	c.1014T>C	c.(1012-1014)taT>taC	p.Y338Y	LRRC8A_ENST00000372599.3_Silent_p.Y338Y|LRRC8A_ENST00000372600.4_Silent_p.Y338Y	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	338					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						TCTGCATGTATACACTGTGGT	0.562													C|||	1324	0.264377	0.4297	0.1513	5008	,	,		20578	0.1746		0.2008	False		,,,				2504	0.2791				p.Y338Y		Atlas-SNP	.											.	LRRC8A	69	.	0			c.T1014C						PASS	.	C	,,	1735,2671	648.2+/-398.7	308,1119,776	199.0	145.0	164.0		1014,1014,1014	4.3	1.0	9	dbSNP_107	164	1596,7004	743.6+/-407.2	141,1314,2845	no	coding-synonymous,coding-synonymous,coding-synonymous	LRRC8A	NM_001127244.1,NM_001127245.1,NM_019594.3	,,	449,2433,3621	CC,CT,TT		18.5581,39.3781,25.6113	,,	338/811,338/811,338/811	131670457	3331,9675	2203	4300	6503	SO:0001819	synonymous_variant	56262	exon3			CATGTATACACTG	AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"""leucine rich repeat containing 8"""	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.1014T>C	9.37:g.131670457T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	104	39	0.375	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Silent	SNP	ENST00000259324.5	37	CCDS35155.1																																																																																			T|0.745;C|0.255	0.255	strong		0.562	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594	
OPN1LW	5956	hgsc.bcm.edu	37	X	153418516	153418516	+	Silent	SNP	G	G	T	rs55676401		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153418516G>T	ENST00000369951.4	+	3	573	c.513G>T	c.(511-513)gtG>gtT	p.V171V	OPN1LW_ENST00000463296.1_3'UTR	NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	171					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)					TGGCCATCGTGGGCATTGCCT	0.582													g|||	751	0.19894	0.2481	0.072	3775	,	,		13237	0.1042		0.0517	False		,,,				2504	0.2209				p.V171V		Atlas-SNP	.											.	OPN1LW	87	.	0			c.G513T						PASS	.	T		1102,2704		176,601,149,853,397	225.0	138.0	169.0		513	-6.6	0.0	X	dbSNP_129	169	472,5908		64,232,112,2078,1520	no	coding-synonymous	OPN1LW	NM_020061.4		240,833,261,2931,1917	TT,TG,T,GG,G		7.3981,28.9543,15.4526		171/365	153418516	1574,8612	2176	4006	6182	SO:0001819	synonymous_variant	5956	exon3			CATCGTGGGCATT	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.513G>T	X.37:g.153418516G>T		Somatic	464	1	0.00215517		WXS	Illumina HiSeq	Phase_I	1088	321	0.295037	NM_020061		Silent	SNP	ENST00000369951.4	37	CCDS14742.1																																																																																			.	.	weak		0.582	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39915677	39915677	+	Missense_Mutation	SNP	G	G	A	rs34603507		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39915677G>A	ENST00000409794.3	+	19	4754	c.3904G>A	c.(3904-3906)Gca>Aca	p.A1302T	PLEKHG2_ENST00000425673.1_Missense_Mutation_p.A1273T|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000458508.2_Intron|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000378550.1_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	1302			A -> T (in dbSNP:rs34603507).		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)			AGGGGCCCCCGCAGCCTCCCG	0.721													G|||	1	0.000199681	0.0008	0.0	5008	,	,		11603	0.0		0.0	False		,,,				2504	0.0				p.A1302T		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G3904A						PASS	.	G	THR/ALA	5,4237		0,5,2116	13.0	16.0	15.0		3904	-7.2	0.0	19	dbSNP_126	15	0,8448		0,0,4224	no	missense	PLEKHG2	NM_022835.2	58	0,5,6340	AA,AG,GG		0.0,0.1179,0.0394	benign	1302/1387	39915677	5,12685	2121	4224	6345	SO:0001583	missense	64857	exon19			GCCCCCGCAGCCT	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.3904G>A	19.37:g.39915677G>A	ENSP00000386733:p.Ala1302Thr	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	26	17	0.653846	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	G	10.97	1.500290	0.26861	0.001179	0.0	ENSG00000090924	ENST00000409794;ENST00000425673	T;T	0.67171	-0.24;-0.25	4.35	-7.16	0.01516	.	1.186420	0.06463	N	0.729685	T	0.34513	0.0900	N	0.05383	-0.06	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.06405	0.002;0.001	T	0.13602	-1.0503	9	.	.	.	.	2.4588	0.04536	0.1357:0.2896:0.4002:0.1745	rs34603507	1273;1302	Q9H7P9-3;Q9H7P9	.;PKHG2_HUMAN	T	1302;1273	ENSP00000386733:A1302T;ENSP00000392906:A1273T	.	A	+	1	0	PLEKHG2	44607517	0.000000	0.05858	0.000000	0.03702	0.833000	0.47200	-0.923000	0.04000	-1.368000	0.02149	-1.305000	0.01319	GCA	G|0.970;A|0.030	0.030	strong		0.721	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
TATDN3	128387	hgsc.bcm.edu	37	1	212969889	212969889	+	Missense_Mutation	SNP	G	G	A	rs55709122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:212969889G>A	ENST00000366974.4	+	3	224	c.130G>A	c.(130-132)Gaa>Aaa	p.E44K	TATDN3_ENST00000531963.1_Missense_Mutation_p.E44K|TATDN3_ENST00000526641.1_Missense_Mutation_p.E44K|TATDN3_ENST00000526997.1_Missense_Mutation_p.E44K|TATDN3_ENST00000525569.1_3'UTR|TATDN3_ENST00000532324.1_Missense_Mutation_p.E44K|TATDN3_ENST00000530441.1_Missense_Mutation_p.E44K|TATDN3_ENST00000366973.4_Missense_Mutation_p.E44K	NM_001042552.2|NM_001042553.2|NM_001146169.1|NM_001146171.1	NP_001036017.1|NP_001036018.1|NP_001139641.1|NP_001139643.1	Q17R31	TATD3_HUMAN	TatD DNase domain containing 3	44					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00699)|all cancers(67;0.0118)|GBM - Glioblastoma multiforme(131;0.0801)|Epithelial(68;0.104)		GGCAGTTGCCGAACATTCAGG	0.289													G|||	8	0.00159744	0.0061	0.0	5008	,	,		13128	0.0		0.0	False		,,,				2504	0.0				p.E44K		Atlas-SNP	.											.	TATDN3	23	.	0			c.G130A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	43,4363	41.6+/-74.8	0,43,2160	38.0	41.0	40.0		130,130,130,130,130	5.8	1.0	1	dbSNP_129	40	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	TATDN3	NM_001042552.2,NM_001042553.2,NM_001146169.1,NM_001146170.1,NM_001146171.1	56,56,56,56,56	0,43,6460	AA,AG,GG		0.0,0.9759,0.3306	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	44/275,44/274,44/241,44/254,44/282	212969889	43,12963	2203	4300	6503	SO:0001583	missense	128387	exon3			GTTGCCGAACATT	AL832248	CCDS31019.1, CCDS41465.1, CCDS53475.1, CCDS53476.1, CCDS53477.1	1q32.3	2008-02-05			ENSG00000203705	ENSG00000203705			27010	protein-coding gene	gene with protein product							Standard	NM_001042552		Approved		uc001hjo.2	Q17R31	OTTHUMG00000036805	ENST00000366974.4:c.130G>A	1.37:g.212969889G>A	ENSP00000355941:p.Glu44Lys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_001146170	A6NGS3|B7Z1C1|B7Z978|B7ZLQ6|E9PJE5|E9PNH3|G3V151|Q4G0L1	Missense_Mutation	SNP	ENST00000366974.4	37	CCDS31019.1	5|5	0.0022893772893772895|0.0022893772893772895	5|5	0.01016260162601626|0.01016260162601626	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	29.3|29.3	4.990408|4.990408	0.93106|0.93106	0.009759|0.009759	0.0|0.0	ENSG00000203705|ENSG00000203705	ENST00000532324;ENST00000366974;ENST00000530441;ENST00000526641;ENST00000531963;ENST00000366973;ENST00000526997;ENST00000530399|ENST00000488246	.|.	.|.	.|.	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.046199|.	0.85682|.	D|.	0.000000|.	T|T	0.69904|0.69904	0.3163|0.3163	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.67145|.	0.995;0.996;0.995;0.989;0.992|.	P;P;P;P;P|.	0.61275|.	0.836;0.836;0.886;0.658;0.769|.	T|T	0.71938|0.71938	-0.4441|-0.4441	9|5	0.29301|.	T|.	0.29|.	-8.3766|-8.3766	18.7217|18.7217	0.91697|0.91697	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs55709122|rs55709122	44;44;44;44;44|.	E9PNH3;G3V151;E9PJE5;Q17R31-2;Q17R31|.	.;.;.;.;TATD3_HUMAN|.	K|Q	44;44;44;44;44;44;44;43|43	.|.	ENSP00000355940:E44K|.	E|R	+|+	1|2	0|0	TATDN3|TATDN3	211036512|211036512	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.952000|0.952000	0.60782|0.60782	4.428000|4.428000	0.59894|0.59894	2.731000|2.731000	0.93534|0.93534	0.555000|0.555000	0.69702|0.69702	GAA|CGA	G|0.997;A|0.003	0.003	strong		0.289	TATDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089396.2	XM_375838	
ULK1	8408	hgsc.bcm.edu	37	12	132404101	132404101	+	Silent	SNP	C	C	T	rs143340589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132404101C>T	ENST00000321867.4	+	25	3120	c.2769C>T	c.(2767-2769)gcC>gcT	p.A923A	ULK1_ENST00000540647.1_Silent_p.A168A	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	923					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		AGATCCGGGCCGGCAAGCTCT	0.662													C|||	7	0.00139776	0.0053	0.0	5008	,	,		16277	0.0		0.0	False		,,,				2504	0.0				p.A923A		Atlas-SNP	.											.	ULK1	92	.	0			c.C2769T						PASS	.	C		29,4377	34.3+/-65.2	0,29,2174	62.0	66.0	65.0		2769	-4.8	0.9	12	dbSNP_134	65	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ULK1	NM_003565.2		0,30,6472	TT,TC,CC		0.0116,0.6582,0.2307		923/1051	132404101	30,12974	2203	4299	6502	SO:0001819	synonymous_variant	8408	exon25			CCGGGCCGGCAAG	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"""ATG1 autophagy related 1 homolog (S. cerevisiae)"""	603168	"""unc-51 (C. elegans)-like kinase 1"", ""unc-51-like kinase 1 (C. elegans)"""			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.2769C>T	12.37:g.132404101C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	77	28	0.363636	NM_003565	Q9UQ28	Silent	SNP	ENST00000321867.4	37	CCDS9274.1																																																																																			C|0.998;T|0.002	0.002	strong		0.662	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3		
KIF21B	23046	hgsc.bcm.edu	37	1	200959305	200959305	+	Silent	SNP	G	G	A	rs2297910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200959305G>A	ENST00000422435.2	-	20	3307	c.2991C>T	c.(2989-2991)acC>acT	p.T997T	KIF21B_ENST00000332129.2_Silent_p.T997T|KIF21B_ENST00000360529.5_Silent_p.T997T|KIF21B_ENST00000461742.2_Silent_p.T997T	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	997					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CCTGGCAGTCGGTGATGCCGT	0.647													G|||	386	0.0770767	0.0953	0.0504	5008	,	,		20650	0.127		0.0119	False		,,,				2504	0.0869				p.T997T		Atlas-SNP	.											.	KIF21B	208	.	0			c.C2991T						PASS	.	G		422,3984	206.8+/-228.3	20,382,1801	87.0	82.0	84.0		2991	-5.0	1.0	1	dbSNP_100	84	32,8568	21.0+/-64.5	0,32,4268	no	coding-synonymous	KIF21B	NM_017596.2		20,414,6069	AA,AG,GG		0.3721,9.5778,3.4907		997/1625	200959305	454,12552	2203	4300	6503	SO:0001819	synonymous_variant	23046	exon20			GCAGTCGGTGATG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.2991C>T	1.37:g.200959305G>A		Somatic	399	0	0		WXS	Illumina HiSeq	Phase_I	285	147	0.515789	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	37	CCDS58056.1																																																																																			G|0.957;A|0.043	0.043	strong		0.647	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
FAM179B	23116	hgsc.bcm.edu	37	14	45473265	45473265	+	Splice_Site	SNP	G	G	A	rs17092470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45473265G>A	ENST00000361577.3	+	4	2554	c.2340G>A	c.(2338-2340)gtG>gtA	p.V780V	KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000361462.2_Splice_Site_p.V780V|FAM179B_ENST00000382233.2_Splice_Site_p.V780V	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	780										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TTATTACAGTGTATGCTAGCC	0.338													G|||	262	0.0523163	0.1899	0.0159	5008	,	,		17095	0.0		0.0	False		,,,				2504	0.0				p.V780V		Atlas-SNP	.											.	FAM179B	115	.	0			c.G2340A						PASS	.	G		688,3718	284.6+/-277.7	50,588,1565	47.0	43.0	44.0		2340	-0.8	0.1	14	dbSNP_123	44	7,8593	5.0+/-18.6	0,7,4293	yes	coding-synonymous-near-splice	FAM179B	NM_015091.2		50,595,5858	AA,AG,GG		0.0814,15.6151,5.3437		780/1721	45473265	695,12311	2203	4300	6503	SO:0001630	splice_region_variant	23116	exon4			TACAGTGTATGCT	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.2339-1G>A	14.37:g.45473265G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_015091	Q68D66|Q6PG27	Silent	SNP	ENST00000361577.3	37	CCDS9681.1																																																																																			G|0.948;A|0.052	0.052	strong		0.338	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	Silent
PDZRN3	23024	hgsc.bcm.edu	37	3	73453325	73453325	+	Silent	SNP	C	C	T	rs2291463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:73453325C>T	ENST00000263666.4	-	4	1254	c.1140G>A	c.(1138-1140)gtG>gtA	p.V380V	PDZRN3_ENST00000466780.1_Silent_p.V37V|PDZRN3_ENST00000535920.1_Silent_p.V102V|PDZRN3_ENST00000479530.1_Silent_p.V97V|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000462146.2_Silent_p.V37V	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	380					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)		AGGGATCCAGCACGGGTGGGC	0.478													C|||	3013	0.601637	0.4811	0.6297	5008	,	,		18193	0.8353		0.5567	False		,,,				2504	0.5501				p.V380V		Atlas-SNP	.											.	PDZRN3	196	.	0			c.G1140A						PASS	.	C		2203,2203	589.8+/-387.2	538,1127,538	126.0	110.0	116.0		1140	-0.8	0.0	3	dbSNP_100	116	4751,3849	610.4+/-395.7	1332,2087,881	no	coding-synonymous	PDZRN3	NM_015009.1		1870,3214,1419	TT,TC,CC		44.7558,50.0,46.5324		380/1067	73453325	6954,6052	2203	4300	6503	SO:0001819	synonymous_variant	23024	exon4			ATCCAGCACGGGT	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.1140G>A	3.37:g.73453325C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	139	68	0.489209	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	37	CCDS33789.1																																																																																			C|0.427;T|0.573	0.573	strong		0.478	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
MYH14	79784	hgsc.bcm.edu	37	19	50720949	50720949	+	Missense_Mutation	SNP	G	G	A	rs34773557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50720949G>A	ENST00000596571.1	+	2	483	c.483G>A	c.(481-483)atG>atA	p.M161I	MYH14_ENST00000262269.8_Missense_Mutation_p.M161I|MYH14_ENST00000598205.1_Missense_Mutation_p.M161I|MYH14_ENST00000601313.1_Missense_Mutation_p.M161I|MYH14_ENST00000425460.1_Missense_Mutation_p.M161I|MYH14_ENST00000440075.2_Missense_Mutation_p.M161I|MYH14_ENST00000376970.2_Missense_Mutation_p.M161I			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	161	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)		TTGTGGAGATGTACCGGGGCA	0.607													G|||	56	0.0111821	0.028	0.013	5008	,	,		18213	0.0		0.0099	False		,,,				2504	0.0				p.M161I		Atlas-SNP	.											.	MYH14	261	.	0			c.G483A						PASS	.	G	ILE/MET,ILE/MET,ILE/MET	119,4229		1,117,2056	89.0	98.0	95.0		483,483,483	4.6	1.0	19	dbSNP_126	95	66,8488		1,64,4212	yes	missense,missense,missense	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	10,10,10	2,181,6268	AA,AG,GG		0.7716,2.7369,1.4339	probably-damaging,probably-damaging,probably-damaging	161/2004,161/2037,161/1996	50720949	185,12717	2174	4277	6451	SO:0001583	missense	79784	exon3			GGAGATGTACCGG	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.483G>A	19.37:g.50720949G>A	ENSP00000472819:p.Met161Ile	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	29	0.013278388278388278	16	0.032520325203252036	5	0.013812154696132596	0	0.0	8	0.010554089709762533	G	17.81	3.481669	0.63849	0.027369	0.007716	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	4.63	4.63	0.57726	Myosin head, motor domain (2);	.	.	.	.	T	0.79907	0.4527	M	0.70595	2.14	0.54753	D	0.999988	P;P;P	0.51791	0.948;0.755;0.711	P;B;B	0.53146	0.719;0.378;0.347	D	0.85829	0.1390	9	0.72032	D	0.01	.	15.3635	0.74499	0.0:0.0:1.0:0.0	rs34773557	161;161;161	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	I	161	ENSP00000406273:M161I;ENSP00000366169:M161I;ENSP00000407879:M161I;ENSP00000262269:M161I	ENSP00000262269:M161I	M	+	3	0	MYH14	55412761	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.482000	0.73613	2.579000	0.87056	0.655000	0.94253	ATG	G|0.987;A|0.013	0.013	strong		0.607	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
CDS2	8760	hgsc.bcm.edu	37	20	5166418	5166418	+	Silent	SNP	G	G	A	rs3818196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5166418G>A	ENST00000460006.1	+	9	1081	c.774G>A	c.(772-774)aaG>aaA	p.K258K	CDS2_ENST00000379070.3_3'UTR|CDS2_ENST00000379062.4_Silent_p.K138K|CDS2_ENST00000535100.1_Silent_p.K79K	NM_003818.3	NP_003809.1	O95674	CDS2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	258					CDP-diacylglycerol biosynthetic process (GO:0016024)|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)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	phosphatidate cytidylyltransferase activity (GO:0004605)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|stomach(1)	14						CCCCGAAGAAGACCTGGGAAG	0.483													G|||	251	0.0501198	0.0408	0.0274	5008	,	,		20392	0.0774		0.0109	False		,,,				2504	0.091				p.K258K		Atlas-SNP	.											.	CDS2	27	.	0			c.G774A						PASS	.	G		163,4243	109.5+/-147.8	1,161,2041	141.0	118.0	126.0		774	4.9	1.0	20	dbSNP_107	126	126,8474	64.9+/-127.2	2,122,4176	no	coding-synonymous	CDS2	NM_003818.3		3,283,6217	AA,AG,GG		1.4651,3.6995,2.2221		258/446	5166418	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	8760	exon9			GAAGAAGACCTGG	AF069532	CCDS13088.1	20p13	2006-03-28			ENSG00000101290	ENSG00000101290	2.7.7.41		1801	protein-coding gene	gene with protein product		603549				9806839, 9889000	Standard	NM_003818		Approved		uc002wls.3	O95674	OTTHUMG00000031801	ENST00000460006.1:c.774G>A	20.37:g.5166418G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	208	95	0.456731	NM_003818	B2RDC6|D3DW04|Q5TDY2|Q5TDY3|Q5TDY4|Q5TDY5|Q9BYK5|Q9NTT2	Silent	SNP	ENST00000460006.1	37	CCDS13088.1																																																																																			G|0.966;A|0.034	0.034	strong		0.483	CDS2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077858.2		
GPR17	2840	hgsc.bcm.edu	37	2	128408747	128408747	+	Silent	SNP	C	C	A	rs34722685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128408747C>A	ENST00000272644.3	+	3	596	c.522C>A	c.(520-522)ctC>ctA	p.L174L	LIMS2_ENST00000324938.5_Intron|GPR17_ENST00000486700.1_3'UTR|LIMS2_ENST00000355119.4_Intron|LIMS2_ENST00000409455.1_Intron|LIMS2_ENST00000409254.1_5'Flank|LIMS2_ENST00000545738.2_Intron|LIMS2_ENST00000409808.2_Intron|GPR17_ENST00000544369.1_Silent_p.L174L|GPR17_ENST00000393018.3_Silent_p.L174L|LIMS2_ENST00000410011.1_Intron|LIMS2_ENST00000410038.1_5'Flank	NM_001161416.1|NM_001161417.1|NM_005291.2	NP_001154888.1|NP_001154889.1|NP_005282.1	Q13304	GPR17_HUMAN	G protein-coupled receptor 17	174					chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)|urinary_tract(1)	19	Colorectal(110;0.1)	Ovarian(717;0.15)		BRCA - Breast invasive adenocarcinoma(221;0.0677)		GCAGGCCCCTCTACGCACACC	0.637													C|||	70	0.0139776	0.0499	0.0058	5008	,	,		18872	0.0		0.0	False		,,,				2504	0.0				p.L174L		Atlas-SNP	.											.	GPR17	56	.	0			c.C522A						PASS	.	C	,,,,,,,	158,4248	106.5+/-144.9	2,154,2047	112.0	99.0	103.0		,,,522,438,438,522,	3.6	1.0	2	dbSNP_126	103	1,8599		0,1,4299	no	intron,intron,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	GPR17,LIMS2	NM_001136037.2,NM_001161403.1,NM_001161404.1,NM_001161415.1,NM_001161416.1,NM_001161417.1,NM_005291.2,NM_017980.4	,,,,,,,	2,155,6346	AA,AC,CC		0.0116,3.586,1.2225	,,,,,,,	,,,174/368,146/340,146/340,174/368,	128408747	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	2840	exon3			GCCCCTCTACGCA		CCDS2148.1	2q21	2014-01-30			ENSG00000144230	ENSG00000144230		"""GPCR / Class A : Orphans"""	4471	protein-coding gene	gene with protein product		603071				8558062	Standard	NM_001161415		Approved		uc002tpc.3	Q13304	OTTHUMG00000131533	ENST00000272644.3:c.522C>A	2.37:g.128408747C>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_005291	A8K9L0|B2R9X0|Q8N5S7|Q9UDZ6|Q9UE21	Silent	SNP	ENST00000272644.3	37	CCDS2148.1																																																																																			C|0.985;A|0.015	0.015	strong		0.637	GPR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254390.1		
APLNR	187	hgsc.bcm.edu	37	11	57004344	57004344	+	Silent	SNP	G	G	T	rs948847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57004344G>T	ENST00000606794.1	-	1	331	c.135C>A	c.(133-135)ggC>ggA	p.G45G		NM_005161.4	NP_005152.1	P35414	APJ_HUMAN	apelin receptor	45					G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation (GO:0007369)|heart development (GO:0007507)|regulation of body fluid levels (GO:0050878)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)	p.G45G(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CCAGACCGTTGCCCGTGGTGC	0.597													G|||	2928	0.584665	0.3835	0.6412	5008	,	,		19084	0.7113		0.5577	False		,,,				2504	0.7137				p.G45G		Atlas-SNP	.											APLNR,colon,carcinoma,0,1	APLNR	62	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C135A						PASS	.	G		1948,2454	549.3+/-377.7	406,1136,659	75.0	72.0	73.0		135	3.3	1.0	11	dbSNP_86	73	4752,3840	608.4+/-395.4	1353,2046,897	no	coding-synonymous	APLNR	NM_005161.4		1759,3182,1556	TT,TG,GG		44.6927,44.2526,48.4377		45/381	57004344	6700,6294	2201	4296	6497	SO:0001819	synonymous_variant	187	exon1			ACCGTTGCCCGTG	U03642	CCDS7950.1	11q12.1	2012-08-08	2008-05-12	2008-05-12	ENSG00000134817	ENSG00000134817			339	protein-coding gene	gene with protein product	"""APJ (apelin) receptor"""	600052	"""angiotensin II receptor-like 1"""	AGTRL1		8294032, 14622440	Standard	NM_005161		Approved	FLJ90771, APJ, APJR	uc001njo.3	P35414	OTTHUMG00000167021	ENST00000606794.1:c.135C>A	11.37:g.57004344G>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_005161		Silent	SNP	ENST00000606794.1	37	CCDS7950.1																																																																																			G|0.455;T|0.545	0.545	strong		0.597	APLNR-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470575.1	NM_005161	
FGD6	55785	hgsc.bcm.edu	37	12	95604547	95604547	+	Silent	SNP	C	C	T	rs4762288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:95604547C>T	ENST00000343958.4	-	2	736	c.513G>A	c.(511-513)ggG>ggA	p.G171G	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Silent_p.G171G|FGD6_ENST00000546711.1_Silent_p.G171G	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	171					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						TTAAAACAACCCCACCCTGGT	0.378													C|||	245	0.0489217	0.0613	0.036	5008	,	,		18637	0.0109		0.0467	False		,,,				2504	0.0828				p.G171G		Atlas-SNP	.											.	FGD6	127	.	0			c.G513A						PASS	.	C		250,4156	145.0+/-179.8	6,238,1959	70.0	69.0	69.0		513	-3.4	0.0	12	dbSNP_111	69	392,8208	125.6+/-184.2	10,372,3918	no	coding-synonymous	FGD6	NM_018351.3		16,610,5877	TT,TC,CC		4.5581,5.6741,4.9362		171/1431	95604547	642,12364	2203	4300	6503	SO:0001819	synonymous_variant	55785	exon2			AACAACCCCACCC	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.513G>A	12.37:g.95604547C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Silent	SNP	ENST00000343958.4	37	CCDS31878.1																																																																																			C|0.948;T|0.052	0.052	strong		0.378	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
WDR66	144406	hgsc.bcm.edu	37	12	122396424	122396424	+	Silent	SNP	C	C	A	rs73415652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122396424C>A	ENST00000288912.4	+	12	2831	c.1977C>A	c.(1975-1977)ccC>ccA	p.P659P	WDR66_ENST00000397454.2_Silent_p.P659P	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	659							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)		CCTACAACCCCGAAGGTATTT	0.488													G|||	372	0.0742812	0.2572	0.0202	5008	,	,		19706	0.0		0.0	False		,,,				2504	0.0184				p.P659P	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C1977A						PASS	.	G	,	729,3035		71,587,1224	182.0	178.0	180.0		1977,1977	-10.6	0.0	12	dbSNP_130	180	8,8194		0,8,4093	no	coding-synonymous,coding-synonymous	WDR66	NM_001178003.1,NM_144668.5	,	71,595,5317	AA,AC,CC		0.0975,19.3677,6.1591	,	659/942,659/1150	122396424	737,11229	1882	4101	5983	SO:0001819	synonymous_variant	144406	exon12			CAACCCCGAAGGT	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.1977C>A	12.37:g.122396424C>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	123	68	0.552846	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Silent	SNP	ENST00000288912.4	37	CCDS41853.1																																																																																			C|0.963;A|0.037	0.037	strong		0.488	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
GSTP1	2950	hgsc.bcm.edu	37	11	67353970	67353970	+	Silent	SNP	T	T	C	rs4891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67353970T>C	ENST00000398606.3	+	7	804	c.555T>C	c.(553-555)agT>agC	p.S185S	GSTP1_ENST00000398603.1_Silent_p.S149S|GSTP1_ENST00000498765.1_3'UTR	NM_000852.3	NP_000843.1	P09211	GSTP1_HUMAN	glutathione S-transferase pi 1	185	GST C-terminal.				cellular response to lipopolysaccharide (GO:0071222)|central nervous system development (GO:0007417)|common myeloid progenitor cell proliferation (GO:0035726)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biosynthetic process (GO:0009890)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of leukocyte proliferation (GO:0070664)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|nitric oxide storage (GO:0035732)|positive regulation of superoxide anion generation (GO:0032930)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of stress-activated MAPK cascade (GO:0032872)|response to reactive oxygen species (GO:0000302)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|TRAF2-GSTP1 complex (GO:0097057)|vesicle (GO:0031982)	dinitrosyl-iron complex binding (GO:0035731)|glutathione transferase activity (GO:0004364)|JUN kinase binding (GO:0008432)|kinase regulator activity (GO:0019207)|nitric oxide binding (GO:0070026)|S-nitrosoglutathione binding (GO:0035730)			central_nervous_system(1)|cervix(1)|endometrium(4)|lung(2)|ovary(1)	9					Busulfan(DB01008)|Carboplatin(DB00958)|Chlorambucil(DB00291)|Cisplatin(DB00515)|Clomipramine(DB01242)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	GGCGCCTCAGTGCCCGGCCCA	0.622													C|||	1783	0.35603	0.5182	0.4885	5008	,	,		18460	0.1736		0.337	False		,,,				2504	0.2505				p.S185S		Atlas-SNP	.											.	GSTP1	21	.	0			c.T555C						PASS	.	C		1846,2220		420,1006,607	40.0	43.0	42.0		555	-8.6	0.0	11	dbSNP_52	42	2844,5488		513,1818,1835	no	coding-synonymous	GSTP1	NM_000852.3		933,2824,2442	CC,CT,TT		34.1335,45.4009,37.8287		185/211	67353970	4690,7708	2033	4166	6199	SO:0001819	synonymous_variant	2950	exon7			CCTCAGTGCCCGG	U12472	CCDS41679.1	11q13.2	2014-09-17	2008-07-18		ENSG00000084207	ENSG00000084207	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4638	protein-coding gene	gene with protein product		134660		FAEES3, GST3		1885604, 7587384, 19915149	Standard	NM_000852		Approved	GSTP	uc001omf.3	P09211	OTTHUMG00000137430	ENST00000398606.3:c.555T>C	11.37:g.67353970T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_000852	O00460|Q15690|Q5TZY3	Silent	SNP	ENST00000398606.3	37	CCDS41679.1																																																																																			T|0.688;C|0.312	0.312	strong		0.622	GSTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268504.1	NM_000852	
CXorf30	645090	hgsc.bcm.edu	37	X	36403036	36403036	+	Missense_Mutation	SNP	A	A	G	rs6527569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:36403036A>G	ENST00000378657.4	+	18	2465	c.1817A>G	c.(1816-1818)cAt>cGt	p.H606R	RP11-87M18.2_ENST00000455438.2_RNA	NM_001098843.4	NP_001092313.2	A6PW82	CX030_HUMAN	chromosome X open reading frame 30	606			H -> R (in dbSNP:rs6527569).							breast(1)|lung(2)|stomach(1)	4						GTCCGTCCACATAATTTTGTC	0.393													G|||	1478	0.391523	0.6278	0.1787	3775	,	,		12771	0.1766		0.0994	False		,,,				2504	0.2515				p.H606R		Atlas-SNP	.											.	CXorf30	76	.	0			c.A1817G						PASS	.	G	ARG/HIS	875,334		273,203,126,41,49	89.0	74.0	78.0		1817	-2.7	0.0	X	dbSNP_116	78	315,2076		20,173,102,607,689	yes	missense	CXorf30	NM_001098843.3	29	293,376,228,648,738	GG,GA,G,AA,A		13.1744,27.6261,33.0556	benign	606/634	36403036	1190,2410	692	1591	2283	SO:0001583	missense	645090	exon19			GTCCACATAATTT		CCDS55396.1	Xp21.1	2014-08-07			ENSG00000205081	ENSG00000205081			27298	protein-coding gene	gene with protein product							Standard	NM_001098843		Approved		uc011mkc.3	A6PW82	OTTHUMG00000021353	ENST00000378657.4:c.1817A>G	X.37:g.36403036A>G	ENSP00000367926:p.His606Arg	Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	378	378	1	NM_001098843		Missense_Mutation	SNP	ENST00000378657.4	37	CCDS55396.1	549	0.3309222423146474	216	0.6878980891719745	47	0.1407185628742515	70	0.1394422310756972	53	0.0748587570621469	G	0.110	-1.140005	0.01728	0.723739	0.131744	ENSG00000205081	ENST00000378653;ENST00000378657	T;T	0.36878	1.23;1.23	5.74	-2.74	0.05932	.	0.539359	0.20448	N	0.092151	T	0.00012	0.0000	N	0.03983	-0.305	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31336	-0.9947	9	0.02654	T	1	1.1351	8.7579	0.34656	0.4957:0.0954:0.4089:0.0	rs6527569;rs17320065;rs56558935;rs6527569	606	A6PW82	CX030_HUMAN	R	891;606	ENSP00000367922:H891R;ENSP00000367926:H606R	ENSP00000367922:H891R	H	+	2	0	CXorf30	36312957	0.020000	0.18652	0.000000	0.03702	0.000000	0.00434	0.154000	0.16343	-1.853000	0.01165	-2.075000	0.00382	CAT	A|0.585;0|0.030	.	strong		0.393	CXorf30-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NP_001092313	
ZFP36	7538	hgsc.bcm.edu	37	19	39898521	39898521	+	Missense_Mutation	SNP	C	C	T	rs2229272		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39898521C>T	ENST00000248673.3	+	2	221	c.163C>T	c.(163-165)Cct>Tct	p.P55S	ZFP36_ENST00000594045.1_3'UTR|MIR4530_ENST00000581459.1_RNA|ZFP36_ENST00000597629.1_Missense_Mutation_p.P61S	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	55			P -> S (in dbSNP:rs2229272).		3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of inflammatory response (GO:0050728)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|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)|regulation of tumor necrosis factor production (GO:0032680)|response to starvation (GO:0042594)|RNA destabilization (GO:0050779)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|AU-rich element binding (GO:0017091)|C-C chemokine binding (GO:0019957)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(5)|pancreas(1)	7	all_cancers(60;6.54e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.53e-06)|Ovarian(47;0.0512)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CTCCCGCCTGCCTGGCCGCTC	0.736													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11689	0.0		0.0	False		,,,				2504	0.0				p.P61S	NSCLC(67;1164 1324 12056 21056 30097)	Atlas-SNP	.											.	ZFP36	19	.	0			c.C181T						PASS	.	C	SER/PRO	3,4271		0,3,2134	15.0	19.0	18.0		163	2.8	1.0	19	dbSNP_98	18	0,8330		0,0,4165	no	missense	ZFP36	NM_003407.2	74	0,3,6299	TT,TC,CC		0.0,0.0702,0.0238	benign	55/327	39898521	3,12601	2137	4165	6302	SO:0001583	missense	7538	exon2			CGCCTGCCTGGCC	M63625	CCDS12534.1, CCDS12534.2	19q13.1	2012-11-27	2012-11-27			ENSG00000128016		"""RING-type (C3HC4) zinc fingers"""	12862	protein-coding gene	gene with protein product		190700	"""zinc finger protein 36, C3H type, homolog (mouse)"""			1699942	Standard	NM_003407		Approved	RNF162A, TIS11, G0S24, TTP, NUP475, tristetraprolin	uc002olh.2	P26651		ENST00000248673.3:c.163C>T	19.37:g.39898521C>T	ENSP00000248673:p.Pro55Ser	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_003407	B2RA54	Missense_Mutation	SNP	ENST00000248673.3	37		2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	11.91	1.779652	0.31502	7.02E-4	0.0	ENSG00000128016	ENST00000248673	T	0.18174	2.23	3.91	2.84	0.33178	.	0.070080	0.56097	D	0.000022	T	0.10809	0.0264	N	0.24115	0.695	0.26691	N	0.971344	B	0.20052	0.041	B	0.18871	0.023	T	0.22347	-1.0219	10	0.29301	T	0.29	-3.1484	10.0703	0.42328	0.2111:0.7889:0.0:0.0	rs2229272	55	P26651	TTP_HUMAN	S	55	ENSP00000248673:P55S	ENSP00000248673:P55S	P	+	1	0	ZFP36	44590361	0.842000	0.29525	1.000000	0.80357	0.750000	0.42670	1.235000	0.32671	0.799000	0.34018	0.549000	0.68633	CCT	C|0.998;T|0.002	0.002	strong		0.736	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
ZBTB8OS	339487	hgsc.bcm.edu	37	1	33099637	33099637	+	Silent	SNP	A	A	G	rs704878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:33099637A>G	ENST00000468695.1	-	3	213	c.195T>C	c.(193-195)ttT>ttC	p.F65F	ZBTB8OS_ENST00000373501.2_Silent_p.F53F|ZBTB8OS_ENST00000492007.1_Intron|ZBTB8OS_ENST00000341885.5_Intron	NM_178547.2	NP_848642.1	Q8IWT0	ARCH_HUMAN	zinc finger and BTB domain containing 8 opposite strand	53					tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	extracellular vesicular exosome (GO:0070062)|tRNA-splicing ligase complex (GO:0072669)	metal ion binding (GO:0046872)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CACATTGCTCAAATGCTTCCT	0.413													G|||	1070	0.213658	0.4947	0.2464	5008	,	,		16261	0.1319		0.0368	False		,,,				2504	0.0767				p.F65F		Atlas-SNP	.											.	ZBTB8OS	9	.	0			c.T195C						PASS	.	G		1870,2536	631.5+/-395.7	423,1024,756	118.0	105.0	110.0		195	3.1	1.0	1	dbSNP_86	110	341,8259	804.3+/-407.3	7,327,3966	no	coding-synonymous	ZBTB8OS	NM_178547.2		430,1351,4722	GG,GA,AA		3.9651,42.4421,16.9998		65/180	33099637	2211,10795	2203	4300	6503	SO:0001819	synonymous_variant	339487	exon3			TTGCTCAAATGCT	AY151084	CCDS365.1	1p35.1	2010-09-30			ENSG00000176261	ENSG00000176261			24094	protein-coding gene	gene with protein product	"""archease"""	615891				12477932	Standard	NM_178547		Approved	ARCH	uc001bvp.3	Q8IWT0	OTTHUMG00000007856	ENST00000468695.1:c.195T>C	1.37:g.33099637A>G		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	259	119	0.459459	NM_178547	Q5TGK5|Q6PDA1|Q8IWS9|Q8NEV6|Q8NEV7	Silent	SNP	ENST00000468695.1	37	CCDS365.1	395	0.18086080586080586	219	0.4451219512195122	79	0.21823204419889503	73	0.12762237762237763	24	0.0316622691292876	G	10.31	1.314977	0.23908	0.424421	0.039651	ENSG00000176261	ENST00000436661	.	.	.	5.35	3.06	0.35304	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.8943	10.6057	0.45392	0.8512:0.0:0.1488:0.0	rs704878	.	.	.	R	64	.	.	X	-	1	0	ZBTB8OS	32872224	1.000000	0.71417	0.994000	0.49952	0.976000	0.68499	1.578000	0.36525	0.115000	0.18071	-1.163000	0.01768	TGA	A|0.831;G|0.169	0.169	strong		0.413	ZBTB8OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021669.3	NM_178547	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209190632	209190632	+	Missense_Mutation	SNP	T	T	G	rs999890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	101	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	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	
TBP	6908	hgsc.bcm.edu	37	6	170878793	170878793	+	Silent	SNP	T	T	C	rs1042327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	106	0	0		WXS	Illumina HiSeq	Phase_I	145	143	0.986207	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	
RHPN2	85415	hgsc.bcm.edu	37	19	33498978	33498978	+	Silent	SNP	A	A	G	rs2163807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33498978A>G	ENST00000254260.3	-	7	737	c.702T>C	c.(700-702)tgT>tgC	p.C234C	RHPN2_ENST00000400226.4_Silent_p.C83C	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	234	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)					TCTGCCGATCACACCGGGTCC	0.627													G|||	2100	0.419329	0.4955	0.3228	5008	,	,		13775	0.2272		0.4652	False		,,,				2504	0.5358				p.C234C		Atlas-SNP	.											.	RHPN2	107	.	0			c.T702C						PASS	.	G		2104,2300		495,1114,593	30.0	26.0	27.0		702	-1.8	0.5	19	dbSNP_96	27	3847,4753		866,2115,1319	no	coding-synonymous	RHPN2	NM_033103.4		1361,3229,1912	GG,GA,AA		44.7326,47.7748,45.7628		234/687	33498978	5951,7053	2202	4300	6502	SO:0001819	synonymous_variant	85415	exon7			CCGATCACACCGG	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.702T>C	19.37:g.33498978A>G		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	153	152	0.993464	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Silent	SNP	ENST00000254260.3	37	CCDS12427.1																																																																																			A|0.580;G|0.420	0.420	strong		0.627	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
CSNK1G1	53944	hgsc.bcm.edu	37	15	64508763	64508763	+	Silent	SNP	G	G	A	rs6494466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:64508763G>A	ENST00000303052.7	-	5	865	c.442C>T	c.(442-444)Ctg>Ttg	p.L148L	CSNK1G1_ENST00000607537.1_Silent_p.L148L|CSNK1G1_ENST00000303032.6_Silent_p.L148L|CTD-2116N17.1_ENST00000606793.1_Silent_p.L121L	NM_022048.3	NP_071331.2	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	13						CAACTTACCAGCTGGATGGCT	0.478													A|||	2431	0.485423	0.9614	0.2089	5008	,	,		19212	0.1419		0.2386	False		,,,				2504	0.6462				p.L148L		Atlas-SNP	.											.	CSNK1G1	56	.	0			c.C442T						PASS	.	A		3701,705	294.1+/-283.0	1552,597,54	71.0	59.0	63.0		442	4.0	1.0	15	dbSNP_116	63	2308,6292	705.1+/-405.5	313,1682,2305	no	coding-synonymous	CSNK1G1	NM_022048.3		1865,2279,2359	AA,AG,GG		26.8372,16.0009,46.2018		148/423	64508763	6009,6997	2203	4300	6503	SO:0001819	synonymous_variant	53944	exon5			TTACCAGCTGGAT	AB042562	CCDS10192.2	15q22.1-q22.31	2013-01-17			ENSG00000169118	ENSG00000169118			2454	protein-coding gene	gene with protein product		606274				11124537	Standard	NM_022048		Approved	CK1gamma1	uc002anf.3	Q9HCP0	OTTHUMG00000133019	ENST00000303052.7:c.442C>T	15.37:g.64508763G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_022048	Q5JPH1|Q96AE9|Q9HCP1	Silent	SNP	ENST00000303052.7	37	CCDS10192.2																																																																																			G|0.548;A|0.451	0.451	strong		0.478	CSNK1G1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256605.1	NM_022048	
GAN	8139	hgsc.bcm.edu	37	16	81398635	81398635	+	Silent	SNP	C	C	T	rs2608555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81398635C>T	ENST00000568107.2	+	8	1455	c.1293C>T	c.(1291-1293)taC>taT	p.Y431Y		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	431					cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				GAGGCTCCTACGGAAAGCTTT	0.498													c|||	757	0.151158	0.1778	0.1225	5008	,	,		17016	0.0407		0.2644	False		,,,				2504	0.1329				p.Y431Y	GBM(106;1239 1507 7582 9741 33976)	Atlas-SNP	.											.	GAN	59	.	0			c.C1293T						PASS	.	T		844,3560	333.3+/-302.9	74,696,1432	72.0	68.0	69.0		1293	-0.5	0.4	16	dbSNP_100	69	2144,6456	367.9+/-334.9	267,1610,2423	no	coding-synonymous	GAN	NM_022041.3		341,2306,3855	TT,TC,CC		24.9302,19.1644,22.9775		431/598	81398635	2988,10016	2202	4300	6502	SO:0001819	synonymous_variant	8139	exon8			CTCCTACGGAAAG	AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"""Kelch-like"", ""BTB/POZ domain containing"""	4137	protein-coding gene	gene with protein product	"""kelch-like family member 16"""	605379	"""giant axonal neuropathy (gigaxonin)"""			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.1293C>T	16.37:g.81398635C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	87	35	0.402299	NM_022041		Silent	SNP	ENST00000568107.2	37	CCDS10935.1																																																																																			C|0.800;T|0.200	0.200	strong		0.498	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3		
BIN1	274	hgsc.bcm.edu	37	2	127816695	127816695	+	Silent	SNP	C	C	T	rs2228955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:127816695C>T	ENST00000316724.5	-	11	1305	c.894G>A	c.(892-894)tcG>tcA	p.S298S	BIN1_ENST00000259238.4_Silent_p.S282S|BIN1_ENST00000393041.3_Silent_p.S267S|BIN1_ENST00000357970.3_Silent_p.S298S|BIN1_ENST00000351659.3_Silent_p.S298S|BIN1_ENST00000376113.2_Silent_p.S282S|BIN1_ENST00000393040.3_Silent_p.S267S|BIN1_ENST00000346226.3_Silent_p.S267S|BIN1_ENST00000348750.4_Silent_p.S267S|BIN1_ENST00000466111.1_5'UTR|BIN1_ENST00000409400.1_Silent_p.S267S|BIN1_ENST00000352848.3_Silent_p.S282S	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	298					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)		CATCTGGAGGCGAAGGGCTCT	0.692													c|||	450	0.0898562	0.0189	0.1311	5008	,	,		11348	0.1587		0.0417	False		,,,				2504	0.135				p.S298S		Atlas-SNP	.											BIN1_ENST00000259238,colon,carcinoma,0,2	BIN1	85	2	0			c.G894A						PASS	.	T	,,,,,,,,,	55,4347		1,53,2147	23.0	29.0	27.0		846,894,894,894,846,801,801,801,801,801	-9.9	0.0	2	dbSNP_131	27	169,8421		2,165,4128	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	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	,,,,,,,,,	3,218,6275	TT,TC,CC		1.9674,1.2494,1.7241	,,,,,,,,,	282/455,298/594,298/551,298/507,282/498,267/519,267/483,267/476,267/440,267/410	127816695	224,12768	2201	4295	6496	SO:0001819	synonymous_variant	274	exon11			TGGAGGCGAAGGG	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.894G>A	2.37:g.127816695C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_139345	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			T|0.033;G|0.270;C|0.678;A|0.019	0.033	strong		0.692	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
C3orf20	84077	hgsc.bcm.edu	37	3	14745857	14745857	+	Missense_Mutation	SNP	G	G	A	rs17040196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:14745857G>A	ENST00000253697.3	+	7	1344	c.892G>A	c.(892-894)Gcc>Acc	p.A298T	C3orf20_ENST00000435614.1_Missense_Mutation_p.A176T|C3orf20_ENST00000412910.1_Missense_Mutation_p.A176T	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	298			A -> T (in dbSNP:rs17040196). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						AGCTGAAAGGGCCACATGGAA	0.493													G|||	1888	0.376997	0.4236	0.4553	5008	,	,		20715	0.3155		0.4175	False		,,,				2504	0.2802				p.A298T		Atlas-SNP	.											.	C3orf20	109	.	0			c.G892A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	1898,2508	544.5+/-376.5	425,1048,730	77.0	79.0	78.0		526,526,892	-3.0	0.0	3	dbSNP_123	78	3657,4943	526.6+/-381.0	788,2081,1431	yes	missense,missense,missense	C3orf20	NM_001184957.1,NM_001184958.1,NM_032137.4	58,58,58	1213,3129,2161	AA,AG,GG		42.5233,43.0776,42.7111	benign,benign,benign	176/783,176/783,298/905	14745857	5555,7451	2203	4300	6503	SO:0001583	missense	84077	exon7			GAAAGGGCCACAT	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.892G>A	3.37:g.14745857G>A	ENSP00000253697:p.Ala298Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	36	0.387097	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	885	0.4052197802197802	231	0.4695121951219512	157	0.43370165745856354	179	0.3129370629370629	318	0.41952506596306066	G	0.390	-0.923774	0.02377	0.430776	0.425233	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.08008	3.43;3.14;3.14	4.91	-3.04	0.05412	.	1.522830	0.03923	N	0.283896	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.16396	0.017	B	0.14578	0.011	T	0.46898	-0.9158	9	0.13108	T	0.6	-1.9366	10.7852	0.46401	0.6556:0.0:0.3444:0.0	rs17040196;rs17852773;rs52799567;rs59251381;rs17040196	298	Q8ND61	CC020_HUMAN	T	298;176;176	ENSP00000253697:A298T;ENSP00000402933:A176T;ENSP00000396081:A176T	ENSP00000253697:A298T	A	+	1	0	C3orf20	14720861	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	-0.499000	0.06413	-0.525000	0.06391	-0.225000	0.12378	GCC	G|0.588;A|0.412	0.412	strong		0.493	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	
SLC2A2	6514	hgsc.bcm.edu	37	3	170732300	170732300	+	Missense_Mutation	SNP	G	G	A	rs5400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:170732300G>A	ENST00000314251.3	-	3	408	c.329C>T	c.(328-330)aCt>aTt	p.T110I	SLC2A2_ENST00000382808.4_Intron	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	110			T -> I (in dbSNP:rs5400). {ECO:0000269|PubMed:7593414, ECO:0000269|PubMed:8063045}.		carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	GAATGATGCAGTCATTCCACC	0.448													A|||	1078	0.215256	0.4894	0.1715	5008	,	,		18629	0.0159		0.1352	False		,,,				2504	0.1636				p.T110I		Atlas-SNP	.											.	SLC2A2	71	.	0			c.C329T	GRCh37	CM941277	SLC2A2	M	rs5400	PASS	.	A	ILE/THR	1970,2436	620.0+/-393.5	446,1078,679	175.0	160.0	165.0		329	6.1	1.0	3	dbSNP_52	165	1147,7453	766.6+/-407.6	71,1005,3224	yes	missense	SLC2A2	NM_000340.1	89	517,2083,3903	AA,AG,GG		13.3372,44.7118,23.9659	benign	110/525	170732300	3117,9889	2203	4300	6503	SO:0001583	missense	6514	exon3			GATGCAGTCATTC	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.329C>T	3.37:g.170732300G>A	ENSP00000323568:p.Thr110Ile	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	37	CCDS3215.1	411	0.18818681318681318	228	0.4634146341463415	70	0.19337016574585636	9	0.015734265734265736	104	0.13720316622691292	A	8.575	0.880856	0.17467	0.447118	0.133372	ENSG00000163581	ENST00000314251	T	0.70399	-0.48	6.08	6.08	0.98989	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.399027	0.29218	N	0.012794	T	0.00012	0.0000	N	0.00016	-2.86	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41945	-0.9480	9	0.02654	T	1	.	12.1128	0.53848	0.9328:0.0:0.0672:0.0	rs5400;rs52828515;rs61638260;rs5400	110	P11168	GTR2_HUMAN	I	110	ENSP00000323568:T110I	ENSP00000323568:T110I	T	-	2	0	SLC2A2	172214994	0.955000	0.32602	0.981000	0.43875	0.991000	0.79684	7.036000	0.76524	1.126000	0.42016	-0.254000	0.11334	ACT	G|0.776;A|0.224	0.224	strong		0.448	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
OR7A10	390892	hgsc.bcm.edu	37	19	14951889	14951889	+	Silent	SNP	A	A	G	rs3752194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	95	0	0		WXS	Illumina HiSeq	Phase_I	91	35	0.384615	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	
CEP170	9859	hgsc.bcm.edu	37	1	243328226	243328226	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:243328226A>G	ENST00000366542.1	-	13	3087	c.3036T>C	c.(3034-3036)agT>agC	p.S1012S	CEP170_ENST00000366544.1_Silent_p.S914S|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000366543.1_Silent_p.S914S|CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000437499.1_RNA	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	1012	Targeting to microtubules.					centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			TTATTCTCCCACTGGACTGAA	0.408																																					p.S1012S		Atlas-SNP	.											.	CEP170	153	.	0			c.T3036C						PASS	.						157.0	139.0	145.0					1																	243328226		1909	4120	6029	SO:0001819	synonymous_variant	9859	exon13			TCTCCCACTGGAC	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.3036T>C	1.37:g.243328226A>G		Somatic	527	0	0		WXS	Illumina HiSeq	Phase_I	616	236	0.383117	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Silent	SNP	ENST00000366542.1	37	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	A	1.317	-0.600452	0.03744	.	.	ENSG00000143702	ENST00000336415	.	.	.	4.37	4.37	0.52481	.	.	.	.	.	T	0.64125	0.2570	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63567	-0.6608	4	.	.	.	-11.7439	12.8963	0.58101	1.0:0.0:0.0:0.0	.	.	.	.	A	976	.	.	V	-	2	0	CEP170	241394849	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	1.938000	0.40203	1.823000	0.53134	0.454000	0.30748	GTG	.	.	none		0.408	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
LRRC55	219527	hgsc.bcm.edu	37	11	56949529	56949529	+	Silent	SNP	C	C	T	rs80306837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56949529C>T	ENST00000497933.1	+	1	309	c.162C>T	c.(160-162)ccC>ccT	p.P54P		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	24	LRRNT.				ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						TTCCCTGGCCCGGGCCACCCC	0.632													C|||	184	0.0367412	0.1339	0.0101	5008	,	,		18733	0.0		0.0	False		,,,				2504	0.0				p.P54P		Atlas-SNP	.											.	LRRC55	52	.	0			c.C162T						PASS	.	C		516,3886	234.9+/-247.6	28,460,1713	43.0	38.0	40.0		162	-11.3	0.8	11	dbSNP_131	40	4,8588	3.7+/-12.6	0,4,4292	no	coding-synonymous	LRRC55	NM_001005210.2		28,464,6005	TT,TC,CC		0.0466,11.7219,4.0018		54/342	56949529	520,12474	2201	4296	6497	SO:0001819	synonymous_variant	219527	exon1			CTGGCCCGGGCCA		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.162C>T	11.37:g.56949529C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_001005210	A7E2U7|B2RN81	Silent	SNP	ENST00000497933.1	37	CCDS31539.1																																																																																			C|0.952;T|0.048	0.048	strong		0.632	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210	
NCF4	4689	hgsc.bcm.edu	37	22	37273742	37273742	+	Silent	SNP	G	G	A	rs11552115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37273742G>A	ENST00000248899.6	+	10	1081	c.897G>A	c.(895-897)tcG>tcA	p.S299S	NCF4_ENST00000397147.4_3'UTR	NM_000631.4	NP_000622.2	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4, 40kDa	299	OPR.				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)|immune response (GO:0006955)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of catalytic activity (GO:0043085)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|membrane (GO:0016020)|NADPH oxidase complex (GO:0043020)|phagolysosome (GO:0032010)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein dimerization activity (GO:0046983)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16					Dextromethorphan(DB00514)	GGCTGCTGTCGGATGAGGACG	0.587													G|||	674	0.134585	0.2655	0.1398	5008	,	,		17155	0.0645		0.0656	False		,,,				2504	0.0971				p.S299S		Atlas-SNP	.											.	NCF4	66	.	0			c.G897A						PASS	.	G	,	958,3448	361.1+/-315.5	94,770,1339	59.0	53.0	55.0		897,	-10.9	0.1	22	dbSNP_120	55	592,8008	157.5+/-211.1	21,550,3729	no	coding-synonymous,utr-3	NCF4	NM_000631.4,NM_013416.3	,	115,1320,5068	AA,AG,GG		6.8837,21.7431,11.9176	,	299/340,	37273742	1550,11456	2203	4300	6503	SO:0001819	synonymous_variant	4689	exon10			GCTGTCGGATGAG	X77094	CCDS13934.1, CCDS13935.1	22q13.1	2014-09-17	2002-08-29		ENSG00000100365	ENSG00000100365			7662	protein-coding gene	gene with protein product	"""neutrophil NADPH oxidase factor 4"""	601488	"""neutrophil cytosolic factor 4 (40kD)"""			8839867	Standard	NM_013416		Approved	p40phox, SH3PXD4	uc003apy.4	Q15080	OTTHUMG00000150548	ENST00000248899.6:c.897G>A	22.37:g.37273742G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	NM_000631	A8K4F9|O60808|Q86U56|Q9BU98|Q9NP45	Silent	SNP	ENST00000248899.6	37	CCDS13934.1																																																																																			G|0.883;A|0.117	0.117	strong		0.587	NCF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318863.1	NM_000631	
DUSP13	51207	hgsc.bcm.edu	37	10	76867899	76867899	+	Missense_Mutation	SNP	T	T	C	rs7912300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76867899T>C	ENST00000372702.3	-	2	281	c.218A>G	c.(217-219)aAg>aGg	p.K73R	DUSP13_ENST00000491677.2_5'UTR|DUSP13_ENST00000607131.1_Intron|DUSP13_ENST00000372700.3_Intron|DUSP13_ENST00000607009.1_5'UTR			Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	81					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)					GTAGAGGCCCTTGTGGGCGGC	0.632													C|||	2271	0.453474	0.5348	0.4452	5008	,	,		18611	0.6438		0.2823	False		,,,				2504	0.3292				p.K73R	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											.	DUSP13	82	.	0			c.A218G						PASS	.	C	ARG/LYS,,	1971,2081		500,971,555	48.0	56.0	53.0		218,,	4.9	1.0	10	dbSNP_116	53	2211,6115		294,1623,2246	yes	missense,intron,intron	DUSP13	NM_001007271.1,NM_001007272.1,NM_001007273.1	26,,	794,2594,2801	CC,CT,TT		26.5554,48.6426,33.7857	,,	73/189,,	76867899	4182,8196	2026	4163	6189	SO:0001583	missense	51207	exon2			AGGCCCTTGTGGG	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	ENST00000372702.3:c.218A>G	10.37:g.76867899T>C	ENSP00000361787:p.Lys73Arg	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	138	57	0.413043	NM_001007271	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Missense_Mutation	SNP	ENST00000372702.3	37	CCDS53542.1	980	0.44871794871794873	257	0.5223577235772358	134	0.3701657458563536	362	0.6328671328671329	227	0.2994722955145119	C	24.0	4.482367	0.84747	0.486426	0.265554	ENSG00000079393	ENST00000372702	D	0.85629	-2.01	4.93	4.93	0.64822	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	.	.	.	.	T	0.00012	0.0000	N	0.05306	-0.075	0.09310	P	1.0	B	0.10296	0.003	B	0.10450	0.005	T	0.47355	-0.9124	8	0.42905	T	0.14	.	12.5486	0.56214	0.0:0.9181:0.0:0.0819	rs7912300;rs57157460;rs7912300	73	Q6B8I1	MDSP_HUMAN	R	73	ENSP00000361787:K73R	ENSP00000361787:K73R	K	-	2	0	DUSP13	76537905	0.996000	0.38824	0.994000	0.49952	0.992000	0.81027	5.371000	0.66150	1.312000	0.45043	-0.119000	0.15052	AAG	T|0.574;C|0.426	0.426	strong		0.632	DUSP13-012	KNOWN	NMD_exception|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401503.3		
WDR81	124997	hgsc.bcm.edu	37	17	1637458	1637458	+	Silent	SNP	G	G	A	rs587780506|rs398088774|rs8065251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1637458G>A	ENST00000409644.1	+	7	5127	c.5127G>A	c.(5125-5127)ccG>ccA	p.P1709P	WDR81_ENST00000545662.1_Silent_p.P340P|WDR81_ENST00000437219.2_Silent_p.P506P|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Silent_p.P658P|WDR81_ENST00000419248.1_Silent_p.P482P|WDR81_ENST00000446363.1_Silent_p.P348P	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1709					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TTGAGGCCCCGCAGCACGTGG	0.672													G|||	1236	0.246805	0.2519	0.2061	5008	,	,		15192	0.1855		0.1978	False		,,,				2504	0.3824				p.P1709P		Atlas-SNP	.											WDR81_ENST00000437219,NS,carcinoma,0,3	WDR81	180	3	0			c.G5127A						PASS	.	G	,,,	1057,3347		118,821,1263	30.0	32.0	31.0		1518,5127,1446,1974	-8.9	0.1	17	dbSNP_116	31	1802,6794		188,1426,2684	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	306,2247,3947	AA,AG,GG		20.9632,24.0009,21.9923	,,,	506/739,1709/1942,482/715,658/891	1637458	2859,10141	2202	4298	6500	SO:0001819	synonymous_variant	124997	exon7			GGCCCCGCAGCAC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.5127G>A	17.37:g.1637458G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			G|0.782;A|0.218	0.218	strong		0.672	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
MUC17	140453	hgsc.bcm.edu	37	7	100680939	100680939	+	Missense_Mutation	SNP	C	C	A	rs36120435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100680939C>A	ENST00000306151.4	+	3	6306	c.6242C>A	c.(6241-6243)gCc>gAc	p.A2081D		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2081	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)					TCTACTGAAGCCAGTTCATCT	0.498													C|||	612	0.122204	0.1997	0.0821	5008	,	,		26174	0.0665		0.1173	False		,,,				2504	0.1084				p.A2081D		Atlas-SNP	.											.	MUC17	804	.	0			c.C6242A						PASS	.	C	ASP/ALA	775,3631	314.9+/-293.9	64,647,1492	172.0	170.0	171.0		6242	-1.2	0.0	7	dbSNP_126	171	983,7617	213.1+/-253.2	56,871,3373	no	missense	MUC17	NM_001040105.1	126	120,1518,4865	AA,AC,CC		11.4302,17.5897,13.5168	benign	2081/4494	100680939	1758,11248	2203	4300	6503	SO:0001583	missense	140453	exon3			CTGAAGCCAGTTC	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.6242C>A	7.37:g.100680939C>A	ENSP00000302716:p.Ala2081Asp	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	220	0.10073260073260074	70	0.14227642276422764	34	0.09392265193370165	29	0.050699300699300696	87	0.11477572559366754	c	3.462	-0.109758	0.06924	0.175897	0.114302	ENSG00000169876	ENST00000306151	T	0.02787	4.16	0.589	-1.18	0.09617	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.49483	P	2.0900000000001473E-4	B	0.14438	0.01	B	0.08055	0.003	T	0.46735	-0.9170	8	0.21540	T	0.41	.	5.2138	0.15332	0.3336:0.6663:0.0:0.0	.	2081	Q685J3	MUC17_HUMAN	D	2081	ENSP00000302716:A2081D	ENSP00000302716:A2081D	A	+	2	0	MUC17	100467659	0.000000	0.05858	0.003000	0.11579	0.020000	0.10135	-0.240000	0.08952	-0.374000	0.07967	0.134000	0.15878	GCC	C|0.880;A|0.120	0.120	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
S1PR1	1901	hgsc.bcm.edu	37	1	101704772	101704772	+	Silent	SNP	C	C	A	rs150493209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:101704772C>A	ENST00000305352.6	+	2	607	c.232C>A	c.(232-234)Cga>Aga	p.R78R	RP4-575N6.4_ENST00000432195.1_RNA|S1PR1_ENST00000475821.1_3'UTR	NM_001400.4	NP_001391.2	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1	78					actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|brain development (GO:0007420)|cardiac muscle tissue growth involved in heart morphogenesis (GO:0003245)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|chemotaxis (GO:0006935)|endothelial cell differentiation (GO:0045446)|G-protein coupled receptor signaling pathway (GO:0007186)|heart trabecula morphogenesis (GO:0061384)|lamellipodium assembly (GO:0030032)|negative regulation of stress fiber assembly (GO:0051497)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bone mineralization (GO:0030500)|regulation of bone resorption (GO:0045124)|regulation of cell adhesion (GO:0030155)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell migration (GO:0072678)|transmission of nerve impulse (GO:0019226)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|sphingolipid binding (GO:0046625)|sphingosine-1-phosphate receptor activity (GO:0038036)			NS(1)|autonomic_ganglia(1)|breast(1)|large_intestine(7)|lung(23)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	43						GAAATTCCACCGACCCATGTA	0.473											OREG0013620	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3	0.000599042	0.0023	0.0	5008	,	,		20524	0.0		0.0	False		,,,				2504	0.0				p.R78R		Atlas-SNP	.											.	S1PR1	87	.	0			c.C232A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	113.0	115.0	114.0		232	5.0	1.0	1	dbSNP_134	114	0,8600		0,0,4300	no	coding-synonymous	S1PR1	NM_001400.4		0,5,6498	AA,AC,CC		0.0,0.1135,0.0384		78/383	101704772	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	1901	exon2			TTCCACCGACCCA	M31210	CCDS777.1	1p21	2012-08-08	2008-04-30	2008-04-30	ENSG00000170989	ENSG00000170989		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"", ""CD molecules"""	3165	protein-coding gene	gene with protein product		601974	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 1"""	EDG1		2160972, 9488656	Standard	NM_001400		Approved	edg-1, D1S3362, CD363	uc001dud.2	P21453	OTTHUMG00000010835	ENST00000305352.6:c.232C>A	1.37:g.101704772C>A		Somatic	164	0	0	1360	WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_001400	D3DT66|Q9BYY4|Q9NYN8	Silent	SNP	ENST00000305352.6	37	CCDS777.1																																																																																			C|1.000;A|0.000	0.000	strong		0.473	S1PR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029908.1	NM_001400	
NPR2	4882	hgsc.bcm.edu	37	9	35802583	35802583	+	Silent	SNP	C	C	T	rs5812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35802583C>T	ENST00000342694.2	+	11	2049	c.1794C>T	c.(1792-1794)taC>taT	p.Y598Y		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	598	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	TCACTGAATACTGTCCTCGTG	0.468													T|||	1565	0.3125	0.4962	0.2334	5008	,	,		20745	0.3819		0.2008	False		,,,				2504	0.1636				p.Y598Y		Atlas-SNP	.											.	NPR2	162	.	0			c.C1794T						PASS	.	T		2011,2395	615.3+/-392.5	468,1075,660	111.0	100.0	104.0		1794	3.1	1.0	9	dbSNP_52	104	1736,6864	736.2+/-407.0	167,1402,2731	no	coding-synonymous	NPR2	NM_003995.3		635,2477,3391	TT,TC,CC		20.186,45.6423,28.8098		598/1048	35802583	3747,9259	2203	4300	6503	SO:0001819	synonymous_variant	4882	exon11			TGAATACTGTCCT	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.1794C>T	9.37:g.35802583C>T		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	196	195	0.994898	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1																																																																																			C|0.695;T|0.305	0.305	strong		0.468	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
CYFIP1	23191	hgsc.bcm.edu	37	15	22939192	22939192	+	Silent	SNP	G	G	A	rs11633474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:22939192G>A	ENST00000313077.7	+	10	1043	c.918G>A	c.(916-918)ccG>ccA	p.P306P	CYFIP1_ENST00000560848.1_Silent_p.P306P	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		AGGTGGTTCCGCTATTTGGGG	0.408													g|||	1653	0.330072	0.3457	0.4741	5008	,	,		15404	0.1141		0.505	False		,,,				2504	0.2495				p.P306P		Atlas-SNP	.											CYFIP1,NS,carcinoma,0,1	CYFIP1	159	1	0			c.G918A						PASS	.	A		1543,2863	482.8+/-359.5	263,1017,923	132.0	142.0	138.0		918	-11.3	0.1	15	dbSNP_120	138	4258,4342	574.3+/-390.0	1083,2092,1125	no	coding-synonymous	CYFIP1	NM_014608.2		1346,3109,2048	AA,AG,GG		49.5116,35.0204,44.6025		306/1254	22939192	5801,7205	2203	4300	6503	SO:0001819	synonymous_variant	23191	exon10			GGTTCCGCTATTT	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.918G>A	15.37:g.22939192G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	176	80	0.454545	NM_014608		Silent	SNP	ENST00000313077.7	37	CCDS10009.1																																																																																			G|0.574;A|0.426	0.426	strong		0.408	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
ZBED2	79413	hgsc.bcm.edu	37	3	111312965	111312965	+	Silent	SNP	A	A	T	rs34083626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:111312965A>T	ENST00000317012.4	-	2	1092	c.84T>A	c.(82-84)atT>atA	p.I28I	CD96_ENST00000352690.4_Intron|CD96_ENST00000438817.2_Intron|CD96_ENST00000283285.5_Intron	NM_024508.4	NP_078784.2	Q9BTP6	ZBED2_HUMAN	zinc finger, BED-type containing 2	28							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(1)|skin(2)	6						CTGTCTCACTAATCTCTTCCT	0.517													A|||	266	0.053115	0.1891	0.0187	5008	,	,		14454	0.0		0.003	False		,,,				2504	0.0				p.I28I		Atlas-SNP	.											.	ZBED2	22	.	0			c.T84A						PASS	.	A	,,	642,3764	274.6+/-272.0	38,566,1599	268.0	221.0	237.0		,84,	0.4	0.0	3	dbSNP_126	237	9,8591	5.7+/-21.5	0,9,4291	no	intron,coding-synonymous,intron	CD96,ZBED2	NM_005816.4,NM_024508.4,NM_198196.2	,,	38,575,5890	TT,TA,AA		0.1047,14.571,5.0054	,,	,28/219,	111312965	651,12355	2203	4300	6503	SO:0001819	synonymous_variant	79413	exon2			CTCACTAATCTCT	BC003536	CCDS2960.2	3p13-q13.2	2013-05-03			ENSG00000177494	ENSG00000177494		"""Zinc fingers, BED-type"""	20710	protein-coding gene	gene with protein product		615246				23533661	Standard	NM_024508		Approved	MGC10796	uc003dxy.3	Q9BTP6	OTTHUMG00000074061	ENST00000317012.4:c.84T>A	3.37:g.111312965A>T		Somatic	265	1	0.00377358		WXS	Illumina HiSeq	Phase_I	304	136	0.447368	NM_024508	D3DN62	Silent	SNP	ENST00000317012.4	37	CCDS2960.2																																																																																			A|0.950;T|0.050	0.050	strong		0.517	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	NM_024508	
PPAP2B	8613	hgsc.bcm.edu	37	1	57002627	57002627	+	Splice_Site	SNP	C	C	T	rs1136164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57002627C>T	ENST00000371250.3	-	2	848	c.297G>A	c.(295-297)gcG>gcA	p.A99A		NM_003713.4	NP_003704.3	O14495	LPP3_HUMAN	phosphatidic acid phosphatase type 2B	99					Bergmann glial cell differentiation (GO:0060020)|blood vessel development (GO:0001568)|canonical Wnt signaling pathway involved in positive regulation of cell-cell adhesion (GO:0044329)|canonical Wnt signaling pathway involved in positive regulation of endothelial cell migration (GO:0044328)|canonical Wnt signaling pathway involved in positive regulation of wound healing (GO:0044330)|dephosphorylation (GO:0016311)|gastrulation with mouth forming second (GO:0001702)|germ cell migration (GO:0008354)|homotypic cell-cell adhesion (GO:0034109)|lipid metabolic process (GO:0006629)|negative regulation of protein phosphorylation (GO:0001933)|phospholipid metabolic process (GO:0006644)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of sphingolipid mediated signaling pathway (GO:1902068)|regulation of Wnt signaling pathway (GO:0030111)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)|sphingosine-1-phosphate phosphatase activity (GO:0042392)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						GGACACTTACCGCGAGGATGG	0.453													C|||	548	0.109425	0.2337	0.0159	5008	,	,		20425	0.1756		0.0119	False		,,,				2504	0.0399				p.A99A		Atlas-SNP	.											.	PPAP2B	30	.	0			c.G297A						PASS	.	C		803,3603	322.3+/-297.6	69,665,1469	200.0	168.0	179.0		297	5.0	1.0	1	dbSNP_129	179	146,8454	71.6+/-134.2	2,142,4156	yes	coding-synonymous-near-splice	PPAP2B	NM_003713.4		71,807,5625	TT,TC,CC		1.6977,18.2251,7.2966		99/312	57002627	949,12057	2203	4300	6503	SO:0001630	splice_region_variant	8613	exon2			ACTTACCGCGAGG	AB000889	CCDS604.1	1p32.2	2009-05-27			ENSG00000162407	ENSG00000162407	3.1.3.4		9229	protein-coding gene	gene with protein product		607125				9305923	Standard	NM_003713		Approved	PAP-2b, LPP3	uc001cyj.2	O14495	OTTHUMG00000008160	ENST00000371250.3:c.297+1G>A	1.37:g.57002627C>T		Somatic	265	1	0.00377358		WXS	Illumina HiSeq	Phase_I	260	113	0.434615	NM_003713	B2R651|D3DQ52|Q5U0F7|Q96GW0|Q99782	Silent	SNP	ENST00000371250.3	37	CCDS604.1																																																																																			C|0.922;T|0.078	0.078	strong		0.453	PPAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022334.2	NM_003713	Silent
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25266547	25266547	+	Missense_Mutation	SNP	C	C	A	rs113273135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:25266547C>A	ENST00000328086.7	-	2	1369	c.566G>T	c.(565-567)cGt>cTt	p.R189L		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	189					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		TAAGGGCCGACGTTCTCGCTT	0.602													C|||	70	0.0139776	0.0477	0.0072	5008	,	,		17212	0.0		0.002	False		,,,				2504	0.0				p.R189L		Atlas-SNP	.											ZKSCAN2,NS,carcinoma,-1,1	ZKSCAN2	90	1	0			c.G566T						PASS	.	C	LEU/ARG	136,4258	98.0+/-136.7	2,132,2063	114.0	99.0	104.0		566	-5.2	0.0	16	dbSNP_132	104	8,8592	5.0+/-18.6	1,6,4293	yes	missense	ZKSCAN2	NM_001012981.4	102	3,138,6356	AA,AC,CC		0.093,3.0951,1.1082	benign	189/968	25266547	144,12850	2197	4300	6497	SO:0001583	missense	342357	exon2			GGCCGACGTTCTC	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	25677	protein-coding gene	gene with protein product			"""zinc finger protein 694"""	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.566G>T	16.37:g.25266547C>A	ENSP00000331626:p.Arg189Leu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	101	58	0.574257	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	24	0.01098901098901099	19	0.03861788617886179	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	0.541	-0.853648	0.02630	0.030951	9.3E-4	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.14144	2.53	5.3	-5.17	0.02849	.	1.318600	0.04683	N	0.412758	T	0.00608	0.0020	N	0.00621	-1.32	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.36456	-0.9747	10	0.12766	T	0.61	0.0	0.7766	0.01033	0.3527:0.1598:0.1131:0.3743	.	189;189	Q63HK3-2;Q63HK3	.;ZKSC2_HUMAN	L	189	ENSP00000331626:R189L	ENSP00000331626:R189L	R	-	2	0	ZKSCAN2	25174048	0.000000	0.05858	0.000000	0.03702	0.100000	0.18952	-0.679000	0.05203	-0.480000	0.06803	-1.467000	0.01014	CGT	C|0.991;A|0.009	0.009	strong		0.602	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
DOCK2	1794	hgsc.bcm.edu	37	5	169111345	169111345	+	Missense_Mutation	SNP	C	C	T	rs78243868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:169111345C>T	ENST00000256935.8	+	8	832	c.752C>T	c.(751-753)aCg>aTg	p.T251M		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	251					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)			AACAAGCAAACGGTCATAAGG	0.488													C|||	51	0.0101837	0.0174	0.0072	5008	,	,		20396	0.0		0.0089	False		,,,				2504	0.0143				p.T251M		Atlas-SNP	.											.	DOCK2	389	.	0			c.C752T						PASS	.	C	MET/THR	103,4303	81.9+/-120.4	1,101,2101	161.0	145.0	150.0		752	-8.5	0.0	5	dbSNP_132	150	73,8527	43.6+/-101.6	0,73,4227	yes	missense	DOCK2	NM_004946.2	81	1,174,6328	TT,TC,CC		0.8488,2.3377,1.3532	benign	251/1831	169111345	176,12830	2203	4300	6503	SO:0001583	missense	1794	exon8			AGCAAACGGTCAT	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.752C>T	5.37:g.169111345C>T	ENSP00000256935:p.Thr251Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	18	0.008241758241758242	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	10.10	1.258109	0.23051	0.023377	0.008488	ENSG00000134516	ENST00000256935	T	0.41758	0.99	5.43	-8.5	0.00927	.	0.745442	0.13119	N	0.412363	T	0.20007	0.0481	L	0.51422	1.61	0.48135	D	0.999598	B	0.12013	0.005	B	0.04013	0.001	T	0.04153	-1.0973	10	0.48119	T	0.1	.	19.7031	0.96063	0.0:0.725:0.0:0.275	.	251	Q92608	DOCK2_HUMAN	M	251	ENSP00000256935:T251M	ENSP00000256935:T251M	T	+	2	0	DOCK2	169043923	0.000000	0.05858	0.034000	0.17996	0.915000	0.54546	-1.014000	0.03641	-1.577000	0.01650	-0.768000	0.03414	ACG	C|0.987;T|0.013	0.013	strong		0.488	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
HSD3B1	3283	hgsc.bcm.edu	37	1	120057002	120057002	+	Missense_Mutation	SNP	T	T	C	rs6205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120057002T>C	ENST00000369413.3	+	4	1001	c.856T>C	c.(856-858)Ttt>Ctt	p.F286L	HSD3B1_ENST00000235547.6_Missense_Mutation_p.F288L|HSD3B1_ENST00000528909.1_Missense_Mutation_p.F286L			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	286			F -> L (in dbSNP:rs6205). {ECO:0000269|PubMed:10391209}.		androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	CAGATGGAGCTTTCCTTTATC	0.473													C|||	790	0.157748	0.4546	0.0793	5008	,	,		20929	0.0595		0.007	False		,,,				2504	0.0685				p.F286L		Atlas-SNP	.											.	HSD3B1	53	.	0			c.T856C						PASS	.	C	LEU/PHE	1681,2725	650.5+/-399.1	322,1037,844	97.0	101.0	100.0		856	-0.2	0.0	1	dbSNP_52	100	33,8567	817.2+/-406.9	0,33,4267	no	missense	HSD3B1	NM_000862.2	22	322,1070,5111	CC,CT,TT		0.3837,38.1525,13.1785	benign	286/374	120057002	1714,11292	2203	4300	6503	SO:0001583	missense	3283	exon4			TGGAGCTTTCCTT	S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5217	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 1"""	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.856T>C	1.37:g.120057002T>C	ENSP00000358421:p.Phe286Leu	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	252	111	0.440476	NM_000862	A8K691|Q14545|Q8IV65	Missense_Mutation	SNP	ENST00000369413.3	37	CCDS903.1	275	0.1259157509157509	220	0.44715447154471544	26	0.0718232044198895	28	0.04895104895104895	1	0.0013192612137203166	C	0	-2.776107	0.00080	0.381525	0.003837	ENSG00000203857	ENST00000369413;ENST00000235547;ENST00000528909	T;T;T	0.58797	0.31;0.31;0.31	3.26	-0.227	0.13102	3-beta hydroxysteroid dehydrogenase/isomerase (1);	0.940200	0.08995	N	0.863819	T	0.02193	0.0068	N	0.00017	-2.84	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.33675	-0.9859	9	0.02654	T	1	-32.4736	3.9526	0.09375	0.3151:0.4743:0.0:0.2106	rs6205;rs52822637;rs61488575;rs6205	288;286	Q5TDG2;P14060	.;3BHS1_HUMAN	L	286;288;286	ENSP00000358421:F286L;ENSP00000235547:F288L;ENSP00000432268:F286L	ENSP00000235547:F288L	F	+	1	0	HSD3B1	119858525	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.805000	0.04530	-0.080000	0.12685	-1.993000	0.00448	TTT	T|0.859;C|0.141	0.141	strong		0.473	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862	
RYR1	6261	hgsc.bcm.edu	37	19	39068641	39068641	+	Silent	SNP	A	A	C	rs1468571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39068641A>C	ENST00000359596.3	+	98	14256	c.14256A>C	c.(14254-14256)acA>acC	p.T4752T	RYR1_ENST00000360985.3_Silent_p.T4747T|RYR1_ENST00000355481.4_Silent_p.T4747T			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4752					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)	TAGAGATCACAGCCCACAATG	0.637													C|||	771	0.153954	0.3427	0.1527	5008	,	,		15062	0.0952		0.0239	False		,,,				2504	0.0941				p.T4752T		Atlas-SNP	.											.	RYR1	708	.	0			c.A14256C						PASS	.	C	,	1243,3163	704.4+/-407.1	183,877,1143	66.0	61.0	62.0		14256,14241	-10.2	0.0	19	dbSNP_88	62	170,8430	811.6+/-407.1	3,164,4133	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	186,1041,5276	CC,CA,AA		1.9767,28.2115,10.8642	,	4752/5039,4747/5034	39068641	1413,11593	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon98			GATCACAGCCCAC	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.14256A>C	19.37:g.39068641A>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	80	48	0.6	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			A|0.871;C|0.128	0.128	strong		0.637	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
PSMB10	5699	hgsc.bcm.edu	37	16	67969531	67969531	+	Silent	SNP	A	A	G	rs14178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67969531A>G	ENST00000358514.4	-	5	790	c.453T>C	c.(451-453)ggT>ggC	p.G151G	CTC-479C5.12_ENST00000573493.1_Missense_Mutation_p.V5A	NM_002801.3	NP_002792.1	P40306	PSB10_HUMAN	proteasome (prosome, macropain) subunit, beta type, 10	151					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)|cell morphogenesis (GO:0000902)|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)|humoral immune response (GO:0006959)|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)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			NS(2)|endometrium(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)	Carfilzomib(DB08889)	GGGGATGCACACCGTAGAGCT	0.652													G|||	734	0.146565	0.4312	0.0793	5008	,	,		17573	0.006		0.0457	False		,,,				2504	0.0583				p.G151G		Atlas-SNP	.											PSMB10,colon,carcinoma,0,1	PSMB10	19	1	0			c.T453C						scavenged	.	G		1633,2763	658.5+/-400.4	312,1009,877	111.0	112.0	112.0		453	-5.4	0.0	16	dbSNP_52	112	429,8171	799.3+/-407.4	13,403,3884	no	coding-synonymous	PSMB10	NM_002801.3		325,1412,4761	GG,GA,AA		4.9884,37.1474,15.8664		151/274	67969531	2062,10934	2198	4300	6498	SO:0001819	synonymous_variant	5699	exon5			ATGCACACCGTAG	Y13640	CCDS10853.1	16q22.1	2008-02-05			ENSG00000205220	ENSG00000205220		"""Proteasome (prosome, macropain) subunits"""	9538	protein-coding gene	gene with protein product		176847		MECL1		8268911	Standard	NM_002801		Approved	LMP10, MGC1665, beta2i	uc002eux.2	P40306	OTTHUMG00000137553	ENST00000358514.4:c.453T>C	16.37:g.67969531A>G		Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	126	54	0.428571	NM_002801	B2R5J4|Q5U098	Silent	SNP	ENST00000358514.4	37	CCDS10853.1																																																																																			A|0.831;G|0.169	0.169	strong		0.652	PSMB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268887.1	NM_002801	
NRAP	4892	hgsc.bcm.edu	37	10	115393948	115393948	+	Missense_Mutation	SNP	C	C	T	rs11196400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115393948C>T	ENST00000359988.3	-	15	1694	c.1450G>A	c.(1450-1452)Gac>Aac	p.D484N	NRAP_ENST00000369360.3_Missense_Mutation_p.D449N|NRAP_ENST00000369358.4_Missense_Mutation_p.D484N|NRAP_ENST00000360478.3_Missense_Mutation_p.D449N	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)		TTCAACTTGTCGATGCTCTGC	0.463													C|||	962	0.192093	0.3094	0.1124	5008	,	,		19731	0.1677		0.1382	False		,,,				2504	0.1708				p.D484N		Atlas-SNP	.											.	NRAP	208	.	0			c.G1450A						PASS	.	C	ASN/ASP,ASN/ASP	1305,3101	442.7+/-346.8	189,927,1087	190.0	163.0	173.0		1345,1450	4.3	0.8	10	dbSNP_120	173	1141,7459	234.7+/-267.5	81,979,3240	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	23,23	270,1906,4327	TT,TC,CC		13.2674,29.6187,18.8067	benign,benign	449/1696,484/1731	115393948	2446,10560	2203	4300	6503	SO:0001583	missense	4892	exon15			ACTTGTCGATGCT		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.1450G>A	10.37:g.115393948C>T	ENSP00000353078:p.Asp484Asn	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	116	67	0.577586	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	396	0.1813186813186813	139	0.28252032520325204	40	0.11049723756906077	99	0.17307692307692307	118	0.15567282321899736	C	17.16	3.317823	0.60524	0.296187	0.132674	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350;ENST00000369343	T;T;T;T	0.19250	2.35;2.41;2.23;2.16	5.17	4.27	0.50696	.	0.050281	0.85682	D	0.000000	T	0.00012	0.0000	L	0.59436	1.845	0.23144	P	0.99822988	P;D;P	0.54047	0.94;0.964;0.94	B;P;B	0.45343	0.211;0.477;0.353	T	0.37079	-0.9721	9	0.54805	T	0.06	.	13.9788	0.64291	0.0:0.9269:0.0:0.0731	rs11196400;rs52831195;rs59150146;rs11196400	484;449;484	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	N	484;449;484;449;213;213	ENSP00000358365:D484N;ENSP00000358367:D449N;ENSP00000353078:D484N;ENSP00000353666:D449N	ENSP00000353078:D484N	D	-	1	0	NRAP	115383938	1.000000	0.71417	0.784000	0.31847	0.409000	0.31022	5.350000	0.66016	1.181000	0.42912	-0.362000	0.07510	GAC	C|0.811;T|0.189	0.189	strong		0.463	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
ITGA4	3676	hgsc.bcm.edu	37	2	182376480	182376480	+	Missense_Mutation	SNP	T	T	A	rs35322532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:182376480T>A	ENST00000397033.2	+	17	2330	c.1900T>A	c.(1900-1902)Tct>Act	p.S634T		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	634			S -> T (in dbSNP:rs35322532).		B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	TTTACAGGTTTCTGCAAAGAT	0.338													T|||	86	0.0171725	0.0605	0.0072	5008	,	,		16437	0.0		0.001	False		,,,				2504	0.0				p.S634T		Atlas-SNP	.											.	ITGA4	142	.	0			c.T1900A						PASS	.	T	THR/SER	206,3446		6,194,1626	148.0	144.0	145.0		1900	4.7	1.0	2	dbSNP_126	145	9,8139		0,9,4065	yes	missense	ITGA4	NM_000885.4	58	6,203,5691	AA,AT,TT		0.1105,5.6407,1.822	possibly-damaging	634/1033	182376480	215,11585	1826	4074	5900	SO:0001583	missense	3676	exon17			CAGGTTTCTGCAA		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"""CD molecules"", ""Integrins"""	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.1900T>A	2.37:g.182376480T>A	ENSP00000380227:p.Ser634Thr	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	18.59	3.657151	0.67586	0.056407	0.001105	ENSG00000115232	ENST00000397033	T	0.50001	0.76	5.87	4.68	0.58851	Integrin alpha-2 (1);	0.170160	0.53938	D	0.000050	T	0.09949	0.0244	L	0.41710	1.295	0.48185	D	0.999603	D;P	0.54397	0.966;0.906	P;P	0.55999	0.646;0.789	T	0.02385	-1.1167	10	0.42905	T	0.14	.	10.2631	0.43438	0.2642:0.0:0.0:0.7358	rs35322532	456;634	Q59H74;P13612	.;ITA4_HUMAN	T	634	ENSP00000380227:S634T	ENSP00000380227:S634T	S	+	1	0	ITGA4	182084725	1.000000	0.71417	0.989000	0.46669	0.992000	0.81027	2.791000	0.47829	1.004000	0.39156	0.529000	0.55759	TCT	T|0.987;A|0.013	0.013	strong		0.338	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
SMCO2	341346	hgsc.bcm.edu	37	12	27628521	27628521	+	Silent	SNP	G	G	C	rs77197438	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27628521G>C	ENST00000535986.1	+	4	369	c.369G>C	c.(367-369)ctG>ctC	p.L123L	SMCO2_ENST00000538647.1_3'UTR|SMCO2_ENST00000298876.4_Intron|SMCO2_ENST00000416383.1_Silent_p.L123L			A6NFE2	SMCO2_HUMAN	single-pass membrane protein with coiled-coil domains 2	123						integral component of membrane (GO:0016021)											GCAGGTGTCTGAAGGGCATGT	0.408													G|||	31	0.0061901	0.0219	0.0029	5008	,	,		17088	0.0		0.0	False		,,,				2504	0.0				p.L123L		Atlas-SNP	.											.	.	.	.	0			c.G369C						PASS	.	G		46,1338		0,46,646	77.0	65.0	68.0		369	-0.8	0.0	12	dbSNP_132	68	1,3181		0,1,1590	no	coding-synonymous	C12orf70	NM_001145010.1		0,47,2236	CC,CG,GG		0.0314,3.3237,1.0293		123/344	27628521	47,4519	692	1591	2283	SO:0001819	synonymous_variant	0	exon5			GTGTCTGAAGGGC		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.369G>C	12.37:g.27628521G>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_001145010		Silent	SNP	ENST00000535986.1	37	CCDS44852.1																																																																																			G|0.993;C|0.007	0.007	strong		0.408	SMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402867.1	NM_001145010	
DIABLO	56616	hgsc.bcm.edu	37	12	122692958	122692958	+	Silent	SNP	C	C	T	rs35426428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122692958C>T	ENST00000443649.3	-	7	1507	c.690G>A	c.(688-690)tcG>tcA	p.S230S	DIABLO_ENST00000267169.6_Silent_p.S177S|RP11-512M8.5_ENST00000535844.1_3'UTR|B3GNT4_ENST00000545141.1_Intron|DIABLO_ENST00000464942.2_Silent_p.S177S|B3GNT4_ENST00000546192.1_3'UTR|DIABLO_ENST00000413918.1_Silent_p.S186S|DIABLO_ENST00000353548.6_Silent_p.S186S	NM_019887.4	NP_063940.1	Q9NR28	DBLOH_HUMAN	diablo, IAP-binding mitochondrial protein	230					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)				breast(1)|endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	7	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000302)|Epithelial(86;0.00051)|BRCA - Breast invasive adenocarcinoma(302;0.223)		CCTCCTGCTCCGACTCAGCCC	0.617													C|||	454	0.090655	0.3283	0.0274	5008	,	,		20976	0.0		0.001	False		,,,				2504	0.0				p.S230S		Atlas-SNP	.											DIABLO,NS,carcinoma,-2,1	DIABLO	16	1	0			c.G690A						PASS	.	C	,	1365,3041	452.8+/-350.1	219,927,1057	113.0	107.0	109.0		690,558	-6.1	0.0	12	dbSNP_126	109	23,8577	16.0+/-53.3	0,23,4277	no	coding-synonymous,coding-synonymous	DIABLO	NM_019887.4,NM_138929.3	,	219,950,5334	TT,TC,CC		0.2674,30.9805,10.672	,	230/240,186/196	122692958	1388,11618	2203	4300	6503	SO:0001819	synonymous_variant	56616	exon7			CTGCTCCGACTCA	AF262240	CCDS9228.1, CCDS9229.1, CCDS73541.1	12q24.31	2011-08-02	2011-03-11		ENSG00000184047	ENSG00000184047			21528	protein-coding gene	gene with protein product	"""second mitochondria-derived activator of caspase"""	605219				12749848, 17237824, 21722859	Standard	NM_019887		Approved	SMAC, DIABLO-S, FLJ25049, FLJ10537, DFNA64	uc010tab.2	Q9NR28	OTTHUMG00000157014	ENST00000443649.3:c.690G>A	12.37:g.122692958C>T		Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_019887	B2RDQ0|Q6W3F3|Q96LV0|Q9BT11|Q9HAV6	Silent	SNP	ENST00000443649.3	37	CCDS9228.1																																																																																			C|0.906;T|0.094	0.094	strong		0.617	DIABLO-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347102.2	NM_019887	
ZNF737	100129842	hgsc.bcm.edu	37	19	20727463	20727463	+	Missense_Mutation	SNP	T	T	C	rs10411329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:20727463T>C	ENST00000427401.4	-	4	1640	c.1546A>G	c.(1546-1548)Aaa>Gaa	p.K516E		NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	516			K -> E (in dbSNP:rs10411329). {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(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						TTAAAGCCTTTGCCACATTCT	0.403													-|||	2092	0.417732	0.3449	0.5202	5008	,	,		20903	0.4395		0.4185	False		,,,				2504	0.4202				p.K516E		Atlas-SNP	.											.	ZNF737	50	.	0			c.A1546G						PASS	.	T	GLU/LYS	490,894		87,316,289	46.0	47.0	47.0		1546	0.8	0.3	19	dbSNP_119	47	1191,1991		221,749,621	no	missense	ZNF737	NM_001159293.1	56	308,1065,910	CC,CT,TT		37.4293,35.4046,36.8156	benign	516/537	20727463	1681,2885	692	1591	2283	SO:0001583	missense	100129842	exon4			AGCCTTTGCCACA	BC015765	CCDS54238.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	32468	protein-coding gene	gene with protein product		603984					Standard	NM_001159293		Approved	ZNF102	uc002npa.3	O75373		ENST00000427401.4:c.1546A>G	19.37:g.20727463T>C	ENSP00000395733:p.Lys516Glu	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	26	16	0.615385	NM_001159293	C9JHM3	Missense_Mutation	SNP	ENST00000427401.4	37	CCDS54238.1	939	0.42994505494505497	168	0.34146341463414637	179	0.494475138121547	267	0.46678321678321677	325	0.4287598944591029	N	12.59	1.984912	0.35036	0.354046	0.374293	ENSG00000237440	ENST00000427401	T	0.27104	1.69	0.801	0.801	0.18679	.	.	.	.	.	T	0.00012	0.0000	L	0.60904	1.88	0.37937	P	0.06779599999999997	B	0.25743	0.133	B	0.30401	0.115	T	0.42666	-0.9438	8	0.87932	D	0	.	3.7037	0.08392	0.0:0.0:0.0:1.0	rs10411329;rs52819273;rs10411329	516	C9JHM3	.	E	516	ENSP00000395733:K516E	ENSP00000395733:K516E	K	-	1	0	ZNF737	20519303	0.006000	0.16342	0.286000	0.24833	0.282000	0.26991	-2.106000	0.01338	0.147000	0.19030	0.145000	0.16022	AAA	T|0.588;C|0.412	0.412	strong		0.403	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289	
PSG3	5671	hgsc.bcm.edu	37	19	43243238	43243238	+	Missense_Mutation	SNP	A	A	G	rs11559136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43243238A>G	ENST00000327495.5	-	2	252	c.68T>C	c.(67-69)tTa>tCa	p.L23S	PSG3_ENST00000595140.1_Missense_Mutation_p.L23S|PSG3_ENST00000490592.1_5'UTR	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	23			L -> S (in dbSNP:rs11559136). {ECO:0000269|PubMed:2302228, ECO:0000269|PubMed:2341148, ECO:0000269|PubMed:2350345, ECO:0000269|PubMed:3265688}.		defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				GTTTAAAAGTAATGCTAGGAG	0.488													.|||	3290	0.656949	0.8911	0.6571	5008	,	,		18478	0.4772		0.5507	False		,,,				2504	0.635				p.L23S		Atlas-SNP	.											.	PSG3	82	.	0			c.T68C						PASS	.	G	SER/LEU	3622,780		1552,518,131	94.0	128.0	117.0		68	1.4	1.0	19	dbSNP_120	117	4533,4063		1246,2041,1011	no	missense	PSG3	NM_021016.3	145	2798,2559,1142	GG,GA,AA		47.2662,17.7192,37.2596	benign	23/429	43243238	8155,4843	2201	4298	6499	SO:0001583	missense	5671	exon2			AAAAGTAATGCTA		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.68T>C	19.37:g.43243238A>G	ENSP00000332215:p.Leu23Ser	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	37	CCDS12611.1	1226	0.5613553113553114	399	0.8109756097560976	208	0.574585635359116	224	0.3916083916083916	395	0.521108179419525	N	0.011	-1.692074	0.00731	0.822808	0.527338	ENSG00000221826	ENST00000327495	T	0.15487	2.42	1.39	1.39	0.22231	.	.	.	.	.	T	0.00012	0.0000	N	0.00020	-2.765	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.31024	-0.9958	8	0.02654	T	1	.	3.985	0.09511	0.2396:0.0:0.7604:0.0	rs11559136;rs12185498;rs58832504	23	Q16557	PSG3_HUMAN	S	23	ENSP00000332215:L23S	ENSP00000332215:L23S	L	-	2	0	PSG3	47935078	0.806000	0.28996	0.977000	0.42913	0.017000	0.09413	0.257000	0.18369	0.159000	0.19401	-0.534000	0.04291	TTA	.	.	weak		0.488	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016	
SLURP1	57152	hgsc.bcm.edu	37	8	143822612	143822612	+	Silent	SNP	G	G	A	rs62636564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143822612G>A	ENST00000246515.1	-	3	286	c.261C>T	c.(259-261)gcC>gcT	p.A87A		NM_020427.2	NP_065160.1	P55000	SLUR1_HUMAN	secreted LY6/PLAUR domain containing 1	87					cell activation (GO:0001775)|cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			breast(1)|lung(7)|ovary(1)	9	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)					TCAGGTGGGCGGCCCCGATGC	0.662													G|||	111	0.0221645	0.0802	0.0072	5008	,	,		15680	0.0		0.0	False		,,,				2504	0.0				p.A87A		Atlas-SNP	.											.	SLURP1	16	.	0			c.C261T						PASS	.	G		250,4156	143.5+/-178.5	7,236,1960	43.0	45.0	45.0		261	-7.5	0.0	8	dbSNP_129	45	5,8593	4.3+/-15.6	0,5,4294	no	coding-synonymous	SLURP1	NM_020427.2		7,241,6254	AA,AG,GG		0.0582,5.6741,1.9609		87/104	143822612	255,12749	2203	4299	6502	SO:0001819	synonymous_variant	57152	exon3			GTGGGCGGCCCCG	AY579080	CCDS6387.1	8q24.3	2004-11-16			ENSG00000126233	ENSG00000126233			18746	protein-coding gene	gene with protein product	"""lymphocyte antigen 6-like secreted"", ""ARS component B"""	606119				11285253, 10211827	Standard	NM_020427		Approved	ARS, ANUP, MDM, ArsB, LY6LS	uc003ywy.3	P55000	OTTHUMG00000164685	ENST00000246515.1:c.261C>T	8.37:g.143822612G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_020427	Q53YJ6|Q6PUA6|Q92483	Silent	SNP	ENST00000246515.1	37	CCDS6387.1																																																																																			G|0.979;A|0.021	0.021	strong		0.662	SLURP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379741.1	NM_020427	
STAP2	55620	hgsc.bcm.edu	37	19	4325433	4325433	+	Silent	SNP	G	G	A	rs1138253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4325433G>A	ENST00000594605.1	-	10	1062	c.939C>T	c.(937-939)ccC>ccT	p.P313P	STAP2_ENST00000597593.1_5'UTR|STAP2_ENST00000600324.1_Silent_p.P313P	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	313	Pro-rich.					cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		CATCTCCAATGGGGGTCACGT	0.597													g|||	2604	0.519968	0.5764	0.4957	5008	,	,		16092	0.6339		0.4294	False		,,,				2504	0.4366				p.P313P		Atlas-SNP	.											.	STAP2	38	.	0			c.C939T						PASS	.		,	2436,1970	619.3+/-393.3	674,1088,441	104.0	104.0	104.0		939,939	4.8	1.0	19	dbSNP_86	104	3855,4745	542.0+/-384.1	876,2103,1321	no	coding-synonymous,coding-synonymous	STAP2	NM_001013841.1,NM_017720.2	,	1550,3191,1762	AA,AG,GG		44.8256,44.7118,48.37	,	313/404,313/450	4325433	6291,6715	2203	4300	6503	SO:0001819	synonymous_variant	55620	exon10			TCCAATGGGGGTC	AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078			30430	protein-coding gene	gene with protein product		607881				10980601, 11441184	Standard	XM_005259592		Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000594605.1:c.939C>T	19.37:g.4325433G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	121	58	0.479339	NM_001013841	A6NKK3|Q9NXI2	Silent	SNP	ENST00000594605.1	37	CCDS45926.1																																																																																			G|0.493;N|0.001	.	strong		0.597	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841	
TEK	7010	hgsc.bcm.edu	37	9	27205021	27205021	+	Silent	SNP	G	G	A	rs542913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:27205021G>A	ENST00000380036.4	+	14	2764	c.2322G>A	c.(2320-2322)agG>agA	p.R774R	TEK_ENST00000519097.1_Silent_p.R627R|TEK_ENST00000406359.4_Silent_p.R731R	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	199	0	0		WXS	Illumina HiSeq	Phase_I	227	103	0.453745	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		
PRDM10	56980	hgsc.bcm.edu	37	11	129830796	129830796	+	Missense_Mutation	SNP	C	C	T	rs11221912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:129830796C>T	ENST00000360871.3	-	2	295	c.64G>A	c.(64-66)Gca>Aca	p.A22T	PRDM10_ENST00000358825.5_Missense_Mutation_p.A22T|PRDM10_ENST00000528746.1_Missense_Mutation_p.A22T	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	22			A -> T (in dbSNP:rs11221912).		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)	p.A22T(1)		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)		TTCACCTGTGCGGCATTCTGT	0.493													C|||	1397	0.278954	0.3949	0.1758	5008	,	,		18326	0.5417		0.0557	False		,,,				2504	0.1544				p.A22T		Atlas-SNP	.											PRDM10,NS,carcinoma,0,1	PRDM10	120	1	1	Substitution - Missense(1)	stomach(1)	c.G64A						PASS	.	C	THR/ALA,THR/ALA	1553,2849	487.6+/-361.0	272,1009,920	139.0	124.0	129.0		64,64	-0.9	0.0	11	dbSNP_120	129	475,8119	139.5+/-196.2	13,449,3835	yes	missense,missense	PRDM10	NM_020228.2,NM_199437.1	58,58	285,1458,4755	TT,TC,CC		5.5271,35.2794,15.6048	benign,benign	22/1161,22/1157	129830796	2028,10968	2201	4297	6498	SO:0001583	missense	56980	exon2			CCTGTGCGGCATT	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.64G>A	11.37:g.129830796C>T	ENSP00000354118:p.Ala22Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	122	49	0.401639	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	37	CCDS8484.1	594	0.27197802197802196	196	0.3983739837398374	54	0.14917127071823205	308	0.5384615384615384	36	0.047493403693931395	C	11.92	1.781863	0.31502	0.352794	0.055271	ENSG00000170325	ENST00000358825;ENST00000360871;ENST00000528746;ENST00000527581;ENST00000531431	T;T;T;T;T	0.52295	2.76;2.75;2.76;0.67;0.68	5.39	-0.936	0.10419	.	0.349382	0.28871	N	0.013866	T	0.00012	0.0000	L	0.27053	0.805	0.22342	P	0.999180817	B;B;B	0.14438	0.01;0.006;0.001	B;B;B	0.12156	0.007;0.002;0.0	T	0.48175	-0.9058	9	0.51188	T	0.08	-3.0822	10.3723	0.44062	0.0:0.611:0.0:0.389	rs11221912;rs58525085;rs11221912	22;22;22	Q9NQV6-4;G3XAE5;Q9NQV6	.;.;PRD10_HUMAN	T	22	ENSP00000351686:A22T;ENSP00000354118:A22T;ENSP00000431262:A22T;ENSP00000432093:A22T;ENSP00000436681:A22T	ENSP00000351686:A22T	A	-	1	0	PRDM10	129336006	0.041000	0.20044	0.002000	0.10522	0.116000	0.19942	0.163000	0.16520	-0.364000	0.08088	-0.143000	0.13931	GCA	C|0.776;T|0.224	0.224	strong		0.493	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
MRC2	9902	hgsc.bcm.edu	37	17	60767303	60767303	+	Missense_Mutation	SNP	G	G	A	rs77299955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60767303G>A	ENST00000303375.5	+	25	4024	c.3622G>A	c.(3622-3624)Ggc>Agc	p.G1208S	MRC2_ENST00000446119.2_Missense_Mutation_p.G74S	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1208	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						GAACTACGTGGGCTGGCAGGA	0.677													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		12596	0.0		0.0	False		,,,				2504	0.0				p.G1208S		Atlas-SNP	.											.	MRC2	126	.	0			c.G3622A						PASS	.	G	SER/GLY	95,4295		0,95,2100	13.0	16.0	15.0		3622	1.8	0.2	17	dbSNP_131	15	1,8567		0,1,4283	yes	missense	MRC2	NM_006039.3	56	0,96,6383	AA,AG,GG		0.0117,2.164,0.7409	benign	1208/1480	60767303	96,12862	2195	4284	6479	SO:0001583	missense	9902	exon25			TACGTGGGCTGGC	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"""CD molecules"", ""C-type lectin domain containing"""	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3622G>A	17.37:g.60767303G>A	ENSP00000307513:p.Gly1208Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	37	CCDS11634.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	G	11.35	1.614242	0.28712	0.02164	1.17E-4	ENSG00000011028	ENST00000303375;ENST00000446119	T;T	0.53423	0.62;0.62	5.16	1.8	0.24995	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.232107	0.49916	N	0.000124	T	0.08133	0.0203	N	0.08118	0	0.23478	N	0.997599	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	T	0.13072	-1.0523	10	0.18276	T	0.48	-17.6713	8.5553	0.33478	0.7771:0.0:0.2229:0.0	.	74;1208	E7EME3;Q9UBG0	.;MRC2_HUMAN	S	1208;74	ENSP00000307513:G1208S;ENSP00000400445:G74S	ENSP00000307513:G1208S	G	+	1	0	MRC2	58121035	0.920000	0.31207	0.177000	0.23020	0.707000	0.40811	1.980000	0.40618	0.124000	0.18369	-0.367000	0.07326	GGC	G|0.991;A|0.009	0.009	strong		0.677	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
CDON	50937	hgsc.bcm.edu	37	11	125891269	125891269	+	Missense_Mutation	SNP	C	C	T	rs3740912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	128	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	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	
KLRF1	51348	hgsc.bcm.edu	37	12	9985915	9985915	+	Missense_Mutation	SNP	G	G	T	rs2232548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9985915G>T	ENST00000279544.3	+	3	265	c.201G>T	c.(199-201)ttG>ttT	p.L67F	KLRF1_ENST00000354855.3_Intron|KLRF1_ENST00000537723.1_Missense_Mutation_p.L67F|KLRF1_ENST00000324214.4_Intron	NM_016523.1	NP_057607	Q9NZS2	KLRF1_HUMAN	killer cell lectin-like receptor subfamily F, member 1	67			L -> F (in dbSNP:rs2232548).		cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|MHC class I receptor activity (GO:0032393)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)	13						AGGGAGTATTGCTAAAATGCC	0.353													G|||	400	0.0798722	0.121	0.0821	5008	,	,		-128	0.0476		0.0775	False		,,,				2504	0.0583				p.L67F		Atlas-SNP	.											.	KLRF1	27	.	0			c.G201T						PASS	.	G	PHE/LEU	380,3320		26,328,1496	96.0	91.0	93.0		201	2.6	1.0	12	dbSNP_98	93	634,7556		31,572,3492	yes	missense	KLRF1	NM_016523.1	22	57,900,4988	TT,TG,GG		7.7411,10.2703,8.5282	benign	67/233	9985915	1014,10876	1850	4095	5945	SO:0001583	missense	51348	exon3			AGTATTGCTAAAA	AF175206	CCDS41750.1	12p13.31	2011-08-30			ENSG00000150045	ENSG00000150045		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	13342	protein-coding gene	gene with protein product		605029				10671213	Standard	NM_001291823		Approved	CLEC5C, NKp80	uc021qux.1	Q9NZS2		ENST00000279544.3:c.201G>T	12.37:g.9985915G>T	ENSP00000279544:p.Leu67Phe	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_016523	Q4KMT5|Q96PR2|Q96PR3|Q9NZS1	Missense_Mutation	SNP	ENST00000279544.3	37	CCDS41750.1	158	0.07234432234432235	57	0.11585365853658537	31	0.0856353591160221	19	0.033216783216783216	51	0.06728232189973615	G	12.20	1.867006	0.32977	0.102703	0.077411	ENSG00000150045	ENST00000279544;ENST00000537723	T;T	0.59083	4.96;0.29	2.57	2.57	0.30868	.	.	.	.	.	T	0.01558	0.0050	L	0.34521	1.04	0.41812	P	0.010024000000000033	D;D	0.89917	0.998;1.0	D;D	0.87578	0.994;0.998	T	0.27739	-1.0065	7	.	.	.	.	8.8546	0.35221	0.0:0.0:1.0:0.0	rs2232548;rs17806460;rs60994638;rs2232548	67;67	Q9NZS2;Q4KN30	KLRF1_HUMAN;.	F	67	ENSP00000279544:L67F;ENSP00000443054:L67F	.	L	+	3	2	KLRF1	9877182	1.000000	0.71417	0.997000	0.53966	0.425000	0.31504	2.285000	0.43487	1.786000	0.52430	0.461000	0.40582	TTG	G|0.914;T|0.086	0.086	strong		0.353	KLRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399535.1	NM_016523	
CRIM1	51232	hgsc.bcm.edu	37	2	36691680	36691680	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:36691680C>T	ENST00000280527.2	+	5	1240	c.873C>T	c.(871-873)tgC>tgT	p.C291C		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	291					insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.C291C(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				GTTTCAGATGCGAGTGTCTCT	0.507																																					p.C291C		Atlas-SNP	.											CRIM1,caecum,carcinoma,0,1	CRIM1	88	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C873T						scavenged	.						194.0	178.0	184.0					2																	36691680		2203	4300	6503	SO:0001819	synonymous_variant	51232	exon5			CAGATGCGAGTGT	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"""cysteine-rich motor neuron 1"""	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.873C>T	2.37:g.36691680C>T		Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	323	4	0.0123839	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Silent	SNP	ENST00000280527.2	37	CCDS1783.1																																																																																			.	.	none		0.507	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441	
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587103	15587103	+	Silent	SNP	C	C	T	rs35973013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15587103C>T	ENST00000340880.4	-	2	858	c.378G>A	c.(376-378)gcG>gcA	p.A126A	PGLYRP2_ENST00000292609.4_Silent_p.A126A	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	126					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)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|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)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						CCTCCAGCCCCGCCAGCAGAG	0.607													C|||	123	0.0245607	0.0477	0.0058	5008	,	,		19723	0.006		0.008	False		,,,				2504	0.0429				p.A126A		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.G378A						PASS	.	C		193,4213	120.4+/-158.0	3,187,2013	100.0	86.0	91.0		378	-10.3	0.1	19	dbSNP_126	91	75,8525	44.0+/-102.2	0,75,4225	no	coding-synonymous	PGLYRP2	NM_052890.3		3,262,6238	TT,TC,CC		0.8721,4.3804,2.0606		126/577	15587103	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	114770	exon2			CAGCCCCGCCAGC	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.378G>A	19.37:g.15587103C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	136	76	0.558824	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Silent	SNP	ENST00000340880.4	37	CCDS12330.2																																																																																			C|0.981;T|0.019	0.019	strong		0.607	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
ZNF678	339500	hgsc.bcm.edu	37	1	227842561	227842561	+	Missense_Mutation	SNP	A	A	G	rs116552491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227842561A>G	ENST00000343776.5	+	4	955	c.610A>G	c.(610-612)Agt>Ggt	p.S204G	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.S259G	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	204					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				GAAAATTCATAGTGGAGAGAA	0.373													A|||	30	0.00599042	0.0212	0.0014	5008	,	,		19312	0.0		0.001	False		,,,				2504	0.0				p.S259G		Atlas-SNP	.											.	ZNF678	137	.	0			c.A775G						PASS	.	A	GLY/SER	77,4327	64.1+/-101.4	0,77,2125	100.0	115.0	110.0		775	0.3	0.0	1	dbSNP_132	110	0,8594		0,0,4297	no	missense	ZNF678	NM_178549.3	56	0,77,6422	GG,GA,AA		0.0,1.7484,0.5924	possibly-damaging	259/581	227842561	77,12921	2202	4297	6499	SO:0001583	missense	339500	exon4			ATTCATAGTGGAG	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"""Zinc fingers, C2H2-type"", ""-"""	28652	protein-coding gene	gene with protein product	"""hypothetical protein MGC42493"""					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.610A>G	1.37:g.227842561A>G	ENSP00000344828:p.Ser204Gly	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	13.99	2.401576	0.42613	0.017484	0.0	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.19669	2.13;2.13	1.49	0.308	0.15815	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10937	0.0267	L	0.58354	1.805	0.24788	N	0.992776	P	0.43938	0.822	B	0.44044	0.439	T	0.13926	-1.0491	9	0.87932	D	0	.	4.1011	0.10014	0.7609:0.0:0.2391:0.0	.	204	Q5SXM1	ZN678_HUMAN	G	204;259	ENSP00000344828:S204G;ENSP00000440403:S259G	ENSP00000344828:S204G	S	+	1	0	ZNF678	225909184	0.232000	0.23762	0.004000	0.12327	0.027000	0.11550	1.213000	0.32407	0.587000	0.29643	0.413000	0.27773	AGT	A|0.996;G|0.004	0.004	strong		0.373	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549	
GOLGA4	2803	hgsc.bcm.edu	37	3	37323569	37323569	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37323569C>T	ENST00000361924.2	+	3	657	c.283C>T	c.(283-285)Cga>Tga	p.R95*	GOLGA4_ENST00000435830.2_Intron|GOLGA4_ENST00000356847.4_Nonsense_Mutation_p.R117*|GOLGA4_ENST00000444882.1_Nonsense_Mutation_p.R95*	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	95					Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GTCTTTGGTACGAACATCTTC	0.488																																					p.R117X		Atlas-SNP	.											GOLGA4,NS,carcinoma,-1,2	GOLGA4	173	2	0			c.C349T						scavenged	.						98.0	98.0	98.0					3																	37323569		2203	4300	6503	SO:0001587	stop_gained	2803	exon4			TTGGTACGAACAT	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.283C>T	3.37:g.37323569C>T	ENSP00000354486:p.Arg95*	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	176	3	0.0170455	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Nonsense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	C	39	7.556932	0.98355	.	.	ENSG00000144674	ENST00000361924;ENST00000444882;ENST00000356847;ENST00000450863	.	.	.	5.8	5.8	0.92144	.	0.000000	0.30565	N	0.009342	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0706	0.97721	0.0:1.0:0.0:0.0	.	.	.	.	X	95;95;117;117	.	ENSP00000349305:R117X	R	+	1	2	GOLGA4	37298573	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.456000	0.60081	2.744000	0.94065	0.655000	0.94253	CGA	.	.	none		0.488	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
CLEC18A	348174	hgsc.bcm.edu	37	16	69988472	69988472	+	Missense_Mutation	SNP	C	C	T	rs75776403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69988472C>T	ENST00000288040.6	+	3	639	c.452C>T	c.(451-453)aCg>aTg	p.T151M	CLEC18A_ENST00000393701.2_Missense_Mutation_p.T151M|CLEC18A_ENST00000568461.1_Missense_Mutation_p.T151M|CLEC18A_ENST00000449317.2_Missense_Mutation_p.T151M	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	151	SCP.			T -> M (in Ref. 2; BAF82573 and 4; AAI41809). {ECO:0000305}.		extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						ACCCACTACACGCAGGTGAGT	0.582													.|||	1592	0.317891	0.1135	0.3228	5008	,	,		20491	0.4901		0.2714	False		,,,				2504	0.4611				p.T151M		Atlas-SNP	.											.	CLEC18A	9	.	0			c.C452T						PASS	.						25.0	23.0	24.0					16																	69988472		2198	4298	6496	SO:0001583	missense	348174	exon4			ACTACACGCAGGT	AF428259	CCDS10886.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157322		"""C-type lectin domain containing"""	30388	protein-coding gene	gene with protein product	"""mannose receptor-like"""					12975309	Standard	NM_001136214		Approved	MRCL	uc010vlo.3	A5D8T8		ENST00000288040.6:c.452C>T	16.37:g.69988472C>T	ENSP00000288040:p.Thr151Met	Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	391	187	0.478261	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Missense_Mutation	SNP	ENST00000288040.6	37	CCDS10886.1	616	0.28205128205128205	54	0.10975609756097561	115	0.31767955801104975	274	0.479020979020979	173	0.22823218997361477	.	15.90	2.969358	0.53614	.	.	ENSG00000157322	ENST00000393701;ENST00000539957;ENST00000545150;ENST00000449317;ENST00000288040	T;T;T	0.16073	2.37;2.37;2.37	1.97	1.97	0.26223	CAP domain (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.95574	3.69	0.23640	P	0.99722994	D;D	0.76494	0.998;0.999	P;P	0.59643	0.861;0.781	T	0.42916	-0.9423	8	.	.	.	.	7.5137	0.27587	0.0:1.0:0.0:0.0	.	151;151	A5D8T8;F8W692	CL18A_HUMAN;.	M	151;151;148;151;151	ENSP00000377304:T151M;ENSP00000413990:T151M;ENSP00000288040:T151M	.	T	+	2	0	CLEC18A	68545973	1.000000	0.71417	0.995000	0.50966	0.105000	0.19272	3.484000	0.53201	1.424000	0.47217	0.184000	0.17185	ACG	C|0.743;T|0.257	0.257	strong		0.582	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619	
C7orf71	285941	hgsc.bcm.edu	37	7	26678910	26678910	+	Silent	SNP	C	C	T	rs111516571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:26678910C>T	ENST00000409974.3	+	2	863	c.147C>T	c.(145-147)ctC>ctT	p.L49L		NM_001145531.1	NP_001139003.1	A4D174	CG071_HUMAN	chromosome 7 open reading frame 71	49																	agaggggcctcggggaagcca	0.527													C|||	474	0.0946486	0.3381	0.0288	5008	,	,		17598	0.004		0.003	False		,,,				2504	0.0				p.L49L		Atlas-SNP	.											.	C7orf71	6	.	0			c.C147T						PASS	.						48.0	63.0	59.0					7																	26678910		692	1591	2283	SO:0001819	synonymous_variant	285941	exon2			GGGCCTCGGGGAA		CCDS47565.1	7p15.2	2009-09-11			ENSG00000222004	ENSG00000222004			22364	protein-coding gene	gene with protein product							Standard	NM_001145531		Approved		uc003syb.3	A4D174	OTTHUMG00000152860	ENST00000409974.3:c.147C>T	7.37:g.26678910C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	21	20	0.952381	NM_001145531		Silent	SNP	ENST00000409974.3	37	CCDS47565.1																																																																																			C|0.925;T|0.075	0.075	strong		0.527	C7orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328272.1	NM_001145531	
TNC	3371	hgsc.bcm.edu	37	9	117848368	117848368	+	Missense_Mutation	SNP	C	C	T	rs61729478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117848368C>T	ENST00000350763.4	-	3	2053	c.1642G>A	c.(1642-1644)Gtg>Atg	p.V548M	TNC_ENST00000341037.4_Missense_Mutation_p.V548M|TNC_ENST00000535648.1_Missense_Mutation_p.V548M|TNC_ENST00000542877.1_Missense_Mutation_p.V548M|TNC_ENST00000340094.3_Missense_Mutation_p.V548M|TNC_ENST00000537320.1_Missense_Mutation_p.V548M|TNC_ENST00000423613.2_Missense_Mutation_p.V548M|TNC_ENST00000346706.3_Missense_Mutation_p.V548M|TNC_ENST00000345230.3_Missense_Mutation_p.V548M	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	548	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						TCATGGCACACGCACTGCCCA	0.587													C|||	32	0.00638978	0.0038	0.0072	5008	,	,		21065	0.0		0.0119	False		,,,				2504	0.0102				p.V548M		Atlas-SNP	.											.	TNC	282	.	0			c.G1642A						PASS	.	C	MET/VAL	41,4365	44.6+/-78.6	0,41,2162	106.0	76.0	86.0		1642	4.1	0.9	9	dbSNP_129	86	123,8477	63.1+/-125.2	1,121,4178	yes	missense	TNC	NM_002160.3	21	1,162,6340	TT,TC,CC		1.4302,0.9305,1.261	benign	548/2202	117848368	164,12842	2203	4300	6503	SO:0001583	missense	3371	exon3			GGCACACGCACTG		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.1642G>A	9.37:g.117848368C>T	ENSP00000265131:p.Val548Met	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	165	108	0.654545	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	15	0.006868131868131868	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	9.105	1.005034	0.19199	0.009305	0.014302	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77	5.95	4.13	0.48395	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);	0.111211	0.64402	N	0.000008	T	0.16471	0.0396	M	0.79614	2.46	0.51767	D	0.999938	D;P	0.55385	0.971;0.52	P;B	0.49953	0.627;0.223	T	0.01245	-1.1407	10	0.59425	D	0.04	.	12.6844	0.56940	0.0:0.8672:0.0:0.1328	.	548;548	E9PC84;P24821	.;TENA_HUMAN	M	548	ENSP00000344400:V548M;ENSP00000438152:V548M;ENSP00000344555:V548M;ENSP00000345861:V548M;ENSP00000265131:V548M;ENSP00000339553:V548M;ENSP00000411406:V548M;ENSP00000443478:V548M;ENSP00000442242:V548M	ENSP00000344400:V548M	V	-	1	0	TNC	116888189	0.008000	0.16893	0.874000	0.34290	0.117000	0.20001	0.248000	0.18198	0.867000	0.35654	-0.222000	0.12452	GTG	C|0.990;T|0.010	0.010	strong		0.587	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
ARID4B	51742	hgsc.bcm.edu	37	1	235383188	235383188	+	Silent	SNP	A	A	G	rs4659654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235383188A>G	ENST00000264183.3	-	16	2000	c.1503T>C	c.(1501-1503)gaT>gaC	p.D501D	ARID4B_ENST00000366603.2_Silent_p.D501D|ARID4B_ENST00000349213.3_Silent_p.D501D	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	501	Glu-rich.				histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			CATCTTTGTCATCCAGATTTT	0.328													G|||	2261	0.451478	0.4433	0.5115	5008	,	,		15454	0.251		0.4791	False		,,,				2504	0.5982				p.D501D		Atlas-SNP	.											ARID4B_ENST00000264183,NS,carcinoma,0,1	ARID4B	142	1	0			c.T1503C						PASS	.	G	,,	2101,2305	601.5+/-389.7	494,1113,596	209.0	191.0	197.0		1503,1503,1503	-1.5	0.0	1	dbSNP_111	197	3988,4610	599.8+/-394.1	924,2140,1235	no	coding-synonymous,coding-synonymous,coding-synonymous	ARID4B	NM_001206794.1,NM_016374.5,NM_031371.3	,,	1418,3253,1831	GG,GA,AA		46.3829,47.685,46.8241	,,	501/1313,501/1313,501/1227	235383188	6089,6915	2203	4299	6502	SO:0001819	synonymous_variant	51742	exon16			TTTGTCATCCAGA	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.1503T>C	1.37:g.235383188A>G		Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	237	237	1	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Silent	SNP	ENST00000264183.3	37	CCDS31061.1																																																																																			A|0.549;G|0.451	0.451	strong		0.328	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	
KRT38	8687	hgsc.bcm.edu	37	17	39595536	39595536	+	Silent	SNP	C	C	T	rs17494404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39595536C>T	ENST00000246646.3	-	3	650	c.651G>A	c.(649-651)gcG>gcA	p.A217A		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)				TGGCCAGGGTCGCATCATCCA	0.637													C|||	245	0.0489217	0.059	0.0346	5008	,	,		17618	0.0496		0.0755	False		,,,				2504	0.0174				p.A217A		Atlas-SNP	.											.	KRT38	63	.	0			c.G651A						PASS	.	C		288,4118	158.9+/-191.5	9,270,1924	82.0	75.0	77.0		651	2.2	0.8	17	dbSNP_123	77	753,7847	180.2+/-229.2	29,695,3576	no	coding-synonymous	KRT38	NM_006771.3		38,965,5500	TT,TC,CC		8.7558,6.5365,8.004		217/457	39595536	1041,11965	2203	4300	6503	SO:0001819	synonymous_variant	8687	exon3			CAGGGTCGCATCA	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.651G>A	17.37:g.39595536C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	68	0.576271	NM_006771	A2RRM5|Q6A164	Silent	SNP	ENST00000246646.3	37	CCDS11392.1																																																																																			C|0.928;T|0.072	0.072	strong		0.637	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
SLC12A2	6558	hgsc.bcm.edu	37	5	127469859	127469859	+	Silent	SNP	A	A	G	rs2228112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:127469859A>G	ENST00000262461.2	+	6	1380	c.1191A>G	c.(1189-1191)gaA>gaG	p.E397E	SLC12A2_ENST00000343225.4_Silent_p.E397E	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	397					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	TTTTCTAGGAACATTCCATAC	0.328													A|||	1975	0.394369	0.7337	0.3977	5008	,	,		17350	0.3294		0.1918	False		,,,				2504	0.2086				p.E397E		Atlas-SNP	.											.	SLC12A2	119	.	0			c.A1191G						PASS	.	A		2732,1674	653.5+/-399.6	854,1024,325	101.0	112.0	108.0		1191	2.5	1.0	5	dbSNP_98	108	1896,6700	334.1+/-320.8	196,1504,2598	no	coding-synonymous	SLC12A2	NM_001046.2		1050,2528,2923	GG,GA,AA		22.0568,37.9936,35.5945		397/1213	127469859	4628,8374	2203	4298	6501	SO:0001819	synonymous_variant	6558	exon6			CTAGGAACATTCC		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"""Solute carriers"""	10911	protein-coding gene	gene with protein product	"""bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1"", ""basolateral Na-K-Cl symporter"", ""protein phosphatase 1, regulatory subunit 141"""	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.1191A>G	5.37:g.127469859A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	132	76	0.575758	NM_001046	Q8N713|Q8WWH7	Silent	SNP	ENST00000262461.2	37	CCDS4144.1																																																																																			A|0.627;C|0.000;G|0.373;T|0.000	0.373	strong		0.328	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046	
CES5A	221223	hgsc.bcm.edu	37	16	55907811	55907811	+	Missense_Mutation	SNP	C	C	T	rs2397965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:55907811C>T	ENST00000290567.9	-	2	333	c.212G>A	c.(211-213)cGa>cAa	p.R71Q	CES5A_ENST00000541580.1_Intron|CES5A_ENST00000518005.1_5'UTR|CES5A_ENST00000319165.9_Missense_Mutation_p.R71Q|CES5A_ENST00000520435.1_Missense_Mutation_p.R71Q|CES5A_ENST00000521992.1_Missense_Mutation_p.R100Q	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	119	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	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	
VCAN	1462	hgsc.bcm.edu	37	5	82834630	82834630	+	Silent	SNP	T	T	C	rs309557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82834630T>C	ENST00000265077.3	+	8	6373	c.5808T>C	c.(5806-5808)ggT>ggC	p.G1936G	VCAN_ENST00000343200.5_Silent_p.G949G|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1936	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	ATTTCAGTGGTGACTTTAGAG	0.438													T|||	2347	0.46865	0.5023	0.5288	5008	,	,		19704	0.3919		0.5258	False		,,,				2504	0.4008				p.G1936G		Atlas-SNP	.											.	VCAN	498	.	0			c.T5808C						PASS	.	T	,,,	2213,2193	588.8+/-387.0	549,1115,539	82.0	84.0	83.0		,2847,,5808	3.3	1.0	5	dbSNP_79	83	4263,4337	573.0+/-389.8	1066,2131,1103	no	intron,coding-synonymous,intron,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	1615,3246,1642	CC,CT,TT		49.5698,49.773,49.7924	,,,	,949/2410,,1936/3397	82834630	6476,6530	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			CAGTGGTGACTTT	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.5808T>C	5.37:g.82834630T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			T|0.507;C|0.493	0.493	strong		0.438	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
GALNT5	11227	hgsc.bcm.edu	37	2	158140806	158140806	+	Missense_Mutation	SNP	G	G	C	rs6759356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:158140806G>C	ENST00000259056.4	+	2	1952	c.1467G>C	c.(1465-1467)caG>caC	p.Q489H		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	489			Q -> H (in dbSNP:rs6759356).		cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|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(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						GTGCAGAGCAGCTAGTTCACA	0.463													G|||	756	0.150958	0.503	0.0749	5008	,	,		20315	0.002		0.0189	False		,,,				2504	0.0184				p.Q489H		Atlas-SNP	.											.	GALNT5	112	.	0			c.G1467C						PASS	.	G	HIS/GLN	1920,2486	548.8+/-377.6	446,1028,729	248.0	206.0	220.0		1467	-1.0	0.9	2	dbSNP_116	220	168,8432	77.5+/-140.1	3,162,4135	yes	missense	GALNT5	NM_014568.1	24	449,1190,4864	CC,CG,GG		1.9535,43.5769,16.0541	probably-damaging	489/941	158140806	2088,10918	2203	4300	6503	SO:0001583	missense	11227	exon2			AGAGCAGCTAGTT	AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4127	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 5"""	615129	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"""			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.1467G>C	2.37:g.158140806G>C	ENSP00000259056:p.Gln489His	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_014568	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	37	CCDS2203.1	301	0.13782051282051283	260	0.5284552845528455	30	0.08287292817679558	0	0.0	11	0.014511873350923483	G	16.12	3.031917	0.54790	0.435769	0.019535	ENSG00000136542	ENST00000259056	T	0.59364	0.27	5.45	-1.03	0.10102	.	0.317119	0.22182	N	0.063498	T	0.00012	0.0000	M	0.72118	2.19	0.38267	P	0.057945000000000024	D	0.63880	0.993	P	0.58210	0.835	T	0.45687	-0.9244	9	0.59425	D	0.04	.	7.229	0.26033	0.4152:0.106:0.4787:0.0	rs6759356;rs52799205;rs6759356	489	Q7Z7M9	GALT5_HUMAN	H	489	ENSP00000259056:Q489H	ENSP00000259056:Q489H	Q	+	3	2	GALNT5	157849052	0.598000	0.26882	0.950000	0.38849	0.865000	0.49528	-0.172000	0.09868	-0.300000	0.08895	-0.140000	0.14226	CAG	G|0.851;C|0.149	0.149	strong		0.463	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568	
C17orf50	146853	hgsc.bcm.edu	37	17	34091130	34091130	+	Missense_Mutation	SNP	C	C	A	rs140052043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34091130C>A	ENST00000285023.4	+	2	150	c.118C>A	c.(118-120)Cag>Aag	p.Q40K	C17orf50_ENST00000588628.1_Missense_Mutation_p.P47Q|C17orf50_ENST00000586491.1_Missense_Mutation_p.Q40K	NM_145272.3	NP_660315.2	Q8WW18	CQ050_HUMAN	chromosome 17 open reading frame 50	40													Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		cgaggaCAACCAGAGGCCGCT	0.692													C|||	43	0.00858626	0.0318	0.0014	5008	,	,		9618	0.0		0.0	False		,,,				2504	0.0				p.Q40K		Atlas-SNP	.											.	C17orf50	4	.	0			c.C118A						PASS	.	C	LYS/GLN	73,3255		1,71,1592	8.0	13.0	11.0		118	-3.7	0.0	17	dbSNP_134	11	2,6858		0,2,3428	yes	missense	C17orf50	NM_145272.3	53	1,73,5020	AA,AC,CC		0.0292,2.1935,0.7362	benign	40/175	34091130	75,10113	1664	3430	5094	SO:0001583	missense	146853	exon2			GACAACCAGAGGC	BC021727	CCDS42298.1	17q12	2014-05-06			ENSG00000154768	ENSG00000270806			29581	protein-coding gene	gene with protein product							Standard	NM_145272		Approved		uc002hjx.3	Q8WW18	OTTHUMG00000188389	ENST00000285023.4:c.118C>A	17.37:g.34091130C>A	ENSP00000285023:p.Gln40Lys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_145272	Q6Q621	Missense_Mutation	SNP	ENST00000285023.4	37	CCDS42298.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	C	6.499	0.460290	0.12342	0.021935	2.92E-4	ENSG00000154768	ENST00000285023	T	0.42513	0.97	1.86	-3.72	0.04411	.	.	.	.	.	T	0.07052	0.0179	N	0.19112	0.55	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.20571	-1.0271	9	0.54805	T	0.06	-3.6237	0.4196	0.00454	0.216:0.2495:0.3138:0.2207	.	40	Q8WW18	CQ050_HUMAN	K	40	ENSP00000285023:Q40K	ENSP00000285023:Q40K	Q	+	1	0	C17orf50	31115243	0.000000	0.05858	0.016000	0.15963	0.022000	0.10575	-0.033000	0.12246	-0.319000	0.08652	-0.502000	0.04539	CAG	C|0.993;A|0.007	0.007	strong		0.692	C17orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449132.1	NM_145272	
PIGN	23556	hgsc.bcm.edu	37	18	59810563	59810563	+	Silent	SNP	A	A	G	rs34227891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	187	0	0		WXS	Illumina HiSeq	Phase_I	168	166	0.988095	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	
TRIM6	117854	hgsc.bcm.edu	37	11	5625784	5625784	+	Silent	SNP	A	A	G	rs3751005	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5625784A>G	ENST00000278302.5	+	3	584	c.444A>G	c.(442-444)ctA>ctG	p.L148L	TRIM6_ENST00000507320.1_5'UTR|TRIM6_ENST00000445329.1_5'UTR|TRIM6_ENST00000380107.1_Silent_p.L122L|AC015691.13_ENST00000394793.2_RNA|TRIM6_ENST00000380097.3_Silent_p.L176L|TRIM6_ENST00000515022.1_Intron|TRIM6_ENST00000506134.1_5'UTR|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Silent_p.L176L	NM_001198645.1|NM_058166.4	NP_001185574.1|NP_477514.1	Q9C030	TRIM6_HUMAN	tripartite motif containing 6	148					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|prostate(2)|stomach(1)	22		Lung NSC(207;2.23e-07)|all_lung(207;1.81e-06)|Medulloblastoma(188;0.00225)|Breast(177;0.0101)|all_neural(188;0.0212)		Epithelial(150;1.12e-45)|BRCA - Breast invasive adenocarcinoma(625;0.00101)|LUSC - Lung squamous cell carcinoma(625;0.192)		AGGAGTCTCTAAAGAAGCTGA	0.438													A|||	431	0.0860623	0.0598	0.0836	5008	,	,		20410	0.1756		0.0109	False		,,,				2504	0.1084				p.L176L		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.A528G						PASS	.	A	,,,,	306,4096	165.8+/-197.2	9,288,1904	127.0	131.0	130.0		528,528,,,444	2.6	1.0	11	dbSNP_107	130	124,8470	64.9+/-127.2	3,118,4176	no	coding-synonymous,coding-synonymous,utr-5,intron,coding-synonymous	TRIM6,TRIM6-TRIM34	NM_001003818.2,NM_001003819.3,NM_001198644.1,NM_001198645.1,NM_058166.4	,,,,	12,406,6080	GG,GA,AA		1.4429,6.9514,3.3087	,,,,	176/517,176/843,,,148/489	5625784	430,12566	2201	4297	6498	SO:0001819	synonymous_variant	445372	exon3			GTCTCTAAAGAAG	AF220030	CCDS31389.1, CCDS31390.1, CCDS55738.1	11p15	2013-01-09	2011-01-25		ENSG00000121236	ENSG00000121236		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16277	protein-coding gene	gene with protein product		607564	"""tripartite motif-containing 6"""			11331580	Standard	NM_058166		Approved	RNF89		Q9C030	OTTHUMG00000150029	ENST00000278302.5:c.444A>G	11.37:g.5625784A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_001003819	A8K2A7|B4DDQ5|Q86WZ8|Q9HCR1	Silent	SNP	ENST00000278302.5	37	CCDS31390.1																																																																																			A|0.949;G|0.051	0.051	strong		0.438	TRIM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143376.2	NM_001003818	
TNS3	64759	hgsc.bcm.edu	37	7	47343079	47343079	+	Missense_Mutation	SNP	A	A	G	rs61731305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47343079A>G	ENST00000398879.1	-	22	3292	c.2926T>C	c.(2926-2928)Tcc>Ccc	p.S976P	TNS3_ENST00000355730.3_Missense_Mutation_p.S736P|TNS3_ENST00000311160.9_Missense_Mutation_p.S976P			Q68CZ2	TENS3_HUMAN	tensin 3	976					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						CTGGTACCGGAGAACTCAGCG	0.652													A|||	50	0.00998403	0.0371	0.0014	5008	,	,		16308	0.0		0.0	False		,,,				2504	0.0				p.S976P		Atlas-SNP	.											.	TNS3	140	.	0			c.T2926C						PASS	.	A	PRO/SER	110,3944		1,108,1918	24.0	30.0	28.0		2926	-4.5	0.0	7	dbSNP_129	28	1,8365		0,1,4182	yes	missense	TNS3	NM_022748.11	74	1,109,6100	GG,GA,AA		0.012,2.7134,0.8937	benign	976/1446	47343079	111,12309	2027	4183	6210	SO:0001583	missense	64759	exon22			TACCGGAGAACTC	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"""SH2 domain containing"""	21616	protein-coding gene	gene with protein product	"""tumor endothelial marker 6"""	606825	"""tensin-like SH2 domain-containing 1"""	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.2926T>C	7.37:g.47343079A>G	ENSP00000381854:p.Ser976Pro	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	94	55	0.585106	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	37	CCDS5506.2	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	A	7.817	0.717014	0.15372	0.027134	1.2E-4	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000545849;ENST00000457718	D;D;D;D	0.94828	-3.07;-3.07;-3.53;-3.23	5.34	-4.47	0.03525	.	1.008340	0.07998	N	0.988200	T	0.56891	0.2016	N	0.08118	0	0.24069	N	0.995984	B	0.02656	0.0	B	0.04013	0.001	T	0.65516	-0.6149	10	0.25751	T	0.34	-5.9377	1.8322	0.03132	0.4155:0.1339:0.3198:0.1308	.	976	Q68CZ2	TENS3_HUMAN	P	976;1086;976;736;432;1079	ENSP00000312143:S976P;ENSP00000381854:S976P;ENSP00000347968:S736P;ENSP00000414358:S1079P	ENSP00000312143:S976P	S	-	1	0	TNS3	47309604	0.942000	0.31987	0.002000	0.10522	0.058000	0.15608	0.267000	0.18552	-0.660000	0.05352	0.528000	0.53228	TCC	A|0.989;G|0.011	0.011	strong		0.652	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748	
PRR12	57479	hgsc.bcm.edu	37	19	50097784	50097784	+	Silent	SNP	T	T	C	rs10414643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	74	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	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	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573759	140573759	+	Missense_Mutation	SNP	C	C	T	rs17844584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140573759C>T	ENST00000239446.4	+	1	1818	c.1634C>T	c.(1633-1635)gCg>gTg	p.A545V		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	545	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)	p.A545V(1)		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)			AGCAGAGAGGCGCTGGTGCGC	0.706													C|||	27	0.00539137	0.0204	0.0	5008	,	,		16480	0.0		0.0	False		,,,				2504	0.0				p.A545V		Atlas-SNP	.											PCDHB10,colon,carcinoma,0,1	PCDHB10	177	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1634T						scavenged	.	C	VAL/ALA	66,4300		0,66,2117	34.0	48.0	43.0		1634	3.5	1.0	5	dbSNP_123	43	0,8560		0,0,4280	no	missense	PCDHB10	NM_018930.3	64	0,66,6397	TT,TC,CC		0.0,1.5117,0.5106	benign	545/801	140573759	66,12860	2183	4280	6463	SO:0001583	missense	56126	exon1			GAGAGGCGCTGGT	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.1634C>T	5.37:g.140573759C>T	ENSP00000239446:p.Ala545Val	Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	145	68	0.468966	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	c	14.35	2.508907	0.44660	0.015117	0.0	ENSG00000120324	ENST00000239446	T	0.01787	4.64	3.53	3.53	0.40419	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00875	0.0029	N	0.16266	0.395	0.09310	N	1	D	0.54047	0.964	P	0.48921	0.595	T	0.53136	-0.8481	9	0.14252	T	0.57	.	7.8479	0.29437	0.0:0.8331:0.0:0.1669	rs17844584	545	Q9UN67	PCDBA_HUMAN	V	545	ENSP00000239446:A545V	ENSP00000239446:A545V	A	+	2	0	PCDHB10	140553943	0.000000	0.05858	0.998000	0.56505	0.980000	0.70556	-0.423000	0.07034	1.994000	0.58287	0.549000	0.68633	GCG	C|0.993;T|0.007	0.007	strong		0.706	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
TIGD7	91151	hgsc.bcm.edu	37	16	3349300	3349300	+	Missense_Mutation	SNP	C	C	G	rs151295470		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3349300C>G	ENST00000396862.1	-	2	3143	c.1315G>C	c.(1315-1317)Gtg>Ctg	p.V439L	TIGD7_ENST00000574598.1_5'Flank|TIGD7_ENST00000268674.2_Missense_Mutation_p.V439L	NM_033208.3	NP_149985.2	Q6NT04	TIGD7_HUMAN	tigger transposable element derived 7	439						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12						TTTAACCACACCCTATCATCA	0.383																																					p.V439L		Atlas-SNP	.											.	TIGD7	41	.	0			c.G1315C						PASS	.	C	LEU/VAL	3,4391	6.2+/-15.9	0,3,2194	162.0	174.0	170.0		1315	-0.7	0.0	16	dbSNP_134	170	0,8600		0,0,4300	yes	missense	TIGD7	NM_033208.3	32	0,3,6494	GG,GC,CC		0.0,0.0683,0.0231	possibly-damaging	439/550	3349300	3,12991	2197	4300	6497	SO:0001583	missense	91151	exon2			ACCACACCCTATC	AF251050	CCDS10500.1	16p13.11	2008-02-05			ENSG00000140993	ENSG00000140993			18331	protein-coding gene	gene with protein product		612969					Standard	NM_033208		Approved	Sancho	uc002cus.3	Q6NT04	OTTHUMG00000129325	ENST00000396862.1:c.1315G>C	16.37:g.3349300C>G	ENSP00000380071:p.Val439Leu	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	300	142	0.473333	NM_033208	Q9BXZ0	Missense_Mutation	SNP	ENST00000396862.1	37	CCDS10500.1	.	.	.	.	.	.	.	.	.	.	C	0.050	-1.253366	0.01457	6.83E-4	0.0	ENSG00000140993	ENST00000426381;ENST00000396862;ENST00000268674	T;T	0.31510	1.49;1.49	4.88	-0.699	0.11277	.	1.396770	0.05259	U	0.515337	T	0.19327	0.0464	N	0.19112	0.55	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.26503	-1.0101	10	0.26408	T	0.33	.	7.8653	0.29533	0.0:0.5056:0.0:0.4944	.	439	Q6NT04	TIGD7_HUMAN	L	439	ENSP00000380071:V439L;ENSP00000268674:V439L	ENSP00000268674:V439L	V	-	1	0	TIGD7	3289301	0.005000	0.15991	0.001000	0.08648	0.291000	0.27294	-0.189000	0.09629	-0.110000	0.12022	-0.150000	0.13652	GTG	C|1.000;G|0.000	0.000	weak		0.383	TIGD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251465.1	NM_033208	
WDR26	80232	hgsc.bcm.edu	37	1	224607296	224607296	+	Silent	SNP	T	T	C	rs142827296	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:224607296T>C	ENST00000414423.2	-	5	979	c.786A>G	c.(784-786)gcA>gcG	p.A262A	WDR26_ENST00000366852.2_3'UTR|WDR26_ENST00000295024.6_Silent_p.A115A	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	262						cytoplasm (GO:0005737)|nucleus (GO:0005634)				biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		GTAGGTCTTCTGCATGGCTAC	0.353													T|||	6	0.00119808	0.0038	0.0	5008	,	,		17617	0.001		0.0	False		,,,				2504	0.0				p.A262A		Atlas-SNP	.											WDR26_ENST00000414423,NS,carcinoma,0,2	WDR26	104	2	0			c.A786G						PASS	.	T	,	8,4398	14.3+/-33.2	0,8,2195	126.0	112.0	117.0		738,786	-1.0	1.0	1	dbSNP_134	117	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	WDR26	NM_001115113.2,NM_025160.6	,	0,8,6495	CC,CT,TT		0.0,0.1816,0.0615	,	246/646,262/662	224607296	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	80232	exon5			GTCTTCTGCATGG	AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"""WD repeat domain containing"""	21208	protein-coding gene	gene with protein product	"""GID complex subunit 7 homolog (S. cerevisiae)"""						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.786A>G	1.37:g.224607296T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_025160	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Silent	SNP	ENST00000414423.2	37	CCDS31037.2																																																																																			T|0.999;C|0.001	0.001	strong		0.353	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160	
SCAF1	58506	hgsc.bcm.edu	37	19	50157980	50157980	+	Silent	SNP	G	G	A	rs61741228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50157980G>A	ENST00000360565.3	+	9	3595	c.3471G>A	c.(3469-3471)ctG>ctA	p.L1157L		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1157					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		CTTTGGGTCTGCCCCCTGGCC	0.672													g|||	32	0.00638978	0.0234	0.0014	5008	,	,		15138	0.0		0.0	False		,,,				2504	0.0				p.L1157L		Atlas-SNP	.											.	SCAF1	78	.	0			c.G3471A						PASS	.			84,4322	71.4+/-109.4	2,80,2121	85.0	77.0	80.0		3471	-1.0	1.0	19	dbSNP_129	80	0,8600		0,0,4300	no	coding-synonymous	SCAF1	NM_021228.2		2,80,6421	AA,AG,GG		0.0,1.9065,0.6459		1157/1313	50157980	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	58506	exon9			GGGTCTGCCCCCT	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.3471G>A	19.37:g.50157980G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Silent	SNP	ENST00000360565.3	37	CCDS33074.1																																																																																			G|0.993;A|0.007	0.007	strong		0.672	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
PINK1	65018	hgsc.bcm.edu	37	1	20975047	20975047	+	Silent	SNP	T	T	C	rs45499398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:20975047T>C	ENST00000321556.4	+	6	1267	c.1173T>C	c.(1171-1173)gaT>gaC	p.D391D	PINK1_ENST00000492302.1_3'UTR|PINK1-AS_ENST00000451424.1_RNA	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	391	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCCTGGCTGATGAGAGCATCG	0.607													T|||	50	0.00998403	0.0356	0.0043	5008	,	,		19352	0.0		0.0	False		,,,				2504	0.0				p.D391D	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.T1173C						PASS	.	T		157,4249	107.8+/-146.2	6,145,2052	65.0	57.0	60.0		1173	-5.2	0.0	1	dbSNP_127	60	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	PINK1	NM_032409.2		6,147,6350	CC,CT,TT		0.0233,3.5633,1.2225		391/582	20975047	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	65018	exon6			GGCTGATGAGAGC	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"""Parkinson disease"""	14581	protein-coding gene	gene with protein product		608309	"""Parkinson disease (autosomal recessive) 6"""	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.1173T>C	1.37:g.20975047T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Silent	SNP	ENST00000321556.4	37	CCDS211.1																																																																																			T|0.989;C|0.011	0.011	strong		0.607	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409	
MUC17	140453	hgsc.bcm.edu	37	7	100678616	100678616	+	Missense_Mutation	SNP	G	G	A	rs113959201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678616G>A	ENST00000306151.4	+	3	3983	c.3919G>A	c.(3919-3921)Ggt>Agt	p.G1307S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1307	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)					TGACACTAAAGGTCCTGTGGT	0.453																																					p.G1307S		Atlas-SNP	.											.	MUC17	804	.	0			c.G3919A						PASS	.						238.0	228.0	231.0					7																	100678616		2203	4300	6503	SO:0001583	missense	140453	exon3			ACTAAAGGTCCTG	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.3919G>A	7.37:g.100678616G>A	ENSP00000302716:p.Gly1307Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	134	19	0.141791	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	2.077	-0.411605	0.04799	.	.	ENSG00000169876	ENST00000306151	T	0.03468	3.92	0.471	-0.942	0.10398	.	.	.	.	.	T	0.01029	0.0034	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39761	-0.9598	8	0.06757	T	0.87	.	.	.	.	.	1307	Q685J3	MUC17_HUMAN	S	1307	ENSP00000302716:G1307S	ENSP00000302716:G1307S	G	+	1	0	MUC17	100465336	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.794000	0.04584	-2.345000	0.00621	-1.616000	0.00795	GGT	G|0.941;A|0.059	0.059	strong		0.453	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FAM101A	144347	hgsc.bcm.edu	37	12	124798797	124798797	+	Missense_Mutation	SNP	C	C	T	rs116090335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124798797C>T	ENST00000389727.3	+	3	377	c.377C>T	c.(376-378)gCg>gTg	p.A126V	FAM101A_ENST00000324038.3_Missense_Mutation_p.A45V|FAM101A_ENST00000546355.1_Missense_Mutation_p.A45V|FAM101A_ENST00000338359.4_Missense_Mutation_p.A45V			Q6ZTI6	F101A_HUMAN	family with sequence similarity 101, member A	126										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)		GTCTTCTATGCGCCCGTACCC	0.622													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18557	0.0		0.0	False		,,,				2504	0.0				p.A45V		Atlas-SNP	.											.	FAM101A	10	.	0			c.C134T						PASS	.	C	VAL/ALA,VAL/ALA	31,4375	37.6+/-69.7	0,31,2172	84.0	72.0	76.0		134,134	0.0	0.1	12	dbSNP_132	76	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	FAM101A,ZNF664-FAM101A	NM_001204299.1,NM_181709.4	64,64	0,32,6471	TT,TC,CC		0.0116,0.7036,0.246	benign,benign	45/136,45/136	124798797	32,12974	2203	4300	6503	SO:0001583	missense	144347	exon3			TCTATGCGCCCGT		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.377C>T	12.37:g.124798797C>T	ENSP00000374377:p.Ala126Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	144	80	0.555556	NM_181709	A5D8T5	Missense_Mutation	SNP	ENST00000389727.3	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	2.675	-0.276668	0.05679	0.007036	1.16E-4	ENSG00000178882	ENST00000324038;ENST00000541200;ENST00000389727;ENST00000546355;ENST00000338359	.	.	.	4.69	0.0271	0.14153	.	0.566604	0.18703	N	0.133527	T	0.13243	0.0321	N	0.10874	0.06	0.28756	N	0.901148	B	0.13145	0.007	B	0.08055	0.003	T	0.10683	-1.0619	9	0.29301	T	0.29	-0.5442	5.5434	0.17051	0.0:0.3925:0.1872:0.4203	.	126	Q6ZTI6	F101A_HUMAN	V	45;45;126;45;45	.	ENSP00000315626:A45V	A	+	2	0	FAM101A	123364750	0.126000	0.22350	0.078000	0.20375	0.034000	0.12701	0.293000	0.19029	0.085000	0.17107	-1.175000	0.01729	GCG	C|0.998;T|0.002	0.002	strong		0.622	FAM101A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_181709	
SLC12A9	56996	hgsc.bcm.edu	37	7	100458795	100458795	+	Silent	SNP	T	T	C	rs314378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100458795T>C	ENST00000354161.3	+	10	1379	c.1254T>C	c.(1252-1254)gcT>gcC	p.A418A	SLC12A9_ENST00000540482.1_Silent_p.A418A|SLC12A9_ENST00000415287.1_Silent_p.A329A|SLC12A9_ENST00000428758.1_Silent_p.A418A|SLC12A9_ENST00000275729.3_Silent_p.A329A	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	418					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)					ACACACTGGCTGCTGTGGTCA	0.622													C|||	2897	0.578474	0.4168	0.6527	5008	,	,		17391	0.8095		0.5159	False		,,,				2504	0.5706				p.A418A		Atlas-SNP	.											.	SLC12A9	81	.	0			c.T1254C						PASS	.	C		1969,2437	620.5+/-393.6	416,1137,650	114.0	99.0	104.0		1254	-10.3	0.0	7	dbSNP_79	104	4504,4096	560.2+/-387.5	1220,2064,1016	no	coding-synonymous	SLC12A9	NM_020246.2		1636,3201,1666	CC,CT,TT		47.6279,44.6891,49.7693		418/915	100458795	6473,6533	2203	4300	6503	SO:0001819	synonymous_variant	56996	exon10			ACTGGCTGCTGTG	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.1254T>C	7.37:g.100458795T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1																																																																																			T|0.465;C|0.535	0.535	strong		0.622	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
COL6A3	1293	hgsc.bcm.edu	37	2	238243369	238243369	+	Silent	SNP	G	G	A	rs10201909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238243369G>A	ENST00000295550.4	-	41	9581	c.9129C>T	c.(9127-9129)cgC>cgT	p.R3043R	COL6A3_ENST00000472056.1_Silent_p.R2436R|COL6A3_ENST00000409809.1_Silent_p.R2837R|COL6A3_ENST00000346358.4_Silent_p.R2843R|COL6A3_ENST00000347401.3_Silent_p.R2842R|COL6A3_ENST00000353578.4_Silent_p.R2837R	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	3043	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|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)		CTCCAATGACGCGGTCCGTGA	0.572													G|||	355	0.0708866	0.2194	0.0375	5008	,	,		17549	0.005		0.0179	False		,,,				2504	0.0164				p.R3043R		Atlas-SNP	.											COL6A3,colon,carcinoma,-1,2	COL6A3	608	2	0			c.C9129T						scavenged	.	G	,,	810,3596	323.7+/-298.2	58,694,1451	72.0	66.0	68.0		9129,7308,8511	-9.8	0.0	2	dbSNP_119	68	169,8431	78.1+/-140.7	1,167,4132	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	59,861,5583	AA,AG,GG		1.9651,18.384,7.5273	,,	3043/3178,2436/2571,2837/2972	238243369	979,12027	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon41			AATGACGCGGTCC	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.9129C>T	2.37:g.238243369G>A		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.933;A|0.067	0.067	strong		0.572	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
CYLC1	1538	hgsc.bcm.edu	37	X	83128911	83128911	+	Missense_Mutation	SNP	G	G	C	rs12008888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:83128911G>C	ENST00000329312.4	+	4	1232	c.1195G>C	c.(1195-1197)Gat>Cat	p.D399H		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	399			D -> H (in dbSNP:rs12008888).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						CAAGAAAAAGGATGCAAAGAA	0.343													G|||	200	0.0529801	0.1384	0.0231	3775	,	,		14297	0.0		0.001	False		,,,				2504	0.0				p.D399H		Atlas-SNP	.											.	CYLC1	272	.	0			c.G1195C						PASS	.	G	HIS/ASP	581,3240		41,402,97,1184,470	30.0	24.0	26.0		1195	3.2	0.0	X	dbSNP_120	26	5,6711		0,5,0,2421,1864	yes	missense	CYLC1	NM_021118.1	81	41,407,97,3605,2334	CC,CG,C,GG,G		0.0744,15.2054,5.5614	probably-damaging	399/652	83128911	586,9951	2194	4290	6484	SO:0001583	missense	1538	exon4			AAAAAGGATGCAA	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"""cylicin 1"""	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1195G>C	X.37:g.83128911G>C	ENSP00000331556:p.Asp399His	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	75	0.045207956600361664	41	0.09234234234234234	5	0.014204545454545454	0	0.0	0	0.0	g	2.122	-0.401166	0.04865	0.152054	7.44E-4	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.28895	1.59	4.12	3.24	0.37175	.	.	.	.	.	T	0.00271	0.0008	L	0.49126	1.545	0.80722	P	0.0	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.98	T	0.06588	-1.0818	8	0.66056	D	0.02	-7.8087	6.0759	0.19915	0.1403:0.0:0.8597:0.0	rs12008888;rs52819056;rs12008888	399;399	P35663;F5H4V5	CYLC1_HUMAN;.	H	399	ENSP00000331556:D399H	ENSP00000331556:D399H	D	+	1	0	CYLC1	83015567	0.979000	0.34478	0.008000	0.14137	0.011000	0.07611	3.108000	0.50337	2.026000	0.59711	0.600000	0.82982	GAT	0|0.017;C|0.055	0.055	strong		0.343	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118	
CST1	1469	hgsc.bcm.edu	37	20	23728528	23728528	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23728528C>T	ENST00000304749.2	-	3	421	c.351G>A	c.(349-351)ttG>ttA	p.L117L	CST1_ENST00000398402.1_Silent_p.L117L	NM_001898.2	NP_001889.2	P01037	CYTN_HUMAN	cystatin SN	117					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.L117L(1)		kidney(1)|large_intestine(1)|lung(8)|ovary(1)|stomach(1)|urinary_tract(1)	13	Lung NSC(19;0.0676)|all_lung(19;0.148)					CGAAAGAGCACAACTGTTTCT	0.527																																					p.L117L		Atlas-SNP	.											CST1,NS,carcinoma,0,2	CST1	37	2	1	Substitution - coding silent(1)	lung(1)	c.G351A						scavenged	.						93.0	81.0	85.0					20																	23728528		2203	4300	6503	SO:0001819	synonymous_variant	1469	exon3			AGAGCACAACTGT	M19169	CCDS13160.1	20p11.2	2008-04-15			ENSG00000170373	ENSG00000170373			2473	protein-coding gene	gene with protein product		123855					Standard	NM_001898		Approved		uc002wtp.3	P01037	OTTHUMG00000032085	ENST00000304749.2:c.351G>A	20.37:g.23728528C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	210	10	0.047619	NM_001898	Q96LE6|Q9UCQ6	Silent	SNP	ENST00000304749.2	37	CCDS13160.1																																																																																			.	.	none		0.527	CST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078351.2	NM_001898	
SYTL2	54843	hgsc.bcm.edu	37	11	85436352	85436352	+	Intron	SNP	G	G	A	rs641393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:85436352G>A	ENST00000528231.1	-	7	1737				SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000354566.3_Missense_Mutation_p.T383M|SYTL2_ENST00000525423.1_Missense_Mutation_p.T383M|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000359152.5_Missense_Mutation_p.T907M	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CGAAATTTCCGTTTGAGAAGG	0.473													G|||	2611	0.521366	0.4062	0.4957	5008	,	,		20487	0.5972		0.6282	False		,,,				2504	0.5072				p.T383M		Atlas-SNP	.											SYTL2,NS,carcinoma,+1,1	SYTL2	231	1	0			c.C1148T						PASS	.	G	,,,MET/THR,MET/THR	1923,2483	530.0+/-372.8	436,1051,716	53.0	54.0	54.0		,,,1148,1148	-0.9	0.8	11	dbSNP_83	54	5429,3167	629.7+/-398.3	1730,1969,599	yes	intron,intron,intron,missense,missense	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,81,81	2166,3020,1315	AA,AG,GG		36.8427,43.645,43.4549	,,,possibly-damaging,possibly-damaging	,,,383/1273,383/1257	85436352	7352,5650	2203	4298	6501	SO:0001627	intron_variant	54843	exon1			ATTTCCGTTTGAG	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2586C>T	11.37:g.85436352G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	1200	0.5494505494505495	204	0.4146341463414634	196	0.5414364640883977	323	0.5646853146853147	477	0.6292875989445911	G	0.463	-0.888140	0.02511	0.43645	0.631573	ENSG00000137501	ENST00000359152;ENST00000354566;ENST00000525423	T;T;T	0.25579	1.79;1.79;1.79	6.16	-0.906	0.10524	.	0.743599	0.12813	N	0.437013	T	0.00012	0.0000	N	0.04508	-0.205	0.43857	P	0.0035410000000000164	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.06405	0.002;0.002;0.002	T	0.37641	-0.9697	8	.	.	.	-6.2622	2.8743	0.05626	0.2165:0.4856:0.0993:0.1986	rs641393;rs17208805;rs52804408;rs58119009;rs641393	383;383;383	Q9HCH5-11;Q9HCH5-7;Q9HCH5-8	.;.;.	M	907;383;383	ENSP00000352065:T907M;ENSP00000346576:T383M;ENSP00000432694:T383M	.	T	-	2	0	SYTL2	85114000	0.000000	0.05858	0.819000	0.32651	0.225000	0.24961	-0.488000	0.06497	-0.026000	0.13895	-0.839000	0.03059	ACG	G|0.451;A|0.549	0.549	strong		0.473	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
SERPINA5	5104	hgsc.bcm.edu	37	14	95054012	95054012	+	Missense_Mutation	SNP	A	A	G	rs6119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95054012A>G	ENST00000554866.1	+	2	427	c.313A>G	c.(313-315)Aag>Gag	p.K105E	SERPINA5_ENST00000553780.1_Missense_Mutation_p.K105E|SERPINA5_ENST00000554276.1_Missense_Mutation_p.K105E|SERPINA5_ENST00000329597.7_Missense_Mutation_p.K105E			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	105			K -> E (in allele PCI*B; dbSNP:rs6119). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:8713781, ECO:0000269|Ref.6}.		fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	AAGCTCAGAGAAGGAGCTGCA	0.592													G|||	1347	0.26897	0.615	0.1182	5008	,	,		19503	0.25		0.0905	False		,,,				2504	0.1115				p.K105E		Atlas-SNP	.											.	SERPINA5	69	.	0			c.A313G						PASS	.	G	GLU/LYS	2260,2146	574.6+/-383.8	585,1090,528	33.0	32.0	32.0		313	2.0	0.0	14	dbSNP_52	32	813,7787	779.3+/-407.7	41,731,3528	yes	missense	SERPINA5	NM_000624.4	56	626,1821,4056	GG,GA,AA		9.4535,48.7063,23.6276	benign	105/407	95054012	3073,9933	2203	4300	6503	SO:0001583	missense	5104	exon3			TCAGAGAAGGAGC	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.313A>G	14.37:g.95054012A>G	ENSP00000451126:p.Lys105Glu	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_000624	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	37	CCDS9928.1	532	0.24358974358974358	289	0.5873983739837398	48	0.13259668508287292	125	0.21853146853146854	70	0.09234828496042216	G	0.126	-1.119664	0.01785	0.512937	0.094535	ENSG00000188488	ENST00000554220;ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000555681;ENST00000554276;ENST00000557598	D;D;D;D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	3.94	2.01	0.26516	Serpin domain (3);	0.758820	0.12020	N	0.507024	T	0.00012	0.0000	N	0.00599	-1.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40664	-0.9551	9	0.02654	T	1	.	4.9873	0.14196	0.08:0.2673:0.5152:0.1375	rs6119;rs3190222;rs61244877;rs6119	105;105	G3V5Q9;P05154	.;IPSP_HUMAN	E	105	ENSP00000450484:K105E;ENSP00000450837:K105E;ENSP00000452469:K105E;ENSP00000451126:K105E;ENSP00000333203:K105E;ENSP00000450745:K105E;ENSP00000451650:K105E;ENSP00000451610:K105E;ENSP00000450485:K105E	ENSP00000333203:K105E	K	+	1	0	SERPINA5	94123765	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	-0.520000	0.06252	0.085000	0.17107	-0.231000	0.12243	AAG	A|0.750;G|0.250	0.250	strong		0.592	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
TMPRSS4	56649	hgsc.bcm.edu	37	11	117982464	117982464	+	Missense_Mutation	SNP	A	A	G	rs12270001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117982464A>G	ENST00000437212.3	+	8	806	c.592A>G	c.(592-594)Aag>Gag	p.K198E	TMPRSS4_ENST00000522824.1_Missense_Mutation_p.K193E|TMPRSS4_ENST00000534111.1_Missense_Mutation_p.K196E|TMPRSS4_ENST00000523251.1_Missense_Mutation_p.K158E|TMPRSS4_ENST00000522307.1_Missense_Mutation_p.K51E			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	198	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.		K -> E (in dbSNP:rs12270001).		proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		AGCCTGTGGGAAGAGCCTGAA	0.602													G|||	605	0.120807	0.2746	0.036	5008	,	,		17485	0.1558		0.008	False		,,,				2504	0.0532				p.K198E		Atlas-SNP	.											.	TMPRSS4	46	.	0			c.A592G						PASS	.	G	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	925,3475	726.9+/-409.8	104,717,1379	63.0	53.0	57.0		577,586,472,592	-2.7	0.1	11	dbSNP_120	57	59,8533	815.5+/-407.0	0,59,4237	yes	missense,missense,missense,missense	TMPRSS4	NM_001083947.1,NM_001173551.1,NM_001173552.1,NM_019894.3	56,56,56,56	104,776,5616	GG,GA,AA		0.6867,21.0227,7.5739	benign,benign,benign,benign	193/433,196/436,158/398,198/438	117982464	984,12008	2200	4296	6496	SO:0001583	missense	56649	exon8			TGTGGGAAGAGCC	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"""Serine peptidases / Transmembrane"""	11878	protein-coding gene	gene with protein product	"""transmembrane serine protease 3"", ""membrane-type serine protease 2"", ""type II membrane serine protease"""	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.592A>G	11.37:g.117982464A>G	ENSP00000416037:p.Lys198Glu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_019894	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	37	CCDS31684.1	242	0.1108058608058608	139	0.28252032520325204	12	0.03314917127071823	85	0.1486013986013986	6	0.0079155672823219	G	0.022	-1.413570	0.01145	0.210227	0.006867	ENSG00000137648	ENST00000534111;ENST00000522307;ENST00000523251;ENST00000437212;ENST00000522824;ENST00000522151	T;T;T;T;T;T	0.60548	0.18;0.18;0.18;0.18;0.18;0.18	4.89	-2.73	0.05950	Peptidase cysteine/serine, trypsin-like (1);Speract/scavenger receptor-related (1);	1.150470	0.06415	N	0.721296	T	0.00012	0.0000	N	0.02011	-0.69	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	0.08269	-1.0730	9	0.02654	T	1	.	6.512	0.22226	0.4509:0.3501:0.199:0.0	rs12270001;rs60127784;rs12270001	173;158;51;198;196	B7Z900;E7ERX8;E7ESG9;Q9NRS4;Q9NRS4-3	.;.;.;TMPS4_HUMAN;.	E	196;51;158;198;193;145	ENSP00000435184:K196E;ENSP00000428814:K51E;ENSP00000429209:K158E;ENSP00000416037:K198E;ENSP00000430547:K193E;ENSP00000428407:K145E	ENSP00000416037:K198E	K	+	1	0	TMPRSS4	117487674	0.000000	0.05858	0.117000	0.21633	0.507000	0.33981	-0.196000	0.09532	-0.937000	0.03719	-0.912000	0.02778	AAG	A|0.911;G|0.089	0.089	strong		0.602	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894	
SCML4	256380	hgsc.bcm.edu	37	6	108029133	108029133	+	Silent	SNP	C	C	T	rs61742583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:108029133C>T	ENST00000369020.3	-	7	1301	c.1056G>A	c.(1054-1056)gtG>gtA	p.V352V	SCML4_ENST00000369022.2_Silent_p.V294V|SCML4_ENST00000369025.2_Silent_p.V110V	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	352	SAM.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		TCACAAACCACACCACGTCCT	0.627													C|||	64	0.0127796	0.0477	0.0014	5008	,	,		18965	0.0		0.0	False		,,,				2504	0.0				p.V352V		Atlas-SNP	.											.	SCML4	65	.	0			c.G1056A						PASS	.	C		75,1309		0,75,617	54.0	63.0	60.0		1056	2.7	0.9	6	dbSNP_129	60	0,3182		0,0,1591	no	coding-synonymous	SCML4	NM_198081.3		0,75,2208	TT,TC,CC		0.0,5.4191,1.6426		352/415	108029133	75,4491	692	1591	2283	SO:0001819	synonymous_variant	256380	exon7			AAACCACACCACG		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.1056G>A	6.37:g.108029133C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	171	78	0.45614	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Silent	SNP	ENST00000369020.3	37	CCDS5060.2																																																																																			C|0.991;T|0.009	0.009	strong		0.627	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
UNC5C	8633	hgsc.bcm.edu	37	4	96106322	96106322	+	Missense_Mutation	SNP	A	A	G	rs2289043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:96106322A>G	ENST00000453304.1	-	13	2510	c.2162T>C	c.(2161-2163)aTg>aCg	p.M721T		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	721			M -> T (in dbSNP:rs2289043). {ECO:0000269|PubMed:9782087}.		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)		CTGTCCTCCCATCTGTCTCTC	0.448													A|||	2477	0.494609	0.0923	0.7507	5008	,	,		17114	0.5694		0.7147	False		,,,				2504	0.5532				p.M721T		Atlas-SNP	.											.	UNC5C	141	.	0			c.T2162C						PASS	.	A	THR/MET	816,3590	325.0+/-298.9	93,630,1480	109.0	103.0	105.0		2162	4.7	1.0	4	dbSNP_100	105	6041,2559	691.7+/-404.5	2147,1747,406	yes	missense	UNC5C	NM_003728.3	81	2240,2377,1886	GG,GA,AA		29.7558,18.5202,47.2782	benign	721/932	96106322	6857,6149	2203	4300	6503	SO:0001583	missense	8633	exon13			CCTCCCATCTGTC	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.2162T>C	4.37:g.96106322A>G	ENSP00000406022:p.Met721Thr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	133	79	0.593985	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	1191	0.5453296703296703	46	0.09349593495934959	260	0.7182320441988951	341	0.5961538461538461	544	0.7176781002638523	A	15.05	2.718955	0.48622	0.185202	0.702442	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.55413	0.84;0.52	5.87	4.71	0.59529	.	0.129840	0.64402	D	0.000001	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	1.0	B	0.27791	0.189	B	0.22386	0.039	T	0.41305	-0.9516	9	0.72032	D	0.01	.	11.4162	0.49954	0.9303:0.0:0.0697:0.0	rs2289043;rs52803176;rs57517044;rs2289043	721	O95185	UNC5C_HUMAN	T	721;680;740	ENSP00000406022:M721T;ENSP00000426924:M740T	ENSP00000328673:M680T	M	-	2	0	UNC5C	96325345	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.106000	0.71511	2.251000	0.74343	0.529000	0.55759	ATG	G|0.520;N|0.000	0.520	strong		0.448	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
GMPPB	29925	hgsc.bcm.edu	37	3	49760073	49760073	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49760073C>T	ENST00000480687.1	-	6	633	c.517G>A	c.(517-519)Gca>Aca	p.A173T	AMIGO3_ENST00000535833.1_5'UTR|GMPPB_ENST00000308375.6_Missense_Mutation_p.A173T|AMIGO3_ENST00000320431.7_5'Flank|GMPPB_ENST00000308388.6_Missense_Mutation_p.A173T			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B	173					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TACATGCCTGCGTTGATCTTA	0.592																																					p.A173T		Atlas-SNP	.											GMPPB,NS,carcinoma,0,1	GMPPB	14	1	0			c.G517A						scavenged	.						121.0	108.0	112.0					3																	49760073		2203	4300	6503	SO:0001583	missense	29925	exon5			TGCCTGCGTTGAT	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.517G>A	3.37:g.49760073C>T	ENSP00000418565:p.Ala173Thr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	167	4	0.0239521	NM_021971	A8K6N5|Q9H7U3	Missense_Mutation	SNP	ENST00000480687.1	37	CCDS2803.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.012612	0.75161	.	.	ENSG00000173540	ENST00000480687;ENST00000308375;ENST00000308388	D;D;D	0.94092	-3.35;-3.35;-3.35	4.58	4.58	0.56647	Nucleotidyl transferase (1);	0.054620	0.64402	D	0.000001	D	0.90655	0.7069	L	0.55834	1.745	0.80722	D	1	P;P	0.50156	0.932;0.902	B;B	0.43783	0.393;0.431	D	0.88432	0.3036	10	0.25106	T	0.35	-10.6477	11.7331	0.51748	0.1762:0.8238:0.0:0.0	.	173;173	Q9Y5P6-2;Q9Y5P6	.;GMPPB_HUMAN	T	173	ENSP00000418565:A173T;ENSP00000309092:A173T;ENSP00000311130:A173T	ENSP00000309092:A173T	A	-	1	0	GMPPB	49735077	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	5.680000	0.68168	2.373000	0.80994	0.462000	0.41574	GCA	.	.	none		0.592	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334	
KLHL31	401265	hgsc.bcm.edu	37	6	53517035	53517035	+	Silent	SNP	G	G	A	rs3823111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:53517035G>A	ENST00000407079.1	-	2	1265	c.1266C>T	c.(1264-1266)taC>taT	p.Y422Y	KLHL31_ENST00000370905.3_Silent_p.Y422Y			Q9H511	KLH31_HUMAN	kelch-like family member 31	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(3)	20	Lung NSC(77;0.0158)					CGCCCGCGGCGTACACGAGCC	0.637													G|||	663	0.132388	0.121	0.0937	5008	,	,		16333	0.2163		0.0596	False		,,,				2504	0.1636				p.Y422Y		Atlas-SNP	.											KLHL31,NS,carcinoma,-2,1	KLHL31	48	1	0			c.C1266T						PASS	.	G		475,3931	222.0+/-238.9	26,423,1754	56.0	58.0	57.0		1266	4.6	1.0	6	dbSNP_107	57	558,8042	151.6+/-206.3	17,524,3759	no	coding-synonymous	KLHL31	NM_001003760.4		43,947,5513	AA,AG,GG		6.4884,10.7808,7.9425		422/635	53517035	1033,11973	2203	4300	6503	SO:0001819	synonymous_variant	401265	exon3			CGCGGCGTACACG		CCDS34478.1	6p12.1	2013-09-27	2013-02-22	2007-01-09	ENSG00000124743	ENSG00000124743		"""Kelch-like"", ""BTB/POZ domain containing"""	21353	protein-coding gene	gene with protein product		610749	"""kelch repeat and BTB (POZ) domain containing 1"", ""kelch-like 31 (Drosophila)"""	KBTBD1			Standard	NM_001003760		Approved	bA345L23.2, BKLHD6	uc003pcb.4	Q9H511	OTTHUMG00000014882	ENST00000407079.1:c.1266C>T	6.37:g.53517035G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	94	62	0.659574	NM_001003760	A6N9J2|B2RP49	Silent	SNP	ENST00000407079.1	37	CCDS34478.1																																																																																			G|0.903;A|0.097	0.097	strong		0.637	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040965.1	NM_001003760	
SH3BP4	23677	hgsc.bcm.edu	37	2	235950002	235950002	+	Missense_Mutation	SNP	G	G	A	rs3731646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:235950002G>A	ENST00000409212.1	+	4	1096	c.589G>A	c.(589-591)Gca>Aca	p.A197T	SH3BP4_ENST00000392011.2_Missense_Mutation_p.A197T|SH3BP4_ENST00000344528.4_Missense_Mutation_p.A197T			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	197			A -> T (in dbSNP:rs3731646). {ECO:0000269|PubMed:16325581}.		cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		CCTTTTTGACGCAGGTACATC	0.532													A|||	1495	0.298522	0.2859	0.3256	5008	,	,		19630	0.4097		0.0915	False		,,,				2504	0.3947				p.A197T		Atlas-SNP	.											.	SH3BP4	109	.	0			c.G589A						PASS	.	A	THR/ALA	1146,3260	714.8+/-408.4	149,848,1206	108.0	105.0	106.0		589	-0.0	0.0	2	dbSNP_107	106	891,7709	778.4+/-407.7	43,805,3452	yes	missense	SH3BP4	NM_014521.2	58	192,1653,4658	AA,AG,GG		10.3605,26.01,15.662	benign	197/964	235950002	2037,10969	2203	4300	6503	SO:0001583	missense	23677	exon4			TTTGACGCAGGTA	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.589G>A	2.37:g.235950002G>A	ENSP00000386862:p.Ala197Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	37	CCDS2513.1	559	0.25595238095238093	142	0.2886178861788618	90	0.24861878453038674	253	0.4423076923076923	74	0.09762532981530343	A	0.006	-2.051408	0.00394	0.2601	0.103605	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000409212;ENST00000344528	T;T;T	0.08984	3.03;3.03;3.03	5.58	-0.0177	0.13967	.	0.553031	0.20798	N	0.085494	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	0.40308	-0.9570	9	0.12430	T	0.62	-1.2388	5.7498	0.18140	0.3802:0.3992:0.2206:0.0	rs3731646;rs60274850;rs3731646	197;197	A8K594;Q9P0V3	.;SH3B4_HUMAN	T	197	ENSP00000375867:A197T;ENSP00000386862:A197T;ENSP00000340237:A197T	ENSP00000340237:A197T	A	+	1	0	SH3BP4	235614741	0.001000	0.12720	0.000000	0.03702	0.052000	0.14988	0.383000	0.20651	-0.176000	0.10707	-0.269000	0.10298	GCA	G|0.786;A|0.214	0.214	strong		0.532	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305760	39305760	+	Missense_Mutation	SNP	C	C	T	rs427961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305760C>T	ENST00000343246.4	-	1	294	c.260G>A	c.(259-261)aGg>aAg	p.R87K		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	87	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)			gcaggtggtcctgcagcaggt	0.657													T|||	184	0.0367412	0.1256	0.0086	5008	,	,		15710	0.001		0.001	False		,,,				2504	0.0102				p.R87K		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.G260A						PASS	.						17.0	23.0	21.0					17																	39305760		2133	4241	6374	SO:0001583	missense	85289	exon1			GTGGTCCTGCAGC	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.260G>A	17.37:g.39305760C>T	ENSP00000340546:p.Arg87Lys	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	6.445	0.450231	0.12223	.	.	ENSG00000198271	ENST00000343246	T	0.00568	6.53	2.87	-5.75	0.02384	.	.	.	.	.	T	0.00468	0.0015	L	0.56769	1.78	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.43893	-0.9363	9	0.10111	T	0.7	.	5.8578	0.18730	0.1977:0.5979:0.0:0.2045	rs427961	92	Q9BYR2	KRA45_HUMAN	K	87	ENSP00000340546:R87K	ENSP00000340546:R87K	R	-	2	0	KRTAP4-5	36559286	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.772000	0.04694	-2.052000	0.00902	-1.408000	0.01128	AGG	T|1.000;|0.000	1.000	weak		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
CYP4A22	284541	hgsc.bcm.edu	37	1	47608983	47608983	+	Missense_Mutation	SNP	G	G	T	rs113777592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47608983G>T	ENST00000371891.3	+	5	584	c.553G>T	c.(553-555)Gtc>Ttc	p.V185F	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000371890.3_Missense_Mutation_p.V185F|CYP4A22_ENST00000294337.3_Missense_Mutation_p.V185F|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	185			V -> F (in allele CYP4A22*10, allele CYP4A22*11, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs113777592). {ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCCTCTGGAGGTCTTTCAGCA	0.542													G|||	1681	0.335663	0.2057	0.232	5008	,	,		19651	0.5536		0.1928	False		,,,				2504	0.5072				p.V185F	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											CYP4A22,colon,carcinoma,-2,1	CYP4A22	60	1	0			c.G553T						scavenged	.	G	PHE/VAL	1006,3400	372.0+/-320.2	107,792,1304	70.0	64.0	66.0		553	-1.9	0.0	1	dbSNP_132	66	1731,6865	315.9+/-312.5	184,1363,2751	no	missense	CYP4A22	NM_001010969.2	50	291,2155,4055	TT,TG,GG		20.1373,22.8325,21.0506	possibly-damaging	185/520	47608983	2737,10265	2203	4298	6501	SO:0001583	missense	284541	exon5			CTGGAGGTCTTTC		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.553G>T	1.37:g.47608983G>T	ENSP00000360958:p.Val185Phe	Somatic	759	4	0.00527009		WXS	Illumina HiSeq	Phase_I	818	318	0.388753	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	613	0.2806776556776557	95	0.19308943089430894	83	0.2292817679558011	298	0.5209790209790209	137	0.18073878627968337	g	12.99	2.104200	0.37145	0.228325	0.201373	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.70516	-0.45;-0.49;-0.49	1.44	-1.89	0.07689	.	0.621999	0.16471	N	0.212985	T	0.00012	0.0000	M	0.63843	1.955	0.45567	P	0.0014880000000000448	P;P	0.46064	0.846;0.872	B;P	0.49597	0.264;0.616	T	0.37478	-0.9704	9	0.62326	D	0.03	.	5.0373	0.14441	0.5021:0.2748:0.2231:0.0	.	185;185	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	F	185	ENSP00000360957:V185F;ENSP00000360958:V185F;ENSP00000294337:V185F	ENSP00000294337:V185F	V	+	1	0	CYP4A22	47381570	0.001000	0.12720	0.002000	0.10522	0.478000	0.33099	-1.183000	0.03079	-0.551000	0.06175	0.194000	0.17425	GTC	G|0.849;T|0.151	0.151	strong		0.542	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
FAM71E2	284418	hgsc.bcm.edu	37	19	55870319	55870319	+	Silent	SNP	C	C	T	rs143731075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55870319C>T	ENST00000424985.3	-	9	2110	c.1917G>A	c.(1915-1917)caG>caA	p.Q639Q	CTD-2105E13.6_ENST00000591954.3_Missense_Mutation_p.R189K	NM_001145402.1	NP_001138874.1	Q8N5Q1	F71E2_HUMAN	family with sequence similarity 71, member E2	639										NS(1)|breast(3)|endometrium(2)|kidney(1)|skin(1)	8						CCAACTTCCCCTGGCCCCTGA	0.617													c|||	91	0.0181709	0.0666	0.0043	5008	,	,		17639	0.0		0.0	False		,,,				2504	0.0				p.Q639Q		Atlas-SNP	.											.	FAM71E2	41	.	0			c.G1917A						PASS	.	C		100,1284		4,92,596	48.0	47.0	48.0		1917	1.8	0.0	19	dbSNP_134	48	0,3182		0,0,1591	no	coding-synonymous	FAM71E2	NM_001145402.1		4,92,2187	TT,TC,CC		0.0,7.2254,2.1901		639/923	55870319	100,4466	692	1591	2283	SO:0001819	synonymous_variant	284418	exon9			CTTCCCCTGGCCC	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.1917G>A	19.37:g.55870319C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_001145402	Q8ND99	Silent	SNP	ENST00000424985.3	37																																																																																				C|0.983;T|0.017	0.017	strong		0.617	FAM71E2-010	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000409063.4	NM_001145402	
SCARF1	8578	hgsc.bcm.edu	37	17	1538561	1538561	+	Missense_Mutation	SNP	G	G	A	rs8072430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1538561G>A	ENST00000263071.4	-	11	2033	c.1984C>T	c.(1984-1986)Cgg>Tgg	p.R662W	SCARF1_ENST00000571272.1_3'UTR|SCARF1_ENST00000348987.3_Missense_Mutation_p.R576W	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	662	Gly-rich.		R -> W (in dbSNP:rs8072430). {ECO:0000269|PubMed:8590280, ECO:0000269|PubMed:9395444}.		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)		AGTGGGGGCCGCCGGTGGCCA	0.682													G|||	105	0.0209665	0.0764	0.0058	5008	,	,		13011	0.0		0.0	False		,,,				2504	0.0				p.R662W		Atlas-SNP	.											.	SCARF1	46	.	0			c.C1984T						PASS	.	G	TRP/ARG,,TRP/ARG	237,3973		10,217,1878	15.0	17.0	17.0		1984,,1726	1.2	0.0	17	dbSNP_116	17	3,8223		0,3,4110	yes	missense,utr-3,missense	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	101,,101	10,220,5988	AA,AG,GG		0.0365,5.6295,1.9299	probably-damaging,,probably-damaging	662/831,,576/745	1538561	240,12196	2105	4113	6218	SO:0001583	missense	8578	exon11			GGGGCCGCCGGTG	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.1984C>T	17.37:g.1538561G>A	ENSP00000263071:p.Arg662Trp	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	68	25	0.367647	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	36	0.016483516483516484	34	0.06910569105691057	2	0.0055248618784530384	0	0.0	0	0.0	G	11.44	1.639770	0.29157	0.056295	3.65E-4	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.35973	1.28;1.28	5.0	1.23	0.21249	.	1.186410	0.06503	N	0.736688	T	0.07908	0.0198	M	0.62723	1.935	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.72075	0.942;0.976	T	0.04930	-1.0917	10	0.72032	D	0.01	-0.2214	6.3298	0.21264	0.1799:0.0:0.5964:0.2237	rs8072430;rs8072430	576;662	Q14162-2;Q14162	.;SREC_HUMAN	W	662;576	ENSP00000263071:R662W;ENSP00000323964:R576W	ENSP00000263071:R662W	R	-	1	2	SCARF1	1485311	0.001000	0.12720	0.008000	0.14137	0.014000	0.08584	0.529000	0.23019	0.433000	0.26313	-0.377000	0.06932	CGG	G|0.979;A|0.021	0.021	strong		0.682	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
PRKG1	5592	hgsc.bcm.edu	37	10	53822344	53822344	+	Silent	SNP	T	T	C	rs113994747	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:53822344T>C	ENST00000401604.2	+	7	1037	c.843T>C	c.(841-843)ctT>ctC	p.L281L	PRKG1_ENST00000373985.1_Silent_p.L269L|PRKG1_ENST00000373975.2_5'UTR|PRKG1_ENST00000373980.4_Silent_p.L296L			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	281	cGMP-binding, low affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		CAGTCTTTCTTAGAACTTTAG	0.403													T|||	106	0.0211661	0.0764	0.0058	5008	,	,		15835	0.0		0.001	False		,,,				2504	0.0				p.L296L		Atlas-SNP	.											.	PRKG1	167	.	0			c.T888C						PASS	.	T	,	299,4107	162.9+/-194.8	15,269,1919	65.0	67.0	66.0		843,888	0.8	1.0	10	dbSNP_132	66	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PRKG1	NM_001098512.2,NM_006258.3	,	15,269,6219	CC,CT,TT		0.0,6.7862,2.2989	,	281/672,296/687	53822344	299,12707	2203	4300	6503	SO:0001819	synonymous_variant	5592	exon7			CTTTCTTAGAACT		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.843T>C	10.37:g.53822344T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	119	68	0.571429	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Silent	SNP	ENST00000401604.2	37	CCDS44399.1																																																																																			T|0.976;C|0.024	0.024	strong		0.403	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
OR1N2	138882	hgsc.bcm.edu	37	9	125315557	125315557	+	Missense_Mutation	SNP	T	T	C	rs1831370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125315557T>C	ENST00000373688.2	+	1	167	c.109T>C	c.(109-111)Tgg>Cgg	p.W37R		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	37			W -> R (in dbSNP:rs1831370). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.W37R(1)		breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						ACTCTCTGAGTGGCCAGAGGA	0.517													C|||	2797	0.558506	0.5946	0.5908	5008	,	,		18962	0.6637		0.4791	False		,,,				2504	0.4601				p.W37R		Atlas-SNP	.											OR1N2,colon,carcinoma,-1,2	OR1N2	51	2	1	Substitution - Missense(1)	stomach(1)	c.T109C						PASS	.	C	ARG/TRP	2528,1878	541.4+/-375.8	714,1100,389	107.0	98.0	101.0		109	-2.6	0.0	9	dbSNP_92	101	4212,4388	583.3+/-391.5	1011,2190,1099	yes	missense	OR1N2	NM_001004457.1	101	1725,3290,1488	CC,CT,TT		48.9767,42.6237,48.1778	benign	37/331	125315557	6740,6266	2203	4300	6503	SO:0001583	missense	138882	exon1			TCTGAGTGGCCAG		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.109T>C	9.37:g.125315557T>C	ENSP00000362792:p.Trp37Arg	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	204	71	0.348039	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Missense_Mutation	SNP	ENST00000373688.2	37	CCDS35123.1	1197	0.5480769230769231	280	0.5691056910569106	211	0.5828729281767956	353	0.6171328671328671	353	0.4656992084432718	C	1.129	-0.653039	0.03480	0.573763	0.489767	ENSG00000171501	ENST00000373688	T	0.01059	5.39	4.31	-2.62	0.06152	.	1.300740	0.05678	N	0.589889	T	0.00012	0.0000	N	0.02842	-0.48	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07927	-1.0747	9	0.28530	T	0.3	.	0.6697	0.00856	0.2434:0.3281:0.1193:0.3093	rs1831370;rs17530879;rs60632643;rs1831370	37	Q8NGR9	OR1N2_HUMAN	R	37	ENSP00000362792:W37R	ENSP00000362792:W37R	W	+	1	0	OR1N2	124355378	0.000000	0.05858	0.002000	0.10522	0.463000	0.32649	-5.227000	0.00139	-0.761000	0.04670	-0.860000	0.03012	TGG	T|0.471;C|0.529	0.529	strong		0.517	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
TMX4	56255	hgsc.bcm.edu	37	20	7963041	7963041	+	Missense_Mutation	SNP	C	C	T	rs2076015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:7963041C>T	ENST00000246024.2	-	8	1122	c.907G>A	c.(907-909)Gga>Aga	p.G303R		NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	303	Glu-rich.		G -> R (in dbSNP:rs2076015). {ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(2)|lung(11)|skin(1)	17						CCGTCCTCTCCTGGGGGCCCC	0.582													C|||	1773	0.354034	0.6483	0.2334	5008	,	,		16298	0.5883		0.0726	False		,,,				2504	0.09				p.G303R		Atlas-SNP	.											.	TMX4	39	.	0			c.G907A						PASS	.	C	ARG/GLY	2456,1950	623.1+/-394.1	683,1090,430	140.0	123.0	129.0		907	-0.6	0.0	20	dbSNP_96	129	581,8019	156.0+/-209.9	22,537,3741	yes	missense	TMX4	NM_021156.2	125	705,1627,4171	TT,TC,CC		6.7558,44.2578,23.3508	benign	303/350	7963041	3037,9969	2203	4300	6503	SO:0001583	missense	56255	exon8			CCTCTCCTGGGGG		CCDS13101.1	20p12	2011-10-19	2009-02-23	2009-02-23	ENSG00000125827	ENSG00000125827		"""Protein disulfide isomerases"""	25237	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 14"""		"""thioredoxin domain containing 13"""	TXNDC13			Standard	NM_021156		Approved	DJ971N18.2, KIAA1162, PDIA14	uc002wmx.1	Q9H1E5	OTTHUMG00000031843	ENST00000246024.2:c.907G>A	20.37:g.7963041C>T	ENSP00000246024:p.Gly303Arg	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	177	175	0.988701	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Missense_Mutation	SNP	ENST00000246024.2	37	CCDS13101.1	764	0.3498168498168498	308	0.6260162601626016	73	0.20165745856353592	325	0.5681818181818182	58	0.07651715039577836	C	2.423	-0.332568	0.05314	0.557422	0.067558	ENSG00000125827	ENST00000246024	T	0.09255	3.0	5.72	-0.564	0.11774	.	0.974158	0.08471	N	0.940949	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33033	-0.9884	9	0.10111	T	0.7	0.0112	5.9282	0.19124	0.0:0.2476:0.1306:0.6218	rs2076015;rs17846062;rs17859056;rs52797785;rs60332072;rs2076015	303	Q9H1E5	TMX4_HUMAN	R	303	ENSP00000246024:G303R	ENSP00000246024:G303R	G	-	1	0	TMX4	7911041	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.068000	0.03447	-0.104000	0.12154	-1.353000	0.01230	GGA	C|0.693;T|0.307	0.307	strong		0.582	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156	
ESYT3	83850	hgsc.bcm.edu	37	3	138176436	138176436	+	Silent	SNP	A	A	G	rs35605373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:138176436A>G	ENST00000389567.4	+	4	717	c.531A>G	c.(529-531)gcA>gcG	p.A177A	ESYT3_ENST00000289135.4_Silent_p.A177A	NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	177	Glycerophospholipid-binding barrel-like domain. {ECO:0000250}.				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						GTGTCAAGGCACACACTAATA	0.587													A|||	118	0.0235623	0.0825	0.013	5008	,	,		20302	0.0		0.0	False		,,,				2504	0.0				p.A177A		Atlas-SNP	.											.	ESYT3	64	.	0			c.A531G						PASS	.	A		310,4096	166.5+/-197.7	5,300,1898	182.0	160.0	168.0		531	-10.9	0.0	3	dbSNP_126	168	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ESYT3	NM_031913.3		5,304,6194	GG,GA,AA		0.0465,7.0359,2.4143		177/887	138176436	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	83850	exon4			CAAGGCACACACT	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.531A>G	3.37:g.138176436A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	154	75	0.487013	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Silent	SNP	ENST00000389567.4	37	CCDS3101.2																																																																																			A|0.975;G|0.025	0.025	strong		0.587	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913	
TNFRSF10D	8793	hgsc.bcm.edu	37	8	23021346	23021346	+	Missense_Mutation	SNP	G	G	A	rs11135703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:23021346G>A	ENST00000312584.3	-	1	197	c.103C>T	c.(103-105)Ccc>Tcc	p.P35S		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	35			P -> S (in TRAIL-R4-B; dbSNP:rs11135703). {ECO:0000269|PubMed:9430226}.		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		AGGATCTTGGGGTCCAGGAGC	0.667											OREG0018632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1302	0.259984	0.2035	0.33	5008	,	,		16479	0.5655		0.1133	False		,,,				2504	0.1227				p.P35S		Atlas-SNP	.											.	TNFRSF10D	21	.	0			c.C103T						PASS	.	G	SER/PRO	925,3481	329.1+/-300.9	90,745,1368	48.0	38.0	41.0		103	0.4	0.0	8	dbSNP_120	41	965,7635	196.3+/-241.3	55,855,3390	yes	missense	TNFRSF10D	NM_003840.3	74	145,1600,4758	AA,AG,GG		11.2209,20.9941,14.5318	possibly-damaging	35/387	23021346	1890,11116	2203	4300	6503	SO:0001583	missense	8793	exon1			TCTTGGGGTCCAG	AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.103C>T	8.37:g.23021346G>A	ENSP00000310263:p.Pro35Ser	Somatic	80	0	0	760	WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_003840	B2R8W0|Q9Y6Q4	Missense_Mutation	SNP	ENST00000312584.3	37	CCDS6038.1	601	0.2751831501831502	90	0.18292682926829268	103	0.2845303867403315	316	0.5524475524475524	92	0.12137203166226913	G	12.01	1.810184	0.32053	0.209941	0.112209	ENSG00000173530	ENST00000312584	D	0.81908	-1.55	1.3	0.373	0.16178	.	0.837879	0.09789	U	0.755623	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	D	0.69078	0.997	P	0.60789	0.879	T	0.35500	-0.9786	9	0.28530	T	0.3	.	3.6311	0.08131	0.2621:0.0:0.7379:0.0	rs11135703;rs58794799	35	Q9UBN6	TR10D_HUMAN	S	35	ENSP00000310263:P35S	ENSP00000310263:P35S	P	-	1	0	TNFRSF10D	23077291	0.007000	0.16637	0.001000	0.08648	0.006000	0.05464	0.836000	0.27545	0.110000	0.17919	0.462000	0.41574	CCC	G|0.820;A|0.180	0.180	strong		0.667	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1		
FBXW9	84261	hgsc.bcm.edu	37	19	12807187	12807187	+	Missense_Mutation	SNP	C	C	T	rs6511833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12807187C>T	ENST00000380339.3	-	1	245	c.209G>A	c.(208-210)aGg>aAg	p.R70K	FBXW9_ENST00000587955.1_Missense_Mutation_p.R70K|FBXW9_ENST00000393261.3_Missense_Mutation_p.R70K|FBXW9_ENST00000544494.1_5'UTR			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	70			R -> K (in dbSNP:rs6511833).		SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						GGCCGAAACCCTGGACGCGGC	0.692													T|||	748	0.149361	0.5333	0.0461	5008	,	,		12421	0.0		0.0109	False		,,,				2504	0.0				p.R70K		Atlas-SNP	.											.	FBXW9	30	.	0			c.G209A						PASS	.	T	LYS/ARG	1544,2262		327,890,686	14.0	18.0	17.0		209	-0.2	0.0	19	dbSNP_116	17	128,8068		4,120,3974	yes	missense	FBXW9	NM_032301.2	26	331,1010,4660	TT,TC,CC		1.5617,40.5675,13.931	benign	70/459	12807187	1672,10330	1903	4098	6001	SO:0001583	missense	84261	exon1			GAAACCCTGGACG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.209G>A	19.37:g.12807187C>T	ENSP00000369696:p.Arg70Lys	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		244	0.11172161172161173	220	0.44715447154471544	17	0.04696132596685083	0	0.0	7	0.009234828496042216	T	7.621	0.676786	0.14841	0.405675	0.015617	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.53857	0.6;0.6	5.0	-0.247	0.13019	.	0.338458	0.20979	N	0.082254	T	0.00012	0.0000	N	0.02916	-0.46	0.46849	P	7.759999999999989E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.41998	-0.9477	9	0.02654	T	1	-7.7148	10.6828	0.45823	0.0:0.4314:0.0:0.5686	rs6511833;rs61227291;rs6511833	70;70	Q5XUX1-2;Q5XUX1-3	.;.	K	70	ENSP00000376945:R70K;ENSP00000369696:R70K	ENSP00000369696:R70K	R	-	2	0	FBXW9	12668187	0.063000	0.20901	0.023000	0.16930	0.194000	0.23727	-0.092000	0.11129	-0.309000	0.08779	-0.521000	0.04368	AGG	C|0.880;T|0.120	0.120	strong		0.692	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
HMMR	3161	hgsc.bcm.edu	37	5	162910136	162910136	+	Missense_Mutation	SNP	A	A	G	rs112257004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162910136A>G	ENST00000358715.3	+	14	1676	c.1640A>G	c.(1639-1641)cAg>cGg	p.Q547R	HMMR_ENST00000432118.2_Missense_Mutation_p.Q461R|HMMR_ENST00000393915.4_Missense_Mutation_p.Q548R|RP11-80G7.1_ENST00000521666.1_RNA|RP11-80G7.1_ENST00000514724.2_RNA|HMMR_ENST00000353866.3_Missense_Mutation_p.Q532R			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	547				Q -> R (in Ref. 3; BAF83266). {ECO:0000305}.	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)	CTCAAGCAACAGGAGGAAGAC	0.358													A|||	46	0.0091853	0.0287	0.0115	5008	,	,		17094	0.0		0.0	False		,,,				2504	0.0				p.Q548R		Atlas-SNP	.											.	HMMR	64	.	0			c.A1643G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	101,4305		1,99,2103	55.0	57.0	57.0		1643,1382,1640,1595	5.3	0.9	5	dbSNP_132	57	0,8594		0,0,4297	yes	missense,missense,missense,missense	HMMR	NM_001142556.1,NM_001142557.1,NM_012484.2,NM_012485.2	43,43,43,43	1,99,6400	GG,GA,AA		0.0,2.2923,0.7769	benign,benign,benign,benign	548/726,461/639,547/725,532/710	162910136	101,12899	2203	4297	6500	SO:0001583	missense	3161	exon14			AGCAACAGGAGGA	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.1640A>G	5.37:g.162910136A>G	ENSP00000351554:p.Gln547Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	128	53	0.414062	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	17	0.007783882783882784	12	0.024390243902439025	5	0.013812154696132596	0	0.0	0	0.0	A	13.18	2.159585	0.38119	0.022923	0.0	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.08282	3.11;3.11;3.11;3.11;3.11	5.33	5.33	0.75918	.	0.292472	0.38326	N	0.001730	T	0.06050	0.0157	L	0.60455	1.87	0.27255	N	0.958781	B;P;P;P	0.36959	0.383;0.51;0.575;0.575	B;B;B;P	0.45232	0.165;0.273;0.394;0.474	T	0.12319	-1.0552	10	0.14656	T	0.56	-11.8252	9.8283	0.40925	0.8474:0.0:0.0:0.1526	.	461;548;532;547	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	R	433;532;548;524;461;547	ENSP00000400527:Q433R;ENSP00000185942:Q532R;ENSP00000377492:Q548R;ENSP00000402673:Q461R;ENSP00000351554:Q547R	ENSP00000185942:Q532R	Q	+	2	0	HMMR	162842714	0.998000	0.40836	0.903000	0.35520	0.684000	0.39900	2.194000	0.42668	2.234000	0.73211	0.533000	0.62120	CAG	A|0.990;G|0.010	0.010	strong		0.358	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	
MMP15	4324	hgsc.bcm.edu	37	16	58079268	58079268	+	Missense_Mutation	SNP	C	C	T	rs141377329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58079268C>T	ENST00000219271.3	+	10	2713	c.1928C>T	c.(1927-1929)aCc>aTc	p.T643I		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	643					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)			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)	CTGGGCCTCACCTACGCGCTG	0.662													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		14760	0.0		0.0	False		,,,				2504	0.0				p.T643I		Atlas-SNP	.											.	MMP15	58	.	0			c.C1928T						PASS	.	C	ILE/THR	39,4355		0,39,2158	124.0	127.0	126.0		1928	3.6	0.0	16	dbSNP_134	126	1,8595		0,1,4297	yes	missense	MMP15	NM_002428.2	89	0,40,6455	TT,TC,CC		0.0116,0.8876,0.3079	benign	643/670	58079268	40,12950	2197	4298	6495	SO:0001583	missense	4324	exon10			GCCTCACCTACGC	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.1928C>T	16.37:g.58079268C>T	ENSP00000219271:p.Thr643Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_002428	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	C	2.732	-0.264139	0.05754	0.008876	1.16E-4	ENSG00000102996	ENST00000219271	T	0.25579	1.79	4.65	3.62	0.41486	Peptidase M10A, matrix metallopeptidase, C-terminal (1);	0.337903	0.33772	N	0.004578	T	0.02970	0.0088	N	0.00186	-1.895	0.26149	N	0.980165	B	0.06786	0.001	B	0.06405	0.002	T	0.40194	-0.9576	10	0.10902	T	0.67	.	5.4497	0.16556	0.0:0.7809:0.0:0.2191	.	643	P51511	MMP15_HUMAN	I	643	ENSP00000219271:T643I	ENSP00000219271:T643I	T	+	2	0	MMP15	56636769	0.999000	0.42202	0.018000	0.16275	0.093000	0.18481	2.919000	0.48836	2.418000	0.82041	0.555000	0.69702	ACC	C|0.997;T|0.003	0.003	strong		0.662	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428	
CCDC66	285331	hgsc.bcm.edu	37	3	56650012	56650012	+	Missense_Mutation	SNP	G	G	C	rs4681904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	60	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	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	
RNF207	388591	hgsc.bcm.edu	37	1	6272078	6272078	+	Missense_Mutation	SNP	G	G	A	rs12073329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6272078G>A	ENST00000377939.4	+	13	1388	c.1261G>A	c.(1261-1263)Gca>Aca	p.A421T	RNF207_ENST00000377948.2_Missense_Mutation_p.R138H	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	421			A -> T (in dbSNP:rs12073329).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		CACGCCCTTCGCAGAGCACTG	0.642													A|||	668	0.133387	0.3487	0.0648	5008	,	,		15200	0.0476		0.0408	False		,,,				2504	0.0746				p.A421T		Atlas-SNP	.											.	RNF207	45	.	0			c.G1261A						PASS	.	A	THR/ALA	1284,3080		193,898,1091	8.0	9.0	9.0		1261	-1.1	0.1	1	dbSNP_120	9	331,8195		10,311,3942	yes	missense	RNF207	NM_207396.2	58	203,1209,5033	AA,AG,GG		3.8822,29.4225,12.5291	benign	421/635	6272078	1615,11275	2182	4263	6445	SO:0001583	missense	388591	exon13			CCCTTCGCAGAGC	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1261G>A	1.37:g.6272078G>A	ENSP00000367173:p.Ala421Thr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	152	74	0.486842	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Missense_Mutation	SNP	ENST00000377939.4	37	CCDS59.2	249|249	0.11401098901098901|0.11401098901098901	167|167	0.3394308943089431|0.3394308943089431	27|27	0.07458563535911603|0.07458563535911603	27|27	0.0472027972027972|0.0472027972027972	28|28	0.036939313984168866|0.036939313984168866	A|A	0.032|0.032	-1.325328|-1.325328	0.01309|0.01309	0.294225|0.294225	0.038822|0.038822	ENSG00000158286|ENSG00000158286	ENST00000377939|ENST00000377948	T|.	0.49720|.	0.77|.	4.36|4.36	-1.06|-1.06	0.10002|0.10002	.|.	0.563614|.	0.18758|.	N|.	0.131998|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01576|0.01576	-0.805|-0.805	0.58432|0.58432	P|P	2.9999999999752447E-6|2.9999999999752447E-6	B|.	0.06786|.	0.001|.	B|.	0.01281|.	0.0|.	T|T	0.45512|0.45512	-0.9256|-0.9256	9|5	0.02654|0.15952	T|T	1|0.53	0.6441|0.6441	7.0283|7.0283	0.24952|0.24952	0.3911:0.0:0.4821:0.1268|0.3911:0.0:0.4821:0.1268	rs12073329;rs12073329|rs12073329;rs12073329	421|.	Q6ZRF8|.	RN207_HUMAN|.	T|H	421|138	ENSP00000367173:A421T|.	ENSP00000367173:A421T|ENSP00000367183:R138H	A|R	+|+	1|2	0|0	RNF207|RNF207	6194665|6194665	0.061000|0.061000	0.20836|0.20836	0.079000|0.079000	0.20413|0.20413	0.106000|0.106000	0.19336|0.19336	0.354000|0.354000	0.20146|0.20146	-0.813000|-0.813000	0.04357|0.04357	-1.390000|-1.390000	0.01156|0.01156	GCA|CGC	G|0.882;A|0.118	0.118	strong		0.642	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
PDLIM7	9260	hgsc.bcm.edu	37	5	176915143	176915143	+	Missense_Mutation	SNP	C	C	T	rs2306764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176915143C>T	ENST00000355841.2	-	10	1042	c.976G>A	c.(976-978)Gcc>Acc	p.A326T	PDLIM7_ENST00000393551.1_3'UTR|PDLIM7_ENST00000359895.2_Missense_Mutation_p.A292T|PDLIM7_ENST00000356618.4_3'UTR	NM_005451.3	NP_005442.2	Q9NR12	PDLI7_HUMAN	PDZ and LIM domain 7 (enigma)	326	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.		A -> T (in dbSNP:rs2306764).		actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|receptor-mediated endocytosis (GO:0006898)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ruffle (GO:0001726)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGAAGATGGCGCCCTTCTCC	0.607													C|||	677	0.135184	0.1339	0.1124	5008	,	,		19401	0.2907		0.0219	False		,,,				2504	0.1094				p.A326T		Atlas-SNP	.											.	PDLIM7	32	.	0			c.G976A						PASS	.	C	THR/ALA,THR/ALA	652,3752	281.1+/-275.7	43,566,1593	134.0	100.0	111.0		976,874	0.8	0.0	5	dbSNP_100	111	203,8397	87.4+/-149.7	1,201,4098	yes	missense,missense	PDLIM7	NM_005451.3,NM_203352.1	58,58	44,767,5691	TT,TC,CC		2.3605,14.8047,6.5749	benign,benign	326/458,292/424	176915143	855,12149	2202	4300	6502	SO:0001583	missense	9260	exon10			AGATGGCGCCCTT	BC001093	CCDS4422.1, CCDS4423.1, CCDS4424.1	5q35.3	2008-02-05			ENSG00000196923	ENSG00000196923			22958	protein-coding gene	gene with protein product		605903				11874232	Standard	NM_005451		Approved	ENIGMA	uc003mhc.1	Q9NR12	OTTHUMG00000130853	ENST00000355841.2:c.976G>A	5.37:g.176915143C>T	ENSP00000348099:p.Ala326Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_005451	Q14250|Q5XG82|Q6NVZ5|Q96C91|Q9BXB8|Q9BXB9	Missense_Mutation	SNP	ENST00000355841.2	37	CCDS4422.1	307	0.14056776556776557	82	0.16666666666666666	32	0.08839779005524862	174	0.3041958041958042	19	0.025065963060686015	C	7.142	0.582016	0.13749	0.148047	0.023605	ENSG00000196923	ENST00000359895;ENST00000355841	D;D	0.86956	-2.19;-2.19	5.26	0.818	0.18778	Zinc finger, LIM-type (4);	0.097403	0.37261	N	0.002172	T	0.00012	0.0000	L	0.28054	0.825	0.09310	P	0.99999415936	P;P	0.47034	0.889;0.854	B;B	0.43413	0.419;0.195	T	0.09952	-1.0651	9	0.13853	T	0.58	.	8.3463	0.32275	0.6479:0.2666:0.0:0.0855	rs2306764	326;292	Q9NR12;Q9NR12-2	PDLI7_HUMAN;.	T	292;326	ENSP00000352964:A292T;ENSP00000348099:A326T	ENSP00000348099:A326T	A	-	1	0	PDLIM7	176847749	0.363000	0.24989	0.031000	0.17742	0.001000	0.01503	1.037000	0.30241	0.199000	0.20427	-0.840000	0.03056	GCC	C|0.916;T|0.084	0.084	strong		0.607	PDLIM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253423.1	NM_005451	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808711	18808711	+	Silent	SNP	G	G	C	rs2992751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:18808711G>C	ENST00000400664.1	+	1	1288	c.1236G>C	c.(1234-1236)ggG>ggC	p.G412G		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	412						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)		CGGTGGCCGGGACCAATTTCT	0.657													G|||	1321	0.263778	0.1725	0.2349	5008	,	,		14427	0.625		0.1173	False		,,,				2504	0.1861				p.G412G		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G1236C						PASS	.	G		845,3561		85,675,1443	27.0	34.0	32.0		1236	2.2	0.8	1	dbSNP_101	32	1051,7549		54,943,3303	no	coding-synonymous	KLHDC7A	NM_152375.2		139,1618,4746	CC,CG,GG		12.2209,19.1784,14.5779		412/778	18808711	1896,11110	2203	4300	6503	SO:0001819	synonymous_variant	127707	exon1			GGCCGGGACCAAT	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.1236G>C	1.37:g.18808711G>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	42	15	0.357143	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																			G|0.795;C|0.205	0.205	strong		0.657	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
GGT1	2678	hgsc.bcm.edu	37	22	25016442	25016442	+	Missense_Mutation	SNP	C	C	T	rs3895576		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25016442C>T	ENST00000400382.1	+	8	1285	c.530C>T	c.(529-531)gCc>gTc	p.A177V	GGT1_ENST00000406383.2_Missense_Mutation_p.A177V|GGT1_ENST00000400380.1_Missense_Mutation_p.A177V|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400383.1_Missense_Mutation_p.A177V|GGT1_ENST00000248923.4_Missense_Mutation_p.A177V			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	177			A -> V (in dbSNP:rs3895576).		arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.A177V(1)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	TTGGCGGCAGCCCTGGAAAAC	0.687																																					p.A177V		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	prostate(1)	c.C530T						scavenged	.						25.0	28.0	27.0					22																	25016442		1906	4095	6001	SO:0001583	missense	2678	exon8			CGGCAGCCCTGGA	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.530C>T	22.37:g.25016442C>T	ENSP00000383232:p.Ala177Val	Somatic	531	14	0.0263653		WXS	Illumina HiSeq	Phase_I	663	44	0.066365	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	14.08	2.430183	0.43122	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383	T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23	3.35	3.35	0.38373	.	0.067565	0.64402	U	0.000018	T	0.09730	0.0239	L	0.56340	1.77	0.09310	N	1	B	0.12013	0.005	B	0.20577	0.03	T	0.15065	-1.0450	10	0.46703	T	0.11	-6.9103	10.3241	0.43783	0.0:0.7987:0.2013:0.0	rs3895576;rs4049845	177	P19440	GGT1_HUMAN	V	177	ENSP00000248923:A177V;ENSP00000393537:A177V;ENSP00000383232:A177V;ENSP00000383233:A177V;ENSP00000383231:A177V;ENSP00000385975:A177V	ENSP00000248923:A177V	A	+	2	0	GGT1	23346442	0.997000	0.39634	0.256000	0.24389	0.047000	0.14425	3.457000	0.53007	1.588000	0.49971	0.455000	0.32223	GCC	.	.	weak		0.687	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
DSPP	1834	hgsc.bcm.edu	37	4	88535831	88535831	+	Missense_Mutation	SNP	G	G	A	rs142316753|rs200378069		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88535831G>A	ENST00000282478.7	+	4	2050	c.2017G>A	c.(2017-2019)Gat>Aat	p.D673N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D673N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	673	Asp/Ser-rich.			D -> DSSDSSS (in Ref. 1; AAF42472). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgacagcagtgatagcagtga	0.488																																					p.D673N		Atlas-SNP	.											.	DSPP	174	.	0			c.G2017A						PASS	.						120.0	136.0	130.0					4																	88535831		1703	3111	4814	SO:0001583	missense	1834	exon5			AGCAGTGATAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2017G>A	4.37:g.88535831G>A	ENSP00000282478:p.Asp673Asn	Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	361	58	0.160665	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	-	3.944	-0.013591	0.07727	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87887	-2.31;-2.31	2.58	2.58	0.30949	.	.	.	.	.	T	0.78672	0.4320	L	0.43923	1.385	0.09310	N	0.999996	P	0.48694	0.914	B	0.40199	0.322	T	0.66512	-0.5905	9	0.21540	T	0.41	-9.092	5.9953	0.19491	0.1666:0.0:0.8334:0.0	.	673	Q9NZW4	DSPP_HUMAN	N	673	ENSP00000382213:D673N;ENSP00000282478:D673N	ENSP00000282478:D673N	D	+	1	0	DSPP	88754855	0.545000	0.26449	0.888000	0.34837	0.025000	0.11179	1.981000	0.40628	1.389000	0.46526	0.165000	0.16767	GAT	.	.	weak		0.488	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
INPP5B	3633	hgsc.bcm.edu	37	1	38411444	38411444	+	Missense_Mutation	SNP	C	C	T	rs56993041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38411444C>T	ENST00000373026.1	-	2	136	c.136G>A	c.(136-138)Ggc>Agc	p.G46S	INPP5B_ENST00000373023.2_Missense_Mutation_p.G46S|INPP5B_ENST00000373024.3_Missense_Mutation_p.G46S|INPP5B_ENST00000373021.1_Missense_Mutation_p.G46S			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	46	PH.		G -> S (in dbSNP:rs56993041).		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)				TCCTGGCCGCCGTGCTCCAGG	0.652													C|||	143	0.0285543	0.1021	0.0115	5008	,	,		15864	0.0		0.0	False		,,,				2504	0.0				p.G46S		Atlas-SNP	.											.	INPP5B	76	.	0			c.G136A						PASS	.	C	SER/GLY	341,3813		12,317,1748	54.0	65.0	61.0		136	4.4	0.0	1	dbSNP_129	61	0,8390		0,0,4195	yes	missense	INPP5B	NM_005540.2	56	12,317,5943	TT,TC,CC		0.0,8.209,2.7184	possibly-damaging	46/914	38411444	341,12203	2077	4195	6272	SO:0001583	missense	3633	exon3			GGCCGCCGTGCTC	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.136G>A	1.37:g.38411444C>T	ENSP00000362117:p.Gly46Ser	Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	215	118	0.548837	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	C	15.32	2.799766	0.50208	0.08209	0.0	ENSG00000204084	ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024;ENST00000373021	D;D;D;T	0.91945	-2.93;-2.93;-2.94;0.96	4.43	4.43	0.53597	.	0.993232	0.08181	N	0.985409	T	0.32763	0.0840	L	0.54323	1.7	0.80722	D	1	P	0.39920	0.695	B	0.32149	0.141	T	0.68047	-0.5512	10	0.51188	T	0.08	.	13.2598	0.60098	0.0:1.0:0.0:0.0	rs56993041;rs61744649	46	P32019-2	.	S	46	ENSP00000362114:G46S;ENSP00000362117:G46S;ENSP00000362115:G46S;ENSP00000362112:G46S	ENSP00000362112:G46S	G	-	1	0	INPP5B	38184031	0.009000	0.17119	0.018000	0.16275	0.185000	0.23345	2.347000	0.44036	2.411000	0.81874	0.563000	0.77884	GGC	C|0.978;T|0.022	0.022	strong		0.652	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
TNXB	7148	hgsc.bcm.edu	37	6	32023903	32023903	+	Missense_Mutation	SNP	G	G	C	rs440160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32023903G>C	ENST00000375244.3	-	24	8393	c.8192C>G	c.(8191-8193)cCg>cGg	p.P2731R	TNXB_ENST00000375247.2_Missense_Mutation_p.P2731R			P22105	TENX_HUMAN	tenascin XB	2789	Fibronectin type-III 19. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						AGGGGGCTCCGGGGCCTCAGT	0.642													G|||	223	0.0445288	0.1036	0.0605	5008	,	,		14531	0.001		0.0427	False		,,,				2504	0.0				p.P2731R		Atlas-SNP	.											.	TNXB	553	.	0			c.C8192G						PASS	.	G	ARG/PRO	201,2183		10,181,1001	40.0	47.0	45.0		8192	4.5	1.0	6	dbSNP_80	45	209,4793		4,201,2296	no	missense	TNXB	NM_019105.6	103	14,382,3297	CC,CG,GG		4.1783,8.4312,5.551	probably-damaging	2731/4243	32023903	410,6976	1192	2501	3693	SO:0001583	missense	7148	exon24			GGCTCCGGGGCCT	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.8192C>G	6.37:g.32023903G>C	ENSP00000364393:p.Pro2731Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		94	0.04304029304029304	42	0.08536585365853659	22	0.06077348066298342	1	0.0017482517482517483	29	0.03825857519788918	G	15.03	2.713296	0.48517	0.084312	0.041783	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.61510	0.47;0.1	4.48	4.48	0.54585	.	.	.	.	.	T	0.65974	0.2743	M	0.82923	2.615	0.28078	N	0.932303	D	0.61080	0.989	P	0.61070	0.883	T	0.60722	-0.7207	9	0.62326	D	0.03	.	12.0664	0.53590	0.0:0.1746:0.8254:0.0	rs440160;rs3948802	2731	P22105-3	.	R	2731	ENSP00000364393:P2731R;ENSP00000364396:P2731R	ENSP00000364393:P2731R	P	-	2	0	TNXB	32131881	0.037000	0.19845	0.989000	0.46669	0.396000	0.30629	0.607000	0.24209	2.317000	0.78254	0.456000	0.33151	CCG	G|0.931;C|0.069	0.069	strong		0.642	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
IKZF1	10320	hgsc.bcm.edu	37	7	50467767	50467767	+	Silent	SNP	C	C	A	rs61731355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:50467767C>A	ENST00000331340.3	+	8	1157	c.1002C>A	c.(1000-1002)ccC>ccA	p.P334P	IKZF1_ENST00000349824.4_Silent_p.P191P|IKZF1_ENST00000346667.4_Silent_p.P104P|IKZF1_ENST00000438033.1_Silent_p.P247P|IKZF1_ENST00000359197.5_Silent_p.P292P|IKZF1_ENST00000439701.1_Silent_p.P292P|IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000343574.5_Silent_p.P247P|IKZF1_ENST00000357364.4_Silent_p.P247P	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	334					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(28)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				TGCAGACGCCCCCGGGCGGTT	0.657			"""D,T"""	BCL6	"""ALL, DLBCL"""								C|||	746	0.148962	0.0908	0.196	5008	,	,		14198	0.0546		0.2296	False		,,,				2504	0.2086				p.P334P		Atlas-SNP	.		"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	IKZF1_ENST00000331340,NS,carcinoma,0,1	IKZF1	613	1	28	Unknown(28)	haematopoietic_and_lymphoid_tissue(28)	c.C1002A						PASS	.	C	,,,,,,,,,,,,	401,3625		19,363,1631	13.0	16.0	15.0		716,581,551,581,455,425,413,155,424,394,292,262,842	-2.3	0.6	7	dbSNP_129	15	1538,6786		155,1228,2779	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	IKZF1	NM_001220765.1,NM_001220766.1,NM_001220767.1,NM_001220768.1,NM_001220769.1,NM_001220770.1,NM_001220771.1,NM_001220772.1,NM_001220773.1,NM_001220774.1,NM_001220775.1,NM_001220776.1,NM_006060.4	,,,,,,,,,,,,	174,1591,4410	AA,AC,CC		18.4767,9.9603,15.7004	,,,,,,,,,,,,	292/478,247/433,237/423,247/433,205/391,195/381,191/377,64/250,151/337,141/327,109/295,99/285,334/520	50467767	1939,10411	2013	4162	6175	SO:0001819	synonymous_variant	10320	exon8			GACGCCCCCGGGC	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13176	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 92"""	603023	"""zinc finger protein, subfamily 1A, 1 (Ikaros)"""	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.1002C>A	7.37:g.50467767C>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Silent	SNP	ENST00000331340.3	37																																																																																				C|0.852;A|0.148	0.148	strong		0.657	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060	
ZNF668	79759	hgsc.bcm.edu	37	16	31075364	31075364	+	Silent	SNP	G	G	A	rs34889904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31075364G>A	ENST00000538906.1	-	2	1201	c.417C>T	c.(415-417)ccC>ccT	p.P139P	ZNF668_ENST00000535577.1_Silent_p.P139P|ZNF668_ENST00000539836.3_Silent_p.P162P|ZNF668_ENST00000426488.2_Silent_p.P162P|ZNF668_ENST00000300849.4_Silent_p.P139P|ZNF668_ENST00000564456.1_5'Flank|AC135050.5_ENST00000568708.1_RNA|ZNF668_ENST00000394983.2_Silent_p.P139P	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	139					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						CACAGCGGAAGGGCAGTTCGC	0.697													G|||	38	0.00758786	0.0257	0.0058	5008	,	,		17086	0.0		0.0	False		,,,				2504	0.0				p.P162P	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C486T						PASS	.	G	,,,	135,4259	84.8+/-123.5	4,127,2066	26.0	23.0	24.0		417,486,417,417	-0.6	1.0	16	dbSNP_126	24	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	4,128,6363	AA,AG,GG		0.0116,3.0724,1.047	,,,	139/620,162/643,139/620,139/620	31075364	136,12854	2197	4298	6495	SO:0001819	synonymous_variant	79759	exon3			GCGGAAGGGCAGT		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.417C>T	16.37:g.31075364G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1																																																																																			G|0.990;A|0.010	0.010	strong		0.697	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
ZNF439	90594	hgsc.bcm.edu	37	19	11977147	11977147	+	Splice_Site	SNP	G	G	A	rs10420385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11977147G>A	ENST00000304030.2	+	1	375		c.e1+1		ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Intron	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439						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						ACCTCTATAGGTAAGGATGAC	0.438													g|||	85	0.0169728	0.0628	0.0029	5008	,	,		18513	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	ZNF439	67	.	0			c.175+1G>A						PASS	.	G		295,4111	161.4+/-193.6	10,275,1918	123.0	124.0	123.0			0.6	0.1	19	dbSNP_119	123	5,8595	3.7+/-12.6	0,5,4295	yes	splice-5	ZNF439	NM_152262.2		10,280,6213	AA,AG,GG		0.0581,6.6954,2.3066			11977147	300,12706	2203	4300	6503	SO:0001630	splice_region_variant	90594	exon1			CTATAGGTAAGGA	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.175+1G>A	19.37:g.11977147G>A		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	244	121	0.495902	NM_152262	Q8IYZ7|Q96SU1	Splice_Site	SNP	ENST00000304030.2	37	CCDS12268.1	49	0.022435897435897436	47	0.09552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	-	5.467	0.271198	0.10349	0.066954	5.81E-4	ENSG00000171291	ENST00000442091;ENST00000304030	.	.	.	0.575	0.575	0.17374	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	rs10420385	.	.	.	.	-1	.	.	.	+	.	.	ZNF439	11838147	0.998000	0.40836	0.097000	0.21041	0.111000	0.19643	3.646000	0.54396	0.577000	0.29470	0.194000	0.17425	.	G|0.968;A|0.032	0.032	strong		0.438	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1		Intron
CEP135	9662	hgsc.bcm.edu	37	4	56837458	56837458	+	Missense_Mutation	SNP	A	A	G	rs141602415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:56837458A>G	ENST00000257287.4	+	10	1257	c.1133A>G	c.(1132-1134)gAa>gGa	p.E378G		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	378					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					TGCCAGAAAGAAAAGGAGAGA	0.294													A|||	4	0.000798722	0.003	0.0	5008	,	,		15338	0.0		0.0	False		,,,				2504	0.0				p.E378G		Atlas-SNP	.											CEP135,NS,carcinoma,+1,1	CEP135	115	1	0			c.A1133G						PASS	.	A	GLY/GLU	25,4381	26.2+/-53.5	0,25,2178	42.0	43.0	43.0		1133	6.0	1.0	4	dbSNP_134	43	0,8600		0,0,4300	yes	missense	CEP135	NM_025009.3	98	0,25,6478	GG,GA,AA		0.0,0.5674,0.1922	probably-damaging	378/1141	56837458	25,12981	2203	4300	6503	SO:0001583	missense	9662	exon10			AGAAAGAAAAGGA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"""KIAA0635"", ""centrosomal protein 4"""	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.1133A>G	4.37:g.56837458A>G	ENSP00000257287:p.Glu378Gly	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	25.9	4.681724	0.88542	0.005674	0.0	ENSG00000174799	ENST00000257287	T	0.53640	0.61	6.04	6.04	0.98038	.	0.091491	0.64402	D	0.000001	T	0.56920	0.2018	M	0.63428	1.95	0.42620	D	0.993343	D	0.69078	0.997	P	0.62885	0.908	T	0.63404	-0.6645	10	0.52906	T	0.07	.	16.5763	0.84648	1.0:0.0:0.0:0.0	.	378	Q66GS9	CP135_HUMAN	G	378	ENSP00000257287:E378G	ENSP00000257287:E378G	E	+	2	0	CEP135	56532215	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.387000	0.73191	2.317000	0.78254	0.459000	0.35465	GAA	A|0.998;G|0.002	0.002	strong		0.294	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009	
LCLAT1	253558	hgsc.bcm.edu	37	2	30863108	30863108	+	Missense_Mutation	SNP	A	A	G	rs12471868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:30863108A>G	ENST00000309052.4	+	7	1077	c.868A>G	c.(868-870)Ata>Gta	p.I290V	LCLAT1_ENST00000491680.2_3'UTR|LCLAT1_ENST00000379509.3_Missense_Mutation_p.I252V|LCLAT1_ENST00000540623.1_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	157	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	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	
C3	718	hgsc.bcm.edu	37	19	6713291	6713291	+	Silent	SNP	C	C	T	rs2230201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6713291C>T	ENST00000245907.6	-	9	1004	c.912G>A	c.(910-912)cgG>cgA	p.R304R		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	304					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	GCAGTACCTTCCGGCTCAGCA	0.642													C|||	1141	0.227835	0.1362	0.1225	5008	,	,		14613	0.4464		0.161	False		,,,				2504	0.2699				p.R304R		Atlas-SNP	.											.	C3	192	.	0			c.G912A						PASS	.	C		523,3883	236.1+/-248.4	25,473,1705	45.0	41.0	42.0		912	-9.0	0.0	19	dbSNP_98	42	1374,7226	263.9+/-285.3	129,1116,3055	no	coding-synonymous	C3	NM_000064.2		154,1589,4760	TT,TC,CC		15.9767,11.8702,14.5856		304/1664	6713291	1897,11109	2203	4300	6503	SO:0001819	synonymous_variant	718	exon9			TACCTTCCGGCTC	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.912G>A	19.37:g.6713291C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	37	CCDS32883.1																																																																																			T|0.156;G|0.000;C|0.844	0.156	strong		0.642	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
SOX9	6662	hgsc.bcm.edu	37	17	70118935	70118935	+	Silent	SNP	C	C	T	rs2229989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:70118935C>T	ENST00000245479.2	+	2	879	c.507C>T	c.(505-507)caC>caT	p.H169H		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	169					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|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 complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			AGAAGGACCACCCGGATTACA	0.682													C|||	684	0.136581	0.0416	0.1254	5008	,	,		11960	0.0139		0.2465	False		,,,				2504	0.2863				p.H169H	Pancreas(42;83 1041 2320 35205 39456)	Atlas-SNP	.											SOX9,NS,carcinoma,0,1	SOX9	91	1	0			c.C507T						PASS	.	C		309,4097	165.8+/-197.2	13,283,1907	54.0	56.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	507	1.6	1.0	17	dbSNP_98	55	1854,6746	325.5+/-317.0	210,1434,2656	no	coding-synonymous	SOX9	NM_000346.3		223,1717,4563	TT,TC,CC		21.5581,7.0132,16.6308		169/510	70118935	2163,10843	2203	4300	6503	SO:0001819	synonymous_variant	6662	exon2			GGACCACCCGGAT	S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"""SRY (sex determining region Y)-boxes"""	11204	protein-coding gene	gene with protein product		608160	"""campomelic dysplasia, autosomal sex-reversal"""	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.507C>T	17.37:g.70118935C>T		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	274	118	0.430657	NM_000346	Q53Y80	Silent	SNP	ENST00000245479.2	37	CCDS11689.1																																																																																			C|0.848;T|0.152	0.152	strong		0.682	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346	
POF1B	79983	hgsc.bcm.edu	37	X	84600948	84600948	+	Missense_Mutation	SNP	T	T	C	rs60768249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:84600948T>C	ENST00000262753.4	-	6	786	c.641A>G	c.(640-642)cAa>cGa	p.Q214R	POF1B_ENST00000373145.3_Missense_Mutation_p.Q214R	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	214						tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						TGTGATGGCTTGGATTTGCTG	0.463													T|||	135	0.0357616	0.0946	0.0144	3775	,	,		12542	0.0		0.0	False		,,,				2504	0.0				p.Q214R		Atlas-SNP	.											.	POF1B	77	.	0			c.A641G						PASS	.	T	ARG/GLN	462,3373		16,338,92,1278,479	234.0	189.0	204.0		641	4.6	0.0	X	dbSNP_129	204	2,6726		0,1,1,2427,1871	yes	missense	POF1B	NM_024921.3	43	16,339,93,3705,2350	CC,CT,C,TT,T		0.0297,12.0469,4.3927	possibly-damaging	214/590	84600948	464,10099	2203	4300	6503	SO:0001583	missense	79983	exon6			ATGGCTTGGATTT	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.641A>G	X.37:g.84600948T>C	ENSP00000262753:p.Gln214Arg	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	202	106	0.524752	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	37	CCDS14452.1	53	0.031946955997588906	32	0.06926406926406926	3	0.008426966292134831	0	0.0	0	0.0	T	6.220	0.408732	0.11812	0.120469	2.97E-4	ENSG00000124429	ENST00000262753;ENST00000373145;ENST00000276124	T;T	0.10763	2.84;2.84	4.56	4.56	0.56223	.	0.364164	0.23070	N	0.052276	T	0.00178	0.0005	L	0.53249	1.67	0.80722	P	0.0	B;B	0.25272	0.058;0.122	B;B	0.25291	0.059;0.04	T	0.05801	-1.0863	9	0.66056	D	0.02	.	9.2182	0.37360	0.0:0.0:0.0:1.0	rs60768249	214;214	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	R	214	ENSP00000262753:Q214R;ENSP00000362238:Q214R	ENSP00000262753:Q214R	Q	-	2	0	POF1B	84487604	0.828000	0.29307	0.049000	0.19019	0.045000	0.14185	3.232000	0.51302	1.775000	0.52247	0.481000	0.45027	CAA	T|0.958;C|0.042	0.042	strong		0.463	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921	
PSG9	5678	hgsc.bcm.edu	37	19	43773574	43773574	+	Missense_Mutation	SNP	G	G	A	rs73037706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43773574G>A	ENST00000270077.3	-	1	106	c.10C>T	c.(10-12)Ctc>Ttc	p.L4F	PSG9_ENST00000593948.1_Missense_Mutation_p.L4F|PSG9_ENST00000596730.1_Missense_Mutation_p.L4F|PSG9_ENST00000418820.2_Missense_Mutation_p.L4F|PSG9_ENST00000291752.5_Missense_Mutation_p.L4F|PSG9_ENST00000244293.7_Missense_Mutation_p.L4F|PSG9_ENST00000443718.3_Missense_Mutation_p.L4F	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	4				L -> F (in Ref. 5; AAA60203). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.L4F(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				GGGGCTGGGAGGGGCCCCATG	0.617													G|||	499	0.0996406	0.2269	0.0331	5008	,	,		16943	0.0873		0.0119	False		,,,				2504	0.0777				p.L4F		Atlas-SNP	.											PSG9,NS,carcinoma,0,1	PSG9	77	1	1	Substitution - Missense(1)	stomach(1)	c.C10T						PASS	.	G	PHE/LEU	828,3578	328.0+/-300.3	86,656,1461	110.0	104.0	106.0		10	1.0	0.0	19	dbSNP_130	106	99,8501	54.4+/-115.2	3,93,4204	no	missense	PSG9	NM_002784.3	22	89,749,5665	AA,AG,GG		1.1512,18.7926,7.1275	benign	4/427	43773574	927,12079	2203	4300	6503	SO:0001583	missense	5678	exon1			CTGGGAGGGGCCC	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.10C>T	19.37:g.43773574G>A	ENSP00000270077:p.Leu4Phe	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	67	40	0.597015	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	37	CCDS12618.1	185	0.08470695970695971	109	0.22154471544715448	13	0.03591160220994475	55	0.09615384615384616	8	0.010554089709762533	g	9.631	1.136353	0.21123	0.187926	0.011512	ENSG00000183668	ENST00000270077;ENST00000291752;ENST00000443718;ENST00000435220;ENST00000244293	T;T;T;T	0.49432	0.78;2.28;2.6;1.47	2.17	0.998	0.19857	.	.	.	.	.	T	0.00039	0.0001	L	0.40543	1.245	0.80722	P	0.0	P;B;D;B;B	0.89917	0.617;0.379;1.0;0.01;0.001	P;B;D;B;B	0.80764	0.533;0.214;0.994;0.03;0.011	T	0.05599	-1.0875	8	0.41790	T	0.15	.	6.3442	0.21341	0.0:0.3377:0.6623:0.0	.	4;4;4;4;4	E7EW65;Q15227;G3XAA7;Q6LEU7;Q00887	.;.;.;.;PSG9_HUMAN	F	4	ENSP00000270077:L4F;ENSP00000291752:L4F;ENSP00000396753:L4F;ENSP00000244293:L4F	ENSP00000244293:L4F	L	-	1	0	PSG9	48465414	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.437000	0.21543	0.209000	0.20645	0.298000	0.19748	CTC	G|0.929;A|0.071	0.071	strong		0.617	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
CD1E	913	hgsc.bcm.edu	37	1	158324425	158324425	+	Missense_Mutation	SNP	A	A	G	rs1065457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000368165.3_Missense_Mutation_p.Q106R|CD1E_ENST00000368164.3_Intron|CD1E_ENST00000464822.1_Intron|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368161.3_Missense_Mutation_p.Q106R|CD1E_ENST00000368156.1_Missense_Mutation_p.Q106R|CD1E_ENST00000368155.3_Missense_Mutation_p.Q106R|CD1E_ENST00000368166.3_Intron|CD1E_ENST00000434258.1_Missense_Mutation_p.Q104R|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000452291.2_Intron|CD1E_ENST00000368160.3_Missense_Mutation_p.Q106R|CD1E_ENST00000444681.2_Intron	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	134	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	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	
OR13C5	138799	hgsc.bcm.edu	37	9	107361312	107361312	+	Missense_Mutation	SNP	T	T	C	rs1851723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361312T>C	ENST00000374779.2	-	1	476	c.383A>G	c.(382-384)aAc>aGc	p.N128S		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						TCTCAGAGGGTTGCAGATAGC	0.522													T|||	1208	0.241214	0.1006	0.366	5008	,	,		20196	0.3819		0.2445	False		,,,				2504	0.1943				p.N128S		Atlas-SNP	.											.	OR13C5	60	.	0			c.A383G						PASS	.	T	SER/ASN	649,3757		108,433,1662	74.0	102.0	93.0		383	3.0	0.9	9	dbSNP_92	93	2026,6574		283,1460,2557	no	missense	OR13C5	NM_001004482.1	46	391,1893,4219	CC,CT,TT		23.5581,14.7299,20.5674	possibly-damaging	128/319	107361312	2675,10331	2203	4300	6503	SO:0001583	missense	138799	exon1			AGAGGGTTGCAGA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.383A>G	9.37:g.107361312T>C	ENSP00000363911:p.Asn128Ser	Somatic	444	2	0.0045045		WXS	Illumina HiSeq	Phase_I	455	281	0.617582	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	611	0.27976190476190477	56	0.11382113821138211	127	0.35082872928176795	225	0.39335664335664333	203	0.2678100263852243	T	5.443	0.266842	0.10294	0.147299	0.235581	ENSG00000255800	ENST00000374779	T	0.01313	5.02	4.17	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	0.617973	0.13202	N	0.405869	T	0.00012	0.0000	L	0.39020	1.185	0.80722	P	0.0	B	0.24317	0.101	B	0.25884	0.064	T	0.40905	-0.9538	9	0.37606	T	0.19	.	3.444	0.07474	0.1978:0.1083:0.0:0.6939	rs1851723;rs59632018	128	Q8NGS8	O13C5_HUMAN	S	128	ENSP00000363911:N128S	ENSP00000363911:N128S	N	-	2	0	OR13C5	106401133	0.000000	0.05858	0.937000	0.37676	0.088000	0.18126	-0.341000	0.07811	0.669000	0.31146	-0.430000	0.05897	AAC	.	.	weak		0.522	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
F5	2153	hgsc.bcm.edu	37	1	169512027	169512027	+	Silent	SNP	T	T	C	rs6021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169512027T>C	ENST00000367797.3	-	13	2502	c.2301A>G	c.(2299-2301)tcA>tcG	p.S767S	F5_ENST00000367796.3_Silent_p.S772S	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	767	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)	TATCTGTGTTTGAAGAAACGA	0.393													C|||	1316	0.26278	0.1679	0.3948	5008	,	,		21933	0.248		0.2535	False		,,,				2504	0.3221				p.S767S		Atlas-SNP	.											.	F5	301	.	0			c.A2301G						PASS	.	C		813,3593	750.9+/-412.2	68,677,1458	165.0	159.0	161.0		2301	0.8	0.0	1	dbSNP_52	161	2355,6245	702.6+/-405.3	299,1757,2244	no	coding-synonymous	F5	NM_000130.4		367,2434,3702	CC,CT,TT		27.3837,18.4521,24.358		767/2225	169512027	3168,9838	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			TGTGTTTGAAGAA	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.2301A>G	1.37:g.169512027T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			T|0.763;C|0.237	0.237	strong		0.393	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79051801	79051801	+	Missense_Mutation	SNP	C	C	A	rs201472223		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:79051801C>A	ENST00000388820.4	-	24	5233	c.5023G>T	c.(5023-5025)Gcc>Tcc	p.A1675S		NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1675					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CGGGAGGGGGCGCCGTGGCTG	0.721																																					p.A1675S		Atlas-SNP	.											ADAMTS7,NS,carcinoma,0,1	ADAMTS7	142	1	0			c.G5023T						PASS	.						7.0	9.0	9.0					15																	79051801		2082	4133	6215	SO:0001583	missense	11173	exon24			AGGGGGCGCCGTG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.5023G>T	15.37:g.79051801C>A	ENSP00000373472:p.Ala1675Ser	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	19	6	0.315789	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	c	1.406	-0.576936	0.03854	.	.	ENSG00000136378	ENST00000388820	T	0.59502	0.26	2.92	0.947	0.19555	.	2.418420	0.02155	U	0.058341	T	0.39627	0.1085	N	0.19112	0.55	0.09310	N	1	B	0.25007	0.116	B	0.23150	0.044	T	0.16600	-1.0397	10	0.09590	T	0.72	.	6.0212	0.19630	0.0:0.7622:0.0:0.2378	.	1675	Q9UKP4	ATS7_HUMAN	S	1675	ENSP00000373472:A1675S	ENSP00000373472:A1675S	A	-	1	0	ADAMTS7	76838856	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.624000	0.24462	0.111000	0.17947	-2.153000	0.00332	GCC	.	.	weak		0.721	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
KRT31	3881	hgsc.bcm.edu	37	17	39553547	39553547	+	Missense_Mutation	SNP	G	G	A	rs6503627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39553547G>A	ENST00000251645.2	-	1	297	c.245C>T	c.(244-246)gCg>gTg	p.A82V		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	82	Coil 1A.|Rod.		A -> V (in dbSNP:rs6503627).		epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				CTCCAGCTCCGCGTTGTCCCG	0.587													G|||	224	0.0447284	0.0371	0.0331	5008	,	,		17472	0.0516		0.0785	False		,,,				2504	0.0215				p.A82V		Atlas-SNP	.											.	KRT31	158	.	0			c.C245T						PASS	.	G	VAL/ALA	173,4233	114.6+/-152.6	4,165,2034	75.0	72.0	73.0		245	4.9	0.8	17	dbSNP_116	73	742,7856	178.9+/-228.2	27,688,3584	no	missense	KRT31	NM_002277.2	64	31,853,5618	AA,AG,GG		8.6299,3.9265,7.0363	benign	82/417	39553547	915,12089	2203	4299	6502	SO:0001583	missense	3881	exon1			AGCTCCGCGTTGT	X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6448	protein-coding gene	gene with protein product	"""hard keratin type I 1"""	601077	"""keratin, hair, acidic, 1"""	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.245C>T	17.37:g.39553547G>A	ENSP00000251645:p.Ala82Val	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	172	98	0.569767	NM_002277	Q9UE12	Missense_Mutation	SNP	ENST00000251645.2	37	CCDS11391.1	129	0.059065934065934064	18	0.036585365853658534	14	0.03867403314917127	32	0.055944055944055944	65	0.08575197889182058	g	15.71	2.913866	0.52439	0.039265	0.086299	ENSG00000094796	ENST00000251645	D	0.89415	-2.51	5.91	4.94	0.65067	Filament (1);	0.000000	0.64402	D	0.000004	T	0.30293	0.0760	M	0.82433	2.59	0.09310	N	1	P	0.44946	0.846	B	0.39840	0.311	T	0.64271	-0.6447	10	0.66056	D	0.02	.	9.7155	0.40272	0.0736:0.1408:0.7856:0.0	rs6503627;rs6503627	82	Q15323	K1H1_HUMAN	V	82	ENSP00000251645:A82V	ENSP00000251645:A82V	A	-	2	0	KRT31	36807073	0.001000	0.12720	0.765000	0.31456	0.981000	0.71138	1.088000	0.30877	1.501000	0.48654	0.655000	0.94253	GCG	G|0.938;A|0.062	0.062	strong		0.587	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277	
PLEC	5339	hgsc.bcm.edu	37	8	144991428	144991428	+	Silent	SNP	G	G	A	rs11998271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144991428G>A	ENST00000322810.4	-	32	13141	c.12972C>T	c.(12970-12972)gaC>gaT	p.D4324D	PLEC_ENST00000345136.3_Silent_p.D4187D|PLEC_ENST00000398774.2_Silent_p.D4155D|PLEC_ENST00000356346.3_Silent_p.D4173D|PLEC_ENST00000527096.1_Silent_p.D4210D|PLEC_ENST00000354589.3_Silent_p.D4187D|PLEC_ENST00000357649.2_Silent_p.D4191D|PLEC_ENST00000436759.2_Silent_p.D4214D|PLEC_ENST00000354958.2_Silent_p.D4165D	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4324	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						TGACCACGCCGTCCGAGGAGG	0.622													G|||	419	0.0836661	0.3011	0.0173	5008	,	,		18486	0.001		0.002	False		,,,				2504	0.0061				p.D4324D		Atlas-SNP	.											.	PLEC	1144	.	0			c.C12972T						PASS	.	G	,,,,,,,	1134,3084		148,838,1123	56.0	63.0	61.0		12642,12519,12495,12972,12465,12561,12573,12561	-4.4	0.9	8	dbSNP_120	61	5,8413		0,5,4204	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	,,,,,,,	148,843,5327	AA,AG,GG		0.0594,26.8848,9.0139	,,,,,,,	4214/4575,4173/4534,4165/4526,4324/4685,4155/4516,4187/4548,4191/4552,4187/4548	144991428	1139,11497	2109	4209	6318	SO:0001819	synonymous_variant	5339	exon32			CACGCCGTCCGAG	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.12972C>T	8.37:g.144991428G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.957;A|0.043	0.043	strong		0.622	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
NRSN2	80023	hgsc.bcm.edu	37	20	330408	330408	+	Missense_Mutation	SNP	C	C	G	rs11556643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:330408C>G	ENST00000382291.3	+	3	361	c.121C>G	c.(121-123)Ctc>Gtc	p.L41V	RP5-1103G7.4_ENST00000442637.1_RNA|NRSN2_ENST00000382285.2_Missense_Mutation_p.L41V|NRSN2_ENST00000608736.1_Missense_Mutation_p.L41V|NRSN2_ENST00000492242.1_Intron	NM_024958.2	NP_079234.1	Q9GZP1	NRSN2_HUMAN	neurensin 2	41			L -> V (in dbSNP:rs11556643).			integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				endometrium(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8		all_cancers(10;0.0834)				AGGCACTGCTCTCAGCGACGA	0.642													C|||	635	0.126797	0.3222	0.0663	5008	,	,		15562	0.0119		0.0457	False		,,,				2504	0.1074				p.L41V		Atlas-SNP	.											.	NRSN2	20	.	0			c.C121G						PASS	.	C	VAL/LEU	1219,3187	416.5+/-337.6	182,855,1166	59.0	57.0	58.0		121	4.2	0.7	20	dbSNP_120	58	483,8117	139.8+/-196.4	15,453,3832	yes	missense	NRSN2	NM_024958.2	32	197,1308,4998	GG,GC,CC		5.6163,27.6668,13.0863	probably-damaging	41/205	330408	1702,11304	2203	4300	6503	SO:0001583	missense	80023	exon3			ACTGCTCTCAGCG	AL136915	CCDS12996.1	20p13	2008-02-04	2006-07-04	2006-07-04	ENSG00000125841	ENSG00000125841			16229	protein-coding gene	gene with protein product		610666	"""chromosome 20 open reading frame 98"""	C20orf98		16527258	Standard	NM_024958		Approved	dJ1103G7.6	uc002wdi.4	Q9GZP1	OTTHUMG00000031628	ENST00000382291.3:c.121C>G	20.37:g.330408C>G	ENSP00000371728:p.Leu41Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	88	33	0.375	NM_024958	A8K3B2|Q6FII5|Q9NUD3	Missense_Mutation	SNP	ENST00000382291.3	37	CCDS12996.1	208	0.09523809523809523	143	0.29065040650406504	20	0.055248618784530384	7	0.012237762237762238	38	0.05013192612137203	C	10.27	1.305091	0.23736	0.276668	0.056163	ENSG00000125841	ENST00000382291;ENST00000382285	T;T	0.17854	2.25;2.25	4.25	4.25	0.50352	.	0.422192	0.22997	N	0.053131	T	0.00012	0.0000	L	0.54323	1.7	0.36941	P	0.10761500000000002	D	0.67145	0.996	D	0.79108	0.992	T	0.31223	-0.9951	9	0.39692	T	0.17	-26.8864	12.0091	0.53276	0.0:1.0:0.0:0.0	rs11556643;rs60937200	41	Q9GZP1	NRSN2_HUMAN	V	41	ENSP00000371728:L41V;ENSP00000371722:L41V	ENSP00000371722:L41V	L	+	1	0	NRSN2	278408	0.922000	0.31269	0.665000	0.29768	0.422000	0.31414	1.965000	0.40471	2.177000	0.69029	0.643000	0.83706	CTC	C|0.879;G|0.121	0.121	strong		0.642	NRSN2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077446.1	NM_024958	
OR10C1	442194	hgsc.bcm.edu	37	6	29408270	29408270	+	Missense_Mutation	SNP	C	C	T	rs2074468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29408270C>T	ENST00000444197.2	+	1	1188	c.478C>T	c.(478-480)Cct>Tct	p.P160S	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	160			P -> S (in dbSNP:rs2074468).			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)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GGGCCACACCCCTTTCATCTT	0.622													T|||	483	0.0964457	0.233	0.0447	5008	,	,		17755	0.0605		0.0258	False		,,,				2504	0.0583				p.P160S		Atlas-SNP	.											.	OR10C1	58	.	0			c.C478T						PASS	.	T	SER/PRO	696,2326		83,530,898	107.0	121.0	116.0		478	0.9	0.8	6	dbSNP_96	116	184,5234		5,174,2530	no	missense	OR10C1	NM_013941.3	74	88,704,3428	TT,TC,CC		3.3961,23.0311,10.4265	benign	160/313	29408270	880,7560	1511	2709	4220	SO:0001583	missense	442194	exon1			CACACCCCTTTCA		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.478C>T	6.37:g.29408270C>T	ENSP00000419119:p.Pro160Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_013941	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	37	CCDS34364.1	236	0.10805860805860806	161	0.32723577235772355	22	0.06077348066298342	33	0.057692307692307696	20	0.026385224274406333	T	0.301	-0.974129	0.02215	0.230311	0.033961	ENSG00000206474	ENST00000444197	T	0.35973	1.28	3.53	0.874	0.19124	GPCR, rhodopsin-like superfamily (1);	0.202127	0.24774	N	0.035708	T	0.02649	0.0080	N	0.01267	-0.92	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.40496	-0.9560	9	0.22109	T	0.4	.	2.0816	0.03636	0.5229:0.0928:0.1348:0.2494	rs2074468;rs17184030;rs52836977;rs2074468	160	Q96KK4	O10C1_HUMAN	S	160	ENSP00000419119:P160S	ENSP00000419119:P160S	P	+	1	0	OR10C1	29516249	0.000000	0.05858	0.838000	0.33150	0.111000	0.19643	-5.395000	0.00125	-0.322000	0.08615	-0.451000	0.05528	CCT	C|0.901;T|0.099	0.099	strong		0.622	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2		
SEC14L6	730005	hgsc.bcm.edu	37	22	30934887	30934887	+	Silent	SNP	G	G	A	rs5753191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30934887G>A	ENST00000402034.2	-	2	56	c.57C>T	c.(55-57)ttC>ttT	p.F19F		NM_001193336.2	NP_001180265.2	B5MCN3	S14L6_HUMAN	SEC14-like 6 (S. cerevisiae)	19						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			lung(3)	3						TGTTCTCCCGGAACTGAGGAC	0.577													.|||	2664	0.531949	0.702	0.4496	5008	,	,		17077	0.4107		0.492	False		,,,				2504	0.5266				p.F19F		Atlas-SNP	.											.	SEC14L6	6	.	0			c.C57T						PASS	.																																			SO:0001819	synonymous_variant	730005	exon2			CTCCCGGAACTGA		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.57C>T	22.37:g.30934887G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_001193336		Silent	SNP	ENST00000402034.2	37	CCDS54518.1																																																																																			G|0.494;A|0.506	0.506	strong		0.577	SEC14L6-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000322022.2		
C11orf95	65998	hgsc.bcm.edu	37	11	63531175	63531175	+	lincRNA	SNP	C	C	G	rs2959886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:63531175C>G	ENST00000433688.1	-	0	1770							C9JLR9	CK095_HUMAN	chromosome 11 open reading frame 95																		CGCCCCGCCACCGCGGCTGGT	0.751													G|||	946	0.188898	0.4372	0.0937	5008	,	,		7651	0.003		0.1372	False		,,,				2504	0.1656				p.R584R		Atlas-SNP	.											.	.	.	.	0			c.G1752C						PASS	.						5.0	9.0	8.0					11																	63531175		637	1527	2164			65998	exon5			CCGCCACCGCGGC	BC000572, AK096306		11q13	2011-11-24			ENSG00000188070	ENSG00000188070			28449	protein-coding gene	gene with protein product		615699				20607705	Standard	NM_001144936		Approved	MGC3032	uc010rmv.2	C9JLR9			11.37:g.63531175C>G		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	14	5	0.357143	NM_001144936	A6NLS7|Q3C1V4	Silent	SNP	ENST00000433688.1	37																																																																																				C|0.857;G|0.143	0.143	strong		0.751	C11orf95-201	KNOWN	basic	lincRNA	lincRNA		NM_001144936	
SEMA5B	54437	hgsc.bcm.edu	37	3	122634665	122634665	+	Missense_Mutation	SNP	G	G	C	rs34037493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122634665G>C	ENST00000357599.3	-	13	2147	c.1761C>G	c.(1759-1761)gaC>gaG	p.D587E	SEMA5B_ENST00000195173.4_Missense_Mutation_p.D587E|SEMA5B_ENST00000451055.2_Missense_Mutation_p.D641E	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	587					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		TGTTGGAGCTGTCCTCGAGTG	0.597													G|||	161	0.0321486	0.1089	0.0216	5008	,	,		18045	0.0		0.002	False		,,,				2504	0.0				p.D641E		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C1923G						PASS	.	G	GLU/ASP	369,4037	187.4+/-214.1	18,333,1852	142.0	134.0	137.0		1761	4.6	1.0	3	dbSNP_126	137	4,8596	3.7+/-12.6	0,4,4296	yes	missense	SEMA5B	NM_001031702.2	45	18,337,6148	CC,CG,GG		0.0465,8.3749,2.8679	benign	587/1152	122634665	373,12633	2203	4300	6503	SO:0001583	missense	54437	exon13			GGAGCTGTCCTCG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.1761C>G	3.37:g.122634665G>C	ENSP00000350215:p.Asp587Glu	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	280	144	0.514286	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	62	0.028388278388278388	51	0.10365853658536585	9	0.024861878453038673	0	0.0	2	0.002638522427440633	G	12.03	1.817110	0.32145	0.083749	4.65E-4	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.00271	0.0008	N	0.11284	0.12	0.54753	D	0.999981	B;B;B	0.27559	0.086;0.181;0.181	B;B;B	0.27500	0.048;0.08;0.08	T	0.11108	-1.0601	10	0.05525	T	0.97	.	14.3689	0.66826	0.0:0.0:1.0:0.0	rs34037493;rs59368219	529;587;587	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	E	587;587;529;641;587	ENSP00000350215:D587E;ENSP00000195173:D587E;ENSP00000389588:D641E;ENSP00000377208:D587E	ENSP00000195173:D587E	D	-	3	2	SEMA5B	124117355	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.083000	0.41615	2.404000	0.81709	0.561000	0.74099	GAC	G|0.970;C|0.030	0.030	strong		0.597	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
RGL3	57139	hgsc.bcm.edu	37	19	11516007	11516007	+	Silent	SNP	T	T	G	rs10416704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11516007T>G	ENST00000380456.3	-	8	1155	c.1092A>C	c.(1090-1092)gcA>gcC	p.A364A	RGL3_ENST00000393423.3_Silent_p.A364A	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	364	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				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						ACCGGCTCACTGCCCCCCAGC	0.662													t|||	1197	0.239018	0.5219	0.1023	5008	,	,		11868	0.251		0.0795	False		,,,				2504	0.1053				p.A364A	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.A1092C						PASS	.	T	,	1990,2416	507.9+/-366.8	447,1096,660	23.0	27.0	25.0		1092,1092	-10.3	0.1	19	dbSNP_119	25	677,7923	159.8+/-213.0	30,617,3653	no	coding-synonymous,coding-synonymous	RGL3	NM_001035223.2,NM_001161616.1	,	477,1713,4313	GG,GT,TT		7.8721,45.1657,20.5059	,	364/711,364/717	11516007	2667,10339	2203	4300	6503	SO:0001819	synonymous_variant	57139	exon8			GCTCACTGCCCCC	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.1092A>C	19.37:g.11516007T>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Silent	SNP	ENST00000380456.3	37	CCDS32910.1																																																																																			T|0.794;G|0.206	0.206	strong		0.662	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73207372	73207372	+	Missense_Mutation	SNP	T	T	A	rs1478453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:73207372T>A	ENST00000426542.2	+	34	4940	c.4920T>A	c.(4918-4920)caT>caA	p.H1640Q	ARHGEF28_ENST00000287898.5_Missense_Mutation_p.H1596Q|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.H560Q|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.H1327Q|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.H1640Q			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1640	Interaction with microtubules. {ECO:0000250}.		H -> Q (in dbSNP:rs1478453). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										TTCCTTTCCATGAAAGCAGCA	0.433													C|||	1514	0.302316	0.3775	0.2205	5008	,	,		21416	0.2242		0.4165	False		,,,				2504	0.2219				p.H1640Q		Atlas-SNP	.											.	.	.	.	0			c.T4920A						PASS	.	C	GLN/HIS,GLN/HIS	1490,2658		283,924,867	34.0	34.0	34.0		4920,4920	-1.8	0.2	5	dbSNP_88	34	3351,5079		686,1979,1550	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	24,24	969,2903,2417	AA,AT,TT		39.7509,35.9209,38.4878	benign,benign	1640/1732,1640/1706	73207372	4841,7737	2074	4215	6289	SO:0001583	missense	64283	exon35			TTTCCATGAAAGC		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.4920T>A	5.37:g.73207372T>A	ENSP00000412175:p.His1640Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	693	0.3173076923076923	168	0.34146341463414637	94	0.2596685082872928	119	0.20804195804195805	312	0.41160949868073876	C	0.326	-0.959181	0.02267	0.359209	0.397509	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.28069	3.28;3.29;3.27;3.05;3.29;3.27;3.1;1.63	5.29	-1.84	0.07809	.	1.137660	0.07014	N	0.825584	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B;B	0.12013	0.001;0.001;0.003;0.005;0.003	B;B;B;B;B	0.08055	0.001;0.001;0.001;0.003;0.003	T	0.44544	-0.9321	9	0.08599	T	0.76	.	0.8513	0.01173	0.1562:0.3484:0.2187:0.2768	rs1478453;rs17553541;rs52807010;rs57886667;rs1478453	1327;1640;1640;560;1640	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	Q	1640;1640;1640;1596;1640;1640;1327;560	ENSP00000296794:H1640Q;ENSP00000441913:H1640Q;ENSP00000441436:H1640Q;ENSP00000287898:H1596Q;ENSP00000411459:H1640Q;ENSP00000412175:H1640Q;ENSP00000296799:H1327Q;ENSP00000421081:H560Q	ENSP00000287898:H1596Q	H	+	3	2	RP11-428C6.1	73243128	0.000000	0.05858	0.192000	0.23308	0.155000	0.21991	-0.559000	0.05971	-1.238000	0.02535	-1.929000	0.00512	CAT	T|0.663;A|0.337	0.337	strong		0.433	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
CRB3	92359	hgsc.bcm.edu	37	19	6466482	6466482	+	Silent	SNP	A	A	G	rs348362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6466482A>G	ENST00000598494.1	+	4	693	c.162A>G	c.(160-162)ccA>ccG	p.P54P	CRB3_ENST00000308243.7_Silent_p.P54P|CRB3_ENST00000600229.1_Silent_p.P54P|CRB3_ENST00000356762.3_Silent_p.P54P			Q9BUF7	CRUM3_HUMAN	crumbs family member 3	54					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein localization to plasma membrane (GO:0072659)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|SH3 domain binding (GO:0017124)			endometrium(1)|large_intestine(1)|lung(1)	3						TGCAGCGTCCAGAAGCCATCA	0.612													G|||	2120	0.423323	0.6233	0.3127	5008	,	,		17782	0.1875		0.5189	False		,,,				2504	0.3763				p.P54P		Atlas-SNP	.											.	CRB3	8	.	0			c.A162G						PASS	.	G	,	2528,1878	540.5+/-375.5	709,1110,384	178.0	156.0	163.0		162,162	2.0	0.0	19	dbSNP_79	163	4733,3867	542.6+/-384.2	1291,2151,858	no	coding-synonymous,coding-synonymous	CRB3	NM_139161.3,NM_174881.2	,	2000,3261,1242	GG,GA,AA		44.9651,42.6237,44.1719	,	54/121,54/124	6466482	7261,5745	2203	4300	6503	SO:0001819	synonymous_variant	92359	exon4			GCGTCCAGAAGCC	AF503290	CCDS12166.1, CCDS12167.1	19p13.3	2014-02-06	2014-02-06		ENSG00000130545	ENSG00000130545			20237	protein-coding gene	gene with protein product		609737	"""crumbs homolog 3 (Drosophila)"""				Standard	XM_005259680		Approved	MGC17303	uc002mez.3	Q9BUF7	OTTHUMG00000181828	ENST00000598494.1:c.162A>G	19.37:g.6466482A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	111	59	0.531532	NM_174881	A8KA91|D6W643|Q8N0V8|Q8WVA0	Silent	SNP	ENST00000598494.1	37	CCDS12167.1																																																																																			A|0.494;G|0.506	0.506	strong		0.612	CRB3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457837.1		
RPL39	6170	hgsc.bcm.edu	37	X	118920652	118920652	+	Silent	SNP	G	G	A	rs79192437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:118920652G>A	ENST00000361575.3	-	3	217	c.151C>T	c.(151-153)Cta>Tta	p.L51L	RPL39_ENST00000468844.1_5'UTR|SNORA69_ENST00000383895.1_RNA	NM_001000.2	NP_000991.1	P62891	RL39_HUMAN	ribosomal protein L39	51					antibacterial humoral response (GO:0019731)|cellular protein metabolic process (GO:0044267)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|innate immune response in mucosa (GO:0002227)|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)|extracellular space (GO:0005615)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|large_intestine(2)	3						ATTCCTTATAGACCCAGCTTG	0.413													G|||	202	0.0535099	0.118	0.0101	3775	,	,		15158	0.0		0.003	False		,,,				2504	0.0368				p.M51L		Atlas-SNP	.											.	RPL39	9	.	0			c.A151T						PASS	.	G		477,3356		29,344,75,1258,496	114.0	103.0	107.0		151	3.8	1.0	X	dbSNP_131	107	10,6714		0,9,1,2417,1871	no	coding-synonymous	RPL39	NM_001000.2		29,353,76,3675,2367	AA,AG,A,GG,G		0.1487,12.4446,4.6131		51/52	118920652	487,10070	2202	4298	6500	SO:0001819	synonymous_variant	6170	exon3			CTTATAGACCCAG		CCDS14586.1	Xq24	2013-03-11			ENSG00000198918	ENSG00000198918		"""L ribosomal proteins"""	10350	protein-coding gene	gene with protein product		300899	"""ribosomal protein L39 pseudogene 42"""	RPL39P42		8764829	Standard	NM_001000		Approved	L39	uc004erx.2	P62891	OTTHUMG00000022278	ENST00000361575.3:c.151C>T	X.37:g.118920652G>A		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	336	334	0.994048	NM_001000	P02404|P39025|Q9BYF2	Missense_Mutation	SNP	ENST00000361575.3	37	CCDS14586.1																																																																																			G|0.953;A|0.047	0.047	strong		0.413	RPL39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058047.1	NM_001000	
GNA13	10672	hgsc.bcm.edu	37	17	63049709	63049709	+	Missense_Mutation	SNP	C	C	T	rs116700192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:63049709C>T	ENST00000439174.2	-	2	666	c.421G>A	c.(421-423)Gtt>Att	p.V141I	GNA13_ENST00000541118.1_Missense_Mutation_p.V46I|RP11-583F2.5_ENST00000581796.1_RNA	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	141					activation of phospholipase D activity (GO:0031584)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|in utero embryonic development (GO:0001701)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(14)|kidney(2)|large_intestine(4)|lung(6)|urinary_tract(1)	34						TGTAAGAAAACCCTTGTTTCC	0.468													C|||	55	0.0109824	0.0408	0.0014	5008	,	,		16418	0.0		0.0	False		,,,				2504	0.0				p.V141I		Atlas-SNP	.											.	GNA13	69	.	0			c.G421A						PASS	.	C	ILE/VAL	193,4213	121.3+/-158.8	4,185,2014	126.0	127.0	127.0		421	3.4	0.0	17	dbSNP_132	127	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GNA13	NM_006572.4	29	4,186,6313	TT,TC,CC		0.0116,4.3804,1.4916	benign	141/378	63049709	194,12812	2203	4300	6503	SO:0001583	missense	10672	exon2			AGAAAACCCTTGT	L22075	CCDS11661.1, CCDS62302.1	17q24.1	2014-09-04			ENSG00000120063	ENSG00000120063			4381	protein-coding gene	gene with protein product		604406				7791744	Standard	NM_006572		Approved	G13, MGC46138	uc002jfc.3	Q14344	OTTHUMG00000179316	ENST00000439174.2:c.421G>A	17.37:g.63049709C>T	ENSP00000400717:p.Val141Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	105	102	0.971429	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Missense_Mutation	SNP	ENST00000439174.2	37	CCDS11661.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	C	13.82	2.351213	0.41700	0.043804	1.16E-4	ENSG00000120063	ENST00000439174;ENST00000541118;ENST00000239138	D;D	0.88818	-2.43;-2.43	5.42	3.44	0.39384	G protein alpha subunit, helical insertion (2);	0.125987	0.30630	N	0.009208	T	0.54431	0.1858	L	0.45470	1.425	0.34370	D	0.691943	B	0.27594	0.182	B	0.31337	0.128	T	0.75269	-0.3377	10	0.37606	T	0.19	.	11.6014	0.51006	0.0:0.8574:0.0:0.1426	.	141	Q14344	GNA13_HUMAN	I	141;46;116	ENSP00000400717:V141I;ENSP00000439647:V46I	ENSP00000239138:V116I	V	-	1	0	GNA13	60480171	0.972000	0.33761	0.014000	0.15608	0.975000	0.68041	2.447000	0.44917	0.664000	0.31047	0.655000	0.94253	GTT	C|0.988;T|0.012	0.012	strong		0.468	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572	
MYOZ3	91977	hgsc.bcm.edu	37	5	150056307	150056307	+	Missense_Mutation	SNP	C	C	A	rs7737542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150056307C>A	ENST00000297130.4	+	7	825	c.626C>A	c.(625-627)aCt>aAt	p.T209N	MYOZ3_ENST00000456566.2_3'UTR|MYOZ3_ENST00000520112.1_Missense_Mutation_p.H125Q|MYOZ3_ENST00000517768.1_Missense_Mutation_p.T209N	NM_001122853.2|NM_133371.4	NP_001116325.1|NP_588612.2			myozenin 3											large_intestine(2)|lung(1)|skin(2)	5		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTGGGGGGCACTTTTCCCAGG	0.632													C|||	592	0.118211	0.3555	0.0202	5008	,	,		14089	0.0853		0.002	False		,,,				2504	0.0204				p.T209N		Atlas-SNP	.											MYOZ3,colon,carcinoma,0,1	MYOZ3	21	1	0			c.C626A						PASS	.	C	ASN/THR,ASN/THR	1280,3126	422.5+/-339.8	172,936,1095	62.0	74.0	70.0		626,626	4.3	0.0	5	dbSNP_116	70	19,8581	14.0+/-48.4	0,19,4281	yes	missense,missense	MYOZ3	NM_001122853.1,NM_133371.3	65,65	172,955,5376	AA,AC,CC		0.2209,29.0513,9.9877	possibly-damaging,possibly-damaging	209/252,209/252	150056307	1299,11707	2203	4300	6503	SO:0001583	missense	91977	exon7			GGGGCACTTTTCC	AF480443	CCDS4309.1	5q33.2	2008-07-18			ENSG00000164591	ENSG00000164591			18565	protein-coding gene	gene with protein product	"""calsarcin 3"", ""FATZ related protein 3"""	610735				11842093	Standard	NM_001122853		Approved	CS-3, CS3, FRP3	uc003lsr.3	Q8TDC0	OTTHUMG00000130077	ENST00000297130.4:c.626C>A	5.37:g.150056307C>A	ENSP00000297130:p.Thr209Asn	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_001122853		Missense_Mutation	SNP	ENST00000297130.4	37	CCDS4309.1	238|238	0.10897435897435898|0.10897435897435898	177|177	0.3597560975609756|0.3597560975609756	9|9	0.024861878453038673|0.024861878453038673	52|52	0.09090909090909091|0.09090909090909091	0|0	0.0|0.0	C|C	7.508|7.508	0.654102|0.654102	0.14580|0.14580	0.290513|0.290513	0.002209|0.002209	ENSG00000164591|ENSG00000164591	ENST00000520112|ENST00000517768;ENST00000297130	.|T;T	.|0.62639	.|0.01;0.01	5.2|5.2	4.33|4.33	0.51752|0.51752	.|.	.|0.966378	.|0.08546	.|N	.|0.929748	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.35414|0.35414	1.06|1.06	0.80722|0.80722	P|P	0.0|0.0	.|P	.|0.44380	.|0.834	.|P	.|0.46362	.|0.514	T|T	0.18808|0.18808	-1.0325|-1.0325	5|9	0.87932|0.27082	D|T	0|0.32	-5.2858|-5.2858	9.7635|9.7635	0.40545|0.40545	0.0:0.9042:0.0:0.0958|0.0:0.9042:0.0:0.0958	rs7737542;rs58997546;rs7737542|rs7737542;rs58997546;rs7737542	.|209	.|Q8TDC0	.|MYOZ3_HUMAN	Q|N	125|209	.|ENSP00000428815:T209N;ENSP00000297130:T209N	ENSP00000429439:H125Q|ENSP00000297130:T209N	H|T	+|+	3|2	2|0	MYOZ3|MYOZ3	150036500|150036500	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.003000|0.003000	0.03518|0.03518	0.613000|0.613000	0.24299|0.24299	1.195000|1.195000	0.43115|0.43115	-0.140000|-0.140000	0.14226|0.14226	CAC|ACT	C|0.887;A|0.113	0.113	strong		0.632	MYOZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252369.1	NM_001122853	
OGFR	11054	hgsc.bcm.edu	37	20	61444845	61444845	+	Silent	SNP	G	G	A	rs112106909		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61444845G>A	ENST00000290291.6	+	7	1903	c.1878G>A	c.(1876-1878)ccG>ccA	p.P626P	OGFR_ENST00000370461.1_Silent_p.P574P	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	626	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].				opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)	p.P626P(2)		endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					GCCCCCGCCCGGCAGGACCTG	0.746																																					p.P626P		Atlas-SNP	.											OGFR,NS,carcinoma,0,3	OGFR	63	3	2	Substitution - coding silent(2)	prostate(2)	c.G1878A						scavenged	.						5.0	8.0	7.0					20																	61444845		1854	3783	5637	SO:0001819	synonymous_variant	11054	exon7			CCGCCCGGCAGGA	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1878G>A	20.37:g.61444845G>A		Somatic	25	1	0.04		WXS	Illumina HiSeq	Phase_I	21	15	0.714286	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Silent	SNP	ENST00000290291.6	37	CCDS13504.1																																																																																			G|0.500;A|0.500	0.500	weak		0.746	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
UBR4	23352	hgsc.bcm.edu	37	1	19403331	19403331	+	Silent	SNP	G	G	A	rs142064832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19403331G>A	ENST00000375254.3	-	105	15417	c.15390C>T	c.(15388-15390)aaC>aaT	p.N5130N	UBR4_ENST00000375224.1_Silent_p.N837N|UBR4_ENST00000375226.2_Silent_p.N5106N|UBR4_ENST00000375267.2_Silent_p.N5151N|UBR4_ENST00000543981.1_Silent_p.N794N|RP5-1126H10.2_ENST00000606379.1_RNA|UBR4_ENST00000429347.2_Silent_p.N653N|UBR4_ENST00000375225.3_Silent_p.N205N|UBR4_ENST00000375217.2_Silent_p.N5123N	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	5130					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)			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)		TGGGCATGTCGTTGTGGCGGA	0.552													G|||	14	0.00279553	0.0106	0.0	5008	,	,		19899	0.0		0.0	False		,,,				2504	0.0				p.N5130N		Atlas-SNP	.											.	UBR4	415	.	0			c.C15390T						PASS	.	G		14,4392	22.3+/-47.3	0,14,2189	199.0	172.0	181.0		15390	-4.1	1.0	1	dbSNP_134	181	0,8600		0,0,4300	no	coding-synonymous	UBR4	NM_020765.2		0,14,6489	AA,AG,GG		0.0,0.3177,0.1076		5130/5184	19403331	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon105			CATGTCGTTGTGG	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.15390C>T	1.37:g.19403331G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	193	88	0.455959	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			G|0.999;A|0.001	0.001	strong		0.552	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
NPHS1	4868	hgsc.bcm.edu	37	19	36334419	36334419	+	Silent	SNP	G	G	A	rs437168	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36334419G>A	ENST00000378910.5	-	17	2288	c.2289C>T	c.(2287-2289)gtC>gtT	p.V763V	NPHS1_ENST00000353632.6_Silent_p.V763V	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	763	Ig-like C2-type 7.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	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)			GATTGGCATCGACAGTGCAGA	0.587													A|||	970	0.19369	0.5113	0.0692	5008	,	,		19940	0.1488		0.0268	False		,,,				2504	0.0706				p.V763V		Atlas-SNP	.											.	NPHS1	165	.	0			c.C2289T	GRCh37	CI024197	NPHS1	I	rs437168	PASS	.	A		1967,2439	619.5+/-393.4	433,1101,669	141.0	125.0	130.0		2289	-4.8	0.0	19	dbSNP_80	130	324,8276	805.1+/-407.3	2,320,3978	no	coding-synonymous	NPHS1	NM_004646.3		435,1421,4647	AA,AG,GG		3.7674,44.6437,17.6149		763/1242	36334419	2291,10715	2203	4300	6503	SO:0001819	synonymous_variant	4868	exon17			GGCATCGACAGTG		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.2289C>T	19.37:g.36334419G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_004646	A6NDH2|C3RX61	Silent	SNP	ENST00000378910.5	37	CCDS32996.1																																																																																			G|0.821;A|0.179	0.179	strong		0.587	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
TPRX1	284355	hgsc.bcm.edu	37	19	48305731	48305731	+	Silent	SNP	G	G	T	rs79291962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48305731G>T	ENST00000322175.3	-	2	692	c.537C>A	c.(535-537)atC>atA	p.I179I	TPRX1_ENST00000543508.1_Silent_p.I169I|TPRX1_ENST00000535759.1_Silent_p.I276I	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	179	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)		ttgggcctgggatcgggcctg	0.662													G|||	40	0.00798722	0.0295	0.0014	5008	,	,		13670	0.0		0.0	False		,,,				2504	0.0				p.I179I	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.C537A						PASS	.	G		80,3372		0,80,1646	15.0	13.0	14.0		537	0.3	0.1	19	dbSNP_131	14	1,6371		0,1,3185	no	coding-synonymous	TPRX1	NM_198479.2		0,81,4831	TT,TG,GG		0.0157,2.3175,0.8245		179/412	48305731	81,9743	1726	3186	4912	SO:0001819	synonymous_variant	284355	exon2			GCCTGGGATCGGG		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.537C>A	19.37:g.48305731G>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	129	60	0.465116	NM_198479	A5D8Y3|B2RPL5	Silent	SNP	ENST00000322175.3	37	CCDS33066.1																																																																																			G|0.993;T|0.007	0.007	strong		0.662	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
URB2	9816	hgsc.bcm.edu	37	1	229772285	229772285	+	Missense_Mutation	SNP	C	C	T	rs115230066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229772285C>T	ENST00000258243.2	+	4	2061	c.1925C>T	c.(1924-1926)tCg>tTg	p.S642L		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	642						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						CTGGAGATCTCGAACCTCCCT	0.468													C|||	6	0.00119808	0.0045	0.0	5008	,	,		21056	0.0		0.0	False		,,,				2504	0.0				p.S642L		Atlas-SNP	.											.	URB2	152	.	0			c.C1925T						PASS	.	C	LEU/SER	10,4396	16.8+/-37.8	0,10,2193	206.0	212.0	210.0		1925	2.9	0.0	1	dbSNP_132	210	0,8600		0,0,4300	yes	missense	URB2	NM_014777.2	145	0,10,6493	TT,TC,CC		0.0,0.227,0.0769	possibly-damaging	642/1525	229772285	10,12996	2203	4300	6503	SO:0001583	missense	9816	exon4			AGATCTCGAACCT	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.1925C>T	1.37:g.229772285C>T	ENSP00000258243:p.Ser642Leu	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	253	130	0.513834	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	6.986	0.551949	0.13374	0.00227	0.0	ENSG00000135763	ENST00000258243	T	0.31769	1.48	4.79	2.91	0.33838	.	1.112010	0.06634	N	0.759866	T	0.26593	0.0650	L	0.51422	1.61	0.09310	N	1	B	0.18968	0.032	B	0.08055	0.003	T	0.21895	-1.0232	9	.	.	.	-2.6001	4.7928	0.13257	0.0:0.4546:0.297:0.2483	.	642	Q14146	URB2_HUMAN	L	642	ENSP00000258243:S642L	.	S	+	2	0	URB2	227838908	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	1.070000	0.30653	1.391000	0.46566	-0.157000	0.13467	TCG	C|0.999;T|0.001	0.001	strong		0.468	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34824636	34824636	+	Missense_Mutation	SNP	A	A	G	rs11755393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:34824636A>G	ENST00000192788.5	+	11	1532	c.1361A>G	c.(1360-1362)cAg>cGg	p.Q454R	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.Q454R	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	454			Q -> R (in dbSNP:rs11755393).				histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						CCTGCCTTTCAGCCTCCAGCA	0.502													G|||	2342	0.467652	0.7723	0.3127	5008	,	,		19636	0.4583		0.3539	False		,,,				2504	0.2924				p.Q454R		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.A1361G						PASS	.	G	ARG/GLN	2549,1303		854,841,231	80.0	79.0	79.0		1361	5.0	0.8	6	dbSNP_120	79	2892,5374		512,1868,1753	yes	missense	UHRF1BP1	NM_017754.3	43	1366,2709,1984	GG,GA,AA		34.9867,33.8266,44.9001	benign	454/1441	34824636	5441,6677	1926	4133	6059	SO:0001583	missense	54887	exon11			CCTTTCAGCCTCC	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.1361A>G	6.37:g.34824636A>G	ENSP00000192788:p.Gln454Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	1020	0.46703296703296704	375	0.7621951219512195	117	0.32320441988950277	265	0.4632867132867133	263	0.3469656992084433	G	8.516	0.867634	0.17250	0.661734	0.349867	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.08008	3.14;3.14	5.93	5.01	0.66863	.	0.890084	0.09897	N	0.741495	T	0.00936	0.0031	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48570	-0.9024	9	0.12430	T	0.62	-1.0536	7.3674	0.26781	0.1453:0.1388:0.7159:0.0	rs11755393;rs52828489;rs11755393	454	Q6BDS2	URFB1_HUMAN	R	454	ENSP00000192788:Q454R;ENSP00000400628:Q454R	ENSP00000192788:Q454R	Q	+	2	0	UHRF1BP1	34932614	0.997000	0.39634	0.794000	0.32065	0.600000	0.36913	2.535000	0.45685	1.546000	0.49388	-0.119000	0.15052	CAG	A|0.531;G|0.469	0.469	strong		0.502	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
ZNF860	344787	hgsc.bcm.edu	37	3	32031622	32031622	+	Missense_Mutation	SNP	T	T	C	rs13087612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:32031622T>C	ENST00000360311.4	+	2	1600	c.1051T>C	c.(1051-1053)Ttc>Ctc	p.F351L		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						TGAAAAGGCTTTCAGGCGTGA	0.398													T|||	2329	0.465056	0.7799	0.3573	5008	,	,		21477	0.4524		0.1968	False		,,,				2504	0.4049				p.F351L		Atlas-SNP	.											ZNF860_ENST00000360311,NS,carcinoma,0,2	ZNF860	96	2	0			c.T1051C						PASS	.	T	LEU/PHE	897,487		298,301,93	48.0	49.0	49.0		1051	0.3	0.0	3	dbSNP_121	49	608,2574		57,494,1040	yes	missense	ZNF860	NM_001137674.2	22	355,795,1133	CC,CT,TT		19.1075,35.1879,32.961	probably-damaging	351/633	32031622	1505,3061	692	1591	2283	SO:0001583	missense	344787	exon2			AAGGCTTTCAGGC	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1051T>C	3.37:g.32031622T>C	ENSP00000373274:p.Phe351Leu	Somatic	390	0	0		WXS	Illumina HiSeq	Phase_I	323	129	0.399381	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	899	0.4116300366300366	373	0.758130081300813	125	0.3453038674033149	248	0.43356643356643354	153	0.20184696569920843	T	14.79	2.640073	0.47153	0.648121	0.191075	ENSG00000197385	ENST00000360311	T	0.46063	0.88	0.345	0.345	0.16011	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.90977	3.165	0.58432	P	5.999999999950489E-6	D	0.63880	0.993	D	0.68192	0.956	T	0.39683	-0.9602	7	.	.	.	.	4.9959	0.14240	0.0:2.0E-4:0.0:0.9998	rs13087612;rs59979195;rs13087612	351	A6NHJ4	ZN860_HUMAN	L	351	ENSP00000373274:F351L	.	F	+	1	0	ZNF860	32006626	0.979000	0.34478	0.003000	0.11579	0.003000	0.03518	5.394000	0.66285	0.332000	0.23536	0.323000	0.21402	TTC	T|0.621;C|0.379	0.379	strong		0.398	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
PADI2	11240	hgsc.bcm.edu	37	1	17413127	17413127	+	Silent	SNP	G	G	A	rs35184728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17413127G>A	ENST00000375486.4	-	7	786	c.723C>T	c.(721-723)taC>taT	p.Y241Y	PADI2_ENST00000375481.1_Silent_p.Y241Y|PADI2_ENST00000444885.2_Missense_Mutation_p.T160I	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	241					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	AGCCACCCGTGTACTTGACCA	0.602													G|||	105	0.0209665	0.0635	0.0072	5008	,	,		17470	0.0159		0.0	False		,,,				2504	0.0				p.Y241Y		Atlas-SNP	.											PADI2,NS,malignant_melanoma,-1,1	PADI2	72	1	0			c.C723T						PASS	.	G		290,4116	159.2+/-191.8	8,274,1921	81.0	85.0	84.0		723	2.6	1.0	1	dbSNP_126	84	0,8600		0,0,4300	no	coding-synonymous	PADI2	NM_007365.2		8,274,6221	AA,AG,GG		0.0,6.5819,2.2297		241/666	17413127	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	11240	exon7			ACCCGTGTACTTG	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.723C>T	1.37:g.17413127G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	110	62	0.563636	NM_007365	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	37	CCDS177.1	42	0.019230769230769232	28	0.056910569105691054	2	0.0055248618784530384	12	0.02097902097902098	0	0.0	G	11.73	1.726689	0.30593	0.065819	0.0	ENSG00000117115	ENST00000444885	T	0.05258	3.47	4.56	2.62	0.31277	.	.	.	.	.	T	0.00328	0.0010	.	.	.	0.24587	N	0.993841	B	0.02656	0.0	B	0.06405	0.002	T	0.45818	-0.9235	8	0.20519	T	0.43	-30.2651	8.7762	0.34762	0.2513:0.0:0.7487:0.0	rs35184728	160	B4DIU3	.	I	160	ENSP00000405894:T160I	ENSP00000405894:T160I	T	-	2	0	PADI2	17285714	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	3.058000	0.49939	1.124000	0.41980	0.460000	0.39030	ACA	G|0.976;A|0.024	0.024	strong		0.602	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
PTH2R	5746	hgsc.bcm.edu	37	2	209353800	209353800	+	Silent	SNP	A	A	G	rs16841294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:209353800A>G	ENST00000272847.2	+	11	1353	c.1140A>G	c.(1138-1140)gtA>gtG	p.V380V	AC019185.4_ENST00000424628.1_RNA|PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	380					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)	TCGTGTTCGTATGCCTGCCTC	0.493													A|||	642	0.128195	0.3495	0.0865	5008	,	,		15681	0.0069		0.0636	False		,,,				2504	0.0501				p.V380V		Atlas-SNP	.											.	PTH2R	92	.	0			c.A1140G						PASS	.	A		1468,2938	471.8+/-356.2	247,974,982	235.0	194.0	208.0		1140	-0.5	0.6	2	dbSNP_123	208	608,7992	159.4+/-212.7	21,566,3713	no	coding-synonymous	PTH2R	NM_005048.2		268,1540,4695	GG,GA,AA		7.0698,33.3182,15.9619		380/551	209353800	2076,10930	2203	4300	6503	SO:0001819	synonymous_variant	5746	exon11			GTTCGTATGCCTG	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.1140A>G	2.37:g.209353800A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	196	196	1	NM_005048	Q8N429	Silent	SNP	ENST00000272847.2	37	CCDS2383.1																																																																																			A|0.858;G|0.142	0.142	strong		0.493	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4458536	4458536	+	Silent	SNP	T	T	C	rs144321472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4458536T>C	ENST00000254718.4	-	1	390	c.84A>G	c.(82-84)ctA>ctG	p.L28L	MYBBP1A_ENST00000381556.2_Silent_p.L28L			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	28	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						TGTGCTTCAATAGGCCATAGC	0.637													C|||	34	0.00678914	0.0234	0.0043	5008	,	,		16162	0.0		0.0	False		,,,				2504	0.0				p.L28L		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.A84G						PASS	.	C	,	77,4327	780.9+/-414.5	1,75,2126	24.0	25.0	25.0		84,84	0.6	0.1	17	dbSNP_134	25	2,8596	790.5+/-407.6	0,2,4297	no	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	1,77,6423	CC,CT,TT		0.0233,1.7484,0.6076	,	28/1333,28/1329	4458536	79,12923	2202	4299	6501	SO:0001819	synonymous_variant	10514	exon1			CTTCAATAGGCCA	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.84A>G	17.37:g.4458536T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			T|0.995;C|0.005	0.005	strong		0.637	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
DERL3	91319	hgsc.bcm.edu	37	22	24179132	24179132	+	Missense_Mutation	SNP	G	G	A	rs1128127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24179132G>A	ENST00000318109.7	-	7	648	c.632C>T	c.(631-633)gCc>gTc	p.A211V	DERL3_ENST00000404056.1_3'UTR|DERL3_ENST00000406855.3_Intron|DERL3_ENST00000464023.1_5'Flank|DERL3_ENST00000476077.1_3'UTR			Q96Q80	DERL3_HUMAN	derlin 3	211			A -> V (in dbSNP:rs1128127). {ECO:0000269|PubMed:14702039}.		endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of endoplasmic reticulum membrane (GO:0030176)				ovary(1)|prostate(1)|skin(1)	3						TTCTGCAGGGGCATCCAGGAG	0.667													G|||	1311	0.261781	0.5446	0.1153	5008	,	,		14544	0.0923		0.1322	False		,,,				2504	0.2914				p.A211V		Atlas-SNP	.											.	DERL3	14	.	0			c.C632T						PASS	.	G	VAL/ALA,,	2009,2395		465,1079,658	27.0	27.0	27.0		632,,	2.3	1.0	22	dbSNP_86	27	1080,7514		70,940,3287	yes	missense,intron,utr-3	DERL3	NM_001002862.2,NM_001135751.1,NM_198440.3	64,,	535,2019,3945	AA,AG,GG		12.5669,45.6176,23.7652	,,	211/236,,	24179132	3089,9909	2202	4297	6499	SO:0001583	missense	91319	exon7			GCAGGGGCATCCA	AB049213	CCDS33615.1, CCDS42986.1, CCDS46672.1	22q11.23	2012-02-01	2012-02-01	2004-11-02	ENSG00000099958	ENSG00000099958			14236	protein-coding gene	gene with protein product		610305	"""chromosome 22 open reading frame 14"", ""Der1-like domain family, member 3"""	C22orf14		15215855	Standard	NM_198440		Approved	FLJ43842, MGC71803, derlin-3, IZP6	uc002zyk.4	Q96Q80	OTTHUMG00000150743	ENST00000318109.7:c.632C>T	22.37:g.24179132G>A	ENSP00000315303:p.Ala211Val	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	316	168	0.531646	NM_001002862	F2Z3B6|Q6ICJ6|Q6PEX0|Q6ZUB5	Missense_Mutation	SNP	ENST00000318109.7	37	CCDS33615.1	442	0.20238095238095238	256	0.5203252032520326	46	0.1270718232044199	41	0.07167832167832168	99	0.13060686015831136	G	14.11	2.437021	0.43224	0.456176	0.125669	ENSG00000099958	ENST00000318109	T	0.23552	1.9	4.95	2.31	0.28768	.	3.136180	0.01583	N	0.021208	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.9999999999839997	P;B	0.47910	0.902;0.007	B;B	0.41510	0.359;0.006	T	0.46748	-0.9169	9	0.30078	T	0.28	.	11.4419	0.50102	0.0:0.0:0.5558:0.4442	rs1128127;rs3177244;rs3184722;rs11543134;rs17408362;rs52811884;rs59644953;rs1128127	201;211	Q96Q80-4;Q96Q80	.;DERL3_HUMAN	V	211	ENSP00000315303:A211V	ENSP00000315303:A211V	A	-	2	0	DERL3	22509132	0.535000	0.26370	0.954000	0.39281	0.983000	0.72400	2.869000	0.48444	0.305000	0.22832	0.650000	0.86243	GCC	G|0.750;A|0.250	0.250	strong		0.667	DERL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319905.1	NM_198440	
SYT7	9066	hgsc.bcm.edu	37	11	61291922	61291922	+	Silent	SNP	A	A	G	rs10897167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61291922A>G	ENST00000263846.4	-	6	1032	c.705T>C	c.(703-705)atT>atC	p.I235I	SYT7_ENST00000535826.1_Silent_p.I354I|SYT7_ENST00000539008.1_Silent_p.I518I|SYT7_ENST00000540677.1_Silent_p.I310I|SYT7_ENST00000542670.1_Silent_p.I443I|SYT7_ENST00000540831.1_5'UTR|SYT7_ENST00000542836.1_Silent_p.I279I	NM_004200.3	NP_004191.2	O43581	SYT7_HUMAN	synaptotagmin VII	235	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|plasma membrane repair (GO:0001778)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			kidney(2)|large_intestine(3)|lung(4)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						ACACCTCCCCAATGGGGTCGT	0.557													G|||	758	0.151358	0.4455	0.0504	5008	,	,		20942	0.002		0.0348	False		,,,				2504	0.0992				p.I310I		Atlas-SNP	.											.	SYT7	39	.	0			c.T930C						PASS	.	G		1686,2718	653.9+/-399.7	348,990,864	87.0	80.0	83.0		705	-7.1	0.6	11	dbSNP_120	83	378,8220	802.4+/-407.3	8,362,3929	no	coding-synonymous	SYT7	NM_004200.2		356,1352,4793	GG,GA,AA		4.3964,38.2834,15.8745		235/404	61291922	2064,10938	2202	4299	6501	SO:0001819	synonymous_variant	9066	exon7			CTCCCCAATGGGG	AF038535	CCDS31577.1, CCDS58139.1, CCDS73298.1	11q12-q13.1	2013-01-21			ENSG00000011347	ENSG00000011347		"""Synaptotagmins"""	11514	protein-coding gene	gene with protein product		604146	"""prostate cancer associated protein 7"""	PCANAP7		9615227	Standard	NM_001252065		Approved	IPCA-7, SYT-VII, MGC150517	uc009ynr.3	O43581	OTTHUMG00000168199	ENST00000263846.4:c.705T>C	11.37:g.61291922A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001252065	F5GZU9|Q08AH6	Silent	SNP	ENST00000263846.4	37	CCDS31577.1																																																																																			A|0.836;G|0.164	0.164	strong		0.557	SYT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398733.1	NM_004200	
NOTCH3	4854	hgsc.bcm.edu	37	19	15276739	15276739	+	Silent	SNP	A	A	G	rs16980398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15276739A>G	ENST00000263388.2	-	30	5601	c.5526T>C	c.(5524-5526)gcT>gcC	p.A1842A		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1842					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CCAGGTGCAAAGCAGTCTCGC	0.622													A|||	610	0.121805	0.4259	0.0346	5008	,	,		16284	0.0		0.007	False		,,,				2504	0.0164				p.A1842A		Atlas-SNP	.											.	NOTCH3	340	.	0			c.T5526C						PASS	.	A		1618,2788	497.7+/-363.9	310,998,895	72.0	56.0	61.0		5526	0.8	1.0	19	dbSNP_123	61	74,8526	40.8+/-97.7	0,74,4226	no	coding-synonymous	NOTCH3	NM_000435.2		310,1072,5121	GG,GA,AA		0.8605,36.7227,13.0094		1842/2322	15276739	1692,11314	2203	4300	6503	SO:0001819	synonymous_variant	4854	exon30			GTGCAAAGCAGTC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.5526T>C	19.37:g.15276739A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	105	62	0.590476	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	37	CCDS12326.1																																																																																			A|0.883;G|0.117	0.117	strong		0.622	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
TCEB3	6924	hgsc.bcm.edu	37	1	24078234	24078234	+	Missense_Mutation	SNP	T	T	C	rs34394004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24078234T>C	ENST00000418390.2	+	4	1488	c.1217T>C	c.(1216-1218)tTg>tCg	p.L406S	TCEB3_ENST00000609199.1_Missense_Mutation_p.L380S	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	406					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)		AAAACTAATTTGGATAGAAAG	0.448											OREG0013232	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	279	0.0557109	0.202	0.0144	5008	,	,		18505	0.0		0.001	False		,,,				2504	0.001				p.L406S		Atlas-SNP	.											.	TCEB3	61	.	0			c.T1217C						PASS	.	C	SER/LEU	741,3665	746.0+/-411.7	66,609,1528	97.0	109.0	105.0		1217	-2.6	0.0	1	dbSNP_126	105	16,8584	812.1+/-407.1	0,16,4284	yes	missense	TCEB3	NM_003198.2	145	66,625,5812	CC,CT,TT		0.186,16.818,5.8204	benign	406/799	24078234	757,12249	2203	4300	6503	SO:0001583	missense	6924	exon4			CTAATTTGGATAG	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.1217T>C	1.37:g.24078234T>C	ENSP00000395574:p.Leu406Ser	Somatic	63	0	0	768	WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_003198	B2R7Q8|Q8IXH1	Missense_Mutation	SNP	ENST00000418390.2	37	CCDS239.2	102	0.046703296703296704	94	0.1910569105691057	8	0.022099447513812154	0	0.0	0	0.0	C	0.011	-1.697264	0.00725	0.16818	0.00186	ENSG00000011007	ENST00000418390	T	0.06768	3.26	5.85	-2.64	0.06114	.	1.391920	0.04481	N	0.377838	T	0.00012	0.0000	N	0.01003	-1.06	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45116	-0.9283	9	0.11794	T	0.64	2.5335	6.9989	0.24799	0.1849:0.3127:0.0:0.5025	rs34394004	406	Q14241	ELOA1_HUMAN	S	406	ENSP00000395574:L406S	ENSP00000395574:L406S	L	+	2	0	TCEB3	23950821	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.017000	0.01445	-1.183000	0.02723	-1.073000	0.02249	TTG	T|0.935;C|0.065	0.065	strong		0.448	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198	
KLF4	9314	hgsc.bcm.edu	37	9	110249415	110249415	+	Silent	SNP	T	T	C	rs45596731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:110249415T>C	ENST00000374672.4	-	4	1631	c.1158A>G	c.(1156-1158)cgA>cgG	p.R386R		NM_004235.4	NP_004226.3	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)	420	Pro-rich.				cellular response to cycloheximide (GO:0071409)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|epidermal cell differentiation (GO:0009913)|epidermis morphogenesis (GO:0048730)|fat cell differentiation (GO:0045444)|mesodermal cell fate determination (GO:0007500)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of muscle hyperplasia (GO:0014740)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic camera-type eye development (GO:0031077)|post-embryonic hemopoiesis (GO:0035166)|regulation of cell differentiation (GO:0045595)|response to retinoic acid (GO:0032526)|stem cell maintenance (GO:0019827)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001010)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(5)|large_intestine(1)|lung(3)|pancreas(1)|prostate(2)	16						GGGGCCACGATCGTCTTCCCC	0.597													T|||	18	0.00359425	0.0129	0.0014	5008	,	,		17148	0.0		0.0	False		,,,				2504	0.0				p.R386R		Atlas-SNP	.											.	KLF4	106	.	0			c.A1158G						PASS	.	T		51,4355	52.3+/-87.9	0,51,2152	192.0	175.0	180.0		1158	4.4	1.0	9	dbSNP_127	180	0,8600		0,0,4300	no	coding-synonymous	KLF4	NM_004235.4		0,51,6452	CC,CT,TT		0.0,1.1575,0.3921		386/480	110249415	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	9314	exon4			CCACGATCGTCTT	AF022184	CCDS6770.2	9q31	2013-01-08			ENSG00000136826	ENSG00000136826		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6348	protein-coding gene	gene with protein product		602253				9422764, 16372018	Standard	NM_004235		Approved	EZF, GKLF	uc004bdg.3	O43474	OTTHUMG00000020449	ENST00000374672.4:c.1158A>G	9.37:g.110249415T>C		Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	269	171	0.635688	NM_004235	B2R8S4|B3KT79|L0R3I6|L0R4N5|P78338|Q5T3J8|Q5T3J9|Q8N717|Q9UNP3	Silent	SNP	ENST00000374672.4	37	CCDS6770.2																																																																																			T|0.996;C|0.004	0.004	strong		0.597	KLF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053556.2	NM_004235	
AAR2	25980	hgsc.bcm.edu	37	20	34828459	34828459	+	Silent	SNP	T	T	C	rs716431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34828459T>C	ENST00000373932.3	+	2	1015	c.669T>C	c.(667-669)gcT>gcC	p.A223A	AAR2_ENST00000397286.3_Silent_p.A223A|AAR2_ENST00000320849.4_Silent_p.A223A	NM_015511.3	NP_056326.2	Q9Y312	AAR2_HUMAN	AAR2 splicing factor homolog (S. cerevisiae)	223																	CCACGCCAGCTGAGATAACCA	0.607													C|||	718	0.143371	0.5098	0.0461	5008	,	,		18079	0.0		0.0109	False		,,,				2504	0.001				p.A223A		Atlas-SNP	.											C20orf4,colon,carcinoma,0,1	.	.	1	0			c.T669C						PASS	.	C		1798,2608		378,1042,783	40.0	41.0	41.0		669	-2.7	0.9	20	dbSNP_86	41	71,8529		1,69,4230	no	coding-synonymous	C20orf4	NM_015511.3		379,1111,5013	CC,CT,TT		0.8256,40.808,14.3703		223/385	34828459	1869,11137	2203	4300	6503	SO:0001819	synonymous_variant	25980	exon2			GCCAGCTGAGATA		CCDS13273.1	20q11.23	2012-07-20	2012-07-20	2012-07-20	ENSG00000131043	ENSG00000131043			15886	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 4"""	C20orf4			Standard	NM_015511		Approved	bA234K24.2	uc002xfc.3	Q9Y312	OTTHUMG00000032380	ENST00000373932.3:c.669T>C	20.37:g.34828459T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	133	72	0.541353	NM_001271874	E1P5S7|Q9H4F9|Q9P1P3|Q9UFK9	Silent	SNP	ENST00000373932.3	37	CCDS13273.1																																																																																			T|0.854;C|0.146	0.146	strong		0.607	AAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079001.2	NM_015511	
HYDIN	54768	hgsc.bcm.edu	37	16	70841703	70841703	+	Missense_Mutation	SNP	A	A	G	rs116730273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70841703A>G	ENST00000393567.2	-	86	15296	c.15146T>C	c.(15145-15147)aTg>aCg	p.M5049T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	5049					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)				GAAGGTCACCATGTGATAGAA	0.527													A|||	27	0.00539137	0.0197	0.0014	5008	,	,		21437	0.0		0.0	False		,,,				2504	0.0				p.M5049T		Atlas-SNP	.											.	HYDIN	788	.	0			c.T15146C						PASS	.	A	THR/MET	39,4047		0,39,2004	124.0	127.0	126.0		15143	3.1	0.0	16	dbSNP_132	126	0,8402		0,0,4201	yes	missense	HYDIN	NM_032821.2	81	0,39,6205	GG,GA,AA		0.0,0.9545,0.3123	benign	5048/5121	70841703	39,12449	2043	4201	6244	SO:0001583	missense	54768	exon86			GTCACCATGTGAT	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.15146T>C	16.37:g.70841703A>G	ENSP00000377197:p.Met5049Thr	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	310	142	0.458065	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	0.004	-2.378729	0.00205	0.009545	0.0	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00705	5.81	6.16	3.06	0.35304	.	7.165540	0.02602	N	0.101146	T	0.00178	0.0005	N	0.00142	-2.005	0.23645	N	0.997212	B	0.09022	0.002	B	0.01281	0.0	T	0.41875	-0.9484	10	0.02654	T	1	.	8.741	0.34558	0.1238:0.0:0.7538:0.1223	.	5048	F8WD23	.	T	5049;5048	ENSP00000377197:M5049T	ENSP00000313052:M5048T	M	-	2	0	HYDIN	69399204	0.030000	0.19436	0.001000	0.08648	0.002000	0.02628	2.046000	0.41260	0.921000	0.36994	-0.924000	0.02725	ATG	A|0.994;G|0.006	0.006	strong		0.527	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
CLTCL1	8218	hgsc.bcm.edu	37	22	19178854	19178854	+	Missense_Mutation	SNP	G	G	A	rs190366603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19178854G>A	ENST00000263200.10	-	27	4357	c.4285C>T	c.(4285-4287)Cgg>Tgg	p.R1429W	CLTCL1_ENST00000353891.5_Missense_Mutation_p.R1429W|CLTCL1_ENST00000427926.1_Missense_Mutation_p.R1429W|CLTCL1_ENST00000442042.2_5'UTR	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1429	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.				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)					TGGTCCAGCCGGGGTGAAAGC	0.493			T	?	ALCL								G|||	3	0.000599042	0.0023	0.0	5008	,	,		16783	0.0		0.0	False		,,,				2504	0.0				p.R1429W		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	CLTCL1,NS,carcinoma,0,1	CLTCL1	115	1	0			c.C4285T						PASS	.	G	TRP/ARG,TRP/ARG	5,3907		0,5,1951	80.0	84.0	83.0		4285,4285	3.6	1.0	22		83	0,8286		0,0,4143	yes	missense,missense	CLTCL1	NM_007098.3,NM_001835.3	101,101	0,5,6094	AA,AG,GG		0.0,0.1278,0.041	benign,benign	1429/1641,1429/1584	19178854	5,12193	1956	4143	6099	SO:0001583	missense	8218	exon27			CCAGCCGGGGTGA		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.4285C>T	22.37:g.19178854G>A	ENSP00000445677:p.Arg1429Trp	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	51	0.579545	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	18.39	3.613700	0.66672	0.001278	0.0	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.20332	2.08;2.08;2.08	3.61	3.61	0.41365	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.40956	0.1138	M	0.92649	3.33	0.80722	D	1	B;B;B	0.33171	0.4;0.318;0.266	B;B;B	0.39217	0.283;0.256;0.294	T	0.57888	-0.7733	10	0.87932	D	0	-17.9135	15.4348	0.75137	0.0:0.0:1.0:0.0	.	1429;252;1429	P53675-2;B7Z1Z7;P53675	.;.;CLH2_HUMAN	W	1429	ENSP00000439662:R1429W;ENSP00000445677:R1429W;ENSP00000441158:R1429W	ENSP00000445677:R1429W	R	-	1	2	CLTCL1	17558854	1.000000	0.71417	0.998000	0.56505	0.787000	0.44495	2.973000	0.49264	1.868000	0.54150	0.585000	0.79938	CGG	G|0.999;A|0.001	0.001	strong		0.493	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
ERLEC1	27248	hgsc.bcm.edu	37	2	54035447	54035447	+	Silent	SNP	A	A	G	rs1127362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:54035447A>G	ENST00000185150.4	+	9	1022	c.891A>G	c.(889-891)caA>caG	p.Q297Q	ASB3_ENST00000498475.2_Intron|ERLEC1_ENST00000378239.5_Intron|GPR75-ASB3_ENST00000352846.3_Intron|ERLEC1_ENST00000405123.3_Silent_p.Q297Q|ASB3_ENST00000406625.2_Intron	NM_015701.4	NP_056516.2	Q96DZ1	ERLEC_HUMAN	endoplasmic reticulum lectin 1	297					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	glycoprotein binding (GO:0001948)	p.Q297Q(1)		endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|stomach(1)|urinary_tract(1)	18						AAGATTTGCAATCAACTAAAG	0.373													A|||	865	0.172724	0.1044	0.2032	5008	,	,		17434	0.1597		0.1799	False		,,,				2504	0.2495				p.Q297Q		Atlas-SNP	.											ERLEC1,NS,carcinoma,0,1	ERLEC1	32	1	1	Substitution - coding silent(1)	stomach(1)	c.A891G						PASS	.	A	,,,	525,3881	240.3+/-251.1	34,457,1712	83.0	83.0	83.0		891,,,891	-9.9	0.2	2	dbSNP_100	83	1658,6942	304.9+/-307.2	164,1330,2806	no	coding-synonymous,intron,intron,coding-synonymous	ERLEC1,GPR75-ASB3	NM_001127397.2,NM_001127398.2,NM_001164165.1,NM_015701.4	,,,	198,1787,4518	GG,GA,AA		19.2791,11.9156,16.7846	,,,	297/458,,,297/484	54035447	2183,10823	2203	4300	6503	SO:0001819	synonymous_variant	27248	exon9			TTTGCAATCAACT	AF131849	CCDS1848.1, CCDS46283.1, CCDS46284.1	2p16	2010-03-19	2009-08-26	2009-08-26	ENSG00000068912	ENSG00000068912			25222	protein-coding gene	gene with protein product	"""erlectin 1"""	611229	"""chromosome 2 open reading frame 30"""	C2orf30		9110174, 8619474, 16531414, 18264092	Standard	NM_015701		Approved	CL25084, XTP3TPB, XTP3-B, ERLECTIN	uc002rxl.3	Q96DZ1	OTTHUMG00000129281	ENST00000185150.4:c.891A>G	2.37:g.54035447A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_015701	B2RDB4|B5MC72|O95901|Q6UWN7|Q9NUY7|Q9UQL4	Silent	SNP	ENST00000185150.4	37	CCDS1848.1																																																																																			A|0.835;G|0.165	0.165	strong		0.373	ERLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251404.1	NM_015701	
KNG1	3827	hgsc.bcm.edu	37	3	186460110	186460110	+	Missense_Mutation	SNP	G	G	C	rs5030087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186460110G>C	ENST00000265023.4	+	10	2137	c.1925G>C	c.(1924-1926)gGc>gCc	p.G642A	RP11-573D15.8_ENST00000609726.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000596329.1_RNA|KNG1_ENST00000287611.2_Intron	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	642			G -> A (in dbSNP:rs5030087).		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		CTCACTGATGGCCTTTCTTAA	0.368													C|||	176	0.0351438	0.0643	0.0389	5008	,	,		22051	0.0129		0.0258	False		,,,				2504	0.0256				p.G642A		Atlas-SNP	.											.	KNG1	129	.	0			c.G1925C						PASS	.	C	,ALA/GLY,	224,3414		3,218,1598	82.0	78.0	80.0		,1925,	4.4	0.6	3	dbSNP_113	80	247,7915		6,235,3840	yes	intron,missense,intron	KNG1	NM_000893.3,NM_001102416.2,NM_001166451.1	,60,	9,453,5438	CC,CG,GG		3.0262,6.1572,3.9915	,benign,	,642/645,	186460110	471,11329	1819	4081	5900	SO:0001583	missense	3827	exon10			CTGATGGCCTTTC		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"""Endogenous ligands"""	6383	protein-coding gene	gene with protein product	"""alpha-2-thiol proteinase inhibitor"", ""bradykinin"""	612358	"""kininogen"""	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.1925G>C	3.37:g.186460110G>C	ENSP00000265023:p.Gly642Ala	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_001102416	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	37	CCDS43183.1	76	0.0347985347985348	31	0.06300813008130081	18	0.049723756906077346	7	0.012237762237762238	20	0.026385224274406333	C	0.007	-1.957041	0.00465	0.061572	0.030262	ENSG00000113889	ENST00000265023	T	0.06933	3.24	5.28	4.4	0.53042	.	0.000000	0.48286	N	0.000184	T	0.00300	0.0009	N	0.00321	-1.65	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48019	-0.9071	9	.	.	.	-5.3869	12.741	0.57253	0.0:0.685:0.315:0.0	rs5030087;rs52826965;rs60387045;rs5030087	642	P01042	KNG1_HUMAN	A	642	ENSP00000265023:G642A	.	G	+	2	0	KNG1	187942804	0.485000	0.25972	0.616000	0.29078	0.006000	0.05464	0.651000	0.24873	0.732000	0.32470	-0.215000	0.12644	GGC	G|0.963;C|0.037	0.037	strong		0.368	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416	
DUSP21	63904	hgsc.bcm.edu	37	X	44703935	44703935	+	Missense_Mutation	SNP	T	T	C	rs1045031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:44703935T>C	ENST00000339042.4	+	1	687	c.557T>C	c.(556-558)aTg>aCg	p.M186T		NM_022076.3	NP_071359.3	Q9H596	DUS21_HUMAN	dual specificity phosphatase 21	186			M -> T (in dbSNP:rs1045031). {ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		peptidyl-tyrosine dephosphorylation (GO:0035335)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|skin(3)	19						GACCTACGTATGATGATATCA	0.438													C|||	936	0.247947	0.5219	0.0692	3775	,	,		14198	0.0357		0.0447	False		,,,				2504	0.1196				p.M186T		Atlas-SNP	.											.	DUSP21	39	.	0			c.T557C						PASS	.	C	THR/MET	2217,1618		537,811,332,284,239	55.0	48.0	50.0		557	-2.3	0.0	X	dbSNP_86	50	416,6312		5,300,106,2123,1766	yes	missense	DUSP21	NM_022076.3	81	542,1111,438,2407,2005	CC,CT,C,TT,T		6.1831,42.1904,24.9266	benign	186/191	44703935	2633,7930	2203	4300	6503	SO:0001583	missense	63904	exon1			TACGTATGATGAT	AF143321	CCDS14264.1	Xp11.4-p11.23	2011-06-09			ENSG00000189037	ENSG00000189037		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	20476	protein-coding gene	gene with protein product		300678				12408986	Standard	NM_022076		Approved		uc004dgd.3	Q9H596	OTTHUMG00000021401	ENST00000339042.4:c.557T>C	X.37:g.44703935T>C	ENSP00000343244:p.Met186Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	133	130	0.977444	NM_022076	Q0VDA6|Q6IAJ6|Q6YDQ8	Missense_Mutation	SNP	ENST00000339042.4	37	CCDS14264.1	325	0.19590114526823388	176	0.5176470588235295	16	0.045714285714285714	19	0.034050179211469536	19	0.025537634408602152	c	0.686	-0.796317	0.02862	0.578096	0.061831	ENSG00000189037	ENST00000339042;ENST00000537377	T	0.03386	3.95	3.95	-2.35	0.06684	.	1.207940	0.05675	N	0.589378	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	0.37174	-0.9717	9	0.09084	T	0.74	.	7.4753	0.27371	0.0:0.4824:0.1352:0.3823	rs1045031;rs3174429;rs59938456;rs1045031	186	Q9H596	DUS21_HUMAN	T	186;185	ENSP00000343244:M186T	ENSP00000343244:M186T	M	+	2	0	DUSP21	44588879	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.238000	0.08977	-1.069000	0.03153	-1.174000	0.01732	ATG	0|0.015;C|0.254	0.254	strong		0.438	DUSP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056323.1	NM_022076	
SLC25A13	10165	hgsc.bcm.edu	37	7	95820500	95820500	+	Silent	SNP	C	C	T	rs78247004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:95820500C>T	ENST00000265631.5	-	7	811	c.675G>A	c.(673-675)tcG>tcA	p.S225S	SLC25A13_ENST00000416240.2_Silent_p.S225S|SLC25A13_ENST00000542654.1_Silent_p.S117S			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	225					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|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)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|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)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	TGTTAAGGAGCGAATTAAATC	0.368													C|||	58	0.0115815	0.0439	0.0	5008	,	,		16454	0.0		0.0	False		,,,				2504	0.0				p.S225S		Atlas-SNP	.											SLC25A13,NS,carcinoma,-1,2	SLC25A13	131	2	0			c.G675A						PASS	.	C	,	161,4245	108.6+/-147.0	4,153,2046	147.0	145.0	146.0		675,675	-10.4	0.1	7	dbSNP_132	146	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC25A13	NM_001160210.1,NM_014251.2	,	4,153,6346	TT,TC,CC		0.0,3.6541,1.2379	,	225/677,225/676	95820500	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	10165	exon7			AAGGAGCGAATTA	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"""Solute carriers"", ""EF-hand domain containing"""	10983	protein-coding gene	gene with protein product	"""mitochondrial aspartate glutamate carrier 2"""	603859	"""solute carrier family 25, member 13 (citrin)"""	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.675G>A	7.37:g.95820500C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Silent	SNP	ENST00000265631.5	37	CCDS5645.1																																																																																			C|0.985;T|0.015	0.015	strong		0.368	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251	
ARRDC2	27106	hgsc.bcm.edu	37	19	18121466	18121466	+	Silent	SNP	C	C	T	rs8100681	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18121466C>T	ENST00000222250.4	+	7	1241	c.1098C>T	c.(1096-1098)gaC>gaT	p.D366D	ARRDC2_ENST00000379656.3_Silent_p.D361D	NM_015683.1	NP_056498.1	Q8TBH0	ARRD2_HUMAN	arrestin domain containing 2	366					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)	12						AGGACCCCGACATGAGCCTTG	0.632													C|||	270	0.0539137	0.1165	0.0288	5008	,	,		17281	0.002		0.0467	False		,,,				2504	0.0481				p.D366D		Atlas-SNP	.											.	ARRDC2	60	.	0			c.C1098T						PASS	.	C	,	498,3908	230.7+/-244.8	27,444,1732	63.0	62.0	63.0		1083,1098	0.2	0.0	19	dbSNP_116	63	432,8168	133.0+/-190.5	14,404,3882	no	coding-synonymous,coding-synonymous	ARRDC2	NM_001025604.1,NM_015683.1	,	41,848,5614	TT,TC,CC		5.0233,11.3028,7.1505	,	361/403,366/408	18121466	930,12076	2203	4300	6503	SO:0001819	synonymous_variant	27106	exon7			CCCCGACATGAGC		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.1098C>T	19.37:g.18121466C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_015683	B2RBG9|O95895|Q6ZRV9|Q8WYG6	Silent	SNP	ENST00000222250.4	37	CCDS12370.1																																																																																			C|0.939;T|0.061	0.061	strong		0.632	ARRDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466845.1	NM_015683	
EPHB3	2049	hgsc.bcm.edu	37	3	184293769	184293769	+	Silent	SNP	T	T	C	rs7652597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184293769T>C	ENST00000330394.2	+	4	1460	c.1008T>C	c.(1006-1008)tgT>tgC	p.C336C	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	336	Cys-rich.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			ACAGTGCCTGTACCAGTGAGT	0.592													C|||	1687	0.336861	0.5598	0.2507	5008	,	,		17691	0.1657		0.3608	False		,,,				2504	0.2485				p.C336C		Atlas-SNP	.											.	EPHB3	114	.	0			c.T1008C						PASS	.	C		2352,2054	568.0+/-382.3	610,1132,461	139.0	129.0	132.0		1008	-5.6	0.9	3	dbSNP_116	132	2842,5758	674.6+/-403.1	482,1878,1940	no	coding-synonymous	EPHB3	NM_004443.3		1092,3010,2401	CC,CT,TT		33.0465,46.6182,39.9354		336/999	184293769	5194,7812	2203	4300	6503	SO:0001819	synonymous_variant	2049	exon4			TGCCTGTACCAGT	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.1008T>C	3.37:g.184293769T>C		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			T|0.621;C|0.379	0.379	strong		0.592	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
CBX2	84733	hgsc.bcm.edu	37	17	77758597	77758597	+	Missense_Mutation	SNP	C	C	T	rs76915888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77758597C>T	ENST00000310942.4	+	5	1459	c.1355C>T	c.(1354-1356)gCg>gTg	p.A452V		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	452					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)			GCCCGCAAGGCGGCCACACTG	0.687													C|||	256	0.0511182	0.1762	0.0259	5008	,	,		15513	0.0		0.005	False		,,,				2504	0.0				p.A452V		Atlas-SNP	.											.	CBX2	50	.	0			c.C1355T						PASS	.	C	VAL/ALA	644,3744		43,558,1593	17.0	18.0	18.0		1355	4.2	0.0	17	dbSNP_131	18	30,8560		0,30,4265	yes	missense	CBX2	NM_005189.2	64	43,588,5858	TT,TC,CC		0.3492,14.6764,5.1934	benign	452/533	77758597	674,12304	2194	4295	6489	SO:0001583	missense	84733	exon5			GCAAGGCGGCCAC	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.1355C>T	17.37:g.77758597C>T	ENSP00000308750:p.Ala452Val	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_005189	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	37	CCDS32757.1	82	0.037545787545787544	71	0.1443089430894309	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	C	5.157	0.214476	0.09810	0.146764	0.003492	ENSG00000173894	ENST00000310942	.	.	.	5.18	4.21	0.49690	.	0.780131	0.11562	N	0.551633	T	0.00109	0.0003	N	0.14661	0.345	0.42207	P	0.008209000000000022	P	0.37997	0.614	B	0.22152	0.038	T	0.09400	-1.0676	8	0.17832	T	0.49	-0.004	12.1569	0.54083	0.0:0.9206:0.0:0.0794	.	452	Q14781	CBX2_HUMAN	V	452	.	ENSP00000308750:A452V	A	+	2	0	CBX2	75373192	0.001000	0.12720	0.009000	0.14445	0.013000	0.08279	1.442000	0.35046	1.191000	0.43056	0.650000	0.86243	GCG	C|0.942;T|0.058	0.058	strong		0.687	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
NFRKB	4798	hgsc.bcm.edu	37	11	129752426	129752426	+	Silent	SNP	G	G	A	rs76967949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:129752426G>A	ENST00000446488.3	-	9	1105	c.1002C>T	c.(1000-1002)gcC>gcT	p.A334A	NFRKB_ENST00000524794.1_Silent_p.A359A|NFRKB_ENST00000304521.5_Silent_p.A334A|NFRKB_ENST00000524746.1_Silent_p.A334A	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	334					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		TTAGCGGCTCGGCCAGGTCCT	0.463													G|||	42	0.00838658	0.0295	0.0043	5008	,	,		17616	0.0		0.0	False		,,,				2504	0.0				p.A359A		Atlas-SNP	.											.	NFRKB	101	.	0			c.C1077T						PASS	.	G	,	177,4225	116.3+/-154.2	5,167,2029	95.0	99.0	98.0		1002,1077	-0.8	0.6	11	dbSNP_131	98	5,8589	4.3+/-15.6	0,5,4292	no	coding-synonymous,coding-synonymous	NFRKB	NM_001143835.1,NM_006165.3	,	5,172,6321	AA,AG,GG		0.0582,4.0209,1.4004	,	334/1300,359/1325	129752426	182,12814	2201	4297	6498	SO:0001819	synonymous_variant	4798	exon8			CGGCTCGGCCAGG		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.1002C>T	11.37:g.129752426G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	85	51	0.6	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	37	CCDS44770.1																																																																																			G|0.985;A|0.015	0.015	strong		0.463	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	
DLGAP5	9787	hgsc.bcm.edu	37	14	55619311	55619311	+	Silent	SNP	A	A	G	rs15870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55619311A>G	ENST00000247191.2	-	16	2334	c.2118T>C	c.(2116-2118)aaT>aaC	p.N706N	DLGAP5_ENST00000395425.2_Silent_p.N706N	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	706					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TACTTACATGATTTTCTTCAA	0.338													G|||	1693	0.338059	0.4145	0.2911	5008	,	,		21438	0.1895		0.4085	False		,,,				2504	0.3487				p.N706N		Atlas-SNP	.											.	DLGAP5	84	.	0			c.T2118C						PASS	.	G	,	1849,2557	630.4+/-395.5	390,1069,744	104.0	103.0	104.0		2118,2118	-1.9	0.0	14	dbSNP_52	104	3465,5135	631.3+/-398.5	727,2011,1562	no	coding-synonymous,coding-synonymous	DLGAP5	NM_001146015.1,NM_014750.4	,	1117,3080,2306	GG,GA,AA		40.2907,41.9655,40.8581	,	706/843,706/847	55619311	5314,7692	2203	4300	6503	SO:0001819	synonymous_variant	9787	exon16			TACATGATTTTCT	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"""discs, large homolog 7 (Drosophila)"""	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.2118T>C	14.37:g.55619311A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Silent	SNP	ENST00000247191.2	37	CCDS9723.1																																																																																			A|0.621;G|0.379	0.379	strong		0.338	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	
RAB25	57111	hgsc.bcm.edu	37	1	156039960	156039960	+	Missense_Mutation	SNP	C	C	T	rs115837676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156039960C>T	ENST00000361084.5	+	5	765	c.524C>T	c.(523-525)gCg>gTg	p.A175V		NM_020387.2	NP_065120.2	P57735	RAB25_HUMAN	RAB25, member RAS oncogene family	175					positive regulation of cell proliferation (GO:0008284)|protein transport (GO:0015031)|pseudopodium organization (GO:0031268)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	Hepatocellular(266;0.158)|all_neural(408;0.195)					GAAATCTTTGCGAAGGTGTCC	0.597													C|||	29	0.00579073	0.0212	0.0014	5008	,	,		18839	0.0		0.0	False		,,,				2504	0.0				p.A175V		Atlas-SNP	.											RAB25,NS,carcinoma,-1,1	RAB25	18	1	0			c.C524T						PASS	.	C	VAL/ALA	100,3904		2,96,1904	65.0	69.0	68.0		524	4.9	0.1	1	dbSNP_132	68	0,8350		0,0,4175	no	missense	RAB25	NM_020387.2	64	2,96,6079	TT,TC,CC		0.0,2.4975,0.8095	benign	175/214	156039960	100,12254	2002	4175	6177	SO:0001583	missense	57111	exon5			TCTTTGCGAAGGT	AF083124	CCDS41413.1	1q22	2008-07-03			ENSG00000132698	ENSG00000132698		"""RAB, member RAS oncogene"""	18238	protein-coding gene	gene with protein product		612942				11697911	Standard	NM_020387		Approved	CATX-8	uc001fnc.3	P57735	OTTHUMG00000017457	ENST00000361084.5:c.524C>T	1.37:g.156039960C>T	ENSP00000354376:p.Ala175Val	Somatic	331	1	0.00302115		WXS	Illumina HiSeq	Phase_I	317	157	0.495268	NM_020387	Q5VYA2|Q8NG24|Q96GB1|Q9BT12	Missense_Mutation	SNP	ENST00000361084.5	37	CCDS41413.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	13.90	2.375470	0.42105	0.024975	0.0	ENSG00000132698	ENST00000361084	T	0.80033	-1.33	5.85	4.94	0.65067	.	0.395029	0.26800	N	0.022433	T	0.48370	0.1496	N	0.11560	0.145	0.09310	N	1	B	0.17465	0.022	B	0.09377	0.004	T	0.50533	-0.8817	10	0.87932	D	0	.	12.4852	0.55868	0.1671:0.8329:0.0:0.0	.	175	P57735	RAB25_HUMAN	V	175	ENSP00000354376:A175V	ENSP00000354376:A175V	A	+	2	0	RAB25	154306584	0.001000	0.12720	0.130000	0.21974	0.895000	0.52256	0.961000	0.29267	1.475000	0.48197	-0.152000	0.13540	GCG	C|0.996;T|0.004	0.004	strong		0.597	RAB25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046185.1		
GRAMD3	65983	hgsc.bcm.edu	37	5	125696127	125696127	+	Missense_Mutation	SNP	A	A	G	rs78682130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125696127A>G	ENST00000513040.1	+	1	304	c.104A>G	c.(103-105)aAg>aGg	p.K35R		NM_001146319.1	NP_001139791.1	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	0						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		AGAGAAGTGAAGCCAGTGGGT	0.488													A|||	118	0.0235623	0.087	0.0043	5008	,	,		21319	0.0		0.0	False		,,,				2504	0.0				p.K35R		Atlas-SNP	.											.	GRAMD3	30	.	0			c.A104G						PASS	.	A	ARG/LYS	87,1297		2,83,607	119.0	112.0	114.0		104	4.2	0.0	5	dbSNP_132	114	0,3182		0,0,1591	yes	missense	GRAMD3	NM_001146319.1	26	2,83,2198	GG,GA,AA		0.0,6.2861,1.9054	benign	35/448	125696127	87,4479	692	1591	2283	SO:0001583	missense	65983	exon1			AAGTGAAGCCAGT	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000513040.1:c.104A>G	5.37:g.125696127A>G	ENSP00000426120:p.Lys35Arg	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	210	80	0.380952	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000513040.1	37	CCDS54891.1	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	A	12.15	1.852185	0.32699	0.062861	0.0	ENSG00000155324	ENST00000513040	T	0.35048	1.33	4.15	4.15	0.48705	.	.	.	.	.	T	0.01061	0.0035	.	.	.	0.34252	D	0.678883	B	0.24186	0.099	B	0.22753	0.041	T	0.12682	-1.0538	8	0.16896	T	0.51	.	9.8683	0.41157	1.0:0.0:0.0:0.0	.	35	B7Z6D8	.	R	35	ENSP00000426120:K35R	ENSP00000426120:K35R	K	+	2	0	GRAMD3	125724026	0.158000	0.22850	0.005000	0.12908	0.006000	0.05464	1.900000	0.39828	2.107000	0.64212	0.460000	0.39030	AAG	A|0.975;G|0.025	0.025	strong		0.488	GRAMD3-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371350.1	NM_023927	
ANKRD18A	253650	hgsc.bcm.edu	37	9	38615698	38615698	+	Missense_Mutation	SNP	C	C	T	rs1832313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	176	0	0		WXS	Illumina HiSeq	Phase_I	164	83	0.506098	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		
CRYBG3	131544	hgsc.bcm.edu	37	3	97660084	97660084	+	Silent	SNP	C	C	T	rs11544446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:97660084C>T	ENST00000182096.4	+	17	2818	c.2754C>T	c.(2752-2754)tgC>tgT	p.C918C	CRYBG3_ENST00000485253.1_3'UTR|CRYBG3_ENST00000389622.2_Silent_p.C125C	NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2866							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						CATCTGTGTGCATTTCTCCCT	0.458													C|||	1008	0.201278	0.112	0.3098	5008	,	,		15472	0.1528		0.2823	False		,,,				2504	0.2117				p.C2866C		Atlas-SNP	.											.	CRYBG3	86	.	0			c.C8598T						PASS	.	C		466,3294		25,416,1439	125.0	118.0	120.0		8598	1.8	0.4	3	dbSNP_120	120	2328,5878		350,1628,2125	no	coding-synonymous	CRYBG3	XM_003118522.2		375,2044,3564	TT,TC,CC		28.3695,12.3936,23.3495		2866/2971	97660084	2794,9172	1880	4103	5983	SO:0001819	synonymous_variant	131544	exon20			TGTGTGCATTTCT			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.2754C>T	3.37:g.97660084C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Silent	SNP	ENST00000182096.4	37																																																																																				C|0.790;T|0.210	0.210	strong		0.458	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605	
NLRP13	126204	hgsc.bcm.edu	37	19	56443519	56443519	+	Silent	SNP	C	C	T	rs12610617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56443519C>T	ENST00000342929.3	-	1	158	c.159G>A	c.(157-159)ccG>ccA	p.P53P	NLRP13_ENST00000588751.1_Silent_p.P53P	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	53	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						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)		AGGGGATACGCGGGAAGTGCC	0.552													C|||	497	0.0992412	0.1157	0.0447	5008	,	,		18654	0.2609		0.0109	False		,,,				2504	0.0399				p.P53P		Atlas-SNP	.											NLRP13,colon,carcinoma,-1,1	NLRP13	220	1	0			c.G159A						PASS	.	C		391,4015	193.0+/-218.2	16,359,1828	57.0	60.0	59.0		159	-1.8	0.0	19	dbSNP_120	59	78,8522	43.6+/-101.6	0,78,4222	no	coding-synonymous	NLRP13	NM_176810.2		16,437,6050	TT,TC,CC		0.907,8.8743,3.606		53/1044	56443519	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon1			GATACGCGGGAAG	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.159G>A	19.37:g.56443519C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			C|0.928;T|0.072	0.072	strong		0.552	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
DPEP2	64174	hgsc.bcm.edu	37	16	68024850	68024850	+	Silent	SNP	A	A	G	rs10500542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:68024850A>G	ENST00000572888.1	-	6	1433	c.783T>C	c.(781-783)caT>caC	p.H261H	DPEP2_ENST00000393847.1_Silent_p.H261H|DPEP2_ENST00000412757.2_Silent_p.H261H			Q9H4A9	DPEP2_HUMAN	dipeptidase 2	261					arachidonic acid metabolic process (GO:0019369)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		CATCTGAGACATGGGATAAGT	0.572													G|||	339	0.0676917	0.2103	0.0202	5008	,	,		19215	0.001		0.007	False		,,,				2504	0.0399				p.H261H		Atlas-SNP	.											.	DPEP2	43	.	0			c.T783C						PASS	.	G		847,3549	332.0+/-302.3	91,665,1442	114.0	113.0	113.0		783	-2.0	1.0	16	dbSNP_119	113	29,8571	17.9+/-57.8	0,29,4271	no	coding-synonymous	DPEP2	NM_022355.2		91,694,5713	GG,GA,AA		0.3372,19.2675,6.7405		261/487	68024850	876,12120	2198	4300	6498	SO:0001819	synonymous_variant	64174	exon7			TGAGACATGGGAT	AJ295149	CCDS10857.1	16q22.1	2011-07-22			ENSG00000167261	ENSG00000167261	3.4.13.19		23028	protein-coding gene	gene with protein product		609925					Standard	NM_022355		Approved		uc002eve.4	Q9H4A9	OTTHUMG00000137542	ENST00000572888.1:c.783T>C	16.37:g.68024850A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	151	67	0.443709	NM_022355	B2RCF8|Q6UX92|Q8TC95	Silent	SNP	ENST00000572888.1	37	CCDS10857.1																																																																																			A|0.942;G|0.058	0.058	strong		0.572	DPEP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437026.1	NM_022355	
TANC1	85461	hgsc.bcm.edu	37	2	160087410	160087410	+	Missense_Mutation	SNP	C	C	T	rs77049231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160087410C>T	ENST00000263635.6	+	27	5710	c.5473C>T	c.(5473-5475)Cat>Tat	p.H1825Y	TANC1_ENST00000454300.1_Missense_Mutation_p.H1719Y	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1825					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GACTGTTTCTCATCTGTACCA	0.453													C|||	220	0.0439297	0.1611	0.0086	5008	,	,		18665	0.0		0.001	False		,,,				2504	0.0				p.H1825Y		Atlas-SNP	.											.	TANC1	157	.	0			c.C5473T						PASS	.	C	,TYR/HIS	476,3394		31,414,1490	76.0	77.0	77.0		,5473	5.2	0.0	2	dbSNP_131	77	2,8310		0,2,4154	yes	utr-3,missense	TANC1	NM_001145909.1,NM_033394.2	,83	31,416,5644	TT,TC,CC		0.0241,12.2997,3.9238	,possibly-damaging	,1825/1862	160087410	478,11704	1935	4156	6091	SO:0001583	missense	85461	exon27			GTTTCTCATCTGT	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.5473C>T	2.37:g.160087410C>T	ENSP00000263635:p.His1825Tyr	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	165	94	0.569697	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	66	0.03021978021978022	64	0.13008130081300814	2	0.0055248618784530384	0	0.0	0	0.0	C	13.58	2.280696	0.40294	0.122997	2.41E-4	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.71817	-0.59;-0.6	6.06	5.18	0.71444	.	0.096342	0.64402	D	0.000001	T	0.01489	0.0048	L	0.56769	1.78	0.23003	P	0.99844134	D	0.56521	0.976	B	0.40636	0.335	T	0.33675	-0.9859	8	.	.	.	.	17.4939	0.87712	0.0:0.876:0.124:0.0	.	1825	Q9C0D5	TANC1_HUMAN	Y	1719;1825	ENSP00000396339:H1719Y;ENSP00000263635:H1825Y	.	H	+	1	0	TANC1	159795656	1.000000	0.71417	0.030000	0.17652	0.010000	0.07245	5.453000	0.66645	1.559000	0.49555	0.655000	0.94253	CAT	C|0.980;T|0.020	0.020	strong		0.453	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
TNRC18	84629	hgsc.bcm.edu	37	7	5352659	5352659	+	Silent	SNP	G	G	T	rs138591330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5352659G>T	ENST00000430969.1	-	27	8211	c.7863C>A	c.(7861-7863)tcC>tcA	p.S2621S	TNRC18_ENST00000399537.4_Silent_p.S2621S	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2621	Ser-rich.						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)		aggaggaggaggaggatgagg	0.652													G|||	2190	0.4373	0.5076	0.5274	5008	,	,		5586	0.246		0.508	False		,,,				2504	0.4029				p.S2621S		Atlas-SNP	.											TNRC18_ENST00000430969,NS,carcinoma,0,3	TNRC18	311	3	0			c.C7863A						PASS	.						5.0	8.0	7.0					7																	5352659		1382	3171	4553	SO:0001819	synonymous_variant	84629	exon27			GGAGGAGGAGGAT	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.7863C>A	7.37:g.5352659G>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1	760	0.34798534798534797	201	0.40853658536585363	151	0.4171270718232044	104	0.18181818181818182	304	0.40105540897097625	N	0.009	-1.858244	0.00558	.	.	ENSG00000182095	ENST00000399544	.	.	.	4.17	-1.59	0.08453	.	0.589271	0.12916	N	0.428578	T	0.00012	0.0000	.	.	.	0.34255	P	0.32071700000000003	.	.	.	.	.	.	T	0.40776	-0.9545	5	0.87932	D	0	.	4.5564	0.12138	0.3329:0.0:0.5125:0.1546	.	.	.	.	H	1134	.	ENSP00000382459:P1134H	P	-	2	0	TNRC18	5319185	1.000000	0.71417	0.029000	0.17559	0.001000	0.01503	0.742000	0.26216	-0.333000	0.08476	-1.713000	0.00713	CCT	G|0.653;T|0.347	0.347	strong		0.652	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
OBSCN	84033	hgsc.bcm.edu	37	1	228476366	228476366	+	Missense_Mutation	SNP	G	G	T	rs3795789|rs386640016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228476366G>T	ENST00000422127.1	+	38	10160	c.10116G>T	c.(10114-10116)gaG>gaT	p.E3372D	OBSCN_ENST00000359599.6_Missense_Mutation_p.E2219D|OBSCN_ENST00000284548.11_Missense_Mutation_p.E3372D|OBSCN_ENST00000570156.2_Missense_Mutation_p.E3801D|OBSCN_ENST00000366709.4_Missense_Mutation_p.E491D|OBSCN_ENST00000366707.4_Missense_Mutation_p.E491D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3372	Ig-like 34.		E -> D (in dbSNP:rs3795789).		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)				GACACCAAGAGAGCATAGAAG	0.607													G|||	480	0.0958466	0.0514	0.0144	5008	,	,		21025	0.3165		0.0258	False		,,,				2504	0.0583				p.E3801D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G11403T						PASS	.	G	ASP/GLU,ASP/GLU	186,3926		8,170,1878	71.0	76.0	75.0		10116,10116	3.2	0.2	1	dbSNP_107	75	125,8281		0,125,4078	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	45,45	8,295,5956	TT,TG,GG		1.487,4.5233,2.4844	possibly-damaging,possibly-damaging	3372/7969,3372/6621	228476366	311,12207	2056	4203	6259	SO:0001583	missense	84033	exon43			CCAAGAGAGCATA	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.10116G>T	1.37:g.228476366G>T	ENSP00000409493:p.Glu3372Asp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	122	63	0.516393	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	208	0.09523809523809523	17	0.034552845528455285	3	0.008287292817679558	167	0.291958041958042	21	0.027704485488126648	G	16.90	3.251180	0.59212	0.045233	0.01487	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37	5.07	3.15	0.36227	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.325170	0.22002	N	0.065982	T	0.00012	0.0000	M	0.87758	2.905	0.38410	P	0.054088000000000025	B;P	0.38863	0.139;0.65	P;P	0.51701	0.472;0.677	T	0.08785	-1.0705	9	0.32370	T	0.25	.	6.4245	0.21762	0.1648:0.0:0.6798:0.1554	rs3795789;rs3795789	3372;3372	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	D	3372;3372;491;491;2219	ENSP00000284548:E3372D;ENSP00000409493:E3372D;ENSP00000355668:E491D;ENSP00000355670:E491D;ENSP00000352613:E2219D	ENSP00000284548:E3372D	E	+	3	2	OBSCN	226542989	0.195000	0.23338	0.215000	0.23724	0.333000	0.28666	0.401000	0.20948	1.121000	0.41925	0.561000	0.74099	GAG	G|0.927;T|0.073	0.073	strong		0.607	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CCDC142	84865	hgsc.bcm.edu	37	2	74708453	74708453	+	Silent	SNP	A	A	T	rs115125840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74708453A>T	ENST00000393965.3	-	3	1551	c.1155T>A	c.(1153-1155)ctT>ctA	p.L385L	CCDC142_ENST00000290418.4_Silent_p.L385L|TTC31_ENST00000233623.5_5'Flank|TTC31_ENST00000410003.1_5'Flank|TTC31_ENST00000442235.2_5'Flank|CCDC142_ENST00000471713.1_5'UTR	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	385										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						AGGATGTGGGAAGGCTGCTCT	0.557													A|||	19	0.00379393	0.0144	0.0	5008	,	,		19536	0.0		0.0	False		,,,				2504	0.0				p.L385L		Atlas-SNP	.											.	CCDC142	40	.	0			c.T1155A						PASS	.	A		32,4374	37.6+/-69.7	0,32,2171	111.0	126.0	121.0		1155	-2.6	0.0	2	dbSNP_132	121	0,8600		0,0,4300	no	coding-synonymous	CCDC142	NM_032779.3		0,32,6471	TT,TA,AA		0.0,0.7263,0.246		385/744	74708453	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	84865	exon3			TGTGGGAAGGCTG	AK075543	CCDS1945.1	2p13.1	2008-02-05			ENSG00000135637	ENSG00000135637			25889	protein-coding gene	gene with protein product							Standard	NM_032779		Approved	FLJ14397	uc002slq.3	Q17RM4	OTTHUMG00000129962	ENST00000393965.3:c.1155T>A	2.37:g.74708453A>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	144	56	0.388889	NM_032779	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Silent	SNP	ENST00000393965.3	37																																																																																				A|0.997;T|0.003	0.003	strong		0.557	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779	
DDX11	1663	hgsc.bcm.edu	37	12	31250830	31250830	+	Missense_Mutation	SNP	C	C	G	rs2911826		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:31250830C>G	ENST00000407793.2	+	18	2025	c.1774C>G	c.(1774-1776)Cag>Gag	p.Q592E	DDX11_ENST00000350437.4_Missense_Mutation_p.Q592E|DDX11_ENST00000228264.6_Missense_Mutation_p.Q566E|DDX11_ENST00000545668.1_Missense_Mutation_p.Q592E|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Missense_Mutation_p.Q592E|DDX11_ENST00000539673.1_3'UTR	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	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	225	0	0		WXS	Illumina HiSeq	Phase_I	290	17	0.0586207	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	
OPN1LW	5956	hgsc.bcm.edu	37	X	153420176	153420176	+	Missense_Mutation	SNP	A	A	G	rs78093925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153420176A>G	ENST00000369951.4	+	4	766	c.706A>G	c.(706-708)Atg>Gtg	p.M236V	OPN1LW_ENST00000463296.1_Intron	NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	236					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)					CGCTATCATCATGCTCTGCTA	0.612													G|||	565	0.149669	0.3192	0.0562	3775	,	,		12001	0.0129		0.0616	False		,,,				2504	0.0297				p.M236V		Atlas-SNP	.											.	OPN1LW	87	.	0			c.A706G						PASS	.	G	VAL/MET	1403,2417		217,767,202,647,356	308.0	226.0	254.0		706	-3.0	0.2	X	dbSNP_131	254	634,6044		36,376,186,2014,1640	yes	missense	OPN1LW	NM_020061.4	21	253,1143,388,2661,1996	GG,GA,G,AA,A		9.4939,36.7277,19.4037	benign	236/365	153420176	2037,8461	2189	4252	6441	SO:0001583	missense	5956	exon4			ATCATCATGCTCT	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.706A>G	X.37:g.153420176A>G	ENSP00000358967:p.Met236Val	Somatic	618	1	0.00161812		WXS	Illumina HiSeq	Phase_I	929	485	0.522067	NM_020061		Missense_Mutation	SNP	ENST00000369951.4	37	CCDS14742.1	210	0.12658227848101267	88	0.2233502538071066	12	0.03428571428571429	4	0.007017543859649123	33	0.04583333333333333	G	0.007	-1.991273	0.00439	0.367277	0.094939	ENSG00000102076	ENST00000369951;ENST00000442922	T;T	0.70282	-0.47;-0.47	4.27	-2.95	0.05564	GPCR, rhodopsin-like superfamily (1);	0.428458	0.24742	N	0.035968	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.40459	-0.9562	9	0.25106	T	0.35	.	7.105	0.25358	0.3272:0.3964:0.2763:0.0	.	236	P04000	OPSR_HUMAN	V	236;99	ENSP00000358967:M236V;ENSP00000402493:M99V	ENSP00000358967:M236V	M	+	1	0	OPN1LW	153073370	0.000000	0.05858	0.239000	0.24122	0.134000	0.20937	-1.488000	0.02308	-0.716000	0.04962	-0.775000	0.03384	ATG	A|0.814;G|0.186	0.186	strong		0.612	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061	
IFNA14	3448	hgsc.bcm.edu	37	9	21239504	21239504	+	Missense_Mutation	SNP	T	T	C	rs140823004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21239504T>C	ENST00000380222.2	-	1	474	c.431A>G	c.(430-432)aAg>aGg	p.K144R		NM_002172.2	NP_002163.2	P01570	IFN14_HUMAN	interferon, alpha 14	144					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)	11				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		GAAGTATTTCTTCACAGCCAG	0.463																																					p.K144R		Atlas-SNP	.											IFNA14,NS,carcinoma,0,1	IFNA14	29	1	0			c.A431G						scavenged	.	T	ARG/LYS	0,4406		0,0,2203	222.0	223.0	223.0		431	-6.8	0.0	9	dbSNP_134	223	1,8599		0,1,4299	no	missense	IFNA14	NM_002172.2	26	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	144/190	21239504	1,13005	2203	4300	6503	SO:0001583	missense	3448	exon1			TATTTCTTCACAG		CCDS6501.1	9p22	2010-08-24			ENSG00000228083	ENSG00000228083		"""Interferons"""	5420	protein-coding gene	gene with protein product		147579				1385305	Standard	NM_002172		Approved	LEIF2H, IFN-alphaH	uc010mis.3	P01570	OTTHUMG00000019665	ENST00000380222.2:c.431A>G	9.37:g.21239504T>C	ENSP00000369571:p.Lys144Arg	Somatic	357	0	0		WXS	Illumina HiSeq	Phase_I	401	47	0.117207	NM_002172	Q5VZ56|Q7M4S1	Missense_Mutation	SNP	ENST00000380222.2	37	CCDS6501.1	.	.	.	.	.	.	.	.	.	.	-	0.215	-1.033570	0.02029	0.0	1.16E-4	ENSG00000228083	ENST00000380222	T	0.03745	3.82	3.38	-6.76	0.01732	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.418930	0.25194	N	0.032432	T	0.00967	0.0032	N	0.02368	-0.58	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.34378	-0.9831	10	0.02654	T	1	.	6.649	0.22951	0.1395:0.2029:0.0:0.6576	.	144	P01570	IFN14_HUMAN	R	144	ENSP00000369571:K144R	ENSP00000369571:K144R	K	-	2	0	IFNA14	21229504	0.000000	0.05858	0.002000	0.10522	0.341000	0.28922	-3.552000	0.00433	-1.276000	0.02414	-1.307000	0.01316	AAG	T|1.000;C|0.000	0.000	strong		0.463	IFNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051894.1	NM_002172	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919302	51919302	+	Missense_Mutation	SNP	T	T	C	rs201376644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51919302T>C	ENST00000339313.5	-	5	990	c.874A>G	c.(874-876)Aac>Gac	p.N292D	SIGLEC10_ENST00000432469.2_Missense_Mutation_p.N209D|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.N234D|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.N292D|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.N234D|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.N244D|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.N292D|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	292	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		AGGACTCTGTTCTGCAGGACC	0.652																																					p.N292D		Atlas-SNP	.											SIGLEC12_ENST00000439889,rectum,carcinoma,0,2	SIGLEC10	112	2	0			c.A874G						PASS	.						19.0	24.0	22.0					19																	51919302		2201	4299	6500	SO:0001583	missense	89790	exon5			CTCTGTTCTGCAG	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.874A>G	19.37:g.51919302T>C	ENSP00000345243:p.Asn292Asp	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	125	13	0.104	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	7.755	0.704152	0.15172	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;T;T;T;T;T;T	0.40476	1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.03	4.37	1.07	0.20283	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.427133	0.19965	N	0.102128	T	0.13841	0.0335	N	0.02854	-0.475	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001	T	0.33701	-0.9858	10	0.02654	T	1	.	7.7519	0.28903	0.0:0.684:0.0:0.316	.	244;292;292;234;234;292	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	D	292;209;292;234;234;244;292;106	ENSP00000342389:N292D;ENSP00000396742:N209D;ENSP00000348646:N292D;ENSP00000408387:N234D;ENSP00000389132:N234D;ENSP00000414324:N244D;ENSP00000345243:N292D;ENSP00000435281:N106D	ENSP00000345243:N292D	N	-	1	0	SIGLEC10	56611114	0.000000	0.05858	0.002000	0.10522	0.047000	0.14425	0.182000	0.16900	-0.072000	0.12864	-1.945000	0.00491	AAC	T|0.998;C|0.002	0.002	strong		0.652	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
ZNF432	9668	hgsc.bcm.edu	37	19	52538428	52538428	+	Silent	SNP	A	A	G	rs11881700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52538428A>G	ENST00000594154.1	-	5	716	c.504T>C	c.(502-504)ggT>ggC	p.G168G	ZNF432_ENST00000221315.5_Silent_p.G168G			O94892	ZN432_HUMAN	zinc finger protein 432	168					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	29		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)		CTTCATAGTTACCATGAAGAA	0.323													A|||	981	0.195887	0.2171	0.1974	5008	,	,		17426	0.124		0.0994	False		,,,				2504	0.3395				p.G168G		Atlas-SNP	.											ZNF432,NS,carcinoma,-1,1	ZNF432	172	1	0			c.T504C						PASS	.	A		952,3452	357.6+/-314.0	104,744,1354	55.0	54.0	55.0		504	0.0	0.0	19	dbSNP_120	55	974,7626	210.4+/-251.3	54,866,3380	yes	coding-synonymous	ZNF432	NM_014650.2		158,1610,4734	GG,GA,AA		11.3256,21.6167,14.8108		168/653	52538428	1926,11078	2202	4300	6502	SO:0001819	synonymous_variant	9668	exon5			ATAGTTACCATGA	AB018341	CCDS12848.1	19q13.41	2013-01-08				ENSG00000256087		"""Zinc fingers, C2H2-type"", ""-"""	20810	protein-coding gene	gene with protein product						9872452	Standard	NM_014650		Approved	KIAA0798	uc002pyk.3	O94892		ENST00000594154.1:c.504T>C	19.37:g.52538428A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	121	75	0.619835	NM_014650		Silent	SNP	ENST00000594154.1	37	CCDS12848.1																																																																																			A|0.839;G|0.161	0.161	strong		0.323	ZNF432-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462410.1	NM_014650	
DDX47	51202	hgsc.bcm.edu	37	12	12980305	12980305	+	Missense_Mutation	SNP	G	G	A	rs373273540		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:12980305G>A	ENST00000358007.3	+	11	1254	c.1232G>A	c.(1231-1233)cGa>cAa	p.R411Q	DDX47_ENST00000352940.4_Missense_Mutation_p.R362Q	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	411					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		AGGTTTGCCCGAATGGTATGC	0.423													G|||	1	0.000199681	0.0	0.0	5008	,	,		21240	0.001		0.0	False		,,,				2504	0.0				p.R411Q		Atlas-SNP	.											DDX47,colon,carcinoma,+1,1	DDX47	37	1	0			c.G1232A						PASS	.						218.0	216.0	217.0					12																	12980305		2203	4300	6503	SO:0001583	missense	51202	exon11			TTGCCCGAATGGT	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"""DEAD-boxes"""	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.1232G>A	12.37:g.12980305G>A	ENSP00000350698:p.Arg411Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	116	73	0.62931	NM_016355	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	37	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.284152	0.40394	.	.	ENSG00000213782	ENST00000352940;ENST00000358007	T;T	0.26957	2.5;1.7	5.75	3.89	0.44902	.	0.066087	0.64402	D	0.000015	T	0.17704	0.0425	L	0.28649	0.875	0.53688	D	0.999974	B;B	0.20887	0.036;0.049	B;B	0.16722	0.016;0.004	T	0.04203	-1.0969	10	0.13108	T	0.6	-5.9575	12.9654	0.58481	0.0:0.1243:0.7461:0.1296	.	362;411	G5E955;Q9H0S4	.;DDX47_HUMAN	Q	362;411	ENSP00000319578:R362Q;ENSP00000350698:R411Q	ENSP00000319578:R362Q	R	+	2	0	DDX47	12871572	1.000000	0.71417	0.983000	0.44433	0.988000	0.76386	7.657000	0.83745	0.746000	0.32786	0.655000	0.94253	CGA	.	.	weak		0.423	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355	
SALL4	57167	hgsc.bcm.edu	37	20	50406646	50406646	+	Silent	SNP	A	A	G	rs143601538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50406646A>G	ENST00000217086.4	-	2	2487	c.2376T>C	c.(2374-2376)aaT>aaC	p.N792N	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	792					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						CGGCTTGACTATTGGCCGGGG	0.547													A|||	4	0.000798722	0.003	0.0	5008	,	,		17547	0.0		0.0	False		,,,				2504	0.0				p.N792N		Atlas-SNP	.											.	SALL4	168	.	0			c.T2376C						PASS	.	A		11,4395	17.9+/-39.9	0,11,2192	79.0	73.0	75.0		2376	2.2	1.0	20	dbSNP_134	75	0,8600		0,0,4300	no	coding-synonymous	SALL4	NM_020436.3		0,11,6492	GG,GA,AA		0.0,0.2497,0.0846		792/1054	50406646	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			TTGACTATTGGCC	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.2376T>C	20.37:g.50406646A>G		Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	302	158	0.523179	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			A|0.999;G|0.001	0.001	strong		0.547	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
NXPE1	120400	hgsc.bcm.edu	37	11	114393066	114393066	+	Missense_Mutation	SNP	A	A	G	rs34993124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:114393066A>G	ENST00000424269.1	-	5	1267	c.1268T>C	c.(1267-1269)aTt>aCt	p.I423T	NXPE1_ENST00000251921.2_Missense_Mutation_p.I281T|NXPE1_ENST00000536271.1_Missense_Mutation_p.I139T			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	423			I -> T (in dbSNP:rs34993124).			extracellular region (GO:0005576)											TAGCCGGTCAATTTCCCGAGG	0.443													A|||	95	0.0189696	0.0651	0.013	5008	,	,		18652	0.0		0.0	False		,,,				2504	0.0				p.I281T		Atlas-SNP	.											.	NXPE1	8	.	0			c.T842C						PASS	.	A	THR/ILE	254,4148	146.1+/-180.8	4,246,1951	147.0	140.0	142.0		842	2.1	0.6	11	dbSNP_126	142	3,8589	3.0+/-9.4	0,3,4293	yes	missense	FAM55A	NM_152315.2	89	4,249,6244	GG,GA,AA		0.0349,5.7701,1.9778	probably-damaging	281/406	114393066	257,12737	2201	4296	6497	SO:0001583	missense	120400	exon6			CGGTCAATTTCCC	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member A"""	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.1268T>C	11.37:g.114393066A>G	ENSP00000411690:p.Ile423Thr	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	161	74	0.459627	NM_152315	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	37		38	0.0173992673992674	34	0.06910569105691057	4	0.011049723756906077	0	0.0	0	0.0	A	27.2	4.809928	0.90707	0.057701	3.49E-4	ENSG00000095110	ENST00000536271;ENST00000251921;ENST00000424269	T;T;T	0.27256	1.68;1.68;1.68	4.44	2.07	0.26955	.	0.082106	0.49916	D	0.000132	T	0.07503	0.0189	M	0.92367	3.3	0.28092	N	0.931779	D	0.76494	0.999	D	0.67382	0.951	T	0.10177	-1.0641	10	0.56958	D	0.05	.	8.0262	0.30438	0.8267:0.0:0.1733:0.0	rs34993124	423	Q8N323	FA55A_HUMAN	T	139;281;423	ENSP00000445200:I139T;ENSP00000251921:I281T;ENSP00000411690:I423T	ENSP00000251921:I281T	I	-	2	0	FAM55A	113898276	0.993000	0.37304	0.643000	0.29450	0.931000	0.56810	1.124000	0.31320	0.298000	0.22638	0.528000	0.53228	ATT	A|0.982;G|0.018	0.018	strong		0.443	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315	
CCDC180	100499483	hgsc.bcm.edu	37	9	100139161	100139161	+	Silent	SNP	A	A	G	rs11581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100139161A>G	ENST00000357054.1	+	49	5861	c.4926A>G	c.(4924-4926)caA>caG	p.Q1642Q	CCDC180_ENST00000529487.1_Silent_p.Q1697Q|CCDC180_ENST00000375202.2_Silent_p.Q1697Q|CCDC180_ENST00000395220.1_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1642						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.Q1642Q(1)									ACACTATCCAAGGCCTGTATG	0.517													G|||	2100	0.419329	0.5726	0.4582	5008	,	,		21290	0.5248		0.1958	False		,,,				2504	0.3057				p.Q1697Q		Atlas-SNP	.											KIAA1529,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.A5091G						PASS	.	G		2343,2063	566.4+/-381.9	643,1057,503	127.0	104.0	112.0		5091	2.1	0.6	9	dbSNP_52	112	1624,6976	739.4+/-407.1	146,1332,2822	no	coding-synonymous	C9orf174	NM_020893.2		789,2389,3325	GG,GA,AA		18.8837,46.8225,30.5013		1697/1702	100139161	3967,9039	2203	4300	6503	SO:0001819	synonymous_variant	0	exon37			TATCCAAGGCCTG	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.4926A>G	9.37:g.100139161A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				A|0.654;G|0.346	0.346	strong		0.517	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
SMC2	10592	hgsc.bcm.edu	37	9	106901506	106901506	+	Silent	SNP	A	A	G	rs16923746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:106901506A>G	ENST00000286398.7	+	25	3792	c.3504A>G	c.(3502-3504)gtA>gtG	p.V1168V	SMC2_ENST00000374787.3_Silent_p.V1168V|SMC2_ENST00000374793.3_Silent_p.V1168V	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	1168					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						TTTCTACAGTAGCCAGATTTA	0.363													A|||	326	0.0650958	0.2209	0.013	5008	,	,		15837	0.0129		0.007	False		,,,				2504	0.0051				p.V1168V		Atlas-SNP	.											.	SMC2	127	.	0			c.A3504G						PASS	.	A	,,	742,3664	302.7+/-287.5	56,630,1517	89.0	89.0	89.0		3504,3504,3504	-3.0	1.0	9	dbSNP_123	89	62,8538	39.3+/-95.6	0,62,4238	no	coding-synonymous,coding-synonymous,coding-synonymous	SMC2	NM_001042550.1,NM_001042551.1,NM_006444.2	,,	56,692,5755	GG,GA,AA		0.7209,16.8407,6.1818	,,	1168/1198,1168/1198,1168/1198	106901506	804,12202	2203	4300	6503	SO:0001819	synonymous_variant	10592	exon25			TACAGTAGCCAGA	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"""Structural maintenance of chromosomes proteins"""	14011	protein-coding gene	gene with protein product		605576	"""SMC2 (structural maintenance of chromosomes 2, yeast)-like 1"", ""SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"""	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.3504A>G	9.37:g.106901506A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	194	66	0.340206	NM_006444	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	37	CCDS35086.1																																																																																			A|0.935;G|0.065	0.065	strong		0.363	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1		
FUT3	2525	hgsc.bcm.edu	37	19	5844792	5844792	+	Missense_Mutation	SNP	A	A	C	rs28362459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5844792A>C	ENST00000303225.6	-	3	693	c.59T>G	c.(58-60)cTg>cGg	p.L20R	FUT3_ENST00000458379.2_Missense_Mutation_p.L20R|AC024592.9_ENST00000589276.1_RNA|FUT3_ENST00000589620.1_Missense_Mutation_p.L20R|FUT3_ENST00000589918.1_Missense_Mutation_p.L20R|FUT3_ENST00000593144.1_5'Flank	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	20			L -> R (in Le(-); dbSNP:rs28362459). {ECO:0000269|PubMed:8063716, ECO:0000269|PubMed:8219240, ECO:0000269|PubMed:8240337, ECO:0000269|PubMed:8801770, ECO:0000269|Ref.5}.		cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						CTGAAATAGCAGTGCGGCCAG	0.612													A|||	1266	0.252796	0.3374	0.2709	5008	,	,		15473	0.2956		0.0984	False		,,,				2504	0.2403				p.L20R	Esophageal Squamous(82;745 1728 24593 44831)	Atlas-SNP	.											FUT3,NS,carcinoma,0,1	FUT3	30	1	0			c.T59G	GRCh37	CM930258	FUT3	M	rs28362459	PASS	.	A	ARG/LEU,ARG/LEU,ARG/LEU,ARG/LEU	1244,3162	381.8+/-324.2	181,882,1140	28.0	26.0	27.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	59,59,59,59	2.3	0.0	19	dbSNP_125	27	846,7754	179.8+/-228.8	43,760,3497	yes	missense,missense,missense,missense	FUT3	NM_000149.3,NM_001097639.1,NM_001097640.1,NM_001097641.1	102,102,102,102	224,1642,4637	CC,CA,AA		9.8372,28.2342,16.0695	probably-damaging,probably-damaging,probably-damaging,probably-damaging	20/362,20/362,20/362,20/362	5844792	2090,10916	2203	4300	6503	SO:0001583	missense	2525	exon3			AATAGCAGTGCGG		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"""CD molecules"", ""Blood group antigens"", ""Fucosyltransferases"""	4014	protein-coding gene	gene with protein product		111100	"""fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"""	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.59T>G	19.37:g.5844792A>C	ENSP00000305603:p.Leu20Arg	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	223	111	0.497758	NM_001097640	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	CCDS12153.1	457	0.20924908424908426	156	0.3170731707317073	79	0.21823204419889503	141	0.2465034965034965	81	0.10686015831134564	A	15.12	2.738382	0.49045	0.282342	0.098372	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.26810	1.71;1.71	2.33	2.33	0.28932	.	0.909833	0.09089	N	0.850153	T	0.00012	0.0000	M	0.79475	2.455	0.32237	P	0.573249	D;D;D;D	0.69078	0.997;0.997;0.997;0.997	D;D;D;D	0.70227	0.968;0.968;0.968;0.968	T	0.22034	-1.0228	9	0.29301	T	0.29	.	8.4913	0.33102	1.0:0.0:0.0:0.0	rs28362459;rs60711378	20;20;20;20	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	R	20	ENSP00000305603:L20R;ENSP00000416443:L20R	ENSP00000305603:L20R	L	-	2	0	FUT3	5795792	0.002000	0.14202	0.024000	0.17045	0.030000	0.12068	0.986000	0.29590	1.010000	0.39314	0.172000	0.16884	CTG	A|0.832;C|0.168	0.168	strong		0.612	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149	
PRDM14	63978	hgsc.bcm.edu	37	8	70964399	70964399	+	Silent	SNP	A	A	G	rs10089937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:70964399A>G	ENST00000276594.2	-	8	1830	c.1629T>C	c.(1627-1629)gaT>gaC	p.D543D		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	543					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|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(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			AGCAGCCATCATCCTCCTTGT	0.498													A|||	3234	0.645767	0.5847	0.6037	5008	,	,		21867	0.7302		0.6143	False		,,,				2504	0.7035				p.D543D	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											.	PRDM14	102	.	0			c.T1629C						PASS	.	A		2701,1705	652.5+/-399.4	825,1051,327	136.0	127.0	130.0		1629	-9.4	0.0	8	dbSNP_119	130	5399,3201	653.0+/-401.0	1698,2003,599	no	coding-synonymous	PRDM14	NM_024504.2		2523,3054,926	GG,GA,AA		37.2209,38.6972,37.7211		543/572	70964399	8100,4906	2203	4300	6503	SO:0001819	synonymous_variant	63978	exon8			GCCATCATCCTCC	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"""Zinc fingers, C2H2-type"""	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1629T>C	8.37:g.70964399A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_024504	Q86UX9	Silent	SNP	ENST00000276594.2	37	CCDS6206.1																																																																																			A|0.364;G|0.636	0.636	strong		0.498	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1		
DHDH	27294	hgsc.bcm.edu	37	19	49442933	49442933	+	Silent	SNP	T	T	C	rs2270939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49442933T>C	ENST00000221403.2	+	4	634	c.594T>C	c.(592-594)tcT>tcC	p.S198S	DHDH_ENST00000522614.1_Silent_p.S198S|DHDH_ENST00000523250.1_Intron	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	198					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		AGAAGATTTCTGTCGTGGGAA	0.537													C|||	2269	0.453075	0.6982	0.2954	5008	,	,		18321	0.5675		0.2058	False		,,,				2504	0.3701				p.S198S		Atlas-SNP	.											.	DHDH	35	.	0			c.T594C						PASS	.	C		2781,1625	500.0+/-364.6	899,983,321	103.0	106.0	105.0		594	-9.9	0.0	19	dbSNP_100	105	1492,7108	749.0+/-407.4	130,1232,2938	no	coding-synonymous	DHDH	NM_014475.3		1029,2215,3259	CC,CT,TT		17.3488,36.8815,32.8541		198/335	49442933	4273,8733	2203	4300	6503	SO:0001819	synonymous_variant	27294	exon4			GATTTCTGTCGTG	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.594T>C	19.37:g.49442933T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_014475		Silent	SNP	ENST00000221403.2	37	CCDS12741.1																																																																																			T|0.623;C|0.377	0.377	strong		0.537	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
SRL	6345	hgsc.bcm.edu	37	16	4245693	4245693	+	Silent	SNP	A	A	G	rs10852643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4245693A>G	ENST00000399609.3	-	5	483	c.471T>C	c.(469-471)cgT>cgC	p.R157R	SRL_ENST00000537996.1_Silent_p.R115R	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	616	Acidic domain, probably binds calcium. {ECO:0000250}.					sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						GTGAGAAGGAACGGGCGCTGT	0.542													G|||	4073	0.813299	0.9652	0.7147	5008	,	,		16758	0.755		0.7286	False		,,,				2504	0.8252				p.R157R		Atlas-SNP	.											.	SRL	56	.	0			c.T471C						PASS	.	G		3670,306		1698,274,16	79.0	84.0	82.0		471	-5.6	0.7	16	dbSNP_120	82	5902,2418		2102,1698,360	no	coding-synonymous	SRL	NM_001098814.1		3800,1972,376	GG,GA,AA		29.0625,7.6962,22.1535		157/474	4245693	9572,2724	1988	4160	6148	SO:0001819	synonymous_variant	6345	exon5			GAAGGAACGGGCG	AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739			11295	protein-coding gene	gene with protein product		604992				2762314	Standard	NM_001098814		Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.471T>C	16.37:g.4245693A>G		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	201	200	0.995025	NM_001098814		Silent	SNP	ENST00000399609.3	37	CCDS42113.1																																																																																			A|0.226;G|0.774	0.774	strong		0.542	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152	
ZCCHC9	84240	hgsc.bcm.edu	37	5	80604427	80604427	+	Silent	SNP	C	C	T	rs149561750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80604427C>T	ENST00000254037.2	+	2	3587	c.432C>T	c.(430-432)ccC>ccT	p.P144P	ZCCHC9_ENST00000380199.5_Silent_p.P144P|ZCCHC9_ENST00000407610.3_Silent_p.P144P|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000438268.2_Silent_p.P144P			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	144					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)		CAGATTGCCCCGCCGCCCTTG	0.473													C|||	2	0.000399361	0.0015	0.0	5008	,	,		14028	0.0		0.0	False		,,,				2504	0.0				p.P144P		Atlas-SNP	.											ZCCHC9,bladder,carcinoma,0,1	ZCCHC9	26	1	0			c.C432T						scavenged	.	C	,,	20,4386	28.1+/-56.4	1,18,2184	87.0	88.0	88.0		432,432,432	-11.9	0.6	5	dbSNP_134	88	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ZCCHC9	NM_001131035.1,NM_001131036.1,NM_032280.2	,,	1,18,6484	TT,TC,CC		0.0,0.4539,0.1538	,,	144/272,144/272,144/272	80604427	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	84240	exon3			TTGCCCCGCCGCC	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.432C>T	5.37:g.80604427C>T		Somatic	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	180	78	0.433333	NM_001131036	B2RAE7|Q9H027	Silent	SNP	ENST00000254037.2	37	CCDS4054.1																																																																																			C|0.998;T|0.002	0.002	strong		0.473	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280	
DNAH17	8632	hgsc.bcm.edu	37	17	76521121	76521121	+	Silent	SNP	T	T	C	rs17729253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76521121T>C	ENST00000585328.1	-	25	3949	c.3825A>G	c.(3823-3825)ctA>ctG	p.L1275L	DNAH17_ENST00000389840.5_Silent_p.L1274L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1274	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)			GCTCCTTCAGTAGGCGGACCT	0.662													.|||	736	0.146965	0.0363	0.2046	5008	,	,		16804	0.0873		0.2634	False		,,,				2504	0.1973				p.L1278L		Atlas-SNP	.											.	DNAH17	347	.	0			c.A3834G						PASS	.	C		226,3916		2,222,1847	64.0	71.0	69.0		3834	4.4	1.0	17	dbSNP_123	69	2221,6211		304,1613,2299	no	coding-synonymous	DNAH17	NM_173628.3		306,1835,4146	CC,CT,TT		26.3401,5.4563,19.4608		1278/4463	76521121	2447,10127	2071	4216	6287	SO:0001819	synonymous_variant	8632	exon25			CTTCAGTAGGCGG	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.3825A>G	17.37:g.76521121T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				T|0.830;C|0.170	0.170	strong		0.662	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
PTPRE	5791	hgsc.bcm.edu	37	10	129871690	129871690	+	Silent	SNP	A	A	G	rs2275803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129871690A>G	ENST00000254667.3	+	17	1833	c.1554A>G	c.(1552-1554)aaA>aaG	p.K518K	PTPRE_ENST00000306042.5_Silent_p.K460K|PTPRE_ENST00000419012.2_Silent_p.K518K	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	518	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.K518K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	GGGAATGGAAATCCCACACTA	0.597													A|||	1296	0.258786	0.2829	0.2435	5008	,	,		20991	0.2599		0.2018	False		,,,				2504	0.2945				p.K518K	Colon(52;977 1184 20575 41685)	Atlas-SNP	.											PTPRE,NS,carcinoma,0,1	PTPRE	132	1	1	Substitution - coding silent(1)	stomach(1)	c.A1554G						PASS	.	A	,	1176,3230	415.2+/-337.1	153,870,1180	119.0	101.0	107.0		1554,1380	1.5	1.0	10	dbSNP_100	107	1752,6848	317.9+/-313.4	185,1382,2733	no	coding-synonymous,coding-synonymous	PTPRE	NM_006504.4,NM_130435.3	,	338,2252,3913	GG,GA,AA		20.3721,26.6909,22.5127	,	518/701,460/643	129871690	2928,10078	2203	4300	6503	SO:0001819	synonymous_variant	5791	exon17			ATGGAAATCCCAC	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.1554A>G	10.37:g.129871690A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_006504	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Silent	SNP	ENST00000254667.3	37	CCDS7657.1																																																																																			G|0.223;N|0.000	0.223	strong		0.597	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1		
CDKN1A	1026	hgsc.bcm.edu	37	6	36652135	36652135	+	Missense_Mutation	SNP	G	G	A	rs566071526		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36652135G>A	ENST00000405375.1	+	2	492	c.257G>A	c.(256-258)cGg>cAg	p.R86Q	CDKN1A_ENST00000373711.2_Missense_Mutation_p.R86Q|CDKN1A_ENST00000448526.2_Missense_Mutation_p.R120Q|CDKN1A_ENST00000244741.5_Missense_Mutation_p.R86Q|CDKN1A_ENST00000478800.1_3'UTR	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	86					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						CGGCGAGGCCGGGATGAGTTG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		18244	0.001		0.0	False		,,,				2504	0.0				p.R86Q		Atlas-SNP	.											CDKN1A,NS,carcinoma,+1,1	CDKN1A	27	1	0			c.G257A						PASS	.						25.0	25.0	25.0					6																	36652135		2203	4300	6503	SO:0001583	missense	1026	exon2			GAGGCCGGGATGA	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.257G>A	6.37:g.36652135G>A	ENSP00000384849:p.Arg86Gln	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	37	CCDS4824.1	.	.	.	.	.	.	.	.	.	.	G	4.718	0.133545	0.09032	.	.	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.16	0.313	0.15842	.	1.118360	0.06876	N	0.801660	T	0.25121	0.0610	L	0.34521	1.04	0.09310	N	1	B;B;B	0.24882	0.113;0.064;0.037	B;B;B	0.16289	0.015;0.006;0.006	T	0.21759	-1.0236	10	0.51188	T	0.08	-1.0186	4.3301	0.11059	0.3607:0.161:0.4783:0.0	.	120;86;86	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	Q	120;86;86;86	ENSP00000409259:R120Q;ENSP00000244741:R86Q;ENSP00000384849:R86Q;ENSP00000362815:R86Q	ENSP00000244741:R86Q	R	+	2	0	CDKN1A	36760113	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.096000	0.11059	-0.131000	0.11578	0.511000	0.50034	CGG	.	.	none		0.652	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467	
GALNT4	8693	hgsc.bcm.edu	37	12	89916781	89916781	+	Missense_Mutation	SNP	G	G	T	rs139995124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:89916781G>T	ENST00000529983.2	-	1	1802	c.1546C>A	c.(1546-1548)Caa>Aaa	p.Q516K	POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.Q513K|POC1B_ENST00000549035.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000549504.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|GALNT4_ENST00000413530.1_Missense_Mutation_p.Q344K|POC1B_ENST00000541909.1_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	516	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				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						GGACAATTTTGCATTCCCACA	0.358													G|||	11	0.00219649	0.0023	0.0	5008	,	,		19748	0.0		0.007	False		,,,				2504	0.001				p.Q516K		Atlas-SNP	.											.	GALNT4	38	.	0			c.C1546A						PASS	.	G	,LYS/GLN,LYS/GLN,LYS/GLN,	5,3649		0,5,1822	71.0	67.0	68.0		,1537,1030,1546,	5.0	1.0	12	dbSNP_134	68	65,8115		0,65,4025	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	,53,53,53,	0,70,5847	TT,TG,GG		0.7946,0.1368,0.5915	,benign,benign,benign,	,513/576,344/407,516/579,	89916781	70,11764	1827	4090	5917	SO:0001583	missense	8693	exon1			AATTTTGCATTCC	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.1546C>A	12.37:g.89916781G>T	ENSP00000436604:p.Gln516Lys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	37	CCDS53817.1	9	0.004120879120879121	3	0.006097560975609756	0	0.0	0	0.0	6	0.0079155672823219	G	11.35	1.612993	0.28712	0.001368	0.007946	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;T;T	0.29397	1.57;1.57;1.57	5.93	4.99	0.66335	Ricin B-related lectin (1);Ricin B lectin (3);	.	.	.	.	T	0.11623	0.0283	N	0.10645	0.015	0.39363	D	0.965958	B;B	0.06786	0.0;0.001	B;B	0.09377	0.003;0.004	T	0.08638	-1.0712	9	0.27785	T	0.31	.	12.0779	0.53655	0.0:0.0:0.7004:0.2996	.	513;516	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	K	513;344;516	ENSP00000447852:Q513K;ENSP00000389686:Q344K;ENSP00000436604:Q516K	ENSP00000436604:Q516K	Q	-	1	0	GALNT4;RP11-1109F11.4	88440912	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.469000	0.73555	2.814000	0.96858	0.591000	0.81541	CAA	G|0.996;T|0.004	0.004	strong		0.358	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12918963	12918963	+	Missense_Mutation	SNP	G	G	T	rs9661554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12918963G>T	ENST00000240189.2	+	2	186	c.99G>T	c.(97-99)agG>agT	p.R33S		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	33			R -> S (in dbSNP:rs9661554).		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)		AGCTGCCCAGGGTGCTCTATC	0.627													.|||	523	0.104433	0.1127	0.0965	5008	,	,		19696	0.128		0.1064	False		,,,				2504	0.0726				p.R33S		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G99T						PASS	.	G	SER/ARG	576,3826	254.9+/-260.3	62,452,1687	100.0	109.0	106.0		99	-1.7	0.0	1	dbSNP_119	106	975,7617	211.0+/-251.7	75,825,3396	no	missense	PRAMEF2	NM_023014.1	110	137,1277,5083	TT,TG,GG		11.3478,13.085,11.9363	probably-damaging	33/475	12918963	1551,11443	2201	4296	6497	SO:0001583	missense	65122	exon2			GCCCAGGGTGCTC		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.99G>T	1.37:g.12918963G>T	ENSP00000240189:p.Arg33Ser	Somatic	454	2	0.00440529		WXS	Illumina HiSeq	Phase_I	518	243	0.469112	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	218	0.09981684981684982	38	0.07723577235772358	34	0.09392265193370165	60	0.1048951048951049	86	0.11345646437994723	G	4.074	0.011518	0.07912	0.13085	0.113478	ENSG00000120952	ENST00000240189	T	0.04551	3.6	0.842	-1.68	0.08212	.	1.537720	0.04347	N	0.355072	T	0.00073	0.0002	M	0.70275	2.135	0.80722	P	0.0	P	0.44776	0.843	P	0.45610	0.487	T	0.31696	-0.9934	9	0.20519	T	0.43	.	4.1361	0.10170	0.5271:0.0:0.4729:0.0	rs9661554	33	O60811	PRAM2_HUMAN	S	33	ENSP00000240189:R33S	ENSP00000240189:R33S	R	+	3	2	PRAMEF2	12841550	0.017000	0.18338	0.000000	0.03702	0.002000	0.02628	-0.372000	0.07504	-0.705000	0.05035	-1.038000	0.02383	AGG	G|0.891;T|0.109	0.109	strong		0.627	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
PTGIR	5739	hgsc.bcm.edu	37	19	47124579	47124579	+	Silent	SNP	C	C	T	rs2229130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47124579C>T	ENST00000291294.2	-	3	1252	c.1119G>A	c.(1117-1119)acG>acA	p.T373T	PTGIR_ENST00000597185.1_Silent_p.T102T|PTGIR_ENST00000598865.1_Silent_p.T161T|PTGIR_ENST00000594275.1_Silent_p.T130T	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	373					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	CTTTGGACGACGTTCCCACGG	0.632													C|||	64	0.0127796	0.0446	0.0072	5008	,	,		16398	0.0		0.0	False		,,,				2504	0.0				p.T373T		Atlas-SNP	.											.	PTGIR	31	.	0			c.G1119A						PASS	.	C		207,4199	121.7+/-159.2	7,193,2003	44.0	47.0	46.0		1119	-9.5	0.0	19	dbSNP_98	46	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	PTGIR	NM_000960.3		7,196,6300	TT,TC,CC		0.0349,4.6981,1.6146		373/387	47124579	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	5739	exon3			GGACGACGTTCCC		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"""GPCR / Class A : Prostanoid receptors"""	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.1119G>A	19.37:g.47124579C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_000960		Silent	SNP	ENST00000291294.2	37	CCDS12686.1																																																																																			C|0.984;T|0.016	0.016	strong		0.632	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1		
IRS4	8471	hgsc.bcm.edu	37	X	107979475	107979475	+	Missense_Mutation	SNP	G	G	A	rs1801162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:107979475G>A	ENST00000372129.2	-	1	176	c.100C>T	c.(100-102)Ctt>Ttt	p.L34F	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	34			L -> F (in dbSNP:rs1801162).		positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GAGGAAAGAAGCGGGGTGGTC	0.642													g|||	185	0.0490066	0.0499	0.0562	3775	,	,		8286	0.002		0.0408	False		,,,				2504	0.0378				p.L34F		Atlas-SNP	.											.	IRS4	253	.	0			c.C100T						PASS	.		PHE/LEU	256,3579		6,206,38,1420,533	28.0	30.0	29.0		100	0.4	0.2	X	dbSNP_89	29	392,6332		7,258,120,2163,1748	yes	missense	IRS4	NM_003604.2	22	13,464,158,3583,2281	AA,AG,A,GG,G		5.8299,6.6754,6.1369	benign	34/1258	107979475	648,9911	2203	4296	6499	SO:0001583	missense	8471	exon1			AAAGAAGCGGGGT	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.100C>T	X.37:g.107979475G>A	ENSP00000361202:p.Leu34Phe	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	158	103	0.651899	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	84	0.05063291139240506	29	0.06016597510373444	14	0.03977272727272727	0	0.0	20	0.02717391304347826	g	10.04	1.241221	0.22711	0.066754	0.058299	ENSG00000133124	ENST00000372129	T	0.38887	1.11	3.24	0.359	0.16088	.	1.235780	0.06363	N	0.712073	T	0.01489	0.0048	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.14200	-1.0481	9	0.30854	T	0.27	-0.1263	3.9713	0.09454	0.2496:0.385:0.3654:0.0	rs1801162;rs52823369	34	O14654	IRS4_HUMAN	F	34	ENSP00000361202:L34F	ENSP00000361202:L34F	L	-	1	0	IRS4	107866131	0.154000	0.22792	0.238000	0.24106	0.652000	0.38707	0.194000	0.17135	-0.030000	0.13804	0.431000	0.28591	CTT	G|0.943;A|0.057	0.057	strong		0.642	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
MYO7B	4648	hgsc.bcm.edu	37	2	128381717	128381717	+	Missense_Mutation	SNP	G	G	A	rs2245408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128381717G>A	ENST00000409816.2	+	28	3823	c.3791G>A	c.(3790-3792)cGg>cAg	p.R1264Q	RP11-286H15.1_ENST00000609697.1_RNA|MYO7B_ENST00000409090.1_Missense_Mutation_p.R117Q|MYO7B_ENST00000389524.4_Missense_Mutation_p.R1264Q|MYO7B_ENST00000428314.1_Missense_Mutation_p.R1264Q			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1264	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.		R -> Q (in dbSNP:rs2245408).			extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GCCATCGCCCGGTGTGAGCAG	0.667													A|||	64	0.0127796	0.0439	0.0086	5008	,	,		17463	0.0		0.0	False		,,,				2504	0.0				p.R1264Q		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3791A						PASS	.	A	GLN/ARG	141,3873		2,137,1868	21.0	26.0	25.0		3791	3.8	1.0	2	dbSNP_100	25	2,8324		0,2,4161	yes	missense	MYO7B	NM_001080527.1	43	2,139,6029	AA,AG,GG		0.024,3.5127,1.1588	benign	1264/2117	128381717	143,12197	2007	4163	6170	SO:0001583	missense	4648	exon29			TCGCCCGGTGTGA		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3791G>A	2.37:g.128381717G>A	ENSP00000386461:p.Arg1264Gln	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	22	0.010073260073260074	19	0.03861788617886179	3	0.008287292817679558	0	0.0	0	0.0	.	9.528	1.110073	0.20714	0.035127	2.4E-4	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000437387;ENST00000409090	T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08	3.76	3.76	0.43208	Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	N	0.000000	T	0.09247	0.0228	N	0.00084	-2.21	0.22562	N	0.998982	B	0.02656	0.0	B	0.01281	0.0	T	0.38308	-0.9667	10	0.02654	T	1	.	9.5173	0.39113	0.9119:0.0:0.0881:0.0	rs2245408;rs2245408	1264	Q6PIF6	MYO7B_HUMAN	Q	1264;1264;117;1264;117;117	ENSP00000374175:R1264Q;ENSP00000415090:R1264Q;ENSP00000386461:R1264Q;ENSP00000404927:R117Q;ENSP00000386850:R117Q	ENSP00000272666:R117Q	R	+	2	0	MYO7B	128098187	1.000000	0.71417	0.998000	0.56505	0.832000	0.47134	4.758000	0.62220	0.809000	0.34255	-0.490000	0.04691	CGG	G|0.990;A|0.010	0.010	strong		0.667	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
TMEM199	147007	hgsc.bcm.edu	37	17	26691916	26691916	+	IGR	SNP	T	T	C	rs2277667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26691916T>C	ENST00000292114.3	+	0	3148				VTN_ENST00000536498.1_Silent_p.L56L|TMEM199_ENST00000509083.1_Intron|VTN_ENST00000438614.1_Silent_p.L56L|SARM1_ENST00000379061.4_Intron|CTB-96E2.2_ENST00000555059.2_Missense_Mutation_p.T131A|VTN_ENST00000431468.1_Silent_p.L57L|CTB-96E2.7_ENST00000577850.1_RNA|CTB-96E2.3_ENST00000591482.1_RNA	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		CCAGCTCCAGTAGCTGCCCTT	0.632													C|||	812	0.162141	0.1853	0.0821	5008	,	,		18306	0.244		0.0785	False		,,,				2504	0.1892				p.L57L		Atlas-SNP	.											.	SEBOX	20	.	0			c.A171G						PASS	.	C		721,3659		65,591,1534	58.0	68.0	64.0		171	3.2	1.0	17	dbSNP_100	64	696,7868		33,630,3619	no	coding-synonymous	SEBOX	NM_001080837.2		98,1221,5153	CC,CT,TT		8.127,16.4612,10.9472		57/217	26691916	1417,11527	2190	4282	6472	SO:0001628	intergenic_variant	645832	exon2			CTCCAGTAGCTGC	AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 32"""	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498		17.37:g.26691916T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_001080837		Silent	SNP	ENST00000292114.3	37	CCDS11228.1																																																																																			T|0.855;C|0.145	0.145	strong		0.632	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464	
PTCRA	171558	hgsc.bcm.edu	37	6	42893328	42893328	+	Missense_Mutation	SNP	T	T	C	rs115331994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42893328T>C	ENST00000304672.1	+	4	835	c.754T>C	c.(754-756)Tgc>Cgc	p.C252R	PTCRA_ENST00000441198.1_Missense_Mutation_p.C227R|PTCRA_ENST00000446507.1_Missense_Mutation_p.C145R	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	252					negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			ACAGGCCTGGTGCTCAAGATC	0.642													T|||	44	0.00878594	0.0257	0.0	5008	,	,		2807	0.0		0.0	False		,,,				2504	0.0102				p.C267R		Atlas-SNP	.											.	PTCRA	24	.	0			c.T799C						PASS	.	T	ARG/CYS	60,4338		0,60,2139	36.0	30.0	32.0		754	-8.4	0.0	6	dbSNP_132	32	2,8594		0,2,4296	yes	missense	PTCRA	NM_138296.2	180	0,62,6435	CC,CT,TT		0.0233,1.3643,0.4771	possibly-damaging	252/282	42893328	62,12932	2199	4298	6497	SO:0001583	missense	171558	exon4			GCCTGGTGCTCAA	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.754T>C	6.37:g.42893328T>C	ENSP00000304447:p.Cys252Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	85	50	0.588235	NM_001243168	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	T	12.26	1.885331	0.33255	0.013643	2.33E-4	ENSG00000171611	ENST00000304672;ENST00000441198;ENST00000446507;ENST00000418903	T;T;T	0.55413	1.23;1.19;0.52	4.17	-8.35	0.00984	.	2.132630	0.02556	N	0.096213	T	0.09774	0.0240	N	0.14661	0.345	0.09310	N	0.999999	B;B;B	0.23806	0.091;0.005;0.005	B;B;B	0.22152	0.038;0.008;0.003	T	0.03166	-1.1065	10	0.72032	D	0.01	.	1.2025	0.01888	0.3397:0.3089:0.1915:0.1599	.	145;227;252	Q6ISU1-2;Q6ISU1-3;Q6ISU1	.;.;PTCRA_HUMAN	R	252;227;145;98	ENSP00000304447:C252R;ENSP00000409550:C227R;ENSP00000392288:C145R	ENSP00000304447:C252R	C	+	1	0	PTCRA	43001306	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-4.585000	0.00212	-3.458000	0.00159	0.533000	0.62120	TGC	T|0.994;C|0.006	0.006	strong		0.642	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296	
SEMA3D	223117	hgsc.bcm.edu	37	7	84697540	84697540	+	Missense_Mutation	SNP	C	C	T	rs148351346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:84697540C>T	ENST00000284136.6	-	5	599	c.556G>A	c.(556-558)Gat>Aat	p.D186N	SEMA3D_ENST00000444867.1_Missense_Mutation_p.D186N	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	186	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						TGCTGAGGATCGAAAGGACAT	0.343													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17192	0.0		0.0	False		,,,				2504	0.0				p.D186N	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.G556A						PASS	.	C	ASN/ASP	13,4393	20.2+/-43.8	0,13,2190	103.0	102.0	102.0		556	5.5	1.0	7	dbSNP_134	102	0,8600		0,0,4300	yes	missense	SEMA3D	NM_152754.2	23	0,13,6490	TT,TC,CC		0.0,0.2951,0.1	probably-damaging	186/778	84697540	13,12993	2203	4300	6503	SO:0001583	missense	223117	exon5			GAGGATCGAAAGG	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"""Semaphorins"", ""Immunoglobulin superfamily / V-set domain containing"""	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.556G>A	7.37:g.84697540C>T	ENSP00000284136:p.Asp186Asn	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	33	5.213062	0.95069	0.002951	0.0	ENSG00000153993	ENST00000284136;ENST00000444867	T;T	0.15017	2.46;2.46	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.28499	0.0705	M	0.72479	2.2	0.80722	D	1	D;P	0.59357	0.985;0.769	P;B	0.54238	0.746;0.404	T	0.01276	-1.1398	10	0.40728	T	0.16	.	19.7307	0.96181	0.0:1.0:0.0:0.0	.	186;186	C9JYT6;O95025	.;SEM3D_HUMAN	N	186	ENSP00000284136:D186N;ENSP00000401366:D186N	ENSP00000284136:D186N	D	-	1	0	SEMA3D	84535476	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.435000	0.80391	2.707000	0.92482	0.655000	0.94253	GAT	C|0.999;T|0.001	0.001	strong		0.343	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84581904	84581904	+	Silent	SNP	T	T	C	rs4842923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:84581904T>C	ENST00000286744.5	+	16	1985	c.1761T>C	c.(1759-1761)cgT>cgC	p.R587R	ADAMTSL3_ENST00000567476.1_Silent_p.R587R	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	587	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.		R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			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)			TGCAGGTCCGTGAGGTGAAGT	0.607													C|||	3436	0.686102	0.8306	0.7248	5008	,	,		17539	0.7202		0.5308	False		,,,				2504	0.5879				p.R587R		Atlas-SNP	.											ADAMTSL3,colon,carcinoma,+1,2	ADAMTSL3	290	2	0			c.T1761C						PASS	.	C		3417,989	369.8+/-319.3	1330,757,116	90.0	81.0	84.0		1761	-9.8	0.0	15	dbSNP_111	84	4624,3976	550.9+/-385.8	1252,2120,928	no	coding-synonymous	ADAMTSL3	NM_207517.2		2582,2877,1044	CC,CT,TT		46.2326,22.4467,38.1747		587/1692	84581904	8041,4965	2203	4300	6503	SO:0001819	synonymous_variant	57188	exon16			GGTCCGTGAGGTG	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.1761T>C	15.37:g.84581904T>C		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_207517	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	37	CCDS10326.1																																																																																			T|0.354;C|0.646	0.646	strong		0.607	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
SBF1	6305	hgsc.bcm.edu	37	22	50885775	50885775	+	Silent	SNP	A	A	G	rs1053744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50885775A>G	ENST00000390679.3	-	39	5665	c.5481T>C	c.(5479-5481)acT>acC	p.T1827T	SBF1_ENST00000380817.3_Silent_p.T1853T|SBF1_ENST00000348911.6_Silent_p.T1828T			O95248	MTMR5_HUMAN	SET binding factor 1	1827	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		TCTCGTCCACAGTCTTAGGGG	0.642													A|||	2509	0.500998	0.4909	0.5389	5008	,	,		13950	0.4673		0.5577	False		,,,				2504	0.4642				p.T1853T		Atlas-SNP	.											.	SBF1	211	.	0			c.T5559C						PASS	.	A		2081,2205		516,1049,578	74.0	83.0	80.0		5559	-2.7	1.0	22	dbSNP_86	80	4607,3887		1282,2043,922	no	coding-synonymous	SBF1	NM_002972.2		1798,3092,1500	GG,GA,AA		45.7617,48.5534,47.6682		1853/1894	50885775	6688,6092	2143	4247	6390	SO:0001819	synonymous_variant	6305	exon40			GTCCACAGTCTTA	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.5481T>C	22.37:g.50885775A>G		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	194	194	1	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37		1149	0.5260989010989011	254	0.516260162601626	201	0.5552486187845304	278	0.486013986013986	416	0.5488126649076517	A	5.172	0.217273	0.09810	0.485534	0.542383	ENSG00000100241	ENST00000418590	.	.	.	3.17	-2.66	0.06077	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999862939	.	.	.	.	.	.	T	0.45862	-0.9232	3	.	.	.	.	6.3706	0.21479	0.5815:0.1763:0.2423:0.0	rs1053744;rs3194350;rs17846548;rs17859623;rs59941368;rs1053744	.	.	.	R	375	.	.	C	-	1	0	SBF1	49232641	0.534000	0.26362	0.991000	0.47740	0.493000	0.33554	0.012000	0.13287	-0.623000	0.05618	-0.609000	0.04063	TGT	G|0.524;N|0.000	0.524	strong		0.642	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
UTP20	27340	hgsc.bcm.edu	37	12	101685852	101685852	+	Silent	SNP	G	G	A	rs11110737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101685852G>A	ENST00000261637.4	+	10	1317	c.1143G>A	c.(1141-1143)ccG>ccA	p.P381P		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	381					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						TTTCCTTGCCGGAGACCCTCA	0.383													G|||	441	0.0880591	0.0219	0.111	5008	,	,		16923	0.0278		0.165	False		,,,				2504	0.1442				p.P381P		Atlas-SNP	.											.	UTP20	222	.	0			c.G1143A						PASS	.	G		187,4219	118.4+/-156.1	5,177,2021	149.0	143.0	145.0		1143	-2.9	0.9	12	dbSNP_120	145	1422,7178	274.5+/-291.2	121,1180,2999	no	coding-synonymous	UTP20	NM_014503.2		126,1357,5020	AA,AG,GG		16.5349,4.2442,12.3712		381/2786	101685852	1609,11397	2203	4300	6503	SO:0001819	synonymous_variant	27340	exon10			CTTGCCGGAGACC	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.1143G>A	12.37:g.101685852G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			G|0.888;A|0.112	0.112	strong		0.383	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
SOWAHD	347454	hgsc.bcm.edu	37	X	118893390	118893390	+	Missense_Mutation	SNP	A	A	G	rs12841259		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:118893390A>G	ENST00000343905.3	+	1	815	c.760A>G	c.(760-762)Acc>Gcc	p.T254A		NM_001105576.2	NP_001099046.1	A6NJG2	SWAHD_HUMAN	sosondowah ankyrin repeat domain family member D	254			T -> A (in dbSNP:rs12841259).														CAGCGGGTGCACCAACCTGAA	0.697													A|||	174	0.0460927	0.0764	0.0072	3775	,	,		10862	0.0377		0.002	False		,,,				2504	0.0286				p.T254A		Atlas-SNP	.											.	.	.	.	0			c.A760G						PASS	.	A	ALA/THR	249,3366		5,194,45,1337,498	7.0	10.0	9.0		760	-7.0	0.0	X	dbSNP_121	9	19,6433		0,15,4,2340,1738	yes	missense	ANKRD58	NM_001105576.2	58	5,209,49,3677,2236	GG,GA,G,AA,A		0.2945,6.888,2.6622	benign	254/316	118893390	268,9799	2079	4097	6176	SO:0001583	missense	347454	exon1			GGGTGCACCAACC		CCDS43984.1	Xq24	2013-01-10	2012-01-12	2012-01-12	ENSG00000187808	ENSG00000187808		"""Ankyrin repeat domain containing"""	32960	protein-coding gene	gene with protein product			"""ankyrin repeat domain 58"""	ANKRD58		22234889	Standard	NM_001105576		Approved		uc010nql.3	A6NJG2	OTTHUMG00000159606	ENST00000343905.3:c.760A>G	X.37:g.118893390A>G	ENSP00000340975:p.Thr254Ala	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	97	59	0.608247	NM_001105576		Missense_Mutation	SNP	ENST00000343905.3	37	CCDS43984.1	67	0.04038577456298975	23	0.04893617021276596	4	0.011111111111111112	20	0.03597122302158273	0	0.0	A	5.179	0.218585	0.09810	0.06888	0.002945	ENSG00000187808	ENST00000343905	T	0.13420	2.59	4.24	-7.04	0.01578	.	.	.	.	.	T	0.00412	0.0013	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.47005	-0.9150	8	0.09084	T	0.74	1.5969	11.8996	0.52675	0.1977:0.1212:0.681:0.0	rs12841259	254	A6NJG2	ANR58_HUMAN	A	254	ENSP00000340975:T254A	ENSP00000340975:T254A	T	+	1	0	ANKRD58	118777418	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-1.267000	0.02839	-1.676000	0.01457	0.314000	0.21332	ACC	A|0.958;G|0.042	0.042	strong		0.697	SOWAHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356469.1	NM_001105576	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32551948	32551948	+	Missense_Mutation	SNP	G	G	A	rs67476479|rs17886882		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32551948G>A	ENST00000360004.5	-	2	413	c.308C>T	c.(307-309)gCg>gTg	p.A103V		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	103	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)		p.A103fs*26(2)		large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GGTGTCCACCGCGGCCCGCGC	0.682										Multiple Myeloma(14;0.17)																											p.A103V		Atlas-SNP	.											HLA-DRB1,brain,glioma,0,2	HLA-DRB1	41	2	2	Deletion - Frameshift(2)	ovary(1)|large_intestine(1)	c.C308T	GRCh37	CX045849	HLA-DRB1	X	rs17886882	scavenged	.						26.0	27.0	26.0					6																	32551948		2106	4192	6298	SO:0001583	missense	3123	exon2			TCCACCGCGGCCC	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.308C>T	6.37:g.32551948G>A	ENSP00000353099:p.Ala103Val	Somatic	31	4	0.129032		WXS	Illumina HiSeq	Phase_I	23	11	0.478261	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	9.035	0.988355	0.18966	.	.	ENSG00000196126	ENST00000360004	T	0.00277	8.34	3.52	-4.93	0.03066	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	2.651270	0.02020	N	0.047686	T	0.00039	0.0001	N	0.02379	-0.575	0.09310	N	1	B	0.31274	0.317	B	0.22152	0.038	T	0.35822	-0.9773	10	0.48119	T	0.1	.	10.1847	0.42991	0.0:0.102:0.2902:0.6078	rs17886882;rs28724091	103	P01911	2B1F_HUMAN	V	103	ENSP00000353099:A103V	ENSP00000353099:A103V	A	-	2	0	HLA-DRB1	32659926	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-3.748000	0.00376	-1.340000	0.02227	-3.004000	0.00076	GCG	.	.	weak		0.682	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
FAM131C	348487	hgsc.bcm.edu	37	1	16385131	16385131	+	Missense_Mutation	SNP	C	C	A	rs1832151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16385131C>A	ENST00000375662.4	-	7	827	c.644G>T	c.(643-645)aGc>aTc	p.S215I	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	215	Pro-rich.		S -> I (in dbSNP:rs1832151).							large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		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;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGGAGGGGCTGGGCGAGGA	0.677																																					p.S215I		Atlas-SNP	.											.	FAM131C	21	.	0			c.G644T						PASS	.						25.0	24.0	25.0					1																	16385131		2030	4181	6211	SO:0001583	missense	348487	exon7			GAGGGGCTGGGCG		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.644G>T	1.37:g.16385131C>A	ENSP00000364814:p.Ser215Ile	Somatic	512	0	0		WXS	Illumina HiSeq	Phase_I	659	195	0.295903	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	37	CCDS41270.1	376	0.17216117216117216	179	0.3638211382113821	57	0.1574585635359116	3	0.005244755244755245	137	0.18073878627968337	C	8.925	0.962089	0.18583	.	.	ENSG00000185519	ENST00000375662	T	0.13901	2.55	4.45	3.53	0.40419	.	0.518857	0.19640	N	0.109468	T	0.00012	0.0000	N	0.22421	0.69	0.45295	P	0.0017059999999999853	B	0.22983	0.078	B	0.19391	0.025	T	0.44772	-0.9306	9	0.52906	T	0.07	-7.2114	7.4371	0.27162	0.0:0.8818:0.0:0.1182	rs1832151;rs3961587	215	Q96AQ9	F131C_HUMAN	I	215	ENSP00000364814:S215I	ENSP00000364814:S215I	S	-	2	0	FAM131C	16257718	0.771000	0.28555	0.979000	0.43373	0.031000	0.12232	1.588000	0.36633	2.054000	0.61138	0.479000	0.44913	AGC	C|0.837;A|0.163	0.163	strong		0.677	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
SEMA7A	8482	hgsc.bcm.edu	37	15	74703022	74703022	+	Silent	SNP	G	G	A	rs2075592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:74703022G>A	ENST00000261918.4	-	14	2492	c.1944C>T	c.(1942-1944)gcC>gcT	p.A648A	SEMA7A_ENST00000543145.2_Silent_p.A634A|SEMA7A_ENST00000542748.1_Silent_p.A483A	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	648					axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						AGAGGGAGGCGGCCAGGGCAC	0.687													G|||	910	0.181709	0.4002	0.036	5008	,	,		16063	0.1915		0.0467	False		,,,				2504	0.1186				p.A648A		Atlas-SNP	.											.	SEMA7A	58	.	0			c.C1944T						PASS	.	G	,,	1413,2981	431.6+/-343.0	229,955,1013	43.0	45.0	44.0		1902,1449,1944	-9.1	0.0	15	dbSNP_96	44	390,8196	120.6+/-179.8	13,364,3916	no	coding-synonymous,coding-synonymous,coding-synonymous	SEMA7A	NM_001146029.1,NM_001146030.1,NM_003612.3	,,	242,1319,4929	AA,AG,GG		4.5423,32.1575,13.8906	,,	634/653,483/502,648/667	74703022	1803,11177	2197	4293	6490	SO:0001819	synonymous_variant	8482	exon14			GGAGGCGGCCAGG	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"""Semaphorins"", ""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10741	protein-coding gene	gene with protein product	"""John Milton Hagen blood group"", ""H-Sema K1"""	607961	"""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A"", ""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"""	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1944C>T	15.37:g.74703022G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Silent	SNP	ENST00000261918.4	37	CCDS10262.1																																																																																			G|0.857;A|0.143	0.143	strong		0.687	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612	
EPHA10	284656	hgsc.bcm.edu	37	1	38185169	38185169	+	Silent	SNP	G	G	A	rs35909785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38185169G>A	ENST00000373048.4	-	15	2672	c.2673C>T	c.(2671-2673)ccC>ccT	p.P891P	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000427468.2_Silent_p.P891P|EPHA10_ENST00000330210.7_Silent_p.P386P|EPHA10_ENST00000540011.1_Intron	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	891	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGGAGAACCTGGGCCGCTCAC	0.617													G|||	496	0.0990415	0.1241	0.0937	5008	,	,		18548	0.2351		0.006	False		,,,				2504	0.0245				p.P891P		Atlas-SNP	.											.	EPHA10	120	.	0			c.C2673T						PASS	.	G		358,3724		13,332,1696	48.0	57.0	54.0		2673	0.9	1.0	1	dbSNP_126	54	46,8336		0,46,4145	no	coding-synonymous	EPHA10	NM_001099439.1		13,378,5841	AA,AG,GG		0.5488,8.7702,3.2413		891/1009	38185169	404,12060	2041	4191	6232	SO:0001819	synonymous_variant	284656	exon15			GAACCTGGGCCGC	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2673C>T	1.37:g.38185169G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	192	88	0.458333	NM_001099439	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	37	CCDS41305.1																																																																																			G|0.936;A|0.064	0.064	strong		0.617	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
GAPDH	2597	hgsc.bcm.edu	37	12	6647109	6647109	+	Silent	SNP	T	T	C	rs1803621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	47	0	0	635	WXS	Illumina HiSeq	Phase_I	55	19	0.345455	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	
DGKH	160851	hgsc.bcm.edu	37	13	42793479	42793479	+	Silent	SNP	G	G	A	rs180870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:42793479G>A	ENST00000337343.4	+	27	3348	c.3327G>A	c.(3325-3327)gaG>gaA	p.E1109E	DGKH_ENST00000379274.2_Silent_p.E973E|DGKH_ENST00000540693.1_Silent_p.E1109E|DGKH_ENST00000261491.5_Silent_p.E1109E|DGKH_ENST00000538674.1_Silent_p.E864E|DGKH_ENST00000536612.1_Silent_p.E973E|DGKH_ENST00000498255.2_3'UTR	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	116	0	0		WXS	Illumina HiSeq	Phase_I	114	112	0.982456	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	
HECA	51696	hgsc.bcm.edu	37	6	139488364	139488364	+	Silent	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139488364C>G	ENST00000367658.2	+	2	1500	c.1215C>G	c.(1213-1215)ctC>ctG	p.L405L	RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.2_ENST00000591102.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000585447.1_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	405					respiratory tube development (GO:0030323)	membrane (GO:0016020)				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		ACCGGGCGCTCCCGGTGTTCG	0.557																																					p.L405L		Atlas-SNP	.											.	HECA	45	.	0			c.C1215G						PASS	.						62.0	57.0	59.0					6																	139488364		2203	4300	6503	SO:0001819	synonymous_variant	51696	exon2			GGCGCTCCCGGTG	AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.1215C>G	6.37:g.139488364C>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	96	59	0.614583	NM_016217		Silent	SNP	ENST00000367658.2	37	CCDS5194.1																																																																																			.	.	none		0.557	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217	
FLII	2314	hgsc.bcm.edu	37	17	18148944	18148944	+	Silent	SNP	C	C	G	rs113208618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18148944C>G	ENST00000327031.4	-	28	3759	c.3534G>C	c.(3532-3534)gtG>gtC	p.V1178V	FLII_ENST00000379450.4_Silent_p.V1092V|FLII_ENST00000578558.1_Intron|FLII_ENST00000579294.1_Silent_p.V1167V|FLII_ENST00000545457.2_Silent_p.V1123V	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1178					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)					ATTTCTCAGTCACTGCAAAGT	0.542													C|||	209	0.0417332	0.1301	0.0259	5008	,	,		22593	0.0079		0.004	False		,,,				2504	0.0072				p.V1178V		Atlas-SNP	.											.	FLII	79	.	0			c.G3534C						PASS	.	C		455,3951	217.1+/-235.6	31,393,1779	221.0	195.0	204.0		3534	3.4	1.0	17	dbSNP_132	204	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous	FLII	NM_002018.2		31,439,6033	GG,GC,CC		0.5349,10.3268,3.8521		1178/1270	18148944	501,12505	2203	4300	6503	SO:0001819	synonymous_variant	2314	exon28			CTCAGTCACTGCA	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.3534G>C	17.37:g.18148944C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	42	0.456522	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	37	CCDS11192.1																																																																																			C|0.964;G|0.036	0.036	strong		0.542	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
TBC1D16	125058	hgsc.bcm.edu	37	17	77984168	77984168	+	Silent	SNP	G	G	A	rs35393459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77984168G>A	ENST00000310924.2	-	3	685	c.570C>T	c.(568-570)gtC>gtT	p.V190V		NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	190							Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			CCTGCGGACTGACCGTCGACA	0.687													G|||	141	0.028155	0.0983	0.0159	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.V190V	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.C570T						PASS	.	G		397,4003	178.3+/-207.1	23,351,1826	29.0	33.0	31.0		570	3.5	0.1	17	dbSNP_126	31	3,8589	3.0+/-9.4	0,3,4293	no	coding-synonymous	TBC1D16	NM_019020.2		23,354,6119	AA,AG,GG		0.0349,9.0227,3.0788		190/768	77984168	400,12592	2200	4296	6496	SO:0001819	synonymous_variant	125058	exon3			CGGACTGACCGTC	AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.570C>T	17.37:g.77984168G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	112	64	0.571429	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Silent	SNP	ENST00000310924.2	37	CCDS11766.1																																																																																			G|0.967;A|0.033	0.033	strong		0.687	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020	
PABPN1L	390748	hgsc.bcm.edu	37	16	88931509	88931509	+	Silent	SNP	G	G	A	rs76746996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88931509G>A	ENST00000419291.2	-	4	498	c.487C>T	c.(487-489)Ctg>Ttg	p.L163L	PABPN1L_ENST00000411789.2_Silent_p.L163L|PABPN1L_ENST00000378358.4_Silent_p.L163L|PABPN1L_ENST00000427766.1_Intron	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	163	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						TGGGCCTCCAGCTCCTCGGCG	0.657													g|||	302	0.0603035	0.174	0.0274	5008	,	,		13404	0.0198		0.0239	False		,,,				2504	0.0092				p.L163L		Atlas-SNP	.											.	PABPN1L	25	.	0			c.C487T						PASS	.	G		492,3414		29,434,1490	12.0	15.0	14.0		487	2.4	1.0	16	dbSNP_132	14	190,8058		1,188,3935	no	coding-synonymous	PABPN1L	NM_001080487.2		30,622,5425	AA,AG,GG		2.3036,12.596,5.6113		163/279	88931509	682,11472	1953	4124	6077	SO:0001819	synonymous_variant	390748	exon4			CCTCCAGCTCCTC		CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"""RNA binding motif (RRM) containing"""	37237	protein-coding gene	gene with protein product	"""embryonic poly(A) binding protein 2"""					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.487C>T	16.37:g.88931509G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_001080487	A1L3B3|A2VDI2	Silent	SNP	ENST00000419291.2	37	CCDS45547.2																																																																																			G|0.953;A|0.047	0.047	strong		0.657	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487	
KAZN	23254	hgsc.bcm.edu	37	1	15438990	15438990	+	Missense_Mutation	SNP	G	G	A	rs10803354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:15438990G>A	ENST00000376030.2	+	14	2410	c.2116G>A	c.(2116-2118)Gca>Aca	p.A706T		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	706			A -> T (in dbSNP:rs10803354). {ECO:0000269|PubMed:14702039}.		keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						CGTCACGCGGGCAGGAAAGGA	0.592													G|||	2214	0.442093	0.264	0.4438	5008	,	,		17210	0.6558		0.3966	False		,,,				2504	0.5082				p.A706T		Atlas-SNP	.											.	KAZN	57	.	0			c.G2116A						PASS	.	G	THR/ALA	1242,3164		170,902,1131	35.0	34.0	34.0		2116	3.6	1.0	1	dbSNP_120	34	3476,5118		700,2076,1521	yes	missense	KAZN	NM_201628.2	58	870,2978,2652	AA,AG,GG		40.4468,28.1888,36.2923	benign	706/776	15438990	4718,8282	2203	4297	6500	SO:0001583	missense	23254	exon14			ACGCGGGCAGGAA	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"""Sterile alpha motif (SAM) domain containing"""	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.2116G>A	1.37:g.15438990G>A	ENSP00000365198:p.Ala706Thr	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	267	265	0.992509	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	37	CCDS152.2	998	0.45695970695970695	125	0.2540650406504065	159	0.43922651933701656	398	0.6958041958041958	316	0.41688654353562005	G	12.78	2.040317	0.35989	0.281888	0.404468	ENSG00000189337	ENST00000376030	T	0.18016	2.24	5.52	3.61	0.41365	.	0.444427	0.19276	N	0.118277	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.9999999999295361	B	0.06786	0.001	B	0.06405	0.002	T	0.21177	-1.0253	9	0.39692	T	0.17	-8.9263	6.3791	0.21523	0.1032:0.2411:0.6557:0.0	rs10803354;rs56962621;rs10803354	706	Q674X7	KAZRN_HUMAN	T	706	ENSP00000365198:A706T	ENSP00000365198:A706T	A	+	1	0	KAZN	15311577	0.998000	0.40836	0.965000	0.40720	0.662000	0.39071	1.505000	0.35736	1.333000	0.45449	0.650000	0.86243	GCA	G|0.601;A|0.399	0.399	strong		0.592	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999	
KRT79	338785	hgsc.bcm.edu	37	12	53215684	53215684	+	Missense_Mutation	SNP	G	G	A	rs73303800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53215684G>A	ENST00000330553.5	-	9	1614	c.1580C>T	c.(1579-1581)aCg>aTg	p.T527M		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	527	Tail.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CGTCTTGACCGTAGTGGTCTT	0.622													G|||	44	0.00878594	0.0318	0.0029	5008	,	,		17021	0.0		0.0	False		,,,				2504	0.0				p.T527M		Atlas-SNP	.											.	KRT79	78	.	0			c.C1580T						PASS	.	G	MET/THR	121,4285	90.6+/-129.3	3,115,2085	58.0	44.0	48.0		1580	4.0	1.0	12	dbSNP_130	48	2,8598	1.2+/-3.3	0,2,4298	yes	missense	KRT79	NM_175834.2	81	3,117,6383	AA,AG,GG		0.0233,2.7463,0.9457	probably-damaging	527/536	53215684	123,12883	2203	4300	6503	SO:0001583	missense	338785	exon9			TTGACCGTAGTGG	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28930	protein-coding gene	gene with protein product	"""keratin 6-like"""	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.1580C>T	12.37:g.53215684G>A	ENSP00000328358:p.Thr527Met	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	37	CCDS8839.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	18.23	3.578041	0.65878	0.027463	2.33E-4	ENSG00000185640	ENST00000330553	D	0.83075	-1.68	3.97	3.97	0.46021	.	0.000000	0.47852	D	0.000213	T	0.75824	0.3902	M	0.61703	1.905	0.37441	D	0.914404	D	0.89917	1.0	D	0.78314	0.991	D	0.85029	0.0916	10	0.72032	D	0.01	.	11.8409	0.52353	0.0:0.0:1.0:0.0	.	527	Q5XKE5	K2C79_HUMAN	M	527	ENSP00000328358:T527M	ENSP00000328358:T527M	T	-	2	0	KRT79	51501951	0.969000	0.33509	1.000000	0.80357	0.997000	0.91878	1.735000	0.38176	2.516000	0.84829	0.655000	0.94253	ACG	G|0.990;A|0.010	0.010	strong		0.622	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834	
ZRANB3	84083	hgsc.bcm.edu	37	2	135976740	135976740	+	Silent	SNP	T	T	C	rs16831460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:135976740T>C	ENST00000264159.6	-	16	2375	c.2259A>G	c.(2257-2259)aaA>aaG	p.K753K	ZRANB3_ENST00000401392.1_Silent_p.K751K|ZRANB3_ENST00000412849.1_5'UTR|ZRANB3_ENST00000536680.1_Silent_p.K751K	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	753					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		AGCTCATCTGTTTTCCATCCT	0.318													T|||	298	0.0595048	0.1528	0.0288	5008	,	,		18227	0.0456		0.0239	False		,,,				2504	0.0061				p.K753K		Atlas-SNP	.											.	ZRANB3	109	.	0			c.A2259G						PASS	.	T		484,3092		34,416,1338	38.0	36.0	36.0		2259	2.7	1.0	2	dbSNP_123	36	153,7955		3,147,3904	no	coding-synonymous	ZRANB3	NM_032143.2		37,563,5242	CC,CT,TT		1.887,13.5347,5.4519		753/1080	135976740	637,11047	1788	4054	5842	SO:0001819	synonymous_variant	84083	exon16			CATCTGTTTTCCA	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"""Zinc fingers, RAN-binding domain containing"""	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.2259A>G	2.37:g.135976740T>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	165	71	0.430303	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Silent	SNP	ENST00000264159.6	37	CCDS46419.1																																																																																			T|0.947;C|0.053	0.053	strong		0.318	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143	
AQP12B	653437	hgsc.bcm.edu	37	2	241622008	241622008	+	Missense_Mutation	SNP	G	G	A	rs187845451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241622008G>A	ENST00000407834.3	-	1	309	c.247C>T	c.(247-249)Cac>Tac	p.H83Y		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	71						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)		GTGACCCCGTGCGCCAGGAAG	0.672													N|||	54	0.0107827	0.0408	0.0	5008	,	,		18265	0.0		0.0	False		,,,				2504	0.0				p.H83Y		Atlas-SNP	.											AQP12B,colon,carcinoma,+2,1	AQP12B	33	1	0			c.C247T						PASS	.		TYR/HIS	141,4265		1,139,2063	50.0	51.0	50.0		247	2.5	0.5	2		50	0,8598		0,0,4299	no	missense	AQP12B	NM_001102467.1	83	1,139,6362	AA,AG,GG		0.0,3.2002,1.0843	probably-damaging	83/308	241622008	141,12863	2203	4299	6502	SO:0001583	missense	653437	exon1			CCCCGTGCGCCAG	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.247C>T	2.37:g.241622008G>A	ENSP00000384894:p.His83Tyr	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	245	98	0.4	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	37	CCDS46560.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	.	13.39	2.223741	0.39300	0.032002	0.0	ENSG00000185176	ENST00000407834	T	0.14516	2.5	2.53	2.53	0.30540	.	0.000000	0.85682	D	0.000000	T	0.10380	0.0254	M	0.80982	2.52	0.44547	D	0.997501	D	0.89917	1.0	D	0.87578	0.998	T	0.02053	-1.1222	9	.	.	.	-1.4545	11.1973	0.48719	0.0:0.0:1.0:0.0	.	83	A6NM10-2	.	Y	83	ENSP00000384894:H83Y	.	H	-	1	0	AQP12B	241270681	1.000000	0.71417	0.528000	0.27938	0.035000	0.12851	8.195000	0.89723	1.720000	0.51447	0.479000	0.44913	CAC	G|0.991;A|0.009	0.009	strong		0.672	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
MUC4	4585	hgsc.bcm.edu	37	3	195506483	195506483	+	Missense_Mutation	SNP	T	T	C	rs201375109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195506483T>C	ENST00000463781.3	-	2	12427	c.11968A>G	c.(11968-11970)Act>Gct	p.T3990A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3990A	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.T3990P(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)		ACTGAGGAAGTGTCGGTGACA	0.592																																					p.T3990A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.A11968G						scavenged	.						10.0	7.0	8.0					3																	195506483		622	1355	1977	SO:0001583	missense	4585	exon2			AGGAAGTGTCGGT	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.11968A>G	3.37:g.195506483T>C	ENSP00000417498:p.Thr3990Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	47	6	0.12766	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	8.956	0.969412	0.18659	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.41;1.5	0.481	-0.864	0.10666	.	0.562686	0.09843	U	0.748557	T	0.21718	0.0523	N	0.14661	0.345	0.09310	N	1	B	0.31790	0.34	B	0.43274	0.414	T	0.40478	-0.9561	9	.	.	.	.	5.8902	0.18909	0.0:0.618:0.0:0.382	.	3862	E7ESK3	.	A	3990	ENSP00000417498:T3990A;ENSP00000420243:T3990A	.	T	-	1	0	MUC4	196991262	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	-2.288000	0.01150	-2.052000	0.00902	-2.075000	0.00382	ACT	C|0.002;G|0.002;T|0.996	0.002	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NUP133	55746	hgsc.bcm.edu	37	1	229622236	229622236	+	Missense_Mutation	SNP	G	G	A	rs35442997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229622236G>A	ENST00000261396.3	-	11	1473	c.1382C>T	c.(1381-1383)cCt>cTt	p.P461L	NUP133_ENST00000537506.1_Missense_Mutation_p.P445L	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	461					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 organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|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)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				AAAAATGATAGGAACACCACC	0.368													G|||	50	0.00998403	0.0325	0.0043	5008	,	,		17685	0.0		0.002	False		,,,				2504	0.002				p.P461L		Atlas-SNP	.											.	NUP133	111	.	0			c.C1382T						PASS	.	G	LEU/PRO	141,4265	99.8+/-138.5	4,133,2066	92.0	93.0	93.0		1382	4.3	0.5	1	dbSNP_126	93	4,8596	4.3+/-15.6	0,4,4296	yes	missense	NUP133	NM_018230.2	98	4,137,6362	AA,AG,GG		0.0465,3.2002,1.1149	benign	461/1157	229622236	145,12861	2203	4300	6503	SO:0001583	missense	55746	exon11			ATGATAGGAACAC		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1382C>T	1.37:g.229622236G>A	ENSP00000261396:p.Pro461Leu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	176	74	0.420455	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	23	0.010531135531135532	22	0.044715447154471545	0	0.0	0	0.0	1	0.0013192612137203166	G	18.11	3.549917	0.65311	0.032002	4.65E-4	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.40225	1.04;1.04;1.04	5.21	4.3	0.51218	WD40/YVTN repeat-like-containing domain (1);	0.251116	0.47093	N	0.000247	T	0.14442	0.0349	M	0.65975	2.015	0.80722	D	1	P	0.47841	0.901	P	0.45276	0.475	T	0.15435	-1.0437	10	0.11485	T	0.65	-6.4934	13.9867	0.64339	0.0737:0.0:0.9263:0.0	rs35442997	461	Q8WUM0	NU133_HUMAN	L	461;461;461;445	ENSP00000261396:P461L;ENSP00000355640:P461L;ENSP00000443496:P445L	ENSP00000261396:P461L	P	-	2	0	NUP133	227688859	1.000000	0.71417	0.535000	0.28026	0.989000	0.77384	6.520000	0.73773	1.321000	0.45227	0.467000	0.42956	CCT	G|0.990;A|0.010	0.010	strong		0.368	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
SLC36A3	285641	hgsc.bcm.edu	37	5	150657130	150657130	+	Missense_Mutation	SNP	G	G	T	rs59596499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150657130G>T	ENST00000335230.3	-	10	1648	c.1237C>A	c.(1237-1239)Ctc>Atc	p.L413I	SLC36A3_ENST00000377713.3_Missense_Mutation_p.L454I	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	413						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)			ATCTCCAGGAGGGCTGGGATG	0.547													G|||	622	0.124201	0.3139	0.0461	5008	,	,		18721	0.0863		0.005	False		,,,				2504	0.0849				p.L454I		Atlas-SNP	.											.	SLC36A3	54	.	0			c.C1360A						PASS	.	G	ILE/LEU,ILE/LEU	1043,3363	384.7+/-325.4	142,759,1302	88.0	79.0	82.0		1360,1237	-6.0	0.0	5	dbSNP_129	82	23,8577	16.6+/-54.9	1,21,4278	yes	missense,missense	SLC36A3	NM_001145017.1,NM_181774.3	5,5	143,780,5580	TT,TG,GG		0.2674,23.6723,8.1962	benign,benign	454/512,413/471	150657130	1066,11940	2203	4300	6503	SO:0001583	missense	285641	exon11			CCAGGAGGGCTGG	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.1237C>A	5.37:g.150657130G>T	ENSP00000334750:p.Leu413Ile	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	111	46	0.414414	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Missense_Mutation	SNP	ENST00000335230.3	37	CCDS4314.1	234	0.10714285714285714	163	0.3313008130081301	19	0.052486187845303865	49	0.08566433566433566	3	0.00395778364116095	G	11.46	1.644841	0.29246	0.236723	0.002674	ENSG00000186334	ENST00000335230;ENST00000377713	T;T	0.02863	4.13;4.13	4.69	-6.03	0.02185	.	0.540122	0.18846	N	0.129540	T	0.00012	0.0000	L	0.52126	1.63	0.32793	P	0.500845	B;B;B	0.25563	0.029;0.129;0.058	B;B;B	0.37387	0.076;0.248;0.044	T	0.46652	-0.9176	9	0.28530	T	0.3	.	0.9335	0.01340	0.3023:0.0965:0.3066:0.2946	rs59596499	454;413;398	Q495N2-3;Q495N2;Q495N2-2	.;S36A3_HUMAN;.	I	413;454	ENSP00000334750:L413I;ENSP00000366942:L454I	ENSP00000334750:L413I	L	-	1	0	SLC36A3	150637323	0.508000	0.26154	0.016000	0.15963	0.599000	0.36880	0.289000	0.18957	-1.471000	0.01886	-0.182000	0.12963	CTC	G|0.915;T|0.085	0.085	strong		0.547	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
AAED1	195827	hgsc.bcm.edu	37	9	99417000	99417000	+	Missense_Mutation	SNP	C	C	T	rs9886834|rs77297714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99417000C>T	ENST00000375234.3	-	2	247	c.248G>A	c.(247-249)aGg>aAg	p.R83K	AAED1_ENST00000464512.1_5'UTR	NM_153698.1	NP_714542.1	Q7RTV5	AAED1_HUMAN	AhpC/TSA antioxidant enzyme domain containing 1	83			R -> K (in dbSNP:rs9886834).														TAAGAAACTCCTGGGGATTTT	0.572													T|||	410	0.081869	0.2912	0.0259	5008	,	,		16276	0.0		0.002	False		,,,				2504	0.0051				p.R83K		Atlas-SNP	.											.	.	.	.	0			c.G248A						PASS	.	T	LYS/ARG	1109,3283		125,859,1212	59.0	58.0	58.0		248	-1.6	0.8	9	dbSNP_119	58	16,8558		0,16,4271	yes	missense	C9orf21	NM_153698.1	26	125,875,5483	TT,TC,CC		0.1866,25.2505,8.6765	benign	83/227	99417000	1125,11841	2196	4287	6483	SO:0001583	missense	195827	exon2			AAACTCCTGGGGA	BK000255	CCDS35073.1	9q22.32	2013-01-07	2012-03-06	2012-03-06	ENSG00000158122	ENSG00000158122			16881	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 21"""	C9orf21			Standard	XM_005251783		Approved		uc004awm.3	Q7RTV5	OTTHUMG00000020299	ENST00000375234.3:c.248G>A	9.37:g.99417000C>T	ENSP00000364382:p.Arg83Lys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	69	41	0.594203	NM_153698	B2RMW4|Q5JU02	Missense_Mutation	SNP	ENST00000375234.3	37	CCDS35073.1	132|132	0.06043956043956044|0.06043956043956044	124|124	0.25203252032520324|0.25203252032520324	8|8	0.022099447513812154|0.022099447513812154	0|0	0.0|0.0	0|0	0.0|0.0	T|T	0.325|0.325	-0.959491|-0.959491	0.02267|0.02267	0.252505|0.252505	0.001866|0.001866	ENSG00000158122|ENSG00000158122	ENST00000411939|ENST00000375234;ENST00000375233	.|T	.|0.39592	.|1.07	4.79|4.79	-1.64|-1.64	0.08318|0.08318	.|Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant (1);Thioredoxin-like fold (2);	.|0.514983	.|0.21661	.|N	.|0.071010	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.20240|0.20240	-1.0281|-1.0281	4|9	.|0.02654	.|T	.|1	-1.013|-1.013	5.5316|5.5316	0.16987|0.16987	0.1376:0.4036:0.0:0.4588|0.1376:0.4036:0.0:0.4588	rs9886834;rs11538195;rs57315001;rs9886834|rs9886834;rs11538195;rs57315001;rs9886834	.|83	.|Q7RTV5	.|CI021_HUMAN	R|K	11|83	.|ENSP00000364382:R83K	.|ENSP00000364381:R83K	G|R	-|-	1|2	0|0	C9orf21|C9orf21	98456821|98456821	0.175000|0.175000	0.23083|0.23083	0.814000|0.814000	0.32528|0.32528	0.098000|0.098000	0.18820|0.18820	-0.008000|-0.008000	0.12788|0.12788	-0.858000|-0.858000	0.04110|0.04110	-1.916000|-1.916000	0.00518|0.00518	GGA|AGG	C|0.901;T|0.099	0.099	strong		0.572	AAED1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053273.1	NM_153698	
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1605983	1605983	+	Missense_Mutation	SNP	G	G	C	rs59007122		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1605983G>C	ENST00000382171.2	-	1	530	c.497C>G	c.(496-498)gCc>gGc	p.A166G	KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	166	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AGAACCACAGGCCCCCTTGGA	0.657																																					p.A166G		Atlas-SNP	.											KRTAP5-1,caecum,carcinoma,0,3	KRTAP5-1	74	3	0			c.C497G						scavenged	.																																			SO:0001583	missense	387264	exon1			CCACAGGCCCCCT	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.497C>G	11.37:g.1605983G>C	ENSP00000371606:p.Ala166Gly	Somatic	239	13	0.0543933		WXS	Illumina HiSeq	Phase_I	245	25	0.102041	NM_001005922		Missense_Mutation	SNP	ENST00000382171.2	37	CCDS31330.1	.	.	.	.	.	.	.	.	.	.	-	0.306	-0.971005	0.02232	.	.	ENSG00000205869	ENST00000382171	T	0.03860	3.78	3.47	2.54	0.30619	.	.	.	.	.	T	0.01189	0.0039	N	0.00134	-2.025	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.44817	-0.9303	9	0.39692	T	0.17	.	5.0286	0.14398	0.0:0.6557:0.2202:0.1241	rs59007122	166	Q6L8H4	KRA51_HUMAN	G	166	ENSP00000371606:A166G	ENSP00000371606:A166G	A	-	2	0	KRTAP5-1	1562559	0.000000	0.05858	0.726000	0.30738	0.031000	0.12232	-0.388000	0.07352	0.444000	0.26612	-0.803000	0.03203	GCC	G|0.500;C|0.500	0.500	weak		0.657	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
RHOT2	89941	hgsc.bcm.edu	37	16	722331	722331	+	Missense_Mutation	SNP	C	C	T	rs3177338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	48	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	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	
CDK11A	728642	hgsc.bcm.edu	37	1	1635022	1635022	+	Silent	SNP	A	A	G	rs1136978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1635022A>G	ENST00000378633.1	-	18	2041	c.1962T>C	c.(1960-1962)agT>agC	p.S654S	CDK11A_ENST00000495016.1_5'Flank|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000378638.2_Silent_p.S617S|CDK11A_ENST00000357760.2_Silent_p.S650S|CDK11A_ENST00000356200.3_Silent_p.S617S|CDK11A_ENST00000358779.5_Silent_p.S641S|CDK11A_ENST00000404249.3_Silent_p.S651S			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	654					apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						CTGGGAGCTCACTGTAGCCGG	0.582																																					p.S651S	Pancreas(186;965 2119 30274 40311 50569)	Atlas-SNP	.											.	CDK11A	38	.	0			c.T1953C						PASS	.	G	,	1303,2143		425,453,845	22.0	49.0	41.0		1953,1923	-5.4	0.0	1	dbSNP_86	41	129,8071		15,99,3986	no	coding-synonymous,coding-synonymous	CDK11A	NM_024011.2,NM_033529.2	,	440,552,4831	GG,GA,AA		1.5732,37.812,12.2961	,	651/781,641/771	1635022	1432,10214	1723	4100	5823	SO:0001819	synonymous_variant	728642	exon18			GAGCTCACTGTAG	AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128		"""Cyclin-dependent kinases"""	1730	protein-coding gene	gene with protein product		116951	"""cell division cycle 2-like 2"", ""cell division cycle 2-like 2 (PITSLRE proteins)"""	CDC2L3, CDC2L2		7920654, 9750192, 19884882	Standard	NM_033529		Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000378633.1:c.1962T>C	1.37:g.1635022A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	109	19	0.174312	NM_024011	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	Silent	SNP	ENST00000378633.1	37																																																																																				A|0.852;G|0.148	0.148	strong		0.582	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011	
AACS	65985	hgsc.bcm.edu	37	12	125587278	125587278	+	Silent	SNP	G	G	A	rs3763984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125587278G>A	ENST00000316519.6	+	6	830	c.624G>A	c.(622-624)gaG>gaA	p.E208E	AACS_ENST00000261686.6_Silent_p.E208E|AACS_ENST00000316543.10_5'Flank	NM_023928.3	NP_076417.2	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	208					adipose tissue development (GO:0060612)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cellular response to testosterone stimulus (GO:0071394)|fatty acid metabolic process (GO:0006631)|liver development (GO:0001889)|positive regulation of insulin secretion (GO:0032024)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to purine-containing compound (GO:0014074)|response to starvation (GO:0042594)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)	acetoacetate-CoA ligase activity (GO:0030729)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|liver(1)|lung(16)|ovary(1)|stomach(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		TCTCTGTGGAGGCTGTTGTCT	0.502													g|||	280	0.0559105	0.0923	0.0245	5008	,	,		19948	0.1131		0.006	False		,,,				2504	0.0215				p.E208E		Atlas-SNP	.											.	AACS	59	.	0			c.G624A						PASS	.	G		326,4080	173.4+/-203.2	9,308,1886	169.0	181.0	177.0		624	1.0	1.0	12	dbSNP_107	177	55,8545	34.8+/-89.0	0,55,4245	no	coding-synonymous	AACS	NM_023928.3		9,363,6131	AA,AG,GG		0.6395,7.399,2.9294		208/673	125587278	381,12625	2203	4300	6503	SO:0001819	synonymous_variant	65985	exon6			TGTGGAGGCTGTT	AK022451	CCDS9263.1	12q24.31	2010-09-29			ENSG00000081760	ENSG00000081760	6.2.1.16	"""Acyl-CoA synthetase family"""	21298	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 1"""	614364				12623130, 17762044	Standard	NM_023928		Approved	FLJ12389, SUR-5, ACSF1	uc001uhc.3	Q86V21	OTTHUMG00000168550	ENST00000316519.6:c.624G>A	12.37:g.125587278G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_023928	Q49AB9|Q49AC3|Q658Q8|Q8IWD2|Q8NEW5|Q9BSJ9|Q9H829|Q9HA19	Silent	SNP	ENST00000316519.6	37	CCDS9263.1																																																																																			G|0.956;A|0.044	0.044	strong		0.502	AACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400202.1	NM_023928	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057766	46057766	+	Missense_Mutation	SNP	G	G	C	rs142146787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057766G>C	ENST00000380095.1	+	1	494	c.432G>C	c.(430-432)caG>caC	p.Q144H	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	144	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CATGCCAGCAGGCCTGCTGTG	0.602													G|||	3	0.000599042	0.0015	0.0	5008	,	,		23205	0.0		0.0	False		,,,				2504	0.001				p.Q144H		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G432C						PASS	.	G	,HIS/GLN	7,4399	12.9+/-30.5	0,7,2196	293.0	265.0	274.0		,432	-0.5	0.1	21	dbSNP_134	274	0,8600		0,0,4300	yes	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,24	0,7,6496	CC,CG,GG		0.0,0.1589,0.0538	,probably-damaging	,144/252	46057766	7,12999	2203	4300	6503	SO:0001583	missense	353333	exon1			CCAGCAGGCCTGC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.432G>C	21.37:g.46057766G>C	ENSP00000369438:p.Gln144His	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	172	53	0.30814	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	g	8.829	0.939468	0.18281	0.001589	0.0	ENSG00000221859	ENST00000380095	T	0.01178	5.22	3.27	-0.456	0.12190	.	.	.	.	.	T	0.05273	0.0140	M	0.91300	3.195	0.09310	N	1	D	0.56746	0.977	P	0.56343	0.796	T	0.12760	-1.0535	9	0.87932	D	0	.	5.8436	0.18647	0.632:0.0:0.368:0.0	.	144	P60014	KR10A_HUMAN	H	144	ENSP00000369438:Q144H	ENSP00000369438:Q144H	Q	+	3	2	KRTAP10-10	44882194	0.000000	0.05858	0.109000	0.21407	0.190000	0.23558	-1.200000	0.03029	0.065000	0.16485	0.461000	0.40582	CAG	G|1.000;C|0.000	0.000	weak		0.602	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
CD109	135228	hgsc.bcm.edu	37	6	74466377	74466377	+	Silent	SNP	C	C	T	rs6453696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74466377C>T	ENST00000287097.5	+	6	757	c.645C>T	c.(643-645)taC>taT	p.Y215Y	CD109_ENST00000422508.2_Silent_p.Y138Y|CD109_ENST00000437994.2_Silent_p.Y215Y			Q6YHK3	CD109_HUMAN	CD109 molecule	215					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						ACCAGACATACTATCAATCAT	0.308													T|||	3347	0.668331	0.7345	0.6816	5008	,	,		15069	0.8452		0.507	False		,,,				2504	0.5532				p.Y215Y		Atlas-SNP	.											.	CD109	170	.	0			c.C645T						PASS	.	T	,,	3181,1225	423.6+/-340.2	1143,895,165	83.0	85.0	85.0		645,414,645	1.0	0.9	6	dbSNP_116	85	4562,4024	551.7+/-386.0	1240,2082,971	no	coding-synonymous,coding-synonymous,coding-synonymous	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	,,	2383,2977,1136	TT,TC,CC		46.867,27.803,40.4018	,,	215/1429,138/1369,215/1446	74466377	7743,5249	2203	4293	6496	SO:0001819	synonymous_variant	135228	exon6			GACATACTATCAA	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.645C>T	6.37:g.74466377C>T		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	214	214	1	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																			C|0.387;T|0.613	0.613	strong		0.308	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
GABRA4	2557	hgsc.bcm.edu	37	4	46995387	46995387	+	Missense_Mutation	SNP	C	C	T	rs16859837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:46995387C>T	ENST00000264318.3	-	1	1037	c.55G>A	c.(55-57)Gcc>Acc	p.A19T	GABRA4_ENST00000509316.1_5'UTR	NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	19			A -> T (in dbSNP:rs16859837).		central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	CGCAGGAGGGCGAAACTGACC	0.582													C|||	59	0.0117812	0.0439	0.0014	5008	,	,		16882	0.0		0.0	False		,,,				2504	0.0				p.A19T	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											.	GABRA4	129	.	0			c.G55A						PASS	.	C	THR/ALA,,	164,4242	109.9+/-148.2	5,154,2044	115.0	109.0	111.0		55,,	1.8	1.0	4	dbSNP_123	111	2,8598	1.2+/-3.3	0,2,4298	yes	missense,intron,intron	GABRA4	NM_000809.3,NM_001204266.1,NM_001204267.1	58,,	5,156,6342	TT,TC,CC		0.0233,3.7222,1.2763	benign,,	19/555,,	46995387	166,12840	2203	4300	6503	SO:0001583	missense	2557	exon1			GGAGGGCGAAACT		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4078	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 4"""	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.55G>A	4.37:g.46995387C>T	ENSP00000264318:p.Ala19Thr	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	194	192	0.989691	NM_000809	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	15.70	2.911015	0.52439	0.037222	2.33E-4	ENSG00000109158	ENST00000264318	T	0.79845	-1.31	4.72	1.79	0.24919	.	0.494117	0.20686	N	0.087559	T	0.17789	0.0427	N	0.08118	0	0.28598	N	0.909322	B	0.06786	0.001	B	0.04013	0.001	T	0.13980	-1.0489	10	0.20519	T	0.43	.	5.9264	0.19114	0.0:0.6558:0.0:0.3442	rs16859837;rs52821342;rs16859837	19	P48169	GBRA4_HUMAN	T	19	ENSP00000264318:A19T	ENSP00000264318:A19T	A	-	1	0	GABRA4	46690144	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.961000	0.40432	0.595000	0.29777	-0.237000	0.12165	GCC	C|0.984;T|0.016	0.016	strong		0.582	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1		
NAV2	89797	hgsc.bcm.edu	37	11	20067064	20067064	+	Silent	SNP	C	C	T	rs7125647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:20067064C>T	ENST00000396087.3	+	15	3918	c.3819C>T	c.(3817-3819)gaC>gaT	p.D1273D	NAV2_ENST00000360655.4_Silent_p.D1186D|NAV2_ENST00000527559.2_Silent_p.D1202D|NAV2-AS2_ENST00000533767.1_RNA|NAV2_ENST00000540292.1_Silent_p.D1204D|NAV2_ENST00000396085.1_Silent_p.D1250D|NAV2_ENST00000349880.4_Silent_p.D1250D|NAV2_ENST00000311043.8_Silent_p.D336D|NAV2_ENST00000533917.1_Silent_p.D336D	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1273					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						ACCAAACAGACAAGGAGAAAG	0.557													T|||	3317	0.66234	0.5983	0.6628	5008	,	,		19526	0.8313		0.5378	False		,,,				2504	0.7025				p.D1273D		Atlas-SNP	.											.	NAV2	255	.	0			c.C3819T						PASS	.	T	,,,	2696,1710	515.2+/-368.8	834,1028,341	68.0	65.0	66.0		3558,1008,3750,3750	-0.5	0.9	11	dbSNP_116	66	4672,3928	547.1+/-385.1	1261,2150,889	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	2095,3178,1230	TT,TC,CC		45.6744,38.8107,43.3492	,,,	1186/2366,336/1494,1250/2430,1250/2433	20067064	7368,5638	2203	4300	6503	SO:0001819	synonymous_variant	89797	exon15			AACAGACAAGGAG	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.3819C>T	11.37:g.20067064C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			C|0.384;T|0.616	0.616	strong		0.557	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
PLIN4	729359	hgsc.bcm.edu	37	19	4512637	4512637	+	Silent	SNP	A	A	G	rs57042059|rs386806138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512637A>G	ENST00000301286.3	-	3	1292	c.1293T>C	c.(1291-1293)aaT>aaC	p.N431N		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	431	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						CTCTGGCCAAATTCATGGCAC	0.552													a|||	834	0.166534	0.559	0.049	5008	,	,		20317	0.0		0.0139	False		,,,				2504	0.0481				p.N431N		Atlas-SNP	.											PLIN4_ENST00000301286,colon,carcinoma,-2,2	PLIN4	191	2	0			c.T1293C						PASS	.	G		2072,1966		663,746,610	121.0	147.0	139.0		1293	-6.8	0.0	19	dbSNP_129	139	154,8212		11,132,4040	no	coding-synonymous	PLIN4	NM_001080400.1		674,878,4650	GG,GA,AA		1.8408,48.6875,17.9458		431/1358	4512637	2226,10178	2019	4183	6202	SO:0001819	synonymous_variant	729359	exon3			GGCCAAATTCATG	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.1293T>C	19.37:g.4512637A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	189	189	1	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			A|0.864;G|0.136	0.136	strong		0.552	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
ZNF618	114991	hgsc.bcm.edu	37	9	116811184	116811184	+	Silent	SNP	G	G	A	rs7852282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116811184G>A	ENST00000374126.5	+	15	1701	c.1602G>A	c.(1600-1602)aaG>aaA	p.K534K	ZNF618_ENST00000288466.7_Silent_p.K441K|ZNF618_ENST00000470105.1_3'UTR			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	534					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						ACCAGGTGAAGGTGAAAGTGA	0.587													G|||	338	0.067492	0.2375	0.0303	5008	,	,		21657	0.0		0.0	False		,,,				2504	0.0031				p.K441K		Atlas-SNP	.											.	ZNF618	184	.	0			c.G1323A						PASS	.	G		796,3538		77,642,1448	27.0	30.0	29.0		1323	3.5	1.0	9	dbSNP_116	29	18,8520		0,18,4251	no	coding-synonymous	ZNF618	NM_133374.2		77,660,5699	AA,AG,GG		0.2108,18.3664,6.3238		441/862	116811184	814,12058	2167	4269	6436	SO:0001819	synonymous_variant	114991	exon14			GGTGAAGGTGAAA	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.1602G>A	9.37:g.116811184G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	38	0.633333	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				G|0.921;A|0.079	0.079	strong		0.587	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
ASPDH	554235	hgsc.bcm.edu	37	19	51017064	51017064	+	Missense_Mutation	SNP	G	G	C	rs7248272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51017064G>C	ENST00000389208.4	-	1	78	c.17C>G	c.(16-18)cCg>cGg	p.P6R	ASPDH_ENST00000597030.1_Intron|JOSD2_ENST00000598418.1_5'Flank|JOSD2_ENST00000391815.3_5'Flank|JOSD2_ENST00000595669.1_5'Flank|ASPDH_ENST00000376916.3_Intron|JOSD2_ENST00000601423.1_5'Flank	NM_001114598.1	NP_001108070.1	A6ND91	ASPD_HUMAN	aspartate dehydrogenase domain containing	6					NAD biosynthetic process (GO:0009435)|NADP catabolic process (GO:0006742)		aspartate dehydrogenase activity (GO:0033735)|NADP binding (GO:0050661)			endometrium(1)|large_intestine(1)|lung(1)	3						CACCCTCCACGGGCCCCTGTC	0.682													G|||	291	0.058107	0.0855	0.0317	5008	,	,		13839	0.121		0.001	False		,,,				2504	0.0337				p.P6R		Atlas-SNP	.											.	ASPDH	22	.	0			c.C17G						PASS	.						28.0	36.0	33.0					19																	51017064		692	1591	2283	SO:0001583	missense	554235	exon1			CTCCACGGGCCCC		CCDS33082.1, CCDS46153.1	19q13.33	2012-10-02			ENSG00000204653	ENSG00000204653			33856	protein-coding gene	gene with protein product							Standard	NM_001024656		Approved		uc010enz.3	A6ND91		ENST00000389208.4:c.17C>G	19.37:g.51017064G>C	ENSP00000373860:p.Pro6Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_001114598	Q6NZ37	Missense_Mutation	SNP	ENST00000389208.4	37	CCDS46153.1	145	0.06639194139194139	56	0.11382113821138211	13	0.03591160220994475	75	0.13111888111888112	1	0.0013192612137203166	G	11.23	1.577637	0.28180	.	.	ENSG00000204653	ENST00000389208	T	0.46063	0.88	3.23	2.19	0.27852	NAD(P)-binding domain (1);	0.461581	0.18443	U	0.141099	T	0.00241	0.0007	L	0.34521	1.04	0.80722	P	0.0	P	0.39157	0.662	B	0.31751	0.135	T	0.05162	-1.0902	9	0.20046	T	0.44	.	5.6409	0.17562	0.1517:0.0:0.8483:0.0	rs7248272	6	A6ND91	ASPD_HUMAN	R	6	ENSP00000373860:P6R	ENSP00000373860:P6R	P	-	2	0	ASPDH	55708876	0.537000	0.26386	0.059000	0.19551	0.116000	0.19942	0.837000	0.27558	1.829000	0.53265	0.462000	0.41574	CCG	G|0.930;C|0.070	0.070	strong		0.682	ASPDH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464861.1	NM_001024656	
ZNF813	126017	hgsc.bcm.edu	37	19	53993670	53993670	+	Missense_Mutation	SNP	G	G	A	rs2617667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53993670G>A	ENST00000396403.4	+	4	312	c.184G>A	c.(184-186)Gca>Aca	p.A62T	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	62	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		A -> T (in dbSNP:rs2617667).		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)	1				GBM - Glioblastoma multiforme(134;0.00619)		CTCATCAACAGCACAAGGCAA	0.368													g|||	1495	0.298522	0.475	0.2406	5008	,	,		21430	0.2421		0.1918	False		,,,				2504	0.2689				p.A62T		Atlas-SNP	.											.	ZNF813	81	.	0			c.G184A						PASS	.	G	THR/ALA	1851,2513	489.2+/-361.4	396,1059,727	89.0	93.0	91.0		184	-1.1	0.0	19	dbSNP_100	91	1648,6938	291.6+/-300.4	158,1332,2803	no	missense	ZNF813	NM_001004301.3	58	554,2391,3530	AA,AG,GG		19.194,42.4152,27.0193	possibly-damaging	62/618	53993670	3499,9451	2182	4293	6475	SO:0001583	missense	126017	exon4			TCAACAGCACAAG	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.184G>A	19.37:g.53993670G>A	ENSP00000379684:p.Ala62Thr	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	168	91	0.541667	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	578	0.26465201465201466	224	0.45528455284552843	83	0.2292817679558011	140	0.24475524475524477	131	0.17282321899736147	G	6.884	0.532613	0.13127	0.424152	0.19194	ENSG00000198346	ENST00000468450;ENST00000396403;ENST00000490956	T;T;T	0.05649	4.08;3.41;5.14	0.678	-1.13	0.09775	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.37330	0.59	B	0.40602	0.334	T	0.37549	-0.9701	8	0.16420	T	0.52	.	4.7006	0.12825	0.0:0.0:0.3779:0.6221	rs2617667;rs52808272;rs56450222;rs59449241;rs2617667	62	Q6ZN06	ZN813_HUMAN	T	9;62;93	ENSP00000419821:A9T;ENSP00000379684:A62T;ENSP00000418289:A93T	ENSP00000379684:A62T	A	+	1	0	ZNF813	58685482	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.243000	0.08915	-0.301000	0.08882	0.205000	0.17691	GCA	G|0.745;A|0.255	0.255	strong		0.368	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
SYK	6850	hgsc.bcm.edu	37	9	93606309	93606309	+	Silent	SNP	G	G	A	rs35758162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:93606309G>A	ENST00000375754.4	+	2	277	c.129G>A	c.(127-129)caG>caA	p.Q43Q	SYK_ENST00000476708.1_3'UTR|SYK_ENST00000375751.4_Silent_p.Q43Q|SYK_ENST00000375747.1_Silent_p.Q43Q|SYK_ENST00000375746.1_Silent_p.Q43Q	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	43	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						TGCTGCGCCAGAGCCGCAACT	0.612			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								G|||	556	0.111022	0.1067	0.1138	5008	,	,		18957	0.0159		0.168	False		,,,				2504	0.1544				p.Q43Q		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.G129A						PASS	.	G	,,,	529,3877	232.6+/-246.1	36,457,1710	60.0	41.0	48.0		129,129,129,129	4.1	1.0	9	dbSNP_126	48	1795,6805	313.7+/-311.4	181,1433,2686	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	217,1890,4396	AA,AG,GG		20.8721,12.0064,17.8687	,,,	43/613,43/636,43/613,43/636	93606309	2324,10682	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon2			GCGCCAGAGCCGC	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.129G>A	9.37:g.93606309G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	88	32	0.363636	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			G|0.847;A|0.153	0.153	strong		0.612	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
DOCK2	1794	hgsc.bcm.edu	37	5	169469088	169469088	+	Silent	SNP	G	G	C	rs6555882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:169469088G>C	ENST00000256935.8	+	38	3908	c.3828G>C	c.(3826-3828)ctG>ctC	p.L1276L	DOCK2_ENST00000520908.1_Silent_p.L768L|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Silent_p.L337L	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1276	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACCGGCAGCTGAAGGAGACGC	0.577													C|||	461	0.0920527	0.2837	0.0317	5008	,	,		19097	0.0		0.0189	False		,,,				2504	0.046				p.L1276L		Atlas-SNP	.											.	DOCK2	389	.	0			c.G3828C						PASS	.	C		1166,3240	713.1+/-408.2	139,888,1176	61.0	54.0	57.0		3828	3.4	1.0	5	dbSNP_116	57	164,8436	811.3+/-407.1	3,158,4139	no	coding-synonymous	DOCK2	NM_004946.2		142,1046,5315	CC,CG,GG		1.907,26.4639,10.226		1276/1831	169469088	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon38			GCAGCTGAAGGAG	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.3828G>C	5.37:g.169469088G>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	242	242	1	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			G|0.867;C|0.133	0.133	strong		0.577	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
LILRA1	11024	hgsc.bcm.edu	37	19	55105722	55105722	+	Missense_Mutation	SNP	G	G	C	rs28524012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55105722G>C	ENST00000251372.3	+	2	195	c.13G>C	c.(13-15)Gtc>Ctc	p.V5L	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Missense_Mutation_p.V5L|LILRA1_ENST00000473156.1_Intron|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	5				V -> L (in Ref. 1; AAB87663). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		GACCCCCATCGTCACAGTCCT	0.582													N|||	1427	0.284944	0.4894	0.268	5008	,	,		16924	0.2778		0.1034	False		,,,				2504	0.2147				p.V5L		Atlas-SNP	.											.	LILRA1	105	.	0			c.G13C						PASS	.	C	LEU/VAL	1320,3086		399,522,1282	88.0	107.0	100.0		13	-0.2	0.0	19	dbSNP_125	100	332,8268		50,232,4018	no	missense	LILRA1	NM_006863.1	32	449,754,5300	CC,CG,GG		3.8605,29.9591,12.7018	benign	5/490	55105722	1652,11354	2203	4300	6503	SO:0001583	missense	11024	exon2			CCCATCGTCACAG	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.13G>C	19.37:g.55105722G>C	ENSP00000251372:p.Val5Leu	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	440	0.20146520146520147	169	0.3434959349593496	78	0.2154696132596685	140	0.24475524475524477	53	0.06992084432717678	C	0.011	-1.736306	0.00681	0.299591	0.038605	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.00470	7.2;7.21	2.42	-0.145	0.13436	.	0.555858	0.15336	N	0.267735	T	0.00012	0.0000	N	0.00089	-2.185	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.0	T	0.31998	-0.9923	9	0.02654	T	1	.	1.1695	0.01823	0.2208:0.407:0.2172:0.155	rs28524012;rs57852452	5;5	O75019-2;O75019	.;LIRA1_HUMAN	L	5	ENSP00000251372:V5L;ENSP00000413715:V5L	ENSP00000251372:V5L	V	+	1	0	LILRA1	59797534	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.526000	0.02229	-0.494000	0.06669	-1.041000	0.02371	GTC	G|0.797;C|0.203	0.203	strong		0.582	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
DUOX1	53905	hgsc.bcm.edu	37	15	45427345	45427345	+	Silent	SNP	C	C	T	rs78022423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45427345C>T	ENST00000321429.4	+	6	758	c.351C>T	c.(349-351)ggC>ggT	p.G117G	DUOX1_ENST00000389037.3_Silent_p.G117G	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	117	Peroxidase-like; mediates peroxidase activity.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		AAACTCCCGGCTGCCCCGCCG	0.647													C|||	111	0.0221645	0.0809	0.0058	5008	,	,		15061	0.0		0.0	False		,,,				2504	0.0				p.G117G		Atlas-SNP	.											.	DUOX1	125	.	0			c.C351T						PASS	.	C	,	295,4099	160.0+/-192.4	11,273,1913	48.0	48.0	48.0		351,351	2.1	1.0	15	dbSNP_131	48	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	DUOX1	NM_017434.3,NM_175940.1	,	11,273,6211	TT,TC,CC		0.0,6.7137,2.271	,	117/1552,117/1552	45427345	295,12695	2197	4298	6495	SO:0001819	synonymous_variant	53905	exon6			TCCCGGCTGCCCC	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.351C>T	15.37:g.45427345C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	206	95	0.461165	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																			C|0.976;T|0.024	0.024	strong		0.647	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
OR7G2	390882	hgsc.bcm.edu	37	19	9213396	9213396	+	Missense_Mutation	SNP	G	G	A	rs7247751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9213396G>A	ENST00000305456.2	-	1	586	c.587C>T	c.(586-588)cCg>cTg	p.P196L		NM_001005193.1	NP_001005193.1	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G, member 2	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|skin(3)	16						GAAGAAGAGCGGGATTTCCAG	0.478													-|||	155	0.0309505	0.1127	0.0086	5008	,	,		21697	0.0		0.0	False		,,,				2504	0.0				p.P196L	Esophageal Squamous(67;143 1448 28637 40648)	Atlas-SNP	.											OR7G2,NS,carcinoma,+1,1	OR7G2	48	1	0			c.C587T						PASS	.	G	LEU/PRO	380,4026	190.9+/-216.7	16,348,1839	98.0	86.0	90.0		587	2.2	0.0	19	dbSNP_116	90	4,8596	3.0+/-9.4	0,4,4296	yes	missense	OR7G2	NM_001005193.1	98	16,352,6135	AA,AG,GG		0.0465,8.6246,2.9525	possibly-damaging	196/346	9213396	384,12622	2203	4300	6503	SO:0001583	missense	390882	exon1			AAGAGCGGGATTT		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.587C>T	19.37:g.9213396G>A	ENSP00000303822:p.Pro196Leu	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	216	102	0.472222	NM_001005193	Q6IFJ4|Q96RA0	Missense_Mutation	SNP	ENST00000305456.2	37	CCDS32897.1	55	0.025183150183150184	54	0.10975609756097561	1	0.0027624309392265192	0	0.0	0	0.0	g	8.801	0.932843	0.18131	0.086246	4.65E-4	ENSG00000170923	ENST00000305456	T	0.37752	1.18	3.27	2.19	0.27852	GPCR, rhodopsin-like superfamily (1);	0.212960	0.23524	U	0.047241	T	0.00637	0.0021	L	0.58583	1.82	0.09310	N	1	P	0.45672	0.864	B	0.40825	0.341	T	0.01262	-1.1402	10	0.66056	D	0.02	.	9.1271	0.36821	0.0:0.0:0.4786:0.5214	rs7247751;rs52817351;rs7247751	175	Q8NG99	OR7G2_HUMAN	L	196	ENSP00000303822:P196L	ENSP00000303822:P196L	P	-	2	0	OR7G2	9074396	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-0.621000	0.05559	0.954000	0.37851	0.545000	0.68477	CCG	G|0.968;A|0.032	0.032	strong		0.478	OR7G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448994.1		
MERTK	10461	hgsc.bcm.edu	37	2	112722854	112722854	+	Splice_Site	SNP	G	G	A	rs7588635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:112722854G>A	ENST00000295408.4	+	5	1101	c.844G>A	c.(844-846)Gca>Aca	p.A282T	MERTK_ENST00000421804.2_Splice_Site_p.A282T|MERTK_ENST00000409780.1_Splice_Site_p.A106T			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	282			A -> T (in dbSNP:rs7588635). {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						CAACATCAAAGGTAAGCAGCA	0.567													G|||	233	0.0465256	0.171	0.0086	5008	,	,		19523	0.0		0.001	False		,,,				2504	0.0				p.A282T		Atlas-SNP	.											.	MERTK	112	.	0			c.G844A						PASS	.	G	THR/ALA	598,3808	255.2+/-260.5	47,504,1652	102.0	80.0	88.0		844	5.8	1.0	2	dbSNP_116	88	6,8594	4.3+/-15.6	0,6,4294	yes	missense-near-splice	MERTK	NM_006343.2	58	47,510,5946	AA,AG,GG		0.0698,13.5724,4.644	benign	282/1000	112722854	604,12402	2203	4300	6503	SO:0001630	splice_region_variant	10461	exon5			ATCAAAGGTAAGC	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.844+1G>A	2.37:g.112722854G>A		Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	201	94	0.467662	NM_006343	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	90	0.04120879120879121	87	0.17682926829268292	3	0.008287292817679558	0	0.0	0	0.0	G	17.78	3.474628	0.63737	0.135724	6.98E-4	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000409780	T;T;T	0.36520	1.25;1.25;1.25	5.75	5.75	0.90469	Immunoglobulin-like fold (1);	0.534882	0.13857	U	0.357982	T	0.00109	0.0003	L	0.58101	1.795	0.30039	P	0.8128029999999999	B	0.32245	0.361	B	0.25140	0.058	T	0.05084	-1.0907	9	0.72032	D	0.01	-0.4319	19.5333	0.95239	0.0:0.0:1.0:0.0	rs7588635;rs17838486;rs7588635	282	Q12866	MERTK_HUMAN	T	282;282;106	ENSP00000295408:A282T;ENSP00000389152:A282T;ENSP00000387277:A106T	ENSP00000295408:A282T	A	+	1	0	MERTK	112439325	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	4.652000	0.61454	2.720000	0.93068	0.563000	0.77884	GCA	G|0.947;A|0.053	0.053	strong		0.567	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		Missense_Mutation
MAN2B2	23324	hgsc.bcm.edu	37	4	6602378	6602378	+	Silent	SNP	G	G	A	rs73796294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6602378G>A	ENST00000285599.3	+	10	1470	c.1434G>A	c.(1432-1434)tcG>tcA	p.S478S	MAN2B2_ENST00000504248.1_Silent_p.S427S	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	478					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						ATTTTGCCTCGGTCTACAACC	0.597													G|||	186	0.0371406	0.1331	0.013	5008	,	,		19561	0.0		0.001	False		,,,				2504	0.0				p.S478S		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G1434A						PASS	.	G		515,3891	236.8+/-248.8	34,447,1722	155.0	122.0	133.0		1434	-7.5	0.0	4	dbSNP_130	133	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	MAN2B2	NM_015274.1		34,453,6016	AA,AG,GG		0.0698,11.6886,4.0058		478/1010	6602378	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	23324	exon10			TGCCTCGGTCTAC	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.1434G>A	4.37:g.6602378G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_015274	Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	37	CCDS33951.1	65	0.02976190476190476	62	0.12601626016260162	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	4.539	0.100114	0.08731	0.116886	6.98E-4	ENSG00000013288	ENST00000505907	.	.	.	4.67	-7.52	0.01341	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.42109	P	0.008626000000000023	.	.	.	.	.	.	T	0.26744	-1.0094	3	.	.	.	-3.5583	0.9855	0.01445	0.1784:0.1741:0.2587:0.3887	.	.	.	.	Q	477	.	.	R	+	2	0	MAN2B2	6653279	0.014000	0.17966	0.003000	0.11579	0.008000	0.06430	-0.480000	0.06559	-1.075000	0.03129	-1.224000	0.01588	CGG	G|0.959;A|0.041	0.041	strong		0.597	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
BRPF3	27154	hgsc.bcm.edu	37	6	36177597	36177597	+	Silent	SNP	C	C	T	rs73730485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36177597C>T	ENST00000357641.6	+	5	2024	c.1771C>T	c.(1771-1773)Ctg>Ttg	p.L591L	BRPF3_ENST00000339717.7_Silent_p.L591L|BRPF3_ENST00000443324.2_Silent_p.L591L|BRPF3_ENST00000543502.1_Silent_p.L591L|BRPF3_ENST00000534400.1_Silent_p.L591L|BRPF3_ENST00000534694.1_Silent_p.L591L	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	591					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						GGAGCTGGAGCTGATGCCATT	0.507													C|||	53	0.0105831	0.0393	0.0014	5008	,	,		20080	0.0		0.0	False		,,,				2504	0.0				p.L591L		Atlas-SNP	.											.	BRPF3	93	.	0			c.C1771T						PASS	.	C		186,4220	118.8+/-156.5	4,178,2021	96.0	84.0	88.0		1771	3.2	1.0	6	dbSNP_130	88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BRPF3	NM_015695.2		4,179,6320	TT,TC,CC		0.0116,4.2215,1.4378		591/1206	36177597	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	27154	exon5			CTGGAGCTGATGC	AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.1771C>T	6.37:g.36177597C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Silent	SNP	ENST00000357641.6	37	CCDS34437.1																																																																																			C|0.987;T|0.013	0.013	strong		0.507	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695	
LRRC16B	90668	hgsc.bcm.edu	37	14	24527220	24527220	+	Silent	SNP	C	C	T	rs4982853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24527220C>T	ENST00000342740.5	+	16	1423	c.1269C>T	c.(1267-1269)taC>taT	p.Y423Y	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	423						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)		GCAGCGCCTACACACTGAGCC	0.657											OREG0022615	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	998	0.199281	0.1014	0.2032	5008	,	,		18014	0.4306		0.0616	False		,,,				2504	0.2321				p.Y423Y		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C1269T						PASS	.	C		442,3964	202.8+/-225.5	21,400,1782	64.0	68.0	67.0		1269	4.2	1.0	14	dbSNP_111	67	476,8124	137.6+/-194.5	11,454,3835	no	coding-synonymous	LRRC16B	NM_138360.3		32,854,5617	TT,TC,CC		5.5349,10.0318,7.0583		423/1373	24527220	918,12088	2203	4300	6503	SO:0001819	synonymous_variant	90668	exon16			CGCCTACACACTG	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.1269C>T	14.37:g.24527220C>T		Somatic	114	0	0	772	WXS	Illumina HiSeq	Phase_I	107	59	0.551402	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																			C|0.898;T|0.102	0.102	strong		0.657	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
GFI1B	8328	hgsc.bcm.edu	37	9	135864547	135864547	+	Missense_Mutation	SNP	G	G	A	rs62638686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135864547G>A	ENST00000339463.3	+	9	1429	c.610G>A	c.(610-612)Gct>Act	p.A204T	GFI1B_ENST00000450530.1_Missense_Mutation_p.A204T|GFI1B_ENST00000372122.1_Missense_Mutation_p.A204T|GFI1B_ENST00000372123.1_Intron|GFI1B_ENST00000534944.1_Intron|GFI1B_ENST00000372124.1_Intron			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	204	Interaction with ARIH2.|Mediates interaction with GATA1.				cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K9 methylation (GO:0051574)|regulation of erythrocyte differentiation (GO:0045646)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II transcription factor binding (GO:0001085)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		CTTCGGCCACGCTGTGAGCCT	0.662													G|||	75	0.014976	0.0537	0.0043	5008	,	,		19398	0.0		0.001	False		,,,				2504	0.0				p.A204T		Atlas-SNP	.											.	GFI1B	37	.	0			c.G610A						PASS	.	G	,THR/ALA	228,4178	134.5+/-170.7	6,216,1981	63.0	50.0	55.0		,610	2.5	0.3	9	dbSNP_129	55	3,8597	2.2+/-6.3	0,3,4297	yes	intron,missense	GFI1B	NM_001135031.1,NM_004188.4	,58	6,219,6278	AA,AG,GG		0.0349,5.1748,1.7761	,benign	,204/331	135864547	231,12775	2203	4300	6503	SO:0001583	missense	8328	exon5			GGCCACGCTGTGA	AF081946	CCDS6957.1, CCDS48049.1	9q34.13	2014-09-17	2007-10-04		ENSG00000165702	ENSG00000165702		"""Zinc fingers, C2H2-type"""	4238	protein-coding gene	gene with protein product		604383	"""growth factor independent 1B (potential regulator of CDKN1A, translocated in CML)"""			9878267	Standard	NM_001135031		Approved		uc004ccg.3	Q5VTD9	OTTHUMG00000020848	ENST00000339463.3:c.610G>A	9.37:g.135864547G>A	ENSP00000344782:p.Ala204Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	121	41	0.338843	NM_004188	O95270|Q5VTD8|Q6FHZ2|Q6T888	Missense_Mutation	SNP	ENST00000339463.3	37	CCDS6957.1	38	0.0173992673992674	34	0.06910569105691057	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	13.62	2.290120	0.40494	0.051748	3.49E-4	ENSG00000165702	ENST00000339463;ENST00000450530;ENST00000372122	T;T;T	0.07800	3.16;3.16;3.16	5.42	2.45	0.29901	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.129163	0.51477	D	0.000098	T	0.00524	0.0017	N	0.21142	0.635	0.47245	D	0.99936	B	0.30727	0.292	B	0.31812	0.136	T	0.44877	-0.9299	10	0.72032	D	0.01	-23.2176	14.0232	0.64571	0.0:0.0:0.6057:0.3943	rs62638686	204	Q5VTD9	GFI1B_HUMAN	T	204	ENSP00000344782:A204T;ENSP00000409546:A204T;ENSP00000361195:A204T	ENSP00000344782:A204T	A	+	1	0	GFI1B	134854368	1.000000	0.71417	0.338000	0.25549	0.016000	0.09150	4.773000	0.62331	0.649000	0.30751	-0.122000	0.15005	GCT	A|0.017;G|0.983;T|0.000	0.017	strong		0.662	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188	
PDZD2	23037	hgsc.bcm.edu	37	5	32087374	32087374	+	Missense_Mutation	SNP	A	A	G	rs157496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32087374A>G	ENST00000438447.1	+	20	4208	c.3820A>G	c.(3820-3822)Acc>Gcc	p.T1274A	PDZD2_ENST00000282493.3_Missense_Mutation_p.T1274A			O15018	PDZD2_HUMAN	PDZ domain containing 2	1274			T -> A (in dbSNP:rs157496). {ECO:0000269|PubMed:9205841}.		cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GCCCAGGGTCACCAAGTGCAA	0.642													G|||	1802	0.359824	0.3396	0.2349	5008	,	,		15983	0.4137		0.2773	False		,,,				2504	0.5051				p.T1274A		Atlas-SNP	.											.	PDZD2	306	.	0			c.A3820G						PASS	.	G	ALA/THR	1489,2917	674.5+/-402.9	239,1011,953	64.0	75.0	71.0		3820	-5.2	0.0	5	dbSNP_79	71	1988,6612	721.7+/-406.4	244,1500,2556	yes	missense	PDZD2	NM_178140.2	58	483,2511,3509	GG,GA,AA		23.1163,33.7948,26.7338	benign	1274/2840	32087374	3477,9529	2203	4300	6503	SO:0001583	missense	23037	exon19			AGGGTCACCAAGT	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3820A>G	5.37:g.32087374A>G	ENSP00000402033:p.Thr1274Ala	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	134	57	0.425373	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	718	0.32875457875457875	172	0.34959349593495936	91	0.2513812154696133	239	0.4178321678321678	216	0.2849604221635884	G	2.516	-0.311796	0.05422	0.337948	0.231163	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.05855	3.38;3.38	3.67	-5.16	0.02857	.	0.732309	0.11815	N	0.526814	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	0.40289	-0.9571	9	0.06494	T	0.89	.	2.0276	0.03523	0.1219:0.2193:0.3799:0.2789	rs157496;rs527617;rs1175728;rs3822361;rs56556053;rs60698662;rs157496	1274	O15018	PDZD2_HUMAN	A	1274;1075;1274	ENSP00000402033:T1274A;ENSP00000282493:T1274A	ENSP00000282493:T1274A	T	+	1	0	PDZD2	32123131	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.248000	0.01189	-1.500000	0.01819	-1.493000	0.00968	ACC	A|0.706;G|0.294	0.294	strong		0.642	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
NOL10	79954	hgsc.bcm.edu	37	2	10712278	10712278	+	Silent	SNP	C	C	T	rs3732114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10712278C>T	ENST00000381685.5	-	21	2091	c.1986G>A	c.(1984-1986)ctG>ctA	p.L662L	NOL10_ENST00000345985.3_Silent_p.L612L|NOL10_ENST00000538384.1_Silent_p.L636L|NOL10_ENST00000542668.1_Silent_p.L612L	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	662						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		CTTGTCGATGCAGTTTCTCAG	0.443													C|||	1535	0.30651	0.5	0.3156	5008	,	,		19280	0.4335		0.1183	False		,,,				2504	0.1012				p.L662L		Atlas-SNP	.											.	NOL10	22	.	0			c.G1986A						PASS	.	C		2024,2382	563.2+/-381.1	482,1060,661	222.0	216.0	218.0		1986	4.0	1.0	2	dbSNP_107	218	955,7645	208.2+/-249.7	55,845,3400	no	coding-synonymous	NOL10	NM_024894.2		537,1905,4061	TT,TC,CC		11.1047,45.9374,22.9048		662/689	10712278	2979,10027	2203	4300	6503	SO:0001819	synonymous_variant	79954	exon21			TCGATGCAGTTTC	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1986G>A	2.37:g.10712278C>T		Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	341	175	0.513196	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Silent	SNP	ENST00000381685.5	37	CCDS1673.2																																																																																			C|0.730;T|0.270	0.270	strong		0.443	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
B9D1	27077	hgsc.bcm.edu	37	17	19246667	19246667	+	Silent	SNP	A	A	G	rs7212549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19246667A>G	ENST00000261499.4	-	7	723	c.580T>C	c.(580-582)Ttg>Ctg	p.L194L	B9D1_ENST00000477478.2_3'UTR|MIR1180_ENST00000408613.1_RNA|B9D1_ENST00000461069.2_Intron|B9D1_ENST00000575403.1_Intron|B9D1_ENST00000395615.1_3'UTR	NM_015681.3	NP_056496.1	Q9UPM9	B9D1_HUMAN	B9 protein domain 1	194					camera-type eye development (GO:0043010)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|in utero embryonic development (GO:0001701)|neuroepithelial cell differentiation (GO:0060563)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)|vasculature development (GO:0001944)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)	hedgehog receptor activity (GO:0008158)			large_intestine(3)|urinary_tract(1)	4	all_cancers(12;2.04e-05)|all_epithelial(12;0.000806)|Hepatocellular(7;0.00345)|Breast(13;0.143)					CTGGGCCCCAACACACCCTGT	0.587													A|||	153	0.0305511	0.0514	0.0029	5008	,	,		18629	0.0079		0.0	False		,,,				2504	0.0767				p.L194L		Atlas-SNP	.											.	B9D1	8	.	0			c.T580C						PASS	.	A		172,4234	113.8+/-151.8	1,170,2032	75.0	68.0	70.0		580	-2.2	0.0	17	dbSNP_116	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	B9D1	NM_015681.3		1,171,6331	GG,GA,AA		0.0116,3.9038,1.3302		194/205	19246667	173,12833	2203	4300	6503	SO:0001819	synonymous_variant	27077	exon7			GCCCCAACACACC	BC002944	CCDS11205.1, CCDS58528.1	17p11.2	2014-09-17			ENSG00000108641	ENSG00000108641			24123	protein-coding gene	gene with protein product	"""endothelial precursor protein B9"""	614144				21493627	Standard	NM_015681		Approved	B9, EPPB9, MKS9	uc010vyr.2	Q9UPM9	OTTHUMG00000059586	ENST00000261499.4:c.580T>C	17.37:g.19246667A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_015681	Q9BU22	Silent	SNP	ENST00000261499.4	37	CCDS11205.1																																																																																			A|0.980;G|0.020	0.020	strong		0.587	B9D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132494.1	NM_015681	
PDK2	5164	hgsc.bcm.edu	37	17	48174908	48174908	+	Silent	SNP	C	C	T	rs9839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48174908C>T	ENST00000503176.1	+	2	401	c.240C>T	c.(238-240)tcC>tcT	p.S80S	PDK2_ENST00000007708.3_Silent_p.S16S	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	80				S -> T (in Ref. 1; AAC42010). {ECO:0000305}.	cellular metabolic process (GO:0044237)|cellular response to nutrient (GO:0031670)|cellular response to reactive oxygen species (GO:0034614)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of gluconeogenesis (GO:0006111)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						GCACACCCTCCGTGCAGCTGG	0.607									Autosomal Dominant Polycystic Kidney Disease				T|||	2179	0.435104	0.4932	0.4395	5008	,	,		22189	0.38		0.2783	False		,,,				2504	0.5716				p.S80S		Atlas-SNP	.											PDK2,NS,carcinoma,0,1	PDK2	41	1	0			c.C240T						PASS	.	T	,,,	2092,2314	605.2+/-390.5	499,1094,610	78.0	65.0	69.0		48,48,240,240	-7.4	0.8	17	dbSNP_105	69	2532,6068	692.8+/-404.6	370,1792,2138	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDK2	NM_001199898.1,NM_001199899.1,NM_001199900.1,NM_002611.4	,,,	869,2886,2748	TT,TC,CC		29.4419,47.4807,35.5528	,,,	16/344,16/344,80/200,80/408	48174908	4624,8382	2203	4300	6503	SO:0001819	synonymous_variant	5164	exon2	Familial Cancer Database	ADPKD	ACCCTCCGTGCAG	L42451	CCDS11559.1, CCDS56039.1	17q21.33	2012-07-18	2005-11-16		ENSG00000005882	ENSG00000005882			8810	protein-coding gene	gene with protein product		602525	"""pyruvate dehydrogenase kinase, isoenzyme 2"""			7499431	Standard	NM_001199898		Approved	PDHK2	uc002iqc.3	Q15119	OTTHUMG00000161948	ENST00000503176.1:c.240C>T	17.37:g.48174908C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_002611	A8K3A7|B3KNW0|Q6P515|Q9BS05	Silent	SNP	ENST00000503176.1	37	CCDS11559.1																																																																																			C|0.639;T|0.361	0.361	strong		0.607	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2	NM_002611	
ZBED5	58486	hgsc.bcm.edu	37	11	10875701	10875701	+	Silent	SNP	A	A	G	rs2232922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:10875701A>G	ENST00000432999.2	-	3	1290	c.792T>C	c.(790-792)gtT>gtC	p.V264V	ZBED5_ENST00000525350.1_Intron|ZBED5_ENST00000413761.2_Silent_p.V264V	NM_001143667.1|NM_021211.3	NP_001137139.1|NP_067034.2	Q49AG3	ZBED5_HUMAN	zinc finger, BED-type containing 5	264							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)	4						tcagtctacaaacaagctctt	0.378													A|||	417	0.0832668	0.2935	0.0346	5008	,	,		21684	0.0		0.005	False		,,,				2504	0.0				p.V264V		Atlas-SNP	.											.	ZBED5	50	.	0			c.T792C						PASS	.	A	,	366,1018		53,260,379	117.0	95.0	101.0		792,792	3.0	1.0	11	dbSNP_98	101	9,3173		0,9,1582	no	coding-synonymous,coding-synonymous	ZBED5	NM_001143667.1,NM_021211.3	,	53,269,1961	GG,GA,AA		0.2828,26.4451,8.2129	,	264/694,264/694	10875701	375,4191	692	1591	2283	SO:0001819	synonymous_variant	58486	exon3			TCTACAAACAAGC	AF205601		11p15.3	2013-05-03			ENSG00000236287	ENSG00000236287		"""Zinc fingers, BED-type"""	30803	protein-coding gene	gene with protein product		615251				10607616, 23533661	Standard	NM_021211		Approved	Buster1	uc009ygh.3	Q49AG3	OTTHUMG00000150341	ENST00000432999.2:c.792T>C	11.37:g.10875701A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_021211	B2RCC1|Q05D82|Q86WW3|Q9NT24|Q9UBJ4	Silent	SNP	ENST00000432999.2	37																																																																																				A|0.896;G|0.104	0.104	strong		0.378	ZBED5-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000317691.1	NM_021211	
ZNF34	80778	hgsc.bcm.edu	37	8	145999080	145999080	+	Silent	SNP	G	G	A	rs7845196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145999080G>A	ENST00000343459.4	-	6	1319	c.1254C>T	c.(1252-1254)ccC>ccT	p.P418P	ZNF34_ENST00000429371.2_Silent_p.P397P			Q8IZ26	ZNF34_HUMAN	zinc finger protein 34	418					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)		TACATTTATAGGGTTTCTCTC	0.413													G|||	388	0.077476	0.2821	0.0216	5008	,	,		20084	0.0		0.0	False		,,,				2504	0.0				p.P418P		Atlas-SNP	.											.	ZNF34	38	.	0			c.C1254T						PASS	.	G		1055,3333	340.7+/-306.4	138,779,1277	49.0	53.0	52.0		1254	1.5	1.0	8	dbSNP_116	52	7,8589	4.3+/-15.6	0,7,4291	no	coding-synonymous	ZNF34	NM_030580.3		138,786,5568	AA,AG,GG		0.0814,24.0428,8.1793		418/561	145999080	1062,11922	2194	4298	6492	SO:0001819	synonymous_variant	80778	exon6			TTTATAGGGTTTC	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.1254C>T	8.37:g.145999080G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	161	85	0.52795	NM_030580	D3DWN1|Q9BSZ0	Silent	SNP	ENST00000343459.4	37	CCDS47945.1																																																																																			G|0.927;A|0.073	0.073	strong		0.413	ZNF34-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382936.1	NM_030580	
LPCAT3	10162	hgsc.bcm.edu	37	12	7125672	7125672	+	Silent	SNP	C	C	G	rs61733160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7125672C>G	ENST00000261407.4	-	1	142	c.57G>C	c.(55-57)ctG>ctC	p.L19L	C1S_ENST00000406697.1_Intron	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	19					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						AACCCGACTGCAGAACCCCCG	0.667													C|||	254	0.0507188	0.1142	0.0216	5008	,	,		-128	0.0188		0.0258	False		,,,				2504	0.044				p.L19L		Atlas-SNP	.											.	LPCAT3	33	.	0			c.G57C						PASS	.	C		419,3987	176.2+/-205.4	18,383,1802	43.0	43.0	43.0		57	3.2	0.0	12	dbSNP_129	43	161,8439	66.7+/-129.0	0,161,4139	no	coding-synonymous	LPCAT3	NM_005768.5		18,544,5941	GG,GC,CC		1.8721,9.5098,4.4595		19/488	7125672	580,12426	2203	4300	6503	SO:0001819	synonymous_variant	10162	exon1			CGACTGCAGAACC	U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"""O-acyltransferase (membrane bound) domain containing 5"", ""membrane bound O-acyltransferase domain containing 5"""	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970	ENST00000261407.4:c.57G>C	12.37:g.7125672C>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	NM_005768	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Silent	SNP	ENST00000261407.4	37	CCDS8572.1																																																																																			C|0.950;G|0.050	0.050	strong		0.667	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768	
KRT33A	3883	hgsc.bcm.edu	37	17	39502398	39502398	+	Silent	SNP	A	A	G	rs16966703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39502398A>G	ENST00000007735.3	-	7	1232	c.1188T>C	c.(1186-1188)tgT>tgC	p.C396C		NM_004138.3	NP_004129.2	O76009	KT33A_HUMAN	keratin 33A	396	Tail.					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)				TGCAAGGCCCACACCGAGCAC	0.557													G|||	626	0.125	0.3321	0.0519	5008	,	,		17134	0.0506		0.0795	False		,,,				2504	0.0204				p.C396C		Atlas-SNP	.											.	KRT33A	53	.	0			c.T1188C						PASS	.	G		1306,3100	698.4+/-406.3	207,892,1104	136.0	120.0	126.0		1188	0.2	0.6	17	dbSNP_123	126	753,7847	785.3+/-407.6	28,697,3575	no	coding-synonymous	KRT33A	NM_004138.2		235,1589,4679	GG,GA,AA		8.7558,29.6414,15.8312		396/405	39502398	2059,10947	2203	4300	6503	SO:0001819	synonymous_variant	3883	exon7			AGGCCCACACCGA	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.1188T>C	17.37:g.39502398A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	190	190	1	NM_004138	B2RA87|Q6NTB9|Q6ZZB9	Silent	SNP	ENST00000007735.3	37	CCDS11388.1																																																																																			A|0.854;G|0.146	0.146	strong		0.557	KRT33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257295.1	NM_004138	
ANKZF1	55139	hgsc.bcm.edu	37	2	220097257	220097257	+	Missense_Mutation	SNP	G	G	C	rs61747682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220097257G>C	ENST00000323348.5	+	5	584	c.410G>C	c.(409-411)aGt>aCt	p.S137T	ATG9A_ENST00000409422.1_5'Flank|ATG9A_ENST00000361242.4_5'Flank|ANKZF1_ENST00000409849.1_5'UTR|ATG9A_ENST00000396761.2_5'Flank|ANKZF1_ENST00000410034.3_Missense_Mutation_p.S137T	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	137						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GACTCAGCCAGTGAGGAGGAC	0.488													g|||	261	0.0521166	0.0998	0.0115	5008	,	,		20738	0.0893		0.0179	False		,,,				2504	0.0133				p.S137T		Atlas-SNP	.											.	ANKZF1	45	.	0			c.G410C						PASS	.	G	THR/SER,THR/SER	392,3474		23,346,1564	66.0	68.0	68.0		410,410	2.6	1.0	2	dbSNP_129	68	91,8165		0,91,4037	yes	missense,missense	ANKZF1	NM_001042410.1,NM_018089.2	58,58	23,437,5601	CC,CG,GG		1.1022,10.1397,3.9845	possibly-damaging,possibly-damaging	137/727,137/727	220097257	483,11639	1933	4128	6061	SO:0001583	missense	55139	exon5			CAGCCAGTGAGGA	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"""Zinc fingers, C2H2-type"", ""Ankyrin repeat domain containing"""	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.410G>C	2.37:g.220097257G>C	ENSP00000321617:p.Ser137Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	117	69	0.589744	NM_001042410	Q9NVZ4	Missense_Mutation	SNP	ENST00000323348.5	37	CCDS42821.1	126	0.057692307692307696	48	0.0975609756097561	5	0.013812154696132596	59	0.10314685314685315	14	0.018469656992084433	G	12.96	2.094842	0.36952	0.101397	0.011022	ENSG00000163516	ENST00000323348;ENST00000453432;ENST00000410034;ENST00000447157	T;T	0.29917	1.55;1.55	5.53	2.64	0.31445	.	0.404321	0.32287	N	0.006307	T	0.00695	0.0023	M	0.63843	1.955	0.35399	P	0.20854399999999995	B;B	0.25809	0.135;0.083	B;B	0.24701	0.055;0.025	T	0.09684	-1.0663	9	0.22109	T	0.4	-1.5062	10.0904	0.42443	0.0718:0.2607:0.6675:0.0	rs61747682	81;137	B4DZT1;Q9H8Y5	.;ANKZ1_HUMAN	T	137;72;137;137	ENSP00000321617:S137T;ENSP00000386337:S137T	ENSP00000321617:S137T	S	+	2	0	ANKZF1	219805501	0.845000	0.29573	1.000000	0.80357	0.988000	0.76386	1.130000	0.31393	1.546000	0.49388	0.655000	0.94253	AGT	G|0.960;C|0.040	0.040	strong		0.488	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261793	39261793	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39261793G>A	ENST00000391415.1	+	1	210	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	51	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						GCTGCTGCAGGCCCCAGTGCT	0.647																																					p.R51R		Atlas-SNP	.											.	KRTAP4-9	110	.	0			c.G153A						PASS	.						16.0	23.0	21.0					17																	39261793		686	1591	2277	SO:0001819	synonymous_variant	100132386	exon1			CTGCAGGCCCCAG	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.153G>A	17.37:g.39261793G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	76	14	0.184211	NM_001146041		Silent	SNP	ENST00000391415.1	37	CCDS54124.1																																																																																			.	.	none		0.647	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
ZNF157	7712	hgsc.bcm.edu	37	X	47272970	47272970	+	Missense_Mutation	SNP	A	A	G	rs61736398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47272970A>G	ENST00000377073.3	+	4	1584	c.1498A>G	c.(1498-1500)Aca>Gca	p.T500A		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	500					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)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						CTGGCGTTGTACAATGAAGAA	0.493													A|||	37	0.00980132	0.025	0.0043	3775	,	,		14772	0.0		0.001	False		,,,				2504	0.0				p.T500A		Atlas-SNP	.											.	ZNF157	46	.	0			c.A1498G						PASS	.	A	ALA/THR	191,3644		3,153,32,1476,539	71.0	60.0	64.0		1498	-2.0	0.0	X	dbSNP_129	64	5,6723		0,4,1,2424,1871	yes	missense	ZNF157	NM_003446.3	58	3,157,33,3900,2410	GG,GA,G,AA,A		0.0743,4.9804,1.8555	benign	500/507	47272970	196,10367	2203	4300	6503	SO:0001583	missense	7712	exon4			CGTTGTACAATGA	U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"""Zinc fingers, C2H2-type"", ""-"""	12942	protein-coding gene	gene with protein product		300024	"""zinc finger protein 157 (HZF22)"""			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.1498A>G	X.37:g.47272970A>G	ENSP00000366273:p.Thr500Ala	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	139	53	0.381295	NM_003446	Q96LE9	Missense_Mutation	SNP	ENST00000377073.3	37	CCDS14278.1	12	0.007233273056057866	4	0.008264462809917356	2	0.005555555555555556	0	0.0	1	0.0013192612137203166	A	2.829	-0.243005	0.05906	0.049804	7.43E-4	ENSG00000147117	ENST00000377073	T	0.06068	3.35	2.85	-1.99	0.07457	.	.	.	.	.	T	0.00637	0.0021	N	0.16790	0.44	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28808	-1.0032	8	0.59425	D	0.04	.	9.8782	0.41216	0.2684:0.0:0.7316:0.0	rs61736398	500	P51786	ZN157_HUMAN	A	500	ENSP00000366273:T500A	ENSP00000366273:T500A	T	+	1	0	ZNF157	47157914	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.258000	0.08733	-0.564000	0.06070	-0.466000	0.05196	ACA	A|0.984;G|0.016	0.016	strong		0.493	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446	
TRPM5	29850	hgsc.bcm.edu	37	11	2428434	2428434	+	Silent	SNP	G	G	A	rs369339407		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2428434G>A	ENST00000155858.6	-	20	3041	c.3033C>T	c.(3031-3033)gcC>gcT	p.A1011A	TRPM5_ENST00000533060.1_Silent_p.A1011A|TRPM5_ENST00000528453.1_Silent_p.A1011A|AC124057.5_ENST00000433035.1_RNA|TRPM5_ENST00000452833.1_Silent_p.A1013A	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)		TGAAGGGCGGGGCCAGGGCGG	0.637																																					p.A1011A	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.C3033T						PASS	.						35.0	34.0	34.0					11																	2428434		2198	4299	6497	SO:0001819	synonymous_variant	29850	exon20			GGGCGGGGCCAGG	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.3033C>T	11.37:g.2428434G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	123	70	0.569106	NM_014555		Silent	SNP	ENST00000155858.6	37	CCDS31340.1																																																																																			.	.	weak		0.637	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
ZNF99	7652	hgsc.bcm.edu	37	19	22941617	22941617	+	Missense_Mutation	SNP	T	T	C	rs58653025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22941617T>C	ENST00000596209.1	-	4	1184	c.1094A>G	c.(1093-1095)gAa>gGa	p.E365G	ZNF99_ENST00000397104.3_Missense_Mutation_p.E274G	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	365					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.E274G(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GGGTTTCTCTTCAGTATGAAT	0.368													C|||	1087	0.217053	0.4206	0.1326	5008	,	,		19505	0.1746		0.1362	False		,,,				2504	0.1288				p.E365G		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	1	1	Substitution - Missense(1)	stomach(1)	c.A1094G						scavenged	.	C	GLY/GLU	1432,2612		250,932,840	69.0	77.0	74.0		821	0.3	0.0	19	dbSNP_129	74	994,7436		67,860,3288	no	missense	ZNF99	NM_001080409.2	98	317,1792,4128	CC,CT,TT		11.7912,35.4105,19.4485	benign	274/912	22941617	2426,10048	2022	4215	6237	SO:0001583	missense	7652	exon4			TTCTCTTCAGTAT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1094A>G	19.37:g.22941617T>C	ENSP00000472969:p.Glu365Gly	Somatic	32	1	0.03125		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	454	0.2078754578754579	203	0.41260162601626016	54	0.14917127071823205	104	0.18181818181818182	93	0.12269129287598944	-	0.008	-1.877054	0.00537	0.354105	0.117912	ENSG00000213973	ENST00000397104	T	0.11821	2.74	1.46	0.302	0.15786	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00496	-1.435	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.44498	-0.9324	8	0.02654	T	1	.	6.1729	0.20427	0.0:0.6931:0.0:0.3069	rs58653025	274	A8MXY4	ZNF99_HUMAN	G	274	ENSP00000380293:E274G	ENSP00000380293:E274G	E	-	2	0	ZNF99	22733457	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.130000	0.10498	-0.501000	0.06605	-0.526000	0.04340	GAA	T|0.811;C|0.189	0.189	strong		0.368	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
IGSF22	283284	hgsc.bcm.edu	37	11	18735947	18735947	+	Missense_Mutation	SNP	T	T	C	rs386751189|rs7125943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18735947T>C	ENST00000513874.1	-	13	1814	c.1675A>G	c.(1675-1677)Atg>Gtg	p.M559V	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	559			M -> V (in dbSNP:rs7125943). {ECO:0000269|PubMed:14702039}.							NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						ACAATCTGCATGCCTGGCAAG	0.602													C|||	3787	0.75619	0.851	0.7075	5008	,	,		20261	0.8125		0.7783	False		,,,				2504	0.5818				p.M559V		Atlas-SNP	.											.	IGSF22	211	.	0			c.A1675G						PASS	.	C	VAL/MET	3391,765		1383,625,70	101.0	107.0	105.0		1675	-2.1	0.0	11	dbSNP_116	105	6295,2107		2362,1571,268	yes	missense	IGSF22	NM_173588.3	21	3745,2196,338	CC,CT,TT		25.0774,18.4071,22.8699	benign	559/1327	18735947	9686,2872	2078	4201	6279	SO:0001583	missense	283284	exon13			TCTGCATGCCTGG	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1675A>G	11.37:g.18735947T>C	ENSP00000421191:p.Met559Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	1730	0.7921245421245421	418	0.8495934959349594	266	0.7348066298342542	461	0.8059440559440559	585	0.7717678100263852	C	0.003	-2.461414	0.00171	0.815929	0.749226	ENSG00000179057	ENST00000513874	T	0.37915	1.17	4.42	-2.12	0.07165	.	0.599024	0.12707	N	0.445853	T	0.00012	0.0000	N	0.00778	-1.195	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25779	-1.0122	9	0.12766	T	0.61	.	11.1401	0.48398	0.0:0.2996:0.0:0.7004	rs7125943;rs52828196;rs57257526;rs7125943	559	D6RGV7	.	V	559	ENSP00000421191:M559V	ENSP00000322422:M559V	M	-	1	0	IGSF22	18692523	0.001000	0.12720	0.001000	0.08648	0.392000	0.30506	-0.173000	0.09854	-0.897000	0.03910	-0.954000	0.02651	ATG	T|0.224;C|0.776	0.776	strong		0.602	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
PCDH15	65217	hgsc.bcm.edu	37	10	55955610	55955610	+	Missense_Mutation	SNP	C	C	T	rs10825269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:55955610C>T	ENST00000320301.6	-	11	1532	c.1138G>A	c.(1138-1140)Ggt>Agt	p.G380S	PCDH15_ENST00000395438.1_Missense_Mutation_p.G380S|PCDH15_ENST00000395430.1_Missense_Mutation_p.G380S|PCDH15_ENST00000414778.1_Missense_Mutation_p.G385S|PCDH15_ENST00000361849.3_Missense_Mutation_p.G380S|PCDH15_ENST00000395432.2_Missense_Mutation_p.G343S|PCDH15_ENST00000373957.3_Missense_Mutation_p.G358S|PCDH15_ENST00000395446.1_Missense_Mutation_p.G380S|PCDH15_ENST00000437009.1_Missense_Mutation_p.G380S|PCDH15_ENST00000395445.1_Missense_Mutation_p.G380S|PCDH15_ENST00000409834.1_5'UTR|PCDH15_ENST00000395440.1_Missense_Mutation_p.G380S|PCDH15_ENST00000373965.2_Missense_Mutation_p.G380S|PCDH15_ENST00000373955.1_Missense_Mutation_p.G380S|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.G358S	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	380	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		G -> S (in dbSNP:rs10825269). {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)				ATGTGTAGACCGGCAAAGGCA	0.383										HNSCC(58;0.16)			T|||	1218	0.243211	0.4871	0.2104	5008	,	,		16076	0.0863		0.1382	False		,,,				2504	0.2065				p.G385S		Atlas-SNP	.											.	PCDH15	1715	.	0			c.G1153A						PASS	.	T	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	1947,2459	622.6+/-394.0	442,1063,698	127.0	122.0	124.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1153,1138,1138,1138,1027,1072,1153,1138,1153,1138,1072,1138	5.2	1.0	10	dbSNP_120	124	1101,7499	768.8+/-407.6	65,971,3264	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	56,56,56,56,56,56,56,56,56,56,56,56	507,2034,3962	TT,TC,CC		12.8023,44.1897,23.4353	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	385/1963,380/1958,380/1887,380/1953,343/1916,358/1936,385/1791,380/1540,385/1683,380/1678,358/1933,380/1956	55955610	3048,9958	2203	4300	6503	SO:0001583	missense	65217	exon12			GTAGACCGGCAAA	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.1138G>A	10.37:g.55955610C>T	ENSP00000322604:p.Gly380Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	454	0.2078754578754579	235	0.47764227642276424	68	0.1878453038674033	49	0.08566433566433566	102	0.1345646437994723	T	5.780	0.328284	0.10956	0.441897	0.128023	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;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	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;2.53;1.25;1.25;1.25;1.25;1.25;1.25;1.25	5.17	5.17	0.71159	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.11201	0.11	0.51767	P	7.00000000000145E-5	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.16396	0.017;0.004;0.004;0.007;0.004;0.007;0.017;0.0;0.014;0.014;0.0;0.0;0.0;0.001;0.007	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.09377	0.004;0.002;0.002;0.003;0.003;0.002;0.004;0.0;0.003;0.003;0.0;0.0;0.001;0.001;0.002	T	0.41448	-0.9508	8	0.05959	T	0.93	.	10.7228	0.46050	0.0:0.0763:0.0:0.9237	rs10825269;rs52818022;rs59807776;rs10825269	358;380;380;385;380;343;380;380;380;380;380;385;380;358;380	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	S	380;385;380;380;380;380;380;343;380;358;358;380;380;385;380;380	ENSP00000363076:G380S;ENSP00000410304:G385S;ENSP00000378826:G380S;ENSP00000378832:G380S;ENSP00000378833:G380S;ENSP00000378827:G380S;ENSP00000378820:G343S;ENSP00000354950:G380S;ENSP00000378821:G358S;ENSP00000363068:G358S;ENSP00000322604:G380S;ENSP00000378818:G380S;ENSP00000412628:G380S;ENSP00000363066:G380S	ENSP00000322604:G380S	G	-	1	0	PCDH15	55625616	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	2.210000	0.42816	0.823000	0.34589	-0.332000	0.08345	GGT	C|0.772;T|0.228	0.228	strong		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
AR	367	hgsc.bcm.edu	37	X	66765627	66765627	+	Silent	SNP	G	G	A	rs6152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:66765627G>A	ENST00000374690.3	+	1	1163	c.639G>A	c.(637-639)gaG>gaA	p.E213E	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Silent_p.E213E|AR_ENST00000504326.1_Silent_p.E213E	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	211	Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	GAGCGAGGGAGGCCTCGGGGG	0.572									Androgen Insensitivity Syndrome				g|||	901	0.238675	0.4932	0.1023	3775	,	,		13539	0.002		0.1083	False		,,,				2504	0.0685				p.E213E		Atlas-SNP	.											.	AR	249	.	0			c.G639A	GRCh37	CM051843	AR	M	rs6152	PASS	.			2312,1523		588,793,343,251,228	34.0	34.0	34.0	http://omim.org/entry/300710	639	3.0	1.0	X	dbSNP_52	34	1057,5671		56,625,320,1747,1552	no	coding-synonymous	AR	NM_000044.3		644,1418,663,1998,1780	AA,AG,A,GG,G		15.7105,39.7132,31.8943		213/921	66765627	3369,7194	2203	4300	6503	SO:0001819	synonymous_variant	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GAGGGAGGCCTCG	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.639G>A	X.37:g.66765627G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent	SNP	ENST00000374690.3	37	CCDS14387.1																																																																																			G|0.700;A|0.300	0.300	strong		0.572	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
USP33	23032	hgsc.bcm.edu	37	1	78201745	78201745	+	Silent	SNP	G	G	T	rs2296227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:78201745G>T	ENST00000370793.1	-	7	889	c.543C>A	c.(541-543)gcC>gcA	p.A181A	USP33_ENST00000370792.3_Silent_p.A181A|USP33_ENST00000357428.1_Silent_p.A181A|USP33_ENST00000370794.3_Silent_p.A150A	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	181					axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						ATTTACCTCTGGCCCTAAGTT	0.358													T|||	2451	0.489417	0.7451	0.2608	5008	,	,		15784	0.4077		0.332	False		,,,				2504	0.5521				p.A181A	Melanoma(152;72 1870 11110 26780 42647)	Atlas-SNP	.											.	USP33	87	.	0			c.C543A						PASS	.	T	,,	2980,1426	464.3+/-353.8	1026,928,249	126.0	121.0	123.0		543,450,543	1.3	1.0	1	dbSNP_100	123	2594,6006	688.8+/-404.3	428,1738,2134	no	coding-synonymous,coding-synonymous,coding-synonymous	USP33	NM_015017.3,NM_201624.1,NM_201626.1	,,	1454,2666,2383	TT,TG,GG		30.1628,32.365,42.8571	,,	181/943,150/912,181/829	78201745	5574,7432	2203	4300	6503	SO:0001819	synonymous_variant	23032	exon7			ACCTCTGGCCCTA	AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"""Ubiquitin-specific peptidases"""	20059	protein-coding gene	gene with protein product		615146	"""ubiquitin specific protease 33"""			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.543C>A	1.37:g.78201745G>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	155	155	1	NM_201626	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Silent	SNP	ENST00000370793.1	37	CCDS678.1																																																																																			G|0.550;T|0.450	0.450	strong		0.358	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017	
ZNF613	79898	hgsc.bcm.edu	37	19	52448669	52448669	+	Silent	SNP	G	G	C	rs11880193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52448669G>C	ENST00000293471.6	+	6	2212	c.1533G>C	c.(1531-1533)ccG>ccC	p.P511P	ZNF613_ENST00000601794.1_3'UTR|ZNF613_ENST00000391794.4_Silent_p.P475P	NM_001031721.3	NP_001026891.2	Q6PF04	ZN613_HUMAN	zinc finger protein 613	511					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(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	19		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		GGGAGAGACCGTATGGATGCT	0.448													C|||	1011	0.201877	0.3654	0.1225	5008	,	,		23946	0.0317		0.1074	False		,,,				2504	0.3098				p.P511P		Atlas-SNP	.											.	ZNF613	62	.	0			c.G1533C						PASS	.	C	,	1287,3119	699.8+/-406.5	175,937,1091	98.0	76.0	84.0		1533,1425	-0.6	0.4	19	dbSNP_120	84	943,7657	776.0+/-407.7	58,827,3415	no	coding-synonymous,coding-synonymous	ZNF613	NM_001031721.3,NM_024840.3	,	233,1764,4506	CC,CG,GG		10.9651,29.2102,17.1459	,	511/618,475/582	52448669	2230,10776	2203	4300	6503	SO:0001819	synonymous_variant	79898	exon6			GAGACCGTATGGA	AK027565	CCDS12844.1, CCDS33089.1	19q13.41	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	25827	protein-coding gene	gene with protein product						12477932	Standard	NM_001031721		Approved	FLJ13590	uc002pxz.2	Q6PF04		ENST00000293471.6:c.1533G>C	19.37:g.52448669G>C		Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	150	150	1	NM_001031721	Q96SS9	Silent	SNP	ENST00000293471.6	37	CCDS33089.1																																																																																			G|0.841;C|0.159	0.159	strong		0.448	ZNF613-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461104.2	NM_024840	
CMYA5	202333	hgsc.bcm.edu	37	5	79030346	79030346	+	Missense_Mutation	SNP	A	A	G	rs16877151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79030346A>G	ENST00000446378.2	+	2	5789	c.5758A>G	c.(5758-5760)Agc>Ggc	p.S1920G		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1920	Poly-Ser.		S -> G (in dbSNP:rs16877151). {ECO:0000269|PubMed:15489334}.		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)		GGATTCCTCTAGCAGCAATGA	0.493													G|||	1378	0.27516	0.5877	0.085	5008	,	,		18729	0.3621		0.0815	False		,,,				2504	0.0971				p.S1920G		Atlas-SNP	.											.	CMYA5	643	.	0			c.A5758G						PASS	.	G	GLY/SER	1940,1962		484,972,495	44.0	44.0	44.0		5758	4.3	0.0	5	dbSNP_123	44	716,7564		40,636,3464	yes	missense	CMYA5	NM_153610.3	56	524,1608,3959	GG,GA,AA		8.6473,49.7181,21.8027	benign	1920/4070	79030346	2656,9526	1951	4140	6091	SO:0001583	missense	202333	exon2			TCCTCTAGCAGCA	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.5758A>G	5.37:g.79030346A>G	ENSP00000394770:p.Ser1920Gly	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	216	214	0.990741	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	625	0.28617216117216115	303	0.6158536585365854	31	0.0856353591160221	232	0.40559440559440557	59	0.07783641160949868	G	0.516	-0.864257	0.02590	0.497181	0.086473	ENSG00000164309	ENST00000446378	T	0.03772	3.81	6.06	4.28	0.50868	.	0.658361	0.13491	N	0.384018	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35076	-0.9803	9	0.02654	T	1	.	6.6284	0.22843	0.1568:0.1467:0.6965:0.0	rs16877151;rs16877151	1920	Q8N3K9	CMYA5_HUMAN	G	1920	ENSP00000394770:S1920G	ENSP00000394770:S1920G	S	+	1	0	CMYA5	79066102	0.001000	0.12720	0.005000	0.12908	0.000000	0.00434	0.743000	0.26231	0.455000	0.26910	-0.828000	0.03084	AGC	A|0.702;G|0.298	0.298	strong		0.493	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
OR2S2	56656	hgsc.bcm.edu	37	9	35957728	35957728	+	Missense_Mutation	SNP	C	C	T	rs2233563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35957728C>T	ENST00000341959.2	-	1	423	c.368G>A	c.(367-369)cGc>cAc	p.R123H		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	123			R -> H (in dbSNP:rs2233563).		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)			GGCCACATAGCGATCAAATGC	0.557													C|||	122	0.024361	0.0915	0.0014	5008	,	,		24963	0.0		0.0	False		,,,				2504	0.0				p.R123H	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											.	OR2S2	46	.	0			c.G368A						PASS	.	C	HIS/ARG	351,4055	182.9+/-210.6	14,323,1866	94.0	80.0	85.0		368	0.8	0.2	9	dbSNP_98	85	3,8597	3.0+/-9.4	0,3,4297	yes	missense	OR2S2	NM_019897.2	29	14,326,6163	TT,TC,CC		0.0349,7.9664,2.7218	possibly-damaging	123/320	35957728	354,12652	2203	4300	6503	SO:0001583	missense	56656	exon1			ACATAGCGATCAA	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.368G>A	9.37:g.35957728C>T	ENSP00000344040:p.Arg123His	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	100	57	0.57	NM_019897	Q2M3L0|Q6IF19|Q96R42	Missense_Mutation	SNP	ENST00000341959.2	37	CCDS6596.2	45	0.020604395604395604	45	0.09146341463414634	0	0.0	0	0.0	0	0.0	C	10.24	1.295956	0.23650	0.079664	3.49E-4	ENSG00000122718	ENST00000341959	T	0.77489	-1.1	4.32	0.775	0.18527	GPCR, rhodopsin-like superfamily (1);	0.388525	0.22144	N	0.064012	T	0.11110	0.0271	M	0.88310	2.945	0.25060	N	0.991077	P	0.47034	0.889	B	0.36504	0.226	T	0.48747	-0.9008	10	0.72032	D	0.01	.	8.045	0.30545	0.0:0.6808:0.0:0.3192	rs2233563;rs2233563	123	Q9NQN1	OR2S1_HUMAN	H	123	ENSP00000344040:R123H	ENSP00000344040:R123H	R	-	2	0	OR2S2	35947728	0.990000	0.36364	0.195000	0.23364	0.101000	0.19017	1.416000	0.34759	0.125000	0.18397	0.655000	0.94253	CGC	C|0.975;T|0.025	0.025	strong		0.557	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897	
PAK7	57144	hgsc.bcm.edu	37	20	9543622	9543622	+	Missense_Mutation	SNP	C	C	T	rs2297345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	104	0	0		WXS	Illumina HiSeq	Phase_I	97	56	0.57732	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		
MUC5B	727897	hgsc.bcm.edu	37	11	1268513	1268513	+	Missense_Mutation	SNP	G	G	C	rs2943529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1268513G>C	ENST00000529681.1	+	31	10461	c.10403G>C	c.(10402-10404)cGc>cCc	p.R3468P	MUC5B_ENST00000447027.1_Missense_Mutation_p.R3471P|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3468	7 X Cys-rich subdomain repeats.|Thr-rich.		R -> P (in dbSNP:rs2943529). {ECO:0000269|PubMed:9013550}.	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)		CACACGGTGCGCACAGCCTGG	0.677													-|||	2474	0.49401	0.4002	0.5591	5008	,	,		19180	0.6558		0.4533	False		,,,				2504	0.4499				p.R3468P		Atlas-SNP	.											.	MUC5B	473	.	0			c.G10403C						PASS	.	C	PRO/ARG	1603,2577		380,843,867	69.0	94.0	86.0		10403	-0.6	0.0	11	dbSNP_101	86	3901,4509		996,1909,1300	no	missense	MUC5B	NM_002458.2	103	1376,2752,2167	CC,CG,GG		46.3853,38.3493,43.7172	benign	3468/5763	1268513	5504,7086	2090	4205	6295	SO:0001583	missense	727897	exon31			CGGTGCGCACAGC	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.10403G>C	11.37:g.1268513G>C	ENSP00000436812:p.Arg3468Pro	Somatic	476	0	0		WXS	Illumina HiSeq	Phase_I	715	422	0.59021	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	1113	0.5096153846153846	200	0.4065040650406504	184	0.5082872928176796	388	0.6783216783216783	341	0.449868073878628	g	3.574	-0.086941	0.07097	0.383493	0.463853	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.22134	1.97;2.15	1.68	-0.591	0.11675	.	.	.	.	.	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B;B	0.21606	0.058;0.0	B;B	0.27500	0.08;0.0	T	0.26087	-1.0113	8	0.87932	D	0	.	5.8264	0.18556	0.0:0.5015:0.371:0.1274	.	3996;3471	A7Y9J9;E9PBJ0	.;.	P	3468;3471;3440;3373	ENSP00000436812:R3468P;ENSP00000415793:R3471P	ENSP00000343037:R3440P	R	+	2	0	MUC5B	1225089	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.554000	0.00926	-0.555000	0.06142	-0.647000	0.03941	CGC	G|0.497;C|0.503	0.503	strong		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ATP2B2	491	hgsc.bcm.edu	37	3	10413715	10413715	+	Silent	SNP	G	G	A	rs2289274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:10413715G>A	ENST00000352432.4	-	11	1506	c.1437C>T	c.(1435-1437)aaC>aaT	p.N479N	ATP2B2_ENST00000360273.2_Silent_p.N479N|ATP2B2_ENST00000343816.4_Silent_p.N465N|ATP2B2_ENST00000397077.1_Silent_p.N434N|ATP2B2_ENST00000383800.4_Silent_p.N434N			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	261	1	0.00383142		WXS	Illumina HiSeq	Phase_I	296	143	0.483108	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	
PTPN13	5783	hgsc.bcm.edu	37	4	87696476	87696476	+	Silent	SNP	G	G	A	rs12499471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:87696476G>A	ENST00000411767.2	+	34	5724	c.5661G>A	c.(5659-5661)acG>acA	p.T1887T	PTPN13_ENST00000511467.1_Silent_p.T1892T|PTPN13_ENST00000427191.2_Silent_p.T1868T|PTPN13_ENST00000436978.1_Silent_p.T1892T|PTPN13_ENST00000316707.6_Silent_p.T1696T			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1887	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TAACACTAACGTGCAACAAAG	0.373													A|||	353	0.0704872	0.1074	0.0677	5008	,	,		19377	0.0079		0.1143	False		,,,				2504	0.0419				p.T1892T		Atlas-SNP	.											.	PTPN13	203	.	0			c.G5676A						PASS	.	A	,,,	373,3357		19,335,1511	81.0	74.0	76.0		5604,5661,5088,5676	-7.1	0.0	4	dbSNP_120	76	999,7205		61,877,3164	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	,,,	80,1212,4675	AA,AG,GG		12.177,10.0,11.4966	,,,	1868/2467,1887/2486,1696/2295,1892/2491	87696476	1372,10562	1865	4102	5967	SO:0001819	synonymous_variant	5783	exon34			ACTAACGTGCAAC		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.5661G>A	4.37:g.87696476G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	151	69	0.456954	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			G|0.906;A|0.094	0.094	strong		0.373	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
MAP10	54627	hgsc.bcm.edu	37	1	232942251	232942251	+	Silent	SNP	A	A	G	rs12048236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232942251A>G	ENST00000418460.1	+	1	1609	c.1482A>G	c.(1480-1482)ctA>ctG	p.L494L		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	352					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)	p.L494L(1)									GGAGTTGTCTAAAGCATCCAA	0.418													A|||	670	0.133786	0.2481	0.0836	5008	,	,		19814	0.1379		0.0517	False		,,,				2504	0.0951				p.L494L		Atlas-SNP	.											KIAA1383_ENST00000418460,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.A1482G						PASS	.	A		847,3011		84,679,1166	67.0	67.0	67.0		1482	0.3	0.0	1	dbSNP_120	67	375,7907		10,355,3776	no	coding-synonymous	KIAA1383	NM_019090.2		94,1034,4942	GG,GA,AA		4.5279,21.9544,10.0659		494/1048	232942251	1222,10918	1929	4141	6070	SO:0001819	synonymous_variant	54627	exon1			TTGTCTAAAGCAT	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.1482A>G	1.37:g.232942251A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Silent	SNP	ENST00000418460.1	37	CCDS44334.1																																																																																			A|0.885;G|0.115	0.115	strong		0.418	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
OR14A16	284532	hgsc.bcm.edu	37	1	247978768	247978768	+	Silent	SNP	G	G	A	rs61740923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247978768G>A	ENST00000357627.1	-	1	263	c.264C>T	c.(262-264)aaC>aaT	p.N88N		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	88						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)|kidney(1)|large_intestine(3)|lung(32)|skin(2)|stomach(1)	45						ATGAAATGGAGTTGTTGTGTA	0.448													g|||	78	0.0155751	0.053	0.0029	5008	,	,		19549	0.0		0.003	False		,,,				2504	0.0031				p.N88N	Ovarian(112;180 1586 15073 21914 33526)	Atlas-SNP	.											.	OR14A16	90	.	0			c.C264T						PASS	.	T		187,4219	120.4+/-158.0	7,173,2023	91.0	91.0	91.0		264	-0.9	0.0	1	dbSNP_129	91	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous	OR14A16	NM_001001966.1		7,192,6304	AA,AG,GG		0.2209,4.2442,1.5839		88/310	247978768	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	284532	exon1			AATGGAGTTGTTG	BK004366	CCDS31097.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000196772	ENSG00000196772		"""GPCR / Class A : Olfactory receptors"""	15022	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AT, member 1"""	OR5AT1			Standard	NM_001001966		Approved		uc001idm.1	Q8NHC5	OTTHUMG00000040199	ENST00000357627.1:c.264C>T	1.37:g.247978768G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	203	84	0.413793	NM_001001966	Q6IF96	Silent	SNP	ENST00000357627.1	37	CCDS31097.1																																																																																			G|0.986;A|0.014	0.014	strong		0.448	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1	NM_001001966	
GDF5	8200	hgsc.bcm.edu	37	20	34022344	34022344	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34022344C>T	ENST00000374372.1	-	4	1372	c.869G>A	c.(868-870)gGc>gAc	p.G290D	GDF5OS_ENST00000374375.1_Missense_Mutation_p.P130S|GDF5_ENST00000374369.3_Missense_Mutation_p.G290D			P43026	GDF5_HUMAN	growth differentiation factor 5	290					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)			CACCTCCCAGCCAGATCCGTC	0.682																																					p.G290D		Atlas-SNP	.											.	GDF5	66	.	0			c.G869A						PASS	.						17.0	19.0	18.0					20																	34022344		2197	4298	6495	SO:0001583	missense	8200	exon2			TCCCAGCCAGATC	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.869G>A	20.37:g.34022344C>T	ENSP00000363492:p.Gly290Asp	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_000557	E1P5Q2|Q96SB1	Missense_Mutation	SNP	ENST00000374372.1	37	CCDS13254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.00|14.00	2.403881|2.403881	0.42613|0.42613	.|.	.|.	ENSG00000125965|ENSG00000204183	ENST00000374369;ENST00000374372|ENST00000374375	T;T|.	0.69806|.	-0.43;-0.43|.	4.56|4.56	4.56|4.56	0.56223|0.56223	Transforming growth factor-beta, N-terminal (1);|.	0.494665|.	0.18574|.	N|.	0.137222|.	T|T	0.41834|0.41834	0.1176|0.1176	L|L	0.47190|0.47190	1.495|1.495	0.29135|0.29135	N|N	0.87936|0.87936	B;P|.	0.34615|.	0.316;0.459|.	B;B|.	0.39465|.	0.3;0.245|.	T|T	0.46693|0.46693	-0.9173|-0.9173	10|6	0.17832|0.87932	T|D	0.49|0	.|.	5.4132|5.4132	0.16360|0.16360	0.0:0.7525:0.0:0.2475|0.0:0.7525:0.0:0.2475	.|.	290;290|.	F1T0J1;P43026|.	.;GDF5_HUMAN|.	D|S	290|130	ENSP00000363489:G290D;ENSP00000363492:G290D|.	ENSP00000363489:G290D|ENSP00000363495:P130S	G|P	-|+	2|1	0|0	GDF5|GDF5OS	33485758|33485758	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.633000|2.633000	0.46519|0.46519	2.353000|2.353000	0.79882|0.79882	0.491000|0.491000	0.48974|0.48974	GGC|CCA	.	.	none		0.682	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2		
PMS2	5395	hgsc.bcm.edu	37	7	6026787	6026787	+	Missense_Mutation	SNP	C	C	T	rs115052399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6026787C>T	ENST00000265849.7	-	11	1714	c.1609G>A	c.(1609-1611)Gag>Aag	p.E537K	PMS2_ENST00000441476.2_Missense_Mutation_p.E431K|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Missense_Mutation_p.E537K|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	537					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)		GGCGCTTTCTCCTGAGAGTCC	0.537			"""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				C|||	28	0.00559105	0.0204	0.0014	5008	,	,		15948	0.0		0.0	False		,,,				2504	0.0				p.E537K		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.G1609A						PASS	.	C	LYS/GLU	55,4351		0,55,2148	78.0	85.0	83.0		1609	3.7	0.0	7	dbSNP_132	83	0,8596		0,0,4298	no	missense	PMS2	NM_000535.5	56	0,55,6446	TT,TC,CC		0.0,1.2483,0.423	benign	537/863	6026787	55,12947	2203	4298	6501	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	CTTTCTCCTGAGA		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.1609G>A	7.37:g.6026787C>T	ENSP00000265849:p.Glu537Lys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	c	11.03	1.519693	0.27211	0.012483	0.0	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;D	0.87179	1.1;1.1;-2.22	5.85	3.72	0.42706	.	0.843000	0.10493	N	0.668254	T	0.67449	0.2894	L	0.38838	1.175	0.09310	N	0.999999	B;B;B	0.21071	0.023;0.001;0.051	B;B;B	0.19391	0.011;0.003;0.025	T	0.58086	-0.7698	10	0.09338	T	0.73	-16.5088	10.2582	0.43410	0.0:0.7388:0.1388:0.1224	.	537;537;431	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	K	537;490;431;537	ENSP00000265849:E537K;ENSP00000392843:E431K;ENSP00000384308:E537K	ENSP00000265849:E537K	E	-	1	0	PMS2	5993313	0.001000	0.12720	0.016000	0.15963	0.016000	0.09150	0.250000	0.18235	1.474000	0.48178	0.650000	0.86243	GAG	C|0.995;T|0.005	0.005	strong		0.537	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
AKAP1	8165	hgsc.bcm.edu	37	17	55183203	55183203	+	Silent	SNP	T	T	C	rs2230772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:55183203T>C	ENST00000337714.3	+	2	611	c.378T>C	c.(376-378)gaT>gaC	p.D126D	AKAP1_ENST00000571629.1_Silent_p.D126D|AKAP1_ENST00000572557.1_Silent_p.D126D|AKAP1_ENST00000314126.3_Silent_p.D126D|AKAP1_ENST00000539273.1_Silent_p.D126D	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	126					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					CACGCAGAGATGACAGTACAA	0.527													t|||	2395	0.478235	0.3548	0.4798	5008	,	,		21186	0.8046		0.4026	False		,,,				2504	0.3855				p.D126D		Atlas-SNP	.											.	AKAP1	73	.	0			c.T378C						PASS	.	T	,,	1526,2880	482.1+/-359.3	260,1006,937	121.0	107.0	111.0		378,378,378	-11.6	0.0	17	dbSNP_98	111	3564,5036	516.3+/-378.8	736,2092,1472	no	coding-synonymous,coding-synonymous,coding-synonymous	AKAP1	NM_001242902.1,NM_001242903.1,NM_003488.3	,,	996,3098,2409	CC,CT,TT		41.4419,34.6346,39.1358	,,	126/904,126/904,126/904	55183203	5090,7916	2203	4300	6503	SO:0001819	synonymous_variant	8165	exon3			CAGAGATGACAGT	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Tudor domain containing"""	367	protein-coding gene	gene with protein product	"""protein kinase anchoring protein 1"", ""dual specificity A-kinase-anchoring protein 1"", ""protein phosphatase 1, regulatory subunit 43"", ""tudor domain containing 17"""	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.378T>C	17.37:g.55183203T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	191	97	0.507853	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Silent	SNP	ENST00000337714.3	37	CCDS11594.1																																																																																			T|0.554;C|0.446	0.446	strong		0.527	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1		
PRR27	401137	hgsc.bcm.edu	37	4	71024552	71024552	+	Missense_Mutation	SNP	C	C	G	rs143985138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71024552C>G	ENST00000344526.5	+	3	772	c.583C>G	c.(583-585)Cca>Gca	p.P195A	C4orf40_ENST00000502294.1_Missense_Mutation_p.P195A	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		195	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GGAACCTTCACCAGCTGAGCC	0.557													C|||	48	0.00958466	0.0348	0.0029	5008	,	,		16492	0.0		0.0	False		,,,				2504	0.0				p.P195A		Atlas-SNP	.											.	C4orf40	19	.	0			c.C583G						PASS	.	C	ALA/PRO	172,4234		1,170,2032	57.0	52.0	54.0		583	-7.9	0.0	4	dbSNP_134	54	1,8599		0,1,4299	yes	missense	C4orf40	NM_214711.3	27	1,171,6331	GG,GC,CC		0.0116,3.9038,1.3302	benign	195/220	71024552	173,12833	2203	4300	6503	SO:0001583	missense	401137	exon3			CCTTCACCAGCTG																												ENST00000344526.5:c.583C>G	4.37:g.71024552C>G	ENSP00000343172:p.Pro195Ala	Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	303	136	0.448845	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	C	5.440	0.266257	0.10294	0.039038	1.16E-4	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.28454	1.61;1.61	3.97	-7.94	0.01152	.	.	.	.	.	T	0.02047	0.0064	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.26538	-1.0100	9	0.02654	T	1	5.212	3.7914	0.08722	0.2107:0.3878:0.3086:0.0929	.	195	Q6MZM9	CD040_HUMAN	A	195	ENSP00000426249:P195A;ENSP00000343172:P195A	ENSP00000343172:P195A	P	+	1	0	C4orf40	71059141	0.001000	0.12720	0.000000	0.03702	0.012000	0.07955	0.133000	0.15912	-1.914000	0.01078	0.411000	0.27672	CCA	C|0.987;G|0.013	0.013	strong		0.557	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
PARK2	5071	hgsc.bcm.edu	37	6	162475167	162475167	+	Missense_Mutation	SNP	T	T	G	rs9456735	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:162475167T>G	ENST00000366898.1	-	5	676	c.574A>C	c.(574-576)Atg>Ctg	p.M192L	PARK2_ENST00000366897.1_Intron|PARK2_ENST00000338468.3_Start_Codon_SNP_p.M1L|PARK2_ENST00000366894.1_Start_Codon_SNP_p.M1L|PARK2_ENST00000366896.1_Intron|PARK2_ENST00000366892.1_Missense_Mutation_p.M192L	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	192			M -> L (in PARK2; unknown pathological significance; dbSNP:rs9456735). {ECO:0000269|PubMed:11971093}.|M -> V (in PARK2; unknown pathological significance; dbSNP:rs9456735). {ECO:0000269|PubMed:12629236}.		adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		TCACCACTCATCCGGTTTGGA	0.398													T|||	95	0.0189696	0.0681	0.0029	5008	,	,		18248	0.0		0.003	False		,,,				2504	0.0				p.M192L		Atlas-SNP	.											.	PARK2	96	.	0			c.A574C	GRCh37	CM024241|CM030925	PARK2	M	rs9456735	PASS	.	T	LEU/MET,,	252,4154	146.1+/-180.8	8,236,1959	141.0	123.0	129.0		574,,	5.4	1.0	6	dbSNP_119	129	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron,intron	PARK2	NM_004562.2,NM_013987.2,NM_013988.2	15,,	8,237,6258	GG,GT,TT		0.0116,5.7195,1.9453	benign,,	192/466,,	162475167	253,12753	2203	4300	6503	SO:0001583	missense	5071	exon5			CACTCATCCGGTT		CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"""Parkinson disease"""	8607	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase"""	602544	"""Parkinson disease (autosomal recessive, juvenile) 2, parkin"", ""parkinson protein 2, E3 ubiquitin protein ligase (parkin)"""			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.574A>C	6.37:g.162475167T>G	ENSP00000355865:p.Met192Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	37	CCDS5281.1	43	0.019688644688644688	40	0.08130081300813008	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	14.04	2.416234	0.42918	0.057195	1.16E-4	ENSG00000185345	ENST00000366898;ENST00000366894;ENST00000338468;ENST00000392134;ENST00000366892;ENST00000366895	D;D;D;D	0.90385	-2.58;-2.33;-2.33;-2.66	5.39	5.39	0.77823	.	0.199863	0.45867	D	0.000329	T	0.79364	0.4433	L	0.41236	1.265	0.29921	N	0.822717	B;B;B	0.17268	0.021;0.001;0.016	B;B;B	0.17722	0.019;0.001;0.003	T	0.74583	-0.3617	10	0.54805	T	0.06	.	11.8193	0.52228	0.0:0.0:0.0:1.0	rs9456735;rs52822498;rs9456735	192;192;1	O60260-5;O60260;Q8NI42	.;PRKN2_HUMAN;.	L	192;1;1;1;192;113	ENSP00000355865:M192L;ENSP00000355860:M1L;ENSP00000343589:M1L;ENSP00000355858:M192L	ENSP00000343589:M1L	M	-	1	0	PARK2	162395157	0.984000	0.35163	0.997000	0.53966	0.944000	0.59088	2.591000	0.46163	2.043000	0.60533	0.533000	0.62120	ATG	T|0.977;G|0.023	0.023	strong		0.398	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1		
MRPL9	65005	hgsc.bcm.edu	37	1	151735545	151735545	+	Silent	SNP	A	A	G	rs1196455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151735545A>G	ENST00000368830.3	-	2	315	c.231T>C	c.(229-231)caT>caC	p.H77H	RP11-98D18.2_ENST00000420382.1_RNA|OAZ3_ENST00000479764.1_5'Flank|MRPL9_ENST00000368829.3_Silent_p.H77H|MRPL9_ENST00000467306.1_5'UTR|OAZ3_ENST00000315067.8_5'UTR|OAZ3_ENST00000453029.2_5'Flank|RP11-98D18.3_ENST00000512280.1_RNA|OAZ3_ENST00000321531.5_5'UTR	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	77					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)			TATAGACGCGATGTCGCCGGT	0.672													A|||	873	0.174321	0.1422	0.1037	5008	,	,		12558	0.3611		0.003	False		,,,				2504	0.2515				p.H77H		Atlas-SNP	.											.	MRPL9	21	.	0			c.T231C						PASS	.	A	,	560,3846	249.0+/-256.6	33,494,1676	54.0	56.0	56.0		,231	2.8	1.0	1	dbSNP_87	56	32,8568	22.2+/-67.0	0,32,4268	no	utr-5,coding-synonymous	OAZ3,MRPL9	NM_001134939.1,NM_031420.2	,	33,526,5944	GG,GA,AA		0.3721,12.7099,4.5517	,	,77/268	151735545	592,12414	2203	4300	6503	SO:0001819	synonymous_variant	65005	exon2			GACGCGATGTCGC	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.231T>C	1.37:g.151735545A>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	194	95	0.489691	NM_031420	B2RD99|Q5SZR2|Q9BSW8	Silent	SNP	ENST00000368830.3	37	CCDS1003.1																																																																																			A|0.908;G|0.092	0.092	strong		0.672	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2	NM_031420	
REL	5966	hgsc.bcm.edu	37	2	61148988	61148988	+	Missense_Mutation	SNP	C	C	G	rs34661029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61148988C>G	ENST00000295025.8	+	11	1498	c.1178C>G	c.(1177-1179)cCc>cGc	p.P393R	REL_ENST00000394479.3_Missense_Mutation_p.P361R	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	393					cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			TCACCTGGGCCCATCTCAAGT	0.512			A		Hodgkin Lymphoma								C|||	34	0.00678914	0.025	0.0014	5008	,	,		16212	0.0		0.0	False		,,,				2504	0.0				p.P393R		Atlas-SNP	.		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	REL	48	.	0			c.C1178G						PASS	.	C	ARG/PRO	93,4313	74.1+/-112.3	0,93,2110	100.0	98.0	99.0		1178	3.6	0.9	2	dbSNP_126	99	1,8599	1.2+/-3.3	0,1,4299	yes	missense	REL	NM_002908.2	103	0,94,6409	GG,GC,CC		0.0116,2.1108,0.7227	benign	393/620	61148988	94,12912	2203	4300	6503	SO:0001583	missense	5966	exon11			CTGGGCCCATCTC	M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.1178C>G	2.37:g.61148988C>G	ENSP00000295025:p.Pro393Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Missense_Mutation	SNP	ENST00000295025.8	37	CCDS1864.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	C	10.88	1.476325	0.26511	0.021108	1.16E-4	ENSG00000162924	ENST00000295025;ENST00000394479	T;T	0.42131	0.98;0.98	5.54	3.63	0.41609	.	0.859295	0.10279	N	0.693783	T	0.12135	0.0295	N	0.08118	0	0.09310	N	1	B;B	0.28128	0.201;0.181	B;B	0.20577	0.014;0.03	T	0.09314	-1.0680	10	0.52906	T	0.07	-22.6802	9.6826	0.40078	0.159:0.6877:0.1533:0.0	rs34661029	361;393	Q17RU2;Q04864	.;REL_HUMAN	R	393;361	ENSP00000295025:P393R;ENSP00000377989:P361R	ENSP00000295025:P393R	P	+	2	0	REL	61002492	0.771000	0.28555	0.926000	0.36857	0.866000	0.49608	1.214000	0.32419	1.345000	0.45676	-0.158000	0.13435	CCC	C|0.993;G|0.007	0.007	strong		0.512	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908	
WDR81	124997	hgsc.bcm.edu	37	17	1640793	1640793	+	Silent	SNP	C	C	T	rs587780510|rs8077638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1640793C>T	ENST00000409644.1	+	10	5640	c.5640C>T	c.(5638-5640)agC>agT	p.S1880S	WDR81_ENST00000545662.1_Silent_p.S511S|WDR81_ENST00000437219.2_Silent_p.S677S|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Silent_p.S829S|WDR81_ENST00000419248.1_Silent_p.S653S|WDR81_ENST00000446363.1_Silent_p.S519S	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1880					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TGTACGGCAGCGAGGTGGTCA	0.597													C|||	1210	0.241613	0.23	0.2075	5008	,	,		22298	0.1865		0.1988	False		,,,				2504	0.3824				p.S1880S		Atlas-SNP	.											WDR81_ENST00000437219,colon,carcinoma,0,6	WDR81	180	6	0			c.C5640T						PASS	.	C	,,,	986,3418	366.8+/-318.0	106,774,1322	229.0	137.0	168.0		2031,5640,1959,2487	2.0	1.0	17	dbSNP_116	168	1799,6801	323.9+/-316.2	186,1427,2687	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	292,2201,4009	TT,TC,CC		20.9186,22.3887,21.4165	,,,	677/739,1880/1942,653/715,829/891	1640793	2785,10219	2202	4300	6502	SO:0001819	synonymous_variant	124997	exon10			CGGCAGCGAGGTG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.5640C>T	17.37:g.1640793C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	153	62	0.405229	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			C|0.789;T|0.211	0.211	strong		0.597	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
LMNTD1	160492	hgsc.bcm.edu	37	12	25672955	25672955	+	Missense_Mutation	SNP	C	C	T	rs35450203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672955C>T	ENST00000282881.6	-	6	939	c.790G>A	c.(790-792)Gct>Act	p.A264T	IFLTD1_ENST00000413632.2_Missense_Mutation_p.A245T|IFLTD1_ENST00000445693.1_Missense_Mutation_p.A201T|IFLTD1_ENST00000539744.1_Missense_Mutation_p.A167T|IFLTD1_ENST00000458174.2_Missense_Mutation_p.A285T	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		264			A -> T (in dbSNP:rs35450203).		cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					TCAACGTCAGCATCTAATTTT	0.383													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13163	0.0		0.0	False		,,,				2504	0.0				p.A285T		Atlas-SNP	.											.	IFLTD1	121	.	0			c.G853A						PASS	.	T	THR/ALA,THR/ALA,THR/ALA,THR/ALA	252,4154	803.0+/-415.7	5,242,1956	123.0	107.0	112.0		601,853,733,790	2.6	1.0	12	dbSNP_126	112	1,8599	818.9+/-406.8	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	58,58,58,58	5,243,6255	TT,TC,CC		0.0116,5.7195,1.9453	benign,benign,benign,benign	201/326,285/410,245/370,264/389	25672955	253,12753	2203	4300	6503	SO:0001583	missense	160492	exon7			CGTCAGCATCTAA																												ENST00000282881.6:c.790G>A	12.37:g.25672955C>T	ENSP00000282881:p.Ala264Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	159	89	0.559748	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	2.163|2.163	-0.391668|-0.391668	0.04932|0.04932	0.057195|0.057195	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000545543|ENST00000543629	T;T;T;T;T;T|.	0.12569|.	2.92;2.9;2.94;2.89;2.67;2.69|.	5.05|5.05	2.61|2.61	0.31194|0.31194	.|.	.|.	.|.	.|.	.|.	T|T	0.00815|0.00815	0.0027|0.0027	N|N	0.01048|0.01048	-1.04|-1.04	0.19300|0.19300	N|N	0.999978|0.999978	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0|.	T|T	0.32188|0.32188	-0.9916|-0.9916	9|5	0.02654|.	T|.	1|.	-2.2559|-2.2559	4.0577|4.0577	0.09824|0.09824	0.3165:0.0877:0.0:0.5958|0.3165:0.0877:0.0:0.5958	rs35450203|rs35450203	201;285;245;264|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	T|Y	264;167;285;201;245;94|38	ENSP00000282881:A264T;ENSP00000443132:A167T;ENSP00000407353:A285T;ENSP00000407043:A201T;ENSP00000393150:A245T;ENSP00000443596:A94T|.	ENSP00000282881:A264T|.	A|C	-|-	1|2	0|0	IFLTD1|IFLTD1	25564222|25564222	0.160000|0.160000	0.22878|0.22878	0.953000|0.953000	0.39169|0.39169	0.671000|0.671000	0.39405|0.39405	0.141000|0.141000	0.16076|0.16076	0.050000|0.050000	0.15949|0.15949	-0.352000|-0.352000	0.07741|0.07741	GCT|TGC	C|0.980;T|0.020	0.020	strong		0.383	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
MB21D1	115004	hgsc.bcm.edu	37	6	74138503	74138503	+	Silent	SNP	G	G	A	rs73754628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74138503G>A	ENST00000370315.3	-	4	1240	c.1146C>T	c.(1144-1146)atC>atT	p.I382I	MB21D1_ENST00000370318.1_Silent_p.I382I	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	382					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						TTTCCTTTTCGATGTGAGAGA	0.328													G|||	280	0.0559105	0.1188	0.0533	5008	,	,		18547	0.0625		0.0189	False		,,,				2504	0.0041				p.I382I		Atlas-SNP	.											.	MB21D1	33	.	0			c.C1146T						PASS	.	G		458,3948	219.7+/-237.4	26,406,1771	105.0	97.0	100.0		1146	1.2	1.0	6	dbSNP_130	100	212,8388	90.4+/-152.6	1,210,4089	no	coding-synonymous	MB21D1	NM_138441.2		27,616,5860	AA,AG,GG		2.4651,10.3949,5.1515		382/523	74138503	670,12336	2203	4300	6503	SO:0001819	synonymous_variant	115004	exon4			CTTTTCGATGTGA	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"""chromosome 6 open reading frame 150"""	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.1146C>T	6.37:g.74138503G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	130	81	0.623077	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Silent	SNP	ENST00000370315.3	37	CCDS4978.1																																																																																			G|0.947;A|0.053	0.053	strong		0.328	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441	
IGSF9B	22997	hgsc.bcm.edu	37	11	133789790	133789790	+	Missense_Mutation	SNP	G	G	C	rs200373794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:133789790G>C	ENST00000321016.8	-	18	4060	c.3830C>G	c.(3829-3831)aCt>aGt	p.T1277S	IGSF9B_ENST00000533871.2_Missense_Mutation_p.T1277S			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1277	Pro-rich.				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)		GGTGGCCAGAGTGGTGAAGCC	0.677													G|||	20	0.00399361	0.0151	0.0	5008	,	,		12387	0.0		0.0	False		,,,				2504	0.0				p.T1277S		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C3830G						PASS	.	G	SER/THR	55,3777		1,53,1862	24.0	32.0	30.0		3830	4.8	0.9	11	dbSNP_132	30	1,8223		0,1,4111	yes	missense	IGSF9B	NM_014987.1	58	1,54,5973	CC,CG,GG		0.0122,1.4353,0.4645	benign	1277/1350	133789790	56,12000	1916	4112	6028	SO:0001583	missense	22997	exon18			GCCAGAGTGGTGA	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.3830C>G	11.37:g.133789790G>C	ENSP00000317980:p.Thr1277Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	G	12.95	2.091421	0.36952	0.014353	1.22E-4	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.65916	0.15;-0.18	4.76	4.76	0.60689	.	0.000000	0.44688	D	0.000431	T	0.37320	0.0999	N	0.12182	0.205	0.38308	D	0.943176	B	0.06786	0.001	B	0.04013	0.001	T	0.35301	-0.9794	10	0.28530	T	0.3	.	17.5598	0.87902	0.0:0.0:1.0:0.0	.	1277	Q9UPX0	TUTLB_HUMAN	S	1277;1119	ENSP00000317980:T1277S;ENSP00000436552:T1119S	ENSP00000317980:T1277S	T	-	2	0	IGSF9B	133295000	1.000000	0.71417	0.926000	0.36857	0.814000	0.46013	8.633000	0.90999	2.484000	0.83849	0.555000	0.69702	ACT	.	.	weak		0.677	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
ZNF280B	140883	hgsc.bcm.edu	37	22	22842484	22842484	+	Missense_Mutation	SNP	C	C	T	rs57235089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:22842484C>T	ENST00000406426.1	-	4	1982	c.1240G>A	c.(1240-1242)Gtc>Atc	p.V414I	ZNF280B_ENST00000360412.2_Missense_Mutation_p.V414I			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	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)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TCAGCAAAGACCGACGATCTA	0.403													C|||	151	0.0301518	0.0877	0.0072	5008	,	,		19574	0.0		0.0099	False		,,,				2504	0.0204				p.V414I		Atlas-SNP	.											.	ZNF280B	67	.	0			c.G1240A						PASS	.	C	ILE/VAL	339,4067	176.9+/-206.0	15,309,1879	131.0	122.0	125.0		1240	-1.6	0.0	22	dbSNP_129	125	106,8494	56.0+/-117.1	2,102,4196	no	missense	ZNF280B	NM_080764.2	29	17,411,6075	TT,TC,CC		1.2326,7.6941,3.4215	benign	414/544	22842484	445,12561	2203	4300	6503	SO:0001583	missense	140883	exon4			CAAAGACCGACGA	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"""zinc finger protein 279"", ""suppressor of hairy wing homolog 2 (Drosophila)"""	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.1240G>A	22.37:g.22842484C>T	ENSP00000385998:p.Val414Ile	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	266	110	0.413534	NM_080764		Missense_Mutation	SNP	ENST00000406426.1	37	CCDS13799.1	38	0.0173992673992674	26	0.052845528455284556	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	0.005	-2.182245	0.00308	0.076941	0.012326	ENSG00000198477	ENST00000406426;ENST00000360412	T;T	0.28069	1.63;1.63	4.32	-1.63	0.08345	Zinc finger, C2H2-like (1);	.	.	.	.	T	0.00695	0.0023	N	0.25890	0.77	0.09310	N	1	B	0.21905	0.062	B	0.18871	0.023	T	0.24764	-1.0151	9	0.06625	T	0.88	5.8306	4.7941	0.13263	0.4233:0.4085:0.0:0.1682	rs57235089;rs61910698	414	Q86YH2	Z280B_HUMAN	I	414	ENSP00000385998:V414I;ENSP00000353586:V414I	ENSP00000353586:V414I	V	-	1	0	ZNF280B	21172484	0.945000	0.32115	0.000000	0.03702	0.099000	0.18886	2.087000	0.41653	-0.168000	0.10853	-0.152000	0.13540	GTC	C|0.973;T|0.027	0.027	strong		0.403	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764	
PTPRS	5802	hgsc.bcm.edu	37	19	5212380	5212380	+	Silent	SNP	C	C	T	rs1064300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5212380C>T	ENST00000587303.1	-	30	4836	c.4737G>A	c.(4735-4737)ccG>ccA	p.P1579P	PTPRS_ENST00000353284.2_Silent_p.P1132P|PTPRS_ENST00000588012.1_Silent_p.P1541P|PTPRS_ENST00000592099.1_Silent_p.P1132P|PTPRS_ENST00000348075.2_Silent_p.P1541P|PTPRS_ENST00000372412.4_Silent_p.P1580P|PTPRS_ENST00000262963.6_Silent_p.P1559P|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000357368.4_Silent_p.P1579P			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	102	0	0		WXS	Illumina HiSeq	Phase_I	118	47	0.398305	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		
FLG2	388698	hgsc.bcm.edu	37	1	152325456	152325456	+	Silent	SNP	G	G	A	rs73007787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152325456G>A	ENST00000388718.5	-	3	4878	c.4806C>T	c.(4804-4806)gcC>gcT	p.A1602A	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1602					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTTGAGATCCGGCTTGGCCGT	0.512													g|||	341	0.0680911	0.2421	0.0231	5008	,	,		26525	0.0		0.005	False		,,,				2504	0.0				p.A1602A		Atlas-SNP	.											.	FLG2	431	.	0			c.C4806T						PASS	.	G		841,3565	331.8+/-302.1	70,701,1432	353.0	305.0	321.0		4806	-7.5	0.0	1	dbSNP_130	321	25,8575	17.9+/-57.8	0,25,4275	no	coding-synonymous	FLG2	NM_001014342.2		70,726,5707	AA,AG,GG		0.2907,19.0876,6.6585		1602/2392	152325456	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			AGATCCGGCTTGG	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.4806C>T	1.37:g.152325456G>A		Somatic	404	1	0.00247525		WXS	Illumina HiSeq	Phase_I	399	226	0.566416	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			G|0.940;A|0.060	0.060	strong		0.512	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
CFTR	1080	hgsc.bcm.edu	37	7	117307108	117307108	+	Silent	SNP	G	G	A	rs1800136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:117307108G>A	ENST00000003084.6	+	27	4521	c.4389G>A	c.(4387-4389)caG>caA	p.Q1463Q	CFTR_ENST00000454343.1_Silent_p.Q1402Q	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1463					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)	CTAAGCCCCAGATTGCTGCTC	0.512									Cystic Fibrosis				A|||	932	0.186102	0.2496	0.1513	5008	,	,		20100	0.0149		0.2525	False		,,,				2504	0.2331				p.Q1463Q		Atlas-SNP	.											.	CFTR	171	.	0			c.G4389A	GRCh37	CS042143	CFTR	S	rs1800136	PASS	.	A		1077,3329	721.4+/-409.2	126,825,1252	56.0	51.0	53.0		4389	-10.9	0.0	7	dbSNP_89	53	1861,6739	729.8+/-406.7	225,1411,2664	no	coding-synonymous	CFTR	NM_000492.3		351,2236,3916	AA,AG,GG		21.6395,24.4439,22.5896		1463/1481	117307108	2938,10068	2203	4300	6503	SO:0001819	synonymous_variant	1080	exon27	Familial Cancer Database	CF	GCCCCAGATTGCT	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.4389G>A	7.37:g.117307108G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	188	84	0.446809	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	37	CCDS5773.1																																																																																			G|0.790;A|0.210	0.210	strong		0.512	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
MMP2	4313	hgsc.bcm.edu	37	16	55523705	55523705	+	Silent	SNP	T	T	C	rs243849|rs201812551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:55523705T>C	ENST00000219070.4	+	7	1658	c.1149T>C	c.(1147-1149)gaT>gaC	p.D383D	MMP2_ENST00000437642.2_Silent_p.D333D|MMP2_ENST00000543485.1_Silent_p.D307D|MMP2_ENST00000570308.1_Silent_p.D307D	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	383	Collagen-binding.|Fibronectin type-II 3. {ECO:0000255|PROSITE-ProRule:PRU00479}.				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)	ACTACGATGATGACCGCAAGT	0.567													C|||	4006	0.79992	0.7005	0.804	5008	,	,		20466	0.8016		0.8419	False		,,,				2504	0.8865				p.D383D		Atlas-SNP	.											.	MMP2	119	.	0			c.T1149C						PASS	.	C	,	3116,1280	435.9+/-344.5	1092,932,174	96.0	79.0	85.0		999,1149	-6.8	0.2	16	dbSNP_79	85	7272,1328	259.9+/-283.0	3074,1124,102	no	coding-synonymous,coding-synonymous	MMP2	NM_001127891.1,NM_004530.4	,	4166,2056,276	CC,CT,TT		15.4419,29.1174,20.0677	,	333/611,383/661	55523705	10388,2608	2198	4300	6498	SO:0001819	synonymous_variant	4313	exon7			CGATGATGACCGC		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.1149T>C	16.37:g.55523705T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_004530	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Silent	SNP	ENST00000219070.4	37	CCDS10752.1																																																																																			T|0.213;C|0.787	0.787	strong		0.567	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3		
KMT2C	58508	hgsc.bcm.edu	37	7	151970811	151970811	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151970811T>C	ENST00000262189.6	-	7	1209	c.991A>G	c.(991-993)Att>Gtt	p.I331V	KMT2C_ENST00000355193.2_Missense_Mutation_p.I331V	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	331					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)										GCTTGGTCAATGTGTTCTGGA	0.393																																					p.I331V		Atlas-SNP	.											.	MLL3	1564	.	0			c.A991G						PASS	.																																			SO:0001583	missense	58508	exon7			GGTCAATGTGTTC	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.991A>G	7.37:g.151970811T>C	ENSP00000262189:p.Ile331Val	Somatic	725	0	0		WXS	Illumina HiSeq	Phase_I	801	39	0.0486891	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.458970	0.43634	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.83992	-1.79;-1.79	4.78	4.78	0.61160	Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.44097	U	0.000493	T	0.72993	0.3530	L	0.34521	1.04	0.80722	D	1	P	0.39094	0.659	B	0.34873	0.191	T	0.71537	-0.4563	10	0.21014	T	0.42	.	14.599	0.68427	0.0:0.0:0.0:1.0	.	331	Q8NEZ4	MLL3_HUMAN	V	331	ENSP00000262189:I331V;ENSP00000347325:I331V	ENSP00000262189:I331V	I	-	1	0	MLL3	151601744	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.185000	0.58330	1.924000	0.55735	0.477000	0.44152	ATT	.	.	none		0.393	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
EEA1	8411	hgsc.bcm.edu	37	12	93196422	93196422	+	Missense_Mutation	SNP	T	T	G	rs10745623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:93196422T>G	ENST00000322349.8	-	19	2692	c.2428A>C	c.(2428-2430)Aaa>Caa	p.K810Q		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	810			K -> Q (in dbSNP:rs10745623). {ECO:0000269|PubMed:7768953, ECO:0000269|Ref.2}.		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						TTCAGGATTTTTTTTTCTTCC	0.308													T|||	3533	0.705471	0.4887	0.7752	5008	,	,		15877	0.9405		0.6292	False		,,,				2504	0.7853				p.K810Q		Atlas-SNP	.											.	EEA1	104	.	0			c.A2428C						PASS	.	T	GLN/LYS	2315,2087	584.3+/-386.0	626,1063,512	71.0	67.0	69.0		2428	-8.0	0.0	12	dbSNP_120	69	5376,3216	638.1+/-399.3	1690,1996,610	yes	missense	EEA1	NM_003566.3	53	2316,3059,1122	GG,GT,TT		37.4302,47.4103,40.8111	benign	810/1412	93196422	7691,5303	2201	4296	6497	SO:0001583	missense	8411	exon19			GGATTTTTTTTTC	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.2428A>C	12.37:g.93196422T>G	ENSP00000317955:p.Lys810Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	1537	0.7037545787545788	244	0.4959349593495935	278	0.7679558011049724	539	0.9423076923076923	476	0.6279683377308707	T	0.729	-0.780529	0.02929	0.525897	0.625698	ENSG00000102189	ENST00000322349	T	0.77229	-1.08	5.65	-7.99	0.01131	.	1.398190	0.04950	N	0.460191	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15141	0.012	B	0.11329	0.006	T	0.25676	-1.0125	9	0.26408	T	0.33	.	9.0371	0.36293	0.0:0.4642:0.3037:0.232	rs10745623;rs52803865;rs60080467;rs10745623	810	Q15075	EEA1_HUMAN	Q	810	ENSP00000317955:K810Q	ENSP00000317955:K810Q	K	-	1	0	EEA1	91720553	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.160000	0.10041	-1.421000	0.02007	-1.614000	0.00798	AAA	T|0.364;G|0.636	0.636	strong		0.308	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
PITRM1	10531	hgsc.bcm.edu	37	10	3214939	3214939	+	Missense_Mutation	SNP	C	C	A	rs199766052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3214939C>A	ENST00000224949.4	-	1	60	c.26G>T	c.(25-27)gGc>gTc	p.G9V	PITRM1_ENST00000451104.2_Silent_p.G11G|PITRM1_ENST00000380989.2_Missense_Mutation_p.G9V			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	9					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						CACACACAGGCCCTGCCGCCC	0.751													C|||	58	0.0115815	0.0416	0.0029	5008	,	,		8716	0.0		0.0	False		,,,				2504	0.001				p.G9V		Atlas-SNP	.											.	PITRM1	109	.	0			c.G26T						PASS	.	C	VAL/GLY,,VAL/GLY	125,3595		1,123,1736	4.0	7.0	6.0		26,33,26	-4.6	0.0	10		6	3,7519		0,3,3758	no	missense,coding-synonymous,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	109,,109	1,126,5494	AA,AC,CC		0.0399,3.3602,1.1386	benign,,benign	9/1039,11/940,9/1038	3214939	128,11114	1860	3761	5621	SO:0001583	missense	10531	exon1			CACAGGCCCTGCC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.26G>T	10.37:g.3214939C>A	ENSP00000224949:p.Gly9Val	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530296	0.27387	0.033602	3.99E-4	ENSG00000107959	ENST00000224949;ENST00000380989	T;T	0.03920	3.76;3.76	3.31	-4.59	0.03400	.	2.102200	0.01907	N	0.039579	T	0.01092	0.0036	.	.	.	0.09310	N	0.999998	B;B	0.18968	0.032;0.019	B;B	0.19391	0.025;0.011	T	0.42699	-0.9436	9	0.30078	T	0.28	.	7.0117	0.24865	0.2341:0.5702:0.1957:0.0	.	9;9	Q5JRX3-2;Q5JRX3	.;PREP_HUMAN	V	9	ENSP00000224949:G9V;ENSP00000370377:G9V	ENSP00000224949:G9V	G	-	2	0	PITRM1	3204939	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.319000	0.08039	-0.576000	0.05974	0.313000	0.20887	GGC	.	.	weak		0.751	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
NBPF7	343505	hgsc.bcm.edu	37	1	120386922	120386922	+	IGR	SNP	A	A	T	rs12068863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120386922A>T								REG4 (32639 upstream) : ADAM30 (49233 downstream)																							TATAGATCTTACTGTATTTGT	0.428											OREG0013730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	371	0.0740815	0.27	0.0202	5008	,	,		20192	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	NBPF7	46	.	0			c.235+2T>A						PASS	.	A		829,3303		91,647,1328	78.0	86.0	83.0			0.7	0.0	1	dbSNP_120	83	22,8414		0,22,4196	no	splice-5	NBPF7	NM_001047980.1		91,669,5524	TT,TA,AA		0.2608,20.0629,6.7712			120386922	851,11717	2066	4218	6284	SO:0001628	intergenic_variant	343505	exon2			GATCTTACTGTAT																													1.37:g.120386922A>T		Somatic	83	0	0	1503	WXS	Illumina HiSeq	Phase_I	109	40	0.366972	NM_001047980		Splice_Site	SNP		37																																																																																				A|0.957;T|0.043	0.043	strong	0	0.428								
TET3	200424	hgsc.bcm.edu	37	2	74275174	74275174	+	Silent	SNP	C	C	T	rs73951129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74275174C>T	ENST00000409262.3	+	1	1725	c.1725C>T	c.(1723-1725)ctC>ctT	p.L575L		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	575					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGGAAGAGCTCATCCGGCAGT	0.602													C|||	79	0.0157748	0.0582	0.0	5008	,	,		17465	0.001		0.001	False		,,,				2504	0.0				p.L575L		Atlas-SNP	.											.	TET3	101	.	0			c.C1725T						PASS	.	C		157,3687		4,149,1769	41.0	45.0	43.0		1725	4.5	1.0	2	dbSNP_130	43	1,8255		0,1,4127	no	coding-synonymous	TET3	NM_144993.1		4,150,5896	TT,TC,CC		0.0121,4.0843,1.3058		575/1661	74275174	158,11942	1922	4128	6050	SO:0001819	synonymous_variant	200424	exon1			AGAGCTCATCCGG		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"""tet oncogene family member 3"""			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.1725C>T	2.37:g.74275174C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	121	65	0.53719	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	37	CCDS46339.1																																																																																			C|0.984;T|0.016	0.016	strong		0.602	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4		
RELA	5970	hgsc.bcm.edu	37	11	65422374	65422374	+	Silent	SNP	C	C	T	rs7116571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65422374C>T	ENST00000406246.3	-	11	1392	c.1131G>A	c.(1129-1131)tcG>tcA	p.S377S	RELA_ENST00000308639.9_Silent_p.S374S|RELA_ENST00000525693.1_3'UTR	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	377				QISQASALA -> RSARPRLG (in Ref. 2; CAA80524). {ECO:0000305}.	acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|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 extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|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)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						gggccaaggccgaggcCTGGC	0.647													C|||	153	0.0305511	0.1074	0.0159	5008	,	,		14470	0.0		0.0	False		,,,				2504	0.0				p.S377S		Atlas-SNP	.											.	RELA	44	.	0			c.G1131A						PASS	.	C	,	346,4040		7,332,1854	10.0	10.0	10.0		1122,1131	-7.6	0.2	11	dbSNP_116	10	6,8576		0,6,4285	no	coding-synonymous,coding-synonymous	RELA	NM_001145138.1,NM_021975.3	,	7,338,6139	TT,TC,CC		0.0699,7.8887,2.7144	,	374/549,377/552	65422374	352,12616	2193	4291	6484	SO:0001819	synonymous_variant	5970	exon11			CAAGGCCGAGGCC	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"""	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1131G>A	11.37:g.65422374C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	NM_021975	Q6GTV1|Q6SLK1	Silent	SNP	ENST00000406246.3	37	CCDS31609.1																																																																																			C|0.965;T|0.035	0.035	strong		0.647	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975	
WWP2	11060	hgsc.bcm.edu	37	16	69967897	69967897	+	Silent	SNP	T	T	C	rs2270841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69967897T>C	ENST00000359154.2	+	17	1808	c.1707T>C	c.(1705-1707)caT>caC	p.H569H	WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000568684.1_Silent_p.H130H|WWP2_ENST00000448661.1_Silent_p.H569H|WWP2_ENST00000356003.2_Silent_p.H569H|WWP2_ENST00000542271.1_Silent_p.H453H|MIR140_ENST00000385282.1_RNA	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	569	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|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 transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TCCTGTCTCATGAGGTGCTCA	0.483													C|||	4280	0.854633	0.947	0.7507	5008	,	,		23109	0.9683		0.7525	False		,,,				2504	0.7914				p.H569H		Atlas-SNP	.											WWP2,NS,carcinoma,0,1	WWP2	88	1	0			c.T1707C						PASS	.	C	,	3941,455	218.1+/-236.3	1767,407,24	186.0	170.0	175.0		1707,390	-3.6	0.8	16	dbSNP_100	175	6380,2220	378.8+/-339.0	2378,1624,298	no	coding-synonymous,coding-synonymous	WWP2	NM_007014.3,NM_199424.1	,	4145,2031,322	CC,CT,TT		25.814,10.3503,20.5833	,	569/871,130/432	69967897	10321,2675	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon17			GTCTCATGAGGTG	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.1707T>C	16.37:g.69967897T>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			T|0.194;C|0.806	0.806	strong		0.483	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
CHST5	23563	hgsc.bcm.edu	37	16	75563352	75563352	+	Missense_Mutation	SNP	C	C	T	rs7206332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75563352C>T	ENST00000336257.3	-	3	2325	c.931G>A	c.(931-933)Gcc>Acc	p.A311T	RP11-77K12.7_ENST00000460606.1_3'UTR|CHST5_ENST00000541075.1_Missense_Mutation_p.A317T	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	311			A -> T (in dbSNP:rs7206332).		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)	24						CCGGTGAAGGCGTAGAGTGCG	0.677													C|||	124	0.0247604	0.0908	0.0058	5008	,	,		15530	0.0		0.0	False		,,,				2504	0.0				p.A311T		Atlas-SNP	.											CHST5,middle_lobe,carcinoma,+1,1	CHST5	47	1	0			c.G931A						PASS	.	C	THR/ALA	322,4070	164.0+/-195.7	15,292,1889	67.0	68.0	67.0		931	2.8	1.0	16	dbSNP_116	67	13,8587	7.7+/-29.5	0,13,4287	yes	missense	CHST5	NM_024533.4	58	15,305,6176	TT,TC,CC		0.1512,7.3315,2.5785	benign	311/412	75563352	335,12657	2196	4300	6496	SO:0001583	missense	23563	exon3			TGAAGGCGTAGAG	AF176839	CCDS10919.1	16q23.1	2008-02-05			ENSG00000135702	ENSG00000135702		"""Sulfotransferases, membrane-bound"""	1973	protein-coding gene	gene with protein product		604817				10491328, 11017086	Standard	NM_024533		Approved	I-GLCNAC-6-ST, FLJ22167	uc002fei.3	Q9GZS9	OTTHUMG00000137610	ENST00000336257.3:c.931G>A	16.37:g.75563352C>T	ENSP00000338783:p.Ala311Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Missense_Mutation	SNP	ENST00000336257.3	37	CCDS10919.1	36	0.016483516483516484	32	0.06504065040650407	4	0.011049723756906077	0	0.0	0	0.0	C	6.674	0.492920	0.12702	0.073315	0.001512	ENSG00000135702	ENST00000336257;ENST00000541075	T;T	0.23950	1.88;1.88	2.84	2.84	0.33178	Sulfotransferase domain (1);	0.322809	0.31495	N	0.007547	T	0.01092	0.0036	L	0.29908	0.895	0.26382	N	0.976729	B;B	0.22851	0.062;0.076	B;B	0.22753	0.024;0.041	T	0.11567	-1.0582	10	0.25751	T	0.34	.	7.8661	0.29539	0.0:0.8684:0.0:0.1316	rs7206332;rs57580922;rs7206332	317;311	Q9GZS9-2;Q9GZS9	.;CHST5_HUMAN	T	311;317	ENSP00000338783:A311T;ENSP00000441220:A317T	ENSP00000338783:A311T	A	-	1	0	CHST5	74120853	0.000000	0.05858	0.995000	0.50966	0.142000	0.21351	0.279000	0.18771	1.583000	0.49898	0.313000	0.20887	GCC	C|0.974;T|0.026	0.026	strong		0.677	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126	
FRAS1	80144	hgsc.bcm.edu	37	4	79437155	79437155	+	Silent	SNP	C	C	T	rs3749487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79437155C>T	ENST00000264895.6	+	66	10817	c.10377C>T	c.(10375-10377)acC>acT	p.T3459T		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3455					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.T3459T(2)|p.T3460T(1)		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						GCTCTGTAACCGCTGACTTCC	0.507													C|||	884	0.176518	0.177	0.1398	5008	,	,		18849	0.2242		0.2058	False		,,,				2504	0.1227				p.T3459T		Atlas-SNP	.											FRAS1_ENST00000264895,NS,carcinoma,0,2	FRAS1	779	2	3	Substitution - coding silent(3)	prostate(3)	c.C10377T						PASS	.	C		762,3516		66,630,1443	69.0	74.0	72.0		10377	-4.6	0.7	4	dbSNP_107	72	1551,6979		140,1271,2854	no	coding-synonymous	FRAS1	NM_025074.6		206,1901,4297	TT,TC,CC		18.1829,17.8121,18.059		3459/4013	79437155	2313,10495	2139	4265	6404	SO:0001819	synonymous_variant	80144	exon66			TGTAACCGCTGAC	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.10377C>T	4.37:g.79437155C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	203	97	0.477833	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	432	0.1978021978021978	96	0.1951219512195122	58	0.16022099447513813	128	0.22377622377622378	150	0.19788918205804748	C	1.309	-0.602724	0.03744	0.178121	0.181829	ENSG00000138759	ENST00000512123	.	.	.	5.97	-4.61	0.03380	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33929	-0.9849	3	.	.	.	.	2.7957	0.05400	0.1827:0.3609:0.0961:0.3603	rs3749487;rs57228815	.	.	.	C	1688	.	.	R	+	1	0	FRAS1	79656179	0.002000	0.14202	0.743000	0.31040	0.168000	0.22595	-1.645000	0.02000	-0.358000	0.08162	-0.606000	0.04082	CGC	C|0.803;T|0.197	0.197	strong		0.507	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CYTH2	9266	hgsc.bcm.edu	37	19	48977479	48977479	+	Silent	SNP	C	C	T	rs61748773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48977479C>T	ENST00000452733.2	+	7	1064	c.588C>T	c.(586-588)aaC>aaT	p.N196N	CYTH2_ENST00000427476.1_Silent_p.N196N			Q99418	CYH2_HUMAN	cytohesin 2	196	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|inositol 1,4,5 trisphosphate binding (GO:0070679)|lipid binding (GO:0008289)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						TCATGCTCAACACCAGTCTCC	0.632													C|||	375	0.0748802	0.2012	0.0389	5008	,	,		15982	0.0546		0.0089	False		,,,				2504	0.0184				p.N196N		Atlas-SNP	.											.	CYTH2	33	.	0			c.C588T						PASS	.	C	,	773,3633	313.8+/-293.3	62,649,1492	125.0	99.0	108.0		588,588	4.1	1.0	19	dbSNP_129	108	165,8435	78.1+/-140.7	1,163,4136	no	coding-synonymous,coding-synonymous	CYTH2	NM_004228.6,NM_017457.5	,	63,812,5628	TT,TC,CC		1.9186,17.5443,7.2121	,	196/400,196/401	48977479	938,12068	2203	4300	6503	SO:0001819	synonymous_variant	9266	exon7			GCTCAACACCAGT	X99753	CCDS12722.1	19q13.32	2014-05-02	2008-08-14	2008-08-14	ENSG00000105443	ENSG00000105443		"""Pleckstrin homology (PH) domain containing"""	9502	protein-coding gene	gene with protein product		602488	"""pleckstrin homology, Sec7 and coiled/coil domains 2 (cytohesin-2)"", ""pleckstrin homology, Sec7 and coiled-coil domains 2"""	PSCD2L, PSCD2		8706128, 8945478, 20525696	Standard	NM_004228		Approved	CTS18.1, Sec7p-L, ARNO, Sec7p-like, cytohesin-2	uc002pjj.4	Q99418	OTTHUMG00000150245	ENST00000452733.2:c.588C>T	19.37:g.48977479C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	194	194	1	NM_017457	A8K8P0|Q8IXY9|Q92958	Silent	SNP	ENST00000452733.2	37	CCDS12722.1																																																																																			C|0.937;T|0.063	0.063	strong		0.632	CYTH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317060.1	NM_004228	
ATM	472	hgsc.bcm.edu	37	11	108143299	108143299	+	Missense_Mutation	SNP	A	A	G	rs3092857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108143299A>G	ENST00000452508.2	+	22	3307	c.3118A>G	c.(3118-3120)Atg>Gtg	p.M1040V	ATM_ENST00000278616.4_Missense_Mutation_p.M1040V			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1040			M -> V (in B-cell non-Hodgkin lymphoma; dbSNP:rs3092857). {ECO:0000269|PubMed:9288106}.		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)	p.M1040V(1)		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)	CTCTGTAAGAATGGCCCTAGT	0.303			"""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)			A|||	71	0.0141773	0.053	0.0014	5008	,	,		17666	0.0		0.0	False		,,,				2504	0.0				p.M1040V		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM_ENST00000278616,colon,carcinoma,-1,7	ATM	1657	7	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A3118G						PASS	.	A	VAL/MET	177,4225	112.5+/-150.6	1,175,2025	112.0	117.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3118	-1.1	1.0	11	dbSNP_103	115	0,8596		0,0,4298	yes	missense	ATM	NM_000051.3	21	1,175,6323	GG,GA,AA		0.0,4.0209,1.3617	benign	1040/3057	108143299	177,12821	2201	4298	6499	SO:0001583	missense	472	exon21	Familial Cancer Database	AT, Louis-Bar syndrome	GTAAGAATGGCCC	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.3118A>G	11.37:g.108143299A>G	ENSP00000388058:p.Met1040Val	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	142	51	0.359155	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	A	0.185	-1.058171	0.01950	0.040209	0.0	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.68624	-0.34;-0.34;-0.34	5.43	-1.09	0.09904	Armadillo-type fold (1);	0.532223	0.22706	N	0.056633	T	0.10380	0.0254	L	0.35723	1.085	0.20926	N	0.999827	B	0.02656	0.0	B	0.01281	0.0	T	0.14531	-1.0469	10	0.02654	T	1	.	6.8803	0.24168	0.4453:0.1325:0.4222:0.0	rs3092857;rs17107892;rs52804880;rs3092857	1040	Q13315	ATM_HUMAN	V	1040	ENSP00000435747:M1040V;ENSP00000278616:M1040V;ENSP00000388058:M1040V	ENSP00000278616:M1040V	M	+	1	0	ATM	107648509	0.995000	0.38212	0.990000	0.47175	0.533000	0.34776	0.324000	0.19610	-0.134000	0.11516	0.533000	0.62120	ATG	A|0.985;G|0.015	0.015	strong		0.303	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
EXOC3	11336	hgsc.bcm.edu	37	5	453583	453583	+	Silent	SNP	C	C	T	rs6871053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:453583C>T	ENST00000512944.1	+	4	652	c.463C>T	c.(463-465)Ctg>Ttg	p.L155L	EXOC3_ENST00000315013.5_Silent_p.L155L	NM_007277.4	NP_009208.2	O60645	EXOC3_HUMAN	exocyst complex component 3	166					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|secretory granule membrane (GO:0030667)				breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(13)|ovary(1)|urinary_tract(1)	23		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CCGGGACGGGCTGATGTACGA	0.597													C|||	175	0.0349441	0.0575	0.0706	5008	,	,		20983	0.0188		0.0129	False		,,,				2504	0.0184				p.L155L		Atlas-SNP	.											.	EXOC3	54	.	0			c.C463T						PASS	.	C		180,3944		7,166,1889	41.0	42.0	41.0		463	4.5	1.0	5	dbSNP_116	41	114,8266		0,114,4076	no	coding-synonymous	EXOC3	NM_007277.4		7,280,5965	TT,TC,CC		1.3604,4.3647,2.3512		155/746	453583	294,12210	2062	4190	6252	SO:0001819	synonymous_variant	11336	exon4			GACGGGCTGATGT	BC034427	CCDS54830.1	5p15.33	2013-01-22	2005-11-01	2005-11-01	ENSG00000180104	ENSG00000180104			30378	protein-coding gene	gene with protein product		608186	"""SEC6-like 1 (S. cerevisiae)"""	SEC6L1		8619474	Standard	XM_005248238		Approved	Sec6p	uc003jba.3	O60645	OTTHUMG00000162205	ENST00000512944.1:c.463C>T	5.37:g.453583C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	147	76	0.517007	NM_007277	Q6P2E8|Q8TEN6|Q8WUW0|Q96DI4	Silent	SNP	ENST00000512944.1	37	CCDS54830.1																																																																																			C|0.972;T|0.028	0.028	strong		0.597	EXOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367882.1	NM_007277	
TGFBI	7045	hgsc.bcm.edu	37	5	135392482	135392482	+	Missense_Mutation	SNP	T	T	G	rs200219644		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:135392482T>G	ENST00000442011.2	+	12	1837	c.1676T>G	c.(1675-1677)tTg>tGg	p.L559W	TGFBI_ENST00000305126.8_Missense_Mutation_p.L559W|TGFBI_ENST00000508076.1_5'Flank	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	559	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGCAGACTCTTGGGTAAAGAC	0.512													T|||	1	0.000199681	0.0	0.0	5008	,	,		19392	0.0		0.001	False		,,,				2504	0.0				p.L559W		Atlas-SNP	.											.	TGFBI	76	.	0			c.T1676G						PASS	.	T	TRP/LEU	3,3871		0,3,1934	43.0	45.0	45.0		1676	5.8	1.0	5		45	0,8266		0,0,4133	yes	missense	TGFBI	NM_000358.2	61	0,3,6067	GG,GT,TT		0.0,0.0774,0.0247	probably-damaging	559/684	135392482	3,12137	1937	4133	6070	SO:0001583	missense	7045	exon12			GACTCTTGGGTAA	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"""transforming growth factor, beta-induced, 68kD"""	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.1676T>G	5.37:g.135392482T>G	ENSP00000416330:p.Leu559Trp	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	216	117	0.541667	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Missense_Mutation	SNP	ENST00000442011.2	37	CCDS47266.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.344323	0.82022	7.74E-4	0.0	ENSG00000120708	ENST00000442011;ENST00000398813;ENST00000305126	D;D	0.92495	-3.05;-3.05	5.75	5.75	0.90469	FAS1 domain (5);	0.345979	0.31636	N	0.007304	D	0.97012	0.9024	M	0.93854	3.465	0.58432	D	0.999999	D;D	0.67145	0.992;0.996	D;D	0.70487	0.969;0.969	D	0.97996	1.0357	10	0.87932	D	0	-1.0597	16.0502	0.80755	0.0:0.0:0.0:1.0	.	292;559	B9ZVW9;Q15582	.;BGH3_HUMAN	W	559;292;559	ENSP00000416330:L559W;ENSP00000306306:L559W	ENSP00000306306:L559W	L	+	2	0	TGFBI	135420381	1.000000	0.71417	1.000000	0.80357	0.737000	0.42083	5.538000	0.67193	2.201000	0.70794	0.496000	0.49642	TTG	.	.	weak		0.512	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		
C2orf44	80304	hgsc.bcm.edu	37	2	24260862	24260862	+	Silent	SNP	A	A	G	rs115270382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:24260862A>G	ENST00000295148.4	-	2	1560	c.1503T>C	c.(1501-1503)agT>agC	p.S501S	C2orf44_ENST00000406895.3_Silent_p.S501S	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	501									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)					TAGACAGAGGACTCTGGATTT	0.488			T	ALK	NSCLC								A|||	27	0.00539137	0.0204	0.0	5008	,	,		17626	0.0		0.0	False		,,,				2504	0.0				p.S501S		Atlas-SNP	.		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	C2orf44	56	.	0			c.T1503C						PASS	.	A	,	136,4270	94.4+/-133.1	2,132,2069	65.0	69.0	68.0		1503,1503	-3.5	0.1	2	dbSNP_132	68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	C2orf44	NM_001142319.1,NM_025203.2	,	2,133,6368	GG,GA,AA		0.0116,3.0867,1.0534	,	501/623,501/722	24260862	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	80304	exon2			CAGAGGACTCTGG	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.1503T>C	2.37:g.24260862A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_025203	D6W532|Q8IYK0|Q9HBP5	Silent	SNP	ENST00000295148.4	37	CCDS1705.1																																																																																			A|0.992;G|0.008	0.008	strong		0.488	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203	
GRIN3A	116443	hgsc.bcm.edu	37	9	104385646	104385646	+	Silent	SNP	A	A	G	rs138253972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:104385646A>G	ENST00000361820.3	-	5	3168	c.2568T>C	c.(2566-2568)gaT>gaC	p.D856D		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	856					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)	TGCAGTCAGCATCTATTGACA	0.413													A|||	5	0.000998403	0.0023	0.0029	5008	,	,		18756	0.0		0.0	False		,,,				2504	0.0				p.D856D		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T2568C						PASS	.	A		7,4399	12.9+/-30.5	0,7,2196	165.0	149.0	154.0		2568	1.7	1.0	9	dbSNP_134	154	0,8600		0,0,4300	no	coding-synonymous	GRIN3A	NM_133445.2		0,7,6496	GG,GA,AA		0.0,0.1589,0.0538		856/1116	104385646	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon5			GTCAGCATCTATT		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.2568T>C	9.37:g.104385646A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	183	121	0.661202	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			A|1.000;G|0.000	0.000	strong		0.413	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
C2CD3	26005	hgsc.bcm.edu	37	11	73796683	73796683	+	Missense_Mutation	SNP	T	T	C	rs1095423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73796683T>C	ENST00000334126.7	-	21	4116	c.3890A>G	c.(3889-3891)tAt>tGt	p.Y1297C	C2CD3_ENST00000313663.7_Missense_Mutation_p.Y1297C			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1297			Y -> C (in dbSNP:rs1095423).		brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					ATTTTCATGATAGACAGCAAA	0.413													T|||	239	0.0477236	0.1747	0.0115	5008	,	,		19547	0.0		0.0	False		,,,				2504	0.0				p.Y1297C		Atlas-SNP	.											.	C2CD3	288	.	0			c.A3890G						PASS	.	T	CYS/TYR	554,3846	248.7+/-256.4	40,474,1686	64.0	62.0	63.0		3890	5.9	1.0	11	dbSNP_86	63	15,8571	11.2+/-40.8	0,15,4278	yes	missense	C2CD3	NM_015531.4	194	40,489,5964	CC,CT,TT		0.1747,12.5909,4.3816	probably-damaging	1297/1964	73796683	569,12417	2200	4293	6493	SO:0001583	missense	26005	exon21			TCATGATAGACAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.3890A>G	11.37:g.73796683T>C	ENSP00000334379:p.Tyr1297Cys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		75	0.034340659340659344	70	0.14227642276422764	5	0.013812154696132596	0	0.0	0	0.0	T	18.08	3.542983	0.65198	0.125909	0.001747	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.46063	0.88;0.88;0.88	5.95	5.95	0.96441	.	0.188748	0.48767	D	0.000167	T	0.00754	0.0025	M	0.68317	2.08	0.29764	P	0.835337	D	0.89917	1.0	D	0.91635	0.999	T	0.29427	-1.0012	9	0.72032	D	0.01	-12.7519	11.7864	0.52045	0.1316:0.0:0.0:0.8684	rs1095423;rs1790396;rs52807296;rs61681570;rs1095423	1297	Q4AC94-1	.	C	1297;1297;1297;105	ENSP00000334379:Y1297C;ENSP00000323339:Y1297C;ENSP00000388750:Y105C	ENSP00000323339:Y1297C	Y	-	2	0	C2CD3	73474331	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.834000	0.55798	2.268000	0.75426	0.533000	0.62120	TAT	T|0.951;C|0.049	0.049	strong		0.413	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
ZNF284	342909	hgsc.bcm.edu	37	19	44590753	44590753	+	Silent	SNP	T	T	C	rs114253786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44590753T>C	ENST00000421176.3	+	5	1338	c.1122T>C	c.(1120-1122)aaT>aaC	p.N374N	ZNF223_ENST00000591793.1_3'UTR|RNU6-902P_ENST00000517212.1_RNA	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	374					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				ATAATTGTAATGTATGTGGGA	0.433													T|||	24	0.00479233	0.0166	0.0029	5008	,	,		21791	0.0		0.0	False		,,,				2504	0.0				p.N374N		Atlas-SNP	.											.	ZNF284	38	.	0			c.T1122C						PASS	.	T		65,4171		0,65,2053	93.0	100.0	98.0		1122	-4.8	0.0	19	dbSNP_132	98	0,8480		0,0,4240	no	coding-synonymous	ZNF284	NM_001037813.2		0,65,6293	CC,CT,TT		0.0,1.5345,0.5112		374/594	44590753	65,12651	2118	4240	6358	SO:0001819	synonymous_variant	342909	exon5			TTGTAATGTATGT	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"""Zinc fingers, C2H2-type"", ""-"""	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.1122T>C	19.37:g.44590753T>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_001037813	Q86WM1	Silent	SNP	ENST00000421176.3	37	CCDS46099.1																																																																																			T|0.995;C|0.005	0.005	strong		0.433	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813	
APOBEC4	403314	hgsc.bcm.edu	37	1	183617105	183617105	+	Missense_Mutation	SNP	A	A	G	rs1174658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	415	0	0		WXS	Illumina HiSeq	Phase_I	411	205	0.498783	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	
ILK	3611	hgsc.bcm.edu	37	11	6630833	6630833	+	Silent	SNP	G	G	A	rs1043390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6630833G>A	ENST00000396751.2	+	8	1275	c.819G>A	c.(817-819)ccG>ccA	p.P273P	RP11-732A19.2_ENST00000527398.1_RNA|TAF10_ENST00000531760.1_5'Flank|ILK_ENST00000537806.1_Silent_p.P139P|ILK_ENST00000420936.2_Silent_p.P273P|ILK_ENST00000528995.1_Silent_p.P212P|ILK_ENST00000299421.4_Silent_p.P273P|ILK_ENST00000526711.1_3'UTR	NM_001014795.1	NP_001014795.1	Q13418	ILK_HUMAN	integrin-linked kinase	273	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell junction assembly (GO:0034329)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|extracellular fibril organization (GO:0043206)|fibroblast migration (GO:0010761)|integrin-mediated signaling pathway (GO:0007229)|myelin assembly (GO:0032288)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|peptidyl-serine phosphorylation (GO:0018105)|platelet aggregation (GO:0070527)|positive regulation of axon extension (GO:0045773)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)		ACTGGATGCCGTATGGATCCC	0.507													A|||	1740	0.347444	0.5303	0.2651	5008	,	,		22842	0.3492		0.2555	False		,,,				2504	0.2515				p.P273P		Atlas-SNP	.											.	ILK	41	.	0			c.G819A						PASS	.	A	,,	2088,2314	603.5+/-390.1	482,1124,595	156.0	141.0	146.0		819,819,819	4.4	1.0	11	dbSNP_86	146	2160,6432	713.4+/-405.9	265,1630,2401	no	coding-synonymous,coding-synonymous,coding-synonymous	ILK	NM_001014794.1,NM_001014795.1,NM_004517.2	,,	747,2754,2996	AA,AG,GG		25.1397,47.433,32.692	,,	273/453,273/453,273/453	6630833	4248,8746	2201	4296	6497	SO:0001819	synonymous_variant	3611	exon9			GATGCCGTATGGA	U40282	CCDS7768.1, CCDS60712.1, CCDS60713.1	11p15.4	2014-09-17			ENSG00000166333	ENSG00000166333		"""Ankyrin repeat domain containing"""	6040	protein-coding gene	gene with protein product		602366				8538749	Standard	NM_004517		Approved		uc001mef.3	Q13418	OTTHUMG00000133407	ENST00000396751.2:c.819G>A	11.37:g.6630833G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	255	117	0.458824	NM_001014794	B7Z1I0|B7Z418|D3DQU0|P57043|Q68DZ3	Silent	SNP	ENST00000396751.2	37	CCDS7768.1																																																																																			G|0.669;A|0.331	0.331	strong		0.507	ILK-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384519.1	NM_004517	
MNT	4335	hgsc.bcm.edu	37	17	2298615	2298615	+	Silent	SNP	T	T	C	rs7213000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2298615T>C	ENST00000174618.4	-	2	612	c.207A>G	c.(205-207)ccA>ccG	p.P69P	MNT_ENST00000575394.1_Intron	NM_020310.2	NP_064706.1	Q99583	MNT_HUMAN	MAX network transcriptional repressor	69					cell aging (GO:0007569)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cell cycle (GO:0051726)|transcription from RNA polymerase II promoter (GO:0006366)	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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			endometrium(4)|large_intestine(5)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	12				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		ggggagccggtggagacagag	0.657													C|||	769	0.153554	0.2617	0.1037	5008	,	,		8879	0.1319		0.0954	False		,,,				2504	0.1247				p.P69P		Atlas-SNP	.											.	MNT	35	.	0			c.A207G						PASS	.	C		1044,3316		124,796,1260	22.0	29.0	26.0		207	-9.9	0.0	17	dbSNP_116	26	700,7834		40,620,3607	no	coding-synonymous	MNT	NM_020310.2		164,1416,4867	CC,CT,TT		8.2025,23.945,13.5257		69/583	2298615	1744,11150	2180	4267	6447	SO:0001819	synonymous_variant	4335	exon2			AGCCGGTGGAGAC	Y13444	CCDS11018.1	17p13.3	2013-11-15	2013-11-15		ENSG00000070444	ENSG00000070444		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	7188	protein-coding gene	gene with protein product	"""myc antagonist"", ""Max-interacting protein"""	603039	"""MAX binding protein"", ""MNT, MAX dimerization protein"""			9598315	Standard	NM_020310		Approved	ROX, MXD6, MAD6, bHLHd3	uc002fur.3	Q99583	OTTHUMG00000090603	ENST00000174618.4:c.207A>G	17.37:g.2298615T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_020310	A8K6D1|D3DTI7|Q1ED38	Silent	SNP	ENST00000174618.4	37	CCDS11018.1																																																																																			T|0.869;C|0.131	0.131	strong		0.657	MNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207158.1	NM_020310	
ALOX15	246	hgsc.bcm.edu	37	17	4539171	4539171	+	Silent	SNP	G	G	T	rs11568113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4539171G>T	ENST00000570836.1	-	9	1140	c.1044C>A	c.(1042-1044)cgC>cgA	p.R348R	ALOX15_ENST00000293761.3_Silent_p.R348R|ALOX15_ENST00000545513.1_Silent_p.R370R|ALOX15_ENST00000574640.1_Silent_p.R309R			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	348	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		AGTCAGAGCTGCGCACCCAGC	0.602													G|||	93	0.0185703	0.0681	0.0043	5008	,	,		20183	0.0		0.0	False		,,,				2504	0.0				p.R348R		Atlas-SNP	.											.	ALOX15	70	.	0			c.C1044A						PASS	.	G		314,4092	169.1+/-199.8	15,284,1904	68.0	70.0	69.0		1044	-7.4	0.6	17	dbSNP_120	69	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	ALOX15	NM_001140.3		15,286,6202	TT,TG,GG		0.0233,7.1266,2.4296		348/663	4539171	316,12690	2203	4300	6503	SO:0001819	synonymous_variant	246	exon8			AGAGCTGCGCACC	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"""Arachidonate lipoxygenases"""	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.1044C>A	17.37:g.4539171G>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	150	77	0.513333	NM_001140	A8K2P4|B7ZA11|Q8N6R7|Q99657	Silent	SNP	ENST00000570836.1	37	CCDS11049.1																																																																																			G|0.973;T|0.027	0.027	strong		0.602	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2		
BCAS1	8537	hgsc.bcm.edu	37	20	52675188	52675188	+	Missense_Mutation	SNP	G	G	T	rs394732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52675188G>T	ENST00000395961.3	-	2	236	c.70C>A	c.(70-72)Cag>Aag	p.Q24K	BCAS1_ENST00000371435.2_Missense_Mutation_p.Q24K|BCAS1_ENST00000411563.1_Intron|BCAS1_ENST00000371440.3_Missense_Mutation_p.Q24K	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	24			Q -> K (in dbSNP:rs394732).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				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)			TACACTACCTGGTAAGTCTCT	0.408													T|||	2885	0.576078	0.8094	0.3199	5008	,	,		15260	0.6339		0.4175	False		,,,				2504	0.546				p.Q24K		Atlas-SNP	.											.	BCAS1	77	.	0			c.C70A						PASS	.	T	LYS/GLN	3283,1123	403.5+/-332.8	1222,839,142	186.0	185.0	185.0		70	-0.3	0.0	20	dbSNP_80	185	3736,4864	617.3+/-396.6	803,2130,1367	yes	missense	BCAS1	NM_003657.2	53	2025,2969,1509	TT,TG,GG		43.4419,25.488,46.0326	benign	24/585	52675188	7019,5987	2203	4300	6503	SO:0001583	missense	8537	exon2			CTACCTGGTAAGT	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.70C>A	20.37:g.52675188G>T	ENSP00000379290:p.Gln24Lys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_003657	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	37	CCDS13444.1	1190	0.5448717948717948	390	0.7926829268292683	135	0.3729281767955801	343	0.5996503496503497	322	0.42480211081794195	T	0.254	-1.004058	0.02112	0.74512	0.434419	ENSG00000064787	ENST00000371440;ENST00000395961;ENST00000371435	T;T;T	0.12039	2.72;2.73;2.73	4.97	-0.322	0.12713	.	0.595161	0.16117	N	0.228808	T	0.00012	0.0000	N	0.00246	-1.78	0.23095	P	0.99830474	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21348	-1.0248	9	0.02654	T	1	-1.2767	5.6521	0.17622	0.0:0.1731:0.3608:0.4661	rs394732;rs17553498;rs52795105;rs57822491;rs394732	24;24	G3XAF7;O75363	.;BCAS1_HUMAN	K	24	ENSP00000360495:Q24K;ENSP00000379290:Q24K;ENSP00000360490:Q24K	ENSP00000360490:Q24K	Q	-	1	0	BCAS1	52108595	0.413000	0.25400	0.031000	0.17742	0.072000	0.16883	0.213000	0.17521	-0.426000	0.07360	-0.256000	0.11100	CAG	A|0.003;C|0.003	.	strong		0.408	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657	
FSCB	84075	hgsc.bcm.edu	37	14	44974966	44974966	+	Missense_Mutation	SNP	G	G	A	rs1959379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:44974966G>A	ENST00000340446.4	-	1	1516	c.1225C>T	c.(1225-1227)Cca>Tca	p.P409S	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	409	Pro-rich.		P -> S (in dbSNP:rs1959379). {ECO:0000269|PubMed:15489334}.			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)		ACTTTAGCTGGGGCCTCTTCA	0.517													G|||	1358	0.271166	0.2859	0.3055	5008	,	,		17836	0.3968		0.1193	False		,,,				2504	0.2536				p.P409S		Atlas-SNP	.											.	FSCB	173	.	0			c.C1225T						PASS	.	G	SER/PRO	1149,3249		151,847,1201	39.0	44.0	42.0		1225	-8.3	0.0	14	dbSNP_92	42	933,7661		53,827,3417	yes	missense	FSCB	NM_032135.3	74	204,1674,4618	AA,AG,GG		10.8564,26.1255,16.0252	possibly-damaging	409/826	44974966	2082,10910	2199	4297	6496	SO:0001583	missense	84075	exon1			TAGCTGGGGCCTC	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.1225C>T	14.37:g.44974966G>A	ENSP00000344579:p.Pro409Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	542	0.24816849816849818	138	0.2804878048780488	97	0.26795580110497236	223	0.38986013986013984	84	0.11081794195250659	G	6.900	0.535552	0.13188	0.261255	0.108564	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.19806	2.12	4.49	-8.33	0.00992	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.44711	-0.9310	8	0.31617	T	0.26	1.5439	3.3091	0.07010	0.4878:0.176:0.2415:0.0947	rs1959379;rs3825631;rs17855637;rs52807156;rs1959379	409	Q5H9T9	FSCB_HUMAN	S	409	ENSP00000344579:P409S	ENSP00000344579:P409S	P	-	1	0	FSCB	44044716	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.632000	0.00870	-1.724000	0.01373	-0.783000	0.03347	CCA	G|0.811;A|0.189	0.189	strong		0.517	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
PAPLN	89932	hgsc.bcm.edu	37	14	73727509	73727509	+	Missense_Mutation	SNP	T	T	G	rs177389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000340738.5_Missense_Mutation_p.M666R|PAPLN_ENST00000381166.3_Missense_Mutation_p.M693R			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	50	0	0		WXS	Illumina HiSeq	Phase_I	54	54	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	
PLEKHH2	130271	hgsc.bcm.edu	37	2	43927568	43927568	+	Silent	SNP	C	C	T	rs17031299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:43927568C>T	ENST00000282406.4	+	8	1581	c.1471C>T	c.(1471-1473)Cta>Tta	p.L491L		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	491					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TGATCTTGATCTAGTTGATGG	0.408													C|||	207	0.0413339	0.0696	0.0346	5008	,	,		21682	0.0347		0.007	False		,,,				2504	0.0501				p.L491L		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.C1471T						PASS	.	C		296,4110	161.4+/-193.6	15,266,1922	177.0	168.0	171.0		1471	3.0	0.8	2	dbSNP_123	171	27,8573	19.8+/-62.0	0,27,4273	no	coding-synonymous	PLEKHH2	NM_172069.3		15,293,6195	TT,TC,CC		0.314,6.7181,2.4835		491/1494	43927568	323,12683	2203	4300	6503	SO:0001819	synonymous_variant	130271	exon8			CTTGATCTAGTTG	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"""Pleckstrin homology (PH) domain containing"""	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.1471C>T	2.37:g.43927568C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	173	90	0.520231	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Silent	SNP	ENST00000282406.4	37	CCDS1812.1																																																																																			C|0.973;T|0.027	0.027	strong		0.408	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069	
AHNAK2	113146	hgsc.bcm.edu	37	14	105408182	105408182	+	Missense_Mutation	SNP	T	T	G	rs9672139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105408182T>G	ENST00000333244.5	-	7	13725	c.13606A>C	c.(13606-13608)Atg>Ctg	p.M4536L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4536			M -> L (in dbSNP:rs9672139).			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)			ACCTCGGGCATGTGGCCTTCT	0.627													-|||	2642	0.527556	0.6331	0.4942	5008	,	,		18365	0.3899		0.498	False		,,,				2504	0.5808				p.M4536L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A13606C						PASS	.	T	LEU/MET	2503,1327		823,857,235	106.0	117.0	113.0		13606	-7.1	0.0	14	dbSNP_119	113	4184,4032		1074,2036,998	no	missense	AHNAK2	NM_138420.2	15	1897,2893,1233	GG,GT,TT		49.075,34.6475,44.4878	benign	4536/5796	105408182	6687,5359	1915	4108	6023	SO:0001583	missense	113146	exon7			CGGGCATGTGGCC	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.13606A>C	14.37:g.105408182T>G	ENSP00000353114:p.Met4536Leu	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	181	180	0.994475	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1093	0.5004578754578755	314	0.6382113821138211	193	0.5331491712707183	204	0.35664335664335667	382	0.503957783641161	T	0.045	-1.271138	0.01421	0.653525	0.50925	ENSG00000185567	ENST00000333244	T	0.01145	5.27	3.56	-7.11	0.01542	.	1.407470	0.05982	U	0.644448	T	0.00012	0.0000	N	0.11255	0.115	0.80722	P	0.0	B	0.14438	0.01	B	0.18561	0.022	T	0.30446	-0.9978	9	0.07813	T	0.8	.	7.3918	0.26913	0.0:0.2516:0.4512:0.2972	rs9672139;rs9672139	4536	Q8IVF2	AHNK2_HUMAN	L	4536	ENSP00000353114:M4536L	ENSP00000353114:M4536L	M	-	1	0	AHNAK2	104479227	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-5.072000	0.00154	-3.139000	0.00234	-0.760000	0.03462	ATG	T|0.501;G|0.499	0.499	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ACACA	31	hgsc.bcm.edu	37	17	35470031	35470031	+	Silent	SNP	T	T	G	rs55811414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:35470031T>G	ENST00000394406.2	-	51	6523	c.6333A>C	c.(6331-6333)cgA>cgC	p.R2111R	ACACA_ENST00000353139.5_Silent_p.R2148R|ACACA_ENST00000335166.5_Silent_p.R2033R|ACACA_ENST00000360679.3_Silent_p.R2053R|ACACA_ENST00000361253.5_Silent_p.R237R	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	2111	Carboxyltransferase.				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)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	ACCTGCTTTCTCGGTCAGCAT	0.552													T|||	221	0.0441294	0.149	0.0274	5008	,	,		19920	0.0		0.004	False		,,,				2504	0.001				p.R2148R	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.A6444C						PASS	.	T	,,,,	461,3945	218.4+/-236.5	26,409,1768	82.0	71.0	75.0		6444,6333,6159,6099,6333	-1.6	1.0	17	dbSNP_129	75	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACACA	NM_198834.1,NM_198836.1,NM_198837.1,NM_198838.1,NM_198839.1	,,,,	26,441,6036	GG,GT,TT		0.3721,10.463,3.7906	,,,,	2148/2384,2111/2347,2053/2289,2033/2269,2111/2347	35470031	493,12513	2203	4300	6503	SO:0001819	synonymous_variant	31	exon51			GCTTTCTCGGTCA	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.6333A>C	17.37:g.35470031T>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																			G|0.034;T|0.966	0.034	strong		0.552	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
ARRDC2	27106	hgsc.bcm.edu	37	19	18123738	18123738	+	Missense_Mutation	SNP	T	T	C	rs7259041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	41	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	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	
GIMAP2	26157	hgsc.bcm.edu	37	7	150390255	150390255	+	Missense_Mutation	SNP	T	T	C	rs115945256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150390255T>C	ENST00000223293.5	+	3	975	c.881T>C	c.(880-882)aTg>aCg	p.M294T		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	294						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(8)|skin(2)|urinary_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTGCACAGCATGTGCAATTTG	0.323													T|||	24	0.00479233	0.0098	0.0014	5008	,	,		22226	0.004		0.0	False		,,,				2504	0.0061				p.M294T		Atlas-SNP	.											.	GIMAP2	39	.	0			c.T881C						PASS	.	T	THR/MET	58,4348	57.4+/-93.9	1,56,2146	117.0	108.0	111.0		881	2.1	0.0	7	dbSNP_132	111	0,8600		0,0,4300	yes	missense	GIMAP2	NM_015660.2	81	1,56,6446	CC,CT,TT		0.0,1.3164,0.4459	possibly-damaging	294/338	150390255	58,12948	2203	4300	6503	SO:0001583	missense	26157	exon3			ACAGCATGTGCAA	AL110151	CCDS5905.1	7q36.1	2014-04-04			ENSG00000106560	ENSG00000106560		"""GTPases, IMAP"""	21789	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 12"""	608085				15474311	Standard	NM_015660		Approved	DKFZp586D0824, HIMAP2, IMAP2, IAN12	uc003who.3	Q9UG22	OTTHUMG00000157488	ENST00000223293.5:c.881T>C	7.37:g.150390255T>C	ENSP00000223293:p.Met294Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_015660	Q96L25	Missense_Mutation	SNP	ENST00000223293.5	37	CCDS5905.1	7	0.003205128205128205	4	0.008130081300813009	0	0.0	3	0.005244755244755245	0	0.0	T	3.694	-0.062952	0.07273	0.013164	0.0	ENSG00000106560	ENST00000223293	T	0.05382	3.45	3.32	2.14	0.27477	.	1.629670	0.03647	N	0.240382	T	0.03739	0.0106	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.37663	-0.9696	10	0.87932	D	0	.	5.2908	0.15725	0.0:0.1378:0.0:0.8622	.	294	Q9UG22	GIMA2_HUMAN	T	294	ENSP00000223293:M294T	ENSP00000223293:M294T	M	+	2	0	GIMAP2	150021188	0.004000	0.15560	0.005000	0.12908	0.008000	0.06430	0.560000	0.23500	0.491000	0.27793	0.533000	0.62120	ATG	T|0.995;C|0.005	0.005	strong		0.323	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660	
RNF122	79845	hgsc.bcm.edu	37	8	33416222	33416222	+	Silent	SNP	C	C	T	rs3735951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	70	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	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	
RGPD4	285190	hgsc.bcm.edu	37	2	108487330	108487330	+	Missense_Mutation	SNP	A	A	G	rs148409227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:108487330A>G	ENST00000408999.3	+	20	2947	c.2870A>G	c.(2869-2871)aAt>aGt	p.N957S	RGPD4_ENST00000354986.4_Missense_Mutation_p.N957S	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	957					protein targeting to Golgi (GO:0000042)			p.N957S(1)		breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						GGCCAGAAGAATGGCCGTGGT	0.403													N|||	2645	0.528155	0.4395	0.4755	5008	,	,		19150	0.3532		0.6889	False		,,,				2504	0.7004				p.N957S		Atlas-SNP	.											RGPD4,NS,carcinoma,0,1	RGPD4	112	1	1	Substitution - Missense(1)	kidney(1)	c.A2870G						scavenged	.						20.0	29.0	27.0					2																	108487330		139	630	769	SO:0001583	missense	285190	exon20			AGAAGAATGGCCG	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.2870A>G	2.37:g.108487330A>G	ENSP00000386810:p.Asn957Ser	Somatic	1693	1	0.000590667		WXS	Illumina HiSeq	Phase_I	1647	1227	0.744991	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	CCDS46381.1	1150	0.5265567765567766	242	0.491869918699187	192	0.5303867403314917	206	0.36013986013986016	510	0.6728232189973615	-	0.009	-1.805932	0.00606	.	.	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.38887	1.11;1.11	2.3	0.885	0.19188	.	.	.	.	.	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.13145	0.007	B	0.12837	0.008	T	0.44636	-0.9315	8	0.08179	T	0.78	-13.4325	7.4662	0.27322	0.7838:0.2162:0.0:0.0	.	957	Q7Z3J3	RGPD4_HUMAN	S	957;957;715	ENSP00000347081:N957S;ENSP00000386810:N957S	ENSP00000347081:N957S	N	+	2	0	RGPD4	107853762	0.963000	0.33076	0.699000	0.30290	0.067000	0.16453	1.479000	0.35453	1.068000	0.40764	0.128000	0.15822	AAT	G|1.000;|0.000	1.000	weak		0.403	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
DSPP	1834	hgsc.bcm.edu	37	4	88535830	88535830	+	Silent	SNP	T	T	C	rs202057495|rs142316753		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88535830T>C	ENST00000282478.7	+	4	2049	c.2016T>C	c.(2014-2016)agT>agC	p.S672S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S672S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	672	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagtgatagcagtg	0.488																																					p.S672S		Atlas-SNP	.											.	DSPP	174	.	0			c.T2016C						PASS	.						121.0	137.0	131.0					4																	88535830		1707	3117	4824	SO:0001819	synonymous_variant	1834	exon5			CAGCAGTGATAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2016T>C	4.37:g.88535830T>C		Somatic	345	0	0		WXS	Illumina HiSeq	Phase_I	362	56	0.154696	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.488	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
C2orf81	388963	hgsc.bcm.edu	37	2	74641624	74641624	+	Silent	SNP	G	G	C	rs2240444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74641624G>C	ENST00000517883.1	-	1	2086	c.1395C>G	c.(1393-1395)ccC>ccG	p.P465P	C2orf81_ENST00000290390.5_Silent_p.P533P			A6NN90	CB081_HUMAN	chromosome 2 open reading frame 81	526										endometrium(3)|kidney(1)	4						GCAGCAACACGGGCTTCCACA	0.622													C|||	2730	0.545128	0.91	0.3271	5008	,	,		16936	0.8244		0.1412	False		,,,				2504	0.3344				p.P533P		Atlas-SNP	.											.	C2orf81	23	.	0			c.C1599G						PASS	.	C		1103,281		439,225,28	39.0	46.0	44.0		1599	-1.6	0.0	2	dbSNP_98	44	423,2759		31,361,1199	no	coding-synonymous	C2orf81	NM_001145054.1		470,586,1227	CC,CG,GG		13.2935,20.3035,33.4209		533/589	74641624	1526,3040	692	1591	2283	SO:0001819	synonymous_variant	388963	exon4			CAACACGGGCTTC	AC005041, CH471053		2p13.1	2012-08-07			ENSG00000159239	ENSG00000159239			34350	protein-coding gene	gene with protein product						15815621	Standard	NM_001145054		Approved	LOC388963, hCG40743	uc010yrq.1	A6NN90	OTTHUMG00000164184	ENST00000517883.1:c.1395C>G	2.37:g.74641624G>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	158	158	1	NM_001145054		Silent	SNP	ENST00000517883.1	37																																																																																				G|0.496;C|0.504	0.504	strong		0.622	C2orf81-002	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000377683.1	NM_001145054	
CREB3L1	90993	hgsc.bcm.edu	37	11	46339011	46339011	+	Missense_Mutation	SNP	G	G	A	rs35652107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46339011G>A	ENST00000529193.1	+	10	1682	c.1231G>A	c.(1231-1233)Gca>Aca	p.A411T	CREB3L1_ENST00000288400.3_Missense_Mutation_p.A411T|CREB3L1_ENST00000534616.1_3'UTR			Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like 1	411			A -> T (in dbSNP:rs35652107).		regulation of bone mineralization (GO:0030500)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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)		FUS/CREB3L1(6)	NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3)	12				GBM - Glioblastoma multiforme(35;0.0285)		CCCCCTGGCCGCAGACGGCGT	0.672			T	FUS	myxofibrosarcoma								G|||	368	0.0734824	0.0847	0.0447	5008	,	,		15933	0.0843		0.0775	False		,,,				2504	0.0634				p.A411T	Pancreas(3;159 194 19597 26278 47995)	Atlas-SNP	.		Dom	yes		11	11p11.2	90993	cAMP responsive element binding protein 3-like 1		M	.	CREB3L1	30	.	0			c.G1231A						PASS	.	G	THR/ALA	310,3666		24,262,1702	38.0	42.0	41.0		1231	-10.2	0.2	11	dbSNP_126	41	629,7693		18,593,3550	yes	missense	CREB3L1	NM_052854.2	58	42,855,5252	AA,AG,GG		7.5583,7.7968,7.6354	benign	411/520	46339011	939,11359	1988	4161	6149	SO:0001583	missense	90993	exon10			CTGGCCGCAGACG		CCDS53620.1	11q11	2013-01-10				ENSG00000157613		"""basic leucine zipper proteins"""	18856	protein-coding gene	gene with protein product	"""BBF-2 homolog (drosophila)"""						Standard	NM_052854		Approved	OASIS	uc021qil.1	Q96BA8		ENST00000529193.1:c.1231G>A	11.37:g.46339011G>A	ENSP00000434939:p.Ala411Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_052854	Q8N2D5|Q96CP0	Missense_Mutation	SNP	ENST00000529193.1	37	CCDS53620.1	188	0.08608058608058608	50	0.1016260162601626	18	0.049723756906077346	62	0.10839160839160839	58	0.07651715039577836	G	3.986	-0.005371	0.07773	0.077968	0.075583	ENSG00000157613	ENST00000529193;ENST00000288400;ENST00000446415	T;T	0.64260	-0.09;-0.09	5.08	-10.2	0.00374	.	1.168090	0.06301	N	0.701005	T	0.00637	0.0021	N	0.13098	0.295	0.80722	P	0.0	B;B	0.19583	0.037;0.001	B;B	0.13407	0.009;0.001	T	0.02567	-1.1140	9	0.10636	T	0.68	-16.3211	8.1366	0.31058	0.1832:0.1525:0.595:0.0693	rs35652107	323;411	Q96BA8-2;Q96BA8	.;CR3L1_HUMAN	T	411;411;323	ENSP00000434939:A411T;ENSP00000288400:A411T	ENSP00000288400:A411T	A	+	1	0	CREB3L1	46295587	0.000000	0.05858	0.202000	0.23494	0.103000	0.19146	-1.101000	0.03336	-1.999000	0.00967	-1.079000	0.02226	GCA	G|0.914;A|0.086	0.086	strong		0.672	CREB3L1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389702.1	NM_052854	
FBN2	2201	hgsc.bcm.edu	37	5	127670412	127670412	+	Splice_Site	SNP	T	T	G	rs28763943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:127670412T>G	ENST00000508053.1	-	37	5072	c.4098A>C	c.(4096-4098)acA>acC	p.T1366T	FBN2_ENST00000508989.1_Splice_Site_p.T1333T|FBN2_ENST00000262464.4_Splice_Site_p.T1366T|FBN2_ENST00000507835.1_Splice_Site_p.T216T			P35556	FBN2_HUMAN	fibrillin 2	1366	EGF-like 21; 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)		GAAACCTACCTGTACATCCTG	0.443													T|||	98	0.0195687	0.0726	0.0029	5008	,	,		21065	0.0		0.0	False		,,,				2504	0.0				p.T1366T		Atlas-SNP	.											.	FBN2	858	.	0			c.A4098C						PASS	.	T		331,4075	174.4+/-204.0	15,301,1887	131.0	117.0	122.0		4098	5.0	1.0	5	dbSNP_125	122	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous-near-splice	FBN2	NM_001999.3		15,304,6184	GG,GT,TT		0.0349,7.5125,2.568		1366/2913	127670412	334,12672	2203	4300	6503	SO:0001630	splice_region_variant	2201	exon31			CCTACCTGTACAT	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.4099+1A>C	5.37:g.127670412T>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			T|0.975;G|0.025	0.025	strong		0.443	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	Silent
GREB1	9687	hgsc.bcm.edu	37	2	11725908	11725908	+	Missense_Mutation	SNP	G	G	A	rs6744817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11725908G>A	ENST00000381486.2	+	9	1336	c.1036G>A	c.(1036-1038)Gtg>Atg	p.V346M	GREB1_ENST00000381483.2_Missense_Mutation_p.V346M|GREB1_ENST00000263834.5_Missense_Mutation_p.V346M|RN7SL674P_ENST00000463397.2_RNA|GREB1_ENST00000234142.5_Missense_Mutation_p.V346M	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	346			V -> M (in dbSNP:rs6744817).			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)		CATGTCCTGCGTGCCGCAGGT	0.522													G|||	493	0.0984425	0.3041	0.036	5008	,	,		22068	0.0317		0.003	False		,,,				2504	0.0317				p.V346M	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.G1036A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	1125,3281	402.6+/-332.4	145,835,1223	88.0	80.0	83.0		1036,1036,1036	-8.3	0.1	2	dbSNP_116	83	29,8571	19.2+/-60.6	0,29,4271	yes	missense,missense,missense	GREB1	NM_014668.3,NM_033090.2,NM_148903.2	21,21,21	145,864,5494	AA,AG,GG		0.3372,25.5334,8.8728	benign,benign,benign	346/1950,346/458,346/410	11725908	1154,11852	2203	4300	6503	SO:0001583	missense	9687	exon9			TCCTGCGTGCCGC		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.1036G>A	2.37:g.11725908G>A	ENSP00000370896:p.Val346Met	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	148	147	0.993243	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	175	0.08012820512820513	142	0.2886178861788618	11	0.03038674033149171	20	0.03496503496503497	2	0.002638522427440633	G	2.542	-0.306091	0.05458	0.255334	0.003372	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000381483;ENST00000234142	T;T;T;T	0.19938	3.11;2.11;2.11;3.11	5.46	-8.28	0.01013	.	0.941025	0.08955	N	0.869523	T	0.00012	0.0000	N	0.11560	0.145	0.48395	P	3.589999999999982E-4	B;B;B	0.19331	0.035;0.008;0.004	B;B;B	0.17979	0.02;0.003;0.005	T	0.44128	-0.9348	9	0.29301	T	0.29	-18.7477	3.0304	0.06104	0.5071:0.2169:0.1333:0.1426	rs6744817;rs6744817	346;346;346	Q4ZG55-2;Q4ZG55-3;Q4ZG55	.;.;GREB1_HUMAN	M	346	ENSP00000370896:V346M;ENSP00000263834:V346M;ENSP00000370892:V346M;ENSP00000234142:V346M	ENSP00000234142:V346M	V	+	1	0	GREB1	11643359	0.150000	0.22732	0.089000	0.20774	0.009000	0.06853	-0.391000	0.07323	-1.342000	0.02222	-0.808000	0.03180	GTG	G|0.906;A|0.094	0.094	strong		0.522	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
TOR1A	1861	hgsc.bcm.edu	37	9	132585058	132585058	+	Silent	SNP	G	G	A	rs2296793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132585058G>A	ENST00000351698.4	-	2	294	c.246C>T	c.(244-246)gcC>gcT	p.A82A	TOR1A_ENST00000473084.1_5'UTR	NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	82					ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)	p.A82A(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				AACCAAACACGGCATTTAAGA	0.488													A|||	1133	0.226238	0.2179	0.2118	5008	,	,		21361	0.2133		0.2753	False		,,,				2504	0.2106				p.A82A		Atlas-SNP	.											TOR1A,NS,carcinoma,0,1	TOR1A	36	1	1	Substitution - coding silent(1)	stomach(1)	c.C246T						PASS	.	A		981,3425	733.0+/-410.4	107,767,1329	167.0	152.0	157.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	246	-10.4	0.0	9	dbSNP_100	157	2066,6534	718.9+/-406.2	263,1540,2497	no	coding-synonymous	TOR1A	NM_000113.2		370,2307,3826	AA,AG,GG		24.0233,22.2651,23.4276		82/333	132585058	3047,9959	2203	4300	6503	SO:0001819	synonymous_variant	1861	exon2			AAACACGGCATTT	AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"""dystonia 1, torsion (autosomal dominant; torsin A)"""	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.246C>T	9.37:g.132585058G>A		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	208	63	0.302885	NM_000113	B2RB58|Q53Y64|Q96CA0	Silent	SNP	ENST00000351698.4	37	CCDS6930.1																																																																																			G|0.763;A|0.237	0.237	strong		0.488	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113	
COL6A2	1292	hgsc.bcm.edu	37	21	47545889	47545889	+	Silent	SNP	C	C	G	rs61735829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47545889C>G	ENST00000300527.4	+	26	2264	c.2160C>G	c.(2158-2160)cgC>cgG	p.R720R	COL6A2_ENST00000357838.4_Silent_p.R720R|COL6A2_ENST00000397763.1_Silent_p.R720R|COL6A2_ENST00000310645.5_Silent_p.R720R|COL6A2_ENST00000409416.1_Silent_p.R720R	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	720	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)		AGAGCCGGCGCCAGAAGACAC	0.637													C|||	82	0.0163738	0.059	0.0058	5008	,	,		14676	0.0		0.0	False		,,,				2504	0.0				p.R720R		Atlas-SNP	.											COL6A2_ENST00000357838,NS,carcinoma,+2,3	COL6A2	351	3	0			c.C2160G						PASS	.	C	,,	227,4179	135.3+/-171.4	6,215,1982	68.0	67.0	67.0		2160,2160,2160	0.1	1.0	21	dbSNP_129	67	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	,,	6,218,6279	GG,GC,CC		0.0349,5.1521,1.7684	,,	720/1020,720/919,720/829	47545889	230,12776	2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			CCGGCGCCAGAAG	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.2160C>G	21.37:g.47545889C>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	166	86	0.518072	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			C|0.982;G|0.018	0.018	strong		0.637	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
KALRN	8997	hgsc.bcm.edu	37	3	124369744	124369744	+	Silent	SNP	C	C	T	rs12106716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124369744C>T	ENST00000291478.5	+	5	823	c.660C>T	c.(658-660)aaC>aaT	p.N220N	KALRN_ENST00000428018.2_Silent_p.N188N|KALRN_ENST00000459915.1_Silent_p.N9N|KALRN_ENST00000360013.3_Silent_p.N1917N|KALRN_ENST00000393496.1_Silent_p.N258N	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1916					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						CTCCTAAAAACCCAGAAGAAG	0.552													C|||	446	0.0890575	0.1339	0.111	5008	,	,		19385	0.001		0.1014	False		,,,				2504	0.091				p.N1917N		Atlas-SNP	.											.	KALRN	556	.	0			c.C5751T						PASS	.	C	,	643,3763	275.7+/-272.7	49,545,1609	93.0	84.0	87.0		5751,660	4.0	1.0	3	dbSNP_120	87	1048,7552	221.5+/-258.9	63,922,3315	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_007064.3	,	112,1467,4924	TT,TC,CC		12.186,14.5937,13.0017	,	1917/2987,220/1290	124369744	1691,11315	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon38			TAAAAACCCAGAA	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	ENST00000291478.5:c.660C>T	3.37:g.124369744C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	22	0.305556	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	37	CCDS3028.1	187	0.08562271062271062	73	0.1483739837398374	43	0.11878453038674033	0	0.0	71	0.09366754617414248	C	1.724	-0.495982	0.04291	0.145937	0.12186	ENSG00000160145	ENST00000354186	.	.	.	4.83	3.96	0.45880	.	.	.	.	.	T	0.00552	0.0018	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.13899	-1.0492	3	.	.	.	.	12.8883	0.58057	0.0:0.9206:0.0:0.0794	rs12106716	.	.	.	I	1886	.	.	T	+	2	0	KALRN	125852434	1.000000	0.71417	1.000000	0.80357	0.210000	0.24377	2.823000	0.48081	1.250000	0.43966	0.655000	0.94253	ACC	C|0.888;T|0.112	0.112	strong		0.552	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947	
CAD	790	hgsc.bcm.edu	37	2	27460968	27460968	+	Silent	SNP	A	A	G	rs1141313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27460968A>G	ENST00000403525.1	+	29	4728	c.4584A>G	c.(4582-4584)gcA>gcG	p.A1528A	CAD_ENST00000264705.4_Silent_p.A1591A			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGCTCACGCAGAGCAGCAAA	0.557													G|||	2277	0.454673	0.8374	0.4683	5008	,	,		21934	0.1488		0.2883	False		,,,				2504	0.4141				p.A1591A		Atlas-SNP	.											CAD,NS,carcinoma,+1,1	CAD	199	1	0			c.A4773G						PASS	.	G		3287,1119	398.1+/-330.7	1233,821,149	102.0	95.0	98.0		4773	-9.6	0.5	2	dbSNP_86	98	2564,6036	690.7+/-404.5	377,1810,2113	no	coding-synonymous	CAD	NM_004341.3		1610,2631,2262	GG,GA,AA		29.814,25.3972,44.9869		1591/2226	27460968	5851,7155	2203	4300	6503	SO:0001819	synonymous_variant	790	exon30			TCACGCAGAGCAG	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.4584A>G	2.37:g.27460968A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	195	194	0.994872	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	37		825	0.37774725274725274	400	0.8130081300813008	152	0.4198895027624309	64	0.11188811188811189	209	0.2757255936675462	G	0.885	-0.727540	0.03158	0.746028	0.29814	ENSG00000084774	ENST00000458503	.	.	.	4.8	-9.6	0.00553	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999980619	.	.	.	.	.	.	T	0.20306	-1.0279	3	.	.	.	-0.1691	2.9165	0.05754	0.3979:0.2642:0.2509:0.0869	rs1141313;rs17855322;rs58779686;rs1141313	.	.	.	R	243	.	.	Q	+	2	0	CAD	27314472	0.000000	0.05858	0.529000	0.27951	0.107000	0.19398	-4.974000	0.00164	-2.338000	0.00627	-1.195000	0.01675	CAG	A|0.568;G|0.432	0.432	strong		0.557	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
FNDC7	163479	hgsc.bcm.edu	37	1	109270563	109270563	+	Silent	SNP	T	T	C	rs4484951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109270563T>C	ENST00000370017.3	+	7	1522	c.1245T>C	c.(1243-1245)aaT>aaC	p.N415N	FNDC7_ENST00000271311.2_Silent_p.N416N	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	415	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				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)		TTGAGTGCAATGACACTACTC	0.483													T|||	206	0.0411342	0.1059	0.0245	5008	,	,		23725	0.0		0.0189	False		,,,				2504	0.0307				p.N415N		Atlas-SNP	.											.	FNDC7	113	.	0			c.T1245C						PASS	.	T		390,4016	196.0+/-220.5	15,360,1828	292.0	247.0	262.0		1245	-0.6	1.0	1	dbSNP_111	262	138,8462	68.4+/-130.8	0,138,4162	no	coding-synonymous	FNDC7	NM_001144937.1		15,498,5990	CC,CT,TT		1.6047,8.8516,4.0597		415/734	109270563	528,12478	2203	4300	6503	SO:0001819	synonymous_variant	163479	exon7			GTGCAATGACACT		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.1245T>C	1.37:g.109270563T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	210	105	0.5	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Silent	SNP	ENST00000370017.3	37	CCDS44185.1	79	0.036172161172161175	55	0.11178861788617886	9	0.024861878453038673	0	0.0	15	0.01978891820580475	T	7.396	0.631779	0.14322	0.088516	0.016047	ENSG00000143107	ENST00000445274	.	.	.	5.73	-0.588	0.11687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.0088	6.4663	0.21983	0.0:0.311:0.2203:0.4687	rs4484951;rs4484951	.	.	.	R	191	.	.	X	+	1	0	FNDC7	109072086	0.058000	0.20735	0.988000	0.46212	0.647000	0.38526	-0.778000	0.04664	-0.346000	0.08312	0.459000	0.35465	TGA	T|0.959;C|0.041	0.041	strong		0.483	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
SLC17A5	26503	hgsc.bcm.edu	37	6	74354175	74354175	+	Silent	SNP	C	C	T	rs472294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74354175C>T	ENST00000355773.5	-	2	514	c.246G>A	c.(244-246)gcG>gcA	p.A82A	SLC17A5_ENST00000481996.1_5'UTR|SLC17A5_ENST00000393019.3_Silent_p.A82A	NM_012434.4	NP_036566.1	Q9NRA2	S17A5_HUMAN	solute carrier family 17 (acidic sugar transporter), member 5	82					amino acid transport (GO:0006865)|anion transport (GO:0006820)|ion transport (GO:0006811)|proton transport (GO:0015992)|sialic acid transport (GO:0015739)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	sialic acid transmembrane transporter activity (GO:0015136)|sugar:proton symporter activity (GO:0005351)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCTCTGGACACGCCTTGGAAG	0.343													C|||	667	0.133187	0.1641	0.1571	5008	,	,		15464	0.1845		0.0726	False		,,,				2504	0.0838				p.A82A		Atlas-SNP	.											.	SLC17A5	42	.	0			c.G246A						PASS	.	C		695,3711	291.5+/-281.6	62,571,1570	74.0	72.0	73.0		246	1.6	0.8	6	dbSNP_83	73	631,7969	162.6+/-215.3	25,581,3694	no	coding-synonymous	SLC17A5	NM_012434.4		87,1152,5264	TT,TC,CC		7.3372,15.7739,10.1953		82/496	74354175	1326,11680	2203	4300	6503	SO:0001819	synonymous_variant	26503	exon2			TGGACACGCCTTG	AJ387747	CCDS4981.1	6q13	2013-07-18	2013-07-18		ENSG00000119899	ENSG00000119899		"""Solute carriers"""	10933	protein-coding gene	gene with protein product		604322	"""sialic acid storage disease"", ""solute carrier family 17 (anion/sugar transporter), member 5"""	SIASD		10581036, 8198127	Standard	NM_012434		Approved	AST, SD, ISSD, NSD, SIALIN, SLD	uc003phn.4	Q9NRA2	OTTHUMG00000015039	ENST00000355773.5:c.246G>A	6.37:g.74354175C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	130	61	0.469231	NM_012434	Q5SZ76|Q8NBR5|Q9UGH0	Silent	SNP	ENST00000355773.5	37	CCDS4981.1																																																																																			C|0.888;T|0.112	0.112	strong		0.343	SLC17A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041228.1		
ZNF841	284371	hgsc.bcm.edu	37	19	52569479	52569479	+	Silent	SNP	G	G	A	rs61738706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52569479G>A	ENST00000426391.2	-	5	1859	c.1308C>T	c.(1306-1308)taC>taT	p.Y436Y	ZNF841_ENST00000594295.1_Silent_p.Y552Y|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000359973.2_Intron|ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000389534.4_Silent_p.Y552Y			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	436					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(4)|kidney(3)|lung(3)	11						GGTATCCACCGTAATTAAAGA	0.403													g|||	110	0.0219649	0.0772	0.0101	5008	,	,		22430	0.0		0.001	False		,,,				2504	0.0				p.Y552Y		Atlas-SNP	.											.	ZNF841	183	.	0			c.C1656T						PASS	.	A		87,1297		3,81,608	93.0	81.0	85.0		1656	-4.5	0.0	19	dbSNP_129	85	0,3182		0,0,1591	no	coding-synonymous	ZNF841	NM_001136499.1		3,81,2199	AA,AG,GG		0.0,6.2861,1.9054		552/925	52569479	87,4479	692	1591	2283	SO:0001819	synonymous_variant	284371	exon7			TCCACCGTAATTA	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.1308C>T	19.37:g.52569479G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Silent	SNP	ENST00000426391.2	37																																																																																				G|0.979;A|0.021	0.021	strong		0.403	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155	
TH	7054	hgsc.bcm.edu	37	11	2190982	2190982	+	Silent	SNP	A	A	G	rs7950050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2190982A>G	ENST00000381178.1	-	3	321	c.303T>C	c.(301-303)gcT>gcC	p.A101A	TH_ENST00000352909.3_Silent_p.A70A|TH_ENST00000333684.5_Silent_p.A74A|TH_ENST00000381175.1_Silent_p.A97A	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	101					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CAAAGGCCACAGCCTCCAGGG	0.697													G|||	168	0.0335463	0.1233	0.0058	5008	,	,		14629	0.0		0.001	False		,,,				2504	0.0				p.A101A		Atlas-SNP	.											.	TH	43	.	0			c.T303C						PASS	.	G	,,	522,3882	744.0+/-411.5	23,476,1703	32.0	34.0	34.0		210,303,291	-1.3	0.1	11	dbSNP_116	34	13,8583	796.2+/-407.5	0,13,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	23,489,5988	GG,GA,AA		0.1512,11.8529,4.1154	,,	70/498,101/529,97/525	2190982	535,12465	2202	4298	6500	SO:0001819	synonymous_variant	7054	exon3			GGCCACAGCCTCC	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.303T>C	11.37:g.2190982A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	116	62	0.534483	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			A|0.952;G|0.048	0.048	strong		0.697	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
WASF3	10810	hgsc.bcm.edu	37	13	27250823	27250823	+	Silent	SNP	T	T	C	rs3764108	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	95	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	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		
POLR3D	661	hgsc.bcm.edu	37	8	22107707	22107707	+	Silent	SNP	C	C	T	rs34435413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22107707C>T	ENST00000397802.4	+	7	1256	c.1041C>T	c.(1039-1041)gaC>gaT	p.D347D	POLR3D_ENST00000306433.4_Silent_p.D347D			P05423	RPC4_HUMAN	polymerase (RNA) III (DNA directed) polypeptide D, 44kDa	347					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	13				Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		TGACTCTGGACGTGACCATGG	0.567													C|||	19	0.00379393	0.0144	0.0	5008	,	,		19108	0.0		0.0	False		,,,				2504	0.0				p.D347D		Atlas-SNP	.											.	POLR3D	26	.	0			c.C1041T						PASS	.	C		78,4328	68.1+/-105.8	0,78,2125	82.0	73.0	76.0		1041	-10.8	0.5	8	dbSNP_126	76	0,8600		0,0,4300	no	coding-synonymous	POLR3D	NM_001722.2		0,78,6425	TT,TC,CC		0.0,1.7703,0.5997		347/399	22107707	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	661	exon8			TCTGGACGTGACC	M17754	CCDS34858.1	8q21	2013-01-21	2003-04-01	2003-04-04	ENSG00000168495	ENSG00000168495		"""RNA polymerase subunits"""	1080	protein-coding gene	gene with protein product		187280	"""BN51 (BHK21) temperature sensitivity complementing"""	BN51T		12391170, 11279001	Standard	NM_001722		Approved	TSBN51, RPC4	uc003xbl.3	P05423	OTTHUMG00000163778	ENST00000397802.4:c.1041C>T	8.37:g.22107707C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_001722	Q6FI28|Q9BPV7|Q9BPZ1|Q9BXB3	Silent	SNP	ENST00000397802.4	37	CCDS34858.1																																																																																			C|0.993;T|0.007	0.007	strong		0.567	POLR3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375434.2	NM_001722	
NECAB3	63941	hgsc.bcm.edu	37	20	32248088	32248088	+	Silent	SNP	C	C	T	rs146604647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:32248088C>T	ENST00000246190.6	-	6	556	c.501G>A	c.(499-501)ctG>ctA	p.L167L	C20orf144_ENST00000375222.3_5'Flank|NECAB3_ENST00000375238.4_Silent_p.L167L|NECAB3_ENST00000606525.1_5'UTR|RP1-63M2.6_ENST00000607224.1_RNA	NM_031232.3	NP_112509.3	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	167					protein metabolic process (GO:0019538)|protein secretion (GO:0009306)|regulation of amyloid precursor protein biosynthetic process (GO:0042984)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|Golgi cis cisterna (GO:0000137)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			large_intestine(3)|lung(5)|skin(2)	10						CCTGGGCCTCCAGGGTATCTG	0.622													C|||	10	0.00199681	0.0076	0.0	5008	,	,		18803	0.0		0.0	False		,,,				2504	0.0				p.L167L		Atlas-SNP	.											.	NECAB3	27	.	0			c.G501A						PASS	.	C	,	24,4058		0,24,2017	48.0	54.0	52.0		501,501	3.9	1.0	20	dbSNP_134	52	0,8376		0,0,4188	no	coding-synonymous,coding-synonymous	NECAB3	NM_031231.3,NM_031232.3	,	0,24,6205	TT,TC,CC		0.0,0.5879,0.1926	,	167/363,167/397	32248088	24,12434	2041	4188	6229	SO:0001819	synonymous_variant	63941	exon6			GGCCTCCAGGGTA	AB039947	CCDS42866.1, CCDS42867.1	20q11.21	2013-01-10	2007-12-06	2007-12-06	ENSG00000125967	ENSG00000125967		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	15851	protein-coding gene	gene with protein product	"""EF-hand calcium binding protein 3"""	612478	"""amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein"""	SYTIP2, APBA2BP		10833507	Standard	NM_031232		Approved	XB51, dJ63M2.4, NIP1, dJ63M2.5, EFCBP3	uc002wzn.4	Q96P71	OTTHUMG00000032264	ENST00000246190.6:c.501G>A	20.37:g.32248088C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_031232	A8K780|E1P5N2|Q5JWF5|Q5JWF6|Q5JWF7|Q86VV1|Q9H433|Q9H8G8|Q9HBW7|Q9HCQ9	Silent	SNP	ENST00000246190.6	37	CCDS42866.1																																																																																			C|0.996;T|0.004	0.004	strong		0.622	NECAB3-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078724.2		
TICRR	90381	hgsc.bcm.edu	37	15	90145118	90145118	+	Silent	SNP	T	T	A	rs202042800		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90145118T>A	ENST00000268138.7	+	12	2583	c.2478T>A	c.(2476-2478)ccT>ccA	p.P826P	TICRR_ENST00000560985.1_Silent_p.P825P			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	826					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)										TTTCTGTGCCTTTTTTGTCAA	0.458													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19991	0.0		0.0	False		,,,				2504	0.0				p.P826P		Atlas-SNP	.											.	.	.	.	0			c.T2478A						PASS	.	T		5,3841		0,5,1918	137.0	125.0	129.0		2478	0.3	0.1	15		129	0,8276		0,0,4138	no	coding-synonymous	C15orf42	NM_152259.3		0,5,6056	AA,AT,TT		0.0,0.13,0.0412		826/1911	90145118	5,12117	1923	4138	6061	SO:0001819	synonymous_variant	90381	exon12			TGTGCCTTTTTTG	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.2478T>A	15.37:g.90145118T>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																			T|1.000;A|0.000	0.000	strong		0.458	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
DNAH9	1770	hgsc.bcm.edu	37	17	11550413	11550413	+	Silent	SNP	T	T	C	rs61745426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11550413T>C	ENST00000262442.4	+	12	2063	c.1995T>C	c.(1993-1995)gaT>gaC	p.D665D	DNAH9_ENST00000454412.2_Silent_p.D665D	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	665	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)		TTTATGAGGATTGGTGCCGGA	0.488													T|||	59	0.0117812	0.0431	0.0029	5008	,	,		16804	0.0		0.0	False		,,,				2504	0.0				p.D665D		Atlas-SNP	.											.	DNAH9	695	.	0			c.T1995C						PASS	.	T		162,4244	110.8+/-149.0	6,150,2047	151.0	128.0	136.0		1995	-0.4	1.0	17	dbSNP_129	136	1,8599		0,1,4299	no	coding-synonymous	DNAH9	NM_001372.3		6,151,6346	CC,CT,TT		0.0116,3.6768,1.2533		665/4487	11550413	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon12			TGAGGATTGGTGC	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.1995T>C	17.37:g.11550413T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	131	59	0.450382	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			T|0.988;C|0.012	0.012	strong		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
IGSF9	57549	hgsc.bcm.edu	37	1	159900655	159900655	+	Missense_Mutation	SNP	G	G	A	rs140306211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159900655G>A	ENST00000368094.1	-	14	1837	c.1640C>T	c.(1639-1641)gCc>gTc	p.A547V	IGSF9_ENST00000361509.3_Missense_Mutation_p.A531V|IGSF9_ENST00000493195.1_5'UTR	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	547	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			AGGACGCTTGGCCCTGGGAGA	0.617													G|||	17	0.00339457	0.0129	0.0	5008	,	,		19874	0.0		0.0	False		,,,				2504	0.0				p.A547V		Atlas-SNP	.											.	IGSF9	123	.	0			c.C1640T						PASS	.	G	VAL/ALA,VAL/ALA	78,4328	67.0+/-104.6	0,78,2125	34.0	35.0	35.0		1640,1592	4.7	1.0	1	dbSNP_134	35	0,8600		0,0,4300	yes	missense,missense	IGSF9	NM_001135050.1,NM_020789.3	64,64	0,78,6425	AA,AG,GG		0.0,1.7703,0.5997	benign,benign	547/1180,531/1164	159900655	78,12928	2203	4300	6503	SO:0001583	missense	57549	exon14			CGCTTGGCCCTGG	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.1640C>T	1.37:g.159900655G>A	ENSP00000357073:p.Ala547Val	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	37	CCDS44254.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	8.888	0.953376	0.18431	0.017703	0.0	ENSG00000085552	ENST00000361509;ENST00000368094	T;T	0.56776	0.44;0.44	4.65	4.65	0.58169	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.165414	0.28700	N	0.014421	T	0.13670	0.0331	N	0.05510	-0.035	0.33488	D	0.588349	B	0.13145	0.007	B	0.20384	0.029	T	0.10337	-1.0634	9	.	.	.	-14.7856	8.6122	0.33808	0.1024:0.0:0.8976:0.0	.	547	Q9P2J2	TUTLA_HUMAN	V	531;547	ENSP00000355049:A531V;ENSP00000357073:A547V	.	A	-	2	0	IGSF9	158167279	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	3.744000	0.55112	2.400000	0.81607	0.462000	0.41574	GCC	G|0.994;A|0.006	0.006	strong		0.617	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789	
SLC13A1	6561	hgsc.bcm.edu	37	7	122787306	122787306	+	Missense_Mutation	SNP	G	G	A	rs10231144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:122787306G>A	ENST00000194130.2	-	7	758	c.719C>T	c.(718-720)aCg>aTg	p.T240M	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	240			T -> M (in dbSNP:rs10231144).		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	GCACAAACACGTAAGTTTACG	0.413													A|||	31	0.0061901	0.0227	0.0014	5008	,	,		20613	0.0		0.0	False		,,,				2504	0.0				p.T240M		Atlas-SNP	.											.	SLC13A1	110	.	0			c.C719T						PASS	.	A	MET/THR	92,4314	818.0+/-416.3	0,92,2111	236.0	180.0	199.0		719	5.0	1.0	7	dbSNP_119	199	1,8599		0,1,4299	yes	missense	SLC13A1	NM_022444.3	81	0,93,6410	AA,AG,GG		0.0116,2.0881,0.7151	benign	240/596	122787306	93,12913	2203	4300	6503	SO:0001583	missense	6561	exon7			AAACACGTAAGTT		CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"""Solute carriers"""	10916	protein-coding gene	gene with protein product		606193	"""solute carrier family 13 (sodium/sulphate symporters), member 1"""			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.719C>T	7.37:g.122787306G>A	ENSP00000194130:p.Thr240Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	136	79	0.580882	NM_022444	Q9H5Z0	Missense_Mutation	SNP	ENST00000194130.2	37	CCDS5786.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	A	3.455	-0.111112	0.06881	0.020881	1.16E-4	ENSG00000081800	ENST00000194130	T	0.63913	-0.07	5.0	5.0	0.66597	.	0.085242	0.85682	N	0.000000	T	0.05914	0.0154	N	0.00030	-2.605	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04946	-1.0916	10	0.13108	T	0.6	.	9.0284	0.36243	0.9119:0.0:0.0881:0.0	rs10231144;rs52791983;rs57837984;rs10231144	240;240	A4D0X1;Q9BZW2	.;S13A1_HUMAN	M	240	ENSP00000194130:T240M	ENSP00000194130:T240M	T	-	2	0	SLC13A1	122574542	1.000000	0.71417	0.997000	0.53966	0.706000	0.40770	6.172000	0.71932	0.772000	0.33382	-0.360000	0.07572	ACG	G|0.989;A|0.011	0.011	strong		0.413	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444	
PCDHGA11	56105	hgsc.bcm.edu	37	5	140802723	140802723	+	Silent	SNP	C	C	T	rs62378456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140802723C>T	ENST00000398587.2	+	1	1962	c.1929C>T	c.(1927-1929)ctC>ctT	p.L643L	PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	643	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCAGAGCCTCGTGGTGGCCG	0.701													c|||	190	0.0379393	0.0756	0.036	5008	,	,		16447	0.001		0.0328	False		,,,				2504	0.0317				p.L643L		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.C1929T						PASS	.	C	,,,,,,,,,,,,,,,,,,,	254,4152	127.8+/-164.7	7,240,1956	41.0	49.0	46.0		,,,1929,,,,,,,,,,,,,,,1929,	-4.8	1.0	5	dbSNP_129	46	315,8281	107.6+/-168.3	6,303,3989	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032091.1,NM_032092.1	,,,,,,,,,,,,,,,,,,,	13,543,5945	TT,TC,CC		3.6645,5.7649,4.3762	,,,,,,,,,,,,,,,,,,,	,,,643/936,,,,,,,,,,,,,,,643/838,	140802723	569,12433	2203	4298	6501	SO:0001819	synonymous_variant	56105	exon1			GAGCCTCGTGGTG	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"""Cadherins / Protocadherins : Clustered"""	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.1929C>T	5.37:g.140802723C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	163	84	0.515337	NM_032091	B7ZVY8|Q9Y5D8|Q9Y5D9	Silent	SNP	ENST00000398587.2	37	CCDS47294.1																																																																																			C|0.963;T|0.037	0.037	strong		0.701	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914	
SGCD	6444	hgsc.bcm.edu	37	5	156184786	156184786	+	Intron	SNP	G	G	A	rs187204080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156184786G>A	ENST00000435422.3	+	7	1183				SGCD_ENST00000337851.4_Intron|SGCD_ENST00000517913.1_Silent_p.*257*|SGCD_ENST00000447401.1_Silent_p.*257*	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)						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)			ATAACTGGTTGACCTCGGAGT	0.448													G|||	14	0.00279553	0.0106	0.0	5008	,	,		17960	0.0		0.0	False		,,,				2504	0.0				p.X257X		Atlas-SNP	.											.	SGCD	52	.	0			c.G770A						PASS	.	G	,,	33,3799		0,33,1883	64.0	63.0	63.0		,,770	0.0	0.0	5		63	0,8268		0,0,4134	no	intron,intron,coding-synonymous	SGCD	NM_000337.5,NM_001128209.1,NM_172244.2	,,	0,33,6017	AA,AG,GG		0.0,0.8612,0.2727	,,	,,257/257	156184786	33,12067	1916	4134	6050	SO:0001627	intron_variant	6444	exon8			CTGGTTGACCTCG	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.696+71G>A	5.37:g.156184786G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	217	98	0.451613	NM_172244	A8K9S9|Q53XA5|Q99644	Silent	SNP	ENST00000435422.3	37	CCDS47327.1																																																																																			G|0.998;A|0.002	0.002	strong		0.448	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3		
ZNF285	26974	hgsc.bcm.edu	37	19	44890817	44890817	+	Silent	SNP	G	G	A	rs73039937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44890817G>A	ENST00000330997.4	-	4	1654	c.1590C>T	c.(1588-1590)caC>caT	p.H530H	ZNF285_ENST00000591679.1_Silent_p.H537H|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Silent_p.H530H	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	211	0	0		WXS	Illumina HiSeq	Phase_I	201	79	0.393035	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	
PXDNL	137902	hgsc.bcm.edu	37	8	52321686	52321686	+	Missense_Mutation	SNP	C	C	T	rs11985241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:52321686C>T	ENST00000356297.4	-	17	2598	c.2498G>A	c.(2497-2499)aGc>aAc	p.S833N	PXDNL_ENST00000543296.1_Missense_Mutation_p.S833N	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	833				S -> N (in Ref. 4; BAD18663). {ECO:0000305}.	hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GCAGACGGAGCTGCACGGCCG	0.672													C|||	771	0.153954	0.1725	0.0778	5008	,	,		10650	0.2768		0.0905	False		,,,				2504	0.1217				p.S833N		Atlas-SNP	.											.	PXDNL	414	.	0			c.G2498A						PASS	.	C	ASN/SER	682,3532		50,582,1475	17.0	21.0	20.0		2498	2.6	0.0	8	dbSNP_120	20	725,7687		33,659,3514	yes	missense	PXDNL	NM_144651.4	46	83,1241,4989	TT,TC,CC		8.6186,16.1841,11.1437	benign	833/1464	52321686	1407,11219	2107	4206	6313	SO:0001583	missense	137902	exon17			ACGGAGCTGCACG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2498G>A	8.37:g.52321686C>T	ENSP00000348645:p.Ser833Asn	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	67	47	0.701493	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	334	0.15293040293040294	85	0.17276422764227642	30	0.08287292817679558	152	0.26573426573426573	67	0.08839050131926121	C	4.452	0.083708	0.08533	0.161841	0.086186	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.73047	-0.71;-0.71	3.56	2.63	0.31362	.	0.000000	0.64402	D	0.000019	T	0.00012	0.0000	L	0.33753	1.03	0.39622	P	0.029958999999999958	B	0.25105	0.118	B	0.23716	0.048	T	0.06935	-1.0799	9	0.40728	T	0.16	.	9.8527	0.41066	0.2068:0.7932:0.0:0.0	rs11985241	833	A1KZ92	PXDNL_HUMAN	N	833	ENSP00000348645:S833N;ENSP00000444865:S833N	ENSP00000348645:S833N	S	-	2	0	PXDNL	52484239	1.000000	0.71417	0.017000	0.16124	0.034000	0.12701	5.229000	0.65316	0.553000	0.29044	0.650000	0.86243	AGC	C|0.853;T|0.147	0.147	strong		0.672	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
C8B	732	hgsc.bcm.edu	37	1	57422511	57422511	+	Missense_Mutation	SNP	C	C	T	rs12067507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57422511C>T	ENST00000371237.4	-	3	388	c.322G>A	c.(322-324)Gaa>Aaa	p.E108K	C8B_ENST00000535057.1_Missense_Mutation_p.E46K|C8B_ENST00000543257.1_Missense_Mutation_p.E56K	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	108	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.		E -> K (in dbSNP:rs12067507).		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)		p.E108K(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						ACACAGTCTTCGACTTCCTTG	0.498													C|||	208	0.0415335	0.0575	0.0331	5008	,	,		20252	0.0		0.0547	False		,,,				2504	0.0552				p.E108K		Atlas-SNP	.											C8B,caecum,carcinoma,0,1	C8B	107	1	1	Substitution - Missense(1)	large_intestine(1)	c.G322A						PASS	.	C	LYS/GLU	288,4118	159.2+/-191.8	8,272,1923	257.0	237.0	244.0		322	4.5	0.9	1	dbSNP_120	244	479,8121	140.5+/-197.0	14,451,3835	yes	missense	C8B	NM_000066.2	56	22,723,5758	TT,TC,CC		5.5698,6.5365,5.8973	probably-damaging	108/592	57422511	767,12239	2203	4300	6503	SO:0001583	missense	732	exon3			AGTCTTCGACTTC	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"""Complement system"""	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.322G>A	1.37:g.57422511C>T	ENSP00000360281:p.Glu108Lys	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	120	63	0.525	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	37	CCDS30730.1	90	0.04120879120879121	34	0.06910569105691057	16	0.04419889502762431	0	0.0	40	0.052770448548812667	C	24.7	4.557566	0.86231	0.065365	0.055698	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	T;T;T	0.27557	2.16;2.16;1.66	5.41	4.47	0.54385	.	0.101764	0.64402	D	0.000002	T	0.05181	0.0138	L	0.37697	1.125	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.987;0.997;0.97	T	0.00918	-1.1515	10	0.35671	T	0.21	-27.0469	15.8821	0.79211	0.0:0.864:0.136:0.0	rs12067507;rs52799290;rs56715593;rs12067507	56;46;108	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	K	108;56;46	ENSP00000360281:E108K;ENSP00000442548:E56K;ENSP00000440113:E46K	ENSP00000360281:E108K	E	-	1	0	C8B	57195099	0.990000	0.36364	0.911000	0.35937	0.704000	0.40688	2.981000	0.49329	1.370000	0.46153	0.650000	0.86243	GAA	C|0.944;T|0.056	0.056	strong		0.498	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2		
CPNE7	27132	hgsc.bcm.edu	37	16	89645345	89645345	+	Missense_Mutation	SNP	C	C	A	rs9944362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89645345C>A	ENST00000268720.5	+	3	568	c.438C>A	c.(436-438)caC>caA	p.H146Q	CPNE7_ENST00000319518.8_Intron	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	146					lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		GCGCTAAGCACTTCCTGTGCT	0.552													C|||	24	0.00479233	0.0174	0.0014	5008	,	,		16713	0.0		0.0	False		,,,				2504	0.0				p.H146Q		Atlas-SNP	.											.	CPNE7	56	.	0			c.C438A						PASS	.	C	GLN/HIS,	41,4355	46.0+/-80.4	1,39,2158	133.0	112.0	119.0		438,	-0.7	0.0	16	dbSNP_119	119	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron	CPNE7	NM_014427.4,NM_153636.2	24,	1,40,6457	AA,AC,CC		0.0116,0.9327,0.3232	,	146/634,	89645345	42,12954	2198	4300	6498	SO:0001583	missense	27132	exon3			TAAGCACTTCCTG	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.438C>A	16.37:g.89645345C>A	ENSP00000268720:p.His146Gln	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	100	58	0.58	NM_014427		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	0.672	-0.801433	0.02841	0.009327	1.16E-4	ENSG00000178773	ENST00000268720	T	0.13089	2.62	0.471	-0.661	0.11417	C2 calcium/lipid-binding domain, CaLB (1);	432.516000	0.00520	U	0.000184	T	0.07324	0.0185	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21965	-1.0230	9	0.15066	T	0.55	.	.	.	.	rs9944362	146	Q9UBL6	CPNE7_HUMAN	Q	146	ENSP00000268720:H146Q	ENSP00000268720:H146Q	H	+	3	2	CPNE7	88172846	0.003000	0.15002	0.001000	0.08648	0.006000	0.05464	0.396000	0.20867	-0.368000	0.08040	0.205000	0.17691	CAC	C|0.998;A|0.002	0.002	strong		0.552	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
OR5L1	219437	hgsc.bcm.edu	37	11	55579068	55579068	+	Silent	SNP	C	C	T	rs575553149		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55579068C>T	ENST00000333973.2	+	1	215	c.126C>T	c.(124-126)aaC>aaT	p.N42N		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	42						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(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TGTTAGCCAACCTGGGCATGA	0.498																																					p.N42N		Atlas-SNP	.											OR5L1,colon,carcinoma,0,3	OR5L1	145	3	0			c.C126T						scavenged	.						325.0	285.0	299.0					11																	55579068		2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			AGCCAACCTGGGC	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.126C>T	11.37:g.55579068C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	214	8	0.0373832	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			.	.	none		0.498	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57077464	57077464	+	Silent	SNP	T	T	C	rs10896602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57077464T>C	ENST00000532437.1	-	5	3032	c.2721A>G	c.(2719-2721)caA>caG	p.Q907Q	TNKS1BP1_ENST00000358252.3_Silent_p.Q907Q|TNKS1BP1_ENST00000530920.1_5'UTR			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	907	Acidic.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TCCCCAAATCTTGGCCCTGCT	0.537													T|||	1661	0.331669	0.4531	0.2522	5008	,	,		19426	0.2827		0.33	False		,,,				2504	0.2761				p.Q907Q		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.A2721G						PASS	.	T		1893,2509	544.2+/-376.5	393,1107,701	190.0	185.0	186.0		2721	-1.2	0.0	11	dbSNP_120	186	2785,5807	442.5+/-360.1	456,1873,1967	no	coding-synonymous	TNKS1BP1	NM_033396.2		849,2980,2668	CC,CT,TT		32.4139,43.0032,36.0012		907/1730	57077464	4678,8316	2201	4296	6497	SO:0001819	synonymous_variant	85456	exon6			CAAATCTTGGCCC	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.2721A>G	11.37:g.57077464T>C		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	182	92	0.505495	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	
VAMP8	8673	hgsc.bcm.edu	37	2	85808737	85808737	+	Silent	SNP	A	A	G	rs1009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85808737A>G	ENST00000263864.5	+	3	357	c.201A>G	c.(199-201)cgA>cgG	p.R67R	VAMP8_ENST00000409760.1_3'UTR|VAMP5_ENST00000306384.4_5'Flank|VAMP8_ENST00000432071.1_Silent_p.R41R	NM_003761.4	NP_003752.2	Q9BV40	VAMP8_HUMAN	vesicle-associated membrane protein 8	67	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				autophagic vacuole fusion (GO:0000046)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|secretory granule membrane (GO:0030667)|SNARE complex (GO:0031201)		p.R67R(1)		breast(1)|endometrium(2)|large_intestine(1)|stomach(2)	6						AGGTGGCTCGAAAATTCTGGT	0.468													G|||	2201	0.439497	0.5976	0.3473	5008	,	,		21409	0.3859		0.4314	False		,,,				2504	0.3548				p.R67R		Atlas-SNP	.											VAMP8,NS,carcinoma,0,1	VAMP8	10	1	1	Substitution - coding silent(1)	stomach(1)	c.A201G						PASS	.	G		2423,1983	557.4+/-379.7	672,1079,452	378.0	321.0	340.0		201	0.4	1.0	2	dbSNP_36	340	3554,5046	629.9+/-398.3	734,2086,1480	no	coding-synonymous	VAMP8	NM_003761.4		1406,3165,1932	GG,GA,AA		41.3256,45.0068,45.9557		67/101	85808737	5977,7029	2203	4300	6503	SO:0001819	synonymous_variant	8673	exon3			GGCTCGAAAATTC	AF053233	CCDS1979.1	2p12-p11.2	2013-02-13	2012-10-17		ENSG00000118640	ENSG00000118640		"""Vesicle-associated membrane proteins"""	12647	protein-coding gene	gene with protein product	"""endobrevin"""	603177				9878266, 9614193	Standard	NM_003761		Approved	EDB	uc002spt.4	Q9BV40	OTTHUMG00000130180	ENST00000263864.5:c.201A>G	2.37:g.85808737A>G		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	252	131	0.519841	NM_003761	O60625|Q53SP9|Q6IB09	Silent	SNP	ENST00000263864.5	37	CCDS1979.1																																																																																			A|0.547;G|0.453	0.453	strong		0.468	VAMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252498.3	NM_003761	
FANCA	2175	hgsc.bcm.edu	37	16	89807233	89807233	+	Silent	SNP	C	C	G	rs11649210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89807233C>G	ENST00000389301.3	-	38	3837	c.3807G>C	c.(3805-3807)ctG>ctC	p.L1269L	ZNF276_ENST00000289816.5_3'UTR|FANCA_ENST00000568369.1_Silent_p.L1269L	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1269					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GATGTGACGACAGCAGGCCCA	0.463			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	691	0.137979	0.1543	0.0346	5008	,	,		17285	0.2629		0.0736	False		,,,				2504	0.1268				p.L1269L		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.G3807C						PASS	.	G	,,	629,3767	764.9+/-413.3	38,553,1607	84.0	77.0	79.0		3807,,	-7.2	0.1	16	dbSNP_120	79	774,7826	781.2+/-407.6	32,710,3558	no	coding-synonymous,utr-3,utr-3	FANCA,ZNF276	NM_000135.2,NM_001113525.1,NM_152287.3	,,	70,1263,5165	GG,GC,CC		9.0,14.3085,10.7956	,,	1269/1456,,	89807233	1403,11593	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon38	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGACGACAGCAGG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3807G>C	16.37:g.89807233C>G		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	206	102	0.495146	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			C|0.892;G|0.108	0.108	strong		0.463	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
PCDHGB7	56099	hgsc.bcm.edu	37	5	140797630	140797630	+	Silent	SNP	G	G	T	rs2015825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140797630G>T	ENST00000398594.2	+	1	204	c.204G>T	c.(202-204)gtG>gtT	p.V68V	PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	68	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)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTGCGAGTGAGCGCGGAGA	0.572													t|||	2709	0.540935	0.8419	0.6182	5008	,	,		14025	0.3244		0.4225	False		,,,				2504	0.4243				p.V68V		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.G204T						PASS	.	T	,,,,,,,,,,,,,,,,,	3121,775		1265,591,92	70.0	77.0	75.0		,,,,,,,,,,,,,,,204,,204	-4.5	0.9	5	dbSNP_92	75	3568,4730		755,2058,1336	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032101.2	,,,,,,,,,,,,,,,,,	2020,2649,1428	TT,TG,GG		42.9983,19.8922,45.1452	,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,68/930,,68/809	140797630	6689,5505	1948	4149	6097	SO:0001819	synonymous_variant	56099	exon1			GCGAGTGAGCGCG	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"""Cadherins / Protocadherins : Clustered"""	8714	other	protocadherin	"""cadherin ME6"""	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.204G>T	5.37:g.140797630G>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	170	167	0.982353	NM_018927	Q9UN63	Silent	SNP	ENST00000398594.2	37	CCDS47293.1																																																																																			G|0.500;T|0.500	0.500	strong		0.572	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927	
LILRA1	11024	hgsc.bcm.edu	37	19	55106778	55106778	+	Missense_Mutation	SNP	G	G	A	rs10418391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55106778G>A	ENST00000251372.3	+	5	754	c.572G>A	c.(571-573)cGc>cAc	p.R191H	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Missense_Mutation_p.R191H|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	191	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		AGCCCGAGTCGCAGGTGGTCG	0.572													g|||	714	0.142572	0.4032	0.0821	5008	,	,		19472	0.004		0.0547	False		,,,				2504	0.0665				p.R191H		Atlas-SNP	.											LILRA1,NS,malignant_melanoma,+1,2	LILRA1	105	2	0			c.G572A						PASS	.	G	HIS/ARG	1642,2764	503.2+/-365.5	295,1052,856	152.0	157.0	156.0		572	-0.3	0.0	19	dbSNP_119	156	410,8190	129.0+/-187.1	10,390,3900	no	missense	LILRA1	NM_006863.1	29	305,1442,4756	AA,AG,GG		4.7674,37.2674,15.7773	benign	191/490	55106778	2052,10954	2203	4300	6503	SO:0001583	missense	11024	exon5			CGAGTCGCAGGTG	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.572G>A	19.37:g.55106778G>A	ENSP00000251372:p.Arg191His	Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	408	194	0.47549	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	251	0.11492673992673992	177	0.3597560975609756	36	0.09944751381215469	2	0.0034965034965034965	36	0.047493403693931395	G	0.013	-1.623243	0.00820	0.372674	0.047674	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.02369	4.32;4.32	2.24	-0.33	0.12683	Immunoglobulin-like fold (1);	1.389240	0.04584	N	0.395426	T	0.00012	0.0000	N	0.03268	-0.37	0.80722	P	0.0	B;B	0.20164	0.042;0.001	B;B	0.11329	0.006;0.0	T	0.42599	-0.9442	9	0.02654	T	1	.	2.0528	0.03574	0.5644:0.0:0.1783:0.2573	rs10418391	191;191	O75019-2;O75019	.;LIRA1_HUMAN	H	191	ENSP00000251372:R191H;ENSP00000413715:R191H	ENSP00000251372:R191H	R	+	2	0	LILRA1	59798590	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.058000	0.11750	-0.319000	0.08652	0.194000	0.17425	CGC	G|0.857;A|0.143	0.143	strong		0.572	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
CCBL2	56267	hgsc.bcm.edu	37	1	89426956	89426956	+	Silent	SNP	C	C	T	rs12063768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89426956C>T	ENST00000260508.4	-	8	1018	c.681G>A	c.(679-681)gaG>gaA	p.E227E	CCBL2_ENST00000370491.3_Silent_p.E193E|CCBL2_ENST00000370485.2_3'UTR|CCBL2_ENST00000446900.2_5'UTR	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	227					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	mitochondrion (GO:0005739)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|kynurenine-glyoxylate transaminase activity (GO:0047315)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|ovary(2)|skin(2)|soft_tissue(1)	18		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)		CTTGCAGTTCCTCTCTGTTAT	0.373													C|||	192	0.0383387	0.1354	0.0159	5008	,	,		20050	0.0		0.002	False		,,,				2504	0.0				p.E227E		Atlas-SNP	.											.	CCBL2	138	.	0			c.G681A						PASS	.	C	,	437,3969	211.8+/-231.9	23,391,1789	170.0	163.0	166.0		681,579	-0.4	0.9	1	dbSNP_120	166	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	CCBL2	NM_001008661.2,NM_001008662.2	,	23,396,6084	TT,TC,CC		0.0581,9.9183,3.3984	,	227/455,193/421	89426956	442,12564	2203	4300	6503	SO:0001819	synonymous_variant	56267	exon8			CAGTTCCTCTCTG	AF091090	CCDS30766.1, CCDS30767.1	1p22.2	2009-06-23			ENSG00000137944	ENSG00000137944			33238	protein-coding gene	gene with protein product		610656				16376499	Standard	NM_001008662		Approved	RBM1, RP11-82K18.3, KAT3	uc001dmp.2	Q6YP21	OTTHUMG00000010617	ENST00000260508.4:c.681G>A	1.37:g.89426956C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Silent	SNP	ENST00000260508.4	37	CCDS30766.1																																																																																			C|0.961;T|0.039	0.039	strong		0.373	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661	
MYO10	4651	hgsc.bcm.edu	37	5	16769273	16769273	+	Missense_Mutation	SNP	G	G	A	rs11750538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16769273G>A	ENST00000513610.1	-	10	1424	c.970C>T	c.(970-972)Cgg>Tgg	p.R324W		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	324	Myosin motor.		R -> W (in dbSNP:rs11750538). {ECO:0000269|PubMed:10984435, ECO:0000269|Ref.3}.		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						GACACTTCCCGAACTTCCTCC	0.403													G|||	2410	0.48123	0.3396	0.4006	5008	,	,		17279	0.5357		0.5984	False		,,,				2504	0.5532				p.R324W		Atlas-SNP	.											.	MYO10	198	.	0			c.C970T						PASS	.	G	TRP/ARG	1489,2349		291,907,721	109.0	100.0	103.0		970	4.8	0.8	5	dbSNP_120	103	4949,3323		1492,1965,679	yes	missense	MYO10	NM_012334.2	101	1783,2872,1400	AA,AG,GG		40.1717,38.7962,46.8373	possibly-damaging	324/2059	16769273	6438,5672	1919	4136	6055	SO:0001583	missense	4651	exon10			CTTCCCGAACTTC	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.970C>T	5.37:g.16769273G>A	ENSP00000421280:p.Arg324Trp	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	1111	0.5086996336996337	173	0.3516260162601626	171	0.4723756906077348	314	0.548951048951049	453	0.5976253298153035	G	8.864	0.947529	0.18356	0.387962	0.598283	ENSG00000145555	ENST00000513610;ENST00000513882	D;D	0.88509	-2.39;-2.39	5.71	4.82	0.62117	Myosin head, motor domain (2);	.	.	.	.	T	0.00012	0.0000	L	0.35723	1.085	0.09310	P	0.999999999999986	D	0.61080	0.989	P	0.53185	0.72	T	0.45190	-0.9278	8	0.45353	T	0.12	.	13.5022	0.61462	0.0:0.0:0.7155:0.2845	rs11750538;rs52826195;rs60590343;rs11750538	324	Q9HD67	MYO10_HUMAN	W	324;335	ENSP00000421280:R324W;ENSP00000421309:R335W	ENSP00000421280:R324W	R	-	1	2	MYO10	16822273	0.997000	0.39634	0.769000	0.31535	0.687000	0.40016	2.849000	0.48286	1.359000	0.45940	0.585000	0.79938	CGG	G|0.492;A|0.507	0.507	strong		0.403	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
KIRREL2	84063	hgsc.bcm.edu	37	19	36353880	36353880	+	Missense_Mutation	SNP	G	G	A	rs35775934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36353880G>A	ENST00000360202.5	+	13	1865	c.1667G>A	c.(1666-1668)aGc>aAc	p.S556N	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Missense_Mutation_p.S521N|KIRREL2_ENST00000347900.6_Missense_Mutation_p.S506N|KIRREL2_ENST00000262625.7_Missense_Mutation_p.S556N	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	556			S -> N (in dbSNP:rs35775934).		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)			CCTGGCAGCAGCGACGGCTCC	0.607													G|||	165	0.0329473	0.121	0.0072	5008	,	,		16611	0.0		0.0	False		,,,				2504	0.0				p.S556N		Atlas-SNP	.											KIRREL2_ENST00000262625,NS,carcinoma,-1,2	KIRREL2	170	2	0			c.G1667A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	503,3901		19,465,1718	38.0	36.0	37.0		1667,1517,1667	3.9	0.9	19	dbSNP_126	37	4,8592		0,4,4294	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	46,46,46	19,469,6012	AA,AG,GG		0.0465,11.4214,3.9	benign,benign,benign	556/634,506/584,556/709	36353880	507,12493	2202	4298	6500	SO:0001583	missense	84063	exon13			GCAGCAGCGACGG	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.1667G>A	19.37:g.36353880G>A	ENSP00000353331:p.Ser556Asn	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	45	0.020604395604395604	39	0.07926829268292683	6	0.016574585635359115	0	0.0	0	0.0	G	13.69	2.311961	0.40895	0.114214	4.65E-4	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658;ENST00000270294	T;T;T	0.65178	-0.13;0.1;-0.14	4.98	3.94	0.45596	.	0.000000	0.45126	D	0.000386	T	0.03651	0.0104	L	0.56769	1.78	0.25267	N	0.989546	D;D;D;D;D	0.71674	0.993;0.998;0.993;0.996;0.996	D;D;D;D;D	0.80764	0.968;0.994;0.968;0.986;0.986	T	0.05451	-1.0884	10	0.21540	T	0.41	-13.9497	8.3131	0.32084	0.1065:0.0:0.8935:0.0	rs35775934	556;536;556;506;556	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	N	556;506;556;536;67	ENSP00000262625:S556N;ENSP00000345067:S506N;ENSP00000353331:S556N	ENSP00000262625:S556N	S	+	2	0	KIRREL2	41045720	0.958000	0.32768	0.945000	0.38365	0.102000	0.19082	1.580000	0.36547	2.321000	0.78463	0.561000	0.74099	AGC	G|0.959;A|0.041	0.041	strong		0.607	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
GPR112	139378	hgsc.bcm.edu	37	X	135429503	135429503	+	Missense_Mutation	SNP	C	C	A	rs4829830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:135429503C>A	ENST00000394143.1	+	6	3929	c.3638C>A	c.(3637-3639)aCc>aAc	p.T1213N	GPR112_ENST00000412101.1_Missense_Mutation_p.T1008N|GPR112_ENST00000370652.1_Missense_Mutation_p.T1213N|GPR112_ENST00000287534.4_Missense_Mutation_p.T1150N|GPR112_ENST00000394141.1_Missense_Mutation_p.T1008N	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1213			T -> N (in dbSNP:rs4829830).		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GTTGATGAGACCACACCCTCA	0.473													c|||	1760	0.466225	0.4289	0.3573	3775	,	,		15390	0.246		0.3797	False		,,,				2504	0.3221				p.T1213N		Atlas-SNP	.											.	GPR112	459	.	0			c.C3638A						PASS	.		ASN/THR	2122,1713		502,805,313,325,258	214.0	183.0	193.0		3638	-1.5	0.0	X	dbSNP_111	193	3220,3508		566,1176,912,686,960	yes	missense	GPR112	NM_153834.3	65	1068,1981,1225,1011,1218	AA,AC,A,CC,C		47.8597,44.6675,49.4272	benign	1213/3081	135429503	5342,5221	2203	4300	6503	SO:0001583	missense	139378	exon6			ATGAGACCACACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.3638C>A	X.37:g.135429503C>A	ENSP00000377699:p.Thr1213Asn	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	232	137	0.590517	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	746	0.4496684749849307	138	0.372972972972973	83	0.2902097902097902	99	0.21063829787234042	190	0.3242320819112628	c	6.546	0.469051	0.12461	0.553325	0.478597	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.33865	1.43;1.43;1.39;1.52;1.39	2.98	-1.46	0.08800	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.15930	0.015;0.001;0.001	B;B;B	0.14578	0.011;0.003;0.001	T	0.46190	-0.9209	8	0.37606	T	0.19	.	0.3457	0.00341	0.2044:0.3206:0.1987:0.2763	rs4829830;rs58174019;rs4829830	1150;1008;1213	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	N	1213;1213;1008;1150;1008	ENSP00000377699:T1213N;ENSP00000359686:T1213N;ENSP00000416526:T1008N;ENSP00000287534:T1150N;ENSP00000377697:T1008N	ENSP00000287534:T1150N	T	+	2	0	GPR112	135257169	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.312000	0.08113	-0.347000	0.08299	-0.313000	0.08912	ACC	0|0.015;A|0.479	0.479	strong		0.473	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
S100A3	6274	hgsc.bcm.edu	37	1	153520203	153520203	+	Silent	SNP	G	G	A	rs41265164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153520203G>A	ENST00000368713.3	-	3	457	c.261C>T	c.(259-261)caC>caT	p.H87H	S100A3_ENST00000368712.1_Silent_p.H87H|S100A4_ENST00000368714.1_Intron|S100A4_ENST00000481009.1_5'Flank|S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000368715.1_5'Flank|S100A4_ENST00000368716.4_5'Flank	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	87						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|liver(1)|lung(1)	3	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)			TGAAGTACTCGTGGCAGTAGA	0.592													G|||	760	0.151757	0.4228	0.1037	5008	,	,		19755	0.0149		0.0517	False		,,,				2504	0.0634				p.H87H		Atlas-SNP	.											.	S100A3	7	.	0			c.C261T						PASS	.	G		1633,2773	502.5+/-365.3	318,997,888	157.0	139.0	145.0		261	-2.6	1.0	1	dbSNP_127	145	466,8134	137.9+/-194.8	16,434,3850	no	coding-synonymous	S100A3	NM_002960.1		334,1431,4738	AA,AG,GG		5.4186,37.0631,16.1387		87/102	153520203	2099,10907	2203	4300	6503	SO:0001819	synonymous_variant	6274	exon3			GTACTCGTGGCAG	BC012893	CCDS1043.1	1q21	2008-02-05	2001-11-28		ENSG00000188015	ENSG00000188015		"""S100 calcium binding proteins"""	10493	protein-coding gene	gene with protein product		176992	"""S100 calcium-binding protein A3"""	S100E		8341667	Standard	NM_002960		Approved		uc001fca.1	P33764	OTTHUMG00000013550	ENST00000368713.3:c.261C>T	1.37:g.153520203G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	146	74	0.506849	NM_002960	D3DV51|Q6FGE4	Silent	SNP	ENST00000368713.3	37	CCDS1043.1																																																																																			A|0.147;C|0.000;G|0.853;T|0.000	0.147	strong		0.592	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960	
ZNF860	344787	hgsc.bcm.edu	37	3	32031615	32031615	+	Missense_Mutation	SNP	A	A	C	rs13064905	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:32031615A>C	ENST00000360311.4	+	2	1593	c.1044A>C	c.(1042-1044)gaA>gaC	p.E348D		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	348					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						AGGTTTGTGAAAAGGCTTTCA	0.393													C|||	2356	0.470447	0.7988	0.3602	5008	,	,		21648	0.4524		0.1968	False		,,,				2504	0.4049				p.E348D		Atlas-SNP	.											.	ZNF860	96	.	0			c.A1044C						PASS	.						45.0	47.0	46.0					3																	32031615		692	1591	2283	SO:0001583	missense	344787	exon2			TTGTGAAAAGGCT	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1044A>C	3.37:g.32031615A>C	ENSP00000373274:p.Glu348Asp	Somatic	380	0	0		WXS	Illumina HiSeq	Phase_I	311	127	0.40836	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	911	0.41712454212454214	385	0.782520325203252	126	0.34806629834254144	248	0.43356643356643354	152	0.20052770448548812	C	3.265	-0.150374	0.06585	.	.	ENSG00000197385	ENST00000360311	T	0.01185	5.21	0.345	0.345	0.16011	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04148	-0.265	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02411	-1.1163	7	.	.	.	.	2.5267	0.04693	0.3212:0.3574:0.3213:0.0	rs13064905;rs61529855;rs13064905	348	A6NHJ4	ZN860_HUMAN	D	348	ENSP00000373274:E348D	.	E	+	3	2	ZNF860	32006619	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	-1.684000	0.01932	-0.518000	0.06452	-0.525000	0.04345	GAA	A|0.614;C|0.386	0.386	strong		0.393	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
PCDHB16	57717	hgsc.bcm.edu	37	5	140563173	140563173	+	Missense_Mutation	SNP	G	G	T	rs28664170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140563173G>T	ENST00000361016.2	+	1	2194	c.1039G>T	c.(1039-1041)Gtg>Ttg	p.V347L		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	347	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> L (in dbSNP:rs28664170).		calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCCCCACAGGTGACCATGTC	0.522													g|||	763	0.152356	0.2579	0.1902	5008	,	,		17783	0.0407		0.1571	False		,,,				2504	0.093				p.V347L		Atlas-SNP	.											.	PCDHB16	159	.	0			c.G1039T						PASS	.	T	LEU/VAL	1042,3364	384.9+/-325.5	115,812,1276	90.0	95.0	93.0		1039	-2.2	0.0	5	dbSNP_125	93	1474,7126	281.2+/-294.9	136,1202,2962	yes	missense	PCDHB16	NM_020957.1	32	251,2014,4238	TT,TG,GG		17.1395,23.6496,19.3449	benign	347/777	140563173	2516,10490	2203	4300	6503	SO:0001583	missense	57717	exon1			CCACAGGTGACCA	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1039G>T	5.37:g.140563173G>T	ENSP00000354293:p.Val347Leu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	329	0.15064102564102563	119	0.241869918699187	63	0.17403314917127072	26	0.045454545454545456	121	0.15963060686015831	G	0.041	-1.283588	0.01398	0.236496	0.171395	ENSG00000196963	ENST00000361016	T	0.01787	4.64	4.47	-2.21	0.06973	Cadherin (2);Cadherin-like (1);	0.600314	0.12637	N	0.451640	T	0.00012	0.0000	N	0.03253	-0.375	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.003	T	0.42498	-0.9448	9	0.02654	T	1	.	0.421	0.00456	0.2557:0.2432:0.1326:0.3685	rs28664170;rs59526747	37;347	O15199;Q9NRJ7	.;PCDBG_HUMAN	L	347	ENSP00000354293:V347L	ENSP00000354293:V347L	V	+	1	0	PCDHB16	140543357	0.000000	0.05858	0.011000	0.14972	0.556000	0.35491	-1.001000	0.03690	0.020000	0.15106	-0.188000	0.12872	GTG	C|0.000;G|0.818;T|0.182	0.182	strong		0.522	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
ORM2	5005	hgsc.bcm.edu	37	9	117094159	117094159	+	Missense_Mutation	SNP	G	G	A	rs148221879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117094159G>A	ENST00000431067.2	+	5	526	c.490G>A	c.(490-492)Gac>Aac	p.D164N	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	164					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	CGAAGCTCTCGACTGCTTGTG	0.572													G|||	14	0.00279553	0.0083	0.0014	5008	,	,		18564	0.0		0.001	False		,,,				2504	0.001				p.D164N	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G490A						PASS	.	G	ASN/ASP	54,4352	53.6+/-89.4	1,52,2150	103.0	99.0	100.0		490	-5.1	0.0	9	dbSNP_134	100	0,8600		0,0,4300	yes	missense	ORM2	NM_000608.2	23	1,52,6450	AA,AG,GG		0.0,1.2256,0.4152		164/202	117094159	54,12952	2203	4300	6503	SO:0001583	missense	5005	exon5			GCTCTCGACTGCT		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.490G>A	9.37:g.117094159G>A	ENSP00000394936:p.Asp164Asn	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	215	152	0.706977	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Missense_Mutation	SNP	ENST00000431067.2	37	CCDS6804.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	G	14.61	2.587382	0.46110	0.012256	0.0	ENSG00000228278	ENST00000431067	T	0.07567	3.18	3.83	-5.07	0.02938	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.832830	0.02642	N	0.105407	T	0.03827	0.0108	L	0.36672	1.1	0.09310	N	1	P	0.39748	0.686	B	0.27076	0.076	T	0.35822	-0.9773	10	0.24483	T	0.36	-2.7618	10.116	0.42591	0.3551:0.0:0.6449:0.0	.	164	P19652	A1AG2_HUMAN	N	164	ENSP00000394936:D164N	ENSP00000394936:D164N	D	+	1	0	ORM2	116133980	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.487000	0.02310	-1.079000	0.03113	0.544000	0.68410	GAC	G|0.997;A|0.003	0.003	strong		0.572	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
CCDC94	55702	hgsc.bcm.edu	37	19	4254375	4254375	+	Silent	SNP	C	C	T	rs11085068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4254375C>T	ENST00000262962.7	+	4	362	c.294C>T	c.(292-294)taC>taT	p.Y98Y		NM_018074.4	NP_060544.2	Q9BW85	CCD94_HUMAN	coiled-coil domain containing 94	98								p.Y98Y(1)		NS(1)|endometrium(1)|lung(2)|ovary(1)|stomach(2)	7				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)		ACACAGACTACACCATGGAGC	0.547													C|||	2092	0.417732	0.5083	0.2695	5008	,	,		19031	0.4435		0.3091	False		,,,				2504	0.4857				p.Y98Y		Atlas-SNP	.											CCDC94,NS,carcinoma,0,1	CCDC94	28	1	1	Substitution - coding silent(1)	stomach(1)	c.C294T						PASS	.			2162,2244	583.2+/-385.8	528,1106,569	117.0	105.0	109.0		294	3.1	1.0	19	dbSNP_120	109	2482,6118	407.3+/-349.1	381,1720,2199	no	coding-synonymous	CCDC94	NM_018074.4		909,2826,2768	TT,TC,CC		28.8605,49.0695,35.7066		98/324	4254375	4644,8362	2203	4300	6503	SO:0001819	synonymous_variant	55702	exon4			AGACTACACCATG	AK001236	CCDS12124.1	19p13.3	2008-02-05				ENSG00000105248			25518	protein-coding gene	gene with protein product						12477932	Standard	NM_018074		Approved	FLJ10374	uc002lzv.4	Q9BW85		ENST00000262962.7:c.294C>T	19.37:g.4254375C>T		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_018074	O75270|Q9H862|Q9NW16	Silent	SNP	ENST00000262962.7	37	CCDS12124.1																																																																																			C|0.632;T|0.368	0.368	strong		0.547	CCDC94-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458007.2	NM_018074	
CLASRP	11129	hgsc.bcm.edu	37	19	45561014	45561014	+	Silent	SNP	A	A	G	rs76953457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45561014A>G	ENST00000221455.3	+	7	569	c.471A>G	c.(469-471)gcA>gcG	p.A157A	CLASRP_ENST00000391953.4_Silent_p.A95A|CLASRP_ENST00000544944.2_Silent_p.A157A	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	157					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						TCAGGCTGGCAGAGAAGAAGG	0.637													A|||	50	0.00998403	0.034	0.0072	5008	,	,		19589	0.0		0.0	False		,,,				2504	0.0				p.A157A		Atlas-SNP	.											.	CLASRP	44	.	0			c.A471G						PASS	.	A		108,4298	85.3+/-124.0	1,106,2096	111.0	99.0	103.0		471	-5.3	0.9	19	dbSNP_131	103	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CLASRP	NM_007056.2		1,107,6395	GG,GA,AA		0.0116,2.4512,0.8381		157/675	45561014	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	11129	exon7			GCTGGCAGAGAAG	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"""Clk4 associating SR-related protein"""		"""splicing factor, arginine/serine-rich 16"""	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.471A>G	19.37:g.45561014A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	37	CCDS12652.2																																																																																			A|0.990;G|0.010	0.010	strong		0.637	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056	
ZNF835	90485	hgsc.bcm.edu	37	19	57176482	57176482	+	Missense_Mutation	SNP	C	C	T	rs12462469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57176482C>T	ENST00000537055.2	-	2	316	c.85G>A	c.(85-87)Gaa>Aaa	p.E29K		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	29			E -> K (in dbSNP:rs12462469). {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						TCCTGGTTTTCCTGCAGGTCC	0.607													.|||	2065	0.41234	0.4531	0.379	5008	,	,		15832	0.4702		0.3131	False		,,,				2504	0.4233				p.E29K		Atlas-SNP	.											.	ZNF835	106	.	0			c.G85A						PASS	.	C	LYS/GLU	1677,2285		367,943,671	75.0	79.0	78.0		85	1.1	0.0	19	dbSNP_120	78	2491,5819		372,1747,2036	yes	missense	ZNF835	NM_001005850.2	56	739,2690,2707	TT,TC,CC		29.9759,42.3271,33.9635	benign	29/538	57176482	4168,8104	1981	4155	6136	SO:0001583	missense	90485	exon2			GGTTTTCCTGCAG	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.85G>A	19.37:g.57176482C>T	ENSP00000444747:p.Glu29Lys	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	148	73	0.493243	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	865	0.39606227106227104	232	0.4715447154471545	128	0.35359116022099446	264	0.46153846153846156	241	0.3179419525065963	C	8.447	0.852126	0.17034	0.423271	0.299759	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.06142	3.34	2.19	1.09	0.20402	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.26318	0.146	B	0.24974	0.057	T	0.38735	-0.9647	8	0.06236	T	0.91	.	6.5636	0.22499	0.0:0.6963:0.3037:0.0	rs12462469	51	Q9Y2P0	ZN835_HUMAN	K	51;29	ENSP00000444747:E29K	ENSP00000341756:E51K	E	-	1	0	ZNF835	61868294	0.000000	0.05858	0.007000	0.13788	0.062000	0.15995	0.145000	0.16157	0.467000	0.27218	0.491000	0.48974	GAA	C|0.621;T|0.379	0.379	strong		0.607	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
EPPK1	83481	hgsc.bcm.edu	37	8	144940474	144940474	+	Silent	SNP	C	C	T	rs56015972		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144940474C>T	ENST00000525985.1	-	2	7019	c.6948G>A	c.(6946-6948)ggG>ggA	p.G2316G				P58107	EPIPL_HUMAN	epiplakin 1	2316						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)			AGATCTGCTGCCCGGTGTAGG	0.706																																					p.G2316G		Atlas-SNP	.											EPPK1,right_lower_lobe,carcinoma,-2,2	EPPK1	199	2	0			c.G6948A						PASS	.	C		17,4343		0,17,2163	198.0	188.0	192.0		6948	-1.0	1.0	8	dbSNP_129	192	4,8524		0,4,4260	no	coding-synonymous	EPPK1	NM_031308.1		0,21,6423	TT,TC,CC		0.0469,0.3899,0.1629		2316/2420	144940474	21,12867	2180	4264	6444	SO:0001819	synonymous_variant	83481	exon1			CTGCTGCCCGGTG	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.6948G>A	8.37:g.144940474C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	184	15	0.0815217	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				C|0.500;T|0.500	0.500	weak		0.706	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
TCN1	6947	hgsc.bcm.edu	37	11	59623433	59623433	+	Silent	SNP	G	G	A	rs1042613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59623433G>A	ENST00000257264.3	-	6	950	c.846C>T	c.(844-846)agC>agT	p.S282S	TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	282	Globular N-terminal alpha domain.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)	p.S282S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CGTTTGGATTGCTGAATGCTC	0.433													a|||	1491	0.297724	0.5484	0.1556	5008	,	,		17327	0.1607		0.2266	False		,,,				2504	0.274				p.S282S		Atlas-SNP	.											TCN1,NS,carcinoma,0,1	TCN1	64	1	1	Substitution - coding silent(1)	stomach(1)	c.C846T						PASS	.			2036,2366	610.4+/-391.6	470,1096,635	129.0	130.0	130.0		846	2.2	0.0	11	dbSNP_86	130	1898,6692	727.3+/-406.6	211,1476,2608	no	coding-synonymous	TCN1	NM_001062.3		681,2572,3243	AA,AG,GG		22.0955,46.2517,30.2802		282/434	59623433	3934,9058	2201	4295	6496	SO:0001819	synonymous_variant	6947	exon6			TGGATTGCTGAAT	J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"""haptocorin"", ""haptocorrin"""	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.846C>T	11.37:g.59623433G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_001062	A8KAC5|Q8WV77	Silent	SNP	ENST00000257264.3	37	CCDS7978.1																																																																																			G|0.704;A|0.296	0.296	strong		0.433	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062	
CAD	790	hgsc.bcm.edu	37	2	27462076	27462076	+	Silent	SNP	C	C	T	rs3739092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27462076C>T	ENST00000403525.1	+	31	5184	c.5040C>T	c.(5038-5040)ccC>ccT	p.P1680P	CAD_ENST00000264705.4_Silent_p.P1743P			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCACCTGCCCCCGCAGGAGG	0.627													C|||	1330	0.265575	0.2716	0.3689	5008	,	,		20316	0.1488		0.2237	False		,,,				2504	0.3476				p.P1743P		Atlas-SNP	.											.	CAD	199	.	0			c.C5229T						PASS	.	C		1049,3357	373.9+/-321.0	127,795,1281	37.0	38.0	38.0		5229	-5.3	0.0	2	dbSNP_107	38	1995,6605	341.3+/-324.0	238,1519,2543	no	coding-synonymous	CAD	NM_004341.3		365,2314,3824	TT,TC,CC		23.1977,23.8084,23.4046		1743/2226	27462076	3044,9962	2203	4300	6503	SO:0001819	synonymous_variant	790	exon32			CCTGCCCCCGCAG	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.5040C>T	2.37:g.27462076C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	37		495	0.22664835164835165	149	0.30284552845528456	112	0.30939226519337015	63	0.11013986013986014	171	0.22559366754617413	C	6.980	0.550843	0.13374	0.238084	0.231977	ENSG00000084774	ENST00000456311	.	.	.	5.16	-5.32	0.02722	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999995955	.	.	.	.	.	.	T	0.20405	-1.0276	5	0.42905	T	0.14	0.856	4.5504	0.12108	0.0831:0.2532:0.4063:0.2573	rs3739092;rs17855323;rs3739092	.	.	.	S	31	.	ENSP00000388740:P31S	P	+	1	0	CAD	27315580	0.000000	0.05858	0.001000	0.08648	0.902000	0.53008	-3.104000	0.00603	-2.352000	0.00616	-1.943000	0.00494	CCC	C|0.773;T|0.227	0.227	strong		0.627	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
SGK223	157285	hgsc.bcm.edu	37	8	8175868	8175868	+	Silent	SNP	C	C	T	rs114026601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8175868C>T	ENST00000520004.1	-	6	4281	c.4017G>A	c.(4015-4017)tcG>tcA	p.S1339S	SGK223_ENST00000330777.4_Silent_p.S1339S			Q86YV5	SG223_HUMAN		1343							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCGCCTCCTCCGAGGTGCCCG	0.682													C|||	123	0.0245607	0.0885	0.0072	5008	,	,		13730	0.0		0.001	False		,,,				2504	0.0				p.S1339S	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G4017A						PASS	.	C		318,3830		13,292,1769	64.0	73.0	70.0		4017	-6.6	0.1	8	dbSNP_132	70	1,8381		0,1,4190	no	coding-synonymous	SGK223	NM_001080826.1		13,293,5959	TT,TC,CC		0.0119,7.6663,2.5459		1339/1403	8175868	319,12211	2074	4191	6265	SO:0001819	synonymous_variant	0	exon5			CTCCTCCGAGGTG																												ENST00000520004.1:c.4017G>A	8.37:g.8175868C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	109	68	0.623853	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			C|0.988;T|0.012	0.012	strong		0.682	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
ZNF638	27332	hgsc.bcm.edu	37	2	71577169	71577169	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71577169T>C	ENST00000409544.1	+	2	1715	c.1085T>C	c.(1084-1086)gTa>gCa	p.V362A	ZNF638_ENST00000377802.2_Missense_Mutation_p.V362A|ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000264447.4_Missense_Mutation_p.V362A|ZNF638_ENST00000355812.3_Missense_Mutation_p.V362A	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	362					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						TCATCTAACGTACATGTTGGA	0.433																																					p.V362A		Atlas-SNP	.											ZNF638,caecum,carcinoma,+1,1	ZNF638	179	1	0			c.T1085C						scavenged	.						121.0	118.0	119.0					2																	71577169		2203	4300	6503	SO:0001583	missense	27332	exon2			CTAACGTACATGT	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.1085T>C	2.37:g.71577169T>C	ENSP00000386433:p.Val362Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	124	2	0.016129	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	T	4.766	0.142467	0.09083	.	.	ENSG00000075292	ENST00000410075;ENST00000544512;ENST00000355812;ENST00000377802;ENST00000264447;ENST00000409544	T;T;T;T;T;T	0.70986	0.07;-0.53;0.69;0.11;1.72;1.72	5.42	3.1	0.35709	.	0.792020	0.11578	N	0.549997	T	0.40222	0.1108	N	0.02539	-0.55	0.23325	N	0.997904	B;B;B;B;B	0.15141	0.012;0.004;0.004;0.002;0.002	B;B;B;B;B	0.10450	0.005;0.002;0.003;0.003;0.002	T	0.28004	-1.0057	10	0.14656	T	0.56	-5.6922	5.8456	0.18663	0.0:0.2085:0.0:0.7915	.	468;362;362;362;362	F5H330;Q14966-4;Q14966-3;Q14966;Q14966-2	.;.;.;ZN638_HUMAN;.	A	362;468;362;362;362;362	ENSP00000386669:V362A;ENSP00000438189:V468A;ENSP00000348066:V362A;ENSP00000367033:V362A;ENSP00000264447:V362A;ENSP00000386433:V362A	ENSP00000264447:V362A	V	+	2	0	ZNF638	71430677	0.997000	0.39634	0.979000	0.43373	0.985000	0.73830	1.328000	0.33758	0.919000	0.36945	0.533000	0.62120	GTA	.	.	none		0.433	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
FBXO41	150726	hgsc.bcm.edu	37	2	73492614	73492614	+	Missense_Mutation	SNP	A	A	T	rs526106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73492614A>T	ENST00000521871.1	-	5	1775	c.1360T>A	c.(1360-1362)Tcc>Acc	p.S454T	FBXO41_ENST00000295133.5_Missense_Mutation_p.S515T|FBXO41_ENST00000520530.2_Missense_Mutation_p.S454T			Q8TF61	FBX41_HUMAN	F-box protein 41	454				S -> T (in Ref. 3; BAB85526). {ECO:0000305}.						breast(2)|central_nervous_system(1)|endometrium(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)	13						GGGGGCTGGGACCGCTCTGAG	0.716													A|||	1654	0.330272	0.2837	0.2421	5008	,	,		11856	0.4752		0.2674	False		,,,				2504	0.3712				p.S454T		Atlas-SNP	.											.	FBXO41	82	.	0			c.T1360A						PASS	.	A	THR/SER	1058,2838		144,770,1034	15.0	18.0	17.0		1360	-0.8	0.9	2	dbSNP_83	17	2135,6093		283,1569,2262	no	missense	FBXO41	NM_001080410.2	58	427,2339,3296	TT,TA,AA		25.948,27.1561,26.3362	benign	454/876	73492614	3193,8931	1948	4114	6062	SO:0001583	missense	150726	exon4			GCTGGGACCGCTC	AB075820	CCDS46337.1, CCDS46337.2	2p13.2	2004-08-24				ENSG00000163013		"""F-boxes /  ""other"""""	29409	protein-coding gene	gene with protein product		609108				11853319	Standard	NM_001080410		Approved	KIAA1940, Fbx41	uc021vjh.1	Q8TF61		ENST00000521871.1:c.1360T>A	2.37:g.73492614A>T	ENSP00000428646:p.Ser454Thr	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	NM_001080410	G3V0Z7|Q2M1V8	Missense_Mutation	SNP	ENST00000521871.1	37	CCDS46337.2	714	0.3269230769230769	138	0.2804878048780488	100	0.27624309392265195	275	0.4807692307692308	201	0.26517150395778366	A	13.31	2.199095	0.38806	0.271561	0.25948	ENSG00000163013	ENST00000295133;ENST00000521871	.	.	.	5.52	-0.818	0.10833	.	0.643686	0.15471	N	0.260595	T	0.00012	0.0000	N	0.14661	0.345	0.44611	P	0.0024170000000000025	.	.	.	.	.	.	T	0.43523	-0.9386	6	0.07030	T	0.85	.	0.8479	0.01166	0.1821:0.347:0.2234:0.2476	rs526106	.	.	.	T	515;454	.	ENSP00000295133:S515T	S	-	1	0	FBXO41	73346122	0.998000	0.40836	0.946000	0.38457	0.962000	0.63368	0.752000	0.26362	-0.113000	0.11958	0.454000	0.30748	TCC	A|0.673;T|0.327	0.327	strong		0.716	FBXO41-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377381.1		
CASP8AP2	9994	hgsc.bcm.edu	37	6	90565242	90565242	+	RNA	SNP	A	A	G	rs369328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90565242A>G	ENST00000551025.1	+	0	1716									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)		TGATGAAAAAATTTAAAGAAA	0.289													G|||	2118	0.422923	0.3502	0.3314	5008	,	,		16871	0.3006		0.5417	False		,,,				2504	0.59				p.K93K	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.A279G						PASS	.	G	,,	1207,2167		264,679,744	14.0	13.0	14.0		279,279,279	-0.1	1.0	6	dbSNP_80	14	3785,3857		1039,1707,1075	no	coding-synonymous,coding-synonymous,coding-synonymous	CASP8AP2	NM_001137667.1,NM_001137668.1,NM_012115.3	,,	1303,2386,1819	GG,GA,AA		49.5289,35.7736,45.3159	,,	93/1967,93/1967,93/1967	90565242	4992,6024	1687	3821	5508			9994	exon5			GAAAAAATTTAAA	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.90565242A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_001137667		Silent	SNP	ENST00000551025.1	37																																																																																				G|0.396;N|0.000	0.396	strong		0.289	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
LPIN1	23175	hgsc.bcm.edu	37	2	11913806	11913806	+	Silent	SNP	G	G	A	rs59909741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11913806G>A	ENST00000256720.2	+	5	750	c.657G>A	c.(655-657)ctG>ctA	p.L219L	LPIN1_ENST00000449576.2_Silent_p.L268L|LPIN1_ENST00000425416.2_Silent_p.L225L|LPIN1_ENST00000396098.1_Silent_p.L225L|LPIN1_ENST00000396099.1_Silent_p.L225L	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	219					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)	p.A220_V221delAV(1)		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)		ACCTCTCCCTGGCTGTGATTT	0.448													G|||	343	0.0684904	0.2451	0.013	5008	,	,		13992	0.0		0.001	False		,,,				2504	0.0092				p.L268L		Atlas-SNP	.											.	LPIN1	99	.	1	Deletion - In frame(1)	kidney(1)	c.G804A						PASS	.	G		939,3467	359.6+/-314.9	93,753,1357	124.0	127.0	126.0		657	-11.0	0.0	2	dbSNP_129	126	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous	LPIN1	NM_145693.1		93,765,5645	AA,AG,GG		0.1395,21.3118,7.312		219/891	11913806	951,12055	2203	4300	6503	SO:0001819	synonymous_variant	23175	exon6			CTCCCTGGCTGTG	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.657G>A	2.37:g.11913806G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																			G|0.937;A|0.063	0.063	strong		0.448	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
IGSF22	283284	hgsc.bcm.edu	37	11	18731905	18731905	+	Silent	SNP	T	T	A	rs114511413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18731905T>A	ENST00000513874.1	-	17	2809	c.2670A>T	c.(2668-2670)ccA>ccT	p.P890P	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	888	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CTGAGCTGGATGGCACACTGG	0.493													T|||	67	0.0133786	0.0484	0.0043	5008	,	,		20918	0.0		0.0	False		,,,				2504	0.0				p.P890P		Atlas-SNP	.											.	IGSF22	211	.	0			c.A2670T						PASS	.	T		123,3791		3,117,1837	119.0	119.0	119.0		2670	-0.4	0.2	11	dbSNP_132	119	3,8295		0,3,4146	no	coding-synonymous	IGSF22	NM_173588.3		3,120,5983	AA,AT,TT		0.0362,3.1426,1.0318		890/1327	18731905	126,12086	1957	4149	6106	SO:0001819	synonymous_variant	283284	exon17			GCTGGATGGCACA	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.2670A>T	11.37:g.18731905T>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_173588	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																			T|0.991;A|0.009	0.009	strong		0.493	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
FAM208A	23272	hgsc.bcm.edu	37	3	56658871	56658871	+	Missense_Mutation	SNP	T	T	C	rs2291498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:56658871T>C	ENST00000493960.2	-	22	4313	c.4303A>G	c.(4303-4305)Ata>Gta	p.I1435V	FAM208A_ENST00000485156.1_Intron|FAM208A_ENST00000431842.2_Missense_Mutation_p.I998V|FAM208A_ENST00000355628.5_Missense_Mutation_p.I1374V	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	177	0	0		WXS	Illumina HiSeq	Phase_I	193	82	0.42487	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	
ZFP28	140612	hgsc.bcm.edu	37	19	57050521	57050521	+	Missense_Mutation	SNP	G	G	A	rs199655023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57050521G>A	ENST00000301318.3	+	1	205	c.134G>A	c.(133-135)gGa>gAa	p.G45E	ZFP28_ENST00000594386.1_3'UTR|ZFP28_ENST00000591844.1_Missense_Mutation_p.G45E|AC005498.3_ENST00000593218.1_lincRNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	45					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)		CCTGCCCGGGGAAGGCCGCGC	0.726													G|||	19	0.00379393	0.0144	0.0	5008	,	,		8689	0.0		0.0	False		,,,				2504	0.0				p.G45E	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.G134A						PASS	.	G	GLU/GLY	32,4078		0,32,2023	6.0	8.0	7.0		134	2.7	1.0	19		7	2,8204		0,2,4101	yes	missense	ZFP28	NM_020828.1	98	0,34,6124	AA,AG,GG		0.0244,0.7786,0.2761	probably-damaging	45/869	57050521	34,12282	2055	4103	6158	SO:0001583	missense	140612	exon1			CCCGGGGAAGGCC		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.134G>A	19.37:g.57050521G>A	ENSP00000301318:p.Gly45Glu	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650497	0.47362	0.007786	2.44E-4	ENSG00000196867	ENST00000301318	T	0.05717	3.4	2.74	2.74	0.32292	.	0.000000	0.31301	U	0.007892	T	0.06280	0.0162	N	0.24115	0.695	0.34331	D	0.687738	D;D	0.89917	0.999;1.0	D;D	0.87578	0.998;0.998	T	0.11227	-1.0596	10	0.06757	T	0.87	.	9.1377	0.36883	0.0:0.0:1.0:0.0	.	45;45	Q8NHY6;A8K0L8	ZFP28_HUMAN;.	E	45	ENSP00000301318:G45E	ENSP00000301318:G45E	G	+	2	0	ZFP28	61742333	0.909000	0.30893	0.986000	0.45419	0.823000	0.46562	0.683000	0.25349	1.817000	0.53016	0.462000	0.41574	GGA	.	.	weak		0.726	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
OR2A4	79541	hgsc.bcm.edu	37	6	132021722	132021722	+	Silent	SNP	G	G	A	rs145289654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:132021722G>A	ENST00000315453.2	-	1	913	c.820C>T	c.(820-822)Ctg>Ttg	p.L274L	ENPP3_ENST00000357639.3_Intron|ENPP3_ENST00000358229.5_Intron|ENPP3_ENST00000414305.1_Intron	NM_030908.1	NP_112170.1	O95047	OR2A4_HUMAN	olfactory receptor, family 2, subfamily A, member 4	274					positive regulation of cytokinesis (GO:0032467)|regulation of actin cytoskeleton organization (GO:0032956)	cleavage furrow (GO:0032154)|Flemming body (GO:0090543)|integral component of membrane (GO:0016021)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|ovary(1)|skin(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.018)|OV - Ovarian serous cystadenocarcinoma(155;0.041)		TGAAACAGCAGGAGATATTTC	0.453													g|||	76	0.0151757	0.0545	0.0058	5008	,	,		22576	0.0		0.0	False		,,,				2504	0.0				p.L274L		Atlas-SNP	.											.	OR2A4	17	.	0			c.C820T						PASS	.	G	,	198,3340		56,86,1627	20.0	30.0	27.0		,820	0.7	0.9	6	dbSNP_134	27	0,8486		0,0,4243	no	intron,coding-synonymous	ENPP3,OR2A4	NM_005021.3,NM_030908.1	,	56,86,5870	AA,AG,GG		0.0,5.5964,1.6467	,	,274/311	132021722	198,11826	1769	4243	6012	SO:0001819	synonymous_variant	79541	exon1			ACAGCAGGAGATA	AC005587	CCDS5149.1	6q23	2012-08-09	2003-05-22		ENSG00000180658	ENSG00000180658		"""GPCR / Class A : Olfactory receptors"""	14729	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 10"""	OR2A10			Standard	NM_030908		Approved		uc011ecd.2	O95047	OTTHUMG00000016316	ENST00000315453.2:c.820C>T	6.37:g.132021722G>A		Somatic	770	2	0.0025974		WXS	Illumina HiSeq	Phase_I	935	254	0.271658	NM_030908	Q0VAR3|Q6IF18|Q9NQN0	Silent	SNP	ENST00000315453.2	37	CCDS5149.1																																																																																			G|0.995;A|0.005	0.005	strong		0.453	OR2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109221.1	NM_030908	
PRKD3	23683	hgsc.bcm.edu	37	2	37506939	37506939	+	Silent	SNP	A	A	G	rs3770761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37506939A>G	ENST00000379066.1	-	8	1884	c.1122T>C	c.(1120-1122)gaT>gaC	p.D374D	PRKD3_ENST00000234179.2_Silent_p.D374D			O94806	KPCD3_HUMAN	protein kinase D3	374					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)				GATCAGATGGATCCAAGAAGA	0.388													A|||	815	0.16274	0.0809	0.2435	5008	,	,		13660	0.3373		0.0795	False		,,,				2504	0.1217				p.D374D	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.T1122C						PASS	.	A		328,4078	173.0+/-202.9	15,298,1890	109.0	107.0	108.0		1122	3.3	1.0	2	dbSNP_107	108	514,8086	145.6+/-201.3	24,466,3810	no	coding-synonymous	PRKD3	NM_005813.3		39,764,5700	GG,GA,AA		5.9767,7.4444,6.4739		374/891	37506939	842,12164	2203	4300	6503	SO:0001819	synonymous_variant	23683	exon7			AGATGGATCCAAG	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.1122T>C	2.37:g.37506939A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1																																																																																			A|0.895;G|0.105	0.105	strong		0.388	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	
ANAPC16	119504	hgsc.bcm.edu	37	10	73992862	73992862	+	Silent	SNP	C	C	G	rs9275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73992862C>G	ENST00000299381.4	+	4	439	c.321C>G	c.(319-321)ccC>ccG	p.P107P	ANAPC16_ENST00000470481.2_3'UTR	NM_001242546.1|NM_001242547.1|NM_001242548.1|NM_173473.3	NP_001229475.1|NP_001229476.1|NP_001229477.1|NP_775744.1	Q96DE5	APC16_HUMAN	anaphase promoting complex subunit 16	107					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	anaphase-promoting complex (GO:0005680)|cytoplasm (GO:0005737)				large_intestine(1)|ovary(1)	2						GATTCACCCCCTCTTCAGGTT	0.542													C|||	364	0.0726837	0.2595	0.0274	5008	,	,		14954	0.0		0.002	False		,,,				2504	0.0				p.P107P		Atlas-SNP	.											.	ANAPC16	10	.	0			c.C321G						PASS	.	C	,,,	919,3487	344.1+/-307.9	90,739,1374	66.0	64.0	65.0		321,321,246,321	-0.3	1.0	10	dbSNP_52	65	13,8587	9.1+/-34.3	0,13,4287	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANAPC16	NM_001242546.1,NM_001242547.1,NM_001242548.1,NM_173473.3	,,,	90,752,5661	GG,GC,CC		0.1512,20.8579,7.1659	,,,	107/111,107/111,82/86,107/111	73992862	932,12074	2203	4300	6503	SO:0001819	synonymous_variant	119504	exon5			CACCCCCTCTTCA	BC009530	CCDS7314.1, CCDS73147.1	10q22.2	2011-08-12	2010-04-06	2010-04-06	ENSG00000166295	ENSG00000166295		"""Anaphase promoting complex subunits"""	26976	protein-coding gene	gene with protein product	"""centromere protein 27"""	613427	"""chromosome 10 open reading frame 104"""	C10orf104		14702039, 20360068	Standard	NM_001242546		Approved	bA570G20.3, FLJ33728, APC16, CENP-27	uc021psp.1	Q96DE5	OTTHUMG00000018433	ENST00000299381.4:c.321C>G	10.37:g.73992862C>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	45	26	0.577778	NM_001242546		Silent	SNP	ENST00000299381.4	37	CCDS7314.1																																																																																			G|0.064;C|0.936	0.064	strong		0.542	ANAPC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048565.2	NM_173473	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21932598	21932598	+	Silent	SNP	G	G	A	rs150973141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21932598G>A	ENST00000374765.4	-	18	1589	c.1389C>T	c.(1387-1389)ttC>ttT	p.F463F	RAP1GAP_ENST00000374761.2_Silent_p.F494F|RAP1GAP_ENST00000374763.2_Silent_p.F463F|RAP1GAP_ENST00000542643.2_Silent_p.F463F|RAP1GAP_ENST00000290101.4_Silent_p.F527F	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	463					GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		TGTTGGGCGCGAAGCTCCCGC	0.682																																					p.F527F		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.C1581T						PASS	.	G	,,	7,4383		0,7,2188	55.0	33.0	40.0		1389,1581,1389	-2.1	0.1	1	dbSNP_134	40	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	RAP1GAP	NM_001145657.1,NM_001145658.1,NM_002885.2	,,	0,7,6484	AA,AG,GG		0.0,0.1595,0.0539	,,	463/682,527/728,463/664	21932598	7,12975	2195	4296	6491	SO:0001819	synonymous_variant	5909	exon18			GGGCGCGAAGCTC	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1389C>T	1.37:g.21932598G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	114	50	0.438596	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			G|0.999;A|0.001	0.001	strong		0.682	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
STAG3	10734	hgsc.bcm.edu	37	7	99799845	99799845	+	Silent	SNP	T	T	A	rs1043915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99799845T>A	ENST00000426455.1	+	24	2852	c.2445T>A	c.(2443-2445)atT>atA	p.I815I	STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000436886.2_3'UTR|GATS_ENST00000543273.1_RNA|STAG3_ENST00000317296.5_Silent_p.I815I|STAG3_ENST00000394018.2_Silent_p.I757I	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	815					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTCAGATGATTGTTGGGGGCC	0.458													T|||	1969	0.393171	0.3343	0.5173	5008	,	,		19641	0.621		0.2664	False		,,,				2504	0.2802				p.I815I		Atlas-SNP	.											.	STAG3	121	.	0			c.T2445A						PASS	.	T	,	1502,2904		245,1012,946	144.0	153.0	150.0		2445,	-0.2	0.1	7	dbSNP_86	150	2263,6337		305,1653,2342	no	coding-synonymous,utr-3	STAG3,GATS	NM_012447.2,NM_178831.6	,	550,2665,3288	AA,AT,TT		26.314,34.0899,28.9482	,	815/1226,	99799845	3765,9241	2203	4300	6503	SO:0001819	synonymous_variant	10734	exon24			GATGATTGTTGGG	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2445T>A	7.37:g.99799845T>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Silent	SNP	ENST00000426455.1	37	CCDS34703.1																																																																																			T|0.679;A|0.321	0.321	strong		0.458	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388757	1388757	+	Missense_Mutation	SNP	T	T	C	rs138170890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1388757T>C	ENST00000324803.4	+	1	3418	c.458T>C	c.(457-459)aTg>aCg	p.M153T		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	153					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)		p.M153T(1)		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)			CACGTGCCCATGCGGAGTGCC	0.697													N|||	566	0.113019	0.0772	0.1657	5008	,	,		14705	0.0139		0.1441	False		,,,				2504	0.1943				p.M153T		Atlas-SNP	.											CRIPAK,colon,carcinoma,0,2	CRIPAK	185	2	1	Substitution - Missense(1)	NS(1)	c.T458C						scavenged	.						78.0	69.0	72.0					4																	1388757		2201	4281	6482	SO:0001583	missense	285464	exon1			TGCCCATGCGGAG	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.458T>C	4.37:g.1388757T>C	ENSP00000323978:p.Met153Thr	Somatic	31	1	0.0322581		WXS	Illumina HiSeq	Phase_I	78	9	0.115385	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	2.748	-0.260796	0.05791	.	.	ENSG00000179979	ENST00000324803	T	0.17370	2.28	0.948	-0.668	0.11392	Post-SET domain (1);	.	.	.	.	T	0.07188	0.0182	N	0.08118	0	0.09310	N	1	B	0.20052	0.041	B	0.14023	0.01	T	0.34304	-0.9834	9	0.38643	T	0.18	.	4.4755	0.11733	0.0:0.2357:0.0:0.7643	.	153	Q8N1N5	CRPAK_HUMAN	T	153	ENSP00000323978:M153T	ENSP00000323978:M153T	M	+	2	0	CRIPAK	1378757	0.000000	0.05858	0.003000	0.11579	0.022000	0.10575	-1.643000	0.02004	-0.155000	0.11098	0.102000	0.15555	ATG	.	.	weak		0.697	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
MRPS9	64965	hgsc.bcm.edu	37	2	105708936	105708936	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:105708936G>C	ENST00000258455.3	+	8	839	c.729G>C	c.(727-729)agG>agC	p.R243S		NM_182640.2	NP_872578.1	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9	243					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						TTGTGCAGAGGTTTCGAAGAA	0.388																																					p.R243S		Atlas-SNP	.											.	MRPS9	32	.	0			c.G729C						PASS	.						140.0	143.0	142.0					2																	105708936		2203	4300	6503	SO:0001583	missense	64965	exon8			GCAGAGGTTTCGA		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.729G>C	2.37:g.105708936G>C	ENSP00000258455:p.Arg243Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_182640	Q6PG40	Missense_Mutation	SNP	ENST00000258455.3	37	CCDS2065.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.580061	0.28180	.	.	ENSG00000135972	ENST00000258455	D	0.92099	-2.97	5.61	1.81	0.25067	.	0.318283	0.38111	N	0.001806	D	0.86896	0.6043	M	0.61703	1.905	0.42674	D	0.993529	B	0.16396	0.017	B	0.10450	0.005	T	0.76602	-0.2899	10	0.39692	T	0.17	-24.4138	2.1982	0.03916	0.2617:0.1209:0.4925:0.1249	.	243	P82933	RT09_HUMAN	S	243	ENSP00000258455:R243S	ENSP00000258455:R243S	R	+	3	2	MRPS9	105075368	0.997000	0.39634	0.988000	0.46212	0.789000	0.44602	0.322000	0.19576	0.115000	0.18071	0.655000	0.94253	AGG	.	.	none		0.388	MRPS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253352.1	NM_182640	
GAB4	128954	hgsc.bcm.edu	37	22	17445710	17445710	+	Silent	SNP	C	C	T	rs5992599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17445710C>T	ENST00000400588.1	-	8	1529	c.1422G>A	c.(1420-1422)acG>acA	p.T474T	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	474										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)				TGATGCTCTGCGTGGAGATGG	0.572													C|||	202	0.0403355	0.1498	0.0058	5008	,	,		19710	0.0		0.0	False		,,,				2504	0.0				p.T474T		Atlas-SNP	.											.	GAB4	95	.	0			c.G1422A						PASS	.	C		504,3876	213.5+/-233.1	31,442,1717	151.0	162.0	158.0		1422	-3.9	0.3	22	dbSNP_114	158	2,8580	2.2+/-6.3	0,2,4289	no	coding-synonymous	GAB4	NM_001037814.1		31,444,6006	TT,TC,CC		0.0233,11.5068,3.9037		474/575	17445710	506,12456	2190	4291	6481	SO:0001819	synonymous_variant	128954	exon8			GCTCTGCGTGGAG	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.1422G>A	22.37:g.17445710C>T		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	259	127	0.490348	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			C|0.954;T|0.046	0.046	strong		0.572	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
USP44	84101	hgsc.bcm.edu	37	12	95927172	95927172	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:95927172A>G	ENST00000258499.3	-	2	1149	c.861T>C	c.(859-861)gtT>gtC	p.V287V	USP44_ENST00000552440.1_Silent_p.V287V|USP44_ENST00000393091.2_Silent_p.V287V|USP44_ENST00000537435.2_Silent_p.V287V	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	287	USP.				mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						ACACCTGAAGAACAGAATTCA	0.378																																					p.V287V		Atlas-SNP	.											.	USP44	83	.	0			c.T861C						PASS	.						77.0	79.0	78.0					12																	95927172		2203	4300	6503	SO:0001819	synonymous_variant	84101	exon2			CTGAAGAACAGAA	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.861T>C	12.37:g.95927172A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_032147	B2RDW3	Silent	SNP	ENST00000258499.3	37	CCDS9053.1																																																																																			.	.	none		0.378	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	
DEAF1	10522	hgsc.bcm.edu	37	11	653968	653968	+	Silent	SNP	T	T	C	rs10615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:653968T>C	ENST00000382409.3	-	11	2071	c.1587A>G	c.(1585-1587)caA>caG	p.Q529Q	DEAF1_ENST00000338675.6_Silent_p.Q454Q|DEAF1_ENST00000525904.1_5'UTR	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	529					anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		CTACCTTGCGTTGGCAGAAGG	0.632													C|||	1426	0.284744	0.6263	0.1369	5008	,	,		16402	0.2202		0.1312	False		,,,				2504	0.1524				p.Q529Q		Atlas-SNP	.											.	DEAF1	47	.	0			c.A1587G						PASS	.	C		2383,2023	563.4+/-381.2	659,1065,479	188.0	148.0	161.0		1587	3.5	1.0	11	dbSNP_116	161	1052,7548	771.0+/-407.7	73,906,3321	no	coding-synonymous	DEAF1	NM_021008.2		732,1971,3800	CC,CT,TT		12.2326,45.9147,26.4109		529/566	653968	3435,9571	2203	4300	6503	SO:0001819	synonymous_variant	10522	exon11			CTTGCGTTGGCAG	AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030		"""Zinc fingers, MYND-type"""	14677	protein-coding gene	gene with protein product		602635	"""deformed epidermal autoregulatory factor 1 (Drosophila)"""			9773984	Standard	XR_428838		Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.1587A>G	11.37:g.653968T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_021008	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Silent	SNP	ENST00000382409.3	37	CCDS31327.1																																																																																			T|0.726;C|0.274	0.274	strong		0.632	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383614.3	NM_021008	
SETD9	133383	hgsc.bcm.edu	37	5	56205559	56205559	+	Silent	SNP	C	C	T	rs80198735	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:56205559C>T	ENST00000285947.2	+	1	473	c.87C>T	c.(85-87)agC>agT	p.S29S	AC008937.3_ENST00000453721.1_RNA|SETD9_ENST00000541720.1_Silent_p.S29S|SETD9_ENST00000475908.1_Intron	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	29							methyltransferase activity (GO:0008168)										TGAACCTAAGCCACAACCCGA	0.687													C|||	53	0.0105831	0.0386	0.0029	5008	,	,		9227	0.0		0.0	False		,,,				2504	0.0				p.S29S		Atlas-SNP	.											.	.	.	.	0			c.C87T						PASS	.	C	,	152,4254	98.9+/-137.6	5,142,2056	49.0	32.0	38.0		87,87	2.4	0.5	5	dbSNP_131	38	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	C5orf35	NM_001171990.1,NM_153706.3	,	5,143,6355	TT,TC,CC		0.0116,3.4498,1.1764	,	29/272,29/300	56205559	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	133383	exon1			CCTAAGCCACAAC	BC036528	CCDS3972.1	5q11.2	2012-02-23	2012-02-23	2012-02-23	ENSG00000155542	ENSG00000155542			28508	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 35"""	C5orf35		20930037	Standard	NM_153706		Approved	MGC33648	uc003jqx.3	Q8NE22	OTTHUMG00000059485	ENST00000285947.2:c.87C>T	5.37:g.56205559C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	98	34	0.346939	NM_153706	F5H713	Silent	SNP	ENST00000285947.2	37	CCDS3972.1																																																																																			C|0.987;T|0.013	0.013	strong		0.687	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706	
COCH	1690	hgsc.bcm.edu	37	14	31355096	31355096	+	Missense_Mutation	SNP	C	C	G	rs1045644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:31355096C>G	ENST00000396618.3	+	11	1111	c.1055C>G	c.(1054-1056)aCt>aGt	p.T352S	RP11-829H16.3_ENST00000556786.1_RNA|COCH_ENST00000382493.4_Missense_Mutation_p.T203S|COCH_ENST00000460581.2_Missense_Mutation_p.T240S|RP11-829H16.3_ENST00000468444.2_RNA|RP11-829H16.3_ENST00000555108.1_RNA|COCH_ENST00000475087.1_Missense_Mutation_p.T352S|RP11-829H16.3_ENST00000555421.1_RNA|COCH_ENST00000216361.4_Missense_Mutation_p.T352S	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	352			T -> S (in dbSNP:rs1045644). {ECO:0000269|Ref.4}.		defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	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;0.00645)		AAGCTGTGCACTCATGAACAA	0.453													C|||	2060	0.411342	0.2141	0.6311	5008	,	,		21277	0.3611		0.6342	False		,,,				2504	0.3446				p.T352S		Atlas-SNP	.											.	COCH	54	.	0			c.C1055G						PASS	.	C	SER/THR,SER/THR	1244,3162	427.8+/-341.7	179,886,1138	108.0	92.0	98.0		1055,1055	4.2	0.5	14	dbSNP_86	98	5415,3185	653.2+/-401.0	1690,2035,575	yes	missense,missense	COCH	NM_001135058.1,NM_004086.2	58,58	1869,2921,1713	GG,GC,CC		37.0349,28.2342,48.8006	benign,benign	352/551,352/551	31355096	6659,6347	2203	4300	6503	SO:0001583	missense	1690	exon11			TGTGCACTCATGA		CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"""coagulation factor C (Limulus polyphemus homolog); cochlin"", ""coagulation factor C homolog, cochlin (Limulus polyphemus)"""	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.1055C>G	14.37:g.31355096C>G	ENSP00000379862:p.Thr352Ser	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	163	82	0.503067	NM_004086	A8K9K9|D3DS84|Q96IU6	Missense_Mutation	SNP	ENST00000396618.3	37	CCDS9640.1	1020|1020	0.46703296703296704|0.46703296703296704	119|119	0.241869918699187|0.241869918699187	222|222	0.6132596685082873|0.6132596685082873	198|198	0.34615384615384615|0.34615384615384615	481|481	0.6345646437994723|0.6345646437994723	C|C	12.49|12.49	1.953829|1.953829	0.34471|0.34471	0.282342|0.282342	0.629651|0.629651	ENSG00000100473|ENSG00000100473	ENST00000542225;ENST00000468826|ENST00000216361;ENST00000396618;ENST00000475087;ENST00000460581;ENST00000382493	.|T;T;T;T;T	.|0.78003	.|-1.14;-1.14;-1.14;-1.14;-1.14	6.02|6.02	4.18|4.18	0.49190|0.49190	.|.	.|0.308394	.|0.40144	.|N	.|0.001171	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00436|0.00436	-1.5|-1.5	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.10296	.|0.003;0.003;0.0	.|B;B;B	.|0.06405	.|0.002;0.002;0.0	T|T	0.44528|0.44528	-0.9322|-0.9322	5|9	0.12430|0.06494	T|T	0.62|0.89	-1.6457|-1.6457	16.9096|16.9096	0.86137|0.86137	0.0:0.7586:0.2414:0.0|0.0:0.7586:0.2414:0.0	rs1045644;rs2076681;rs3168862;rs17367681;rs52825530;rs1045644|rs1045644;rs2076681;rs3168862;rs17367681;rs52825530;rs1045644	.|203;352;352	.|E7EN67;Q96IU6;O43405	.|.;.;COCH_HUMAN	V|S	240;236|352;352;352;240;203	.|ENSP00000216361:T352S;ENSP00000379862:T352S;ENSP00000451528:T352S;ENSP00000451713:T240S;ENSP00000371933:T203S	ENSP00000440215:L240V|ENSP00000216361:T352S	L|T	+|+	1|2	0|0	COCH|COCH	30424847|30424847	0.002000|0.002000	0.14202|0.14202	0.454000|0.454000	0.27019|0.27019	0.988000|0.988000	0.76386|0.76386	1.416000|1.416000	0.34759|0.34759	0.846000|0.846000	0.35142|0.35142	0.650000|0.650000	0.86243|0.86243	CTC|ACT	C|0.529;G|0.471	0.471	strong		0.453	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086	
OR11A1	26531	hgsc.bcm.edu	37	6	29395180	29395180	+	Missense_Mutation	SNP	A	A	G	rs61978565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29395180A>G	ENST00000377149.1	-	5	711	c.239T>C	c.(238-240)aTg>aCg	p.M80T	OR11A1_ENST00000377148.1_Missense_Mutation_p.M80T|OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377147.2_Missense_Mutation_p.M80T			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, 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)	p.M80T(1)		cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						CATTTTTGGCATCACTGCGGA	0.483													A|||	219	0.04373	0.1384	0.0115	5008	,	,		19957	0.0119		0.0129	False		,,,				2504	0.0031				p.M80T		Atlas-SNP	.											OR11A1,NS,carcinoma,0,1	OR11A1	30	1	1	Substitution - Missense(1)	pancreas(1)	c.T239C						PASS	.	A	THR/MET	369,2651		26,317,1167	70.0	63.0	66.0		239	3.8	0.9	6	dbSNP_129	66	34,5384		0,34,2675	yes	missense	OR11A1	NM_013937.2	81	26,351,3842	GG,GA,AA		0.6275,12.2185,4.776	benign	80/316	29395180	403,8035	1510	2709	4219	SO:0001583	missense	26531	exon1			TTTGGCATCACTG		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.239T>C	6.37:g.29395180A>G	ENSP00000366354:p.Met80Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	75	44	0.586667	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	37	CCDS34363.1	102	0.046703296703296704	74	0.15040650406504066	7	0.019337016574585635	10	0.017482517482517484	11	0.014511873350923483	A	8.985	0.976299	0.18736	0.122185	0.006275	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.02974	4.09;4.09;4.09	3.78	3.78	0.43462	GPCR, rhodopsin-like superfamily (1);	0.297272	0.18047	U	0.153413	T	0.00524	0.0017	N	0.01209	-0.955	0.18873	N	0.999989	B	0.13594	0.008	B	0.14578	0.011	T	0.51028	-0.8757	10	0.56958	D	0.05	-9.2563	11.5265	0.50582	1.0:0.0:0.0:0.0	.	80	Q9GZK7	O11A1_HUMAN	T	80	ENSP00000366353:M80T;ENSP00000366354:M80T;ENSP00000366352:M80T	ENSP00000366352:M80T	M	-	2	0	OR11A1	29503159	0.000000	0.05858	0.925000	0.36789	0.702000	0.40608	0.971000	0.29396	1.569000	0.49696	0.333000	0.21579	ATG	A|0.957;G|0.043	0.043	strong		0.483	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1		
RIPPLY2	134701	hgsc.bcm.edu	37	6	84563147	84563147	+	Silent	SNP	G	G	A	rs9353143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84563147G>A	ENST00000369689.1	+	1	163	c.12G>A	c.(10-12)gcG>gcA	p.A4A	RIPPLY2_ENST00000369687.1_5'Flank	NM_001009994.1	NP_001009994.1	Q5TAB7	RIPP2_HUMAN	ripply transcriptional repressor 2	4					bone morphogenesis (GO:0060349)|determination of left/right symmetry (GO:0007368)|Notch signaling pathway (GO:0007219)|ossification (GO:0001503)|post-anal tail morphogenesis (GO:0036342)|regulation of gene expression (GO:0010468)|somite rostral/caudal axis specification (GO:0032525)|somitogenesis (GO:0001756)	nucleus (GO:0005634)				large_intestine(2)|lung(4)|urinary_tract(1)	7						TGGAGAACGCGGGAGGCGCAG	0.697													A|||	1469	0.293331	0.6596	0.2752	5008	,	,		13517	0.2619		0.0825	False		,,,				2504	0.0603				p.A4A		Atlas-SNP	.											RIPPLY2,rectum,carcinoma,0,1	RIPPLY2	17	1	0			c.G12A						PASS	.	A		1259,1859		244,771,544	3.0	4.0	4.0		12	-3.7	0.0	6	dbSNP_119	4	433,5751		28,377,2687	no	coding-synonymous	RIPPLY2	NM_001009994.1		272,1148,3231	AA,AG,GG		7.0019,40.3784,18.1896		4/129	84563147	1692,7610	1559	3092	4651	SO:0001819	synonymous_variant	134701	exon1			GAACGCGGGAGGC	BC130460	CCDS34493.1	6q14.2	2013-07-23	2013-07-23	2008-05-07	ENSG00000203877	ENSG00000203877			21390	protein-coding gene	gene with protein product		609891	"""chromosome 6 open reading frame 159"", ""ripply2 homolog (zebrafish)"""	C6orf159			Standard	NM_001009994		Approved	dJ237I15.1	uc003pke.3	Q5TAB7	OTTHUMG00000015117	ENST00000369689.1:c.12G>A	6.37:g.84563147G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_001009994	Q5TAB6	Silent	SNP	ENST00000369689.1	37	CCDS34493.1																																																																																			G|0.692;A|0.308	0.308	strong		0.697	RIPPLY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041360.1	NM_001009994	
FLG	2312	hgsc.bcm.edu	37	1	152280471	152280471	+	Missense_Mutation	SNP	C	C	G	rs78179835		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152280471C>G	ENST00000368799.1	-	3	6926	c.6891G>C	c.(6889-6891)gaG>gaC	p.E2297D	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	714	3	0.00420168		WXS	Illumina HiSeq	Phase_I	799	460	0.57572	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	
VWA2	340706	hgsc.bcm.edu	37	10	116008497	116008497	+	Missense_Mutation	SNP	G	G	A	rs9664945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	208	0	0		WXS	Illumina HiSeq	Phase_I	248	143	0.576613	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	
IDUA	3425	hgsc.bcm.edu	37	4	995868	995868	+	Silent	SNP	C	C	T	rs114806891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:995868C>T	ENST00000247933.4	+	7	979	c.891C>T	c.(889-891)aaC>aaT	p.N297N	IDUA_ENST00000453894.1_Nonsense_Mutation_p.R284*|IDUA_ENST00000514224.1_Silent_p.N165N	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	297					carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCATTTACAACGACGAGGCGG	0.682													C|||	150	0.0299521	0.0076	0.0548	5008	,	,		13632	0.0208		0.0557	False		,,,				2504	0.0256				p.N297N		Atlas-SNP	.											.	IDUA	33	.	0			c.C891T						PASS	.	C		65,4275		0,65,2105	24.0	26.0	26.0		891	-1.2	1.0	4	dbSNP_132	26	549,7959		21,507,3726	no	coding-synonymous	IDUA	NM_000203.3		21,572,5831	TT,TC,CC		6.4528,1.4977,4.779		297/654	995868	614,12234	2170	4254	6424	SO:0001819	synonymous_variant	3425	exon7			TTACAACGACGAG	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.891C>T	4.37:g.995868C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	18	0.327273	NM_000203	B3KWK6	Silent	SNP	ENST00000247933.4	37	CCDS3343.1	73	0.033424908424908424	7	0.014227642276422764	21	0.058011049723756904	11	0.019230769230769232	34	0.044854881266490766	C	32	5.173413	0.94807	0.014977	0.064528	ENSG00000127415	ENST00000453894	.	.	.	4.91	-1.16	0.09678	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	0.484	10.2778	0.43521	0.0:0.3858:0.0:0.6142	.	.	.	.	X	284	.	ENSP00000396458:R284X	R	+	1	2	IDUA	985868	0.070000	0.21116	0.992000	0.48379	0.911000	0.54048	-0.575000	0.05861	-0.247000	0.09597	-0.254000	0.11334	CGA	C|0.965;T|0.035	0.035	strong		0.682	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
SUN2	25777	hgsc.bcm.edu	37	22	39134715	39134715	+	Silent	SNP	T	T	C	rs1062687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39134715T>C	ENST00000405510.1	-	17	2182	c.1824A>G	c.(1822-1824)caA>caG	p.Q608Q	RP3-508I15.19_ENST00000418803.1_RNA|SUN2_ENST00000216064.4_Silent_p.Q608Q|SUN2_ENST00000405018.1_Silent_p.Q629Q|SUN2_ENST00000406622.1_Silent_p.Q608Q|RP3-508I15.20_ENST00000609428.1_RNA|SUN2_ENST00000411587.2_Silent_p.Q597Q|RP3-508I15.14_ENST00000416406.1_RNA|RP3-508I15.18_ENST00000420118.1_RNA	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	608	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						CGGCGAAGCCTTGTGGCCCCT	0.622													C|||	1923	0.383986	0.556	0.2046	5008	,	,		17697	0.4603		0.2982	False		,,,				2504	0.2883				p.Q629Q		Atlas-SNP	.											.	SUN2	59	.	0			c.A1887G						PASS	.	C	,,	2258,2148	573.8+/-383.6	577,1104,522	66.0	70.0	69.0		1887,1824,1824	2.4	1.0	22	dbSNP_86	69	2565,6035	685.2+/-404.0	375,1815,2110	no	coding-synonymous,coding-synonymous,coding-synonymous	SUN2	NM_001199579.1,NM_001199580.1,NM_015374.2	,,	952,2919,2632	CC,CT,TT		29.8256,48.7517,37.0829	,,	629/739,608/718,608/718	39134715	4823,8183	2203	4300	6503	SO:0001819	synonymous_variant	25777	exon16			GAAGCCTTGTGGC	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"""unc-84 homolog B (C. elegans)"""	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.1824A>G	22.37:g.39134715T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_001199579	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Silent	SNP	ENST00000405510.1	37	CCDS13978.1																																																																																			T|0.620;C|0.380;A|0.000	0.380	strong		0.622	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332	
HMCN1	83872	hgsc.bcm.edu	37	1	186043899	186043899	+	Silent	SNP	T	T	C	rs77026548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186043899T>C	ENST00000271588.4	+	53	8395	c.8166T>C	c.(8164-8166)aaT>aaC	p.N2722N	HMCN1_ENST00000367492.2_Silent_p.N2722N	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2722	Ig-like C2-type 25.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATCATGTTAATATTGCTGCGA	0.383													T|||	153	0.0305511	0.1104	0.0086	5008	,	,		14973	0.0		0.001	False		,,,				2504	0.0				p.N2722N		Atlas-SNP	.											.	HMCN1	797	.	0			c.T8166C						PASS	.	T		425,3981	208.2+/-229.3	24,377,1802	113.0	109.0	110.0		8166	-2.0	0.1	1	dbSNP_131	110	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	HMCN1	NM_031935.2		24,383,6096	CC,CT,TT		0.0698,9.6459,3.3139		2722/5636	186043899	431,12575	2203	4300	6503	SO:0001819	synonymous_variant	83872	exon53			TGTTAATATTGCT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8166T>C	1.37:g.186043899T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			T|0.967;C|0.033	0.033	strong		0.383	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
AKAP11	11215	hgsc.bcm.edu	37	13	42876290	42876290	+	Silent	SNP	A	A	C	rs41288311	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:42876290A>C	ENST00000025301.2	+	8	3583	c.3408A>C	c.(3406-3408)acA>acC	p.T1136T		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1136					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)		CACCTGCTACACCACCTTCTA	0.408													A|||	357	0.0712859	0.1233	0.0576	5008	,	,		20338	0.002		0.1252	False		,,,				2504	0.0266				p.T1136T		Atlas-SNP	.											.	AKAP11	146	.	0			c.A3408C						PASS	.	A		568,3838	247.2+/-255.5	40,488,1675	101.0	108.0	106.0		3408	-0.2	1.0	13	dbSNP_127	106	1119,7481	231.7+/-265.6	85,949,3266	no	coding-synonymous	AKAP11	NM_016248.3		125,1437,4941	CC,CA,AA		13.0116,12.8915,12.9709		1136/1902	42876290	1687,11319	2203	4300	6503	SO:0001819	synonymous_variant	11215	exon8			TGCTACACCACCT	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.3408A>C	13.37:g.42876290A>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	188	100	0.531915	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			A|0.882;C|0.118	0.118	strong		0.408	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
KLHL26	55295	hgsc.bcm.edu	37	19	18779728	18779728	+	Silent	SNP	C	C	T	rs73533829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18779728C>T	ENST00000300976.4	+	3	1611	c.1521C>T	c.(1519-1521)ggC>ggT	p.G507G	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	507										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						TGGGTGCCGGCGGCCGCATCT	0.667													C|||	49	0.00978435	0.034	0.0043	5008	,	,		14368	0.0		0.001	False		,,,				2504	0.0				p.G507G		Atlas-SNP	.											.	KLHL26	43	.	0			c.C1521T						PASS	.	C		121,4283		1,119,2082	37.0	38.0	37.0		1521	-6.0	0.1	19	dbSNP_130	37	4,8576		0,4,4286	no	coding-synonymous	KLHL26	NM_018316.1		1,123,6368	TT,TC,CC		0.0466,2.7475,0.9627		507/616	18779728	125,12859	2202	4290	6492	SO:0001819	synonymous_variant	55295	exon3			TGCCGGCGGCCGC		CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"""Kelch-like"", ""BTB/POZ domain containing"""	25623	protein-coding gene	gene with protein product			"""kelch-like 26 (Drosophila)"""				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.1521C>T	19.37:g.18779728C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.988;T|0.012	0.012	strong		0.667	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316	
FIGLA	344018	hgsc.bcm.edu	37	2	71012604	71012604	+	Silent	SNP	G	G	A	rs7566541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71012604G>A	ENST00000332372.6	-	3	556	c.552C>T	c.(550-552)caC>caT	p.H184H		NM_001004311.3	NP_001004311.2	Q6QHK4	FIGLA_HUMAN	folliculogenesis specific basic helix-loop-helix	184					multicellular organismal development (GO:0007275)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)			endometrium(2)|lung(3)	5						GGCGACAAGCGTGTGCTGGCT	0.468													A|||	3995	0.797724	0.9743	0.7032	5008	,	,		17286	0.9067		0.5905	False		,,,				2504	0.727				p.H184H		Atlas-SNP	.											.	FIGLA	23	.	0			c.C552T						PASS	.	A		3780,418		1696,388,15	249.0	247.0	248.0		552	-3.1	0.0	2	dbSNP_116	248	4744,3686		1343,2058,814	no	coding-synonymous	FIGLA	NM_001004311.3		3039,2446,829	AA,AG,GG		43.7248,9.9571,32.4992		184/220	71012604	8524,4104	2099	4215	6314	SO:0001819	synonymous_variant	344018	exon3			ACAAGCGTGTGCT	BC039536	CCDS46320.1	2p13.3	2013-05-21			ENSG00000183733	ENSG00000183733		"""Basic helix-loop-helix proteins"""	24669	protein-coding gene	gene with protein product	"""factor in the germline alpha"""	608697				12468641	Standard	NM_001004311		Approved	bHLHc8	uc002she.1	Q6QHK4	OTTHUMG00000153440	ENST00000332372.6:c.552C>T	2.37:g.71012604G>A		Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	190	189	0.994737	NM_001004311		Silent	SNP	ENST00000332372.6	37	CCDS46320.1																																																																																			G|0.225;A|0.774	0.774	strong		0.468	FIGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331214.1	NM_001004311	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59500117	59500117	+	Silent	SNP	T	T	C	rs61753957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:59500117T>C	ENST00000307144.4	+	1	1076	c.978T>C	c.(976-978)atT>atC	p.I326I	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	326			I -> T (in dbSNP:rs3825937). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						CCACCATAATTAAGGGCCTCT	0.398													T|||	529	0.105631	0.2216	0.0865	5008	,	,		19286	0.0397		0.0517	False		,,,				2504	0.0859				p.I326I		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.T978C						PASS	.	T	,	786,3596	294.4+/-283.1	67,652,1472	80.0	86.0	84.0		,978	1.5	1.0	15	dbSNP_129	84	502,8074	140.9+/-197.4	17,468,3803	no	intron,coding-synonymous	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,	84,1120,5275	CC,CT,TT		5.8535,17.937,9.9398	,	,326/382	59500117	1288,11670	2191	4288	6479	SO:0001819	synonymous_variant	92483	exon1			CATAATTAAGGGC	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.978T>C	15.37:g.59500117T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_033195	Q6DUY4|Q96LI2	Silent	SNP	ENST00000307144.4	37	CCDS10171.1																																																																																			T|0.912;C|0.088	0.088	strong		0.398	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
FHAD1	114827	hgsc.bcm.edu	37	1	15668276	15668276	+	Missense_Mutation	SNP	G	G	A	rs763821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:15668276G>A	ENST00000375998.4	+	14	1951	c.1951G>A	c.(1951-1953)Gga>Aga	p.G651R	FHAD1_ENST00000417793.1_Missense_Mutation_p.G651R|FHAD1_ENST00000358897.4_Missense_Mutation_p.G651R|RP3-467K16.2_ENST00000428747.1_RNA|FHAD1_ENST00000375999.3_Missense_Mutation_p.G651R|FHAD1_ENST00000471347.1_3'UTR			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	651										skin(1)|stomach(1)	2						CTTTACTGCAGGAAAAGCTGC	0.483													A|||	1732	0.345847	0.4849	0.4078	5008	,	,		19750	0.0407		0.4006	False		,,,				2504	0.3722				p.G651R		Atlas-SNP	.											.	FHAD1	78	.	0			c.G1951A						PASS	.	A	ARG/GLY	701,683		175,351,166	121.0	104.0	109.0		1951	0.6	0.1	1	dbSNP_86	109	1271,1911		260,751,580	yes	missense	FHAD1	NM_052929.1	125	435,1102,746	AA,AG,GG		39.9434,49.3497,43.1888	benign	651/1413	15668276	1972,2594	692	1591	2283	SO:0001583	missense	114827	exon15			ACTGCAGGAAAAG	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.1951G>A	1.37:g.15668276G>A	ENSP00000365166:p.Gly651Arg	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	137	71	0.518248	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		707|707	0.32371794871794873|0.32371794871794873	222|222	0.45121951219512196|0.45121951219512196	149|149	0.4116022099447514|0.4116022099447514	27|27	0.0472027972027972|0.0472027972027972	309|309	0.4076517150395778|0.4076517150395778	A|A	0.027|0.027	-1.360892|-1.360892	0.01245|0.01245	0.506503|0.506503	0.399434|0.399434	ENSG00000142621|ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998|ENST00000444385	D;D;D;D|.	0.83075|.	-1.68;-1.68;-1.68;-1.68|.	4.25|4.25	0.616|0.616	0.17613|0.17613	.|.	1.273770|.	0.05473|.	N|.	0.553503|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.47778|0.47778	P|P	4.809999999999537E-4|4.809999999999537E-4	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.46484|0.46484	-0.9188|-0.9188	9|4	0.15952|.	T|.	0.53|.	0.275|0.275	9.4141|9.4141	0.38510|0.38510	0.3119:0.0:0.6881:0.0|0.3119:0.0:0.6881:0.0	rs763821;rs59846471;rs763821|rs763821;rs59846471;rs763821	651|.	B1AJZ9|.	FHAD1_HUMAN|.	R|K	651|7	ENSP00000351770:G651R;ENSP00000407615:G651R;ENSP00000365167:G651R;ENSP00000365166:G651R|.	ENSP00000351770:G651R|.	G|R	+|+	1|2	0|0	FHAD1|FHAD1	15540863|15540863	0.877000|0.877000	0.30153|0.30153	0.072000|0.072000	0.20136|0.20136	0.212000|0.212000	0.24457|0.24457	-0.010000|-0.010000	0.12743|0.12743	-0.271000|-0.271000	0.09272|0.09272	-0.361000|-0.361000	0.07541|0.07541	GGA|AGG	G|0.653;A|0.347	0.347	strong		0.483	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
PCYT1B	9468	hgsc.bcm.edu	37	X	24637193	24637193	+	Silent	SNP	A	A	C	rs7060616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24637193A>C	ENST00000379144.2	-	2	256	c.126T>G	c.(124-126)acT>acG	p.T42T	PCYT1B_ENST00000356768.4_Silent_p.T42T|PCYT1B_ENST00000379145.1_Silent_p.T24T	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	42					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)			breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	GGGCAGGTGCAGTCAGGGTCT	0.488													A|||	397	0.105166	0.2761	0.0303	3775	,	,		13195	0.0		0.008	False		,,,				2504	0.0031				p.T42T		Atlas-SNP	.											.	PCYT1B	88	.	0			c.T126G						PASS	.	A	,,	1367,2468		221,714,211,697,360	98.0	85.0	89.0		72,126,126	-0.3	1.0	X	dbSNP_116	89	117,6610		1,82,33,2345,1838	no	coding-synonymous,coding-synonymous,coding-synonymous	PCYT1B	NM_001163264.1,NM_001163265.1,NM_004845.4	,,	222,796,244,3042,2198	CC,CA,C,AA,A		1.7393,35.6454,14.0504	,,	24/352,42/331,42/370	24637193	1484,9078	2203	4299	6502	SO:0001819	synonymous_variant	9468	exon2			AGGTGCAGTCAGG	AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"""phosphate cytidylyltransferase 1, choline, beta isoform"""			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.126T>G	X.37:g.24637193A>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_004845	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Silent	SNP	ENST00000379144.2	37	CCDS14213.1																																																																																			A|0.861;C|0.139	0.139	strong		0.488	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845	
ITGAM	3684	hgsc.bcm.edu	37	16	31289396	31289396	+	Missense_Mutation	SNP	T	T	C	rs1143680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31289396T>C	ENST00000287497.8	+	12	1397	c.1322T>C	c.(1321-1323)aTg>aCg	p.M441T	ITGAM_ENST00000544665.3_Missense_Mutation_p.M441T			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	441			M -> T (in dbSNP:rs11861251). {ECO:0000269|PubMed:15489334}.		activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						AACACTGGCATGTGGGAGTCC	0.572													T|||	466	0.0930511	0.1876	0.0692	5008	,	,		17377	0.003		0.1302	False		,,,				2504	0.0368				p.M441T		Atlas-SNP	.											.	ITGAM	137	.	0			c.T1322C						PASS	.	T	THR/MET,THR/MET	728,3420		65,598,1411	53.0	54.0	54.0		1322,1322	-0.1	0.0	16	dbSNP_120	54	1270,7150		97,1076,3037	yes	missense,missense	ITGAM	NM_000632.3,NM_001145808.1	81,81	162,1674,4448	CC,CT,TT		15.0831,17.5506,15.8975	benign,benign	441/1153,441/1154	31289396	1998,10570	2074	4210	6284	SO:0001583	missense	3684	exon12			CTGGCATGTGGGA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.1322T>C	16.37:g.31289396T>C	ENSP00000287497:p.Met441Thr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	152	93	0.611842	NM_000632	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	228	0.1043956043956044	104	0.21138211382113822	26	0.0718232044198895	1	0.0017482517482517483	97	0.1279683377308707	T	0.426	-0.905663	0.02453	0.175506	0.150831	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.10860	2.83;2.83	4.44	-0.0783	0.13715	.	.	.	.	.	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45731	-0.9241	8	0.12103	T	0.63	.	3.7061	0.08401	0.0:0.4606:0.1859:0.3535	rs11861251;rs52822161;rs58631826;rs11861251	441;441	Q4VAK1;P11215	.;ITAM_HUMAN	T	441	ENSP00000441691:M441T;ENSP00000287497:M441T	ENSP00000287497:M441T	M	+	2	0	ITGAM	31196897	0.000000	0.05858	0.017000	0.16124	0.066000	0.16364	-1.014000	0.03641	-0.078000	0.12730	-0.366000	0.07423	ATG	T|0.871;C|0.129	0.129	strong		0.572	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632	
ARSH	347527	hgsc.bcm.edu	37	X	2933323	2933323	+	Missense_Mutation	SNP	C	C	T	rs61997197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:2933323C>T	ENST00000381130.2	+	4	653	c.653C>T	c.(652-654)aCt>aTt	p.T218I		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	218					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)				TATGGATTTACTCGACGTTGG	0.463													C|||	122	0.0323179	0.0877	0.0086	3775	,	,		14570	0.0		0.0	False		,,,				2504	0.0				p.T218I		Atlas-SNP	.											.	ARSH	72	.	0			c.C653T						PASS	.	C	ILE/THR	491,3344		32,349,78,1251,493	164.0	113.0	131.0		653	-7.5	0.0	X	dbSNP_129	131	6,6722		0,4,2,2424,1870	yes	missense	ARSH	NM_001011719.1	89	32,353,80,3675,2363	TT,TC,T,CC,C		0.0892,12.8031,4.7051	benign	218/563	2933323	497,10066	2203	4300	6503	SO:0001583	missense	347527	exon4			GATTTACTCGACG	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.653C>T	X.37:g.2933323C>T	ENSP00000370522:p.Thr218Ile	Somatic	273	1	0.003663		WXS	Illumina HiSeq	Phase_I	281	123	0.437722	NM_001011719		Missense_Mutation	SNP	ENST00000381130.2	37	CCDS35198.1	45	0.027124773960216998	29	0.06223175965665236	2	0.00558659217877095	0	0.0	0	0.0	C	2.305	-0.359233	0.05138	0.128031	8.92E-4	ENSG00000205667	ENST00000381130	D	0.93953	-3.32	4.03	-7.5	0.01351	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	2.073320	0.02352	N	0.076063	T	0.03011	0.0089	N	0.01134	-0.995	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.62291	-0.6885	9	0.17832	T	0.49	.	12.9274	0.58268	0.0:0.1984:0.0:0.8016	rs61997197	218	Q5FYA8	ARSH_HUMAN	I	218	ENSP00000370522:T218I	ENSP00000370522:T218I	T	+	2	0	ARSH	2943323	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.122000	0.15687	-2.070000	0.00881	-0.248000	0.11899	ACT	C|0.952;T|0.048	0.048	strong		0.463	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
DUSP27	92235	hgsc.bcm.edu	37	1	167095163	167095163	+	Missense_Mutation	SNP	G	G	C	rs267745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167095163G>C	ENST00000361200.2	+	6	961	c.795G>C	c.(793-795)gaG>gaC	p.E265D	DUSP27_ENST00000485151.1_3'UTR|DUSP27_ENST00000443333.1_Missense_Mutation_p.E265D|DUSP27_ENST00000271385.5_Missense_Mutation_p.E265D			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	265			E -> D (in dbSNP:rs267745). {ECO:0000269|PubMed:15489334}.		protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						ACCCCAATGAGGGCTTCCTGA	0.587													C|||	3215	0.641973	0.888	0.4597	5008	,	,		19822	0.872		0.4751	False		,,,				2504	0.3732				p.E265D		Atlas-SNP	.											.	DUSP27	235	.	0			c.G795C						PASS	.	C	ASP/GLU	3677,729	302.1+/-287.2	1536,605,62	77.0	76.0	76.0		795	-4.6	0.8	1	dbSNP_79	76	4153,4447	588.8+/-392.4	1003,2147,1150	yes	missense	DUSP27	NM_001080426.1	45	2539,2752,1212	CC,CG,GG		48.2907,16.5456,39.797	benign	265/1159	167095163	7830,5176	2203	4300	6503	SO:0001583	missense	92235	exon5			CAATGAGGGCTTC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.795G>C	1.37:g.167095163G>C	ENSP00000354483:p.Glu265Asp	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	1439	0.6588827838827839	417	0.8475609756097561	181	0.5	508	0.8881118881118881	333	0.4393139841688654	C	2.612	-0.290557	0.05568	0.834544	0.482907	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	D;D;D	0.85484	-1.99;-1.99;-1.99	5.55	-4.59	0.03400	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.312145	0.34802	N	0.003677	T	0.30386	0.0763	N	0.04787	-0.16	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.34428	-0.9829	9	0.02654	T	1	-28.9626	2.8034	0.05421	0.1828:0.2921:0.0838:0.4413	rs267745;rs12734908;rs52812145;rs61430367;rs267745	265	Q5VZP5	DUS27_HUMAN	D	265	ENSP00000354483:E265D;ENSP00000271385:E265D;ENSP00000404874:E265D	ENSP00000271385:E265D	E	+	3	2	DUSP27	165361787	0.000000	0.05858	0.815000	0.32552	0.967000	0.64934	-2.213000	0.01224	-0.793000	0.04475	-0.756000	0.03474	GAG	G|0.373;C|0.627	0.627	strong		0.587	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
MUC17	140453	hgsc.bcm.edu	37	7	100682275	100682275	+	Silent	SNP	A	A	G	rs4386914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100682275A>G	ENST00000306151.4	+	3	7642	c.7578A>G	c.(7576-7578)ccA>ccG	p.P2526P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2526	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)					GCACCACGCCAGTGGCCAGTC	0.483													G|||	1194	0.238419	0.351	0.1023	5008	,	,		27860	0.253		0.1213	False		,,,				2504	0.2883				p.P2526P		Atlas-SNP	.											.	MUC17	804	.	0			c.A7578G						PASS	.	G		1346,3060	693.0+/-405.6	209,928,1066	245.0	265.0	258.0		7578	-0.7	0.0	7	dbSNP_111	258	991,7609	773.5+/-407.7	56,879,3365	no	coding-synonymous	MUC17	NM_001040105.1		265,1807,4431	GG,GA,AA		11.5233,30.5493,17.9686		2526/4494	100682275	2337,10669	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CACGCCAGTGGCC	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.7578A>G	7.37:g.100682275A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	163	80	0.490798	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			A|0.835;G|0.165	0.165	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TNFRSF1B	7133	hgsc.bcm.edu	37	1	12253003	12253003	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12253003G>A	ENST00000376259.3	+	6	724	c.635G>A	c.(634-636)gGg>gAg	p.G212E	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	212					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)	ATGGCCCCAGGGGCAGTACAC	0.617																																					p.G212E		Atlas-SNP	.											.	TNFRSF1B	28	.	0			c.G635A						PASS	.						165.0	121.0	136.0					1																	12253003		2203	4300	6503	SO:0001583	missense	7133	exon6			CCCCAGGGGCAGT	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.635G>A	1.37:g.12253003G>A	ENSP00000365435:p.Gly212Glu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_001066	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Missense_Mutation	SNP	ENST00000376259.3	37	CCDS145.1	.	.	.	.	.	.	.	.	.	.	G	3.321	-0.138774	0.06669	.	.	ENSG00000028137	ENST00000376259;ENST00000400863	D	0.86097	-2.07	3.31	-0.714	0.11219	.	2.871980	0.01167	N	0.006766	T	0.75273	0.3827	L	0.38953	1.18	0.09310	N	1	B	0.15473	0.013	B	0.12837	0.008	T	0.60840	-0.7183	10	0.02654	T	1	0.0033	6.2978	0.21095	0.4784:0.0:0.5216:0.0	.	212	P20333	TNR1B_HUMAN	E	212	ENSP00000365435:G212E	ENSP00000365435:G212E	G	+	2	0	TNFRSF1B	12175590	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.169000	0.09911	-0.138000	0.11434	-0.812000	0.03155	GGG	.	.	none		0.617	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066	
FOXC1	2296	hgsc.bcm.edu	37	6	1612243	1612243	+	Silent	SNP	T	T	G	rs73406891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:1612243T>G	ENST00000380874.2	+	1	1563	c.1563T>G	c.(1561-1563)tcT>tcG	p.S521S		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	521					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		TGAACAACTCTCCAGTGAACG	0.602													T|||	160	0.0319489	0.115	0.0101	5008	,	,		9192	0.0		0.001	False		,,,				2504	0.0				p.S521S	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.T1563G						PASS	.	T		452,3950	202.1+/-225.0	23,406,1772	64.0	47.0	52.0		1563	-4.6	1.0	6	dbSNP_130	52	4,8594	1.2+/-3.3	0,4,4295	no	coding-synonymous	FOXC1	NM_001453.2		23,410,6067	GG,GT,TT		0.0465,10.2681,3.5077		521/554	1612243	456,12544	2201	4299	6500	SO:0001819	synonymous_variant	2296	exon1			CAACTCTCCAGTG	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"""Forkhead boxes"""	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.1563T>G	6.37:g.1612243T>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	61	24	0.393443	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Silent	SNP	ENST00000380874.2	37	CCDS4473.1																																																																																			T|0.963;G|0.037	0.037	strong		0.602	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1		
SALL4	57167	hgsc.bcm.edu	37	20	50407162	50407162	+	Silent	SNP	T	T	C	rs6021437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50407162T>C	ENST00000217086.4	-	2	1971	c.1860A>G	c.(1858-1860)acA>acG	p.T620T	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	620					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCTTAATGGATGTGTTGGTTC	0.527													C|||	1913	0.381989	0.1982	0.3415	5008	,	,		20729	0.6071		0.336	False		,,,				2504	0.4744				p.T620T		Atlas-SNP	.											.	SALL4	168	.	0			c.A1860G						PASS	.	C		962,3444	731.0+/-410.2	105,752,1346	72.0	62.0	66.0		1860	-6.3	0.0	20	dbSNP_114	66	2967,5633	665.6+/-402.3	522,1923,1855	no	coding-synonymous	SALL4	NM_020436.3		627,2675,3201	CC,CT,TT		34.5,21.8339,30.2091		620/1054	50407162	3929,9077	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			AATGGATGTGTTG	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1860A>G	20.37:g.50407162T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	213	97	0.455399	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		
TBC1D8B	54885	hgsc.bcm.edu	37	X	106083304	106083304	+	Silent	SNP	A	A	G	rs56825776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:106083304A>G	ENST00000357242.5	+	9	1554	c.1380A>G	c.(1378-1380)tcA>tcG	p.S460S	TBC1D8B_ENST00000310452.2_Silent_p.S460S|TBC1D8B_ENST00000276175.3_Silent_p.S454S	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	460							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AGGAACAGTCATGGAAAATAC	0.343													A|||	263	0.0696689	0.1876	0.0202	3775	,	,		13833	0.0		0.001	False		,,,				2504	0.0				p.S460S		Atlas-SNP	.											.	TBC1D8B	181	.	0			c.A1380G						PASS	.	A	,	857,2978		87,555,128,990,443	116.0	108.0	111.0		1380,1380	-3.8	1.0	X	dbSNP_129	111	2,6726		0,1,1,2427,1871	no	coding-synonymous,coding-synonymous	TBC1D8B	NM_017752.2,NM_198881.1	,	87,556,129,3417,2314	GG,GA,G,AA,A		0.0297,22.3468,8.1322	,	460/1121,460/633	106083304	859,9704	2203	4300	6503	SO:0001819	synonymous_variant	54885	exon9			ACAGTCATGGAAA	AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"""EF-hand domain containing"""	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.1380A>G	X.37:g.106083304A>G		Somatic	338	1	0.00295858		WXS	Illumina HiSeq	Phase_I	318	318	1	NM_198881	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Silent	SNP	ENST00000357242.5	37	CCDS14522.1																																																																																			A|0.923;G|0.077	0.077	strong		0.343	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752	
GATA3	2625	hgsc.bcm.edu	37	10	8100632	8100632	+	Silent	SNP	T	T	C	rs2228254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:8100632T>C	ENST00000346208.3	+	3	1061	c.606T>C	c.(604-606)cgT>cgC	p.R202R	GATA3_ENST00000461472.1_3'UTR|GATA3_ENST00000379328.3_Silent_p.R202R			P23771	GATA3_HUMAN	GATA binding protein 3	202					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						CCCACTCCCGTGGCAGCATGA	0.687			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""						T|||	189	0.0377396	0.1392	0.0058	5008	,	,		14132	0.0		0.001	False		,,,				2504	0.0				p.R202R		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.T606C						PASS	.	T	,	504,3902	227.8+/-242.9	31,442,1730	85.0	77.0	80.0		606,606	-11.1	0.4	10	dbSNP_98	80	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous,coding-synonymous	GATA3	NM_001002295.1,NM_002051.2	,	31,444,6027	CC,CT,TT		0.0233,11.4389,3.8911	,	202/445,202/444	8100632	506,12498	2203	4299	6502	SO:0001819	synonymous_variant	2625	exon3			CTCCCGTGGCAGC	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.606T>C	10.37:g.8100632T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_002051	Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	37	CCDS7083.1																																																																																			T|0.959;C|0.041	0.041	strong		0.687	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808465	18808465	+	Silent	SNP	T	T	A	rs3007718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:18808465T>A	ENST00000400664.1	+	1	1042	c.990T>A	c.(988-990)gcT>gcA	p.A330A		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	330						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)		GAACAGGGGCTGCCTCGGGAG	0.692													A|||	3369	0.672724	0.6611	0.7277	5008	,	,		13211	0.8948		0.6113	False		,,,				2504	0.4836				p.A330A		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.T990A						PASS	.	A		2912,1478		987,938,270	15.0	18.0	17.0		990	-3.7	0.0	1	dbSNP_101	17	5388,3184		1724,1940,622	no	coding-synonymous	KLHDC7A	NM_152375.2		2711,2878,892	AA,AT,TT		37.1442,33.6674,35.9667		330/778	18808465	8300,4662	2195	4286	6481	SO:0001819	synonymous_variant	127707	exon1			AGGGGCTGCCTCG	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.990T>A	1.37:g.18808465T>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																			T|0.328;A|0.672	0.672	strong		0.692	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
SETD1A	9739	hgsc.bcm.edu	37	16	30978324	30978324	+	Silent	SNP	C	C	A	rs11866157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30978324C>A	ENST00000262519.8	+	9	3311	c.2625C>A	c.(2623-2625)atC>atA	p.I875I		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	875					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CTACGGGCATCGAGGCTTTCG	0.607													C|||	150	0.0299521	0.1104	0.0058	5008	,	,		14627	0.0		0.0	False		,,,				2504	0.0				p.I875I		Atlas-SNP	.											.	SETD1A	143	.	0			c.C2625A						PASS	.	C		357,4037		14,329,1854	30.0	27.0	28.0		2625	-7.1	0.9	16	dbSNP_120	28	4,8594		0,4,4295	no	coding-synonymous	SETD1A	NM_014712.1		14,333,6149	AA,AC,CC		0.0465,8.1247,2.7786		875/1708	30978324	361,12631	2197	4299	6496	SO:0001819	synonymous_variant	9739	exon9			GGGCATCGAGGCT	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.2625C>A	16.37:g.30978324C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Silent	SNP	ENST00000262519.8	37	CCDS32435.1																																																																																			C|0.968;A|0.032	0.032	strong		0.607	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712	
UNC93A	54346	hgsc.bcm.edu	37	6	167719436	167719436	+	Missense_Mutation	SNP	G	G	A	rs2072767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:167719436G>A	ENST00000230256.3	+	6	1049	c.874G>A	c.(874-876)Gtc>Atc	p.V292I	UNC93A_ENST00000366829.2_Missense_Mutation_p.V250I	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	292			V -> I (in dbSNP:rs2072767). {ECO:0000269|PubMed:12381271}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CATCCAGTTCGTCGGCTACGT	0.612													G|||	1404	0.280351	0.2587	0.2349	5008	,	,		20543	0.2629		0.2753	False		,,,				2504	0.365				p.V292I		Atlas-SNP	.											.	UNC93A	66	.	0			c.G874A						PASS	.	G	ILE/VAL,ILE/VAL	1158,3248	409.7+/-335.1	153,852,1198	285.0	237.0	253.0		748,874	3.9	0.0	6	dbSNP_96	253	2187,6413	373.3+/-337.0	263,1661,2376	yes	missense,missense	UNC93A	NM_001143947.1,NM_018974.3	29,29	416,2513,3574	AA,AG,GG		25.4302,26.2823,25.7189	benign,benign	250/416,292/458	167719436	3345,9661	2203	4300	6503	SO:0001583	missense	54346	exon6			CAGTTCGTCGGCT	AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"""unc93 (C.elegans) homolog A"""			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.874G>A	6.37:g.167719436G>A	ENSP00000230256:p.Val292Ile	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	175	82	0.468571	NM_018974	B3KRP5|Q4QQJ4|Q5JZD6	Missense_Mutation	SNP	ENST00000230256.3	37	CCDS5300.1	590	0.27014652014652013	141	0.2865853658536585	88	0.2430939226519337	157	0.2744755244755245	204	0.2691292875989446	G	10.35	1.326484	0.24080	0.262823	0.254302	ENSG00000112494	ENST00000230256;ENST00000366829	T;T	0.16457	2.34;2.62	4.73	3.87	0.44632	Major facilitator superfamily domain, general substrate transporter (1);	0.131212	0.50627	N	0.000115	T	0.04588	0.0125	L	0.49256	1.55	0.19945	P	0.9999408312	P;P	0.51351	0.944;0.506	B;B	0.35073	0.195;0.078	T	0.19160	-1.0314	9	0.09084	T	0.74	-39.111	12.2369	0.54520	0.083:0.0:0.917:0.0	rs2072767;rs56604367;rs58276443;rs2072767	250;292	Q4QQJ4;Q86WB7	.;UN93A_HUMAN	I	292;250	ENSP00000230256:V292I;ENSP00000355794:V250I	ENSP00000230256:V292I	V	+	1	0	UNC93A	167639426	1.000000	0.71417	0.021000	0.16686	0.154000	0.21943	5.362000	0.66098	1.003000	0.39130	-0.222000	0.12452	GTC	G|0.732;A|0.268	0.268	strong		0.612	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974	
MSRB2	22921	hgsc.bcm.edu	37	10	23408278	23408278	+	Silent	SNP	C	C	T	rs7427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:23408278C>T	ENST00000376510.3	+	4	445	c.342C>T	c.(340-342)tcC>tcT	p.S114S	MSRB2_ENST00000468633.1_3'UTR	NM_012228.3	NP_036360.3	Q9Y3D2	MSRB2_HUMAN	methionine sulfoxide reductase B2	114					actin filament polymerization (GO:0030041)|protein repair (GO:0030091)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)	actin binding (GO:0003779)|peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	9					L-Methionine(DB00134)	CTTCGTTTTCCGAGGCTCATG	0.502													C|||	1130	0.225639	0.2315	0.1571	5008	,	,		20241	0.123		0.327	False		,,,				2504	0.2679				p.S114S	Esophageal Squamous(89;1240 1363 4973 30188 42299)	Atlas-SNP	.											.	MSRB2	21	.	0			c.C342T						PASS	.	C		906,3100		97,712,1194	106.0	107.0	107.0		342	-10.5	0.6	10	dbSNP_52	107	2897,5443		477,1943,1750	no	coding-synonymous	MSRB2	NM_012228.3		574,2655,2944	TT,TC,CC		34.7362,22.6161,30.8035		114/183	23408278	3803,8543	2003	4170	6173	SO:0001819	synonymous_variant	22921	exon4			GTTTTCCGAGGCT	AF122004	CCDS41495.1	10p12	2004-12-07	2004-12-06	2004-12-07	ENSG00000148450	ENSG00000148450			17061	protein-coding gene	gene with protein product		613782	"""methionine sulfoxide reductase B"""	MSRB		8749308, 10375640	Standard	NM_012228		Approved	PILB, CGI-131, CBS1, CBS-1	uc001iro.3	Q9Y3D2	OTTHUMG00000017812	ENST00000376510.3:c.342C>T	10.37:g.23408278C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_012228	Q17R44|Q4G1C7|Q9Y5W6	Silent	SNP	ENST00000376510.3	37	CCDS41495.1																																																																																			C|0.746;T|0.254	0.254	strong		0.502	MSRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047205.1	NM_012228	
SMG6	23293	hgsc.bcm.edu	37	17	2091765	2091765	+	Missense_Mutation	SNP	C	C	T	rs903160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2091765C>T	ENST00000263073.6	-	11	2964	c.2914G>A	c.(2914-2916)Gca>Aca	p.A972T	SMG6_ENST00000544865.1_Missense_Mutation_p.A941T|SMG6_ENST00000354901.4_Missense_Mutation_p.A64T|SMG6_ENST00000536871.2_Missense_Mutation_p.A64T	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	972			A -> T (in dbSNP:rs903160).		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						CCCAGAGCTGCGGCTTGTTCC	0.587													C|||	2022	0.403754	0.5499	0.3012	5008	,	,		20170	0.3264		0.3091	False		,,,				2504	0.456				p.A972T	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.G2914A						PASS	.	C	THR/ALA,THR/ALA	2166,2240	583.1+/-385.7	532,1102,569	63.0	57.0	59.0		2821,2914	2.5	1.0	17	dbSNP_86	59	2644,5956	426.6+/-355.3	424,1796,2080	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	58,58	956,2898,2649	TT,TC,CC		30.7442,49.1602,36.9829	benign,benign	941/1389,972/1420	2091765	4810,8196	2203	4300	6503	SO:0001583	missense	23293	exon11			GAGCTGCGGCTTG	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.2914G>A	17.37:g.2091765C>T	ENSP00000263073:p.Ala972Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	775	0.35485347985347987	268	0.5447154471544715	109	0.3011049723756906	158	0.2762237762237762	240	0.316622691292876	C	13.05	2.122399	0.37436	0.491602	0.307442	ENSG00000070366	ENST00000263073;ENST00000544865;ENST00000536871	T;T;T	0.28069	1.63;1.63;1.63	4.64	2.5	0.30297	.	0.140304	0.46145	D	0.000318	T	0.00012	0.0000	N	0.02539	-0.55	0.34659	P	0.277548	B	0.02656	0.0	B	0.04013	0.001	T	0.46076	-0.9217	9	0.23891	T	0.37	-5.3127	4.3033	0.10935	0.0:0.5427:0.0:0.4573	rs903160;rs52800764;rs56856254;rs903160	972	Q86US8	EST1A_HUMAN	T	972;941;64	ENSP00000263073:A972T;ENSP00000443920:A941T;ENSP00000440283:A64T	ENSP00000263073:A972T	A	-	1	0	SMG6	2038515	0.996000	0.38824	0.997000	0.53966	0.992000	0.81027	1.791000	0.38744	1.176000	0.42840	0.561000	0.74099	GCA	C|0.626;T|0.374	0.374	strong		0.587	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
TARBP1	6894	hgsc.bcm.edu	37	1	234529552	234529552	+	Silent	SNP	C	C	T	rs2175594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	168	0	0		WXS	Illumina HiSeq	Phase_I	136	61	0.448529	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	
MGAT1	4245	hgsc.bcm.edu	37	5	180218668	180218668	+	Missense_Mutation	SNP	A	A	G	rs634501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180218668A>G	ENST00000446023.2	-	3	2054	c.1304T>C	c.(1303-1305)cTg>cCg	p.L435P	MGAT1_ENST00000427865.2_Missense_Mutation_p.L435P|MGAT1_ENST00000307826.4_Missense_Mutation_p.L435P|MGAT1_ENST00000393340.3_Missense_Mutation_p.L435P|MGAT1_ENST00000333055.3_Missense_Mutation_p.L435P	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	435			L -> P (in dbSNP:rs634501). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1827260, ECO:0000269|Ref.4}.		carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|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)			CTCCCACGTCAGTGGGGGCGC	0.622													G|||	3671	0.733027	0.879	0.5576	5008	,	,		15523	0.5526		0.7455	False		,,,				2504	0.8333				p.L435P		Atlas-SNP	.											MGAT1,NS,carcinoma,0,1	MGAT1	48	1	0			c.T1304C						PASS	.	G	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	3693,713	279.9+/-275.1	1556,581,66	38.0	41.0	40.0		1304,1304,1304,1304,1304	3.8	0.7	5	dbSNP_83	40	6294,2306	363.1+/-333.0	2306,1682,312	yes	missense,missense,missense,missense,missense	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	98,98,98,98,98	3862,2263,378	GG,GA,AA		26.814,16.1825,23.2124	benign,benign,benign,benign,benign	435/446,435/446,435/446,435/446,435/446	180218668	9987,3019	2203	4300	6503	SO:0001583	missense	4245	exon3			CACGTCAGTGGGG	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.1304T>C	5.37:g.180218668A>G	ENSP00000404718:p.Leu435Pro	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	1352	0.6190476190476191	356	0.7235772357723578	195	0.5386740331491713	293	0.5122377622377622	508	0.6701846965699209	G	0.413	-0.912114	0.02415	0.838175	0.73186	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865	D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68	4.96	3.79	0.43588	.	0.498752	0.20868	N	0.084227	T	0.00012	0.0000	N	0.00926	-1.1	0.43347	P	0.0045960000000000445	B	0.02656	0.0	B	0.08055	0.003	T	0.41088	-0.9528	9	0.30854	T	0.27	-3.7269	7.0726	0.25187	0.1439:0.0:0.1564:0.6997	rs634501;rs17856087;rs60466398;rs634501	435	P26572	MGAT1_HUMAN	P	435;435;435;435;292;435	ENSP00000332073:L435P;ENSP00000311888:L435P;ENSP00000404718:L435P;ENSP00000377010:L435P;ENSP00000402838:L435P	ENSP00000311888:L435P	L	-	2	0	MGAT1	180151274	0.001000	0.12720	0.654000	0.29608	0.025000	0.11179	0.597000	0.24059	0.470000	0.27294	-1.059000	0.02297	CTG	A|0.273;G|0.727	0.727	strong		0.622	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
MYH11	4629	hgsc.bcm.edu	37	16	15931975	15931975	+	Silent	SNP	G	G	A	rs28570191|rs587781074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:15931975G>A	ENST00000300036.5	-	2	244	c.135C>T	c.(133-135)ttC>ttT	p.F45F	MYH11_ENST00000576790.2_Silent_p.F45F|MYH11_ENST00000396324.3_Silent_p.F45F|MYH11_ENST00000452625.2_Silent_p.F45F	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	45					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGGCTGCCTCGAAGCCCTGCT	0.562			T	CBFB	AML								G|||	220	0.0439297	0.1543	0.0231	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0				p.F45F		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.C135T						PASS	.	G	,,,	591,3803	261.9+/-264.6	42,507,1648	166.0	156.0	159.0		135,135,135,135	-0.4	1.0	16	dbSNP_125	159	17,8583	11.9+/-42.8	0,17,4283	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	,,,	42,524,5931	AA,AG,GG		0.1977,13.4502,4.6791	,,,	45/1946,45/1980,45/1973,45/1939	15931975	608,12386	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon2			TGCCTCGAAGCCC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.135C>T	16.37:g.15931975G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	58	0.591837	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			G|0.951;A|0.049	0.049	strong		0.562	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
USP29	57663	hgsc.bcm.edu	37	19	57641887	57641887	+	Missense_Mutation	SNP	A	A	G	rs74511605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57641887A>G	ENST00000254181.4	+	4	2298	c.1844A>G	c.(1843-1845)cAa>cGa	p.Q615R	USP29_ENST00000598197.1_Missense_Mutation_p.Q615R	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	615	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GATGCAAGCCAAGAGCAGCAT	0.493													A|||	12	0.00239617	0.0091	0.0	5008	,	,		20449	0.0		0.0	False		,,,				2504	0.0				p.Q615R		Atlas-SNP	.											.	USP29	186	.	0			c.A1844G						PASS	.	A	ARG/GLN	50,4356	51.6+/-87.1	0,50,2153	73.0	72.0	72.0		1844	1.4	0.0	19	dbSNP_131	72	0,8600		0,0,4300	yes	missense	USP29	NM_020903.2	43	0,50,6453	GG,GA,AA		0.0,1.1348,0.3844	benign	615/923	57641887	50,12956	2203	4300	6503	SO:0001583	missense	57663	exon4			CAAGCCAAGAGCA		CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"""Ubiquitin-specific peptidases"""	18563	protein-coding gene	gene with protein product		609546	"""ubiquitin specific protease 29"""			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.1844A>G	19.37:g.57641887A>G	ENSP00000254181:p.Gln615Arg	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	120	74	0.616667	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	A	0.013	-1.643501	0.00792	0.011348	0.0	ENSG00000131864	ENST00000254181	T	0.74002	-0.8	2.43	1.4	0.22301	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.	.	.	.	T	0.37571	0.1008	N	0.11313	0.125	0.09310	N	1	B	0.14805	0.011	B	0.14578	0.011	T	0.32402	-0.9908	9	0.02654	T	1	0.0203	4.2465	0.10674	0.8306:0.0:0.1694:0.0	.	615	Q9HBJ7	UBP29_HUMAN	R	615	ENSP00000254181:Q615R	ENSP00000254181:Q615R	Q	+	2	0	USP29	62333699	0.021000	0.18746	0.003000	0.11579	0.085000	0.17905	2.747000	0.47475	0.347000	0.23924	0.383000	0.25322	CAA	A|0.995;G|0.005	0.005	strong		0.493	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1		
ZNF497	162968	hgsc.bcm.edu	37	19	58868480	58868480	+	Missense_Mutation	SNP	G	G	T	rs12609654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58868480G>T	ENST00000311044.3	-	3	710	c.522C>A	c.(520-522)caC>caA	p.H174Q	A1BG-AS1_ENST00000600686.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000595302.1_RNA|CTD-2619J13.9_ENST00000599952.1_RNA|ZNF497_ENST00000425453.3_Missense_Mutation_p.H174Q|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000593960.1_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	180	0	0		WXS	Illumina HiSeq	Phase_I	246	120	0.487805	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	
SERPINA5	5104	hgsc.bcm.edu	37	14	95053891	95053891	+	Silent	SNP	C	C	T	rs6111|rs386780205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95053891C>T	ENST00000554866.1	+	2	306	c.192C>T	c.(190-192)agC>agT	p.S64S	SERPINA5_ENST00000553780.1_Silent_p.S64S|SERPINA5_ENST00000554276.1_Silent_p.S64S|SERPINA5_ENST00000329597.7_Silent_p.S64S			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	64			S -> N (in dbSNP:rs6115). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1714450, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:2173165, ECO:0000269|PubMed:3027058, ECO:0000269|PubMed:8471250, ECO:0000269|PubMed:8713781, ECO:0000269|Ref.6}.		fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CCAGCCAGAGCATCTTCTTCT	0.622													C|||	1366	0.272764	0.612	0.1167	5008	,	,		18414	0.2748		0.0905	False		,,,				2504	0.1104				p.S64S		Atlas-SNP	.											.	SERPINA5	69	.	0			c.C192T						PASS	.	C		2148,2258		574,1000,629	34.0	35.0	35.0		192	1.2	0.3	14	dbSNP_52	35	751,7849		41,669,3590	no	coding-synonymous	SERPINA5	NM_000624.4		615,1669,4219	TT,TC,CC		8.7326,48.7517,22.2897		64/407	95053891	2899,10107	2203	4300	6503	SO:0001819	synonymous_variant	5104	exon3			CCAGAGCATCTTC	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.192C>T	14.37:g.95053891C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_000624	Q07616|Q9UG30	Silent	SNP	ENST00000554866.1	37	CCDS9928.1																																																																																			C|0.783;T|0.217	0.217	strong		0.622	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
FLG	2312	hgsc.bcm.edu	37	1	152280759	152280759	+	Silent	SNP	A	A	G	rs2338554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152280759A>G	ENST00000368799.1	-	3	6638	c.6603T>C	c.(6601-6603)gaT>gaC	p.D2201D	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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						PASS	.	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	439	0	0		WXS	Illumina HiSeq	Phase_I	710	707	0.995775	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	
ZBED4	9889	hgsc.bcm.edu	37	22	50279749	50279749	+	Silent	SNP	C	C	T	rs61731524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50279749C>T	ENST00000216268.5	+	2	2916	c.2439C>T	c.(2437-2439)atC>atT	p.I813I		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	813						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		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)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		ACGCCAGCATCGGGAAGACGC	0.617													C|||	18	0.00359425	0.0083	0.0029	5008	,	,		19867	0.0		0.0	False		,,,				2504	0.0051				p.I813I		Atlas-SNP	.											.	ZBED4	102	.	0			c.C2439T						PASS	.	C		14,4392	20.2+/-43.8	0,14,2189	38.0	38.0	38.0		2439	-9.5	0.2	22	dbSNP_129	38	0,8598		0,0,4299	no	coding-synonymous	ZBED4	NM_014838.2		0,14,6488	TT,TC,CC		0.0,0.3177,0.1077		813/1172	50279749	14,12990	2203	4299	6502	SO:0001819	synonymous_variant	9889	exon2			CAGCATCGGGAAG	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.2439C>T	22.37:g.50279749C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Silent	SNP	ENST00000216268.5	37	CCDS33677.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
CC2D2A	57545	hgsc.bcm.edu	37	4	15516389	15516389	+	Silent	SNP	C	C	T	rs2286976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:15516389C>T	ENST00000503292.1	+	10	957	c.777C>T	c.(775-777)caC>caT	p.H259H	CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000424120.1_Silent_p.H259H|CC2D2A_ENST00000389652.5_Silent_p.H210H|CC2D2A_ENST00000413206.1_Silent_p.H259H	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	259					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						GCTTAGATCACGTGGCTGACG	0.428													C|||	481	0.0960463	0.0431	0.0303	5008	,	,		18626	0.3492		0.0268	False		,,,				2504	0.0245				p.H259H		Atlas-SNP	.											.	CC2D2A	158	.	0			c.C777T						PASS	.	C		200,3754		3,194,1780	142.0	142.0	142.0		777	-8.1	0.0	4	dbSNP_100	142	228,8098		1,226,3936	no	coding-synonymous	CC2D2A	NM_001080522.2		4,420,5716	TT,TC,CC		2.7384,5.0582,3.4853		259/1621	15516389	428,11852	1977	4163	6140	SO:0001819	synonymous_variant	57545	exon10			AGATCACGTGGCT	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.777C>T	4.37:g.15516389C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	125	57	0.456	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	37	CCDS47026.1																																																																																			C|0.900;T|0.100	0.100	strong		0.428	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522	
COL4A1	1282	hgsc.bcm.edu	37	13	110813709	110813709	+	Silent	SNP	G	G	A	rs1133219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	48	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	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		
DSG1	1828	hgsc.bcm.edu	37	18	28919913	28919913	+	Missense_Mutation	SNP	G	G	A	rs34302455|rs200575647|rs386802123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28919913G>A	ENST00000257192.4	+	11	1824	c.1612G>A	c.(1612-1614)Gat>Aat	p.D538N		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	538			D -> N (in dbSNP:rs34302455).		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)			CGGAGCCAAAGATTTGTTATC	0.413													G|||	746	0.148962	0.2421	0.0994	5008	,	,		16728	0.0665		0.0845	False		,,,				2504	0.2096				p.D538N		Atlas-SNP	.											DSG1,NS,carcinoma,0,1	DSG1	176	1	0			c.G1612A						PASS	.	G	ASN/ASP	8,4398		1,6,2196	98.0	97.0	97.0		1612	-1.4	0.0	18	dbSNP_126	97	2,8598		1,0,4299	yes	missense	DSG1	NM_001942.2	23	2,6,6495	AA,AG,GG		0.0233,0.1816,0.0769	benign	538/1050	28919913	10,12996	2203	4300	6503	SO:0001583	missense	1828	exon11			GCCAAAGATTTGT	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.1612G>A	18.37:g.28919913G>A	ENSP00000257192:p.Asp538Asn	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	108	42	0.388889	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	247	0.1130952380952381	117	0.23780487804878048	40	0.11049723756906077	34	0.05944055944055944	56	0.07387862796833773	G	0.049	-1.257018	0.01457	0.001816	2.33E-4	ENSG00000134760	ENST00000257192	T	0.57107	0.42	1.12	-1.36	0.09085	.	7739.210000	0.00166	N	0.000000	T	0.00012	0.0000	L	0.36672	1.1	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.05037	-1.0910	9	0.12766	T	0.61	.	4.3923	0.11346	0.4926:0.0:0.5074:0.0	rs34302455	538	Q02413	DSG1_HUMAN	N	538	ENSP00000257192:D538N	ENSP00000257192:D538N	D	+	1	0	DSG1	27173911	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.282000	0.08445	-0.601000	0.05783	-0.652000	0.03908	GAT	G|0.894;A|0.106	0.106	strong		0.413	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
SEMG2	6407	hgsc.bcm.edu	37	20	43851101	43851101	+	Silent	SNP	T	T	C	rs2233902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43851101T>C	ENST00000372769.3	+	2	918	c.828T>C	c.(826-828)gaT>gaC	p.D276D		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	276	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				TCAGTCAAGATCAAGAGCATG	0.398													T|||	79	0.0157748	0.0484	0.0101	5008	,	,		22551	0.0		0.004	False		,,,				2504	0.0041				p.D276D		Atlas-SNP	.											.	SEMG2	92	.	0			c.T828C						PASS	.	T		177,4229	114.6+/-152.6	3,171,2029	93.0	90.0	91.0		828	-1.5	0.0	20	dbSNP_98	91	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous	SEMG2	NM_003008.2		3,189,6311	CC,CT,TT		0.2093,4.0172,1.4993		276/583	43851101	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	6407	exon2			TCAAGATCAAGAG		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"""Semenogelin 2"""	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.828T>C	20.37:g.43851101T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	151	78	0.516556	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Silent	SNP	ENST00000372769.3	37	CCDS13346.1																																																																																			T|0.985;C|0.015	0.015	strong		0.398	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008	
PDHX	8050	hgsc.bcm.edu	37	11	34938310	34938310	+	Silent	SNP	T	T	C	rs1049307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34938310T>C	ENST00000227868.4	+	1	192	c.108T>C	c.(106-108)tcT>tcC	p.S36S	APIP_ENST00000395787.3_5'Flank|PDHX_ENST00000448838.3_Intron|APIP_ENST00000527830.1_5'Flank|PDHX_ENST00000430469.2_Silent_p.S36S|APIP_ENST00000278359.5_5'Flank			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	36					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)			TTGGGTGGTCTGTAAGCCGCG	0.637													T|||	965	0.192692	0.4395	0.1052	5008	,	,		13072	0.0873		0.1173	False		,,,				2504	0.1074				p.S36S		Atlas-SNP	.											.	PDHX	40	.	0			c.T108C						PASS	.	T	,,	1719,2683		349,1021,831	37.0	39.0	38.0		,108,108	0.4	0.0	11	dbSNP_86	38	946,7650		57,832,3409	no	intron,coding-synonymous,coding-synonymous	PDHX	NM_001135024.1,NM_001166158.1,NM_003477.2	,,	406,1853,4240	CC,CT,TT		11.0051,39.0504,20.5032	,,	,36/275,36/502	34938310	2665,10333	2201	4298	6499	SO:0001819	synonymous_variant	8050	exon1			GTGGTCTGTAAGC	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.108T>C	11.37:g.34938310T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Silent	SNP	ENST00000227868.4	37	CCDS7896.1																																																																																			T|0.802;C|0.198	0.198	strong		0.637	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
PWWP2B	170394	hgsc.bcm.edu	37	10	134218802	134218802	+	Silent	SNP	G	G	T	rs76160300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134218802G>T	ENST00000305233.5	+	2	857	c.798G>T	c.(796-798)gtG>gtT	p.V266V	PWWP2B_ENST00000368609.4_Silent_p.V266V	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	266										central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)		AGGGAGAGGTGGTCAAGATCC	0.701													G|||	36	0.0071885	0.0272	0.0	5008	,	,		12729	0.0		0.0	False		,,,				2504	0.0				p.V266V		Atlas-SNP	.											.	PWWP2B	33	.	0			c.G798T						PASS	.	G	,	107,4271		1,105,2083	15.0	20.0	19.0		798,798	-1.2	1.0	10	dbSNP_131	19	1,8565		0,1,4282	no	coding-synonymous,coding-synonymous	PWWP2B	NM_001098637.1,NM_138499.3	,	1,106,6365	TT,TG,GG		0.0117,2.444,0.8344	,	266/500,266/591	134218802	108,12836	2189	4283	6472	SO:0001819	synonymous_variant	170394	exon2			AGAGGTGGTCAAG	AK128663	CCDS7667.2	10q26.3	2009-06-03	2007-10-22	2007-10-22	ENSG00000171813	ENSG00000171813			25150	protein-coding gene	gene with protein product			"""PWWP domain containing 2"""	PWWP2			Standard	NM_001098637		Approved	bA432J24.1, FLJ46823	uc001lll.4	Q6NUJ5	OTTHUMG00000019286	ENST00000305233.5:c.798G>T	10.37:g.134218802G>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	93	52	0.55914	NM_001098637	A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Silent	SNP	ENST00000305233.5	37	CCDS7667.2																																																																																			G|0.993;T|0.007	0.007	strong		0.701	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499	
SFXN5	94097	hgsc.bcm.edu	37	2	73226090	73226090	+	Silent	SNP	G	G	A	rs12233055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	87	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	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	
C12orf40	283461	hgsc.bcm.edu	37	12	40085906	40085906	+	Missense_Mutation	SNP	A	A	T	rs73270414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:40085906A>T	ENST00000324616.5	+	11	1557	c.1403A>T	c.(1402-1404)aAg>aTg	p.K468M	C12orf40_ENST00000405531.3_Missense_Mutation_p.K468M	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	468										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						ATATCTACTAAGAAAATCTGT	0.244													A|||	650	0.129792	0.0658	0.098	5008	,	,		13634	0.1766		0.162	False		,,,				2504	0.1575				p.K468M		Atlas-SNP	.											C12orf40,fourth_ventricle,glioma,0,1	C12orf40	118	1	0			c.A1403T						PASS	.	A	MET/LYS	277,3257		11,255,1501	28.0	26.0	27.0		1403	1.7	0.4	12	dbSNP_130	27	1306,6626		108,1090,2768	yes	missense	C12orf40	NM_001031748.2	95	119,1345,4269	TT,TA,AA		16.465,7.8381,13.806	benign	468/653	40085906	1583,9883	1767	3966	5733	SO:0001583	missense	283461	exon11			CTACTAAGAAAAT	AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.1403A>T	12.37:g.40085906A>T	ENSP00000317671:p.Lys468Met	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	128	78	0.609375	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	281	0.12866300366300365	29	0.05894308943089431	40	0.11049723756906077	97	0.16958041958041958	115	0.1517150395778364	A	4.175	0.031040	0.08101	0.078381	0.16465	ENSG00000180116	ENST00000405531;ENST00000324616	T;T	0.53206	0.63;0.72	2.84	1.66	0.24008	.	0.915548	0.09122	N	0.845588	T	0.00109	0.0003	N	0.24115	0.695	0.33319	P	0.432906	B	0.16603	0.018	B	0.20767	0.031	T	0.12760	-1.0535	9	0.38643	T	0.18	.	5.995	0.19489	0.7306:0.2694:0.0:0.0	.	468	Q86WS4	CL040_HUMAN	M	468	ENSP00000383897:K468M;ENSP00000317671:K468M	ENSP00000317671:K468M	K	+	2	0	C12orf40	38372173	0.046000	0.20272	0.429000	0.26710	0.178000	0.23041	0.308000	0.19314	0.475000	0.27415	0.379000	0.24179	AAG	A|0.858;T|0.142	0.142	strong		0.244	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599	
WDR87	83889	hgsc.bcm.edu	37	19	38376804	38376804	+	Missense_Mutation	SNP	T	T	C	rs78748271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38376804T>C	ENST00000303868.5	-	6	7614	c.7390A>G	c.(7390-7392)Acc>Gcc	p.T2464A	WDR87_ENST00000447313.2_Missense_Mutation_p.T2503A	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2464										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						ATAAATGGGGTCTTTAAGTCC	0.463													T|||	144	0.028754	0.1051	0.0072	5008	,	,		19760	0.0		0.0	False		,,,				2504	0.0				p.T2464A		Atlas-SNP	.											.	WDR87	191	.	0			c.A7390G						PASS	.	T	ALA/THR	156,1228		13,130,549	123.0	107.0	112.0		7390	1.7	0.0	19	dbSNP_132	112	0,3182		0,0,1591	yes	missense	WDR87	NM_031951.3	58	13,130,2140	CC,CT,TT		0.0,11.2717,3.4166	benign	2464/2874	38376804	156,4410	692	1591	2283	SO:0001583	missense	83889	exon6			ATGGGGTCTTTAA	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.7390A>G	19.37:g.38376804T>C	ENSP00000368025:p.Thr2464Ala	Somatic	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	299	147	0.491639	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	38	0.0173992673992674	35	0.07113821138211382	3	0.008287292817679558	0	0.0	0	0.0	T	5.593	0.294248	0.10567	0.112717	0.0	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.10573	2.86;2.86	3.84	1.68	0.24146	.	.	.	.	.	T	0.00144	0.0004	N	0.14661	0.345	0.09310	N	1	B;B	0.30793	0.295;0.088	B;B	0.32211	0.142;0.068	T	0.45026	-0.9289	9	0.45353	T	0.12	.	6.465	0.21977	0.3971:0.0:0.0:0.6029	.	2464;2503	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	A	2503;2464	ENSP00000405012:T2503A;ENSP00000368025:T2464A	ENSP00000368025:T2464A	T	-	1	0	WDR87	43068644	0.032000	0.19561	0.001000	0.08648	0.005000	0.04900	0.878000	0.28126	0.282000	0.22254	-0.341000	0.08007	ACC	T|0.979;C|0.021	0.021	strong		0.463	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
CYP2F1	1572	hgsc.bcm.edu	37	19	41627868	41627868	+	Missense_Mutation	SNP	G	G	A	rs80319612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41627868G>A	ENST00000331105.2	+	6	724	c.652G>A	c.(652-654)Gac>Aac	p.D218N		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	218			D -> N (in allele CYP2F1*3 and in allele CYP2F1*4; dbSNP:rs80319612).		naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						CCAGTTGTACGACATCTTCCC	0.592													N|||	1987	0.396765	0.5265	0.4841	5008	,	,		12536	0.2877		0.3091	False		,,,				2504	0.362				p.D218N		Atlas-SNP	.											.	CYP2F1	60	.	0			c.G652A						PASS	.	A	ASN/ASP	2228,2176		565,1098,539	63.0	66.0	65.0		652	3.0	0.9	19	dbSNP_131	65	2521,6077		380,1761,2158	no	missense	CYP2F1	NM_000774.3	23	945,2859,2697	AA,AG,GG		29.3208,49.4096,36.5251	benign	218/492	41627868	4749,8253	2202	4299	6501	SO:0001583	missense	1572	exon6			TTGTACGACATCT	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"""Cytochrome P450s"""	2632	protein-coding gene	gene with protein product		124070	"""cytochrome P450, subfamily IIF, polypeptide 1"""	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.652G>A	19.37:g.41627868G>A	ENSP00000333534:p.Asp218Asn	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	206	204	0.990291	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	37	CCDS12572.1	827	0.37866300366300365	269	0.5467479674796748	160	0.4419889502762431	156	0.2727272727272727	242	0.31926121372031663	N	0.008	-1.929886	0.00488	0.505904	0.293208	ENSG00000197446	ENST00000331105	T	0.69685	-0.42	3.04	3.04	0.35103	.	0.050287	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00642	-1.3	0.51482	P	7.699999999999374E-5	B;B;B	0.25272	0.122;0.001;0.001	B;B;B	0.16722	0.016;0.001;0.001	T	0.45411	-0.9263	9	0.02654	T	1	.	6.7434	0.23449	0.8737:0.0:0.1263:0.0	rs305974;rs4803377;rs62117447;rs305974	4;218;218	B4DL83;Q32MN5;P24903	.;.;CP2F1_HUMAN	N	218	ENSP00000333534:D218N	ENSP00000333534:D218N	D	+	1	0	CYP2F1	46319708	0.000000	0.05858	0.905000	0.35620	0.009000	0.06853	-0.513000	0.06305	0.241000	0.21283	-2.092000	0.00371	GAC	G|0.637;A|0.363	0.363	strong		0.592	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
DNAH3	55567	hgsc.bcm.edu	37	16	21049286	21049286	+	Missense_Mutation	SNP	C	C	T	rs16970832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:21049286C>T	ENST00000261383.3	-	34	4746	c.4747G>A	c.(4747-4749)Gtt>Att	p.V1583I	DNAH3_ENST00000415178.1_Missense_Mutation_p.V1583I	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1583	AAA 1. {ECO:0000250}.		V -> I (in dbSNP:rs16970832).		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)		TAGGTCGCAACGATCTTCTGG	0.547													C|||	248	0.0495208	0.1808	0.0101	5008	,	,		21358	0.0		0.002	False		,,,				2504	0.0				p.V1583I		Atlas-SNP	.											.	DNAH3	1142	.	0			c.G4747A						PASS	.	C	ILE/VAL	675,3727	286.9+/-279.0	56,563,1582	88.0	66.0	74.0		4747	5.8	1.0	16	dbSNP_123	74	7,8593	3.7+/-12.6	0,7,4293	yes	missense	DNAH3	NM_017539.1	29	56,570,5875	TT,TC,CC		0.0814,15.3339,5.2453	probably-damaging	1583/4117	21049286	682,12320	2201	4300	6501	SO:0001583	missense	55567	exon34			TCGCAACGATCTT	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.4747G>A	16.37:g.21049286C>T	ENSP00000261383:p.Val1583Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	60	0.625	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	79	0.036172161172161175	77	0.1565040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	32	5.164216	0.94727	0.153339	8.14E-4	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.06608	3.28;3.28	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000001	T	0.00109	0.0003	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.00076	-1.2118	10	0.36615	T	0.2	.	19.9616	0.97254	0.0:1.0:0.0:0.0	rs16970832;rs56565035;rs16970832	1583	Q8TD57	DYH3_HUMAN	I	1583	ENSP00000261383:V1583I;ENSP00000394245:V1583I	ENSP00000261383:V1583I	V	-	1	0	DNAH3	20956787	1.000000	0.71417	0.998000	0.56505	0.731000	0.41821	7.764000	0.85297	2.724000	0.93272	0.561000	0.74099	GTT	C|0.944;T|0.056	0.056	strong		0.547	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ACVRL1	94	hgsc.bcm.edu	37	12	52306898	52306898	+	Missense_Mutation	SNP	C	C	T	rs199542304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52306898C>T	ENST00000388922.4	+	3	360	c.77C>T	c.(76-78)cCg>cTg	p.P26L	ACVRL1_ENST00000550683.1_Missense_Mutation_p.P40L|ACVRL1_ENST00000419526.2_Intron	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	26					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	CCTGTGAAGCCGTCTCGGGGC	0.657													C|||	2	0.000399361	0.0	0.0	5008	,	,		14365	0.002		0.0	False		,,,				2504	0.0				p.P26L		Atlas-SNP	.											.	ACVRL1	60	.	0			c.C77T						PASS	.	C	LEU/PRO,LEU/PRO	1,4371		0,1,2185	13.0	15.0	14.0		77,77	5.8	0.9	12		14	1,8567		0,1,4283	yes	missense,missense	ACVRL1	NM_000020.2,NM_001077401.1	98,98	0,2,6468	TT,TC,CC		0.0117,0.0229,0.0155	possibly-damaging,possibly-damaging	26/504,26/504	52306898	2,12938	2186	4284	6470	SO:0001583	missense	94	exon3			TGAAGCCGTCTCG	L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567			175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2		8397373, 8640225	Standard	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	ENST00000388922.4:c.77C>T	12.37:g.52306898C>T	ENSP00000373574:p.Pro26Leu	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	42	12	0.285714	NM_000020	A6NGA8	Missense_Mutation	SNP	ENST00000388922.4	37	CCDS31804.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427822	0.62733	2.29E-4	1.17E-4	ENSG00000139567	ENST00000388922;ENST00000267008;ENST00000547400;ENST00000550683	D;D;D	0.92149	-2.98;-2.98;-2.98	5.76	5.76	0.90799	.	0.343290	0.21467	N	0.074075	T	0.80649	0.4663	N	0.08118	0	0.80722	D	1	P	0.43750	0.816	B	0.27380	0.079	D	0.83667	0.0164	10	0.44086	T	0.13	.	15.4529	0.75290	0.0:1.0:0.0:0.0	.	26	P37023	ACVL1_HUMAN	L	26;26;40;40	ENSP00000373574:P26L;ENSP00000446724:P40L;ENSP00000447884:P40L	ENSP00000267008:P26L	P	+	2	0	ACVRL1	50593165	0.004000	0.15560	0.898000	0.35279	0.512000	0.34134	0.741000	0.26202	2.716000	0.92895	0.655000	0.94253	CCG	.	.	weak		0.657	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2		
CACNA2D1	781	hgsc.bcm.edu	37	7	81588636	81588636	+	Silent	SNP	G	G	A	rs1229502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:81588636G>A	ENST00000356253.5	-	38	3405	c.3150C>T	c.(3148-3150)ccC>ccT	p.P1050P	CACNA2D1_ENST00000535308.1_Silent_p.P250P|CACNA2D1_ENST00000356860.3_Silent_p.P1038P			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	95	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	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			
ACSL3	2181	hgsc.bcm.edu	37	2	223783841	223783841	+	Silent	SNP	G	G	A	rs13000358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:223783841G>A	ENST00000357430.3	+	7	1257	c.726G>A	c.(724-726)ccG>ccA	p.P242P	AC097461.4_ENST00000446709.1_RNA|ACSL3_ENST00000392066.3_Silent_p.P242P	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	242					brain development (GO:0007420)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty acid import (GO:0044539)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)|positive regulation of phosphatidylcholine biosynthetic process (GO:2001247)|positive regulation of secretion (GO:0051047)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)|skin(2)	22		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	GAAAGCCACCGACCTGGTCCG	0.483			T	ETV1	prostate								g|||	113	0.0225639	0.0113	0.0346	5008	,	,		16458	0.0		0.0537	False		,,,				2504	0.0204				p.P242P		Atlas-SNP	.		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	.	ACSL3	107	.	0			c.G726A						PASS	.	G	,	85,4321	72.5+/-110.5	0,85,2118	120.0	102.0	108.0		726,726	-11.3	0.0	2	dbSNP_121	108	466,8134	138.1+/-194.9	14,438,3848	no	coding-synonymous,coding-synonymous	ACSL3	NM_004457.3,NM_203372.1	,	14,523,5966	AA,AG,GG		5.4186,1.9292,4.2365	,	242/721,242/721	223783841	551,12455	2203	4300	6503	SO:0001819	synonymous_variant	2181	exon6			GCCACCGACCTGG	D89053	CCDS2455.1	2q34-q35	2008-02-05	2004-02-19	2004-02-20	ENSG00000123983	ENSG00000123983		"""Acyl-CoA synthetase family"""	3570	protein-coding gene	gene with protein product		602371	"""fatty-acid-Coenzyme A ligase, long-chain 3"""	FACL3			Standard	NM_004457		Approved	ACS3, PRO2194	uc002vnj.3	O95573	OTTHUMG00000133160	ENST00000357430.3:c.726G>A	2.37:g.223783841G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	225	107	0.475556	NM_203372	Q60I92|Q8IUM9	Silent	SNP	ENST00000357430.3	37	CCDS2455.1																																																																																			G|0.963;A|0.037	0.037	strong		0.483	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457	
MYO18B	84700	hgsc.bcm.edu	37	22	26222454	26222454	+	Missense_Mutation	SNP	C	C	T	rs9624909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26222454C>T	ENST00000407587.2	+	14	2943	c.2774C>T	c.(2773-2775)tCa>tTa	p.S925L	MYO18B_ENST00000335473.7_Missense_Mutation_p.S925L|MYO18B_ENST00000536101.1_Missense_Mutation_p.S925L			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	925	Myosin motor.		S -> L (in dbSNP:rs9624909). {ECO:0000269|PubMed:12547197}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GCTGTGGTCTCACTCATCAAC	0.547													C|||	706	0.140974	0.1838	0.1801	5008	,	,		18425	0.0		0.2386	False		,,,				2504	0.1002				p.S925L		Atlas-SNP	.											.	MYO18B	322	.	0			c.C2774T						PASS	.	C	LEU/SER	741,3173		77,587,1293	162.0	154.0	156.0		2774	4.3	1.0	22	dbSNP_119	156	1803,6501		195,1413,2544	yes	missense	MYO18B	NM_032608.5	145	272,2000,3837	TT,TC,CC		21.7124,18.932,20.8217	probably-damaging	925/2568	26222454	2544,9674	1957	4152	6109	SO:0001583	missense	84700	exon14			TGGTCTCACTCAT	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.2774C>T	22.37:g.26222454C>T	ENSP00000386096:p.Ser925Leu	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	216	103	0.476852	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		355	0.16254578754578755	88	0.17886178861788618	77	0.212707182320442	2	0.0034965034965034965	188	0.24802110817941952	C	23.3	4.397818	0.83120	0.18932	0.217124	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.87966	-2.32;-2.32;-2.32	4.26	4.26	0.50523	Myosin head, motor domain (2);	0.078134	0.53938	D	0.000060	T	0.00144	0.0004	L	0.56769	1.78	0.22500	P	0.999043338	D;D;D;D	0.58268	0.978;0.982;0.972;0.978	P;P;P;P	0.58620	0.756;0.842;0.67;0.756	T	0.00000	-1.2891	9	0.52906	T	0.07	.	15.2478	0.73521	0.0:1.0:0.0:0.0	rs9624909;rs52810539;rs58212376;rs9624909	438;925;925;925	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	L	925	ENSP00000441229:S925L;ENSP00000334563:S925L;ENSP00000386096:S925L	ENSP00000334563:S925L	S	+	2	0	MYO18B	24552454	1.000000	0.71417	0.989000	0.46669	0.851000	0.48451	4.541000	0.60670	1.923000	0.55706	0.462000	0.41574	TCA	C|0.835;T|0.165	0.165	strong		0.547	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
JRK	8629	hgsc.bcm.edu	37	8	143746399	143746399	+	RNA	SNP	T	T	C	rs73379623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746399T>C	ENST00000507178.2	-	0	1411							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)				tatggcatcgttcatgttgta	0.602													T|||	63	0.0125799	0.0469	0.0014	5008	,	,		18767	0.0		0.0	False		,,,				2504	0.0				p.N360S		Atlas-SNP	.											.	.	.	.	0			c.A1079G						PASS	.	T	SER/ASN,SER/ASN	137,3981		0,137,1922	9.0	10.0	10.0		1079,1079	1.4	0.0	8	dbSNP_130	10	1,8401		0,1,4200	yes	missense,missense	JRK	NM_001077527.1,NM_003724.2	46,46	0,138,6122	CC,CT,TT		0.0119,3.3269,1.1022	benign,benign	360/557,360/569	143746399	138,12382	2059	4201	6260			8629	exon2			GCATCGTTCATGT	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.143746399T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				T|0.992;C|0.008	0.008	strong		0.602	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
AKR7A3	22977	hgsc.bcm.edu	37	1	19612477	19612477	+	Missense_Mutation	SNP	C	C	T	rs2231198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19612477C>T	ENST00000361640.4	-	3	952	c.412G>A	c.(412-414)Gtg>Atg	p.V138M		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	138			V -> M (in dbSNP:rs2231198). {ECO:0000269|PubMed:10383892, ECO:0000269|PubMed:15489334}.		cellular aldehyde metabolic process (GO:0006081)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)	13		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CCAAGCTCCACGAACTTGCCC	0.612													C|||	2320	0.463259	0.3646	0.5432	5008	,	,		19169	0.6905		0.3817	False		,,,				2504	0.3896				p.V138M		Atlas-SNP	.											.	AKR7A3	30	.	0			c.G412A						PASS	.	C	MET/VAL	1614,2784		319,976,904	58.0	54.0	55.0		412	3.0	1.0	1	dbSNP_98	55	3110,5490		564,1982,1754	no	missense	AKR7A3	NM_012067.2	21	883,2958,2658	TT,TC,CC		36.1628,36.6985,36.3441	benign	138/332	19612477	4724,8274	2199	4300	6499	SO:0001583	missense	22977	exon3			GCTCCACGAACTT	AF040639	CCDS193.1	1p36.13	2008-05-14			ENSG00000162482	ENSG00000162482		"""Aldo-keto reductases"""	390	protein-coding gene	gene with protein product		608477				10383892	Standard	NM_012067		Approved		uc001bbv.1	O95154	OTTHUMG00000002523	ENST00000361640.4:c.412G>A	1.37:g.19612477C>T	ENSP00000355377:p.Val138Met	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	219	101	0.461187	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Missense_Mutation	SNP	ENST00000361640.4	37	CCDS193.1	1072	0.4908424908424908	187	0.3800813008130081	194	0.5359116022099447	411	0.7185314685314685	280	0.36939313984168864	.	6.831	0.522560	0.13066	0.366985	0.361628	ENSG00000162482	ENST00000361640	T	0.23348	1.91	3.04	3.04	0.35103	NADP-dependent oxidoreductase domain (3);	0.240515	0.40640	N	0.001046	T	0.00012	0.0000	M	0.82823	2.61	0.41505	P	0.011692999999999953	B	0.32543	0.375	B	0.24974	0.057	T	0.34453	-0.9828	9	0.41790	T	0.15	.	5.9087	0.19016	0.0:0.8521:0.0:0.1479	rs2231198;rs11539611;rs13374777;rs17852954;rs59246333	138	O95154	ARK73_HUMAN	M	138	ENSP00000355377:V138M	ENSP00000355377:V138M	V	-	1	0	AKR7A3	19485064	1.000000	0.71417	1.000000	0.80357	0.263000	0.26337	2.346000	0.44027	1.542000	0.49330	0.194000	0.17425	GTG	C|0.603;T|0.397	0.397	strong		0.612	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067	
CLEC4D	338339	hgsc.bcm.edu	37	12	8667897	8667897	+	Missense_Mutation	SNP	A	A	G	rs4304840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:8667897A>G	ENST00000299665.2	+	2	287	c.94A>G	c.(94-96)Agt>Ggt	p.S32G		NM_080387.4	NP_525126.2	Q8WXI8	CLC4D_HUMAN	C-type lectin domain family 4, member D	32			S -> G (in dbSNP:rs4304840). {ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Lung SC(5;0.184)					CTTACTTCTCAGTGTCTGTTT	0.378													A|||	1504	0.300319	0.5923	0.1844	5008	,	,		-128	0.122		0.2475	False		,,,				2504	0.226				p.S32G		Atlas-SNP	.											.	CLEC4D	46	.	0			c.A94G						PASS	.	A	GLY/SER	2420,1986	618.2+/-393.1	668,1084,451	232.0	197.0	209.0		94	-0.3	0.3	12	dbSNP_111	209	1987,6613	348.8+/-327.2	249,1489,2562	yes	missense	CLEC4D	NM_080387.4	56	917,2573,3013	GG,GA,AA		23.1047,45.0749,33.8844	benign	32/216	8667897	4407,8599	2203	4300	6503	SO:0001583	missense	338339	exon2			CTTCTCAGTGTCT	AF411850	CCDS8593.1	12p13.31	2005-09-21	2005-02-09	2005-02-11		ENSG00000166527		"""C-type lectin domain containing"""	14554	protein-coding gene	gene with protein product		609964	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 8"""	CLECSF8			Standard	NM_080387		Approved	Mpcl	uc001qun.3	Q8WXI8		ENST00000299665.2:c.94A>G	12.37:g.8667897A>G	ENSP00000299665:p.Ser32Gly	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	240	100	0.416667	NM_080387	Q8N5J5	Missense_Mutation	SNP	ENST00000299665.2	37	CCDS8593.1	621	0.28434065934065933	279	0.5670731707317073	66	0.18232044198895028	88	0.15384615384615385	188	0.24802110817941952	a	0.126	-1.119811	0.01785	0.549251	0.231047	ENSG00000166527	ENST00000382064;ENST00000299665	T;T	0.05513	3.43;3.7	3.36	-0.299	0.12808	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.52501	P	4.199999999998649E-5	B	0.10296	0.003	B	0.04013	0.001	T	0.29518	-1.0009	8	0.36615	T	0.2	.	7.1227	0.25454	0.7959:0.0:0.2041:0.0	rs4304840;rs60537162;rs4304840	32	Q8WXI8	CLC4D_HUMAN	G	32	ENSP00000371496:S32G;ENSP00000299665:S32G	ENSP00000299665:S32G	S	+	1	0	CLEC4D	8559164	0.031000	0.19500	0.321000	0.25320	0.003000	0.03518	-0.178000	0.09782	-0.089000	0.12484	-1.335000	0.01260	AGT	A|0.678;G|0.322	0.322	strong		0.378	CLEC4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400565.1	NM_080387	
FCGBP	8857	hgsc.bcm.edu	37	19	40384035	40384035	+	Missense_Mutation	SNP	G	G	A	rs367618328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40384035G>A	ENST00000221347.6	-	21	9582	c.9575C>T	c.(9574-9576)gCg>gTg	p.A3192V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3192	TIL 7.					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)			CACGAAACCCGCGTCGCACTG	0.662													G|||	65	0.0129792	0.0446	0.0058	5008	,	,		24198	0.001		0.001	False		,,,				2504	0.0				p.A3192V		Atlas-SNP	.											FCGBP,NS,haematopoietic_neoplasm,-1,1	FCGBP	416	1	0			c.C9575T						scavenged	.	G	VAL/ALA	47,2527		0,47,1240	4.0	4.0	4.0		9575	-4.6	0.0	19		4	1,5829		0,1,2914	no	missense	FCGBP	NM_003890.2	64	0,48,4154	AA,AG,GG		0.0172,1.826,0.5712	possibly-damaging	3192/5406	40384035	48,8356	1287	2915	4202	SO:0001583	missense	8857	exon21			AAACCCGCGTCGC	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.9575C>T	19.37:g.40384035G>A	ENSP00000221347:p.Ala3192Val	Somatic	585	1	0.0017094		WXS	Illumina HiSeq	Phase_I	639	130	0.203443	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	7.646	0.681900	0.14907	0.01826	1.72E-4	ENSG00000090920	ENST00000221347	T	0.30981	1.51	3.48	-4.63	0.03359	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	.	.	.	.	T	0.18676	0.0448	L	0.49350	1.555	0.09310	N	1	D	0.56287	0.975	P	0.54372	0.75	T	0.25082	-1.0142	9	0.33141	T	0.24	.	7.6572	0.28381	0.0999:0.0:0.2726:0.6275	.	3192	Q9Y6R7	FCGBP_HUMAN	V	3192	ENSP00000221347:A3192V	ENSP00000221347:A3192V	A	-	2	0	FCGBP	45075875	0.000000	0.05858	0.001000	0.08648	0.033000	0.12548	-0.286000	0.08399	-0.448000	0.07128	-0.513000	0.04457	GCG	.	.	weak		0.662	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CEP68	23177	hgsc.bcm.edu	37	2	65299766	65299766	+	Silent	SNP	T	T	C	rs55952639	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:65299766T>C	ENST00000377990.2	+	3	1739	c.1536T>C	c.(1534-1536)gaT>gaC	p.D512D	CEP68_ENST00000546106.1_Silent_p.D512D|CEP68_ENST00000537589.1_Silent_p.D124D|CEP68_ENST00000260569.4_Intron|CEP68_ENST00000497039.1_Intron|RAB1A_ENST00000494188.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	512					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						CCACTGGGGATATCAAAGGGC	0.567													T|||	1052	0.210064	0.4054	0.1585	5008	,	,		20962	0.2421		0.0567	False		,,,				2504	0.1074				p.D512D		Atlas-SNP	.											.	CEP68	69	.	0			c.T1536C						PASS	.	T		1428,2978	429.9+/-342.4	230,968,1005	80.0	92.0	88.0		1536	-1.5	0.0	2	dbSNP_129	88	503,8097	140.8+/-197.2	16,471,3813	yes	coding-synonymous	CEP68	NM_015147.2		246,1439,4818	CC,CT,TT		5.8488,32.4103,14.847		512/758	65299766	1931,11075	2203	4300	6503	SO:0001819	synonymous_variant	23177	exon3			TGGGGATATCAAA	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.1536T>C	2.37:g.65299766T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Silent	SNP	ENST00000377990.2	37	CCDS1880.2																																																																																			T|0.848;C|0.152	0.152	strong		0.567	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
ATP8A1	10396	hgsc.bcm.edu	37	4	42576646	42576646	+	Missense_Mutation	SNP	C	C	T	rs61755862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:42576646C>T	ENST00000381668.5	-	14	1516	c.1285G>A	c.(1285-1287)Gtt>Att	p.V429I	ATP8A1_ENST00000264449.10_Missense_Mutation_p.V429I	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	429					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	CCATAAGCAACTCCCGCTATG	0.343													C|||	126	0.0251597	0.0923	0.0058	5008	,	,		17551	0.0		0.0	False		,,,				2504	0.0				p.V429I		Atlas-SNP	.											ATP8A1_ENST00000264449,NS,carcinoma,+1,2	ATP8A1	206	2	0			c.G1285A						PASS	.	C	ILE/VAL,ILE/VAL	297,4109	159.6+/-192.1	13,271,1919	55.0	56.0	56.0		1285,1285	3.4	1.0	4	dbSNP_129	56	2,8596	1.2+/-3.3	0,2,4297	yes	missense,missense	ATP8A1	NM_001105529.1,NM_006095.2	29,29	13,273,6216	TT,TC,CC		0.0233,6.7408,2.2993	benign,benign	429/1150,429/1165	42576646	299,12705	2203	4299	6502	SO:0001583	missense	10396	exon14			AAGCAACTCCCGC	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"""ATPases / P-type"""	13531	protein-coding gene	gene with protein product		609542	"""ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"""			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1285G>A	4.37:g.42576646C>T	ENSP00000371084:p.Val429Ile	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	190	84	0.442105	NM_001105529	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	C	4.770	0.143139	0.09083	0.067408	2.33E-4	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.74947	-0.89;-0.89	5.27	3.4	0.38934	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.068109	0.64402	D	0.000017	T	0.04137	0.0115	N	0.11845	0.185	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.03325	-1.1048	10	0.09338	T	0.73	.	6.9831	0.24713	0.0:0.6446:0.0:0.3554	.	429;429;429	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	I	429	ENSP00000371084:V429I;ENSP00000264449:V429I	ENSP00000264449:V429I	V	-	1	0	ATP8A1	42271403	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	0.657000	0.24963	1.459000	0.47892	0.591000	0.81541	GTT	C|0.975;T|0.025	0.025	strong		0.343	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095	
ZNF257	113835	hgsc.bcm.edu	37	19	22256347	22256347	+	Silent	SNP	G	G	A	rs10423157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22256347G>A	ENST00000594947.1	+	3	351	c.207G>A	c.(205-207)gaG>gaA	p.E69E	ZNF257_ENST00000600162.1_Silent_p.E69E	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGAGACATGAGATGGTAGCCA	0.438													G|||	556	0.111022	0.4054	0.0274	5008	,	,		16022	0.0		0.0	False		,,,				2504	0.001				p.E69E		Atlas-SNP	.											.	ZNF257	156	.	0			c.G207A						PASS	.	G		1613,2793	496.2+/-363.5	291,1031,881	133.0	145.0	141.0		207	-1.7	0.0	19	dbSNP_119	141	17,8583	11.2+/-40.8	0,17,4283	no	coding-synonymous	ZNF257	NM_033468.2		291,1048,5164	AA,AG,GG		0.1977,36.6092,12.5327		69/564	22256347	1630,11376	2203	4300	6503	SO:0001819	synonymous_variant	113835	exon3			ACATGAGATGGTA	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"""Zinc fingers, C2H2-type"", ""-"""	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.207G>A	19.37:g.22256347G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_033468	B3KPS4|E9PG34|Q8NE34	Silent	SNP	ENST00000594947.1	37	CCDS46030.1																																																																																			G|0.927;A|0.073	0.073	strong		0.438	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1		
OR52E6	390078	hgsc.bcm.edu	37	11	5862731	5862731	+	Missense_Mutation	SNP	A	A	G	rs10838719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5862731A>G	ENST00000329322.5	-	1	396	c.397T>C	c.(397-399)Tgg>Cgg	p.W133R	TRIM5_ENST00000380027.1_Intron|OR52E6_ENST00000379946.2_Missense_Mutation_p.W137R	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	133			W -> R (in dbSNP:rs10838719).			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)		ATGGTGTACCAAAGAGGTTTG	0.473													A|||	1940	0.38738	0.2352	0.389	5008	,	,		21277	0.4593		0.5258	False		,,,				2504	0.3753				p.W133R		Atlas-SNP	.											OR52E6,NS,carcinoma,+2,2	OR52E6	70	2	0			c.T397C						PASS	.	A	ARG/TRP	1206,3196	418.7+/-338.4	169,868,1164	207.0	187.0	194.0		397	-6.9	0.0	11	dbSNP_120	194	4339,4253	579.2+/-390.9	1071,2197,1028	no	missense	OR52E6	NM_001005167.1	101	1240,3065,2192	GG,GA,AA		49.4995,27.3966,42.6735	benign	133/314	5862731	5545,7449	2201	4296	6497	SO:0001583	missense	390078	exon1			TGTACCAAAGAGG	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.397T>C	11.37:g.5862731A>G	ENSP00000328878:p.Trp133Arg	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	202	88	0.435644	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	864	0.3956043956043956	94	0.1910569105691057	141	0.38950276243093923	250	0.4370629370629371	379	0.5	a	0.012	-1.656056	0.00779	0.273966	0.505005	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.32272	1.46;1.46	3.45	-6.91	0.01649	GPCR, rhodopsin-like superfamily (1);	1.171350	0.06439	N	0.725641	T	0.00012	0.0000	N	0.00000	-4.27	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.53034	-0.8495	9	0.02654	T	1	.	5.0066	0.14291	0.3246:0.0:0.2032:0.4721	rs10838719	133	Q96RD3	O52E6_HUMAN	R	133;137	ENSP00000328878:W133R;ENSP00000369279:W137R	ENSP00000328878:W133R	W	-	1	0	OR52E6	5819307	0.000000	0.05858	0.000000	0.03702	0.882000	0.50991	-0.533000	0.06157	-1.517000	0.01780	-0.319000	0.08680	TGG	A|0.622;G|0.378	0.378	strong		0.473	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
KLHL20	27252	hgsc.bcm.edu	37	1	173735378	173735378	+	Silent	SNP	T	T	C	rs7536773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173735378T>C	ENST00000209884.4	+	8	1381	c.1245T>C	c.(1243-1245)ctT>ctC	p.L415L	KLHL20_ENST00000546011.1_Silent_p.L226L	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	415					cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)			breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						GAGGCTTTCTTTATGCTGTGG	0.433													C|||	555	0.110823	0.3971	0.0346	5008	,	,		15265	0.0		0.006	False		,,,				2504	0.0				p.L415L	GBM(159;862 2695 6559 23041)	Atlas-SNP	.											.	KLHL20	54	.	0			c.T1245C						PASS	.	C		1333,3073	695.2+/-405.9	197,939,1067	285.0	261.0	269.0		1245	0.1	1.0	1	dbSNP_116	269	31,8569	818.0+/-406.9	0,31,4269	no	coding-synonymous	KLHL20	NM_014458.3		197,970,5336	CC,CT,TT		0.3605,30.2542,10.4875		415/610	173735378	1364,11642	2203	4300	6503	SO:0001819	synonymous_variant	27252	exon8			CTTTCTTTATGCT	AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"""Kelch-like"", ""BTB/POZ domain containing"""	25056	protein-coding gene	gene with protein product			"""kelch-like 20 (Drosophila)"""			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.1245T>C	1.37:g.173735378T>C		Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	330	135	0.409091	NM_014458	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Silent	SNP	ENST00000209884.4	37	CCDS1310.1																																																																																			T|0.875;C|0.125	0.125	strong		0.433	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458	
INSR	3643	hgsc.bcm.edu	37	19	7163154	7163154	+	Silent	SNP	G	G	A	rs2963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7163154G>A	ENST00000302850.5	-	9	2060	c.1918C>T	c.(1918-1920)Ctg>Ttg	p.L640L	AC010311.1_ENST00000581768.1_RNA|INSR_ENST00000341500.5_Silent_p.L640L	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	640	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)"""	TTCCACTTCAGAATAATCTGG	0.517													A|||	800	0.159744	0.2723	0.0692	5008	,	,		15100	0.0367		0.0646	False		,,,				2504	0.2965				p.L640L		Atlas-SNP	.											.	INSR	265	.	0			c.C1918T						PASS	.	A	,	1034,3372	723.9+/-409.4	118,798,1287	163.0	167.0	166.0		1918,1918	-6.3	0.0	19	dbSNP_36	166	681,7919	788.0+/-407.6	33,615,3652	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	151,1413,4939	AA,AG,GG		7.9186,23.468,13.1862	,	640/1383,640/1371	7163154	1715,11291	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon9			ACTTCAGAATAAT	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.1918C>T	19.37:g.7163154G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	176	68	0.386364	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			G|0.876;A|0.124	0.124	strong		0.517	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
RAB40AL	282808	hgsc.bcm.edu	37	X	102192321	102192321	+	Silent	SNP	A	A	G	rs61745027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192321A>G	ENST00000218249.5	+	1	122	c.75A>G	c.(73-75)gtA>gtG	p.V25V	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	25					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						ACAGGGACGTAGGCAAGAGTG	0.677													.|||	995	0.263576	0.4123	0.0692	3775	,	,		9952	0.1171		0.005	False		,,,				2504	0.2853				p.V25V		Atlas-SNP	.											.	RAB40AL	33	.	0			c.A75G						PASS	.	G		1452,2377		316,553,267,762,300	51.0	69.0	63.0		75	0.8	0.4	X	dbSNP_129	63	26,6701		0,20,6,2408,1865	no	coding-synonymous	RAB40AL	NM_001031834.1		316,573,273,3170,2165	GG,GA,G,AA,A		0.3865,37.9211,14.0015		25/279	102192321	1478,9078	2198	4299	6497	SO:0001819	synonymous_variant	282808	exon1			GGACGTAGGCAAG	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"""Ras like GTPase"""	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.75A>G	X.37:g.102192321A>G		Somatic	331	1	0.00302115		WXS	Illumina HiSeq	Phase_I	259	258	0.996139	NM_001031834	Q495H3	Silent	SNP	ENST00000218249.5	37	CCDS35353.1																																																																																			A|0.824;G|0.176	0.176	strong		0.677	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834	
PARP10	84875	hgsc.bcm.edu	37	8	145058539	145058539	+	Missense_Mutation	SNP	T	T	C	rs80304851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145058539T>C	ENST00000313028.7	-	6	1613	c.1519A>G	c.(1519-1521)Agc>Ggc	p.S507G	PARP10_ENST00000533665.1_5'Flank|PARP10_ENST00000525773.1_Missense_Mutation_p.S519G|PARP10_ENST00000524918.1_Missense_Mutation_p.S507G	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	507					negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CAGCTAATGCTGCCCAGCAGG	0.627													T|||	438	0.0874601	0.239	0.0519	5008	,	,		18012	0.0218		0.0398	False		,,,				2504	0.0245				p.S507G		Atlas-SNP	.											.	PARP10	57	.	0			c.A1519G						PASS	.		GLY/SER	923,3481		96,731,1375	26.0	29.0	28.0		1519	4.2	1.0	8	dbSNP_131	28	374,8226		9,356,3935	yes	missense	PARP10	NM_032789.3	56	105,1087,5310	CC,CT,TT		4.3488,20.9582,9.9739	benign	507/1026	145058539	1297,11707	2202	4300	6502	SO:0001583	missense	84875	exon6			TAATGCTGCCCAG	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"""Poly (ADP-ribose) polymerases"""	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.1519A>G	8.37:g.145058539T>C	ENSP00000325618:p.Ser507Gly	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Missense_Mutation	SNP	ENST00000313028.7	37	CCDS34960.1	181	0.08287545787545787	112	0.22764227642276422	23	0.06353591160220995	15	0.026223776223776224	31	0.040897097625329816	T	17.16	3.319537	0.60524	0.209582	0.043488	ENSG00000178685	ENST00000524918;ENST00000534861;ENST00000313028;ENST00000525773	T;T;T	0.22336	1.96;1.99;1.99	4.21	4.21	0.49690	.	0.000000	0.56097	D	0.000036	T	0.00012	0.0000	M	0.69823	2.125	0.30588	P	0.761803	B;D	0.54207	0.207;0.965	B;P	0.52343	0.101;0.696	T	0.14559	-1.0468	9	0.66056	D	0.02	.	6.4009	0.21638	0.0:0.1136:0.0:0.8864	.	519;507	E9PNI7;Q53GL7	.;PAR10_HUMAN	G	507;213;507;519	ENSP00000431620:S507G;ENSP00000325618:S507G;ENSP00000434776:S519G	ENSP00000325618:S507G	S	-	1	0	PARP10	145130527	0.967000	0.33354	0.988000	0.46212	0.587000	0.36485	1.982000	0.40638	1.549000	0.49425	0.450000	0.29827	AGC	T|0.903;C|0.097	0.097	strong		0.627	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33881385	33881385	+	Missense_Mutation	SNP	G	G	C	rs16891862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:33881385G>C	ENST00000504830.1	-	2	663	c.328C>G	c.(328-330)Caa>Gaa	p.Q110E	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.Q110E|ADAMTS12_ENST00000515401.1_Missense_Mutation_p.Q110E	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	110			Q -> E (in dbSNP:rs16891862).		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						AGAAATCCTTGATTGACCGTC	0.478										HNSCC(64;0.19)			G|||	63	0.0125799	0.0446	0.0058	5008	,	,		20577	0.0		0.0	False		,,,				2504	0.0				p.Q110E		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.C328G						PASS	.	G	GLU/GLN	137,4269	97.1+/-135.8	5,127,2071	118.0	113.0	115.0		328	2.2	0.0	5	dbSNP_123	115	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ADAMTS12	NM_030955.2	29	5,128,6370	CC,CG,GG		0.0116,3.1094,1.061	benign	110/1595	33881385	138,12868	2203	4300	6503	SO:0001583	missense	81792	exon2			ATCCTTGATTGAC	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.328C>G	5.37:g.33881385G>C	ENSP00000422554:p.Gln110Glu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	164	72	0.439024	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	15	0.006868131868131868	12	0.024390243902439025	3	0.008287292817679558	0	0.0	0	0.0	G	5.178	0.218364	0.09810	0.031094	1.16E-4	ENSG00000151388	ENST00000504830;ENST00000352040;ENST00000515401	T;T;T	0.05513	3.43;3.43;3.43	5.65	2.19	0.27852	Peptidase M12B, propeptide (1);	1.682860	0.03218	N	0.177161	T	0.01940	0.0061	L	0.42245	1.32	0.09310	N	1	B;B;B	0.21309	0.0;0.054;0.001	B;B;B	0.19666	0.001;0.026;0.02	T	0.42666	-0.9438	10	0.16420	T	0.52	.	2.8766	0.05632	0.1002:0.3354:0.3077:0.2567	rs16891862;rs52818503;rs16891862	110;110;110	P58397-3;D6REX0;P58397	.;.;ATS12_HUMAN	E	110	ENSP00000422554:Q110E;ENSP00000344847:Q110E;ENSP00000421638:Q110E	ENSP00000344847:Q110E	Q	-	1	0	ADAMTS12	33917142	0.018000	0.18449	0.001000	0.08648	0.807000	0.45602	0.455000	0.21843	0.100000	0.17581	0.467000	0.42956	CAA	C|0.011;G|0.989	0.011	strong		0.478	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
SLC5A8	160728	hgsc.bcm.edu	37	12	101551065	101551065	+	Missense_Mutation	SNP	G	G	A	rs113062899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101551065G>A	ENST00000536262.2	-	15	2383	c.1825C>T	c.(1825-1827)Cgt>Tgt	p.R609C		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTTCACAAACGAGTCCCATTG	0.378													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		19406	0.0		0.0	False		,,,				2504	0.0				p.R609C	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.C1825T						PASS	.	G	CYS/ARG	145,4261	100.7+/-139.4	0,145,2058	136.0	119.0	125.0		1825	5.2	1.0	12	dbSNP_132	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC5A8	NM_145913.3	180	0,146,6357	AA,AG,GG		0.0116,3.291,1.1226	probably-damaging	609/611	101551065	146,12860	2203	4300	6503	SO:0001583	missense	160728	exon15			ACAAACGAGTCCC	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"""Solute carriers"""	19119	protein-coding gene	gene with protein product		608044	"""solute carrier family 5 (iodide transporter), member 8"""			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1825C>T	12.37:g.101551065G>A	ENSP00000445340:p.Arg609Cys	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	118	67	0.567797	NM_145913		Missense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	G	15.83	2.949451	0.53186	0.03291	1.16E-4	ENSG00000256870	ENST00000536262	D	0.86230	-2.09	5.15	5.15	0.70609	.	0.710763	0.13338	N	0.395349	T	0.55577	0.1929	L	0.47716	1.5	0.40861	D	0.983839	D	0.56968	0.978	B	0.43623	0.425	T	0.77590	-0.2531	10	0.87932	D	0	.	15.919	0.79544	0.0:0.0:1.0:0.0	.	609	Q8N695	SC5A8_HUMAN	C	609	ENSP00000445340:R609C	ENSP00000445340:R609C	R	-	1	0	SLC5A8	100075196	1.000000	0.71417	1.000000	0.80357	0.510000	0.34073	3.942000	0.56614	2.574000	0.86865	0.655000	0.94253	CGT	G|0.987;A|0.013	0.013	strong		0.378	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913	
TBC1D2	55357	hgsc.bcm.edu	37	9	100995721	100995721	+	Missense_Mutation	SNP	A	A	G	rs879369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100995721A>G	ENST00000375064.1	-	4	796	c.758T>C	c.(757-759)tTg>tCg	p.L253S	TBC1D2_ENST00000375066.5_Missense_Mutation_p.L253S|TBC1D2_ENST00000342112.5_Missense_Mutation_p.L35S	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	77	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	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	
PARP15	165631	hgsc.bcm.edu	37	3	122296638	122296638	+	Missense_Mutation	SNP	G	G	A	rs1875272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122296638G>A	ENST00000464300.2	+	1	190	c.124G>A	c.(124-126)Gtg>Atg	p.V42M	PARP15_ENST00000483793.1_Missense_Mutation_p.V42M	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	42				V -> M (in Ref. 4; AAY64451). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		GGCGGGGAGCGTGCTGCCGGC	0.697													G|||	1182	0.236022	0.2564	0.33	5008	,	,		14132	0.247		0.2197	False		,,,				2504	0.1472				p.V42M		Atlas-SNP	.											PARP15_ENST00000464300,NS,carcinoma,0,1	PARP15	115	1	0			c.G124A						PASS	.						27.0	30.0	29.0					3																	122296638		692	1591	2283	SO:0001583	missense	165631	exon1			GGGAGCGTGCTGC	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.124G>A	3.37:g.122296638G>A	ENSP00000417214:p.Val42Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	116	68	0.586207	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	554	0.25366300366300365	125	0.2540650406504065	105	0.2900552486187845	155	0.270979020979021	169	0.22295514511873352	G	10.71	1.427298	0.25726	.	.	ENSG00000173200	ENST00000464300;ENST00000483793	T;T	0.15139	2.62;2.45	2.55	0.535	0.17133	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.999999999950489E-6	P	0.39551	0.678	B	0.20577	0.03	T	0.47799	-0.9089	7	0.52906	T	0.07	.	4.5242	0.11973	0.1537:0.229:0.6174:0.0	rs1875272;rs1875272	42	C9J7L3	.	M	42	ENSP00000417214:V42M;ENSP00000417785:V42M	ENSP00000417214:V42M	V	+	1	0	PARP15	123779328	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.711000	0.05019	0.116000	0.18110	0.561000	0.74099	GTG	G|0.744;A|0.256	0.256	strong		0.697	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
THEG	51298	hgsc.bcm.edu	37	19	373531	373531	+	Splice_Site	SNP	C	C	T	rs73489977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:373531C>T	ENST00000342640.4	-	4	546	c.504G>A	c.(502-504)tgG>tgA	p.W168*	THEG_ENST00000346878.2_Splice_Site_p.R144R	NM_016585.4	NP_057669.1	Q9P2T0	THEG_HUMAN	theg spermatid protein	168					cell differentiation (GO:0030154)|chaperone-mediated protein complex assembly (GO:0051131)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)				NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)|soft_tissue(1)	29		all_cancers(10;1.13e-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)		ACACAGAGGGCCTGGAATAAG	0.677													C|||	186	0.0371406	0.1339	0.0115	5008	,	,		15295	0.0		0.001	False		,,,				2504	0.0				p.W168X		Atlas-SNP	.											.	THEG	58	.	0			c.G504A						PASS	.	C	stop/TRP,	514,3892	229.4+/-244.0	23,468,1712	44.0	39.0	41.0		504,432	3.0	1.0	19	dbSNP_130	41	3,8597	3.0+/-9.4	0,3,4297	yes	stop-gained-near-splice,coding-synonymous-near-splice	THEG	NM_016585.3,NM_199202.1	,	23,471,6009	TT,TC,CC		0.0349,11.6659,3.9751	,	168/380,144/356	373531	517,12489	2203	4300	6503	SO:0001630	splice_region_variant	51298	exon4			AGAGGGCCTGGAA	AF268610	CCDS12025.1, CCDS12026.1	19p13.3	2012-02-24	2012-02-24		ENSG00000105549	ENSG00000105549			13706	protein-coding gene	gene with protein product	"""cancer/testis antigen 56"""	609503	"""Theg homolog (mouse)"""			11173852	Standard	NM_016585		Approved	CT56, THEG1	uc002lol.3	Q9P2T0	OTTHUMG00000165491	ENST00000342640.4:c.504-1G>A	19.37:g.373531C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	166	86	0.518072	NM_016585	A6NMJ8	Nonsense_Mutation	SNP	ENST00000342640.4	37	CCDS12025.1	61	0.027930402930402932	56	0.11382113821138211	5	0.013812154696132596	0	0.0	0	0.0	C	16.59	3.166200	0.57476	0.116659	3.49E-4	ENSG00000105549	ENST00000342640	.	.	.	3.03	3.03	0.35002	.	0.466367	0.16510	N	0.211261	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	9.7902	0.40702	0.0:1.0:0.0:0.0	.	.	.	.	X	168	.	ENSP00000340088:W168X	W	-	3	0	THEG	324531	1.000000	0.71417	0.985000	0.45067	0.153000	0.21895	3.225000	0.51246	2.008000	0.58898	0.561000	0.74099	TGG	C|0.960;T|0.040	0.040	strong		0.677	THEG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384431.2		Nonsense_Mutation
HOMEZ	57594	hgsc.bcm.edu	37	14	23744844	23744844	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23744844C>T	ENST00000357460.5	-	2	1757	c.1593G>A	c.(1591-1593)gaG>gaA	p.E531E	HOMEZ_ENST00000561013.1_Silent_p.E533E|HOMEZ_ENST00000431326.2_Silent_p.E533E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	531	Glu-rich.				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)		cctcctcctcctcttcctcat	0.493																																					p.E531E		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G1593A						PASS	.						37.0	36.0	36.0					14																	23744844		2196	4286	6482	SO:0001819	synonymous_variant	57594	exon2			CTCCTCCTCTTCC	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.1593G>A	14.37:g.23744844C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	114	7	0.0614035	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			.	.	none		0.493	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
IGSF22	283284	hgsc.bcm.edu	37	11	18729367	18729367	+	Silent	SNP	G	G	T	rs57253324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18729367G>T	ENST00000513874.1	-	20	3403	c.3264C>A	c.(3262-3264)atC>atA	p.I1088I	IGSF22_ENST00000510673.1_5'Flank|RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	693										NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CGCGCACATGGATGTCATAGC	0.532													G|||	553	0.110423	0.1778	0.1239	5008	,	,		21190	0.0615		0.0686	False		,,,				2504	0.1033				p.I1088I		Atlas-SNP	.											.	IGSF22	211	.	0			c.C3264A						PASS	.	G		237,1147		17,203,472	152.0	124.0	133.0		3264	3.0	0.0	11	dbSNP_129	133	218,2964		7,204,1380	no	coding-synonymous	IGSF22	NM_173588.3		24,407,1852	TT,TG,GG		6.851,17.1243,9.965		1088/1327	18729367	455,4111	692	1591	2283	SO:0001819	synonymous_variant	283284	exon20			CACATGGATGTCA	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.3264C>A	11.37:g.18729367G>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_173588	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																			G|0.901;T|0.099	0.099	strong		0.532	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
IDUA	3425	hgsc.bcm.edu	37	4	994452	994452	+	Silent	SNP	C	C	T	rs3755954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:994452C>T	ENST00000247933.4	+	3	440	c.352C>T	c.(352-354)Ctg>Ttg	p.L118L	IDUA_ENST00000453894.1_Silent_p.L71L|IDUA_ENST00000514224.1_5'UTR	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	118					carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGACGGGTACCTGGACCTTCT	0.672													C|||	812	0.162141	0.1626	0.2046	5008	,	,		16145	0.1478		0.2505	False		,,,				2504	0.0552				p.L118L		Atlas-SNP	.											.	IDUA	33	.	0			c.C352T						PASS	.	C		859,3543	333.3+/-302.9	105,649,1447	71.0	63.0	66.0		352	-0.7	0.6	4	dbSNP_107	66	2075,6525	358.1+/-331.0	250,1575,2475	yes	coding-synonymous	IDUA	NM_000203.3		355,2224,3922	TT,TC,CC		24.1279,19.5139,22.5658		118/654	994452	2934,10068	2201	4300	6501	SO:0001819	synonymous_variant	3425	exon3			GGGTACCTGGACC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.352C>T	4.37:g.994452C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	242	121	0.5	NM_000203	B3KWK6	Silent	SNP	ENST00000247933.4	37	CCDS3343.1																																																																																			C|0.784;T|0.216	0.216	strong		0.672	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
KL	9365	hgsc.bcm.edu	37	13	33628193	33628193	+	Missense_Mutation	SNP	G	G	C	rs9527025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33628193G>C	ENST00000380099.3	+	2	1117	c.1109G>C	c.(1108-1110)tGc>tCc	p.C370S	KL_ENST00000426690.2_Missense_Mutation_p.C63S|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	370	Glycosyl hydrolase-1 1.		C -> S (in allele KL-VS; associated with V-352; dbSNP:rs9527025). {ECO:0000269|PubMed:11792841, ECO:0000269|PubMed:15677572}.		acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TTTGCTCTTTGCTTTGGACCC	0.423													C|||	651	0.129992	0.2005	0.0821	5008	,	,		19195	0.0		0.1938	False		,,,				2504	0.137				p.C370S		Atlas-SNP	.											.	KL	106	.	0			c.G1109C	GRCh37	CM022034	KL	M	rs9527025	PASS	.	C	SER/CYS	816,3590	749.3+/-412.0	74,668,1461	176.0	181.0	180.0		1109	5.9	1.0	13	dbSNP_119	180	1411,7189	752.4+/-407.4	116,1179,3005	yes	missense	KL	NM_004795.3	112	190,1847,4466	CC,CG,GG		16.407,18.5202,17.1229	benign	370/1013	33628193	2227,10779	2203	4300	6503	SO:0001583	missense	9365	exon2			CTCTTTGCTTTGG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1109G>C	13.37:g.33628193G>C	ENSP00000369442:p.Cys370Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	114	49	0.429825	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	37	CCDS9347.1	287	0.13141025641025642	93	0.18902439024390244	41	0.1132596685082873	0	0.0	153	0.20184696569920843	C	7.622	0.677076	0.14841	0.185202	0.16407	ENSG00000133116	ENST00000426690;ENST00000380099	T;T	0.27402	1.67;1.82	5.9	5.9	0.94986	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00020	-2.78	0.43029	P	0.005404999999999993	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30534	-0.9975	9	0.23891	T	0.37	-32.9193	17.3287	0.87257	0.0:0.8748:0.1252:0.0	rs9527025;rs52797932;rs9527025	370;63	Q9UEF7;B3KUJ4	KLOT_HUMAN;.	S	63;370	ENSP00000399513:C63S;ENSP00000369442:C370S	ENSP00000369442:C370S	C	+	2	0	KL	32526193	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	5.982000	0.70532	1.527000	0.49086	-0.120000	0.15030	TGC	G|0.848;C|0.152	0.152	strong		0.423	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
IQUB	154865	hgsc.bcm.edu	37	7	123119990	123119990	+	Silent	SNP	T	T	C	rs10500091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:123119990T>C	ENST00000466202.1	-	8	1845	c.1269A>G	c.(1267-1269)caA>caG	p.Q423Q	IQUB_ENST00000434450.1_Silent_p.Q423Q|IQUB_ENST00000324698.6_Silent_p.Q423Q	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	423					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)				breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						CAGTAAAAGATTGGTTAATAC	0.378													T|||	1128	0.22524	0.0507	0.2478	5008	,	,		17942	0.3879		0.2853	False		,,,				2504	0.2157				p.Q423Q		Atlas-SNP	.											.	IQUB	117	.	0			c.A1269G						PASS	.	T		445,3961	212.5+/-232.4	22,401,1780	108.0	98.0	101.0		1269	-10.5	0.1	7	dbSNP_119	101	2325,6273	390.1+/-343.2	306,1713,2280	no	coding-synonymous	IQUB	NM_178827.4		328,2114,4060	CC,CT,TT		27.0412,10.0999,21.3011		423/792	123119990	2770,10234	2203	4299	6502	SO:0001819	synonymous_variant	154865	exon8			AAAAGATTGGTTA	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.1269A>G	7.37:g.123119990T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	165	85	0.515152	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Silent	SNP	ENST00000466202.1	37	CCDS5787.1																																																																																			T|0.782;C|0.218	0.218	strong		0.378	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
IL16	3603	hgsc.bcm.edu	37	15	81589340	81589340	+	Silent	SNP	C	C	T	rs201624502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81589340C>T	ENST00000302987.4	+	12	1974	c.1974C>T	c.(1972-1974)gcC>gcT	p.A658A	IL16_ENST00000394660.2_Silent_p.A658A|IL16_ENST00000560230.1_3'UTR|IL16_ENST00000394652.2_5'UTR			Q14005	IL16_HUMAN	interleukin 16	658					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GTGCCTCTGCCGGCTGCCCAG	0.592													C|||	6	0.00119808	0.0045	0.0	5008	,	,		18755	0.0		0.0	False		,,,				2504	0.0				p.A658A		Atlas-SNP	.											.	IL16	254	.	0			c.C1974T						PASS	.	C	,,	8,3906		0,8,1949	34.0	39.0	37.0		1974,,1974	-3.6	0.0	15		37	0,8326		0,0,4163	no	coding-synonymous,utr-5,coding-synonymous	IL16	NM_001172128.1,NM_004513.5,NM_172217.3	,,	0,8,6112	TT,TC,CC		0.0,0.2044,0.0654	,,	658/1332,,658/1333	81589340	8,12232	1957	4163	6120	SO:0001819	synonymous_variant	3603	exon13			CTCTGCCGGCTGC	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1974C>T	15.37:g.81589340C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	173	89	0.514451	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
MRS2	57380	hgsc.bcm.edu	37	6	24403377	24403377	+	Missense_Mutation	SNP	C	C	T	rs2295651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24403377C>T	ENST00000378386.3	+	1	196	c.103C>T	c.(103-105)Ccc>Tcc	p.P35S	MRS2_ENST00000274747.7_Missense_Mutation_p.P35S|MRS2_ENST00000378353.1_Missense_Mutation_p.P35S|MRS2_ENST00000535061.1_Missense_Mutation_p.P35S|MRS2_ENST00000443868.2_Missense_Mutation_p.P35S|MRS2_ENST00000543597.1_5'UTR|MRS2_ENST00000483634.1_3'UTR	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	35			P -> S (in dbSNP:rs2295651).			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						TGTGGGTCCTCCCGTTGCTGC	0.697													C|||	353	0.0704872	0.0711	0.0259	5008	,	,		16380	0.122		0.0089	False		,,,				2504	0.1115				p.P35S		Atlas-SNP	.											.	MRS2	31	.	0			c.C103T						PASS	.	C	SER/PRO	253,4153	137.3+/-173.1	10,233,1960	37.0	36.0	37.0		103	3.2	0.0	6	dbSNP_100	37	72,8526	41.7+/-99.0	0,72,4227	yes	missense	MRS2	NM_020662.2	74	10,305,6187	TT,TC,CC		0.8374,5.7422,2.4992	benign	35/444	24403377	325,12679	2203	4299	6502	SO:0001583	missense	57380	exon1			GGTCCTCCCGTTG	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.103C>T	6.37:g.24403377C>T	ENSP00000367637:p.Pro35Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Missense_Mutation	SNP	ENST00000378386.3	37	CCDS4552.1	136	0.06227106227106227	41	0.08333333333333333	13	0.03591160220994475	73	0.12762237762237763	9	0.011873350923482849	C	12.31	1.899706	0.33535	0.057422	0.008374	ENSG00000124532	ENST00000274747;ENST00000535061;ENST00000378386;ENST00000378353;ENST00000443868	T;T;T;T;T	0.45276	0.9;1.42;1.59;1.01;1.58	5.0	3.17	0.36434	.	0.795244	0.10907	N	0.621033	T	0.13286	0.0322	N	0.24115	0.695	0.46609	P	8.709999999999551E-4	B;B;B;B	0.29301	0.002;0.241;0.144;0.0	B;B;B;B	0.27500	0.002;0.08;0.037;0.002	T	0.09640	-1.0665	9	0.51188	T	0.08	-0.2459	7.8229	0.29298	0.0:0.8047:0.0:0.1953	rs2295651;rs2295651	35;35;35;35	F5GWH3;B4DQL2;Q9HD23;Q9HD23-2	.;.;MRS2_HUMAN;.	S	35	ENSP00000274747:P35S;ENSP00000441839:P35S;ENSP00000367637:P35S;ENSP00000367604:P35S;ENSP00000399585:P35S	ENSP00000274747:P35S	P	+	1	0	MRS2	24511356	0.000000	0.05858	0.002000	0.10522	0.101000	0.19017	-0.180000	0.09754	1.309000	0.44985	0.643000	0.83706	CCC	C|0.961;T|0.039	0.039	strong		0.697	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1		
OR13C5	138799	hgsc.bcm.edu	37	9	107360922	107360922	+	Missense_Mutation	SNP	A	A	G	rs1851724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107360922A>G	ENST00000374779.2	-	1	866	c.773T>C	c.(772-774)aTg>aCg	p.M258T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	258			M -> T (in dbSNP:rs1851724).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CTTCATGTACATGAGGAAGAT	0.443													A|||	3390	0.676917	0.7466	0.5937	5008	,	,		20659	0.9573		0.4235	False		,,,				2504	0.6135				p.M258T		Atlas-SNP	.											OR13C5,NS,lymphoid_neoplasm,0,1	OR13C5	60	1	0			c.T773C						PASS	.	A	THR/MET	3165,1241	706.6+/-407.4	1144,877,182	137.0	123.0	128.0		773	4.0	0.9	9	dbSNP_92	128	3648,4952	525.3+/-380.7	806,2036,1458	yes	missense	OR13C5	NM_001004482.1	81	1950,2913,1640	GG,GA,AA		42.4186,28.1661,47.6165	possibly-damaging	258/319	107360922	6813,6193	2203	4300	6503	SO:0001583	missense	138799	exon1			ATGTACATGAGGA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.773T>C	9.37:g.107360922A>G	ENSP00000363911:p.Met258Thr	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	217	141	0.64977	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	1440	0.6593406593406593	349	0.709349593495935	207	0.5718232044198895	550	0.9615384615384616	334	0.44063324538258575	A	14.53	2.562208	0.45694	0.718339	0.424186	ENSG00000255800	ENST00000374779	T	0.00164	8.64	4.03	4.03	0.46877	GPCR, rhodopsin-like superfamily (1);	0.395212	0.18447	U	0.140947	T	0.00012	0.0000	L	0.41492	1.28	0.45806	P	0.0013180000000000414	P	0.39601	0.68	P	0.45406	0.479	T	0.48536	-0.9027	9	0.51188	T	0.08	.	6.0217	0.19632	0.8838:0.0:0.1162:0.0	rs1851724;rs52797012;rs61541229;rs1851724	258	Q8NGS8	O13C5_HUMAN	T	258	ENSP00000363911:M258T	ENSP00000363911:M258T	M	-	2	0	OR13C5	106400743	0.036000	0.19791	0.947000	0.38551	0.290000	0.27261	1.107000	0.31110	1.704000	0.51252	0.347000	0.21830	ATG	A|0.421;G|0.579	0.579	strong		0.443	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
PSAP	5660	hgsc.bcm.edu	37	10	73574948	73574948	+	IGR	SNP	C	C	T	rs73277900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73574948C>T	ENST00000394936.3	-	0	2866				CDH23_ENST00000224721.6_Silent_p.N3331N|CDH23_ENST00000398788.3_Silent_p.N1086N|CDH23_ENST00000475158.1_3'UTR			P07602	SAP_HUMAN	prosaposin						blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						TCGAGCGCAACGCCCGCACAG	0.637													C|||	106	0.0211661	0.0756	0.0072	5008	,	,		17511	0.0		0.001	False		,,,				2504	0.0				p.N3326N		Atlas-SNP	.											.	CDH23	365	.	0			c.C9978T						PASS	.	C	,,,,	260,4058		7,246,1906	21.0	28.0	26.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3258,3153,669,564,9978	-0.8	1.0	10	dbSNP_130	26	3,8497		0,3,4247	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171933.1,NM_001171934.1,NM_001171935.1,NM_001171936.1,NM_022124.5	,,,,	7,249,6153	TT,TC,CC		0.0353,6.0213,2.0518	,,,,	1086/1115,1051/1080,223/252,188/217,3326/3355	73574948	263,12555	2159	4250	6409	SO:0001628	intergenic_variant	64072	exon68			GCGCAACGCCCGC	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"""Endogenous ligands"""	9498	protein-coding gene	gene with protein product	"""variant Gaucher disease and variant metachromatic leukodystrophy"""	176801	"""sphingolipid activator protein-1"""	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429		10.37:g.73574948C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_022124	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Silent	SNP	ENST00000394936.3	37	CCDS7311.1																																																																																			C|0.984;T|0.016	0.016	strong		0.637	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778	
YEATS2	55689	hgsc.bcm.edu	37	3	183432983	183432983	+	Silent	SNP	C	C	T	rs3736535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183432983C>T	ENST00000305135.5	+	2	228	c.33C>T	c.(31-33)acC>acT	p.T11T		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	11					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TCAAAGAAACCGACCCTGATT	0.348													C|||	948	0.189297	0.1377	0.3256	5008	,	,		17209	0.2937		0.1382	False		,,,				2504	0.1074				p.T11T		Atlas-SNP	.											.	YEATS2	111	.	0			c.C33T						PASS	.	C		580,3174		46,488,1343	121.0	123.0	122.0		33	-11.3	0.4	3	dbSNP_107	122	1316,6900		119,1078,2911	no	coding-synonymous	YEATS2	NM_018023.4		165,1566,4254	TT,TC,CC		16.0175,15.4502,15.8396		11/1423	183432983	1896,10074	1877	4108	5985	SO:0001819	synonymous_variant	55689	exon2			AGAAACCGACCCT	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.33C>T	3.37:g.183432983C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	176	105	0.596591	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Silent	SNP	ENST00000305135.5	37	CCDS43175.1																																																																																			C|0.804;T|0.196	0.196	strong		0.348	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
CDH16	1014	hgsc.bcm.edu	37	16	66945947	66945947	+	Missense_Mutation	SNP	C	C	T	rs61735427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:66945947C>T	ENST00000299752.4	-	13	1838	c.1645G>A	c.(1645-1647)Gcc>Acc	p.A549T	CDH16_ENST00000568632.1_Missense_Mutation_p.A452T|CDH16_ENST00000394055.3_Missense_Mutation_p.A549T|CDH16_ENST00000570262.1_Missense_Mutation_p.A469T|CDH16_ENST00000565796.1_Missense_Mutation_p.A549T	NM_001204744.1|NM_001204745.1|NM_004062.3	NP_001191673.1|NP_001191674.1|NP_004053.1	O75309	CAD16_HUMAN	cadherin 16, KSP-cadherin	549	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.A549S(1)		endometrium(1)|kidney(3)|large_intestine(10)|lung(15)|ovary(2)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		GTCACCGTGGCGGTGGCTCCA	0.632													C|||	367	0.0732827	0.1747	0.0159	5008	,	,		17094	0.0466		0.0209	False		,,,				2504	0.0583				p.A549T		Atlas-SNP	.											.	CDH16	91	.	1	Substitution - Missense(1)	kidney(1)	c.G1645A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	644,3756	275.4+/-272.5	48,548,1604	73.0	69.0	70.0		1645,1645,1354,1645	3.3	1.0	16	dbSNP_129	70	152,8448	74.2+/-136.8	1,150,4149	yes	missense,missense,missense,missense	CDH16	NM_001204744.1,NM_001204745.1,NM_001204746.1,NM_004062.3	58,58,58,58	49,698,5753	TT,TC,CC		1.7674,14.6364,6.1231	benign,benign,benign,benign	549/808,549/791,452/733,549/830	66945947	796,12204	2200	4300	6500	SO:0001583	missense	1014	exon13			CCGTGGCGGTGGC	AF016272	CCDS10823.1, CCDS56002.1, CCDS58471.1, CCDS58472.1	16q22.1	2010-01-26			ENSG00000166589	ENSG00000166589		"""Cadherins / Major cadherins"""	1755	protein-coding gene	gene with protein product		603118				9721215, 7615566	Standard	NM_004062		Approved		uc002eql.3	O75309	OTTHUMG00000137518	ENST00000299752.4:c.1645G>A	16.37:g.66945947C>T	ENSP00000299752:p.Ala549Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_004062	B4DPA8|H3BPD3|Q6UW93	Missense_Mutation	SNP	ENST00000299752.4	37	CCDS10823.1	130	0.05952380952380952	86	0.17479674796747968	8	0.022099447513812154	21	0.03671328671328671	15	0.01978891820580475	C	11.69	1.715168	0.30413	0.146364	0.017674	ENSG00000166589	ENST00000394055;ENST00000299752;ENST00000544875	T;T	0.50548	0.74;0.74	5.25	3.26	0.37387	Cadherin (4);Cadherin-like (1);	0.189569	0.44688	N	0.000424	T	0.00144	0.0004	L	0.37800	1.135	0.21290	P	0.999738213	P;P;P	0.52692	0.944;0.955;0.955	P;B;P	0.48598	0.447;0.406;0.583	T	0.04870	-1.0921	9	0.29301	T	0.29	-6.4677	8.4964	0.33130	0.0:0.8095:0.0:0.1905	.	549;549;549	O75309-2;B2R7S8;O75309	.;.;CAD16_HUMAN	T	549;549;513	ENSP00000377619:A549T;ENSP00000299752:A549T	ENSP00000299752:A549T	A	-	1	0	CDH16	65503448	0.961000	0.32948	0.994000	0.49952	0.027000	0.11550	1.892000	0.39748	1.350000	0.45770	0.462000	0.41574	GCC	C|0.942;T|0.058	0.058	strong		0.632	CDH16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268839.2	NM_004062	
POLQ	10721	hgsc.bcm.edu	37	3	121251924	121251924	+	Silent	SNP	C	C	T	rs41390550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121251924C>T	ENST00000264233.5	-	6	1001	c.873G>A	c.(871-873)ccG>ccA	p.P291P	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	291					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)		ACTCCAAAAGCGGTACAGGGC	0.428								DNA polymerases (catalytic subunits)					C|||	107	0.0213658	0.0749	0.0115	5008	,	,		17115	0.0		0.0	False		,,,				2504	0.0				p.P291P	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G873A						PASS	.	C		267,4139	152.5+/-186.2	7,253,1943	94.0	93.0	93.0		873	0.1	1.0	3	dbSNP_127	93	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	POLQ	NM_199420.3		7,257,6239	TT,TC,CC		0.0465,6.0599,2.0837		291/2591	121251924	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	10721	exon6			CAAAAGCGGTACA	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.873G>A	3.37:g.121251924C>T		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	260	117	0.45	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	37	CCDS33833.1																																																																																			C|0.982;T|0.018	0.018	strong		0.428	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
MT-CO2	4513	hgsc.bcm.edu	37	M	8027	8027	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:8027G>A	ENST00000361739.1	+	1	442	c.442G>A	c.(442-444)Gcc>Acc	p.A148T	MT-TS1_ENST00000387416.2_RNA|MT-TN_ENST00000387400.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TY_ENST00000387409.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-ND4L_ENST00000361335.1_5'Flank|MT-ATP6_ENST00000361899.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-ND3_ENST00000361227.2_5'Flank			P00403	COX2_HUMAN	mitochondrially encoded cytochrome c oxidase II	148			A -> T. {ECO:0000269|PubMed:8277847}.		cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|respiratory chain complex IV (GO:0045277)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)			endometrium(5)|kidney(8)|lung(2)|pancreas(3)|prostate(1)	19						TCCCGATTGAAGCCCCCATTC	0.468																																					p.A148T		Atlas-SNP	.											.	.	.	.	0			c.G442A						PASS	.																																			SO:0001583	missense	5743	exon1			ATTGAAGCCCCCA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198712	ENSG00000198712		"""Mitochondrial respiratory chain complex / Complex IV"""	7421	protein-coding gene	gene with protein product		516040	"""cytochrome c oxidase II"""	MTCO2		1712754, 1989603	Standard			Approved	COX2, CO2		P00403		ENST00000361739.1:c.442G>A	M.37:g.8027G>A	ENSP00000354876:p.Ala148Thr	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	14	13	0.928571	ENST00000361739	Q37526	Missense_Mutation	SNP	ENST00000361739.1	37																																																																																				.	.	none		0.468	MT-CO2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024029	
FAM188B	84182	hgsc.bcm.edu	37	7	30915263	30915263	+	Missense_Mutation	SNP	A	A	G	rs10216063|rs386711774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30915263A>G	ENST00000265299.6	+	15	2040	c.1963A>G	c.(1963-1965)Atg>Gtg	p.M655V	INMT-FAM188B_ENST00000458257.1_3'UTR|AQP1_ENST00000509504.1_Missense_Mutation_p.M118V|AQP1_ENST00000434909.2_Start_Codon_SNP_p.M1V	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	655			M -> V (in dbSNP:rs10216063).							endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GCATTACAACATGTGCCAGGT	0.512													G|||	2302	0.459665	0.8775	0.1816	5008	,	,		21485	0.4157		0.162	False		,,,				2504	0.4438				p.M655V		Atlas-SNP	.											.	FAM188B	62	.	0			c.A1963G						PASS	.	G	VAL/MET	2708,1348		1046,616,366	164.0	167.0	166.0		1963	5.7	0.8	7	dbSNP_119	166	1184,7228		125,934,3147	yes	missense	FAM188B	NM_032222.2	21	1171,1550,3513	GG,GA,AA		14.0751,33.2347,31.2159	benign	655/758	30915263	3892,8576	2028	4206	6234	SO:0001583	missense	84182	exon15			TACAACATGTGCC	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.1963A>G	7.37:g.30915263A>G	ENSP00000265299:p.Met655Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_032222	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	37	CCDS43565.1	721	0.3301282051282051	346	0.7032520325203252	71	0.19613259668508287	199	0.3479020979020979	105	0.13852242744063326	G	4.533	0.098978	0.08681	0.667653	0.140751	ENSG00000106125;ENSG00000106125;ENSG00000240583;ENSG00000250424	ENST00000265299;ENST00000409881;ENST00000434909;ENST00000509504	T;D;T	0.86297	1.68;-2.1;1.68	5.67	5.67	0.87782	.	0.126950	0.53938	N	0.000052	T	0.00012	0.0000	N	0.00246	-1.78	0.09310	P	1.0	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.48547	-0.9026	9	0.87932	D	0	-8.7791	12.7176	0.57123	0.0796:0.0:0.9204:0.0	rs10216063;rs59668602;rs10216063	1;175;655	B4E220;B8ZZX1;Q4G0A6	.;.;F188B_HUMAN	V	655;175;1;118	ENSP00000265299:M655V;ENSP00000395059:M1V;ENSP00000421315:M118V	ENSP00000265299:M655V	M	+	1	0	RP5-877J2.1;FAM188B;AQP1	30881788	1.000000	0.71417	0.791000	0.31998	0.852000	0.48524	4.590000	0.61013	1.434000	0.47414	-0.128000	0.14901	ATG	A|0.726;G|0.274	0.274	strong		0.512	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
C7orf72	100130988	hgsc.bcm.edu	37	7	50173702	50173702	+	Splice_Site	SNP	A	A	G	rs78990563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:50173702A>G	ENST00000297001.6	+	4	778		c.e4-1			NM_001161834.2	NP_001155306	A4D263	CG072_HUMAN	chromosome 7 open reading frame 72											NS(1)|breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|prostate(2)	9						ATAACTTCATAGAGCTTATGA	0.348													A|||	11	0.00219649	0.0083	0.0	5008	,	,		19208	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	C7orf72	26	.	0			c.729-2A>G						PASS	.						60.0	52.0	55.0					7																	50173702		692	1591	2283	SO:0001630	splice_region_variant	100130988	exon4			CTTCATAGAGCTT		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.729-1A>G	7.37:g.50173702A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_001161834	A6NDX9	Splice_Site	SNP	ENST00000297001.6	37	CCDS47585.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	A	16.77	3.215312	0.58452	.	.	ENSG00000164500	ENST00000297001	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7596	0.57356	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C7orf72	50144248	1.000000	0.71417	0.974000	0.42286	0.738000	0.42128	4.739000	0.62080	2.254000	0.74563	0.528000	0.53228	.	A|0.997;G|0.003	0.003	strong		0.348	C7orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342124.1	NM_001161834	Intron
TUBGCP2	10844	hgsc.bcm.edu	37	10	135106718	135106718	+	Silent	SNP	G	G	A	rs3008344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135106718G>A	ENST00000252936.3	-	6	888	c.849C>T	c.(847-849)ttC>ttT	p.F283F	RP11-122K13.12_ENST00000424450.1_RNA|TUBGCP2_ENST00000417178.2_Silent_p.F153F|TUBGCP2_ENST00000368563.2_Silent_p.F283F|TUBGCP2_ENST00000368562.1_5'Flank|TUBGCP2_ENST00000543663.1_Silent_p.F311F			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	283					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		GCCCGTACTCGAAGGAAGACT	0.547													G|||	16	0.00319489	0.0106	0.0014	5008	,	,		20270	0.0		0.001	False		,,,				2504	0.0				p.F311F		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.C933T						PASS	.	G		48,4358	50.2+/-85.5	0,48,2155	60.0	58.0	59.0		849	-6.7	0.8	10	dbSNP_101	59	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	TUBGCP2	NM_006659.2		0,51,6452	AA,AG,GG		0.0349,1.0894,0.3921		283/903	135106718	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	10844	exon8			GTACTCGAAGGAA	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.849C>T	10.37:g.135106718G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	37	CCDS7676.1																																																																																			G|0.996;A|0.004	0.004	strong		0.547	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1		
HECTD4	283450	hgsc.bcm.edu	37	12	112667675	112667675	+	Silent	SNP	T	T	G	rs1005902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:112667675T>G	ENST00000430131.2	-	40	6225	c.5080A>C	c.(5080-5082)Aga>Cga	p.R1694R	HECTD4_ENST00000550722.1_Silent_p.R1970R|HECTD4_ENST00000377560.5_Silent_p.R1944R			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1694					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)										ATCAGTGCTCTAGACAGAACC	0.453													G|||	3146	0.628195	0.8502	0.4078	5008	,	,		21588	0.8899		0.2614	False		,,,				2504	0.592				p.R1982R		Atlas-SNP	.											.	.	.	.	0			c.A5944C						PASS	.	G		2895,969		1091,713,128	59.0	56.0	57.0		5830	6.0	1.0	12	dbSNP_86	57	2213,6039		280,1653,2193	yes	coding-synonymous	C12orf51	NM_001109662.2		1371,2366,2321	GG,GT,TT		26.8177,25.0776,42.1591		1944/4247	112667675	5108,7008	1932	4126	6058	SO:0001819	synonymous_variant	283450	exon41			GTGCTCTAGACAG	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.5080A>C	12.37:g.112667675T>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																				T|0.381;G|0.619	0.619	strong		0.453	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
SLC41A1	254428	hgsc.bcm.edu	37	1	205767885	205767885	+	Silent	SNP	G	G	A	rs708727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:205767885G>A	ENST00000367137.3	-	6	1770	c.756C>T	c.(754-756)aaC>aaT	p.N252N	SLC41A1_ENST00000468057.1_5'UTR	NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	252					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	17	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			GTGTGGCCACGTTGTCTGGGT	0.577													G|||	708	0.141374	0.0227	0.2291	5008	,	,		18060	0.003		0.3966	False		,,,				2504	0.1196				p.N252N		Atlas-SNP	.											SLC41A1,colon,carcinoma,0,1	SLC41A1	46	1	0			c.C756T						PASS	.	G		368,4038	187.4+/-214.1	24,320,1859	103.0	96.0	99.0		756	-2.1	1.0	1	dbSNP_86	99	3492,5108	511.3+/-377.7	710,2072,1518	no	coding-synonymous	SLC41A1	NM_173854.4		734,2392,3377	AA,AG,GG		40.6047,8.3522,29.6786		252/514	205767885	3860,9146	2203	4300	6503	SO:0001819	synonymous_variant	254428	exon6			GGCCACGTTGTCT	AJ514402	CCDS30988.1	1q32.1	2013-07-17	2013-07-17		ENSG00000133065	ENSG00000133065		"""Solute carriers"""	19429	protein-coding gene	gene with protein product		610801				12810078, 18367447	Standard	NM_173854		Approved	MgtE	uc001hdh.1	Q8IVJ1	OTTHUMG00000036000	ENST00000367137.3:c.756C>T	1.37:g.205767885G>A		Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	318	158	0.496855	NM_173854	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Silent	SNP	ENST00000367137.3	37	CCDS30988.1																																																																																			G|0.751;A|0.249	0.249	strong		0.577	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1		
TTN	7273	hgsc.bcm.edu	37	2	179571448	179571448	+	Missense_Mutation	SNP	A	A	G	rs4893852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.I8474T|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron			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	105	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	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	
CRAMP1L	57585	hgsc.bcm.edu	37	16	1664931	1664931	+	Silent	SNP	T	T	C	rs11539468|rs7201813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1664931T>C	ENST00000397412.3	+	2	390	c.291T>C	c.(289-291)gaT>gaC	p.D97D	IFT140_ENST00000426508.2_5'Flank|CRAMP1L_ENST00000436138.3_Silent_p.D97D|CRAMP1L_ENST00000293925.5_Silent_p.D97D			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	97						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						CCAGGAAGGATCCTCCGAGCG	0.761													C|||	3511	0.701078	0.9092	0.6383	5008	,	,		9970	0.7371		0.4016	False		,,,				2504	0.7352				p.D97D		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.T291C						PASS	.						5.0	9.0	8.0					16																	1664931		639	1533	2172	SO:0001819	synonymous_variant	57585	exon1			GAAGGATCCTCCG	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.291T>C	16.37:g.1664931T>C		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Silent	SNP	ENST00000397412.3	37	CCDS10440.2																																																																																			T|0.365;C|0.635	0.635	strong		0.761	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		
POLRMT	5442	hgsc.bcm.edu	37	19	622834	622834	+	Missense_Mutation	SNP	C	C	G	rs146178977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:622834C>G	ENST00000588649.2	-	7	1526	c.1442G>C	c.(1441-1443)cGg>cCg	p.R481P	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	481					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)		CAGGAGCATCCGCACCACCTC	0.716													c|||	17	0.00339457	0.0129	0.0	5008	,	,		14871	0.0		0.0	False		,,,				2504	0.0				p.R481P		Atlas-SNP	.											.	POLRMT	91	.	0			c.G1442C						PASS	.	C	PRO/ARG	33,4365		0,33,2166	23.0	22.0	22.0		1442	-8.0	0.0	19	dbSNP_134	22	0,8598		0,0,4299	no	missense	POLRMT	NM_005035.3	103	0,33,6465	GG,GC,CC		0.0,0.7503,0.2539	benign	481/1231	622834	33,12963	2199	4299	6498	SO:0001583	missense	5442	exon7			AGCATCCGCACCA		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.1442G>C	19.37:g.622834C>G	ENSP00000465759:p.Arg481Pro	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	36	0.642857	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	10.38	1.332902	0.24167	0.007503	0.0	ENSG00000099821	ENST00000215591	T	0.41758	0.99	4.01	-8.03	0.01114	.	0.937015	0.08876	N	0.880708	T	0.17577	0.0422	N	0.08118	0	0.09310	N	1	B	0.27594	0.182	B	0.32724	0.151	T	0.32295	-0.9912	10	0.30854	T	0.27	-0.4611	17.4545	0.87603	0.0:0.1116:0.0:0.8884	.	481	O00411	RPOM_HUMAN	P	481	ENSP00000215591:R481P	ENSP00000215591:R481P	R	-	2	0	POLRMT	573834	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.305000	0.08188	-2.543000	0.00484	-2.079000	0.00380	CGG	C|0.997;G|0.003	0.003	strong		0.716	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
PTPRF	5792	hgsc.bcm.edu	37	1	44058265	44058265	+	Silent	SNP	C	C	A	rs3828151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44058265C>A	ENST00000359947.4	+	11	2146	c.1806C>A	c.(1804-1806)gcC>gcA	p.A602A	PTPRF_ENST00000438120.1_Silent_p.A602A|PTPRF_ENST00000372414.3_Silent_p.A602A|PTPRF_ENST00000422171.2_Silent_p.A61A|PTPRF_ENST00000372413.3_Silent_p.A602A	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	602	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)				CCCGCACAGCCCAGTCCAGTA	0.612													A|||	2236	0.446486	0.4561	0.317	5008	,	,		16880	0.5585		0.3966	False		,,,				2504	0.4611				p.A602A		Atlas-SNP	.											.	PTPRF	172	.	0			c.C1806A						PASS	.	A	,	2013,2393	614.4+/-392.4	468,1077,658	76.0	64.0	68.0		1806,1806	1.9	1.0	1	dbSNP_107	68	3472,5128	635.2+/-398.9	704,2064,1532	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	1172,3141,2190	AA,AC,CC		40.3721,45.6877,42.1728	,	602/1908,602/1899	44058265	5485,7521	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon11			CACAGCCCAGTCC	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.1806C>A	1.37:g.44058265C>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	913|913	0.41804029304029305|0.41804029304029305	197|197	0.40040650406504064|0.40040650406504064	122|122	0.3370165745856354|0.3370165745856354	290|290	0.506993006993007|0.506993006993007	304|304	0.40105540897097625|0.40105540897097625	A|A	9.385|9.385	1.073889|1.073889	0.20147|0.20147	0.456877|0.456877	0.403721|0.403721	ENSG00000142949|ENSG00000142949	ENST00000429895|ENST00000412568;ENST00000414879	.|.	.|.	.|.	4.49|4.49	1.93|1.93	0.25924|0.25924	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49283|0.49283	-0.8956|-0.8956	3|3	.|.	.|.	.|.	.|.	8.3188|8.3188	0.32117|0.32117	0.5905:0.3314:0.0781:0.0|0.5905:0.3314:0.0781:0.0	rs3828151;rs17849099;rs3828151|rs3828151;rs17849099;rs3828151	.|.	.|.	.|.	H|T	259|270;127	.|.	.|.	P|P	+|+	2|1	0|0	PTPRF|PTPRF	43830852|43830852	0.005000|0.005000	0.15991|0.15991	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	-1.256000|-1.256000	0.02869|0.02869	0.311000|0.311000	0.23014|0.23014	-0.363000|-0.363000	0.07495|0.07495	CCC|CCA	C|0.581;A|0.419	0.419	strong		0.612	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
HIST1H2AL	8332	hgsc.bcm.edu	37	6	27833342	27833342	+	Silent	SNP	C	C	T	rs11966705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27833342C>T	ENST00000357320.2	+	1	309	c.210C>T	c.(208-210)gcC>gcT	p.A70A		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	70						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						CGGGCAACGCCGCCCGCGACA	0.657													C|||	123	0.0245607	0.0703	0.0144	5008	,	,		15159	0.005		0.0119	False		,,,				2504	0.0031				p.A70A		Atlas-SNP	.											.	HIST1H2AL	14	.	0			c.C210T						PASS	.	C		329,4077		11,307,1885	78.0	83.0	81.0		210	1.8	1.0	6	dbSNP_120	81	48,8552		0,48,4252	no	coding-synonymous	HIST1H2AL	NM_003511.2		11,355,6137	TT,TC,CC		0.5581,7.4671,2.8987		70/131	27833342	377,12629	2203	4300	6503	SO:0001819	synonymous_variant	8332	exon1			CAACGCCGCCCGC	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.210C>T	6.37:g.27833342C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	248	122	0.491935	NM_003511	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000357320.2	37	CCDS4634.1																																																																																			C|0.975;T|0.025	0.025	strong		0.657	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511	
CDC37L1	55664	hgsc.bcm.edu	37	9	4685008	4685008	+	Silent	SNP	C	C	T	rs2295967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:4685008C>T	ENST00000381854.3	+	2	466	c.264C>T	c.(262-264)tcC>tcT	p.S88S	CDC37L1_ENST00000479095.1_3'UTR|CDC37L1_ENST00000381858.1_Silent_p.S88S	NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	88	Self-association.					cytoplasm (GO:0005737)				breast(1)|kidney(1)|lung(2)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		ATTCTGAGTCCTTGGATCAGG	0.453													C|||	899	0.179513	0.0333	0.111	5008	,	,		19935	0.376		0.0865	False		,,,				2504	0.319				p.S88S		Atlas-SNP	.											.	CDC37L1	19	.	0			c.C264T						PASS	.	C		216,4190	133.3+/-169.7	6,204,1993	143.0	137.0	139.0		264	5.7	1.0	9	dbSNP_100	139	784,7816	185.0+/-232.9	35,714,3551	no	coding-synonymous	CDC37L1	NM_017913.2		41,918,5544	TT,TC,CC		9.1163,4.9024,7.6888		88/338	4685008	1000,12006	2203	4300	6503	SO:0001819	synonymous_variant	55664	exon2			TGAGTCCTTGGAT	AK000497	CCDS6454.1	9p24.1	2013-01-17	2013-01-17		ENSG00000106993	ENSG00000106993			17179	protein-coding gene	gene with protein product		610346	"""CDC37 cell division cycle 37 homolog (S. cerevisiae)-like 1"", ""cell division cycle 37 homolog (S. cerevisiae)-like 1"""				Standard	NM_017913		Approved	HARC, FLJ20639, CDC37B	uc003zio.3	Q7L3B6	OTTHUMG00000019465	ENST00000381854.3:c.264C>T	9.37:g.4685008C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	137	73	0.532847	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	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609097	32609097	+	Silent	SNP	T	T	C	rs553033826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	160	160	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	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	
SBNO2	22904	hgsc.bcm.edu	37	19	1122147	1122147	+	Silent	SNP	G	G	A	rs2072280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1122147G>A	ENST00000361757.3	-	11	1377	c.1140C>T	c.(1138-1140)ttC>ttT	p.F380F	SBNO2_ENST00000438103.2_Silent_p.F323F|SBNO2_ENST00000587024.1_Silent_p.F380F	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	83	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	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	
SLC26A4	5172	hgsc.bcm.edu	37	7	107342294	107342294	+	Missense_Mutation	SNP	T	T	G	rs17154335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107342294T>G	ENST00000265715.3	+	17	2050	c.1826T>G	c.(1825-1827)gTt>gGt	p.V609G	SLC26A4_ENST00000544569.1_Missense_Mutation_p.V196G|SLC26A4_ENST00000543100.1_Missense_Mutation_p.V178G|SLC26A4_ENST00000541474.1_Missense_Mutation_p.V170G|SLC26A4_ENST00000480841.1_3'UTR	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	609	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.		V -> G (in dbSNP:rs17154335). {ECO:0000269|PubMed:15689455, ECO:0000269|PubMed:19204907}.		chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	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)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						AGTGATGCTGTTTCAACAAAT	0.343									Pendred syndrome				G|||	229	0.0457268	0.1657	0.0115	5008	,	,		21715	0.0		0.002	False		,,,				2504	0.0				p.V609G		Atlas-SNP	.											.	SLC26A4	117	.	0			c.T1826G	GRCh37	CM050323	SLC26A4	M	rs17154335	PASS	.	G	GLY/VAL	629,3777	767.8+/-413.5	43,543,1617	97.0	96.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1826	5.8	0.9	7	dbSNP_123	96	7,8593	818.9+/-406.8	0,7,4293	yes	missense	SLC26A4	NM_000441.1	109	43,550,5910	GG,GT,TT		0.0814,14.276,4.8901	benign	609/781	107342294	636,12370	2203	4300	6503	SO:0001583	missense	5172	exon17	Familial Cancer Database	Goiter-Deafness syndrome	ATGCTGTTTCAAC	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"""Solute carriers"""	8818	protein-coding gene	gene with protein product	"""pendrin"""	605646	"""solute carrier family 26, member 4"""	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.1826T>G	7.37:g.107342294T>G	ENSP00000265715:p.Val609Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_000441	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	37	CCDS5746.1	78	0.03571428571428571	71	0.1443089430894309	7	0.019337016574585635	0	0.0	0	0.0	G	14.16	2.453089	0.43531	0.14276	8.14E-4	ENSG00000091137	ENST00000265715;ENST00000541474;ENST00000544569;ENST00000543100	D;D;D;D	0.94793	-3.2;-3.47;-3.52;-3.51	5.83	5.83	0.93111	Sulphate transporter/antisigma-factor antagonist STAS (3);	0.120219	0.56097	N	0.000035	T	0.02304	0.0071	N	0.00237	-1.79	0.30149	P	0.80322	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.57493	-0.7802	9	0.20046	T	0.44	.	16.5365	0.84373	0.0:0.0:0.8681:0.1319	rs17154335;rs17154335	170;196;609	F5H104;B7Z6M6;O43511	.;.;S26A4_HUMAN	G	609;170;196;178	ENSP00000265715:V609G;ENSP00000439743:V170G;ENSP00000437427:V196G;ENSP00000441209:V178G	ENSP00000265715:V609G	V	+	2	0	SLC26A4	107129530	1.000000	0.71417	0.889000	0.34880	0.977000	0.68977	3.712000	0.54875	1.478000	0.48253	-0.121000	0.15023	GTT	T|0.952;G|0.048	0.048	strong		0.343	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441	
CELSR3	1951	hgsc.bcm.edu	37	3	48699134	48699134	+	Silent	SNP	G	G	T	rs76423828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48699134G>T	ENST00000164024.4	-	1	1214	c.934C>A	c.(934-936)Cgg>Agg	p.R312R	RP11-148G20.1_ENST00000421275.1_RNA|CELSR3_ENST00000544264.1_Silent_p.R312R	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	312					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AAGCGTGCCCGGTTCGCCGAG	0.701													G|||	29	0.00579073	0.0212	0.0014	5008	,	,		14032	0.0		0.0	False		,,,				2504	0.0				p.R312R		Atlas-SNP	.											.	CELSR3	237	.	0			c.C934A						PASS	.	G		51,4315		0,51,2132	39.0	43.0	42.0		934	1.4	0.0	3	dbSNP_131	42	1,8499		0,1,4249	no	coding-synonymous	CELSR3	NM_001407.2		0,52,6381	TT,TG,GG		0.0118,1.1681,0.4042		312/3313	48699134	52,12814	2183	4250	6433	SO:0001819	synonymous_variant	1951	exon1			GTGCCCGGTTCGC	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.934C>A	3.37:g.48699134G>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_001407	O75092	Silent	SNP	ENST00000164024.4	37	CCDS2775.1																																																																																			G|0.995;T|0.005	0.005	strong		0.701	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
ARHGAP26	23092	hgsc.bcm.edu	37	5	142254679	142254679	+	Silent	SNP	A	A	G	rs185200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:142254679A>G	ENST00000274498.4	+	3	633	c.255A>G	c.(253-255)agA>agG	p.R85R	ARHGAP26_ENST00000378004.3_Silent_p.R85R	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	85					actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCCAGCAAGATCTTTGCAGG	0.483													G|||	3374	0.673722	0.8979	0.5058	5008	,	,		19158	0.8581		0.3091	False		,,,				2504	0.6748				p.R85R		Atlas-SNP	.											.	ARHGAP26	57	.	0			c.A255G						PASS	.	G	,	3440,966	362.4+/-316.1	1350,740,113	114.0	103.0	107.0		255,255	2.6	1.0	5	dbSNP_79	107	2569,6031	690.7+/-404.5	378,1813,2109	no	coding-synonymous,coding-synonymous	ARHGAP26	NM_001135608.1,NM_015071.4	,	1728,2553,2222	GG,GA,AA		29.8721,21.9246,46.2018	,	85/760,85/815	142254679	6009,6997	2203	4300	6503	SO:0001819	synonymous_variant	23092	exon3			AGCAAGATCTTTG	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"""Rho GTPase activating proteins"""	17073	protein-coding gene	gene with protein product	"""GTPase regulator associated with the focal adhesion kinase pp125"""	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.255A>G	5.37:g.142254679A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	132	55	0.416667	NM_015071	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Silent	SNP	ENST00000274498.4	37	CCDS4277.1																																																																																			A|0.466;G|0.534	0.534	strong		0.483	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071	
CCDC101	112869	hgsc.bcm.edu	37	16	28602991	28602991	+	Silent	SNP	A	A	G	rs11401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:28602991A>G	ENST00000317058.3	+	10	1033	c.846A>G	c.(844-846)agA>agG	p.R282R		NM_138414.2	NP_612423.1	Q96ES7	SGF29_HUMAN	coiled-coil domain containing 101	282	SGF29 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00851}.				chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|histone H3 acetylation (GO:0043966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|SAGA-type complex (GO:0070461)	methylated histone binding (GO:0035064)			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)	10						TGGCTCAGAGATACGTGGTGG	0.582													.|||	872	0.174121	0.1619	0.2017	5008	,	,		19643	0.2212		0.1571	False		,,,				2504	0.1401				p.R282R		Atlas-SNP	.											.	CCDC101	24	.	0			c.A846G						PASS	.	G		746,3648		59,628,1510	131.0	115.0	121.0		846	2.8	1.0	16	dbSNP_52	121	1497,7103		126,1245,2929	no	coding-synonymous	CCDC101	NM_138414.2		185,1873,4439	GG,GA,AA		17.407,16.9777,17.2618		282/294	28602991	2243,10751	2197	4300	6497	SO:0001819	synonymous_variant	112869	exon10			TCAGAGATACGTG	AK057008	CCDS10635.1	16p11.2	2010-08-03			ENSG00000176476	ENSG00000176476			25156	protein-coding gene	gene with protein product	"""SAGA-associated factor 29 homolog (yeast)"""	613374				17334388	Standard	NM_138414		Approved	FLJ32446, SGF29	uc002dqf.3	Q96ES7	OTTHUMG00000131763	ENST00000317058.3:c.846A>G	16.37:g.28602991A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	NM_138414	Q96MF5	Silent	SNP	ENST00000317058.3	37	CCDS10635.1																																																																																			A|0.832;G|0.168	0.168	strong		0.582	CCDC101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254691.1	NM_138414	
ZNF404	342908	hgsc.bcm.edu	37	19	44378009	44378009	+	Silent	SNP	A	A	C	rs74424854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44378009A>C	ENST00000587539.1	-	3	356	c.357T>G	c.(355-357)ccT>ccG	p.P119P	ZNF404_ENST00000324394.6_Silent_p.P117P	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	119					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)				TCTTATGTAGAGGAAGGGATT	0.353													A|||	394	0.0786741	0.2753	0.0418	5008	,	,		17922	0.0		0.001	False		,,,				2504	0.0				p.P116P		Atlas-SNP	.											ZNF404,NS,carcinoma,-1,1	ZNF404	46	1	0			c.T348G						PASS	.	A		841,2813		107,627,1093	129.0	142.0	138.0		357	-0.6	0.0	19	dbSNP_132	138	12,8172		0,12,4080	no	coding-synonymous	ZNF404	NM_001033719.2		107,639,5173	CC,CA,AA		0.1466,23.0159,7.2056		119/553	44378009	853,10985	1827	4092	5919	SO:0001819	synonymous_variant	342908	exon2			ATGTAGAGGAAGG	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.357T>G	19.37:g.44378009A>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	115	36	0.313043	NM_001033719	A4FU30|K7ELF2	Silent	SNP	ENST00000587539.1	37	CCDS59394.1																																																																																			A|0.939;C|0.061	0.061	strong		0.353	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719	
LILRA2	11027	hgsc.bcm.edu	37	19	55087313	55087313	+	Missense_Mutation	SNP	T	T	G	rs7249811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55087313T>G	ENST00000251377.3	+	7	1125	c.992T>G	c.(991-993)gTc>gGc	p.V331G	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA2_ENST00000391738.3_Missense_Mutation_p.V331G|LILRA2_ENST00000391737.1_Missense_Mutation_p.V319G|LILRA2_ENST00000251376.3_Missense_Mutation_p.V331G|LILRB1_ENST00000418536.2_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	331	Ig-like C2-type 4.		V -> G (in dbSNP:rs7249811).		defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		GTGCAGCCGGTCCCCACAGTA	0.602													N|||	632	0.126198	0.2421	0.0879	5008	,	,		15959	0.0079		0.0934	False		,,,				2504	0.1524				p.V331G		Atlas-SNP	.											.	LILRA2	99	.	0			c.T992G						PASS	.	G	GLY/VAL,GLY/VAL	945,3461	734.6+/-410.6	100,745,1358	60.0	54.0	56.0		992,992	1.1	0.0	19	dbSNP_116	56	883,7717	778.8+/-407.7	46,791,3463	yes	missense,missense	LILRA2	NM_001130917.1,NM_006866.2	109,109	146,1536,4821	GG,GT,TT		10.2674,21.448,14.0551	,	331/484,331/467	55087313	1828,11178	2203	4300	6503	SO:0001583	missense	11027	exon6			AGCCGGTCCCCAC	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.992T>G	19.37:g.55087313T>G	ENSP00000251377:p.Val331Gly	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	184	102	0.554348	NM_001130917	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	224	0.10256410256410256	122	0.24796747967479674	35	0.09668508287292818	1	0.0017482517482517483	66	0.0870712401055409	G	0.007	-2.005715	0.00426	0.21448	0.102674	ENSG00000239998	ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T	0.00651	5.97;5.97;5.97;5.97	2.19	1.08	0.20341	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.944611	0.08659	N	0.912726	T	0.00012	0.0000	N	0.00016	-2.865	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	0.34675	-0.9819	8	.	.	.	.	4.5973	0.12336	0.0:0.2474:0.4991:0.2535	rs7249811;rs16985580;rs52813341;rs7249811	319;331;331	A8MZH0;Q8N149;Q8N149-2	.;LIRA2_HUMAN;.	G	331;331;331;319	ENSP00000251377:V331G;ENSP00000375618:V331G;ENSP00000251376:V331G;ENSP00000375617:V319G	.	V	+	2	0	LILRA2	59779125	0.012000	0.17670	0.001000	0.08648	0.015000	0.08874	0.672000	0.25187	0.032000	0.15435	-0.292000	0.09595	GTC	T|0.876;G|0.124	0.124	strong		0.602	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2		
GPR151	134391	hgsc.bcm.edu	37	5	145894896	145894896	+	Missense_Mutation	SNP	G	G	C	rs7709485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:145894896G>C	ENST00000311104.2	-	1	857	c.781C>G	c.(781-783)Ctc>Gtc	p.L261V		NM_194251.2	NP_919227.2	Q8TDV0	GP151_HUMAN	G protein-coupled receptor 151	261			L -> V (in dbSNP:rs7709485).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(2)	14			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGCCACAAGAGAGCAGAGATG	0.502													G|||	1713	0.342053	0.2519	0.183	5008	,	,		19667	0.7669		0.1958	False		,,,				2504	0.2894				p.L261V	Pancreas(78;420 1386 18535 37114 49710)	Atlas-SNP	.											.	GPR151	35	.	0			c.C781G						PASS	.	G	VAL/LEU	1027,3379	378.5+/-322.9	120,787,1296	59.0	61.0	61.0		781	-1.6	0.0	5	dbSNP_116	61	1726,6874	314.9+/-312.0	172,1382,2746	yes	missense	GPR151	NM_194251.2	32	292,2169,4042	CC,CG,GG		20.0698,23.3091,21.1672	benign	261/420	145894896	2753,10253	2203	4300	6503	SO:0001583	missense	134391	exon1			ACAAGAGAGCAGA	AY255557	CCDS34266.1	5q32	2012-08-21						"""GPCR / Class A : Orphans"""	23624	protein-coding gene	gene with protein product	"""galanin receptor 4"""					12679517	Standard	NM_194251		Approved	PGR7, GALR4	uc003lod.1	Q8TDV0		ENST00000311104.2:c.781C>G	5.37:g.145894896G>C	ENSP00000308733:p.Leu261Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_194251	Q86SN8|Q8NGV2	Missense_Mutation	SNP	ENST00000311104.2	37	CCDS34266.1	792	0.3626373626373626	114	0.23170731707317074	79	0.21823204419889503	457	0.798951048951049	142	0.18733509234828497	G	0.255	-1.003594	0.02128	0.233091	0.200698	ENSG00000173250	ENST00000311104	T	0.37584	1.19	5.91	-1.58	0.08479	GPCR, rhodopsin-like superfamily (1);	0.302038	0.34110	N	0.004255	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.09022	0.002	B	0.14578	0.011	T	0.33033	-0.9884	9	0.13853	T	0.58	.	9.1674	0.37060	0.0:0.4239:0.2966:0.2795	rs7709485;rs17506353;rs52809074;rs58222574;rs7709485	261	Q8TDV0	GP151_HUMAN	V	261	ENSP00000308733:L261V	ENSP00000308733:L261V	L	-	1	0	GPR151	145875089	0.004000	0.15560	0.002000	0.10522	0.022000	0.10575	-0.025000	0.12413	-0.538000	0.06281	-0.175000	0.13238	CTC	G|0.723;C|0.277	0.277	strong		0.502	GPR151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373457.1	NM_194251	
RPP40	10799	hgsc.bcm.edu	37	6	4996543	4996543	+	Missense_Mutation	SNP	C	C	T	rs62385118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4996543C>T	ENST00000380051.2	-	6	715	c.671G>A	c.(670-672)aGc>aAc	p.S224N	RPP40_ENST00000464646.1_Missense_Mutation_p.S164N|RPP40_ENST00000319533.5_Missense_Mutation_p.S201N	NM_006638.2	NP_006629.2	O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	224					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			NS(1)|breast(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	14	Ovarian(93;0.11)	all_hematologic(90;0.0895)				CAGCTCGCTGCTCTGCAGCAC	0.542													C|||	233	0.0465256	0.0673	0.036	5008	,	,		18498	0.0387		0.0278	False		,,,				2504	0.0532				p.S224N		Atlas-SNP	.											.	RPP40	36	.	0			c.G671A						PASS	.	C	ASN/SER	284,4122	157.8+/-190.6	6,272,1925	74.0	73.0	73.0		671	4.4	0.9	6	dbSNP_129	73	293,8307	108.2+/-168.9	5,283,4012	yes	missense	RPP40	NM_006638.2	46	11,555,5937	TT,TC,CC		3.407,6.4458,4.4364	probably-damaging	224/364	4996543	577,12429	2203	4300	6503	SO:0001583	missense	10799	exon6			TCGCTGCTCTGCA	U94317	CCDS34333.1, CCDS69040.1, CCDS75391.1	6p25.1	2012-05-21	2007-06-26	2004-03-19	ENSG00000124787	ENSG00000124787			20992	protein-coding gene	gene with protein product		606117	"""ribonuclease P1"", ""ribonuclease P 40kDa subunit"""	RNASEP1		9630247	Standard	NM_006638		Approved	bA428J1.3	uc003mwl.3	O75818	OTTHUMG00000014168	ENST00000380051.2:c.671G>A	6.37:g.4996543C>T	ENSP00000369391:p.Ser224Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_006638	Q5VX97|Q8WVK8	Missense_Mutation	SNP	ENST00000380051.2	37	CCDS34333.1	81	0.03708791208791209	21	0.042682926829268296	16	0.04419889502762431	23	0.04020979020979021	21	0.027704485488126648	C	10.66	1.412049	0.25465	0.064458	0.03407	ENSG00000124787	ENST00000380051;ENST00000319533;ENST00000464646	T;T;T	0.43688	0.94;0.94;0.94	5.33	4.45	0.53987	.	0.088244	0.85682	D	0.000000	T	0.28333	0.0700	M	0.80028	2.48	0.41127	D	0.985859	B;B	0.22746	0.016;0.074	B;B	0.21360	0.016;0.034	T	0.22208	-1.0223	10	0.17369	T	0.5	-17.1227	14.3979	0.67022	0.1489:0.8511:0.0:0.0	rs62385118	201;224	O75818-2;O75818	.;RPP40_HUMAN	N	224;201;164	ENSP00000369391:S224N;ENSP00000317998:S201N;ENSP00000419431:S164N	ENSP00000317998:S201N	S	-	2	0	RPP40	4941542	0.954000	0.32549	0.900000	0.35374	0.020000	0.10135	2.169000	0.42434	1.223000	0.43536	-0.188000	0.12872	AGC	C|0.956;T|0.044	0.044	strong		0.542	RPP40-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039733.2	NM_006638	
OR4K13	390433	hgsc.bcm.edu	37	14	20502779	20502779	+	Missense_Mutation	SNP	C	C	T	rs144683363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20502779C>T	ENST00000315693.2	-	1	140	c.139G>A	c.(139-141)Gtg>Atg	p.V47M	AL359218.1_ENST00000580563.1_RNA	NM_001004714.1	NP_001004714.1	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K, member 13	47						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)		GTCACAGTCACCAAGATGAGC	0.423													C|||	55	0.0109824	0.0393	0.0043	5008	,	,		21594	0.0		0.0	False		,,,				2504	0.0				p.V47M		Atlas-SNP	.											.	OR4K13	68	.	0			c.G139A						PASS	.	C	MET/VAL	178,4228		4,170,2029	109.0	99.0	102.0		139	-1.9	0.0	14	dbSNP_134	102	1,8599		0,1,4299	yes	missense	OR4K13	NM_001004714.1	21	4,171,6328	TT,TC,CC		0.0116,4.0399,1.3763	possibly-damaging	47/305	20502779	179,12827	2203	4300	6503	SO:0001583	missense	390433	exon1			CAGTCACCAAGAT		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.139G>A	14.37:g.20502779C>T	ENSP00000319322:p.Val47Met	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_001004714	Q6IF13	Missense_Mutation	SNP	ENST00000315693.2	37	CCDS32028.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	.	10.51	1.369413	0.24771	0.040399	1.16E-4	ENSG00000176253	ENST00000315693	T	0.01113	5.32	3.75	-1.86	0.07760	GPCR, rhodopsin-like superfamily (1);	0.760143	0.10674	U	0.647227	T	0.00241	0.0007	L	0.49571	1.57	0.09310	N	1	B	0.31077	0.307	B	0.22601	0.04	T	0.44682	-0.9312	10	0.52906	T	0.07	.	4.8534	0.13547	0.0:0.3611:0.2819:0.357	.	47	Q8NH42	OR4KD_HUMAN	M	47	ENSP00000319322:V47M	ENSP00000319322:V47M	V	-	1	0	OR4K13	19572619	0.000000	0.05858	0.011000	0.14972	0.005000	0.04900	-0.485000	0.06520	-0.020000	0.14032	-0.335000	0.08231	GTG	C|0.985;T|0.015	0.015	strong		0.423	OR4K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410344.1		
DAD1	1603	hgsc.bcm.edu	37	14	23044004	23044004	+	Silent	SNP	C	C	T	rs386775535|rs1051154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23044004C>T	ENST00000250498.4	-	2	452	c.341G>A	c.(340-342)tGa>tAa	p.*114*	DAD1_ENST00000538631.1_Intron|DAD1_ENST00000543337.1_Silent_p.*86*|DAD1_ENST00000489532.2_5'Flank	NM_001344.2	NP_001335.1	P61803	DAD1_HUMAN	defender against cell death 1	0					apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			large_intestine(2)|ovary(2)|prostate(1)	5	all_cancers(95;5.49e-05)			GBM - Glioblastoma multiforme(265;0.0156)		GAGAATGAGTCAGCCAACAAA	0.408													C|||	460	0.091853	0.2731	0.036	5008	,	,		19696	0.001		0.0537	False		,,,				2504	0.0194				p.X114X		Atlas-SNP	.											.	DAD1	8	.	0			c.G341A						PASS	.	C		1007,3399	374.2+/-321.1	101,805,1297	133.0	130.0	131.0		341	5.7	1.0	14	dbSNP_86	131	390,8210	125.0+/-183.6	8,374,3918	no	coding-synonymous	DAD1	NM_001344.2		109,1179,5215	TT,TC,CC		4.5349,22.8552,10.7412		114/114	23044004	1397,11609	2203	4300	6503	SO:0001819	synonymous_variant	1603	exon2			ATGAGTCAGCCAA	AK223129	CCDS9571.1	14q11.2	2013-03-06			ENSG00000129562	ENSG00000129562			2664	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 2 homolog (S. cerevisiae)"", ""oligosaccharyltransferase subunit 2 (non-catalytic)"""	600243					Standard	NM_001344		Approved	OST2	uc001wgl.2	P61803	OTTHUMG00000028685	ENST00000250498.4:c.341G>A	14.37:g.23044004C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_001344	D3DS25|O08552|O70364|P46966|P46968|Q6FGA3|Q96GB7	Silent	SNP	ENST00000250498.4	37	CCDS9571.1																																																																																			C|0.901;T|0.099	0.099	strong		0.408	DAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071617.2	NM_001344	
HOMEZ	57594	hgsc.bcm.edu	37	14	23746269	23746269	+	Silent	SNP	C	C	G	rs1057119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23746269C>G	ENST00000357460.5	-	2	332	c.168G>C	c.(166-168)acG>acC	p.T56T	HOMEZ_ENST00000561013.1_Silent_p.T58T|HOMEZ_ENST00000431326.2_Silent_p.T58T	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	56					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)		GGGCTGCTTGCGTCCACACAA	0.552													G|||	914	0.182508	0.1059	0.2104	5008	,	,		18237	0.1766		0.2624	False		,,,				2504	0.1902				p.T56T		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G168C						PASS	.	G		488,3634		31,426,1604	125.0	120.0	122.0		168	1.0	1.0	14	dbSNP_86	122	1820,6600		210,1400,2600	no	coding-synonymous	HOMEZ	NM_020834.2		241,1826,4204	GG,GC,CC		21.6152,11.8389,18.4022		56/551	23746269	2308,10234	2061	4210	6271	SO:0001819	synonymous_variant	57594	exon2			TGCTTGCGTCCAC	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.168G>C	14.37:g.23746269C>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	181	88	0.486188	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			C|0.797;G|0.203	0.203	strong		0.552	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
SUN1	23353	hgsc.bcm.edu	37	7	883088	883088	+	Missense_Mutation	SNP	G	G	A	rs116520953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:883088G>A	ENST00000405266.1	+	5	613	c.589G>A	c.(589-591)Gtg>Atg	p.V197M	SUN1_ENST00000457378.2_Missense_Mutation_p.V218M|SUN1_ENST00000425407.2_Missense_Mutation_p.V147M|SUN1_ENST00000401592.1_Missense_Mutation_p.V197M|SUN1_ENST00000403868.1_Missense_Mutation_p.V197M|SUN1_ENST00000389574.3_Missense_Mutation_p.V147M|SUN1_ENST00000452783.2_Intron|SUN1_ENST00000456758.2_Missense_Mutation_p.V255M			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	197					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						GCGCAAGGACGTGCTCACGGC	0.592													.|||	32	0.00638978	0.0234	0.0014	5008	,	,		13852	0.0		0.0	False		,,,				2504	0.0				p.V218M		Atlas-SNP	.											.	SUN1	157	.	0			c.G652A						PASS	.	G	MET/VAL,,MET/VAL,MET/VAL,MET/VAL	82,3924		2,78,1923	94.0	112.0	107.0		589,,652,589,439	-0.1	0.0	7	dbSNP_132	107	1,8309		0,1,4154	yes	missense,intron,missense,missense,missense	SUN1	NM_001130965.2,NM_001171944.1,NM_001171945.1,NM_001171946.1,NM_025154.5	21,,21,21,21	2,79,6077	AA,AG,GG		0.012,2.0469,0.6739	benign,,benign,benign,benign	197/786,,218/279,197/258,147/703	883088	83,12233	2003	4155	6158	SO:0001583	missense	23353	exon7			AAGGACGTGCTCA	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.589G>A	7.37:g.883088G>A	ENSP00000384116:p.Val197Met	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	73	43	0.589041	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37		7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	15.86	2.959220	0.53400	0.020469	1.2E-4	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407;ENST00000429178	T;T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89	4.4	-0.0819	0.13701	.	1.178380	0.05856	N	0.622191	T	0.11707	0.0285	N	0.19112	0.55	0.09310	N	1	B;P;P;B	0.37038	0.038;0.532;0.579;0.079	B;B;B;B	0.27380	0.035;0.079;0.045;0.024	T	0.09907	-1.0653	10	0.33141	T	0.24	-2.952	5.938	0.19177	0.2089:0.0:0.6586:0.1325	.	197;218;147;197	E9PF23;F8WD13;O94901-5;O94901-3	.;.;.;.	M	255;147;218;197;197;197;197;147;28	ENSP00000388743:V255M;ENSP00000374225:V147M;ENSP00000395952:V218M;ENSP00000384116:V197M;ENSP00000384015:V197M;ENSP00000383947:V197M;ENSP00000392309:V147M;ENSP00000409909:V28M	ENSP00000297445:V197M	V	+	1	0	SUN1	849614	0.003000	0.15002	0.000000	0.03702	0.084000	0.17831	0.577000	0.23758	-0.272000	0.09259	0.591000	0.81541	GTG	G|0.996;A|0.004	0.004	strong		0.592	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
CHD5	26038	hgsc.bcm.edu	37	1	6211183	6211183	+	Silent	SNP	G	G	A	rs9434711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6211183G>A	ENST00000262450.3	-	7	1002	c.903C>T	c.(901-903)ttC>ttT	p.F301F	CHD5_ENST00000378021.1_5'UTR	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)		TGGCGCTGTCGAAGTCCGACT	0.602													G|||	2535	0.50619	0.6906	0.2089	5008	,	,		19415	0.6528		0.3002	False		,,,				2504	0.5286				p.F301F		Atlas-SNP	.											.	CHD5	267	.	0			c.C903T						PASS	.			2701,1705	652.2+/-399.4	834,1033,336	98.0	84.0	88.0		903	-6.9	0.9	1	dbSNP_119	88	2423,6177	401.7+/-347.2	348,1727,2225	no	coding-synonymous	CHD5	NM_015557.2		1182,2760,2561	AA,AG,GG		28.1744,38.6972,39.3972		301/1955	6211183	5124,7882	2203	4300	6503	SO:0001819	synonymous_variant	26038	exon7			GCTGTCGAAGTCC	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.903C>T	1.37:g.6211183G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	147	77	0.52381	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			G|0.588;A|0.412	0.412	strong		0.602	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
PSKH2	85481	hgsc.bcm.edu	37	8	87060793	87060793	+	Silent	SNP	T	T	A	rs28483271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87060793T>A	ENST00000276616.2	-	3	1130	c.1056A>T	c.(1054-1056)ggA>ggT	p.G352G		NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	352							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			ACTGTGCAGATCCAGGACTCT	0.498													T|||	124	0.0247604	0.0885	0.0101	5008	,	,		16173	0.0		0.0	False		,,,				2504	0.0				p.G352G		Atlas-SNP	.											.	PSKH2	79	.	0			c.A1056T						PASS	.	T		302,4104	164.0+/-195.7	9,284,1910	113.0	117.0	115.0		1056	-0.0	0.5	8	dbSNP_125	115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PSKH2	NM_033126.1		9,285,6209	AA,AT,TT		0.0116,6.8543,2.3297		352/386	87060793	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	85481	exon3			TGCAGATCCAGGA	AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.1056A>T	8.37:g.87060793T>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	142	69	0.485915	NM_033126	A0AV22	Silent	SNP	ENST00000276616.2	37	CCDS6240.1																																																																																			T|0.966;A|0.034	0.034	strong		0.498	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
ORM2	5005	hgsc.bcm.edu	37	9	117093856	117093856	+	Missense_Mutation	SNP	G	G	A	rs142633392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117093856G>A	ENST00000431067.2	+	4	374	c.338G>A	c.(337-339)cGa>cAa	p.R113Q	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	113					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	GAGGGAGGCCGAGAACATGTT	0.537													-|||	29	0.00579073	0.0197	0.0029	5008	,	,		18793	0.0		0.001	False		,,,				2504	0.0				p.R113Q	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G338A						PASS	.	G	GLN/ARG	77,4329		1,75,2127	132.0	116.0	121.0		338	-5.9	0.0	9	dbSNP_134	121	0,8600		0,0,4300	yes	missense	ORM2	NM_000608.2	43	1,75,6427	AA,AG,GG		0.0,1.7476,0.592		113/202	117093856	77,12929	2203	4300	6503	SO:0001583	missense	5005	exon4			GAGGCCGAGAACA		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.338G>A	9.37:g.117093856G>A	ENSP00000394936:p.Arg113Gln	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	216	135	0.625	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Missense_Mutation	SNP	ENST00000431067.2	37	CCDS6804.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	-	0.084	-1.178327	0.01633	0.017476	0.0	ENSG00000228278	ENST00000431067	T	0.08008	3.14	2.95	-5.9	0.02275	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.906400	0.02445	N	0.084964	T	0.03095	0.0091	L	0.37561	1.115	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.24476	-1.0159	10	0.20519	T	0.43	4.2497	6.8017	0.23754	0.121:0.0928:0.6382:0.148	.	113	P19652	A1AG2_HUMAN	Q	113	ENSP00000394936:R113Q	ENSP00000394936:R113Q	R	+	2	0	ORM2	116133677	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.988000	0.00319	-4.920000	0.00027	-2.326000	0.00250	CGA	G|0.995;A|0.005	0.005	strong		0.537	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
PCLO	27445	hgsc.bcm.edu	37	7	82785096	82785096	+	Silent	SNP	G	G	A	rs61744360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:82785096G>A	ENST00000333891.9	-	2	1198	c.861C>T	c.(859-861)gaC>gaT	p.D287D	PCLO_ENST00000423517.2_Silent_p.D287D	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						CCCTTACTATGTCTGCCTGTT	0.512													G|||	12	0.00239617	0.0068	0.0029	5008	,	,		18830	0.0		0.0	False		,,,				2504	0.001				p.D287D		Atlas-SNP	.											.	PCLO	1506	.	0			c.C861T						PASS	.	G	,	25,4119		0,25,2047	122.0	111.0	114.0		861,861	-1.0	0.0	7	dbSNP_129	114	0,8422		0,0,4211	no	coding-synonymous,coding-synonymous	PCLO	NM_014510.2,NM_033026.5	,	0,25,6258	AA,AG,GG		0.0,0.6033,0.1989	,	287/4936,287/5143	82785096	25,12541	2072	4211	6283	SO:0001819	synonymous_variant	27445	exon2			TACTATGTCTGCC	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.861C>T	7.37:g.82785096G>A		Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	270	125	0.462963	NM_014510		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			G|0.998;A|0.002	0.002	strong		0.512	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
GPR179	440435	hgsc.bcm.edu	37	17	36487412	36487412	+	Silent	SNP	G	G	A	rs111770829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36487412G>A	ENST00000342292.4	-	11	2060	c.2040C>T	c.(2038-2040)gaC>gaT	p.D680D		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	680					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TCTTCAGCTCGTCCTGTGGGG	0.587													G|||	133	0.0265575	0.0998	0.0014	5008	,	,		18185	0.0		0.0	False		,,,				2504	0.0				p.D680D		Atlas-SNP	.											.	GPR179	170	.	0			c.C2040T						PASS	.	G		294,3810		10,274,1768	45.0	50.0	48.0		2040	-9.7	0.5	17	dbSNP_132	48	3,8383		0,3,4190	no	coding-synonymous	GPR179	NM_001004334.2		10,277,5958	AA,AG,GG		0.0358,7.1637,2.3779		680/2368	36487412	297,12193	2052	4193	6245	SO:0001819	synonymous_variant	440435	exon11			CAGCTCGTCCTGT		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.2040C>T	17.37:g.36487412G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	205	92	0.44878	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			G|0.981;A|0.019	0.019	strong		0.587	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
CHIA	27159	hgsc.bcm.edu	37	1	111862074	111862074	+	Silent	SNP	C	C	T	rs2820092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111862074C>T	ENST00000369740.1	+	11	1264	c.1161C>T	c.(1159-1161)ctC>ctT	p.L387L	CHIA_ENST00000430615.1_Silent_p.L279L|CHIA_ENST00000353665.6_Silent_p.L226L|CHIA_ENST00000483391.1_Silent_p.L226L|CHIA_ENST00000451398.2_Silent_p.L226L|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000343320.6_Silent_p.L387L	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	128	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	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		
RPS16	6217	hgsc.bcm.edu	37	19	39923952	39923952	+	Silent	SNP	G	G	A	rs17627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	204	0	0		WXS	Illumina HiSeq	Phase_I	162	76	0.469136	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	
AOAH	313	hgsc.bcm.edu	37	7	36656001	36656001	+	Silent	SNP	C	C	T	rs3735387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:36656001C>T	ENST00000258749.5	-	11	1230	c.831G>A	c.(829-831)gcG>gcA	p.A277A	AOAH_ENST00000535891.1_Silent_p.A245A|AOAH_ENST00000431169.1_Silent_p.A277A	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	277					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						ACATCTGCGACGCTGTGATCC	0.458													C|||	225	0.0449281	0.0068	0.0994	5008	,	,		19476	0.0992		0.003	False		,,,				2504	0.045				p.A277A		Atlas-SNP	.											.	AOAH	79	.	0			c.G831A						PASS	.	C	,,	69,4337	62.9+/-100.1	0,69,2134	83.0	71.0	75.0		831,735,831	-3.8	0.9	7	dbSNP_107	75	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	AOAH	NM_001177506.1,NM_001177507.1,NM_001637.3	,,	0,72,6431	TT,TC,CC		0.0349,1.566,0.5536	,,	277/689,245/544,277/576	36656001	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	313	exon11			CTGCGACGCTGTG	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.831G>A	7.37:g.36656001C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	71	41	0.577465	NM_001637	A4D1Y5|B7Z490|Q53F13	Silent	SNP	ENST00000258749.5	37	CCDS5448.1																																																																																			C|0.978;T|0.022	0.022	strong		0.458	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	
ABHD12B	145447	hgsc.bcm.edu	37	14	51368610	51368610	+	Missense_Mutation	SNP	A	A	G	rs28564871|rs386777431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:51368610A>G	ENST00000337334.2	+	10	859	c.844A>G	c.(844-846)Atc>Gtc	p.I282V	PYGL_ENST00000532462.1_Intron|ABHD12B_ENST00000395752.1_Missense_Mutation_p.I175V|ABHD12B_ENST00000353130.1_Missense_Mutation_p.I205V	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	282			I -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.				hydrolase activity (GO:0016787)	p.I205V(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					AGACAAAATAATCTTTCCTAA	0.313													G|||	1421	0.283746	0.1649	0.3876	5008	,	,		18507	0.4573		0.2028	False		,,,				2504	0.2751				p.I282V		Atlas-SNP	.											ABHD12B_ENST00000337334,colon,carcinoma,-1,5	ABHD12B	53	5	1	Substitution - Missense(1)	breast(1)	c.A844G						PASS	.	G	VAL/ILE,VAL/ILE	673,3733	760.5+/-413.0	54,565,1584	75.0	72.0	73.0		844,613	3.3	1.0	14	dbSNP_125	73	1637,6955	738.4+/-407.1	151,1335,2810	yes	missense,missense	ABHD12B	NM_001206673.1,NM_181814.1	29,29	205,1900,4394	GG,GA,AA		19.0526,15.2746,17.772	benign,benign	282/363,205/286	51368610	2310,10688	2203	4296	6499	SO:0001583	missense	145447	exon10			AAAATAATCTTTC	BG698443	CCDS9702.1, CCDS55916.1	14q21.3	2009-10-09	2007-04-03	2007-04-03	ENSG00000131969	ENSG00000131969		"""Abhydrolase domain containing"""	19837	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 29"""	C14orf29			Standard	NM_181814		Approved	BEM46L3	uc001wys.3	Q7Z5M8	OTTHUMG00000140286	ENST00000337334.2:c.844A>G	14.37:g.51368610A>G	ENSP00000336693:p.Ile282Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	90	35	0.388889	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Missense_Mutation	SNP	ENST00000337334.2	37	CCDS55916.1	657	0.3008241758241758	90	0.18292682926829268	139	0.3839779005524862	268	0.46853146853146854	160	0.21108179419525067	G	6.676	0.493340	0.12702	0.152746	0.190526	ENSG00000131969	ENST00000353130;ENST00000337334;ENST00000395752	T;T;T	0.41065	2.23;1.01;2.27	5.24	3.35	0.38373	.	0.502898	0.21095	N	0.080253	T	0.00012	0.0000	N	0.11789	0.175	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.47611	-0.9104	9	0.09843	T	0.71	-9.4496	5.205	0.15285	0.175:0.0:0.6608:0.1641	rs28564871;rs28564871	282;205	Q7Z5M8;Q7Z5M8-2	AB12B_HUMAN;.	V	205;282;175	ENSP00000343951:I205V;ENSP00000336693:I282V;ENSP00000379101:I175V	ENSP00000336693:I282V	I	+	1	0	ABHD12B	50438360	0.799000	0.28903	0.998000	0.56505	0.960000	0.62799	0.331000	0.19733	0.401000	0.25424	-0.119000	0.15052	ATC	A|0.765;G|0.235	0.235	strong		0.313	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1		
ABCC10	89845	hgsc.bcm.edu	37	6	43412935	43412935	+	Silent	SNP	T	T	C	rs2125740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43412935T>C	ENST00000372530.4	+	14	3128	c.2913T>C	c.(2911-2913)taT>taC	p.Y971Y	ABCC10_ENST00000244533.3_Silent_p.Y943Y	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	971	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	TCACCGTGTATGCGACCATTG	0.602													T|||	271	0.0541134	0.1974	0.0115	5008	,	,		17679	0.0		0.002	False		,,,				2504	0.0				p.Y971Y		Atlas-SNP	.											.	ABCC10	118	.	0			c.T2913C						PASS	.	T	,	845,3561	334.7+/-303.5	72,701,1430	132.0	102.0	112.0		2913,2829	-6.0	0.3	6	dbSNP_96	112	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous	ABCC10	NM_001198934.1,NM_033450.2	,	72,706,5725	CC,CT,TT		0.0581,19.1784,6.5354	,	971/1493,943/1465	43412935	850,12156	2203	4300	6503	SO:0001819	synonymous_variant	89845	exon14			CGTGTATGCGACC	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.2913T>C	6.37:g.43412935T>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	234	103	0.440171	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	37	CCDS56430.1																																																																																			T|0.940;C|0.060	0.060	strong		0.602	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
MYH14	79784	hgsc.bcm.edu	37	19	50760716	50760716	+	Silent	SNP	C	C	G	rs378811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50760716C>G	ENST00000596571.1	+	15	2082	c.2082C>G	c.(2080-2082)cgC>cgG	p.R694R	MYH14_ENST00000440075.2_Silent_p.R735R|MYH14_ENST00000262269.8_Silent_p.R735R|MYH14_ENST00000425460.1_Silent_p.R702R|MYH14_ENST00000376970.2_Silent_p.R727R|MYH14_ENST00000601313.1_Silent_p.R735R|MYH14_ENST00000598205.1_Silent_p.R702R			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	694	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)		GTTTTGTCCGCTGCATTGTCC	0.612													C|||	1792	0.357827	0.3374	0.3026	5008	,	,		19529	0.374		0.4026	False		,,,				2504	0.362				p.R735R		Atlas-SNP	.											MYH14_ENST00000262269,NS,carcinoma,0,4	MYH14	261	4	0			c.C2205G						PASS	.	C	,,	1336,2946		217,902,1022	31.0	34.0	33.0		2106,2205,2082	4.5	1.0	19	dbSNP_80	33	3603,4903		771,2061,1421	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	988,2963,2443	GG,GC,CC		42.3583,31.2004,38.6221	,,	702/2004,735/2037,694/1996	50760716	4939,7849	2141	4253	6394	SO:0001819	synonymous_variant	79784	exon18			TGTCCGCTGCATT	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.2082C>G	19.37:g.50760716C>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			C|0.617;G|0.383	0.383	strong		0.612	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
PAX2	5076	hgsc.bcm.edu	37	10	102568983	102568983	+	Silent	SNP	A	A	C	rs1800898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102568983A>C	ENST00000428433.1	+	8	1528	c.978A>C	c.(976-978)ccA>ccC	p.P326P	PAX2_ENST00000355243.3_Silent_p.P303P|PAX2_ENST00000556085.1_Silent_p.P302P|PAX2_ENST00000370296.2_Silent_p.P326P|PAX2_ENST00000361791.3_Silent_p.P303P	NM_003987.3|NM_003990.3	NP_003978|NP_003981.2	Q02962	PAX2_HUMAN	paired box 2	326					aging (GO:0007568)|axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cell fate determination (GO:0001709)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucose stimulus (GO:0071333)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|glial cell differentiation (GO:0010001)|inner ear morphogenesis (GO:0042472)|mesenchymal to epithelial transition (GO:0060231)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|mesonephric duct development (GO:0072177)|mesonephric tubule formation (GO:0072172)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric nephron tubule formation (GO:0072289)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytolysis (GO:0045918)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of programmed cell death (GO:0043069)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|neural tube closure (GO:0001843)|optic chiasma development (GO:0061360)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|optic nerve development (GO:0021554)|optic nerve morphogenesis (GO:0021631)|optic nerve structural organization (GO:0021633)|pancreas development (GO:0031016)|paramesonephric duct development (GO:0061205)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of optic nerve formation (GO:2000597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|protein kinase B signaling (GO:0043491)|reactive oxygen species metabolic process (GO:0072593)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of metanephros size (GO:0035566)|response to nutrient levels (GO:0031667)|retinal pigment epithelium development (GO:0003406)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|ureter development (GO:0072189)|ureter maturation (GO:0035799)|ureter morphogenesis (GO:0072197)|urogenital system development (GO:0001655)|vestibulocochlear nerve formation (GO:0021650)|visual perception (GO:0007601)	centriolar satellite (GO:0034451)|lysosome (GO:0005764)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|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 (GO:0000982)|superoxide-generating NADPH oxidase activity (GO:0016175)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		AGACATACCCAGTTGTGACTG	0.607													C|||	1882	0.375799	0.8215	0.2363	5008	,	,		18525	0.0982		0.2594	False		,,,				2504	0.2781				p.P326P		Atlas-SNP	.											.	PAX2	83	.	0			c.A978C						PASS	.	C	,,,,	3261,1145	406.2+/-333.8	1229,803,171	77.0	67.0	70.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	909,978,909,909,978	-8.4	0.0	10	dbSNP_89	70	2458,6142	695.6+/-404.8	357,1744,2199	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PAX2	NM_000278.3,NM_003987.3,NM_003988.3,NM_003989.3,NM_003990.3	,,,,	1586,2547,2370	CC,CA,AA		28.5814,25.9873,43.972	,,,,	303/395,326/418,303/397,303/410,326/433	102568983	5719,7287	2203	4300	6503	SO:0001819	synonymous_variant	5076	exon8			ATACCCAGTTGTG		CCDS7499.1, CCDS41561.1	10q24.31	2011-06-20	2007-07-12		ENSG00000075891	ENSG00000075891		"""Paired boxes"", ""Homeoboxes / PRD class"""	8616	protein-coding gene	gene with protein product		167409	"""paired box gene 2"""			8431641, 7981748	Standard	NM_003990		Approved		uc001krk.4	Q02962	OTTHUMG00000018913	ENST00000428433.1:c.978A>C	10.37:g.102568983A>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_003987	Q15105|Q15110|Q15837|Q5SZP2|Q5SZP3	Silent	SNP	ENST00000428433.1	37	CCDS53569.1																																																																																			A|0.594;C|0.406	0.406	strong		0.607	PAX2-202	KNOWN	basic|CCDS	protein_coding	protein_coding			
KCTD18	130535	hgsc.bcm.edu	37	2	201355106	201355106	+	Missense_Mutation	SNP	G	G	A	rs13018579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	100	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	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	
CCT3	7203	hgsc.bcm.edu	37	1	156281999	156281999	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156281999G>A	ENST00000295688.3	-	11	1268	c.988C>T	c.(988-990)Cgg>Tgg	p.R330W	CCT3_ENST00000472765.2_Missense_Mutation_p.R285W|CCT3_ENST00000368261.3_Missense_Mutation_p.R285W|CCT3_ENST00000368259.2_Missense_Mutation_p.R292W	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	330					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					CTGACTATCCGGGCCCCACAG	0.468																																					p.R330W		Atlas-SNP	.											.	CCT3	61	.	0			c.C988T						PASS	.						57.0	61.0	60.0					1																	156281999		2203	4300	6503	SO:0001583	missense	7203	exon11			CTATCCGGGCCCC	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"""Heat Shock Proteins / Chaperonins"""	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.988C>T	1.37:g.156281999G>A	ENSP00000295688:p.Arg330Trp	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	37	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	G	27.7	4.856417	0.91355	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	6.15	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.88822	0.6541	M	0.88512	2.96	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.997;0.997	D;D;D	0.69307	0.963;0.949;0.949	D	0.91190	0.4983	10	0.72032	D	0.01	-15.521	14.8519	0.70303	0.0:0.0:0.8555:0.1445	.	292;329;330	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	W	330;292;285;285	ENSP00000295688:R330W;ENSP00000357242:R292W;ENSP00000357244:R285W;ENSP00000431543:R285W	ENSP00000295688:R330W	R	-	1	2	CCT3	154548623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.908000	0.87438	1.610000	0.50200	0.643000	0.83706	CGG	.	.	none		0.468	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998	
PCDH12	51294	hgsc.bcm.edu	37	5	141331098	141331098	+	Missense_Mutation	SNP	G	G	A	rs115735066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141331098G>A	ENST00000231484.3	-	2	4148	c.2938C>T	c.(2938-2940)Cac>Tac	p.H980Y	AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	980					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)			TTTCCTCGGTGGTTTGGTTTG	0.547											OREG0016877	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	44	0.00878594	0.0318	0.0029	5008	,	,		20762	0.0		0.0	False		,,,				2504	0.0				p.H980Y		Atlas-SNP	.											.	PCDH12	133	.	0			c.C2938T						PASS	.	G	TYR/HIS	104,4302	81.4+/-119.9	0,104,2099	113.0	103.0	106.0		2938	6.1	1.0	5	dbSNP_132	106	0,8600		0,0,4300	yes	missense	PCDH12	NM_016580.2	83	0,104,6399	AA,AG,GG		0.0,2.3604,0.7996	probably-damaging	980/1185	141331098	104,12902	2203	4300	6503	SO:0001583	missense	51294	exon2			CTCGGTGGTTTGG	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.2938C>T	5.37:g.141331098G>A	ENSP00000231484:p.His980Tyr	Somatic	106	0	0	1663	WXS	Illumina HiSeq	Phase_I	118	45	0.381356	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	17.98	3.520092	0.64747	0.023604	0.0	ENSG00000113555	ENST00000231484	T	0.52754	0.65	6.08	6.08	0.98989	.	0.107907	0.64402	D	0.000003	T	0.21022	0.0506	M	0.62723	1.935	0.42331	D	0.992297	P	0.43788	0.817	B	0.39339	0.297	T	0.15809	-1.0424	10	0.36615	T	0.2	.	11.4227	0.49991	0.0811:0.0:0.9189:0.0	.	980	Q9NPG4	PCD12_HUMAN	Y	980	ENSP00000231484:H980Y	ENSP00000231484:H980Y	H	-	1	0	PCDH12	141311282	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.297000	0.65704	2.894000	0.99253	0.655000	0.94253	CAC	G|0.991;A|0.009	0.009	strong		0.547	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
C10orf12	26148	hgsc.bcm.edu	37	10	98742021	98742021	+	Silent	SNP	C	C	T	rs7098255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98742021C>T	ENST00000286067.2	+	1	981	c.874C>T	c.(874-876)Ctg>Ttg	p.L292L		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	292								p.L292L(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		TAAGCCGAACCTGAGCAGCTC	0.562													C|||	701	0.139976	0.0492	0.1282	5008	,	,		19757	0.2808		0.0229	False		,,,				2504	0.2464				p.L292L		Atlas-SNP	.											C10orf12,NS,carcinoma,0,1	C10orf12	94	1	1	Substitution - coding silent(1)	stomach(1)	c.C874T						PASS	.	C		204,4202	128.2+/-165.1	5,194,2004	66.0	70.0	69.0		874	5.1	0.0	10	dbSNP_116	69	197,8403	85.6+/-148.0	2,193,4105	no	coding-synonymous	C10orf12	NM_015652.2		7,387,6109	TT,TC,CC		2.2907,4.63,3.0832		292/1248	98742021	401,12605	2203	4300	6503	SO:0001819	synonymous_variant	26148	exon1			CCGAACCTGAGCA	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.874C>T	10.37:g.98742021C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_015652	Q9H945|Q9Y457	Silent	SNP	ENST00000286067.2	37	CCDS7452.1																																																																																			C|0.931;T|0.069	0.069	strong		0.562	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
SCIN	85477	hgsc.bcm.edu	37	7	12675690	12675690	+	Missense_Mutation	SNP	G	G	A	rs35385652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12675690G>A	ENST00000297029.5	+	10	1441	c.1340G>A	c.(1339-1341)cGa>cAa	p.R447Q	SCIN_ENST00000445618.2_Missense_Mutation_p.R200Q|SCIN_ENST00000519209.1_Missense_Mutation_p.R200Q	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	447	Ca(2+)-dependent actin binding.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		AATGCCACACGAGATGAGCTG	0.463													G|||	144	0.028754	0.0272	0.0346	5008	,	,		20478	0.0		0.0567	False		,,,				2504	0.0276				p.R447Q		Atlas-SNP	.											.	SCIN	105	.	0			c.G1340A						PASS	.	G	GLN/ARG,GLN/ARG	132,3910		1,130,1890	87.0	87.0	87.0		1340,599	3.8	0.5	7	dbSNP_126	87	372,8006		10,352,3827	yes	missense,missense	SCIN	NM_001112706.2,NM_033128.3	43,43	11,482,5717	AA,AG,GG		4.4402,3.2657,4.058	benign,benign	447/716,200/469	12675690	504,11916	2021	4189	6210	SO:0001583	missense	85477	exon10			CCACACGAGATGA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.1340G>A	7.37:g.12675690G>A	ENSP00000297029:p.Arg447Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	58	0.026556776556776556	10	0.02032520325203252	10	0.027624309392265192	0	0.0	38	0.05013192612137203	G	0.271	-0.993087	0.02145	0.032657	0.044402	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.52526	0.66;0.66;0.66	5.55	3.75	0.43078	Gelsolin domain (1);	0.182576	0.45606	D	0.000357	T	0.01627	0.0052	N	0.00272	-1.73	0.31397	N	0.67714	B	0.16603	0.018	B	0.12837	0.008	T	0.23619	-1.0183	10	0.02654	T	1	-16.0247	8.981	0.35966	0.2803:0.0:0.7197:0.0	rs35385652	447	Q9Y6U3	ADSV_HUMAN	Q	447;200;200	ENSP00000297029:R447Q;ENSP00000430997:R200Q;ENSP00000390189:R200Q	ENSP00000297029:R447Q	R	+	2	0	SCIN	12642215	0.046000	0.20272	0.474000	0.27266	0.141000	0.21300	0.525000	0.22956	0.714000	0.32081	-0.123000	0.14984	CGA	G|0.972;A|0.028	0.028	strong		0.463	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
PHACTR4	65979	hgsc.bcm.edu	37	1	28800380	28800380	+	Missense_Mutation	SNP	C	C	A	rs61785974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:28800380C>A	ENST00000373839.3	+	7	1399	c.1138C>A	c.(1138-1140)Cta>Ata	p.L380I	PHACTR4_ENST00000373836.3_Missense_Mutation_p.L390I|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	380	Pro-rich.				actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		ATCCTTAGATCTACACCAGGA	0.507													C|||	1127	0.22504	0.3048	0.2666	5008	,	,		14282	0.0704		0.3111	False		,,,				2504	0.1585				p.L390I		Atlas-SNP	.											.	PHACTR4	64	.	0			c.C1168A						PASS	.	C	ILE/LEU,ILE/LEU	1153,2617		192,769,924	81.0	81.0	81.0		1138,1168	3.3	0.2	1	dbSNP_129	81	2233,5989		282,1669,2160	yes	missense,missense	PHACTR4	NM_001048183.1,NM_023923.3	5,5	474,2438,3084	AA,AC,CC		27.1588,30.5836,28.2355	possibly-damaging,possibly-damaging	380/703,390/713	28800380	3386,8606	1885	4111	5996	SO:0001583	missense	65979	exon6			TTAGATCTACACC	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"""Phosphatase and actin regulators"""	25793	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 124"""	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1138C>A	1.37:g.28800380C>A	ENSP00000362945:p.Leu380Ile	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	56	35	0.625	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	37	CCDS41293.1	560	0.2564102564102564	168	0.34146341463414637	100	0.27624309392265195	54	0.0944055944055944	238	0.31398416886543534	C	5.460	0.270018	0.10349	0.305836	0.271588	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.24908	1.84;1.83	5.22	3.3	0.37823	.	1.100460	0.06835	N	0.794600	T	0.00012	0.0000	L	0.54323	1.7	0.38745	P	0.04601200000000005	B;B	0.31548	0.328;0.22	B;B	0.28011	0.085;0.024	T	0.41980	-0.9478	9	0.19590	T	0.45	-5.1431	5.4783	0.16708	0.1624:0.676:0.0:0.1616	rs61785974	390;380	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	I	380;390;379	ENSP00000362945:L380I;ENSP00000362942:L390I	ENSP00000362942:L390I	L	+	1	2	PHACTR4	28672967	0.235000	0.23794	0.237000	0.24090	0.250000	0.25880	1.307000	0.33516	0.731000	0.32448	0.655000	0.94253	CTA	C|0.726;A|0.274	0.274	strong		0.507	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923	
MUC17	140453	hgsc.bcm.edu	37	7	100680120	100680120	+	Missense_Mutation	SNP	C	C	A	rs147991653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100680120C>A	ENST00000306151.4	+	3	5487	c.5423C>A	c.(5422-5424)aCt>aAt	p.T1808N		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1808	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.T1808N(1)		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)					GAAGGAATGACTCCATTAACA	0.512													-|||	4	0.000798722	0.0008	0.0	5008	,	,		25905	0.003		0.0	False		,,,				2504	0.0				p.T1808N		Atlas-SNP	.											MUC17,extremity,malignant_melanoma,0,2	MUC17	804	2	1	Substitution - Missense(1)	skin(1)	c.C5423A						scavenged	.						246.0	249.0	248.0					7																	100680120		2203	4300	6503	SO:0001583	missense	140453	exon3			GAATGACTCCATT	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.5423C>A	7.37:g.100680120C>A	ENSP00000302716:p.Thr1808Asn	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	205	10	0.0487805	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	76	0.0347985347985348	28	0.056910569105691054	21	0.058011049723756904	12	0.02097902097902098	15	0.01978891820580475	c	0.142	-1.100945	0.01843	.	.	ENSG00000169876	ENST00000306151	T	0.02177	4.41	0.471	-0.615	0.11587	.	.	.	.	.	T	0.00210	0.0006	N	0.19112	0.55	0.09310	N	1	D	0.58620	0.983	B	0.40677	0.337	T	0.51988	-0.8635	8	0.32370	T	0.25	.	.	.	.	.	1808	Q685J3	MUC17_HUMAN	N	1808	ENSP00000302716:T1808N	ENSP00000302716:T1808N	T	+	2	0	MUC17	100466840	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	0.305000	0.19254	-0.243000	0.09653	-1.404000	0.01136	ACT	C|0.975;A|0.025	0.025	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SSPO	23145	hgsc.bcm.edu	37	7	149509048	149509048	+	RNA	SNP	C	C	T	rs115723456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149509048C>T	ENST00000378016.2	+	0	9594							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)			GTTCAGCCTCCTGTGGCCCTG	0.697													C|||	70	0.0139776	0.053	0.0	5008	,	,		15590	0.0		0.0	False		,,,				2504	0.0				p.S3198S		Atlas-SNP	.											.	.	.	.	0			c.C9594T						PASS	.	C		162,3908		5,152,1878	30.0	35.0	34.0		9604	0.7	1.0	7	dbSNP_132	34	0,8344		0,0,4172	no	coding-notMod3	SSPO	NM_198455.2		5,152,6050	TT,TC,CC		0.0,3.9803,1.305			149509048	162,12252	2035	4172	6207			23145	exon68			AGCCTCCTGTGGC	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.149509048C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.989;T|0.011	0.011	strong		0.697	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
PLEKHG3	26030	hgsc.bcm.edu	37	14	65197791	65197791	+	Silent	SNP	C	C	A	rs61742295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:65197791C>A	ENST00000394691.1	+	7	900	c.753C>A	c.(751-753)ggC>ggA	p.G251G	PLEKHG3_ENST00000247226.7_Silent_p.G195G			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	251	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)		AAGAGGATGGCTTTGAGGTGG	0.577													C|||	215	0.0429313	0.0787	0.0115	5008	,	,		20782	0.0357		0.0099	False		,,,				2504	0.0583				p.G195G		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.C585A						PASS	.	C		308,4098	166.2+/-197.5	13,282,1908	169.0	150.0	157.0		585	4.4	1.0	14	dbSNP_129	157	79,8521	46.3+/-105.2	0,79,4221	no	coding-synonymous	PLEKHG3	NM_015549.1		13,361,6129	AA,AC,CC		0.9186,6.9905,2.9755		195/1164	65197791	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	26030	exon5			GGATGGCTTTGAG	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.753C>A	14.37:g.65197791C>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	125	73	0.584	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Silent	SNP	ENST00000394691.1	37																																																																																				C|0.974;A|0.026	0.026	strong		0.577	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549	
PIGT	51604	hgsc.bcm.edu	37	20	44052992	44052992	+	Silent	SNP	G	G	A	rs13217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44052992G>A	ENST00000279036.6	+	10	1451	c.1371G>A	c.(1369-1371)acG>acA	p.T457T	PIGT_ENST00000341555.5_Silent_p.T263T|PIGT_ENST00000535404.1_Silent_p.T302T|PIGT_ENST00000279035.9_Silent_p.T355T|PIGT_ENST00000545755.1_Silent_p.T195T|PIGT_ENST00000372689.5_Silent_p.T390T|PIGT_ENST00000543458.2_Silent_p.T401T	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	102	0	0		WXS	Illumina HiSeq	Phase_I	134	62	0.462687	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	
RGS3	5998	hgsc.bcm.edu	37	9	116279880	116279880	+	Silent	SNP	T	T	C	rs35270441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116279880T>C	ENST00000374140.2	+	17	1943	c.1734T>C	c.(1732-1734)taT>taC	p.Y578Y	RGS3_ENST00000317613.6_Silent_p.Y466Y|RGS3_ENST00000374136.1_Silent_p.Y204Y|RGS3_ENST00000394646.3_Silent_p.Y297Y|RGS3_ENST00000350696.5_Silent_p.Y578Y|RGS3_ENST00000343817.5_Silent_p.Y297Y	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	578					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						TGCTGCTGTATGAAGGGAGGA	0.537													C|||	417	0.0832668	0.1785	0.0663	5008	,	,		15392	0.0		0.0964	False		,,,				2504	0.0389				p.Y578Y		Atlas-SNP	.											.	RGS3	251	.	0			c.T1734C						PASS	.	C	,,	803,3603	750.3+/-412.1	87,629,1487	99.0	100.0	99.0		1398,891,1734	-4.2	0.8	9	dbSNP_126	99	861,7739	780.3+/-407.7	39,783,3478	no	coding-synonymous,coding-synonymous,coding-synonymous	RGS3	NM_017790.3,NM_130795.2,NM_144488.4	,,	126,1412,4965	CC,CT,TT		10.0116,18.2251,12.7941	,,	466/603,297/918,578/1199	116279880	1664,11342	2203	4300	6503	SO:0001819	synonymous_variant	5998	exon17			GCTGTATGAAGGG	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.1734T>C	9.37:g.116279880T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	82	60	0.731707	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Silent	SNP	ENST00000374140.2	37	CCDS43869.1	184	0.08424908424908426	81	0.16463414634146342	27	0.07458563535911603	0	0.0	76	0.10026385224274406	C	8.330	0.826272	0.16749	0.182251	0.100116	ENSG00000138835	ENST00000496113	.	.	.	4.88	-4.22	0.03800	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999665589	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.128	0.31010	0.1119:0.2787:0.0:0.6094	rs35270441;rs61749205	.	.	.	R	33	.	.	X	+	1	0	RGS3	115319701	0.008000	0.16893	0.781000	0.31783	0.895000	0.52256	-1.812000	0.01726	-1.163000	0.02793	-1.476000	0.00998	TGA	T|0.889;C|0.111	0.111	strong		0.537	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
MAT1A	4143	hgsc.bcm.edu	37	10	82034854	82034854	+	Silent	SNP	T	T	C	rs10788546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:82034854T>C	ENST00000372213.3	-	7	1130	c.870A>G	c.(868-870)gtA>gtG	p.V290V	MAT1A_ENST00000485270.1_5'UTR	NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	290					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	CTGAGCGGTCTACCTTGGTGT	0.617													C|||	4211	0.840855	0.9266	0.7781	5008	,	,		15774	0.9712		0.6412	False		,,,				2504	0.8405				p.V290V		Atlas-SNP	.											.	MAT1A	52	.	0			c.A870G						PASS	.	C		3841,561		1681,479,41	39.0	39.0	39.0		870	4.1	1.0	10	dbSNP_120	39	5379,3217		1700,1979,619	no	coding-synonymous	MAT1A	NM_000429.2		3381,2458,660	CC,CT,TT		37.4244,12.7442,29.066		290/396	82034854	9220,3778	2201	4298	6499	SO:0001819	synonymous_variant	4143	exon7			GCGGTCTACCTTG		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"""S-adenosylmethionine synthetase"""	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.870A>G	10.37:g.82034854T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_000429	D3DWD5|Q5QP09	Silent	SNP	ENST00000372213.3	37	CCDS7365.1																																																																																			T|0.235;C|0.765	0.765	strong		0.617	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573655	140573655	+	Silent	SNP	C	C	T	rs17844572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140573655C>T	ENST00000239446.4	+	1	1714	c.1530C>T	c.(1528-1530)aaC>aaT	p.N510N		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	510	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(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)			ACGCGGACAACGGCCACCTGT	0.692													C|||	79	0.0157748	0.0582	0.0029	5008	,	,		18416	0.0		0.0	False		,,,				2504	0.0				p.N510N		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C1530T						PASS	.	C		182,4224	107.8+/-146.2	5,172,2026	102.0	119.0	113.0		1530	1.7	0.9	5	dbSNP_123	113	0,8594		0,0,4297	no	coding-synonymous	PCDHB10	NM_018930.3		5,172,6323	TT,TC,CC		0.0,4.1307,1.4		510/801	140573655	182,12818	2203	4297	6500	SO:0001819	synonymous_variant	56126	exon1			GGACAACGGCCAC	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.1530C>T	5.37:g.140573655C>T		Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	395	107	0.270886	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.986;T|0.014	0.014	strong		0.692	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
ZAK	51776	hgsc.bcm.edu	37	2	174103160	174103160	+	Silent	SNP	T	T	C	rs3739103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:174103160T>C	ENST00000375213.3	+	15	1341	c.1263T>C	c.(1261-1263)atT>atC	p.I421I	MLK7-AS1_ENST00000423106.2_RNA|MLTK_ENST00000409176.2_Silent_p.I421I|MLK7-AS1_ENST00000422703.1_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		421					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										CACCACTAATTAAGGTAAGTA	0.343													T|||	750	0.14976	0.056	0.085	5008	,	,		19343	0.5575		0.0249	False		,,,				2504	0.0307				p.I421I		Atlas-SNP	.											.	ZAK	62	.	0			c.T1263C						PASS	.	T		193,3633		4,185,1724	117.0	111.0	113.0		1263	1.6	1.0	2	dbSNP_107	113	229,8049		3,223,3913	no	coding-synonymous	ZAK	NM_016653.2		7,408,5637	CC,CT,TT		2.7664,5.0444,3.4865		421/801	174103160	422,11682	1913	4139	6052	SO:0001819	synonymous_variant	0	exon15			ACTAATTAAGGTA																												ENST00000375213.3:c.1263T>C	2.37:g.174103160T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	145	64	0.441379	NM_016653	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Silent	SNP	ENST00000375213.3	37	CCDS42777.1																																																																																			T|0.850;C|0.150	0.150	strong		0.343	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1		
SATB2	23314	hgsc.bcm.edu	37	2	200233357	200233357	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:200233357C>T	ENST00000417098.1	-	6	1487	c.671G>A	c.(670-672)aGa>aAa	p.R224K	SATB2_ENST00000443023.1_Missense_Mutation_p.R165K|SATB2_ENST00000428695.1_Intron|SATB2_ENST00000260926.5_Missense_Mutation_p.R224K|SATB2_ENST00000484124.1_5'UTR|SATB2_ENST00000457245.1_Missense_Mutation_p.R224K	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	224					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TTTATACCATCTCCCAAACTC	0.323																																					p.R224K	Colon(30;262 767 11040 24421 36230)	Atlas-SNP	.											SATB2,colon,carcinoma,+1,1	SATB2	134	1	0			c.G671A						scavenged	.						102.0	99.0	100.0					2																	200233357		2203	4300	6503	SO:0001583	missense	23314	exon7			TACCATCTCCCAA	AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"""Homeoboxes / CUT class"""	21637	protein-coding gene	gene with protein product		608148	"""SATB family member 2"""				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.671G>A	2.37:g.200233357C>T	ENSP00000401112:p.Arg224Lys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	108	2	0.0185185	NM_015265	A8K5Z8|Q3ZB87|Q4V763	Missense_Mutation	SNP	ENST00000417098.1	37	CCDS2327.1	.	.	.	.	.	.	.	.	.	.	C	35	5.573914	0.96553	.	.	ENSG00000119042	ENST00000417098;ENST00000443023;ENST00000260926;ENST00000457245	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.78194	0.4245	L	0.34521	1.04	0.52099	D	0.999948	P	0.47106	0.89	P	0.49887	0.625	T	0.77115	-0.2707	10	0.44086	T	0.13	-12.6975	20.1518	0.98089	0.0:1.0:0.0:0.0	.	224	Q9UPW6	SATB2_HUMAN	K	224;165;224;224	ENSP00000401112:R224K;ENSP00000388764:R165K;ENSP00000260926:R224K;ENSP00000405420:R224K	ENSP00000260926:R224K	R	-	2	0	SATB2	199941602	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.769000	0.95229	0.491000	0.48974	AGA	.	.	none		0.323	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265	
COL6A3	1293	hgsc.bcm.edu	37	2	238277573	238277573	+	Silent	SNP	C	C	A	rs2645774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238277573C>A	ENST00000295550.4	-	10	4985	c.4533G>T	c.(4531-4533)ggG>ggT	p.G1511G	COL6A3_ENST00000472056.1_Silent_p.G904G|COL6A3_ENST00000409809.1_Silent_p.G1305G|COL6A3_ENST00000346358.4_Silent_p.G1311G|COL6A3_ENST00000347401.3_Silent_p.G1310G|COL6A3_ENST00000353578.4_Silent_p.G1305G	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1511	Nonhelical region.|VWFA 8. {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)		TCAGTGGGGACCCCCCTCTGA	0.562													C|||	1330	0.265575	0.295	0.3084	5008	,	,		18618	0.256		0.2177	False		,,,				2504	0.2546				p.G1511G		Atlas-SNP	.											.	COL6A3	608	.	0			c.G4533T						PASS	.	C	,,	1224,3182	421.5+/-339.4	163,898,1142	47.0	48.0	48.0		4533,2712,3915	-5.6	0.0	2	dbSNP_100	48	1824,6776	321.3+/-315.0	208,1408,2684	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	371,2306,3826	AA,AC,CC		21.2093,27.7803,23.4353	,,	1511/3178,904/2571,1305/2972	238277573	3048,9958	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon10			TGGGGACCCCCCT	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.4533G>T	2.37:g.238277573C>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	104	45	0.432692	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.757;A|0.243	0.243	strong		0.562	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
TTC38	55020	hgsc.bcm.edu	37	22	46664431	46664431	+	Silent	SNP	C	C	G	rs9627359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46664431C>G	ENST00000381031.3	+	2	130	c.54C>G	c.(52-54)ctC>ctG	p.L18L	TTC38_ENST00000445282.2_Silent_p.L18L	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	18						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						ATGCGAGGCTCCCGCTCTCCA	0.607													C|||	743	0.148363	0.4788	0.062	5008	,	,		14364	0.001		0.0358	False		,,,				2504	0.0307				p.L18L		Atlas-SNP	.											.	TTC38	40	.	0			c.C54G						PASS	.	C		1763,2619		358,1047,786	39.0	49.0	46.0		54	-3.5	0.3	22	dbSNP_119	46	305,8267		2,301,3983	no	coding-synonymous	TTC38	NM_017931.2		360,1348,4769	GG,GC,CC		3.5581,40.2328,15.9642		18/470	46664431	2068,10886	2191	4286	6477	SO:0001819	synonymous_variant	55020	exon2			GAGGCTCCCGCTC		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.54C>G	22.37:g.46664431C>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_017931	Q8WV27|Q9NWP8	Silent	SNP	ENST00000381031.3	37	CCDS43030.1																																																																																			C|0.912;G|0.088	0.088	strong		0.607	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
AIRE	326	hgsc.bcm.edu	37	21	45712983	45712983	+	Silent	SNP	T	T	C	rs61737072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45712983T>C	ENST00000291582.5	+	10	1330	c.1203T>C	c.(1201-1203)ccT>ccC	p.P401P	AIRE_ENST00000329347.4_Intron|AIRE_ENST00000355347.4_Silent_p.P194P	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	401					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)		CGGCTCCGCCTTCTGCAGCCC	0.677									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				T|||	232	0.0463259	0.1649	0.0202	5008	,	,		10975	0.0		0.0	False		,,,				2504	0.0				p.P401P		Atlas-SNP	.											.	AIRE	61	.	0			c.T1203C						PASS	.	T	,	665,3717		60,545,1586	22.0	26.0	24.0		1203,612	-2.4	0.0	21	dbSNP_129	24	2,8586		0,2,4292	no	coding-synonymous,coding-synonymous	AIRE	NM_000383.2,NM_000658.2	,	60,547,5878	CC,CT,TT		0.0233,15.1757,5.1426	,	401/546,204/349	45712983	667,12303	2191	4294	6485	SO:0001819	synonymous_variant	326	exon10	Familial Cancer Database	APECED	TCCGCCTTCTGCA	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.1203T>C	21.37:g.45712983T>C		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			T|0.951;C|0.049	0.049	strong		0.677	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
DENND2A	27147	hgsc.bcm.edu	37	7	140244560	140244560	+	Missense_Mutation	SNP	C	C	T	rs2293177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140244560C>T	ENST00000275884.6	-	13	2602	c.2185G>A	c.(2185-2187)Gaa>Aaa	p.E729K	DENND2A_ENST00000492720.1_Missense_Mutation_p.E729K|DENND2A_ENST00000496613.1_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	86	0	0		WXS	Illumina HiSeq	Phase_I	85	26	0.305882	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	
MSH2	4436	hgsc.bcm.edu	37	2	47637439	47637439	+	Silent	SNP	C	C	T	rs1800151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47637439C>T	ENST00000233146.2	+	3	796	c.573C>T	c.(571-573)ctC>ctT	p.L191L	MSH2_ENST00000543555.1_Silent_p.L125L|MSH2_ENST00000406134.1_Silent_p.L191L	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	191					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGGCTCTCCTCATCCAGATTG	0.463			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				C|||	97	0.019369	0.0696	0.0072	5008	,	,		15087	0.0		0.0	False		,,,				2504	0.0				p.L191L		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.C573T						PASS	.	C		254,4152	146.9+/-181.5	4,246,1953	182.0	176.0	178.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	573	1.6	1.0	2	dbSNP_89	178	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	MSH2	NM_000251.1		4,250,6249	TT,TC,CC		0.0465,5.7649,1.9837		191/935	47637439	258,12748	2203	4300	6503	SO:0001819	synonymous_variant	4436	exon3	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	TCTCCTCATCCAG	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.573C>T	2.37:g.47637439C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	129	55	0.426357	NM_000251	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																			C|0.977;T|0.023	0.023	strong		0.463	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
IL10RA	3587	hgsc.bcm.edu	37	11	117870257	117870257	+	Silent	SNP	C	C	T	rs146193205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117870257C>T	ENST00000227752.3	+	7	1758	c.1638C>T	c.(1636-1638)gcC>gcT	p.A546A	IL10RA_ENST00000545409.1_Silent_p.A397A|IL10RA_ENST00000541785.1_Silent_p.A526A|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	546					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		ATGACCTTGCCCCTCTAGGCT	0.592													C|||	3	0.000599042	0.0023	0.0	5008	,	,		19108	0.0		0.0	False		,,,				2504	0.0				p.A546A		Atlas-SNP	.											.	IL10RA	46	.	0			c.C1638T						PASS	.	C		6,4394	11.4+/-27.6	0,6,2194	51.0	48.0	49.0		1638	-0.1	0.0	11	dbSNP_134	49	0,8592		0,0,4296	no	coding-synonymous	IL10RA	NM_001558.3		0,6,6490	TT,TC,CC		0.0,0.1364,0.0462		546/579	117870257	6,12986	2200	4296	6496	SO:0001819	synonymous_variant	3587	exon7			CCTTGCCCCTCTA	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.1638C>T	11.37:g.117870257C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	37	CCDS8388.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
TBC1D1	23216	hgsc.bcm.edu	37	4	37962186	37962186	+	Intron	SNP	G	G	C	rs6811863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:37962186G>C	ENST00000261439.4	+	3	772				TBC1D1_ENST00000508802.1_Intron|PTTG2_ENST00000504686.1_Missense_Mutation_p.R44P	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						GTTTTAACACGACGTTTTGGC	0.463													C|||	3655	0.729832	0.6967	0.7017	5008	,	,		19910	0.9583		0.5746	False		,,,				2504	0.7188				p.R44P		Atlas-SNP	.											.	PTTG2	15	.	0			c.G131C						PASS	.	C	PRO/ARG,	3099,1303	406.4+/-333.9	1113,873,215	71.0	75.0	74.0		131,	-4.0	0.0	4	dbSNP_116	74	4855,3745	526.1+/-380.9	1365,2125,810	yes	missense,intron	PTTG2,TBC1D1	NM_006607.2,NM_015173.2	103,	2478,2998,1025	CC,CG,GG		43.5465,29.6002,38.8248	possibly-damaging,	44/192,	37962186	7954,5048	2201	4300	6501	SO:0001627	intron_variant	10744	exon1			TAACACGACGTTT	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.418-53944G>C	4.37:g.37962186G>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	223	223	1	NM_006607	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	37	CCDS33972.1	1589	0.7275641025641025	343	0.6971544715447154	251	0.6933701657458563	557	0.9737762237762237	438	0.5778364116094987	C	1.255	-0.617482	0.03663	0.703998	0.564535	ENSG00000250254	ENST00000504686	T	0.37915	1.17	2.02	-4.04	0.04010	.	.	.	.	.	T	0.00012	0.0000	N	0.00035	-2.545	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44267	-0.9339	8	0.02654	T	1	.	1.3883	0.02245	0.4846:0.2124:0.1647:0.1384	rs6811863;rs16994115;rs52800308;rs58556101;rs6811863	44	Q9NZH5-2	.	P	44	ENSP00000424261:R44P	ENSP00000424261:R44P	R	+	2	0	PTTG2	37638581	0.013000	0.17824	0.000000	0.03702	0.001000	0.01503	-0.042000	0.12063	-1.494000	0.01833	-1.544000	0.00907	CGA	G|0.275;C|0.725	0.725	strong		0.463	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
PER3	8863	hgsc.bcm.edu	37	1	7890064	7890064	+	Silent	SNP	A	A	G	rs12023156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:7890064A>G	ENST00000361923.2	+	18	3205	c.3030A>G	c.(3028-3030)acA>acG	p.T1010T	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Silent_p.T1019T	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1010	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.		Missing (associated with eveningness and better cognitive performance during sleep deprivation exepriments; dbSNP:rs57875989).|T -> I (in dbSNP:rs12033719).		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)		CTCTGTCCACAGGATCGCCTC	0.577													G|||	1226	0.244808	0.2421	0.2118	5008	,	,		10880	0.1478		0.2863	False		,,,				2504	0.3292				p.T1010T		Atlas-SNP	.											.	PER3	95	.	0			c.A3030G						PASS	.						93.0	74.0	80.0					1																	7890064		2203	4297	6500	SO:0001819	synonymous_variant	8863	exon18			GTCCACAGGATCG	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.3030A>G	1.37:g.7890064A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	282	135	0.478723	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1	599	0.2742673992673993	129	0.2621951219512195	101	0.27900552486187846	118	0.2062937062937063	251	0.3311345646437995	G	1.865	-0.461664	0.04508	.	.	ENSG00000049246	ENST00000539773	.	.	.	0.119	0.119	0.14685	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	rs12023156	.	.	.	.	-1	.	.	.	+	.	.	PER3	7812651	0.005000	0.15991	0.054000	0.19295	0.063000	0.16089	0.651000	0.24873	0.235000	0.21160	0.232000	0.17820	.	A|0.714;G|0.286	0.286	strong		0.577	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
SCNN1B	6338	hgsc.bcm.edu	37	16	23379279	23379279	+	Splice_Site	SNP	C	C	T	rs250563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23379279C>T	ENST00000343070.2	+	5	1055	c.879C>T	c.(877-879)ttC>ttT	p.F293F	SCNN1B_ENST00000568923.1_Splice_Site_p.F266F|SCNN1B_ENST00000568085.1_Splice_Site_p.F293F|SCNN1B_ENST00000307331.5_Splice_Site_p.F338F	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	293					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	GAACTGAATTCGGTGAGTTTT	0.522													C|||	425	0.0848642	0.2504	0.0447	5008	,	,		21131	0.0		0.0616	False		,,,				2504	0.001				p.F293F		Atlas-SNP	.											.	SCNN1B	81	.	0			c.C879T						PASS	.	C		915,3479	351.8+/-311.4	80,755,1362	177.0	134.0	148.0		879	-7.9	0.2	16	dbSNP_79	148	446,8154	134.3+/-191.7	10,426,3864	yes	coding-synonymous-near-splice	SCNN1B	NM_000336.2		90,1181,5226	TT,TC,CC		5.186,20.8239,10.4741		293/641	23379279	1361,11633	2197	4300	6497	SO:0001630	splice_region_variant	6338	exon5			TGAATTCGGTGAG	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10600	protein-coding gene	gene with protein product	"""Liddle syndrome"""	600760	"""sodium channel, nonvoltage-gated 1, beta"", ""sodium channel, non-voltage-gated 1, beta"""				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.880+1C>T	16.37:g.23379279C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	155	81	0.522581	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Silent	SNP	ENST00000343070.2	37	CCDS10609.1																																																																																			C|0.894;T|0.106	0.106	strong		0.522	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2		Silent
FNDC3B	64778	hgsc.bcm.edu	37	3	171969077	171969077	+	Missense_Mutation	SNP	C	C	G	rs7652177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:171969077C>G	ENST00000336824.4	+	6	635	c.536C>G	c.(535-537)aCc>aGc	p.T179S	FNDC3B_ENST00000416957.1_Missense_Mutation_p.T179S|FNDC3B_ENST00000415807.2_Missense_Mutation_p.T179S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	179			T -> S (in dbSNP:rs7652177). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15564382, ECO:0000269|Ref.5}.		cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.T179S(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		GGAATGTCAACCTACATCACC	0.388													G|||	3229	0.644768	0.9228	0.5634	5008	,	,		16403	0.5536		0.5169	False		,,,				2504	0.5521				p.T179S		Atlas-SNP	.											FNDC3B,NS,carcinoma,0,1	FNDC3B	118	1	1	Substitution - Missense(1)	stomach(1)	c.C536G						PASS	.	G	SER/THR,SER/THR	3758,648	277.2+/-273.6	1605,548,50	49.0	53.0	51.0		536,536	6.0	1.0	3	dbSNP_116	51	4236,4364	581.3+/-391.2	1028,2180,1092	yes	missense,missense	FNDC3B	NM_001135095.1,NM_022763.3	58,58	2633,2728,1142	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	49.2558,14.7072,38.5361	benign,benign	179/1205,179/1205	171969077	7994,5012	2203	4300	6503	SO:0001583	missense	64778	exon6			TGTCAACCTACAT	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.536C>G	3.37:g.171969077C>G	ENSP00000338523:p.Thr179Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	107	104	0.971963	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	37	CCDS3217.1	1336	0.6117216117216118	449	0.9126016260162602	209	0.5773480662983426	289	0.5052447552447552	389	0.5131926121372031	G	9.197	1.027387	0.19512	0.852928	0.492558	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957;ENST00000443501	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.98	5.98	0.97165	.	0.114990	0.85682	N	0.000000	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34079	-0.9843	9	0.07325	T	0.83	-17.7311	17.4819	0.87674	0.0:0.1242:0.8758:0.0	rs7652177;rs17281567;rs52833274;rs60495250;rs7652177	179;179	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	S	179;179;179;152	ENSP00000411242:T179S;ENSP00000338523:T179S;ENSP00000389094:T179S;ENSP00000389064:T152S	ENSP00000338523:T179S	T	+	2	0	FNDC3B	173451771	1.000000	0.71417	0.996000	0.52242	0.891000	0.51852	4.977000	0.63792	1.554000	0.49487	-0.187000	0.12897	ACC	C|0.384;G|0.616	0.616	strong		0.388	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
STPG2	285555	hgsc.bcm.edu	37	4	99027137	99027137	+	Silent	SNP	T	T	C	rs2865979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:99027137T>C	ENST00000295268.3	-	5	668	c.579A>G	c.(577-579)ctA>ctG	p.L193L		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	193																	TTATTTCATATAGTCGTGGGA	0.274													T|||	1880	0.375399	0.4425	0.2882	5008	,	,		15184	0.2758		0.4026	False		,,,				2504	0.4213				p.L193L		Atlas-SNP	.											.	.	.	.	0			c.A579G						PASS	.	T		1962,2436	542.8+/-376.1	451,1060,688	85.0	88.0	87.0		579	1.1	0.9	4	dbSNP_101	87	3402,5194	491.9+/-373.2	692,2018,1588	no	coding-synonymous	C4orf37	NM_174952.2		1143,3078,2276	CC,CT,TT		39.5765,44.6112,41.2806		193/460	99027137	5364,7630	2199	4298	6497	SO:0001819	synonymous_variant	285555	exon5			TTCATATAGTCGT	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.579A>G	4.37:g.99027137T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_174952		Silent	SNP	ENST00000295268.3	37	CCDS3645.1																																																																																			T|0.607;C|0.393	0.393	strong		0.274	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
HSD17B4	3295	hgsc.bcm.edu	37	5	118861713	118861713	+	Missense_Mutation	SNP	A	A	G	rs11205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118861713A>G	ENST00000256216.6	+	19	1808	c.1675A>G	c.(1675-1677)Att>Gtt	p.I559V	HSD17B4_ENST00000504811.1_Missense_Mutation_p.I584V|HSD17B4_ENST00000510025.1_Missense_Mutation_p.I535V|HSD17B4_ENST00000515320.1_Missense_Mutation_p.I541V|HSD17B4_ENST00000522415.1_3'UTR|HSD17B4_ENST00000414835.2_Missense_Mutation_p.I419V|HSD17B4_ENST00000509514.1_Missense_Mutation_p.I297V|HSD17B4_ENST00000513628.1_Missense_Mutation_p.I422V	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	559	Enoyl-CoA hydratase 2.|MaoC-like.		I -> V (in dbSNP:rs11205). {ECO:0000269|PubMed:14702039}.		alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.I559V(1)		breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		ATTCAAGGCAATTAAGGTAAA	0.313													A|||	2004	0.40016	0.4092	0.4683	5008	,	,		15465	0.4177		0.4125	False		,,,				2504	0.3088				p.I584V	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											HSD17B4,NS,carcinoma,0,1	HSD17B4	63	1	1	Substitution - Missense(1)	prostate(1)	c.A1750G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	1741,2663	519.1+/-369.9	341,1059,802	148.0	142.0	144.0		1675,1750,1621	5.4	1.0	5	dbSNP_52	144	3518,5082	512.7+/-378.0	717,2084,1499	yes	missense,missense,missense	HSD17B4	NM_000414.3,NM_001199291.1,NM_001199292.1	29,29,29	1058,3143,2301	GG,GA,AA		40.907,39.5322,40.4414	benign,benign,benign	559/737,584/762,541/719	118861713	5259,7745	2202	4300	6502	SO:0001583	missense	3295	exon20			AAGGCAATTAAGG		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.1675A>G	5.37:g.118861713A>G	ENSP00000256216:p.Ile559Val	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Missense_Mutation	SNP	ENST00000256216.6	37	CCDS4126.1	888	0.4065934065934066	181	0.3678861788617886	164	0.4530386740331492	213	0.3723776223776224	330	0.43535620052770446	A	14.61	2.587740	0.46110	0.395322	0.40907	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628;ENST00000509514	T;T;T;T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4;-1.4;-1.4;-1.4	5.39	5.39	0.77823	MaoC-like dehydratase (1);	0.046452	0.85682	D	0.000000	T	0.00012	0.0000	L	0.28740	0.885	0.09310	P	0.9999982734	P;B;B;B;B	0.42827	0.791;0.223;0.418;0.094;0.118	B;B;B;B;B	0.40534	0.332;0.204;0.088;0.264;0.17	T	0.34527	-0.9825	9	0.39692	T	0.17	-21.7798	14.3833	0.66926	1.0:0.0:0.0:0.0	rs11205;rs1130646;rs3189732;rs11539470;rs11740179;rs16918307;rs17342666;rs60097041;rs11205	584;541;535;297;559	F5HE57;E9PB82;E7EWE5;E7EPL9;P51659	.;.;.;.;DHB4_HUMAN	V	559;541;535;584;419;422;297	ENSP00000256216:I559V;ENSP00000424613:I541V;ENSP00000424940:I535V;ENSP00000420914:I584V;ENSP00000411960:I419V;ENSP00000425993:I422V;ENSP00000426272:I297V	ENSP00000256216:I559V	I	+	1	0	HSD17B4	118889612	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	3.836000	0.55813	2.050000	0.60909	0.482000	0.46254	ATT	A|0.591;G|0.409	0.409	strong		0.313	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	
AADACL3	126767	hgsc.bcm.edu	37	1	12779560	12779560	+	Silent	SNP	T	T	C	rs3010876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12779560T>C	ENST00000359318.5	+	2	286	c.81T>C	c.(79-81)gaT>gaC	p.D27D	AADACL3_ENST00000332530.3_Intron	NM_001103170.1	NP_001096640.1	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3	27							hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	15	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TAAAGTATGATCCCGATGTTG	0.483													C|||	4254	0.849441	0.9228	0.8818	5008	,	,		8510	0.7817		0.83	False		,,,				2504	0.817				p.D27D		Atlas-SNP	.											.	AADACL3	84	.	0			c.T81C						PASS	.	C	,	3581,333		1636,309,12	157.0	162.0	160.0		,81	-6.3	0.0	1	dbSNP_101	160	6892,1418		2864,1164,127	no	intron,coding-synonymous	AADACL3	NM_001103169.1,NM_001103170.1	,	4500,1473,139	CC,CT,TT		17.0638,8.5079,14.3243	,	,27/351	12779560	10473,1751	1957	4155	6112	SO:0001819	synonymous_variant	126767	exon2			GTATGATCCCGAT		CCDS41253.1	1p36.21	2014-07-17			ENSG00000188984	ENSG00000188984			32037	protein-coding gene	gene with protein product							Standard	XM_006710337		Approved	OTTHUMG00000001887	uc009vnn.1	Q5VUY0	OTTHUMG00000001887	ENST00000359318.5:c.81T>C	1.37:g.12779560T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_001103170	B3KXR9|Q5VUY1	Silent	SNP	ENST00000359318.5	37	CCDS41253.1																																																																																			T|0.148;C|0.852	0.852	strong		0.483	AADACL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005324.2	NM_001103170	
IGSF10	285313	hgsc.bcm.edu	37	3	151165106	151165106	+	Missense_Mutation	SNP	T	T	G	rs35491609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151165106T>G	ENST00000282466.3	-	4	2662	c.2663A>C	c.(2662-2664)cAa>cCa	p.Q888P		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	888					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GGATGAATGTTGATTGGTTGT	0.428													T|||	37	0.00738818	0.0272	0.0014	5008	,	,		22524	0.0		0.0	False		,,,				2504	0.0				p.Q888P		Atlas-SNP	.											IGSF10,NS,carcinoma,-1,1	IGSF10	279	1	0			c.A2663C						PASS	.	T	PRO/GLN	99,4307	79.3+/-117.8	0,99,2104	356.0	355.0	355.0		2663	-5.0	0.0	3	dbSNP_126	355	0,8600		0,0,4300	yes	missense	IGSF10	NM_178822.4	76	0,99,6404	GG,GT,TT		0.0,2.2469,0.7612	benign	888/2624	151165106	99,12907	2203	4300	6503	SO:0001583	missense	285313	exon4			GAATGTTGATTGG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.2663A>C	3.37:g.151165106T>G	ENSP00000282466:p.Gln888Pro	Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	348	156	0.448276	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	T	10.97	1.500447	0.26861	0.022469	0.0	ENSG00000152580	ENST00000282466	T	0.68903	-0.36	5.41	-5.03	0.02973	.	0.536026	0.15865	N	0.240805	T	0.20333	0.0489	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.16541	-1.0399	10	0.20519	T	0.43	.	7.7274	0.28767	0.0:0.217:0.3727:0.4103	rs35491609	888	Q6WRI0	IGS10_HUMAN	P	888	ENSP00000282466:Q888P	ENSP00000282466:Q888P	Q	-	2	0	IGSF10	152647796	0.000000	0.05858	0.000000	0.03702	0.347000	0.29111	-0.226000	0.09139	-0.598000	0.05806	0.482000	0.46254	CAA	T|0.992;G|0.008	0.008	strong		0.428	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
ZNF516	9658	hgsc.bcm.edu	37	18	74091235	74091235	+	Silent	SNP	G	G	C	rs621265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:74091235G>C	ENST00000443185.2	-	4	3152	c.2835C>G	c.(2833-2835)gcC>gcG	p.A945A	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	945					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)		GCTTGCTATTGGCCGAGGGCT	0.672													C|||	526	0.105032	0.3132	0.0418	5008	,	,		14120	0.0149		0.0378	False		,,,				2504	0.0307				p.A945A		Atlas-SNP	.											.	ZNF516	102	.	0			c.C2835G						PASS	.	C		796,2754		68,660,1047	21.0	25.0	24.0		2835	0.1	0.0	18	dbSNP_83	24	172,7672		1,170,3751	no	coding-synonymous	ZNF516	NM_014643.3		69,830,4798	CC,CG,GG		2.1928,22.4225,8.4957		945/1164	74091235	968,10426	1775	3922	5697	SO:0001819	synonymous_variant	9658	exon4			GCTATTGGCCGAG	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.2835C>G	18.37:g.74091235G>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_014643		Silent	SNP	ENST00000443185.2	37																																																																																				G|0.898;C|0.102	0.102	strong		0.672	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
TEP1	7011	hgsc.bcm.edu	37	14	20876253	20876253	+	Missense_Mutation	SNP	A	A	G	rs1760897	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20876253A>G	ENST00000262715.5	-	2	386	c.346T>C	c.(346-348)Tct>Cct	p.S116P	TEP1_ENST00000556935.1_Missense_Mutation_p.S116P	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	116			S -> P (in dbSNP:rs1760897). {ECO:0000269|PubMed:9020079}.		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)		TTTAGACTAGAGAGGGTGGCC	0.517													G|||	1799	0.359225	0.5439	0.3012	5008	,	,		23338	0.1825		0.3211	False		,,,				2504	0.3722				p.S116P		Atlas-SNP	.											.	TEP1	224	.	0			c.T346C						PASS	.	G	PRO/SER	2249,2157	581.0+/-385.3	566,1117,520	107.0	109.0	109.0		346	-0.6	0.0	14	dbSNP_89	109	2731,5869	681.9+/-403.8	446,1839,2015	yes	missense	TEP1	NM_007110.4	74	1012,2956,2535	GG,GA,AA		31.7558,48.956,38.29	benign	116/2628	20876253	4980,8026	2203	4300	6503	SO:0001583	missense	7011	exon2			GACTAGAGAGGGT		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.346T>C	14.37:g.20876253A>G	ENSP00000262715:p.Ser116Pro	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	183	84	0.459016	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	742	0.33974358974358976	262	0.532520325203252	115	0.31767955801104975	113	0.19755244755244755	252	0.3324538258575198	G	0.010	-1.778725	0.00634	0.51044	0.317558	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000556549	T;T;T	0.26223	1.75;1.75;1.75	5.08	-0.634	0.11516	.	0.736857	0.12656	N	0.450073	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43245	-0.9403	9	0.02654	T	1	-4.0792	3.387	0.07276	0.2777:0.0:0.2821:0.4401	rs1760897;rs3748335;rs52804943;rs61199362;rs1760897	116;116	G3V5X7;Q99973	.;TEP1_HUMAN	P	116	ENSP00000262715:S116P;ENSP00000452574:S116P;ENSP00000452240:S116P	ENSP00000262715:S116P	S	-	1	0	TEP1	19946093	0.000000	0.05858	0.007000	0.13788	0.327000	0.28475	-0.657000	0.05335	-0.134000	0.11516	-0.755000	0.03482	TCT	A|0.635;G|0.365	0.365	strong		0.517	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
MTRR	4552	hgsc.bcm.edu	37	5	7885907	7885907	+	Missense_Mutation	SNP	C	C	G	rs10064631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:7885907C>G	ENST00000264668.2	+	7	1108	c.1078C>G	c.(1078-1080)Ctt>Gtt	p.L360V	MTRR_ENST00000440940.2_Missense_Mutation_p.L333V|MTRR_ENST00000341013.6_3'UTR	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	360	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.		L -> V (in dbSNP:rs10064631). {ECO:0000269|PubMed:10484769}.		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)	AAGACTGCAGCTTGAAGATAA	0.468													C|||	199	0.0397364	0.1445	0.0115	5008	,	,		17404	0.0		0.0	False		,,,				2504	0.0				p.L360V		Atlas-SNP	.											.	MTRR	74	.	0			c.C1078G	GRCh37	CM992646	MTRR	M	rs10064631	PASS	.	C	VAL/LEU,VAL/LEU	639,3767	275.4+/-272.5	46,547,1610	109.0	109.0	109.0		997,1078	5.8	1.0	5	dbSNP_119	109	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	MTRR	NM_002454.2,NM_024010.2	32,32	46,555,5902	GG,GC,CC		0.093,14.503,4.9746	probably-damaging,probably-damaging	333/699,360/726	7885907	647,12359	2203	4300	6503	SO:0001583	missense	4552	exon7			CTGCAGCTTGAAG	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.1078C>G	5.37:g.7885907C>G	ENSP00000264668:p.Leu360Val	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	197	92	0.467005	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	75	0.034340659340659344	71	0.1443089430894309	4	0.011049723756906077	0	0.0	0	0.0	C	15.42	2.826850	0.50739	0.14503	9.3E-4	ENSG00000124275	ENST00000264668;ENST00000440940	T;T	0.39406	1.08;1.08	5.83	5.83	0.93111	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.00524	0.0017	M	0.66378	2.025	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.00119	-1.2031	10	0.31617	T	0.26	-27.2783	13.3424	0.60553	0.0:0.9283:0.0:0.0717	rs10064631;rs10064631	360	Q9UBK8	MTRR_HUMAN	V	360;333	ENSP00000264668:L360V;ENSP00000402510:L333V	ENSP00000264668:L360V	L	+	1	0	MTRR	7938907	1.000000	0.71417	0.991000	0.47740	0.034000	0.12701	4.189000	0.58358	2.753000	0.94483	0.650000	0.86243	CTT	C|0.948;G|0.052	0.052	strong		0.468	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
ABCA1	19	hgsc.bcm.edu	37	9	107578478	107578478	+	Silent	SNP	C	C	T	rs2230807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107578478C>T	ENST00000374736.3	-	25	4078	c.3684G>A	c.(3682-3684)cgG>cgA	p.R1228R		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1228					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)	GGTCTGAGAGCCGGTCATCAA	0.488													C|||	316	0.063099	0.2269	0.0231	5008	,	,		18611	0.0		0.0	False		,,,				2504	0.0				p.R1228R		Atlas-SNP	.											.	ABCA1	244	.	0			c.G3684A						PASS	.	C		778,3628	314.7+/-293.7	70,638,1495	159.0	165.0	163.0		3684	-2.1	1.0	9	dbSNP_98	163	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	ABCA1	NM_005502.3		70,647,5786	TT,TC,CC		0.1047,17.6577,6.0511		1228/2262	107578478	787,12219	2203	4300	6503	SO:0001819	synonymous_variant	19	exon25			TGAGAGCCGGTCA	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.3684G>A	9.37:g.107578478C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	158	87	0.550633	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			T|0.049;G|0.134	0.049	strong		0.488	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
ACHE	43	hgsc.bcm.edu	37	7	100490077	100490077	+	Silent	SNP	G	G	A	rs7636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100490077G>A	ENST00000412389.1	-	2	1586	c.1431C>T	c.(1429-1431)ccC>ccT	p.P477P	ACHE_ENST00000411582.1_Silent_p.P477P|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000428317.1_Silent_p.P477P|ACHE_ENST00000419336.2_Silent_p.P389P|ACHE_ENST00000241069.5_Silent_p.P477P|ACHE_ENST00000302913.4_Silent_p.P477P			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	477					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	CGTAGCCGTGGGGCACCCCCA	0.617													G|||	527	0.105232	0.2897	0.0663	5008	,	,		13694	0.002		0.0527	False		,,,				2504	0.044				p.P477P		Atlas-SNP	.											.	ACHE	80	.	0			c.C1431T						PASS	.	G	,	1006,3400	372.5+/-320.4	128,750,1325	45.0	45.0	45.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1431,1431	3.9	1.0	7	dbSNP_52	45	411,8189	128.7+/-186.9	14,383,3903	yes	coding-synonymous,coding-synonymous	ACHE	NM_000665.3,NM_015831.2	,	142,1133,5228	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	4.7791,22.8325,10.895	,	477/615,477/618	100490077	1417,11589	2203	4300	6503	SO:0001819	synonymous_variant	43	exon3			GCCGTGGGGCACC		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"""Blood group antigens"""	108	protein-coding gene	gene with protein product	"""Yt blood group"""	100740	"""acetylcholinesterase (YT blood group)"", ""acetylcholinesterase (Yt blood group)"", ""acetylcholinesterase"""	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1431C>T	7.37:g.100490077G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	101	42	0.415842	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Silent	SNP	ENST00000412389.1	37	CCDS5709.1																																																																																			G|0.887;A|0.113	0.113	strong		0.617	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831	
SETD3	84193	hgsc.bcm.edu	37	14	99927594	99927594	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:99927594C>T	ENST00000331768.5	-	4	439	c.280G>A	c.(280-282)Gag>Aag	p.E94K	SETD3_ENST00000329331.3_Missense_Mutation_p.E94K|SETD3_ENST00000453938.1_Intron|SETD3_ENST00000436070.2_Missense_Mutation_p.E94K	NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	94	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				TCAAAACCCTCGACAGAAGCC	0.388																																					p.E94K		Atlas-SNP	.											SETD3,colon,carcinoma,+2,1	SETD3	56	1	0			c.G280A						scavenged	.						106.0	110.0	108.0					14																	99927594		2203	4300	6503	SO:0001583	missense	84193	exon4			AACCCTCGACAGA	AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"""chromosome 14 open reading frame 154"""	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.280G>A	14.37:g.99927594C>T	ENSP00000327436:p.Glu94Lys	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	166	4	0.0240964	NM_032233	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Missense_Mutation	SNP	ENST00000331768.5	37	CCDS9951.1	.	.	.	.	.	.	.	.	.	.	C	19.49	3.837613	0.71373	.	.	ENSG00000183576	ENST00000331768;ENST00000329331;ENST00000436070	T;T;T	0.14266	2.52;2.52;2.52	5.45	4.57	0.56435	.	0.313213	0.35013	N	0.003506	T	0.08313	0.0207	L	0.41824	1.3	0.58432	D	0.999998	P;P;P	0.42649	0.633;0.786;0.564	B;B;B	0.25884	0.029;0.064;0.054	T	0.16867	-1.0388	10	0.08179	T	0.78	-19.4543	14.3822	0.66919	0.0:0.929:0.0:0.071	.	94;94;94	Q6NXR6;A0PJU3;Q86TU7	.;.;SETD3_HUMAN	K	94	ENSP00000327436:E94K;ENSP00000327910:E94K;ENSP00000408602:E94K	ENSP00000327910:E94K	E	-	1	0	SETD3	98997347	1.000000	0.71417	0.961000	0.40146	0.999000	0.98932	7.744000	0.85034	1.441000	0.47550	0.655000	0.94253	GAG	.	.	none		0.388	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233	
USP45	85015	hgsc.bcm.edu	37	6	99893938	99893938	+	Silent	SNP	T	T	C	rs4504482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:99893938T>C	ENST00000327681.6	-	14	2242	c.1710A>G	c.(1708-1710)ggA>ggG	p.G570G	USP45_ENST00000392738.2_Silent_p.G250G|USP45_ENST00000500704.2_Silent_p.G570G|USP45_ENST00000369233.2_Silent_p.G522G|USP45_ENST00000539675.1_Intron	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	40	0	0		WXS	Illumina HiSeq	Phase_I	37	36	0.972973	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	
ARMCX2	9823	hgsc.bcm.edu	37	X	100912065	100912065	+	Silent	SNP	C	C	T	rs78189978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:100912065C>T	ENST00000328766.5	-	5	963	c.510G>A	c.(508-510)gcG>gcA	p.A170A	ARMCX2_ENST00000356824.4_Silent_p.A170A|ARMCX2_ENST00000467416.1_5'Flank|ARMCX2_ENST00000330154.2_Silent_p.A170A	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	170	Ala-rich.					integral component of membrane (GO:0016021)				NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(6)|prostate(1)|skin(1)	29						TGGAAGTCTCCGCTTCTCTGG	0.652													C|||	57	0.0150993	0.0416	0.0029	3775	,	,		11432	0.0		0.0	False		,,,				2504	0.0				p.A170A		Atlas-SNP	.											.	ARMCX2	75	.	0			c.G510A						PASS	.	C	,	213,3621		7,168,31,1457,539	28.0	29.0	28.0		510,510	-0.1	0.0	X	dbSNP_131	28	1,6713		0,1,0,2427,1858	no	coding-synonymous,coding-synonymous	ARMCX2	NM_014782.5,NM_177949.2	,	7,169,31,3884,2397	TT,TC,T,CC,C		0.0149,5.5556,2.0288	,	170/633,170/633	100912065	214,10334	2202	4286	6488	SO:0001819	synonymous_variant	9823	exon5			AGTCTCCGCTTCT	AB011084	CCDS14490.1	Xq21.33-q22.2	2014-03-21			ENSG00000184867	ENSG00000184867		"""Armadillo repeat containing"""	16869	protein-coding gene	gene with protein product		300363				9628581, 11162520, 16221301, 22569362	Standard	XM_005278109		Approved	ALEX2, KIAA0512, GASP9	uc004eif.3	Q7L311	OTTHUMG00000022038	ENST00000328766.5:c.510G>A	X.37:g.100912065C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	74	46	0.621622	NM_014782	O60267|Q5H9D9	Silent	SNP	ENST00000328766.5	37	CCDS14490.1																																																																																			C|0.981;T|0.019	0.019	strong		0.652	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057586.1	NM_014782	
SLC4A7	9497	hgsc.bcm.edu	37	3	27442336	27442336	+	Silent	SNP	G	G	A	rs3736312	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:27442336G>A	ENST00000295736.5	-	16	2389	c.2319C>T	c.(2317-2319)aaC>aaT	p.N773N	SLC4A7_ENST00000455077.1_Silent_p.N654N|SLC4A7_ENST00000388777.4_Silent_p.N323N|SLC4A7_ENST00000440156.1_Silent_p.N769N|SLC4A7_ENST00000446700.1_Silent_p.N765N|SLC4A7_ENST00000445684.1_Silent_p.N769N|SLC4A7_ENST00000435667.2_Silent_p.N658N|SLC4A7_ENST00000437179.1_Silent_p.N654N|SLC4A7_ENST00000428386.1_Silent_p.N649N|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000454389.1_Silent_p.N782N	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	773					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CATTGCTGGGGTTTGGAGGTT	0.313													G|||	642	0.128195	0.0446	0.1614	5008	,	,		17831	0.0565		0.2247	False		,,,				2504	0.1922				p.N773N		Atlas-SNP	.											.	SLC4A7	119	.	0			c.C2319T						PASS	.	G		354,4052	182.6+/-210.3	9,336,1858	152.0	149.0	150.0		2319	1.3	1.0	3	dbSNP_107	150	2129,6465	365.1+/-333.8	264,1601,2432	no	coding-synonymous	SLC4A7	NM_003615.3		273,1937,4290	AA,AG,GG		24.7731,8.0345,19.1		773/1215	27442336	2483,10517	2203	4297	6500	SO:0001819	synonymous_variant	9497	exon16			GCTGGGGTTTGGA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2319C>T	3.37:g.27442336G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	160	75	0.46875	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			G|0.828;A|0.172	0.172	strong		0.313	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
MYO18B	84700	hgsc.bcm.edu	37	22	26423477	26423477	+	Missense_Mutation	SNP	G	G	A	rs7284177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26423477G>A	ENST00000407587.2	+	43	7709	c.7540G>A	c.(7540-7542)Ggc>Agc	p.G2514S	MYO18B_ENST00000335473.7_Missense_Mutation_p.G2513S|MYO18B_ENST00000536101.1_Missense_Mutation_p.G2513S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2513	Poly-Ser.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CTCATCCTCCGGCTCCATCGT	0.587													A|||	352	0.0702875	0.2005	0.0259	5008	,	,		18932	0.004		0.0179	False		,,,				2504	0.0481				p.G2513S		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7537A						PASS	.	A	SER/GLY	695,3407		58,579,1414	53.0	55.0	55.0		7537	1.8	1.0	22	dbSNP_116	55	146,8242		1,144,4049	yes	missense	MYO18B	NM_032608.5	56	59,723,5463	AA,AG,GG		1.7406,16.943,6.7334	benign	2513/2568	26423477	841,11649	2051	4194	6245	SO:0001583	missense	84700	exon43			TCCTCCGGCTCCA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7540G>A	22.37:g.26423477G>A	ENSP00000386096:p.Gly2514Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	56	21	0.375	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		123	0.05631868131868132	92	0.18699186991869918	13	0.03591160220994475	4	0.006993006993006993	14	0.018469656992084433	A	4.656	0.121893	0.08931	0.16943	0.017406	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.85088	-1.92;-1.92;-1.94	5.17	1.8	0.24995	.	0.170297	0.37437	N	0.002083	T	0.00109	0.0003	N	0.00729	-1.24	0.54753	P	1.0999999999983245E-5	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.002;0.002	T	0.12426	-1.0548	9	0.02654	T	1	.	4.0444	0.09766	0.4128:0.0:0.4136:0.1736	rs7284177;rs52837742;rs59696890;rs7284177	2026;2515;2513;2514;2513	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	S	2513;2513;2514	ENSP00000441229:G2513S;ENSP00000334563:G2513S;ENSP00000386096:G2514S	ENSP00000334563:G2513S	G	+	1	0	MYO18B	24753477	0.459000	0.25768	0.958000	0.39756	0.893000	0.52053	0.694000	0.25512	-0.007000	0.14345	-0.361000	0.07541	GGC	G|0.931;A|0.069	0.069	strong		0.587	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
NMU	10874	hgsc.bcm.edu	37	4	56466734	56466734	+	Missense_Mutation	SNP	G	G	T	rs12108463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:56466734G>T	ENST00000264218.3	-	8	549	c.444C>A	c.(442-444)ttC>ttA	p.F148L	NMU_ENST00000505262.1_Missense_Mutation_p.F121L|NMU_ENST00000507338.1_Missense_Mutation_p.F123L|NMU_ENST00000511469.1_Missense_Mutation_p.F132L|NMU_ENST00000515325.1_5'UTR	NM_006681.2	NP_006672.1	P48645	NMU_HUMAN	neuromedin U	148			F -> L (in dbSNP:rs12108463).		digestion (GO:0007586)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of hormone secretion (GO:0046887)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic transmission (GO:0050806)|regulation of smooth muscle contraction (GO:0006940)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|terminal bouton (GO:0043195)	receptor binding (GO:0005102)			lung(3)|ovary(1)|urinary_tract(1)	5	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)		AGGGACTTTGGAATTCTTCCT	0.299													G|||	209	0.0417332	0.1543	0.0072	5008	,	,		17523	0.0		0.0	False		,,,				2504	0.0				p.F148L		Atlas-SNP	.											.	NMU	17	.	0			c.C444A						PASS	.	G	LEU/PHE	585,3821	251.8+/-258.4	41,503,1659	54.0	59.0	57.0		444	-3.0	0.2	4	dbSNP_120	57	5,8585	3.7+/-12.6	0,5,4290	yes	missense	NMU	NM_006681.2	22	41,508,5949	TT,TG,GG		0.0582,13.2773,4.5399	benign	148/175	56466734	590,12406	2203	4295	6498	SO:0001583	missense	10874	exon8			ACTTTGGAATTCT	X76029	CCDS3501.1, CCDS75125.1	4q12	2013-02-26			ENSG00000109255	ENSG00000109255		"""Endogenous ligands"""	7859	protein-coding gene	gene with protein product	"""prepro-NMU"""	605103				7619205	Standard	XM_005265713		Approved		uc003hbc.3	P48645	OTTHUMG00000102161	ENST00000264218.3:c.444C>A	4.37:g.56466734G>T	ENSP00000264218:p.Phe148Leu	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	213	91	0.42723	NM_006681		Missense_Mutation	SNP	ENST00000264218.3	37	CCDS3501.1	64	0.029304029304029304	62	0.12601626016260162	2	0.0055248618784530384	0	0.0	0	0.0	G	4.096	0.015910	0.07959	0.132773	5.82E-4	ENSG00000109255	ENST00000511469;ENST00000264218;ENST00000505262;ENST00000541393;ENST00000507338	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	4.72	-2.96	0.05547	.	0.703326	0.13471	N	0.385414	T	0.00144	0.0004	N	0.11064	0.09	0.09310	N	0.999996	B	0.09022	0.002	B	0.08055	0.003	T	0.13019	-1.0525	10	0.07813	T	0.8	-6.4377	2.1008	0.03679	0.3758:0.1231:0.3762:0.1249	rs12108463;rs52827993;rs12108463	148	P48645	NMU_HUMAN	L	132;148;121;131;123	ENSP00000422399:F132L;ENSP00000264218:F148L;ENSP00000424246:F121L;ENSP00000422870:F123L	ENSP00000264218:F148L	F	-	3	2	NMU	56161491	0.165000	0.22948	0.173000	0.22940	0.971000	0.66376	-1.188000	0.03064	-0.684000	0.05183	0.585000	0.79938	TTC	G|0.960;T|0.040	0.040	strong		0.299	NMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220006.2		
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39280162	39280162	+	Silent	SNP	A	A	G	rs28515113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39280162A>G	ENST00000394014.1	-	1	257	c.213T>C	c.(211-213)tgT>tgC	p.C71C		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	71	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].					keratin filament (GO:0045095)		p.C71C(3)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGGTGGTCCTACAGCAGGTGG	0.677													A|||	863	0.172324	0.4357	0.1138	5008	,	,		14227	0.1389		0.0477	False		,,,				2504	0.0204				p.C71C		Atlas-SNP	.											KRTAP4-12,colon,carcinoma,0,3	KRTAP4-12	32	3	3	Substitution - coding silent(3)	large_intestine(3)	c.T213C						scavenged	.	A		192,3702		9,174,1764	31.0	55.0	47.0		213	-2.0	0.0	17	dbSNP_125	47	5,8543		0,5,4269	no	coding-synonymous	KRTAP4-12	NM_031854.2		9,179,6033	GG,GA,AA		0.0585,4.9307,1.5833		71/202	39280162	197,12245	1947	4274	6221	SO:0001819	synonymous_variant	83755	exon1			GGTCCTACAGCAG	AJ406943	CCDS32649.1	17q21.2	2013-06-25			ENSG00000213416	ENSG00000213416		"""Keratin associated proteins"""	16776	protein-coding gene	gene with protein product						11279113	Standard	NM_031854		Approved	KAP4.12	uc002hwa.3	Q9BQ66	OTTHUMG00000133632	ENST00000394014.1:c.213T>C	17.37:g.39280162A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_031854	A3KMC5|Q495I0	Silent	SNP	ENST00000394014.1	37	CCDS32649.1																																																																																			A|0.891;G|0.109	0.109	strong		0.677	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1		
TG	7038	hgsc.bcm.edu	37	8	133898949	133898949	+	Silent	SNP	C	C	T	rs61741629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133898949C>T	ENST00000220616.4	+	9	1372	c.1332C>T	c.(1330-1332)atC>atT	p.I444I	TG_ENST00000377869.1_Silent_p.I444I	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	444					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)		AAGAAGCCATCCGAGCAATTT	0.502													C|||	124	0.0247604	0.0923	0.0029	5008	,	,		18045	0.0		0.0	False		,,,				2504	0.0				p.I444I		Atlas-SNP	.											.	TG	416	.	0			c.C1332T						PASS	.	C		332,4074	169.1+/-199.8	19,294,1890	73.0	80.0	78.0		1332	-1.0	0.0	8	dbSNP_129	78	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TG	NM_003235.4		19,296,6188	TT,TC,CC		0.0233,7.5352,2.568		444/2769	133898949	334,12672	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon9			AGCCATCCGAGCA	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.1332C>T	8.37:g.133898949C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	68	42	0.617647	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																			C|0.971;T|0.029	0.029	strong		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
VAMP8	8673	hgsc.bcm.edu	37	2	85806266	85806266	+	Silent	SNP	C	C	T	rs3731828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85806266C>T	ENST00000263864.5	+	2	294	c.138C>T	c.(136-138)aaC>aaT	p.N46N	VAMP8_ENST00000409760.1_Silent_p.N46N|VAMP8_ENST00000432071.1_Silent_p.N20N	NM_003761.4	NP_003752.2	Q9BV40	VAMP8_HUMAN	vesicle-associated membrane protein 8	46	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				autophagic vacuole fusion (GO:0000046)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|secretory granule membrane (GO:0030667)|SNARE complex (GO:0031201)		p.N46N(1)		breast(1)|endometrium(2)|large_intestine(1)|stomach(2)	6						ATCTCCGCAACAAGACAGAGG	0.542													C|||	1419	0.283347	0.3971	0.2161	5008	,	,		17696	0.3085		0.2982	False		,,,				2504	0.136				p.N46N		Atlas-SNP	.											VAMP8,NS,carcinoma,0,1	VAMP8	10	1	1	Substitution - coding silent(1)	stomach(1)	c.C138T						PASS	.	C		1556,2850	452.8+/-350.1	282,992,929	39.0	38.0	38.0		138	2.9	1.0	2	dbSNP_107	38	2352,6248	362.0+/-332.6	325,1702,2273	no	coding-synonymous	VAMP8	NM_003761.4		607,2694,3202	TT,TC,CC		27.3488,35.3155,30.0477		46/101	85806266	3908,9098	2203	4300	6503	SO:0001819	synonymous_variant	8673	exon2			CCGCAACAAGACA	AF053233	CCDS1979.1	2p12-p11.2	2013-02-13	2012-10-17		ENSG00000118640	ENSG00000118640		"""Vesicle-associated membrane proteins"""	12647	protein-coding gene	gene with protein product	"""endobrevin"""	603177				9878266, 9614193	Standard	NM_003761		Approved	EDB	uc002spt.4	Q9BV40	OTTHUMG00000130180	ENST00000263864.5:c.138C>T	2.37:g.85806266C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_003761	O60625|Q53SP9|Q6IB09	Silent	SNP	ENST00000263864.5	37	CCDS1979.1																																																																																			C|0.698;T|0.302	0.302	strong		0.542	VAMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252498.3	NM_003761	
FAM129A	116496	hgsc.bcm.edu	37	1	184764351	184764351	+	Silent	SNP	G	G	A	rs35543943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:184764351G>A	ENST00000367511.3	-	14	2740	c.2547C>T	c.(2545-2547)gaC>gaT	p.D849D	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	849	Glu-rich.				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						GGCAGATGGGGTCAGAACCTA	0.597													G|||	479	0.095647	0.3457	0.0274	5008	,	,		19839	0.0		0.003	False		,,,				2504	0.0				p.D849D		Atlas-SNP	.											.	FAM129A	98	.	0			c.C2547T						PASS	.	G		1198,3208	418.3+/-338.2	175,848,1180	95.0	75.0	82.0		2547	3.8	0.0	1	dbSNP_126	82	27,8573	17.3+/-56.4	0,27,4273	no	coding-synonymous	FAM129A	NM_052966.2		175,875,5453	AA,AG,GG		0.314,27.1902,9.4187		849/929	184764351	1225,11781	2203	4300	6503	SO:0001819	synonymous_variant	116496	exon14			GATGGGGTCAGAA	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.2547C>T	1.37:g.184764351G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Silent	SNP	ENST00000367511.3	37	CCDS1364.1																																																																																			A|0.101;C|0.000;G|0.899;T|0.000	0.101	strong		0.597	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1		
DSP	1832	hgsc.bcm.edu	37	6	7577260	7577260	+	Silent	SNP	C	C	T	rs2064217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7577260C>T	ENST00000379802.3	+	20	3203	c.2862C>T	c.(2860-2862)tgC>tgT	p.C954C	DSP_ENST00000418664.2_Silent_p.C954C	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	954	Globular 1.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.C954C(1)		biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		CTGAACTTTGCGCCAATTCAA	0.323													C|||	1378	0.27516	0.4039	0.2363	5008	,	,		18325	0.1915		0.2266	False		,,,				2504	0.2648				p.C954C		Atlas-SNP	.											DSP,NS,carcinoma,0,1	DSP	306	1	1	Substitution - coding silent(1)	stomach(1)	c.C2862T						PASS	.	C	,	1640,2766	502.2+/-365.2	310,1020,873	88.0	84.0	85.0		2862,2862	2.1	1.0	6	dbSNP_94	85	1856,6742	329.9+/-319.0	194,1468,2637	no	coding-synonymous,coding-synonymous	DSP	NM_001008844.1,NM_004415.2	,	504,2488,3510	TT,TC,CC		21.5864,37.222,26.884	,	954/2273,954/2872	7577260	3496,9508	2203	4299	6502	SO:0001819	synonymous_variant	1832	exon20			ACTTTGCGCCAAT	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.2862C>T	6.37:g.7577260C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	147	71	0.482993	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																			C|0.737;T|0.263	0.263	strong		0.323	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
ZNF746	155061	hgsc.bcm.edu	37	7	149174758	149174758	+	Silent	SNP	G	G	A	rs61746598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149174758G>A	ENST00000340622.3	-	5	889	c.609C>T	c.(607-609)ggC>ggT	p.G203G	ZNF746_ENST00000458143.2_Silent_p.G203G			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	203					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			ACGCCTCCACGCCCAGGGCCT	0.667													G|||	174	0.0347444	0.1248	0.013	5008	,	,		16240	0.0		0.0	False		,,,				2504	0.0				p.G203G		Atlas-SNP	.											.	ZNF746	68	.	0			c.C609T						PASS	.	G	,	528,3878	228.1+/-243.1	33,462,1708	27.0	30.0	29.0		609,609	-6.2	0.7	7	dbSNP_129	29	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous,coding-synonymous	ZNF746	NM_001163474.1,NM_152557.4	,	33,465,6005	AA,AG,GG		0.0349,11.9837,4.0827	,	203/646,203/645	149174758	531,12475	2203	4300	6503	SO:0001819	synonymous_variant	155061	exon5			CTCCACGCCCAGG	AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"""Zinc fingers, C2H2-type"", ""-"""	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.609C>T	7.37:g.149174758G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_001163474	A8K6Z9|Q6ZRF9	Silent	SNP	ENST00000340622.3	37	CCDS5897.1																																																																																			G|0.960;A|0.040	0.040	strong		0.667	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557	
FLG2	388698	hgsc.bcm.edu	37	1	152326516	152326516	+	Missense_Mutation	SNP	T	T	C	rs16833974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152326516T>C	ENST00000388718.5	-	3	3818	c.3746A>G	c.(3745-3747)cAt>cGt	p.H1249R	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1249	Ser-rich.		H -> R (in dbSNP:rs16833974).		establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGACTGGCTATGTCTAGTGGT	0.478													T|||	341	0.0680911	0.2421	0.0231	5008	,	,		25196	0.0		0.005	False		,,,				2504	0.0				p.H1249R		Atlas-SNP	.											.	FLG2	431	.	0			c.A3746G						PASS	.	T	ARG/HIS	842,3564	332.0+/-302.3	71,700,1432	263.0	245.0	251.0		3746	2.5	0.0	1	dbSNP_123	251	25,8575	17.9+/-57.8	0,25,4275	yes	missense	FLG2	NM_001014342.2	29	71,725,5707	CC,CT,TT		0.2907,19.1103,6.6662	possibly-damaging	1249/2392	152326516	867,12139	2203	4300	6503	SO:0001583	missense	388698	exon3			TGGCTATGTCTAG	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.3746A>G	1.37:g.152326516T>C	ENSP00000373370:p.His1249Arg	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	349	175	0.501433	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	118	0.05402930402930403	112	0.22764227642276422	4	0.011049723756906077	0	0.0	2	0.002638522427440633	T	9.679	1.148853	0.21288	0.191103	0.002907	ENSG00000143520	ENST00000388718	T	0.37752	1.18	3.64	2.47	0.30058	.	.	.	.	.	T	0.09468	0.0233	L	0.52266	1.64	0.80722	P	0.0	P	0.39480	0.675	B	0.28638	0.092	T	0.17410	-1.0370	8	0.16420	T	0.52	-0.2453	7.1344	0.25521	0.0:0.0:0.2304:0.7696	rs16833974;rs16833974	1249	Q5D862	FILA2_HUMAN	R	1249	ENSP00000373370:H1249R	ENSP00000373370:H1249R	H	-	2	0	FLG2	150593140	0.000000	0.05858	0.001000	0.08648	0.076000	0.17211	-0.219000	0.09228	0.384000	0.24942	0.254000	0.18369	CAT	T|0.932;C|0.068	0.068	strong		0.478	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
FANCA	2175	hgsc.bcm.edu	37	16	89809319	89809319	+	Silent	SNP	T	T	C	rs1800358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89809319T>C	ENST00000389301.3	-	37	3684	c.3654A>G	c.(3652-3654)ccA>ccG	p.P1218P	FANCA_ENST00000568369.1_Silent_p.P1218P	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1218					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GGTTGGGTGCTGGGGAGGCAG	0.542			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	789	0.157548	0.2216	0.0389	5008	,	,		18197	0.2629		0.0765	False		,,,				2504	0.1299				p.P1218P		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.A3654G						PASS	.	C		924,3472	736.3+/-410.8	87,750,1361	71.0	71.0	71.0		3654	-9.7	0.0	16	dbSNP_89	71	791,7809	783.2+/-407.6	36,719,3545	no	coding-synonymous	FANCA	NM_000135.2		123,1469,4906	CC,CT,TT		9.1977,21.0191,13.1964		1218/1456	89809319	1715,11281	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon37	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGGTGCTGGGGAG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3654A>G	16.37:g.89809319T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	39	0.423913	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			T|0.874;C|0.126	0.126	strong		0.542	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
MAP10	54627	hgsc.bcm.edu	37	1	232940953	232940953	+	Missense_Mutation	SNP	T	T	C	rs10797593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232940953T>C	ENST00000418460.1	+	1	311	c.184T>C	c.(184-186)Tca>Cca	p.S62P		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	0					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)	p.S62P(1)									CTCAGCATTATCATCAATTGT	0.403													T|||	595	0.11881	0.1861	0.0836	5008	,	,		20854	0.1369		0.0567	False		,,,				2504	0.0982				p.S62P		Atlas-SNP	.											KIAA1383_ENST00000418460,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.T184C						PASS	.	T	PRO/SER	687,3111		57,573,1269	158.0	161.0	160.0		184	0.2	0.0	1	dbSNP_120	160	386,7856		10,366,3745	yes	missense	KIAA1383	NM_019090.2	74	67,939,5014	CC,CT,TT		4.6833,18.0885,8.912		62/1048	232940953	1073,10967	1899	4121	6020	SO:0001583	missense	54627	exon1			GCATTATCATCAA	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.184T>C	1.37:g.232940953T>C	ENSP00000403208:p.Ser62Pro	Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	206	100	0.485437	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	221	0.10119047619047619	81	0.16463414634146342	29	0.08011049723756906	69	0.12062937062937062	42	0.055408970976253295	T	13.54	2.268241	0.40095	0.180885	0.046833	ENSG00000212916	ENST00000418460	.	.	.	2.64	0.208	0.15221	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.15607	-1.0431	4	0.87932	D	0	.	2.0711	0.03614	0.2587:0.1527:0.0:0.5886	rs10797593;rs52796164;rs10797593	.	.	.	P	62	.	ENSP00000403208:S62P	S	+	1	0	KIAA1383	231007576	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.732000	0.04904	0.018000	0.15052	0.260000	0.18958	TCA	T|0.893;C|0.107	0.107	strong		0.403	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
RBM34	23029	hgsc.bcm.edu	37	1	235324298	235324298	+	Silent	SNP	T	T	C	rs2295815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	58	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	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	
AGBL1	123624	hgsc.bcm.edu	37	15	86940673	86940673	+	Silent	SNP	C	C	T	rs1367647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:86940673C>T	ENST00000441037.2	+	17	2408	c.2313C>T	c.(2311-2313)acC>acT	p.T771T	AGBL1_ENST00000389298.3_Silent_p.T502T|AGBL1_ENST00000421325.2_Silent_p.T771T	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	771					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TGAAGGGTACCTTGGAGTTCC	0.493													C|||	556	0.111022	0.0598	0.1844	5008	,	,		17522	0.0605		0.1024	False		,,,				2504	0.1892				p.T771T		Atlas-SNP	.											.	AGBL1	151	.	0			c.C2313T						PASS	.	C		281,3743		10,261,1741	144.0	141.0	142.0		2313	4.5	1.0	15	dbSNP_88	142	1071,7267		70,931,3168	no	coding-synonymous	AGBL1	NM_152336.2		80,1192,4909	TT,TC,CC		12.8448,6.9831,10.9367		771/1067	86940673	1352,11010	2012	4169	6181	SO:0001819	synonymous_variant	123624	exon17			GGGTACCTTGGAG	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2313C>T	15.37:g.86940673C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	168	67	0.39881	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			C|0.912;T|0.088	0.088	strong		0.493	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
VPS25	84313	hgsc.bcm.edu	37	17	40931054	40931054	+	Silent	SNP	T	T	C	rs3744239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40931054T>C	ENST00000253794.2	+	6	538	c.498T>C	c.(496-498)acT>acC	p.T166T	WNK4_ENST00000246914.5_5'Flank	NM_032353.2	NP_115729.1	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25 homolog (S. cerevisiae)	166					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 membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)	5		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		AGATCATCACTGTCAGCGATG	0.562													C|||	691	0.137979	0.382	0.0346	5008	,	,		20764	0.0387		0.005	False		,,,				2504	0.1207				p.T166T		Atlas-SNP	.											.	VPS25	11	.	0			c.T498C						PASS	.	C		1440,2966	681.5+/-404.0	241,958,1004	92.0	80.0	84.0		498	-9.1	0.0	17	dbSNP_107	84	19,8581	818.5+/-406.9	0,19,4281	no	coding-synonymous	VPS25	NM_032353.2		241,977,5285	CC,CT,TT		0.2209,32.6827,11.2179		166/177	40931054	1459,11547	2203	4300	6503	SO:0001819	synonymous_variant	84313	exon6			CATCACTGTCAGC	AB014763	CCDS11438.1	17q21.31	2014-02-12	2006-04-04		ENSG00000131475	ENSG00000131475			28122	protein-coding gene	gene with protein product		610907	"""vacuolar protein sorting 25 (yeast)"""			15511219	Standard	NM_032353		Approved	MGC10540, EAP20, DERP9	uc002ibi.3	Q9BRG1		ENST00000253794.2:c.498T>C	17.37:g.40931054T>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	157	86	0.547771	NM_032353	B2R581	Silent	SNP	ENST00000253794.2	37	CCDS11438.1																																																																																			T|0.877;C|0.123	0.123	strong		0.562	VPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452383.1	NM_032353	
MUC17	140453	hgsc.bcm.edu	37	7	100683053	100683053	+	Missense_Mutation	SNP	A	A	G	rs200821451		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100683053A>G	ENST00000306151.4	+	3	8420	c.8356A>G	c.(8356-8358)Act>Gct	p.T2786A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2786	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)					CACCACTTCTACTGAAGCCAG	0.473																																					p.T2786A		Atlas-SNP	.											.	MUC17	804	.	0			c.A8356G						PASS	.						252.0	247.0	248.0					7																	100683053		2203	4300	6503	SO:0001583	missense	140453	exon3			ACTTCTACTGAAG	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.8356A>G	7.37:g.100683053A>G	ENSP00000302716:p.Thr2786Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	174	26	0.149425	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	4.579	0.107573	0.08780	.	.	ENSG00000169876	ENST00000306151	T	0.01902	4.57	1.21	-2.42	0.06542	.	.	.	.	.	T	0.02494	0.0076	L	0.34521	1.04	0.09310	N	1	P	0.46578	0.88	P	0.50270	0.636	T	0.31806	-0.9930	9	0.16420	T	0.52	.	3.7487	0.08558	0.2781:0.0:0.5022:0.2197	.	2786	Q685J3	MUC17_HUMAN	A	2786	ENSP00000302716:T2786A	ENSP00000302716:T2786A	T	+	1	0	MUC17	100469773	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.827000	0.04424	-1.279000	0.02405	-1.567000	0.00876	ACT	A|0.999;G|0.001	0.001	weak		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
IL12RB2	3595	hgsc.bcm.edu	37	1	67787286	67787286	+	Splice_Site	SNP	T	T	C	rs2307147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:67787286T>C	ENST00000262345.1	+	3	718	c.78T>C	c.(76-78)gaT>gaC	p.D26D	IL12RB2_ENST00000544434.1_Splice_Site_p.D26D|IL12RB2_ENST00000371000.1_Splice_Site_p.D26D|IL12RB2_ENST00000541374.1_Splice_Site_p.D26D	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	26					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						TTATTGCAGATGCGTGCAAGA	0.388													T|||	324	0.0646965	0.2383	0.013	5008	,	,		20536	0.0		0.0	False		,,,				2504	0.0				p.D26D		Atlas-SNP	.											.	IL12RB2	94	.	0			c.T78C						PASS	.	T		901,3505	347.5+/-309.5	88,725,1390	103.0	94.0	97.0		78	-1.2	1.0	1	dbSNP_100	97	9,8591	5.7+/-21.5	0,9,4291	yes	coding-synonymous-near-splice	IL12RB2	NM_001559.2		88,734,5681	CC,CT,TT		0.1047,20.4494,6.9968		26/863	67787286	910,12096	2203	4300	6503	SO:0001630	splice_region_variant	3595	exon3			TGCAGATGCGTGC	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.77-1T>C	1.37:g.67787286T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Silent	SNP	ENST00000262345.1	37	CCDS638.1																																																																																			T|0.926;C|0.074	0.074	strong		0.388	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	Silent
ADAM30	11085	hgsc.bcm.edu	37	1	120436751	120436751	+	Missense_Mutation	SNP	T	T	C	rs35273427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120436751T>C	ENST00000369400.1	-	1	2367	c.2209A>G	c.(2209-2211)Aca>Gca	p.T737A		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	737	5 X 9 AA approximate repeats.		T -> A (in dbSNP:rs35273427).		binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		ACAGTTTTTGTTTTAGATTCT	0.368													t|||	812	0.162141	0.3306	0.0865	5008	,	,		17633	0.0407		0.0606	False		,,,				2504	0.2178				p.T737A		Atlas-SNP	.											.	ADAM30	88	.	0			c.A2209G						PASS	.	T	ALA/THR	1222,3184	422.1+/-339.6	178,866,1159	196.0	205.0	202.0		2209	-1.9	0.0	1	dbSNP_126	202	495,8105	142.5+/-198.7	22,451,3827	yes	missense	ADAM30	NM_021794.3	58	200,1317,4986	CC,CT,TT		5.7558,27.7349,13.2016	benign	737/791	120436751	1717,11289	2203	4300	6503	SO:0001583	missense	11085	exon1			TTTTTGTTTTAGA	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"""ADAM metallopeptidase domain containing"""	208	protein-coding gene	gene with protein product		604779	"""a disintegrin and metalloproteinase domain 30"""				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.2209A>G	1.37:g.120436751T>C	ENSP00000358407:p.Thr737Ala	Somatic	350	1	0.00285714		WXS	Illumina HiSeq	Phase_I	384	213	0.554688	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	260	0.11904761904761904	175	0.3556910569105691	30	0.08287292817679558	12	0.02097902097902098	43	0.05672823218997362	T	0.064	-1.217896	0.01542	0.277349	0.057558	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.01126	5.3	2.55	-1.93	0.07594	.	2.259650	0.03871	U	0.275554	T	0.00271	0.0008	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.45293	-0.9271	9	0.23891	T	0.37	.	7.691	0.28567	0.0:0.5507:0.0:0.4493	rs35273427;rs61752483	737	Q9UKF2	ADA30_HUMAN	A	737	ENSP00000358407:T737A	ENSP00000358407:T737A	T	-	1	0	ADAM30	120238274	0.330000	0.24705	0.000000	0.03702	0.009000	0.06853	-0.024000	0.12435	-0.586000	0.05898	0.482000	0.46254	ACA	T|0.878;C|0.122	0.122	strong		0.368	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794	
C2orf16	84226	hgsc.bcm.edu	37	2	27802457	27802457	+	Silent	SNP	T	T	C	rs12329054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27802457T>C	ENST00000408964.2	+	1	3069	c.3018T>C	c.(3016-3018)ggT>ggC	p.G1006G	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1006						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CGTTCAATGGTATATCCCAAG	0.443													T|||	55	0.0109824	0.0378	0.0043	5008	,	,		20778	0.0		0.002	False		,,,				2504	0.0				p.G1006G		Atlas-SNP	.											.	C2orf16	357	.	0			c.T3018C						PASS	.	T		122,3976		3,116,1930	101.0	100.0	100.0		3018	-0.3	0.1	2	dbSNP_120	100	3,8421		0,3,4209	no	coding-synonymous	C2orf16	NM_032266.3		3,119,6139	CC,CT,TT		0.0356,2.9771,0.9982		1006/1985	27802457	125,12397	2049	4212	6261	SO:0001819	synonymous_variant	84226	exon1			CAATGGTATATCC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3018T>C	2.37:g.27802457T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	59	0.578431	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			T|0.986;C|0.014	0.014	strong		0.443	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
CDH9	1007	hgsc.bcm.edu	37	5	26988424	26988424	+	Missense_Mutation	SNP	T	T	C	rs2288467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:26988424T>C	ENST00000231021.4	-	2	189	c.17A>G	c.(16-18)tAt>tGt	p.Y6C		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	6			Y -> C (in dbSNP:rs2288467). {ECO:0000269|PubMed:15489334}.		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						TAATGGTATATAATGGTAAGT	0.333													C|||	1632	0.325879	0.4894	0.2536	5008	,	,		15500	0.1518		0.4712	False		,,,				2504	0.1861				p.Y6C	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A17G						PASS	.	C	CYS/TYR	2289,2117	576.3+/-384.2	594,1101,508	119.0	125.0	123.0		17	2.7	0.0	5	dbSNP_100	123	4297,4303	575.6+/-390.2	1094,2109,1097	yes	missense	CDH9	NM_016279.3	194	1688,3210,1605	CC,CT,TT		49.9651,48.0481,49.3618	benign	6/790	26988424	6586,6420	2203	4300	6503	SO:0001583	missense	1007	exon2			GGTATATAATGGT	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.17A>G	5.37:g.26988424T>C	ENSP00000231021:p.Tyr6Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	811	0.37133699633699635	240	0.4878048780487805	107	0.2955801104972376	98	0.17132867132867133	366	0.48284960422163586	C	0.009	-1.810275	0.00600	0.519519	0.499651	ENSG00000113100	ENST00000231021;ENST00000513289;ENST00000511822	T;T;T	0.56941	0.5;0.43;1.97	5.47	2.69	0.31865	.	0.598700	0.17677	N	0.165778	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.47302	-0.9128	8	.	.	.	.	4.1531	0.10247	0.3976:0.3825:0.0:0.2199	rs2288467;rs17499800;rs52812429;rs59304285;rs2288467	6;6	E7EPN0;Q9ULB4	.;CADH9_HUMAN	C	6	ENSP00000231021:Y6C;ENSP00000426239:Y6C;ENSP00000422538:Y6C	.	Y	-	2	0	CDH9	27024181	0.868000	0.29978	0.003000	0.11579	0.062000	0.15995	0.105000	0.15333	0.021000	0.15133	-0.349000	0.07799	TAT	C|0.447;N|0.000	0.447	strong		0.333	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
TMEM30A	55754	hgsc.bcm.edu	37	6	75994151	75994151	+	Silent	SNP	A	A	G	rs240374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:75994151A>G	ENST00000230461.6	-	1	533	c.204T>C	c.(202-204)atT>atC	p.I68I	RP1-234P15.4_ENST00000607221.1_lincRNA|TMEM30A_ENST00000475111.2_Silent_p.I68I	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	67	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	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	
FASN	2194	hgsc.bcm.edu	37	17	80039481	80039481	+	Silent	SNP	G	G	A	rs1140616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80039481G>A	ENST00000306749.2	-	37	6620	c.6402C>T	c.(6400-6402)atC>atT	p.I2134I	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2134	Acyl carrier. {ECO:0000255|PROSITE- ProRule:PRU00258}.				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)	GCTCACCCAGGATGTGTGCCA	0.642													.|||	1522	0.303914	0.1823	0.2867	5008	,	,		14395	0.2996		0.4791	False		,,,				2504	0.3047				p.I2134I	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C6402T						PASS	.	G		990,3412	353.1+/-312.0	108,774,1319	42.0	41.0	41.0		6402	1.7	1.0	17	dbSNP_86	41	4501,4097	569.4+/-389.2	1196,2109,994	no	coding-synonymous	FASN	NM_004104.4		1304,2883,2313	AA,AG,GG		47.6506,22.4898,42.2385		2134/2512	80039481	5491,7509	2201	4299	6500	SO:0001819	synonymous_variant	2194	exon37			ACCCAGGATGTGT	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.6402C>T	17.37:g.80039481G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	67	39	0.58209	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	37	CCDS11801.1																																																																																			G|0.632;A|0.368	0.368	strong		0.642	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
ABCC6	368	hgsc.bcm.edu	37	16	16259497	16259497	+	Missense_Mutation	SNP	G	G	T	rs60707953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16259497G>T	ENST00000205557.7	-	23	3318	c.3289C>A	c.(3289-3291)Ctc>Atc	p.L1097I		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1097	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.		L -> I (in dbSNP:rs60707953).		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)	CCAGCGTAGAGGAGAAACAGT	0.612													G|||	38	0.00758786	0.0242	0.0058	5008	,	,		17411	0.0		0.002	False		,,,				2504	0.0				p.L1097I		Atlas-SNP	.											.	ABCC6	110	.	0			c.C3289A						PASS	.	G	ILE/LEU	94,4300	71.4+/-109.4	1,92,2104	58.0	51.0	54.0		3289	-0.2	0.9	16	dbSNP_129	54	7,8591	4.3+/-15.6	0,7,4292	yes	missense	ABCC6	NM_001171.5	5	1,99,6396	TT,TG,GG		0.0814,2.1393,0.7774	benign	1097/1504	16259497	101,12891	2197	4299	6496	SO:0001583	missense	368	exon23			CGTAGAGGAGAAA	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.3289C>A	16.37:g.16259497G>T	ENSP00000205557:p.Leu1097Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	G	8.586	0.883526	0.17467	0.021393	8.14E-4	ENSG00000091262	ENST00000205557	D	0.89681	-2.55	5.38	-0.254	0.12992	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.180137	0.27482	U	0.019165	T	0.63367	0.2505	L	0.33710	1.025	0.80722	D	1	D	0.53619	0.961	P	0.48089	0.566	T	0.68205	-0.5470	10	0.20519	T	0.43	.	5.9149	0.19050	0.3303:0.2203:0.4494:0.0	rs60707953;rs61731991	1097	O95255	MRP6_HUMAN	I	1097	ENSP00000205557:L1097I	ENSP00000205557:L1097I	L	-	1	0	ABCC6	16166998	0.280000	0.24249	0.932000	0.37286	0.098000	0.18820	0.223000	0.17719	0.247000	0.21414	0.561000	0.74099	CTC	G|0.992;T|0.008	0.008	strong		0.612	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
IQCF1	132141	hgsc.bcm.edu	37	3	51930850	51930850	+	Missense_Mutation	SNP	T	T	C	rs57859638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	142	0	0		WXS	Illumina HiSeq	Phase_I	157	62	0.394904	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	
DLK1	8788	hgsc.bcm.edu	37	14	101200514	101200514	+	Missense_Mutation	SNP	G	G	T	rs116078181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101200514G>T	ENST00000341267.4	+	5	675	c.433G>T	c.(433-435)Gtg>Ttg	p.V145L	DLK1_ENST00000331224.6_Missense_Mutation_p.V145L	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	145	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)				AGGCACCTGCGTGGATGATGA	0.652													G|||	93	0.0185703	0.0696	0.0014	5008	,	,		12961	0.0		0.0	False		,,,				2504	0.0				p.V145L		Atlas-SNP	.											.	DLK1	57	.	0			c.G433T						PASS	.	G	LEU/VAL	197,4207		7,183,2012	45.0	43.0	44.0		433	3.2	1.0	14	dbSNP_132	44	0,8598		0,0,4299	yes	missense	DLK1	NM_003836.5	32	7,183,6311	TT,TG,GG		0.0,4.4732,1.5152	possibly-damaging	145/384	101200514	197,12805	2202	4299	6501	SO:0001583	missense	8788	exon5			ACCTGCGTGGATG	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.433G>T	14.37:g.101200514G>T	ENSP00000340292:p.Val145Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	89	54	0.606742	NM_003836	P15803|Q96DW5	Missense_Mutation	SNP	ENST00000341267.4	37	CCDS9963.1	37	0.01694139194139194	37	0.07520325203252033	0	0.0	0	0.0	0	0.0	G	15.51	2.856381	0.51376	0.044732	0.0	ENSG00000185559	ENST00000341267;ENST00000331224	T;T	0.71817	-0.6;-0.6	4.1	3.18	0.36537	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.432951	0.20458	N	0.091958	T	0.10981	0.0268	L	0.28776	0.89	0.80722	D	1	D;P	0.67145	0.996;0.926	D;P	0.64595	0.927;0.542	T	0.37820	-0.9689	10	0.30854	T	0.27	.	5.9295	0.19130	0.2969:0.0:0.7031:0.0	.	145;145	P80370-2;P80370	.;DLK1_HUMAN	L	145	ENSP00000340292:V145L;ENSP00000331081:V145L	ENSP00000331081:V145L	V	+	1	0	DLK1	100270267	0.812000	0.29077	0.997000	0.53966	0.813000	0.45954	1.136000	0.31467	1.981000	0.57761	0.491000	0.48974	GTG	G|0.981;T|0.019	0.019	strong		0.652	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
AQP12A	375318	hgsc.bcm.edu	37	2	241631616	241631616	+	Silent	SNP	T	T	C	rs11889147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241631616T>C	ENST00000337801.4	+	2	318	c.249T>C	c.(247-249)acT>acC	p.T83T	AQP12A_ENST00000429564.1_Silent_p.T95T|AC011298.2_ENST00000407635.2_lincRNA	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	83						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)		CCAACCCCACTGTGTCCCTGC	0.677													N|||	405	0.0808706	0.2073	0.0461	5008	,	,		13202	0.0268		0.0129	False		,,,				2504	0.0603				p.T83T		Atlas-SNP	.											AQP12A,NS,carcinoma,0,1	AQP12A	32	1	0			c.T249C						scavenged	.			436,3770		66,304,1733	35.0	51.0	46.0		249	-5.1	0.2	2	dbSNP_120	46	29,8485		1,27,4229	no	coding-synonymous	AQP12A	NM_198998.1		67,331,5962	CC,CT,TT		0.3406,10.3661,3.6557		83/296	241631616	465,12255	2103	4257	6360	SO:0001819	synonymous_variant	375318	exon2			CCCCACTGTGTCC	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.249T>C	2.37:g.241631616T>C		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_198998		Silent	SNP	ENST00000337801.4	37																																																																																				T|0.958;C|0.042	0.042	strong		0.677	AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998	
DDX43	55510	hgsc.bcm.edu	37	6	74125283	74125283	+	Silent	SNP	T	T	C	rs138615882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74125283T>C	ENST00000370336.4	+	15	1967	c.1809T>C	c.(1807-1809)atT>atC	p.I603I	MB21D1_ENST00000370318.1_Intron	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	603	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						CTGAATTGATTAATATTCTGG	0.383													T|||	13	0.00259585	0.0098	0.0	5008	,	,		16489	0.0		0.0	False		,,,				2504	0.0				p.I603I		Atlas-SNP	.											.	DDX43	69	.	0			c.T1809C						PASS	.	T		33,4373	37.6+/-69.7	1,31,2171	110.0	109.0	109.0		1809	0.9	1.0	6	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous	DDX43	NM_018665.2		1,31,6471	CC,CT,TT		0.0,0.749,0.2537		603/649	74125283	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	55510	exon15			ATTGATTAATATT		CCDS4977.1	6q13	2014-01-21			ENSG00000080007	ENSG00000080007		"""DEAD-boxes"""	18677	protein-coding gene	gene with protein product	"""cancer/testis antigen 13"""	606286				10919659	Standard	NM_018665		Approved	HAGE, DKFZp434H2114, CT13	uc003pgw.3	Q9NXZ2	OTTHUMG00000015033	ENST00000370336.4:c.1809T>C	6.37:g.74125283T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_018665	B4E0C8|Q6NXR1	Silent	SNP	ENST00000370336.4	37	CCDS4977.1																																																																																			T|0.997;C|0.003	0.003	strong		0.383	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665	
SEC16B	89866	hgsc.bcm.edu	37	1	177929940	177929940	+	Silent	SNP	G	G	A	rs7413442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:177929940G>A	ENST00000308284.6	-	7	1011	c.922C>T	c.(922-924)Ctg>Ttg	p.L308L	SEC16B_ENST00000464631.2_Silent_p.L309L|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	308					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						ATGCTGTGCAGTTCAACAAGG	0.542													G|||	1392	0.277955	0.5719	0.2003	5008	,	,		19999	0.1944		0.1819	False		,,,				2504	0.1207				p.L308L		Atlas-SNP	.											.	SEC16B	92	.	0			c.C922T						PASS	.	G		2005,2213		490,1025,594	42.0	46.0	45.0		922	-0.2	0.9	1	dbSNP_116	45	1459,7027		128,1203,2912	no	coding-synonymous	SEC16B	NM_033127.2		618,2228,3506	AA,AG,GG		17.193,47.5344,27.267		308/1061	177929940	3464,9240	2109	4243	6352	SO:0001819	synonymous_variant	89866	exon7			TGTGCAGTTCAAC	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.922C>T	1.37:g.177929940G>A		Somatic	234	2	0.00854701		WXS	Illumina HiSeq	Phase_I	210	210	1	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			G|0.727;A|0.273	0.273	strong		0.542	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
DEK	7913	hgsc.bcm.edu	37	6	18264210	18264210	+	Silent	SNP	G	G	A	rs11544757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:18264210G>A	ENST00000397239.3	-	2	456	c.9C>T	c.(7-9)gcC>gcT	p.A3A	DEK_ENST00000244776.7_Silent_p.A3A	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	3					chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			CAGGGGCCGAGGCGGACATGC	0.672			T	NUP214	AML								G|||	824	0.164537	0.031	0.1124	5008	,	,		12151	0.246		0.2087	False		,,,				2504	0.2526				p.A3A		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31	.	0			c.C9T						PASS	.	G	,	297,4109	154.0+/-187.5	10,277,1916	25.0	27.0	26.0		9,9	-1.1	0.0	6	dbSNP_120	26	1789,6811	306.2+/-307.8	198,1393,2709	no	coding-synonymous,coding-synonymous	DEK	NM_001134709.1,NM_003472.3	,	208,1670,4625	AA,AG,GG		20.8023,6.7408,16.0388	,	3/342,3/376	18264210	2086,10920	2203	4300	6503	SO:0001819	synonymous_variant	7913	exon2			GGCCGAGGCGGAC	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"""DEK oncogene (DNA binding)"", ""DEK oncogene"""			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.9C>T	6.37:g.18264210G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Silent	SNP	ENST00000397239.3	37	CCDS34344.1																																																																																			G|0.838;C|0.000;A|0.162	0.162	strong		0.672	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4		
TMCC3	57458	hgsc.bcm.edu	37	12	94976084	94976084	+	Silent	SNP	T	T	C	rs3747552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:94976084T>C	ENST00000261226.4	-	2	440	c.309A>G	c.(307-309)gcA>gcG	p.A103A	TMCC3_ENST00000551457.1_Silent_p.A72A	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	103						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						GCTGCTTGTCTGCGTTGTTCA	0.453													C|||	3502	0.699281	0.9266	0.6095	5008	,	,		19833	0.6002		0.5775	False		,,,				2504	0.683				p.A103A		Atlas-SNP	.											.	TMCC3	63	.	0			c.A309G						PASS	.	C		3795,611	267.7+/-268.0	1645,505,53	155.0	142.0	146.0		309	-11.2	0.0	12	dbSNP_107	146	4855,3745	533.1+/-382.3	1393,2069,838	no	coding-synonymous	TMCC3	NM_020698.2		3038,2574,891	CC,CT,TT		43.5465,13.8675,33.4922		103/478	94976084	8650,4356	2203	4300	6503	SO:0001819	synonymous_variant	57458	exon2			CTTGTCTGCGTTG	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"""Transmembrane and coiled-coil domain containing"""	29199	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 3"""			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.309A>G	12.37:g.94976084T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	160	82	0.5125	NM_020698	Q8IWB2	Silent	SNP	ENST00000261226.4	37	CCDS31877.1																																																																																			T|0.335;C|0.665	0.665	strong		0.453	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
FBLN2	2199	hgsc.bcm.edu	37	3	13679203	13679203	+	Silent	SNP	G	G	A	rs1061375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:13679203G>A	ENST00000295760.7	+	17	3408	c.3339G>A	c.(3337-3339)acG>acA	p.T1113T	FBLN2_ENST00000535798.1_Silent_p.T1139T|FBLN2_ENST00000492059.1_Silent_p.T1160T|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	208	0	0		WXS	Illumina HiSeq	Phase_I	233	123	0.527897	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	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68023989	68023989	+	Missense_Mutation	SNP	G	G	C	rs149253165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:68023989G>C	ENST00000329153.5	+	4	325	c.193G>C	c.(193-195)Ggt>Cgt	p.G65R		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	65						cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		TTTTCAGGTGGGTGTCATGGA	0.507													G|||	40	0.00798722	0.028	0.0043	5008	,	,		19812	0.0		0.0	False		,,,				2504	0.0				p.G65R		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G193C						PASS	.	G	ARG/GLY	87,3815		0,87,1864	74.0	88.0	83.0		193	2.5	1.0	14	dbSNP_134	83	1,8305		0,1,4152	yes	missense	PLEKHH1	NM_020715.2	125	0,88,6016	CC,CG,GG		0.012,2.2296,0.7208	benign	65/1365	68023989	88,12120	1951	4153	6104	SO:0001583	missense	57475	exon4			CAGGTGGGTGTCA	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.193G>C	14.37:g.68023989G>C	ENSP00000330278:p.Gly65Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	92	52	0.565217	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	16	0.007326007326007326	13	0.026422764227642278	3	0.008287292817679558	0	0.0	0	0.0	G	2.631	-0.286399	0.05605	0.022296	1.2E-4	ENSG00000054690	ENST00000329153	T	0.04083	3.71	5.41	2.47	0.30058	.	0.335067	0.36303	N	0.002673	T	0.00936	0.0031	L	0.28014	0.82	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.42207	-0.9465	10	0.02654	T	1	.	7.9764	0.30157	0.2765:0.0:0.7235:0.0	.	65	Q9ULM0	PKHH1_HUMAN	R	65	ENSP00000330278:G65R	ENSP00000330278:G65R	G	+	1	0	PLEKHH1	67093742	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.637000	0.24659	0.349000	0.23975	-0.254000	0.11334	GGT	G|0.993;C|0.007	0.007	strong		0.507	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
PARP14	54625	hgsc.bcm.edu	37	3	122419151	122419151	+	Missense_Mutation	SNP	G	G	A	rs201474464		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122419151G>A	ENST00000474629.2	+	6	2016	c.1750G>A	c.(1750-1752)Gcc>Acc	p.A584T		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	584					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TTCTTCTGAAGCCCTGTTAGA	0.398													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21056	0.0		0.0	False		,,,				2504	0.0				p.A584T		Atlas-SNP	.											PARP14_ENST00000474629,caecum,carcinoma,-2,2	PARP14	242	2	0			c.G1750A						PASS	.	G	THR/ALA	10,3702		0,10,1846	38.0	35.0	36.0		1750	3.5	0.0	3		36	0,8178		0,0,4089	yes	missense	PARP14	NM_017554.2	58	0,10,5935	AA,AG,GG		0.0,0.2694,0.0841	benign	584/1802	122419151	10,11880	1856	4089	5945	SO:0001583	missense	54625	exon6			TCTGAAGCCCTGT	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1750G>A	3.37:g.122419151G>A	ENSP00000418194:p.Ala584Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	32	0.415584	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	G	8.583	0.882878	0.17467	0.002694	0.0	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.09817	2.94	5.34	3.52	0.40303	.	0.755868	0.11822	N	0.526062	T	0.06690	0.0171	N	0.22421	0.69	0.09310	N	1	B;B	0.15473	0.005;0.013	B;B	0.09377	0.002;0.004	T	0.33343	-0.9872	10	0.02654	T	1	.	11.1929	0.48696	0.1539:0.0:0.8461:0.0	.	584;584	Q460N5-4;Q460N5	.;PAR14_HUMAN	T	584;503	ENSP00000418194:A584T	ENSP00000381228:A503T	A	+	1	0	PARP14	123901841	0.558000	0.26554	0.005000	0.12908	0.634000	0.38068	2.752000	0.47516	1.494000	0.48533	-0.142000	0.14014	GCC	.	.	weak		0.398	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
SNED1	25992	hgsc.bcm.edu	37	2	241973223	241973223	+	Silent	SNP	C	C	T	rs61746865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241973223C>T	ENST00000310397.8	+	3	573	c.573C>T	c.(571-573)atC>atT	p.I191I	SNED1_ENST00000342631.6_Silent_p.I191I|SNED1_ENST00000401884.1_Silent_p.I191I|SNED1_ENST00000405547.3_Silent_p.I191I|AC005237.4_ENST00000458377.1_RNA	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	191	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		ATGAGTCCATCGTGTGGACCA	0.622													C|||	480	0.0958466	0.2231	0.0245	5008	,	,		19626	0.0754		0.0159	False		,,,				2504	0.0777				p.I191I		Atlas-SNP	.											.	SNED1	76	.	0			c.C573T						PASS	.	C		772,3510		76,620,1445	60.0	64.0	63.0		573	3.7	0.7	2	dbSNP_129	63	93,8353		1,91,4131	no	coding-synonymous	SNED1	NM_001080437.1		77,711,5576	TT,TC,CC		1.1011,18.029,6.796		191/1414	241973223	865,11863	2141	4223	6364	SO:0001819	synonymous_variant	25992	exon3			GTCCATCGTGTGG	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.573C>T	2.37:g.241973223C>T		Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	332	165	0.496988	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																			C|0.940;T|0.060	0.060	strong		0.622	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
TG	7038	hgsc.bcm.edu	37	8	134042164	134042164	+	Missense_Mutation	SNP	C	C	T	rs61742878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134042164C>T	ENST00000220616.4	+	41	7175	c.7135C>T	c.(7135-7137)Cgc>Tgc	p.R2379C	TG_ENST00000377869.1_Missense_Mutation_p.R2322C|TG_ENST00000519543.1_Missense_Mutation_p.R512C|TG_ENST00000542445.1_Missense_Mutation_p.R749C	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2379					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)		GGACCCTCGGCGCGTGTCCCT	0.667													C|||	22	0.00439297	0.0166	0.0	5008	,	,		14003	0.0		0.0	False		,,,				2504	0.0				p.R2379C		Atlas-SNP	.											TG,NS,carcinoma,0,4	TG	416	4	0			c.C7135T						PASS	.	C	CYS/ARG	54,4352	54.2+/-90.2	0,54,2149	47.0	49.0	48.0		7135	4.2	0.6	8	dbSNP_129	48	0,8596		0,0,4298	yes	missense	TG	NM_003235.4	180	0,54,6447	TT,TC,CC		0.0,1.2256,0.4153	probably-damaging	2379/2769	134042164	54,12948	2203	4298	6501	SO:0001583	missense	7038	exon41			CCTCGGCGCGTGT	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.7135C>T	8.37:g.134042164C>T	ENSP00000220616:p.Arg2379Cys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	124	49	0.395161	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	7|7	0.003205128205128205|0.003205128205128205	7|7	0.014227642276422764|0.014227642276422764	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	15.00|15.00	2.701863|2.701863	0.48307|0.48307	0.012256|0.012256	0.0|0.0	ENSG00000042832|ENSG00000042832	ENST00000519178;ENST00000518108|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	.|T;T;T;T	.|0.65364	.|-0.15;-0.15;-0.15;-0.15	5.13|5.13	4.22|4.22	0.49857|0.49857	.|Carboxylesterase, type B (1);	.|0.761860	.|0.12170	.|N	.|0.493098	T|T	0.69993|0.69993	0.3173|0.3173	M|M	0.72576|0.72576	2.205|2.205	0.09310|0.09310	N|N	0.999993|0.999993	.|D;D;D	.|0.89917	.|1.0;0.999;0.999	.|D;P;D	.|0.63192	.|0.912;0.899;0.912	T|T	0.63853|0.63853	-0.6543|-0.6543	5|10	.|0.87932	.|D	.|0	.|.	13.7454|13.7454	0.62872|0.62872	0.1544:0.8456:0.0:0.0|0.1544:0.8456:0.0:0.0	rs61742878|rs61742878	.|512;749;2379	.|E7EVM0;F5GWW5;P01266	.|.;.;THYG_HUMAN	V|C	834;174|2322;1185;2379;749;512	.|ENSP00000367100:R2322C;ENSP00000220616:R2379C;ENSP00000441693:R749C;ENSP00000430430:R512C	.|ENSP00000220616:R2379C	A|R	+|+	2|1	0|0	TG|TG	134111346|134111346	0.060000|0.060000	0.20803|0.20803	0.550000|0.550000	0.28217|0.28217	0.384000|0.384000	0.30261|0.30261	2.504000|2.504000	0.45416|0.45416	2.407000|2.407000	0.81776|0.81776	0.485000|0.485000	0.47835|0.47835	GCG|CGC	C|0.995;T|0.005	0.005	strong		0.667	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
TRPM2	7226	hgsc.bcm.edu	37	21	45786709	45786709	+	Missense_Mutation	SNP	G	G	A	rs45544142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45786709G>A	ENST00000397928.1	+	4	941	c.496G>A	c.(496-498)Gtc>Atc	p.V166I	TRPM2_ENST00000300482.5_Missense_Mutation_p.V166I|TRPM2_ENST00000397932.2_Missense_Mutation_p.V166I|TRPM2_ENST00000300481.9_Missense_Mutation_p.V166I	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	166			V -> I (in dbSNP:rs45544142). {ECO:0000269|Ref.6}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GGGGCTGGACGTCCCCAATCT	0.612													G|||	148	0.0295527	0.1044	0.0101	5008	,	,		16186	0.003		0.0	False		,,,				2504	0.0				p.V166I		Atlas-SNP	.											.	TRPM2	196	.	0			c.G496A						PASS	.	G	ILE/VAL	454,3952	216.4+/-235.1	24,406,1773	61.0	57.0	58.0		496	2.3	0.1	21	dbSNP_127	58	6,8594	4.3+/-15.6	0,6,4294	yes	missense	TRPM2	NM_003307.3	29	24,412,6067	AA,AG,GG		0.0698,10.3041,3.5368	benign	166/1504	45786709	460,12546	2203	4300	6503	SO:0001583	missense	7226	exon4			CTGGACGTCCCCA	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.496G>A	21.37:g.45786709G>A	ENSP00000381023:p.Val166Ile	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	60	0.027472527472527472	55	0.11178861788617886	3	0.008287292817679558	2	0.0034965034965034965	0	0.0	G	5.471	0.271913	0.10349	0.103041	6.98E-4	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	4.12	2.28	0.28536	.	0.459727	0.21621	U	0.071660	T	0.00754	0.0025	L	0.39397	1.21	0.09310	N	1	B;B	0.23377	0.084;0.039	B;B	0.17433	0.018;0.007	T	0.02821	-1.1106	10	0.22109	T	0.4	-28.3824	5.9165	0.19057	0.2468:0.1389:0.6143:0.0	rs45544142;rs61747092	166;166	E9PGK7;O94759	.;TRPM2_HUMAN	I	166	ENSP00000300482:V166I;ENSP00000381023:V166I;ENSP00000300481:V166I;ENSP00000381026:V166I	ENSP00000300481:V166I	V	+	1	0	TRPM2	44611137	0.000000	0.05858	0.110000	0.21437	0.394000	0.30568	0.164000	0.16542	0.314000	0.23086	0.297000	0.19635	GTC	G|0.962;A|0.038	0.038	strong		0.612	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
OR6K3	391114	hgsc.bcm.edu	37	1	158687224	158687224	+	Missense_Mutation	SNP	G	G	A	rs857703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158687224G>A	ENST00000368146.1	-	1	729	c.730C>T	c.(730-732)Ccc>Tcc	p.P244S	OR6K3_ENST00000368145.1_Missense_Mutation_p.P228S			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	244			P -> S (in dbSNP:rs857703). {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)	p.P244S(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					TCAGAAGAGGGAATCCTCAAT	0.438													G|||	1404	0.280351	0.09	0.389	5008	,	,		23447	0.4474		0.3946	False		,,,				2504	0.1708				p.P228S		Atlas-SNP	.											OR6K3,NS,carcinoma,0,1	OR6K3	101	1	1	Substitution - Missense(1)	stomach(1)	c.C682T						PASS	.	G	SER/PRO	589,3817	259.5+/-263.1	47,495,1661	107.0	96.0	100.0		682	0.8	0.0	1	dbSNP_86	100	3247,5353	487.5+/-372.1	610,2027,1663	yes	missense	OR6K3	NM_001005327.2	74	657,2522,3324	AA,AG,GG		37.7558,13.3681,29.4941	benign	228/316	158687224	3836,9170	2203	4300	6503	SO:0001583	missense	391114	exon1			AAGAGGGAATCCT	AB065633	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			ENSG00000203757	ENSG00000203757		"""GPCR / Class A : Olfactory receptors"""	15030	protein-coding gene	gene with protein product							Standard	NM_001005327		Approved		uc021pbn.1	Q8NGY3	OTTHUMG00000022770	ENST00000368146.1:c.730C>T	1.37:g.158687224G>A	ENSP00000357128:p.Pro244Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_001005327	Q5VUV0|Q6IFR5	Missense_Mutation	SNP	ENST00000368146.1	37		732	0.33516483516483514	56	0.11382113821138211	140	0.3867403314917127	238	0.4160839160839161	298	0.39313984168865435	G	13.46	2.243764	0.39697	0.133681	0.377558	ENSG00000203757	ENST00000368145;ENST00000368146	T;T	0.36878	1.23;1.23	3.77	0.813	0.18749	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.12987	0.0315	L	0.45137	1.4	0.80722	P	0.0	B	0.23128	0.08	B	0.24006	0.05	T	0.10776	-1.0615	8	0.48119	T	0.1	.	7.9959	0.30267	0.2855:0.0:0.7145:0.0	rs857703;rs52791601;rs56909898;rs857703	244	Q8NGY3	OR6K3_HUMAN	S	228;244	ENSP00000357127:P228S;ENSP00000357128:P244S	ENSP00000357127:P228S	P	-	1	0	OR6K3	156953848	0.000000	0.05858	0.001000	0.08648	0.627000	0.37826	-0.113000	0.10774	0.055000	0.16094	0.467000	0.42956	CCC	G|0.696;A|0.304	0.304	strong		0.438	OR6K3-201	KNOWN	basic	protein_coding	protein_coding			
SLC2A14	144195	hgsc.bcm.edu	37	12	7967071	7967071	+	Silent	SNP	G	G	A	rs11837392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7967071G>A	ENST00000543909.1	-	16	2163	c.1404C>T	c.(1402-1404)gcC>gcT	p.A468A	SLC2A14_ENST00000340749.5_Silent_p.A445A|SLC2A14_ENST00000396589.2_Silent_p.A468A|SLC2A14_ENST00000431042.2_Silent_p.A445A|SLC2A14_ENST00000542546.1_Silent_p.A359A|SLC2A14_ENST00000535295.1_Silent_p.A359A|SLC2A14_ENST00000542505.1_Silent_p.A109A|SLC2A14_ENST00000539924.1_Silent_p.A483A			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	468					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)		AGAAGGTAAAGGCCAAGAAGG	0.453													G|||	603	0.120407	0.1846	0.1081	5008	,	,		-128	0.1895		0.0199	False		,,,				2504	0.0746				p.A468A		Atlas-SNP	.											.	SLC2A14	78	.	0			c.C1404T						PASS	.	G		572,3834	217.1+/-235.6	49,474,1680	70.0	71.0	71.0		1404	1.5	0.8	12	dbSNP_120	71	167,8433	67.3+/-129.8	5,157,4138	no	coding-synonymous	SLC2A14	NM_153449.2		54,631,5818	AA,AG,GG		1.9419,12.9823,5.682		468/521	7967071	739,12267	2203	4300	6503	SO:0001819	synonymous_variant	144195	exon12			GGTAAAGGCCAAG	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.1404C>T	12.37:g.7967071G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	110	47	0.427273	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Silent	SNP	ENST00000543909.1	37	CCDS8585.1																																																																																			.	.	weak		0.453	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449	
MBLAC1	255374	hgsc.bcm.edu	37	7	99725466	99725466	+	Missense_Mutation	SNP	G	G	T	rs78225840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99725466G>T	ENST00000398075.2	+	2	847	c.448G>T	c.(448-450)Ggt>Tgt	p.G150C	RP11-506M12.1_ENST00000494221.1_RNA	NM_203397.1	NP_981942.1	A4D2B0	MBLC1_HUMAN	metallo-beta-lactamase domain containing 1	150							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|skin(1)	7						CCACGGGCTGGGTGAGGGGCA	0.746													G|||	125	0.0249601	0.09	0.0086	5008	,	,		12011	0.0		0.0	False		,,,				2504	0.0				p.G150C		Atlas-SNP	.											.	MBLAC1	13	.	0			c.G448T						PASS	.	G	CYS/GLY	289,3345		6,277,1534	9.0	11.0	10.0		448	-1.4	0.0	7	dbSNP_131	10	2,8064		0,2,4031	yes	missense	MBLAC1	NM_203397.1	159	6,279,5565	TT,TG,GG		0.0248,7.9527,2.4872	benign	150/267	99725466	291,11409	1817	4033	5850	SO:0001583	missense	255374	exon2			GGGCTGGGTGAGG	BC031288	CCDS43620.1	7q22	2014-02-12	2009-04-08		ENSG00000214309	ENSG00000214309			22180	protein-coding gene	gene with protein product							Standard	XM_005250250		Approved	MGC49416	uc003utp.3	A4D2B0	OTTHUMG00000154846	ENST00000398075.2:c.448G>T	7.37:g.99725466G>T	ENSP00000381150:p.Gly150Cys	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	49	27	0.55102	NM_203397	Q8N5X8	Missense_Mutation	SNP	ENST00000398075.2	37	CCDS43620.1	37	0.01694139194139194	31	0.06300813008130081	3	0.008287292817679558	3	0.005244755244755245	0	0.0	G	8.154	0.788075	0.16258	0.079527	2.48E-4	ENSG00000214309	ENST00000398075	T	0.30448	1.53	4.35	-1.38	0.09027	Beta-lactamase-like (2);	0.393038	0.20783	N	0.085752	T	0.00936	0.0031	L	0.46819	1.47	0.09310	N	1	B	0.10296	0.003	B	0.17979	0.02	T	0.11060	-1.0603	10	0.38643	T	0.18	.	1.2154	0.01913	0.4798:0.1516:0.204:0.1646	.	150	A4D2B0	MBLC1_HUMAN	C	150	ENSP00000381150:G150C	ENSP00000381150:G150C	G	+	1	0	MBLAC1	99563402	0.000000	0.05858	0.005000	0.12908	0.332000	0.28634	0.180000	0.16860	-0.294000	0.08973	0.561000	0.74099	GGT	G|0.980;T|0.020	0.020	strong		0.746	MBLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337353.1	NM_203397	
ZNF398	57541	hgsc.bcm.edu	37	7	148851273	148851273	+	Missense_Mutation	SNP	G	G	C	rs3801979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:148851273G>C	ENST00000475153.1	+	2	528	c.261G>C	c.(259-261)gaG>gaC	p.E87D	ZNF398_ENST00000426851.2_5'UTR|ZNF398_ENST00000420008.2_5'UTR|ZNF398_ENST00000483892.1_5'UTR|ZNF398_ENST00000485111.1_3'UTR|ZNF398_ENST00000335901.4_5'UTR|ZNF398_ENST00000491174.1_5'UTR|ZNF398_ENST00000540950.1_Missense_Mutation_p.E92D			Q8TD17	ZN398_HUMAN	zinc finger protein 398	87			E -> D (in dbSNP:rs3801979). {ECO:0000269|PubMed:14702039}.		positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)	25	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			CAGTTACCGAGCTTGGGAACC	0.602													G|||	350	0.0698882	0.0893	0.0778	5008	,	,		16475	0.0536		0.0855	False		,,,				2504	0.0389				p.E87D		Atlas-SNP	.											ZNF398,colon,carcinoma,+2,1	ZNF398	54	1	0			c.G261C						PASS	.	G	,ASP/GLU	342,4064	178.7+/-207.4	18,306,1879	64.0	66.0	65.0		,261	0.6	0.9	7	dbSNP_107	65	709,7891	174.0+/-224.4	29,651,3620	yes	utr-5,missense	ZNF398	NM_020781.3,NM_170686.2	,45	47,957,5499	CC,CG,GG		8.2442,7.7621,8.0809	,benign	,87/643	148851273	1051,11955	2203	4300	6503	SO:0001583	missense	57541	exon2			TACCGAGCTTGGG	AB037760	CCDS5894.1, CCDS47739.1	7q35	2013-01-08			ENSG00000197024	ENSG00000197024		"""Zinc fingers, C2H2-type"", ""-"""	18373	protein-coding gene	gene with protein product						11779858	Standard	NM_170686		Approved	ZER6, KIAA1339, P51, P71	uc003wfl.3	Q8TD17	OTTHUMG00000158970	ENST00000475153.1:c.261G>C	7.37:g.148851273G>C	ENSP00000420418:p.Glu87Asp	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_170686	A8K384|B4E377|Q8TD18|Q9P2K7|Q9UDV8	Missense_Mutation	SNP	ENST00000475153.1	37	CCDS5894.1	150	0.06868131868131869	41	0.08333333333333333	24	0.06629834254143646	35	0.06118881118881119	50	0.06596306068601583	G	13.10	2.137377	0.37728	0.077621	0.082442	ENSG00000197024	ENST00000475153;ENST00000540950	D;D	0.81659	-1.52;-1.52	5.18	0.615	0.17608	.	0.403521	0.21112	N	0.079980	T	0.07188	0.0182	N	0.11789	0.175	0.09310	P	0.9999999999555069	B;B	0.06786	0.0;0.001	B;B	0.10450	0.002;0.005	T	0.24657	-1.0154	9	0.33940	T	0.23	-5.7211	7.1697	0.25712	0.0:0.2554:0.4316:0.313	rs3801979;rs52825319;rs3801979	92;87	B4DXA9;Q8TD17	.;ZN398_HUMAN	D	87;92	ENSP00000420418:E87D;ENSP00000439340:E92D	ENSP00000420418:E87D	E	+	3	2	ZNF398	148482206	0.931000	0.31567	0.949000	0.38748	0.925000	0.55904	-0.236000	0.09003	0.141000	0.18875	0.655000	0.94253	GAG	G|0.925;C|0.075	0.075	strong		0.602	ZNF398-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352722.2		
C3orf20	84077	hgsc.bcm.edu	37	3	14755617	14755617	+	Missense_Mutation	SNP	C	C	G	rs6790129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:14755617C>G	ENST00000253697.3	+	8	1716	c.1264C>G	c.(1264-1266)Cta>Gta	p.L422V	C3orf20_ENST00000435614.1_Missense_Mutation_p.L300V|C3orf20_ENST00000412910.1_Missense_Mutation_p.L300V|C3orf20_ENST00000495387.1_3'UTR	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	422			L -> V (in dbSNP:rs6790129). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CTTGCTGGCCCTATTCAATAC	0.502													C|||	1898	0.378994	0.4244	0.4568	5008	,	,		21186	0.3234		0.4175	False		,,,				2504	0.2802				p.L422V		Atlas-SNP	.											.	C3orf20	109	.	0			c.C1264G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU	1899,2507	544.0+/-376.4	426,1047,730	94.0	85.0	88.0		898,898,1264	1.6	0.9	3	dbSNP_116	88	3660,4940	526.9+/-381.1	789,2082,1429	yes	missense,missense,missense	C3orf20	NM_001184957.1,NM_001184958.1,NM_032137.4	32,32,32	1215,3129,2159	GG,GC,CC		42.5581,43.1003,42.7418	probably-damaging,probably-damaging,probably-damaging	300/783,300/783,422/905	14755617	5559,7447	2203	4300	6503	SO:0001583	missense	84077	exon8			CTGGCCCTATTCA	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.1264C>G	3.37:g.14755617C>G	ENSP00000253697:p.Leu422Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	135	71	0.525926	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	893	0.4088827838827839	231	0.4695121951219512	158	0.43646408839779005	186	0.32517482517482516	318	0.41952506596306066	C	14.99	2.701572	0.48307	0.431003	0.425581	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.13901	2.55;2.55;2.55	5.56	1.57	0.23409	.	0.000000	0.39544	N	0.001330	T	0.00012	0.0000	M	0.61703	1.905	0.37651	P	0.07758200000000004	P	0.46142	0.873	P	0.45681	0.49	T	0.45160	-0.9280	9	0.30078	T	0.28	-9.4692	2.0532	0.03575	0.1608:0.5113:0.1558:0.172	rs6790129;rs17856869;rs56928522;rs6790129	422	Q8ND61	CC020_HUMAN	V	422;300;300	ENSP00000253697:L422V;ENSP00000402933:L300V;ENSP00000396081:L300V	ENSP00000253697:L422V	L	+	1	2	C3orf20	14730621	0.773000	0.28580	0.948000	0.38648	0.746000	0.42486	-0.090000	0.11163	0.306000	0.22856	0.591000	0.81541	CTA	C|0.582;G|0.418	0.418	strong		0.502	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	
TYW1	55253	hgsc.bcm.edu	37	7	66648199	66648199	+	Silent	SNP	G	G	A	rs55756354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:66648199G>A	ENST00000359626.5	+	14	1949	c.1785G>A	c.(1783-1785)ggG>ggA	p.G595G		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	595					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				TGTCCCTGGGGAATCCTGACT	0.537																																					p.G595G		Atlas-SNP	.											.	TYW1	71	.	0			c.G1785A						PASS	.	G		1246,3160		124,998,1081	59.0	45.0	50.0		1785	0.6	0.1	7	dbSNP_129	50	1785,6805		158,1469,2668	no	coding-synonymous	TYW1	NM_018264.2		282,2467,3749	AA,AG,GG		20.78,28.2796,23.3226		595/733	66648199	3031,9965	2203	4295	6498	SO:0001819	synonymous_variant	55253	exon14			CCTGGGGAATCCT	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1785G>A	7.37:g.66648199G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	127	44	0.346457	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	37	CCDS5538.1																																																																																			.	.	weak		0.537	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
TTLL11	158135	hgsc.bcm.edu	37	9	124633018	124633018	+	Silent	SNP	C	C	T	rs16911064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124633018C>T	ENST00000321582.5	-	7	1948	c.1761G>A	c.(1759-1761)caG>caA	p.Q587Q	TTLL11_ENST00000474723.1_5'UTR	NM_001139442.1	NP_001132914.1	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	0					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						GTTTTTCAAGCTGCTGAGACC	0.488													C|||	88	0.0175719	0.0613	0.0058	5008	,	,		21797	0.0		0.003	False		,,,				2504	0.0				p.Q587Q		Atlas-SNP	.											.	TTLL11	67	.	0			c.G1761A						PASS	.	C		96,1288		2,92,598	142.0	125.0	130.0		1761	1.6	0.8	9	dbSNP_123	130	0,3182		0,0,1591	no	coding-synonymous	TTLL11	NM_001139442.1		2,92,2189	TT,TC,CC		0.0,6.9364,2.1025		587/801	124633018	96,4470	692	1591	2283	SO:0001819	synonymous_variant	158135	exon7			TTCAAGCTGCTGA	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"""Tubulin tyrosine ligase-like family"""	18113	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 20"""	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000321582.5:c.1761G>A	9.37:g.124633018C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	132	67	0.507576	NM_001139442		Silent	SNP	ENST00000321582.5	37	CCDS48012.1																																																																																			C|0.983;T|0.017	0.017	strong		0.488	TTLL11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_088486	
ZNF385B	151126	hgsc.bcm.edu	37	2	180311444	180311444	+	Missense_Mutation	SNP	T	T	C	rs2271761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:180311444T>C	ENST00000410066.1	-	7	1327	c.724A>G	c.(724-726)Agt>Ggt	p.S242G	ZNF385B_ENST00000336917.5_Missense_Mutation_p.S140G|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409343.1_Missense_Mutation_p.S166G|ZNF385B_ENST00000409692.1_Missense_Mutation_p.S140G	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	242	Interaction with p53/TP53.		S -> G (in dbSNP:rs2271761).		intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			AATGAGCCACTTTCAGAGCTT	0.463													T|||	355	0.0708866	0.2012	0.0231	5008	,	,		15950	0.0248		0.0179	False		,,,				2504	0.0307				p.S242G	Colon(155;204 2491 32774 51842)	Atlas-SNP	.											.	ZNF385B	68	.	0			c.A724G						PASS	.	T	GLY/SER,GLY/SER,GLY/SER	738,3668	300.1+/-286.2	62,614,1527	112.0	124.0	120.0		496,418,724	0.4	1.0	2	dbSNP_100	120	90,8510	50.6+/-110.7	1,88,4211	yes	missense,missense,missense	ZNF385B	NM_001113397.1,NM_001113398.1,NM_152520.4	56,56,56	63,702,5738	CC,CT,TT		1.0465,16.7499,6.3663	benign,benign,benign	166/396,140/370,242/472	180311444	828,12178	2203	4300	6503	SO:0001583	missense	151126	exon7			AGCCACTTTCAGA	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"""zinc finger protein 533"""	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.724A>G	2.37:g.180311444T>C	ENSP00000386845:p.Ser242Gly	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	184	91	0.494565	NM_152520	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Missense_Mutation	SNP	ENST00000410066.1	37	CCDS33339.1	137	0.06272893772893773	97	0.19715447154471544	8	0.022099447513812154	17	0.02972027972027972	15	0.01978891820580475	T	10.77	1.444391	0.25987	0.167499	0.010465	ENSG00000144331	ENST00000410066;ENST00000336917;ENST00000409343;ENST00000409692;ENST00000457304	T;T;T;T;T	0.32515	1.46;1.45;1.46;1.45;1.47	5.83	0.387	0.16259	.	0.960097	0.08778	N	0.895163	T	0.00012	0.0000	N	0.01705	-0.755	0.53688	P	2.5000000000052758E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41251	-0.9519	9	0.19590	T	0.45	-12.4103	9.1717	0.37086	0.0:0.4936:0.0:0.5064	rs2271761;rs52802430;rs2271761	242;166	Q569K4;Q569K4-2	Z385B_HUMAN;.	G	242;140;166;140;140	ENSP00000386845:S242G;ENSP00000338225:S140G;ENSP00000386379:S166G;ENSP00000386507:S140G;ENSP00000394038:S140G	ENSP00000338225:S140G	S	-	1	0	ZNF385B	180019689	0.521000	0.26258	0.983000	0.44433	0.975000	0.68041	0.643000	0.24750	-0.004000	0.14419	-0.408000	0.06270	AGT	T|0.937;C|0.063	0.063	strong		0.463	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520	
IL17RA	23765	hgsc.bcm.edu	37	22	17589983	17589983	+	Missense_Mutation	SNP	G	G	A	rs189025188		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17589983G>A	ENST00000319363.6	+	13	2007	c.1874G>A	c.(1873-1875)cGc>cAc	p.R625H		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	625					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		CCCCTGGTGCGCGAGCCTGGC	0.677													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13392	0.0		0.0	False		,,,				2504	0.0				p.R625H		Atlas-SNP	.											.	IL17RA	62	.	0			c.G1874A						PASS	.	G	HIS/ARG	1,4309		0,1,2154	7.0	6.0	6.0		1874	-4.2	0.0	22		6	0,8498		0,0,4249	no	missense	IL17RA	NM_014339.5	29	0,1,6403	AA,AG,GG		0.0,0.0232,0.0078	benign	625/867	17589983	1,12807	2155	4249	6404	SO:0001583	missense	23765	exon13			TGGTGCGCGAGCC	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"""Interleukins and interleukin receptors"", ""CD molecules"""	5985	protein-coding gene	gene with protein product		605461	"""interleukin 17 receptor"""	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.1874G>A	22.37:g.17589983G>A	ENSP00000320936:p.Arg625His	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	16	12	0.75	NM_014339	O43844|Q20WK1	Missense_Mutation	SNP	ENST00000319363.6	37	CCDS13739.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	7.477	0.647869	0.14516	2.32E-4	0.0	ENSG00000177663	ENST00000425985;ENST00000319363	T	0.07800	3.16	5.1	-4.19	0.03835	.	0.588863	0.17907	N	0.157988	T	0.04363	0.0120	N	0.21583	0.68	0.09310	N	1	B;B	0.17038	0.01;0.02	B;B	0.10450	0.002;0.005	T	0.31475	-0.9942	10	0.37606	T	0.19	-15.8275	7.1335	0.25515	0.4871:0.0:0.4036:0.1092	.	573;625	D3YTB4;Q96F46	.;I17RA_HUMAN	H	573;625	ENSP00000320936:R625H	ENSP00000320936:R625H	R	+	2	0	IL17RA	15969983	0.000000	0.05858	0.016000	0.15963	0.002000	0.02628	-0.188000	0.09642	-0.559000	0.06110	-0.254000	0.11334	CGC	G|0.999;A|0.001	0.001	strong		0.677	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339	
MED12L	116931	hgsc.bcm.edu	37	3	150911405	150911405	+	Silent	SNP	T	T	C	rs3732755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150911405T>C	ENST00000474524.1	+	14	2135	c.2097T>C	c.(2095-2097)taT>taC	p.Y699Y	MED12L_ENST00000309237.4_Silent_p.Y734Y|MED12L_ENST00000273432.4_Silent_p.Y559Y|MED12L_ENST00000422248.2_Silent_p.Y699Y	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	699						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)			CATCTAATTATGACCTCCTTC	0.373													C|||	710	0.141773	0.2579	0.049	5008	,	,		18675	0.2153		0.0149	False		,,,				2504	0.1053				p.Y699Y		Atlas-SNP	.											.	MED12L	271	.	0			c.T2097C						PASS	.	C		1018,3388	728.6+/-410.0	125,768,1310	140.0	140.0	140.0		2097	-3.9	1.0	3	dbSNP_107	140	100,8500	814.7+/-407.0	0,100,4200	no	coding-synonymous	MED12L	NM_053002.4		125,868,5510	CC,CT,TT		1.1628,23.1049,8.596		699/2146	150911405	1118,11888	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon14			TAATTATGACCTC	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.2097T>C	3.37:g.150911405T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1	249	0.11401098901098901	107	0.21747967479674796	15	0.04143646408839779	117	0.20454545454545456	10	0.013192612137203167	C	8.490	0.861903	0.17178	0.231049	0.011628	ENSG00000144893	ENST00000480026	.	.	.	5.18	-3.91	0.04168	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999962	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.2088	15.0425	0.71803	0.0:0.4498:0.0:0.5502	rs3732755;rs3732755	.	.	.	R	49	.	.	X	+	1	0	MED12L	152394095	0.685000	0.27652	0.953000	0.39169	0.908000	0.53690	-0.358000	0.07641	-0.987000	0.03494	-0.826000	0.03091	TGA	T|0.896;C|0.104	0.104	strong		0.373	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
ZNF594	84622	hgsc.bcm.edu	37	17	5085247	5085247	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085247T>C	ENST00000399604.4	-	1	2445	c.2305A>G	c.(2305-2307)Acc>Gcc	p.T769A	ZNF594_ENST00000575779.1_Missense_Mutation_p.T769A			Q96JF6	ZN594_HUMAN	zinc finger protein 594	769					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)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CCCTGGAAGGTCCTACTACAC	0.413																																					p.T769A		Atlas-SNP	.											.	ZNF594	89	.	0			c.A2305G						PASS	.						207.0	208.0	208.0					17																	5085247		1990	4182	6172	SO:0001583	missense	84622	exon2			GGAAGGTCCTACT	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.2305A>G	17.37:g.5085247T>C	ENSP00000382513:p.Thr769Ala	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	98	16	0.163265	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.220840	0.00286	.	.	ENSG00000180626	ENST00000399604	T	0.14022	2.54	0.98	-0.251	0.13003	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04907	0.0132	N	0.12831	0.26	0.09310	N	1	B	0.18310	0.027	B	0.04013	0.001	T	0.42616	-0.9441	9	0.02654	T	1	.	4.0333	0.09719	0.0:0.2705:0.0:0.7295	.	769	Q96JF6	ZN594_HUMAN	A	769	ENSP00000382513:T769A	ENSP00000382513:T769A	T	-	1	0	ZNF594	5025971	0.000000	0.05858	0.002000	0.10522	0.239000	0.25481	-1.239000	0.02916	0.413000	0.25759	0.240000	0.17902	ACC	.	.	none		0.413	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
FAM46C	54855	hgsc.bcm.edu	37	1	118166195	118166195	+	Silent	SNP	C	C	T	rs10923359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118166195C>T	ENST00000369448.3	+	2	952	c.705C>T	c.(703-705)aaC>aaT	p.N235N		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	235										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		CCACCAAGAACCCAGAAGAAA	0.527			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			C|||	85	0.0169728	0.0613	0.0058	5008	,	,		18879	0.0		0.0	False		,,,				2504	0.0				p.N235N		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C705T						PASS	.	C		207,4199	127.4+/-164.3	6,195,2002	69.0	74.0	72.0		705	4.8	1.0	1	dbSNP_120	72	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FAM46C	NM_017709.3		6,197,6300	TT,TC,CC		0.0233,4.6981,1.607		235/392	118166195	209,12797	2203	4300	6503	SO:0001819	synonymous_variant	54855	exon2			CAAGAACCCAGAA	BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.705C>T	1.37:g.118166195C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	128	56	0.4375	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Silent	SNP	ENST00000369448.3	37	CCDS896.1																																																																																			C|0.979;T|0.021	0.021	strong		0.527	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412259	105412259	+	Missense_Mutation	SNP	G	G	C	rs2819426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105412259G>C	ENST00000333244.5	-	7	9648	c.9529C>G	c.(9529-9531)Ctg>Gtg	p.L3177V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3177			L -> V (in dbSNP:rs2819426).			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)			GGGAGGCTCAGGTCGGCCTCC	0.602													.|||	2168	0.432907	0.6536	0.3487	5008	,	,		14725	0.3552		0.2654	False		,,,				2504	0.4468				p.L3177V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C9529G						PASS	.	C	VAL/LEU	2252,1580		807,638,471	146.0	117.0	127.0		9529	1.8	0.0	14	dbSNP_100	127	916,6182		218,480,2851	no	missense	AHNAK2	NM_138420.2	32	1025,1118,3322	CC,CG,GG		12.905,41.2317,28.9844	benign	3177/5796	105412259	3168,7762	1916	3549	5465	SO:0001583	missense	113146	exon7			GGCTCAGGTCGGC	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.9529C>G	14.37:g.105412259G>C	ENSP00000353114:p.Leu3177Val	Somatic	393	0	0		WXS	Illumina HiSeq	Phase_I	393	392	0.997455	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	748	0.3424908424908425	278	0.5650406504065041	135	0.3729281767955801	160	0.27972027972027974	175	0.23087071240105542	c	0.005	-2.226234	0.00283	0.587683	0.12905	ENSG00000185567	ENST00000333244	T	0.00737	5.76	2.74	1.81	0.25067	.	.	.	.	.	T	0.00012	0.0000	N	0.00424	-1.51	0.80722	P	0.0	B	0.12630	0.006	B	0.10450	0.005	T	0.10730	-1.0617	8	0.06236	T	0.91	.	3.2516	0.06816	0.1662:0.4128:0.324:0.0971	rs60311708	3177	Q8IVF2	AHNK2_HUMAN	V	3177	ENSP00000353114:L3177V	ENSP00000353114:L3177V	L	-	1	2	AHNAK2	104483304	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.764000	0.00784	-0.043000	0.13513	-0.671000	0.03813	CTG	G|0.657;C|0.343	0.343	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ERICH6B	220081	hgsc.bcm.edu	37	13	46170898	46170898	+	Silent	SNP	C	C	T	rs78950901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:46170898C>T	ENST00000298738.2	-	3	407	c.243G>A	c.(241-243)aaG>aaA	p.K81K		NM_182542.2	NP_872348.2	Q5W0A0	ERI6B_HUMAN		81	Glu-rich.									breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)	5						actcttcctccttcAAGTATT	0.478													C|||	54	0.0107827	0.0386	0.0043	5008	,	,		22241	0.0		0.0	False		,,,				2504	0.0				p.K81K		Atlas-SNP	.											.	FAM194B	42	.	0			c.G243A						PASS	.	-		53,1331		0,53,639	243.0	195.0	210.0		243	-4.5	0.0	13	dbSNP_132	210	0,3182		0,0,1591	no	coding-synonymous	FAM194B	NM_182542.2		0,53,2230	TT,TC,CC		0.0,3.8295,1.1608		81/697	46170898	53,4513	692	1591	2283	SO:0001819	synonymous_variant	220081	exon3			TTCCTCCTTCAAG																												ENST00000298738.2:c.243G>A	13.37:g.46170898C>T		Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	334	163	0.488024	NM_182542	Q96MB5	Silent	SNP	ENST00000298738.2	37	CCDS45045.1																																																																																			C|0.987;T|0.013	0.013	strong		0.478	FAM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044781.3		
PIF1	80119	hgsc.bcm.edu	37	15	65108939	65108939	+	Missense_Mutation	SNP	A	A	G	rs138069301		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65108939A>G	ENST00000268043.4	-	12	1794	c.1700T>C	c.(1699-1701)aTt>aCt	p.I567T	PIF1_ENST00000333425.6_Missense_Mutation_p.I567T|PIF1_ENST00000559239.1_Missense_Mutation_p.I567T					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						GCCCAGAGAAATCTCCACACA	0.612																																					p.I567T		Atlas-SNP	.											.	PIF1	43	.	0			c.T1700C						PASS	.	A	THR/ILE	1,4399		0,1,2199	42.0	38.0	39.0		1700	5.7	1.0	15	dbSNP_134	39	0,8592		0,0,4296	no	missense	PIF1	NM_025049.2	89	0,1,6495	GG,GA,AA		0.0,0.0227,0.0077	possibly-damaging	567/642	65108939	1,12991	2200	4296	6496	SO:0001583	missense	80119	exon12			AGAGAAATCTCCA	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.1700T>C	15.37:g.65108939A>G	ENSP00000268043:p.Ile567Thr	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	174	84	0.482759	NM_025049		Missense_Mutation	SNP	ENST00000268043.4	37	CCDS10195.2	.	.	.	.	.	.	.	.	.	.	A	19.18	3.777475	0.70107	2.27E-4	0.0	ENSG00000140451	ENST00000268043;ENST00000333425	T;T	0.48836	0.8;0.8	5.73	5.73	0.89815	.	0.045148	0.85682	D	0.000000	T	0.64000	0.2559	M	0.75085	2.285	0.80722	D	1	P	0.51653	0.947	P	0.56751	0.805	T	0.68573	-0.5373	10	0.87932	D	0	-13.5461	13.9753	0.64268	1.0:0.0:0.0:0.0	.	567	Q9H611	PIF1_HUMAN	T	567	ENSP00000268043:I567T;ENSP00000328174:I567T	ENSP00000268043:I567T	I	-	2	0	PIF1	62895992	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.272000	0.95707	2.186000	0.69663	0.533000	0.62120	ATT	A|1.000;G|0.000	0.000	weak		0.612	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049	
SLC35D3	340146	hgsc.bcm.edu	37	6	137245567	137245567	+	Missense_Mutation	SNP	C	C	A	rs116512494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:137245567C>A	ENST00000331858.4	+	2	1149	c.984C>A	c.(982-984)gaC>gaA	p.D328E		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	328					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		TAAGTGGAGACCAGCTGCCGT	0.622													C|||	50	0.00998403	0.0371	0.0014	5008	,	,		17722	0.0		0.0	False		,,,				2504	0.0				p.D328E		Atlas-SNP	.											.	SLC35D3	33	.	0			c.C984A						PASS	.	C	GLU/ASP	110,4296	78.3+/-116.7	1,108,2094	28.0	30.0	29.0		984	0.3	1.0	6	dbSNP_132	29	0,8600		0,0,4300	yes	missense	SLC35D3	NM_001008783.1	45	1,108,6394	AA,AC,CC		0.0,2.4966,0.8458	benign	328/417	137245567	110,12896	2203	4300	6503	SO:0001583	missense	340146	exon2			TGGAGACCAGCTG		CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"""Solute carriers"""	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.984C>A	6.37:g.137245567C>A	ENSP00000333591:p.Asp328Glu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	105	59	0.561905	NM_001008783	B4DI58|Q5QNZ6|Q6NX71	Missense_Mutation	SNP	ENST00000331858.4	37	CCDS34544.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	C	12.85	2.061537	0.36373	0.024966	0.0	ENSG00000182747	ENST00000331858	T	0.54279	0.58	5.99	0.297	0.15762	.	0.219154	0.44902	D	0.000414	T	0.14141	0.0342	N	0.19112	0.55	0.35092	D	0.764393	B	0.06786	0.001	B	0.04013	0.001	T	0.03306	-1.1050	10	0.37606	T	0.19	-11.3298	5.2593	0.15563	0.134:0.399:0.0:0.467	.	328	Q5M8T2	S35D3_HUMAN	E	328	ENSP00000333591:D328E	ENSP00000333591:D328E	D	+	3	2	SLC35D3	137287260	0.998000	0.40836	0.996000	0.52242	0.699000	0.40488	0.450000	0.21762	0.106000	0.17784	0.609000	0.83330	GAC	C|0.988;A|0.012	0.012	strong		0.622	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017	
MORC1	27136	hgsc.bcm.edu	37	3	108677821	108677821	+	Silent	SNP	C	C	A	rs2197737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108677821C>A	ENST00000483760.1	-	27	2926	c.2883G>T	c.(2881-2883)tcG>tcT	p.S961S	MORC1_ENST00000232603.5_Silent_p.S982S					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						CTTAATTTTCCGaagtctttt	0.259													A|||	1530	0.305511	0.3933	0.2421	5008	,	,		15335	0.1071		0.3678	False		,,,				2504	0.3722				p.S982S		Atlas-SNP	.											MORC1,NS,carcinoma,0,1	MORC1	211	1	0			c.G2946T						PASS	.	A		1752,2644		356,1040,802	30.0	31.0	31.0		2946	3.1	0.0	3	dbSNP_96	31	3009,5577		531,1947,1815	no	coding-synonymous	MORC1	NM_014429.3		887,2987,2617	AA,AC,CC		35.0454,39.8544,36.6739		982/985	108677821	4761,8221	2198	4293	6491	SO:0001819	synonymous_variant	27136	exon28			ATTTTCCGAAGTC	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.2883G>T	3.37:g.108677821C>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_014429		Silent	SNP	ENST00000483760.1	37																																																																																				C|0.656;A|0.344	0.344	strong		0.259	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
EPOR	2057	hgsc.bcm.edu	37	19	11489049	11489049	+	Missense_Mutation	SNP	G	G	C	rs35423344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11489049G>C	ENST00000222139.6	-	8	1242	c.1138C>G	c.(1138-1140)Ccg>Gcg	p.P380A	EPOR_ENST00000592375.2_3'UTR	NM_000121.3	NP_000112.1	P19235	EPOR_HUMAN	erythropoietin receptor	380			P -> A (in dbSNP:rs35423344).		brain development (GO:0007420)|decidualization (GO:0046697)|erythropoietin-mediated signaling pathway (GO:0038162)|heart development (GO:0007507)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	erythropoietin receptor activity (GO:0004900)|identical protein binding (GO:0042802)			endometrium(1)|lung(2)|ovary(1)|urinary_tract(1)	5					Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)|Epoetin Zeta(DB08923)|Peginesatide(DB08894)	TCACTGGGCGGGTTCCGGGGC	0.617											OREG0025254	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	306	0.0611022	0.2231	0.0144	5008	,	,		17759	0.0		0.001	False		,,,				2504	0.0				p.P380A		Atlas-SNP	.											.	EPOR	26	.	0			c.C1138G						PASS	.	G	ALA/PRO	863,3543	335.5+/-303.9	79,705,1419	58.0	56.0	57.0		1138	4.5	0.2	19	dbSNP_126	57	11,8589	6.4+/-24.3	0,11,4289	yes	missense	EPOR	NM_000121.3	27	79,716,5708	CC,CG,GG		0.1279,19.5869,6.72	probably-damaging	380/509	11489049	874,12132	2203	4300	6503	SO:0001583	missense	2057	exon8			TGGGCGGGTTCCG	M34986	CCDS12260.1	19p13.3-p13.2	2013-02-11				ENSG00000187266		"""Fibronectin type III domain containing"""	3416	protein-coding gene	gene with protein product		133171					Standard	NM_000121		Approved		uc002mrj.2	P19235		ENST00000222139.6:c.1138C>G	19.37:g.11489049G>C	ENSP00000222139:p.Pro380Ala	Somatic	32	0	0	672	WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_000121	B2RCG4|Q15443|Q2M205	Missense_Mutation	SNP	ENST00000222139.6	37	CCDS12260.1	109	0.04990842490842491	105	0.21341463414634146	4	0.011049723756906077	0	0.0	0	0.0	G	10.08	1.251233	0.22880	0.195869	0.001279	ENSG00000187266	ENST00000222139	T	0.59364	0.27	4.51	4.51	0.55191	.	0.229422	0.36778	N	0.002409	T	0.00109	0.0003	M	0.67953	2.075	0.42246	P	0.008044000000000051	D	0.76494	0.999	P	0.60609	0.877	T	0.11591	-1.0581	9	0.14656	T	0.56	-28.7314	12.5811	0.56391	0.0:0.0:1.0:0.0	rs35423344;rs57359971	380	P19235	EPOR_HUMAN	A	380	ENSP00000222139:P380A	ENSP00000222139:P380A	P	-	1	0	EPOR	11350049	0.629000	0.27146	0.196000	0.23383	0.027000	0.11550	3.028000	0.49705	2.320000	0.78422	0.650000	0.86243	CCG	G|0.941;C|0.059	0.059	strong		0.617	EPOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458791.1		
DSPP	1834	hgsc.bcm.edu	37	4	88536451	88536451	+	Silent	SNP	C	C	T	rs111205176|rs149201255		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88536451C>T	ENST00000282478.7	+	4	2670	c.2637C>T	c.(2635-2637)agC>agT	p.S879S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S879S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	879	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcagtgacagcagtgatagca	0.493																																					p.S879S		Atlas-SNP	.											DSPP,colon,carcinoma,0,1	DSPP	174	1	0			c.C2637T						scavenged	.						71.0	84.0	80.0					4																	88536451		1629	2928	4557	SO:0001819	synonymous_variant	1834	exon5			TGACAGCAGTGAT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2637C>T	4.37:g.88536451C>T		Somatic	283	1	0.00353357		WXS	Illumina HiSeq	Phase_I	334	35	0.10479	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.493	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
MMP20	9313	hgsc.bcm.edu	37	11	102477395	102477395	+	Missense_Mutation	SNP	A	A	G	rs1784423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:102477395A>G	ENST00000260228.2	-	6	836	c.824T>C	c.(823-825)gTa>gCa	p.V275A	RP11-817J15.2_ENST00000542119.1_RNA|MMP20_ENST00000544938.1_5'UTR|RP11-817J15.2_ENST00000544115.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	294					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	CCCCAGGAATACTTTCCGAGG	0.527													G|||	2103	0.419928	0.2625	0.4424	5008	,	,		19891	0.4325		0.4364	False		,,,				2504	0.5869				p.V275A		Atlas-SNP	.											.	MMP20	52	.	0			c.T824C						PASS	.	G	ALA/VAL	1359,3047	692.2+/-405.5	203,953,1047	97.0	97.0	97.0		824	4.5	0.0	11	dbSNP_89	97	3927,4671	604.8+/-394.9	867,2193,1239	yes	missense	MMP20	NM_004771.3	64	1070,3146,2286	GG,GA,AA		45.6734,30.8443,40.649	benign	275/484	102477395	5286,7718	2203	4299	6502	SO:0001583	missense	9313	exon6			AGGAATACTTTCC	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.824T>C	11.37:g.102477395A>G	ENSP00000260228:p.Val275Ala	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	152	81	0.532895	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	876	0.4010989010989011	129	0.2621951219512195	170	0.4696132596685083	248	0.43356643356643354	329	0.4340369393139842	G	0.012	-1.683853	0.00745	0.308443	0.456734	ENSG00000137674	ENST00000260228	T	0.12361	2.69	5.45	4.53	0.55603	.	1.200790	0.05857	N	0.622272	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44892	-0.9298	9	0.07175	T	0.84	.	7.9149	0.29812	0.2475:0.0:0.7525:0.0	rs1784423;rs1784423	275	O60882	MMP20_HUMAN	A	275	ENSP00000260228:V275A	ENSP00000260228:V275A	V	-	2	0	MMP20	101982605	0.005000	0.15991	0.017000	0.16124	0.020000	0.10135	0.727000	0.25999	0.855000	0.35359	-0.128000	0.14901	GTA	G|0.400;N|0.000	0.400	strong		0.527	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
SCOC	60592	hgsc.bcm.edu	37	4	141294814	141294814	+	Missense_Mutation	SNP	G	G	C	rs2271430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:141294814G>C	ENST00000608372.1	+	1	151	c.124G>C	c.(124-126)Gtg>Ctg	p.V42L	SCOC_ENST00000502535.1_5'Flank|RP11-425I13.3_ENST00000512692.2_RNA|SCOC_ENST00000394201.4_5'UTR|RP11-425I13.3_ENST00000608178.1_RNA|RP11-425I13.3_ENST00000609616.1_RNA|SCOC_ENST00000394205.3_Intron|SCOC_ENST00000338517.4_Intron|SCOC_ENST00000506322.1_Intron|SCOC_ENST00000394203.3_Intron|SCOC_ENST00000512749.1_Intron|SCOC_ENST00000506597.1_Missense_Mutation_p.V42L|SCOC_ENST00000510586.1_5'UTR			Q9UIL1	SCOC_HUMAN	short coiled-coil protein	42					positive regulation of macroautophagy (GO:0016239)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5	all_hematologic(180;0.162)					GTTGGTCCAAGTGTCCCGGCC	0.711													G|||	607	0.121206	0.0855	0.1095	5008	,	,		13039	0.2302		0.0775	False		,,,				2504	0.1104				p.V42L		Atlas-SNP	.											SCOC_ENST00000394201,NS,carcinoma,0,1	SCOC	11	1	0			c.G124C						PASS	.	G	,LEU/VAL,LEU/VAL,,,LEU/VAL,,	145,1239		10,125,557	50.0	59.0	56.0		,124,124,,,124,,	3.3	0.0	4	dbSNP_100	56	283,2899		11,261,1319	yes	intron,missense,missense,intron,intron,missense,intron,intron	SCOC	NM_001153446.1,NM_001153484.1,NM_001153552.1,NM_001153585.1,NM_001153635.1,NM_001153663.1,NM_001153690.1,NM_032547.2	,32,32,,,32,,	21,386,1876	CC,CG,GG		8.8938,10.4769,9.3736	,,,,,,,	,42/160,42/132,,,42/159,,	141294814	428,4138	692	1591	2283	SO:0001583	missense	60592	exon1			GTCCAAGTGTCCC	AK027797	CCDS3750.1, CCDS54806.1, CCDS54807.1	4q28.3	2014-05-22	2003-03-19		ENSG00000153130	ENSG00000153130			20335	protein-coding gene	gene with protein product			"""short coiled coil protein"""			11303027	Standard	NM_032547		Approved	HRIHFB2072, SCOCO	uc011che.1	Q9UIL1	OTTHUMG00000133416	ENST00000608372.1:c.124G>C	4.37:g.141294814G>C	ENSP00000477352:p.Val42Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	115	62	0.53913	NM_001153484	B7WPH7|D3DNY7|E9PB65|Q6P5T9|Q7L2Y0|Q7Z4P2|Q96JY9|Q9BZB2	Missense_Mutation	SNP	ENST00000608372.1	37	CCDS54806.1	233	0.10668498168498168	50	0.1016260162601626	37	0.10220994475138122	101	0.17657342657342656	45	0.059366754617414245	G	11.66	1.706169	0.30232	0.104769	0.088938	ENSG00000153130	ENST00000394201;ENST00000506597	.	.	.	5.17	3.31	0.37934	.	1.941280	0.03143	N	0.166893	T	0.00073	0.0002	N	0.24115	0.695	0.51012	P	9.999999999998899E-5	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.05321	-1.0892	8	0.41790	T	0.15	-16.3881	6.4476	0.21885	0.0982:0.1853:0.7164:0.0	rs2271430;rs17226920;rs52830427;rs2271430	42;42	E9PB65;Q9UIL1	.;SCOC_HUMAN	L	42	.	ENSP00000377751:V42L	V	+	1	0	SCOC	141514264	0.006000	0.16342	0.001000	0.08648	0.035000	0.12851	1.368000	0.34216	1.303000	0.44873	0.563000	0.77884	GTG	G|0.887;C|0.113	0.113	strong		0.711	SCOC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257274.2		
CES4A	283848	hgsc.bcm.edu	37	16	67037054	67037054	+	Missense_Mutation	SNP	A	A	C	rs61744399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67037054A>C	ENST00000326686.5	+	6	772	c.772A>C	c.(772-774)Agt>Cgt	p.S258R	CES4A_ENST00000398354.1_Missense_Mutation_p.S258R|CES4A_ENST00000540579.1_Missense_Mutation_p.S160R|CES4A_ENST00000541479.1_Missense_Mutation_p.S281R|CES4A_ENST00000338718.4_Missense_Mutation_p.S281R|CES4A_ENST00000540947.2_Missense_Mutation_p.S258R|CES4A_ENST00000535696.1_Missense_Mutation_p.S164R			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	258						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						TTTCATCACTAGTAACCCACT	0.542													C|||	1677	0.334864	0.8033	0.1715	5008	,	,		21997	0.2312		0.0755	False		,,,				2504	0.1912				p.S258R		Atlas-SNP	.											.	CES4A	24	.	0			c.A772C						PASS	.	C	ARG/SER,ARG/SER,ARG/SER	2521,1475		801,919,278	91.0	90.0	90.0		478,490,772	1.6	0.0	16	dbSNP_129	90	632,7720		31,570,3575	yes	missense,missense,missense	CES4A	NM_001190201.1,NM_001190202.1,NM_173815.6	110,110,110	832,1489,3853	CC,CA,AA		7.567,36.9119,25.5345	benign,benign,benign	160/464,164/375,258/469	67037054	3153,9195	1998	4176	6174	SO:0001583	missense	283848	exon6			ATCACTAGTAACC	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"""Carboxylesterases"""	26741	protein-coding gene	gene with protein product			"""carboxylesterase 8 (putative)"""	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.772A>C	16.37:g.67037054A>C	ENSP00000314145:p.Ser258Arg	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	155	66	0.425806	NM_173815	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Missense_Mutation	SNP	ENST00000326686.5	37		632	0.2893772893772894	386	0.7845528455284553	61	0.1685082872928177	129	0.22552447552447552	56	0.07387862796833773	c	10.71	1.426257	0.25726	0.630881	0.07567	ENSG00000172824	ENST00000540947;ENST00000541479;ENST00000338718;ENST00000398354;ENST00000326686;ENST00000538199;ENST00000540579;ENST00000535696	T;T;T;T;T;T;T;T	0.68624	0.28;0.28;0.28;0.28;-0.34;0.28;-0.34;0.28	5.17	1.61	0.23674	Carboxylesterase, type B (1);	3.156810	0.01089	N	0.005151	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B;B;B;B	0.13145	0.007;0.0;0.0;0.0	B;B;B;B	0.16722	0.012;0.0;0.016;0.001	T	0.45991	-0.9223	9	0.25106	T	0.35	.	2.6837	0.05101	0.3927:0.3632:0.0:0.2441	rs61744399	164;281;258;281	Q5XG92-7;F8WEE9;Q5XG92;F5H5S4	.;.;EST4A_HUMAN;.	R	258;281;281;258;258;221;160;164	ENSP00000444052:S258R;ENSP00000443175:S281R;ENSP00000340714:S281R;ENSP00000381397:S258R;ENSP00000314145:S258R;ENSP00000441103:S221R;ENSP00000441907:S160R;ENSP00000441644:S164R	ENSP00000314145:S258R	S	+	1	0	CES4A	65594555	0.000000	0.05858	0.048000	0.18961	0.178000	0.23041	-0.283000	0.08433	0.205000	0.20568	-0.211000	0.12701	AGT	A|0.791;C|0.209	0.209	strong		0.542	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173815	
IDO2	169355	hgsc.bcm.edu	37	8	39871135	39871135	+	Silent	SNP	C	C	T	rs2001923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39871135C>T	ENST00000389060.4	+	9	771	c.771C>T	c.(769-771)tcC>tcT	p.S257S	IDO2_ENST00000343295.4_3'UTR|IDO2_ENST00000502986.2_Silent_p.S270S			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	257					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						AAGGAGTTTCCCAAGAGCCCC	0.498													C|||	381	0.0760783	0.1785	0.0692	5008	,	,		17581	0.002		0.0577	False		,,,				2504	0.0378				p.S270S		Atlas-SNP	.											IDO2_ENST00000502986,trunk,malignant_melanoma,+1,1	IDO2	78	1	0			c.C810T						PASS	.	C		646,3172		54,538,1317	103.0	99.0	100.0		810	-4.0	0.0	8	dbSNP_92	100	462,7788		13,436,3676	no	coding-synonymous	IDO2	NM_194294.2		67,974,4993	TT,TC,CC		5.6,16.9199,9.1813		270/421	39871135	1108,10960	1909	4125	6034	SO:0001819	synonymous_variant	169355	exon10			AGTTTCCCAAGAG	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"""indoleamine-pyrrole 2,3 dioxygenase-like 1"""	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.771C>T	8.37:g.39871135C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	NM_194294	A4UD41	Silent	SNP	ENST00000389060.4	37																																																																																				C|0.932;T|0.068	0.068	strong		0.498	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
PCDHA8	56140	hgsc.bcm.edu	37	5	140222534	140222534	+	Missense_Mutation	SNP	C	C	A	rs6889154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140222534C>A	ENST00000531613.1	+	1	1628	c.1628C>A	c.(1627-1629)cCg>cAg	p.P543Q	PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.P543Q|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	543	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(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)			GCGGGCGTGCCGCCTCTGGGC	0.687													.|||	85	0.0169728	0.0635	0.0014	5008	,	,		15269	0.0		0.0	False		,,,				2504	0.0				p.P543Q		Atlas-SNP	.											PCDHA8_ENST00000531613,NS,carcinoma,-1,6	PCDHA8	366	6	0			c.C1628A						PASS	.	C	,,,,,,,GLN/PRO,,,GLN/PRO	287,4097		26,235,1931	52.0	61.0	58.0		,,,,,,,1628,,,1628	3.7	0.9	5	dbSNP_116	58	2,8524		0,2,4261	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	,,,,,,,76,,,76	26,237,6192	AA,AC,CC		0.0235,6.5465,2.2386	,,,,,,,,,,	,,,,,,,543/951,,,543/815	140222534	289,12621	2192	4263	6455	SO:0001583	missense	56140	exon1			GCGTGCCGCCTCT	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.1628C>A	5.37:g.140222534C>A	ENSP00000434655:p.Pro543Gln	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	17.62	3.434270	0.62955	0.065465	2.35E-4	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.55588	0.51;0.51	3.72	3.72	0.42706	Cadherin (4);Cadherin-like (1);	0.000000	0.36555	U	0.002521	T	0.22166	0.0534	M	0.87180	2.865	0.46376	D	0.999014	D;D	0.76494	0.999;0.999	D;D	0.80764	0.991;0.994	T	0.66396	-0.5934	10	0.87932	D	0	.	15.9202	0.79556	0.0:1.0:0.0:0.0	rs6889154	543;543	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	Q	543	ENSP00000434655:P543Q;ENSP00000367363:P543Q	ENSP00000367363:P543Q	P	+	2	0	PCDHA8	140202718	1.000000	0.71417	0.869000	0.34112	0.258000	0.26162	7.317000	0.79018	1.790000	0.52503	0.306000	0.20318	CCG	C|0.978;A|0.022	0.022	strong		0.687	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
PLXND1	23129	hgsc.bcm.edu	37	3	129289752	129289752	+	Silent	SNP	C	C	T	rs2285365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129289752C>T	ENST00000324093.4	-	19	3805	c.3627G>A	c.(3625-3627)caG>caA	p.Q1209Q	PLXND1_ENST00000393239.1_Silent_p.Q1209Q	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1209					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						ACTCGTGACTCTGGAGCCCCA	0.612													C|||	735	0.146765	0.3495	0.0519	5008	,	,		18385	0.1032		0.0388	False		,,,				2504	0.0961				p.Q1209Q	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.G3627A						PASS	.	C		1357,3049	453.2+/-350.3	208,941,1054	246.0	260.0	255.0		3627	3.9	1.0	3	dbSNP_100	255	306,8294	109.8+/-170.3	8,290,4002	no	coding-synonymous	PLXND1	NM_015103.2		216,1231,5056	TT,TC,CC		3.5581,30.7989,12.7864		1209/1926	129289752	1663,11343	2203	4300	6503	SO:0001819	synonymous_variant	23129	exon19			GTGACTCTGGAGC	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.3627G>A	3.37:g.129289752C>T		Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	299	151	0.505017	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			C|0.857;T|0.143	0.143	strong		0.612	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
FAM209B	388799	hgsc.bcm.edu	37	20	55111273	55111273	+	Silent	SNP	C	C	T	rs2296128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:55111273C>T	ENST00000371325.1	+	2	391	c.295C>T	c.(295-297)Cta>Tta	p.L99L		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	99						integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TCGCACTCCACTAAAGAAAAA	0.398													C|||	549	0.109625	0.0219	0.0346	5008	,	,		21036	0.4524		0.002	False		,,,				2504	0.0389				p.L99L		Atlas-SNP	.											.	.	.	.	0			c.C295T						PASS	.	C		109,4297	83.9+/-122.4	0,109,2094	94.0	95.0	95.0		295	-3.6	0.0	20	dbSNP_100	95	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	C20orf107	NM_001013646.2		0,119,6384	TT,TC,CC		0.1163,2.4739,0.915		99/172	55111273	119,12887	2203	4300	6503	SO:0001819	synonymous_variant	388799	exon2			ACTCCACTAAAGA	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.295C>T	20.37:g.55111273C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	112	61	0.544643	NM_001013646	Q3KRB5	Silent	SNP	ENST00000371325.1	37	CCDS33494.1																																																																																			C|0.937;T|0.063	0.063	strong		0.398	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
TTLL2	83887	hgsc.bcm.edu	37	6	167754702	167754702	+	Silent	SNP	C	C	T	rs909546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:167754702C>T	ENST00000239587.5	+	3	1402	c.1314C>T	c.(1312-1314)gaC>gaT	p.D438D		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	438					cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CCAACATCGACGCTGCAAAAA	0.428													C|||	2571	0.513379	0.6437	0.4265	5008	,	,		23083	0.6181		0.3966	False		,,,				2504	0.411				p.D438D		Atlas-SNP	.											TTLL2,NS,carcinoma,0,1	TTLL2	82	1	0			c.C1314T						PASS	.	C		2691,1715	650.3+/-399.0	823,1045,335	102.0	95.0	98.0		1314	-0.3	0.0	6	dbSNP_86	98	3605,4995	521.5+/-379.9	736,2133,1431	no	coding-synonymous	TTLL2	NM_031949.4		1559,3178,1766	TT,TC,CC		41.9186,38.9242,48.4084		438/593	167754702	6296,6710	2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			CATCGACGCTGCA	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1314C>T	6.37:g.167754702C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	37	CCDS5301.1																																																																																			C|0.503;A|0.003	.	strong		0.428	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
MUC6	4588	hgsc.bcm.edu	37	11	1017307	1017307	+	Missense_Mutation	SNP	G	G	A	rs372717767		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017307G>A	ENST00000421673.2	-	31	5544	c.5494C>T	c.(5494-5496)Cct>Tct	p.P1832S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1832	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			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)		GTGGTGTGAGGGTGTGATGGG	0.552																																					p.P1832S		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	0			c.C5494T						scavenged	.	G	SER/PRO	152,4250		0,152,2049	780.0	761.0	767.0		5494	-1.4	0.0	11		767	139,8451		0,139,4156	no	missense	MUC6	NM_005961.2	74	0,291,6205	AA,AG,GG		1.6182,3.453,2.2398	benign	1832/2440	1017307	291,12701	2201	4295	6496	SO:0001583	missense	4588	exon31			TGTGAGGGTGTGA	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.5494C>T	11.37:g.1017307G>A	ENSP00000406861:p.Pro1832Ser	Somatic	1136	14	0.0123239		WXS	Illumina HiSeq	Phase_I	1352	173	0.127959	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.706398	0.30232	0.03453	0.016182	ENSG00000184956	ENST00000421673	T	0.20200	2.09	3.21	-1.4	0.08968	.	.	.	.	.	T	0.10035	0.0246	M	0.65975	2.015	0.09310	N	1	P	0.45078	0.85	P	0.51657	0.676	T	0.08868	-1.0701	9	0.35671	T	0.21	.	3.0139	0.06053	0.3177:0.0:0.3661:0.3162	.	1832	Q6W4X9	MUC6_HUMAN	S	1832	ENSP00000406861:P1832S	ENSP00000406861:P1832S	P	-	1	0	MUC6	1007307	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.644000	0.02002	-0.414000	0.07495	-0.643000	0.03959	CCT	.	.	weak		0.552	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
GDF15	9518	hgsc.bcm.edu	37	19	18499151	18499151	+	Silent	SNP	C	C	T	rs1059022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18499151C>T	ENST00000252809.3	+	2	365	c.333C>T	c.(331-333)ccC>ccT	p.P111P	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	111					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						CCGCCCTTCCCGAGGGGCTCC	0.701											OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	863	0.172324	0.3601	0.1556	5008	,	,		12390	0.0069		0.175	False		,,,				2504	0.0982				p.P111P		Atlas-SNP	.											GDF15,NS,carcinoma,0,1	GDF15	31	1	0			c.C333T						PASS	.	C		1414,2934		255,904,1015	17.0	21.0	19.0		333	-8.6	0.0	19	dbSNP_86	19	1497,7063		143,1211,2926	no	coding-synonymous	GDF15	NM_004864.2		398,2115,3941	TT,TC,CC		17.4883,32.5207,22.5519		111/309	18499151	2911,9997	2174	4280	6454	SO:0001819	synonymous_variant	9518	exon2			CCTTCCCGAGGGG	BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"""prostate differentiation factor"""	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988		ENST00000252809.3:c.333C>T	19.37:g.18499151C>T		Somatic	92	0	0	726	WXS	Illumina HiSeq	Phase_I	129	62	0.48062	NM_004864	O14629|P78360|Q9BWA0|Q9NRT0	Silent	SNP	ENST00000252809.3	37	CCDS12376.1																																																																																			C|0.799;T|0.201	0.201	strong		0.701	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864	
NUDCD1	84955	hgsc.bcm.edu	37	8	110302047	110302047	+	Missense_Mutation	SNP	T	T	G	rs2980619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110302047T>G	ENST00000239690.4	-	5	1130	c.756A>C	c.(754-756)ttA>ttC	p.L252F	NUDCD1_ENST00000427660.2_Missense_Mutation_p.L223F	NM_032869.3	NP_116258.2			NudC domain containing 1											breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(2)|skin(1)	25	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)			GAACAAATGTTAAAGACTTGT	0.338													G|||	3361	0.671126	0.8941	0.6888	5008	,	,		13349	0.5218		0.4841	False		,,,				2504	0.7035				p.L252F		Atlas-SNP	.											.	NUDCD1	58	.	0			c.A756C						PASS	.	G	PHE/LEU,PHE/LEU	3700,706	294.4+/-283.1	1549,602,52	74.0	75.0	75.0		669,756	3.8	0.3	8	dbSNP_101	75	4656,3944	548.7+/-385.4	1241,2174,885	yes	missense,missense	NUDCD1	NM_001128211.1,NM_032869.3	22,22	2790,2776,937	GG,GT,TT		45.8605,16.0236,35.7527	benign,benign	223/555,252/584	110302047	8356,4650	2203	4300	6503	SO:0001583	missense	84955	exon5			AAATGTTAAAGAC	AF283302	CCDS6312.1, CCDS47910.1	8q23	2005-02-07			ENSG00000120526	ENSG00000120526			24306	protein-coding gene	gene with protein product		606109				11416219	Standard	NM_032869		Approved	CML66, FLJ14991	uc003ynb.4	Q96RS6	OTTHUMG00000164931	ENST00000239690.4:c.756A>C	8.37:g.110302047T>G	ENSP00000239690:p.Leu252Phe	Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	370	370	1	NM_032869		Missense_Mutation	SNP	ENST00000239690.4	37	CCDS6312.1	1354	0.61996336996337	425	0.8638211382113821	247	0.6823204419889503	313	0.5472027972027972	369	0.4868073878627968	G	0.024	-1.391632	0.01185	0.839764	0.541395	ENSG00000120526	ENST00000239690;ENST00000427660	T;T	0.16597	2.33;2.33	5.69	3.81	0.43845	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00057	-2.36	0.50632	P	1.2000000000000899E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33189	-0.9878	9	0.02654	T	1	-0.4768	7.738	0.28825	0.1458:0.0:0.7241:0.1301	rs2980619;rs17856026;rs17857287;rs52825694;rs60760734;rs2980619	165;252;223	Q96RS6-3;Q96RS6;Q96RS6-2	.;NUDC1_HUMAN;.	F	252;223	ENSP00000239690:L252F;ENSP00000410707:L223F	ENSP00000239690:L252F	L	-	3	2	NUDCD1	110371223	1.000000	0.71417	0.277000	0.24703	0.139000	0.21198	2.429000	0.44758	0.293000	0.22520	-0.770000	0.03390	TTA	G|0.634;N|0.000	0.634	strong		0.338	NUDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380996.1	NM_032869	
CLUH	23277	hgsc.bcm.edu	37	17	2604698	2604698	+	Silent	SNP	G	G	A	rs115717445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2604698G>A	ENST00000570628.2	-	6	852	c.747C>T	c.(745-747)gtC>gtT	p.V249V	CLUH_ENST00000435359.1_Silent_p.V249V|CLUH_ENST00000538975.1_Silent_p.V249V			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	249					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											CGGTGATGCTGACTTGCCGGT	0.632													G|||	21	0.00419329	0.0159	0.0	5008	,	,		14270	0.0		0.0	False		,,,				2504	0.0				p.V249V		Atlas-SNP	.											.	.	.	.	0			c.C747T						PASS	.	G		48,4218		0,48,2085	27.0	34.0	32.0		747	1.3	1.0	17	dbSNP_132	32	0,8468		0,0,4234	yes	coding-synonymous	KIAA0664	NM_015229.3		0,48,6319	AA,AG,GG		0.0,1.1252,0.3769		249/1310	2604698	48,12686	2133	4234	6367	SO:0001819	synonymous_variant	23277	exon6			GATGCTGACTTGC	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"""KIAA0664"""	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.747C>T	17.37:g.2604698G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	87	53	0.609195	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	37	CCDS45572.1																																																																																			G|0.993;A|0.007	0.007	strong		0.632	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
DPP8	54878	hgsc.bcm.edu	37	15	65772698	65772698	+	Silent	SNP	T	T	C	rs352461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65772698T>C	ENST00000341861.5	-	10	2786	c.1206A>G	c.(1204-1206)ctA>ctG	p.L402L	DPP8_ENST00000321118.7_Silent_p.L402L|DPP8_ENST00000358939.4_Silent_p.L386L|DPP8_ENST00000321147.6_Silent_p.L402L|DPP8_ENST00000559233.1_Silent_p.L402L|DPP8_ENST00000300141.6_Silent_p.L386L|DPP8_ENST00000339244.5_Intron	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	402					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						ACACTATCTGTAGGCGAGTCT	0.403													C|||	610	0.121805	0.3306	0.0432	5008	,	,		16261	0.0456		0.0457	False		,,,				2504	0.0521				p.L402L		Atlas-SNP	.											.	DPP8	78	.	0			c.A1206G						PASS	.	C	,,,	1237,3165	704.2+/-407.1	177,883,1141	91.0	86.0	87.0		1158,1158,1206,1206	-8.9	0.4	15	dbSNP_79	87	507,8091	796.4+/-407.5	16,475,3808	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DPP8	NM_017743.4,NM_130434.3,NM_197960.2,NM_197961.2	,,,	193,1358,4949	CC,CT,TT		5.8967,28.1009,13.4154	,,,	386/783,386/883,402/899,402/848	65772698	1744,11256	2201	4299	6500	SO:0001819	synonymous_variant	54878	exon11			TATCTGTAGGCGA	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"""dipeptidyl peptidase VIII"", ""dipeptidyl peptidase IV-related protein-1"", ""prolyl dipeptidase DPP8"""	606819	"""dipeptidylpeptidase 8"""			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.1206A>G	15.37:g.65772698T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Silent	SNP	ENST00000341861.5	37	CCDS10207.1																																																																																			T|0.871;C|0.129	0.129	strong		0.403	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743	
CUBN	8029	hgsc.bcm.edu	37	10	16918972	16918972	+	Silent	SNP	A	A	G	rs1801241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:16918972A>G	ENST00000377833.4	-	57	9095	c.9030T>C	c.(9028-9030)gcT>gcC	p.A3010A		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3010	CUB 22. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.A3010A(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAACCGGCCCAGCGATGGTGA	0.488													G|||	1239	0.247404	0.354	0.2882	5008	,	,		17623	0.3065		0.0855	False		,,,				2504	0.18				p.A3010A		Atlas-SNP	.											CUBN,NS,carcinoma,0,1	CUBN	515	1	1	Substitution - coding silent(1)	stomach(1)	c.T9030C						PASS	.	G		1441,2965	682.7+/-404.2	242,957,1004	121.0	105.0	111.0		9030	-6.2	0.0	10	dbSNP_89	111	494,8106	797.5+/-407.4	16,462,3822	no	coding-synonymous	CUBN	NM_001081.3		258,1419,4826	GG,GA,AA		5.7442,32.7054,14.8777		3010/3624	16918972	1935,11071	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon57			CGGCCCAGCGATG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.9030T>C	10.37:g.16918972A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			A|0.814;G|0.186	0.186	strong		0.488	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
MXRA8	54587	hgsc.bcm.edu	37	1	1290408	1290408	+	Silent	SNP	A	A	G	rs147996767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1290408A>G	ENST00000309212.6	-	5	633	c.603T>C	c.(601-603)gcT>gcC	p.A201A	MXRA8_ENST00000342753.4_Silent_p.A100A|MXRA8_ENST00000445648.2_Silent_p.A201A|MXRA8_ENST00000477278.2_Silent_p.A192A	NM_001282582.1|NM_032348.2	NP_001269511.1|NP_115724.1	Q9BRK3	MXRA8_HUMAN	matrix-remodelling associated 8	201	Ig-like V-type 2.				establishment of glial blood-brain barrier (GO:0060857)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)	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;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CCACCTGTTGAGCCTCCTCCA	0.751													-|||	361	0.0720847	0.2579	0.0274	5008	,	,		8344	0.0		0.001	False		,,,				2504	0.0				p.A201A		Atlas-SNP	.											.	MXRA8	28	.	0			c.T603C						PASS	.			722,3238		65,592,1323	7.0	9.0	9.0		603	-0.7	1.0	1	dbSNP_134	9	6,7864		0,6,3929	no	coding-synonymous	MXRA8	NM_032348.2		65,598,5252	GG,GA,AA		0.0762,18.2323,6.1538		201/443	1290408	728,11102	1980	3935	5915	SO:0001819	synonymous_variant	54587	exon5			CTGTTGAGCCTCC	BC006213	CCDS24.1, CCDS59950.1, CCDS59951.1, CCDS59952.1	1p36.33	2013-01-11			ENSG00000162576	ENSG00000162576		"""Immunoglobulin superfamily / V-set domain containing"""	7542	protein-coding gene	gene with protein product	"""limitrin"""					14603461	Standard	XM_005244758		Approved	DKFZp586E2023	uc001aew.3	Q9BRK3	OTTHUMG00000002973	ENST00000309212.6:c.603T>C	1.37:g.1290408A>G		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_032348	B3KTR6|B4DE34|Q5TA39|Q96KC3	Silent	SNP	ENST00000309212.6	37	CCDS24.1																																																																																			A|0.939;G|0.061	0.061	strong		0.751	MXRA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008282.2	NM_032348	
TELO2	9894	hgsc.bcm.edu	37	16	1555589	1555589	+	Missense_Mutation	SNP	A	A	G	rs386787714|rs2248128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	80	80	1	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	
ZSCAN10	84891	hgsc.bcm.edu	37	16	3140601	3140601	+	Silent	SNP	C	C	T	rs140690870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3140601C>T	ENST00000252463.2	-	5	756	c.669G>A	c.(667-669)gaG>gaA	p.E223E	ZSCAN10_ENST00000538082.2_Silent_p.E141E|ZSCAN10_ENST00000572548.1_3'UTR|ZSCAN10_ENST00000575108.1_5'UTR	NM_032805.1	NP_116194.1	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	223					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(3)|endometrium(3)|kidney(1)|lung(8)|ovary(2)|prostate(1)|skin(4)|urinary_tract(1)	24						CCCCTTTGGGCTCTTCTTGTT	0.592													C|||	25	0.00499201	0.0182	0.0014	5008	,	,		15976	0.0		0.0	False		,,,				2504	0.0				p.E223E		Atlas-SNP	.											.	ZSCAN10	63	.	0			c.G669A						PASS	.	C		77,4279		1,75,2102	33.0	36.0	35.0		669	-6.0	0.0	16	dbSNP_134	35	0,8496		0,0,4248	no	coding-synonymous	ZSCAN10	NM_032805.1		1,75,6350	TT,TC,CC		0.0,1.7677,0.5991		223/726	3140601	77,12775	2178	4248	6426	SO:0001819	synonymous_variant	84891	exon5			TTTGGGCTCTTCT	AA206569	CCDS10493.1, CCDS61813.1, CCDS61814.1	16p13.3	2013-01-08	2007-02-20	2007-02-20		ENSG00000130182		"""-"", ""Zinc fingers, C2H2-type"""	12997	protein-coding gene	gene with protein product			"""zinc finger protein 206"""	ZNF206		9653642	Standard	NM_032805		Approved		uc002ctv.1	Q96SZ4		ENST00000252463.2:c.669G>A	16.37:g.3140601C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	30	11	0.366667	NM_032805	B3KQD3|H0YFS6|Q1WWM2	Silent	SNP	ENST00000252463.2	37	CCDS10493.1																																																																																			C|0.991;T|0.009	0.009	strong		0.592	ZSCAN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437124.2	NM_032805	
MAN2B1	4125	hgsc.bcm.edu	37	19	12772165	12772165	+	Missense_Mutation	SNP	G	G	A	rs1054487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12772165G>A	ENST00000456935.2	-	7	975	c.935C>T	c.(934-936)aCt>aTt	p.T312I	MAN2B1_ENST00000221363.4_Missense_Mutation_p.T312I|MAN2B1_ENST00000495617.1_5'Flank	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	312			T -> I (in dbSNP:rs1054487). {ECO:0000269|PubMed:22161967, ECO:0000269|PubMed:9915946}.		cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGTCATCACAGTGTGGTTGGT	0.527													A|||	1642	0.327875	0.584	0.281	5008	,	,		20649	0.0615		0.4036	False		,,,				2504	0.2117				p.T312I		Atlas-SNP	.											MAN2B1,NS,adenoma,0,1	MAN2B1	91	1	0			c.C935T						PASS	.	A	ILE/THR,ILE/THR	2366,2040	561.6+/-380.8	647,1072,484	210.0	173.0	186.0		935,935	-2.2	0.0	19	dbSNP_86	186	3533,5067	632.4+/-398.6	703,2127,1470	yes	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	89,89	1350,3199,1954	AA,AG,GG		41.0814,46.3005,45.356	benign,benign	312/1012,312/1011	12772165	5899,7107	2203	4300	6503	SO:0001583	missense	4125	exon7			ATCACAGTGTGGT		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.935C>T	19.37:g.12772165G>A	ENSP00000395473:p.Thr312Ile	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	155	67	0.432258	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		
TRMT12	55039	hgsc.bcm.edu	37	8	125463544	125463544	+	Silent	SNP	T	T	C	rs11556913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:125463544T>C	ENST00000328599.3	+	1	497	c.376T>C	c.(376-378)Ttg>Ctg	p.L126L	TRMT12_ENST00000521443.1_Intron	NM_017956.3	NP_060426.2	Q53H54	TYW2_HUMAN	tRNA methyltransferase 12 homolog (S. cerevisiae)	126					tRNA processing (GO:0008033)		transferase activity (GO:0016740)			breast(2)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GTCAGCCGAGTTGGAGGCTGA	0.542													T|||	948	0.189297	0.0696	0.3429	5008	,	,		20402	0.0982		0.3748	False		,,,				2504	0.1452				p.L126L		Atlas-SNP	.											.	TRMT12	28	.	0			c.T376C						PASS	.	T		541,3865	245.6+/-254.5	40,461,1702	69.0	68.0	68.0		376	-0.3	0.3	8	dbSNP_120	68	2994,5606	462.8+/-365.8	514,1966,1820	no	coding-synonymous	TRMT12	NM_017956.3		554,2427,3522	CC,CT,TT		34.814,12.2787,27.1798		126/449	125463544	3535,9471	2203	4300	6503	SO:0001819	synonymous_variant	55039	exon1			GCCGAGTTGGAGG	AF313041	CCDS6349.1	8q24.13	2011-05-09	2006-11-16		ENSG00000183665	ENSG00000183665			26091	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 2"""	611244	"""tRNA methyltranferase 12 homolog (S. cerevisiae)"""			16005430, 17150819	Standard	NM_017956		Approved	FLJ20772, Trm12, TYW2	uc003yra.4	Q53H54	OTTHUMG00000165022	ENST00000328599.3:c.376T>C	8.37:g.125463544T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	136	78	0.573529	NM_017956	Q6PKB9|Q96F21|Q9NWK6	Silent	SNP	ENST00000328599.3	37	CCDS6349.1																																																																																			A|0.000;C|0.268;G|0.000;T|0.731	0.268	strong		0.542	TRMT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381465.1	NM_017956	
SNTG2	54221	hgsc.bcm.edu	37	2	1168781	1168781	+	Missense_Mutation	SNP	C	C	A	rs28505970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1168781C>A	ENST00000308624.5	+	8	632	c.503C>A	c.(502-504)tCc>tAc	p.S168Y	SNTG2_ENST00000407292.1_Intron|SNTG2_ENST00000467759.1_3'UTR	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	168			S -> Y (in dbSNP:rs28505970).		central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)	p.S168Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		GCTGCAGGGTCCCCAGGGCCA	0.532													C|||	1033	0.20627	0.3608	0.098	5008	,	,		17456	0.1042		0.169	False		,,,				2504	0.2178				p.S168Y		Atlas-SNP	.											SNTG2,NS,carcinoma,0,1	SNTG2	125	1	1	Substitution - Missense(1)	stomach(1)	c.C503A						PASS	.	C	TYR/SER	1210,2802		192,826,988	115.0	122.0	120.0		503	4.6	1.0	2	dbSNP_125	120	1260,7098		95,1070,3014	yes	missense	SNTG2	NM_018968.3	144	287,1896,4002	AA,AC,CC		15.0754,30.1595,19.9677	probably-damaging	168/540	1168781	2470,9900	2006	4179	6185	SO:0001583	missense	54221	exon8			CAGGGTCCCCAGG	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.503C>A	2.37:g.1168781C>A	ENSP00000311837:p.Ser168Tyr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_018968	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	37	CCDS46220.1	390	0.17857142857142858	173	0.3516260162601626	35	0.09668508287292818	55	0.09615384615384616	127	0.16754617414248021	C	14.49	2.550271	0.45383	0.301595	0.150754	ENSG00000172554	ENST00000308624	T	0.54866	0.55	4.58	4.58	0.56647	.	0.062085	0.64402	D	0.000003	T	0.00012	0.0000	M	0.72479	2.2	0.09310	P	1.0	D	0.76494	0.999	D	0.83275	0.996	T	0.06023	-1.0850	9	0.66056	D	0.02	.	15.1671	0.72837	0.0:1.0:0.0:0.0	rs28505970	168	Q9NY99	SNTG2_HUMAN	Y	168	ENSP00000311837:S168Y	ENSP00000311837:S168Y	S	+	2	0	SNTG2	1158781	1.000000	0.71417	0.974000	0.42286	0.065000	0.16274	4.969000	0.63735	2.067000	0.61834	0.643000	0.83706	TCC	C|0.822;A|0.178	0.178	strong		0.532	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103124135	103124135	+	Silent	SNP	T	T	G	rs11225634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:103124135T>G	ENST00000375735.2	+	66	10308	c.10164T>G	c.(10162-10164)acT>acG	p.T3388T	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Silent_p.T3395T	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	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	194	118	0.608247	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	
OR1L1	26737	hgsc.bcm.edu	37	9	125424164	125424164	+	Missense_Mutation	SNP	C	C	T	rs111803762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125424164C>T	ENST00000373686.1	+	1	320	c.320C>T	c.(319-321)aCg>aTg	p.T107M	OR1L1_ENST00000309623.1_Missense_Mutation_p.T57M			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	107						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						CGTCTCCAGACGCCCATGTAC	0.463													.|||	67	0.0133786	0.0477	0.0058	5008	,	,		21488	0.0		0.0	False		,,,				2504	0.0				p.T57M		Atlas-SNP	.											OR1L1,caecum,carcinoma,0,1	OR1L1	54	1	0			c.C170T						PASS	.	C	MET/THR	147,4259	102.1+/-140.7	3,141,2059	133.0	124.0	127.0		170	1.0	0.2	9	dbSNP_132	127	1,8599		0,1,4299	yes	missense	OR1L1	NM_001005236.3	81	3,142,6358	TT,TC,CC		0.0116,3.3364,1.1379	probably-damaging	57/311	125424164	148,12858	2203	4300	6503	SO:0001583	missense	26737	exon1			TCCAGACGCCCAT		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.320C>T	9.37:g.125424164C>T	ENSP00000362790:p.Thr107Met	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	226	151	0.668142	NM_001005236	Q5T7Z3|Q6IFN2	Missense_Mutation	SNP	ENST00000373686.1	37		27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	C	14.01	2.408566	0.42715	0.033364	1.16E-4	ENSG00000173679	ENST00000373686;ENST00000309623	T;T	0.00481	7.11;7.11	3.11	1.01	0.19927	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00178	0.0005	L	0.58428	1.81	0.09310	N	0.999997	D	0.59357	0.985	P	0.55391	0.775	T	0.54077	-0.8347	9	0.72032	D	0.01	.	9.8389	0.40987	0.511:0.489:0.0:0.0	.	107	Q8NH94	OR1L1_HUMAN	M	107;57	ENSP00000362790:T107M;ENSP00000310773:T57M	ENSP00000310773:T57M	T	+	2	0	OR1L1	124463985	0.000000	0.05858	0.188000	0.23233	0.075000	0.17131	-1.376000	0.02561	0.095000	0.17434	0.313000	0.20887	ACG	C|0.987;T|0.013	0.013	strong		0.463	OR1L1-201	KNOWN	basic	protein_coding	protein_coding			
DNAH10	196385	hgsc.bcm.edu	37	12	124270467	124270467	+	Silent	SNP	C	C	T	rs116310078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124270467C>T	ENST00000409039.3	+	9	1247	c.1222C>T	c.(1222-1224)Ctg>Ttg	p.L408L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	408	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)		AGTGGTCAACCTGCGGACTTT	0.438													C|||	28	0.00559105	0.0212	0.0	5008	,	,		19731	0.0		0.0	False		,,,				2504	0.0				p.L408L		Atlas-SNP	.											.	DNAH10	888	.	0			c.C1222T						PASS	.	C		76,4330	65.8+/-103.3	0,76,2127	86.0	77.0	80.0		1222	4.4	1.0	12	dbSNP_132	80	1,8599		0,1,4299	no	coding-synonymous	DNAH10	NM_207437.3		0,77,6426	TT,TC,CC		0.0116,1.7249,0.592		408/4472	124270467	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	196385	exon9			GTCAACCTGCGGA	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.1222C>T	12.37:g.124270467C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.994;T|0.006	0.006	strong		0.438	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
PCDHA5	56143	hgsc.bcm.edu	37	5	140202821	140202821	+	Silent	SNP	C	C	G	rs80008076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140202821C>G	ENST00000529859.1	+	1	1461	c.1461C>G	c.(1459-1461)gcC>gcG	p.A487A	PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000378126.3_Silent_p.A487A|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Silent_p.A487A|PCDHA1_ENST00000504120.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	487	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)	p.A487A(2)		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)			AGGAGAACGCCCTGGTGTCCT	0.667													.|||	72	0.014377	0.0537	0.0014	5008	,	,		18355	0.0		0.0	False		,,,				2504	0.0				p.A487A		Atlas-SNP	.											PCDHA5_ENST00000529859,NS,carcinoma,0,2	PCDHA5	361	2	2	Substitution - coding silent(2)	lung(2)	c.C1461G						PASS	.	G	,,,,,,	227,4179	797.7+/-415.4	9,209,1985	68.0	73.0	71.0		,,,,1461,,1461	2.0	1.0	5	dbSNP_131	71	1,8599	814.7+/-407.0	0,1,4299	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	,,,,,,	9,210,6284	GG,GC,CC		0.0116,5.1521,1.753	,,,,,,	,,,,487/937,,487/817	140202821	228,12778	2203	4300	6503	SO:0001819	synonymous_variant	56143	exon1			GAACGCCCTGGTG	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.1461C>G	5.37:g.140202821C>G		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	276	145	0.525362	NM_018908	O75284|Q8N4R3	Silent	SNP	ENST00000529859.1	37	CCDS54917.1																																																																																			C|0.983;G|0.017	0.017	strong		0.667	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
ITGAX	3687	hgsc.bcm.edu	37	16	31382464	31382464	+	Silent	SNP	G	G	C	rs2230426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31382464G>C	ENST00000268296.4	+	15	1891	c.1770G>C	c.(1768-1770)ggG>ggC	p.G590G	ITGAX_ENST00000562522.1_Silent_p.G590G	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	590					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						CACTGAGCGGGGGTCAAGACC	0.637													G|||	223	0.0445288	0.1619	0.0115	5008	,	,		17382	0.0		0.001	False		,,,				2504	0.0				p.G590G		Atlas-SNP	.											.	ITGAX	198	.	0			c.G1770C						PASS	.	G		552,3842	239.0+/-250.2	39,474,1684	60.0	66.0	64.0		1770	2.3	1.0	16	dbSNP_98	64	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ITGAX	NM_000887.3		39,479,5979	CC,CG,GG		0.0581,12.5626,4.2866		590/1164	31382464	557,12437	2197	4300	6497	SO:0001819	synonymous_variant	3687	exon15			GAGCGGGGGTCAA	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.1770G>C	16.37:g.31382464G>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	77	36	0.467532	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	37	CCDS10711.1																																																																																			G|0.961;C|0.039	0.039	strong		0.637	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
COL12A1	1303	hgsc.bcm.edu	37	6	75899300	75899300	+	Missense_Mutation	SNP	T	T	G	rs75535959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:75899300T>G	ENST00000322507.8	-	6	935	c.626A>C	c.(625-627)aAa>aCa	p.K209T	COL12A1_ENST00000416123.2_Missense_Mutation_p.K209T|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Missense_Mutation_p.K209T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	209	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ATATGGAATTTTTTTTATTGC	0.318													T|||	138	0.0275559	0.1006	0.0072	5008	,	,		18044	0.0		0.0	False		,,,				2504	0.0				p.K209T		Atlas-SNP	.											.	COL12A1	385	.	0			c.A626C						PASS	.	T	THR/LYS,	278,3348		12,254,1547	123.0	114.0	117.0		626,	0.4	1.0	6	dbSNP_131	117	2,8142		0,2,4070	yes	missense,intron	COL12A1	NM_004370.5,NM_080645.2	78,	12,256,5617	GG,GT,TT		0.0246,7.6669,2.3789	benign,	209/3064,	75899300	280,11490	1813	4072	5885	SO:0001583	missense	1303	exon6			GGAATTTTTTTTA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.626A>C	6.37:g.75899300T>G	ENSP00000325146:p.Lys209Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	91	50	0.549451	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	53	0.024267399267399268	50	0.1016260162601626	3	0.008287292817679558	0	0.0	0	0.0	T	7.405	0.633502	0.14322	0.076669	2.46E-4	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.78481	-1.18;-1.18;-1.18	5.65	0.435	0.16544	von Willebrand factor, type A (3);	0.422713	0.24285	N	0.039863	T	0.43433	0.1247	L	0.31926	0.97	0.25462	N	0.987905	B	0.14438	0.01	B	0.16289	0.015	T	0.38950	-0.9637	10	0.22706	T	0.39	.	10.6931	0.45884	0.0:0.4407:0.0:0.5593	.	209	Q99715	COCA1_HUMAN	T	209	ENSP00000325146:K209T;ENSP00000412864:K209T;ENSP00000421216:K209T	ENSP00000325146:K209T	K	-	2	0	COL12A1	75956020	0.989000	0.36119	0.995000	0.50966	0.916000	0.54674	0.615000	0.24329	-0.134000	0.11516	0.533000	0.62120	AAA	T|0.984;G|0.016	0.016	strong		0.318	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
LGI2	55203	hgsc.bcm.edu	37	4	25005193	25005193	+	Silent	SNP	G	G	A	rs2232028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:25005193G>A	ENST00000382114.4	-	8	1703	c.1518C>T	c.(1516-1518)taC>taT	p.Y506Y		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	506						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)				GCGCCTGCACGTAAATCTCCT	0.408													A|||	3835	0.765775	0.9115	0.6455	5008	,	,		17150	0.9742		0.4632	False		,,,				2504	0.7505				p.Y506Y		Atlas-SNP	.											.	LGI2	62	.	0			c.C1518T						PASS	.	A		3719,687	287.8+/-279.5	1570,579,54	92.0	102.0	98.0		1518	-3.8	0.7	4	dbSNP_98	98	3924,4676	605.9+/-395.0	933,2058,1309	no	coding-synonymous	LGI2	NM_018176.3		2503,2637,1363	AA,AG,GG		45.6279,15.5924,41.2348		506/546	25005193	7643,5363	2203	4300	6503	SO:0001819	synonymous_variant	55203	exon8			CTGCACGTAAATC	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.1518C>T	4.37:g.25005193G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	163	72	0.441718	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Silent	SNP	ENST00000382114.4	37	CCDS3431.1																																																																																			G|0.332;A|0.668	0.668	strong		0.408	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1		
ZBTB7B	51043	hgsc.bcm.edu	37	1	154987526	154987526	+	Silent	SNP	C	C	T	rs11264295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:154987526C>T	ENST00000368426.3	+	3	527	c.390C>T	c.(388-390)atC>atT	p.I130I	ZBTB7B_ENST00000487542.1_3'UTR|ZBTB7B_ENST00000417934.2_Silent_p.I164I|ZBTB7B_ENST00000535420.1_Silent_p.I130I|ZBTB7B_ENST00000292176.2_Silent_p.I130I	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	130					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TGCTGGAGATCCCGTGTGTCA	0.617													C|||	3094	0.617812	0.4592	0.6671	5008	,	,		16567	0.9058		0.4513	False		,,,				2504	0.6718				p.I164I		Atlas-SNP	.											ZBTB7B,NS,carcinoma,0,1	ZBTB7B	69	1	0			c.C492T						PASS	.	C		2075,2331		472,1131,600	41.0	45.0	43.0		390	0.6	0.9	1	dbSNP_120	43	3651,4949		771,2109,1420	no	coding-synonymous	ZBTB7B	NM_015872.2		1243,3240,2020	TT,TC,CC		42.4535,47.0949,44.0258		130/540	154987526	5726,7280	2203	4300	6503	SO:0001819	synonymous_variant	51043	exon4			GGAGATCCCGTGT	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	18668	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 15"""	607646	"""zinc finger protein 67 homolog (mouse)"""	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.390C>T	1.37:g.154987526C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Silent	SNP	ENST00000368426.3	37	CCDS1081.1																																																																																			C|0.487;T|0.513	0.513	strong		0.617	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872	
APC	324	hgsc.bcm.edu	37	5	112175240	112175240	+	Missense_Mutation	SNP	G	G	C	rs1801166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112175240G>C	ENST00000457016.1	+	16	4329	c.3949G>C	c.(3949-3951)Gaa>Caa	p.E1317Q	APC_ENST00000257430.4_Missense_Mutation_p.E1317Q|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.E1317Q			P25054	APC_HUMAN	adenomatous polyposis coli	1317	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.		E -> Q (may contribute to colorectal tumor development; dbSNP:rs1801166). {ECO:0000269|PubMed:9724771}.		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.E1317Q(5)|p.E1317*(3)|p.E1317fs*4(3)|p.?(1)|p.K1192fs*3(1)|p.A1316fs*9(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)		TAGGTCAGCTGAAGATCCTGT	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|||	15	0.00299521	0.003	0.0029	5008	,	,		21730	0.0		0.006	False		,,,				2504	0.0031				p.E1317Q	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,bladder,carcinoma,0,14	APC	4158	14	14	Substitution - Missense(5)|Deletion - Frameshift(5)|Substitution - Nonsense(3)|Unknown(1)	large_intestine(9)|stomach(1)|soft_tissue(1)|urinary_tract(1)|lung(1)|skin(1)	c.G3949C	GRCh37	CM980089	APC	M	rs1801166	PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU	28,4376	33.5+/-64.1	0,28,2174	60.0	61.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3949,3949,3895	5.2	0.7	5	dbSNP_89	61	80,8520	46.3+/-105.2	1,78,4221	yes	missense,missense,missense	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	29,29,29	1,106,6395	CC,CG,GG		0.9302,0.6358,0.8305	benign,benign,benign	1317/2844,1317/2844,1299/2826	112175240	108,12896	2202	4300	6502	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,	TCAGCTGAAGATC	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.3949G>C	5.37:g.112175240G>C	ENSP00000413133:p.Glu1317Gln	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	162	54	0.333333	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	8	0.003663003663003663	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	9.512	1.105897	0.20632	0.006358	0.009302	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90324	-2.65;-2.65;-2.65	6.03	5.15	0.70609	.	0.502603	0.24048	N	0.042028	T	0.80325	0.4602	N	0.24115	0.695	0.37326	A	0.90977	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.79045	-0.1964	8	.	.	.	-16.8737	17.2207	0.86956	0.0:0.1257:0.8742:0.0	rs1801166;rs52811293	1319;1317	Q4LE70;P25054	.;APC_HUMAN	Q	1317	ENSP00000413133:E1317Q;ENSP00000257430:E1317Q;ENSP00000427089:E1317Q	.	E	+	1	0	APC	112203139	1.000000	0.71417	0.685000	0.30070	0.277000	0.26821	6.359000	0.73060	1.533000	0.49186	0.655000	0.94253	GAA	G|0.992;C|0.008	0.008	strong		0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
MUC17	140453	hgsc.bcm.edu	37	7	100678013	100678013	+	Missense_Mutation	SNP	G	G	A	rs75312831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678013G>A	ENST00000306151.4	+	3	3380	c.3316G>A	c.(3316-3318)Gtg>Atg	p.V1106M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1106	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)					ACTAACAAGTGTGCCTGTCAG	0.507																																					p.V1106M		Atlas-SNP	.											MUC17,NS,carcinoma,-2,1	MUC17	804	1	0			c.G3316A						scavenged	.	A	MET/VAL	242,4164	121.3+/-158.8	0,242,1961	496.0	393.0	428.0		3316	-1.6	0.0	7	dbSNP_131	428	151,8449	62.8+/-124.8	0,151,4149	no	missense	MUC17	NM_001040105.1	21	0,393,6110	AA,AG,GG		1.7558,5.4925,3.0217	benign	1106/4494	100678013	393,12613	2203	4300	6503	SO:0001583	missense	140453	exon3			ACAAGTGTGCCTG	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.3316G>A	7.37:g.100678013G>A	ENSP00000302716:p.Val1106Met	Somatic	166	2	0.0120482		WXS	Illumina HiSeq	Phase_I	379	65	0.171504	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	0.067	-1.211056	0.01555	0.054925	0.017558	ENSG00000169876	ENST00000306151	T	0.02763	4.17	0.801	-1.6	0.08426	.	.	.	.	.	T	0.00241	0.0007	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.01281	0.0	T	0.43475	-0.9389	9	0.28530	T	0.3	.	0.7416	0.00975	0.3295:0.1734:0.324:0.173	.	1106	Q685J3	MUC17_HUMAN	M	1106	ENSP00000302716:V1106M	ENSP00000302716:V1106M	V	+	1	0	MUC17	100464733	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.810000	0.01729	-2.966000	0.00288	-1.214000	0.01621	GTG	A|0.022;G|0.978	0.022	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
VIT	5212	hgsc.bcm.edu	37	2	37035866	37035866	+	Silent	SNP	G	G	T	rs36048308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37035866G>T	ENST00000389975.3	+	14	1898	c.1596G>T	c.(1594-1596)acG>acT	p.T532T	VIT_ENST00000497382.1_Silent_p.T201T|VIT_ENST00000379241.3_Silent_p.T510T|VIT_ENST00000401530.1_Silent_p.T511T|VIT_ENST00000404084.1_Silent_p.T484T|VIT_ENST00000379242.3_Silent_p.T547T	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	532	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				ACACGGACACGCGCATCGGGG	0.582													G|||	359	0.0716853	0.2458	0.0274	5008	,	,		21942	0.0079		0.001	False		,,,				2504	0.0061				p.T547T		Atlas-SNP	.											.	VIT	138	.	0			c.G1641T						PASS	.	G	,,,	1007,3399	374.4+/-321.2	116,775,1312	81.0	78.0	79.0		1596,1533,1530,1641	-9.3	0.0	2	dbSNP_126	79	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VIT	NM_001177969.1,NM_001177970.1,NM_001177971.1,NM_053276.3	,,,	116,803,5584	TT,TG,GG		0.3256,22.8552,7.9579	,,,	532/679,511/658,510/657,547/694	37035866	1035,11971	2203	4300	6503	SO:0001819	synonymous_variant	5212	exon15			GGACACGCGCATC	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.1596G>T	2.37:g.37035866G>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_053276	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Silent	SNP	ENST00000389975.3	37	CCDS54347.1																																																																																			G|0.925;T|0.075	0.075	strong		0.582	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			
PRDM8	56978	hgsc.bcm.edu	37	4	81124596	81124596	+	Silent	SNP	G	G	C	rs12780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:81124596G>C	ENST00000504452.1	+	8	2819	c.1980G>C	c.(1978-1980)cgG>cgC	p.R660R	PRDM8_ENST00000339711.4_Silent_p.R660R|PRDM8_ENST00000415738.2_Silent_p.R660R			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	660					corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						TGGTGAAGCGGCGGCGAGAGG	0.572													G|||	1745	0.348442	0.1672	0.3372	5008	,	,		12837	0.626		0.2724	False		,,,				2504	0.3937				p.R660R		Atlas-SNP	.											PRDM8,colon,carcinoma,0,1	PRDM8	44	1	0			c.G1980C						PASS	.	G	,	746,3544		70,606,1469	32.0	38.0	36.0		1980,1980	1.1	1.0	4	dbSNP_52	36	2160,6384		289,1582,2401	no	coding-synonymous,coding-synonymous	PRDM8	NM_001099403.1,NM_020226.3	,	359,2188,3870	CC,CG,GG		25.2809,17.3893,22.643	,	660/690,660/690	81124596	2906,9928	2145	4272	6417	SO:0001819	synonymous_variant	56978	exon4			GAAGCGGCGGCGA	AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.1980G>C	4.37:g.81124596G>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_001099403	A8K7X2|Q6IQ36	Silent	SNP	ENST00000504452.1	37	CCDS43243.1																																																																																			G|0.671;C|0.329	0.329	strong		0.572	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1		
ATP10A	57194	hgsc.bcm.edu	37	15	25924539	25924539	+	Silent	SNP	T	T	C	rs1047700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25924539T>C	ENST00000356865.6	-	21	4560	c.4449A>G	c.(4447-4449)caA>caG	p.Q1483Q		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1483					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GGTCTGGCCCTTGAAGTCCTG	0.473													C|||	1334	0.266374	0.4153	0.3386	5008	,	,		13468	0.2748		0.1382	False		,,,				2504	0.137				p.Q1483Q		Atlas-SNP	.											.	ATP10A	270	.	0			c.A4449G						PASS	.	C		1631,2775	643.7+/-397.9	298,1035,870	58.0	63.0	61.0		4449	-4.4	0.0	15	dbSNP_86	61	1339,7261	749.9+/-407.4	99,1141,3060	no	coding-synonymous	ATP10A	NM_024490.3		397,2176,3930	CC,CT,TT		15.5698,37.0177,22.8356		1483/1500	25924539	2970,10036	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon21			TGGCCCTTGAAGT	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.4449A>G	15.37:g.25924539T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			T|0.749;C|0.251	0.251	strong		0.473	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
KIF21B	23046	hgsc.bcm.edu	37	1	200967687	200967687	+	Silent	SNP	C	C	G	rs61740473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200967687C>G	ENST00000422435.2	-	14	2218	c.1902G>C	c.(1900-1902)gcG>gcC	p.A634A	KIF21B_ENST00000332129.2_Silent_p.A634A|KIF21B_ENST00000360529.5_Silent_p.A634A|KIF21B_ENST00000461742.2_Silent_p.A634A	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	634					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CGGCCAGGTCCGCCTGGAAGT	0.597													C|||	383	0.0764776	0.2791	0.0173	5008	,	,		18558	0.0		0.001	False		,,,				2504	0.001				p.A634A		Atlas-SNP	.											.	KIF21B	208	.	0			c.G1902C						PASS	.	C		1092,3314	393.5+/-328.9	128,836,1239	71.0	67.0	68.0		1902	-10.3	0.8	1	dbSNP_129	68	42,8558	28.5+/-78.6	1,40,4259	no	coding-synonymous	KIF21B	NM_017596.2		129,876,5498	GG,GC,CC		0.4884,24.7844,8.7191		634/1625	200967687	1134,11872	2203	4300	6503	SO:0001819	synonymous_variant	23046	exon14			CAGGTCCGCCTGG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.1902G>C	1.37:g.200967687C>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	37	CCDS58056.1																																																																																			C|0.920;G|0.080	0.080	strong		0.597	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
AHNAK2	113146	hgsc.bcm.edu	37	14	105408030	105408030	+	Silent	SNP	A	A	G	rs9671643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105408030A>G	ENST00000333244.5	-	7	13877	c.13758T>C	c.(13756-13758)gaT>gaC	p.D4586D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4586						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)			ACACCTCCACATCGGGGGCCA	0.647													G|||	2782	0.555511	0.6437	0.5144	5008	,	,		18618	0.4117		0.5338	False		,,,				2504	0.636				p.D4586D		Atlas-SNP	.											AHNAK2_ENST00000333244,caecum,carcinoma,-2,1	AHNAK2	719	1	0			c.T13758C						PASS	.	G		2655,1279		904,847,216	94.0	106.0	102.0		13758	-4.7	0.0	14	dbSNP_119	102	4494,3794		1234,2026,884	no	coding-synonymous	AHNAK2	NM_138420.2		2138,2873,1100	GG,GA,AA		45.777,32.5114,41.5071		4586/5796	105408030	7149,5073	1967	4144	6111	SO:0001819	synonymous_variant	113146	exon7			CTCCACATCGGGG	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.13758T>C	14.37:g.105408030A>G		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	181	181	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.469;G|0.531	0.531	strong		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
URB2	9816	hgsc.bcm.edu	37	1	229772932	229772932	+	Missense_Mutation	SNP	A	A	G	rs3811474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229772932A>G	ENST00000258243.2	+	4	2708	c.2572A>G	c.(2572-2574)Aaa>Gaa	p.K858E		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	858						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						CAGATTTGCAAAAGCTGGACC	0.502													A|||	998	0.199281	0.1952	0.2421	5008	,	,		20179	0.4315		0.0636	False		,,,				2504	0.0746				p.K858E		Atlas-SNP	.											.	URB2	152	.	0			c.A2572G						PASS	.	A	GLU/LYS	844,3562	332.5+/-302.5	85,674,1444	86.0	90.0	89.0		2572	2.6	0.0	1	dbSNP_107	89	553,8047	150.6+/-205.5	14,525,3761	yes	missense	URB2	NM_014777.2	56	99,1199,5205	GG,GA,AA		6.4302,19.1557,10.7412	possibly-damaging	858/1525	229772932	1397,11609	2203	4300	6503	SO:0001583	missense	9816	exon4			TTTGCAAAAGCTG	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.2572A>G	1.37:g.229772932A>G	ENSP00000258243:p.Lys858Glu	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	162	74	0.45679	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	489	0.2239010989010989	99	0.20121951219512196	75	0.20718232044198895	271	0.4737762237762238	44	0.05804749340369393	A	7.495	0.651409	0.14516	0.191557	0.064302	ENSG00000135763	ENST00000258243	T	0.30182	1.54	4.95	2.59	0.31030	.	0.631054	0.17336	N	0.177928	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.21381	0.055	B	0.20955	0.032	T	0.47249	-0.9132	8	.	.	.	-2.8656	2.4527	0.04522	0.6029:0.1342:0.1332:0.1297	rs3811474;rs61291674;rs3811474	858	Q14146	URB2_HUMAN	E	858	ENSP00000258243:K858E	.	K	+	1	0	URB2	227839555	0.017000	0.18338	0.001000	0.08648	0.505000	0.33919	2.475000	0.45162	0.831000	0.34780	0.477000	0.44152	AAA	A|0.836;G|0.164	0.164	strong		0.502	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
EIF4G1	1981	hgsc.bcm.edu	37	3	184045410	184045410	+	Missense_Mutation	SNP	T	T	C	rs2230570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184045410T>C	ENST00000346169.2	+	25	3969	c.3698T>C	c.(3697-3699)cTg>cCg	p.L1233P	EIF4G1_ENST00000342981.4_Missense_Mutation_p.L1234P|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000435046.2_Missense_Mutation_p.L1037P|EIF4G1_ENST00000427845.1_Missense_Mutation_p.L1147P|EIF4G1_ENST00000350481.5_Missense_Mutation_p.L1069P|EIF4G1_ENST00000414031.1_Missense_Mutation_p.L1193P|EIF4G1_ENST00000352767.3_Missense_Mutation_p.L1240P|EIF4G1_ENST00000434061.2_Missense_Mutation_p.L1038P|EIF4G1_ENST00000424196.1_Missense_Mutation_p.L1240P|EIF4G1_ENST00000392537.2_Missense_Mutation_p.L1146P|EIF4G1_ENST00000382330.3_Missense_Mutation_p.L1240P|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000441154.1_Missense_Mutation_p.L1070P|EIF4G1_ENST00000411531.1_Missense_Mutation_p.L1194P|EIF4G1_ENST00000319274.6_Missense_Mutation_p.L1233P	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1233			L -> P (in dbSNP:rs2230570). {ECO:0000269|PubMed:21907011}.		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)			GTGAGCCCCCTGAAGGCGGCT	0.507													C|||	172	0.034345	0.0961	0.0317	5008	,	,		20121	0.0		0.0219	False		,,,				2504	0.001				p.L1240P		Atlas-SNP	.											.	EIF4G1	151	.	0			c.T3719C						PASS	.	C	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	362,4044		12,338,1853	74.0	83.0	80.0		3719,3719,3113,3701,3698,3206,3437	0.5	0.0	3	dbSNP_98	80	183,8417		2,179,4119	yes	missense,missense,missense,missense,missense,missense,missense	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	98,98,98,98,98,98,98	14,517,5972	CC,CT,TT		2.1279,8.2161,4.1904	benign,benign,benign,benign,benign,benign,benign	1240/1607,1240/1607,1038/1405,1234/1601,1233/1600,1069/1436,1146/1513	184045410	545,12461	2203	4300	6503	SO:0001583	missense	1981	exon26			GCCCCCTGAAGGC	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.3698T>C	3.37:g.184045410T>C	ENSP00000316879:p.Leu1233Pro	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	37	CCDS3259.1	74	0.03388278388278388	43	0.08739837398373984	11	0.03038674033149171	0	0.0	20	0.026385224274406333	C	4.699	0.129922	0.08981	0.082161	0.021279	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000382330;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000441154;ENST00000434061;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.03496	4.09;4.09;4.01;4.09;3.91;4.09;4.01;4.09;4.09;4.09;4.08;3.92;3.92;3.92	5.2	0.492	0.16872	.	0.571971	0.20603	N	0.089109	T	0.00073	0.0002	N	0.01048	-1.04	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.48317	-0.9046	10	0.21014	T	0.42	-0.5527	10.8334	0.46673	0.0:0.6479:0.0:0.3521	rs2230570;rs2230570	1240;1234;1233	E9PFM1;D3DNT2;Q04637	.;.;IF4G1_HUMAN	P	1233;1193;1146;1240;1069;1240;1147;1234;1233;1240;1194;1070;1038;1037	ENSP00000316879:L1233P;ENSP00000391935:L1193P;ENSP00000376320:L1146P;ENSP00000371767:L1240P;ENSP00000317600:L1069P;ENSP00000338020:L1240P;ENSP00000407682:L1147P;ENSP00000343450:L1234P;ENSP00000323737:L1233P;ENSP00000416255:L1240P;ENSP00000395974:L1194P;ENSP00000399858:L1070P;ENSP00000411826:L1038P;ENSP00000404754:L1037P	ENSP00000323737:L1233P	L	+	2	0	EIF4G1	185528104	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.936000	0.28938	-0.315000	0.08703	-1.536000	0.00914	CTG	T|0.960;C|0.040	0.040	strong		0.507	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
OR5L2	26338	hgsc.bcm.edu	37	11	55594869	55594869	+	Missense_Mutation	SNP	G	G	A	rs56711116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55594869G>A	ENST00000378397.1	+	1	175	c.175G>A	c.(175-177)Gtg>Atg	p.V59M		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	59			V -> M (in dbSNP:rs56711116).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V59M(1)		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)				CCACACCCCCGTGTACTTTTT	0.468										HNSCC(27;0.073)			N|||	537	0.107228	0.1952	0.0461	5008	,	,		20056	0.0843		0.0924	False		,,,				2504	0.0706				p.V59M		Atlas-SNP	.											OR5L2,colon,carcinoma,0,2	OR5L2	135	2	1	Substitution - Missense(1)	stomach(1)	c.G175A						PASS	.	A	MET/VAL	658,3742		64,530,1606	244.0	226.0	232.0		175	5.3	1.0	11	dbSNP_129	232	702,7890		32,638,3626	no	missense	OR5L2	NM_001004739.1	21	96,1168,5232	AA,AG,GG		8.1704,14.9545,10.468	benign	59/312	55594869	1360,11632	2200	4296	6496	SO:0001583	missense	26338	exon1			ACCCCCGTGTACT	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.175G>A	11.37:g.55594869G>A	ENSP00000367650:p.Val59Met	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	283	149	0.526502	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	169	0.07738095238095238	62	0.12601626016260162	19	0.052486187845303865	35	0.06118881118881119	53	0.06992084432717678	.	1.359	-0.589350	0.03799	0.149545	0.081704	ENSG00000205030	ENST00000378397	T	0.01197	5.19	5.31	5.31	0.75309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000012	T	0.00012	0.0000	N	0.00005	-3.255	0.53005	P	3.6999999999953737E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.25882	-1.0119	9	0.02654	T	1	-56.956	10.8374	0.46696	0.9241:0.0:0.0759:0.0	rs56711116;rs61739473	59	Q8NGL0	OR5L2_HUMAN	M	59	ENSP00000367650:V59M	ENSP00000367650:V59M	V	+	1	0	OR5L2	55351445	1.000000	0.71417	0.999000	0.59377	0.249000	0.25844	3.918000	0.56432	0.965000	0.38133	-0.377000	0.06932	GTG	G|0.901;A|0.099	0.099	strong		0.468	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464934	39464934	+	Missense_Mutation	SNP	G	G	A	rs150797223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39464934G>A	ENST00000391352.1	-	1	571	c.572C>T	c.(571-573)cCt>cTt	p.P191L		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	191	11 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						GCAGAGGACAGGCTGGCAGGA	0.587													G|||	32	0.00638978	0.0242	0.0	5008	,	,		23787	0.0		0.0	False		,,,				2504	0.0				p.P191L		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.C572T						PASS	.																																			SO:0001583	missense	100505753	exon1			AGGACAGGCTGGC	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.572C>T	17.37:g.39464934G>A	ENSP00000375147:p.Pro191Leu	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	190	86	0.452632	NM_001146182		Missense_Mutation	SNP	ENST00000391352.1	37	CCDS56032.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	13.44	2.236547	0.39498	.	.	ENSG00000212657	ENST00000391352	T	0.02158	4.42	4.22	4.22	0.49857	.	.	.	.	.	T	0.01870	0.0059	N	0.24115	0.695	0.45704	D	0.998617	.	.	.	.	.	.	T	0.57418	-0.7815	7	0.87932	D	0	.	14.8704	0.70453	0.0:0.0:1.0:0.0	.	.	.	.	L	191	ENSP00000375147:P191L	ENSP00000375147:P191L	P	-	2	0	KRTAP16-1	36718460	0.423000	0.25482	0.702000	0.30337	0.002000	0.02628	2.042000	0.41222	2.605000	0.88082	0.655000	0.94253	CCT	G|0.995;A|0.005	0.005	strong		0.587	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
MAP9	79884	hgsc.bcm.edu	37	4	156274377	156274377	+	Missense_Mutation	SNP	T	T	C	rs1058992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:156274377T>C	ENST00000311277.4	-	11	1759	c.1496A>G	c.(1495-1497)aAg>aGg	p.K499R	AC097467.2_ENST00000597939.1_RNA|AC097467.2_ENST00000599555.2_RNA|AC097467.2_ENST00000609254.1_RNA|AC097467.2_ENST00000595229.1_RNA|AC097467.2_ENST00000608544.1_RNA|AC097467.2_ENST00000609716.1_RNA|MAP9_ENST00000515654.1_Missense_Mutation_p.K475R|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000593387.2_RNA|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000601977.1_RNA|AC097467.2_ENST00000417474.1_RNA|AC097467.2_ENST00000608092.1_RNA|AC097467.2_ENST00000609486.1_RNA|AC097467.2_ENST00000608463.1_RNA|AC097467.2_ENST00000610249.1_RNA|AC097467.2_ENST00000598252.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	499			K -> R (in dbSNP:rs1058992).		cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)		p.K499R(1)		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)		TTCAGTTTTCTTCTTGTTTTT	0.333													T|||	2048	0.408946	0.6104	0.3228	5008	,	,		14025	0.5863		0.2247	False		,,,				2504	0.2045				p.K499R		Atlas-SNP	.											MAP9,NS,carcinoma,0,1	MAP9	79	1	1	Substitution - Missense(1)	prostate(1)	c.A1496G						scavenged	.	T	ARG/LYS	2319,2085	603.3+/-390.1	631,1057,514	108.0	104.0	106.0		1496	4.1	1.0	4	dbSNP_86	106	1857,6739	332.3+/-320.0	193,1471,2634	yes	missense	MAP9	NM_001039580.1	26	824,2528,3148	CC,CT,TT		21.6031,47.3433,32.1231	probably-damaging	499/648	156274377	4176,8824	2202	4298	6500	SO:0001583	missense	79884	exon11			GTTTTCTTCTTGT	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.1496A>G	4.37:g.156274377T>C	ENSP00000310593:p.Lys499Arg	Somatic	241	2	0.00829876		WXS	Illumina HiSeq	Phase_I	231	108	0.467532	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	37	CCDS35493.1	921	0.4217032967032967	307	0.6239837398373984	104	0.287292817679558	329	0.5751748251748252	181	0.23878627968337732	T	10.92	1.487296	0.26686	0.526567	0.216031	ENSG00000164114	ENST00000311277;ENST00000515654	T;T	0.09445	2.98;2.98	5.23	4.05	0.47172	.	0.402707	0.28700	N	0.014428	T	0.00012	0.0000	M	0.69823	2.125	0.09310	P	0.9999999999743422	B;B;B	0.32203	0.169;0.36;0.169	B;B;B	0.32022	0.091;0.139;0.091	T	0.19321	-1.0309	9	0.19147	T	0.46	-13.891	8.6845	0.34229	0.0:0.0879:0.0:0.9121	rs17357030	474;499;499	B4DVG9;B9EJB6;Q49MG5	.;.;MAP9_HUMAN	R	499;475	ENSP00000310593:K499R;ENSP00000427402:K475R	ENSP00000310593:K499R	K	-	2	0	MAP9	156493827	0.914000	0.31030	1.000000	0.80357	0.991000	0.79684	0.012000	0.13287	0.930000	0.37217	0.533000	0.62120	AAG	T|0.652;C|0.348	0.348	strong		0.333	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	
SNX5	27131	hgsc.bcm.edu	37	20	17923043	17923043	+	Silent	SNP	G	G	A	rs17349809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:17923043G>A	ENST00000377768.3	-	14	1485	c.1173C>T	c.(1171-1173)gtC>gtT	p.V391V	SNX5_ENST00000377759.4_Silent_p.V391V|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	391	BAR.				intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						GCAAAAGGGAGACATTGTTCT	0.408													G|||	148	0.0295527	0.1097	0.0014	5008	,	,		18450	0.0		0.001	False		,,,				2504	0.001				p.V391V		Atlas-SNP	.											.	SNX5	38	.	0			c.C1173T						PASS	.	G	,	452,3954	217.8+/-236.0	19,414,1770	111.0	101.0	105.0		1173,1173	1.0	1.0	20	dbSNP_123	105	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	SNX5	NM_014426.2,NM_152227.1	,	19,418,6066	AA,AG,GG		0.0465,10.2587,3.5061	,	391/405,391/405	17923043	456,12550	2203	4300	6503	SO:0001819	synonymous_variant	27131	exon13			AAGGGAGACATTG	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"""Sorting nexins"""	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.1173C>T	20.37:g.17923043G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	125	66	0.528	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	37	CCDS13130.1																																																																																			G|1.000;|0.000	.	weak		0.408	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
DENND2A	27147	hgsc.bcm.edu	37	7	140227184	140227184	+	Silent	SNP	C	C	T	rs76760136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140227184C>T	ENST00000275884.6	-	14	2856	c.2439G>A	c.(2437-2439)ccG>ccA	p.P813P	DENND2A_ENST00000496613.1_Silent_p.P813P|DENND2A_ENST00000537639.1_Silent_p.P813P			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	813	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				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)					GGAAGGGCGTCGGCGAGCACA	0.672													C|||	35	0.00698882	0.0257	0.0014	5008	,	,		17558	0.0		0.0	False		,,,				2504	0.0				p.P813P		Atlas-SNP	.											.	DENND2A	132	.	0			c.G2439A						PASS	.	C		59,4119		0,59,2030	12.0	18.0	16.0		2439	-2.2	0.4	7	dbSNP_132	16	0,8420		0,0,4210	no	coding-synonymous	DENND2A	NM_015689.3		0,59,6240	TT,TC,CC		0.0,1.4122,0.4683		813/1010	140227184	59,12539	2089	4210	6299	SO:0001819	synonymous_variant	27147	exon13			GGGCGTCGGCGAG	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.2439G>A	7.37:g.140227184C>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	209	113	0.54067	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	10.80	1.452752	0.26074	0.014122	0.0	ENSG00000146966	ENST00000469373	T	0.36340	1.26	5.04	-2.21	0.06973	.	.	.	.	.	T	0.29458	0.0734	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43228	-0.9404	6	0.87932	D	0	-17.1724	10.9649	0.47406	0.0:0.2873:0.2046:0.5082	.	.	.	.	Q	141	ENSP00000420145:R141Q	ENSP00000417673:R794Q	R	-	2	0	DENND2A	139873653	0.155000	0.22806	0.413000	0.26509	0.012000	0.07955	-0.761000	0.04751	-0.836000	0.04229	-1.134000	0.01955	CGA	C|0.995;T|0.005	0.005	strong		0.672	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
ATP2C1	27032	hgsc.bcm.edu	37	3	130698205	130698205	+	Silent	SNP	C	C	T	rs114319700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130698205C>T	ENST00000510168.1	+	19	2233	c.1683C>T	c.(1681-1683)gcC>gcT	p.A561A	ATP2C1_ENST00000507488.2_Silent_p.A545A|ATP2C1_ENST00000428331.2_Silent_p.A561A|ATP2C1_ENST00000422190.2_Silent_p.A561A|ATP2C1_ENST00000505330.1_Silent_p.A545A|ATP2C1_ENST00000508532.1_Silent_p.A561A|ATP2C1_ENST00000504381.1_Silent_p.A506A|ATP2C1_ENST00000513801.1_Silent_p.A545A|ATP2C1_ENST00000328560.8_Silent_p.A561A|ATP2C1_ENST00000533801.2_Silent_p.A556A|ATP2C1_ENST00000359644.3_Silent_p.A561A|ATP2C1_ENST00000504948.1_Silent_p.A545A|ATP2C1_ENST00000393221.4_Silent_p.A595A			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	561					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CACTCATTGCCTCAGGAGTAT	0.413									Hailey-Hailey disease				C|||	19	0.00379393	0.0129	0.0014	5008	,	,		17464	0.001		0.0	False		,,,				2504	0.0				p.A595A	Esophageal Squamous(99;456 1443 27647 34099 42636)	Atlas-SNP	.											.	ATP2C1	94	.	0			c.C1785T						PASS	.	C	,,,,,,,,,,	60,4346	57.4+/-93.9	0,60,2143	121.0	118.0	119.0		1683,1683,1683,1683,1785,1785,1668,1635,1635,1683,1683	4.8	1.0	3	dbSNP_132	119	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2C1	NM_001001485.2,NM_001001486.1,NM_001001487.1,NM_001199179.1,NM_001199180.1,NM_001199181.1,NM_001199182.1,NM_001199183.1,NM_001199184.1,NM_001199185.1,NM_014382.3	,,,,,,,,,,	0,60,6443	TT,TC,CC		0.0,1.3618,0.4613	,,,,,,,,,,	561/889,561/950,561/940,561/920,595/974,595/954,556/945,545/924,545/904,561/889,561/920	130698205	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	27032	exon18	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	CATTGCCTCAGGA	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"""ATPases / P-type"""	13211	protein-coding gene	gene with protein product	"""secretory pathway Ca2+/Mn2+ ATPase 1"", ""calcium-transporting ATPase type 2C member 1"""	604384	"""benign chronic pemphigus (Hailey-Hailey disease)"""	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.1683C>T	3.37:g.130698205C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	146	87	0.59589	NM_001199181	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Silent	SNP	ENST00000510168.1	37	CCDS46914.1	8	0.003663003663003663	7	0.014227642276422764	0	0.0	1	0.0017482517482517483	0	0.0	C	10.04	1.240288	0.22711	0.013618	0.0	ENSG00000017260	ENST00000504612	.	.	.	5.68	4.8	0.61643	.	.	.	.	.	T	0.49847	0.1581	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53549	-0.8423	4	.	.	.	.	7.3917	0.26913	0.1283:0.6805:0.1237:0.0676	.	.	.	.	L	515	.	.	P	+	2	0	ATP2C1	132180895	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.225000	0.32551	1.386000	0.46466	0.655000	0.94253	CCT	C|0.995;T|0.005	0.005	strong		0.413	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486	
OR10C1	442194	hgsc.bcm.edu	37	6	29408555	29408555	+	Missense_Mutation	SNP	C	C	A	rs17177674|rs386698374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29408555C>A	ENST00000444197.2	+	1	1473	c.763C>A	c.(763-765)Ctc>Atc	p.L255I	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	255			L -> I (in dbSNP:rs17177674).			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)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TGGCACCGCACTCTTTATCTA	0.577													A|||	316	0.063099	0.152	0.0562	5008	,	,		18037	0.0456		0.0159	False		,,,				2504	0.0143				p.L255I		Atlas-SNP	.											.	OR10C1	58	.	0			c.C763A						PASS	.	A	ILE/LEU	7,3015		3,1,1507	266.0	299.0	287.0		763	-0.9	0.3	6	dbSNP_123	287	0,5418		0,0,2709	yes	missense	OR10C1	NM_013941.3	5	3,1,4216	AA,AC,CC		0.0,0.2316,0.0829	benign	255/313	29408555	7,8433	1511	2709	4220	SO:0001583	missense	442194	exon1			ACCGCACTCTTTA		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.763C>A	6.37:g.29408555C>A	ENSP00000419119:p.Leu255Ile	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	181	67	0.370166	NM_013941	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	37	CCDS34364.1	122	0.055860805860805864	78	0.15853658536585366	17	0.04696132596685083	21	0.03671328671328671	6	0.0079155672823219	A	0.077	-1.189974	0.01607	0.002316	0.0	ENSG00000206474	ENST00000444197	T	0.38887	1.11	3.35	-0.944	0.10392	GPCR, rhodopsin-like superfamily (1);	0.187137	0.25854	N	0.027868	T	0.03348	0.0097	N	0.04959	-0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.25467	-1.0131	9	0.02654	T	1	.	1.5125	0.02499	0.4005:0.2621:0.0821:0.2553	rs17177674	255	Q96KK4	O10C1_HUMAN	I	255	ENSP00000419119:L255I	ENSP00000419119:L255I	L	+	1	0	OR10C1	29516534	0.000000	0.05858	0.285000	0.24819	0.893000	0.52053	-1.344000	0.02639	-0.373000	0.07979	-0.318000	0.08688	CTC	C|0.946;A|0.054	0.054	strong		0.577	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2		
KRT28	162605	hgsc.bcm.edu	37	17	38955961	38955961	+	Missense_Mutation	SNP	G	G	A	rs4624233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38955961G>A	ENST00000306658.7	-	1	250	c.185C>T	c.(184-186)gCt>gTt	p.A62V		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				GGCACCACCAGCATGGCTCCC	0.542													G|||	1465	0.292532	0.2958	0.134	5008	,	,		18308	0.4077		0.1938	False		,,,				2504	0.3834				p.A62V	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.C185T						PASS	.	G	VAL/ALA	1277,3129	433.5+/-343.6	192,893,1118	73.0	74.0	74.0		185	1.4	0.0	17	dbSNP_111	74	1596,7004	296.2+/-302.8	149,1298,2853	yes	missense	KRT28	NM_181535.3	64	341,2191,3971	AA,AG,GG		18.5581,28.9832,22.0898	benign	62/465	38955961	2873,10133	2203	4300	6503	SO:0001583	missense	162605	exon1			CCACCAGCATGGC	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30842	protein-coding gene	gene with protein product			"""keratin 25D"""	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.185C>T	17.37:g.38955961G>A	ENSP00000305263:p.Ala62Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_181535		Missense_Mutation	SNP	ENST00000306658.7	37	CCDS11376.1	580	0.26556776556776557	148	0.3008130081300813	57	0.1574585635359116	231	0.40384615384615385	144	0.18997361477572558	G	5.492	0.275848	0.10403	0.289832	0.185581	ENSG00000173908	ENST00000306658	T	0.75821	-0.97	5.08	1.35	0.21983	.	0.852841	0.10182	N	0.705705	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.10450	0.005	T	0.31447	-0.9943	9	0.17369	T	0.5	.	5.8448	0.18659	0.2198:0.4563:0.3239:0.0	rs4624233;rs61130906;rs4624233	62	Q7Z3Y7	K1C28_HUMAN	V	62	ENSP00000305263:A62V	ENSP00000305263:A62V	A	-	2	0	KRT28	36209487	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.548000	0.06048	0.623000	0.30267	0.650000	0.86243	GCT	G|0.752;A|0.248	0.248	strong		0.542	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535	
DSPP	1834	hgsc.bcm.edu	37	4	88537258	88537258	+	Silent	SNP	T	T	C	rs199966097		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88537258T>C	ENST00000282478.7	+	4	3477	c.3444T>C	c.(3442-3444)agT>agC	p.S1148S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1148S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1148	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.S1148S(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagtgaaagcagcg	0.562																																					p.S1148S		Atlas-SNP	.											DSPP,NS,carcinoma,0,2	DSPP	174	2	1	Substitution - coding silent(1)	kidney(1)	c.T3444C						PASS	.						47.0	63.0	57.0					4																	88537258		1566	2841	4407	SO:0001819	synonymous_variant	1834	exon5			CAGCAGTGAAAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3444T>C	4.37:g.88537258T>C		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	291	63	0.216495	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.562	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
UBE3C	9690	hgsc.bcm.edu	37	7	157000176	157000176	+	Silent	SNP	T	T	C	rs2301914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	172	0	0		WXS	Illumina HiSeq	Phase_I	161	161	1	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	
RSL1D1	26156	hgsc.bcm.edu	37	16	11940390	11940390	+	Silent	SNP	T	T	C	rs8052900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11940390T>C	ENST00000571133.1	-	5	675	c.603A>G	c.(601-603)acA>acG	p.T201T	RSL1D1_ENST00000542106.1_5'UTR	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	201					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)	p.T201T(1)		NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						TGTTTAAGACTGTTCCACCTA	0.333													C|||	3523	0.703474	0.9788	0.7983	5008	,	,		18858	0.4355		0.6551	False		,,,				2504	0.59				p.T201T		Atlas-SNP	.											RSL1D1,NS,carcinoma,0,1	RSL1D1	40	1	1	Substitution - coding silent(1)	stomach(1)	c.A603G						scavenged	.	C		4084,310	165.1+/-196.6	1898,288,11	102.0	101.0	101.0		603	-3.7	0.0	16	dbSNP_116	101	5715,2885	450.9+/-362.5	1882,1951,467	no	coding-synonymous	RSL1D1	NM_015659.2		3780,2239,478	CC,CT,TT		33.5465,7.0551,24.5883		201/491	11940390	9799,3195	2197	4300	6497	SO:0001819	synonymous_variant	26156	exon5			TAAGACTGTTCCA	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.603A>G	16.37:g.11940390T>C		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Silent	SNP	ENST00000571133.1	37	CCDS10551.1																																																																																			T|0.271;C|0.729	0.729	strong		0.333	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659	
OR10G3	26533	hgsc.bcm.edu	37	14	22038162	22038162	+	Silent	SNP	A	A	C	rs17197261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:22038162A>C	ENST00000303532.1	-	1	713	c.714T>G	c.(712-714)gcT>gcG	p.A238A		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	238						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)		AAGTTGAAAAAGCCCGGCGCC	0.567													A|||	420	0.0838658	0.0091	0.2882	5008	,	,		17272	0.0407		0.1153	False		,,,				2504	0.0521				p.A238A		Atlas-SNP	.											.	OR10G3	40	.	0			c.T714G						PASS	.	A		124,4282	92.0+/-130.7	0,124,2079	74.0	83.0	80.0		714	-0.6	1.0	14	dbSNP_123	80	1113,7487	231.9+/-265.7	66,981,3253	no	coding-synonymous	OR10G3	NM_001005465.1		66,1105,5332	CC,CA,AA		12.9419,2.8143,9.511		238/314	22038162	1237,11769	2203	4300	6503	SO:0001819	synonymous_variant	26533	exon1			TGAAAAAGCCCGG		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.714T>G	14.37:g.22038162A>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	173	81	0.468208	NM_001005465	Q6IET7|Q96R77	Silent	SNP	ENST00000303532.1	37	CCDS32046.1																																																																																			A|0.916;C|0.084	0.084	strong		0.567	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
EPHA10	284656	hgsc.bcm.edu	37	1	38188736	38188736	+	Missense_Mutation	SNP	G	G	A	rs146568133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38188736G>A	ENST00000373048.4	-	10	1936	c.1937C>T	c.(1936-1938)aCg>aTg	p.T646M	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000427468.2_Missense_Mutation_p.T646M|EPHA10_ENST00000330210.7_Missense_Mutation_p.T141M|EPHA10_ENST00000540011.1_Missense_Mutation_p.T141M	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	646	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCTCTCCAGCGTGACGCTTTT	0.617													G|||	5	0.000998403	0.003	0.0	5008	,	,		19137	0.0		0.001	False		,,,				2504	0.0				p.T646M		Atlas-SNP	.											.	EPHA10	120	.	0			c.C1937T						PASS	.	G	MET/THR	16,4208		0,16,2096	53.0	59.0	57.0		1937	0.7	0.6	1	dbSNP_134	57	3,8429		0,3,4213	yes	missense	EPHA10	NM_001099439.1	81	0,19,6309	AA,AG,GG		0.0356,0.3788,0.1501	probably-damaging	646/1009	38188736	19,12637	2112	4216	6328	SO:0001583	missense	284656	exon10			TCCAGCGTGACGC	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.1937C>T	1.37:g.38188736G>A	ENSP00000362139:p.Thr646Met	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	6.575	0.474435	0.12521	0.003788	3.56E-4	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000540011;ENST00000373048	D;D;T;D	0.83250	-1.7;-1.7;2.32;-1.7	3.96	0.672	0.17935	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.805996	0.10139	N	0.711048	T	0.66005	0.2746	L	0.41632	1.29	0.21579	N	0.99964	B	0.22851	0.076	B	0.17433	0.018	T	0.60321	-0.7286	10	0.66056	D	0.02	.	3.9999	0.09576	0.2121:0.0:0.4597:0.3283	.	646	Q5JZY3	EPHAA_HUMAN	M	141;646;141;646	ENSP00000330379:T141M;ENSP00000397746:T646M;ENSP00000441822:T141M;ENSP00000362139:T646M	ENSP00000330379:T141M	T	-	2	0	EPHA10	37961323	0.800000	0.28916	0.606000	0.28943	0.055000	0.15305	1.113000	0.31184	0.274000	0.22072	-0.657000	0.03884	ACG	G|0.999;A|0.001	0.001	strong		0.617	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
POM121L2	94026	hgsc.bcm.edu	37	6	27279877	27279877	+	Missense_Mutation	SNP	T	T	C	rs11965377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27279877T>C	ENST00000444565.1	-	1	72	c.73A>G	c.(73-75)Agg>Ggg	p.R25G	POM121L2_ENST00000377451.2_Missense_Mutation_p.R25G	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	25										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						TTCGTGGGCCTCTCGGGCAAG	0.637													T|||	101	0.0201677	0.053	0.0144	5008	,	,		14836	0.005		0.0129	False		,,,				2504	0.0031				p.R25G		Atlas-SNP	.											.	POM121L2	61	.	0			c.A73G						PASS	.	T	GLY/ARG	69,1315		1,67,624	16.0	23.0	21.0		73	-2.2	0.0	6	dbSNP_120	21	22,3160		0,22,1569	yes	missense	POM121L2	NM_033482.3	125	1,89,2193	CC,CT,TT		0.6914,4.9855,1.993	benign	25/1036	27279877	91,4475	692	1591	2283	SO:0001583	missense	94026	exon1			TGGGCCTCTCGGG	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.73A>G	6.37:g.27279877T>C	ENSP00000392726:p.Arg25Gly	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	95	39	0.410526	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	58	0.026556776556776556	34	0.06910569105691057	8	0.022099447513812154	4	0.006993006993006993	12	0.0158311345646438	T	9.921	1.212259	0.22289	0.049855	0.006914	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.16457	2.34;2.34	3.19	-2.24	0.06909	.	.	.	.	.	T	0.05135	0.0137	M	0.62723	1.935	0.09310	N	1	B	0.14012	0.009	B	0.13407	0.009	T	0.40021	-0.9585	9	0.39692	T	0.17	.	4.1196	0.10099	0.0:0.4172:0.2106:0.3722	rs11965377;rs11965377	25	C9J1I7	.	G	25	ENSP00000366671:R25G;ENSP00000392726:R25G	ENSP00000366671:R25G	R	-	1	2	POM121L2	27387856	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.165000	0.16564	-0.445000	0.07159	0.459000	0.35465	AGG	T|0.968;C|0.032	0.032	strong		0.637	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
RGPD3	653489	hgsc.bcm.edu	37	2	107040572	107040572	+	Missense_Mutation	SNP	T	T	C	rs3870235		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:107040572T>C	ENST00000409886.3	-	20	3938	c.3851A>G	c.(3850-3852)cAc>cGc	p.H1284R	RGPD3_ENST00000304514.7_Missense_Mutation_p.H1284R	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1284					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						CTCATCAAAGTGGAAAAGATT	0.403																																					p.H1284R		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,0,4	RGPD3	316	4	0			c.A3851G						scavenged	.						183.0	135.0	149.0					2																	107040572		659	1516	2175	SO:0001583	missense	653489	exon20			TCAAAGTGGAAAA		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.3851A>G	2.37:g.107040572T>C	ENSP00000386588:p.His1284Arg	Somatic	1255	0	0		WXS	Illumina HiSeq	Phase_I	221	212	0.959276	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-2.926314	0.00054	.	.	ENSG00000153165	ENST00000409886;ENST00000304514	T;T	0.34859	1.34;1.34	2.35	2.35	0.29111	.	.	.	.	.	T	0.10723	0.0262	N	0.00926	-1.1	0.45261	P	0.0017359999999999598	B	0.02656	0.0	B	0.01281	0.0	T	0.30937	-0.9961	8	0.10636	T	0.68	-3.2817	7.1563	0.25639	0.0:0.8506:0.0:0.1494	.	1284	A6NKT7	RGPD3_HUMAN	R	1284	ENSP00000386588:H1284R;ENSP00000303659:H1284R	ENSP00000303659:H1284R	H	-	2	0	RGPD3	106407004	1.000000	0.71417	0.999000	0.59377	0.042000	0.13812	4.693000	0.61753	0.328000	0.23435	-1.128000	0.01989	CAC	.	.	weak		0.403	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
TAF2	6873	hgsc.bcm.edu	37	8	120744349	120744349	+	Missense_Mutation	SNP	T	T	C	rs956748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120744349T>C	ENST00000378164.2	-	26	3713	c.3415A>G	c.(3415-3417)Aca>Gca	p.T1139A		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	1139			T -> A (in dbSNP:rs956748).		G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TTGGAGGCTGTAGATTCCTTA	0.423													T|||	905	0.180711	0.4766	0.0677	5008	,	,		20051	0.0159		0.0577	False		,,,				2504	0.1575				p.T1139A		Atlas-SNP	.											.	TAF2	204	.	0			c.A3415G						PASS	.	T	ALA/THR	1847,2559	535.9+/-374.3	380,1087,736	318.0	296.0	304.0		3415	-11.0	0.0	8	dbSNP_86	304	579,8021	155.8+/-209.8	22,535,3743	yes	missense	TAF2	NM_003184.3	58	402,1622,4479	CC,CT,TT		6.7326,41.9201,18.6529	benign	1139/1200	120744349	2426,10580	2203	4300	6503	SO:0001583	missense	6873	exon26			AGGCTGTAGATTC	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.3415A>G	8.37:g.120744349T>C	ENSP00000367406:p.Thr1139Ala	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	37	CCDS34937.1	310	0.14194139194139194	242	0.491869918699187	21	0.058011049723756904	2	0.0034965034965034965	45	0.059366754617414245	T	8.725	0.915254	0.17907	0.419201	0.067326	ENSG00000064313	ENST00000378164;ENST00000529653	T;T	0.29655	2.54;1.56	6.02	-11.0	0.00169	.	1.047070	0.07380	N	0.887402	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	0.40194	-0.9576	9	0.07030	T	0.85	-16.5437	12.0127	0.53297	0.0:0.5701:0.2142:0.2156	rs956748;rs52827029;rs60909112;rs956748	1139	Q6P1X5	TAF2_HUMAN	A	1139;315	ENSP00000367406:T1139A;ENSP00000436750:T315A	ENSP00000367406:T1139A	T	-	1	0	TAF2	120813530	0.000000	0.05858	0.000000	0.03702	0.351000	0.29236	-0.780000	0.04654	-2.521000	0.00497	-0.256000	0.11100	ACA	T|0.823;C|0.177	0.177	strong		0.423	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
LTV1	84946	hgsc.bcm.edu	37	6	144183376	144183376	+	Silent	SNP	T	T	C	rs56155985	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:144183376T>C	ENST00000367576.5	+	8	1193	c.1059T>C	c.(1057-1059)atT>atC	p.I353I	ZC2HC1B_ENST00000237275.6_5'Flank|ZC2HC1B_ENST00000539295.1_5'Flank	NM_032860.3	NP_116249.2	Q96GA3	LTV1_HUMAN	LTV1 ribosome biogenesis factor	353						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)		GTGAATCTATTTGTAGTAAGT	0.388													T|||	353	0.0704872	0.2368	0.0346	5008	,	,		18790	0.0		0.0139	False		,,,				2504	0.002				p.I353I		Atlas-SNP	.											.	LTV1	48	.	0			c.T1059C						PASS	.	T		781,3625	313.3+/-293.0	72,637,1494	91.0	90.0	90.0		1059	0.3	1.0	6	dbSNP_129	90	89,8511	50.2+/-110.2	1,87,4212	no	coding-synonymous	LTV1	NM_032860.3		73,724,5706	CC,CT,TT		1.0349,17.7258,6.6892		353/476	144183376	870,12136	2203	4300	6503	SO:0001819	synonymous_variant	84946	exon8			ATCTATTTGTAGT	BC009855	CCDS5201.1	6q24.2	2014-02-03	2014-02-03	2006-02-06	ENSG00000135521	ENSG00000135521			21173	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 93"", ""LTV1 homolog (S. cerevisiae)"""	C6orf93			Standard	NM_032860		Approved	FLJ14909, dJ468K18.4	uc003qjs.3	Q96GA3	OTTHUMG00000015733	ENST00000367576.5:c.1059T>C	6.37:g.144183376T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_032860	Q96JX8	Silent	SNP	ENST00000367576.5	37	CCDS5201.1																																																																																			T|0.936;C|0.064	0.064	strong		0.388	LTV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042532.1	NM_032860	
EVI5L	115704	hgsc.bcm.edu	37	19	7914022	7914022	+	Silent	SNP	C	C	T	rs554853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7914022C>T	ENST00000270530.4	+	4	739	c.543C>T	c.(541-543)aaC>aaT	p.N181N	EVI5L_ENST00000538904.2_Silent_p.N181N	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	181	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						TCCTCTTCAACGTCATGAAGG	0.647													C|||	83	0.0165735	0.0567	0.0101	5008	,	,		19132	0.0		0.001	False		,,,				2504	0.0				p.N181N		Atlas-SNP	.											.	EVI5L	43	.	0			c.C543T						PASS	.	C	,	232,4172	131.4+/-167.9	8,216,1978	34.0	30.0	32.0		543,543	-7.8	0.7	19	dbSNP_83	32	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous	EVI5L	NM_001159944.1,NM_145245.3	,	8,221,6273	TT,TC,CC		0.0581,5.2679,1.8225	,	181/806,181/795	7914022	237,12767	2202	4300	6502	SO:0001819	synonymous_variant	115704	exon3			CTTCAACGTCATG	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.543C>T	19.37:g.7914022C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_001159944	B9A6I9	Silent	SNP	ENST00000270530.4	37	CCDS12188.1																																																																																			C|0.984;T|0.016	0.016	strong		0.647	EVI5L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461347.1	NM_145245	
SMOC1	64093	hgsc.bcm.edu	37	14	70418881	70418881	+	Silent	SNP	G	G	A	rs3742909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:70418881G>A	ENST00000381280.4	+	2	379	c.126G>A	c.(124-126)caG>caA	p.Q42Q	SMOC1_ENST00000361956.3_Silent_p.Q42Q|SMOC1_ENST00000555917.1_3'UTR	NM_001034852.2|NM_022137.5	NP_001030024.1|NP_071420.1	Q9H4F8	SMOC1_HUMAN	SPARC related modular calcium binding 1	42	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165)	basement membrane (GO:0005604)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GTGACCCACAGTGCAACCTCC	0.507													G|||	1087	0.217053	0.0076	0.3718	5008	,	,		20143	0.375		0.2634	False		,,,				2504	0.18				p.Q42Q		Atlas-SNP	.											.	SMOC1	61	.	0			c.G126A						PASS	.	G	,	272,4134	153.7+/-187.2	12,248,1943	126.0	116.0	120.0		126,126	4.5	1.0	14	dbSNP_107	120	2163,6437	372.1+/-336.5	259,1645,2396	no	coding-synonymous,coding-synonymous	SMOC1	NM_001034852.2,NM_022137.5	,	271,1893,4339	AA,AG,GG		25.1512,6.1734,18.7221	,	42/436,42/435	70418881	2435,10571	2203	4300	6503	SO:0001819	synonymous_variant	64093	exon2			CCCACAGTGCAAC	AJ249900	CCDS9798.1, CCDS32110.1	14q24.1	2010-08-05			ENSG00000198732	ENSG00000198732			20318	protein-coding gene	gene with protein product		608488				12130637	Standard	NM_001034852		Approved		uc001xlt.2	Q9H4F8		ENST00000381280.4:c.126G>A	14.37:g.70418881G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_001034852	A8K1S3|B2R7P5|Q96F78	Silent	SNP	ENST00000381280.4	37	CCDS9798.1																																																																																			G|0.784;A|0.216	0.216	strong		0.507	SMOC1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412467.1		
UBA1	7317	hgsc.bcm.edu	37	X	47070261	47070261	+	Silent	SNP	G	G	A	rs2230147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47070261G>A	ENST00000335972.6	+	19	2403	c.2220G>A	c.(2218-2220)ccG>ccA	p.P740P	UBA1_ENST00000377269.3_Silent_p.P188P|UBA1_ENST00000377351.4_Silent_p.P740P	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	740					cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CAGGAGCGCCGTTCTGGTCTG	0.537													G|||	364	0.0964238	0.2648	0.0202	3775	,	,		14687	0.0		0.0	False		,,,				2504	0.0				p.P740P		Atlas-SNP	.											.	UBA1	89	.	0			c.G2220A						PASS	.	G	,	1067,2768		149,620,149,863,422	105.0	81.0	89.0		2220,2220	-9.5	0.0	X	dbSNP_98	89	14,6714		0,10,4,2418,1868	no	coding-synonymous,coding-synonymous	UBA1	NM_003334.3,NM_153280.2	,	149,630,153,3281,2290	AA,AG,A,GG,G		0.2081,27.8227,10.2338	,	740/1059,740/1059	47070261	1081,9482	2203	4300	6503	SO:0001819	synonymous_variant	7317	exon19			AGCGCCGTTCTGG	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"""Ubiquitin-like modifier activating enzymes"""	12469	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog (yeast)"", ""POC20 centriolar protein homolog (Chlamydomonas)"""	314370	"""ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)"", ""ubiquitin-activating enzyme E1"""	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.2220G>A	X.37:g.47070261G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	180	94	0.522222	NM_153280	Q5JRR8|Q96E13	Silent	SNP	ENST00000335972.6	37	CCDS14275.1																																																																																			0|0.004;A|0.126	0.126	strong		0.537	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	
PCDHB4	56131	hgsc.bcm.edu	37	5	140503278	140503278	+	Silent	SNP	T	T	C	rs535776973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140503278T>C	ENST00000194152.1	+	1	1698	c.1698T>C	c.(1696-1698)aaT>aaC	p.N566N	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	566					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCTGCAGAATGGCTCCGCGC	0.701													C|||	29	0.00579073	0.0219	0.0	5008	,	,		15744	0.0		0.0	False		,,,				2504	0.0				p.N566N		Atlas-SNP	.											PCDHB4,NS,carcinoma,+1,1	PCDHB4	177	1	0			c.T1698C						scavenged	.						19.0	23.0	22.0					5																	140503278		2185	4269	6454	SO:0001819	synonymous_variant	56131	exon1			GCAGAATGGCTCC	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1698T>C	5.37:g.140503278T>C		Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	65	24	0.369231	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			.	.	none		0.701	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
DDX11	1663	hgsc.bcm.edu	37	12	31256905	31256905	+	Missense_Mutation	SNP	T	T	C	rs1046458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:31256905T>C	ENST00000407793.2	+	27	3102	c.2851T>C	c.(2851-2853)Tgc>Cgc	p.C951R	DDX11_ENST00000350437.4_3'UTR|DDX11_ENST00000228264.6_3'UTR|DDX11_ENST00000545668.1_Missense_Mutation_p.C951R|DDX11_ENST00000251758.5_3'UTR	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	951			C -> R (in dbSNP:rs1046458).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GAGTCCAGAGTGCTGCCAGGA	0.592										Multiple Myeloma(12;0.14)			C|||	3197	0.638379	0.708	0.6153	5008	,	,		16557	0.8105		0.4553	False		,,,				2504	0.5716				p.C951R		Atlas-SNP	.											.	DDX11	188	.	0			c.T2851C						PASS	.						19.0	32.0	27.0					12																	31256905		1309	2289	3598	SO:0001583	missense	1663	exon27			CCAGAGTGCTGCC	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.2851T>C	12.37:g.31256905T>C	ENSP00000384703:p.Cys951Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	136	63	0.463235	NM_001257144	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	1181	0.5407509157509157	301	0.6117886178861789	189	0.5220994475138122	420	0.7342657342657343	271	0.3575197889182058	C	0.031	-1.335212	0.01287	.	.	ENSG00000013573	ENST00000407793;ENST00000545668	T;T	0.72725	-0.68;-0.68	1.38	-2.53	0.06326	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.53005	P	3.900000000001125E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.39292	-0.9621	7	.	.	.	.	4.767	0.13137	0.0:0.1951:0.2372:0.5677	rs1046458;rs3175510;rs4031272;rs60595330	951	Q96FC9	DDX11_HUMAN	R	951	ENSP00000384703:C951R;ENSP00000440402:C951R	.	C	+	1	0	DDX11	31148172	0.000000	0.05858	0.011000	0.14972	0.005000	0.04900	-0.876000	0.04201	-1.616000	0.01572	-1.518000	0.00936	TGC	T|0.458;C|0.542	0.542	strong		0.592	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
IL5RA	3568	hgsc.bcm.edu	37	3	3139957	3139957	+	Missense_Mutation	SNP	T	T	C	rs2290610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:3139957T>C	ENST00000446632.2	-	6	959	c.385A>G	c.(385-387)Att>Gtt	p.I129V	IL5RA_ENST00000456302.1_Missense_Mutation_p.I129V|IL5RA_ENST00000418488.2_Missense_Mutation_p.I129V|IL5RA_ENST00000430514.2_Missense_Mutation_p.I129V|IL5RA_ENST00000311981.8_Missense_Mutation_p.I129V|IL5RA_ENST00000445864.2_Intron|IL5RA_ENST00000383846.1_Missense_Mutation_p.I129V|IL5RA_ENST00000256452.3_Missense_Mutation_p.I129V|IL5RA_ENST00000438560.1_Missense_Mutation_p.I129V	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	129			I -> V (in dbSNP:rs2290610). {ECO:0000269|PubMed:1732409, ECO:0000269|Ref.6}.		cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)			cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		AAATTCACAATTGAGGTTCCA	0.403													T|||	2144	0.428115	0.4047	0.3991	5008	,	,		21287	0.4097		0.3489	False		,,,				2504	0.5808				p.I129V	GBM(169;430 2801 24955 28528)	Atlas-SNP	.											.	IL5RA	55	.	0			c.A385G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1726,2680	515.0+/-368.8	340,1046,817	164.0	167.0	166.0		385,385,385,385,385,385	-4.2	0.0	3	dbSNP_100	166	3152,5448	478.0+/-369.8	581,1990,1729	yes	missense,missense,missense,missense,missense,missense	IL5RA	NM_000564.4,NM_175724.2,NM_175725.2,NM_175726.3,NM_175727.2,NM_175728.2	29,29,29,29,29,29	921,3036,2546	CC,CT,TT		36.6512,39.1739,37.5058	benign,benign,benign,benign,benign,benign	129/421,129/334,129/336,129/421,129/334,129/336	3139957	4878,8128	2203	4300	6503	SO:0001583	missense	3568	exon6			TCACAATTGAGGT	M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"""Interleukins and interleukin receptors"", ""CD molecules"""	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.385A>G	3.37:g.3139957T>C	ENSP00000412209:p.Ile129Val	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_001243099	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Missense_Mutation	SNP	ENST00000446632.2	37	CCDS2559.1	831	0.3804945054945055	218	0.44308943089430897	147	0.40607734806629836	209	0.36538461538461536	257	0.3390501319261214	T	0	-2.617110	0.00118	0.391739	0.366512	ENSG00000091181	ENST00000446632;ENST00000438560;ENST00000256452;ENST00000418488;ENST00000383846;ENST00000311981;ENST00000430514;ENST00000456302;ENST00000445701	T;T;T;T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6	5.72	-4.22	0.03800	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.265650	0.05345	N	0.530869	T	0.00012	0.0000	N	0.04655	-0.195	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.08055	0.003;0.001;0.002;0.002;0.003	T	0.38243	-0.9670	9	0.02654	T	1	-3.3836	12.8508	0.57856	0.0:0.3013:0.0:0.6987	rs2290610;rs17659966;rs17882248;rs60525995;rs2290610	129;129;129;129;129	B4E2G0;Q01344-3;Q01344-2;Q01344;E7ERY4	.;.;.;IL5RA_HUMAN;.	V	129	ENSP00000412209:I129V;ENSP00000390753:I129V;ENSP00000256452:I129V;ENSP00000388858:I129V;ENSP00000373358:I129V;ENSP00000309196:I129V;ENSP00000400400:I129V;ENSP00000392059:I129V;ENSP00000398117:I129V	ENSP00000256452:I129V	I	-	1	0	IL5RA	3114957	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.613000	0.05610	-1.344000	0.02216	-1.601000	0.00813	ATT	T|0.610;C|0.390	0.390	strong		0.403	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2		
LRRC16B	90668	hgsc.bcm.edu	37	14	24533539	24533539	+	Missense_Mutation	SNP	C	C	A	rs10146906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	57	0	0		WXS	Illumina HiSeq	Phase_I	48	24	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	
FCGBP	8857	hgsc.bcm.edu	37	19	40364011	40364011	+	Silent	SNP	G	G	A	rs78835791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40364011G>A	ENST00000221347.6	-	31	14638	c.14631C>T	c.(14629-14631)tcC>tcT	p.S4877S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4877	VWFD 12. {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)			CATAGGAGCAGGAGCCATGCA	0.602													G|||	61	0.0121805	0.0439	0.0029	5008	,	,		20928	0.0		0.001	False		,,,				2504	0.0				p.S4877S		Atlas-SNP	.											.	FCGBP	416	.	0			c.C14631T						PASS	.	G		151,4255	103.8+/-142.4	1,149,2053	94.0	82.0	86.0		14631	4.0	1.0	19	dbSNP_131	86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FCGBP	NM_003890.2		1,150,6352	AA,AG,GG		0.0116,3.4271,1.1687		4877/5406	40364011	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon31			GGAGCAGGAGCCA	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.14631C>T	19.37:g.40364011G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.988;A|0.012	0.012	strong		0.602	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
RGMA	56963	hgsc.bcm.edu	37	15	93588657	93588657	+	Silent	SNP	G	G	A	rs61733836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:93588657G>A	ENST00000329082.7	-	4	1195	c.924C>T	c.(922-924)gaC>gaT	p.D308D	RGMA_ENST00000542321.2_Silent_p.D292D|RGMA_ENST00000538818.1_Silent_p.D199D|RGMA_ENST00000425933.2_Silent_p.D292D|RGMA_ENST00000557420.1_3'UTR|RGMA_ENST00000543599.1_Silent_p.D292D|RGMA_ENST00000557301.1_Silent_p.D316D|RGMA_ENST00000556658.1_Silent_p.D199D	NM_020211.2	NP_064596	Q96B86	RGMA_HUMAN	repulsive guidance molecule family member a	308					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|neural tube closure (GO:0001843)|regulation of BMP signaling pathway (GO:0030510)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	9	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)			GACCCTGGCTGTCCCAGTCCT	0.647													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		18464	0.0		0.0	False		,,,				2504	0.0				p.D316D		Atlas-SNP	.											.	RGMA	49	.	0			c.C948T						PASS	.	G	,,,,,	93,4121		3,87,2017	27.0	34.0	32.0		948,876,876,876,876,924	4.8	1.0	15	dbSNP_129	32	0,8432		0,0,4216	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RGMA	NM_001166283.1,NM_001166286.1,NM_001166287.1,NM_001166288.1,NM_001166289.1,NM_020211.2	,,,,,	3,87,6233	AA,AG,GG		0.0,2.2069,0.7354	,,,,,	316/459,292/435,292/435,292/435,292/435,308/451	93588657	93,12553	2107	4216	6323	SO:0001819	synonymous_variant	56963	exon4			CTGGCTGTCCCAG	AL390083	CCDS45357.1, CCDS53973.1, CCDS53974.1	15q26.1	2013-11-06	2013-11-06			ENSG00000182175			30308	protein-coding gene	gene with protein product		607362	"""RGM domain family, member A"""			15975920	Standard	NM_020211		Approved	RGM, RGMa	uc010urc.2	Q96B86		ENST00000329082.7:c.924C>T	15.37:g.93588657G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001166283	B2RTW1|B7Z5S8|F5GXQ7|F5GZU6|G3V518|Q0JV97|Q8NC80|Q9H0E6|Q9NPM3	Silent	SNP	ENST00000329082.7	37	CCDS45357.1																																																																																			G|0.994;A|0.006	0.006	strong		0.647	RGMA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415091.1	NM_020211	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411852	105411852	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105411852T>C	ENST00000333244.5	-	7	10055	c.9936A>G	c.(9934-9936)aaA>aaG	p.K3312K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3312						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)			GCATCTTGAATTTGGGCATTT	0.622																																					p.K3312K		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-1,1	AHNAK2	719	1	0			c.A9936G						scavenged	.						205.0	199.0	201.0					14																	105411852		2003	4164	6167	SO:0001819	synonymous_variant	113146	exon7			CTTGAATTTGGGC	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.9936A>G	14.37:g.105411852T>C		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	298	7	0.0234899	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.	.	none		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
COL28A1	340267	hgsc.bcm.edu	37	7	7514235	7514235	+	Missense_Mutation	SNP	C	C	G	rs6952195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:7514235C>G	ENST00000399429.3	-	15	1439	c.1299G>C	c.(1297-1299)gaG>gaC	p.E433D		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	433			E -> D (in dbSNP:rs6952195).		cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E433D(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		ACAGTACCTTCTCCCCTTTGA	0.413													G|||	1694	0.338259	0.6536	0.2565	5008	,	,		15040	0.2113		0.2117	False		,,,				2504	0.2311				p.E433D		Atlas-SNP	.											COL28A1,NS,carcinoma,0,1	COL28A1	113	1	1	Substitution - Missense(1)	stomach(1)	c.G1299C						PASS	.	G	ASP/GLU	2084,1636		601,882,377	135.0	136.0	135.0		1299	2.8	1.0	7	dbSNP_116	135	1671,6547		153,1365,2591	yes	missense	COL28A1	NM_001037763.2	45	754,2247,2968	GG,GC,CC		20.3334,43.9785,31.4542	benign	433/1126	7514235	3755,8183	1860	4109	5969	SO:0001583	missense	340267	exon15			TACCTTCTCCCCT	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.1299G>C	7.37:g.7514235C>G	ENSP00000382356:p.Glu433Asp	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	699	0.32005494505494503	335	0.6808943089430894	94	0.2596685082872928	115	0.20104895104895104	155	0.20448548812664907	G	1.123	-0.654628	0.03480	0.560215	0.203334	ENSG00000215018	ENST00000399429;ENST00000399419	T	0.74421	-0.84	4.7	2.82	0.32997	.	0.095250	0.38778	N	0.001569	T	0.00012	0.0000	L	0.28192	0.835	0.54753	P	1.399999999995849E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47289	-0.9129	9	0.10636	T	0.68	-4.2027	2.9265	0.05786	0.1009:0.1805:0.5319:0.1867	rs6952195;rs9771165;rs52835781;rs6952195	433;433	Q2UY09-2;Q2UY09	.;COSA1_HUMAN	D	433	ENSP00000382356:E433D	ENSP00000382347:E433D	E	-	3	2	COL28A1	7480760	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	0.669000	0.25142	0.275000	0.22094	-0.127000	0.14921	GAG	C|0.712;G|0.288	0.288	strong		0.413	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
SSPO	23145	hgsc.bcm.edu	37	7	149485059	149485059	+	RNA	SNP	T	T	C	rs709060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149485059T>C	ENST00000378016.2	+	0	3814							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)			GGAGCTCTGCTGTGAGTGTGC	0.617													C|||	524	0.104633	0.1445	0.0865	5008	,	,		17191	0.0942		0.0954	False		,,,				2504	0.0838				p.S1272P		Atlas-SNP	.											.	.	.	.	0			c.T3814C						PASS	.	C		495,3563		29,437,1563	12.0	17.0	15.0		3818	3.8	1.0	7	dbSNP_86	15	730,7600		32,666,3467	yes	coding-notMod3-near-splice	SSPO	NM_198455.2		61,1103,5030	CC,CT,TT		8.7635,12.1981,9.8886			149485059	1225,11163	2029	4165	6194			23145	exon26			CTCTGCTGTGAGT	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.149485059T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.893;C|0.107	0.107	strong		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
TBP	6908	hgsc.bcm.edu	37	6	170871055	170871055	+	Silent	SNP	G	G	A	rs112928724|rs369312237		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170871055G>A	ENST00000392092.2	+	3	510	c.231G>A	c.(229-231)caG>caA	p.Q77Q	TBP_ENST00000230354.6_Silent_p.Q77Q|TBP_ENST00000540980.1_Silent_p.Q57Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	77	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		aacagcagcagcagcagcagc	0.572																																					p.Q77Q		Atlas-SNP	.											TBP,colon,carcinoma,0,2	TBP	58	2	0			c.G231A						scavenged	.						14.0	18.0	17.0					6																	170871055		1934	3804	5738	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.231G>A	6.37:g.170871055G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	64	3	0.046875	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			G|0.500;A|0.500	0.500	weak		0.572	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
LRRC52	440699	hgsc.bcm.edu	37	1	165532746	165532746	+	Missense_Mutation	SNP	T	T	A	rs17407838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:165532746T>A	ENST00000294818.1	+	2	917	c.627T>A	c.(625-627)gaT>gaA	p.D209E	RP11-280O1.2_ENST00000421273.1_RNA|RP11-280O1.2_ENST00000438275.1_RNA|RP11-280O1.2_ENST00000416424.1_RNA	NM_001005214.3	NP_001005214.2	Q8N7C0	LRC52_HUMAN	leucine rich repeat containing 52	209	LRRCT.		D -> E (in dbSNP:rs17407838).		ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)	18	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TCTTAGATGATCTAAATGCCA	0.572													T|||	293	0.0585064	0.1006	0.062	5008	,	,		20087	0.0		0.1034	False		,,,				2504	0.0133				p.D209E		Atlas-SNP	.											.	LRRC52	50	.	0			c.T627A						PASS	.	T	GLU/ASP	411,3995	198.1+/-222.0	14,383,1806	45.0	37.0	40.0		627	-8.6	0.0	1	dbSNP_123	40	905,7695	195.9+/-241.0	54,797,3449	yes	missense	LRRC52	NM_001005214.3	45	68,1180,5255	AA,AT,TT		10.5233,9.3282,10.1184	benign	209/314	165532746	1316,11690	2203	4300	6503	SO:0001583	missense	440699	exon2			AGATGATCTAAAT	AK098677	CCDS30930.1	1q23.3	2008-02-05			ENSG00000162763	ENSG00000162763			32156	protein-coding gene	gene with protein product		615218					Standard	NM_001005214		Approved	FLJ25811	uc001gde.2	Q8N7C0	OTTHUMG00000034625	ENST00000294818.1:c.627T>A	1.37:g.165532746T>A	ENSP00000294818:p.Asp209Glu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_001005214	A2RUN7|Q5T9K5	Missense_Mutation	SNP	ENST00000294818.1	37	CCDS30930.1	144	0.06593406593406594	49	0.09959349593495935	21	0.058011049723756904	0	0.0	74	0.09762532981530343	T	0.006	-2.043824	0.00398	0.093282	0.105233	ENSG00000162763	ENST00000294818	T	0.64803	-0.12	4.28	-8.56	0.00904	.	0.544586	0.19975	N	0.101883	T	0.07188	0.0182	N	0.08118	0	0.24481	P	0.994347	B	0.02656	0.0	B	0.01281	0.0	T	0.14924	-1.0455	9	0.02654	T	1	.	4.7372	0.12993	0.1777:0.3642:0.3582:0.0998	rs17407838;rs52823561;rs17407838	209	Q8N7C0	LRC52_HUMAN	E	209	ENSP00000294818:D209E	ENSP00000294818:D209E	D	+	3	2	LRRC52	163799370	0.000000	0.05858	0.000000	0.03702	0.400000	0.30750	-4.590000	0.00211	-3.350000	0.00181	-1.123000	0.02005	GAT	T|0.917;A|0.083	0.083	strong		0.572	LRRC52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083793.1	NM_001005214	
SLC6A16	28968	hgsc.bcm.edu	37	19	49793620	49793620	+	Silent	SNP	C	C	T	rs34817563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49793620C>T	ENST00000335875.4	-	12	2212	c.1971G>A	c.(1969-1971)ccG>ccA	p.P657P	SLC6A16_ENST00000454748.3_3'UTR	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	657					neurotransmitter transport (GO:0006836)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		GCAGTGCCCACGGTGGGTATG	0.488													T|||	106	0.0211661	0.0711	0.0144	5008	,	,		20056	0.0		0.001	False		,,,				2504	0.001				p.P657P		Atlas-SNP	.											.	SLC6A16	62	.	0			c.G1971A						PASS	.	T		221,3697		6,209,1744	68.0	66.0	67.0		1971	-4.6	0.0	19	dbSNP_126	67	2,8306		0,2,4152	no	coding-synonymous	SLC6A16	NM_014037.2		6,211,5896	TT,TC,CC		0.0241,5.6406,1.824		657/737	49793620	223,12003	1959	4154	6113	SO:0001819	synonymous_variant	28968	exon12			TGCCCACGGTGGG	AF265578	CCDS42590.1	19q13.33	2013-05-22			ENSG00000063127	ENSG00000063127		"""Solute carriers"""	13622	protein-coding gene	gene with protein product	"""NTT5 protein"""	607972	"""solute carrier family 6 (neurotransmitter transporter), member 16"""			10471414, 11112352	Standard	XM_005258820		Approved	NTT5	uc002pmz.3	Q9GZN6		ENST00000335875.4:c.1971G>A	19.37:g.49793620C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_014037	Q8IYV4|Q9Y5I9	Silent	SNP	ENST00000335875.4	37	CCDS42590.1																																																																																			C|0.989;T|0.011	0.011	strong		0.488	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037	
KIF4A	24137	hgsc.bcm.edu	37	X	69573639	69573639	+	Silent	SNP	C	C	T	rs1199429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:69573639C>T	ENST00000374403.3	+	15	1738	c.1656C>T	c.(1654-1656)ccC>ccT	p.P552P	KIF4A_ENST00000374388.3_Silent_p.P552P	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	552					anterograde axon cargo transport (GO:0008089)|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)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						AACTGCAGCCCATTCAGTACC	0.428													C|||	450	0.119205	0.2791	0.0375	3775	,	,		13843	0.0		0.0398	False		,,,				2504	0.0153				p.P552P		Atlas-SNP	.											.	KIF4A	118	.	0			c.C1656T						PASS	.	C		1337,2496		210,717,200,705,369	46.0	39.0	41.0		1656	-0.2	1.0	X	dbSNP_87	41	323,6400		4,225,90,2199,1777	no	coding-synonymous	KIF4A	NM_012310.4		214,942,290,2904,2146	TT,TC,T,CC,C		4.8044,34.8813,15.7257		552/1233	69573639	1660,8896	2201	4295	6496	SO:0001819	synonymous_variant	24137	exon15			GCAGCCCATTCAG	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"""Kinesins"""	13339	protein-coding gene	gene with protein product	"""chromokinesin"""	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1656C>T	X.37:g.69573639C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	250	109	0.436	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Silent	SNP	ENST00000374403.3	37	CCDS14401.1																																																																																			0|0.003;T|0.145	0.145	strong		0.428	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	
LYPLA1	10434	hgsc.bcm.edu	37	8	54967638	54967638	+	Missense_Mutation	SNP	A	A	C	rs76859468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:54967638A>C	ENST00000316963.3	-	6	535	c.342T>G	c.(340-342)atT>atG	p.I114M	LYPLA1_ENST00000519926.1_5'UTR|LYPLA1_ENST00000343231.6_Missense_Mutation_p.I98M|LYPLA1_ENST00000522007.1_Intron	NM_001279360.1|NM_006330.2	NP_001266289.1|NP_006321.1	O75608	LYPA1_HUMAN	lysophospholipase I	114					fatty acid metabolic process (GO:0006631)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|nitric oxide metabolic process (GO:0046209)|protein depalmitoylation (GO:0002084)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	lysophospholipase activity (GO:0004622)|palmitoyl-(protein) hydrolase activity (GO:0008474)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)	6		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)			ACCCTCCCAAAATAATTCTGT	0.328													A|||	56	0.0111821	0.0401	0.0043	5008	,	,		16168	0.0		0.0	False		,,,				2504	0.0				p.I114M		Atlas-SNP	.											.	LYPLA1	15	.	0			c.T342G						PASS	.	A	MET/ILE	211,4195	127.4+/-164.3	6,199,1998	60.0	58.0	59.0		342	5.2	1.0	8	dbSNP_131	59	1,8591	1.2+/-3.3	0,1,4295	yes	missense	LYPLA1	NM_006330.2	10	6,200,6293	CC,CA,AA		0.0116,4.7889,1.631	benign	114/231	54967638	212,12786	2203	4296	6499	SO:0001583	missense	10434	exon6			TCCCAAAATAATT	AF081281	CCDS6157.1, CCDS64899.1, CCDS75738.1, CCDS75739.1	8q11.23-q12.1	2008-05-15			ENSG00000120992	ENSG00000120992	3.1.1.5		6737	protein-coding gene	gene with protein product		605599				10064899	Standard	NM_006330		Approved	LPL1	uc003xry.3	O75608	OTTHUMG00000164313	ENST00000316963.3:c.342T>G	8.37:g.54967638A>C	ENSP00000320043:p.Ile114Met	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	223	108	0.484305	NM_006330	O43202|Q9UQF9	Missense_Mutation	SNP	ENST00000316963.3	37	CCDS6157.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	A	12.13	1.846250	0.32606	0.047889	1.16E-4	ENSG00000120992	ENST00000316963;ENST00000523751;ENST00000343231;ENST00000521171;ENST00000518546;ENST00000521352;ENST00000519926;ENST00000521898	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65	5.23	5.23	0.72850	Phospholipase/carboxylesterase/thioesterase (1);	0.223460	0.46145	D	0.000313	T	0.05547	0.0146	L	0.45744	1.44	0.80722	D	1	B;B;B	0.33549	0.417;0.392;0.073	B;B;B	0.41666	0.363;0.259;0.105	T	0.05649	-1.0872	10	0.51188	T	0.08	-5.5049	5.7137	0.17948	0.7698:0.0:0.0798:0.1504	.	114;98;114	B4DP64;O75608-2;O75608	.;.;LYPA1_HUMAN	M	114;114;98;23;98;50;114;92	ENSP00000320043:I114M;ENSP00000344477:I98M;ENSP00000428729:I98M;ENSP00000428306:I50M;ENSP00000430791:I92M	ENSP00000320043:I114M	I	-	3	3	LYPLA1	55130191	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.404000	0.34623	2.103000	0.63969	0.528000	0.53228	ATT	A|0.983;C|0.017	0.017	strong		0.328	LYPLA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378238.1		
TACSTD2	4070	hgsc.bcm.edu	37	1	59042181	59042181	+	Missense_Mutation	SNP	G	G	T	rs14008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:59042181G>T	ENST00000371225.2	-	1	985	c.648C>A	c.(646-648)gaC>gaA	p.D216E		NM_002353.2	NP_002344.2	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	216			D -> E (in dbSNP:rs14008). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8382772}.		cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell motility (GO:2000146)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of stem cell differentiation (GO:2000738)|regulation of epithelial cell proliferation (GO:0050678)|ureteric bud morphogenesis (GO:0060675)|visual perception (GO:0007601)	basal plasma membrane (GO:0009925)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)					all_cancers(7;6.54e-05)					CGATATCCACGTCACCGGCGG	0.647													G|||	787	0.157149	0.3449	0.0533	5008	,	,		14915	0.1379		0.0497	False		,,,				2504	0.1074				p.D216E		Atlas-SNP	.											.	TACSTD2	6	.	0			c.C648A						PASS	.	G	GLU/ASP	1358,3034		216,926,1054	14.0	17.0	16.0		648	0.2	1.0	1	dbSNP_52	16	579,8011		27,525,3743	yes	missense	TACSTD2	NM_002353.2	45	243,1451,4797	TT,TG,GG		6.7404,30.9199,14.9207	benign	216/324	59042181	1937,11045	2196	4295	6491	SO:0001583	missense	4070	exon1			ATCCACGTCACCG	X77753	CCDS609.1	1p32	2008-02-05			ENSG00000184292	ENSG00000184292			11530	protein-coding gene	gene with protein product		137290		M1S1		8382772, 11306819	Standard	NM_002353		Approved	TROP2, GA733-1, EGP-1	uc001cyz.4	P09758	OTTHUMG00000010067	ENST00000371225.2:c.648C>A	1.37:g.59042181G>T	ENSP00000360269:p.Asp216Glu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_002353	Q15658|Q6FG48|Q7Z7Q4|Q96QD2	Missense_Mutation	SNP	ENST00000371225.2	37	CCDS609.1	273	0.125	135	0.27439024390243905	19	0.052486187845303865	82	0.14335664335664336	37	0.048812664907651716	G	8.456	0.854221	0.17106	0.309199	0.067404	ENSG00000184292	ENST00000371225	T	0.77489	-1.1	4.64	0.165	0.14995	.	0.406641	0.24611	N	0.037056	T	0.00012	0.0000	N	0.16098	0.37	0.35294	P	0.21758299999999997	B	0.21520	0.057	B	0.17979	0.02	T	0.10086	-1.0645	9	0.31617	T	0.26	-12.9943	5.1262	0.14886	0.3106:0.2655:0.4239:0.0	rs14008;rs232837;rs481082;rs59139961;rs14008	216	P09758	TACD2_HUMAN	E	216	ENSP00000360269:D216E	ENSP00000360269:D216E	D	-	3	2	TACSTD2	58814769	0.969000	0.33509	1.000000	0.80357	0.193000	0.23685	-0.111000	0.10807	0.146000	0.19002	0.561000	0.74099	GAC	G|0.865;T|0.135	0.135	strong		0.647	TACSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027818.1	NM_002353	
WWC3	55841	hgsc.bcm.edu	37	X	10106971	10106971	+	Missense_Mutation	SNP	C	C	T	rs377116582		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:10106971C>T	ENST00000380861.4	+	21	3470	c.3079C>T	c.(3079-3081)Cgg>Tgg	p.R1027W	WWC3_ENST00000454666.1_Missense_Mutation_p.R1027W	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	1027					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						GGAGGCCGAGCGGCAGGTGGG	0.711																																					p.R1027W		Atlas-SNP	.											.	WWC3	142	.	0			c.C3079T						PASS	.	C	TRP/ARG	2,3724		0,1,1,1592,539	8.0	9.0	9.0		3079	-6.4	0.5	X		9	1,6500		0,1,0,2373,1753	no	missense	WWC3	NM_015691.3	101	0,2,1,3965,2292	TT,TC,T,CC,C		0.0154,0.0537,0.0293	probably-damaging	1027/1093	10106971	3,10224	2133	4127	6260	SO:0001583	missense	55841	exon21			GCCGAGCGGCAGG	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.3079C>T	X.37:g.10106971C>T	ENSP00000370242:p.Arg1027Trp	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	19	16	0.842105	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632188	0.67015	5.37E-4	1.54E-4	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543412	T;T	0.44482	0.92;0.92	4.8	-6.37	0.01963	.	0.044151	0.85682	D	0.000000	T	0.56396	0.1982	M	0.67953	2.075	0.43032	D	0.994601	D	0.76494	0.999	D	0.74348	0.983	T	0.64748	-0.6334	9	.	.	.	-20.9116	18.8956	0.92421	0.2618:0.7382:0.0:0.0	.	1027	Q9ULE0	WWC3_HUMAN	W	1027;1027;522	ENSP00000370242:R1027W;ENSP00000399584:R1027W	.	R	+	1	2	WWC3	10066971	1.000000	0.71417	0.517000	0.27799	0.613000	0.37349	2.008000	0.40893	-1.390000	0.02087	-0.436000	0.05848	CGG	.	.	weak		0.711	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
TACSTD2	4070	hgsc.bcm.edu	37	1	59041940	59041940	+	Missense_Mutation	SNP	T	T	C	rs114373153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:59041940T>C	ENST00000371225.2	-	1	1226	c.889A>G	c.(889-891)Atc>Gtc	p.I297V		NM_002353.2	NP_002344.2	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	297					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)					CGGTTGGTGATCACCAGgacg	0.622													T|||	149	0.0297524	0.1082	0.0043	5008	,	,		14669	0.0		0.003	False		,,,				2504	0.0				p.I297V		Atlas-SNP	.											.	TACSTD2	6	.	0			c.A889G						PASS	.	T	VAL/ILE	398,4008	195.0+/-219.7	18,362,1823	50.0	46.0	47.0		889	1.0	0.8	1	dbSNP_132	47	6,8594	4.3+/-15.6	0,6,4294	yes	missense	TACSTD2	NM_002353.2	29	18,368,6117	CC,CT,TT		0.0698,9.0331,3.1063	benign	297/324	59041940	404,12602	2203	4300	6503	SO:0001583	missense	4070	exon1			TGGTGATCACCAG	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.889A>G	1.37:g.59041940T>C	ENSP00000360269:p.Ile297Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	61	0.580952	NM_002353	Q15658|Q6FG48|Q7Z7Q4|Q96QD2	Missense_Mutation	SNP	ENST00000371225.2	37	CCDS609.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	T	3.973	-0.008046	0.07773	0.090331	6.98E-4	ENSG00000184292	ENST00000371225	T	0.76448	-1.02	4.59	0.995	0.19838	.	0.178739	0.48286	N	0.000189	T	0.00936	0.0031	N	0.12422	0.21	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.01071	-1.1461	10	0.11182	T	0.66	-9.0532	3.5124	0.07713	0.1616:0.2884:0.0:0.5501	.	297	P09758	TACD2_HUMAN	V	297	ENSP00000360269:I297V	ENSP00000360269:I297V	I	-	1	0	TACSTD2	58814528	0.005000	0.15991	0.797000	0.32132	0.803000	0.45373	-0.133000	0.10451	0.004000	0.14682	0.533000	0.62120	ATC	T|0.965;C|0.035	0.035	strong		0.622	TACSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027818.1	NM_002353	
ACAN	176	hgsc.bcm.edu	37	15	89401825	89401825	+	Silent	SNP	T	T	C	rs35676128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89401825T>C	ENST00000561243.1	+	11	6009	c.6009T>C	c.(6007-6009)taT>taC	p.Y2003Y	ACAN_ENST00000439576.2_Silent_p.Y2003Y|ACAN_ENST00000352105.7_Silent_p.Y2003Y|ACAN_ENST00000559004.1_Silent_p.Y2003Y			P16112	PGCA_HUMAN	aggrecan	2013	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GTACTCCATATTTTAGTGGGG	0.532													T|||	127	0.0253594	0.0507	0.0274	5008	,	,		18222	0.0347		0.002	False		,,,				2504	0.0041				p.Y2003Y		Atlas-SNP	.											.	ACAN	220	.	0			c.T6009C						PASS	.	T	,	136,3582		3,130,1726	47.0	47.0	47.0		6009,6009	2.8	0.9	15	dbSNP_126	47	12,8188		0,12,4088	no	coding-synonymous,coding-synonymous	ACAN	NM_001135.3,NM_013227.3	,	3,142,5814	CC,CT,TT		0.1463,3.6579,1.2418	,	2003/2432,2003/2531	89401825	148,11770	1859	4100	5959	SO:0001819	synonymous_variant	176	exon12			TCCATATTTTAGT	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.6009T>C	15.37:g.89401825T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																			T|0.985;C|0.015	0.015	strong		0.532	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
TAS2R20	259295	hgsc.bcm.edu	37	12	11149711	11149711	+	Missense_Mutation	SNP	C	C	A	rs10845279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11149711C>A	ENST00000538986.1	-	1	763	c.764G>T	c.(763-765)cGa>cTa	p.R255L	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	255			R -> L (in dbSNP:rs10845279). {ECO:0000269|PubMed:15496549}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R255Q(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						TTCTTTTGGTCGCATCTTAAA	0.373													C|||	2119	0.423123	0.0651	0.3847	5008	,	,		18928	0.755		0.3827	False		,,,				2504	0.6339				p.R255L		Atlas-SNP	.											TAS2R20,colon,carcinoma,0,1	TAS2R20	17	1	1	Substitution - Missense(1)	large_intestine(1)	c.G764T						scavenged	.	C	LEU/ARG	442,3964	212.8+/-232.6	18,406,1779	110.0	109.0	109.0		764	-5.3	0.0	12	dbSNP_120	109	3016,5584	465.2+/-366.4	544,1928,1828	yes	missense	TAS2R20	NM_176889.2	102	562,2334,3607	AA,AC,CC		35.0698,10.0318,26.5877	benign	255/310	11149711	3458,9548	2203	4300	6503	SO:0001583	missense	259295	exon1			TTTGGTCGCATCT	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.764G>T	12.37:g.11149711C>A	ENSP00000441624:p.Arg255Leu	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	169	72	0.426035	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	898	0.41117216117216115	33	0.06707317073170732	155	0.4281767955801105	426	0.7447552447552448	284	0.37467018469656993	C	0.008	-1.921931	0.00498	0.100318	0.350698	ENSG00000255837	ENST00000538986	T	0.00753	5.74	2.66	-5.32	0.02722	.	2.067560	0.05057	N	0.479233	T	0.00012	0.0000	N	0.00017	-2.83	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46638	-0.9177	9	0.02654	T	1	.	4.8332	0.13451	0.2999:0.1236:0.0:0.5765	rs10845279;rs60755728;rs10845279	255	P59543	T2R20_HUMAN	L	255	ENSP00000441624:R255L	ENSP00000441624:R255L	R	-	2	0	TAS2R20	11040978	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.312000	0.02720	-1.408000	0.02040	-0.383000	0.06682	CGA	C|0.671;A|0.329	0.329	strong		0.373	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
C2orf83	56918	hgsc.bcm.edu	37	2	228493211	228493211	+	Missense_Mutation	SNP	G	G	A	rs28739019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228493211G>A	ENST00000264387.4	-	2	220	c.134C>T	c.(133-135)tCg>tTg	p.S45L	C2orf83_ENST00000409066.1_Missense_Mutation_p.S45L	NM_020161.3	NP_064546.3	Q53S99	CB083_HUMAN	chromosome 2 open reading frame 83	45			S -> L (in dbSNP:rs28739019).		transport (GO:0006810)	membrane (GO:0016020)		p.S45L(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(2)	11						ggcttttggcgagggctttgc	0.453													G|||	1702	0.339856	0.466	0.3084	5008	,	,		18142	0.2143		0.2575	False		,,,				2504	0.4059				p.S45L		Atlas-SNP	.											C2orf83,NS,carcinoma,0,1	C2orf83	15	1	1	Substitution - Missense(1)	stomach(1)	c.C134T						PASS	.	G	LEU/SER,LEU/SER	1129,1525		247,635,445	237.0	203.0	215.0		134,134	-1.4	0.0	2	dbSNP_125	215	1185,3433		172,841,1296	yes	missense,missense	C2orf83	NM_001162483.1,NM_020161.3	145,145	419,1476,1741	AA,AG,GG		25.6605,42.5396,31.8207	possibly-damaging,possibly-damaging	45/97,45/151	228493211	2314,4958	1327	2309	3636	SO:0001583	missense	56918	exon2			TTTGGCGAGGGCT		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.134C>T	2.37:g.228493211G>A	ENSP00000264387:p.Ser45Leu	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	167	69	0.413174	NM_020161	A2RRG6|B8ZZI8|Q9NPW4	Missense_Mutation	SNP	ENST00000264387.4	37	CCDS33388.1	627	0.28708791208791207	208	0.42276422764227645	108	0.2983425414364641	127	0.22202797202797203	184	0.24274406332453827	.	4.677	0.125929	0.08931	0.425396	0.256605	ENSG00000042304	ENST00000264387;ENST00000409066	T;T	0.69806	0.17;-0.43	0.694	-1.36	0.09085	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.35151	-0.9800	7	0.56958	D	0.05	.	.	.	.	rs28739019	45;45	B8ZZI8;Q53S99	.;CB083_HUMAN	L	45	ENSP00000264387:S45L;ENSP00000387149:S45L	ENSP00000264387:S45L	S	-	2	0	C2orf83	228201455	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.928000	0.00332	-0.756000	0.04703	-0.751000	0.03497	TCG	G|0.709;A|0.291	0.291	strong		0.453	C2orf83-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331607.1	NM_020161	
TRIP6	7205	hgsc.bcm.edu	37	7	100468284	100468284	+	Silent	SNP	A	A	G	rs1054391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100468284A>G	ENST00000200457.4	+	6	1278	c.918A>G	c.(916-918)gtA>gtG	p.V306V		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	306	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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)					GCTGCTTTGTATGTTCTACAT	0.627													G|||	2805	0.560104	0.3585	0.6513	5008	,	,		17643	0.8095		0.5149	False		,,,				2504	0.5573				p.V306V		Atlas-SNP	.											TRIP6,colon,carcinoma,0,1	TRIP6	45	1	0			c.A918G						PASS	.	G		1745,2661	648.6+/-398.7	325,1095,783	171.0	149.0	156.0		918	4.9	1.0	7	dbSNP_86	156	4501,4099	560.6+/-387.6	1220,2061,1019	no	coding-synonymous	TRIP6	NM_003302.2		1545,3156,1802	GG,GA,AA		47.6628,39.6051,48.024		306/477	100468284	6246,6760	2203	4300	6503	SO:0001819	synonymous_variant	7205	exon6			CTTTGTATGTTCT	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.918A>G	7.37:g.100468284A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	183	183	1	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Silent	SNP	ENST00000200457.4	37	CCDS5708.1	1254	0.5741758241758241	177	0.3597560975609756	225	0.6215469613259669	462	0.8076923076923077	390	0.5145118733509235	g	11.14	1.550900	0.27739	0.396051	0.523372	ENSG00000087077	ENST00000429658	.	.	.	5.79	4.91	0.64330	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22941	-1.0202	3	.	.	.	.	8.0257	0.30436	0.1038:0.4175:0.4787:0.0	rs1054391;rs3173641;rs17849646;rs61138970;rs1054391	.	.	.	C	80	.	.	Y	+	2	0	TRIP6	100306220	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.009000	0.29886	0.806000	0.34183	-0.142000	0.14014	TAT	A|0.482;G|0.518	0.518	strong		0.627	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302	
MACROD2	140733	hgsc.bcm.edu	37	20	14066276	14066276	+	Missense_Mutation	SNP	C	C	T	rs2990505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:14066276C>T	ENST00000310348.4	+	3	173	c.173C>T	c.(172-174)aCt>aTt	p.T58I	MACROD2_ENST00000217246.4_Missense_Mutation_p.T58I			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	58			T -> I (in dbSNP:rs2990505). {ECO:0000269|PubMed:14702039}.		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)	p.T58I(1)		breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				GAAGAAAATACTCAGGAAACA	0.313													C|||	1291	0.257788	0.3056	0.2983	5008	,	,		12783	0.1895		0.2346	False		,,,				2504	0.2587				p.T58I		Atlas-SNP	.											C20orf133,NS,carcinoma,0,1	MACROD2	34	1	1	Substitution - Missense(1)	stomach(1)	c.C173T						scavenged	.	C	ILE/THR	1061,2531		162,737,897	59.0	54.0	55.0		173	4.8	1.0	20	dbSNP_101	55	1704,6412		192,1320,2546	yes	missense	MACROD2	NM_080676.5	89	354,2057,3443	TT,TC,CC		20.9956,29.5379,23.6163	benign	58/426	14066276	2765,8943	1796	4058	5854	SO:0001583	missense	140733	exon3			AAAATACTCAGGA	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.173C>T	20.37:g.14066276C>T	ENSP00000309809:p.Thr58Ile	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	109	44	0.40367	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	542	0.24816849816849818	158	0.32113821138211385	98	0.27071823204419887	114	0.1993006993006993	172	0.22691292875989447	C	12.51	1.960781	0.34565	0.295379	0.209956	ENSG00000172264	ENST00000217246;ENST00000310348	T;T	0.39997	1.05;1.05	5.76	4.81	0.61882	.	1.553840	0.03488	N	0.216141	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	0.9999999999999948	B;B	0.26975	0.099;0.165	B;B	0.30105	0.015;0.111	T	0.06826	-1.0805	9	0.48119	T	0.1	0.6917	12.9468	0.58376	0.0:0.9198:0.0:0.0802	rs2990505;rs52812396;rs59845301;rs2990505	58;58	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	I	58	ENSP00000217246:T58I;ENSP00000309809:T58I	ENSP00000217246:T58I	T	+	2	0	MACROD2	14014276	0.996000	0.38824	0.985000	0.45067	0.976000	0.68499	2.427000	0.44740	2.724000	0.93272	0.585000	0.79938	ACT	C|0.749;T|0.251	0.251	strong		0.313	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	
MRPS27	23107	hgsc.bcm.edu	37	5	71519664	71519664	+	Missense_Mutation	SNP	C	C	T	rs3209157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71519664C>T	ENST00000261413.5	-	10	890	c.851G>A	c.(850-852)gGt>gAt	p.G284D	MRPS27_ENST00000457646.4_Missense_Mutation_p.G228D|MRPS27_ENST00000513900.1_Missense_Mutation_p.G298D|MRPS27_ENST00000522562.1_5'UTR	NM_015084.2	NP_055899.2	Q92552	RT27_HUMAN	mitochondrial ribosomal protein S27	284			G -> D (polymorphism confirmed at protein level; dbSNP:rs3209157). {ECO:0000269|PubMed:17488105, ECO:0000269|PubMed:9039502}.			mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)		CAGCACTGCACCCAGCACATC	0.502													T|||	1332	0.265974	0.3147	0.1974	5008	,	,		17501	0.0218		0.4056	False		,,,				2504	0.3569				p.G284D		Atlas-SNP	.											MRPS27,NS,neuroblastoma,-1,1	MRPS27	23	1	0			c.G851A						scavenged	.	T	ASP/GLY	1455,2951	680.1+/-403.8	257,941,1005	64.0	63.0	63.0		851	6.2	0.8	5	dbSNP_105	63	3202,5398	652.1+/-400.9	617,1968,1715	yes	missense	MRPS27	NM_015084.2	94	874,2909,2720	TT,TC,CC		37.2326,33.0232,35.8066	benign	284/415	71519664	4657,8349	2203	4300	6503	SO:0001583	missense	23107	exon10			ACTGCACCCAGCA	D87453	CCDS4013.1, CCDS68890.1, CCDS75257.1	5q13.2	2012-09-13			ENSG00000113048	ENSG00000113048		"""Mitochondrial ribosomal proteins / small subunits"""	14512	protein-coding gene	gene with protein product		611989					Standard	NM_015084		Approved	KIAA0264	uc003kbz.4	Q92552	OTTHUMG00000100951	ENST00000261413.5:c.851G>A	5.37:g.71519664C>T	ENSP00000261413:p.Gly284Asp	Somatic	101	2	0.019802		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_015084	B4DRT2|Q6P1S1	Missense_Mutation	SNP	ENST00000261413.5	37	CCDS4013.1	548	0.2509157509157509	141	0.2865853658536585	76	0.20994475138121546	9	0.015734265734265736	322	0.42480211081794195	T	0.020	-1.444956	0.01089	0.330232	0.372326	ENSG00000113048	ENST00000261413;ENST00000457646;ENST00000513900;ENST00000508863	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	6.16	6.16	0.99307	.	0.384491	0.32785	N	0.005656	T	0.00012	0.0000	N	0.00500	-1.43	0.09310	P	0.9999999999636834	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.42916	-0.9423	9	0.13470	T	0.59	-7.2913	7.8391	0.29387	0.0:0.0691:0.1375:0.7933	rs3209157;rs11557157;rs17375461;rs17410278;rs52791834;rs17375461	298;65;284	B4DRT2;E7ETN4;Q92552	.;.;RT27_HUMAN	D	284;228;298;228	ENSP00000261413:G284D;ENSP00000428120:G228D;ENSP00000426941:G298D;ENSP00000426176:G228D	ENSP00000261413:G284D	G	-	2	0	MRPS27	71555420	0.970000	0.33590	0.774000	0.31636	0.002000	0.02628	1.751000	0.38339	1.152000	0.42452	-0.269000	0.10298	GGT	T|0.258;G|0.146	0.258	strong		0.502	MRPS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218560.2	NM_015084	
MOB3A	126308	hgsc.bcm.edu	37	19	2078409	2078409	+	Silent	SNP	A	A	G	rs2074893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2078409A>G	ENST00000357066.3	-	3	530	c.151T>C	c.(151-153)Ttg>Ctg	p.L51L	MOB3A_ENST00000592280.1_Silent_p.L51L|MOB3A_ENST00000592143.1_Intron	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	51						intracellular (GO:0005622)	metal ion binding (GO:0046872)										CCCGGGGGCAACTGCACGGCC	0.652													G|||	2042	0.407748	0.6702	0.2579	5008	,	,		14489	0.1964		0.3618	False		,,,				2504	0.4243				p.L51L		Atlas-SNP	.											.	.	.	.	0			c.T151C						PASS	.	G		2808,1598	493.4+/-362.7	898,1012,293	53.0	56.0	55.0		151	2.0	1.0	19	dbSNP_96	55	2976,5624	664.4+/-402.2	523,1930,1847	no	coding-synonymous	MOB3A	NM_130807.2		1421,2942,2140	GG,GA,AA		34.6047,36.2687,44.4718		51/218	2078409	5784,7222	2203	4300	6503	SO:0001819	synonymous_variant	126308	exon3			GGGGCAACTGCAC	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.151T>C	19.37:g.2078409A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			A|0.578;G|0.422	0.422	strong		0.652	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
IGSF3	3321	hgsc.bcm.edu	37	1	117146319	117146319	+	Silent	SNP	C	C	T	rs61730486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117146319C>T	ENST00000369486.3	-	6	2316	c.1551G>A	c.(1549-1551)gtG>gtA	p.V517V	IGSF3_ENST00000318837.6_Silent_p.V537V|IGSF3_ENST00000369483.1_Silent_p.V537V	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	517	Ig-like C2-type 4.				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)		CCACTGCCCGCACCCATTCAG	0.607													C|||	267	0.0533147	0.1157	0.0115	5008	,	,		16536	0.0635		0.0	False		,,,				2504	0.0429				p.V537V		Atlas-SNP	.											.	IGSF3	294	.	0			c.G1611A						PASS	.	C	,	408,3998	202.5+/-225.2	11,386,1806	63.0	55.0	58.0		1551,1611	2.0	1.0	1	dbSNP_129	58	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous,coding-synonymous	IGSF3	NM_001007237.1,NM_001542.2	,	11,394,6098	TT,TC,CC		0.093,9.2601,3.1985	,	517/1195,537/1215	117146319	416,12590	2203	4300	6503	SO:0001819	synonymous_variant	3321	exon7			TGCCCGCACCCAT	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.1551G>A	1.37:g.117146319C>T		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	200	105	0.525	NM_001542	A6NJZ6|A6NMC7	Silent	SNP	ENST00000369486.3	37	CCDS30813.1																																																																																			C|0.965;T|0.035	0.035	strong		0.607	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
NEB	4703	hgsc.bcm.edu	37	2	152518847	152518847	+	Silent	SNP	G	G	A	rs77547727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152518847G>A	ENST00000172853.10	-	46	5919	c.5772C>T	c.(5770-5772)taC>taT	p.Y1924Y	NEB_ENST00000603639.1_Silent_p.Y1924Y|NEB_ENST00000409198.1_Silent_p.Y1924Y|NEB_ENST00000604864.1_Silent_p.Y1924Y|NEB_ENST00000397345.3_Silent_p.Y1924Y|NEB_ENST00000427231.2_Silent_p.Y1924Y			P20929	NEBU_HUMAN	nebulin	1924					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)		AGTCAGCCTTGTACTGATTCT	0.398													G|||	135	0.0269569	0.034	0.0043	5008	,	,		17232	0.0843		0.001	False		,,,				2504	0.001				p.Y1924Y		Atlas-SNP	.											.	NEB	1697	.	0			c.C5772T						PASS	.	G	,,	101,3589		0,101,1744	84.0	80.0	81.0		5772,5772,5772	3.0	1.0	2	dbSNP_132	81	3,8185		0,3,4091	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	0,104,5835	AA,AG,GG		0.0366,2.7371,0.8756	,,	1924/8526,1924/8526,1924/6670	152518847	104,11774	1845	4094	5939	SO:0001819	synonymous_variant	4703	exon46			AGCCTTGTACTGA	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.5772C>T	2.37:g.152518847G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				G|0.971;A|0.029	0.029	strong		0.398	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
TEX2	55852	hgsc.bcm.edu	37	17	62291105	62291105	+	Missense_Mutation	SNP	G	G	A	rs28605685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62291105G>A	ENST00000583097.1	-	2	645	c.473C>T	c.(472-474)aCc>aTc	p.T158I	TEX2_ENST00000584379.1_Missense_Mutation_p.T158I|TEX2_ENST00000258991.3_Missense_Mutation_p.T158I			Q8IWB9	TEX2_HUMAN	testis expressed 2	158			T -> I (in dbSNP:rs28605685).		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)		GGAAGAACTGGTTTTCTGCTC	0.527													G|||	349	0.0696885	0.2481	0.0303	5008	,	,		19789	0.0		0.0	False		,,,				2504	0.0				p.T158I		Atlas-SNP	.											.	TEX2	89	.	0			c.C473T						PASS	.	G	ILE/THR	921,3485	353.1+/-312.0	101,719,1383	72.0	67.0	69.0		473	5.8	1.0	17	dbSNP_125	69	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TEX2	NM_018469.3	89	101,722,5680	AA,AG,GG		0.0349,20.9033,7.1044	probably-damaging	158/1135	62291105	924,12082	2203	4300	6503	SO:0001583	missense	55852	exon2			GAACTGGTTTTCT	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.473C>T	17.37:g.62291105G>A	ENSP00000462665:p.Thr158Ile	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	37		117	0.05357142857142857	104	0.21138211382113822	13	0.03591160220994475	0	0.0	0	0.0	G	11.37	1.618083	0.28801	0.209033	3.49E-4	ENSG00000136478	ENST00000258991	T	0.50001	0.76	5.82	5.82	0.92795	.	0.186533	0.44902	D	0.000409	T	0.00039	0.0001	N	0.14661	0.345	0.22771	P	0.99875152	D;P	0.53462	0.96;0.933	P;B	0.48795	0.59;0.386	T	0.02161	-1.1203	9	0.52906	T	0.07	-18.3683	20.1054	0.97890	0.0:0.0:1.0:0.0	rs28605685	158;158	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	I	158	ENSP00000258991:T158I	ENSP00000258991:T158I	T	-	2	0	TEX2	59644837	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	4.538000	0.60650	2.757000	0.94681	0.655000	0.94253	ACC	G|0.937;A|0.063	0.063	strong		0.527	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469	
MUC17	140453	hgsc.bcm.edu	37	7	100679754	100679754	+	Missense_Mutation	SNP	C	C	G	rs4992073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100679754C>G	ENST00000306151.4	+	3	5121	c.5057C>G	c.(5056-5058)aCt>aGt	p.T1686S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1686	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)					TCAACTTATACTGAAGGAAGA	0.468																																					p.T1686S		Atlas-SNP	.											.	MUC17	804	.	0			c.C5057G						PASS	.						191.0	206.0	201.0					7																	100679754		2203	4300	6503	SO:0001583	missense	140453	exon3			CTTATACTGAAGG	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.5057C>G	7.37:g.100679754C>G	ENSP00000302716:p.Thr1686Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	119	39	0.327731	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.307	-0.970357	0.02232	.	.	ENSG00000169876	ENST00000306151	T	0.01963	4.53	0.932	-1.86	0.07760	.	.	.	.	.	T	0.00845	0.0028	N	0.02539	-0.55	0.09310	N	1	B	0.20261	0.043	B	0.08055	0.003	T	0.46062	-0.9218	9	0.05436	T	0.98	.	6.7353	0.23405	0.0:0.4292:0.5708:0.0	rs4992073	1686	Q685J3	MUC17_HUMAN	S	1686	ENSP00000302716:T1686S	ENSP00000302716:T1686S	T	+	2	0	MUC17	100466474	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.458000	0.06737	-0.486000	0.06744	-3.678000	0.00024	ACT	C|0.973;G|0.027	0.027	strong		0.468	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ATHL1	80162	hgsc.bcm.edu	37	11	293188	293188	+	Silent	SNP	T	T	C	rs12801980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:293188T>C	ENST00000409548.2	+	8	1411	c.1296T>C	c.(1294-1296)caT>caC	p.H432H	ATHL1_ENST00000409655.1_Silent_p.H255H|ATHL1_ENST00000409479.1_Silent_p.H459H	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	432					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		ACGAGTACCATTCAGGGGTCA	0.602													t|||	2007	0.400759	0.3585	0.3718	5008	,	,		14854	0.3998		0.3668	False		,,,				2504	0.5143				p.H432H		Atlas-SNP	.											.	ATHL1	88	.	0			c.T1296C						PASS	.	T		1434,2972	466.4+/-354.5	245,944,1014	236.0	205.0	216.0		1296	-4.6	0.0	11	dbSNP_121	216	2969,5631	461.2+/-365.4	510,1949,1841	no	coding-synonymous	ATHL1	NM_025092.4		755,2893,2855	CC,CT,TT		34.5233,32.5465,33.8536		432/738	293188	4403,8603	2203	4300	6503	SO:0001819	synonymous_variant	80162	exon8			GTACCATTCAGGG	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.1296T>C	11.37:g.293188T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																			C|0.344;N|0.000	0.344	strong		0.602	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
PIK3R5	23533	hgsc.bcm.edu	37	17	8790473	8790473	+	Silent	SNP	G	G	A	rs61761067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8790473G>A	ENST00000447110.1	-	12	1969	c.1845C>T	c.(1843-1845)gaC>gaT	p.D615D	PIK3R5_ENST00000581552.1_Silent_p.D615D|PIK3R5_ENST00000584803.1_Silent_p.D615D	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	615					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						CATACCAGGGGTCCAGCATGC	0.607													G|||	159	0.0317492	0.1135	0.0101	5008	,	,		20471	0.0		0.002	False		,,,				2504	0.0				p.D615D	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.C1845T						PASS	.	G	,	436,3970	211.2+/-231.4	16,404,1783	155.0	111.0	126.0		1845,1845	2.8	1.0	17	dbSNP_129	126	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	16,411,6076	AA,AG,GG		0.0814,9.8956,3.4061	,	615/881,615/881	8790473	443,12563	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon12			CCAGGGGTCCAGC	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.1845C>T	17.37:g.8790473G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	201	109	0.542289	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			G|0.969;A|0.031	0.031	strong		0.607	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
RIMBP3B	440804	hgsc.bcm.edu	37	22	21742598	21742598	+	Missense_Mutation	SNP	G	G	A	rs468931		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21742598G>A	ENST00000434111.1	+	1	4936	c.4451G>A	c.(4450-4452)aGg>aAg	p.R1484K	SCARNA18_ENST00000516505.1_RNA|SCARNA17_ENST00000516211.1_RNA|RN7SKP63_ENST00000363187.1_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	911	0	0		WXS	Illumina HiSeq	Phase_I	988	205	0.20749	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	
ASXL1	171023	hgsc.bcm.edu	37	20	31022480	31022480	+	Silent	SNP	C	C	T	rs79865730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31022480C>T	ENST00000375687.4	+	13	2389	c.1965C>T	c.(1963-1965)acC>acT	p.T655T	ASXL1_ENST00000306058.5_Silent_p.T650T	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	655	Gly-rich.|Interaction with NCOA1. {ECO:0000250}.				bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.T639_G659>PPWD(1)|p.A640_S664>PCSGG(1)|p.T655fs*8(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						GCGGGGCCACCGATGAGGGAG	0.701			"""F, N, Mis"""		"""MDS, CMML"""								C|||	39	0.00778754	0.025	0.0043	5008	,	,		12008	0.0		0.003	False		,,,				2504	0.0				p.T655T		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	3	Complex - deletion inframe(2)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(3)	c.C1965T						PASS	.	C		53,4213		1,51,2081	8.0	9.0	9.0		1965	1.2	1.0	20	dbSNP_131	9	2,8376		0,2,4187	no	coding-synonymous	ASXL1	NM_015338.5		1,53,6268	TT,TC,CC		0.0239,1.2424,0.435		655/1542	31022480	55,12589	2133	4189	6322	SO:0001819	synonymous_variant	171023	exon12			GGCCACCGATGAG	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.1965C>T	20.37:g.31022480C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	54	33	0.611111	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	37	CCDS13201.1																																																																																			C|0.993;T|0.007	0.007	strong		0.701	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026122	176026122	+	Silent	SNP	C	C	T	rs142779818|rs550332435|rs3797464|rs371149640|rs386695335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176026122C>T	ENST00000303991.4	-	2	891	c.714G>A	c.(712-714)ttG>ttA	p.L238L		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	238				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCACCTTTCTCAAAGACCCAG	0.488																																					p.L238L		Atlas-SNP	.											GPRIN1,rectum,carcinoma,-1,2	GPRIN1	77	2	0			c.G714A						scavenged	.						90.0	94.0	93.0					5																	176026122		2171	4246	6417	SO:0001819	synonymous_variant	114787	exon2			CTTTCTCAAAGAC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.714G>A	5.37:g.176026122C>T		Somatic	101	22	0.217822		WXS	Illumina HiSeq	Phase_I	102	26	0.254902	NM_052899	C9JM70|Q8ND74|Q96PZ4	Silent	SNP	ENST00000303991.4	37	CCDS4405.1																																																																																			.	.	weak		0.488	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
TRDMT1	1787	hgsc.bcm.edu	37	10	17204187	17204187	+	Missense_Mutation	SNP	G	G	A	rs11254413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:17204187G>A	ENST00000377799.3	-	4	348	c.301C>T	c.(301-303)Cat>Tat	p.H101Y	TRDMT1_ENST00000351358.4_Intron|TRDMT1_ENST00000377766.5_Intron|TRDMT1_ENST00000488990.1_Intron|TRDMT1_ENST00000412821.3_Intron|TRDMT1_ENST00000452380.2_5'UTR|TRDMT1_ENST00000457442.2_Missense_Mutation_p.H42Y|TRDMT1_ENST00000358282.7_Intron	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	101	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.		H -> Y (in dbSNP:rs11254413). {ECO:0000269|PubMed:15489334}.		C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	TCTAGAATATGTAAGAAGCTA	0.348													A|||	1928	0.384984	0.4039	0.4265	5008	,	,		15672	0.2599		0.494	False		,,,				2504	0.3466				p.H101Y		Atlas-SNP	.											.	TRDMT1	46	.	0			c.C301T						PASS	.	A	TYR/HIS	1898,2508	625.3+/-394.5	417,1064,722	125.0	135.0	132.0		301	-2.2	0.4	10	dbSNP_120	132	3897,4703	605.4+/-394.9	894,2109,1297	yes	missense	TRDMT1	NM_004412.5	83	1311,3173,2019	AA,AG,GG		45.314,43.0776,44.5564	benign	101/392	17204187	5795,7211	2203	4300	6503	SO:0001583	missense	1787	exon4			GAATATGTAAGAA	AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"""DNA (cytosine-5-)-methyltransferase 2"""	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.301C>T	10.37:g.17204187G>A	ENSP00000367030:p.His101Tyr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	96	34	0.354167	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Missense_Mutation	SNP	ENST00000377799.3	37	CCDS7114.1	846	0.3873626373626374	180	0.36585365853658536	157	0.43370165745856354	147	0.256993006993007	362	0.47757255936675463	A	0.023	-1.403758	0.01165	0.430776	0.45314	ENSG00000107614	ENST00000377799;ENST00000457442	D;T	0.83837	-1.77;0.96	6.07	-2.15	0.07102	.	0.270142	0.43579	N	0.000550	T	0.00012	0.0000	N	0.16066	0.365	0.28965	P	0.889615	B;B	0.14805	0.0;0.011	B;B	0.24541	0.001;0.054	T	0.19192	-1.0313	9	0.06625	T	0.88	-4.2663	13.9397	0.64048	0.5764:0.0:0.4236:0.0	rs11254413;rs17857339;rs52789833;rs11254413	42;101	E7EMI8;O14717	.;TRDMT_HUMAN	Y	101;42	ENSP00000367030:H101Y;ENSP00000412256:H42Y	ENSP00000367030:H101Y	H	-	1	0	TRDMT1	17244193	0.130000	0.22417	0.408000	0.26446	0.422000	0.31414	0.633000	0.24598	-0.550000	0.06183	-1.036000	0.02392	CAT	G|0.579;A|0.421	0.421	strong		0.348	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412	
GANC	2595	hgsc.bcm.edu	37	15	42585099	42585099	+	Missense_Mutation	SNP	A	A	G	rs16973015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42585099A>G	ENST00000318010.8	+	5	736	c.496A>G	c.(496-498)Att>Gtt	p.I166V	GANC_ENST00000566442.1_Missense_Mutation_p.I166V	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	166			I -> V (in dbSNP:rs16973015).		carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	GCATCTACAGATTCTTCACAA	0.363													A|||	64	0.0127796	0.0212	0.0058	5008	,	,		20822	0.0		0.008	False		,,,				2504	0.0245				p.I166V		Atlas-SNP	.											.	GANC	57	.	0			c.A496G						PASS	.	A	VAL/ILE	63,4343	59.9+/-96.7	0,63,2140	128.0	123.0	125.0		496	0.4	0.9	15	dbSNP_123	125	39,8559	26.8+/-75.7	0,39,4260	yes	missense	GANC	NM_198141.2	29	0,102,6400	GG,GA,AA		0.4536,1.4299,0.7844	benign	166/915	42585099	102,12902	2203	4299	6502	SO:0001583	missense	2595	exon5			CTACAGATTCTTC	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.496A>G	15.37:g.42585099A>G	ENSP00000326227:p.Ile166Val	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	170	99	0.582353	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Missense_Mutation	SNP	ENST00000318010.8	37	CCDS10084.1	22	0.010073260073260074	13	0.026422764227642278	4	0.011049723756906077	0	0.0	5	0.006596306068601583	A	2.471	-0.321955	0.05386	0.014299	0.004536	ENSG00000214013	ENST00000318010	T	0.15487	2.42	5.27	0.387	0.16259	Glycoside hydrolase-type carbohydrate-binding (1);	1.002620	0.08037	N	0.994447	T	0.02342	0.0072	N	0.08118	0	0.19575	N	0.999961	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40553	-0.9557	10	0.25106	T	0.35	-0.2169	5.5278	0.16967	0.4019:0.2069:0.3911:0.0	rs16973015;rs52796001;rs16973015	166;166	Q8TET4;Q2M2A3	GANC_HUMAN;.	V	166	ENSP00000326227:I166V	ENSP00000326227:I166V	I	+	1	0	GANC	40372391	0.078000	0.21339	0.939000	0.37840	0.098000	0.18820	0.247000	0.18179	-0.089000	0.12484	0.528000	0.53228	ATT	A|0.989;G|0.011	0.011	strong		0.363	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
AHNAK2	113146	hgsc.bcm.edu	37	14	105410183	105410183	+	Missense_Mutation	SNP	T	T	C	rs10438246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105410183T>C	ENST00000333244.5	-	7	11724	c.11605A>G	c.(11605-11607)Atg>Gtg	p.M3869V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3869			M -> V (in dbSNP:rs10438246).			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)			AGGAGTTTCATGTCCACCTGG	0.602													.|||	2784	0.555911	0.643	0.5144	5008	,	,		18090	0.4127		0.5348	False		,,,				2504	0.637				p.M3869V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A11605G						PASS	.	C	VAL/MET	2678,1266		920,838,214	130.0	137.0	135.0		11605	-2.0	0.0	14	dbSNP_119	135	4528,3782		1252,2024,879	yes	missense	AHNAK2	NM_138420.2	21	2172,2862,1093	CC,CT,TT		45.5114,32.0994,41.1947	benign	3869/5796	105410183	7206,5048	1972	4155	6127	SO:0001583	missense	113146	exon7			GTTTCATGTCCAC	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.11605A>G	14.37:g.105410183T>C	ENSP00000353114:p.Met3869Val	Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	254	254	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1148	0.5256410256410257	324	0.6585365853658537	200	0.5524861878453039	222	0.3881118881118881	402	0.5303430079155673	t	0.010	-1.780679	0.00634	0.679006	0.544886	ENSG00000185567	ENST00000333244	T	0.00882	5.58	3.67	-2.03	0.07365	.	.	.	.	.	T	0.00012	0.0000	N	0.00985	-1.075	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.01834	-1.1264	8	0.12430	T	0.62	.	6.3549	0.21397	0.0:0.5117:0.1168:0.3714	rs10438246;rs59225031;rs10438246	3869	Q8IVF2	AHNK2_HUMAN	V	3869	ENSP00000353114:M3869V	ENSP00000353114:M3869V	M	-	1	0	AHNAK2	104481228	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.234000	0.00546	-0.909000	0.03852	-2.717000	0.00132	ATG	T|0.456;C|0.544	0.544	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
NUP98	4928	hgsc.bcm.edu	37	11	3714489	3714489	+	Silent	SNP	C	C	T	rs1875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:3714489C>T	ENST00000324932.7	-	27	4704	c.4284G>A	c.(4282-4284)gcG>gcA	p.A1428A	NUP98_ENST00000359171.4_Silent_p.A1428A|NUP98_ENST00000355260.3_Silent_p.A1428A|NUP98_ENST00000488828.1_5'Flank|snoU13_ENST00000458786.1_RNA	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1445					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|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)|nuclear pore organization (GO:0006999)|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)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		ACATGCTGAGCGCCCTAGAAA	0.448			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML								C|||	1381	0.275759	0.3608	0.0965	5008	,	,		17398	0.3185		0.1938	False		,,,				2504	0.3282				p.A1428A		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.G4284A						PASS	.	C	,	1444,2958	470.0+/-355.6	241,962,998	163.0	163.0	163.0		4284,4284	-4.2	1.0	11	dbSNP_36	163	1465,7131	279.7+/-294.1	138,1189,2971	no	coding-synonymous,coding-synonymous	NUP98	NM_016320.4,NM_139132.3	,	379,2151,3969	TT,TC,CC		17.0428,32.8033,22.3804	,	1428/1801,1428/1727	3714489	2909,10089	2201	4298	6499	SO:0001819	synonymous_variant	4928	exon27			GCTGAGCGCCCTA	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.4284G>A	11.37:g.3714489C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	76	29	0.381579	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Silent	SNP	ENST00000324932.7	37	CCDS7746.1	546	0.25	178	0.3617886178861789	38	0.10497237569060773	186	0.32517482517482516	144	0.18997361477572558	C	10.09	1.253636	0.22965	0.328033	0.170428	ENSG00000110713	ENST00000429801	.	.	.	5.65	-4.15	0.03881	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.30851	-0.9964	5	0.62326	D	0.03	-17.5027	0.5337	0.00633	0.382:0.1448:0.1736:0.2996	rs1875;rs3740668;rs17173889;rs58248468;rs1875	.	.	.	T	381	.	ENSP00000413146:A381T	A	-	1	0	NUP98	3671065	0.410000	0.25376	0.989000	0.46669	0.919000	0.55068	-0.501000	0.06398	-0.463000	0.06973	-1.397000	0.01146	GCT	C|0.757;N|0.000	.	strong		0.448	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
SSPO	23145	hgsc.bcm.edu	37	7	149486367	149486367	+	RNA	SNP	C	C	A	rs855692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149486367C>A	ENST00000378016.2	+	0	4343							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)			ACGGATGAGCCGAGCTATCCG	0.687													A|||	158	0.0315495	0.1029	0.0115	5008	,	,		16290	0.004		0.0	False		,,,				2504	0.0102				p.P1448Q		Atlas-SNP	.											.	.	.	.	0			c.C4343A						PASS	.	A		317,4079		13,291,1894	24.0	28.0	27.0		4347	0.9	0.5	7	dbSNP_86	27	5,8583		0,5,4289	yes	coding-notMod3	SSPO	NM_198455.2		13,296,6183	AA,AC,CC		0.0582,7.2111,2.48			149486367	322,12662	2198	4294	6492			23145	exon30			ATGAGCCGAGCTA	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.149486367C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	87	47	0.54023	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.968;A|0.032	0.032	strong		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
NIM1K	167359	hgsc.bcm.edu	37	5	43245922	43245922	+	Silent	SNP	C	C	T	rs13176855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:43245922C>T	ENST00000512796.1	+	2	1544	c.45C>T	c.(43-45)caC>caT	p.H15H	NIM1_ENST00000326035.2_Silent_p.H15H			Q8IY84	NIM1_HUMAN		15					protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)										TGAACCCCCACTATGCCCGGT	0.617													C|||	1439	0.28734	0.2905	0.2622	5008	,	,		20469	0.1409		0.4344	False		,,,				2504	0.3006				p.H15H		Atlas-SNP	.											.	.	.	.	0			c.C45T						PASS	.	C		1291,3115	437.0+/-344.8	196,899,1108	128.0	121.0	123.0		45	3.8	0.8	5	dbSNP_121	123	3631,4969	523.2+/-380.3	774,2083,1443	no	coding-synonymous	NIM1	NM_153361.2		970,2982,2551	TT,TC,CC		42.2209,29.301,37.8441		15/437	43245922	4922,8084	2203	4300	6503	SO:0001819	synonymous_variant	0	exon2			CCCCCACTATGCC																												ENST00000512796.1:c.45C>T	5.37:g.43245922C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	154	75	0.487013	NM_153361	B3KVM1	Silent	SNP	ENST00000512796.1	37	CCDS3943.1																																																																																			C|0.645;T|0.355	0.355	strong		0.617	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1		
ZNF717	100131827	hgsc.bcm.edu	37	3	75786748	75786748	+	Missense_Mutation	SNP	C	C	T	rs112332186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75786748C>T	ENST00000478296.1	-	4	2152	c.1876G>A	c.(1876-1878)Gat>Aat	p.D626N	ZNF717_ENST00000422325.1_Missense_Mutation_p.D676N|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.D669N|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	666					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TTCATTACATCCATACGGTTT	0.393																																					p.D676N		Atlas-SNP	.											.	ZNF717	160	.	0			c.G2026A						PASS	.						18.0	18.0	18.0					3																	75786748		627	1550	2177	SO:0001583	missense	100131827	exon5			TTACATCCATACG	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1876G>A	3.37:g.75786748C>T	ENSP00000419377:p.Asp626Asn	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	45	26	0.577778	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		1056	0.4835164835164835	175	0.3556910569105691	183	0.505524861878453	279	0.48776223776223776	419	0.5527704485488126	.	4.850	0.157969	0.09236	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.07327	3.2;3.2;3.2	1.57	-3.14	0.05250	.	.	.	.	.	T	0.00012	0.0000	N	0.00738	-1.235	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41270	-0.9518	8	0.49607	T	0.09	.	5.6215	0.17459	0.0:0.2842:0.5029:0.2129	.	676	C9JSV9	.	N	626;676;669	ENSP00000419377:D626N;ENSP00000409514:D676N;ENSP00000383643:D669N	ENSP00000383643:D669N	D	-	1	0	ZNF717	75869438	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.568000	0.02144	-2.019000	0.00942	-1.616000	0.00795	GAT	C|0.516;T|0.484	0.484	strong		0.393	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
OR10X1	128367	hgsc.bcm.edu	37	1	158549511	158549511	+	Missense_Mutation	SNP	A	A	G	rs863363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	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	
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53636000	53636000	+	Silent	SNP	G	G	A	rs4784320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53636000G>A	ENST00000379925.3	-	27	3986	c.3936C>T	c.(3934-3936)gaC>gaT	p.D1312D	RPGRIP1L_ENST00000262135.4_Silent_p.D1232D|RPGRIP1L_ENST00000563746.1_Silent_p.D1278D	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1312					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)				AAGCCTCCAAGTCATCTCTGT	0.448													G|||	585	0.116813	0.3389	0.0461	5008	,	,		17548	0.001		0.0298	False		,,,				2504	0.0757				p.D1312D		Atlas-SNP	.											RPGRIP1L,colon,carcinoma,0,1	RPGRIP1L	118	1	0			c.C3936T						PASS	.	G	,	1170,3226	411.9+/-335.9	162,846,1190	103.0	86.0	91.0		3696,3936	2.6	0.4	16	dbSNP_111	91	320,8280	112.7+/-172.9	6,308,3986	no	coding-synonymous,coding-synonymous	RPGRIP1L	NM_001127897.1,NM_015272.2	,	168,1154,5176	AA,AG,GG		3.7209,26.6151,11.4651	,	1232/1236,1312/1316	53636000	1490,11506	2198	4300	6498	SO:0001819	synonymous_variant	23322	exon27			CTCCAAGTCATCT		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.3936C>T	16.37:g.53636000G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	141	77	0.546099	NM_015272	A0PJ88|Q9Y2K8	Silent	SNP	ENST00000379925.3	37	CCDS32447.1																																																																																			G|0.889;A|0.111	0.111	strong		0.448	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
GABRG3	2567	hgsc.bcm.edu	37	15	27573968	27573968	+	Silent	SNP	T	T	C	rs140674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:27573968T>C	ENST00000333743.6	+	5	761	c.507T>C	c.(505-507)gcT>gcC	p.A169A	GABRG3_ENST00000555083.1_Silent_p.A169A	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	169					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)	CCATCAATGCTGAGTGCCAGC	0.602													C|||	745	0.148762	0.4017	0.0476	5008	,	,		19692	0.0635		0.0169	False		,,,				2504	0.1022				p.A169A	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.T507C						PASS	.	C		1375,2907		231,913,997	74.0	77.0	76.0		507	-10.7	0.0	15	dbSNP_78	76	134,8364		4,126,4119	no	coding-synonymous	GABRG3	NM_033223.4		235,1039,5116	CC,CT,TT		1.5768,32.1112,11.8075		169/468	27573968	1509,11271	2141	4249	6390	SO:0001819	synonymous_variant	2567	exon5			CAATGCTGAGTGC		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.507T>C	15.37:g.27573968T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	156	68	0.435897	NM_001270873	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1	271	0.12408424908424909	200	0.4065040650406504	23	0.06353591160220995	39	0.06818181818181818	9	0.011873350923482849	C	7.549	0.662224	0.14645	0.321112	0.015768	ENSG00000182256	ENST00000557596	.	.	.	5.35	-10.7	0.00240	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999908	.	.	.	.	.	.	T	0.33163	-0.9879	3	.	.	.	.	1.2369	0.01955	0.1779:0.3201:0.1976:0.3044	rs140674;rs4129457	.	.	.	P	2	.	.	L	+	2	0	GABRG3	25156714	0.000000	0.05858	0.039000	0.18376	0.662000	0.39071	-2.239000	0.01198	-2.502000	0.00509	-2.107000	0.00358	CTG	T|0.896;C|0.104	0.104	strong		0.602	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
AFP	174	hgsc.bcm.edu	37	4	74316461	74316461	+	Silent	SNP	C	C	T	rs115622472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:74316461C>T	ENST00000395792.2	+	11	1519	c.1419C>T	c.(1417-1419)ggC>ggT	p.G473G	AFP_ENST00000226359.2_Silent_p.G473G	NM_001134.1	NP_001125.1	P02771	FETA_HUMAN	alpha-fetoprotein	473	Albumin 3. {ECO:0000255|PROSITE- ProRule:PRU00769}.				ovulation from ovarian follicle (GO:0001542)|progesterone metabolic process (GO:0042448)|SMAD protein signal transduction (GO:0060395)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(3)|lung(13)|ovary(1)|skin(1)|urinary_tract(1)	22	Breast(15;0.00102)		Epithelial(6;2.42e-05)|all cancers(17;0.000268)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGGCCTGTGGCGAGGGAGCGG	0.522									Alpha-Fetoprotein, Hereditary Persistence of				C|||	22	0.00439297	0.0159	0.0014	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0				p.G473G		Atlas-SNP	.											.	AFP	60	.	0			c.C1419T						PASS	.	C		76,4330	67.6+/-105.2	0,76,2127	156.0	134.0	142.0		1419	-9.9	0.1	4	dbSNP_132	142	3,8597		0,3,4297	no	coding-synonymous	AFP	NM_001134.1		0,79,6424	TT,TC,CC		0.0349,1.7249,0.6074		473/610	74316461	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	174	exon11	Familial Cancer Database	HPAFP	CTGTGGCGAGGGA	V01514	CCDS3556.1	4q13.3	2012-05-16			ENSG00000081051	ENSG00000081051			317	protein-coding gene	gene with protein product		104150		HPAFP			Standard	NM_001134		Approved	FETA	uc003hgz.1	P02771	OTTHUMG00000130011	ENST00000395792.2:c.1419C>T	4.37:g.74316461C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	161	70	0.434783	NM_001134	B2RBU3	Silent	SNP	ENST00000395792.2	37	CCDS3556.1																																																																																			C|0.994;T|0.006	0.006	strong		0.522	AFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252284.3		
FRAS1	80144	hgsc.bcm.edu	37	4	79455714	79455714	+	Silent	SNP	C	C	G	rs4975070	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79455714C>G	ENST00000264895.6	+	71	11477	c.11037C>G	c.(11035-11037)ccC>ccG	p.P3679P		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3675					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						TAATGGATCCCAATACATCTG	0.448													C|||	2579	0.514976	0.3086	0.4395	5008	,	,		20789	0.7758		0.4632	False		,,,				2504	0.6319				p.P3679P		Atlas-SNP	.											.	FRAS1	779	.	0			c.C11037G						PASS	.	C		1279,2509		215,849,830	128.0	115.0	119.0		11037	3.2	1.0	4	dbSNP_111	119	3593,4649		791,2011,1319	no	coding-synonymous	FRAS1	NM_025074.6		1006,2860,2149	GG,GC,CC		43.5938,33.7645,40.4988		3679/4013	79455714	4872,7158	1894	4121	6015	SO:0001819	synonymous_variant	80144	exon71			GGATCCCAATACA	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.11037C>G	4.37:g.79455714C>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	1143	0.5233516483516484	172	0.34959349593495936	163	0.45027624309392267	453	0.791958041958042	355	0.4683377308707124	C	6.186	0.402486	0.11696	0.337645	0.435938	ENSG00000138759	ENST00000512123	.	.	.	5.05	3.2	0.36748	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33523	-0.9865	3	.	.	.	.	9.0976	0.36649	0.2536:0.6722:0.0:0.0741	rs4975070;rs61687904;rs4975070	.	.	.	E	1908	.	.	Q	+	1	0	FRAS1	79674738	0.997000	0.39634	1.000000	0.80357	0.777000	0.43975	0.493000	0.22451	2.336000	0.79503	0.591000	0.81541	CAA	C|0.485;G|0.515	0.515	strong		0.448	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CRY1	1407	hgsc.bcm.edu	37	12	107395106	107395106	+	Silent	SNP	A	A	G	rs8192440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:107395106A>G	ENST00000008527.5	-	5	1503	c.636T>C	c.(634-636)ggT>ggC	p.G212G		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	212					blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						CAGTTTCTCCACCTGGCCACA	0.348													G|||	3955	0.789736	0.857	0.7579	5008	,	,		17073	0.9554		0.6282	False		,,,				2504	0.7168				p.G212G		Atlas-SNP	.											CRY1,NS,carcinoma,-2,1	CRY1	74	1	0			c.T636C						PASS	.	G		3618,788	316.3+/-294.6	1494,630,79	100.0	103.0	102.0		636	-11.4	0.7	12	dbSNP_117	102	5367,3233	486.6+/-371.9	1642,2083,575	no	coding-synonymous	CRY1	NM_004075.3		3136,2713,654	GG,GA,AA		37.593,17.8847,30.9165		212/587	107395106	8985,4021	2203	4300	6503	SO:0001819	synonymous_variant	1407	exon5			TTCTCCACCTGGC	BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"""cryptochrome 1 (photolyase-like)"""	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.636T>C	12.37:g.107395106A>G		Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	267	128	0.479401	NM_004075		Silent	SNP	ENST00000008527.5	37	CCDS9112.1																																																																																			A|0.264;G|0.736	0.736	strong		0.348	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075	
FAM83B	222584	hgsc.bcm.edu	37	6	54805074	54805074	+	Missense_Mutation	SNP	C	C	G	rs9475076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:54805074C>G	ENST00000306858.7	+	5	1421	c.1305C>G	c.(1303-1305)agC>agG	p.S435R	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	435			S -> R (in dbSNP:rs9475076).							autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					GCTATGTAAGCCACCACAACA	0.448													C|||	288	0.057508	0.2088	0.0144	5008	,	,		18486	0.0		0.002	False		,,,				2504	0.0				p.S435R		Atlas-SNP	.											.	FAM83B	186	.	0			c.C1305G						PASS	.	C	ARG/SER	795,3611	321.0+/-296.9	67,661,1475	65.0	69.0	67.0		1305	0.8	0.0	6	dbSNP_119	67	16,8584	10.5+/-38.8	0,16,4284	yes	missense	FAM83B	NM_001010872.1	110	67,677,5759	GG,GC,CC		0.186,18.0436,6.2356	benign	435/1012	54805074	811,12195	2203	4300	6503	SO:0001583	missense	222584	exon5			TGTAAGCCACCAC	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.1305C>G	6.37:g.54805074C>G	ENSP00000304078:p.Ser435Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	110	54	0.490909	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	112	0.05128205128205128	105	0.21341463414634146	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	1.045	-0.677640	0.03378	0.180436	0.00186	ENSG00000168143	ENST00000306858	T	0.08546	3.08	5.56	0.802	0.18686	.	1.270360	0.05003	N	0.469411	T	0.02807	0.0084	L	0.47716	1.5	0.80722	P	0.0	P	0.34780	0.468	B	0.27500	0.08	T	0.43572	-0.9383	9	0.42905	T	0.14	-0.061	9.8787	0.41220	0.0:0.4374:0.0:0.5626	rs9475076;rs52793316;rs9475076	435	Q5T0W9	FA83B_HUMAN	R	435	ENSP00000304078:S435R	ENSP00000304078:S435R	S	+	3	2	FAM83B	54913033	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.071000	0.14594	-0.074000	0.12820	-0.137000	0.14449	AGC	C|0.945;G|0.055	0.055	strong		0.448	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
KERA	11081	hgsc.bcm.edu	37	12	91449990	91449990	+	Silent	SNP	C	C	T	rs2735333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:91449990C>T	ENST00000266719.3	-	2	316	c.69G>A	c.(67-69)gtG>gtA	p.V23V		NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan	23					carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						AGACCTGCCTCACACTTCTAG	0.423													C|||	3105	0.620008	0.2443	0.7046	5008	,	,		17837	0.7976		0.7962	False		,,,				2504	0.7035				p.V23V		Atlas-SNP	.											.	KERA	62	.	0			c.G69A						PASS	.	C		1534,2870	484.8+/-360.1	268,998,936	92.0	73.0	79.0		69	4.1	1.0	12	dbSNP_100	79	6699,1901	724.4+/-406.5	2613,1473,214	no	coding-synonymous	KERA	NM_007035.3		2881,2471,1150	TT,TC,CC		22.1047,34.832,36.6887		23/353	91449990	8233,4771	2202	4300	6502	SO:0001819	synonymous_variant	11081	exon2			CTGCCTCACACTT	AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	6309	protein-coding gene	gene with protein product	"""keratocan proteoglycan"""	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.69G>A	12.37:g.91449990C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	68	40	0.588235	NM_007035		Silent	SNP	ENST00000266719.3	37	CCDS9037.1																																																																																			C|0.364;T|0.636	0.636	strong		0.423	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035	
SLCO5A1	81796	hgsc.bcm.edu	37	8	70588878	70588878	+	Silent	SNP	T	T	C	rs10448034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	91	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	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	
KIAA0319	9856	hgsc.bcm.edu	37	6	24551729	24551729	+	Silent	SNP	T	T	C	rs807535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24551729T>C	ENST00000378214.3	-	20	3497	c.2973A>G	c.(2971-2973)aaA>aaG	p.K991K	KIAA0319_ENST00000430948.2_Silent_p.K946K|KIAA0319_ENST00000537886.1_Intron|KIAA0319_ENST00000543707.1_Silent_p.K991K|KIAA0319_ENST00000535378.1_Silent_p.K982K	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	991					negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						ACTTTGTTTTTTTCCTGATTT	0.403													T|||	488	0.0974441	0.0832	0.0951	5008	,	,		21561	0.0764		0.1272	False		,,,				2504	0.1094				p.K991K		Atlas-SNP	.											.	KIAA0319	117	.	0			c.A2973G						PASS	.	T	,,,,	415,3991	198.7+/-222.5	20,375,1808	319.0	261.0	281.0		2946,2973,2838,,2973	-9.1	0.1	6	dbSNP_86	281	1152,7448	233.0+/-266.5	75,1002,3223	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	KIAA0319	NM_001168374.1,NM_001168375.1,NM_001168376.1,NM_001168377.1,NM_014809.3	,,,,	95,1377,5031	CC,CT,TT		13.3953,9.419,12.0483	,,,,	982/1064,991/1073,946/1028,,991/1073	24551729	1567,11439	2203	4300	6503	SO:0001819	synonymous_variant	9856	exon20			TGTTTTTTTCCTG	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.2973A>G	6.37:g.24551729T>C		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	245	245	1	NM_001168375	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Silent	SNP	ENST00000378214.3	37	CCDS34348.1																																																																																			A|0.006;C|0.112	0.112	strong		0.403	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
BTN2A1	11120	hgsc.bcm.edu	37	6	26468319	26468319	+	Silent	SNP	C	C	T	rs3734541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26468319C>T	ENST00000312541.5	+	8	1374	c.1126C>T	c.(1126-1128)Cta>Tta	p.L376L	BTN2A1_ENST00000541522.1_Silent_p.L315L|BTN2A1_ENST00000429381.1_3'UTR|BTN2A1_ENST00000469185.1_Intron	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	376	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						GCCTTGTGTCCTAGGCCGGGA	0.567													C|||	714	0.142572	0.4312	0.0821	5008	,	,		22312	0.0427		0.0159	False		,,,				2504	0.0286				p.L376L		Atlas-SNP	.											.	BTN2A1	118	.	0			c.C1126T						PASS	.	C	,,,	1741,2665	521.9+/-370.6	356,1029,818	160.0	154.0	156.0		943,,1126,	2.0	0.9	6	dbSNP_107	156	120,8480	61.7+/-123.6	0,120,4180	no	coding-synonymous,intron,coding-synonymous,utr-3	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	,,,	356,1149,4998	TT,TC,CC		1.3953,39.5143,14.3088	,,,	315/467,,376/528,	26468319	1861,11145	2203	4300	6503	SO:0001819	synonymous_variant	11120	exon8			TGTGTCCTAGGCC	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.1126C>T	6.37:g.26468319C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Silent	SNP	ENST00000312541.5	37	CCDS4613.1																																																																																			C|0.870;T|0.130	0.130	strong		0.567	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
LRIG1	26018	hgsc.bcm.edu	37	3	66434643	66434643	+	Missense_Mutation	SNP	T	T	C	rs2306272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:66434643T>C	ENST00000273261.3	-	14	2367	c.1843A>G	c.(1843-1845)Atg>Gtg	p.M615V	LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000383703.3_Missense_Mutation_p.M639V	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	615	Ig-like C2-type 2.		M -> V (in dbSNP:rs2306272). {ECO:0000269|PubMed:11414704, ECO:0000269|PubMed:17974005}.		innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		AGGCGGGCCATGGTGGTGGTC	0.577													T|||	1814	0.36222	0.1513	0.2435	5008	,	,		17527	0.7341		0.2922	False		,,,				2504	0.4202				p.M615V		Atlas-SNP	.											.	LRIG1	138	.	0			c.A1843G						PASS	.	T	VAL/MET	637,3769	274.6+/-272.0	45,547,1611	192.0	184.0	186.0		1843	5.0	1.0	3	dbSNP_100	186	2358,6242	394.7+/-344.8	337,1684,2279	yes	missense	LRIG1	NM_015541.2	21	382,2231,3890	CC,CT,TT		27.4186,14.4576,23.0278	benign	615/1094	66434643	2995,10011	2203	4300	6503	SO:0001583	missense	26018	exon14			GGGCCATGGTGGT	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1843A>G	3.37:g.66434643T>C	ENSP00000273261:p.Met615Val	Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	337	159	0.47181	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	830	0.38003663003663	82	0.16666666666666666	106	0.292817679558011	418	0.7307692307692307	224	0.2955145118733509	T	8.389	0.839336	0.16891	0.144576	0.274186	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.65916	1.06;-0.18	6.17	5.0	0.66597	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.379169	0.31936	N	0.006822	T	0.00012	0.0000	N	0.05467	-0.045	0.34993	P	0.24476699999999996	B;B	0.13145	0.006;0.007	B;B	0.19666	0.015;0.026	T	0.37596	-0.9699	9	0.27082	T	0.32	.	12.8497	0.57850	0.1223:0.0:0.0:0.8776	rs2306272;rs52808080;rs59543444;rs2306272	639;615	Q96JA1-2;Q96JA1	.;LRIG1_HUMAN	V	615;639;518	ENSP00000273261:M615V;ENSP00000373208:M639V	ENSP00000273261:M615V	M	-	1	0	LRIG1	66517333	0.990000	0.36364	0.989000	0.46669	0.306000	0.27790	6.232000	0.72313	1.126000	0.42016	0.533000	0.62120	ATG	T|0.707;C|0.293	0.293	strong		0.577	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
NCLN	56926	hgsc.bcm.edu	37	19	3207422	3207422	+	Silent	SNP	T	T	C	rs3816054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3207422T>C	ENST00000246117.4	+	14	2018	c.1587T>C	c.(1585-1587)gcT>gcC	p.A529A	NCLN_ENST00000590671.1_Silent_p.A455A	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	529					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)		TGCTCCTGGCTGTTGGCATTG	0.662													C|||	1337	0.266973	0.3525	0.1772	5008	,	,		16588	0.4097		0.0656	False		,,,				2504	0.2751				p.A529A		Atlas-SNP	.											.	NCLN	27	.	0			c.T1587C						PASS	.	C		1323,3083	690.7+/-405.3	208,907,1088	126.0	120.0	122.0		1587	-3.8	0.4	19	dbSNP_107	122	408,8192	795.4+/-407.5	10,388,3902	no	coding-synonymous	NCLN	NM_020170.3		218,1295,4990	CC,CT,TT		4.7442,30.0272,13.3092		529/564	3207422	1731,11275	2203	4300	6503	SO:0001819	synonymous_variant	56926	exon14			CCTGGCTGTTGGC	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.1587T>C	19.37:g.3207422T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_020170	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Silent	SNP	ENST00000246117.4	37	CCDS32869.1																																																																																			T|0.820;C|0.180	0.180	strong		0.662	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1	NM_020170	
MED12L	116931	hgsc.bcm.edu	37	3	151082923	151082923	+	Silent	SNP	T	T	C	rs1463725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151082923T>C	ENST00000474524.1	+	20	3047	c.3009T>C	c.(3007-3009)aaT>aaC	p.N1003N	P2RY12_ENST00000302632.3_Intron|MED12L_ENST00000273432.4_Silent_p.N863N	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1003						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)			TCAGTGACAATGCGGCCAATC	0.483													T|||	961	0.191893	0.2247	0.196	5008	,	,		16584	0.3532		0.0427	False		,,,				2504	0.1319				p.N1003N		Atlas-SNP	.											.	MED12L	271	.	0			c.T3009C						PASS	.	T	,	799,3607	319.1+/-295.9	66,667,1470	211.0	200.0	204.0		,3009	-5.0	0.7	3	dbSNP_88	204	497,8103	143.4+/-199.5	20,457,3823	no	intron,coding-synonymous	P2RY12,MED12L	NM_022788.3,NM_053002.4	,	86,1124,5293	CC,CT,TT		5.7791,18.1344,9.9646	,	,1003/2146	151082923	1296,11710	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon20			TGACAATGCGGCC	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.3009T>C	3.37:g.151082923T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			T|0.856;C|0.144	0.144	strong		0.483	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
PTX4	390667	hgsc.bcm.edu	37	16	1536114	1536114	+	Silent	SNP	C	C	A	rs79788206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536114C>A	ENST00000447419.2	-	3	1288	c.1263G>T	c.(1261-1263)gtG>gtT	p.V421V	PTX4_ENST00000293922.1_Silent_p.V416V|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	421	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						ACATGCTCCCCACGAAGGCCT	0.637													C|||	88	0.0175719	0.0635	0.0058	5008	,	,		17747	0.0		0.0	False		,,,				2504	0.0				p.V416V		Atlas-SNP	.											.	PTX4	46	.	0			c.G1248T						PASS	.	C		286,4112	139.6+/-175.2	5,276,1918	67.0	65.0	66.0		1248	4.2	1.0	16	dbSNP_131	66	0,8600		0,0,4300	no	coding-synonymous	PTX4	NM_001013658.1		5,276,6218	AA,AC,CC		0.0,6.503,2.2003		416/474	1536114	286,12712	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GCTCCCCACGAAG		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.1263G>T	16.37:g.1536114C>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				C|0.976;A|0.024	0.024	strong		0.637	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
ZFPL1	7542	hgsc.bcm.edu	37	11	64854812	64854812	+	Missense_Mutation	SNP	G	G	A	rs35251366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64854812G>A	ENST00000294258.3	+	7	805	c.653G>A	c.(652-654)cGg>cAg	p.R218Q	AP003068.6_ENST00000525544.2_5'Flank	NM_006782.3	NP_006773.2	O95159	ZFPL1_HUMAN	zinc finger protein-like 1	218			R -> Q (in dbSNP:rs35251366).		regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11						TATGATACGCGGGATGATGAC	0.597													G|||	194	0.038738	0.0734	0.0303	5008	,	,		17531	0.0317		0.0258	False		,,,				2504	0.0184				p.R218Q		Atlas-SNP	.											.	ZFPL1	25	.	0			c.G653A						PASS	.	G	GLN/ARG	248,4154	143.5+/-178.5	6,236,1959	88.0	91.0	90.0		653	4.6	1.0	11	dbSNP_126	90	160,8434	77.2+/-139.8	3,154,4140	yes	missense	ZFPL1	NM_006782.3	43	9,390,6099	AA,AG,GG		1.8618,5.6338,3.1394	possibly-damaging	218/311	64854812	408,12588	2201	4297	6498	SO:0001583	missense	7542	exon7			ATACGCGGGATGA		CCDS8092.1	11q13	2013-01-08			ENSG00000162300	ENSG00000162300			12868	protein-coding gene	gene with protein product	"""zinc-finger protein in MEN1 region"""					9653652	Standard	NM_006782		Approved	D11S750, MCG4	uc001ocq.1	O95159	OTTHUMG00000165597	ENST00000294258.3:c.653G>A	11.37:g.64854812G>A	ENSP00000294258:p.Arg218Gln	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	154	68	0.441558	NM_006782	A8K7E9|O14616|Q9UID0	Missense_Mutation	SNP	ENST00000294258.3	37	CCDS8092.1	82	0.037545787545787544	33	0.06707317073170732	14	0.03867403314917127	19	0.033216783216783216	16	0.021108179419525065	G	22.1	4.248880	0.80024	0.056338	0.018618	ENSG00000162300	ENST00000294258	T	0.45668	0.89	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.09774	0.0240	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.04440	-1.0951	10	0.29301	T	0.29	-20.8505	15.2787	0.73764	0.0:0.0:1.0:0.0	rs35251366;rs35251366	218	O95159	ZFPL1_HUMAN	Q	218	ENSP00000294258:R218Q	ENSP00000294258:R218Q	R	+	2	0	ZFPL1	64611388	1.000000	0.71417	0.986000	0.45419	0.950000	0.60333	8.025000	0.88777	2.537000	0.85549	0.650000	0.86243	CGG	G|0.966;A|0.034	0.034	strong		0.597	ZFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385196.1	NM_006782	
CERCAM	51148	hgsc.bcm.edu	37	9	131196704	131196704	+	Silent	SNP	G	G	A	rs7259	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131196704G>A	ENST00000372838.4	+	11	1745	c.1347G>A	c.(1345-1347)aaG>aaA	p.K449K	CERCAM_ENST00000372842.1_Silent_p.K371K|RP11-339B21.10_ENST00000610052.1_RNA	NM_016174.4	NP_057258.3	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule	449					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|leukocyte cell-cell adhesion (GO:0007159)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|pancreas(2)	20						TCGGACGGAAGCAGGTGAACC	0.662													G|||	1884	0.376198	0.6604	0.2089	5008	,	,		16087	0.4048		0.2117	False		,,,				2504	0.2505				p.K449K		Atlas-SNP	.											.	CERCAM	104	.	0			c.G1347A						PASS	.	G		2657,1749	623.6+/-394.2	814,1029,360	43.0	49.0	47.0		1347	3.4	1.0	9	dbSNP_52	47	1567,7033	281.2+/-294.9	134,1299,2867	no	coding-synonymous	CERCAM	NM_016174.4		948,2328,3227	AA,AG,GG		18.2209,39.6959,32.4773		449/596	131196704	4224,8782	2203	4300	6503	SO:0001819	synonymous_variant	51148	exon11			ACGGAAGCAGGTG	AB040935	CCDS6901.2, CCDS69675.1	9q34.13	2008-02-05	2007-10-17	2007-10-17	ENSG00000167123	ENSG00000167123			23723	protein-coding gene	gene with protein product	"""glycosyltransferase 25 domain containing 3"""		"""cerebral cell adhesion molecule"""	CEECAM1		10608765	Standard	NM_016174		Approved	GLT25D3, CerCAM	uc004buz.4	Q5T4B2	OTTHUMG00000020747	ENST00000372838.4:c.1347G>A	9.37:g.131196704G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_016174	A7MD00|C4AMA2|Q0VDF3|Q2VPJ4|Q4KMP2|Q5T4B1|Q8N107|Q96EZ5|Q9P226|Q9UMW5	Silent	SNP	ENST00000372838.4	37	CCDS6901.2																																																																																			G|0.673;A|0.327	0.327	strong		0.662	CERCAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054435.2	NM_016174	
NLRC5	84166	hgsc.bcm.edu	37	16	57071167	57071167	+	Silent	SNP	G	G	A	rs137919442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57071167G>A	ENST00000262510.6	+	15	2997	c.2772G>A	c.(2770-2772)gcG>gcA	p.A924A	NLRC5_ENST00000308149.7_Silent_p.A924A|NLRC5_ENST00000539144.1_Silent_p.A924A|NLRC5_ENST00000436936.1_Silent_p.A924A	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	924					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)				CCGTGAGTGCGTGCTGGACCC	0.622													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18115	0.0		0.0	False		,,,				2504	0.0				p.A924A		Atlas-SNP	.											.	NLRC5	186	.	0			c.G2772A						PASS	.	G		20,4376	26.2+/-53.5	0,20,2178	119.0	103.0	108.0		2772	-6.2	0.0	16	dbSNP_134	108	0,8600		0,0,4300	no	coding-synonymous	NLRC5	NM_032206.3		0,20,6478	AA,AG,GG		0.0,0.455,0.1539		924/1867	57071167	20,12976	2198	4300	6498	SO:0001819	synonymous_variant	84166	exon14			GAGTGCGTGCTGG	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.2772G>A	16.37:g.57071167G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	67	23	0.343284	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	g	3.650	-0.071627	0.07228	0.00455	0.0	ENSG00000140853	ENST00000538805	.	.	.	3.5	-6.21	0.02065	.	.	.	.	.	T	0.19685	0.0473	.	.	.	0.19300	N	0.99997	.	.	.	.	.	.	T	0.25950	-1.0117	4	.	.	.	.	7.5874	0.28002	0.4148:0.309:0.2761:0.0	.	.	.	.	M	677	.	.	V	+	1	0	NLRC5	55628668	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.843000	0.00736	-1.778000	0.01282	-1.694000	0.00725	GTG	G|0.998;A|0.002	0.002	strong		0.622	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
OR2M3	127062	hgsc.bcm.edu	37	1	248366792	248366792	+	Silent	SNP	T	T	C	rs12562957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248366792T>C	ENST00000456743.1	+	1	461	c.423T>C	c.(421-423)tgT>tgC	p.C141C		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	141						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CTAAAATTTGTGGACTTATGA	0.453													T|||	1232	0.246006	0.171	0.255	5008	,	,		19737	0.3542		0.1451	False		,,,				2504	0.3333				p.C141C		Atlas-SNP	.											.	OR2M3	116	.	0			c.T423C						PASS	.	T		688,3718	290.4+/-280.9	61,566,1576	208.0	208.0	208.0		423	-0.0	0.0	1	dbSNP_120	208	1258,7342	251.1+/-277.7	90,1078,3132	no	coding-synonymous	OR2M3	NM_001004689.1		151,1644,4708	CC,CT,TT		14.6279,15.6151,14.9623		141/313	248366792	1946,11060	2203	4300	6503	SO:0001819	synonymous_variant	127062	exon1			AATTTGTGGACTT		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"""GPCR / Class A : Olfactory receptors"""	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.423T>C	1.37:g.248366792T>C		Somatic	423	0	0		WXS	Illumina HiSeq	Phase_I	416	206	0.495192	NM_001004689	B9EH06|Q6IEY0	Silent	SNP	ENST00000456743.1	37	CCDS31107.1																																																																																			T|0.828;C|0.172	0.172	strong		0.453	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689	
USP34	9736	hgsc.bcm.edu	37	2	61415492	61415492	+	Silent	SNP	A	A	G	rs14170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	94	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	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		
ICAM3	3385	hgsc.bcm.edu	37	19	10449358	10449358	+	Splice_Site	SNP	T	T	C	rs7258015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10449358T>C	ENST00000160262.5	-	2	551	c.343A>G	c.(343-345)Agg>Ggg	p.R115G	ICAM3_ENST00000589261.1_Splice_Site_p.R38G	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	115			R -> G (in dbSNP:rs7258015). {ECO:0000269|PubMed:1448174, ECO:0000269|PubMed:8459213}.		extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			GTCGACTCACTGTACACGGTG	0.547													T|||	896	0.178914	0.1392	0.1744	5008	,	,		19949	0.1141		0.2356	False		,,,				2504	0.2444				p.R115G		Atlas-SNP	.											ICAM3,colon,carcinoma,0,1	ICAM3	29	1	0			c.A343G						PASS	.	T	GLY/ARG	745,3661	304.1+/-288.3	56,633,1514	76.0	59.0	65.0		343	-11.5	0.0	19	dbSNP_116	65	1967,6633	344.9+/-325.5	238,1491,2571	yes	missense-near-splice	ICAM3	NM_002162.3	125	294,2124,4085	CC,CT,TT		22.8721,16.9088,20.8519	benign	115/548	10449358	2712,10294	2203	4300	6503	SO:0001630	splice_region_variant	3385	exon2			ACTCACTGTACAC		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.343+1A>G	19.37:g.10449358T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_002162	Q6PD68	Missense_Mutation	SNP	ENST00000160262.5	37	CCDS12235.1	382	0.1749084249084249	58	0.11788617886178862	69	0.19060773480662985	70	0.12237762237762238	185	0.24406332453825857	T	12.32	1.901485	0.33535	0.169088	0.228721	ENSG00000076662	ENST00000160262	T	0.24350	1.86	5.75	-11.5	0.00074	Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal (1);Intercellular adhesion molecule, N-terminal (1);Immunoglobulin-like fold (1);	0.854576	0.10072	N	0.719602	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.20739	-1.0266	8	.	.	.	-3.8943	6.787	0.23679	0.0633:0.391:0.1209:0.4248	rs7258015;rs58067369;rs7258015	38;115	B7Z6W6;P32942	.;ICAM3_HUMAN	G	115	ENSP00000160262:R115G	.	R	-	1	2	ICAM3	10310358	0.022000	0.18835	0.001000	0.08648	0.172000	0.22775	-2.406000	0.01044	-2.000000	0.00965	-0.213000	0.12676	AGG	T|0.809;C|0.191	0.191	strong		0.547	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		Missense_Mutation
WDR93	56964	hgsc.bcm.edu	37	15	90281452	90281452	+	Missense_Mutation	SNP	G	G	A	rs35389334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90281452G>A	ENST00000268130.7	+	16	2047	c.1946G>A	c.(1945-1947)cGt>cAt	p.R649H	WDR93_ENST00000560294.1_Missense_Mutation_p.R621H|WDR93_ENST00000444934.2_Missense_Mutation_p.R366H	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	649					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			AGATGTGAGCGTTTCCTCCAG	0.473													G|||	102	0.0203674	0.0756	0.0029	5008	,	,		17358	0.0		0.0	False		,,,				2504	0.0				p.R649H		Atlas-SNP	.											WDR93,colon,carcinoma,+1,1	WDR93	63	1	0			c.G1946A						PASS	.	G	HIS/ARG	251,4149	143.8+/-178.8	7,237,1956	165.0	167.0	166.0		1946	-10.5	0.0	15	dbSNP_126	166	2,8596	2.2+/-6.3	0,2,4297	yes	missense	WDR93	NM_020212.1	29	7,239,6253	AA,AG,GG		0.0233,5.7045,1.9465	possibly-damaging	649/687	90281452	253,12745	2200	4299	6499	SO:0001583	missense	56964	exon16			GTGAGCGTTTCCT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1946G>A	15.37:g.90281452G>A	ENSP00000268130:p.Arg649His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	130	72	0.553846	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	G	11.54	1.670012	0.29693	0.057045	2.33E-4	ENSG00000140527	ENST00000268130;ENST00000444934	T;T	0.43294	1.95;0.95	5.27	-10.5	0.00291	.	3.609450	0.00520	N	0.000193	T	0.00608	0.0020	N	0.22421	0.69	0.09310	N	1	P;P	0.50943	0.859;0.94	B;B	0.41571	0.276;0.36	T	0.38520	-0.9657	10	0.40728	T	0.16	3.3554	5.7049	0.17903	0.3798:0.0:0.2483:0.3718	rs35389334	621;649	Q6P2C0-2;Q6P2C0	.;WDR93_HUMAN	H	649;366	ENSP00000268130:R649H;ENSP00000403871:R366H	ENSP00000268130:R649H	R	+	2	0	WDR93	88082456	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.725000	0.00808	-2.790000	0.00356	-0.156000	0.13503	CGT	G|0.977;A|0.023	0.023	strong		0.473	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
SEMA5A	9037	hgsc.bcm.edu	37	5	9122926	9122926	+	Silent	SNP	C	C	T	rs6894626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:9122926C>T	ENST00000382496.5	-	14	2288	c.1623G>A	c.(1621-1623)ggG>ggA	p.G541G		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	541	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						CACCAAAGTGCCCATCCACGG	0.542																																					p.G541G		Atlas-SNP	.											.	SEMA5A	236	.	0			c.G1623A						PASS	.	T		1126,3280	681.5+/-404.0	125,876,1202	60.0	61.0	61.0		1623	-1.7	0.3	5	dbSNP_116	61	454,8146	765.0+/-407.6	8,438,3854	no	coding-synonymous	SEMA5A	NM_003966.2		133,1314,5056	TT,TC,CC		5.2791,25.5561,12.1482		541/1075	9122926	1580,11426	2203	4300	6503	SO:0001819	synonymous_variant	9037	exon14			AAAGTGCCCATCC	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1623G>A	5.37:g.9122926C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	188	77	0.409574	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																			C|0.837;T|0.163	0.163	strong		0.542	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
IL4I1	259307	hgsc.bcm.edu	37	19	50393743	50393743	+	Silent	SNP	A	A	G	rs61740372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50393743A>G	ENST00000391826.2	-	8	1030	c.888T>C	c.(886-888)gaT>gaC	p.D296D	IL4I1_ENST00000595948.1_Silent_p.D318D|MIR4750_ENST00000584564.1_RNA|IL4I1_ENST00000341114.3_Silent_p.D318D	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	296						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	GCACGTGCACATCGTGCGGTC	0.692											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	83	0.0165735	0.059	0.0072	5008	,	,		12580	0.0		0.0	False		,,,				2504	0.0				p.D318D		Atlas-SNP	.											.	IL4I1	50	.	0			c.T954C						PASS	.	A	,	242,4162	131.8+/-168.3	9,224,1969	28.0	27.0	27.0		888,954	-7.9	0.0	19	dbSNP_129	27	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	IL4I1	NM_152899.1,NM_172374.1	,	9,225,6268	GG,GA,AA		0.0116,5.495,1.8687	,	296/568,318/590	50393743	243,12761	2202	4300	6502	SO:0001819	synonymous_variant	259307	exon10			GTGCACATCGTGC	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.888T>C	19.37:g.50393743A>G		Somatic	63	0	0	969	WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_172374	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Silent	SNP	ENST00000391826.2	37	CCDS12787.1																																																																																			A|0.982;G|0.018	0.018	strong		0.692	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1		
TBCD	6904	hgsc.bcm.edu	37	17	80887123	80887123	+	Missense_Mutation	SNP	G	G	T	rs8072406	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80887123G>T	ENST00000355528.4	+	31	2958	c.2828G>T	c.(2827-2829)gGa>gTa	p.G943V	TBCD_ENST00000539345.2_Missense_Mutation_p.G943V	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	943			G -> V (in dbSNP:rs8072406).		'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)			CCCCACCGAGGAGAACTGGAA	0.637													G|||	119	0.023762	0.084	0.0101	5008	,	,		19308	0.0		0.001	False		,,,				2504	0.0				p.G943V		Atlas-SNP	.											.	TBCD	94	.	0			c.G2828T						PASS	.	G	VAL/GLY	333,3793		15,303,1745	62.0	66.0	65.0		2828	-10.3	0.0	17	dbSNP_116	65	2,8418		0,2,4208	yes	missense	TBCD	NM_005993.4	109	15,305,5953	TT,TG,GG		0.0238,8.0708,2.6702	possibly-damaging	943/1193	80887123	335,12211	2063	4210	6273	SO:0001583	missense	6904	exon31			ACCGAGGAGAACT	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.2828G>T	17.37:g.80887123G>T	ENSP00000347719:p.Gly943Val	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	45	0.020604395604395604	42	0.08536585365853659	3	0.008287292817679558	0	0.0	0	0.0	G	8.712	0.912371	0.17907	0.080708	2.38E-4	ENSG00000141556	ENST00000355528;ENST00000334614	T	0.29917	1.55	5.13	-10.3	0.00346	Armadillo-type fold (1);Tubulin-specific chaperone D, C-terminal (1);	1.128570	0.06621	N	0.757363	T	0.00666	0.0022	L	0.40543	1.245	0.09310	N	1	B;B;B	0.32010	0.351;0.238;0.351	B;B;B	0.31101	0.076;0.124;0.108	T	0.02933	-1.1092	9	.	.	.	.	11.0645	0.47968	0.6996:0.1867:0.1137:0.0	rs8072406;rs8072406	694;943;943	F8WC00;Q9BTW9;Q9BTW9-4	.;TBCD_HUMAN;.	V	943;694	ENSP00000347719:G943V	.	G	+	2	0	TBCD	78480412	0.019000	0.18553	0.000000	0.03702	0.011000	0.07611	0.131000	0.15870	-2.089000	0.00860	-0.165000	0.13383	GGA	G|0.974;T|0.026	0.026	strong		0.637	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
SAMM50	25813	hgsc.bcm.edu	37	22	44386281	44386281	+	Silent	SNP	C	C	T	rs7587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44386281C>T	ENST00000350028.4	+	14	1516	c.1359C>T	c.(1357-1359)ggC>ggT	p.G453G	SAMM50_ENST00000396202.3_Silent_p.G243G	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	453					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)				TACAGACAGGCGACAGGTACG	0.478													C|||	1116	0.222843	0.1604	0.1657	5008	,	,		17728	0.3621		0.2068	False		,,,				2504	0.2209				p.G453G		Atlas-SNP	.											.	SAMM50	30	.	0			c.C1359T						PASS	.	C		754,3652	307.2+/-289.9	67,620,1516	138.0	104.0	115.0		1359	-9.7	0.0	22	dbSNP_52	115	1906,6694	338.2+/-322.6	219,1468,2613	no	coding-synonymous	SAMM50	NM_015380.4		286,2088,4129	TT,TC,CC		22.1628,17.113,20.4521		453/470	44386281	2660,10346	2203	4300	6503	SO:0001819	synonymous_variant	25813	exon14			GACAGGCGACAGG	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.1359C>T	22.37:g.44386281C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Silent	SNP	ENST00000350028.4	37	CCDS14055.1																																																																																			T|0.178;G|0.125	0.178	strong		0.478	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
DDX5	1655	hgsc.bcm.edu	37	17	62499163	62499163	+	Silent	SNP	C	C	T	rs56025355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62499163C>T	ENST00000225792.5	-	8	1265	c.864G>A	c.(862-864)caG>caA	p.Q288Q	DDX5_ENST00000578804.1_Silent_p.Q288Q|DDX5_ENST00000450599.2_Silent_p.Q209Q|DDX5_ENST00000580026.1_5'Flank|MIR5047_ENST00000579212.1_RNA|MIR3064_ENST00000581130.1_RNA	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	288	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			CTTCAGCAAGCTGTCTTACTT	0.398			T	ETV4	prostate								C|||	19	0.00379393	0.0015	0.0029	5008	,	,		20101	0.0		0.0149	False		,,,				2504	0.0				p.Q288Q	NSCLC(22;406 813 4871 19580 40307)	Atlas-SNP	.		Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	.	DDX5	101	.	0			c.G864A						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	180.0	174.0	176.0		864	3.9	1.0	17	dbSNP_129	176	83,8517	48.9+/-108.6	0,83,4217	no	coding-synonymous	DDX5	NM_004396.3		0,93,6410	TT,TC,CC		0.9651,0.227,0.7151		288/615	62499163	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	1655	exon8			AGCAAGCTGTCTT	AF015812	CCDS11659.1	17q21	2012-07-27	2012-02-23		ENSG00000108654	ENSG00000108654		"""DEAD-boxes"""	2746	protein-coding gene	gene with protein product		180630	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 5"""	HLR1, G17P1		22156369, 18698352	Standard	NM_004396		Approved	p68	uc002jek.2	P17844	OTTHUMG00000178936	ENST00000225792.5:c.864G>A	17.37:g.62499163C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	169	68	0.402367	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Silent	SNP	ENST00000225792.5	37	CCDS11659.1																																																																																			C|0.993;T|0.007	0.007	strong		0.398	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396	
PCDHA5	56143	hgsc.bcm.edu	37	5	140202132	140202132	+	Missense_Mutation	SNP	A	A	G	rs61730633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140202132A>G	ENST00000529859.1	+	1	772	c.772A>G	c.(772-774)Aca>Gca	p.T258A	PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.T258A|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.T258A|PCDHA1_ENST00000504120.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	258	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)|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)			ACCAAGTGGGACATTAGTTAT	0.353													.|||	28	0.00559105	0.0212	0.0	5008	,	,		19252	0.0		0.0	False		,,,				2504	0.0				p.T258A		Atlas-SNP	.											.	PCDHA5	361	.	0			c.A772G						PASS	.	A	,,,,ALA/THR,,ALA/THR	104,4302	76.8+/-115.0	0,104,2099	62.0	65.0	64.0		,,,,772,,772	4.1	0.1	5	dbSNP_129	64	0,8598		0,0,4299	yes	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,58,,58	0,104,6398	GG,GA,AA		0.0,2.3604,0.7998	,,,,,,	,,,,258/937,,258/817	140202132	104,12900	2203	4299	6502	SO:0001583	missense	56143	exon1			AGTGGGACATTAG	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.772A>G	5.37:g.140202132A>G	ENSP00000436557:p.Thr258Ala	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	126	52	0.412698	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	A	15.50	2.851517	0.51270	0.023604	0.0	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.57107	0.42;0.42;0.42	4.11	4.11	0.48088	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.46983	0.1421	M	0.82517	2.595	0.29191	N	0.875842	P;P;P	0.49862	0.929;0.913;0.913	P;P;B	0.62382	0.901;0.596;0.444	T	0.58042	-0.7706	9	0.62326	D	0.03	.	8.9776	0.35946	0.9105:0.0:0.0895:0.0	rs61730633	258;258;258	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	A	258	ENSP00000433416:T258A;ENSP00000436557:T258A;ENSP00000367366:T258A	ENSP00000367366:T258A	T	+	1	0	PCDHA5	140182316	0.275000	0.24201	0.125000	0.21846	0.947000	0.59692	2.543000	0.45752	1.624000	0.50355	0.533000	0.62120	ACA	A|0.993;G|0.007	0.007	strong		0.353	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
TNFRSF25	8718	hgsc.bcm.edu	37	1	6524649	6524649	+	Silent	SNP	T	T	C	rs35137293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6524649T>C	ENST00000356876.3	-	4	513	c.426A>G	c.(424-426)ctA>ctG	p.L142L	TNFRSF25_ENST00000351959.5_Silent_p.L142L|TNFRSF25_ENST00000348333.3_Silent_p.L97L|TNFRSF25_ENST00000461703.2_5'UTR|TNFRSF25_ENST00000377782.3_Silent_p.L142L|TNFRSF25_ENST00000351748.3_Intron	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	142					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|central_nervous_system(2)|endometrium(1)|lung(4)|prostate(1)|stomach(1)	10	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		CCCCGCAGTCTAGGCATGGTT	0.627													t|||	104	0.0207668	0.0734	0.0072	5008	,	,		16978	0.0		0.002	False		,,,				2504	0.0				p.L142L		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.A426G						PASS	.	T	,,,,,	262,4144	147.6+/-182.1	5,252,1946	52.0	56.0	54.0		426,426,426,426,291,	-6.5	0.0	1	dbSNP_126	54	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	TNFRSF25	NM_001039664.1,NM_003790.2,NM_148965.1,NM_148966.1,NM_148967.1,NM_148970.1	,,,,,	5,258,6240	CC,CT,TT		0.0698,5.9464,2.0606	,,,,,	142/182,142/418,142/427,142/381,97/373,	6524649	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	8718	exon4			GCAGTCTAGGCAT	U72763	CCDS71.1, CCDS72.1, CCDS73.1, CCDS74.1, CCDS75.1	1p36.2	2008-02-05	2002-12-20	2002-12-20	ENSG00000215788	ENSG00000215788		"""Tumor necrosis factor receptor superfamily"""	11910	protein-coding gene	gene with protein product		603366	"""tumor necrosis factor receptor superfamily, member 12 (translocating chain-association membrane protein)"""	TNFRSF12		9052839, 8934525	Standard	NM_003790		Approved	DR3, TRAMP, WSL-1, LARD, WSL-LR, DDR3, TR3, APO-3	uc001anh.3	Q93038	OTTHUMG00000000831	ENST00000356876.3:c.426A>G	1.37:g.6524649T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_148966	B1ALX2|B1ALX3|B7ZLL7|O00275|O00276|O00277|O00278|O00279|O00280|O14865|O14866|P78507|P78515|Q17RU4|Q92983|Q93036|Q93037|Q99722|Q99830|Q99831|Q9BY86|Q9UME0|Q9UME1|Q9UME5	Silent	SNP	ENST00000356876.3	37	CCDS71.1																																																																																			T|0.978;C|0.022	0.022	strong		0.627	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965	
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22960655	22960655	+	Silent	SNP	C	C	T	rs10107827|rs374790272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22960655C>T	ENST00000356864.3	+	1	553	c.21C>T	c.(19-21)acC>acT	p.T7T	TNFRSF10C_ENST00000520607.1_Intron|TNFRSF10C_ENST00000397703.2_Silent_p.T47T|TNFRSF10C_ENST00000540813.1_5'UTR	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	7					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)		TCCCCAAGACCCTAAAGTTCG	0.716													C|||	208	0.0415335	0.149	0.0101	5008	,	,		14742	0.0		0.004	False		,,,				2504	0.0				p.T7T		Atlas-SNP	.											.	TNFRSF10C	30	.	0			c.C21T						PASS	.	C		438,3966	169.8+/-200.3	25,388,1789	80.0	59.0	66.0		21	0.8	0.0	8	dbSNP_119	66	12,8586	5.0+/-18.6	0,12,4287	no	coding-synonymous	TNFRSF10C	NM_003841.3		25,400,6076	TT,TC,CC		0.1396,9.9455,3.461		7/260	22960655	450,12552	2202	4299	6501	SO:0001819	synonymous_variant	8794	exon1			CAAGACCCTAAAG	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.21C>T	8.37:g.22960655C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Silent	SNP	ENST00000356864.3	37	CCDS6037.1																																																																																			.	.	alt		0.716	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
BPIFA3	128861	hgsc.bcm.edu	37	20	31812923	31812923	+	Missense_Mutation	SNP	G	G	A	rs3818222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31812923G>A	ENST00000375454.3	+	4	616	c.406G>A	c.(406-408)Gta>Ata	p.V136I	BPIFA3_ENST00000490499.1_3'UTR|BPIFA3_ENST00000375452.3_Missense_Mutation_p.V100I	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	136			V -> I (in dbSNP:rs3818222).			extracellular region (GO:0005576)	lipid binding (GO:0008289)										TAACAACATCGTAAAGATGTG	0.507													A|||	3327	0.664337	0.789	0.428	5008	,	,		22625	0.8115		0.5229	False		,,,				2504	0.6575				p.V136I		Atlas-SNP	.											.	.	.	.	0			c.G406A						PASS	.	A	ILE/VAL,ILE/VAL	3204,1202	419.1+/-338.5	1169,866,168	165.0	157.0	160.0		298,406	-5.5	0.0	20	dbSNP_107	160	4382,4218	571.0+/-389.5	1122,2138,1040	yes	missense,missense	BPIFA3	NM_001042439.1,NM_178466.3	29,29	2291,3004,1208	AA,AG,GG		49.0465,27.281,41.6731	benign,benign	100/219,136/255	31812923	7586,5420	2203	4300	6503	SO:0001583	missense	128861	exon4			AACATCGTAAAGA		CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"""BPI fold containing"""	16204	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 71"""	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.406G>A	20.37:g.31812923G>A	ENSP00000364603:p.Val136Ile	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_178466	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	37	CCDS13216.2	1412	0.6465201465201466	381	0.774390243902439	167	0.4613259668508287	465	0.8129370629370629	399	0.5263852242744064	A	0.188	-1.055829	0.01965	0.72719	0.509535	ENSG00000131059	ENST00000375454;ENST00000375452	T;T	0.04809	3.55;3.55	3.49	-5.46	0.02608	.	1.231100	0.05853	N	0.621586	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.30060	-0.9991	9	0.02654	T	1	-0.0358	4.4607	0.11665	0.2017:0.1397:0.5209:0.1376	rs3818222;rs13041676;rs61303950;rs3818222	100;136	Q9BQP9-2;Q9BQP9	.;BPIA3_HUMAN	I	136;100	ENSP00000364603:V136I;ENSP00000364601:V100I	ENSP00000364601:V100I	V	+	1	0	BPIFA3	31276584	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.653000	0.01986	-1.846000	0.01175	-0.521000	0.04368	GTA	G|0.380;A|0.620	0.620	strong		0.507	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466	
ZNF879	345462	hgsc.bcm.edu	37	5	178459283	178459283	+	Missense_Mutation	SNP	A	A	G	rs17078988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:178459283A>G	ENST00000444149.2	+	5	522	c.334A>G	c.(334-336)Aca>Gca	p.T112A	ZNF879_ENST00000519896.1_3'UTR	NM_001136116.1	NP_001129588.1	B4DU55	ZN879_HUMAN	zinc finger protein 879	112					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						AATTGATGGCACATTTGACTT	0.333													G|||	1824	0.364217	0.5182	0.255	5008	,	,		18690	0.4276		0.2237	False		,,,				2504	0.3129				p.T112A		Atlas-SNP	.											.	ZNF879	41	.	0			c.A334G						PASS	.	G	ALA/THR	618,766		138,342,212	98.0	83.0	87.0		334	-2.4	0.0	5	dbSNP_123	87	706,2476		76,554,961	yes	missense	ZNF879	NM_001136116.1	58	214,896,1173	GG,GA,AA		22.1873,44.6532,28.9969	benign	112/564	178459283	1324,3242	692	1591	2283	SO:0001583	missense	345462	exon5			GATGGCACATTTG	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.334A>G	5.37:g.178459283A>G	ENSP00000414887:p.Thr112Ala	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	96	42	0.4375	NM_001136116		Missense_Mutation	SNP	ENST00000444149.2	37	CCDS47352.1	768	0.3516483516483517	243	0.49390243902439024	100	0.27624309392265195	244	0.42657342657342656	181	0.23878627968337732	G	0	-2.590623	0.00126	0.446532	0.221873	ENSG00000234284	ENST00000444149;ENST00000522442	T;T	0.06142	3.34;5.87	4.32	-2.37	0.06643	.	.	.	.	.	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	0.42137	-0.9469	8	0.07030	T	0.85	0.427	1.2422	0.01965	0.3576:0.2448:0.2425:0.1551	rs17078988;rs52795425;rs17078988	112	B4DU55	ZN879_HUMAN	A	112	ENSP00000414887:T112A;ENSP00000428477:T112A	ENSP00000414887:T112A	T	+	1	0	ZNF879	178391889	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-2.139000	0.01302	-1.063000	0.03177	-4.156000	0.00010	ACA	A|0.634;G|0.366	0.366	strong		0.333	ZNF879-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374447.1	NM_001136116	
APEX2	27301	hgsc.bcm.edu	37	X	55033238	55033238	+	Silent	SNP	A	A	G	rs6651872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:55033238A>G	ENST00000374987.3	+	6	993	c.927A>G	c.(925-927)gcA>gcG	p.A309A	ALAS2_ENST00000498636.1_5'Flank	NM_014481.2	NP_055296.2	Q9UBZ4	APEX2_HUMAN	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	309					base-excision repair (GO:0006284)|cell cycle (GO:0007049)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1)	21						CTGTGGGTGCAGTCTTGAGTG	0.582								Other BER factors					A|||	33	0.00874172	0.025	0.0	3775	,	,		14084	0.0		0.0	False		,,,				2504	0.0				p.A309A		Atlas-SNP	.											.	APEX2	50	.	0			c.A927G						PASS	.	A		211,3624		3,173,32,1456,539	52.0	46.0	48.0		927	-1.7	0.8	X	dbSNP_116	48	1,6727		0,0,1,2428,1871	no	coding-synonymous	APEX2	NM_014481.2		3,173,33,3884,2410	GG,GA,G,AA,A		0.0149,5.502,2.007		309/519	55033238	212,10351	2203	4300	6503	SO:0001819	synonymous_variant	27301	exon6			GGGTGCAGTCTTG	AB021260	CCDS14365.1	Xp11.23	2014-02-18			ENSG00000169188	ENSG00000169188	4.2.99.18		17889	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 2"""	300773				11376153	Standard	NM_014481		Approved	APEXL2, APE2, XTH2, ZGRF2	uc004dtz.4	Q9UBZ4	OTTHUMG00000021642	ENST00000374987.3:c.927A>G	X.37:g.55033238A>G		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	257	140	0.544747	NM_014481	Q9Y5X7	Silent	SNP	ENST00000374987.3	37	CCDS14365.1																																																																																			A|0.975;0|0.005	.	strong		0.582	APEX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056845.1		
FAM181B	220382	hgsc.bcm.edu	37	11	82443672	82443672	+	Missense_Mutation	SNP	C	C	G	rs6592081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:82443672C>G	ENST00000329203.3	-	1	1234	c.1100G>C	c.(1099-1101)cGg>cCg	p.R367P		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	367	Pro-rich.		R -> P (in dbSNP:rs6592081).							large_intestine(1)|lung(2)|prostate(1)	4						CAAATGGCCCCGCCCGTCCTC	0.706													G|||	3205	0.639976	0.8949	0.5764	5008	,	,		10642	0.6319		0.3608	False		,,,				2504	0.636				p.R367P		Atlas-SNP	.											.	FAM181B	14	.	0			c.G1100C						PASS	.	G	PRO/ARG	2058,1152		682,694,229	2.0	3.0	3.0		1100	3.3	0.0	11	dbSNP_116	3	2285,4835		476,1333,1751	yes	missense	FAM181B	NM_175885.3	103	1158,2027,1980	GG,GC,CC		32.0927,35.8879,42.0426	benign	367/427	82443672	4343,5987	1605	3560	5165	SO:0001583	missense	220382	exon1			TGGCCCCGCCCGT	AK095054, BC039262	CCDS31648.1	11q14.1	2011-11-30			ENSG00000182103	ENSG00000182103			28512	protein-coding gene	gene with protein product						12477932	Standard	NM_175885		Approved	LOC220382, MGC33846	uc001ozp.3	A6NEQ2	OTTHUMG00000166869	ENST00000329203.3:c.1100G>C	11.37:g.82443672C>G	ENSP00000365295:p.Arg367Pro	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_175885	B2RWP1	Missense_Mutation	SNP	ENST00000329203.3	37	CCDS31648.1	1303	0.5966117216117216	438	0.8902439024390244	195	0.5386740331491713	388	0.6783216783216783	282	0.3720316622691293	G	0.357	-0.941794	0.02322	0.641121	0.320927	ENSG00000182103	ENST00000329203	T	0.29142	1.58	5.27	3.26	0.37387	.	0.262193	0.23708	N	0.045345	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24261	-1.0165	8	.	.	.	.	14.2854	0.66243	0.0:0.4276:0.5724:0.0	rs6592081	367	A6NEQ2	F181B_HUMAN	P	367	ENSP00000365295:R367P	.	R	-	2	0	FAM181B	82121320	0.136000	0.22515	0.002000	0.10522	0.827000	0.46813	1.620000	0.36976	0.610000	0.30035	-0.216000	0.12614	CGG	C|0.402;G|0.598	0.598	strong		0.706	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885	
ZNF492	57615	hgsc.bcm.edu	37	19	22847072	22847072	+	Missense_Mutation	SNP	G	G	C	rs146300593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	531	2	0.00376648		WXS	Illumina HiSeq	Phase_I	465	341	0.733333	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	
MCC	4163	hgsc.bcm.edu	37	5	112406862	112406862	+	Silent	SNP	G	G	A	rs2227950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112406862G>A	ENST00000302475.4	-	10	1847	c.1284C>T	c.(1282-1284)gcC>gcT	p.A428A	MCC_ENST00000515367.2_Silent_p.A365A|MCC_ENST00000408903.3_Silent_p.A618A|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	428					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.A618A(1)|p.A428A(1)		endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		TCATCCTCTCGGCATTGCTTT	0.483													G|||	1671	0.333666	0.354	0.2853	5008	,	,		19595	0.3462		0.3151	False		,,,				2504	0.3466				p.A618A		Atlas-SNP	.											MCC_ENST00000408903,colon,carcinoma,-1,4	MCC	234	4	2	Substitution - coding silent(2)	stomach(2)	c.C1854T						PASS	.	G	,	1380,3024	455.1+/-350.9	223,934,1045	265.0	221.0	236.0		1854,1284	-9.4	0.1	5	dbSNP_98	236	2825,5775	446.1+/-361.2	460,1905,1935	no	coding-synonymous,coding-synonymous	MCC	NM_001085377.1,NM_002387.2	,	683,2839,2980	AA,AG,GG		32.8488,31.3351,32.3362	,	618/1020,428/830	112406862	4205,8799	2202	4300	6502	SO:0001819	synonymous_variant	4163	exon12			CCTCTCGGCATTG		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1284C>T	5.37:g.112406862G>A		Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	231	229	0.991342	NM_001085377	D3DT05|Q6ZR04	Silent	SNP	ENST00000302475.4	37	CCDS4111.1																																																																																			T|0.062;G|0.554;C|0.125;A|0.259	0.259	strong		0.483	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
TRPM3	80036	hgsc.bcm.edu	37	9	73151970	73151970	+	Silent	SNP	C	C	T	rs3739776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:73151970C>T	ENST00000377110.3	-	25	4266	c.4023G>A	c.(4021-4023)tcG>tcA	p.S1341S	TRPM3_ENST00000377106.1_Silent_p.S1213S|TRPM3_ENST00000358082.3_Silent_p.S1203S|TRPM3_ENST00000357533.2_Silent_p.S1345S|TRPM3_ENST00000396285.1_Silent_p.S1200S|TRPM3_ENST00000360823.2_Silent_p.S1203S|TRPM3_ENST00000408909.2_Silent_p.S1200S|TRPM3_ENST00000396280.5_Silent_p.S1190S|TRPM3_ENST00000377105.1_Silent_p.S1200S|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396292.4_Silent_p.S1213S|TRPM3_ENST00000423814.3_Silent_p.S1368S			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1366					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						TCATATTGACCGAATAGAAAG	0.458													C|||	2815	0.562101	0.5703	0.5706	5008	,	,		20165	0.6954		0.5815	False		,,,				2504	0.3875				p.S1341S		Atlas-SNP	.											.	TRPM3	700	.	0			c.G4023A						PASS	.	C	,,,,,,	2542,1864	633.4+/-396.0	729,1084,390	93.0	98.0	97.0		4023,3564,3600,3534,3570,3639,3609	-11.7	0.5	9	dbSNP_107	97	4734,3866	607.1+/-395.2	1307,2120,873	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPM3	NM_001007471.2,NM_020952.4,NM_024971.5,NM_206944.3,NM_206945.3,NM_206946.3,NM_206947.3	,,,,,,	2036,3204,1263	TT,TC,CC		44.9535,42.3059,44.0566	,,,,,,	1341/1708,1188/1555,1200/1567,1178/1545,1190/1557,1213/1580,1203/1570	73151970	7276,5730	2203	4300	6503	SO:0001819	synonymous_variant	80036	exon25			ATTGACCGAATAG	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.4023G>A	9.37:g.73151970C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	187	187	1	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377110.3	37	CCDS43835.1	1320	0.6043956043956044	279	0.5670731707317073	193	0.5331491712707183	404	0.7062937062937062	444	0.5857519788918206	C	1.188	-0.636184	0.03557	0.576941	0.550465	ENSG00000083067	ENST00000396280	.	.	.	6.17	-11.7	0.00046	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22226	P	0.999273448	.	.	.	.	.	.	T	0.32693	-0.9897	3	.	.	.	-2.9687	7.3724	0.26808	0.1495:0.4854:0.0821:0.283	rs3739776;rs59345790;rs3739776	.	.	.	S	1190	.	.	G	-	1	0	TRPM3	72341790	0.007000	0.16637	0.493000	0.27502	0.877000	0.50540	-1.088000	0.03379	-1.804000	0.01241	-2.455000	0.00206	GGT	C|0.427;T|0.573	0.573	strong		0.458	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945	
ENPP1	5167	hgsc.bcm.edu	37	6	132211534	132211534	+	Silent	SNP	A	A	G	rs1804025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:132211534A>G	ENST00000360971.2	+	25	2681	c.2661A>G	c.(2659-2661)gcA>gcG	p.A887A		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	887	Nuclease.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	TACACAGAGCACGGATCACAG	0.388													A|||	396	0.0790735	0.2368	0.0331	5008	,	,		20304	0.0		0.0318	False		,,,				2504	0.0286				p.A887A	Colon(104;336 1535 5856 11019 33782)	Atlas-SNP	.											ENPP1,larynx,carcinoma,+2,1	ENPP1	108	1	0			c.A2661G						PASS	.	A		908,3498	351.1+/-311.1	93,722,1388	136.0	126.0	130.0		2661	-2.7	1.0	6	dbSNP_89	130	162,8438	76.3+/-139.0	0,162,4138	no	coding-synonymous	ENPP1	NM_006208.2		93,884,5526	GG,GA,AA		1.8837,20.6083,8.227		887/926	132211534	1070,11936	2203	4300	6503	SO:0001819	synonymous_variant	5167	exon25			CAGAGCACGGATC	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.2661A>G	6.37:g.132211534A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_006208	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Silent	SNP	ENST00000360971.2	37	CCDS5150.2																																																																																			A|0.915;G|0.085	0.085	strong		0.388	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2		
PAX8	7849	hgsc.bcm.edu	37	2	113994191	113994191	+	Silent	SNP	G	G	A	rs112872760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113994191G>A	ENST00000429538.3	-	8	1079	c.885C>T	c.(883-885)taC>taT	p.Y295Y	AC016683.6_ENST00000431844.2_RNA|AC016683.6_ENST00000437551.1_RNA|AC016683.6_ENST00000333145.5_RNA|AC016683.6_ENST00000436293.2_RNA|AC016683.6_ENST00000556070.1_RNA|AC016683.6_ENST00000456685.1_RNA|AC016683.6_ENST00000422956.2_RNA|AC016683.6_ENST00000553869.2_RNA|AC016683.6_ENST00000445745.1_RNA|PAX8_ENST00000397647.3_Intron|PAX8_ENST00000263334.5_Silent_p.Y295Y|PAX8_ENST00000263335.7_Intron|PAX8_ENST00000348715.5_Silent_p.Y295Y|AC016683.6_ENST00000451179.1_RNA	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	295					anatomical structure morphogenesis (GO:0009653)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular response to gonadotropin stimulus (GO:0071371)|central nervous system development (GO:0007417)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesonephros development (GO:0001823)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric nephron tubule formation (GO:0072289)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|otic vesicle development (GO:0071599)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|regulation of apoptotic process (GO:0042981)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of thyroid-stimulating hormone secretion (GO:2000612)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone signaling pathway (GO:0038194)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid-stimulating hormone receptor activity (GO:0004996)|transcription regulatory region DNA binding (GO:0044212)		PAX8/PPARG(117)	breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|skin(1)	20						CCACCACGGGGTAGGTCTGGT	0.682			T	PPARG	follicular thyroid		Thyroid dysgenesis						G|||	8	0.00159744	0.0061	0.0	5008	,	,		14226	0.0		0.0	False		,,,				2504	0.0				p.Y295Y	Ovarian(188;7 2067 9084 29802 29892)	Atlas-SNP	.		Dom	yes		2	2q12-q14	7849	paired box gene 8	yes	E	.	PAX8	42	.	0			c.C885T						PASS	.	G	,,,	25,4077		0,25,2026	34.0	41.0	38.0		885,885,,	3.7	1.0	2	dbSNP_132	38	1,8367		0,1,4183	no	coding-synonymous,coding-synonymous,intron,intron	PAX8	NM_003466.3,NM_013952.3,NM_013953.3,NM_013992.3	,,,	0,26,6209	AA,AG,GG		0.012,0.6095,0.2085	,,,	295/451,295/399,,	113994191	26,12444	2051	4184	6235	SO:0001819	synonymous_variant	7849	exon8			CACGGGGTAGGTC	X69699	CCDS42735.1, CCDS42736.1, CCDS46398.1, CCDS46399.1	2q13	2011-06-20	2007-07-12		ENSG00000125618	ENSG00000125618		"""Paired boxes"", ""Homeoboxes / PRD class"""	8622	protein-coding gene	gene with protein product		167415	"""paired box gene 8"""			8431641, 7981748	Standard	NM_003466		Approved		uc010yxt.2	Q06710	OTTHUMG00000128529	ENST00000429538.3:c.885C>T	2.37:g.113994191G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_013952	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Silent	SNP	ENST00000429538.3	37	CCDS46398.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	16.70	3.196529	0.58126	0.006095	1.2E-4	ENSG00000125618	ENST00000468980	.	.	.	5.58	3.7	0.42460	.	.	.	.	.	T	0.51143	0.1657	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50566	-0.8813	4	.	.	.	.	9.3385	0.38065	0.1849:0.0:0.8151:0.0	.	.	.	.	S	81	.	.	P	-	1	0	PAX8	113710662	1.000000	0.71417	0.997000	0.53966	0.812000	0.45895	2.702000	0.47102	0.646000	0.30693	-0.345000	0.07892	CCC	G|0.999;A|0.001	0.001	strong		0.682	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5		
NLRP12	91662	hgsc.bcm.edu	37	19	54327313	54327313	+	Missense_Mutation	SNP	C	C	A	rs34436714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54327313C>A	ENST00000324134.6	-	1	284	c.116G>T	c.(115-117)gGa>gTa	p.G39V	NLRP12_ENST00000535162.1_Missense_Mutation_p.G39V|NLRP12_ENST00000391772.1_Missense_Mutation_p.G39V|NLRP12_ENST00000354278.3_Missense_Mutation_p.G39V|NLRP12_ENST00000351894.4_Missense_Mutation_p.G39V|NLRP12_ENST00000391775.3_Missense_Mutation_p.G39V|NLRP12_ENST00000391773.1_Missense_Mutation_p.G39V|NLRP12_ENST00000345770.5_Missense_Mutation_p.G39V	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	39	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.		G -> V (in dbSNP:rs34436714).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		CTTGCCTTCTCCCAGCTCTGT	0.607													C|||	1280	0.255591	0.3858	0.2291	5008	,	,		16894	0.1776		0.2008	False		,,,				2504	0.2352				p.K39M		Atlas-SNP	.											.	NLRP12	236	.	0			c.A116T						PASS	.	C	VAL/GLY	1619,2787	499.3+/-364.4	299,1021,883	62.0	58.0	60.0		116	4.5	0.1	19	dbSNP_126	60	1851,6749	329.8+/-318.9	195,1461,2644	yes	missense	NLRP12	NM_144687.2	109	494,2482,3527	AA,AC,CC		21.5233,36.7453,26.68	probably-damaging	39/1062	54327313	3470,9536	2203	4300	6503	SO:0001583	missense	91662	exon1			CCTTCTCCCAGCT	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.116G>T	19.37:g.54327313C>A	ENSP00000319377:p.Gly39Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	147	67	0.455782	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	536	0.2454212454212454	213	0.4329268292682927	87	0.24033149171270718	83	0.1451048951048951	153	0.20184696569920843	C	13.08	2.130976	0.37630	0.367453	0.215233	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13;0.13	4.48	4.48	0.54585	Pyrin (2);DEATH-like (2);	0.183793	0.25991	N	0.027001	T	0.00012	0.0000	L	0.60845	1.875	0.09310	P	0.9999999899703	B;B;B;B	0.25772	0.134;0.028;0.111;0.051	B;B;B;B	0.25614	0.052;0.021;0.062;0.03	T	0.38672	-0.9650	9	0.36615	T	0.2	.	13.0212	0.58789	0.0:1.0:0.0:0.0	rs34436714;rs58032372;rs34436714	39;39;39;39	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	V	39	ENSP00000319377:G39V;ENSP00000438030:G39V;ENSP00000340473:G39V;ENSP00000346231:G39V;ENSP00000375655:G39V;ENSP00000375653:G39V;ENSP00000375652:G39V	ENSP00000319377:G39V	G	-	2	0	NLRP12	59019125	0.013000	0.17824	0.079000	0.20413	0.188000	0.23474	1.465000	0.35299	2.224000	0.72417	0.305000	0.20034	GGA	C|0.741;A|0.259	0.259	strong		0.607	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
TRPC7	57113	hgsc.bcm.edu	37	5	135692575	135692575	+	Silent	SNP	G	G	A	rs2546661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:135692575G>A	ENST00000513104.1	-	2	783	c.501C>T	c.(499-501)ccC>ccT	p.P167P	TRPC7_ENST00000355180.3_Silent_p.P167P|TRPC7_ENST00000426057.2_Silent_p.P167P	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	167					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCAGGATGATGGGCGTGATGT	0.647													G|||	1346	0.26877	0.4312	0.2075	5008	,	,		19100	0.3641		0.164	False		,,,				2504	0.1022				p.P167P		Atlas-SNP	.											.	TRPC7	126	.	0			c.C501T						PASS	.	G	,,	1622,2784	481.4+/-359.1	283,1056,864	134.0	144.0	140.0		501,501,501	3.5	1.0	5	dbSNP_100	140	1368,7232	261.7+/-284.0	114,1140,3046	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPC7	NM_001167576.1,NM_001167577.1,NM_020389.2	,,	397,2196,3910	AA,AG,GG		15.907,36.8134,22.9894	,,	167/747,167/802,167/863	135692575	2990,10016	2203	4300	6503	SO:0001819	synonymous_variant	57113	exon2			GATGATGGGCGTG	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.501C>T	5.37:g.135692575G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	131	76	0.580153	NM_001167576	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Silent	SNP	ENST00000513104.1	37	CCDS47267.2	593	0.2715201465201465	220	0.44715447154471544	65	0.17955801104972377	182	0.3181818181818182	126	0.1662269129287599	G	9.734	1.163071	0.21538	0.368134	0.15907	ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753	.	.	.	5.27	3.46	0.39613	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47911	-0.9080	3	.	.	.	-21.3621	4.6145	0.12418	0.2104:0.0:0.5183:0.2713	rs2546661;rs3777161;rs57153548;rs2546661	.	.	.	Y	167	.	.	H	-	1	0	TRPC7	135720474	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.481000	0.22260	0.762000	0.33152	0.655000	0.94253	CAT	G|0.723;A|0.277	0.277	strong		0.647	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389	
ZSCAN12	9753	hgsc.bcm.edu	37	6	28359170	28359170	+	Silent	SNP	A	A	G	rs2859348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28359170A>G	ENST00000361028.1	-	4	1042	c.897T>C	c.(895-897)gaT>gaC	p.D299D	ZSCAN12_ENST00000396827.3_Silent_p.D299D			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12	299					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|urinary_tract(1)	6						TGTAGGGTCTATCTCCAGTAT	0.423													a|||	3208	0.640575	0.9697	0.4942	5008	,	,		20015	0.5952		0.4583	False		,,,				2504	0.5337				p.D299D		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.T897C						PASS	.	A		1203,181		526,151,15	131.0	118.0	122.0		897	-0.2	1.0	6	dbSNP_100	122	1421,1761		315,791,485	no	coding-synonymous	ZSCAN12	NM_001163391.1		841,942,500	GG,GA,AA		44.6574,13.078,42.5318		299/612	28359170	2624,1942	692	1591	2283	SO:0001819	synonymous_variant	9753	exon4			GGGTCTATCTCCA	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"""-"", ""Zinc fingers, C2H2-type"""	13172	protein-coding gene	gene with protein product		603978	"""zinc finger protein 305"", ""zinc finger protein 96"""	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.897T>C	6.37:g.28359170A>G		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	192	192	1	NM_001163391	O43724	Silent	SNP	ENST00000361028.1	37																																																																																				A|0.407;G|0.593	0.593	strong		0.423	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724	
RP1L1	94137	hgsc.bcm.edu	37	8	10467647	10467647	+	Missense_Mutation	SNP	G	G	C	rs200373757		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10467647G>C	ENST00000382483.3	-	4	4184	c.3961C>G	c.(3961-3963)Cag>Gag	p.Q1321E		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1337	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)		tcctctaactgcaccgcctct	0.468																																					p.Q1321E		Atlas-SNP	.											RP1L1,NS,haematopoietic_neoplasm,0,1	RP1L1	453	1	0			c.C3961G						PASS	.	G	GLU/GLN	169,3739		2,165,1787	136.0	135.0	135.0		3961	-0.1	0.0	8	dbSNP_132	135	336,7932		0,336,3798	yes	missense	RP1L1	NM_178857.5	29	2,501,5585	CC,CG,GG		4.0639,4.3245,4.1475	benign	1321/2401	10467647	505,11671	1954	4134	6088	SO:0001583	missense	94137	exon4			CTAACTGCACCGC	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.3961C>G	8.37:g.10467647G>C	ENSP00000371923:p.Gln1321Glu	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	188	12	0.0638298	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	74	0.03388278388278388	30	0.06097560975609756	12	0.03314917127071823	2	0.0034965034965034965	30	0.0395778364116095	G	0.013	-1.632212	0.00806	0.043245	0.040639	ENSG00000183638	ENST00000382483	T	0.04758	3.56	2.13	-0.127	0.13510	.	1.785720	0.03751	N	0.256541	T	0.00328	0.0010	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.18263	0.021	T	0.45396	-0.9264	10	0.39692	T	0.17	-2.9969	0.6548	0.00832	0.1593:0.191:0.288:0.3617	.	1321	A6NKC6	.	E	1321	ENSP00000371923:Q1321E	ENSP00000371923:Q1321E	Q	-	1	0	RP1L1	10505057	0.000000	0.05858	0.016000	0.15963	0.072000	0.16883	-0.930000	0.03972	1.010000	0.39314	0.313000	0.20887	CAG	G|0.966;C|0.034	0.034	strong		0.468	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
B4GALNT4	338707	hgsc.bcm.edu	37	11	372157	372157	+	Missense_Mutation	SNP	C	C	T	rs34063493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:372157C>T	ENST00000329962.6	+	2	200	c.200C>T	c.(199-201)gCg>gTg	p.A67V		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	67			A -> V (in dbSNP:rs34063493).		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)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		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)		GTCCACGCTGCGCCATCCACA	0.647													.|||	1881	0.375599	0.4887	0.3098	5008	,	,		19615	0.3859		0.2952	False		,,,				2504	0.3415				p.A67V		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.C200T						PASS	.	T	VAL/ALA	1576,1900		360,856,522	65.0	57.0	60.0		200	-4.0	0.0	11	dbSNP_126	60	1762,4752		249,1264,1744	yes	missense	B4GALNT4	NM_178537.4	64	609,2120,2266	TT,TC,CC		27.0494,45.3395,33.4134	benign	67/1040	372157	3338,6652	1738	3257	4995	SO:0001583	missense	338707	exon2			ACGCTGCGCCATC	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.200C>T	11.37:g.372157C>T	ENSP00000328277:p.Ala67Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	107	42	0.392523	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	37	CCDS7694.1	817	0.3740842490842491	223	0.4532520325203252	119	0.3287292817679558	245	0.42832167832167833	230	0.3034300791556728	c	3.145	-0.175445	0.06421	0.453395	0.270494	ENSG00000182272	ENST00000329962	T	0.04862	3.54	3.52	-3.99	0.04069	.	2.616520	0.02606	N	0.101596	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.46610	-0.9179	9	0.02654	T	1	-0.5022	10.2695	0.43475	0.0:0.4536:0.0:0.5464	rs34063493;rs59064726	67	Q76KP1	B4GN4_HUMAN	V	67	ENSP00000328277:A67V	ENSP00000328277:A67V	A	+	2	0	B4GALNT4	362157	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.321000	0.08018	-0.770000	0.04614	-1.740000	0.00687	GCG	A|0.000;C|0.629;G|0.000;T|0.371	0.371	strong		0.647	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
ADAM18	8749	hgsc.bcm.edu	37	8	39468128	39468128	+	Missense_Mutation	SNP	A	A	T	rs73605945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39468128A>T	ENST00000265707.5	+	6	470	c.425A>T	c.(424-426)cAa>cTa	p.Q142L	ADAM18_ENST00000520772.1_Missense_Mutation_p.Q142L|ADAM18_ENST00000541111.1_Intron|ADAM18_ENST00000379866.1_Missense_Mutation_p.Q142L	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	142					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)			ATAATTTATCAAATGAAAAAT	0.328													A|||	181	0.0361422	0.1203	0.0144	5008	,	,		15463	0.0		0.0089	False		,,,				2504	0.0031				p.Q142L		Atlas-SNP	.											.	ADAM18	169	.	0			c.A425T						PASS	.	A	LEU/GLN,LEU/GLN	505,3901	221.7+/-238.7	22,461,1720	47.0	49.0	48.0		425,425	4.1	1.0	8	dbSNP_130	48	49,8547	29.0+/-79.6	0,49,4249	yes	missense,missense	ADAM18	NM_001190956.1,NM_014237.2	113,113	22,510,5969	TT,TA,AA		0.57,11.4616,4.2609	probably-damaging,probably-damaging	142/183,142/740	39468128	554,12448	2203	4298	6501	SO:0001583	missense	8749	exon6			TTTATCAAATGAA	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.425A>T	8.37:g.39468128A>T	ENSP00000265707:p.Gln142Leu	Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	280	125	0.446429	NM_001190956	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	75	0.034340659340659344	66	0.13414634146341464	6	0.016574585635359115	0	0.0	3	0.00395778364116095	A	15.82	2.946102	0.53079	0.114616	0.0057	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000520772;ENST00000522198	T;T;T	0.12465	5.29;4.82;2.68	5.25	4.07	0.47477	.	0.000000	0.47093	D	0.000245	T	0.00144	0.0004	N	0.08118	0	0.80722	D	1	D;D;D	0.63046	0.98;0.967;0.992	P;P;P	0.60286	0.872;0.749;0.84	T	0.34179	-0.9839	10	0.41790	T	0.15	.	7.8609	0.29509	0.9058:0.0:0.0942:0.0	.	142;142;142	Q9Y3Q7-2;Q9Y3Q7;Q6IRW9	.;ADA18_HUMAN;.	L	142;142;142;98	ENSP00000265707:Q142L;ENSP00000369195:Q142L;ENSP00000429908:Q142L	ENSP00000265707:Q142L	Q	+	2	0	ADAM18	39587285	1.000000	0.71417	1.000000	0.80357	0.291000	0.27294	2.766000	0.47629	2.206000	0.71126	0.533000	0.62120	CAA	A|0.964;T|0.036	0.036	strong		0.328	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
PTCRA	171558	hgsc.bcm.edu	37	6	42891022	42891022	+	Missense_Mutation	SNP	G	G	A	rs9471966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42891022G>A	ENST00000304672.1	+	2	397	c.316G>A	c.(316-318)Gtc>Atc	p.V106I	PTCRA_ENST00000441198.1_Missense_Mutation_p.V81I|PTCRA_ENST00000446507.1_Intron	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	106			V -> I (in dbSNP:rs9471966). {ECO:0000269|PubMed:15489334}.		negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			GGAGCCTTTGGTCTGCCACAC	0.632													G|||	1204	0.240415	0.3994	0.2133	5008	,	,		21832	0.0238		0.2893	False		,,,				2504	0.2178				p.V106I		Atlas-SNP	.											.	PTCRA	24	.	0			c.G316A						PASS	.	G	ILE/VAL	1522,2884	483.3+/-359.7	264,994,945	82.0	68.0	73.0		316	4.8	1.0	6	dbSNP_119	73	2278,6322	383.5+/-340.8	285,1708,2307	yes	missense	PTCRA	NM_138296.2	29	549,2702,3252	AA,AG,GG		26.4884,34.5438,29.2173	benign	106/282	42891022	3800,9206	2203	4300	6503	SO:0001583	missense	171558	exon2			CCTTTGGTCTGCC	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.316G>A	6.37:g.42891022G>A	ENSP00000304447:p.Val106Ile	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	208	107	0.514423	NM_138296	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	511	0.23397435897435898	201	0.40853658536585363	83	0.2292817679558011	15	0.026223776223776224	212	0.2796833773087071	G	23.0	4.362653	0.82353	0.345438	0.264884	ENSG00000171611	ENST00000304672;ENST00000441198	T;T	0.54279	0.58;0.58	5.69	4.82	0.62117	Immunoglobulin-like fold (1);	0.000000	0.42682	D	0.000670	T	0.46698	0.1406	L	0.36672	1.1	0.09310	P	0.9999999999999986	D;D	0.65815	0.995;0.98	P;P	0.61800	0.894;0.691	T	0.51919	-0.8644	9	0.52906	T	0.07	-35.6978	9.6018	0.39609	0.0925:0.0:0.9075:0.0	rs9471966;rs52795622;rs58242015;rs9471966	81;106	Q6ISU1-3;Q6ISU1	.;PTCRA_HUMAN	I	106;81	ENSP00000304447:V106I;ENSP00000409550:V81I	ENSP00000304447:V106I	V	+	1	0	PTCRA	42999000	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	3.635000	0.54309	2.668000	0.90789	0.650000	0.86243	GTC	G|0.729;A|0.271	0.271	strong		0.632	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296	
ATP10D	57205	hgsc.bcm.edu	37	4	47560163	47560163	+	Silent	SNP	C	C	A	rs11729411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:47560163C>A	ENST00000273859.3	+	12	2576	c.2307C>A	c.(2305-2307)atC>atA	p.I769I	AC092597.3_ENST00000508081.1_RNA	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	769					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)	p.I769I(1)		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						TCCTACACATCCTGCCCTTTG	0.483													C|||	1125	0.224641	0.1785	0.2925	5008	,	,		20635	0.2986		0.2127	False		,,,				2504	0.1748				p.I769I		Atlas-SNP	.											ATP10D,NS,carcinoma,0,1	ATP10D	168	1	1	Substitution - coding silent(1)	stomach(1)	c.C2307A						PASS	.	C		849,3557	334.9+/-303.7	87,675,1441	141.0	120.0	127.0		2307	3.2	1.0	4	dbSNP_120	127	1925,6675	340.3+/-323.5	217,1491,2592	no	coding-synonymous	ATP10D	NM_020453.3		304,2166,4033	AA,AC,CC		22.3837,19.2692,21.3286		769/1427	47560163	2774,10232	2203	4300	6503	SO:0001819	synonymous_variant	57205	exon12			ACACATCCTGCCC	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.2307C>A	4.37:g.47560163C>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	176	175	0.994318	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Silent	SNP	ENST00000273859.3	37	CCDS3476.1																																																																																			C|0.779;A|0.221	0.221	strong		0.483	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
PSME4	23198	hgsc.bcm.edu	37	2	54133744	54133744	+	Silent	SNP	T	T	C	rs805316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:54133744T>C	ENST00000404125.1	-	26	2989	c.2934A>G	c.(2932-2934)tcA>tcG	p.S978S	PSME4_ENST00000421748.2_Silent_p.S122S	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	978					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)	p.S864S(1)		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)			CCTGACTGTATGAACTTGTAG	0.363													T|||	1071	0.213858	0.1082	0.2205	5008	,	,		18843	0.1558		0.2664	False		,,,				2504	0.3579				p.S978S		Atlas-SNP	.											PSME4,NS,carcinoma,0,1	PSME4	247	1	1	Substitution - coding silent(1)	stomach(1)	c.A2934G						PASS	.	T		581,3825	258.6+/-262.5	38,505,1660	165.0	163.0	164.0		2934	-3.0	1.0	2	dbSNP_86	164	2403,6197	399.1+/-346.3	332,1739,2229	no	coding-synonymous	PSME4	NM_014614.2		370,2244,3889	CC,CT,TT		27.9419,13.1866,22.9433		978/1844	54133744	2984,10022	2203	4300	6503	SO:0001819	synonymous_variant	23198	exon26			ACTGTATGAACTT	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.2934A>G	2.37:g.54133744T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	165	68	0.412121	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																			T|0.784;C|0.216	0.216	strong		0.363	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
BSN	8927	hgsc.bcm.edu	37	3	49698695	49698695	+	Silent	SNP	T	T	C	rs149210839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49698695T>C	ENST00000296452.4	+	6	9531	c.9417T>C	c.(9415-9417)cgT>cgC	p.R3139R		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3139					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)		CTGATAGCCGTGCCCCACTGC	0.602													T|||	14	0.00279553	0.0098	0.0014	5008	,	,		16801	0.0		0.0	False		,,,				2504	0.0				p.R3139R		Atlas-SNP	.											.	BSN	272	.	0			c.T9417C						PASS	.	T		26,4380	32.6+/-62.9	0,26,2177	67.0	53.0	58.0		9417	-2.3	0.0	3	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous	BSN	NM_003458.3		0,26,6477	CC,CT,TT		0.0,0.5901,0.1999		3139/3927	49698695	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	8927	exon6			TAGCCGTGCCCCA	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.9417T>C	3.37:g.49698695T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	154	70	0.454545	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			T|0.998;C|0.002	0.002	strong		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
DACT2	168002	hgsc.bcm.edu	37	6	168708793	168708793	+	Silent	SNP	C	C	G	rs10945500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:168708793C>G	ENST00000366795.3	-	4	1732	c.1644G>C	c.(1642-1644)cgG>cgC	p.R548R	DACT2_ENST00000610183.1_Silent_p.R378R|DACT2_ENST00000366796.3_Intron|DACT2_ENST00000607983.1_Silent_p.R140R	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	548					epithelial cell morphogenesis (GO:0003382)|hematopoietic progenitor cell differentiation (GO:0002244)|inner medullary collecting duct development (GO:0072061)|negative regulation of cell adhesion (GO:0007162)|negative regulation of nodal signaling pathway (GO:1900108)|skin development (GO:0043588)	mitochondrion (GO:0005739)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)|transcription factor binding (GO:0008134)			endometrium(1)	1		Breast(66;1.46e-05)|Ovarian(120;0.0728)		OV - Ovarian serous cystadenocarcinoma(33;5.33e-21)|BRCA - Breast invasive adenocarcinoma(81;1.18e-06)|GBM - Glioblastoma multiforme(31;0.000957)		GGGCTGGCCTCCGCTGGAGCC	0.706													C|||	1287	0.256989	0.4251	0.1902	5008	,	,		10832	0.122		0.2475	False		,,,				2504	0.226				p.R548R		Atlas-SNP	.											.	DACT2	46	.	0			c.G1644C						PASS	.						14.0	20.0	18.0					6																	168708793		692	1588	2280	SO:0001819	synonymous_variant	168002	exon4			TGGCCTCCGCTGG	AF318336	CCDS47519.1, CCDS69241.1, CCDS75554.1	6q27	2013-05-15	2013-05-15	2003-09-17	ENSG00000164488	ENSG00000164488			21231	protein-coding gene	gene with protein product		608966	"""chromosome 6 open reading frame 116"", ""dapper homolog 2, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 2 (Xenopus laevis)"""	C6orf116			Standard	NM_001286351		Approved	bA503C24.7, DAPPER2	uc003qwq.3	Q5SW24	OTTHUMG00000016046	ENST00000366795.3:c.1644G>C	6.37:g.168708793C>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	27	15	0.555556	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Silent	SNP	ENST00000366795.3	37	CCDS47519.1																																																																																			C|0.753;G|0.247	0.247	strong		0.706	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
PLIN4	729359	hgsc.bcm.edu	37	19	4510850	4510850	+	Missense_Mutation	SNP	G	G	A	rs145519622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4510850G>A	ENST00000301286.3	-	3	3079	c.3080C>T	c.(3079-3081)gCg>gTg	p.A1027V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1027						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						GGCCCCTGTCGCCACGTTCCC	0.647													G|||	60	0.0119808	0.0303	0.0086	5008	,	,		18497	0.0		0.0129	False		,,,				2504	0.001				p.A1027V		Atlas-SNP	.											.	PLIN4	191	.	0			c.C3080T						PASS	.		VAL/ALA	115,4157		3,109,2024	70.0	79.0	76.0		3080	3.5	0.0	19	dbSNP_134	76	93,8415		1,91,4162	yes	missense	PLIN4	NM_001080400.1	64	4,200,6186	AA,AG,GG		1.0931,2.6919,1.6275	benign	1027/1358	4510850	208,12572	2136	4254	6390	SO:0001583	missense	729359	exon3			CCTGTCGCCACGT	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.3080C>T	19.37:g.4510850G>A	ENSP00000301286:p.Ala1027Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	24	0.01098901098901099	11	0.022357723577235773	4	0.011049723756906077	0	0.0	9	0.011873350923482849	G	12.83	2.056289	0.36277	0.026919	0.010931	ENSG00000167676	ENST00000301286	T	0.09723	2.95	4.56	3.49	0.39957	.	0.000000	0.35970	U	0.002866	T	0.02649	0.0080	L	0.58510	1.815	0.09310	N	1	P	0.39831	0.69	B	0.32533	0.147	T	0.24977	-1.0145	10	0.14252	T	0.57	-30.7309	8.97	0.35901	0.1077:0.0:0.8923:0.0	.	1027	Q96Q06	PLIN4_HUMAN	V	1027	ENSP00000301286:A1027V	ENSP00000301286:A1027V	A	-	2	0	PLIN4	4461850	0.287000	0.24315	0.009000	0.14445	0.046000	0.14306	1.486000	0.35530	0.892000	0.36259	0.500000	0.49745	GCG	G|0.988;A|0.012	0.012	strong		0.647	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
CACNA2D2	9254	hgsc.bcm.edu	37	3	50418547	50418547	+	Silent	SNP	G	G	T	rs56287038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:50418547G>T	ENST00000479441.1	-	7	662	c.663C>A	c.(661-663)atC>atA	p.I221I	CACNA2D2_ENST00000435965.1_Silent_p.I221I|CACNA2D2_ENST00000360963.3_Silent_p.I152I|CACNA2D2_ENST00000266039.3_Silent_p.I221I|CACNA2D2_ENST00000424201.2_Silent_p.I221I|CACNA2D2_ENST00000395083.1_Silent_p.I221I|CACNA2D2_ENST00000423994.2_Silent_p.I221I|CACNA2D2_ENST00000429770.1_Silent_p.I221I			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	221					energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GCTCATTGAGGATGACAGTGG	0.612													G|||	587	0.117212	0.3517	0.0562	5008	,	,		13903	0.0		0.0318	False		,,,				2504	0.0521				p.I221I		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.C663A						PASS	.	G	,,	1314,3092	441.6+/-346.4	227,860,1116	123.0	128.0	126.0		663,663,663	4.6	1.0	3	dbSNP_129	126	287,8313	106.6+/-167.4	8,271,4021	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA2D2	NM_001005505.1,NM_001174051.1,NM_006030.2	,,	235,1131,5137	TT,TG,GG		3.3372,29.823,12.3097	,,	221/1146,221/1151,221/1144	50418547	1601,11405	2203	4300	6503	SO:0001819	synonymous_variant	9254	exon7			ATTGAGGATGACA	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"""Calcium channel subunits"""	1400	protein-coding gene	gene with protein product	"""gene 26"""	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.663C>A	3.37:g.50418547G>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	83	26	0.313253	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Silent	SNP	ENST00000479441.1	37	CCDS54588.1																																																																																			G|0.887;T|0.113	0.113	strong		0.612	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030	
LGI4	163175	hgsc.bcm.edu	37	19	35617639	35617639	+	Silent	SNP	C	C	G	rs1687998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35617639C>G	ENST00000310123.3	-	8	1353	c.834G>C	c.(832-834)ccG>ccC	p.P278P	LGI4_ENST00000392225.3_Missense_Mutation_p.R304P|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	278					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CGAAGAGGCTCGGGCCCAGCA	0.741													C|||	1718	0.343051	0.2965	0.2493	5008	,	,		12239	0.254		0.3708	False		,,,				2504	0.5358				p.P278P		Atlas-SNP	.											.	LGI4	32	.	0			c.G834C						PASS	.	C		730,2116		146,438,839	2.0	3.0	3.0		834	-8.7	0.4	19	dbSNP_89	3	1965,4439		401,1163,1638	no	coding-synonymous	LGI4	NM_139284.2		547,1601,2477	GG,GC,CC		30.6839,25.65,29.1351		278/538	35617639	2695,6555	1423	3202	4625	SO:0001819	synonymous_variant	163175	exon8			GAGGCTCGGGCCC	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.834G>C	19.37:g.35617639C>G		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_139284	B2RN53|B9EGS7|Q5M8T1	Silent	SNP	ENST00000310123.3	37	CCDS12444.1	663	0.30357142857142855	157	0.31910569105691056	85	0.23480662983425415	131	0.229020979020979	290	0.38258575197889183	C	8.226	0.803486	0.16397	0.2565	0.306839	ENSG00000153902	ENST00000392225	T	0.63417	-0.04	4.35	-8.69	0.00855	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.39978	P	0.025124000000000035	.	.	.	.	.	.	T	0.14172	-1.0482	4	.	.	.	.	7.4446	0.27203	0.0993:0.1544:0.588:0.1583	rs1687998;rs17712562;rs59273846	.	.	.	P	304	ENSP00000376059:R304P	.	R	-	2	0	LGI4	40309479	0.000000	0.05858	0.378000	0.26068	0.633000	0.38033	-0.796000	0.04575	-1.234000	0.02548	-0.802000	0.03209	CGA	C|0.694;G|0.306	0.306	strong		0.741	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1		
AXDND1	126859	hgsc.bcm.edu	37	1	179363114	179363114	+	Missense_Mutation	SNP	G	G	C	rs139341288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179363114G>C	ENST00000367618.3	+	10	1327	c.940G>C	c.(940-942)Gtg>Ctg	p.V314L	AXDND1_ENST00000461179.2_3'UTR|AXDND1_ENST00000457238.2_Missense_Mutation_p.V314L	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	314										NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						AACTCAGCGAGTGATGGACCA	0.378													G|||	21	0.00419329	0.0159	0.0	5008	,	,		17593	0.0		0.0	False		,,,				2504	0.0				p.V314L		Atlas-SNP	.											.	AXDND1	142	.	0			c.G940C						PASS	.	G	LEU/VAL	55,4351	55.5+/-91.7	1,53,2149	153.0	150.0	151.0		940	-8.5	0.4	1	dbSNP_134	151	0,8600		0,0,4300	yes	missense	AXDND1	NM_144696.4	32	1,53,6449	CC,CG,GG		0.0,1.2483,0.4229	benign	314/1013	179363114	55,12951	2203	4300	6503	SO:0001583	missense	126859	exon10			CAGCGAGTGATGG	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.940G>C	1.37:g.179363114G>C	ENSP00000356590:p.Val314Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	11.60	1.686179	0.29962	0.012483	0.0	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000457238;ENST00000434088	T;T;T	0.44083	2.23;0.93;2.25	5.33	-8.49	0.00931	.	1.179580	0.05606	N	0.577214	T	0.15609	0.0376	N	0.17474	0.49	0.09310	N	0.999999	B;B;B	0.11235	0.001;0.002;0.004	B;B;B	0.11329	0.005;0.005;0.006	T	0.16748	-1.0392	10	0.24483	T	0.36	-0.2882	8.4441	0.32833	0.3562:0.1866:0.4572:0.0	.	272;314;314	E9PCJ4;Q5T1B0;F5GWM2	.;AXDN1_HUMAN;.	L	314;272;314;248	ENSP00000356590:V314L;ENSP00000416712:V314L;ENSP00000391716:V248L	ENSP00000353471:V272L	V	+	1	0	AXDND1	177629737	0.041000	0.20044	0.412000	0.26496	0.994000	0.84299	-1.684000	0.01932	-1.766000	0.01302	-0.152000	0.13540	GTG	G|0.997;C|0.003	0.003	strong		0.378	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	
ZNF699	374879	hgsc.bcm.edu	37	19	9415754	9415754	+	Silent	SNP	T	T	C	rs73504761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9415754T>C	ENST00000591998.1	-	2	270	c.42A>G	c.(40-42)agA>agG	p.R14R	ZNF699_ENST00000588336.1_Intron|ZNF699_ENST00000308650.3_Silent_p.R14R			Q32M78	ZN699_HUMAN	zinc finger protein 699	14					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(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TTACCTGTATTCTATTTTTCT	0.368													C|||	215	0.0429313	0.1422	0.0231	5008	,	,		18816	0.0109		0.0	False		,,,				2504	0.0				p.R14R		Atlas-SNP	.											.	ZNF699	67	.	0			c.A42G						PASS	.	C		477,3215		23,431,1392	155.0	148.0	150.0		42	0.0	0.0	19	dbSNP_130	150	10,8172		0,10,4081	no	coding-synonymous	ZNF699	NM_198535.1		23,441,5473	CC,CT,TT		0.1222,12.9198,4.1014		14/643	9415754	487,11387	1846	4091	5937	SO:0001819	synonymous_variant	374879	exon1			CTGTATTCTATTT	BC109268	CCDS42495.1	19p13.2	2013-01-08				ENSG00000196110		"""Zinc fingers, C2H2-type"", ""-"""	24750	protein-coding gene	gene with protein product	hangover homolog (Drosophila)	609571				16940975	Standard	NM_198535		Approved	FLJ38144, hang	uc002mlc.1	Q32M78		ENST00000591998.1:c.42A>G	19.37:g.9415754T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_198535	Q8N9A1	Silent	SNP	ENST00000591998.1	37	CCDS42495.1																																																																																			T|0.975;C|0.025	0.025	strong		0.368	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535	
OR10K1	391109	hgsc.bcm.edu	37	1	158435573	158435573	+	Silent	SNP	C	C	G	rs76205582|rs386635902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158435573C>G	ENST00000289451.2	+	1	302	c.222C>G	c.(220-222)acC>acG	p.T74T		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, member 1	74						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)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					TTTGCTATACCTTTGTCATTG	0.458													C|||	189	0.0377396	0.1354	0.013	5008	,	,		24689	0.0		0.001	False		,,,				2504	0.0				p.T74T		Atlas-SNP	.											.	OR10K1	80	.	0			c.C222G						PASS	.	C		503,3903	214.8+/-234.0	27,449,1727	209.0	190.0	196.0		222	-0.3	1.0	1	dbSNP_131	196	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	OR10K1	NM_001004473.1		27,457,6019	GG,GC,CC		0.093,11.4163,3.929		74/314	158435573	511,12495	2203	4300	6503	SO:0001819	synonymous_variant	391109	exon1			CTATACCTTTGTC	AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"""GPCR / Class A : Olfactory receptors"""	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.222C>G	1.37:g.158435573C>G		Somatic	489	1	0.00204499		WXS	Illumina HiSeq	Phase_I	474	205	0.432489	NM_001004473	Q6IFS2	Silent	SNP	ENST00000289451.2	37	CCDS30897.1																																																																																			C|0.966;G|0.034	0.034	strong		0.458	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1		
NALCN	259232	hgsc.bcm.edu	37	13	101720300	101720300	+	Silent	SNP	T	T	G	rs1289556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:101720300T>G	ENST00000251127.6	-	39	4497	c.4416A>C	c.(4414-4416)atA>atC	p.I1472I		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1472					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGTTCCATATTATTTGAAAGT	0.363													G|||	2018	0.402955	0.7519	0.2752	5008	,	,		19628	0.1171		0.3608	False		,,,				2504	0.3599				p.I1472I		Atlas-SNP	.											.	NALCN	431	.	0			c.A4416C						PASS	.	G		3159,1247	428.3+/-341.8	1136,887,180	123.0	119.0	120.0		4416	5.9	1.0	13	dbSNP_87	120	3118,5482	657.8+/-401.5	580,1958,1762	no	coding-synonymous	NALCN	NM_052867.2		1716,2845,1942	GG,GT,TT		36.2558,28.3023,48.2623		1472/1739	101720300	6277,6729	2203	4300	6503	SO:0001819	synonymous_variant	259232	exon39			CCATATTATTTGA	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.4416A>C	13.37:g.101720300T>G		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																			T|0.558;G|0.442	0.442	strong		0.363	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
ARPC5	10092	hgsc.bcm.edu	37	1	183599638	183599638	+	Silent	SNP	C	C	T	rs2231240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:183599638C>T	ENST00000359856.6	-	3	417	c.351G>A	c.(349-351)ccG>ccA	p.P117P	ARPC5_ENST00000367534.1_Silent_p.P117P|ARPC5_ENST00000462965.1_5'UTR|ARPC5_ENST00000294742.6_Silent_p.P120P	NM_005717.3	NP_005708.1	O15511	ARPC5_HUMAN	actin related protein 2/3 complex, subunit 5, 16kDa	117					actin cytoskeleton organization (GO:0030036)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|large_intestine(1)|lung(2)	4						TATTGTCAGACGGGCTCTCAA	0.343													C|||	537	0.107228	0.2262	0.0403	5008	,	,		18489	0.1091		0.0318	False		,,,				2504	0.0695				p.P120P	Melanoma(136;1596 1789 3041 4830 41075)	Atlas-SNP	.											.	ARPC5	6	.	0			c.G360A						PASS	.	C		853,3553	334.9+/-303.7	79,695,1429	72.0	72.0	72.0		351	-2.7	1.0	1	dbSNP_98	72	242,8358	95.6+/-157.4	1,240,4059	no	coding-synonymous	ARPC5	NM_005717.2		80,935,5488	TT,TC,CC		2.814,19.36,8.4192		117/152	183599638	1095,11911	2203	4300	6503	SO:0001819	synonymous_variant	10092	exon3			GTCAGACGGGCTC	AF017807	CCDS1357.1, CCDS58050.1	1q	2011-07-06	2002-08-29		ENSG00000162704	ENSG00000162704		"""Actin related protein 2/3 complex subunits"""	708	protein-coding gene	gene with protein product	"""Arp2/3 protein complex subunit p16"""	604227	"""actin related protein 2/3 complex, subunit 5 (16 kD)"""			9359840, 9230079	Standard	NM_005717		Approved	p16-Arc, ARC16, dJ127C7.3	uc021pgb.2	O15511	OTTHUMG00000035326	ENST00000359856.6:c.351G>A	1.37:g.183599638C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_001270439	A6NEC4|Q6PG42	Silent	SNP	ENST00000359856.6	37	CCDS1357.1																																																																																			C|0.918;T|0.082	0.082	strong		0.343	ARPC5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000085477.1	NM_005717	
CEACAM5	1048	hgsc.bcm.edu	37	19	42221418	42221418	+	Missense_Mutation	SNP	G	G	A	rs75927810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42221418G>A	ENST00000221992.6	+	5	1117	c.1003G>A	c.(1003-1005)Gtg>Atg	p.V335M	CEACAM5_ENST00000405816.1_Missense_Mutation_p.V335M|CEACAM5_ENST00000398599.4_Missense_Mutation_p.V334M|CEA_ENST00000598976.1_Intron	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	335	Ig-like 4.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CTCCAACCCCGTGGAGGATGA	0.532													g|||	97	0.019369	0.0688	0.0072	5008	,	,		21742	0.0		0.001	False		,,,				2504	0.0				p.V335M		Atlas-SNP	.											CEACAM5,NS,carcinoma,-2,1	CEACAM5	84	1	0			c.G1003A						PASS	.	G	MET/VAL	231,4175	135.7+/-171.8	6,219,1978	143.0	144.0	144.0		1003	-5.6	0.0	19	dbSNP_131	144	7,8593	5.7+/-21.5	0,7,4293	yes	missense	CEACAM5	NM_004363.2	21	6,226,6271	AA,AG,GG		0.0814,5.2429,1.8299	benign	335/703	42221418	238,12768	2203	4300	6503	SO:0001583	missense	1048	exon5			AACCCCGTGGAGG	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1003G>A	19.37:g.42221418G>A	ENSP00000221992:p.Val335Met	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	172	91	0.52907	NM_004363	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	CCDS12584.1	25|25	0.011446886446886446|0.011446886446886446	19|19	0.03861788617886179|0.03861788617886179	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	7.757|7.757	0.704676|0.704676	0.15172|0.15172	0.052429|0.052429	8.14E-4|8.14E-4	ENSG00000105388|ENSG00000105388	ENST00000398599|ENST00000221992;ENST00000405816	.|T;T	.|0.72167	.|-0.63;-0.63	2.77|2.77	-5.55|-5.55	0.02536|0.02536	.|Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|.	.|.	.|.	.|.	T|T	0.38852|0.38852	0.1056|0.1056	M|M	0.83603|0.83603	2.65|2.65	0.09310|0.09310	N|N	1|1	.|P;D	.|0.63880	.|0.881;0.993	.|P;D	.|0.64042	.|0.572;0.921	T|T	0.60697|0.60697	-0.7212|-0.7212	5|9	.|0.56958	.|D	.|0.05	.|.	0.9149|0.9149	0.01302|0.01302	0.3457:0.1551:0.3423:0.1569|0.3457:0.1551:0.3423:0.1569	.|.	.|335;335	.|P06731;Q53G30	.|CEAM5_HUMAN;.	H|M	330|335	.|ENSP00000221992:V335M;ENSP00000385072:V335M	.|ENSP00000221992:V335M	R|V	+|+	2|1	0|0	CEACAM5|CEACAM5	46913258|46913258	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-1.341000|-1.341000	0.02647|0.02647	-1.658000|-1.658000	0.01490|0.01490	-0.706000|-0.706000	0.03657|0.03657	CGT|GTG	G|0.985;A|0.015	0.015	strong		0.532	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	
KRT3	3850	hgsc.bcm.edu	37	12	53189428	53189428	+	Silent	SNP	C	C	A	rs148531142|rs184322044		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	159	0	0		WXS	Illumina HiSeq	Phase_I	173	38	0.219653	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	
MPRIP	23164	hgsc.bcm.edu	37	17	17030129	17030129	+	Silent	SNP	G	G	A	rs140002644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17030129G>A	ENST00000341712.4	+	4	381	c.381G>A	c.(379-381)gaG>gaA	p.E127E	MPRIP_ENST00000395811.5_Silent_p.E127E|MPRIP_ENST00000395804.3_Silent_p.E127E|MPRIP_ENST00000444976.1_Silent_p.E127E			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	127	Interaction with F-actin. {ECO:0000250}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CTGAGAAGGAGCATTTCATCC	0.587													G|||	3	0.000599042	0.0023	0.0	5008	,	,		20330	0.0		0.0	False		,,,				2504	0.0				p.E127E		Atlas-SNP	.											.	MPRIP	87	.	0			c.G381A						PASS	.	G	,	21,4385	28.1+/-56.4	0,21,2182	92.0	89.0	90.0		381,381	3.4	1.0	17	dbSNP_134	90	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MPRIP	NM_015134.3,NM_201274.3	,	0,21,6482	AA,AG,GG		0.0,0.4766,0.1615	,	127/1039,127/1026	17030129	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	23164	exon4			GAAGGAGCATTTC	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"""Pleckstrin homology (PH) domain containing"""	30321	protein-coding gene	gene with protein product	"""Rho interacting protein 3"""	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.381G>A	17.37:g.17030129G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	136	52	0.382353	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Silent	SNP	ENST00000341712.4	37	CCDS32578.1																																																																																			G|0.998;A|0.002	0.002	strong		0.587	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	
OPRL1	4987	hgsc.bcm.edu	37	20	62729843	62729843	+	Silent	SNP	A	A	G	rs34874539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62729843A>G	ENST00000349451.3	+	6	1216	c.804A>G	c.(802-804)gtA>gtG	p.V268V	OPRL1_ENST00000355631.4_Silent_p.V268V|OPRL1_ENST00000336866.2_Silent_p.V268V	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	268					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavior (GO:0007610)|opioid receptor signaling pathway (GO:0038003)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|nociceptin receptor activity (GO:0001626)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					TGCTGGTGGTAGTGGCTGTGT	0.672													G|||	99	0.0197684	0.0719	0.0058	5008	,	,		16073	0.0		0.0	False		,,,				2504	0.0				p.V268V		Atlas-SNP	.											.	OPRL1	47	.	0			c.A804G						PASS	.		,,	263,4139	793.7+/-415.2	9,245,1947	70.0	63.0	65.0		804,804,804	1.0	1.0	20	dbSNP_126	65	1,8593		0,1,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	OPRL1	NM_000913.4,NM_001200019.1,NM_182647.2	,,	9,246,6243	GG,GA,AA		0.0116,5.9746,2.0314	,,	268/371,268/371,268/371	62729843	264,12732	2201	4297	6498	SO:0001819	synonymous_variant	4987	exon4			GGTGGTAGTGGCT		CCDS13556.1	20q13.33	2012-08-08			ENSG00000125510	ENSG00000125510		"""GPCR / Class A : Opioid receptors"""	8155	protein-coding gene	gene with protein product	"""LC132 receptor-like"", ""orphanin FQ receptor"", ""kappa3-related opioid receptor"""	602548				8137918	Standard	NM_000913		Approved	NOCIR, ORL1, OOR, KOR-3	uc021wgs.1	P41146	OTTHUMG00000033027	ENST00000349451.3:c.804A>G	20.37:g.62729843A>G		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	224	114	0.508929	NM_000913	Q8TD34|Q8WYH9|Q9H4K4	Silent	SNP	ENST00000349451.3	37	CCDS13556.1																																																																																			A|0.979;G|0.021	0.021	strong		0.672	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647	
MTCL1	23255	hgsc.bcm.edu	37	18	8825399	8825399	+	Silent	SNP	C	C	T	rs16954339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:8825399C>T	ENST00000306329.11	+	13	4848	c.4848C>T	c.(4846-4848)tcC>tcT	p.S1616S	SOGA2_ENST00000518815.1_Silent_p.S622S|SOGA2_ENST00000359865.3_Silent_p.S1297S|SOGA2_ENST00000517570.1_Silent_p.S1256S|SOGA2_ENST00000400050.3_Silent_p.S1256S|SOGA2_ENST00000306285.7_Silent_p.S622S																							CCATCTGCTCCGGCCCTGGCG	0.592													T|||	520	0.103834	0.2216	0.0836	5008	,	,		19797	0.0774		0.0318	False		,,,				2504	0.0603				p.S1297S		Atlas-SNP	.											.	.	.	.	0			c.C3891T						PASS	.	T		883,3523	731.8+/-410.3	95,693,1415	47.0	41.0	43.0		3891	-5.5	0.0	18	dbSNP_123	43	345,8255	790.9+/-407.6	10,325,3965	no	coding-synonymous	CCDC165	NM_015210.3		105,1018,5380	TT,TC,CC		4.0116,20.0409,9.4418		1297/1587	8825399	1228,11778	2203	4300	6503	SO:0001819	synonymous_variant	23255	exon15			CTGCTCCGGCCCT																												ENST00000306329.11:c.4848C>T	18.37:g.8825399C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	136	68	0.5	NM_015210		Silent	SNP	ENST00000306329.11	37																																																																																				C|0.905;T|0.095	0.095	strong		0.592	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
HMCN1	83872	hgsc.bcm.edu	37	1	186101539	186101539	+	Missense_Mutation	SNP	A	A	G	rs10911825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186101539A>G	ENST00000271588.4	+	86	13539	c.13310A>G	c.(13309-13311)cAa>cGa	p.Q4437R	HMCN1_ENST00000367492.2_Missense_Mutation_p.Q4437R	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4437			Q -> R (in dbSNP:rs10911825).		response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTGACTCTGCAAAGTAAGCTG	0.368													A|||	2426	0.484425	0.6498	0.4841	5008	,	,		17276	0.5685		0.2634	False		,,,				2504	0.4018				p.Q4437R		Atlas-SNP	.											.	HMCN1	797	.	0			c.A13310G						PASS	.	A	ARG/GLN	2553,1853	618.3+/-393.1	774,1005,424	80.0	76.0	77.0		13310	5.4	1.0	1	dbSNP_120	77	2258,6340	370.6+/-335.9	308,1642,2349	yes	missense	HMCN1	NM_031935.2	43	1082,2647,2773	GG,GA,AA		26.2619,42.0563,36.9963	probably-damaging	4437/5636	186101539	4811,8193	2203	4299	6502	SO:0001583	missense	83872	exon86			CTCTGCAAAGTAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.13310A>G	1.37:g.186101539A>G	ENSP00000271588:p.Gln4437Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1038	0.47527472527472525	324	0.6585365853658537	163	0.45027624309392267	341	0.5961538461538461	210	0.2770448548812665	A	22.4	4.290972	0.80914	0.579437	0.262619	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.72167	1.58;-0.63	5.37	5.37	0.77165	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.55743	1.74	0.09310	P	0.99999941475	P	0.41008	0.735	P	0.44772	0.46	T	0.44636	-0.9315	9	0.13853	T	0.58	.	15.6642	0.77213	1.0:0.0:0.0:0.0	rs10911825;rs10911825	4437	Q96RW7	HMCN1_HUMAN	R	4437	ENSP00000271588:Q4437R;ENSP00000356462:Q4437R	ENSP00000271588:Q4437R	Q	+	2	0	HMCN1	184368162	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	8.537000	0.90631	2.141000	0.66446	0.533000	0.62120	CAA	A|0.569;G|0.431	0.431	strong		0.368	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
NUP155	9631	hgsc.bcm.edu	37	5	37299007	37299007	+	Silent	SNP	G	G	A	rs216400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37299007G>A	ENST00000231498.3	-	32	3959	c.3756C>T	c.(3754-3756)ggC>ggT	p.G1252G	NUP155_ENST00000513532.1_Silent_p.G1188G|NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000381843.2_Silent_p.G1193G	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	1252					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)			CATAAATTTTGCCAAGGAGAA	0.408													G|||	150	0.0299521	0.1112	0.0043	5008	,	,		18740	0.0		0.0	False		,,,				2504	0.0				p.G1252G		Atlas-SNP	.											.	NUP155	116	.	0			c.C3756T						PASS	.	G	,	437,3969	210.5+/-231.0	24,389,1790	134.0	119.0	124.0		3579,3756	0.7	1.0	5	dbSNP_79	124	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NUP155	NM_004298.2,NM_153485.1	,	24,390,6089	AA,AG,GG		0.0116,9.9183,3.3677	,	1193/1333,1252/1392	37299007	438,12568	2203	4300	6503	SO:0001819	synonymous_variant	9631	exon32			AATTTTGCCAAGG	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.3756C>T	5.37:g.37299007G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	108	40	0.37037	NM_153485	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	37	CCDS3921.1																																																																																			G|0.967;A|0.033	0.033	strong		0.408	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298	
GSDMD	79792	hgsc.bcm.edu	37	8	144641514	144641514	+	Silent	SNP	G	G	T	rs7840446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144641514G>T	ENST00000526406.1	+	5	892	c.9G>T	c.(7-9)tcG>tcT	p.S3S	GSDMD_ENST00000262580.4_Silent_p.S3S|GSDMD_ENST00000533063.1_Silent_p.S51S	NM_001166237.1	NP_001159709.1	P57764	GSDMD_HUMAN	gasdermin D	3					cellular response to extracellular stimulus (GO:0031668)					breast(1)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	12						GCATGGGGTCGGCCTTTGAGC	0.627													G|||	165	0.0329473	0.121	0.0058	5008	,	,		10930	0.0		0.001	False		,,,				2504	0.0				p.S3S		Atlas-SNP	.											.	GSDMD	28	.	0			c.G9T						PASS	.	G	,	383,4023	190.2+/-216.2	15,353,1835	63.0	58.0	60.0		9,9	-9.4	0.0	8	dbSNP_116	60	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous,coding-synonymous	GSDMD	NM_001166237.1,NM_024736.6	,	15,357,6130	TT,TG,GG		0.0465,8.6927,2.976	,	3/485,3/485	144641514	387,12617	2203	4299	6502	SO:0001819	synonymous_variant	79792	exon5			GGGGTCGGCCTTT	AK096216	CCDS34956.1	8q24.3	2008-07-31	2008-07-31	2008-07-31		ENSG00000104518			25697	protein-coding gene	gene with protein product			"""gasdermin domain containing 1"""	GSDMDC1		15289881, 17350798	Standard	NM_024736		Approved	FLJ12150, DF5L	uc003yyg.3	P57764		ENST00000526406.1:c.9G>T	8.37:g.144641514G>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	79	48	0.607595	NM_001166237	D3DWJ9|Q96Q98	Silent	SNP	ENST00000526406.1	37	CCDS34956.1																																																																																			G|0.971;T|0.029	0.029	strong		0.627	GSDMD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382046.3	NM_024736	
ABCC6	368	hgsc.bcm.edu	37	16	16281007	16281007	+	Missense_Mutation	SNP	A	A	G	rs12931472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16281007A>G	ENST00000205557.7	-	14	1870	c.1841T>C	c.(1840-1842)gTc>gCc	p.V614A	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	614			V -> A (in dbSNP:rs12931472). {ECO:0000269|PubMed:10835642, ECO:0000269|PubMed:11536079, ECO:0000269|PubMed:11776382, ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:19339160}.		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)	TGAGTCTACGACACCAGGGTC	0.602											OREG0023640	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1700	0.339457	0.3328	0.4957	5008	,	,		16349	0.1518		0.5	False		,,,				2504	0.2658				p.V614A		Atlas-SNP	.											.	ABCC6	110	.	0			c.T1841C						PASS	.	G	ALA/VAL	1687,2707	649.8+/-398.9	316,1055,826	50.0	41.0	44.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1841	3.8	0.0	16	dbSNP_121	44	4342,4258	571.3+/-389.5	1096,2150,1054	yes	missense	ABCC6	NM_001171.5	64	1412,3205,1880	GG,GA,AA		49.5116,38.3933,46.3983	benign	614/1504	16281007	6029,6965	2197	4300	6497	SO:0001583	missense	368	exon14			TCTACGACACCAG	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.1841T>C	16.37:g.16281007A>G	ENSP00000205557:p.Val614Ala	Somatic	76	0	0	709	WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	817	0.3740842490842491	178	0.3617886178861789	174	0.48066298342541436	91	0.1590909090909091	374	0.49340369393139843	G	4.895	0.166267	0.09339	0.383933	0.504884	ENSG00000091262	ENST00000205557;ENST00000456970;ENST00000546056	D;D	0.90069	-2.56;-2.61	4.84	3.85	0.44370	.	0.663319	0.12998	N	0.421879	T	0.00012	0.0000	N	0.03983	-0.305	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38672	-0.9650	9	0.19147	T	0.46	.	3.5818	0.07957	0.0941:0.1734:0.5664:0.1661	rs12931472;rs52812178;rs56825606;rs12931472	626;614	F5GWQ0;O95255	.;MRP6_HUMAN	A	614;614;626	ENSP00000205557:V614A;ENSP00000405002:V614A	ENSP00000205557:V614A	V	-	2	0	ABCC6	16188508	0.006000	0.16342	0.002000	0.10522	0.011000	0.07611	1.037000	0.30241	0.432000	0.26286	-0.215000	0.12644	GTC	A|0.599;G|0.400	0.400	strong		0.602	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
ZNF461	92283	hgsc.bcm.edu	37	19	37134737	37134737	+	Missense_Mutation	SNP	T	T	C	rs10419469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37134737T>C	ENST00000588268.1	-	5	487	c.260A>G	c.(259-261)aAt>aGt	p.N87S	ZNF461_ENST00000540605.2_5'Flank|ZNF461_ENST00000360357.4_Intron	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	87			N -> S (in dbSNP:rs10419469).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			caagaaattattgtgaaatcc	0.274													T|||	447	0.0892572	0.1785	0.0677	5008	,	,		16955	0.0685		0.0577	False		,,,				2504	0.0378				p.N87S		Atlas-SNP	.											.	ZNF461	73	.	0			c.A260G						PASS	.	T	SER/ASN	294,1550		22,250,650	106.0	94.0	97.0		260	0.6	0.1	19	dbSNP_119	97	307,3845		13,281,1782	yes	missense	ZNF461	NM_153257.2	46	35,531,2432	CC,CT,TT		7.394,15.9436,10.0233	possibly-damaging	87/564	37134737	601,5395	922	2076	2998	SO:0001583	missense	92283	exon5			AAATTATTGTGAA	BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"""Zinc fingers, C2H2-type"", ""-"""	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.260A>G	19.37:g.37134737T>C	ENSP00000467931:p.Asn87Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	37	CCDS54257.1	229	0.10485347985347986	113	0.22967479674796748	29	0.08011049723756906	48	0.08391608391608392	39	0.051451187335092345	T	2.014	-0.426386	0.04701	0.159436	0.07394	ENSG00000197808	ENST00000396893;ENST00000396892	.	.	.	0.625	0.625	0.17665	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	P	0.34587	0.458	B	0.39152	0.292	T	0.28332	-1.0047	6	0.48119	T	0.1	.	.	.	.	rs10419469;rs56479571;rs10419469	87	Q8TAF7	ZN461_HUMAN	S	87;22	.	ENSP00000380101:N22S	N	-	2	0	ZNF461	41826577	0.087000	0.21565	0.058000	0.19502	0.641000	0.38312	0.533000	0.23082	0.488000	0.27723	0.164000	0.16699	AAT	T|0.892;C|0.108	0.108	strong		0.274	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257	
BMP15	9210	hgsc.bcm.edu	37	X	50659280	50659280	+	Silent	SNP	C	C	T	rs17003221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:50659280C>T	ENST00000252677.3	+	2	852	c.852C>T	c.(850-852)agC>agT	p.S284S		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	284					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					CAAAACATAGCGGGCCTGAAA	0.527													t|||	694	0.183841	0.3918	0.0591	3775	,	,		11819	0.0615		0.003	False		,,,				2504	0.0716				p.S284S		Atlas-SNP	.											.	BMP15	62	.	0			c.C852T						PASS	.	T		1730,2105		341,793,255,498,316	90.0	77.0	81.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	852	-2.8	0.0	X	dbSNP_123	81	37,6690		0,30,7,2398,1864	no	coding-synonymous	BMP15	NM_005448.2		341,823,262,2896,2180	TT,TC,T,CC,C		0.55,45.1108,16.7298		284/393	50659280	1767,8795	2203	4299	6502	SO:0001819	synonymous_variant	9210	exon2			ACATAGCGGGCCT	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"""Bone morphogenetic proteins"""	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.852C>T	X.37:g.50659280C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	145	62	0.427586	NM_005448	Q17RM6|Q5JST1|Q9UMS1	Silent	SNP	ENST00000252677.3	37	CCDS14334.1																																																																																			C|0.811;0|0.015	.	strong		0.527	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448	
RIMS2	9699	hgsc.bcm.edu	37	8	104513156	104513156	+	Silent	SNP	C	C	A	rs78505067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104513156C>A	ENST00000406091.3	+	1	42	c.42C>A	c.(40-42)atC>atA	p.I14I	RP11-1C8.4_ENST00000523422.1_RNA|RP11-1C8.4_ENST00000517376.1_RNA	NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	14					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TGGCTCCCATCCCGGCGGCCT	0.677										HNSCC(12;0.0054)			C|||	38	0.00758786	0.0257	0.0058	5008	,	,		10505	0.0		0.0	False		,,,				2504	0.0				p.I14I		Atlas-SNP	.											.	RIMS2	1357	.	0			c.C42A						PASS	.	C		67,3591		1,65,1763	14.0	17.0	16.0		42	1.2	1.0	8	dbSNP_132	16	0,8116		0,0,4058	no	coding-synonymous	RIMS2	NM_001100117.2		1,65,5821	AA,AC,CC		0.0,1.8316,0.5691		14/1350	104513156	67,11707	1829	4058	5887	SO:0001819	synonymous_variant	9699	exon1			TCCCATCCCGGCG	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000406091.3:c.42C>A	8.37:g.104513156C>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000406091.3	37	CCDS55269.1																																																																																			C|0.994;A|0.006	0.006	strong		0.677	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001100117	
KIF12	113220	hgsc.bcm.edu	37	9	116859631	116859631	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116859631C>T	ENST00000374118.3	-	4	419	c.182G>A	c.(181-183)cGg>cAg	p.R61Q	KIF12_ENST00000473174.1_Intron	NM_138424.1	NP_612433.1	Q96FN5	KIF12_HUMAN	kinesin family member 12	194	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	17						TTCCACCACCCGCAGCTGCTC	0.622																																					p.R61Q		Atlas-SNP	.											KIF12,NS,carcinoma,-1,1	KIF12	35	1	0			c.G182A						scavenged	.						37.0	40.0	39.0					9																	116859631		2203	4300	6503	SO:0001583	missense	113220	exon4			ACCACCCGCAGCT	BC010626	CCDS6801.1	9q33.1	2008-02-05			ENSG00000136883	ENSG00000136883		"""Kinesins"""	21495	protein-coding gene	gene with protein product		611278					Standard	NM_138424		Approved		uc004bif.3	Q96FN5	OTTHUMG00000020533	ENST00000374118.3:c.182G>A	9.37:g.116859631C>T	ENSP00000363232:p.Arg61Gln	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	226	4	0.0176991	NM_138424	Q5TBE0	Missense_Mutation	SNP	ENST00000374118.3	37	CCDS6801.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.672966	0.29693	.	.	ENSG00000136883	ENST00000374118;ENST00000259410	T	0.74842	-0.88	5.44	3.36	0.38483	Kinesin, motor domain (4);	0.541938	0.17542	N	0.170484	T	0.54175	0.1842	N	0.16266	0.395	0.31159	N	0.70452	B	0.22080	0.064	B	0.16289	0.015	T	0.54912	-0.8222	10	0.49607	T	0.09	.	5.373	0.16150	0.0:0.7195:0.0:0.2805	.	194	Q96FN5	KIF12_HUMAN	Q	61;194	ENSP00000363232:R61Q	ENSP00000259410:R194Q	R	-	2	0	KIF12	115899452	0.139000	0.22563	0.996000	0.52242	0.408000	0.30992	1.023000	0.30065	1.290000	0.44636	0.555000	0.69702	CGG	.	.	none		0.622	KIF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053751.1	NM_138424	
C11orf53	341032	hgsc.bcm.edu	37	11	111156523	111156523	+	Missense_Mutation	SNP	G	G	T	rs74649813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:111156523G>T	ENST00000280325.4	+	4	602	c.455G>T	c.(454-456)tGg>tTg	p.W152L		NM_198498.1	NP_940900.1	Q8IXP5	CK053_HUMAN	chromosome 11 open reading frame 53	152										endometrium(1)|large_intestine(2)|lung(3)|skin(2)	8		all_cancers(61;2.05e-09)|Melanoma(852;4.04e-05)|all_epithelial(67;6.15e-05)|all_hematologic(158;0.000826)|Acute lymphoblastic leukemia(157;0.000966)|all_neural(223;0.0332)|Medulloblastoma(222;0.0425)|Breast(348;0.147)		Epithelial(105;1.7e-06)|BRCA - Breast invasive adenocarcinoma(274;3.16e-06)|all cancers(92;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0507)		GGCTCAAGCTGGGGGTCATCC	0.642													G|||	223	0.0445288	0.1589	0.0187	5008	,	,		21186	0.0		0.0	False		,,,				2504	0.0				p.W152L		Atlas-SNP	.											C11orf53,NS,haematopoietic_neoplasm,-1,1	C11orf53	17	1	0			c.G455T						PASS	.	G	LEU/TRP	526,3876	237.4+/-249.2	36,454,1711	75.0	72.0	73.0		455	5.2	1.0	11	dbSNP_131	73	3,8591	2.2+/-6.3	0,3,4294	yes	missense	C11orf53	NM_198498.1	61	36,457,6005	TT,TG,GG		0.0349,11.9491,4.0705	probably-damaging	152/237	111156523	529,12467	2201	4297	6498	SO:0001583	missense	341032	exon4			CAAGCTGGGGGTC	BC039669	CCDS31674.1	11q23.1	2012-05-31			ENSG00000150750	ENSG00000150750			30527	protein-coding gene	gene with protein product						12477932	Standard	NM_198498		Approved	MGC50104	uc001plc.3	Q8IXP5	OTTHUMG00000166656	ENST00000280325.4:c.455G>T	11.37:g.111156523G>T	ENSP00000280325:p.Trp152Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	56	34	0.607143	NM_198498		Missense_Mutation	SNP	ENST00000280325.4	37	CCDS31674.1	86	0.039377289377289376	77	0.1565040650406504	9	0.024861878453038673	0	0.0	0	0.0	G	18.56	3.650861	0.67472	0.119491	3.49E-4	ENSG00000150750	ENST00000280325	.	.	.	5.15	5.15	0.70609	.	0.069080	0.64402	D	0.000009	T	0.00754	0.0025	M	0.67953	2.075	0.24566	P	0.99394883	D	0.89917	1.0	D	0.87578	0.998	T	0.23833	-1.0177	8	0.12103	T	0.63	-12.1586	16.1285	0.81410	0.0:0.0:1.0:0.0	.	152	Q8IXP5	CK053_HUMAN	L	152	.	ENSP00000280325:W152L	W	+	2	0	C11orf53	110661733	1.000000	0.71417	0.995000	0.50966	0.655000	0.38815	6.849000	0.75414	2.402000	0.81655	0.561000	0.74099	TGG	G|0.961;T|0.039	0.039	strong		0.642	C11orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390989.1	NM_198498	
ZNF846	162993	hgsc.bcm.edu	37	19	9868764	9868764	+	Missense_Mutation	SNP	C	C	G	rs60387559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9868764C>G	ENST00000397902.2	-	6	1402	c.989G>C	c.(988-990)cGa>cCa	p.R330P	ZNF846_ENST00000588267.1_Missense_Mutation_p.R201P|ZNF846_ENST00000592859.1_Missense_Mutation_p.R201P|ZNF846_ENST00000586293.1_3'UTR	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	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)	p.R330Q(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						AGTGTGAATTCGCATGTGTAA	0.388													N|||	64	0.0127796	0.0461	0.0043	5008	,	,		23084	0.0		0.0	False		,,,				2504	0.0				p.R330P		Atlas-SNP	.											ZNF846,NS,carcinoma,0,3	ZNF846	61	3	1	Substitution - Missense(1)	large_intestine(1)	c.G989C						PASS	.	C	PRO/ARG	247,4097		17,213,1942	63.0	68.0	66.0		989	-3.1	0.0	19	dbSNP_129	66	0,8586		0,0,4293	yes	missense	ZNF846	NM_001077624.1	103	17,213,6235	GG,GC,CC		0.0,5.686,1.9103	probably-damaging	330/534	9868764	247,12683	2172	4293	6465	SO:0001583	missense	162993	exon6			TGAATTCGCATGT	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.989G>C	19.37:g.9868764C>G	ENSP00000380999:p.Arg330Pro	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	.	15.85	2.955405	0.53293	0.05686	0.0	ENSG00000196605	ENST00000397902	T	0.25749	1.78	2.01	-3.1	0.05315	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07143	0.0181	M	0.89840	3.065	0.09310	N	1	D	0.71674	0.998	P	0.58013	0.831	T	0.08554	-1.0716	8	.	.	.	.	3.6327	0.08138	0.1949:0.251:0.0:0.5541	rs60387559	330	Q147U1	ZN846_HUMAN	P	330	ENSP00000380999:R330P	.	R	-	2	0	ZNF846	9729764	0.000000	0.05858	0.000000	0.03702	0.688000	0.40055	-1.594000	0.02094	-0.747000	0.04759	0.456000	0.33151	CGA	C|0.992;G|0.007;T|0.000	0.007	strong		0.388	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624	
MARCH10	162333	hgsc.bcm.edu	37	17	60813954	60813954	+	Silent	SNP	A	A	G	rs8068372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60813954A>G	ENST00000311269.5	-	6	1549	c.1275T>C	c.(1273-1275)atT>atC	p.I425I	MARCH10_ENST00000544856.2_Silent_p.I424I|RP11-156L14.1_ENST00000584597.1_RNA|RP11-156L14.1_ENST00000577270.1_RNA|MARCH10_ENST00000456609.2_Silent_p.I425I|RP11-156L14.1_ENST00000579201.1_RNA|MARCH10_ENST00000583600.1_Silent_p.I463I|RP11-156L14.1_ENST00000582564.1_RNA	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	425					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						GTTCCACAGAAATACAATCAC	0.428													A|||	278	0.0555112	0.2057	0.0072	5008	,	,		20942	0.0		0.001	False		,,,				2504	0.0				p.I425I		Atlas-SNP	.											.	MARCH10	102	.	0			c.T1275C						PASS	.	A	,	645,3761	274.6+/-272.0	43,559,1601	87.0	79.0	82.0		1275,1275	-0.7	0.0	17	dbSNP_116	82	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	MARCH10	NM_001100875.1,NM_152598.2	,	43,565,5895	GG,GA,AA		0.0698,14.6391,5.0054	,	425/809,425/809	60813954	651,12355	2203	4300	6503	SO:0001819	synonymous_variant	162333	exon6			CACAGAAATACAA	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	26655	protein-coding gene	gene with protein product		613337	"""ring finger protein 190"", ""membrane-associated ring finger (C3HC4) 10"""	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.1275T>C	17.37:g.60813954A>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	163	71	0.435583	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Silent	SNP	ENST00000311269.5	37	CCDS11635.1																																																																																			A|0.952;G|0.048	0.048	strong		0.428	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598	
SERPINI2	5276	hgsc.bcm.edu	37	3	167164187	167164187	+	Silent	SNP	A	A	G	rs2272138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:167164187A>G	ENST00000476257.1	-	9	1432	c.1134T>C	c.(1132-1134)aaT>aaC	p.N378N	SERPINI2_ENST00000471111.1_Silent_p.N378N|SERPINI2_ENST00000461846.1_Silent_p.N378N|SERPINI2_ENST00000264677.4_Silent_p.N378N			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	378					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						TACCTGTTGGATTATGCTTCA	0.348													G|||	1182	0.236022	0.4251	0.2277	5008	,	,		18166	0.2927		0.0924	False		,,,				2504	0.0757				p.N388N		Atlas-SNP	.											.	SERPINI2	85	.	0			c.T1164C						PASS	.	G		1719,2687	647.5+/-398.6	351,1017,835	97.0	108.0	104.0		1134	0.7	1.0	3	dbSNP_100	104	826,7772	779.4+/-407.7	41,744,3514	no	coding-synonymous	SERPINI2	NM_006217.3		392,1761,4349	GG,GA,AA		9.6069,39.015,19.5709		378/406	167164187	2545,10459	2203	4299	6502	SO:0001819	synonymous_variant	5276	exon9			TGTTGGATTATGC	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.1134T>C	3.37:g.167164187A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_001012303		Silent	SNP	ENST00000476257.1	37	CCDS3200.1																																																																																			A|0.775;G|0.225	0.225	strong		0.348	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
GPRIN3	285513	hgsc.bcm.edu	37	4	90170015	90170015	+	Missense_Mutation	SNP	C	C	A	rs114960901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:90170015C>A	ENST00000609438.1	-	2	1765	c.1247G>T	c.(1246-1248)gGg>gTg	p.G416V	GPRIN3_ENST00000333209.4_Missense_Mutation_p.G416V	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	416										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		TTTAAGGACCCCACCTGGTAG	0.507													C|||	41	0.0081869	0.0295	0.0029	5008	,	,		19599	0.0		0.0	False		,,,				2504	0.0				p.G416V		Atlas-SNP	.											GPRIN3,colon,carcinoma,+1,1	GPRIN3	90	1	0			c.G1247T						PASS	.	C	VAL/GLY	114,4292	85.8+/-124.5	1,112,2090	108.0	112.0	110.0		1247	2.8	0.0	4	dbSNP_132	110	1,8599		0,1,4299	yes	missense	GPRIN3	NM_198281.2	109	1,113,6389	AA,AC,CC		0.0116,2.5874,0.8842	benign	416/777	90170015	115,12891	2203	4300	6503	SO:0001583	missense	285513	exon2			AGGACCCCACCTG	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.1247G>T	4.37:g.90170015C>A	ENSP00000476603:p.Gly416Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	190	95	0.5	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	C	10.41	1.341579	0.24339	0.025874	1.16E-4	ENSG00000185477	ENST00000333209	T	0.11385	2.78	5.38	2.81	0.32909	.	0.502634	0.14825	N	0.296209	T	0.01592	0.0051	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.34129	-0.9841	10	0.45353	T	0.12	-1.3894	1.9135	0.03292	0.1497:0.0899:0.2415:0.5188	.	416	Q6ZVF9	GRIN3_HUMAN	V	416	ENSP00000328672:G416V	ENSP00000328672:G416V	G	-	2	0	GPRIN3	90389038	0.000000	0.05858	0.014000	0.15608	0.026000	0.11368	-0.091000	0.11146	1.050000	0.40346	-0.290000	0.09829	GGG	C|0.991;A|0.009	0.009	strong		0.507	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370660	26370660	+	Missense_Mutation	SNP	G	G	A	rs12205731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26370660G>A	ENST00000356386.2	+	5	732	c.544G>A	c.(544-546)Gcc>Acc	p.A182T	BTN3A2_ENST00000396934.3_Missense_Mutation_p.A159T|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000377708.2_Missense_Mutation_p.A182T|BTN3A2_ENST00000396948.1_Missense_Mutation_p.A182T|BTN3A2_ENST00000508906.2_Missense_Mutation_p.A140T|BTN3A2_ENST00000527422.1_Missense_Mutation_p.A182T	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	182			A -> T (in dbSNP:rs12205731). {ECO:0000269|PubMed:14702039}.		interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						GTGGAGCAACGCCAAGGGAGA	0.552													G|||	315	0.0628994	0.0598	0.0519	5008	,	,		18361	0.0883		0.1024	False		,,,				2504	0.0082				p.A182T		Atlas-SNP	.											.	BTN3A2	44	.	0			c.G544A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	230,4176	136.1+/-172.1	4,222,1977	131.0	117.0	122.0		544,544,475,418,544	-3.4	0.0	6	dbSNP_120	122	638,7962	164.2+/-216.6	30,578,3692	no	missense,missense,missense,missense,missense	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	58,58,58,58,58	34,800,5669	AA,AG,GG		7.4186,5.2202,6.6738	benign,benign,benign,benign,benign	182/335,182/335,159/312,140/293,182/335	26370660	868,12138	2203	4300	6503	SO:0001583	missense	11118	exon3			AGCAACGCCAAGG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.544G>A	6.37:g.26370660G>A	ENSP00000348751:p.Ala182Thr	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	218	113	0.518349	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	195	0.08928571428571429	25	0.0508130081300813	20	0.055248618784530384	68	0.11888111888111888	82	0.10817941952506596	g	2.133	-0.398753	0.04865	0.052202	0.074186	ENSG00000186470	ENST00000532865;ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T;T	0.75704	-0.96;3.3;3.3;3.3;3.3;3.3;3.3	2.31	-3.42	0.04825	Immunoglobulin-like fold (1);	.	.	.	.	T	0.32406	0.0828	L	0.31294	0.92	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.0	T	0.02596	-1.1136	8	0.23302	T	0.38	.	5.2155	0.15340	0.0:0.3589:0.278:0.3631	rs12205731	159;182	F8W6E0;P78410	.;BT3A2_HUMAN	T	140;182;182;182;159;182;182;140	ENSP00000435952:A140T;ENSP00000432138:A182T;ENSP00000348751:A182T;ENSP00000380140:A159T;ENSP00000366937:A182T;ENSP00000380152:A182T;ENSP00000442687:A140T	ENSP00000348751:A182T	A	+	1	0	BTN3A2	26478639	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.675000	0.01947	-0.821000	0.04312	0.405000	0.27470	GCC	G|0.927;A|0.073	0.073	strong		0.552	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
SGK223	157285	hgsc.bcm.edu	37	8	8176770	8176770	+	Missense_Mutation	SNP	C	C	T	rs28533138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8176770C>T	ENST00000520004.1	-	6	3379	c.3115G>A	c.(3115-3117)Gtg>Atg	p.V1039M	SGK223_ENST00000330777.4_Missense_Mutation_p.V1039M			Q86YV5	SG223_HUMAN		1041	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TGCACGGGCACGGACGGGCTG	0.617													C|||	160	0.0319489	0.115	0.0086	5008	,	,		14630	0.0		0.002	False		,,,				2504	0.0				p.V1039M	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G3115A						PASS	.	C	MET/VAL	347,3795		11,325,1735	41.0	49.0	46.0		3115	5.3	1.0	8	dbSNP_125	46	14,8330		0,14,4158	yes	missense	SGK223	NM_001080826.1	21	11,339,5893	TT,TC,CC		0.1678,8.3776,2.8912	probably-damaging	1039/1403	8176770	361,12125	2071	4172	6243	SO:0001583	missense	0	exon5			CGGGCACGGACGG																												ENST00000520004.1:c.3115G>A	8.37:g.8176770C>T	ENSP00000428054:p.Val1039Met	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	58	0.026556776556776556	55	0.11178861788617886	3	0.008287292817679558	0	0.0	0	0.0	C	18.72	3.684827	0.68157	0.083776	0.001678	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.32515	1.45;1.45	5.33	5.33	0.75918	Protein kinase, catalytic domain (1);	0.318706	0.31809	N	0.007027	T	0.00496	0.0016	L	0.27053	0.805	0.46028	D	0.998827	D	0.58268	0.982	P	0.45449	0.481	T	0.00225	-1.1901	10	0.72032	D	0.01	.	14.0559	0.64769	0.0:0.8492:0.1508:0.0	rs28533138	1039	Q86YV5	SG223_HUMAN	M	1039	ENSP00000330930:V1039M;ENSP00000428054:V1039M	ENSP00000330930:V1039M	V	-	1	0	AC068353.1	8214180	1.000000	0.71417	0.959000	0.39883	0.726000	0.41606	4.871000	0.63042	2.670000	0.90874	0.467000	0.42956	GTG	C|0.982;T|0.018	0.018	strong		0.617	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
TMEM57	55219	hgsc.bcm.edu	37	1	25757607	25757607	+	Silent	SNP	C	C	T	rs114403991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:25757607C>T	ENST00000374343.4	+	1	197	c.18C>T	c.(16-18)gcC>gcT	p.A6A	TMEM57_ENST00000399763.3_Silent_p.A6A|RHCE_ENST00000349320.3_5'Flank|TMEM57_ENST00000399766.3_Silent_p.A6A	NM_018202.4	NP_060672.2	Q8N5G2	MACOI_HUMAN	transmembrane protein 57	6					brain development (GO:0007420)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|synapse (GO:0045202)				breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)		GGCGGAACGCCGACTGCAGTA	0.761													C|||	56	0.0111821	0.0371	0.0086	5008	,	,		5510	0.0		0.001	False		,,,				2504	0.0				p.A6A		Atlas-SNP	.											.	TMEM57	72	.	0			c.C18T						PASS	.	C		61,4291		0,61,2115	11.0	13.0	12.0		18	-0.5	1.0	1	dbSNP_132	12	1,8539		0,1,4269	no	coding-synonymous	TMEM57	NM_018202.4		0,62,6384	TT,TC,CC		0.0117,1.4017,0.4809		6/665	25757607	62,12830	2176	4270	6446	SO:0001819	synonymous_variant	55219	exon1			GAACGCCGACTGC	AK001609	CCDS30638.1, CCDS60034.1	1p36.11	2008-02-05			ENSG00000204178	ENSG00000204178			25572	protein-coding gene	gene with protein product		610301				12459264, 15255972	Standard	XM_005245931		Approved	FLJ10747	uc001bkk.3	Q8N5G2	OTTHUMG00000003473	ENST00000374343.4:c.18C>T	1.37:g.25757607C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	55	34	0.618182	NM_018202	B1AK00|Q2TLX5|Q2TLX6|Q9NVG6	Silent	SNP	ENST00000374343.4	37	CCDS30638.1																																																																																			C|0.992;T|0.008	0.008	strong		0.761	TMEM57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009659.2	NM_018202	
DSPP	1834	hgsc.bcm.edu	37	4	88535878	88535878	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88535878T>C	ENST00000282478.7	+	4	2097	c.2064T>C	c.(2062-2064)gaT>gaC	p.D688D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D688D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	688	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgatagtagtgaca	0.468																																					p.D688D		Atlas-SNP	.											.	DSPP	174	.	0			c.T2064C						PASS	.						118.0	132.0	127.0					4																	88535878		1673	3064	4737	SO:0001819	synonymous_variant	1834	exon5			CAGTGATAGTAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2064T>C	4.37:g.88535878T>C		Somatic	339	0	0		WXS	Illumina HiSeq	Phase_I	345	36	0.104348	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.468	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
PTGIS	5740	hgsc.bcm.edu	37	20	48140682	48140682	+	Silent	SNP	C	C	T	rs5628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48140682C>T	ENST00000244043.4	-	6	797	c.768G>A	c.(766-768)ctG>ctA	p.L256L	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	256					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	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)|prostaglandin-I synthase activity (GO:0008116)	p.L256L(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	GGTAACTCTCCAGCCATTTGC	0.627													C|||	620	0.123802	0.2027	0.121	5008	,	,		19573	0.1002		0.0646	False		,,,				2504	0.1043				p.L256L		Atlas-SNP	.											PTGIS,NS,carcinoma,0,1	PTGIS	60	1	1	Substitution - coding silent(1)	stomach(1)	c.G768A						PASS	.	C		679,3727	286.0+/-278.5	48,583,1572	127.0	105.0	113.0		768	4.3	1.0	20	dbSNP_52	113	525,8075	147.4+/-202.8	11,503,3786	no	coding-synonymous	PTGIS	NM_000961.3		59,1086,5358	TT,TC,CC		6.1047,15.4108,9.2573		256/501	48140682	1204,11802	2203	4300	6503	SO:0001819	synonymous_variant	5740	exon6			ACTCTCCAGCCAT		CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"""Cytochrome P450s"""	9603	protein-coding gene	gene with protein product	"""cytochrome P450, family 8, subfamily A, polypeptide 1"""	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.768G>A	20.37:g.48140682C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	208	108	0.519231	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Silent	SNP	ENST00000244043.4	37	CCDS13419.1																																																																																			C|0.897;T|0.103	0.103	strong		0.627	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2		
CCDC91	55297	hgsc.bcm.edu	37	12	28603112	28603112	+	Missense_Mutation	SNP	A	A	G	rs1133028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:28603112A>G	ENST00000545336.1	+	12	1200	c.781A>G	c.(781-783)Atg>Gtg	p.M261V	CCDC91_ENST00000381256.1_Missense_Mutation_p.M225V|CCDC91_ENST00000306172.5_Missense_Mutation_p.M231V|CCDC91_ENST00000381259.1_Missense_Mutation_p.M261V|CCDC91_ENST00000540401.1_3'UTR|CCDC91_ENST00000539107.1_Missense_Mutation_p.M225V			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	261	Homodimerization.		M -> V (in dbSNP:rs1133028).		protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					GCTCCTTGAAATGCTAGATAC	0.368													A|||	652	0.130192	0.4418	0.0605	5008	,	,		16544	0.0		0.0209	False		,,,				2504	0.0051				p.M261V		Atlas-SNP	.											.	CCDC91	63	.	0			c.A781G						PASS	.	A	VAL/MET	1612,2786		297,1018,884	60.0	71.0	67.0		781	4.8	1.0	12	dbSNP_86	67	175,8413		0,175,4119	yes	missense	CCDC91	NM_018318.3	21	297,1193,5003	GG,GA,AA		2.0377,36.653,13.761	benign	261/442	28603112	1787,11199	2199	4294	6493	SO:0001583	missense	55297	exon8			CTTGAAATGCTAG	AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"""GGA binding partner"""					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.781A>G	12.37:g.28603112A>G	ENSP00000438040:p.Met261Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_018318	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Missense_Mutation	SNP	ENST00000545336.1	37	CCDS8716.1	227	0.10393772893772894	197	0.40040650406504064	20	0.055248618784530384	0	0.0	10	0.013192612137203167	A	9.597	1.127791	0.20959	0.36653	0.020377	ENSG00000123106	ENST00000540794;ENST00000536154;ENST00000539107;ENST00000536442;ENST00000545336;ENST00000545737;ENST00000381259;ENST00000381256;ENST00000306172	T;T;T;T;T;T;T;T;T	0.52983	0.64;1.36;1.03;1.63;1.62;1.63;1.62;1.03;1.61	5.98	4.85	0.62838	.	0.214977	0.42420	N	0.000705	T	0.00012	0.0000	N	0.08118	0	0.41847	P	0.009843999999999964	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41980	-0.9478	9	0.11485	T	0.65	-9.2621	9.29	0.37780	0.9181:0.0:0.0819:0.0	rs1133028;rs3194433;rs11049614;rs61569269;rs1133028	225;261;231	Q7Z6B0-3;Q7Z6B0;Q7Z6B0-2	.;CCD91_HUMAN;.	V	57;1;225;261;261;261;261;225;231	ENSP00000441714:M57V;ENSP00000444440:M1V;ENSP00000440513:M225V;ENSP00000445660:M261V;ENSP00000438040:M261V;ENSP00000442544:M261V;ENSP00000370658:M261V;ENSP00000370655:M225V;ENSP00000305075:M231V	ENSP00000305075:M231V	M	+	1	0	CCDC91	28494379	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.951000	0.56684	1.099000	0.41499	0.482000	0.46254	ATG	A|0.875;G|0.125	0.125	strong		0.368	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1	NM_018318	
OR10T2	128360	hgsc.bcm.edu	37	1	158368915	158368915	+	Silent	SNP	G	G	T	rs56704148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158368915G>T	ENST00000334438.1	-	1	341	c.342C>A	c.(340-342)ctC>ctA	p.L114L		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	114						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)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					CAGCAATGAGGAGGCAGTTGG	0.498													G|||	46	0.0091853	0.034	0.0014	5008	,	,		21129	0.0		0.0	False		,,,				2504	0.0				p.L114L		Atlas-SNP	.											.	OR10T2	76	.	0			c.C342A						PASS	.	G		139,4267	98.0+/-136.7	5,129,2069	122.0	121.0	121.0		342	-1.0	1.0	1	dbSNP_129	121	0,8600		0,0,4300	no	coding-synonymous	OR10T2	NM_001004475.1		5,129,6369	TT,TG,GG		0.0,3.1548,1.0687		114/315	158368915	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	128360	exon1			AATGAGGAGGCAG	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.342C>A	1.37:g.158368915G>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	NM_001004475	Q6IF98	Silent	SNP	ENST00000334438.1	37	CCDS30895.1																																																																																			G|0.989;T|0.011	0.011	strong		0.498	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
SPATA17	128153	hgsc.bcm.edu	37	1	217824488	217824488	+	Silent	SNP	T	T	C	rs143446051		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:217824488T>C	ENST00000366933.4	+	3	263	c.208T>C	c.(208-210)Tta>Cta	p.L70L		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	70	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		GAGAAGTTTCTTAGGCAGAAA	0.299													T|||	1	0.000199681	0.0	0.0	5008	,	,		18465	0.0		0.001	False		,,,				2504	0.0				p.L70L		Atlas-SNP	.											.	SPATA17	59	.	0			c.T208C						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	84.0	94.0	91.0		208	2.5	1.0	1	dbSNP_134	91	15,8569	10.5+/-38.8	0,15,4277	no	coding-synonymous	SPATA17	NM_138796.2		0,16,6479	CC,CT,TT		0.1747,0.0227,0.1232		70/362	217824488	16,12974	2203	4292	6495	SO:0001819	synonymous_variant	128153	exon3			AGTTTCTTAGGCA	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"""IQ motif containing H"""	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.208T>C	1.37:g.217824488T>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	217	104	0.479263	NM_138796	A5D6N2	Silent	SNP	ENST00000366933.4	37	CCDS1519.1																																																																																			T|0.998;C|0.002	0.002	strong		0.299	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796	
RRP7A	27341	hgsc.bcm.edu	37	22	42910142	42910142	+	Missense_Mutation	SNP	C	C	T	rs61731241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42910142C>T	ENST00000323013.6	-	6	742	c.727G>A	c.(727-729)Gcc>Acc	p.A243T	SERHL_ENST00000359906.2_RNA	NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	243							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						TGCTGCCAGGCGTAGAAGTTG	0.667													C|||	247	0.0493211	0.1793	0.013	5008	,	,		21135	0.0		0.001	False		,,,				2504	0.0				p.A243T		Atlas-SNP	.											.	RRP7A	25	.	0			c.G727A						PASS	.	C	THR/ALA	589,3817		31,527,1645	53.0	36.0	42.0		727	3.7	0.9	22	dbSNP_129	42	18,8582		0,18,4282	yes	missense	RRP7A	NM_015703.4	58	31,545,5927	TT,TC,CC		0.2093,13.3681,4.6671	benign	243/281	42910142	607,12399	2203	4300	6503	SO:0001583	missense	27341	exon6			GCCAGGCGTAGAA	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.727G>A	22.37:g.42910142C>T	ENSP00000321449:p.Ala243Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Missense_Mutation	SNP	ENST00000323013.6	37	CCDS14036.1	84	0.038461538461538464	78	0.15853658536585366	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	.	6.304	0.424130	0.11928	0.133681	0.002093	ENSG00000189306	ENST00000323013	T	0.22539	1.95	3.66	3.66	0.41972	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.164932	0.53938	D	0.000046	T	0.00039	0.0001	N	0.03999	-0.3	0.21967	P	0.999444231	P;B	0.45396	0.857;0.364	B;B	0.35510	0.204;0.121	T	0.42292	-0.9460	9	0.16420	T	0.52	-28.9794	15.7164	0.77672	0.0:1.0:0.0:0.0	.	243;66	Q9Y3A4;Q9NSQ0	RRP7A_HUMAN;RRP7B_HUMAN	T	243	ENSP00000321449:A243T	ENSP00000321449:A243T	A	-	1	0	RRP7A	41240086	0.995000	0.38212	0.922000	0.36590	0.018000	0.09664	3.198000	0.51035	1.747000	0.51819	0.205000	0.17691	GCC	C|0.958;T|0.042	0.042	strong		0.667	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703	
TMCO3	55002	hgsc.bcm.edu	37	13	114154419	114154419	+	Silent	SNP	G	G	A	rs2260159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114154419G>A	ENST00000434316.2	+	4	1130	c.771G>A	c.(769-771)aaG>aaA	p.K257K	TMCO3_ENST00000375391.1_Silent_p.K257K|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	257						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			TTTTGACCAAGCCCAGAGATT	0.463													.|||	1019	0.203474	0.4092	0.1369	5008	,	,		16314	0.1488		0.1292	False		,,,				2504	0.1053				p.K257K		Atlas-SNP	.											.	TMCO3	77	.	0			c.G771A						PASS	.	G		1511,2895	481.5+/-359.1	256,999,948	119.0	120.0	120.0		771	1.5	0.9	13	dbSNP_100	120	1086,7514	226.2+/-262.0	62,962,3276	yes	coding-synonymous	TMCO3	NM_017905.4		318,1961,4224	AA,AG,GG		12.6279,34.2941,19.9677		257/678	114154419	2597,10409	2203	4300	6503	SO:0001819	synonymous_variant	55002	exon4			GACCAAGCCCAGA	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.771G>A	13.37:g.114154419G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																			G|0.796;A|0.204	0.204	strong		0.463	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
WDR63	126820	hgsc.bcm.edu	37	1	85594466	85594466	+	Missense_Mutation	SNP	G	G	A	rs709783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:85594466G>A	ENST00000294664.6	+	21	2573	c.2393G>A	c.(2392-2394)cGc>cAc	p.R798H	WDR63_ENST00000370596.1_Missense_Mutation_p.R759H|WDR63_ENST00000326813.8_Missense_Mutation_p.R759H	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	798			R -> H (in dbSNP:rs709783).							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)		ACATTAAGTCGCCCTTCCACC	0.323													G|||	1090	0.217652	0.3245	0.2406	5008	,	,		18925	0.2133		0.1829	False		,,,				2504	0.0971				p.R798H		Atlas-SNP	.											WDR63,colon,carcinoma,0,1	WDR63	91	1	0			c.G2393A						PASS	.	G	HIS/ARG	1338,3068	427.6+/-341.6	215,908,1080	76.0	78.0	78.0		2393	3.5	1.0	1	dbSNP_86	78	1448,7152	274.5+/-291.2	132,1184,2984	yes	missense	WDR63	NM_145172.3	29	347,2092,4064	AA,AG,GG		16.8372,30.3677,21.4209	benign	798/892	85594466	2786,10220	2203	4300	6503	SO:0001583	missense	126820	exon21			TAAGTCGCCCTTC		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.2393G>A	1.37:g.85594466G>A	ENSP00000294664:p.Arg798His	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	189	95	0.502645	NM_145172	A8K988|Q96L72|Q96NU4	Missense_Mutation	SNP	ENST00000294664.6	37	CCDS702.1	520	0.23809523809523808	160	0.3252032520325203	93	0.2569060773480663	134	0.23426573426573427	133	0.17546174142480211	G	1.362	-0.588500	0.03799	0.303677	0.168372	ENSG00000162643	ENST00000370596;ENST00000326813;ENST00000294664;ENST00000484007	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.81	3.49	0.39957	.	0.394740	0.30686	N	0.009081	T	0.06050	0.0157	N	0.01529	-0.815	0.37425	P	0.08620499999999998	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.20773	-1.0265	9	0.30078	T	0.28	-11.261	9.9147	0.41427	0.8588:0.0:0.1412:0.0	rs709783;rs11564847;rs17121817;rs57576192;rs709783	759;798	Q8IWG1-2;Q8IWG1	.;WDR63_HUMAN	H	759;759;798;80	ENSP00000359628:R759H;ENSP00000317463:R759H;ENSP00000294664:R798H;ENSP00000435544:R80H	ENSP00000294664:R798H	R	+	2	0	WDR63	85367054	0.925000	0.31364	1.000000	0.80357	0.760000	0.43138	1.110000	0.31147	0.466000	0.27193	-0.384000	0.06662	CGC	G|0.780;A|0.220	0.220	strong		0.323	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172	
OBSL1	23363	hgsc.bcm.edu	37	2	220427347	220427347	+	Silent	SNP	G	G	T	rs10804275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220427347G>T	ENST00000404537.1	-	8	2786	c.2730C>A	c.(2728-2730)gcC>gcA	p.A910A	OBSL1_ENST00000373876.1_Silent_p.A910A|OBSL1_ENST00000373873.4_Silent_p.A910A|OBSL1_ENST00000265318.4_Silent_p.A910A|OBSL1_ENST00000289656.3_Silent_p.A497A|OBSL1_ENST00000603926.1_Silent_p.A910A|RP11-256I23.2_ENST00000597192.1_RNA	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	110	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	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		
DDX55	57696	hgsc.bcm.edu	37	12	124090655	124090655	+	Silent	SNP	C	C	T	rs7973689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124090655C>T	ENST00000238146.4	+	3	245	c.195C>T	c.(193-195)atC>atT	p.I65I	DDX55_ENST00000538744.1_Silent_p.I65I	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	65	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					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)		CTTTTGTCATCCCCATCCTGG	0.428													C|||	364	0.0726837	0.2315	0.0202	5008	,	,		20720	0.0		0.0159	False		,,,				2504	0.0286				p.I65I		Atlas-SNP	.											.	DDX55	51	.	0			c.C195T						PASS	.	C		764,3642	308.0+/-290.3	67,630,1506	81.0	76.0	77.0		195	1.6	1.0	12	dbSNP_116	77	163,8437	74.2+/-136.8	0,163,4137	no	coding-synonymous	DDX55	NM_020936.1		67,793,5643	TT,TC,CC		1.8953,17.34,7.1275		65/601	124090655	927,12079	2203	4300	6503	SO:0001819	synonymous_variant	57696	exon3			TGTCATCCCCATC	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.195C>T	12.37:g.124090655C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	105	56	0.533333	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Silent	SNP	ENST00000238146.4	37	CCDS9251.1																																																																																			C|0.929;T|0.071	0.071	strong		0.428	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
FAM179B	23116	hgsc.bcm.edu	37	14	45432870	45432870	+	Missense_Mutation	SNP	G	G	C	rs3825629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45432870G>C	ENST00000361577.3	+	1	1460	c.1246G>C	c.(1246-1248)Gaa>Caa	p.E416Q	KLHL28_ENST00000553817.1_5'Flank|FAM179B_ENST00000361462.2_Missense_Mutation_p.E416Q|KLHL28_ENST00000355081.2_5'Flank|KLHL28_ENST00000396128.4_5'Flank|FAM179B_ENST00000382233.2_Missense_Mutation_p.E416Q	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	416			E -> Q (in dbSNP:rs3825629).							endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TGGCACACTTGAAGTCCTGCA	0.428													C|||	943	0.188299	0.4637	0.0879	5008	,	,		8589	0.1022		0.0626	False		,,,				2504	0.1053				p.E416Q		Atlas-SNP	.											.	FAM179B	115	.	0			c.G1246C						PASS	.	C	GLN/GLU	1661,2745	657.7+/-400.3	302,1057,844	105.0	106.0	106.0		1246	4.3	1.0	14	dbSNP_107	106	471,8129	798.2+/-407.4	14,443,3843	yes	missense	FAM179B	NM_015091.2	29	316,1500,4687	CC,CG,GG		5.4767,37.6986,16.3924	benign	416/1721	45432870	2132,10874	2203	4300	6503	SO:0001583	missense	23116	exon1			ACACTTGAAGTCC	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.1246G>C	14.37:g.45432870G>C	ENSP00000355045:p.Glu416Gln	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	23	15	0.652174	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	367	0.16804029304029305	222	0.45121951219512196	34	0.09392265193370165	57	0.09965034965034965	54	0.0712401055408971	C	0.399	-0.919512	0.02396	0.376986	0.054767	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233	T;T;T	0.38887	1.11;1.11;1.11	4.28	4.28	0.50868	Armadillo-like helical (1);Armadillo-type fold (1);	0.084949	0.47455	N	0.000224	T	0.00012	0.0000	N	0.16656	0.425	0.49798	P	1.7100000000003224E-4	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.001;0.002	T	0.42999	-0.9418	9	0.12766	T	0.61	-3.5298	13.087	0.59146	0.0:0.5058:0.4942:0.0	rs3825629;rs57443716;rs3825629	416;416;416;416	Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2	.;.;F179B_HUMAN;.	Q	416	ENSP00000355045:E416Q;ENSP00000354917:E416Q;ENSP00000371668:E416Q	ENSP00000354917:E416Q	E	+	1	0	FAM179B	44502620	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.982000	0.49337	1.155000	0.42497	-0.225000	0.12378	GAA	G|0.836;C|0.164	0.164	strong		0.428	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	
TBX18	9096	hgsc.bcm.edu	37	6	85446965	85446965	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:85446965G>A	ENST00000369663.5	-	8	1599	c.1262C>T	c.(1261-1263)gCc>gTc	p.A421V	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	421					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		GCCTGAGCGGGCACAGGCAGA	0.597																																					p.A421V		Atlas-SNP	.											TBX18,colon,carcinoma,0,1	TBX18	131	1	0			c.C1262T						scavenged	.						96.0	90.0	92.0					6																	85446965		2203	4300	6503	SO:0001583	missense	9096	exon8			GAGCGGGCACAGG	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"""T-boxes"""	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1262C>T	6.37:g.85446965G>A	ENSP00000358677:p.Ala421Val	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	276	4	0.0144928	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Missense_Mutation	SNP	ENST00000369663.5	37	CCDS34495.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.790408	0.50102	.	.	ENSG00000112837	ENST00000369663	D	0.87809	-2.3	5.18	5.18	0.71444	.	0.663219	0.16235	N	0.223391	T	0.74786	0.3762	L	0.27053	0.805	0.38020	D	0.934815	P	0.41313	0.745	B	0.44278	0.445	T	0.72484	-0.4279	10	0.17369	T	0.5	.	14.3045	0.66375	0.0:0.1486:0.8514:0.0	.	421	O95935	TBX18_HUMAN	V	421	ENSP00000358677:A421V	ENSP00000358677:A421V	A	-	2	0	TBX18	85503684	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	4.279000	0.58953	2.409000	0.81822	0.585000	0.79938	GCC	.	.	none		0.597	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508	
NCF1	653361	hgsc.bcm.edu	37	7	74193718	74193718	+	Silent	SNP	C	C	T	rs17356100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:74193718C>T	ENST00000289473.4	+	4	415	c.345C>T	c.(343-345)ctC>ctT	p.L115L	NCF1_ENST00000443956.3_3'UTR	NM_000265.4	NP_000256.4	P14598	NCF1_HUMAN	neutrophil cytosolic factor 1	115	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)|cell proliferation (GO:0008283)|cellular defense response (GO:0006968)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|leukotriene metabolic process (GO:0006691)|negative regulation of smooth muscle contraction (GO:0045986)|neutrophil mediated killing of fungus (GO:0070947)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|protein targeting to membrane (GO:0006612)|respiratory burst (GO:0045730)|respiratory burst involved in defense response (GO:0002679)|response to yeast (GO:0001878)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagolysosome (GO:0032010)|rough endoplasmic reticulum (GO:0005791)	electron carrier activity (GO:0009055)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)	p.L115L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10					Dextromethorphan(DB00514)	CCCACCTCCTCGACTTCTTCA	0.637																																					p.L115L		Atlas-SNP	.											NCF1,NS,carcinoma,0,1	NCF1	26	1	1	Substitution - coding silent(1)	endometrium(1)	c.C345T						scavenged	.																																			SO:0001819	synonymous_variant	653361	exon4			CCTCCTCGACTTC	M25665	CCDS34657.1	7q11.23	2014-09-17	2008-07-31		ENSG00000158517	ENSG00000158517			7660	protein-coding gene	gene with protein product	"""NADPH oxidase organizer 2"", ""chronic granulomatous disease, autosomal 1"""	608512	"""neutrophil cytosolic factor 1 (47kD, chronic granulomatous disease, autosomal 1)"""				Standard	NM_000265		Approved	p47phox, NOXO2, NCF1A, SH3PXD1A	uc022aft.1	P14598	OTTHUMG00000149965	ENST00000289473.4:c.345C>T	7.37:g.74193718C>T		Somatic	396	0	0		WXS	Illumina HiSeq	Phase_I	362	76	0.209945	NM_000265	A6NEH2|A8K7S9|O43842|Q2PP07|Q53FR5|Q9BU90|Q9BXI7|Q9BXI8|Q9UDV9|Q9UMU2	Silent	SNP	ENST00000289473.4	37	CCDS34657.1																																																																																			C|0.500;T|0.500	0.500	weak		0.637	NCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314560.1	NM_000265	
LAMB4	22798	hgsc.bcm.edu	37	7	107756510	107756510	+	Missense_Mutation	SNP	A	A	G	rs35644375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107756510A>G	ENST00000388781.3	-	3	214	c.131T>C	c.(130-132)aTg>aCg	p.M44T	LAMB4_ENST00000418464.1_Missense_Mutation_p.M44T|LAMB4_ENST00000388780.3_Missense_Mutation_p.M44T|LAMB4_ENST00000414450.2_Missense_Mutation_p.M44T|LAMB4_ENST00000205386.4_Missense_Mutation_p.M44T	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	44	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.		M -> T (in dbSNP:rs35644375).		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						AGAAGAAGCCATAAGCTGCGT	0.512													G|||	503	0.100439	0.3631	0.0317	5008	,	,		19458	0.0		0.001	False		,,,				2504	0.0				p.M44T		Atlas-SNP	.											.	LAMB4	253	.	0			c.T131C						PASS	.	G	THR/MET	1279,3127	700.8+/-406.7	186,907,1110	105.0	106.0	106.0		131	2.8	0.0	7	dbSNP_126	106	32,8568	817.9+/-406.9	0,32,4268	yes	missense	LAMB4	NM_007356.2	81	186,939,5378	GG,GA,AA		0.3721,29.0286,10.08	benign	44/1762	107756510	1311,11695	2203	4300	6503	SO:0001583	missense	22798	exon3			GAAGCCATAAGCT	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.131T>C	7.37:g.107756510A>G	ENSP00000373433:p.Met44Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	190	0.08699633699633699	177	0.3597560975609756	13	0.03591160220994475	0	0.0	0	0.0	G	0.019	-1.450644	0.01080	0.290286	0.003721	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78;-0.78	5.6	2.81	0.32909	Laminin, N-terminal (3);	0.560407	0.16178	N	0.225961	T	0.00012	0.0000	N	0.00099	-2.14	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26849	-1.0091	9	0.06625	T	0.88	.	6.7977	0.23734	0.2544:0.0:0.6319:0.1136	rs35644375;rs60836843	44	A4D0S4	LAMB4_HUMAN	T	44	ENSP00000205386:M44T;ENSP00000373433:M44T;ENSP00000373432:M44T;ENSP00000402353:M44T;ENSP00000402265:M44T	ENSP00000205386:M44T	M	-	2	0	LAMB4	107543746	0.000000	0.05858	0.003000	0.11579	0.082000	0.17680	0.434000	0.21494	0.049000	0.15920	-0.735000	0.03563	ATG	A|0.908;G|0.092	0.092	strong		0.512	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
PRAMEF11	440560	hgsc.bcm.edu	37	1	12885289	12885289	+	Silent	SNP	G	G	T	rs200907281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12885289G>T	ENST00000535591.1	-	4	1017	c.822C>A	c.(820-822)ctC>ctA	p.L274L	RP5-845O24.8_ENST00000438401.1_lincRNA	NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	274					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.L274L(3)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						GGCACTGGGAGAGATGCTTCA	0.458													.|||	1958	0.390974	0.1899	0.3501	5008	,	,		13255	0.6895		0.4553	False		,,,				2504	0.318				p.L274L		Atlas-SNP	.											PRAMEF11,NS,carcinoma,0,7	PRAMEF11	72	7	3	Substitution - coding silent(3)	kidney(2)|endometrium(1)	c.C822A						scavenged	.						67.0	40.0	49.0					1																	12885289		582	1168	1750	SO:0001819	synonymous_variant	440560	exon4			CTGGGAGAGATGC	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.822C>A	1.37:g.12885289G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	60	6	0.1	NM_001146344		Silent	SNP	ENST00000535591.1	37	CCDS53268.1																																																																																			T|1.000;|0.000	1.000	weak		0.458	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
FANCI	55215	hgsc.bcm.edu	37	15	89849413	89849413	+	Silent	SNP	C	C	A	rs114810692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89849413C>A	ENST00000310775.7	+	32	3611	c.3525C>A	c.(3523-3525)gcC>gcA	p.A1175A	FANCI_ENST00000300027.8_Silent_p.A1115A	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	1175					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CACTTACAGCCCTTGTCAGAT	0.512								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	33	0.00658946	0.0242	0.0014	5008	,	,		19687	0.0		0.0	False		,,,				2504	0.0				p.A1175A		Atlas-SNP	.											.	FANCI	129	.	0			c.C3525A						PASS	.	C	,	75,4325	66.4+/-103.9	0,75,2125	109.0	96.0	100.0		3525,3345	-10.8	0.6	15	dbSNP_132	100	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous	FANCI	NM_001113378.1,NM_018193.2	,	0,76,6423	AA,AC,CC		0.0116,1.7045,0.5847	,	1175/1329,1115/1269	89849413	76,12922	2200	4299	6499	SO:0001819	synonymous_variant	55215	exon32	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TACAGCCCTTGTC	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.3525C>A	15.37:g.89849413C>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Silent	SNP	ENST00000310775.7	37	CCDS45346.1																																																																																			C|0.994;A|0.006	0.006	strong		0.512	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
SCN3B	55800	hgsc.bcm.edu	37	11	123516316	123516316	+	Silent	SNP	G	G	A	rs115752338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123516316G>A	ENST00000392770.2	-	2	1000	c.198C>T	c.(196-198)ccC>ccT	p.P66P	SCN3B_ENST00000530277.1_Silent_p.P66P|SCN3B_ENST00000299333.3_Silent_p.P66P	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	66	Ig-like C2-type.				atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|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 depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|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)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	TACCGCCCTCGGGCCTGTAGA	0.597													A|||	46	0.0091853	0.0325	0.0043	5008	,	,		19339	0.0		0.0	False		,,,				2504	0.0				p.P66P		Atlas-SNP	.											.	SCN3B	53	.	0			c.C198T						PASS	.	A	,	118,4286	815.4+/-416.2	2,114,2086	131.0	135.0	134.0		198,198	-11.9	0.0	11	dbSNP_132	134	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	SCN3B	NM_001040151.1,NM_018400.3	,	2,114,6385	AA,AG,GG		0.0,2.6794,0.9076	,	66/216,66/216	123516316	118,12884	2202	4299	6501	SO:0001819	synonymous_variant	55800	exon2			GCCCTCGGGCCTG	AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"", ""Immunoglobulin superfamily / V-set domain containing"""	20665	protein-coding gene	gene with protein product		608214	"""sodium channel, voltage-gated, type III, beta"""			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.198C>T	11.37:g.123516316G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	112	68	0.607143	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Silent	SNP	ENST00000392770.2	37	CCDS8442.1																																																																																			G|0.990;A|0.010	0.010	strong		0.597	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400	
TMEM218	219854	hgsc.bcm.edu	37	11	124972114	124972114	+	Silent	SNP	G	G	A	rs7114520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124972114G>A	ENST00000279968.4	-	3	347	c.24C>T	c.(22-24)gtC>gtT	p.V8V	TMEM218_ENST00000529583.1_Silent_p.V8V|TMEM218_ENST00000532407.1_Silent_p.V8V|TMEM218_ENST00000527271.1_Silent_p.V8V|TMEM218_ENST00000526175.1_Silent_p.V8V|TMEM218_ENST00000455225.1_Silent_p.V8V|TMEM218_ENST00000528724.1_Silent_p.V8V|TMEM218_ENST00000527766.1_Silent_p.V8V|TMEM218_ENST00000531909.1_Silent_p.V8V|TMEM218_ENST00000529609.1_Silent_p.V8V|TMEM218_ENST00000531262.1_Intron|TMEM218_ENST00000532156.1_Silent_p.V8V			A2RU14	TM218_HUMAN	transmembrane protein 218	8						integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						CGCCCGCACCGACTCCGAGCA	0.682													G|||	294	0.0587061	0.1861	0.0115	5008	,	,		12552	0.001		0.008	False		,,,				2504	0.0317				p.V43V		Atlas-SNP	.											.	TMEM218	14	.	0			c.C129T						PASS	.	G		735,3661	293.8+/-282.8	52,631,1515	42.0	43.0	43.0		24	0.9	1.0	11	dbSNP_116	43	70,8520	41.7+/-99.0	0,70,4225	no	coding-synonymous	TMEM218	NM_001080546.1		52,701,5740	AA,AG,GG		0.8149,16.7197,6.199		8/116	124972114	805,12181	2198	4295	6493	SO:0001819	synonymous_variant	219854	exon4			CGCACCGACTCCG		CCDS31715.1	11q24.2	2008-08-08			ENSG00000150433	ENSG00000150433			27344	protein-coding gene	gene with protein product							Standard	NM_001258238		Approved		uc031qeu.1	A2RU14		ENST00000279968.4:c.24C>T	11.37:g.124972114G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_001258243	B7ZM48	Silent	SNP	ENST00000279968.4	37	CCDS31715.1																																																																																			G|0.946;A|0.054	0.054	strong		0.682	TMEM218-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386849.1	NM_001080546	
FLG	2312	hgsc.bcm.edu	37	1	152277055	152277055	+	Missense_Mutation	SNP	C	C	G	rs2065955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152277055C>G	ENST00000368799.1	-	3	10342	c.10307G>C	c.(10306-10308)gGa>gCa	p.G3436A	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	399	0	0		WXS	Illumina HiSeq	Phase_I	364	330	0.906593	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	
MED15	51586	hgsc.bcm.edu	37	22	20909389	20909389	+	Silent	SNP	G	G	A	rs147554746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:20909389G>A	ENST00000263205.7	+	5	474	c.405G>A	c.(403-405)ggG>ggA	p.G135G	MED15_ENST00000425759.2_Intron|MED15_ENST00000542773.1_Intron|MED15_ENST00000382974.2_Intron|MED15_ENST00000406969.1_Silent_p.G109G|MED15_ENST00000292733.7_Silent_p.G135G|MED15_ENST00000541476.1_Silent_p.G109G	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	135					gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			GGACCTCGGGGATGGCCCCTC	0.612													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17772	0.0		0.0	False		,,,				2504	0.0				p.G135G		Atlas-SNP	.											.	MED15	68	.	0			c.G405A						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	29.0	29.0	29.0		405,405	-2.0	1.0	22	dbSNP_134	29	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MED15	NM_001003891.1,NM_015889.3	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	135/789,135/749	20909389	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51586	exon5			CTCGGGGATGGCC	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.405G>A	22.37:g.20909389G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_015889	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Silent	SNP	ENST00000263205.7	37	CCDS33602.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.36	1.615678	0.28801	2.27E-4	0.0	ENSG00000099917	ENST00000423862	.	.	.	5.46	-2.03	0.07365	.	.	.	.	.	T	0.39279	0.1072	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31724	-0.9933	4	.	.	.	.	1.4274	0.02326	0.2499:0.2738:0.3381:0.1381	.	.	.	.	N	76	.	.	D	+	1	0	MED15	19239389	0.446000	0.25665	0.981000	0.43875	0.986000	0.74619	-0.516000	0.06282	-0.109000	0.12044	-0.225000	0.12378	GAT	G|1.000;A|0.000	0.000	strong		0.612	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037580	33037580	+	Missense_Mutation	SNP	T	T	G	rs36013091|rs2308911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33037580T>G	ENST00000419277.1	-	3	313	c.184A>C	c.(184-186)Atg>Ctg	p.M62L	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.M62L	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	62	Alpha-1.		M -> K (in dbSNP:rs2308912).|M -> L (in dbSNP:rs2308911).|M -> Q (in allele DPA1*01:06, allele DPA1*02:01, allele DPA1*02:02 and allele DPA1*02:04; requires 2 nucleotide substitutions; dbSNP:rs36013091).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						ACATAGAACATCTCATCTTCA	0.488													.|||	2159	0.43111	0.5794	0.2795	5008	,	,		19572	0.6508		0.1869	False		,,,				2504	0.363				p.M62L		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.A184C						PASS	.	T	LEU/MET,LEU/MET,LEU/MET	45,2975		3,39,1468	62.0	87.0	78.0		184,184,184	-6.0	0.0	6	dbSNP_126	78	7,5411		0,7,2702	no	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	15,15,15	3,46,4170	GG,GT,TT		0.1292,1.4901,0.6163	benign,benign,benign	62/261,62/261,62/261	33037580	52,8386	1510	2709	4219	SO:0001583	missense	3113	exon2			AGAACATCTCATC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.184A>C	6.37:g.33037580T>G	ENSP00000393566:p.Met62Leu	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	760	0.34798534798534797	239	0.48577235772357724	78	0.2154696132596685	329	0.5751748251748252	114	0.1503957783641161	T	0.001	-3.735704	0.00005	0.014901	0.001292	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.00623	6.15;6.15;6.15	3.0	-5.99	0.02213	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	2.490280	0.02659	U	0.107291	T	0.00109	0.0003	N	0.13003	0.285	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48502	-0.9030	9	0.02654	T	1	.	2.9736	0.05930	0.092:0.1781:0.3519:0.378	rs2308911;rs12722001;rs52808337	62	P20036	DPA1_HUMAN	L	62	ENSP00000393566:M62L;ENSP00000402872:M62L;ENSP00000390929:M62L	ENSP00000393566:M62L	M	-	1	0	HLA-DPA1	33145558	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	-2.357000	0.01086	-3.633000	0.00129	-1.423000	0.01107	ATG	T|0.716;G|0.284	0.284	strong		0.488	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
ZNF292	23036	hgsc.bcm.edu	37	6	87969341	87969341	+	Silent	SNP	G	G	A	rs16878809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:87969341G>A	ENST00000369577.3	+	8	6037	c.5994G>A	c.(5992-5994)ccG>ccA	p.P1998P	ZNF292_ENST00000339907.4_Silent_p.P1993P	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1998						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AAAATGTGCCGGCCTCACGAA	0.388													G|||	390	0.0778754	0.2171	0.0375	5008	,	,		17704	0.001		0.0447	False		,,,				2504	0.0317				p.P1998P		Atlas-SNP	.											.	ZNF292	479	.	0			c.G5994A						PASS	.	G		678,2966		59,560,1203	16.0	15.0	15.0		5994	2.1	0.0	6	dbSNP_123	15	303,7837		5,293,3772	no	coding-synonymous	ZNF292	NM_015021.1		64,853,4975	AA,AG,GG		3.7224,18.6059,8.3248		1998/2724	87969341	981,10803	1822	4070	5892	SO:0001819	synonymous_variant	23036	exon8			TGTGCCGGCCTCA	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.5994G>A	6.37:g.87969341G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Silent	SNP	ENST00000369577.3	37	CCDS47457.1																																																																																			G|0.910;A|0.090	0.090	strong		0.388	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
SLC26A3	1811	hgsc.bcm.edu	37	7	107423254	107423254	+	Silent	SNP	C	C	T	rs3735605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107423254C>T	ENST00000340010.5	-	11	1483	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	SLC26A3_ENST00000422236.2_Silent_p.A398A	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	433					anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						TTTGTAGAGGCGCCAGGAGAA	0.413													C|||	756	0.150958	0.0552	0.1369	5008	,	,		18734	0.2758		0.175	False		,,,				2504	0.137				p.A433A		Atlas-SNP	.											SLC26A3,caecum,carcinoma,0,1	SLC26A3	120	1	0			c.G1299A						PASS	.	C		328,4078	174.4+/-204.0	16,296,1891	86.0	85.0	85.0		1299	-0.1	0.1	7	dbSNP_107	85	1523,7077	287.5+/-298.3	148,1227,2925	no	coding-synonymous	SLC26A3	NM_000111.2		164,1523,4816	TT,TC,CC		17.7093,7.4444,14.2319		433/765	107423254	1851,11155	2203	4300	6503	SO:0001819	synonymous_variant	1811	exon11			TAGAGGCGCCAGG	L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"""Solute carriers"""	3018	protein-coding gene	gene with protein product		126650	"""congenital chloride diarrhea"", ""solute carrier family 26, member 3"""	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.1299G>A	7.37:g.107423254C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_000111		Silent	SNP	ENST00000340010.5	37	CCDS5748.1																																																																																			C|0.847;T|0.153	0.153	strong		0.413	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111	
HELB	92797	hgsc.bcm.edu	37	12	66700273	66700273	+	Silent	SNP	G	G	A	rs12227179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:66700273G>A	ENST00000247815.4	+	3	815	c.756G>A	c.(754-756)ccG>ccA	p.P252P		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	252					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)		GTACACATCCGTGGAAACTTG	0.363													G|||	343	0.0684904	0.0802	0.013	5008	,	,		17951	0.1468		0.003	False		,,,				2504	0.0787				p.P252P		Atlas-SNP	.											.	HELB	90	.	0			c.G756A						PASS	.	G		304,4102	164.4+/-196.0	6,292,1905	100.0	106.0	104.0		756	-5.3	0.9	12	dbSNP_120	104	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	HELB	NM_033647.2		6,319,6178	AA,AG,GG		0.314,6.8997,2.545		252/1088	66700273	331,12675	2203	4300	6503	SO:0001819	synonymous_variant	92797	exon3			ACATCCGTGGAAA	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.756G>A	12.37:g.66700273G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	83	33	0.39759	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Silent	SNP	ENST00000247815.4	37	CCDS8976.1																																																																																			G|0.966;A|0.034	0.034	strong		0.363	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
RBM19	9904	hgsc.bcm.edu	37	12	114358449	114358449	+	Silent	SNP	C	C	T	rs79120696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114358449C>T	ENST00000545145.2	-	19	2430	c.2352G>A	c.(2350-2352)ccG>ccA	p.P784P	RBM19_ENST00000392561.3_Silent_p.P784P|RBM19_ENST00000261741.5_Silent_p.P784P	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	784	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)					GGGCTTGCTCCGGCTTCCTGT	0.562													C|||	384	0.0766773	0.2716	0.0317	5008	,	,		16543	0.0		0.003	False		,,,				2504	0.0				p.P784P		Atlas-SNP	.											.	RBM19	117	.	0			c.G2352A						PASS	.	C	,,	1093,3313	394.4+/-329.3	152,789,1262	237.0	239.0	238.0		2352,2352,2352	-10.0	0.3	12	dbSNP_131	238	10,8590	5.7+/-21.5	0,10,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	152,799,5552	TT,TC,CC		0.1163,24.8071,8.4807	,,	784/961,784/961,784/961	114358449	1103,11903	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon19			TTGCTCCGGCTTC	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.2352G>A	12.37:g.114358449C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			C|0.917;T|0.083	0.083	strong		0.562	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
GPRC6A	222545	hgsc.bcm.edu	37	6	117127551	117127551	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117127551G>A	ENST00000310357.3	-	3	1338	c.1317C>T	c.(1315-1317)aaC>aaT	p.N439N	GPRC6A_ENST00000368549.3_Silent_p.N439N|GPRC6A_ENST00000530250.1_Intron	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	439					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		GTTGAAAGGCGTTGGGGTTCT	0.438																																					p.N439N		Atlas-SNP	.											.	GPRC6A	152	.	0			c.C1317T						PASS	.						96.0	85.0	88.0					6																	117127551		2203	4299	6502	SO:0001819	synonymous_variant	222545	exon3			AAAGGCGTTGGGG	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1317C>T	6.37:g.117127551G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			.	.	none		0.438	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
SPEG	10290	hgsc.bcm.edu	37	2	220315970	220315970	+	Silent	SNP	G	G	A	rs10932806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220315970G>A	ENST00000312358.7	+	5	2358	c.2226G>A	c.(2224-2226)aaG>aaA	p.K742K	SPEG_ENST00000396698.1_Silent_p.K638K|SPEG_ENST00000396695.2_5'UTR|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	112	0	0		WXS	Illumina HiSeq	Phase_I	87	47	0.54023	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	
AXDND1	126859	hgsc.bcm.edu	37	1	179504043	179504043	+	Missense_Mutation	SNP	C	C	G	rs6658180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179504043C>G	ENST00000367618.3	+	25	3364	c.2977C>G	c.(2977-2979)Caa>Gaa	p.Q993E		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	993	Glu-rich.		Q -> E (in dbSNP:rs6658180).							NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agaagaacaacaagaagaaga	0.323													C|||	1910	0.38139	0.2496	0.4035	5008	,	,		17574	0.4256		0.4115	False		,,,				2504	0.4673				p.Q993E		Atlas-SNP	.											.	AXDND1	142	.	0			c.C2977G						PASS	.	C	GLU/GLN	1137,3151		169,799,1176	50.0	54.0	53.0		2977	-4.9	0.0	1	dbSNP_116	53	3113,5457		585,1943,1757	yes	missense	AXDND1	NM_144696.4	29	754,2742,2933	GG,GC,CC		36.3244,26.5159,33.0534	benign	993/1013	179504043	4250,8608	2144	4285	6429	SO:0001583	missense	126859	exon25			GAACAACAAGAAG	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2977C>G	1.37:g.179504043C>G	ENSP00000356590:p.Gln993Glu	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	236	116	0.491525	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	825	0.37774725274725274	103	0.20934959349593496	157	0.43370165745856354	263	0.4597902097902098	302	0.39841688654353563	C	0.003	-2.521003	0.00149	0.265159	0.363244	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.15256	2.44;2.46	2.47	-4.94	0.03057	.	2.583780	0.01561	N	0.020132	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	0.43310	-0.9399	9	0.10111	T	0.7	-6.7708	0.9261	0.01325	0.4226:0.1628:0.2568:0.1578	rs6658180;rs6658180	877;993	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	E	993;877;853	ENSP00000356590:Q993E;ENSP00000391716:Q853E	ENSP00000353471:Q877E	Q	+	1	0	AXDND1	177770666	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.633000	0.02022	-1.372000	0.02137	-1.284000	0.01376	CAA	C|0.671;G|0.329	0.329	strong		0.323	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	
TRPM5	29850	hgsc.bcm.edu	37	11	2435956	2435956	+	Missense_Mutation	SNP	C	C	T	rs4929982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2435956C>T	ENST00000155858.6	-	11	1741	c.1733G>A	c.(1732-1734)cGg>cAg	p.R578Q	TRPM5_ENST00000533060.1_Missense_Mutation_p.R578Q|TRPM5_ENST00000528453.1_Missense_Mutation_p.R578Q|TRPM5_ENST00000452833.1_Missense_Mutation_p.R580Q	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)		AAGGGCCAGCCGCTCGTATTT	0.721													T|||	2649	0.528954	0.4924	0.5663	5008	,	,		13260	0.6597		0.4533	False		,,,				2504	0.4949				p.R578Q	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1733A						PASS	.	T	GLN/ARG	1688,2054		457,774,640	4.0	6.0	5.0		1733	3.8	1.0	11	dbSNP_111	5	3146,4326		788,1570,1378	no	missense	TRPM5	NM_014555.3	43	1245,2344,2018	TT,TC,CC		42.1039,45.1096,43.1068	benign	578/1166	2435956	4834,6380	1871	3736	5607	SO:0001583	missense	29850	exon11			GCCAGCCGCTCGT	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.1733G>A	11.37:g.2435956C>T	ENSP00000155858:p.Arg578Gln	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	1179	0.5398351648351648	259	0.5264227642276422	196	0.5414364640883977	381	0.666083916083916	343	0.4525065963060686	T	7.351	0.622828	0.14193	0.451096	0.421039	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03	3.83	3.83	0.44106	.	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00179	-1.91	0.54753	P	1.799999999996249E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.46105	-0.9215	9	0.02654	T	1	-25.6987	7.4097	0.27011	0.0:0.1022:0.0:0.8978	rs4929982;rs56720767	578;580;578	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	Q	572;578;580;578;578;578	ENSP00000434383:R572Q;ENSP00000155858:R578Q;ENSP00000387965:R580Q;ENSP00000434121:R578Q;ENSP00000436809:R578Q	ENSP00000155858:R578Q	R	-	2	0	TRPM5	2392532	1.000000	0.71417	1.000000	0.80357	0.247000	0.25773	2.934000	0.48956	0.646000	0.30693	-0.490000	0.04691	CGG	C|0.459;T|0.541	0.541	strong		0.721	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
KRT40	125115	hgsc.bcm.edu	37	17	39134528	39134528	+	Missense_Mutation	SNP	G	G	A	rs16968862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	68	0	0		WXS	Illumina HiSeq	Phase_I	83	28	0.337349	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	
GRAMD3	65983	hgsc.bcm.edu	37	5	125696124	125696124	+	Missense_Mutation	SNP	T	T	A	rs79046516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125696124T>A	ENST00000513040.1	+	1	301	c.101T>A	c.(100-102)gTg>gAg	p.V34E		NM_001146319.1	NP_001139791.1	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	0						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		GGGAGAGAAGTGAAGCCAGTG	0.488													T|||	118	0.0235623	0.087	0.0043	5008	,	,		21249	0.0		0.0	False		,,,				2504	0.0				p.V34E		Atlas-SNP	.											.	GRAMD3	30	.	0			c.T101A						PASS	.						123.0	116.0	119.0					5																	125696124		692	1591	2283	SO:0001583	missense	65983	exon1			GAGAAGTGAAGCC	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000513040.1:c.101T>A	5.37:g.125696124T>A	ENSP00000426120:p.Val34Glu	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	215	82	0.381395	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000513040.1	37	CCDS54891.1	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	T	9.413	1.081098	0.20309	.	.	ENSG00000155324	ENST00000513040	T	0.36878	1.23	4.15	-5.51	0.02568	.	.	.	.	.	T	0.00496	0.0016	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18429	-1.0337	8	0.02654	T	1	.	2.4366	0.04485	0.2542:0.0881:0.4343:0.2234	.	34	B7Z6D8	.	E	34	ENSP00000426120:V34E	ENSP00000426120:V34E	V	+	2	0	GRAMD3	125724023	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.306000	0.08178	-0.956000	0.03631	-1.304000	0.01323	GTG	T|0.975;A|0.025	0.025	strong		0.488	GRAMD3-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371350.1	NM_023927	
NRCAM	4897	hgsc.bcm.edu	37	7	107790417	107790417	+	Missense_Mutation	SNP	C	C	T	rs74708699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107790417C>T	ENST00000425651.2	-	30	3852	c.3853G>A	c.(3853-3855)Gct>Act	p.A1285T	NRCAM_ENST00000351718.4_Missense_Mutation_p.A1164T|NRCAM_ENST00000379024.4_Missense_Mutation_p.A1173T|NRCAM_ENST00000522550.2_5'UTR|NRCAM_ENST00000413765.2_Missense_Mutation_p.A1161T|NRCAM_ENST00000379028.3_Missense_Mutation_p.A1285T	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1285					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						TTTCCTTCAGCCGGCTCTTTC	0.428													C|||	36	0.0071885	0.0272	0.0	5008	,	,		15356	0.0		0.0	False		,,,				2504	0.0				p.A1285T		Atlas-SNP	.											.	NRCAM	267	.	0			c.G3853A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	115,4291	87.8+/-126.4	0,115,2088	161.0	150.0	154.0		3853,3574,3517,3481,3490	5.3	0.5	7	dbSNP_131	154	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense,missense,missense	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	58,58,58,58,58	0,118,6385	TT,TC,CC		0.0349,2.6101,0.9073	benign,benign,benign,benign,benign	1285/1305,1192/1212,1173/1193,1161/1181,1164/1184	107790417	118,12888	2203	4300	6503	SO:0001583	missense	4897	exon30			CTTCAGCCGGCTC		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3853G>A	7.37:g.107790417C>T	ENSP00000401244:p.Ala1285Thr	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	175	93	0.531429	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	12.19	1.863087	0.32884	0.026101	3.49E-4	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000437386;ENST00000351718;ENST00000379024;ENST00000425651	T;T;T;T;T	0.58940	0.34;0.57;0.3;0.35;0.34	6.17	5.3	0.74995	.	0.344041	0.33290	N	0.005080	T	0.15912	0.0383	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B;B;P	0.47106	0.01;0.001;0.144;0.021;0.036;0.001;0.89	B;B;B;B;B;B;B	0.37833	0.021;0.002;0.17;0.011;0.016;0.004;0.259	T	0.09228	-1.0684	10	0.13108	T	0.6	.	15.699	0.77528	0.0:0.9348:0.0:0.0652	.	1289;131;1161;1173;1164;1285;68	Q92823-5;B4DFP9;Q92823-3;E9PDA4;Q92823-4;Q92823;Q6QRP2	.;.;.;.;.;NRCAM_HUMAN;.	T	1289;1285;1161;129;1164;1173;1285	ENSP00000368314:A1285T;ENSP00000407858:A1161T;ENSP00000325269:A1164T;ENSP00000368310:A1173T;ENSP00000401244:A1285T	ENSP00000325269:A1164T	A	-	1	0	NRCAM	107577653	1.000000	0.71417	0.514000	0.27761	0.983000	0.72400	5.115000	0.64655	1.630000	0.50440	0.655000	0.94253	GCT	C|0.990;T|0.010	0.010	strong		0.428	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
QRICH2	84074	hgsc.bcm.edu	37	17	74287594	74287594	+	Missense_Mutation	SNP	G	G	A	rs2279054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74287594G>A	ENST00000262765.5	-	4	2895	c.2716C>T	c.(2716-2718)Cac>Tac	p.H906Y		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	906			H -> Y (in dbSNP:rs2279054).							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						TGATCTGGGTGTGTAGATCCC	0.512													G|||	2043	0.407947	0.4955	0.2925	5008	,	,		19958	0.5714		0.2704	False		,,,				2504	0.3446				p.H906Y		Atlas-SNP	.											QRICH2,colon,carcinoma,0,1	QRICH2	143	1	0			c.C2716T						PASS	.	G	TYR/HIS	2114,2292	578.5+/-384.7	507,1100,596	129.0	110.0	116.0		2716	1.0	0.0	17	dbSNP_100	116	2414,6186	398.9+/-346.3	329,1756,2215	yes	missense	QRICH2	NM_032134.1	83	836,2856,2811	AA,AG,GG		28.0698,47.98,34.8147	benign	906/1664	74287594	4528,8478	2203	4300	6503	SO:0001583	missense	84074	exon4			CTGGGTGTGTAGA	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.2716C>T	17.37:g.74287594G>A	ENSP00000262765:p.His906Tyr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	171	105	0.614035	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	874	0.4001831501831502	250	0.508130081300813	100	0.27624309392265195	332	0.5804195804195804	192	0.2532981530343008	G	10.16	1.273492	0.23221	0.4798	0.280698	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08458	3.09	4.65	0.958	0.19619	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P;P	0.47604	0.898;0.898	B;B	0.43867	0.434;0.434	T	0.24977	-1.0145	8	0.56958	D	0.05	1.1817	6.476	0.22037	0.1089:0.4498:0.4413:0.0	rs2279054;rs52813589;rs59976711;rs2279054	906;906	B5MD94;Q9H0J4	.;QRIC2_HUMAN	Y	906	ENSP00000262765:H906Y	ENSP00000262765:H906Y	H	-	1	0	QRICH2	71799189	0.195000	0.23338	0.000000	0.03702	0.036000	0.12997	-0.210000	0.09345	0.475000	0.27415	0.462000	0.41574	CAC	G|0.615;A|0.385	0.385	strong		0.512	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
PCDHB7	56129	hgsc.bcm.edu	37	5	140553917	140553917	+	Missense_Mutation	SNP	G	G	A	rs17844455|rs386692906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140553917G>A	ENST00000231137.3	+	1	1675	c.1501G>A	c.(1501-1503)Gcc>Acc	p.A501T		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	501	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(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)			CCTGCCCCTCGCCTCCCTGGT	0.677													G|||	759	0.151558	0.2572	0.1902	5008	,	,		16812	0.0417		0.1531	False		,,,				2504	0.093				p.A501T		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G1501A						PASS	.	G	THR/ALA	1024,3382	361.4+/-315.7	114,796,1293	85.0	88.0	87.0		1501	-1.2	0.0	5	dbSNP_123	87	1416,7184	259.8+/-282.9	120,1176,3004	no	missense	PCDHB7	NM_018940.2	58	234,1972,4297	AA,AG,GG		16.4651,23.241,18.7606	benign	501/794	140553917	2440,10566	2203	4300	6503	SO:0001583	missense	56129	exon1			CCCCTCGCCTCCC	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.1501G>A	5.37:g.140553917G>A	ENSP00000231137:p.Ala501Thr	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	276	118	0.427536	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	327	0.14972527472527472	121	0.2459349593495935	63	0.17403314917127072	26	0.045454545454545456	117	0.15435356200527706	g	4.524	0.097227	0.08681	0.23241	0.164651	ENSG00000113212	ENST00000231137;ENST00000543636	T	0.03181	4.02	4.34	-1.25	0.09405	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.13003	0.285	0.51482	P	7.40000000000185E-5	B	0.31519	0.327	B	0.24394	0.053	T	0.49293	-0.8955	8	0.38643	T	0.18	.	2.328	0.04228	0.1632:0.1009:0.3896:0.3463	rs17844455	501	Q9Y5E2	PCDB7_HUMAN	T	501;284	ENSP00000231137:A501T	ENSP00000231137:A501T	A	+	1	0	PCDHB7	140534101	0.000000	0.05858	0.009000	0.14445	0.023000	0.10783	-1.352000	0.02619	0.062000	0.16340	-0.261000	0.10672	GCC	G|0.825;A|0.175	0.175	strong		0.677	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643252	1643252	+	Silent	SNP	A	A	G	rs190925107		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1643252A>G	ENST00000399682.1	-	1	116	c.72T>C	c.(70-72)tgT>tgC	p.C24C		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0						keratin filament (GO:0045095)		p.C24C(5)		NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		agccagagccacagcccccac	0.687																																					p.C24C		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,6	KRTAP5-4	78	6	5	Substitution - coding silent(5)	endometrium(4)|prostate(1)	c.T72C						scavenged	.																																			SO:0001819	synonymous_variant	387267	exon1			AGAGCCACAGCCC	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.72T>C	11.37:g.1643252A>G		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	343	72	0.209913	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				A|0.950;G|0.050	0.050	strong		0.687	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
TMPRSS2	7113	hgsc.bcm.edu	37	21	42852497	42852497	+	Missense_Mutation	SNP	C	C	T	rs12329760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:42852497C>T	ENST00000332149.5	-	6	612	c.478G>A	c.(478-480)Gtg>Atg	p.V160M	TMPRSS2_ENST00000458356.1_Missense_Mutation_p.V160M|TMPRSS2_ENST00000398585.3_Missense_Mutation_p.V197M	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	160	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.		V -> M (in dbSNP:rs12329760). {ECO:0000269|PubMed:11414763, ECO:0000269|PubMed:17918732, ECO:0000269|PubMed:9325052}.		positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.V160M(1)	TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				GATGAGTACACCTGAAGGATG	0.507			T	"""ERG, ETV1, ETV4, ETV5"""	prostate								C|||	1309	0.261382	0.2867	0.1542	5008	,	,		20708	0.3621		0.2356	False		,,,				2504	0.226				p.V197M		Atlas-SNP	.		Dom	yes		21	21q22.3	7113	"""transmembrane protease, serine 2"""		E	TMPRSS2_ENST00000332149,NS,carcinoma,0,1	TMPRSS2	148	1	1	Substitution - Missense(1)	stomach(1)	c.G589A						PASS	.	C	MET/VAL,MET/VAL	1279,3127	433.5+/-343.6	183,913,1107	62.0	53.0	56.0		589,478	4.2	1.0	21	dbSNP_120	56	1860,6740	330.6+/-319.3	222,1416,2662	yes	missense,missense	TMPRSS2	NM_001135099.1,NM_005656.3	21,21	405,2329,3769	TT,TC,CC		21.6279,29.0286,24.135	probably-damaging,probably-damaging	197/530,160/493	42852497	3139,9867	2203	4300	6503	SO:0001583	missense	7113	exon6			AGTACACCTGAAG	U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"""Serine peptidases / Transmembrane"""	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.478G>A	21.37:g.42852497C>T	ENSP00000330330:p.Val160Met	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	129	52	0.403101	NM_001135099	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Missense_Mutation	SNP	ENST00000332149.5	37	CCDS33564.1	634	0.2902930402930403	145	0.29471544715447157	69	0.19060773480662985	230	0.4020979020979021	190	0.25065963060686014	C	18.40	3.615593	0.66672	0.290286	0.216279	ENSG00000184012	ENST00000332149;ENST00000398585;ENST00000458356;ENST00000454499;ENST00000424093	T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75	5.12	4.23	0.50019	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.307523	0.26812	N	0.022371	T	0.00012	0.0000	M	0.85462	2.755	0.28298	P	0.9232503	D;D	0.76494	0.999;0.997	D;D	0.65773	0.938;0.937	T	0.10847	-1.0612	9	0.66056	D	0.02	.	9.9163	0.41436	0.0:0.9025:0.0:0.0975	rs12329760;rs60283747;rs12329760	197;160	F8WES1;O15393	.;TMPS2_HUMAN	M	160;197;160;160;120	ENSP00000330330:V160M;ENSP00000381588:V197M;ENSP00000391216:V160M;ENSP00000389006:V160M;ENSP00000397846:V120M	ENSP00000330330:V160M	V	-	1	0	TMPRSS2	41774367	1.000000	0.71417	0.999000	0.59377	0.756000	0.42949	1.578000	0.36525	2.392000	0.81423	0.561000	0.74099	GTG	C|0.744;T|0.256	0.256	strong		0.507	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1		
PTPRN2	5799	hgsc.bcm.edu	37	7	157959870	157959870	+	Silent	SNP	G	G	T	rs112343839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157959870G>T	ENST00000389418.4	-	6	672	c.663C>A	c.(661-663)ctC>ctA	p.L221L	PTPRN2_ENST00000409483.1_Silent_p.L183L|PTPRN2_ENST00000389416.4_Silent_p.L204L|PTPRN2_ENST00000389413.3_Silent_p.L221L|PTPRN2_ENST00000404321.2_Silent_p.L244L	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	221					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GGAGCTGGCCGAGGGTCCGCG	0.667													G|||	49	0.00978435	0.034	0.0043	5008	,	,		16342	0.0		0.001	False		,,,				2504	0.0				p.L221L		Atlas-SNP	.											.	PTPRN2	243	.	0			c.C663A						PASS	.		,,	161,4245	105.6+/-144.1	5,151,2047	40.0	39.0	39.0		663,612,663	-1.8	0.0	7	dbSNP_132	39	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	5,151,6347	TT,TG,GG		0.0,3.6541,1.2379	,,	221/1016,204/999,221/987	157959870	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	5799	exon6			CTGGCCGAGGGTC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.663C>A	7.37:g.157959870G>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			G|0.985;T|0.015	0.015	strong		0.667	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
SLC6A14	11254	hgsc.bcm.edu	37	X	115568993	115568993	+	Silent	SNP	T	T	A	rs12720074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:115568993T>A	ENST00000371900.4	+	2	172	c.84T>A	c.(82-84)ggT>ggA	p.G28G		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	28					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TCCATGTTGGTGAAAATGATG	0.388													T|||	204	0.0540397	0.0144	0.0331	3775	,	,		10878	0.0139		0.0736	False		,,,				2504	0.0757				p.G28G		Atlas-SNP	.											.	SLC6A14	56	.	0			c.T84A						PASS	.	T		161,3674		1,135,24,1496,547	170.0	174.0	173.0		84	1.2	0.9	X	dbSNP_121	173	588,6140		18,393,159,2017,1713	no	coding-synonymous	SLC6A14	NM_007231.3		19,528,183,3513,2260	AA,AT,A,TT,T		8.7396,4.1982,7.0908		28/643	115568993	749,9814	2203	4300	6503	SO:0001819	synonymous_variant	11254	exon2			TGTTGGTGAAAAT	AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"""Solute carriers"""	11047	protein-coding gene	gene with protein product		300444	"""solute carrier family 6 (neurotransmitter transporter), member 14"""			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.84T>A	X.37:g.115568993T>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	78	55	0.705128	NM_007231	Q5H942	Silent	SNP	ENST00000371900.4	37	CCDS14570.1																																																																																			0|0.018;A|0.063	0.063	strong		0.388	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1		
CENPE	1062	hgsc.bcm.edu	37	4	104066461	104066461	+	Missense_Mutation	SNP	A	A	G	rs2615542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:104066461A>G	ENST00000265148.3	-	32	4692	c.4603T>C	c.(4603-4605)Ttt>Ctt	p.F1535L	CENPE_ENST00000380026.3_Missense_Mutation_p.F1510L	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1535			F -> L (in dbSNP:rs2615542). {ECO:0000269|PubMed:1406971}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.F1535L(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TTTATATTAAATTGTTCCTCT	0.299													G|||	607	0.121206	0.062	0.1153	5008	,	,		16276	0.1409		0.2207	False		,,,				2504	0.0828				p.F1535L		Atlas-SNP	.											CENPE,NS,carcinoma,0,1	CENPE	253	1	1	Substitution - Missense(1)	stomach(1)	c.T4603C						PASS	.	G	LEU/PHE	281,4121	778.4+/-414.3	8,265,1928	47.0	46.0	46.0		4603	-2.4	0.0	4	dbSNP_100	46	1768,6828	720.6+/-406.3	195,1378,2725	yes	missense	CENPE	NM_001813.2	22	203,1643,4653	GG,GA,AA		20.5677,6.3835,15.764	benign	1535/2702	104066461	2049,10949	2201	4298	6499	SO:0001583	missense	1062	exon32			TATTAAATTGTTC	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.4603T>C	4.37:g.104066461A>G	ENSP00000265148:p.Phe1535Leu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	347	0.15888278388278387	39	0.07926829268292683	51	0.1408839779005525	74	0.12937062937062938	183	0.24142480211081793	G	0.006	-2.062430	0.00386	0.063835	0.205677	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.62639	0.01;0.15	4.44	-2.42	0.06542	.	.	.	.	.	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	0.07654	-1.0761	8	0.02654	T	1	.	0.4903	0.00563	0.3766:0.2373:0.1466:0.2394	rs2615542;rs17282727;rs52815493;rs60897952;rs2615542	1510;1535	Q02224-3;Q02224	.;CENPE_HUMAN	L	1535;1535;1510	ENSP00000265148:F1535L;ENSP00000369365:F1510L	ENSP00000265148:F1535L	F	-	1	0	CENPE	104285910	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	-0.886000	0.04157	-0.433000	0.07286	-0.231000	0.12243	TTT	A|0.848;G|0.152	0.152	strong		0.299	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
OPN3	23596	hgsc.bcm.edu	37	1	241755348	241755348	+	IGR	SNP	C	C	T	rs1053230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241755348C>T	ENST00000366554.2	-	0	2620				KMO_ENST00000366557.4_Missense_Mutation_p.R418C|OPN3_ENST00000469376.1_5'Flank|KMO_ENST00000366558.3_Missense_Mutation_p.R439C|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	72	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	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	
PPP1R1B	84152	hgsc.bcm.edu	37	17	37791894	37791894	+	Silent	SNP	A	A	G	rs34257414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37791894A>G	ENST00000254079.4	+	6	949	c.480A>G	c.(478-480)gaA>gaG	p.E160E	PPP1R1B_ENST00000394267.2_Silent_p.E124E|STARD3_ENST00000544210.2_5'Flank|STARD3_ENST00000580611.1_5'Flank|STARD3_ENST00000336308.5_5'Flank|PPP1R1B_ENST00000580825.1_Silent_p.E160E|PPP1R1B_ENST00000579000.1_Silent_p.E127E|PPP1R1B_ENST00000394265.1_Silent_p.E124E|STARD3_ENST00000394250.4_5'Flank	NM_032192.3	NP_115568.2	Q9UD71	PPR1B_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1B	160					intracellular signal transduction (GO:0035556)|negative regulation of catalytic activity (GO:0043086)|negative regulation of female receptivity (GO:0007621)|negative regulation of protein kinase activity (GO:0006469)|regulation of catalytic activity (GO:0050790)|response to amphetamine (GO:0001975)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	protein kinase inhibitor activity (GO:0004860)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 1 regulator activity (GO:0008599)			kidney(1)|large_intestine(1)|liver(1)|lung(2)	5	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)			AGGGTCTGGAAGGGCCCTGGG	0.587													G|||	94	0.01877	0.0711	0.0	5008	,	,		19292	0.0		0.0	False		,,,				2504	0.0				p.E160E		Atlas-SNP	.											.	PPP1R1B	9	.	0			c.A480G						PASS	.	G	,,	206,4200	784.3+/-414.7	3,200,2000	74.0	85.0	81.0		372,480,372	2.1	1.0	17	dbSNP_126	81	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PPP1R1B	NM_001242464.1,NM_032192.3,NM_181505.3	,,	3,200,6300	GG,GA,AA		0.0,4.6754,1.5839	,,	124/169,160/205,124/169	37791894	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	84152	exon6			TCTGGAAGGGCCC	AI124650	CCDS11339.1, CCDS11340.1	17q12	2012-04-17	2008-07-31		ENSG00000131771	ENSG00000131771	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9287	protein-coding gene	gene with protein product	"""dopamine and cAMP regulated phosphoprotein"""	604399				8120638	Standard	NM_032192		Approved	DARPP-32, FLJ20940	uc002hrz.3	Q9UD71	OTTHUMG00000133210	ENST00000254079.4:c.480A>G	17.37:g.37791894A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_032192	Q547V9|Q547W0|Q9H7G1	Silent	SNP	ENST00000254079.4	37	CCDS11339.1																																																																																			A|0.979;G|0.021	0.021	strong		0.587	PPP1R1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256925.2	NM_032192	
SLC9A8	23315	hgsc.bcm.edu	37	20	48472098	48472098	+	Silent	SNP	A	A	G	rs35137210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48472098A>G	ENST00000361573.2	+	8	735	c.693A>G	c.(691-693)gcA>gcG	p.A231A	SLC9A8_ENST00000539601.1_Silent_p.A12A|SLC9A8_ENST00000541138.1_5'UTR|SLC9A8_ENST00000417961.1_Silent_p.A247A			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	231					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			TCAACGATGCAGTCTCCATTG	0.463													A|||	18	0.00359425	0.0136	0.0	5008	,	,		22384	0.0		0.0	False		,,,				2504	0.0				p.A247A		Atlas-SNP	.											.	SLC9A8	63	.	0			c.A741G						PASS	.	A		60,4346	56.2+/-92.4	0,60,2143	107.0	92.0	97.0		693	-10.5	0.0	20	dbSNP_126	97	0,8600		0,0,4300	no	coding-synonymous	SLC9A8	NM_015266.1		0,60,6443	GG,GA,AA		0.0,1.3618,0.4613		231/582	48472098	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	23315	exon8			CGATGCAGTCTCC	AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"""Solute carriers"""	20728	protein-coding gene	gene with protein product		612730	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 8"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 8"""			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.693A>G	20.37:g.48472098A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	161	85	0.52795	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																			A|0.994;G|0.006	0.006	strong		0.463	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524	
FLG	2312	hgsc.bcm.edu	37	1	152276626	152276626	+	Missense_Mutation	SNP	G	G	C	rs3126075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276626G>C	ENST00000368799.1	-	3	10771	c.10736C>G	c.(10735-10737)aCg>aGg	p.T3579R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	564	0	0		WXS	Illumina HiSeq	Phase_I	483	480	0.993789	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	
SLC19A3	80704	hgsc.bcm.edu	37	2	228566993	228566993	+	Silent	SNP	G	G	A	rs34080459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228566993G>A	ENST00000258403.3	-	2	113	c.42C>T	c.(40-42)taC>taT	p.Y14Y	SLC19A3_ENST00000409287.1_Silent_p.Y14Y|SLC19A3_ENST00000541617.1_5'UTR	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	14					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)			breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	TCACAGTGGGGTAAATCCAGG	0.383													G|||	79	0.0157748	0.0537	0.0086	5008	,	,		19039	0.001		0.001	False		,,,				2504	0.0				p.Y14Y		Atlas-SNP	.											.	SLC19A3	62	.	0			c.C42T						PASS	.	G		221,4185	134.9+/-171.1	6,209,1988	108.0	115.0	113.0		42	1.7	1.0	2	dbSNP_126	113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC19A3	NM_025243.3		6,210,6287	AA,AG,GG		0.0116,5.0159,1.7069		14/497	228566993	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	80704	exon2			AGTGGGGTAAATC	AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"""Solute carriers"""	16266	protein-coding gene	gene with protein product	"""thiamine transporter 2"""	606152	"""solute carrier family 19, member 3"""			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.42C>T	2.37:g.228566993G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_025243		Silent	SNP	ENST00000258403.3	37	CCDS2468.1																																																																																			G|0.982;A|0.018	0.018	strong		0.383	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1		
PKD1L1	168507	hgsc.bcm.edu	37	7	47920345	47920345	+	Silent	SNP	G	G	A	rs62447081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	119	0	0		WXS	Illumina HiSeq	Phase_I	144	57	0.395833	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	
ROBO1	6091	hgsc.bcm.edu	37	3	78676701	78676701	+	Silent	SNP	T	T	C	rs116125749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:78676701T>C	ENST00000464233.1	-	26	3758	c.3645A>G	c.(3643-3645)ccA>ccG	p.P1215P	ROBO1_ENST00000436010.2_Silent_p.P1176P|ROBO1_ENST00000467549.1_Silent_p.P1115P|ROBO1_ENST00000495273.1_Silent_p.P1170P	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1215					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)		GCACGGGACATGGCATTTCTT	0.413													T|||	52	0.0103834	0.0371	0.0043	5008	,	,		19868	0.0		0.0	False		,,,				2504	0.0				p.P1215P		Atlas-SNP	.											.	ROBO1	833	.	0			c.A3645G						PASS	.	T	,,	114,3892		1,112,1890	59.0	70.0	67.0		3345,3645,3510	-1.6	1.0	3	dbSNP_132	67	1,8321		0,1,4160	no	coding-synonymous,coding-synonymous,coding-synonymous	ROBO1	NM_001145845.1,NM_002941.3,NM_133631.3	,,	1,113,6050	CC,CT,TT		0.012,2.8457,0.9328	,,	1115/1552,1215/1652,1170/1607	78676701	115,12213	2003	4161	6164	SO:0001819	synonymous_variant	6091	exon26			GGGACATGGCATT	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.3645A>G	3.37:g.78676701T>C		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	244	120	0.491803	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	T	5.980	0.364753	0.11296	0.028457	1.2E-4	ENSG00000169855	ENST00000472273	.	.	.	5.29	-1.6	0.08426	.	.	.	.	.	T	0.17152	0.0412	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17137	-1.0379	4	.	.	.	.	1.2302	0.01942	0.174:0.1782:0.1809:0.4669	.	.	.	.	R	142	.	.	H	-	2	0	ROBO1	78759391	0.944000	0.32072	0.963000	0.40424	0.670000	0.39368	0.033000	0.13754	-0.468000	0.06922	-1.447000	0.01057	CAT	T|0.991;C|0.009	0.009	strong		0.413	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
SPINK5	11005	hgsc.bcm.edu	37	5	147480080	147480080	+	Missense_Mutation	SNP	G	G	A	rs2303064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147480080G>A	ENST00000256084.7	+	13	1198	c.1156G>A	c.(1156-1158)Gat>Aat	p.D386N	SPINK5_ENST00000359874.3_Missense_Mutation_p.D386N|SPINK5_ENST00000398454.1_Missense_Mutation_p.D386N|SPINK5_ENST00000476608.1_3'UTR	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	386	Kazal-like 6. {ECO:0000255|PROSITE- ProRule:PRU00798}.		D -> N (in dbSNP:rs2303064).		anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAGAGAACGATCCTATCCA	0.493													G|||	1744	0.348243	0.559	0.1614	5008	,	,		17510	0.4246		0.1213	False		,,,				2504	0.3507				p.D386N		Atlas-SNP	.											.	SPINK5	245	.	0			c.G1156A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP	1800,2126		404,992,567	159.0	155.0	156.0		1156,1156,1156	3.8	0.2	5	dbSNP_100	156	1044,7304		52,940,3182	yes	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	23,23,23	456,1932,3749	AA,AG,GG		12.506,45.8482,23.1709	benign,benign,benign	386/1095,386/917,386/1065	147480080	2844,9430	1963	4174	6137	SO:0001583	missense	11005	exon13			GAGAACGATCCTA	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1156G>A	5.37:g.147480080G>A	ENSP00000256084:p.Asp386Asn	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	660	0.3021978021978022	247	0.5020325203252033	59	0.16298342541436464	257	0.4493006993006993	97	0.1279683377308707	G	10.88	1.476580	0.26511	0.458482	0.12506	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.04654	3.58;3.58;3.58;3.58	4.69	3.82	0.43975	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.189270	0.25349	N	0.031317	T	0.00012	0.0000	L	0.61387	1.9	0.51482	P	7.100000000004325E-5	P;P;P;B	0.40970	0.455;0.689;0.734;0.4	B;B;B;B	0.37780	0.125;0.167;0.258;0.12	T	0.38308	-0.9667	9	0.28530	T	0.3	-8.6523	9.1943	0.37217	0.0998:0.0:0.9002:0.0	rs2303064;rs17860503;rs52823786;rs59833491;rs2303064	367;386;386;386	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	N	386;386;367;386	ENSP00000381472:D386N;ENSP00000352936:D386N;ENSP00000421519:D367N;ENSP00000256084:D386N	ENSP00000256084:D386N	D	+	1	0	SPINK5	147460273	0.377000	0.25106	0.164000	0.22755	0.362000	0.29581	1.896000	0.39789	1.349000	0.45751	0.591000	0.81541	GAT	G|0.688;A|0.312	0.312	strong		0.493	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
CHAT	1103	hgsc.bcm.edu	37	10	50824619	50824619	+	Missense_Mutation	SNP	G	G	A	rs3810950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50824619G>A	ENST00000337653.2	+	2	511	c.358G>A	c.(358-360)Gca>Aca	p.A120T	CHAT_ENST00000351556.3_Missense_Mutation_p.A2T|CHAT_ENST00000395559.2_Missense_Mutation_p.A2T|CHAT_ENST00000460699.1_3'UTR|CHAT_ENST00000455728.2_Missense_Mutation_p.A2T|CHAT_ENST00000395562.2_Missense_Mutation_p.A38T|CHAT_ENST00000339797.1_Missense_Mutation_p.A2T	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	120			A -> T (in dbSNP:rs3810950). {ECO:0000269|PubMed:11172068, ECO:0000269|PubMed:1388731, ECO:0000269|PubMed:15489334}.		adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	CCGTAAGATGGCAGCAAAAAC	0.557													G|||	804	0.160543	0.0053	0.1671	5008	,	,		18114	0.1696		0.2316	False		,,,				2504	0.2832				p.A120T		Atlas-SNP	.											CHAT,NS,carcinoma,-1,1	CHAT	162	1	0			c.G358A	GRCh37	CM025920	CHAT	M	rs3810950	PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	228,4178	131.4+/-167.9	7,214,1982	114.0	85.0	95.0		4,112,4,358,4,4,4	3.0	0.0	10	dbSNP_107	95	2144,6456	354.6+/-329.6	263,1618,2419	yes	missense,missense,missense,missense,missense,missense,missense	CHAT	NM_001142929.1,NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3,NM_020985.3,NM_020986.3	58,58,58,58,58,58,58	270,1832,4401	AA,AG,GG		24.9302,5.1748,18.2377	benign,benign,benign,benign,benign,benign,benign	2/631,38/667,2/631,120/749,2/631,2/631,2/631	50824619	2372,10634	2203	4300	6503	SO:0001583	missense	1103	exon2			AAGATGGCAGCAA	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.358G>A	10.37:g.50824619G>A	ENSP00000337103:p.Ala120Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	332	0.152014652014652	5	0.01016260162601626	77	0.212707182320442	87	0.1520979020979021	163	0.21503957783641162	G	6.004	0.369097	0.11352	0.051748	0.249302	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	D;D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-1.9;-1.95;-1.92	3.96	3.03	0.35002	.	0.678932	0.14323	N	0.326861	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B	0.25609	0.13;0.014	B;B	0.29942	0.109;0.005	T	0.05386	-1.0888	9	0.17369	T	0.5	-2.7401	5.388	0.16227	0.1117:0.222:0.6664:0.0	rs3810950;rs17775591;rs60084580;rs3810950	2;120	F8W8I2;P28329	.;CLAT_HUMAN	T	2;2;2;120;38;2	ENSP00000343486:A2T;ENSP00000345878:A2T;ENSP00000378926:A2T;ENSP00000337103:A120T;ENSP00000378929:A38T;ENSP00000390521:A2T	ENSP00000337103:A120T	A	+	1	0	CHAT	50494625	0.048000	0.20356	0.004000	0.12327	0.745000	0.42441	2.188000	0.42612	1.229000	0.43630	0.655000	0.94253	GCA	G|0.762;A|0.237	0.237	strong		0.557	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
AMACR	23600	hgsc.bcm.edu	37	5	34008100	34008100	+	Missense_Mutation	SNP	C	C	T	rs3195676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34008100C>T	ENST00000335606.6	-	1	113	c.25G>A	c.(25-27)Gtg>Atg	p.V9M	AMACR_ENST00000514195.1_5'UTR|AMACR_ENST00000382085.3_Missense_Mutation_p.V9M|AMACR_ENST00000426255.2_Missense_Mutation_p.V9M|AMACR_ENST00000382072.2_Missense_Mutation_p.V9M|AMACR_ENST00000512079.1_Missense_Mutation_p.V9M|RP11-1084J3.4_ENST00000382079.3_Intron|AMACR_ENST00000382068.3_Missense_Mutation_p.V9M|AMACR_ENST00000502637.1_Missense_Mutation_p.V9M|AMACR_ENST00000441713.2_Missense_Mutation_p.V9M	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	9			V -> M (in dbSNP:rs3195676). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.5, ECO:0000269|Ref.6, ECO:0000269|Ref.9}.		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						GACAGCTCCACGACCGAGATG	0.692													C|||	1437	0.286941	0.1415	0.4078	5008	,	,		13433	0.3542		0.505	False		,,,				2504	0.1043				p.V9M		Atlas-SNP	.											AMACR,NS,carcinoma,0,3	AMACR	38	3	0			c.G25A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	920,3464		111,698,1383	22.0	23.0	23.0		25,25,25	-9.4	0.0	5	dbSNP_105	23	4492,4084		1195,2102,991	yes	missense,missense,missense	AMACR	NM_001167595.1,NM_014324.5,NM_203382.2	21,21,21	1306,2800,2374	TT,TC,CC		47.6213,20.9854,41.7593	benign,benign,benign	9/395,9/383,9/199	34008100	5412,7548	2192	4288	6480	SO:0001583	missense	23600	exon1			GCTCCACGACCGA	AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.25G>A	5.37:g.34008100C>T	ENSP00000334424:p.Val9Met	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_014324	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	833	0.3814102564102564	75	0.1524390243902439	164	0.4530386740331492	203	0.3548951048951049	391	0.5158311345646438	C	17.23	3.337535	0.60963	0.209854	0.523787	ENSG00000242110	ENST00000335606;ENST00000382072;ENST00000382085;ENST00000502637;ENST00000441713	T;T;T;T;T	0.58652	0.32;0.32;0.32;0.32;0.32	4.72	-9.44	0.00603	CoA-transferase family III domain (2);	0.597947	0.17508	N	0.171723	T	0.00012	0.0000	M	0.93062	3.375	0.09310	P	0.999999999608215	P;B;B;P;B	0.46987	0.888;0.24;0.155;0.858;0.155	B;B;B;P;B	0.48488	0.301;0.092;0.026;0.579;0.026	T	0.48570	-0.9024	9	0.62326	D	0.03	-4.4361	14.2962	0.66316	0.4513:0.0933:0.4554:0.0	rs3195676;rs17850511;rs3195676	9;9;9;9;9	Q6VRU4;F8W9N1;D6RB81;Q9UHK6-4;Q9UHK6	.;.;.;.;AMACR_HUMAN	M	9	ENSP00000334424:V9M;ENSP00000371504:V9M;ENSP00000371517:V9M;ENSP00000424351:V9M;ENSP00000403800:V9M	ENSP00000334424:V9M	V	-	1	0	AMACR	34043857	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.233000	0.02934	-3.351000	0.00181	-1.104000	0.02111	GTG	C|0.609;T|0.391	0.391	strong		0.692	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188023	140188023	+	Silent	SNP	C	C	T	rs7702779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140188023C>T	ENST00000530339.1	+	1	1251	c.1251C>T	c.(1249-1251)agC>agT	p.S417S	PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Silent_p.S417S|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.S417S|PCDHA1_ENST00000504120.2_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	417	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			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)			ACCGCGAGAGCGTGTCAGCCT	0.612													.|||	285	0.0569089	0.208	0.013	5008	,	,		19748	0.0		0.001	False		,,,				2504	0.0				p.S417S		Atlas-SNP	.											.	PCDHA4	419	.	0			c.C1251T						PASS	.	C	,,,,,	797,3609	321.8+/-297.3	66,665,1472	155.0	146.0	149.0		,,,1251,,1251	-9.0	0.0	5	dbSNP_116	149	2,8598	2.2+/-6.3	0,2,4298	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	,,,,,	66,667,5770	TT,TC,CC		0.0233,18.089,6.1433	,,,,,	,,,417/948,,417/799	140188023	799,12207	2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CGAGAGCGTGTCA	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.1251C>T	5.37:g.140188023C>T		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	295	151	0.511864	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			C|0.944;T|0.056	0.056	strong		0.612	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
TRIM39	56658	hgsc.bcm.edu	37	6	30297529	30297529	+	Silent	SNP	T	T	C	rs2057727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30297529T>C	ENST00000396547.1	+	2	595	c.435T>C	c.(433-435)gaT>gaC	p.D145D	HCG18_ENST00000426882.1_RNA|TRIM39-RPP21_ENST00000513556.1_Silent_p.D57D|TRIM39_ENST00000376659.5_Silent_p.D145D|TRIM39_ENST00000376656.4_Silent_p.D145D|HCG18_ENST00000412685.2_RNA|TRIM39_ENST00000396551.3_Silent_p.D145D|HCG18_ENST00000413358.2_RNA|TRIM39_ENST00000396548.1_Silent_p.D145D|TRIM39_ENST00000540416.1_Silent_p.D145D			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	145					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						CACTGGACGATGCTACACAGG	0.537													C|||	1907	0.380791	0.3222	0.4539	5008	,	,		20492	0.506		0.2525	False		,,,				2504	0.411				p.D145D		Atlas-SNP	.											.	TRIM39	56	.	0			c.T435C						PASS	.	C	,,	879,2137		122,635,751	60.0	64.0	63.0		435,435,435	-1.6	0.6	6	dbSNP_94	63	1357,4057		165,1027,1515	yes	coding-synonymous,coding-synonymous,coding-synonymous	TRIM39,TRIM39-RPP21	NM_001199119.1,NM_021253.3,NM_172016.2	,,	287,1662,2266	CC,CT,TT		25.0646,29.1446,26.5243	,,	145/504,145/519,145/489	30297529	2236,6194	1508	2707	4215	SO:0001819	synonymous_variant	56658	exon3			GGACGATGCTACA	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.435T>C	6.37:g.30297529T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Silent	SNP	ENST00000396547.1	37	CCDS34377.1	746	0.3415750915750916	156	0.3170731707317073	147	0.40607734806629836	270	0.47202797202797203	173	0.22823218997361477	C	9.049	0.991596	0.18966	0.291446	0.250646	ENSG00000204599	ENST00000420746	.	.	.	5.35	-1.57	0.08506	.	.	.	.	.	T	0.17704	0.0425	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.18241	-1.0343	3	.	.	.	.	6.5398	0.22375	0.118:0.3956:0.0:0.4864	rs2057727;rs6939906;rs17194831;rs17850232;rs61139874;rs2057727	.	.	.	T	75	.	.	M	+	2	0	TRIM39	30405508	0.037000	0.19845	0.565000	0.28409	0.944000	0.59088	-1.096000	0.03353	-0.658000	0.05366	-0.227000	0.12334	ATG	T|0.696;C|0.304	0.304	strong		0.537	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	
GATAD2B	57459	hgsc.bcm.edu	37	1	153788927	153788927	+	Silent	SNP	G	G	A	rs114813239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153788927G>A	ENST00000368655.4	-	7	1281	c.1038C>T	c.(1036-1038)gcC>gcT	p.A346A		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	346	CR2; histone tail-binding.				ATP-dependent chromatin remodeling (GO:0043044)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	38	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCTGTGAGTTGGCAGCATCAG	0.537													G|||	51	0.0101837	0.0371	0.0029	5008	,	,		19938	0.0		0.0	False		,,,				2504	0.0				p.A346A		Atlas-SNP	.											.	GATAD2B	62	.	0			c.C1038T						PASS	.	G		139,4267	99.4+/-138.0	2,135,2066	105.0	83.0	90.0		1038	4.2	1.0	1	dbSNP_132	90	0,8600		0,0,4300	no	coding-synonymous	GATAD2B	NM_020699.2		2,135,6366	AA,AG,GG		0.0,3.1548,1.0687		346/594	153788927	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	57459	exon7			TGAGTTGGCAGCA	AF411836	CCDS1054.1	1q21.3	2013-01-25			ENSG00000143614	ENSG00000143614		"""GATA zinc finger domain containing"""	30778	protein-coding gene	gene with protein product	"""transcription repressor p66 beta component of the MeCP1 complex"""	614998				10574461, 11756549	Standard	NM_020699		Approved	P66beta	uc001fdb.4	Q8WXI9	OTTHUMG00000037162	ENST00000368655.4:c.1038C>T	1.37:g.153788927G>A		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	307	144	0.469055	NM_020699	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Silent	SNP	ENST00000368655.4	37	CCDS1054.1																																																																																			G|0.987;A|0.013	0.013	strong		0.537	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699	
ZNF804B	219578	hgsc.bcm.edu	37	7	88964196	88964196	+	Missense_Mutation	SNP	T	T	A	rs801840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88964196T>A	ENST00000333190.4	+	4	2509	c.1900T>A	c.(1900-1902)Ttt>Att	p.F634I		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	634			F -> I (in dbSNP:rs801840). {ECO:0000269|PubMed:12690205}.				metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			CATCTCTAGGTTTAAAAAGCA	0.418										HNSCC(36;0.09)			A|||	2607	0.520567	0.7738	0.3415	5008	,	,		19885	0.7153		0.2346	False		,,,				2504	0.3988				p.F634I		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T1900A						PASS	.	A	ILE/PHE	3011,1395	456.1+/-351.2	1021,969,213	80.0	84.0	83.0		1900	4.3	0.7	7	dbSNP_86	83	2036,6564	719.1+/-406.2	234,1568,2498	yes	missense	ZNF804B	NM_181646.2	21	1255,2537,2711	AA,AT,TT		23.6744,31.6614,38.8052	benign	634/1350	88964196	5047,7959	2203	4300	6503	SO:0001583	missense	219578	exon4			TCTAGGTTTAAAA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1900T>A	7.37:g.88964196T>A	ENSP00000329638:p.Phe634Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	1073	0.4913003663003663	374	0.7601626016260162	130	0.35911602209944754	390	0.6818181818181818	179	0.23614775725593667	A	6.795	0.515659	0.12944	0.683386	0.236744	ENSG00000182348	ENST00000333190	T	0.04015	3.73	5.48	4.33	0.51752	.	0.169739	0.42294	D	0.000738	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.06643	-1.0815	9	0.51188	T	0.08	-4.6357	7.8499	0.29448	0.8102:0.0:0.0666:0.1232	rs801840;rs1721758;rs56634318;rs801840	634	A4D1E1	Z804B_HUMAN	I	634	ENSP00000329638:F634I	ENSP00000329638:F634I	F	+	1	0	ZNF804B	88802132	1.000000	0.71417	0.702000	0.30337	0.028000	0.11728	3.085000	0.50151	0.518000	0.28383	-0.265000	0.10407	TTT	T|0.483;A|0.517	0.517	strong		0.418	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
MT-ND4L	4539	hgsc.bcm.edu	37	M	10586	10586	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10586G>A	ENST00000361335.1	+	1	117	c.117G>A	c.(115-117)tcG>tcA	p.S39S	MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03901	NU4LM_HUMAN	mitochondrially encoded NADH dehydrogenase 4L	39					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(2)|kidney(2)	5						ATAATACTATCGCTGTTCATT	0.418																																					p.S39S		Atlas-SNP	.											.	.	.	.	0			c.G117A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ACTATCGCTGTTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000212907	ENSG00000212907	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7460	protein-coding gene	gene with protein product	"""complex I ND4L subunit"", ""NADH-ubiquinone oxidoreductase chain 4L"""	516004	"""NADH dehydrogenase 4L"""	MTND4L			Standard			Approved	ND4L, NAD4L		P03901		ENST00000361335.1:c.117G>A	M.37:g.10586G>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	ENST00000361335		Silent	SNP	ENST00000361335.1	37																																																																																				.	.	none		0.418	MT-ND4L-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024034	
SYMPK	8189	hgsc.bcm.edu	37	19	46319415	46319415	+	Silent	SNP	G	G	C	rs1132645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46319415G>C	ENST00000245934.7	-	26	3625	c.3381C>G	c.(3379-3381)gcC>gcG	p.A1127A	SYMPK_ENST00000598155.1_5'UTR|RSPH6A_ENST00000597055.1_5'Flank|RSPH6A_ENST00000221538.3_5'Flank	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	1127					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)		CTGGGGCCGGGGCCAAGGTCA	0.652													G|||	1793	0.358027	0.2905	0.232	5008	,	,		11505	0.6409		0.3181	False		,,,				2504	0.2883				p.A1127A		Atlas-SNP	.											.	SYMPK	104	.	0			c.C3381G						PASS	.						3.0	3.0	3.0					19																	46319415		1528	3134	4662	SO:0001819	synonymous_variant	8189	exon26			GGCCGGGGCCAAG	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.3381C>G	19.37:g.46319415G>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			G|0.613;C|0.387	0.387	strong		0.652	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
RAI14	26064	hgsc.bcm.edu	37	5	34824555	34824555	+	Missense_Mutation	SNP	G	G	T	rs1048944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34824555G>T	ENST00000265109.3	+	15	2895	c.2608G>T	c.(2608-2610)Gct>Tct	p.A870S	RAI14_ENST00000506376.1_Missense_Mutation_p.A862S|RAI14_ENST00000503673.1_Missense_Mutation_p.A870S|RAI14_ENST00000515799.1_Missense_Mutation_p.A873S|RAI14_ENST00000428746.2_Missense_Mutation_p.A870S|RAI14_ENST00000512629.1_Missense_Mutation_p.A841S|RAI14_ENST00000397449.1_Missense_Mutation_p.A863S	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	870			A -> S (in dbSNP:rs1048944). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GAAAAGATACGCTGAGAGCTC	0.368													T|||	2186	0.436502	0.2859	0.5879	5008	,	,		19028	0.369		0.4891	False		,,,				2504	0.5481				p.A873S		Atlas-SNP	.											.	RAI14	100	.	0			c.G2617T						PASS	.	T	SER/ALA,SER/ALA,SER/ALA,SER/ALA,SER/ALA,SER/ALA	1385,3015		252,881,1067	29.0	30.0	29.0		2608,2608,2521,2584,2617,2608	4.4	0.1	5	dbSNP_86	29	4233,4355		1061,2111,1122	yes	missense,missense,missense,missense,missense,missense	RAI14	NM_001145520.1,NM_001145521.1,NM_001145522.1,NM_001145523.1,NM_001145525.1,NM_015577.2	99,99,99,99,99,99	1313,2992,2189	TT,TG,GG		49.2897,31.4773,43.2553	benign,benign,benign,benign,benign,benign	870/981,870/981,841/952,862/973,873/984,870/981	34824555	5618,7370	2200	4294	6494	SO:0001583	missense	26064	exon17			AGATACGCTGAGA	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.2608G>T	5.37:g.34824555G>T	ENSP00000265109:p.Ala870Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	62	38	0.612903	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	928	0.4249084249084249	149	0.30284552845528456	212	0.585635359116022	198	0.34615384615384615	369	0.4868073878627968	T	9.574	1.121851	0.20877	0.314773	0.492897	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02;2.02	5.63	4.43	0.53597	.	.	.	.	.	T	0.00012	0.0000	N	0.00670	-1.27	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.39961	-0.9588	8	0.10111	T	0.7	-2.7917	8.8112	0.34967	0.1267:0.0:0.133:0.7403	rs1048944;rs3189001;rs52791950;rs60733664	862;841;873;870	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	S	870;841;870;870;873;862;863	ENSP00000265109:A870S;ENSP00000422377:A841S;ENSP00000388725:A870S;ENSP00000422942:A870S;ENSP00000427123:A873S;ENSP00000423854:A862S;ENSP00000380591:A863S	ENSP00000265109:A870S	A	+	1	0	RAI14	34860312	0.249000	0.23941	0.132000	0.22025	0.973000	0.67179	0.620000	0.24403	0.385000	0.24970	-0.375000	0.07067	GCT	A|0.004;C|0.007	.	strong		0.368	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
WDR34	89891	hgsc.bcm.edu	37	9	131398633	131398633	+	Silent	SNP	C	C	T	rs61744155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131398633C>T	ENST00000372715.2	-	4	690	c.630G>A	c.(628-630)ccG>ccA	p.P210P	WDR34_ENST00000483181.1_5'Flank	NM_052844.3	NP_443076.2	Q96EX3	WDR34_HUMAN	WD repeat domain 34	210						axoneme (GO:0005930)|centriole (GO:0005814)|ciliary basal body (GO:0036064)				central_nervous_system(2)|lung(5)|skin(1)|urinary_tract(1)	9						CCACGGCCGACGGCTGCTGGG	0.682													C|||	77	0.0153754	0.056	0.0043	5008	,	,		16542	0.0		0.0	False		,,,				2504	0.0				p.P210P		Atlas-SNP	.											.	WDR34	29	.	0			c.G630A						PASS	.	C		252,4150	136.5+/-172.5	10,232,1959	56.0	49.0	51.0		630	-5.2	0.0	9	dbSNP_129	51	5,8589	3.7+/-12.6	0,5,4292	no	coding-synonymous	WDR34	NM_052844.3		10,237,6251	TT,TC,CC		0.0582,5.7247,1.9775		210/537	131398633	257,12739	2201	4297	6498	SO:0001819	synonymous_variant	89891	exon4			GGCCGACGGCTGC	BC011874	CCDS6906.2	9q34.11	2013-11-15	2013-02-19	2013-02-19	ENSG00000119333	ENSG00000119333		"""WD repeat domain containing"""	28296	protein-coding gene	gene with protein product		613363				19521662, 21953912, 24183451	Standard	NM_052844		Approved	DIC5, MGC20486, bA216B9.3, FAP133	uc004bvq.1	Q96EX3	OTTHUMG00000020750	ENST00000372715.2:c.630G>A	9.37:g.131398633C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	110	30	0.272727	NM_052844	Q5VXV4|Q9BV46	Silent	SNP	ENST00000372715.2	37	CCDS6906.2																																																																																			C|0.978;T|0.022	0.022	strong		0.682	WDR34-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054463.1	NM_052844	
DCAF11	80344	hgsc.bcm.edu	37	14	24587639	24587639	+	Missense_Mutation	SNP	G	G	A	rs3825584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24587639G>A	ENST00000446197.3	+	7	1347	c.620G>A	c.(619-621)cGt>cAt	p.R207H	DCAF11_ENST00000560171.1_3'UTR|RP11-468E2.6_ENST00000558325.1_5'Flank|DCAF11_ENST00000396936.1_Missense_Mutation_p.R107H|DCAF11_ENST00000396941.4_Missense_Mutation_p.R181H|DCAF11_ENST00000559115.1_Missense_Mutation_p.R207H	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	155	0	0		WXS	Illumina HiSeq	Phase_I	168	77	0.458333	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		
FUCA2	2519	hgsc.bcm.edu	37	6	143816869	143816869	+	Missense_Mutation	SNP	G	G	A	rs151156975		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:143816869G>A	ENST00000002165.6	-	7	1434	c.1379C>T	c.(1378-1380)gCt>gTt	p.A460V	RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	460					fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		CAGGGCTAGAGCCCAGCCCCA	0.453																																					p.A460V		Atlas-SNP	.											.	FUCA2	28	.	0			c.C1379T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	98.0	82.0	87.0		1379	5.4	0.8	6	dbSNP_134	87	1,8599	1.2+/-3.3	0,1,4299	no	missense	FUCA2	NM_032020.4	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	460/468	143816869	1,13005	2203	4300	6503	SO:0001583	missense	2519	exon7			GCTAGAGCCCAGC	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1379C>T	6.37:g.143816869G>A	ENSP00000002165:p.Ala460Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	120	66	0.55	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	.	.	.	.	.	.	.	.	.	.	G	2.438	-0.329383	0.05314	0.0	1.16E-4	ENSG00000001036	ENST00000002165	T	0.50001	0.76	5.44	5.44	0.79542	.	0.495248	0.23750	N	0.044936	T	0.10423	0.0255	N	0.05383	-0.06	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.12041	-1.0563	10	0.02654	T	1	-0.6766	12.588	0.56428	0.0758:0.0:0.9242:0.0	.	460	Q9BTY2	FUCO2_HUMAN	V	460	ENSP00000002165:A460V	ENSP00000002165:A460V	A	-	2	0	FUCA2	143858562	0.998000	0.40836	0.842000	0.33263	0.068000	0.16541	6.197000	0.72100	2.575000	0.86900	0.650000	0.86243	GCT	G|1.000;A|0.000	0.000	weak		0.453	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
OR5L2	26338	hgsc.bcm.edu	37	11	55595116	55595116	+	Missense_Mutation	SNP	G	G	C	rs75822385|rs35214936|rs386753701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55595116G>C	ENST00000378397.1	+	1	422	c.422G>C	c.(421-423)cGt>cCt	p.R141P		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	141						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)				CAGAAGCTGCGTGTGGAGCTG	0.517										HNSCC(27;0.073)			N|||	446	0.0890575	0.1293	0.0403	5008	,	,		21243	0.0843		0.0924	False		,,,				2504	0.0706				p.R141P		Atlas-SNP	.											OR5L2,NS,carcinoma,+1,1	OR5L2	135	1	0			c.G422C						PASS	.						211.0	182.0	192.0					11																	55595116		2200	4296	6496	SO:0001583	missense	26338	exon1			AGCTGCGTGTGGA	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.422G>C	11.37:g.55595116G>C	ENSP00000367650:p.Arg141Pro	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	286	128	0.447552	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	.	.	.	.	.	.	.	.	.	.	.	11.49	1.653845	0.29425	.	.	ENSG00000205030	ENST00000378397	T	0.37058	1.22	5.18	4.26	0.50523	GPCR, rhodopsin-like superfamily (1);	0.359940	0.24334	N	0.039423	T	0.48003	0.1476	M	0.63843	1.955	0.09310	N	1	P	0.38395	0.629	P	0.51055	0.657	T	0.43442	-0.9391	10	0.87932	D	0	-1.0929	9.6016	0.39607	0.1634:0.0:0.8366:0.0	.	141	Q8NGL0	OR5L2_HUMAN	P	141	ENSP00000367650:R141P	ENSP00000367650:R141P	R	+	2	0	OR5L2	55351692	0.036000	0.19791	0.083000	0.20561	0.052000	0.14988	2.184000	0.42575	1.346000	0.45694	0.626000	0.83405	CGT	A|0.002;C|0.069;G|0.929	0.069	strong		0.517	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
CSTB	1476	hgsc.bcm.edu	37	21	45196136	45196136	+	Silent	SNP	C	C	A	rs4533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45196136C>A	ENST00000291568.5	-	1	190	c.15G>T	c.(13-15)gcG>gcT	p.A5A		NM_000100.3	NP_000091.1	P04080	CYTB_HUMAN	cystatin B (stefin B)	5					adult locomotory behavior (GO:0008344)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			lung(1)|prostate(1)	2				STAD - Stomach adenocarcinoma(101;0.168)		TGGCGGAGGGCGCCCCGCACA	0.746													C|||	86	0.0171725	0.062	0.0058	5008	,	,		9141	0.0		0.0	False		,,,				2504	0.0				p.A5A	Esophageal Squamous(58;831 1093 17019 29789 35147)	Atlas-SNP	.											.	CSTB	3	.	0			c.G15T						PASS	.	C		142,3048		0,142,1453	4.0	7.0	6.0		15	1.4	0.0	21	dbSNP_52	6	2,5900		0,2,2949	no	coding-synonymous	CSTB	NM_000100.2		0,144,4402	AA,AC,CC		0.0339,4.4514,1.5838		5/99	45196136	144,8948	1595	2951	4546	SO:0001819	synonymous_variant	1476	exon1			GGAGGGCGCCCCG	L03558	CCDS13701.1	21q22.3	2014-09-17			ENSG00000160213	ENSG00000160213			2482	protein-coding gene	gene with protein product		601145		EPM1, STFB		8596935	Standard	NM_000100		Approved	CST6, PME	uc002zdr.4	P04080	OTTHUMG00000086886	ENST00000291568.5:c.15G>T	21.37:g.45196136C>A		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_000100		Silent	SNP	ENST00000291568.5	37	CCDS13701.1																																																																																			C|0.988;A|0.012	0.012	strong		0.746	CSTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195689.1	NM_000100	
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978128	45978128	+	Silent	SNP	G	G	A	rs186210430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45978128G>A	ENST00000391620.1	-	1	515	c.471C>T	c.(469-471)tcC>tcT	p.S157S	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	157	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						GGAGGGACACGGAGGAGGAGG	0.692													G|||	70	0.0139776	0.0484	0.0086	5008	,	,		16657	0.0		0.0	False		,,,				2504	0.0				p.S157S		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.C471T						PASS	.	G	,	263,4143	147.3+/-181.8	4,255,1944	90.0	98.0	95.0		,471	-5.3	0.0	21		95	0,8600		0,0,4300	no	intron,coding-synonymous	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,	4,255,6244	AA,AG,GG		0.0,5.9691,2.0221	,	,157/222	45978128	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	386682	exon1			GGACACGGAGGAG	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.471C>T	21.37:g.45978128G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	189	99	0.52381	NM_198696	A3KN67|Q70LJ4	Silent	SNP	ENST00000391620.1	37	CCDS42956.1																																																																																			G|0.992;A|0.008	0.008	strong		0.692	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
TRIML1	339976	hgsc.bcm.edu	37	4	189061010	189061010	+	Missense_Mutation	SNP	A	A	G	rs111308948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:189061010A>G	ENST00000332517.3	+	1	438	c.298A>G	c.(298-300)Acc>Gcc	p.T100A	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	100					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		GAGGATGCCCACCACTGCCAA	0.647													G|||	203	0.0405351	0.1445	0.0159	5008	,	,		18008	0.0		0.001	False		,,,				2504	0.0				p.T100A	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											.	TRIML1	126	.	0			c.A298G						PASS	.	G	ALA/THR	538,3868	767.9+/-413.5	40,458,1705	41.0	40.0	41.0		298	3.3	0.0	4	dbSNP_132	41	0,8600		0,0,4300	yes	missense	TRIML1	NM_178556.3	58	40,458,6005	GG,GA,AA		0.0,12.2106,4.1366	benign	100/469	189061010	538,12468	2203	4300	6503	SO:0001583	missense	339976	exon1			ATGCCCACCACTG	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"""RING-type (C3HC4) zinc fingers"""	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.298A>G	4.37:g.189061010A>G	ENSP00000327738:p.Thr100Ala	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	156	73	0.467949	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	37	CCDS3851.1	78	0.03571428571428571	71	0.1443089430894309	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	G	0.714	-0.786047	0.02907	0.122106	0.0	ENSG00000184108	ENST00000332517	T	0.61040	0.14	5.06	3.27	0.37495	.	0.559255	0.16346	N	0.218439	T	0.00144	0.0004	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05649	-1.0872	9	0.42905	T	0.14	-6.5562	4.0011	0.09580	0.191:0.0:0.6206:0.1884	.	100	Q8N9V2	TRIML_HUMAN	A	100	ENSP00000327738:T100A	ENSP00000327738:T100A	T	+	1	0	TRIML1	189298004	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.371000	0.20450	0.776000	0.33473	-0.215000	0.12644	ACC	A|0.962;G|0.038	0.038	strong		0.647	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556	
NFATC1	4772	hgsc.bcm.edu	37	18	77211764	77211764	+	Silent	SNP	T	T	C	rs15350	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:77211764T>C	ENST00000427363.2	+	6	1851	c.1851T>C	c.(1849-1851)tcT>tcC	p.S617S	NFATC1_ENST00000587635.1_Missense_Mutation_p.L589P|NFATC1_ENST00000586434.1_Silent_p.S604S|NFATC1_ENST00000397790.2_Silent_p.S145S|NFATC1_ENST00000253506.5_Silent_p.S617S|NFATC1_ENST00000592223.1_Silent_p.S604S|NFATC1_ENST00000329101.4_Silent_p.S604S|NFATC1_ENST00000545796.1_Silent_p.S145S|NFATC1_ENST00000318065.5_Silent_p.S604S|NFATC1_ENST00000591814.1_Silent_p.S617S|NFATC1_ENST00000542384.1_Silent_p.S617S			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	617					calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	TGGTCCTGTCTGGCCACAACT	0.612													C|||	1425	0.284545	0.4569	0.17	5008	,	,		18388	0.3849		0.1262	False		,,,				2504	0.1922				p.S617S	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.T1851C						PASS	.	C	,,,,	1791,2615	641.0+/-397.4	361,1069,773	104.0	99.0	101.0		1851,1812,435,1812,1851	-4.1	0.7	18	dbSNP_119	101	1334,7266	757.0+/-407.5	109,1116,3075	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	,,,,	470,2185,3848	CC,CT,TT		15.5116,40.6491,24.0274	,,,,	617/826,604/931,145/354,604/813,617/717	77211764	3125,9881	2203	4300	6503	SO:0001819	synonymous_variant	4772	exon6			CCTGTCTGGCCAC	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.1851T>C	18.37:g.77211764T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Silent	SNP	ENST00000427363.2	37																																																																																				T|0.727;C|0.273	0.273	strong		0.612	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
HERC3	8916	hgsc.bcm.edu	37	4	89625427	89625427	+	Missense_Mutation	SNP	G	G	C	rs1804080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:89625427G>C	ENST00000402738.1	+	24	3075	c.2836G>C	c.(2836-2838)Gaa>Caa	p.E946Q	HERC3_ENST00000543130.1_Missense_Mutation_p.E390Q|HERC3_ENST00000264345.3_Missense_Mutation_p.E946Q	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	946			E -> Q (in dbSNP:rs1804080).		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)		GGAAGAACTGGAAGAGGTAAG	0.512													G|||	933	0.186302	0.1906	0.2017	5008	,	,		17767	0.2381		0.166	False		,,,				2504	0.137				p.E946Q		Atlas-SNP	.											.	HERC3	82	.	0			c.G2836C						PASS	.	G	GLN/GLU	851,3555	334.4+/-303.4	81,689,1433	150.0	147.0	148.0		2836	3.5	0.9	4	dbSNP_89	148	1331,7269	261.6+/-283.9	107,1117,3076	yes	missense	HERC3	NM_014606.1	29	188,1806,4509	CC,CG,GG		15.4767,19.3146,16.7769	probably-damaging	946/1051	89625427	2182,10824	2203	4300	6503	SO:0001583	missense	8916	exon24			GAACTGGAAGAGG	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.2836G>C	4.37:g.89625427G>C	ENSP00000385684:p.Glu946Gln	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	184	97	0.527174	NM_014606	A8K1S5|Q8IXX3	Missense_Mutation	SNP	ENST00000402738.1	37	CCDS34028.1	421	0.19276556776556777	88	0.17886178861788618	67	0.1850828729281768	134	0.23426573426573427	132	0.1741424802110818	G	19.18	3.776833	0.70107	0.193146	0.154767	ENSG00000138641	ENST00000402738;ENST00000264345;ENST00000543130	T;T;T	0.57907	0.37;0.37;0.37	5.26	3.51	0.40186	HECT (4);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	L	0.41079	1.255	0.09310	P	0.99999808362	D	0.89917	1.0	D	0.97110	1.0	T	0.03684	-1.1013	9	0.39692	T	0.17	.	10.8765	0.46915	0.0704:0.1307:0.7989:0.0	rs1804080;rs3737486;rs52837068;rs3737486	946	Q15034	HERC3_HUMAN	Q	946;946;390	ENSP00000385684:E946Q;ENSP00000264345:E946Q;ENSP00000441703:E390Q	ENSP00000264345:E946Q	E	+	1	0	HERC3	89844450	1.000000	0.71417	0.873000	0.34254	0.932000	0.56968	6.588000	0.74076	0.763000	0.33175	0.655000	0.94253	GAA	G|0.801;C|0.199	0.199	strong		0.512	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606	
NT5C1B	93034	hgsc.bcm.edu	37	2	18757501	18757501	+	Silent	SNP	G	G	C	rs3902946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:18757501G>C	ENST00000359846.2	-	9	1535	c.1458C>G	c.(1456-1458)ctC>ctG	p.L486L	NT5C1B_ENST00000304081.4_Silent_p.L426L|NT5C1B-RDH14_ENST00000532967.1_Silent_p.L486L|NT5C1B_ENST00000600945.1_Silent_p.L486L	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	486					nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				AGAATTTGTCGAGCCCATGCT	0.398													C|||	1574	0.314297	0.6649	0.3127	5008	,	,		17787	0.1081		0.1948	False		,,,				2504	0.1769				p.L503L		Atlas-SNP	.											.	NT5C1B	72	.	0			c.C1509G						PASS	.	C	,,,,,,	2591,1815	530.8+/-373.0	754,1083,366	81.0	76.0	78.0		1458,1407,1509,1464,1284,1458,1278	2.0	1.0	2	dbSNP_108	78	1796,6804	732.6+/-406.8	195,1406,2699	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NT5C1B,NT5C1B-RDH14	NM_001002006.2,NM_001199086.1,NM_001199087.1,NM_001199088.1,NM_001199103.1,NM_001199104.1,NM_033253.3	,,,,,,	949,2489,3065	CC,CG,GG		20.8837,41.1938,33.7306	,,,,,,	486/611,469/594,503/628,488/613,428/651,486/603,426/551	18757501	4387,8619	2203	4300	6503	SO:0001819	synonymous_variant	93034	exon9			TTTGTCGAGCCCA	AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.1458C>G	2.37:g.18757501G>C		Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	419	206	0.491647	NM_001199087	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Silent	SNP	ENST00000359846.2	37	CCDS33150.1	648	0.2967032967032967	323	0.6565040650406504	104	0.287292817679558	64	0.11188811188811189	157	0.20712401055408972	C	0.259	-1.000911	0.02128	0.588062	0.208837	ENSG00000185013	ENST00000418427	.	.	.	5.33	1.98	0.26296	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.41034	-0.9531	3	.	.	.	-1.9764	6.9441	0.24508	0.0:0.5707:0.1303:0.299	rs3902946;rs58362593;rs3902946	.	.	.	G	141	.	.	R	-	1	2	NT5C1B	18620982	0.389000	0.25205	1.000000	0.80357	0.042000	0.13812	-0.321000	0.08018	0.324000	0.23333	-0.120000	0.15030	CGA	G|0.689;C|0.311	0.311	strong		0.398	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1		
CPN2	1370	hgsc.bcm.edu	37	3	194062821	194062821	+	Missense_Mutation	SNP	G	G	A	rs146126834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:194062821G>A	ENST00000323830.3	-	2	700	c.611C>T	c.(610-612)gCg>gTg	p.A204V	CPN2_ENST00000429275.1_Missense_Mutation_p.A204V	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	204					protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)	p.A204V(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		ACCAGAGAGCGCGTTGTTGCT	0.617													G|||	13	0.00259585	0.0083	0.0014	5008	,	,		20075	0.0		0.001	False		,,,				2504	0.0				p.A204V		Atlas-SNP	.											CPN2,NS,carcinoma,0,1	CPN2	56	1	1	Substitution - Missense(1)	endometrium(1)	c.C611T						PASS	.	G	VAL/ALA	46,4360	48.2+/-83.0	0,46,2157	47.0	52.0	50.0		611	-3.7	0.0	3	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CPN2	NM_001080513.2	64	0,47,6456	AA,AG,GG		0.0116,1.044,0.3614	benign	204/546	194062821	47,12959	2203	4300	6503	SO:0001583	missense	1370	exon2			GAGAGCGCGTTGT	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"""carboxypeptidase N, polypeptide 2, 83kD"""	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.611C>T	3.37:g.194062821G>A	ENSP00000319464:p.Ala204Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	142	77	0.542253	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	5.618	0.298668	0.10622	0.01044	1.16E-4	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.57907	0.37;0.37	4.77	-3.7	0.04437	.	1.593460	0.04366	N	0.358343	T	0.19127	0.0459	N	0.25031	0.7	0.09310	N	1	P	0.39520	0.676	B	0.25759	0.063	T	0.14531	-1.0469	10	0.29301	T	0.29	.	1.8943	0.03254	0.2691:0.1002:0.1357:0.495	.	204	P22792	CPN2_HUMAN	V	204	ENSP00000319464:A204V;ENSP00000402232:A204V	ENSP00000319464:A204V	A	-	2	0	CPN2	195544516	0.000000	0.05858	0.000000	0.03702	0.297000	0.27493	-2.161000	0.01278	-0.371000	0.08004	-0.305000	0.09177	GCG	G|0.996;A|0.004	0.004	strong		0.617	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513	
USP34	9736	hgsc.bcm.edu	37	2	61433919	61433919	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61433919T>C	ENST00000398571.2	-	71	9098	c.9022A>G	c.(9022-9024)Aca>Gca	p.T3008A	USP34_ENST00000472689.1_5'Flank	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3008					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)			TAAGGGCGTGTAGACTTCAAA	0.388																																					p.T3008A		Atlas-SNP	.											.	USP34	334	.	0			c.A9022G						PASS	.						69.0	64.0	66.0					2																	61433919		1842	4099	5941	SO:0001583	missense	9736	exon71			GGCGTGTAGACTT	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.9022A>G	2.37:g.61433919T>C	ENSP00000381577:p.Thr3008Ala	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.32|16.32	3.090012|3.090012	0.55968|0.55968	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398571|ENST00000411912	T|.	0.64438|.	-0.1|.	5.82|5.82	5.82|5.82	0.92795|0.92795	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53351|0.53351	0.1791|0.1791	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	P|.	0.52842|.	0.956|.	D|.	0.65010|.	0.931|.	T|T	0.50074|0.50074	-0.8870|-0.8870	10|5	0.19590|.	T|.	0.45|.	.|.	16.19|16.19	0.81981|0.81981	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	3008|.	Q70CQ2|.	UBP34_HUMAN|.	A|C	2856;3008|767	ENSP00000381577:T3008A|.	ENSP00000263989:T2856A|.	T|Y	-|-	1|2	0|0	USP34|USP34	61287423|61287423	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	6.295000|6.295000	0.72744|0.72744	2.225000|2.225000	0.72522|0.72522	0.460000|0.460000	0.39030|0.39030	ACA|TAC	.	.	none		0.388	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
TRAM1L1	133022	hgsc.bcm.edu	37	4	118005458	118005458	+	Silent	SNP	C	C	T	rs35809332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:118005458C>T	ENST00000310754.4	-	1	1278	c.1092G>A	c.(1090-1092)agG>agA	p.R364R		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	364					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22						ATTTCTCTTTCCTCTTTGGCG	0.378													C|||	56	0.0111821	0.0401	0.0043	5008	,	,		18119	0.0		0.0	False		,,,				2504	0.0				p.R364R		Atlas-SNP	.											.	TRAM1L1	55	.	0			c.G1092A						PASS	.	C		161,4245	94.8+/-133.5	4,153,2046	135.0	140.0	138.0		1092	2.9	1.0	4	dbSNP_126	138	0,8600		0,0,4300	no	coding-synonymous	TRAM1L1	NM_152402.2		4,153,6346	TT,TC,CC		0.0,3.6541,1.2379		364/370	118005458	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	133022	exon1			CTCTTTCCTCTTT	AK074617	CCDS3707.1	4q26	2008-02-05			ENSG00000174599	ENSG00000174599			28371	protein-coding gene	gene with protein product						12477932	Standard	NM_152402		Approved	MGC26568	uc003ibv.4	Q8N609	OTTHUMG00000132956	ENST00000310754.4:c.1092G>A	4.37:g.118005458C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	199	94	0.472362	NM_152402	Q8N2L7	Silent	SNP	ENST00000310754.4	37	CCDS3707.1																																																																																			C|0.987;T|0.013	0.013	strong		0.378	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402	
LILRA6	79168	hgsc.bcm.edu	37	19	54745665	54745665	+	Missense_Mutation	SNP	C	C	T	rs1052966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54745665C>T	ENST00000396365.2	-	4	484	c.445G>A	c.(445-447)Gga>Aga	p.G149R	LILRA6_ENST00000391735.3_Missense_Mutation_p.G149R|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Missense_Mutation_p.G149R|LILRA6_ENST00000270464.5_Missense_Mutation_p.G149R|LILRA6_ENST00000419410.2_Missense_Mutation_p.G149R|LILRA6_ENST00000245621.5_Missense_Mutation_p.G149R	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	149			G -> R (in dbSNP:rs1052966).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.G149R(2)		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)		TGGTGATATCCCTTCTGTGAG	0.582																																					p.G149R		Atlas-SNP	.											LILRA6,NS,carcinoma,+1,4	LILRA6	75	4	2	Substitution - Missense(2)	large_intestine(2)	c.G445A						scavenged	.						25.0	40.0	35.0					19																	54745665		2106	4268	6374	SO:0001583	missense	79168	exon4			GATATCCCTTCTG	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.445G>A	19.37:g.54745665C>T	ENSP00000379651:p.Gly149Arg	Somatic	475	0	0		WXS	Illumina HiSeq	Phase_I	853	103	0.12075	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825878	0.32237	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;3.85;2.76;2.76	3.1	-6.21	0.02065	Immunoglobulin-like fold (1);	2.192950	0.01626	N	0.023278	T	0.12050	0.0293	L	0.39326	1.205	0.09310	N	1	P;B;P;P;B;P	0.41978	0.64;0.037;0.767;0.555;0.383;0.716	P;B;B;B;B;B	0.47044	0.535;0.085;0.444;0.211;0.344;0.276	T	0.27773	-1.0064	10	0.44086	T	0.13	.	4.765	0.13128	0.0:0.4155:0.3207:0.2638	rs1052966;rs3193450;rs13346484	149;149;149;149;149;149	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	R	149	ENSP00000390120:G149R;ENSP00000270464:G149R;ENSP00000411227:G149R;ENSP00000375615:G149R;ENSP00000379651:G149R;ENSP00000245621:G149R	ENSP00000245621:G149R	G	-	1	0	LILRA6	59437477	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-2.553000	0.00927	-1.315000	0.02297	0.162000	0.16502	GGA	C|0.972;T|0.028	0.028	strong		0.582	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
EXT2	2132	hgsc.bcm.edu	37	11	44129386	44129386	+	Missense_Mutation	SNP	A	A	G	rs4755779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44129386A>G	ENST00000343631.3	+	2	253	c.124A>G	c.(124-126)Atg>Gtg	p.M42V	EXT2_ENST00000533608.1_Missense_Mutation_p.M42V|EXT2_ENST00000395673.3_Missense_Mutation_p.M75V|EXT2_ENST00000358681.4_Missense_Mutation_p.M42V			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	42			M -> V (in dbSNP:rs4755779).		carbohydrate metabolic process (GO:0005975)|cell differentiation (GO:0030154)|cellular polysaccharide biosynthetic process (GO:0033692)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm formation (GO:0001707)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|lung(17)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	32						TGCCACTGGCATGTTTCAGTT	0.527			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Hereditary Multiple Exostoses				A|||	65	0.0129792	0.0492	0.0	5008	,	,		19628	0.0		0.0	False		,,,				2504	0.0				p.M75V		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	.	EXT2	129	.	0			c.A223G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	215,4191	132.1+/-168.6	3,209,1991	158.0	164.0	162.0		223,124,124	-1.5	1.0	11	dbSNP_111	162	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	EXT2	NM_000401.3,NM_001178083.1,NM_207122.1	21,21,21	3,210,6290	GG,GA,AA		0.0116,4.8797,1.6608	benign,benign,benign	75/752,42/729,42/719	44129386	216,12790	2203	4300	6503	SO:0001583	missense	2132	exon2	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	ACTGGCATGTTTC		CCDS7908.1, CCDS53618.1, CCDS53619.1	11p12-p11	2014-09-17	2013-03-01		ENSG00000151348	ENSG00000151348	2.4.1.224, 2.4.1.225	"""Exostosin glycosyltransferase family"""	3513	protein-coding gene	gene with protein product	"""Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"""	608210	"""exostoses (multiple) 2"", ""exostosin 2"""			8162019, 9576285	Standard	NM_000401		Approved	SOTV	uc001mya.3	Q93063	OTTHUMG00000166498	ENST00000343631.3:c.124A>G	11.37:g.44129386A>G	ENSP00000342656:p.Met42Val	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	204	98	0.480392	NM_000401	B2R5Z6|C9JU51|J3KPT2|O15288	Missense_Mutation	SNP	ENST00000343631.3	37	CCDS7908.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	A	9.644	1.139669	0.21205	0.048797	1.16E-4	ENSG00000151348	ENST00000533608;ENST00000532479;ENST00000527014;ENST00000358681;ENST00000395673;ENST00000343631	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.45	-1.52	0.08637	.	0.204155	0.64402	N	0.000019	T	0.03095	0.0091	N	0.24115	0.695	0.43814	D	0.996377	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	0.17018	-1.0383	10	0.07990	T	0.79	-5.2768	8.2837	0.31915	0.5707:0.1043:0.3249:0.0	rs4755779;rs52810595;rs4755779	42;42;42;42;55	Q6NUL1;C9JU51;Q93063-2;Q93063;D3DR24	.;.;.;EXT2_HUMAN;.	V	42;42;42;42;75;42	ENSP00000431173:M42V;ENSP00000433827:M42V;ENSP00000434716:M42V;ENSP00000351509:M42V;ENSP00000379032:M75V;ENSP00000342656:M42V	ENSP00000342656:M42V	M	+	1	0	EXT2	44085962	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	1.323000	0.33701	-0.161000	0.10983	0.528000	0.53228	ATG	A|0.981;G|0.019	0.019	strong		0.527	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401	
OBSCN	84033	hgsc.bcm.edu	37	1	228504486	228504486	+	Silent	SNP	G	G	A	rs372827129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228504486G>A	ENST00000422127.1	+	51	13406	c.13362G>A	c.(13360-13362)acG>acA	p.T4454T	OBSCN_ENST00000284548.11_Silent_p.T4454T|OBSCN_ENST00000570156.2_Silent_p.T5411T|OBSCN_ENST00000366709.4_Silent_p.T1573T|OBSCN_ENST00000366707.4_Silent_p.T2088T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4454	Ig-like 46.				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)				TCACCTGCACGCTCAGCGAGG	0.672													g|||	36	0.0071885	0.0272	0.0	5008	,	,		15193	0.0		0.0	False		,,,				2504	0.0				p.T5411T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G16233A						PASS	.		,	111,4087		0,111,1988	16.0	21.0	19.0		13362,13362	-0.1	0.1	1		19	0,8410		0,0,4205	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,111,6193	AA,AG,GG		0.0,2.6441,0.8804	,	4454/7969,4454/6621	228504486	111,12497	2099	4205	6304	SO:0001819	synonymous_variant	84033	exon62			CTGCACGCTCAGC	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.13362G>A	1.37:g.228504486G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	99	60	0.606061	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		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
BUB1B	701	hgsc.bcm.edu	37	15	40453430	40453430	+	Silent	SNP	G	G	T	rs7168394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40453430G>T	ENST00000287598.6	+	1	204	c.9G>T	c.(7-9)gcG>gcT	p.A3A	BUB1B_ENST00000560120.1_3'UTR|BUB1B_ENST00000412359.3_Silent_p.A3A	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	3					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)		GGATGGCGGCGGTGAAGAAGG	0.637			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				G|||	335	0.066893	0.2458	0.0144	5008	,	,		17894	0.0		0.0	False		,,,				2504	0.0				p.A3A		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.G9T						PASS	.	G		761,3645	297.3+/-284.7	70,621,1512	66.0	54.0	58.0		9	1.1	0.0	15	dbSNP_116	58	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous	BUB1B	NM_001211.5		70,639,5794	TT,TG,GG		0.2093,17.2719,5.9895		3/1051	40453430	779,12227	2203	4300	6503	SO:0001819	synonymous_variant	701	exon1	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GGCGGCGGTGAAG	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.9G>T	15.37:g.40453430G>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	136	74	0.544118	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			G|0.922;T|0.078	0.078	strong		0.637	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
NACA2	342538	hgsc.bcm.edu	37	17	59668275	59668275	+	Silent	SNP	T	T	A	rs61739271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:59668275T>A	ENST00000521764.1	-	1	288	c.267A>T	c.(265-267)acA>acT	p.T89T		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	89	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					TAGTAACTCCTGTAACCTGTA	0.443													T|||	198	0.0395367	0.1415	0.0144	5008	,	,		21980	0.0		0.001	False		,,,				2504	0.0				p.T89T		Atlas-SNP	.											.	NACA2	33	.	0			c.A267T						PASS	.	T		554,3852	249.6+/-257.0	38,478,1687	231.0	226.0	228.0		267	0.8	1.0	17	dbSNP_129	228	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NACA2	NM_199290.3		38,480,5985	AA,AT,TT		0.0233,12.5738,4.275		89/216	59668275	556,12450	2203	4300	6503	SO:0001819	synonymous_variant	342538	exon1			AACTCCTGTAACC	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"""alpha-NAC protein"""	609274	"""nascent-polypeptide-associated complex alpha polypeptide-like"""	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.267A>T	17.37:g.59668275T>A		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	257	134	0.521401	NM_199290	Q2VIR9	Silent	SNP	ENST00000521764.1	37	CCDS11630.1																																																																																			T|0.957;A|0.043	0.043	strong		0.443	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290	
ZNF469	84627	hgsc.bcm.edu	37	16	88495021	88495021	+	Silent	SNP	C	C	A	rs74032864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88495021C>A	ENST00000437464.1	+	1	1143	c.1143C>A	c.(1141-1143)ccC>ccA	p.P381P	ZNF469_ENST00000565624.1_Silent_p.P381P	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	381	Pro-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)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						AAATCCTTCCCGAAAGACCAC	0.617													C|||	256	0.0511182	0.1838	0.0187	5008	,	,		14646	0.0		0.0	False		,,,				2504	0.0				p.P381P		Atlas-SNP	.											.	ZNF469	121	.	0			c.C1143A						PASS	.						7.0	9.0	8.0					16																	88495021		683	1565	2248	SO:0001819	synonymous_variant	84627	exon1			CCTTCCCGAAAGA	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.1143C>A	16.37:g.88495021C>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			C|0.956;A|0.044	0.044	strong		0.617	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
MUC17	140453	hgsc.bcm.edu	37	7	100679752	100679752	+	Silent	SNP	T	T	C	rs4992072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100679752T>C	ENST00000306151.4	+	3	5119	c.5055T>C	c.(5053-5055)taT>taC	p.Y1685Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1685	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)					CCTCAACTTATACTGAAGGAA	0.468																																					p.Y1685Y		Atlas-SNP	.											.	MUC17	804	.	0			c.T5055C						PASS	.						192.0	206.0	201.0					7																	100679752		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTTATACTGAA	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.5055T>C	7.37:g.100679752T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	119	38	0.319328	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.980;C|0.020	0.020	strong		0.468	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238453	71238453	+	Missense_Mutation	SNP	G	G	C	rs147685834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71238453G>C	ENST00000398536.4	+	1	141	c.107G>C	c.(106-108)tGt>tCt	p.C36S		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	36	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						TCCAGCTGCTGTGTGCCCGTC	0.682													g|||	1257	0.250998	0.2088	0.2233	5008	,	,		10723	0.2877		0.1918	False		,,,				2504	0.3507				p.C36S		Atlas-SNP	.											KRTAP5-7,NS,carcinoma,0,1	KRTAP5-7	23	1	0			c.G107C						PASS	.	G	SER/CYS	856,3544		65,726,1409	69.0	90.0	83.0		107	1.8	1.0	11	dbSNP_134	83	1314,7270		110,1094,3088	no	missense	KRTAP5-7	NM_001012503.1	112	175,1820,4497	CC,CG,GG		15.3075,19.4545,16.7129	possibly-damaging	36/166	71238453	2170,10814	2200	4292	6492	SO:0001583	missense	440050	exon1			GCTGCTGTGTGCC	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"""Keratin associated proteins"""	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.107G>C	11.37:g.71238453G>C	ENSP00000417330:p.Cys36Ser	Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	361	164	0.454294	NM_001012503	B2RNM3|Q701N5	Missense_Mutation	SNP	ENST00000398536.4	37	CCDS41682.1	497	0.22756410256410256	100	0.2032520325203252	86	0.23756906077348067	173	0.30244755244755245	138	0.1820580474934037	N	6.704	0.498625	0.12762	0.194545	0.153075	ENSG00000244411	ENST00000398536	T	0.01397	4.94	1.8	1.8	0.24995	.	.	.	.	.	T	0.00012	0.0000	M	0.89658	3.05	0.43608	P	0.004022999999999999	P	0.47106	0.89	P	0.54965	0.765	T	0.33624	-0.9861	8	0.54805	T	0.06	.	7.1256	0.25469	0.0:0.0:1.0:0.0	.	36	Q6L8G8	KRA57_HUMAN	S	36	ENSP00000417330:C36S	ENSP00000417330:C36S	C	+	2	0	KRTAP5-7	70916101	1.000000	0.71417	0.978000	0.43139	0.179000	0.23085	3.185000	0.50934	1.345000	0.45676	0.281000	0.19383	TGT	G|0.807;C|0.193	0.193	strong		0.682	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1		
TAS2R30	259293	hgsc.bcm.edu	37	12	11286688	11286688	+	Silent	SNP	C	C	T	rs375822837		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11286688C>T	ENST00000539585.1	-	1	555	c.156G>A	c.(154-156)gcG>gcA	p.A52A	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	52					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						CTCTGGAGACCGCCAGAGCAG	0.388																																					p.A52A		Atlas-SNP	.											.	TAS2R30	28	.	0			c.G156A						PASS	.	C		2,4110		0,2,2054	78.0	79.0	79.0		156	-5.4	0.0	12		79	0,8504		0,0,4252	no	coding-synonymous	TAS2R30	NM_001097643.1		0,2,6306	TT,TC,CC		0.0,0.0486,0.0159		52/320	11286688	2,12614	2056	4252	6308	SO:0001819	synonymous_variant	259293	exon1			GGAGACCGCCAGA	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19112	protein-coding gene	gene with protein product		613963	"""taste receptor, type 2, member 47"""	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.156G>A	12.37:g.11286688C>T		Somatic	305	1	0.00327869		WXS	Illumina HiSeq	Phase_I	357	187	0.52381	NM_001097643	Q645X7	Silent	SNP	ENST00000539585.1	37	CCDS53750.1																																																																																			.	.	weak		0.388	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643	
RHPN2	85415	hgsc.bcm.edu	37	19	33493200	33493200	+	Missense_Mutation	SNP	G	G	A	rs200623446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33493200G>A	ENST00000254260.3	-	9	1093	c.1058C>T	c.(1057-1059)gCg>gTg	p.A353V	RHPN2_ENST00000400226.4_Missense_Mutation_p.A202V	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	353	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)					GGCCAGGGCCGCGTAGTGGTG	0.637																																					p.A353V		Atlas-SNP	.											RHPN2,caecum,carcinoma,-1,17	RHPN2	107	17	0			c.C1058T						scavenged	.						50.0	48.0	49.0					19																	33493200		2203	4300	6503	SO:0001583	missense	85415	exon9			AGGGCCGCGTAGT	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.1058C>T	19.37:g.33493200G>A	ENSP00000254260:p.Ala353Val	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	201	5	0.0248756	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	G	10.17	1.276172	0.23307	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.18810	2.19;2.19	4.61	-4.16	0.03869	BRO1 domain (3);	1.055030	0.07227	N	0.861852	T	0.14830	0.0358	L	0.39898	1.24	0.09310	N	1	B	0.18013	0.025	B	0.15484	0.013	T	0.36114	-0.9761	10	0.30078	T	0.28	0.2931	7.8623	0.29517	0.0:0.2524:0.4684:0.2792	.	353	Q8IUC4	RHPN2_HUMAN	V	353;83;202	ENSP00000254260:A353V;ENSP00000402244:A202V	ENSP00000254260:A353V	A	-	2	0	RHPN2	38185040	0.000000	0.05858	0.001000	0.08648	0.375000	0.29983	0.178000	0.16820	-0.540000	0.06265	0.455000	0.32223	GCG	G|0.935;A|0.065	0.065	strong		0.637	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
SUPT16H	11198	hgsc.bcm.edu	37	14	21841524	21841524	+	Silent	SNP	A	A	G	rs75576875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21841524A>G	ENST00000216297.2	-	2	470	c.132T>C	c.(130-132)atT>atC	p.I44I		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	44					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|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)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		TGGCATAAACAATTTCTTCAT	0.378													A|||	80	0.0159744	0.059	0.0029	5008	,	,		18715	0.0		0.0	False		,,,				2504	0.0				p.I44I		Atlas-SNP	.											.	SUPT16H	84	.	0			c.T132C						PASS	.	A		224,4182	134.9+/-171.1	5,214,1984	179.0	159.0	166.0		132	1.9	1.0	14	dbSNP_132	166	0,8600	1.2+/-3.3	0,0,4300	no	coding-synonymous	SUPT16H	NM_007192.3		5,214,6284	GG,GA,AA		0.0,5.084,1.7223		44/1048	21841524	224,12782	2203	4300	6503	SO:0001819	synonymous_variant	11198	exon2			ATAAACAATTTCT	AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 140 kDa subunit"""	605012	"""suppressor of Ty (S.cerevisiae) 16 homolog"""			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.132T>C	14.37:g.21841524A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	170	84	0.494118	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Silent	SNP	ENST00000216297.2	37	CCDS9569.1																																																																																			A|0.985;G|0.015	0.015	strong		0.378	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2		
PCNXL3	399909	hgsc.bcm.edu	37	11	65392695	65392695	+	Silent	SNP	C	C	T	rs1205259	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65392695C>T	ENST00000355703.3	+	17	3512	c.2973C>T	c.(2971-2973)ctC>ctT	p.L991L		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	991						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						TCTGTGGCCTCCTGGTGGCAC	0.632													C|||	1178	0.235224	0.3245	0.2421	5008	,	,		13681	0.1349		0.337	False		,,,				2504	0.1084				p.L991L		Atlas-SNP	.											.	PCNXL3	140	.	0			c.C2973T						PASS	.	C		1463,2935		241,981,977	45.0	48.0	47.0		2973	2.6	1.0	11	dbSNP_87	47	2975,5607		519,1937,1835	no	coding-synonymous	PCNXL3	NM_032223.2		760,2918,2812	TT,TC,CC		34.6656,33.2651,34.1911		991/2035	65392695	4438,8542	2199	4291	6490	SO:0001819	synonymous_variant	399909	exon17			TGGCCTCCTGGTG	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.2973C>T	11.37:g.65392695C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	37	CCDS44650.1																																																																																			C|0.733;T|0.267	0.267	strong		0.632	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
NCEH1	57552	hgsc.bcm.edu	37	3	172365832	172365832	+	Missense_Mutation	SNP	T	T	G	rs2302815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:172365832T>G	ENST00000475381.1	-	2	444	c.211A>C	c.(211-213)Aaa>Caa	p.K71Q	NCEH1_ENST00000273512.3_Missense_Mutation_p.K103Q|NCEH1_ENST00000543711.1_Intron|NCEH1_ENST00000538775.1_Missense_Mutation_p.K103Q			Q6PIU2	NCEH1_HUMAN	neutral cholesterol ester hydrolase 1	71			K -> Q (in dbSNP:rs2302815).		lipid catabolic process (GO:0016042)|protein dephosphorylation (GO:0006470)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carboxylic ester hydrolase activity (GO:0052689)|phosphate ion binding (GO:0042301)|serine hydrolase activity (GO:0017171)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15						GCGCTTTTTTTGCCAAAAGAA	0.512													T|||	681	0.135982	0.2345	0.1167	5008	,	,		19776	0.0833		0.1054	False		,,,				2504	0.1022				p.K103Q		Atlas-SNP	.											NCEH1,NS,adenoma,0,1	NCEH1	63	1	0			c.A307C						PASS	.	T	,,GLN/LYS,GLN/LYS	926,3480	351.6+/-311.3	110,706,1387	76.0	76.0	76.0		,,307,307	4.8	1.0	3	dbSNP_100	76	806,7794	186.2+/-233.7	48,710,3542	yes	utr-5,intron,missense,missense	NCEH1	NM_001146277.1,NM_001146278.1,NM_020792.4,NM_001146276.1	,,53,53	158,1416,4929	GG,GT,TT		9.3721,21.0168,13.3169	,,benign,benign	,,103/441,103/449	172365832	1732,11274	2203	4300	6503	SO:0001583	missense	57552	exon2			TTTTTTTGCCAAA	AB037784	CCDS54681.1, CCDS54682.1	3q26.31	2009-07-23	2009-07-23	2009-07-23	ENSG00000144959	ENSG00000144959			29260	protein-coding gene	gene with protein product		613234	"""arylacetamide deacetylase-like 1"""	AADACL1		10718198	Standard	NM_001146276		Approved	KIAA1363, NCEH	uc011bpx.2	Q6PIU2	OTTHUMG00000156872	ENST00000475381.1:c.211A>C	3.37:g.172365832T>G	ENSP00000418571:p.Lys71Gln	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	132	80	0.606061	NM_020792	B7Z2K4|B7Z3A1|B7Z5U2|B7Z906|B7ZAW6|F5H7K4|Q86WZ1|Q9P2I4	Missense_Mutation	SNP	ENST00000475381.1	37		275	0.1259157509157509	97	0.19715447154471544	37	0.10220994475138122	60	0.1048951048951049	81	0.10686015831134564	T	10.66	1.413799	0.25465	0.210168	0.093721	ENSG00000144959	ENST00000475381;ENST00000538775;ENST00000273512	T;T;T	0.04454	3.64;3.62;3.62	5.96	4.78	0.61160	.	0.672964	0.16446	N	0.214069	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	0.999999999938841	B;B	0.26081	0.141;0.017	B;B	0.20577	0.03;0.005	T	0.44862	-0.9300	9	0.25106	T	0.35	-14.7722	12.521	0.56058	0.0:0.0:0.397:0.603	rs2302815;rs59554414;rs2302815	103;71	F5H7K4;Q6PIU2	.;NCEH1_HUMAN	Q	71;103;103	ENSP00000418571:K71Q;ENSP00000442464:K103Q;ENSP00000273512:K103Q	ENSP00000273512:K103Q	K	-	1	0	NCEH1	173848526	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	2.082000	0.41605	1.039000	0.40074	0.533000	0.62120	AAA	T|0.868;G|0.132	0.132	strong		0.512	NCEH1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346367.3	NM_020792	
ZCCHC9	84240	hgsc.bcm.edu	37	5	80608363	80608363	+	Splice_Site	SNP	A	A	C	rs144053491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80608363A>C	ENST00000254037.2	+	5	3853	c.698A>C	c.(697-699)gAg>gCg	p.E233A	ZCCHC9_ENST00000407610.3_Splice_Site_p.E233A|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000380199.5_Splice_Site_p.E233A|ZCCHC9_ENST00000438268.2_Splice_Site_p.E233A			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	233					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)		TCCTTTACAGAGCGAATGGTC	0.368													A|||	2	0.000399361	0.0015	0.0	5008	,	,		20172	0.0		0.0	False		,,,				2504	0.0				p.E233A		Atlas-SNP	.											.	ZCCHC9	26	.	0			c.A698C						PASS	.	A	ALA/GLU,ALA/GLU,ALA/GLU	19,4387	27.2+/-55.0	1,17,2185	75.0	73.0	74.0		698,698,698	5.9	0.9	5	dbSNP_134	74	0,8600		0,0,4300	yes	missense-near-splice,missense-near-splice,missense-near-splice	ZCCHC9	NM_001131035.1,NM_001131036.1,NM_032280.2	107,107,107	1,17,6485	CC,CA,AA		0.0,0.4312,0.1461	benign,benign,benign	233/272,233/272,233/272	80608363	19,12987	2203	4300	6503	SO:0001630	splice_region_variant	84240	exon6			TTACAGAGCGAAT	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.698-1A>C	5.37:g.80608363A>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_001131036	B2RAE7|Q9H027	Missense_Mutation	SNP	ENST00000254037.2	37	CCDS4054.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	10.88	1.474400	0.26423	0.004312	0.0	ENSG00000131732	ENST00000254037;ENST00000407610;ENST00000380199;ENST00000438268	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.89	5.89	0.94794	.	0.392038	0.30302	N	0.009933	T	0.20047	0.0482	N	0.03608	-0.345	0.29325	N	0.867064	B	0.06786	0.001	B	0.06405	0.002	T	0.13072	-1.0523	9	.	.	.	.	11.9071	0.52719	0.8547:0.1453:0.0:0.0	.	233	Q8N567	ZCHC9_HUMAN	A	233	ENSP00000254037:E233A;ENSP00000385047:E233A;ENSP00000369546:E233A;ENSP00000412637:E233A	.	E	+	2	0	ZCCHC9	80644119	0.991000	0.36638	0.942000	0.38095	0.749000	0.42624	2.913000	0.48790	2.246000	0.74042	0.533000	0.62120	GAG	A|0.998;C|0.002	0.002	strong		0.368	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280	Missense_Mutation
MUC4	4585	hgsc.bcm.edu	37	3	195507851	195507851	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507851C>G	ENST00000463781.3	-	2	11059	c.10600G>C	c.(10600-10602)Gcc>Ccc	p.A3534P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3534P	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)		AGAGGCGTGGCGTGACCGGTG	0.612																																					p.A3534P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G10600C						PASS	.						31.0	30.0	31.0					3																	195507851		674	1579	2253	SO:0001583	missense	4585	exon2			GCGTGGCGTGACC	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.10600G>C	3.37:g.195507851C>G	ENSP00000417498:p.Ala3534Pro	Somatic	473	1	0.00211416		WXS	Illumina HiSeq	Phase_I	242	142	0.586777	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	8.586	0.883527	0.17467	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.55	0.743	-0.725	0.11174	.	0.326178	0.13539	U	0.380396	T	0.14098	0.0341	N	0.19112	0.55	0.09310	N	1	B	0.31581	0.329	B	0.28784	0.094	T	0.20371	-1.0277	9	.	.	.	.	4.4534	0.11631	0.0:0.67:0.0:0.33	.	3406	E7ESK3	.	P	3534	ENSP00000417498:A3534P;ENSP00000420243:A3534P	.	A	-	1	0	MUC4	196992630	0.000000	0.05858	0.019000	0.16419	0.019000	0.09904	-1.527000	0.02227	0.088000	0.17205	0.089000	0.15464	GCC	.	.	none		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SNX9	51429	hgsc.bcm.edu	37	6	158330765	158330765	+	Silent	SNP	G	G	A	rs3211067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:158330765G>A	ENST00000392185.3	+	8	945	c.774G>A	c.(772-774)agG>agA	p.R258R		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	258	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		CAGATCCCAGGAAAGGCTCCA	0.408													G|||	1028	0.205272	0.2239	0.1383	5008	,	,		20959	0.1369		0.2485	False		,,,				2504	0.2536				p.R258R		Atlas-SNP	.											.	SNX9	43	.	0			c.G774A						PASS	.	G		966,3440	367.1+/-318.1	107,752,1344	170.0	166.0	167.0		774	2.8	1.0	6	dbSNP_105	167	2020,6580	352.5+/-328.7	248,1524,2528	no	coding-synonymous	SNX9	NM_016224.3		355,2276,3872	AA,AG,GG		23.4884,21.9246,22.9586		258/596	158330765	2986,10020	2203	4300	6503	SO:0001819	synonymous_variant	51429	exon8			TCCCAGGAAAGGC	AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"""Sorting nexins"""	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.774G>A	6.37:g.158330765G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_016224	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Silent	SNP	ENST00000392185.3	37	CCDS5253.1																																																																																			G|0.778;A|0.222	0.222	strong		0.408	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1		
FKTN	2218	hgsc.bcm.edu	37	9	108380355	108380355	+	Silent	SNP	C	C	A	rs17309806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:108380355C>A	ENST00000223528.2	+	8	1150	c.1026C>A	c.(1024-1026)ctC>ctA	p.L342L	FKTN_ENST00000448551.2_Silent_p.L342L|FKTN_ENST00000357998.5_Silent_p.L342L|FKTN_ENST00000602661.1_Silent_p.L342L|FKTN_ENST00000540160.1_Intron	NM_006731.2	NP_006722.2	O75072	FKTN_HUMAN	fukutin	342					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						GACTTCCGCTCAAACACAAAT	0.328													C|||	893	0.178315	0.2088	0.2248	5008	,	,		16658	0.0903		0.2724	False		,,,				2504	0.0982				p.L342L		Atlas-SNP	.											.	FKTN	47	.	0			c.C1026A						PASS	.	C	,,	1051,3355	357.6+/-314.0	133,785,1285	41.0	41.0	41.0		1026,1026,1026	3.0	1.0	9	dbSNP_123	41	2731,5865	418.5+/-352.8	394,1943,1961	no	coding-synonymous,coding-synonymous,coding-synonymous	FKTN	NM_001079802.1,NM_001198963.1,NM_006731.2	,,	527,2728,3246	AA,AC,CC		31.7706,23.8538,29.0878	,,	342/462,342/431,342/462	108380355	3782,9220	2203	4298	6501	SO:0001819	synonymous_variant	2218	exon8			TCCGCTCAAACAC		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.1026C>A	9.37:g.108380355C>A		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	235	159	0.676596	NM_006731	B4DUX9|J3KP13|Q3MIJ1|Q96TE1|Q9P295	Silent	SNP	ENST00000223528.2	37	CCDS6766.1	460	0.21062271062271062	97	0.19715447154471544	87	0.24033149171270718	57	0.09965034965034965	219	0.28891820580474936	C	7.979	0.750751	0.15778	0.238538	0.317706	ENSG00000106692	ENST00000457847	.	.	.	6.02	2.98	0.34508	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999988	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.8012	1.8877	0.03241	0.203:0.4984:0.1286:0.17	rs17309806;rs17309806	.	.	.	X	39	.	.	S	+	2	0	FKTN	107420176	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.601000	0.24119	1.563000	0.49615	-0.142000	0.14014	TCA	C|0.750;A|0.250	0.250	strong		0.328	FKTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053505.1	NM_006731	
COL27A1	85301	hgsc.bcm.edu	37	9	116931666	116931666	+	Missense_Mutation	SNP	A	A	T	rs2567705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	46	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	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	
RHPN2	85415	hgsc.bcm.edu	37	19	33493201	33493201	+	Missense_Mutation	SNP	C	C	T	rs201601538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33493201C>T	ENST00000254260.3	-	9	1092	c.1057G>A	c.(1057-1059)Gcg>Acg	p.A353T	RHPN2_ENST00000400226.4_Missense_Mutation_p.A202T	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	353	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.A353T(2)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					GCCAGGGCCGCGTAGTGGTGG	0.642																																					p.A353T		Atlas-SNP	.											RHPN2,caecum,carcinoma,0,17	RHPN2	107	17	2	Substitution - Missense(2)	central_nervous_system(2)	c.G1057A						scavenged	.						51.0	48.0	49.0					19																	33493201		2203	4300	6503	SO:0001583	missense	85415	exon9			GGGCCGCGTAGTG	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.1057G>A	19.37:g.33493201C>T	ENSP00000254260:p.Ala353Thr	Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	203	5	0.0246305	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	6.623	0.483344	0.12581	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.17691	2.26;2.26	4.61	-0.585	0.11698	BRO1 domain (3);	1.055030	0.07227	N	0.861852	T	0.07279	0.0184	N	0.11560	0.145	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.41378	-0.9512	10	0.13853	T	0.58	0.2931	3.9219	0.09247	0.1643:0.3914:0.0:0.4443	.	353	Q8IUC4	RHPN2_HUMAN	T	353;83;202	ENSP00000254260:A353T;ENSP00000402244:A202T	ENSP00000254260:A353T	A	-	1	0	RHPN2	38185041	0.000000	0.05858	0.006000	0.13384	0.362000	0.29581	-0.172000	0.09868	0.142000	0.18901	-0.373000	0.07131	GCG	C|0.929;T|0.070	0.070	strong		0.642	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519244	48519244	+	Silent	SNP	A	A	G	rs35792818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48519244A>G	ENST00000339841.2	+	4	481	c.303A>G	c.(301-303)tcA>tcG	p.S101S	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	101	Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		TGTGGTGCTCAGTCACCTCTG	0.507													g|||	810	0.161741	0.2103	0.1254	5008	,	,		21204	0.0724		0.1531	False		,,,				2504	0.2229				p.S101S		Atlas-SNP	.											ELSPBP1,NS,NS,+1,1	ELSPBP1	29	1	0			c.A303G						PASS	.	G		885,3521	742.5+/-411.4	86,713,1404	136.0	115.0	122.0		303	-7.1	0.3	19	dbSNP_126	122	1294,7306	759.1+/-407.5	91,1112,3097	no	coding-synonymous	ELSPBP1	NM_022142.4		177,1825,4501	GG,GA,AA		15.0465,20.0862,16.7538		101/224	48519244	2179,10827	2203	4300	6503	SO:0001819	synonymous_variant	64100	exon4			GTGCTCAGTCACC	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.303A>G	19.37:g.48519244A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_022142	Q96RT0|Q9H4C8	Silent	SNP	ENST00000339841.2	37	CCDS12708.1																																																																																			A|0.837;G|0.163	0.163	strong		0.507	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
MRC1	4360	hgsc.bcm.edu	37	10	17891705	17891705	+	Missense_Mutation	SNP	A	A	G	rs1926736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	460	0	0		WXS	Illumina HiSeq	Phase_I	264	263	0.996212	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		
CD101	9398	hgsc.bcm.edu	37	1	117560058	117560058	+	Missense_Mutation	SNP	C	C	G	rs17235773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117560058C>G	ENST00000256652.4	+	5	1633	c.1575C>G	c.(1573-1575)agC>agG	p.S525R	CD101_ENST00000369470.1_Missense_Mutation_p.S525R	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	525	Ig-like C2-type 4.		S -> R (in dbSNP:rs17235773).		cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GAGATCTGAGCTGGACTCAGA	0.473													C|||	169	0.033746	0.0522	0.0461	5008	,	,		22414	0.0		0.0596	False		,,,				2504	0.0082				p.S525R		Atlas-SNP	.											.	CD101	95	.	0			c.C1575G						PASS	.	C	ARG/SER	304,4102	164.0+/-195.7	8,288,1907	71.0	74.0	73.0		1575	2.6	0.4	1	dbSNP_123	73	558,8042	151.8+/-206.5	22,514,3764	yes	missense	CD101	NM_004258.3	110	30,802,5671	GG,GC,CC		6.4884,6.8997,6.6277	probably-damaging	525/1022	117560058	862,12144	2203	4300	6503	SO:0001583	missense	9398	exon5			TCTGAGCTGGACT	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.1575C>G	1.37:g.117560058C>G	ENSP00000256652:p.Ser525Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	171	86	0.502924	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	93	0.042582417582417584	31	0.06300813008130081	15	0.04143646408839779	0	0.0	47	0.06200527704485488	C	15.24	2.776063	0.49786	0.068997	0.064884	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.22336	1.96;1.96	4.52	2.59	0.31030	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.767080	0.12461	N	0.466920	T	0.14874	0.0359	M	0.62723	1.935	0.29048	N	0.884698	P	0.50710	0.938	P	0.50314	0.637	T	0.07731	-1.0757	10	0.72032	D	0.01	0.0806	5.94	0.19187	0.0:0.6883:0.2048:0.107	rs17235773	525	Q93033	IGSF2_HUMAN	R	525	ENSP00000256652:S525R;ENSP00000358482:S525R	ENSP00000256652:S525R	S	+	3	2	CD101	117361581	0.066000	0.20996	0.440000	0.26846	0.797000	0.45037	0.049000	0.14099	0.611000	0.30052	0.655000	0.94253	AGC	C|0.944;G|0.056	0.056	strong		0.473	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
CHD1L	9557	hgsc.bcm.edu	37	1	146757092	146757092	+	Missense_Mutation	SNP	A	A	C	rs13374920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:146757092A>C	ENST00000369258.4	+	17	1966	c.1946A>C	c.(1945-1947)gAa>gCa	p.E649A	CHD1L_ENST00000431239.1_Missense_Mutation_p.E555A|CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000361293.5_Missense_Mutation_p.E368A|CHD1L_ENST00000369259.3_Missense_Mutation_p.E445A	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	649			E -> A (in dbSNP:rs13374920).		ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					AAAAGACAAGAAGCAGCTGCC	0.493													A|||	114	0.0227636	0.0825	0.0058	5008	,	,		19571	0.0		0.0	False		,,,				2504	0.001				p.E649A		Atlas-SNP	.											CHD1L,right_upper_lobe,carcinoma,+1,1	CHD1L	72	1	0			c.A1946C						PASS	.	A	ALA/GLU	307,4099	165.8+/-197.2	8,291,1904	148.0	146.0	147.0		1946	3.4	1.0	1	dbSNP_121	147	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CHD1L	NM_004284.3	107	8,296,6199	CC,CA,AA		0.0581,6.9678,2.3989	possibly-damaging	649/898	146757092	312,12694	2203	4300	6503	SO:0001583	missense	9557	exon17			GACAAGAAGCAGC	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.1946A>C	1.37:g.146757092A>C	ENSP00000358262:p.Glu649Ala	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	183	95	0.519126	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	37	CCDS927.1	47	0.02152014652014652	46	0.09349593495934959	1	0.0027624309392265192	0	0.0	0	0.0	A	8.801	0.932825	0.18131	0.069678	5.81E-4	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000361293	D;T;D;D	0.89810	-2.57;-1.43;-2.45;-1.55	5.78	3.4	0.38934	.	0.337634	0.31809	N	0.007040	T	0.76765	0.4033	L	0.43152	1.355	0.44098	D	0.996861	P;B;B	0.39181	0.663;0.419;0.339	B;B;B	0.38921	0.285;0.151;0.04	T	0.74481	-0.3651	10	0.49607	T	0.09	.	10.1412	0.42736	0.6754:0.3246:0.0:0.0	rs13374920;rs52828089;rs13374920	555;445;649	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	A	555;445;649;368	ENSP00000389031:E555A;ENSP00000358263:E445A;ENSP00000358262:E649A;ENSP00000355100:E368A	ENSP00000355100:E368A	E	+	2	0	CHD1L	145223716	1.000000	0.71417	0.989000	0.46669	0.006000	0.05464	2.163000	0.42377	0.418000	0.25898	-0.446000	0.05623	GAA	A|0.976;C|0.024	0.024	strong		0.493	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284	
ACSM5	54988	hgsc.bcm.edu	37	16	20435314	20435314	+	Missense_Mutation	SNP	C	C	T	rs73545426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20435314C>T	ENST00000331849.4	+	6	991	c.844C>T	c.(844-846)Ctc>Ttc	p.L282F		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	282					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						AGCCTGGACTCTCTTCTCTGC	0.493													C|||	329	0.0656949	0.171	0.0101	5008	,	,		19468	0.0466		0.0179	False		,,,				2504	0.0317				p.L282F		Atlas-SNP	.											.	ACSM5	101	.	0			c.C844T						PASS	.	C	PHE/LEU	616,3790	268.3+/-268.4	36,544,1623	172.0	150.0	157.0		844	2.5	1.0	16	dbSNP_131	157	179,8421	81.8+/-144.4	2,175,4123	no	missense	ACSM5	NM_017888.2	22	38,719,5746	TT,TC,CC		2.0814,13.9809,6.1126	benign	282/580	20435314	795,12211	2203	4300	6503	SO:0001583	missense	54988	exon6			TGGACTCTCTTCT		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.844C>T	16.37:g.20435314C>T	ENSP00000327916:p.Leu282Phe	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	151	77	0.509934	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	128	0.05860805860805861	75	0.1524390243902439	5	0.013812154696132596	33	0.057692307692307696	15	0.01978891820580475	C	10.50	1.368117	0.24771	0.139809	0.020814	ENSG00000183549	ENST00000331849	T	0.48836	0.8	4.56	2.45	0.29901	AMP-dependent synthetase/ligase (1);	0.703467	0.12754	N	0.441902	T	0.00178	0.0005	L	0.32530	0.975	0.38292	D	0.942747	B	0.16802	0.019	B	0.20955	0.032	T	0.20840	-1.0263	10	0.31617	T	0.26	-11.7114	2.5546	0.04756	0.1501:0.5145:0.1466:0.1889	.	282	Q6NUN0	ACSM5_HUMAN	F	282	ENSP00000327916:L282F	ENSP00000327916:L282F	L	+	1	0	ACSM5	20342815	0.001000	0.12720	0.989000	0.46669	0.989000	0.77384	-0.554000	0.06006	1.116000	0.41820	0.655000	0.94253	CTC	C|0.938;T|0.062	0.062	strong		0.493	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
DMKN	93099	hgsc.bcm.edu	37	19	36002393	36002393	+	Missense_Mutation	SNP	C	C	T	rs56743379|rs58579970|rs11667007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002393C>T	ENST00000339686.3	-	5	1014	c.838G>A	c.(838-840)Ggc>Agc	p.G280S	DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000451297.2_Missense_Mutation_p.G280S|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.G280S|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.G280S|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.G280S|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.G280S	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	280	Gly-rich.		G -> S (in dbSNP:rs11667007). {ECO:0000269|PubMed:17380110}.			extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			ccactgctgccgccactgctg	0.637																																					p.G280S		Atlas-SNP	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.G838A						PASS	.						26.0	20.0	22.0					19																	36002393		2167	4203	6370	SO:0001583	missense	93099	exon5			TGCTGCCGCCACT	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.838G>A	19.37:g.36002393C>T	ENSP00000342012:p.Gly280Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	673	0.30815018315018317	210	0.4268292682926829	75	0.20718232044198895	240	0.4195804195804196	148	0.19525065963060687	C	1.811	-0.474606	0.04414	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07;1.07	3.22	-6.45	0.01914	.	1.501560	0.04069	N	0.307709	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P;P;P;P;P	0.45428	0.858;0.858;0.858;0.858;0.749	B;B;B;B;B	0.29942	0.061;0.109;0.109;0.109;0.061	T	0.37244	-0.9714	9	0.07482	T	0.82	5.4478	5.8619	0.18752	0.149:0.2427:0.0:0.6083	rs11667007	280;280;280;280;280	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	S	280	ENSP00000342012:G280S;ENSP00000394908:G280S;ENSP00000415277:G280S;ENSP00000414743:G280S;ENSP00000388404:G280S;ENSP00000409513:G280S	ENSP00000342012:G280S	G	-	1	0	DMKN	40694233	0.008000	0.16893	0.000000	0.03702	0.008000	0.06430	-0.639000	0.05446	-1.330000	0.02255	-0.291000	0.09656	GGC	C|0.691;T|0.309	0.309	strong		0.637	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
DNAJC11	55735	hgsc.bcm.edu	37	1	6705874	6705874	+	Missense_Mutation	SNP	G	G	C	rs200454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6705874G>C	ENST00000377577.5	-	8	992	c.869C>G	c.(868-870)aCc>aGc	p.T290S	DNAJC11_ENST00000465508.1_5'Flank|DNAJC11_ENST00000377573.5_Missense_Mutation_p.T200S|DNAJC11_ENST00000294401.7_Missense_Mutation_p.T290S|DNAJC11_ENST00000542246.1_Missense_Mutation_p.T252S|DNAJC11_ENST00000349363.6_Intron	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	290			T -> A (in dbSNP:rs200454).|T -> S (in dbSNP:rs200454). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		GAAGTGGCTGGTTTTAGTGTC	0.592													G|||	807	0.161142	0.1982	0.3559	5008	,	,		17937	0.002		0.2266	False		,,,				2504	0.0695				p.T290S		Atlas-SNP	.											.	DNAJC11	93	.	0			c.C869G						PASS	.	G	SER/THR	986,3420	353.3+/-312.1	113,760,1330	138.0	131.0	133.0		869	4.3	1.0	1	dbSNP_79	133	1771,6829	306.6+/-308.0	170,1431,2699	yes	missense	DNAJC11	NM_018198.3	58	283,2191,4029	CC,CG,GG		20.593,22.3786,21.1979	benign	290/560	6705874	2757,10249	2203	4300	6503	SO:0001583	missense	55735	exon8			TGGCTGGTTTTAG	AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"""Heat shock proteins / DNAJ (HSP40)"""	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.869C>G	1.37:g.6705874G>C	ENSP00000366800:p.Thr290Ser	Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Missense_Mutation	SNP	ENST00000377577.5	37	CCDS87.1	406	0.1858974358974359	113	0.22967479674796748	118	0.3259668508287293	2	0.0034965034965034965	173	0.22823218997361477	G	9.833	1.188875	0.21954	0.223786	0.20593	ENSG00000007923	ENST00000377577;ENST00000294401;ENST00000542246;ENST00000377573;ENST00000426784	T;T;T;T;T	0.22336	2.56;2.55;2.29;1.96;2.51	5.27	4.33	0.51752	.	0.136479	0.64402	D	0.000003	T	0.00012	0.0000	N	0.11427	0.14	0.24466	P	0.99441492	B;B;B	0.12013	0.0;0.003;0.005	B;B;B	0.10450	0.0;0.005;0.002	T	0.42582	-0.9443	9	0.09084	T	0.74	-16.7799	12.0357	0.53423	0.0:0.0:0.6861:0.3139	rs200454;rs201177;rs3949837;rs200454	200;290;290	B4DGD5;Q9NVH1-3;Q9NVH1	.;.;DJC11_HUMAN	S	290;290;252;200;320	ENSP00000366800:T290S;ENSP00000294401:T290S;ENSP00000444020:T252S;ENSP00000366796:T200S;ENSP00000410194:T320S	ENSP00000294401:T290S	T	-	2	0	DNAJC11	6628461	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.913000	0.39956	1.172000	0.42781	0.650000	0.86243	ACC	G|0.786;C|0.214	0.214	strong		0.592	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198	
FAHD1	81889	hgsc.bcm.edu	37	16	1877494	1877494	+	Silent	SNP	T	T	C	rs3743854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1877494T>C	ENST00000427358.2	+	1	270	c.264T>C	c.(262-264)gcT>gcC	p.A88A	HAGH_ENST00000566709.1_5'Flank|FAHD1_ENST00000382666.4_Silent_p.A88A|HAGH_ENST00000455446.2_5'Flank|FAHD1_ENST00000382668.4_Silent_p.A88A|HAGH_ENST00000397353.2_5'Flank|HAGH_ENST00000397356.3_5'Flank	NM_031208.3	NP_112485.1	Q6P587	FAHD1_HUMAN	fumarylacetoacetate hydrolase domain containing 1	88						cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetylpyruvate hydrolase activity (GO:0018773)|acylpyruvate hydrolase activity (GO:0047621)|fumarylpyruvate hydrolase activity (GO:0034545)|metal ion binding (GO:0046872)			NS(1)|large_intestine(1)|liver(1)|ovary(2)|urinary_tract(1)	6						TCCCCGAGGCTGCGGCCATGG	0.677													C|||	1007	0.201078	0.1831	0.2262	5008	,	,		18027	0.1746		0.1809	False		,,,				2504	0.2556				p.A88A		Atlas-SNP	.											.	FAHD1	18	.	0			c.T264C						PASS	.	C	,,	775,3617		82,611,1503	33.0	36.0	35.0		264,264,264	1.3	1.0	16	dbSNP_107	35	1312,7276		110,1092,3092	no	coding-synonymous,coding-synonymous,coding-synonymous	FAHD1	NM_001018104.2,NM_001142398.1,NM_031208.3	,,	192,1703,4595	CC,CT,TT		15.2771,17.6457,16.0786	,,	88/249,88/227,88/225	1877494	2087,10893	2196	4294	6490	SO:0001819	synonymous_variant	81889	exon1			CGAGGCTGCGGCC	BC063017	CCDS10448.1, CCDS32367.1, CCDS45380.1	16p13.3	2011-10-21	2004-08-19	2004-08-26	ENSG00000180185	ENSG00000180185			14169	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 36"""	C16orf36		21878618	Standard	NM_001018104		Approved	DKFZP566J2046	uc002cnd.3	Q6P587	OTTHUMG00000128663	ENST00000427358.2:c.264T>C	16.37:g.1877494T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_031208	B1AK40|B1AK41|Q6FIC7|Q96RY1|Q9H0N6	Silent	SNP	ENST00000427358.2	37	CCDS10448.1																																																																																			T|0.840;C|0.160	0.160	strong		0.677	FAHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250550.2	NM_001018104	
DENND6B	414918	hgsc.bcm.edu	37	22	50752258	50752258	+	Silent	SNP	G	G	A	rs115446109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50752258G>A	ENST00000413817.3	-	14	1259	c.1188C>T	c.(1186-1188)ctC>ctT	p.L396L	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	396					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										GCAGCCGTTTGAGCAGCGCCT	0.677													G|||	61	0.0121805	0.0446	0.0029	5008	,	,		10156	0.0		0.0	False		,,,				2504	0.0				p.L396L		Atlas-SNP	.											.	.	.	.	0			c.C1188T						PASS	.	G		202,3980		3,196,1892	34.0	40.0	38.0		1188	1.0	1.0	22	dbSNP_132	38	2,8408		0,2,4203	no	coding-synonymous	FAM116B	NM_001001794.3		3,198,6095	AA,AG,GG		0.0238,4.8302,1.6201		396/586	50752258	204,12388	2091	4205	6296	SO:0001819	synonymous_variant	414918	exon14			CCGTTTGAGCAGC	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.1188C>T	22.37:g.50752258G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1																																																																																			G|0.984;A|0.016	0.016	strong		0.677	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
DUSP27	92235	hgsc.bcm.edu	37	1	167095768	167095768	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167095768G>A	ENST00000361200.2	+	6	1566	c.1400G>A	c.(1399-1401)cGc>cAc	p.R467H	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.R467H|DUSP27_ENST00000271385.5_Missense_Mutation_p.R467H			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	467					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R467H(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						AGGAGGCGCCGCGCAGACTCG	0.652																																					p.R467H		Atlas-SNP	.											DUSP27,NS,carcinoma,0,2	DUSP27	235	2	1	Substitution - Missense(1)	lung(1)	c.G1400A						PASS	.						21.0	21.0	21.0					1																	167095768		2202	4300	6502	SO:0001583	missense	92235	exon5			GGCGCCGCGCAGA	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1400G>A	1.37:g.167095768G>A	ENSP00000354483:p.Arg467His	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	98	13	0.132653	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.155451	0.38021	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03607	3.87;3.87;3.87	5.02	4.1	0.47936	.	0.086313	0.49305	D	0.000150	T	0.02649	0.0080	M	0.67953	2.075	0.30396	N	0.780517	B	0.19817	0.039	B	0.12156	0.007	T	0.12268	-1.0554	10	0.87932	D	0	-16.6929	13.7869	0.63115	0.076:0.0:0.924:0.0	.	467	Q5VZP5	DUS27_HUMAN	H	467	ENSP00000354483:R467H;ENSP00000271385:R467H;ENSP00000404874:R467H	ENSP00000271385:R467H	R	+	2	0	DUSP27	165362392	0.650000	0.27331	0.790000	0.31976	0.263000	0.26337	2.340000	0.43974	2.291000	0.77112	0.643000	0.83706	CGC	.	.	none		0.652	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
TNPO2	30000	hgsc.bcm.edu	37	19	12812169	12812169	+	Silent	SNP	A	A	G	rs16978628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12812169A>G	ENST00000592287.1	-	24	2793	c.2685T>C	c.(2683-2685)taT>taC	p.Y895Y	TNPO2_ENST00000588216.1_Silent_p.Y885Y|TNPO2_ENST00000441499.1_Silent_p.Y885Y|TNPO2_ENST00000425528.1_Silent_p.Y895Y|TNPO2_ENST00000356861.5_Silent_p.Y885Y|TNPO2_ENST00000450764.2_Silent_p.Y885Y	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	895					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CCTAGACCCCATAGAAAGCCG	0.567													G|||	808	0.161342	0.5787	0.0476	5008	,	,		13813	0.0		0.0099	False		,,,				2504	0.0				p.Y895Y		Atlas-SNP	.											.	TNPO2	108	.	0			c.T2685C						PASS	.	G	,,	1742,2040		428,886,577	54.0	57.0	56.0		2655,2685,2655	-4.6	1.0	19	dbSNP_123	56	127,8085		1,125,3980	no	coding-synonymous,coding-synonymous,coding-synonymous	TNPO2	NM_001136195.1,NM_001136196.1,NM_013433.4	,,	429,1011,4557	GG,GA,AA		1.5465,46.0603,15.5828	,,	885/888,895/898,885/888	12812169	1869,10125	1891	4106	5997	SO:0001819	synonymous_variant	30000	exon24			GACCCCATAGAAA	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"""Importins"""	19998	protein-coding gene	gene with protein product	"""importin 3"", ""karyopherin beta 2b"""	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.2685T>C	19.37:g.12812169A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	67	27	0.402985	NM_001136196	O14655|Q6IN77	Silent	SNP	ENST00000592287.1	37	CCDS45991.1																																																																																			A|0.843;G|0.157	0.157	strong		0.567	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433	
WWP1	11059	hgsc.bcm.edu	37	8	87414308	87414308	+	Silent	SNP	A	A	G	rs10106066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87414308A>G	ENST00000517970.1	+	8	907	c.600A>G	c.(598-600)caA>caG	p.Q200Q	WWP1_ENST00000349423.2_Intron|WWP1_ENST00000265428.4_Silent_p.Q200Q|WWP1_ENST00000341922.2_Intron	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	200					central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						CTCTAGTCCAAAACTCATGCT	0.408													A|||	265	0.0529153	0.1921	0.013	5008	,	,		16493	0.0		0.001	False		,,,				2504	0.001				p.Q200Q		Atlas-SNP	.											.	WWP1	97	.	0			c.A600G						PASS	.	A		678,3728	286.0+/-278.5	47,584,1572	119.0	105.0	109.0		600	-4.8	0.0	8	dbSNP_119	109	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	WWP1	NM_007013.3		47,589,5867	GG,GA,AA		0.0581,15.3881,5.2514		200/923	87414308	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	11059	exon8			AGTCCAAAACTCA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.600A>G	8.37:g.87414308A>G		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	196	104	0.530612	NM_007013	O00307|Q5YLC1|Q96BP4	Silent	SNP	ENST00000517970.1	37	CCDS6242.1																																																																																			.	.	weak		0.408	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013	
PRAMEF12	390999	hgsc.bcm.edu	37	1	12835868	12835868	+	Missense_Mutation	SNP	T	T	C	rs1812242|rs386628595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12835868T>C	ENST00000357726.4	+	2	497	c.470T>C	c.(469-471)aTg>aCg	p.M157T		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	157			M -> T (in dbSNP:rs1812242).		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)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	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;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AAGAATGGGATGCTGGATGAA	0.532													t|||	3588	0.716454	0.5696	0.8213	5008	,	,		19544	0.7183		0.7982	False		,,,				2504	0.7546				p.M157T		Atlas-SNP	.											.	PRAMEF12	69	.	0			c.T470C						PASS	.	C	THR/MET	2673,1733		810,1053,340	119.0	125.0	123.0		470	-2.4	0.0	1	dbSNP_92	123	6910,1690		2754,1402,144	yes	missense	PRAMEF12	NM_001080830.1	81	3564,2455,484	CC,CT,TT		19.6512,39.3327,26.3186	benign	157/484	12835868	9583,3423	2203	4300	6503	SO:0001583	missense	390999	exon2			ATGGGATGCTGGA		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"""-"""	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.470T>C	1.37:g.12835868T>C	ENSP00000350358:p.Met157Thr	Somatic	401	0	0		WXS	Illumina HiSeq	Phase_I	388	387	0.997423	NM_001080830		Missense_Mutation	SNP	ENST00000357726.4	37	CCDS41254.1	1611	0.7376373626373627	283	0.5752032520325203	294	0.8121546961325967	418	0.7307692307692307	616	0.8126649076517151	.	0.004	-2.316973	0.00235	0.606673	0.803488	ENSG00000116726	ENST00000357726	T	0.00949	5.51	2.67	-2.39	0.06602	.	2.671990	0.01490	N	0.017038	T	0.00012	0.0000	N	0.00077	-2.24	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31194	-0.9952	9	0.14656	T	0.56	.	5.42	0.16396	0.0:0.2483:0.5078:0.2439	rs1812242;rs2076217;rs56421762;rs59705408;rs1812242	157	O95522	PRA12_HUMAN	T	157	ENSP00000350358:M157T	ENSP00000350358:M157T	M	+	2	0	PRAMEF12	12758455	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.543000	0.02194	-0.966000	0.03587	-0.684000	0.03749	ATG	T|0.256;G|0.003	.	strong		0.532	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760	
SLC9C2	284525	hgsc.bcm.edu	37	1	173552703	173552703	+	Silent	SNP	G	G	A	rs16828416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173552703G>A	ENST00000367714.3	-	6	1004	c.582C>T	c.(580-582)atC>atT	p.I194I	SLC9C2_ENST00000536496.1_Silent_p.I92I|RP3-436N22.3_ENST00000431459.1_RNA	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	194					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										AAATTGATGCGATGCTACAAA	0.303													G|||	344	0.0686901	0.2466	0.0245	5008	,	,		16936	0.0		0.0	False		,,,				2504	0.001				p.I194I		Atlas-SNP	.											.	.	.	.	0			c.C582T						PASS	.	G		996,3410	357.6+/-314.0	113,770,1320	55.0	60.0	58.0		582	0.1	0.0	1	dbSNP_123	58	6,8590	5.0+/-18.6	0,6,4292	yes	coding-synonymous	SLC9A11	NM_178527.3		113,776,5612	AA,AG,GG		0.0698,22.6055,7.7065		194/1125	173552703	1002,12000	2203	4298	6501	SO:0001819	synonymous_variant	284525	exon6			TGATGCGATGCTA	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.582C>T	1.37:g.173552703G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	202	98	0.485149	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	37	CCDS1308.1																																																																																			G|0.910;A|0.090	0.090	strong		0.303	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
ARMC5	79798	hgsc.bcm.edu	37	16	31477442	31477442	+	Silent	SNP	T	T	C	rs116201073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31477442T>C	ENST00000563544.1	+	7	2586	c.2040T>C	c.(2038-2040)ggT>ggC	p.G680G	ARMC5_ENST00000412665.2_Silent_p.G324G|ARMC5_ENST00000408912.3_Silent_p.G775G|ARMC5_ENST00000457010.2_3'UTR|ARMC5_ENST00000268314.4_Silent_p.G680G|ARMC5_ENST00000538189.1_Silent_p.G712G			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	680										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						AGCAGGGTGGTCTCCGGCTCC	0.647													C|||	122	0.024361	0.0893	0.0058	5008	,	,		15259	0.0		0.0	False		,,,				2504	0.0				p.G680G		Atlas-SNP	.											ARMC5,NS,carcinoma,0,1	ARMC5	94	1	0			c.T2040C						scavenged	.	C	,	253,3943		8,237,1853	31.0	36.0	34.0		2040,	3.0	1.0	16	dbSNP_132	34	1,8425		0,1,4212	no	coding-synonymous,utr-3	ARMC5	NM_001105247.1,NM_024742.2	,	8,238,6065	CC,CT,TT		0.0119,6.0296,2.0124	,	680/936,	31477442	254,12368	2098	4213	6311	SO:0001819	synonymous_variant	79798	exon6			GGGTGGTCTCCGG	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.2040T>C	16.37:g.31477442T>C		Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001105247	Q86WM9|Q9H7P8|Q9H925	Silent	SNP	ENST00000563544.1	37	CCDS45472.1																																																																																			T|0.974;C|0.026	0.026	strong		0.647	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
XAB2	56949	hgsc.bcm.edu	37	19	7692132	7692132	+	Silent	SNP	G	G	A	rs4134824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7692132G>A	ENST00000358368.4	-	4	556	c.519C>T	c.(517-519)ctC>ctT	p.L173L	PET100_ENST00000594797.1_5'Flank|XAB2_ENST00000534844.1_Silent_p.L170L|CTD-3214H19.4_ENST00000595866.1_5'Flank|PET100_ENST00000456958.3_5'Flank|PET100_ENST00000601406.1_5'Flank	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	173					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						GGCTCACCTTGAGGAAGCGCC	0.597								Direct reversal of damage;Nucleotide excision repair (NER)					G|||	32	0.00638978	0.0242	0.0	5008	,	,		18719	0.0		0.0	False		,,,				2504	0.0				p.L173L		Atlas-SNP	.											.	XAB2	69	.	0			c.C519T						PASS	.	G		115,4291	87.3+/-125.9	2,111,2090	54.0	56.0	56.0		519	4.0	1.0	19	dbSNP_108	56	0,8600		0,0,4300	no	coding-synonymous	XAB2	NM_020196.2		2,111,6390	AA,AG,GG		0.0,2.6101,0.8842		173/856	7692132	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	56949	exon4			CACCTTGAGGAAG	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.519C>T	19.37:g.7692132G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	37	CCDS32892.1																																																																																			G|0.990;A|0.010	0.010	strong		0.597	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
OR9K2	441639	hgsc.bcm.edu	37	12	55523685	55523685	+	Missense_Mutation	SNP	C	C	T	rs12303066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	203	0	0		WXS	Illumina HiSeq	Phase_I	205	107	0.521951	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		
MAN2B1	4125	hgsc.bcm.edu	37	19	12760200	12760200	+	Silent	SNP	G	G	A	rs35880640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12760200G>A	ENST00000456935.2	-	19	2350	c.2310C>T	c.(2308-2310)ccC>ccT	p.P770P	MAN2B1_ENST00000221363.4_Silent_p.P769P|CTD-2192J16.22_ENST00000597692.1_5'Flank	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	770					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						TTCCTGCCACGGGCTCCGTCT	0.552													G|||	127	0.0253594	0.0756	0.0159	5008	,	,		15027	0.0		0.0109	False		,,,				2504	0.0051				p.P770P		Atlas-SNP	.											MAN2B1,colon,carcinoma,-1,1	MAN2B1	91	1	0			c.C2310T						PASS	.	G	,	288,4118	157.4+/-190.3	11,266,1926	84.0	60.0	68.0		2310,2307	-9.3	0.0	19	dbSNP_126	68	93,8507	51.1+/-111.2	1,91,4208	no	coding-synonymous,coding-synonymous	MAN2B1	NM_000528.3,NM_001173498.1	,	12,357,6134	AA,AG,GG		1.0814,6.5365,2.9294	,	770/1012,769/1011	12760200	381,12625	2203	4300	6503	SO:0001819	synonymous_variant	4125	exon19			TGCCACGGGCTCC		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.2310C>T	19.37:g.12760200G>A		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	242	130	0.53719	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Silent	SNP	ENST00000456935.2	37	CCDS32919.1																																																																																			G|0.975;A|0.025	0.025	strong		0.552	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
ZNF510	22869	hgsc.bcm.edu	37	9	99521150	99521150	+	Silent	SNP	T	T	C	rs61735521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99521150T>C	ENST00000375231.1	-	6	2612	c.1962A>G	c.(1960-1962)aaA>aaG	p.K654K	ZNF510_ENST00000223428.4_Silent_p.K654K			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	654					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(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				ATTCATAAGATTTCTCCCCAC	0.383													T|||	174	0.0347444	0.1278	0.0072	5008	,	,		18490	0.0		0.0	False		,,,				2504	0.0				p.K654K		Atlas-SNP	.											.	ZNF510	59	.	0			c.A1962G						PASS	.	T		448,3958	211.8+/-231.9	22,404,1777	101.0	107.0	105.0		1962	-0.6	0.0	9	dbSNP_129	105	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF510	NM_014930.1		22,406,6075	CC,CT,TT		0.0233,10.168,3.4599		654/684	99521150	450,12556	2203	4300	6503	SO:0001819	synonymous_variant	22869	exon6			ATAAGATTTCTCC	AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"""Zinc fingers, C2H2-type"", ""-"""	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.1962A>G	9.37:g.99521150T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	162	103	0.635802	NM_014930	Q5SZP5	Silent	SNP	ENST00000375231.1	37	CCDS35074.1																																																																																			T|0.970;C|0.030	0.030	strong		0.383	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930	
MUC17	140453	hgsc.bcm.edu	37	7	100676409	100676409	+	Missense_Mutation	SNP	C	C	T	rs34834039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100676409C>T	ENST00000306151.4	+	3	1776	c.1712C>T	c.(1711-1713)cCa>cTa	p.P571L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	571	59 X approximate tandem repeats.|Ser-rich.		P -> L (in dbSNP:rs34834039).		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)					GGAAGCACTCCATTAACAAAC	0.493													C|||	602	0.120208	0.1967	0.0821	5008	,	,		27512	0.0645		0.1173	False		,,,				2504	0.1043				p.P571L		Atlas-SNP	.											.	MUC17	804	.	0			c.C1712T						PASS	.	C	LEU/PRO	773,3633	314.4+/-293.6	63,647,1493	287.0	298.0	294.0		1712	0.4	0.0	7	dbSNP_126	294	982,7618	212.9+/-253.1	56,870,3374	yes	missense	MUC17	NM_001040105.1	98	119,1517,4867	TT,TC,CC		11.4186,17.5443,13.4938	benign	571/4494	100676409	1755,11251	2203	4300	6503	SO:0001583	missense	140453	exon3			GCACTCCATTAAC	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.1712C>T	7.37:g.100676409C>T	ENSP00000302716:p.Pro571Leu	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	155	72	0.464516	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	221	0.10119047619047619	69	0.1402439024390244	34	0.09392265193370165	29	0.050699300699300696	89	0.11741424802110818	C	2.299	-0.360703	0.05103	0.175443	0.114186	ENSG00000169876	ENST00000306151	T	0.03242	4.0	0.401	0.401	0.16338	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	1.0000000000287557E-6	B	0.24963	0.115	B	0.09377	0.004	T	0.46816	-0.9164	8	0.16420	T	0.52	.	6.7501	0.23482	0.0:0.9999:0.0:1.0E-4	rs34834039	571	Q685J3	MUC17_HUMAN	L	571	ENSP00000302716:P571L	ENSP00000302716:P571L	P	+	2	0	MUC17	100463129	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	0.756000	0.26419	0.496000	0.27904	0.501000	0.49751	CCA	C|0.880;T|0.120	0.120	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SETMAR	6419	hgsc.bcm.edu	37	3	4358210	4358210	+	Silent	SNP	A	A	G	rs7647539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:4358210A>G	ENST00000358065.4	+	3	1402	c.1335A>G	c.(1333-1335)cgA>cgG	p.R445R	SETMAR_ENST00000425863.1_Silent_p.R306R|SUMF1_ENST00000534863.1_Intron	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	445	Mariner transposase Hsmar1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		cggtcgttcgacatttgaagc	0.423								Chromatin Structure					G|||	2081	0.415535	0.8865	0.2954	5008	,	,		14865	0.1062		0.3559	False		,,,				2504	0.2444				p.R445R		Atlas-SNP	.											.	SETMAR	30	.	0			c.A1335G						PASS	.	G		3505,895		1406,693,101	13.0	15.0	14.0		1335	0.2	0.7	3	dbSNP_116	14	2843,5743		487,1869,1937	no	coding-synonymous	SETMAR	NM_006515.3		1893,2562,2038	GG,GA,AA		33.112,20.3409,48.8834		445/685	4358210	6348,6638	2200	4293	6493	SO:0001819	synonymous_variant	6419	exon3			CGTTCGACATTTG	U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.1335A>G	3.37:g.4358210A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_006515	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Silent	SNP	ENST00000358065.4	37	CCDS2563.2																																																																																			A|0.558;G|0.442	0.442	strong		0.423	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515	
TEP1	7011	hgsc.bcm.edu	37	14	20849169	20849169	+	Silent	SNP	G	G	A	rs2228039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20849169G>A	ENST00000262715.5	-	33	4723	c.4683C>T	c.(4681-4683)ttC>ttT	p.F1561F	TEP1_ENST00000545983.1_5'UTR|TEP1_ENST00000556935.1_Silent_p.F1453F	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1561					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)		GGTTGGTAAGGAACTTCGAAA	0.527													A|||	288	0.057508	0.093	0.036	5008	,	,		18921	0.001		0.0676	False		,,,				2504	0.0726				p.F1561F		Atlas-SNP	.											.	TEP1	224	.	0			c.C4683T						PASS	.	A		378,4028	791.5+/-415.1	16,346,1841	69.0	63.0	65.0		4683	-1.8	0.9	14	dbSNP_98	65	565,8035	793.8+/-407.5	20,525,3755	no	coding-synonymous	TEP1	NM_007110.4		36,871,5596	AA,AG,GG		6.5698,8.5792,7.2505		1561/2628	20849169	943,12063	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon33			GGTAAGGAACTTC		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.4683C>T	14.37:g.20849169G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			G|0.935;A|0.065	0.065	strong		0.527	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
KRT24	192666	hgsc.bcm.edu	37	17	38859664	38859664	+	Silent	SNP	G	G	A	rs61237409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38859664G>A	ENST00000264651.2	-	1	338	c.282C>T	c.(280-282)ggC>ggT	p.G94G		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	94	Gly-rich.|Head.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				CAGAGACCCCGCCAAAGCTAG	0.572													G|||	192	0.0383387	0.1384	0.0115	5008	,	,		13481	0.0		0.001	False		,,,				2504	0.0				p.G94G	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.	KRT24	60	.	0			c.C282T						PASS	.	G		416,3990	201.1+/-224.2	22,372,1809	95.0	118.0	110.0		282	-8.3	0.0	17	dbSNP_129	110	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	KRT24	NM_019016.2		22,375,6106	AA,AG,GG		0.0349,9.4417,3.2216		94/526	38859664	419,12587	2203	4300	6503	SO:0001819	synonymous_variant	192666	exon1			GACCCCGCCAAAG		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.282C>T	17.37:g.38859664G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	56	28	0.5	NM_019016	Q9NXG7	Silent	SNP	ENST00000264651.2	37	CCDS11372.1																																																																																			G|0.969;A|0.031	0.031	strong		0.572	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016	
MGAT5B	146664	hgsc.bcm.edu	37	17	74921129	74921129	+	Silent	SNP	C	C	T	rs34056052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74921129C>T	ENST00000569840.2	+	9	1681	c.1107C>T	c.(1105-1107)caC>caT	p.H369H	MGAT5B_ENST00000428789.2_Silent_p.H380H|MGAT5B_ENST00000301618.4_Silent_p.H369H	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	369					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)	p.H369H(1)		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						CCGACTACCACGGCCTGCAGC	0.627													C|||	295	0.0589058	0.0166	0.072	5008	,	,		10333	0.0784		0.0954	False		,,,				2504	0.0491				p.H380H		Atlas-SNP	.											MGAT5B,NS,carcinoma,0,2	MGAT5B	98	2	1	Substitution - coding silent(1)	stomach(1)	c.C1140T						PASS	.	C	,,	111,4295	84.4+/-122.9	0,111,2092	94.0	86.0	89.0		1107,1107,1140	-4.1	1.0	17	dbSNP_126	89	773,7827	181.8+/-230.4	39,695,3566	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	39,806,5658	TT,TC,CC		8.9884,2.5193,6.7969	,,	369/793,369/791,380/802	74921129	884,12122	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon8			CTACCACGGCCTG	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.1107C>T	17.37:g.74921129C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			C|0.932;T|0.068	0.068	strong		0.627	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592284	1592284	+	Intron	SNP	G	G	A	rs1135196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1592284G>A	ENST00000381605.4	-	1	141				SIRPB1_ENST00000568365.1_Missense_Mutation_p.T51I|SIRPB1_ENST00000279477.7_Missense_Mutation_p.T51I|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000381596.1_5'UTR|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						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						GCAGTGCAGAGTGGCCGACTC	0.552													g|||	3350	0.66893	0.739	0.5331	5008	,	,		8196	0.7669		0.5318	False		,,,				2504	0.7106				p.T51I		Atlas-SNP	.											.	SIRPB1	83	.	0			c.C152T						PASS	.						59.0	67.0	65.0					20																	1592284		446	1337	1783	SO:0001627	intron_variant	10326	exon2			TGCAGAGTGGCCG	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.76+8230C>T	20.37:g.1592284G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	173	58	0.33526	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	1306	0.597985347985348	353	0.717479674796748	188	0.5193370165745856	406	0.7097902097902098	359	0.4736147757255937	.	14.38	2.519337	0.44866	.	.	ENSG00000101307	ENST00000279477;ENST00000381596	T	0.02890	4.12	2.61	1.63	0.23807	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.70275	2.135	0.09310	P	0.99999999105145	P	0.49862	0.929	P	0.58077	0.832	T	0.10177	-1.0641	8	0.59425	D	0.04	.	5.1542	0.15027	0.1762:0.0:0.8238:0.0	rs1135196;rs3197727	51	Q5TFQ8	SIRBL_HUMAN	I	51	ENSP00000279477:T51I	ENSP00000279477:T51I	T	-	2	0	SIRPB1	1540284	0.961000	0.32948	0.830000	0.32933	0.019000	0.09904	0.679000	0.25291	0.406000	0.25560	0.205000	0.17691	ACT	G|0.420;A|0.580	0.580	strong		0.552	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
XYLT1	64131	hgsc.bcm.edu	37	16	17211545	17211545	+	Missense_Mutation	SNP	C	C	T	rs7200466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:17211545C>T	ENST00000261381.6	-	11	2599	c.2515G>A	c.(2515-2517)Gtt>Att	p.V839I		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	839			V -> I (in dbSNP:rs7200466).		cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AGAGGCGCAACGAGGAATTTG	0.547													C|||	318	0.0634984	0.2322	0.0144	5008	,	,		18992	0.0		0.001	False		,,,				2504	0.0				p.V839I		Atlas-SNP	.											.	XYLT1	147	.	0			c.G2515A						PASS	.	C	ILE/VAL	849,3545	334.4+/-303.4	80,689,1428	74.0	70.0	72.0		2515	4.2	0.7	16	dbSNP_116	72	19,8581	10.5+/-38.8	0,19,4281	yes	missense	XYLT1	NM_022166.3	29	80,708,5709	TT,TC,CC		0.2209,19.3218,6.68	possibly-damaging	839/960	17211545	868,12126	2197	4300	6497	SO:0001583	missense	64131	exon11			GCGCAACGAGGAA	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.2515G>A	16.37:g.17211545C>T	ENSP00000261381:p.Val839Ile	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	182	90	0.494505	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	110	0.05036630036630037	104	0.21138211382113822	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	12.04	1.818446	0.32145	0.193218	0.002209	ENSG00000103489	ENST00000261381	T	0.08984	3.03	5.11	4.16	0.48862	.	0.119796	0.64402	D	0.000019	T	0.00012	0.0000	L	0.42008	1.315	0.27093	P	0.9628188	B	0.25521	0.128	B	0.22753	0.041	T	0.40040	-0.9584	9	0.35671	T	0.21	-12.9866	8.7024	0.34334	0.0:0.7608:0.0:0.2392	rs7200466;rs52799636;rs7200466	839	Q86Y38	XYLT1_HUMAN	I	839	ENSP00000261381:V839I	ENSP00000261381:V839I	V	-	1	0	XYLT1	17119046	0.156000	0.22821	0.746000	0.31095	0.884000	0.51177	0.636000	0.24644	1.273000	0.44346	-0.251000	0.11542	GTT	C|0.934;T|0.066	0.066	strong		0.547	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
TRMT44	152992	hgsc.bcm.edu	37	4	8472839	8472839	+	Silent	SNP	C	C	T	rs17202499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:8472839C>T	ENST00000389737.4	+	10	1956	c.1956C>T	c.(1954-1956)aaC>aaT	p.N652N		NM_152544.2	NP_689757.2	Q8IYL2	TRM44_HUMAN	tRNA methyltransferase 44 homolog (S. cerevisiae)	652					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										AAGTAGCCAACGAGCTGGACA	0.547													T|||	97	0.019369	0.003	0.0202	5008	,	,		16156	0.0		0.0398	False		,,,				2504	0.0399				p.N652N		Atlas-SNP	.											.	TRMT44	7	.	0			c.C1956T						PASS	.	T		34,4372	822.9+/-416.5	0,34,2169	106.0	122.0	116.0		1956	-9.0	0.0	4	dbSNP_123	116	323,8277	804.9+/-407.3	9,305,3986	no	coding-synonymous	METTL19	NM_152544.2		9,339,6155	TT,TC,CC		3.7558,0.7717,2.7449		652/758	8472839	357,12649	2203	4300	6503	SO:0001819	synonymous_variant	152992	exon10			AGCCAACGAGCTG	AK093044	CCDS3402.1, CCDS3402.2	4p16.1	2012-06-12	2012-06-12	2012-06-12	ENSG00000155275	ENSG00000155275			26653	protein-coding gene	gene with protein product	"""tRNA methyltransferase 44 homolog (S. cerevisiae)"""	614309	"""chromosome 4 open reading frame 23"", ""methyltransferase like 19"""	C4orf23, METTL19		21658913	Standard	NM_152544		Approved	FLJ35725, TRM44	uc003glg.2	Q8IYL2	OTTHUMG00000160935	ENST00000389737.4:c.1956C>T	4.37:g.8472839C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	89	54	0.606742	NM_152544	Q8NA95	Silent	SNP	ENST00000389737.4	37	CCDS3402.2																																																																																			C|0.977;T|0.023	0.023	strong		0.547	TRMT44-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359197.2	NM_152544	
ZBBX	79740	hgsc.bcm.edu	37	3	167051726	167051726	+	Silent	SNP	A	A	G	rs10936530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:167051726A>G	ENST00000392766.2	-	10	916	c.576T>C	c.(574-576)ttT>ttC	p.F192F	ZBBX_ENST00000307529.5_Silent_p.F192F|ZBBX_ENST00000455345.2_Silent_p.F192F|ZBBX_ENST00000392764.1_Silent_p.F163F|ZBBX_ENST00000392767.2_Silent_p.F192F|ZBBX_ENST00000469220.1_Intron	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	192						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						CATCCTTTATAAACTGATGGG	0.308													A|||	2306	0.460463	0.4584	0.4395	5008	,	,		14921	0.6637		0.341	False		,,,				2504	0.3916				p.F192F		Atlas-SNP	.											ZBBX_ENST00000455345,NS,carcinoma,-2,2	ZBBX	299	2	0			c.T576C						PASS	.	A	,,	1533,2057		322,889,584	107.0	94.0	98.0		576,489,576	-1.6	0.5	3	dbSNP_120	98	2668,5474		422,1824,1825	no	coding-synonymous,coding-synonymous,coding-synonymous	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	,,	744,2713,2409	GG,GA,AA		32.7684,42.7019,35.808	,,	192/840,163/772,192/801	167051726	4201,7531	1795	4071	5866	SO:0001819	synonymous_variant	79740	exon10			CTTTATAAACTGA	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.576T>C	3.37:g.167051726A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	37	CCDS3199.2																																																																																			A|0.557;G|0.443	0.443	strong		0.308	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
PTPN13	5783	hgsc.bcm.edu	37	4	87696623	87696623	+	Silent	SNP	C	C	T	rs148059206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:87696623C>T	ENST00000411767.2	+	35	5772	c.5709C>T	c.(5707-5709)agC>agT	p.S1903S	PTPN13_ENST00000511467.1_Silent_p.S1908S|PTPN13_ENST00000427191.2_Silent_p.S1884S|PTPN13_ENST00000436978.1_Silent_p.S1908S|PTPN13_ENST00000316707.6_Silent_p.S1712S			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1903	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		GTCATGACAGCCTTTATCAAG	0.353													C|||	9	0.00179712	0.0068	0.0	5008	,	,		20073	0.0		0.0	False		,,,				2504	0.0				p.S1908S		Atlas-SNP	.											.	PTPN13	203	.	0			c.C5724T						PASS	.	C	,,,	20,3920		0,20,1950	94.0	89.0	90.0		5652,5709,5136,5724	1.0	0.3	4	dbSNP_134	90	1,8343		0,1,4171	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	,,,	0,21,6121	TT,TC,CC		0.012,0.5076,0.171	,,,	1884/2467,1903/2486,1712/2295,1908/2491	87696623	21,12263	1970	4172	6142	SO:0001819	synonymous_variant	5783	exon35			TGACAGCCTTTAT		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.5709C>T	4.37:g.87696623C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			C|0.999;T|0.001	0.001	strong		0.353	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
TCOF1	6949	hgsc.bcm.edu	37	5	149759201	149759201	+	Missense_Mutation	SNP	C	C	T	rs114689020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149759201C>T	ENST00000504761.2	+	17	2765	c.2765C>T	c.(2764-2766)tCg>tTg	p.S922L	TCOF1_ENST00000323668.7_Missense_Mutation_p.S845L|TCOF1_ENST00000394269.3_Missense_Mutation_p.S922L|TCOF1_ENST00000451292.1_Missense_Mutation_p.S922L|TCOF1_ENST00000377797.3_Missense_Mutation_p.S922L|TCOF1_ENST00000445265.2_Missense_Mutation_p.S845L|TCOF1_ENST00000439160.2_Missense_Mutation_p.S922L|TCOF1_ENST00000506063.1_3'UTR|TCOF1_ENST00000513346.1_Missense_Mutation_p.S922L			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	922					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACAGGGCCTTCGGCTGCCCAG	0.632													C|||	114	0.0227636	0.0787	0.0101	5008	,	,		19801	0.0		0.003	False		,,,				2504	0.0				p.S922L		Atlas-SNP	.											.	TCOF1	154	.	0			c.C2765T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER	281,4125	157.4+/-190.3	14,253,1936	54.0	60.0	58.0		2534,2765,2765,2765,2534,2765	0.4	0.0	5	dbSNP_132	58	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense,missense,missense,missense,missense	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	145,145,145,145,145,145	14,264,6225	TT,TC,CC		0.1279,6.3777,2.2451	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	845/1412,922/959,922/1489,922/1452,845/1413,922/1451	149759201	292,12714	2203	4300	6503	SO:0001583	missense	6949	exon17			GGCCTTCGGCTGC		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.2765C>T	5.37:g.149759201C>T	ENSP00000421655:p.Ser922Leu	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	142	75	0.528169	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	43	0.019688644688644688	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	13.10	2.136775	0.37728	0.063777	0.001279	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000394269;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T;T	0.74947	-0.01;-0.01;-0.01;-0.01;-0.02;-0.01;-0.89;-0.01;-0.87	5.63	0.389	0.16269	Treacher Collins syndrome, treacle (1);	1.572510	0.03797	N	0.263889	T	0.05823	0.0152	N	0.11560	0.145	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B	0.04013	0.0;0.001;0.001;0.001;0.001;0.001;0.001	T	0.25293	-1.0136	10	0.66056	D	0.02	1.7592	4.6859	0.12757	0.1423:0.5093:0.0:0.3484	.	431;922;845;922;922;845;922	B4DRA2;Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8;Q13428-5	.;.;.;.;TCOF_HUMAN;.;.	L	922;922;845;845;922;922;922;922;922	ENSP00000400939:S922L;ENSP00000367028:S922L;ENSP00000409944:S845L;ENSP00000325223:S845L;ENSP00000406888:S922L;ENSP00000377811:S922L;ENSP00000390717:S922L;ENSP00000421655:S922L;ENSP00000427484:S922L	ENSP00000325223:S845L	S	+	2	0	TCOF1	149739394	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.568000	0.05909	0.103000	0.17682	-0.254000	0.11334	TCG	C|0.979;T|0.021	0.021	strong		0.632	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
MVP	9961	hgsc.bcm.edu	37	16	29856082	29856082	+	Missense_Mutation	SNP	G	G	A	rs35916172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:29856082G>A	ENST00000357402.5	+	11	2041	c.1903G>A	c.(1903-1905)Gtc>Atc	p.V635I	MVP_ENST00000395353.1_Missense_Mutation_p.V635I	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	635			V -> I (in dbSNP:rs35916172).		cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						CGGGCTGGTGGTCAGCAGTGT	0.647													G|||	63	0.0125799	0.0439	0.0058	5008	,	,		16638	0.0		0.001	False		,,,				2504	0.0				p.V635I		Atlas-SNP	.											.	MVP	80	.	0			c.G1903A						PASS	.	G	ILE/VAL,ILE/VAL	151,4243	106.0+/-144.5	0,151,2046	80.0	81.0	81.0		1903,1903	5.0	1.0	16	dbSNP_126	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	MVP	NM_005115.4,NM_017458.3	29,29	0,152,6345	AA,AG,GG		0.0116,3.4365,1.1698	benign,benign	635/894,635/894	29856082	152,12842	2197	4300	6497	SO:0001583	missense	9961	exon11			CTGGTGGTCAGCA	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"""lung resistance-related protein"""	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.1903G>A	16.37:g.29856082G>A	ENSP00000349977:p.Val635Ile	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	37	CCDS10656.1	17	0.007783882783882784	16	0.032520325203252036	0	0.0	0	0.0	1	0.0013192612137203166	G	7.470	0.646386	0.14451	0.034365	1.16E-4	ENSG00000013364	ENST00000357402;ENST00000395353	T;T	0.39406	1.08;1.08	5.91	4.96	0.65561	Shoulder domain (1);	0.103708	0.64402	N	0.000003	T	0.08980	0.0222	N	0.20881	0.62	0.80722	D	1	B	0.18610	0.029	B	0.25140	0.058	T	0.04664	-1.0935	10	0.02654	T	1	-17.7157	9.1044	0.36689	0.1639:0.0:0.836:0.0	rs35916172;rs35916172	635	Q14764	MVP_HUMAN	I	635	ENSP00000349977:V635I;ENSP00000378760:V635I	ENSP00000349977:V635I	V	+	1	0	MVP	29763583	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.270000	0.51600	1.513000	0.48852	0.655000	0.94253	GTC	G|0.985;A|0.015	0.015	strong		0.647	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115	
CD72	971	hgsc.bcm.edu	37	9	35612978	35612978	+	Missense_Mutation	SNP	G	G	A	rs34791102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35612978G>A	ENST00000396757.1	-	7	865	c.701C>T	c.(700-702)cCg>cTg	p.P234L	CD72_ENST00000259633.4_Missense_Mutation_p.P234L|CD72_ENST00000490239.1_5'UTR			P21854	CD72_HUMAN	CD72 molecule	234	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		P -> L (in dbSNP:rs34791102).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor binding (GO:0005102)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(5)|liver(1)|lung(6)	12			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CCATCCCGACGGACAGCAGGT	0.423													g|||	309	0.0617013	0.1377	0.0216	5008	,	,		22020	0.005		0.0646	False		,,,				2504	0.0429				p.P234L		Atlas-SNP	.											.	CD72	20	.	0			c.C701T						PASS	.	A	LEU/PRO	553,3853	248.1+/-256.1	39,475,1689	128.0	115.0	119.0		701	3.8	0.3	9	dbSNP_126	119	459,8141	137.1+/-194.1	13,433,3854	yes	missense	CD72	NM_001782.2	98	52,908,5543	AA,AG,GG		5.3372,12.5511,7.781	probably-damaging	234/360	35612978	1012,11994	2203	4300	6503	SO:0001583	missense	971	exon6			CCCGACGGACAGC		CCDS6581.1	9p	2008-07-21	2006-03-28		ENSG00000137101	ENSG00000137101		"""CD molecules"""	1696	protein-coding gene	gene with protein product		107272	"""CD72 antigen"""			2044654, 1711157	Standard	NM_001782		Approved	LYB2, CD72b	uc003zxb.2	P21854	OTTHUMG00000019870	ENST00000396757.1:c.701C>T	9.37:g.35612978G>A	ENSP00000379980:p.Pro234Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_001782		Missense_Mutation	SNP	ENST00000396757.1	37	CCDS6581.1	113	0.051739926739926737	53	0.10772357723577236	4	0.011049723756906077	3	0.005244755244755245	53	0.06992084432717678	g	6.100	0.386632	0.11524	0.125511	0.053372	ENSG00000137101	ENST00000396757;ENST00000396759;ENST00000259633	T;T	0.61158	0.13;0.13	5.64	3.81	0.43845	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (1);	0.306603	0.28414	N	0.015435	T	0.00724	0.0024	M	0.78637	2.42	0.38189	D	0.939854	P;P	0.45986	0.87;0.87	B;B	0.31812	0.136;0.136	T	0.00883	-1.1528	10	0.59425	D	0.04	-8.2535	11.3314	0.49479	0.1584:0.0:0.8416:0.0	rs34791102;rs34791102	234;234	Q5TLG3;P21854	.;CD72_HUMAN	L	234	ENSP00000379980:P234L;ENSP00000259633:P234L	ENSP00000259633:P234L	P	-	2	0	CD72	35602978	0.735000	0.28153	0.325000	0.25375	0.008000	0.06430	0.807000	0.27140	0.352000	0.24053	-0.713000	0.03633	CCG	G|0.929;A|0.071	0.071	strong		0.423	CD72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052336.1	NM_001782	
RAB40AL	282808	hgsc.bcm.edu	37	X	102192885	102192885	+	Silent	SNP	G	G	A	rs7876193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192885G>A	ENST00000218249.5	+	1	686	c.639G>A	c.(637-639)ccG>ccA	p.P213P	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	213	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						ACAAGCTCCCGCTCCCCATTG	0.592													.|||	68	0.0180132	0.0477	0.0058	3775	,	,		13822	0.0		0.0	False		,,,				2504	0.001				p.P213P		Atlas-SNP	.											.	RAB40AL	33	.	0			c.G639A						PASS	.	G		213,3622		4,171,34,1457,537	145.0	117.0	127.0		639	-0.3	0.4	X	dbSNP_116	127	0,6728		0,0,0,2428,1872	no	coding-synonymous	RAB40AL	NM_001031834.1		4,171,34,3885,2409	AA,AG,A,GG,G		0.0,5.5541,2.0165		213/279	102192885	213,10350	2203	4300	6503	SO:0001819	synonymous_variant	282808	exon1			GCTCCCGCTCCCC	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"""Ras like GTPase"""	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.639G>A	X.37:g.102192885G>A		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	310	111	0.358065	NM_001031834	Q495H3	Silent	SNP	ENST00000218249.5	37	CCDS35353.1																																																																																			G|0.981;A|0.019	0.019	strong		0.592	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834	
PEAR1	375033	hgsc.bcm.edu	37	1	156878531	156878531	+	Silent	SNP	T	T	C	rs11264580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	75	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	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	
TENM1	10178	hgsc.bcm.edu	37	X	123775824	123775824	+	Missense_Mutation	SNP	T	T	C	rs16999334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:123775824T>C	ENST00000371130.3	-	11	1957	c.1894A>G	c.(1894-1896)Atg>Gtg	p.M632V	TENM1_ENST00000422452.2_Missense_Mutation_p.M632V	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	632	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.		M -> V (in dbSNP:rs16999334).		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)										TTGGAACACATTGGGTCTAGG	0.468													T|||	168	0.0445033	0.121	0.0086	3775	,	,		14477	0.0		0.001	False		,,,				2504	0.001				p.M632V		Atlas-SNP	.											.	.	.	.	0			c.A1894G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	562,3273		49,384,80,1199,491	196.0	175.0	182.0		1894,1891,1894	4.2	1.0	X	dbSNP_123	182	3,6725		0,3,0,2425,1872	yes	missense,missense,missense	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	21,21,21	49,387,80,3624,2363	CC,CT,C,TT,T		0.0446,14.6545,5.3489	benign,benign,benign	632/2733,631/2732,632/2726	123775824	565,9998	2203	4300	6503	SO:0001583	missense	10178	exon11			AACACATTGGGTC	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.1894A>G	X.37:g.123775824T>C	ENSP00000360171:p.Met632Val	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	159	56	0.352201	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	59	0.03556359252561784	41	0.08836206896551724	3	0.008379888268156424	0	0.0	0	0.0	T	13.41	2.228398	0.39399	0.146545	4.46E-4	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.03212	4.01;4.01	5.32	4.15	0.48705	Epidermal growth factor-like (1);	0.119478	0.56097	D	0.000024	T	0.00039	0.0001	N	0.21373	0.66	0.27607	P	0.9487963	B;B;B	0.27351	0.176;0.111;0.006	B;B;B	0.17098	0.016;0.017;0.005	T	0.48864	-0.8997	9	0.38643	T	0.18	.	10.3355	0.43847	0.0:0.0784:0.0:0.9216	rs16999334;rs52832334;rs58243564;rs16999334	631;632;632	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	V	632	ENSP00000360171:M632V;ENSP00000403954:M632V	ENSP00000360171:M632V	M	-	1	0	ODZ1	123603505	0.989000	0.36119	1.000000	0.80357	0.978000	0.69477	2.162000	0.42367	0.675000	0.31264	0.481000	0.45027	ATG	0|0.018;C|0.053	0.053	strong		0.468	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
LRP2	4036	hgsc.bcm.edu	37	2	170062078	170062078	+	Silent	SNP	G	G	C	rs13397109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170062078G>C	ENST00000263816.3	-	41	7911	c.7626C>G	c.(7624-7626)cgC>cgG	p.R2542R		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2542					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)"""	CAATGGGTACGCGGAAGTTTC	0.488													C|||	683	0.136382	0.3563	0.0576	5008	,	,		16972	0.0		0.0547	False		,,,				2504	0.1196				p.R2542R		Atlas-SNP	.											LRP2,NS,carcinoma,-2,1	LRP2	751	1	0			c.C7626G						scavenged	.	C		1345,3061	694.4+/-405.8	196,953,1054	123.0	114.0	117.0		7626	3.8	0.7	2	dbSNP_121	117	446,8154	799.3+/-407.4	8,430,3862	no	coding-synonymous	LRP2	NM_004525.2		204,1383,4916	CC,CG,GG		5.186,30.5266,13.7706		2542/4656	170062078	1791,11215	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon41			GGGTACGCGGAAG		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.7626C>G	2.37:g.170062078G>C		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			G|0.878;C|0.122	0.122	strong		0.488	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
SLC30A5	64924	hgsc.bcm.edu	37	5	68417643	68417643	+	Silent	SNP	C	C	T	rs164578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68417643C>T	ENST00000396591.3	+	13	2302	c.1692C>T	c.(1690-1692)caC>caT	p.H564H	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	564	His-rich loop.				cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		GCCATTCACACCATATGCATG	0.493													T|||	2122	0.423722	0.326	0.4207	5008	,	,		15173	0.5397		0.4245	False		,,,				2504	0.4376				p.H564H		Atlas-SNP	.											.	SLC30A5	54	.	0			c.C1692T						PASS	.	T		1472,2934	677.5+/-403.4	239,994,970	94.0	79.0	84.0		1692	2.1	1.0	5	dbSNP_79	84	3722,4878	614.5+/-396.2	830,2062,1408	no	coding-synonymous	SLC30A5	NM_022902.3		1069,3056,2378	TT,TC,CC		43.2791,33.409,39.9354		564/766	68417643	5194,7812	2203	4300	6503	SO:0001819	synonymous_variant	64924	exon13			TTCACACCATATG	AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"""Solute carriers"""	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.1692C>T	5.37:g.68417643C>T		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	266	122	0.458647	NM_022902	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Silent	SNP	ENST00000396591.3	37	CCDS3996.1																																																																																			C|0.589;T|0.411	0.411	strong		0.493	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2		
AKAP7	9465	hgsc.bcm.edu	37	6	131490324	131490324	+	Missense_Mutation	SNP	C	C	T	rs115301121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:131490324C>T	ENST00000431975.2	+	5	598	c.500C>T	c.(499-501)cCc>cTc	p.P167L	AKAP7_ENST00000541650.1_Missense_Mutation_p.P166L|AKAP7_ENST00000368123.4_Missense_Mutation_p.P145L|AKAP7_ENST00000366358.2_Intron	NM_016377.3	NP_057461.2	Q9P0M2	AKA7G_HUMAN	A kinase (PRKA) anchor protein 7	167						cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|nucleotide binding (GO:0000166)|protein kinase A binding (GO:0051018)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|stomach(1)	13	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		TTGACTTTGCCCTTTCAAGGG	0.373													C|||	26	0.00519169	0.0197	0.0	5008	,	,		17471	0.0		0.0	False		,,,				2504	0.0				p.P167L		Atlas-SNP	.											.	AKAP7	61	.	0			c.C500T						PASS	.	C	LEU/PRO	80,4326	68.7+/-106.4	3,74,2126	130.0	133.0	132.0		500	5.9	1.0	6	dbSNP_132	132	2,8598	1.2+/-3.3	0,2,4298	yes	missense	AKAP7	NM_016377.3	98	3,76,6424	TT,TC,CC		0.0233,1.8157,0.6305	benign	167/349	131490324	82,12924	2203	4300	6503	SO:0001583	missense	9465	exon5			CTTTGCCCTTTCA	AF047715	CCDS5142.1, CCDS5143.1, CCDS5144.1, CCDS5142.2	6q23.2	2012-10-24			ENSG00000118507	ENSG00000118507		"""A-kinase anchor proteins"""	377	protein-coding gene	gene with protein product		604693				9545239	Standard	NM_016377		Approved	AKAP18, AKAP15	uc003qck.4	O43687	OTTHUMG00000015563	ENST00000431975.2:c.500C>T	6.37:g.131490324C>T	ENSP00000405252:p.Pro167Leu	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	210	104	0.495238	NM_016377	B4DUC3|Q9HCZ8	Missense_Mutation	SNP	ENST00000431975.2	37	CCDS5142.2	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	25.2	4.613160	0.87359	0.018157	2.33E-4	ENSG00000118507	ENST00000431975;ENST00000541650;ENST00000368123	T;T;T	0.62941	-0.01;-0.01;-0.01	5.9	5.9	0.94986	RNA ligase/cyclic nucleotide phosphodiesterase (1);Protein kinase A anchor protein, nuclear localisation signal domain (1);	0.159801	0.56097	D	0.000021	T	0.63022	0.2476	M	0.73598	2.24	0.58432	D	0.999999	D;P	0.53312	0.959;0.945	P;P	0.50440	0.62;0.641	T	0.62077	-0.6930	10	0.33141	T	0.24	-11.449	15.779	0.78246	0.0:1.0:0.0:0.0	.	166;167	F5GXD1;Q9P0M2	.;AKA7G_HUMAN	L	167;166;145	ENSP00000405252:P167L;ENSP00000441048:P166L;ENSP00000357105:P145L	ENSP00000357105:P145L	P	+	2	0	AKAP7	131532017	0.998000	0.40836	1.000000	0.80357	0.984000	0.73092	4.775000	0.62346	2.788000	0.95919	0.650000	0.86243	CCC	C|0.993;T|0.007	0.007	strong		0.373	AKAP7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042209.2	NM_004842	
MMP20	9313	hgsc.bcm.edu	37	11	102477377	102477377	+	Missense_Mutation	SNP	G	G	T	rs1784424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:102477377G>T	ENST00000260228.2	-	6	854	c.842C>A	c.(841-843)aCt>aAt	p.T281N	RP11-817J15.2_ENST00000542119.1_RNA|MMP20_ENST00000544938.1_5'UTR|RP11-817J15.2_ENST00000544115.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	300					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	ATGGGGCAGAGTGGGCTTCCC	0.532													G|||	2103	0.419928	0.2625	0.4424	5008	,	,		20032	0.4325		0.4364	False		,,,				2504	0.5869				p.T281N		Atlas-SNP	.											.	MMP20	52	.	0			c.C842A						PASS	.	G	ASN/THR	1360,3046	451.8+/-349.8	204,952,1047	113.0	109.0	110.0		842	2.3	0.2	11	dbSNP_89	110	3926,4672	547.7+/-385.2	867,2192,1240	yes	missense	MMP20	NM_004771.3	65	1071,3144,2287	TT,TG,GG		45.6618,30.867,40.649	benign	281/484	102477377	5286,7718	2203	4299	6502	SO:0001583	missense	9313	exon6			GGCAGAGTGGGCT	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.842C>A	11.37:g.102477377G>T	ENSP00000260228:p.Thr281Asn	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	166	90	0.542169	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	876	0.4010989010989011	129	0.2621951219512195	170	0.4696132596685083	248	0.43356643356643354	329	0.4340369393139842	G	0.027	-1.362562	0.01235	0.30867	0.456618	ENSG00000137674	ENST00000260228	T	0.14516	2.5	5.45	2.3	0.28687	.	0.506134	0.22203	N	0.063204	T	0.00012	0.0000	L	0.34521	1.04	0.53688	P	2.599999999997049E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.46317	-0.9200	9	0.16420	T	0.52	.	8.1778	0.31292	0.1424:0.0:0.6217:0.2359	rs1784424;rs52816330;rs1784424	281	O60882	MMP20_HUMAN	N	281	ENSP00000260228:T281N	ENSP00000260228:T281N	T	-	2	0	MMP20	101982587	0.576000	0.26700	0.164000	0.22755	0.001000	0.01503	0.646000	0.24797	0.417000	0.25871	-0.813000	0.03139	ACT	G|0.598;T|0.402	0.402	strong		0.532	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
STARD13	90627	hgsc.bcm.edu	37	13	33684221	33684221	+	Missense_Mutation	SNP	C	C	T	rs140868444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33684221C>T	ENST00000336934.5	-	12	2952	c.2836G>A	c.(2836-2838)Gac>Aac	p.D946N	STARD13_ENST00000399365.3_Missense_Mutation_p.D828N|STARD13_ENST00000255486.4_Missense_Mutation_p.D938N	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	946	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				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)		GGGTTCCCGTCGCCCACCTTG	0.547											OREG0022359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	13	0.00259585	0.0098	0.0	5008	,	,		18177	0.0		0.0	False		,,,				2504	0.0				p.D946N		Atlas-SNP	.											.	STARD13	100	.	0			c.G2836A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	51,4355	53.6+/-89.4	0,51,2152	36.0	35.0	35.0		2482,2836,2812	5.3	0.9	13	dbSNP_134	35	0,8600		0,0,4300	yes	missense,missense,missense	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	23,23,23	0,51,6452	TT,TC,CC		0.0,1.1575,0.3921	probably-damaging,probably-damaging,probably-damaging	828/996,946/1114,938/1106	33684221	51,12955	2203	4300	6503	SO:0001583	missense	90627	exon12			TCCCGTCGCCCAC	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.2836G>A	13.37:g.33684221C>T	ENSP00000338785:p.Asp946Asn	Somatic	64	0	0	841	WXS	Illumina HiSeq	Phase_I	48	14	0.291667	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	35	5.458396	0.96240	0.011575	0.0	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934	T;T;T	0.34859	1.34;1.34;1.34	5.34	5.34	0.76211	Lipid-binding START (3);START-like domain (1);	0.000000	0.85682	D	0.000000	T	0.53690	0.1812	M	0.90650	3.135	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.77004	0.954;0.989;0.982	T	0.71573	-0.4552	10	0.87932	D	0	.	19.4036	0.94640	0.0:1.0:0.0:0.0	.	911;946;938	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	N	828;938;946	ENSP00000382300:D828N;ENSP00000255486:D938N;ENSP00000338785:D946N	ENSP00000255486:D938N	D	-	1	0	STARD13	32582221	1.000000	0.71417	0.931000	0.37212	0.958000	0.62258	7.689000	0.84165	2.657000	0.90304	0.655000	0.94253	GAC	C|0.996;T|0.004	0.004	strong		0.547	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
HBS1L	10767	hgsc.bcm.edu	37	6	135287533	135287533	+	Silent	SNP	A	A	G	rs13064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135287533A>G	ENST00000367837.5	-	17	2183	c.1977T>C	c.(1975-1977)ttT>ttC	p.F659F	HBS1L_ENST00000415177.2_Silent_p.F594F|HBS1L_ENST00000527578.1_Silent_p.F495F|HBS1L_ENST00000367824.4_Silent_p.F495F|HBS1L_ENST00000445176.2_Silent_p.F383F|HBS1L_ENST00000367826.2_Silent_p.F617F	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	659					signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		CCAGCTCTTTAAAGTCTTTAT	0.368													A|||	1299	0.259385	0.1906	0.2378	5008	,	,		16977	0.245		0.3549	False		,,,				2504	0.2843				p.F659F		Atlas-SNP	.											.	HBS1L	75	.	0			c.T1977C						PASS	.	A	,	1011,3395	376.8+/-322.2	113,785,1305	143.0	136.0	138.0		1851,1977	-9.0	0.4	6	dbSNP_52	138	3205,5395	484.5+/-371.4	595,2015,1690	no	coding-synonymous,coding-synonymous	HBS1L	NM_001145158.1,NM_006620.3	,	708,2800,2995	GG,GA,AA		37.2674,22.946,32.4158	,	617/643,659/685	135287533	4216,8790	2203	4300	6503	SO:0001819	synonymous_variant	10767	exon17			CTCTTTAAAGTCT	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.1977T>C	6.37:g.135287533A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1																																																																																			A|0.692;G|0.308	0.308	strong		0.368	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
ATP10A	57194	hgsc.bcm.edu	37	15	25959298	25959298	+	Missense_Mutation	SNP	T	T	C	rs141928852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25959298T>C	ENST00000356865.6	-	10	1978	c.1867A>G	c.(1867-1869)Agc>Ggc	p.S623G		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	623					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CCGATGCTGCTGCAGCCTGAG	0.617													T|||	18	0.00359425	0.0136	0.0	5008	,	,		14466	0.0		0.0	False		,,,				2504	0.0				p.S623G		Atlas-SNP	.											.	ATP10A	270	.	0			c.A1867G						PASS	.	T	GLY/SER	50,4356	43.8+/-77.6	0,50,2153	44.0	49.0	47.0		1867	0.6	1.0	15	dbSNP_134	47	0,8600		0,0,4300	yes	missense	ATP10A	NM_024490.3	56	0,50,6453	CC,CT,TT		0.0,1.1348,0.3844	benign	623/1500	25959298	50,12956	2203	4300	6503	SO:0001583	missense	57194	exon10			TGCTGCTGCAGCC	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1867A>G	15.37:g.25959298T>C	ENSP00000349325:p.Ser623Gly	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	11.14	1.550168	0.27652	0.011348	0.0	ENSG00000206190	ENST00000356865	T	0.11604	2.76	4.21	0.576	0.17380	HAD-like domain (1);	0.310582	0.37761	N	0.001944	T	0.04907	0.0132	L	0.35723	1.085	0.41036	D	0.985193	B	0.17038	0.02	B	0.20384	0.029	T	0.34527	-0.9825	10	0.28530	T	0.3	-9.6357	5.3687	0.16127	0.0:0.1605:0.149:0.6905	.	623	O60312	AT10A_HUMAN	G	623	ENSP00000349325:S623G	ENSP00000349325:S623G	S	-	1	0	ATP10A	23510391	1.000000	0.71417	0.952000	0.39060	0.450000	0.32258	3.499000	0.53310	-0.061000	0.13110	0.533000	0.62120	AGC	T|0.997;C|0.003	0.003	strong		0.617	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
NACC2	138151	hgsc.bcm.edu	37	9	138905136	138905136	+	Silent	SNP	C	C	T	rs2280486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138905136C>T	ENST00000371753.1	-	4	1222	c.1164G>A	c.(1162-1164)acG>acA	p.T388T	NACC2_ENST00000467669.1_5'Flank|NACC2_ENST00000277554.2_Silent_p.T388T			Q96BF6	NACC2_HUMAN	NACC family member 2, BEN and BTB (POZ) domain containing	388	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.				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						TGTTGGCCAGCGTGTTCCTGG	0.672													C|||	2325	0.464257	0.5469	0.4741	5008	,	,		11939	0.4494		0.4284	False		,,,				2504	0.3978				p.T388T		Atlas-SNP	.											.	NACC2	16	.	0			c.G1164A						PASS	.	C		2254,2150	576.4+/-384.2	586,1082,534	43.0	47.0	46.0		1164	-9.9	0.6	9	dbSNP_100	46	3615,4977	512.0+/-377.8	765,2085,1446	no	coding-synonymous	NACC2	NM_144653.4		1351,3167,1980	TT,TC,CC		42.074,48.8193,45.16		388/588	138905136	5869,7127	2202	4296	6498	SO:0001819	synonymous_variant	138151	exon5			GGCCAGCGTGTTC	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.1164G>A	9.37:g.138905136C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	199	71	0.356784	NM_144653		Silent	SNP	ENST00000371753.1	37	CCDS6993.1																																																																																			C|0.543;T|0.457	0.457	strong		0.672	NACC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055040.1	NM_144653	
TTC5	91875	hgsc.bcm.edu	37	14	20757804	20757804	+	Silent	SNP	C	C	A	rs3737220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	76	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	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	
APOB	338	hgsc.bcm.edu	37	2	21231524	21231524	+	Missense_Mutation	SNP	G	G	A	rs676210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:21231524G>A	ENST00000233242.1	-	26	8343	c.8216C>T	c.(8215-8217)cCa>cTa	p.P2739L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2739			P -> L (in dbSNP:rs676210). {ECO:0000269|PubMed:22095935, ECO:0000269|PubMed:2216805, ECO:0000269|PubMed:9490296}.		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGGAATTCTGGTATGTGAAG	0.398													G|||	1834	0.366214	0.1241	0.2493	5008	,	,		21164	0.7192		0.2177	False		,,,				2504	0.5654				p.P2739L		Atlas-SNP	.											.	APOB	761	.	0			c.C8216T	GRCh37	CM980093	APOB	M	rs676210	PASS	.	G	LEU/PRO	694,3712	289.5+/-280.5	52,590,1561	185.0	186.0	186.0		8216	5.2	1.0	2	dbSNP_83	186	1862,6738	331.8+/-319.8	227,1408,2665	yes	missense	APOB	NM_000384.2	98	279,1998,4226	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	21.6512,15.7512,19.6525	probably-damaging	2739/4564	21231524	2556,10450	2203	4300	6503	SO:0001583	missense	338	exon26			AATTCTGGTATGT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8216C>T	2.37:g.21231524G>A	ENSP00000233242:p.Pro2739Leu	Somatic	269	1	0.00371747		WXS	Illumina HiSeq	Phase_I	310	170	0.548387	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	737	0.3374542124542125	77	0.1565040650406504	79	0.21823204419889503	406	0.7097902097902098	175	0.23087071240105542	G	24.9	4.580663	0.86748	0.157512	0.216512	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01185	5.21	5.22	5.22	0.72569	.	0.000000	0.52532	D	0.000061	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.08597	-1.0714	9	0.87932	D	0	.	18.7715	0.91893	0.0:0.0:1.0:0.0	rs676210;rs17240903;rs52830519;rs60113879;rs676210	2739	P04114	APOB_HUMAN	L	2739	ENSP00000233242:P2739L	ENSP00000233242:P2739L	P	-	2	0	APOB	21085029	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.803000	0.99136	2.437000	0.82529	0.561000	0.74099	CCA	G|0.731;A|0.269	0.269	strong		0.398	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
MAD1L1	8379	hgsc.bcm.edu	37	7	2257612	2257612	+	Silent	SNP	G	G	A	rs6951493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2257612G>A	ENST00000406869.1	-	7	1220	c.663C>T	c.(661-663)caC>caT	p.H221H	MAD1L1_ENST00000265854.7_Silent_p.H221H|MAD1L1_ENST00000486340.1_5'Flank|MAD1L1_ENST00000402746.1_Silent_p.H129H|MAD1L1_ENST00000399654.2_Silent_p.H221H			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	221					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)		TCTGCTGCTCGTGGTCTGCTC	0.517													G|||	1831	0.365615	0.2587	0.389	5008	,	,		18844	0.5139		0.338	False		,,,				2504	0.3691				p.H221H		Atlas-SNP	.											.	MAD1L1	81	.	0			c.C663T						PASS	.	G	,,	1291,2991		224,843,1074	244.0	269.0	260.0		663,663,663	-10.8	0.0	7	dbSNP_116	260	2982,5504		551,1880,1812	no	coding-synonymous,coding-synonymous,coding-synonymous	MAD1L1	NM_001013836.1,NM_001013837.1,NM_003550.2	,,	775,2723,2886	AA,AG,GG		35.1402,30.1495,33.4665	,,	221/719,221/719,221/719	2257612	4273,8495	2141	4243	6384	SO:0001819	synonymous_variant	8379	exon7			CTGCTCGTGGTCT	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.663C>T	7.37:g.2257612G>A		Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	263	263	1	NM_003550	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Silent	SNP	ENST00000406869.1	37	CCDS43539.1																																																																																			G|0.639;A|0.361	0.361	strong		0.517	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550	
TEP1	7011	hgsc.bcm.edu	37	14	20850093	20850093	+	Missense_Mutation	SNP	C	C	T	rs1713456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20850093C>T	ENST00000262715.5	-	30	4443	c.4403G>A	c.(4402-4404)tGc>tAc	p.C1468Y	TEP1_ENST00000545983.1_5'UTR|TEP1_ENST00000556935.1_Missense_Mutation_p.C1360Y	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1468	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		C -> Y (in dbSNP:rs1713456).		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)		CTGGACGAGGCAGGCAAACGG	0.612													T|||	1198	0.239217	0.4448	0.1888	5008	,	,		17667	0.0992		0.1889	False		,,,				2504	0.1933				p.C1468Y		Atlas-SNP	.											TEP1,NS,carcinoma,+1,1	TEP1	224	1	0			c.G4403A						PASS	.	T	TYR/CYS	1672,2734	655.1+/-399.9	327,1018,858	147.0	132.0	137.0		4403	3.8	1.0	14	dbSNP_89	137	1579,7021	744.7+/-407.2	141,1297,2862	yes	missense	TEP1	NM_007110.4	194	468,2315,3720	TT,TC,CC		18.3605,37.9483,24.9962	benign	1468/2628	20850093	3251,9755	2203	4300	6503	SO:0001583	missense	7011	exon30			ACGAGGCAGGCAA		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.4403G>A	14.37:g.20850093C>T	ENSP00000262715:p.Cys1468Tyr	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	486	0.22252747252747251	213	0.4329268292682927	73	0.20165745856353592	50	0.08741258741258741	150	0.19788918205804748	T	0.800	-0.755646	0.03019	0.379483	0.183605	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.43688	1.01;0.94	4.98	3.82	0.43975	.	0.431628	0.25302	N	0.031653	T	0.00012	0.0000	N	0.00170	-1.935	0.09310	P	0.999999999813782	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45175	-0.9279	9	0.02654	T	1	-6.2294	4.6463	0.12574	0.1671:0.0917:0.0:0.7411	rs1713456;rs2228029;rs52817703;rs60076485;rs1713456	1360;811;1468	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	Y	1468;1468;1360	ENSP00000262715:C1468Y;ENSP00000452574:C1360Y	ENSP00000262715:C1468Y	C	-	2	0	TEP1	19919933	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	0.613000	0.24299	0.325000	0.23359	-0.521000	0.04368	TGC	C|0.754;A|0.001	.	strong		0.612	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
CCAR1	55749	hgsc.bcm.edu	37	10	70549579	70549579	+	Silent	SNP	G	G	A	rs11594683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70549579G>A	ENST00000265872.6	+	24	3419	c.3300G>A	c.(3298-3300)tcG>tcA	p.S1100S	CCAR1_ENST00000535016.1_Silent_p.S1085S|CCAR1_ENST00000543719.1_Silent_p.S1085S	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	1100					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						TAAAGATTTCGGAAAACATGA	0.328													G|||	203	0.0405351	0.0408	0.0634	5008	,	,		11157	0.006		0.0596	False		,,,				2504	0.0399				p.S1100S		Atlas-SNP	.											.	CCAR1	118	.	0			c.G3300A						PASS	.	G		152,4254	98.9+/-137.6	3,146,2054	49.0	53.0	52.0		3300	3.4	1.0	10	dbSNP_120	52	556,8018	148.9+/-204.1	18,520,3749	no	coding-synonymous	CCAR1	NM_018237.2		21,666,5803	AA,AG,GG		6.4847,3.4498,5.4545		1100/1151	70549579	708,12272	2203	4287	6490	SO:0001819	synonymous_variant	55749	exon24			GATTTCGGAAAAC	AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.3300G>A	10.37:g.70549579G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	166	69	0.415663	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Silent	SNP	ENST00000265872.6	37	CCDS7282.1																																																																																			G|0.947;A|0.053	0.053	strong		0.328	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237	
ABCC12	94160	hgsc.bcm.edu	37	16	48180311	48180311	+	Missense_Mutation	SNP	T	T	G	rs16945901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48180311T>G	ENST00000311303.3	-	1	370	c.25A>C	c.(25-27)Atc>Ctc	p.I9L	ABCC12_ENST00000448542.1_Missense_Mutation_p.I9L|ABCC12_ENST00000416054.1_Missense_Mutation_p.I9L	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	9			I -> L (in dbSNP:rs16945901).			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)				AGATCTGAGATAAGGTAGGGT	0.552													T|||	189	0.0377396	0.1399	0.0058	5008	,	,		20637	0.0		0.0	False		,,,				2504	0.0				p.I9L		Atlas-SNP	.											.	ABCC12	190	.	0			c.A25C						PASS	.	T	LEU/ILE	477,3925	225.9+/-241.6	24,429,1748	108.0	96.0	100.0		25	5.4	1.0	16	dbSNP_123	100	7,8593	4.3+/-15.6	0,7,4293	yes	missense	ABCC12	NM_033226.2	5	24,436,6041	GG,GT,TT		0.0814,10.836,3.7225	possibly-damaging	9/1360	48180311	484,12518	2201	4300	6501	SO:0001583	missense	94160	exon1			CTGAGATAAGGTA	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.25A>C	16.37:g.48180311T>G	ENSP00000311030:p.Ile9Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	74	0.03388278388278388	72	0.14634146341463414	2	0.0055248618784530384	0	0.0	0	0.0	T	17.20	3.327928	0.60743	0.10836	8.14E-4	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939;ENST00000416054;ENST00000527640	D;D;D;D	0.92911	-2.8;-3.04;-3.13;-2.66	5.41	5.41	0.78517	.	0.208161	0.39687	N	0.001292	T	0.01976	0.0062	N	0.25144	0.715	0.34860	P	0.257501	B;B	0.21821	0.061;0.007	B;B	0.16289	0.015;0.003	T	0.56914	-0.7900	9	0.02654	T	1	.	11.8356	0.52321	0.0:0.0:0.0:1.0	rs16945901;rs59437921;rs16945901	9;9	Q96J65-2;Q96J65	.;MRP9_HUMAN	L	9	ENSP00000311030:I9L;ENSP00000401855:I9L;ENSP00000413046:I9L;ENSP00000436647:I9L	ENSP00000311030:I9L	I	-	1	0	ABCC12	46737812	0.989000	0.36119	0.994000	0.49952	0.960000	0.62799	1.976000	0.40579	2.022000	0.59522	0.496000	0.49642	ATC	T|0.955;G|0.045	0.045	strong		0.552	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
PPEF2	5470	hgsc.bcm.edu	37	4	76788564	76788564	+	Missense_Mutation	SNP	C	C	T	rs34155925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:76788564C>T	ENST00000286719.7	-	14	2014	c.1658G>A	c.(1657-1659)aGa>aAa	p.R553K		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	553			R -> K (in dbSNP:rs34155925).		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)			CTCCTCCACTCTGCTAATCCT	0.403													C|||	639	0.127596	0.4531	0.0346	5008	,	,		19539	0.0079		0.002	False		,,,				2504	0.0061				p.R553K	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.G1658A						PASS	.	C	LYS/ARG	1783,2623	524.1+/-371.2	357,1069,777	55.0	57.0	57.0		1658	4.3	1.0	4	dbSNP_126	57	21,8579	14.0+/-48.4	0,21,4279	yes	missense	PPEF2	NM_006239.2	26	357,1090,5056	TT,TC,CC		0.2442,40.4675,13.8705	benign	553/754	76788564	1804,11202	2203	4300	6503	SO:0001583	missense	5470	exon14			TCCACTCTGCTAA	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.1658G>A	4.37:g.76788564C>T	ENSP00000286719:p.Arg553Lys	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	136	66	0.485294	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	251	0.11492673992673992	239	0.48577235772357724	9	0.024861878453038673	2	0.0034965034965034965	1	0.0013192612137203166	C	12.33	1.906038	0.33628	0.404675	0.002442	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.05081	3.5	6.04	4.31	0.51392	.	4.318100	0.00508	N	0.000165	T	0.00012	0.0000	L	0.55990	1.75	0.21627	P	0.999610337	B;B	0.30146	0.27;0.031	B;B	0.41946	0.371;0.015	T	0.47611	-0.9104	9	0.46703	T	0.11	1.3252	5.7123	0.17941	0.0:0.6724:0.1619:0.1657	rs34155925;rs57342715	553;553	O14830-2;O14830	.;PPE2_HUMAN	K	553	ENSP00000286719:R553K	ENSP00000286719:R553K	R	-	2	0	PPEF2	77007588	0.978000	0.34361	1.000000	0.80357	0.979000	0.70002	1.205000	0.32308	1.571000	0.49722	0.561000	0.74099	AGA	C|0.877;T|0.123	0.123	strong		0.403	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239	
TATDN2	9797	hgsc.bcm.edu	37	3	10312113	10312113	+	Missense_Mutation	SNP	T	T	C	rs61730105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:10312113T>C	ENST00000287652.4	+	4	2298	c.1247T>C	c.(1246-1248)aTg>aCg	p.M416T	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Missense_Mutation_p.M416T	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	416					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						CGGAGCCGCATGAGTGATTAT	0.577													T|||	171	0.0341454	0.121	0.0159	5008	,	,		18447	0.0		0.0	False		,,,				2504	0.0				p.M416T		Atlas-SNP	.											.	TATDN2	59	.	0			c.T1247C						PASS	.	T	THR/MET	464,3942	218.1+/-236.3	25,414,1764	89.0	89.0	89.0		1247	-0.9	0.0	3	dbSNP_129	89	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TATDN2	NM_014760.3	81	25,417,6061	CC,CT,TT		0.0349,10.5311,3.5907	benign	416/762	10312113	467,12539	2203	4300	6503	SO:0001583	missense	9797	exon4			GCCGCATGAGTGA	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.1247T>C	3.37:g.10312113T>C	ENSP00000287652:p.Met416Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	161	87	0.540373	NM_014760	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	37	CCDS33698.1	74	0.03388278388278388	64	0.13008130081300814	10	0.027624309392265192	0	0.0	0	0.0	T	7.134	0.580500	0.13686	0.105311	3.49E-4	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.32023	1.47;1.47	4.65	-0.863	0.10669	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25012	-1.0144	8	0.62326	D	0.03	0.6533	1.7362	0.02942	0.1368:0.1699:0.1409:0.5524	rs61730105	416	Q93075	TATD2_HUMAN	T	416	ENSP00000287652:M416T;ENSP00000408736:M416T	ENSP00000287652:M416T	M	+	2	0	TATDN2	10287113	0.011000	0.17503	0.047000	0.18901	0.386000	0.30323	0.184000	0.16939	-0.057000	0.13199	0.524000	0.50904	ATG	T|0.957;C|0.043	0.043	strong		0.577	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
CAMK2D	817	hgsc.bcm.edu	37	4	114438740	114438740	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:114438740C>T	ENST00000342666.5	-	9	674	c.675G>A	c.(673-675)caG>caA	p.Q225Q	CAMK2D_ENST00000454265.2_Silent_p.Q225Q|CAMK2D_ENST00000394526.2_Silent_p.Q225Q|CAMK2D_ENST00000418639.2_Silent_p.Q225Q|CAMK2D_ENST00000514328.1_Silent_p.Q225Q|CAMK2D_ENST00000394522.3_Silent_p.Q225Q|CAMK2D_ENST00000296402.5_Silent_p.Q225Q|CAMK2D_ENST00000515496.1_Silent_p.Q225Q|CAMK2D_ENST00000511664.1_Silent_p.Q225Q|CAMK2D_ENST00000379773.2_Silent_p.Q225Q|CAMK2D_ENST00000508738.1_Silent_p.Q225Q|CAMK2D_ENST00000429180.1_Silent_p.Q225Q|CAMK2D_ENST00000505990.1_Silent_p.Q225Q|CAMK2D_ENST00000394524.3_Silent_p.Q225Q			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		CAGCCTTGATCTGCTGATAGA	0.383																																					p.Q225Q		Atlas-SNP	.											.	CAMK2D	55	.	0			c.G675A						PASS	.						129.0	131.0	130.0					4																	114438740		2203	4300	6503	SO:0001819	synonymous_variant	817	exon9			CTTGATCTGCTGA	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.675G>A	4.37:g.114438740C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	85	4	0.0470588	NM_172128	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Silent	SNP	ENST00000342666.5	37	CCDS3703.1																																																																																			.	.	none		0.383	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2		
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249183	71249183	+	Missense_Mutation	SNP	T	T	C	rs55921335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	258	0	0		WXS	Illumina HiSeq	Phase_I	235	101	0.429787	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	
MUC4	4585	hgsc.bcm.edu	37	3	195511524	195511524	+	Silent	SNP	G	G	A	rs201351734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511524G>A	ENST00000463781.3	-	2	7386	c.6927C>T	c.(6925-6927)gaC>gaT	p.D2309D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D2309D	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)		CTGAGGAAGCGTCGGTGACAT	0.582																																					p.D2309D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,5	MUC4	1505	5	0			c.C6927T						scavenged	.						4.0	5.0	5.0					3																	195511524		476	1230	1706	SO:0001819	synonymous_variant	4585	exon2			GGAAGCGTCGGTG	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.6927C>T	3.37:g.195511524G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	114	20	0.175439	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|0.967;A|0.033	0.033	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
C17orf53	78995	hgsc.bcm.edu	37	17	42225250	42225250	+	Missense_Mutation	SNP	G	G	A	rs35879996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42225250G>A	ENST00000319977.4	+	3	316	c.79G>A	c.(79-81)Gca>Aca	p.A27T	C17orf53_ENST00000585683.1_Missense_Mutation_p.A27T|C17orf53_ENST00000245382.6_Missense_Mutation_p.A27T	NM_001171251.1|NM_024032.3	NP_001164722.1|NP_076937.2	Q8N3J3	CQ053_HUMAN	chromosome 17 open reading frame 53	27										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)		TGTGGAGGATGCAGAGAACCG	0.532													G|||	94	0.01877	0.0681	0.0058	5008	,	,		20182	0.0		0.0	False		,,,				2504	0.0				p.A27T		Atlas-SNP	.											.	C17orf53	59	.	0			c.G79A						PASS	.	G	THR/ALA,THR/ALA	223,4183	127.4+/-164.3	2,219,1982	57.0	58.0	58.0		79,79	2.0	1.0	17	dbSNP_126	58	5,8595	3.7+/-12.6	0,5,4295	yes	missense,missense	C17orf53	NM_001171251.1,NM_024032.3	58,58	2,224,6277	AA,AG,GG		0.0581,5.0613,1.753	probably-damaging,probably-damaging	27/647,27/648	42225250	228,12778	2203	4300	6503	SO:0001583	missense	78995	exon3			GAGGATGCAGAGA	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.79G>A	17.37:g.42225250G>A	ENSP00000313500:p.Ala27Thr	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_001171251	A8K7A9|Q9BWM9|Q9HAI1	Missense_Mutation	SNP	ENST00000319977.4	37	CCDS11477.1	34	0.015567765567765568	31	0.06300813008130081	3	0.008287292817679558	0	0.0	0	0.0	G	18.70	3.679486	0.68042	0.050613	5.81E-4	ENSG00000125319	ENST00000319977;ENST00000245382;ENST00000253405	T;T	0.52057	0.68;0.68	5.28	2.05	0.26809	.	0.355277	0.25487	N	0.030330	T	0.07098	0.0180	L	0.46157	1.445	0.27350	N	0.956269	P;B;P	0.51537	0.946;0.15;0.946	P;B;P	0.48677	0.586;0.044;0.586	T	0.01834	-1.1264	10	0.40728	T	0.16	-5.352	7.9308	0.29901	0.3513:0.0:0.6487:0.0	rs35879996	27;27;27	A8K7A9;Q8N3J3-3;Q8N3J3	.;.;CQ053_HUMAN	T	27	ENSP00000313500:A27T;ENSP00000245382:A27T	ENSP00000245382:A27T	A	+	1	0	C17orf53	39580776	0.992000	0.36948	1.000000	0.80357	0.960000	0.62799	2.005000	0.40864	0.797000	0.33971	0.561000	0.74099	GCA	G|0.983;A|0.017	0.017	strong		0.532	C17orf53-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457697.1	NM_024032	
PXDN	7837	hgsc.bcm.edu	37	2	1642736	1642736	+	Missense_Mutation	SNP	C	C	T	rs61747868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1642736C>T	ENST00000252804.4	-	21	4138	c.4088G>A	c.(4087-4089)gGg>gAg	p.G1363E		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1363					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)		GAGATGTTCCCCCTGTCTCCC	0.527													C|||	49	0.00978435	0.034	0.0043	5008	,	,		20724	0.0		0.001	False		,,,				2504	0.0				p.G1363E		Atlas-SNP	.											.	PXDN	255	.	0			c.G4088A						PASS	.	C	GLU/GLY	96,4162		1,94,2034	103.0	106.0	105.0		4088	3.2	0.0	2	dbSNP_129	105	5,8489		0,5,4242	yes	missense	PXDN	NM_012293.1	98	1,99,6276	TT,TC,CC		0.0589,2.2546,0.792	benign	1363/1480	1642736	101,12651	2129	4247	6376	SO:0001583	missense	7837	exon21			TGTTCCCCCTGTC	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.4088G>A	2.37:g.1642736C>T	ENSP00000252804:p.Gly1363Glu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	0.157	-1.085078	0.01888	0.022546	5.89E-4	ENSG00000130508	ENST00000252804	T	0.58652	0.32	5.07	3.21	0.36854	.	1.792660	0.02747	N	0.116942	T	0.22205	0.0535	L	0.36672	1.1	0.09310	N	1	B	0.16603	0.018	B	0.18263	0.021	T	0.24728	-1.0152	10	0.02654	T	1	-1.7644	7.7153	0.28700	0.0:0.7222:0.0:0.2778	.	1363	Q92626	PXDN_HUMAN	E	1363	ENSP00000252804:G1363E	ENSP00000252804:G1363E	G	-	2	0	PXDN	1621743	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.343000	0.19944	0.604000	0.29930	0.563000	0.77884	GGG	C|0.992;T|0.008	0.008	strong		0.527	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
OR2Z1	284383	hgsc.bcm.edu	37	19	8841461	8841461	+	Missense_Mutation	SNP	G	G	A	rs61746162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8841461G>A	ENST00000324060.2	+	1	146	c.71G>A	c.(70-72)cGc>cAc	p.R24H		NM_001004699.1	NP_001004699.1	Q8NG97	OR2Z1_HUMAN	olfactory receptor, family 2, subfamily Z, member 1	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCAGGATCACGCCAGCTCCTC	0.527													G|||	68	0.0135783	0.0507	0.0014	5008	,	,		19929	0.0		0.0	False		,,,				2504	0.0				p.R24H		Atlas-SNP	.											.	OR2Z1	53	.	0			c.G71A						PASS	.	G	HIS/ARG	238,4168	141.1+/-176.5	4,230,1969	100.0	88.0	92.0		71	-8.7	0.0	19	dbSNP_129	92	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR2Z1	NM_001004699.1	29	4,231,6268	AA,AG,GG		0.0116,5.4017,1.8376	benign	24/315	8841461	239,12767	2203	4300	6503	SO:0001583	missense	284383	exon1			GATCACGCCAGCT	AC008753	CCDS32895.1	19p13.2	2013-09-20	2002-11-13		ENSG00000181733	ENSG00000181733		"""GPCR / Class A : Olfactory receptors"""	15391	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily Z, member 2"""	OR2Z2			Standard	NM_001004699		Approved		uc010xkg.2	Q8NG97	OTTHUMG00000182195	ENST00000324060.2:c.71G>A	19.37:g.8841461G>A	ENSP00000316284:p.Arg24His	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	192	109	0.567708	NM_001004699	B9EH50|Q6IFK0|Q96R25	Missense_Mutation	SNP	ENST00000324060.2	37	CCDS32895.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	G	0.055	-1.239798	0.01493	0.054017	1.16E-4	ENSG00000181733	ENST00000324060	T	0.02787	4.16	4.33	-8.66	0.00866	.	2.040040	0.01847	N	0.035693	T	0.00210	0.0006	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46965	-0.9153	10	0.23302	T	0.38	.	3.2173	0.06704	0.446:0.2768:0.1843:0.0929	rs61746162	24	Q8NG97	OR2Z1_HUMAN	H	24	ENSP00000316284:R24H	ENSP00000316284:R24H	R	+	2	0	OR2Z1	8702461	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.436000	0.01019	-2.268000	0.00685	-1.131000	0.01979	CGC	G|0.984;A|0.016	0.016	strong		0.527	OR2Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459954.1		
ACACB	32	hgsc.bcm.edu	37	12	109617728	109617728	+	Missense_Mutation	SNP	A	A	G	rs16940029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109617728A>G	ENST00000338432.7	+	11	1773	c.1654A>G	c.(1654-1656)Atc>Gtc	p.I552V	ACACB_ENST00000377848.3_Missense_Mutation_p.I552V|ACACB_ENST00000543080.1_3'UTR|ACACB_ENST00000377854.5_Missense_Mutation_p.I552V			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	552	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.		I -> V (in dbSNP:rs16940029).		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)	ACAGTGTGCCATCCGCCTGGC	0.512													G|||	395	0.0788738	0.2375	0.0403	5008	,	,		18543	0.0179		0.0239	False		,,,				2504	0.0112				p.I552V		Atlas-SNP	.											.	ACACB	330	.	0			c.A1654G						PASS	.	G	VAL/ILE	909,3497	739.8+/-411.1	96,717,1390	80.0	69.0	73.0		1654	4.9	0.9	12	dbSNP_123	73	154,8446	812.4+/-407.1	0,154,4146	yes	missense	ACACB	NM_001093.3	29	96,871,5536	GG,GA,AA		1.7907,20.631,8.1732	benign	552/2459	109617728	1063,11943	2203	4300	6503	SO:0001583	missense	32	exon10			TGTGCCATCCGCC	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.1654A>G	12.37:g.109617728A>G	ENSP00000341044:p.Ile552Val	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	211	110	0.521327	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	170	0.07783882783882784	129	0.2621951219512195	11	0.03038674033149171	13	0.022727272727272728	17	0.022427440633245383	G	4.992	0.184305	0.09495	0.20631	0.017907	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	D;D;D	0.96802	-4.13;-4.13;-4.13	4.86	4.86	0.63082	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.000000	0.85682	N	0.000000	T	0.00039	0.0001	N	0.00419	-1.52	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.50816	-0.8783	9	0.02654	T	1	.	13.3307	0.60485	0.077:0.0:0.923:0.0	rs16940029;rs17848853;rs60034155;rs16940029	552	O00763	ACACB_HUMAN	V	552	ENSP00000341044:I552V;ENSP00000367079:I552V;ENSP00000367085:I552V	ENSP00000341044:I552V	I	+	1	0	ACACB	108102111	1.000000	0.71417	0.950000	0.38849	0.515000	0.34225	6.663000	0.74431	1.049000	0.40321	-0.119000	0.15052	ATC	A|0.917;G|0.083	0.083	strong		0.512	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
STT3A	3703	hgsc.bcm.edu	37	11	125488404	125488404	+	Silent	SNP	C	C	T	rs17140116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:125488404C>T	ENST00000529196.1	+	17	2117	c.1911C>T	c.(1909-1911)tgC>tgT	p.C637C	STT3A_ENST00000392708.4_Silent_p.C637C|STT3A_ENST00000531491.1_Silent_p.C545C			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	637					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		TGCTCAACTGCCTCATGTACA	0.413													C|||	557	0.111222	0.27	0.062	5008	,	,		16908	0.0308		0.0736	False		,,,				2504	0.0532				p.C637C		Atlas-SNP	.											.	STT3A	52	.	0			c.C1911T						PASS	.	C		1016,3386	377.5+/-322.5	113,790,1298	153.0	137.0	142.0		1911	2.4	1.0	11	dbSNP_123	142	579,8019	155.1+/-209.2	18,543,3738	no	coding-synonymous	STT3A	NM_152713.3		131,1333,5036	TT,TC,CC		6.7341,23.0804,12.2692		637/706	125488404	1595,11405	2201	4299	6500	SO:0001819	synonymous_variant	3703	exon16			CAACTGCCTCATG	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"""dolichyl-diphosphooligosaccharide protein glycotransferase"""	601134	"""integral membrane protein 1"", ""STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)"", ""STT3A, cataylic subunit of the oligosaccharyltransferase complex"""	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.1911C>T	11.37:g.125488404C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	75	29	0.386667	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	37	CCDS8458.1																																																																																			C|0.878;T|0.122	0.122	strong		0.413	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
FAM205A	259308	hgsc.bcm.edu	37	9	34726524	34726524	+	Missense_Mutation	SNP	G	G	A	rs1810820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:34726524G>A	ENST00000378788.3	-	4	752	c.713C>T	c.(712-714)aCg>aTg	p.T238M		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	238						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						GTTGCTCTGCGTCATCTCCTC	0.557													A|||	1156	0.230831	0.4123	0.1873	5008	,	,		18475	0.0813		0.17	False		,,,				2504	0.2331				p.T238M		Atlas-SNP	.											.	FAM205A	45	.	0			c.C713T						PASS	.	A	MET/THR	536,848		106,324,262	44.0	40.0	41.0		713	1.4	0.0	9	dbSNP_92	41	555,2627		51,453,1087	no	missense	FAM205A	NM_001141917.1	81	157,777,1349	AA,AG,GG		17.4419,38.7283,23.894	benign	238/1336	34726524	1091,3475	692	1591	2283	SO:0001583	missense	259308	exon4			CTCTGCGTCATCT		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.713C>T	9.37:g.34726524G>A	ENSP00000417711:p.Thr238Met	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	396	0.1813186813186813	165	0.3353658536585366	72	0.19889502762430938	33	0.057692307692307696	126	0.1662269129287599	A	0.083	-1.179611	0.01633	0.387283	0.174419	ENSG00000205108	ENST00000378788	T	0.23552	1.9	3.85	1.37	0.22104	.	728.057000	0.00481	U	0.000125	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43589	-0.9382	9	0.15066	T	0.55	.	6.2973	0.21093	0.662:0.0:0.338:0.0	rs1810820;rs60648957	238	Q6ZU69	F205A_HUMAN	M	238	ENSP00000417711:T238M	ENSP00000417711:T238M	T	-	2	0	RP11-195F19.10	34716524	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.127000	0.10547	-0.108000	0.12066	-0.381000	0.06696	ACG	G|0.815;A|0.185	0.185	strong		0.557	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
OR7A10	390892	hgsc.bcm.edu	37	19	14952189	14952189	+	Silent	SNP	G	G	T	rs114596415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14952189G>T	ENST00000248058.1	-	1	500	c.501C>A	c.(499-501)ccC>ccA	p.P167P		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	167						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)					GTGTACAAAAGGGCAGTGGCA	0.418													.|||	115	0.0229633	0.0832	0.0058	5008	,	,		22672	0.0		0.001	False		,,,				2504	0.0				p.P167P		Atlas-SNP	.											OR7A10,NS,carcinoma,-2,1	OR7A10	33	1	0			c.C501A						PASS	.	G		235,4171	137.7+/-173.5	8,219,1976	81.0	79.0	80.0		501	-4.2	0.0	19	dbSNP_132	80	1,8599		0,1,4299	no	coding-synonymous	OR7A10	NM_001005190.1		8,220,6275	TT,TG,GG		0.0116,5.3336,1.8145		167/310	14952189	236,12770	2203	4300	6503	SO:0001819	synonymous_variant	390892	exon1			ACAAAAGGGCAGT		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.501C>A	19.37:g.14952189G>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	152	74	0.486842	NM_001005190	Q6IFP0|Q96R97	Silent	SNP	ENST00000248058.1	37	CCDS32936.1																																																																																			G|0.980;T|0.020	0.020	strong		0.418	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
ASMTL	8623	hgsc.bcm.edu	37	X	1531701	1531701	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1531701C>T	ENST00000381317.3	-	12	1601	c.1569G>A	c.(1567-1569)ctG>ctA	p.L523L	ASMTL_ENST00000416733.2_Silent_p.L447L|ASMTL-AS1_ENST00000425740.2_RNA|ASMTL_ENST00000534940.1_Silent_p.L465L|ASMTL_ENST00000381333.4_Silent_p.L507L|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000602357.1_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	523	ASMT-like.					cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGATCCGGCACAGGACGTACA	0.562													c|||	95	0.0189696	0.0703	0.0014	5008	,	,		16507	0.0		0.001	False		,,,				2504	0.0				p.L523L		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1569A						PASS	.		,,	280,3766		9,262,1752	160.0	174.0	169.0		1395,1521,1569	-1.9	0.0	X	dbSNP_134	169	2,8348		0,2,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	,,	9,264,5925	TT,TC,CC		0.024,6.9204,2.2749	,,	465/564,507/606,523/622	1531701	282,12114	2023	4175	6198	SO:0001819	synonymous_variant	8623	exon12			CCGGCACAGGACG	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.1569G>A	X.37:g.1531701C>T		Somatic	404	1	0.00247525		WXS	Illumina HiSeq	Phase_I	448	211	0.470982	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Silent	SNP	ENST00000381317.3	37	CCDS43917.1																																																																																			C|0.981;T|0.019	0.019	strong		0.562	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
ATP1A4	480	hgsc.bcm.edu	37	1	160129273	160129273	+	Silent	SNP	G	G	A	rs61734686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160129273G>A	ENST00000368081.4	+	6	1206	c.735G>A	c.(733-735)ctG>ctA	p.L245L		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	245					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGAACCCTCTGGAGACCCGAA	0.507													G|||	53	0.0105831	0.0401	0.0	5008	,	,		17615	0.0		0.0	False		,,,				2504	0.0				p.L245L		Atlas-SNP	.											.	ATP1A4	167	.	0			c.G735A						PASS	.	G		96,4310	77.3+/-115.6	3,90,2110	97.0	100.0	99.0		735	2.6	1.0	1	dbSNP_129	99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATP1A4	NM_144699.3		3,91,6409	AA,AG,GG		0.0116,2.1788,0.7458		245/1030	160129273	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	480	exon6			CCCTCTGGAGACC	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"""ATPases / P-type"""	14073	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-4"", ""sodium pump subunit alpha-4"", ""sodium-potassium ATPase catalytic subunit alpha-4"""	607321	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 2"""	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.735G>A	1.37:g.160129273G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	37	CCDS1197.1																																																																																			G|0.992;A|0.008	0.008	strong		0.507	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	
TM9SF3	56889	hgsc.bcm.edu	37	10	98287792	98287792	+	Silent	SNP	G	G	T	rs12779720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98287792G>T	ENST00000371142.4	-	12	1753	c.1537C>A	c.(1537-1539)Cgg>Agg	p.R513R		NM_020123.3	NP_064508.3	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3	513						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)	15		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		ACTTACCACCGGTAATCTTCT	0.368													T|||	1164	0.232428	0.2958	0.3573	5008	,	,		16783	0.1548		0.2018	False		,,,				2504	0.1697				p.R513R		Atlas-SNP	.											.	TM9SF3	45	.	0			c.C1537A						PASS	.	T		1204,3202	707.1+/-407.5	172,860,1171	103.0	99.0	100.0		1537	4.8	0.9	10	dbSNP_121	100	1475,7123	749.0+/-407.4	124,1227,2948	no	coding-synonymous	TM9SF3	NM_020123.3		296,2087,4119	TT,TG,GG		17.1552,27.3264,20.6014		513/590	98287792	2679,10325	2203	4299	6502	SO:0001819	synonymous_variant	56889	exon12			ACCACCGGTAATC	AF160213, AF269150	CCDS7450.1	10q24.2	2006-04-12			ENSG00000077147	ENSG00000077147			21529	protein-coding gene	gene with protein product						11530251, 11595169	Standard	NM_020123		Approved	SMBP	uc001kmm.4	Q9HD45	OTTHUMG00000018834	ENST00000371142.4:c.1537C>A	10.37:g.98287792G>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	151	79	0.523179	NM_020123	Q5TB57|Q6UWE7|Q9NWL8|Q9P0G9|Q9UHW8	Silent	SNP	ENST00000371142.4	37	CCDS7450.1																																																																																			G|0.783;T|0.217	0.217	strong		0.368	TM9SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049610.2	NM_020123	
FLNA	2316	hgsc.bcm.edu	37	X	153581214	153581214	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153581214C>A	ENST00000369850.3	-	39	6541	c.6305G>T	c.(6304-6306)tGc>tTc	p.C2102F	FLNA_ENST00000422373.1_Missense_Mutation_p.C2094F|FLNA_ENST00000360319.4_Missense_Mutation_p.C2094F|FLNA_ENST00000344736.4_Missense_Mutation_p.C2062F|FLNA_ENST00000369856.3_Missense_Mutation_p.C235F|FLNA_ENST00000498491.1_5'Flank	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	2102					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)					GGTGACCCTGCACGTCCCGTC	0.607																																					p.C2102F		Atlas-SNP	.											.	FLNA	373	.	0			c.G6305T						PASS	.						108.0	109.0	109.0					X																	153581214		2157	4239	6396	SO:0001583	missense	2316	exon39			ACCCTGCACGTCC	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.6305G>T	X.37:g.153581214C>A	ENSP00000358866:p.Cys2102Phe	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	182	41	0.225275	NM_001110556	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.241318	0.58995	.	.	ENSG00000196924	ENST00000360319;ENST00000422373;ENST00000369850;ENST00000369856;ENST00000344736;ENST00000444578	D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	5.64	5.64	0.86602	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.90477	0.7017	M	0.73217	2.22	0.80722	D	1	D;D;B;B	0.71674	0.994;0.998;0.407;0.407	P;D;B;B	0.67900	0.89;0.954;0.356;0.356	D	0.91224	0.5009	10	0.72032	D	0.01	.	18.7428	0.91780	0.0:1.0:0.0:0.0	.	235;2094;2102;2102	E9PHF0;P21333-2;P21333;E9KL45	.;.;FLNA_HUMAN;.	F	2094;2094;2102;235;2062;83	ENSP00000353467:C2094F;ENSP00000416926:C2094F;ENSP00000358866:C2102F;ENSP00000358872:C235F;ENSP00000358863:C2062F;ENSP00000397824:C83F	ENSP00000358863:C2062F	C	-	2	0	FLNA	153234408	1.000000	0.71417	0.989000	0.46669	0.513000	0.34164	7.779000	0.85648	2.372000	0.80975	0.513000	0.50165	TGC	.	.	none		0.607	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
BZRAP1	9256	hgsc.bcm.edu	37	17	56389732	56389732	+	Missense_Mutation	SNP	T	T	C	rs9913145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56389732T>C	ENST00000343736.4	-	17	2613	c.2450A>G	c.(2449-2451)cAa>cGa	p.Q817R	BZRAP1_ENST00000355701.3_Missense_Mutation_p.Q817R|BZRAP1_ENST00000268893.6_Missense_Mutation_p.Q757R			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	817	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Q -> R (in dbSNP:rs9913145). {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)					TAGCTCCACTTGCTCAGGAGG	0.687													C|||	888	0.177316	0.2239	0.1225	5008	,	,		15864	0.25		0.1203	False		,,,				2504	0.137				p.Q817R		Atlas-SNP	.											.	BZRAP1	287	.	0			c.A2450G						PASS	.	C	ARG/GLN,ARG/GLN	930,3476	699.3+/-406.5	101,728,1374	24.0	24.0	24.0		2450,2270	1.2	0.2	17	dbSNP_119	24	976,7620	741.0+/-407.1	64,848,3386	yes	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	43,43	165,1576,4760	CC,CT,TT		11.3541,21.1076,14.6593	benign,benign	817/1858,757/1798	56389732	1906,11096	2203	4298	6501	SO:0001583	missense	9256	exon17			TCCACTTGCTCAG	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.2450A>G	17.37:g.56389732T>C	ENSP00000345824:p.Gln817Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	360	0.16483516483516483	91	0.18495934959349594	39	0.10773480662983426	138	0.24125874125874125	92	0.12137203166226913	C	0.083	-1.180536	0.01633	0.211076	0.113541	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.04119	3.7;3.7;3.7	4.33	1.25	0.21368	Fibronectin, type III (2);	0.192734	0.43110	N	0.000608	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	0.48234	-0.9053	9	0.23302	T	0.38	.	5.1515	0.15011	0.0:0.4079:0.1574:0.4347	rs9913145;rs57932613;rs9913145	817;757;817	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	R	817;817;757	ENSP00000347929:Q817R;ENSP00000345824:Q817R;ENSP00000268893:Q757R	ENSP00000268893:Q757R	Q	-	2	0	BZRAP1	53744731	0.001000	0.12720	0.235000	0.24058	0.417000	0.31264	-0.112000	0.10791	-0.008000	0.14320	-0.355000	0.07637	CAA	T|0.850;C|0.150	0.150	strong		0.687	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
FBF1	85302	hgsc.bcm.edu	37	17	73913827	73913827	+	Silent	SNP	G	G	T	rs150139322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73913827G>T	ENST00000586717.1	-	22	2722	c.2449C>A	c.(2449-2451)Cgg>Agg	p.R817R	FBF1_ENST00000319129.5_Silent_p.R816R|FBF1_ENST00000389570.4_Silent_p.R817R			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	817					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TCCAGCAGCCGGCTCTGCTCA	0.697													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17377	0.0		0.0	False		,,,				2504	0.0				p.R816R		Atlas-SNP	.											.	FBF1	48	.	0			c.C2446A						PASS	.	G		36,4118		0,36,2041	25.0	29.0	28.0		2446	3.9	1.0	17	dbSNP_134	28	1,8413		0,1,4206	no	coding-synonymous	FBF1	NM_001080542.1		0,37,6247	TT,TG,GG		0.0119,0.8666,0.2944		816/1134	73913827	37,12531	2077	4207	6284	SO:0001819	synonymous_variant	85302	exon22			GCAGCCGGCTCTG	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.2449C>A	17.37:g.73913827G>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	185	85	0.459459	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	37																																																																																				G|0.997;T|0.003	0.003	strong		0.697	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
LRAT	9227	hgsc.bcm.edu	37	4	155665820	155665820	+	Silent	SNP	G	G	A	rs17031981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155665820G>A	ENST00000336356.3	+	2	595	c.342G>A	c.(340-342)gaG>gaA	p.E114E	LRAT_ENST00000507827.1_Silent_p.E114E	NM_004744.3	NP_004735.2	O95237	LRAT_HUMAN	lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)	114					phototransduction, visible light (GO:0007603)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|rough endoplasmic reticulum (GO:0005791)	phosphatidylcholine-retinol O-acyltransferase activity (GO:0047173)|retinoic acid binding (GO:0001972)|retinol binding (GO:0019841)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)	16	all_hematologic(180;0.215)	Renal(120;0.0458)			Vitamin A(DB00162)	ACACAGTGGAGGACTTCGCCT	0.582													G|||	484	0.0966454	0.3404	0.0274	5008	,	,		17535	0.0109		0.001	False		,,,				2504	0.0031				p.E114E		Atlas-SNP	.											.	LRAT	29	.	0			c.G342A						PASS	.	G		1395,3011	459.4+/-352.3	215,965,1023	65.0	66.0	66.0		342	3.8	1.0	4	dbSNP_123	66	24,8576	17.3+/-56.4	0,24,4276	no	coding-synonymous	LRAT	NM_004744.3		215,989,5299	AA,AG,GG		0.2791,31.6614,10.9103		114/231	155665820	1419,11587	2203	4300	6503	SO:0001819	synonymous_variant	9227	exon2			AGTGGAGGACTTC	AF071510	CCDS3789.1	4q32.1	2014-01-28			ENSG00000121207	ENSG00000121207	2.3.1.135		6685	protein-coding gene	gene with protein product		604863				9920938	Standard	XM_006714412		Approved	LCA14	uc003ion.1	O95237	OTTHUMG00000161418	ENST00000336356.3:c.342G>A	4.37:g.155665820G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_004744	A8K983|Q8N716	Silent	SNP	ENST00000336356.3	37	CCDS3789.1																																																																																			G|0.910;A|0.090	0.090	strong		0.582	LRAT-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365246.1	NM_004744	
OR5L2	26338	hgsc.bcm.edu	37	11	55595115	55595115	+	Missense_Mutation	SNP	C	C	T	rs35214936|rs71490506|rs386753701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55595115C>T	ENST00000378397.1	+	1	421	c.421C>T	c.(421-423)Cgt>Tgt	p.R141C		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	141						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R141C(1)		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)				TCAGAAGCTGCGTGTGGAGCT	0.517										HNSCC(27;0.073)			N|||	449	0.0896565	0.1309	0.0403	5008	,	,		21374	0.0853		0.0924	False		,,,				2504	0.0706				p.R141C		Atlas-SNP	.											OR5L2,NS,carcinoma,0,1	OR5L2	135	1	1	Substitution - Missense(1)	stomach(1)	c.C421T						PASS	.						211.0	182.0	192.0					11																	55595115		2200	4296	6496	SO:0001583	missense	26338	exon1			AAGCTGCGTGTGG	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.421C>T	11.37:g.55595115C>T	ENSP00000367650:p.Arg141Cys	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	282	127	0.450355	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	146	0.06684981684981685	47	0.09552845528455285	17	0.04696132596685083	36	0.06293706293706294	46	0.06068601583113457	.	0.003	-2.453880	0.00175	.	.	ENSG00000205030	ENST00000378397	T	0.34275	1.37	5.18	0.994	0.19832	GPCR, rhodopsin-like superfamily (1);	0.359940	0.24334	N	0.039423	T	0.00178	0.0005	N	0.00084	-2.21	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.06405	0.002	T	0.37009	-0.9724	9	0.02654	T	1	-1.0929	8.8173	0.35004	0.0:0.2583:0.0:0.7417	.	141	Q8NGL0	OR5L2_HUMAN	C	141	ENSP00000367650:R141C	ENSP00000367650:R141C	R	+	1	0	OR5L2	55351691	0.010000	0.17322	0.064000	0.19789	0.051000	0.14879	0.390000	0.20768	-0.004000	0.14419	-0.389000	0.06534	CGT	C|0.913;G|0.000;T|0.087	0.087	strong		0.517	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
GSTM5	2949	hgsc.bcm.edu	37	1	110257836	110257836	+	Silent	SNP	T	T	C	rs386634508|rs67757008|rs61744262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110257836T>C	ENST00000256593.3	+	7	599	c.541T>C	c.(541-543)Ttg>Ctg	p.L181L	GSTM5_ENST00000492718.1_3'UTR|GSTM5_ENST00000369813.1_Silent_p.L140L|GSTM5_ENST00000369812.5_Silent_p.L200L	NM_000851.3	NP_000842.2	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5	181	GST C-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)			NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	CTTCCTAAACTTGAAGGACTT	0.483													T|||	703	0.140375	0.3941	0.0663	5008	,	,		19875	0.001		0.0845	False		,,,				2504	0.0511				p.L181L		Atlas-SNP	.											GSTM5,brain,glioma,0,4	GSTM5	89	4	0			c.T541C						PASS	.						176.0	197.0	190.0					1																	110257836		2203	4300	6503	SO:0001819	synonymous_variant	2949	exon7			CTAAACTTGAAGG	L02321	CCDS811.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134201	ENSG00000134201	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4637	protein-coding gene	gene with protein product		138385	"""glutathione S-transferase M5"""			8473333	Standard	NM_000851		Approved		uc001dyn.3	P46439	OTTHUMG00000011644	ENST00000256593.3:c.541T>C	1.37:g.110257836T>C		Somatic	537	2	0.00372439		WXS	Illumina HiSeq	Phase_I	577	284	0.492201	NM_000851	A8K0V8|Q6PD78	Silent	SNP	ENST00000256593.3	37	CCDS811.1																																																																																			CAAATC|0.500;TAAACT|0.500	.	alt		0.483	GSTM5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032200.1	NM_000851	
CPVL	54504	hgsc.bcm.edu	37	7	29070320	29070320	+	Missense_Mutation	SNP	C	C	T	rs1052200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:29070320C>T	ENST00000409850.1	-	16	1839	c.1193G>A	c.(1192-1194)cGc>cAc	p.R398H	CPVL_ENST00000265394.5_Missense_Mutation_p.R398H|CPVL_ENST00000396276.3_Missense_Mutation_p.R398H			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	398			R -> H (in dbSNP:rs1052200). {ECO:0000269|PubMed:11401439, 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						CATCAAGGAGCGCTCTGTCAG	0.463													C|||	1029	0.205471	0.1604	0.281	5008	,	,		19449	0.2649		0.1521	False		,,,				2504	0.2065				p.R398H		Atlas-SNP	.											.	CPVL	60	.	0			c.G1193A						PASS	.	C	HIS/ARG,HIS/ARG	695,3711	291.3+/-281.4	48,599,1556	128.0	126.0	127.0		1193,1193	2.0	1.0	7	dbSNP_86	127	1227,7373	247.5+/-275.5	89,1049,3162	yes	missense,missense	CPVL	NM_019029.2,NM_031311.3	29,29	137,1648,4718	TT,TC,CC		14.2674,15.7739,14.7778	benign,benign	398/477,398/477	29070320	1922,11084	2203	4300	6503	SO:0001583	missense	54504	exon12			AAGGAGCGCTCTG	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.1193G>A	7.37:g.29070320C>T	ENSP00000387164:p.Arg398His	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	209	109	0.521531	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Missense_Mutation	SNP	ENST00000409850.1	37	CCDS5419.1	420	0.19230769230769232	69	0.1402439024390244	81	0.22375690607734808	150	0.26223776223776224	120	0.158311345646438	C	9.868	1.198280	0.22037	0.157739	0.142674	ENSG00000106066	ENST00000265394;ENST00000396276;ENST00000455893;ENST00000409850	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.71	1.97	0.26223	.	0.161882	0.53938	N	0.000047	T	0.00012	0.0000	L	0.56199	1.76	0.22305	P	0.99921311	P	0.35612	0.512	B	0.31614	0.133	T	0.37103	-0.9720	9	0.15499	T	0.54	0.0711	9.3878	0.38354	0.0:0.7059:0.0:0.2941	rs1052200;rs3192630;rs52825107;rs61626281;rs1052200	398	Q9H3G5	CPVL_HUMAN	H	398;398;63;398	ENSP00000265394:R398H;ENSP00000379572:R398H;ENSP00000403580:R63H;ENSP00000387164:R398H	ENSP00000265394:R398H	R	-	2	0	CPVL	29036845	0.998000	0.40836	0.995000	0.50966	0.051000	0.14879	1.058000	0.30504	0.364000	0.24374	-0.203000	0.12734	CGC	C|0.836;T|0.163	0.163	strong		0.463	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
DBNL	28988	hgsc.bcm.edu	37	7	44099664	44099664	+	Silent	SNP	T	T	C	rs11552797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44099664T>C	ENST00000448521.1	+	12	1163	c.1065T>C	c.(1063-1065)gcT>gcC	p.A355A	DBNL_ENST00000490734.2_Silent_p.A261A|DBNL_ENST00000494774.1_Silent_p.A356A|DBNL_ENST00000497184.1_3'UTR|DBNL_ENST00000468694.1_Silent_p.A364A|DBNL_ENST00000456905.1_Silent_p.A307A|DBNL_ENST00000440166.1_Silent_p.A252A|DBNL_ENST00000452943.1_Silent_p.A331A	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	355					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|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)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)	p.A356A(1)		breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						AGCAAGGTGCTGGCTCTGAGC	0.607													C|||	1337	0.266973	0.4387	0.2882	5008	,	,		20099	0.1141		0.2406	False		,,,				2504	0.2045				p.A364A	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											DBNL,NS,carcinoma,0,1	DBNL	26	1	1	Substitution - coding silent(1)	stomach(1)	c.T1092C						PASS	.	C	,,	1849,2557	629.4+/-395.3	390,1069,744	54.0	46.0	48.0		1065,1092,1068	-7.6	0.0	7	dbSNP_120	48	1992,6608	721.0+/-406.3	239,1514,2547	no	coding-synonymous,coding-synonymous,coding-synonymous	DBNL	NM_001014436.2,NM_001122956.1,NM_014063.6	,,	629,2583,3291	CC,CT,TT		23.1628,41.9655,29.5325	,,	355/431,364/440,356/432	44099664	3841,9165	2203	4300	6503	SO:0001819	synonymous_variant	28988	exon12			AGGTGCTGGCTCT	AF151364	CCDS34622.1, CCDS34623.1, CCDS47579.1, CCDS64633.1, CCDS64634.1	7p13	2004-07-22			ENSG00000136279	ENSG00000136279			2696	protein-coding gene	gene with protein product		610106				10087302	Standard	NM_014063		Approved	SH3P7, HIP-55	uc003tjq.4	Q9UJU6	OTTHUMG00000155350	ENST00000448521.1:c.1065T>C	7.37:g.44099664T>C		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	225	225	1	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Silent	SNP	ENST00000448521.1	37	CCDS34623.1	558|558	0.2554945054945055|0.2554945054945055	194|194	0.3943089430894309|0.3943089430894309	106|106	0.292817679558011|0.292817679558011	68|68	0.11888111888111888|0.11888111888111888	190|190	0.25065963060686014|0.25065963060686014	C|C	11.21|11.21	1.572572|1.572572	0.28092|0.28092	0.419655|0.419655	0.231628|0.231628	ENSG00000136279|ENSG00000136279	ENST00000452661|ENST00000432854	.|.	.|.	.|.	5.53|5.53	-7.58|-7.58	0.01313|0.01313	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.03296|0.03296	-1.1051|-1.1051	3|3	.|.	.|.	.|.	-2.7619|-2.7619	18.0703|18.0703	0.89404|0.89404	0.0:0.6938:0.0:0.3062|0.0:0.6938:0.0:0.3062	rs11552797;rs11764534;rs17358190;rs59746704;rs11552797|rs11552797;rs11764534;rs17358190;rs59746704;rs11552797	.|.	.|.	.|.	P|R	63|284	.|.	.|.	L|W	+|+	2|1	0|0	DBNL|DBNL	44066189|44066189	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.541000|0.541000	0.35023|0.35023	-0.487000|-0.487000	0.06505|0.06505	-1.961000|-1.961000	0.01016|0.01016	-1.095000|-1.095000	0.02154|0.02154	CTG|TGG	T|0.715;C|0.285	0.285	strong		0.607	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063	
SPTB	6710	hgsc.bcm.edu	37	14	65242044	65242044	+	Silent	SNP	C	C	T	rs184528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:65242044C>T	ENST00000389721.5	-	22	4673	c.4641G>A	c.(4639-4641)gcG>gcA	p.A1547A	SPTB_ENST00000542895.1_Silent_p.A1547A|SPTB_ENST00000556626.1_Silent_p.A1547A|SPTB_ENST00000389722.3_Silent_p.A1547A|SPTB_ENST00000389720.3_Silent_p.A1547A	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1547					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)		CGATCTCCGCCGCCTCCACCA	0.672													C|||	2064	0.412141	0.7746	0.2493	5008	,	,		19430	0.3671		0.1938	False		,,,				2504	0.3088				p.A1547A		Atlas-SNP	.											.	SPTB	378	.	0			c.G4641A						PASS	.	C	,	2996,1410	675.0+/-403.0	1028,940,235	32.0	26.0	28.0		4641,4641	-5.0	0.0	14	dbSNP_79	28	1518,7082	281.7+/-295.2	114,1290,2896	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	1142,2230,3131	TT,TC,CC		17.6512,32.0018,34.7071	,	1547/2138,1547/2329	65242044	4514,8492	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon22			CTCCGCCGCCTCC		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.4641G>A	14.37:g.65242044C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	152	78	0.513158	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			C|0.642;T|0.358	0.358	strong		0.672	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
OR4D9	390199	hgsc.bcm.edu	37	11	59283299	59283299	+	Missense_Mutation	SNP	T	T	C	rs79922105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59283299T>C	ENST00000329328.3	+	1	914	c.914T>C	c.(913-915)cTa>cCa	p.L305P		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	305						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(14)|prostate(5)|upper_aerodigestive_tract(1)	26						AAGAGACGGCTAGGACAATCA	0.383													T|||	108	0.0215655	0.0802	0.0029	5008	,	,		20633	0.0		0.0	False		,,,				2504	0.0				p.L305P		Atlas-SNP	.											.	OR4D9	47	.	0			c.T914C						PASS	.	T	PRO/LEU	260,4142	140.0+/-175.5	8,244,1949	54.0	56.0	55.0		914	2.3	0.0	11	dbSNP_132	55	1,8589		0,1,4294	yes	missense	OR4D9	NM_001004711.1	98	8,245,6243	CC,CT,TT		0.0116,5.9064,2.0089	possibly-damaging	305/315	59283299	261,12731	2201	4295	6496	SO:0001583	missense	390199	exon1			GACGGCTAGGACA	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"""GPCR / Class A : Olfactory receptors"""	15178	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily D, member 9 pseudogene"""				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.914T>C	11.37:g.59283299T>C	ENSP00000328563:p.Leu305Pro	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	83	26	0.313253	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	T	6.379	0.438092	0.12104	0.059064	1.16E-4	ENSG00000172742	ENST00000329328	T	0.38887	1.11	3.47	2.29	0.28610	.	0.257134	0.20056	U	0.100183	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.18263	0.021	T	0.09975	-1.0650	10	0.37606	T	0.19	.	4.1407	0.10191	0.208:0.0:0.2151:0.5769	.	305	Q8NGE8	OR4D9_HUMAN	P	305	ENSP00000328563:L305P	ENSP00000328563:L305P	L	+	2	0	OR4D9	59039875	0.003000	0.15002	0.001000	0.08648	0.002000	0.02628	1.303000	0.33470	0.480000	0.27534	-0.490000	0.04691	CTA	T|0.980;C|0.020	0.020	strong		0.383	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711	
ATP13A4	84239	hgsc.bcm.edu	37	3	193120627	193120627	+	Silent	SNP	C	C	T	rs61733355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:193120627C>T	ENST00000342695.4	-	30	3727	c.3405G>A	c.(3403-3405)ctG>ctA	p.L1135L	ATP13A4_ENST00000482964.1_5'UTR|ATP13A4_ENST00000400270.2_Silent_p.L151L|ATP13A4_ENST00000392443.3_Silent_p.L1116L	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1135						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		TCATCATCCACAGGGCTCGAT	0.448													C|||	72	0.014377	0.0522	0.0043	5008	,	,		18910	0.0		0.0	False		,,,				2504	0.0				p.L1135L		Atlas-SNP	.											.	ATP13A4	154	.	0			c.G3405A						PASS	.	C		237,4169	139.2+/-174.8	10,217,1976	74.0	71.0	72.0		3405	0.0	1.0	3	dbSNP_129	72	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ATP13A4	NM_032279.2		10,220,6273	TT,TC,CC		0.0349,5.379,1.8453		1135/1197	193120627	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon30			CATCCACAGGGCT	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.3405G>A	3.37:g.193120627C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	146	63	0.431507	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			C|0.982;T|0.018	0.018	strong		0.448	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
YPEL1	29799	hgsc.bcm.edu	37	22	22049783	22049783	+	IGR	SNP	C	C	T	rs12484060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:22049783C>T	ENST00000339468.3	-	0	4329				PPIL2_ENST00000456792.2_Missense_Mutation_p.A467V|PPIL2_ENST00000335025.8_3'UTR|PPIL2_ENST00000406385.1_3'UTR|PPIL2_ENST00000398831.3_3'UTR|PPIL2_ENST00000492445.2_3'UTR|PPIL2_ENST00000412327.1_Silent_p.S521S|PPIL2_ENST00000446951.1_3'UTR	NM_013313.3	NP_037445.1	O60688	YPEL1_HUMAN	yippee-like 1 (Drosophila)							nucleus (GO:0005634)				breast(1)|large_intestine(1)|lung(1)	3	Colorectal(54;0.105)					CTGGTAGCAGCAGGTTGGCCG	0.607													C|||	1832	0.365815	0.4032	0.3473	5008	,	,		17350	0.4425		0.3211	False		,,,				2504	0.2955				p.S521S		Atlas-SNP	.											.	PPIL2	38	.	0			c.C1563T						PASS	.	C	,,	1675,2723		325,1025,849	24.0	22.0	23.0		,,1563	0.9	0.1	22	dbSNP_120	23	2935,5665		512,1911,1877	no	utr-3,utr-3,coding-synonymous	PPIL2	NM_014337.3,NM_148175.2,NM_148176.2	,,	837,2936,2726	TT,TC,CC		34.1279,38.0855,35.467	,,	,,521/528	22049783	4610,8388	2199	4300	6499	SO:0001628	intergenic_variant	23759	exon20			TAGCAGCAGGTTG	AF060862	CCDS13794.1	22q11.2	2008-02-04	2001-11-28		ENSG00000100027	ENSG00000100027			12845	protein-coding gene	gene with protein product		608082	"""yippee (Drosophila) homolog-like 1"""			11473580	Standard	NM_013313		Approved		uc002zvl.3	O60688	OTTHUMG00000150830		22.37:g.22049783C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	207	95	0.458937	NM_148176	Q65ZA1|Q6GLI6	Silent	SNP	ENST00000339468.3	37	CCDS13794.1	846	0.3873626373626374	206	0.4186991869918699	133	0.3674033149171271	263	0.4597902097902098	244	0.32189973614775724	C	15.10	2.732309	0.48939	0.380855	0.341279	ENSG00000100023	ENST00000456792	T	0.25085	1.82	3.28	0.931	0.19460	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.39086	P	0.038999000000000006	B	0.26935	0.164	B	0.17433	0.018	T	0.47032	-0.9148	7	0.37606	T	0.19	.	11.6688	0.51389	0.0:0.6561:0.3439:0.0	rs12484060;rs12484060	467	E7EW80	.	V	467	ENSP00000396228:A467V	ENSP00000396228:A467V	A	+	2	0	PPIL2	20379783	0.015000	0.18098	0.080000	0.20451	0.572000	0.35998	0.725000	0.25970	0.196000	0.20367	0.558000	0.71614	GCA	C|0.616;T|0.384	0.384	strong		0.607	YPEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320245.1	NM_013313	
GPR98	84059	hgsc.bcm.edu	37	5	90445889	90445889	+	Missense_Mutation	SNP	A	A	G	rs77469944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:90445889A>G	ENST00000405460.2	+	88	18571	c.18475A>G	c.(18475-18477)Atg>Gtg	p.M6159V	GPR98_ENST00000425867.2_Missense_Mutation_p.M1820V	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	6159					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)		ACACAACCAAATGTGTTGCCC	0.408													A|||	370	0.0738818	0.1732	0.0144	5008	,	,		16423	0.0516		0.003	False		,,,				2504	0.0777				p.M6159V		Atlas-SNP	.											.	GPR98	605	.	0			c.A18475G						PASS	.	A	VAL/MET	445,3291		31,383,1454	68.0	62.0	64.0		18475	4.7	0.1	5	dbSNP_131	64	17,8157		0,17,4070	yes	missense	GPR98	NM_032119.3	21	31,400,5524	GG,GA,AA		0.208,11.9111,3.8791	benign	6159/6307	90445889	462,11448	1868	4087	5955	SO:0001583	missense	84059	exon88			AACCAAATGTGTT	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.18475A>G	5.37:g.90445889A>G	ENSP00000384582:p.Met6159Val	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	90	48	0.533333	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	115	0.052655677655677656	88	0.17886178861788618	6	0.016574585635359115	19	0.033216783216783216	2	0.002638522427440633	A	10.67	1.414200	0.25465	0.119111	0.00208	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.20200	2.17;2.09	5.89	4.73	0.59995	.	0.294608	0.37483	N	0.002072	T	0.00039	0.0001	N	0.14661	0.345	0.52099	P	5.900000000003125E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.36065	-0.9763	8	.	.	.	.	7.6783	0.28499	0.6751:0.2482:0.0767:0.0	.	1820;6159;1820	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	V	6159;6159;1820	ENSP00000384582:M6159V;ENSP00000392618:M1820V	.	M	+	1	0	GPR98	90481645	1.000000	0.71417	0.111000	0.21465	0.712000	0.41017	3.387000	0.52501	1.049000	0.40321	0.533000	0.62120	ATG	A|0.957;G|0.043	0.043	strong		0.408	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
NOP9	161424	hgsc.bcm.edu	37	14	24772373	24772373	+	Missense_Mutation	SNP	C	C	T	rs147123517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24772373C>T	ENST00000267425.3	+	6	1330	c.1237C>T	c.(1237-1239)Cgc>Tgc	p.R413C	NOP9_ENST00000396802.3_Missense_Mutation_p.R413C	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	413							poly(A) RNA binding (GO:0044822)										GGGGGCCTGTCGCAGAGTTGG	0.557													C|||	8	0.00159744	0.0	0.0014	5008	,	,		16884	0.0		0.007	False		,,,				2504	0.0				p.R413C		Atlas-SNP	.											.	.	.	.	0			c.C1237T						PASS	.	C	CYS/ARG	4,4402	6.2+/-15.9	0,4,2199	70.0	71.0	71.0		1237	4.2	1.0	14	dbSNP_134	71	45,8555	30.1+/-81.4	0,45,4255	yes	missense	C14orf21	NM_174913.1	180	0,49,6454	TT,TC,CC		0.5233,0.0908,0.3767	probably-damaging	413/637	24772373	49,12957	2203	4300	6503	SO:0001583	missense	161424	exon6			GCCTGTCGCAGAG		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.1237C>T	14.37:g.24772373C>T	ENSP00000267425:p.Arg413Cys	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	37	CCDS9624.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.19	3.567896	0.65651	9.08E-4	0.005233	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.32753	1.48;1.44	5.16	4.25	0.50352	.	0.224065	0.38897	N	0.001525	T	0.35189	0.0923	L	0.54323	1.7	0.43536	D	0.995829	D	0.76494	0.999	P	0.59288	0.855	T	0.23013	-1.0200	10	0.52906	T	0.07	-4.9362	11.1833	0.48642	0.4521:0.5479:0.0:0.0	.	413	Q86U38	CN021_HUMAN	C	413	ENSP00000267425:R413C;ENSP00000380020:R413C	ENSP00000267425:R413C	R	+	1	0	C14orf21	23842213	0.869000	0.29996	1.000000	0.80357	0.909000	0.53808	0.630000	0.24553	1.356000	0.45884	0.563000	0.77884	CGC	C|0.996;T|0.004	0.004	strong		0.557	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
ZNF98	148198	hgsc.bcm.edu	37	19	22575777	22575777	+	Missense_Mutation	SNP	T	T	C	rs200167484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	59	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	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	
FBXO39	162517	hgsc.bcm.edu	37	17	6683215	6683215	+	Missense_Mutation	SNP	C	C	T	rs4796555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:6683215C>T	ENST00000321535.4	+	2	158	c.28C>T	c.(28-30)Ccc>Tcc	p.P10S		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	10			P -> S (in dbSNP:rs4796555).							NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	26						ACTGATCCAGCCCCAAGACCA	0.537													C|||	1626	0.324681	0.2148	0.2896	5008	,	,		20496	0.6151		0.2107	False		,,,				2504	0.316				p.P10S		Atlas-SNP	.											.	FBXO39	50	.	0			c.C28T						PASS	.	C	SER/PRO	958,3448	361.6+/-315.8	107,744,1352	89.0	85.0	86.0		28	2.3	0.9	17	dbSNP_111	86	1879,6721	334.2+/-320.9	213,1453,2634	yes	missense	FBXO39	NM_153230.2	74	320,2197,3986	TT,TC,CC		21.8488,21.7431,21.813	possibly-damaging	10/443	6683215	2837,10169	2203	4300	6503	SO:0001583	missense	162517	exon2			ATCCAGCCCCAAG	BC034782	CCDS11082.1	17p13.2	2014-01-21			ENSG00000177294	ENSG00000177294		"""F-boxes /  ""other"""""	28565	protein-coding gene	gene with protein product		609106				12477932	Standard	NM_153230		Approved	MGC35179, Fbx39, CT144	uc010vtg.2	Q8N4B4	OTTHUMG00000102062	ENST00000321535.4:c.28C>T	17.37:g.6683215C>T	ENSP00000321386:p.Pro10Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_153230		Missense_Mutation	SNP	ENST00000321535.4	37	CCDS11082.1	740	0.33882783882783885	109	0.22154471544715448	92	0.2541436464088398	380	0.6643356643356644	159	0.20976253298153033	C	12.69	2.013227	0.35511	0.217431	0.218488	ENSG00000177294	ENST00000321535	T	0.54279	0.58	5.56	2.26	0.28386	.	0.525149	0.18834	N	0.129870	T	0.00012	0.0000	L	0.27053	0.805	0.43338	P	0.004612999999999978	B	0.17465	0.022	B	0.14023	0.01	T	0.44221	-0.9342	9	0.10902	T	0.67	-13.5396	4.7906	0.13247	0.1528:0.6137:0.1485:0.085	rs4796555;rs17794696;rs52829409;rs56480343;rs60341795;rs4796555	10	Q8N4B4	FBX39_HUMAN	S	10	ENSP00000321386:P10S	ENSP00000321386:P10S	P	+	1	0	FBXO39	6623939	0.046000	0.20272	0.902000	0.35471	0.970000	0.65996	0.928000	0.28831	0.813000	0.34350	0.561000	0.74099	CCC	C|0.730;N|0.000	.	strong		0.537	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230	
IRGQ	126298	hgsc.bcm.edu	37	19	44096772	44096772	+	Silent	SNP	C	C	T	rs114508854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44096772C>T	ENST00000602269.1	-	2	1463	c.1278G>A	c.(1276-1278)gaG>gaA	p.E426E	L34079.2_ENST00000594374.1_Intron|IRGQ_ENST00000601520.1_Intron|IRGQ_ENST00000422989.1_Silent_p.E426E			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	426	IRG-type G.									endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				GCGGCGGCGCCTCCTCCAGCA	0.687													C|||	128	0.0255591	0.0613	0.0029	5008	,	,		13730	0.0308		0.0	False		,,,				2504	0.0143				p.E426E		Atlas-SNP	.											.	IRGQ	40	.	0			c.G1278A						PASS	.	C		173,4233	106.5+/-144.9	4,165,2034	39.0	44.0	42.0		1278	2.0	0.9	19	dbSNP_132	42	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	IRGQ	NM_001007561.2		4,169,6330	TT,TC,CC		0.0465,3.9265,1.3609		426/624	44096772	177,12829	2203	4300	6503	SO:0001819	synonymous_variant	126298	exon3			CGGCGCCTCCTCC	AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"""immunity-related GTPase family, Q1"""	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.1278G>A	19.37:g.44096772C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_001007561	B2RNP3	Silent	SNP	ENST00000602269.1	37	CCDS33040.1																																																																																			C|0.981;T|0.019	0.019	strong		0.687	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561	
NBPF7	343505	hgsc.bcm.edu	37	1	120378702	120378702	+	IGR	SNP	A	A	G	rs10158823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120378702A>G								REG4 (24419 upstream) : ADAM30 (57453 downstream)																							CTTTCTGTTCAACTAGTGCCA	0.488													a|||	405	0.0808706	0.295	0.0216	5008	,	,		21265	0.0		0.0	False		,,,				2504	0.0				p.V348V		Atlas-SNP	.											.	NBPF7	46	.	0			c.T1044C						PASS	.	A		848,3086		97,654,1216	107.0	106.0	107.0		1044	-0.1	0.0	1	dbSNP_119	107	21,8319		0,21,4149	no	coding-synonymous	NBPF7	NM_001047980.1		97,675,5365	GG,GA,AA		0.2518,21.5557,7.08		348/422	120378702	869,11405	1967	4170	6137	SO:0001628	intergenic_variant	343505	exon7			CTGTTCAACTAGT																													1.37:g.120378702A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	203	105	0.517241	NM_001047980		Silent	SNP		37																																																																																				A|0.919;G|0.081	0.081	strong	0	0.488								
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197609	39197609	+	Missense_Mutation	SNP	C	C	A	rs138200823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39197609C>A	ENST00000306271.4	-	1	104	c.41G>T	c.(40-42)tGc>tTc	p.C14F		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	14			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)			ACTGGTGGAGCAGCTGGGAAA	0.597													c|||	498	0.0994409	0.1838	0.1124	5008	,	,		15162	0.1409		0.0169	False		,,,				2504	0.0184				p.C14F		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.G41T						PASS	.						45.0	55.0	52.0					17																	39197609		1959	4162	6121	SO:0001583	missense	81851	exon1			GTGGAGCAGCTGG	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.41G>T	17.37:g.39197609C>A	ENSP00000305975:p.Cys14Phe	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	184	46	0.25	NM_030967	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	108	0.04945054945054945	40	0.08130081300813008	18	0.049723756906077346	44	0.07692307692307693	6	0.0079155672823219	C	10.59	1.391756	0.25118	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.33216	1.42	4.56	2.52	0.30459	.	.	.	.	.	T	0.03136	0.0092	M	0.92604	3.325	0.27968	P	0.9365203	B	0.22146	0.065	B	0.20767	0.031	T	0.41734	-0.9492	8	0.66056	D	0.02	.	11.8299	0.52288	0.3171:0.6829:0.0:0.0	.	14	Q07627	KRA11_HUMAN	F	14	ENSP00000305975:C14F	ENSP00000305975:C14F	C	-	2	0	KRTAP1-1	36451135	0.993000	0.37304	0.993000	0.49108	0.637000	0.38172	0.435000	0.21510	0.840000	0.34995	-0.182000	0.12963	TGC	C|0.950;A|0.050	0.050	strong		0.597	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
IFIH1	64135	hgsc.bcm.edu	37	2	163124051	163124051	+	Missense_Mutation	SNP	C	C	T	rs1990760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:163124051C>T	ENST00000263642.2	-	15	3231	c.2836G>A	c.(2836-2838)Gca>Aca	p.A946T		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	946			A -> T (associated with susceptibility to IDDM19; dbSNP:rs1990760). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16699517}.		cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						TTTTGCAGTGCTTTGTTTTCT	0.383													C|||	1786	0.356629	0.1256	0.3905	5008	,	,		19813	0.1865		0.6054	False		,,,				2504	0.5644				p.A946T		Atlas-SNP	.											.	IFIH1	102	.	0			c.G2836A	GRCh37	CM066881	IFIH1	M	rs1990760	PASS	.	C	THR/ALA	816,3590	325.3+/-299.0	85,646,1472	185.0	154.0	165.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2836	3.9	1.0	2	dbSNP_92	165	5185,3415	639.0+/-399.4	1583,2019,698	yes	missense	IFIH1	NM_022168.2	58	1668,2665,2170	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	39.7093,18.5202,46.1402	benign	946/1026	163124051	6001,7005	2203	4300	6503	SO:0001583	missense	64135	exon15			GCAGTGCTTTGTT	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.2836G>A	2.37:g.163124051C>T	ENSP00000263642:p.Ala946Thr	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	801	0.36675824175824173	56	0.11382113821138211	162	0.44751381215469616	123	0.21503496503496503	460	0.6068601583113457	C	4.264	0.048000	0.08243	0.185202	0.602907	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.43294	0.95	4.74	3.87	0.44632	C-terminal domain of RIG-I (1);	0.453841	0.25469	N	0.030455	T	0.00012	0.0000	L	0.40543	1.245	0.30279	P	0.791512	B	0.24533	0.105	B	0.19946	0.027	T	0.42447	-0.9451	9	0.12766	T	0.61	-12.3172	7.7307	0.28786	0.0:0.6931:0.0:0.3069	rs1990760;rs3761653;rs34707823;rs52819809;rs58100036;rs1990760	946	Q9BYX4	IFIH1_HUMAN	T	946	ENSP00000263642:A946T	ENSP00000263642:A946T	A	-	1	0	IFIH1	162832297	0.975000	0.34042	0.991000	0.47740	0.226000	0.24999	0.669000	0.25142	1.243000	0.43853	0.585000	0.79938	GCA	C|0.588;T|0.412	0.412	strong		0.383	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168	
CHPF	79586	hgsc.bcm.edu	37	2	220405230	220405230	+	Silent	SNP	G	G	A	rs6436154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220405230G>A	ENST00000243776.6	-	4	1451	c.1203C>T	c.(1201-1203)caC>caT	p.H401H	CHPF_ENST00000535926.1_Silent_p.H239H	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	401					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)|mitochondrion (GO:0005739)	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(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		AGGAGAAAGCGTGCTGCTCCG	0.662													G|||	1558	0.311102	0.2065	0.4841	5008	,	,		17051	0.2748		0.4523	False		,,,				2504	0.2219				p.H401H		Atlas-SNP	.											.	CHPF	56	.	0			c.C1203T						PASS	.	G	,	1157,3247	387.2+/-326.4	135,887,1180	29.0	32.0	31.0		717,1203	-6.0	0.0	2	dbSNP_116	31	3978,4620	529.0+/-381.5	939,2100,1260	no	coding-synonymous,coding-synonymous	CHPF	NM_001195731.1,NM_024536.5	,	1074,2987,2440	AA,AG,GG		46.2666,26.2716,39.4939	,	239/614,401/776	220405230	5135,7867	2202	4299	6501	SO:0001819	synonymous_variant	79586	exon4			GAAAGCGTGCTGC	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24291	protein-coding gene	gene with protein product	"""chondroitin sulfate synthase 2"""	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1203C>T	2.37:g.220405230G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Silent	SNP	ENST00000243776.6	37	CCDS2443.1																																																																																			G|0.613;A|0.387	0.387	strong		0.662	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536	
MICA	100507436	hgsc.bcm.edu	37	6	31378387	31378387	+	Silent	SNP	T	T	C	rs1063631|rs386699190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31378387T>C	ENST00000449934.2	+	2	192	c.138T>C	c.(136-138)ctT>ctC	p.L46L	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)				CAGGGTTTCTTGCTGAGGTAC	0.532													c|||	1829	0.365216	0.4788	0.4078	5008	,	,		19543	0.3016		0.3141	False		,,,				2504	0.2996				p.L46L		Atlas-SNP	.											MICA,bladder,carcinoma,0,1	MICA	21	1	0			c.T138C						PASS	.	C		573,811		132,309,251	19.0	21.0	21.0		138	-5.8	0.0	6	dbSNP_86	21	881,2301		126,629,836	no	coding-synonymous	MICA	NM_001177519.1		258,938,1087	CC,CT,TT		27.687,41.4017,31.8441		46/333	31378387	1454,3112	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon2			GTTTCTTGCTGAG	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.138T>C	6.37:g.31378387T>C		Somatic	314	1	0.00318471		WXS	Illumina HiSeq	Phase_I	266	266	1	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			T|0.642;C|0.358	0.358	strong		0.532	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324254	39324254	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324254G>A	ENST00000391356.2	-	1	170	c.171C>T	c.(169-171)tcC>tcT	p.S57S		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	57	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				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)			tgcagcagctggagatacagc	0.642																																					p.S57S		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.C171T						PASS	.						3.0	4.0	4.0					17																	39324254		1542	3395	4937	SO:0001819	synonymous_variant	85290	exon1			GCAGCTGGAGATA	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.171C>T	17.37:g.39324254G>A		Somatic	434	0	0		WXS	Illumina HiSeq	Phase_I	210	33	0.157143	NM_033187		Silent	SNP	ENST00000391356.2	37	CCDS42331.1																																																																																			.	.	none		0.642	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
IQGAP3	128239	hgsc.bcm.edu	37	1	156539169	156539169	+	Splice_Site	SNP	G	G	A	rs370931618		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156539169G>A	ENST00000361170.2	-	2	134	c.124C>T	c.(124-126)Cgc>Tgc	p.R42C		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	42	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)					TCCGCTCACCGCTTGGCCTCC	0.557													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13122	0.0		0.0	False		,,,				2504	0.0				p.R42C		Atlas-SNP	.											.	IQGAP3	146	.	0			c.C124T						PASS	.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	43.0	36.0	39.0		124	5.0	1.0	1		39	0,8600		0,0,4300	no	missense-near-splice	IQGAP3	NM_178229.4	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	42/1632	156539169	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	128239	exon2			CTCACCGCTTGGC	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.125+1C>T	1.37:g.156539169G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053545	0.75960	2.27E-4	0.0	ENSG00000183856	ENST00000361170	D	0.95554	-3.74	4.97	4.97	0.65823	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.97139	0.9065	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97567	1.0102	10	0.72032	D	0.01	-13.4997	16.978	0.86319	0.0:0.0:1.0:0.0	.	42	Q86VI3	IQGA3_HUMAN	C	42	ENSP00000354451:R42C	ENSP00000354451:R42C	R	-	1	0	IQGAP3	154805793	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	2.887000	0.48586	2.592000	0.87571	0.467000	0.42956	CGC	.	.	none		0.557	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	Missense_Mutation
DNAH6	1768	hgsc.bcm.edu	37	2	84752784	84752784	+	Silent	SNP	A	A	C	rs73945104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:84752784A>C	ENST00000237449.6	+	2	329	c.321A>C	c.(319-321)ccA>ccC	p.P107P	DNAH6_ENST00000398278.2_Silent_p.P107P|DNAH6_ENST00000468661.1_3'UTR|DNAH6_ENST00000389394.3_Silent_p.P107P			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	107	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						TTAAACGTCCAGTAAGCATAG	0.348													A|||	65	0.0129792	0.0477	0.0029	5008	,	,		16979	0.0		0.0	False		,,,				2504	0.0				p.P107P		Atlas-SNP	.											.	DNAH6	194	.	0			c.A321C						PASS	.						114.0	92.0	98.0					2																	84752784		692	1591	2283	SO:0001819	synonymous_variant	1768	exon3			ACGTCCAGTAAGC	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.321A>C	2.37:g.84752784A>C		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	261	130	0.498084	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			A|0.989;C|0.011	0.011	strong		0.348	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
THBS1	7057	hgsc.bcm.edu	37	15	39874396	39874396	+	Missense_Mutation	SNP	T	T	G	rs41515347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39874396T>G	ENST00000260356.5	+	3	235	c.70T>G	c.(70-72)Tct>Gct	p.S24A		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	24			S -> A (in dbSNP:rs41515347).		activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		TCTAACAGAGTCTGGCGGAGA	0.597													T|||	183	0.0365415	0.1241	0.0101	5008	,	,		18737	0.0099		0.001	False		,,,				2504	0.001				p.S24A		Atlas-SNP	.											.	THBS1	106	.	0			c.T70G						PASS	.	T	ALA/SER	457,3939	207.2+/-228.6	28,401,1769	36.0	39.0	38.0		70	4.0	1.0	15	dbSNP_127	38	7,8579	5.7+/-21.5	0,7,4286	yes	missense	THBS1	NM_003246.2	99	28,408,6055	GG,GT,TT		0.0815,10.3958,3.5742	benign	24/1171	39874396	464,12518	2198	4293	6491	SO:0001583	missense	7057	exon3			ACAGAGTCTGGCG		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.70T>G	15.37:g.39874396T>G	ENSP00000260356:p.Ser24Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	73	0.033424908424908424	62	0.12601626016260162	5	0.013812154696132596	5	0.008741258741258742	1	0.0013192612137203166	T	17.25	3.342644	0.61073	0.103958	8.15E-4	ENSG00000137801	ENST00000260356;ENST00000397591	T;T	0.78003	-1.14;0.73	5.17	4.02	0.46733	Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.35708	N	0.003030	T	0.02727	0.0082	N	0.22421	0.69	0.32910	D	0.514417	D	0.58268	0.982	D	0.67548	0.952	T	0.52586	-0.8556	10	0.34782	T	0.22	-12.2229	11.4375	0.50076	0.0:0.0:0.1511:0.8489	rs41515347;rs61731227	24	P07996	TSP1_HUMAN	A	24	ENSP00000260356:S24A;ENSP00000380720:S24A	ENSP00000260356:S24A	S	+	1	0	THBS1	37661688	1.000000	0.71417	0.993000	0.49108	0.712000	0.41017	5.745000	0.68672	0.947000	0.37659	0.460000	0.39030	TCT	T|0.969;G|0.031	0.031	strong		0.597	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
IKBKAP	8518	hgsc.bcm.edu	37	9	111651620	111651620	+	Missense_Mutation	SNP	A	A	T	rs3204145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:111651620A>T	ENST00000374647.5	-	29	3521	c.3214T>A	c.(3214-3216)Tgt>Agt	p.C1072S	IKBKAP_ENST00000467959.1_5'UTR|IKBKAP_ENST00000537196.1_Missense_Mutation_p.C723S	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	1072			C -> S (in dbSNP:rs3204145). {ECO:0000269|PubMed:11179008, ECO:0000269|PubMed:17974005}.		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						ACCTGGGCACACTCTTCCAAA	0.433													A|||	1231	0.245807	0.3245	0.1585	5008	,	,		18947	0.2937		0.172	False		,,,				2504	0.228				p.C1072S		Atlas-SNP	.											.	IKBKAP	122	.	0			c.T3214A						PASS	.	A	SER/CYS	1341,3065	448.8+/-348.8	196,949,1058	169.0	161.0	164.0		3214	5.5	1.0	9	dbSNP_105	164	1423,7177	273.7+/-290.8	129,1165,3006	yes	missense	IKBKAP	NM_003640.3	112	325,2114,4064	TT,TA,AA		16.5465,30.4358,21.2517	benign	1072/1333	111651620	2764,10242	2203	4300	6503	SO:0001583	missense	8518	exon29			GGGCACACTCTTC	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.3214T>A	9.37:g.111651620A>T	ENSP00000363779:p.Cys1072Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	99	65	0.656566	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	37	CCDS6773.1	489	0.2239010989010989	142	0.2886178861788618	49	0.13535911602209943	165	0.28846153846153844	133	0.17546174142480211	A	16.58	3.162160	0.57368	0.304358	0.165465	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.26223	1.75;1.75	5.51	5.51	0.81932	.	0.176099	0.48767	D	0.000171	T	0.00012	0.0000	N	0.08118	0	0.47065	P	6.930000000000547E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.32824	-0.9892	9	0.66056	D	0.02	-4.7817	13.5727	0.61856	1.0:0.0:0.0:0.0	rs3204145;rs3824462;rs56566330;rs60095549;rs3204145	1072	O95163	ELP1_HUMAN	S	1072;723	ENSP00000363779:C1072S;ENSP00000439367:C723S	ENSP00000363779:C1072S	C	-	1	0	IKBKAP	110691441	1.000000	0.71417	0.995000	0.50966	0.842000	0.47809	6.550000	0.73905	2.080000	0.62538	0.533000	0.62120	TGT	A|0.773;T|0.227	0.227	strong		0.433	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
LIPE	3991	hgsc.bcm.edu	37	19	42910416	42910416	+	Silent	SNP	C	C	T	rs28657829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42910416C>T	ENST00000244289.4	-	7	2538	c.2262G>A	c.(2260-2262)ccG>ccA	p.P754P	LIPE_ENST00000602000.1_5'Flank|LIPE-AS1_ENST00000593491.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000599276.1_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	754					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				GCATTGTGGCCGGGTAGGCTG	0.662													C|||	103	0.0205671	0.0726	0.0072	5008	,	,		14500	0.0		0.002	False		,,,				2504	0.0				p.P754P		Atlas-SNP	.											LIPE,rectum,carcinoma,-1,1	LIPE	83	1	0			c.G2262A						PASS	.	C		229,4177	131.4+/-167.9	6,217,1980	47.0	45.0	45.0		2262	-10.2	0.1	19	dbSNP_125	45	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	LIPE	NM_005357.2		6,227,6270	TT,TC,CC		0.1163,5.1975,1.8376		754/1077	42910416	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	3991	exon7			TGTGGCCGGGTAG	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2262G>A	19.37:g.42910416C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	124	56	0.451613	NM_005357	Q3LRT2|Q6NSL7	Silent	SNP	ENST00000244289.4	37	CCDS12607.1																																																																																			C|0.978;T|0.022	0.022	strong		0.662	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357	
WDR49	151790	hgsc.bcm.edu	37	3	167217960	167217960	+	Silent	SNP	C	C	T	rs13061106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:167217960C>T	ENST00000308378.3	-	14	2261	c.1956G>A	c.(1954-1956)gaG>gaA	p.E652E	WDR49_ENST00000479765.1_Intron|WDR49_ENST00000476376.1_Silent_p.E477E|WDR49_ENST00000453925.2_Silent_p.E617E	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	652										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						GTGACGGGGCCTCCAGAATTT	0.423													C|||	937	0.187101	0.1815	0.2205	5008	,	,		16496	0.3849		0.0915	False		,,,				2504	0.0654				p.E652E		Atlas-SNP	.											.	WDR49	188	.	0			c.G1956A						PASS	.	C		695,3711	285.5+/-278.2	67,561,1575	126.0	144.0	138.0		1956	-0.5	0.0	3	dbSNP_121	138	775,7825	181.9+/-230.5	36,703,3561	no	coding-synonymous	WDR49	NM_178824.3		103,1264,5136	TT,TC,CC		9.0116,15.7739,11.3025		652/698	167217960	1470,11536	2203	4300	6503	SO:0001819	synonymous_variant	151790	exon14			CGGGGCCTCCAGA	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.1956G>A	3.37:g.167217960C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_178824	Q8N297	Silent	SNP	ENST00000308378.3	37	CCDS3201.1	444	0.2032967032967033	96	0.1951219512195122	69	0.19060773480662985	211	0.3688811188811189	68	0.08970976253298153	C	0.006	-2.109061	0.00353	0.157739	0.090116	ENSG00000174776	ENST00000472600	.	.	.	5.13	-0.538	0.11868	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44682	-0.9312	3	.	.	.	.	4.782	0.13206	0.0:0.4402:0.1516:0.4082	rs13061106;rs57499876	.	.	.	K	629	.	.	R	-	2	0	WDR49	168700654	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.058000	0.14301	-0.185000	0.10550	0.467000	0.42956	AGG	C|0.862;T|0.138	0.138	strong		0.423	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824	
ODF2	4957	hgsc.bcm.edu	37	9	131260808	131260808	+	Missense_Mutation	SNP	C	C	G	rs16930426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131260808C>G	ENST00000434106.3	+	19	2492	c.2129C>G	c.(2128-2130)aCc>aGc	p.T710S	ODF2_ENST00000604420.1_Missense_Mutation_p.T710S|ODF2_ENST00000351030.3_Missense_Mutation_p.T705S|ODF2_ENST00000372807.5_Missense_Mutation_p.T705S|ODF2_ENST00000393527.3_Missense_Mutation_p.T686S|ODF2_ENST00000444119.2_Missense_Mutation_p.T686S	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	710			T -> S (in dbSNP:rs16930426).		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						GAATGTGGGACCctggcaagg	0.542													C|||	106	0.0211661	0.0749	0.0086	5008	,	,		20036	0.0		0.001	False		,,,				2504	0.0				p.T774S		Atlas-SNP	.											.	ODF2	227	.	0			c.C2321G						PASS	.	C	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	330,4076	173.0+/-202.9	15,300,1888	73.0	62.0	66.0		2114,2129,2057,2129,2321	3.8	0.3	9	dbSNP_123	66	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense,missense,missense	ODF2	NM_001242352.1,NM_001242353.1,NM_002540.4,NM_153433.1,NM_153435.1	58,58,58,58,58	15,304,6184	GG,GC,CC		0.0465,7.4898,2.568	benign,benign,benign,benign,benign	705/825,710/830,686/806,710/830,774/894	131260808	334,12672	2203	4300	6503	SO:0001583	missense	4957	exon19			GTGGGACCCTGGC	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.2129C>G	9.37:g.131260808C>G	ENSP00000403453:p.Thr710Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	117	76	0.649573	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	45	0.020604395604395604	41	0.08333333333333333	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	9.645	1.139924	0.21205	0.074898	4.65E-4	ENSG00000136811	ENST00000351030;ENST00000372796;ENST00000303890	T;T;T	0.20069	2.1;2.11;2.1	5.67	3.8	0.43715	.	1.035180	0.07583	N	0.920674	T	0.00468	0.0015	N	0.01576	-0.805	0.25699	N	0.985609	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	0.09997	-1.0649	10	0.05721	T	0.95	-0.0175	15.5266	0.75915	0.0:0.6681:0.3319:0.0	rs16930426;rs52827709;rs16930426	705;55;710;686	Q5BJF6-4;Q6PJQ8;Q5BJF6;Q5BJF6-3	.;.;ODFP2_HUMAN;.	S	705;710;686	ENSP00000342581:T705S;ENSP00000361882:T710S;ENSP00000307781:T686S	ENSP00000307781:T686S	T	+	2	0	ODF2	130300629	0.000000	0.05858	0.265000	0.24526	0.689000	0.40095	0.677000	0.25262	0.685000	0.31468	-0.211000	0.12701	ACC	C|0.971;G|0.029	0.029	strong		0.542	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
SPAG4	6676	hgsc.bcm.edu	37	20	34208869	34208869	+	Silent	SNP	G	G	A	rs34962502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34208869G>A	ENST00000374273.3	+	12	1351	c.1239G>A	c.(1237-1239)acG>acA	p.T413T		NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	413	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			CCCGTTTCACGTGCTTGTATC	0.557													G|||	51	0.0101837	0.0378	0.0014	5008	,	,		15888	0.0		0.0	False		,,,				2504	0.0				p.T413T		Atlas-SNP	.											SPAG4,colon,carcinoma,+1,1	SPAG4	36	1	0			c.G1239A						PASS	.	G		183,4223	118.4+/-156.1	4,175,2024	82.0	83.0	83.0		1239	-11.1	0.2	20	dbSNP_126	83	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous	SPAG4	NM_003116.1		4,177,6322	AA,AG,GG		0.0233,4.1534,1.4224		413/438	34208869	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	6676	exon12			TTTCACGTGCTTG	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.1239G>A	20.37:g.34208869G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	116	66	0.568965	NM_003116	O43648	Silent	SNP	ENST00000374273.3	37	CCDS13259.1																																																																																			G|0.986;A|0.014	0.014	strong		0.557	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73163965	73163965	+	Missense_Mutation	SNP	C	C	A	rs2973558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:73163965C>A	ENST00000426542.2	+	19	2358	c.2338C>A	c.(2338-2340)Cat>Aat	p.H780N	ARHGEF28_ENST00000287898.5_Missense_Mutation_p.H780N|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.H780N|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.H780N|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.H780N|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.H467N|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.H780N			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	780			H -> N (in dbSNP:rs2973558).		central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										TGAGAGTGACCATAACAGCTG	0.502													A|||	1115	0.222644	0.177	0.3631	5008	,	,		18281	0.1389		0.3012	False		,,,				2504	0.1902				p.H780N		Atlas-SNP	.											.	.	.	.	0			c.C2338A						PASS	.	A	ASN/HIS,ASN/HIS	792,3138		87,618,1260	56.0	55.0	55.0		2338,2338	-0.6	0.0	5	dbSNP_101	55	2584,5732		406,1772,1980	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	68,68	493,2390,3240	AA,AC,CC		31.0726,20.1527,27.5682	benign,benign	780/1732,780/1706	73163965	3376,8870	1965	4158	6123	SO:0001583	missense	64283	exon20			AGTGACCATAACA		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2338C>A	5.37:g.73163965C>A	ENSP00000412175:p.His780Asn	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	150	79	0.526667	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	528	0.24175824175824176	92	0.18699186991869918	122	0.3370165745856354	78	0.13636363636363635	236	0.3113456464379947	A	10.03	1.238640	0.22711	0.201527	0.310726	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.09073	3.27;3.27;3.27;3.02;3.27;3.27;3.11	5.27	-0.557	0.11800	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.09022	0.001;0.001;0.001;0.002	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47724	-0.9095	8	0.32370	T	0.25	.	9.0502	0.36372	0.4623:0.0982:0.4395:0.0	rs2973558;rs52798984;rs57008739;rs2973558	467;780;780;780	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	N	780;780;780;780;780;780;467	ENSP00000296794:H780N;ENSP00000441913:H780N;ENSP00000441436:H780N;ENSP00000287898:H780N;ENSP00000411459:H780N;ENSP00000412175:H780N;ENSP00000296799:H467N	ENSP00000287898:H780N	H	+	1	0	RP11-428C6.1	73199721	0.000000	0.05858	0.044000	0.18714	0.936000	0.57629	-0.252000	0.08806	-0.418000	0.07450	-0.539000	0.04255	CAT	C|0.764;A|0.236	0.236	strong		0.502	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
TRIM6	117854	hgsc.bcm.edu	37	11	5629607	5629607	+	Silent	SNP	G	G	A	rs10769121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5629607G>A	ENST00000278302.5	+	5	896	c.756G>A	c.(754-756)gtG>gtA	p.V252V	TRIM6_ENST00000507320.1_Silent_p.V77V|TRIM6_ENST00000445329.1_Silent_p.V77V|TRIM6_ENST00000380107.1_Silent_p.V226V|AC015691.13_ENST00000394793.2_RNA|TRIM6_ENST00000380097.3_Silent_p.V280V|TRIM6_ENST00000515022.1_Silent_p.V77V|TRIM6_ENST00000506134.1_Silent_p.V77V|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Silent_p.V280V|TRIM6_ENST00000481603.1_3'UTR	NM_001198645.1|NM_058166.4	NP_001185574.1|NP_477514.1	Q9C030	TRIM6_HUMAN	tripartite motif containing 6	252					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.V280V(2)		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)		CCTAGGATGTGAGTGATGTCA	0.443													G|||	1987	0.396765	0.5643	0.3559	5008	,	,		22825	0.4335		0.2326	False		,,,				2504	0.3303				p.V280V		Atlas-SNP	.											TRIM6-TRIM34,NS,carcinoma,0,2	TRIM6-TRIM34	68	2	2	Substitution - coding silent(2)	stomach(2)	c.G840A						PASS	.	G	,,,,	2224,2178	592.9+/-387.9	563,1098,540	305.0	215.0	246.0		840,840,231,231,756	2.6	1.0	11	dbSNP_120	246	2128,6466	364.7+/-333.6	257,1614,2426	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRIM6,TRIM6-TRIM34	NM_001003818.2,NM_001003819.3,NM_001198644.1,NM_001198645.1,NM_058166.4	,,,,	820,2712,2966	AA,AG,GG		24.7615,49.4775,33.4872	,,,,	280/517,280/843,77/314,77/314,252/489	5629607	4352,8644	2201	4297	6498	SO:0001819	synonymous_variant	445372	exon5			GGATGTGAGTGAT	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.756G>A	11.37:g.5629607G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	197	93	0.472081	NM_001003819	A8K2A7|B4DDQ5|Q86WZ8|Q9HCR1	Silent	SNP	ENST00000278302.5	37	CCDS31390.1																																																																																			G|0.632;A|0.368	0.368	strong		0.443	TRIM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143376.2	NM_001003818	
CFAP46	54777	hgsc.bcm.edu	37	10	134748281	134748281	+	Missense_Mutation	SNP	G	G	A	rs74460040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134748281G>A	ENST00000368586.5	-	8	941	c.841C>T	c.(841-843)Cgc>Tgc	p.R281C	TTC40_ENST00000368582.2_Missense_Mutation_p.R281C|TTC40_ENST00000368585.3_Missense_Mutation_p.R281C	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GAGGGAAAGCGCTGGTGGTTG	0.378													G|||	134	0.0267572	0.0613	0.0346	5008	,	,		18945	0.0		0.0268	False		,,,				2504	0.002				p.R281C		Atlas-SNP	.											.	TTC40	100	.	0			c.C841T						PASS	.	G	CYS/ARG	195,4211	124.1+/-161.4	5,185,2013	98.0	93.0	95.0		841	1.0	0.0	10	dbSNP_131	95	148,8452	72.3+/-134.9	1,146,4153	yes	missense	C10orf93	NM_173572.3	180	6,331,6166	AA,AG,GG		1.7209,4.4258,2.6372	probably-damaging	281/406	134748281	343,12663	2203	4300	6503	SO:0001583	missense	54777	exon8			GAAAGCGCTGGTG																												ENST00000368586.5:c.841C>T	10.37:g.134748281G>A	ENSP00000357575:p.Arg281Cys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	52	0.023809523809523808	24	0.04878048780487805	13	0.03591160220994475	0	0.0	15	0.01978891820580475	G	14.76	2.631822	0.46944	0.044258	0.017209	ENSG00000171811	ENST00000368586;ENST00000368582;ENST00000368585	T;T;T	0.55588	0.51;0.51;0.51	4.08	0.967	0.19674	.	0.829047	0.10271	N	0.694809	T	0.14700	0.0355	L	0.47716	1.5	0.09310	N	1	D	0.71674	0.998	P	0.53649	0.731	T	0.11446	-1.0587	10	0.59425	D	0.04	.	4.147	0.10220	0.1146:0.0:0.4685:0.4169	.	281	Q5SR76-1	.	C	281	ENSP00000357575:R281C;ENSP00000357571:R281C;ENSP00000357574:R281C	ENSP00000357571:R281C	R	-	1	0	C10orf93	134598271	0.007000	0.16637	0.001000	0.08648	0.208000	0.24298	0.015000	0.13355	0.385000	0.24970	0.609000	0.83330	CGC	G|0.972;A|0.028	0.028	strong		0.378	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
AVL9	23080	hgsc.bcm.edu	37	7	32613020	32613020	+	Silent	SNP	A	A	G	rs1993050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:32613020A>G	ENST00000318709.4	+	12	1781	c.1560A>G	c.(1558-1560)acA>acG	p.T520T	AVL9_ENST00000409301.1_Silent_p.T520T|AVL9_ENST00000404479.1_Intron	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	520					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)		p.T520T(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TGGCTGCCACACTGCAATTAG	0.458													A|||	2848	0.56869	0.3933	0.7147	5008	,	,		17731	0.6677		0.6551	False		,,,				2504	0.5112				p.T520T		Atlas-SNP	.											AVL9,NS,carcinoma,0,1	AVL9	66	1	1	Substitution - coding silent(1)	stomach(1)	c.A1560G						PASS	.	A		1900,2506	546.3+/-377.0	416,1068,719	89.0	77.0	81.0		1560	-11.0	0.2	7	dbSNP_92	81	5691,2909	671.1+/-402.8	1902,1887,511	no	coding-synonymous	AVL9	NM_015060.1		2318,2955,1230	GG,GA,AA		33.8256,43.123,41.6346		520/649	32613020	7591,5415	2203	4300	6503	SO:0001819	synonymous_variant	23080	exon12			TGCCACACTGCAA	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1560A>G	7.37:g.32613020A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	122	58	0.47541	NM_015060	Q92573	Silent	SNP	ENST00000318709.4	37	CCDS34613.1																																																																																			A|0.420;G|0.580	0.580	strong		0.458	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
OR10G4	390264	hgsc.bcm.edu	37	11	123886648	123886648	+	Silent	SNP	T	T	C	rs397832341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123886648T>C	ENST00000320891.4	+	1	367	c.367T>C	c.(367-369)Ttg>Ctg	p.L123L		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		TGATCGCTACTTGGCCATCAG	0.567													t|||	2	0.000399361	0.0008	0.0	5008	,	,		23929	0.0		0.0	False		,,,				2504	0.001				p.L123L		Atlas-SNP	.											OR10G4,right_lower_lobe,carcinoma,-2,1	OR10G4	77	1	0			c.T367C						scavenged	.																																			SO:0001819	synonymous_variant	390264	exon1			CGCTACTTGGCCA	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.367T>C	11.37:g.123886648T>C		Somatic	1243	0	0		WXS	Illumina HiSeq	Phase_I	939	202	0.215122	NM_001004462	Q6IEW0	Silent	SNP	ENST00000320891.4	37	CCDS31702.1																																																																																			.	.	none		0.567	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
MYH14	79784	hgsc.bcm.edu	37	19	50810405	50810405	+	Silent	SNP	C	C	T	rs201839634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50810405C>T	ENST00000596571.1	+	38	5655	c.5655C>T	c.(5653-5655)ctC>ctT	p.L1885L	CTB-191K22.5_ENST00000595563.1_RNA|MYH14_ENST00000440075.2_Silent_p.L1926L|MYH14_ENST00000262269.8_Silent_p.L1926L|MYH14_ENST00000425460.1_Silent_p.L1893L|MYH14_ENST00000376970.2_Silent_p.L1918L|MYH14_ENST00000601313.1_Silent_p.L1926L|MYH14_ENST00000598205.1_Silent_p.L1893L			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1885					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)		CTGACCAGCTCCGGGACCAGG	0.592													C|||	2	0.000399361	0.0015	0.0	5008	,	,		20297	0.0		0.0	False		,,,				2504	0.0				p.L1926L		Atlas-SNP	.											.	MYH14	261	.	0			c.C5778T						PASS	.	C	,,	2,3712		0,2,1855	39.0	49.0	46.0		5679,5778,5655	2.0	1.0	19		46	0,7216		0,0,3608	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	0,2,5463	TT,TC,CC		0.0,0.0539,0.0183	,,	1893/2004,1926/2037,1885/1996	50810405	2,10928	1857	3608	5465	SO:0001819	synonymous_variant	79784	exon41			CCAGCTCCGGGAC	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.5655C>T	19.37:g.50810405C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
SSPO	23145	hgsc.bcm.edu	37	7	149509064	149509064	+	RNA	SNP	T	T	C	rs73727632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149509064T>C	ENST00000378016.2	+	0	9610							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)			CCCTGCCCGGTGCCATCGGCA	0.697													C|||	332	0.0662939	0.2126	0.0245	5008	,	,		14721	0.004		0.005	False		,,,				2504	0.0256				p.C3204R		Atlas-SNP	.											.	.	.	.	0			c.T9610C						PASS	.	C		736,3280		63,610,1335	27.0	33.0	31.0		9620	3.6	0.6	7	dbSNP_130	31	51,8257		0,51,4103	yes	coding-notMod3	SSPO	NM_198455.2		63,661,5438	CC,CT,TT		0.6139,18.3267,6.3859			149509064	787,11537	2008	4154	6162			23145	exon68			GCCCGGTGCCATC	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.149509064T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.949;C|0.051	0.051	strong		0.697	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
SPON2	10417	hgsc.bcm.edu	37	4	1165748	1165748	+	Missense_Mutation	SNP	T	T	C	rs6836335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1165748T>C	ENST00000290902.5	-	2	444	c.112A>G	c.(112-114)Aga>Gga	p.R38G	SPON2_ENST00000431380.1_Missense_Mutation_p.R38G	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	38	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.		R -> G (in dbSNP:rs6836335).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		GCCAGGGCTCTGGCGGAACAG	0.692													T|||	690	0.13778	0.2943	0.0994	5008	,	,		12371	0.001		0.1312	False		,,,				2504	0.1012				p.R38G		Atlas-SNP	.											.	SPON2	22	.	0			c.A112G						PASS	.	T	GLY/ARG,GLY/ARG,GLY/ARG	1280,3118		190,900,1109	36.0	49.0	45.0		112,112,112	0.2	0.0	4	dbSNP_116	45	1039,7541		64,911,3315	yes	missense,missense,missense	SPON2	NM_001128325.2,NM_001199021.1,NM_012445.3	125,125,125	254,1811,4424	CC,CT,TT		12.1096,29.1041,17.8687	benign,benign,benign	38/332,38/332,38/332	1165748	2319,10659	2199	4290	6489	SO:0001583	missense	10417	exon2			GGGCTCTGGCGGA	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"""Mindin"", ""M-spondin"""	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.112A>G	4.37:g.1165748T>C	ENSP00000290902:p.Arg38Gly	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	146	62	0.424658	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Missense_Mutation	SNP	ENST00000290902.5	37	CCDS3347.1	280	0.1282051282051282	139	0.28252032520325204	42	0.11602209944751381	1	0.0017482517482517483	98	0.12928759894459102	T	12.21	1.868543	0.32977	0.291041	0.121096	ENSG00000159674	ENST00000290902;ENST00000431380;ENST00000503765;ENST00000515004;ENST00000502483	T;T;T;T;T	0.32515	2.95;2.95;1.52;1.46;1.45	4.74	0.199	0.15175	Spondin, N-terminal (1);	0.838802	0.10780	N	0.634936	T	0.00012	0.0000	L	0.53249	1.67	0.54753	P	1.0999999999983245E-5	P;P;B	0.37688	0.605;0.459;0.28	B;B;B	0.36464	0.225;0.017;0.019	T	0.32079	-0.9920	9	0.25751	T	0.34	.	2.1123	0.03706	0.1008:0.322:0.2969:0.2803	rs6836335;rs6836335	38;38;38	D6RB12;D3DVN9;Q9BUD6	.;.;SPON2_HUMAN	G	38	ENSP00000290902:R38G;ENSP00000394832:R38G;ENSP00000424542:R38G;ENSP00000425871:R38G;ENSP00000422516:R38G	ENSP00000290902:R38G	R	-	1	2	SPON2	1155748	0.792000	0.28813	0.001000	0.08648	0.067000	0.16453	1.458000	0.35223	-0.012000	0.14223	0.334000	0.21626	AGA	T|0.847;C|0.153	0.153	strong		0.692	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2		
SPATA31E1	286234	hgsc.bcm.edu	37	9	90501514	90501514	+	Missense_Mutation	SNP	C	C	G	rs4076794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:90501514C>G	ENST00000325643.5	+	4	2178	c.2112C>G	c.(2110-2112)gaC>gaG	p.D704E		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	704			D -> E (in dbSNP:rs4076794). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGTTCTCTGACAAGGGGTGCT	0.602													.|||	1492	0.297923	0.6142	0.2882	5008	,	,		18485	0.253		0.1103	False		,,,				2504	0.1166				p.D704E		Atlas-SNP	.											C9orf79,middle_lobe,carcinoma,+1,2	.	.	2	0			c.C2112G						PASS	.	G	GLU/ASP	2348,2058	555.7+/-379.3	619,1110,474	50.0	64.0	59.0		2112	-3.8	0.0	9	dbSNP_108	59	812,7786	770.1+/-407.7	38,736,3525	yes	missense	C9orf79	NM_178828.4	45	657,1846,3999	GG,GC,CC		9.4441,46.709,24.3002	benign	704/1446	90501514	3160,9844	2203	4299	6502	SO:0001583	missense	286234	exon4			CTCTGACAAGGGG	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.2112C>G	9.37:g.90501514C>G	ENSP00000322640:p.Asp704Glu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	72	48	0.666667	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	632	0.2893772893772894	305	0.6199186991869918	95	0.26243093922651933	141	0.2465034965034965	91	0.12005277044854881	g	0.010	-1.758496	0.00657	0.53291	0.094441	ENSG00000177992	ENST00000325643;ENST00000539327	T	0.06218	3.33	2.47	-3.84	0.04256	.	8.130670	0.00166	N	0.000000	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.12013	0.005;0.001	B;B	0.06405	0.002;0.001	T	0.45542	-0.9254	9	0.02654	T	1	.	1.9593	0.03383	0.2337:0.4335:0.1834:0.1494	rs4076794;rs4076794	704;356	Q6ZUB1;Q8NA33	CI079_HUMAN;.	E	704;356	ENSP00000322640:D704E	ENSP00000322640:D704E	D	+	3	2	C9orf79	89691334	0.066000	0.20996	0.000000	0.03702	0.003000	0.03518	0.004000	0.13106	-1.590000	0.01623	-0.224000	0.12420	GAC	C|0.751;G|0.249	0.249	strong		0.602	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
C2CD2	25966	hgsc.bcm.edu	37	21	43319180	43319180	+	Missense_Mutation	SNP	T	T	C	rs9981024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43319180T>C	ENST00000380486.3	-	13	2093	c.1852A>G	c.(1852-1854)Act>Gct	p.T618A	C2CD2_ENST00000329623.7_Missense_Mutation_p.T463A	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	618			T -> A (in dbSNP:rs9981024).			cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						TTTTTGGCAGTGCCCGGCTCC	0.627													t|||	303	0.0605032	0.1452	0.0288	5008	,	,		17060	0.0387		0.0239	False		,,,				2504	0.0286				p.T618A		Atlas-SNP	.											.	C2CD2	47	.	0			c.A1852G						PASS	.	T	ALA/THR,ALA/THR	626,3780	262.8+/-265.1	58,510,1635	48.0	57.0	54.0		1852,1387	-3.7	0.0	21	dbSNP_119	54	135,8465	65.3+/-127.6	0,135,4165	yes	missense,missense	C2CD2	NM_015500.1,NM_199050.2	58,58	58,645,5800	CC,CT,TT		1.5698,14.2079,5.8511	benign,benign	618/697,463/542	43319180	761,12245	2203	4300	6503	SO:0001583	missense	25966	exon13			TGGCAGTGCCCGG	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"""TMEM24-like"""		"""chromosome 21 open reading frame 25"""	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1852A>G	21.37:g.43319180T>C	ENSP00000369853:p.Thr618Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	37	CCDS42933.1	130|130	0.05952380952380952|0.05952380952380952	84|84	0.17073170731707318|0.17073170731707318	10|10	0.027624309392265192|0.027624309392265192	24|24	0.04195804195804196|0.04195804195804196	12|12	0.0158311345646438|0.0158311345646438	t|t	0.010|0.010	-1.751969|-1.751969	0.00663|0.00663	0.142079|0.142079	0.015698|0.015698	ENSG00000157617|ENSG00000157617	ENST00000449165|ENST00000329623;ENST00000380486	.|T;T	.|0.39787	.|1.06;1.06	4.67|4.67	-3.68|-3.68	0.04463|0.04463	.|.	.|1.139230	.|0.06249	.|N	.|0.691768	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.01576|0.01576	-0.805|-0.805	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.26467|0.26467	-1.0102|-1.0102	4|9	.|0.20046	.|T	.|0.44	-0.6039|-0.6039	14.4289|14.4289	0.67236|0.67236	0.0:0.2751:0.0:0.7249|0.0:0.2751:0.0:0.7249	rs9981024;rs9981024|rs9981024;rs9981024	.|618	.|Q9Y426	.|CU025_HUMAN	R|A	103|463;618	.|ENSP00000329302:T463A;ENSP00000369853:T618A	.|ENSP00000329302:T463A	H|T	-|-	2|1	0|0	C2CD2|C2CD2	42192249|42192249	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.017000|0.017000	0.09413|0.09413	-0.874000|-0.874000	0.04210|0.04210	-0.968000|-0.968000	0.03578|0.03578	-1.070000|-1.070000	0.02257|0.02257	CAC|ACT	T|0.938;C|0.062	0.062	strong		0.627	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
CCDC108	255101	hgsc.bcm.edu	37	2	219895548	219895548	+	Missense_Mutation	SNP	C	C	A	rs56411706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219895548C>A	ENST00000341552.5	-	9	1107	c.1024G>T	c.(1024-1026)Gcc>Tcc	p.A342S	CCDC108_ENST00000410037.1_Missense_Mutation_p.A277S|CCDC108_ENST00000453220.1_Missense_Mutation_p.A342S|CCDC108_ENST00000409865.3_Missense_Mutation_p.A331S|CCDC108_ENST00000441968.1_Missense_Mutation_p.A342S	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	342						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCAGCTGGGCGCACTTGGCT	0.637													C|||	858	0.171326	0.3222	0.1066	5008	,	,		15229	0.1726		0.0964	False		,,,				2504	0.089				p.A342S		Atlas-SNP	.											.	CCDC108	208	.	0			c.G1024T						PASS	.	C	SER/ALA	1234,3172	418.3+/-338.2	173,888,1142	38.0	40.0	39.0		1024	2.0	0.9	2	dbSNP_129	39	849,7751	193.2+/-239.0	37,775,3488	yes	missense	CCDC108	NM_194302.2	99	210,1663,4630	AA,AC,CC		9.8721,28.0073,16.0157	possibly-damaging	342/1926	219895548	2083,10923	2203	4300	6503	SO:0001583	missense	255101	exon9			GCTGGGCGCACTT	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.1024G>T	2.37:g.219895548C>A	ENSP00000340776:p.Ala342Ser	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	358	0.16391941391941392	149	0.30284552845528456	37	0.10220994475138122	99	0.17307692307692307	73	0.09630606860158311	C	11.61	1.689268	0.29962	0.280073	0.098721	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220;ENST00000409865;ENST00000410037;ENST00000441164	T;T;T;T;T	0.06449	3.57;3.57;3.57;3.3;3.31	4.97	1.99	0.26369	.	0.318910	0.22850	N	0.054861	T	0.00012	0.0000	L	0.55481	1.735	0.09310	P	1.0	P;P	0.39535	0.677;0.677	B;B	0.41374	0.355;0.355	T	0.51371	-0.8714	9	0.23302	T	0.38	-17.5074	9.2326	0.37446	0.0:0.3853:0.5221:0.0925	rs56411706	331;342	E9PG25;Q6ZU64	.;CC108_HUMAN	S	342;342;342;331;277;276	ENSP00000340776:A342S;ENSP00000413377:A342S;ENSP00000409117:A342S;ENSP00000386945:A331S;ENSP00000386258:A277S	ENSP00000340776:A342S	A	-	1	0	CCDC108	219603792	0.118000	0.22208	0.898000	0.35279	0.492000	0.33523	0.250000	0.18235	0.654000	0.30846	-0.259000	0.10710	GCC	C|0.847;A|0.153	0.153	strong		0.637	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
HTT	3064	hgsc.bcm.edu	37	4	3148570	3148570	+	Missense_Mutation	SNP	G	G	A	rs35892913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:3148570G>A	ENST00000355072.5	+	25	3335	c.3190G>A	c.(3190-3192)Gtt>Att	p.V1064I		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1064			V -> I (in dbSNP:rs35892913).		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)		GAGCTGTACCGTTGGGATGGC	0.463													G|||	118	0.0235623	0.003	0.0259	5008	,	,		20235	0.0		0.0736	False		,,,				2504	0.0225				p.V1064I		Atlas-SNP	.											.	HTT	221	.	0			c.G3190A						PASS	.	G	ILE/VAL	54,3962		1,52,1955	311.0	311.0	311.0		3190	3.8	0.1	4	dbSNP_126	311	496,7854		6,484,3685	yes	missense	HTT	NM_002111.6	29	7,536,5640	AA,AG,GG		5.9401,1.3446,4.4477	benign	1064/3143	3148570	550,11816	2008	4175	6183	SO:0001583	missense	3064	exon25			TGTACCGTTGGGA	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.3190G>A	4.37:g.3148570G>A	ENSP00000347184:p.Val1064Ile	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	203	96	0.472906	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	56	0.02564102564102564	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	46	0.06068601583113457	G	2.349	-0.349196	0.05173	0.013446	0.059401	ENSG00000197386	ENST00000355072	T	0.05199	3.48	4.68	3.84	0.44239	Armadillo-type fold (1);	0.186617	0.46145	D	0.000316	T	0.00440	0.0014	N	0.20685	0.6	0.26172	N	0.97984	B	0.20164	0.042	B	0.13407	0.009	T	0.44832	-0.9302	10	0.20519	T	0.43	.	7.9796	0.30175	0.2354:0.0:0.7646:0.0	rs35892913	1064	P42858	HD_HUMAN	I	1064	ENSP00000347184:V1064I	ENSP00000347184:V1064I	V	+	1	0	HTT	3118368	1.000000	0.71417	0.062000	0.19696	0.145000	0.21501	3.671000	0.54576	1.210000	0.43336	-0.244000	0.11960	GTT	G|0.955;A|0.045	0.045	strong		0.463	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
TMEM247	388946	hgsc.bcm.edu	37	2	46707812	46707812	+	Missense_Mutation	SNP	G	G	A	rs79819367		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:46707812G>A	ENST00000434431.1	+	2	386	c.386G>A	c.(385-387)cGg>cAg	p.R129Q		NM_001145051.2	NP_001138523.1	A6NEH6	TM247_HUMAN	transmembrane protein 247	129						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											CAGCGGCAGCGGCAGCACGAG	0.657																																					p.R129Q		Atlas-SNP	.											.	.	.	.	0			c.G386A						PASS	.						29.0	39.0	36.0					2																	46707812		692	1591	2283	SO:0001583	missense	388946	exon2			GGCAGCGGCAGCA		CCDS56117.1	2p21	2012-04-11			ENSG00000187600	ENSG00000187600			42967	protein-coding gene	gene with protein product							Standard	NM_001145051		Approved		uc010yod.3	A6NEH6	OTTHUMG00000153137	ENST00000434431.1:c.386G>A	2.37:g.46707812G>A	ENSP00000388684:p.Arg129Gln	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	215	17	0.0790698	NM_001145051		Missense_Mutation	SNP	ENST00000434431.1	37	CCDS56117.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316551	0.81469	.	.	ENSG00000187600	ENST00000434431	.	.	.	4.76	4.76	0.60689	.	0.000000	0.37857	N	0.001912	T	0.65933	0.2739	L	0.34521	1.04	.	.	.	D	0.89917	1.0	D	0.81914	0.995	T	0.72597	-0.4245	8	0.59425	D	0.04	-29.3943	14.7885	0.69821	0.0:0.0:1.0:0.0	.	129	A6NEH6	YB028_HUMAN	Q	129	.	ENSP00000388684:R129Q	R	+	2	0	AC018682.6	46561316	1.000000	0.71417	1.000000	0.80357	0.624000	0.37722	4.719000	0.61937	2.484000	0.83849	0.563000	0.77884	CGG	A|1.000;|0.000	1.000	weak		0.657	TMEM247-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329726.1	NM_001145051	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011547	46011547	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011547G>A	ENST00000400368.1	-	1	839	c.819C>T	c.(817-819)ccC>ccT	p.P273P	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	273	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CAGAGCAGACGGGCACACAGC	0.652																																					p.P273P		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C819T						PASS	.						114.0	115.0	115.0					21																	46011547		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			GCAGACGGGCACA	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.819C>T	21.37:g.46011547G>A		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	330	34	0.10303	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.652	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
ATXN1	6310	hgsc.bcm.edu	37	6	16328115	16328115	+	Missense_Mutation	SNP	T	T	C	rs143125796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:16328115T>C	ENST00000244769.4	-	8	1363	c.427A>G	c.(427-429)Atc>Gtc	p.I143V	ATXN1_ENST00000436367.1_Missense_Mutation_p.I143V	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	143					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)				TGTGATGGGATGAAGCTGGCA	0.657													T|||	2	0.000399361	0.0015	0.0	5008	,	,		14675	0.0		0.0	False		,,,				2504	0.0				p.I143V		Atlas-SNP	.											.	ATXN1	117	.	0			c.A427G						PASS	.	T	VAL/ILE,VAL/ILE	4,4402	8.1+/-20.4	0,4,2199	73.0	79.0	77.0		427,427	1.0	1.0	6	dbSNP_134	77	0,8600		0,0,4300	no	missense,missense	ATXN1	NM_000332.3,NM_001128164.1	29,29	0,4,6499	CC,CT,TT		0.0,0.0908,0.0308	possibly-damaging,possibly-damaging	143/816,143/816	16328115	4,13002	2203	4300	6503	SO:0001583	missense	6310	exon7			ATGGGATGAAGCT	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.427A>G	6.37:g.16328115T>C	ENSP00000244769:p.Ile143Val	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	T	8.212	0.800596	0.16397	9.08E-4	0.0	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.45276	0.9;0.9	5.11	1.04	0.20106	.	0.101815	0.64402	D	0.000004	T	0.14874	0.0359	L	0.46157	1.445	0.41711	D	0.989452	B	0.27229	0.172	B	0.18871	0.023	T	0.04635	-1.0937	10	0.38643	T	0.18	-15.4984	7.2098	0.25927	0.0:0.0733:0.2756:0.6511	.	143	P54253	ATX1_HUMAN	V	143	ENSP00000244769:I143V;ENSP00000416360:I143V	ENSP00000244769:I143V	I	-	1	0	ATXN1	16436094	1.000000	0.71417	1.000000	0.80357	0.147000	0.21601	3.031000	0.49728	0.264000	0.21851	-0.456000	0.05471	ATC	T|0.999;C|0.001	0.001	strong		0.657	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144879485	144879485	+	Missense_Mutation	SNP	G	G	C	rs113467089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144879485G>C	ENST00000369354.3	-	27	4154	c.3965C>G	c.(3964-3966)aCa>aGa	p.T1322R	RP4-791M13.5_ENST00000531288.1_RNA|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.T1458R|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.T1458R|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.T1322R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.T1278R|AL138796.1_ENST00000582173.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1322					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)		ACTAGCCAGTGTTGAGCCCCG	0.522			T	PDGFRB	MPD								.|||	215	0.0429313	0.0613	0.0144	5008	,	,		35647	0.0734		0.0179	False		,,,				2504	0.0327				p.T1322R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C3965G						PASS	.	G	ARG/THR,ARG/THR,ARG/THR	227,4179	123.7+/-161.0	0,227,1976	114.0	129.0	124.0		3965,3965,3833	1.1	0.0	1	dbSNP_132	124	171,8421	71.6+/-134.2	0,171,4125	yes	missense,missense,missense	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1	71,71,71	0,398,6101	CC,CG,GG		1.9902,5.1521,3.062	benign,benign,benign	1322/2347,1322/2363,1278/2241	144879485	398,12600	2203	4296	6499	SO:0001583	missense	9659	exon27			GCCAGTGTTGAGC	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.3965C>G	1.37:g.144879485G>C	ENSP00000358360:p.Thr1322Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	92	21	0.228261	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	105	0.04807692307692308	36	0.07317073170731707	6	0.016574585635359115	49	0.08566433566433566	14	0.018469656992084433	G	10.67	1.416543	0.25552	0.051521	0.019902	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01705	4.68;4.74;4.74;4.76;4.75	5.09	1.14	0.20703	.	.	.	.	.	T	0.00552	0.0018	L	0.36672	1.1	0.09310	N	1	B;B	0.29341	0.144;0.242	B;B	0.31614	0.061;0.133	T	0.43621	-0.9380	9	0.17832	T	0.49	.	7.3415	0.26640	0.4627:0.0:0.5373:0.0	.	1278;1322	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	R	1278;1322;1322;1458;1458	ENSP00000327209:T1278R;ENSP00000358360:T1322R;ENSP00000358363:T1322R;ENSP00000435654:T1458R;ENSP00000358366:T1458R	ENSP00000327209:T1278R	T	-	2	0	PDE4DIP	143590842	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.450000	0.21762	0.058000	0.16222	-0.810000	0.03169	ACA	G|0.665;C|0.335	0.335	strong		0.522	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
GML	2765	hgsc.bcm.edu	37	8	143922620	143922620	+	Missense_Mutation	SNP	C	C	T	rs3764795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143922620C>T	ENST00000220940.1	+	3	250	c.160C>T	c.(160-162)Cgc>Tgc	p.R54C		NM_002066.2	NP_002057.1	Q99445	GML_HUMAN	glycosylphosphatidylinositol anchored molecule like	54	UPAR/Ly6.		R -> C (in dbSNP:rs3764795).		apoptotic process (GO:0006915)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of cell proliferation (GO:0008285)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(1)|large_intestine(6)|lung(8)	18	all_cancers(97;4.26e-11)|all_epithelial(106;1.85e-08)|Lung NSC(106;0.000274)|all_lung(105;0.000755)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TCATATTAGGCGCTGTATGAC	0.463													c|||	1050	0.209665	0.1687	0.1311	5008	,	,		24940	0.4772		0.0497	False		,,,				2504	0.2096				p.R54C		Atlas-SNP	.											.	GML	34	.	0			c.C160T						PASS	.	C	CYS/ARG	670,3736		46,578,1579	220.0	181.0	194.0		160	2.5	1.0	8	dbSNP_107	194	461,8139		16,429,3855	yes	missense	GML	NM_002066.2	180	62,1007,5434	TT,TC,CC		5.3605,15.2065,8.696	probably-damaging	54/159	143922620	1131,11875	2203	4300	6503	SO:0001583	missense	2765	exon3			ATTAGGCGCTGTA	D84290	CCDS6391.1	8q24.3	2014-05-14	2012-11-02						4375	protein-coding gene	gene with protein product		602370	"""GPI anchored molecule like protein"", ""glycosylphosphatidylinositol anchored molecule like protein"""			8934543, 9169150	Standard	NM_002066		Approved	LY6DL	uc003yxg.3	Q99445		ENST00000220940.1:c.160C>T	8.37:g.143922620C>T	ENSP00000220940:p.Arg54Cys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	195	91	0.466667	NM_002066	A0AVF6|O00686|O00731	Missense_Mutation	SNP	ENST00000220940.1	37	CCDS6391.1	431	0.19734432234432234	78	0.15853658536585366	46	0.1270718232044199	269	0.47027972027972026	38	0.05013192612137203	N	15.17	2.754520	0.49362	0.152065	0.053605	ENSG00000104499	ENST00000522728;ENST00000220940	T;T	0.22743	1.94;1.94	3.43	2.55	0.30701	Ly-6 antigen / uPA receptor -like (1);CD59 antigen, conserved site (1);	0.537042	0.15823	N	0.242906	T	0.00012	0.0000	L	0.58101	1.795	0.24373	P	0.99482382	D	0.89917	1.0	D	0.67900	0.954	T	0.46952	-0.9154	9	0.51188	T	0.08	-17.6019	6.8583	0.24052	0.0:0.8706:0.0:0.1294	rs3764795;rs56577850;rs60074823;rs3764795	54	Q99445	GML_HUMAN	C	54	ENSP00000430799:R54C;ENSP00000220940:R54C	ENSP00000220940:R54C	R	+	1	0	GML	143919622	0.832000	0.29368	0.957000	0.39632	0.103000	0.19146	0.608000	0.24223	1.001000	0.39076	0.650000	0.86243	CGC	C|0.855;T|0.145	0.145	strong		0.463	GML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379659.1	NM_002066	
CMTM2	146225	hgsc.bcm.edu	37	16	66613525	66613525	+	Silent	SNP	G	G	A	rs11553598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:66613525G>A	ENST00000268595.2	+	1	166	c.15G>A	c.(13-15)gcG>gcA	p.A5A	RP11-403P17.2_ENST00000568430.1_RNA|CMTM2_ENST00000379486.2_Silent_p.A5A	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	5					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)		CACCTAAGGCGGCAAAGGGGG	0.597													G|||	719	0.14357	0.1944	0.0937	5008	,	,		13817	0.1895		0.0835	False		,,,				2504	0.1247				p.A5A		Atlas-SNP	.											CMTM2,NS,carcinoma,+1,2	CMTM2	33	2	0			c.G15A						scavenged	.	G	,	842,3560	327.5+/-300.1	73,696,1432	65.0	64.0	64.0		15,15	-6.4	0.0	16	dbSNP_120	64	730,7870	175.5+/-225.5	40,650,3610	no	coding-synonymous,coding-synonymous	CMTM2	NM_001199317.1,NM_144673.2	,	113,1346,5042	AA,AG,GG		8.4884,19.1277,12.0904	,	5/196,5/249	66613525	1572,11430	2201	4300	6501	SO:0001819	synonymous_variant	146225	exon1			TAAGGCGGCAAAG	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.15G>A	16.37:g.66613525G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_001199317	Q5I2A4|Q8N7E5	Silent	SNP	ENST00000268595.2	37	CCDS10814.1																																																																																			G|0.874;A|0.126	0.126	strong		0.597	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1		
HPS4	89781	hgsc.bcm.edu	37	22	26860269	26860269	+	Missense_Mutation	SNP	G	G	C	rs2014410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26860269G>C	ENST00000398145.2	-	11	1943	c.1327C>G	c.(1327-1329)Ctc>Gtc	p.L443V	HPS4_ENST00000336873.5_Missense_Mutation_p.L443V|HPS4_ENST00000402105.3_Missense_Mutation_p.L438V|HPS4_ENST00000493455.2_5'Flank|HPS4_ENST00000398141.1_Missense_Mutation_p.L456V	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	70	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	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	
SMCHD1	23347	hgsc.bcm.edu	37	18	2667005	2667005	+	Silent	SNP	T	T	C	rs7239096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2667005T>C	ENST00000320876.6	+	3	737	c.399T>C	c.(397-399)taT>taC	p.Y133Y	SMCHD1_ENST00000261598.8_Silent_p.Y133Y	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	133					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						ATGAATATTATGCCAGTGAAG	0.378													T|||	159	0.0317492	0.1142	0.0101	5008	,	,		20279	0.0		0.001	False		,,,				2504	0.0				p.Y133Y		Atlas-SNP	.											.	SMCHD1	88	.	0			c.T399C						PASS	.	T		429,3325		30,369,1478	83.0	72.0	76.0		399	5.6	1.0	18	dbSNP_116	76	7,8219		0,7,4106	no	coding-synonymous	SMCHD1	NM_015295.2		30,376,5584	CC,CT,TT		0.0851,11.4278,3.6394		133/2006	2667005	436,11544	1877	4113	5990	SO:0001819	synonymous_variant	23347	exon3			ATATTATGCCAGT	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.399T>C	18.37:g.2667005T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			T|0.974;C|0.026	0.026	strong		0.378	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
TSPAN9	10867	hgsc.bcm.edu	37	12	3389559	3389559	+	Silent	SNP	C	C	T	rs877089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:3389559C>T	ENST00000011898.5	+	6	503	c.342C>T	c.(340-342)aaC>aaT	p.N114N	TSPAN9_ENST00000492305.1_3'UTR|TSPAN9_ENST00000537971.1_Silent_p.N114N|TSPAN9_ENST00000407263.1_Silent_p.N114N	NM_006675.4	NP_006666.1	O75954	TSN9_HUMAN	tetraspanin 9	114						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)				endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			TGAACGAGAACGCCAAGAAGG	0.617													c|||	104	0.0207668	0.0598	0.0173	5008	,	,		18186	0.0		0.0099	False		,,,				2504	0.0031				p.N114N		Atlas-SNP	.											.	TSPAN9	20	.	0			c.C342T						PASS	.		,	237,4169	138.4+/-174.2	3,231,1969	136.0	92.0	107.0		342,342	-3.5	1.0	12	dbSNP_86	107	130,8470	65.6+/-127.9	1,128,4171	no	coding-synonymous,coding-synonymous	TSPAN9	NM_001168320.1,NM_006675.4	,	4,359,6140	TT,TC,CC		1.5116,5.379,2.8218	,	114/240,114/240	3389559	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	10867	exon6			CGAGAACGCCAAG	AF089749	CCDS8520.1	12p13.33-p13.32	2013-02-14			ENSG00000011105	ENSG00000011105		"""Tetraspanins"""	21640	protein-coding gene	gene with protein product		613137				10719184, 11739647	Standard	NM_006675		Approved	NET-5	uc021qtd.1	O75954	OTTHUMG00000150333	ENST00000011898.5:c.342C>T	12.37:g.3389559C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	38	13	0.342105	NM_006675	D3DUQ7|Q53FV2|Q6FGJ8	Silent	SNP	ENST00000011898.5	37	CCDS8520.1																																																																																			C|0.974;T|0.026	0.026	strong		0.617	TSPAN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317606.2	NM_006675	
OR6C4	341418	hgsc.bcm.edu	37	12	55945856	55945856	+	Silent	SNP	A	A	G	rs57386660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55945856A>G	ENST00000394256.2	+	1	874	c.846A>G	c.(844-846)ttA>ttG	p.L282L	RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|AC009779.1_ENST00000584743.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	282						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(3)|lung(5)|skin(1)	11						TTACTCCCTTACTGAATCCCT	0.358													.|||	594	0.11861	0.3623	0.0231	5008	,	,		19169	0.0913		0.002	False		,,,				2504	0.0051				p.L282L		Atlas-SNP	.											.	OR6C4	34	.	0			c.A846G						PASS	.	G		1317,3089	695.5+/-405.9	199,919,1085	57.0	57.0	57.0		846	-0.8	0.0	12	dbSNP_129	57	22,8578	816.5+/-406.9	0,22,4278	no	coding-synonymous	OR6C4	NM_001005494.1		199,941,5363	GG,GA,AA		0.2558,29.8911,10.2952		282/310	55945856	1339,11667	2203	4300	6503	SO:0001819	synonymous_variant	341418	exon1			TCCCTTACTGAAT	BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"""GPCR / Class A : Olfactory receptors"""	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.846A>G	12.37:g.55945856A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_001005494	A8MZG7|B2RNN2|Q6IFK1	Silent	SNP	ENST00000394256.2	37	CCDS31827.1																																																																																			A|0.902;G|0.098	0.098	strong		0.358	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1		
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377424	49377424	+	Missense_Mutation	SNP	G	G	A	rs11541192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49377424G>A	ENST00000200453.5	+	2	1203	c.934G>A	c.(934-936)Ggt>Agt	p.G312S		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	312	Glu-rich.		G -> S (in dbSNP:rs11541192). {ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		TGAAGAGGAGGGTGAGGTCAA	0.612													G|||	765	0.152756	0.2474	0.1023	5008	,	,		18553	0.0179		0.1849	False		,,,				2504	0.1667				p.G312S		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G934A						PASS	.	G	SER/GLY	1136,3270	402.4+/-332.3	149,838,1216	68.0	74.0	72.0		934	4.3	0.0	19	dbSNP_120	72	1651,6949	302.0+/-305.7	153,1345,2802	yes	missense	PPP1R15A	NM_014330.3	56	302,2183,4018	AA,AG,GG		19.1977,25.783,21.4286	possibly-damaging	312/675	49377424	2787,10219	2203	4300	6503	SO:0001583	missense	23645	exon2			GAGGAGGGTGAGG	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.934G>A	19.37:g.49377424G>A	ENSP00000200453:p.Gly312Ser	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	165	74	0.448485	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	295	0.13507326007326007	105	0.21341463414634146	40	0.11049723756906077	12	0.02097902097902098	138	0.1820580474934037	G	15.27	2.783964	0.49891	0.25783	0.191977	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05139	3.49	4.26	4.26	0.50523	.	1.634130	0.03436	N	0.208525	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	P	0.34662	0.462	B	0.30855	0.121	T	0.38993	-0.9635	9	0.12103	T	0.63	0.3771	12.5678	0.56320	0.0:0.0:1.0:0.0	rs11541192;rs52818639	312	O75807	PR15A_HUMAN	S	312;152;270	ENSP00000200453:G312S	ENSP00000200453:G312S	G	+	1	0	PPP1R15A	54069236	0.001000	0.12720	0.002000	0.10522	0.007000	0.05969	0.442000	0.21628	2.078000	0.62432	0.650000	0.86243	GGT	G|0.811;A|0.189	0.189	strong		0.612	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
TTN	7273	hgsc.bcm.edu	37	2	179613258	179613258	+	Intron	SNP	A	A	C	rs72648906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179613258A>C	ENST00000591111.1	-	45	10585				TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Silent_p.S4623S|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000578746.1_RNA			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)			CTCCTATATGAGAATACATTT	0.368													A|||	104	0.0207668	0.0764	0.0043	5008	,	,		18443	0.0		0.0	False		,,,				2504	0.0				p.S4623S		Atlas-SNP	.											.	TTN	18412	.	0			c.T13869G						PASS	.	A	,,,,	244,4160	139.2+/-174.8	7,230,1965	99.0	109.0	106.0		,,13869,,	3.5	1.0	2	dbSNP_130	106	6,8590	3.7+/-12.6	0,6,4292	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	7,236,6257	CC,CA,AA		0.0698,5.5404,1.9231	,,,,	,,4623/5605,,	179613258	250,12750	2202	4298	6500	SO:0001627	intron_variant	7273	exon46			TATATGAGAATAC	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.10360+4592T>G	2.37:g.179613258A>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	202	97	0.480198	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|0.977;C|0.023	0.023	strong		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MTERF4	130916	hgsc.bcm.edu	37	2	242036797	242036797	+	Missense_Mutation	SNP	A	A	G	rs2286323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242036797A>G	ENST00000391980.2	-	3	624	c.566T>C	c.(565-567)aTg>aCg	p.M189T	MTERFD2_ENST00000407095.3_Missense_Mutation_p.M189T|MTERFD2_ENST00000406593.1_Start_Codon_SNP_p.M1T|MTERFD2_ENST00000495694.1_Intron|MTERFD2_ENST00000464344.2_Intron	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		189			M -> T (in dbSNP:rs2286323).		rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		CTGCTGGCGCATGGTGAAAAT	0.443													A|||	555	0.110823	0.0855	0.0836	5008	,	,		21765	0.2073		0.0964	False		,,,				2504	0.0798				p.M189T		Atlas-SNP	.											.	MTERFD2	33	.	0			c.T566C						PASS	.	A	THR/MET	376,4030	189.9+/-215.9	18,340,1845	102.0	92.0	95.0		566	4.9	1.0	2	dbSNP_100	95	726,7874	177.3+/-227.0	23,680,3597	yes	missense	MTERFD2	NM_182501.3	81	41,1020,5442	GG,GA,AA		8.4419,8.5338,8.473	probably-damaging	189/382	242036797	1102,11904	2203	4300	6503	SO:0001583	missense	130916	exon3			TGGCGCATGGTGA																												ENST00000391980.2:c.566T>C	2.37:g.242036797A>G	ENSP00000375840:p.Met189Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_182501	A8K6K0|Q9P0E0	Missense_Mutation	SNP	ENST00000391980.2	37	CCDS2544.1	271	0.12408424908424909	45	0.09146341463414634	28	0.07734806629834254	127	0.22202797202797203	71	0.09366754617414248	A	16.12	3.032414	0.54790	0.085338	0.084419	ENSG00000122085	ENST00000414146;ENST00000391980;ENST00000406593;ENST00000439144;ENST00000424798;ENST00000407095	T;T;T;T;T;T	0.16743	2.77;2.87;2.32;2.87;2.87;2.87	4.91	4.91	0.64330	.	0.135789	0.49305	D	0.000151	T	0.00039	0.0001	M	0.72118	2.19	0.26979	P	0.9654062	D;D	0.57257	0.979;0.979	P;P	0.60236	0.871;0.76	T	0.17228	-1.0376	9	0.23891	T	0.37	-20.7559	14.2242	0.65848	1.0:0.0:0.0:0.0	rs2286323;rs61153316;rs2286323	189;189	B4DKD5;Q7Z6M4	.;MTER2_HUMAN	T	26;189;1;42;182;189	ENSP00000401409:M26T;ENSP00000375840:M189T;ENSP00000384998:M1T;ENSP00000414989:M42T;ENSP00000409023:M182T;ENSP00000385630:M189T	ENSP00000241527:M189T	M	-	2	0	MTERFD2	241685470	1.000000	0.71417	0.996000	0.52242	0.216000	0.24613	4.145000	0.58065	1.837000	0.53436	0.383000	0.25322	ATG	A|0.894;G|0.106	0.106	strong		0.443	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4		
C17orf77	146723	hgsc.bcm.edu	37	17	72588326	72588326	+	Missense_Mutation	SNP	A	A	C	rs493430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72588326A>C	ENST00000392620.1	+	3	503	c.141A>C	c.(139-141)agA>agC	p.R47S	C17orf77_ENST00000328023.2_Missense_Mutation_p.R47S|CD300LD_ENST00000375352.1_Missense_Mutation_p.S6A	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	47			R -> S (in dbSNP:rs493430). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)		p.S6A(1)|p.R47S(1)		breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						AGCAGCAGAGATGGGGACAGC	0.562													C|||	3377	0.674321	0.8298	0.5533	5008	,	,		19392	0.5714		0.675	False		,,,				2504	0.6554				p.R47S		Atlas-SNP	.											CD300LD,NS,carcinoma,0,2	C17orf77	31	2	2	Substitution - Missense(2)	prostate(2)	c.A141C						PASS	.	C	ALA/SER,SER/ARG	3570,836	329.9+/-301.2	1457,656,90	80.0	81.0	81.0		16,141	2.1	0.0	17	dbSNP_83	81	5730,2870	452.1+/-362.9	1920,1890,490	yes	missense,missense	C17orf77,CD300LD	NM_001115152.1,NM_152460.2	99,110	3377,2546,580	CC,CA,AA		33.3721,18.9741,28.4945	benign,benign	6/195,47/244	72588326	9300,3706	2203	4300	6503	SO:0001583	missense	146723	exon3			GCAGAGATGGGGA		CCDS32721.1	17q25.1	2006-01-16			ENSG00000182352	ENSG00000182352			26480	protein-coding gene	gene with protein product							Standard	NM_152460		Approved	FLJ31882	uc002jla.1	Q96MU5	OTTHUMG00000067611	ENST00000392620.1:c.141A>C	17.37:g.72588326A>C	ENSP00000376396:p.Arg47Ser	Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_152460		Missense_Mutation	SNP	ENST00000392620.1	37	CCDS32721.1	1451|1451	0.6643772893772893|0.6643772893772893	410|410	0.8333333333333334|0.8333333333333334	203|203	0.5607734806629834|0.5607734806629834	312|312	0.5454545454545454|0.5454545454545454	526|526	0.6939313984168866|0.6939313984168866	C|C	9.137|9.137	1.012840|1.012840	0.19277|0.19277	0.810259|0.810259	0.666279|0.666279	ENSG00000182352|ENSG00000204345	ENST00000392620;ENST00000328023|ENST00000375352	T;T|T	0.55413|0.03496	0.52;0.52|3.91	4.18|4.18	2.12|2.12	0.27331|0.27331	.|.	.|1.782210	.|0.03819	.|N	.|0.267140	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	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	0.26395|0.26395	-1.0104|-1.0104	6|8	.|0.02654	.|T	.|1	.|.	3.4548|3.4548	0.07511|0.07511	0.1736:0.5607:0.1681:0.0976|0.1736:0.5607:0.1681:0.0976	rs493430;rs61489654;rs493430|rs493430;rs61489654;rs493430	47|6	Q96MU5|Q6UXZ3	CQ077_HUMAN|CLM4_HUMAN	S|A	47|6	ENSP00000376396:R47S;ENSP00000329353:R47S|ENSP00000364501:S6A	.|ENSP00000364501:S6A	R|S	+|-	3|1	2|0	C17orf77|CD300LD	70099921|70099921	0.000000|0.000000	0.05858|0.05858	0.025000|0.025000	0.17156|0.17156	0.002000|0.002000	0.02628|0.02628	-0.793000|-0.793000	0.04589|0.04589	0.142000|0.142000	0.18901|0.18901	-0.167000|-0.167000	0.13348|0.13348	AGA|TCT	A|0.306;C|0.694	0.694	strong		0.562	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460	
RORB	6096	hgsc.bcm.edu	37	9	77245265	77245265	+	Silent	SNP	C	C	T	rs41307459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:77245265C>T	ENST00000396204.2	+	2	108	c.108C>T	c.(106-108)atC>atT	p.I36I	RORB_ENST00000376896.3_Silent_p.I25I			Q92753	RORB_HUMAN	RAR-related orphan receptor B	36					amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	ACGGAGTCATCACATGTGAAG	0.443													C|||	12	0.00239617	0.0	0.0014	5008	,	,		19502	0.0		0.0099	False		,,,				2504	0.001				p.I25I		Atlas-SNP	.											.	RORB	89	.	0			c.C75T						PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	164.0	134.0	144.0		75	5.3	1.0	9	dbSNP_127	144	53,8547	33.3+/-86.6	0,53,4247	no	coding-synonymous	RORB	NM_006914.3		0,60,6443	TT,TC,CC		0.6163,0.1589,0.4613		25/460	77245265	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	6096	exon2			AGTCATCACATGT	Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"""Nuclear hormone receptors"""	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.108C>T	9.37:g.77245265C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	135	51	0.377778	NM_006914	Q8WX73	Silent	SNP	ENST00000396204.2	37																																																																																				C|0.996;T|0.004	0.004	strong		0.443	RORB-201	KNOWN	basic	protein_coding	protein_coding			
SRM	6723	hgsc.bcm.edu	37	1	11114940	11114940	+	Silent	SNP	G	G	T	rs13616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11114940G>T	ENST00000376957.2	-	8	971	c.891C>A	c.(889-891)gcC>gcA	p.A297A		NM_003132.2	NP_003123.2	P19623	SPEE_HUMAN	spermidine synthase	297					cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)|spermidine synthase activity (GO:0004766)			large_intestine(1)|lung(1)|urinary_tract(1)	3	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)	STAD - Stomach adenocarcinoma(5;0.228)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)	S-Adenosylmethionine(DB00118)	CATCATTCAGGGCCTGGAGGG	0.716													G|||	840	0.167732	0.2481	0.1167	5008	,	,		10717	0.1806		0.0249	False		,,,				2504	0.229				p.A297A		Atlas-SNP	.											SRM,NS,carcinoma,0,1	SRM	18	1	0			c.C891A						PASS	.	G		913,3493	335.5+/-303.9	104,705,1394	32.0	35.0	34.0		891	2.2	1.0	1	dbSNP_52	34	195,8405	84.5+/-147.0	3,189,4108	no	coding-synonymous	SRM	NM_003132.2		107,894,5502	TT,TG,GG		2.2674,20.7217,8.5191		297/303	11114940	1108,11898	2203	4300	6503	SO:0001819	synonymous_variant	6723	exon8			ATTCAGGGCCTGG	BC033106	CCDS125.1	1p36-p22	2010-11-08			ENSG00000116649	ENSG00000116649	2.5.1.16		11296	protein-coding gene	gene with protein product		182891		SRML1		2344393	Standard	NM_003132		Approved	SPS1	uc001arz.1	P19623	OTTHUMG00000002119	ENST00000376957.2:c.891C>A	1.37:g.11114940G>T		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	186	96	0.516129	NM_003132	B1AKP9|Q15511	Silent	SNP	ENST00000376957.2	37	CCDS125.1																																																																																			G|0.906;T|0.094	0.094	strong		0.716	SRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006056.1	NM_003132	
WRN	7486	hgsc.bcm.edu	37	8	30954338	30954338	+	Silent	SNP	C	C	T	rs11574263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:30954338C>T	ENST00000298139.5	+	17	2202	c.1953C>T	c.(1951-1953)ggC>ggT	p.G651G		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	651	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		GTAACATGGGCCTGCTCCAGC	0.338			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				C|||	20	0.00399361	0.0144	0.0014	5008	,	,		16879	0.0		0.0	False		,,,				2504	0.0				p.G651G	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.C1953T						PASS	.	C		78,4328	67.0+/-104.6	2,74,2127	92.0	91.0	91.0		1953	2.1	0.0	8	dbSNP_120	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WRN	NM_000553.4		2,76,6425	TT,TC,CC		0.0233,1.7703,0.6151		651/1433	30954338	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	7486	exon17	Familial Cancer Database	WS, Adult Progeria	CATGGGCCTGCTC		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1953C>T	8.37:g.30954338C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	29	12	0.413793	NM_000553	A1KYY9	Silent	SNP	ENST00000298139.5	37	CCDS6082.1																																																																																			C|0.997;T|0.003	0.003	strong		0.338	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
NPL	80896	hgsc.bcm.edu	37	1	182787951	182787951	+	Silent	SNP	C	C	T	rs10911142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182787951C>T	ENST00000367553.1	+	9	654	c.610C>T	c.(610-612)Ctg>Ttg	p.L204L	NPL_ENST00000258317.2_Silent_p.L204L|NPL_ENST00000367555.1_Intron|NPL_ENST00000367552.2_Intron|NPL_ENST00000367554.3_Silent_p.L185L|NPL_ENST00000463899.1_3'UTR	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	204					carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)			breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						TGATTAGCAACTGTTGAGTGC	0.403													C|||	464	0.0926518	0.2723	0.036	5008	,	,		19954	0.0089		0.0119	False		,,,				2504	0.0593				p.L204L		Atlas-SNP	.											.	NPL	55	.	0			c.C610T						PASS	.	C	,,,,	1075,3331	383.7+/-325.0	138,799,1266	75.0	82.0	80.0		553,,610,610,610	4.6	1.0	1	dbSNP_120	80	79,8521	44.9+/-103.4	0,79,4221	no	coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	NPL	NM_001200050.1,NM_001200051.1,NM_001200052.1,NM_001200056.1,NM_030769.2	,,,,	138,878,5487	TT,TC,CC		0.9186,24.3985,8.8728	,,,,	185/302,,204/231,204/285,204/321	182787951	1154,11852	2203	4300	6503	SO:0001819	synonymous_variant	80896	exon10			TAGCAACTGTTGA	AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"""dihydrodipicolinate synthetase homolog 1 (E. coli)"""	611412	"""chromosome 1 open reading frame 13"""	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.610C>T	1.37:g.182787951C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	94	33	0.351064	NM_001200052	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Silent	SNP	ENST00000367553.1	37	CCDS1350.1	145	0.06639194139194139	124	0.25203252032520324	13	0.03591160220994475	2	0.0034965034965034965	6	0.0079155672823219	C	8.004	0.755994	0.15846	0.243985	0.009186	ENSG00000135838	ENST00000445965	.	.	.	5.48	4.57	0.56435	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.04281	-1.0963	4	0.36615	T	0.2	-15.183	12.0975	0.53763	0.0:0.9196:0.0:0.0804	rs10911142;rs59052567;rs10911142	.	.	.	I	119	.	ENSP00000414118:T119I	T	+	2	0	NPL	181054574	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	3.179000	0.50887	1.309000	0.44985	0.655000	0.94253	ACT	C|0.918;T|0.082	0.082	strong		0.403	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769	
EPB41L1	2036	hgsc.bcm.edu	37	20	34782156	34782156	+	Silent	SNP	G	G	A	rs111865221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34782156G>A	ENST00000338074.2	+	12	1484	c.1323G>A	c.(1321-1323)tcG>tcA	p.S441S	EPB41L1_ENST00000373941.1_Silent_p.S441S|EPB41L1_ENST00000441639.1_Silent_p.S379S|EPB41L1_ENST00000202028.5_Silent_p.S379S|EPB41L1_ENST00000373946.3_Silent_p.S410S|EPB41L1_ENST00000373950.2_Silent_p.S344S	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	441					cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					GCCCAGCCTCGGTCAGCGAGA	0.627													G|||	32	0.00638978	0.0234	0.0014	5008	,	,		20291	0.0		0.0	False		,,,				2504	0.0				p.S441S		Atlas-SNP	.											.	EPB41L1	111	.	0			c.G1323A						PASS	.	G	,	93,4313	77.8+/-116.1	2,89,2112	60.0	52.0	55.0		1323,1137	-10.4	0.0	20	dbSNP_132	55	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	EPB41L1	NM_012156.2,NM_177996.1	,	2,89,6412	AA,AG,GG		0.0,2.1108,0.7151	,	441/882,379/780	34782156	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	2036	exon13			AGCCTCGGTCAGC	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.1323G>A	20.37:g.34782156G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	170	77	0.452941	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Silent	SNP	ENST00000338074.2	37	CCDS13271.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	G	1.735	-0.493136	0.04322	0.021108	0.0	ENSG00000088367	ENST00000451082	.	.	.	5.18	-10.4	0.00318	.	.	.	.	.	T	0.16514	0.0397	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72204	-0.4361	4	.	.	.	.	1.9428	0.03350	0.0936:0.1922:0.346:0.3681	.	.	.	.	Q	19	.	.	R	+	2	0	EPB41L1	34245570	0.000000	0.05858	0.002000	0.10522	0.521000	0.34408	-9.217000	0.00013	-7.995000	0.00000	-3.875000	0.00017	CGG	G|0.991;A|0.009	0.009	strong		0.627	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156	
ATP8B2	57198	hgsc.bcm.edu	37	1	154320942	154320942	+	Silent	SNP	A	A	G	rs2297607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:154320942A>G	ENST00000368489.3	+	27	3321	c.3321A>G	c.(3319-3321)acA>acG	p.T1107T		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	1093					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGCTCACCACAGTCGTCTGCA	0.607													G|||	993	0.198283	0.2867	0.1499	5008	,	,		9793	0.126		0.2366	False		,,,				2504	0.1483				p.T1107T		Atlas-SNP	.											.	ATP8B2	158	.	0			c.A3321G						PASS	.	G		1100,3306	719.8+/-409.0	144,812,1247	92.0	76.0	81.0		3321	-9.1	0.3	1	dbSNP_100	81	1956,6644	724.7+/-406.5	242,1472,2586	no	coding-synonymous	ATP8B2	NM_020452.3		386,2284,3833	GG,GA,AA		22.7442,24.966,23.4968		1107/1224	154320942	3056,9950	2203	4300	6503	SO:0001819	synonymous_variant	57198	exon27			CACCACAGTCGTC	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"""ATPases / P-type"""	13534	protein-coding gene	gene with protein product		605867	"""ATPase, class I, type 8B, member 2"""			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.3321A>G	1.37:g.154320942A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Silent	SNP	ENST00000368489.3	37	CCDS1066.1																																																																																			G|0.226;N|0.000	0.226	strong		0.607	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452	
CENPE	1062	hgsc.bcm.edu	37	4	104102563	104102563	+	Silent	SNP	T	T	C	rs17217250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:104102563T>C	ENST00000265148.3	-	12	1103	c.1014A>G	c.(1012-1014)gtA>gtG	p.V338V	CENPE_ENST00000380026.3_Silent_p.V338V|CENPE_ENST00000509120.1_5'UTR	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	338					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.V338V(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CATCAGTTGATACCTCATTAA	0.294													T|||	599	0.119609	0.0552	0.1153	5008	,	,		14600	0.1419		0.2207	False		,,,				2504	0.0828				p.V338V		Atlas-SNP	.											CENPE,NS,carcinoma,0,1	CENPE	253	1	1	Substitution - coding silent(1)	stomach(1)	c.A1014G						PASS	.	T		250,4146	142.3+/-177.5	8,234,1956	62.0	62.0	62.0		1014	-3.2	1.0	4	dbSNP_123	62	1770,6810	313.0+/-311.1	193,1384,2713	no	coding-synonymous	CENPE	NM_001813.2		201,1618,4669	CC,CT,TT		20.6294,5.687,15.5672		338/2702	104102563	2020,10956	2198	4290	6488	SO:0001819	synonymous_variant	1062	exon12			AGTTGATACCTCA	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.1014A>G	4.37:g.104102563T>C		Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	344	168	0.488372	NM_001813	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	37	CCDS34042.1																																																																																			T|0.840;C|0.160	0.160	strong		0.294	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SPATA16	83893	hgsc.bcm.edu	37	3	172835290	172835290	+	Missense_Mutation	SNP	C	C	T	rs1515441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:172835290C>T	ENST00000351008.3	-	2	415	c.232G>A	c.(232-234)Gag>Aag	p.E78K		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	78			E -> K (in dbSNP:rs1515441). {ECO:0000269|PubMed:17665087}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			GCTGCTTTCTCTAAATCATTG	0.368													c|||	855	0.170727	0.0968	0.183	5008	,	,		22524	0.3095		0.0994	False		,,,				2504	0.1922				p.E78K		Atlas-SNP	.											SPATA16,NS,carcinoma,+2,1	SPATA16	111	1	0			c.G232A						PASS	.	G	LYS/GLU	454,3952	218.1+/-236.3	19,416,1768	375.0	351.0	359.0		232	4.4	1.0	3	dbSNP_88	359	1054,7546	223.1+/-260.0	66,922,3312	yes	missense	SPATA16	NM_031955.5	56	85,1338,5080	TT,TC,CC		12.2558,10.3041,11.5946	benign	78/570	172835290	1508,11498	2203	4300	6503	SO:0001583	missense	83893	exon2			CTTTCTCTAAATC	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.232G>A	3.37:g.172835290C>T	ENSP00000341765:p.Glu78Lys	Somatic	278	1	0.00359712		WXS	Illumina HiSeq	Phase_I	339	168	0.495575	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	37	CCDS3221.1	366	0.16758241758241757	42	0.08536585365853659	57	0.1574585635359116	198	0.34615384615384615	69	0.09102902374670185	c	15.01	2.705345	0.48412	0.103041	0.122558	ENSG00000144962	ENST00000351008	T	0.18657	2.2	5.27	4.4	0.53042	.	0.357463	0.23908	N	0.043374	T	0.00012	0.0000	N	0.24115	0.695	0.42855	P	0.005901999999999963	P	0.38504	0.634	B	0.33620	0.167	T	0.47611	-0.9104	9	0.52906	T	0.07	-12.1553	14.1264	0.65222	0.0:0.8498:0.1502:0.0	rs1515441;rs52836878;rs61569686;rs1515441	78	Q9BXB7	SPT16_HUMAN	K	78	ENSP00000341765:E78K	ENSP00000341765:E78K	E	-	1	0	SPATA16	174317984	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.559000	0.36320	1.227000	0.43598	-0.127000	0.14921	GAG	C|0.831;T|0.169	0.169	strong		0.368	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955	
RAD1	5810	hgsc.bcm.edu	37	5	34914829	34914829	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34914829T>C	ENST00000382038.2	-	2	1588	c.169A>G	c.(169-171)Aag>Gag	p.K57E	BRIX1_ENST00000336767.5_5'Flank|RAD1_ENST00000341754.4_Missense_Mutation_p.K57E	NM_002853.3	NP_002844.1	O60671	RAD1_HUMAN	RAD1 checkpoint DNA exonuclease	57					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|meiotic recombination checkpoint (GO:0051598)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|substantia nigra development (GO:0021762)	chromosome (GO:0005694)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|damaged DNA binding (GO:0003684)|exodeoxyribonuclease III activity (GO:0008853)			endometrium(3)|large_intestine(1)|lung(5)|urinary_tract(1)	10	all_lung(31;0.000107)	Lung NSC(810;5.19e-05)|Ovarian(839;0.0448)|Breast(839;0.198)	COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			TGCACACACTTTGCATTTTCC	0.383								Other conserved DNA damage response genes																													p.K57E		Atlas-SNP	.											RAD1,colon,carcinoma,+2,1	RAD1	17	1	0			c.A169G						scavenged	.						176.0	162.0	167.0					5																	34914829		2203	4300	6503	SO:0001583	missense	5810	exon2			CACACTTTGCATT	AF074717	CCDS3905.1	5p13	2014-08-08	2014-08-08		ENSG00000113456	ENSG00000113456	3.1.11.2		9806	protein-coding gene	gene with protein product	"""exonuclease homolog RAD1"", ""checkpoint control protein HRAD1"", ""cell cycle checkpoint protein Hrad1"", ""Rad1-like DNA damage checkpoint"", ""DNA repair exonuclease REC1"""	603153	"""RAD1 (S. pombe) homolog"", ""RAD1 homolog (S. pombe)"""			9716408, 9828137	Standard	NR_026591		Approved	HRAD1, REC1	uc003jix.3	O60671	OTTHUMG00000090783	ENST00000382038.2:c.169A>G	5.37:g.34914829T>C	ENSP00000371469:p.Lys57Glu	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	182	3	0.0164835	NM_002853	O75572|O95304|Q1W161|Q5KSM0|Q5KSM1|Q9UEP1	Missense_Mutation	SNP	ENST00000382038.2	37	CCDS3905.1	.	.	.	.	.	.	.	.	.	.	T	35	5.455151	0.96223	.	.	ENSG00000113456	ENST00000382038;ENST00000341754;ENST00000542494	T;T	0.17854	2.25;2.25	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.48943	0.1528	M	0.88906	2.99	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	T	0.58160	-0.7685	10	0.72032	D	0.01	.	16.0193	0.80468	0.0:0.0:0.0:1.0	.	57	O60671	RAD1_HUMAN	E	57	ENSP00000371469:K57E;ENSP00000340879:K57E	ENSP00000313467:K57E	K	-	1	0	RAD1	34950586	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	7.368000	0.79567	2.190000	0.69967	0.533000	0.62120	AAG	.	.	none		0.383	RAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207567.1	NM_002853	
CELSR1	9620	hgsc.bcm.edu	37	22	46932079	46932079	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46932079G>A	ENST00000262738.3	-	1	988	c.989C>T	c.(988-990)aCg>aTg	p.T330M	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Missense_Mutation_p.T330M	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	330	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)		GCGCGGCGGCGTACTGTAGTC	0.647																																					p.T330M		Atlas-SNP	.											.	CELSR1	242	.	0			c.C989T						PASS	.						116.0	95.0	102.0					22																	46932079		2201	4300	6501	SO:0001583	missense	9620	exon1			GGCGGCGTACTGT	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.989C>T	22.37:g.46932079G>A	ENSP00000262738:p.Thr330Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	G	3.466	-0.109044	0.06924	.	.	ENSG00000075275	ENST00000262738;ENST00000395964	T;T	0.01838	4.61;4.61	4.32	-0.683	0.11335	Cadherin (4);Cadherin-like (1);	0.310145	0.26203	U	0.025732	T	0.01800	0.0057	L	0.35854	1.095	0.09310	N	0.999999	P	0.34522	0.455	B	0.32805	0.153	T	0.48305	-0.9047	10	0.32370	T	0.25	.	6.6282	0.22841	0.1613:0.2739:0.5649:0.0	.	330	Q9NYQ6	CELR1_HUMAN	M	330	ENSP00000262738:T330M;ENSP00000379293:T330M	ENSP00000262738:T330M	T	-	2	0	CELSR1	45310743	0.376000	0.25098	0.741000	0.31004	0.009000	0.06853	3.037000	0.49775	-0.001000	0.14495	-0.391000	0.06502	ACG	.	.	none		0.647	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
ZNF577	84765	hgsc.bcm.edu	37	19	52376448	52376448	+	Silent	SNP	A	A	G	rs9807843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52376448A>G	ENST00000301399.5	-	7	1160	c.795T>C	c.(793-795)acT>acC	p.T265T	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Silent_p.T206T|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000451628.2_Silent_p.T206T	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GTTTCTCTCCAGTATGTGATC	0.488													A|||	854	0.170527	0.295	0.1427	5008	,	,		20808	0.0427		0.0358	False		,,,				2504	0.2924				p.T265T		Atlas-SNP	.											.	ZNF577	63	.	0			c.T795C						PASS	.	A	,	1178,3228		167,844,1192	62.0	58.0	59.0		618,795	-0.4	0.1	19	dbSNP_119	59	165,8435		1,163,4136	no	coding-synonymous,coding-synonymous	ZNF577	NM_001135590.1,NM_032679.2	,	168,1007,5328	GG,GA,AA		1.9186,26.7363,10.326	,	206/427,265/486	52376448	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	84765	exon7			CTCTCCAGTATGT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.795T>C	19.37:g.52376448A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	91	34	0.373626	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			A|0.899;G|0.101	0.101	strong		0.488	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
KIAA1407	57577	hgsc.bcm.edu	37	3	113699599	113699599	+	Missense_Mutation	SNP	C	C	G	rs35546981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113699599C>G	ENST00000295878.3	-	14	2351	c.2205G>C	c.(2203-2205)caG>caC	p.Q735H	KIAA1407_ENST00000545063.1_3'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	735										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						TTGCTTCCAGCTGCTGGTTCC	0.363													C|||	5	0.000998403	0.003	0.0014	5008	,	,		18688	0.0		0.0	False		,,,				2504	0.0				p.Q735H		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G2205C						PASS	.	C	HIS/GLN	32,4374	37.6+/-69.7	0,32,2171	170.0	161.0	164.0		2205	3.8	1.0	3	dbSNP_126	164	0,8600		0,0,4300	yes	missense	KIAA1407	NM_020817.1	24	0,32,6471	GG,GC,CC		0.0,0.7263,0.246	probably-damaging	735/937	113699599	32,12974	2203	4300	6503	SO:0001583	missense	57577	exon14			TTCCAGCTGCTGG	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2205G>C	3.37:g.113699599C>G	ENSP00000295878:p.Gln735His	Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	266	121	0.454887	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	37	CCDS2977.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	C	17.30	3.354777	0.61293	0.007263	0.0	ENSG00000163617	ENST00000295878	T	0.33216	1.42	5.57	3.75	0.43078	.	0.298923	0.36932	N	0.002326	T	0.24160	0.0585	L	0.59436	1.845	0.80722	D	1	B	0.21071	0.051	B	0.21917	0.037	T	0.07693	-1.0759	10	0.56958	D	0.05	.	12.7141	0.57105	0.2994:0.7006:0.0:0.0	rs35546981	735	Q8NCU4	K1407_HUMAN	H	735	ENSP00000295878:Q735H	ENSP00000295878:Q735H	Q	-	3	2	KIAA1407	115182289	0.988000	0.35896	1.000000	0.80357	0.940000	0.58332	0.569000	0.23638	0.797000	0.33971	0.591000	0.81541	CAG	C|0.997;G|0.003	0.003	strong		0.363	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
LILRB3	11025	hgsc.bcm.edu	37	19	54721090	54721090	+	Missense_Mutation	SNP	A	A	G	rs141841040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54721090A>G	ENST00000391750.1	-	14	1904	c.1768T>C	c.(1768-1770)Tcc>Ccc	p.S590P	LILRB3_ENST00000245620.9_Missense_Mutation_p.S591P|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.S607P|LILRB3_ENST00000346401.6_Missense_Mutation_p.S602P|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000440558.2_Missense_Mutation_p.S590P|LILRA6_ENST00000270464.5_Missense_Mutation_p.S591P|LILRA6_ENST00000419410.2_Missense_Mutation_p.S591P|LILRB3_ENST00000424807.1_Missense_Mutation_p.S590P			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	590					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.S590P(4)		endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACATCCTGGGAGGCTTCAGAT	0.637													.|||	94	0.01877	0.0446	0.0029	5008	,	,		16037	0.0179		0.001	False		,,,				2504	0.0143				p.S591P		Atlas-SNP	.											LILRB3,NS,carcinoma,0,4	LILRB3	67	4	4	Substitution - Missense(4)	prostate(3)|stomach(1)	c.T1771C						scavenged	.	G	PRO/SER,PRO/SER	94,4312		6,82,2115	81.0	85.0	84.0		1771,1768	-0.7	0.1	19	dbSNP_134	84	3,8597		0,3,4297	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	74,74	6,85,6412	GG,GA,AA		0.0349,2.1335,0.7458	benign,benign	591/633,590/632	54721090	97,12909	2203	4300	6503	SO:0001583	missense	11025	exon13			CCTGGGAGGCTTC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1768T>C	19.37:g.54721090A>G	ENSP00000375630:p.Ser590Pro	Somatic	407	16	0.039312		WXS	Illumina HiSeq	Phase_I	395	16	0.0405063	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	21	0.009615384615384616	10	0.02032520325203252	1	0.0027624309392265192	10	0.017482517482517484	0	0.0	a	0.017	-1.509272	0.00984	0.021335	3.49E-4	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00462	7.39;7.39;7.3;7.37;7.26;7.39;7.39;7.4	3.13	-0.713	0.11223	.	.	.	.	.	T	0.00039	0.0001	N	0.00138	-2.015	0.23519	N	0.997507	B;B;B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.08055	0.001;0.002;0.0;0.001;0.003;0.001;0.001	T	0.38520	-0.9657	9	0.02654	T	1	.	2.8979	0.05696	0.2298:0.0:0.3986:0.3716	.	607;590;591;602;607;590;591	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	P	590;590;602;591;607;590;591;591	ENSP00000375630:S590P;ENSP00000412771:S590P;ENSP00000345184:S602P;ENSP00000245620:S591P;ENSP00000384274:S607P;ENSP00000390120:S590P;ENSP00000270464:S591P;ENSP00000411227:S591P	ENSP00000270464:S591P	S	-	1	0	LILRB3;LILRA6	59412902	0.006000	0.16342	0.050000	0.19076	0.117000	0.20001	-0.196000	0.09532	-0.237000	0.09739	-0.368000	0.07277	TCC	A|0.988;G|0.012	0.012	strong		0.637	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
NMI	9111	hgsc.bcm.edu	37	2	152138522	152138522	+	Silent	SNP	T	T	C	rs3771886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152138522T>C	ENST00000243346.5	-	3	587	c.117A>G	c.(115-117)caA>caG	p.Q39Q		NM_004688.2	NP_004679.2	Q13287	NMI_HUMAN	N-myc (and STAT) interactor	39					inflammatory response (GO:0006954)|JAK-STAT cascade (GO:0007259)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription cofactor activity (GO:0003712)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.0571)		CCTTCTTTAGTTGAATATTTT	0.313													T|||	2783	0.555711	0.646	0.6297	5008	,	,		15950	0.4365		0.5577	False		,,,				2504	0.502				p.Q39Q		Atlas-SNP	.											.	NMI	21	.	0			c.A117G						PASS	.	T		2790,1614	656.1+/-400.0	886,1018,298	82.0	83.0	83.0		117	-5.1	0.0	2	dbSNP_107	83	4968,3624	620.6+/-397.1	1429,2110,757	no	coding-synonymous	NMI	NM_004688.2		2315,3128,1055	CC,CT,TT		42.1788,36.6485,40.3047		39/308	152138522	7758,5238	2202	4296	6498	SO:0001819	synonymous_variant	9111	exon3			CTTTAGTTGAATA	U32849	CCDS2192.1	2q23	2008-05-23			ENSG00000123609	ENSG00000123609			7854	protein-coding gene	gene with protein product		603525				8668343, 9989503	Standard	NM_004688		Approved		uc002txi.2	Q13287	OTTHUMG00000131867	ENST00000243346.5:c.117A>G	2.37:g.152138522T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	106	63	0.59434	NM_004688	B5BU69|Q53TI8|Q9BVE5	Silent	SNP	ENST00000243346.5	37	CCDS2192.1																																																																																			T|0.430;C|0.570	0.570	strong		0.313	NMI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254817.2	NM_004688	
NRAP	4892	hgsc.bcm.edu	37	10	115411598	115411598	+	Silent	SNP	C	C	A	rs4918861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115411598C>A	ENST00000359988.3	-	7	883	c.639G>T	c.(637-639)ctG>ctT	p.L213L	NRAP_ENST00000369360.3_Silent_p.L213L|NRAP_ENST00000369358.4_Silent_p.L213L|NRAP_ENST00000360478.3_Silent_p.L213L	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TGCTCCGTAGCAGCTCAGGAG	0.522													C|||	1325	0.264577	0.3306	0.2248	5008	,	,		20859	0.2163		0.2684	False		,,,				2504	0.2495				p.L213L		Atlas-SNP	.											.	NRAP	208	.	0			c.G639T						PASS	.	C	,	1511,2895	482.8+/-359.5	263,985,955	105.0	81.0	89.0		639,639	2.9	1.0	10	dbSNP_111	89	2389,6211	397.4+/-345.7	335,1719,2246	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	598,2704,3201	AA,AC,CC		27.7791,34.2941,29.9862	,	213/1696,213/1731	115411598	3900,9106	2203	4300	6503	SO:0001819	synonymous_variant	4892	exon7			CCGTAGCAGCTCA		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.639G>T	10.37:g.115411598C>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			C|0.712;A|0.288	0.288	strong		0.522	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
OR2L8	391190	hgsc.bcm.edu	37	1	248112754	248112754	+	Missense_Mutation	SNP	T	T	C	rs201126494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248112754T>C	ENST00000357191.3	+	1	595	c.595T>C	c.(595-597)Ttt>Ctt	p.F199L	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			GGGCACAGTGTTTTTGAGTGC	0.483																																					p.F199L		Atlas-SNP	.											.	OR2L8	92	.	0			c.T595C						PASS	.						145.0	45.0	79.0					1																	248112754		2203	4297	6500	SO:0001583	missense	391190	exon1			ACAGTGTTTTTGA	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"""GPCR / Class A : Olfactory receptors"""	15014	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily L, member 8"""				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.595T>C	1.37:g.248112754T>C	ENSP00000349719:p.Phe199Leu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	344	46	0.133721	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	37	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	7.762	0.705616	0.15172	.	.	ENSG00000196936	ENST00000357191	T	0.00042	8.84	1.79	0.313	0.15842	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33732	U	0.004607	T	0.00144	0.0004	N	0.13235	0.315	0.09310	N	1	D	0.58970	0.984	P	0.59948	0.866	T	0.52230	-0.8603	10	0.51188	T	0.08	.	2.0669	0.03605	0.463:0.2458:0.0:0.2912	.	199	Q8NGY9	OR2L8_HUMAN	L	199	ENSP00000349719:F199L	ENSP00000349719:F199L	F	+	1	0	OR2L8	246179377	0.000000	0.05858	0.788000	0.31933	0.689000	0.40095	-0.139000	0.10358	0.833000	0.34828	0.392000	0.25879	TTT	T|0.945;C|0.055	0.055	strong		0.483	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2		
WDR27	253769	hgsc.bcm.edu	37	6	170038674	170038674	+	Silent	SNP	T	T	C	rs115828649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170038674T>C	ENST00000448612.1	-	18	1939	c.1830A>G	c.(1828-1830)cgA>cgG	p.R610R	WDR27_ENST00000333572.6_Silent_p.R610R|WDR27_ENST00000423258.1_Silent_p.R483R|WDR27_ENST00000546525.1_5'UTR	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	580						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		CCGACCACATTCGCAGGGTCC	0.602													c|||	140	0.0279553	0.0817	0.0259	5008	,	,		14584	0.005		0.005	False		,,,				2504	0.0041				p.R610R		Atlas-SNP	.											.	WDR27	129	.	0			c.A1830G						PASS	.	C	,	320,3712		12,296,1708	18.0	21.0	20.0		1449,1830	2.5	0.0	6	dbSNP_132	20	35,8287		0,35,4126	no	coding-synonymous,coding-synonymous	WDR27	NM_001202550.1,NM_182552.4	,	12,331,5834	CC,CT,TT		0.4206,7.9365,2.8736	,	483/731,610/896	170038674	355,11999	2016	4161	6177	SO:0001819	synonymous_variant	253769	exon18			CCACATTCGCAGG	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"""WD repeat domain containing"""	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.1830A>G	6.37:g.170038674T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_182552	A5PLM8|C9JGV0|Q5T066	Silent	SNP	ENST00000448612.1	37	CCDS47520.2																																																																																			T|0.959;C|0.041	0.041	strong		0.602	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552	
TTYH2	94015	hgsc.bcm.edu	37	17	72248482	72248482	+	Missense_Mutation	SNP	C	C	A	rs9892705|rs386799126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72248482C>A	ENST00000269346.4	+	11	1300	c.1226C>A	c.(1225-1227)gCa>gAa	p.A409E	TTYH2_ENST00000529107.1_Missense_Mutation_p.A388E|TTYH2_ENST00000441391.2_Missense_Mutation_p.A88E	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	409			A -> E (in dbSNP:rs9892705).			chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						ATGATCTGTGCAGGGCCAAGG	0.637													C|||	295	0.0589058	0.0855	0.0187	5008	,	,		18201	0.0139		0.0268	False		,,,				2504	0.1309				p.A409E		Atlas-SNP	.											TTYH2,NS,carcinoma,-1,1	TTYH2	63	1	0			c.C1226A						PASS	.																																			SO:0001583	missense	94015	exon11			TCTGTGCAGGGCC		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.1226C>A	17.37:g.72248482C>A	ENSP00000269346:p.Ala409Glu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	72	0.03296703296703297	45	0.09146341463414634	5	0.013812154696132596	8	0.013986013986013986	14	0.018469656992084433	C	13.77	2.334926	0.41297	.	.	ENSG00000141540	ENST00000269346;ENST00000529107;ENST00000441391	T;T;T	0.12672	2.66;2.66;2.66	5.79	-0.188	0.13264	.	0.267026	0.42172	D	0.000749	T	0.01061	0.0035	M	0.75447	2.3	0.20873	N	0.999837	D;P	0.61080	0.989;0.933	P;P	0.61940	0.896;0.799	T	0.01130	-1.1442	10	0.87932	D	0	-1.7086	10.0355	0.42127	0.0:0.616:0.0:0.384	rs9892705;rs9892705	388;409	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	E	409;388;88	ENSP00000269346:A409E;ENSP00000433089:A388E;ENSP00000394576:A88E	ENSP00000269346:A409E	A	+	2	0	TTYH2	69760077	0.001000	0.12720	0.000000	0.03702	0.081000	0.17604	0.353000	0.20130	-0.213000	0.10094	-0.748000	0.03510	GCA	C|0.959;A|0.041	0.041	strong		0.637	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
MUC17	140453	hgsc.bcm.edu	37	7	100677409	100677409	+	Silent	SNP	G	G	A	rs150735476	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	106	0	0		WXS	Illumina HiSeq	Phase_I	159	34	0.213836	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	
ST8SIA3	51046	hgsc.bcm.edu	37	18	55027334	55027334	+	Silent	SNP	G	G	T	rs112792874|rs1153626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:55027334G>T	ENST00000324000.3	+	4	3003	c.969G>T	c.(967-969)ccG>ccT	p.P323P		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	323					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|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)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		GATTTTGGCCGTTTGGATTTG	0.433																																					p.P323P		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.G969T						PASS	.	T		1710,2696	652.4+/-399.4	333,1044,826	129.0	117.0	121.0		969	3.5	1.0	18	dbSNP_87	121	1344,7256	756.2+/-407.5	98,1148,3054	no	coding-synonymous	ST8SIA3	NM_015879.2		431,2192,3880	TT,TG,GG		15.6279,38.8107,23.4815		323/381	55027334	3054,9952	2203	4300	6503	SO:0001819	synonymous_variant	51046	exon4			TTGGCCGTTTGGA	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"""Sialyltransferases"""	14269	protein-coding gene	gene with protein product	"""ST8Sia III"""	609478	"""sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"""	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.969G>T	18.37:g.55027334G>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	183	82	0.448087	NM_015879	A8K0F2|Q6B085|Q9NS41	Silent	SNP	ENST00000324000.3	37	CCDS32834.1																																																																																			T|0.282;G|0.718;A|0.000	0.282	strong		0.433	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879	
DMD	1756	hgsc.bcm.edu	37	X	31496426	31496426	+	Missense_Mutation	SNP	T	T	C	rs1800278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:31496426T>C	ENST00000357033.4	-	59	8940	c.8734A>G	c.(8734-8736)Aat>Gat	p.N2912D	DMD_ENST00000378707.3_Missense_Mutation_p.N452D|DMD_ENST00000541735.1_Missense_Mutation_p.N452D|DMD_ENST00000378677.2_Missense_Mutation_p.N2908D|DMD_ENST00000445312.1_5'Flank|DMD_ENST00000343523.2_Missense_Mutation_p.N452D|DMD_ENST00000474231.1_Missense_Mutation_p.N452D|DMD_ENST00000359836.1_Missense_Mutation_p.N452D	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	2912			N -> D (in dbSNP:rs1800278). {ECO:0000269|PubMed:12359139}.		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)				CACTCAGTATTGACCTCCTCA	0.493													T|||	140	0.0370861	0.0628	0.0202	3775	,	,		13854	0.0308		0.0099	False		,,,				2504	0.002				p.N2912D		Atlas-SNP	.											.	DMD	2127	.	0			c.A8734G	GRCh37	CM940361	DMD	M	rs1800278	PASS	.	T	ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN	276,3557		9,216,42,1406,529	72.0	68.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	8710,8734,8365,8722,8365,4711,4702,1354,547,1354,1354,1354,1354	1.7	1.0	X	dbSNP_89	69	57,6671		0,39,18,2389,1854	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3,NM_004011.3,NM_004012.3,NM_004013.2,NM_004014.2,NM_004020.3,NM_004021.2,NM_004022.2,NM_004023.2	23,23,23,23,23,23,23,23,23,23,23,23,23	9,255,60,3795,2383	CC,CT,C,TT,T		0.8472,7.2006,3.1531	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	2904/3678,2912/3686,2789/3563,2908/3682,2789/3563,1571/2345,1568/2342,452/1226,183/957,452/1116,452/1244,452/1231,452/1134	31496426	333,10228	2202	4300	6502	SO:0001583	missense	1756	exon59			CAGTATTGACCTC	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.8734A>G	X.37:g.31496426T>C	ENSP00000354923:p.Asn2912Asp	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	210	95	0.452381	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	65|65	0.03918022905364678|0.03918022905364678	23|23	0.04852320675105485|0.04852320675105485	6|6	0.016853932584269662|0.016853932584269662	9|9	0.01601423487544484|0.01601423487544484	8|8	0.010610079575596816|0.010610079575596816	T|T	12.09|12.09	1.833296|1.833296	0.32421|0.32421	0.072006|0.072006	0.008472|0.008472	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231|ENST00000465285	T;T;T;T;T;T;T;T|.	0.36520|.	1.25;1.25;1.25;1.25;1.25;1.25;1.25;1.25|.	5.4|5.4	1.66|1.66	0.24008|0.24008	.|.	0.359998|.	0.19479|.	U|.	0.113242|.	T|T	0.01189|0.01189	0.0039|0.0039	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	P|P	5.000000000032756E-6|5.000000000032756E-6	B;B;B;B;B;B;B;B;B;B;B|.	0.30482|.	0.281;0.081;0.0;0.081;0.081;0.007;0.019;0.019;0.167;0.257;0.101|.	B;B;B;B;B;B;B;B;B;B;B|.	0.43701|.	0.428;0.021;0.0;0.014;0.014;0.026;0.012;0.012;0.045;0.074;0.122|.	T|T	0.17137|0.17137	-1.0379|-1.0379	9|4	0.33141|.	T|.	0.24|.	.|.	1.6458|1.6458	0.02761|0.02761	0.139:0.1519:0.1415:0.5676|0.139:0.1519:0.1415:0.5676	rs1800278;rs17340811;rs1800278|rs1800278;rs17340811;rs1800278	2904;2912;2908;1571;1568;452;452;452;452;452;2789|.	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3|.	.;DMD_HUMAN;.;.;.;.;.;.;.;.;.|.	D|R	2904;1571;1568;608;2908;2912;452;452;2912;2789;452;452;452|640	ENSP00000350765:N608D;ENSP00000367948:N2908D;ENSP00000354923:N2912D;ENSP00000352894:N452D;ENSP00000340057:N452D;ENSP00000367979:N452D;ENSP00000444119:N452D;ENSP00000417123:N452D|.	ENSP00000340057:N452D|.	N|Q	-|-	1|2	0|0	DMD|DMD	31406347|31406347	0.025000|0.025000	0.19082|0.19082	0.980000|0.980000	0.43619|0.43619	0.997000|0.997000	0.91878|0.91878	0.508000|0.508000	0.22692|0.22692	0.276000|0.276000	0.22118|0.22118	0.430000|0.430000	0.28490|0.28490	AAT|CAA	T|0.963;0|0.002	.	strong		0.493	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
CFAP57	149465	hgsc.bcm.edu	37	1	43638436	43638436	+	Silent	SNP	G	G	T	rs6695238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43638436G>T	ENST00000372492.4	+	2	336	c.12G>T	c.(10-12)gtG>gtT	p.V4V	EBNA1BP2_ENST00000431635.2_5'Flank|EBNA1BP2_ENST00000236051.2_5'Flank|WDR65_ENST00000528956.1_Silent_p.V4V|EBNA1BP2_ENST00000472982.1_5'Flank	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		4										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGTCAGCCGTGGTAGCTCAGA	0.547													G|||	341	0.0680911	0.1899	0.0576	5008	,	,		10442	0.001		0.0368	False		,,,				2504	0.0123				p.V4V		Atlas-SNP	.											.	WDR65	76	.	0			c.G12T						PASS	.	G	,,	714,3692	295.6+/-283.7	65,584,1554	116.0	104.0	108.0		12,12,12	2.1	1.0	1	dbSNP_116	108	354,8246	119.5+/-178.9	6,342,3952	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	71,926,5506	TT,TG,GG		4.1163,16.2052,8.2116	,,	4/699,4/699,4/699	43638436	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon2			AGCCGTGGTAGCT																												ENST00000372492.4:c.12G>T	1.37:g.43638436G>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				G|0.920;T|0.080	0.080	strong		0.547	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
OR10Z1	128368	hgsc.bcm.edu	37	1	158576472	158576472	+	Missense_Mutation	SNP	C	C	T	rs76424590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158576472C>T	ENST00000361284.1	+	1	244	c.244C>T	c.(244-246)Ctc>Ttc	p.L82F		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	82						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)					CCCTAGAATGCTCTCTGGCCT	0.542													C|||	190	0.0379393	0.1377	0.0086	5008	,	,		20262	0.0		0.002	False		,,,				2504	0.0				p.L82F		Atlas-SNP	.											OR10Z1,NS,carcinoma,-2,1	OR10Z1	99	1	0			c.C244T						PASS	.	C	PHE/LEU	525,3881	238.7+/-250.0	33,459,1711	203.0	209.0	207.0		244	5.4	1.0	1	dbSNP_131	207	12,8588	9.1+/-34.3	0,12,4288	yes	missense	OR10Z1	NM_001004478.1	22	33,471,5999	TT,TC,CC		0.1395,11.9156,4.1289	probably-damaging	82/314	158576472	537,12469	2203	4300	6503	SO:0001583	missense	128368	exon1			AGAATGCTCTCTG	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.244C>T	1.37:g.158576472C>T	ENSP00000354707:p.Leu82Phe	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	210	93	0.442857	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	68	0.031135531135531136	66	0.13414634146341464	2	0.0055248618784530384	0	0.0	0	0.0	C	17.17	3.321840	0.60634	0.119156	0.001395	ENSG00000198967	ENST00000361284	T	0.00419	7.48	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36778	N	0.002405	T	0.01222	0.0040	H	0.97077	3.935	0.26251	P	0.97873	D	0.89917	1.0	D	0.80764	0.994	T	0.03296	-1.1051	9	0.87932	D	0	.	13.5532	0.61745	0.1563:0.8437:0.0:0.0	.	82	Q8NGY1	O10Z1_HUMAN	F	82	ENSP00000354707:L82F	ENSP00000354707:L82F	L	+	1	0	OR10Z1	156843096	0.996000	0.38824	0.997000	0.53966	0.647000	0.38526	1.184000	0.32053	2.783000	0.95769	0.655000	0.94253	CTC	C|0.962;T|0.038	0.038	strong		0.542	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478	
RALGDS	5900	hgsc.bcm.edu	37	9	135974054	135974054	+	Missense_Mutation	SNP	C	C	T	rs143209866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135974054C>T	ENST00000372050.3	-	18	2686	c.2665G>A	c.(2665-2667)Gtg>Atg	p.V889M	RALGDS_ENST00000393157.3_Missense_Mutation_p.V888M|RALGDS_ENST00000542690.1_Missense_Mutation_p.V960M|RALGDS_ENST00000372062.3_Missense_Mutation_p.V860M|RALGDS_ENST00000393160.3_Missense_Mutation_p.V834M|RALGDS_ENST00000372047.3_Missense_Mutation_p.V877M|RALGDS_ENST00000469972.1_5'UTR	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	889					neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		TTGACCTTCACTCCCTTGGTG	0.542			T	CIITA	"""PMBL, Hodgkin Lymphona, """								C|||	4	0.000798722	0.003	0.0	5008	,	,		21550	0.0		0.0	False		,,,				2504	0.0				p.V889M	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.G2665A						PASS	.	C	MET/VAL,MET/VAL	19,4387	26.2+/-53.5	0,19,2184	116.0	93.0	100.0		2500,2665	2.5	0.8	9	dbSNP_134	100	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	RALGDS	NM_001042368.1,NM_006266.2	21,21	0,20,6483	TT,TC,CC		0.0116,0.4312,0.1538	possibly-damaging,possibly-damaging	834/860,889/915	135974054	20,12986	2203	4300	6503	SO:0001583	missense	5900	exon18			CCTTCACTCCCTT	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.2665G>A	9.37:g.135974054C>T	ENSP00000361120:p.Val889Met	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	189	65	0.343915	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Missense_Mutation	SNP	ENST00000372050.3	37	CCDS6959.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	10.20	1.285630	0.23478	0.004312	1.16E-4	ENSG00000160271	ENST00000372050;ENST00000372047;ENST00000393160;ENST00000393157;ENST00000542690;ENST00000372062	T;T;T;T;T;T	0.40476	1.52;1.04;1.52;1.5;1.68;1.03	5.37	2.55	0.30701	.	0.458064	0.20879	N	0.084033	T	0.34716	0.0907	L	0.46157	1.445	0.19945	N	0.999946	B;P;P;P;P;B	0.51240	0.349;0.943;0.694;0.758;0.943;0.35	B;B;B;B;B;B	0.41271	0.057;0.352;0.295;0.173;0.352;0.077	T	0.18053	-1.0349	10	0.72032	D	0.01	.	9.9724	0.41763	0.0:0.7793:0.0:0.2207	.	960;860;834;888;877;889	F5H6M6;E7ER93;Q6KH11;E7ERZ0;Q6PCE1;Q12967	.;.;.;.;.;GNDS_HUMAN	M	889;877;834;888;960;860	ENSP00000361120:V889M;ENSP00000361117:V877M;ENSP00000376867:V834M;ENSP00000376864:V888M;ENSP00000437518:V960M;ENSP00000361132:V860M	ENSP00000361117:V877M	V	-	1	0	RALGDS	134963875	0.000000	0.05858	0.797000	0.32132	0.292000	0.27327	0.038000	0.13862	0.259000	0.21709	0.561000	0.74099	GTG	C|0.998;T|0.002	0.002	strong		0.542	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
ATP6V0D2	245972	hgsc.bcm.edu	37	8	87162515	87162515	+	Missense_Mutation	SNP	G	G	A	rs10094744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87162515G>A	ENST00000285393.3	+	6	956	c.814G>A	c.(814-816)Gga>Aga	p.G272R	CTD-3118D11.2_ENST00000522679.1_RNA	NM_152565.1	NP_689778.1	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2	272			G -> R (in dbSNP:rs10094744).		ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen ion transmembrane transporter activity (GO:0015078)			breast(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|prostate(1)	27						GGATCATTACGGAGTATGTGA	0.453													G|||	152	0.0303514	0.1089	0.0115	5008	,	,		18274	0.0		0.0	False		,,,				2504	0.0				p.G272R		Atlas-SNP	.											.	ATP6V0D2	61	.	0			c.G814A						PASS	.	G	ARG/GLY	421,3985	204.5+/-226.7	19,383,1801	100.0	90.0	94.0		814	5.3	0.1	8	dbSNP_119	94	5,8595	4.3+/-15.6	0,5,4295	yes	missense	ATP6V0D2	NM_152565.1	125	19,388,6096	AA,AG,GG		0.0581,9.5552,3.2754	benign	272/351	87162515	426,12580	2203	4300	6503	SO:0001583	missense	245972	exon6			CATTACGGAGTAT	AY079172	CCDS6241.1	8q21.3	2014-01-28	2006-01-20	2002-05-24	ENSG00000147614	ENSG00000147614		"""ATPases / V-type"""	18266	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 38kD, V0 subunit d isoform 2"", ""ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 2"", ""ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D2"""			12384298	Standard	NM_152565		Approved	FLJ38708, VMA6, ATP6D2	uc003ydp.1	Q8N8Y2	OTTHUMG00000163637	ENST00000285393.3:c.814G>A	8.37:g.87162515G>A	ENSP00000285393:p.Gly272Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_152565		Missense_Mutation	SNP	ENST00000285393.3	37	CCDS6241.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	G	14.33	2.504335	0.44558	0.095552	5.81E-4	ENSG00000147614	ENST00000285393	T	0.29917	1.55	6.17	5.27	0.74061	.	0.585174	0.17628	N	0.167492	T	0.00724	0.0024	L	0.48642	1.525	0.23689	N	0.997107	D	0.53462	0.96	B	0.38194	0.267	T	0.01940	-1.1243	10	0.40728	T	0.16	-22.0686	16.0952	0.81114	0.0:0.0:0.8659:0.1341	rs10094744;rs52810720;rs10094744	272	Q8N8Y2	VA0D2_HUMAN	R	272	ENSP00000285393:G272R	ENSP00000285393:G272R	G	+	1	0	ATP6V0D2	87231631	0.153000	0.22777	0.096000	0.21009	0.040000	0.13550	3.075000	0.50073	2.941000	0.99782	0.655000	0.94253	GGA	G|0.970;A|0.030	0.030	strong		0.453	ATP6V0D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374651.1	NM_152565	
C11orf44	283171	hgsc.bcm.edu	37	11	130542882	130542882	+	Silent	SNP	C	C	T	rs7933829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:130542882C>T	ENST00000317019.2	+	1	32	c.9C>T	c.(7-9)ctC>ctT	p.L3L		NM_001271983.1	NP_001258912.1	Q8N8P7	CK044_HUMAN	chromosome 11 open reading frame 44	3						extracellular region (GO:0005576)				central_nervous_system(1)	1						ACATGGTCCTCCTCTGTCTCT	0.587													C|||	1310	0.261581	0.3638	0.1988	5008	,	,		15454	0.3274		0.1928	False		,,,				2504	0.1708				p.L3L		Atlas-SNP	.											.	C11orf44	6	.	0			c.C9T						PASS	.	C		478,906		83,312,297	62.0	55.0	57.0			1.0	0.0	11	dbSNP_116	57	708,2474		89,530,972	no	intergenic				172,842,1269	TT,TC,CC		22.2502,34.5376,25.9746			130542882	1186,3380	692	1591	2283	SO:0001819	synonymous_variant	283171	exon1			GGTCCTCCTCTGT	AK096377	CCDS8489.1	11q24.3	2005-10-27			ENSG00000175728	ENSG00000175728			26805	protein-coding gene	gene with protein product							Standard	NM_001271983		Approved	FLJ39058	uc031qfg.1	Q8N8P7	OTTHUMG00000150705	ENST00000317019.2:c.9C>T	11.37:g.130542882C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	125	46	0.368	NM_001271983		Silent	SNP	ENST00000317019.2	37																																																																																				C|0.739;T|0.261	0.261	strong		0.587	C11orf44-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000319680.1	NM_173580	
ZP4	57829	hgsc.bcm.edu	37	1	238046056	238046056	+	Missense_Mutation	SNP	G	G	A	rs35187146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:238046056G>A	ENST00000366570.4	-	11	1639	c.1481C>T	c.(1480-1482)cCt>cTt	p.P494L	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	494					acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CTTTTCTGGAGGGTCCTTAGT	0.418													G|||	98	0.0195687	0.0681	0.0101	5008	,	,		18510	0.0		0.001	False		,,,				2504	0.0				p.P494L	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.C1481T						PASS	.	G	LEU/PRO	232,4174	136.1+/-172.1	4,224,1975	113.0	113.0	113.0		1481	3.3	0.0	1	dbSNP_126	113	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZP4	NM_021186.3	98	4,225,6274	AA,AG,GG		0.0116,5.2655,1.7915	benign	494/541	238046056	233,12773	2203	4300	6503	SO:0001583	missense	57829	exon11			TCTGGAGGGTCCT	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.1481C>T	1.37:g.238046056G>A	ENSP00000355529:p.Pro494Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	13.86	2.362971	0.41902	0.052655	1.16E-4	ENSG00000116996	ENST00000366570	T	0.75154	-0.91	4.2	3.29	0.37713	.	1.113200	0.06962	N	0.816574	T	0.11750	0.0286	L	0.38175	1.15	0.09310	N	1	B	0.18741	0.03	B	0.12837	0.008	T	0.13737	-1.0498	10	0.11485	T	0.65	-6.9559	8.323	0.32140	0.1076:0.0:0.8924:0.0	rs35187146	494	Q12836	ZP4_HUMAN	L	494	ENSP00000355529:P494L	ENSP00000355529:P494L	P	-	2	0	ZP4	236112679	0.088000	0.21588	0.002000	0.10522	0.836000	0.47400	2.346000	0.44027	1.146000	0.42352	-0.126000	0.14955	CCT	G|0.985;A|0.015	0.015	strong		0.418	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
CES5A	221223	hgsc.bcm.edu	37	16	55883667	55883667	+	Missense_Mutation	SNP	T	T	C	rs545527146		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:55883667T>C	ENST00000290567.9	-	11	1413	c.1292A>G	c.(1291-1293)tAc>tGc	p.Y431C	CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000518005.1_Missense_Mutation_p.Y325C|CES5A_ENST00000319165.9_Intron|CES5A_ENST00000520435.1_Missense_Mutation_p.Y401C|CES5A_ENST00000521992.1_Missense_Mutation_p.Y460C	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	431						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						CTCATAGAAGTAGACAGGTGC	0.557																																					p.Y460C		Atlas-SNP	.											.	CES5A	206	.	0			c.A1379G						PASS	.						77.0	68.0	71.0					16																	55883667		1568	3582	5150	SO:0001583	missense	221223	exon12			TAGAAGTAGACAG	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.1292A>G	16.37:g.55883667T>C	ENSP00000290567:p.Tyr431Cys	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	.	.	.	.	.	.	.	.	.	.	.	15.85	2.955162	0.53293	.	.	ENSG00000159398	ENST00000521992;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.03	5.03	0.67393	Carboxylesterase, type B (1);	0.181974	0.27084	N	0.021018	D	0.92665	0.7669	H	0.98802	4.335	0.49483	D	0.999795	D	0.89917	1.0	D	0.91635	0.999	D	0.95007	0.8148	10	0.87932	D	0	.	13.3257	0.60459	0.0:0.0:0.0:1.0	.	431	Q6NT32	EST5A_HUMAN	C	460;325;431;401;211	ENSP00000428864:Y460C;ENSP00000428571:Y325C;ENSP00000290567:Y431C;ENSP00000428887:Y401C	ENSP00000290567:Y431C	Y	-	2	0	CES5A	54441168	1.000000	0.71417	0.999000	0.59377	0.526000	0.34562	4.597000	0.61062	2.194000	0.70268	0.379000	0.24179	TAC	.	.	none		0.557	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	
MLLT4	4301	hgsc.bcm.edu	37	6	168315978	168315978	+	Silent	SNP	G	G	C	rs3213590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:168315978G>C	ENST00000447894.2	+	18	2409	c.2409G>C	c.(2407-2409)gtG>gtC	p.V803V	MLLT4_ENST00000400822.3_Silent_p.V802V|MLLT4_ENST00000392112.1_Silent_p.V787V|MLLT4_ENST00000366806.2_Silent_p.V803V|MLLT4_ENST00000351017.4_Silent_p.V810V|MLLT4_ENST00000344191.4_Silent_p.V803V|MLLT4_ENST00000392108.3_Silent_p.V803V			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	803	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		ATAGATTGGTGACCGACCCAG	0.547			T	MLL	AL								G|||	946	0.188898	0.2103	0.2104	5008	,	,		19363	0.1954		0.0775	False		,,,				2504	0.2526				p.V803V		Atlas-SNP	.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	.	MLLT4	351	.	0			c.G2409C						PASS	.	G	,	723,3683	300.1+/-286.2	51,621,1531	122.0	96.0	105.0		2409,2361	-1.4	0.7	6	dbSNP_106	105	678,7922	170.7+/-221.8	26,626,3648	no	coding-synonymous,coding-synonymous	MLLT4	NM_001040000.2,NM_001207008.1	,	77,1247,5179	CC,CG,GG		7.8837,16.4094,10.772	,	803/1652,787/1744	168315978	1401,11605	2203	4300	6503	SO:0001819	synonymous_variant	4301	exon18			ATTGGTGACCGAC	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.2409G>C	6.37:g.168315978G>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	210	86	0.409524	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				G|0.880;C|0.120	0.120	strong		0.547	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
PRDM8	56978	hgsc.bcm.edu	37	4	81124299	81124299	+	Silent	SNP	C	C	T	rs150632206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:81124299C>T	ENST00000504452.1	+	8	2522	c.1683C>T	c.(1681-1683)tcC>tcT	p.S561S	PRDM8_ENST00000339711.4_Silent_p.S561S|PRDM8_ENST00000415738.2_Silent_p.S561S			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	561					corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						GTTGCGGGTCCCTGCCGAGCG	0.746													C|||	105	0.0209665	0.0764	0.0058	5008	,	,		7601	0.0		0.0	False		,,,				2504	0.0				p.S561S		Atlas-SNP	.											.	PRDM8	44	.	0			c.C1683T						PASS	.	C	,	100,2254		0,100,1077	2.0	3.0	3.0		1683,1683	-2.1	1.0	4	dbSNP_134	3	1,5715		0,1,2857	no	coding-synonymous,coding-synonymous	PRDM8	NM_001099403.1,NM_020226.3	,	0,101,3934	TT,TC,CC		0.0175,4.2481,1.2515	,	561/690,561/690	81124299	101,7969	1177	2858	4035	SO:0001819	synonymous_variant	56978	exon4			CGGGTCCCTGCCG	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.1683C>T	4.37:g.81124299C>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001099403	A8K7X2|Q6IQ36	Silent	SNP	ENST00000504452.1	37	CCDS43243.1																																																																																			C|0.982;T|0.018	0.018	strong		0.746	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1		
MUC4	4585	hgsc.bcm.edu	37	3	195510266	195510266	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195510266A>C	ENST00000463781.3	-	2	8644	c.8185T>G	c.(8185-8187)Tca>Gca	p.S2729A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S2729A	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)		CCTGTGGATGATGAGGAAGTG	0.552																																					p.S2729A		Atlas-SNP	.											MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	0			c.T8185G						scavenged	.						2.0	2.0	2.0					3																	195510266		261	672	933	SO:0001583	missense	4585	exon2			TGGATGATGAGGA	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.8185T>G	3.37:g.195510266A>C	ENSP00000417498:p.Ser2729Ala	Somatic	79	2	0.0253165		WXS	Illumina HiSeq	Phase_I	69	18	0.26087	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	.	.	.	.	.	.	.	.	.	.	-	1.325	-0.598449	0.03744	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.54;1.53	1.02	-0.144	0.13440	.	.	.	.	.	T	0.10594	0.0259	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.25293	-1.0136	5	.	.	.	.	0.3308	0.00318	0.2449:0.2997:0.2433:0.2122	.	.	.	.	A	2729	ENSP00000417498:S2729A;ENSP00000420243:S2729A	.	S	-	1	0	MUC4	196993365	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-2.757000	0.00788	-2.087000	0.00862	-2.380000	0.00233	TCA	.	.	none		0.552	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PDE9A	5152	hgsc.bcm.edu	37	21	44119120	44119120	+	Splice_Site	SNP	C	C	T	rs74697345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44119120C>T	ENST00000291539.6	+	4	321	c.261C>T	c.(259-261)tcC>tcT	p.S87S	PDE9A_ENST00000398236.3_Splice_Site_p.S61S|PDE9A_ENST00000335440.6_Splice_Site_p.R64*|PDE9A_ENST00000335512.4_Splice_Site_p.S87S|PDE9A_ENST00000539837.1_Intron|PDE9A_ENST00000398229.3_Intron|PDE9A_ENST00000328862.6_Splice_Site_p.S61S|PDE9A_ENST00000398225.3_Splice_Site_p.S46S|PDE9A_ENST00000398224.3_Splice_Site_p.S20S|PDE9A_ENST00000398234.3_Splice_Site_p.S46S|PDE9A_ENST00000398227.3_Intron|PDE9A_ENST00000380328.2_Splice_Site_p.R113*|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000349112.3_Splice_Site_p.R38*|PDE9A_ENST00000398232.3_Splice_Site_p.S20S	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	87					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)	p.S87S(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	AGCAACTCTCCGGTAAGGCCC	0.448													T|||	49	0.00978435	0.0348	0.0043	5008	,	,		14460	0.0		0.0	False		,,,				2504	0.0				p.R113X		Atlas-SNP	.											PDE9A,colon,carcinoma,0,1	PDE9A	69	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C337T						PASS	.	T	,,stop/ARG,stop/ARG,,,,,,,,stop/ARG,,,,,,,,	155,4251	812.6+/-416.1	1,153,2049	85.0	78.0	80.0		261,60,112,337,138,,,183,,,,190,,,60,138,183,,,261	-4.7	0.9	21	dbSNP_132	80	3,8597	819.0+/-406.8	0,3,4297	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,stop-gained-near-splice,stop-gained-near-splice,coding-synonymous-near-splice,intron,intron,coding-synonymous-near-splice,intron,utr-5,intron,stop-gained-near-splice,utr-5,intron,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,utr-5,utr-5,coding-synonymous-near-splice	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	,,,,,,,,,,,,,,,,,,,	1,156,6346	TT,TC,CC		0.0349,3.5179,1.2148	,,,,,,,,,,,,,,,,,,,	87/534,20/467,38/466,113/541,46/493,,,61/508,,,,64/492,,,20/527,46/553,61/568,,,87/594	44119120	158,12848	2203	4300	6503	SO:0001630	splice_region_variant	5152	exon5			ACTCTCCGGTAAG	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.262+1C>T	21.37:g.44119120C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_001001570	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Nonsense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	t	15.04	2.716118	0.48622	0.035179	3.49E-4	ENSG00000160191	ENST00000380328;ENST00000335440;ENST00000349112	.	.	.	4.19	-4.74	0.03249	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.8976	0.29715	0.1418:0.5569:0.0:0.3013	.	.	.	.	X	113;64;38	.	ENSP00000335365:R64X	R	+	1	2	PDE9A	42992189	0.847000	0.29606	0.876000	0.34364	0.886000	0.51366	-0.556000	0.05992	-1.122000	0.02945	-0.439000	0.05793	CGA	C|0.990;T|0.010	0.010	strong		0.448	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		Silent
CCDC105	126402	hgsc.bcm.edu	37	19	15122104	15122104	+	Missense_Mutation	SNP	G	G	T	rs199904661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15122104G>T	ENST00000292574.3	+	1	549	c.467G>T	c.(466-468)cGc>cTc	p.R156L	SLC1A6_ENST00000430939.2_5'Flank	NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	156						extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						CAGCTGCTGCGCCAGCGCGAG	0.692													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		14563	0.0		0.0	False		,,,				2504	0.0				p.R156L		Atlas-SNP	.											.	CCDC105	53	.	0			c.G467T						PASS	.	G	LEU/ARG	163,3785		3,157,1814	7.0	8.0	7.0		467	2.8	1.0	19	dbSNP_134	7	3,8257		0,3,4127	yes	missense	CCDC105	NM_173482.2	102	3,160,5941	TT,TG,GG		0.0363,4.1287,1.3598	probably-damaging	156/500	15122104	166,12042	1974	4130	6104	SO:0001583	missense	126402	exon1			TGCTGCGCCAGCG	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.467G>T	19.37:g.15122104G>T	ENSP00000292574:p.Arg156Leu	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	44	30	0.681818	NM_173482	Q8N7T5|Q8NDL5	Missense_Mutation	SNP	ENST00000292574.3	37	CCDS12322.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	G	17.67	3.446054	0.63178	0.041287	3.63E-4	ENSG00000160994	ENST00000292574	T	0.02579	4.24	3.82	2.78	0.32641	.	0.117336	0.34603	N	0.003821	T	0.01765	0.0056	M	0.67953	2.075	0.25682	N	0.985784	D	0.69078	0.997	D	0.63957	0.92	T	0.05517	-1.0880	10	0.49607	T	0.09	-17.7965	6.322	0.21223	0.1376:0.0:0.8624:0.0	.	156	Q8IYK2	CC105_HUMAN	L	156	ENSP00000292574:R156L	ENSP00000292574:R156L	R	+	2	0	CCDC105	14983104	0.402000	0.25311	0.998000	0.56505	0.645000	0.38454	1.363000	0.34159	1.678000	0.50952	0.462000	0.41574	CGC	G|0.993;T|0.007	0.007	strong		0.692	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482	
CTSC	1075	hgsc.bcm.edu	37	11	88027209	88027209	+	Missense_Mutation	SNP	T	T	C	rs3888798	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:88027209T>C	ENST00000227266.5	-	7	1471	c.1357A>G	c.(1357-1359)Ata>Gta	p.I453V		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	453			I -> V (rare polymorphism; dbSNP:rs3888798). {ECO:0000269|PubMed:11180012}.		aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)			large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GCCACTGCTATGCTCTCAATT	0.463													T|||	420	0.0838658	0.0802	0.1023	5008	,	,		16827	0.1151		0.0517	False		,,,				2504	0.0767				p.I453V		Atlas-SNP	.											.	CTSC	46	.	0			c.A1357G	GRCh37	CM086741	CTSC	M	rs3888798	PASS	.	T	VAL/ILE	302,4100	163.6+/-195.4	11,280,1910	87.0	82.0	84.0		1357	6.0	1.0	11	dbSNP_108	84	332,8266	115.7+/-175.5	6,320,3973	yes	missense	CTSC	NM_001814.4	29	17,600,5883	CC,CT,TT		3.8614,6.8605,4.8769	possibly-damaging	453/464	88027209	634,12366	2201	4299	6500	SO:0001583	missense	1075	exon7			CTGCTATGCTCTC	AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"""Cathepsins"""	2528	protein-coding gene	gene with protein product	"""dipeptidyl peptidase 1"""	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.1357A>G	11.37:g.88027209T>C	ENSP00000227266:p.Ile453Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_001814	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	ENST00000227266.5	37	CCDS8282.1	186	0.08516483516483517	35	0.07113821138211382	27	0.07458563535911603	75	0.13111888111888112	49	0.06464379947229551	T	24.7	4.556481	0.86231	0.068605	0.038614	ENSG00000109861	ENST00000393302;ENST00000227266	D	0.86627	-2.15	5.97	5.97	0.96955	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.06280	0.0162	N	0.20574	0.59	0.80722	D	1	P;B	0.39759	0.687;0.444	P;B	0.52909	0.713;0.307	T	0.53585	-0.8418	9	.	.	.	.	16.4504	0.83984	0.0:0.0:0.0:1.0	rs3888798;rs4581448;rs56447948;rs3888798	436;453	B4DJQ8;P53634	.;CATC_HUMAN	V	436;453	ENSP00000227266:I453V	.	I	-	1	0	CTSC	87666857	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.156000	0.71840	2.288000	0.76882	0.533000	0.62120	ATA	T|0.939;C|0.061	0.061	strong		0.463	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814	
DOCK5	80005	hgsc.bcm.edu	37	8	25149590	25149590	+	Silent	SNP	G	G	A	rs35475676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:25149590G>A	ENST00000276440.7	+	6	416	c.372G>A	c.(370-372)ctG>ctA	p.L124L	DOCK5_ENST00000481100.1_Silent_p.L124L	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	124					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)		CGTACAGCCTGATCGAGTGGC	0.483													G|||	59	0.0117812	0.0416	0.0058	5008	,	,		18104	0.0		0.0	False		,,,				2504	0.0				p.L124L	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.G372A						PASS	.	G		213,4193	121.7+/-159.2	8,197,1998	38.0	36.0	36.0		372	3.7	1.0	8	dbSNP_126	36	0,8600		0,0,4300	yes	coding-synonymous	DOCK5	NM_024940.6		8,197,6298	AA,AG,GG		0.0,4.8343,1.6377		124/1871	25149590	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	80005	exon6			CAGCCTGATCGAG		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.372G>A	8.37:g.25149590G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1																																																																																			G|0.983;A|0.017	0.017	strong		0.483	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
DMGDH	29958	hgsc.bcm.edu	37	5	78328560	78328560	+	Silent	SNP	G	G	A	rs1805072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:78328560G>A	ENST00000255189.3	-	9	1495	c.1467C>T	c.(1465-1467)ggC>ggT	p.G489G	DMGDH_ENST00000380311.4_Silent_p.G288G|DMGDH_ENST00000540686.1_Silent_p.G109G	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	489					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		GCTGCTCCCAGCCAGCATGGA	0.542													G|||	995	0.198682	0.2398	0.134	5008	,	,		17116	0.1399		0.1988	False		,,,				2504	0.2495				p.G489G		Atlas-SNP	.											.	DMGDH	88	.	0			c.C1467T						PASS	.	G		1005,3401	374.6+/-321.3	101,803,1299	127.0	129.0	129.0		1467	4.6	1.0	5	dbSNP_89	129	1621,6979	300.8+/-305.1	162,1297,2841	no	coding-synonymous	DMGDH	NM_013391.2		263,2100,4140	AA,AG,GG		18.8488,22.8098,20.1907		489/867	78328560	2626,10380	2203	4300	6503	SO:0001819	synonymous_variant	29958	exon9			CTCCCAGCCAGCA	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.1467C>T	5.37:g.78328560G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_013391	B2RBN0|B4E1J9	Silent	SNP	ENST00000255189.3	37	CCDS4044.1																																																																																			G|0.796;A|0.204	0.204	strong		0.542	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
CIAPIN1	57019	hgsc.bcm.edu	37	16	57474740	57474740	+	Missense_Mutation	SNP	G	G	T	rs11557672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57474740G>T	ENST00000569979.1	-	1	147	c.101C>A	c.(100-102)gCg>gAg	p.A34E	CIAPIN1_ENST00000569246.1_5'UTR|CIAPIN1_ENST00000569370.1_Missense_Mutation_p.A34E|CIAPIN1_ENST00000567518.1_Missense_Mutation_p.A34E|CIAPIN1_ENST00000568940.1_Missense_Mutation_p.A34E|CIAPIN1_ENST00000394391.4_Missense_Mutation_p.A34E|CIAPIN1_ENST00000565961.1_Missense_Mutation_p.A34E					cytokine induced apoptosis inhibitor 1											cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						GCCGGTTAACGCTTGAAGCTT	0.522													G|||	73	0.0145767	0.0499	0.0086	5008	,	,		18615	0.0		0.001	False		,,,				2504	0.0				p.A34E		Atlas-SNP	.											.	CIAPIN1	17	.	0			c.C101A						PASS	.	G	GLU/ALA	142,3808		2,138,1835	86.0	84.0	85.0		101	-10.0	0.0	16	dbSNP_120	85	3,8331		0,3,4164	no	missense	CIAPIN1	NM_020313.2	107	2,141,5999	TT,TG,GG		0.036,3.5949,1.1804	benign	34/313	57474740	145,12139	1975	4167	6142	SO:0001583	missense	57019	exon2			GTTAACGCTTGAA	AF248964	CCDS10781.2	16q21	2012-09-20			ENSG00000005194	ENSG00000005194			28050	protein-coding gene	gene with protein product		608943				10493829, 11230166	Standard	XM_005256061		Approved	Anamorsin	uc002ell.1	Q6FI81	OTTHUMG00000133457	ENST00000569979.1:c.101C>A	16.37:g.57474740G>T	ENSP00000458000:p.Ala34Glu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	138	56	0.405797	NM_020313		Missense_Mutation	SNP	ENST00000569979.1	37		31	0.014194139194139194	26	0.052845528455284556	5	0.013812154696132596	0	0.0	0	0.0	G	4.538	0.099964	0.08681	0.035949	3.6E-4	ENSG00000005194	ENST00000394391	T	0.28666	1.6	4.98	-9.96	0.00443	.	1.395360	0.05048	N	0.477654	T	0.01976	0.0062	L	0.33753	1.03	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.0	B;B;B	0.08055	0.002;0.003;0.001	T	0.18935	-1.0321	10	0.05959	T	0.93	1.2775	3.7895	0.08715	0.0939:0.1347:0.3108:0.4606	rs11557672;rs16957069;rs11557672	34;34;34	B4DHB9;Q6FI81-3;Q6FI81	.;.;CPIN1_HUMAN	E	34	ENSP00000377914:A34E	ENSP00000377914:A34E	A	-	2	0	CIAPIN1	56032241	0.000000	0.05858	0.009000	0.14445	0.950000	0.60333	-1.034000	0.03567	-2.690000	0.00404	-0.295000	0.09555	GCG	G|0.975;T|0.025	0.025	strong		0.522	CIAPIN1-010	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432580.1	NM_020313	
C2orf54	79919	hgsc.bcm.edu	37	2	241826517	241826517	+	Silent	SNP	C	C	T	rs12616061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241826517C>T	ENST00000388934.4	-	5	1472	c.1314G>A	c.(1312-1314)aaG>aaA	p.K438K	C2orf54_ENST00000402775.2_Silent_p.K270K|C2orf54_ENST00000307486.8_Silent_p.K289K	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	438										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)		GAGTCCTGGTCTTCTGGAAGA	0.587													C|||	635	0.126797	0.1377	0.1167	5008	,	,		20194	0.3105		0.003	False		,,,				2504	0.0573				p.K438K		Atlas-SNP	.											.	C2orf54	14	.	0			c.G1314A						PASS	.	C	,	434,3532		24,386,1573	86.0	91.0	90.0		1314,810	4.5	1.0	2	dbSNP_120	90	27,8301		0,27,4137	no	coding-synonymous,coding-synonymous	C2orf54	NM_001085437.1,NM_024861.2	,	24,413,5710	TT,TC,CC		0.3242,10.943,3.7498	,	438/448,270/280	241826517	461,11833	1983	4164	6147	SO:0001819	synonymous_variant	79919	exon5			CCTGGTCTTCTGG	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.1314G>A	2.37:g.241826517C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	37	CCDS42839.1																																																																																			C|0.888;T|0.112	0.112	strong		0.587	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
SRGN	5552	hgsc.bcm.edu	37	10	70863699	70863699	+	Silent	SNP	C	C	T	rs4892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70863699C>T	ENST00000242465.3	+	3	340	c.300C>T	c.(298-300)tcC>tcT	p.S100S	SRGN_ENST00000462445.1_3'UTR	NM_002727.2	NP_002718.2	P10124	SRGN_HUMAN	serglycin	100	9 X 2 AA tandem repeats of [SF]-G.				biomineral tissue development (GO:0031214)|blood coagulation (GO:0007596)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|maintenance of granzyme B location in T cell secretory granule (GO:0033382)|maintenance of protease location in mast cell secretory granule (GO:0033373)|mast cell secretory granule organization (GO:0033364)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine secretion (GO:0050710)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein processing (GO:0016485)|T cell secretory granule organization (GO:0033371)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|platelet alpha granule lumen (GO:0031093)|zymogen granule (GO:0042588)				large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(3)	7						GCTTCGGCTCCGGCTCCGGCT	0.463													C|||	430	0.0858626	0.2663	0.049	5008	,	,		16308	0.0367		0.004	False		,,,				2504	0.0031				p.S100S		Atlas-SNP	.											SRGN,mouth,carcinoma,+1,1	SRGN	15	1	0			c.C300T						PASS	.	C		1043,3363	384.0+/-325.1	122,799,1282	74.0	68.0	70.0		300	-7.3	0.5	10	dbSNP_52	70	14,8586	9.1+/-34.3	0,14,4286	no	coding-synonymous	SRGN	NM_002727.2		122,813,5568	TT,TC,CC		0.1628,23.6723,8.127		100/159	70863699	1057,11949	2203	4300	6503	SO:0001819	synonymous_variant	5552	exon3			CGGCTCCGGCTCC	BC015516	CCDS7285.1	10q22.1	2007-02-16	2007-02-15	2007-02-15	ENSG00000122862	ENSG00000122862		"""Proteoglycans / Extracellular Matrix : Other"""	9361	protein-coding gene	gene with protein product	"""serglycin proteoglycan"""	177040	"""proteoglycan 1, secretory granule"""	PRG, PRG1			Standard	NR_036430		Approved	PPG	uc001joz.3	P10124	OTTHUMG00000018369	ENST00000242465.3:c.300C>T	10.37:g.70863699C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_002727	B2R4L7|Q5VW06	Silent	SNP	ENST00000242465.3	37	CCDS7285.1																																																																																			C|0.925;T|0.075	0.075	strong		0.463	SRGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048379.1	NM_002727	
QRICH2	84074	hgsc.bcm.edu	37	17	74273299	74273299	+	Missense_Mutation	SNP	G	G	A	rs73350377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74273299G>A	ENST00000262765.5	-	16	4891	c.4712C>T	c.(4711-4713)cCg>cTg	p.P1571L		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1571										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						AAGGTGCTGCGGGCGGCTGCG	0.637													G|||	665	0.132788	0.4047	0.0447	5008	,	,		16722	0.0367		0.0229	False		,,,				2504	0.0399				p.P1571L		Atlas-SNP	.											.	QRICH2	143	.	0			c.C4712T						PASS	.	G	LEU/PRO	1502,2904	470.0+/-355.6	256,990,957	49.0	55.0	53.0		4712	-2.5	1.0	17	dbSNP_130	53	149,8451	69.7+/-132.2	0,149,4151	yes	missense	QRICH2	NM_032134.1	98	256,1139,5108	AA,AG,GG		1.7326,34.0899,12.6941	benign	1571/1664	74273299	1651,11355	2203	4300	6503	SO:0001583	missense	84074	exon16			TGCTGCGGGCGGC	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.4712C>T	17.37:g.74273299G>A	ENSP00000262765:p.Pro1571Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	264	0.12087912087912088	210	0.4268292682926829	14	0.03867403314917127	23	0.04020979020979021	17	0.022427440633245383	G	6.235	0.411412	0.11812	0.340899	0.017326	ENSG00000129646	ENST00000262765	T	0.06687	3.27	5.63	-2.54	0.06307	.	.	.	.	.	T	0.00012	0.0000	N	0.00563	-1.375	0.30329	P	0.786859	B	0.11235	0.004	B	0.04013	0.001	T	0.41928	-0.9481	8	0.08599	T	0.76	-2.6518	6.1923	0.20530	0.5337:0.0:0.3521:0.1141	.	1571	Q9H0J4	QRIC2_HUMAN	L	1571	ENSP00000262765:P1571L	ENSP00000262765:P1571L	P	-	2	0	QRICH2	71784894	0.003000	0.15002	0.963000	0.40424	0.148000	0.21650	-0.053000	0.11846	-0.396000	0.07703	-0.459000	0.05422	CCG	G|0.879;A|0.121	0.121	strong		0.637	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
C4orf29	80167	hgsc.bcm.edu	37	4	128949929	128949929	+	Missense_Mutation	SNP	C	C	A	rs60505265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:128949929C>A	ENST00000444616.1	+	10	1246	c.999C>A	c.(997-999)agC>agA	p.S333R	C4orf29_ENST00000398965.1_Missense_Mutation_p.S333R|C4orf29_ENST00000388795.5_Missense_Mutation_p.S285R			Q0P651	CD029_HUMAN	chromosome 4 open reading frame 29	333						extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						AAGAACAAAGCAGAAACAGTC	0.353													A|||	439	0.0876597	0.0499	0.0908	5008	,	,		16709	0.2718		0.0199	False		,,,				2504	0.0164				p.S333R		Atlas-SNP	.											.	C4orf29	58	.	0			c.C999A						PASS	.	A	ARG/SER	180,3580		3,174,1703	69.0	68.0	68.0		999	2.3	1.0	4	dbSNP_129	68	109,8109		0,109,4000	yes	missense	C4orf29	NM_001039717.1	110	3,283,5703	AA,AC,CC		1.3264,4.7872,2.4128	benign	333/415	128949929	289,11689	1880	4109	5989	SO:0001583	missense	80167	exon10			ACAAAGCAGAAAC	AK024759	CCDS47131.1	4q28.2	2008-02-05			ENSG00000164074	ENSG00000164074			26111	protein-coding gene	gene with protein product						12477932	Standard	XM_006714318		Approved	FLJ21106	uc021xrt.1	Q0P651	OTTHUMG00000133304	ENST00000444616.1:c.999C>A	4.37:g.128949929C>A	ENSP00000397229:p.Ser333Arg	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	146	63	0.431507	NM_001039717	A1A4W8|A1A4W9|Q9H7A7	Missense_Mutation	SNP	ENST00000444616.1	37		243	0.11126373626373626	21	0.042682926829268296	34	0.09392265193370165	168	0.2937062937062937	20	0.026385224274406333	A	3.744	-0.052957	0.07362	0.047872	0.013264	ENSG00000164074	ENST00000454347;ENST00000398961;ENST00000398965;ENST00000444616;ENST00000388795;ENST00000545758;ENST00000437077	.	.	.	4.87	2.29	0.28610	.	0.536720	0.22287	N	0.062052	T	0.00012	0.0000	N	0.00554	-1.385	0.58432	P	8.000000000008E-6	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.39781	-0.9597	8	0.09338	T	0.73	-22.5133	4.8553	0.13555	0.5075:0.2999:0.1925:0.0	rs60505265	285;333	B7WP89;Q0P651	.;CD029_HUMAN	R	333;164;333;333;285;251;240	.	ENSP00000373447:S285R	S	+	3	2	C4orf29	129169379	1.000000	0.71417	0.956000	0.39512	0.687000	0.40016	1.111000	0.31159	0.323000	0.23307	-0.264000	0.10439	AGC	C|0.909;A|0.091	0.091	strong		0.353	C4orf29-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257098.1	NM_001039717	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34827085	34827085	+	Missense_Mutation	SNP	A	A	T	rs9469913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:34827085A>T	ENST00000192788.5	+	14	3123	c.2952A>T	c.(2950-2952)caA>caT	p.Q984H	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.Q984H	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	984			Q -> H (in dbSNP:rs9469913).				histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						GCAGAACCCAAGCCTCCAGCT	0.572													A|||	952	0.190096	0.4569	0.1196	5008	,	,		22281	0.0228		0.1402	False		,,,				2504	0.1033				p.Q984H		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.A2952T						PASS	.	A	HIS/GLN	1464,2618		250,964,827	46.0	50.0	48.0		2952	-5.2	0.0	6	dbSNP_119	48	1444,6894		132,1180,2857	yes	missense	UHRF1BP1	NM_017754.3	24	382,2144,3684	TT,TA,AA		17.3183,35.8648,23.4138	possibly-damaging	984/1441	34827085	2908,9512	2041	4169	6210	SO:0001583	missense	54887	exon14			AACCCAAGCCTCC	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.2952A>T	6.37:g.34827085A>T	ENSP00000192788:p.Gln984His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	399	0.18269230769230768	234	0.47560975609756095	47	0.1298342541436464	13	0.022727272727272728	105	0.13852242744063326	A	13.88	2.368353	0.42003	0.358648	0.173183	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.09163	3.01;3.01	5.52	-5.18	0.02840	.	0.566831	0.19078	N	0.123328	T	0.02193	0.0068	N	0.19112	0.55	0.80722	P	0.0	B	0.18863	0.031	B	0.13407	0.009	T	0.35895	-0.9770	9	0.34782	T	0.22	-11.9099	15.6301	0.76899	0.316:0.0:0.684:0.0	rs9469913;rs52800736;rs9469913	984	Q6BDS2	URFB1_HUMAN	H	984	ENSP00000192788:Q984H;ENSP00000400628:Q984H	ENSP00000192788:Q984H	Q	+	3	2	UHRF1BP1	34935063	0.000000	0.05858	0.007000	0.13788	0.776000	0.43924	0.028000	0.13644	-0.862000	0.04089	0.482000	0.46254	CAA	A|0.822;T|0.178	0.178	strong		0.572	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
TRAF3IP3	80342	hgsc.bcm.edu	37	1	209933659	209933659	+	Missense_Mutation	SNP	G	G	A	rs78296889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:209933659G>A	ENST00000367024.1	+	3	791	c.275G>A	c.(274-276)cGg>cAg	p.R92Q	TRAF3IP3_ENST00000367026.3_Missense_Mutation_p.R92Q|TRAF3IP3_ENST00000010338.4_Missense_Mutation_p.R92Q|TRAF3IP3_ENST00000367025.3_Missense_Mutation_p.R92Q|TRAF3IP3_ENST00000400959.3_Missense_Mutation_p.R92Q			Q9Y228	T3JAM_HUMAN	TRAF3 interacting protein 3	92						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32				OV - Ovarian serous cystadenocarcinoma(81;0.045)		CCCTCCAGGCGGCCAGGACAG	0.597													G|||	87	0.0173722	0.0628	0.0058	5008	,	,		17422	0.0		0.0	False		,,,				2504	0.0				p.R92Q		Atlas-SNP	.											.	TRAF3IP3	68	.	0			c.G275A						PASS	.	G	GLN/ARG	220,4186	125.7+/-162.9	4,212,1987	25.0	26.0	25.0		275	1.8	0.0	1	dbSNP_132	25	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TRAF3IP3	NM_025228.2	43	4,215,6284	AA,AG,GG		0.0349,4.9932,1.7146	possibly-damaging	92/552	209933659	223,12783	2203	4300	6503	SO:0001583	missense	80342	exon3			CCAGGCGGCCAGG		CCDS1490.1, CCDS1490.2, CCDS73023.1	1q32.3-q41	2008-02-05			ENSG00000009790	ENSG00000009790			30766	protein-coding gene	gene with protein product	"""TRAF3 interacting Jun N terminal kinase (JNK) activating modulator"""	608255				14572659	Standard	XR_247044		Approved	T3JAM	uc001hho.3	Q9Y228	OTTHUMG00000036480	ENST00000367024.1:c.275G>A	1.37:g.209933659G>A	ENSP00000355991:p.Arg92Gln	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	158	65	0.411392	NM_025228	A1L464|A6NIU9|Q2YDB5|Q4VY06|Q7Z706	Missense_Mutation	SNP	ENST00000367024.1	37	CCDS1490.2	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	G	11.69	1.712561	0.30322	0.049932	3.49E-4	ENSG00000009790	ENST00000400959;ENST00000367025;ENST00000458110;ENST00000367026;ENST00000367024;ENST00000010338	T;T;T;T;T	0.46819	0.86;0.87;0.91;0.87;0.91	4.69	1.75	0.24633	.	2.341960	0.02012	N	0.047071	T	0.05044	0.0135	L	0.44542	1.39	0.09310	N	1	B;D;B;P	0.56746	0.003;0.977;0.007;0.938	B;P;B;B	0.46718	0.003;0.525;0.007;0.308	T	0.12682	-1.0538	10	0.13108	T	0.6	-7.597	7.4585	0.27280	0.2986:0.0:0.7014:0.0	.	92;92;92;92	Q9Y228;Q9Y228-2;Q9Y228-3;E2QRE5	T3JAM_HUMAN;.;.;.	Q	92;92;75;92;92;92	ENSP00000383743:R92Q;ENSP00000355992:R92Q;ENSP00000355993:R92Q;ENSP00000355991:R92Q;ENSP00000010338:R92Q	ENSP00000010338:R92Q	R	+	2	0	TRAF3IP3	208000282	0.000000	0.05858	0.008000	0.14137	0.006000	0.05464	-0.029000	0.12329	0.523000	0.28482	-0.448000	0.05591	CGG	G|0.984;A|0.016	0.016	strong		0.597	TRAF3IP3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088734.2		
CBX8	57332	hgsc.bcm.edu	37	17	77768654	77768654	+	Missense_Mutation	SNP	C	C	A	rs4889891|rs113547221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77768654C>A	ENST00000269385.4	-	5	1067	c.950G>T	c.(949-951)gGg>gTg	p.G317V	CBX8_ENST00000485449.1_5'Flank	NM_020649.2	NP_065700.1	Q9HC52	CBX8_HUMAN	chromobox homolog 8	317			G -> V (in dbSNP:rs4889891). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.		histone ubiquitination (GO:0016574)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	methylated histone binding (GO:0035064)|single-stranded RNA binding (GO:0003727)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)	14			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			CAGGCCCCCCCCAGAGCTGGG	0.682													A|||	3052	0.609425	0.8411	0.6902	5008	,	,		13737	0.4097		0.4702	False		,,,				2504	0.5879				p.G317V		Atlas-SNP	.											CBX8,colon,carcinoma,-1,3	CBX8	42	3	0			c.G950T						PASS	.	A	VAL/GLY	3348,972		1301,746,113	11.0	14.0	13.0		950	3.4	0.2	17	dbSNP_111	13	4278,4180		1125,2028,1076	yes	missense	CBX8	NM_020649.2	109	2426,2774,1189	AA,AC,CC		49.4207,22.5,40.3193	benign	317/390	77768654	7626,5152	2160	4229	6389	SO:0001583	missense	57332	exon5			CCCCCCCCAGAGC	AF174482	CCDS11765.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141570	ENSG00000141570			15962	protein-coding gene	gene with protein product	"""polycomb 3"", ""Pc class 3 homolog (Drosophila)"""		"""chromobox homolog 8 (Drosophila Pc class)"""			10825164	Standard	NM_020649		Approved	RC1, HPC3, PC3	uc002jxd.2	Q9HC52	OTTHUMG00000150416	ENST00000269385.4:c.950G>T	17.37:g.77768654C>A	ENSP00000269385:p.Gly317Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	47	29	0.617021	NM_020649	Q96H39|Q9NR07	Missense_Mutation	SNP	ENST00000269385.4	37	CCDS11765.1	1206	0.5521978021978022	390	0.7926829268292683	249	0.6878453038674033	204	0.35664335664335667	363	0.4788918205804749	a	0.003	-2.575191	0.00131	0.775	0.505793	ENSG00000141570	ENST00000269385	T	0.39406	1.08	4.47	3.36	0.38483	.	2.413210	0.01433	N	0.014826	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	0.48514	-0.9029	9	0.28530	T	0.3	-2.0212	10.8184	0.46591	0.6985:0.3015:0.0:0.0	rs4889891;rs17855399;rs17858507;rs61324260;rs4889891	317	Q9HC52	CBX8_HUMAN	V	317	ENSP00000269385:G317V	ENSP00000269385:G317V	G	-	2	0	CBX8	75383249	0.000000	0.05858	0.182000	0.23118	0.361000	0.29550	0.443000	0.21644	0.317000	0.23160	-0.383000	0.06682	GGG	C|0.433;A|0.567	0.567	strong		0.682	CBX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318011.1	NM_020649	
SBNO2	22904	hgsc.bcm.edu	37	19	1119963	1119963	+	Silent	SNP	A	A	G	rs2074921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1119963A>G	ENST00000361757.3	-	12	1446	c.1209T>C	c.(1207-1209)gcT>gcC	p.A403A	SBNO2_ENST00000438103.2_Silent_p.A346A|SBNO2_ENST00000587024.1_Silent_p.A403A	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	71	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	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	
ASAH1	427	hgsc.bcm.edu	37	8	17928811	17928811	+	Missense_Mutation	SNP	C	C	T	rs1071645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17928811C>T	ENST00000262097.6	-	3	525	c.214G>A	c.(214-216)Gtg>Atg	p.V72M	ASAH1_ENST00000381733.4_Missense_Mutation_p.V88M|ASAH1_ENST00000417108.2_Missense_Mutation_p.V7M|ASAH1_ENST00000520051.1_5'Flank|ASAH1_ENST00000520781.1_Missense_Mutation_p.V72M|ASAH1_ENST00000314146.10_Missense_Mutation_p.V95M	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	72			V -> M (in dbSNP:rs1071645). {ECO:0000269|PubMed:10993717, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8955159, ECO:0000269|Ref.2}.		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)		TAGCATACCACTGGTGCCTTG	0.303													T|||	2106	0.420527	0.2504	0.5735	5008	,	,		15607	0.373		0.4761	False		,,,				2504	0.5337				p.V95M		Atlas-SNP	.											.	ASAH1	71	.	0			c.G283A						PASS	.	T	MET/VAL,MET/VAL,MET/VAL	1275,3131	685.6+/-404.6	194,887,1122	164.0	132.0	143.0		283,262,214	-3.3	0.0	8	dbSNP_86	143	4243,4357	564.2+/-388.3	1031,2181,1088	yes	missense,missense,missense	ASAH1	NM_001127505.1,NM_004315.4,NM_177924.3	21,21,21	1225,3068,2210	TT,TC,CC		49.3372,28.9378,42.4266	benign,benign,benign	95/390,88/412,72/396	17928811	5518,7488	2203	4300	6503	SO:0001583	missense	427	exon4			ATACCACTGGTGC	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	ENST00000262097.6:c.214G>A	8.37:g.17928811C>T	ENSP00000262097:p.Val72Met	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_001127505	E9PDS0|Q6W898|Q96AS2	Missense_Mutation	SNP	ENST00000262097.6	37	CCDS6006.1	925	0.42353479853479853	147	0.29878048780487804	219	0.6049723756906077	204	0.35664335664335667	355	0.4683377308707124	T	8.835	0.940822	0.18281	0.289378	0.493372	ENSG00000104763	ENST00000262097;ENST00000381733;ENST00000520781;ENST00000417108;ENST00000314146	T;T;T;T;T	0.52057	0.79;0.79;0.79;0.79;0.68	5.1	-3.27	0.05048	.	1.506130	0.03689	N	0.246842	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.09377	0.0;0.003;0.004;0.004	T	0.41556	-0.9502	9	0.35671	T	0.21	-4.7588	6.9396	0.24486	0.2468:0.5673:0.1013:0.0846	rs1071645;rs1804720;rs3190053;rs3190062;rs11538151;rs12544854;rs17416573;rs17845496;rs17858382;rs52809253;rs60844591;rs12544854	95;88;72;72	E9PDS0;Q13510-2;E7EMM4;Q13510	.;.;.;ASAH1_HUMAN	M	72;88;72;7;95	ENSP00000262097:V72M;ENSP00000371152:V88M;ENSP00000427751:V72M;ENSP00000394125:V7M;ENSP00000326970:V95M	ENSP00000262097:V72M	V	-	1	0	ASAH1	17973091	0.212000	0.23540	0.000000	0.03702	0.002000	0.02628	0.402000	0.20965	-1.107000	0.03004	-2.194000	0.00310	GTG	T|0.339;G|0.122	0.339	strong		0.303	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	
GABRR2	2570	hgsc.bcm.edu	37	6	89967498	89967498	+	Missense_Mutation	SNP	G	G	A	rs282129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	272	0	0		WXS	Illumina HiSeq	Phase_I	255	118	0.462745	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		
EPS8L3	79574	hgsc.bcm.edu	37	1	110299691	110299691	+	Missense_Mutation	SNP	G	G	A	rs11102001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110299691G>A	ENST00000361965.4	-	12	1172	c.1066C>T	c.(1066-1068)Cca>Tca	p.P356S	EPS8L3_ENST00000494151.1_5'Flank|EPS8L3_ENST00000369805.3_Missense_Mutation_p.P357S|EPS8L3_ENST00000361852.4_Missense_Mutation_p.P356S|RP4-735C1.4_ENST00000431955.1_RNA	NM_133181.3	NP_573444.2	Q8TE67	ES8L3_HUMAN	EPS8-like 3	356			P -> S (in dbSNP:rs11102001).			cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	32		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		CTCTCAGGTGGGCTTAGACAG	0.587													G|||	787	0.157149	0.4297	0.1254	5008	,	,		17783	0.0089		0.0557	False		,,,				2504	0.0685				p.P357S		Atlas-SNP	.											.	EPS8L3	73	.	0			c.C1069T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	1606,2800	497.4+/-363.8	317,972,914	130.0	128.0	129.0		1066,1066,1069	4.5	0.3	1	dbSNP_120	129	540,8060	148.8+/-204.0	16,508,3776	yes	missense,missense,missense	EPS8L3	NM_024526.3,NM_133181.3,NM_139053.2	74,74,74	333,1480,4690	AA,AG,GG		6.2791,36.4503,16.5001	benign,benign,benign	356/564,356/594,357/595	110299691	2146,10860	2203	4300	6503	SO:0001583	missense	79574	exon12			CAGGTGGGCTTAG	AK025175	CCDS813.1, CCDS814.1, CCDS815.1	1p13.2	2008-02-05			ENSG00000198758	ENSG00000198758			21297	protein-coding gene	gene with protein product		614989				12620401	Standard	NM_139053		Approved	FLJ21522, MGC16817	uc001dyq.2	Q8TE67	OTTHUMG00000011651	ENST00000361965.4:c.1066C>T	1.37:g.110299691G>A	ENSP00000355255:p.Pro356Ser	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_139053	A8K833|Q5T8Q6|Q5T8Q7|Q5T8Q8|Q96E47|Q9H719	Missense_Mutation	SNP	ENST00000361965.4	37	CCDS814.1	306	0.1401098901098901	213	0.4329268292682927	42	0.11602209944751381	7	0.012237762237762238	44	0.05804749340369393	G	11.09	1.537501	0.27475	0.364503	0.062791	ENSG00000198758	ENST00000361852;ENST00000369805;ENST00000361965	T;T;T	0.42131	0.98;0.98;0.98	5.44	4.53	0.55603	.	0.428536	0.27168	N	0.020610	T	0.09730	0.0239	L	0.31926	0.97	0.58432	P	2.9999999999752447E-6	B;B;B;P	0.36683	0.024;0.422;0.021;0.565	B;B;B;B	0.33254	0.031;0.119;0.017;0.16	T	0.08472	-1.0720	9	0.02654	T	1	-3.1063	8.4648	0.32949	0.1763:0.0:0.8237:0.0	rs11102001;rs52793050;rs59692712;rs11102001	356;356;356;357	A8K2J6;Q8TE67-2;Q8TE67;Q8TE67-3	.;.;ES8L3_HUMAN;.	S	356;357;356	ENSP00000354551:P356S;ENSP00000358820:P357S;ENSP00000355255:P356S	ENSP00000354551:P356S	P	-	1	0	EPS8L3	110101214	0.000000	0.05858	0.256000	0.24389	0.704000	0.40688	0.109000	0.15417	1.307000	0.44944	0.585000	0.79938	CCA	G|0.831;A|0.169	0.169	strong		0.587	EPS8L3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032234.1	NM_024526	
MYO5A	4644	hgsc.bcm.edu	37	15	52662388	52662388	+	Missense_Mutation	SNP	C	C	T	rs189981926		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52662388C>T	ENST00000399231.3	-	22	3287	c.3044G>A	c.(3043-3045)cGa>cAa	p.R1015Q	MYO5A_ENST00000399233.2_Missense_Mutation_p.R1015Q|MYO5A_ENST00000553916.1_Missense_Mutation_p.R1015Q|MYO5A_ENST00000358212.6_Missense_Mutation_p.R1015Q|MYO5A_ENST00000356338.6_Missense_Mutation_p.R1015Q	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1015					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)		TTGTTTGTATCGATCTGCATG	0.468													C|||	1	0.000199681	0.0	0.0	5008	,	,		18553	0.001		0.0	False		,,,				2504	0.0				p.R1015Q		Atlas-SNP	.											MYO5A,NS,carcinoma,-1,1	MYO5A	145	1	0			c.G3044A						scavenged	.						221.0	204.0	210.0					15																	52662388		1958	4137	6095	SO:0001583	missense	4644	exon22			TTGTATCGATCTG		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.3044G>A	15.37:g.52662388C>T	ENSP00000382177:p.Arg1015Gln	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	193	2	0.0103627	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	12.22	1.873305	0.33069	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24	5.49	-0.393	0.12438	.	0.470824	0.25089	N	0.033224	T	0.08537	0.0212	N	0.17474	0.49	0.09310	N	1	B;B	0.18863	0.002;0.031	B;B	0.15870	0.001;0.014	T	0.24905	-1.0147	10	0.37606	T	0.19	.	7.1256	0.25469	0.1109:0.4008:0.0:0.4883	.	1015;1015	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	Q	1015;549;1015;1015;1015;645;1015	ENSP00000382177:R1015Q;ENSP00000382179:R1015Q;ENSP00000348693:R1015Q;ENSP00000350945:R1015Q;ENSP00000451109:R1015Q	ENSP00000348693:R1015Q	R	-	2	0	MYO5A	50449680	0.020000	0.18652	0.923000	0.36655	0.667000	0.39255	-0.617000	0.05584	-0.178000	0.10672	-0.797000	0.03246	CGA	C|1.000;T|0.000	0.000	strong		0.468	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
PPP1R26	9858	hgsc.bcm.edu	37	9	138376649	138376649	+	Missense_Mutation	SNP	T	T	C	rs3748192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138376649T>C	ENST00000356818.2	+	4	842	c.293T>C	c.(292-294)gTc>gCc	p.V98A	PPP1R26_ENST00000605660.1_Missense_Mutation_p.V98A|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000401470.3_Missense_Mutation_p.V98A|PPP1R26_ENST00000605286.1_Missense_Mutation_p.V98A|PPP1R26_ENST00000604351.1_Missense_Mutation_p.V98A	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	98			V -> A (in dbSNP:rs3748192). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GCGTTGGCTGTCTGTGGTCTC	0.627													C|||	2095	0.418331	0.2905	0.4899	5008	,	,		16315	0.6528		0.2117	False		,,,				2504	0.5112				p.V98A		Atlas-SNP	.											KIAA0649,NS,carcinoma,0,1	.	.	1	0			c.T293C						PASS	.	C	ALA/VAL	1113,3291		132,849,1221	41.0	48.0	46.0		293	3.4	0.1	9	dbSNP_107	46	1777,6821		195,1387,2717	no	missense	KIAA0649	NM_014811.3	64	327,2236,3938	CC,CT,TT		20.6676,25.2725,22.2273	benign	98/1210	138376649	2890,10112	2202	4299	6501	SO:0001583	missense	9858	exon4			TGGCTGTCTGTGG	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.293T>C	9.37:g.138376649T>C	ENSP00000349274:p.Val98Ala	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	50	34	0.68	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	833	0.3814102564102564	122	0.24796747967479674	158	0.43646408839779005	394	0.6888111888111889	159	0.20976253298153033	C	0.007	-2.011636	0.00422	0.252725	0.206676	ENSG00000196422	ENST00000356818;ENST00000401470	T;T	0.46063	0.88;0.88	4.39	3.41	0.39046	.	0.854487	0.10136	N	0.711490	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	0.45116	-0.9283	9	0.02654	T	1	-12.6961	7.3836	0.26870	0.2105:0.6922:0.0:0.0973	rs3748192;rs17846422;rs17859468;rs3748192	98	Q5T8A7	PPR26_HUMAN	A	98	ENSP00000349274:V98A;ENSP00000385826:V98A	ENSP00000349274:V98A	V	+	2	0	KIAA0649	137516470	0.006000	0.16342	0.106000	0.21319	0.067000	0.16453	1.185000	0.32065	1.085000	0.41206	-0.119000	0.15052	GTC	T|0.723;C|0.277	0.277	strong		0.627	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
LRRC38	126755	hgsc.bcm.edu	37	1	13802325	13802325	+	Missense_Mutation	SNP	T	T	C	rs3013105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:13802325T>C	ENST00000376085.3	-	2	1328	c.874A>G	c.(874-876)Aag>Gag	p.K292E		NM_001010847.1	NP_001010847.1	Q5VT99	LRC38_HUMAN	leucine rich repeat containing 38	292			K -> E (in dbSNP:rs3013105).		ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CAGTCATCCTTGTCCTCGTCT	0.557													C|||	2314	0.462061	0.5242	0.3357	5008	,	,		20308	0.62		0.3837	False		,,,				2504	0.3855				p.K292E		Atlas-SNP	.											LRRC38,NS,meningioma,0,1	LRRC38	12	1	0			c.A874G						PASS	.																																			SO:0001583	missense	126755	exon2			CATCCTTGTCCTC	BC016048	CCDS53269.1	1p36.21	2008-02-05			ENSG00000162494	ENSG00000162494			27005	protein-coding gene	gene with protein product		615212				12477932	Standard	NM_001010847		Approved		uc001avb.3	Q5VT99	OTTHUMG00000007918	ENST00000376085.3:c.874A>G	1.37:g.13802325T>C	ENSP00000365253:p.Lys292Glu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001010847	Q96B32	Missense_Mutation	SNP	ENST00000376085.3	37	CCDS53269.1	1039	0.4757326007326007	254	0.516260162601626	134	0.3701657458563536	362	0.6328671328671329	289	0.3812664907651715	.	0.018	-1.483234	0.01027	.	.	ENSG00000162494	ENST00000376085	T	0.59224	0.28	5.25	5.25	0.73442	.	0.491849	0.20946	N	0.082822	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	0.46005	-0.9222	9	0.02654	T	1	.	5.2956	0.15751	0.1637:0.6687:0.0:0.1676	rs3013105;rs3795751;rs60739508;rs3013105	292	Q5VT99	LRC38_HUMAN	E	292	ENSP00000365253:K292E	ENSP00000365253:K292E	K	-	1	0	LRRC38	13674912	0.048000	0.20356	0.701000	0.30321	0.084000	0.17831	1.002000	0.29796	1.225000	0.43566	-0.215000	0.12644	AAG	C|0.487;N|0.000	0.487	strong		0.557	LRRC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021793.1		
KCNG4	93107	hgsc.bcm.edu	37	16	84270650	84270650	+	Missense_Mutation	SNP	C	C	T	rs61743417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84270650C>T	ENST00000308251.4	-	2	510	c.442G>A	c.(442-444)Gcc>Acc	p.A148T	KCNG4_ENST00000568181.1_Missense_Mutation_p.A148T	NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	148					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						CCCCAGTAGGCCAGCTCCTCC	0.667													C|||	149	0.0297524	0.1097	0.0058	5008	,	,		16764	0.0		0.0	False		,,,				2504	0.0				p.A148T		Atlas-SNP	.											KCNG4,NS,carcinoma,0,1	KCNG4	71	1	0			c.G442A						PASS	.	C	THR/ALA	380,4020	191.6+/-217.2	19,342,1839	42.0	43.0	42.0		442	-1.0	0.6	16	dbSNP_129	42	0,8600		0,0,4300	yes	missense	KCNG4	NM_172347.2	58	19,342,6139	TT,TC,CC		0.0,8.6364,2.9231	benign	148/520	84270650	380,12620	2200	4300	6500	SO:0001583	missense	93107	exon2			AGTAGGCCAGCTC	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.442G>A	16.37:g.84270650C>T	ENSP00000312129:p.Ala148Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	142	59	0.415493	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	48	0.02197802197802198	47	0.09552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	C	4.103	0.017220	0.07959	0.086364	0.0	ENSG00000168418	ENST00000308251	T	0.76709	-1.04	5.11	-1.05	0.10036	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.951541	0.08816	N	0.889546	T	0.02727	0.0082	N	0.11818	0.18	0.09310	N	0.999999	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.01215	-1.1416	10	0.16896	T	0.51	.	9.62	0.39716	0.0:0.3441:0.0:0.6559	.	148;148	Q8TDN1;Q8TDN1-2	KCNG4_HUMAN;.	T	148	ENSP00000312129:A148T	ENSP00000312129:A148T	A	-	1	0	KCNG4	82828151	0.000000	0.05858	0.631000	0.29282	0.993000	0.82548	-0.583000	0.05807	-0.538000	0.06281	-0.275000	0.10095	GCC	C|0.971;T|0.029	0.029	strong		0.667	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
NLRP7	199713	hgsc.bcm.edu	37	19	55441971	55441971	+	Silent	SNP	G	G	A	rs61746780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55441971G>A	ENST00000590030.1	-	8	2746	c.2706C>T	c.(2704-2706)gcC>gcT	p.A902A	NLRP7_ENST00000340844.2_Silent_p.A902A|NLRP7_ENST00000448121.2_Silent_p.A874A|NLRP7_ENST00000446217.1_Silent_p.A930A|NLRP7_ENST00000328092.5_Silent_p.A874A|NLRP7_ENST00000588756.1_Silent_p.A902A|NLRP7_ENST00000592784.1_Silent_p.A902A			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	902							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)		TGAGGCTGCAGGCTTCTTGGA	0.463													.|||	128	0.0255591	0.09	0.0086	5008	,	,		17972	0.0		0.002	False		,,,				2504	0.001				p.A902A		Atlas-SNP	.											.	NLRP7	411	.	0			c.C2706T						PASS	.	G	,,	368,4038	187.4+/-214.1	15,338,1850	132.0	126.0	128.0		2706,2622,2706	-1.7	0.0	19	dbSNP_129	128	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	,,	15,342,6146	AA,AG,GG		0.0465,8.3522,2.8602	,,	902/1038,874/1010,902/981	55441971	372,12634	2203	4300	6503	SO:0001819	synonymous_variant	199713	exon9			GCTGCAGGCTTCT	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.2706C>T	19.37:g.55441971G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	111	63	0.567568	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			G|0.976;A|0.024	0.024	strong		0.463	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
ACSL5	51703	hgsc.bcm.edu	37	10	114181773	114181773	+	Missense_Mutation	SNP	A	A	G	rs12254915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:114181773A>G	ENST00000393081.1	+	16	1763	c.1456A>G	c.(1456-1458)Aca>Gca	p.T486A	RP11-324O2.6_ENST00000424422.1_RNA|ACSL5_ENST00000354655.4_Missense_Mutation_p.T486A|ACSL5_ENST00000369410.3_Missense_Mutation_p.T268A|ACSL5_ENST00000433418.1_Missense_Mutation_p.T486A|ACSL5_ENST00000354273.4_Missense_Mutation_p.T486A|ACSL5_ENST00000356116.1_Missense_Mutation_p.T542A	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	486			T -> A (in dbSNP:rs12254915).		cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|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)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		GAACTACTTTACAGTGAATAA	0.458													A|||	75	0.014976	0.0552	0.0029	5008	,	,		20705	0.0		0.0	False		,,,				2504	0.0				p.T542A		Atlas-SNP	.											.	ACSL5	51	.	0			c.A1624G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	193,4213	122.9+/-160.3	2,189,2012	135.0	132.0	133.0		1624,1456,1456	0.6	0.7	10	dbSNP_120	133	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	ACSL5	NM_016234.3,NM_203379.1,NM_203380.1	58,58,58	2,190,6311	GG,GA,AA		0.0116,4.3804,1.4916	benign,benign,benign	542/740,486/684,486/684	114181773	194,12812	2203	4300	6503	SO:0001583	missense	51703	exon16			TACTTTACAGTGA	AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142		"""Acyl-CoA synthetase family"""	16526	protein-coding gene	gene with protein product	"""FACL5 for fatty acid coenzyme A ligase 5"", ""long-chain acyl-CoA synthetase 5"", ""long-chain fatty acid coenzyme A ligase 5"", ""fatty-acid-Coenzyme A ligase, long-chain 5"""	605677	"""fatty-acid-Coenzyme A ligase, long-chain 5"""	FACL5		11127823	Standard	NM_016234		Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.1456A>G	10.37:g.114181773A>G	ENSP00000376796:p.Thr486Ala	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	70	22	0.314286	NM_016234	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Missense_Mutation	SNP	ENST00000393081.1	37	CCDS7573.1	25	0.011446886446886446	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	0	0.0	A	2.991	-0.208102	0.06180	0.043804	1.16E-4	ENSG00000197142	ENST00000354655;ENST00000393081;ENST00000356116;ENST00000433418;ENST00000354273;ENST00000369410	T;T;T;T;T;T	0.09630	2.96;2.96;2.96;2.96;2.96;2.96	5.86	0.636	0.17729	AMP-dependent synthetase/ligase (1);	0.395320	0.28724	N	0.014342	T	0.00356	0.0011	N	0.00405	-1.535	0.09310	N	0.999999	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	0.44283	-0.9338	10	0.02654	T	1	-2.9242	8.9257	0.35639	0.2131:0.0:0.462:0.3249	rs12254915;rs52833907;rs12254915	268;486;542;486	B4DX30;A6GV77;Q9ULC5-3;Q9ULC5	.;.;.;ACSL5_HUMAN	A	486;486;542;486;486;268	ENSP00000346680:T486A;ENSP00000376796:T486A;ENSP00000348429:T542A;ENSP00000403647:T486A;ENSP00000346223:T486A;ENSP00000358418:T268A	ENSP00000346223:T486A	T	+	1	0	ACSL5	114171763	0.994000	0.37717	0.677000	0.29947	0.906000	0.53458	1.059000	0.30517	-0.131000	0.11578	-0.270000	0.10280	ACA	A|0.982;G|0.018	0.018	strong		0.458	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1	NM_016234	
PTBP1	5725	hgsc.bcm.edu	37	19	804612	804612	+	Silent	SNP	C	C	T	rs4986235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:804612C>T	ENST00000349038.4	+	6	589	c.516C>T	c.(514-516)gaC>gaT	p.D172D	PTBP1_ENST00000356948.6_Silent_p.D172D|MIR4745_ENST00000577608.1_RNA|PTBP1_ENST00000394601.4_Silent_p.D172D|PTBP1_ENST00000350092.4_Intron	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	172					alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		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;0.000172)|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)		CGGCCGTGGACGCAGGGATGG	0.692													C|||	421	0.0840655	0.0567	0.1513	5008	,	,		13240	0.0377		0.0944	False		,,,				2504	0.1104				p.D172D		Atlas-SNP	.											.	PTBP1	43	.	0			c.C516T						PASS	.	C	,,,	286,4114		9,268,1923	41.0	43.0	43.0		516,516,516,	-6.4	0.3	19	dbSNP_111	43	783,7811		25,733,3539	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	34,1001,5462	TT,TC,CC		9.111,6.5,8.2269	,,,	172/558,172/551,172/532,	804612	1069,11925	2200	4297	6497	SO:0001819	synonymous_variant	5725	exon6			CGTGGACGCAGGG	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.516C>T	19.37:g.804612C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_031990	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.922;T|0.078	0.078	strong		0.692	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
KRT78	196374	hgsc.bcm.edu	37	12	53242389	53242389	+	Missense_Mutation	SNP	G	G	A	rs116117459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53242389G>A	ENST00000304620.4	-	1	389	c.326C>T	c.(325-327)aCg>aTg	p.T109M	KRT78_ENST00000359499.4_5'Flank	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	109	Head.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						GGTCTCCTGCGTCCGCACCAC	0.567													G|||	67	0.0133786	0.0507	0.0	5008	,	,		16189	0.0		0.0	False		,,,				2504	0.0				p.T109M		Atlas-SNP	.											.	KRT78	41	.	0			c.C326T						PASS	.	G	MET/THR	254,4152	145.7+/-180.5	5,244,1954	106.0	88.0	94.0		326	4.2	1.0	12	dbSNP_132	94	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KRT78	NM_173352.2	81	5,245,6253	AA,AG,GG		0.0116,5.7649,1.9606	probably-damaging	109/521	53242389	255,12751	2203	4300	6503	SO:0001583	missense	196374	exon1			TCCTGCGTCCGCA	AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.326C>T	12.37:g.53242389G>A	ENSP00000306261:p.Thr109Met	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	187	89	0.475936	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Missense_Mutation	SNP	ENST00000304620.4	37	CCDS8840.1	31	0.014194139194139194	31	0.06300813008130081	0	0.0	0	0.0	0	0.0	G	20.4	3.978126	0.74360	0.057649	1.16E-4	ENSG00000170423	ENST00000304620	T	0.77877	-1.13	5.18	4.22	0.49857	.	.	.	.	.	T	0.56485	0.1988	M	0.90369	3.11	0.25830	N	0.984172	D	0.89917	1.0	D	0.65874	0.939	T	0.67364	-0.5689	9	0.72032	D	0.01	.	13.5578	0.61770	0.0:0.0:0.8437:0.1563	.	109	Q8N1N4	K2C78_HUMAN	M	109	ENSP00000306261:T109M	ENSP00000306261:T109M	T	-	2	0	KRT78	51528656	0.080000	0.21391	0.977000	0.42913	0.994000	0.84299	2.068000	0.41471	2.575000	0.86900	0.491000	0.48974	ACG	G|0.983;A|0.017	0.017	strong		0.567	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352	
WHAMM	123720	hgsc.bcm.edu	37	15	83499766	83499766	+	Missense_Mutation	SNP	G	G	A	rs3814281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83499766G>A	ENST00000286760.4	+	9	2156	c.2057G>A	c.(2056-2058)cGt>cAt	p.R686H		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	686	Mediates actin nucleation. {ECO:0000269|PubMed:18614018}.		R -> H (in dbSNP:rs3814281).		actin filament organization (GO:0007015)|actin filament reorganization (GO:0090527)|ER to Golgi vesicle-mediated transport (GO:0006888)|focal adhesion assembly (GO:0048041)|lamellipodium assembly (GO:0030032)|membrane tubulation (GO:0097320)|positive regulation of actin nucleation (GO:0051127)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|Golgi membrane (GO:0000139)	Arp2/3 complex binding (GO:0071933)|GTP-Rho binding (GO:0017049)|microtubule binding (GO:0008017)			endometrium(6)|large_intestine(5)|lung(1)|prostate(1)	13						GACCAGCCACGTCCTCTAGTG	0.557													G|||	884	0.176518	0.0893	0.1066	5008	,	,		13192	0.2044		0.1223	False		,,,				2504	0.3712				p.R686H		Atlas-SNP	.											.	WHAMM	63	.	0			c.G2057A						PASS	.	G	HIS/ARG	399,3911		22,355,1778	87.0	92.0	90.0		2057	-1.0	0.0	15	dbSNP_107	90	1183,7365		93,997,3184	yes	missense	WHAMM	NM_001080435.1	29	115,1352,4962	AA,AG,GG		13.8395,9.2575,12.3036	benign	686/810	83499766	1582,11276	2155	4274	6429	SO:0001583	missense	123720	exon9			AGCCACGTCCTCT	AK126887	CCDS45333.1	15q25.2	2009-02-18	2009-02-18	2009-02-18	ENSG00000156232	ENSG00000156232			30493	protein-coding gene	gene with protein product		612393	"""WAS protein homology region 2 domain containing 1"""	WHDC1		11853319, 18226259, 18614018, 18812086	Standard	XM_005272422		Approved	KIAA1971	uc002bje.3	Q8TF30		ENST00000286760.4:c.2057G>A	15.37:g.83499766G>A	ENSP00000286760:p.Arg686His	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_001080435	Q8N1J9	Missense_Mutation	SNP	ENST00000286760.4	37	CCDS45333.1	292	0.1336996336996337	57	0.11585365853658537	41	0.1132596685082873	102	0.17832167832167833	92	0.12137203166226913	G	10.84	1.463252	0.26248	0.092575	0.138395	ENSG00000156232	ENST00000286760;ENST00000234505	T	0.08370	3.1	4.58	-1.03	0.10102	.	1.727280	0.03091	N	0.159766	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.13145	0.007	B	0.06405	0.002	T	0.45056	-0.9287	9	0.14252	T	0.57	.	11.8047	0.52147	0.0:0.0:0.6383:0.3617	rs3814281;rs52812483;rs57439210;rs3814281	686	Q8TF30	WHAMM_HUMAN	H	686	ENSP00000286760:R686H	ENSP00000234505:R686H	R	+	2	0	WHAMM	81296820	0.000000	0.05858	0.001000	0.08648	0.451000	0.32288	-0.434000	0.06939	-0.351000	0.08249	-1.135000	0.01939	CGT	G|0.866;A|0.134	0.134	strong		0.557	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1		
BEST1	7439	hgsc.bcm.edu	37	11	61719387	61719387	+	Silent	SNP	T	T	C	rs1800007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61719387T>C	ENST00000378043.4	+	2	752	c.109T>C	c.(109-111)Tta>Cta	p.L37L	BEST1_ENST00000378042.3_5'UTR|BEST1_ENST00000449131.2_Intron|BEST1_ENST00000534553.1_Intron|BEST1_ENST00000435278.2_Silent_p.L37L|BEST1_ENST00000301774.9_Intron	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	37					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						TGGCGAGTTCTTAATCTTCCT	0.572													T|||	3408	0.680511	0.7988	0.5893	5008	,	,		15117	0.8978		0.3052	False		,,,				2504	0.7474				p.L37L		Atlas-SNP	.											.	BEST1	85	.	0			c.T109C						PASS	.	T	,	3153,1251	703.6+/-407.0	1136,881,185	112.0	114.0	113.0		,109	-1.9	0.9	11	dbSNP_89	113	2663,5935	428.0+/-355.8	435,1793,2071	no	intron,coding-synonymous	BEST1	NM_001139443.1,NM_004183.3	,	1571,2674,2256	CC,CT,TT		30.9723,28.406,44.7316	,	,37/586	61719387	5816,7186	2202	4299	6501	SO:0001819	synonymous_variant	7439	exon2			GAGTTCTTAATCT	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.109T>C	11.37:g.61719387T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			T|0.448;C|0.552	0.552	strong		0.572	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
UACA	55075	hgsc.bcm.edu	37	15	70960422	70960422	+	Silent	SNP	C	C	T	rs61742861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70960422C>T	ENST00000322954.6	-	16	2786	c.2601G>A	c.(2599-2601)gaG>gaA	p.E867E	UACA_ENST00000560441.1_Silent_p.E852E|UACA_ENST00000539319.1_Silent_p.E758E|UACA_ENST00000379983.2_Silent_p.E854E	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	867					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TCATTTTAACCTCTTCATGGG	0.333													C|||	75	0.014976	0.0552	0.0029	5008	,	,		19447	0.0		0.0	False		,,,				2504	0.0				p.E867E		Atlas-SNP	.											.	UACA	235	.	0			c.G2601A						PASS	.	C	,	195,4201	120.0+/-157.7	3,189,2006	96.0	90.0	92.0		2562,2601	2.6	0.6	15	dbSNP_129	92	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	3,190,6303	TT,TC,CC		0.0116,4.4359,1.5086	,	854/1404,867/1417	70960422	196,12796	2198	4298	6496	SO:0001819	synonymous_variant	55075	exon16			TTTAACCTCTTCA	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.2601G>A	15.37:g.70960422C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			C|0.985;T|0.015	0.015	strong		0.333	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
PDE4DIP	9659	hgsc.bcm.edu	37	1	144863438	144863438	+	Missense_Mutation	SNP	G	G	T	rs140993521		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144863438G>T	ENST00000369354.3	-	37	6154	c.5965C>A	c.(5965-5967)Cag>Aag	p.Q1989K	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.Q2074K|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.Q2125K|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.Q1989K|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.Q1883K			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1989					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)		AGCTTGTGCTGCAGTCTGACC	0.527			T	PDGFRB	MPD																																p.Q1989K		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,NS,carcinoma,0,2	PDE4DIP	817	2	0			c.C5965A						scavenged	.						180.0	167.0	171.0					1																	144863438		2203	4300	6503	SO:0001583	missense	9659	exon37			TGTGCTGCAGTCT	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.5965C>A	1.37:g.144863438G>T	ENSP00000358360:p.Gln1989Lys	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	287	15	0.0522648	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.4|22.4	4.291537|4.291537	0.80914|0.80914	.|.	.|.	ENSG00000178104|ENSG00000178104	ENST00000530130|ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	.|T;T;T;T;T	.|0.03124	.|4.04;4.09;4.08;4.17;4.14	4.83|4.83	4.83|4.83	0.62350|0.62350	.|.	.|.	.|.	.|.	.|.	.|T	.|0.05777	.|0.0151	M|M	0.77313|0.77313	2.365|2.365	0.36029|0.36029	D|D	0.839278|0.839278	.|P;B	.|0.46784	.|0.884;0.261	.|P;B	.|0.46076	.|0.503;0.297	.|T	.|0.06250	.|-1.0837	.|9	.|0.66056	.|D	.|0.02	.|.	15.7693|15.7693	0.78152|0.78152	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1883;1989	.|Q5VU43-3;Q5VU43	.|.;MYOME_HUMAN	X|K	145|1883;1989;1989;2074;2125	.|ENSP00000327209:Q1883K;ENSP00000358360:Q1989K;ENSP00000358363:Q1989K;ENSP00000435654:Q2074K;ENSP00000358366:Q2125K	.|ENSP00000327209:Q1883K	C|Q	-|-	3|1	2|0	PDE4DIP|PDE4DIP	143574795|143574795	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.800000|0.800000	0.45204|0.45204	4.045000|4.045000	0.57368|0.57368	2.407000|2.407000	0.81776|0.81776	0.484000|0.484000	0.47621|0.47621	TGC|CAG	.	.	weak		0.527	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
PAPPA2	60676	hgsc.bcm.edu	37	1	176564092	176564092	+	Missense_Mutation	SNP	C	C	T	rs34698817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:176564092C>T	ENST00000367662.3	+	3	2516	c.1352C>T	c.(1351-1353)gCg>gTg	p.A451V	PAPPA2_ENST00000367661.3_Missense_Mutation_p.A451V	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	451	Metalloprotease.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						GAGGAGGAAGCGACTGACTTG	0.532													C|||	17	0.00339457	0.0113	0.0029	5008	,	,		21732	0.0		0.0	False		,,,				2504	0.0				p.A451V		Atlas-SNP	.											PAPPA2_ENST00000367661,NS,carcinoma,-1,1	PAPPA2	665	1	0			c.C1352T						PASS	.	C	VAL/ALA,VAL/ALA	29,4195		0,29,2083	99.0	105.0	103.0		1352,1352	2.4	0.0	1	dbSNP_126	103	0,8456		0,0,4228	yes	missense,missense	PAPPA2	NM_020318.2,NM_021936.2	64,64	0,29,6311	TT,TC,CC		0.0,0.6866,0.2287	benign,benign	451/1792,451/828	176564092	29,12651	2112	4228	6340	SO:0001583	missense	60676	exon3			AGGAAGCGACTGA	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1352C>T	1.37:g.176564092C>T	ENSP00000356634:p.Ala451Val	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	6	0.0027472527472527475	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	0	0.0	C	0.118	-1.128701	0.01756	0.006866	0.0	ENSG00000116183	ENST00000367662;ENST00000367661	T;T	0.30448	4.78;1.53	4.87	2.4	0.29515	.	1.625110	0.03455	N	0.211229	T	0.12732	0.0309	N	0.14661	0.345	0.09310	N	1	B;B	0.15473	0.008;0.013	B;B	0.08055	0.003;0.001	T	0.18871	-1.0323	10	0.18276	T	0.48	0.1753	3.9845	0.09509	0.1568:0.3405:0.0:0.5026	rs34698817	451;451	Q9BXP8;A9Z1Y8	PAPP2_HUMAN;.	V	451	ENSP00000356634:A451V;ENSP00000356633:A451V	ENSP00000356633:A451V	A	+	2	0	PAPPA2	174830715	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.277000	0.18734	0.230000	0.21059	-0.300000	0.09419	GCG	C|0.997;T|0.003	0.003	strong		0.532	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
AARS2	57505	hgsc.bcm.edu	37	6	44270189	44270189	+	Missense_Mutation	SNP	A	A	T	rs35967387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44270189A>T	ENST00000244571.4	-	18	2428	c.2426T>A	c.(2425-2427)cTg>cAg	p.L809Q	AARS2_ENST00000491573.1_5'Flank|RP11-444E17.6_ENST00000505802.1_Intron|TMEM151B_ENST00000438774.2_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCGGCTCCCCAGACTCAGCCG	0.632													T|||	114	0.0227636	0.0847	0.0029	5008	,	,		18406	0.0		0.0	False		,,,				2504	0.0				p.L809Q		Atlas-SNP	.											.	AARS2	77	.	0			c.T2426A						PASS	.	T	GLN/LEU	256,4150	795.4+/-415.3	5,246,1952	41.0	46.0	44.0		2426	0.2	1.0	6	dbSNP_126	44	1,8599		0,1,4299	yes	missense	AARS2	NM_020745.2	113	5,247,6251	TT,TA,AA		0.0116,5.8103,1.976	benign	809/986	44270189	257,12749	2203	4300	6503	SO:0001583	missense	57505	exon18			CTCCCCAGACTCA	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	21022	protein-coding gene	gene with protein product	"""alanine tRNA ligase 2, mitochondrial"""	612035	"""alanyl-tRNA synthetase like"", ""alanyl-tRNA synthetase 2, mitochondrial (putative)"""	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.2426T>A	6.37:g.44270189A>T	ENSP00000244571:p.Leu809Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	131	66	0.503817	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	37	CCDS34464.1	48	0.02197802197802198	47	0.09552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	T	1.128	-0.653372	0.03480	0.058103	1.16E-4	ENSG00000124608	ENST00000244571	T	0.63913	-0.07	5.32	0.155	0.14906	.	1.197330	0.05517	N	0.561479	T	0.09113	0.0225	N	0.01048	-1.04	0.22947	N	0.998524	B	0.02656	0.0	B	0.01281	0.0	T	0.09250	-1.0683	10	0.12103	T	0.63	-10.1928	4.7087	0.12861	0.2367:0.3061:0.0:0.4572	rs35967387	809	Q5JTZ9	SYAM_HUMAN	Q	809	ENSP00000244571:L809Q	ENSP00000244571:L809Q	L	-	2	0	AARS2	44378167	0.362000	0.24980	0.961000	0.40146	0.084000	0.17831	-0.656000	0.05342	-0.185000	0.10550	-0.983000	0.02560	CTG	A|0.977;T|0.023	0.023	strong		0.632	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745	
NCOA3	8202	hgsc.bcm.edu	37	20	46279866	46279866	+	Silent	SNP	A	A	G	rs578139784|rs112826888|rs1132443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:46279866A>G	ENST00000371998.3	+	20	3983	c.3792A>G	c.(3790-3792)caA>caG	p.Q1264Q	NCOA3_ENST00000372004.3_Silent_p.Q1260Q|NCOA3_ENST00000371997.3_Silent_p.Q1255Q|NCOA3_ENST00000341724.6_Silent_p.Q1190Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1264	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)			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						agcagcagcaacagcaacagc	0.567													G|||	599	0.119609	0.2186	0.0663	5008	,	,		14499	0.0873		0.0726	False		,,,				2504	0.1053				p.Q1264Q		Atlas-SNP	.											NCOA3,colon,carcinoma,0,1	NCOA3	156	1	0			c.A3792G						PASS	.	G	,,,	561,3841		126,309,1766	56.0	66.0	62.0		3789,3765,3780,3792	0.0	0.2	20	dbSNP_86	62	436,8164		30,376,3894	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	156,685,5660	GG,GA,AA		5.0698,12.7442,7.6681	,,,	1263/1424,1255/1416,1260/1421,1264/1425	46279866	997,12005	2201	4300	6501	SO:0001819	synonymous_variant	8202	exon20			GCAGCAACAGCAA	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.3792A>G	20.37:g.46279866A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	34	32	0.941176	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			A|0.870;G|0.130	0.130	strong		0.567	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
FLI1	2313	hgsc.bcm.edu	37	11	128675292	128675292	+	Silent	SNP	T	T	A	rs7113191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:128675292T>A	ENST00000527786.2	+	6	1176	c.687T>A	c.(685-687)gcT>gcA	p.A229A	FLI1_ENST00000344954.6_Silent_p.A196A|FLI1_ENST00000281428.8_Silent_p.A163A|FLI1_ENST00000525560.1_Silent_p.A36A|FLI1_ENST00000534087.2_Silent_p.A196A	NM_001271010.1|NM_002017.4	NP_001257939.1|NP_002008.2	Q01543	FLI1_HUMAN	Fli-1 proto-oncogene, ETS transcription factor	229					blood circulation (GO:0008015)|cell differentiation (GO:0030154)|hemostasis (GO:0007599)|megakaryocyte development (GO:0035855)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/FLI1(2569)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(2)	31	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		GAAGAGGAGCTTGGGGCAATA	0.398			T	EWSR1	Ewing sarcoma								t|||	877	0.17512	0.2579	0.1254	5008	,	,		21079	0.1706		0.1093	False		,,,				2504	0.1708				p.A229A		Atlas-SNP	.		Dom	yes		11	11q24	2313	Friend leukemia virus integration 1		M	.	FLI1	72	.	0			c.T687A						PASS	.	A	,	916,2778		125,666,1056	77.0	76.0	76.0		588,687	-0.8	0.6	11	dbSNP_116	76	890,7286		47,796,3245	no	coding-synonymous,coding-synonymous	FLI1	NM_001167681.2,NM_002017.3	,	172,1462,4301	AA,AT,TT		10.8855,24.797,15.2148	,	196/420,229/453	128675292	1806,10064	1847	4088	5935	SO:0001819	synonymous_variant	2313	exon6			AGGAGCTTGGGGC	M98833	CCDS44768.1, CCDS53725.1, CCDS59230.1, CCDS59231.1	11q24.1-q24.3	2014-09-17	2013-08-07		ENSG00000151702	ENSG00000151702			3749	protein-coding gene	gene with protein product		193067	"""Friend leukemia virus integration 1"""			1765382	Standard	NM_001167681		Approved	SIC-1, EWSR2	uc010sbu.2	Q01543	OTTHUMG00000165792	ENST00000527786.2:c.687T>A	11.37:g.128675292T>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_002017	B2R8H2|B4DFV4|B4DTC6|G3V183|Q14319|Q92480|Q9UE07	Silent	SNP	ENST00000527786.2	37	CCDS44768.1																																																																																			T|0.855;A|0.145	0.145	strong		0.398	FLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386226.2	NM_002017	
IGSF5	150084	hgsc.bcm.edu	37	21	41137499	41137499	+	Silent	SNP	A	A	G	rs12626544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	78	0	0		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	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		
GKN1	56287	hgsc.bcm.edu	37	2	69204671	69204671	+	Silent	SNP	A	A	T	rs9808077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69204671A>T	ENST00000377938.2	+	2	162	c.99A>T	c.(97-99)ctA>ctT	p.L33L		NM_019617.3	NP_062563.3	Q9NS71	GKN1_HUMAN	gastrokine 1	33					digestion (GO:0007586)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|secretory granule (GO:0030141)				breast(2)|large_intestine(4)|lung(5)	11						CTCCTGCCCTAGCTAACTATG	0.363													T|||	1429	0.285343	0.4062	0.2219	5008	,	,		19096	0.3581		0.0954	False		,,,				2504	0.2873				p.L33L		Atlas-SNP	.											.	GKN1	24	.	0			c.A99T						PASS	.	T		1562,2844	669.1+/-402.1	269,1024,910	187.0	162.0	171.0		99	2.6	0.2	2	dbSNP_119	171	742,7858	785.4+/-407.6	46,650,3604	no	coding-synonymous	GKN1	NM_019617.3		315,1674,4514	TT,TA,AA		8.6279,35.4517,17.7149		33/200	69204671	2304,10702	2203	4300	6503	SO:0001819	synonymous_variant	56287	exon2			TGCCCTAGCTAAC	AY139182	CCDS1891.2	2p13.3	2012-10-10			ENSG00000169605	ENSG00000169605		"""BRICHOS domain containing"""	23217	protein-coding gene	gene with protein product	"""BRICHOS domain containing 1"""	606402				12851218, 11562744	Standard	NM_019617		Approved	AMP18, CA11, BRICD1	uc002sfc.3	Q9NS71	OTTHUMG00000129574	ENST00000377938.2:c.99A>T	2.37:g.69204671A>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	176	176	1	NM_019617	Q8IUA9	Silent	SNP	ENST00000377938.2	37	CCDS1891.2																																																																																			A|0.804;T|0.196	0.196	strong		0.363	GKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251769.2	NM_019617	
NFKBID	84807	hgsc.bcm.edu	37	19	36387881	36387881	+	Missense_Mutation	SNP	A	A	G	rs8113704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36387881A>G	ENST00000396901.1	-	5	659	c.86T>C	c.(85-87)gTg>gCg	p.V29A	NFKBID_ENST00000352614.2_Missense_Mutation_p.V181A|NFKBID_ENST00000585544.1_5'Flank|NFKBID_ENST00000606253.1_Missense_Mutation_p.V29A	NM_139239.1	NP_640332.1	Q8NI38	IKBD_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, delta	29			V -> A (in dbSNP:rs8113704).		inflammatory response (GO:0006954)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|positive regulation of thymocyte apoptotic process (GO:0070245)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	14						AGCTCGGGCCACCTCCAGCGA	0.617													G|||	988	0.197284	0.5333	0.0778	5008	,	,		15936	0.1151		0.0318	False		,,,				2504	0.0828				p.V29A		Atlas-SNP	.											.	NFKBID	30	.	0			c.T86C						PASS	.	G	ALA/VAL	1756,2146		402,952,597	47.0	52.0	50.0		86	4.7	0.0	19	dbSNP_116	50	387,7893		2,383,3755	yes	missense	NFKBID	NM_139239.1	64	404,1335,4352	GG,GA,AA		4.6739,45.0026,17.5915	benign	29/314	36387881	2143,10039	1951	4140	6091	SO:0001583	missense	84807	exon5			CGGGCCACCTCCA	AF385434	CCDS42552.1	19q13.12	2013-01-10				ENSG00000167604		"""Ankyrin repeat domain containing"""	15671	protein-coding gene	gene with protein product						12477932	Standard	NM_139239		Approved	TA-NFKBH, IkappaBNS	uc002oci.1	Q8NI38		ENST00000396901.1:c.86T>C	19.37:g.36387881A>G	ENSP00000380109:p.Val29Ala	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	170	169	0.994118	NM_139239	Q8NI39|Q9BRG9	Missense_Mutation	SNP	ENST00000396901.1	37	CCDS42552.1	350	0.16025641025641027	216	0.43902439024390244	31	0.0856353591160221	78	0.13636363636363635	25	0.032981530343007916	G	0.008	-1.933930	0.00488	0.450026	0.046739	ENSG00000167604	ENST00000352614;ENST00000396901	T;T	0.54071	0.59;1.2	4.74	4.74	0.60224	.	1.395380	0.04214	N	0.332260	T	0.00012	0.0000	N	0.02539	-0.55	0.54753	P	2.0000000000020002E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40213	-0.9575	9	0.07030	T	0.85	.	6.1006	0.20045	0.0951:0.0:0.7206:0.1843	rs8113704;rs58139929;rs8113704	181;29	Q8NI38-2;Q8NI38	.;IKBD_HUMAN	A	181;29	ENSP00000252985:V181A;ENSP00000380109:V29A	ENSP00000252985:V181A	V	-	2	0	NFKBID	41079721	0.500000	0.26091	0.038000	0.18304	0.149000	0.21700	2.646000	0.46630	1.245000	0.43885	-0.215000	0.12644	GTG	A|0.840;G|0.160	0.160	strong		0.617	NFKBID-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452927.3	NM_032721	
FBXL6	26233	hgsc.bcm.edu	37	8	145579962	145579962	+	Missense_Mutation	SNP	C	C	T	rs77494279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145579962C>T	ENST00000331890.5	-	7	1287	c.1223G>A	c.(1222-1224)cGg>cAg	p.R408Q	SLC52A2_ENST00000402965.1_5'Flank|TMEM249_ENST00000531225.1_5'Flank|FBXL6_ENST00000455319.2_Missense_Mutation_p.R402Q|SLC52A2_ENST00000329994.2_5'Flank|FBXL6_ENST00000526524.1_5'UTR|SLC52A2_ENST00000540505.1_5'Flank|SLC52A2_ENST00000530047.1_5'Flank|TMEM249_ENST00000398633.3_5'Flank|SLC52A2_ENST00000532887.1_5'Flank|SLC52A2_ENST00000527078.1_5'Flank|SLC52A2_ENST00000526752.1_5'Flank	NM_012162.2	NP_036294.2	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6	408					protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)		ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|lung(3)|ovary(1)	5	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;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			CTGCTGACCCCGACATGGCAG	0.642																																					p.R408Q		Atlas-SNP	.											FBXL6,colon,carcinoma,0,1	FBXL6	26	1	0			c.G1223A						scavenged	.						37.0	38.0	37.0					8																	145579962		2199	4296	6495	SO:0001583	missense	26233	exon7			TGACCCCGACATG	AF174592	CCDS6422.1, CCDS47942.1	8q24.3	2011-06-09			ENSG00000182325	ENSG00000182325		"""F-boxes / Leucine-rich repeats"""	13603	protein-coding gene	gene with protein product		609076				10531035, 10531037	Standard	NM_012162		Approved	FBL6	uc003zcb.3	Q8N531	OTTHUMG00000165169	ENST00000331890.5:c.1223G>A	8.37:g.145579962C>T	ENSP00000330098:p.Arg408Gln	Somatic	52	6	0.115385		WXS	Illumina HiSeq	Phase_I	55	7	0.127273	NM_012162	Q53G43|Q9H5W9|Q9UKC7	Missense_Mutation	SNP	ENST00000331890.5	37	CCDS6422.1	.	.	.	.	.	.	.	.	.	.	C	2.320	-0.355930	0.05138	.	.	ENSG00000182325	ENST00000455319;ENST00000331890	T;T	0.23147	5.54;1.92	4.72	2.42	0.29668	.	0.526222	0.16851	N	0.196922	T	0.11410	0.0278	N	0.15975	0.35	0.23559	N	0.99742	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.29610	-1.0006	10	0.16420	T	0.52	-1.2663	4.1831	0.10385	0.0:0.125:0.2883:0.5867	.	408;402	Q8N531;Q8N531-2	FBXL6_HUMAN;.	Q	402;408	ENSP00000403873:R402Q;ENSP00000330098:R408Q	ENSP00000330098:R408Q	R	-	2	0	FBXL6	145550770	0.000000	0.05858	1.000000	0.80357	0.021000	0.10359	-0.300000	0.08243	0.656000	0.30886	-0.481000	0.04817	CGG	C|0.932;T|0.068	0.068	strong		0.642	FBXL6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382413.1	NM_024555	
BST1	683	hgsc.bcm.edu	37	4	15709252	15709252	+	Missense_Mutation	SNP	G	G	A	rs2302464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	191	2	0.0104712		WXS	Illumina HiSeq	Phase_I	165	72	0.436364	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	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110534512	110534512	+	Silent	SNP	G	G	A	rs1563578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	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	
LILRA4	23547	hgsc.bcm.edu	37	19	54848125	54848125	+	Silent	SNP	C	C	T	rs138326444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54848125C>T	ENST00000291759.4	-	6	1298	c.1242G>A	c.(1240-1242)gaG>gaA	p.E414E	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	414					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)		AGACCACGAGCTCCAGGGGCT	0.597													C|||	110	0.0219649	0.0598	0.0101	5008	,	,		17485	0.0		0.0099	False		,,,				2504	0.0143				p.E414E		Atlas-SNP	.											.	LILRA4	91	.	0			c.G1242A						PASS	.						86.0	72.0	77.0					19																	54848125		2203	4300	6503	SO:0001819	synonymous_variant	23547	exon6			CACGAGCTCCAGG	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.1242G>A	19.37:g.54848125C>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	271	42	0.154982	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																			C|0.999;T|0.001	0.001	weak		0.597	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
LRIT3	345193	hgsc.bcm.edu	37	4	110791453	110791453	+	Silent	SNP	T	T	C	rs9994891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:110791453T>C	ENST00000594814.1	+	4	1548	c.1548T>C	c.(1546-1548)acT>acC	p.T516T	LRIT3_ENST00000379920.3_Silent_p.T471T|LRIT3_ENST00000327908.3_Silent_p.T333T|LRIT3_ENST00000409621.2_Silent_p.T333T	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	516	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		CTGCAGTGACTGTGTTGTATT	0.473													T|||	588	0.117412	0.4228	0.0346	5008	,	,		22015	0.001		0.004	False		,,,				2504	0.0				p.T516T		Atlas-SNP	.											.	LRIT3	107	.	0			c.T1548C						PASS	.	T		1599,2807	496.0+/-363.4	295,1009,899	152.0	139.0	144.0		1413	-6.0	0.0	4	dbSNP_119	144	61,8539	36.4+/-91.3	1,59,4240	no	coding-synonymous	LRIT3	NM_198506.2		296,1068,5139	CC,CT,TT		0.7093,36.2914,12.7633		471/635	110791453	1660,11346	2203	4300	6503	SO:0001819	synonymous_variant	345193	exon4			AGTGACTGTGTTG	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1548T>C	4.37:g.110791453T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	151	148	0.980132	NM_198506	C9J1C2|Q6ZTG1	Silent	SNP	ENST00000594814.1	37	CCDS3688.3																																																																																			T|0.866;C|0.134	0.134	strong		0.473	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
C5orf42	65250	hgsc.bcm.edu	37	5	37226888	37226888	+	Silent	SNP	A	A	G	rs115435816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37226888A>G	ENST00000508244.1	-	11	1902	c.1809T>C	c.(1807-1809)acT>acC	p.T603T	C5orf42_ENST00000274258.7_5'UTR|C5orf42_ENST00000425232.2_Silent_p.T603T			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	603						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			AAAAAAAATGAGTGATACAAA	0.284													A|||	92	0.0183706	0.0673	0.0043	5008	,	,		18803	0.0		0.0	False		,,,				2504	0.0				p.T603T		Atlas-SNP	.											.	C5orf42	422	.	0			c.T1809C						PASS	.	A		89,1295		5,79,608	46.0	38.0	40.0		1809	4.1	1.0	5	dbSNP_132	40	1,3175		0,1,1587	no	coding-synonymous	C5orf42	NM_023073.3		5,80,2195	GG,GA,AA		0.0315,6.4306,1.9737		603/3198	37226888	90,4470	692	1588	2280	SO:0001819	synonymous_variant	65250	exon12			AAAATGAGTGATA		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.1809T>C	5.37:g.37226888A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			A|0.984;G|0.016	0.016	strong		0.284	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
HMGB1	3146	hgsc.bcm.edu	37	13	31037445	31037445	+	Silent	SNP	T	T	C	rs983723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:31037445T>C	ENST00000405805.1	-	3	1135	c.195A>G	c.(193-195)aaA>aaG	p.K65K	HMGB1_ENST00000341423.5_Silent_p.K65K|HMGB1_ENST00000399494.1_Silent_p.K65K|HMGB1_ENST00000399489.1_Silent_p.K65K|HMGB1_ENST00000339872.4_Silent_p.K65K|HMGB1_ENST00000326004.4_Silent_p.K65K|HMGB1_ENST00000468384.1_5'Flank			P09429	HMGB1_HUMAN	high mobility group box 1	65					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		CCTTGTCCGCTTTTGCCATAT	0.368													C|||	399	0.0796725	0.292	0.0159	5008	,	,		19065	0.0		0.002	False		,,,				2504	0.0				p.K65K		Atlas-SNP	.											.	HMGB1	21	.	0			c.A195G						PASS	.	C		996,3410	684.5+/-404.4	121,754,1328	57.0	64.0	62.0		195	3.4	1.0	13	dbSNP_86	62	7,8593	813.0+/-407.0	0,7,4293	no	coding-synonymous	HMGB1	NM_002128.4		121,761,5621	CC,CT,TT		0.0814,22.6055,7.7118		65/216	31037445	1003,12003	2203	4300	6503	SO:0001819	synonymous_variant	3146	exon3			GTCCGCTTTTGCC	D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403		"""High-mobility group / Canonical"""	4983	protein-coding gene	gene with protein product	"""high mobility group box 1"", ""Sulfoglucuronyl carbohydrate binding protein"", ""Amphoterin"", ""high mobility group protein 1"""	163905	"""high-mobility group (nonhistone chromosomal) protein 1"", ""high-mobility group box 1"""	HMG1		8661151, 11279268	Standard	NM_002128		Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.195A>G	13.37:g.31037445T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_002128	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Silent	SNP	ENST00000405805.1	37	CCDS9335.1																																																																																			T|0.941;C|0.059	0.059	strong		0.368	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128	
LRP4	4038	hgsc.bcm.edu	37	11	46918529	46918529	+	Silent	SNP	C	C	T	rs879721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46918529C>T	ENST00000378623.1	-	8	1055	c.813G>A	c.(811-813)acG>acA	p.T271T		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	271	LDL-receptor class A 7. {ECO:0000255|PROSITE-ProRule:PRU00124}.				dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		ACTGTTCTGCCGTACACATGG	0.552													T|||	309	0.0617013	0.2239	0.0173	5008	,	,		17998	0.0		0.001	False		,,,				2504	0.0				p.T271T		Atlas-SNP	.											.	LRP4	160	.	0			c.G813A						PASS	.	T		770,3632	753.5+/-412.4	68,634,1499	113.0	100.0	104.0		813	-11.6	0.0	11	dbSNP_86	104	3,8595	819.0+/-406.8	0,3,4296	no	coding-synonymous	LRP4	NM_002334.3		68,637,5795	TT,TC,CC		0.0349,17.492,5.9462		271/1906	46918529	773,12227	2201	4299	6500	SO:0001819	synonymous_variant	4038	exon8			TTCTGCCGTACAC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.813G>A	11.37:g.46918529C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	37	CCDS31478.1																																																																																			C|0.943;T|0.057	0.057	strong		0.552	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
C8B	732	hgsc.bcm.edu	37	1	57415310	57415310	+	Missense_Mutation	SNP	G	G	A	rs12085435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57415310G>A	ENST00000371237.4	-	6	848	c.782C>T	c.(781-783)cCt>cTt	p.P261L	C8B_ENST00000535057.1_Missense_Mutation_p.P199L|C8B_ENST00000543257.1_Missense_Mutation_p.P209L	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	261	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.		P -> L (in dbSNP:rs12085435).		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						AAATATTCCAGGTATTTTAAA	0.348													G|||	211	0.0421326	0.0575	0.0375	5008	,	,		18532	0.0		0.0547	False		,,,				2504	0.0552				p.P261L		Atlas-SNP	.											.	C8B	107	.	0			c.C782T						PASS	.	G	LEU/PRO	286,4120	158.1+/-190.9	8,270,1925	123.0	124.0	124.0		782	0.9	0.0	1	dbSNP_120	124	478,8122	140.1+/-196.7	14,450,3836	yes	missense	C8B	NM_000066.2	98	22,720,5761	AA,AG,GG		5.5581,6.4911,5.8742	benign	261/592	57415310	764,12242	2203	4300	6503	SO:0001583	missense	732	exon6			ATTCCAGGTATTT	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"""Complement system"""	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.782C>T	1.37:g.57415310G>A	ENSP00000360281:p.Pro261Leu	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	140	56	0.4	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	37	CCDS30730.1	92	0.04212454212454213	34	0.06910569105691057	18	0.049723756906077346	0	0.0	40	0.052770448548812667	G	10.43	1.347429	0.24426	0.064911	0.055581	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	T;T;T	0.27557	1.84;1.85;1.66	5.19	0.854	0.19007	Membrane attack complex component/perforin (MACPF) domain (1);	2.075460	0.02088	N	0.052888	T	0.03011	0.0089	M	0.63428	1.95	0.45594	P	0.001466999999999996	B;B;B	0.15141	0.007;0.012;0.002	B;B;B	0.16289	0.015;0.015;0.002	T	0.17107	-1.0380	9	0.35671	T	0.21	0.0672	9.3642	0.38215	0.0677:0.0:0.5616:0.3708	rs12085435;rs52790403;rs12085435	209;199;261	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	L	261;209;199	ENSP00000360281:P261L;ENSP00000442548:P209L;ENSP00000440113:P199L	ENSP00000360281:P261L	P	-	2	0	C8B	57187898	0.016000	0.18221	0.000000	0.03702	0.006000	0.05464	0.513000	0.22770	0.222000	0.20900	-0.293000	0.09583	CCT	G|0.944;A|0.056	0.056	strong		0.348	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2		
GMNN	51053	hgsc.bcm.edu	37	6	24781719	24781719	+	Missense_Mutation	SNP	G	G	C	rs2307307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24781719G>C	ENST00000230056.3	+	4	476	c.144G>C	c.(142-144)ttG>ttC	p.L48F	GMNN_ENST00000356509.3_Missense_Mutation_p.L48F	NM_015895.4	NP_056979.1	O75496	GEMI_HUMAN	geminin, DNA replication inhibitor	48			L -> F (in dbSNP:rs2307307).		mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	10						CCGCAGGCTTGTCCAAAAGGA	0.343													G|||	433	0.0864617	0.2511	0.0331	5008	,	,		11233	0.0347		0.003	False		,,,				2504	0.0409				p.L48F		Atlas-SNP	.											.	GMNN	19	.	0			c.G144C						PASS	.	G	PHE/LEU	969,3437	348.7+/-310.1	119,731,1353	49.0	54.0	53.0		144	-3.5	0.0	6	dbSNP_100	53	60,8540	36.9+/-92.0	0,60,4240	yes	missense	GMNN	NM_015895.3	22	119,791,5593	CC,CG,GG		0.6977,21.9927,7.9117	probably-damaging	48/210	24781719	1029,11977	2203	4300	6503	SO:0001583	missense	51053	exon4			AGGCTTGTCCAAA	AF067855	CCDS4560.1	6p21.32	2008-10-31			ENSG00000112312	ENSG00000112312			17493	protein-coding gene	gene with protein product		602842				9635433	Standard	NM_001251989		Approved	Gem	uc003nem.3	O75496	OTTHUMG00000014363	ENST00000230056.3:c.144G>C	6.37:g.24781719G>C	ENSP00000230056:p.Leu48Phe	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_001251991	B3KMM8|Q9H1Z1	Missense_Mutation	SNP	ENST00000230056.3	37	CCDS4560.1	147	0.0673076923076923	112	0.22764227642276422	13	0.03591160220994475	20	0.03496503496503497	2	0.002638522427440633	G	9.323	1.058570	0.19987	0.219927	0.006977	ENSG00000112312	ENST00000356509;ENST00000230056;ENST00000378054;ENST00000476555;ENST00000378059	T;T;T;T;T	0.16073	2.37;2.37;2.37;2.37;2.37	5.49	-3.46	0.04767	.	0.887861	0.10144	N	0.710528	T	0.07098	0.0180	M	0.68317	2.08	0.80722	P	0.0	P	0.50369	0.934	P	0.49887	0.625	T	0.17198	-1.0377	9	0.10111	T	0.7	-33.3703	3.7543	0.08579	0.3203:0.1172:0.4467:0.1159	rs2307307;rs52823028;rs59360716;rs2307307	48	O75496	GEMI_HUMAN	F	48	ENSP00000348902:L48F;ENSP00000230056:L48F;ENSP00000367293:L48F;ENSP00000419584:L48F;ENSP00000367298:L48F	ENSP00000230056:L48F	L	+	3	2	GMNN	24889698	0.185000	0.23213	0.000000	0.03702	0.011000	0.07611	0.264000	0.18497	-0.400000	0.07656	-1.110000	0.02074	TTG	G|0.932;C|0.068	0.068	strong		0.343	GMNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040021.2	NM_015895	
HLA-G	3135	hgsc.bcm.edu	37	6	29795993	29795993	+	Silent	SNP	G	G	A	rs1130355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29795993G>A	ENST00000360323.6	+	2	267	c.243G>A	c.(241-243)ccG>ccA	p.P81P	HLA-G_ENST00000428701.1_Silent_p.P81P|HLA-G_ENST00000376828.2_Silent_p.P86P|HLA-G_ENST00000376818.3_Silent_p.P81P|HLA-G_ENST00000376815.3_Silent_p.P81P			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	81	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)|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						AGGAGGGGCCGGAGTATTGGG	0.647													g|||	2726	0.544329	0.5083	0.4654	5008	,	,		13086	0.6032		0.4324	False		,,,				2504	0.7035				p.P81P		Atlas-SNP	.											.	HLA-G	90	.	0			c.G243A						PASS	.	G		1537,1485		391,755,365	55.0	35.0	42.0		243	0.8	1.0	6	dbSNP_86	42	2509,2909		599,1311,799	no	coding-synonymous	HLA-G	NM_002127.5		990,2066,1164	AA,AG,GG		46.3086,49.1396,47.9384		81/339	29795993	4046,4394	1511	2709	4220	SO:0001819	synonymous_variant	3135	exon3			GGGGCCGGAGTAT		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.243G>A	6.37:g.29795993G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	110	35	0.318182	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			G|0.500;A|0.500	0.500	strong		0.647	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
PRR3	80742	hgsc.bcm.edu	37	6	30529622	30529622	+	Missense_Mutation	SNP	G	G	A	rs3888778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30529622G>A	ENST00000376560.3	+	3	640	c.181G>A	c.(181-183)Ggt>Agt	p.G61S	PRR3_ENST00000376557.3_Missense_Mutation_p.G40S|PRR3_ENST00000498336.1_3'UTR	NM_025263.3	NP_079539.2	P79522	PRR3_HUMAN	proline rich 3	61	Pro-rich.		G -> S (in dbSNP:rs3888778). {ECO:0000269|PubMed:15489334}.				metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						TCTTCACAGAGGTCCTCCAGG	0.507													G|||	166	0.033147	0.0862	0.0259	5008	,	,		17768	0.0208		0.0109	False		,,,				2504	0.002				p.G61S		Atlas-SNP	.											.	PRR3	5	.	0			c.G181A						PASS	.	G	SER/GLY,SER/GLY	137,2249		3,131,1059	9.0	9.0	9.0		118,181	3.9	1.0	6	dbSNP_108	9	47,4983		0,47,2468	yes	missense,missense	PRR3	NM_001077497.2,NM_025263.3	56,56	3,178,3527	AA,AG,GG		0.9344,5.7418,2.4811	possibly-damaging,possibly-damaging	40/168,61/189	30529622	184,7232	1193	2515	3708	SO:0001583	missense	80742	exon3			CACAGAGGTCCTC	AK074531	CCDS43440.1, CCDS43441.1	6p21.32	2013-01-18	2004-05-27		ENSG00000204576	ENSG00000204576		"""Zinc fingers, CCCH-type domain containing"""	21149	protein-coding gene	gene with protein product			"""proline-rich polpeptide 3"""				Standard	NM_025263		Approved	CAT56, Em:AB014077.1, Em:AB023052.2	uc003nqi.2	P79522	OTTHUMG00000031037	ENST00000376560.3:c.181G>A	6.37:g.30529622G>A	ENSP00000365744:p.Gly61Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_025263	A1A4H4|Q5RJB5|Q5STN6	Missense_Mutation	SNP	ENST00000376560.3	37	CCDS43440.1	75	0.034340659340659344	41	0.08333333333333333	10	0.027624309392265192	17	0.02972027972027972	7	0.009234828496042216	G	18.14	3.558222	0.65538	0.057418	0.009344	ENSG00000204576	ENST00000376560;ENST00000376555;ENST00000376557	T;T	0.61392	0.79;0.11	4.8	3.93	0.45458	.	0.000000	0.44097	D	0.000490	T	0.28665	0.0710	N	0.14661	0.345	0.35071	D	0.762444	D;P	0.55385	0.971;0.952	P;B	0.46585	0.521;0.322	T	0.33471	-0.9867	10	0.87932	D	0	-4.6812	8.9334	0.35684	0.1014:0.0:0.8986:0.0	rs3888778;rs4559118;rs3888778	40;61	P79522-2;P79522	.;PRR3_HUMAN	S	61;126;40	ENSP00000365744:G61S;ENSP00000365740:G40S	ENSP00000365738:G126S	G	+	1	0	PRR3	30637601	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.111000	0.57838	1.243000	0.43853	0.655000	0.94253	GGT	G|0.963;A|0.037	0.037	strong		0.507	PRR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076033.2	NM_025263	
SLC38A5	92745	hgsc.bcm.edu	37	X	48326270	48326270	+	Silent	SNP	C	C	T	rs34099520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48326270C>T	ENST00000376876.3	-	2	885	c.42G>A	c.(40-42)tcG>tcA	p.S14S	SLC38A5_ENST00000317669.5_Silent_p.S14S|SLC38A5_ENST00000376875.1_5'Flank			Q8WUX1	S38A5_HUMAN	solute carrier family 38, member 5	14					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)			breast(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	19						CCACAGCATCCGAAGGGAGGG	0.557													C|||	15	0.00397351	0.0113	0.0	3775	,	,		13307	0.0		0.0	False		,,,				2504	0.0				p.S14S		Atlas-SNP	.											.	SLC38A5	98	.	0			c.G42A						PASS	.	C		45,3790		1,34,9,1597,562	58.0	47.0	51.0		42	-2.4	0.0	X	dbSNP_126	51	1,6725		0,0,1,2428,1869	no	coding-synonymous	SLC38A5	NM_033518.2		1,34,10,4025,2431	TT,TC,T,CC,C		0.0149,1.1734,0.4356		14/473	48326270	46,10515	2203	4298	6501	SO:0001819	synonymous_variant	92745	exon3			AGCATCCGAAGGG	AF276889	CCDS14293.1	Xp11.23	2013-05-22			ENSG00000017483	ENSG00000017483		"""Solute carriers"""	18070	protein-coding gene	gene with protein product		300649				11243884	Standard	NM_033518		Approved	SN2, JM24	uc010nid.3	Q8WUX1	OTTHUMG00000024117	ENST00000376876.3:c.42G>A	X.37:g.48326270C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	145	64	0.441379	NM_033518	B3KT20|B5MDE6|B7WPJ9|Q6PIW9|Q8WYU2|Q96PQ4	Silent	SNP	ENST00000376876.3	37	CCDS14293.1																																																																																			C|0.997;T|0.003	0.003	strong		0.557	SLC38A5-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060724.1	NM_033518	
RRP7A	27341	hgsc.bcm.edu	37	22	42908976	42908976	+	Silent	SNP	G	G	A	rs145348367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42908976G>A	ENST00000323013.6	-	7	798	c.783C>T	c.(781-783)ttC>ttT	p.F261F	SERHL_ENST00000359906.2_RNA	NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	261							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.F261F(1)		central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						TGTCCTCCTCGAACTTCTTGC	0.662																																					p.F261F		Atlas-SNP	.											RRP7A,NS,carcinoma,0,2	RRP7A	25	2	1	Substitution - coding silent(1)	skin(1)	c.C783T						PASS	.						47.0	39.0	42.0					22																	42908976		2203	4299	6502	SO:0001819	synonymous_variant	27341	exon7			CTCCTCGAACTTC	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.783C>T	22.37:g.42908976G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	228	26	0.114035	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Silent	SNP	ENST00000323013.6	37	CCDS14036.1																																																																																			G|0.983;A|0.017	0.017	strong		0.662	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703	
ORC5	5001	hgsc.bcm.edu	37	7	103844599	103844599	+	Missense_Mutation	SNP	T	T	A	rs2307413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103844599T>A	ENST00000297431.4	-	2	298	c.156A>T	c.(154-156)aaA>aaT	p.K52N	ORC5_ENST00000545943.1_5'UTR|ORC5_ENST00000447452.2_Missense_Mutation_p.K52N|ORC5_ENST00000485726.1_5'UTR	NM_002553.3	NP_002544.1	O43913	ORC5_HUMAN	origin recognition complex, subunit 5	52			K -> N (in dbSNP:rs2307413).		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			kidney(1)|large_intestine(2)|lung(9)|pancreas(1)|upper_aerodigestive_tract(1)	14						CCTCTAAAGTTTTCAACAACG	0.299													T|||	72	0.014377	0.053	0.0029	5008	,	,		17463	0.0		0.0	False		,,,				2504	0.0				p.K52N		Atlas-SNP	.											.	ORC5	48	.	0			c.A156T						PASS	.	T	ASN/LYS,ASN/LYS	219,4183	128.6+/-165.4	8,203,1990	59.0	60.0	59.0		156,156	2.7	1.0	7	dbSNP_100	59	2,8594	1.2+/-3.3	0,2,4296	yes	missense,missense	ORC5	NM_002553.3,NM_181747.3	94,94	8,205,6286	AA,AT,TT		0.0233,4.975,1.7003	benign,benign	52/436,52/325	103844599	221,12777	2201	4298	6499	SO:0001583	missense	5001	exon2			TAAAGTTTTCAAC		CCDS5734.1, CCDS47681.1	7q22.1	2014-06-13	2010-10-12	2010-10-12	ENSG00000164815	ENSG00000164815			8491	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 117"""	602331	"""origin recognition complex, subunit 5 (yeast homolog)-like"", ""origin recognition complex, subunit 5-like (yeast)"", ""origin recognition complex, subunit 5 homolog (yeast)"""	ORC5L		9417919, 9829972	Standard	NM_002553		Approved	Orc5p, ORC5T, PPP1R117	uc003vcb.3	O43913	OTTHUMG00000157275	ENST00000297431.4:c.156A>T	7.37:g.103844599T>A	ENSP00000297431:p.Lys52Asn	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_002553	A4D0P8|O60590|O95268	Missense_Mutation	SNP	ENST00000297431.4	37	CCDS5734.1	33	0.01510989010989011	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	0	0.0	T	10.43	1.347141	0.24426	0.04975	2.33E-4	ENSG00000164815	ENST00000297431;ENST00000447452	T;T	0.62941	-0.01;-0.01	5.16	2.74	0.32292	.	0.189382	0.56097	D	0.000033	T	0.05364	0.0142	N	0.17474	0.49	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.002;0.003;0.002	T	0.02431	-1.1160	10	0.23302	T	0.38	.	3.8148	0.08811	0.1211:0.0725:0.371:0.4354	rs2307413;rs16873425;rs52800217;rs2307413	52;52;52	A4D0P7;O43913-2;O43913	.;.;ORC5_HUMAN	N	52	ENSP00000297431:K52N;ENSP00000395747:K52N	ENSP00000297431:K52N	K	-	3	2	ORC5	103631835	0.995000	0.38212	1.000000	0.80357	0.913000	0.54294	0.264000	0.18497	0.294000	0.22547	-0.438000	0.05819	AAA	T|0.985;A|0.015	0.015	strong		0.299	ORC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348286.1	NM_002553	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411091	105411091	+	Missense_Mutation	SNP	G	G	A	rs143814844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105411091G>A	ENST00000333244.5	-	7	10816	c.10697C>T	c.(10696-10698)aCg>aTg	p.T3566M	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3566						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)		p.T3566M(1)		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)			CACTTTGGGCGTCTTTAAACT	0.612													.|||	367	0.0732827	0.267	0.0173	5008	,	,		17318	0.0		0.002	False		,,,				2504	0.0				p.T3566M		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	1	Substitution - Missense(1)	prostate(1)	c.C10697T						PASS	.	A	MET/THR	783,2917		107,569,1174	98.0	113.0	108.0		10697	1.6	0.0	14	dbSNP_134	108	10,8158		0,10,4074	no	missense	AHNAK2	NM_138420.2	81	107,579,5248	AA,AG,GG		0.1224,21.1622,6.6818	benign	3566/5796	105411091	793,11075	1850	4084	5934	SO:0001583	missense	113146	exon7			TTGGGCGTCTTTA	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.10697C>T	14.37:g.105411091G>A	ENSP00000353114:p.Thr3566Met	Somatic	241	2	0.00829876		WXS	Illumina HiSeq	Phase_I	257	254	0.988327	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	80	0.03663003663003663	75	0.1524390243902439	5	0.013812154696132596	0	0.0	0	0.0	a	2.924	-0.222471	0.06061	0.211622	0.001224	ENSG00000185567	ENST00000333244	T	0.00745	5.75	4.06	1.63	0.23807	.	1.601890	0.05251	U	0.513995	T	0.00012	0.0000	N	0.00086	-2.195	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39461	-0.9613	9	0.33940	T	0.23	.	4.4622	0.11671	0.5589:0.1614:0.2797:0.0	rs2819442	3566	Q8IVF2	AHNK2_HUMAN	M	3566	ENSP00000353114:T3566M	ENSP00000353114:T3566M	T	-	2	0	AHNAK2	104482136	0.000000	0.05858	0.042000	0.18584	0.008000	0.06430	-0.778000	0.04664	-0.237000	0.09739	-1.140000	0.01884	ACG	G|0.971;A|0.029	0.029	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
HIRA	7290	hgsc.bcm.edu	37	22	19340928	19340928	+	Silent	SNP	G	G	A	rs34000365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19340928G>A	ENST00000263208.5	-	23	3055	c.2799C>T	c.(2797-2799)caC>caT	p.H933H	HIRA_ENST00000546308.1_3'UTR|HIRA_ENST00000340170.4_Silent_p.H726H|HIRA_ENST00000541063.1_Silent_p.H889H	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	933	Interaction with histone H4.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					GGCGGTACTCGTGGCTGGACT	0.622													G|||	35	0.00698882	0.0257	0.0014	5008	,	,		20446	0.0		0.0	False		,,,				2504	0.0				p.H933H		Atlas-SNP	.											.	HIRA	100	.	0			c.C2799T						PASS	.	G		124,4282	91.1+/-129.8	3,118,2082	73.0	48.0	57.0		2799	-2.7	1.0	22	dbSNP_126	57	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	HIRA	NM_003325.3		3,126,6374	AA,AG,GG		0.093,2.8143,1.0149		933/1018	19340928	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	7290	exon23			GTACTCGTGGCTG	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"""WD repeat domain containing"""	4916	protein-coding gene	gene with protein product	"""DiGeorge critical region gene 1"""	600237	"""HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)"", ""HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"""	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.2799C>T	22.37:g.19340928G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_003325	Q05BU9|Q8IXN2	Silent	SNP	ENST00000263208.5	37	CCDS13759.1																																																																																			G|0.990;A|0.010	0.010	strong		0.622	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325	
RARS2	57038	hgsc.bcm.edu	37	6	88229953	88229953	+	Missense_Mutation	SNP	G	G	A	rs138460258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88229953G>A	ENST00000369536.5	-	13	1102	c.1057C>T	c.(1057-1059)Cat>Tat	p.H353Y	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	353					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)		TGCTGAAAATGCTTTTTTTGT	0.333													G|||	3	0.000599042	0.0015	0.0014	5008	,	,		17566	0.0		0.0	False		,,,				2504	0.0				p.H353Y		Atlas-SNP	.											.	RARS2	61	.	0			c.C1057T						PASS	.	G	TYR/HIS	1,4405	2.1+/-5.4	0,1,2202	203.0	194.0	197.0		1057	5.8	1.0	6	dbSNP_134	197	0,8600		0,0,4300	no	missense	RARS2	NM_020320.3	83	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	353/579	88229953	1,13005	2203	4300	6503	SO:0001583	missense	57038	exon13			GAAAATGCTTTTT	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.1057C>T	6.37:g.88229953G>A	ENSP00000358549:p.His353Tyr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	25.9	4.688534	0.88639	2.27E-4	0.0	ENSG00000146282	ENST00000369536	T	0.62232	0.04	5.76	5.76	0.90799	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.79701	0.4491	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81291	-0.0999	10	0.72032	D	0.01	.	19.975	0.97300	0.0:0.0:1.0:0.0	.	353	Q5T160	SYRM_HUMAN	Y	353	ENSP00000358549:H353Y	ENSP00000358549:H353Y	H	-	1	0	RARS2	88286672	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.939000	0.92951	2.724000	0.93272	0.585000	0.79938	CAT	G|1.000;A|0.000	0.000	strong		0.333	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
TAF1C	9013	hgsc.bcm.edu	37	16	84212928	84212928	+	Silent	SNP	G	G	A	rs3743642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84212928G>A	ENST00000567759.1	-	14	2411	c.2229C>T	c.(2227-2229)ccC>ccT	p.P743P	TAF1C_ENST00000570117.1_Silent_p.P411P|TAF1C_ENST00000378541.4_Silent_p.P743P|TAF1C_ENST00000541676.1_Silent_p.P650P|TAF1C_ENST00000341690.6_Silent_p.P649P|TAF1C_ENST00000566732.1_Silent_p.P717P	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	743					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						TCTGTCTCCCGGGCTCCGAGG	0.672													G|||	771	0.153954	0.1914	0.0634	5008	,	,		13013	0.1498		0.1064	False		,,,				2504	0.2209				p.P743P		Atlas-SNP	.											.	TAF1C	60	.	0			c.C2229T						PASS	.	G	,	774,3600		65,644,1478	13.0	17.0	16.0		2229,1947	-3.5	0.0	16	dbSNP_107	16	772,7788		40,692,3548	no	coding-synonymous,coding-synonymous	TAF1C	NM_005679.3,NM_139353.2	,	105,1336,5026	AA,AG,GG		9.0187,17.6955,11.953	,	743/870,649/776	84212928	1546,11388	2187	4280	6467	SO:0001819	synonymous_variant	9013	exon14			TCTCCCGGGCTCC	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.2229C>T	16.37:g.84212928G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	37	CCDS32496.1																																																																																			G|0.867;A|0.133	0.133	strong		0.672	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
TM2D1	83941	hgsc.bcm.edu	37	1	62190780	62190780	+	Missense_Mutation	SNP	A	A	G	rs200054903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62190780A>G	ENST00000606498.1	-	1	33	c.13T>C	c.(13-15)Tgg>Cgg	p.W5R	TM2D1_ENST00000294613.5_Missense_Mutation_p.W5R|TM2D1_ENST00000371180.2_Missense_Mutation_p.W67R|TM2D1_ENST00000371177.2_Missense_Mutation_p.W5R			Q9BX74	TM2D1_HUMAN	TM2 domain containing 1	5					apoptotic signaling pathway (GO:0097190)	integral component of plasma membrane (GO:0005887)	beta-amyloid binding (GO:0001540)|G-protein coupled receptor activity (GO:0004930)			large_intestine(2)|lung(3)|ovary(1)	6						CCAGACGGCCAGGCGGCCGCC	0.652													A|||	31	0.0061901	0.0219	0.0029	5008	,	,		16840	0.0		0.0	False		,,,				2504	0.0				p.W5R		Atlas-SNP	.											TM2D1_ENST00000371177,right_upper_lobe,carcinoma,+1,3	TM2D1	37	3	0			c.T13C						PASS	.	A	ARG/TRP	54,3760		0,54,1853	35.0	41.0	39.0		13	-6.0	0.0	1		39	0,8178		0,0,4089	no	missense	TM2D1	NM_032027.2	101	0,54,5942	GG,GA,AA		0.0,1.4158,0.4503	benign	5/208	62190780	54,11938	1907	4089	5996	SO:0001583	missense	83941	exon1			ACGGCCAGGCGGC	AF353990	CCDS65554.1	1p32.1	2008-02-05			ENSG00000162604	ENSG00000162604			24142	protein-coding gene	gene with protein product		610080				11278849, 12553667	Standard	NM_032027		Approved	BBP	uc001czz.1	Q9BX74	OTTHUMG00000008466	ENST00000606498.1:c.13T>C	1.37:g.62190780A>G	ENSP00000475700:p.Trp5Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	57	34	0.596491	NM_032027	A6NDA8	Missense_Mutation	SNP	ENST00000606498.1	37		.	.	.	.	.	.	.	.	.	.	A	13.04	2.117243	0.37339	0.014158	0.0	ENSG00000162604	ENST00000371180;ENST00000294613;ENST00000371178;ENST00000371177	.	.	.	4.69	-5.98	0.02220	.	1.041710	0.07590	N	0.921834	T	0.17789	0.0427	L	0.38531	1.155	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33292	-0.9874	9	0.72032	D	0.01	3.1902	0.4995	0.00577	0.1994:0.2683:0.1696:0.3628	.	5	Q9BX74	TM2D1_HUMAN	R	67;5;5;5	.	ENSP00000294613:W5R	W	-	1	0	TM2D1	61963368	0.061000	0.20836	0.000000	0.03702	0.034000	0.12701	-0.222000	0.09190	-0.981000	0.03520	0.379000	0.24179	TGG	.	.	weak		0.652	TM2D1-012	KNOWN	non_canonical_U12|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470779.2	NM_032027	
WDR44	54521	hgsc.bcm.edu	37	X	117528142	117528142	+	Silent	SNP	C	C	T	rs6603401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:117528142C>T	ENST00000254029.3	+	5	1346	c.951C>T	c.(949-951)acC>acT	p.T317T	WDR44_ENST00000371822.5_Silent_p.T292T|WDR44_ENST00000371825.3_Silent_p.T317T	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	317						endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.T317T(2)		breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						AAATAGTTACCGCCCAGGTTG	0.433													T|||	2177	0.576689	0.7156	0.451	3775	,	,		14217	0.4395		0.1581	False		,,,				2504	0.3231				p.T317T		Atlas-SNP	.											.	WDR44	188	.	2	Substitution - coding silent(2)	stomach(2)	c.C951T						PASS	.	T	,,	3246,589		1172,407,495,53,76	121.0	120.0	121.0		951,876,951	2.9	1.0	X	dbSNP_116	121	1413,5315		101,797,414,1530,1458	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR44	NM_001184965.1,NM_001184966.1,NM_019045.4	,,	1273,1204,909,1583,1534	TT,TC,T,CC,C		21.0018,15.3585,44.1068	,,	317/906,292/825,317/914	117528142	4659,5904	2203	4300	6503	SO:0001819	synonymous_variant	54521	exon5			AGTTACCGCCCAG	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"""WD repeat domain containing"""	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.951C>T	X.37:g.117528142C>T		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	226	154	0.681416	NM_001184965	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Silent	SNP	ENST00000254029.3	37	CCDS14572.1	875	0.5274261603375527	238	0.8561151079136691	99	0.38671875	172	0.42574257425742573	90	0.12968299711815562	T	10.12	1.263062	0.23051	0.846415	0.210018	ENSG00000131725	ENST00000371848	.	.	.	5.51	2.9	0.33743	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14420	-1.0473	3	.	.	.	-13.3646	2.8866	0.05663	0.1348:0.0751:0.2745:0.5156	rs6603401;rs57593030;rs6603401	.	.	.	C	217	.	.	R	+	1	0	WDR44	117412170	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	0.982000	0.29539	0.220000	0.20860	-0.314000	0.08810	CGC	C|0.475;T|0.525	0.525	strong		0.433	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045	
GET4	51608	hgsc.bcm.edu	37	7	931960	931960	+	Silent	SNP	G	G	A	rs11543218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:931960G>A	ENST00000265857.3	+	6	745	c.651G>A	c.(649-651)acG>acA	p.T217T	GET4_ENST00000407192.1_Silent_p.T164T	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	217					tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)				breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TGGTCTTCACGACGTACACCC	0.562													G|||	286	0.0571086	0.1589	0.0288	5008	,	,		14499	0.0		0.0388	False		,,,				2504	0.0174				p.T217T		Atlas-SNP	.											.	GET4	17	.	0			c.G651A						PASS	.	G		674,3732	284.0+/-277.4	60,554,1589	99.0	103.0	102.0		651	-11.0	0.3	7	dbSNP_120	102	306,8294	110.2+/-170.6	7,292,4001	no	coding-synonymous	GET4	NM_015949.2		67,846,5590	AA,AG,GG		3.5581,15.2973,7.535		217/328	931960	980,12026	2203	4300	6503	SO:0001819	synonymous_variant	51608	exon6			CTTCACGACGTAC	AK023560	CCDS5317.1	7p22.3	2010-08-05	2010-03-24	2010-03-24	ENSG00000239857	ENSG00000239857			21690	protein-coding gene	gene with protein product	"""CGI-20 protein"", ""conserved edge protein"", ""transmembrane domain recognition complex, 35kDa"""	612056	"""chromosome 7 open reading frame 20"""	C7orf20		10810093, 20106980, 20676083	Standard	NM_015949		Approved	CGI-20, H_NH1244M04.5, CEE, TRC35	uc003sjl.1	Q7L5D6	OTTHUMG00000112459	ENST00000265857.3:c.651G>A	7.37:g.931960G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_015949	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	Silent	SNP	ENST00000265857.3	37	CCDS5317.1																																																																																			G|0.929;A|0.071	0.071	strong		0.562	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000231930.1	NM_015949	
ADIPOR2	79602	hgsc.bcm.edu	37	12	1893077	1893077	+	Silent	SNP	C	C	A	rs35854772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:1893077C>A	ENST00000357103.4	+	7	1121	c.870C>A	c.(868-870)atC>atA	p.I290I		NM_024551.2	NP_078827.2	Q86V24	ADR2_HUMAN	adiponectin receptor 2	290					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|female pregnancy (GO:0007565)|heart development (GO:0007507)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of cell growth (GO:0030308)|positive regulation of glucose import (GO:0046326)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|receptor activity (GO:0004872)			endometrium(1)|large_intestine(3)|lung(7)|stomach(1)	12	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			TGAGTGGAATCATTCCTACCT	0.493													C|||	513	0.102436	0.1952	0.0663	5008	,	,		18446	0.0258		0.1252	False		,,,				2504	0.0583				p.I290I		Atlas-SNP	.											.	ADIPOR2	30	.	0			c.C870A						PASS	.	C		858,3548	335.5+/-303.9	88,682,1433	99.0	92.0	94.0		870	5.7	1.0	12	dbSNP_126	94	1047,7553	221.5+/-258.9	58,931,3311	no	coding-synonymous	ADIPOR2	NM_024551.2		146,1613,4744	AA,AC,CC		12.1744,19.4734,14.6471		290/387	1893077	1905,11101	2203	4300	6503	SO:0001819	synonymous_variant	79602	exon7			TGGAATCATTCCT	AY424280	CCDS8511.1	12p13	2012-08-22			ENSG00000006831	ENSG00000006831		"""GPCR / Unclassified : Adiponectin receptors"""	24041	protein-coding gene	gene with protein product		607946				12802337	Standard	NM_024551		Approved	PAQR2, ACDCR2	uc001qjm.3	Q86V24	OTTHUMG00000130139	ENST00000357103.4:c.870C>A	12.37:g.1893077C>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	183	87	0.47541	NM_024551	Q53YY5|Q9H737	Silent	SNP	ENST00000357103.4	37	CCDS8511.1																																																																																			C|0.873;A|0.127	0.127	strong		0.493	ADIPOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252447.2	NM_024551	
TAS2R8	50836	hgsc.bcm.edu	37	12	10959031	10959031	+	Silent	SNP	C	C	T	rs1548803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	167	0	0		WXS	Illumina HiSeq	Phase_I	165	72	0.436364	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		
FBRSL1	57666	hgsc.bcm.edu	37	12	133084874	133084874	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133084874G>A	ENST00000434748.2	+	2	1447	c.427G>A	c.(427-429)Ggg>Agg	p.G143R	FBRSL1_ENST00000542061.1_3'UTR|FBRSL1_ENST00000261673.6_Missense_Mutation_p.G70R	NM_001142641.1	NP_001136113.1	Q9HCM7	FBSL_HUMAN	fibrosin-like 1	143							poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(1)|stomach(1)	4						AGGCAGCCCCGGGCAGGACCT	0.697																																					p.G143R		Atlas-SNP	.											.	FBRSL1	47	.	0			c.G427A						PASS	.						33.0	46.0	42.0					12																	133084874		692	1590	2282	SO:0001583	missense	57666	exon2			AGCCCCGGGCAGG		CCDS45010.1	12q24.33	2008-12-09			ENSG00000112787	ENSG00000112787			29308	protein-coding gene	gene with protein product						10997877	Standard	NM_001142641		Approved	KIAA1545	uc001ukf.3	Q9HCM7	OTTHUMG00000167991	ENST00000434748.2:c.427G>A	12.37:g.133084874G>A	ENSP00000396160:p.Gly143Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_001142641	Q86XQ1	Missense_Mutation	SNP	ENST00000434748.2	37	CCDS45010.1	.	.	.	.	.	.	.	.	.	.	G	4.618	0.114914	0.08831	.	.	ENSG00000112787	ENST00000434748;ENST00000261673	T;T	0.28069	1.63;1.63	4.3	1.29	0.21616	.	.	.	.	.	T	0.10895	0.0266	N	0.11427	0.14	0.09310	N	1	B	0.32893	0.389	B	0.21546	0.035	T	0.26087	-1.0113	9	0.07325	T	0.83	.	6.0554	0.19809	0.184:0.156:0.66:0.0	.	143	Q9HCM7	FBSL_HUMAN	R	143;70	ENSP00000396160:G143R;ENSP00000261673:G70R	ENSP00000261673:G70R	G	+	1	0	FBRSL1	131594947	0.000000	0.05858	0.010000	0.14722	0.309000	0.27889	0.228000	0.17814	0.160000	0.19432	-0.275000	0.10095	GGG	.	.	none		0.697	FBRSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397404.2		
KRT33B	3884	hgsc.bcm.edu	37	17	39521248	39521248	+	Missense_Mutation	SNP	A	A	C	rs71373411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39521248A>C	ENST00000251646.3	-	6	929	c.880T>G	c.(880-882)Tac>Gac	p.Y294D		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	294	Coil 2.|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)				TCCAGAGAGTATCGCTGTGGT	0.552													C|||	679	0.135583	0.3707	0.0548	5008	,	,		17851	0.0506		0.0795	False		,,,				2504	0.0204				p.Y294D		Atlas-SNP	.											.	KRT33B	46	.	0			c.T880G						PASS	.	C	ASP/TYR	1361,3021	679.7+/-403.7	281,799,1111	41.0	48.0	46.0		880	-2.5	0.2	17	dbSNP_130	46	742,7858	784.1+/-407.6	28,686,3586	yes	missense	KRT33B	NM_002279.3	160	309,1485,4697	CC,CA,AA		8.6279,31.0589,16.1994	benign	294/405	39521248	2103,10879	2191	4300	6491	SO:0001583	missense	3884	exon6			GAGAGTATCGCTG	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.880T>G	17.37:g.39521248A>C	ENSP00000251646:p.Tyr294Asp	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	37	CCDS11389.1	279	0.12774725274725274	161	0.32723577235772355	22	0.06077348066298342	31	0.05419580419580419	65	0.08575197889182058	c	0.003	-2.479716	0.00165	0.310589	0.086279	ENSG00000131738	ENST00000251646	D	0.87491	-2.26	4.85	-2.45	0.06481	Filament (1);	0.276012	0.32175	N	0.006477	T	0.00012	0.0000	N	0.00024	-2.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38585	-0.9654	9	0.02654	T	1	.	4.0897	0.09963	0.1027:0.4167:0.1035:0.3771	.	294	Q14525	KT33B_HUMAN	D	294	ENSP00000251646:Y294D	ENSP00000251646:Y294D	Y	-	1	0	KRT33B	36774774	0.000000	0.05858	0.152000	0.22495	0.076000	0.17211	-3.151000	0.00582	-0.437000	0.07243	-2.126000	0.00345	TAC	A|0.853;C|0.147	0.147	strong		0.552	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
LPIN3	64900	hgsc.bcm.edu	37	20	39977300	39977300	+	Missense_Mutation	SNP	G	G	C	rs150562240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:39977300G>C	ENST00000373257.3	+	4	421	c.330G>C	c.(328-330)tgG>tgC	p.W110C		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	110					fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				CCATCCCTTGGGGGGGTCTGT	0.662																																					p.W110C		Atlas-SNP	.											.	LPIN3	69	.	0			c.G330C						PASS	.	G	CYS/TRP	0,4406		0,0,2203	33.0	37.0	36.0		330	2.2	1.0	20	dbSNP_134	36	3,8597	1.2+/-3.3	0,3,4297	yes	missense	LPIN3	NM_022896.1	215	0,3,6500	CC,CG,GG		0.0349,0.0,0.0231	benign	110/852	39977300	3,13003	2203	4300	6503	SO:0001583	missense	64900	exon4			CCCTTGGGGGGGT	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"""lipin 3-like"""	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.330G>C	20.37:g.39977300G>C	ENSP00000362354:p.Trp110Cys	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Missense_Mutation	SNP	ENST00000373257.3	37	CCDS33469.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.606536	0.28623	0.0	3.49E-4	ENSG00000132793	ENST00000373257	T	0.76316	-1.01	4.22	2.19	0.27852	Lipin, N-terminal (1);	0.299857	0.26016	N	0.026860	T	0.53753	0.1816	N	0.08118	0	0.46874	D	0.999231	B;B	0.18968	0.002;0.032	B;B	0.19391	0.005;0.025	T	0.30592	-0.9973	9	.	.	.	-2.1502	8.2485	0.31704	0.0:0.1724:0.6488:0.1788	.	110;110	Q9BQK8-2;Q9BQK8	.;LPIN3_HUMAN	C	110	ENSP00000362354:W110C	.	W	+	3	0	LPIN3	39410714	1.000000	0.71417	0.971000	0.41717	0.955000	0.61496	2.688000	0.46984	0.488000	0.27723	0.557000	0.71058	TGG	G|0.999;C|0.001	0.001	strong		0.662	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896	
OSCAR	126014	hgsc.bcm.edu	37	19	54599119	54599119	+	Missense_Mutation	SNP	G	G	A	rs1110643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54599119G>A	ENST00000284648.6	-	5	870	c.673C>T	c.(673-675)Cgg>Tgg	p.R225W	OSCAR_ENST00000351806.4_Intron|OSCAR_ENST00000391761.1_Missense_Mutation_p.R214W|OSCAR_ENST00000391760.1_3'UTR|OSCAR_ENST00000356532.3_Intron|OSCAR_ENST00000359649.4_Missense_Mutation_p.R229W|OSCAR_ENST00000358375.4_Intron			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor	225						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|skin(1)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)					gaggcgggccgggCCTCAGGG	0.697													G|||	37	0.00738818	0.0272	0.0014	5008	,	,		11125	0.0		0.0	False		,,,				2504	0.0				p.R229W		Atlas-SNP	.											.	OSCAR	22	.	0			c.C685T						PASS	.	G	,,,TRP/ARG	77,4115		0,77,2019	7.0	8.0	8.0		,,,685	-4.1	0.0	19	dbSNP_86	8	0,8172		0,0,4086	yes	intron,intron,intron,missense	OSCAR	NM_130771.3,NM_133168.3,NM_133169.3,NM_206818.1	,,,101	0,77,6105	AA,AG,GG		0.0,1.8368,0.6228	,,,benign	,,,229/287	54599119	77,12287	2096	4086	6182	SO:0001583	missense	126014	exon5			CGGGCCGGGCCTC	AK130199	CCDS12873.1, CCDS12874.1, CCDS12875.1, CCDS12876.1, CCDS62789.1, CCDS74444.1	19q13.42	2013-01-29			ENSG00000170909	ENSG00000170909		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29960	protein-coding gene	gene with protein product		606862				11805147	Standard	NM_206818		Approved		uc002qda.3	Q8IYS5	OTTHUMG00000064966	ENST00000284648.6:c.673C>T	19.37:g.54599119G>A	ENSP00000365808:p.Arg225Trp	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_206818	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Missense_Mutation	SNP	ENST00000284648.6	37		12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	14.75	2.627173	0.46944	0.018368	0.0	ENSG00000170909	ENST00000391761;ENST00000359649;ENST00000284648	T;T;T	0.00524	6.82;6.85;6.83	2.03	-4.06	0.03986	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.09310	N	0.999999	D;D;D	0.71674	0.997;0.998;0.996	B;P;P	0.50136	0.428;0.632;0.48	T	0.40664	-0.9551	9	0.02654	T	1	.	0.9438	0.01361	0.1669:0.2216:0.3875:0.2239	rs1110643	225;214;229	Q8IYS5;Q8IYS5-4;Q8IYS5-7	OSCAR_HUMAN;.;.	W	214;229;225	ENSP00000375641:R214W;ENSP00000352671:R229W;ENSP00000365808:R225W	ENSP00000365808:R225W	R	-	1	2	OSCAR	59290931	0.010000	0.17322	0.005000	0.12908	0.115000	0.19883	-0.599000	0.05700	-0.941000	0.03700	0.289000	0.19496	CGG	G|0.993;A|0.007	0.007	strong		0.697	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169	
CDK2	1017	hgsc.bcm.edu	37	12	56360876	56360876	+	Silent	SNP	G	G	A	rs2069398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56360876G>A	ENST00000266970.4	+	1	324	c.84G>A	c.(82-84)gaG>gaA	p.E28E	RP11-973D8.4_ENST00000554022.1_RNA|PMEL_ENST00000550464.1_5'Flank|PMEL_ENST00000449260.2_5'Flank|PMEL_ENST00000548493.1_5'Flank|PMEL_ENST00000360714.4_5'Flank|CDK2_ENST00000553376.1_Silent_p.E28E|PMEL_ENST00000539511.1_5'Flank|PMEL_ENST00000550447.1_5'Flank|PMEL_ENST00000536427.1_5'Flank|PMEL_ENST00000548689.1_5'Flank|PMEL_ENST00000548747.1_5'Flank|PMEL_ENST00000552882.1_5'Flank|CDK2_ENST00000354056.4_Silent_p.E28E|CDK2_ENST00000440311.2_Silent_p.E28E	NM_001798.3	NP_001789.2	P24941	CDK2_HUMAN	cyclin-dependent kinase 2	28	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			LTGEV -> STGQM (in Ref. 5; BAA32794). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|blood coagulation (GO:0007596)|cellular response to nitric oxide (GO:0071732)|centrosome duplication (GO:0051298)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone phosphorylation (GO:0016572)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|mitotic nuclear division (GO:0007067)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transport (GO:0006813)|Ras protein signal transduction (GO:0007265)|regulation of gene silencing (GO:0060968)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	Cajal body (GO:0015030)|centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|condensed chromosome (GO:0000793)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|X chromosome (GO:0000805)|Y chromosome (GO:0000806)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	18			UCEC - Uterine corpus endometrioid carcinoma (6;0.123)|OV - Ovarian serous cystadenocarcinoma(18;0.235)		Bosutinib(DB06616)	TGACGGGAGAGGTGGTGGCGC	0.572													A|||	592	0.118211	0.3207	0.0764	5008	,	,		15851	0.001		0.0656	False		,,,				2504	0.0491				p.E28E		Atlas-SNP	.											.	CDK2	27	.	0			c.G84A						PASS	.	A	,	1226,3180	699.7+/-406.5	171,884,1148	133.0	125.0	128.0		84,84	2.3	1.0	12	dbSNP_96	128	665,7935	785.3+/-407.6	23,619,3658	no	coding-synonymous,coding-synonymous	CDK2	NM_001798.3,NM_052827.2	,	194,1503,4806	AA,AG,GG		7.7326,27.8257,14.5394	,	28/299,28/265	56360876	1891,11115	2203	4300	6503	SO:0001819	synonymous_variant	1017	exon1			GGGAGAGGTGGTG	M68520	CCDS8898.1, CCDS8899.1	12q13	2011-11-08				ENSG00000123374		"""Cyclin-dependent kinases"""	1771	protein-coding gene	gene with protein product		116953				1717994, 8275715	Standard	NM_001798		Approved		uc001sit.4	P24941		ENST00000266970.4:c.84G>A	12.37:g.56360876G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_052827	A8K7C6|O75100	Silent	SNP	ENST00000266970.4	37	CCDS8898.1																																																																																			G|0.871;A|0.129	0.129	strong		0.572	CDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409650.1		
ZNF812	729648	hgsc.bcm.edu	37	19	9801668	9801668	+	Missense_Mutation	SNP	T	T	C	rs113307466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9801668T>C	ENST00000457674.2	-	5	1029	c.511A>G	c.(511-513)Aga>Gga	p.R171G	ZNF812_ENST00000536819.1_5'UTR	NM_001199814.1	NP_001186743.1	P0C7V5	ZN812_HUMAN	zinc finger protein 812	171					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						AAGCCTTTTCTACATTCCTTA	0.378													.|||	323	0.0644968	0.2186	0.0216	5008	,	,		21792	0.0159		0.001	False		,,,				2504	0.002				p.R171G		Atlas-SNP	.											.	ZNF812	27	.	0			c.A511G						PASS	.																																			SO:0001583	missense	729648	exon6			CTTTTCTACATTC		CCDS54215.1	19p13.2	2014-04-02			ENSG00000224689	ENSG00000224689		"""Zinc fingers, C2H2-type"", ""-"""	33242	protein-coding gene	gene with protein product							Standard	NM_001199814		Approved		uc021uop.1	P0C7V5	OTTHUMG00000167867	ENST00000457674.2:c.511A>G	19.37:g.9801668T>C	ENSP00000395629:p.Arg171Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	53	0.630952	NM_001199814		Missense_Mutation	SNP	ENST00000457674.2	37	CCDS54215.1	114	0.0521978021978022	98	0.1991869918699187	8	0.022099447513812154	7	0.012237762237762238	1	0.0013192612137203166	c	0.004	-2.256732	0.00265	.	.	ENSG00000224689	ENST00000457674	T	0.21031	2.03	1.42	-2.83	0.05769	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00032	-2.58	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30238	-0.9985	8	0.02654	T	1	.	9.8025	0.40773	0.0:0.7424:0.0:0.2576	.	171	P0C7V5	ZN812_HUMAN	G	171	ENSP00000395629:R171G	ENSP00000395629:R171G	R	-	1	2	ZNF812	9662668	0.039000	0.19947	0.009000	0.14445	0.021000	0.10359	0.296000	0.19083	-1.714000	0.01390	-1.273000	0.01405	AGA	T|0.946;C|0.054	0.054	strong		0.378	ZNF812-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396726.1		
IL27RA	9466	hgsc.bcm.edu	37	19	14142705	14142705	+	Silent	SNP	C	C	T	rs113593439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14142705C>T	ENST00000263379.2	+	1	146	c.21C>T	c.(19-21)gcC>gcT	p.A7A	CTB-55O6.4_ENST00000590528.1_RNA	NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	7				A -> G (in Ref. 3; AAG27297 and 5; AAQ89235). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						GCAGGGGCGCCCCTTTCTGGC	0.721													C|||	588	0.117412	0.1641	0.1282	5008	,	,		11265	0.12		0.0517	False		,,,				2504	0.1115				p.A7A	Colon(164;1849 1896 4443 37792 47834)	Atlas-SNP	.											IL27RA,NS,haematopoietic_neoplasm,0,2	IL27RA	56	2	0			c.C21T						PASS	.	C		560,3818		37,486,1666	11.0	13.0	12.0		21	-1.2	0.0	19	dbSNP_132	12	524,8042		18,488,3777	no	coding-synonymous	IL27RA	NM_004843.2		55,974,5443	TT,TC,CC		6.1172,12.7912,8.3745		7/637	14142705	1084,11860	2189	4283	6472	SO:0001819	synonymous_variant	9466	exon1			GGGCGCCCCTTTC	AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	17290	protein-coding gene	gene with protein product	"""T-cell cytokine receptor type 1"""	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.21C>T	19.37:g.14142705C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_004843	A0N0L1|O60624	Silent	SNP	ENST00000263379.2	37	CCDS12303.1																																																																																			C|0.891;T|0.109	0.109	strong		0.721	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843	
STRN4	29888	hgsc.bcm.edu	37	19	47226434	47226434	+	Missense_Mutation	SNP	C	C	T	rs10409124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47226434C>T	ENST00000263280.6	-	13	1751	c.1702G>A	c.(1702-1704)Gtc>Atc	p.V568I	STRN4_ENST00000594357.2_5'UTR|STRN4_ENST00000391910.3_Missense_Mutation_p.V575I|STRN4_ENST00000539396.1_Missense_Mutation_p.V449I	NM_001039877.1|NM_013403.2	NP_001034966.1|NP_037535.2	Q9NRL3	STRN4_HUMAN	striatin, calmodulin binding protein 4	568			V -> I (in dbSNP:rs10409124).			cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		CAGATGCGGACGGTGCCATCA	0.716													C|||	412	0.0822684	0.264	0.0216	5008	,	,		16216	0.0347		0.006	False		,,,				2504	0.0072				p.V575I		Atlas-SNP	.											.	STRN4	33	.	0			c.G1723A						PASS	.	C	ILE/VAL,ILE/VAL	805,3499		65,675,1412	13.0	14.0	14.0		1702,1723	-5.2	0.6	19	dbSNP_119	14	12,8472		0,12,4230	yes	missense,missense	STRN4	NM_013403.2,NM_001039877.1	29,29	65,687,5642	TT,TC,CC		0.1414,18.7035,6.3888	benign,benign	568/754,575/761	47226434	817,11971	2152	4242	6394	SO:0001583	missense	29888	exon13			TGCGGACGGTGCC	AF212940	CCDS12690.1, CCDS42581.1	19q13.32	2013-01-10			ENSG00000090372	ENSG00000090372		"""WD repeat domain containing"""	15721	protein-coding gene	gene with protein product		614767				10748158	Standard	XM_006723171		Approved	zinedin, ZIN	uc002pfm.3	Q9NRL3		ENST00000263280.6:c.1702G>A	19.37:g.47226434C>T	ENSP00000263280:p.Val568Ile	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	160	61	0.38125	NM_001039877	A0A024R0V2|B4DQH7|F8VYA6|Q8NE53	Missense_Mutation	SNP	ENST00000263280.6	37	CCDS12690.1	169	0.07738095238095238	143	0.29065040650406504	8	0.022099447513812154	13	0.022727272727272728	5	0.006596306068601583	C	10.15	1.272265	0.23221	0.187035	0.001414	ENSG00000090372	ENST00000391910;ENST00000263280;ENST00000539396	T;T;T	0.57107	0.42;0.42;0.42	5.0	-5.24	0.02789	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.502804	0.19890	N	0.103752	T	0.00012	0.0000	L	0.35249	1.045	0.09310	P	0.9999999999991201	B;B	0.17667	0.023;0.002	B;B	0.23716	0.048;0.003	T	0.26538	-1.0100	9	0.07325	T	0.83	-19.3301	13.0542	0.58971	0.0:0.4098:0.0:0.5902	rs10409124;rs10409124	575;568	F8VYA6;Q9NRL3	.;STRN4_HUMAN	I	575;568;449	ENSP00000375777:V575I;ENSP00000263280:V568I;ENSP00000440901:V449I	ENSP00000263280:V568I	V	-	1	0	STRN4	51918274	0.016000	0.18221	0.576000	0.28549	0.411000	0.31082	0.299000	0.19138	-0.694000	0.05113	0.313000	0.20887	GTC	C|0.912;T|0.088	0.088	strong		0.716	STRN4-001	KNOWN	NMD_exception|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466607.2		
ZNF331	55422	hgsc.bcm.edu	37	19	54080279	54080279	+	Silent	SNP	T	T	C	rs1351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54080279T>C	ENST00000253144.9	+	7	1798	c.465T>C	c.(463-465)ggT>ggC	p.G155G	ZNF331_ENST00000511154.1_Silent_p.G155G|ZNF331_ENST00000411977.2_Silent_p.G155G|ZNF331_ENST00000511593.2_Silent_p.G155G|ZNF331_ENST00000512387.1_Silent_p.G155G|ZNF331_ENST00000513265.1_Intron|ZNF331_ENST00000449416.1_Silent_p.G155G|ZNF331_ENST00000513999.1_Silent_p.G155G	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	155					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)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		TCCATACTGGTGAGAAACCTT	0.408			T	?	follicular thyroid adenoma								C|||	544	0.108626	0.3071	0.0706	5008	,	,		19205	0.0		0.0726	False		,,,				2504	0.0164				p.G155G		Atlas-SNP	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	ZNF331_ENST00000253144,NS,carcinoma,+2,1	ZNF331	66	1	0			c.T465C						scavenged	.	C	,,	1110,3296	718.8+/-408.9	125,860,1218	97.0	103.0	101.0		465,465,465	-7.3	0.2	19	dbSNP_36	101	570,8030	793.4+/-407.5	17,536,3747	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF331	NM_001079906.1,NM_001079907.1,NM_018555.5	,,	142,1396,4965	CC,CT,TT		6.6279,25.1929,12.9171	,,	155/464,155/464,155/464	54080279	1680,11326	2203	4300	6503	SO:0001819	synonymous_variant	55422	exon5			TACTGGTGAGAAA	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"""Zinc fingers, C2H2-type"", ""-"""	15489	protein-coding gene	gene with protein product	"""rearranged in thyroid adenomas"""	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.465T>C	19.37:g.54080279T>C		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_001253801	Q96GJ4	Silent	SNP	ENST00000253144.9	37	CCDS33102.1																																																																																			T|0.881;C|0.119	0.119	strong		0.408	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555	
MGAT5B	146664	hgsc.bcm.edu	37	17	74878259	74878259	+	Missense_Mutation	SNP	G	G	A	rs571264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74878259G>A	ENST00000569840.2	+	3	782	c.208G>A	c.(208-210)Gtc>Atc	p.V70I	MGAT5B_ENST00000428789.2_Missense_Mutation_p.V81I|MGAT5B_ENST00000565675.1_Missense_Mutation_p.V70I|MGAT5B_ENST00000374998.3_3'UTR|MGAT5B_ENST00000301618.4_Missense_Mutation_p.V70I	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	70			V -> I (in dbSNP:rs571264).		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						GTCCCGCGGCGTCCTGCGCAA	0.687													G|||	2005	0.400359	0.6558	0.3905	5008	,	,		17448	0.3839		0.1431	False		,,,				2504	0.3436				p.V81I		Atlas-SNP	.											MGAT5B,colon,carcinoma,0,1	MGAT5B	98	1	0			c.G241A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	2496,1910		730,1036,437	28.0	27.0	28.0		208,208,241	2.2	0.2	17	dbSNP_83	28	1153,7439		85,983,3228	yes	missense,missense,missense	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	29,29,29	815,2019,3665	AA,AG,GG		13.4195,43.35,28.0735	possibly-damaging,possibly-damaging,possibly-damaging	70/793,70/791,81/802	74878259	3649,9349	2203	4296	6499	SO:0001583	missense	146664	exon2			CGCGGCGTCCTGC	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.208G>A	17.37:g.74878259G>A	ENSP00000456037:p.Val70Ile	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	152	81	0.532895	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Missense_Mutation	SNP	ENST00000569840.2	37	CCDS59299.1	765	0.35027472527472525	305	0.6199186991869918	121	0.3342541436464088	226	0.3951048951048951	113	0.14907651715039577	G	13.67	2.305690	0.40795	0.5665	0.134195	ENSG00000167889	ENST00000374998;ENST00000301618;ENST00000428789	T;T	0.50548	0.75;0.74	5.23	2.18	0.27775	.	0.315088	0.29225	N	0.012769	T	0.00012	0.0000	L	0.47716	1.5	0.41383	P	0.012440000000000007	B;B	0.17667	0.023;0.023	B;B	0.12156	0.007;0.004	T	0.40478	-0.9561	9	0.42905	T	0.14	-22.276	7.172	0.25724	0.2805:0.0:0.7195:0.0	rs571264;rs771729;rs60952655;rs571264	81;70	Q3V5L5-2;Q3V5L5-5	.;.	I	70;70;81	ENSP00000301618:V70I;ENSP00000391227:V81I	ENSP00000301618:V70I	V	+	1	0	MGAT5B	72389854	0.992000	0.36948	0.232000	0.24009	0.597000	0.36814	2.029000	0.41098	0.224000	0.20940	-0.258000	0.10820	GTC	G|0.665;A|0.335	0.335	strong		0.687	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
SGCG	6445	hgsc.bcm.edu	37	13	23853547	23853547	+	Silent	SNP	C	C	T	rs35628352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23853547C>T	ENST00000218867.3	+	5	559	c.435C>T	c.(433-435)aaC>aaT	p.N145N	SGCG_ENST00000545013.1_Silent_p.N145N|SGCG_ENST00000537476.1_Silent_p.N145N	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	145					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		TCAACTCCAACGACGGCAAGC	0.383													C|||	47	0.00938498	0.031	0.0072	5008	,	,		17239	0.0		0.001	False		,,,				2504	0.0				p.N145N		Atlas-SNP	.											.	SGCG	64	.	0			c.C435T						PASS	.	C		130,4276	93.9+/-132.6	2,126,2075	98.0	90.0	93.0		435	-3.5	0.4	13	dbSNP_126	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SGCG	NM_000231.2		2,127,6374	TT,TC,CC		0.0116,2.9505,1.0072		145/292	23853547	131,12875	2203	4300	6503	SO:0001819	synonymous_variant	6445	exon5			CTCCAACGACGGC	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"""Maghrebian myopathy (autosomal recessive)"", ""35kD dystrophin-associated glycoprotein"", ""limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)"", ""gamma sarcoglycan"""	608896	"""sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"""	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.435C>T	13.37:g.23853547C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	109	59	0.541284	NM_000231	Q32M32|Q5T9J6	Silent	SNP	ENST00000218867.3	37	CCDS9299.1																																																																																			C|0.991;T|0.009	0.009	strong		0.383	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231	
CPAMD8	27151	hgsc.bcm.edu	37	19	17081707	17081707	+	Missense_Mutation	SNP	G	G	T	rs9305083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17081707G>T	ENST00000443236.1	-	18	2379	c.2348C>A	c.(2347-2349)cCc>cAc	p.P783H	CPAMD8_ENST00000388925.4_3'UTR	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	736						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						TTACCTGGGGGGGTGCCTGGA	0.572													G|||	520	0.103834	0.3608	0.036	5008	,	,		16421	0.0		0.0129	False		,,,				2504	0.0051				p.P783H		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C2348A						PASS	.	G	HIS/PRO	1156,2704		169,818,943	26.0	29.0	28.0		2348	-3.2	0.2	19	dbSNP_119	28	180,8074		3,174,3950	yes	missense	CPAMD8	NM_015692.2	77	172,992,4893	TT,TG,GG		2.1808,29.9482,11.0286	possibly-damaging	783/1933	17081707	1336,10778	1930	4127	6057	SO:0001583	missense	27151	exon18			CTGGGGGGGTGCC	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.2348C>A	19.37:g.17081707G>T	ENSP00000402505:p.Pro783His	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	222|222	0.10164835164835165|0.10164835164835165	191|191	0.3882113821138211|0.3882113821138211	19|19	0.052486187845303865|0.052486187845303865	0|0	0.0|0.0	12|12	0.0158311345646438|0.0158311345646438	G|G	11.55|11.55	1.673598|1.673598	0.29693|0.29693	0.299482|0.299482	0.021808|0.021808	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	3.19|3.19	-3.22|-3.22	0.05125|0.05125	.|.	1.230310|1.230310	0.06279|0.06279	N|U	0.697038|0.697038	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	P|.	0.51653|.	0.947|.	B|.	0.40741|.	0.339|.	T|T	0.44329|0.44329	-0.9335|-0.9335	8|6	0.42905|0.14252	T|T	0.14|0.57	.|.	0.9563|0.9563	0.01386|0.01386	0.342:0.161:0.3358:0.1611|0.342:0.161:0.3358:0.1611	rs9305083;rs52812668;rs9305083|rs9305083;rs52812668;rs9305083	736|.	Q8IZJ3|.	CPMD8_HUMAN|.	H|T	783|794	.|.	ENSP00000291440:P783H|ENSP00000402505:P794T	P|P	-|-	2|1	0|0	CPAMD8|CPAMD8	16942707|16942707	0.013000|0.013000	0.17824|0.17824	0.179000|0.179000	0.23059|0.23059	0.258000|0.258000	0.26162|0.26162	0.758000|0.758000	0.26447|0.26447	-0.437000|-0.437000	0.07243|0.07243	-1.045000|-1.045000	0.02358|0.02358	CCC|CCC	G|0.914;T|0.086	0.086	strong		0.572	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
FAM69C	125704	hgsc.bcm.edu	37	18	72103782	72103782	+	Missense_Mutation	SNP	T	T	C	rs2278154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:72103782T>C	ENST00000343998.6	-	4	1222	c.1214A>G	c.(1213-1215)cAa>cGa	p.Q405R	FAM69C_ENST00000400291.2_Missense_Mutation_p.Q106R	NM_001044369.2	NP_001037834.2	Q0P6D2	FA69C_HUMAN	family with sequence similarity 69, member C	405						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|ovary(2)	5						TTGGAGGAGTTGGCGAAGCTT	0.582													C|||	1678	0.335064	0.3419	0.2997	5008	,	,		13728	0.2589		0.3797	False		,,,				2504	0.3834				p.Q405R		Atlas-SNP	.											.	FAM69C	45	.	0			c.A1214G						PASS	.	C	ARG/GLN	1222,2620		199,824,898	32.0	35.0	34.0		1214	4.1	0.0	18	dbSNP_100	34	3165,5081		615,1935,1573	yes	missense	FAM69C	NM_001044369.2	43	814,2759,2471	CC,CT,TT		38.3822,31.8064,36.2922	benign	405/420	72103782	4387,7701	1921	4123	6044	SO:0001583	missense	125704	exon4			AGGAGTTGGCGAA	BC019628	CCDS42445.2	18q22.3	2012-08-03	2009-07-23	2009-07-23	ENSG00000187773	ENSG00000187773			31729	protein-coding gene	gene with protein product		614544	"""chromosome 18 open reading frame 51"""	C18orf51		21334309	Standard	NM_001044369		Approved		uc002llk.3	Q0P6D2	OTTHUMG00000156984	ENST00000343998.6:c.1214A>G	18.37:g.72103782T>C	ENSP00000344331:p.Gln405Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_001044369		Missense_Mutation	SNP	ENST00000343998.6	37	CCDS42445.2	724	0.3315018315018315	174	0.35365853658536583	115	0.31767955801104975	152	0.26573426573426573	283	0.3733509234828496	C	1.680	-0.506740	0.04231	0.318064	0.383822	ENSG00000187773	ENST00000400291;ENST00000343998	.	.	.	4.95	4.08	0.47627	.	0.507764	0.20656	N	0.088114	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	0.42344	-0.9457	8	0.12766	T	0.61	-9.8332	8.5284	0.33319	0.0:0.6981:0.0:0.3019	rs2278154;rs56640189;rs2278154	405	Q0P6D2	FA69C_HUMAN	R	106;405	.	ENSP00000344331:Q405R	Q	-	2	0	FAM69C	70254762	0.003000	0.15002	0.021000	0.16686	0.285000	0.27093	1.315000	0.33608	0.639000	0.30564	-0.220000	0.12472	CAA	T|0.666;C|0.334	0.334	strong		0.582	FAM69C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346971.2	XM_058931	
SORCS1	114815	hgsc.bcm.edu	37	10	108367020	108367020	+	Silent	SNP	C	C	T	rs7082289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:108367020C>T	ENST00000263054.6	-	23	3076	c.3069G>A	c.(3067-3069)gcG>gcA	p.A1023A	SORCS1_ENST00000344440.6_Silent_p.A1023A|SORCS1_ENST00000369698.1_Silent_p.A558A|SORCS1_ENST00000478809.2_5'UTR	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1023					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)		CAGGGAGCACCGCCACCAGGA	0.552													C|||	1187	0.237021	0.323	0.0994	5008	,	,		19392	0.2401		0.0765	False		,,,				2504	0.3804				p.A1023A		Atlas-SNP	.											.	SORCS1	534	.	0			c.G3069A						PASS	.	C	,,,,,	1246,3160	428.5+/-341.9	184,878,1141	70.0	67.0	68.0		3069,3069,3069,3069,3069,3069	-11.8	0.0	10	dbSNP_116	68	721,7879	175.9+/-225.9	31,659,3610	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	,,,,,	215,1537,4751	TT,TC,CC		8.3837,28.2796,15.1238	,,,,,	1023/1199,1023/1180,1023/1131,1023/1160,1023/1180,1023/1169	108367020	1967,11039	2203	4300	6503	SO:0001819	synonymous_variant	114815	exon23			GAGCACCGCCACC	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.3069G>A	10.37:g.108367020C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1	358	0.16391941391941392	135	0.27439024390243905	36	0.09944751381215469	125	0.21853146853146854	62	0.08179419525065963	C	5.613	0.297926	0.10622	0.282796	0.083837	ENSG00000108018	ENST00000452214	.	.	.	5.92	-11.8	0.00035	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999955085	.	.	.	.	.	.	T	0.23976	-1.0173	3	.	.	.	-22.0366	9.601	0.39603	0.055:0.1218:0.2746:0.5486	rs7082289;rs60556865;rs7082289	.	.	.	Q	38	.	.	R	-	2	0	SORCS1	108357010	0.000000	0.05858	0.001000	0.08648	0.710000	0.40934	-2.984000	0.00661	-5.598000	0.00012	-0.136000	0.14681	CGG	C|0.839;T|0.161	0.161	strong		0.552	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
C5	727	hgsc.bcm.edu	37	9	123783934	123783934	+	Silent	SNP	T	T	C	rs10985126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:123783934T>C	ENST00000223642.1	-	11	1184	c.1155A>G	c.(1153-1155)ggA>ggG	p.G385G		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	385					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	TTACTGGGACTCCTCCTACCA	0.393													C|||	1208	0.241214	0.4418	0.1037	5008	,	,		19524	0.244		0.167	False		,,,				2504	0.1411				p.G385G		Atlas-SNP	.											C5,NS,adenoma,0,1	C5	124	1	0			c.A1155G						PASS	.	C		1677,2729	653.1+/-399.5	318,1041,844	189.0	177.0	181.0		1155	1.9	0.2	9	dbSNP_120	181	1548,7052	745.4+/-407.3	141,1266,2893	no	coding-synonymous	C5	NM_001735.2		459,2307,3737	CC,CT,TT		18.0,38.0617,24.7962		385/1677	123783934	3225,9781	2203	4300	6503	SO:0001819	synonymous_variant	727	exon11			TGGGACTCCTCCT	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.1155A>G	9.37:g.123783934T>C		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	285	97	0.340351	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	37	CCDS6826.1																																																																																			T|0.764;C|0.236	0.236	strong		0.393	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276888	71276888	+	Silent	SNP	T	T	C	rs12793134		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	180	19	0.105556	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		
CYP3A5	1577	hgsc.bcm.edu	37	7	99262835	99262835	+	Silent	SNP	C	C	T	rs10264272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99262835C>T	ENST00000222982.4	-	7	723	c.624G>A	c.(622-624)aaG>aaA	p.K208K	CYP3A5_ENST00000343703.5_Silent_p.K198K|CYP3A5_ENST00000480723.1_5'Flank|CYP3A5_ENST00000339843.2_3'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	208					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TTAGGAACTTCTTAGTGCTCT	0.378													C|||	223	0.0445288	0.1543	0.0231	5008	,	,		18786	0.0		0.003	False		,,,				2504	0.0				p.K208K		Atlas-SNP	.											.	CYP3A5	46	.	0			c.G624A	GRCh37	CS015291	CYP3A5	S	rs10264272	PASS	.	C		530,3876	238.4+/-249.8	43,444,1716	113.0	108.0	110.0		624	2.9	0.0	7	dbSNP_119	110	7,8593	3.7+/-12.6	0,7,4293	no	coding-synonymous	CYP3A5	NM_000777.3		43,451,6009	TT,TC,CC		0.0814,12.0291,4.1289		208/503	99262835	537,12469	2203	4300	6503	SO:0001819	synonymous_variant	1577	exon7			GAACTTCTTAGTG	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.624G>A	7.37:g.99262835C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	160	72	0.45	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Silent	SNP	ENST00000222982.4	37	CCDS5672.1																																																																																			C|0.952;T|0.048	0.048	strong		0.378	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
ABCC11	85320	hgsc.bcm.edu	37	16	48234381	48234381	+	Missense_Mutation	SNP	G	G	A	rs41282045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48234381G>A	ENST00000394747.1	-	14	2237	c.1888C>T	c.(1888-1890)Cgg>Tgg	p.R630W	ABCC11_ENST00000537808.1_Missense_Mutation_p.R630W|ABCC11_ENST00000356608.2_Missense_Mutation_p.R630W|ABCC11_ENST00000353782.5_Missense_Mutation_p.R630W|ABCC11_ENST00000394748.1_Missense_Mutation_p.R630W	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	630	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|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)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	TTGAGGCCCCGCTCTCCAATC	0.597													G|||	13	0.00259585	0.003	0.0043	5008	,	,		18082	0.0		0.004	False		,,,				2504	0.002				p.R630W		Atlas-SNP	.											.	ABCC11	177	.	0			c.C1888T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	12,4390	19.1+/-41.9	0,12,2189	46.0	38.0	41.0		1888,1888,1888	1.2	1.0	16	dbSNP_127	41	61,8539	37.8+/-93.5	0,61,4239	yes	missense,missense,missense	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	101,101,101	0,73,6428	AA,AG,GG		0.7093,0.2726,0.5615	probably-damaging,probably-damaging,probably-damaging	630/1383,630/1383,630/1345	48234381	73,12929	2201	4300	6501	SO:0001583	missense	85320	exon14			GGCCCCGCTCTCC	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.1888C>T	16.37:g.48234381G>A	ENSP00000378230:p.Arg630Trp	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	6	0.0027472527472527475	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	20.3	3.968770	0.74131	0.002726	0.007093	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53	5.61	1.19	0.21007	ABC transporter, transmembrane domain, type 1 (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.067924	0.64402	N	0.000016	D	0.85375	0.5682	M	0.91561	3.22	0.80722	D	1	B;D	0.89917	0.333;1.0	B;D	0.97110	0.061;1.0	D	0.83707	0.0185	10	0.87932	D	0	-11.3458	4.1375	0.10178	0.1727:0.0:0.5052:0.3221	rs41282045	630;630	Q96J66-2;Q96J66	.;ABCCB_HUMAN	W	630	ENSP00000311326:R630W;ENSP00000349017:R630W;ENSP00000378231:R630W;ENSP00000378230:R630W;ENSP00000438530:R630W	ENSP00000311326:R630W	R	-	1	2	ABCC11	46791882	0.945000	0.32115	0.999000	0.59377	0.784000	0.44337	0.691000	0.25467	0.316000	0.23135	0.655000	0.94253	CGG	G|0.996;A|0.004	0.004	strong		0.597	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
KRT72	140807	hgsc.bcm.edu	37	12	52985293	52985293	+	Silent	SNP	A	A	G	rs12824366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52985293A>G	ENST00000537672.2	-	5	928	c.918T>C	c.(916-918)atT>atC	p.I306I	KRT72_ENST00000354310.4_Silent_p.I306I|KRT72_ENST00000398066.3_Silent_p.I118I|KRT72_ENST00000293745.2_Silent_p.I306I	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	306	Coil 2.|Rod.					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)		TCTTTAGGGCAATCTCCTCGT	0.597													G|||	1865	0.372404	0.1914	0.2406	5008	,	,		21236	0.5655		0.3638	False		,,,				2504	0.5204				p.I306I		Atlas-SNP	.											.	KRT72	70	.	0			c.T918C						PASS	.	G	,,	1138,3268	716.0+/-408.5	156,826,1221	156.0	117.0	130.0		918,918,918	-3.6	0.0	12	dbSNP_121	130	3279,5321	647.6+/-400.4	598,2083,1619	no	coding-synonymous,coding-synonymous,coding-synonymous	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	,,	754,2909,2840	GG,GA,AA		38.1279,25.8284,33.9612	,,	306/512,306/470,306/512	52985293	4417,8589	2203	4300	6503	SO:0001819	synonymous_variant	140807	exon5			TAGGGCAATCTCC	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.918T>C	12.37:g.52985293A>G		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	259	121	0.467181	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Silent	SNP	ENST00000537672.2	37	CCDS8833.1																																																																																			A|0.651;G|0.349	0.349	strong		0.597	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
CACNG6	59285	hgsc.bcm.edu	37	19	54501540	54501540	+	Missense_Mutation	SNP	C	C	T	rs78495589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54501540C>T	ENST00000252729.2	+	2	969	c.379C>T	c.(379-381)Cgc>Tgc	p.R127C	CACNG6_ENST00000346968.2_Missense_Mutation_p.R127C|CACNG6_ENST00000352529.1_Intron	NM_145814.1	NP_665813.1	Q9BXT2	CCG6_HUMAN	calcium channel, voltage-dependent, gamma subunit 6	127					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)		GGAGAATGCACGCATCTTTCA	0.502													C|||	79	0.0157748	0.0567	0.0058	5008	,	,		18465	0.0		0.0	False		,,,				2504	0.0				p.R127C		Atlas-SNP	.											.	CACNG6	42	.	0			c.C379T						PASS	.	C	,CYS/ARG,CYS/ARG	179,4227		5,169,2029	104.0	93.0	97.0		,379,379	5.4	0.2	19	dbSNP_131	97	1,8599		0,1,4299	yes	intron,missense,missense	CACNG6	NM_031897.2,NM_145814.1,NM_145815.1	,180,180	5,170,6328	TT,TC,CC		0.0116,4.0626,1.384	,possibly-damaging,possibly-damaging	,127/261,127/215	54501540	180,12826	2203	4300	6503	SO:0001583	missense	59285	exon2			AATGCACGCATCT	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.379C>T	19.37:g.54501540C>T	ENSP00000252729:p.Arg127Cys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	56	38	0.678571	NM_145815		Missense_Mutation	SNP	ENST00000252729.2	37	CCDS12870.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	.	16.01	3.000193	0.54147	0.040626	1.16E-4	ENSG00000130433	ENST00000252729;ENST00000346968	T;T	0.31769	1.48;1.48	5.36	5.36	0.76844	.	0.633990	0.14809	N	0.297160	T	0.03608	0.0103	N	0.22421	0.69	0.40471	D	0.980344	D;D	0.61697	0.987;0.99	P;P	0.48114	0.555;0.567	T	0.01039	-1.1472	10	0.62326	D	0.03	-13.2984	14.9705	0.71229	0.0:1.0:0.0:0.0	.	127;127	A6NFR2;Q9BXT2	.;CCG6_HUMAN	C	127	ENSP00000252729:R127C;ENSP00000319097:R127C	ENSP00000252729:R127C	R	+	1	0	CACNG6	59193352	0.024000	0.19004	0.244000	0.24202	0.499000	0.33736	2.549000	0.45803	2.685000	0.91497	0.655000	0.94253	CGC	C|0.986;T|0.014	0.014	strong		0.502	CACNG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139359.1		
CEP85L	387119	hgsc.bcm.edu	37	6	118953755	118953755	+	Silent	SNP	T	T	C	rs9320659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118953755T>C	ENST00000368491.3	-	2	714	c.93A>G	c.(91-93)gcA>gcG	p.A31A	CEP85L_ENST00000360290.3_5'UTR|CEP85L_ENST00000392500.3_Silent_p.A34A|CEP85L_ENST00000419517.2_Silent_p.A31A|CEP85L_ENST00000368488.5_Silent_p.A34A	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	31						centrosome (GO:0005813)|cytoplasm (GO:0005737)											CAGGTAGCCATGCTGATGAAT	0.388													T|||	163	0.0325479	0.0582	0.0159	5008	,	,		17382	0.0		0.0179	False		,,,				2504	0.0583				p.A34A		Atlas-SNP	.											.	CEP85L	26	.	0			c.A102G						PASS	.	T	,,	199,3547		4,191,1678	79.0	74.0	76.0		93,102,93	1.9	1.0	6	dbSNP_119	76	163,8055		2,159,3948	no	coding-synonymous,coding-synonymous,coding-synonymous	C6orf204	NM_001042475.2,NM_001178035.1,NM_206921.2	,,	6,350,5626	CC,CT,TT		1.9835,5.3123,3.0257	,,	31/806,34/809,31/497	118953755	362,11602	1873	4109	5982	SO:0001819	synonymous_variant	387119	exon3			TAGCCATGCTGAT	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.93A>G	6.37:g.118953755T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Silent	SNP	ENST00000368491.3	37	CCDS43498.1																																																																																			T|0.980;C|0.020	0.020	strong		0.388	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
OR2T5	401993	hgsc.bcm.edu	37	1	248652011	248652011	+	Missense_Mutation	SNP	A	A	T	rs150528589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248652011A>T	ENST00000366473.2	+	1	127	c.122A>T	c.(121-123)aAg>aTg	p.K41M		NM_001004697.1	NP_001004697.1	Q6IEZ7	OR2T5_HUMAN	olfactory receptor, family 2, subfamily T, member 5	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K41M(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(2)|pancreas(1)|skin(2)	9	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)			GTTTTCCTGAAGGCGTTGTCT	0.478													.|||	1961	0.391573	0.7307	0.2147	5008	,	,		28057	0.3542		0.1889	False		,,,				2504	0.3057				p.K41M		Atlas-SNP	.											OR2T5,NS,other,0,1	OR2T5	17	1	1	Substitution - Missense(1)	pancreas(1)	c.A122T						scavenged	.	T	MET/LYS	2044,2150		554,936,607	81.0	103.0	96.0		122	1.3	0.2	1	dbSNP_134	96	674,7914		4,666,3624	no	missense	OR2T5	NM_001004697.1	95	558,1602,4231	TT,TA,AA		7.8482,48.7363,21.2643	benign	41/316	248652011	2718,10064	2097	4294	6391	SO:0001583	missense	401993	exon1			TCCTGAAGGCGTT	BK004465	CCDS31118.1	1q44	2012-08-09			ENSG00000203661	ENSG00000203661		"""GPCR / Class A : Olfactory receptors"""	15017	protein-coding gene	gene with protein product							Standard	NM_001004697		Approved		uc001iem.1	Q6IEZ7	OTTHUMG00000040481	ENST00000366473.2:c.122A>T	1.37:g.248652011A>T	ENSP00000355429:p.Lys41Met	Somatic	944	2	0.00211864		WXS	Illumina HiSeq	Phase_I	788	343	0.435279	NM_001004697		Missense_Mutation	SNP	ENST00000366473.2	37	CCDS31118.1	.	.	.	.	.	.	.	.	.	.	t	0.019	-1.457006	0.01071	0.487363	0.078482	ENSG00000203661	ENST00000366473	T	0.00424	7.45	2.64	1.27	0.21489	.	0.130450	0.36409	N	0.002609	T	0.00012	0.0000	N	0.00023	-2.71	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18398	-1.0338	9	0.02654	T	1	.	7.1342	0.25519	0.3491:0.0:0.0:0.6509	.	41	Q6IEZ7	OR2T5_HUMAN	M	41	ENSP00000355429:K41M	ENSP00000355429:K41M	K	+	2	0	OR2T5	246718634	0.007000	0.16637	0.198000	0.23420	0.062000	0.15995	1.733000	0.38156	0.108000	0.17862	-1.793000	0.00626	AAG	A|0.250;T|0.750	0.750	weak		0.478	OR2T5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097422.1	NM_001004697	
APCDD1L	164284	hgsc.bcm.edu	37	20	57042665	57042665	+	Missense_Mutation	SNP	A	A	G	rs7265854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:57042665A>G	ENST00000371149.3	-	3	468	c.238T>C	c.(238-240)Tac>Cac	p.Y80H	APCDD1L_ENST00000439429.1_Missense_Mutation_p.Y91H	NM_153360.1	NP_699191.1	Q8NCL9	APCDL_HUMAN	adenomatosis polyposis coli down-regulated 1-like	80			Y -> H (in dbSNP:rs7265854).			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)			CGGCTGGGGTAGAAGGTGTAG	0.672													A|||	619	0.123602	0.0643	0.1945	5008	,	,		12434	0.3026		0.0199	False		,,,				2504	0.0757				p.Y80H		Atlas-SNP	.											.	APCDD1L	48	.	0			c.T238C						PASS	.	A	HIS/TYR	312,4094	152.9+/-186.6	10,292,1901	25.0	27.0	26.0		238	3.5	0.8	20	dbSNP_116	26	273,8327	97.7+/-159.3	1,271,4028	yes	missense	APCDD1L	NM_153360.1	83	11,563,5929	GG,GA,AA		3.1744,7.0813,4.4979	benign	80/502	57042665	585,12421	2203	4300	6503	SO:0001583	missense	164284	exon3			TGGGGTAGAAGGT	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.238T>C	20.37:g.57042665A>G	ENSP00000360191:p.Tyr80His	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	167	86	0.51497	NM_153360		Missense_Mutation	SNP	ENST00000371149.3	37	CCDS13467.1	277	0.12683150183150182	34	0.06910569105691057	55	0.15193370165745856	172	0.3006993006993007	16	0.021108179419525065	A	11.96	1.793593	0.31685	0.070813	0.031744	ENSG00000198768	ENST00000371149;ENST00000439429	T;T	0.20332	2.08;2.08	4.65	3.55	0.40652	.	0.338322	0.31660	N	0.007268	T	0.00012	0.0000	L	0.56769	1.78	0.42321	P	0.007743000000000055	B;B	0.17667	0.023;0.004	B;B	0.18871	0.023;0.004	T	0.36261	-0.9755	9	0.30078	T	0.28	-12.3582	10.0012	0.41929	0.9189:0.0:0.0811:0.0	rs7265854;rs7265854	91;80	F5H6V6;Q8NCL9	.;APCDL_HUMAN	H	80;91	ENSP00000360191:Y80H;ENSP00000413261:Y91H	ENSP00000360191:Y80H	Y	-	1	0	APCDD1L	56476071	1.000000	0.71417	0.805000	0.32314	0.934000	0.57294	3.483000	0.53194	0.651000	0.30788	0.454000	0.30748	TAC	A|0.920;G|0.080	0.080	strong		0.672	APCDD1L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000079881.2	NM_153360	
SRGAP2-AS1	100873165	hgsc.bcm.edu	37	1	121116732	121116732	+	lincRNA	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:121116732C>T	ENST00000437515.1	-	0	329					NR_104189.1																						CATCAAAGCCCAGAATGAGTA	0.428																																					p.Q97X		Atlas-SNP	.											.	.	.	.	0			c.C289T						PASS	.																																					100996712	exon3			AAAGCCCAGAATG																													1.37:g.121116732C>T		Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	272	11	0.0404412	NM_001271887		Nonsense_Mutation	SNP	ENST00000437515.1	37																																																																																				.	.	none		0.428	RP11-343N15.1-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000098477.2		
CST4	1472	hgsc.bcm.edu	37	20	23669584	23669584	+	Missense_Mutation	SNP	A	A	T	rs73902131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23669584A>T	ENST00000217423.3	-	1	93	c.23T>A	c.(22-24)cTg>cAg	p.L8Q		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	8					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CAGGAGTAGCAGGGTACACAG	0.602													.|||	170	0.0339457	0.1225	0.0115	5008	,	,		15657	0.0		0.0	False		,,,				2504	0.0				p.L8Q		Atlas-SNP	.											.	CST4	37	.	0			c.T23A						PASS	.	A	GLN/LEU	411,3995	201.5+/-224.5	18,375,1810	53.0	52.0	52.0		23	0.4	0.0	20	dbSNP_130	52	3,8597	2.2+/-6.3	0,3,4297	yes	missense	CST4	NM_001899.2	113	18,378,6107	TT,TA,AA		0.0349,9.3282,3.1831	possibly-damaging	8/142	23669584	414,12592	2203	4300	6503	SO:0001583	missense	1472	exon1			AGTAGCAGGGTAC		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.23T>A	20.37:g.23669584A>T	ENSP00000217423:p.Leu8Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	122	48	0.393443	NM_001899	Q9UBI5|Q9UCS9	Missense_Mutation	SNP	ENST00000217423.3	37	CCDS13159.1	58	0.026556776556776556	51	0.10365853658536585	7	0.019337016574585635	0	0.0	0	0.0	A	2.719	-0.266983	0.05754	0.093282	3.49E-4	ENSG00000101441	ENST00000217423	T	0.08458	3.09	1.45	0.431	0.16523	.	1.397050	0.04408	N	0.365592	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	P	0.50156	0.932	B	0.34991	0.193	T	0.28522	-1.0041	10	0.54805	T	0.06	.	3.6086	0.08052	0.2712:0.0:0.7288:0.0	.	8	P01036	CYTS_HUMAN	Q	8	ENSP00000217423:L8Q	ENSP00000217423:L8Q	L	-	2	0	CST4	23617584	0.005000	0.15991	0.001000	0.08648	0.003000	0.03518	1.018000	0.30002	0.157000	0.19338	-0.483000	0.04790	CTG	A|0.964;T|0.036	0.036	strong		0.602	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899	
MUC20	200958	hgsc.bcm.edu	37	3	195452679	195452679	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195452679C>T	ENST00000447234.2	+	2	1331	c.1205C>T	c.(1204-1206)cCg>cTg	p.P402L	MUC20_ENST00000445522.2_Missense_Mutation_p.P367L|MUC20_ENST00000436408.1_Missense_Mutation_p.P402L|MUC20_ENST00000320736.6_Missense_Mutation_p.P231L	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	402					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)		TCATGGTCCCCGGGATCTGAC	0.577																																					p.P231L		Atlas-SNP	.											.	MUC20	84	.	0			c.C692T						PASS	.						4.0	3.0	4.0					3																	195452679		1669	3676	5345	SO:0001583	missense	200958	exon3			GGTCCCCGGGATC	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.1205C>T	3.37:g.195452679C>T	ENSP00000414350:p.Pro402Leu	Somatic	609	0	0		WXS	Illumina HiSeq	Phase_I	990	191	0.192929	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	c	0.869	-0.732706	0.03135	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.11169	3.13;3.17;3.42;2.8	3.26	-6.52	0.01872	.	0.588934	0.14297	N	0.328508	T	0.02848	0.0085	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30995	-0.9959	10	0.87932	D	0	10.2224	0.1188	0.00063	0.242:0.2215:0.2078:0.3286	.	231	E9PH32	.	L	402;231;402;367	ENSP00000414350:P402L;ENSP00000325431:P231L;ENSP00000396774:P402L;ENSP00000405629:P367L	ENSP00000325431:P231L	P	+	2	0	MUC20	196938350	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.247000	0.02893	-2.014000	0.00948	-0.972000	0.02603	CCG	.	.	none		0.577	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919079	12919079	+	Missense_Mutation	SNP	C	C	G	rs9659529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919079C>G	ENST00000240189.2	+	2	302	c.215C>G	c.(214-216)aCg>aGg	p.T72R		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	72			T -> R (in dbSNP:rs9659529).		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)		CTGATGAAGACGCTTCATCTG	0.557													.|||	540	0.107827	0.1263	0.098	5008	,	,		22731	0.127		0.1064	False		,,,				2504	0.0716				p.T72R		Atlas-SNP	.											PRAMEF2,caecum,carcinoma,-1,2	PRAMEF2	85	2	0			c.C215G						PASS	.	T	ARG/THR	623,3779	268.6+/-268.5	67,489,1645	153.0	163.0	160.0		215	-1.7	0.1	1	dbSNP_119	160	960,7632	209.4+/-250.6	62,836,3398	no	missense	PRAMEF2	NM_023014.1	71	129,1325,5043	GG,GC,CC		11.1732,14.1527,12.1825	possibly-damaging	72/475	12919079	1583,11411	2201	4296	6497	SO:0001583	missense	65122	exon2			TGAAGACGCTTCA		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.215C>G	1.37:g.12919079C>G	ENSP00000240189:p.Thr72Arg	Somatic	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	348	167	0.479885	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	230	0.10531135531135531	46	0.09349593495934959	35	0.09668508287292818	62	0.10839160839160839	87	0.11477572559366754	c	1.758	-0.487598	0.04352	0.141527	0.111732	ENSG00000120952	ENST00000240189	T	0.11277	2.79	0.842	-1.68	0.08212	.	4.218360	0.00582	N	0.000330	T	0.00178	0.0005	L	0.50919	1.6	0.80722	P	0.0	P	0.41643	0.758	D	0.64237	0.923	T	0.14476	-1.0471	9	0.25106	T	0.35	.	4.1359	0.10170	0.0:0.4732:0.0:0.5268	rs9659529;rs9659529	72	O60811	PRAM2_HUMAN	R	72	ENSP00000240189:T72R	ENSP00000240189:T72R	T	+	2	0	PRAMEF2	12841666	0.000000	0.05858	0.064000	0.19789	0.045000	0.14185	-0.129000	0.10515	-0.704000	0.05042	-1.031000	0.02408	ACG	C|0.887;G|0.113	0.113	strong		0.557	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
PLIN4	729359	hgsc.bcm.edu	37	19	4511944	4511944	+	Silent	SNP	A	A	G	rs143131726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4511944A>G	ENST00000301286.3	-	3	1985	c.1986T>C	c.(1984-1986)aaT>aaC	p.N662N		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	662	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						CTTTGGCCACATTCACAGCAC	0.577													A|||	40	0.00798722	0.0303	0.0	5008	,	,		25673	0.0		0.0	False		,,,				2504	0.0				p.N662N		Atlas-SNP	.											.	PLIN4	191	.	0			c.T1986C						PASS	.	A		115,4007		6,103,1952	96.0	106.0	103.0		1986	-10.3	0.0	19	dbSNP_134	103	1,8383		0,1,4191	no	coding-synonymous	PLIN4	NM_001080400.1		6,104,6143	GG,GA,AA		0.0119,2.7899,0.9276		662/1358	4511944	116,12390	2061	4192	6253	SO:0001819	synonymous_variant	729359	exon3			GGCCACATTCACA	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.1986T>C	19.37:g.4511944A>G		Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	306	134	0.437909	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			A|0.994;G|0.006	0.006	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
FBN2	2201	hgsc.bcm.edu	37	5	127622491	127622491	+	Missense_Mutation	SNP	T	T	C	rs32209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:127622491T>C	ENST00000508053.1	-	61	7905	c.6931A>G	c.(6931-6933)Atg>Gtg	p.M2311V	FBN2_ENST00000262464.4_Missense_Mutation_p.M2311V			P35556	FBN2_HUMAN	fibrillin 2	2311	EGF-like 39; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		M -> V (in dbSNP:rs32209).		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)		TTCTTACACATCATGCCCCTA	0.448													T|||	1166	0.232827	0.2511	0.0648	5008	,	,		20513	0.5873		0.0417	False		,,,				2504	0.1585				p.M2311V		Atlas-SNP	.											.	FBN2	858	.	0			c.A6931G						PASS	.	T	VAL/MET	914,3492	351.3+/-311.2	98,718,1387	141.0	124.0	130.0		6931	5.3	1.0	5	dbSNP_76	130	358,8242	119.9+/-179.2	7,344,3949	yes	missense	FBN2	NM_001999.3	21	105,1062,5336	CC,CT,TT		4.1628,20.7444,9.7801	benign	2311/2913	127622491	1272,11734	2203	4300	6503	SO:0001583	missense	2201	exon55			TACACATCATGCC	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.6931A>G	5.37:g.127622491T>C	ENSP00000424571:p.Met2311Val	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	138	75	0.543478	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	522	0.23901098901098902	114	0.23170731707317074	23	0.06353591160220995	349	0.6101398601398601	36	0.047493403693931395	T	11.77	1.738740	0.30774	0.207444	0.041628	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.86694	-2.16;-2.16	5.34	5.34	0.76211	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.065955	0.64402	D	0.000005	T	0.00012	0.0000	N	0.01576	-0.805	0.28809	P	0.898348	B	0.02656	0.0	B	0.04013	0.001	T	0.39921	-0.9590	9	0.28530	T	0.3	.	10.1516	0.42796	0.0:0.0741:0.0:0.9259	rs32209;rs1617952;rs17697639;rs52791218;rs60140231;rs32209	2311	P35556	FBN2_HUMAN	V	2311	ENSP00000262464:M2311V;ENSP00000424571:M2311V	ENSP00000262464:M2311V	M	-	1	0	FBN2	127650390	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	2.147000	0.42226	2.367000	0.80283	0.528000	0.53228	ATG	T|0.831;C|0.169	0.169	strong		0.448	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
DNHD1	144132	hgsc.bcm.edu	37	11	6579354	6579354	+	Silent	SNP	G	G	C	rs16915382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	103	0	0		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	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	
COL20A1	57642	hgsc.bcm.edu	37	20	61945439	61945439	+	Missense_Mutation	SNP	G	G	C	rs147670144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61945439G>C	ENST00000358894.6	+	19	2474	c.2374G>C	c.(2374-2376)Gcc>Ccc	p.A792P	COL20A1_ENST00000435874.1_Missense_Mutation_p.A799P|COL20A1_ENST00000326996.6_Missense_Mutation_p.A792P|COL20A1_ENST00000422202.1_Missense_Mutation_p.A799P	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	792	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					TGTGCCAGGAGCCAGGAGCCA	0.642													C|||	321	0.0640974	0.0832	0.036	5008	,	,		18224	0.0139		0.0527	False		,,,				2504	0.1217				p.A792P		Atlas-SNP	.											.	COL20A1	137	.	0			c.G2374C						PASS	.	C	PRO/ALA	292,4010		13,266,1872	39.0	46.0	44.0		2374	-0.2	0.9	20	dbSNP_134	44	491,7981		17,457,3762	yes	missense	COL20A1	NM_020882.2	27	30,723,5634	CC,CG,GG		5.7956,6.7875,6.1296	benign	792/1285	61945439	783,11991	2151	4236	6387	SO:0001583	missense	57642	exon19			CCAGGAGCCAGGA	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.2374G>C	20.37:g.61945439G>C	ENSP00000351767:p.Ala792Pro	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	113	0.051739926739926737	39	0.07926829268292683	17	0.04696132596685083	8	0.013986013986013986	49	0.06464379947229551	C	1.915	-0.449644	0.04572	0.067875	0.057956	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	3.57	-0.153	0.13403	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.810534	0.10939	N	0.617427	T	0.00815	0.0027	N	0.00841	-1.15	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.13176	-1.0519	9	0.27082	T	0.32	.	1.6125	0.02696	0.3773:0.3339:0.1721:0.1166	.	799;792	Q9P218-2;Q9P218	.;COKA1_HUMAN	P	792;792;799;799	ENSP00000351767:A792P;ENSP00000323077:A792P;ENSP00000408690:A799P;ENSP00000414753:A799P	ENSP00000323077:A792P	A	+	1	0	COL20A1	61415884	0.000000	0.05858	0.937000	0.37676	0.108000	0.19459	0.041000	0.13927	-0.137000	0.11455	-0.670000	0.03821	GCC	G|0.946;C|0.054	0.054	strong		0.642	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
P2RX7	5027	hgsc.bcm.edu	37	12	121622380	121622380	+	Missense_Mutation	SNP	C	C	G	rs2230913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121622380C>G	ENST00000546057.1	+	13	1706	c.1563C>G	c.(1561-1563)caC>caG	p.H521Q	P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000328963.5_Missense_Mutation_p.H351Q|RP11-340F14.5_ENST00000569999.1_RNA|P2RX7_ENST00000541446.1_Missense_Mutation_p.H232Q|P2RX7_ENST00000535250.1_Missense_Mutation_p.H431Q	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	521			H -> Q (in dbSNP:rs2230913).		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)					TGTCCAGACACGTCCTGCAGT	0.627													C|||	223	0.0445288	0.1619	0.013	5008	,	,		17902	0.0		0.0	False		,,,				2504	0.0				p.H521Q		Atlas-SNP	.											.	P2RX7	53	.	0			c.C1563G						PASS	.	C	GLN/HIS	615,3791	246.2+/-254.9	43,529,1631	35.0	31.0	32.0		1563	-10.4	0.0	12	dbSNP_98	32	7,8593	4.3+/-15.6	0,7,4293	yes	missense	P2RX7	NM_002562.5	24	43,536,5924	GG,GC,CC		0.0814,13.9582,4.7824	benign	521/596	121622380	622,12384	2203	4300	6503	SO:0001583	missense	5027	exon13			CAGACACGTCCTG	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.1563C>G	12.37:g.121622380C>G	ENSP00000442349:p.His521Gln	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	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	81	0.03708791208791209	75	0.1524390243902439	6	0.016574585635359115	0	0.0	0	0.0	C	0.024	-1.393088	0.01185	0.139582	8.14E-4	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.04454	4.5;4.13;4.29;3.62	5.21	-10.4	0.00318	.	2.829390	0.01180	N	0.007078	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.40194	-0.9576	9	0.21540	T	0.41	.	3.5355	0.07793	0.0826:0.2354:0.3527:0.3294	rs2230913;rs2230913	351;232;431;521	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	Q	521;351;431;232	ENSP00000442349:H521Q;ENSP00000330696:H351Q;ENSP00000442572:H431Q;ENSP00000437471:H232Q	ENSP00000330696:H351Q	H	+	3	2	P2RX7	120106763	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-6.209000	0.00076	-4.138000	0.00070	-1.865000	0.00557	CAC	C|0.955;G|0.045;T|0.000	0.045	strong		0.627	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
TMEM2	23670	hgsc.bcm.edu	37	9	74360395	74360395	+	Silent	SNP	T	T	C	rs76670837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:74360395T>C	ENST00000377044.4	-	4	1112	c.573A>G	c.(571-573)gcA>gcG	p.A191A	TMEM2_ENST00000377066.5_Silent_p.A191A	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	191	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		GGCATTTTTCTGCTCCAATAT	0.413													T|||	302	0.0603035	0.0998	0.0591	5008	,	,		18601	0.0		0.0934	False		,,,				2504	0.0358				p.A191A		Atlas-SNP	.											.	TMEM2	112	.	0			c.A573G						PASS	.	T	,	364,4042	186.4+/-213.3	16,332,1855	100.0	101.0	101.0		573,573	5.9	1.0	9	dbSNP_132	101	576,8024	155.2+/-209.3	25,526,3749	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	41,858,5604	CC,CT,TT		6.6977,8.2615,7.2274	,	191/1321,191/1384	74360395	940,12066	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon4			TTTTTCTGCTCCA		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.573A>G	9.37:g.74360395T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	91	55	0.604396	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			T|0.926;C|0.074	0.074	strong		0.413	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65347922	65347922	+	Silent	SNP	G	G	A	rs78852393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65347922G>A	ENST00000309295.4	+	6	871	c.606G>A	c.(604-606)ccG>ccA	p.P202P		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	202						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						CAGGAGCCCCGGAGGCCCGGG	0.622													G|||	97	0.019369	0.0688	0.0058	5008	,	,		17515	0.0		0.002	False		,,,				2504	0.0				p.P202P		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G606A						PASS	.	G		270,3658		8,254,1702	61.0	66.0	65.0		606	-6.2	0.6	11	dbSNP_131	65	2,8312		0,2,4155	no	coding-synonymous	EHBP1L1	NM_001099409.1		8,256,5857	AA,AG,GG		0.0241,6.8737,2.2219		202/1524	65347922	272,11970	1964	4157	6121	SO:0001819	synonymous_variant	254102	exon6			AGCCCCGGAGGCC	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.606G>A	11.37:g.65347922G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	54	36	0.666667	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1																																																																																			G|0.990;A|0.010	0.010	strong		0.622	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
OR5H14	403273	hgsc.bcm.edu	37	3	97868523	97868523	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:97868523G>A	ENST00000437310.1	+	1	354	c.294G>A	c.(292-294)aaG>aaA	p.K98K	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	98						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						CTGAATGCAAGATACAGTTGT	0.383																																					p.K98K		Atlas-SNP	.											OR5H14,NS,carcinoma,0,1	OR5H14	56	1	0			c.G294A						scavenged	.						206.0	213.0	211.0					3																	97868523		2203	4299	6502	SO:0001819	synonymous_variant	403273	exon1			ATGCAAGATACAG		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.294G>A	3.37:g.97868523G>A		Somatic	506	0	0		WXS	Illumina HiSeq	Phase_I	508	7	0.0137795	NM_001005514	B9EH15	Silent	SNP	ENST00000437310.1	37	CCDS33798.1																																																																																			.	.	none		0.383	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
OR2T2	401992	hgsc.bcm.edu	37	1	248616408	248616408	+	Missense_Mutation	SNP	C	C	T	rs67700848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248616408C>T	ENST00000342927.3	+	1	332	c.310C>T	c.(310-312)Ctc>Ttc	p.L104F		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCAGATCTTCCTCTACCTGAC	0.532																																					p.L104F		Atlas-SNP	.											OR2T2,NS,carcinoma,-2,1	OR2T2	73	1	0			c.C310T						PASS	.						300.0	329.0	320.0					1																	248616408		2203	4300	6503	SO:0001583	missense	401992	exon1			ATCTTCCTCTACC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.310C>T	1.37:g.248616408C>T	ENSP00000343062:p.Leu104Phe	Somatic	1131	0	0		WXS	Illumina HiSeq	Phase_I	1137	257	0.226033	NM_001004136	B2RNM1|B9EH01	Missense_Mutation	SNP	ENST00000342927.3	37	CCDS31116.1	.	.	.	.	.	.	.	.	.	.	c	0.006	-2.038068	0.00402	.	.	ENSG00000196240	ENST00000342927	T	0.00495	6.99	3.59	-0.635	0.11512	GPCR, rhodopsin-like superfamily (1);	0.681714	0.12783	N	0.439555	T	0.00210	0.0006	N	0.04768	-0.165	0.80722	P	0.0	B	0.13594	0.008	B	0.14023	0.01	T	0.23904	-1.0175	9	0.02654	T	1	.	8.1475	0.31121	0.0:0.3677:0.0:0.6323	.	104	Q6IF00	OR2T2_HUMAN	F	104	ENSP00000343062:L104F	ENSP00000343062:L104F	L	+	1	0	OR2T2	246683031	0.000000	0.05858	0.036000	0.18154	0.224000	0.24922	-0.885000	0.04161	-0.046000	0.13446	0.298000	0.19748	CTC	C|0.875;T|0.125	0.125	strong		0.532	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
RIMS2	9699	hgsc.bcm.edu	37	8	105261725	105261725	+	Silent	SNP	G	G	A	rs59975412|rs2028945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:105261725G>A	ENST00000436393.2	+	26	3895	c.3654G>A	c.(3652-3654)caG>caA	p.Q1218Q	RIMS2_ENST00000262231.10_Silent_p.Q1039Q|RIMS2_ENST00000507740.1_Silent_p.Q1014Q|RIMS2_ENST00000406091.3_Silent_p.Q1200Q|RIMS2_ENST00000339750.2_Silent_p.Q136Q			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1262					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			GTGACATTCAGGTAGGAATGA	0.418										HNSCC(12;0.0054)			G|||	1182	0.236022	0.1316	0.2579	5008	,	,		15861	0.5357		0.0765	False		,,,				2504	0.2168				p.Q1200Q		Atlas-SNP	.											.	RIMS2	1357	.	0			c.G3600A						PASS	.	G	,	425,3307		20,385,1461	69.0	69.0	69.0		3600,3042	3.7	1.0	8	dbSNP_94	69	544,7624		21,502,3561	no	coding-synonymous,coding-synonymous	RIMS2	NM_001100117.2,NM_014677.4	,	41,887,5022	AA,AG,GG		6.6601,11.388,8.1429	,	1200/1350,1014/1164	105261725	969,10931	1866	4084	5950	SO:0001819	synonymous_variant	9699	exon22			CATTCAGGTAGGA	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.3654G>A	8.37:g.105261725G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	89	53	0.595506	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000436393.2	37																																																																																				.	.	weak		0.418	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117	
EFCAB5	374786	hgsc.bcm.edu	37	17	28407876	28407876	+	Silent	SNP	T	T	G	rs7221743	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:28407876T>G	ENST00000394835.3	+	17	3495	c.3303T>G	c.(3301-3303)ggT>ggG	p.G1101G	EFCAB5_ENST00000320856.5_Silent_p.G977G|EFCAB5_ENST00000394832.2_Intron	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1101							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						ATTATAATGGTTCATTCCTGG	0.443													G|||	2858	0.570687	0.9402	0.4669	5008	,	,		20119	0.2897		0.5656	False		,,,				2504	0.4397				p.G1101G		Atlas-SNP	.											.	EFCAB5	122	.	0			c.T3303G						PASS	.	G		3282,490		1430,422,34	87.0	84.0	85.0		3303	-3.8	0.9	17	dbSNP_116	85	4465,3755		1217,2031,862	no	coding-synonymous	EFCAB5	NM_198529.3		2647,2453,896	GG,GT,TT		45.6813,12.9905,35.3986		1101/1504	28407876	7747,4245	1886	4110	5996	SO:0001819	synonymous_variant	374786	exon17			TAATGGTTCATTC	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.3303T>G	17.37:g.28407876T>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	37	CCDS11254.2																																																																																			T|0.418;G|0.582	0.582	strong		0.443	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
HCN2	610	hgsc.bcm.edu	37	19	607984	607984	+	Silent	SNP	G	G	C	rs3752158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:607984G>C	ENST00000251287.2	+	4	1292	c.1239G>C	c.(1237-1239)ctG>ctC	p.L413L		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	413					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)		GGAGTGAACTGTACTCCTTCG	0.652													G|||	684	0.136581	0.2587	0.1124	5008	,	,		17579	0.131		0.0636	False		,,,				2504	0.0695				p.L413L	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.G1239C						PASS	.	G		940,3464		103,734,1365	72.0	48.0	56.0		1239	-6.3	0.8	19	dbSNP_107	56	552,8048		18,516,3766	no	coding-synonymous	HCN2	NM_001194.3		121,1250,5131	CC,CG,GG		6.4186,21.3442,11.4734		413/890	607984	1492,11512	2202	4300	6502	SO:0001819	synonymous_variant	610	exon4			TGAACTGTACTCC	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.1239G>C	19.37:g.607984G>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			G|0.864;C|0.136;A|0.000	0.136	strong		0.652	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
HRC	3270	hgsc.bcm.edu	37	19	49657526	49657526	+	Silent	SNP	G	G	A	rs150557795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657526G>A	ENST00000252825.4	-	1	1155	c.969C>T	c.(967-969)gaC>gaT	p.D323D	HRC_ENST00000595625.1_Silent_p.D323D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	323	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		CCTTTCTGTGGTCTTGGTGCC	0.542													G|||	63	0.0125799	0.0401	0.0029	5008	,	,		27949	0.0		0.005	False		,,,				2504	0.0031				p.D323D	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											HRC,NS,carcinoma,0,1	HRC	85	1	0			c.C969T						scavenged	.						212.0	161.0	178.0					19																	49657526		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			TCTGTGGTCTTGG		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.969C>T	19.37:g.49657526G>A		Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	283	36	0.127208	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			G|0.999;A|0.001	0.001	weak		0.542	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
CHPF2	54480	hgsc.bcm.edu	37	7	150935367	150935367	+	Missense_Mutation	SNP	C	C	T	rs76509585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150935367C>T	ENST00000035307.2	+	4	3432	c.1919C>T	c.(1918-1920)cCg>cTg	p.P640L	RP4-548D19.3_ENST00000607902.1_RNA|MIR671_ENST00000390183.1_RNA|CHPF2_ENST00000495645.1_Missense_Mutation_p.P632L	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	640	Gly/Pro-rich.				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						CCAGGGCCCCCGGGGGCTGGC	0.657													C|||	77	0.0153754	0.0545	0.0072	5008	,	,		13615	0.0		0.0	False		,,,				2504	0.0				p.P640L		Atlas-SNP	.											.	CHPF2	52	.	0			c.C1919T						PASS	.	C	LEU/PRO	169,4233		1,167,2033	19.0	22.0	21.0		1919	2.9	0.0	7	dbSNP_131	21	1,8597		0,1,4298	yes	missense	CHPF2	NM_019015.1	98	1,168,6331	TT,TC,CC		0.0116,3.8392,1.3077	probably-damaging	640/773	150935367	170,12830	2201	4299	6500	SO:0001583	missense	54480	exon4			GGCCCCCGGGGGC	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.1919C>T	7.37:g.150935367C>T	ENSP00000035307:p.Pro640Leu	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	38	10	0.263158	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	37	CCDS34779.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	C	10.20	1.283741	0.23392	0.038392	1.16E-4	ENSG00000033100	ENST00000495645;ENST00000035307	T;T	0.15372	2.43;2.43	4.81	2.92	0.33932	.	0.129772	0.36002	N	0.002859	T	0.01627	0.0052	N	0.08118	0	0.21147	N	0.999775	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32214	-0.9915	10	0.30078	T	0.28	-5.8196	9.1096	0.36718	0.0:0.8523:0.0:0.1477	.	640;632	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	L	632;640	ENSP00000418914:P632L;ENSP00000035307:P640L	ENSP00000035307:P640L	P	+	2	0	CHPF2	150566300	0.009000	0.17119	0.015000	0.15790	0.410000	0.31052	0.945000	0.29056	0.573000	0.29400	0.655000	0.94253	CCG	C|0.988;T|0.012	0.012	strong		0.657	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
RNF145	153830	hgsc.bcm.edu	37	5	158596032	158596032	+	Silent	SNP	G	G	A	rs61732785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:158596032G>A	ENST00000424310.2	-	8	1329	c.970C>T	c.(970-972)Ctg>Ttg	p.L324L	RNF145_ENST00000519865.1_Silent_p.L324L|RNF145_ENST00000521606.2_Silent_p.L341L|RNF145_ENST00000518802.1_Silent_p.L354L|RNF145_ENST00000520638.1_Silent_p.L338L|RNF145_ENST00000274542.2_Silent_p.L352L	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	324						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGCACTGCCAGGATTAACAGC	0.373													G|||	71	0.0141773	0.053	0.0014	5008	,	,		17610	0.0		0.0	False		,,,				2504	0.0				p.L354L		Atlas-SNP	.											RNF145,right_upper_lobe,carcinoma,+2,1	RNF145	110	1	0			c.C1060T						PASS	.	G	,,,,	200,4206	124.1+/-161.4	2,196,2005	116.0	119.0	118.0		1060,1021,1012,970,1054	4.2	1.0	5	dbSNP_129	118	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RNF145	NM_001199380.1,NM_001199381.1,NM_001199382.1,NM_001199383.1,NM_144726.2	,,,,	2,199,6302	AA,AG,GG		0.0349,4.5393,1.5608	,,,,	354/694,341/681,338/678,324/664,352/692	158596032	203,12803	2203	4300	6503	SO:0001819	synonymous_variant	153830	exon8			CTGCCAGGATTAA	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.970C>T	5.37:g.158596032G>A		Somatic	334	1	0.00299401		WXS	Illumina HiSeq	Phase_I	353	167	0.473088	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Silent	SNP	ENST00000424310.2	37	CCDS56390.1																																																																																			G|0.985;A|0.015	0.015	strong		0.373	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726	
GYG1	2992	hgsc.bcm.edu	37	3	148714662	148714662	+	Missense_Mutation	SNP	A	A	T	rs35054019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148714662A>T	ENST00000345003.4	+	4	752	c.452A>T	c.(451-453)cAt>cTt	p.H151L	GYG1_ENST00000483267.1_Missense_Mutation_p.H151L|GYG1_ENST00000296048.6_Missense_Mutation_p.H151L|GYG1_ENST00000484197.1_Missense_Mutation_p.H151L	NM_004130.3	NP_004121.2	P46976	GLYG_HUMAN	glycogenin 1	151					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogenin glucosyltransferase activity (GO:0008466)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(3)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CAGCTGTTGCATCTTGCTTCT	0.433													A|||	46	0.0091853	0.0348	0.0	5008	,	,		19931	0.0		0.0	False		,,,				2504	0.0				p.H151L		Atlas-SNP	.											.	GYG1	29	.	0			c.A452T						PASS	.	A	LEU/HIS,LEU/HIS,LEU/HIS	137,4269	98.5+/-137.1	1,135,2067	76.0	70.0	72.0		452,452,452	1.1	0.1	3	dbSNP_126	72	0,8600		0,0,4300	yes	missense,missense,missense	GYG1	NM_001184720.1,NM_001184721.1,NM_004130.3	99,99,99	1,135,6367	TT,TA,AA		0.0,3.1094,1.0534	benign,benign,benign	151/334,151/280,151/351	148714662	137,12869	2203	4300	6503	SO:0001583	missense	2992	exon4			TGTTGCATCTTGC	AF087942	CCDS3139.1, CCDS54654.1, CCDS54655.1	3q24-q25.1	2013-02-22	2005-11-04	2005-11-04	ENSG00000163754	ENSG00000163754	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4699	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	603942	"""glycogenin"""	GYG		8602861	Standard	NM_004130		Approved		uc003ewn.3	P46976	OTTHUMG00000159533	ENST00000345003.4:c.452A>T	3.37:g.148714662A>T	ENSP00000340736:p.His151Leu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	179	85	0.47486	NM_004130	D3DNH0|D3DNH1|D3DNH2|Q6FHZ1|Q9UNV0	Missense_Mutation	SNP	ENST00000345003.4	37	CCDS3139.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	A	11.23	1.576606	0.28092	0.031094	0.0	ENSG00000163754	ENST00000345003;ENST00000296048;ENST00000483267;ENST00000484197;ENST00000492285;ENST00000461191	T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	6.11	1.11	0.20524	.	0.519143	0.23943	N	0.043027	T	0.24431	0.0592	L	0.33339	1.005	0.20873	N	0.999833	B;B;B;B	0.13145	0.001;0.007;0.001;0.0	B;B;B;B	0.20184	0.004;0.028;0.01;0.005	T	0.31861	-0.9928	10	0.59425	D	0.04	-35.2266	9.9467	0.41613	0.7509:0.0:0.2491:0.0	rs35054019	151;151;151;151	G5E9W8;D3DNH0;P46976-2;P46976	.;.;.;GLYG_HUMAN	L	151;151;151;151;105;151	ENSP00000340736:H151L;ENSP00000296048:H151L;ENSP00000419499:H151L;ENSP00000420683:H151L;ENSP00000418297:H105L;ENSP00000420247:H151L	ENSP00000296048:H151L	H	+	2	0	GYG1	150197352	0.258000	0.24033	0.099000	0.21106	0.896000	0.52359	1.243000	0.32767	-0.028000	0.13850	-0.261000	0.10672	CAT	A|0.990;T|0.010	0.010	strong		0.433	GYG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356046.1	NM_004130	
MUC4	4585	hgsc.bcm.edu	37	3	195516980	195516980	+	Missense_Mutation	SNP	A	A	G	rs11923648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195516980A>G	ENST00000463781.3	-	2	1930	c.1471T>C	c.(1471-1473)Tca>Cca	p.S491P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S491P	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	496					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)		CTGGAGAATGAGGAAGGCCAT	0.488													N|||	193	0.0385383	0.0915	0.0144	5008	,	,		20450	0.002		0.0239	False		,,,				2504	0.0368				p.S491P		Atlas-SNP	.											.	MUC4	1505	.	0			c.T1471C						PASS	.		,,PRO/SER	380,3620		20,340,1640	125.0	119.0	121.0		,,1471	-4.6	0.0	3	dbSNP_120	121	193,8179		0,193,3993	yes	intron,intron,missense	MUC4	NM_004532.5,NM_138297.4,NM_018406.6	,,74	20,533,5633	GG,GA,AA		2.3053,9.5,4.6314	,,benign	,,491/5413	195516980	573,11799	2000	4186	6186	SO:0001583	missense	4585	exon2			AGAATGAGGAAGG	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.1471T>C	3.37:g.195516980A>G	ENSP00000417498:p.Ser491Pro	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	171	78	0.45614	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	71	0.03250915750915751	44	0.08943089430894309	9	0.024861878453038673	1	0.0017482517482517483	17	0.022427440633245383	-	2.431	-0.330925	0.05314	0.095	0.023053	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.48522	0.81;0.83	2.3	-4.61	0.03380	.	.	.	.	.	T	0.00637	0.0021	N	0.24115	0.695	0.09310	N	1	B;B	0.21225	0.053;0.002	B;B	0.17433	0.018;0.003	T	0.07443	-1.0772	9	0.38643	T	0.18	.	3.1524	0.06493	0.3217:0.0:0.3748:0.3035	rs11923648;rs52831761;rs58093545;rs11923648	491;496	E7ESK3;Q99102	.;MUC4_HUMAN	P	491;491;465	ENSP00000417498:S491P;ENSP00000420243:S491P	ENSP00000376209:S465P	S	-	1	0	MUC4	197001375	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.854000	0.01664	-1.560000	0.01686	-0.630000	0.03990	TCA	A|0.960;G|0.040	0.040	strong		0.488	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55331419	55331419	+	Missense_Mutation	SNP	C	C	T	rs143886704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55331419C>T	ENST00000391728.4	+	4	640	c.607C>T	c.(607-609)Ccc>Tcc	p.P203S	KIR3DL1_ENST00000402254.2_Missense_Mutation_p.P203S|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.P203S|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.P203S|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.P203S|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.P108S	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	92	0	0		WXS	Illumina HiSeq	Phase_I	204	104	0.509804	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	
ZNF385C	201181	hgsc.bcm.edu	37	17	40180910	40180910	+	Silent	SNP	G	G	A	rs7208473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40180910G>A	ENST00000436535.3	-	5	861	c.861C>T	c.(859-861)gcC>gcT	p.A287A	ZNF385C_ENST00000461831.1_5'Flank			Q66K41	Z385C_HUMAN	zinc finger protein 385C	205						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	3		all_cancers(22;0.00127)|Breast(137;0.00104)|all_epithelial(22;0.0126)				TGCTTCCCACGGCAGCTGCCG	0.637													G|||	75	0.014976	0.0567	0.0	5008	,	,		19369	0.0		0.0	False		,,,				2504	0.0				p.A207A		Atlas-SNP	.											.	ZNF385C	7	.	0			c.C621T						PASS	.																																			SO:0001819	synonymous_variant	201181	exon5			TCCCACGGCAGCT	BC067901	CCDS74065.1	17q21.2	2012-10-05			ENSG00000187595	ENSG00000187595			33722	protein-coding gene	gene with protein product							Standard	NM_001242704		Approved		uc021txr.1	Q66K41	OTTHUMG00000132073	ENST00000436535.3:c.861C>T	17.37:g.40180910G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_001242704	Q4G0J1	Silent	SNP	ENST00000436535.3	37																																																																																				G|0.989;A|0.011	0.011	strong		0.637	ZNF385C-001	NOVEL	not_organism_supported|mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000347740.3	NM_001013624	
TRPM1	4308	hgsc.bcm.edu	37	15	31323360	31323360	+	Splice_Site	SNP	T	T	G	rs181499296	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31323360T>G	ENST00000256552.6	-	23	3100	c.2953A>C	c.(2953-2955)Atg>Ctg	p.M985L	RP11-348B17.1_ENST00000561299.1_RNA|RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000542188.1_Splice_Site_p.M1002L|TRPM1_ENST00000397795.2_Splice_Site_p.M963L	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)		ATGTCGATCATCTGAGTAAGG	0.493													T|||	4	0.000798722	0.0023	0.0014	5008	,	,		22528	0.0		0.0	False		,,,				2504	0.0				p.M1002L		Atlas-SNP	.											.	TRPM1	183	.	0			c.A3004C						PASS	.	T	LEU/MET	8,4150		0,8,2071	68.0	66.0	66.0		2887	5.9	1.0	15		66	0,8476		0,0,4238	yes	missense-near-splice	TRPM1	NM_002420.4	15	0,8,6309	GG,GT,TT		0.0,0.1924,0.0633	possibly-damaging	963/1604	31323360	8,12626	2079	4238	6317	SO:0001630	splice_region_variant	4308	exon22			CGATCATCTGAGT	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.2953-1A>C	15.37:g.31323360T>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	126	46	0.365079	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	T	21.6	4.177858	0.78564	0.001924	0.0	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.73363	-0.74;-0.74;-0.74	5.92	5.92	0.95590	Ion transport (1);	0.000000	0.85682	D	0.000000	T	0.79718	0.4494	L	0.33485	1.01	0.58432	D	0.999997	D;D	0.59767	0.986;0.983	P;D	0.64687	0.8;0.928	T	0.81803	-0.0765	10	0.72032	D	0.01	-46.9433	16.371	0.83361	0.0:0.0:0.0:1.0	.	957;963	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	L	963;1002;985;963	ENSP00000380897:M963L;ENSP00000437849:M1002L;ENSP00000256552:M985L	ENSP00000256552:M985L	M	-	1	0	TRPM1	29110652	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.296000	0.72751	2.267000	0.75376	0.477000	0.44152	ATG	T|0.999;G|0.001	0.001	strong		0.493	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	Missense_Mutation
OR51F2	119694	hgsc.bcm.edu	37	11	4843119	4843119	+	Silent	SNP	C	C	T	rs142530902		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4843119C>T	ENST00000322110.5	+	1	569	c.504C>T	c.(502-504)gcC>gcT	p.A168A	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004753.1	NP_001004753.1	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F, member 2	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		GAAATGTTGCCGTCATGTTGC	0.443																																					p.A168A		Atlas-SNP	.											.	OR51F2	72	.	0			c.C504T						PASS	.	C		2,4400	6.2+/-15.9	0,2,2199	336.0	287.0	303.0		504	-1.1	1.0	11	dbSNP_134	303	0,8596		0,0,4298	no	coding-synonymous	OR51F2	NM_001004753.1		0,2,6497	TT,TC,CC		0.0,0.0454,0.0154		168/343	4843119	2,12996	2201	4298	6499	SO:0001819	synonymous_variant	119694	exon1			TGTTGCCGTCATG	BK004281	CCDS31361.1	11p15.4	2012-08-09			ENSG00000176925	ENSG00000176925		"""GPCR / Class A : Olfactory receptors"""	15197	protein-coding gene	gene with protein product							Standard	NM_001004753		Approved		uc010qyn.2	Q8NH61	OTTHUMG00000066508	ENST00000322110.5:c.504C>T	11.37:g.4843119C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	143	83	0.58042	NM_001004753	Q6IFI1	Silent	SNP	ENST00000322110.5	37	CCDS31361.1																																																																																			C|1.000;T|0.000	0.000	weak		0.443	OR51F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142181.1	NM_001004753	
ATP1A2	477	hgsc.bcm.edu	37	1	160090993	160090993	+	Silent	SNP	G	G	A	rs61734527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160090993G>A	ENST00000361216.3	+	3	218	c.129G>A	c.(127-129)aaG>aaA	p.K43K	ATP1A2_ENST00000392233.3_Silent_p.K43K	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	43					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			ATGACCACAAGCTGTCCTTGG	0.537													G|||	33	0.00658946	0.0242	0.0014	5008	,	,		21718	0.0		0.0	False		,,,				2504	0.0				p.K43K		Atlas-SNP	.											.	ATP1A2	167	.	0			c.G129A						PASS	.	G		122,4284	90.2+/-128.9	2,118,2083	229.0	232.0	231.0		129	3.7	1.0	1	dbSNP_129	231	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATP1A2	NM_000702.3		2,119,6382	AA,AG,GG		0.0116,2.769,0.9457		43/1021	160090993	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	477	exon3			CCACAAGCTGTCC	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.129G>A	1.37:g.160090993G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	77	29	0.376623	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	37	CCDS1196.1																																																																																			G|0.991;A|0.009	0.009	strong		0.537	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	
ABLIM1	3983	hgsc.bcm.edu	37	10	116335246	116335246	+	Silent	SNP	G	G	A	rs985273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116335246G>A	ENST00000277895.5	-	3	589	c.492C>T	c.(490-492)ttC>ttT	p.F164F	ABLIM1_ENST00000369252.4_Silent_p.F104F|ABLIM1_ENST00000533213.2_Silent_p.F104F	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	164	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)	p.F104F(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		CGCCCTCCACGAACTCCCCAC	0.537													G|||	1525	0.304513	0.475	0.3602	5008	,	,		19474	0.2321		0.2078	False		,,,				2504	0.2086				p.F164F		Atlas-SNP	.											ABLIM1,NS,carcinoma,0,1	ABLIM1	131	1	1	Substitution - coding silent(1)	stomach(1)	c.C492T						PASS	.	G	,,	1935,2471	549.1+/-377.7	436,1063,704	141.0	113.0	122.0		312,312,492	-3.2	1.0	10	dbSNP_86	122	1537,7063	289.4+/-299.3	147,1243,2910	no	coding-synonymous,coding-synonymous,coding-synonymous	ABLIM1	NM_001003407.1,NM_001003408.1,NM_002313.5	,,	583,2306,3614	AA,AG,GG		17.8721,43.9174,26.6954	,,	104/719,104/747,164/779	116335246	3472,9534	2203	4300	6503	SO:0001819	synonymous_variant	3983	exon3			CTCCACGAACTCC	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.492C>T	10.37:g.116335246G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	170	170	1	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Silent	SNP	ENST00000277895.5	37	CCDS7590.1																																																																																			G|0.719;A|0.281	0.281	strong		0.537	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3		
KRT84	3890	hgsc.bcm.edu	37	12	52778947	52778947	+	Silent	SNP	A	A	G	rs1791631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52778947A>G	ENST00000257951.3	-	1	489	c.423T>C	c.(421-423)acT>acC	p.T141T	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	141	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TCTTGTTCACAGTCACAGCTG	0.547													A|||	1691	0.33766	0.6354	0.3242	5008	,	,		18746	0.1954		0.2068	False		,,,				2504	0.226				p.T141T		Atlas-SNP	.											.	KRT84	61	.	0			c.T423C						PASS	.	A		2513,1893	628.2+/-395.1	741,1031,431	173.0	176.0	175.0		423	2.8	1.0	12	dbSNP_89	175	1805,6795	324.5+/-316.5	180,1445,2675	no	coding-synonymous	KRT84	NM_033045.3		921,2476,3106	GG,GA,AA		20.9884,42.9641,33.2001		141/601	52778947	4318,8688	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon1			GTTCACAGTCACA	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.423T>C	12.37:g.52778947A>G		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.685;G|0.315	0.315	strong		0.547	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
ESPL1	9700	hgsc.bcm.edu	37	12	53670545	53670545	+	Missense_Mutation	SNP	C	C	A	rs1318648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53670545C>A	ENST00000257934.4	+	8	1933	c.1842C>A	c.(1840-1842)agC>agA	p.S614R	ESPL1_ENST00000552462.1_Missense_Mutation_p.S614R	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	614			S -> R (in dbSNP:rs1318648).		apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TGGAGCTGAGCCCCGAGGAGA	0.637													C|||	3171	0.633187	0.4024	0.5994	5008	,	,		19167	0.8194		0.6372	False		,,,				2504	0.773				p.S614R	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C1842A						PASS	.	C	ARG/SER	1887,2519		394,1099,710	50.0	54.0	53.0		1842	1.2	1.0	12	dbSNP_88	53	5491,3105		1770,1951,577	yes	missense	ESPL1	NM_012291.4	110	2164,3050,1287	AA,AC,CC		36.1215,42.828,43.2549	probably-damaging	614/2121	53670545	7378,5624	2203	4298	6501	SO:0001583	missense	9700	exon8			GCTGAGCCCCGAG	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.1842C>A	12.37:g.53670545C>A	ENSP00000257934:p.Ser614Arg	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	1355	0.6204212454212454	203	0.41260162601626016	221	0.6104972375690608	462	0.8076923076923077	469	0.6187335092348285	C	16.80	3.223939	0.58668	0.42828	0.638785	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.14144	2.53;2.53	5.11	1.25	0.21368	.	0.144838	0.64402	D	0.000007	T	0.00012	0.0000	M	0.68317	2.08	0.38397	P	0.054444999999999966	D	0.71674	0.998	P	0.61940	0.896	T	0.10567	-1.0624	9	0.46703	T	0.11	.	8.7053	0.34351	0.0:0.6008:0.0:0.3992	rs1318648;rs3817539;rs52811463;rs59896279;rs1318648	614	Q14674	ESPL1_HUMAN	R	614;289;614	ENSP00000257934:S614R;ENSP00000449831:S614R	ENSP00000257934:S614R	S	+	3	2	ESPL1	51956812	0.553000	0.26513	0.996000	0.52242	0.994000	0.84299	-0.161000	0.10026	0.341000	0.23771	0.650000	0.86243	AGC	C|0.400;N|0.000	.	strong		0.637	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
GLRA1	2741	hgsc.bcm.edu	37	5	151231140	151231140	+	Silent	SNP	C	C	G	rs76872663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:151231140C>G	ENST00000455880.2	-	7	1009	c.723G>C	c.(721-723)cgG>cgC	p.R241R	GLRA1_ENST00000471351.2_5'UTR|GLRA1_ENST00000545569.1_Silent_p.R158R|GLRA1_ENST00000274576.4_Silent_p.R241R			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	241					acrosome reaction (GO:0007340)|action potential (GO:0001508)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|muscle contraction (GO:0006936)|negative regulation of transmission of nerve impulse (GO:0051970)|neuromuscular process controlling posture (GO:0050884)|neuropeptide signaling pathway (GO:0007218)|positive regulation of acrosome reaction (GO:2000344)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|external side of plasma membrane (GO:0009897)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|taurine binding (GO:0030977)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	23		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CCAGGTGGAACCGGGCCTCAA	0.483													C|||	25	0.00499201	0.0189	0.0	5008	,	,		22610	0.0		0.0	False		,,,				2504	0.0				p.R241R		Atlas-SNP	.											GLRA1,NS,carcinoma,-2,1	GLRA1	61	1	0			c.G723C						PASS	.	C	,	68,4338	60.5+/-97.4	0,68,2135	92.0	89.0	90.0		723,723	-1.0	1.0	5	dbSNP_132	90	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GLRA1	NM_000171.3,NM_001146040.1	,	0,68,6435	GG,GC,CC		0.0,1.5433,0.5228	,	241/450,241/458	151231140	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	2741	exon7			GTGGAACCGGGCC		CCDS4320.1, CCDS54942.1	5q33.1	2012-02-07	2008-01-24		ENSG00000145888	ENSG00000145888		"""Ligand-gated ion channels / Glycine receptors"""	4326	protein-coding gene	gene with protein product	"""startle disease/hyperekplexia"", ""stiff person syndrome"""	138491	"""glycine receptor, alpha 1 (startle disease/hyperekplexia)"""	STHE		1355335, 8298642	Standard	NM_000171		Approved		uc003lut.3	P23415	OTTHUMG00000130121	ENST00000455880.2:c.723G>C	5.37:g.151231140C>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	145	76	0.524138	NM_000171	B2R6T3|Q14C77|Q6DJV9	Silent	SNP	ENST00000455880.2	37	CCDS54942.1																																																																																			C|0.994;G|0.006	0.006	strong		0.483	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1		
NFATC3	4775	hgsc.bcm.edu	37	16	68224786	68224786	+	Missense_Mutation	SNP	C	C	G	rs77352556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:68224786C>G	ENST00000346183.3	+	9	2238	c.2214C>G	c.(2212-2214)gaC>gaG	p.D738E	SNORA48_ENST00000391143.1_RNA|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Missense_Mutation_p.D738E|NFATC3_ENST00000329524.4_Missense_Mutation_p.D738E|NFATC3_ENST00000349223.5_Missense_Mutation_p.D738E	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	738					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|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)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		GTTCACATGACAGTGTACTGT	0.478													C|||	46	0.0091853	0.0333	0.0029	5008	,	,		21238	0.0		0.0	False		,,,				2504	0.0				p.D738E		Atlas-SNP	.											.	NFATC3	190	.	0			c.C2214G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP	88,4308	74.1+/-112.3	2,84,2112	109.0	92.0	97.0		2214,2214,2214	-1.8	0.9	16	dbSNP_131	97	0,8600		0,0,4300	yes	missense,missense,missense	NFATC3	NM_004555.3,NM_173163.2,NM_173165.2	45,45,45	2,84,6412	GG,GC,CC		0.0,2.0018,0.6771	benign,benign,benign	738/1069,738/1066,738/1076	68224786	88,12908	2198	4300	6498	SO:0001583	missense	4775	exon9			ACATGACAGTGTA	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.2214C>G	16.37:g.68224786C>G	ENSP00000300659:p.Asp738Glu	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	231	128	0.554113	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	37	CCDS10860.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	C	9.959	1.222209	0.22457	0.020018	0.0	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524;ENST00000535127	T;T;T	0.11604	2.76;2.76;2.76	5.55	-1.84	0.07809	.	1.004540	0.07995	N	0.987827	T	0.01353	0.0044	M	0.65975	2.015	0.38233	D	0.941091	B;B;B;B	0.13145	0.001;0.006;0.007;0.001	B;B;B;B	0.16289	0.004;0.015;0.007;0.004	T	0.46062	-0.9218	10	0.06099	T	0.92	-3.3363	6.3098	0.21159	0.0:0.2985:0.3225:0.379	.	738;738;738;738	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	E	738;738;738;259	ENSP00000264008:D738E;ENSP00000300659:D738E;ENSP00000331324:D738E	ENSP00000331324:D738E	D	+	3	2	NFATC3	66782287	0.992000	0.36948	0.876000	0.34364	0.316000	0.28119	0.366000	0.20365	-0.220000	0.09988	0.557000	0.71058	GAC	C|0.991;G|0.009	0.009	strong		0.478	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555	
TEX10	54881	hgsc.bcm.edu	37	9	103064530	103064530	+	Silent	SNP	G	G	A	rs7472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:103064530G>A	ENST00000374902.4	-	15	2909	c.2733C>T	c.(2731-2733)ttC>ttT	p.F911F	TEX10_ENST00000535814.1_Silent_p.F895F|TEX10_ENST00000477648.1_5'UTR	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	911						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		TATACACGTTGAAGCAGTAAT	0.448													G|||	3140	0.626997	0.6188	0.611	5008	,	,		18565	0.8542		0.329	False		,,,				2504	0.7219				p.F911F		Atlas-SNP	.											.	TEX10	99	.	0			c.C2733T						PASS	.	G	,	2581,1825	638.1+/-396.9	750,1081,372	153.0	130.0	137.0		2685,2733	5.3	1.0	9	dbSNP_52	137	2933,5667	456.2+/-364.0	503,1927,1870	no	coding-synonymous,coding-synonymous	TEX10	NM_001161584.1,NM_017746.3	,	1253,3008,2242	AA,AG,GG		34.1047,41.4208,42.3958	,	895/914,911/930	103064530	5514,7492	2203	4300	6503	SO:0001819	synonymous_variant	54881	exon15			CACGTTGAAGCAG	AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"""testis expressed gene 10"", ""testis expressed sequence 10"""			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.2733C>T	9.37:g.103064530G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_017746	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Silent	SNP	ENST00000374902.4	37	CCDS6748.1																																																																																			G|0.502;A|0.498	0.498	strong		0.448	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919983	12919983	+	Silent	SNP	G	G	A	rs77138000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919983G>A	ENST00000240189.2	+	3	810	c.723G>A	c.(721-723)agG>agA	p.R241R		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	241					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)		TTTTCTCCAGGTGCCATCATT	0.448													.|||	671	0.133986	0.2806	0.1052	5008	,	,		22571	0.0169		0.1103	False		,,,				2504	0.1012				p.R241R		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G723A						PASS	.	G		1048,3358	376.8+/-322.2	143,762,1298	111.0	114.0	113.0		723	-0.5	0.0	1	dbSNP_131	113	928,7670	203.2+/-246.3	73,782,3444	no	coding-synonymous	PRAMEF2	NM_023014.1		216,1544,4742	AA,AG,GG		10.7932,23.7857,15.1953		241/475	12919983	1976,11028	2203	4299	6502	SO:0001819	synonymous_variant	65122	exon3			CTCCAGGTGCCAT		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.723G>A	1.37:g.12919983G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	187	78	0.417112	NM_023014		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			G|0.863;A|0.137	0.137	strong		0.448	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
HEATR1	55127	hgsc.bcm.edu	37	1	236760181	236760181	+	Silent	SNP	G	G	A	rs12135515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:236760181G>A	ENST00000366582.3	-	6	813	c.699C>T	c.(697-699)gaC>gaT	p.D233D	HEATR1_ENST00000366581.2_Silent_p.D233D|HEATR1_ENST00000483073.1_5'UTR	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	233					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TGTCTGATACGTCCTCTGCAG	0.443													G|||	93	0.0185703	0.0356	0.0115	5008	,	,		16828	0.005		0.0139	False		,,,				2504	0.0194				p.D233D		Atlas-SNP	.											.	HEATR1	197	.	0			c.C699T						PASS	.	G		186,4220	119.2+/-156.9	3,180,2020	133.0	128.0	130.0		699	-3.7	0.0	1	dbSNP_120	130	147,8453	71.6+/-134.2	2,143,4155	no	coding-synonymous	HEATR1	NM_018072.5		5,323,6175	AA,AG,GG		1.7093,4.2215,2.5604		233/2145	236760181	333,12673	2203	4300	6503	SO:0001819	synonymous_variant	55127	exon6			TGATACGTCCTCT	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"""UTP10, small subunit (SSU) processome component, homolog (yeast)"""					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.699C>T	1.37:g.236760181G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Silent	SNP	ENST00000366582.3	37	CCDS31066.1																																																																																			G|0.979;A|0.021	0.021	strong		0.443	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853	
CMYA5	202333	hgsc.bcm.edu	37	5	79026539	79026539	+	Missense_Mutation	SNP	A	A	C	rs57544556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79026539A>C	ENST00000446378.2	+	2	1982	c.1951A>C	c.(1951-1953)Agc>Cgc	p.S651R		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	651			S -> R (in dbSNP:rs57544556).		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)		p.S651R(1)		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)		TACATCTGAGAGCTCTCTCTC	0.468													C|||	1357	0.270966	0.5734	0.0821	5008	,	,		20577	0.3621		0.0815	False		,,,				2504	0.0971				p.S651R		Atlas-SNP	.											CMYA5,NS,carcinoma,0,1	CMYA5	643	1	1	Substitution - Missense(1)	stomach(1)	c.A1951C						PASS	.	C	ARG/SER	1850,2030		449,952,539	58.0	58.0	58.0		1951	0.2	0.0	5	dbSNP_129	58	716,7564		40,636,3464	yes	missense	CMYA5	NM_153610.3	110	489,1588,4003	CC,CA,AA		8.6473,47.6804,21.102	benign	651/4070	79026539	2566,9594	1940	4140	6080	SO:0001583	missense	202333	exon2			TCTGAGAGCTCTC	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.1951A>C	5.37:g.79026539A>C	ENSP00000394770:p.Ser651Arg	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	187	186	0.994652	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	621	0.28434065934065933	300	0.6097560975609756	30	0.08287292817679558	232	0.40559440559440557	59	0.07783641160949868	C	1.268	-0.613993	0.03690	0.476804	0.086473	ENSG00000164309	ENST00000446378	T	0.36878	1.23	5.52	0.216	0.15258	.	1.487380	0.04113	N	0.315010	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	0.44375	-0.9332	9	0.33940	T	0.23	.	2.5551	0.04758	0.3556:0.3891:0.1156:0.1397	rs57544556;rs62621916	651	Q8N3K9	CMYA5_HUMAN	R	651	ENSP00000394770:S651R	ENSP00000394770:S651R	S	+	1	0	CMYA5	79062295	0.000000	0.05858	0.013000	0.15412	0.000000	0.00434	-1.852000	0.01667	0.043000	0.15746	-0.770000	0.03390	AGC	A|0.757;C|0.243	0.243	strong		0.468	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
H1FOO	132243	hgsc.bcm.edu	37	3	129267915	129267915	+	Silent	SNP	T	T	C	rs60616647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129267915T>C	ENST00000324382.2	+	3	455	c.450T>C	c.(448-450)ggT>ggC	p.G150G	H1FOO_ENST00000503977.1_Silent_p.G11G	NM_153833.1	NP_722575.1	Q8IZA3	H1FOO_HUMAN	H1 histone family, member O, oocyte-specific	150					meiotic nuclear division (GO:0007126)|negative regulation of stem cell differentiation (GO:2000737)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of DNA methylation (GO:0044030)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|female germ cell nucleus (GO:0001674)|nucleosome (GO:0000786)|nucleus (GO:0005634)	nucleosomal DNA binding (GO:0031492)			endometrium(1)|lung(4)|skin(1)	6						GGAGAGCGGGTGAGGCCAAGG	0.607													C|||	315	0.0628994	0.2277	0.0202	5008	,	,		16740	0.0		0.0	False		,,,				2504	0.0				p.G150G		Atlas-SNP	.											.	H1FOO	20	.	0			c.T450C						PASS	.	C		795,3611	723.7+/-409.4	75,645,1483	30.0	30.0	30.0		450	-5.2	0.0	3	dbSNP_129	30	10,8590	800.0+/-407.4	0,10,4290	no	coding-synonymous	H1FOO	NM_153833.1		75,655,5773	CC,CT,TT		0.1163,18.0436,6.1895		150/347	129267915	805,12201	2203	4300	6503	SO:0001819	synonymous_variant	132243	exon3			AGCGGGTGAGGCC	AY158091	CCDS3064.1	3q21.3	2011-01-27			ENSG00000178804	ENSG00000178804		"""Histones / Replication-independent"""	18463	protein-coding gene	gene with protein product						12408966	Standard	NM_153833		Approved		uc003emu.3	Q8IZA3	OTTHUMG00000159541	ENST00000324382.2:c.450T>C	3.37:g.129267915T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_153833	Q86WT7	Silent	SNP	ENST00000324382.2	37	CCDS3064.1																																																																																			T|0.938;C|0.062	0.062	strong		0.607	H1FOO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356100.3	NM_153833	
ZC3H4	23211	hgsc.bcm.edu	37	19	47575170	47575170	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47575170T>C	ENST00000253048.5	-	13	2048	c.2011A>G	c.(2011-2013)Atg>Gtg	p.M671V	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	671	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		TAGGGCATCATTGGAGGGCCG	0.617																																					p.M671V		Atlas-SNP	.											.	ZC3H4	96	.	0			c.A2011G						PASS	.						33.0	39.0	37.0					19																	47575170		2040	4187	6227	SO:0001583	missense	23211	exon13			GCATCATTGGAGG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2011A>G	19.37:g.47575170T>C	ENSP00000253048:p.Met671Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	117	63	0.538462	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	37	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	T	11.74	1.728939	0.30684	.	.	ENSG00000130749	ENST00000253048	T	0.18174	2.23	5.35	5.35	0.76521	.	0.784041	0.11696	N	0.538401	T	0.13415	0.0325	L	0.34521	1.04	0.46499	D	0.999079	B	0.31485	0.325	B	0.21917	0.037	T	0.12167	-1.0558	10	0.15499	T	0.54	.	14.3108	0.66415	0.0:0.0:0.0:1.0	.	671	Q9UPT8	ZC3H4_HUMAN	V	671	ENSP00000253048:M671V	ENSP00000253048:M671V	M	-	1	0	ZC3H4	52267010	1.000000	0.71417	0.982000	0.44146	0.507000	0.33981	6.886000	0.75611	2.028000	0.59812	0.523000	0.50628	ATG	.	.	none		0.617	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
ZNF471	57573	hgsc.bcm.edu	37	19	57036012	57036012	+	Missense_Mutation	SNP	G	G	T	rs11667052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57036012G>T	ENST00000308031.5	+	5	709	c.576G>T	c.(574-576)atG>atT	p.M192I	ZNF471_ENST00000591537.1_Intron|ZNF471_ENST00000593197.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	192			M -> I (in dbSNP:rs11667052). {ECO:0000269|PubMed:10718198}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		AAAATTCTATGGTAATAAAAC	0.299													G|||	920	0.183706	0.2337	0.1398	5008	,	,		18537	0.0526		0.2813	False		,,,				2504	0.182				p.M192I	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.G576T						PASS	.	G	ILE/MET	1006,3392		119,768,1312	26.0	28.0	27.0		576	1.7	0.0	19	dbSNP_120	27	2159,6419		308,1543,2438	yes	missense	ZNF471	NM_020813.2	10	427,2311,3750	TT,TG,GG		25.169,22.874,24.3912	benign	192/627	57036012	3165,9811	2199	4289	6488	SO:0001583	missense	57573	exon5			TTCTATGGTAATA	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"""Zinc fingers, C2H2-type"", ""-"""	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.576G>T	19.37:g.57036012G>T	ENSP00000309161:p.Met192Ile	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	428	0.19597069597069597	120	0.24390243902439024	59	0.16298342541436464	34	0.05944055944055944	215	0.2836411609498681	G	1.290	-0.607754	0.03717	0.22874	0.25169	ENSG00000196263	ENST00000308031	T	0.14516	2.5	3.87	1.71	0.24356	.	.	.	.	.	T	0.00012	0.0000	N	0.00399	-1.545	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46205	-0.9208	8	0.23302	T	0.38	.	6.9352	0.24463	0.3009:0.0:0.6991:0.0	rs11667052;rs52814044;rs58037293;rs11667052	192	Q9BX82	ZN471_HUMAN	I	192	ENSP00000309161:M192I	ENSP00000309161:M192I	M	+	3	0	ZNF471	61727824	.	.	0.001000	0.08648	0.789000	0.44602	.	.	0.427000	0.26145	-0.253000	0.11424	ATG	G|0.792;T|0.208	0.208	strong		0.299	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813	
BPIFB3	359710	hgsc.bcm.edu	37	20	31661399	31661399	+	Silent	SNP	C	C	T	rs114341725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31661399C>T	ENST00000375494.3	+	15	1419	c.1419C>T	c.(1417-1419)acC>acT	p.T473T		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	473					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.T473T(1)									TTGTGCTGACCGTGGCATCCT	0.552													C|||	27	0.00539137	0.0204	0.0	5008	,	,		19225	0.0		0.0	False		,,,				2504	0.0				p.T473T		Atlas-SNP	.											C20orf185,caecum,carcinoma,+2,1	.	.	1	1	Substitution - coding silent(1)	lung(1)	c.C1419T						scavenged	.	C		71,4335	65.3+/-102.7	0,71,2132	237.0	182.0	201.0		1419	-2.5	1.0	20	dbSNP_132	201	0,8600		0,0,4300	yes	coding-synonymous	BPIFB3	NM_182658.1		0,71,6432	TT,TC,CC		0.0,1.6114,0.5459		473/477	31661399	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	359710	exon15			GCTGACCGTGGCA	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1419C>T	20.37:g.31661399C>T		Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	218	109	0.5	NM_182658	Q5TDX7	Silent	SNP	ENST00000375494.3	37	CCDS13212.1																																																																																			C|0.993;T|0.007	0.007	strong		0.552	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
PLIN4	729359	hgsc.bcm.edu	37	19	4512933	4512933	+	Missense_Mutation	SNP	C	C	A	rs200149931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512933C>A	ENST00000301286.3	-	3	996	c.997G>T	c.(997-999)Gtg>Ttg	p.V333L		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	333	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						CCTTTGGCCACATTCATGGCA	0.567													c|||	558	0.111422	0.357	0.0403	5008	,	,		19414	0.0		0.0129	False		,,,				2504	0.046				p.V333L		Atlas-SNP	.											.	PLIN4	191	.	0			c.G997T						PASS	.						43.0	56.0	52.0					19																	4512933		1884	4141	6025	SO:0001583	missense	729359	exon3			TGGCCACATTCAT	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.997G>T	19.37:g.4512933C>A	ENSP00000301286:p.Val333Leu	Somatic	372	1	0.00268817		WXS	Illumina HiSeq	Phase_I	245	66	0.269388	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	c	12.09	1.832474	0.32421	.	.	ENSG00000167676	ENST00000301286	T	0.04654	3.58	4.59	-1.78	0.07957	.	0.731989	0.12146	N	0.495324	T	0.06462	0.0166	M	0.76838	2.35	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.33240	-0.9876	10	0.41790	T	0.15	-13.7794	4.0634	0.09849	0.1545:0.4657:0.0:0.3798	.	333	Q96Q06	PLIN4_HUMAN	L	333	ENSP00000301286:V333L	ENSP00000301286:V333L	V	-	1	0	PLIN4	4463933	.	.	0.007000	0.13788	0.002000	0.02628	.	.	-0.231000	0.09825	0.462000	0.41574	GTG	C|0.989;A|0.011	0.011	strong		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
ZNF229	7772	hgsc.bcm.edu	37	19	44933706	44933706	+	Missense_Mutation	SNP	C	C	T	rs57014690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44933706C>T	ENST00000588931.1	-	6	1683	c.1250G>A	c.(1249-1251)aGc>aAc	p.S417N	CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000291187.4_Missense_Mutation_p.S411N|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	417			S -> N (in dbSNP:rs57014690).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				AAGCACTGAGCTGTAACTGAA	0.522													C|||	814	0.16254	0.1929	0.3213	5008	,	,		20844	0.1558		0.1024	False		,,,				2504	0.0777				p.S417N		Atlas-SNP	.											ZNF229,tonsil,carcinoma,0,1	ZNF229	123	1	0			c.G1250A						scavenged	.	C	ASN/SER	751,3651	285.2+/-278.0	70,611,1520	89.0	100.0	96.0		1250	2.8	0.0	19	dbSNP_129	96	939,7661	203.5+/-246.5	60,819,3421	yes	missense	ZNF229	NM_014518.2	46	130,1430,4941	TT,TC,CC		10.9186,17.0604,12.998	benign	417/826	44933706	1690,11312	2201	4300	6501	SO:0001583	missense	7772	exon6			ACTGAGCTGTAAC	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1250G>A	19.37:g.44933706C>T	ENSP00000466519:p.Ser417Asn	Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	363	0.1662087912087912	102	0.2073170731707317	101	0.27900552486187846	83	0.1451048951048951	77	0.10158311345646438	C	11.10	1.539651	0.27563	0.170604	0.109186	ENSG00000167383	ENST00000291187	.	.	.	3.86	2.79	0.32731	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.53561	1.675	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.12553	-1.0543	7	0.24483	T	0.36	.	6.4046	0.21658	0.0:0.6895:0.0:0.3105	rs57014690;rs61740849	417	Q9UJW7	ZN229_HUMAN	N	417	.	ENSP00000291187:S417N	S	-	2	0	ZNF229	49625546	0.000000	0.05858	0.042000	0.18584	0.554000	0.35429	-1.359000	0.02602	1.694000	0.51137	0.609000	0.83330	AGC	C|0.848;T|0.152	0.152	strong		0.522	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
PRPF4	9128	hgsc.bcm.edu	37	9	116053895	116053895	+	Silent	SNP	C	C	T	rs146201781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116053895C>T	ENST00000374198.4	+	14	1626	c.1524C>T	c.(1522-1524)gcC>gcT	p.A508A	PRPF4_ENST00000374199.4_Silent_p.A507A	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	508					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						AGCTCATAGCCACTTGCTCAT	0.517													C|||	7	0.00139776	0.0045	0.0014	5008	,	,		19015	0.0		0.0	False		,,,				2504	0.0				p.A508A		Atlas-SNP	.											.	PRPF4	56	.	0			c.C1524T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	88.0	80.0	83.0		1524	3.9	1.0	9	dbSNP_134	83	0,8600		0,0,4300	no	coding-synonymous	PRPF4	NM_004697.3		0,14,6489	TT,TC,CC		0.0,0.3177,0.1076		508/523	116053895	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9128	exon14			CATAGCCACTTGC	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"""WD repeat domain containing"""	17349	protein-coding gene	gene with protein product	"""PRP4/STK/WD splicing factor"", ""U4/U6 small nuclear ribonucleoprotein Prp4"""	607795	"""PRP4 pre-mRNA processing factor 4 homolog (yeast)"""			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.1524C>T	9.37:g.116053895C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	122	78	0.639344	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Silent	SNP	ENST00000374198.4	37	CCDS6791.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011409	46011409	+	Silent	SNP	G	G	A	rs144363824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011409G>A	ENST00000400368.1	-	1	977	c.957C>T	c.(955-957)ccC>ccT	p.P319P	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	319	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						AGGAGGGGACGGGCACGCAGC	0.697													.|||	155	0.0309505	0.1127	0.0086	5008	,	,		18795	0.0		0.0	False		,,,				2504	0.0				p.P319P		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C957T						PASS	.						70.0	85.0	80.0					21																	46011409		2201	4300	6501	SO:0001819	synonymous_variant	386674	exon1			GGGGACGGGCACG	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.957C>T	21.37:g.46011409G>A		Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	265	54	0.203774	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			G|0.975;A|0.025	0.025	strong		0.697	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
JRK	8629	hgsc.bcm.edu	37	8	143746414	143746414	+	RNA	SNP	G	G	A	rs115218091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746414G>A	ENST00000507178.2	-	0	1396							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)				gttgtagcgggcatgggggcc	0.617													G|||	63	0.0125799	0.0469	0.0014	5008	,	,		18410	0.0		0.0	False		,,,				2504	0.0				p.A355V		Atlas-SNP	.											.	.	.	.	0			c.C1064T						PASS	.	G	VAL/ALA,VAL/ALA	67,3943		0,67,1938	8.0	9.0	9.0		1064,1064	3.7	0.0	8	dbSNP_132	9	1,8323		0,1,4161	yes	missense,missense	JRK	NM_001077527.1,NM_003724.2	64,64	0,68,6099	AA,AG,GG		0.012,1.6708,0.5513	benign,benign	355/557,355/569	143746414	68,12266	2005	4162	6167			8629	exon2			TAGCGGGCATGGG	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.143746414G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				G|0.991;A|0.009	0.009	strong		0.617	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
SYNPO2	171024	hgsc.bcm.edu	37	4	119948046	119948046	+	Missense_Mutation	SNP	A	A	C	rs17263971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:119948046A>C	ENST00000429713.2	+	3	704	c.522A>C	c.(520-522)caA>caC	p.Q174H	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.Q174H|SYNPO2_ENST00000434046.2_Missense_Mutation_p.Q174H	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	174			Q -> H (in dbSNP:rs17263971).			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						CTGACTCCCAAAGAGGACGCG	0.557													A|||	1110	0.221645	0.2133	0.219	5008	,	,		18571	0.1577		0.2644	False		,,,				2504	0.2566				p.Q174H		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A522C						PASS	.	A	HIS/GLN,HIS/GLN,HIS/GLN	1006,3400	342.8+/-307.3	115,776,1312	36.0	41.0	40.0		522,522,522	-1.5	0.0	4	dbSNP_123	40	2140,6460	354.8+/-329.6	264,1612,2424	yes	missense,missense,missense	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	24,24,24	379,2388,3736	CC,CA,AA		24.8837,22.8325,24.1888	benign,benign,benign	174/1094,174/1110,174/1262	119948046	3146,9860	2203	4300	6503	SO:0001583	missense	171024	exon3			CTCCCAAAGAGGA	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.522A>C	4.37:g.119948046A>C	ENSP00000395143:p.Gln174His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	463|463	0.211996336996337|0.211996336996337	87|87	0.17682926829268292|0.17682926829268292	88|88	0.2430939226519337|0.2430939226519337	90|90	0.15734265734265734|0.15734265734265734	198|198	0.2612137203166227|0.2612137203166227	A|A	6.546|6.546	0.469035|0.469035	0.12461|0.12461	0.228325|0.228325	0.248837|0.248837	ENSG00000172403|ENSG00000172403	ENST00000504178|ENST00000307142;ENST00000429713;ENST00000434046	.|T;T;T	.|0.09073	.|3.02;3.03;3.02	5.24|5.24	-1.52|-1.52	0.08637|0.08637	.|.	.|1.114660	.|0.06829	.|N	.|0.793679	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	P|P	0.0|0.0	.|P;B;B	.|0.41569	.|0.755;0.0;0.0	.|B;B;B	.|0.37346	.|0.247;0.001;0.001	T|T	0.44143|0.44143	-0.9347|-0.9347	4|9	.|0.30854	.|T	.|0.27	0.4447|0.4447	5.7472|5.7472	0.18126|0.18126	0.4363:0.2693:0.2945:0.0|0.4363:0.2693:0.2945:0.0	rs17263971;rs17263971|rs17263971;rs17263971	.|174;174;174	.|Q9UMS6-2;E9PEM2;Q9UMS6	.|.;.;SYNP2_HUMAN	Q|H	126|174	.|ENSP00000306015:Q174H;ENSP00000395143:Q174H;ENSP00000390965:Q174H	.|ENSP00000306015:Q174H	K|Q	+|+	1|3	0|2	SYNPO2|SYNPO2	120167494|120167494	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.201000|0.201000	0.24016|0.24016	-0.045000|-0.045000	0.12003|0.12003	-0.240000|-0.240000	0.09696|0.09696	0.455000|0.455000	0.32223|0.32223	AAG|CAA	A|0.774;C|0.226	0.226	strong		0.557	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
SSTR5	6755	hgsc.bcm.edu	37	16	1128901	1128901	+	Silent	SNP	C	C	T	rs35128939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1128901C>T	ENST00000293897.4	+	1	121	c.33C>T	c.(31-33)agC>agT	p.S11S	SSTR5_ENST00000562758.1_Silent_p.S11S|SSTR5_ENST00000397547.2_Silent_p.S11S|SSTR5-AS1_ENST00000569832.1_RNA	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	11					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytokinesis (GO:0032467)|regulation of insulin secretion (GO:0050796)|somatostatin signaling pathway (GO:0038170)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			endometrium(2)|lung(5)|prostate(1)|skin(1)	9		Hepatocellular(780;0.00369)			Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	CCACGCCCAGCTGGAACGCCT	0.731													C|||	17	0.00339457	0.0121	0.0014	5008	,	,		13446	0.0		0.0	False		,,,				2504	0.0				p.S11S		Atlas-SNP	.											.	SSTR5	36	.	0			c.C33T						PASS	.	C	,	44,4262		0,44,2109	10.0	11.0	11.0		33,33	3.8	1.0	16	dbSNP_126	11	0,8488		0,0,4244	no	coding-synonymous,coding-synonymous	SSTR5	NM_001053.3,NM_001172560.1	,	0,44,6353	TT,TC,CC		0.0,1.0218,0.3439	,	11/365,11/365	1128901	44,12750	2153	4244	6397	SO:0001819	synonymous_variant	6755	exon2			GCCCAGCTGGAAC	D16827	CCDS10429.1	16p13.3	2012-08-08			ENSG00000162009	ENSG00000162009		"""GPCR / Class A : Somatostatin receptors"""	11334	protein-coding gene	gene with protein product		182455				7607700	Standard	NM_001053		Approved		uc021taf.1	P35346	OTTHUMG00000047842	ENST00000293897.4:c.33C>T	16.37:g.1128901C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	24	5	0.208333	NM_001172560	P34988|Q541E0|Q9UJI5	Silent	SNP	ENST00000293897.4	37	CCDS10429.1																																																																																			C|0.997;T|0.003	0.003	strong		0.731	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1		
SLC3A2	6520	hgsc.bcm.edu	37	11	62648748	62648748	+	Silent	SNP	C	C	T	rs73487878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62648748C>T	ENST00000377890.2	+	4	724	c.556C>T	c.(556-558)Ctg>Ttg	p.L186L	SLC3A2_ENST00000377889.2_Silent_p.L124L|SLC3A2_ENST00000377891.2_Silent_p.L187L|SLC3A2_ENST00000377892.1_Silent_p.L217L|SLC3A2_ENST00000535296.1_Silent_p.L155L|SLC3A2_ENST00000536981.1_5'Flank|SLC3A2_ENST00000338663.7_Silent_p.L85L	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	186					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						CTGGGCACTGCTGCTGCTCTT	0.687											OREG0021031	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	116	0.0231629	0.0809	0.0101	5008	,	,		13125	0.0		0.002	False		,,,				2504	0.0				p.L187L		Atlas-SNP	.											.	SLC3A2	55	.	0			c.C559T						PASS	.	C	,,,	239,4153		11,217,1968	15.0	16.0	16.0		559,370,253,556	5.0	1.0	11	dbSNP_130	16	1,8579		0,1,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC3A2	NM_001012662.2,NM_001012664.2,NM_001013251.2,NM_002394.5	,,,	11,218,6257	TT,TC,CC		0.0117,5.4417,1.8501	,,,	187/632,124/569,85/530,186/631	62648748	240,12732	2196	4290	6486	SO:0001819	synonymous_variant	6520	exon4			GCACTGCTGCTGC		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"""Solute carriers"""	11026	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43"", ""antigen defined by monoclonal antibody 4F2"", ""heavy chain"", ""4F2 heavy chain"", ""CD98 heavy chain"", ""monoclonal antibody 44D7"", ""4F2 cell-surface antigen heavy chain"", ""lymphocyte activation antigen 4F2 large subunit"""	158070	"""solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"""	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.556C>T	11.37:g.62648748C>T		Somatic	57	0	0	1062	WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_001012662	Q13543	Silent	SNP	ENST00000377890.2	37	CCDS8039.2																																																																																			C|0.975;T|0.025	0.025	strong		0.687	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661	
TCP10L2	401285	hgsc.bcm.edu	37	6	167585652	167585652	+	Missense_Mutation	SNP	A	A	C	rs59203630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:167585652A>C	ENST00000366832.2	+	2	151	c.20A>C	c.(19-21)gAg>gCg	p.E7A		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	7										endometrium(1)|kidney(2)|lung(3)	6						GGTCAGCTCGAGGCCAGGGAG	0.672													A|||	197	0.0393371	0.1422	0.013	5008	,	,		18107	0.0		0.0	False		,,,				2504	0.0				p.E7A		Atlas-SNP	.											.	TCP10L2	41	.	0			c.A20C						PASS	.	A	ALA/GLU	207,1177		20,167,505	21.0	31.0	28.0		20	-2.1	0.0	6	dbSNP_129	28	0,3182		0,0,1591	no	missense	TCP10L2	NM_001145121.1	107	20,167,2096	CC,CA,AA		0.0,14.9566,4.5335	possibly-damaging	7/354	167585652	207,4359	692	1591	2283	SO:0001583	missense	401285	exon2			AGCTCGAGGCCAG		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.20A>C	6.37:g.167585652A>C	ENSP00000355797:p.Glu7Ala	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	177	173	0.977401	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	75	0.034340659340659344	73	0.1483739837398374	2	0.0055248618784530384	0	0.0	0	0.0	a	11.90	1.775977	0.31411	0.149566	0.0	ENSG00000166984	ENST00000486697;ENST00000366832	T	0.20200	2.09	2.61	-2.13	0.07144	.	.	.	.	.	T	0.10852	0.0265	L	0.51422	1.61	0.80722	P	0.0	D	0.58268	0.982	P	0.52554	0.702	T	0.04811	-1.0925	8	0.62326	D	0.03	.	3.0393	0.06133	0.4685:0.2327:0.2987:0.0	rs59203630	7	B9ZVM9	TCP2L_HUMAN	A	7	ENSP00000355797:E7A	ENSP00000283507:E7A	E	+	2	0	TCP10L2	167505642	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.176000	0.16782	-0.554000	0.06150	-0.863000	0.03009	GAG	A|0.966;C|0.034	0.034	strong		0.672	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
MTG2	26164	hgsc.bcm.edu	37	20	60768497	60768497	+	Silent	SNP	C	C	T	rs2236527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60768497C>T	ENST00000370823.3	+	2	39	c.21C>T	c.(19-21)ttC>ttT	p.F7F	MTG2_ENST00000536470.1_Intron|MTG2_ENST00000436421.2_Silent_p.F7F	NM_015666.3	NP_056481.1	Q9H4K7	MTG2_HUMAN	mitochondrial ribosome-associated GTPase 2	7					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)										CAAGGTGTTTCTCAGCAAGAT	0.547													C|||	1094	0.21845	0.174	0.1282	5008	,	,		20152	0.4881		0.1173	False		,,,				2504	0.1687				p.F7F		Atlas-SNP	.											.	GTPBP5	43	.	0			c.C21T						PASS	.	C		591,3815	262.8+/-265.1	36,519,1648	101.0	103.0	102.0		21	4.1	0.0	20	dbSNP_98	102	1032,7568	219.1+/-257.3	64,904,3332	no	coding-synonymous	GTPBP5	NM_015666.3		100,1423,4980	TT,TC,CC		12.0,13.4135,12.4789		7/407	60768497	1623,11383	2203	4300	6503	SO:0001819	synonymous_variant	26164	exon2			GTGTTTCTCAGCA	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.21C>T	20.37:g.60768497C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	190	82	0.431579	NM_015666	A6NDR3|B4DR85|Q96I17|Q9NVG9|Q9UFR4	Silent	SNP	ENST00000370823.3	37	CCDS13492.1																																																																																			C|0.827;T|0.173	0.173	strong		0.547	MTG2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079989.1	NM_015666	
MUC16	94025	hgsc.bcm.edu	37	19	9048342	9048342	+	Missense_Mutation	SNP	C	C	T	rs10854118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	149	0	0		WXS	Illumina HiSeq	Phase_I	153	75	0.490196	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	
C3orf52	79669	hgsc.bcm.edu	37	3	111821747	111821747	+	Missense_Mutation	SNP	A	A	G	rs16859190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:111821747A>G	ENST00000264848.5	+	3	390	c.331A>G	c.(331-333)Atc>Gtc	p.I111V	C3orf52_ENST00000431717.2_Missense_Mutation_p.I111V|C3orf52_ENST00000430855.1_Missense_Mutation_p.I111V	NM_024616.2	NP_078892	Q5BVD1	TTMP_HUMAN	chromosome 3 open reading frame 52	111			I -> V (in dbSNP:rs16859190).			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						AACATTCTTCATCATGCTGAA	0.363													G|||	618	0.123403	0.2799	0.0591	5008	,	,		19051	0.0605		0.0368	False		,,,				2504	0.1115				p.I111V		Atlas-SNP	.											.	C3orf52	28	.	0			c.A331G						PASS	.	G	VAL/ILE,VAL/ILE	831,2907		83,665,1121	75.0	69.0	71.0		331,331	2.6	0.2	3	dbSNP_123	71	250,7962		3,244,3859	yes	missense,missense	C3orf52	NM_001171747.1,NM_024616.2	29,29	86,909,4980	GG,GA,AA		3.0443,22.2311,9.046	benign,benign	111/251,111/218	111821747	1081,10869	1869	4106	5975	SO:0001583	missense	79669	exon3			TTCTTCATCATGC	AY830714	CCDS46887.1, CCDS54620.1	3q13.2	2006-01-30			ENSG00000114529	ENSG00000114529			26255	protein-coding gene	gene with protein product	"""TPA induced trans-membrane protein"""	611956				15737651	Standard	NM_024616		Approved	FLJ23186, TTMP	uc011bhs.2	Q5BVD1	OTTHUMG00000159230	ENST00000264848.5:c.331A>G	3.37:g.111821747A>G	ENSP00000264848:p.Ile111Val	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	185	88	0.475676	NM_001171747	B4DNV2|B4E0Z2|Q96AJ4|Q9H5Q1	Missense_Mutation	SNP	ENST00000264848.5	37	CCDS46887.1	225|225	0.10302197802197802|0.10302197802197802	142|142	0.2886178861788618|0.2886178861788618	23|23	0.06353591160220995|0.06353591160220995	34|34	0.05944055944055944|0.05944055944055944	26|26	0.03430079155672823|0.03430079155672823	G|G	0.004|0.004	-2.336876|-2.336876	0.00224|0.00224	0.222311|0.222311	0.030443|0.030443	ENSG00000114529|ENSG00000114529	ENST00000484828|ENST00000430855;ENST00000431717;ENST00000264848	.|T;T;T	.|0.09445	.|2.98;2.98;2.98	5.66|5.66	2.6|2.6	0.31112|0.31112	.|.	.|0.242891	.|0.33040	.|N	.|0.005345	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01576|0.01576	-0.805|-0.805	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;0.001	T|T	0.45440|0.45440	-0.9261|-0.9261	4|9	.|0.02654	.|T	.|1	-31.071|-31.071	3.6032|3.6032	0.08032|0.08032	0.4011:0.1919:0.407:0.0|0.4011:0.1919:0.407:0.0	rs16859190;rs52821979;rs16859190|rs16859190;rs52821979;rs16859190	.|111;111;111	.|Q5BVD1-2;Q5BVD1-3;Q5BVD1	.|.;.;TTMP_HUMAN	R|V	101|111	.|ENSP00000390333:I111V;ENSP00000399392:I111V;ENSP00000264848:I111V	.|ENSP00000264848:I111V	H|I	+|+	2|1	0|0	C3orf52|C3orf52	113304437|113304437	0.000000|0.000000	0.05858|0.05858	0.168000|0.168000	0.22838|0.22838	0.051000|0.051000	0.14879|0.14879	-0.301000|-0.301000	0.08232|0.08232	-0.028000|-0.028000	0.13850|0.13850	-0.684000|-0.684000	0.03749|0.03749	CAT|ATC	A|0.895;G|0.105	0.105	strong		0.363	C3orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353961.1	NM_024616	
PTPRQ	374462	hgsc.bcm.edu	37	12	80936082	80936082	+	Silent	SNP	C	C	T	rs11114503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	119	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	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	
IDO2	169355	hgsc.bcm.edu	37	8	39873053	39873053	+	Missense_Mutation	SNP	G	G	A	rs72632016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39873053G>A	ENST00000389060.4	+	10	1156	c.1156G>A	c.(1156-1158)Gca>Aca	p.A386T	IDO2_ENST00000343295.4_3'UTR|IDO2_ENST00000502986.2_Missense_Mutation_p.A399T			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	386					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						AGGTGGAACCGCAGTTATGAG	0.542													G|||	403	0.0804712	0.1884	0.0634	5008	,	,		20875	0.0119		0.0527	False		,,,				2504	0.046				p.A399T		Atlas-SNP	.											.	IDO2	78	.	0			c.G1195A						PASS	.	G	THR/ALA	714,3226		64,586,1320	115.0	113.0	114.0		1195	1.1	0.0	8	dbSNP_130	114	431,7867		11,409,3729	yes	missense	IDO2	NM_194294.2	58	75,995,5049	AA,AG,GG		5.194,18.1218,9.3561	benign	399/421	39873053	1145,11093	1970	4149	6119	SO:0001583	missense	169355	exon11			GGAACCGCAGTTA	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"""indoleamine-pyrrole 2,3 dioxygenase-like 1"""	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.1156G>A	8.37:g.39873053G>A	ENSP00000426447:p.Ala386Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_194294	A4UD41	Missense_Mutation	SNP	ENST00000389060.4	37		168	0.07692307692307693	94	0.1910569105691057	25	0.06906077348066299	9	0.015734265734265736	40	0.052770448548812667	G	2.319	-0.355979	0.05138	0.181218	0.05194	ENSG00000188676	ENST00000502986;ENST00000389060	T;T	0.46063	0.88;0.88	6.03	1.1	0.20463	.	0.717381	0.14006	N	0.347782	T	0.00039	0.0001	L	0.58810	1.83	0.80722	P	0.0	B;B	0.18013	0.025;0.021	B;B	0.12837	0.003;0.008	T	0.14839	-1.0458	8	.	.	.	.	1.1148	0.01712	0.1961:0.2391:0.3413:0.2235	.	399;386	F5H5G0;Q6ZQW0	.;I23O2_HUMAN	T	399;386	ENSP00000443432:A399T;ENSP00000426447:A386T	.	A	+	1	0	IDO2	39992210	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	-0.312000	0.08113	-0.080000	0.12685	0.655000	0.94253	GCA	G|0.929;A|0.071	0.071	strong		0.542	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
MUC4	4585	hgsc.bcm.edu	37	3	195508524	195508524	+	Silent	SNP	G	G	A	rs141064104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508524G>A	ENST00000463781.3	-	2	10386	c.9927C>T	c.(9925-9927)caC>caT	p.H3309H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.H3309H	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.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(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)		GAGGAGTGGCGTGACCTGTGG	0.567													.|||	179	0.0357428	0.1293	0.0101	5008	,	,		9468	0.0		0.001	False		,,,				2504	0.0				p.H3309H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	2	Deletion - In frame(2)	stomach(2)	c.C9927T						PASS	.						18.0	18.0	18.0					3																	195508524		659	1500	2159	SO:0001819	synonymous_variant	4585	exon2			AGTGGCGTGACCT	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.9927C>T	3.37:g.195508524G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	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|0.950;A|0.050	0.050	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GRXCR1	389207	hgsc.bcm.edu	37	4	42895308	42895308	+	Missense_Mutation	SNP	G	G	A	rs78136490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	122	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	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	
ADRB1	153	hgsc.bcm.edu	37	10	115804123	115804123	+	Silent	SNP	C	C	T	rs373125312		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115804123C>T	ENST00000369295.2	+	1	318	c.232C>T	c.(232-234)Ctg>Ttg	p.L78L		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	78					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	GGGCAATGTGCTGGTGATCGT	0.657																																					p.L78L		Atlas-SNP	.											.	ADRB1	16	.	0			c.C232T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	43.0	39.0	40.0		232	2.1	1.0	10		40	0,8600		0,0,4300	no	coding-synonymous	ADRB1	NM_000684.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		78/478	115804123	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	153	exon1			AATGTGCTGGTGA	J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"""GPCR / Class A : Adrenoceptors : beta"""	285	protein-coding gene	gene with protein product		109630	"""adrenergic, beta-1-, receptor"""	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.232C>T	10.37:g.115804123C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_000684	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Silent	SNP	ENST00000369295.2	37	CCDS7586.1																																																																																			.	.	none		0.657	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1		
SLC14A2	8170	hgsc.bcm.edu	37	18	43246156	43246156	+	Missense_Mutation	SNP	G	G	A	rs9960464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:43246156G>A	ENST00000255226.6	+	12	2345	c.1529G>A	c.(1528-1530)cGa>cAa	p.R510Q	SLC14A2_ENST00000586448.1_Missense_Mutation_p.R510Q|SLC14A2_ENST00000589658.1_5'UTR	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	510			R -> Q (in dbSNP:rs9960464). {ECO:0000269|PubMed:11502588, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)	p.R510Q(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTTCCCTATCGATACCGGAAG	0.512											OREG0024946	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	1870	0.373403	0.2867	0.4712	5008	,	,		17597	0.3423		0.4314	False		,,,				2504	0.3937				p.R510Q		Atlas-SNP	.											SLC14A2,NS,carcinoma,0,1	SLC14A2	121	1	1	Substitution - Missense(1)	stomach(1)	c.G1529A						PASS	.	G	GLN/ARG,GLN/ARG	1446,2960	469.2+/-355.4	225,996,982	160.0	126.0	138.0		1529,1529	-11.7	0.0	18	dbSNP_119	138	3848,4752	541.7+/-384.0	826,2196,1278	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	43,43	1051,3192,2260	AA,AG,GG		44.7442,32.8189,40.7043	benign,benign	510/921,510/921	43246156	5294,7712	2203	4300	6503	SO:0001583	missense	8170	exon13			CCTATCGATACCG	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.1529G>A	18.37:g.43246156G>A	ENSP00000255226:p.Arg510Gln	Somatic	119	0	0	914	WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	839	0.3841575091575092	138	0.2804878048780488	175	0.48342541436464087	192	0.3356643356643357	334	0.44063324538258575	g	7.576	0.667826	0.14710	0.328189	0.447442	ENSG00000132874	ENST00000255226	T	0.32515	1.45	6.04	-11.7	0.00046	.	1.340750	0.04528	N	0.385873	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40924	-0.9537	9	0.13108	T	0.6	3.2061	6.7344	0.23401	0.1347:0.579:0.0671:0.2192	rs9960464;rs52828182;rs59892831;rs9960464	510	Q15849	UT2_HUMAN	Q	510	ENSP00000255226:R510Q	ENSP00000255226:R510Q	R	+	2	0	SLC14A2	41500154	0.000000	0.05858	0.000000	0.03702	0.146000	0.21551	-0.763000	0.04740	-1.612000	0.01579	-0.405000	0.06341	CGA	G|0.615;A|0.385	0.385	strong		0.512	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
NUDT6	11162	hgsc.bcm.edu	37	4	123814170	123814170	+	Missense_Mutation	SNP	G	G	A	rs138619142		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:123814170G>A	ENST00000304430.5	-	5	797	c.764C>T	c.(763-765)gCg>gTg	p.A255V	FGF2_ENST00000264498.3_3'UTR|FGF2_ENST00000608478.1_3'UTR|NUDT6_ENST00000339154.2_Missense_Mutation_p.A86V|NUDT6_ENST00000502270.1_Missense_Mutation_p.A86V|NUDT6_ENST00000608639.1_5'Flank	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	255	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)			endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						TTCAGTCTTCGCCAGGTCATT	0.433													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18368	0.0		0.0	False		,,,				2504	0.0				p.A255V		Atlas-SNP	.											.	NUDT6	50	.	0			c.C764T						PASS	.	G	,VAL/ALA,VAL/ALA	15,4391	22.3+/-47.3	0,15,2188	134.0	125.0	128.0		,764,257	-3.6	0.0	4	dbSNP_134	128	0,8600		0,0,4300	yes	utr-3,missense,missense	FGF2,NUDT6	NM_002006.4,NM_007083.3,NM_198041.1	,64,64	0,15,6488	AA,AG,GG		0.0,0.3404,0.1153	,benign,benign	,255/317,86/148	123814170	15,12991	2203	4300	6503	SO:0001583	missense	11162	exon5			GTCTTCGCCAGGT	AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"""Nudix motif containing"""	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.764C>T	4.37:g.123814170G>A	ENSP00000306070:p.Ala255Val	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	231	114	0.493506	NM_007083	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	37	CCDS43268.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.606796	0.00842	0.003404	0.0	ENSG00000170917	ENST00000304430;ENST00000339154;ENST00000502270	T;T;T	0.29397	1.57;1.57;1.57	5.11	-3.64	0.04515	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.356862	0.31312	N	0.007867	T	0.14960	0.0361	L	0.41124	1.26	0.38646	D	0.951723	B	0.31241	0.315	B	0.24006	0.05	T	0.43410	-0.9393	10	0.02654	T	1	-8.3014	10.6191	0.45470	0.2019:0.0:0.6699:0.1282	.	255	P53370	NUDT6_HUMAN	V	255;86;86	ENSP00000306070:A255V;ENSP00000344011:A86V;ENSP00000424117:A86V	ENSP00000306070:A255V	A	-	2	0	NUDT6	124033620	0.857000	0.29778	0.016000	0.15963	0.203000	0.24098	1.354000	0.34056	-0.254000	0.09500	-0.312000	0.09012	GCG	G|0.998;A|0.002	0.002	strong		0.433	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083	
TTC29	83894	hgsc.bcm.edu	37	4	147824864	147824864	+	Missense_Mutation	SNP	G	G	A	rs17610219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:147824864G>A	ENST00000325106.4	-	6	644	c.418C>T	c.(418-420)Cat>Tat	p.H140Y	TTC29_ENST00000513335.1_Missense_Mutation_p.H166Y|TTC29_ENST00000398886.4_Missense_Mutation_p.H166Y	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	140			H -> Y (in dbSNP:rs17610219). {ECO:0000269|Ref.1, ECO:0000269|Ref.2}.							breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					AAGTTATTATGTACATCTTCG	0.388													A|||	2745	0.548123	0.6581	0.5908	5008	,	,		17171	0.5526		0.3598	False		,,,				2504	0.5583				p.H140Y		Atlas-SNP	.											.	TTC29	63	.	0			c.C418T						PASS	.	A	TYR/HIS	2143,1549		631,881,334	51.0	49.0	50.0		418	5.6	0.9	4	dbSNP_123	50	3041,5165		543,1955,1605	yes	missense	TTC29	NM_031956.2	83	1174,2836,1939	AA,AG,GG		37.0583,41.9556,43.5703	benign	140/476	147824864	5184,6714	1846	4103	5949	SO:0001583	missense	83894	exon6			TATTATGTACATC	AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"""Tetratricopeptide (TTC) repeat domain containing"""	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.418C>T	4.37:g.147824864G>A	ENSP00000316740:p.His140Tyr	Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_031956	A4GU95|Q9BXB6	Missense_Mutation	SNP	ENST00000325106.4	37	CCDS47141.1	1071	0.49038461538461536	317	0.6443089430894309	184	0.5082872928176796	312	0.5454545454545454	258	0.3403693931398417	A	0.010	-1.746363	0.00669	0.580444	0.370583	ENSG00000137473	ENST00000513335;ENST00000398886;ENST00000325106;ENST00000398883;ENST00000504425	T;T;T;T	0.15603	2.41;2.41;2.41;2.41	5.62	5.62	0.85841	.	0.133718	0.52532	N	0.000067	T	0.00012	0.0000	N	0.00052	-2.395	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	0.43245	-0.9403	9	0.02654	T	1	-9.3104	10.4294	0.44398	0.9266:0.0:0.0734:0.0	rs17610219;rs17856717;rs56419348;rs57564073;rs17610219	140;166;140	E7EQ14;G5E9Z5;Q8NA56	.;.;TTC29_HUMAN	Y	166;166;140;140;140	ENSP00000423505:H166Y;ENSP00000381861:H166Y;ENSP00000316740:H140Y;ENSP00000425778:H140Y	ENSP00000316740:H140Y	H	-	1	0	TTC29	148044314	0.997000	0.39634	0.939000	0.37840	0.040000	0.13550	4.637000	0.61346	0.967000	0.38186	-0.269000	0.10298	CAT	G|0.507;A|0.493	0.493	strong		0.388	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956	
FGD3	89846	hgsc.bcm.edu	37	9	95766336	95766336	+	Silent	SNP	C	C	T	rs201073654		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95766336C>T	ENST00000375482.3	+	5	1093	c.597C>T	c.(595-597)ggC>ggT	p.G199G	FGD3_ENST00000416701.2_Silent_p.G199G|FGD3_ENST00000337352.6_Silent_p.G199G	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	199	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)|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)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						TCATCATGGGCATATTCTCTA	0.582											OREG0019318	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G199G		Atlas-SNP	.											.	FGD3	116	.	0			c.C597T						PASS	.	C	,	1,4183		0,1,2091	77.0	81.0	80.0		597,597	-0.6	1.0	9		80	0,8488		0,0,4244	no	coding-synonymous,coding-synonymous	FGD3	NM_001083536.1,NM_033086.2	,	0,1,6335	TT,TC,CC		0.0,0.0239,0.0079	,	199/726,199/726	95766336	1,12671	2092	4244	6336	SO:0001819	synonymous_variant	89846	exon5			CATGGGCATATTC	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16027	protein-coding gene	gene with protein product			"""FGD1 family, member 3"""			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.597C>T	9.37:g.95766336C>T		Somatic	99	0	0	1315	WXS	Illumina HiSeq	Phase_I	93	60	0.645161	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Silent	SNP	ENST00000375482.3	37	CCDS43849.1																																																																																			C|1.000;T|0.000	0.000	strong		0.582	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086	
ERCC5	2073	hgsc.bcm.edu	37	13	103519119	103519119	+	Silent	SNP	G	G	A	rs73573973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103519119G>A	ENST00000355739.4	+	11	3880	c.2457G>A	c.(2455-2457)cgG>cgA	p.R819R	ERCC5_ENST00000375954.1_Silent_p.R52R|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.A1245T	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	819	I-domain.				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)					TTGGAGCGCGGCATGTCTATA	0.423			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	35	0.00698882	0.0257	0.0014	5008	,	,		18124	0.0		0.0	False		,,,				2504	0.0				p.R1273R		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	ERCC5,NS,carcinoma,+2,1	.	.	1	0			c.G3819A						PASS	.	G	,	91,4315	75.2+/-113.4	2,87,2114	57.0	58.0	58.0		2457,3819	3.1	1.0	13	dbSNP_130	58	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	2,87,6414	AA,AG,GG		0.0,2.0654,0.6997	,	819/1187,1273/1641	103519119	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	0	exon19	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGCGCGGCATGTC	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.2457G>A	13.37:g.103519119G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			G|0.994;A|0.006	0.006	strong		0.423	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
PLEKHS1	79949	hgsc.bcm.edu	37	10	115531790	115531790	+	Missense_Mutation	SNP	C	C	T	rs143039412		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115531790C>T	ENST00000369310.3	+	7	1158	c.596C>T	c.(595-597)gCc>gTc	p.A199V	PLEKHS1_ENST00000354462.3_5'UTR|PLEKHS1_ENST00000361048.1_Missense_Mutation_p.A205V|PLEKHS1_ENST00000369312.4_Missense_Mutation_p.A117V|PLEKHS1_ENST00000369309.1_Missense_Mutation_p.A19V	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	199																	TTATCAGAAGCCACTCAAGAT	0.353													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21165	0.0		0.0	False		,,,				2504	0.0				p.A205V		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.C614T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	3,4403	4.2+/-10.8	0,3,2200	147.0	137.0	140.0		350,350,614,596	2.6	0.0	10	dbSNP_134	140	0,8600		0,0,4300	no	missense,missense,missense,missense	C10orf81	NM_001193434.1,NM_001193435.1,NM_024889.4,NM_182601.1	64,64,64,64	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign,benign,benign,benign	117/367,117/367,205/364,199/466	115531790	3,13003	2203	4300	6503	SO:0001583	missense	79949	exon8			CAGAAGCCACTCA	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.596C>T	10.37:g.115531790C>T	ENSP00000358316:p.Ala199Val	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	126	56	0.444444	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	37	CCDS53580.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.843362	0.32606	6.81E-4	0.0	ENSG00000148735	ENST00000361048;ENST00000369312;ENST00000369310;ENST00000369309	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.63	2.59	0.31030	.	1.116260	0.06460	N	0.729232	T	0.13970	0.0338	N	0.08118	0	0.09310	N	1	B;B;B;B	0.31077	0.307;0.009;0.049;0.043	B;B;B;B	0.23419	0.046;0.005;0.019;0.03	T	0.17198	-1.0377	10	0.36615	T	0.2	-21.7194	3.245	0.06794	0.1867:0.5589:0.1595:0.095	.	199;199;199;205	Q5SXH7;Q5SXH7-5;Q5SXH7-2;Q5SXH7-4	CJ081_HUMAN;.;.;.	V	205;117;199;19	ENSP00000354332:A205V;ENSP00000358318:A117V;ENSP00000358316:A199V;ENSP00000358315:A19V	ENSP00000354332:A205V	A	+	2	0	C10orf81	115521780	0.002000	0.14202	0.002000	0.10522	0.072000	0.16883	0.513000	0.22770	1.390000	0.46547	0.650000	0.86243	GCC	C|1.000;T|0.000	0.000	weak		0.353	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889	
PCLO	27445	hgsc.bcm.edu	37	7	82585803	82585803	+	Missense_Mutation	SNP	G	G	C	rs114445550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:82585803G>C	ENST00000333891.9	-	5	4803	c.4466C>G	c.(4465-4467)tCc>tGc	p.S1489C	PCLO_ENST00000423517.2_Missense_Mutation_p.S1489C	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						GTCCTTGCTGGAAGGAATATC	0.358													G|||	19	0.00379393	0.0144	0.0	5008	,	,		21243	0.0		0.0	False		,,,				2504	0.0				p.S1489C		Atlas-SNP	.											.	PCLO	1506	.	0			c.C4466G						PASS	.	G	CYS/SER,CYS/SER	50,3644		0,50,1797	112.0	103.0	106.0		4466,4466	3.6	0.0	7	dbSNP_132	106	0,8172		0,0,4086	yes	missense,missense	PCLO	NM_014510.2,NM_033026.5	112,112	0,50,5883	CC,CG,GG		0.0,1.3535,0.4214	possibly-damaging,possibly-damaging	1489/4936,1489/5143	82585803	50,11816	1847	4086	5933	SO:0001583	missense	27445	exon5			TTGCTGGAAGGAA	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.4466C>G	7.37:g.82585803G>C	ENSP00000334319:p.Ser1489Cys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	0.586	-0.834971	0.02713	0.013535	0.0	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17370	2.28;2.28	5.43	3.57	0.40892	.	.	.	.	.	T	0.17408	0.0418	L	0.47716	1.5	0.09310	N	0.999996	P;P	0.49253	0.921;0.921	P;P	0.50378	0.518;0.639	T	0.04041	-1.0982	9	0.87932	D	0	.	10.4646	0.44600	0.0726:0.1355:0.7919:0.0	.	1489;1489	Q9Y6V0-5;Q9Y6V0-6	.;.	C	1420;1489;1489	ENSP00000334319:S1489C;ENSP00000388393:S1489C	ENSP00000334319:S1489C	S	-	2	0	PCLO	82423739	0.976000	0.34144	0.012000	0.15200	0.080000	0.17528	3.139000	0.50577	1.265000	0.44215	0.650000	0.86243	TCC	G|0.997;C|0.003	0.003	strong		0.358	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
TSC22D1	8848	hgsc.bcm.edu	37	13	45149662	45149662	+	Silent	SNP	G	G	A	rs9525984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:45149662G>A	ENST00000458659.2	-	1	1039	c.549C>T	c.(547-549)gcC>gcT	p.A183A	TSC22D1_ENST00000501704.2_Silent_p.A183A|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	183					negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		CAGGTGTCTCGGCTTCCTGGA	0.532													G|||	264	0.0527157	0.0166	0.0937	5008	,	,		19095	0.001		0.1163	False		,,,				2504	0.0603				p.A183A		Atlas-SNP	.											.	TSC22D1	88	.	0			c.C549T						PASS	.	G		142,4264	98.0+/-136.7	1,140,2062	66.0	70.0	69.0		549	-4.1	0.9	13	dbSNP_119	69	1064,7536	223.6+/-260.3	71,922,3307	no	coding-synonymous	TSC22D1	NM_183422.3		72,1062,5369	AA,AG,GG		12.3721,3.2229,9.2726		183/1074	45149662	1206,11800	2203	4300	6503	SO:0001819	synonymous_variant	8848	exon1			TGTCTCGGCTTCC	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.549C>T	13.37:g.45149662G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	217	106	0.488479	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Silent	SNP	ENST00000458659.2	37	CCDS31966.1																																																																																			G|0.924;A|0.076	0.076	strong		0.532	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022	
ASL	435	hgsc.bcm.edu	37	7	65551782	65551782	+	Silent	SNP	G	G	A	rs115468878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:65551782G>A	ENST00000304874.9	+	8	678	c.576G>A	c.(574-576)aaG>aaA	p.K192K	AC068533.7_ENST00000450043.1_5'Flank|ASL_ENST00000380839.4_Intron|ASL_ENST00000395332.3_Silent_p.K192K|ASL_ENST00000395331.3_Silent_p.K192K	NM_000048.3	NP_000039.2	P04424	ARLY_HUMAN	argininosuccinate lyase	192					arginine biosynthetic process via ornithine (GO:0042450)|arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|internal protein amino acid acetylation (GO:0006475)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	argininosuccinate lyase activity (GO:0004056)			breast(3)|endometrium(3)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	18					L-Arginine(DB00125)	AGGTGCGGAAGCGGATCAATG	0.687													g|||	29	0.00579073	0.0212	0.0014	5008	,	,		17651	0.0		0.0	False		,,,				2504	0.0				p.K192K		Atlas-SNP	.											.	ASL	39	.	0			c.G576A						PASS	.	A	,,,	95,4307		1,93,2107	27.0	28.0	28.0		576,576,576,	1.8	1.0	7	dbSNP_132	28	0,8584		0,0,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ASL	NM_000048.3,NM_001024943.1,NM_001024944.1,NM_001024946.1	,,,	1,93,6399	AA,AG,GG		0.0,2.1581,0.7316	,,,	192/465,192/465,192/445,	65551782	95,12891	2201	4292	6493	SO:0001819	synonymous_variant	435	exon8			GCGGAAGCGGATC		CCDS5531.1, CCDS47597.1, CCDS47598.1	7q11.21	2012-10-02			ENSG00000126522	ENSG00000126522	4.3.2.1		746	protein-coding gene	gene with protein product		608310					Standard	NM_001024943		Approved		uc003tuo.3	P04424	OTTHUMG00000022876	ENST00000304874.9:c.576G>A	7.37:g.65551782G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_000048	E7EMI0|E9PE48|Q6LDS5|Q96HS2	Silent	SNP	ENST00000304874.9	37	CCDS5531.1																																																																																			G|0.993;A|0.007	0.007	strong		0.687	ASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251695.2	NM_000048	
IMPG1	3617	hgsc.bcm.edu	37	6	76640781	76640781	+	Missense_Mutation	SNP	C	C	T	rs3734313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	171	74	0.432749	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	
ZNF577	84765	hgsc.bcm.edu	37	19	52376040	52376040	+	Silent	SNP	G	G	A	rs10407707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52376040G>A	ENST00000301399.5	-	7	1568	c.1203C>T	c.(1201-1203)agC>agT	p.S401S	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Silent_p.S342S|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000451628.2_Silent_p.S342S	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	401					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GTATGAGTTCGCTCATGTATA	0.443													A|||	854	0.170527	0.295	0.1427	5008	,	,		19180	0.0427		0.0358	False		,,,				2504	0.2924				p.S401S		Atlas-SNP	.											.	ZNF577	63	.	0			c.C1203T						PASS	.	A	,	1177,3229		167,843,1193	109.0	115.0	113.0		1026,1203	-0.6	0.0	19	dbSNP_119	113	165,8435		1,163,4136	no	coding-synonymous,coding-synonymous	ZNF577	NM_001135590.1,NM_032679.2	,	168,1006,5329	AA,AG,GG		1.9186,26.7136,10.3183	,	342/427,401/486	52376040	1342,11664	2203	4300	6503	SO:0001819	synonymous_variant	84765	exon7			GAGTTCGCTCATG	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1203C>T	19.37:g.52376040G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	113	48	0.424779	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			G|0.892;A|0.108	0.108	strong		0.443	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
JAG2	3714	hgsc.bcm.edu	37	14	105622157	105622157	+	Silent	SNP	G	G	A	rs61750261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105622157G>A	ENST00000331782.3	-	4	1048	c.645C>T	c.(643-645)aaC>aaT	p.N215N	RP11-44N21.4_ENST00000548203.1_RNA|JAG2_ENST00000347004.2_Silent_p.N215N	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	215	DSL. {ECO:0000255|PROSITE- ProRule:PRU00377}.				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)		CGAAAAAGTCGTTGCGGGGCC	0.637													G|||	147	0.029353	0.1074	0.0072	5008	,	,		16759	0.0		0.0	False		,,,				2504	0.0				p.N215N		Atlas-SNP	.											.	JAG2	69	.	0			c.C645T						PASS	.	G	,	361,4031	179.7+/-208.2	15,331,1850	85.0	62.0	70.0		645,645	-3.3	1.0	14	dbSNP_129	70	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous,coding-synonymous	JAG2	NM_002226.3,NM_145159.1	,	15,332,6146	AA,AG,GG		0.0116,8.2195,2.7876	,	215/1239,215/1201	105622157	362,12624	2196	4297	6493	SO:0001819	synonymous_variant	3714	exon4			AAAGTCGTTGCGG	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.645C>T	14.37:g.105622157G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	153	68	0.444444	NM_145159	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	CCDS9998.1																																																																																			G|0.974;A|0.026	0.026	strong		0.637	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
PCDHA9	9752	hgsc.bcm.edu	37	5	140229925	140229925	+	Silent	SNP	G	G	C	rs58792000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140229925G>C	ENST00000532602.1	+	1	2878	c.1845G>C	c.(1843-1845)acG>acC	p.T615T	PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000378122.3_Silent_p.T615T|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	615	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCAGAAACGGCCAGCGCGA	0.687													.|||	325	0.0648962	0.2315	0.0187	5008	,	,		16120	0.0		0.006	False		,,,				2504	0.0				p.T615T	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G1845C						PASS	.	G	,,,,,,,,,,,	892,3500		144,604,1448	61.0	66.0	64.0		1845,,,,,,,,,,,1845	2.4	0.0	5	dbSNP_129	64	19,8521		1,17,4252	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_014005.3,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_031857.1	,,,,,,,,,,,	145,621,5700	CC,CG,GG		0.2225,20.3097,7.0445	,,,,,,,,,,,	615/843,,,,,,,,,,,615/951	140229925	911,12021	2196	4270	6466	SO:0001819	synonymous_variant	9752	exon1			AGAAACGGCCAGC	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1845G>C	5.37:g.140229925G>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	211	111	0.526066	NM_031857	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																			G|0.937;C|0.063	0.063	strong		0.687	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
BPIFA2	140683	hgsc.bcm.edu	37	20	31756954	31756954	+	Start_Codon_SNP	SNP	G	G	A	rs17124277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31756954G>A	ENST00000253362.2	+	2	149	c.3G>A	c.(1-3)atG>atA	p.M1I	BPIFA2_ENST00000354932.5_Start_Codon_SNP_p.M1I			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	1						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										GACAAAAGATGCTTCAGCTTT	0.473													G|||	140	0.0279553	0.0991	0.0058	5008	,	,		20080	0.0		0.005	False		,,,				2504	0.0				p.M1I		Atlas-SNP	.											.	.	.	.	0			c.G3A						PASS	.	G	ILE/MET	400,4006	199.1+/-222.7	14,372,1817	149.0	134.0	139.0		3	4.2	1.0	20	dbSNP_123	139	17,8583	12.6+/-44.7	0,17,4283	yes	missense	BPIFA2	NM_080574.2	10	14,389,6100	AA,AG,GG		0.1977,9.0785,3.2062	probably-damaging	1/250	31756954	417,12589	2203	4300	6503	SO:0001582	initiator_codon_variant	140683	exon2			AAAGATGCTTCAG	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.3G>A	20.37:g.31756954G>A	ENSP00000253362:p.Met1Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	116	47	0.405172	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	59	0.027014652014652016	52	0.10569105691056911	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	18.40	3.615032	0.66672	0.090785	0.001977	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.33654	1.4;1.4	4.22	4.22	0.49857	.	0.093315	0.47455	D	0.000230	T	0.01905	0.0060	.	.	.	0.09310	P	0.9999999999804186	D	0.89917	1.0	D	0.80764	0.994	T	0.35001	-0.9806	8	0.87932	D	0	-13.9353	12.3777	0.55289	0.0:0.0:1.0:0.0	rs17124277;rs52823533;rs17124277	1	Q96DR5	BPIA2_HUMAN	I	1	ENSP00000253362:M1I;ENSP00000347012:M1I	ENSP00000253362:M1I	M	+	3	0	BPIFA2	31220615	1.000000	0.71417	0.998000	0.56505	0.876000	0.50452	3.596000	0.54024	2.633000	0.89246	0.591000	0.81541	ATG	G|0.963;A|0.037	0.037	strong		0.473	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	Missense_Mutation
CCDC183	84960	hgsc.bcm.edu	37	9	139694569	139694569	+	Missense_Mutation	SNP	A	A	C	rs7859194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139694569A>C	ENST00000338005.6	+	4	421	c.386A>C	c.(385-387)gAc>gCc	p.D129A	KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.D159A|RP11-216L13.18_ENST00000471502.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		129			D -> A (in dbSNP:rs7859194).							biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		CTGGAGCTGGACAGCCTGCGG	0.682													C|||	1376	0.27476	0.3381	0.2968	5008	,	,		9043	0.2421		0.2157	False		,,,				2504	0.2679				p.D129A		Atlas-SNP	.											.	KIAA1984	39	.	0			c.A386C						PASS	.	C	ALA/ASP	963,2909		140,683,1113	10.0	12.0	12.0		386	-3.1	0.0	9	dbSNP_116	12	1531,6531		185,1161,2685	no	missense	KIAA1984	NM_001039374.4	126	325,1844,3798	CC,CA,AA		18.9903,24.8709,20.8983	benign	129/535	139694569	2494,9440	1936	4031	5967	SO:0001583	missense	84960	exon4			AGCTGGACAGCCT																												ENST00000338005.6:c.386A>C	9.37:g.139694569A>C	ENSP00000338013:p.Asp129Ala	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	535	0.24496336996336995	158	0.32113821138211385	97	0.26795580110497236	122	0.21328671328671328	158	0.20844327176781002	C	5.124	0.208555	0.09757	0.248709	0.189903	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.11604	2.76	4.95	-3.07	0.05363	.	0.822281	0.09595	N	0.780992	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	0.45145	-0.9281	9	0.09843	T	0.71	-0.1055	5.2268	0.15399	0.6236:0.1793:0.1142:0.0829	rs7859194;rs60792782;rs7859194	129	Q5T5S1	K1984_HUMAN	A	129	ENSP00000338013:D129A	ENSP00000338013:D129A	D	+	2	0	KIAA1984	138814390	0.000000	0.05858	0.004000	0.12327	0.086000	0.17979	-0.016000	0.12613	-0.448000	0.07128	-0.358000	0.07595	GAC	A|0.754;C|0.246	0.246	strong		0.682	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
MVP	9961	hgsc.bcm.edu	37	16	29841950	29841950	+	Missense_Mutation	SNP	G	G	A	rs142997389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:29841950G>A	ENST00000357402.5	+	2	218	c.80G>A	c.(79-81)cGt>cAt	p.R27H	MVP_ENST00000452209.2_Missense_Mutation_p.V11M|MVP_ENST00000395353.1_Missense_Mutation_p.R27H|MVP_ENST00000566554.1_3'UTR	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	27					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						AACGTGTCCCGTGTGGAGGTC	0.597													G|||	40	0.00798722	0.0287	0.0029	5008	,	,		15564	0.0		0.0	False		,,,				2504	0.0				p.R27H		Atlas-SNP	.											.	MVP	80	.	0			c.G80A						PASS	.	G	HIS/ARG,HIS/ARG	112,4282	88.2+/-126.9	0,112,2085	135.0	97.0	110.0		80,80	0.5	0.2	16	dbSNP_134	110	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	MVP	NM_005115.4,NM_017458.3	29,29	0,114,6383	AA,AG,GG		0.0233,2.5489,0.8773	benign,benign	27/894,27/894	29841950	114,12880	2197	4300	6497	SO:0001583	missense	9961	exon2			TGTCCCGTGTGGA	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"""lung resistance-related protein"""	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.80G>A	16.37:g.29841950G>A	ENSP00000349977:p.Arg27His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	37	CCDS10656.1	12|12	0.005494505494505495|0.005494505494505495	12|12	0.024390243902439025|0.024390243902439025	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	14.62|14.62	2.588764|2.588764	0.46110|0.46110	0.025489|0.025489	2.33E-4|2.33E-4	ENSG00000013364|ENSG00000013364	ENST00000357402;ENST00000395353|ENST00000452209	T;T|.	0.33865|.	1.39;1.39|.	5.82|5.82	0.469|0.469	0.16741|0.16741	.|.	0.109460|.	0.64402|.	N|.	0.000005|.	T|T	0.35998|0.35998	0.0951|0.0951	M|M	0.85197|0.85197	2.74|2.74	0.21675|0.21675	N|N	0.999591|0.999591	B|.	0.28400|.	0.21|.	B|.	0.27500|.	0.08|.	T|T	0.47509|0.47509	-0.9112|-0.9112	10|6	0.48119|0.87932	T|D	0.1|0	-4.9453|-4.9453	9.041|9.041	0.36319|0.36319	0.3672:0.0:0.6328:0.0|0.3672:0.0:0.6328:0.0	.|.	27|.	Q14764|.	MVP_HUMAN|.	H|M	27|11	ENSP00000349977:R27H;ENSP00000378760:R27H|.	ENSP00000349977:R27H|ENSP00000387916:V11M	R|V	+|+	2|1	0|0	MVP|MVP	29749451|29749451	0.915000|0.915000	0.31059|0.31059	0.191000|0.191000	0.23289|0.23289	0.606000|0.606000	0.37113|0.37113	1.270000|1.270000	0.33086|0.33086	0.110000|0.110000	0.17919|0.17919	-0.224000|-0.224000	0.12420|0.12420	CGT|GTG	G|0.991;A|0.009	0.009	strong		0.597	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115	
ITGA5	3678	hgsc.bcm.edu	37	12	54795410	54795410	+	Silent	SNP	A	A	G	rs73322228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:54795410A>G	ENST00000293379.4	-	23	2607	c.2346T>C	c.(2344-2346)ttT>ttC	p.F782F	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	782					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						CGGAGAGCCGAAAGGAAACCA	0.582													G|||	250	0.0499201	0.1074	0.0086	5008	,	,		22245	0.0069		0.004	False		,,,				2504	0.093				p.F782F		Atlas-SNP	.											.	ITGA5	99	.	0			c.T2346C						PASS	.	G		499,3907	779.6+/-414.4	30,439,1734	164.0	139.0	148.0		2346	4.9	1.0	12	dbSNP_130	148	82,8518	815.5+/-407.0	0,82,4218	no	coding-synonymous	ITGA5	NM_002205.2		30,521,5952	GG,GA,AA		0.9535,11.3255,4.4672		782/1050	54795410	581,12425	2203	4300	6503	SO:0001819	synonymous_variant	3678	exon23			GAGCCGAAAGGAA		CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"""CD molecules"", ""Integrins"""	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.2346T>C	12.37:g.54795410A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	171	72	0.421053	NM_002205	Q96HA5	Silent	SNP	ENST00000293379.4	37	CCDS8880.1																																																																																			A|0.960;G|0.040	0.040	strong		0.582	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1		
TMPRSS3	64699	hgsc.bcm.edu	37	21	43803167	43803167	+	Missense_Mutation	SNP	T	T	C	rs2839500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43803167T>C	ENST00000291532.3	-	8	1712	c.757A>G	c.(757-759)Atc>Gtc	p.I253V	TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.I253V|TMPRSS3_ENST00000398405.1_Missense_Mutation_p.I251V|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.I337V|TMPRSS3_ENST00000433957.2_Missense_Mutation_p.I253V	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	253	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		I -> V (in dbSNP:rs2839500). {ECO:0000269|PubMed:11424922}.		cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						GCAGCAGTGATGATCCACAGG	0.592													C|||	1208	0.241214	0.3041	0.134	5008	,	,		20674	0.3323		0.1113	False		,,,				2504	0.272				p.I253V		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.A757G						PASS	.	C	VAL/ILE,VAL/ILE	1196,3210	708.6+/-407.6	161,874,1168	75.0	64.0	68.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	757,757	4.6	0.5	21	dbSNP_100	68	887,7713	778.9+/-407.7	37,813,3450	yes	missense,missense	TMPRSS3	NM_024022.2,NM_032405.1	29,29	198,1687,4618	CC,CT,TT		10.314,27.1448,16.0157	benign,benign	253/455,253/345	43803167	2083,10923	2203	4300	6503	SO:0001583	missense	64699	exon8			CAGTGATGATCCA	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.757A>G	21.37:g.43803167T>C	ENSP00000291532:p.Ile253Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	48	0.585366	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	37	CCDS13686.1	494	0.2261904761904762	154	0.3130081300813008	54	0.14917127071823205	203	0.3548951048951049	83	0.10949868073878628	C	0.696	-0.792701	0.02884	0.271448	0.10314	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	T;T;T;T;T	0.80994	0.25;-1.44;-1.44;0.25;-1.44	5.5	4.59	0.56863	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.159777	0.42053	N	0.000763	T	0.00012	0.0000	N	0.11698	0.16	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.14980	-1.0453	8	.	.	.	.	8.2005	0.31421	0.0:0.5343:0.3254:0.1403	rs2839500;rs52817606;rs60045807;rs2839500	253;253;253	P57727-3;P57727-5;P57727	.;.;TMPS3_HUMAN	V	253;253;251;337;253	ENSP00000291532:I253V;ENSP00000411013:I253V;ENSP00000381442:I251V;ENSP00000369762:I337V;ENSP00000381434:I253V	.	I	-	1	0	TMPRSS3	42676236	0.025000	0.19082	0.465000	0.27155	0.794000	0.44872	0.113000	0.15499	0.658000	0.30925	-0.186000	0.12905	ATC	A|0.006;C|0.194	0.194	strong		0.592	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		
CASP8	841	hgsc.bcm.edu	37	2	202149696	202149696	+	Silent	SNP	G	G	A	rs1045487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:202149696G>A	ENST00000432109.2	+	9	1149	c.960G>A	c.(958-960)aaG>aaA	p.K320K	CASP8_ENST00000264275.5_Silent_p.K337K|CASP8_ENST00000323492.7_Silent_p.K305K|CASP8_ENST00000264274.9_Silent_p.K236K|CASP8_ENST00000358485.4_Silent_p.K379K|CASP8_ENST00000392266.3_3'UTR|CASP8_ENST00000392259.2_3'UTR	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	320					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						ATGGAGACAAGGGCATCATCT	0.478										HNSCC(4;0.00038)			G|||	878	0.175319	0.2602	0.0504	5008	,	,		18997	0.1885		0.0417	False		,,,				2504	0.273				p.K379K	Melanoma(82;831 1348 20716 36952 40159)	Atlas-SNP	.											.	CASP8	272	.	0			c.G1137A						PASS	.	G	,,,,	942,3464	355.9+/-313.2	85,772,1346	174.0	147.0	156.0		915,1137,1011,960,915	0.8	1.0	2	dbSNP_86	156	439,8161	133.8+/-191.2	10,419,3871	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASP8	NM_001080124.1,NM_001080125.1,NM_001228.4,NM_033355.3,NM_033356.3	,,,,	95,1191,5217	AA,AG,GG		5.1047,21.3799,10.6182	,,,,	305/465,379/539,337/497,320/480,305/465	202149696	1381,11625	2203	4300	6503	SO:0001819	synonymous_variant	841	exon8			AGACAAGGGCATC	U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"""Caspases"""	1509	protein-coding gene	gene with protein product		601763	"""caspase 8, apoptosis-related cysteine protease"""			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	ENST00000432109.2:c.960G>A	2.37:g.202149696G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Silent	SNP	ENST00000432109.2	37	CCDS2342.1																																																																																			G|0.862;A|0.138	0.138	strong		0.478	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228	
CEP350	9857	hgsc.bcm.edu	37	1	179983153	179983153	+	Missense_Mutation	SNP	A	A	G	rs111349041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179983153A>G	ENST00000367607.3	+	10	1983	c.1565A>G	c.(1564-1566)gAc>gGc	p.D522G		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	522					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TTAAATAAGGACTTTTTACCT	0.378													A|||	63	0.0125799	0.0461	0.0029	5008	,	,		19374	0.0		0.0	False		,,,				2504	0.0				p.D522G		Atlas-SNP	.											.	CEP350	418	.	0			c.A1565G						PASS	.	A	GLY/ASP	160,4246	106.0+/-144.5	4,152,2047	43.0	43.0	43.0		1565	5.6	1.0	1	dbSNP_132	43	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CEP350	NM_014810.4	94	4,154,6345	GG,GA,AA		0.0233,3.6314,1.2456	possibly-damaging	522/3118	179983153	162,12844	2203	4300	6503	SO:0001583	missense	9857	exon10			ATAAGGACTTTTT	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.1565A>G	1.37:g.179983153A>G	ENSP00000356579:p.Asp522Gly	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	46	0.613333	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	A	19.07	3.755539	0.69648	0.036314	2.33E-4	ENSG00000135837	ENST00000367607	D	0.89485	-2.52	5.6	5.6	0.85130	.	0.122043	0.36555	N	0.002523	T	0.73345	0.3575	M	0.65975	2.015	0.46901	D	0.999242	P;P	0.49635	0.78;0.926	B;P	0.47673	0.265;0.554	T	0.81703	-0.0812	9	.	.	.	.	15.7476	0.77958	1.0:0.0:0.0:0.0	.	522;522	E7EU22;Q5VT06	.;CE350_HUMAN	G	522	ENSP00000356579:D522G	.	D	+	2	0	CEP350	178249776	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.597000	0.74118	2.251000	0.74343	0.528000	0.53228	GAC	A|0.986;G|0.014	0.014	strong		0.378	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
NCF4	4689	hgsc.bcm.edu	37	22	37260123	37260123	+	Silent	SNP	G	G	A	rs10854695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37260123G>A	ENST00000248899.6	+	2	253	c.69G>A	c.(67-69)tcG>tcA	p.S23S	CTA-833B7.2_ENST00000431290.1_RNA|CTA-833B7.2_ENST00000330602.2_RNA|NCF4_ENST00000397147.4_Silent_p.S23S	NM_000631.4	NP_000622.2	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4, 40kDa	23	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)|immune response (GO:0006955)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of catalytic activity (GO:0043085)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|membrane (GO:0016020)|NADPH oxidase complex (GO:0043020)|phagolysosome (GO:0032010)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein dimerization activity (GO:0046983)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16					Dextromethorphan(DB00514)	TTGCCATCTCGGCCAACATTG	0.527													G|||	492	0.0982428	0.2504	0.098	5008	,	,		19272	0.0734		0.003	False		,,,				2504	0.0164				p.S23S		Atlas-SNP	.											NCF4_ENST00000397147,NS,carcinoma,+1,2	NCF4	66	2	0			c.G69A						PASS	.	G	,	879,3527	342.3+/-307.1	79,721,1403	208.0	179.0	189.0		69,69	-1.5	1.0	22	dbSNP_120	189	11,8589	9.1+/-34.3	0,11,4289	no	coding-synonymous,coding-synonymous	NCF4	NM_000631.4,NM_013416.3	,	79,732,5692	AA,AG,GG		0.1279,19.9501,6.843	,	23/340,23/349	37260123	890,12116	2203	4300	6503	SO:0001819	synonymous_variant	4689	exon2			CATCTCGGCCAAC	X77094	CCDS13934.1, CCDS13935.1	22q13.1	2014-09-17	2002-08-29		ENSG00000100365	ENSG00000100365			7662	protein-coding gene	gene with protein product	"""neutrophil NADPH oxidase factor 4"""	601488	"""neutrophil cytosolic factor 4 (40kD)"""			8839867	Standard	NM_013416		Approved	p40phox, SH3PXD4	uc003apy.4	Q15080	OTTHUMG00000150548	ENST00000248899.6:c.69G>A	22.37:g.37260123G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_000631	A8K4F9|O60808|Q86U56|Q9BU98|Q9NP45	Silent	SNP	ENST00000248899.6	37	CCDS13934.1																																																																																			G|0.930;A|0.070	0.070	strong		0.527	NCF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318863.1	NM_000631	
KLHDC7B	113730	hgsc.bcm.edu	37	22	50987843	50987843	+	Silent	SNP	C	C	T	rs61746062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50987843C>T	ENST00000395676.2	+	1	1382	c.1248C>T	c.(1246-1248)taC>taT	p.Y416Y	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	416										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)		AATGCCTGTACAGCATGGAGT	0.682													C|||	434	0.0866613	0.1762	0.0375	5008	,	,		14164	0.004		0.0875	False		,,,				2504	0.0849				p.Y416Y		Atlas-SNP	.											.	KLHDC7B	39	.	0			c.C1248T						PASS	.	C		735,3671	293.0+/-282.3	65,605,1533	75.0	73.0	74.0		1248	5.3	1.0	22	dbSNP_129	74	751,7847	176.6+/-226.4	32,687,3580	no	coding-synonymous	KLHDC7B	NM_138433.3		97,1292,5113	TT,TC,CC		8.7346,16.6818,11.4273		416/595	50987843	1486,11518	2203	4299	6502	SO:0001819	synonymous_variant	113730	exon1			CCTGTACAGCATG	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.1248C>T	22.37:g.50987843C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_138433		Silent	SNP	ENST00000395676.2	37	CCDS14097.2																																																																																			C|0.896;T|0.104	0.104	strong		0.682	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433	
OR51Q1	390061	hgsc.bcm.edu	37	11	5443739	5443739	+	Silent	SNP	T	T	C	rs2736587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5443739T>C	ENST00000300778.4	+	1	399	c.309T>C	c.(307-309)ttT>ttC	p.F103F	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGCTCAGTTTTTCTTCCTTC	0.517													C|||	2272	0.453674	0.2799	0.3991	5008	,	,		22512	0.7024		0.3986	False		,,,				2504	0.5276				p.F103F		Atlas-SNP	.											.	OR51Q1	79	.	0			c.T309C						PASS	.	C		1332,3070	694.1+/-405.8	203,926,1072	157.0	138.0	144.0		309	-10.0	0.0	11	dbSNP_100	144	3373,5221	641.9+/-399.7	676,2021,1600	no	coding-synonymous	OR51Q1	NM_001004757.2		879,2947,2672	CC,CT,TT		39.2483,30.259,36.2034		103/318	5443739	4705,8291	2201	4297	6498	SO:0001819	synonymous_variant	390061	exon1			TCAGTTTTTCTTC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.309T>C	11.37:g.5443739T>C		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_001004757	B2RNN1	Silent	SNP	ENST00000300778.4	37	CCDS31381.1																																																																																			T|0.601;C|0.399	0.399	strong		0.517	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
QRFP	347148	hgsc.bcm.edu	37	9	133768987	133768987	+	Missense_Mutation	SNP	T	T	C	rs111763002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133768987T>C	ENST00000343079.1	-	1	238	c.239A>G	c.(238-240)gAg>gGg	p.E80G		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)		GCCAGCATGCTCTCTGCCCGA	0.667													T|||	95	0.0189696	0.0582	0.0173	5008	,	,		18583	0.0		0.006	False		,,,				2504	0.0				p.E80G		Atlas-SNP	.											.	QRFP	14	.	0			c.A239G						PASS	.	T	GLY/GLU	197,4209	120.0+/-157.7	7,183,2013	62.0	65.0	64.0		239	-2.3	0.0	9	dbSNP_132	64	48,8552	29.0+/-79.6	0,48,4252	yes	missense	QRFP	NM_198180.1	98	7,231,6265	CC,CT,TT		0.5581,4.4712,1.8837	benign	80/137	133768987	245,12761	2203	4300	6503	SO:0001583	missense	347148	exon1			GCATGCTCTCTGC	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.239A>G	9.37:g.133768987T>C	ENSP00000345487:p.Glu80Gly	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	145	95	0.655172	NM_198180		Missense_Mutation	SNP	ENST00000343079.1	37	CCDS6936.1	30	0.013736263736263736	22	0.044715447154471545	6	0.016574585635359115	0	0.0	2	0.002638522427440633	T	13.86	2.362823	0.41902	0.044712	0.005581	ENSG00000188710	ENST00000343079	T	0.50813	0.73	4.65	-2.29	0.06805	.	0.447428	0.19611	N	0.110130	T	0.09905	0.0243	L	0.52573	1.65	0.09310	N	1	B	0.11235	0.004	B	0.17722	0.019	T	0.12066	-1.0562	10	0.54805	T	0.06	-1.6953	5.0319	0.14413	0.0:0.2479:0.2911:0.461	.	80	P83859	OX26_HUMAN	G	80	ENSP00000345487:E80G	ENSP00000345487:E80G	E	-	2	0	QRFP	132758808	0.000000	0.05858	0.000000	0.03702	0.254000	0.26022	-1.142000	0.03203	-0.649000	0.05430	0.379000	0.24179	GAG	T|0.983;C|0.017	0.017	strong		0.667	QRFP-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254566.1	NM_198180	
STAU2	27067	hgsc.bcm.edu	37	8	74526081	74526081	+	Silent	SNP	G	G	A	rs28728027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:74526081G>A	ENST00000521451.1	-	4	505	c.129C>T	c.(127-129)cgC>cgT	p.R43R	STAU2_ENST00000523558.1_Silent_p.R91R|STAU2_ENST00000522509.1_Silent_p.R231R|STAU2_ENST00000521727.1_Silent_p.R243R|STAU2_ENST00000517542.1_Silent_p.R225R|STAU2_ENST00000519961.1_Silent_p.R263R|STAU2_ENST00000521210.1_Silent_p.R159R|STAU2_ENST00000355780.5_Silent_p.R231R|STAU2_ENST00000522695.1_Silent_p.R231R|STAU2_ENST00000524300.1_Silent_p.R263R			Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	263	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)	19	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			TGGTCGCAGCGCGCTTCTTGG	0.418													G|||	28	0.00559105	0.0189	0.0043	5008	,	,		15334	0.0		0.0	False		,,,				2504	0.0				p.R263R		Atlas-SNP	.											STAU2_ENST00000524300,NS,carcinoma,-1,3	STAU2	148	3	0			c.C789T						PASS	.	G	,,,,,,	79,4327	68.1+/-105.8	1,77,2125	88.0	83.0	85.0		789,693,477,273,693,675,693	-11.9	0.3	8	dbSNP_125	85	3,8597	2.2+/-6.3	0,3,4297	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STAU2	NM_001164380.1,NM_001164381.1,NM_001164382.1,NM_001164383.1,NM_001164384.1,NM_001164385.1,NM_014393.2	,,,,,,	1,80,6422	AA,AG,GG		0.0349,1.793,0.6305	,,,,,,	263/571,231/539,159/505,91/399,231/480,225/474,231/480	74526081	82,12924	2203	4300	6503	SO:0001819	synonymous_variant	27067	exon9			CGCAGCGCGCTTC	Y19062	CCDS6214.1, CCDS55244.1, CCDS55245.1, CCDS55246.1, CCDS55247.1, CCDS55248.1	8q21.11	2013-06-05	2013-06-05		ENSG00000040341	ENSG00000040341			11371	protein-coding gene	gene with protein product		605920	"""staufen (Drosophila, RNA-binding protein) homolog 2"", ""staufen, RNA binding protein, homolog 2 (Drosophila)"""			10585778	Standard	NM_014393		Approved	39K2	uc003xzm.3	Q9NUL3	OTTHUMG00000164499	ENST00000521451.1:c.129C>T	8.37:g.74526081G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_001164380	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	Silent	SNP	ENST00000521451.1	37																																																																																				G|0.995;A|0.005	0.005	strong		0.418	STAU2-006	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000379006.4	NM_001164380	
ZNF70	7621	hgsc.bcm.edu	37	22	24087319	24087319	+	Silent	SNP	A	A	C	rs2070451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24087319A>C	ENST00000341976.3	-	2	469	c.9T>G	c.(7-9)gtT>gtG	p.V3V		NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	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)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						TTGCTGGGGGAACCTCCATTG	0.443													A|||	832	0.166134	0.1732	0.1225	5008	,	,		19789	0.2966		0.1034	False		,,,				2504	0.1176				p.V3V		Atlas-SNP	.											.	ZNF70	49	.	0			c.T9G						PASS	.	A		794,3612	306.9+/-289.7	71,652,1480	77.0	77.0	77.0		9	1.1	0.7	22	dbSNP_96	77	802,7798	181.8+/-230.4	46,710,3544	no	coding-synonymous	ZNF70	NM_021916.2		117,1362,5024	CC,CA,AA		9.3256,18.0209,12.2713		3/447	24087319	1596,11410	2203	4300	6503	SO:0001819	synonymous_variant	7621	exon2			TGGGGGAACCTCC	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.9T>G	22.37:g.24087319A>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	120	64	0.533333	NM_021916		Silent	SNP	ENST00000341976.3	37	CCDS13812.1																																																																																			A|0.865;C|0.135	0.135	strong		0.443	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319881.1	NM_021916	
IFT52	51098	hgsc.bcm.edu	37	20	42252587	42252587	+	Silent	SNP	G	G	A	rs73274323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42252587G>A	ENST00000373030.3	+	10	955	c.825G>A	c.(823-825)gaG>gaA	p.E275E	IFT52_ENST00000373039.4_Silent_p.E275E	NM_016004.2	NP_057088.2	Q9Y366	IFT52_HUMAN	intraflagellar transport 52	275					cilium morphogenesis (GO:0060271)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube formation (GO:0001841)|regulation of protein processing (GO:0070613)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)	protein C-terminus binding (GO:0008022)			endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GGAATCGAGAGTGTCTCCAGG	0.517													G|||	68	0.0135783	0.0492	0.0043	5008	,	,		20452	0.0		0.0	False		,,,				2504	0.0				p.E275E		Atlas-SNP	.											.	IFT52	40	.	0			c.G825A						PASS	.	G		229,4177	136.5+/-172.5	8,213,1982	220.0	181.0	194.0		825	3.5	1.0	20	dbSNP_130	194	0,8600		0,0,4300	no	coding-synonymous	IFT52	NM_016004.2		8,213,6282	AA,AG,GG		0.0,5.1975,1.7607		275/438	42252587	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	51098	exon10			TCGAGAGTGTCTC	AF151811	CCDS33470.1	20q12-q13.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000101052	ENSG00000101052		"""Intraflagellar transport homologs"""	15901	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 9"", ""intraflagellar transport 52 homolog (Chlamydomonas)"""	C20orf9		10810093	Standard	NM_016004		Approved	CGI-53, NGD5, dJ1028D15.1, NGD2	uc002xkw.3	Q9Y366	OTTHUMG00000032513	ENST00000373030.3:c.825G>A	20.37:g.42252587G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	127	56	0.440945	NM_016004	B3KMA1|E1P5W9|Q5H8Z0|Q9H1G3|Q9H1G4|Q9H1H2	Silent	SNP	ENST00000373030.3	37	CCDS33470.1																																																																																			G|0.980;A|0.020	0.020	strong		0.517	IFT52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079317.1	NM_016004	
ROR1	4919	hgsc.bcm.edu	37	1	64643650	64643650	+	Silent	SNP	C	C	T	rs35586842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:64643650C>T	ENST00000371079.1	+	9	2301	c.1926C>T	c.(1924-1926)tcC>tcT	p.S642S	ROR1_ENST00000545203.1_Silent_p.S93S	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	642	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						AAATTTACTCCGCTGATTACT	0.448													C|||	122	0.024361	0.0885	0.0058	5008	,	,		18919	0.0		0.001	False		,,,				2504	0.0				p.S642S		Atlas-SNP	.											.	ROR1	113	.	0			c.C1926T						PASS	.	C		346,4060	177.3+/-206.3	12,322,1869	62.0	64.0	64.0		1926	-11.8	0.3	1	dbSNP_126	64	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ROR1	NM_005012.2		12,326,6165	TT,TC,CC		0.0465,7.8529,2.6911		642/938	64643650	350,12656	2203	4300	6503	SO:0001819	synonymous_variant	4919	exon9			TTACTCCGCTGAT	M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"""Immunoglobulin superfamily / I-set domain containing"""	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.1926C>T	1.37:g.64643650C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	126	76	0.603175	NM_005012	Q5VVX6|Q66K77|Q92776	Silent	SNP	ENST00000371079.1	37	CCDS626.1																																																																																			C|0.972;T|0.028	0.028	strong		0.448	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012	
CLEC4F	165530	hgsc.bcm.edu	37	2	71044076	71044076	+	Missense_Mutation	SNP	T	T	C	rs61754946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71044076T>C	ENST00000272367.2	-	4	513	c.437A>G	c.(436-438)aAt>aGt	p.N146S	CLEC4F_ENST00000426626.1_Missense_Mutation_p.N146S	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	146					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						GATGTCAGCATTGGTGTTTCC	0.473													C|||	95	0.0189696	0.0703	0.0029	5008	,	,		20407	0.0		0.0	False		,,,				2504	0.0				p.N146S	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.A437G						PASS	.	C	SER/ASN	282,4124	800.8+/-415.6	6,270,1927	142.0	120.0	127.0		437	-2.8	0.0	2	dbSNP_129	127	1,8599		0,1,4299	yes	missense	CLEC4F	NM_173535.2	46	6,271,6226	CC,CT,TT		0.0116,6.4004,2.1759	benign	146/590	71044076	283,12723	2203	4300	6503	SO:0001583	missense	165530	exon4			TCAGCATTGGTGT	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.437A>G	2.37:g.71044076T>C	ENSP00000272367:p.Asn146Ser	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	254	112	0.440945	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	0.067	-1.210900	0.01555	0.064004	1.16E-4	ENSG00000152672	ENST00000272367;ENST00000426626	T;T	0.01854	4.6;4.63	5.15	-2.79	0.05841	.	0.560537	0.16319	N	0.219645	T	0.00109	0.0003	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40346	-0.9568	10	0.02654	T	1	.	6.1052	0.20069	0.0:0.2149:0.2644:0.5207	.	146;146	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	S	146	ENSP00000272367:N146S;ENSP00000390581:N146S	ENSP00000272367:N146S	N	-	2	0	CLEC4F	70897584	0.066000	0.20996	0.001000	0.08648	0.003000	0.03518	0.005000	0.13129	-0.464000	0.06963	-1.201000	0.01664	AAT	T|0.979;C|0.021	0.021	strong		0.473	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
SSPO	23145	hgsc.bcm.edu	37	7	149489443	149489443	+	RNA	SNP	C	C	A	rs893603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149489443C>A	ENST00000378016.2	+	0	5596							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)			TGTGTGGCCCCGGCAGTGCCC	0.697													C|||	202	0.0403355	0.1029	0.0144	5008	,	,		16052	0.004		0.003	False		,,,				2504	0.0501				p.R1866R		Atlas-SNP	.											.	.	.	.	0			c.C5596A						PASS	.	C		301,3865		12,277,1794	13.0	21.0	19.0		5600	-1.9	0.1	7	dbSNP_86	19	18,8382		0,18,4182	no	coding-notMod3	SSPO	NM_198455.2		12,295,5976	AA,AC,CC		0.2143,7.2252,2.5386			149489443	319,12247	2083	4200	6283			23145	exon37			TGGCCCCGGCAGT	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.149489443C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	112	37	0.330357	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.975;A|0.025	0.025	strong		0.697	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
ZNF76	7629	hgsc.bcm.edu	37	6	35263009	35263009	+	Missense_Mutation	SNP	C	C	T	rs73745177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35263009C>T	ENST00000373953.3	+	14	1963	c.1697C>T	c.(1696-1698)tCg>tTg	p.S566L	DEF6_ENST00000316637.5_5'Flank|ZNF76_ENST00000440666.2_Missense_Mutation_p.S540L|DEF6_ENST00000542066.1_5'Flank|ZNF76_ENST00000339411.5_Missense_Mutation_p.S511L	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	566					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						ACAACAGTGTCGGAGAGTGGC	0.627													C|||	27	0.00539137	0.0151	0.0086	5008	,	,		19071	0.0		0.0	False		,,,				2504	0.001				p.S566L	Esophageal Squamous(52;92 1039 20612 23956 34676)	Atlas-SNP	.											.	ZNF76	37	.	0			c.C1697T						PASS	.	C	LEU/SER	71,4333	62.9+/-100.1	0,71,2131	58.0	45.0	49.0		1697	5.9	0.3	6	dbSNP_130	49	4,8596	2.2+/-6.3	0,4,4296	yes	missense	ZNF76	NM_003427.3	145	0,75,6427	TT,TC,CC		0.0465,1.6122,0.5767	benign	566/571	35263009	75,12929	2202	4300	6502	SO:0001583	missense	7629	exon14			CAGTGTCGGAGAG	M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"""Zinc fingers, C2H2-type"""	13149	protein-coding gene	gene with protein product		194549	"""zinc finger protein 76 (expressed in testis)"""	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.1697C>T	6.37:g.35263009C>T	ENSP00000363064:p.Ser566Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_003427	Q9BQB2	Missense_Mutation	SNP	ENST00000373953.3	37	CCDS4801.1	9	0.004120879120879121	6	0.012195121951219513	3	0.008287292817679558	0	0.0	0	0.0	C	16.72	3.202287	0.58234	0.016122	4.65E-4	ENSG00000065029	ENST00000373953;ENST00000440666;ENST00000339411	T;T;T	0.10005	2.95;2.95;2.92	5.91	5.91	0.95273	.	0.306088	0.18150	N	0.150126	T	0.04137	0.0115	N	0.22421	0.69	0.09310	N	1	B;B	0.23806	0.046;0.091	B;B	0.12837	0.008;0.007	T	0.24225	-1.0166	10	0.72032	D	0.01	.	17.0178	0.86424	0.0:1.0:0.0:0.0	.	511;566	P36508-2;P36508	.;ZNF76_HUMAN	L	566;540;511	ENSP00000363064:S566L;ENSP00000392243:S540L;ENSP00000344097:S511L	ENSP00000344097:S511L	S	+	2	0	ZNF76	35370987	0.090000	0.21635	0.330000	0.25442	0.994000	0.84299	2.471000	0.45127	2.793000	0.96121	0.655000	0.94253	TCG	C|0.994;T|0.006	0.006	strong		0.627	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427	
ADIPOQ	9370	hgsc.bcm.edu	37	3	186570892	186570892	+	Silent	SNP	T	T	G	rs2241766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186570892T>G	ENST00000412955.2	+	2	186	c.45T>G	c.(43-45)ggT>ggG	p.G15G	ADIPOQ_ENST00000320741.2_Silent_p.G15G|ADIPOQ-AS1_ENST00000422718.1_RNA|ADIPOQ_ENST00000444204.2_Silent_p.G15G			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	15					adiponectin-activated signaling pathway (GO:0033211)|brown fat cell differentiation (GO:0050873)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to insulin stimulus (GO:0032869)|circadian rhythm (GO:0007623)|detection of oxidative stress (GO:0070994)|fatty acid beta-oxidation (GO:0006635)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|low-density lipoprotein particle clearance (GO:0034383)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of hormone secretion (GO:0046888)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular protein transport (GO:0090317)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metanephric mesenchymal cell migration (GO:2000590)|negative regulation of phagocytosis (GO:0050765)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of receptor binding (GO:1900121)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of synaptic transmission (GO:0050805)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|positive regulation of blood pressure (GO:0045777)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of metanephric glomerular visceral epithelial cell development (GO:2000478)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myeloid cell apoptotic process (GO:0033034)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal albumin absorption (GO:2000534)|positive regulation of signal transduction (GO:0009967)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|regulation of glucose metabolic process (GO:0010906)|response to activity (GO:0014823)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to linoleic acid (GO:0070543)|response to nutrient (GO:0007584)|response to sucrose (GO:0009744)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|sialic acid binding (GO:0033691)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(2)	16	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)		CTCTGCCCGGTCATGACCAGG	0.622													T|||	758	0.151358	0.0356	0.1859	5008	,	,		17033	0.2986		0.1322	False		,,,				2504	0.1513				p.G15G		Atlas-SNP	.											ADIPOQ,colon,carcinoma,+2,2	ADIPOQ	35	2	0			c.T45G	GRCh37	CM032392	ADIPOQ	M	rs2241766	PASS	.	T	,	212,4194	128.6+/-165.4	5,202,1996	88.0	81.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	45,45	-1.2	0.0	3	dbSNP_98	84	991,7609	214.5+/-254.1	64,863,3373	no	coding-synonymous,coding-synonymous	ADIPOQ	NM_001177800.1,NM_004797.3	,	69,1065,5369	GG,GT,TT		11.5233,4.8116,9.2496	,	15/245,15/245	186570892	1203,11803	2203	4300	6503	SO:0001819	synonymous_variant	9370	exon3			GCCCGGTCATGAC	D45371	CCDS3284.1	3q27	2013-02-26	2005-01-24	2005-01-27	ENSG00000181092	ENSG00000181092		"""Endogenous ligands"""	13633	protein-coding gene	gene with protein product	"""adipose most abundant gene transcript 1"", ""adiponectin precursor"""	605441	"""adipocyte, C1Q and collagen domain containing"""	ACDC		7592907, 8631877	Standard	NM_001177800		Approved	ACRP30, AdipoQ, apM1, GBP28, adiponectin	uc003fra.3	Q15848	OTTHUMG00000156521	ENST00000412955.2:c.45T>G	3.37:g.186570892T>G		Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	305	144	0.472131	NM_001177800	Q58EX9	Silent	SNP	ENST00000412955.2	37	CCDS3284.1																																																																																			T|0.885;G|0.115	0.115	strong		0.622	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344490.2	NM_004797	
NPNT	255743	hgsc.bcm.edu	37	4	106819089	106819089	+	Silent	SNP	C	C	T	rs147630398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:106819089C>T	ENST00000379987.2	+	2	319	c.103C>T	c.(103-105)Cta>Tta	p.L35L	NPNT_ENST00000514622.1_Silent_p.L35L|NPNT_ENST00000506666.1_Silent_p.L35L|NPNT_ENST00000427316.2_Silent_p.L35L|NPNT_ENST00000453617.2_Silent_p.L35L|NPNT_ENST00000305572.8_Silent_p.L35L	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	35					branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		ATCGATTGGCCTATGTCGTTA	0.468													C|||	7	0.00139776	0.0	0.0029	5008	,	,		18023	0.0		0.002	False		,,,				2504	0.0031				p.L35L		Atlas-SNP	.											.	NPNT	69	.	0			c.C103T						PASS	.	C	,,,,	2,4404	4.2+/-10.8	0,2,2201	135.0	123.0	127.0		103,103,103,103,103	5.8	1.0	4	dbSNP_134	127	13,8587	9.8+/-36.6	0,13,4287	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPNT	NM_001033047.2,NM_001184690.1,NM_001184691.1,NM_001184692.1,NM_001184693.1	,,,,	0,15,6488	TT,TC,CC		0.1512,0.0454,0.1153	,,,,	35/566,35/583,35/596,35/537,35/567	106819089	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	255743	exon2			ATTGGCCTATGTC		CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07							27405	protein-coding gene	gene with protein product		610306				15754038	Standard	NM_001033047		Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000379987.2:c.103C>T	4.37:g.106819089C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	205	113	0.55122	NM_001184692	A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Silent	SNP	ENST00000379987.2	37	CCDS34046.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	6.225	0.409722	0.11812	4.54E-4	0.001512	ENSG00000168743	ENST00000514837	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	T	0.57592	0.2064	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59700	-0.7405	4	.	.	.	.	12.8916	0.58073	0.0:0.9222:0.0:0.0778	.	.	.	.	L	11	.	.	P	+	2	0	NPNT	107038538	1.000000	0.71417	1.000000	0.80357	0.488000	0.33401	1.277000	0.33167	2.746000	0.94184	0.655000	0.94253	CCT	C|0.999;T|0.001	0.001	strong		0.468	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1	NM_198278	
PCDHGB6	56100	hgsc.bcm.edu	37	5	140788264	140788264	+	Silent	SNP	C	C	T	rs58047392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140788264C>T	ENST00000520790.1	+	1	495	c.495C>T	c.(493-495)aaC>aaT	p.N165N	PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	165	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(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)			TAAACATAAACTCAATTAAAG	0.343													.|||	995	0.198682	0.3064	0.1902	5008	,	,		18324	0.1528		0.1014	False		,,,				2504	0.2065				p.N165N		Atlas-SNP	.											.	PCDHGB6	120	.	0			c.C495T						PASS	.	C	,,,,,,,,,,,,,,,	1141,2505		187,767,869	30.0	30.0	30.0		,,,,,,,,,,,,,495,,495	3.2	0.9	5	dbSNP_129	30	1000,7176		63,874,3151	no	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032100.1	,,,,,,,,,,,,,,,	250,1641,4020	TT,TC,CC		12.2309,31.2946,18.1103	,,,,,,,,,,,,,,,	,,,,,,,,,,,,,165/931,,165/821	140788264	2141,9681	1823	4088	5911	SO:0001819	synonymous_variant	56100	exon1			CATAAACTCAATT	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.495C>T	5.37:g.140788264C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_032100	Q9Y5C5	Silent	SNP	ENST00000520790.1	37	CCDS54929.1																																																																																			C|0.824;T|0.176	0.176	strong		0.343	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926	
DTX2	113878	hgsc.bcm.edu	37	7	76109877	76109877	+	Silent	SNP	G	G	A	rs149301449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:76109877G>A	ENST00000324432.5	+	4	561	c.51G>A	c.(49-51)gcG>gcA	p.A17A	DTX2_ENST00000446600.1_Intron|DTX2_ENST00000446820.2_Silent_p.A17A|DTX2_ENST00000413936.2_Silent_p.A17A|DTX2_ENST00000430490.2_Silent_p.A17A|AC007078.4_ENST00000479299.2_RNA|DTX2_ENST00000472426.1_3'UTR|DTX2_ENST00000307569.8_Silent_p.A17A	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	17	WWE 1. {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						CCAGCCCCGCGGCTGTGGCCG	0.642													.|||	15	0.00299521	0.0083	0.0014	5008	,	,		18307	0.003		0.0	False		,,,				2504	0.0				p.A17A		Atlas-SNP	.											.	DTX2	64	.	0			c.G51A						PASS	.	G	,,,	16,4390		0,16,2187	28.0	29.0	29.0		51,51,51,51	4.2	1.0	7	dbSNP_134	29	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	0,16,6483	AA,AG,GG		0.0,0.3631,0.1231	,,,	17/623,17/623,17/576,17/623	76109877	16,12982	2203	4296	6499	SO:0001819	synonymous_variant	113878	exon1			CCCCGCGGCTGTG		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.51G>A	7.37:g.76109877G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	238	135	0.567227	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			G|0.997;A|0.003	0.003	strong		0.642	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
AKNA	80709	hgsc.bcm.edu	37	9	117130838	117130838	+	Missense_Mutation	SNP	C	C	T	rs138188658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117130838C>T	ENST00000307564.4	-	5	1615	c.1454G>A	c.(1453-1455)aGc>aAc	p.S485N	AKNA_ENST00000223791.3_5'UTR|AKNA_ENST00000374075.5_Missense_Mutation_p.S404N|AKNA_ENST00000374088.3_Missense_Mutation_p.S485N|AKNA_ENST00000312033.3_Missense_Mutation_p.S485N	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	485					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						CGTGTGGATGCTGTGGTTGGG	0.652													C|||	18	0.00359425	0.0113	0.0029	5008	,	,		18213	0.0		0.001	False		,,,				2504	0.0				p.S485N		Atlas-SNP	.											.	AKNA	119	.	0			c.G1454A						PASS	.	C	ASN/SER	61,4345	56.8+/-93.2	0,61,2142	80.0	54.0	63.0		1454	4.0	0.6	9	dbSNP_134	63	0,8600		0,0,4300	yes	missense	AKNA	NM_030767.4	46	0,61,6442	TT,TC,CC		0.0,1.3845,0.469	probably-damaging	485/1440	117130838	61,12945	2203	4300	6503	SO:0001583	missense	80709	exon5			TGGATGCTGTGGT	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.1454G>A	9.37:g.117130838C>T	ENSP00000303769:p.Ser485Asn	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	120	66	0.55	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	5	0.0022893772893772895	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	0	0.0	C	6.631	0.484937	0.12641	0.013845	0.0	ENSG00000106948	ENST00000307564;ENST00000394582;ENST00000374088;ENST00000374075;ENST00000312033	T;T;T;T	0.33654	2.63;2.63;2.63;1.4	4.87	3.97	0.46021	.	0.575422	0.18059	N	0.153006	T	0.23886	0.0578	L	0.56769	1.78	0.09310	N	0.999995	B;B	0.30937	0.079;0.301	B;B	0.27715	0.037;0.082	T	0.15780	-1.0425	10	0.41790	T	0.15	-10.4751	7.9366	0.29933	0.1595:0.755:0.0:0.0855	.	485;404	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	N	485;326;485;404;485	ENSP00000303769:S485N;ENSP00000363201:S485N;ENSP00000363188:S404N;ENSP00000309222:S485N	ENSP00000303769:S485N	S	-	2	0	AKNA	116170659	0.924000	0.31332	0.604000	0.28916	0.007000	0.05969	0.647000	0.24812	1.279000	0.44446	-0.140000	0.14226	AGC	C|0.996;T|0.004	0.004	strong		0.652	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632820	32632820	+	Missense_Mutation	SNP	C	C	G	rs1130375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32632820C>G	ENST00000399084.1	-	3	312	c.134G>C	c.(133-135)gGc>gCc	p.G45A	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.G45A|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.G45A|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.G45A			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	40	0	0		WXS	Illumina HiSeq	Phase_I	25	24	0.96	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	
VSIG10	54621	hgsc.bcm.edu	37	12	118511726	118511726	+	Missense_Mutation	SNP	C	C	T	rs9668527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:118511726C>T	ENST00000359236.5	-	5	1273	c.997G>A	c.(997-999)Gtg>Atg	p.V333M		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	333	Ig-like C2-type 4.		V -> M (in dbSNP:rs9668527).			integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						GCCCCAGACACCTGGCATGTA	0.567													C|||	297	0.0593051	0.1089	0.0331	5008	,	,		18792	0.1071		0.001	False		,,,				2504	0.0215				p.V333M		Atlas-SNP	.											.	VSIG10	41	.	0			c.G997A						PASS	.	C	MET/VAL	357,3523		18,321,1601	51.0	51.0	51.0		997	4.6	1.0	12	dbSNP_119	51	11,8293		0,11,4141	yes	missense	VSIG10	NM_019086.5	21	18,332,5742	TT,TC,CC		0.1325,9.201,3.0204	probably-damaging	333/541	118511726	368,11816	1940	4152	6092	SO:0001583	missense	54621	exon5			CAGACACCTGGCA		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.997G>A	12.37:g.118511726C>T	ENSP00000352172:p.Val333Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_019086	Q9NWQ7	Missense_Mutation	SNP	ENST00000359236.5	37	CCDS44992.1	132	0.06043956043956044	60	0.12195121951219512	10	0.027624309392265192	62	0.10839160839160839	0	0.0	C	17.32	3.358775	0.61403	0.09201	0.001325	ENSG00000176834	ENST00000359236	T	0.75154	-0.91	5.52	4.57	0.56435	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.188421	0.26079	N	0.026463	T	0.09247	0.0228	M	0.86343	2.81	0.34487	P	0.29544800000000004	D	0.89917	1.0	D	0.81914	0.995	T	0.64101	-0.6486	9	0.56958	D	0.05	-22.4971	11.6729	0.51413	0.1376:0.7294:0.133:0.0	rs9668527;rs52810002;rs9668527	333	Q8N0Z9	VSI10_HUMAN	M	333	ENSP00000352172:V333M	ENSP00000352172:V333M	V	-	1	0	VSIG10	116996109	0.578000	0.26717	0.955000	0.39395	0.722000	0.41435	1.748000	0.38308	2.626000	0.88956	0.555000	0.69702	GTG	C|0.937;T|0.063	0.063	strong		0.567	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
C9orf114	51490	hgsc.bcm.edu	37	9	131588888	131588888	+	Missense_Mutation	SNP	G	G	C	rs6478854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131588888G>C	ENST00000361256.5	-	5	429	c.389C>G	c.(388-390)aCa>aGa	p.T130R		NM_016390.3	NP_057474.2	Q5T280	CI114_HUMAN	chromosome 9 open reading frame 114	130			T -> R (in dbSNP:rs6478854). {ECO:0000269|PubMed:15489334}.				poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(4)|ovary(1)	7						CCCAACTCCTGTGAATTCCCC	0.587													G|||	2311	0.461462	0.7602	0.2536	5008	,	,		18444	0.3601		0.2942	False		,,,				2504	0.4816				p.T130R		Atlas-SNP	.											.	C9orf114	28	.	0			c.C389G						PASS	.	G	ARG/THR	2973,1433	683.1+/-404.2	996,981,226	56.0	56.0	56.0		389	-4.3	0.9	9	dbSNP_116	56	2493,6107	409.2+/-349.7	337,1819,2144	yes	missense	C9orf114	NM_016390.2	71	1333,2800,2370	CC,CG,GG		28.9884,32.5238,42.0268	benign	130/377	131588888	5466,7540	2203	4300	6503	SO:0001583	missense	51490	exon5			ACTCCTGTGAATT		CCDS6913.1	9q34.11	2014-05-29			ENSG00000198917	ENSG00000198917			26933	protein-coding gene	gene with protein product	"""centromere protein 32"""					20813266	Standard	NM_016390		Approved	HSPC109, CENP-32	uc004bwd.3	Q5T280	OTTHUMG00000020762	ENST00000361256.5:c.389C>G	9.37:g.131588888G>C	ENSP00000354812:p.Thr130Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	49	12	0.244898	NM_016390	Q0D2P6|Q6P469|Q6PGP9|Q6PIJ1|Q6PJV9	Missense_Mutation	SNP	ENST00000361256.5	37	CCDS6913.1	870|870	0.3983516483516483|0.3983516483516483	370|370	0.7520325203252033|0.7520325203252033	101|101	0.27900552486187846|0.27900552486187846	208|208	0.36363636363636365|0.36363636363636365	191|191	0.2519788918205805|0.2519788918205805	G|G	10.12|10.12	1.263936|1.263936	0.23136|0.23136	0.674762|0.674762	0.289884|0.289884	ENSG00000198917|ENSG00000198917	ENST00000372618|ENST00000361256	.|T	.|0.41065	.|1.01	5.62|5.62	-4.31|-4.31	0.03698|0.03698	.|.	0.428510|.	0.28914|.	N|.	0.013729|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.39633|0.39633	1.23|1.23	0.52099|0.52099	P|P	5.999999999994898E-5|5.999999999994898E-5	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	T|T	0.44436|0.44436	-0.9328|-0.9328	6|8	0.02654|0.15952	T|T	1|0.53	-0.1618|-0.1618	1.7504|1.7504	0.02970|0.02970	0.2463:0.1486:0.1088:0.4963|0.2463:0.1486:0.1088:0.4963	rs6478854;rs11540575;rs17855860;rs56866944;rs6478854|rs6478854;rs11540575;rs17855860;rs56866944;rs6478854	.|130	.|Q5T280	.|CI114_HUMAN	E|R	130|130	.|ENSP00000354812:T130R	ENSP00000361701:Q130E|ENSP00000354812:T130R	Q|T	-|-	1|2	0|0	C9orf114|C9orf114	130628709|130628709	0.001000|0.001000	0.12720|0.12720	0.892000|0.892000	0.35008|0.35008	0.880000|0.880000	0.50808|0.50808	-0.159000|-0.159000	0.10056|0.10056	-0.654000|-0.654000	0.05394|0.05394	-0.143000|-0.143000	0.13931|0.13931	CAG|ACA	G|0.583;C|0.417	0.417	strong		0.587	C9orf114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054500.1	NM_016390	
CCDC37	348807	hgsc.bcm.edu	37	3	126137456	126137456	+	Silent	SNP	T	T	C	rs76764772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126137456T>C	ENST00000352312.1	+	7	588	c.489T>C	c.(487-489)taT>taC	p.Y163Y	CCDC37_ENST00000393425.1_Silent_p.Y164Y|CCDC37_ENST00000505024.1_Silent_p.Y164Y	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	163										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		GCCCCCAGTATGCCCTGGATG	0.667													T|||	283	0.0565096	0.2057	0.0159	5008	,	,		14709	0.0		0.0	False		,,,				2504	0.0				p.Y163Y		Atlas-SNP	.											.	CCDC37	69	.	0			c.T489C						PASS	.	T		794,3608		80,634,1487	34.0	36.0	35.0		489	-6.4	0.0	3	dbSNP_131	35	10,8588		0,10,4289	no	coding-synonymous	CCDC37	NM_182628.2		80,644,5776	CC,CT,TT		0.1163,18.0373,6.1846		163/612	126137456	804,12196	2201	4299	6500	SO:0001819	synonymous_variant	348807	exon7			CCAGTATGCCCTG	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.489T>C	3.37:g.126137456T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																			T|0.941;C|0.059	0.059	strong		0.667	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
POTEG	404785	hgsc.bcm.edu	37	14	19553677	19553677	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:19553677C>T	ENST00000409832.3	+	1	313	c.261C>T	c.(259-261)gaC>gaT	p.D87D		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	87										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						GAGACCACGACGACTCTGCTA	0.612																																					p.D87D		Atlas-SNP	.											POTEG,NS,carcinoma,0,2	POTEG	118	2	0			c.C261T						scavenged	.						74.0	96.0	89.0					14																	19553677		1962	4007	5969	SO:0001819	synonymous_variant	404785	exon1			CCACGACGACTCT		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.261C>T	14.37:g.19553677C>T		Somatic	704	1	0.00142045		WXS	Illumina HiSeq	Phase_I	1110	83	0.0747748	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Silent	SNP	ENST00000409832.3	37	CCDS32018.1																																																																																			.	.	none		0.612	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
USP40	55230	hgsc.bcm.edu	37	2	234394487	234394487	+	Missense_Mutation	SNP	G	G	A	rs1048603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234394487G>A	ENST00000427112.2	-	28	3366	c.3331C>T	c.(3331-3333)Cgt>Tgt	p.R1111C	USP40_ENST00000450966.1_Missense_Mutation_p.R1123C|USP40_ENST00000251722.6_Missense_Mutation_p.R1111C|USP40_ENST00000496298.1_5'UTR			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1111			R -> C (in dbSNP:rs1048603).		ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		ACGGGAAGACGATAGAAATCG	0.562													A|||	2004	0.40016	0.7489	0.2709	5008	,	,		17737	0.1944		0.3618	False		,,,				2504	0.272				p.R1123C		Atlas-SNP	.											.	USP40	174	.	0			c.C3367T						PASS	.	A	CYS/ARG	2480,1328		819,842,243	21.0	24.0	23.0		3367	-2.4	0.0	2	dbSNP_86	23	2595,5643		414,1767,1938	yes	missense	USP40	NM_018218.2	180	1233,2609,2181	AA,AG,GG		31.5004,34.8739,42.1302	benign	1123/1248	234394487	5075,6971	1904	4119	6023	SO:0001583	missense	55230	exon28			GAAGACGATAGAA	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3331C>T	2.37:g.234394487G>A	ENSP00000387898:p.Arg1111Cys	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	238	238	1	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	805	0.3685897435897436	351	0.7134146341463414	96	0.26519337016574585	96	0.16783216783216784	262	0.34564643799472294	A	7.624	0.677480	0.14841	0.651261	0.315004	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.04603	3.59;3.59;3.59	5.75	-2.41	0.06562	.	1.068780	0.07073	N	0.835760	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.22800	-1.0206	9	0.45353	T	0.12	.	12.5667	0.56314	0.429:0.5121:0.0588:0.0	rs1048603;rs3188607;rs17668936;rs52816184;rs58082988;rs1048603	1123	Q9NVE5-3	.	C	1123;1111;1111	ENSP00000415434:R1123C;ENSP00000251722:R1111C;ENSP00000387898:R1111C	ENSP00000251722:R1111C	R	-	1	0	USP40	234059226	0.316000	0.24580	0.000000	0.03702	0.138000	0.21146	0.262000	0.18460	-0.485000	0.06754	-1.189000	0.01698	CGT	G|0.604;T|0.006	.	strong		0.562	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
UHMK1	127933	hgsc.bcm.edu	37	1	162467927	162467927	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:162467927C>G	ENST00000489294.1	+	1	295	c.137C>G	c.(136-138)cCt>cGt	p.P46R	UHMK1_ENST00000538489.1_Missense_Mutation_p.P46R|UHMK1_ENST00000282169.8_3'UTR|UHMK1_ENST00000545294.1_Intron	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	46	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)			endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			TGCGGCAACCCTGGCTCGCCC	0.697																																					p.P46R		Atlas-SNP	.											UHMK1_ENST00000489294,NS,carcinoma,0,2	UHMK1	65	2	0			c.C137G						PASS	.						11.0	14.0	13.0					1																	162467927		2186	4284	6470	SO:0001583	missense	127933	exon1			GCAACCCTGGCTC	BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332		"""RNA binding motif (RRM) containing"""	19683	protein-coding gene	gene with protein product		608849				12093740, 12782393	Standard	NM_175866		Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.137C>G	1.37:g.162467927C>G	ENSP00000420270:p.Pro46Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_175866	A8K8K4|G3V1M1|Q96C22	Missense_Mutation	SNP	ENST00000489294.1	37	CCDS1239.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.374293	0.42105	.	.	ENSG00000152332	ENST00000538489;ENST00000489294	T;T	0.19669	2.13;2.13	4.94	4.94	0.65067	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.064455	0.64402	D	0.000006	T	0.05044	0.0135	N	0.16166	0.38	.	.	.	P;B	0.35821	0.523;0.324	B;B	0.24541	0.054;0.053	T	0.23332	-1.0191	9	0.39692	T	0.17	-9.9211	13.8569	0.63534	0.0:1.0:0.0:0.0	.	46;46	Q8TAS1-2;Q8TAS1	.;UHMK1_HUMAN	R	46	ENSP00000446416:P46R;ENSP00000420270:P46R	ENSP00000420270:P46R	P	+	2	0	UHMK1	160734551	0.781000	0.28676	0.811000	0.32455	0.991000	0.79684	3.781000	0.55394	2.715000	0.92844	0.655000	0.94253	CCT	.	.	none		0.697	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076788.1	NM_175866	
CLEC4F	165530	hgsc.bcm.edu	37	2	71046536	71046536	+	Silent	SNP	G	G	A	rs17006361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71046536G>A	ENST00000272367.2	-	3	295	c.219C>T	c.(217-219)gcC>gcT	p.A73A	CLEC4F_ENST00000426626.1_Silent_p.A73A	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	73					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						CCAGAATTACGGCTTGCACAG	0.532													A|||	198	0.0395367	0.143	0.013	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.A73A	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											CLEC4F,NS,carcinoma,0,3	CLEC4F	95	3	0			c.C219T						PASS	.	A		584,3822	259.8+/-263.3	32,520,1651	124.0	107.0	112.0		219	-0.0	0.0	2	dbSNP_123	112	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CLEC4F	NM_173535.2		32,523,5948	AA,AG,GG		0.0349,13.2547,4.5133		73/590	71046536	587,12419	2203	4300	6503	SO:0001819	synonymous_variant	165530	exon3			AATTACGGCTTGC	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.219C>T	2.37:g.71046536G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	167	85	0.508982	NM_173535	A4QPA5	Silent	SNP	ENST00000272367.2	37	CCDS1910.1																																																																																			G|0.948;A|0.052	0.052	strong		0.532	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102514227	102514227	+	Silent	SNP	T	T	C	rs13749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102514227T>C	ENST00000360184.4	+	73	13244	c.13080T>C	c.(13078-13080)acT>acC	p.T4360T	RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557242.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4360					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.T4360T(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ACGCAGAGACTGAGAAGAAGA	0.597													C|||	1739	0.347244	0.6505	0.2392	5008	,	,		15280	0.2897		0.1421	False		,,,				2504	0.2843				p.T4360T		Atlas-SNP	.											DYNC1H1,NS,carcinoma,0,1	DYNC1H1	395	1	1	Substitution - coding silent(1)	stomach(1)	c.T13080C						scavenged	.	C		2522,1884	542.8+/-376.1	727,1068,408	160.0	107.0	125.0		13080	-8.9	0.5	14	dbSNP_52	125	1427,7173	752.5+/-407.4	137,1153,3010	no	coding-synonymous	DYNC1H1	NM_001376.4		864,2221,3418	CC,CT,TT		16.593,42.7599,30.3629		4360/4647	102514227	3949,9057	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon73			AGAGACTGAGAAG	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.13080T>C	14.37:g.102514227T>C		Somatic	60	1	0.0166667		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			T|0.681;C|0.319	0.319	strong		0.597	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
ALK	238	hgsc.bcm.edu	37	2	30143259	30143259	+	Silent	SNP	G	G	T	rs192127241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:30143259G>T	ENST00000389048.3	-	1	1173	c.267C>A	c.(265-267)ggC>ggA	p.G89G	ALK_ENST00000431873.1_Silent_p.G89G	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	89					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)	GAGCTAGCGAGCCGCGGGCCT	0.721			"""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				G|||	16	0.00319489	0.0113	0.0014	5008	,	,		11936	0.0		0.0	False		,,,				2504	0.0				p.G89G		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C267A						PASS	.	G		73,4275		0,73,2101	12.0	14.0	13.0		267	2.2	0.3	2		13	0,8484		0,0,4242	no	coding-synonymous	ALK	NM_004304.4		0,73,6343	TT,TG,GG		0.0,1.6789,0.5689		89/1621	30143259	73,12759	2174	4242	6416	SO:0001819	synonymous_variant	238	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TAGCGAGCCGCGG	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.267C>A	2.37:g.30143259G>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.998;T|0.002	0.002	strong		0.721	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
APEH	327	hgsc.bcm.edu	37	3	49721798	49721798	+	IGR	SNP	C	C	A	rs13085791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49721798C>A	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Silent_p.R655R|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TCTCACTCTCCCGCACACGTC	0.597													C|||	1046	0.208866	0.2632	0.1729	5008	,	,		21198	0.0565		0.3241	False		,,,				2504	0.1994				p.R655R		Atlas-SNP	.											.	MST1	84	.	0			c.G1965T						PASS	.	C		1184,3222	408.9+/-334.8	153,878,1172	55.0	57.0	56.0		1965	-6.0	0.0	3	dbSNP_121	56	2576,6024	406.4+/-348.8	399,1778,2123	no	coding-synonymous	MST1	NM_020998.3		552,2656,3295	AA,AC,CC		29.9535,26.8724,28.9097		655/726	49721798	3760,9246	2203	4300	6503	SO:0001628	intergenic_variant	4485	exon17			ACTCTCCCGCACA	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49721798C>A		Somatic	372	1	0.00268817		WXS	Illumina HiSeq	Phase_I	367	189	0.514986	NM_020998	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	37	CCDS2801.1	515	0.2358058608058608	148	0.3008130081300813	83	0.2292817679558011	37	0.06468531468531469	247	0.3258575197889182	C	5.900	0.350100	0.11182	0.268724	0.299535	ENSG00000173531	ENST00000448220	.	.	.	5.59	-5.99	0.02213	.	.	.	.	.	.	.	.	.	.	.	0.23023	P	0.99841852	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.6906	0.02851	0.1818:0.3582:0.266:0.194	rs13085791;rs13085791	.	.	.	X	125	.	.	G	-	1	0	MST1	49696802	0.000000	0.05858	0.001000	0.08648	0.939000	0.58152	-1.124000	0.03260	-1.376000	0.02126	0.655000	0.94253	GGA	C|0.725;A|0.275	0.275	strong		0.597	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
OR8B12	219858	hgsc.bcm.edu	37	11	124413491	124413491	+	Silent	SNP	C	C	T	rs61746453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124413491C>T	ENST00000306842.2	-	1	84	c.60G>A	c.(58-60)ccG>ccA	p.P20P		NM_001005195.1	NP_001005195.1	Q8NGG6	OR8BC_HUMAN	olfactory receptor, family 8, subfamily B, member 12	20						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)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		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;0.0213)		TCCGCAGTCCCGGCTGGTGGG	0.542													C|||	139	0.0277556	0.1021	0.0058	5008	,	,		18064	0.0		0.0	False		,,,				2504	0.0				p.P20P		Atlas-SNP	.											OR8B12,bladder,carcinoma,-1,1	OR8B12	66	1	0			c.G60A						PASS	.	C		321,4081	155.5+/-188.7	7,307,1887	47.0	51.0	49.0		60	-5.8	0.0	11	dbSNP_129	49	16,8582	10.5+/-38.8	0,16,4283	no	coding-synonymous	OR8B12	NM_001005195.1		7,323,6170	TT,TC,CC		0.1861,7.2921,2.5923		20/311	124413491	337,12663	2201	4299	6500	SO:0001819	synonymous_variant	219858	exon1			CAGTCCCGGCTGG		CCDS31711.1	11q24.2	2013-09-24			ENSG00000170953	ENSG00000170953		"""GPCR / Class A : Olfactory receptors"""	15307	protein-coding gene	gene with protein product							Standard	NM_001005195		Approved		uc010sam.2	Q8NGG6	OTTHUMG00000165922	ENST00000306842.2:c.60G>A	11.37:g.124413491C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001005195	B2RNF6|Q6IEW8|Q96RC7	Silent	SNP	ENST00000306842.2	37	CCDS31711.1																																																																																			C|0.974;T|0.026	0.026	strong		0.542	OR8B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387061.1		
PCNP	57092	hgsc.bcm.edu	37	3	101293097	101293097	+	Missense_Mutation	SNP	A	A	G	rs116752753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101293097A>G	ENST00000265260.3	+	1	159	c.38A>G	c.(37-39)aAg>aGg	p.K13R	PCNP_ENST00000486406.1_3'UTR|PCNP_ENST00000469941.1_5'UTR|PCNP_ENST00000296024.5_Missense_Mutation_p.K13R	NM_020357.1	NP_065090.1	Q8WW12	PCNP_HUMAN	PEST proteolytic signal containing nuclear protein	13					cell cycle (GO:0007049)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)				large_intestine(1)|lung(1)	2						AAGCCTGAAAAGTCGCAGCGA	0.677													A|||	49	0.00978435	0.0363	0.0014	5008	,	,		12760	0.0		0.0	False		,,,				2504	0.0				p.K13R		Atlas-SNP	.											.	PCNP	8	.	0			c.A38G						PASS	.	A	ARG/LYS	87,3257		0,87,1585	23.0	27.0	26.0		38	2.6	0.9	3	dbSNP_132	26	1,6167		0,1,3083	yes	missense	PCNP	NM_020357.1	26	0,88,4668	GG,GA,AA		0.0162,2.6017,0.9251	benign	13/179	101293097	88,9424	1672	3084	4756	SO:0001583	missense	57092	exon1			CTGAAAAGTCGCA		CCDS2942.1	3q12.3	2006-03-09			ENSG00000081154	ENSG00000081154			30023	protein-coding gene	gene with protein product		615210				12176013	Standard	NM_020357		Approved		uc003dva.3	Q8WW12	OTTHUMG00000159108	ENST00000265260.3:c.38A>G	3.37:g.101293097A>G	ENSP00000265260:p.Lys13Arg	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	210	114	0.542857	NM_020357	B2RBE7|D3DN52|Q53GF3|Q6AI44|Q96CU3|Q9NS81	Missense_Mutation	SNP	ENST00000265260.3	37	CCDS2942.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	A	15.73	2.921230	0.52653	0.026017	1.62E-4	ENSG00000081154	ENST00000265260;ENST00000296024	.	.	.	5.08	2.59	0.31030	.	2.264980	0.01941	N	0.041900	T	0.06735	0.0172	N	0.08118	0	0.27175	N	0.960801	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.14868	-1.0457	9	0.27785	T	0.31	.	1.8535	0.03174	0.5685:0.1752:0.0887:0.1676	.	13;13	Q8WW12-2;Q8WW12	.;PCNP_HUMAN	R	13	.	ENSP00000265260:K13R	K	+	2	0	PCNP	102775787	1.000000	0.71417	0.891000	0.34965	0.933000	0.57130	1.646000	0.37249	0.366000	0.24427	-0.336000	0.08194	AAG	A|0.993;G|0.007	0.007	strong		0.677	PCNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353338.2	NM_020357	
NCL	4691	hgsc.bcm.edu	37	2	232320281	232320281	+	Silent	SNP	G	G	A	rs78372304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:232320281G>A	ENST00000322723.4	-	13	2127	c.1887C>T	c.(1885-1887)gcC>gcT	p.A629A	SNORA75_ENST00000384158.1_RNA|SNORD20_ENST00000384550.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	629	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CGTCTTCCATGGCCTCCTTGG	0.488													.|||	26	0.00519169	0.0189	0.0014	5008	,	,		21137	0.0		0.0	False		,,,				2504	0.0				p.A629A		Atlas-SNP	.											.	NCL	80	.	0			c.C1887T						PASS	.	G		73,4333	65.3+/-102.7	2,69,2132	209.0	222.0	218.0		1887	2.1	1.0	2	dbSNP_131	218	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NCL	NM_005381.2		2,71,6430	AA,AG,GG		0.0233,1.6568,0.5767		629/711	232320281	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	4691	exon13			TTCCATGGCCTCC		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.1887C>T	2.37:g.232320281G>A		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	210	109	0.519048	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	37	CCDS33397.1																																																																																			G|0.994;A|0.006	0.006	strong		0.488	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381	
ZNF577	84765	hgsc.bcm.edu	37	19	52376126	52376126	+	Missense_Mutation	SNP	C	C	T	rs10407547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52376126C>T	ENST00000301399.5	-	7	1482	c.1117G>A	c.(1117-1119)Gag>Aag	p.E373K	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.E314K|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000451628.2_Missense_Mutation_p.E314K	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	373			E -> K (in dbSNP:rs10407547).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TGAGTTTTCTCATGTTTAATG	0.443													T|||	853	0.170327	0.2943	0.1427	5008	,	,		20105	0.0427		0.0358	False		,,,				2504	0.2924				p.E373K		Atlas-SNP	.											ZNF577,NS,carcinoma,+2,1	ZNF577	63	1	0			c.G1117A						PASS	.	T	LYS/GLU,LYS/GLU	1174,3232		166,842,1195	88.0	93.0	91.0		940,1117	0.6	0.0	19	dbSNP_119	91	165,8435		1,163,4136	yes	missense,missense	ZNF577	NM_001135590.1,NM_032679.2	56,56	167,1005,5331	TT,TC,CC		1.9186,26.6455,10.2952	benign,benign	314/427,373/486	52376126	1339,11667	2203	4300	6503	SO:0001583	missense	84765	exon7			TTTTCTCATGTTT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1117G>A	19.37:g.52376126C>T	ENSP00000301399:p.Glu373Lys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	121	47	0.38843	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	37	CCDS12842.2	219	0.10027472527472528	117	0.23780487804878048	50	0.13812154696132597	25	0.043706293706293704	27	0.03562005277044855	.	3.005	-0.205122	0.06180	0.266455	0.019186	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	3.06	0.647	0.17796	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00483	-1.445	0.54753	P	1.0999999999983245E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.34453	-0.9828	8	0.39692	T	0.17	.	4.5198	0.11954	0.0:0.2481:0.3579:0.394	rs10407547;rs52794334;rs10407547	373;314	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	K	373;314;314;373	ENSP00000301399:E373K;ENSP00000413476:E314K;ENSP00000389652:E314K;ENSP00000404509:E373K	ENSP00000301399:E373K	E	-	1	0	ZNF577	57067938	0.000000	0.05858	0.003000	0.11579	0.301000	0.27625	-0.180000	0.09754	-0.011000	0.14247	-0.254000	0.11334	GAG	C|0.892;T|0.108	0.108	strong		0.443	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
MYH6	4624	hgsc.bcm.edu	37	14	23861811	23861811	+	Missense_Mutation	SNP	A	A	G	rs365990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	167	0	0		WXS	Illumina HiSeq	Phase_I	177	83	0.468927	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		
LGI3	203190	hgsc.bcm.edu	37	8	22005939	22005939	+	Missense_Mutation	SNP	C	C	T	rs559732127		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22005939C>T	ENST00000306317.2	-	8	1670	c.1381G>A	c.(1381-1383)Gcc>Acc	p.A461T	LGI3_ENST00000424267.2_Missense_Mutation_p.A437T	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	461					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		GAGGGCAGGGCCTGCACCTCC	0.657													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15389	0.0		0.0	False		,,,				2504	0.0				p.A461T		Atlas-SNP	.											.	LGI3	44	.	0			c.G1381A						PASS	.						30.0	30.0	30.0					8																	22005939		2203	4300	6503	SO:0001583	missense	203190	exon8			GCAGGGCCTGCAC	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.1381G>A	8.37:g.22005939C>T	ENSP00000302297:p.Ala461Thr	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_139278	A5PLP2|Q86TL4|Q8N296	Missense_Mutation	SNP	ENST00000306317.2	37	CCDS6025.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.122032	0.37436	.	.	ENSG00000168481	ENST00000306317;ENST00000424267	T;T	0.78924	-1.22;-1.22	5.19	5.19	0.71726	Six-bladed beta-propeller, TolB-like (1);	0.062211	0.64402	D	0.000004	T	0.49372	0.1553	N	0.01686	-0.76	0.35162	D	0.770725	B;B	0.16396	0.017;0.008	B;B	0.18561	0.022;0.012	T	0.55970	-0.8056	10	0.12430	T	0.62	-31.0187	9.7807	0.40647	0.0:0.9063:0.0:0.0937	.	437;461	A5PLP2;Q8N145	.;LGI3_HUMAN	T	461;437	ENSP00000302297:A461T;ENSP00000399121:A437T	ENSP00000302297:A461T	A	-	1	0	LGI3	22061884	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.203000	0.51075	2.396000	0.81511	0.561000	0.74099	GCC	.	.	none		0.657	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1		
PRODH2	58510	hgsc.bcm.edu	37	19	36304143	36304143	+	Missense_Mutation	SNP	G	G	A	rs138605929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36304143G>A	ENST00000301175.3	-	1	58	c.41C>T	c.(40-42)tCc>tTc	p.S14F		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	14					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)			aacactttgggaggccaagac	0.423													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		21126	0.0		0.0	False		,,,				2504	0.0				p.S14F		Atlas-SNP	.											.	PRODH2	68	.	0			c.C41T						PASS	.	G	PHE/SER	79,4327	54.9+/-90.9	0,79,2124	60.0	54.0	56.0		41	0.4	0.0	19	dbSNP_134	56	0,8600		0,0,4300	no	missense	PRODH2	NM_021232.1	155	0,79,6424	AA,AG,GG		0.0,1.793,0.6074	possibly-damaging	14/537	36304143	79,12927	2203	4300	6503	SO:0001583	missense	58510	exon1			CTTTGGGAGGCCA	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.41C>T	19.37:g.36304143G>A	ENSP00000301175:p.Ser14Phe	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	43	28	0.651163	NM_021232		Missense_Mutation	SNP	ENST00000301175.3	37	CCDS12478.1	9	0.004120879120879121	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	G	6.284	0.420467	0.11928	0.01793	0.0	ENSG00000250799	ENST00000301175	T	0.06849	3.25	0.36	0.36	0.16097	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	P	0.39520	0.676	P	0.45558	0.485	T	0.41034	-0.9531	8	0.56958	D	0.05	.	.	.	.	.	14	Q9UF12	PROD2_HUMAN	F	14	ENSP00000301175:S14F	ENSP00000301175:S14F	S	-	2	0	PRODH2	40995983	0.037000	0.19845	0.031000	0.17742	0.030000	0.12068	0.477000	0.22196	0.469000	0.27268	0.472000	0.43445	TCC	G|0.992;A|0.008	0.008	strong		0.423	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	
NLN	57486	hgsc.bcm.edu	37	5	65084101	65084101	+	Missense_Mutation	SNP	A	A	G	rs6863012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:65084101A>G	ENST00000380985.5	+	8	1293	c.1115A>G	c.(1114-1116)aAg>aGg	p.K372R	NLN_ENST00000502464.1_Missense_Mutation_p.K268R	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	372			K -> R (in dbSNP:rs6863012).			mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		GAGGAACTCAAGTATTCCATA	0.408													A|||	276	0.0551118	0.1944	0.0202	5008	,	,		20583	0.0		0.004	False		,,,				2504	0.001				p.K372R		Atlas-SNP	.											.	NLN	51	.	0			c.A1115G						PASS	.	A	ARG/LYS	803,3603	319.3+/-296.1	63,677,1463	131.0	135.0	133.0		1115	6.1	1.0	5	dbSNP_116	133	32,8568	22.8+/-68.1	0,32,4268	yes	missense	NLN	NM_020726.4	26	63,709,5731	GG,GA,AA		0.3721,18.2251,6.4201	benign	372/705	65084101	835,12171	2203	4300	6503	SO:0001583	missense	57486	exon8			AACTCAAGTATTC	AJ300837	CCDS3989.1	5q12.3	2008-02-05	2005-03-31		ENSG00000123213	ENSG00000123213	3.4.24.16		16058	protein-coding gene	gene with protein product		611530	"""angiotensin binding protein"""	AGTBP		10574462	Standard	NM_020726		Approved	KIAA1226	uc003juf.3	Q9BYT8	OTTHUMG00000097803	ENST00000380985.5:c.1115A>G	5.37:g.65084101A>G	ENSP00000370372:p.Lys372Arg	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	170	88	0.517647	NM_020726	Q9ULJ4	Missense_Mutation	SNP	ENST00000380985.5	37	CCDS3989.1	108	0.04945054945054945	101	0.20528455284552846	7	0.019337016574585635	0	0.0	0	0.0	A	10.38	1.333268	0.24167	0.182251	0.003721	ENSG00000123213	ENST00000380985;ENST00000502464;ENST00000340159;ENST00000511299	T;T;T	0.08458	3.09;3.09;3.09	6.07	6.07	0.98685	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.045838	0.85682	D	0.000000	T	0.00012	0.0000	N	0.12961	0.28	0.19575	P	0.9999611304	B;B;D	0.64830	0.001;0.004;0.994	B;B;D	0.73708	0.001;0.008;0.981	T	0.56366	-0.7991	9	0.12430	T	0.62	-22.309	16.6406	0.85098	1.0:0.0:0.0:0.0	rs6863012;rs6863012	67;372;372	Q96K48;Q9BYT8;Q9BQD0	.;NEUL_HUMAN;.	R	372;268;372;100	ENSP00000370372:K372R;ENSP00000423214:K268R;ENSP00000427417:K100R	ENSP00000339283:K372R	K	+	2	0	NLN	65119857	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.934000	0.70138	2.326000	0.78906	0.533000	0.62120	AAG	A|0.936;G|0.064	0.064	strong		0.408	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1		
C4BPA	722	hgsc.bcm.edu	37	1	207305069	207305069	+	Silent	SNP	A	A	C	rs6663608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207305069A>C	ENST00000367070.3	+	8	1262	c.1068A>C	c.(1066-1068)ccA>ccC	p.P356P		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	356	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						GATGGACCCCATACCAAGGAT	0.368													A|||	276	0.0551118	0.1967	0.0187	5008	,	,		20256	0.0		0.001	False		,,,				2504	0.002				p.P356P		Atlas-SNP	.											.	C4BPA	70	.	0			c.A1068C						PASS	.	A		733,3673	284.3+/-277.5	69,595,1539	117.0	101.0	106.0		1068	-8.7	0.0	1	dbSNP_116	106	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	C4BPA	NM_000715.3		69,601,5833	CC,CA,AA		0.0698,16.6364,5.682		356/598	207305069	739,12267	2203	4300	6503	SO:0001819	synonymous_variant	722	exon8			GACCCCATACCAA	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"""complement component 4-binding protein, alpha"""	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.1068A>C	1.37:g.207305069A>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_000715	Q5VVQ8	Silent	SNP	ENST00000367070.3	37	CCDS1477.1																																																																																			A|0.930;C|0.070	0.070	strong		0.368	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		
COL6A5	256076	hgsc.bcm.edu	37	3	130188009	130188009	+	Silent	SNP	C	C	T	rs59160673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130188009C>T	ENST00000432398.2	+	38	7655	c.7161C>T	c.(7159-7161)ggC>ggT	p.G2387G	COL6A5_ENST00000265379.6_Silent_p.G2387G	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2387	Nonhelical region.|VWFA 10. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						TTTTTATTGGCCATGCCTTGC	0.388													C|||	67	0.0133786	0.0499	0.0014	5008	,	,		23052	0.0		0.0	False		,,,				2504	0.0				p.G2387G		Atlas-SNP	.											.	COL6A5	205	.	0			c.C7161T						PASS	.	C		164,3580		2,160,1710	118.0	106.0	110.0		7161	1.4	0.9	3	dbSNP_129	110	0,8222		0,0,4111	no	coding-synonymous	COL6A5	NM_153264.5		2,160,5821	TT,TC,CC		0.0,4.3803,1.3705		2387/2527	130188009	164,11802	1872	4111	5983	SO:0001819	synonymous_variant	256076	exon38			TATTGGCCATGCC	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.7161C>T	3.37:g.130188009C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37		19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	C	4.754	0.140218	0.09083	0.043803	0.0	ENSG00000172752	ENST00000512836	.	.	.	5.35	1.44	0.22558	.	.	.	.	.	T	0.22126	0.0533	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.10382	-1.0632	4	.	.	.	.	6.4978	0.22152	0.0:0.6424:0.1312:0.2264	rs59160673	.	.	.	S	639	.	.	P	+	1	0	COL6A5	131670699	0.738000	0.28186	0.950000	0.38849	0.667000	0.39255	-0.305000	0.08188	-0.018000	0.14079	-0.137000	0.14449	CCA	C|0.989;T|0.011	0.011	strong		0.388	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
ARSG	22901	hgsc.bcm.edu	37	17	66391232	66391232	+	Silent	SNP	A	A	G	rs7342975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66391232A>G	ENST00000448504.2	+	10	1906	c.1110A>G	c.(1108-1110)ccA>ccG	p.P370P	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Silent_p.P206P	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	370					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)			ACATTTTTCCAACTGTGGTAG	0.592													G|||	575	0.114816	0.2776	0.036	5008	,	,		20652	0.1478		0.0239	False		,,,				2504	0.0102				p.P370P		Atlas-SNP	.											.	ARSG	55	.	0			c.A1110G						PASS	.	G		1140,3266	715.3+/-408.5	152,836,1215	151.0	118.0	129.0		1110	2.0	1.0	17	dbSNP_116	129	121,8479	813.8+/-407.0	1,119,4180	no	coding-synonymous	ARSG	NM_014960.3		153,955,5395	GG,GA,AA		1.407,25.8738,9.6955		370/526	66391232	1261,11745	2203	4300	6503	SO:0001819	synonymous_variant	22901	exon10			TTTTCCAACTGTG	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.1110A>G	17.37:g.66391232A>G		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	220	104	0.472727	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	37	CCDS11676.1																																																																																			A|0.894;G|0.106	0.106	strong		0.592	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
TNS1	7145	hgsc.bcm.edu	37	2	218682771	218682771	+	Silent	SNP	A	A	G	rs3796026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218682771A>G	ENST00000171887.4	-	24	4424	c.3972T>C	c.(3970-3972)ggT>ggC	p.G1324G	TNS1_ENST00000419504.1_Silent_p.G1311G|TNS1_ENST00000430930.1_Silent_p.G1303G	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1324					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)		TAGAATAGCCACCATAGGCCA	0.657													A|||	1667	0.332867	0.2443	0.4121	5008	,	,		16095	0.246		0.4056	False		,,,				2504	0.411				p.G1324G		Atlas-SNP	.											.	TNS1	251	.	0			c.T3972C						PASS	.	A		1033,3371		148,737,1317	21.0	22.0	22.0		3972	-6.1	1.0	2	dbSNP_107	22	3418,5176		734,1950,1613	no	coding-synonymous	TNS1	NM_022648.4		882,2687,2930	GG,GA,AA		39.7719,23.4559,34.2437		1324/1736	218682771	4451,8547	2202	4297	6499	SO:0001819	synonymous_variant	7145	exon24			ATAGCCACCATAG	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.3972T>C	2.37:g.218682771A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			A|0.689;G|0.311	0.311	strong		0.657	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
MUC4	4585	hgsc.bcm.edu	37	3	195509170	195509170	+	Missense_Mutation	SNP	A	A	G	rs71634716|rs202189117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509170A>G	ENST00000463781.3	-	2	9740	c.9281T>C	c.(9280-9282)cTt>cCt	p.L3094P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L3094P	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)		TACTGAGGAAAGGCTGGTGAC	0.602																																					p.L3094P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.T9281C						scavenged	.						13.0	10.0	11.0					3																	195509170		667	1550	2217	SO:0001583	missense	4585	exon2			GAGGAAAGGCTGG	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.9281T>C	3.37:g.195509170A>G	ENSP00000417498:p.Leu3094Pro	Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	293	35	0.119454	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	6.319	0.427039	0.11987	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37235	1.27;1.21	1.18	1.18	0.20946	.	.	.	.	.	T	0.14485	0.0350	N	0.14661	0.345	0.30615	N	0.75912	P	0.47604	0.898	B	0.34180	0.177	T	0.13737	-1.0498	8	.	.	.	.	4.1756	0.10349	0.6345:0.3655:0.0:0.0	.	2966	E7ESK3	.	P	3094	ENSP00000417498:L3094P;ENSP00000420243:L3094P	.	L	-	2	0	MUC4	196993949	.	.	0.016000	0.15963	0.000000	0.00434	.	.	0.577000	0.29470	0.000000	0.15137	CTT	A|0.994;G|0.006	0.006	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OBFC1	79991	hgsc.bcm.edu	37	10	105657363	105657363	+	Silent	SNP	C	C	G	rs11191853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	87	0	0		WXS	Illumina HiSeq	Phase_I	117	115	0.982906	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	
ANKRD20A1	84210	hgsc.bcm.edu	37	9	67938633	67938633	+	Missense_Mutation	SNP	G	G	T	rs200989194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:67938633G>T	ENST00000377477.2	+	6	880	c.768G>T	c.(766-768)aaG>aaT	p.K256N	RNU6-368P_ENST00000391117.1_RNA	NM_032250.3	NP_115626.2	Q5TYW2	A20A1_HUMAN	ankyrin repeat domain 20 family, member A1	256						plasma membrane (GO:0005886)		p.K256N(2)		kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	11						AACATAAAAAGAAGATACTTA	0.249																																					p.K256N		Atlas-SNP	.											ANKRD20A1,bladder,carcinoma,0,3	ANKRD20A1	16	3	2	Substitution - Missense(2)	urinary_tract(1)|kidney(1)	c.G768T						scavenged	.						9.0	11.0	10.0					9																	67938633		1501	3099	4600	SO:0001583	missense	84210	exon6			TAAAAAGAAGATA	AL136793	CCDS6620.1	9p12	2014-04-16	2005-08-23	2005-08-23	ENSG00000196774	ENSG00000260691		"""Ankyrin repeat domain containing"""	23665	protein-coding gene	gene with protein product			"""ankyrin repeat domain 20A"""	ANKRD20A			Standard	NM_032250		Approved	DKFZp434A171		Q5TYW2	OTTHUMG00000188594	ENST00000377477.2:c.768G>T	9.37:g.67938633G>T	ENSP00000366697:p.Lys256Asn	Somatic	851	5	0.00587544		WXS	Illumina HiSeq	Phase_I	570	10	0.0175439	NM_032250	Q9H0H6	Missense_Mutation	SNP	ENST00000377477.2	37	CCDS6620.1	.	.	.	.	.	.	.	.	.	.	.	8.301	0.819993	0.16678	.	.	ENSG00000196774	ENST00000377477	T	0.37752	1.18	1.4	-1.97	0.07503	Ankyrin repeat-containing domain (2);	.	.	.	.	T	0.13372	0.0324	N	0.05230	-0.09	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.19745	-1.0296	9	0.29301	T	0.29	.	1.5748	0.02622	0.4716:0.0:0.2145:0.3139	.	256	Q5TYW2	A20A1_HUMAN	N	256	ENSP00000366697:K256N	ENSP00000366697:K256N	K	+	3	2	ANKRD20A1	67528453	0.778000	0.28640	0.019000	0.16419	0.050000	0.14768	0.163000	0.16520	-0.458000	0.07023	-1.594000	0.00841	AAG	G|0.990;T|0.010	0.010	strong		0.249	ANKRD20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083800.1		
GTPBP10	85865	hgsc.bcm.edu	37	7	89982132	89982132	+	Silent	SNP	T	T	C	rs6972561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	37	0	0	1271	WXS	Illumina HiSeq	Phase_I	47	28	0.595745	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	
LRP5L	91355	hgsc.bcm.edu	37	22	25753321	25753321	+	Silent	SNP	G	G	A	rs9624807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	169	0	0		WXS	Illumina HiSeq	Phase_I	209	102	0.488038	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	
APBA2	321	hgsc.bcm.edu	37	15	29347019	29347019	+	Missense_Mutation	SNP	T	T	C	rs8040932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:29347019T>C	ENST00000558402.1	+	5	1531	c.932T>C	c.(931-933)cTg>cCg	p.L311P	APBA2_ENST00000558259.1_Missense_Mutation_p.L311P|APBA2_ENST00000411764.1_Missense_Mutation_p.L311P|APBA2_ENST00000558330.1_Missense_Mutation_p.L311P|APBA2_ENST00000561069.1_Missense_Mutation_p.L311P			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	311			L -> P (in dbSNP:rs8040932). {ECO:0000269|PubMed:15489334}.		in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		GAAGAGAGGCTGAAGTGGCCC	0.657													C|||	1559	0.311302	0.7526	0.2161	5008	,	,		15988	0.1319		0.1889	False		,,,				2504	0.093				p.L311P		Atlas-SNP	.											.	APBA2	132	.	0			c.T932C						PASS	.	C	PRO/LEU,PRO/LEU	2931,1443		1016,899,272	15.0	18.0	17.0		932,932	4.2	1.0	15	dbSNP_116	17	1542,6980		153,1236,2872	yes	missense,missense	APBA2	NM_001130414.1,NM_005503.3	98,98	1169,2135,3144	CC,CT,TT		18.0943,32.9904,34.6852	benign,benign	311/738,311/750	29347019	4473,8423	2187	4261	6448	SO:0001583	missense	321	exon3			AGAGGCTGAAGTG	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.932T>C	15.37:g.29347019T>C	ENSP00000453293:p.Leu311Pro	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	660	0.3021978021978022	355	0.7215447154471545	84	0.23204419889502761	75	0.13111888111888112	146	0.19261213720316622	C	0.015	-1.548992	0.00926	0.670096	0.180943	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.20069	2.1	5.24	4.25	0.50352	.	0.127759	0.52532	N	0.000075	T	0.00012	0.0000	N	0.00230	-1.795	0.33447	P	0.41681199999999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37291	-0.9712	9	0.05833	T	0.94	.	6.1462	0.20287	0.3547:0.5468:0.0:0.0986	rs8040932;rs8040932	311;311	E9PGI4;Q99767	.;APBA2_HUMAN	P	311	ENSP00000409312:L311P	ENSP00000219865:L311P	L	+	2	0	APBA2	27134311	1.000000	0.71417	0.998000	0.56505	0.134000	0.20937	2.721000	0.47260	1.201000	0.43203	-0.128000	0.14901	CTG	T|0.681;C|0.319	0.319	strong		0.657	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
APPL1	26060	hgsc.bcm.edu	37	3	57303684	57303684	+	Missense_Mutation	SNP	A	A	G	rs11544593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:57303684A>G	ENST00000288266.3	+	22	2246	c.2099A>G	c.(2098-2100)gAa>gGa	p.E700G	ASB14_ENST00000487349.1_Intron|ASB14_ENST00000389601.3_Intron	NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	700			E -> G (in dbSNP:rs11544593).		apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)			breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		GATTTGGGAGAAGGAGGAAAG	0.443													A|||	364	0.0726837	0.0068	0.1282	5008	,	,		17962	0.004		0.159	False		,,,				2504	0.1043				p.E700G		Atlas-SNP	.											.	APPL1	59	.	0			c.A2099G						PASS	.	A	,GLY/GLU,	191,4215	121.7+/-159.2	3,185,2015	153.0	147.0	149.0		,2099,	5.7	1.0	3	dbSNP_120	149	1470,7130	279.9+/-294.2	132,1206,2962	yes	intron,missense,intron	APPL1,ASB14	NM_001142733.2,NM_012096.2,NM_130387.5	,98,	135,1391,4977	GG,GA,AA		17.093,4.335,12.771	,benign,	,700/710,	57303684	1661,11345	2203	4300	6503	SO:0001583	missense	26060	exon22			TGGGAGAAGGAGG	AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"""Pleckstrin homology (PH) domain containing"""	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.2099A>G	3.37:g.57303684A>G	ENSP00000288266:p.Glu700Gly	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_012096	Q9P2B9	Missense_Mutation	SNP	ENST00000288266.3	37	CCDS2882.1	191	0.08745421245421245	8	0.016260162601626018	54	0.14917127071823205	2	0.0034965034965034965	127	0.16754617414248021	A	11.55	1.671067	0.29693	0.04335	0.17093	ENSG00000157500	ENST00000288266	T	0.12361	2.69	5.65	5.65	0.86999	.	0.113216	0.64402	D	0.000012	T	0.00039	0.0001	L	0.29908	0.895	0.09310	P	1.0	P	0.34522	0.455	B	0.30105	0.111	T	0.36841	-0.9731	9	0.49607	T	0.09	.	16.1611	0.81712	1.0:0.0:0.0:0.0	rs11544593;rs61231163;rs11544593	700	Q9UKG1	DP13A_HUMAN	G	700	ENSP00000288266:E700G	ENSP00000288266:E700G	E	+	2	0	APPL1	57278724	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.689000	0.91265	2.272000	0.75746	0.460000	0.39030	GAA	A|0.892;G|0.108	0.108	strong		0.443	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096	
LRRC8C	84230	hgsc.bcm.edu	37	1	90179470	90179470	+	Silent	SNP	A	A	G	rs34576461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:90179470A>G	ENST00000370454.4	+	3	1596	c.1341A>G	c.(1339-1341)caA>caG	p.Q447Q	LRRC8C_ENST00000479252.1_Intron|RP11-302M6.4_ENST00000370453.5_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	447					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		CAGAGTTGCAATCTCTAAAAC	0.423													A|||	99	0.0197684	0.0703	0.0086	5008	,	,		19984	0.0		0.0	False		,,,				2504	0.0				p.Q447Q		Atlas-SNP	.											.	LRRC8C	73	.	0			c.A1341G						PASS	.	A		281,4125	158.5+/-191.2	11,259,1933	88.0	84.0	85.0		1341	-0.5	1.0	1	dbSNP_126	85	0,8600		0,0,4300	no	coding-synonymous	LRRC8C	NM_032270.4		11,259,6233	GG,GA,AA		0.0,6.3777,2.1605		447/804	90179470	281,12725	2203	4300	6503	SO:0001819	synonymous_variant	84230	exon3			GTTGCAATCTCTA		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"""hypothetical protein AD158"""	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.1341A>G	1.37:g.90179470A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_032270	B3KXS9|Q29RV6|Q9H075	Silent	SNP	ENST00000370454.4	37	CCDS725.1																																																																																			A|0.979;G|0.021	0.021	strong		0.423	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270	
MYO7B	4648	hgsc.bcm.edu	37	2	128364787	128364787	+	Missense_Mutation	SNP	G	G	C	rs201386852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128364787G>C	ENST00000409816.2	+	20	2463	c.2431G>C	c.(2431-2433)Gtg>Ctg	p.V811L	MYO7B_ENST00000389524.4_Missense_Mutation_p.V811L|MYO7B_ENST00000428314.1_Missense_Mutation_p.V811L			Q6PIF6	MYO7B_HUMAN	myosin VIIB	811	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GCAGATCCTCGTGGGCTTTGA	0.632													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17201	0.0		0.0	False		,,,				2504	0.0				p.V811L		Atlas-SNP	.											.	MYO7B	359	.	0			c.G2431C						PASS	.	G	LEU/VAL	8,3810		0,8,1901	7.0	9.0	8.0		2431	-6.2	0.1	2		8	0,7854		0,0,3927	yes	missense	MYO7B	NM_001080527.1	32	0,8,5828	CC,CG,GG		0.0,0.2095,0.0685	benign	811/2117	128364787	8,11664	1909	3927	5836	SO:0001583	missense	4648	exon21			ATCCTCGTGGGCT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.2431G>C	2.37:g.128364787G>C	ENSP00000386461:p.Val811Leu	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	180	93	0.516667	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	G	4.550	0.102047	0.08731	0.002095	0.0	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.86627	-2.15;-2.15;-2.15	5.6	-6.22	0.02058	.	0.757314	0.11581	N	0.549776	T	0.52901	0.1763	N	0.01352	-0.895	0.09310	N	0.999991	B	0.02656	0.0	B	0.04013	0.001	T	0.59177	-0.7503	10	0.07990	T	0.79	.	1.1174	0.01717	0.1671:0.2857:0.2377:0.3095	.	811	Q6PIF6	MYO7B_HUMAN	L	811	ENSP00000374175:V811L;ENSP00000415090:V811L;ENSP00000386461:V811L	ENSP00000374175:V811L	V	+	1	0	MYO7B	128081257	0.000000	0.05858	0.057000	0.19452	0.727000	0.41649	-0.731000	0.04909	-1.131000	0.02910	-0.344000	0.07964	GTG	.	.	weak		0.632	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
SBNO2	22904	hgsc.bcm.edu	37	19	1109577	1109577	+	Silent	SNP	C	C	T	rs200767766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1109577C>T	ENST00000361757.3	-	28	3381	c.3144G>A	c.(3142-3144)ctG>ctA	p.L1048L	SBNO2_ENST00000438103.2_Silent_p.L991L|SBNO2_ENST00000587024.1_Silent_p.L1038L	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	1048					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)		CCTCCCACTTCAGGCCGCGGT	0.697													C|||	31	0.0061901	0.0234	0.0	5008	,	,		7099	0.0		0.0	False		,,,				2504	0.0				p.L1048L		Atlas-SNP	.											.	SBNO2	112	.	0			c.G3144A						PASS	.	C	,	57,3687		0,57,1815	7.0	9.0	8.0		2973,3144	2.3	1.0	19		8	0,8122		0,0,4061	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	0,57,5876	TT,TC,CC		0.0,1.5224,0.4804	,	991/1310,1048/1367	1109577	57,11809	1872	4061	5933	SO:0001819	synonymous_variant	22904	exon28			CCACTTCAGGCCG	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.3144G>A	19.37:g.1109577C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			C|0.986;T|0.014	0.014	strong		0.697	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412138	105412138	+	Missense_Mutation	SNP	A	A	G	rs200384326		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105412138A>G	ENST00000333244.5	-	7	9769	c.9650T>C	c.(9649-9651)cTc>cCc	p.L3217P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3217						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)			AGCTCCCTCGAGAACGTGGCC	0.602																																					p.L3217P		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,neuroblastoma,0,1	AHNAK2	719	1	0			c.T9650C						PASS	.						112.0	72.0	85.0					14																	105412138		1914	4004	5918	SO:0001583	missense	113146	exon7			CCCTCGAGAACGT	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.9650T>C	14.37:g.105412138A>G	ENSP00000353114:p.Leu3217Pro	Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	335	30	0.0895522	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	2.736	-0.263306	0.05754	.	.	ENSG00000185567	ENST00000333244	T	0.00554	6.64	2.59	2.59	0.31030	.	.	.	.	.	T	0.00178	0.0005	N	0.00128	-2.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17837	-1.0356	8	0.30078	T	0.28	.	5.3502	0.16032	0.1716:0.0:0.8284:0.0	.	3217	Q8IVF2	AHNK2_HUMAN	P	3217	ENSP00000353114:L3217P	ENSP00000353114:L3217P	L	-	2	0	AHNAK2	104483183	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	-0.587000	0.05780	0.297000	0.22615	-0.971000	0.02607	CTC	.	.	weak		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TRDMT1	1787	hgsc.bcm.edu	37	10	17216556	17216556	+	Silent	SNP	C	C	T	rs2273734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:17216556C>T	ENST00000377799.3	-	2	215	c.168G>A	c.(166-168)acG>acA	p.T56T	TRDMT1_ENST00000351358.4_Silent_p.T56T|TRDMT1_ENST00000377766.5_Silent_p.T56T|TRDMT1_ENST00000488990.1_Silent_p.T56T|TRDMT1_ENST00000412821.3_Silent_p.T56T|TRDMT1_ENST00000457442.2_Missense_Mutation_p.R23Q|TRDMT1_ENST00000358282.7_Silent_p.T56T	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	56	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	TCACTTCAATCGTCTTGGCAA	0.383													T|||	1921	0.383586	0.4002	0.4265	5008	,	,		18412	0.2599		0.494	False		,,,				2504	0.3446				p.T56T		Atlas-SNP	.											.	TRDMT1	46	.	0			c.G168A						PASS	.	T		1874,2532	631.1+/-395.6	411,1052,740	130.0	114.0	119.0		168	-0.2	1.0	10	dbSNP_100	119	3900,4700	605.8+/-395.0	894,2112,1294	no	coding-synonymous	TRDMT1	NM_004412.5		1305,3164,2034	TT,TC,CC		45.3488,42.5329,44.3949		56/392	17216556	5774,7232	2203	4300	6503	SO:0001819	synonymous_variant	1787	exon2			TTCAATCGTCTTG	AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"""DNA (cytosine-5-)-methyltransferase 2"""	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.168G>A	10.37:g.17216556C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Silent	SNP	ENST00000377799.3	37	CCDS7114.1	842|842	0.38553113553113555|0.38553113553113555	175|175	0.3556910569105691|0.3556910569105691	158|158	0.43646408839779005|0.43646408839779005	147|147	0.256993006993007|0.256993006993007	362|362	0.47757255936675463|0.47757255936675463	T|T	1.165|1.165	-0.642762|-0.642762	0.03531|0.03531	0.425329|0.425329	0.453488|0.453488	ENSG00000107614|ENSG00000107614	ENST00000313936;ENST00000436968|ENST00000457442	.|T	.|0.42513	.|0.97	5.35|5.35	-0.151|-0.151	0.13411|0.13411	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999921|0.9999999999999921	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.44605|0.44605	-0.9317|-0.9317	3|7	.|0.87932	.|D	.|0	-12.7603|-12.7603	0.7609|0.7609	0.01007|0.01007	0.2203:0.1366:0.2313:0.4118|0.2203:0.1366:0.2313:0.4118	rs2273734;rs17465066;rs17854514;rs58298820;rs2273734|rs2273734;rs17465066;rs17854514;rs58298820;rs2273734	.|23	.|E7EMI8	.|.	N|Q	36|23	.|ENSP00000412256:R23Q	.|ENSP00000412256:R23Q	D|R	-|-	1|2	0|0	TRDMT1|TRDMT1	17256562|17256562	0.919000|0.919000	0.31177|0.31177	0.998000|0.998000	0.56505|0.56505	0.151000|0.151000	0.21798|0.21798	-0.303000|-0.303000	0.08210|0.08210	-0.112000|-0.112000	0.11979|0.11979	-1.584000|-1.584000	0.00852|0.00852	GAT|CGA	C|0.581;T|0.419	0.419	strong		0.383	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412	
OR10A4	283297	hgsc.bcm.edu	37	11	6898663	6898663	+	Missense_Mutation	SNP	G	G	A	rs10839635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	74	0	0		WXS	Illumina HiSeq	Phase_I	73	28	0.383562	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	
PLA2G4F	255189	hgsc.bcm.edu	37	15	42448659	42448659	+	Missense_Mutation	SNP	C	C	A	rs636604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42448659C>A	ENST00000382396.4	-	1	175	c.89G>T	c.(88-90)gGc>gTc	p.G30V	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.G30V			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	30			G -> V (in dbSNP:rs636604).		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)		CCACAGAGGGCCCCTCTTCTC	0.627													C|||	482	0.096246	0.1536	0.1268	5008	,	,		16677	0.0853		0.0089	False		,,,				2504	0.0982				p.G30V		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.G89T						PASS	.	C	VAL/GLY	509,3883		24,461,1711	22.0	20.0	21.0		89	-1.4	0.0	15	dbSNP_83	21	47,8517		0,47,4235	yes	missense	PLA2G4F	NM_213600.3	109	24,508,5946	AA,AC,CC		0.5488,11.5893,4.2914	possibly-damaging	30/850	42448659	556,12400	2196	4282	6478	SO:0001583	missense	255189	exon1			AGAGGGCCCCTCT		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.89G>T	15.37:g.42448659C>A	ENSP00000371833:p.Gly30Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_213600	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	37	CCDS32204.1	184	0.08424908424908426	79	0.16056910569105692	47	0.1298342541436464	53	0.09265734265734266	5	0.006596306068601583	C	9.721	1.159787	0.21454	0.115893	0.005488	ENSG00000168907	ENST00000397272;ENST00000382396;ENST00000357924;ENST00000443825	T;T	0.01397	4.94;4.98	5.41	-1.43	0.08884	.	0.682863	0.13279	N	0.399921	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	B	0.28713	0.22	B	0.27500	0.08	T	0.46925	-0.9156	9	0.59425	D	0.04	-0.0074	6.7828	0.23657	0.0:0.3251:0.129:0.5459	rs636604;rs52813203;rs636604	30	Q68DD2	PA24F_HUMAN	V	30	ENSP00000380442:G30V;ENSP00000371833:G30V	ENSP00000350604:G30V	G	-	2	0	PLA2G4F	40235951	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.066000	0.14489	-0.449000	0.07117	-0.136000	0.14681	GGC	C|0.939;A|0.061	0.061	strong		0.627	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
ADAM28	10863	hgsc.bcm.edu	37	8	24207399	24207399	+	Silent	SNP	G	G	C	rs7829944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24207399G>C	ENST00000265769.4	+	19	2123	c.2013G>C	c.(2011-2013)gtG>gtC	p.V671V	RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000397649.3_Missense_Mutation_p.A420P|RP11-624C23.1_ENST00000518988.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	671					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TGGTTGGGGTGCTGTTCCCAA	0.493													G|||	363	0.072484	0.0847	0.0173	5008	,	,		13610	0.1052		0.0298	False		,,,				2504	0.1053				p.V671V	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.G2013C						PASS	.	G		378,4028	190.5+/-216.4	15,348,1840	184.0	174.0	177.0		2013	3.2	1.0	8	dbSNP_116	177	239,8361	95.6+/-157.4	3,233,4064	no	coding-synonymous	ADAM28	NM_014265.4		18,581,5904	CC,CG,GG		2.7791,8.5792,4.744		671/776	24207399	617,12389	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon19			TGGGGTGCTGTTC	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.2013G>C	8.37:g.24207399G>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	140	62	0.442857	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1	148	0.06776556776556776	58	0.11788617886178862	6	0.016574585635359115	58	0.10139860139860139	26	0.03430079155672823	G	11.44	1.638722	0.29157	0.085792	0.027791	ENSG00000042980	ENST00000397649;ENST00000521629;ENST00000518326	T	0.02121	4.44	5.12	3.24	0.37175	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.45452	P	0.0015779999999999683	.	.	.	.	.	.	T	0.33266	-0.9875	5	0.72032	D	0.01	.	6.8032	0.23762	0.0951:0.0:0.7268:0.1781	rs7829944;rs7829944	.	.	.	P	420;304;97	ENSP00000380770:A420P	ENSP00000380770:A420P	A	+	1	0	ADAM28	24263344	1.000000	0.71417	0.999000	0.59377	0.052000	0.14988	1.615000	0.36922	1.257000	0.44085	0.442000	0.29010	GCT	G|0.947;C|0.053	0.053	strong		0.493	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
PIH1D1	55011	hgsc.bcm.edu	37	19	49950298	49950298	+	Missense_Mutation	SNP	C	C	T	rs13394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49950298C>T	ENST00000262265.5	-	7	905	c.670G>A	c.(670-672)Gtt>Att	p.V224I	PIH1D1_ENST00000596049.1_Missense_Mutation_p.V224I|PIH1D1_ENST00000602226.1_5'UTR	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	224			V -> I (in dbSNP:rs13394). {ECO:0000269|PubMed:15489334}.		box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		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;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		GGGAGGTCAACTTCGGCCAAG	0.592													T|||	3450	0.688898	0.9274	0.6441	5008	,	,		18710	0.4177		0.7545	False		,,,				2504	0.6104				p.V224I		Atlas-SNP	.											PIH1D1,bladder,carcinoma,+1,1	PIH1D1	23	1	0			c.G670A						PASS	.	T	ILE/VAL	3935,471	221.7+/-238.7	1757,421,25	111.0	113.0	113.0		670	2.7	1.0	19	dbSNP_52	113	6597,2003	350.3+/-327.8	2521,1555,224	yes	missense	PIH1D1	NM_017916.2	29	4278,1976,249	TT,TC,CC		23.2907,10.69,19.022	benign	224/291	49950298	10532,2474	2203	4300	6503	SO:0001583	missense	55011	exon7			GGTCAACTTCGGC	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.670G>A	19.37:g.49950298C>T	ENSP00000262265:p.Val224Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_017916	B4DGN7|B4E2X7|Q9BVL0	Missense_Mutation	SNP	ENST00000262265.5	37	CCDS12765.1	1476	0.6758241758241759	455	0.9247967479674797	240	0.6629834254143646	223	0.38986013986013984	558	0.7361477572559367	T	0.623	-0.820476	0.02755	0.8931	0.767093	ENSG00000104872	ENST00000262265	T	0.16196	2.36	4.76	2.67	0.31697	.	0.125124	0.51477	N	0.000095	T	0.00012	0.0000	N	0.05574	-0.02	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.38993	-0.9635	9	0.02654	T	1	-3.9055	5.9494	0.19237	0.0:0.3278:0.0:0.6722	rs13394;rs1127153;rs3182727;rs17239224;rs17357674;rs58359049;rs13394	224	Q9NWS0	PIHD1_HUMAN	I	224	ENSP00000262265:V224I	ENSP00000262265:V224I	V	-	1	0	PIH1D1	54642110	0.974000	0.33945	1.000000	0.80357	0.592000	0.36648	0.159000	0.16442	0.425000	0.26087	-0.254000	0.11334	GTT	C|0.264;N|0.000	.	strong		0.592	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916	
SGK223	157285	hgsc.bcm.edu	37	8	8176540	8176540	+	Silent	SNP	C	C	T	rs116402506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8176540C>T	ENST00000520004.1	-	6	3609	c.3345G>A	c.(3343-3345)gcG>gcA	p.A1115A	SGK223_ENST00000330777.4_Silent_p.A1115A			Q86YV5	SG223_HUMAN		1117	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCCGCTCGTACGCCTCGGGCT	0.667													C|||	318	0.0634984	0.2231	0.0274	5008	,	,		10206	0.0		0.003	False		,,,				2504	0.001				p.A1115A	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G3345A						PASS	.	C		726,3448		70,586,1431	77.0	86.0	83.0		3345	-11.0	0.0	8	dbSNP_132	83	13,8401		0,13,4194	no	coding-synonymous	SGK223	NM_001080826.1		70,599,5625	TT,TC,CC		0.1545,17.3934,5.8707		1115/1403	8176540	739,11849	2087	4207	6294	SO:0001819	synonymous_variant	0	exon5			CTCGTACGCCTCG																												ENST00000520004.1:c.3345G>A	8.37:g.8176540C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			C|0.970;T|0.030	0.030	strong		0.667	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
ZP1	22917	hgsc.bcm.edu	37	11	60642633	60642633	+	Silent	SNP	C	C	T	rs112864814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60642633C>T	ENST00000278853.5	+	11	1686	c.1686C>T	c.(1684-1686)gaC>gaT	p.D562D		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	562					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						ACCGTAATGACACTGCCAGGC	0.627													C|||	78	0.0155751	0.056	0.0029	5008	,	,		19463	0.0		0.002	False		,,,				2504	0.0				p.D562D		Atlas-SNP	.											.	ZP1	69	.	0			c.C1686T						PASS	.	C		240,4166	142.3+/-177.5	3,234,1966	69.0	73.0	72.0		1686	-4.2	0.0	11	dbSNP_132	72	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ZP1	NM_207341.2		3,235,6264	TT,TC,CC		0.0116,5.4471,1.8533		562/639	60642633	241,12763	2203	4299	6502	SO:0001819	synonymous_variant	22917	exon11			TAATGACACTGCC	BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"""Zona pellucida glycoproteins"""	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.1686C>T	11.37:g.60642633C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	126	60	0.47619	NM_207341		Silent	SNP	ENST00000278853.5	37	CCDS31572.1																																																																																			C|0.980;T|0.020	0.020	strong		0.627	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341	
LIPM	340654	hgsc.bcm.edu	37	10	90580012	90580012	+	Silent	SNP	C	C	T	rs12255753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90580012C>T	ENST00000404743.4	+	9	1193	c.1026C>T	c.(1024-1026)gtC>gtT	p.V342V	ANKRD22_ENST00000476963.1_5'Flank|LIPM_ENST00000539337.1_Silent_p.V302V	NM_001128215.1	NP_001121687.1	Q5VYY2	LIPM_HUMAN	lipase, family member M	342					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)|skin(1)	7						GGTACAGAGTCAGAGATATGA	0.428													C|||	166	0.033147	0.1225	0.0058	5008	,	,		21904	0.0		0.0	False		,,,				2504	0.0				p.V342V		Atlas-SNP	.											.	LIPM	17	.	0			c.C1026T						PASS	.	C	,	140,1244		8,124,560	87.0	72.0	77.0		1026,	-3.5	0.4	10	dbSNP_120	77	2,3180		0,2,1589	no	coding-synonymous,utr-3	ANKRD22,LIPM	NM_001128215.1,NM_144590.2	,	8,126,2149	TT,TC,CC		0.0629,10.1156,3.1099	,	342/424,	90580012	142,4424	692	1591	2283	SO:0001819	synonymous_variant	340654	exon9			CAGAGTCAGAGAT		CCDS44457.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000173239	ENSG00000173239			23455	protein-coding gene	gene with protein product		613923	"""lipase-like, ab-hydrolase domain containing 3"""	LIPL3			Standard	NM_001128215		Approved	bA304I5.1	uc009xtm.1	Q5VYY2	OTTHUMG00000018698	ENST00000404743.4:c.1026C>T	10.37:g.90580012C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	31	9	0.290323	NM_001128215	A6PVS3|B2RXK7|B5MCR3	Silent	SNP	ENST00000404743.4	37	CCDS44457.1																																																																																			C|0.969;T|0.031	0.031	strong		0.428	LIPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049261.3	XM_291663	
KCNK2	3776	hgsc.bcm.edu	37	1	215342573	215342573	+	Silent	SNP	C	C	T	rs17024342	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:215342573C>T	ENST00000444842.2	+	4	657	c.507C>T	c.(505-507)ggC>ggT	p.G169G	KCNK2_ENST00000391894.2_Silent_p.G154G|KCNK2_ENST00000391895.2_Silent_p.G165G	NM_001017425.2|NM_014217.3	NP_001017425.2|NP_055032.1	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2	169					G-protein coupled receptor signaling pathway (GO:0007186)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|potassium ion leak channel activity (GO:0022841)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)|Dronedarone(DB04855)	GCACAGAAGGCGGCAAAATAT	0.363													C|||	686	0.136981	0.4107	0.0504	5008	,	,		13682	0.004		0.0467	False		,,,				2504	0.0583				p.G169G		Atlas-SNP	.											.	KCNK2	135	.	0			c.C507T						PASS	.	C	,,	1433,2973	464.5+/-353.9	258,917,1028	150.0	154.0	153.0		495,507,462	-10.4	0.3	1	dbSNP_123	153	351,8249	117.7+/-177.3	3,345,3952	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNK2	NM_001017424.2,NM_001017425.2,NM_014217.3	,,	261,1262,4980	TT,TC,CC		4.0814,32.5238,13.7167	,,	165/423,169/427,154/412	215342573	1784,11222	2203	4300	6503	SO:0001819	synonymous_variant	3776	exon4			AGAAGGCGGCAAA	AF004711	CCDS31024.1, CCDS41466.1, CCDS41467.1	1q41	2012-03-07			ENSG00000082482	ENSG00000082482		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6277	protein-coding gene	gene with protein product		603219				9721223, 16382106	Standard	NM_001017424		Approved	K2p2.1, TREK-1	uc001hkr.4	O95069	OTTHUMG00000037017	ENST00000444842.2:c.507C>T	1.37:g.215342573C>T		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	217	95	0.437788	NM_001017425	A1Z1V3|A8K618|B2RCS4|B7ZL56|D3DTA5|Q5DP47|Q5DP48|Q9NRT2|Q9UNE3	Silent	SNP	ENST00000444842.2	37	CCDS41467.1	268	0.1227106227106227	206	0.4186991869918699	20	0.055248618784530384	2	0.0034965034965034965	40	0.052770448548812667	C	4.793	0.147440	0.09134	0.325238	0.040814	ENSG00000082482	ENST00000366948	.	.	.	6.16	-10.4	0.00318	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999838	.	.	.	.	.	.	T	0.31806	-0.9930	4	0.35671	T	0.21	.	4.9176	0.13853	0.249:0.0687:0.0939:0.5884	rs17024342;rs17024342	.	.	.	V	126	.	ENSP00000355915:A126V	A	+	2	0	KCNK2	213409196	0.176000	0.23096	0.271000	0.24616	0.932000	0.56968	-0.545000	0.06069	-1.555000	0.01697	-0.759000	0.03464	GCG	C|0.859;T|0.141	0.141	strong		0.363	KCNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089856.2	NM_014217	
FANCA	2175	hgsc.bcm.edu	37	16	89874756	89874756	+	Missense_Mutation	SNP	G	G	A	rs17232246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89874756G>A	ENST00000389301.3	-	6	572	c.542C>T	c.(541-543)gCg>gTg	p.A181V	FANCA_ENST00000534992.1_Missense_Mutation_p.A181V|FANCA_ENST00000563673.1_Missense_Mutation_p.A181V|FANCA_ENST00000389302.3_Missense_Mutation_p.A181V|FANCA_ENST00000543736.1_Missense_Mutation_p.A149V|FANCA_ENST00000568369.1_Missense_Mutation_p.A181V	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	181			A -> V (in FA; dbSNP:rs17232246).		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)		ATGCCACACCGCTTCAAGCAA	0.398			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	267	0.0533147	0.1959	0.0115	5008	,	,		18304	0.0		0.0	False		,,,				2504	0.0				p.A181V		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.C542T						PASS	.	G	VAL/ALA,VAL/ALA	738,3658	304.9+/-288.7	64,610,1524	137.0	129.0	131.0		542,542	2.8	0.3	16	dbSNP_123	131	4,8596	2.2+/-6.3	0,4,4296	yes	missense,missense	FANCA	NM_000135.2,NM_001018112.1	64,64	64,614,5820	AA,AG,GG		0.0465,16.788,5.7094	benign,benign	181/1456,181/298	89874756	742,12254	2198	4300	6498	SO:0001583	missense	2175	exon6	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CACACCGCTTCAA	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.542C>T	16.37:g.89874756G>A	ENSP00000373952:p.Ala181Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	194	87	0.448454	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	65	0.02976190476190476	61	0.12398373983739837	4	0.011049723756906077	0	0.0	0	0.0	G	7.667	0.686109	0.14973	0.16788	4.65E-4	ENSG00000187741	ENST00000389301;ENST00000389302;ENST00000534992;ENST00000543736	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.77	2.81	0.32909	.	0.147328	0.30879	N	0.008682	T	0.00109	0.0003	L	0.58669	1.825	0.32276	N	0.568249	P;B;B;B;B;P	0.48230	0.907;0.241;0.06;0.06;0.06;0.907	B;B;B;B;B;B	0.33295	0.161;0.064;0.012;0.019;0.012;0.161	T	0.04165	-1.0972	10	0.38643	T	0.18	-6.3506	9.5774	0.39465	0.1724:0.0:0.8276:0.0	rs17232246	181;149;181;181;181;181	B4DRI7;Q0VAP4;A0PJU8;F5H8D5;O15360-2;O15360	.;.;.;.;.;FANCA_HUMAN	V	181;181;181;149	ENSP00000373952:A181V;ENSP00000373953:A181V;ENSP00000443675:A181V;ENSP00000443409:A149V	ENSP00000373952:A181V	A	-	2	0	FANCA	88402257	0.730000	0.28100	0.335000	0.25508	0.047000	0.14425	0.788000	0.26872	0.517000	0.28361	-0.924000	0.02725	GCG	G|0.950;A|0.050	0.050	strong		0.398	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
ARHGEF10	9639	hgsc.bcm.edu	37	8	1905222	1905222	+	Silent	SNP	A	A	G	rs146227529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:1905222A>G	ENST00000398564.1	+	29	3903	c.3903A>G	c.(3901-3903)tcA>tcG	p.S1301S	ARHGEF10_ENST00000262112.6_Silent_p.S1272S|ARHGEF10_ENST00000520359.1_Silent_p.S1238S|ARHGEF10_ENST00000349830.3_Silent_p.S1276S|ARHGEF10_ENST00000521927.1_3'UTR|ARHGEF10_ENST00000518288.1_Silent_p.S1300S			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1301	Ser-rich.				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)		AGCACAGATCAGAGGACAGCA	0.572													A|||	16	0.00319489	0.0106	0.0029	5008	,	,		17994	0.0		0.0	False		,,,				2504	0.0				p.S1276S		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.A3828G						PASS	.	A		40,4366	44.6+/-78.6	1,38,2164	71.0	67.0	68.0		3828	-11.4	0.0	8	dbSNP_134	68	0,8600		0,0,4300	no	coding-synonymous	ARHGEF10	NM_014629.2		1,38,6464	GG,GA,AA		0.0,0.9079,0.3076		1276/1345	1905222	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon29			CAGATCAGAGGAC	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.3903A>G	8.37:g.1905222A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				A|0.996;G|0.004	0.004	strong		0.572	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
MYO5B	4645	hgsc.bcm.edu	37	18	47455923	47455923	+	Silent	SNP	C	C	T	rs2298628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47455923C>T	ENST00000285039.7	-	17	2348	c.2049G>A	c.(2047-2049)gtG>gtA	p.V683V		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	683	Myosin motor.				endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TCGTCTCCAACACCCCGCAGG	0.527													C|||	2060	0.411342	0.3782	0.3948	5008	,	,		15159	0.2688		0.5507	False		,,,				2504	0.4714				p.V683V		Atlas-SNP	.											.	MYO5B	178	.	0			c.G2049A						PASS	.	C		1662,2190		356,950,620	29.0	30.0	30.0		2049	2.5	0.9	18	dbSNP_100	30	4564,3704		1267,2030,837	no	coding-synonymous	MYO5B	NM_001080467.2		1623,2980,1457	TT,TC,CC		44.7992,43.1464,48.6304		683/1849	47455923	6226,5894	1926	4134	6060	SO:0001819	synonymous_variant	4645	exon17			CTCCAACACCCCG	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.2049G>A	18.37:g.47455923C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	44	26	0.590909	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			C|0.563;T|0.437	0.437	strong		0.527	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
CHRNA1	1134	hgsc.bcm.edu	37	2	175613477	175613477	+	Missense_Mutation	SNP	T	T	A	rs6739001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:175613477T>A	ENST00000261007.5	-	9	1214	c.1148A>T	c.(1147-1149)gAc>gTc	p.D383V	AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000348749.5_Missense_Mutation_p.D358V|CHRNA1_ENST00000409219.1_Intron|CHRNA1_ENST00000409542.1_Missense_Mutation_p.D276V	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	383			D -> V (in dbSNP:rs6739001).		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)	AATCTTTTTGTCTTGCTTTTC	0.408											OREG0015079	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	94	0.01877	0.0703	0.0014	5008	,	,		19250	0.0		0.0	False		,,,				2504	0.0				p.D383V		Atlas-SNP	.											.	CHRNA1	92	.	0			c.A1148T						PASS	.	T	VAL/ASP,VAL/ASP	251,4155	144.6+/-179.5	5,241,1957	137.0	130.0	133.0		1073,1148	5.5	1.0	2	dbSNP_116	133	1,8599		0,1,4299	yes	missense,missense	CHRNA1	NM_000079.3,NM_001039523.2	152,152	5,242,6256	AA,AT,TT		0.0116,5.6968,1.9376	benign,benign	358/458,383/483	175613477	252,12754	2203	4300	6503	SO:0001583	missense	1134	exon9			TTTTTGTCTTGCT	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.1148A>T	2.37:g.175613477T>A	ENSP00000261007:p.Asp383Val	Somatic	175	0	0	1924	WXS	Illumina HiSeq	Phase_I	134	59	0.440298	NM_001039523	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	37	CCDS33331.1	37	0.01694139194139194	37	0.07520325203252033	0	0.0	0	0.0	0	0.0	T	14.25	2.478393	0.44044	0.056968	1.16E-4	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542	D;D;D	0.85773	-2.03;-2.03;-2.03	5.51	5.51	0.81932	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.943943	0.09150	N	0.841683	T	0.19967	0.0480	L	0.27053	0.805	0.80722	D	1	B;B	0.23540	0.003;0.087	B;B	0.25759	0.007;0.063	T	0.48559	-0.9025	10	0.40728	T	0.16	.	11.8621	0.52471	0.0:0.0:0.1458:0.8542	rs6739001;rs52820919;rs6739001	358;383	Q53SH4;P02708	.;ACHA_HUMAN	V	358;383;276	ENSP00000261008:D358V;ENSP00000261007:D383V;ENSP00000387026:D276V	ENSP00000261007:D383V	D	-	2	0	CHRNA1	175321723	0.997000	0.39634	0.998000	0.56505	0.992000	0.81027	2.634000	0.46528	2.217000	0.71921	0.533000	0.62120	GAC	T|0.971;A|0.029	0.029	strong		0.408	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1		
EPHX1	2052	hgsc.bcm.edu	37	1	226032896	226032896	+	Silent	SNP	T	T	C	rs2234700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226032896T>C	ENST00000366837.4	+	9	1412	c.1216T>C	c.(1216-1218)Ttg>Ctg	p.L406L	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Silent_p.L406L	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	406				L -> F (in Ref. 3; CAA68486). {ECO:0000305}.	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)			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)					TTTTGAGCTATTGCACACGCC	0.572													t|||	106	0.0211661	0.0741	0.0043	5008	,	,		13351	0.001		0.0	False		,,,				2504	0.0041				p.L406L		Atlas-SNP	.											.	EPHX1	57	.	0			c.T1216C						PASS	.	C	,	208,4198	127.8+/-164.7	7,194,2002	102.0	93.0	96.0		1216,1216	-10.0	0.0	1	dbSNP_98	96	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	EPHX1	NM_000120.3,NM_001136018.2	,	7,194,6302	CC,CT,TT		0.0,4.7208,1.5993	,	406/456,406/456	226032896	208,12798	2203	4300	6503	SO:0001819	synonymous_variant	2052	exon9			GAGCTATTGCACA	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.1216T>C	1.37:g.226032896T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	147	78	0.530612	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	37	CCDS1547.1																																																																																			T|0.980;C|0.020	0.020	strong		0.572	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
DCDC1	341019	hgsc.bcm.edu	37	11	31327316	31327316	+	Silent	SNP	C	C	T	rs2616815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:31327316C>T	ENST00000452803.1	-	6	801	c.600G>A	c.(598-600)gaG>gaA	p.E200E	RP1-296L11.1_ENST00000528872.1_RNA|DCDC1_ENST00000597505.1_Silent_p.E200E	NM_181807.3	NP_861523.2	P59894	DCDC1_HUMAN	doublecortin domain containing 1	200	Doublecortin. {ECO:0000255|PROSITE- ProRule:PRU00072}.				intracellular signal transduction (GO:0035556)					central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|pancreas(2)|prostate(1)|skin(1)|stomach(1)	31	Lung SC(675;0.225)					CTGTGCACTCCTCCAGCAGCT	0.428													T|||	3404	0.679712	0.9357	0.7032	5008	,	,		15827	0.3839		0.674	False		,,,				2504	0.6278				p.E200E		Atlas-SNP	.											.	DCDC1	74	.	0			c.G600A						PASS	.	T		3972,432	209.8+/-230.5	1792,388,22	82.0	84.0	83.0		600	0.7	0.0	11	dbSNP_100	83	5600,2998	464.9+/-366.4	1799,2002,498	no	coding-synonymous	DCDC1	NM_181807.3		3591,2390,520	TT,TC,CC		34.8686,9.8093,26.3806		200/355	31327316	9572,3430	2202	4299	6501	SO:0001819	synonymous_variant	341019	exon6			GCACTCCTCCAGC	AY247970	CCDS7872.1	11p14.1	2013-05-22			ENSG00000170959	ENSG00000170959			20625	protein-coding gene	gene with protein product		608062				12820024	Standard	NM_181807		Approved		uc001msv.3	P59894	OTTHUMG00000150144	ENST00000452803.1:c.600G>A	11.37:g.31327316C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	NM_181807	A6PVL6|B7WNX6|Q6ZU04	Silent	SNP	ENST00000452803.1	37	CCDS7872.1																																																																																			C|0.298;T|0.702	0.702	strong		0.428	DCDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316531.1	NM_181807	
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744310	31744310	+	Missense_Mutation	SNP	G	G	C	rs3804010	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31744310G>C	ENST00000399889.2	-	1	247	c.222C>G	c.(220-222)agC>agG	p.S74R		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	74	5 X 10 AA approximate repeats.		S -> R (in dbSNP:rs3804010).			intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						TCTGGCAGGGGCTGGACTCCA	0.612													G|||	756	0.150958	0.2943	0.0994	5008	,	,		19292	0.0615		0.1223	False		,,,				2504	0.1155				p.S74R		Atlas-SNP	.											KRTAP13-2,NS,carcinoma,-1,1	KRTAP13-2	29	1	0			c.C222G						PASS	.	G	ARG/SER	1217,3189	421.5+/-339.4	176,865,1162	57.0	58.0	58.0		222	-9.5	0.0	21	dbSNP_107	58	928,7672	204.4+/-247.1	65,798,3437	no	missense	KRTAP13-2	NM_181621.3	110	241,1663,4599	CC,CG,GG		10.7907,27.6214,16.4924	benign	74/176	31744310	2145,10861	2203	4300	6503	SO:0001583	missense	337959	exon1			GCAGGGGCTGGAC	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"""Keratin associated proteins"""	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.222C>G	21.37:g.31744310G>C	ENSP00000382777:p.Ser74Arg	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	172	96	0.55814	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	311	0.1423992673992674	156	0.3170731707317073	40	0.11049723756906077	32	0.055944055944055944	83	0.10949868073878628	G	0.102	-1.151315	0.01700	0.276214	0.107907	ENSG00000182816	ENST00000399889	T	0.03212	4.01	4.75	-9.5	0.00584	.	0.139488	0.31859	N	0.006944	T	0.00012	0.0000	N	0.26042	0.785	0.80722	P	0.0	B	0.16802	0.019	B	0.18871	0.023	T	0.38265	-0.9669	9	0.23891	T	0.37	.	4.9289	0.13907	0.1888:0.503:0.1447:0.1635	rs3804010;rs52828905;rs56923242;rs3804010	74	Q52LG2	KR132_HUMAN	R	74	ENSP00000382777:S74R	ENSP00000382777:S74R	S	-	3	2	KRTAP13-2	30666181	0.000000	0.05858	0.000000	0.03702	0.952000	0.60782	-4.043000	0.00307	-3.351000	0.00181	0.655000	0.94253	AGC	G|0.841;C|0.159	0.159	strong		0.612	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1		
SSR1	6745	hgsc.bcm.edu	37	6	7310259	7310259	+	Missense_Mutation	SNP	A	A	G	rs10004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000479365.1_Missense_Mutation_p.L28S|SSR1_ENST00000474597.1_Missense_Mutation_p.L28S|SSR1_ENST00000489567.1_Missense_Mutation_p.L28S|SSR1_ENST00000462112.1_Missense_Mutation_p.L28S|SSR1_ENST00000488834.1_5'UTR|SSR1_ENST00000397511.2_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	96	0	0		WXS	Illumina HiSeq	Phase_I	116	63	0.543103	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		
DISP1	84976	hgsc.bcm.edu	37	1	223178226	223178226	+	Missense_Mutation	SNP	A	A	G	rs61743732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:223178226A>G	ENST00000284476.6	+	8	3651	c.3487A>G	c.(3487-3489)Agt>Ggt	p.S1163G		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1163					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)		TACAAGTCCCAGTGACAAGGG	0.453													A|||	129	0.0257588	0.093	0.0058	5008	,	,		23051	0.0		0.002	False		,,,				2504	0.0				p.S1163G		Atlas-SNP	.											.	DISP1	145	.	0			c.A3487G						PASS	.	A	GLY/SER	372,4034	188.8+/-215.1	12,348,1843	85.0	89.0	88.0		3487	1.6	0.0	1	dbSNP_129	88	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DISP1	NM_032890.3	56	12,351,6140	GG,GA,AA		0.0349,8.443,2.8833	benign	1163/1525	223178226	375,12631	2203	4300	6503	SO:0001583	missense	84976	exon10			AGTCCCAGTGACA	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.3487A>G	1.37:g.223178226A>G	ENSP00000284476:p.Ser1163Gly	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	28	12	0.428571	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	56	0.02564102564102564	53	0.10772357723577236	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	0.004	-2.279509	0.00254	0.08443	3.49E-4	ENSG00000154309	ENST00000284476	D	0.91351	-2.83	5.66	1.56	0.23342	.	0.630262	0.17522	N	0.171240	T	0.03477	0.0100	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30880	-0.9963	10	0.05436	T	0.98	-4.8804	7.9026	0.29744	0.1384:0.2477:0.6138:0.0	rs61743732	1163	Q96F81	DISP1_HUMAN	G	1163	ENSP00000284476:S1163G	ENSP00000284476:S1163G	S	+	1	0	DISP1	221244849	0.084000	0.21492	0.004000	0.12327	0.204000	0.24138	2.705000	0.47127	0.030000	0.15379	-0.415000	0.06103	AGT	A|0.971;G|0.029	0.029	strong		0.453	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
ARHGEF37	389337	hgsc.bcm.edu	37	5	149006640	149006640	+	Splice_Site	SNP	C	C	T	rs9324624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149006640C>T	ENST00000333677.6	+	11	1629	c.1466C>T	c.(1465-1467)cCg>cTg	p.P489L		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	489			P -> L (in dbSNP:rs9324624). {ECO:0000269|PubMed:14702039}.			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						CTCTCCCAGCCGCTCCTTCCA	0.557													C|||	1881	0.375599	0.4871	0.3617	5008	,	,		19217	0.1706		0.5109	False		,,,				2504	0.3067				p.P489L		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.C1466T						PASS	.	C	LEU/PRO	1886,2224		449,988,618	91.0	99.0	96.0		1466	4.5	1.0	5	dbSNP_119	96	4076,4342		985,2106,1118	yes	missense-near-splice	ARHGEF37	NM_001001669.2	98	1434,3094,1736	TT,TC,CC		48.4201,45.8881,47.5894	probably-damaging	489/676	149006640	5962,6566	2055	4209	6264	SO:0001630	splice_region_variant	389337	exon11			CCCAGCCGCTCCT	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1465-1C>T	5.37:g.149006640C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	880	0.40293040293040294	264	0.5365853658536586	144	0.39779005524861877	90	0.15734265734265734	382	0.503957783641161	C	20.2	3.944542	0.73672	0.458881	0.484201	ENSG00000183111	ENST00000333677	T	0.56611	0.45	5.39	4.53	0.55603	.	0.353536	0.33670	N	0.004670	T	0.00012	0.0000	L	0.58101	1.795	0.20873	P	0.999832131	D	0.89917	1.0	D	0.69307	0.963	T	0.50180	-0.8858	9	0.54805	T	0.06	.	12.358	0.55186	0.0:0.9212:0.0:0.0788	rs9324624;rs52802137;rs57196632;rs9324624	489	A1IGU5	ARH37_HUMAN	L	489	ENSP00000328083:P489L	ENSP00000328083:P489L	P	+	2	0	ARHGEF37	148986833	1.000000	0.71417	0.983000	0.44433	0.956000	0.61745	5.321000	0.65846	1.281000	0.44480	-0.219000	0.12488	CCG	C|0.590;T|0.410	0.410	strong		0.557	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	Missense_Mutation
TBC1D9B	23061	hgsc.bcm.edu	37	5	179300131	179300131	+	Silent	SNP	T	T	C	rs269469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179300131T>C	ENST00000356834.3	-	13	2341	c.2304A>G	c.(2302-2304)aaA>aaG	p.K768K	TBC1D9B_ENST00000444477.2_5'Flank|TBC1D9B_ENST00000355235.3_Silent_p.K768K|TBC1D9B_ENST00000519746.1_5'Flank	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	768						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CATAGGACACTTTCAGGAGCT	0.612													T|||	624	0.124601	0.4455	0.0432	5008	,	,		17765	0.0		0.005	False		,,,				2504	0.0				p.K768K		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.A2304G						PASS	.	T	,	1538,2866	480.4+/-358.8	282,974,946	56.0	56.0	56.0		2304,2304	-0.1	1.0	5	dbSNP_79	56	15,8585	9.1+/-34.3	0,15,4285	no	coding-synonymous,coding-synonymous	TBC1D9B	NM_015043.3,NM_198868.2	,	282,989,5231	CC,CT,TT		0.1744,34.9228,11.9425	,	768/1234,768/1251	179300131	1553,11451	2202	4300	6502	SO:0001819	synonymous_variant	23061	exon13			GGACACTTTCAGG	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"""EF-hand domain containing"""	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.2304A>G	5.37:g.179300131T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	139	60	0.431655	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	37	CCDS43408.1																																																																																			T|0.899;C|0.101	0.101	strong		0.612	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043	
EGFR	1956	hgsc.bcm.edu	37	7	55238087	55238087	+	Intron	SNP	C	C	T	rs10258429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:55238087C>T	ENST00000275493.2	+	16	2057				EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Intron|EGFR_ENST00000454757.2_Intron|EGFR_ENST00000344576.2_Silent_p.H656H	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor						activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GCGTGTCCCACCAGAGCGGGA	0.512		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	563	0.11242	0.2398	0.049	5008	,	,		20745	0.0496		0.0736	False		,,,				2504	0.09				p.H656H		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	.	EGFR	20426	.	0			c.C1968T						PASS	.	C	,	922,3484	352.1+/-311.5	101,720,1382	108.0	89.0	95.0		,1968	2.4	0.0	7	dbSNP_119	95	606,7994	158.6+/-212.1	23,560,3717	no	intron,coding-synonymous	EGFR	NM_005228.3,NM_201284.1	,	124,1280,5099	TT,TC,CC		7.0465,20.926,11.7484	,	,656/706	55238087	1528,11478	2203	4300	6503	SO:0001627	intron_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GTCCCACCAGAGC		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1881-781C>T	7.37:g.55238087C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	147	79	0.537415	NM_201284	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.889;T|0.111	0.111	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558384	140558384	+	Missense_Mutation	SNP	C	C	T	rs116452537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140558384C>T	ENST00000239444.2	+	1	1014	c.769C>T	c.(769-771)Cca>Tca	p.P257S	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	257	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)			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)			TGAGGACAGTCCAATAAGCTT	0.458													C|||	27	0.00539137	0.0204	0.0	5008	,	,		15847	0.0		0.0	False		,,,				2504	0.0				p.P257S		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C769T						PASS	.	C	SER/PRO	68,4338	61.7+/-98.7	1,66,2136	209.0	277.0	254.0		769	3.3	0.9	5	dbSNP_132	254	0,8600		0,0,4300	yes	missense	PCDHB8	NM_019120.3	74	1,66,6436	TT,TC,CC		0.0,1.5433,0.5228	benign	257/802	140558384	68,12938	2203	4300	6503	SO:0001583	missense	56128	exon1			GACAGTCCAATAA	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.769C>T	5.37:g.140558384C>T	ENSP00000239444:p.Pro257Ser	Somatic	469	1	0.0021322		WXS	Illumina HiSeq	Phase_I	285	140	0.491228	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	c	13.53	2.263792	0.39995	0.015433	0.0	ENSG00000120322	ENST00000239444	T	0.54279	0.58	4.25	3.33	0.38152	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.41971	0.1182	M	0.79011	2.435	0.32980	D	0.523474	B	0.26935	0.164	B	0.33690	0.168	T	0.67604	-0.5628	9	0.62326	D	0.03	.	13.5777	0.61883	0.0:0.8433:0.1567:0.0	.	257	Q9UN66	PCDB8_HUMAN	S	257	ENSP00000239444:P257S	ENSP00000239444:P257S	P	+	1	0	PCDHB8	140538568	0.033000	0.19621	0.908000	0.35775	0.609000	0.37215	2.681000	0.46926	1.911000	0.55334	0.585000	0.79938	CCA	C|0.994;T|0.006	0.006	strong		0.458	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
PDGFRB	5159	hgsc.bcm.edu	37	5	149509508	149509508	+	Missense_Mutation	SNP	G	G	A	rs74943037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149509508G>A	ENST00000261799.4	-	10	1860	c.1391C>T	c.(1390-1392)aCg>aTg	p.T464M		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	464	Ig-like C2-type 5.				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)	p.T464M(1)		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)	CCCCAGCAGCGTGGGCGGCAG	0.612			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""						OREG0016927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	138	0.0275559	0.0953	0.0115	5008	,	,		20674	0.001		0.003	False		,,,				2504	0.0				p.T464M		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	PDGFRB,NS,carcinoma,0,1	PDGFRB	142	1	1	Substitution - Missense(1)	stomach(1)	c.C1391T						scavenged	.	G	MET/THR	393,4013	195.3+/-220.0	26,341,1836	102.0	74.0	84.0		1391	3.8	0.8	5	dbSNP_131	84	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PDGFRB	NM_002609.3	81	26,344,6133	AA,AG,GG		0.0349,8.9197,3.0447	probably-damaging	464/1107	149509508	396,12610	2203	4300	6503	SO:0001583	missense	5159	exon10			AGCAGCGTGGGCG	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.1391C>T	5.37:g.149509508G>A	ENSP00000261799:p.Thr464Met	Somatic	100	1	0.01	1725	WXS	Illumina HiSeq	Phase_I	133	58	0.43609	NM_002609	B5A957|Q8N5L4	Missense_Mutation	SNP	ENST00000261799.4	37	CCDS4303.1	56	0.02564102564102564	51	0.10365853658536585	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	6.709	0.499568	0.12762	0.089197	3.49E-4	ENSG00000113721	ENST00000261799;ENST00000544453	T	0.76316	-1.01	4.64	3.76	0.43208	.	0.276731	0.27821	N	0.017704	T	0.06462	0.0166	L	0.59436	1.845	0.27164	N	0.961099	P;B	0.45634	0.863;0.122	B;B	0.39531	0.302;0.022	T	0.04140	-1.0974	10	0.33940	T	0.23	.	12.9704	0.58510	0.0865:0.0:0.9135:0.0	.	464;464	A8KAM8;P09619	.;PGFRB_HUMAN	M	464;134	ENSP00000261799:T464M	ENSP00000261799:T464M	T	-	2	0	PDGFRB	149489701	0.297000	0.24408	0.838000	0.33150	0.007000	0.05969	0.467000	0.22035	0.583000	0.29574	-1.598000	0.00824	ACG	G|0.972;A|0.028	0.028	strong		0.612	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
CCDC183	84960	hgsc.bcm.edu	37	9	139693596	139693596	+	Missense_Mutation	SNP	T	T	C	rs945386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139693596T>C	ENST00000338005.6	+	2	148	c.113T>C	c.(112-114)aTg>aCg	p.M38T	KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.M94T|RP11-216L13.18_ENST00000471502.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		38			M -> T (in dbSNP:rs945386).							biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		AAAGAGAATATGGACCAGAAC	0.637													C|||	1369	0.273363	0.3374	0.2968	5008	,	,		18525	0.2421		0.2147	False		,,,				2504	0.2628				p.M38T		Atlas-SNP	.											.	KIAA1984	39	.	0			c.T113C						PASS	.	C	THR/MET	1221,2859		191,839,1010	53.0	62.0	59.0		113	1.0	0.0	9	dbSNP_86	59	1821,6553		208,1405,2574	yes	missense	KIAA1984	NM_001039374.4	81	399,2244,3584	CC,CT,TT		21.7459,29.9265,24.4259	benign	38/535	139693596	3042,9412	2040	4187	6227	SO:0001583	missense	84960	exon2			AGAATATGGACCA																												ENST00000338005.6:c.113T>C	9.37:g.139693596T>C	ENSP00000338013:p.Met38Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	539	0.2467948717948718	160	0.3252032520325203	98	0.27071823204419887	124	0.21678321678321677	157	0.20712401055408972	C	1.102	-0.660878	0.03454	0.299265	0.217459	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.10960	2.82	3.91	1.02	0.19986	.	0.979372	0.08252	N	0.974461	T	0.00012	0.0000	N	0.02142	-0.665	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.49312	-0.8953	9	0.20519	T	0.43	-3.8689	7.3765	0.26831	0.0:0.6152:0.0:0.3848	rs945386;rs945386	38	Q5T5S1	K1984_HUMAN	T	38	ENSP00000338013:M38T	ENSP00000338013:M38T	M	+	2	0	KIAA1984	138813417	0.207000	0.23482	0.025000	0.17156	0.000000	0.00434	0.284000	0.18864	-0.124000	0.11724	-0.994000	0.02522	ATG	T|0.759;C|0.241	0.241	strong		0.637	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651412	1651412	+	Silent	SNP	G	G	C	rs569811286		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1651412G>C	ENST00000399676.2	+	1	380	c.342G>C	c.(340-342)ggG>ggC	p.G114G		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	114	8 X 4 AA repeats of C-C-X-P.			Missing (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)		p.G114G(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)		CCTGTGGGGGGTCCAAGGGGG	0.706													N|||	1	0.000199681	0.0	0.0	5008	,	,		3556	0.001		0.0	False		,,,				2504	0.0				p.G114G		Atlas-SNP	.											KRTAP5-5,NS,carcinoma,+1,2	KRTAP5-5	86	2	1	Substitution - coding silent(1)	prostate(1)	c.G342C						scavenged	.						20.0	31.0	27.0					11																	1651412		2083	4147	6230	SO:0001819	synonymous_variant	439915	exon1			TGGGGGGTCCAAG	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.342G>C	11.37:g.1651412G>C		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	127	7	0.0551181	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			.	.	none		0.706	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
SLC22A7	10864	hgsc.bcm.edu	37	6	43270151	43270151	+	Splice_Site	SNP	C	C	T	rs2270860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43270151C>T	ENST00000372585.5	+	8	1370	c.1275C>T	c.(1273-1275)tcC>tcT	p.S425S	SLC22A7_ENST00000372589.3_Splice_Site_p.S423S|SLC22A7_ENST00000372574.3_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	20	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_153320	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Silent	SNP	ENST00000372585.5	37	CCDS4893.2																																																																																			C|0.562;T|0.436	0.436	strong		0.667	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1		Silent
TMEM241	85019	hgsc.bcm.edu	37	18	20953720	20953720	+	Missense_Mutation	SNP	G	G	A	rs8099409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:20953720G>A	ENST00000383233.3	-	7	443	c.391C>T	c.(391-393)Ctc>Ttc	p.L131F	TMEM241_ENST00000542162.1_Missense_Mutation_p.L131F|TMEM241_ENST00000450466.2_Missense_Mutation_p.L10F	NM_032933.4	NP_116322.3	Q24JQ0	TM241_HUMAN	transmembrane protein 241	131			L -> F (in dbSNP:rs8099409). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)											GCCAGGAGGAGGAGGGCACTG	0.498													A|||	2056	0.410543	0.4735	0.3184	5008	,	,		23579	0.4147		0.4881	False		,,,				2504	0.3067				p.L131F		Atlas-SNP	.											.	.	.	.	0			c.C391T						PASS	.	A	PHE/LEU	2128,2278	598.1+/-389.0	521,1086,596	100.0	96.0	98.0		391	3.6	1.0	18	dbSNP_116	98	4231,4369	581.9+/-391.3	1069,2093,1138	yes	missense	C18orf45	NM_032933.4	22	1590,3179,1734	AA,AG,GG		49.1977,48.2978,48.8928	benign	131/297	20953720	6359,6647	2203	4300	6503	SO:0001583	missense	85019	exon7			GGAGGAGGAGGGC	BC082984	CCDS11876.2	18q11.2	2011-11-25	2011-11-25	2011-11-25	ENSG00000134490	ENSG00000134490			31723	protein-coding gene	gene with protein product		615430	"""chromosome 18 open reading frame 45"""	C18orf45		12477932	Standard	NM_032933		Approved	MGC11386, FLJ44259	uc002kuf.3	Q24JQ0	OTTHUMG00000131771	ENST00000383233.3:c.391C>T	18.37:g.20953720G>A	ENSP00000372720:p.Leu131Phe	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_032933	I0J130|Q6ZTS7|Q6ZW41	Missense_Mutation	SNP	ENST00000383233.3	37	CCDS11876.2	988|988	0.4523809523809524|0.4523809523809524	245|245	0.49796747967479676|0.49796747967479676	136|136	0.3756906077348066|0.3756906077348066	228|228	0.3986013986013986|0.3986013986013986	379|379	0.5|0.5	A|A	10.86|10.86	1.468430|1.468430	0.26335|0.26335	0.482978|0.482978	0.491977|0.491977	ENSG00000134490|ENSG00000134490	ENST00000450466;ENST00000383233;ENST00000542162|ENST00000497608	T;T;T|.	0.76448|.	1.05;1.05;-1.02|.	5.99|5.99	3.62|3.62	0.41486|0.41486	.|.	0.258118|.	0.34460|.	N|.	0.003958|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00926|0.00926	-1.1|-1.1	0.09310|0.09310	P|P	0.9999999999782435|0.9999999999782435	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.45833|0.45833	-0.9234|-0.9234	9|4	0.28530|.	T|.	0.3|.	-25.2792|-25.2792	7.6304|7.6304	0.28236|0.28236	0.7613:0.0:0.2387:0.0|0.7613:0.0:0.2387:0.0	rs8099409;rs52817169;rs59773270;rs8099409|rs8099409;rs52817169;rs59773270;rs8099409	131|.	Q24JQ0|.	CR045_HUMAN|.	F|L	10;131;131|130	ENSP00000414899:L10F;ENSP00000372720:L131F;ENSP00000440152:L131F|.	ENSP00000372720:L131F|.	L|P	-|-	1|2	0|0	C18orf45|C18orf45	19207718|19207718	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.754000|0.754000	0.42855|0.42855	2.411000|2.411000	0.44600|0.44600	0.171000|0.171000	0.19730|0.19730	-0.982000|-0.982000	0.02568|0.02568	CTC|CCT	G|0.541;A|0.459	0.459	strong		0.498	TMEM241-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254702.3	NM_032933	
UPF3A	65110	hgsc.bcm.edu	37	13	115047305	115047305	+	Missense_Mutation	SNP	G	G	A	rs3752105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	80	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	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		
IFRD2	7866	hgsc.bcm.edu	37	3	50326883	50326883	+	Silent	SNP	A	A	G	rs78165652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:50326883A>G	ENST00000429673.2	-	7	965	c.966T>C	c.(964-966)ctT>ctC	p.L322L	IFRD2_ENST00000336089.4_Silent_p.L424L|IFRD2_ENST00000484043.1_5'Flank|IFRD2_ENST00000417626.2_Silent_p.L258L|IFRD2_ENST00000436390.1_Silent_p.L258L			Q12894	IFRD2_HUMAN	interferon-related developmental regulator 2	322						nucleus (GO:0005634)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CCTACCTGTCAAGGATGTGGC	0.632													A|||	30	0.00599042	0.0008	0.0101	5008	,	,		17527	0.0		0.0179	False		,,,				2504	0.0041				p.L322L		Atlas-SNP	.											.	IFRD2	34	.	0			c.T966C						PASS	.	A		9,3949		0,9,1970	13.0	16.0	15.0		966	-4.9	0.9	3	dbSNP_132	15	149,8185		2,145,4020	no	coding-synonymous	IFRD2	NM_006764.4		2,154,5990	GG,GA,AA		1.7879,0.2274,1.2854		322/507	50326883	158,12134	1979	4167	6146	SO:0001819	synonymous_variant	7866	exon7			CCTGTCAAGGATG	U09585		3p21.3	2008-07-18			ENSG00000214706	ENSG00000214706			5457	protein-coding gene	gene with protein product	"""interferon-related protein"""	602725				9050919	Standard	NM_006764		Approved	SKMc15, SM15, IFNRP	uc011bdp.2	Q12894	OTTHUMG00000156935	ENST00000429673.2:c.966T>C	3.37:g.50326883A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	159	70	0.440252	NM_006764	Q9BVB4|Q9UJ88	Silent	SNP	ENST00000429673.2	37	CCDS46831.1																																																																																			A|0.992;G|0.008	0.008	strong		0.632	IFRD2-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006764	
PARP4	143	hgsc.bcm.edu	37	13	25009288	25009288	+	Missense_Mutation	SNP	C	C	T	rs1050114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25009288C>T	ENST00000381989.3	-	31	4096	c.3991G>A	c.(3991-3993)Gcc>Acc	p.A1331T		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1331				A -> 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)		TGAGCGCGGGCAGTCGGGGGA	0.478													c|||	283	0.0565096	0.1959	0.0216	5008	,	,		19228	0.0		0.0089	False		,,,				2504	0.0				p.A1331T		Atlas-SNP	.											.	PARP4	142	.	0			c.G3991A						PASS	.	C	THR/ALA	719,3687	298.4+/-285.3	55,609,1539	83.0	90.0	88.0		3991	-2.3	0.0	13	dbSNP_86	88	58,8542	35.9+/-90.5	0,58,4242	yes	missense	PARP4	NM_006437.3	58	55,667,5781	TT,TC,CC		0.6744,16.3187,5.9742	benign	1331/1725	25009288	777,12229	2203	4300	6503	SO:0001583	missense	143	exon31			CGCGGGCAGTCGG	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.3991G>A	13.37:g.25009288C>T	ENSP00000371419:p.Ala1331Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	158	81	0.512658	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	112	0.05128205128205128	101	0.20528455284552846	4	0.011049723756906077	0	0.0	7	0.009234828496042216	c	2.703	-0.270503	0.05716	0.163187	0.006744	ENSG00000102699	ENST00000381989	T	0.01745	4.66	2.49	-2.35	0.06684	.	1.812460	0.03814	U	0.266463	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.28026	0.198	B	0.14578	0.011	T	0.48198	-0.9056	9	0.13108	T	0.6	.	11.1398	0.48396	0.0:0.2639:0.7361:0.0	rs1050114;rs3190398;rs52820789;rs58911394;rs1050114	1331	Q9UKK3	PARP4_HUMAN	T	1331	ENSP00000371419:A1331T	ENSP00000371419:A1331T	A	-	1	0	PARP4	23907288	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.045000	0.01410	-0.249000	0.09569	0.313000	0.20887	GCC	C|0.940;T|0.060	0.060	strong		0.478	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
RCC2	55920	hgsc.bcm.edu	37	1	17739586	17739586	+	Silent	SNP	G	G	A	rs942457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17739586G>A	ENST00000375436.4	-	10	1483	c.1296C>T	c.(1294-1296)atC>atT	p.I432I	AC004824.1_ENST00000583469.1_RNA|RCC2_ENST00000375433.3_Silent_p.I432I	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	196	0	0		WXS	Illumina HiSeq	Phase_I	236	110	0.466102	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	
IGFALS	3483	hgsc.bcm.edu	37	16	1841033	1841033	+	Silent	SNP	G	G	A	rs17559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1841033G>A	ENST00000215539.3	-	2	1496	c.1386C>T	c.(1384-1386)taC>taT	p.Y462Y	IGFALS_ENST00000415638.3_Silent_p.Y500Y			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit	462					cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						AGAGCAGCAGGTACTCCAGCT	0.716													G|||	1283	0.25619	0.4818	0.0922	5008	,	,		15016	0.1548		0.0934	False		,,,				2504	0.3395				p.Y500Y		Atlas-SNP	.											IGFALS,NS,carcinoma,0,1	IGFALS	29	1	0			c.C1500T						scavenged	.	G	,	1637,2645		297,1043,801	16.0	18.0	17.0		1500,1386	2.7	1.0	16	dbSNP_63	17	755,7657		34,687,3485	no	coding-synonymous,coding-synonymous	IGFALS	NM_001146006.1,NM_004970.2	,	331,1730,4286	AA,AG,GG		8.9753,38.2298,18.8435	,	500/644,462/606	1841033	2392,10302	2141	4206	6347	SO:0001819	synonymous_variant	3483	exon2			CAGCAGGTACTCC	M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638	ENST00000215539.3:c.1386C>T	16.37:g.1841033G>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	8	6	0.75	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		
ZFHX4	79776	hgsc.bcm.edu	37	8	77690563	77690563	+	Silent	SNP	T	T	C	rs16939357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:77690563T>C	ENST00000521891.2	+	4	3661	c.3213T>C	c.(3211-3213)caT>caC	p.H1071H	ZFHX4_ENST00000517683.1_3'UTR|ZFHX4_ENST00000455469.2_Silent_p.H1045H|ZFHX4_ENST00000050961.6_Silent_p.H1045H|ZFHX4_ENST00000518282.1_Silent_p.H1045H	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1045					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)			CGGTGAAGCATCAGCAGACTG	0.512										HNSCC(33;0.089)			T|||	1677	0.334864	0.5983	0.2147	5008	,	,		19847	0.3929		0.167	False		,,,				2504	0.1769				p.H1071H		Atlas-SNP	.											.	ZFHX4	878	.	0			c.T3213C						PASS	.	T		2200,1942		598,1004,469	151.0	161.0	158.0		3213	3.2	1.0	8	dbSNP_123	158	1300,7112		102,1096,3008	no	coding-synonymous	ZFHX4	NM_024721.4		700,2100,3477	CC,CT,TT		15.4541,46.8856,27.8796		1071/3617	77690563	3500,9054	2071	4206	6277	SO:0001819	synonymous_variant	79776	exon4			GAAGCATCAGCAG		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.3213T>C	8.37:g.77690563T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																			T|0.674;C|0.326	0.326	strong		0.512	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
DNAH5	1767	hgsc.bcm.edu	37	5	13902220	13902220	+	Missense_Mutation	SNP	T	T	C	rs1530498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	65	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	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	
NEIL3	55247	hgsc.bcm.edu	37	4	178283474	178283474	+	Missense_Mutation	SNP	A	A	G	rs35418725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:178283474A>G	ENST00000264596.3	+	10	1785	c.1667A>G	c.(1666-1668)cAt>cGt	p.H556R		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	556			H -> R (in dbSNP:rs35418725). {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)		TTCTGCAACCATGGCAAGCGT	0.383								Base excision repair (BER), DNA glycosylases					A|||	24	0.00479233	0.0174	0.0014	5008	,	,		19183	0.0		0.0	False		,,,				2504	0.0				p.H556R		Atlas-SNP	.											.	NEIL3	89	.	0			c.A1667G						PASS	.	A	ARG/HIS	74,4332	60.5+/-97.4	0,74,2129	93.0	94.0	94.0		1667	3.5	1.0	4	dbSNP_126	94	0,8600		0,0,4300	yes	missense	NEIL3	NM_018248.2	29	0,74,6429	GG,GA,AA		0.0,1.6795,0.569	possibly-damaging	556/606	178283474	74,12932	2203	4300	6503	SO:0001583	missense	55247	exon10			GCAACCATGGCAA	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.1667A>G	4.37:g.178283474A>G	ENSP00000264596:p.His556Arg	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	A	17.52	3.409952	0.62399	0.016795	0.0	ENSG00000109674	ENST00000264596	T	0.26223	1.75	4.63	3.45	0.39498	Zinc finger, GRF-type (1);	0.000000	0.85682	D	0.000000	T	0.42017	0.1184	H	0.94542	3.55	0.58432	D	0.999995	D	0.64830	0.994	D	0.70487	0.969	T	0.61936	-0.6960	10	0.87932	D	0	-19.9676	10.3252	0.43790	0.9223:0.0:0.0777:0.0	rs35418725	556	Q8TAT5	NEIL3_HUMAN	R	556	ENSP00000264596:H556R	ENSP00000264596:H556R	H	+	2	0	NEIL3	178520468	1.000000	0.71417	0.983000	0.44433	0.753000	0.42808	8.872000	0.92352	0.937000	0.37394	0.402000	0.26972	CAT	A|0.996;G|0.004	0.004	strong		0.383	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
GLT1D1	144423	hgsc.bcm.edu	37	12	129360518	129360518	+	Missense_Mutation	SNP	G	G	A	rs73438369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:129360518G>A	ENST00000442111.2	+	2	216	c.128G>A	c.(127-129)aGc>aAc	p.S43N	GLT1D1_ENST00000542193.1_5'UTR|GLT1D1_ENST00000281703.6_Missense_Mutation_p.S43N|GLT1D1_ENST00000537468.1_Missense_Mutation_p.S32N			Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1	43					biosynthetic process (GO:0009058)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)		GACTTTGAAAGCCGATCTGAG	0.488													G|||	82	0.0163738	0.059	0.0058	5008	,	,		16943	0.0		0.0	False		,,,				2504	0.0				p.S43N		Atlas-SNP	.											.	GLT1D1	48	.	0			c.G128A						PASS	.	G	ASN/SER	227,4179	135.3+/-171.4	3,221,1979	162.0	164.0	163.0		128	4.7	0.1	12	dbSNP_130	163	3,8597	3.7+/-12.6	0,3,4297	yes	missense	GLT1D1	NM_144669.1	46	3,224,6276	AA,AG,GG		0.0349,5.1521,1.7684	probably-damaging	43/267	129360518	230,12776	2203	4300	6503	SO:0001583	missense	144423	exon2			TTGAAAGCCGATC		CCDS9265.1	12q24.32	2013-02-22			ENSG00000151948	ENSG00000151948		"""Glycosyltransferase group 1 domain containing"""	26483	protein-coding gene	gene with protein product							Standard	NM_144669		Approved	FLJ31978	uc001uhx.1	Q96MS3	OTTHUMG00000168437	ENST00000442111.2:c.128G>A	12.37:g.129360518G>A	ENSP00000394692:p.Ser43Asn	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	72	0.476821	NM_144669	Q86XG8	Missense_Mutation	SNP	ENST00000442111.2	37		31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	G	13.77	2.334875	0.41297	0.051521	3.49E-4	ENSG00000151948	ENST00000442111;ENST00000281703;ENST00000537468	T;T;T	0.79247	-1.25;0.74;0.69	5.54	4.65	0.58169	.	0.144833	0.64402	N	0.000006	T	0.46678	0.1405	M	0.77616	2.38	0.32213	N	0.576306	D;B	0.89917	1.0;0.037	D;B	0.76071	0.987;0.039	T	0.74163	-0.3754	10	0.22706	T	0.39	-25.057	9.1417	0.36908	0.0789:0.1461:0.775:0.0	.	32;43	F5H088;Q96MS3-2	.;.	N	43;43;32	ENSP00000394692:S43N;ENSP00000281703:S43N;ENSP00000438158:S32N	ENSP00000281703:S43N	S	+	2	0	GLT1D1	127926471	0.963000	0.33076	0.145000	0.22337	0.327000	0.28475	1.719000	0.38011	1.320000	0.45209	0.655000	0.94253	AGC	G|0.981;A|0.019	0.019	strong		0.488	GLT1D1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000399740.1	NM_144669	
DAGLA	747	hgsc.bcm.edu	37	11	61511498	61511498	+	Missense_Mutation	SNP	C	C	T	rs3741252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61511498C>T	ENST00000257215.5	+	20	2782	c.2666C>T	c.(2665-2667)cCg>cTg	p.P889L	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	889			P -> L (in dbSNP:rs3741252).		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)		GGTGGCGGGCCGGCCTCCCGC	0.706													c|||	896	0.178914	0.3086	0.0504	5008	,	,		12076	0.2569		0.0954	False		,,,				2504	0.1002				p.P889L		Atlas-SNP	.											.	DAGLA	109	.	0			c.C2666T						PASS	.	T	LEU/PRO	1066,3312		114,838,1237	18.0	21.0	20.0		2666	-5.5	0.0	11	dbSNP_107	20	565,7987		18,529,3729	yes	missense	DAGLA	NM_006133.2	98	132,1367,4966	TT,TC,CC		6.6066,24.349,12.6141	benign	889/1043	61511498	1631,11299	2189	4276	6465	SO:0001583	missense	747	exon20			GCGGGCCGGCCTC	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.2666C>T	11.37:g.61511498C>T	ENSP00000257215:p.Pro889Leu	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	17	12	0.705882	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	37	CCDS31578.1	474	0.21703296703296704	171	0.3475609756097561	21	0.058011049723756904	214	0.3741258741258741	68	0.08970976253298153	c	0	-2.791726	0.00077	0.24349	0.066066	ENSG00000134780	ENST00000257215	T	0.20463	2.07	3.1	-5.51	0.02568	.	3.006760	0.01066	N	0.004721	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	0.38222	-0.9671	9	0.11485	T	0.65	3.2016	9.9369	0.41556	0.0:0.3231:0.0967:0.5803	rs3741252	889	Q9Y4D2	DGLA_HUMAN	L	889	ENSP00000257215:P889L	ENSP00000257215:P889L	P	+	2	0	DAGLA	61268074	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.895000	0.00707	-1.994000	0.00972	-3.260000	0.00049	CCG	C|0.840;T|0.160	0.160	strong		0.706	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
USHBP1	83878	hgsc.bcm.edu	37	19	17370190	17370190	+	Silent	SNP	T	T	G	rs11880383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17370190T>G	ENST00000252597.3	-	7	1127	c.954A>C	c.(952-954)ctA>ctC	p.L318L	USHBP1_ENST00000431146.2_Silent_p.L254L	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						TGTATCCCTGTAGCACAGCTG	0.557													G|||	1505	0.300519	0.4902	0.2795	5008	,	,		20871	0.2788		0.1551	False		,,,				2504	0.2311				p.L318L		Atlas-SNP	.											USHBP1,NS,carcinoma,-2,1	USHBP1	85	1	0			c.A954C						PASS	.	G		1978,2428	619.5+/-393.4	440,1098,665	83.0	79.0	80.0		954	-5.1	0.9	19	dbSNP_120	80	1159,7441	766.0+/-407.6	77,1005,3218	no	coding-synonymous	USHBP1	NM_031941.3		517,2103,3883	GG,GT,TT		13.4767,44.8933,24.1196		318/704	17370190	3137,9869	2203	4300	6503	SO:0001819	synonymous_variant	83878	exon7			TCCCTGTAGCACA	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.954A>C	19.37:g.17370190T>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			T|0.737;G|0.263	0.263	strong		0.557	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
PCDHGA12	26025	hgsc.bcm.edu	37	5	140867347	140867347	+	Intron	SNP	C	C	T	rs1423149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140867347C>T	ENST00000252085.3	+	2	2566				PCDHGB4_ENST00000519479.1_Intron|PCDHGC5_ENST00000252087.1_5'Flank|PCDHGA11_ENST00000518882.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTAACTGTTTCGTGAATTAAC	0.438																																					p.F869F		Atlas-SNP	.											.	PCDHGC4	91	.	0			c.C2607T						PASS	.	C	,,,,,,,,,,,,,,,,,,,,,,,	680,1686		93,494,596	88.0	86.0	87.0		,,,,,,,,,,,,,,,,,,,,,,,2607	2.4	0.6	5	dbSNP_88	87	207,4269		4,199,2035	no	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGC4,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_018928.2,NM_032088.1,NM_032092.1,NM_032403.1,NM_032406.1	,,,,,,,,,,,,,,,,,,,,,,,	97,693,2631	TT,TC,CC		4.6247,28.7405,12.964	,,,,,,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,,,,,,869/872	140867347	887,5955	1183	2238	3421	SO:0001627	intron_variant	56098	exon1			CTGTTTCGTGAAT	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"""Cadherins / Protocadherins : Clustered"""	8699	other	protocadherin	"""fibroblast cadherin FIB3"""	603059	"""cadherin 21"""	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.2425-7027C>T	5.37:g.140867347C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_032406	O15100|Q6UW70|Q9Y5D7	Silent	SNP	ENST00000252085.3	37	CCDS4260.1																																																																																			C|0.866;T|0.134	0.134	strong		0.438	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735	
NPNT	255743	hgsc.bcm.edu	37	4	106859549	106859549	+	Missense_Mutation	SNP	G	G	C	rs35132891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:106859549G>C	ENST00000379987.2	+	5	693	c.477G>C	c.(475-477)caG>caC	p.Q159H	NPNT_ENST00000453617.2_Missense_Mutation_p.Q176H|NPNT_ENST00000305572.8_Missense_Mutation_p.Q159H|NPNT_ENST00000427316.2_Missense_Mutation_p.Q189H|NPNT_ENST00000506666.1_Missense_Mutation_p.Q189H|NPNT_ENST00000514622.1_Missense_Mutation_p.Q159H	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	159	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.		Q -> H (in dbSNP:rs35132891). {ECO:0000269|PubMed:12975309}.		branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		CTGGCCTGCAGCTGGCTCCTG	0.517													G|||	1626	0.324681	0.4607	0.3329	5008	,	,		17415	0.1825		0.334	False		,,,				2504	0.272				p.Q189H		Atlas-SNP	.											.	NPNT	69	.	0			c.G567C						PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN	1810,2596	530.8+/-373.0	369,1072,762	70.0	66.0	67.0		477,528,567,477,567	3.5	1.0	4	dbSNP_126	67	2797,5803	443.5+/-360.4	457,1883,1960	yes	missense,missense,missense,missense,missense	NPNT	NM_001033047.2,NM_001184690.1,NM_001184691.1,NM_001184692.1,NM_001184693.1	24,24,24,24,24	826,2955,2722	CC,CG,GG		32.5233,41.0803,35.4221	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	159/566,176/583,189/596,159/537,189/567	106859549	4607,8399	2203	4300	6503	SO:0001583	missense	255743	exon6			CCTGCAGCTGGCT		CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07							27405	protein-coding gene	gene with protein product		610306				15754038	Standard	NM_001033047		Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000379987.2:c.477G>C	4.37:g.106859549G>C	ENSP00000369323:p.Gln159His	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001184691	A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Missense_Mutation	SNP	ENST00000379987.2	37	CCDS34046.1	692|692	0.31684981684981683|0.31684981684981683	212|212	0.43089430894308944|0.43089430894308944	127|127	0.35082872928176795|0.35082872928176795	113|113	0.19755244755244755|0.19755244755244755	240|240	0.316622691292876|0.316622691292876	G|G	17.26|17.26	3.344923|3.344923	0.61073|0.61073	0.410803|0.410803	0.325233|0.325233	ENSG00000168743|ENSG00000168743	ENST00000514837|ENST00000504304;ENST00000379987;ENST00000453617;ENST00000427316;ENST00000514622;ENST00000305572;ENST00000506666;ENST00000503451	.|T;D;D;D;D;D;D;D	.|0.87491	.|1.3;-2.26;-2.26;-2.26;-2.26;-2.26;-2.26;-2.26	5.22|5.22	3.49|3.49	0.39957|0.39957	.|Epidermal growth factor-like (1);	.|0.049867	.|0.85682	.|D	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.65975|0.65975	2.015|2.015	0.26849|0.26849	P|P	0.9681974|0.9681974	.|D;B;B;D;B;D;D	.|0.69078	.|0.997;0.112;0.23;0.989;0.23;0.996;0.995	.|D;B;B;D;B;D;D	.|0.66847	.|0.931;0.082;0.082;0.921;0.082;0.93;0.947	T|T	0.01013|0.01013	-1.1481|-1.1481	4|9	.|0.72032	.|D	.|0.01	.|.	8.6958|8.6958	0.34296|0.34296	0.2933:0.0:0.7067:0.0|0.2933:0.0:0.7067:0.0	rs35132891|rs35132891	.|159;189;189;176;206;159;159	.|E9PF04;E9PE64;E9PCQ1;E9PCK8;D6RH31;Q6UXI9-2;Q6UXI9	.|.;.;.;.;.;.;NPNT_HUMAN	P|H	136|55;159;176;189;159;159;189;206	.|ENSP00000426951:Q55H;ENSP00000369323:Q159H;ENSP00000402884:Q176H;ENSP00000389252:Q189H;ENSP00000422044:Q159H;ENSP00000302557:Q159H;ENSP00000422474:Q189H;ENSP00000426146:Q206H	.|ENSP00000302557:Q159H	A|Q	+|+	1|3	0|2	NPNT|NPNT	107078998|107078998	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.935000|0.935000	0.57460|0.57460	3.803000|3.803000	0.55560|0.55560	0.698000|0.698000	0.31739|0.31739	-0.122000|-0.122000	0.15005|0.15005	GCT|CAG	G|0.658;C|0.342	0.342	strong		0.517	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1	NM_198278	
UBE3D	90025	hgsc.bcm.edu	37	6	83667045	83667045	+	Missense_Mutation	SNP	C	C	T	rs7739323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	101	0	0		WXS	Illumina HiSeq	Phase_I	138	62	0.449275	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	
MAATS1	89876	hgsc.bcm.edu	37	3	119445139	119445139	+	Silent	SNP	A	A	G	rs9835381	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119445139A>G	ENST00000273390.5	+	7	881	c.804A>G	c.(802-804)aaA>aaG	p.K268K		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	268						mitochondrion (GO:0005739)											AGAGGAGGAAAATGATGAATG	0.517													G|||	70	0.0139776	0.0514	0.0014	5008	,	,		19708	0.0		0.0	False		,,,				2504	0.001				p.K268K		Atlas-SNP	.											.	.	.	.	0			c.A804G						PASS	.	G		209,4197	807.1+/-415.9	3,203,1997	69.0	67.0	67.0		804	4.6	1.0	3	dbSNP_119	67	4,8596	819.0+/-406.8	1,2,4297	no	coding-synonymous	C3orf15	NM_033364.3		4,205,6294	GG,GA,AA		0.0465,4.7435,1.6377		268/768	119445139	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	89876	exon7			GAGGAAAATGATG	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.804A>G	3.37:g.119445139A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	131	62	0.473282	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Silent	SNP	ENST00000273390.5	37	CCDS2994.1																																																																																			A|0.983;G|0.017	0.017	strong		0.517	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
FBXL14	144699	hgsc.bcm.edu	37	12	1702561	1702561	+	Silent	SNP	G	G	A	rs35524129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:1702561G>A	ENST00000339235.3	-	1	770	c.672C>T	c.(670-672)tcC>tcT	p.S224S	WNT5B_ENST00000537031.1_Intron|FBXL14_ENST00000543278.1_5'Flank	NM_152441.2	NP_689654.1	Q8N1E6	FXL14_HUMAN	F-box and leucine-rich repeat protein 14	224					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	8	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00115)			TCAGCCCTCGGGAGATGTGCT	0.657													g|||	234	0.0467252	0.1006	0.013	5008	,	,		20364	0.0675		0.0169	False		,,,				2504	0.0072				p.S224S		Atlas-SNP	.											.	FBXL14	19	.	0			c.C672T						PASS	.	A		330,4076	169.8+/-200.3	14,302,1887	40.0	37.0	38.0		672	-1.1	1.0	12	dbSNP_126	38	112,8488	57.9+/-119.4	1,110,4189	no	coding-synonymous	FBXL14	NM_152441.2		15,412,6076	AA,AG,GG		1.3023,7.4898,3.3984		224/419	1702561	442,12564	2203	4300	6503	SO:0001819	synonymous_variant	144699	exon1			CCCTCGGGAGATG	BC028132	CCDS8509.1	12p13.33	2011-06-09			ENSG00000171823	ENSG00000171823		"""F-boxes / Leucine-rich repeats"""	28624	protein-coding gene	gene with protein product		609081				12477932	Standard	NM_152441		Approved	MGC40195, Fbl14	uc001qjh.3	Q8N1E6	OTTHUMG00000090369	ENST00000339235.3:c.672C>T	12.37:g.1702561G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_152441		Silent	SNP	ENST00000339235.3	37	CCDS8509.1																																																																																			G|0.964;A|0.036	0.036	strong		0.657	FBXL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206741.1	NM_152441	
ACVRL1	94	hgsc.bcm.edu	37	12	52308344	52308344	+	Silent	SNP	G	G	A	rs1058563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52308344G>A	ENST00000388922.4	+	6	1030	c.747G>A	c.(745-747)gtG>gtA	p.V249V	ACVRL1_ENST00000550683.1_Silent_p.V263V|ACVRL1_ENST00000419526.2_Silent_p.V75V	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	ATAACACAGTGTTGCTCAGAC	0.592													G|||	231	0.0461262	0.1619	0.0159	5008	,	,		10490	0.0		0.006	False		,,,				2504	0.0				p.V249V		Atlas-SNP	.											.	ACVRL1	60	.	0			c.G747A						PASS	.	G	,	576,3830	254.3+/-259.9	37,502,1664	94.0	71.0	79.0		747,747	1.9	0.4	12	dbSNP_86	79	17,8583	11.2+/-40.8	0,17,4283	no	coding-synonymous,coding-synonymous	ACVRL1	NM_000020.2,NM_001077401.1	,	37,519,5947	AA,AG,GG		0.1977,13.0731,4.5594	,	249/504,249/504	52308344	593,12413	2203	4300	6503	SO:0001819	synonymous_variant	94	exon6			CACAGTGTTGCTC	L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567			175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2		8397373, 8640225	Standard	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	ENST00000388922.4:c.747G>A	12.37:g.52308344G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	221	113	0.511312	NM_000020	A6NGA8	Silent	SNP	ENST00000388922.4	37	CCDS31804.1																																																																																			G|0.957;A|0.043	0.043	strong		0.592	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2		
AIFM1	9131	hgsc.bcm.edu	37	X	129283520	129283520	+	Silent	SNP	A	A	G	rs1139851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:129283520A>G	ENST00000287295.3	-	3	503	c.273T>C	c.(271-273)gaT>gaC	p.D91D	AIFM1_ENST00000346424.2_Intron|AIFM1_ENST00000319908.3_Silent_p.D87D|AIFM1_ENST00000535724.1_Silent_p.D4D	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	91					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	ATCTTTTTTCATCCTCTTTCA	0.383													G|||	1854	0.491126	0.5825	0.3588	3775	,	,		13492	0.1438		0.3171	False		,,,				2504	0.3793				p.D91D		Atlas-SNP	.											.	AIFM1	75	.	0			c.T273C						PASS	.	G	,,,	2712,1121		833,639,407,159,164	208.0	184.0	192.0		273,273,261,	3.7	0.1	X	dbSNP_86	192	2672,4056		387,1157,741,884,1131	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	AIFM1	NM_001130847.3,NM_004208.3,NM_145812.2,NM_145813.2	,,,	1220,1796,1148,1043,1295	GG,GA,G,AA,A		39.7146,29.246,49.02	,,,	91/325,91/614,87/610,	129283520	5384,5177	2202	4300	6502	SO:0001819	synonymous_variant	9131	exon3			TTTTTCATCCTCT	AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"""programmed cell death 8 (apoptosis-inducing factor)"", ""neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"""	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.273T>C	X.37:g.129283520A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	141	58	0.411348	NM_001130847	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Silent	SNP	ENST00000287295.3	37	CCDS14618.1																																																																																			0|0.004;G|0.504	0.504	strong		0.383	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2		
SLC6A11	6538	hgsc.bcm.edu	37	3	10976876	10976876	+	Silent	SNP	A	A	G	rs2245532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:10976876A>G	ENST00000254488.2	+	13	1803	c.1737A>G	c.(1735-1737)acA>acG	p.T579T		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	579					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)	CGGAGGGGACACTGCCCGAGG	0.642													G|||	1677	0.334864	0.5363	0.2954	5008	,	,		18258	0.1012		0.4254	False		,,,				2504	0.2382				p.T579T		Atlas-SNP	.											.	SLC6A11	87	.	0			c.A1737G						PASS	.	G		2318,2088	573.2+/-383.5	592,1134,477	104.0	100.0	101.0		1737	-8.4	0.0	3	dbSNP_100	101	3523,5077	632.1+/-398.6	741,2041,1518	no	coding-synonymous	SLC6A11	NM_014229.1		1333,3175,1995	GG,GA,AA		40.9651,47.3899,44.91		579/633	10976876	5841,7165	2203	4300	6503	SO:0001819	synonymous_variant	6538	exon13			GGGGACACTGCCC	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.1737A>G	3.37:g.10976876A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	184	90	0.48913	NM_014229	B2R6U6|Q8IYC9	Silent	SNP	ENST00000254488.2	37	CCDS2602.1																																																																																			A|0.595;G|0.405	0.405	strong		0.642	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229	
DDX49	54555	hgsc.bcm.edu	37	19	19035080	19035080	+	Missense_Mutation	SNP	G	G	C	rs143159618		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19035080G>C	ENST00000247003.4	+	7	882	c.815G>C	c.(814-816)aGc>aCc	p.S272T	DDX49_ENST00000599156.1_3'UTR|AC002985.3_ENST00000596918.1_Intron|DDX49_ENST00000438170.2_Missense_Mutation_p.S165T	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	272	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	18			Epithelial(12;0.0289)			CGCAAATTCAGCTTCCCCACC	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17489	0.0		0.0	False		,,,				2504	0.0				p.S272T		Atlas-SNP	.											.	DDX49	37	.	0			c.G815C						PASS	.	G	THR/SER	6,4400	11.4+/-27.6	0,6,2197	122.0	71.0	88.0		815	-2.3	0.8	19	dbSNP_134	88	0,8600		0,0,4300	no	missense	DDX49	NM_019070.4	58	0,6,6497	CC,CG,GG		0.0,0.1362,0.0461	benign	272/484	19035080	6,13000	2203	4300	6503	SO:0001583	missense	54555	exon7			AATTCAGCTTCCC		CCDS12390.1	19p12	2008-02-05				ENSG00000105671		"""DEAD-boxes"""	18684	protein-coding gene	gene with protein product							Standard	NM_019070		Approved	FLJ10432	uc002nkq.2	Q9Y6V7		ENST00000247003.4:c.815G>C	19.37:g.19035080G>C	ENSP00000247003:p.Ser272Thr	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	231	99	0.428571	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Missense_Mutation	SNP	ENST00000247003.4	37	CCDS12390.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.320348	0.41096	0.001362	0.0	ENSG00000105671	ENST00000247003;ENST00000438170	T;T	0.04862	3.54;3.54	5.03	-2.29	0.06805	Helicase, C-terminal (3);	0.775582	0.12437	N	0.469041	T	0.05410	0.0143	N	0.19112	0.55	0.24060	N	0.996013	B;B	0.06786	0.001;0.001	B;B	0.19946	0.027;0.027	T	0.29119	-1.0022	10	0.72032	D	0.01	-7.7016	15.0157	0.71581	0.3142:0.0:0.6858:0.0	.	272;272	A8K7A1;Q9Y6V7	.;DDX49_HUMAN	T	272;165	ENSP00000247003:S272T;ENSP00000395377:S165T	ENSP00000247003:S272T	S	+	2	0	DDX49	18896080	0.161000	0.22892	0.824000	0.32777	0.934000	0.57294	0.102000	0.15272	-1.026000	0.03330	-0.339000	0.08088	AGC	G|1.000;C|0.000	0.000	weak		0.617	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070	
OR1E1	8387	hgsc.bcm.edu	37	17	3301246	3301246	+	Silent	SNP	G	G	A	rs11078447	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3301246G>A	ENST00000322608.2	-	1	458	c.459C>T	c.(457-459)acC>acT	p.T153T		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	153					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(2)|lung(5)	10						TGGCATGGAAGGTGGTCAGCA	0.542													G|||	110	0.0219649	0.0772	0.0115	5008	,	,		22193	0.0		0.0	False		,,,				2504	0.0				p.T153T		Atlas-SNP	.											.	OR1E1	37	.	0			c.C459T						PASS	.	G		240,4166	140.8+/-176.2	5,230,1968	77.0	61.0	66.0		459	-9.4	0.0	17	dbSNP_120	66	2,8598		0,2,4298	no	coding-synonymous	OR1E1	NM_003553.2		5,232,6266	AA,AG,GG		0.0233,5.4471,1.8607		153/315	3301246	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	8387	exon1			ATGGAAGGTGGTC	U04642	CCDS11024.1	17p13.3	2012-08-09			ENSG00000180016	ENSG00000180016		"""GPCR / Class A : Olfactory receptors"""	8189	protein-coding gene	gene with protein product				OR1E9P, OR1E5, OR1E6		8004088, 1370859	Standard	NM_003553		Approved	OR17-2, HGM071, OR17-32, OR13-66	uc002fvj.1	P30953	OTTHUMG00000090643	ENST00000322608.2:c.459C>T	17.37:g.3301246G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	243	121	0.497942	NM_003553	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Silent	SNP	ENST00000322608.2	37	CCDS11024.1																																																																																			G|0.983;A|0.017	0.017	strong		0.542	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1	NM_003553	
GADL1	339896	hgsc.bcm.edu	37	3	30842517	30842517	+	Missense_Mutation	SNP	C	C	A	rs61738477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:30842517C>A	ENST00000282538.5	-	12	1264	c.1114G>T	c.(1114-1116)Gat>Tat	p.D372Y	GADL1_ENST00000454381.3_Missense_Mutation_p.D372Y	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	372					carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						TAGCTCACATCATAGAATTTA	0.418													C|||	22	0.00439297	0.0144	0.0043	5008	,	,		19418	0.0		0.0	False		,,,				2504	0.0				p.D372Y		Atlas-SNP	.											.	GADL1	91	.	0			c.G1114T						PASS	.	C	TYR/ASP	66,4340	60.5+/-97.4	1,64,2138	132.0	117.0	122.0		1114	5.5	1.0	3	dbSNP_129	122	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GADL1	NM_207359.2	160	1,65,6437	AA,AC,CC		0.0116,1.498,0.5151	probably-damaging	372/522	30842517	67,12939	2203	4300	6503	SO:0001583	missense	339896	exon12			TCACATCATAGAA	AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644			27949	protein-coding gene	gene with protein product		615601					Standard	NM_207359		Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.1114G>T	3.37:g.30842517C>A	ENSP00000282538:p.Asp372Tyr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	122	46	0.377049	NM_207359		Missense_Mutation	SNP	ENST00000282538.5	37	CCDS2649.2	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	26.6	4.752769	0.89753	0.01498	1.16E-4	ENSG00000144644	ENST00000282538;ENST00000454381	T;T	0.43688	0.94;0.94	5.47	5.47	0.80525	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.052957	0.64402	D	0.000001	T	0.68696	0.3029	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80311	-0.1436	10	0.87932	D	0	.	19.3171	0.94218	0.0:1.0:0.0:0.0	.	372	Q6ZQY3	GADL1_HUMAN	Y	372	ENSP00000282538:D372Y;ENSP00000427059:D372Y	ENSP00000282538:D372Y	D	-	1	0	GADL1	30817521	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	7.487000	0.81328	2.571000	0.86741	0.585000	0.79938	GAT	C|0.996;A|0.004	0.004	strong		0.418	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359	
CLUAP1	23059	hgsc.bcm.edu	37	16	3556398	3556398	+	Missense_Mutation	SNP	G	G	T	rs34115694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3556398G>T	ENST00000576634.1	+	3	346	c.202G>T	c.(202-204)Gca>Tca	p.A68S	LA16c-306E5.3_ENST00000574423.2_RNA|CLUAP1_ENST00000341633.5_Missense_Mutation_p.A68S|CLUAP1_ENST00000571025.1_Missense_Mutation_p.A68S|CLUAP1_ENST00000417763.2_5'UTR	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	68			A -> S (in dbSNP:rs34115694).		cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						CTTCATTAAGGCAATTGCCCA	0.438													G|||	130	0.0259585	0.0968	0.0029	5008	,	,		18976	0.0		0.0	False		,,,				2504	0.0				p.A68S		Atlas-SNP	.											.	CLUAP1	32	.	0			c.G202T						PASS	.	G	SER/ALA	337,4057	178.7+/-207.4	8,321,1868	158.0	139.0	146.0		202	5.5	1.0	16	dbSNP_126	146	3,8597	3.0+/-9.4	0,3,4297	yes	missense	CLUAP1	NM_015041.1	99	8,324,6165	TT,TG,GG		0.0349,7.6695,2.6166	benign	68/414	3556398	340,12654	2197	4300	6497	SO:0001583	missense	23059	exon3			ATTAAGGCAATTG	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.202G>T	16.37:g.3556398G>T	ENSP00000460850:p.Ala68Ser	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	101	63	0.623762	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	60	0.027472527472527472	59	0.11991869918699187	1	0.0027624309392265192	0	0.0	0	0.0	G	16.19	3.053615	0.55218	0.076695	3.49E-4	ENSG00000103351	ENST00000341633	T	0.43688	0.94	5.49	5.49	0.81192	.	0.046661	0.85682	D	0.000000	T	0.00384	0.0012	N	0.11789	0.175	0.80722	D	1	P	0.39903	0.694	B	0.39339	0.297	T	0.03969	-1.0988	10	0.12766	T	0.61	-16.0476	17.213	0.86935	0.0:0.0:1.0:0.0	rs34115694	68	Q96AJ1	CLUA1_HUMAN	S	68	ENSP00000344392:A68S	ENSP00000344392:A68S	A	+	1	0	CLUAP1	3496399	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.503000	0.81632	2.745000	0.94114	0.557000	0.71058	GCA	G|0.974;T|0.026	0.026	strong		0.438	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
RGL4	266747	hgsc.bcm.edu	37	22	24034288	24034288	+	Missense_Mutation	SNP	A	A	G	rs738786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24034288A>G	ENST00000290691.5	+	1	1241	c.71A>G	c.(70-72)cAg>cGg	p.Q24R	KB-1572G7.2_ENST00000421064.1_RNA|AP000347.2_ENST00000417194.1_RNA|RGL4_ENST00000401461.1_Intron|GUSBP11_ENST00000455485.1_RNA	NM_153615.1	NP_705843.1	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4	24			Q -> R (in dbSNP:rs738786). {ECO:0000269|PubMed:15489334}.		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						GCTGTGCTCCAGGGCCTTTGG	0.592													a|||	2755	0.55012	0.4372	0.6167	5008	,	,		17897	0.6071		0.5328	False		,,,				2504	0.6145				p.Q24R		Atlas-SNP	.											.	RGL4	29	.	0			c.A71G						PASS	.	A	ARG/GLN	1974,2432	554.0+/-378.9	465,1044,694	88.0	85.0	86.0		71	-0.7	0.0	22	dbSNP_86	86	4432,4168	587.2+/-392.2	1145,2142,1013	yes	missense	RGL4	NM_153615.1	43	1610,3186,1707	GG,GA,AA		48.4651,44.8025,49.2542	benign	24/474	24034288	6406,6600	2203	4300	6503	SO:0001583	missense	266747	exon1			TGCTCCAGGGCCT		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.71A>G	22.37:g.24034288A>G	ENSP00000290691:p.Gln24Arg	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_153615	Q495L8	Missense_Mutation	SNP	ENST00000290691.5	37	CCDS13811.1	1198	0.5485347985347986	225	0.4573170731707317	204	0.56353591160221	350	0.6118881118881119	419	0.5527704485488126	a	8.519	0.868317	0.17250	0.448025	0.515349	ENSG00000159496	ENST00000290691;ENST00000382833;ENST00000423392	T;T	0.29655	1.56;1.56	1.77	-0.665	0.11403	.	0.217217	0.22467	U	0.059673	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P;P	0.39094	0.618;0.659	B;B	0.42959	0.027;0.403	T	0.38628	-0.9652	9	0.05959	T	0.93	.	2.363	0.04312	0.3523:0.4384:0.0:0.2093	rs738786;rs58826212;rs738786	24;24	E9PH87;Q8IZJ4	.;RGDSR_HUMAN	R	24	ENSP00000290691:Q24R;ENSP00000402142:Q24R	ENSP00000290691:Q24R	Q	+	2	0	RGL4	22364288	0.490000	0.26012	0.000000	0.03702	0.005000	0.04900	-0.294000	0.08309	-0.151000	0.11176	0.443000	0.29094	CAG	A|0.483;G|0.517	0.517	strong		0.592	RGL4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319711.1	NM_153615	
GAB2	9846	hgsc.bcm.edu	37	11	77937800	77937800	+	Silent	SNP	G	G	A	rs2248407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77937800G>A	ENST00000361507.4	-	4	1003	c.918C>T	c.(916-918)ttC>ttT	p.F306F	GAB2_ENST00000340149.2_Silent_p.F268F|GAB2_ENST00000526030.1_5'Flank	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	306					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)			GGAGGTCCCCGAACTCCCTGC	0.557													A|||	1582	0.315895	0.3888	0.3285	5008	,	,		17019	0.3978		0.1789	False		,,,				2504	0.2648				p.F306F		Atlas-SNP	.											.	GAB2	63	.	0			c.C918T						PASS	.	A	,	1490,2910	676.3+/-403.2	249,992,959	68.0	64.0	65.0		804,918	-1.1	1.0	11	dbSNP_100	65	1378,7206	754.1+/-407.5	116,1146,3030	no	coding-synonymous,coding-synonymous	GAB2	NM_012296.3,NM_080491.2	,	365,2138,3989	AA,AG,GG		16.0531,33.8636,22.0887	,	268/639,306/677	77937800	2868,10116	2200	4292	6492	SO:0001819	synonymous_variant	9846	exon4			GTCCCCGAACTCC	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.918C>T	11.37:g.77937800G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	182	104	0.571429	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Silent	SNP	ENST00000361507.4	37	CCDS8259.1																																																																																			G|0.738;A|0.262	0.262	strong		0.557	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491	
ITGA2	3673	hgsc.bcm.edu	37	5	52351876	52351876	+	Silent	SNP	A	A	G	rs3212523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	100	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	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	
ACSM2A	123876	hgsc.bcm.edu	37	16	20471487	20471487	+	Missense_Mutation	SNP	G	G	C	rs137947890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20471487G>C	ENST00000573854.1	+	2	165	c.51G>C	c.(49-51)caG>caC	p.Q17H	ACSM2A_ENST00000536134.1_5'UTR|ACSM2A_ENST00000396104.2_Missense_Mutation_p.Q17H|ACSM2A_ENST00000575558.1_Intron|ACSM2A_ENST00000417235.2_Intron|ACSM2A_ENST00000424070.1_Missense_Mutation_p.Q17H|ACSM2A_ENST00000219054.6_Missense_Mutation_p.Q17H|ACSM2A_ENST00000575690.1_Missense_Mutation_p.Q17H	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	17					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						GGGGTACTCAGATGTCCAGCC	0.493													G|||	85	0.0169728	0.0635	0.0014	5008	,	,		18245	0.0		0.0	False		,,,				2504	0.0				p.Q17H		Atlas-SNP	.											.	ACSM2A	120	.	0			c.G51C						PASS	.	G	HIS/GLN	220,4186	133.7+/-170.0	8,204,1991	46.0	48.0	47.0		51	1.0	0.0	16	dbSNP_134	47	5,8589	4.3+/-15.6	0,5,4292	no	missense	ACSM2A	NM_001010845.2	24	8,209,6283	CC,CG,GG		0.0582,4.9932,1.7308	benign	17/578	20471487	225,12775	2203	4297	6500	SO:0001583	missense	123876	exon3			TACTCAGATGTCC	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"""Acyl-CoA synthetase family"""	32017	protein-coding gene	gene with protein product		614358	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.51G>C	16.37:g.20471487G>C	ENSP00000459451:p.Gln17His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	120	68	0.566667	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	30	0.013736263736263736	29	0.05894308943089431	0	0.0	0	0.0	1	0.0013192612137203166	G	7.282	0.609329	0.14066	0.049932	5.82E-4	ENSG00000183747	ENST00000219054;ENST00000424070;ENST00000396104	T;T;T	0.43688	0.94;2.24;0.94	3.28	1.03	0.20045	.	0.746597	0.11304	N	0.577908	T	0.02380	0.0073	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15407	-1.0438	10	0.14252	T	0.57	-4.0391	5.9796	0.19399	0.1217:0.1954:0.6829:0.0	.	17	Q08AH3	ACS2A_HUMAN	H	17	ENSP00000219054:Q17H;ENSP00000394904:Q17H;ENSP00000379411:Q17H	ENSP00000219054:Q17H	Q	+	3	2	ACSM2A	20378988	0.000000	0.05858	0.001000	0.08648	0.661000	0.39034	0.388000	0.20735	0.709000	0.31976	0.454000	0.30748	CAG	.	.	weak		0.493	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845	
MUC4	4585	hgsc.bcm.edu	37	3	195511788	195511788	+	Silent	SNP	G	G	A	rs71291863		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511788G>A	ENST00000463781.3	-	2	7122	c.6663C>T	c.(6661-6663)caC>caT	p.H2221H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.H2221H	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)		GAGGGATGGCGTGACCTGTGG	0.597																																					p.H2221H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C6663T						PASS	.						34.0	32.0	32.0					3																	195511788		677	1584	2261	SO:0001819	synonymous_variant	4585	exon2			GATGGCGTGACCT	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.6663C>T	3.37:g.195511788G>A		Somatic	394	0	0		WXS	Illumina HiSeq	Phase_I	202	37	0.183168	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																																																																																			.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FBXW9	84261	hgsc.bcm.edu	37	19	12805431	12805431	+	Missense_Mutation	SNP	T	T	C	rs10424623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12805431T>C	ENST00000380339.3	-	3	691	c.655A>G	c.(655-657)Act>Gct	p.T219A	FBXW9_ENST00000587955.1_Missense_Mutation_p.T209A|FBXW9_ENST00000393261.3_Missense_Mutation_p.T219A|FBXW9_ENST00000544494.1_5'UTR			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	219			T -> A (in dbSNP:rs10424623).		SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						TTTCGCTTAGTGCCTAAGGTC	0.562													T|||	748	0.149361	0.534	0.0461	5008	,	,		19047	0.0		0.0099	False		,,,				2504	0.0				p.T219A		Atlas-SNP	.											.	FBXW9	30	.	0			c.A655G						PASS	.	T	ALA/THR	1743,2441		372,999,721	65.0	74.0	71.0		655	2.1	0.2	19	dbSNP_119	71	133,8305		1,131,4087	yes	missense	FBXW9	NM_032301.2	58	373,1130,4808	CC,CT,TT		1.5762,41.6587,14.8629	benign	219/459	12805431	1876,10746	2092	4219	6311	SO:0001583	missense	84261	exon3			GCTTAGTGCCTAA	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.655A>G	19.37:g.12805431T>C	ENSP00000369696:p.Thr219Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		244	0.11172161172161173	220	0.44715447154471544	17	0.04696132596685083	0	0.0	7	0.009234828496042216	T	5.162	0.215402	0.09810	0.416587	0.015762	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.51325	1.74;0.71	4.29	2.11	0.27256	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.565790	0.18087	N	0.152109	T	0.00012	0.0000	N	0.24115	0.695	0.21386	P	0.999707688	B;B;B	0.17268	0.013;0.009;0.021	B;B;B	0.16289	0.014;0.015;0.009	T	0.46219	-0.9207	9	0.32370	T	0.25	-17.2872	5.0146	0.14330	0.162:0.0922:0.0:0.7458	rs10424623	209;219;219	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	A	219	ENSP00000376945:T219A;ENSP00000369696:T219A	ENSP00000369696:T219A	T	-	1	0	FBXW9	12666431	0.259000	0.24043	0.235000	0.24058	0.003000	0.03518	0.704000	0.25661	0.190000	0.20209	0.379000	0.24179	ACT	T|0.921;C|0.079	0.079	strong		0.562	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
SPTA1	6708	hgsc.bcm.edu	37	1	158632531	158632531	+	Missense_Mutation	SNP	T	T	C	rs7547313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158632531T>C	ENST00000368147.4	-	17	2605	c.2425A>G	c.(2425-2427)Atc>Gtc	p.I809V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	809			I -> V (in dbSNP:rs7547313).		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)					GTCTCTTGGATCCAGGCCTCC	0.502													T|||	516	0.103035	0.3707	0.0331	5008	,	,		16779	0.0		0.003	False		,,,				2504	0.0				p.I809V		Atlas-SNP	.											SPTA1,NS,carcinoma,+2,1	SPTA1	720	1	0			c.A2425G						PASS	.	T	VAL/ILE	1083,2813		165,753,1030	100.0	103.0	102.0		2425	4.3	1.0	1	dbSNP_116	102	19,8255		0,19,4118	yes	missense	SPTA1	NM_003126.2	29	165,772,5148	CC,CT,TT		0.2296,27.7977,9.0551	possibly-damaging	809/2420	158632531	1102,11068	1948	4137	6085	SO:0001583	missense	6708	exon17			CTTGGATCCAGGC	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.2425A>G	1.37:g.158632531T>C	ENSP00000357129:p.Ile809Val	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	205	104	0.507317	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	183	0.08379120879120878	172	0.34959349593495936	11	0.03038674033149171	0	0.0	0	0.0	T	21.0	4.080651	0.76528	0.277977	0.002296	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.39787	1.06;1.06	4.28	4.28	0.50868	.	0.000000	0.32852	N	0.005568	T	0.40196	0.1107	L	0.37466	1.105	0.22531	P	0.999012003	D	0.76494	0.999	D	0.91635	0.999	T	0.38824	-0.9643	9	0.44086	T	0.13	.	10.915	0.47131	0.0:0.0:0.0:1.0	rs7547313;rs7547313	809	P02549	SPTA1_HUMAN	V	809	ENSP00000357130:I809V;ENSP00000357129:I809V	ENSP00000357129:I809V	I	-	1	0	SPTA1	156899155	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.011000	0.76359	1.786000	0.52430	0.460000	0.39030	ATC	T|0.946;C|0.054	0.054	strong		0.502	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
CYP4F12	66002	hgsc.bcm.edu	37	19	15791066	15791066	+	Missense_Mutation	SNP	C	C	T	rs61731193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791066C>T	ENST00000550308.1	+	4	736	c.356C>T	c.(355-357)cCc>cTc	p.P119L	CYP4F12_ENST00000324632.10_Missense_Mutation_p.P119L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	119					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GCCATTGCACCCAAGGATAAT	0.567													.|||	103	0.0205671	0.0734	0.0072	5008	,	,		20736	0.0		0.001	False		,,,				2504	0.0				p.P119L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C356T						PASS	.	T	LEU/PRO	247,4133		2,243,1945	143.0	146.0	145.0		356	-1.3	0.0	19	dbSNP_129	145	3,8579		0,3,4288	yes	missense	CYP4F12	NM_023944.3	98	2,246,6233	TT,TC,CC		0.035,5.6393,1.9287	possibly-damaging	119/525	15791066	250,12712	2190	4291	6481	SO:0001583	missense	66002	exon4			TTGCACCCAAGGA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.356C>T	19.37:g.15791066C>T	ENSP00000448998:p.Pro119Leu	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	355	89	0.250704	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	40	0.018315018315018316	37	0.07520325203252033	3	0.008287292817679558	0	0.0	0	0.0	.	7.772	0.707735	0.15239	0.056393	3.5E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.69175	-0.38;-0.38	2.36	-1.32	0.09201	.	0.825497	0.10255	N	0.696720	T	0.07863	0.0197	L	0.59912	1.85	0.09310	N	1	B;B;B	0.26512	0.151;0.046;0.014	B;B;B	0.36766	0.232;0.168;0.098	T	0.46857	-0.9161	10	0.52906	T	0.07	.	5.4101	0.16344	0.0:0.5515:0.0:0.4485	rs61731193	119;119;119	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	L	119	ENSP00000448998:P119L;ENSP00000321821:P119L	ENSP00000321821:P119L	P	+	2	0	CYP4F12	15652066	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.870000	0.04228	-0.186000	0.10533	-1.139000	0.01908	CCC	C|0.988;T|0.012	0.012	strong		0.567	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
GPR144	347088	hgsc.bcm.edu	37	9	127231763	127231763	+	Missense_Mutation	SNP	G	G	A	rs114565703|rs386738474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127231763G>A	ENST00000334810.1	+	16	2495	c.2495G>A	c.(2494-2496)cGc>cAc	p.R832H				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	832					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						TCCAGTGCCCGCCGCCGTGCC	0.642													G|||	95	0.0189696	0.0681	0.0058	5008	,	,		17367	0.001		0.0	False		,,,				2504	0.0				p.R832H		Atlas-SNP	.											.	GPR144	33	.	0			c.G2495A						PASS	.	G	HIS/ARG	113,1271		6,101,585	29.0	36.0	34.0		2495	1.2	1.0	9	dbSNP_132	34	1,3181		0,1,1590	yes	missense	GPR144	NM_001161808.1	29	6,102,2175	AA,AG,GG		0.0314,8.1647,2.4967	probably-damaging	832/964	127231763	114,4452	692	1591	2283	SO:0001583	missense	347088	exon16			GTGCCCGCCGCCG	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.2495G>A	9.37:g.127231763G>A	ENSP00000335156:p.Arg832His	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	143	137	0.958042	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	41	0.018772893772893772	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	0	0.0	G	13.71	2.318318	0.40996	0.081647	3.14E-4	ENSG00000180264	ENST00000334810	T	0.44881	0.91	4.22	1.21	0.21127	GPCR, family 2-like (1);	.	.	.	.	T	0.02342	0.0072	M	0.66506	2.035	0.35385	D	0.790234	P	0.36535	0.557	B	0.34093	0.175	T	0.09640	-1.0665	9	0.62326	D	0.03	.	8.9349	0.35693	0.2619:0.0:0.7381:0.0	.	832	Q7Z7M1	GP144_HUMAN	H	832	ENSP00000335156:R832H	ENSP00000335156:R832H	R	+	2	0	GPR144	126271584	0.917000	0.31117	0.993000	0.49108	0.883000	0.51084	0.680000	0.25306	-0.057000	0.13199	0.462000	0.41574	CGC	G|0.975;A|0.025	0.025	strong		0.642	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
PLEKHN1	84069	hgsc.bcm.edu	37	1	909238	909238	+	Missense_Mutation	SNP	G	G	C	rs3829740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:909238G>C	ENST00000379409.2	+	13	1646	c.1616G>C	c.(1615-1617)cGt>cCt	p.R539P	PLEKHN1_ENST00000379410.3_Missense_Mutation_p.R487P|PLEKHN1_ENST00000379407.3_Missense_Mutation_p.R452P			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	539			R -> P (in dbSNP:rs3829740). {ECO:0000269|PubMed:11230166}.							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)		CAGAGTGCACGTGGACCCACG	0.692													C|||	3889	0.776558	0.8169	0.6931	5008	,	,		15120	0.8869		0.6183	False		,,,				2504	0.8303				p.R487P		Atlas-SNP	.											.	PLEKHN1	49	.	0			c.G1460C						PASS	.	C	PRO/ARG,PRO/ARG	3431,963	343.3+/-307.6	1335,761,101	27.0	33.0	31.0		1355,1460	2.5	0.0	1	dbSNP_107	31	5009,3579	498.1+/-374.7	1490,2029,775	yes	missense,missense	PLEKHN1	NM_001160184.1,NM_032129.2	103,103	2825,2790,876	CC,CG,GG		41.6744,21.9162,34.9869	benign,benign	452/577,487/612	909238	8440,4542	2197	4294	6491	SO:0001583	missense	84069	exon14			GTGCACGTGGACC	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.1616G>C	1.37:g.909238G>C	ENSP00000368719:p.Arg539Pro	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_032129	Q494U2|Q5SV98|Q9H0M7	Missense_Mutation	SNP	ENST00000379409.2	37		1609	0.7367216117216118	399	0.8109756097560976	242	0.6685082872928176	508	0.8881118881118881	460	0.6068601583113457	C	2.592	-0.294888	0.05568	0.780838	0.583256	ENSG00000187583	ENST00000379410;ENST00000379407;ENST00000379409	T;T;T	0.41758	0.99;1.0;1.0	4.65	2.45	0.29901	.	0.680154	0.13101	N	0.413783	T	0.00012	0.0000	N	0.02539	-0.55	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	0.15752	-1.0426	9	0.30078	T	0.28	.	2.6504	0.04998	0.0:0.354:0.2625:0.3834	rs3829740;rs3892468;rs59832503	452;539;487	Q494U1-3;Q494U1;Q494U1-2	.;PKHN1_HUMAN;.	P	487;452;539	ENSP00000368720:R487P;ENSP00000368717:R452P;ENSP00000368719:R539P	ENSP00000368717:R452P	R	+	2	0	PLEKHN1	899101	0.000000	0.05858	0.007000	0.13788	0.004000	0.04260	0.311000	0.19380	0.456000	0.26937	-0.546000	0.04227	CGT	G|0.322;C|0.678	0.678	strong		0.692	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129	
OBSCN	84033	hgsc.bcm.edu	37	1	228471379	228471379	+	Silent	SNP	G	G	C	rs56168609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228471379G>C	ENST00000422127.1	+	33	8957	c.8913G>C	c.(8911-8913)cgG>cgC	p.R2971R	OBSCN_ENST00000359599.6_Silent_p.R1818R|OBSCN_ENST00000284548.11_Silent_p.R2971R|OBSCN_ENST00000570156.2_Silent_p.R3400R|OBSCN_ENST00000366709.4_Silent_p.R90R|OBSCN_ENST00000366707.4_Silent_p.R90R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2971	Ig-like 29.				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)				TGACCCTGCGGCTCACCATCA	0.677													g|||	1153	0.230232	0.1989	0.3242	5008	,	,		17988	0.1528		0.3499	False		,,,				2504	0.1626				p.R3400R		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,+1,4	OBSCN	2142	4	0			c.G10200C						PASS	.		,	1049,3203		133,783,1210	36.0	44.0	41.0		8913,8913	0.3	0.1	1	dbSNP_129	41	3121,5357		597,1927,1715	yes	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	730,2710,2925	CC,CG,GG		36.8129,24.6707,32.7573	,	2971/7969,2971/6621	228471379	4170,8560	2126	4239	6365	SO:0001819	synonymous_variant	84033	exon38			CCTGCGGCTCACC	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.8913G>C	1.37:g.228471379G>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	169	86	0.508876	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																																																																																			G|0.721;C|0.279	0.279	strong		0.677	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
LCT	3938	hgsc.bcm.edu	37	2	136574968	136574968	+	Silent	SNP	G	G	C	rs35093754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:136574968G>C	ENST00000264162.2	-	6	1660	c.1650C>G	c.(1648-1650)ggC>ggG	p.G550G	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	550	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)	CGGTGCCATAGCCTGCGTAGC	0.577													G|||	251	0.0501198	0.1059	0.0202	5008	,	,		16966	0.0516		0.0288	False		,,,				2504	0.0164				p.G550G		Atlas-SNP	.											.	LCT	309	.	0			c.C1650G						PASS	.	G		483,3923	226.2+/-241.8	31,421,1751	85.0	80.0	82.0		1650	0.9	1.0	2	dbSNP_126	82	186,8414	82.3+/-144.9	3,180,4117	no	coding-synonymous	LCT	NM_002299.2		34,601,5868	CC,CG,GG		2.1628,10.9623,5.1438		550/1928	136574968	669,12337	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon6			GCCATAGCCTGCG	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.1650C>G	2.37:g.136574968G>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.950;C|0.050	0.050	strong		0.577	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
NEB	4703	hgsc.bcm.edu	37	2	152346979	152346979	+	Missense_Mutation	SNP	T	T	C	rs1061305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152346979T>C	ENST00000172853.10	-	147	19783	c.19636A>G	c.(19636-19638)Atc>Gtc	p.I6546V	NEB_ENST00000603639.1_Missense_Mutation_p.I8402V|RIF1_ENST00000457745.1_Intron|NEB_ENST00000409198.1_Missense_Mutation_p.I6546V|NEB_ENST00000604864.1_Missense_Mutation_p.I8402V|NEB_ENST00000509223.2_Missense_Mutation_p.I315V|NEB_ENST00000397345.3_Missense_Mutation_p.I8402V|NEB_ENST00000397336.2_Missense_Mutation_p.I377V|NEB_ENST00000498015.2_5'Flank|NEB_ENST00000427231.2_Missense_Mutation_p.I8402V			P20929	NEBU_HUMAN	nebulin	6546	Interaction with SVIL.		I -> V (in dbSNP:rs1061305). {ECO:0000269|PubMed:7739042}.		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)		CCCCCACTGATGCTTAGTGCA	0.542													T|||	1674	0.334265	0.4599	0.3458	5008	,	,		16667	0.254		0.3738	False		,,,				2504	0.1984				p.I8437V		Atlas-SNP	.											.	NEB	1697	.	0			c.A25309G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	1744,2344		390,964,690	61.0	62.0	62.0		19636,25204,25204	0.4	1.0	2	dbSNP_86	62	3495,4927		743,2009,1459	yes	missense,missense,missense	NEB	NM_004543.4,NM_001164508.1,NM_001164507.1	29,29,29	1133,2973,2149	CC,CT,TT		41.4985,42.6614,41.8785	benign,benign,benign	6546/6670,8402/8526,8402/8526	152346979	5239,7271	2044	4211	6255	SO:0001583	missense	4703	exon181			CACTGATGCTTAG	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.19636A>G	2.37:g.152346979T>C	ENSP00000172853:p.Ile6546Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		811	0.37133699633699635	247	0.5020325203252033	119	0.3287292817679558	162	0.28321678321678323	283	0.3733509234828496	T	11.50	1.658056	0.29425	0.426614	0.414985	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000397336;ENST00000509223	T;T;T;T;T;T;T	0.05855	3.5;3.52;3.52;3.38;3.5;4.08;4.27	5.4	0.397	0.16314	.	0.399381	0.30602	N	0.009272	T	0.00012	0.0000	N	0.22421	0.69	0.45108	P	0.00187499999999996	B;B;B;B	0.15930	0.0;0.0;0.001;0.015	B;B;B;B	0.23018	0.0;0.001;0.0;0.043	T	0.40289	-0.9571	9	0.13853	T	0.58	.	5.4834	0.16737	0.0:0.2949:0.2439:0.4612	rs1061305;rs3202355;rs17198024;rs57151876;rs1061305	315;377;6546;8402	B7Z6B9;B7Z6P9;P20929;F8WCL5	.;.;NEBU_HUMAN;.	V	6546;8402;8402;2502;2884;6546;377;315	ENSP00000386259:I6546V;ENSP00000380505:I8402V;ENSP00000416578:I8402V;ENSP00000410961:I2884V;ENSP00000172853:I6546V;ENSP00000380497:I377V;ENSP00000427083:I315V	ENSP00000172853:I6546V	I	-	1	0	NEB	152055225	0.776000	0.28616	0.997000	0.53966	0.961000	0.63080	-0.696000	0.05104	0.051000	0.15978	0.379000	0.24179	ATC	T|0.628;C|0.370	0.370	strong		0.542	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
FBN3	84467	hgsc.bcm.edu	37	19	8150393	8150393	+	Missense_Mutation	SNP	C	C	T	rs17160151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8150393C>T	ENST00000600128.1	-	56	7355	c.6941G>A	c.(6940-6942)aGc>aAc	p.S2314N	FBN3_ENST00000601739.1_Missense_Mutation_p.S2314N|FBN3_ENST00000270509.2_Missense_Mutation_p.S2314N			Q75N90	FBN3_HUMAN	fibrillin 3	2314	TB 9.		S -> N (in dbSNP:rs17160151).			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						CTCACTGCTGCTGGACAGAGA	0.672													C|||	349	0.0696885	0.2549	0.0159	5008	,	,		15574	0.0		0.001	False		,,,				2504	0.0				p.S2314N		Atlas-SNP	.											.	FBN3	300	.	0			c.G6941A						PASS	.	C	ASN/SER	998,3396		110,778,1309	12.0	13.0	12.0		6941	2.3	0.0	19	dbSNP_123	12	19,8551		1,17,4267	yes	missense	FBN3	NM_032447.3	46	111,795,5576	TT,TC,CC		0.2217,22.7128,7.8448	probably-damaging	2314/2810	8150393	1017,11947	2197	4285	6482	SO:0001583	missense	84467	exon55			CTGCTGCTGGACA		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.6941G>A	19.37:g.8150393C>T	ENSP00000470498:p.Ser2314Asn	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	139	0.06364468864468864	134	0.27235772357723576	4	0.011049723756906077	1	0.0017482517482517483	0	0.0	C	16.20	3.056882	0.55325	0.227128	0.002217	ENSG00000142449	ENST00000270509;ENST00000341066	D	0.90844	-2.74	4.72	2.31	0.28768	Matrix fibril-associated (2);TGF-beta binding (1);	0.056067	0.64402	U	0.000001	T	0.00144	0.0004	M	0.73962	2.25	0.37731	P	0.07474400000000003	D;P	0.71674	0.998;0.896	D;P	0.83275	0.996;0.596	T	0.00000	-1.2854	9	0.31617	T	0.26	.	13.4093	0.60933	0.0:0.5983:0.4017:0.0	rs17160151;rs17160151	2314;420	Q75N90;Q6ZNB8	FBN3_HUMAN;.	N	2314;420	ENSP00000270509:S2314N	ENSP00000270509:S2314N	S	-	2	0	FBN3	8056393	1.000000	0.71417	0.041000	0.18516	0.142000	0.21351	1.586000	0.36611	2.170000	0.68504	0.491000	0.48974	AGC	C|0.903;T|0.097	0.097	strong		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
NR5A1	2516	hgsc.bcm.edu	37	9	127245070	127245070	+	Silent	SNP	C	C	T	rs79833327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127245070C>T	ENST00000373588.4	-	7	1549	c.1353G>A	c.(1351-1353)ctG>ctA	p.L451L		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	451	Important for dimerization.				adrenal gland development (GO:0030325)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|hormone metabolic process (GO:0042445)|intracellular receptor signaling pathway (GO:0030522)|luteinization (GO:0001553)|maintenance of protein location in nucleus (GO:0051457)|male gonad development (GO:0008584)|multicellular organismal aging (GO:0010259)|negative regulation of female gonad development (GO:2000195)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|primary sex determination (GO:0007538)|regulation of steroid biosynthetic process (GO:0050810)|tissue development (GO:0009888)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)	2						TTTCGATGAGCAGGTTGTTGC	0.697													C|||	45	0.00898562	0.0333	0.0014	5008	,	,		11167	0.0		0.0	False		,,,				2504	0.0				p.L451L		Atlas-SNP	.											.	NR5A1	32	.	0			c.G1353A						PASS	.	C		214,4188	122.1+/-159.5	5,204,1992	64.0	45.0	51.0		1353	3.9	1.0	9	dbSNP_131	51	2,8594		0,2,4296	no	coding-synonymous	NR5A1	NM_004959.4		5,206,6288	TT,TC,CC		0.0233,4.8614,1.6618		451/462	127245070	216,12782	2201	4298	6499	SO:0001819	synonymous_variant	2516	exon7			GATGAGCAGGTTG	D88155	CCDS6856.1	9q33	2013-01-16			ENSG00000136931	ENSG00000136931		"""Nuclear hormone receptors"""	7983	protein-coding gene	gene with protein product		184757		FTZF1		7789992	Standard	NM_004959		Approved	FTZ1, SF-1, ELP, AD4BP	uc004boo.1	Q13285	OTTHUMG00000020655	ENST00000373588.4:c.1353G>A	9.37:g.127245070C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	115	42	0.365217	NM_004959	O15196|Q5T6F5	Silent	SNP	ENST00000373588.4	37	CCDS6856.1																																																																																			C|0.983;T|0.017	0.017	strong		0.697	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959	
ECH1	1891	hgsc.bcm.edu	37	19	39308190	39308190	+	Silent	SNP	C	C	T	rs15570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39308190C>T	ENST00000221418.4	-	4	607	c.375G>A	c.(373-375)tcG>tcA	p.S125S	AC104534.2_ENST00000594558.1_RNA|AC104534.3_ENST00000594769.1_Missense_Mutation_p.R295Q	NM_001398.2	NP_001389.2	Q13011	ECH1_HUMAN	enoyl CoA hydratase 1, peroxisomal	125					fatty acid beta-oxidation (GO:0006635)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	isomerase activity (GO:0016853)|receptor binding (GO:0005102)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	6	all_cancers(60;9.36e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			GCAGGATGTCCGAAGCCATGT	0.562													c|||	903	0.180312	0.2057	0.1225	5008	,	,		19650	0.1012		0.1282	False		,,,				2504	0.3221				p.S125S		Atlas-SNP	.											.	ECH1	14	.	0			c.G375A						PASS	.	C		878,3528	339.4+/-305.8	88,702,1413	77.0	60.0	66.0		375	-10.5	0.0	19	dbSNP_123	66	1158,7442	237.1+/-269.0	73,1012,3215	no	coding-synonymous	ECH1	NM_001398.2		161,1714,4628	TT,TC,CC		13.4651,19.9274,15.6543		125/329	39308190	2036,10970	2203	4300	6503	SO:0001819	synonymous_variant	1891	exon4			GATGTCCGAAGCC	U16660	CCDS33014.1	19q13.1	2010-04-30	2010-04-30			ENSG00000104823			3149	protein-coding gene	gene with protein product		600696	"""enoyl Coenzyme A hydratase 1, peroxisomal"""			7558027	Standard	XM_005258610		Approved	HPXEL		Q13011		ENST00000221418.4:c.375G>A	19.37:g.39308190C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_001398	A8K745|Q8WVX0|Q96EZ9	Silent	SNP	ENST00000221418.4	37	CCDS33014.1																																																																																			C|0.851;T|0.149	0.149	strong		0.562	ECH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462650.1		
ZC3H3	23144	hgsc.bcm.edu	37	8	144522387	144522387	+	Nonsense_Mutation	SNP	G	G	T	rs2272754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144522387G>T	ENST00000262577.5	-	11	2670	c.2639C>A	c.(2638-2640)tCa>tAa	p.S880*		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	880	Poly-Ser.				mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			Gggaggggatgaggaggagga	0.652													G|||	560	0.111821	0.0363	0.1167	5008	,	,		17078	0.2431		0.1461	False		,,,				2504	0.0399				p.S880X		Atlas-SNP	.											.	ZC3H3	75	.	0			c.C2639A						PASS	.	G	stop/SER	220,4186		8,204,1991	29.0	28.0	29.0		2639	1.1	0.0	8	dbSNP_100	29	943,7655		116,711,3472	yes	stop-gained	ZC3H3	NM_015117.2		124,915,5463	TT,TG,GG		10.9677,4.9932,8.9434		880/949	144522387	1163,11841	2203	4299	6502	SO:0001587	stop_gained	23144	exon11			GGGGATGAGGAGG	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"""Zinc fingers, CCCH-type domain containing"""	28972	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 3"""	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.2639C>A	8.37:g.144522387G>T	ENSP00000262577:p.Ser880*	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	108	62	0.574074	NM_015117	Q14163|Q8N4E2|Q9BUS4	Nonsense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	273	0.125	25	0.0508130081300813	42	0.11602209944751381	122	0.21328671328671328	84	0.11081794195250659	G	27.7	4.854259	0.91355	0.049932	0.109677	ENSG00000014164	ENST00000262577	.	.	.	4.25	1.07	0.20283	.	2.759650	0.01499	N	0.017425	.	.	.	.	.	.	0.09310	P	0.9999999999699166	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	2.0487	8.7374	0.34537	0.0967:0.5505:0.3527:0.0	rs2272754	.	.	.	X	880	.	ENSP00000262577:S880X	S	-	2	0	ZC3H3	144593530	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.528000	0.06193	-0.133000	0.11537	-0.444000	0.05651	TCA	G|0.879;T|0.121	0.121	strong		0.652	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
ITPR3	3710	hgsc.bcm.edu	37	6	33648144	33648144	+	Silent	SNP	C	C	T	rs11967839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33648144C>T	ENST00000374316.5	+	33	5323	c.4263C>T	c.(4261-4263)taC>taT	p.Y1421Y	ITPR3_ENST00000605930.1_Silent_p.Y1421Y			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1421					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	ACCACTGCTACGTGGACACGG	0.607													C|||	572	0.114217	0.2958	0.0375	5008	,	,		16528	0.0585		0.0447	False		,,,				2504	0.0521				p.Y1421Y		Atlas-SNP	.											.	ITPR3	409	.	0			c.C4263T						PASS	.	C		1037,3369	382.3+/-324.4	121,795,1287	63.0	57.0	59.0		4263	-4.0	0.9	6	dbSNP_120	59	392,8208	126.5+/-185.0	11,370,3919	no	coding-synonymous	ITPR3	NM_002224.3		132,1165,5206	TT,TC,CC		4.5581,23.5361,10.9872		1421/2672	33648144	1429,11577	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon32			CTGCTACGTGGAC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.4263C>T	6.37:g.33648144C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	50	30	0.6	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.890;T|0.110	0.110	strong		0.607	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
ZFPM1	161882	hgsc.bcm.edu	37	16	88599023	88599023	+	Splice_Site	SNP	A	A	G	rs56041036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88599023A>G	ENST00000319555.3	+	8	1270	c.948A>G	c.(946-948)ggA>ggG	p.G316G	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	316					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)		GTGTTCCAGGAGAGCGGCCCT	0.662													a|||	741	0.147963	0.0741	0.1484	5008	,	,		16600	0.3591		0.0974	False		,,,				2504	0.0818				p.G316G	Pancreas(49;850 1106 29641 32847 38344)	Atlas-SNP	.											ZFPM1,NS,carcinoma,0,1	ZFPM1	32	1	0			c.A948G						PASS	.	A		345,4013		17,311,1851	29.0	27.0	28.0		948	0.6	1.0	16	dbSNP_129	28	652,7914		21,610,3652	yes	coding-synonymous-near-splice	ZFPM1	NM_153813.2		38,921,5503	GG,GA,AA		7.6115,7.9165,7.7143		316/1007	88599023	997,11927	2179	4283	6462	SO:0001630	splice_region_variant	161882	exon8			TCCAGGAGAGCGG	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.947-1A>G	16.37:g.88599023A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	168	76	0.452381	NM_153813		Silent	SNP	ENST00000319555.3	37	CCDS32502.1																																																																																			A|0.879;G|0.121	0.121	strong		0.662	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		Silent
DENND5A	23258	hgsc.bcm.edu	37	11	9286515	9286515	+	Silent	SNP	C	C	T	rs75717840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9286515C>T	ENST00000328194.3	-	1	422	c.102G>A	c.(100-102)gaG>gaA	p.E34E	DENND5A_ENST00000530044.1_Silent_p.E34E	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	34					positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CACCCGACAGCTCGTCCGGCT	0.711													C|||	104	0.0207668	0.0772	0.0029	5008	,	,		8908	0.0		0.0	False		,,,				2504	0.0				p.E34E		Atlas-SNP	.											.	DENND5A	84	.	0			c.G102A						PASS	.	C		216,3890		5,206,1842	6.0	7.0	6.0		102	1.3	0.2	11	dbSNP_132	6	4,8126		0,4,4061	no	coding-synonymous	DENND5A	NM_015213.3		5,210,5903	TT,TC,CC		0.0492,5.2606,1.798		34/1288	9286515	220,12016	2053	4065	6118	SO:0001819	synonymous_variant	23258	exon1			CGACAGCTCGTCC	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.102G>A	11.37:g.9286515C>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	42	25	0.595238	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Silent	SNP	ENST00000328194.3	37	CCDS31423.1																																																																																			C|0.980;T|0.020	0.020	strong		0.711	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	
AMOTL1	154810	hgsc.bcm.edu	37	11	94602457	94602457	+	Silent	SNP	G	G	A	rs181764487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94602457G>A	ENST00000433060.2	+	12	2724	c.2583G>A	c.(2581-2583)acG>acA	p.T861T	AMOTL1_ENST00000317829.8_Silent_p.T811T|AMOTL1_ENST00000317837.9_Silent_p.T448T	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	861					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)				CCTCCACTACGGCAGCCAGCA	0.632													G|||	20	0.00399361	0.0106	0.0072	5008	,	,		14338	0.0		0.0	False		,,,				2504	0.001				p.T861T		Atlas-SNP	.											AMOTL1,NS,carcinoma,+1,2	AMOTL1	95	2	0			c.G2583A						PASS	.	G		24,4298		0,24,2137	25.0	34.0	31.0		2583	-10.3	0.0	11		31	2,8548		0,2,4273	no	coding-synonymous	AMOTL1	NM_130847.2		0,26,6410	AA,AG,GG		0.0234,0.5553,0.202		861/957	94602457	26,12846	2161	4275	6436	SO:0001819	synonymous_variant	154810	exon12			CACTACGGCAGCC	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.2583G>A	11.37:g.94602457G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	139	69	0.496403	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Silent	SNP	ENST00000433060.2	37	CCDS44712.1																																																																																			G|0.995;A|0.005	0.005	strong		0.632	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
TTC28	23331	hgsc.bcm.edu	37	22	28378450	28378450	+	Missense_Mutation	SNP	T	T	C	rs61744744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:28378450T>C	ENST00000397906.2	-	23	7346	c.7205A>G	c.(7204-7206)aAt>aGt	p.N2402S	TTC28-AS1_ENST00000417497.1_RNA|TTC28-AS1_ENST00000419253.1_RNA|TTC28-AS1_ENST00000434221.1_RNA|TTC28-AS1_ENST00000430525.1_RNA|TTC28-AS1_ENST00000452612.1_RNA|TTC28-AS1_ENST00000424161.1_RNA|TTC28-AS1_ENST00000425112.1_RNA|TTC28-AS1_ENST00000435348.1_RNA|TTC28-AS1_ENST00000453632.1_RNA|TTC28-AS1_ENST00000454741.1_RNA|TTC28-AS1_ENST00000430853.1_RNA|TTC28-AS1_ENST00000454996.1_RNA	NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	2402					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						CTCCTTCTTATTGTGCCGTGG	0.562													T|||	54	0.0107827	0.0393	0.0029	5008	,	,		16058	0.0		0.0	False		,,,				2504	0.0				p.N2402S		Atlas-SNP	.											.	TTC28	84	.	0			c.A7205G						PASS	.	T	SER/ASN	51,1333		1,49,642	48.0	49.0	49.0		7205	1.0	1.0	22	dbSNP_129	49	0,3182		0,0,1591	yes	missense	TTC28	NM_001145418.1	46	1,49,2233	CC,CT,TT		0.0,3.685,1.117	benign	2402/2482	28378450	51,4515	692	1591	2283	SO:0001583	missense	23331	exon23			TTCTTATTGTGCC	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.7205A>G	22.37:g.28378450T>C	ENSP00000381003:p.Asn2402Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	105	44	0.419048	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Missense_Mutation	SNP	ENST00000397906.2	37	CCDS46678.1	32	0.014652014652014652	30	0.06097560975609756	2	0.0055248618784530384	0	0.0	0	0.0	T	7.189	0.591145	0.13812	0.03685	0.0	ENSG00000100154	ENST00000397906	D	0.87029	-2.2	4.85	0.981	0.19756	.	0.332930	0.31188	N	0.008081	T	0.14830	0.0358	N	0.01576	-0.805	0.21256	N	0.999749	B	0.02656	0.0	B	0.01281	0.0	T	0.37731	-0.9693	10	0.07644	T	0.81	-8.3766	6.7827	0.23654	0.0:0.5722:0.0:0.4278	.	2402	Q96AY4	TTC28_HUMAN	S	2402	ENSP00000381003:N2402S	ENSP00000381003:N2402S	N	-	2	0	TTC28	26708450	0.994000	0.37717	0.998000	0.56505	0.993000	0.82548	0.376000	0.20535	0.289000	0.22422	0.533000	0.62120	AAT	T|0.988;C|0.012	0.012	strong		0.562	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
LILRA1	11024	hgsc.bcm.edu	37	19	55107354	55107354	+	Silent	SNP	C	C	G	rs61739190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55107354C>G	ENST00000251372.3	+	6	1094	c.912C>G	c.(910-912)tcC>tcG	p.S304S	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	304	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		ACAACCTCTCCTCCGAGTGGT	0.677													g|||	807	0.161142	0.4009	0.0994	5008	,	,		15138	0.0079		0.0924	False		,,,				2504	0.1094				p.S304S		Atlas-SNP	.											.	LILRA1	105	.	0			c.C912G						PASS	.						32.0	48.0	43.0					19																	55107354		2200	4299	6499	SO:0001819	synonymous_variant	11024	exon6			CCTCTCCTCCGAG	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.912C>G	19.37:g.55107354C>G		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	157	70	0.44586	NM_006863	O75018|Q3MJA6	Silent	SNP	ENST00000251372.3	37	CCDS12901.1																																																																																			C|0.920;G|0.080	0.080	strong		0.677	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
PKP1	5317	hgsc.bcm.edu	37	1	201286771	201286771	+	Silent	SNP	C	C	T	rs1722779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201286771C>T	ENST00000352845.3	+	5	918	c.918C>T	c.(916-918)gcC>gcT	p.A306A	PKP1_ENST00000475988.1_3'UTR|PKP1_ENST00000263946.3_Silent_p.A306A|PKP1_ENST00000367324.3_Silent_p.A306A			Q13835	PKP1_HUMAN	plakophilin 1	306					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						TCCAGCAGGCCGCGGCAGGGG	0.647													C|||	844	0.16853	0.1316	0.1945	5008	,	,		17421	0.2302		0.1978	False		,,,				2504	0.1063				p.A306A		Atlas-SNP	.											.	PKP1	127	.	0			c.C918T						PASS	.	C	,	584,3818		41,502,1658	27.0	29.0	28.0		918,918	-11.1	0.0	1	dbSNP_89	28	1794,6806		192,1410,2698	no	coding-synonymous,coding-synonymous	PKP1	NM_000299.3,NM_001005337.2	,	233,1912,4356	TT,TC,CC		20.8605,13.2667,18.2895	,	306/748,306/727	201286771	2378,10624	2201	4300	6501	SO:0001819	synonymous_variant	5317	exon5			GCAGGCCGCGGCA	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"""Armadillo repeat containing"""	9023	protein-coding gene	gene with protein product	"""ectodermal dysplasia/skin fragility syndrome"""	601975	"""plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"""			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.918C>T	1.37:g.201286771C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	204	104	0.509804	NM_001005337	O00645|Q14CA0|Q15152	Silent	SNP	ENST00000352845.3	37	CCDS30966.1																																																																																			T|0.178;C|0.822;A|0.000	0.178	strong		0.647	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
ZNF804B	219578	hgsc.bcm.edu	37	7	88965992	88965992	+	Missense_Mutation	SNP	T	T	G	rs115968745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88965992T>G	ENST00000333190.4	+	4	4305	c.3696T>G	c.(3694-3696)atT>atG	p.I1232M		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1232							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ACCTCCCTATTGCTCATCTAC	0.468										HNSCC(36;0.09)			T|||	32	0.00638978	0.0212	0.0058	5008	,	,		20365	0.0		0.0	False		,,,				2504	0.0				p.I1232M		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T3696G						PASS	.	T	MET/ILE	63,4343	59.3+/-96.0	0,63,2140	209.0	180.0	190.0		3696	-9.7	0.4	7	dbSNP_132	190	0,8600		0,0,4300	yes	missense	ZNF804B	NM_181646.2	10	0,63,6440	GG,GT,TT		0.0,1.4299,0.4844	possibly-damaging	1232/1350	88965992	63,12943	2203	4300	6503	SO:0001583	missense	219578	exon4			CCCTATTGCTCAT	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.3696T>G	7.37:g.88965992T>G	ENSP00000329638:p.Ile1232Met	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	193	93	0.481865	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	T	8.308	0.821452	0.16678	0.014299	0.0	ENSG00000182348	ENST00000333190	T	0.05319	3.46	4.84	-9.68	0.00528	.	0.284991	0.30611	N	0.009243	T	0.02342	0.0072	L	0.51422	1.61	0.09310	N	1	D	0.56035	0.974	P	0.48030	0.564	T	0.00807	-1.1558	10	0.56958	D	0.05	-13.7335	4.6179	0.12435	0.0977:0.4312:0.0933:0.3778	.	1232	A4D1E1	Z804B_HUMAN	M	1232	ENSP00000329638:I1232M	ENSP00000329638:I1232M	I	+	3	3	ZNF804B	88803928	0.240000	0.23847	0.392000	0.26245	0.014000	0.08584	-0.152000	0.10159	-1.527000	0.01758	-0.899000	0.02877	ATT	T|0.996;G|0.004	0.004	strong		0.468	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
C3orf70	285382	hgsc.bcm.edu	37	3	184801099	184801099	+	Missense_Mutation	SNP	G	G	A	rs61747892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184801099G>A	ENST00000335012.2	-	2	639	c.449C>T	c.(448-450)cCg>cTg	p.P150L		NM_001025266.1	NP_001020437.1	A6NLC5	CC070_HUMAN	chromosome 3 open reading frame 70	150										breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|urinary_tract(1)	13						ATGTGGTGCCGGCTGCTTCTG	0.438													G|||	132	0.0263578	0.0953	0.0072	5008	,	,		20751	0.0		0.001	False		,,,				2504	0.0				p.P150L		Atlas-SNP	.											C3orf70,colon,carcinoma,+1,1	C3orf70	29	1	0			c.C449T						scavenged	.	G	LEU/PRO	310,4096	166.5+/-197.7	11,288,1904	93.0	89.0	90.0		449	2.4	0.7	3	dbSNP_129	90	4,8596	3.0+/-9.4	0,4,4296	yes	missense	C3orf70	NM_001025266.1	98	11,292,6200	AA,AG,GG		0.0465,7.0359,2.4143	benign	150/251	184801099	314,12692	2203	4300	6503	SO:0001583	missense	285382	exon2			GGTGCCGGCTGCT		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.449C>T	3.37:g.184801099G>A	ENSP00000334974:p.Pro150Leu	Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	193	92	0.476684	NM_001025266	B2RNY2|B9EH83	Missense_Mutation	SNP	ENST00000335012.2	37	CCDS33900.1	46	0.021062271062271064	41	0.08333333333333333	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	13.41	2.229873	0.39399	0.070359	4.65E-4	ENSG00000187068	ENST00000335012	.	.	.	5.28	2.44	0.29823	.	0.223003	0.46758	N	0.000268	T	0.02571	0.0078	L	0.27053	0.805	0.51767	D	0.99993	B	0.06786	0.001	B	0.04013	0.001	T	0.02958	-1.1089	9	0.72032	D	0.01	.	5.8005	0.18412	0.2262:0.0:0.6363:0.1375	.	150	A6NLC5	CC070_HUMAN	L	150	.	ENSP00000334974:P150L	P	-	2	0	C3orf70	186283793	0.939000	0.31865	0.741000	0.31004	0.927000	0.56198	2.310000	0.43708	0.197000	0.20387	0.655000	0.94253	CCG	G|0.972;A|0.028	0.028	strong		0.438	C3orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345323.1	NM_001025266	
TTBK1	84630	hgsc.bcm.edu	37	6	43251608	43251608	+	Missense_Mutation	SNP	C	C	T	rs146633224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43251608C>T	ENST00000259750.4	+	14	3213	c.3130C>T	c.(3130-3132)Cgc>Tgc	p.R1044C		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1044					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			CTCCCCCAGACGCCATGCTAT	0.662													C|||	16	0.00319489	0.0098	0.0043	5008	,	,		14735	0.0		0.0	False		,,,				2504	0.0				p.R1044C		Atlas-SNP	.											.	TTBK1	124	.	0			c.C3130T						PASS	.	C	CYS/ARG	39,4331		0,39,2146	31.0	29.0	30.0		3130	4.0	0.6	6	dbSNP_134	30	8,8470		0,8,4231	yes	missense	TTBK1	NM_032538.1	180	0,47,6377	TT,TC,CC		0.0944,0.8924,0.3658	possibly-damaging	1044/1322	43251608	47,12801	2185	4239	6424	SO:0001583	missense	84630	exon14			CCCAGACGCCATG	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.3130C>T	6.37:g.43251608C>T	ENSP00000259750:p.Arg1044Cys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	6	0.0027472527472527475	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.159	1.018106	0.19355	0.008924	9.44E-4	ENSG00000146216	ENST00000259750	T	0.54279	0.58	4.84	3.96	0.45880	.	1.368680	0.04907	N	0.452377	T	0.29914	0.0748	L	0.52573	1.65	0.21740	N	0.99957	B	0.06786	0.001	B	0.04013	0.001	T	0.37407	-0.9707	10	0.87932	D	0	.	8.0444	0.30540	0.0:0.7512:0.1604:0.0883	.	1044	Q5TCY1	TTBK1_HUMAN	C	1044	ENSP00000259750:R1044C	ENSP00000259750:R1044C	R	+	1	0	TTBK1	43359586	0.000000	0.05858	0.580000	0.28601	0.346000	0.29079	0.210000	0.17455	1.155000	0.42497	0.462000	0.41574	CGC	C|0.997;T|0.003	0.003	strong		0.662	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
MUC17	140453	hgsc.bcm.edu	37	7	100678483	100678483	+	Silent	SNP	C	C	T	rs73168390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678483C>T	ENST00000306151.4	+	3	3850	c.3786C>T	c.(3784-3786)acC>acT	p.T1262T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1262	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)					CTCCTACAACCGCTGAAGGTA	0.522																																					p.T1262T		Atlas-SNP	.											.	MUC17	804	.	0			c.C3786T						PASS	.	C		577,3829		0,577,1626	285.0	275.0	278.0		3786	-1.3	0.0	7	dbSNP_130	278	376,8224		0,376,3924	no	coding-synonymous	MUC17	NM_001040105.1		0,953,5550	TT,TC,CC		4.3721,13.0958,7.3274		1262/4494	100678483	953,12053	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TACAACCGCTGAA	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.3786C>T	7.37:g.100678483C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	139	26	0.18705	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			C|0.975;T|0.025	0.025	strong		0.522	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
RECQL	5965	hgsc.bcm.edu	37	12	21643223	21643223	+	Missense_Mutation	SNP	C	C	T	rs1065751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21643223C>T	ENST00000444129.2	-	4	772	c.304G>A	c.(304-306)Gta>Ata	p.V102I	RECQL_ENST00000421138.2_Missense_Mutation_p.V102I	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	102	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		V -> I (in dbSNP:rs1065751).		DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)	membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						GCCATTGTTACGTTAATAGTT	0.368								Other identified genes with known or suspected DNA repair function					C|||	225	0.0449281	0.1634	0.013	5008	,	,		15171	0.0		0.0	False		,,,				2504	0.0				p.V102I		Atlas-SNP	.											.	RECQL	45	.	0			c.G304A						PASS	.	C	ILE/VAL,ILE/VAL	617,3789	266.5+/-267.3	44,529,1630	122.0	123.0	123.0		304,304	5.3	0.1	12	dbSNP_86	123	4,8596	2.2+/-6.3	0,4,4296	yes	missense,missense	RECQL	NM_002907.3,NM_032941.2	29,29	44,533,5926	TT,TC,CC		0.0465,14.0036,4.7747	benign,benign	102/650,102/650	21643223	621,12385	2203	4300	6503	SO:0001583	missense	5965	exon5			TTGTTACGTTAAT	D37984	CCDS31756.1	12p12.1	2014-03-07	2014-03-07	2014-03-07	ENSG00000004700	ENSG00000004700			9948	protein-coding gene	gene with protein product	"""DNA helicase Q1-like"""	600537	"""RecQ protein-like (DNA helicase Q1-like)"""			7527136, 7961977	Standard	NM_002907		Approved	RecQ1, RecQL1	uc001rex.3	P46063	OTTHUMG00000169131	ENST00000444129.2:c.304G>A	12.37:g.21643223C>T	ENSP00000416739:p.Val102Ile	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_032941	A8K6G2	Missense_Mutation	SNP	ENST00000444129.2	37	CCDS31756.1	85	0.03891941391941392	80	0.16260162601626016	5	0.013812154696132596	0	0.0	0	0.0	C	15.74	2.923245	0.52653	0.140036	4.65E-4	ENSG00000004700	ENST00000444129;ENST00000421138;ENST00000396093;ENST00000314748;ENST00000542432;ENST00000536240	T;T;T;T;T;T	0.75477	-0.94;-0.94;2.49;2.49;2.49;0.93	5.29	5.29	0.74685	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.529047	0.19411	N	0.114924	T	0.00552	0.0018	L	0.36672	1.1	0.31263	P	0.6926570000000001	B	0.16166	0.016	B	0.14023	0.01	T	0.23332	-1.0191	9	0.66056	D	0.02	-2.6848	19.2899	0.94095	0.0:1.0:0.0:0.0	rs1065751;rs1065751	102	P46063	RECQ1_HUMAN	I	102	ENSP00000416739:V102I;ENSP00000395449:V102I;ENSP00000379400:V102I;ENSP00000318727:V102I;ENSP00000445555:V102I;ENSP00000439069:V102I	ENSP00000318727:V102I	V	-	1	0	RECQL	21534490	0.985000	0.35326	0.113000	0.21522	0.868000	0.49771	4.862000	0.62976	2.615000	0.88500	0.650000	0.86243	GTA	T|0.045;G|0.039	0.045	strong		0.368	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907	
CCDC65	85478	hgsc.bcm.edu	37	12	49310831	49310831	+	Missense_Mutation	SNP	A	A	G	rs140228766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49310831A>G	ENST00000320516.4	+	4	737	c.549A>G	c.(547-549)atA>atG	p.I183M	CCDC65_ENST00000266984.5_Missense_Mutation_p.I183M|RP11-302B13.5_ENST00000398092.4_Intron	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	183										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						AGAACTATATAGATTCTGAGT	0.433													A|||	8	0.00159744	0.0053	0.0014	5008	,	,		21739	0.0		0.0	False		,,,				2504	0.0				p.I183M		Atlas-SNP	.											.	CCDC65	41	.	0			c.A549G						PASS	.	A	MET/ILE	15,4391	22.3+/-47.3	0,15,2188	107.0	95.0	99.0		549	-3.4	0.0	12	dbSNP_134	99	1,8599		0,1,4299	yes	missense	CCDC65	NM_033124.4	10	0,16,6487	GG,GA,AA		0.0116,0.3404,0.123	benign	183/485	49310831	16,12990	2203	4300	6503	SO:0001583	missense	85478	exon4			CTATATAGATTCT		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.549A>G	12.37:g.49310831A>G	ENSP00000312706:p.Ile183Met	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	175	68	0.388571	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Missense_Mutation	SNP	ENST00000320516.4	37	CCDS8772.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	11.22	1.573482	0.28092	0.003404	1.16E-4	ENSG00000139537	ENST00000266984;ENST00000320516	T;T	0.02472	4.28;4.28	5.32	-3.4	0.04853	.	0.540717	0.18922	N	0.127459	T	0.01454	0.0047	L	0.44542	1.39	0.21220	N	0.999755	B	0.02656	0.0	B	0.06405	0.002	T	0.40059	-0.9583	10	0.46703	T	0.11	-3.8361	1.8254	0.03119	0.4013:0.2222:0.2683:0.1081	.	183	Q8IXS2	CCD65_HUMAN	M	183	ENSP00000266984:I183M;ENSP00000312706:I183M	ENSP00000266984:I183M	I	+	3	3	CCDC65	47597098	0.000000	0.05858	0.049000	0.19019	0.979000	0.70002	-0.846000	0.04336	-0.658000	0.05366	-0.274000	0.10170	ATA	A|0.999;G|0.001	0.001	strong		0.433	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
ESRRG	2104	hgsc.bcm.edu	37	1	216692741	216692741	+	Silent	SNP	C	C	T	rs10863247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:216692741C>T	ENST00000408911.3	-	6	1038	c.885G>A	c.(883-885)gcG>gcA	p.A295A	ESRRG_ENST00000359162.2_Silent_p.A272A|ESRRG_ENST00000366940.2_Silent_p.A272A|ESRRG_ENST00000366937.1_Silent_p.A307A|ESRRG_ENST00000360012.3_Silent_p.A272A|ESRRG_ENST00000493603.1_Silent_p.A272A|ESRRG_ENST00000493748.1_Silent_p.A272A|ESRRG_ENST00000361395.2_Silent_p.A272A|ESRRG_ENST00000361525.3_Silent_p.A272A|ESRRG_ENST00000487276.1_Silent_p.A272A|ESRRG_ENST00000366938.2_Silent_p.A272A|ESRRG_ENST00000391890.3_Silent_p.A279A|ESRRG_ENST00000463665.1_Silent_p.A233A	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	295					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|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)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	TCATCTGGTCCGCCAGGGACA	0.453													C|||	467	0.0932508	0.3351	0.0288	5008	,	,		17022	0.0		0.004	False		,,,				2504	0.0				p.A307A		Atlas-SNP	.											.	ESRRG	111	.	0			c.G921A						PASS	.	C	,,,	1256,3150	429.1+/-342.1	193,870,1140	56.0	55.0	56.0		816,885,816,816	-3.2	1.0	1	dbSNP_120	56	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRRG	NM_001134285.2,NM_001438.3,NM_206594.2,NM_206595.2	,,,	193,888,5422	TT,TC,CC		0.2093,28.5066,9.7955	,,,	272/436,295/459,272/436,272/436	216692741	1274,11732	2203	4300	6503	SO:0001819	synonymous_variant	2104	exon7			CTGGTCCGCCAGG	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"""Nuclear hormone receptors"""	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.885G>A	1.37:g.216692741C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	34	10	0.294118	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Silent	SNP	ENST00000408911.3	37	CCDS41468.1																																																																																			C|0.910;T|0.090	0.090	strong		0.453	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595	
POMT1	10585	hgsc.bcm.edu	37	9	134393834	134393834	+	Silent	SNP	A	A	G	rs62620174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:134393834A>G	ENST00000372228.3	+	14	1520	c.1341A>G	c.(1339-1341)gaA>gaG	p.E447E	POMT1_ENST00000402686.3_Silent_p.E425E|POMT1_ENST00000354713.4_Silent_p.E395E|RP11-334J6.6_ENST00000415423.1_RNA|POMT1_ENST00000404875.2_Silent_p.E308E|POMT1_ENST00000423007.1_Silent_p.E425E|POMT1_ENST00000341012.7_Silent_p.E371E|POMT1_ENST00000419118.2_Silent_p.E273E|POMT1_ENST00000485278.1_3'UTR|POMT1_ENST00000541219.1_Silent_p.E203E	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	447	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				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)		TTTTGCAGGAAATTGTGAACA	0.418													A|||	111	0.0221645	0.0794	0.0086	5008	,	,		22316	0.0		0.0	False		,,,				2504	0.0				p.E447E		Atlas-SNP	.											.	POMT1	59	.	0			c.A1341G						PASS	.	A	,,,,	283,4123	154.4+/-187.8	8,267,1928	192.0	202.0	198.0		1275,1113,1275,924,1341	0.8	1.0	9	dbSNP_129	198	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	POMT1	NM_001077365.1,NM_001077366.1,NM_001136113.1,NM_001136114.1,NM_007171.3	,,,,	8,267,6228	GG,GA,AA		0.0,6.4231,2.1759	,,,,	425/726,371/672,425/726,308/609,447/748	134393834	283,12723	2203	4300	6503	SO:0001819	synonymous_variant	10585	exon14			GCAGGAAATTGTG	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.1341A>G	9.37:g.134393834A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	115	68	0.591304	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Silent	SNP	ENST00000372228.3	37	CCDS6943.1																																																																																			A|0.976;G|0.024	0.024	strong		0.418	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171	
OR5R1	219479	hgsc.bcm.edu	37	11	56185689	56185689	+	Missense_Mutation	SNP	A	A	G	rs7931261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	23	0	0		WXS	Illumina HiSeq	Phase_I	37	21	0.567568	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	
RAPGEF5	9771	hgsc.bcm.edu	37	7	22202117	22202117	+	Silent	SNP	G	G	A	rs12592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:22202117G>A	ENST00000401957.2	-	3	664	c.417C>T	c.(415-417)gaC>gaT	p.D139D	RAPGEF5_ENST00000344041.6_Silent_p.D289D			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	139	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				nervous system development (GO:0007399)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)	GTP-dependent protein binding (GO:0030742)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|ovary(1)	6						TACGCGGAACGTCTGAGTTTT	0.343													A|||	2976	0.594249	0.6815	0.438	5008	,	,		19331	0.6062		0.5557	False		,,,				2504	0.6145				p.D289D		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.C867T						PASS	.	A		2428,1258		802,824,217	75.0	74.0	74.0		867	-0.1	1.0	7	dbSNP_52	74	4501,3669		1249,2003,833	no	coding-synonymous	RAPGEF5	NM_012294.3		2051,2827,1050	AA,AG,GG		44.9082,34.1291,41.557		289/731	22202117	6929,4927	1843	4085	5928	SO:0001819	synonymous_variant	9771	exon13			CGGAACGTCTGAG	D87467	CCDS55093.1	7p15.3	2004-03-01			ENSG00000136237	ENSG00000136237			16862	protein-coding gene	gene with protein product	"""M-Ras-regulated GEF"""	609527				9039502, 10486569	Standard	NM_012294		Approved	KIAA0277, GFR, MR-GEF	uc003svg.3	Q92565	OTTHUMG00000152525	ENST00000401957.2:c.417C>T	7.37:g.22202117G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_012294	A4D140|Q8IXU5	Silent	SNP	ENST00000401957.2	37																																																																																				G|0.404;A|0.596	0.596	strong		0.343	RAPGEF5-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000326590.2	NM_012294	
ZBTB7C	201501	hgsc.bcm.edu	37	18	45566903	45566903	+	Silent	SNP	T	T	C	rs114461217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:45566903T>C	ENST00000588982.1	-	3	1077	c.576A>G	c.(574-576)acA>acG	p.T192T	ZBTB7C_ENST00000332053.2_Silent_p.T192T|ZBTB7C_ENST00000590800.1_Silent_p.T192T|ZBTB7C_ENST00000535628.2_Silent_p.T192T|ZBTB7C_ENST00000586438.1_Silent_p.T192T			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	192							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						TGAGATGGTCTGTCTTGGAAG	0.567													C|||	43	0.00858626	0.0295	0.0043	5008	,	,		18424	0.0		0.001	False		,,,				2504	0.0				p.T192T		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.A576G						PASS	.	C		134,4272	814.1+/-416.2	2,130,2071	110.0	107.0	108.0		576	-2.0	1.0	18	dbSNP_132	108	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous	ZBTB7C	NM_001039360.2		2,132,6369	CC,CT,TT		0.0233,3.0413,1.0457		192/620	45566903	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	201501	exon2			ATGGTCTGTCTTG	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	31700	protein-coding gene	gene with protein product			"""zinc finger and BTB domain containing 36"""	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.576A>G	18.37:g.45566903T>C		Somatic	365	1	0.00273973		WXS	Illumina HiSeq	Phase_I	376	168	0.446809	NM_001039360	O73453	Silent	SNP	ENST00000588982.1	37	CCDS32830.1																																																																																			T|0.990;C|0.010	0.010	strong		0.567	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360	
TFCP2L1	29842	hgsc.bcm.edu	37	2	121981950	121981950	+	Silent	SNP	A	A	G	rs11890430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	88	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	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	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276657	71276657	+	Silent	SNP	A	A	G	rs71049990|rs200855172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71276657A>G	ENST00000398531.1	+	1	49	c.24A>G	c.(22-24)ggA>ggG	p.G8G	KRTAP5-10_ENST00000376536.4_Silent_p.G8G	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	8						keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GCTGCTCCGGAGGCTGTGGCT	0.667																																					p.G8G		Atlas-SNP	.											KRTAP5-10,NS,carcinoma,0,2	KRTAP5-10	37	2	0			c.A24G						scavenged	.						44.0	53.0	50.0					11																	71276657		2162	4267	6429	SO:0001819	synonymous_variant	387273	exon1			CTCCGGAGGCTGT	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.24A>G	11.37:g.71276657A>G		Somatic	358	58	0.162011		WXS	Illumina HiSeq	Phase_I	307	39	0.127036	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			.	.	none		0.667	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
KRT31	3881	hgsc.bcm.edu	37	17	39553676	39553676	+	Missense_Mutation	SNP	G	G	C	rs6503628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39553676G>C	ENST00000251645.2	-	1	168	c.116C>G	c.(115-117)gCc>gGc	p.A39G		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	39	Head.		A -> G (in dbSNP:rs6503628).		epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				GCTCACATTGGCGGGGATGTT	0.657													G|||	15	0.00299521	0.0113	0.0	5008	,	,		15172	0.0		0.0	False		,,,				2504	0.0				p.A39G		Atlas-SNP	.											.	KRT31	158	.	0			c.C116G						PASS	.	G	GLY/ALA	45,4361	43.1+/-76.7	0,45,2158	59.0	61.0	60.0		116	4.9	1.0	17	dbSNP_116	60	0,8600		0,0,4300	no	missense	KRT31	NM_002277.2	60	0,45,6458	CC,CG,GG		0.0,1.0213,0.346	benign	39/417	39553676	45,12961	2203	4300	6503	SO:0001583	missense	3881	exon1			ACATTGGCGGGGA	X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6448	protein-coding gene	gene with protein product	"""hard keratin type I 1"""	601077	"""keratin, hair, acidic, 1"""	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.116C>G	17.37:g.39553676G>C	ENSP00000251645:p.Ala39Gly	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	205	90	0.439024	NM_002277	Q9UE12	Missense_Mutation	SNP	ENST00000251645.2	37	CCDS11391.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	g	6.953	0.545683	0.13312	0.010213	0.0	ENSG00000094796	ENST00000251645	D	0.82167	-1.58	5.87	4.9	0.64082	.	0.000000	0.64402	D	0.000004	T	0.61476	0.2350	L	0.28400	0.85	0.32486	N	0.54088	B	0.12013	0.005	B	0.10450	0.005	T	0.60209	-0.7308	10	0.06365	T	0.9	.	8.4419	0.32820	0.2275:0.0:0.7725:0.0	rs6503628;rs6503628	39	Q15323	K1H1_HUMAN	G	39	ENSP00000251645:A39G	ENSP00000251645:A39G	A	-	2	0	KRT31	36807202	0.992000	0.36948	1.000000	0.80357	0.902000	0.53008	2.205000	0.42770	1.500000	0.48636	0.650000	0.86243	GCC	G|0.997;C|0.003	0.003	strong		0.657	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277	
C9orf84	158401	hgsc.bcm.edu	37	9	114454735	114454735	+	Silent	SNP	T	T	C	rs73656294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114454735T>C	ENST00000318737.4	-	25	3458	c.3330A>G	c.(3328-3330)tcA>tcG	p.S1110S	C9orf84_ENST00000394779.3_Silent_p.S1071S|C9orf84_ENST00000374287.3_Silent_p.S1110S|C9orf84_ENST00000394777.4_Silent_p.S1036S	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1110										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						AAATTTGCGGTGATTTTGTTA	0.323													T|||	67	0.0133786	0.0477	0.0058	5008	,	,		18851	0.0		0.0	False		,,,				2504	0.0				p.S1110S		Atlas-SNP	.											.	C9orf84	207	.	0			c.A3330G						PASS	.	T	,	151,4255		2,147,2054	53.0	58.0	57.0		3213,3330	3.0	1.0	9	dbSNP_130	57	1,8589		0,1,4294	no	coding-synonymous,coding-synonymous	C9orf84	NM_001080551.1,NM_173521.3	,	2,148,6348	CC,CT,TT		0.0116,3.4271,1.1696	,	1071/1406,1110/1445	114454735	152,12844	2203	4295	6498	SO:0001819	synonymous_variant	158401	exon25			TTGCGGTGATTTT	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.3330A>G	9.37:g.114454735T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	40	9	0.225	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	37	CCDS6781.3																																																																																			T|0.988;C|0.012	0.012	strong		0.323	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
LYST	1130	hgsc.bcm.edu	37	1	235971802	235971802	+	Silent	SNP	G	G	A	rs16832868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235971802G>A	ENST00000389794.3	-	5	2490	c.2316C>T	c.(2314-2316)gaC>gaT	p.D772D	LYST_ENST00000389793.2_Silent_p.D772D|LYST_ENST00000536965.1_Silent_p.D772D			Q99698	LYST_HUMAN	lysosomal trafficking regulator	772					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)			TCTGAAGCACGTCCTGAGGCA	0.468													G|||	309	0.0617013	0.2201	0.0245	5008	,	,		17331	0.0		0.001	False		,,,				2504	0.0				p.D772D		Atlas-SNP	.											.	LYST	370	.	0			c.C2316T						PASS	.	G		827,3579	328.3+/-300.5	75,677,1451	88.0	86.0	87.0		2316	3.5	1.0	1	dbSNP_123	87	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous	LYST	NM_000081.2		75,687,5741	AA,AG,GG		0.1163,18.7699,6.4355		772/3802	235971802	837,12169	2203	4300	6503	SO:0001819	synonymous_variant	1130	exon5			AAGCACGTCCTGA	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.2316C>T	1.37:g.235971802G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	173	90	0.520231	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			G|0.934;A|0.066	0.066	strong		0.468	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
KIF16B	55614	hgsc.bcm.edu	37	20	16492163	16492163	+	Silent	SNP	T	T	C	rs16997775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:16492163T>C	ENST00000354981.2	-	6	613	c.456A>G	c.(454-456)gaA>gaG	p.E152E	KIF16B_ENST00000355755.3_Silent_p.E152E|KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000408042.1_Silent_p.E152E	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	152	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						CGTTATAAATTTCTAAGTAGC	0.353													T|||	114	0.0227636	0.084	0.0029	5008	,	,		17037	0.0		0.001	False		,,,				2504	0.0				p.E152E		Atlas-SNP	.											.	KIF16B	305	.	0			c.A456G						PASS	.	T	,,	254,4152	141.9+/-177.2	7,240,1956	43.0	43.0	43.0		456,456,456	3.2	1.0	20	dbSNP_123	43	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	,,	7,241,6255	CC,CT,TT		0.0116,5.7649,1.9606	,,	152/1267,152/1393,152/1318	16492163	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	55614	exon6			ATAAATTTCTAAG	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.456A>G	20.37:g.16492163T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	37	CCDS13122.1																																																																																			T|0.978;C|0.022	0.022	strong		0.353	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
GNB2L1	10399	hgsc.bcm.edu	37	5	180665123	180665123	+	Silent	SNP	G	G	A	rs11540200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180665123G>A	ENST00000512805.1	-	6	1161	c.753C>T	c.(751-753)gcC>gcT	p.A251A	GNB2L1_ENST00000511566.1_Intron|GNB2L1_ENST00000376817.4_Silent_p.A207A|GNB2L1_ENST00000511900.1_Silent_p.A203A|GNB2L1_ENST00000514455.1_Silent_p.A35A|GNB2L1_ENST00000505461.1_5'Flank|GNB2L1_ENST00000504726.1_Intron	NM_006098.4	NP_006089.1	P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1	251					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cell cycle (GO:0007049)|gastrulation (GO:0007369)|negative regulation of cell growth (GO:0030308)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron death (GO:1903208)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of translation (GO:0017148)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of cell migration (GO:0030335)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of gastrulation (GO:2000543)|positive regulation of GTPase activity (GO:0043547)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein phosphorylation (GO:0001934)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein localization (GO:0032880)|rhythmic process (GO:0048511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|small ribosomal subunit (GO:0015935)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|ion channel inhibitor activity (GO:0008200)|poly(A) RNA binding (GO:0044822)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase inhibitor activity (GO:0030292)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)			lung(3)|skin(2)	5	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)		TGGGGCCTGTGGCAGCACACA	0.522													G|||	104	0.0207668	0.0772	0.0029	5008	,	,		19698	0.0		0.0	False		,,,				2504	0.0				p.A251A		Atlas-SNP	.											.	GNB2L1	22	.	0			c.C753T						PASS	.	G		300,4106	161.4+/-193.6	13,274,1916	140.0	125.0	130.0		753	2.2	1.0	5	dbSNP_120	130	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GNB2L1	NM_006098.4		13,277,6213	AA,AG,GG		0.0349,6.8089,2.3297		251/318	180665123	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	10399	exon6			GCCTGTGGCAGCA	M24194	CCDS34324.1	5q35.3	2013-01-10				ENSG00000204628		"""WD repeat domain containing"""	4399	protein-coding gene	gene with protein product	"""Receptor for Activated C Kinase 1"""	176981				8302854, 2499885	Standard	NM_006098		Approved	Gnb2-rs1, RACK1, H12.3	uc003mni.1	P63244		ENST00000512805.1:c.753C>T	5.37:g.180665123G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	168	75	0.446429	NM_006098	B3KTJ0|D3DWS0|P25388|P99049|Q53HU2|Q5J8M6|Q5VLR4|Q6FH47	Silent	SNP	ENST00000512805.1	37	CCDS34324.1	38|38	0.0173992673992674|0.0173992673992674	38|38	0.07723577235772358|0.07723577235772358	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	9.424|9.424	1.083839|1.083839	0.20309|0.20309	0.068089|0.068089	3.49E-4|3.49E-4	ENSG00000204628|ENSG00000204628	ENST00000509148;ENST00000502905;ENST00000504128|ENST00000507756;ENST00000509535	.|.	.|.	.|.	5.91|5.91	2.24|2.24	0.28232|0.28232	.|.	.|.	.|.	.|.	.|.	T|T	0.04770|0.04770	0.0129|0.0129	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.01630|0.01630	-1.1308|-1.1308	4|4	.|.	.|.	.|.	-15.4052|-15.4052	4.7881|4.7881	0.13234|0.13234	0.2979:0.0:0.5646:0.1376|0.2979:0.0:0.5646:0.1376	rs11540200;rs17851237|rs11540200;rs17851237	.|.	.|.	.|.	Y|L	25;132;158|182;109	.|.	.|.	H|P	-|-	1|2	0|0	GNB2L1|GNB2L1	180597729|180597729	0.998000|0.998000	0.40836|0.40836	0.973000|0.973000	0.42090|0.42090	0.780000|0.780000	0.44128|0.44128	0.478000|0.478000	0.22212|0.22212	0.142000|0.142000	0.18901|0.18901	-0.812000|-0.812000	0.03155|0.03155	CAC|CCA	G|0.977;A|0.023	0.023	strong		0.522	GNB2L1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372943.2	NM_006098	
PRAMEF4	400735	hgsc.bcm.edu	37	1	12942961	12942961	+	Missense_Mutation	SNP	A	A	C	rs4625290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12942961A>C	ENST00000235349.5	-	2	325	c.255T>G	c.(253-255)gaT>gaG	p.D85E		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	85			D -> E (in dbSNP:rs4625290).		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)		CATCCAGCCCATCGAGCACAG	0.627													a|||	524	0.104633	0.0946	0.1009	5008	,	,		18029	0.1399		0.1133	False		,,,				2504	0.0757				p.D85E		Atlas-SNP	.											.	PRAMEF4	62	.	0			c.T255G						PASS	.	A	GLU/ASP	507,3873		62,383,1745	52.0	53.0	53.0		255	-1.3	0.0	1	dbSNP_111	53	999,7571		105,789,3391	no	missense	PRAMEF4	NM_001009611.2	45	167,1172,5136	CC,CA,AA		11.6569,11.5753,11.6293	benign	85/479	12942961	1506,11444	2190	4285	6475	SO:0001583	missense	400735	exon2			CAGCCCATCGAGC		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.255T>G	1.37:g.12942961A>C	ENSP00000235349:p.Asp85Glu	Somatic	434	0	0		WXS	Illumina HiSeq	Phase_I	512	239	0.466797	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	217	0.09935897435897435	38	0.07723577235772358	32	0.08839779005524862	62	0.10839160839160839	85	0.11213720316622691	a	1.703	-0.501150	0.04261	0.115753	0.116569	ENSG00000243073	ENST00000235349	T	0.05199	3.48	1.48	-1.32	0.09201	.	0.744226	0.12606	N	0.454302	T	0.00073	0.0002	N	0.24115	0.695	0.09310	N	1	B	0.15930	0.015	B	0.18871	0.023	T	0.46789	-0.9166	10	0.14656	T	0.56	.	1.5274	0.02528	0.4816:0.0:0.213:0.3054	rs4625290	85	O60810	PRAM4_HUMAN	E	85	ENSP00000235349:D85E	ENSP00000235349:D85E	D	-	3	2	PRAMEF4	12865548	0.000000	0.05858	0.004000	0.12327	0.005000	0.04900	-0.665000	0.05286	-0.377000	0.07930	0.329000	0.21502	GAT	A|0.894;C|0.106	0.106	strong		0.627	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
STT3A	3703	hgsc.bcm.edu	37	11	125476252	125476252	+	Silent	SNP	C	C	G	rs34964592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:125476252C>G	ENST00000529196.1	+	9	878	c.672C>G	c.(670-672)ctC>ctG	p.L224L	STT3A_ENST00000392708.4_Silent_p.L224L|STT3A_ENST00000531491.1_Silent_p.L132L			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	224					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		TCCACGTCCTCGTGCTGATGC	0.473													G|||	519	0.103634	0.2436	0.0605	5008	,	,		17944	0.0308		0.0716	False		,,,				2504	0.0532				p.L224L		Atlas-SNP	.											.	STT3A	52	.	0			c.C672G						PASS	.	G		917,3485	738.5+/-411.0	88,741,1372	371.0	316.0	335.0		672	2.2	1.0	11	dbSNP_126	335	578,8020	793.3+/-407.5	18,542,3739	no	coding-synonymous	STT3A	NM_152713.3		106,1283,5111	GG,GC,CC		6.7225,20.8314,11.5		224/706	125476252	1495,11505	2201	4299	6500	SO:0001819	synonymous_variant	3703	exon8			CGTCCTCGTGCTG	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"""dolichyl-diphosphooligosaccharide protein glycotransferase"""	601134	"""integral membrane protein 1"", ""STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)"", ""STT3A, cataylic subunit of the oligosaccharyltransferase complex"""	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.672C>G	11.37:g.125476252C>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	199	80	0.40201	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	37	CCDS8458.1																																																																																			C|0.891;G|0.109	0.109	strong		0.473	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
ADAM32	203102	hgsc.bcm.edu	37	8	39091546	39091546	+	Missense_Mutation	SNP	G	G	A	rs114068623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39091546G>A	ENST00000379907.4	+	16	1890	c.1763G>A	c.(1762-1764)cGa>cAa	p.R588Q	ADAM32_ENST00000437682.2_Missense_Mutation_p.R489Q|ADAM32_ENST00000519315.1_Missense_Mutation_p.R482Q	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	588						integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			AAATTGCCTCGAACAGTTCCA	0.353													G|||	42	0.00838658	0.0318	0.0	5008	,	,		13545	0.0		0.0	False		,,,				2504	0.0				p.R588Q		Atlas-SNP	.											.	ADAM32	70	.	0			c.G1763A						PASS	.	G	GLN/ARG	96,3584		1,94,1745	63.0	55.0	58.0		1763	-9.3	0.0	8	dbSNP_132	58	0,8154		0,0,4077	yes	missense	ADAM32	NM_145004.5	43	1,94,5822	AA,AG,GG		0.0,2.6087,0.8112	possibly-damaging	588/788	39091546	96,11738	1840	4077	5917	SO:0001583	missense	203102	exon16			TGCCTCGAACAGT	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1763G>A	8.37:g.39091546G>A	ENSP00000369238:p.Arg588Gln	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	37	CCDS47846.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	G	5.640	0.302788	0.10678	0.026087	0.0	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907	T;T;T	0.21361	2.01;2.01;2.01	4.66	-9.32	0.00643	ADAM, cysteine-rich (2);	10.959300	0.00735	U	0.000979	T	0.01905	0.0060	N	0.05383	-0.06	0.09310	N	1	P;P;P	0.51351	0.559;0.944;0.694	B;B;B	0.38755	0.148;0.281;0.067	T	0.41034	-0.9531	10	0.11182	T	0.66	.	2.6264	0.04930	0.1635:0.1349:0.4716:0.23	.	489;482;588	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	Q	489;482;588	ENSP00000405978:R489Q;ENSP00000429422:R482Q;ENSP00000369238:R588Q	ENSP00000369238:R588Q	R	+	2	0	ADAM32	39210703	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.001000	0.00652	-2.751000	0.00374	-0.781000	0.03364	CGA	G|0.990;A|0.010	0.010	strong		0.353	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
ATP1A1	476	hgsc.bcm.edu	37	1	116932921	116932921	+	Silent	SNP	G	G	A	rs11540956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:116932921G>A	ENST00000295598.5	+	9	1362	c.1110G>A	c.(1108-1110)acG>acA	p.T370T	ATP1A1_ENST00000369496.4_Silent_p.T339T|ATP1A1_ENST00000537345.1_Silent_p.T370T	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	370					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	tgggGTCCACGTCCACCATCT	0.458													G|||	406	0.0810703	0.2474	0.0216	5008	,	,		16845	0.0		0.0298	False		,,,				2504	0.0348				p.T370T		Atlas-SNP	.											.	ATP1A1	87	.	0			c.G1110A						PASS	.	G	,,	857,3549	337.3+/-304.8	88,681,1434	82.0	73.0	76.0		1110,1110,1017	-5.5	1.0	1	dbSNP_120	76	229,8371	93.3+/-155.3	3,223,4074	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP1A1	NM_000701.7,NM_001160233.1,NM_001160234.1	,,	91,904,5508	AA,AG,GG		2.6628,19.4507,8.35	,,	370/1024,370/1024,339/993	116932921	1086,11920	2203	4300	6503	SO:0001819	synonymous_variant	476	exon9			GTCCACGTCCACC	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"""ATPases / P-type"""	799	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-1"", ""sodium pump subunit alpha-1"", ""sodium-potassium ATPase catalytic subunit alpha-1"""	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1110G>A	1.37:g.116932921G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	148	67	0.452703	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Silent	SNP	ENST00000295598.5	37	CCDS887.1																																																																																			G|0.903;A|0.097	0.097	strong		0.458	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233	
DPY19L2	283417	hgsc.bcm.edu	37	12	64062132	64062132	+	Silent	SNP	G	G	A	rs11175111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:64062132G>A	ENST00000324472.4	-	1	225	c.42C>T	c.(40-42)tcC>tcT	p.S14S	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	14					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GGCTGCGGCCGGAAGATTGCA	0.617													G|||	457	0.091254	0.121	0.0231	5008	,	,		14854	0.1329		0.0119	False		,,,				2504	0.138				p.S14S		Atlas-SNP	.											.	DPY19L2	97	.	0			c.C42T						PASS	.	G		338,3996		13,312,1842	12.0	15.0	14.0		42	0.5	0.0	12	dbSNP_120	14	130,8398		1,128,4135	no	coding-synonymous	DPY19L2	NM_173812.4		14,440,5977	AA,AG,GG		1.5244,7.7988,3.6386		14/759	64062132	468,12394	2167	4264	6431	SO:0001819	synonymous_variant	283417	exon1			GCGGCCGGAAGAT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.42C>T	12.37:g.64062132G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Silent	SNP	ENST00000324472.4	37	CCDS31851.1																																																																																			G|0.957;A|0.043	0.043	strong		0.617	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
CENPF	1063	hgsc.bcm.edu	37	1	214814571	214814571	+	Silent	SNP	C	C	T	rs3795521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:214814571C>T	ENST00000366955.3	+	12	3058	c.2890C>T	c.(2890-2892)Cta>Tta	p.L964L		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CATCATTTCTCTAAATAAAAG	0.358													C|||	1197	0.239018	0.0522	0.317	5008	,	,		18098	0.122		0.499	False		,,,				2504	0.2894				p.L964L	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,NS,carcinoma,0,2	CENPF	321	2	0			c.C2890T						PASS	.	C		506,3842		51,404,1719	50.0	56.0	54.0		2890	2.2	0.0	1	dbSNP_107	54	4412,4166		1141,2130,1018	no	coding-synonymous	CENPF	NM_016343.3		1192,2534,2737	TT,TC,CC		48.5661,11.6375,38.0473		964/3115	214814571	4918,8008	2174	4289	6463	SO:0001819	synonymous_variant	1063	exon12			ATTTCTCTAAATA	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.2890C>T	1.37:g.214814571C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	81	30	0.37037	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																			C|0.681;T|0.319	0.319	strong		0.358	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
IPO7	10527	hgsc.bcm.edu	37	11	9456506	9456506	+	Silent	SNP	T	T	C	rs148344816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9456506T>C	ENST00000379719.3	+	19	2242	c.2100T>C	c.(2098-2100)taT>taC	p.Y700Y	CTD-2371O3.2_ENST00000531111.1_RNA	NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	700					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		TTCATAATTATGTAACAGTTG	0.308													T|||	6	0.00119808	0.0045	0.0	5008	,	,		19628	0.0		0.0	False		,,,				2504	0.0				p.Y700Y		Atlas-SNP	.											.	IPO7	72	.	0			c.T2100C						PASS	.	T		23,4379	29.9+/-59.1	0,23,2178	119.0	115.0	116.0		2100	3.3	1.0	11	dbSNP_134	116	0,8588		0,0,4294	no	coding-synonymous	IPO7	NM_006391.2		0,23,6472	CC,CT,TT		0.0,0.5225,0.1771		700/1039	9456506	23,12967	2201	4294	6495	SO:0001819	synonymous_variant	10527	exon19			TAATTATGTAACA	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"""Importins"""	9852	protein-coding gene	gene with protein product		605586	"""RAN binding protein 7"""	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.2100T>C	11.37:g.9456506T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	89	55	0.617977	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Silent	SNP	ENST00000379719.3	37	CCDS31425.1																																																																																			T|0.998;C|0.002	0.002	strong		0.308	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391	
ELTD1	64123	hgsc.bcm.edu	37	1	79392756	79392756	+	Missense_Mutation	SNP	C	C	A	rs12754818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:79392756C>A	ENST00000370742.3	-	8	961	c.898G>T	c.(898-900)Gta>Tta	p.V300L		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	300			V -> L (in dbSNP:rs12754818). {ECO:0000269|PubMed:11050079, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		TTATAATATACAAATGCAACT	0.279													A|||	3108	0.620607	0.4939	0.6844	5008	,	,		16163	0.7044		0.6183	False		,,,				2504	0.6626				p.V300L		Atlas-SNP	.											.	ELTD1	143	.	0			c.G898T						PASS	.	A	LEU/VAL	1884,1704		511,862,421	55.0	51.0	52.0		898	3.7	1.0	1	dbSNP_121	52	5209,2935		1644,1921,507	yes	missense	ELTD1	NM_022159.3	32	2155,2783,928	AA,AC,CC		36.0388,47.4916,39.5414	benign	300/691	79392756	7093,4639	1794	4072	5866	SO:0001583	missense	64123	exon8			AATATACAAATGC	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.898G>T	1.37:g.79392756C>A	ENSP00000359778:p.Val300Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	1361	0.6231684981684982	236	0.4796747967479675	243	0.6712707182320442	414	0.7237762237762237	468	0.6174142480211082	a	2.652	-0.281777	0.05642	0.525084	0.639612	ENSG00000162618	ENST00000370742	T	0.11930	2.73	6.02	3.74	0.42951	Domain of unknown function DUF3497 (1);	0.066165	0.64402	N	0.000012	T	0.00815	0.0027	N	0.00483	-1.445	0.53005	P	3.2999999999949736E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.46748	-0.9169	8	.	.	.	.	5.2641	0.15589	0.5899:0.1427:0.2674:0.0	rs12754818;rs17845775;rs17858735;rs52801657;rs61009919;rs12754818	300	Q9HBW9	ELTD1_HUMAN	L	300	ENSP00000359778:V300L	.	V	-	1	0	ELTD1	79165344	1.000000	0.71417	0.997000	0.53966	0.909000	0.53808	1.538000	0.36094	0.187000	0.20147	-0.406000	0.06334	GTA	C|0.374;A|0.625	0.625	strong		0.279	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
DCAF12L2	340578	hgsc.bcm.edu	37	X	125299467	125299467	+	Missense_Mutation	SNP	G	G	T	rs10126452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:125299467G>T	ENST00000360028.2	-	1	467	c.441C>A	c.(439-441)caC>caA	p.H147Q	DCAF12L2_ENST00000538699.1_Missense_Mutation_p.H147Q			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	147			H -> Q (in dbSNP:rs10126452).							NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						CGCAGCCCTGGTGGGCCTGGG	0.642													T|||	2113	0.559735	0.6293	0.4294	3775	,	,		11489	0.3859		0.2525	False		,,,				2504	0.3476				p.H147Q		Atlas-SNP	.											.	DCAF12L2	157	.	0			c.C441A						PASS	.	T	GLN/HIS	2959,876		974,575,436,83,135	76.0	79.0	78.0		441	-2.2	0.0	X	dbSNP_119	78	2000,4726		221,987,571,1219,1301	no	missense	DCAF12L2	NM_001013628.2	24	1195,1562,1007,1302,1436	TT,TG,T,GG,G		29.7354,22.8422,46.9558	benign	147/464	125299467	4959,5602	2203	4299	6502	SO:0001583	missense	340578	exon1			GCCCTGGTGGGCC	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"""WD repeat domain containing"""	32950	protein-coding gene	gene with protein product			"""WD repeat domain 40C"""	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.441C>A	X.37:g.125299467G>T	ENSP00000353128:p.His147Gln	Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	272	271	0.996324	NM_001013628	B2RN42	Missense_Mutation	SNP	ENST00000360028.2	37	CCDS43991.1	863	0.5201928872814949	218	0.7077922077922078	100	0.36231884057971014	146	0.35784313725490197	131	0.19969512195121952	t	0.001	-3.105942	0.00033	0.771578	0.297354	ENSG00000198354	ENST00000538699;ENST00000360028	T;T	0.25250	1.81;1.81	3.89	-2.22	0.06952	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	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	0.40459	-0.9562	8	0.02654	T	1	.	0.7994	0.01072	0.1634:0.2374:0.3197:0.2795	rs10126452;rs61089575	147	Q5VW00	DC122_HUMAN	Q	147	ENSP00000441489:H147Q;ENSP00000353128:H147Q	ENSP00000353128:H147Q	H	-	3	2	DCAF12L2	125127148	1.000000	0.71417	0.000000	0.03702	0.001000	0.01503	0.736000	0.26130	-0.650000	0.05423	-3.105000	0.00063	CAC	G|0.479;T|0.521	0.521	strong		0.642	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628	
TREX2	11219	hgsc.bcm.edu	37	X	152710238	152710238	+	Silent	SNP	A	A	G	rs386828553|rs916046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:152710238A>G	ENST00000334497.2	-	11	1921	c.780T>C	c.(778-780)cgT>cgC	p.R260R	TREX2_ENST00000370232.1_Silent_p.R260R|HAUS7_ENST00000484394.1_5'Flank|TREX2_ENST00000330912.2_Silent_p.R217R|TREX2_ENST00000393862.2_Silent_p.R217R|TREX2_ENST00000414588.1_Silent_p.R259R|TREX2_ENST00000338525.2_Silent_p.R217R|TREX2_ENST00000370231.2_Silent_p.R217R|TREX2_ENST00000402951.1_Silent_p.R260R			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	260					DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)	nucleus (GO:0005634)	3'-5'-exodeoxyribonuclease activity (GO:0008296)|exodeoxyribonuclease III activity (GO:0008853)|magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)			endometrium(4)|large_intestine(2)|lung(3)|ovary(2)	11	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGGCCCACCCACGGGCCTGCT	0.687								Editing and processing nucleases					G|||	436	0.115497	0.2973	0.0346	3775	,	,		11075	0.001		0.005	False		,,,				2504	0.0133				p.R217R		Atlas-SNP	.											.	TREX2	36	.	0			c.T651C						PASS	.	G		1264,2539		169,744,182,714,367	13.0	12.0	12.0		651	-2.5	0.0	X	dbSNP_86	12	47,6646		0,36,11,2388,1834	no	coding-synonymous	TREX2	NM_080701.3		169,780,193,3102,2201	GG,GA,G,AA,A		0.7022,33.2369,12.4905		217/237	152710238	1311,9185	2176	4269	6445	SO:0001819	synonymous_variant	11219	exon2			CCACCCACGGGCC	AF151107	CCDS35437.1	Xq28	2012-05-08			ENSG00000183479	ENSG00000183479			12270	protein-coding gene	gene with protein product		300370				10391904	Standard	NM_080701		Approved		uc011myp.2	Q9BQ50	OTTHUMG00000159319	ENST00000334497.2:c.780T>C	X.37:g.152710238A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	141	35	0.248227	NM_080701	Q45F08|Q9UN77	Silent	SNP	ENST00000334497.2	37																																																																																				A|0.851;0|0.006	.	strong		0.687	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701	
DDX31	64794	hgsc.bcm.edu	37	9	135493792	135493792	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135493792G>A	ENST00000372159.3	-	18	2216	c.2065C>T	c.(2065-2067)Cga>Tga	p.R689*	DDX31_ENST00000372153.1_Intron|DDX31_ENST00000438527.3_Nonsense_Mutation_p.R560*	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	689						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		ACTGTGGCTCGCTCTCGGATT	0.507																																					p.R689X		Atlas-SNP	.											.	DDX31	76	.	0			c.C2065T						PASS	.						105.0	93.0	97.0					9																	135493792		2203	4300	6503	SO:0001587	stop_gained	64794	exon18			TGGCTCGCTCTCG	AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"""DEAD-boxes"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16715	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 25"""		"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"""				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.2065C>T	9.37:g.135493792G>A	ENSP00000361232:p.Arg689*	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	120	48	0.4	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Nonsense_Mutation	SNP	ENST00000372159.3	37	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	G	40	8.126157	0.98667	.	.	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000438527	.	.	.	5.7	5.7	0.88788	.	0.264197	0.35320	N	0.003292	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-6.5596	13.6113	0.62080	0.0:0.0:0.8456:0.1544	.	.	.	.	X	689;689;560	.	ENSP00000361228:R689X	R	-	1	2	DDX31	134483613	1.000000	0.71417	0.965000	0.40720	0.956000	0.61745	3.757000	0.55212	2.686000	0.91538	0.591000	0.81541	CGA	.	.	none		0.507	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620	
STK36	27148	hgsc.bcm.edu	37	2	219561778	219561778	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219561778T>C	ENST00000295709.3	+	23	2882	c.2603T>C	c.(2602-2604)cTa>cCa	p.L868P	STK36_ENST00000392106.2_Missense_Mutation_p.L847P|STK36_ENST00000440309.1_Missense_Mutation_p.L868P|STK36_ENST00000392105.3_Missense_Mutation_p.L847P	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)		AAGGCTAGCCTAATCAGGGAT	0.517																																					p.L868P		Atlas-SNP	.											STK36,right_upper_lobe,carcinoma,-1,1	STK36	111	1	0			c.T2603C						scavenged	.						179.0	193.0	188.0					2																	219561778		2203	4300	6503	SO:0001583	missense	27148	exon23			CTAGCCTAATCAG	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.2603T>C	2.37:g.219561778T>C	ENSP00000295709:p.Leu868Pro	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	2	0.0188679	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.947|4.947	0.175950|0.175950	0.09443|0.09443	.|.	.|.	ENSG00000163482|ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309|ENST00000431040	T;T;T;T|.	0.74947|.	-0.66;-0.76;-0.89;-0.66|.	4.91|4.91	3.72|3.72	0.42706|0.42706	.|.	0.547095|.	0.14203|.	N|.	0.334579|.	T|.	0.24699|.	0.0599|.	N|N	0.19112|0.19112	0.55|0.55	0.24723|0.24723	N|N	0.993134|0.993134	B;B;B|.	0.09022|.	0.002;0.001;0.001|.	B;B;B|.	0.08055|.	0.002;0.003;0.001|.	T|.	0.19516|.	-1.0303|.	10|.	0.51188|.	T|.	0.08|.	-2.2083|-2.2083	8.1141|8.1141	0.30933|0.30933	0.0:0.101:0.0:0.899|0.0:0.101:0.0:0.899	.|.	847;847;868|.	A8MU99;Q9NRP7-2;Q9NRP7|.	.;.;STK36_HUMAN|.	P|Q	868;847;847;868|61	ENSP00000295709:L868P;ENSP00000375955:L847P;ENSP00000375954:L847P;ENSP00000394095:L868P|.	ENSP00000295709:L868P|.	L|X	+|+	2|1	0|0	STK36|STK36	219270022|219270022	0.298000|0.298000	0.24417|0.24417	0.593000|0.593000	0.28771|0.28771	0.003000|0.003000	0.03518|0.03518	0.643000|0.643000	0.24750|0.24750	0.847000|0.847000	0.35167|0.35167	0.533000|0.533000	0.62120|0.62120	CTA|TAA	.	.	none		0.517	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
SERPINB4	6318	hgsc.bcm.edu	37	18	61310738	61310738	+	Missense_Mutation	SNP	T	T	C	rs55883719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61310738T>C	ENST00000341074.5	-	2	189	c.74A>G	c.(73-75)aAc>aGc	p.N25S	SERPINB4_ENST00000356424.6_Missense_Mutation_p.N25S	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	25					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						GAAGATGTTGTTCTCTTTTGA	0.428													T|||	278	0.0555112	0.1989	0.0144	5008	,	,		19831	0.0		0.004	False		,,,				2504	0.001				p.N25S		Atlas-SNP	.											.	SERPINB4	89	.	0			c.A74G						PASS	.	T	SER/ASN	663,3743	282.2+/-276.4	47,569,1587	277.0	244.0	255.0		74	1.3	0.0	18	dbSNP_129	255	13,8587	9.8+/-36.6	0,13,4287	no	missense	SERPINB4	NM_002974.2	46	47,582,5874	CC,CT,TT		0.1512,15.0477,5.1976		25/391	61310738	676,12330	2203	4300	6503	SO:0001583	missense	6318	exon2			ATGTTGTTCTCTT	X89015	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073		"""Serine (or cysteine) peptidase inhibitors"""	10570	protein-coding gene	gene with protein product	"""squamous cell carcinoma antigen 2"""	600518	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"""	SCCA2		7724531, 14630915, 24172014	Standard	NM_175041		Approved	PI11, LEUPIN, SCCA-2, SCCA1		P48594	OTTHUMG00000060405	ENST00000341074.5:c.74A>G	18.37:g.61310738T>C	ENSP00000343445:p.Asn25Ser	Somatic	550	0	0		WXS	Illumina HiSeq	Phase_I	547	254	0.464351	NM_002974	A8K847	Missense_Mutation	SNP	ENST00000341074.5	37	CCDS11986.1	97|97	0.044413919413919416|0.044413919413919416	89|89	0.18089430894308944|0.18089430894308944	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	T|T	4.847|4.847	0.157400|0.157400	0.09236|0.09236	0.150477|0.150477	0.001512|0.001512	ENSG00000206073|ENSG00000206073	ENST00000341074;ENST00000356424;ENST00000436264|ENST00000413673	D;D;D|.	0.83837|.	-1.77;-1.77;-1.77|.	3.83|3.83	1.31|1.31	0.21738|0.21738	Serpin domain (3);|.	1.227650|.	0.06602|.	N|.	0.754050|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.20445|0.20445	0.575|0.575	0.80722|0.80722	P|P	0.0|0.0	B;P|.	0.36183|.	0.102;0.542|.	B;B|.	0.34991|.	0.108;0.193|.	T|T	0.22836|0.22836	-1.0205|-1.0205	9|4	0.66056|.	D|.	0.02|.	.|.	4.2735|4.2735	0.10797|0.10797	0.0:0.277:0.1709:0.5521|0.0:0.277:0.1709:0.5521	rs55883719|rs55883719	25;25|.	P48594;Q9BYF7|.	SPB4_HUMAN;.|.	S|A	25|27	ENSP00000343445:N25S;ENSP00000348795:N25S;ENSP00000399796:N25S|.	ENSP00000343445:N25S|.	N|T	-|-	2|1	0|0	SERPINB4|SERPINB4	59461718|59461718	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.034000|0.034000	0.12701|0.12701	-0.758000|-0.758000	0.04766|0.04766	0.168000|0.168000	0.19655|0.19655	0.416000|0.416000	0.27883|0.27883	AAC|ACA	.	.	weak		0.428	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2	NM_175041	
C17orf74	201243	hgsc.bcm.edu	37	17	7330437	7330437	+	Missense_Mutation	SNP	A	A	G	rs3892554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7330437A>G	ENST00000333870.3	+	3	1201	c.1127A>G	c.(1126-1128)cAg>cGg	p.Q376R	RP11-104H15.7_ENST00000575310.1_RNA|C17orf74_ENST00000574034.1_3'UTR	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	376			Q -> R (in dbSNP:rs3892554).			integral component of membrane (GO:0016021)				cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	22		Prostate(122;0.157)				TACAGCTCCCAGGACCCCCGT	0.677													G|||	275	0.0549121	0.1997	0.0144	5008	,	,		15995	0.0		0.001	False		,,,				2504	0.0				p.Q376R		Atlas-SNP	.											.	C17orf74	56	.	0			c.A1127G						PASS	.	G	ARG/GLN	610,3590		52,506,1542	26.0	33.0	31.0		1127	3.8	0.9	17	dbSNP_108	31	6,8406		0,6,4200	yes	missense	C17orf74	NM_175734.4	43	52,512,5742	GG,GA,AA		0.0713,14.5238,4.8842	benign	376/502	7330437	616,11996	2100	4206	6306	SO:0001583	missense	201243	exon3			GCTCCCAGGACCC	BC044816	CCDS42255.1	17p13.1	2012-05-30			ENSG00000184560	ENSG00000184560			27315	protein-coding gene	gene with protein product						12477932	Standard	NM_175734		Approved		uc002ggw.3	Q0P670	OTTHUMG00000178190	ENST00000333870.3:c.1127A>G	17.37:g.7330437A>G	ENSP00000328061:p.Gln376Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_175734		Missense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	94	0.04304029304029304	89	0.18089430894308944	5	0.013812154696132596	0	0.0	0	0.0	G	0.011	-1.711549	0.00712	0.145238	7.13E-4	ENSG00000184560	ENST00000333870	T	0.21734	1.99	4.81	3.84	0.44239	.	0.000000	0.40144	N	0.001179	T	0.00012	0.0000	N	0.02247	-0.625	0.09310	P	0.9999999828706	B	0.02656	0.0	B	0.01281	0.0	T	0.37776	-0.9691	9	0.02654	T	1	-11.9907	8.1233	0.30984	0.1913:0.0:0.8087:0.0	rs3892554;rs4069866;rs3892554	376	Q0P670	CQ074_HUMAN	R	376	ENSP00000328061:Q376R	ENSP00000328061:Q376R	Q	+	2	0	C17orf74	7271161	0.809000	0.29036	0.909000	0.35828	0.004000	0.04260	0.841000	0.27613	0.574000	0.29417	-1.383000	0.01170	CAG	A|0.955;G|0.045	0.045	strong		0.677	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734	
RCBTB1	55213	hgsc.bcm.edu	37	13	50141345	50141345	+	Missense_Mutation	SNP	G	G	A	rs4942848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:50141345G>A	ENST00000378302.2	-	3	331	c.71C>T	c.(70-72)gCg>gTg	p.A24V	RCBTB1_ENST00000546015.1_Missense_Mutation_p.A24V|RCBTB1_ENST00000258646.3_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	125	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	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	
AGXT2	64902	hgsc.bcm.edu	37	5	34998877	34998877	+	Missense_Mutation	SNP	C	C	A	rs16899974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34998877C>A	ENST00000231420.6	-	14	1692	c.1492G>T	c.(1492-1494)Gta>Tta	p.V498L		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	498			V -> L (in dbSNP:rs16899974). {ECO:0000269|Ref.3}.		cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	AATACTTCTACTGCAAAATCA	0.373													C|||	1180	0.235623	0.0461	0.2608	5008	,	,		21622	0.4216		0.2266	False		,,,				2504	0.2914				p.V498L		Atlas-SNP	.											.	AGXT2	89	.	0			c.G1492T						PASS	.	C	LEU/VAL	333,4073	175.1+/-204.6	9,315,1879	203.0	182.0	189.0		1492	3.8	1.0	5	dbSNP_123	189	1972,6628	346.5+/-326.2	219,1534,2547	yes	missense	AGXT2	NM_031900.3	32	228,1849,4426	AA,AC,CC		22.9302,7.5579,17.7226	benign	498/515	34998877	2305,10701	2203	4300	6503	SO:0001583	missense	64902	exon14			CTTCTACTGCAAA	AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"""beta-alanine-pyruvate aminotransferase"", ""beta-ALAAT II"""	612471	"""alanine-glyoxylate aminotransferase 2"""			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.1492G>T	5.37:g.34998877C>A	ENSP00000231420:p.Val498Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_031900	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Missense_Mutation	SNP	ENST00000231420.6	37	CCDS3908.1	519	0.23763736263736263	20	0.04065040650406504	93	0.2569060773480663	240	0.4195804195804196	166	0.21899736147757257	C	9.105	1.005038	0.19199	0.075579	0.229302	ENSG00000113492	ENST00000231420	T	0.17691	2.26	5.69	3.85	0.44370	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.481828	0.23060	N	0.052393	T	0.00012	0.0000	L	0.43152	1.355	0.42398	P	0.007441000000000031	B;B	0.23591	0.088;0.002	B;B	0.22753	0.041;0.006	T	0.46816	-0.9164	9	0.16420	T	0.52	-17.7656	10.6159	0.45449	0.1359:0.7889:0.0:0.0753	rs16899974;rs52832203;rs60642487;rs16899974	423;498	E9PDL7;Q9BYV1	.;AGT2_HUMAN	L	498	ENSP00000231420:V498L	ENSP00000231420:V498L	V	-	1	0	AGXT2	35034634	0.992000	0.36948	0.981000	0.43875	0.050000	0.14768	1.044000	0.30329	0.313000	0.23062	-0.813000	0.03139	GTA	C|0.795;A|0.205	0.205	strong		0.373	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900	
MUC17	140453	hgsc.bcm.edu	37	7	100695138	100695138	+	Missense_Mutation	SNP	G	G	A	rs73168398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100695138G>A	ENST00000306151.4	+	9	13062	c.12998G>A	c.(12997-12999)cGg>cAg	p.R4333Q		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4333					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)					GTGGAGTACCGGGACCAGAAG	0.572													G|||	536	0.107029	0.1021	0.0778	5008	,	,		19865	0.124		0.1143	False		,,,				2504	0.1094				p.R4333Q		Atlas-SNP	.											.	MUC17	804	.	0			c.G12998A						PASS	.	G	GLN/ARG	479,3927	226.2+/-241.8	25,429,1749	160.0	143.0	149.0		12998	0.1	0.0	7	dbSNP_130	149	936,7664	206.8+/-248.7	54,828,3418	yes	missense	MUC17	NM_001040105.1	43	79,1257,5167	AA,AG,GG		10.8837,10.8715,10.8796	benign	4333/4494	100695138	1415,11591	2203	4300	6503	SO:0001583	missense	140453	exon9			AGTACCGGGACCA	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.12998G>A	7.37:g.100695138G>A	ENSP00000302716:p.Arg4333Gln	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	217	0.09935897435897435	32	0.06504065040650407	27	0.07458563535911603	70	0.12237762237762238	88	0.11609498680738786	G	7.977	0.750437	0.15778	0.108715	0.108837	ENSG00000169876	ENST00000306151	T	0.43294	0.95	4.17	0.0575	0.14323	.	.	.	.	.	T	0.00144	0.0004	N	0.00926	-1.1	0.80722	P	0.0	B	0.32203	0.36	B	0.15052	0.012	T	0.23904	-1.0175	8	0.18710	T	0.47	.	6.1801	0.20465	0.6597:0.0:0.3403:0.0	.	4333	Q685J3	MUC17_HUMAN	Q	4333	ENSP00000302716:R4333Q	ENSP00000302716:R4333Q	R	+	2	0	MUC17	100481858	0.001000	0.12720	0.043000	0.18650	0.012000	0.07955	-0.054000	0.11826	-0.016000	0.14127	-0.658000	0.03865	CGG	G|0.898;A|0.102	0.102	strong		0.572	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CACNA1A	773	hgsc.bcm.edu	37	19	13563767	13563767	+	Silent	SNP	G	G	A	rs1800039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13563767G>A	ENST00000360228.5	-	3	461	c.462C>T	c.(460-462)gcC>gcT	p.A154A	CACNA1A_ENST00000573710.2_Silent_p.A154A	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	154					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CAAACCCAAGGGCAATGATTT	0.493													G|||	48	0.00958466	0.0356	0.0014	5008	,	,		21794	0.0		0.0	False		,,,				2504	0.0				p.A154A		Atlas-SNP	.											.	CACNA1A	715	.	0			c.C462T						PASS	.	G	,,,,	82,3876		1,80,1898	154.0	150.0	151.0		462,462,462,462,462	2.4	1.0	19	dbSNP_89	151	5,8333		0,5,4164	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	1,85,6062	AA,AG,GG		0.06,2.0718,0.7075	,,,,	154/2267,154/2262,154/2507,154/2264,154/2513	13563767	87,12209	1979	4169	6148	SO:0001819	synonymous_variant	773	exon3			CCCAAGGGCAATG	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.462C>T	19.37:g.13563767G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	216	98	0.453704	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			G|0.992;A|0.008	0.008	strong		0.493	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
CFAP46	54777	hgsc.bcm.edu	37	10	134626383	134626383	+	Silent	SNP	C	C	T	rs7090011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134626383C>T	ENST00000368586.5	-	55	7507	c.7407G>A	c.(7405-7407)caG>caA	p.Q2469Q	TTC40_ENST00000263170.5_Silent_p.Q630Q	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TGCCCAGGGCCTGCTCCCACT	0.562													C|||	171	0.0341454	0.1188	0.0173	5008	,	,		13691	0.0		0.002	False		,,,				2504	0.0				p.Q2469Q		Atlas-SNP	.											.	TTC40	100	.	0			c.G7407A						PASS	.	C		456,3950	215.5+/-234.4	29,398,1776	52.0	54.0	53.0		2343	3.9	0.9	10	dbSNP_116	53	9,8591	5.7+/-21.5	0,9,4291	no	coding-synonymous	C10orf92	NM_001200049.1		29,407,6067	TT,TC,CC		0.1047,10.3495,3.5753		781/1028	134626383	465,12541	2203	4300	6503	SO:0001819	synonymous_variant	54777	exon55			CAGGGCCTGCTCC																												ENST00000368586.5:c.7407G>A	10.37:g.134626383C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	21	8	0.380952	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			C|0.966;T|0.034	0.034	strong		0.562	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
MUC6	4588	hgsc.bcm.edu	37	11	1017522	1017522	+	Missense_Mutation	SNP	T	T	G	rs199592093		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017522T>G	ENST00000421673.2	-	31	5329	c.5279A>C	c.(5278-5280)gAa>gCa	p.E1760A		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1760	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			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)		TGAGGTGACTTCAGGATGGTG	0.567																																					p.E1760A		Atlas-SNP	.											.	MUC6	408	.	0			c.A5279C						PASS	.						751.0	715.0	727.0					11																	1017522		2200	4294	6494	SO:0001583	missense	4588	exon31			GTGACTTCAGGAT	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.5279A>C	11.37:g.1017522T>G	ENSP00000406861:p.Glu1760Ala	Somatic	957	0	0		WXS	Illumina HiSeq	Phase_I	1236	124	0.100324	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	-	0.655	-0.808100	0.02819	.	.	ENSG00000184956	ENST00000421673	T	0.20332	2.08	0.235	0.235	0.15431	.	.	.	.	.	T	0.25195	0.0612	L	0.38175	1.15	0.09310	N	1	D	0.67145	0.996	D	0.70227	0.968	T	0.11966	-1.0566	8	0.05833	T	0.94	.	.	.	.	.	1760	Q6W4X9	MUC6_HUMAN	A	1760	ENSP00000406861:E1760A	ENSP00000406861:E1760A	E	-	2	0	MUC6	1007522	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	-3.356000	0.00499	0.263000	0.21812	0.260000	0.18958	GAA	.	.	weak		0.567	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
IL1RAPL2	26280	hgsc.bcm.edu	37	X	104992963	104992963	+	Silent	SNP	T	T	C	rs3764765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:104992963T>C	ENST00000372582.1	+	9	1815	c.1059T>C	c.(1057-1059)taT>taC	p.Y353Y	IL1RAPL2_ENST00000485671.1_3'UTR|IL1RAPL2_ENST00000344799.4_Silent_p.Y353Y	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	353					central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						ATTTAATCTATAAAATTGAGC	0.383													C|||	826	0.218808	0.1687	0.0591	3775	,	,		11961	0.2351		0.0805	False		,,,				2504	0.2495				p.Y353Y		Atlas-SNP	.											.	IL1RAPL2	105	.	0			c.T1059C						PASS	.	C		771,3064		73,513,112,1046,459	86.0	77.0	80.0		1059	5.0	1.0	X	dbSNP_107	80	606,6122		24,379,179,2025,1693	no	coding-synonymous	IL1RAPL2	NM_017416.1		97,892,291,3071,2152	CC,CT,C,TT,T		9.0071,20.1043,13.0361		353/687	104992963	1377,9186	2203	4300	6503	SO:0001819	synonymous_variant	26280	exon9			AATCTATAAAATT	AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1059T>C	X.37:g.104992963T>C		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	299	100	0.334448	NM_017416	Q2M3U3|Q9NZN0	Silent	SNP	ENST00000372582.1	37	CCDS14517.1																																																																																			T|0.833;C|0.167	0.167	strong		0.383	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416	
OR10G4	390264	hgsc.bcm.edu	37	11	123886466	123886466	+	Missense_Mutation	SNP	C	C	T	rs12422129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123886466C>T	ENST00000320891.4	+	1	185	c.185C>T	c.(184-186)aCc>aTc	p.T62I		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T62I(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		TACTTCCTCACCAACCTGTCC	0.552													N|||	447	0.0892572	0.112	0.1542	5008	,	,		23112	0.1478		0.007	False		,,,				2504	0.0368				p.T62I		Atlas-SNP	.											OR10G4,NS,carcinoma,0,1	OR10G4	77	1	1	Substitution - Missense(1)	stomach(1)	c.C185T						scavenged	.	C	ILE/THR	415,3985	195.0+/-219.7	26,363,1811	39.0	31.0	34.0		185	2.6	1.0	11	dbSNP_120	34	30,8494	17.3+/-56.4	0,30,4232	no	missense	OR10G4	NM_001004462.1	89	26,393,6043	TT,TC,CC		0.3519,9.4318,3.4432	benign	62/312	123886466	445,12479	2200	4262	6462	SO:0001583	missense	390264	exon1			TCCTCACCAACCT	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.185C>T	11.37:g.123886466C>T	ENSP00000325076:p.Thr62Ile	Somatic	658	0	0		WXS	Illumina HiSeq	Phase_I	696	318	0.456897	NM_001004462	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	214	0.09798534798534798	57	0.11585365853658537	64	0.17679558011049723	87	0.1520979020979021	6	0.0079155672823219	c	11.28	1.592265	0.28357	0.094318	0.003519	ENSG00000254737	ENST00000320891	T	0.01092	5.35	3.49	2.57	0.30868	GPCR, rhodopsin-like superfamily (1);	0.653762	0.13418	N	0.389385	T	0.00012	0.0000	L	0.28504	0.86	0.50813	P	1.0500000000002174E-4	P	0.37176	0.586	B	0.39617	0.305	T	0.51919	-0.8644	9	0.66056	D	0.02	.	4.6639	0.12655	0.0:0.4691:0.3243:0.2066	rs12422129	62	Q8NGN3	O10G4_HUMAN	I	62	ENSP00000325076:T62I	ENSP00000325076:T62I	T	+	2	0	OR10G4	123391676	0.000000	0.05858	0.989000	0.46669	0.902000	0.53008	0.003000	0.13083	0.829000	0.34733	-0.192000	0.12808	ACC	T|1.000;|0.000	1.000	weak		0.552	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
SLC35G6	643664	hgsc.bcm.edu	37	17	7385774	7385774	+	Silent	SNP	C	C	T	rs201649944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7385774C>T	ENST00000412468.2	+	2	586	c.471C>T	c.(469-471)taC>taT	p.Y157Y	ZBTB4_ENST00000311403.4_Intron|ZBTB4_ENST00000380599.4_5'Flank|POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	157	EamA 1.					integral component of membrane (GO:0016021)											TCAGTGGCTACGACTGGTGTG	0.602													c|||	3	0.000599042	0.0023	0.0	5008	,	,		20504	0.0		0.0	False		,,,				2504	0.0				p.Y157Y		Atlas-SNP	.											.	.	.	.	0			c.C471T						PASS	.	T	,	8,4398	14.3+/-33.2	0,8,2195	182.0	174.0	176.0		471,	-5.2	0.9	17		176	0,8600		0,0,4300	no	coding-synonymous,intron	ZBTB4,SLC35G6	NM_001102614.1,NM_020899.3	,	0,8,6495	TT,TC,CC		0.0,0.1816,0.0615	,	157/339,	7385774	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	643664	exon2			TGGCTACGACTGG		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.471C>T	17.37:g.7385774C>T		Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	235	120	0.510638	NM_001102614		Silent	SNP	ENST00000412468.2	37	CCDS45603.1																																																																																			C|0.999;T|0.001	0.001	weak		0.602	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
LIFR	3977	hgsc.bcm.edu	37	5	38523529	38523529	+	Missense_Mutation	SNP	C	C	T	rs140538535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38523529C>T	ENST00000263409.4	-	5	715	c.553G>A	c.(553-555)Gta>Ata	p.V185I	LIFR_ENST00000453190.2_Missense_Mutation_p.V185I|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	185					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					ACTAATTTTACGAGCTCCATA	0.338			T	PLAG1	salivary adenoma								C|||	11	0.00219649	0.0076	0.0014	5008	,	,		16786	0.0		0.0	False		,,,				2504	0.0				p.V185I	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	LIFR_ENST00000263409,NS,carcinoma,0,2	LIFR	348	2	0			c.G553A						PASS	.	C	ILE/VAL,ILE/VAL	11,4395	15.5+/-35.6	0,11,2192	79.0	86.0	84.0		553,553	1.8	0.0	5	dbSNP_134	84	0,8600		0,0,4300	yes	missense,missense	LIFR	NM_001127671.1,NM_002310.5	29,29	0,11,6492	TT,TC,CC		0.0,0.2497,0.0846	possibly-damaging,possibly-damaging	185/1098,185/1098	38523529	11,12995	2203	4300	6503	SO:0001583	missense	3977	exon5			ATTTTACGAGCTC	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.553G>A	5.37:g.38523529C>T	ENSP00000263409:p.Val185Ile	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	267	115	0.430712	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	C	8.760	0.923346	0.18056	0.002497	0.0	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.65916	-0.18;-0.18	5.53	1.82	0.25136	Immunoglobulin-like fold (1);	0.720295	0.13949	N	0.351669	T	0.49355	0.1552	L	0.49513	1.565	0.09310	N	1	B	0.25809	0.135	B	0.10450	0.005	T	0.29088	-1.0023	10	0.23302	T	0.38	-9.8342	7.3065	0.26451	0.0:0.6505:0.0:0.3495	.	185	P42702	LIFR_HUMAN	I	185	ENSP00000263409:V185I;ENSP00000398368:V185I	ENSP00000263409:V185I	V	-	1	0	LIFR	38559286	0.000000	0.05858	0.023000	0.16930	0.988000	0.76386	-0.741000	0.04855	0.044000	0.15775	0.655000	0.94253	GTA	C|0.999;T|0.001	0.001	strong		0.338	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
MYLK	4638	hgsc.bcm.edu	37	3	123419733	123419733	+	Missense_Mutation	SNP	A	A	G	rs3732486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:123419733A>G	ENST00000475616.1	-	15	2581	c.2582T>C	c.(2581-2583)cTa>cCa	p.L861P	MYLK_ENST00000360304.3_Missense_Mutation_p.L861P|MYLK_ENST00000359169.1_Missense_Mutation_p.L861P|MYLK_ENST00000346322.5_Missense_Mutation_p.L792P|MYLK_ENST00000360772.3_Missense_Mutation_p.L861P|MYLK_ENST00000510775.1_5'Flank			Q15746	MYLK_HUMAN	myosin light chain kinase	861			L -> P (in dbSNP:rs3732486).		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)		TTCCTCCTCTAGCCAACCCTG	0.652													G|||	1397	0.278954	0.3351	0.0576	5008	,	,		13379	0.5526		0.0358	False		,,,				2504	0.3282				p.L861P		Atlas-SNP	.											.	MYLK	224	.	0			c.T2582C						PASS	.	G	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	1145,3261		147,851,1205	55.0	61.0	59.0		2582,2375,2582,2375	4.8	0.9	3	dbSNP_107	59	154,8446		2,150,4148	no	missense,missense,missense,missense	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	98,98,98,98	149,1001,5353	GG,GA,AA		1.7907,25.9873,9.9877	benign,benign,benign,benign	861/1915,792/1846,861/1864,792/1795	123419733	1299,11707	2203	4300	6503	SO:0001583	missense	4638	exon18			TCCTCTAGCCAAC	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.2582T>C	3.37:g.123419733A>G	ENSP00000418335:p.Leu861Pro	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	520	0.23809523809523808	165	0.3353658536585366	22	0.06077348066298342	300	0.5244755244755245	33	0.04353562005277045	G	10.64	1.406282	0.25378	0.259873	0.017907	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.66638	-0.22;-0.19;-0.22;-0.19;-0.19	4.77	4.77	0.60923	.	.	.	.	.	T	0.00012	0.0000	N	0.00436	-1.5	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;0.001;0.001;0.0	T	0.41215	-0.9521	8	0.28530	T	0.3	.	11.6377	0.51213	0.0828:0.0:0.9172:0.0	rs3732486;rs3732486	861;792;861;792;861	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	P	861;861;861;792;861	ENSP00000354004:L861P;ENSP00000353452:L861P;ENSP00000352088:L861P;ENSP00000320622:L792P;ENSP00000418335:L861P	ENSP00000320622:L792P	L	-	2	0	MYLK	124902423	0.002000	0.14202	0.858000	0.33744	0.839000	0.47603	0.535000	0.23114	1.257000	0.44085	-0.215000	0.12644	CTA	A|0.858;G|0.142	0.142	strong		0.652	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
MORN2	729967	hgsc.bcm.edu	37	2	39108693	39108693	+	Silent	SNP	G	G	A	rs6756998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:39108693G>A	ENST00000410014.1	+	4	490	c.111G>A	c.(109-111)aaG>aaA	p.K37K	MORN2_ENST00000340556.6_Silent_p.K37K|MORN2_ENST00000409665.1_Silent_p.K37K|MORN2_ENST00000409077.2_Intron|MORN2_ENST00000409131.2_Silent_p.K15K			Q502X0	MORN2_HUMAN	MORN repeat containing 2	37										breast(1)	1						ATGGGGCAAAGTATACTGGAA	0.308													G|||	81	0.0161741	0.0582	0.0058	5008	,	,		14852	0.0		0.0	False		,,,				2504	0.0				p.K37K		Atlas-SNP	.											.	MORN2	3	.	0			c.G111A						PASS	.						83.0	71.0	75.0					2																	39108693		692	1590	2282	SO:0001819	synonymous_variant	729967	exon4			GGCAAAGTATACT	AY367766	CCDS46262.1	2p22.1	2010-06-04			ENSG00000188010	ENSG00000188010			30166	protein-coding gene	gene with protein product						12477932	Standard	NM_001145450		Approved	MOPT	uc010fak.3	Q502X0	OTTHUMG00000128589	ENST00000410014.1:c.111G>A	2.37:g.39108693G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_001145450	Q6UL00	Silent	SNP	ENST00000410014.1	37	CCDS46262.1																																																																																			G|0.983;A|0.017	0.017	strong		0.308	MORN2-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331568.1	NM_194270	
ASXL1	171023	hgsc.bcm.edu	37	20	31024488	31024488	+	Missense_Mutation	SNP	C	C	T	rs6057581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31024488C>T	ENST00000375687.4	+	13	4397	c.3973C>T	c.(3973-3975)Ctt>Ttt	p.L1325F	ASXL1_ENST00000306058.5_Missense_Mutation_p.L1320F	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1325			L -> F (in dbSNP:rs6057581).		bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CCCGATGCCTCTTCCTGCTGA	0.572			"""F, N, Mis"""		"""MDS, CMML"""								C|||	145	0.0289537	0.1044	0.0058	5008	,	,		17355	0.0		0.003	False		,,,				2504	0.0				p.L1325F		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.C3973T						PASS	.	C	PHE/LEU	386,4020	187.4+/-214.1	13,360,1830	41.0	44.0	43.0		3973	1.3	0.0	20	dbSNP_114	43	4,8596	3.7+/-12.6	0,4,4296	yes	missense	ASXL1	NM_015338.5	22	13,364,6126	TT,TC,CC		0.0465,8.7608,2.9986	probably-damaging	1325/1542	31024488	390,12616	2203	4300	6503	SO:0001583	missense	171023	exon12			ATGCCTCTTCCTG	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3973C>T	20.37:g.31024488C>T	ENSP00000364839:p.Leu1325Phe	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	47	0.02152014652014652	42	0.08536585365853659	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.497	1.102092	0.20632	0.087608	4.65E-4	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.16597	2.33;2.33	4.56	1.29	0.21616	.	0.227351	0.28011	N	0.016945	T	0.00580	0.0019	L	0.36672	1.1	0.09310	N	1	D;D	0.64830	0.994;0.994	P;P	0.59221	0.854;0.854	T	0.09164	-1.0687	10	0.16896	T	0.51	-9.4128	1.2537	0.01987	0.1414:0.4193:0.1563:0.2829	rs6057581;rs6057581	1320;1325	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	F	1325;1325;1325;1246;1320	ENSP00000364839:L1325F;ENSP00000305119:L1320F	ENSP00000305119:L1320F	L	+	1	0	ASXL1	30488149	0.000000	0.05858	0.010000	0.14722	0.276000	0.26787	-0.141000	0.10327	0.336000	0.23639	0.561000	0.74099	CTT	C|0.971;T|0.029	0.029	strong		0.572	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	
FAM71F2	346653	hgsc.bcm.edu	37	7	128315889	128315889	+	Missense_Mutation	SNP	A	A	T	rs6971819	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:128315889A>T	ENST00000480462.1	+	2	447	c.341A>T	c.(340-342)gAc>gTc	p.D114V	FAM71F2_ENST00000378704.3_Missense_Mutation_p.D105V|FAM71F2_ENST00000460349.1_3'UTR|FAM71F2_ENST00000477515.1_Missense_Mutation_p.D114V			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	46	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	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		
KCNJ6	3763	hgsc.bcm.edu	37	21	39087236	39087236	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:39087236C>T	ENST00000609713.1	-	3	813	c.224G>A	c.(223-225)cGc>cAc	p.R75H	KCNJ6-IT1_ENST00000435001.1_RNA|KCNJ6_ENST00000288309.6_Missense_Mutation_p.R75H	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	75					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	GGTCAGGTAGCGATAGGTCTC	0.463																																					p.R75H	Pancreas(48;379 1118 2936 19024 28214)	Atlas-SNP	.											KCNJ6,NS,carcinoma,-1,1	KCNJ6	58	1	0			c.G224A						scavenged	.						235.0	221.0	225.0					21																	39087236		2023	4164	6187	SO:0001583	missense	3763	exon3			AGGTAGCGATAGG	U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.224G>A	21.37:g.39087236C>T	ENSP00000477437:p.Arg75His	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	282	3	0.0106383	NM_002240	Q3MJ74|Q53WW6	Missense_Mutation	SNP	ENST00000609713.1	37	CCDS42927.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.909633	0.92107	.	.	ENSG00000157542	ENST00000400482;ENST00000288309	D;D	0.96856	-4.15;-4.15	5.95	5.95	0.96441	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.000000	0.85682	D	0.000000	D	0.98661	0.9551	M	0.93106	3.38	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.99050	1.0827	10	0.87932	D	0	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	75	P48051	IRK6_HUMAN	H	75	ENSP00000383330:R75H;ENSP00000288309:R75H	ENSP00000288309:R75H	R	-	2	0	KCNJ6	38009106	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	CGC	.	.	none		0.463	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194828.2	NM_002240	
CDC14A	8556	hgsc.bcm.edu	37	1	100856380	100856380	+	Splice_Site	SNP	A	A	C	rs28361212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100856380A>C	ENST00000336454.3	+	4	664	c.309A>C	c.(307-309)gcA>gcC	p.A103A	CDC14A_ENST00000544534.1_Splice_Site_p.A103A|CDC14A_ENST00000370125.2_Splice_Site_p.A103A|CDC14A_ENST00000370124.3_Splice_Site_p.A103A|CDC14A_ENST00000361544.6_Splice_Site_p.A103A|CDC14A_ENST00000542213.1_Splice_Site_p.A45A	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	103	A.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		GTGCCTATGCAGTAAGTACCT	0.378													G|||	482	0.096246	0.3533	0.0202	5008	,	,		19271	0.0		0.001	False		,,,				2504	0.0				p.A103A		Atlas-SNP	.											.	CDC14A	65	.	0			c.A309C						PASS	.	G	,,	1374,3032		208,958,1037	99.0	97.0	98.0		309,309,309	-11.2	0.1	1	dbSNP_125	98	3,8597		0,3,4297	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	208,961,5334	CC,CA,AA		0.0349,31.1847,10.5874	,,	103/595,103/624,103/384	100856380	1377,11629	2203	4300	6503	SO:0001630	splice_region_variant	8556	exon4			CTATGCAGTAAGT	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1718	protein-coding gene	gene with protein product		603504	"""CDC10 (cell division cycle 10, S. cerevisiae, homolog)"", ""CDC14 cell division cycle 14 homolog A (S. cerevisiae)"""			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.309+1A>C	1.37:g.100856380A>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			A|0.885;C|0.115	0.115	strong		0.378	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	Silent
PRKG1	5592	hgsc.bcm.edu	37	10	53921655	53921655	+	Silent	SNP	T	T	C	rs56047641	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:53921655T>C	ENST00000401604.2	+	9	1157	c.963T>C	c.(961-963)ttT>ttC	p.F321F	PRKG1_ENST00000373985.1_Silent_p.F309F|PRKG1_ENST00000373975.2_Silent_p.F39F|PRKG1_ENST00000373980.4_Silent_p.F336F			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	321	cGMP-binding, low affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		ACAGCTCTTTTAAACATTTGA	0.338													C|||	357	0.0712859	0.1944	0.0115	5008	,	,		17583	0.0605		0.001	False		,,,				2504	0.0307				p.F336F		Atlas-SNP	.											.	PRKG1	167	.	0			c.T1008C						PASS	.	C	,	722,3684	754.6+/-412.5	55,612,1536	156.0	147.0	150.0		963,1008	3.5	1.0	10	dbSNP_129	150	11,8589	816.8+/-406.9	0,11,4289	no	coding-synonymous,coding-synonymous	PRKG1	NM_001098512.2,NM_006258.3	,	55,623,5825	CC,CT,TT		0.1279,16.3867,5.6359	,	321/672,336/687	53921655	733,12273	2203	4300	6503	SO:0001819	synonymous_variant	5592	exon9			CTCTTTTAAACAT		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.963T>C	10.37:g.53921655T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Silent	SNP	ENST00000401604.2	37	CCDS44399.1																																																																																			T|0.947;C|0.053	0.053	strong		0.338	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TDRD5	163589	hgsc.bcm.edu	37	1	179621253	179621253	+	Missense_Mutation	SNP	G	G	T	rs147309264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179621253G>T	ENST00000367614.1	+	13	2440	c.2081G>T	c.(2080-2082)gGt>gTt	p.G694V	TDRD5_ENST00000444136.1_Missense_Mutation_p.G694V|TDRD5_ENST00000294848.8_Missense_Mutation_p.G694V	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	694					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						ACAGAACTGGGTTATCCTTCC	0.403													G|||	16	0.00319489	0.0121	0.0	5008	,	,		16263	0.0		0.0	False		,,,				2504	0.0				p.G694V		Atlas-SNP	.											.	TDRD5	149	.	0			c.G2081T						PASS	.	G	VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY	39,4367	44.6+/-78.6	0,39,2164	103.0	97.0	99.0		2081,2081,2081,746,2081	2.4	0.0	1	dbSNP_134	99	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_001199092.1,NM_173533.3	109,109,109,109,109	0,39,6464	TT,TG,GG		0.0,0.8852,0.2999	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	694/1036,694/1036,694/982,249/537,694/982	179621253	39,12967	2203	4300	6503	SO:0001583	missense	163589	exon13			AACTGGGTTATCC	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2081G>T	1.37:g.179621253G>T	ENSP00000356586:p.Gly694Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	215	107	0.497674	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	10.14	1.269759	0.23221	0.008852	0.0	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.34859	2.61;2.61;2.85;1.34	5.28	2.41	0.29592	.	1.593960	0.03140	N	0.166439	T	0.28433	0.0703	L	0.44542	1.39	0.19775	N	0.999957	P;B	0.35872	0.525;0.265	B;B	0.39971	0.315;0.167	T	0.19257	-1.0311	10	0.26408	T	0.33	-22.1301	7.4534	0.27252	0.3467:0.0:0.6533:0.0	.	694;694	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	V	694;694;694;150	ENSP00000356586:G694V;ENSP00000294848:G694V;ENSP00000406052:G694V;ENSP00000410744:G150V	ENSP00000294848:G694V	G	+	2	0	TDRD5	177887876	0.005000	0.15991	0.016000	0.15963	0.936000	0.57629	0.997000	0.29731	0.244000	0.21351	-0.259000	0.10710	GGT	G|0.997;T|0.003	0.003	strong		0.403	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
FGD6	55785	hgsc.bcm.edu	37	12	95604664	95604664	+	Silent	SNP	A	A	G	rs4762289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:95604664A>G	ENST00000343958.4	-	2	619	c.396T>C	c.(394-396)gtT>gtC	p.V132V	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Silent_p.V132V|FGD6_ENST00000546711.1_Silent_p.V132V	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	132					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						GGGGCTCTAAAACAAGCTGCT	0.353													A|||	238	0.047524	0.056	0.036	5008	,	,		19927	0.0109		0.0467	False		,,,				2504	0.0828				p.V132V		Atlas-SNP	.											.	FGD6	127	.	0			c.T396C						PASS	.	A		237,4169	135.3+/-171.4	4,229,1970	112.0	115.0	114.0		396	2.5	1.0	12	dbSNP_111	114	392,8208	125.5+/-184.1	10,372,3918	no	coding-synonymous	FGD6	NM_018351.3		14,601,5888	GG,GA,AA		4.5581,5.379,4.8362		132/1431	95604664	629,12377	2203	4300	6503	SO:0001819	synonymous_variant	55785	exon2			CTCTAAAACAAGC	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.396T>C	12.37:g.95604664A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	161	78	0.484472	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Silent	SNP	ENST00000343958.4	37	CCDS31878.1																																																																																			A|0.949;G|0.051	0.051	strong		0.353	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
CFAP74	85452	hgsc.bcm.edu	37	1	1887245	1887245	+	IGR	SNP	G	G	A	rs28575980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	91	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	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								
DSPP	1834	hgsc.bcm.edu	37	4	88535868	88535868	+	Missense_Mutation	SNP	A	A	G	rs199719429		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88535868A>G	ENST00000282478.7	+	4	2087	c.2054A>G	c.(2053-2055)aAc>aGc	p.N685S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.N685S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	685	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gacagcagcaacagcagtgat	0.483																																					p.N685S		Atlas-SNP	.											DSPP,NS,carcinoma,-1,2	DSPP	174	2	0			c.A2054G						PASS	.						116.0	132.0	127.0					4																	88535868		1684	3089	4773	SO:0001583	missense	1834	exon5			GCAGCAACAGCAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2054A>G	4.37:g.88535868A>G	ENSP00000282478:p.Asn685Ser	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	347	59	0.170029	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	-	4.290	0.052936	0.08291	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87809	-2.3;-2.3	1.5	0.247	0.15521	.	.	.	.	.	T	0.69287	0.3094	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.54833	-0.8234	9	0.02654	T	1	0.1107	4.5905	0.12304	0.7937:0.0:0.2063:0.0	.	685	Q9NZW4	DSPP_HUMAN	S	685	ENSP00000382213:N685S;ENSP00000282478:N685S	ENSP00000282478:N685S	N	+	2	0	DSPP	88754892	0.003000	0.15002	0.026000	0.17262	0.014000	0.08584	1.419000	0.34793	0.077000	0.16863	0.139000	0.15985	AAC	.	.	weak		0.483	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
MKI67	4288	hgsc.bcm.edu	37	10	129903592	129903592	+	Missense_Mutation	SNP	G	G	A	rs45549235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129903592G>A	ENST00000368654.3	-	13	6887	c.6512C>T	c.(6511-6513)gCa>gTa	p.A2171V	MKI67_ENST00000368653.3_Missense_Mutation_p.A1811V	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2171	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)				TACACTTGCTGCTGGGTCCAG	0.498													G|||	365	0.0728834	0.0303	0.0029	5008	,	,		19867	0.1558		0.0169	False		,,,				2504	0.1524				p.A2171V		Atlas-SNP	.											.	MKI67	363	.	0			c.C6512T						PASS	.	G	VAL/ALA,VAL/ALA	111,4295	86.3+/-125.0	0,111,2092	162.0	150.0	154.0		5432,6512	-4.9	0.0	10	dbSNP_127	154	80,8520	47.2+/-106.3	2,76,4222	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	64,64	2,187,6314	AA,AG,GG		0.9302,2.5193,1.4686	possibly-damaging,possibly-damaging	1811/2897,2171/3257	129903592	191,12815	2203	4300	6503	SO:0001583	missense	4288	exon13			CTTGCTGCTGGGT	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.6512C>T	10.37:g.129903592G>A	ENSP00000357643:p.Ala2171Val	Somatic	507	2	0.00394477		WXS	Illumina HiSeq	Phase_I	466	227	0.487124	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	124	0.056776556776556776	11	0.022357723577235773	0	0.0	96	0.16783216783216784	17	0.022427440633245383	G	12.58	1.982018	0.34942	0.025193	0.009302	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02280	4.36;4.36	4.79	-4.89	0.03103	.	2.259380	0.02081	N	0.052303	T	0.00012	0.0000	L	0.31845	0.965	0.80722	P	0.0	P;P;D	0.61080	0.582;0.708;0.989	B;B;P	0.62298	0.208;0.227;0.9	T	0.37911	-0.9685	9	0.27082	T	0.32	.	1.6494	0.02768	0.2213:0.1286:0.1356:0.5145	rs45549235	2170;1811;2171	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	V	2171;1811;2170	ENSP00000357643:A2171V;ENSP00000357642:A1811V	ENSP00000357642:A1811V	A	-	2	0	MKI67	129793582	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.011000	0.13264	-0.713000	0.04981	-0.258000	0.10820	GCA	G|0.973;A|0.027	0.027	strong		0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
SYNDIG1L	646658	hgsc.bcm.edu	37	14	74876181	74876181	+	Silent	SNP	T	T	G	rs12590672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74876181T>G	ENST00000554823.1	-	1	328	c.267A>C	c.(265-267)acA>acC	p.T89T	SYNDIG1L_ENST00000331628.3_Silent_p.T89T			A6NDD5	SYN1L_HUMAN	synapse differentiation inducing 1-like	89					response to biotic stimulus (GO:0009607)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(8)|pancreas(1)|prostate(1)|skin(1)	14						CTGTGAAGCTTGTCTCACAGC	0.647													G|||	2307	0.460663	0.472	0.4222	5008	,	,		14317	0.4454		0.494	False		,,,				2504	0.454				p.T89T		Atlas-SNP	.											.	SYNDIG1L	24	.	0			c.A267C						PASS	.	G		1773,2063		420,933,565	42.0	45.0	44.0		267	1.7	1.0	14	dbSNP_120	44	4113,4145		1033,2047,1049	no	coding-synonymous	SYNDIG1L	NM_001105579.1		1453,2980,1614	GG,GT,TT		49.8062,46.22,48.6688		89/239	74876181	5886,6208	1918	4129	6047	SO:0001819	synonymous_variant	646658	exon2			GAAGCTTGTCTCA		CCDS41970.1	14q24.3	2011-06-30	2011-06-30	2011-06-30		ENSG00000183379			32388	protein-coding gene	gene with protein product	"""caudate-and putamen-enriched sequence"", ""interferon induced transmembrane protein domain containing 4"""	609999	"""transmembrane protein 90A"""	TMEM90A		16359841	Standard	NM_001105579		Approved	capucin, IFITMD4	uc001xpx.2	A6NDD5		ENST00000554823.1:c.267A>C	14.37:g.74876181T>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_001105579		Silent	SNP	ENST00000554823.1	37	CCDS41970.1																																																																																			T|0.508;G|0.492	0.492	strong		0.647	SYNDIG1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412341.1	XM_938515	
IFT140	9742	hgsc.bcm.edu	37	16	1637998	1637998	+	Missense_Mutation	SNP	G	G	A	rs8058674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1637998G>A	ENST00000426508.2	-	8	1201	c.838C>T	c.(838-840)Cgg>Tgg	p.R280W	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	280			R -> Q (in dbSNP:rs35404373).		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)				ATGTCTGCCCGGCGGCCGGTT	0.622													G|||	98	0.0195687	0.0734	0.0014	5008	,	,		16114	0.0		0.0	False		,,,				2504	0.0				p.R280W		Atlas-SNP	.											.	IFT140	128	.	0			c.C838T						PASS	.	G	TRP/ARG	276,4122	153.7+/-187.2	7,262,1930	43.0	37.0	39.0		838	3.2	0.0	16	dbSNP_116	39	1,8599	1.2+/-3.3	0,1,4299	no	missense	IFT140	NM_014714.3	101	7,263,6229	AA,AG,GG		0.0116,6.2756,2.1311	probably-damaging	280/1463	1637998	277,12721	2199	4300	6499	SO:0001583	missense	9742	exon8			CTGCCCGGCGGCC	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.838C>T	16.37:g.1637998G>A	ENSP00000406012:p.Arg280Trp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	94	50	0.531915	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	37	0.01694139194139194	36	0.07317073170731707	1	0.0027624309392265192	0	0.0	0	0.0	G	11.60	1.686901	0.29962	0.062756	1.16E-4	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.30448	1.53	5.32	3.15	0.36227	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.748429	0.13091	N	0.414548	T	0.01976	0.0062	L	0.60455	1.87	0.09310	N	1	D	0.60160	0.987	B	0.42653	0.394	T	0.15809	-1.0424	10	0.54805	T	0.06	.	2.9009	0.05705	0.3065:0.2411:0.4525:0.0	rs8058674	280	Q96RY7	IF140_HUMAN	W	280	ENSP00000406012:R280W	ENSP00000380562:R280W	R	-	1	2	IFT140	1577999	0.021000	0.18746	0.008000	0.14137	0.002000	0.02628	1.743000	0.38258	1.241000	0.43820	-0.136000	0.14681	CGG	G|0.978;A|0.022	0.022	strong		0.622	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
KLK14	43847	hgsc.bcm.edu	37	19	51582090	51582090	+	Silent	SNP	G	G	A	rs79507858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51582090G>A	ENST00000156499.2	-	6	851	c.633C>T	c.(631-633)ggC>ggT	p.G211G	KLK14_ENST00000391802.1_Silent_p.G211G			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	211	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		AGTCCTTCCCGCCCTGGGGAA	0.542													g|||	153	0.0305511	0.1089	0.0115	5008	,	,		18957	0.0		0.001	False		,,,				2504	0.0				p.G211G	GBM(117;2161 2172 2448 22911)	Atlas-SNP	.											.	KLK14	49	.	0			c.C633T						PASS	.			376,3538		15,346,1596	234.0	237.0	236.0		633	-9.0	0.2	19	dbSNP_131	236	7,8311		0,7,4152	no	coding-synonymous	KLK14	NM_022046.4		15,353,5748	AA,AG,GG		0.0842,9.6065,3.1311		211/268	51582090	383,11849	1957	4159	6116	SO:0001819	synonymous_variant	43847	exon6			CTTCCCGCCCTGG	AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"""Kallikreins"""	6362	protein-coding gene	gene with protein product		606135	"""kallikrein 14"""			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.633C>T	19.37:g.51582090G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_022046	A7UNK5|Q1RMZ2|Q6B089	Silent	SNP	ENST00000156499.2	37	CCDS12823.2																																																																																			G|0.981;A|0.019	0.019	strong		0.542	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046	
ASMTL	8623	hgsc.bcm.edu	37	X	1522325	1522325	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1522325C>T	ENST00000381317.3	-	13	1735	c.1703G>A	c.(1702-1704)cGc>cAc	p.R568H	ASMTL_ENST00000416733.2_Missense_Mutation_p.R492H|ASMTL-AS1_ENST00000425740.2_RNA|ASMTL_ENST00000534940.1_Missense_Mutation_p.R510H|ASMTL_ENST00000381333.4_Missense_Mutation_p.R552H|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000443929.1_RNA|ASMTL-AS1_ENST00000602357.1_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	568	ASMT-like.					cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CATCAGGGCGCGCTGCGCCAC	0.652													c|||	99	0.0197684	0.0726	0.0043	5008	,	,		19958	0.0		0.0	False		,,,				2504	0.0				p.R568H		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1703A						PASS	.		HIS/ARG,HIS/ARG,HIS/ARG	309,3951		11,287,1832	78.0	86.0	84.0		1529,1655,1703	1.3	0.0	X	dbSNP_134	84	4,8470		0,4,4233	no	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	29,29,29	11,291,6065	TT,TC,CC		0.0472,7.2535,2.458	possibly-damaging,possibly-damaging,possibly-damaging	510/564,552/606,568/622	1522325	313,12421	2130	4237	6367	SO:0001583	missense	8623	exon13			AGGGCGCGCTGCG	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.1703G>A	X.37:g.1522325C>T	ENSP00000370718:p.Arg568His	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	192	100	0.520833	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	50	0.022893772893772892	50	0.1016260162601626	0	0.0	0	0.0	0	0.0	c	4.831	0.154519	0.09236	0.072535	4.72E-4	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	1.31	1.31	0.21738	O-methyltransferase, family 2 (1);	0.432093	0.20024	U	0.100843	T	0.00724	0.0024	L	0.50333	1.59	0.25285	N	0.989409	D;D;D	0.76494	0.998;0.999;0.999	D;D;P	0.64506	0.926;0.909;0.908	T	0.04481	-1.0948	10	0.13108	T	0.6	.	5.3914	0.16245	0.0:0.6424:0.3576:0.0	.	492;552;568	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	H	492;510;552;568	ENSP00000410578:R492H;ENSP00000446410:R510H;ENSP00000370734:R552H;ENSP00000370718:R568H	ENSP00000370718:R568H	R	-	2	0	ASMTL	1482325	0.000000	0.05858	0.001000	0.08648	0.046000	0.14306	-2.266000	0.01171	0.693000	0.31634	0.115000	0.15696	CGC	C|0.977;T|0.023	0.023	strong		0.652	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
NDFIP2	54602	hgsc.bcm.edu	37	13	80094993	80094993	+	Missense_Mutation	SNP	C	C	T	rs55887763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:80094993C>T	ENST00000218652.7	+	2	422	c.370C>T	c.(370-372)Cct>Tct	p.P124S	NDFIP2_ENST00000494647.1_3'UTR	NM_001161407.1|NM_019080.2	NP_001154879.1|NP_061953.2	Q9NV92	NFIP2_HUMAN	Nedd4 family interacting protein 2	124			P -> S (in dbSNP:rs55887763).		negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of transporter activity (GO:0032410)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			NS(1)|breast(1)|endometrium(2)|kidney(3)|lung(3)|ovary(2)|prostate(1)|skin(1)	14		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0196)		AGAGCAGCCACCTACTTCAAA	0.403													T|||	254	0.0507188	0.1838	0.0101	5008	,	,		15571	0.0		0.004	False		,,,				2504	0.0				p.P124S		Atlas-SNP	.											.	NDFIP2	23	.	0			c.C370T						PASS	.	T	SER/PRO,SER/PRO	641,3765	767.1+/-413.5	43,555,1605	89.0	82.0	84.0		370,370	5.8	0.3	13	dbSNP_129	84	2,8598	819.2+/-406.8	0,2,4298	yes	missense,missense	NDFIP2	NM_001161407.1,NM_019080.2	74,74	43,557,5903	TT,TC,CC		0.0233,14.5483,4.9439	benign,benign	124/317,124/337	80094993	643,12363	2203	4300	6503	SO:0001583	missense	54602	exon2			CAGCCACCTACTT	AB032991	CCDS31998.1	13q22.1	2011-05-18			ENSG00000102471	ENSG00000102471			18537	protein-coding gene	gene with protein product		610041				10574461, 12050153	Standard	NM_019080		Approved	KIAA1165, N4wbp5a	uc001vlf.3	Q9NV92	OTTHUMG00000017136	ENST00000218652.7:c.370C>T	13.37:g.80094993C>T	ENSP00000218652:p.Pro124Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_019080	Q7Z2H3|Q7Z428|Q8TAR3|Q9ULQ5	Missense_Mutation	SNP	ENST00000218652.7	37	CCDS31998.1	102	0.046703296703296704	99	0.20121951219512196	3	0.008287292817679558	0	0.0	0	0.0	T	1.479	-0.557610	0.03967	0.145483	2.33E-4	ENSG00000102471	ENST00000218652;ENST00000487865	T;T	0.25912	1.78;1.77	5.75	5.75	0.90469	.	0.192068	0.47455	N	0.000229	T	0.00012	0.0000	N	0.00210	-1.845	0.49213	P	2.3799999999996047E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29274	-1.0017	9	0.02654	T	1	-11.3844	11.0315	0.47776	0.0:0.0739:0.0:0.9261	rs55887763;rs58237612	30;124	B4DGY6;Q9NV92	.;NFIP2_HUMAN	S	124;41	ENSP00000218652:P124S;ENSP00000419200:P41S	ENSP00000218652:P124S	P	+	1	0	NDFIP2	78992994	0.995000	0.38212	0.331000	0.25455	0.299000	0.27559	3.411000	0.52672	1.003000	0.39130	-0.254000	0.11334	CCT	C|0.952;T|0.048	0.048	strong		0.403	NDFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045380.2		
ZNF189	7743	hgsc.bcm.edu	37	9	104170580	104170580	+	Missense_Mutation	SNP	A	A	G	rs148414030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:104170580A>G	ENST00000339664.2	+	3	659	c.530A>G	c.(529-531)cAg>cGg	p.Q177R	ZNF189_ENST00000259395.4_Missense_Mutation_p.Q135R|ZNF189_ENST00000374861.3_Missense_Mutation_p.Q163R	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	177					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)				AAACCTTTTCAGTGCAATGAA	0.408													A|||	6	0.00119808	0.0045	0.0	5008	,	,		21632	0.0		0.0	False		,,,				2504	0.0				p.Q177R		Atlas-SNP	.											.	ZNF189	79	.	0			c.A530G						PASS	.	A	ARG/GLN,ARG/GLN	19,4387	25.3+/-52.1	0,19,2184	82.0	82.0	82.0		530,404	4.6	1.0	9	dbSNP_134	82	0,8600		0,0,4300	yes	missense,missense	ZNF189	NM_003452.2,NM_197977.1	43,43	0,19,6484	GG,GA,AA		0.0,0.4312,0.1461	benign,benign	177/627,135/585	104170580	19,12987	2203	4300	6503	SO:0001583	missense	7743	exon3			CTTTTCAGTGCAA	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.530A>G	9.37:g.104170580A>G	ENSP00000342019:p.Gln177Arg	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	158	102	0.64557	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	A	9.515	1.106655	0.20714	0.004312	0.0	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.19105	2.17;2.17;2.17	4.55	4.55	0.56014	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46442	D	0.000288	T	0.18841	0.0452	N	0.13235	0.315	0.27578	N	0.949673	B;B;B	0.34372	0.056;0.451;0.262	B;P;B	0.47102	0.115;0.537;0.115	T	0.10359	-1.0633	10	0.54805	T	0.06	.	7.7508	0.28896	0.8138:0.0:0.0:0.1862	.	162;163;177	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	R	163;177;135	ENSP00000363995:Q163R;ENSP00000342019:Q177R;ENSP00000259395:Q135R	ENSP00000259395:Q135R	Q	+	2	0	ZNF189	103210401	0.000000	0.05858	0.995000	0.50966	0.991000	0.79684	0.093000	0.15086	2.272000	0.75746	0.460000	0.39030	CAG	A|0.998;G|0.002	0.002	strong		0.408	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
FLG	2312	hgsc.bcm.edu	37	1	152286002	152286002	+	Missense_Mutation	SNP	T	T	C	rs386635459|rs2011331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152286002T>C	ENST00000368799.1	-	3	1395	c.1360A>G	c.(1360-1362)Aca>Gca	p.T454A	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_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	434	0	0		WXS	Illumina HiSeq	Phase_I	457	457	1	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	
CCNH	902	hgsc.bcm.edu	37	5	86695228	86695228	+	Silent	SNP	A	A	T	rs150856919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:86695228A>T	ENST00000256897.4	-	7	1079	c.855T>A	c.(853-855)ctT>ctA	p.L285L	CCNH_ENST00000508855.1_Silent_p.L211L|CCNH_ENST00000504878.1_Silent_p.L211L	NM_001239.3	NP_001230.1	P51946	CCNH_HUMAN	cyclin H	285					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|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)|viral process (GO:0016032)	cyclin-dependent protein kinase activating kinase holoenzyme complex (GO:0019907)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|TFIIK complex (GO:0070985)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|kinase activity (GO:0016301)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(2)|ovary(2)	15		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;9.01e-39)|Epithelial(54;5.08e-33)|all cancers(79;4.28e-28)		CGTTAAGTGCAAGCTCAGCAG	0.388								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																													p.L285L		Atlas-SNP	.											.	CCNH	40	.	0			c.T855A						PASS	.	A	,	4,4402	8.1+/-20.4	0,4,2199	221.0	187.0	198.0		696,855	4.5	1.0	5	dbSNP_134	198	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CCNH	NM_001199189.1,NM_001239.3	,	0,4,6499	TT,TA,AA		0.0,0.0908,0.0308	,	232/271,285/324	86695228	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	902	exon7			AAGTGCAAGCTCA	U12685	CCDS4064.1	5q13.3-q14	2014-03-28			ENSG00000134480	ENSG00000134480		"""General transcription factor IIH complex subunits"""	1594	protein-coding gene	gene with protein product	"""CDK-activating kinase complex subunit"", ""cyclin-dependent kinase-activating kinase complex subunit"", ""MO15-associated protein"", ""CAK complex subunit"""	601953				9465303	Standard	NM_001239		Approved	p34, p37, CycH	uc003kjb.3	P51946	OTTHUMG00000119077	ENST00000256897.4:c.855T>A	5.37:g.86695228A>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_001239	Q53X72|Q8TBL9	Silent	SNP	ENST00000256897.4	37	CCDS4064.1																																																																																			A|1.000;T|0.000	0.000	strong		0.388	CCNH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239291.3	NM_001239	
SLC8A3	6547	hgsc.bcm.edu	37	14	70634546	70634546	+	Silent	SNP	C	C	T	rs7161524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:70634546C>T	ENST00000381269.2	-	2	1347	c.594G>A	c.(592-594)aaG>aaA	p.K198K	SLC8A3_ENST00000528359.1_Silent_p.K198K|SLC8A3_ENST00000357887.3_Silent_p.K198K|SLC8A3_ENST00000356921.2_Silent_p.K198K|SLC8A3_ENST00000534137.1_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	123	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	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		
PKD1	5310	hgsc.bcm.edu	37	16	2147500	2147500	+	Missense_Mutation	SNP	C	C	G	rs61747420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2147500C>G	ENST00000262304.4	-	33	10433	c.10225G>C	c.(10225-10227)Gtg>Ctg	p.V3409L	PKD1_ENST00000423118.1_Missense_Mutation_p.V3408L|RP11-304L19.1_ENST00000570072.1_RNA|RP11-304L19.3_ENST00000565937.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3409					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						GGCCAGCACACCAGACTGCAG	0.672													c|||	257	0.0513179	0.1861	0.0159	5008	,	,		17089	0.0		0.0	False		,,,				2504	0.0				p.V3409L		Atlas-SNP	.											.	PKD1	184	.	0			c.G10225C						PASS	.	C	LEU/VAL,LEU/VAL	543,3827		29,485,1671	18.0	18.0	18.0		10222,10225	2.2	1.0	16	dbSNP_129	18	6,8516		0,6,4255	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	32,32	29,491,5926	GG,GC,CC		0.0704,12.4256,4.2585	benign,benign	3408/4303,3409/4304	2147500	549,12343	2185	4261	6446	SO:0001583	missense	5310	exon33			AGCACACCAGACT	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.10225G>C	16.37:g.2147500C>G	ENSP00000262304:p.Val3409Leu	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_001009944	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	94	0.04304029304029304	88	0.17886178861788618	6	0.016574585635359115	0	0.0	0	0.0	C	5.233	0.228566	0.09916	0.124256	7.04E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.36699	1.24;1.26	4.44	2.24	0.28232	.	0.926325	0.09170	N	0.839061	T	0.00073	0.0002	L	0.56769	1.78	0.50039	P	1.5799999999999148E-4	B;B	0.30146	0.27;0.021	B;B	0.29598	0.104;0.012	T	0.16041	-1.0416	9	0.25106	T	0.35	.	4.1741	0.10343	0.0:0.5308:0.2145:0.2547	rs61747420	3408;3409	P98161-3;P98161	.;PKD1_HUMAN	L	3409;3408;2743	ENSP00000262304:V3409L;ENSP00000399501:V3408L	ENSP00000262304:V3409L	V	-	1	0	PKD1	2087501	0.000000	0.05858	0.994000	0.49952	0.018000	0.09664	0.114000	0.15520	1.044000	0.40200	0.555000	0.69702	GTG	C|0.948;G|0.052	0.052	strong		0.672	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
MUC4	4585	hgsc.bcm.edu	37	3	195481111	195481111	+	Missense_Mutation	SNP	G	G	T	rs73079395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195481111G>T	ENST00000346145.4	-	18	2632	c.2593C>A	c.(2593-2595)Ctg>Atg	p.L865M	MUC4_ENST00000349607.4_Missense_Mutation_p.L814M|MUC4_ENST00000475231.1_Missense_Mutation_p.L5049M|MUC4_ENST00000463781.3_Missense_Mutation_p.L5101M	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1858	Ser-rich.				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)		TCCCCAGTCAGGTTTGGAGGG	0.662													.|||	325	0.0648962	0.2322	0.0245	5008	,	,		15840	0.0		0.001	False		,,,				2504	0.0				p.L5101M		Atlas-SNP	.											.	MUC4	1505	.	0			c.C15301A						PASS	.	G	MET/LEU,MET/LEU,MET/LEU	900,3506		99,702,1402	63.0	67.0	65.0		2593,15301,2440	1.3	0.6	3	dbSNP_130	65	6,8594		0,6,4294	yes	missense,missense,missense	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	15,15,15	99,708,5696	TT,TG,GG		0.0698,20.4267,6.966	possibly-damaging,possibly-damaging,possibly-damaging	865/1177,5101/5413,814/1126	195481111	906,12100	2203	4300	6503	SO:0001583	missense	4585	exon19			CAGTCAGGTTTGG	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.2593C>A	3.37:g.195481111G>T	ENSP00000304207:p.Leu865Met	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	307	155	0.504886	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	113	0.051739926739926737	106	0.21544715447154472	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	.	8.877	0.950622	0.18431	0.204267	6.98E-4	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.46451	0.87;1.23;1.21;1.16	4.96	1.32	0.21799	.	0.408184	0.20459	N	0.091933	T	0.00039	0.0001	L	0.43757	1.38	0.80722	P	0.0	P;B;P;B;B;P	0.39352	0.554;0.254;0.494;0.057;0.057;0.669	B;B;B;B;B;B	0.42112	0.078;0.118;0.19;0.015;0.015;0.376	T	0.15292	-1.0442	9	0.32370	T	0.25	-1.7434	12.0729	0.53626	0.0:0.0:0.611:0.389	.	4973;814;865;5101;5049;1806	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	M	814;865;5101;5049;1601	ENSP00000338109:L814M;ENSP00000304207:L865M;ENSP00000417498:L5101M;ENSP00000420243:L5049M	ENSP00000304207:L865M	L	-	1	2	MUC4	196966782	0.986000	0.35501	0.621000	0.29145	0.157000	0.22087	0.811000	0.27198	0.329000	0.23460	0.436000	0.28706	CTG	G|0.924;T|0.076	0.076	strong		0.662	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
PKD1L1	168507	hgsc.bcm.edu	37	7	47925485	47925485	+	Missense_Mutation	SNP	T	T	G	rs113527998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47925485T>G	ENST00000289672.2	-	18	3054	c.3004A>C	c.(3004-3006)Act>Cct	p.T1002P		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1002	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						GGAGCTGAAGTGGCAGGTTGG	0.607													G|||	199	0.0397364	0.1407	0.0101	5008	,	,		16333	0.0		0.005	False		,,,				2504	0.001				p.T1002P		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A3004C						PASS	.	G	PRO/THR	657,3749	765.5+/-413.4	51,555,1597	86.0	87.0	86.0		3004	0.5	0.0	7	dbSNP_132	86	85,8515	815.6+/-407.0	1,83,4216	yes	missense	PKD1L1	NM_138295.3	38	52,638,5813	GG,GT,TT		0.9884,14.9115,5.7051	benign	1002/2850	47925485	742,12264	2203	4300	6503	SO:0001583	missense	168507	exon18			CTGAAGTGGCAGG	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.3004A>C	7.37:g.47925485T>G	ENSP00000289672:p.Thr1002Pro	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	198	81	0.409091	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	88	0.040293040293040296	81	0.16463414634146342	4	0.011049723756906077	0	0.0	3	0.00395778364116095	G	8.197	0.797394	0.16327	0.149115	0.009884	ENSG00000158683	ENST00000289672	T	0.20332	2.08	4.97	0.5	0.16919	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	2744.040000	0.00166	N	0.000000	T	0.00039	0.0001	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25779	-1.0122	9	0.29301	T	0.29	0.945	0.5519	0.00664	0.2174:0.1517:0.32:0.3108	.	1002	Q8TDX9	PK1L1_HUMAN	P	1002	ENSP00000289672:T1002P	ENSP00000289672:T1002P	T	-	1	0	PKD1L1	47892010	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.139000	0.16036	-0.344000	0.08338	-0.132000	0.14878	ACT	T|0.950;G|0.050	0.050	strong		0.607	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
DDX25	29118	hgsc.bcm.edu	37	11	125778305	125778305	+	Silent	SNP	C	C	T	rs34007659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:125778305C>T	ENST00000263576.6	+	6	569	c.414C>T	c.(412-414)aaC>aaT	p.N138N	RP11-680F20.9_ENST00000533033.2_RNA|DDX25_ENST00000525943.1_3'UTR	NM_013264.4	NP_037396.3	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 25	138	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)	10	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)		GACCCCAGAACCTCATAGCAC	0.428													C|||	85	0.0169728	0.0613	0.0043	5008	,	,		20960	0.0		0.001	False		,,,				2504	0.0				p.N138N		Atlas-SNP	.											.	DDX25	65	.	0			c.C414T						PASS	.	C		201,3635		5,191,1722	170.0	163.0	165.0		414	2.3	1.0	11	dbSNP_126	165	5,8241		0,5,4118	no	coding-synonymous	DDX25	NM_013264.3		5,196,5840	TT,TC,CC		0.0606,5.2398,1.705		138/484	125778305	206,11876	1918	4123	6041	SO:0001819	synonymous_variant	29118	exon6			CCAGAACCTCATA	AF155140	CCDS44766.1	11q24	2012-02-23	2012-02-23		ENSG00000109832	ENSG00000109832		"""DEAD-boxes"""	18698	protein-coding gene	gene with protein product	"""gonadotropin-regulated testicular RNA helicase"""	607663	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 25"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 25"""			10608860, 15096601	Standard	NM_013264		Approved	GRTH	uc001qcz.5	Q9UHL0	OTTHUMG00000165859	ENST00000263576.6:c.414C>T	11.37:g.125778305C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	146	83	0.568493	NM_013264	B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Silent	SNP	ENST00000263576.6	37	CCDS44766.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	8.677	0.904182	0.17760	0.052398	6.06E-4	ENSG00000109832	ENST00000530129	.	.	.	5.18	2.26	0.28386	.	.	.	.	.	T	0.10165	0.0249	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03773	-1.1005	4	.	.	.	-6.705	4.4905	0.11812	0.0:0.4806:0.1565:0.3629	rs34007659	.	.	.	S	150	.	.	P	+	1	0	DDX25	125283515	0.994000	0.37717	1.000000	0.80357	0.995000	0.86356	0.292000	0.19011	0.269000	0.21961	0.591000	0.81541	CCT	C|0.985;T|0.015	0.015	strong		0.428	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3	NM_013264	
SUPV3L1	6832	hgsc.bcm.edu	37	10	70940066	70940066	+	Silent	SNP	C	C	T	rs12251842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70940066C>T	ENST00000359655.4	+	1	79	c.19C>T	c.(19-21)Cta>Tta	p.L7L	SUPV3L1_ENST00000483572.1_3'UTR	NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	7					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						CTCCCGTGCCCTATTGTGGGC	0.706													C|||	232	0.0463259	0.1672	0.0144	5008	,	,		16416	0.0		0.001	False		,,,				2504	0.0				p.L7L		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.C19T						PASS	.	C		575,3829	214.1+/-233.5	41,493,1668	25.0	29.0	28.0		19	0.8	0.6	10	dbSNP_120	28	4,8594	2.2+/-6.3	0,4,4295	no	coding-synonymous	SUPV3L1	NM_003171.3		41,497,5963	TT,TC,CC		0.0465,13.0563,4.4532		7/787	70940066	579,12423	2202	4299	6501	SO:0001819	synonymous_variant	6832	exon1			CGTGCCCTATTGT	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.19C>T	10.37:g.70940066C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_003171	A8K301|O43630	Silent	SNP	ENST00000359655.4	37	CCDS7287.1																																																																																			C|0.962;T|0.038	0.038	strong		0.706	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171	
HIPK4	147746	hgsc.bcm.edu	37	19	40895493	40895493	+	Missense_Mutation	SNP	G	G	A	rs79236726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40895493G>A	ENST00000291823.2	-	1	601	c.317C>T	c.(316-318)gCg>gTg	p.A106V		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	106	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in dbSNP:rs34434715). {ECO:0000269|PubMed:17344846}.		histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			GGGGAGGGGCGCGAAGTTGTT	0.577													G|||	32	0.00638978	0.0242	0.0	5008	,	,		9839	0.0		0.0	False		,,,				2504	0.0				p.A106V		Atlas-SNP	.											HIPK4_ENST00000291823,colon,carcinoma,+1,2	HIPK4	100	2	0			c.C317T						scavenged	.	G	VAL/ALA	104,4302	82.4+/-120.9	2,100,2101	58.0	62.0	61.0		317	2.9	0.7	19	dbSNP_131	61	0,8600		0,0,4300	yes	missense	HIPK4	NM_144685.3	64	2,100,6401	AA,AG,GG		0.0,2.3604,0.7996	possibly-damaging	106/617	40895493	104,12902	2203	4300	6503	SO:0001583	missense	147746	exon1			AGGGGCGCGAAGT	BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.317C>T	19.37:g.40895493G>A	ENSP00000291823:p.Ala106Val	Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	37	CCDS12555.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	14.62	2.590686	0.46214	0.023604	0.0	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.63255	-0.03	5.08	2.91	0.33838	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	0.51477	D	0.000083	T	0.27241	0.0668	N	0.04787	-0.16	0.34206	D	0.67376	P	0.50528	0.936	P	0.46419	0.516	T	0.54357	-0.8306	10	0.52906	T	0.07	.	9.804	0.40781	0.0:0.2864:0.5655:0.1481	.	106	Q8NE63	HIPK4_HUMAN	V	106;71	ENSP00000291823:A106V	ENSP00000291823:A106V	A	-	2	0	HIPK4	45587333	0.003000	0.15002	0.726000	0.30738	0.995000	0.86356	1.122000	0.31295	0.708000	0.31955	0.462000	0.41574	GCG	G|0.992;A|0.008	0.008	strong		0.577	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685	
NUP62	23636	hgsc.bcm.edu	37	19	50412516	50412516	+	Silent	SNP	C	C	T	rs1984656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50412516C>T	ENST00000596217.1	-	2	2436	c.549G>A	c.(547-549)acG>acA	p.T183T	NUP62_ENST00000352066.3_Silent_p.T183T|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000413454.1_Silent_p.T183T|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000597723.1_Silent_p.T183T|NUP62_ENST00000422090.2_Silent_p.T183T|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000597029.1_Silent_p.T183T			P37198	NUP62_HUMAN	nucleoporin 62kDa	183	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)		TGGCAGGTGCCGTGGGCTGGG	0.627													C|||	109	0.0217652	0.0613	0.0245	5008	,	,		14325	0.0		0.0099	False		,,,				2504	0.001				p.T183T		Atlas-SNP	.											.	NUP62	50	.	0			c.G549A						PASS	.	C	,,,,,	196,4210	122.5+/-159.9	13,170,2020	67.0	69.0	68.0		549,549,549,549,549,	-10.1	0.0	19	dbSNP_92	68	90,8510	51.5+/-111.7	2,86,4212	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	,,,,,	15,256,6232	TT,TC,CC		1.0465,4.4485,2.199	,,,,,	183/523,183/523,183/523,183/523,183/523,	50412516	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	23636	exon3			AGGTGCCGTGGGC	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.549G>A	19.37:g.50412516C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	225	120	0.533333	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	37	CCDS12788.1																																																																																			C|0.978;T|0.022	0.022	strong		0.627	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719	
PHC1	1911	hgsc.bcm.edu	37	12	9086898	9086898	+	Missense_Mutation	SNP	A	A	G	rs1049925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9086898A>G	ENST00000543824.1	+	11	2409	c.2077A>G	c.(2077-2079)Act>Gct	p.T693A	PHC1_ENST00000544916.1_Missense_Mutation_p.T693A|PHC1_ENST00000536844.1_Missense_Mutation_p.T299A|PHC1_ENST00000433083.2_Missense_Mutation_p.T648A			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	693			T -> A (in dbSNP:rs1049925). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		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						GAATGCTAATACTCCAAGCAG	0.448													A|||	1770	0.353435	0.1551	0.3818	5008	,	,		-128	0.4107		0.4274	False		,,,				2504	0.4663				p.T693A		Atlas-SNP	.											.	PHC1	67	.	0			c.A2077G						PASS	.	A	ALA/THR	868,3538	335.2+/-303.8	82,704,1417	102.0	96.0	98.0		2077	0.9	0.1	12	dbSNP_86	98	3806,4794	524.3+/-380.5	784,2238,1278	yes	missense	PHC1	NM_004426.2	58	866,2942,2695	GG,GA,AA		44.2558,19.7004,35.9373	benign	693/1005	9086898	4674,8332	2203	4300	6503	SO:0001583	missense	1911	exon10			GCTAATACTCCAA	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.2077A>G	12.37:g.9086898A>G	ENSP00000440674:p.Thr693Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Missense_Mutation	SNP	ENST00000543824.1	37	CCDS8597.1	803	0.3676739926739927	71	0.1443089430894309	135	0.3729281767955801	268	0.46853146853146854	329	0.4340369393139842	A	8.336	0.827685	0.16749	0.197004	0.442558	ENSG00000111752	ENST00000543824;ENST00000251757;ENST00000433083;ENST00000544916;ENST00000536844	T;T;T;T;T	0.36340	1.99;1.99;1.99;1.99;1.26	5.32	0.937	0.19494	.	0.365346	0.27008	N	0.021396	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	0.47861	-0.9084	9	0.25106	T	0.35	-4.416	3.3522	0.07156	0.425:0.3732:0.0766:0.1252	rs1049925;rs12818486;rs16915798;rs17294227;rs17729971;rs52819214;rs59173968;rs1049925	693	P78364	PHC1_HUMAN	A	693;693;648;693;299	ENSP00000440674:T693A;ENSP00000251757:T693A;ENSP00000399194:T648A;ENSP00000437659:T693A;ENSP00000440488:T299A	ENSP00000251757:T693A	T	+	1	0	PHC1	8978165	0.000000	0.05858	0.105000	0.21289	0.907000	0.53573	-0.529000	0.06186	-0.009000	0.14296	0.533000	0.62120	ACT	A|0.630;G|0.370	0.370	strong		0.448	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	
SSPO	23145	hgsc.bcm.edu	37	7	149498903	149498903	+	RNA	SNP	T	T	C	rs2074689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149498903T>C	ENST00000378016.2	+	0	7355							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)			ATGCCTACCATGGCCCTGCCT	0.617													C|||	1074	0.214457	0.5658	0.0994	5008	,	,		17959	0.0833		0.0636	False		,,,				2504	0.1115				p.M2452T		Atlas-SNP	.											.	.	.	.	0			c.T7355C						PASS	.	C		1836,2350		375,1086,632	49.0	51.0	50.0		7359	1.8	0.0	7	dbSNP_96	50	547,7891		27,493,3699	no	coding-notMod3	SSPO	NM_198455.2		402,1579,4331	CC,CT,TT		6.4826,43.8605,18.8767			149498903	2383,10241	2093	4219	6312			23145	exon50			CTACCATGGCCCT	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.149498903T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.858;C|0.142	0.142	strong		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
LRFN3	79414	hgsc.bcm.edu	37	19	36430465	36430465	+	Silent	SNP	A	A	C	rs2242590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36430465A>C	ENST00000588831.1	+	3	1192	c.138A>C	c.(136-138)ccA>ccC	p.P46P	LRFN3_ENST00000246529.3_Silent_p.P46P			Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III domain containing 3	46	LRRNT.				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)			TGCTGTGCCCAGGGGCAGGCC	0.721													A|||	793	0.158347	0.382	0.1009	5008	,	,		14139	0.126		0.0268	False		,,,				2504	0.0654				p.P46P		Atlas-SNP	.											.	LRFN3	43	.	0			c.A138C						PASS	.	A		1285,3057		187,911,1073	14.0	17.0	16.0		138	-9.2	0.7	19	dbSNP_98	16	287,8231		2,283,3974	no	coding-synonymous	LRFN3	NM_024509.1		189,1194,5047	CC,CA,AA		3.3693,29.5947,12.224		46/629	36430465	1572,11288	2171	4259	6430	SO:0001819	synonymous_variant	79414	exon2			GTGCCCAGGGGCA	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.138A>C	19.37:g.36430465A>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_024509	Q6UY10	Silent	SNP	ENST00000588831.1	37	CCDS12483.1																																																																																			A|0.876;C|0.124	0.124	strong		0.721	LRFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457403.2	NM_024509	
GJB5	2709	hgsc.bcm.edu	37	1	35223345	35223345	+	Silent	SNP	G	G	A	rs3738345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35223345G>A	ENST00000338513.1	+	2	587	c.414G>A	c.(412-414)aaG>aaA	p.K138K	GJB4_ENST00000339480.1_5'Flank	NM_005268.3	NP_005259.1	O95377	CXB5_HUMAN	gap junction protein, beta 5, 31.1kDa	138					cell communication (GO:0007154)|epidermis development (GO:0008544)|labyrinthine layer morphogenesis (GO:0060713)|spongiotrophoblast differentiation (GO:0060708)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)		p.K138K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)	10		Myeloproliferative disorder(586;0.0393)				TAGTGTTCAAGGCGAGCGTGG	0.557													G|||	1320	0.263578	0.4826	0.2378	5008	,	,		21205	0.1062		0.2535	False		,,,				2504	0.1585				p.K138K		Atlas-SNP	.											GJB5,NS,carcinoma,0,1	GJB5	35	1	1	Substitution - coding silent(1)	stomach(1)	c.G414A						PASS	.	G		1877,2529	541.7+/-375.8	389,1099,715	129.0	114.0	119.0		414	3.0	1.0	1	dbSNP_107	119	2155,6445	370.3+/-335.8	259,1637,2404	no	coding-synonymous	GJB5	NM_005268.2		648,2736,3119	AA,AG,GG		25.0581,42.601,31.0011		138/274	35223345	4032,8974	2203	4300	6503	SO:0001819	synonymous_variant	2709	exon2			GTTCAAGGCGAGC	BC004379	CCDS382.1	1p34.3	2008-05-14	2007-11-06		ENSG00000189280	ENSG00000189280		"""Ion channels / Gap junction proteins (connexins)"""	4287	protein-coding gene	gene with protein product	"""connexin 31.1"""	604493	"""gap junction protein, beta 5 (connexin 31.1)"", ""gap junction protein, beta 5"""			9843209	Standard	NM_005268		Approved	CX31.1	uc001bxu.4	O95377	OTTHUMG00000004053	ENST00000338513.1:c.414G>A	1.37:g.35223345G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_005268	Q9UPA3	Silent	SNP	ENST00000338513.1	37	CCDS382.1																																																																																			G|0.718;A|0.282	0.282	strong		0.557	GJB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011561.1	NM_005268	
MYO9B	4650	hgsc.bcm.edu	37	19	17305781	17305781	+	Missense_Mutation	SNP	T	T	G	rs45541337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17305781T>G	ENST00000594824.1	+	22	3692	c.3545T>G	c.(3544-3546)gTc>gGc	p.V1182G	MYO9B_ENST00000595618.1_Missense_Mutation_p.V1182G|MYO9B_ENST00000397274.2_Missense_Mutation_p.V1182G			Q13459	MYO9B_HUMAN	myosin IXB	1182	Tail.				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						TCCAGAAGGGTCACCCAGGAG	0.537													T|||	402	0.0802716	0.2504	0.0418	5008	,	,		17207	0.0		0.0338	False		,,,				2504	0.0082				p.V1182G		Atlas-SNP	.											.	MYO9B	264	.	0			c.T3545G						PASS	.	T	GLY/VAL,GLY/VAL	842,3328		69,704,1312	55.0	65.0	61.0		3545,3545	2.0	0.0	19	dbSNP_127	61	263,8161		7,249,3956	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	109,109	76,953,5268	GG,GT,TT		3.122,20.1918,8.774	benign,benign	1182/2023,1182/2158	17305781	1105,11489	2085	4212	6297	SO:0001583	missense	4650	exon22			GAAGGGTCACCCA		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.3545T>G	19.37:g.17305781T>G	ENSP00000471367:p.Val1182Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		163	0.07463369963369963	125	0.2540650406504065	14	0.03867403314917127	0	0.0	24	0.0316622691292876	T	6.891	0.533897	0.13188	0.201918	0.03122	ENSG00000099331	ENST00000397274	D	0.84370	-1.84	5.28	1.95	0.26073	.	0.533191	0.16583	N	0.208110	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.14805	0.011;0.011;0.011	B;B;B	0.13407	0.009;0.009;0.009	T	0.02553	-1.1142	9	0.22706	T	0.39	.	4.4561	0.11643	0.1763:0.632:0.0:0.1917	rs45541337	1182;1182;1188	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	G	1182	ENSP00000380444:V1182G	ENSP00000380444:V1182G	V	+	2	0	MYO9B	17166781	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	0.044000	0.13992	0.210000	0.20664	-0.366000	0.07423	GTC	T|0.934;G|0.066	0.066	strong		0.537	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
GIMAP5	55340	hgsc.bcm.edu	37	7	150439554	150439554	+	Silent	SNP	G	G	A	rs61751040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150439554G>A	ENST00000358647.3	+	3	694	c.327G>A	c.(325-327)ccG>ccA	p.P109P	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	109	AIG1-type G.				myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCTCTGCCCCGGGGCCCCACG	0.592													G|||	297	0.0593051	0.1785	0.0173	5008	,	,		18120	0.0159		0.0	False		,,,				2504	0.0337				p.P313P		Atlas-SNP	.											GIMAP5,NS,carcinoma,+1,1	.	.	1	0			c.G939A						scavenged	.	G	,	661,3745	280.5+/-275.4	42,577,1584	75.0	76.0	76.0		939,327	-8.3	0.0	7	dbSNP_129	76	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	GIMAP5,GIMAP1-GIMAP5	NM_001199577.1,NM_018384.4	,	42,589,5872	AA,AG,GG		0.1395,15.0023,5.1745	,	313/512,109/308	150439554	673,12333	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			TGCCCCGGGGCCC	AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"""GTPases, IMAP"""	18005	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 5"""	608086	"""immune associated nucleotide 4 like 1 (mouse)"""	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.327G>A	7.37:g.150439554G>A		Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_001199577	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Silent	SNP	ENST00000358647.3	37	CCDS5907.1																																																																																			G|0.953;A|0.047	0.047	strong		0.592	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384	
DGKH	160851	hgsc.bcm.edu	37	13	42772717	42772717	+	Silent	SNP	G	G	T	rs9533031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:42772717G>T	ENST00000337343.4	+	18	2292	c.2271G>T	c.(2269-2271)ccG>ccT	p.P757P	DGKH_ENST00000379274.2_Silent_p.P621P|DGKH_ENST00000540693.1_Silent_p.P757P|DGKH_ENST00000261491.5_Silent_p.P757P|DGKH_ENST00000538674.1_Silent_p.P512P|DGKH_ENST00000536612.1_Silent_p.P621P|DGKH_ENST00000498255.2_3'UTR	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	99	0	0		WXS	Illumina HiSeq	Phase_I	111	63	0.567568	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	
TRPC6	7225	hgsc.bcm.edu	37	11	101347093	101347093	+	Silent	SNP	A	A	G	rs12366144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:101347093A>G	ENST00000344327.3	-	6	2107	c.1683T>C	c.(1681-1683)aaT>aaC	p.N561N	TRPC6_ENST00000360497.4_Silent_p.N506N|TRPC6_ENST00000348423.4_Silent_p.N445N|TRPC6_ENST00000532133.1_Intron	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	561					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		TCAAAGTATCATTTGCGTCAA	0.373													A|||	1497	0.298922	0.5832	0.2046	5008	,	,		21717	0.0724		0.2495	False		,,,				2504	0.2658				p.N561N	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											.	TRPC6	132	.	0			c.T1683C						PASS	.	A		2299,2107	601.6+/-389.7	605,1089,509	106.0	91.0	96.0		1683	3.4	1.0	11	dbSNP_120	96	2044,6554	354.2+/-329.4	243,1558,2498	no	coding-synonymous	TRPC6	NM_004621.5		848,2647,3007	GG,GA,AA		23.773,47.8212,33.3974		561/932	101347093	4343,8661	2203	4299	6502	SO:0001819	synonymous_variant	7225	exon6			AGTATCATTTGCG	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12338	protein-coding gene	gene with protein product		603652	"""focal segmental glomerulosclerosis 2"""	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.1683T>C	11.37:g.101347093A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Silent	SNP	ENST00000344327.3	37	CCDS8311.1																																																																																			A|0.699;G|0.301	0.301	strong		0.373	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621	
OR10G7	390265	hgsc.bcm.edu	37	11	123909524	123909524	+	Missense_Mutation	SNP	G	G	A	rs201246927		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909524G>A	ENST00000330487.5	-	1	193	c.185C>T	c.(184-186)aCc>aTc	p.T62I		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	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)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		GGACAGGTTGGTGAGGAAGTA	0.547																																					p.T62I		Atlas-SNP	.											OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	0			c.C185T						scavenged	.						21.0	21.0	21.0					11																	123909524		2195	4272	6467	SO:0001583	missense	390265	exon1			AGGTTGGTGAGGA	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.185C>T	11.37:g.123909524G>A	ENSP00000329689:p.Thr62Ile	Somatic	624	0	0		WXS	Illumina HiSeq	Phase_I	468	56	0.119658	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	58	0.026556776556776556	21	0.042682926829268296	17	0.04696132596685083	17	0.02972027972027972	3	0.00395778364116095	G	9.581	1.123605	0.20959	.	.	ENSG00000182634	ENST00000330487	T	0.01092	5.35	3.53	1.5	0.22942	GPCR, rhodopsin-like superfamily (1);	0.649434	0.13528	N	0.381190	T	0.00241	0.0007	L	0.28694	0.88	0.22213	N	0.999283	B	0.06786	0.001	B	0.15052	0.012	T	0.48875	-0.8996	10	0.66056	D	0.02	.	5.9703	0.19349	0.1371:0.3547:0.5082:0.0	.	62	Q8NGN6	O10G7_HUMAN	I	62	ENSP00000329689:T62I	ENSP00000329689:T62I	T	-	2	0	OR10G7	123414734	0.000000	0.05858	0.928000	0.36995	0.900000	0.52787	-0.620000	0.05565	0.261000	0.21753	0.557000	0.71058	ACC	A|1.000;|0.000	1.000	weak		0.547	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
ARL5C	390790	hgsc.bcm.edu	37	17	37317566	37317566	+	Silent	SNP	C	C	A	rs11653423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37317566C>A	ENST00000269586.7	-	4	293	c.294G>T	c.(292-294)cgG>cgT	p.R98R	ARL5C_ENST00000583123.1_5'Flank|ARL5C_ENST00000444555.1_Silent_p.R98R	NM_001143968.1	NP_001137440.1	A6NH57	ARL5C_HUMAN	ADP-ribosylation factor-like 5C	98					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)										TGGTCAGCAGCCGATCCCGGT	0.567													C|||	436	0.0870607	0.3124	0.0317	5008	,	,		17838	0.0		0.001	False		,,,				2504	0.0				p.R98R		Atlas-SNP	.											.	ARL5C	3	.	0			c.G294T						PASS	.	C		378,1006		50,278,364	45.0	37.0	39.0		294	-2.4	0.0	17	dbSNP_120	39	13,3169		0,13,1578	no	coding-synonymous	ARL5C	NM_001143968.1		50,291,1942	AA,AC,CC		0.4085,27.3121,8.5633		98/180	37317566	391,4175	692	1591	2283	SO:0001819	synonymous_variant	390790	exon4			CAGCAGCCGATCC		CCDS45664.1	17q12	2014-05-09	2005-11-08	2005-11-08	ENSG00000141748	ENSG00000141748		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	31111	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 12"""	ARL12			Standard	NM_001143968		Approved		uc010wea.2	A6NH57		ENST00000269586.7:c.294G>T	17.37:g.37317566C>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_001143968		Silent	SNP	ENST00000269586.7	37	CCDS45664.1																																																																																			C|0.933;A|0.067	0.067	strong		0.567	ARL5C-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444566.1	NM_001143968	
FBN3	84467	hgsc.bcm.edu	37	19	8196645	8196645	+	Missense_Mutation	SNP	G	G	A	rs61729592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8196645G>A	ENST00000600128.1	-	15	2197	c.1783C>T	c.(1783-1785)Cgc>Tgc	p.R595C	FBN3_ENST00000601739.1_Missense_Mutation_p.R595C|FBN3_ENST00000270509.2_Missense_Mutation_p.R595C			Q75N90	FBN3_HUMAN	fibrillin 3	595	EGF-like 7; 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						CACTGGCAGCGGAAGGAGCCC	0.672													G|||	11	0.00219649	0.0083	0.0	5008	,	,		15081	0.0		0.0	False		,,,				2504	0.0				p.R595C		Atlas-SNP	.											.	FBN3	300	.	0			c.C1783T						PASS	.	G	CYS/ARG	23,4383		0,23,2180	22.0	23.0	22.0		1783	3.0	0.9	19	dbSNP_129	22	1,8595		0,1,4297	yes	missense	FBN3	NM_032447.3	180	0,24,6477	AA,AG,GG		0.0116,0.522,0.1846	probably-damaging	595/2810	8196645	24,12978	2203	4298	6501	SO:0001583	missense	84467	exon14			GGCAGCGGAAGGA		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.1783C>T	19.37:g.8196645G>A	ENSP00000470498:p.Arg595Cys	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	181	96	0.530387	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	g	13.30	2.197312	0.38806	0.00522	1.16E-4	ENSG00000142449	ENST00000270509	D	0.92545	-3.06	3.02	3.02	0.34903	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.063744	0.64402	U	0.000009	D	0.93419	0.7901	M	0.85041	2.73	0.52501	D	0.999955	D	0.65815	0.995	P	0.58077	0.832	D	0.93900	0.7187	10	0.87932	D	0	.	13.9673	0.64216	0.0:0.0:1.0:0.0	.	595	Q75N90	FBN3_HUMAN	C	595	ENSP00000270509:R595C	ENSP00000270509:R595C	R	-	1	0	FBN3	8102645	0.999000	0.42202	0.856000	0.33681	0.121000	0.20230	2.263000	0.43293	1.227000	0.43598	0.185000	0.17295	CGC	G|0.996;A|0.004	0.004	strong		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
RHOT2	89941	hgsc.bcm.edu	37	16	719592	719592	+	Missense_Mutation	SNP	G	G	A	rs11557858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:719592G>A	ENST00000315082.4	+	5	376	c.262G>A	c.(262-264)Gcc>Acc	p.A88T	RHOT2_ENST00000569943.2_Intron	NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	88	Miro 1.				cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				CTCTGAGGAGGCCACCATTGA	0.622													G|||	1387	0.276957	0.5348	0.1801	5008	,	,		18724	0.2946		0.1153	False		,,,				2504	0.1452				p.A88T		Atlas-SNP	.											.	RHOT2	35	.	0			c.G262A						PASS	.	G	THR/ALA	2063,2333	566.1+/-381.8	477,1109,612	156.0	102.0	121.0		262	-1.1	0.8	16	dbSNP_120	121	1092,7502	227.2+/-262.7	63,966,3268	yes	missense	RHOT2	NM_138769.1	58	540,2075,3880	AA,AG,GG		12.7065,46.929,24.2879	benign	88/619	719592	3155,9835	2198	4297	6495	SO:0001583	missense	89941	exon5			GAGGAGGCCACCA	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"""EF-hand domain containing"""	21169	protein-coding gene	gene with protein product	"""mitochondrial Rho (MIRO) GTPase 2"""	613889	"""chromosome 16 open reading frame 39"", ""ras homolog gene family, member T2"""	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.262G>A	16.37:g.719592G>A	ENSP00000321971:p.Ala88Thr	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Missense_Mutation	SNP	ENST00000315082.4	37	CCDS10417.1	552	0.25274725274725274	259	0.5264227642276422	48	0.13259668508287292	169	0.29545454545454547	76	0.10026385224274406	G	8.543	0.873637	0.17322	0.46929	0.127065	ENSG00000140983	ENST00000315082	T	0.76968	-1.06	5.07	-1.08	0.09936	MIRO (1);	0.589164	0.18158	N	0.149874	T	0.00012	0.0000	N	0.05608	-0.01	0.51233	P	8.399999999997299E-5	B	0.06786	0.001	B	0.12837	0.008	T	0.43507	-0.9387	9	0.13853	T	0.58	-5.7558	6.5124	0.22228	0.3047:0.0:0.5681:0.1272	rs11557858;rs28637938	88	Q8IXI1	MIRO2_HUMAN	T	88	ENSP00000321971:A88T	ENSP00000321971:A88T	A	+	1	0	RHOT2	659593	0.026000	0.19158	0.822000	0.32727	0.564000	0.35744	0.433000	0.21477	0.169000	0.19679	0.555000	0.69702	GCC	G|0.760;A|0.240	0.240	strong		0.622	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769	
PEX6	5190	hgsc.bcm.edu	37	6	42932080	42932080	+	Missense_Mutation	SNP	G	G	A	rs115180949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42932080G>A	ENST00000304611.8	-	17	3005	c.2936C>T	c.(2935-2937)gCc>gTc	p.A979V	PEX6_ENST00000244546.4_3'UTR	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	979					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)			CTCCTAGCAGGCAGCAAACTT	0.637													G|||	47	0.00938498	0.034	0.0029	5008	,	,		17507	0.0		0.0	False		,,,				2504	0.0				p.A979V		Atlas-SNP	.											.	PEX6	44	.	0			c.C2936T						PASS	.	G	VAL/ALA	85,4321		0,85,2118	36.0	38.0	37.0		2936	5.0	1.0	6	dbSNP_132	37	3,8595		0,3,4296	yes	missense	PEX6	NM_000287.3	64	0,88,6414	AA,AG,GG		0.0349,1.9292,0.6767	possibly-damaging	979/981	42932080	88,12916	2203	4299	6502	SO:0001583	missense	5190	exon17			TAGCAGGCAGCAA	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.2936C>T	6.37:g.42932080G>A	ENSP00000303511:p.Ala979Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	37	CCDS4877.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	G	36	5.602210	0.96614	0.019292	3.49E-4	ENSG00000124587	ENST00000304611	D	0.95377	-3.69	5.9	5.03	0.67393	.	0.307721	0.39985	N	0.001217	D	0.93119	0.7809	L	0.33485	1.01	0.80722	D	1	D	0.57257	0.979	P	0.52554	0.702	D	0.93230	0.6616	10	0.52906	T	0.07	-12.279	15.0391	0.71774	0.0698:0.0:0.9302:0.0	.	979	Q13608	PEX6_HUMAN	V	979	ENSP00000303511:A979V	ENSP00000303511:A979V	A	-	2	0	PEX6	43040058	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.035000	0.64158	2.803000	0.96430	0.609000	0.83330	GCC	G|0.993;A|0.007	0.007	strong		0.637	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287	
GLDC	2731	hgsc.bcm.edu	37	9	6587176	6587176	+	Silent	SNP	G	G	A	rs74461075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:6587176G>A	ENST00000321612.6	-	15	1965	c.1815C>T	c.(1813-1815)ctC>ctT	p.L605L		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	605					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)	CATAACCTGTGAGTTCACACA	0.418													G|||	71	0.0141773	0.0514	0.0043	5008	,	,		19260	0.0		0.0	False		,,,				2504	0.0				p.L605L		Atlas-SNP	.											.	GLDC	118	.	0			c.C1815T						PASS	.	G		173,4233	112.9+/-151.0	3,167,2033	117.0	112.0	114.0		1815	3.5	1.0	9	dbSNP_131	114	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GLDC	NM_000170.2		3,169,6331	AA,AG,GG		0.0233,3.9265,1.3455		605/1021	6587176	175,12831	2203	4300	6503	SO:0001819	synonymous_variant	2731	exon15			ACCTGTGAGTTCA	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.1815C>T	9.37:g.6587176G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			G|0.987;A|0.013	0.013	strong		0.418	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
FAM187B	148109	hgsc.bcm.edu	37	19	35719577	35719577	+	Missense_Mutation	SNP	G	G	A	rs34873156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35719577G>A	ENST00000324675.3	-	1	55	c.7C>T	c.(7-9)Ccc>Tcc	p.P3S		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	3			P -> S (in dbSNP:rs34873156). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						CACAGCATGGGTGGCATGGTG	0.612													-|||	864	0.172524	0.112	0.2435	5008	,	,		16647	0.0159		0.3718	False		,,,				2504	0.1605				p.P3S		Atlas-SNP	.											.	FAM187B	28	.	0			c.C7T						PASS	.	G	SER/PRO	590,3804		38,514,1645	25.0	28.0	27.0		7	-3.6	0.0	19	dbSNP_126	27	3231,5367		596,2039,1664	yes	missense	FAM187B	NM_152481.1	74	634,2553,3309	AA,AG,GG		37.5785,13.4274,29.4104	benign	3/370	35719577	3821,9171	2197	4299	6496	SO:0001583	missense	148109	exon1			GCATGGGTGGCAT	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.7C>T	19.37:g.35719577G>A	ENSP00000323355:p.Pro3Ser	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	43	15	0.348837	NM_152481	Q8N7G6	Missense_Mutation	SNP	ENST00000324675.3	37	CCDS12448.1	458	0.2097069597069597	65	0.13211382113821138	92	0.2541436464088398	14	0.024475524475524476	287	0.3786279683377309	G	2.096	-0.407252	0.04832	0.134274	0.375785	ENSG00000177558	ENST00000324675	T	0.21543	2.0	5.3	-3.6	0.04570	.	0.804889	0.11107	N	0.599034	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.46034	-0.9220	9	0.09338	T	0.73	-17.2885	2.0071	0.03480	0.128:0.3374:0.2819:0.2527	rs34873156;rs62111448	3	Q17R55	F187B_HUMAN	S	3	ENSP00000323355:P3S	ENSP00000323355:P3S	P	-	1	0	FAM187B	40411417	0.000000	0.05858	0.013000	0.15412	0.002000	0.02628	-1.237000	0.02922	-0.394000	0.07727	-1.105000	0.02106	CCC	G|0.721;A|0.279	0.279	strong		0.612	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481	
QRICH2	84074	hgsc.bcm.edu	37	17	74300497	74300497	+	Splice_Site	SNP	G	G	A	rs73996306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74300497G>A	ENST00000262765.5	-	3	385	c.206C>T	c.(205-207)gCg>gTg	p.A69V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	69										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						CTGGTTCACCGCTTGTGAGGC	0.572													G|||	432	0.086262	0.205	0.0303	5008	,	,		16207	0.0605		0.0308	False		,,,				2504	0.0491				p.A69V		Atlas-SNP	.											.	QRICH2	143	.	0			c.C206T						PASS	.	G	VAL/ALA	821,3585	323.2+/-298.0	72,677,1454	44.0	39.0	40.0		206	-8.6	0.0	17	dbSNP_130	40	224,8376	91.6+/-153.7	5,214,4081	yes	missense-near-splice	QRICH2	NM_032134.1	64	77,891,5535	AA,AG,GG		2.6047,18.6337,8.0348	benign	69/1664	74300497	1045,11961	2203	4300	6503	SO:0001630	splice_region_variant	84074	exon3			TTCACCGCTTGTG	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.207+1C>T	17.37:g.74300497G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	175	0.08012820512820513	105	0.21341463414634146	9	0.024861878453038673	38	0.06643356643356643	23	0.030343007915567283	G	6.762	0.509446	0.12883	0.186337	0.026047	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08102	3.13	4.3	-8.6	0.00889	.	.	.	.	.	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B	0.28584	0.216	B	0.22386	0.039	T	0.07290	-1.0780	8	0.30854	T	0.27	3.7254	3.628	0.08120	0.3878:0.3569:0.1652:0.0901	.	69	Q9H0J4	QRIC2_HUMAN	V	69	ENSP00000262765:A69V	ENSP00000262765:A69V	A	-	2	0	QRICH2	71812092	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-4.213000	0.00273	-3.605000	0.00133	-0.300000	0.09419	GCG	G|0.919;A|0.081	0.081	strong		0.572	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	Missense_Mutation
LCE1C	353133	hgsc.bcm.edu	37	1	152777874	152777874	+	Silent	SNP	T	T	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152777874T>A	ENST00000607093.1	-	1	80	c.81A>T	c.(79-81)ccA>ccT	p.P27P	LCE1C_ENST00000368768.1_Silent_p.P27P			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	27	Pro-rich.				keratinization (GO:0031424)					NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1)	9	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ggggacactttggggTGgggc	0.647																																					p.P27P		Atlas-SNP	.											.	LCE1C	40	.	0			c.A81T						PASS	.						46.0	47.0	46.0					1																	152777874		2203	4300	6503	SO:0001819	synonymous_variant	353133	exon2			ACACTTTGGGGTG		CCDS1026.1	1q21.3	2008-02-05			ENSG00000197084	ENSG00000197084		"""Late cornified envelopes"""	29464	protein-coding gene	gene with protein product		612605				11698679	Standard	NM_001276331		Approved	LEP3	uc001fap.1	Q5T751	OTTHUMG00000012445	ENST00000607093.1:c.81A>T	1.37:g.152777874T>A		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	403	21	0.0521092	NM_178351		Silent	SNP	ENST00000607093.1	37	CCDS1026.1																																																																																			.	.	none		0.647	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351	
LILRB3	11025	hgsc.bcm.edu	37	19	54721337	54721337	+	Missense_Mutation	SNP	G	G	A	rs75437884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54721337G>A	ENST00000391750.1	-	13	1736	c.1600C>T	c.(1600-1602)Cac>Tac	p.H534Y	LILRB3_ENST00000245620.9_Missense_Mutation_p.H535Y|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.H551Y|LILRB3_ENST00000346401.6_Missense_Mutation_p.H546Y|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000440558.2_Missense_Mutation_p.H534Y|LILRA6_ENST00000270464.5_Missense_Mutation_p.H535Y|LILRA6_ENST00000419410.2_Missense_Mutation_p.H535Y|LILRB3_ENST00000424807.1_Missense_Mutation_p.H534Y			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	534					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TCTTCATCGTGTGGGCTCTGC	0.577																																					p.H535Y		Atlas-SNP	.											LILRB3,NS,lymphoid_neoplasm,+2,1	LILRB3	67	1	0			c.C1603T						PASS	.	G	TYR/HIS,TYR/HIS	47,4355	43.1+/-76.7	0,47,2154	76.0	81.0	80.0		1603,1600	-1.2	0.0	19	dbSNP_131	80	1,8597		0,1,4298	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	83,83	0,48,6452	AA,AG,GG		0.0116,1.0677,0.3692	possibly-damaging,possibly-damaging	535/633,534/632	54721337	48,12952	2201	4299	6500	SO:0001583	missense	11025	exon12			CATCGTGTGGGCT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1600C>T	19.37:g.54721337G>A	ENSP00000375630:p.His534Tyr	Somatic	534	0	0		WXS	Illumina HiSeq	Phase_I	384	90	0.234375	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	G	10.80	1.452361	0.26074	0.010677	1.16E-4	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00487	7.1;7.1;7.07;7.07;7.05;7.1;7.07;7.09	2.47	-1.25	0.09405	.	.	.	.	.	T	0.00384	0.0012	L	0.54323	1.7	0.09310	N	1	D;B;D;P;B;P;P	0.56968	0.969;0.009;0.978;0.832;0.411;0.536;0.593	P;B;P;B;B;B;B	0.51615	0.65;0.004;0.675;0.249;0.059;0.031;0.32	T	0.51164	-0.8740	9	0.33141	T	0.24	.	5.0801	0.14651	0.1499:0.4983:0.3518:0.0	.	551;534;535;546;551;534;535	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	Y	534;534;546;535;551;534;535;535	ENSP00000375630:H534Y;ENSP00000412771:H534Y;ENSP00000345184:H546Y;ENSP00000245620:H535Y;ENSP00000384274:H551Y;ENSP00000390120:H534Y;ENSP00000270464:H535Y;ENSP00000411227:H535Y	ENSP00000270464:H535Y	H	-	1	0	LILRB3;LILRA6	59413149	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.974000	0.03794	-0.122000	0.11766	-0.506000	0.04501	CAC	G|0.996;A|0.004	0.004	strong		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
ACSM5	54988	hgsc.bcm.edu	37	16	20435262	20435262	+	Silent	SNP	T	T	G	rs12103211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20435262T>G	ENST00000331849.4	+	6	939	c.792T>G	c.(790-792)tcT>tcG	p.S264S		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	264					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						TGACCGAATCTGACATCTTCT	0.473													G|||	765	0.152756	0.3646	0.0634	5008	,	,		20759	0.0615		0.0487	False		,,,				2504	0.1309				p.S264S		Atlas-SNP	.											.	ACSM5	101	.	0			c.T792G						PASS	.	G		1453,2953	681.4+/-404.0	239,975,989	196.0	183.0	187.0		792	-5.5	0.2	16	dbSNP_120	187	498,8102	796.9+/-407.5	14,470,3816	no	coding-synonymous	ACSM5	NM_017888.2		253,1445,4805	GG,GT,TT		5.7907,32.9778,15.0008		264/580	20435262	1951,11055	2203	4300	6503	SO:0001819	synonymous_variant	54988	exon6			CGAATCTGACATC		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.792T>G	16.37:g.20435262T>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	176	176	1	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Silent	SNP	ENST00000331849.4	37	CCDS10585.1																																																																																			T|0.853;G|0.147	0.147	strong		0.473	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
ANKRD33	341405	hgsc.bcm.edu	37	12	52282873	52282873	+	Missense_Mutation	SNP	A	A	T	rs697636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52282873A>T	ENST00000340970.4	+	3	385	c.14A>T	c.(13-15)tAc>tTc	p.Y5F	ANKRD33_ENST00000301190.6_Missense_Mutation_p.Y140F|ANKRD33_ENST00000538991.1_Intron|ANKRD33_ENST00000547119.1_3'UTR			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	5			Y -> F (in dbSNP:rs697636). {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)		GTCGCATGCTACCACGGCTTC	0.612													A|||	1622	0.323882	0.1241	0.4135	5008	,	,		18189	0.4216		0.3062	False		,,,				2504	0.4479				p.Y140F		Atlas-SNP	.											.	ANKRD33	33	.	0			c.A419T						PASS	.	A	PHE/TYR,PHE/TYR	634,3772	273.7+/-271.5	50,534,1619	98.0	100.0	100.0		14,419	1.5	0.9	12	dbSNP_86	100	2800,5800	443.6+/-360.4	437,1926,1937	yes	missense,missense	ANKRD33	NM_001130015.1,NM_182608.3	22,22	487,2460,3556	TT,TA,AA		32.5581,14.3895,26.4032	possibly-damaging,possibly-damaging	5/273,140/453	52282873	3434,9572	2203	4300	6503	SO:0001583	missense	341405	exon3			CATGCTACCACGG		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.14A>T	12.37:g.52282873A>T	ENSP00000344690:p.Tyr5Phe	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	37	CCDS44892.1	697	0.3191391941391941	64	0.13008130081300814	130	0.35911602209944754	259	0.4527972027972028	244	0.32189973614775724	A	6.397	0.441362	0.12164	0.143895	0.325581	ENSG00000167612	ENST00000301190;ENST00000340970	T;T	0.63913	-0.07;-0.07	3.98	1.46	0.22682	Ankyrin repeat-containing domain (3);	0.617999	0.14988	N	0.286846	T	0.00012	0.0000	L	0.31294	0.92	0.58432	P	1.0000000000287557E-6	B;D	0.61697	0.134;0.99	B;P	0.57911	0.038;0.829	T	0.36939	-0.9727	9	0.16896	T	0.51	-0.332	6.7499	0.23482	0.7939:0.0:0.2061:0.0	rs697636;rs1690235;rs17700775;rs59137362;rs697636	5;140	Q7Z3H0;Q7Z3H0-2	ANR33_HUMAN;.	F	140;5	ENSP00000301190:Y140F;ENSP00000344690:Y5F	ENSP00000301190:Y140F	Y	+	2	0	ANKRD33	50569140	0.005000	0.15991	0.930000	0.37139	0.049000	0.14656	-0.226000	0.09139	0.181000	0.19994	0.379000	0.24179	TAC	A|0.714;N|0.001	.	strong		0.612	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
OR10A2	341276	hgsc.bcm.edu	37	11	6891704	6891704	+	Missense_Mutation	SNP	T	T	C	rs10839632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	164	0	0		WXS	Illumina HiSeq	Phase_I	176	96	0.545455	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	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552717	43552717	+	Silent	SNP	G	G	C	rs147243132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43552717G>C	ENST00000430334.3	-	4	805	c.672C>G	c.(670-672)tcC>tcG	p.S224S	PLEKHM1_ENST00000421073.2_Silent_p.S135S	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	224					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CTGAAGAATGGGAAATGGAAT	0.562													G|||	412	0.0822684	0.0378	0.1556	5008	,	,		21763	0.001		0.1958	False		,,,				2504	0.0573				p.S224S		Atlas-SNP	.											PLEKHM1,caecum,carcinoma,-1,1	PLEKHM1	69	1	0			c.C672G						PASS	.						25.0	23.0	24.0					17																	43552717		2202	4294	6496	SO:0001819	synonymous_variant	9842	exon4			AGAATGGGAAATG	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.672C>G	17.37:g.43552717G>C		Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	358	148	0.413408	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			G|0.873;C|0.127	0.127	strong		0.562	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
MGAT1	4245	hgsc.bcm.edu	37	5	180219842	180219842	+	Missense_Mutation	SNP	C	C	T	rs34344788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180219842C>T	ENST00000446023.2	-	3	880	c.130G>A	c.(130-132)Gat>Aat	p.D44N	MGAT1_ENST00000427865.2_Missense_Mutation_p.D44N|MGAT1_ENST00000307826.4_Missense_Mutation_p.D44N|MGAT1_ENST00000393340.3_Missense_Mutation_p.D44N|MGAT1_ENST00000333055.3_Missense_Mutation_p.D44N	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	44					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|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)			GGGTCGCCATCGAGAGCGCTG	0.677													C|||	46	0.0091853	0.0333	0.0029	5008	,	,		14178	0.0		0.0	False		,,,				2504	0.0				p.D44N		Atlas-SNP	.											.	MGAT1	48	.	0			c.G130A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	81,4255		0,81,2087	10.0	11.0	10.0		130,130,130,130,130	3.0	0.0	5	dbSNP_126	10	1,8491		0,1,4245	yes	missense,missense,missense,missense,missense	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	23,23,23,23,23	0,82,6332	TT,TC,CC		0.0118,1.8681,0.6392	benign,benign,benign,benign,benign	44/446,44/446,44/446,44/446,44/446	180219842	82,12746	2168	4246	6414	SO:0001583	missense	4245	exon3			CGCCATCGAGAGC	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.130G>A	5.37:g.180219842C>T	ENSP00000404718:p.Asp44Asn	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	C	0.065	-1.214664	0.01555	0.018681	1.18E-4	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865;ENST00000504671;ENST00000506889;ENST00000514283;ENST00000512695;ENST00000506269;ENST00000514438;ENST00000502678;ENST00000513431	T;T;T;T;T;T;T;T;T;T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48	4.75	2.97	0.34412	.	0.746358	0.12755	N	0.441841	T	0.39682	0.1087	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.26224	-1.0109	10	0.15952	T	0.53	-3.9185	10.5598	0.45140	0.0:0.8532:0.0:0.1468	rs34344788	44	P26572	MGAT1_HUMAN	N	44	ENSP00000332073:D44N;ENSP00000311888:D44N;ENSP00000404718:D44N;ENSP00000377010:D44N;ENSP00000402838:D44N;ENSP00000424891:D44N;ENSP00000425988:D44N;ENSP00000424382:D44N;ENSP00000427116:D44N;ENSP00000422906:D44N;ENSP00000421738:D44N;ENSP00000422588:D44N;ENSP00000423401:D44N	ENSP00000311888:D44N	D	-	1	0	MGAT1	180152448	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.842000	0.27627	0.691000	0.31592	-1.523000	0.00931	GAT	C|0.993;T|0.007	0.007	strong		0.677	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
OBSCN	84033	hgsc.bcm.edu	37	1	228437772	228437772	+	Silent	SNP	G	G	A	rs12080655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228437772G>A	ENST00000422127.1	+	14	4184	c.4140G>A	c.(4138-4140)gaG>gaA	p.E1380E	OBSCN_ENST00000570156.2_Silent_p.E1472E|OBSCN_ENST00000284548.11_Silent_p.E1380E|OBSCN_ENST00000366707.4_De_novo_Start_InFrame|OBSCN_ENST00000366709.4_De_novo_Start_InFrame	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1380	Ig-like 14.				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)				CCCAGACAGAGGTGACGTGGT	0.642													G|||	306	0.0611022	0.0537	0.0072	5008	,	,		16429	0.1746		0.003	False		,,,				2504	0.0521				p.E1472E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G4416A						PASS	.	G	,	221,3917		8,205,1856	79.0	82.0	81.0		4140,4140	3.2	0.8	1	dbSNP_120	81	21,8375		0,21,4177	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	8,226,6033	AA,AG,GG		0.2501,5.3407,1.9307	,	1380/7969,1380/6621	228437772	242,12292	2069	4198	6267	SO:0001819	synonymous_variant	84033	exon15			GACAGAGGTGACG	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.4140G>A	1.37:g.228437772G>A		Somatic	354	1	0.00282486		WXS	Illumina HiSeq	Phase_I	376	182	0.484043	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																																																																																			G|0.955;A|0.045	0.045	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
JPH2	57158	hgsc.bcm.edu	37	20	42743454	42743454	+	Silent	SNP	A	A	G	rs6093935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42743454A>G	ENST00000372980.3	-	5	2945	c.2073T>C	c.(2071-2073)ttT>ttC	p.F691F		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	691					calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			GGAGGTGAACAAAGAGGATGG	0.622													G|||	1289	0.257388	0.469	0.219	5008	,	,		18425	0.1101		0.3101	False		,,,				2504	0.0961				p.F691F		Atlas-SNP	.											.	JPH2	86	.	0			c.T2073C						PASS	.	G		1973,2431	592.6+/-387.8	437,1099,666	117.0	75.0	89.0		2073	-0.3	1.0	20	dbSNP_114	89	2636,5964	668.3+/-402.5	404,1828,2068	no	coding-synonymous	JPH2	NM_020433.4		841,2927,2734	GG,GA,AA		30.6512,44.8002,35.4429		691/697	42743454	4609,8395	2202	4300	6502	SO:0001819	synonymous_variant	57158	exon5			GTGAACAAAGAGG	AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.2073T>C	20.37:g.42743454A>G		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_020433	E1P5X1|O95913|Q5JY74|Q9UJN4	Silent	SNP	ENST00000372980.3	37	CCDS13325.1																																																																																			A|0.685;G|0.315	0.315	strong		0.622	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1		
GBP3	2635	hgsc.bcm.edu	37	1	89474818	89474818	+	Missense_Mutation	SNP	A	A	G	rs17433780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89474818A>G	ENST00000370481.4	-	10	1691	c.1471T>C	c.(1471-1473)Tgt>Cgt	p.C491R		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)		GCTTTTACACATTCCACTGTG	0.403													G|||	1303	0.260184	0.2587	0.2637	5008	,	,		19099	0.2113		0.3201	False		,,,				2504	0.2485				p.C491R		Atlas-SNP	.											.	GBP3	53	.	0			c.T1471C						PASS	.	G	ARG/CYS	1125,3281	717.2+/-408.7	148,829,1226	114.0	99.0	104.0		1471	1.7	0.0	1	dbSNP_123	104	2722,5878	681.7+/-403.7	401,1920,1979	yes	missense	GBP3	NM_018284.2	180	549,2749,3205	GG,GA,AA		31.6512,25.5334,29.5787	benign	491/596	89474818	3847,9159	2203	4300	6503	SO:0001583	missense	2635	exon10			TTACACATTCCAC	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.1471T>C	1.37:g.89474818A>G	ENSP00000359512:p.Cys491Arg	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	209	207	0.990431	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	591	0.2706043956043956	121	0.2459349593495935	110	0.30386740331491713	121	0.21153846153846154	239	0.3153034300791557	G	0.005	-2.172454	0.00315	0.255334	0.316512	ENSG00000117226	ENST00000370482;ENST00000370481;ENST00000445969	T;T	0.01665	4.7;4.7	3.66	1.68	0.24146	Guanylate-binding protein, C-terminal (3);	0.436137	0.23646	N	0.045977	T	0.00109	0.0003	N	0.00030	-2.61	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14671	-1.0464	9	0.02654	T	1	.	5.9743	0.19369	0.0963:0.0:0.5746:0.329	rs17433780;rs56622173;rs17433780	357;491	F6X827;Q9H0R5	.;GBP3_HUMAN	R	459;491;71	ENSP00000359512:C491R;ENSP00000415087:C71R	ENSP00000359512:C491R	C	-	1	0	GBP3	89247406	0.045000	0.20229	0.027000	0.17364	0.000000	0.00434	0.409000	0.21082	0.025000	0.15241	-0.971000	0.02607	TGT	A|0.714;G|0.286	0.286	strong		0.403	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	
ARL5C	390790	hgsc.bcm.edu	37	17	37319029	37319029	+	Missense_Mutation	SNP	T	T	G	rs544198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37319029T>G	ENST00000269586.7	-	3	189	c.190A>C	c.(190-192)Atg>Ctg	p.M64L	ARL5C_ENST00000583123.1_5'Flank|ARL5C_ENST00000444555.1_Missense_Mutation_p.M64L	NM_001143968.1	NP_001137440.1	A6NH57	ARL5C_HUMAN	ADP-ribosylation factor-like 5C	64					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)										ATGTCCCACATGAAGAAGTGG	0.542													T|||	1178	0.235224	0.3154	0.1801	5008	,	,		19789	0.256		0.2386	False		,,,				2504	0.1411				p.M64L		Atlas-SNP	.											.	ARL5C	3	.	0			c.A190C						PASS	.	T	LEU/MET	436,948		68,300,324	114.0	89.0	97.0		190	0.9	1.0	17	dbSNP_83	97	609,2573		54,501,1036	yes	missense	ARL5C	NM_001143968.1	15	122,801,1360	GG,GT,TT		19.1389,31.5029,22.8866	possibly-damaging	64/180	37319029	1045,3521	692	1591	2283	SO:0001583	missense	390790	exon3			CCCACATGAAGAA		CCDS45664.1	17q12	2014-05-09	2005-11-08	2005-11-08	ENSG00000141748	ENSG00000141748		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	31111	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 12"""	ARL12			Standard	NM_001143968		Approved		uc010wea.2	A6NH57		ENST00000269586.7:c.190A>C	17.37:g.37319029T>G	ENSP00000269586:p.Met64Leu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_001143968		Missense_Mutation	SNP	ENST00000269586.7	37	CCDS45664.1	547	0.25045787545787546	160	0.3252032520325203	74	0.20441988950276244	137	0.2395104895104895	176	0.23218997361477572	T	12.05	1.820876	0.32237	0.315029	0.191389	ENSG00000141748	ENST00000444555;ENST00000269586	T;T	0.79940	-1.32;-1.32	4.28	0.877	0.19145	Small GTP-binding protein domain (1);	0.186935	0.45361	D	0.000368	T	0.00012	0.0000	L	0.29908	0.895	0.29742	P	0.837041	B	0.23990	0.095	B	0.37650	0.255	T	0.19063	-1.0317	9	0.87932	D	0	-24.2929	7.0499	0.25067	0.0:0.2888:0.0:0.7112	rs544198;rs52817936;rs59543438;rs544198	64	A6NH57	ARL5C_HUMAN	L	64	ENSP00000387615:M64L;ENSP00000269586:M64L	ENSP00000269586:M64L	M	-	1	0	ARL5C	34572555	0.336000	0.24757	0.999000	0.59377	0.013000	0.08279	0.606000	0.24194	0.022000	0.15160	-0.250000	0.11733	ATG	T|0.752;G|0.248	0.248	strong		0.542	ARL5C-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444566.1	NM_001143968	
MIA	8190	hgsc.bcm.edu	37	19	41281700	41281700	+	Silent	SNP	C	C	T	rs2233156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41281700C>T	ENST00000263369.3	+	2	337	c.171C>T	c.(169-171)ccC>ccT	p.P57P	RAB4B_ENST00000357052.2_5'Flank|MIA_ENST00000594436.1_Silent_p.P57P|RAB4B-EGLN2_ENST00000594136.1_5'Flank|MIA_ENST00000597784.1_Silent_p.P57P|RAB4B_ENST00000594800.1_5'Flank|MIA-RAB4B_ENST00000600729.1_Silent_p.P57P	NM_006533.3	NP_006524.1	Q16674	MIA_HUMAN	melanoma inhibitory activity	57	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell proliferation (GO:0008283)	extracellular space (GO:0005615)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)	GBM - Glioblastoma multiforme(1328;0.0199)		ACATGGCCCCCGACTGCCGAT	0.602													C|||	410	0.081869	0.0877	0.0403	5008	,	,		15818	0.1835		0.0417	False		,,,				2504	0.0399				p.P57P		Atlas-SNP	.											.	MIA	16	.	0			c.C171T						PASS	.	C	,	409,3997	201.5+/-224.5	14,381,1808	67.0	63.0	64.0		171,171	-9.9	0.6	19	dbSNP_98	64	381,8219	123.9+/-182.7	7,367,3926	no	coding-synonymous,coding-synonymous	MIA	NM_001202553.1,NM_006533.3	,	21,748,5734	TT,TC,CC		4.4302,9.2828,6.0741	,	57/132,57/132	41281700	790,12216	2203	4300	6503	SO:0001819	synonymous_variant	8190	exon3			GGCCCCCGACTGC	X75450	CCDS12566.1	19q13.2	2012-10-15			ENSG00000261857	ENSG00000261857			7076	protein-coding gene	gene with protein product		601340				7923218, 8661134	Standard	NM_006533		Approved	CD-RAP	uc021uuu.1	Q16674		ENST00000263369.3:c.171C>T	19.37:g.41281700C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_001202553	Q6FHV3	Silent	SNP	ENST00000263369.3	37	CCDS12566.1																																																																																			C|0.913;A|0.000	.	strong		0.602	MIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463162.1		
ZNF326	284695	hgsc.bcm.edu	37	1	90493026	90493026	+	Silent	SNP	G	G	A	rs10922744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:90493026G>A	ENST00000340281.4	+	12	1658	c.1515G>A	c.(1513-1515)gaG>gaA	p.E505E	ZNF326_ENST00000455342.2_Silent_p.E299E|ZNF326_ENST00000370447.3_Silent_p.E416E	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	505	Glu-rich.				mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		atgaagatgaggaagaagaag	0.443													G|||	3165	0.631989	0.4667	0.7032	5008	,	,		16829	0.8899		0.5706	False		,,,				2504	0.6022				p.E505E		Atlas-SNP	.											.	ZNF326	60	.	0			c.G1515A						PASS	.	G		2181,2225	583.5+/-385.8	537,1107,559	87.0	86.0	87.0		1515	-9.7	0.0	1	dbSNP_120	87	4786,3814	610.0+/-395.6	1320,2146,834	no	coding-synonymous	ZNF326	NM_182976.2		1857,3253,1393	AA,AG,GG		44.3488,49.5007,46.4324		505/583	90493026	6967,6039	2203	4300	6503	SO:0001819	synonymous_variant	284695	exon12			AGATGAGGAAGAA	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"""Zinc fingers, C2H2-type"""	14104	protein-coding gene	gene with protein product	"""ZNF-protein interacting with nuclear mRNPs and DBC1"""	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1515G>A	1.37:g.90493026G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	191	101	0.528796	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Silent	SNP	ENST00000340281.4	37	CCDS727.1																																																																																			A|0.588;G|0.412	0.588	strong		0.443	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781	
USP6	9098	hgsc.bcm.edu	37	17	5039138	5039138	+	Silent	SNP	C	C	T	rs3213878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5039138C>T	ENST00000574788.1	+	17	2809	c.579C>T	c.(577-579)acC>acT	p.T193T	USP6_ENST00000304328.5_5'UTR|USP6_ENST00000250066.6_Silent_p.T193T|USP6_ENST00000332776.4_Silent_p.T193T			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	193	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GCCACATCACCGCCTTGTTCC	0.607			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								C|||	490	0.0978435	0.1853	0.0375	5008	,	,		20475	0.0774		0.1143	False		,,,				2504	0.0266				p.T193T		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C579T						PASS	.	C		682,3724	287.2+/-279.2	60,562,1581	126.0	110.0	115.0		579	-1.7	0.2	17	dbSNP_106	115	949,7651	208.0+/-249.6	52,845,3403	no	coding-synonymous	USP6	NM_004505.2		112,1407,4984	TT,TC,CC		11.0349,15.4789,12.5404		193/1407	5039138	1631,11375	2203	4300	6503	SO:0001819	synonymous_variant	9098	exon9			CATCACCGCCTTG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.579C>T	17.37:g.5039138C>T		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	21	10	0.47619	NM_004505	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	37	CCDS11069.2																																																																																			C|0.883;T|0.117	0.117	strong		0.607	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
LILRB2	10288	hgsc.bcm.edu	37	19	54782401	54782401	+	Missense_Mutation	SNP	G	G	C	rs7247055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782401G>C	ENST00000391749.4	-	7	1242	c.971C>G	c.(970-972)aCa>aGa	p.T324R	LILRB2_ENST00000391746.1_Missense_Mutation_p.T324R|LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000314446.5_Missense_Mutation_p.T324R|LILRB2_ENST00000434421.1_Missense_Mutation_p.T208R|LILRB2_ENST00000391748.1_Missense_Mutation_p.T324R	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	324			T -> R (in dbSNP:rs7247055).		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)		GATGAAGGGTGTGCCACGGAT	0.607													.|||	680	0.135783	0.4554	0.0432	5008	,	,		15732	0.0298		0.004	False		,,,				2504	0.0143				p.T324R		Atlas-SNP	.											.	LILRB2	94	.	0			c.C971G						PASS	.	C	ARG/THR,ARG/THR	316,4048	742.9+/-411.4	34,248,1900	43.0	58.0	53.0		971,971	-4.8	0.0	19	dbSNP_116	53	5,8595	818.2+/-406.9	0,5,4295	no	missense,missense	LILRB2	NM_001080978.2,NM_005874.3	71,71	34,253,6195	CC,CG,GG		0.0581,7.2411,2.4761	benign,benign	324/598,324/599	54782401	321,12643	2182	4300	6482	SO:0001583	missense	10288	exon7			AAGGGTGTGCCAC	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.971C>G	19.37:g.54782401G>C	ENSP00000375629:p.Thr324Arg	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	173	67	0.387283	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	122	0.055860805860805864	110	0.22357723577235772	6	0.016574585635359115	6	0.01048951048951049	0	0.0	C	0.004	-2.302758	0.00240	0.072411	5.81E-4	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00691	5.84;5.84;5.84;5.84;5.84	2.41	-4.83	0.03161	Immunoglobulin-like fold (1);	1.088530	0.07309	N	0.875526	T	0.00012	0.0000	N	0.04768	-0.165	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.11329	0.006;0.006;0.006	T	0.36286	-0.9754	9	0.07644	T	0.81	.	5.7157	0.17958	0.0:0.3226:0.3802:0.2972	rs7247055;rs59296089	324;341;324	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	R	324;324;324;324;208	ENSP00000375628:T324R;ENSP00000319960:T324R;ENSP00000375629:T324R;ENSP00000375626:T324R;ENSP00000410117:T208R	ENSP00000319960:T324R	T	-	2	0	LILRB2	59474213	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.114000	0.01329	-1.085000	0.03088	-2.204000	0.00303	ACA	G|0.964;C|0.036	0.036	strong		0.607	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
KCNT1	57582	hgsc.bcm.edu	37	9	138662273	138662273	+	Silent	SNP	G	G	A	rs17038714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138662273G>A	ENST00000263604.3	+	17	1692	c.1692G>A	c.(1690-1692)gcG>gcA	p.A564A	KCNT1_ENST00000371757.2_Silent_p.A583A|KCNT1_ENST00000487664.1_Silent_p.A538A|KCNT1_ENST00000488444.2_Silent_p.A564A|KCNT1_ENST00000490355.2_Silent_p.A564A|KCNT1_ENST00000298480.5_Silent_p.A583A|KCNT1_ENST00000486577.2_Silent_p.A544A|KCNT1_ENST00000491806.2_Silent_p.A550A			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	564	RCK N-terminal.				potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		TCACCTACGCGGCCTTCCACG	0.647													G|||	1780	0.355431	0.4924	0.1772	5008	,	,		15769	0.4147		0.2217	False		,,,				2504	0.3732				p.A583A		Atlas-SNP	.											.	KCNT1	139	.	0			c.G1749A						PASS	.	G		2074,2330	558.6+/-380.0	487,1100,615	86.0	66.0	73.0		1749	-3.1	1.0	9	dbSNP_123	73	1784,6816	317.8+/-313.4	193,1398,2709	no	coding-synonymous	KCNT1	NM_020822.2		680,2498,3324	AA,AG,GG		20.7442,47.0936,29.6678		583/1236	138662273	3858,9146	2202	4300	6502	SO:0001819	synonymous_variant	57582	exon17			CTACGCGGCCTTC	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.1692G>A	9.37:g.138662273G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Silent	SNP	ENST00000263604.3	37																																																																																				G|0.695;A|0.305	0.305	strong		0.647	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822	
C4A	720	hgsc.bcm.edu	37	6	31963860	31963860	+	Missense_Mutation	SNP	C	C	G	rs79299066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31963860C>G	ENST00000428956.2	+	26	3443	c.3359C>G	c.(3358-3360)cCc>cGc	p.P1120R	C4A_ENST00000498271.1_Missense_Mutation_p.P1120R	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1120					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	TTCCAGGACCCCTGTCCAGTG	0.617													c|||	18	0.00359425	0.0129	0.0014	5008	,	,		18899	0.0		0.0	False		,,,				2504	0.0				p.L1120R		Atlas-SNP	.											.	C4A	15	.	0			c.T3359G						PASS	.	T	ARG/PRO	18,3112		0,18,1547	76.0	76.0	76.0		3359	1.5	0.2	6	dbSNP_134	76	0,7074		0,0,3537	no	missense	C4A	NM_007293.2	103	0,18,5084	GG,GC,CC		0.0,0.5751,0.1764	probably-damaging	1120/1745	31963860	18,10186	1565	3537	5102	SO:0001583	missense	720	exon26			AGGACCCCTGTCC	L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731		"""Blood group antigens"", ""Complement system"""	1323	protein-coding gene	gene with protein product		120810	"""complement component 4A"""				Standard	NM_001252204		Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.3359C>G	6.37:g.31963860C>G	ENSP00000396688:p.Pro1120Arg	Somatic	750	0	0		WXS	Illumina HiSeq	Phase_I	527	256	0.485768	NM_007293	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	Missense_Mutation	SNP	ENST00000428956.2	37	CCDS47404.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	c	5.827	0.336826	0.11013	0.005751	0.0	ENSG00000244731	ENST00000428956;ENST00000498271	T;T	0.32515	1.45;1.45	3.35	1.45	0.22620	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	.	.	.	.	T	0.10723	0.0262	N	0.04260	-0.245	0.50813	D	0.999896	D;D	0.63046	0.992;0.992	D;D	0.66847	0.947;0.947	T	0.07424	-1.0773	9	0.12766	T	0.61	.	6.0472	0.19766	0.1829:0.699:0.0:0.1182	.	1120;1120	A6H8M8;P0C0L4	.;CO4A_HUMAN	R	1120	ENSP00000396688:P1120R;ENSP00000420212:P1120R	ENSP00000396688:P1120R	P	+	2	0	C4A	.	0.021000	0.18746	0.151000	0.22473	0.084000	0.17831	-0.000000	0.12993	-0.041000	0.13558	-2.139000	0.00339	CCC	.	.	alt		0.617	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293	
EYS	346007	hgsc.bcm.edu	37	6	66042231	66042231	+	Intron	SNP	T	T	G	rs12207746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:66042231T>G	ENST00000370621.3	-	11	2293				EYS_ENST00000503581.1_Intron|EYS_ENST00000393380.2_Missense_Mutation_p.I616L|EYS_ENST00000370616.2_Intron			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)						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						attcttacgataaatcccacc	0.303													t|||	572	0.114217	0.2496	0.0533	5008	,	,		16246	0.0427		0.0785	False		,,,				2504	0.0849				p.I616L		Atlas-SNP	.											.	EYS	527	.	0			c.A1846C						PASS	.	T	,LEU/ILE	324,1060		36,252,404	190.0	170.0	176.0		,1846	1.0	0.0	6	dbSNP_120	176	237,2945		8,221,1362	yes	intron,missense	EYS	NM_001142800.1,NM_001142801.1	,5	44,473,1766	GG,GT,TT		7.4481,23.4104,12.2865	,	,616/620	66042231	561,4005	692	1591	2283	SO:0001627	intron_variant	346007	exon12			TTACGATAAATCC		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.1766+2641A>C	6.37:g.66042231T>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		230	0.10531135531135531	135	0.27439024390243905	19	0.052486187845303865	14	0.024475524475524476	62	0.08179419525065963	t	8.337	0.827841	0.16749	0.234104	0.074481	ENSG00000188107	ENST00000393380	D	0.90069	-2.61	1.01	1.01	0.19927	.	.	.	.	.	T	0.77458	0.4133	L	0.52011	1.625	0.80722	P	0.0	P	0.41784	0.762	B	0.43386	0.418	T	0.70310	-0.4907	8	0.87932	D	0	.	4.2312	0.10604	0.0:0.0:0.0:1.0	rs12207746;rs12207746	616	Q5SZM4	.	L	616	ENSP00000377042:I616L	ENSP00000377042:I616L	I	-	1	0	EYS	66098952	0.004000	0.15560	0.005000	0.12908	0.013000	0.08279	0.969000	0.29370	0.704000	0.31869	0.247000	0.18012	ATC	T|0.889;G|0.111	0.111	strong		0.303	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
GCN1L1	10985	hgsc.bcm.edu	37	12	120608031	120608031	+	Silent	SNP	A	A	G	rs2286050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:120608031A>G	ENST00000300648.6	-	15	1473	c.1461T>C	c.(1459-1461)acT>acC	p.T487T	AC004812.1_ENST00000582675.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	487					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)					CAACCCCTTCAGTGATGGTGG	0.567													A|||	1447	0.288938	0.3101	0.1297	5008	,	,		20192	0.5655		0.1541	False		,,,				2504	0.227				p.T487T		Atlas-SNP	.											.	GCN1L1	207	.	0			c.T1461C						PASS	.	A		1140,3030		166,808,1111	109.0	115.0	113.0		1461	-11.7	0.5	12	dbSNP_100	113	1244,7210		114,1016,3097	no	coding-synonymous	GCN1L1	NM_006836.1		280,1824,4208	GG,GA,AA		14.7149,27.3381,18.8847		487/2672	120608031	2384,10240	2085	4227	6312	SO:0001819	synonymous_variant	10985	exon15			CCCTTCAGTGATG	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.1461T>C	12.37:g.120608031A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																			A|0.709;G|0.291	0.291	strong		0.567	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
MUC4	4585	hgsc.bcm.edu	37	3	195512219	195512219	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512219C>T	ENST00000463781.3	-	2	6691	c.6232G>A	c.(6232-6234)Gcc>Acc	p.A2078T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2078T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		AGAGGGGTGGCGTGACCTGTG	0.567																																					p.A2078T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G6232A						PASS	.						19.0	20.0	20.0					3																	195512219		687	1571	2258	SO:0001583	missense	4585	exon2			GGGTGGCGTGACC	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.6232G>A	3.37:g.195512219C>T	ENSP00000417498:p.Ala2078Thr	Somatic	439	1	0.0022779		WXS	Illumina HiSeq	Phase_I	220	75	0.340909	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	10.32	1.317466	0.23908	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.44;1.45	.	.	.	.	.	.	.	.	T	0.19446	0.0467	N	0.19112	0.55	0.53005	P	3.100000000000325E-5	D	0.53312	0.959	P	0.45971	0.499	T	0.23226	-1.0194	6	.	.	.	.	5.844	0.18652	0.0:0.9991:0.0:9.0E-4	.	2078	E7ESK3	.	T	2078	ENSP00000417498:A2078T;ENSP00000420243:A2078T	.	A	-	1	0	MUC4	196996614	0.000000	0.05858	0.046000	0.18839	0.072000	0.16883	-1.788000	0.01763	0.064000	0.16427	0.064000	0.15345	GCC	.	.	none		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR2A25	392138	hgsc.bcm.edu	37	7	143771408	143771408	+	Silent	SNP	G	G	C	rs59319753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143771408G>C	ENST00000408898.2	+	1	134	c.96G>C	c.(94-96)ctG>ctC	p.L32L		NM_001004488.1	NP_001004488.1	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A, member 25	32						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)					TCTTCTCCCTGTTCTACATCT	0.527													.|||	1689	0.33726	0.2186	0.4467	5008	,	,		19151	0.628		0.2107	False		,,,				2504	0.2505				p.L32L		Atlas-SNP	.											.	OR2A25	66	.	0			c.G96C						PASS	.	G		899,3507	336.5+/-304.4	82,735,1386	80.0	84.0	83.0		96	0.6	1.0	7	dbSNP_129	83	1794,6806	320.0+/-314.4	190,1414,2696	no	coding-synonymous	OR2A25	NM_001004488.1		272,2149,4082	CC,CG,GG		20.8605,20.404,20.7058		32/311	143771408	2693,10313	2203	4300	6503	SO:0001819	synonymous_variant	392138	exon1			CTCCCTGTTCTAC		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.96G>C	7.37:g.143771408G>C		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	313	148	0.472843	NM_001004488	B2RNC9	Silent	SNP	ENST00000408898.2	37	CCDS43669.1																																																																																			G|0.684;C|0.316	0.316	strong		0.527	OR2A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350000.1		
BIRC8	112401	hgsc.bcm.edu	37	19	53793162	53793162	+	Missense_Mutation	SNP	C	C	T	rs35880972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53793162C>T	ENST00000426466.1	-	1	1713	c.466G>A	c.(466-468)Gct>Act	p.A156T		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	156			A -> T (in dbSNP:rs35880972).		apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		TCTTTCTGAGCGCTCACTAGA	0.413													c|||	346	0.0690895	0.2466	0.0274	5008	,	,		18539	0.0		0.001	False		,,,				2504	0.0				p.A156T		Atlas-SNP	.											.	BIRC8	54	.	0			c.G466A						PASS	.	C	THR/ALA	885,3521	343.3+/-307.6	86,713,1404	102.0	102.0	102.0		466	-0.8	0.0	19	dbSNP_126	102	8,8592	5.0+/-18.6	0,8,4292	yes	missense	BIRC8	NM_033341.4	58	86,721,5696	TT,TC,CC		0.093,20.0862,6.8661	probably-damaging	156/237	53793162	893,12113	2203	4300	6503	SO:0001583	missense	112401	exon1			TCTGAGCGCTCAC	AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"""Baculoviral IAP repeat containing"""	14878	protein-coding gene	gene with protein product	"""IAP-like protein 2"", ""inhibitor of apoptosis-like protein 2"""		"""baculoviral IAP repeat-containing 8"""			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.466G>A	19.37:g.53793162C>T	ENSP00000412957:p.Ala156Thr	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	221	101	0.457014	NM_033341	Q6IPY1|Q96RW5	Missense_Mutation	SNP	ENST00000426466.1	37	CCDS12863.1	120	0.054945054945054944	111	0.22560975609756098	9	0.024861878453038673	0	0.0	0	0.0	C	8.392	0.840001	0.16891	0.200862	9.3E-4	ENSG00000163098	ENST00000426466	T	0.37915	1.17	0.628	-0.793	0.10922	.	.	.	.	.	T	0.00012	0.0000	M	0.79475	2.455	0.80722	P	0.0	P	0.37500	0.597	B	0.23852	0.049	T	0.06862	-1.0803	8	0.42905	T	0.14	-4.5555	5.2502	0.15517	0.0:0.7589:0.0:0.2411	rs35880972	156	Q96P09	BIRC8_HUMAN	T	156	ENSP00000412957:A156T	ENSP00000412957:A156T	A	-	1	0	BIRC8	58484974	0.119000	0.22226	0.005000	0.12908	0.004000	0.04260	0.493000	0.22451	-0.150000	0.11195	-0.356000	0.07607	GCT	C|0.937;T|0.063	0.063	strong		0.413	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341	
UBA7	7318	hgsc.bcm.edu	37	3	49845526	49845526	+	Missense_Mutation	SNP	T	T	C	rs2230149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49845526T>C	ENST00000333486.3	-	20	2608	c.2450A>G	c.(2449-2451)cAt>cGt	p.H817R	MIR5193_ENST00000584510.1_RNA	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	817			H -> R (in dbSNP:rs2230149).		cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		AAAGTCCACATGGAAGTTGCT	0.567													T|||	138	0.0275559	0.0983	0.0072	5008	,	,		22642	0.0		0.003	False		,,,				2504	0.0				p.H817R		Atlas-SNP	.											.	UBA7	64	.	0			c.A2450G						PASS	.	T	ARG/HIS	325,4081	171.6+/-201.8	20,285,1898	94.0	87.0	89.0		2450	5.3	0.9	3	dbSNP_98	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	UBA7	NM_003335.2	29	20,286,6197	CC,CT,TT		0.0116,7.3763,2.5065	probably-damaging	817/1013	49845526	326,12680	2203	4300	6503	SO:0001583	missense	7318	exon20			TCCACATGGAAGT	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"""Ubiquitin-like modifier activating enzymes"""	12471	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)"", ""UBA7, ubiquitin-activating enzyme E1"""	191325	"""ubiquitin-activating enzyme E1-like"""	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267	ENST00000333486.3:c.2450A>G	3.37:g.49845526T>C	ENSP00000333266:p.His817Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_003335	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	37	CCDS2805.1	46	0.021062271062271064	41	0.08333333333333333	3	0.008287292817679558	0	0.0	2	0.002638522427440633	T	22.6	4.310618	0.81358	0.073763	1.16E-4	ENSG00000182179	ENST00000333486	T	0.47177	0.85	5.34	5.34	0.76211	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.177580	0.53938	D	0.000047	T	0.19446	0.0467	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70263	-0.4920	10	0.87932	D	0	-17.9904	15.6299	0.76899	0.0:0.0:0.0:1.0	rs2230149;rs2234387;rs2230149	817	P41226	UBA7_HUMAN	R	817	ENSP00000333266:H817R	ENSP00000333266:H817R	H	-	2	0	UBA7	49820530	1.000000	0.71417	0.902000	0.35471	0.771000	0.43674	5.762000	0.68809	2.169000	0.68431	0.459000	0.35465	CAT	T|0.973;C|0.027	0.027	strong		0.567	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335	
SACS	26278	hgsc.bcm.edu	37	13	23905481	23905481	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23905481C>T	ENST00000382292.3	-	9	12807	c.12534G>A	c.(12532-12534)ccG>ccA	p.P4178P	SACS_ENST00000402364.1_Silent_p.P3428P|SACS_ENST00000382298.3_Silent_p.P4178P			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4178					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CATATTCTCCCGGGTAAAAAA	0.413																																					p.P4178P		Atlas-SNP	.											.	SACS	871	.	0			c.G12534A						PASS	.						108.0	113.0	111.0					13																	23905481		2203	4300	6503	SO:0001819	synonymous_variant	26278	exon10			TTCTCCCGGGTAA	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.12534G>A	13.37:g.23905481C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	59	0.561905	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			.	.	none		0.413	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
REV3L	5980	hgsc.bcm.edu	37	6	111695304	111695304	+	Silent	SNP	A	A	G	rs3218589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:111695304A>G	ENST00000358835.3	-	14	4708	c.4254T>C	c.(4252-4254)aaT>aaC	p.N1418N	REV3L_ENST00000368802.3_Silent_p.N1418N|REV3L_ENST00000435970.1_Silent_p.N1340N|REV3L_ENST00000368805.1_Silent_p.N1418N			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1418					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		AATGCAAAAAATTAGGGGTAT	0.388								DNA polymerases (catalytic subunits)					A|||	6	0.00119808	0.0045	0.0	5008	,	,		19794	0.0		0.0	False		,,,				2504	0.0				p.N1418N		Atlas-SNP	.											.	REV3L	386	.	0			c.T4254C						PASS	.	A		18,4388	25.3+/-52.1	0,18,2185	149.0	133.0	138.0		4254	3.7	1.0	6	dbSNP_106	138	0,8600		0,0,4300	no	coding-synonymous	REV3L	NM_002912.3		0,18,6485	GG,GA,AA		0.0,0.4085,0.1384		1418/3131	111695304	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	5980	exon13			CAAAAAATTAGGG	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.4254T>C	6.37:g.111695304A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	147	76	0.517007	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																			A|0.999;G|0.001	0.001	strong		0.388	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
ITGA2	3673	hgsc.bcm.edu	37	5	52368472	52368472	+	Silent	SNP	C	C	T	rs3212583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:52368472C>T	ENST00000296585.5	+	19	2519	c.2376C>T	c.(2374-2376)gaC>gaT	p.D792D		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	792					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)				GTGGTGAGGACGGACTTTGCA	0.358													T|||	557	0.111222	0.23	0.0663	5008	,	,		15873	0.0317		0.0885	False		,,,				2504	0.0879				p.D792D		Atlas-SNP	.											.	ITGA2	211	.	0			c.C2376T						PASS	.	T		896,3508	739.1+/-411.0	84,728,1390	85.0	76.0	79.0		2376	3.3	0.9	5	dbSNP_106	79	829,7771	779.2+/-407.7	40,749,3511	no	coding-synonymous	ITGA2	NM_002203.3		124,1477,4901	TT,TC,CC		9.6395,20.3451,13.2651		792/1182	52368472	1725,11279	2202	4300	6502	SO:0001819	synonymous_variant	3673	exon19			TGAGGACGGACTT		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.2376C>T	5.37:g.52368472C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	73	44	0.60274	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			C|0.875;T|0.125	0.125	strong		0.358	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
C1orf94	84970	hgsc.bcm.edu	37	1	34663180	34663180	+	Silent	SNP	G	G	A	rs3795412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:34663180G>A	ENST00000488417.1	+	2	795	c.675G>A	c.(673-675)agG>agA	p.R225R	C1orf94_ENST00000373374.3_Silent_p.R35R	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	225										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				CAGAGGACAGGGGCCGCATCC	0.547													G|||	576	0.115016	0.1346	0.1124	5008	,	,		20597	0.0575		0.164	False		,,,				2504	0.0992				p.R225R		Atlas-SNP	.											.	C1orf94	156	.	0			c.G675A						PASS	.	G	,	694,3712	292.7+/-282.2	47,600,1556	87.0	76.0	80.0		675,105	0.7	0.0	1	dbSNP_107	80	1680,6920	307.8+/-308.6	170,1340,2790	yes	coding-synonymous,coding-synonymous	C1orf94	NM_001134734.1,NM_032884.3	,	217,1940,4346	AA,AG,GG		19.5349,15.7512,18.2531	,	225/599,35/409	34663180	2374,10632	2203	4300	6503	SO:0001819	synonymous_variant	84970	exon2			GGACAGGGGCCGC	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.675G>A	1.37:g.34663180G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	89	31	0.348315	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	37	CCDS44108.1																																																																																			G|0.833;A|0.167	0.167	strong		0.547	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
OBSCN	84033	hgsc.bcm.edu	37	1	228565325	228565325	+	Silent	SNP	C	C	T	rs61743077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228565325C>T	ENST00000422127.1	+	102	23459	c.23415C>T	c.(23413-23415)ctC>ctT	p.L7805L	OBSCN_ENST00000570156.2_Silent_p.L8762L|OBSCN_ENST00000366707.4_Silent_p.L5439L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7805	Protein kinase 2. {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)				ACAACCTGCTCAAGGTCGTGG	0.562													C|||	54	0.0107827	0.0386	0.0029	5008	,	,		21756	0.0		0.001	False		,,,				2504	0.0				p.L8762L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C26286T						PASS	.	C		187,4189		1,185,2002	95.0	97.0	96.0		23415	-2.4	0.9	1	dbSNP_129	96	0,8542		0,0,4271	no	coding-synonymous	OBSCN	NM_001098623.1		1,185,6273	TT,TC,CC		0.0,4.2733,1.4476		7805/7969	228565325	187,12731	2188	4271	6459	SO:0001819	synonymous_variant	84033	exon113			CCTGCTCAAGGTC	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.23415C>T	1.37:g.228565325C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	170	94	0.552941	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	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	C	15.09	2.729743	0.48833	0.042733	0.0	ENSG00000154358	ENST00000441106	.	.	.	5.14	-2.38	0.06622	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.2	0.31419	0.0:0.1855:0.4897:0.3248	rs61743077	.	.	.	X	2422	.	.	Q	+	1	0	OBSCN	226631948	0.995000	0.38212	0.873000	0.34254	0.884000	0.51177	0.219000	0.17641	-0.368000	0.08040	0.313000	0.20887	CAA	C|0.992;T|0.008	0.008	strong		0.562	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SF3B3	23450	hgsc.bcm.edu	37	16	70569215	70569215	+	Silent	SNP	A	A	T	rs33910368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70569215A>T	ENST00000302516.5	+	6	928	c.717A>T	c.(715-717)ccA>ccT	p.P239P	SNORD111_ENST00000408139.1_RNA	NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	239					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				TCACAGTTCCAGGAGGGTCAG	0.428													A|||	2355	0.470248	0.2874	0.4135	5008	,	,		18512	0.5804		0.4155	False		,,,				2504	0.7004				p.P239P		Atlas-SNP	.											.	SF3B3	99	.	0			c.A717T						PASS	.	A		1292,3104	437.0+/-344.8	190,912,1096	207.0	212.0	210.0		717	-9.7	0.8	16	dbSNP_126	210	3632,4968	522.8+/-380.2	780,2072,1448	no	coding-synonymous	SF3B3	NM_012426.4		970,2984,2544	TT,TA,AA		42.2326,29.3904,37.8886		239/1218	70569215	4924,8072	2198	4300	6498	SO:0001819	synonymous_variant	23450	exon6			AGTTCCAGGAGGG	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"""splicing factor 3b, subunit 3, 130kD"""			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.717A>T	16.37:g.70569215A>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	179	179	1	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Silent	SNP	ENST00000302516.5	37	CCDS10894.1																																																																																			A|0.596;T|0.404	0.404	strong		0.428	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426	
RNF213	57674	hgsc.bcm.edu	37	17	78263514	78263514	+	Silent	SNP	G	G	A	rs17853713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78263514G>A	ENST00000582970.1	+	6	1133	c.990G>A	c.(988-990)aaG>aaA	p.K330K	RNF213_ENST00000319921.4_Silent_p.K330K|RNF213_ENST00000456466.1_Silent_p.K330K|RNF213_ENST00000508628.2_Silent_p.K379K	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	330					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)	p.K379K(1)|p.K330K(1)		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)			AAGTCGGTAAGAATGAACAAG	0.517													A|||	1103	0.220248	0.4508	0.1254	5008	,	,		16476	0.0665		0.165	False		,,,				2504	0.1912				p.K330K		Atlas-SNP	.											RNF213_ENST00000411702,NS,carcinoma,0,2	RNF213	766	2	2	Substitution - coding silent(2)	stomach(2)	c.G990A						scavenged	.	A	,	1740,2666	647.5+/-398.6	351,1038,814	67.0	71.0	70.0		1137,990	-1.2	0.0	17	dbSNP_123	70	1622,6978	742.2+/-407.2	152,1318,2830	no	coding-synonymous,coding-synonymous	RNF213	NM_020914.4,NM_020954.2	,	503,2356,3644	AA,AG,GG		18.8605,39.4916,25.8496	,	379/5257,330/1064	78263514	3362,9644	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon6			CGGTAAGAATGAA	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.990G>A	17.37:g.78263514G>A		Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	94	37	0.393617	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																																																																																			G|0.760;A|0.240	0.240	strong		0.517	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
RANBP3L	202151	hgsc.bcm.edu	37	5	36257134	36257134	+	Missense_Mutation	SNP	G	G	A	rs16902872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36257134G>A	ENST00000296604.3	-	10	1297	c.812C>T	c.(811-813)gCt>gTt	p.A271V	RANBP3L_ENST00000515759.1_Missense_Mutation_p.A271V|RANBP3L_ENST00000502994.1_Missense_Mutation_p.A296V	NM_145000.3	NP_659437.3	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like	271			A -> V (in dbSNP:rs16902872).		intracellular transport (GO:0046907)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	16	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			GAATGCAGCAGCTGATTCAAT	0.363													G|||	434	0.0866613	0.3132	0.0245	5008	,	,		15384	0.0		0.003	False		,,,				2504	0.0				p.A296V		Atlas-SNP	.											.	RANBP3L	41	.	0			c.C887T						PASS	.	G	VAL/ALA,VAL/ALA	1170,3236	408.6+/-334.7	146,878,1179	107.0	99.0	102.0		887,812	5.4	1.0	5	dbSNP_123	102	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	RANBP3L	NM_001161429.1,NM_145000.3	64,64	146,882,5475	AA,AG,GG		0.0465,26.5547,9.0266	probably-damaging,probably-damaging	296/491,271/466	36257134	1174,11832	2203	4300	6503	SO:0001583	missense	202151	exon11			GCAGCAGCTGATT	BC047660	CCDS3918.1, CCDS54843.1	5p13.2	2008-02-05			ENSG00000164188	ENSG00000164188			26353	protein-coding gene	gene with protein product						12477932	Standard	NM_145000		Approved	FLJ25422	uc011cow.2	Q86VV4	OTTHUMG00000131110	ENST00000296604.3:c.812C>T	5.37:g.36257134G>A	ENSP00000296604:p.Ala271Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	136	75	0.551471	NM_001161429	B7Z866|E9PGP9|Q96LK2	Missense_Mutation	SNP	ENST00000296604.3	37	CCDS3918.1	167	0.07646520146520147	158	0.32113821138211385	7	0.019337016574585635	0	0.0	2	0.002638522427440633	G	29.6	5.023090	0.93462	0.265547	4.65E-4	ENSG00000164188	ENST00000296604;ENST00000502994;ENST00000515759	T;T;T	0.59364	1.43;1.4;0.27	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000002	T	0.00012	0.0000	M	0.68952	2.095	0.18873	P	0.9999869983	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00621	-1.1640	9	0.87932	D	0	-18.1197	18.337	0.90291	0.0:0.0:1.0:0.0	rs16902872;rs52805488;rs16902872	296;271	E9PGP9;Q86VV4	.;RNB3L_HUMAN	V	271;296;271	ENSP00000296604:A271V;ENSP00000421853:A296V;ENSP00000421149:A271V	ENSP00000296604:A271V	A	-	2	0	RANBP3L	36292891	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.191000	0.77763	2.697000	0.92050	0.591000	0.81541	GCT	G|0.906;A|0.094	0.094	strong		0.363	RANBP3L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253773.2	NM_145000	
PARM1	25849	hgsc.bcm.edu	37	4	75938236	75938236	+	Silent	SNP	A	A	G	rs1062293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:75938236A>G	ENST00000307428.7	+	2	857	c.645A>G	c.(643-645)gtA>gtG	p.V215V	RP11-44F21.2_ENST00000513770.1_RNA|PARM1_ENST00000513238.1_Intron	NM_015393.3	NP_056208.2	Q6UWI2	PARM1_HUMAN	prostate androgen-regulated mucin-like protein 1	215					positive regulation of telomerase activity (GO:0051973)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)		p.V215V(1)		cervix(1)|endometrium(2)|lung(4)|ovary(1)	8						CTGAGCCAGTACCCCAGGAGA	0.572													G|||	2072	0.413738	0.4244	0.3473	5008	,	,		19214	0.2143		0.5338	False		,,,				2504	0.5286				p.V215V		Atlas-SNP	.											PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	1	Substitution - coding silent(1)	stomach(1)	c.A645G						scavenged	.	G		1816,2422		414,988,717	109.0	119.0	116.0		645	4.6	0.0	4	dbSNP_86	116	4211,4267		1041,2129,1069	no	coding-synonymous	PARM1	NM_015393.3		1455,3117,1786	GG,GA,AA		49.6697,42.8504,47.397		215/311	75938236	6027,6689	2119	4239	6358	SO:0001819	synonymous_variant	25849	exon2			GCCAGTACCCCAG	AK022311	CCDS47077.1	4q13.3-q21.3	2010-02-17	2009-09-28		ENSG00000169116	ENSG00000169116			24536	protein-coding gene	gene with protein product	"""Prostatic androgen-repressed message 1"", ""Castration-induced prostatic apoptosis-related protein 1"", ""WSC4, cell wall integrity and stress response component 4 homolog (S. cerevisiae)"""					10499539, 12772192, 18027867	Standard	NM_015393		Approved	DKFZP564O0823, Cipar1, WSC4	uc003hih.2	Q6UWI2	OTTHUMG00000160827	ENST00000307428.7:c.645A>G	4.37:g.75938236A>G		Somatic	163	2	0.0122699		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_015393	B3KMQ9|Q96DV8|Q9Y4S1	Silent	SNP	ENST00000307428.7	37	CCDS47077.1																																																																																			A|0.598;G|0.402	0.402	strong		0.572	PARM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362494.1	NM_015393	
LAMA5	3911	hgsc.bcm.edu	37	20	60884473	60884473	+	Silent	SNP	C	C	T	rs115306720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60884473C>T	ENST00000252999.3	-	80	11073	c.11007G>A	c.(11005-11007)gcG>gcA	p.A3669A	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3669	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)			ACCGGTTCACCGCCAGCCTCC	0.706													C|||	143	0.0285543	0.1044	0.0058	5008	,	,		7633	0.0		0.001	False		,,,				2504	0.0				p.A3669A		Atlas-SNP	.											.	LAMA5	268	.	0			c.G11007A						PASS	.			311,3885		5,301,1792	7.0	9.0	9.0		11007	1.9	0.0	20	dbSNP_132	9	2,8320		0,2,4159	no	coding-synonymous	LAMA5	NM_005560.3		5,303,5951	TT,TC,CC		0.024,7.4118,2.5004		3669/3696	60884473	313,12205	2098	4161	6259	SO:0001819	synonymous_variant	3911	exon80			GTTCACCGCCAGC	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.11007G>A	20.37:g.60884473C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	32	21	0.65625	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			C|0.976;T|0.024	0.024	strong		0.706	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
CFHR2	3080	hgsc.bcm.edu	37	1	196887411	196887411	+	Intron	SNP	T	T	C	rs200907976		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:196887411T>C	ENST00000367421.3	+	2	135				CFHR4_ENST00000367418.2_Missense_Mutation_p.Y291H|CFHR4_ENST00000367416.2_Missense_Mutation_p.Y537H|CFHR4_ENST00000251424.4_Missense_Mutation_p.Y291H|CFHR4_ENST00000608469.1_Missense_Mutation_p.Y161H			P36980	FHR2_HUMAN	complement factor H-related 2							extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						TGACATAAAATATTATGCAAA	0.294													T|||	1	0.000199681	0.0	0.0014	5008	,	,		15761	0.0		0.0	False		,,,				2504	0.0				p.Y538H		Atlas-SNP	.											.	CFHR4	141	.	0			c.T1612C						PASS	.	T	HIS/TYR,HIS/TYR,HIS/TYR	6,4396	11.4+/-27.6	1,4,2196	112.0	122.0	119.0		1612,1609,871	-6.5	0.0	1		119	0,8598		0,0,4299	yes	missense,missense,missense	CFHR4	NM_001201550.2,NM_001201551.1,NM_006684.4	83,83,83	1,4,6495	CC,CT,TT		0.0,0.1363,0.0462	benign,benign,benign	538/579,537/578,291/332	196887411	6,12994	2201	4299	6500	SO:0001627	intron_variant	10877	exon10			ATAAAATATTATG	X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"""Complement system"""	4890	protein-coding gene	gene with protein product		600889	"""H factor (complement)-like 3"""	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367421.3:c.59-31174T>C	1.37:g.196887411T>C		Somatic	354	1	0.00282486		WXS	Illumina HiSeq	Phase_I	393	216	0.549618	NM_001201550	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367421.3	37		.	.	.	.	.	.	.	.	.	.	T	10.95	1.496577	0.26861	0.001363	0.0	ENSG00000134365	ENST00000367416;ENST00000367418;ENST00000251424;ENST00000538553	D;D;D	0.82984	-1.67;-1.67;-1.67	3.24	-6.48	0.01896	Complement control module (1);	.	.	.	.	T	0.60130	0.2245	N	0.08118	0	0.09310	N	1	B;D;P	0.58970	0.069;0.984;0.826	B;P;B	0.46796	0.032;0.527;0.188	T	0.58901	-0.7554	9	0.23302	T	0.38	.	0.0302	0.00005	0.2859:0.209:0.2273:0.2777	.	537;538;291	C9J7J7;Q5DVJ7;Q92496	.;.;FHR4_HUMAN	H	537;291;291;291	ENSP00000356386:Y537H;ENSP00000356388:Y291H;ENSP00000251424:Y291H	ENSP00000251424:Y291H	Y	+	1	0	CFHR4	195154034	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-3.116000	0.00597	-2.574000	0.00466	-0.483000	0.04790	TAT	.	.	weak		0.294	CFHR2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005666	
RPS6KB2	6199	hgsc.bcm.edu	37	11	67202156	67202156	+	Missense_Mutation	SNP	C	C	T	rs13859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67202156C>T	ENST00000312629.5	+	14	1304	c.1259C>T	c.(1258-1260)gCc>gTc	p.A420V	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	420	Pro-rich.		A -> V (in dbSNP:rs13859). {ECO:0000269|PubMed:10490847, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9804755, ECO:0000269|PubMed:9878560}.		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)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			AGCCCCCGGGCCCCCGTCAGG	0.657													C|||	2438	0.486821	0.8079	0.5692	5008	,	,		17451	0.3264		0.4225	False		,,,				2504	0.226				p.A420V		Atlas-SNP	.											RPS6KB2_ENST00000312629,NS,carcinoma,0,2	RPS6KB2	92	2	0			c.C1259T						PASS	.	C	VAL/ALA	2835,1023		1045,745,139	12.0	13.0	13.0		1259	4.4	1.0	11	dbSNP_52	13	3510,4694		792,1926,1384	yes	missense	RPS6KB2	NM_003952.2	64	1837,2671,1523	TT,TC,CC		42.784,26.5163,47.3968	benign	420/483	67202156	6345,5717	1929	4102	6031	SO:0001583	missense	6199	exon14			CCCGGGCCCCCGT	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"""ribosomal protein S6 kinase, 70kD, polypeptide 2"""			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.1259C>T	11.37:g.67202156C>T	ENSP00000308413:p.Ala420Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	89	0.978022	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	37	CCDS41677.1	1093	0.5004578754578755	381	0.774390243902439	195	0.5386740331491713	182	0.3181818181818182	335	0.4419525065963061	C	14.64	2.596768	0.46318	0.734837	0.42784	ENSG00000175634	ENST00000312629	T	0.68331	-0.32	4.45	4.45	0.53987	.	0.068776	0.56097	D	0.000031	T	0.00012	0.0000	N	0.08118	0	0.09310	P	1.0	B	0.10296	0.003	B	0.13407	0.009	T	0.39210	-0.9625	9	0.51188	T	0.08	.	15.058	0.71930	0.0:1.0:0.0:0.0	rs13859;rs1132410;rs1790751;rs3178163;rs3193142;rs11558387;rs17296783	420	Q9UBS0	KS6B2_HUMAN	V	420	ENSP00000308413:A420V	ENSP00000308413:A420V	A	+	2	0	RPS6KB2	66958732	1.000000	0.71417	0.998000	0.56505	0.220000	0.24768	6.850000	0.75420	2.300000	0.77407	0.462000	0.41574	GCC	C|0.515;T|0.485	0.485	strong		0.657	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952	
ALDH8A1	64577	hgsc.bcm.edu	37	6	135254034	135254034	+	Silent	SNP	G	G	A	rs114000920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135254034G>A	ENST00000265605.2	-	5	797	c.729C>T	c.(727-729)agC>agT	p.S243S	ALDH8A1_ENST00000367845.2_Silent_p.S243S|ALDH8A1_ENST00000367847.2_Silent_p.S193S	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	243					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		AGTGGGGAGCGCTCAGCTGGG	0.647													G|||	58	0.0115815	0.0416	0.0043	5008	,	,		17286	0.0		0.0	False		,,,				2504	0.0				p.S243S		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.C729T						PASS	.	G	,,	126,4280	91.6+/-130.3	2,122,2079	68.0	70.0	69.0		579,729,729	-2.7	1.0	6	dbSNP_132	69	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH8A1	NM_001193480.1,NM_022568.3,NM_170771.2	,,	2,124,6377	AA,AG,GG		0.0233,2.8597,0.9842	,,	193/438,243/488,243/434	135254034	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	64577	exon5			GGGAGCGCTCAGC	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"""Aldehyde dehydrogenases"""	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.729C>T	6.37:g.135254034G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Silent	SNP	ENST00000265605.2	37	CCDS5171.1																																																																																			G|0.987;A|0.013	0.013	strong		0.647	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2		
BPIFB3	359710	hgsc.bcm.edu	37	20	31644436	31644436	+	Silent	SNP	A	A	C	rs35539872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31644436A>C	ENST00000375494.3	+	2	213	c.213A>C	c.(211-213)ggA>ggC	p.G71G	AL121756.1_ENST00000579962.1_RNA	NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	71	Leu-rich.				innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TGGGCTCAGGAGGGCTGCTTG	0.617													A|||	232	0.0463259	0.1679	0.0144	5008	,	,		17539	0.0		0.0	False		,,,				2504	0.0				p.G71G		Atlas-SNP	.											.	.	.	.	0			c.A213C						PASS	.	A		604,3802	265.9+/-266.9	52,500,1651	89.0	90.0	90.0		213	0.8	0.6	20	dbSNP_126	90	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	BPIFB3	NM_182658.1		52,505,5946	CC,CA,AA		0.0581,13.7086,4.6825		71/477	31644436	609,12397	2203	4300	6503	SO:0001819	synonymous_variant	359710	exon2			CTCAGGAGGGCTG	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.213A>C	20.37:g.31644436A>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_182658	Q5TDX7	Silent	SNP	ENST00000375494.3	37	CCDS13212.1																																																																																			A|0.957;C|0.043	0.043	strong		0.617	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
MRGPRX3	117195	hgsc.bcm.edu	37	11	18159406	18159406	+	Silent	SNP	C	C	G	rs28628238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18159406C>G	ENST00000396275.2	+	3	1018	c.657C>G	c.(655-657)ctC>ctG	p.L219L		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TGACCATCCTCCTCACAGTGC	0.542													.|||	273	0.0545128	0.1952	0.0216	5008	,	,		20315	0.0		0.0	False		,,,				2504	0.0				p.L219L		Atlas-SNP	.											.	MRGPRX3	59	.	0			c.C657G						PASS	.	G		816,3584	748.0+/-411.9	83,650,1467	113.0	107.0	109.0		657	1.3	0.3	11	dbSNP_125	109	5,8581	818.5+/-406.9	0,5,4288	no	coding-synonymous	MRGPRX3	NM_054031.3		83,655,5755	GG,GC,CC		0.0582,18.5455,6.3222		219/323	18159406	821,12165	2200	4293	6493	SO:0001819	synonymous_variant	117195	exon3			CATCCTCCTCACA		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.657C>G	11.37:g.18159406C>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Silent	SNP	ENST00000396275.2	37	CCDS7830.1																																																																																			C|0.948;G|0.052	0.052	strong		0.542	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031	
B4GALT3	8703	hgsc.bcm.edu	37	1	161141862	161141862	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161141862C>T	ENST00000319769.5	-	8	1148	c.926G>A	c.(925-927)cGt>cAt	p.R309H	B4GALT3_ENST00000367998.1_Missense_Mutation_p.R309H|PPOX_ENST00000535223.1_Intron|B4GALT3_ENST00000470882.1_5'UTR|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000432542.2_Intron	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	309					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)	ATTCTGGGTACGGACCAGGAG	0.502																																					p.R309H		Atlas-SNP	.											.	B4GALT3	39	.	0			c.G926A						PASS	.						73.0	77.0	76.0					1																	161141862		2203	4300	6503	SO:0001583	missense	8703	exon8			TGGGTACGGACCA	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.926G>A	1.37:g.161141862C>T	ENSP00000320965:p.Arg309His	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_003779	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Missense_Mutation	SNP	ENST00000319769.5	37	CCDS1222.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.940163	0.34283	.	.	ENSG00000158850	ENST00000319769;ENST00000407555;ENST00000367998;ENST00000367997	T;T	0.35421	1.31;1.31	5.28	4.35	0.52113	.	0.213738	0.49305	D	0.000153	T	0.09730	0.0239	N	0.13235	0.315	0.45307	D	0.998302	P	0.38167	0.621	B	0.34722	0.188	T	0.08146	-1.0736	10	0.13470	T	0.59	.	13.4642	0.61243	0.0:0.9213:0.0:0.0787	.	309	O60512	B4GT3_HUMAN	H	309;286;309;309	ENSP00000320965:R309H;ENSP00000356977:R309H	ENSP00000320965:R309H	R	-	2	0	B4GALT3	159408486	0.954000	0.32549	0.999000	0.59377	0.999000	0.98932	2.130000	0.42064	2.746000	0.94184	0.655000	0.94253	CGT	.	.	none		0.502	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779	
MYH11	4629	hgsc.bcm.edu	37	16	15841534	15841534	+	Silent	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:15841534G>T	ENST00000300036.5	-	19	2413	c.2304C>A	c.(2302-2304)atC>atA	p.I768I	MYH11_ENST00000576790.2_Silent_p.I768I|MYH11_ENST00000396324.3_Silent_p.I775I|MYH11_ENST00000452625.2_Silent_p.I775I	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	768	Actin-binding. {ECO:0000250}.|Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TTCGGAAGAAGATTTTGCTCT	0.512			T	CBFB	AML																																p.I775I		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.C2325A						PASS	.						97.0	93.0	94.0					16																	15841534		2197	4300	6497	SO:0001819	synonymous_variant	4629	exon20			GAAGAAGATTTTG	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.2304C>A	16.37:g.15841534G>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	96	55	0.572917	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			.	.	none		0.512	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
ZNF689	115509	hgsc.bcm.edu	37	16	30616317	30616317	+	Silent	SNP	A	A	G	rs34007971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30616317A>G	ENST00000287461.3	-	3	1108	c.771T>C	c.(769-771)ggT>ggC	p.G257G	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	257					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			GGGGTTTTTCACCTGTGTGTG	0.602													G|||	360	0.071885	0.2595	0.0187	5008	,	,		16142	0.0		0.003	False		,,,				2504	0.001				p.G257G		Atlas-SNP	.											.	ZNF689	48	.	0			c.T771C						PASS	.	G		1032,3362	725.7+/-409.6	123,786,1288	86.0	80.0	82.0		771	-8.2	0.1	16	dbSNP_126	82	33,8567	817.8+/-406.9	1,31,4268	no	coding-synonymous	ZNF689	NM_138447.1		124,817,5556	GG,GA,AA		0.3837,23.4866,8.1961		257/501	30616317	1065,11929	2197	4300	6497	SO:0001819	synonymous_variant	115509	exon3			TTTTTCACCTGTG	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"""Zinc fingers, C2H2-type"", ""-"""	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.771T>C	16.37:g.30616317A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_138447	Q658J5	Silent	SNP	ENST00000287461.3	37	CCDS10686.1																																																																																			A|0.917;G|0.083	0.083	strong		0.602	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447	
PLEKHA6	22874	hgsc.bcm.edu	37	1	204198209	204198209	+	Silent	SNP	A	A	G	rs3795571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204198209A>G	ENST00000272203.3	-	19	2923	c.2607T>C	c.(2605-2607)caT>caC	p.H869H	PLEKHA6_ENST00000414478.1_Silent_p.H889H	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	869										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)			TGTCTACCTCATGGATGCTGC	0.632													G|||	2566	0.51238	0.6967	0.5389	5008	,	,		19143	0.4802		0.4344	False		,,,				2504	0.3579				p.H869H		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.T2607C						PASS	.	G		2912,1494	475.3+/-357.3	971,970,262	41.0	43.0	42.0		2607	-2.6	1.0	1	dbSNP_107	42	3938,4662	598.8+/-394.0	891,2156,1253	no	coding-synonymous	PLEKHA6	NM_014935.2		1862,3126,1515	GG,GA,AA		45.7907,33.9083,47.332		869/1049	204198209	6850,6156	2203	4300	6503	SO:0001819	synonymous_variant	22874	exon19			TACCTCATGGATG	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.2607T>C	1.37:g.204198209A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_014935	A7MD51|Q5VTI6	Silent	SNP	ENST00000272203.3	37	CCDS1444.1																																																																																			A|0.469;G|0.531	0.531	strong		0.632	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
KIAA1211L	343990	hgsc.bcm.edu	37	2	99412654	99412654	+	Missense_Mutation	SNP	C	C	T	rs73962467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99412654C>T	ENST00000397899.2	-	9	3009	c.2678G>A	c.(2677-2679)cGg>cAg	p.R893Q		NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	893																	CCCCTGCTTCCGGTCCACAGC	0.507													C|||	33	0.00658946	0.0219	0.0058	5008	,	,		19267	0.0		0.0	False		,,,				2504	0.0				p.R893Q		Atlas-SNP	.											.	.	.	.	0			c.G2678A						PASS	.	C	GLN/ARG	69,3687		3,63,1812	145.0	141.0	143.0		2678	0.3	0.2	2	dbSNP_130	143	1,8221		0,1,4110	yes	missense	C2orf55	NM_207362.2	43	3,64,5922	TT,TC,CC		0.0122,1.8371,0.5844	benign	893/963	99412654	70,11908	1878	4111	5989	SO:0001583	missense	343990	exon9			TGCTTCCGGTCCA	BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 55"""	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.2678G>A	2.37:g.99412654C>T	ENSP00000380996:p.Arg893Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_207362		Missense_Mutation	SNP	ENST00000397899.2	37	CCDS42720.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	5.887	0.347744	0.11126	0.018371	1.22E-4	ENSG00000196872	ENST00000397899	T	0.39592	1.07	5.17	0.328	0.15918	.	1.201180	0.05934	N	0.635672	T	0.06188	0.0160	N	0.11427	0.14	0.09310	N	1	B	0.19706	0.038	B	0.15870	0.014	T	0.14755	-1.0461	10	0.02654	T	1	-0.9202	3.636	0.08148	0.0:0.3473:0.1965:0.4562	.	893	Q6NV74	CB055_HUMAN	Q	893	ENSP00000380996:R893Q	ENSP00000380996:R893Q	R	-	2	0	C2orf55	98779086	0.996000	0.38824	0.172000	0.22920	0.097000	0.18754	0.215000	0.17562	0.182000	0.20032	0.563000	0.77884	CGG	C|0.991;T|0.009	0.009	strong		0.507	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362	
NEB	4703	hgsc.bcm.edu	37	2	152497088	152497088	+	Silent	SNP	G	G	A	rs61730771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152497088G>A	ENST00000172853.10	-	61	8613	c.8466C>T	c.(8464-8466)caC>caT	p.H2822H	NEB_ENST00000603639.1_Silent_p.H2822H|NEB_ENST00000409198.1_Silent_p.H2822H|NEB_ENST00000604864.1_Silent_p.H2822H|NEB_ENST00000397345.3_Silent_p.H2822H|NEB_ENST00000427231.2_Silent_p.H2822H			P20929	NEBU_HUMAN	nebulin	2822					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)		TCTTGGCCACGTGCATGGACC	0.527													G|||	162	0.0323482	0.0575	0.0101	5008	,	,		17198	0.0079		0.0209	False		,,,				2504	0.0511				p.H2822H		Atlas-SNP	.											.	NEB	1697	.	0			c.C8466T						PASS	.	G	,,	162,3768		4,154,1807	280.0	263.0	269.0		8466,8466,8466	-5.7	0.9	2	dbSNP_129	269	151,8169		1,149,4010	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	5,303,5817	AA,AG,GG		1.8149,4.1221,2.5551	,,	2822/8526,2822/8526,2822/6670	152497088	313,11937	1965	4160	6125	SO:0001819	synonymous_variant	4703	exon61			GGCCACGTGCATG	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.8466C>T	2.37:g.152497088G>A		Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	323	190	0.588235	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				G|0.977;A|0.023	0.023	strong		0.527	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
PIK3AP1	118788	hgsc.bcm.edu	37	10	98469734	98469734	+	Missense_Mutation	SNP	G	G	A	rs73334383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98469734G>A	ENST00000339364.5	-	2	139	c.20C>T	c.(19-21)cCc>cTc	p.P7L		NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	7					negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		GCATCCTCTGGGCACCCCTGG	0.597													G|||	61	0.0121805	0.0416	0.0086	5008	,	,		17446	0.0		0.0	False		,,,				2504	0.0				p.P7L		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.C20T						PASS	.	G	LEU/PRO	128,4168		2,124,2022	52.0	43.0	46.0		20	-9.5	0.0	10	dbSNP_130	46	2,8428		0,2,4213	yes	missense	PIK3AP1	NM_152309.2	98	2,126,6235	AA,AG,GG		0.0237,2.9795,1.0215	benign	7/806	98469734	130,12596	2148	4215	6363	SO:0001583	missense	118788	exon2			CCTCTGGGCACCC	AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.20C>T	10.37:g.98469734G>A	ENSP00000339826:p.Pro7Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Missense_Mutation	SNP	ENST00000339364.5	37	CCDS31259.1	26	0.011904761904761904	21	0.042682926829268296	5	0.013812154696132596	0	0.0	0	0.0	G	2.065	-0.414443	0.04766	0.029795	2.37E-4	ENSG00000155629	ENST00000339364	T	0.09255	3.0	4.73	-9.46	0.00597	.	2.649450	0.01208	N	0.007761	T	0.00906	0.0030	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26467	-1.0102	10	0.22109	T	0.4	4.4446	5.2642	0.15589	0.1057:0.174:0.5472:0.173	.	7	Q6ZUJ8	BCAP_HUMAN	L	7	ENSP00000339826:P7L	ENSP00000339826:P7L	P	-	2	0	PIK3AP1	98459724	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.446000	0.06837	-2.205000	0.00742	-0.345000	0.07892	CCC	G|0.987;A|0.013	0.013	strong		0.597	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309	
AIFM3	150209	hgsc.bcm.edu	37	22	21333605	21333605	+	Missense_Mutation	SNP	G	G	C	rs61356271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21333605G>C	ENST00000399167.2	+	17	1763	c.1523G>C	c.(1522-1524)aGc>aCc	p.S508T	AIFM3_ENST00000399163.2_Missense_Mutation_p.S508T|AIFM3_ENST00000465606.1_3'UTR|XXbac-B135H6.18_ENST00000610278.1_lincRNA|AIFM3_ENST00000333607.6_Missense_Mutation_p.S508T|AIFM3_ENST00000405089.1_Missense_Mutation_p.S514T|AIFM3_ENST00000440238.2_Missense_Mutation_p.S508T|AIFM3_ENST00000335375.5_Missense_Mutation_p.S496T|LZTR1_ENST00000215739.8_5'Flank	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	508			S -> T (in dbSNP:rs61356271).		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)			GCGGAGATGAGCACTGTGCCC	0.672													g|||	270	0.0539137	0.1936	0.0202	5008	,	,		12709	0.0		0.0	False		,,,				2504	0.0				p.S514T		Atlas-SNP	.											.	AIFM3	49	.	0			c.G1541C						PASS	.	C	THR/SER,THR/SER,THR/SER	570,3784		38,494,1645	32.0	25.0	27.0		1523,1541,1523	0.2	0.8	22	dbSNP_129	27	8,8502		0,8,4247	yes	missense,missense,missense	AIFM3	NM_001018060.2,NM_001146288.1,NM_144704.2	58,58,58	38,502,5892	CC,CG,GG		0.094,13.0914,4.4932	,,	508/599,514/605,508/606	21333605	578,12286	2177	4255	6432	SO:0001583	missense	150209	exon17			AGATGAGCACTGT	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.1523G>C	22.37:g.21333605G>C	ENSP00000382120:p.Ser508Thr	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	183	98	0.535519	NM_001146288	B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Missense_Mutation	SNP	ENST00000399167.2	37	CCDS13786.1	83	0.038003663003663	75	0.1524390243902439	8	0.022099447513812154	0	0.0	0	0.0	g	5.235	0.228779	0.09916	0.130914	9.4E-4	ENSG00000183773	ENST00000399167;ENST00000399163;ENST00000405089;ENST00000335375;ENST00000440238;ENST00000333607	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	4.65	0.178	0.15058	FAD/NAD-linked reductase, dimerisation (1);	0.334108	0.35772	N	0.003000	T	0.00109	0.0003	N	0.16266	0.395	0.54753	P	1.2000000000012001E-5	B;B;B;B	0.22983	0.078;0.05;0.05;0.029	B;B;B;B	0.18561	0.022;0.022;0.022;0.01	T	0.24333	-1.0163	9	0.10636	T	0.68	-15.7117	5.9493	0.19237	0.3378:0.1331:0.5291:0.0	rs61356271	496;514;508;508	B7Z9S7;Q96NN9-2;Q96NN9-3;Q96NN9	.;.;.;AIFM3_HUMAN	T	508;508;514;496;508;508	ENSP00000382120:S508T;ENSP00000382116:S508T;ENSP00000385800:S514T;ENSP00000335369:S496T;ENSP00000390798:S508T;ENSP00000327671:S508T	ENSP00000327671:S508T	S	+	2	0	AIFM3	19663605	0.785000	0.28726	0.846000	0.33378	0.236000	0.25371	0.863000	0.27913	-0.250000	0.09555	-2.308000	0.00257	AGC	G|0.946;C|0.054	0.054	strong		0.672	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704	
EFR3B	22979	hgsc.bcm.edu	37	2	25359422	25359422	+	Silent	SNP	G	G	A	rs3731631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:25359422G>A	ENST00000403714.3	+	14	1698	c.1515G>A	c.(1513-1515)ctG>ctA	p.L505L	EFR3B_ENST00000405108.1_Silent_p.L357L|EFR3B_ENST00000402191.1_Silent_p.L470L|EFR3B_ENST00000401432.3_Silent_p.L505L	NM_014971.1	NP_055786.1	Q9Y2G0	EFR3B_HUMAN	EFR3 homolog B (S. cerevisiae)	505										endometrium(1)	1						TCCTGAAGCTGAAAGTGGACA	0.572													G|||	1476	0.294728	0.3169	0.2954	5008	,	,		20989	0.3948		0.3022	False		,,,				2504	0.1534				p.L505L		Atlas-SNP	.											.	EFR3B	29	.	0			c.G1515A						PASS	.	G		412,972		66,280,346	119.0	95.0	102.0		1515	1.1	1.0	2	dbSNP_107	102	965,2217		141,683,767	yes	coding-synonymous	EFR3B	NM_014971.1		207,963,1113	AA,AG,GG		30.3268,29.7688,30.1577		505/818	25359422	1377,3189	692	1591	2283	SO:0001819	synonymous_variant	22979	exon14			GAAGCTGAAAGTG	AB023170	CCDS46231.1	2p24.1	2008-02-05	2007-11-14	2007-11-14	ENSG00000084710	ENSG00000084710			29155	protein-coding gene	gene with protein product			"""KIAA0953"""	KIAA0953		10231032	Standard	NM_014971		Approved	FLJ37871	uc010eyh.3	Q9Y2G0	OTTHUMG00000151988	ENST00000403714.3:c.1515G>A	2.37:g.25359422G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	79	29	0.367089	NM_014971	B7WPL8|Q86XU6	Silent	SNP	ENST00000403714.3	37	CCDS46231.1																																																																																			G|0.665;A|0.335	0.335	strong		0.572	EFR3B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324808.1	NM_014971	
PAMR1	25891	hgsc.bcm.edu	37	11	35492351	35492351	+	Silent	SNP	G	G	A	rs16927500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:35492351G>A	ENST00000378880.2	-	5	955	c.510C>T	c.(508-510)agC>agT	p.S170S	PAMR1_ENST00000378878.3_Intron|PAMR1_ENST00000532848.1_Silent_p.S130S|PAMR1_ENST00000534803.1_5'UTR|PAMR1_ENST00000278360.3_Silent_p.S170S	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	170	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						CAAACTCCAGGCTCAACATGA	0.557													A|||	464	0.0926518	0.2595	0.0591	5008	,	,		22839	0.0377		0.0249	False		,,,				2504	0.0174				p.S170S		Atlas-SNP	.											.	PAMR1	85	.	0			c.C510T						PASS	.	A	,	1006,3398	729.6+/-410.1	95,816,1291	111.0	80.0	90.0		510,510	1.5	1.0	11	dbSNP_123	90	183,8413	810.9+/-407.1	3,177,4118	no	coding-synonymous,coding-synonymous	PAMR1	NM_001001991.1,NM_015430.2	,	98,993,5409	AA,AG,GG		2.1289,22.8429,9.1462	,	170/721,170/738	35492351	1189,11811	2202	4298	6500	SO:0001819	synonymous_variant	25891	exon5			CTCCAGGCTCAAC		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.510C>T	11.37:g.35492351G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	123	71	0.577236	NM_001001991	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Silent	SNP	ENST00000378880.2	37	CCDS31460.1																																																																																			G|0.906;A|0.094	0.094	strong		0.557	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430	
BFSP2	8419	hgsc.bcm.edu	37	3	133191385	133191385	+	Missense_Mutation	SNP	C	C	A	rs79087781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133191385C>A	ENST00000302334.2	+	6	1309	c.1220C>A	c.(1219-1221)gCc>gAc	p.A407D		NM_003571.2	NP_003562.1	Q13515	BFSP2_HUMAN	beaded filament structural protein 2, phakinin	407	Tail.				cell maturation (GO:0048469)|intermediate filament cytoskeleton organization (GO:0045104)|lens fiber cell development (GO:0070307)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|urinary_tract(1)	13						TCCTACCACGCCCTGCTGGAC	0.562													C|||	167	0.0333466	0.028	0.0274	5008	,	,		15989	0.0258		0.0388	False		,,,				2504	0.047				p.A407D		Atlas-SNP	.											.	BFSP2	48	.	0			c.C1220A						PASS	.	C	ASP/ALA	143,4263		2,139,2062	19.0	22.0	21.0		1220	2.3	1.0	3	dbSNP_131	21	379,8221		7,365,3928	yes	missense	BFSP2	NM_003571.2	126	9,504,5990	AA,AC,CC		4.407,3.2456,4.0135	benign	407/416	133191385	522,12484	2203	4300	6503	SO:0001583	missense	8419	exon6			ACCACGCCCTGCT	U48224	CCDS33859.1	3q22.1	2013-01-16			ENSG00000170819	ENSG00000170819		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1041	protein-coding gene	gene with protein product		603212					Standard	NM_003571		Approved	CP47, CP49, LIFL-L, phakinin	uc003epn.1	Q13515	OTTHUMG00000159719	ENST00000302334.2:c.1220C>A	3.37:g.133191385C>A	ENSP00000304987:p.Ala407Asp	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	135	76	0.562963	NM_003571	Q14D32|Q9HBW5	Missense_Mutation	SNP	ENST00000302334.2	37	CCDS33859.1	73	0.033424908424908424	14	0.028455284552845527	12	0.03314917127071823	14	0.024475524475524476	33	0.04353562005277045	c	16.65	3.182012	0.57800	0.032456	0.04407	ENSG00000170819	ENST00000302334	D	0.88664	-2.41	5.13	2.27	0.28462	Filament (1);	0.338987	0.25025	N	0.033740	T	0.61565	0.2357	L	0.40543	1.245	0.40914	D	0.98425	P	0.48911	0.917	P	0.47891	0.56	T	0.70579	-0.4833	10	0.33141	T	0.24	-7.807	7.5614	0.27853	0.0:0.5855:0.2261:0.1883	.	407	Q13515	BFSP2_HUMAN	D	407	ENSP00000304987:A407D	ENSP00000304987:A407D	A	+	2	0	BFSP2	134674075	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	3.010000	0.49559	0.568000	0.29311	0.556000	0.70494	GCC	C|0.964;A|0.036	0.036	strong		0.562	BFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357031.1		
MUC4	4585	hgsc.bcm.edu	37	3	195515550	195515550	+	Silent	SNP	G	G	C	rs59408218|rs386670090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515550G>C	ENST00000463781.3	-	2	3360	c.2901C>G	c.(2899-2901)acC>acG	p.T967T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T967T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	972	Ser-rich.				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)		TGAGGGCCGTGGTGAAGGTTT	0.572													.|||	684	0.136581	0.4319	0.0504	5008	,	,		24447	0.004		0.0348	False		,,,				2504	0.0399				p.T967T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C2901G						PASS	.		,,	1583,2793		264,1055,869	129.0	134.0	132.0		,2901,	0.4	0.0	3	dbSNP_129	132	249,8281		0,249,4016	yes	intron,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	264,1304,4885	CC,CG,GG		2.9191,36.1746,14.1949	,,	,967/5413,	195515550	1832,11074	2188	4265	6453	SO:0001819	synonymous_variant	4585	exon2			GGCCGTGGTGAAG	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.2901C>G	3.37:g.195515550G>C		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	301	300	0.996678	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;C|0.103	0.103	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DSC3	1825	hgsc.bcm.edu	37	18	28610988	28610988	+	Missense_Mutation	SNP	C	C	T	rs276938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28610988C>T	ENST00000360428.4	-	3	385	c.305G>A	c.(304-306)aGg>aAg	p.R102K	DSC3_ENST00000434452.1_Missense_Mutation_p.R102K	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	102			R -> K (in dbSNP:rs276938).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			TGTCTGTTTCCTTTTGTCAGA	0.363													C|||	2181	0.435503	0.32	0.3401	5008	,	,		15601	0.6776		0.3549	False		,,,				2504	0.4928				p.R102K		Atlas-SNP	.											.	DSC3	225	.	0			c.G305A						PASS	.	C	LYS/ARG,LYS/ARG	1498,2908	474.4+/-357.0	253,992,958	102.0	92.0	95.0		305,305	1.6	0.0	18	dbSNP_79	95	2760,5840	437.2+/-358.5	443,1874,1983	yes	missense,missense	DSC3	NM_001941.3,NM_024423.2	26,26	696,2866,2941	TT,TC,CC		32.093,33.9991,32.7387	benign,benign	102/897,102/840	28610988	4258,8748	2203	4300	6503	SO:0001583	missense	1825	exon3			TGTTTCCTTTTGT	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.305G>A	18.37:g.28610988C>T	ENSP00000353608:p.Arg102Lys	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_024423	A6NN35|Q14200|Q9HAZ9	Missense_Mutation	SNP	ENST00000360428.4	37	CCDS32810.1	941	0.4308608058608059	161	0.32723577235772355	127	0.35082872928176795	393	0.6870629370629371	260	0.34300791556728233	C	2.166	-0.391109	0.04932	0.339991	0.32093	ENSG00000134762	ENST00000360428;ENST00000434452	T;T	0.60299	0.2;0.2	5.28	1.64	0.23874	Cadherin prodomain-like (1);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.01800	-0.715	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.38564	-0.9655	8	0.32370	T	0.25	.	5.0997	0.14753	0.0:0.1586:0.2902:0.5512	rs276938;rs1098250;rs1303279;rs52831455;rs58484203;rs276938	102;102	Q14574;Q14574-2	DSC3_HUMAN;.	K	102	ENSP00000353608:R102K;ENSP00000392068:R102K	ENSP00000353608:R102K	R	-	2	0	DSC3	26864986	0.013000	0.17824	0.014000	0.15608	0.005000	0.04900	1.229000	0.32600	0.134000	0.18681	-1.224000	0.01588	AGG	T|0.384;G|0.001	0.384	strong		0.363	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
P2RX7	5027	hgsc.bcm.edu	37	12	121615103	121615103	+	Missense_Mutation	SNP	G	G	A	rs1718119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121615103G>A	ENST00000546057.1	+	11	1185	c.1042G>A	c.(1042-1044)Gct>Act	p.A348T	P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000328963.5_Missense_Mutation_p.A178T|P2RX7_ENST00000541446.1_Missense_Mutation_p.A59T|P2RX7_ENST00000535250.1_Missense_Mutation_p.A258T	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	348			A -> T (in dbSNP:rs1718119). {ECO:0000269|PubMed:9826911}.		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)					TCCCCAGGCCGCTGTGTTCAT	0.498													A|||	1615	0.322484	0.4599	0.2003	5008	,	,		20159	0.1419		0.3827	False		,,,				2504	0.3476				p.A348T		Atlas-SNP	.											P2RX7,NS,carcinoma,0,1	P2RX7	53	1	0			c.G1042A						scavenged	.	A	THR/ALA	2007,2399	614.4+/-392.4	454,1099,650	138.0	121.0	127.0		1042	5.6	1.0	12	dbSNP_89	127	3418,5182	639.4+/-399.5	723,1972,1605	yes	missense	P2RX7	NM_002562.5	58	1177,3071,2255	AA,AG,GG		39.7442,45.5515,41.7115	benign	348/596	121615103	5425,7581	2203	4300	6503	SO:0001583	missense	5027	exon11			CAGGCCGCTGTGT	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.1042G>A	12.37:g.121615103G>A	ENSP00000442349:p.Ala348Thr	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	143	65	0.454545	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	673	0.30815018315018317	231	0.4695121951219512	76	0.20994475138121546	73	0.12762237762237763	293	0.3865435356200528	A	6.616	0.482145	0.12581	0.455515	0.397442	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.03580	3.88;3.88;3.88;3.88	5.62	5.62	0.85841	.	0.382952	0.23821	N	0.044240	T	0.00012	0.0000	N	0.00112	-2.095	0.52501	P	4.199999999998649E-5	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.38887	-0.9640	9	0.02654	T	1	.	7.4513	0.27240	0.8325:0.0:0.1675:0.0	rs1718119;rs2230910;rs17525154;rs52812840;rs58430687;rs1718119	178;59;258;348	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	T	348;178;258;59	ENSP00000442349:A348T;ENSP00000330696:A178T;ENSP00000442572:A258T;ENSP00000437471:A59T	ENSP00000330696:A178T	A	+	1	0	P2RX7	120099486	0.976000	0.34144	0.978000	0.43139	0.854000	0.48673	0.672000	0.25187	0.980000	0.38523	-0.332000	0.08345	GCT	G|0.628;N|0.001	.	strong		0.498	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
OR13D1	286365	hgsc.bcm.edu	37	9	107457532	107457532	+	Missense_Mutation	SNP	C	C	T	rs10761073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107457532C>T	ENST00000318763.5	+	1	873	c.830C>T	c.(829-831)tCg>tTg	p.S277L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	277			S -> L (in dbSNP:rs10761073). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						TCAGCGCACTCGATTGTGGTC	0.388													T|||	3835	0.765775	0.8593	0.6643	5008	,	,		21481	0.9901		0.506	False		,,,				2504	0.7474				p.S277L		Atlas-SNP	.											OR13D1,colon,carcinoma,+1,1	OR13D1	42	1	0			c.C830T						PASS	.	T	LEU/SER	3599,807	318.0+/-295.4	1480,639,84	175.0	169.0	171.0		830	1.4	0.0	9	dbSNP_120	171	4429,4171	568.1+/-388.9	1169,2091,1040	yes	missense	OR13D1	NM_001004484.1	145	2649,2730,1124	TT,TC,CC		48.5,18.3159,38.2746	benign	277/347	107457532	8028,4978	2203	4300	6503	SO:0001583	missense	286365	exon1			CGCACTCGATTGT		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"""GPCR / Class A : Olfactory receptors"""	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.830C>T	9.37:g.107457532C>T	ENSP00000317357:p.Ser277Leu	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	210	77	0.366667	NM_001004484	B9EIS1|Q6IFL1	Missense_Mutation	SNP	ENST00000318763.5	37	CCDS35094.1	1606	0.7353479853479854	409	0.8313008130081301	238	0.6574585635359116	567	0.9912587412587412	392	0.5171503957783641	T	0.001	-2.996412	0.00044	0.816841	0.515	ENSG00000179055	ENST00000318763	T	0.26957	1.7	3.87	1.4	0.22301	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35291	N	0.003311	T	0.00012	0.0000	N	0.00000	-4.525	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.46247	-0.9205	9	0.02654	T	1	.	5.1409	0.14959	0.1374:0.1771:0.0:0.6855	rs10761073;rs61440455;rs10761073	277	Q8NGV5	O13D1_HUMAN	L	277	ENSP00000317357:S277L	ENSP00000317357:S277L	S	+	2	0	OR13D1	106497353	0.496000	0.26059	0.001000	0.08648	0.001000	0.01503	4.054000	0.57434	-0.522000	0.06417	-2.611000	0.00159	TCG	C|0.321;T|0.679	0.679	strong		0.388	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
MED24	9862	hgsc.bcm.edu	37	17	38186106	38186106	+	Silent	SNP	C	C	T	rs11555255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38186106C>T	ENST00000394128.2	-	13	1242	c.1161G>A	c.(1159-1161)gcG>gcA	p.A387A	SNORD124_ENST00000459577.1_RNA|MED24_ENST00000501516.3_Silent_p.A406A|MED24_ENST00000356271.3_Silent_p.A374A|MED24_ENST00000394127.2_Silent_p.A374A|MED24_ENST00000394126.1_Silent_p.A412A	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	387					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)					GCTCTCGGTCCGCTTTGCTGT	0.557													C|||	528	0.105431	0.1551	0.1182	5008	,	,		20173	0.006		0.164	False		,,,				2504	0.0716				p.A387A		Atlas-SNP	.											.	MED24	89	.	0			c.G1161A						PASS	.	C	,	737,3669	304.1+/-288.3	63,611,1529	221.0	165.0	184.0		1122,1161	-4.2	0.2	17	dbSNP_120	184	1401,7199	270.7+/-289.1	115,1171,3014	no	coding-synonymous,coding-synonymous	MED24	NM_001079518.1,NM_014815.3	,	178,1782,4543	TT,TC,CC		16.2907,16.7272,16.4386	,	374/977,387/990	38186106	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	9862	exon13			TCGGTCCGCTTTG	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.1161G>A	17.37:g.38186106C>T		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	218	112	0.513761	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1																																																																																			T|0.119;G|0.156;C|0.699;A|0.025	0.119	strong		0.557	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
MUC4	4585	hgsc.bcm.edu	37	3	195510158	195510158	+	Missense_Mutation	SNP	G	G	C	rs200688112		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195510158G>C	ENST00000463781.3	-	2	8752	c.8293C>G	c.(8293-8295)Cac>Gac	p.H2765D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H2765D	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)		GGGGTGGCGTGACCTGTGGAT	0.572																																					p.H2765D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+2,4	MUC4	1505	4	0			c.C8293G						scavenged	.						27.0	17.0	20.0					3																	195510158		686	1525	2211	SO:0001583	missense	4585	exon2			TGGCGTGACCTGT	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.8293C>G	3.37:g.195510158G>C	ENSP00000417498:p.His2765Asp	Somatic	186	7	0.0376344		WXS	Illumina HiSeq	Phase_I	227	61	0.268722	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	.	.	.	.	.	.	.	.	.	.	-	3.418	-0.118798	0.06838	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.53;1.52	1.02	-2.03	0.07365	.	.	.	.	.	T	0.12008	0.0292	N	0.19112	0.55	0.09310	N	1	P	0.35139	0.486	B	0.22601	0.04	T	0.16630	-1.0396	8	.	.	.	.	2.6372	0.04961	0.2435:0.0:0.4859:0.2706	.	2637	E7ESK3	.	D	2765	ENSP00000417498:H2765D;ENSP00000420243:H2765D	.	H	-	1	0	MUC4	196994937	0.000000	0.05858	0.004000	0.12327	0.121000	0.20230	-1.116000	0.03286	-0.817000	0.04335	0.074000	0.15403	CAC	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
VENTX	27287	hgsc.bcm.edu	37	10	135051543	135051543	+	Missense_Mutation	SNP	T	T	C	rs2240892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135051543T>C	ENST00000325980.9	+	1	636	c.125T>C	c.(124-126)cTg>cCg	p.L42P		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	42			L -> P (in dbSNP:rs2240892). {ECO:0000269|PubMed:15489334}.		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)		GACTTCTCCCTGGGGAGCCTC	0.716													T|||	1221	0.24381	0.2943	0.1859	5008	,	,		12549	0.376		0.1123	False		,,,				2504	0.2157				p.L42P		Atlas-SNP	.											VENTX,caecum,carcinoma,0,1	VENTX	24	1	0			c.T125C						PASS	.	T	PRO/LEU	737,3379		49,639,1370	5.0	7.0	6.0		125	-2.4	0.0	10	dbSNP_98	6	776,7542		42,692,3425	no	missense	VENTX	NM_014468.2	98	91,1331,4795	CC,CT,TT		9.3292,17.9057,12.1682	benign	42/259	135051543	1513,10921	2058	4159	6217	SO:0001583	missense	27287	exon1			TCTCCCTGGGGAG	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.125T>C	10.37:g.135051543T>C	ENSP00000357556:p.Leu42Pro	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	72	19	0.263889	NM_014468	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	37	CCDS7675.1	489	0.2239010989010989	143	0.29065040650406504	71	0.19613259668508287	190	0.3321678321678322	85	0.11213720316622691	T	2.856	-0.237276	0.05944	0.179057	0.093292	ENSG00000151650	ENST00000325980	T	0.43294	0.95	1.78	-2.36	0.06663	.	1.462090	0.04704	N	0.416452	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	0.32079	-0.9920	9	0.33940	T	0.23	.	0.8221	0.01113	0.1484:0.1943:0.2644:0.393	rs2240892;rs60200993;rs2240892	42	O95231	VENTX_HUMAN	P	42	ENSP00000357556:L42P	ENSP00000357556:L42P	L	+	2	0	VENTX	134901533	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.183000	0.09712	-0.933000	0.03737	-1.572000	0.00871	CTG	T|0.766;C|0.234	0.234	strong		0.716	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468	
TDG	6996	hgsc.bcm.edu	37	12	104376693	104376693	+	Missense_Mutation	SNP	G	G	A	rs4135113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:104376693G>A	ENST00000392872.3	+	5	829	c.595G>A	c.(595-597)Ggc>Agc	p.G199S	TDG_ENST00000544861.1_Missense_Mutation_p.G56S|TDG_ENST00000542036.1_Silent_p.P22P|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000266775.9_Missense_Mutation_p.G195S	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	199			G -> S (in dbSNP:rs4135113). {ECO:0000269|Ref.2}.		base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		GACCACGCCCGGCAGCAAAGA	0.468								Base excision repair (BER), DNA glycosylases					G|||	507	0.101238	0.2005	0.0706	5008	,	,		17924	0.1399		0.0368	False		,,,				2504	0.0153				p.G199S		Atlas-SNP	.											.	TDG	43	.	0			c.G595A						PASS	.	G	SER/GLY	721,3685	292.4+/-282.0	43,635,1525	89.0	85.0	86.0		595	4.5	1.0	12	dbSNP_108	86	204,8396	88.4+/-150.7	2,200,4098	yes	missense	TDG	NM_003211.4	56	45,835,5623	AA,AG,GG		2.3721,16.364,7.1121	benign	199/411	104376693	925,12081	2203	4300	6503	SO:0001583	missense	6996	exon5			ACGCCCGGCAGCA	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.595G>A	12.37:g.104376693G>A	ENSP00000376611:p.Gly199Ser	Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	336	144	0.428571	NM_003211	Q8IUZ6|Q8IZM3	Missense_Mutation	SNP	ENST00000392872.3	37	CCDS9095.1	228	0.1043956043956044	78	0.15853658536585366	26	0.0718232044198895	96	0.16783216783216784	28	0.036939313984168866	G	16.23	3.065256	0.55432	0.16364	0.023721	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000537100	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.4	4.51	0.55191	Uracil-DNA glycosylase-like (3);	0.050795	0.85682	N	0.000000	T	0.00109	0.0003	L	0.28115	0.83	0.09310	P	1.0	P;B	0.46142	0.873;0.432	P;B	0.45167	0.472;0.256	T	0.06127	-1.0844	9	0.32370	T	0.25	-18.5352	14.391	0.66978	0.0713:0.0:0.9287:0.0	rs4135113;rs52816514;rs58847150;rs4135113	199;199	B2R848;Q13569	.;TDG_HUMAN	S	199;195;56;192	ENSP00000376611:G199S;ENSP00000266775:G195S;ENSP00000445899:G56S;ENSP00000439825:G192S	ENSP00000266775:G195S	G	+	1	0	TDG	102900823	1.000000	0.71417	0.977000	0.42913	0.597000	0.36814	6.743000	0.74848	1.280000	0.44463	-0.222000	0.12452	GGC	G|0.911;A|0.089	0.089	strong		0.468	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
CCDC27	148870	hgsc.bcm.edu	37	1	3688030	3688030	+	Silent	SNP	C	C	G	rs3737592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3688030C>G	ENST00000294600.2	+	12	1998	c.1914C>G	c.(1912-1914)ccC>ccG	p.P638P	SMIM1_ENST00000444870.2_5'Flank|SMIM1_ENST00000561886.1_5'Flank	NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	638										breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		AAGTGCCCCCCCTGCAACAGT	0.562													C|||	557	0.111222	0.2874	0.072	5008	,	,		16386	0.0198		0.0805	False		,,,				2504	0.0266				p.P638P		Atlas-SNP	.											CCDC27,caecum,carcinoma,+2,1	CCDC27	79	1	0			c.C1914G						PASS	.	C		1078,3328	391.9+/-328.3	124,830,1249	87.0	98.0	94.0		1914	-8.0	0.0	1	dbSNP_107	94	713,7887	175.5+/-225.5	35,643,3622	no	coding-synonymous	CCDC27	NM_152492.2		159,1473,4871	GG,GC,CC		8.2907,24.4666,13.7706		638/657	3688030	1791,11215	2203	4300	6503	SO:0001819	synonymous_variant	148870	exon12			GCCCCCCCTGCAA		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.1914C>G	1.37:g.3688030C>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_152492	Q5TBV3|Q96M50	Silent	SNP	ENST00000294600.2	37	CCDS50.1																																																																																			C|0.876;G|0.124	0.124	strong		0.562	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
OR10S1	219873	hgsc.bcm.edu	37	11	123847473	123847473	+	Missense_Mutation	SNP	A	A	G	rs55944888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123847473A>G	ENST00000531945.1	-	1	1015	c.926T>C	c.(925-927)gTg>gCg	p.V309A		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		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)		AGCATGCTTCACCTCCTTGTT	0.527													A|||	577	0.115216	0.0552	0.1585	5008	,	,		21721	0.1081		0.1829	False		,,,				2504	0.1033				p.V309A		Atlas-SNP	.											.	OR10S1	78	.	0			c.T926C						PASS	.	A	ALA/VAL	332,4072	174.8+/-204.3	17,298,1887	81.0	78.0	79.0		926	4.8	0.9	11	dbSNP_129	79	1454,7144	277.4+/-292.8	120,1214,2965	yes	missense	OR10S1	NM_001004474.1	64	137,1512,4852	GG,GA,AA		16.9109,7.5386,13.7363	possibly-damaging	309/332	123847473	1786,11216	2202	4299	6501	SO:0001583	missense	219873	exon1			TGCTTCACCTCCT	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"""GPCR / Class A : Olfactory receptors"""	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.926T>C	11.37:g.123847473A>G	ENSP00000431914:p.Val309Ala	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	37	CCDS31701.1	274	0.12545787545787546	16	0.032520325203252036	65	0.17955801104972377	68	0.11888111888111888	125	0.16490765171503957	A	9.610	1.131046	0.21041	0.075386	0.169109	ENSG00000196248	ENST00000531945	T	0.39592	1.07	4.82	4.82	0.62117	.	0.000000	0.31989	U	0.006759	T	0.00109	0.0003	M	0.67569	2.06	0.80722	P	0.0	B	0.20368	0.044	B	0.15870	0.014	T	0.07366	-1.0776	9	0.87932	D	0	-20.1912	14.1878	0.65617	1.0:0.0:0.0:0.0	rs55944888	309	Q8NGN2	O10S1_HUMAN	A	309	ENSP00000431914:V309A	ENSP00000431914:V309A	V	-	2	0	OR10S1	123352683	0.440000	0.25618	0.900000	0.35374	0.282000	0.26991	5.304000	0.65744	2.004000	0.58718	0.460000	0.39030	GTG	A|0.862;G|0.138	0.138	strong		0.527	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474	
PDIA2	64714	hgsc.bcm.edu	37	16	334580	334580	+	Silent	SNP	G	G	C	rs432925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:334580G>C	ENST00000219406.6	+	2	411	c.393G>C	c.(391-393)ccG>ccC	p.P131P	PDIA2_ENST00000404312.1_Silent_p.P131P	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	131	Thioredoxin 1. {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)				GCACGCACCCGGAGGAGTACA	0.677													g|||	1234	0.246406	0.32	0.2089	5008	,	,		15702	0.119		0.2913	False		,,,				2504	0.2587				p.P131P		Atlas-SNP	.											.	PDIA2	51	.	0			c.G393C						PASS	.	G		1233,3005		191,851,1077	34.0	40.0	38.0		393	-8.9	0.4	16	dbSNP_80	38	2417,6025		353,1711,2157	no	coding-synonymous	PDIA2	NM_006849.2		544,2562,3234	CC,CG,GG		28.6307,29.0939,28.7855		131/526	334580	3650,9030	2119	4221	6340	SO:0001819	synonymous_variant	64714	exon2			GCACCCGGAGGAG	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.393G>C	16.37:g.334580G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Silent	SNP	ENST00000219406.6	37	CCDS42089.1	508	0.2326007326007326	142	0.2886178861788618	81	0.22375690607734808	69	0.12062937062937062	216	0.2849604221635884	g	0.088	-1.171117	0.01660	0.290939	0.286307	ENSG00000185615	ENST00000456379	.	.	.	4.47	-8.93	0.00771	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999673342	.	.	.	.	.	.	T	0.20840	-1.0263	3	.	.	.	.	2.4162	0.04437	0.1433:0.1924:0.3952:0.2691	rs432925	.	.	.	P	128	.	.	R	+	2	0	PDIA2	274581	0.000000	0.05858	0.433000	0.26760	0.013000	0.08279	-1.350000	0.02624	-2.615000	0.00443	-1.077000	0.02231	CGG	G|0.756;C|0.244	0.244	strong		0.677	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414559	105414559	+	Missense_Mutation	SNP	T	T	C	rs11845746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105414559T>C	ENST00000333244.5	-	7	7348	c.7229A>G	c.(7228-7230)aAg>aGg	p.K2410R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2410			K -> R (in dbSNP:rs11845746).			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)			TTTGGGCATCTTGAAACTGGG	0.627													.|||	283	0.0565096	0.2073	0.0115	5008	,	,		17440	0.0		0.001	False		,,,				2504	0.0				p.K2410R		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A7229G						PASS	.	T	ARG/LYS	591,3093		71,449,1322	130.0	145.0	140.0		7229	2.9	0.5	14	dbSNP_120	140	5,8187		0,5,4091	no	missense	AHNAK2	NM_138420.2	26	71,454,5413	CC,CT,TT		0.061,16.0423,5.0185	probably-damaging	2410/5796	105414559	596,11280	1842	4096	5938	SO:0001583	missense	113146	exon7			GGCATCTTGAAAC	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.7229A>G	14.37:g.105414559T>C	ENSP00000353114:p.Lys2410Arg	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	240	236	0.983333	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	86	0.039377289377289376	82	0.16666666666666666	4	0.011049723756906077	0	0.0	0	0.0	-	12.77	2.037786	0.35989	0.160423	6.1E-4	ENSG00000185567	ENST00000333244	T	0.01265	5.08	4.08	2.93	0.34026	.	.	.	.	.	T	0.00039	0.0001	M	0.90759	3.145	0.49915	P	1.6599999999999948E-4	D	0.69078	0.997	D	0.77004	0.989	T	0.11767	-1.0574	8	0.39692	T	0.17	.	7.5349	0.27704	0.0:0.181:0.0:0.819	rs11845746;rs34729166;rs52811002;rs11845746	2410	Q8IVF2	AHNK2_HUMAN	R	2410	ENSP00000353114:K2410R	ENSP00000353114:K2410R	K	-	2	0	AHNAK2	104485604	0.002000	0.14202	0.526000	0.27913	0.064000	0.16182	0.833000	0.27504	0.468000	0.27243	0.397000	0.26171	AAG	T|0.967;C|0.033	0.033	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
HYDIN	54768	hgsc.bcm.edu	37	16	71015329	71015329	+	Missense_Mutation	SNP	G	G	T	rs78763837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71015329G>T	ENST00000393567.2	-	29	4625	c.4475C>A	c.(4474-4476)cCc>cAc	p.P1492H		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1492					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GCAGATTTGGGGAAAGATTCC	0.483													G|||	2340	0.467252	0.4455	0.5591	5008	,	,		18143	0.5645		0.328	False		,,,				2504	0.4744				p.P1492H		Atlas-SNP	.											LOC652153,NS,haematopoietic_neoplasm,0,2	HYDIN	788	2	0			c.C4475A						PASS	.						66.0	66.0	66.0					16																	71015329		1844	4072	5916	SO:0001583	missense	54768	exon29			ATTTGGGGAAAGA	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.4475C>A	16.37:g.71015329G>T	ENSP00000377197:p.Pro1492His	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	160	65	0.40625	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	964	0.4413919413919414	233	0.4735772357723577	184	0.5082872928176796	312	0.5454545454545454	235	0.3100263852242744	G	24.0	4.480970	0.84747	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01221	5.15	4.26	4.26	0.50523	.	0.000000	0.33023	U	0.005376	T	0.00012	0.0000	M	0.80183	2.485	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.45056	-0.9287	9	0.49607	T	0.09	.	16.6224	0.84934	0.0:0.0:1.0:0.0	.	1491	F8WD23	.	H	1492;1491	ENSP00000377197:P1492H	ENSP00000313052:P1491H	P	-	2	0	HYDIN	69572830	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.105000	0.94246	2.083000	0.62718	0.603000	0.83216	CCC	.	.	weak		0.483	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
ZNF782	158431	hgsc.bcm.edu	37	9	99581440	99581440	+	Missense_Mutation	SNP	T	T	C	rs35403084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99581440T>C	ENST00000481138.1	-	6	1526	c.865A>G	c.(865-867)Aca>Gca	p.T289A	ZNF782_ENST00000535338.1_Missense_Mutation_p.T157A|ZNF782_ENST00000466833.1_5'Flank	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	289			T -> A (in dbSNP:rs35403084).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				TTCCCTCCTGTGAGAGTTTTG	0.363													T|||	174	0.0347444	0.1278	0.0072	5008	,	,		19195	0.0		0.0	False		,,,				2504	0.0				p.T289A		Atlas-SNP	.											.	ZNF782	64	.	0			c.A865G						PASS	.	T	ALA/THR	440,3966	207.8+/-229.1	21,398,1784	84.0	88.0	86.0		865	0.7	0.0	9	dbSNP_126	86	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZNF782	NM_001001662.1	58	21,400,6082	CC,CT,TT		0.0233,9.9864,3.3984	benign	289/700	99581440	442,12564	2203	4300	6503	SO:0001583	missense	158431	exon6			CTCCTGTGAGAGT	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.865A>G	9.37:g.99581440T>C	ENSP00000419397:p.Thr289Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	92	57	0.619565	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	55|55	0.025183150183150184|0.025183150183150184	52|52	0.10569105691056911|0.10569105691056911	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	11.19|11.19	1.564629|1.564629	0.27915|0.27915	0.099864|0.099864	2.33E-4|2.33E-4	ENSG00000196597|ENSG00000196597	ENST00000289032|ENST00000481138;ENST00000535338	.|T;T	.|0.05996	.|3.5;3.36	3.29|3.29	0.74|0.74	0.18330|0.18330	.|Zinc finger, C2H2 (1);	.|1.047330	.|0.07644	.|N	.|0.930840	T|T	0.00144|0.00144	0.0004|0.0004	L|L	0.45051|0.45051	1.395|1.395	0.20821|0.20821	N|N	0.999841|0.999841	.|P	.|0.37525	.|0.598	.|B	.|0.32211	.|0.142	T|T	0.44757|0.44757	-0.9307|-0.9307	5|10	.|0.42905	.|T	.|0.14	.|.	8.5445|8.5445	0.33413|0.33413	0.0:0.0:0.3768:0.6232|0.0:0.0:0.3768:0.6232	rs35403084|rs35403084	.|289	.|Q6ZMW2	.|ZN782_HUMAN	R|A	277|289;157	.|ENSP00000419397:T289A;ENSP00000440624:T157A	.|ENSP00000419397:T289A	H|T	-|-	2|1	0|0	ZNF782|ZNF782	98621261|98621261	0.044000|0.044000	0.20184|0.20184	0.000000|0.000000	0.03702|0.03702	0.137000|0.137000	0.21094|0.21094	1.139000|1.139000	0.31504|0.31504	0.142000|0.142000	0.18901|0.18901	0.524000|0.524000	0.50904|0.50904	CAC|ACA	T|0.971;C|0.029	0.029	strong		0.363	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
MUC17	140453	hgsc.bcm.edu	37	7	100679136	100679136	+	Missense_Mutation	SNP	T	T	C	rs7780935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100679136T>C	ENST00000306151.4	+	3	4503	c.4439T>C	c.(4438-4440)gTt>gCt	p.V1480A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1480	59 X approximate tandem repeats.|Ser-rich.		V -> A (in dbSNP:rs7780935). {ECO:0000269|PubMed:9299468}.		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)					ACAACTCCTGTTGACTCTAAC	0.483													T|||	657	0.13119	0.2322	0.085	5008	,	,		25204	0.0665		0.1173	False		,,,				2504	0.1084				p.V1480A		Atlas-SNP	.											.	MUC17	804	.	0			c.T4439C						PASS	.	T	ALA/VAL	909,3497	350.0+/-310.6	93,723,1387	157.0	165.0	162.0		4439	-2.2	0.0	7	dbSNP_116	162	987,7609	213.4+/-253.3	57,873,3368	no	missense	MUC17	NM_001040105.1	64	150,1596,4755	CC,CT,TT		11.4821,20.631,14.5824	benign	1480/4494	100679136	1896,11106	2203	4298	6501	SO:0001583	missense	140453	exon3			CTCCTGTTGACTC	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.4439T>C	7.37:g.100679136T>C	ENSP00000302716:p.Val1480Ala	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	237	0.10851648351648352	87	0.17682926829268292	34	0.09392265193370165	30	0.05244755244755245	86	0.11345646437994723	t	1.397	-0.579307	0.03854	0.20631	0.114821	ENSG00000169876	ENST00000306151	T	0.02631	4.22	1.09	-2.18	0.07037	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.14438	0.01	B	0.08055	0.003	T	0.41928	-0.9481	8	0.07644	T	0.81	.	2.0054	0.03476	0.2509:0.0:0.3084:0.4408	rs7780935	1480	Q685J3	MUC17_HUMAN	A	1480	ENSP00000302716:V1480A	ENSP00000302716:V1480A	V	+	2	0	MUC17	100465856	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.010000	0.03656	-1.218000	0.02601	0.113000	0.15668	GTT	T|0.875;C|0.125	0.125	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
DMRT2	10655	hgsc.bcm.edu	37	9	1056517	1056517	+	Silent	SNP	C	C	G	rs16928356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:1056517C>G	ENST00000358146.2	+	3	930	c.930C>G	c.(928-930)acC>acG	p.T310T	DMRT2_ENST00000302441.6_Silent_p.T310T|DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000382251.3_Silent_p.T310T|DMRT2_ENST00000382255.3_3'UTR			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	310					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)		TTGATTTAACCATGCAGTATT	0.438													C|||	263	0.052516	0.1876	0.0173	5008	,	,		20652	0.0		0.003	False		,,,				2504	0.0				p.T310T		Atlas-SNP	.											.	DMRT2	70	.	0			c.C930G						PASS	.	C	,,	699,3707	291.5+/-281.6	55,589,1559	85.0	88.0	87.0		,,930	3.7	1.0	9	dbSNP_123	87	3,8597	1.2+/-3.3	0,3,4297	no	utr-3,utr-3,coding-synonymous	DMRT2	NM_001130865.2,NM_006557.6,NM_181872.4	,,	55,592,5856	GG,GC,CC		0.0349,15.8647,5.3975	,,	,,310/562	1056517	702,12304	2203	4300	6503	SO:0001819	synonymous_variant	10655	exon4			TTTAACCATGCAG	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.930C>G	9.37:g.1056517C>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Silent	SNP	ENST00000358146.2	37	CCDS6444.1																																																																																			C|0.951;G|0.049	0.049	strong		0.438	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557	
KIAA0368	23392	hgsc.bcm.edu	37	9	114146832	114146832	+	Silent	SNP	C	C	T	rs16916040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114146832C>T	ENST00000338205.5	-	33	3870	c.3651G>A	c.(3649-3651)gcG>gcA	p.A1217A	KIAA0368_ENST00000259335.4_Silent_p.A1395A|KIAA0368_ENST00000374378.3_5'UTR			Q5VYK3	ECM29_HUMAN	KIAA0368	1223					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)		p.A1395A(1)		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						CTAGTTCTGCCGCTTTTCGTA	0.403													T|||	481	0.0960463	0.1861	0.0187	5008	,	,		19176	0.1627		0.0119	False		,,,				2504	0.047				p.A1395A		Atlas-SNP	.											KIAA0368,NS,carcinoma,0,2	KIAA0368	144	2	1	Substitution - coding silent(1)	stomach(1)	c.G4185A						PASS	.	T		553,3193		43,467,1363	105.0	105.0	105.0		4185	-1.4	1.0	9	dbSNP_123	105	112,8080		0,112,3984	no	coding-synonymous	KIAA0368	NM_001080398.1		43,579,5347	TT,TC,CC		1.3672,14.7624,5.5704		1395/2018	114146832	665,11273	1873	4096	5969	SO:0001819	synonymous_variant	23392	exon35			TTCTGCCGCTTTT	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.3651G>A	9.37:g.114146832C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	135	82	0.607407	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				C|0.908;T|0.092	0.092	strong		0.403	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
DNAH5	1767	hgsc.bcm.edu	37	5	13701422	13701422	+	Missense_Mutation	SNP	G	G	T	rs113425437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13701422G>T	ENST00000265104.4	-	77	13566	c.13462C>A	c.(13462-13464)Ccc>Acc	p.P4488T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4488					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)					AATCCCTGGGGGTTAAAAAAA	0.418									Kartagener syndrome				G|||	207	0.0413339	0.149	0.0144	5008	,	,		14515	0.0		0.0	False		,,,				2504	0.0				p.P4488T		Atlas-SNP	.											.	DNAH5	868	.	0			c.C13462A						PASS	.	G	THR/PRO	586,3820	256.1+/-261.0	32,522,1649	77.0	84.0	82.0		13462	4.9	1.0	5	dbSNP_132	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DNAH5	NM_001369.2	38	32,523,5948	TT,TG,GG		0.0116,13.3,4.5133	probably-damaging	4488/4625	13701422	587,12419	2203	4300	6503	SO:0001583	missense	1767	exon77	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCTGGGGGTTAAA	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.13462C>A	5.37:g.13701422G>T	ENSP00000265104:p.Pro4488Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	73	41	0.561644	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	58	0.026556776556776556	53	0.10772357723577236	5	0.013812154696132596	0	0.0	0	0.0	G	24.4	4.523833	0.85600	0.133	1.16E-4	ENSG00000039139	ENST00000265104	T	0.16196	2.36	5.78	4.91	0.64330	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.00440	0.0014	M	0.67953	2.075	0.80722	D	1	D	0.55385	0.971	D	0.73708	0.981	T	0.00011	-1.2433	10	0.87932	D	0	.	14.6237	0.68605	0.0697:0.0:0.9303:0.0	.	4488	Q8TE73	DYH5_HUMAN	T	4488	ENSP00000265104:P4488T	ENSP00000265104:P4488T	P	-	1	0	DNAH5	13754422	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.987000	0.88182	1.454000	0.47793	0.591000	0.81541	CCC	G|0.961;T|0.039	0.039	strong		0.418	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
MZT2A	653784	hgsc.bcm.edu	37	2	132241731	132241731	+	Missense_Mutation	SNP	T	T	C	rs75021268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:132241731T>C	ENST00000309451.6	-	3	425	c.380A>G	c.(379-381)cAc>cGc	p.H127R	MZT2A_ENST00000410036.2_5'UTR	NM_001085365.1	NP_001078834.1	Q6P582	MZT2A_HUMAN	mitotic spindle organizing protein 2A	127						centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				breast(1)|lung(1)	2						GGATCCCTCGTGGTTGCTGCG	0.642													.|||	841	0.167931	0.4607	0.1037	5008	,	,		16385	0.004		0.0924	False		,,,				2504	0.0644				p.H127R		Atlas-SNP	.											.	MZT2A	6	.	0			c.A380G						PASS	.	C	ARG/HIS	1790,2616	600.5+/-389.5	380,1030,793	52.0	64.0	60.0		380	1.3	0.0	2	dbSNP_131	60	788,7812	769.9+/-407.6	41,706,3553	no	missense	MZT2A	NM_001085365.1	29	421,1736,4346	CC,CT,TT		9.1628,40.6264,19.8216	benign	127/159	132241731	2578,10428	2203	4300	6503	SO:0001583	missense	653784	exon3			CCCTCGTGGTTGC	BC018206	CCDS42758.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000173272	ENSG00000173272			33187	protein-coding gene	gene with protein product	"""mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A"""	613449	"""family with sequence similarity 128, member A"""	FAM128A		20360068	Standard	NM_001085365		Approved	MOZART2A	uc002tsw.4	Q6P582	OTTHUMG00000153606	ENST00000309451.6:c.380A>G	2.37:g.132241731T>C	ENSP00000311500:p.His127Arg	Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	271	137	0.505535	NM_001085365	Q3SWV8|Q8WVB2	Missense_Mutation	SNP	ENST00000309451.6	37	CCDS42758.1	338	0.15476190476190477	236	0.4796747967479675	39	0.10773480662983426	2	0.0034965034965034965	61	0.08047493403693931	c	0.001	-3.004465	0.00044	0.406264	0.091628	ENSG00000173272	ENST00000309451	T	0.17691	2.26	2.23	1.32	0.21799	.	0.121674	0.52532	N	0.000065	T	0.00012	0.0000	N	0.00159	-1.955	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44003	-0.9356	9	0.02654	T	1	-6.1763	6.2716	0.20956	0.0:0.7112:0.0:0.2888	.	127	Q6P582	MZT2A_HUMAN	R	127	ENSP00000311500:H127R	ENSP00000311500:H127R	H	-	2	0	MZT2A	131958201	0.962000	0.33011	0.044000	0.18714	0.006000	0.05464	2.095000	0.41729	-0.092000	0.12417	-1.160000	0.01791	CAC	T|0.872;C|0.128	0.128	strong		0.642	MZT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331811.2		
MOB3C	148932	hgsc.bcm.edu	37	1	47080741	47080741	+	Intron	SNP	C	C	T	rs12029680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47080741C>T	ENST00000319928.3	-	1	181				MOB3C_ENST00000477318.1_Intron|MOB3C_ENST00000371940.1_5'UTR|MOB3C_ENST00000271139.8_Missense_Mutation_p.R3H|MKNK1_ENST00000545730.1_Intron	NM_201403.2	NP_958805.1	Q70IA8	MOB3C_HUMAN	MOB kinase activator 3C								metal ion binding (GO:0046872)										GAGATTTCTGCGCTTCATTTG	0.517													C|||	1674	0.334265	0.5272	0.3516	5008	,	,		15350	0.246		0.2684	False		,,,				2504	0.2198				p.R3H		Atlas-SNP	.											.	MOB3C	1	.	0			c.G8A						PASS	.	C	HIS/ARG,	2141,2265	580.9+/-385.2	522,1097,584	67.0	67.0	67.0		8,	-6.2	0.0	1	dbSNP_120	67	2178,6422	371.8+/-336.4	255,1668,2377	yes	missense,intron	MOB3C	NM_145279.4,NM_201403.2	29,	777,2765,2961	TT,TC,CC		25.3256,48.5928,33.2078	,	3/269,	47080741	4319,8687	2203	4300	6503	SO:0001627	intron_variant	148932	exon1			TTTCTGCGCTTCA	AK091808	CCDS539.1, CCDS540.1	1p34.1	2011-09-28	2011-09-28	2011-09-28	ENSG00000142961	ENSG00000142961		"""MOB kinase activators"""	29800	protein-coding gene	gene with protein product			"""MOB1, Mps One Binder kinase activator-like 2C (yeast)"""	MOBKL2C		12477932	Standard	NM_145279		Approved	MOB1E	uc001cqe.4	Q70IA8	OTTHUMG00000007989	ENST00000319928.3:c.49+1641G>A	1.37:g.47080741C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	149	62	0.416107	NM_145279	D3DQ22|Q0VA98|Q5TC10|Q5TC11|Q8NAZ2|Q8NF28	Missense_Mutation	SNP	ENST00000319928.3	37	CCDS540.1	717	0.3282967032967033	248	0.5040650406504065	134	0.3701657458563536	146	0.25524475524475526	189	0.24934036939313983	C	9.051	0.992086	0.18966	0.485928	0.253256	ENSG00000142961	ENST00000271139	.	.	.	3.12	-6.24	0.02046	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.22977	-1.0201	4	0.87932	D	0	.	9.3601	0.38190	0.0:0.1714:0.1148:0.7139	rs12029680;rs52809751;rs60956522;rs12029680	.	.	.	H	3	.	ENSP00000271139:R3H	R	-	2	0	MOBKL2C	46853328	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.176000	0.00571	-2.577000	0.00464	-0.743000	0.03520	CGC	C|0.666;T|0.334	0.334	strong		0.517	MOB3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145279	
NLRP14	338323	hgsc.bcm.edu	37	11	7064457	7064457	+	Silent	SNP	T	T	C	rs76429148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7064457T>C	ENST00000299481.4	+	4	1546	c.1200T>C	c.(1198-1200)ttT>ttC	p.F400F		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	400	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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)		CAGCTCTGTTTACCTGCTATA	0.512													T|||	276	0.0551118	0.1483	0.0389	5008	,	,		20476	0.0		0.0249	False		,,,				2504	0.0286				p.F400F		Atlas-SNP	.											.	NLRP14	187	.	0			c.T1200C						PASS	.	T		620,3782	268.9+/-268.7	58,504,1639	150.0	144.0	146.0		1200	-0.5	0.0	11	dbSNP_132	146	315,8277	112.1+/-172.3	5,305,3986	no	coding-synonymous	NLRP14	NM_176822.3		63,809,5625	CC,CT,TT		3.6662,14.0845,7.1956		400/1094	7064457	935,12059	2201	4296	6497	SO:0001819	synonymous_variant	338323	exon4			TCTGTTTACCTGC	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.1200T>C	11.37:g.7064457T>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	147	65	0.442177	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	37	CCDS7776.1																																																																																			T|0.938;C|0.062	0.062	strong		0.512	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
OR8K1	390157	hgsc.bcm.edu	37	11	56113923	56113923	+	Silent	SNP	C	C	T	rs61745885	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56113923C>T	ENST00000279783.2	+	1	503	c.409C>T	c.(409-411)Ctg>Ttg	p.L137L		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	137						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L137M(1)		large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					TAAACCTCTTCTGTACGTGAT	0.403										HNSCC(65;0.19)			C|||	35	0.00698882	0.0242	0.0029	5008	,	,		21543	0.0		0.001	False		,,,				2504	0.0				p.L137L		Atlas-SNP	.											OR8K1,shoulder,malignant_melanoma,0,1	OR8K1	93	1	1	Substitution - Missense(1)	skin(1)	c.C409T						PASS	.	C		108,4294	83.4+/-121.9	2,104,2095	213.0	211.0	211.0		409	3.1	0.9	11	dbSNP_129	211	3,8589	2.2+/-6.3	0,3,4293	no	coding-synonymous	OR8K1	NM_001002907.1		2,107,6388	TT,TC,CC		0.0349,2.4534,0.8542		137/320	56113923	111,12883	2201	4296	6497	SO:0001819	synonymous_variant	390157	exon1			CCTCTTCTGTACG	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.409C>T	11.37:g.56113923C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Silent	SNP	ENST00000279783.2	37	CCDS31528.1																																																																																			C|0.993;T|0.007	0.007	strong		0.403	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
LNP1	348801	hgsc.bcm.edu	37	3	100170634	100170634	+	Silent	SNP	T	T	C	rs9848109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.						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	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	118	18	0.152542	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		
MCM2	4171	hgsc.bcm.edu	37	3	127340583	127340583	+	Silent	SNP	C	C	T	rs6794323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127340583C>T	ENST00000265056.7	+	16	2926	c.2682C>T	c.(2680-2682)gaC>gaT	p.D894D	MCM2_ENST00000468414.1_3'UTR	NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	894					cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						TCAGCCACGACCTGAAAAGGA	0.498													C|||	319	0.0636981	0.2269	0.0231	5008	,	,		22127	0.0		0.003	False		,,,				2504	0.0				p.D894D		Atlas-SNP	.											.	MCM2	79	.	0			c.C2682T						PASS	.	C		764,3642	311.1+/-291.9	56,652,1495	99.0	93.0	95.0		2682	4.5	1.0	3	dbSNP_116	95	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	MCM2	NM_004526.2		56,660,5787	TT,TC,CC		0.093,17.34,5.9357		894/905	127340583	772,12234	2203	4300	6503	SO:0001819	synonymous_variant	4171	exon16			CCACGACCTGAAA	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"""mitotin"""	116945	"""minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)"", ""MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"""	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.2682C>T	3.37:g.127340583C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Silent	SNP	ENST00000265056.7	37	CCDS3043.1	133	0.060897435897435896	124	0.25203252032520324	9	0.024861878453038673	0	0.0	0	0.0	C	2.284	-0.364112	0.05103	0.1734	9.3E-4	ENSG00000073111	ENST00000491422	.	.	.	5.38	4.5	0.54988	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.23013	-1.0200	3	.	.	.	-47.6264	6.5614	0.22489	0.0:0.6888:0.0:0.3112	rs6794323;rs17538760;rs56589702;rs6794323	.	.	.	I	826	.	.	T	+	2	0	MCM2	128823273	1.000000	0.71417	0.993000	0.49108	0.308000	0.27856	1.539000	0.36104	1.263000	0.44181	0.313000	0.20887	ACC	C|0.930;T|0.070	0.070	strong		0.498	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1		
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24250809	24250809	+	Missense_Mutation	SNP	T	T	C	rs77012108	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24250809T>C	ENST00000256412.4	+	3	462	c.242T>C	c.(241-243)aTc>aCc	p.I81T	ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.I2T|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.I2T|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	81					immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TATCAGATGATCTTAAATGGA	0.303													t|||	120	0.0239617	0.087	0.0072	5008	,	,		16054	0.0		0.0	False		,,,				2504	0.0				p.I81T	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											ADAMDEC1,arm,malignant_melanoma,-1,1	ADAMDEC1	69	1	0			c.T242C						PASS	.	C	THR/ILE,THR/ILE,THR/ILE	356,4050	176.6+/-205.7	19,318,1866	64.0	68.0	66.0		5,5,242	-10.9	0.0	8	dbSNP_131	66	2,8594	2.2+/-6.3	0,2,4296	yes	missense,missense,missense	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	89,89,89	19,320,6162	CC,CT,TT		0.0233,8.0799,2.7534	benign,benign,benign	2/392,2/392,81/471	24250809	358,12644	2203	4298	6501	SO:0001583	missense	27299	exon3			AGATGATCTTAAA	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.242T>C	8.37:g.24250809T>C	ENSP00000256412:p.Ile81Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	127	68	0.535433	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	t	0.013	-1.643647	0.00792	0.080799	2.33E-4	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.04758	3.56;4.16;4.16	5.47	-10.9	0.00192	Peptidase M12B, propeptide (1);	1.393200	0.04190	N	0.328203	T	0.00144	0.0004	N	0.10837	0.055	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.41088	-0.9528	10	0.09843	T	0.71	0.1711	6.3932	0.21599	0.0997:0.5309:0.2221:0.1472	.	81	O15204	ADEC1_HUMAN	T	81;2;2	ENSP00000256412:I81T;ENSP00000442592:I2T;ENSP00000428993:I2T	ENSP00000256412:I81T	I	+	2	0	ADAMDEC1	24306754	0.000000	0.05858	0.001000	0.08648	0.254000	0.26022	-2.948000	0.00679	-1.756000	0.01318	-0.359000	0.07587	ATC	T|0.973;C|0.027	0.027	strong		0.303	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
TPPP3	51673	hgsc.bcm.edu	37	16	67424122	67424122	+	Silent	SNP	G	G	A	rs11552319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67424122G>A	ENST00000564104.1	-	3	1327	c.486C>T	c.(484-486)agC>agT	p.S162S	RNU1-123P_ENST00000458950.1_RNA|TPPP3_ENST00000290942.5_Silent_p.S162S|TPPP3_ENST00000393957.2_Silent_p.S162S|TPPP3_ENST00000562206.1_Silent_p.S162S			Q9BW30	TPPP3_HUMAN	tubulin polymerization-promoting protein family member 3	162					microtubule bundle formation (GO:0001578)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	tubulin binding (GO:0015631)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0336)|Epithelial(162;0.0781)		TCTTGTAGGCGCTCACGTAGC	0.627													g|||	477	0.0952476	0.2413	0.0504	5008	,	,		18160	0.003		0.0388	False		,,,				2504	0.0828				p.S162S		Atlas-SNP	.											.	TPPP3	13	.	0			c.C486T						PASS	.		,	890,3506	343.8+/-307.8	91,708,1399	109.0	85.0	93.0		486,486	0.6	1.0	16	dbSNP_120	93	354,8246	119.2+/-178.6	9,336,3955	no	coding-synonymous,coding-synonymous	TPPP3	NM_015964.2,NM_016140.2	,	100,1044,5354	AA,AG,GG		4.1163,20.2457,9.5722	,	162/177,162/177	67424122	1244,11752	2198	4300	6498	SO:0001819	synonymous_variant	51673	exon5			GTAGGCGCTCACG	BC000691	CCDS10835.1	16q22.1	2008-02-05			ENSG00000159713	ENSG00000159713			24162	protein-coding gene	gene with protein product						15590652, 17105200	Standard	XM_005255979		Approved	CGI-38, p25gamma, p20	uc002etb.3	Q9BW30	OTTHUMG00000137516	ENST00000564104.1:c.486C>T	16.37:g.67424122G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	NM_016140	Q49AH9|Q9Y326|Q9Y6H0	Silent	SNP	ENST00000564104.1	37	CCDS10835.1																																																																																			G|0.897;A|0.103	0.103	strong		0.627	TPPP3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421787.2	NM_015964	
VWF	7450	hgsc.bcm.edu	37	12	6103281	6103281	+	Silent	SNP	A	A	T	rs11537642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6103281A>T	ENST00000261405.5	-	37	6599	c.6345T>A	c.(6343-6345)acT>acA	p.T2115T		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2115	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GCCGCTGCACAGTCCATTCCT	0.557													A|||	277	0.0553115	0.1982	0.0202	5008	,	,		20224	0.0		0.001	False		,,,				2504	0.0				p.T2115T		Atlas-SNP	.											.	VWF	338	.	0			c.T6345A						PASS	.	A		660,3746	280.2+/-275.2	55,550,1598	94.0	79.0	84.0		6345	-10.3	0.0	12	dbSNP_120	84	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	VWF	NM_000552.3		55,554,5894	TT,TA,AA		0.0465,14.9796,5.1053		2115/2814	6103281	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon37			CTGCACAGTCCAT		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.6345T>A	12.37:g.6103281A>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	88	36	0.409091	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			A|0.955;T|0.045	0.045	strong		0.557	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
EEF2	1938	hgsc.bcm.edu	37	19	3980852	3980852	+	Silent	SNP	G	G	A	rs140573073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3980852G>A	ENST00000309311.6	-	8	1225	c.1137C>T	c.(1135-1137)gaC>gaT	p.D379D	EEF2_ENST00000600720.1_5'Flank|SNORD37_ENST00000384048.1_RNA	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	379					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)		TGGCAGCCTCGTCGTCCGGGG	0.652													G|||	14	0.00279553	0.0106	0.0	5008	,	,		15721	0.0		0.0	False		,,,				2504	0.0				p.D379D	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											.	EEF2	57	.	0			c.C1137T						PASS	.	G		39,4347		0,39,2154	13.0	11.0	12.0		1137	-7.7	0.6	19	dbSNP_134	12	0,8556		0,0,4278	no	coding-synonymous	EEF2	NM_001961.3		0,39,6432	AA,AG,GG		0.0,0.8892,0.3013		379/859	3980852	39,12903	2193	4278	6471	SO:0001819	synonymous_variant	1938	exon8			AGCCTCGTCGTCC	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.1137C>T	19.37:g.3980852G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_001961	B2RMP5|D6W618|Q58J86	Silent	SNP	ENST00000309311.6	37	CCDS12117.1																																																																																			G|0.997;A|0.003	0.003	strong		0.652	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961	
CCDC130	81576	hgsc.bcm.edu	37	19	13875453	13875453	+	IGR	SNP	C	C	T	rs141796284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13875453C>T	ENST00000586600.1	+	0	1922				MRI1_ENST00000319545.8_Silent_p.D17D|MRI1_ENST00000040663.6_Silent_p.D17D			P13994	CC130_HUMAN	coiled-coil domain containing 130						response to virus (GO:0009615)					endometrium(2)|kidney(1)|large_intestine(3)|ovary(1)|skin(2)|urinary_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)			AGATCCTAGACCAGCTGCTGC	0.706													C|||	22	0.00439297	0.0159	0.0014	5008	,	,		6970	0.0		0.0	False		,,,				2504	0.0				p.D17D		Atlas-SNP	.											.	MRI1	35	.	0			c.C51T						PASS	.	C	,	91,4295		0,91,2102	24.0	27.0	26.0		51,51	4.1	1.0	19	dbSNP_134	26	1,8565		0,1,4282	no	coding-synonymous,coding-synonymous	MRI1	NM_001031727.2,NM_032285.2	,	0,92,6384	TT,TC,CC		0.0117,2.0748,0.7103	,	17/370,17/323	13875453	92,12860	2193	4283	6476	SO:0001628	intergenic_variant	84245	exon1			CCTAGACCAGCTG	AF250306	CCDS12296.1	19p13.13	2008-02-05				ENSG00000104957			28118	protein-coding gene	gene with protein product						3203696	Standard	NM_030818		Approved	MGC10471	uc002mxc.1	P13994			19.37:g.13875453C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	48	0.390244	NM_001031727	Q9BQ72	Silent	SNP	ENST00000586600.1	37	CCDS12296.1																																																																																			C|0.993;T|0.007	0.007	strong		0.706	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818	
PLEKHA6	22874	hgsc.bcm.edu	37	1	204199614	204199614	+	Missense_Mutation	SNP	C	C	T	rs10900562	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204199614C>T	ENST00000272203.3	-	18	2826	c.2510G>A	c.(2509-2511)aGg>aAg	p.R837K	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.R857K	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	837			R -> K (in dbSNP:rs10900562). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15489334}.							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)			CCGCTTCTCCCTCATGGAGCC	0.652													T|||	2557	0.510583	0.6914	0.5375	5008	,	,		13874	0.4802		0.4334	False		,,,				2504	0.3579				p.R837K		Atlas-SNP	.											PLEKHA6,colon,carcinoma,0,1	PLEKHA6	115	1	0			c.G2510A						PASS	.	T	LYS/ARG	2895,1507		980,935,286	22.0	21.0	22.0		2510	2.9	1.0	1	dbSNP_120	22	3909,4671		909,2091,1290	yes	missense	PLEKHA6	NM_014935.2	26	1889,3026,1576	TT,TC,CC		45.5594,34.2344,47.589	benign	837/1049	204199614	6804,6178	2201	4290	6491	SO:0001583	missense	22874	exon18			TTCTCCCTCATGG	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.2510G>A	1.37:g.204199614C>T	ENSP00000272203:p.Arg837Lys	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	165	161	0.975758	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	1131	0.5178571428571429	332	0.6747967479674797	193	0.5331491712707183	277	0.48426573426573427	329	0.4340369393139842	T	9.062	0.994763	0.19043	0.657656	0.455594	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.22743	1.94;2.4	5.24	2.91	0.33838	.	0.157126	0.56097	N	0.000034	T	0.00012	0.0000	N	0.10972	0.075	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.30707	-0.9969	9	0.15499	T	0.54	-21.9669	9.0092	0.36131	0.0:0.216:0.0:0.7839	rs10900562;rs58953574;rs10900562	837	Q9Y2H5	PKHA6_HUMAN	K	837;857	ENSP00000272203:R837K;ENSP00000402046:R857K	ENSP00000272203:R837K	R	-	2	0	PLEKHA6	202466237	1.000000	0.71417	0.999000	0.59377	0.790000	0.44656	3.200000	0.51051	0.026000	0.15269	-1.390000	0.01156	AGG	C|0.466;T|0.534	0.534	strong		0.652	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
ENGASE	64772	hgsc.bcm.edu	37	17	77079576	77079576	+	Silent	SNP	A	A	G	rs61756761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77079576A>G	ENST00000579016.1	+	9	1155	c.1155A>G	c.(1153-1155)cgA>cgG	p.R385R	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	385						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						TCTGGGGCCGACTGGAGCGTT	0.612													G|||	682	0.136182	0.357	0.0677	5008	,	,		20375	0.0476		0.0577	False		,,,				2504	0.0583				p.R385R		Atlas-SNP	.											ENGASE,NS,carcinoma,+1,1	ENGASE	55	1	0			c.A1155G						PASS	.	G		1152,3078		150,852,1113	92.0	102.0	99.0		1155	5.5	0.9	17	dbSNP_129	99	481,7973		9,463,3755	no	coding-synonymous	ENGASE	NM_001042573.1		159,1315,4868	GG,GA,AA		5.6896,27.234,12.8745		385/744	77079576	1633,11051	2115	4227	6342	SO:0001819	synonymous_variant	64772	exon9			GGGCCGACTGGAG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1155A>G	17.37:g.77079576A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	169	86	0.508876	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			A|0.902;G|0.098	0.098	strong		0.612	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
FBN2	2201	hgsc.bcm.edu	37	5	127873114	127873114	+	Silent	SNP	G	G	C	rs73348287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:127873114G>C	ENST00000508053.1	-	7	1157	c.183C>G	c.(181-183)ccC>ccG	p.P61P	FBN2_ENST00000508989.1_Silent_p.P61P|FBN2_ENST00000262464.4_Silent_p.P61P			P35556	FBN2_HUMAN	fibrillin 2	61					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)		CGCGATACTCGGGCGCTAGAA	0.721													G|||	498	0.0994409	0.2133	0.0576	5008	,	,		11323	0.005		0.0845	False		,,,				2504	0.0879				p.P61P		Atlas-SNP	.											.	FBN2	858	.	0			c.C183G						PASS	.	G		745,3649		71,603,1523	17.0	20.0	19.0		183	-8.2	0.1	5	dbSNP_130	19	742,7852		39,664,3594	no	coding-synonymous	FBN2	NM_001999.3		110,1267,5117	CC,CG,GG		8.6339,16.9549,11.449		61/2913	127873114	1487,11501	2197	4297	6494	SO:0001819	synonymous_variant	2201	exon1			ATACTCGGGCGCT	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.183C>G	5.37:g.127873114G>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			G|0.894;C|0.106	0.106	strong		0.721	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
ZNF763	284390	hgsc.bcm.edu	37	19	12089903	12089903	+	Silent	SNP	G	G	A	rs112017572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12089903G>A	ENST00000358987.3	+	4	1291	c.1164G>A	c.(1162-1164)gcG>gcA	p.A388A	ZNF763_ENST00000343949.5_Silent_p.A391A|ZNF763_ENST00000538752.1_Silent_p.A408A|ZNF763_ENST00000590798.1_Silent_p.A408A|ZNF763_ENST00000545530.1_Silent_p.A266A			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	388					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)	p.A390A(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						CTAAGAATGCGCTCTGGAGAA	0.393													a|||	398	0.0794728	0.2103	0.0317	5008	,	,		22553	0.0218		0.0378	False		,,,				2504	0.0389				p.A391A		Atlas-SNP	.											ZNF763,caecum,carcinoma,+2,3	ZNF763	31	3	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G1173A						PASS	.	A		819,3565	683.6+/-404.3	81,657,1454	59.0	65.0	63.0		1173	1.4	0.0	19	dbSNP_132	63	256,8336	789.1+/-407.6	3,250,4043	no	coding-synonymous	ZNF763	NM_001012753.1		84,907,5497	AA,AG,GG		2.9795,18.6816,8.2845		391/398	12089903	1075,11901	2192	4296	6488	SO:0001819	synonymous_variant	284390	exon4			GAATGCGCTCTGG	AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"""Zinc fingers, C2H2-type"", ""-"""	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.1164G>A	19.37:g.12089903G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	40	26	0.65	NM_001012753	B3KRU3|B4DRE7	Silent	SNP	ENST00000358987.3	37																																																																																				G|0.941;A|0.059	0.059	strong		0.393	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753	
MEGF8	1954	hgsc.bcm.edu	37	19	42853782	42853782	+	Silent	SNP	T	T	C	rs28621009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42853782T>C	ENST00000251268.6	+	14	2430	c.2430T>C	c.(2428-2430)aaT>aaC	p.N810N	MEGF8_ENST00000334370.4_Silent_p.N743N	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	810					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				GCCAGCTCAATGGCTCGGCAG	0.647													C|||	833	0.166334	0.354	0.1254	5008	,	,		15678	0.0645		0.0586	False		,,,				2504	0.1575				p.N810N		Atlas-SNP	.											.	MEGF8	358	.	0			c.T2430C						PASS	.	C		1445,2961	674.5+/-402.9	241,963,999	60.0	62.0	62.0		2229	-9.1	0.5	19	dbSNP_125	62	471,8129	794.0+/-407.5	12,447,3841	no	coding-synonymous	MEGF8	NM_001410.2		253,1410,4840	CC,CT,TT		5.4767,32.7962,14.7317		743/2779	42853782	1916,11090	2203	4300	6503	SO:0001819	synonymous_variant	1954	exon14			GCTCAATGGCTCG	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.2430T>C	19.37:g.42853782T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																				T|0.835;C|0.165	0.165	strong		0.647	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
DDX27	55661	hgsc.bcm.edu	37	20	47849904	47849904	+	Missense_Mutation	SNP	C	C	T	rs145681733		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47849904C>T	ENST00000371764.4	+	10	1195	c.1186C>T	c.(1186-1188)Cgc>Tgc	p.R396C	DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	396	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TTCCCACCACCGCCAGACCAT	0.582																																					p.R396C		Atlas-SNP	.											.	DDX27	74	.	0			c.C1186T						PASS	.	C	CYS/ARG	0,4406		0,0,2203	87.0	69.0	75.0		1186	6.0	1.0	20	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense	DDX27	NM_017895.7	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	396/797	47849904	1,13005	2203	4300	6503	SO:0001583	missense	55661	exon10			CACCACCGCCAGA	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.1186C>T	20.37:g.47849904C>T	ENSP00000360828:p.Arg396Cys	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.700821	0.88924	0.0	1.16E-4	ENSG00000124228	ENST00000371764	T	0.49432	0.78	5.97	5.97	0.96955	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71929	0.3398	M	0.81614	2.55	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74234	-0.3731	10	0.87932	D	0	-14.1308	17.9218	0.88969	0.0:1.0:0.0:0.0	.	396	Q96GQ7	DDX27_HUMAN	C	396	ENSP00000360828:R396C	ENSP00000360828:R396C	R	+	1	0	DDX27	47283311	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.548000	0.53670	2.837000	0.97791	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	weak		0.582	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		
C7orf71	285941	hgsc.bcm.edu	37	7	26678881	26678881	+	Missense_Mutation	SNP	G	G	A	rs78525926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:26678881G>A	ENST00000409974.3	+	2	834	c.118G>A	c.(118-120)Ggc>Agc	p.G40S		NM_001145531.1	NP_001139003.1	A4D174	CG071_HUMAN	chromosome 7 open reading frame 71	40																	gagacaaggcggctacctgca	0.537													G|||	197	0.0393371	0.1377	0.013	5008	,	,		16554	0.004		0.002	False		,,,				2504	0.0				p.G40S		Atlas-SNP	.											.	C7orf71	6	.	0			c.G118A						PASS	.	G	SER/GLY	155,1229		13,129,550	62.0	81.0	75.0		118	-0.7	0.0	7	dbSNP_132	75	3,3179		0,3,1588	yes	missense	C7orf71	NM_001145531.1	56	13,132,2138	AA,AG,GG		0.0943,11.1994,3.4604	possibly-damaging	40/170	26678881	158,4408	692	1591	2283	SO:0001583	missense	285941	exon2			CAAGGCGGCTACC		CCDS47565.1	7p15.2	2009-09-11			ENSG00000222004	ENSG00000222004			22364	protein-coding gene	gene with protein product							Standard	NM_001145531		Approved		uc003syb.3	A4D174	OTTHUMG00000152860	ENST00000409974.3:c.118G>A	7.37:g.26678881G>A	ENSP00000386749:p.Gly40Ser	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_001145531		Missense_Mutation	SNP	ENST00000409974.3	37	CCDS47565.1	65	0.02976190476190476	59	0.11991869918699187	4	0.011049723756906077	2	0.0034965034965034965	0	0.0	g	6.292	0.421888	0.11928	0.111994	9.43E-4	ENSG00000222004	ENST00000409974	.	.	.	0.374	-0.714	0.11219	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	P	0.39404	0.672	B	0.18871	0.023	T	0.29274	-1.0017	7	0.28530	T	0.3	.	.	.	.	.	40	A4D174	CG071_HUMAN	S	40	.	ENSP00000386749:G40S	G	+	1	0	C7orf71	26645406	0.022000	0.18835	0.013000	0.15412	0.012000	0.07955	-0.172000	0.09868	-0.482000	0.06782	-0.478000	0.04885	GGC	G|0.964;A|0.036	0.036	strong		0.537	C7orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328272.1	NM_001145531	
ATP6AP2	10159	hgsc.bcm.edu	37	X	40464822	40464822	+	Missense_Mutation	SNP	G	G	C	rs35798522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40464822G>C	ENST00000378438.4	+	9	1026	c.868G>C	c.(868-870)Gca>Cca	p.A290P	ATP6AP2_ENST00000535539.1_Missense_Mutation_p.A258P|ATP6AP2_ENST00000535777.1_Missense_Mutation_p.A212P|ATP6AP2_ENST00000544975.1_Missense_Mutation_p.A214P	NM_005765.2	NP_005756.2	O75787	RENR_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 2	290			A -> P (in dbSNP:rs35798522).		angiotensin maturation (GO:0002003)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|eye pigmentation (GO:0048069)|head morphogenesis (GO:0060323)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of Wnt signaling pathway (GO:0030177)|proteolysis (GO:0006508)|regulation of MAPK cascade (GO:0043408)|rostrocaudal neural tube patterning (GO:0021903)	cell body (GO:0044297)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(2)	4						GAAGAACCCAGCAAGTCCCTA	0.343													G|||	83	0.0219868	0.0613	0.0029	3775	,	,		13663	0.0		0.0	False		,,,				2504	0.0				p.A290P		Atlas-SNP	.											.	ATP6AP2	45	.	0			c.G868C						PASS	.	G	PRO/ALA	239,3596		5,190,39,1437,532	61.0	57.0	58.0		868	-8.4	0.0	X	dbSNP_126	58	0,6726		0,0,0,2427,1872	yes	missense	ATP6AP2	NM_005765.2	27	5,190,39,3864,2404	CC,CG,C,GG,G		0.0,6.2321,2.263	benign	290/351	40464822	239,10322	2203	4299	6502	SO:0001583	missense	10159	exon9			AACCCAGCAAGTC	AF248966	CCDS14252.1	Xp11.4	2014-06-17	2003-08-28	2003-08-29	ENSG00000182220	ENSG00000182220			18305	protein-coding gene	gene with protein product	"""prorenin receptor"", ""renin receptor"""	300556	"""ATPase, H+ transporting, lysosomal interacting protein 2"""	ATP6IP2		9556572, 11590366	Standard	NM_005765		Approved	M8-9, APT6M8-9, ATP6M8-9, PRR, RENR	uc004det.3	O75787	OTTHUMG00000024103	ENST00000378438.4:c.868G>C	X.37:g.40464822G>C	ENSP00000367697:p.Ala290Pro	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_005765	B7Z9I3|Q5QTQ7|Q6T7F5|Q8NBP3|Q8NG15|Q96FV6|Q96LB5|Q9H2P8|Q9UG89	Missense_Mutation	SNP	ENST00000378438.4	37	CCDS14252.1	29|29	0.017480409885473176|0.017480409885473176	19|19	0.04025423728813559|0.04025423728813559	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	14.15|14.15	2.450072|2.450072	0.43531|0.43531	0.062321|0.062321	0.0|0.0	ENSG00000182220|ENSG00000182220	ENST00000535539;ENST00000378438;ENST00000544975;ENST00000535777|ENST00000423649	T;T;T;T|.	0.45276|.	0.9;0.9;0.9;0.9|.	5.65|5.65	-8.41|-8.41	0.00961|0.00961	.|.	1.054090|.	0.07412|.	N|.	0.892481|.	T|T	0.00845|0.00845	0.0028|0.0028	N|N	0.03608|0.03608	-0.345|-0.345	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.29531|.	0.0;0.0;0.0;0.247|.	B;B;B;B|.	0.32289|.	0.0;0.002;0.0;0.143|.	T|T	0.15263|0.15263	-1.0443|-1.0443	9|4	0.28530|.	T|.	0.3|.	-34.4303|-34.4303	1.913|1.913	0.03291|0.03291	0.1093:0.2223:0.4974:0.171|0.1093:0.2223:0.4974:0.171	rs35798522|rs35798522	212;258;214;290|.	B7Z1I9;B7Z9I3;B7Z413;O75787|.	.;.;.;RENR_HUMAN|.	P|T	258;290;214;212|230	ENSP00000438415:A258P;ENSP00000367697:A290P;ENSP00000440459:A214P;ENSP00000441536:A212P|.	ENSP00000367697:A290P|.	A|S	+|+	1|2	0|0	ATP6AP2|ATP6AP2	40349766|40349766	0.019000|0.019000	0.18553|0.18553	0.000000|0.000000	0.03702|0.03702	0.689000|0.689000	0.40095|0.40095	1.088000|1.088000	0.30877|0.30877	-3.069000|-3.069000	0.00254|0.00254	0.600000|0.600000	0.82982|0.82982	GCA|AGC	G|0.977;C|0.023	0.023	strong		0.343	ATP6AP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060679.1	NM_005765	
ORM2	5005	hgsc.bcm.edu	37	9	117094200	117094200	+	Silent	SNP	C	C	T	rs1826232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117094200C>T	ENST00000431067.2	+	5	567	c.531C>T	c.(529-531)gaC>gaT	p.D177D	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	177					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	TGTACACCGACTGGAAAAAGG	0.567													T|||	747	0.149161	0.4894	0.0403	5008	,	,		18828	0.0605		0.002	False		,,,				2504	0.0092				p.D177D	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											ORM2,face,carcinoma,-2,1	ORM2	13	1	0			c.C531T						PASS	.	T		1790,2616	641.6+/-397.5	383,1024,796	92.0	92.0	92.0		531	-4.5	0.0	9	dbSNP_92	92	20,8580	818.0+/-406.9	0,20,4280	no	coding-synonymous	ORM2	NM_000608.2		383,1044,5076	TT,TC,CC		0.2326,40.6264,13.9167		177/202	117094200	1810,11196	2203	4300	6503	SO:0001819	synonymous_variant	5005	exon5			CACCGACTGGAAA		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.531C>T	9.37:g.117094200C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	160	49	0.30625	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Silent	SNP	ENST00000431067.2	37	CCDS6804.1																																																																																			C|0.873;T|0.127	0.127	strong		0.567	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
CSRP2BP	57325	hgsc.bcm.edu	37	20	18142564	18142564	+	Silent	SNP	A	A	G	rs3828013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:18142564A>G	ENST00000435364.3	+	5	1124	c.783A>G	c.(781-783)aaA>aaG	p.K261K	CSRP2BP_ENST00000377681.3_Silent_p.K260K|CSRP2BP_ENST00000489634.2_Silent_p.K133K	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	261					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)	p.K261K(2)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						TAAAAGAGAAAAGGTCTCGAA	0.443													A|||	590	0.117812	0.0446	0.1455	5008	,	,		18468	0.1349		0.1302	False		,,,				2504	0.1667				p.K261K		Atlas-SNP	.											CSRP2BP,NS,carcinoma,0,2	CSRP2BP	80	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.A783G						PASS	.	A		317,4089	160.3+/-192.7	17,283,1903	119.0	138.0	132.0		783	-1.0	0.9	20	dbSNP_107	132	1067,7533	219.9+/-257.8	71,925,3304	no	coding-synonymous	CSRP2BP	NM_020536.4		88,1208,5207	GG,GA,AA		12.407,7.1947,10.6412		261/783	18142564	1384,11622	2203	4300	6503	SO:0001819	synonymous_variant	57325	exon5			AGAGAAAAGGTCT	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.783A>G	20.37:g.18142564A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	102	59	0.578431	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Silent	SNP	ENST00000435364.3	37	CCDS13133.1																																																																																			A|0.896;G|0.104	0.104	strong		0.443	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536	
MRS2	57380	hgsc.bcm.edu	37	6	24412530	24412530	+	Silent	SNP	G	G	T	rs61733147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24412530G>T	ENST00000378386.3	+	5	588	c.495G>T	c.(493-495)cgG>cgT	p.R165R	MRS2_ENST00000274747.7_3'UTR|MRS2_ENST00000378353.1_Silent_p.R165R|MRS2_ENST00000535061.1_Silent_p.R115R|MRS2_ENST00000443868.2_Silent_p.R168R|MRS2_ENST00000543597.1_5'UTR|MRS2_ENST00000483634.1_3'UTR	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	165						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						GGCTGTTCCGGGAACTCCCTT	0.383													G|||	355	0.0708866	0.0734	0.0259	5008	,	,		15993	0.122		0.0089	False		,,,				2504	0.1104				p.R165R		Atlas-SNP	.											.	MRS2	31	.	0			c.G495T						PASS	.	G		265,4141	149.2+/-183.4	10,245,1948	114.0	109.0	111.0		495	2.7	1.0	6	dbSNP_129	111	72,8528	42.6+/-100.3	0,72,4228	no	coding-synonymous	MRS2	NM_020662.2		10,317,6176	TT,TG,GG		0.8372,6.0145,2.5911		165/444	24412530	337,12669	2203	4300	6503	SO:0001819	synonymous_variant	57380	exon5			GTTCCGGGAACTC	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.495G>T	6.37:g.24412530G>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	211	211	1	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	37	CCDS4552.1																																																																																			G|0.964;T|0.036	0.036	strong		0.383	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1		
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186168	39186168	+	Missense_Mutation	SNP	A	A	C	rs8074887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39186168A>C	ENST00000377747.4	-	1	188	c.163T>G	c.(163-165)Tct>Gct	p.S55A	KRTAP1-5_ENST00000361883.5_5'Flank	NM_001257305.1	NP_001244234.1	P0C5Y4	KRA14_HUMAN	keratin associated protein 1-4	55						keratin filament (GO:0045095)				lung(1)	1						GTGCTCACAGATCCACCGCTG	0.642													N|||	2243	0.447883	0.5469	0.4769	5008	,	,		17366	0.4692		0.2803	False		,,,				2504	0.4438				p.S55A		Atlas-SNP	.											.	KRTAP1-4	4	.	0			c.T163G						PASS	.																																			SO:0001583	missense	728255	exon1			TCACAGATCCACC	AC007455	CCDS58548.1	17q21.2	2010-06-22			ENSG00000204887	ENSG00000204887		"""Keratin associated proteins"""	18904	protein-coding gene	gene with protein product		608821					Standard	NM_001257305		Approved	KAP1.4	uc031raf.1	P0C5Y4	OTTHUMG00000133631	ENST00000377747.4:c.163T>G	17.37:g.39186168A>C	ENSP00000366976:p.Ser55Ala	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	62	0.508197	NM_001257305	A6NJ92	Missense_Mutation	SNP	ENST00000377747.4	37	CCDS58548.1	895	0.4097985347985348	259	0.5264227642276422	154	0.425414364640884	272	0.4755244755244755	210	0.2770448548812665	C	1.670	-0.509272	0.04231	.	.	ENSG00000204887	ENST00000377747	T	0.21191	2.02	4.76	1.2	0.21068	.	2.529240	0.02416	N	0.082099	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.42899	-0.9424	6	0.10111	T	0.7	.	7.0566	0.25104	0.3262:0.3555:0.3182:0.0	rs8074887;rs52814666	.	.	.	A	55	ENSP00000366976:S55A	ENSP00000366976:S55A	S	-	1	0	KRTAP1-4	36439694	0.009000	0.17119	0.240000	0.24138	0.014000	0.08584	0.019000	0.13444	0.245000	0.21373	-0.121000	0.15023	TCT	A|0.588;C|0.412	0.412	strong		0.642	KRTAP1-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257776.3		
ADAM28	10863	hgsc.bcm.edu	37	8	24199218	24199218	+	Missense_Mutation	SNP	C	C	A	rs36041430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24199218C>A	ENST00000265769.4	+	16	1888	c.1778C>A	c.(1777-1779)aCa>aAa	p.T593K	RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000397649.3_Missense_Mutation_p.T340K|RP11-624C23.1_ENST00000518988.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	593	Cys-rich.		T -> K (in dbSNP:rs36041430).		spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		CCTGAAGACACAAGTCAAGAA	0.413													C|||	489	0.0976438	0.1929	0.0202	5008	,	,		12518	0.1012		0.0298	False		,,,				2504	0.09				p.T593K	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.C1778A						PASS	.	C	LYS/THR	766,3640	310.8+/-291.8	75,616,1512	205.0	194.0	198.0		1778	-11.7	0.0	8	dbSNP_126	198	239,8361	95.6+/-157.4	3,233,4064	yes	missense	ADAM28	NM_014265.4	78	78,849,5576	AA,AC,CC		2.7791,17.3854,7.7272	benign	593/776	24199218	1005,12001	2203	4300	6503	SO:0001583	missense	10863	exon16			AAGACACAAGTCA	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.1778C>A	8.37:g.24199218C>A	ENSP00000265769:p.Thr593Lys	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	164	95	0.579268	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	201|201	0.09203296703296704|0.09203296703296704	117|117	0.23780487804878048|0.23780487804878048	6|6	0.016574585635359115|0.016574585635359115	53|53	0.09265734265734266|0.09265734265734266	25|25	0.032981530343007916|0.032981530343007916	C|C	0.745|0.745	-0.774986|-0.774986	0.02951|0.02951	0.173854|0.173854	0.027791|0.027791	ENSG00000042980|ENSG00000042980	ENST00000521629;ENST00000518326|ENST00000265769;ENST00000397649	.|T;T	.|0.01599	.|4.84;4.74	5.84|5.84	-11.7|-11.7	0.00046|0.00046	.|ADAM, cysteine-rich (1);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25201|0.25201	0.72|0.72	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.12013	.|0.005;0.005	.|B;B	.|0.10450	.|0.005;0.005	T|T	0.47497|0.47497	-0.9113|-0.9113	4|8	.|0.34782	.|T	.|0.22	.|.	0.1176|0.1176	0.00062|0.00062	0.2723:0.182:0.2334:0.3123|0.2723:0.182:0.2334:0.3123	rs36041430|rs36041430	.|593;593	.|B2RMV5;Q9UKQ2	.|.;ADA28_HUMAN	Q|K	225;18|593;340	.|ENSP00000265769:T593K;ENSP00000380770:T340K	.|ENSP00000265769:T593K	H|T	+|+	3|2	2|0	ADAM28|ADAM28	24255163|24255163	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.010000|0.010000	0.07245|0.07245	-1.443000|-1.443000	0.02405|0.02405	-2.607000|-2.607000	0.00447|0.00447	-0.947000|-0.947000	0.02670|0.02670	CAC|ACA	C|0.922;A|0.078	0.078	strong		0.413	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
COG2	22796	hgsc.bcm.edu	37	1	230796533	230796533	+	Silent	SNP	T	T	G	rs16852160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230796533T>G	ENST00000366669.4	+	3	379	c.264T>G	c.(262-264)ctT>ctG	p.L88L	COG2_ENST00000366668.3_Silent_p.L88L|COG2_ENST00000534989.1_Silent_p.L29L|COG2_ENST00000535166.1_5'UTR	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	88					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				TCAACCAGCTTTCTGTGCCTT	0.423													T|||	161	0.0321486	0.1127	0.0115	5008	,	,		16141	0.001		0.001	False		,,,				2504	0.002				p.L88L		Atlas-SNP	.											.	COG2	61	.	0			c.T264G						PASS	.	T	,	436,3970	208.8+/-229.8	20,396,1787	221.0	178.0	193.0		264,264	-0.9	1.0	1	dbSNP_123	193	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous,coding-synonymous	COG2	NM_001145036.1,NM_007357.2	,	20,409,6074	GG,GT,TT		0.1512,9.8956,3.4523	,	88/738,88/739	230796533	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	22796	exon3			CCAGCTTTCTGTG	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.264T>G	1.37:g.230796533T>G		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	245	105	0.428571	NM_007357	Q86U99	Silent	SNP	ENST00000366669.4	37	CCDS1584.1																																																																																			T|0.962;G|0.038	0.038	strong		0.423	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
INHA	3623	hgsc.bcm.edu	37	2	220439826	220439826	+	Missense_Mutation	SNP	G	G	A	rs12720061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220439826G>A	ENST00000243786.2	+	2	859	c.679G>A	c.(679-681)Ggg>Agg	p.G227R		NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	227			G -> R (in dbSNP:rs12720061).		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)		ACCCAGTGGAGGGGAGAGAGC	0.687													G|||	165	0.0329473	0.1225	0.0043	5008	,	,		18962	0.0		0.0	False		,,,				2504	0.0				p.G227R		Atlas-SNP	.											.	INHA	30	.	0			c.G679A	GRCh37	CM041026	INHA	M	rs12720061	PASS	.	G	ARG/GLY	400,4006	195.7+/-220.2	17,366,1820	38.0	41.0	40.0		679	5.5	0.9	2	dbSNP_121	40	4,8596	3.7+/-12.6	0,4,4296	yes	missense	INHA	NM_002191.3	125	17,370,6116	AA,AG,GG		0.0465,9.0785,3.1063	benign	227/367	220439826	404,12602	2203	4300	6503	SO:0001583	missense	3623	exon2			AGTGGAGGGGAGA		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.679G>A	2.37:g.220439826G>A	ENSP00000243786:p.Gly227Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	139	75	0.539568	NM_002191	A8K8H5	Missense_Mutation	SNP	ENST00000243786.2	37	CCDS2444.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	G	13.05	2.120959	0.37436	0.090785	4.65E-4	ENSG00000123999	ENST00000243786	D	0.84944	-1.92	5.48	5.48	0.80851	.	0.394385	0.24085	N	0.041686	T	0.08935	0.0221	L	0.41079	1.255	0.25639	N	0.986228	B	0.21905	0.062	B	0.17722	0.019	T	0.16424	-1.0403	9	.	.	.	-13.0624	9.3942	0.38392	0.0778:0.145:0.7772:0.0	rs12720061;rs57625669	227	P05111	INHA_HUMAN	R	227	ENSP00000243786:G227R	.	G	+	1	0	INHA	220148070	0.002000	0.14202	0.937000	0.37676	0.995000	0.86356	1.128000	0.31369	2.564000	0.86499	0.561000	0.74099	GGG	G|0.973;A|0.027	0.027	strong		0.687	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1		
GPR116	221395	hgsc.bcm.edu	37	6	46826319	46826319	+	Silent	SNP	C	C	G	rs150389766		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46826319C>G	ENST00000283296.7	-	17	3609	c.3321G>C	c.(3319-3321)ctG>ctC	p.L1107L	GPR116_ENST00000456426.2_Silent_p.L965L|GPR116_ENST00000265417.7_Silent_p.L1107L|GPR116_ENST00000545669.1_Silent_p.L536L|GPR116_ENST00000362015.4_Silent_p.L1107L	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	1107					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)			GCATGAGGCCCAGTGTCAGCA	0.512													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20103	0.0		0.0	False		,,,				2504	0.0				p.L1107L	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.G3321C						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	50.0	51.0	51.0		3321,3321	3.6	1.0	6	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GPR116	NM_001098518.1,NM_015234.4	,	0,1,6502	GG,GC,CC		0.0,0.0227,0.0077	,	1107/1347,1107/1347	46826319	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	221395	exon17			GAGGCCCAGTGTC	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.3321G>C	6.37:g.46826319C>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	139	61	0.438849	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	37	CCDS4919.1																																																																																			C|1.000;G|0.000	0.000	weak		0.512	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
CCDC155	147872	hgsc.bcm.edu	37	19	49920719	49920719	+	Silent	SNP	C	C	T	rs79452032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49920719C>T	ENST00000447857.3	+	20	1846	c.1641C>T	c.(1639-1641)ccC>ccT	p.P547P		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	547						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						CCCCACCTCCCACCTGGCCCC	0.632													c|||	104	0.0207668	0.0673	0.013	5008	,	,		14619	0.0		0.006	False		,,,				2504	0.0				p.P547P		Atlas-SNP	.											.	CCDC155	46	.	0			c.C1641T						PASS	.			159,4033		5,149,1942	47.0	49.0	48.0		1641	-1.5	0.9	19	dbSNP_132	48	33,8283		1,31,4126	no	coding-synonymous	CCDC155	NM_144688.4		6,180,6068	TT,TC,CC		0.3968,3.7929,1.535		547/563	49920719	192,12316	2096	4158	6254	SO:0001819	synonymous_variant	147872	exon20			ACCTCCCACCTGG		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.1641C>T	19.37:g.49920719C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_144688	Q96MC3	Silent	SNP	ENST00000447857.3	37	CCDS46140.1																																																																																			C|0.987;T|0.013	0.013	strong		0.632	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688	
ASAH2	56624	hgsc.bcm.edu	37	10	52005153	52005153	+	Silent	SNP	A	A	G	rs7097319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:52005153A>G	ENST00000395526.4	-	2	188	c.189T>C	c.(187-189)gcT>gcC	p.A63A	ASAH2_ENST00000329428.6_Silent_p.A44A|ASAH2_ENST00000447815.1_Silent_p.A63A	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	63					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ceramidase activity (GO:0017040)			large_intestine(1)|lung(9)|urinary_tract(1)	11						AGCGTTGGGCAGCTGTGGAGC	0.507													G|||	1663	0.332069	0.5719	0.1888	5008	,	,		13467	0.4276		0.0934	False		,,,				2504	0.2566				p.A63A		Atlas-SNP	.											ASAH2_ENST00000395526,NS,carcinoma,-1,2	ASAH2	69	2	0			c.T189C						scavenged	.	G	,	2234,2172	583.8+/-385.9	584,1066,553	71.0	81.0	78.0		189,189	1.4	0.0	10	dbSNP_116	78	821,7779	781.9+/-407.6	36,749,3515	no	coding-synonymous,coding-synonymous	ASAH2	NM_001143974.1,NM_019893.2	,	620,1815,4068	GG,GA,AA		9.5465,49.2964,23.4892	,	63/746,63/781	52005153	3055,9951	2203	4300	6503	SO:0001819	synonymous_variant	56624	exon2			TTGGGCAGCTGTG	AF250847	CCDS7239.2, CCDS44398.1	10q11.23	2008-08-11			ENSG00000188611	ENSG00000188611			18860	protein-coding gene	gene with protein product		611202				10781606	Standard	NM_019893		Approved		uc001jjd.3	Q9NR71	OTTHUMG00000018223	ENST00000395526.4:c.189T>C	10.37:g.52005153A>G		Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	194	69	0.35567	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Silent	SNP	ENST00000395526.4	37	CCDS7239.2																																																																																			A|0.738;G|0.262	0.262	strong		0.507	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893	
METTL21A	151194	hgsc.bcm.edu	37	2	208478055	208478055	+	Silent	SNP	A	A	G	rs17520056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:208478055A>G	ENST00000411432.1	-	4	588	c.372T>C	c.(370-372)acT>acC	p.T124T	METTL21A_ENST00000432416.1_Intron|METTL21A_ENST00000426075.1_Silent_p.T124T|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000448823.2_3'UTR|METTL21A_ENST00000406927.2_Silent_p.T124T|METTL21A_ENST00000477919.1_5'Flank|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000272839.3_Silent_p.T142T|METTL21A_ENST00000442521.1_Silent_p.T124T|METTL21A_ENST00000448007.2_Silent_p.T124T	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	124					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)	p.T124T(1)		endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						TTTGTCCCCAAGTCAGCTCCT	0.368													A|||	1741	0.347644	0.233	0.3617	5008	,	,		20308	0.372		0.3072	False		,,,				2504	0.5092				p.T124T		Atlas-SNP	.											METTL21A,NS,carcinoma,0,1	METTL21A	24	1	1	Substitution - coding silent(1)	stomach(1)	c.T372C						PASS	.	A	,	1099,3307	392.8+/-328.6	138,823,1242	83.0	83.0	83.0		372,372	-5.0	0.9	2	dbSNP_123	83	2724,5876	432.7+/-357.2	427,1870,2003	no	coding-synonymous,coding-synonymous	METTL21A	NM_001127395.1,NM_145280.4	,	565,2693,3245	GG,GA,AA		31.6744,24.9433,29.3941	,	124/219,124/219	208478055	3823,9183	2203	4300	6503	SO:0001819	synonymous_variant	151194	exon4			TCCCCAAGTCAGC	AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 557b"", ""heat shock protein 70kDa lysine (K) methyltransferase"""	615257	"""family with sequence similarity 119, member A"""	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.372T>C	2.37:g.208478055A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_145280	Q53RV0|Q8N1Z9|Q96GH6	Silent	SNP	ENST00000411432.1	37	CCDS2376.1																																																																																			A|0.705;G|0.295	0.295	strong		0.368	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280	
MIER2	54531	hgsc.bcm.edu	37	19	327182	327182	+	Silent	SNP	C	C	T	rs7256086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:327182C>T	ENST00000264819.4	-	5	454	c.444G>A	c.(442-444)ccG>ccA	p.P148P	MIER2_ENST00000592722.1_5'Flank	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	148					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)		AGGTCACGGACGGGGTGAGGT	0.527													C|||	682	0.136182	0.2799	0.1988	5008	,	,		17693	0.0248		0.1133	False		,,,				2504	0.0358				p.P148P		Atlas-SNP	.											MIER2,lower_third,carcinoma,-1,1	MIER2	51	1	0			c.G444A						scavenged	.	C		1126,3280		137,852,1214	228.0	203.0	212.0		444	-8.3	0.2	19	dbSNP_116	212	802,7798		37,728,3535	no	coding-synonymous	MIER2	NM_017550.1		174,1580,4749	TT,TC,CC		9.3256,25.5561,14.8239		148/546	327182	1928,11078	2203	4300	6503	SO:0001819	synonymous_variant	54531	exon5			CACGGACGGGGTG	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.444G>A	19.37:g.327182C>T		Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	110	61	0.554545	NM_017550	Q9ULM7	Silent	SNP	ENST00000264819.4	37	CCDS32855.1																																																																																			C|0.849;T|0.151	0.151	strong		0.527	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843	
CEACAM1	634	hgsc.bcm.edu	37	19	43031369	43031369	+	Missense_Mutation	SNP	G	G	A	rs8110904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43031369G>A	ENST00000161559.6	-	2	382	c.248C>T	c.(247-249)gCa>gTa	p.A83V	CEACAM1_ENST00000358394.3_Missense_Mutation_p.A83V|CEACAM1_ENST00000308072.4_Missense_Mutation_p.A43V|CEACAM1_ENST00000599389.1_Missense_Mutation_p.A83V|CEACAM1_ENST00000403444.3_Missense_Mutation_p.A83V|CEACAM1_ENST00000352591.5_Missense_Mutation_p.A83V|CEACAM1_ENST00000351134.3_Missense_Mutation_p.A83V|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000403461.1_Missense_Mutation_p.A83V|LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000594688.1_RNA	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	83	Ig-like V-type.		A -> V (in dbSNP:rs8110904). {ECO:0000269|Ref.9}.		angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	AGTTCCTATTGCATATCCTAC	0.507													a|||	526	0.105032	0.3707	0.0447	5008	,	,		20268	0.0		0.005	False		,,,				2504	0.0				p.A83V		Atlas-SNP	.											.	CEACAM1	43	.	0			c.C248T						PASS	.	A	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	1359,3047		96,1167,940	318.0	255.0	276.0		248,248,248,248,248,248	-6.2	0.0	19	dbSNP_116	276	22,8578		0,22,4278	yes	missense,missense,missense,missense,missense,missense	CEACAM1	NM_001024912.2,NM_001184813.1,NM_001184815.1,NM_001184816.1,NM_001205344.1,NM_001712.4	64,64,64,64,64,64	96,1189,5218	AA,AG,GG		0.2558,30.8443,10.6182	benign,benign,benign,benign,benign,benign	83/465,83/431,83/462,83/369,83/469,83/527	43031369	1381,11625	2203	4300	6503	SO:0001583	missense	634	exon2			CCTATTGCATATC	M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.248C>T	19.37:g.43031369G>A	ENSP00000161559:p.Ala83Val	Somatic	449	1	0.00222717		WXS	Illumina HiSeq	Phase_I	456	238	0.52193	NM_001184816	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	199	0.09111721611721611	176	0.35772357723577236	18	0.049723756906077346	0	0.0	5	0.006596306068601583	a	0.459	-0.889785	0.02511	0.308443	0.002558	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000351134;ENST00000446434;ENST00000378065;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000308072;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01;0.01;0.01	3.76	-6.23	0.02052	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00053	-2.39	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.001;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B	0.08055	0.002;0.001;0.0;0.001;0.001;0.003;0.002;0.001;0.001;0.001	T	0.04140	-1.0974	8	0.02654	T	1	.	2.5662	0.04784	0.2081:0.1227:0.4308:0.2384	rs8110904;rs10408262;rs12979523;rs60053543;rs8110904	83;83;83;83;83;83;83;83;83;83	P13688-7;P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;.;CEAM1_HUMAN	V	83;83;83;110;43;83;83;83;43;83;83;83	ENSP00000161559:A83V;ENSP00000351165:A83V;ENSP00000325946:A83V;ENSP00000244291:A83V;ENSP00000384709:A83V;ENSP00000384083:A83V;ENSP00000312184:A43V	ENSP00000161559:A83V	A	-	2	0	CEACAM1	47723209	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.328000	0.00510	-2.234000	0.00715	-0.361000	0.07541	GCA	G|0.900;A|0.100	0.100	strong		0.507	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712	
TPH2	121278	hgsc.bcm.edu	37	12	72372862	72372862	+	Silent	SNP	A	A	G	rs7305115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72372862A>G	ENST00000333850.3	+	7	1077	c.936A>G	c.(934-936)ccA>ccG	p.P312P		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	312					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	TCTACACCCCAGAACCGTGAG	0.512													G|||	2713	0.541733	0.6044	0.4856	5008	,	,		17921	0.4494		0.5825	False		,,,				2504	0.5501				p.P312P		Atlas-SNP	.											TPH2,colon,carcinoma,+1,1	TPH2	81	1	0			c.A936G	GRCh37	CM077900	TPH2	M	rs7305115	PASS	.	G		2591,1815	531.5+/-373.2	766,1059,378	126.0	126.0	126.0		936	-10.5	0.1	12	dbSNP_116	126	4977,3623	522.3+/-380.1	1439,2099,762	no	coding-synonymous	TPH2	NM_173353.3		2205,3158,1140	GG,GA,AA		42.1279,41.1938,41.8115		312/491	72372862	7568,5438	2203	4300	6503	SO:0001819	synonymous_variant	121278	exon7			CACCCCAGAACCG	AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.936A>G	12.37:g.72372862A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_173353	A6NGA4|Q14CB0	Silent	SNP	ENST00000333850.3	37	CCDS31859.1																																																																																			A|0.439;G|0.561	0.561	strong		0.512	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353	
ZNF227	7770	hgsc.bcm.edu	37	19	44732658	44732658	+	Silent	SNP	C	C	G	rs922063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44732658C>G	ENST00000313040.7	+	4	325	c.120C>G	c.(118-120)ctC>ctG	p.L40L	ZNF227_ENST00000586228.1_Missense_Mutation_p.R27G|ZNF227_ENST00000589005.1_5'UTR|ZNF227_ENST00000589237.1_3'UTR|ZNF227_ENST00000391961.2_5'UTR|ZNF227_ENST00000589707.1_5'UTR	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	40	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)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				TGCGACTGCTCGATCTTACCC	0.498													G|||	1018	0.203275	0.5439	0.2147	5008	,	,		17872	0.1052		0.0278	False		,,,				2504	0.0164				p.L40L		Atlas-SNP	.											.	ZNF227	62	.	0			c.C120G						PASS	.	G		2102,2304	601.8+/-389.8	505,1092,606	246.0	217.0	227.0		120	2.7	1.0	19	dbSNP_86	227	121,8479	814.2+/-407.0	4,113,4183	no	coding-synonymous	ZNF227	NM_182490.1		509,1205,4789	GG,GC,CC		1.407,47.7077,17.0921		40/800	44732658	2223,10783	2203	4300	6503	SO:0001819	synonymous_variant	7770	exon4			ACTGCTCGATCTT	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.120C>G	19.37:g.44732658C>G		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	273	271	0.992674	NM_182490	B3KRU7|B7Z5P9	Silent	SNP	ENST00000313040.7	37	CCDS12636.1																																																																																			C|0.816;G|0.184	0.184	strong		0.498	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490	
GPANK1	7918	hgsc.bcm.edu	37	6	31631907	31631907	+	Silent	SNP	G	G	A	rs928814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31631907G>A	ENST00000375906.1	-	3	1033	c.349C>T	c.(349-351)Ctg>Ttg	p.L117L	GPANK1_ENST00000375893.2_Silent_p.L117L|CSNK2B-LY6G5B-1181_ENST00000375880.2_5'Flank|CSNK2B_ENST00000375866.2_5'Flank|GPANK1_ENST00000375900.4_Silent_p.L117L|Y_RNA_ENST00000364337.1_RNA|GPANK1_ENST00000375896.4_Silent_p.L117L|CSNK2B_ENST00000375885.4_5'Flank|CSNK2B_ENST00000375865.2_5'Flank|CSNK2B_ENST00000375882.2_5'Flank|GPANK1_ENST00000375895.2_Silent_p.L117L	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	117							nucleic acid binding (GO:0003676)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						AGTTCTGGCAGGTCCCCCTCC	0.587													G|||	273	0.0545128	0.1263	0.0692	5008	,	,		16734	0.0179		0.0249	False		,,,				2504	0.0153				p.L117L		Atlas-SNP	.											.	GPANK1	19	.	0			c.C349T						PASS	.	G	,,,,	482,3924	227.8+/-242.9	25,432,1746	89.0	83.0	85.0		349,349,349,349,349	-4.9	0.1	6	dbSNP_86	85	232,8368	95.0+/-156.8	3,226,4071	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPANK1	NM_001199237.1,NM_001199238.1,NM_001199239.1,NM_001199240.1,NM_033177.3	,,,,	28,658,5817	AA,AG,GG		2.6977,10.9396,5.4898	,,,,	117/357,117/357,117/357,117/357,117/357	31631907	714,12292	2203	4300	6503	SO:0001819	synonymous_variant	7918	exon3			CTGGCAGGTCCCC		CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"""Ankyrin repeat domain containing"", ""G patch domain containing"""	13920	protein-coding gene	gene with protein product	"""G patch domain containing 10"", ""ankyrin repeat domain 59"""	142610	"""HLA-B associated transcript 4"""	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.349C>T	6.37:g.31631907G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	177	85	0.480226	NM_001199238	A6NG25|B0UXA2|Q5SQ49	Silent	SNP	ENST00000375906.1	37	CCDS4711.1																																																																																			G|0.935;A|0.065	0.065	strong		0.587	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2	NM_033177	
NACAD	23148	hgsc.bcm.edu	37	7	45124708	45124708	+	Silent	SNP	C	C	T	rs13438759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:45124708C>T	ENST00000490531.2	-	2	1090	c.1071G>A	c.(1069-1071)acG>acA	p.T357T		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	357					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						AGGAGGCAGACGTGCTGTCCT	0.622													C|||	518	0.103435	0.2958	0.0303	5008	,	,		18963	0.0		0.0209	False		,,,				2504	0.0869				p.T357T		Atlas-SNP	.											.	NACAD	44	.	0			c.G1071A						PASS	.	C		328,1056		37,254,401	43.0	43.0	43.0		1071	-8.4	0.0	7	dbSNP_121	43	80,3102		3,74,1514	no	coding-synonymous	NACAD	NM_001146334.1		40,328,1915	TT,TC,CC		2.5141,23.6994,8.9356		357/1563	45124708	408,4158	692	1591	2283	SO:0001819	synonymous_variant	23148	exon2			GGCAGACGTGCTG	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.1071G>A	7.37:g.45124708C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_001146334		Silent	SNP	ENST00000490531.2	37	CCDS47582.1																																																																																			C|0.918;T|0.082	0.082	strong		0.622	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
KCNN1	3780	hgsc.bcm.edu	37	19	18084724	18084724	+	Silent	SNP	C	C	T	rs77030907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18084724C>T	ENST00000222249.9	+	3	346	c.27C>T	c.(25-27)agC>agT	p.S9S	RNA5SP468_ENST00000516782.1_RNA	NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	9					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	ACAATGGCAGCGTGGGGCGGC	0.756													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		12575	0.0		0.0	False		,,,				2504	0.0				p.S9S		Atlas-SNP	.											.	KCNN1	74	.	0			c.C27T						PASS	.						3.0	3.0	3.0					19																	18084724		1475	3351	4826	SO:0001819	synonymous_variant	3780	exon3			TGGCAGCGTGGGG	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.27C>T	19.37:g.18084724C>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	12	7	0.583333	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				C|0.990;T|0.010	0.010	strong		0.756	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
EVC	2121	hgsc.bcm.edu	37	4	5743512	5743512	+	Missense_Mutation	SNP	T	T	C	rs6414624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:5743512T>C	ENST00000264956.6	+	6	956	c.772T>C	c.(772-774)Tac>Cac	p.Y258H	EVC_ENST00000509451.1_Missense_Mutation_p.Y258H|EVC_ENST00000382674.2_Missense_Mutation_p.Y258H	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	258			Y -> H (in dbSNP:rs6414624). {ECO:0000269|PubMed:10700184}.		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)				TGATGAACTATACCAGAAGAT	0.289													T|||	3730	0.744808	0.5015	0.7839	5008	,	,		15627	0.9048		0.7932	False		,,,				2504	0.8313				p.Y258H		Atlas-SNP	.											.	EVC	90	.	0			c.T772C						PASS	.	T	HIS/TYR	2284,2120	571.5+/-383.1	597,1090,515	50.0	52.0	51.0		772	2.7	0.8	4	dbSNP_116	51	6902,1688	727.5+/-406.6	2770,1362,163	yes	missense	EVC	NM_153717.2	83	3367,2452,678	CC,CT,TT		19.6508,48.1381,29.3058	probably-damaging	258/993	5743512	9186,3808	2202	4295	6497	SO:0001583	missense	2121	exon6			GAACTATACCAGA	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.772T>C	4.37:g.5743512T>C	ENSP00000264956:p.Tyr258His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	1689	0.7733516483516484	263	0.5345528455284553	295	0.8149171270718232	523	0.9143356643356644	608	0.8021108179419525	T	5.677	0.309460	0.10733	0.518619	0.803492	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.55588	0.51;0.51;0.64	5.12	2.72	0.32119	.	0.735547	0.13245	N	0.402567	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	B	0.14012	0.009	B	0.16722	0.016	T	0.28073	-1.0055	9	0.20046	T	0.44	.	8.084	0.30760	0.0:0.1664:0.0:0.8336	rs6414624;rs57157110;rs6414624	258	P57679	EVC_HUMAN	H	258	ENSP00000264956:Y258H;ENSP00000372120:Y258H;ENSP00000426774:Y258H	ENSP00000264956:Y258H	Y	+	1	0	EVC	5794413	0.946000	0.32159	0.785000	0.31869	0.188000	0.23474	1.926000	0.40084	0.309000	0.22966	0.533000	0.62120	TAC	T|0.274;C|0.726	0.726	strong		0.289	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
AKNA	80709	hgsc.bcm.edu	37	9	117099574	117099574	+	Silent	SNP	A	A	G	rs148856699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117099574A>G	ENST00000307564.4	-	22	4241	c.4080T>C	c.(4078-4080)ccT>ccC	p.P1360P	AKNA_ENST00000223791.3_Silent_p.P820P|AKNA_ENST00000374075.5_Silent_p.P1279P|AKNA_ENST00000374079.4_Silent_p.P305P|AKNA_ENST00000374088.3_Silent_p.P1360P|AKNA_ENST00000492875.1_5'UTR	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1360					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TAGGTCCTGCAGGCGCATAGT	0.652													G|||	29	0.00579073	0.0197	0.0029	5008	,	,		10995	0.0		0.001	False		,,,				2504	0.0				p.P1360P		Atlas-SNP	.											.	AKNA	119	.	0			c.T4080C						PASS	.	G		77,4329	810.3+/-416.0	1,75,2127	41.0	44.0	43.0		4080	-5.6	0.0	9	dbSNP_134	43	0,8598		0,0,4299	no	coding-synonymous	AKNA	NM_030767.4		1,75,6426	GG,GA,AA		0.0,1.7476,0.5921		1360/1440	117099574	77,12927	2203	4299	6502	SO:0001819	synonymous_variant	80709	exon22			TCCTGCAGGCGCA	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.4080T>C	9.37:g.117099574A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	147	99	0.673469	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	G	8.193	0.796449	0.16327	0.017476	0.0	ENSG00000106948	ENST00000320310	.	.	.	5.0	-5.55	0.02536	.	.	.	.	.	T	0.09202	0.0227	.	.	.	0.21822	N	0.999529	.	.	.	.	.	.	T	0.24476	-1.0159	4	.	.	.	-1.4841	3.3389	0.07111	0.561:0.1076:0.2123:0.119	.	.	.	.	P	371	.	.	L	-	2	0	AKNA	116139395	0.000000	0.05858	0.014000	0.15608	0.849000	0.48306	-0.506000	0.06359	-1.037000	0.03283	-0.349000	0.07799	CTG	A|0.995;G|0.005	0.005	strong		0.652	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
DSPP	1834	hgsc.bcm.edu	37	4	88537198	88537198	+	Missense_Mutation	SNP	C	C	A	rs200796238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88537198C>A	ENST00000282478.7	+	4	3417	c.3384C>A	c.(3382-3384)gaC>gaA	p.D1128E	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1128E			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1128	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgacagcagcgaca	0.562													c|||	1321	0.263778	0.4508	0.3141	5008	,	,		16090	0.1438		0.2167	False		,,,				2504	0.1472				p.D1128E		Atlas-SNP	.											DSPP,NS,lymphoid_neoplasm,+1,1	DSPP	174	1	0			c.C3384A						scavenged	.						16.0	22.0	20.0					4																	88537198		1228	2388	3616	SO:0001583	missense	1834	exon5			CAGTGACAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3384C>A	4.37:g.88537198C>A	ENSP00000282478:p.Asp1128Glu	Somatic	78	17	0.217949		WXS	Illumina HiSeq	Phase_I	100	40	0.4	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	t	2.566	-0.300758	0.05495	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88201	-2.35;-2.35	1.66	-3.2	0.05156	.	.	.	.	.	T	0.74884	0.3775	L	0.34521	1.04	0.80722	P	0.0	P	0.35714	0.517	B	0.27500	0.08	T	0.66571	-0.5890	8	0.10902	T	0.67	-7.8266	6.7032	0.23236	0.0:0.4356:0.0:0.5644	.	1128	Q9NZW4	DSPP_HUMAN	E	1128	ENSP00000382213:D1128E;ENSP00000282478:D1128E	ENSP00000282478:D1128E	D	+	3	2	DSPP	88756222	0.786000	0.28738	0.017000	0.16124	0.009000	0.06853	-0.054000	0.11826	-1.162000	0.02797	-0.730000	0.03578	GAC	.	.	weak		0.562	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
NPR2	4882	hgsc.bcm.edu	37	9	35811215	35811215	+	IGR	SNP	C	C	T	rs73444820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35811215C>T	ENST00000342694.2	+	0	3686				SPAG8_ENST00000484764.1_Silent_p.P274P|SPAG8_ENST00000396638.2_Silent_p.P276P|SPAG8_ENST00000479751.1_5'UTR|AL133410.1_ENST00000582432.1_RNA|HINT2_ENST00000474908.1_5'Flank|SPAG8_ENST00000340291.2_Silent_p.P276P	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)			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)	ACTGGCCCCGCGGCAAAGTTT	0.507													c|||	99	0.0197684	0.0734	0.0029	5008	,	,		17255	0.0		0.0	False		,,,				2504	0.0				p.P276P		Atlas-SNP	.											SPAG8_ENST00000396638,caecum,carcinoma,0,2	SPAG8	67	2	0			c.G828A						scavenged	.	C	,	276,4130	148.0+/-182.4	7,262,1934	95.0	109.0	104.0		828,828	0.7	1.0	9	dbSNP_130	104	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous,coding-synonymous	SPAG8	NM_001039592.1,NM_172312.1	,	7,265,6231	TT,TC,CC		0.0349,6.2642,2.1452	,	276/486,276/502	35811215	279,12727	2203	4300	6503	SO:0001628	intergenic_variant	26206	exon2			GCCCCGCGGCAAA	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.35811215C>T		Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	100	71	0.71	NM_001039592	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	c	6.691	0.496043	0.12762	0.062642	3.49E-4	ENSG00000137098	ENST00000497810	.	.	.	5.65	0.724	0.18236	.	.	.	.	.	T	0.11410	0.0278	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.05500	-1.0881	4	.	.	.	-7.0172	7.2861	0.26340	0.0:0.4303:0.0:0.5697	.	.	.	.	H	274	.	.	R	-	2	0	SPAG8	35801215	0.477000	0.25909	0.964000	0.40570	0.648000	0.38561	-1.146000	0.03191	0.200000	0.20447	-0.285000	0.09966	CGC	C|0.978;T|0.022	0.022	strong		0.507	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713625	32713625	+	Missense_Mutation	SNP	C	C	T	rs116163401		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	468	0	0		WXS	Illumina HiSeq	Phase_I	488	91	0.186475	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	
SERPINE3	647174	hgsc.bcm.edu	37	13	51936079	51936079	+	Silent	SNP	T	T	C	rs74084815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:51936079T>C	ENST00000521255.1	+	7	1281	c.1221T>C	c.(1219-1221)tcT>tcC	p.S407S	SERPINE3_ENST00000524365.1_Intron|RP11-24B19.4_ENST00000602881.1_RNA|SERPINE3_ENST00000400389.4_Intron|RP11-24B19.3_ENST00000602636.1_RNA	NM_001101320.1	NP_001094790.1	A8MV23	SERP3_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3	407					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(2)	2						AGTGTCTCTCTAGCAACAAGG	0.378													T|||	41	0.0081869	0.031	0.0	5008	,	,		16300	0.0		0.0	False		,,,				2504	0.0				p.S407S		Atlas-SNP	.											.	SERPINE3	37	.	0			c.T1221C						PASS	.	T	,,	102,3578		2,98,1740	133.0	120.0	124.0		,1221,	3.2	0.9	13	dbSNP_130	124	0,8172		0,0,4086	no	utr-3,coding-synonymous,utr-3	INTS6,SERPINE3	NM_001039937.1,NM_001101320.1,NM_012141.2	,,	2,98,5826	CC,CT,TT		0.0,2.7717,0.8606	,,	,407/425,	51936079	102,11750	1840	4086	5926	SO:0001819	synonymous_variant	647174	exon7			TCTCTCTAGCAAC	AX772926	CCDS53870.1	13q14.3	2014-02-18			ENSG00000253309	ENSG00000253309		"""Serine (or cysteine) peptidase inhibitors"""	24774	protein-coding gene	gene with protein product						24172014	Standard	NM_001101320		Approved		uc001vfh.2	A8MV23	OTTHUMG00000016943	ENST00000521255.1:c.1221T>C	13.37:g.51936079T>C		Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	202	95	0.470297	NM_001101320	B1V8P3	Silent	SNP	ENST00000521255.1	37	CCDS53870.1																																																																																			T|0.992;C|0.008	0.008	strong		0.378	SERPINE3-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045021.2	NM_001101320	
NACAD	23148	hgsc.bcm.edu	37	7	45122464	45122464	+	Missense_Mutation	SNP	A	A	C	rs10243185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:45122464A>C	ENST00000490531.2	-	2	3334	c.3315T>G	c.(3313-3315)gaT>gaG	p.D1105E		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1105			D -> E (in dbSNP:rs10243185).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						CAGGAGGCGCATCGGGGACCT	0.662													C|||	2432	0.485623	0.6755	0.464	5008	,	,		17039	0.3026		0.3877	False		,,,				2504	0.5337				p.D1105E		Atlas-SNP	.											.	NACAD	44	.	0			c.T3315G						PASS	.	C	GLU/ASP	907,477		295,317,80	55.0	58.0	57.0		3315	0.3	0.0	7	dbSNP_119	57	1299,1883		260,779,552	yes	missense	NACAD	NM_001146334.1	45	555,1096,632	CC,CA,AA		40.8234,34.4653,48.3136	benign	1105/1563	45122464	2206,2360	692	1591	2283	SO:0001583	missense	23148	exon2			AGGCGCATCGGGG	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.3315T>G	7.37:g.45122464A>C	ENSP00000420477:p.Asp1105Glu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	953	0.43635531135531136	343	0.6971544715447154	164	0.4530386740331492	152	0.26573426573426573	294	0.38786279683377306	c	0.055	-1.239931	0.01493	0.655347	0.408234	ENSG00000136274	ENST00000490531	T	0.09255	3.0	3.42	0.273	0.15650	.	.	.	.	.	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	0.34204	-0.9838	8	0.02654	T	1	0.9154	5.8426	0.18643	0.543:0.3569:0.0:0.1001	rs10243185	1105	O15069	NACAD_HUMAN	E	1105	ENSP00000420477:D1105E	ENSP00000420477:D1105E	D	-	3	2	NACAD	45088989	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.091000	0.03369	-0.358000	0.08162	-0.757000	0.03467	GAT	A|0.565;C|0.435	0.435	strong		0.662	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
IL16	3603	hgsc.bcm.edu	37	15	81582868	81582868	+	Silent	SNP	G	G	A	rs8031107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81582868G>A	ENST00000302987.4	+	10	1407	c.1407G>A	c.(1405-1407)caG>caA	p.Q469Q	IL16_ENST00000394660.2_Silent_p.Q469Q			Q14005	IL16_HUMAN	interleukin 16	469					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						AGAGGCATCAGTGGAGTCTGG	0.413													G|||	2932	0.585463	0.7474	0.4222	5008	,	,		18859	0.5407		0.4801	False		,,,				2504	0.637				p.Q469Q		Atlas-SNP	.											IL16_ENST00000302987,right_upper_lobe,carcinoma,+1,2	IL16	254	2	0			c.G1407A						PASS	.	G	,	2604,1200		910,784,208	131.0	138.0	136.0		1407,1407	-0.4	1.0	15	dbSNP_116	136	3677,4575		821,2035,1270	no	coding-synonymous,coding-synonymous	IL16	NM_001172128.1,NM_172217.3	,	1731,2819,1478	AA,AG,GG		44.5589,31.5457,47.9015	,	469/1332,469/1333	81582868	6281,5775	1902	4126	6028	SO:0001819	synonymous_variant	3603	exon11			GCATCAGTGGAGT	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1407G>A	15.37:g.81582868G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	165	162	0.981818	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																			G|0.455;A|0.545	0.545	strong		0.413	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
ROBO4	54538	hgsc.bcm.edu	37	11	124765511	124765511	+	Missense_Mutation	SNP	T	T	G	rs60888551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124765511T>G	ENST00000306534.3	-	6	1363	c.878A>C	c.(877-879)cAg>cCg	p.Q293P	ROBO4_ENST00000533054.1_Missense_Mutation_p.Q148P|ROBO4_ENST00000526899.1_5'Flank	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	293	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CGGAGCTCCCTGGCCTCCCGG	0.657													T|||	366	0.0730831	0.2557	0.0202	5008	,	,		15539	0.0		0.0129	False		,,,				2504	0.001				p.Q293P		Atlas-SNP	.											.	ROBO4	130	.	0			c.A878C						PASS	.	T	PRO/GLN	667,3699		42,583,1558	34.0	43.0	40.0		878	0.9	0.6	11	dbSNP_129	40	44,8504		1,42,4231	yes	missense	ROBO4	NM_019055.5	76	43,625,5789	GG,GT,TT		0.5147,15.2771,5.5057	benign	293/1008	124765511	711,12203	2183	4274	6457	SO:0001583	missense	54538	exon6			GCTCCCTGGCCTC	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.878A>C	11.37:g.124765511T>G	ENSP00000304945:p.Gln293Pro	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	93	31	0.333333	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	37	CCDS8455.1	127	0.05815018315018315	108	0.21951219512195122	10	0.027624309392265192	0	0.0	9	0.011873350923482849	T	7.456	0.643746	0.14451	0.152771	0.005147	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.64438	-0.1;0.26	4.72	0.925	0.19424	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.438357	0.17070	N	0.188195	T	0.00039	0.0001	L	0.29908	0.895	0.48341	P	3.670000000000062E-4	B;B	0.10296	0.002;0.003	B;B	0.08055	0.003;0.002	T	0.06303	-1.0834	9	0.30078	T	0.28	.	5.9357	0.19165	0.0:0.0891:0.3409:0.57	rs60888551	183;293	Q8WZ75-3;Q8WZ75	.;ROBO4_HUMAN	P	293;183;148	ENSP00000304945:Q293P;ENSP00000437129:Q148P	ENSP00000304945:Q293P	Q	-	2	0	ROBO4	124270721	0.108000	0.22018	0.642000	0.29436	0.276000	0.26787	0.391000	0.20784	0.293000	0.22520	0.459000	0.35465	CAG	T|0.952;G|0.048	0.048	strong		0.657	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465389	39465389	+	Silent	SNP	T	T	A	rs12451604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	117	0	0		WXS	Illumina HiSeq	Phase_I	137	62	0.452555	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	
NLRP11	204801	hgsc.bcm.edu	37	19	56303806	56303806	+	Missense_Mutation	SNP	A	A	C	rs80143194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56303806A>C	ENST00000589093.1	-	7	2467	c.2374T>G	c.(2374-2376)Tgc>Ggc	p.C792G	NLRP11_ENST00000360133.3_Missense_Mutation_p.C738G|NLRP11_ENST00000589824.2_Missense_Mutation_p.C738G|NLRP11_ENST00000443188.1_Missense_Mutation_p.C792G|NLRP11_ENST00000592953.1_Missense_Mutation_p.C693G			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	792							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		AGGGCGCTGCAGCAATTTTCA	0.498													A|||	151	0.0301518	0.1097	0.0086	5008	,	,		19216	0.0		0.0	False		,,,				2504	0.0				p.C792G		Atlas-SNP	.											.	NLRP11	139	.	0			c.T2374G						PASS	.	A	GLY/CYS	357,4049	184.0+/-211.4	11,335,1857	110.0	102.0	105.0		2374	-0.1	0.0	19	dbSNP_131	105	7,8593	4.3+/-15.6	0,7,4293	yes	missense	NLRP11	NM_145007.3	159	11,342,6150	CC,CA,AA		0.0814,8.1026,2.7987	probably-damaging	792/1034	56303806	364,12642	2203	4300	6503	SO:0001583	missense	204801	exon9			CGCTGCAGCAATT	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.2374T>G	19.37:g.56303806A>C	ENSP00000466285:p.Cys792Gly	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	41	0.018772893772893772	40	0.08130081300813008	1	0.0027624309392265192	0	0.0	0	0.0	A	10.23	1.292437	0.23564	0.081026	8.14E-4	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.53423	0.62;0.62	2.18	-0.114	0.13564	.	.	.	.	.	T	0.10637	0.0260	M	0.93062	3.375	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.71656	0.942;0.974	T	0.24368	-1.0162	9	0.87932	D	0	.	2.8277	0.05490	0.5109:0.3169:0.1722:0.0	.	792;738	P59045;P59045-2	NAL11_HUMAN;.	G	792;738	ENSP00000409898:C792G;ENSP00000353251:C738G	ENSP00000353251:C738G	C	-	1	0	NLRP11	60995618	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.262000	0.18460	-0.089000	0.12484	-0.340000	0.08031	TGC	A|0.976;C|0.024	0.024	strong		0.498	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
C5orf52	100190949	hgsc.bcm.edu	37	5	157106968	157106968	+	Silent	SNP	C	C	T	rs6892478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:157106968C>T	ENST00000409999.3	+	3	503	c.441C>T	c.(439-441)agC>agT	p.S147S		NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	147										endometrium(2)|lung(1)	3						CCGTGAACAGCAACCGGTACT	0.498													.|||	828	0.165335	0.2912	0.1326	5008	,	,		18596	0.0734		0.1551	False		,,,				2504	0.1237				p.S147S		Atlas-SNP	.											.	C5orf52	17	.	0			c.C441T						PASS	.	C		348,1036		42,264,386	123.0	120.0	121.0		441	1.0	0.0	5	dbSNP_116	121	439,2743		34,371,1186	no	coding-synonymous	C5orf52	NM_001145132.1		76,635,1572	TT,TC,CC		13.7964,25.1445,17.2361		147/160	157106968	787,3779	692	1591	2283	SO:0001819	synonymous_variant	100190949	exon3			GAACAGCAACCGG	BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.441C>T	5.37:g.157106968C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_001145132		Silent	SNP	ENST00000409999.3	37	CCDS47329.1																																																																																			C|0.837;G|0.000;T|0.162	0.162	strong		0.498	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335664.1	NM_001145132	
C10orf62	414157	hgsc.bcm.edu	37	10	99350017	99350017	+	Missense_Mutation	SNP	G	G	C	rs7093840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99350017G>C	ENST00000370640.3	+	1	568	c.363G>C	c.(361-363)gaG>gaC	p.E121D	HOGA1_ENST00000370647.4_Intron|HOGA1_ENST00000370646.4_Intron|PI4K2A_ENST00000370649.3_Intron|PI4K2A_ENST00000555577.1_Intron	NM_001009997.2	NP_001009997.2	Q5T681	CJ062_HUMAN	chromosome 10 open reading frame 62	121			E -> D (in dbSNP:rs7093840). {ECO:0000269|PubMed:15489334}.							endometrium(2)|kidney(1)|lung(1)	4		Colorectal(252;0.162)		Epithelial(162;9.58e-11)|all cancers(201;8.62e-09)		CCACTGATGAGGCCACGTGGG	0.612													G|||	1327	0.264976	0.3124	0.2896	5008	,	,		17502	0.1369		0.3082	False		,,,				2504	0.271				p.E121D		Atlas-SNP	.											.	C10orf62	14	.	0			c.G363C						PASS	.	G	ASP/GLU,,	1472,2934	464.7+/-354.0	252,968,983	42.0	45.0	44.0		363,,	-0.3	0.4	10	dbSNP_116	44	2699,5901	425.6+/-355.0	414,1871,2015	yes	missense,intron,intron	HOGA1,C10orf62	NM_001009997.2,NM_001134670.1,NM_138413.3	45,,	666,2839,2998	CC,CG,GG		31.3837,33.409,32.0698	benign,,	121/224,,	99350017	4171,8835	2203	4300	6503	SO:0001583	missense	414157	exon1			TGATGAGGCCACG		CCDS31261.1	10q24.2	2012-05-31			ENSG00000203942	ENSG00000203942			23294	protein-coding gene	gene with protein product							Standard	NM_001009997		Approved	bA548K23.1	uc001koa.3	Q5T681	OTTHUMG00000018858	ENST00000370640.3:c.363G>C	10.37:g.99350017G>C	ENSP00000359674:p.Glu121Asp	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_001009997	Q49A70|Q8N3Y6	Missense_Mutation	SNP	ENST00000370640.3	37	CCDS31261.1	555	0.2541208791208791	168	0.34146341463414637	91	0.2513812154696133	71	0.12412587412587413	225	0.29683377308707126	G	7.559	0.664348	0.14710	0.33409	0.313837	ENSG00000203942	ENST00000370640	T	0.51325	0.71	5.27	-0.32	0.12721	.	0.532357	0.15253	N	0.272205	T	0.00012	0.0000	N	0.12182	0.205	0.43214	P	0.0049120000000000275	B	0.20052	0.041	B	0.20184	0.028	T	0.43065	-0.9414	9	0.20519	T	0.43	-6.3121	4.6706	0.12687	0.1697:0.0:0.3888:0.4415	rs7093840;rs17853720;rs7093840	121	Q5T681	CJ062_HUMAN	D	121	ENSP00000359674:E121D	ENSP00000359674:E121D	E	+	3	2	C10orf62	99340007	0.000000	0.05858	0.396000	0.26296	0.743000	0.42351	-0.377000	0.07456	-0.074000	0.12820	0.643000	0.83706	GAG	G|0.706;C|0.294	0.294	strong		0.612	C10orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049723.1	NM_001009997	
LCE5A	254910	hgsc.bcm.edu	37	1	152484129	152484129	+	Missense_Mutation	SNP	G	G	A	rs2105117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152484129G>A	ENST00000334269.2	+	2	295	c.119G>A	c.(118-120)tGt>tAt	p.C40Y	CRCT1_ENST00000368790.3_5'Flank	NM_178438.4	NP_848525.1	Q5TCM9	LCE5A_HUMAN	late cornified envelope 5A	40	Cys-rich.		C -> Y (in dbSNP:rs2105117).		keratinization (GO:0031424)					lung(3)|ovary(1)|prostate(3)	7	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTCCCCAGTGTTCAGCCCCA	0.612													G|||	2614	0.521965	0.3132	0.5346	5008	,	,		15690	0.6111		0.6223	False		,,,				2504	0.6002				p.C40Y		Atlas-SNP	.											.	LCE5A	15	.	0			c.G119A						PASS	.	G	TYR/CYS	1549,2857	487.8+/-361.0	277,995,931	93.0	86.0	88.0		119	0.9	0.0	1	dbSNP_96	88	5425,3175	655.0+/-401.2	1716,1993,591	yes	missense	LCE5A	NM_178438.4	194	1993,2988,1522	AA,AG,GG		36.9186,35.1566,46.3786	benign	40/119	152484129	6974,6032	2203	4300	6503	SO:0001583	missense	254910	exon2			CCCAGTGTTCAGC	BI670518	CCDS1011.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000186207	ENSG00000186207		"""Late cornified envelopes"""	16614	protein-coding gene	gene with protein product		612619	"""small proline rich-like (epidermal differentiation complex) 5A"""	SPRL5A		11698679	Standard	NM_178438		Approved	LEP18	uc001ezy.3	Q5TCM9	OTTHUMG00000014401	ENST00000334269.2:c.119G>A	1.37:g.152484129G>A	ENSP00000333952:p.Cys40Tyr	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	184	91	0.494565	NM_178438		Missense_Mutation	SNP	ENST00000334269.2	37	CCDS1011.1	1216	0.5567765567765568	161	0.32723577235772355	210	0.580110497237569	367	0.6416083916083916	478	0.6306068601583114	G	0.982	-0.696693	0.03279	0.351566	0.630814	ENSG00000186207	ENST00000334269	T	0.03982	3.74	1.84	0.898	0.19264	.	.	.	.	.	T	0.01695	0.0054	L	0.54323	1.7	0.80722	P	0.0	B	0.15719	0.014	B	0.08055	0.003	T	0.37407	-0.9707	8	0.56958	D	0.05	.	4.2828	0.10841	0.2119:0.0:0.7881:0.0	rs2105117;rs17657912;rs52814697;rs58898265;rs2105117	40	Q5TCM9	LCE5A_HUMAN	Y	40	ENSP00000333952:C40Y	ENSP00000333952:C40Y	C	+	2	0	LCE5A	150750753	0.001000	0.12720	0.009000	0.14445	0.794000	0.44872	0.308000	0.19314	0.324000	0.23333	0.195000	0.17529	TGT	G|0.469;A|0.531	0.531	strong		0.612	LCE5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040059.1	NM_178438	
SDC4	6385	hgsc.bcm.edu	37	20	43976991	43976991	+	Missense_Mutation	SNP	A	A	G	rs2228384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43976991A>G	ENST00000372733.3	-	1	73	c.34T>C	c.(34-36)Ttc>Ctc	p.F12L	SDC4_ENST00000537976.1_5'UTR	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	12			F -> L (in dbSNP:rs4458268). {ECO:0000269|PubMed:1500433, ECO:0000269|Ref.6}.		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|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)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)		SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				CCTACGAAGAACAGCAGCAGC	0.736			T	ROS1	NSCLC								G|||	1564	0.3123	0.1324	0.3012	5008	,	,		7892	0.4216		0.3807	False		,,,				2504	0.3804				p.F12L		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	SDC4,NS,carcinoma,0,1	SDC4	16	1	0			c.T34C						PASS	.	G	LEU/PHE	704,3632		68,568,1532	14.0	16.0	16.0		34	1.9	0.7	20	dbSNP_111	16	2893,5617		542,1809,1904	yes	missense	SDC4	NM_002999.3	22	610,2377,3436	GG,GA,AA		33.9953,16.2362,28.0009	benign	12/199	43976991	3597,9249	2168	4255	6423	SO:0001583	missense	6385	exon1			CGAAGAACAGCAG	X67016, D13292	CCDS13350.1	20q12	2010-03-25	2007-02-15		ENSG00000124145	ENSG00000124145		"""Proteoglycans / Cell Surface : Syndecans"""	10661	protein-coding gene	gene with protein product	"""syndecan proteoglycan 4"""	600017	"""syndecan 4 (amphiglycan, ryudocan)"""			7916598, 1500433	Standard	NM_002999		Approved	SYND4, amphiglycan, ryudocan	uc002xnu.3	P31431	OTTHUMG00000033083	ENST00000372733.3:c.34T>C	20.37:g.43976991A>G	ENSP00000361818:p.Phe12Leu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	67	24	0.358209	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	37	CCDS13350.1	735	0.33653846153846156	49	0.09959349593495935	128	0.35359116022099446	262	0.458041958041958	296	0.39050131926121373	G	11.74	1.727977	0.30593	0.162362	0.339953	ENSG00000124145	ENST00000372733	T	0.26660	1.72	3.88	1.9	0.25705	.	1.457070	0.04340	N	0.353868	T	0.00012	0.0000	N	0.00210	-1.845	0.09310	P	0.99999838508	B	0.02656	0.0	B	0.01281	0.0	T	0.44314	-0.9336	9	0.09590	T	0.72	-1.4689	5.8347	0.18601	0.3534:0.0:0.6466:0.0	rs4458268;rs17173359;rs60954343;rs4458268	12	P31431	SDC4_HUMAN	L	12	ENSP00000361818:F12L	ENSP00000361818:F12L	F	-	1	0	SDC4	43410405	0.991000	0.36638	0.736000	0.30914	0.806000	0.45545	0.205000	0.17356	0.091000	0.17302	-0.186000	0.12905	TTC	A|0.686;G|0.314	0.314	strong		0.736	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999	
ERBB3	2065	hgsc.bcm.edu	37	12	56487201	56487201	+	Silent	SNP	T	T	C	rs2229046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56487201T>C	ENST00000267101.3	+	12	1787	c.1347T>C	c.(1345-1347)atT>atC	p.I449I	ERBB3_ENST00000553131.1_5'Flank|ERBB3_ENST00000415288.2_Silent_p.I390I|ERBB3_ENST00000450146.2_Intron	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	449					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			TGAAGGAAATTAGTGCTGGGC	0.502													T|||	248	0.0495208	0.0749	0.0403	5008	,	,		19177	0.001		0.0726	False		,,,				2504	0.0481				p.I449I		Atlas-SNP	.											.	ERBB3	350	.	0			c.T1347C						PASS	.	T		357,4049	184.0+/-211.4	10,337,1856	101.0	104.0	103.0		1347	-9.1	0.7	12	dbSNP_98	103	600,8000	158.2+/-211.7	27,546,3727	no	coding-synonymous	ERBB3	NM_001982.3		37,883,5583	CC,CT,TT		6.9767,8.1026,7.3581		449/1343	56487201	957,12049	2203	4300	6503	SO:0001819	synonymous_variant	2065	exon12			GGAAATTAGTGCT	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"""lethal congenital contracture syndrome 2"""	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.1347T>C	12.37:g.56487201T>C		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	170	97	0.570588	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Silent	SNP	ENST00000267101.3	37	CCDS31833.1																																																																																			T|0.932;C|0.068	0.068	strong		0.502	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		
ST3GAL5	8869	hgsc.bcm.edu	37	2	86088311	86088311	+	Missense_Mutation	SNP	T	T	C	rs1138484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86088311T>C	ENST00000377332.3	-	3	419	c.311A>G	c.(310-312)cAt>cGt	p.H104R	ST3GAL5_ENST00000393805.1_Missense_Mutation_p.H76R|ST3GAL5_ENST00000484728.1_5'UTR|ST3GAL5_ENST00000525834.2_Missense_Mutation_p.H104R|ST3GAL5_ENST00000393808.3_Missense_Mutation_p.H81R	NM_003896.3	NP_003887.3	Q9UNP4	SIAT9_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	104			H -> R (in dbSNP:rs3731824). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9822625, ECO:0000269|Ref.2}.		carbohydrate metabolic process (GO:0005975)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	lactosylceramide alpha-2,3-sialyltransferase activity (GO:0047291)|neolactotetraosylceramide alpha-2,3-sialyltransferase activity (GO:0004513)|sialyltransferase activity (GO:0008373)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15						AACCTTTACATGGTCAGGGTC	0.338													C|||	1047	0.209065	0.0605	0.1527	5008	,	,		20921	0.2937		0.1968	False		,,,				2504	0.3753				p.H104R		Atlas-SNP	.											.	ST3GAL5	51	.	0			c.A311G						PASS	.	C	ARG/HIS,ARG/HIS	334,4072	795.3+/-415.3	17,300,1886	116.0	109.0	111.0		242,311	5.0	0.7	2	dbSNP_107	111	1705,6895	737.1+/-407.0	173,1359,2768	yes	missense,missense	ST3GAL5	NM_001042437.1,NM_003896.3	29,29	190,1659,4654	CC,CT,TT		19.8256,7.5806,15.6774	benign,benign	81/396,104/419	86088311	2039,10967	2203	4300	6503	SO:0001583	missense	8869	exon3			TTTACATGGTCAG	AB018356	CCDS1986.2, CCDS42705.1	2p11.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000115525	ENSG00000115525	2.4.99.9	"""Sialyltransferases"""	10872	protein-coding gene	gene with protein product		604402	"""sialyltransferase 9 (CMP-NeuAc:lactosylceramide alpha-2,3-sialyltransferase; GM3 synthase)"""	SIAT9		9822625	Standard	NM_003896		Approved	ST3GalV, SIATGM3S	uc002sqq.1	Q9UNP4	OTTHUMG00000130171	ENST00000377332.3:c.311A>G	2.37:g.86088311T>C	ENSP00000366549:p.His104Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_003896	B3KM82|D6W5L9|O94902|Q53QU1|Q6NZX4|Q6YFL1	Missense_Mutation	SNP	ENST00000377332.3	37	CCDS1986.2	405	0.18543956043956045	28	0.056910569105691054	73	0.20165745856353592	169	0.29545454545454547	135	0.17810026385224276	C	0.240	-1.014477	0.02095	0.075806	0.198256	ENSG00000115525	ENST00000393808;ENST00000393805;ENST00000377332;ENST00000455892;ENST00000525834	T;T;T;T;T	0.36878	1.71;1.71;1.72;1.23;1.29	5.84	4.96	0.65561	.	0.494910	0.22557	N	0.058515	T	0.00012	0.0000	N	0.01168	-0.975	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	0.35798	-0.9774	9	0.02654	T	1	-4.2027	9.0708	0.36491	0.0:0.8325:0.0:0.1675	rs3731824;rs52830384;rs60063777;rs3731824	104;104;81	G3V199;Q9UNP4;Q9UNP4-3	.;SIAT9_HUMAN;.	R	81;76;104;76;104	ENSP00000377397:H81R;ENSP00000377394:H76R;ENSP00000366549:H104R;ENSP00000401375:H76R;ENSP00000433607:H104R	ENSP00000306247:H104R	H	-	2	0	ST3GAL5	85941822	0.674000	0.27549	0.655000	0.29622	0.439000	0.31926	0.845000	0.27668	0.821000	0.34540	-0.119000	0.15052	CAT	T|0.829;C|0.171	0.171	strong		0.338	ST3GAL5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252486.1	NM_003896	
OR52H1	390067	hgsc.bcm.edu	37	11	5565906	5565906	+	Missense_Mutation	SNP	A	A	G	rs7934354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5565906A>G	ENST00000322653.4	-	1	873	c.848T>C	c.(847-849)aTg>aCg	p.M283T	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	283			M -> T (in dbSNP:rs7934354).			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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATTGGCAAACATGATGTGGAA	0.448													A|||	855	0.170727	0.1619	0.1124	5008	,	,		22980	0.3671		0.0219	False		,,,				2504	0.1748				p.M283T		Atlas-SNP	.											.	OR52H1	46	.	0			c.T848C						PASS	.	A	THR/MET	611,3791	270.4+/-269.6	44,523,1634	212.0	200.0	204.0		848	5.2	1.0	11	dbSNP_116	204	171,8423	78.9+/-141.6	1,169,4127	yes	missense	OR52H1	NM_001005289.1	81	45,692,5761	GG,GA,AA		1.9898,13.8801,6.0172	benign	283/321	5565906	782,12214	2201	4297	6498	SO:0001583	missense	390067	exon1			GCAAACATGATGT	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.848T>C	11.37:g.5565906A>G	ENSP00000326259:p.Met283Thr	Somatic	336	1	0.00297619		WXS	Illumina HiSeq	Phase_I	287	147	0.512195	NM_001005289	B9EH26|Q6IF79	Missense_Mutation	SNP	ENST00000322653.4	37	CCDS31386.1	340	0.15567765567765568	85	0.17276422764227642	28	0.07734806629834254	208	0.36363636363636365	19	0.025065963060686015	A	13.74	2.326455	0.41197	0.138801	0.019898	ENSG00000181616	ENST00000322653	T	0.00137	8.68	5.22	5.22	0.72569	GPCR, rhodopsin-like superfamily (1);	0.337248	0.29145	N	0.013005	T	0.00012	0.0000	N	0.21583	0.68	0.37226	P	0.09451699999999996	P	0.34699	0.464	B	0.36092	0.217	T	0.48502	-0.9030	9	0.87932	D	0	.	13.9278	0.63972	1.0:0.0:0.0:0.0	rs7934354;rs56428950;rs58313900;rs7934354	283	Q8NGJ2	O52H1_HUMAN	T	283	ENSP00000326259:M283T	ENSP00000326259:M283T	M	-	2	0	OR52H1	5522482	0.009000	0.17119	1.000000	0.80357	0.965000	0.64279	2.635000	0.46537	1.968000	0.57251	0.528000	0.53228	ATG	A|0.887;G|0.113	0.113	strong		0.448	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
TACC2	10579	hgsc.bcm.edu	37	10	123843946	123843946	+	Missense_Mutation	SNP	C	C	T	rs60531929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123843946C>T	ENST00000369005.1	+	4	2271	c.1931C>T	c.(1930-1932)aCg>aTg	p.T644M	TACC2_ENST00000515273.1_Missense_Mutation_p.T644M|TACC2_ENST00000515603.1_Missense_Mutation_p.T644M|TACC2_ENST00000453444.2_Missense_Mutation_p.T644M|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000334433.3_Missense_Mutation_p.T644M|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	644					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GCTGGGCACACGGACGGGCCC	0.612													C|||	150	0.0299521	0.1036	0.0173	5008	,	,		18351	0.0		0.001	False		,,,				2504	0.0				p.T644M		Atlas-SNP	.											.	TACC2	271	.	0			c.C1931T						PASS	.	C	,MET/THR	445,3961	208.8+/-229.8	26,393,1784	37.0	35.0	35.0		,1931	-10.0	0.0	10	dbSNP_129	35	9,8591	5.0+/-18.6	0,9,4291	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,81	26,402,6075	TT,TC,CC		0.1047,10.0999,3.4907	,possibly-damaging	,644/2949	123843946	454,12552	2203	4300	6503	SO:0001583	missense	10579	exon4			GGCACACGGACGG	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.1931C>T	10.37:g.123843946C>T	ENSP00000358001:p.Thr644Met	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	47	0.02152014652014652	41	0.08333333333333333	6	0.016574585635359115	0	0.0	0	0.0	C	6.831	0.522532	0.13066	0.100999	0.001047	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.03413	3.96;3.94;3.94;3.96;3.94	5.02	-10.0	0.00425	.	3.389020	0.01191	N	0.007326	T	0.00073	0.0002	N	0.14661	0.345	0.09310	N	1	P;P;P	0.42757	0.789;0.789;0.789	B;B;B	0.29785	0.107;0.107;0.107	T	0.45659	-0.9246	10	0.45353	T	0.12	11.5241	1.2386	0.01958	0.331:0.1646:0.0943:0.41	rs60531929	644;644;644	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	M	644;644;644;644;644;634	ENSP00000358001:T644M;ENSP00000424467:T644M;ENSP00000427618:T644M;ENSP00000334280:T644M;ENSP00000395048:T644M	ENSP00000334280:T644M	T	+	2	0	TACC2	123833936	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.942000	0.00167	-1.779000	0.01280	0.561000	0.74099	ACG	C|0.965;T|0.035	0.035	strong		0.612	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
CYP2D6	1565	hgsc.bcm.edu	37	22	42523636	42523636	+	Splice_Site	SNP	C	C	A	rs1135831|rs3915951		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42523636C>A	ENST00000360608.5	-	7	1100	c.986G>T	c.(985-987)cGc>cTc	p.R329L	NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|CYP2D6_ENST00000389970.3_Splice_Site_p.R329L|NDUFA6-AS1_ENST00000417327.1_RNA|CYP2D6_ENST00000359033.4_Splice_Site_p.R278L|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA	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	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	157	14	0.089172	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
ROS1	6098	hgsc.bcm.edu	37	6	117725578	117725578	+	Silent	SNP	T	T	A	rs2243378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117725578T>A	ENST00000368508.3	-	5	501	c.303A>T	c.(301-303)ctA>ctT	p.L101L	ROS1_ENST00000368507.3_Silent_p.L110L|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	101	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		GAGCAGTTGGTAGGTCTGCAT	0.453			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								A|||	3381	0.67512	0.9244	0.5231	5008	,	,		17193	0.5675		0.502	False		,,,				2504	0.7352				p.L101L		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.A303T						PASS	.	A		3785,621	267.7+/-268.0	1638,509,56	89.0	88.0	88.0		303	-3.9	0.0	6	dbSNP_98	88	4008,4592	599.6+/-394.1	942,2124,1234	no	coding-synonymous	ROS1	NM_002944.2		2580,2633,1290	AA,AT,TT		46.6047,14.0944,40.0815		101/2348	117725578	7793,5213	2203	4300	6503	SO:0001819	synonymous_variant	6098	exon5			AGTTGGTAGGTCT	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.303A>T	6.37:g.117725578T>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																			T|0.406;A|0.594	0.594	strong		0.453	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
GRIK3	2899	hgsc.bcm.edu	37	1	37325477	37325477	+	Missense_Mutation	SNP	A	A	C	rs6691840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:37325477A>C	ENST00000373091.3	-	6	944	c.928T>G	c.(928-930)Tcc>Gcc	p.S310A	GRIK3_ENST00000373093.4_Missense_Mutation_p.S310A|GRIK3_ENST00000462621.1_5'Flank	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	310			S -> A (in dbSNP:rs6691840). {ECO:0000269|PubMed:11124978, ECO:0000269|PubMed:7719709}.		adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CCAGACTCGGACCGGGGAGCT	0.587													C|||	1533	0.30611	0.6203	0.2709	5008	,	,		15135	0.0446		0.2952	False		,,,				2504	0.1871				p.S310A		Atlas-SNP	.											.	GRIK3	195	.	0			c.T928G	GRCh37	CM025291	GRIK3	M	rs6691840	PASS	.	C	ALA/SER	2371,2035	558.9+/-380.1	676,1019,508	61.0	66.0	64.0		928	3.8	0.0	1	dbSNP_116	64	2295,6305	701.5+/-405.2	308,1679,2313	yes	missense	GRIK3	NM_000831.3	99	984,2698,2821	CC,CA,AA		26.686,46.187,35.8757	benign	310/920	37325477	4666,8340	2203	4300	6503	SO:0001583	missense	2899	exon6			ACTCGGACCGGGG	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.928T>G	1.37:g.37325477A>C	ENSP00000362183:p.Ser310Ala	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	140	61	0.435714	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	37	CCDS416.1	638	0.29212454212454214	290	0.5894308943089431	99	0.27348066298342544	18	0.03146853146853147	231	0.30474934036939316	C	3.703	-0.061061	0.07317	0.53813	0.26686	ENSG00000163873	ENST00000373091;ENST00000373093	T;T	0.21361	2.01;2.01	5.7	3.85	0.44370	Extracellular ligand-binding receptor (1);	0.386683	0.29225	N	0.012766	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	0.06405	0.002;0.001	T	0.46925	-0.9156	9	0.02654	T	1	.	3.8289	0.08865	0.1225:0.5114:0.2339:0.1322	rs6691840;rs6691840	310;310	A9Z1Z8;Q13003	.;GRIK3_HUMAN	A	310	ENSP00000362183:S310A;ENSP00000362185:S310A	ENSP00000362183:S310A	S	-	1	0	GRIK3	37098064	0.539000	0.26402	0.030000	0.17652	0.303000	0.27691	0.914000	0.28624	0.365000	0.24400	-0.121000	0.15023	TCC	A|0.660;C|0.340	0.340	strong		0.587	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831	
GPR110	266977	hgsc.bcm.edu	37	6	46976812	46976812	+	Missense_Mutation	SNP	T	T	C	rs1226475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46976812T>C	ENST00000371253.2	-	11	2574	c.2359A>G	c.(2359-2361)Atc>Gtc	p.I787V	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.I590V	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	787			I -> V (in dbSNP:rs1226475).		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						CCCACGCGGATGATGGTGGCC	0.547													C|||	1039	0.207468	0.4924	0.1499	5008	,	,		17465	0.1776		0.0089	False		,,,				2504	0.0982				p.I787V		Atlas-SNP	.											.	GPR110	102	.	0			c.A2359G						PASS	.	C	VAL/ILE	1650,2756	658.4+/-400.4	301,1048,854	69.0	72.0	71.0		2359	-2.8	0.0	6	dbSNP_87	71	68,8532	816.3+/-406.9	0,68,4232	yes	missense	GPR110	NM_153840.2	29	301,1116,5086	CC,CT,TT		0.7907,37.4489,13.2093	benign	787/911	46976812	1718,11288	2203	4300	6503	SO:0001583	missense	266977	exon11			CGCGGATGATGGT	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.2359A>G	6.37:g.46976812T>C	ENSP00000360299:p.Ile787Val	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	146	63	0.431507	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	37	CCDS34471.1	395	0.18086080586080586	236	0.4796747967479675	44	0.12154696132596685	107	0.18706293706293706	8	0.010554089709762533	C	0.004	-2.307123	0.00240	0.374489	0.007907	ENSG00000153292	ENST00000371253;ENST00000283297	T;T	0.32023	1.47;1.47	5.9	-2.84	0.05751	GPCR, family 2-like (1);	1.234140	0.05613	N	0.578468	T	0.05181	0.0138	N	0.10916	0.065	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.36696	-0.9737	9	0.16420	T	0.52	-0.9218	12.6954	0.57001	0.0:0.0893:0.0829:0.8278	rs1226475;rs1762331;rs52807982;rs1226475	787	Q5T601	GP110_HUMAN	V	787;590	ENSP00000360299:I787V;ENSP00000283297:I590V	ENSP00000283297:I590V	I	-	1	0	GPR110	47084771	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-0.155000	0.10115	-1.185000	0.02716	-0.755000	0.03482	ATC	T|0.836;C|0.164	0.164	strong		0.547	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
MED16	10025	hgsc.bcm.edu	37	19	879943	879943	+	Silent	SNP	G	G	A	rs201392672|rs76403059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:879943G>A	ENST00000589119.1	-	7	1346	c.1347C>T	c.(1345-1347)caC>caT	p.H449H	MED16_ENST00000325464.1_Silent_p.H449H|MED16_ENST00000606828.1_Intron|MED16_ENST00000312090.6_Silent_p.H449H|MED16_ENST00000269814.4_Silent_p.H449H|MED16_ENST00000395808.3_Silent_p.H449H			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	449					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)		TCACCTTCCCGTGGCTGTCAA	0.672													C|||	25	0.00499201	0.0182	0.0	5008	,	,		15050	0.0		0.001	False		,,,				2504	0.0				p.H449H		Atlas-SNP	.											MED16,colon,carcinoma,0,1	MED16	61	1	0			c.C1347T						PASS	.	C		34,4270		0,34,2118	13.0	11.0	12.0		1347	-7.9	0.9	19	dbSNP_131	12	3,8491		0,3,4244	yes	coding-synonymous	MED16	NM_005481.2		0,37,6362	AA,AG,GG		0.0353,0.79,0.2891		449/878	879943	37,12761	2152	4247	6399	SO:0001819	synonymous_variant	10025	exon8			CTTCCCGTGGCTG	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.1347C>T	19.37:g.879943G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	121	48	0.396694	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1																																																																																			.	.	weak		0.672	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133918372	133918372	+	Silent	SNP	G	G	A	rs10870252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:133918372G>A	ENST00000298622.4	+	1	198	c.60G>A	c.(58-60)gcG>gcA	p.A20A		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	20						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)		CCCTCGCGGCGCTGCAGGCGG	0.667													G|||	1173	0.234225	0.3941	0.1412	5008	,	,		15314	0.2907		0.175	False		,,,				2504	0.0869				p.A20A		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.G60A						PASS	.	G		1332,2794		223,886,954	17.0	23.0	21.0		60	-7.6	0.0	10	dbSNP_120	21	1493,6905		139,1215,2845	no	coding-synonymous	JAKMIP3	NM_001105521.2		362,2101,3799	AA,AG,GG		17.778,32.2831,22.5567		20/845	133918372	2825,9699	2063	4199	6262	SO:0001819	synonymous_variant	282973	exon1			CGCGGCGCTGCAG	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.60G>A	10.37:g.133918372G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	171	87	0.508772	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																			G|0.741;A|0.259	0.259	strong		0.667	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
FBP2	8789	hgsc.bcm.edu	37	9	97325726	97325726	+	Silent	SNP	A	A	G	rs41281154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:97325726A>G	ENST00000375337.3	-	6	789	c.723T>C	c.(721-723)taT>taC	p.Y241Y	PCAT7_ENST00000452148.2_RNA	NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	241					carbohydrate metabolic process (GO:0005975)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(3)|lung(5)	9		Acute lymphoblastic leukemia(62;0.136)				ACCTGGCCCCATAGGGAGCAC	0.562													.|||	655	0.130791	0.2413	0.111	5008	,	,		20161	0.124		0.0298	False		,,,				2504	0.1063				p.Y241Y		Atlas-SNP	.											.	FBP2	26	.	0			c.T723C						PASS	.	A		955,3451		112,731,1360	120.0	106.0	111.0		723	1.0	1.0	9	dbSNP_127	111	193,8407		3,187,4110	no	coding-synonymous	FBP2	NM_003837.2		115,918,5470	GG,GA,AA		2.2442,21.675,8.8267		241/340	97325726	1148,11858	2203	4300	6503	SO:0001819	synonymous_variant	8789	exon6			GGCCCCATAGGGA	Y10812	CCDS6711.1	9q22.3	2012-08-13			ENSG00000130957	ENSG00000130957	3.1.3.11		3607	protein-coding gene	gene with protein product		603027				9678974	Standard	NM_003837		Approved		uc004auv.3	O00757	OTTHUMG00000020269	ENST00000375337.3:c.723T>C	9.37:g.97325726A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	24	0.303797	NM_003837	Q17R39|Q6FI53	Silent	SNP	ENST00000375337.3	37	CCDS6711.1																																																																																			A|0.912;G|0.088	0.088	strong		0.562	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837	
LCN8	138307	hgsc.bcm.edu	37	9	139649701	139649701	+	Missense_Mutation	SNP	C	C	T	rs144857499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139649701C>T	ENST00000371688.3	-	5	711	c.416G>A	c.(415-417)cGg>cAg	p.R139Q	LCN8_ENST00000482893.1_5'UTR	NM_178469.3	NP_848564.2	Q6JVE9	LCN8_HUMAN	lipocalin 8	162					response to hormone (GO:0009725)|transport (GO:0006810)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	10	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)		CTCACCAGGCCGGGCCGCCAG	0.682													C|||	7	0.00139776	0.0045	0.0014	5008	,	,		14888	0.0		0.0	False		,,,				2504	0.0				p.R139Q		Atlas-SNP	.											.	LCN8	14	.	0			c.G416A						PASS	.	C	GLN/ARG	25,4379	30.8+/-60.4	0,25,2177	39.0	48.0	45.0		416	1.9	0.2	9	dbSNP_134	45	1,8599		0,1,4299	yes	missense	LCN8	NM_178469.3	43	0,26,6476	TT,TC,CC		0.0116,0.5677,0.1999	probably-damaging	139/153	139649701	26,12978	2202	4300	6502	SO:0001583	missense	138307	exon5			CCAGGCCGGGCCG	AK124003	CCDS35183.1	9q34.3	2011-10-24	2005-01-11		ENSG00000204001	ENSG00000204001		"""Lipocalins"""	27038	protein-coding gene	gene with protein product		612902	"""chromosome 9 open reading frame 137"", ""lipocalin 5"""	LCN5			Standard	XM_005266058		Approved		uc004cjb.1	Q6JVE9	OTTHUMG00000020942	ENST00000371688.3:c.416G>A	9.37:g.139649701C>T	ENSP00000360753:p.Arg139Gln	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	80	55	0.6875	NM_178469	A1L4A8|A6NMN9|Q5T5R4	Missense_Mutation	SNP	ENST00000371688.3	37	CCDS35183.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	9.456	1.091903	0.20471	0.005677	1.16E-4	ENSG00000204001	ENST00000371688	T	0.34667	1.35	2.76	1.85	0.25348	.	.	.	.	.	T	0.14700	0.0355	N	0.24115	0.695	0.09310	N	1	B	0.23490	0.086	B	0.15870	0.014	T	0.15723	-1.0427	9	0.28530	T	0.3	.	5.487	0.16755	0.0:0.8418:0.0:0.1582	.	139	Q6JVE9-2	.	Q	139	ENSP00000360753:R139Q	ENSP00000360753:R139Q	R	-	2	0	LCN8	138769522	0.058000	0.20735	0.229000	0.23960	0.549000	0.35272	0.257000	0.18369	0.731000	0.32448	0.491000	0.48974	CGG	C|0.997;T|0.003	0.003	strong		0.682	LCN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055109.1	NM_178469	
NUP133	55746	hgsc.bcm.edu	37	1	229623338	229623338	+	Missense_Mutation	SNP	T	T	C	rs1065674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229623338T>C	ENST00000261396.3	-	10	1308	c.1217A>G	c.(1216-1218)cAg>cGg	p.Q406R	NUP133_ENST00000537506.1_Missense_Mutation_p.Q390R	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	406			Q -> R (in dbSNP:rs1065674).		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 organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|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)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GACCGTCAACTGACACAAAAT	0.338													C|||	1519	0.303315	0.5802	0.3271	5008	,	,		16738	0.1607		0.2097	False		,,,				2504	0.1554				p.Q406R		Atlas-SNP	.											.	NUP133	111	.	0			c.A1217G						PASS	.	C	ARG/GLN	2321,2085	571.2+/-383.0	600,1121,482	83.0	85.0	84.0		1217	2.2	0.4	1	dbSNP_86	84	1863,6737	729.6+/-406.7	201,1461,2638	yes	missense	NUP133	NM_018230.2	43	801,2582,3120	CC,CT,TT		21.6628,47.3218,32.1698	benign	406/1157	229623338	4184,8822	2203	4300	6503	SO:0001583	missense	55746	exon10			GTCAACTGACACA		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1217A>G	1.37:g.229623338T>C	ENSP00000261396:p.Gln406Arg	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	612	0.2802197802197802	275	0.5589430894308943	100	0.27624309392265195	80	0.13986013986013987	157	0.20712401055408972	C	0.017	-1.505721	0.00992	0.526782	0.216628	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.35605	1.3;1.3;1.3	5.07	2.2	0.27929	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.167226	0.56097	N	0.000039	T	0.00012	0.0000	N	0.01015	-1.05	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48525	-0.9028	9	0.02654	T	1	-5.5753	9.3235	0.37980	0.0:0.583:0.0:0.417	rs1065674;rs17355666;rs60689296;rs1065674	406	Q8WUM0	NU133_HUMAN	R	406;406;406;390	ENSP00000261396:Q406R;ENSP00000355640:Q406R;ENSP00000443496:Q390R	ENSP00000261396:Q406R	Q	-	2	0	NUP133	227689961	0.910000	0.30920	0.355000	0.25773	0.580000	0.36256	1.748000	0.38308	0.029000	0.15352	-1.952000	0.00485	CAG	T|0.691;C|0.309	0.309	strong		0.338	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
OR2L8	391190	hgsc.bcm.edu	37	1	248112554	248112554	+	Missense_Mutation	SNP	T	T	C	rs202165563		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248112554T>C	ENST00000357191.3	+	1	395	c.395T>C	c.(394-396)cTc>cCc	p.L132P	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L132P(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			CTCCACTATCTCATCCGCATG	0.433																																					p.L132P		Atlas-SNP	.											OR2L8,trunk,malignant_melanoma,0,1	OR2L8	92	1	1	Substitution - Missense(1)	skin(1)	c.T395C						scavenged	.						294.0	255.0	269.0					1																	248112554		2203	4300	6503	SO:0001583	missense	391190	exon1			ACTATCTCATCCG	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"""GPCR / Class A : Olfactory receptors"""	15014	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily L, member 8"""				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.395T>C	1.37:g.248112554T>C	ENSP00000349719:p.Leu132Pro	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	338	41	0.121302	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	37	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.779851	0.00079	.	.	ENSG00000196936	ENST00000357191	T	0.00648	5.99	1.64	-3.28	0.05033	GPCR, rhodopsin-like superfamily (1);	0.569254	0.13211	N	0.405136	T	0.00210	0.0006	N	0.00554	-1.385	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32402	-0.9908	10	0.02654	T	1	.	2.9738	0.05930	0.1117:0.4051:0.1115:0.3717	.	132	Q8NGY9	OR2L8_HUMAN	P	132	ENSP00000349719:L132P	ENSP00000349719:L132P	L	+	2	0	OR2L8	246179177	0.000000	0.05858	0.002000	0.10522	0.242000	0.25591	-4.646000	0.00204	-2.286000	0.00670	-2.951000	0.00084	CTC	.	.	weak		0.433	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2		
MUC5B	727897	hgsc.bcm.edu	37	11	1271582	1271582	+	Missense_Mutation	SNP	C	C	T	rs200110193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1271582C>T	ENST00000529681.1	+	31	13530	c.13472C>T	c.(13471-13473)aCc>aTc	p.T4491I	MUC5B_ENST00000447027.1_Missense_Mutation_p.T4494I|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4491	23 X approximate tandem repeats, Ser/Thr- rich.|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)		CCCACAGTCACCAGCTCCAAA	0.642													C|||	68	0.0135783	0.0469	0.0086	5008	,	,		18910	0.0		0.0	False		,,,				2504	0.0				p.T4491I		Atlas-SNP	.											.	MUC5B	473	.	0			c.C13472T						PASS	.	C	ILE/THR	95,4235		2,91,2072	114.0	152.0	139.0		13472	0.4	0.0	11		139	0,8520		0,0,4260	no	missense	MUC5B	NM_002458.2	89	2,91,6332	TT,TC,CC		0.0,2.194,0.7393	probably-damaging	4491/5763	1271582	95,12755	2165	4260	6425	SO:0001583	missense	727897	exon31			CAGTCACCAGCTC	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.13472C>T	11.37:g.1271582C>T	ENSP00000436812:p.Thr4491Ile	Somatic	827	2	0.00241838		WXS	Illumina HiSeq	Phase_I	596	279	0.468121	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	-	1.101	-0.661133	0.03454	0.02194	0.0	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000535652	T;T	0.25749	1.78;1.97	0.399	0.399	0.16325	.	.	.	.	.	T	0.22475	0.0542	L	0.60455	1.87	0.09310	N	1	D;D	0.58970	0.984;0.984	P;P	0.59595	0.86;0.86	T	0.08351	-1.0726	8	0.87932	D	0	.	.	.	.	.	4964;4494	A7Y9J9;E9PBJ0	.;.	I	4491;4494;4435;4341;270	ENSP00000436812:T4491I;ENSP00000415793:T4494I	ENSP00000343037:T4435I	T	+	2	0	MUC5B	1228158	0.000000	0.05858	0.019000	0.16419	0.023000	0.10783	-0.180000	0.09754	0.440000	0.26502	0.162000	0.16502	ACC	.	.	weak		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SMC1B	27127	hgsc.bcm.edu	37	22	45741416	45741416	+	Missense_Mutation	SNP	T	T	A	rs61737925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45741416T>A	ENST00000357450.4	-	24	3529	c.3530A>T	c.(3529-3531)cAg>cTg	p.Q1177L	SMC1B_ENST00000404354.3_Missense_Mutation_p.Q1103L	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1177					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)		CATCTGAAACTGGTCTTGAGT	0.448													T|||	55	0.0109824	0.0408	0.0014	5008	,	,		18744	0.0		0.0	False		,,,				2504	0.0				p.Q1177L		Atlas-SNP	.											.	SMC1B	215	.	0			c.A3530T						PASS	.	T	LEU/GLN	155,3629		4,147,1741	133.0	127.0	129.0		3530	5.6	1.0	22	dbSNP_129	129	0,8236		0,0,4118	yes	missense	SMC1B	NM_148674.3	113	4,147,5859	AA,AT,TT		0.0,4.0962,1.2895	probably-damaging	1177/1236	45741416	155,11865	1892	4118	6010	SO:0001583	missense	27127	exon24			TGAAACTGGTCTT	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.3530A>T	22.37:g.45741416T>A	ENSP00000350036:p.Gln1177Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	148	78	0.527027	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	T	18.42	3.620931	0.66787	0.040962	0.0	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.77358	2.94;-1.09	5.61	5.61	0.85477	.	0.105145	0.42682	D	0.000676	T	0.46580	0.1400	L	0.43152	1.355	0.28411	N	0.91821	P;P	0.41848	0.763;0.573	P;B	0.44897	0.463;0.236	T	0.62779	-0.6782	10	0.40728	T	0.16	.	15.8023	0.78463	0.0:0.0:0.0:1.0	rs61737925	1103;1177	Q8NDV3-2;Q8NDV3-3	.;.	L	1177;1103	ENSP00000350036:Q1177L;ENSP00000385902:Q1103L	ENSP00000350036:Q1177L	Q	-	2	0	SMC1B	44120080	1.000000	0.71417	0.991000	0.47740	0.981000	0.71138	3.975000	0.56859	2.142000	0.66516	0.397000	0.26171	CAG	T|0.960;A|0.040	0.040	strong		0.448	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
WBSCR27	155368	hgsc.bcm.edu	37	7	73249092	73249092	+	Missense_Mutation	SNP	C	C	T	rs73369956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73249092C>T	ENST00000297873.4	-	6	768	c.719G>A	c.(718-720)cGa>cAa	p.R240Q		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	240										NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				CAACCTGGGTCGCCTTCCACT	0.632													C|||	173	0.0345447	0.1263	0.0072	5008	,	,		17029	0.0		0.001	False		,,,				2504	0.0				p.R240Q		Atlas-SNP	.											.	WBSCR27	21	.	0			c.G719A						PASS	.	C	GLN/ARG	448,3958	210.2+/-230.7	22,404,1777	47.0	43.0	44.0		719	-4.9	0.0	7	dbSNP_130	44	2,8598	2.2+/-6.3	0,2,4298	yes	missense	WBSCR27	NM_152559.2	43	22,406,6075	TT,TC,CC		0.0233,10.168,3.4599	benign	240/246	73249092	450,12556	2203	4300	6503	SO:0001583	missense	155368	exon6			CTGGGTCGCCTTC	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.719G>A	7.37:g.73249092C>T	ENSP00000297873:p.Arg240Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_152559		Missense_Mutation	SNP	ENST00000297873.4	37	CCDS5561.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	C	9.306	1.054385	0.19907	0.10168	2.33E-4	ENSG00000165171	ENST00000297873	T	0.36520	1.25	4.67	-4.88	0.03113	.	0.739448	0.13097	N	0.414080	T	0.00144	0.0004	N	0.02011	-0.69	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.25398	-1.0133	10	0.19147	T	0.46	-0.2142	2.1565	0.03814	0.1345:0.2371:0.1332:0.4952	.	240	Q8N6F8	WBS27_HUMAN	Q	240	ENSP00000297873:R240Q	ENSP00000297873:R240Q	R	-	2	0	WBSCR27	72887028	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-3.365000	0.00496	-0.582000	0.05929	0.549000	0.68633	CGA	C|0.962;T|0.038	0.038	strong		0.632	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559	
AMER1	139285	hgsc.bcm.edu	37	X	63410110	63410110	+	Silent	SNP	T	T	C	rs61730681	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:63410110T>C	ENST00000330258.3	-	2	3329	c.3057A>G	c.(3055-3057)caA>caG	p.Q1019Q	AMER1_ENST00000374869.3_Intron|AMER1_ENST00000403336.1_Intron	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	1019	Pro-rich.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									GACGAGCTAGTTGAGGCCCAG	0.567													C|||	1022	0.270728	0.7012	0.0937	3775	,	,		13676	0.003		0.0119	False		,,,				2504	0.0153				p.Q1019Q		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.A3057G						PASS	.	C		2803,865		883,571,466,95,104	54.0	61.0	58.0		3057	1.9	0.7	X	dbSNP_129	58	101,6502		0,78,23,2314,1796	no	coding-synonymous	FAM123B	NM_152424.3		883,649,489,2409,1900	CC,CT,C,TT,T		1.5296,23.5823,28.2738		1019/1136	63410110	2904,7367	2119	4211	6330	SO:0001819	synonymous_variant	139285	exon2			AGCTAGTTGAGGC	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.3057A>G	X.37:g.63410110T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_152424	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	37	CCDS14377.2																																																																																			T|0.758;C|0.242	0.242	strong		0.567	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
UBE2M	9040	hgsc.bcm.edu	37	19	59067585	59067585	+	Silent	SNP	G	G	A	rs8105097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:59067585G>A	ENST00000253023.3	-	6	1001	c.423C>T	c.(421-423)ccC>ccT	p.P141P	AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|CHMP2A_ENST00000601220.1_5'Flank|CHMP2A_ENST00000312547.2_5'Flank|CHMP2A_ENST00000600118.1_5'Flank	NM_003969.3	NP_003960.1	P61081	UBC12_HUMAN	ubiquitin-conjugating enzyme E2M	141					cellular protein modification process (GO:0006464)|positive regulation of neuron apoptotic process (GO:0043525)|protein neddylation (GO:0045116)|protein ubiquitination (GO:0016567)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|NEDD8 ligase activity (GO:0019788)|ribosomal S6-glutamic acid ligase activity (GO:0018169)|ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	5		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GTGGGTCCTCGGGGTTGGGCT	0.617													G|||	389	0.0776757	0.2617	0.0274	5008	,	,		15085	0.005		0.003	False		,,,				2504	0.0164				p.P141P		Atlas-SNP	.											.	UBE2M	14	.	0			c.C423T						PASS	.	G		1004,3402	374.9+/-321.4	124,756,1323	63.0	67.0	66.0		423	-8.8	0.5	19	dbSNP_116	66	15,8585	10.5+/-38.8	0,15,4285	no	coding-synonymous	UBE2M	NM_003969.3		124,771,5608	AA,AG,GG		0.1744,22.7871,7.8348		141/184	59067585	1019,11987	2203	4300	6503	SO:0001819	synonymous_variant	9040	exon6			GTCCTCGGGGTTG	AB012191	CCDS12987.1	19q13.43	2011-05-19	2011-05-19		ENSG00000130725	ENSG00000130725		"""Ubiquitin-conjugating enzymes E2"""	12491	protein-coding gene	gene with protein product		603173	"""ubiquitin-conjugating enzyme E2M (homologous to yeast UBC12)"", ""ubiquitin-conjugating enzyme E2M (UBC12 homolog, yeast)"""			9694792	Standard	NM_003969		Approved	hUbc12, UBC12	uc002qtl.4	P61081		ENST00000253023.3:c.423C>T	19.37:g.59067585G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	131	54	0.412214	NM_003969	O76069|Q8VC50	Silent	SNP	ENST00000253023.3	37	CCDS12987.1																																																																																			G|0.907;A|0.093	0.093	strong		0.617	UBE2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467097.1	NM_003969	
ABCC1	4363	hgsc.bcm.edu	37	16	16138322	16138322	+	Silent	SNP	T	T	C	rs246221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16138322T>C	ENST00000399410.3	+	8	1000	c.825T>C	c.(823-825)gtT>gtC	p.V275V	ABCC1_ENST00000349029.5_Silent_p.V275V|ABCC1_ENST00000399408.2_Silent_p.V275V|ABCC1_ENST00000345148.5_Silent_p.V275V|ABCC1_ENST00000351154.5_Silent_p.V275V|ABCC1_ENST00000346370.5_Silent_p.V275V	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	275					arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CGGTGAAGGTTGTGTACTCCT	0.582													C|||	2127	0.42472	0.7118	0.3617	5008	,	,		17677	0.4425		0.3171	False		,,,				2504	0.1738				p.V275V		Atlas-SNP	.											.	ABCC1	156	.	0			c.T825C						PASS	.	C	,,,,	2485,1507		792,901,303	63.0	63.0	63.0		825,825,825,825,825	-5.3	0.0	16	dbSNP_79	63	2451,5883		345,1761,2061	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	1137,2662,2364	CC,CT,TT		29.4096,37.7505,40.0454	,,,,	275/1532,275/1473,275/1476,275/1417,275/1467	16138322	4936,7390	1996	4167	6163	SO:0001819	synonymous_variant	4363	exon8			GAAGGTTGTGTAC	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.825T>C	16.37:g.16138322T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	122	47	0.385246	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			T|0.563;C|0.437	0.437	strong		0.582	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
SMC3	9126	hgsc.bcm.edu	37	10	112349422	112349422	+	Silent	SNP	T	T	C	rs75323904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:112349422T>C	ENST00000361804.4	+	14	1491	c.1365T>C	c.(1363-1365)taT>taC	p.Y455Y		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	455					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		ACAGAAAATATTACGAAGTAA	0.284													T|||	249	0.0497204	0.1135	0.0447	5008	,	,		19657	0.0		0.0417	False		,,,				2504	0.0266				p.Y455Y		Atlas-SNP	.											.	SMC3	103	.	0			c.T1365C						PASS	.	T		466,3938	205.8+/-227.6	29,408,1765	29.0	30.0	29.0		1365	-0.4	1.0	10	dbSNP_132	29	378,8216	121.1+/-180.3	5,368,3924	no	coding-synonymous	SMC3	NM_005445.3		34,776,5689	CC,CT,TT		4.3984,10.5813,6.4933		455/1218	112349422	844,12154	2202	4297	6499	SO:0001819	synonymous_variant	9126	exon14			AAAATATTACGAA	AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"""Structural maintenance of chromosomes proteins"", ""Proteoglycans / Extracellular Matrix : Other"""	2468	protein-coding gene	gene with protein product	"""bamacan proteoglycan"""	606062	"""chondroitin sulfate proteoglycan 6 (bamacan)"""	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.1365T>C	10.37:g.112349422T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	189	95	0.502645	NM_005445	A8K156|O60464|Q5T482	Silent	SNP	ENST00000361804.4	37	CCDS31285.1																																																																																			T|0.942;C|0.058	0.058	strong		0.284	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445	
HELZ2	85441	hgsc.bcm.edu	37	20	62198686	62198686	+	Silent	SNP	G	G	A	rs3827025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62198686G>A	ENST00000467148.1	-	6	2094	c.2025C>T	c.(2023-2025)tgC>tgT	p.C675C	HELZ2_ENST00000427522.2_Silent_p.C106C|HELZ2_ENST00000479540.1_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	675	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)										TGAGGGCCTCGCACTCCAGCA	0.687													G|||	1088	0.217252	0.5439	0.1427	5008	,	,		14601	0.0317		0.0686	False		,,,				2504	0.1728				p.C675C		Atlas-SNP	.											.	.	.	.	0			c.C2025T						PASS	.	G	,	1869,2437		420,1029,704	14.0	17.0	16.0		2025,318	-6.2	1.0	20	dbSNP_107	16	626,7848		29,568,3640	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	449,1597,4344	AA,AG,GG		7.3873,43.4046,19.5227	,	675/2650,106/2081	62198686	2495,10285	2153	4237	6390	SO:0001819	synonymous_variant	85441	exon7			GGCCTCGCACTCC	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.2025C>T	20.37:g.62198686G>A		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			G|0.823;A|0.177	0.177	strong		0.687	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259709	71259709	+	Silent	SNP	C	C	T	rs180808688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71259709C>T	ENST00000528743.2	+	1	244	c.6C>T	c.(4-6)ggC>ggT	p.G2G		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	2					epidermis development (GO:0008544)	keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						GAACCATGGGCTGCTGTGGCT	0.642													c|||	10	0.00199681	0.0068	0.0014	5008	,	,		17898	0.0		0.0	False		,,,				2504	0.0				p.G2G		Atlas-SNP	.											.	KRTAP5-9	19	.	0			c.C6T						PASS	.	C		32,4366		0,32,2167	84.0	95.0	91.0		6	1.6	1.0	11		91	0,8588		0,0,4294	no	coding-synonymous	KRTAP5-9	NM_005553.3		0,32,6461	TT,TC,CC		0.0,0.7276,0.2464		2/170	71259709	32,12954	2199	4294	6493	SO:0001819	synonymous_variant	3846	exon1			CATGGGCTGCTGT	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.6C>T	11.37:g.71259709C>T		Somatic	453	1	0.00220751		WXS	Illumina HiSeq	Phase_I	521	234	0.449136	NM_005553	Q14564|Q3MIP8	Silent	SNP	ENST00000528743.2	37	CCDS53677.1																																																																																			C|0.999;T|0.001	0.001	strong		0.642	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
CRTAC1	55118	hgsc.bcm.edu	37	10	99696031	99696031	+	Missense_Mutation	SNP	G	G	A	rs80014629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99696031G>A	ENST00000370597.3	-	3	672	c.317C>T	c.(316-318)gCg>gTg	p.A106V	CRTAC1_ENST00000370591.2_Missense_Mutation_p.A106V|CRTAC1_ENST00000298819.4_Missense_Mutation_p.A106V	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	106						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.A106V(1)		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)		GTCCCGCAGCGCGTAGTAGGG	0.617													G|||	7	0.00139776	0.0053	0.0	5008	,	,		18551	0.0		0.0	False		,,,				2504	0.0				p.A106V		Atlas-SNP	.											CRTAC1,NS,carcinoma,0,2	CRTAC1	86	2	1	Substitution - Missense(1)	endometrium(1)	c.C317T						PASS	.	G	VAL/ALA,VAL/ALA	18,4388	24.3+/-50.5	0,18,2185	66.0	54.0	58.0		317,317	4.8	1.0	10	dbSNP_131	58	0,8600		0,0,4300	yes	missense,missense	CRTAC1	NM_001206528.2,NM_018058.6	64,64	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	benign,benign	106/646,106/662	99696031	18,12988	2203	4300	6503	SO:0001583	missense	55118	exon3			CGCAGCGCGTAGT	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.317C>T	10.37:g.99696031G>A	ENSP00000359629:p.Ala106Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	ENST00000370597.3	37	CCDS31266.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	14.45	2.537920	0.45176	0.004085	0.0	ENSG00000095713	ENST00000413387;ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591	T;T;T;T;T	0.75050	1.37;-0.9;1.27;-0.05;-0.06	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	L	0.57536	1.79	0.80722	D	1	P;P	0.50710	0.68;0.938	B;B	0.43386	0.089;0.418	T	0.68239	-0.5461	10	0.15066	T	0.55	-16.5833	17.7665	0.88480	0.0:0.0:1.0:0.0	.	106;106	Q9NQ79-2;Q9NQ79	.;CRAC1_HUMAN	V	2;106;106;98;106	ENSP00000408445:A2V;ENSP00000359629:A106V;ENSP00000298819:A106V;ENSP00000310810:A98V;ENSP00000359623:A106V	ENSP00000298819:A106V	A	-	2	0	CRTAC1	99686021	1.000000	0.71417	0.958000	0.39756	0.350000	0.29205	7.675000	0.84002	2.204000	0.70986	0.313000	0.20887	GCG	G|0.999;A|0.001	0.001	strong		0.617	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
PCNXL2	80003	hgsc.bcm.edu	37	1	233225848	233225848	+	Silent	SNP	T	T	C	rs12059884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	152	0	0		WXS	Illumina HiSeq	Phase_I	131	67	0.51145	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	
GPR110	266977	hgsc.bcm.edu	37	6	46977458	46977458	+	Missense_Mutation	SNP	T	T	C	rs937057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46977458T>C	ENST00000371253.2	-	11	1928	c.1713A>G	c.(1711-1713)atA>atG	p.I571M	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.I374M	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	571	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						GTGACATCAATATGGAGAAGG	0.453													C|||	1040	0.207668	0.4932	0.1499	5008	,	,		21255	0.1776		0.0089	False		,,,				2504	0.0982				p.I571M		Atlas-SNP	.											.	GPR110	102	.	0			c.A1713G						PASS	.	C	MET/ILE	1651,2755	658.3+/-400.4	302,1047,854	143.0	125.0	131.0		1713	-2.6	0.6	6	dbSNP_86	131	69,8531	816.3+/-406.9	0,69,4231	yes	missense	GPR110	NM_153840.2	10	302,1116,5085	CC,CT,TT		0.8023,37.4716,13.2247	benign	571/911	46977458	1720,11286	2203	4300	6503	SO:0001583	missense	266977	exon11			CATCAATATGGAG	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.1713A>G	6.37:g.46977458T>C	ENSP00000360299:p.Ile571Met	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	106	43	0.40566	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	37	CCDS34471.1	395	0.18086080586080586	236	0.4796747967479675	44	0.12154696132596685	107	0.18706293706293706	8	0.010554089709762533	C	9.181	1.023651	0.19433	0.374716	0.008023	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000283297	T;T	0.71934	-0.61;-0.61	5.76	-2.6	0.06190	GPS domain (3);	0.807401	0.11522	N	0.555607	T	0.28995	0.0720	L	0.35723	1.085	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.15870	0.014	T	0.08186	-1.0734	9	0.42905	T	0.14	-2.1745	0.262	0.00220	0.3495:0.1815:0.1606:0.3084	rs937057;rs52812684;rs937057	571	Q5T601	GP110_HUMAN	M	571;571;374	ENSP00000360299:I571M;ENSP00000283297:I374M	ENSP00000283297:I374M	I	-	3	3	GPR110	47085417	0.293000	0.24371	0.591000	0.28745	0.952000	0.60782	-0.285000	0.08410	-0.827000	0.04278	-0.227000	0.12334	ATA	T|0.832;C|0.168	0.168	strong		0.453	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
EAPP	55837	hgsc.bcm.edu	37	14	34985645	34985645	+	Silent	SNP	G	G	A	rs7797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:34985645G>A	ENST00000250454.3	-	6	810	c.729C>T	c.(727-729)gcC>gcT	p.A243A		NM_018453.3	NP_060923.2	Q56P03	EAPP_HUMAN	E2F-associated phosphoprotein	243					negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2)	12	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00342)|Epithelial(34;0.18)	GBM - Glioblastoma multiforme(112;0.0196)		CTGCCTTCTCGGCAGCATCTT	0.448													G|||	1387	0.276957	0.2897	0.219	5008	,	,		18456	0.1905		0.3678	False		,,,				2504	0.2965				p.A243A		Atlas-SNP	.											.	EAPP	28	.	0			c.C729T						PASS	.	G		1303,2659		223,857,901	242.0	239.0	240.0		729	-3.0	0.0	14	dbSNP_52	240	3090,5210		569,1952,1629	no	coding-synonymous	EAPP	NM_018453.3		792,2809,2530	AA,AG,GG		37.2289,32.8874,35.8261		243/286	34985645	4393,7869	1981	4150	6131	SO:0001819	synonymous_variant	55837	exon6			CTTCTCGGCAGCA	AF217512	CCDS41941.1	14q13	2007-03-26	2007-03-26	2007-03-26		ENSG00000129518			19312	protein-coding gene	gene with protein product		609486	"""chromosome 14 open reading frame 11"""	C14orf11		15716352	Standard	NM_018453		Approved	BM036, FLJ20578	uc001wsd.1	Q56P03		ENST00000250454.3:c.729C>T	14.37:g.34985645G>A		Somatic	298	1	0.0033557		WXS	Illumina HiSeq	Phase_I	260	145	0.557692	NM_018453	Q9BVF4|Q9NWV5|Q9NZ86	Silent	SNP	ENST00000250454.3	37	CCDS41941.1																																																																																			G|0.697;A|0.303	0.303	strong		0.448	EAPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409847.1	NM_018453	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417766	105417766	+	Missense_Mutation	SNP	G	G	A	rs2396457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417766G>A	ENST00000333244.5	-	7	4141	c.4022C>T	c.(4021-4023)tCt>tTt	p.S1341F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1341						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)			GCCTGGGGCAGACACCCCGAA	0.607													.|||	1575	0.314497	0.5658	0.1225	5008	,	,		13647	0.2937		0.1004	False		,,,				2504	0.3528				p.S1341F		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4022T						PASS	.	G	PHE/SER	105,3549		16,73,1738	128.0	119.0	122.0		4022	3.4	0.0	14	dbSNP_100	122	18,6534		1,16,3259	no	missense	AHNAK2	NM_138420.2	155	17,89,4997	AA,AG,GG		0.2747,2.8736,1.2052	probably-damaging	1341/5796	105417766	123,10083	1827	3276	5103	SO:0001583	missense	113146	exon7			GGGGCAGACACCC	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.4022C>T	14.37:g.105417766G>A	ENSP00000353114:p.Ser1341Phe	Somatic	386	1	0.00259067		WXS	Illumina HiSeq	Phase_I	263	263	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	453	0.20741758241758243	248	0.5040650406504065	43	0.11878453038674033	130	0.22727272727272727	32	0.04221635883905013	-	14.71	2.616236	0.46631	0.028736	0.002747	ENSG00000185567	ENST00000333244	T	0.00753	5.74	4.31	3.4	0.38934	.	.	.	.	.	T	0.00012	0.0000	M	0.92122	3.275	0.80722	P	0.0	D	0.89917	1.0	D	0.76575	0.988	T	0.33471	-0.9867	8	0.48119	T	0.1	-6.8464	12.9494	0.58391	0.0:0.0:0.8363:0.1637	.	1341	Q8IVF2	AHNK2_HUMAN	F	1341	ENSP00000353114:S1341F	ENSP00000353114:S1341F	S	-	2	0	AHNAK2	104488811	0.695000	0.27747	0.002000	0.10522	0.000000	0.00434	3.065000	0.49994	0.791000	0.33826	-0.500000	0.04577	TCT	G|0.824;A|0.176	0.176	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
PIGR	5284	hgsc.bcm.edu	37	1	207106478	207106478	+	Missense_Mutation	SNP	G	G	A	rs291102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207106478G>A	ENST00000356495.4	-	7	1922	c.1739C>T	c.(1738-1740)gCt>gTt	p.A580V	PIGR_ENST00000487208.1_5'Flank	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	580			A -> V (in dbSNP:rs291102).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)	p.A580V(1)		central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ATCAGGAGCAGCGTCTGCCTT	0.537													G|||	1336	0.266773	0.7632	0.1931	5008	,	,		20941	0.121		0.0258	False		,,,				2504	0.046				p.A580V		Atlas-SNP	.											PIGR,rectum,carcinoma,-1,3	PIGR	98	3	1	Substitution - Missense(1)	stomach(1)	c.C1739T	GRCh37	CM035762	PIGR	M	rs291102	PASS	.	G	VAL/ALA	2890,1516	674.5+/-402.9	975,940,288	66.0	65.0	66.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1739	1.1	0.0	1	dbSNP_79	66	252,8348	98.4+/-159.9	7,238,4055	yes	missense	PIGR	NM_002644.3	64	982,1178,4343	AA,AG,GG		2.9302,34.4076,24.1581	benign	580/765	207106478	3142,9864	2203	4300	6503	SO:0001583	missense	5284	exon7			GGAGCAGCGTCTG		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"""Immunoglobulin superfamily / V-set domain containing"""	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1739C>T	1.37:g.207106478G>A	ENSP00000348888:p.Ala580Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_002644	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	37	CCDS1474.1	504	0.23076923076923078	360	0.7317073170731707	73	0.20165745856353592	59	0.10314685314685315	12	0.0158311345646438	G	6.784	0.513547	0.12944	0.655924	0.029302	ENSG00000162896	ENST00000356495	T	0.16324	2.35	2.02	1.08	0.20341	.	1.246790	0.05490	N	0.556394	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.13594	0.008	B	0.09377	0.004	T	0.32613	-0.9900	9	0.31617	T	0.26	-32.5565	4.7313	0.12966	0.1905:0.0:0.8095:0.0	rs291102;rs508707;rs1150259;rs52792010;rs57447753;rs291102	580	P01833	PIGR_HUMAN	V	580	ENSP00000348888:A580V	ENSP00000348888:A580V	A	-	2	0	PIGR	205173101	0.001000	0.12720	0.008000	0.14137	0.004000	0.04260	0.523000	0.22925	0.422000	0.26005	-0.300000	0.09419	GCT	G|0.748;T|0.004	.	strong		0.537	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644	
GPR39	2863	hgsc.bcm.edu	37	2	133175152	133175152	+	Silent	SNP	C	C	T	rs34714906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:133175152C>T	ENST00000329321.3	+	1	1006	c.537C>T	c.(535-537)ccC>ccT	p.P179P		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	179					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTGAGTACCCCCTGGTGAACG	0.622													C|||	370	0.0738818	0.2269	0.0231	5008	,	,		18360	0.0357		0.0	False		,,,				2504	0.0184				p.P179P		Atlas-SNP	.											.	GPR39	60	.	0			c.C537T						PASS	.	C		802,3604	323.2+/-298.0	54,694,1455	72.0	65.0	67.0		537	-6.0	0.2	2	dbSNP_126	67	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	GPR39	NM_001508.2		54,703,5746	TT,TC,CC		0.1047,18.2025,6.2356		179/454	133175152	811,12195	2203	4300	6503	SO:0001819	synonymous_variant	2863	exon1			GTACCCCCTGGTG	AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.537C>T	2.37:g.133175152C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	96	36	0.375	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	Silent	SNP	ENST00000329321.3	37	CCDS2170.1																																																																																			C|0.926;T|0.074	0.074	strong		0.622	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1		
CFAP46	54777	hgsc.bcm.edu	37	10	134698626	134698626	+	Missense_Mutation	SNP	T	T	C	rs73393250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134698626T>C	ENST00000368586.5	-	27	3708	c.3608A>G	c.(3607-3609)aAc>aGc	p.N1203S	TTC40_ENST00000368582.2_Missense_Mutation_p.N1203S	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTGGATGGCGTTGTTGTAGCA	0.572													C|||	672	0.134185	0.3608	0.0418	5008	,	,		15794	0.0198		0.0249	False		,,,				2504	0.1237				p.N1203S		Atlas-SNP	.											.	TTC40	100	.	0			c.A3608G						PASS	.																																			SO:0001583	missense	54777	exon27			ATGGCGTTGTTGT																												ENST00000368586.5:c.3608A>G	10.37:g.134698626T>C	ENSP00000357575:p.Asn1203Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	220	0.10073260073260074	179	0.3638211382113821	13	0.03591160220994475	12	0.02097902097902098	16	0.021108179419525065	C	0.901	-0.722113	0.03182	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.45668	2.87;0.89	4.16	1.74	0.24563	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.38693	-0.9649	5	0.38643	T	0.18	.	9.5036	0.39033	0.0:0.1788:0.0:0.8212	.	.	.	.	S	1203	ENSP00000357575:N1203S;ENSP00000357571:N1203S	ENSP00000357571:N1203S	N	-	2	0	C10orf93	134548616	0.400000	0.25295	0.007000	0.13788	0.003000	0.03518	1.216000	0.32443	-0.245000	0.09625	-1.247000	0.01520	AAC	T|0.913;C|0.087	0.087	strong		0.572	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
ASGR2	433	hgsc.bcm.edu	37	17	7011225	7011225	+	Splice_Site	SNP	T	T	G	rs61731746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7011225T>G	ENST00000380952.2	-	5	618	c.354A>C	c.(352-354)ggA>ggC	p.G118G	ASGR2_ENST00000355035.5_Splice_Site_p.G118G|ASGR2_ENST00000446679.2_Splice_Site_p.G99G|ASGR2_ENST00000254850.7_Splice_Site_p.G94G	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	118					bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)	p.G118G(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	CCACGCTGCCTCCTGGAAGCG	0.652													T|||	584	0.116613	0.2738	0.0461	5008	,	,		18665	0.0952		0.0507	False		,,,				2504	0.044				p.G118G		Atlas-SNP	.											ASGR2,NS,carcinoma,0,1	ASGR2	38	1	1	Substitution - coding silent(1)	stomach(1)	c.A354C						PASS	.	T	,,,,	1075,3331	391.2+/-328.0	142,791,1270	193.0	132.0	152.0		354,339,354,282,297	-0.1	0.7	17	dbSNP_129	152	387,8213	125.1+/-183.8	15,357,3928	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ASGR2	NM_001181.4,NM_001201352.1,NM_080912.3,NM_080913.3,NM_080914.2	,,,,	157,1148,5198	GG,GT,TT		4.5,24.3985,11.241	,,,,	118/312,113/307,118/312,94/288,99/293	7011225	1462,11544	2203	4300	6503	SO:0001630	splice_region_variant	433	exon5			GCTGCCTCCTGGA	M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"""C-type lectin domain containing"""	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.353-1A>C	17.37:g.7011225T>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Silent	SNP	ENST00000380952.2	37	CCDS32544.1																																																																																			T|0.891;G|0.109	0.109	strong		0.652	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914	Silent
GANC	2595	hgsc.bcm.edu	37	15	42631976	42631976	+	Silent	SNP	G	G	A	rs35039186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42631976G>A	ENST00000318010.8	+	17	2193	c.1953G>A	c.(1951-1953)aaG>aaA	p.K651K		NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	651					carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)	p.K651K(1)		breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	TGAACACCAAGCGACGAGAGC	0.572													G|||	473	0.0944489	0.1399	0.062	5008	,	,		17061	0.002		0.0845	False		,,,				2504	0.1616				p.K651K		Atlas-SNP	.											GANC,brain,glioma,0,1	GANC	57	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G1953A						PASS	.	G		615,3791	266.5+/-267.3	45,525,1633	72.0	65.0	67.0		1953	4.2	1.0	15	dbSNP_126	67	693,7905	173.2+/-223.7	31,631,3637	no	coding-synonymous	GANC	NM_198141.2		76,1156,5270	AA,AG,GG		8.06,13.9582,10.0584		651/915	42631976	1308,11696	2203	4299	6502	SO:0001819	synonymous_variant	2595	exon17			CACCAAGCGACGA	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.1953G>A	15.37:g.42631976G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	121	119	0.983471	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Silent	SNP	ENST00000318010.8	37	CCDS10084.1																																																																																			G|0.910;A|0.090	0.090	strong		0.572	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
BMP1	649	hgsc.bcm.edu	37	8	22067070	22067070	+	Silent	SNP	C	C	T	rs4076619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22067070C>T	ENST00000306385.5	+	19	3358	c.2688C>T	c.(2686-2688)gcC>gcT	p.A896A	BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	896	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)		TCATTGTGGCCGAGGAAGGCT	0.587													C|||	771	0.153954	0.4584	0.0375	5008	,	,		18697	0.1042		0.0	False		,,,				2504	0.0348				p.A896A		Atlas-SNP	.											.	BMP1	131	.	0			c.C2688T						PASS	.	C		1738,2668	519.4+/-370.0	353,1032,818	294.0	219.0	245.0		2688	-9.5	0.2	8	dbSNP_108	245	12,8588	7.7+/-29.5	0,12,4288	no	coding-synonymous	BMP1	NM_006129.4		353,1044,5106	TT,TC,CC		0.1395,39.4462,13.4553		896/987	22067070	1750,11256	2203	4300	6503	SO:0001819	synonymous_variant	649	exon19			TGTGGCCGAGGAA		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.2688C>T	8.37:g.22067070C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	169	168	0.994083	NM_006129	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			A|0.000;C|0.871;G|0.000;T|0.129	0.129	strong		0.587	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
APBA1	320	hgsc.bcm.edu	37	9	72131577	72131577	+	Missense_Mutation	SNP	A	A	C	rs34788368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:72131577A>C	ENST00000265381.4	-	2	772	c.550T>G	c.(550-552)Tcc>Gcc	p.S184A		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	184			S -> A (in dbSNP:rs34788368).		axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						TAGGGCTCGGAGTAGGGCTCG	0.662													C|||	1018	0.203275	0.3245	0.1787	5008	,	,		12120	0.2976		0.0736	False		,,,				2504	0.093				p.S184A		Atlas-SNP	.											.	APBA1	96	.	0			c.T550G						PASS	.	C	ALA/SER	1219,3185		172,875,1155	35.0	32.0	33.0		550	5.1	1.0	9	dbSNP_126	33	773,7821		31,711,3555	yes	missense	APBA1	NM_001163.3	99	203,1586,4710	CC,CA,AA		8.9946,27.6794,15.3254	benign	184/838	72131577	1992,11006	2202	4297	6499	SO:0001583	missense	320	exon2			GCTCGGAGTAGGG	AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.550T>G	9.37:g.72131577A>C	ENSP00000265381:p.Ser184Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_001163	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	ENST00000265381.4	37	CCDS6630.1	439	0.20100732600732601	162	0.32926829268292684	62	0.1712707182320442	161	0.28146853146853146	54	0.0712401055408971	C	0.026	-1.373835	0.01214	0.276794	0.089946	ENSG00000107282	ENST00000265381	T	0.03889	3.77	5.08	5.08	0.68730	.	0.126810	0.53938	N	0.000046	T	0.00012	0.0000	N	0.04880	-0.145	0.45515	P	0.0015260000000000273	B	0.02656	0.0	B	0.04013	0.001	T	0.44892	-0.9298	9	0.02654	T	1	.	15.3975	0.74808	0.1406:0.8594:0.0:0.0	rs34788368;rs62567207	184	Q02410	APBA1_HUMAN	A	184	ENSP00000265381:S184A	ENSP00000265381:S184A	S	-	1	0	APBA1	71321397	1.000000	0.71417	1.000000	0.80357	0.130000	0.20726	2.801000	0.47908	1.295000	0.44724	-0.217000	0.12591	TCC	A|0.828;C|0.172	0.172	strong		0.662	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163	
MYOM2	9172	hgsc.bcm.edu	37	8	2048831	2048831	+	Missense_Mutation	SNP	A	A	G	rs968381	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2048831A>G	ENST00000262113.4	+	20	2747	c.2606A>G	c.(2605-2607)aAc>aGc	p.N869S	MYOM2_ENST00000523438.1_Missense_Mutation_p.N294S	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	869	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.		N -> S (in dbSNP:rs968381). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505783}.		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)		ACAACAGCCAACCGTTATTTA	0.527													A|||	2306	0.460463	0.6831	0.3573	5008	,	,		18243	0.4048		0.335	False		,,,				2504	0.4192				p.N869S		Atlas-SNP	.											MYOM2,NS,carcinoma,0,1	MYOM2	251	1	0			c.A2606G						PASS	.	A	SER/ASN	2828,1578	659.7+/-400.6	920,988,295	65.0	70.0	68.0		2606	4.4	0.0	8	dbSNP_86	68	2853,5747	443.3+/-360.3	494,1865,1941	yes	missense	MYOM2	NM_003970.2	46	1414,2853,2236	GG,GA,AA		33.1744,35.8148,43.6798	benign	869/1466	2048831	5681,7325	2203	4300	6503	SO:0001583	missense	9172	exon20			CAGCCAACCGTTA		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.2606A>G	8.37:g.2048831A>G	ENSP00000262113:p.Asn869Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	928	0.4249084249084249	318	0.6463414634146342	133	0.3674033149171271	227	0.3968531468531469	250	0.32981530343007914	A	5.934	0.356400	0.11239	0.641852	0.331744	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.56941	0.43;0.43	5.55	4.38	0.52667	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.278757	0.39210	N	0.001422	T	0.00012	0.0000	L	0.33137	0.985	0.53688	P	2.199999999996649E-5	B	0.15473	0.013	B	0.17979	0.02	T	0.41502	-0.9505	9	0.34782	T	0.22	.	11.4648	0.50232	0.9293:0.0:0.0707:0.0	rs968381;rs3758066;rs17857421;rs52824117;rs57664364;rs968381	869	P54296	MYOM2_HUMAN	S	869;294	ENSP00000262113:N869S;ENSP00000428396:N294S	ENSP00000262113:N869S	N	+	2	0	MYOM2	2036238	0.543000	0.26434	0.016000	0.15963	0.004000	0.04260	3.935000	0.56560	0.937000	0.37394	0.523000	0.50628	AAC	A|0.561;G|0.439	0.439	strong		0.527	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
ARL10	285598	hgsc.bcm.edu	37	5	175793532	175793532	+	Silent	SNP	C	C	T	rs2303666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:175793532C>T	ENST00000310389.5	+	2	429	c.333C>T	c.(331-333)ggC>ggT	p.G111G	MIR1271_ENST00000408537.1_RNA	NM_173664.4	NP_775935.1	Q8N8L6	ARL10_HUMAN	ADP-ribosylation factor-like 10	111					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(2)|lung(1)|ovary(1)	4	all_cancers(89;0.0064)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	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;0.000178)	Kidney(146;0.0965)		CCACCTGGGGCTTCAACTCCG	0.637													C|||	574	0.114617	0.0628	0.1585	5008	,	,		17243	0.1121		0.1272	False		,,,				2504	0.1431				p.G111G		Atlas-SNP	.											.	ARL10	19	.	0			c.C333T						PASS	.	C		336,4070	175.5+/-204.9	12,312,1879	76.0	80.0	79.0		333	2.2	1.0	5	dbSNP_100	79	1136,7464	234.7+/-267.5	73,990,3237	no	coding-synonymous	ARL10	NM_173664.4		85,1302,5116	TT,TC,CC		13.2093,7.626,11.3179		111/245	175793532	1472,11534	2203	4300	6503	SO:0001819	synonymous_variant	285598	exon2			CTGGGGCTTCAAC	BK001673	CCDS4400.1	5q35.3	2014-05-09	2005-11-03	2005-11-03	ENSG00000175414	ENSG00000175414		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	22042	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 10A"""	ARL10A			Standard	NM_173664		Approved		uc003mec.1	Q8N8L6	OTTHUMG00000130655	ENST00000310389.5:c.333C>T	5.37:g.175793532C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_173664		Silent	SNP	ENST00000310389.5	37	CCDS4400.1																																																																																			C|0.894;T|0.106	0.106	strong		0.637	ARL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253145.2	NM_173664	
TEP1	7011	hgsc.bcm.edu	37	14	20845521	20845521	+	Silent	SNP	A	A	C	rs2229101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20845521A>C	ENST00000262715.5	-	41	6046	c.6006T>G	c.(6004-6006)ctT>ctG	p.L2002L	TEP1_ENST00000545983.1_Silent_p.L340L|TEP1_ENST00000556935.1_Silent_p.L1894L	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2002					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)		AGAGGGACTGAAGGGAGCATT	0.587													A|||	295	0.0589058	0.09	0.036	5008	,	,		14898	0.002		0.0676	False		,,,				2504	0.0828				p.L2002L		Atlas-SNP	.											.	TEP1	224	.	0			c.T6006G						PASS	.	A		370,4036	189.2+/-215.4	17,336,1850	58.0	51.0	53.0		6006	-3.9	0.2	14	dbSNP_98	53	567,8033	153.4+/-207.8	19,529,3752	no	coding-synonymous	TEP1	NM_007110.4		36,865,5602	CC,CA,AA		6.593,8.3976,7.2044		2002/2628	20845521	937,12069	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon41			GGACTGAAGGGAG		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.6006T>G	14.37:g.20845521A>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	92	47	0.51087	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			A|0.936;C|0.064	0.064	strong		0.587	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
PMVK	10654	hgsc.bcm.edu	37	1	154904840	154904840	+	Silent	SNP	T	T	C	rs1891805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:154904840T>C	ENST00000368467.3	-	2	452	c.147A>G	c.(145-147)gaA>gaG	p.E49E		NM_006556.3	NP_006547.1	Q15126	PMVK_HUMAN	phosphomevalonate kinase	49					cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|response to cholesterol (GO:0070723)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|phosphomevalonate kinase activity (GO:0004631)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.142)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GAGCATACTGTTCCTTGAGTG	0.577													C|||	1036	0.206869	0.6407	0.0836	5008	,	,		17611	0.0		0.0636	False		,,,				2504	0.0685				p.E49E		Atlas-SNP	.											.	PMVK	17	.	0			c.A147G						PASS	.	C		2511,1895	543.3+/-376.2	746,1019,438	107.0	94.0	99.0		147	0.6	1.0	1	dbSNP_92	99	555,8045	793.4+/-407.5	12,531,3757	no	coding-synonymous	PMVK	NM_006556.3		758,1550,4195	CC,CT,TT		6.4535,43.0095,23.5737		49/193	154904840	3066,9940	2203	4300	6503	SO:0001819	synonymous_variant	10654	exon2			ATACTGTTCCTTG	L77213	CCDS1073.1	1q21.3	2012-09-20			ENSG00000163344	ENSG00000163344	2.7.4.2		9141	protein-coding gene	gene with protein product		607622				8663599, 10191291	Standard	NM_006556		Approved	PMK, PMKA, HUMPMKI	uc001ffq.3	Q15126	OTTHUMG00000037415	ENST00000368467.3:c.147A>G	1.37:g.154904840T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_006556	Q5TZW9	Silent	SNP	ENST00000368467.3	37	CCDS1073.1																																																																																			T|0.769;C|0.231	0.231	strong		0.577	PMVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091088.1	NM_006556	
IKBKE	9641	hgsc.bcm.edu	37	1	206665052	206665052	+	Missense_Mutation	SNP	C	C	T	rs12059562	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206665052C>T	ENST00000367120.3	+	18	2178	c.1805C>T	c.(1804-1806)gCg>gTg	p.A602V	C1orf147_ENST00000367119.1_3'UTR|IKBKE_ENST00000537984.1_Missense_Mutation_p.A517V	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	602	Interaction with DDX3X.		A -> V (in dbSNP:rs12059562). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					AAGTATCAAGCGTCCTTAGTC	0.557													C|||	1159	0.23143	0.2534	0.2478	5008	,	,		22562	0.4613		0.0099	False		,,,				2504	0.181				p.A602V		Atlas-SNP	.											.	IKBKE	77	.	0			c.C1805T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	1037,3369	382.5+/-324.5	125,787,1291	108.0	103.0	105.0		1550,1805,1805	1.4	0.0	1	dbSNP_120	105	24,8576	18.5+/-59.3	0,24,4276	yes	missense,missense,missense	IKBKE	NM_001193321.1,NM_001193322.1,NM_014002.3	64,64,64	125,811,5567	TT,TC,CC		0.2791,23.5361,8.1578	benign,benign,benign	517/632,602/658,602/717	206665052	1061,11945	2203	4300	6503	SO:0001583	missense	9641	exon18			ATCAAGCGTCCTT	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.1805C>T	1.37:g.206665052C>T	ENSP00000356087:p.Ala602Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	37	CCDS30996.1	426	0.19505494505494506	116	0.23577235772357724	61	0.1685082872928177	243	0.42482517482517484	6	0.0079155672823219	C	8.314	0.822823	0.16678	0.235361	0.002791	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.16196	2.36;2.36	5.55	1.36	0.22044	.	0.519447	0.20919	N	0.083317	T	0.00012	0.0000	N	0.17082	0.46	0.43603	P	0.004031000000000007	B;B	0.14805	0.008;0.011	B;B	0.09377	0.004;0.004	T	0.48547	-0.9026	9	0.27785	T	0.31	-4.9091	3.4142	0.07369	0.1793:0.5308:0.0:0.2899	rs12059562;rs52806460;rs12059562	517;602	Q3B754;Q14164	.;IKKE_HUMAN	V	602;517	ENSP00000356087:A602V;ENSP00000444529:A517V	ENSP00000356087:A602V	A	+	2	0	IKBKE	204731675	0.023000	0.18921	0.030000	0.17652	0.396000	0.30629	-0.021000	0.12504	0.295000	0.22570	-0.258000	0.10820	GCG	C|0.864;T|0.136	0.136	strong		0.557	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
DUOXA2	405753	hgsc.bcm.edu	37	15	45409732	45409732	+	Intron	SNP	C	C	G	rs61751061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45409732C>G	ENST00000323030.5	+	6	1054				DUOXA1_ENST00000430224.2_Missense_Mutation_p.R433P|DUOXA1_ENST00000558996.1_3'UTR|DUOXA1_ENST00000267803.4_Missense_Mutation_p.R478P|DUOXA1_ENST00000559014.1_Missense_Mutation_p.R478P	NM_207581.3	NP_997464.2	Q1HG44	DOXA2_HUMAN	dual oxidase maturation factor 2						hydrogen peroxide metabolic process (GO:0042743)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)							all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		AGGTGTGTGGCGGGAGGTAAC	0.512													G|||	846	0.16893	0.4297	0.1873	5008	,	,		16774	0.0446		0.0686	False		,,,				2504	0.0348				p.R478P		Atlas-SNP	.											.	DUOXA1	32	.	0			c.G1433C						PASS	.	G	PRO/ARG,	1631,2717		315,1001,858	44.0	47.0	46.0		1433,	-2.6	0.0	15	dbSNP_129	46	567,7937		34,499,3719	yes	missense,intron	DUOXA1,DUOXA2	NM_144565.2,NM_207581.3	103,	349,1500,4577	GG,GC,CC		6.6675,37.5115,17.1024	possibly-damaging,	478/484,	45409732	2198,10654	2174	4252	6426	SO:0001627	intron_variant	90527	exon11			GTGTGGCGGGAGG	BX537581	CCDS10118.2	15q21.1	2008-10-30		2006-07-25	ENSG00000140274	ENSG00000140274			32698	protein-coding gene	gene with protein product		612772				16651268	Standard	NM_207581		Approved		uc001zuo.3	Q1HG44	OTTHUMG00000131354	ENST00000323030.5:c.770-182C>G	15.37:g.45409732C>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	193	76	0.393782	NM_144565	B2RPI9|H0YNQ6	Missense_Mutation	SNP	ENST00000323030.5	37	CCDS10118.2	322	0.14743589743589744	196	0.3983739837398374	46	0.1270718232044199	29	0.050699300699300696	51	0.06728232189973615	G	3.775	-0.046821	0.07407	0.375115	0.066675	ENSG00000140254	ENST00000267803;ENST00000430224	T;T	0.61510	0.52;0.1	1.31	-2.61	0.06171	.	.	.	.	.	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	0.32666	-0.9898	8	0.87932	D	0	.	4.9129	0.13831	0.2498:0.3294:0.4207:0.0	rs61751061	433;478	B5M0C0;A8K9Q6	.;.	P	478;433	ENSP00000267803:R478P;ENSP00000415512:R433P	ENSP00000267803:R478P	R	-	2	0	DUOXA1	43197024	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.424000	0.07025	-3.110000	0.00242	-4.100000	0.00011	CGC	C|0.819;G|0.181	0.181	strong		0.512	DUOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254142.1	NM_207581	
GPANK1	7918	hgsc.bcm.edu	37	6	31630241	31630241	+	Silent	SNP	C	C	T	rs7992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31630241C>T	ENST00000375906.1	-	4	1557	c.873G>A	c.(871-873)agG>agA	p.R291R	GPANK1_ENST00000375893.2_Silent_p.R291R|GPANK1_ENST00000375900.4_Silent_p.R291R|Y_RNA_ENST00000364337.1_RNA|C6orf47_ENST00000375911.1_5'Flank|GPANK1_ENST00000375896.4_Silent_p.R291R|C6orf47-AS1_ENST00000422049.1_RNA|CSNK2B_ENST00000375885.4_5'Flank|GPANK1_ENST00000375895.2_Silent_p.R291R	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	291	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.						nucleic acid binding (GO:0003676)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						CTTCCTGGTCCCTCTTGAGGA	0.652													C|||	2058	0.410942	0.6135	0.4078	5008	,	,		17114	0.369		0.2952	False		,,,				2504	0.3016				p.R291R		Atlas-SNP	.											.	GPANK1	19	.	0			c.G873A						PASS	.	C	,,,,	1649,1373		451,747,313	81.0	83.0	82.0		873,873,873,873,873	1.8	1.0	6	dbSNP_52	82	1446,3972		198,1050,1461	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPANK1	NM_001199237.1,NM_001199238.1,NM_001199239.1,NM_001199240.1,NM_033177.3	,,,,	649,1797,1774	TT,TC,CC		26.6888,45.4335,36.6706	,,,,	291/357,291/357,291/357,291/357,291/357	31630241	3095,5345	1511	2709	4220	SO:0001819	synonymous_variant	7918	exon4			CTGGTCCCTCTTG		CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"""Ankyrin repeat domain containing"", ""G patch domain containing"""	13920	protein-coding gene	gene with protein product	"""G patch domain containing 10"", ""ankyrin repeat domain 59"""	142610	"""HLA-B associated transcript 4"""	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.873G>A	6.37:g.31630241C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	241	100	0.414938	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	
KIAA0922	23240	hgsc.bcm.edu	37	4	154525446	154525446	+	Silent	SNP	A	A	C	rs17030219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:154525446A>C	ENST00000409663.3	+	25	3331	c.3279A>C	c.(3277-3279)tcA>tcC	p.S1093S	KIAA0922_ENST00000409959.3_Silent_p.S1094S|KIAA0922_ENST00000440693.1_Silent_p.S1010S	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1093						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)				TTAAAACTTCAGAGAACACAG	0.408													A|||	52	0.0103834	0.0378	0.0014	5008	,	,		19441	0.0		0.001	False		,,,				2504	0.0				p.S1094S		Atlas-SNP	.											.	KIAA0922	214	.	0			c.A3282C						PASS	.	A	,	171,4235	111.6+/-149.8	2,167,2034	51.0	52.0	52.0		3282,3279	1.9	0.5	4	dbSNP_123	52	1,8599		0,1,4299	yes	coding-synonymous,coding-synonymous	KIAA0922	NM_001131007.1,NM_015196.3	,	2,168,6333	CC,CA,AA		0.0116,3.8811,1.3225	,	1094/1611,1093/1610	154525446	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	23240	exon25			AACTTCAGAGAAC	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.3279A>C	4.37:g.154525446A>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	134	75	0.559702	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																			A|0.987;C|0.013	0.013	strong		0.408	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
AVPI1	60370	hgsc.bcm.edu	37	10	99439541	99439541	+	Missense_Mutation	SNP	G	G	C	rs2275047	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99439541G>C	ENST00000370626.3	-	2	689	c.122C>G	c.(121-123)gCc>gGc	p.A41G		NM_021732.2	NP_068378.2	Q5T686	AVPI1_HUMAN	arginine vasopressin-induced 1	41			A -> G (in dbSNP:rs2275047). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15498874, ECO:0000269|Ref.3}.		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)		TTGAAACAGGGCTTGGATCTG	0.662													C|||	2545	0.508187	0.6982	0.438	5008	,	,		17525	0.4742		0.3579	False		,,,				2504	0.4908				p.A41G		Atlas-SNP	.											AVPI1,NS,carcinoma,0,2	AVPI1	16	2	0			c.C122G						PASS	.	C	GLY/ALA	2846,1560		944,958,301	38.0	29.0	32.0		122	5.1	1.0	10	dbSNP_100	32	3408,5192		678,2052,1570	yes	missense	AVPI1	NM_021732.2	60	1622,3010,1871	CC,CG,GG		39.6279,35.4063,48.0855	benign	41/148	99439541	6254,6752	2203	4300	6503	SO:0001583	missense	60370	exon2			AACAGGGCTTGGA	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.122C>G	10.37:g.99439541G>C	ENSP00000359660:p.Ala41Gly	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_021732	Q53G32|Q9H2R9|Q9HBN9	Missense_Mutation	SNP	ENST00000370626.3	37	CCDS7470.1	1018	0.4661172161172161	339	0.6890243902439024	149	0.4116022099447514	261	0.4562937062937063	269	0.3548812664907652	C	4.439	0.081327	0.08533	0.645937	0.396279	ENSG00000119986	ENST00000370626	T	0.28895	1.59	5.09	5.09	0.68999	.	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.24870	-1.0148	8	0.32370	T	0.25	0.0051	13.3971	0.60861	0.0:0.6982:0.3018:0.0	rs2275047;rs17856022;rs52810646;rs57044806;rs2275047	41	Q5T686	AVPI1_HUMAN	G	41	ENSP00000359660:A41G	ENSP00000359660:A41G	A	-	2	0	AVPI1	99429531	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	1.539000	0.36104	1.383000	0.46405	-0.216000	0.12614	GCC	G|0.524;C|0.476	0.476	strong		0.662	AVPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049736.1	NM_021732	
PDE5A	8654	hgsc.bcm.edu	37	4	120440278	120440278	+	Missense_Mutation	SNP	A	A	G	rs116396619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:120440278A>G	ENST00000354960.3	-	14	2241	c.1922T>C	c.(1921-1923)cTg>cCg	p.L641P	PDE5A_ENST00000394439.1_Missense_Mutation_p.L589P|PDE5A_ENST00000512739.1_5'Flank|RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000264805.5_Missense_Mutation_p.L599P	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	641	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	AAGTATCTCCAGGTCAGTCAG	0.408													A|||	26	0.00519169	0.0174	0.0029	5008	,	,		18416	0.0		0.001	False		,,,				2504	0.0				p.L641P		Atlas-SNP	.											.	PDE5A	83	.	0			c.T1922C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	58,4348	56.8+/-93.2	0,58,2145	125.0	104.0	111.0		1922,1796,1766	5.5	1.0	4	dbSNP_132	111	0,8600		0,0,4300	yes	missense,missense,missense	PDE5A	NM_001083.3,NM_033430.2,NM_033437.3	98,98,98	0,58,6445	GG,GA,AA		0.0,1.3164,0.4459	probably-damaging,probably-damaging,probably-damaging	641/876,599/834,589/824	120440278	58,12948	2203	4300	6503	SO:0001583	missense	8654	exon14			ATCTCCAGGTCAG	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"""Phosphodiesterases"""	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1922T>C	4.37:g.120440278A>G	ENSP00000347046:p.Leu641Pro	Somatic	241	1	0.00414938		WXS	Illumina HiSeq	Phase_I	261	129	0.494253	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	37	CCDS3713.1	7	0.003205128205128205	6	0.012195121951219513	0	0.0	0	0.0	1	0.0013192612137203166	A	20.9	4.064397	0.76187	0.013164	0.0	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	D;D;D	0.85702	-2.02;-2.02;-2.02	5.46	5.46	0.80206	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	D	0.91520	0.7322	H	0.94964	3.605	0.80722	D	1	D;D	0.63046	0.992;0.989	D;D	0.72982	0.979;0.916	D	0.92792	0.6249	10	0.87932	D	0	.	9.4099	0.38485	0.9202:0.0:0.0798:0.0	.	641;599	O76074;O76074-2	PDE5A_HUMAN;.	P	641;589;599	ENSP00000347046:L641P;ENSP00000377957:L589P;ENSP00000264805:L599P	ENSP00000264805:L599P	L	-	2	0	PDE5A	120659726	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.113000	0.77095	2.081000	0.62600	0.533000	0.62120	CTG	A|0.996;G|0.004	0.004	strong		0.408	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	
FBN3	84467	hgsc.bcm.edu	37	19	8196499	8196499	+	Silent	SNP	G	G	A	rs3813774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8196499G>A	ENST00000600128.1	-	15	2343	c.1929C>T	c.(1927-1929)tgC>tgT	p.C643C	FBN3_ENST00000601739.1_Silent_p.C643C|FBN3_ENST00000270509.2_Silent_p.C643C			Q75N90	FBN3_HUMAN	fibrillin 3	643	TB 3.					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						GATTGGCACAGCAGCACTCGG	0.652													G|||	690	0.13778	0.2103	0.0533	5008	,	,		16673	0.2262		0.0805	False		,,,				2504	0.0675				p.C643C		Atlas-SNP	.											.	FBN3	300	.	0			c.C1929T						PASS	.	G		783,3623	314.7+/-293.7	64,655,1484	59.0	60.0	60.0		1929	1.6	0.9	19	dbSNP_107	60	504,8096	144.7+/-200.5	16,472,3812	no	coding-synonymous	FBN3	NM_032447.3		80,1127,5296	AA,AG,GG		5.8605,17.7712,9.8954		643/2810	8196499	1287,11719	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon14			GGCACAGCAGCAC		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.1929C>T	19.37:g.8196499G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	220	102	0.463636	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.878;A|0.122	0.122	strong		0.652	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
AXIN1	8312	hgsc.bcm.edu	37	16	347184	347184	+	Silent	SNP	A	A	G	rs214252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:347184A>G	ENST00000262320.3	-	7	2198	c.1827T>C	c.(1825-1827)gcT>gcC	p.A609A	AXIN1_ENST00000481769.1_5'Flank|AXIN1_ENST00000354866.3_Silent_p.A609A	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	609	Interaction with PPP2CA.|Interaction with RNF111.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				TCCCCGACTCAGCCTTCTTGG	0.612													A|||	1048	0.209265	0.4281	0.17	5008	,	,		14273	0.0546		0.2237	False		,,,				2504	0.0859				p.A609A		Atlas-SNP	.											.	AXIN1	290	.	0			c.T1827C						PASS	.	A	,	1696,2710	513.6+/-368.4	325,1046,832	192.0	187.0	189.0		1827,1827	-10.3	0.0	16	dbSNP_79	189	1958,6642	345.8+/-325.9	232,1494,2574	no	coding-synonymous,coding-synonymous	AXIN1	NM_003502.3,NM_181050.2	,	557,2540,3406	GG,GA,AA		22.7674,38.493,28.0947	,	609/863,609/827	347184	3654,9352	2203	4300	6503	SO:0001819	synonymous_variant	8312	exon7			CGACTCAGCCTTC	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	903	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 49"""	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1827T>C	16.37:g.347184A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Silent	SNP	ENST00000262320.3	37	CCDS10405.1																																																																																			A|0.746;G|0.254	0.254	strong		0.612	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		
MATN2	4147	hgsc.bcm.edu	37	8	99028811	99028811	+	Silent	SNP	G	G	A	rs79255841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:99028811G>A	ENST00000520016.1	+	10	1741	c.1617G>A	c.(1615-1617)tcG>tcA	p.S539S	MATN2_ENST00000254898.5_Silent_p.S539S|MATN2_ENST00000522025.2_Silent_p.S255S|MATN2_ENST00000524308.1_Silent_p.S498S|MATN2_ENST00000521689.1_Silent_p.S539S			O00339	MATN2_HUMAN	matrilin 2	539	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			GTGAACATTCGTGTGTAAGCA	0.418													G|||	139	0.0277556	0.0953	0.0187	5008	,	,		19696	0.0		0.0	False		,,,				2504	0.0				p.S539S		Atlas-SNP	.											MATN2_ENST00000520016,NS,carcinoma,+1,2	MATN2	165	2	0			c.G1617A						PASS	.	G	,	355,3435		11,333,1551	108.0	102.0	104.0		1617,1617	-11.3	0.0	8	dbSNP_132	104	4,8248		0,4,4122	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	11,337,5673	AA,AG,GG		0.0485,9.3668,2.9812	,	539/957,539/938	99028811	359,11683	1895	4126	6021	SO:0001819	synonymous_variant	4147	exon11			ACATTCGTGTGTA	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.1617G>A	8.37:g.99028811G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	204	104	0.509804	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	41	0.018772893772893772	35	0.07113821138211382	6	0.016574585635359115	0	0.0	0	0.0	G	0.127	-1.118394	0.01785	0.093668	4.85E-4	ENSG00000132561	ENST00000518154;ENST00000517321	.	.	.	5.67	-11.3	0.00108	.	.	.	.	.	T	0.01156	0.0038	.	.	.	0.52099	D	0.999946	.	.	.	.	.	.	T	0.30851	-0.9964	4	.	.	.	-0.062	1.117	0.01716	0.232:0.3145:0.2304:0.2231	.	.	.	.	M	322;14	.	.	V	+	1	0	MATN2	99097987	0.000000	0.05858	0.012000	0.15200	0.010000	0.07245	-6.461000	0.00065	-2.310000	0.00650	-1.185000	0.01705	GTG	G|0.976;A|0.024	0.024	strong		0.418	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
IPO4	79711	hgsc.bcm.edu	37	14	24652350	24652350	+	Silent	SNP	G	G	A	rs377303706		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24652350G>A	ENST00000354464.6	-	23	2429	c.2253C>T	c.(2251-2253)gtC>gtT	p.V751V	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	751					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		AGGATGGCACGACTCGGGCCA	0.667																																					p.V751V		Atlas-SNP	.											.	IPO4	74	.	0			c.C2253T						PASS	.	C		6,4192		0,6,2093	42.0	48.0	46.0		2253	4.0	1.0	14		46	0,8460		0,0,4230	no	coding-synonymous	IPO4	NM_024658.3		0,6,6323	AA,AG,GG		0.0,0.1429,0.0474		751/1082	24652350	6,12652	2099	4230	6329	SO:0001819	synonymous_variant	79711	exon23			TGGCACGACTCGG	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.2253C>T	14.37:g.24652350G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	136	72	0.529412	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	37	CCDS9616.1																																																																																			.	.	weak		0.667	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
FGD6	55785	hgsc.bcm.edu	37	12	95603098	95603098	+	Silent	SNP	G	G	A	rs17023760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:95603098G>A	ENST00000343958.4	-	2	2185	c.1962C>T	c.(1960-1962)ctC>ctT	p.L654L	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Silent_p.L654L|FGD6_ENST00000546711.1_Silent_p.L654L	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	654					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						TGGTGTCTCCGAGTTGGCTAC	0.448													G|||	248	0.0495208	0.0628	0.0375	5008	,	,		19534	0.0109		0.0467	False		,,,				2504	0.0828				p.L654L		Atlas-SNP	.											.	FGD6	127	.	0			c.C1962T						PASS	.	G		274,4132	153.7+/-187.2	6,262,1935	86.0	89.0	88.0		1962	-12.1	0.0	12	dbSNP_123	88	393,8207	125.0+/-183.6	10,373,3917	no	coding-synonymous	FGD6	NM_018351.3		16,635,5852	AA,AG,GG		4.5698,6.2188,5.1284		654/1431	95603098	667,12339	2203	4300	6503	SO:0001819	synonymous_variant	55785	exon2			GTCTCCGAGTTGG	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.1962C>T	12.37:g.95603098G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	180	91	0.505556	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Silent	SNP	ENST00000343958.4	37	CCDS31878.1																																																																																			G|0.947;A|0.053	0.053	strong		0.448	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
TAS2R40	259286	hgsc.bcm.edu	37	7	142919731	142919731	+	Missense_Mutation	SNP	C	C	A	rs10260248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142919731C>A	ENST00000408947.3	+	1	602	c.560C>A	c.(559-561)tCt>tAt	p.S187Y	AC073342.1_ENST00000595842.1_5'Flank	NM_176882.1	NP_795363.1	P59535	T2R40_HUMAN	taste receptor, type 2, member 40	187			S -> Y (in dbSNP:rs10260248).		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)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8	Melanoma(164;0.059)					AAGTACTTCTCTGAGACCAAT	0.463													C|||	410	0.081869	0.1384	0.0692	5008	,	,		20855	0.0218		0.0577	False		,,,				2504	0.1012				p.S187Y		Atlas-SNP	.											.	TAS2R40	64	.	0			c.C560A						PASS	.	C	TYR/SER	509,3291		39,431,1430	129.0	122.0	124.0		560	2.1	1.0	7	dbSNP_119	124	491,7769		18,455,3657	yes	missense	TAS2R40	NM_176882.1	144	57,886,5087	AA,AC,CC		5.9443,13.3947,8.2919	benign	187/324	142919731	1000,11060	1900	4130	6030	SO:0001583	missense	259286	exon1			ACTTCTCTGAGAC	AF494229	CCDS43662.1	7q34	2012-08-22	2003-12-16		ENSG00000221937	ENSG00000221937		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18885	protein-coding gene	gene with protein product		613964	"""G protein-coupled receptor 60"""	GPR60		12379855	Standard	NM_176882		Approved		uc011ksx.2	P59535	OTTHUMG00000152638	ENST00000408947.3:c.560C>A	7.37:g.142919731C>A	ENSP00000386210:p.Ser187Tyr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_176882	A4D2I2|Q645W6	Missense_Mutation	SNP	ENST00000408947.3	37	CCDS43662.1	148	0.06776556776556776	67	0.13617886178861788	32	0.08839779005524862	14	0.024475524475524476	35	0.04617414248021108	C	0.053	-1.244212	0.01481	0.133947	0.059443	ENSG00000221937	ENST00000408947	T	0.00824	5.65	5.17	2.07	0.26955	.	1.746340	0.03832	U	0.269255	T	0.00039	0.0001	M	0.71206	2.165	0.80722	P	0.0	P	0.41673	0.759	B	0.41374	0.355	T	0.48293	-0.9048	9	0.48119	T	0.1	.	7.0987	0.25325	0.0:0.6061:0.2139:0.18	rs10260248;rs52793975;rs58497743;rs10260248	187	P59535	T2R40_HUMAN	Y	187	ENSP00000386210:S187Y	ENSP00000386210:S187Y	S	+	2	0	TAS2R40	142629853	0.000000	0.05858	0.994000	0.49952	0.678000	0.39670	-0.804000	0.04535	1.149000	0.42402	0.655000	0.94253	TCT	C|0.932;A|0.068	0.068	strong		0.463	TAS2R40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327097.1		
BRINP1	1620	hgsc.bcm.edu	37	9	121929575	121929575	+	Silent	SNP	T	T	C	rs28453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:121929575T>C	ENST00000265922.3	-	8	2534	c.2073A>G	c.(2071-2073)tcA>tcG	p.S691S	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	691					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											GGAGCATCACTGACGAAGAGG	0.572													C|||	933	0.186302	0.5136	0.1124	5008	,	,		18193	0.004		0.0915	False		,,,				2504	0.0818				p.S691S		Atlas-SNP	.											.	DBC1	194	.	0			c.A2073G						PASS	.	C		1908,2498	626.9+/-394.8	431,1046,726	130.0	127.0	128.0		2073	-11.0	0.0	9	dbSNP_79	128	717,7883	786.8+/-407.6	35,647,3618	no	coding-synonymous	DBC1	NM_014618.2		466,1693,4344	CC,CT,TT		8.3372,43.3046,20.183		691/762	121929575	2625,10381	2203	4300	6503	SO:0001819	synonymous_variant	1620	exon8			CATCACTGACGAA	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"""deleted in bladder cancer chromosome region candidate 1"", ""deleted in bladder cancer 1"""	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.2073A>G	9.37:g.121929575T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	207	77	0.371981	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																			T|0.797;C|0.203	0.203	strong		0.572	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
THNSL2	55258	hgsc.bcm.edu	37	2	88478341	88478341	+	Missense_Mutation	SNP	C	C	A	rs34136143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:88478341C>A	ENST00000324166.5	+	4	2302	c.611C>A	c.(610-612)aCt>aAt	p.T204N	THNSL2_ENST00000358591.2_Missense_Mutation_p.T204N|THNSL2_ENST00000343544.4_Missense_Mutation_p.T204N|THNSL2_ENST00000402102.1_Missense_Mutation_p.T204N|THNSL2_ENST00000449349.1_Missense_Mutation_p.T172N|THNSL2_ENST00000377254.3_Missense_Mutation_p.T204N|THNSL2_ENST00000496844.1_3'UTR	NM_018271.4	NP_060741.3	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2 (S. cerevisiae)	204			T -> N (in dbSNP:rs34136143).		2-oxobutyrate biosynthetic process (GO:0046360)|dephosphorylation (GO:0016311)|serine family amino acid catabolic process (GO:0009071)	extracellular space (GO:0005615)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|serine binding (GO:0070905)			breast(4)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	27						CCGATCAAGACTGTGTTTGCC	0.552													C|||	221	0.0441294	0.0779	0.0144	5008	,	,		18531	0.005		0.0109	False		,,,				2504	0.0941				p.T204N		Atlas-SNP	.											.	THNSL2	66	.	0			c.C611A						PASS	.	C	ASN/THR	309,4097	166.2+/-197.5	9,291,1903	194.0	174.0	180.0		611	4.1	1.0	2	dbSNP_126	180	82,8518	48.9+/-108.6	0,82,4218	yes	missense	THNSL2	NM_018271.4	65	9,373,6121	AA,AC,CC		0.9535,7.0132,3.0063	benign	204/485	88478341	391,12615	2203	4300	6503	SO:0001583	missense	55258	exon4			TCAAGACTGTGTT		CCDS2002.2, CCDS58718.1, CCDS74539.1	2p11.2	2007-06-20			ENSG00000144115	ENSG00000144115			25602	protein-coding gene	gene with protein product		611261				17034760	Standard	NM_018271		Approved	FLJ10916	uc021vkr.1	Q86YJ6	OTTHUMG00000130314	ENST00000324166.5:c.611C>A	2.37:g.88478341C>A	ENSP00000327323:p.Thr204Asn	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	204	204	1	NM_018271	B3KTB1|B5MDX8|B7WPF8|D9ZZB8|Q6P2M7|Q6PI27|Q9NV54	Missense_Mutation	SNP	ENST00000324166.5	37	CCDS2002.2	54	0.024725274725274724	38	0.07723577235772358	7	0.019337016574585635	0	0.0	9	0.011873350923482849	C	9.986	1.229403	0.22542	0.070132	0.009535	ENSG00000144115	ENST00000358591;ENST00000377254;ENST00000402102;ENST00000449349;ENST00000544063;ENST00000343544;ENST00000324166	T;T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83;2.83	5.08	4.07	0.47477	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.601847	0.16677	N	0.204129	T	0.00300	0.0009	N	0.03016	-0.435	0.22880	N	0.998614	B;B;B;B	0.11235	0.001;0.0;0.004;0.001	B;B;B;B	0.09377	0.003;0.001;0.001;0.004	T	0.32161	-0.9917	10	0.59425	D	0.04	.	10.4043	0.44248	0.3747:0.6253:0.0:0.0	rs34136143	46;204;172;204	A8K0C1;Q86YJ6;C9JU10;Q86YJ6-2	.;THNS2_HUMAN;.;.	N	204;204;204;172;46;204;204	ENSP00000351402:T204N;ENSP00000366464:T204N;ENSP00000384475:T204N;ENSP00000407553:T172N;ENSP00000339563:T204N;ENSP00000327323:T204N	ENSP00000327323:T204N	T	+	2	0	THNSL2	88259456	0.998000	0.40836	0.951000	0.38953	0.214000	0.24535	4.088000	0.57678	2.553000	0.86117	0.561000	0.74099	ACT	C|0.974;A|0.026	0.026	strong		0.552	THNSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252662.1	NM_018271	
BRSK1	84446	hgsc.bcm.edu	37	19	55815159	55815159	+	Silent	SNP	C	C	A	rs17851415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55815159C>A	ENST00000309383.1	+	12	1528	c.1251C>A	c.(1249-1251)acC>acA	p.T417T	BRSK1_ENST00000590333.1_Silent_p.T433T|BRSK1_ENST00000326848.7_Silent_p.T112T	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	123	0	0		WXS	Illumina HiSeq	Phase_I	111	49	0.441441	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	
FSD2	123722	hgsc.bcm.edu	37	15	83428192	83428192	+	Missense_Mutation	SNP	C	C	T	rs1108134	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83428192C>T	ENST00000334574.8	-	13	2339	c.2158G>A	c.(2158-2160)Gaa>Aaa	p.E720K	RP11-752G15.6_ENST00000561107.1_RNA|FSD2_ENST00000541889.1_Missense_Mutation_p.E675K|RP11-752G15.6_ENST00000558174.1_RNA|RP11-752G15.6_ENST00000559366.1_RNA			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	720	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		E -> K (in dbSNP:rs1108134).							breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						TGCACAAATTCGTGAAGCTGA	0.348													c|||	481	0.0960463	0.1256	0.1628	5008	,	,		20459	0.001		0.16	False		,,,				2504	0.0409				p.E720K		Atlas-SNP	.											.	FSD2	45	.	0			c.G2158A						PASS	.		LYS/GLU	526,3170		32,462,1354	71.0	69.0	69.0		2158	1.7	0.0	15	dbSNP_86	69	1379,6823		109,1161,2831	yes	missense	FSD2	NM_001007122.2	56	141,1623,4185	TT,TC,CC		16.813,14.2316,16.0111	benign	720/750	83428192	1905,9993	1848	4101	5949	SO:0001583	missense	123722	exon13			CAAATTCGTGAAG	AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"""Fibronectin type III domain containing"""	18024	protein-coding gene	gene with protein product			"""SPRY domain containing 1"""	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.2158G>A	15.37:g.83428192C>T	ENSP00000335651:p.Glu720Lys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001007122	B3KVG1|B7ZM02	Missense_Mutation	SNP	ENST00000334574.8	37	CCDS45332.1	257	0.11767399267399267	74	0.15040650406504066	64	0.17679558011049723	4	0.006993006993006993	115	0.1517150395778364	c	7.367	0.626101	0.14257	0.142316	0.16813	ENSG00000186628	ENST00000334574;ENST00000541889	T;T	0.15834	2.39;2.39	5.86	1.71	0.24356	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.577689	0.18596	N	0.136589	T	0.00039	0.0001	L	0.52573	1.65	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.001	T	0.31943	-0.9925	9	0.17832	T	0.49	0.0763	6.7726	0.23602	0.0658:0.2404:0.5729:0.1209	rs1108134;rs4262919;rs61477553;rs1108134	675;720	B7ZM02;A1L4K1	.;FSD2_HUMAN	K	720;675	ENSP00000335651:E720K;ENSP00000444078:E675K	ENSP00000335651:E720K	E	-	1	0	FSD2	81225246	0.878000	0.30173	0.001000	0.08648	0.483000	0.33249	2.146000	0.42216	0.496000	0.27904	-0.836000	0.03065	GAA	C|0.869;T|0.131	0.131	strong		0.348	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122	
ABCA2	20	hgsc.bcm.edu	37	9	139916833	139916833	+	Silent	SNP	T	T	G	rs35590326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139916833T>G	ENST00000371605.3	-	5	681	c.534A>C	c.(532-534)gcA>gcC	p.A178A	ABCA2_ENST00000265662.5_Silent_p.A179A|ABCA2_ENST00000492260.1_5'UTR|ABCA2_ENST00000341511.6_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	132	2	0.0151515		WXS	Illumina HiSeq	Phase_I	149	94	0.630872	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	
FAM47C	442444	hgsc.bcm.edu	37	X	37029254	37029254	+	Missense_Mutation	SNP	A	A	C	rs1995914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37029254A>C	ENST00000358047.3	+	1	2823	c.2771A>C	c.(2770-2772)aAt>aCt	p.N924T		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	924			N -> T (in dbSNP:rs1995914).							breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						AAAATCCAGAATGCACCAAAT	0.453													N|||	1396	0.369801	0.6445	0.2392	3775	,	,		15358	0.0982		0.0785	False		,,,				2504	0.2045				p.N924T		Atlas-SNP	.											.	FAM47C	267	.	0			c.A2771C						PASS	.	C	THR/ASN	2991,842		1003,538,447,90,124	85.0	87.0	86.0		2771	-1.7	0.0	X	dbSNP_92	86	783,5945		26,499,232,1903,1640	yes	missense	FAM47C	NM_001013736.2	65	1029,1037,679,1993,1764	CC,CA,C,AA,A		11.6379,21.9671,35.7353	benign	924/1036	37029254	3774,6787	2202	4300	6502	SO:0001583	missense	442444	exon1			TCCAGAATGCACC	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2771A>C	X.37:g.37029254A>C	ENSP00000367913:p.Asn924Thr	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	174	172	0.988506	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	495	0.298372513562387	216	0.7058823529411765	54	0.16981132075471697	37	0.06801470588235294	43	0.05922865013774105	C	0.001	-3.759422	0.00005	0.780329	0.116379	ENSG00000198173	ENST00000358047	T	0.42131	0.98	0.829	-1.66	0.08265	.	.	.	.	.	T	0.00012	0.0000	N	0.00823	-1.155	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.45789	-0.9237	7	0.14252	T	0.57	.	.	.	.	rs1995914;rs52815039;rs59553201;rs1995914	924	Q5HY64	FA47C_HUMAN	T	924	ENSP00000367913:N924T	ENSP00000367913:N924T	N	+	2	0	FAM47C	36939175	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.842000	0.04354	-4.876000	0.00028	-4.602000	0.00004	AAT	A|0.631;C|0.369	0.369	strong		0.453	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
SMYD1	150572	hgsc.bcm.edu	37	2	88396120	88396120	+	Silent	SNP	G	G	A	rs2919882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:88396120G>A	ENST00000419482.2	+	6	790	c.705G>A	c.(703-705)gaG>gaA	p.E235E	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.E222E	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	235	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						TCAGAATTGAGCTCCGGGCCC	0.507													G|||	1572	0.313898	0.4244	0.2579	5008	,	,		20526	0.1627		0.3559	False		,,,				2504	0.317				p.E235E		Atlas-SNP	.											.	SMYD1	95	.	0			c.G705A						PASS	.	G		1785,2621	525.7+/-371.7	357,1071,775	97.0	96.0	96.0		705	1.7	1.0	2	dbSNP_101	96	3132,5468	473.3+/-368.6	569,1994,1737	no	coding-synonymous	SMYD1	NM_198274.3		926,3065,2512	AA,AG,GG		36.4186,40.5129,37.8056		235/491	88396120	4917,8089	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon6			AATTGAGCTCCGG	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.705G>A	2.37:g.88396120G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			G|0.647;A|0.353	0.353	strong		0.507	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
FRY	10129	hgsc.bcm.edu	37	13	32759183	32759183	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:32759183C>T	ENST00000380250.3	+	26	3713	c.3217C>T	c.(3217-3219)Cgc>Tgc	p.R1073C		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1073						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R1073C(1)		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)		GGACTTGACCCGCATGCTCCT	0.418																																					p.R1073C		Atlas-SNP	.											FRY,NS,carcinoma,-1,2	FRY	312	2	1	Substitution - Missense(1)	prostate(1)	c.C3217T						scavenged	.						136.0	131.0	133.0					13																	32759183		1851	4089	5940	SO:0001583	missense	10129	exon26			TTGACCCGCATGC	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.3217C>T	13.37:g.32759183C>T	ENSP00000369600:p.Arg1073Cys	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	189	3	0.015873	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.934865	0.73442	.	.	ENSG00000073910	ENST00000380250	T	0.27256	1.68	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.48607	0.1509	M	0.74647	2.275	0.80722	D	1	D	0.89917	1.0	D	0.66351	0.943	T	0.39881	-0.9592	10	0.41790	T	0.15	.	14.3247	0.66512	0.1483:0.8517:0.0:0.0	.	1073	Q5TBA9	FRY_HUMAN	C	1073	ENSP00000369600:R1073C	ENSP00000369600:R1073C	R	+	1	0	FRY	31657183	0.992000	0.36948	1.000000	0.80357	0.929000	0.56500	2.934000	0.48956	2.675000	0.91044	0.650000	0.86243	CGC	.	.	none		0.418	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
DDX53	168400	hgsc.bcm.edu	37	X	23019317	23019317	+	Missense_Mutation	SNP	G	G	T	rs5925720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:23019317G>T	ENST00000327968.5	+	1	1231	c.1143G>T	c.(1141-1143)atG>atT	p.M381I	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	381	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		M -> I (in dbSNP:rs5925720).			nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						CAGATAAAATGCTGGATATGG	0.413													G|||	610	0.161589	0.0008	0.0432	3775	,	,		15089	0.2073		0.0885	False		,,,				2504	0.2873				p.M381I		Atlas-SNP	.											.	DDX53	76	.	0			c.G1143T						PASS	.	G	ILE/MET	67,3768		0,54,13,1578,558	112.0	110.0	110.0		1143	4.3	0.5	X	dbSNP_114	110	789,5939		28,494,239,1906,1633	yes	missense	DDX53	NM_182699.3	10	28,548,252,3484,2191	TT,TG,T,GG,G		11.7271,1.7471,8.1038	probably-damaging	381/632	23019317	856,9707	2203	4300	6503	SO:0001583	missense	168400	exon1			TAAAATGCTGGAT	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"""DEAD-boxes"""	20083	protein-coding gene	gene with protein product	"""cancer associated gene"", ""cancer/testis antigen 26"""						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.1143G>T	X.37:g.23019317G>T	ENSP00000368667:p.Met381Ile	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_182699	Q0D2N2|Q6NVV4	Missense_Mutation	SNP	ENST00000327968.5	37	CCDS35214.1	191	0.11512959614225438	0	0.0	11	0.03125	69	0.13745019920318724	52	0.07222222222222222	G	16.81	3.227200	0.58668	0.017471	0.117271	ENSG00000184735	ENST00000327968	T	0.14766	2.48	4.3	4.3	0.51218	RNA helicase, ATP-dependent, DEAD-box, conserved site (1);DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00356	0.0011	M	0.84846	2.72	0.19575	P	0.9999620347	D	0.89917	1.0	D	0.91635	0.999	T	0.04467	-1.0949	9	0.87932	D	0	0.0312	13.7336	0.62804	0.0:0.0:1.0:0.0	rs5925720;rs58250497;rs5925720	381	Q86TM3	DDX53_HUMAN	I	381	ENSP00000368667:M381I	ENSP00000368667:M381I	M	+	3	0	DDX53	22929238	1.000000	0.71417	0.491000	0.27477	0.478000	0.33099	8.508000	0.90525	1.894000	0.54839	0.600000	0.82982	ATG	G|0.902;T|0.098	0.098	strong		0.413	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580967	140580967	+	Silent	SNP	T	T	G	rs149572646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140580967T>G	ENST00000354757.3	+	1	1620	c.1620T>G	c.(1618-1620)gcT>gcG	p.A540A	PCDHB11_ENST00000536699.1_Silent_p.A175A	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	540	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCTCCCCGGCTTTGAGCAGCG	0.687																																					p.A540A		Atlas-SNP	.											.	PCDHB11	162	.	0			c.T1620G						PASS	.						32.0	44.0	40.0					5																	140580967		2202	4297	6499	SO:0001819	synonymous_variant	56125	exon1			CCCGGCTTTGAGC	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.1620T>G	5.37:g.140580967T>G		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	392	48	0.122449	NM_018931	B4DSF7|Q2M223	Silent	SNP	ENST00000354757.3	37	CCDS4253.1																																																																																			T|0.998;G|0.002	0.002	strong		0.687	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
GPATCH1	55094	hgsc.bcm.edu	37	19	33605312	33605312	+	Missense_Mutation	SNP	T	T	C	rs10421769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33605312T>C	ENST00000170564.2	+	15	2497	c.2183T>C	c.(2182-2184)tTa>tCa	p.L728S		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	728			L -> S (in dbSNP:rs10421769). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		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)					GCACCAGAATTATCCGCAAAT	0.458													C|||	3857	0.770168	0.9697	0.7017	5008	,	,		18803	0.9901		0.3489	False		,,,				2504	0.7556				p.L728S	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.T2183C						PASS	.	C	SER/LEU	3851,555	247.8+/-255.9	1691,469,43	65.0	71.0	69.0		2183	5.3	0.0	19	dbSNP_119	69	3121,5479	657.3+/-401.5	558,2005,1737	yes	missense	GPATCH1	NM_018025.2	145	2249,2474,1780	CC,CT,TT		36.2907,12.5965,46.394	benign	728/932	33605312	6972,6034	2203	4300	6503	SO:0001583	missense	55094	exon15			CAGAATTATCCGC	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.2183T>C	19.37:g.33605312T>C	ENSP00000170564:p.Leu728Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Missense_Mutation	SNP	ENST00000170564.2	37	CCDS12428.1	1530	0.7005494505494505	476	0.967479674796748	225	0.6215469613259669	567	0.9912587412587412	262	0.34564643799472294	C	3.637	-0.074302	0.07184	0.874035	0.362907	ENSG00000076650	ENST00000170564	T	0.17854	2.25	5.32	5.32	0.75619	.	0.723385	0.14206	N	0.334384	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.35276	-0.9795	9	0.08837	T	0.75	-0.0798	11.6747	0.51424	0.0:0.9185:0.0:0.0815	rs10421769;rs17317363;rs57920383;rs10421769	728;728	B2RDX4;Q9BRR8	.;GPTC1_HUMAN	S	728	ENSP00000170564:L728S	ENSP00000170564:L728S	L	+	2	0	GPATCH1	38297152	0.012000	0.17670	0.002000	0.10522	0.003000	0.03518	2.751000	0.47508	1.248000	0.43934	-0.128000	0.14901	TTA	T|0.380;C|0.620	0.620	strong		0.458	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
ATP13A5	344905	hgsc.bcm.edu	37	3	193081122	193081122	+	Missense_Mutation	SNP	G	G	T	rs12637558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:193081122G>T	ENST00000342358.4	-	3	404	c.287C>A	c.(286-288)tCc>tAc	p.S96Y		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	96			S -> Y (in dbSNP:rs12637558). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.S96F(1)|p.S96Y(1)		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)		CTTCAGTGTGGATAAGTAGAG	0.398													G|||	2083	0.415935	0.2133	0.4337	5008	,	,		18153	0.5764		0.4125	False		,,,				2504	0.5153				p.S96Y		Atlas-SNP	.											ATP13A5,NS,carcinoma,0,2	ATP13A5	171	2	2	Substitution - Missense(2)	ovary(1)|NS(1)	c.C287A						PASS	.	G	TYR/SER	1146,3260	409.1+/-334.9	155,836,1212	98.0	96.0	97.0		287	4.2	1.0	3	dbSNP_120	97	3666,4934	527.1+/-381.1	807,2052,1441	yes	missense	ATP13A5	NM_198505.2	144	962,2888,2653	TT,TG,GG		42.6279,26.01,36.9983	probably-damaging	96/1219	193081122	4812,8194	2203	4300	6503	SO:0001583	missense	344905	exon3			AGTGTGGATAAGT	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.287C>A	3.37:g.193081122G>T	ENSP00000341942:p.Ser96Tyr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	893	0.4088827838827839	119	0.241869918699187	143	0.39502762430939226	323	0.5646853146853147	308	0.40633245382585753	G	16.92	3.255259	0.59321	0.2601	0.426279	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.44881	0.91;0.91	5.06	4.17	0.49024	.	0.195010	0.36893	N	0.002353	T	0.00012	0.0000	M	0.73962	2.25	0.29320	P	0.867429	P	0.36733	0.567	B	0.41764	0.366	T	0.48980	-0.8986	9	0.59425	D	0.04	-6.0887	13.2983	0.60311	0.0:0.0:0.84:0.16	rs12637558;rs59613984	96	Q4VNC0	AT135_HUMAN	Y	96;118	ENSP00000341942:S96Y;ENSP00000389416:S118Y	ENSP00000341942:S96Y	S	-	2	0	ATP13A5	194563816	1.000000	0.71417	0.987000	0.45799	0.953000	0.61014	3.546000	0.53656	1.428000	0.47296	0.655000	0.94253	TCC	G|0.618;T|0.382	0.382	strong		0.398	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
CFTR	1080	hgsc.bcm.edu	37	7	117282644	117282644	+	Silent	SNP	A	A	G	rs1800130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:117282644A>G	ENST00000003084.6	+	23	4002	c.3870A>G	c.(3868-3870)ccA>ccG	p.P1290P	AC000111.6_ENST00000456270.1_RNA|CFTR_ENST00000454343.1_Silent_p.P1229P	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1290	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	GAGTGATACCACAGGTGAGCA	0.368									Cystic Fibrosis				G|||	343	0.0684904	0.177	0.0303	5008	,	,		18315	0.001		0.0398	False		,,,				2504	0.0481				p.P1290P		Atlas-SNP	.											.	CFTR	171	.	0			c.A3870G						PASS	.	G		665,3741	762.6+/-413.1	48,569,1586	83.0	78.0	80.0		3870	-4.3	1.0	7	dbSNP_89	80	255,8345	807.5+/-407.2	7,241,4052	no	coding-synonymous	CFTR	NM_000492.3		55,810,5638	GG,GA,AA		2.9651,15.0931,7.0737		1290/1481	117282644	920,12086	2203	4300	6503	SO:0001819	synonymous_variant	1080	exon23	Familial Cancer Database	CF	GATACCACAGGTG	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.3870A>G	7.37:g.117282644A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	29	0.345238	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	37	CCDS5773.1																																																																																			A|0.927;G|0.073	0.073	strong		0.368	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
MYOM1	8736	hgsc.bcm.edu	37	18	3067278	3067278	+	Silent	SNP	A	A	G	rs2230164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3067278A>G	ENST00000356443.4	-	38	5373	c.5040T>C	c.(5038-5040)ggT>ggC	p.G1680G	MYOM1_ENST00000261606.7_Silent_p.G1584G|MYOM1_ENST00000400569.3_Silent_p.G1680G	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1680					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						CCTTCTTGCCACCTTTCAGGG	0.567													G|||	2977	0.594449	0.8533	0.4207	5008	,	,		16407	0.5308		0.4652	False		,,,				2504	0.5665				p.G1680G		Atlas-SNP	.											MYOM1,colon,carcinoma,0,1	MYOM1	192	1	0			c.T5040C						PASS	.	G	,	3376,978		1313,750,114	19.0	26.0	24.0		5040,4752	-2.1	0.0	18	dbSNP_98	24	3990,4564		936,2118,1223	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	2249,2868,1337	GG,GA,AA		46.6448,22.4621,42.9346	,	1680/1686,1584/1590	3067278	7366,5542	2177	4277	6454	SO:0001819	synonymous_variant	8736	exon38			CTTGCCACCTTTC	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.5040T>C	18.37:g.3067278A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			A|0.424;G|0.576	0.576	strong		0.567	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
ZNF280C	55609	hgsc.bcm.edu	37	X	129349295	129349295	+	Silent	SNP	T	T	G	rs209238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:129349295T>G	ENST00000370978.4	-	15	2004	c.1851A>C	c.(1849-1851)ggA>ggC	p.G617G		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	617					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						ACTTGTGAATTCCCCGACGAC	0.318													T|||	1969	0.521589	0.5681	0.353	3775	,	,		12569	0.2738		0.3151	False		,,,				2504	0.3885				p.G617G		Atlas-SNP	.											.	ZNF280C	63	.	0			c.A1851C						PASS	.	T		2618,1217		769,679,401,184,170	77.0	81.0	80.0		1851	3.2	0.8	X	dbSNP_79	80	2698,4030		394,1164,746,870,1126	no	coding-synonymous	ZNF280C	NM_017666.4		1163,1843,1147,1054,1296	GG,GT,G,TT,T		40.1011,31.734,49.6734		617/738	129349295	5316,5247	2203	4300	6503	SO:0001819	synonymous_variant	55609	exon15			GTGAATTCCCCGA	AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 3 (Drosophila)"""	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.1851A>C	X.37:g.129349295T>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	130	46	0.353846	NM_017666	A8K2V8|Q9NXR3	Silent	SNP	ENST00000370978.4	37	CCDS14622.1																																																																																			0|0.003;G|0.509	0.509	strong		0.318	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666	
TRIM16	10626	hgsc.bcm.edu	37	17	15532430	15532430	+	Silent	SNP	G	G	A	rs7225221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15532430G>A	ENST00000578237.1	-	11	2049	c.1194C>T	c.(1192-1194)acC>acT	p.T398T	TRIM16_ENST00000336708.7_Silent_p.T398T|RP11-385D13.1_ENST00000455584.2_Silent_p.T398T|TRIM16_ENST00000579219.1_Missense_Mutation_p.P95L|TRIM16_ENST00000416464.2_Silent_p.T268T|TRIM16_ENST00000577886.1_Silent_p.T182T			O95361	TRI16_HUMAN	tripartite motif containing 16	398	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		CCCAGGGCGTGGTGTTGGTGA	0.587													G|||	309	0.0617013	0.2269	0.0115	5008	,	,		19836	0.0		0.001	False		,,,				2504	0.0				p.T398T		Atlas-SNP	.											.	TRIM16	45	.	0			c.C1194T						PASS	.	G		746,3660		67,612,1524	44.0	42.0	43.0		1194	-1.7	0.8	17	dbSNP_116	43	5,8587		0,5,4291	no	coding-synonymous	TRIM16	NM_006470.3		67,617,5815	AA,AG,GG		0.0582,16.9315,5.7778		398/565	15532430	751,12247	2203	4296	6499	SO:0001819	synonymous_variant	10626	exon9			GGGCGTGGTGTTG	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"""Tripartite motif containing / Tripartite motif containing"""	17241	protein-coding gene	gene with protein product	"""estrogen-responsive B box protein"""	609505	"""tripartite motif-containing 16"""			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.1194C>T	17.37:g.15532430G>A		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	324	142	0.438272	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Silent	SNP	ENST00000578237.1	37	CCDS11171.1	87	0.03983516483516483	83	0.16869918699186992	4	0.011049723756906077	0	0.0	0	0.0	.	12.03	1.816778	0.32145	0.169315	5.82E-4	ENSG00000251537	ENST00000455584	.	.	.	4.53	-1.68	0.08212	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999999986	.	.	.	.	.	.	T	0.23726	-1.0180	3	.	.	.	.	5.0704	0.14604	0.0891:0.4085:0.378:0.1244	rs7225221	.	.	.	L	413	.	.	P	-	2	0	RP11-385D13.1	15473155	0.983000	0.35010	0.789000	0.31954	0.992000	0.81027	0.170000	0.16663	0.096000	0.17463	0.650000	0.86243	CCA	G|0.953;A|0.047	0.047	strong		0.587	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	
RBL2	5934	hgsc.bcm.edu	37	16	53503934	53503934	+	Silent	SNP	G	G	A	rs1131220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53503934G>A	ENST00000262133.6	+	15	2219	c.2082G>A	c.(2080-2082)acG>acA	p.T694T	RBL2_ENST00000544545.1_Intron|RBL2_ENST00000379935.4_3'UTR	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	694	Pocket; binds E1A.|Spacer.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						ATGGAGGGACGCCTGGGCGCA	0.547													g|||	2531	0.505391	0.8517	0.4049	5008	,	,		17469	0.1786		0.4662	False		,,,				2504	0.4857				p.T694T		Atlas-SNP	.											.	RBL2	115	.	0			c.G2082A						PASS	.	A		3382,1014	728.0+/-409.9	1314,754,130	76.0	75.0	75.0		2082	1.0	0.4	16	dbSNP_86	75	4177,4423	565.4+/-388.5	1028,2121,1151	no	coding-synonymous	RBL2	NM_005611.3		2342,2875,1281	AA,AG,GG		48.5698,23.0664,41.8359		694/1140	53503934	7559,5437	2198	4300	6498	SO:0001819	synonymous_variant	5934	exon15			AGGGACGCCTGGG	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2082G>A	16.37:g.53503934G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Silent	SNP	ENST00000262133.6	37	CCDS10748.1																																																																																			G|0.461;A|0.539	0.539	strong		0.547	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
NEFH	4744	hgsc.bcm.edu	37	22	29886341	29886341	+	Silent	SNP	C	C	T	rs61744118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:29886341C>T	ENST00000310624.6	+	4	2745	c.2712C>T	c.(2710-2712)ccC>ccT	p.P904P		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	910	Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAAAAGTCCCCACCCCAGAGA	0.502													C|||	49	0.00978435	0.0363	0.0014	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0				p.P904P		Atlas-SNP	.											.	NEFH	178	.	0			c.C2712T						PASS	.	C		129,4277	88.7+/-127.4	2,125,2076	55.0	60.0	59.0		2712	-6.6	0.0	22	dbSNP_129	59	0,8600		0,0,4300	no	coding-synonymous	NEFH	NM_021076.3		2,125,6376	TT,TC,CC		0.0,2.9278,0.9918		904/1021	29886341	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	4744	exon4			AGTCCCCACCCCA		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.2712C>T	22.37:g.29886341C>T		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			C|0.990;T|0.010	0.010	strong		0.502	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
SPTA1	6708	hgsc.bcm.edu	37	1	158618320	158618320	+	Silent	SNP	G	G	A	rs34773716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158618320G>A	ENST00000368147.4	-	26	3873	c.3693C>T	c.(3691-3693)gaC>gaT	p.D1231D		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1231					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)					GGGGTACGAGGTCCCTTTCAA	0.498													G|||	134	0.0267572	0.0938	0.013	5008	,	,		14013	0.0		0.001	False		,,,				2504	0.0				p.D1231D		Atlas-SNP	.											SPTA1,NS,carcinoma,-2,1	SPTA1	720	1	0			c.C3693T						PASS	.	G		250,3612		10,230,1691	115.0	116.0	115.0		3693	-0.7	0.4	1	dbSNP_126	115	5,8249		0,5,4122	yes	coding-synonymous	SPTA1	NM_003126.2		10,235,5813	AA,AG,GG		0.0606,6.4733,2.1047		1231/2420	158618320	255,11861	1931	4127	6058	SO:0001819	synonymous_variant	6708	exon26			TACGAGGTCCCTT	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.3693C>T	1.37:g.158618320G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	80	53	0.6625	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			G|0.988;A|0.012	0.012	strong		0.498	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
CCDC116	164592	hgsc.bcm.edu	37	22	21988602	21988602	+	Missense_Mutation	SNP	C	C	T	rs861853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	31	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	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	
DSG1	1828	hgsc.bcm.edu	37	18	28934681	28934681	+	Missense_Mutation	SNP	A	A	T	rs3752095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28934681A>T	ENST00000257192.4	+	15	2734	c.2522A>T	c.(2521-2523)tAc>tTc	p.Y841F	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578119.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG1_ENST00000462981.2_Missense_Mutation_p.Y200F|RP11-534N16.1_ENST00000581452.1_RNA	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	841			Y -> F (in dbSNP:rs3752095).		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)			ACCGAGTCTTACACCACCTCT	0.527													A|||	578	0.115415	0.1256	0.0836	5008	,	,		21622	0.0813		0.1412	False		,,,				2504	0.1329				p.Y841F		Atlas-SNP	.											.	DSG1	176	.	0			c.A2522T						PASS	.	A	PHE/TYR	611,3795	265.9+/-266.9	39,533,1631	223.0	187.0	199.0		2522	5.8	1.0	18	dbSNP_107	199	1169,7431	239.9+/-270.8	70,1029,3201	yes	missense	DSG1	NM_001942.2	22	109,1562,4832	TT,TA,AA		13.593,13.8675,13.686	probably-damaging	841/1050	28934681	1780,11226	2203	4300	6503	SO:0001583	missense	1828	exon15			AGTCTTACACCAC	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.2522A>T	18.37:g.28934681A>T	ENSP00000257192:p.Tyr841Phe	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	190	95	0.5	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	254	0.1163003663003663	65	0.13211382113821138	36	0.09944751381215469	48	0.08391608391608392	105	0.13852242744063326	A	13.18	2.158766	0.38119	0.138675	0.13593	ENSG00000134760	ENST00000257192	T	0.69175	-0.38	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000011	T	0.03348	0.0097	M	0.88775	2.98	0.22185	P	0.999301881	D	0.76494	0.999	D	0.72982	0.979	T	0.50423	-0.8830	9	0.72032	D	0.01	.	16.0817	0.81010	1.0:0.0:0.0:0.0	rs3752095;rs17715907;rs52827858;rs59956720;rs3752095	841	Q02413	DSG1_HUMAN	F	841	ENSP00000257192:Y841F	ENSP00000257192:Y841F	Y	+	2	0	DSG1	27188679	1.000000	0.71417	0.998000	0.56505	0.847000	0.48162	6.414000	0.73318	2.206000	0.71126	0.383000	0.25322	TAC	A|0.864;T|0.136	0.136	strong		0.527	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
AIRE	326	hgsc.bcm.edu	37	21	45705988	45705988	+	Silent	SNP	T	T	C	rs3746964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45705988T>C	ENST00000291582.5	+	1	226	c.99T>C	c.(97-99)gcT>gcC	p.A33A		NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	33	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.				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)		ACGCGCTGGCTGACCACGACG	0.716									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				C|||	1199	0.239417	0.5651	0.1153	5008	,	,		6613	0.2788		0.0249	False		,,,				2504	0.0675				p.A33A		Atlas-SNP	.											.	AIRE	61	.	0			c.T99C						PASS	.	C		1412,2352		236,940,706	6.0	6.0	6.0		99	-2.6	0.9	21	dbSNP_107	6	125,7321		2,121,3600	no	coding-synonymous	AIRE	NM_000383.2		238,1061,4306	CC,CT,TT		1.6788,37.5133,13.711		33/546	45705988	1537,9673	1882	3723	5605	SO:0001819	synonymous_variant	326	exon1	Familial Cancer Database	APECED	GCTGGCTGACCAC	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.99T>C	21.37:g.45705988T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			T|0.716;C|0.284	0.284	strong		0.716	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
RNF216	54476	hgsc.bcm.edu	37	7	5765034	5765034	+	Silent	SNP	C	C	T	rs77500990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5765034C>T	ENST00000425013.2	-	8	1478	c.1254G>A	c.(1252-1254)ctG>ctA	p.L418L	RNF216_ENST00000389902.3_Silent_p.L475L	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	418					apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		TTTCTGGTGACAGCTCCTGCC	0.368													c|||	17	0.00339457	0.0129	0.0	5008	,	,		20317	0.0		0.0	False		,,,				2504	0.0				p.L475L		Atlas-SNP	.											.	RNF216	71	.	0			c.G1425A						PASS	.	C	,	52,4354	51.6+/-87.1	0,52,2151	143.0	123.0	130.0		1425,1254	-3.0	1.0	7	dbSNP_131	130	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	RNF216	NM_207111.3,NM_207116.2	,	0,58,6445	TT,TC,CC		0.0698,1.1802,0.4459	,	475/924,418/867	5765034	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	54476	exon8			TGGTGACAGCTCC	AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"""RING-type (C3HC4) zinc fingers"""	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.1254G>A	7.37:g.5765034C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	150	79	0.526667	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Silent	SNP	ENST00000425013.2	37	CCDS34595.1																																																																																			C|0.996;T|0.004	0.004	strong		0.368	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111	
PLA2G1B	5319	hgsc.bcm.edu	37	12	120762765	120762765	+	Silent	SNP	C	C	T	rs5637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:120762765C>T	ENST00000308366.4	-	3	329	c.294G>A	c.(292-294)tcG>tcA	p.S98S	PLA2G1B_ENST00000423423.3_Intron|PLA2G1B_ENST00000549767.1_Silent_p.S69S	NM_000928.2	NP_000919.1	P04054	PA21B_HUMAN	phospholipase A2, group IB (pancreas)	98					actin filament organization (GO:0007015)|activation of MAPK activity (GO:0000187)|activation of phospholipase A2 activity (GO:0032431)|antibacterial humoral response (GO:0019731)|arachidonic acid secretion (GO:0050482)|cellular response to insulin stimulus (GO:0032869)|defense response to Gram-positive bacterium (GO:0050830)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response in mucosa (GO:0002227)|interleukin-8 production (GO:0032637)|intracellular signal transduction (GO:0035556)|leukotriene biosynthetic process (GO:0019370)|multicellular organismal lipid catabolic process (GO:0044240)|neutrophil chemotaxis (GO:0030593)|neutrophil mediated immunity (GO:0002446)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine metabolic process (GO:0046470)|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 metabolic process (GO:0006644)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of immune response (GO:0050778)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule (GO:0030141)	bile acid binding (GO:0032052)|calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|phospholipase A2 activity (GO:0004623)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(3)|skin(2)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)				Niflumic Acid(DB04552)|Sulfasalazine(DB00795)	AGCCAGAGCACGAGTATGAAT	0.493											OREG0022189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1056	0.210863	0.4592	0.147	5008	,	,		19390	0.0794		0.1392	False		,,,				2504	0.1299				p.S98S	NSCLC(64;1781 1795 22266 42732)|Esophageal Squamous(30;459 829 25326 35148)	Atlas-SNP	.											.	PLA2G1B	8	.	0			c.G294A						PASS	.	C		1737,2669	518.3+/-369.7	350,1037,816	212.0	180.0	191.0		294	-10.1	0.0	12	dbSNP_52	191	1276,7324	252.6+/-278.6	92,1092,3116	no	coding-synonymous	PLA2G1B	NM_000928.2		442,2129,3932	TT,TC,CC		14.8372,39.4235,23.1662		98/149	120762765	3013,9993	2203	4300	6503	SO:0001819	synonymous_variant	5319	exon3			AGAGCACGAGTAT		CCDS9195.1	12q24.31	2013-09-19			ENSG00000170890	ENSG00000170890	3.1.1.4		9030	protein-coding gene	gene with protein product		172410		PLA2, PPLA2, PLA2A		8175726	Standard	NM_000928		Approved		uc001tyd.3	P04054	OTTHUMG00000169343	ENST00000308366.4:c.294G>A	12.37:g.120762765C>T		Somatic	273	0	0	1506	WXS	Illumina HiSeq	Phase_I	261	260	0.996169	NM_000928	B2R4H5|Q3KPI1	Silent	SNP	ENST00000308366.4	37	CCDS9195.1																																																																																			C|0.786;T|0.214	0.214	strong		0.493	PLA2G1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403626.1		
TNC	3371	hgsc.bcm.edu	37	9	117853022	117853022	+	Silent	SNP	C	C	T	rs944510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117853022C>T	ENST00000350763.4	-	2	687	c.276G>A	c.(274-276)gtG>gtA	p.V92V	TNC_ENST00000341037.4_Silent_p.V92V|TNC_ENST00000535648.1_Silent_p.V92V|TNC_ENST00000542877.1_Silent_p.V92V|TNC_ENST00000340094.3_Silent_p.V92V|TNC_ENST00000537320.1_Silent_p.V92V|TNC_ENST00000423613.2_Silent_p.V92V|TNC_ENST00000346706.3_Silent_p.V92V|TNC_ENST00000345230.3_Silent_p.V92V	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	92					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)	p.V92V(1)		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						TTTCCCCATCCACTGTGTGCT	0.592													C|||	2238	0.446885	0.6014	0.5216	5008	,	,		19059	0.2837		0.4463	False		,,,				2504	0.3538				p.V92V		Atlas-SNP	.											TNC,NS,carcinoma,0,1	TNC	282	1	1	Substitution - coding silent(1)	stomach(1)	c.G276A						PASS	.	C		2480,1926	625.1+/-394.5	700,1080,423	215.0	210.0	211.0		276	-1.1	0.6	9	dbSNP_86	211	3789,4811	537.4+/-383.2	843,2103,1354	no	coding-synonymous	TNC	NM_002160.3		1543,3183,1777	TT,TC,CC		44.0581,43.7131,48.2008		92/2202	117853022	6269,6737	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon2			CCCATCCACTGTG		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.276G>A	9.37:g.117853022C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	126	125	0.992063	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																			C|0.530;T|0.470	0.470	strong		0.592	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
CUBN	8029	hgsc.bcm.edu	37	10	16979714	16979714	+	Missense_Mutation	SNP	T	T	C	rs41289305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:16979714T>C	ENST00000377833.4	-	39	5868	c.5803A>G	c.(5803-5805)Agc>Ggc	p.S1935G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1935	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.		S -> G (in dbSNP:rs41289305).		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)	CCAGTGGAGCTGAAAGATTCA	0.443													T|||	440	0.0878594	0.0189	0.1326	5008	,	,		14269	0.0387		0.165	False		,,,				2504	0.1207				p.S1935G		Atlas-SNP	.											.	CUBN	515	.	0			c.A5803G						PASS	.	T	GLY/SER	216,4190	127.4+/-164.3	7,202,1994	69.0	74.0	72.0		5803	0.0	0.1	10	dbSNP_127	72	1671,6929	306.6+/-308.0	174,1323,2803	yes	missense	CUBN	NM_001081.3	56	181,1525,4797	CC,CT,TT		19.4302,4.9024,14.5087	benign	1935/3624	16979714	1887,11119	2203	4300	6503	SO:0001583	missense	8029	exon39			TGGAGCTGAAAGA	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.5803A>G	10.37:g.16979714T>C	ENSP00000367064:p.Ser1935Gly	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	202	0.0924908424908425	14	0.028455284552845527	46	0.1270718232044199	21	0.03671328671328671	121	0.15963060686015831	T	8.719	0.913980	0.17907	0.049024	0.194302	ENSG00000107611	ENST00000377833	T	0.34667	1.35	5.14	0.0435	0.14221	CUB (5);	0.158448	0.29932	N	0.010840	T	0.00039	0.0001	M	0.70903	2.155	0.80722	P	0.0	P	0.35527	0.507	B	0.37550	0.253	T	0.07809	-1.0753	9	0.23302	T	0.38	.	5.0229	0.14370	0.0:0.3313:0.1561:0.5126	rs41289305;rs61841446	1935	O60494	CUBN_HUMAN	G	1935	ENSP00000367064:S1935G	ENSP00000367064:S1935G	S	-	1	0	CUBN	17019720	0.192000	0.23301	0.136000	0.22124	0.696000	0.40369	0.548000	0.23314	0.036000	0.15547	0.482000	0.46254	AGC	T|0.874;C|0.126	0.126	strong		0.443	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
BDP1	55814	hgsc.bcm.edu	37	5	70800475	70800475	+	Missense_Mutation	SNP	C	C	T	rs3761966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70800475C>T	ENST00000358731.4	+	16	2532	c.2269C>T	c.(2269-2271)Cgt>Tgt	p.R757C	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	757			R -> C (in dbSNP:rs3761966). {ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:15489334}.		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		AGATCAATCGCGTAAAGATTT	0.343													C|||	1621	0.323682	0.1067	0.4928	5008	,	,		16692	0.505		0.335	False		,,,				2504	0.2986				p.R757C		Atlas-SNP	.											.	BDP1	204	.	0			c.C2269T						PASS	.	C	CYS/ARG	547,3127		37,473,1327	89.0	81.0	84.0		2269	-0.2	0.0	5	dbSNP_107	84	2808,5364		507,1794,1785	yes	missense	BDP1	NM_018429.2	180	544,2267,3112	TT,TC,CC		34.3612,14.8884,28.3218	benign	757/2625	70800475	3355,8491	1837	4086	5923	SO:0001583	missense	55814	exon16			CAATCGCGTAAAG	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.2269C>T	5.37:g.70800475C>T	ENSP00000351575:p.Arg757Cys	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	253	144	0.56917	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	750	0.3434065934065934	49	0.09959349593495935	159	0.43922651933701656	291	0.5087412587412588	251	0.3311345646437995	C	0.484	-0.878384	0.02550	0.148884	0.343612	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000451951;ENST00000444711	T	0.09445	2.98	4.92	-0.211	0.13172	.	0.828507	0.10896	N	0.622116	T	0.00012	0.0000	N	0.01003	-1.06	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	0.37709	-0.9694	9	0.35671	T	0.21	.	3.227	0.06735	0.1743:0.2987:0.0:0.527	rs3761966;rs58491588;rs3761966	757;757;757	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	C	757;757;337;757	ENSP00000351575:R757C	ENSP00000351575:R757C	R	+	1	0	BDP1	70836231	0.000000	0.05858	0.004000	0.12327	0.005000	0.04900	-0.258000	0.08733	-0.150000	0.11195	-0.247000	0.11927	CGT	C|0.667;T|0.333	0.333	strong		0.343	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
ZNF880	400713	hgsc.bcm.edu	37	19	52888048	52888048	+	Silent	SNP	G	G	A	rs324124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	41	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	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	
OR51F1	256892	hgsc.bcm.edu	37	11	4790868	4790868	+	Missense_Mutation	SNP	T	T	C	rs75972277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4790868T>C	ENST00000380383.1	-	1	300	c.301A>G	c.(301-303)Atc>Gtc	p.I101V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.I94V			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	101						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)		TATAGACTGATTTCACGTGCC	0.428													T|||	230	0.0459265	0.1649	0.0159	5008	,	,		22485	0.0		0.001	False		,,,				2504	0.0				p.I94V		Atlas-SNP	.											.	OR51F1	60	.	0			c.A280G						PASS	.	T	VAL/ILE	655,3747	277.2+/-273.6	49,557,1595	78.0	75.0	76.0		280	1.3	0.2	11	dbSNP_132	76	12,8584	7.7+/-29.5	0,12,4286	yes	missense	OR51F1	NM_001004752.1	29	49,569,5881	CC,CT,TT		0.1396,14.8796,5.1316	probably-damaging	94/313	4790868	667,12331	2201	4298	6499	SO:0001583	missense	256892	exon1			GACTGATTTCACG	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.301A>G	11.37:g.4790868T>C	ENSP00000369744:p.Ile101Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	83	33	0.39759	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		96	0.04395604395604396	91	0.18495934959349594	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	t	14.41	2.525656	0.44969	0.148796	0.001396	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00590	6.36;6.36	4.91	1.3	0.21679	GPCR, rhodopsin-like superfamily (1);	0.114787	0.38381	N	0.001718	T	0.00012	0.0000	M	0.87097	2.86	0.24681	N	0.993366	D	0.67145	0.996	D	0.80764	0.994	T	0.45527	-0.9255	10	0.46703	T	0.11	.	8.2938	0.31973	0.0:0.2382:0.0:0.7618	.	101	A6NGY5	O51F1_HUMAN	V	94;101	ENSP00000345163:I94V;ENSP00000369744:I101V	ENSP00000345163:I94V	I	-	1	0	OR51F1	4747444	0.937000	0.31787	0.237000	0.24090	0.676000	0.39594	1.729000	0.38115	0.058000	0.16222	0.473000	0.43528	ATC	T|0.955;C|0.045	0.045	strong		0.428	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
P2RX6	9127	hgsc.bcm.edu	37	22	21377301	21377301	+	Silent	SNP	C	C	A	rs1548411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21377301C>A	ENST00000413302.2	+	5	682	c.534C>A	c.(532-534)ccC>ccA	p.P178P	P2RX6_ENST00000402329.3_3'UTR|P2RX6_ENST00000443995.3_Silent_p.P125P|P2RX6_ENST00000336296.2_Silent_p.P168P|P2RX6_ENST00000401443.1_Silent_p.P152P			O15547	P2RX6_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 6	178					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|channel activity (GO:0015267)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)										GTTGGTGCCCCGTGGAGAGTG	0.577													A|||	3157	0.630391	0.7587	0.67	5008	,	,		18740	0.6349		0.5358	False		,,,				2504	0.5215				p.P178P		Atlas-SNP	.											.	.	.	.	0			c.C534A						PASS	.	A	,	3215,1191	418.3+/-338.2	1193,829,181	163.0	162.0	162.0		456,534	-10.6	0.3	22	dbSNP_88	162	4505,4095	561.9+/-387.9	1201,2103,996	no	coding-synonymous,coding-synonymous	P2RX6	NM_001159554.1,NM_005446.3	,	2394,2932,1177	AA,AC,CC		47.6163,27.0313,40.6428	,	152/416,178/442	21377301	7720,5286	2203	4300	6503	SO:0001819	synonymous_variant	9127	exon5			GTGCCCCGTGGAG		CCDS13788.2, CCDS54504.1	22q11.21	2012-01-17	2008-03-28	2008-03-28	ENSG00000099957	ENSG00000099957		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8538	protein-coding gene	gene with protein product		608077	"""purinergic receptor P2X-like 1, orphan receptor"""	P2RXL1		9242461, 10591208, 8786426	Standard	NM_005446		Approved	P2XM, MGC129625, P2X6	uc010gsu.1	O15547	OTTHUMG00000150689	ENST00000413302.2:c.534C>A	22.37:g.21377301C>A		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	163	163	1	NM_005446	F6V3D7|Q32MB6|Q58F04|Q6IC33|Q9UL50	Silent	SNP	ENST00000413302.2	37	CCDS13788.2																																																																																			C|0.383;A|0.617	0.617	strong		0.577	P2RX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319625.2	NM_005446	
DDX59	83479	hgsc.bcm.edu	37	1	200635560	200635560	+	Silent	SNP	T	T	C	rs3795633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200635560T>C	ENST00000331314.6	-	2	522	c.309A>G	c.(307-309)ccA>ccG	p.P103P	DDX59_ENST00000367348.3_Silent_p.P103P|DDX59_ENST00000447706.2_Silent_p.P103P	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	103						cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						TGGGTTCCCCTGGTTCTGCCC	0.478													C|||	1094	0.21845	0.1664	0.2392	5008	,	,		20274	0.4365		0.0696	False		,,,				2504	0.2025				p.P103P		Atlas-SNP	.											.	DDX59	117	.	0			c.A309G						PASS	.	C		639,3767	766.3+/-413.4	47,545,1611	67.0	67.0	67.0		309	-10.7	0.2	1	dbSNP_107	67	535,8065	795.2+/-407.5	11,513,3776	no	coding-synonymous	DDX59	NM_001031725.4		58,1058,5387	CC,CT,TT		6.2209,14.503,9.0266		103/620	200635560	1174,11832	2203	4300	6503	SO:0001819	synonymous_variant	83479	exon2			TTCCCCTGGTTCT	BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"""Zinc fingers, HIT-type"", ""DEAD-boxes"""	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.309A>G	1.37:g.200635560T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_001031725	Q6PJL2|Q8IVW3|Q9H0W3	Silent	SNP	ENST00000331314.6	37	CCDS30964.1																																																																																			T|0.871;C|0.129	0.129	strong		0.478	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19704422	19704422	+	Missense_Mutation	SNP	T	T	A	rs8134187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:19704422T>A	ENST00000284885.3	-	14	1666	c.1633A>T	c.(1633-1635)Agc>Tgc	p.S545C		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	545	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.		S -> C (in dbSNP:rs8134187).			brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TTAGGGTAGCTGTTTGGAAAG	0.428													T|||	277	0.0553115	0.202	0.0115	5008	,	,		17236	0.0		0.002	False		,,,				2504	0.0				p.S545C		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A1633T						PASS	.	T	CYS/SER	707,3699	295.9+/-283.9	60,587,1556	148.0	149.0	149.0		1633	1.7	0.7	21	dbSNP_116	149	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMPRSS15	NM_002772.2	112	60,589,5854	AA,AT,TT		0.0233,16.0463,5.4513	probably-damaging	545/1020	19704422	709,12297	2203	4300	6503	SO:0001583	missense	5651	exon14			GGTAGCTGTTTGG		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1633A>T	21.37:g.19704422T>A	ENSP00000284885:p.Ser545Cys	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	80	0.03663003663003663	73	0.1483739837398374	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	T	17.24	3.338863	0.60963	0.160463	2.33E-4	ENSG00000154646	ENST00000284885	T	0.19669	2.13	5.43	1.7	0.24286	CUB (5);	0.918548	0.09459	N	0.799265	T	0.00210	0.0006	M	0.86502	2.82	0.47094	P	6.829999999999892E-4	D	0.63046	0.992	P	0.57101	0.813	T	0.04373	-1.0956	8	.	.	.	.	8.8856	0.35400	0.0:0.2218:0.0:0.7782	rs8134187;rs52812192;rs8134187	545	P98073	ENTK_HUMAN	C	545	ENSP00000284885:S545C	.	S	-	1	0	TMPRSS15	18626293	0.208000	0.23494	0.691000	0.30163	0.977000	0.68977	0.449000	0.21744	0.107000	0.17824	-0.263000	0.10527	AGC	T|0.954;A|0.046	0.046	strong		0.428	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
MUC4	4585	hgsc.bcm.edu	37	3	195511816	195511816	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511816G>T	ENST00000463781.3	-	2	7094	c.6635C>A	c.(6634-6636)aCc>aAc	p.T2212N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2212N	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)		GGAAGGGCTGGTGACAGGAAG	0.602																																					p.T2212N		Atlas-SNP	.											MUC4_ENST00000463781,bladder,carcinoma,+1,2	MUC4	1505	2	0			c.C6635A						scavenged	.						38.0	31.0	33.0					3																	195511816		690	1590	2280	SO:0001583	missense	4585	exon2			GGGCTGGTGACAG	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.6635C>A	3.37:g.195511816G>T	ENSP00000417498:p.Thr2212Asn	Somatic	416	0	0		WXS	Illumina HiSeq	Phase_I	289	7	0.0242215	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	8.380	0.837203	0.16891	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36699	1.24;1.35	.	.	.	.	.	.	.	.	T	0.37758	0.1015	N	0.19112	0.55	0.24507	N	0.994228	D	0.61697	0.99	D	0.69142	0.962	T	0.21552	-1.0242	6	.	.	.	.	.	.	.	.	2212	E7ESK3	.	N	2212	ENSP00000417498:T2212N;ENSP00000420243:T2212N	.	T	-	2	0	MUC4	196996211	0.002000	0.14202	0.088000	0.20740	0.028000	0.11728	0.172000	0.16704	0.488000	0.27723	0.064000	0.15345	ACC	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CD109	135228	hgsc.bcm.edu	37	6	74497009	74497009	+	Missense_Mutation	SNP	A	A	G	rs2351528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	70	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	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	
DISP2	85455	hgsc.bcm.edu	37	15	40662501	40662501	+	Silent	SNP	G	G	A	rs4514650	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40662501G>A	ENST00000267889.3	+	8	4275	c.4188G>A	c.(4186-4188)acG>acA	p.T1396T	RP11-64K12.4_ENST00000558421.1_RNA|LINC00594_ENST00000561261.1_lincRNA	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	48	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	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	
ZNF7	7553	hgsc.bcm.edu	37	8	146068322	146068322	+	Silent	SNP	C	C	T	rs9004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:146068322C>T	ENST00000528372.1	+	5	2070	c.1830C>T	c.(1828-1830)taC>taT	p.Y610Y	ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000325241.6_Silent_p.Y610Y|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000446747.2_Silent_p.Y621Y|ZNF7_ENST00000544249.1_Silent_p.Y514Y			P17097	ZNF7_HUMAN	zinc finger protein 7	610					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		AGTGGTTTTACGAATATGGGA	0.448													C|||	1544	0.308307	0.2345	0.2262	5008	,	,		18618	0.3204		0.3052	False		,,,				2504	0.4571				p.Y610Y		Atlas-SNP	.											.	ZNF7	62	.	0			c.C1830T						PASS	.	C		1094,3312	395.8+/-329.8	144,806,1253	71.0	75.0	73.0		1830	-4.3	0.3	8	dbSNP_52	73	2751,5849	434.7+/-357.8	404,1943,1953	no	coding-synonymous	ZNF7	NM_003416.2		548,2749,3206	TT,TC,CC		31.9884,24.8298,29.5633		610/687	146068322	3845,9161	2203	4300	6503	SO:0001819	synonymous_variant	7553	exon5			GTTTTACGAATAT	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"""Zinc fingers, C2H2-type"", ""-"""	13139	protein-coding gene	gene with protein product		194531	"""zinc finger protein 7 (KOX 4, clone HF.16)"""			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.1830C>T	8.37:g.146068322C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Silent	SNP	ENST00000528372.1	37	CCDS6435.1																																																																																			C|0.716;T|0.284	0.284	strong		0.448	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416	
ENGASE	64772	hgsc.bcm.edu	37	17	77079854	77079854	+	Silent	SNP	A	A	G	rs61729127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77079854A>G	ENST00000579016.1	+	10	1263	c.1263A>G	c.(1261-1263)gtA>gtG	p.V421V	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	421						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						AAGAGGCGGTAGGGCCCTGGT	0.652													G|||	405	0.0808706	0.2912	0.0231	5008	,	,		17851	0.0		0.003	False		,,,				2504	0.001				p.V421V		Atlas-SNP	.											.	ENGASE	55	.	0			c.A1263G						PASS	.	G		847,3141		93,661,1240	50.0	59.0	56.0		1263	4.9	0.9	17	dbSNP_129	56	31,8303		0,31,4136	no	coding-synonymous	ENGASE	NM_001042573.1		93,692,5376	GG,GA,AA		0.372,21.2387,7.1255		421/744	77079854	878,11444	1994	4167	6161	SO:0001819	synonymous_variant	64772	exon10			GGCGGTAGGGCCC	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1263A>G	17.37:g.77079854A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			A|0.956;G|0.044	0.044	strong		0.652	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
RHOT2	89941	hgsc.bcm.edu	37	16	720960	720960	+	Silent	SNP	C	C	T	rs3743912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:720960C>T	ENST00000315082.4	+	10	822	c.708C>T	c.(706-708)aaC>aaT	p.N236N		NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	236					cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				TGTGCAGGAACGTGGCGGGCG	0.692													C|||	1070	0.213658	0.3124	0.1614	5008	,	,		8514	0.3036		0.1054	False		,,,				2504	0.136				p.N236N		Atlas-SNP	.											.	RHOT2	35	.	0			c.C708T						PASS	.	C		1159,3225	371.0+/-319.8	154,851,1187	27.0	30.0	29.0		708	-7.7	0.4	16	dbSNP_107	29	1030,7552	205.5+/-247.9	54,922,3315	no	coding-synonymous	RHOT2	NM_138769.1		208,1773,4502	TT,TC,CC		12.0019,26.437,16.8826		236/619	720960	2189,10777	2192	4291	6483	SO:0001819	synonymous_variant	89941	exon10			CAGGAACGTGGCG	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"""EF-hand domain containing"""	21169	protein-coding gene	gene with protein product	"""mitochondrial Rho (MIRO) GTPase 2"""	613889	"""chromosome 16 open reading frame 39"", ""ras homolog gene family, member T2"""	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.708C>T	16.37:g.720960C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Silent	SNP	ENST00000315082.4	37	CCDS10417.1																																																																																			C|0.824;T|0.176	0.176	strong		0.692	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769	
HAGH	3029	hgsc.bcm.edu	37	16	1869907	1869907	+	Silent	SNP	G	G	A	rs17849371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1869907G>A	ENST00000397356.3	-	4	829	c.423C>T	c.(421-423)tcC>tcT	p.S141S	HAGH_ENST00000566709.1_Silent_p.S93S|HAGH_ENST00000455446.2_Silent_p.S141S|HAGH_ENST00000397353.2_Silent_p.S93S	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	141					glutathione biosynthetic process (GO:0006750)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			kidney(2)|lung(1)|ovary(1)|skin(1)	5		Hepatocellular(780;0.00335)			Glutathione(DB00143)	CCTGCAGTGTGGACAGGTGAG	0.627													G|||	218	0.0435304	0.1528	0.0173	5008	,	,		16762	0.0		0.004	False		,,,				2504	0.0				p.S141S	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-SNP	.											.	HAGH	20	.	0			c.C423T						PASS	.	G	,	574,3824	251.5+/-258.2	41,492,1666	104.0	82.0	90.0		279,423	-1.1	0.5	16	dbSNP_123	90	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	HAGH	NM_001040427.1,NM_005326.4	,	41,499,5959	AA,AG,GG		0.0814,13.0514,4.4699	,	93/261,141/309	1869907	581,12417	2199	4300	6499	SO:0001819	synonymous_variant	3029	exon4			CAGTGTGGACAGG	X90999	CCDS32366.1, CCDS10447.2, CCDS66900.1	16p13.3	2012-10-02	2003-11-04		ENSG00000063854	ENSG00000063854	3.1.2.6		4805	protein-coding gene	gene with protein product		138760	"""hydroxyacyl glutathione hydrolase"""			3025077, 7327557	Standard	NM_001286249		Approved	GLO2, GLXII, HAGH1	uc002cna.3	Q16775	OTTHUMG00000128662	ENST00000397356.3:c.423C>T	16.37:g.1869907G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	28	0.358974	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	37	CCDS10447.2																																																																																			G|0.958;A|0.042	0.042	strong		0.627	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326	
C14orf80	283643	hgsc.bcm.edu	37	14	105957446	105957446	+	5'Flank	SNP	G	G	A	rs76864584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105957446G>A	ENST00000392523.4	+	0	0				CRIP1_ENST00000551180.1_3'UTR|C14orf80_ENST00000329886.7_Missense_Mutation_p.G3S|C14orf80_ENST00000354560.6_5'Flank|C14orf80_ENST00000551054.1_3'UTR|C14orf80_ENST00000450383.1_5'Flank|C14orf80_ENST00000392522.3_5'Flank|C14orf80_ENST00000334656.7_Missense_Mutation_p.G3S|C14orf80_ENST00000392527.1_Missense_Mutation_p.G3S			Q86SX3	CN080_HUMAN	chromosome 14 open reading frame 80											central_nervous_system(1)	1		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.239)		ATGCATGTCCGGCCAGCGCGG	0.627													G|||	273	0.0545128	0.202	0.0086	5008	,	,		12847	0.0		0.0	False		,,,				2504	0.0				p.G3S		Atlas-SNP	.											.	C14orf80	19	.	0			c.G7A						PASS	.						115.0	102.0	106.0					14																	105957446		692	1591	2283	SO:0001631	upstream_gene_variant	283643	exon2			ATGTCCGGCCAGC		CCDS45180.1, CCDS45181.1, CCDS45182.1, CCDS55955.1	14q32.33	2012-09-25			ENSG00000185347	ENSG00000185347			20127	protein-coding gene	gene with protein product							Standard	NM_001134875		Approved		uc001yrn.3	Q86SX3	OTTHUMG00000170426		14.37:g.105957446G>A	Exception_encountered	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	168	91	0.541667	NM_001134877	B5MDG3|E9PAQ4|Q86TT3|Q86TT4|Q86TT5|Q96B41|Q9H7H4	Missense_Mutation	SNP	ENST00000392523.4	37		96	0.04395604395604396	91	0.18495934959349594	5	0.013812154696132596	0	0.0	0	0.0	G	12.89	2.073301	0.36566	.	.	ENSG00000185347	ENST00000329886;ENST00000427614;ENST00000455454;ENST00000432805;ENST00000392527;ENST00000443229;ENST00000334656	.	.	.	1.43	0.424	0.16468	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	D;D	0.62365	0.991;0.991	P;P	0.45610	0.487;0.487	T	0.17471	-1.0368	7	0.87932	D	0	.	6.8588	0.24056	0.0:0.0:0.7222:0.2778	.	3;3	B5MDG3;Q86SX3-3	.;.	S	3	.	ENSP00000333010:G3S	G	+	1	0	C14orf80	105028491	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.549000	0.02182	-0.096000	0.12329	-0.708000	0.03648	GGC	G|0.956;A|0.044	0.044	strong		0.627	C14orf80-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409090.1	NM_001134875	
P2RY11	5032	hgsc.bcm.edu	37	19	10224548	10224548	+	Missense_Mutation	SNP	G	G	A	rs3745601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10224548G>A	ENST00000321826.4	+	2	443	c.259G>A	c.(259-261)Gcc>Acc	p.A87T	PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.A507T|PPAN_ENST00000556468.1_Missense_Mutation_p.A507T|PPAN-P2RY11_ENST00000428358.1_3'UTR	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11	87			A -> T (in dbSNP:rs3745601).		activation of adenylate cyclase activity (GO:0007190)|adenosine receptor signaling pathway (GO:0001973)|calcium-mediated signaling (GO:0019722)|cellular response to ATP (GO:0071318)|defense response (GO:0006952)|G-protein coupled receptor signaling pathway (GO:0007186)|neuronal signal transduction (GO:0023041)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|neurotransmitter receptor activity (GO:0030594)|receptor activity (GO:0004872)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)	16			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			CCCGCTGGCCGCCTACCTCTA	0.677											OREG0025230	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	914	0.182508	0.1142	0.1585	5008	,	,		16337	0.3304		0.1083	False		,,,				2504	0.2157				p.A507T		Atlas-SNP	.											.	PPAN-P2RY11	81	.	0			c.G1519A						PASS	.	G	THR/ALA,THR/ALA,	479,3927	221.3+/-238.5	19,441,1743	31.0	29.0	30.0		1519,259,	3.5	1.0	19	dbSNP_107	30	978,7620	209.8+/-250.9	58,862,3379	yes	missense,missense,utr-3	P2RY11,PPAN-P2RY11	NM_001040664.2,NM_002566.4,NM_001198690.1	58,58,	77,1303,5122	AA,AG,GG		11.3747,10.8715,11.2042	probably-damaging,probably-damaging,	507/795,87/375,	10224548	1457,11547	2203	4299	6502	SO:0001583	missense	692312	exon13			CTGGCCGCCTACC	AF030335	CCDS12226.1	19p13.2	2012-08-08			ENSG00000244165	ENSG00000244165		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8540	protein-coding gene	gene with protein product		602697				9405388	Standard	NM_002566		Approved	P2Y11		Q96G91	OTTHUMG00000150166	ENST00000321826.4:c.259G>A	19.37:g.10224548G>A	ENSP00000323872:p.Ala87Thr	Somatic	63	0	0	663	WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_001040664	B2R8X9|O43190|Q9BYU4|Q9H170	Missense_Mutation	SNP	ENST00000321826.4	37	CCDS12226.1	390	0.17857142857142858	62	0.12601626016260162	53	0.1464088397790055	193	0.3374125874125874	82	0.10817941952506596	G	16.86	3.239499	0.58995	0.108715	0.113747	ENSG00000243207;ENSG00000130810;ENSG00000244165	ENST00000393796;ENST00000556468;ENST00000321826	T;T;T	0.37915	1.17;1.17;1.17	4.62	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.824795	0.10482	U	0.669521	T	0.00012	0.0000	L	0.46670	1.46	0.43179	P	0.005009999999999959	D	0.63046	0.992	P	0.55965	0.788	T	0.36286	-0.9754	9	0.22706	T	0.39	.	11.8118	0.52188	0.0:0.0:0.7753:0.2247	rs3745601;rs59821413;rs3745601	87	Q96G91	P2Y11_HUMAN	T	507;507;87	ENSP00000377385:A507T;ENSP00000450710:A507T;ENSP00000323872:A87T	ENSP00000323872:A87T	A	+	1	0	PPAN;P2RY11;PPAN-P2RY11	10085548	0.000000	0.05858	0.997000	0.53966	0.348000	0.29142	-0.044000	0.12023	2.411000	0.81874	0.561000	0.74099	GCC	G|0.855;A|0.145	0.145	strong		0.677	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
SYT15	83849	hgsc.bcm.edu	37	10	46969312	46969312	+	Missense_Mutation	SNP	G	G	A	rs55894256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:46969312G>A	ENST00000374321.4	-	2	215	c.149C>T	c.(148-150)aCa>aTa	p.T50I	SYT15_ENST00000503753.1_Missense_Mutation_p.T50I|SYT15_ENST00000374325.3_Missense_Mutation_p.T50I|SYT15_ENST00000374323.4_Intron|RP11-38L15.3_ENST00000506914.1_RNA	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						GGAGGCAGCTGTGGTGGCCAT	0.642													G|||	240	0.0479233	0.0038	0.0793	5008	,	,		34618	0.0		0.1153	False		,,,				2504	0.0654				p.T50I	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											SYT15_ENST00000416127,NS,carcinoma,0,3	SYT15	165	3	0			c.C149T						PASS	.	G	ILE/THR,ILE/THR	65,4257		0,65,2096	36.0	47.0	43.0		149,149	0.3	0.0	10	dbSNP_129	43	869,7679		0,869,3405	yes	missense,missense	SYT15	NM_031912.4,NM_181519.2	89,89	0,934,5501	AA,AG,GG		10.1661,1.5039,7.2572	benign,benign	50/422,50/391	46969312	934,11936	2161	4274	6435	SO:0001583	missense	83849	exon2			GCAGCTGTGGTGG	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.149C>T	10.37:g.46969312G>A	ENSP00000363441:p.Thr50Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	154	33	0.214286	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	107	0.04899267399267399	3	0.006097560975609756	24	0.06629834254143646	0	0.0	80	0.10554089709762533	g	9.886	1.203012	0.22121	0.015039	0.101661	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374321	T;T;T	0.13778	2.56;2.56;2.79	4.08	0.285	0.15705	.	.	.	.	.	T	0.00178	0.0005	N	0.16478	0.41	0.09310	N	1	B;B	0.10296	0.0;0.003	B;B	0.08055	0.001;0.003	T	0.40384	-0.9566	9	0.34782	T	0.22	.	7.0107	0.24861	0.1047:0.3786:0.5167:0.0	rs55894256;rs61854277	50;50	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	I	50	ENSP00000363445:T50I;ENSP00000427607:T50I;ENSP00000363441:T50I	ENSP00000363441:T50I	T	-	2	0	SYT15	46389318	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.305000	0.08188	-0.039000	0.13602	0.467000	0.42956	ACA	G|0.950;A|0.050	0.050	strong		0.642	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	
OR2T4	127074	hgsc.bcm.edu	37	1	248524974	248524974	+	Missense_Mutation	SNP	A	A	G	rs57795102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248524974A>G	ENST00000366475.1	+	1	92	c.92A>G	c.(91-93)aAt>aGt	p.N31S		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	31			N -> S (in dbSNP:rs57795102).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCAATGGCCAATATCACCTGG	0.478													a|||	348	0.0694888	0.2337	0.0331	5008	,	,		15454	0.002		0.0109	False		,,,				2504	0.0031				p.N31S		Atlas-SNP	.											OR2T4,NS,adenocarcinoma,-1,1	OR2T4	126	1	0			c.A92G						PASS	.	A	SER/ASN	939,3461		137,665,1398	112.0	96.0	102.0		92	0.2	0.1	1	dbSNP_129	102	98,8342		12,74,4134	yes	missense	OR2T4	NM_001004696.1	46	149,739,5532	GG,GA,AA		1.1611,21.3409,8.0763	benign	31/349	248524974	1037,11803	2200	4220	6420	SO:0001583	missense	127074	exon1			TGGCCAATATCAC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.92A>G	1.37:g.248524974A>G	ENSP00000355431:p.Asn31Ser	Somatic	775	1	0.00129032		WXS	Illumina HiSeq	Phase_I	800	387	0.48375	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	149	0.06822344322344322	130	0.26422764227642276	10	0.027624309392265192	0	0.0	9	0.011873350923482849	A	3.277	-0.147841	0.06627	0.213409	0.011611	ENSG00000196944	ENST00000366475	T	0.36340	1.26	0.189	0.189	0.15119	.	1.272670	0.05590	N	0.574537	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.11235	0.004	B	0.09377	0.004	T	0.34428	-0.9829	8	0.25751	T	0.34	.	.	.	.	rs57795102	31	Q8NH00	OR2T4_HUMAN	S	31	ENSP00000355431:N31S	ENSP00000355431:N31S	N	+	2	0	OR2T4	246591597	0.000000	0.05858	0.062000	0.19696	0.036000	0.12997	-0.514000	0.06298	0.250000	0.21479	0.248000	0.18094	AAT	A|0.925;G|0.075	0.075	strong		0.478	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
DLC1	10395	hgsc.bcm.edu	37	8	12952293	12952293	+	Silent	SNP	C	C	T	rs658856	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:12952293C>T	ENST00000276297.4	-	12	3910	c.3501G>A	c.(3499-3501)tcG>tcA	p.S1167S	DLC1_ENST00000512044.2_Silent_p.S764S|DLC1_ENST00000520226.1_Silent_p.S656S|DLC1_ENST00000510318.1_5'UTR|DLC1_ENST00000358919.2_Silent_p.S730S	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	1167	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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						GAAAGGTTTCCGAGAGTTTGT	0.438													C|||	565	0.112819	0.2526	0.0591	5008	,	,		21601	0.0258		0.0557	False		,,,				2504	0.1104				p.S1167S		Atlas-SNP	.											DLC1,caecum,carcinoma,-1,1	DLC1	411	1	0			c.G3501A						PASS	.	C	,,	1006,3400	375.4+/-321.6	103,800,1300	107.0	99.0	102.0		1968,2190,3501	-9.9	0.1	8	dbSNP_83	102	460,8140	137.0+/-194.0	8,444,3848	no	coding-synonymous,coding-synonymous,coding-synonymous	DLC1	NM_001164271.1,NM_006094.4,NM_182643.2	,,	111,1244,5148	TT,TC,CC		5.3488,22.8325,11.2717	,,	656/1018,730/1092,1167/1529	12952293	1466,11540	2203	4300	6503	SO:0001819	synonymous_variant	10395	exon12			GGTTTCCGAGAGT	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.3501G>A	8.37:g.12952293C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	126	50	0.396825	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																			C|0.888;T|0.112	0.112	strong		0.438	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
GGT7	2686	hgsc.bcm.edu	37	20	33451148	33451148	+	Silent	SNP	G	G	A	rs11546155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33451148G>A	ENST00000336431.5	-	2	417	c.373C>T	c.(373-375)Ctg>Ttg	p.L125L		NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	125					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						TGCATGACCAGCGCCACGGTG	0.647													g|||	693	0.138379	0.1362	0.0533	5008	,	,		13649	0.1071		0.1074	False		,,,				2504	0.2658				p.L125L		Atlas-SNP	.											GGT7,NS,carcinoma,0,2	GGT7	41	2	0			c.C373T						PASS	.			635,3771	263.8+/-265.7	43,549,1611	35.0	32.0	33.0		373	5.3	0.8	20	dbSNP_120	33	1202,7398	236.0+/-268.3	90,1022,3188	no	coding-synonymous	GGT7	NM_178026.2		133,1571,4799	AA,AG,GG		13.9767,14.4122,14.1243		125/663	33451148	1837,11169	2203	4300	6503	SO:0001819	synonymous_variant	2686	exon2			TGACCAGCGCCAC	AL049709	CCDS13242.2	20q11.22	2008-11-24	2008-03-10	2008-03-10	ENSG00000131067	ENSG00000131067		"""Gamma-glutamyltransferases"""	4259	protein-coding gene	gene with protein product		612342	"""gamma-glutamyltransferase-like 3"""	GGTL5, GGTL3		8104871, 18357469	Standard	NM_178026		Approved	D20S101, dJ18C9.2	uc002xay.3	Q9UJ14	OTTHUMG00000032314	ENST00000336431.5:c.373C>T	20.37:g.33451148G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	227	96	0.422908	NM_178026	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Silent	SNP	ENST00000336431.5	37	CCDS13242.2																																																																																			G|0.875;A|0.125	0.125	strong		0.647	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2	NM_178026	
DBH	1621	hgsc.bcm.edu	37	9	136507577	136507577	+	Silent	SNP	C	C	T	rs5322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136507577C>T	ENST00000393056.2	+	3	747	c.735C>T	c.(733-735)caC>caT	p.H245H		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	245					behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	CTCGGCACCACATTATCAAGG	0.612													C|||	102	0.0203674	0.0333	0.0101	5008	,	,		20395	0.003		0.0159	False		,,,				2504	0.0327				p.H245H		Atlas-SNP	.											.	DBH	86	.	0			c.C735T						PASS	.	C		145,4261	97.1+/-135.8	0,145,2058	49.0	45.0	46.0		735	2.3	1.0	9	dbSNP_52	46	169,8431	74.8+/-137.4	2,165,4133	no	coding-synonymous	DBH	NM_000787.3		2,310,6191	TT,TC,CC		1.9651,3.291,2.4143		245/618	136507577	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	1621	exon3			GCACCACATTATC	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.735C>T	9.37:g.136507577C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	54	38	0.703704	NM_000787	Q5T381|Q96AG2	Silent	SNP	ENST00000393056.2	37	CCDS6977.2																																																																																			C|0.978;T|0.022	0.022	strong		0.612	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
CEP162	22832	hgsc.bcm.edu	37	6	84856409	84856409	+	Silent	SNP	T	T	C	rs9449804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84856409T>C	ENST00000403245.3	-	25	3981	c.3867A>G	c.(3865-3867)aaA>aaG	p.K1289K	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_Silent_p.K1213K	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TTCTTACCTCTTTCTGTAGAA	0.308													T|||	454	0.090655	0.2973	0.036	5008	,	,		16911	0.006		0.0169	False		,,,				2504	0.0133				p.K1289K		Atlas-SNP	.											.	KIAA1009	119	.	0			c.A3867G						PASS	.	T		1113,3285		164,785,1250	32.0	32.0	32.0		3867	-4.6	0.9	6	dbSNP_119	32	131,8451		6,119,4166	no	coding-synonymous	KIAA1009	NM_014895.2		170,904,5416	CC,CT,TT		1.5265,25.307,9.584		1289/1404	84856409	1244,11736	2199	4291	6490	SO:0001819	synonymous_variant	22832	exon25			TACCTCTTTCTGT																												ENST00000403245.3:c.3867A>G	6.37:g.84856409T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_014895		Silent	SNP	ENST00000403245.3	37	CCDS34494.2																																																																																			T|0.900;C|0.100	0.100	strong		0.308	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
ABCC4	10257	hgsc.bcm.edu	37	13	95953517	95953517	+	Missense_Mutation	SNP	G	G	T	rs11568681	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:95953517G>T	ENST00000376887.4	-	1	166	c.52C>A	c.(52-54)Ctc>Atc	p.L18I	ABCC4_ENST00000538287.1_Missense_Mutation_p.L18I|ABCC4_ENST00000431522.1_Missense_Mutation_p.L18I|ABCC4_ENST00000536256.1_Missense_Mutation_p.L18I|ABCC4_ENST00000412704.1_Missense_Mutation_p.L18I	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	18			L -> I (in dbSNP:rs11568681). {ECO:0000269|PubMed:12105214, ECO:0000269|PubMed:9661885}.		blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	CGTGAGCAGAGGTTCGCGTCC	0.731													G|||	96	0.0191693	0.0113	0.0101	5008	,	,		8925	0.0238		0.0139	False		,,,				2504	0.0368				p.L18I		Atlas-SNP	.											.	ABCC4	248	.	0			c.C52A						PASS	.	G	ILE/LEU,ILE/LEU	56,4346		0,56,2145	42.0	34.0	37.0		52,52	2.8	1.0	13	dbSNP_126	37	177,8421		1,175,4123	yes	missense,missense	ABCC4	NM_001105515.1,NM_005845.3	5,5	1,231,6268	TT,TG,GG		2.0586,1.2721,1.7923	benign,benign	18/860,18/1326	95953517	233,12767	2201	4299	6500	SO:0001583	missense	10257	exon1			AGCAGAGGTTCGC	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.52C>A	13.37:g.95953517G>T	ENSP00000366084:p.Leu18Ile	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	36	0.4	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	37	CCDS9474.1	37	0.01694139194139194	10	0.02032520325203252	4	0.011049723756906077	14	0.024475524475524476	9	0.011873350923482849	G	9.770	1.172476	0.21704	0.012721	0.020586	ENSG00000125257	ENST00000412704;ENST00000376887;ENST00000536256;ENST00000431522;ENST00000538287	T;T;T;T;T	0.76578	-0.44;-0.44;-0.44;-0.44;-1.03	3.7	2.84	0.33178	.	0.221391	0.39544	N	0.001328	T	0.48857	0.1523	L	0.35854	1.095	0.38911	D	0.957549	B;B;B;B	0.30937	0.243;0.016;0.001;0.301	B;B;B;B	0.32677	0.04;0.02;0.003;0.15	T	0.51911	-0.8645	10	0.16420	T	0.52	.	9.1873	0.37178	0.0:0.2234:0.7766:0.0	rs11568681;rs45493095;rs11568681	18;18;18;18	B7Z3Q7;O15439-2;Q8IVZ4;O15439	.;.;.;MRP4_HUMAN	I	18	ENSP00000388657:L18I;ENSP00000366084:L18I;ENSP00000442024:L18I;ENSP00000398562:L18I;ENSP00000440160:L18I	ENSP00000366084:L18I	L	-	1	0	ABCC4	94751518	1.000000	0.71417	1.000000	0.80357	0.384000	0.30261	0.299000	0.19138	0.868000	0.35678	0.305000	0.20034	CTC	G|0.982;T|0.018	0.018	strong		0.731	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
NEB	4703	hgsc.bcm.edu	37	2	152547268	152547268	+	Silent	SNP	G	G	A	rs373946448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152547268G>A	ENST00000172853.10	-	24	2430	c.2283C>T	c.(2281-2283)gcC>gcT	p.A761A	NEB_ENST00000603639.1_Silent_p.A761A|NEB_ENST00000409198.1_Silent_p.A761A|NEB_ENST00000604864.1_Silent_p.A761A|NEB_ENST00000397345.3_Silent_p.A761A|NEB_ENST00000427231.2_Silent_p.A761A			P20929	NEBU_HUMAN	nebulin	761					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)		TGTTGAGCTGGGCTTGCAACA	0.398													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18181	0.0		0.0	False		,,,				2504	0.0				p.A761A		Atlas-SNP	.											.	NEB	1697	.	0			c.C2283T						PASS	.	G	,,	11,3913		0,11,1951	112.0	112.0	112.0		2283,2283,2283	0.6	1.0	2		112	0,8302		0,0,4151	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	0,11,6102	AA,AG,GG		0.0,0.2803,0.09	,,	761/8526,761/8526,761/6670	152547268	11,12215	1962	4151	6113	SO:0001819	synonymous_variant	4703	exon24			GAGCTGGGCTTGC	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.2283C>T	2.37:g.152547268G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	170	91	0.535294	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.	.	weak		0.398	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
RBMXL3	139804	hgsc.bcm.edu	37	X	114424508	114424508	+	Silent	SNP	G	G	T	rs12848233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:114424508G>T	ENST00000424776.3	+	1	546	c.504G>T	c.(502-504)tcG>tcT	p.S168S	LRCH2_ENST00000317135.8_Intron|LRCH2_ENST00000538422.1_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	168							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						CCACGCCGTCGAGCCTGGCTC	0.706													g|||	328	0.0868874	0.1233	0.0274	3775	,	,		11575	0.0407		0.0457	False		,,,				2504	0.0603				p.S168S		Atlas-SNP	.											.	RBMXL3	83	.	0			c.G504T						PASS	.						6.0	9.0	8.0					X																	114424508		652	1508	2160	SO:0001819	synonymous_variant	139804	exon1			GCCGTCGAGCCTG	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.504G>T	X.37:g.114424508G>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	17	11	0.647059	NM_001145346	B4DXC0	Silent	SNP	ENST00000424776.3	37	CCDS55478.1																																																																																			G|0.915;T|0.085	0.085	strong		0.706	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
VWF	7450	hgsc.bcm.edu	37	12	6094249	6094249	+	Missense_Mutation	SNP	C	C	T	rs62641242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6094249C>T	ENST00000261405.5	-	40	7192	c.6938G>A	c.(6937-6939)cGc>cAc	p.R2313H		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2313	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	TGCATTCTGGCGGAGGCGGGC	0.597													C|||	5	0.000998403	0.0015	0.0014	5008	,	,		17767	0.0		0.002	False		,,,				2504	0.0				p.R2313H		Atlas-SNP	.											.	VWF	338	.	0			c.G6938A	GRCh37	CM070320	VWF	M	rs62641242	PASS	.	C	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	92.0	88.0	89.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6938	-2.6	0.1	12	dbSNP_129	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	VWF	NM_000552.3	29	0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308	possibly-damaging	2313/2814	6094249	4,13002	2203	4300	6503	SO:0001583	missense	7450	exon40			TTCTGGCGGAGGC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.6938G>A	12.37:g.6094249C>T	ENSP00000261405:p.Arg2313His	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	154	82	0.532468	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	6.785	0.513843	0.12944	6.81E-4	1.16E-4	ENSG00000110799	ENST00000261405	T	0.36699	1.24	5.33	-2.61	0.06171	von Willebrand factor, type C (3);	1.093970	0.07212	N	0.859422	T	0.22003	0.0530	N	0.14661	0.345	0.26288	N	0.978165	B	0.17268	0.021	B	0.12837	0.008	T	0.27739	-1.0065	10	0.38643	T	0.18	.	11.7285	0.51722	0.0:0.3397:0.0:0.6603	rs62641242	2313	P04275	VWF_HUMAN	H	2313	ENSP00000261405:R2313H	ENSP00000261405:R2313H	R	-	2	0	VWF	5964510	0.001000	0.12720	0.067000	0.19924	0.135000	0.20990	-0.426000	0.07008	-0.496000	0.06650	0.561000	0.74099	CGC	C|0.999;T|0.001	0.001	strong		0.597	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244166	11244166	+	Silent	SNP	G	G	C	rs35720106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11244166G>C	ENST00000531678.1	-	1	746	c.663C>G	c.(661-663)acC>acG	p.T221T	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	221					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.T221T(1)		endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TGTGGACCTTGGTGCTGGGAT	0.398													.|||	3199	0.638778	0.1218	0.7205	5008	,	,		13366	0.9405		0.7793	False		,,,				2504	0.8241				p.T221T		Atlas-SNP	.											TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	1	Substitution - coding silent(1)	prostate(1)	c.C663G						PASS	.						130.0	112.0	118.0					12																	11244166		2176	4249	6425	SO:0001819	synonymous_variant	259289	exon1			GACCTTGGTGCTG	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.663C>G	12.37:g.11244166G>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	173	140	0.809249	NM_176884	P59546|Q645X4	Silent	SNP	ENST00000531678.1	37	CCDS53749.1																																																																																			G|0.614;C|0.386	0.386	strong		0.398	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
IL21R	50615	hgsc.bcm.edu	37	16	27460437	27460437	+	Missense_Mutation	SNP	G	G	A	rs3093386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27460437G>A	ENST00000337929.3	+	9	1923	c.1450G>A	c.(1450-1452)Ggc>Agc	p.G484S	IL21R_ENST00000395755.1_Missense_Mutation_p.G484S|IL21R_ENST00000395754.4_Missense_Mutation_p.G484S|IL21R_ENST00000564089.1_Missense_Mutation_p.G484S|IL21R-AS1_ENST00000563191.1_RNA	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	484			G -> S (in dbSNP:rs3093386). {ECO:0000269|Ref.4}.		interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						ACCCCTGGCCGGCCTGGATAT	0.677			T	BCL6	NHL								G|||	180	0.0359425	0.1324	0.0058	5008	,	,		18816	0.0		0.001	False		,,,				2504	0.0				p.G506S		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.G1516A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	415,3979		26,363,1808	42.0	39.0	40.0		1450,1450,1516	2.6	0.9	16	dbSNP_103	40	3,8597		0,3,4297	yes	missense,missense,missense	IL21R	NM_021798.3,NM_181078.2,NM_181079.4	56,56,56	26,366,6105	AA,AG,GG		0.0349,9.4447,3.2169	benign,benign,benign	484/539,484/539,506/561	27460437	418,12576	2197	4300	6497	SO:0001583	missense	50615	exon10			CTGGCCGGCCTGG	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"""Interleukins and interleukin receptors"", ""CD molecules"""	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1450G>A	16.37:g.27460437G>A	ENSP00000338010:p.Gly484Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	37	CCDS10630.1	64	0.029304029304029304	59	0.11991869918699187	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	14.35	2.509511	0.44660	0.094447	3.49E-4	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.15952	2.38;2.38;2.38	4.9	2.64	0.31445	.	0.231408	0.37437	N	0.002082	T	0.00144	0.0004	L	0.50919	1.6	0.29586	N	0.848826	P	0.42357	0.777	B	0.30179	0.112	T	0.16512	-1.0400	10	0.15952	T	0.53	-30.5288	4.0671	0.09866	0.124:0.0:0.6404:0.2356	rs3093386;rs61328560;rs3093386	484	Q9HBE5	IL21R_HUMAN	S	484	ENSP00000338010:G484S;ENSP00000379104:G484S;ENSP00000379103:G484S	ENSP00000338010:G484S	G	+	1	0	IL21R	27367938	0.055000	0.20627	0.916000	0.36221	0.741000	0.42261	0.087000	0.14958	2.271000	0.75665	0.561000	0.74099	GGC	G|0.962;A|0.038	0.038	strong		0.677	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078	
ALDH3A2	224	hgsc.bcm.edu	37	17	19559770	19559770	+	Missense_Mutation	SNP	C	C	T	rs115977487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19559770C>T	ENST00000176643.6	+	4	1009	c.563C>T	c.(562-564)gCg>gTg	p.A188V	ALDH3A2_ENST00000395575.2_Missense_Mutation_p.A188V|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.A188V|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.A188V|ALDH3A2_ENST00000579855.1_Missense_Mutation_p.A188V			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	188					cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1)	13	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)					GGAAACACTGCGGTTGGCAAA	0.438													C|||	67	0.0133786	0.0499	0.0014	5008	,	,		21110	0.0		0.0	False		,,,				2504	0.0				p.A188V		Atlas-SNP	.											.	ALDH3A2	41	.	0			c.C563T						PASS	.	C	VAL/ALA,VAL/ALA	141,4265	101.2+/-139.8	3,135,2065	115.0	108.0	111.0		563,563	1.2	0.0	17	dbSNP_132	111	0,8600		0,0,4300	yes	missense,missense	ALDH3A2	NM_000382.2,NM_001031806.1	64,64	3,135,6365	TT,TC,CC		0.0,3.2002,1.0841	benign,benign	188/486,188/509	19559770	141,12865	2203	4300	6503	SO:0001583	missense	224	exon4			ACACTGCGGTTGG	L47162	CCDS11210.1, CCDS32589.1	17p11.2	2010-05-07			ENSG00000072210	ENSG00000072210	1.2.1.3	"""Aldehyde dehydrogenases"""	403	protein-coding gene	gene with protein product	"""fatty aldehyde dehydrogenase"""	609523		SLS, ALDH10		7894487	Standard	NM_000382		Approved	FALDH	uc002gwa.1	P51648	OTTHUMG00000059471	ENST00000176643.6:c.563C>T	17.37:g.19559770C>T	ENSP00000176643:p.Ala188Val	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	265	135	0.509434	NM_001031806	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	37	CCDS11210.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	C	5.442	0.266672	0.10294	0.032002	0.0	ENSG00000072210	ENST00000176643;ENST00000395575;ENST00000339618	D;D;D	0.85484	-1.99;-1.99;-1.99	5.71	1.24	0.21308	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.860604	0.10663	N	0.648524	T	0.40791	0.1131	M	0.68317	2.08	0.09310	N	1	P;P	0.44044	0.825;0.79	B;B	0.34873	0.191;0.12	T	0.53878	-0.8376	10	0.31617	T	0.26	-0.0192	4.0327	0.09716	0.1051:0.5293:0.2073:0.1584	.	188;188	P51648;P51648-2	AL3A2_HUMAN;.	V	188	ENSP00000176643:A188V;ENSP00000378942:A188V;ENSP00000345774:A188V	ENSP00000176643:A188V	A	+	2	0	ALDH3A2	19500362	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	0.212000	0.17497	0.336000	0.23639	0.467000	0.42956	GCG	C|0.990;T|0.010	0.010	strong		0.438	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1		
VWA3A	146177	hgsc.bcm.edu	37	16	22155629	22155629	+	Missense_Mutation	SNP	A	A	G	rs9937453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	279	0	0		WXS	Illumina HiSeq	Phase_I	299	149	0.498328	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		
DDX51	317781	hgsc.bcm.edu	37	12	132628285	132628285	+	Silent	SNP	G	G	A	rs191101265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132628285G>A	ENST00000397333.3	-	2	512	c.474C>T	c.(472-474)gtC>gtT	p.V158V	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	158					rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		CCAGGCCGGGGACCAGGGGTC	0.761													g|||	215	0.0429313	0.0492	0.0043	5008	,	,		10654	0.0476		0.0219	False		,,,				2504	0.0787				p.V158V		Atlas-SNP	.											.	DDX51	33	.	0			c.C474T						PASS	.			71,2853		0,71,1391	3.0	4.0	3.0		474	-1.3	0.0	12		3	17,6853		0,17,3418	no	coding-synonymous	DDX51	NM_175066.3		0,88,4809	AA,AG,GG		0.2475,2.4282,0.8985		158/667	132628285	88,9706	1462	3435	4897	SO:0001819	synonymous_variant	317781	exon2			GCCGGGGACCAGG	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"""DEAD-boxes"""	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.474C>T	12.37:g.132628285G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	16	6	0.375	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Silent	SNP	ENST00000397333.3	37	CCDS41865.1																																																																																			G|0.968;A|0.032	0.032	strong		0.761	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
ZNF470	388566	hgsc.bcm.edu	37	19	57085769	57085769	+	Missense_Mutation	SNP	G	G	C	rs10421285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57085769G>C	ENST00000330619.8	+	4	753	c.67G>C	c.(67-69)Gtg>Ctg	p.V23L	ZNF470_ENST00000391709.3_Missense_Mutation_p.V23L|ZNF470_ENST00000601902.1_Missense_Mutation_p.V23L	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	23	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> L (in dbSNP:rs10421285). {ECO:0000269|PubMed:15302581}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V23L(1)		endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		TTAGGGTTCAGTGACTTTCAC	0.403													G|||	2123	0.423922	0.6657	0.3357	5008	,	,		20025	0.2788		0.3698	False		,,,				2504	0.365				p.V23L		Atlas-SNP	.											ZNF470,NS,carcinoma,0,1	ZNF470	103	1	1	Substitution - Missense(1)	stomach(1)	c.G67C						PASS	.	G	LEU/VAL	2705,1701	652.9+/-399.5	827,1051,325	182.0	166.0	171.0		67	-3.1	0.0	19	dbSNP_119	171	3139,5461	478.2+/-369.8	605,1929,1766	yes	missense	ZNF470	NM_001001668.3	32	1432,2980,2091	CC,CG,GG		36.5,38.6064,44.9331	benign	23/718	57085769	5844,7162	2203	4300	6503	SO:0001583	missense	388566	exon4			GGTTCAGTGACTT	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"""Zinc fingers, C2H2-type"", ""-"""	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.67G>C	19.37:g.57085769G>C	ENSP00000333223:p.Val23Leu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	37	CCDS33122.1	867	0.39697802197802196	317	0.6443089430894309	127	0.35082872928176795	147	0.256993006993007	276	0.3641160949868074	G	7.600	0.672565	0.14776	0.613936	0.365	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.04862	3.54;3.54	3.58	-3.06	0.05379	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	L	0.53671	1.685	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.31364	-0.9946	8	0.21540	T	0.41	.	4.4059	0.11409	0.4026:0.3162:0.2812:0.0	rs10421285;rs56621387;rs10421285	23	Q6ECI4	ZN470_HUMAN	L	23	ENSP00000375590:V23L;ENSP00000333223:V23L	ENSP00000333223:V23L	V	+	1	0	ZNF470	61777581	0.661000	0.27430	0.034000	0.17996	0.830000	0.47004	0.740000	0.26188	-0.621000	0.05633	-0.182000	0.12963	GTG	G|0.566;C|0.434	0.434	strong		0.403	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668	
NOS2	4843	hgsc.bcm.edu	37	17	26092631	26092631	+	Silent	SNP	A	A	G	rs1060822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26092631A>G	ENST00000313735.6	-	20	2591	c.2358T>C	c.(2356-2358)ggT>ggC	p.G786G		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	786	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GCTCCAGGATACCTTGGACCA	0.652													G|||	3660	0.730831	0.8071	0.6484	5008	,	,		17955	0.6706		0.6143	False		,,,				2504	0.8681				p.G786G		Atlas-SNP	.											.	NOS2	113	.	0			c.T2358C						PASS	.	G		3409,983		1331,747,118	33.0	37.0	36.0		2358	1.5	1.0	17	dbSNP_86	36	5255,3333		1637,1981,676	no	coding-synonymous	NOS2	NM_000625.4		2968,2728,794	GG,GA,AA		38.81,22.3816,33.2512		786/1154	26092631	8664,4316	2196	4294	6490	SO:0001819	synonymous_variant	4843	exon20			CAGGATACCTTGG	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2358T>C	17.37:g.26092631A>G		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	159	159	1	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																			A|0.322;G|0.678	0.678	strong		0.652	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713608	32713608	+	Silent	SNP	G	G	A	rs199931222		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32713608G>A	ENST00000374940.3	+	3	474	c.372G>A	c.(370-372)acG>acA	p.T124T		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	124	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)"""	TTCCTGTGACGCTGGGTCAGC	0.512																																					p.T124T		Atlas-SNP	.											HLA-DQA2,colon,carcinoma,+1,1	HLA-DQA2	27	1	0			c.G372A						PASS	.						199.0	156.0	171.0					6																	32713608		1511	2709	4220	SO:0001819	synonymous_variant	3118	exon3			TGTGACGCTGGGT		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.372G>A	6.37:g.32713608G>A		Somatic	436	0	0		WXS	Illumina HiSeq	Phase_I	426	57	0.133803	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	37	CCDS4753.1																																																																																			G|0.998;A|0.002	0.002	weak		0.512	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
TTPAL	79183	hgsc.bcm.edu	37	20	43117986	43117986	+	Missense_Mutation	SNP	C	C	G	rs59069332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43117986C>G	ENST00000372904.3	+	6	976	c.833C>G	c.(832-834)gCt>gGt	p.A278G	TTPAL_ENST00000372906.2_3'UTR|TTPAL_ENST00000262605.4_Missense_Mutation_p.A278G	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	278	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		A -> G (in dbSNP:rs59069332).			intracellular (GO:0005622)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|skin(5)	18						GGGGGCACGGCTGGGGAGCTG	0.527													C|||	125	0.0249601	0.0923	0.0043	5008	,	,		20272	0.0		0.0	False		,,,				2504	0.0				p.A278G		Atlas-SNP	.											.	TTPAL	31	.	0			c.C833G						PASS	.	C	GLY/ALA,GLY/ALA	308,4098	166.2+/-197.5	16,276,1911	67.0	64.0	65.0		833,833	6.2	0.3	20	dbSNP_129	65	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TTPAL	NM_001039199.1,NM_024331.3	60,60	16,278,6209	GG,GC,CC		0.0233,6.9905,2.3835	benign,benign	278/343,278/343	43117986	310,12696	2203	4300	6503	SO:0001583	missense	79183	exon5			GCACGGCTGGGGA	BC003071	CCDS13332.2	20q13.12	2008-06-23	2008-06-23	2008-06-23	ENSG00000124120	ENSG00000124120			16114	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 121"""	C20orf121			Standard	NM_024331		Approved	dJ179M20.3	uc002xmd.2	Q9BTX7	OTTHUMG00000032536	ENST00000372904.3:c.833C>G	20.37:g.43117986C>G	ENSP00000361995:p.Ala278Gly	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	144	83	0.576389	NM_001039199	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Missense_Mutation	SNP	ENST00000372904.3	37	CCDS13332.2	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	C	13.21	2.168458	0.38315	0.069905	2.33E-4	ENSG00000124120	ENST00000262605;ENST00000372904;ENST00000456317	D;D;D	0.84516	-1.86;-1.86;-1.86	6.17	6.17	0.99709	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.045191	0.85682	D	0.000000	T	0.24236	0.0587	N	0.03016	-0.435	0.80722	D	1	D;D	0.71674	0.998;0.982	P;P	0.62089	0.898;0.505	T	0.70174	-0.4944	10	0.21540	T	0.41	-16.9013	20.8794	0.99867	0.0:1.0:0.0:0.0	rs59069332	215;278	B2RA57;Q9BTX7	.;TTPAL_HUMAN	G	278;278;244	ENSP00000262605:A278G;ENSP00000361995:A278G;ENSP00000412720:A244G	ENSP00000262605:A278G	A	+	2	0	TTPAL	42551400	1.000000	0.71417	0.336000	0.25522	0.456000	0.32438	5.874000	0.69652	2.941000	0.99782	0.655000	0.94253	GCT	C|0.976;G|0.024	0.024	strong		0.527	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331	
CSMD1	64478	hgsc.bcm.edu	37	8	3432586	3432586	+	Silent	SNP	T	T	G	rs146006696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:3432586T>G	ENST00000520002.1	-	11	1783	c.1228A>C	c.(1228-1230)Aga>Cga	p.R410R	CSMD1_ENST00000542608.1_Silent_p.R409R|CSMD1_ENST00000602557.1_Silent_p.R410R|CSMD1_ENST00000602723.1_Silent_p.R410R|CSMD1_ENST00000537824.1_Silent_p.R409R|CSMD1_ENST00000539096.1_Silent_p.R409R|CSMD1_ENST00000400186.3_Silent_p.R410R			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	410						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)		CCACATGTTCTCGCTGGAAAC	0.413													T|||	54	0.0107827	0.0393	0.0029	5008	,	,		20627	0.0		0.0	False		,,,				2504	0.0				p.R409R		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A1225C						PASS	.	T		97,3963		2,93,1935	60.0	68.0	65.0		1225	2.6	0.8	8	dbSNP_134	65	0,8358		0,0,4179	no	coding-synonymous	CSMD1	NM_033225.5		2,93,6114	GG,GT,TT		0.0,2.3892,0.7811		409/3565	3432586	97,12321	2030	4179	6209	SO:0001819	synonymous_variant	64478	exon10			ATGTTCTCGCTGG			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.1228A>C	8.37:g.3432586T>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37																																																																																				T|0.988;G|0.012	0.012	strong		0.413	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
SCN4A	6329	hgsc.bcm.edu	37	17	62029006	62029006	+	Silent	SNP	A	A	G	rs79893125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62029006A>G	ENST00000435607.1	-	14	2707	c.2631T>C	c.(2629-2631)gaT>gaC	p.D877D	SCN4A_ENST00000578147.1_Silent_p.D877D	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	877					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)	CCTTCTTCTCATCCTCGGGGG	0.657													G|||	485	0.096845	0.3026	0.0303	5008	,	,		13158	0.0169		0.0199	False		,,,				2504	0.0276				p.D877D		Atlas-SNP	.											.	SCN4A	205	.	0			c.T2631C						PASS	.	G		974,2962		135,704,1129	55.0	64.0	61.0		2631	-7.0	0.1	17	dbSNP_131	61	153,8095		6,141,3977	no	coding-synonymous	SCN4A	NM_000334.4		141,845,5106	GG,GA,AA		1.855,24.7459,9.2498		877/1837	62029006	1127,11057	1968	4124	6092	SO:0001819	synonymous_variant	6329	exon14			CTTCTCATCCTCG	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.2631T>C	17.37:g.62029006A>G		Somatic	305	1	0.00327869		WXS	Illumina HiSeq	Phase_I	332	155	0.466867	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			A|0.936;G|0.064	0.064	strong		0.657	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
FANCA	2175	hgsc.bcm.edu	37	16	89836323	89836323	+	Missense_Mutation	SNP	C	C	T	rs7195066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89836323C>T	ENST00000389301.3	-	26	2456	c.2426G>A	c.(2425-2427)gGt>gAt	p.G809D	FANCA_ENST00000567284.2_5'Flank|FANCA_ENST00000568369.1_Missense_Mutation_p.G809D	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	809			G -> D (common polymorphism; dbSNP:rs7195066). {ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:9371798, ECO:0000269|PubMed:9399890, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		AAGGCCAGCACCAGGTGCAGG	0.617			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				T|||	3339	0.666733	0.7398	0.5821	5008	,	,		17886	0.9881		0.3221	False		,,,				2504	0.6513				p.G809D		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,NS,carcinoma,0,1	FANCA	99	1	0			c.G2426A						PASS	.	T	ASP/GLY	2895,1501	476.3+/-357.6	953,989,256	92.0	68.0	76.0		2426	-0.2	0.0	16	dbSNP_116	76	2702,5898	682.3+/-403.8	438,1826,2036	yes	missense	FANCA	NM_000135.2	94	1391,2815,2292	TT,TC,CC		31.4186,34.1447,43.0671	benign	809/1456	89836323	5597,7399	2198	4300	6498	SO:0001583	missense	2175	exon26	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CCAGCACCAGGTG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.2426G>A	16.37:g.89836323C>T	ENSP00000373952:p.Gly809Asp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	1344	0.6153846153846154	348	0.7073170731707317	190	0.5248618784530387	565	0.9877622377622378	241	0.3179419525065963	T	3.507	-0.100499	0.06967	0.658553	0.314186	ENSG00000187741	ENST00000389301	D	0.84442	-1.85	3.13	-0.167	0.13347	.	0.597657	0.15671	N	0.250384	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27054	-1.0085	9	0.18710	T	0.47	-0.0117	2.3692	0.04326	0.1117:0.3478:0.3548:0.1856	rs7195066;rs17233043;rs60022722;rs7195066	809;809	B4DRI7;O15360	.;FANCA_HUMAN	D	809	ENSP00000373952:G809D	ENSP00000373952:G809D	G	-	2	0	FANCA	88363824	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.305000	0.19254	-0.200000	0.10300	-1.562000	0.00884	GGT	C|0.485;T|0.515	0.515	strong		0.617	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
ZNF358	140467	hgsc.bcm.edu	37	19	7585762	7585762	+	Missense_Mutation	SNP	G	G	C	rs116797831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7585762G>C	ENST00000597229.1	+	2	1804	c.1634G>C	c.(1633-1635)aGc>aCc	p.S545T	ZNF358_ENST00000394341.2_Missense_Mutation_p.S545T|MCOLN1_ENST00000264079.6_5'Flank|CTD-2207O23.11_ENST00000602083.1_RNA	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN	zinc finger protein 358	545					embryonic forelimb morphogenesis (GO:0035115)|neural tube development (GO:0021915)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|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)|cervix(1)|kidney(1)|lung(1)|skin(2)	8						GGCACTGTCAGCCCAGCCCTC	0.662													G|||	130	0.0259585	0.0938	0.0072	5008	,	,		16199	0.0		0.001	False		,,,				2504	0.0				p.S545T		Atlas-SNP	.											.	ZNF358	41	.	0			c.G1634C						PASS	.	G	THR/SER	369,4037	182.9+/-210.6	14,341,1848	88.0	70.0	76.0		1634	4.0	1.0	19	dbSNP_132	76	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ZNF358	NM_018083.4	58	14,344,6145	CC,CG,GG		0.0349,8.3749,2.8602	possibly-damaging	545/569	7585762	372,12634	2203	4300	6503	SO:0001583	missense	140467	exon2			CTGTCAGCCCAGC	AK001252	CCDS32890.2	19p13.2	2013-01-08			ENSG00000198816	ENSG00000198816		"""Zinc fingers, C2H2-type"""	16838	protein-coding gene	gene with protein product							Standard	NM_018083		Approved	FLJ10390, ZFEND	uc002mgn.2	Q9NW07		ENST00000597229.1:c.1634G>C	19.37:g.7585762G>C	ENSP00000472305:p.Ser545Thr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	207	117	0.565217	NM_018083	Q9BTM7	Missense_Mutation	SNP	ENST00000597229.1	37	CCDS32890.2	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	14.68	2.606694	0.46527	0.083749	3.49E-4	ENSG00000198816	ENST00000361576;ENST00000394341	T	0.07021	3.23	4.04	4.04	0.47022	.	.	.	.	.	T	0.00412	0.0013	N	0.24115	0.695	0.24806	N	0.992677	B	0.22851	0.076	B	0.18263	0.021	T	0.20672	-1.0268	9	0.72032	D	0.01	.	14.4919	0.67657	0.0:0.0:1.0:0.0	.	545	Q9NW07	ZN358_HUMAN	T	545	ENSP00000377873:S545T	ENSP00000354703:S545T	S	+	2	0	ZNF358	7491762	0.463000	0.25799	0.996000	0.52242	0.375000	0.29983	2.534000	0.45676	2.547000	0.85894	0.655000	0.94253	AGC	G|0.977;C|0.023	0.023	strong		0.662	ZNF358-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316747.1		
SLC26A6	65010	hgsc.bcm.edu	37	3	48664473	48664473	+	Missense_Mutation	SNP	C	C	T	rs59643945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48664473C>T	ENST00000395550.2	-	18	1956	c.1909G>A	c.(1909-1911)Gat>Aat	p.D637N	SLC26A6_ENST00000337000.8_Missense_Mutation_p.D529N|SLC26A6_ENST00000358747.6_Missense_Mutation_p.D616N|SLC26A6_ENST00000420764.2_Missense_Mutation_p.D636N|SLC26A6_ENST00000455886.2_Missense_Mutation_p.D601N|SLC26A6_ENST00000383733.3_Missense_Mutation_p.D618N			Q9BXS9	S26A6_HUMAN	solute carrier family 26 (anion exchanger), member 6	637	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				angiotensin-activated signaling pathway (GO:0038166)|anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular response to cAMP (GO:0071320)|cellular response to fructose stimulus (GO:0071332)|cellular response to interferon-gamma (GO:0071346)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|epithelial fluid transport (GO:0042045)|formate transport (GO:0015724)|intestinal absorption (GO:0050892)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|mannitol transport (GO:0015797)|oxalate transport (GO:0019532)|oxalic acid secretion (GO:0046724)|positive regulation of dipeptide transmembrane transport (GO:2001150)|protein kinase C signaling (GO:0070528)|regulation of intracellular pH (GO:0051453)|sperm capacitation (GO:0048240)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transepithelial chloride transport (GO:0030321)|transepithelial transport (GO:0070633)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|chloride channel complex (GO:0034707)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle membrane (GO:0012506)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|chloride transmembrane transporter activity (GO:0015108)|efflux transmembrane transporter activity (GO:0015562)|formate efflux transmembrane transporter activity (GO:0015660)|formate transmembrane transporter activity (GO:0015499)|formate uptake transmembrane transporter activity (GO:0015659)|oxalate transmembrane transporter activity (GO:0019531)|PDZ domain binding (GO:0030165)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)		SLC26A6/PRKAR2A(2)	NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		TCCATCTTATCTCCTGAGCTC	0.597													C|||	329	0.0656949	0.2231	0.0346	5008	,	,		18821	0.0		0.008	False		,,,				2504	0.002				p.D637N	NSCLC(13;369 479 28271 30152 44026)	Atlas-SNP	.											.	SLC26A6	45	.	0			c.G1909A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	695,3405		68,559,1423	92.0	98.0	96.0		1846,1909,1906,1852	-0.5	0.0	3	dbSNP_129	96	49,8343		0,49,4147	yes	missense,missense,missense,missense	SLC26A6	NM_001040454.1,NM_022911.2,NM_134263.2,NM_134426.2	23,23,23,23	68,608,5570	TT,TC,CC		0.5839,16.9512,5.9558	benign,benign,benign,benign	616/739,637/760,636/759,618/741	48664473	744,11748	2050	4196	6246	SO:0001583	missense	65010	exon18			TCTTATCTCCTGA	AF279265	CCDS43087.1, CCDS46824.1, CCDS46825.1, CCDS46826.1, CCDS63627.1, CCDS63628.1	3p21.31	2013-08-05	2013-07-18		ENSG00000225697	ENSG00000225697		"""Solute carriers"""	14472	protein-coding gene	gene with protein product	"""pendrin-like protein 1"", ""pendrin L1"", ""sulfate anion transporter"", ""anion transporter 1"""	610068	"""solute carrier family 26, member 6"""			11087667, 11247665	Standard	NM_022911		Approved	DKFZp586E1422		Q9BXS9	OTTHUMG00000186381	ENST00000395550.2:c.1909G>A	3.37:g.48664473C>T	ENSP00000378920:p.Asp637Asn	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	175	96	0.548571	NM_022911	B4DMZ1|Q548A7|Q96Q90|Q9NQU1	Missense_Mutation	SNP	ENST00000395550.2	37	CCDS43087.1	116	0.05311355311355311	101	0.20528455284552846	11	0.03038674033149171	0	0.0	4	0.005277044854881266	C	9.598	1.128019	0.20959	0.169512	0.005839	ENSG00000225697	ENST00000420764;ENST00000395550;ENST00000383733;ENST00000337000;ENST00000447978;ENST00000358747;ENST00000455886	D;D;D;D;D;D	0.92545	-2.95;-2.93;-3.05;-2.96;-2.93;-3.06	3.63	-0.494	0.12034	Sulphate transporter/antisigma-factor antagonist STAS (3);	.	.	.	.	T	0.00241	0.0007	N	0.10972	0.075	0.80722	P	0.0	B;B;B;B;B;B;B	0.21905	0.004;0.0;0.005;0.0;0.001;0.0;0.062	B;B;B;B;B;B;B	0.28638	0.013;0.001;0.009;0.002;0.006;0.003;0.092	T	0.24548	-1.0157	8	0.51188	T	0.08	.	3.7251	0.08472	0.0:0.4123:0.1909:0.3969	rs59643945	601;631;529;618;636;637;4023	B4DMZ1;Q86YZ4;G3XAC1;Q9BXS9-2;Q548A7;Q9BXS9;Q5Y190	.;.;.;.;.;S26A6_HUMAN;.	N	636;637;618;529;631;616;601	ENSP00000404684:D636N;ENSP00000378920:D637N;ENSP00000373239:D618N;ENSP00000337648:D529N;ENSP00000351597:D616N;ENSP00000401066:D601N	ENSP00000337648:D529N	D	-	1	0	SLC26A6	48639477	0.001000	0.12720	0.000000	0.03702	0.151000	0.21798	0.206000	0.17375	-0.112000	0.11979	-0.339000	0.08088	GAT	C|0.962;T|0.038	0.038	strong		0.597	SLC26A6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345040.1	NM_022911	
PRPF18	8559	hgsc.bcm.edu	37	10	13658436	13658436	+	Silent	SNP	G	G	A	rs11258476	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:13658436G>A	ENST00000378572.3	+	9	991	c.831G>A	c.(829-831)gcG>gcA	p.A277A		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	277					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						TTGGAAATGCGCCTTGGCCCA	0.413													G|||	335	0.066893	0.1687	0.013	5008	,	,		21058	0.0407		0.0	False		,,,				2504	0.0634				p.A277A		Atlas-SNP	.											.	PRPF18	32	.	0			c.G831A						PASS	.	G		616,3790	267.1+/-267.6	48,520,1635	152.0	141.0	145.0		831	-6.8	1.0	10	dbSNP_120	145	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	PRPF18	NM_003675.3		48,528,5927	AA,AG,GG		0.093,13.9809,4.7978		277/343	13658436	624,12382	2203	4300	6503	SO:0001819	synonymous_variant	8559	exon9			AAATGCGCCTTGG	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.831G>A	10.37:g.13658436G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_003675	Q5T9P9|Q9BUI9	Silent	SNP	ENST00000378572.3	37	CCDS7100.1																																																																																			G|0.943;A|0.057	0.057	strong		0.413	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1		
RP1L1	94137	hgsc.bcm.edu	37	8	10470764	10470764	+	Missense_Mutation	SNP	T	T	G	rs75814156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10470764T>G	ENST00000382483.3	-	4	1067	c.844A>C	c.(844-846)Aac>Cac	p.N282H		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	282					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)		ACCGGGGGGTTGCTAGGACCA	0.672													T|||	113	0.0225639	0.084	0.0029	5008	,	,		15048	0.0		0.0	False		,,,				2504	0.0				p.N282H		Atlas-SNP	.											RP1L1,NS,carcinoma,+2,1	RP1L1	453	1	0			c.A844C						PASS	.	T	HIS/ASN	236,3690		8,220,1735	55.0	62.0	60.0		844	0.6	0.0	8	dbSNP_131	60	2,8288		0,2,4143	yes	missense	RP1L1	NM_178857.5	68	8,222,5878	GG,GT,TT		0.0241,6.0112,1.9483	probably-damaging	282/2401	10470764	238,11978	1963	4145	6108	SO:0001583	missense	94137	exon4			GGGGGTTGCTAGG	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.844A>C	8.37:g.10470764T>G	ENSP00000371923:p.Asn282His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	40	13	0.325	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	49	0.022435897435897436	49	0.09959349593495935	0	0.0	0	0.0	0	0.0	T	13.74	2.326457	0.41197	0.060112	2.41E-4	ENSG00000183638	ENST00000382483	T	0.04360	3.64	4.67	0.552	0.17230	.	0.788418	0.10319	N	0.688987	T	0.00144	0.0004	N	0.14661	0.345	0.09310	N	1	D	0.58970	0.984	P	0.46796	0.527	T	0.49960	-0.8883	10	0.59425	D	0.04	-5.163	5.688	0.17813	0.0:0.5952:0.1546:0.2502	.	282	A6NKC6	.	H	282	ENSP00000371923:N282H	ENSP00000371923:N282H	N	-	1	0	RP1L1	10508174	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.263000	0.18478	-0.050000	0.13356	-0.643000	0.03959	AAC	T|0.984;G|0.016	0.016	strong		0.672	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
AHNAK2	113146	hgsc.bcm.edu	37	14	105412541	105412541	+	Missense_Mutation	SNP	C	C	T	rs386781092|rs12433837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105412541C>T	ENST00000333244.5	-	7	9366	c.9247G>A	c.(9247-9249)Gtc>Atc	p.V3083I	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3083						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)			GGGCCCTTGACATCTATCTGG	0.627													.|||	2597	0.51857	0.5855	0.4669	5008	,	,		14076	0.3978		0.4871	False		,,,				2504	0.6217				p.V3083I		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G9247A						PASS	.	C	ILE/VAL	1179,2461		500,179,1141	65.0	75.0	72.0		9247	-7.4	0.0	14	dbSNP_120	72	1915,6185		820,275,2955	no	missense	AHNAK2	NM_138420.2	29	1320,454,4096	TT,TC,CC		23.642,32.3901,26.3543	benign	3083/5796	105412541	3094,8646	1820	4050	5870	SO:0001583	missense	113146	exon7			CCTTGACATCTAT	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.9247G>A	14.37:g.105412541C>T	ENSP00000353114:p.Val3083Ile	Somatic	262	2	0.00763359		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	734	0.3360805860805861	213	0.4329268292682927	143	0.39502762430939226	144	0.2517482517482518	234	0.3087071240105541	N	0	-2.588210	0.00128	0.323901	0.23642	ENSG00000185567	ENST00000333244	T	0.00642	6.02	3.7	-7.4	0.01397	.	.	.	.	.	T	0.00012	0.0000	N	0.05306	-0.075	0.80722	P	0.0	B	0.29862	0.259	B	0.30495	0.116	T	0.35674	-0.9779	8	0.37606	T	0.19	-12.5853	3.4855	0.07618	0.104:0.4381:0.2093:0.2485	rs41390046;rs41498447	3083	Q8IVF2	AHNK2_HUMAN	I	3083	ENSP00000353114:V3083I	ENSP00000353114:V3083I	V	-	1	0	AHNAK2	104483586	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.871000	0.01640	-1.892000	0.01108	-2.149000	0.00334	GTC	C|0.760;T|0.240	0.240	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ENPP1	5167	hgsc.bcm.edu	37	6	132172368	132172368	+	Missense_Mutation	SNP	A	A	C	rs1044498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:132172368A>C	ENST00000360971.2	+	4	537	c.517A>C	c.(517-519)Aag>Cag	p.K173Q		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	173	SMB 2. {ECO:0000255|PROSITE- ProRule:PRU00350}.		K -> Q (associated with NIDDM; dbSNP:rs1044498). {ECO:0000269|PubMed:10453738, ECO:0000269|PubMed:10480624, ECO:0000269|PubMed:16186408, ECO:0000269|PubMed:20034067}.		3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	CTGCAAGGACAAGGGCGACTG	0.493													C|||	1714	0.342252	0.8835	0.196	5008	,	,		15825	0.0962		0.1332	False		,,,				2504	0.183				p.K173Q	Colon(104;336 1535 5856 11019 33782)	Atlas-SNP	.											.	ENPP1	108	.	0			c.A517C	GRCh37	CM993455	ENPP1	M	rs1044498	PASS	.	C	GLN/LYS	3310,1096	393.3+/-328.8	1262,786,155	133.0	127.0	129.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	517	3.4	0.0	6	dbSNP_86	129	1245,7355	761.3+/-407.6	92,1061,3147	yes	missense	ENPP1	NM_006208.2	53	1354,1847,3302	CC,CA,AA		14.4767,24.8752,35.0223	benign	173/926	132172368	4555,8451	2203	4300	6503	SO:0001583	missense	5167	exon4			AAGGACAAGGGCG	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.517A>C	6.37:g.132172368A>C	ENSP00000354238:p.Lys173Gln	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_006208	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Missense_Mutation	SNP	ENST00000360971.2	37	CCDS5150.2	640	0.29304029304029305	427	0.8678861788617886	59	0.16298342541436464	62	0.10839160839160839	92	0.12137203166226913	C	11.34	1.610895	0.28712	0.751248	0.144767	ENSG00000197594	ENST00000360971	T	0.43294	0.95	5.55	3.39	0.38822	Somatomedin B domain (4);	0.811774	0.11213	N	0.587550	T	0.21186	0.0510	L	0.46885	1.475	0.80722	P	0.0	B	0.22604	0.072	B	0.26310	0.068	T	0.06607	-1.0817	9	0.27785	T	0.31	-0.3225	14.3354	0.66586	0.8272:0.1728:0.0:0.0	rs1044498;rs1801642;rs3184275;rs17847048;rs52820331;rs1044498	173	P22413	ENPP1_HUMAN	Q	173	ENSP00000354238:K173Q	ENSP00000354238:K173Q	K	+	1	0	ENPP1	132214061	0.097000	0.21791	0.001000	0.08648	0.926000	0.56050	1.966000	0.40481	0.174000	0.19809	-0.187000	0.12897	AAG	A|0.655;C|0.345	0.345	strong		0.493	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2		
IPO4	79711	hgsc.bcm.edu	37	14	24647814	24647814	+	IGR	SNP	T	T	C	rs1885711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24647814T>C	ENST00000354464.6	-	0	3646				REC8_ENST00000559919.1_Silent_p.P332P|REC8_ENST00000311457.3_Silent_p.P332P	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4						DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CTACACAGCCTATGGTGCAGC	0.567													C|||	3669	0.732628	0.9092	0.6614	5008	,	,		15515	0.87		0.507	False		,,,				2504	0.635				p.P332P		Atlas-SNP	.											.	REC8	47	.	0			c.T996C						PASS	.	C	,	3049,681		1247,555,63	53.0	60.0	58.0		996,996	-5.9	0.2	14	dbSNP_92	58	4041,4167		995,2051,1058	no	coding-synonymous,coding-synonymous	REC8	NM_001048205.1,NM_005132.2	,	2242,2606,1121	CC,CT,TT		49.2325,18.2574,40.6098	,	332/547,332/547	24647814	7090,4848	1865	4104	5969	SO:0001628	intergenic_variant	9985	exon13			ACAGCCTATGGTG	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801		14.37:g.24647814T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_001048205	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	37	CCDS9616.1																																																																																			T|0.305;C|0.695	0.695	strong		0.567	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28331573	28331573	+	Missense_Mutation	SNP	T	T	A	rs213227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28331573T>A	ENST00000377255.3	+	6	1035	c.738T>A	c.(736-738)caT>caA	p.H246Q	ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.H98Q|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.H246Q	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	246	KRAB.		H -> Q (in dbSNP:rs213227).		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						AGGAGAACCATGGCAGCCTGG	0.463													T|||	244	0.048722	0.1278	0.0346	5008	,	,		18669	0.0119		0.0189	False		,,,				2504	0.0204				p.H246Q		Atlas-SNP	.											.	ZKSCAN3	50	.	0			c.T738A						PASS	.	T	GLN/HIS,GLN/HIS,GLN/HIS	459,3947		25,409,1769	81.0	74.0	76.0		738,294,738	0.5	0.0	6	dbSNP_79	76	135,8465		1,133,4166	yes	missense,missense,missense	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	24,24,24	26,542,5935	AA,AT,TT		1.5698,10.4176,4.5671	benign,benign,benign	246/539,98/391,246/539	28331573	594,12412	2203	4300	6503	SO:0001583	missense	80317	exon5			GAACCATGGCAGC	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.738T>A	6.37:g.28331573T>A	ENSP00000366465:p.His246Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	90	0.04120879120879121	53	0.10772357723577236	14	0.03867403314917127	11	0.019230769230769232	12	0.0158311345646438	.	12.65	2.001597	0.35320	0.104176	0.015698	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.01725	4.67;4.67;4.67	2.98	0.46	0.16684	Krueppel-associated box (3);	.	.	.	.	T	0.00468	0.0015	L	0.29908	0.895	0.80722	P	0.0	P	0.35821	0.523	B	0.33392	0.163	T	0.47983	-0.9074	8	0.25751	T	0.34	.	3.8184	0.08825	0.0:0.2424:0.4061:0.3515	rs213227;rs61181430;rs213227	246	Q9BRR0	ZKSC3_HUMAN	Q	246;98;246	ENSP00000252211:H246Q;ENSP00000341883:H98Q;ENSP00000366465:H246Q	ENSP00000252211:H246Q	H	+	3	2	ZKSCAN3	28439552	0.000000	0.05858	0.002000	0.10522	0.920000	0.55202	-0.612000	0.05616	0.086000	0.17137	0.460000	0.39030	CAT	T|0.958;A|0.042	0.042	strong		0.463	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
TAAR2	9287	hgsc.bcm.edu	37	6	132938817	132938817	+	Silent	SNP	G	G	A	rs61745666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:132938817G>A	ENST00000367931.1	-	2	527	c.528C>T	c.(526-528)ttC>ttT	p.F176F	TAAR2_ENST00000537809.1_Silent_p.F131F|TAAR2_ENST00000275191.2_Silent_p.F131F			Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2	176					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)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)	23	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		AGACCACCCCGAAGGCAAATG	0.443													G|||	971	0.19389	0.5287	0.1196	5008	,	,		19402	0.0893		0.0239	False		,,,				2504	0.0767				p.F176F		Atlas-SNP	.											TAAR2,colon,carcinoma,0,1	TAAR2	45	1	0			c.C528T						PASS	.	G	,	2102,2304	575.0+/-383.9	515,1072,616	61.0	57.0	59.0		528,393	-1.5	0.3	6	dbSNP_129	59	166,8434	76.3+/-139.0	2,162,4136	yes	coding-synonymous,coding-synonymous	TAAR2	NM_001033080.1,NM_014626.3	,	517,1234,4752	AA,AG,GG		1.9302,47.7077,17.4381	,	176/352,131/307	132938817	2268,10738	2203	4300	6503	SO:0001819	synonymous_variant	9287	exon2			CACCCCGAAGGCA	AF112460	CCDS34541.1, CCDS5157.1	6q24	2012-08-08	2005-02-23	2005-02-24	ENSG00000146378	ENSG00000146378		"""GPCR / Class A : Trace amine associated receptors"""	4514	protein-coding gene	gene with protein product		604849	"""G protein-coupled receptor 58"""	GPR58		10684976, 15718104	Standard	NM_014626		Approved		uc003qdl.1	Q9P1P5	OTTHUMG00000015585	ENST00000367931.1:c.528C>T	6.37:g.132938817G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_001033080	Q5QD02|Q6NWS1|Q6NWS2|Q6NWS3	Silent	SNP	ENST00000367931.1	37	CCDS34541.1																																																																																			A|0.164;G|0.836;T|0.000	0.164	strong		0.443	TAAR2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390735.1	NM_014626	
ADAD2	161931	hgsc.bcm.edu	37	16	84230500	84230500	+	Silent	SNP	A	A	C	rs2303243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84230500A>C	ENST00000315906.5	+	10	1724	c.1672A>C	c.(1672-1674)Agg>Cgg	p.R558R	RP11-486L19.2_ENST00000561900.1_RNA|ADAD2_ENST00000268624.3_Silent_p.R640R|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	558	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						GGAGGCTCGCAGGCAGCTGTC	0.677													C|||	1608	0.321086	0.5764	0.245	5008	,	,		14316	0.1984		0.3101	False		,,,				2504	0.1677				p.R640R		Atlas-SNP	.											ADAD2,NS,carcinoma,0,1	ADAD2	46	1	0			c.A1918C						scavenged	.	C	,	2284,2090		620,1044,523	12.0	12.0	12.0		1672,1918	4.0	1.0	16	dbSNP_100	12	2473,6103		392,1689,2207	no	coding-synonymous,coding-synonymous	ADAD2	NM_001145400.1,NM_139174.3	,	1012,2733,2730	CC,CA,AA		28.8363,47.7824,36.7336	,	558/584,640/666	84230500	4757,8193	2187	4288	6475	SO:0001819	synonymous_variant	161931	exon11			GCTCGCAGGCAGC	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.1672A>C	16.37:g.84230500A>C		Somatic	180	2	0.0111111		WXS	Illumina HiSeq	Phase_I	166	165	0.993976	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	37	CCDS45536.1																																																																																			A|0.666;C|0.334	0.334	strong		0.677	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
TRPM2	7226	hgsc.bcm.edu	37	21	45825818	45825818	+	Silent	SNP	C	C	T	rs17004645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45825818C>T	ENST00000397928.1	+	18	3133	c.2688C>T	c.(2686-2688)cgC>cgT	p.R896R	TRPM2_ENST00000300482.5_Silent_p.R896R|TRPM2_ENST00000397932.2_Silent_p.R896R|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000300481.9_Silent_p.R876R	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	896					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						ACCCCGGGCGCGTCATCCTCT	0.612													t|||	18	0.00359425	0.0136	0.0	5008	,	,		17476	0.0		0.0	False		,,,				2504	0.0				p.R896R		Atlas-SNP	.											TRPM2,NS,carcinoma,+1,1	TRPM2	196	1	0			c.C2688T						PASS	.	T		64,4342	814.1+/-416.2	3,58,2142	87.0	90.0	89.0		2688	1.1	0.8	21	dbSNP_123	89	0,8598		0,0,4299	no	coding-synonymous	TRPM2	NM_003307.3		3,58,6441	TT,TC,CC		0.0,1.4526,0.4922		896/1504	45825818	64,12940	2203	4299	6502	SO:0001819	synonymous_variant	7226	exon18			CGGGCGCGTCATC	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2688C>T	21.37:g.45825818C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																			C|0.993;T|0.007	0.007	strong		0.612	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
TDP1	55775	hgsc.bcm.edu	37	14	90451500	90451500	+	Silent	SNP	A	A	G	rs17126522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:90451500A>G	ENST00000335725.4	+	10	1327	c.1077A>G	c.(1075-1077)ccA>ccG	p.P359P	TDP1_ENST00000393454.2_Silent_p.P359P|TDP1_ENST00000555880.1_Silent_p.P359P|TDP1_ENST00000393452.3_Silent_p.P359P|TDP1_ENST00000357382.3_Silent_p.P120P	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	359					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		GTTCAACCCCAGGACGCTTTC	0.284								Repair of DNA-protein crosslinks					A|||	301	0.0601038	0.171	0.0288	5008	,	,		15009	0.0079		0.0179	False		,,,				2504	0.0297				p.P359P		Atlas-SNP	.											.	TDP1	47	.	0			c.A1077G						PASS	.	A	,	597,3809	246.5+/-255.1	44,509,1650	60.0	58.0	58.0		1077,1077	-11.2	0.7	14	dbSNP_123	58	171,8421	79.2+/-141.9	2,167,4127	no	coding-synonymous,coding-synonymous	TDP1	NM_001008744.1,NM_018319.3	,	46,676,5777	GG,GA,AA		1.9902,13.5497,5.9086	,	359/609,359/609	90451500	768,12230	2203	4296	6499	SO:0001819	synonymous_variant	55775	exon10			AACCCCAGGACGC	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.1077A>G	14.37:g.90451500A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	162	80	0.493827	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Silent	SNP	ENST00000335725.4	37	CCDS9888.1																																																																																			A|0.938;G|0.062	0.062	strong		0.284	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319	
FLG	2312	hgsc.bcm.edu	37	1	152284344	152284344	+	Silent	SNP	T	T	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284344T>G	ENST00000368799.1	-	3	3053	c.3018A>C	c.(3016-3018)ggA>ggC	p.G1006G	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1006	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)			CGTGAGGAGTTCCTGATTGTC	0.582									Ichthyosis																												p.G1006G		Atlas-SNP	.											FLG,NS,carcinoma,-2,1	FLG	900	1	0			c.A3018C						scavenged	.						295.0	297.0	296.0					1																	152284344		2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGGAGTTCCTGAT	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.3018A>C	1.37:g.152284344T>G		Somatic	546	2	0.003663		WXS	Illumina HiSeq	Phase_I	568	29	0.0510563	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			.	.	none		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
BPIFC	254240	hgsc.bcm.edu	37	22	32843312	32843312	+	Silent	SNP	G	G	A	rs28733723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32843312G>A	ENST00000397452.1	-	4	371	c.261C>T	c.(259-261)gcC>gcT	p.A87A	BPIFC_ENST00000432451.2_5'UTR|BPIFC_ENST00000534972.1_5'UTR|BPIFC_ENST00000300399.3_Silent_p.A87A			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	87						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										GAAATGAAAAGGCACTGATTT	0.463													G|||	147	0.029353	0.1074	0.0072	5008	,	,		18029	0.0		0.0	False		,,,				2504	0.0				p.A87A		Atlas-SNP	.											.	.	.	.	0			c.C261T						PASS	.	G		387,4019	189.2+/-215.4	14,359,1830	98.0	90.0	93.0		261	1.2	1.0	22	dbSNP_125	93	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	BPIFC	NM_174932.2		14,362,6127	AA,AG,GG		0.0349,8.7835,2.9986		87/508	32843312	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	254240	exon3			TGAAAAGGCACTG	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.261C>T	22.37:g.32843312G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_174932	A2RRF1	Silent	SNP	ENST00000397452.1	37	CCDS13906.1																																																																																			G|0.968;A|0.032	0.032	strong		0.463	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
OGDH	4967	hgsc.bcm.edu	37	7	44747499	44747499	+	Silent	SNP	G	G	A	rs2070606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44747499G>A	ENST00000222673.5	+	23	3015	c.2973G>A	c.(2971-2973)gcG>gcA	p.A991A	OGDH_ENST00000447398.1_Silent_p.A1002A|OGDH_ENST00000449767.1_Silent_p.A987A|OGDH_ENST00000543843.1_Silent_p.A942A|OGDH_ENST00000439616.2_Silent_p.A841A|OGDH_ENST00000444676.1_Silent_p.A1006A	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	991					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)	GGGACCCAGCGGCTGCTCCAG	0.647													G|||	1177	0.235024	0.4145	0.0706	5008	,	,		16733	0.3641		0.0219	False		,,,				2504	0.1953				p.A991A		Atlas-SNP	.											.	OGDH	145	.	0			c.G2973A						PASS	.	G	,	1540,2866	483.3+/-359.7	282,976,945	49.0	47.0	48.0		2961,2973	-10.0	0.0	7	dbSNP_96	48	142,8458	68.4+/-130.8	2,138,4160	no	coding-synonymous,coding-synonymous	OGDH	NM_001165036.1,NM_002541.3	,	284,1114,5105	AA,AG,GG		1.6512,34.9523,12.9325	,	987/1020,991/1024	44747499	1682,11324	2203	4300	6503	SO:0001819	synonymous_variant	4967	exon23			CCCAGCGGCTGCT	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.2973G>A	7.37:g.44747499G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	72	20	0.277778	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Silent	SNP	ENST00000222673.5	37	CCDS34627.1																																																																																			G|0.856;A|0.144	0.144	strong		0.647	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1		
NOXO1	124056	hgsc.bcm.edu	37	16	2030029	2030029	+	Silent	SNP	C	C	T	rs34358073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2030029C>T	ENST00000397280.4	-	5	573	c.570G>A	c.(568-570)gaG>gaA	p.E190E	NOXO1_ENST00000354249.4_Silent_p.E184E|NOXO1_ENST00000566005.1_Silent_p.E189E|AC005606.1_ENST00000598236.1_5'Flank|TBL3_ENST00000568546.1_3'UTR|NOXO1_ENST00000356120.4_Silent_p.E185E			Q8NFA2	NOXO1_HUMAN	NADPH oxidase organizer 1	190	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				extracellular matrix disassembly (GO:0022617)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of respiratory burst (GO:0060263)|superoxide metabolic process (GO:0006801)	NADPH oxidase complex (GO:0043020)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|phospholipid binding (GO:0005543)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			lung(2)	2					Ecabet(DB05265)	CGTCCAGGCTCTCCTGGGCCT	0.652													C|||	194	0.038738	0.1415	0.0086	5008	,	,		16170	0.0		0.001	False		,,,				2504	0.0				p.E190E	Pancreas(104;2811 2841 4129)|Esophageal Squamous(25;910 1225 43728)	Atlas-SNP	.											.	NOXO1	13	.	0			c.G570A						PASS	.	C	,,	442,3932		20,402,1765	15.0	20.0	18.0		552,555,570	-0.2	0.0	16	dbSNP_126	18	3,8593		0,3,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	NOXO1	NM_144603.2,NM_172167.1,NM_172168.1	,,	20,405,6060	TT,TC,CC		0.0349,10.1052,3.431	,,	184/371,185/372,190/377	2030029	445,12525	2187	4298	6485	SO:0001819	synonymous_variant	124056	exon5			CAGGCTCTCCTGG	AF532985	CCDS10454.1, CCDS10455.1, CCDS42101.1, CCDS58406.1	16p13.3	2008-02-05			ENSG00000196408	ENSG00000196408			19404	protein-coding gene	gene with protein product		611256					Standard	NM_144603		Approved	P41NOXA, P41NOXB, P41NOXC, SH3PXD5, SNX28	uc002cnx.4	Q8NFA2	OTTHUMG00000128707	ENST00000397280.4:c.570G>A	16.37:g.2030029C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_172168	Q86YM1|Q8NFA3|Q96B73	Silent	SNP	ENST00000397280.4	37	CCDS42101.1																																																																																			C|0.966;T|0.034	0.034	strong		0.652	NOXO1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250612.1		
UBD	10537	hgsc.bcm.edu	37	6	29523670	29523670	+	Missense_Mutation	SNP	C	C	A	rs7757931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29523670C>A	ENST00000377050.4	-	2	708	c.485G>T	c.(484-486)tGt>tTt	p.C162F	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	162	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		C -> F (in dbSNP:rs7757931).		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						CCCTCCAATACAATAACATGC	0.453													c|||	1000	0.199681	0.4758	0.1052	5008	,	,		20877	0.1488		0.0268	False		,,,				2504	0.1237				p.C162F		Atlas-SNP	.											.	UBD	13	.	0			c.G485T						PASS	.	T	PHE/CYS	1319,1703		277,765,469	95.0	101.0	99.0		485	2.5	0.0	6	dbSNP_116	99	153,5265		2,149,2558	yes	missense	UBD	NM_006398.3	205	279,914,3027	AA,AC,CC		2.8239,43.6466,17.4408	probably-damaging	162/166	29523670	1472,6968	1511	2709	4220	SO:0001583	missense	10537	exon2			CCAATACAATAAC	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.485G>T	6.37:g.29523670C>A	ENSP00000366249:p.Cys162Phe	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	165	84	0.509091	NM_006398	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Missense_Mutation	SNP	ENST00000377050.4	37	CCDS4662.1	393	0.17994505494505494	252	0.5121951219512195	41	0.1132596685082873	84	0.14685314685314685	16	0.021108179419525065	c	12.76	2.033591	0.35893	0.436466	0.028239	ENSG00000213886	ENST00000377050	T	0.10668	2.85	5.32	2.53	0.30540	Ubiquitin supergroup (1);	0.421202	0.17243	U	0.181443	T	0.03220	0.0094	L	0.42245	1.32	0.58432	P	1.0000000000287557E-6	B	0.21606	0.058	B	0.21360	0.034	T	0.28870	-1.0030	9	0.87932	D	0	-2.9037	5.6173	0.17438	0.0:0.6607:0.1616:0.1777	rs7757931;rs17184276	162	O15205	UBD_HUMAN	F	162	ENSP00000366249:C162F	ENSP00000366249:C162F	C	-	2	0	UBD	29631649	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.098000	0.15189	0.219000	0.20840	-0.165000	0.13383	TGT	C|0.831;A|0.169	0.169	strong		0.453	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076628.3		
ZMYND8	23613	hgsc.bcm.edu	37	20	45867852	45867852	+	Missense_Mutation	SNP	A	A	G	rs2275801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:45867852A>G	ENST00000311275.7	-	15	2508	c.2255T>C	c.(2254-2256)gTg>gCg	p.V752A	ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000262975.4_Missense_Mutation_p.V752A|ZMYND8_ENST00000352431.2_Missense_Mutation_p.V772A|ZMYND8_ENST00000355972.4_Missense_Mutation_p.V752A|ZMYND8_ENST00000372023.3_Missense_Mutation_p.V747A|ZMYND8_ENST00000540497.1_Missense_Mutation_p.V700A|ZMYND8_ENST00000458360.2_Intron|ZMYND8_ENST00000536340.1_Missense_Mutation_p.V779A|ZMYND8_ENST00000360911.3_Missense_Mutation_p.V747A|ZMYND8_ENST00000461685.1_Missense_Mutation_p.V772A|ZMYND8_ENST00000396281.4_Missense_Mutation_p.V752A|ZMYND8_ENST00000446994.2_Missense_Mutation_p.V689A|ZMYND8_ENST00000471951.2_Missense_Mutation_p.V772A	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	752			V -> A (in dbSNP:rs2275801). {ECO:0000269|Ref.3}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			ATGGCTGCCCACCGTCGTGGA	0.572													G|||	1640	0.327476	0.6399	0.1772	5008	,	,		16000	0.247		0.0557	False		,,,				2504	0.3742				p.V772A		Atlas-SNP	.											.	ZMYND8	166	.	0			c.T2315C						PASS	.	G	ALA/VAL,ALA/VAL,ALA/VAL	2358,2048	539.8+/-375.3	632,1094,477	60.0	75.0	70.0		2315,2315,2240	5.4	0.0	20	dbSNP_100	70	570,8030	771.2+/-407.7	27,516,3757	yes	missense,missense,missense	ZMYND8	NM_012408.3,NM_183047.1,NM_183048.1	64,64,64	659,1610,4234	GG,GA,AA		6.6279,46.4821,22.5127	benign,benign,benign	772/1161,772/1189,747/1136	45867852	2928,10078	2203	4300	6503	SO:0001583	missense	23613	exon15			CTGCCCACCGTCG	U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"""Zinc fingers, MYND-type"", ""Zinc fingers, PHD-type"""	9397	protein-coding gene	gene with protein product		615713	"""protein kinase C binding protein 1"""	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.2255T>C	20.37:g.45867852A>G	ENSP00000312237:p.Val752Ala	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_183047	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Missense_Mutation	SNP	ENST00000311275.7	37		555	0.2541208791208791	313	0.6361788617886179	60	0.16574585635359115	146	0.25524475524475526	36	0.047493403693931395	G	0.089	-1.169650	0.01660	0.535179	0.066279	ENSG00000101040	ENST00000360911;ENST00000311275;ENST00000262975;ENST00000471951;ENST00000352431;ENST00000396281;ENST00000536340;ENST00000355972;ENST00000446994;ENST00000461685;ENST00000372023;ENST00000540497	T;T;T;T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;1.25;1.25;1.25;1.25	5.38	5.38	0.77491	.	0.922586	0.09196	N	0.835269	T	0.00012	0.0000	N	0.00621	-1.32	0.58432	P	1.999999999946489E-6	B;B;B;B;B;B;B;B;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;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.001;0.001;0.0;0.001;0.0;0.001;0.0;0.0;0.0;0.0;0.0;0.0	T	0.44697	-0.9311	9	0.02654	T	1	-18.1125	11.426	0.50012	0.1451:0.0:0.8549:0.0	rs2275801;rs52806673;rs60735070;rs2275801	779;747;747;727;746;772;752;747;772;772;752;689;747;700;700;752	F5H0X3;Q2HXV7;Q2HXV3;Q5TH11;Q5JV90;Q9ULU4-7;Q9ULU4-9;Q9ULU4-14;Q9ULU4-12;Q9ULU4-13;Q9ULU4;B3KVL2;Q2HXV9;Q2HXV1;Q2HXV4;B7Z2A8	.;.;.;.;.;.;.;.;.;.;PKCB1_HUMAN;.;.;.;.;.	A	747;752;753;773;772;752;779;752;689;772;747;700	ENSP00000354166:V747A;ENSP00000312237:V752A;ENSP00000335537:V772A;ENSP00000379577:V752A;ENSP00000439800:V779A;ENSP00000348246:V752A;ENSP00000396725:V689A;ENSP00000418210:V772A;ENSP00000361093:V747A;ENSP00000443086:V700A	ENSP00000262975:V753A	V	-	2	0	ZMYND8	45301259	0.250000	0.23951	0.029000	0.17559	0.155000	0.21991	3.397000	0.52572	1.274000	0.44362	-0.186000	0.12905	GTG	A|0.741;C|0.002	.	strong		0.572	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047	
RPH3A	22895	hgsc.bcm.edu	37	12	113312971	113312971	+	Missense_Mutation	SNP	G	G	T	rs2189473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113312971G>T	ENST00000389385.4	+	11	1376	c.879G>T	c.(877-879)caG>caT	p.Q293H	RPH3A_ENST00000548866.1_Missense_Mutation_p.Q244H|RPH3A_ENST00000420983.2_Missense_Mutation_p.Q293H|RPH3A_ENST00000543106.2_Missense_Mutation_p.Q293H|RPH3A_ENST00000551052.1_Missense_Mutation_p.Q289H|RPH3A_ENST00000447659.2_Missense_Mutation_p.Q244H|RPH3A_ENST00000549913.2_3'UTR|RPH3A_ENST00000415485.3_Missense_Mutation_p.Q293H	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	293	Pro-rich.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		AGCCTGGGCAGCCAGGTACCT	0.627													G|||	277	0.0553115	0.143	0.0159	5008	,	,		17975	0.0595		0.001	False		,,,				2504	0.0164				p.Q293H		Atlas-SNP	.											.	RPH3A	98	.	0			c.G879T						PASS	.	G	HIS/GLN,HIS/GLN	393,3849		20,353,1748	8.0	9.0	9.0		879,867	2.1	1.0	12	dbSNP_96	9	31,8293		0,31,4131	yes	missense,missense	RPH3A	NM_001143854.1,NM_014954.3	24,24	20,384,5879	TT,TG,GG		0.3724,9.2645,3.3742	possibly-damaging,possibly-damaging	293/695,289/691	113312971	424,12142	2121	4162	6283	SO:0001583	missense	22895	exon11			TGGGCAGCCAGGT	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"""Synaptotagmins"""	17056	protein-coding gene	gene with protein product		612159	"""rabphilin 3A homolog (mouse)"""			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.879G>T	12.37:g.113312971G>T	ENSP00000374036:p.Gln293His	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	41	0.594203	NM_001143854	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	37	CCDS44979.1	104	0.047619047619047616	68	0.13821138211382114	8	0.022099447513812154	28	0.04895104895104895	0	0.0	G	11.82	1.754151	0.31046	0.092645	0.003724	ENSG00000089169	ENST00000543106;ENST00000389385;ENST00000447659;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983	T;T;T;T;T;T;T	0.61392	0.11;0.11;0.11;0.11;0.11;0.11;0.11	5.2	2.13	0.27403	.	0.464810	0.17806	N	0.161391	T	0.00440	0.0014	L	0.40543	1.245	0.41476	P	0.011866999999999961	B;B;B;P	0.36315	0.32;0.412;0.412;0.547	B;B;B;B	0.41036	0.264;0.259;0.259;0.346	T	0.08186	-1.0734	9	0.48119	T	0.1	.	5.7825	0.18314	0.2717:0.1571:0.5713:0.0	rs2189473	244;293;293;289	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	H	293;293;244;289;293;244;293	ENSP00000440384:Q293H;ENSP00000374036:Q293H;ENSP00000413254:Q244H;ENSP00000448297:Q289H;ENSP00000405357:Q293H;ENSP00000450347:Q244H;ENSP00000408889:Q293H	ENSP00000374036:Q293H	Q	+	3	2	RPH3A	111797354	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	1.152000	0.31663	0.595000	0.29777	0.460000	0.39030	CAG	G|0.954;T|0.046	0.046	strong		0.627	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954	
JRK	8629	hgsc.bcm.edu	37	8	143746107	143746107	+	RNA	SNP	C	C	T	rs61747165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746107C>T	ENST00000507178.2	-	0	1703							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)				cctctgctggcgacgtggcag	0.682													C|||	63	0.0125799	0.0469	0.0014	5008	,	,		16019	0.0		0.0	False		,,,				2504	0.0				p.S457S		Atlas-SNP	.											.	.	.	.	0			c.G1371A						PASS	.	C	,	147,3827		0,147,1840	17.0	19.0	18.0		1371,1371	-6.5	0.0	8	dbSNP_129	18	1,8225		0,1,4112	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	0,148,5952	TT,TC,CC		0.0122,3.699,1.2131	,	457/557,457/569	143746107	148,12052	1987	4113	6100			8629	exon2			TGCTGGCGACGTG	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.143746107C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	52	38	0.730769	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				C|0.992;T|0.008	0.008	strong		0.682	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
PLIN4	729359	hgsc.bcm.edu	37	19	4512642	4512642	+	Missense_Mutation	SNP	T	T	C	rs60931060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512642T>C	ENST00000301286.3	-	3	1287	c.1288A>G	c.(1288-1290)Atg>Gtg	p.M430V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	430	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						GCCAAATTCATGGCACCAGTC	0.557													t|||	554	0.110623	0.354	0.036	5008	,	,		20240	0.0		0.0139	False		,,,				2504	0.0481				p.M430V		Atlas-SNP	.											PLIN4,NS,carcinoma,+2,1	PLIN4	191	1	0			c.A1288G						scavenged	.	T	VAL/MET	1251,2777		263,725,1026	115.0	143.0	134.0		1288	-1.6	0.0	19	dbSNP_129	134	147,8219		7,133,4043	yes	missense	PLIN4	NM_001080400.1	21	270,858,5069	CC,CT,TT		1.7571,31.0576,11.2797	benign	430/1358	4512642	1398,10996	2014	4183	6197	SO:0001583	missense	729359	exon3			AATTCATGGCACC	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.1288A>G	19.37:g.4512642T>C	ENSP00000301286:p.Met430Val	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	184	51	0.277174	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	171	0.0782967032967033	157	0.31910569105691056	8	0.022099447513812154	0	0.0	6	0.0079155672823219	t	0.011	-1.723632	0.00694	0.310576	0.017571	ENSG00000167676	ENST00000301286	T	0.02763	4.17	4.56	-1.61	0.08399	.	0.632463	0.14898	N	0.291974	T	0.00012	0.0000	N	0.11154	0.105	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42378	-0.9455	9	0.10377	T	0.69	-6.7095	9.7431	0.40431	0.0:0.4332:0.0:0.5668	rs60931060	430	Q96Q06	PLIN4_HUMAN	V	430	ENSP00000301286:M430V	ENSP00000301286:M430V	M	-	1	0	PLIN4	4463642	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-5.288000	0.00134	-0.826000	0.04284	-0.782000	0.03352	ATG	T|0.935;C|0.065	0.065	strong		0.557	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
RASGRP3	25780	hgsc.bcm.edu	37	2	33774761	33774761	+	Silent	SNP	T	T	C	rs2276590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:33774761T>C	ENST00000403687.3	+	14	2225	c.1485T>C	c.(1483-1485)caT>caC	p.H495H	RASGRP3_ENST00000407811.1_Silent_p.H494H|RASGRP3_ENST00000402538.3_Silent_p.H495H	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	495					MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)	p.H495H(1)		large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					GATTTATCCATAATTTTCAGG	0.398													T|||	675	0.134784	0.1543	0.0432	5008	,	,		20953	0.3095		0.007	False		,,,				2504	0.1247				p.H495H		Atlas-SNP	.											RASGRP3,NS,carcinoma,0,1	RASGRP3	87	1	1	Substitution - coding silent(1)	stomach(1)	c.T1485C						scavenged	.	T	,,	464,3262		22,420,1421	160.0	142.0	147.0		1485,1482,1485	2.5	1.0	2	dbSNP_100	147	34,8192		0,34,4079	no	coding-synonymous,coding-synonymous,coding-synonymous	RASGRP3	NM_001139488.1,NM_015376.2,NM_170672.2	,,	22,454,5500	CC,CT,TT		0.4133,12.453,4.1667	,,	495/691,494/690,495/691	33774761	498,11454	1863	4113	5976	SO:0001819	synonymous_variant	25780	exon15			TATCCATAATTTT	AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"""EF-hand domain containing"""	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.1485T>C	2.37:g.33774761T>C		Somatic	322	2	0.00621118		WXS	Illumina HiSeq	Phase_I	313	134	0.428115	NM_170672	D6W583|O94931|Q53SD7	Silent	SNP	ENST00000403687.3	37	CCDS46256.1																																																																																			T|0.872;C|0.128	0.128	strong		0.398	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376	
ARHGAP17	55114	hgsc.bcm.edu	37	16	24942272	24942272	+	Missense_Mutation	SNP	T	T	A	rs111463480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24942272T>A	ENST00000289968.6	-	19	2417	c.2348A>T	c.(2347-2349)aAc>aTc	p.N783I	ARHGAP17_ENST00000303665.5_Missense_Mutation_p.N705I|ARHGAP17_ENST00000441763.2_3'UTR	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	783	Pro-rich.				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)		AGTTTCAGGGTTACCCCCTGC	0.632													T|||	3	0.000599042	0.0023	0.0	5008	,	,		14279	0.0		0.0	False		,,,				2504	0.0				p.N783I		Atlas-SNP	.											.	ARHGAP17	138	.	0			c.A2348T						PASS	.	T	ILE/ASN,ILE/ASN	1,4393	2.1+/-5.4	0,1,2196	71.0	80.0	77.0		2348,2114	5.1	0.6	16	dbSNP_132	77	0,8600		0,0,4300	no	missense,missense	ARHGAP17	NM_001006634.1,NM_018054.4	149,149	0,1,6496	AA,AT,TT		0.0,0.0228,0.0077	possibly-damaging,possibly-damaging	783/882,705/804	24942272	1,12993	2197	4300	6497	SO:0001583	missense	55114	exon19			TCAGGGTTACCCC	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.2348A>T	16.37:g.24942272T>A	ENSP00000289968:p.Asn783Ile	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	179	76	0.424581	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Missense_Mutation	SNP	ENST00000289968.6	37	CCDS32409.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	12.57	1.977941	0.34942	2.28E-4	0.0	ENSG00000140750	ENST00000289968;ENST00000303665;ENST00000455311	T;T	0.21361	2.01;2.06	5.13	5.13	0.70059	.	0.588411	0.14194	N	0.335149	T	0.34658	0.0905	L	0.44542	1.39	0.80722	D	1	B;B;D;P;P	0.64830	0.343;0.232;0.994;0.736;0.729	B;B;P;B;B	0.59703	0.134;0.063;0.862;0.205;0.372	T	0.02294	-1.1181	10	0.52906	T	0.07	.	12.8937	0.58087	0.0:0.0:0.0:1.0	.	705;783;316;616;344	Q68EM7-2;Q68EM7;Q68EM7-7;B4DWE9;B4DVF3	.;RHG17_HUMAN;.;.;.	I	783;705;783	ENSP00000289968:N783I;ENSP00000303130:N705I	ENSP00000289968:N783I	N	-	2	0	ARHGAP17	24849773	0.994000	0.37717	0.604000	0.28916	0.012000	0.07955	1.696000	0.37773	1.923000	0.55706	0.528000	0.53228	AAC	T|0.999;A|0.001	0.001	strong		0.632	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054	
INSR	3643	hgsc.bcm.edu	37	19	7184518	7184518	+	Silent	SNP	G	G	A	rs891087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	105	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	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		
USHBP1	83878	hgsc.bcm.edu	37	19	17366313	17366313	+	Missense_Mutation	SNP	C	C	T	rs12459398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17366313C>T	ENST00000252597.3	-	10	1746	c.1573G>A	c.(1573-1575)Gtg>Atg	p.V525M	USHBP1_ENST00000431146.2_Missense_Mutation_p.V461M|AC010646.3_ENST00000594059.1_5'Flank	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						AGCAGGAGCACGTGAGCTGGA	0.701													C|||	1348	0.269169	0.3132	0.268	5008	,	,		14664	0.2788		0.2197	False		,,,				2504	0.2515				p.V525M		Atlas-SNP	.											.	USHBP1	85	.	0			c.G1573A						PASS	.	C	MET/VAL	1348,3058	434.3+/-343.9	197,954,1052	38.0	40.0	39.0		1573	-5.5	0.0	19	dbSNP_120	39	1750,6850	304.0+/-306.7	165,1420,2715	no	missense	USHBP1	NM_031941.3	21	362,2374,3767	TT,TC,CC		20.3488,30.5946,23.8198	benign	525/704	17366313	3098,9908	2203	4300	6503	SO:0001583	missense	83878	exon10			GGAGCACGTGAGC	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1573G>A	19.37:g.17366313C>T	ENSP00000252597:p.Val525Met	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	49	0.644737	NM_031941		Missense_Mutation	SNP	ENST00000252597.3	37	CCDS12353.1	580	0.26556776556776557	178	0.3617886178861789	87	0.24033149171270718	154	0.2692307692307692	161	0.21240105540897097	C	6.299	0.423219	0.11928	0.305946	0.203488	ENSG00000130307	ENST00000252597;ENST00000431146	T;T	0.17854	2.25;2.25	4.92	-5.46	0.02608	.	2.347010	0.01907	N	0.039582	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	B;B	0.20671	0.019;0.047	B;B	0.09377	0.004;0.004	T	0.40515	-0.9559	9	0.46703	T	0.11	0.1015	8.5648	0.33534	0.0:0.1432:0.4915:0.3653	rs12459398	461;525	B4DUE8;Q8N6Y0	.;USBP1_HUMAN	M	525;461	ENSP00000252597:V525M;ENSP00000407902:V461M	ENSP00000252597:V525M	V	-	1	0	USHBP1	17227313	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.146000	0.03191	-1.191000	0.02695	-0.882000	0.02950	GTG	C|0.765;T|0.235	0.235	strong		0.701	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
KIRREL2	84063	hgsc.bcm.edu	37	19	36350474	36350474	+	Missense_Mutation	SNP	G	G	A	rs34494265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36350474G>A	ENST00000360202.5	+	5	812	c.614G>A	c.(613-615)cGg>cAg	p.R205Q	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Missense_Mutation_p.R205Q|KIRREL2_ENST00000347900.6_Missense_Mutation_p.R155Q|KIRREL2_ENST00000262625.7_Missense_Mutation_p.R205Q	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	205	Ig-like C2-type 2.				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)		p.R205L(2)		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)			TTTGTCTGCCGGGCCCGGAGC	0.627													G|||	91	0.0181709	0.0673	0.0029	5008	,	,		17806	0.0		0.0	False		,,,				2504	0.0				p.R205Q		Atlas-SNP	.											.	KIRREL2	170	.	2	Substitution - Missense(2)	lung(2)	c.G614A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	235,4171	139.2+/-174.8	4,227,1972	64.0	63.0	63.0		614,464,614	3.7	1.0	19	dbSNP_126	63	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	43,43,43	4,228,6271	AA,AG,GG		0.0116,5.3336,1.8145	possibly-damaging,possibly-damaging,possibly-damaging	205/634,155/584,205/709	36350474	236,12770	2203	4300	6503	SO:0001583	missense	84063	exon5			TCTGCCGGGCCCG	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.614G>A	19.37:g.36350474G>A	ENSP00000353331:p.Arg205Gln	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	G	13.26	2.183768	0.38609	0.053336	1.16E-4	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202	T;T;T	0.74632	-0.86;-0.86;-0.86	4.72	3.68	0.42216	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.203139	0.24398	N	0.038876	T	0.19366	0.0465	L	0.47078	1.49	0.25543	N	0.987161	B;P;P;P	0.38863	0.438;0.65;0.597;0.597	B;B;B;B	0.30716	0.119;0.119;0.072;0.072	T	0.22208	-1.0223	10	0.20519	T	0.43	-18.1018	8.1639	0.31215	0.106:0.0:0.894:0.0	rs34494265;rs34494265	205;205;155;205	F1T0I2;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;KIRR2_HUMAN;.;.	Q	205;155;205	ENSP00000262625:R205Q;ENSP00000345067:R155Q;ENSP00000353331:R205Q	ENSP00000262625:R205Q	R	+	2	0	KIRREL2	41042314	1.000000	0.71417	0.994000	0.49952	0.292000	0.27327	3.165000	0.50778	2.623000	0.88846	0.549000	0.68633	CGG	G|0.982;A|0.018	0.018	strong		0.627	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
ACSM5	54988	hgsc.bcm.edu	37	16	20430678	20430678	+	Missense_Mutation	SNP	G	G	A	rs7192210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20430678G>A	ENST00000331849.4	+	4	691	c.544G>A	c.(544-546)Gaa>Aaa	p.E182K	ACSM5_ENST00000575584.1_Missense_Mutation_p.E182K	NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	182			E -> K (in dbSNP:rs7192210).		fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						CATCAGTGCCGAATGCCCCTC	0.592													G|||	495	0.0988419	0.2564	0.0173	5008	,	,		18285	0.0496		0.0179	False		,,,				2504	0.0777				p.E182K		Atlas-SNP	.											.	ACSM5	101	.	0			c.G544A						PASS	.	G	LYS/GLU	993,3413	371.7+/-320.1	110,773,1320	73.0	62.0	65.0		544	4.7	0.9	16	dbSNP_116	65	183,8417	82.6+/-145.2	3,177,4120	no	missense	ACSM5	NM_017888.2	56	113,950,5440	AA,AG,GG		2.1279,22.5374,9.042	benign	182/580	20430678	1176,11830	2203	4300	6503	SO:0001583	missense	54988	exon4			AGTGCCGAATGCC		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.544G>A	16.37:g.20430678G>A	ENSP00000327916:p.Glu182Lys	Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	219	219	1	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	177	0.08104395604395605	121	0.2459349593495935	8	0.022099447513812154	33	0.057692307692307696	15	0.01978891820580475	G	8.211	0.800421	0.16397	0.225374	0.021279	ENSG00000183549	ENST00000331849	T	0.39592	1.07	4.65	4.65	0.58169	AMP-dependent synthetase/ligase (1);	0.374166	0.25759	N	0.028498	T	0.00012	0.0000	L	0.41124	1.26	0.30506	P	0.769902	B	0.10296	0.003	B	0.08055	0.003	T	0.11891	-1.0569	9	0.23302	T	0.38	-16.6401	13.3868	0.60801	0.0:0.2663:0.7337:0.0	rs7192210;rs52789304;rs60520050;rs7192210	182	Q6NUN0	ACSM5_HUMAN	K	182	ENSP00000327916:E182K	ENSP00000327916:E182K	E	+	1	0	ACSM5	20338179	0.126000	0.22350	0.944000	0.38274	0.067000	0.16453	0.906000	0.28517	2.561000	0.86390	0.650000	0.86243	GAA	G|0.904;A|0.096	0.096	strong		0.592	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
TTC4	7268	hgsc.bcm.edu	37	1	55188382	55188382	+	Silent	SNP	C	C	T	rs11550481	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55188382C>T	ENST00000371281.3	+	5	591	c.504C>T	c.(502-504)gcC>gcT	p.A168A	MROH7-TTC4_ENST00000414150.2_3'UTR|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	168								p.A168A(1)		breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						AACACTTTGCCGAGGCCGTGA	0.478													T|||	648	0.129393	0.1694	0.0288	5008	,	,		20579	0.128		0.0616	False		,,,				2504	0.2178				p.A168A		Atlas-SNP	.											TTC4,NS,carcinoma,0,1	TTC4	21	1	1	Substitution - coding silent(1)	stomach(1)	c.C504T						PASS	.	T		796,3610	751.5+/-412.2	81,634,1488	143.0	142.0	142.0		504	-10.3	0.5	1	dbSNP_120	142	436,8164	800.0+/-407.4	10,416,3874	no	coding-synonymous	TTC4	NM_004623.4		91,1050,5362	TT,TC,CC		5.0698,18.0663,9.4726		168/388	55188382	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	7268	exon5			CTTTGCCGAGGCC		CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"""Tetratricopeptide (TTC) repeat domain containing"""	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.504C>T	1.37:g.55188382C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Silent	SNP	ENST00000371281.3	37	CCDS596.1																																																																																			C|0.892;T|0.108	0.108	strong		0.478	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623	
RNF213	57674	hgsc.bcm.edu	37	17	78272294	78272294	+	Missense_Mutation	SNP	C	C	T	rs72849841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78272294C>T	ENST00000582970.1	+	11	2329	c.2186C>T	c.(2185-2187)cCg>cTg	p.P729L	RNF213_ENST00000319921.4_Missense_Mutation_p.P729L|RNF213_ENST00000456466.1_Missense_Mutation_p.P729L|RNF213_ENST00000508628.2_Missense_Mutation_p.P778L	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	729					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TCCTTCTCACCGTTCCGGGAA	0.572													c|||	570	0.113818	0.1997	0.0692	5008	,	,		17967	0.0149		0.1402	False		,,,				2504	0.1043				p.P729L		Atlas-SNP	.											RNF213_ENST00000456466,colon,carcinoma,-1,3	RNF213	766	3	0			c.C2186T						PASS	.	C	LEU/PRO,LEU/PRO	707,3699	295.6+/-283.7	56,595,1552	82.0	70.0	74.0		2333,2186	2.1	0.0	17	dbSNP_130	74	1182,7418	239.4+/-270.5	82,1018,3200	yes	missense,missense	RNF213	NM_020914.4,NM_020954.2	98,98	138,1613,4752	TT,TC,CC		13.7442,16.0463,14.5241	benign,benign	778/5257,729/1064	78272294	1889,11117	2203	4300	6503	SO:0001583	missense	57674	exon11			TCTCACCGTTCCG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.2186C>T	17.37:g.78272294C>T	ENSP00000464087:p.Pro729Leu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	144	54	0.375	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	245	0.11217948717948718	112	0.22764227642276422	27	0.07458563535911603	9	0.015734265734265736	97	0.1279683377308707	c	1.845	-0.466542	0.04476	0.160463	0.137442	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.14144	2.53;2.53	4.45	2.14	0.27477	.	0.990181	0.08196	N	0.982985	T	0.00012	0.0000	N	0.08118	0	0.51767	P	6.399999999995298E-5	B;B	0.23806	0.045;0.091	B;B	0.17098	0.017;0.017	T	0.42582	-0.9443	9	0.48119	T	0.1	-14.6717	10.3194	0.43756	0.4867:0.5133:0.0:0.0	.	729;729	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	L	729;778;729;729	ENSP00000392123:P729L;ENSP00000324392:P729L	ENSP00000324392:P729L	P	+	2	0	RNF213	75886889	0.001000	0.12720	0.040000	0.18447	0.004000	0.04260	0.629000	0.24538	0.300000	0.22699	-0.280000	0.10049	CCG	C|0.869;T|0.131	0.131	strong		0.572	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
TCP11L1	55346	hgsc.bcm.edu	37	11	33065394	33065394	+	Silent	SNP	C	C	T	rs1064005	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:33065394C>T	ENST00000334274.4	+	2	475	c.75C>T	c.(73-75)ctC>ctT	p.L25L	TCP11L1_ENST00000531632.2_Silent_p.L25L|TCP11L1_ENST00000530171.1_3'UTR|TCP11L1_ENST00000432887.1_Silent_p.L25L	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	25						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						AGGAAGGCCTCGAAGATGCTG	0.408													C|||	1991	0.397564	0.4576	0.4467	5008	,	,		19560	0.4226		0.3986	False		,,,				2504	0.2546				p.L25L		Atlas-SNP	.											.	TCP11L1	40	.	0			c.C75T						PASS	.	C	,	1991,2413	558.9+/-380.1	435,1121,646	199.0	205.0	203.0		75,75	-2.0	1.0	11	dbSNP_86	203	3417,5179	505.6+/-376.4	691,2035,1572	yes	coding-synonymous,coding-synonymous	TCP11L1	NM_001145541.1,NM_018393.3	,	1126,3156,2218	TT,TC,CC		39.751,45.2089,41.6	,	25/510,25/510	33065394	5408,7592	2202	4298	6500	SO:0001819	synonymous_variant	55346	exon2			AGGCCTCGAAGAT	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.75C>T	11.37:g.33065394C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_001145541	D3DR01|Q8IVX4	Silent	SNP	ENST00000334274.4	37	CCDS7882.1																																																																																			C|0.583;T|0.417	0.417	strong		0.408	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393	
GOLGA3	2802	hgsc.bcm.edu	37	12	133358984	133358984	+	Silent	SNP	A	A	G	rs76963006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133358984A>G	ENST00000450791.2	-	16	3546	c.3363T>C	c.(3361-3363)ctT>ctC	p.L1121L	GOLGA3_ENST00000456883.2_Silent_p.L1121L|GOLGA3_ENST00000204726.3_Silent_p.L1121L			Q08378	GOGA3_HUMAN	golgin A3	1121					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)		CGAGGCCCGTAAGCTTCCCTT	0.498													A|||	41	0.0081869	0.0303	0.0014	5008	,	,		19000	0.0		0.0	False		,,,				2504	0.0				p.L1121L		Atlas-SNP	.											.	GOLGA3	234	.	0			c.T3363C						PASS	.	A		117,4289	88.7+/-127.4	1,115,2087	216.0	201.0	207.0		3363	-8.6	0.0	12	dbSNP_132	207	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GOLGA3	NM_005895.3		1,116,6386	GG,GA,AA		0.0116,2.6555,0.9073		1121/1499	133358984	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	2802	exon17			GCCCGTAAGCTTC	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.3363T>C	12.37:g.133358984A>G		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	201	107	0.532338	NM_005895	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Silent	SNP	ENST00000450791.2	37	CCDS9281.1																																																																																			A|0.990;G|0.010	0.010	strong		0.498	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
ZNF618	114991	hgsc.bcm.edu	37	9	116812084	116812084	+	Silent	SNP	C	C	T	rs7856141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116812084C>T	ENST00000374126.5	+	15	2601	c.2502C>T	c.(2500-2502)aaC>aaT	p.N834N	ZNF618_ENST00000288466.7_Silent_p.N741N|ZNF618_ENST00000470105.1_3'UTR			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	834					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						AGCTCATCAACGAGGTGAAGG	0.637													C|||	339	0.0676917	0.1271	0.0605	5008	,	,		19158	0.0		0.0895	False		,,,				2504	0.0399				p.N741N		Atlas-SNP	.											.	ZNF618	184	.	0			c.C2223T						PASS	.	C		488,3642		20,448,1597	61.0	68.0	65.0		2223	-11.3	0.1	9	dbSNP_116	65	707,7651		34,639,3506	no	coding-synonymous	ZNF618	NM_133374.2		54,1087,5103	TT,TC,CC		8.459,11.816,9.5692		741/862	116812084	1195,11293	2065	4179	6244	SO:0001819	synonymous_variant	114991	exon14			CATCAACGAGGTG	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.2502C>T	9.37:g.116812084C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	73	24	0.328767	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				C|0.923;T|0.077	0.077	strong		0.637	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
TATDN1	83940	hgsc.bcm.edu	37	8	125498547	125498547	+	IGR	SNP	C	C	T	rs3812471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:125498547C>T	ENST00000276692.6	-	0	1018				RNF139_ENST00000303545.3_Silent_p.Y219Y|RP11-158K1.3_ENST00000518639.1_RNA	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1						DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ATCGAATTTACGGATTACAGT	0.398													T|||	2859	0.570887	0.7912	0.4755	5008	,	,		22796	0.4355		0.494	False		,,,				2504	0.5593				p.Y219Y		Atlas-SNP	.											.	RNF139	57	.	0			c.C657T						PASS	.	T		3097,1309	439.6+/-345.7	1095,907,201	208.0	210.0	209.0		657	0.4	1.0	8	dbSNP_107	209	3997,4603	599.4+/-394.1	908,2181,1211	no	coding-synonymous	RNF139	NM_007218.3		2003,3088,1412	TT,TC,CC		46.4767,29.7095,45.4559		219/665	125498547	7094,5912	2203	4300	6503	SO:0001628	intergenic_variant	11236	exon2			AATTTACGGATTA	AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068		8.37:g.125498547C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_007218	B2R5J0|Q8TD02|Q9BY40	Silent	SNP	ENST00000276692.6	37	CCDS6351.1																																																																																			C|0.445;T|0.555	0.555	strong		0.398	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026	
RGS3	5998	hgsc.bcm.edu	37	9	116356549	116356549	+	Intron	SNP	C	C	G	rs113405588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116356549C>G	ENST00000374140.2	+	23	3289				RGS3_ENST00000462143.1_Intron|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000350696.5_Intron|RGS3_ENST00000374134.3_Intron|RGS3_ENST00000343817.5_Intron|RGS3_ENST00000462403.1_Missense_Mutation_p.P117R|RGS3_ENST00000342620.5_Intron	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						GTGGGGGGCCCTACAGAGATG	0.662													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		13726	0.0		0.0	False		,,,				2504	0.0				p.P117R		Atlas-SNP	.											.	RGS3	251	.	0			c.C350G						PASS	.	C	,,,,ARG/PRO	206,4196		8,190,2003	37.0	45.0	42.0		,,,,350	5.2	0.8	9	dbSNP_132	42	1,8595		0,1,4297	yes	intron,intron,intron,intron,missense	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4,NM_144489.2	,,,,103	8,191,6300	GG,GC,CC		0.0116,4.6797,1.5926	,,,,	,,,,117/312	116356549	207,12791	2201	4298	6499	SO:0001627	intron_variant	5998	exon1			GGGGCCCTACAGA	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.3081-161C>G	9.37:g.116356549C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	42	0.583333	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	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	C	14.66	2.600389	0.46423	0.046797	1.16E-4	ENSG00000138835	ENST00000462403	T	0.65364	-0.15	5.23	5.23	0.72850	.	.	.	.	.	T	0.09949	0.0244	N	0.14661	0.345	0.47819	D	0.99952	P	0.41313	0.745	B	0.36418	0.224	T	0.14200	-1.0481	9	0.49607	T	0.09	.	11.4969	0.50413	0.1792:0.8208:0.0:0.0	.	117	Q5VZ06	.	R	117	ENSP00000436168:P117R	ENSP00000436168:P117R	P	+	2	0	RGS3	115396370	0.373000	0.25073	0.808000	0.32385	0.977000	0.68977	2.249000	0.43169	2.442000	0.82660	0.558000	0.71614	CCT	C|0.988;G|0.012	0.012	strong		0.662	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
OR2D3	120775	hgsc.bcm.edu	37	11	6942952	6942952	+	Silent	SNP	T	T	C	rs2035844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6942952T>C	ENST00000317834.3	+	1	748	c.720T>C	c.(718-720)acT>acC	p.T240T		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|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)		TTATCTCCACTGTTATCCAGA	0.463													T|||	2040	0.407348	0.6241	0.3329	5008	,	,		20687	0.4464		0.1948	False		,,,				2504	0.3456				p.T240T		Atlas-SNP	.											.	OR2D3	51	.	0			c.T720C						PASS	.	T		2479,1923	626.0+/-394.6	692,1095,414	110.0	98.0	102.0		720	-0.1	1.0	11	dbSNP_94	102	1701,6891	310.0+/-309.6	172,1357,2767	no	coding-synonymous	OR2D3	NM_001004684.1		864,2452,3181	CC,CT,TT		19.7975,43.6847,32.1687		240/331	6942952	4180,8814	2201	4296	6497	SO:0001819	synonymous_variant	120775	exon1			CTCCACTGTTATC	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.720T>C	11.37:g.6942952T>C		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	319	151	0.473354	NM_001004684	B2RP06|Q6IFG8|Q96R51	Silent	SNP	ENST00000317834.3	37	CCDS31417.1																																																																																			T|0.667;C|0.333	0.333	strong		0.463	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
SYTL5	94122	hgsc.bcm.edu	37	X	37967868	37967868	+	Silent	SNP	T	T	C	rs5918476	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37967868T>C	ENST00000357972.5	+	12	1896	c.1350T>C	c.(1348-1350)taT>taC	p.Y450Y	TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000456733.2_Silent_p.Y472Y|SYTL5_ENST00000297875.2_Silent_p.Y450Y			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	450	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						TCAAGTCATATCTTCTTCCTG	0.343													C|||	1611	0.426755	0.6475	0.2983	3775	,	,		13487	0.0615		0.1938	False		,,,				2504	0.2975				p.Y472Y		Atlas-SNP	.											.	SYTL5	72	.	0			c.T1416C						PASS	.	C	,,	2927,906		959,574,435,98,136	72.0	58.0	63.0		1416,1350,1350	2.2	1.0	X	dbSNP_114	63	1673,5053		148,905,472,1375,1398	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL5	NM_001163334.1,NM_001163335.1,NM_138780.2	,,	1107,1479,907,1473,1534	CC,CT,C,TT,T		24.8736,23.6368,43.5647	,,	472/753,450/731,450/731	37967868	4600,5959	2202	4298	6500	SO:0001819	synonymous_variant	94122	exon12			GTCATATCTTCTT		CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"""exophilin 9"""						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.1350T>C	X.37:g.37967868T>C		Somatic	384	0	0		WXS	Illumina HiSeq	Phase_I	349	172	0.492837	NM_001163334	A2RRF2	Silent	SNP	ENST00000357972.5	37	CCDS14244.1																																																																																			T|0.570;C|0.430	0.430	strong		0.343	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780	
RP1L1	94137	hgsc.bcm.edu	37	8	10467130	10467130	+	Missense_Mutation	SNP	G	G	A	rs138261433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10467130G>A	ENST00000382483.3	-	4	4701	c.4478C>T	c.(4477-4479)gCc>gTc	p.A1493V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1573					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)		GGTGGGTTGGGCCTGCGTGTG	0.647													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		16042	0.0		0.0	False		,,,				2504	0.0				p.A1493V		Atlas-SNP	.											.	RP1L1	453	.	0			c.C4478T						PASS	.	G	VAL/ALA	69,3877		0,69,1904	33.0	38.0	37.0		4478	-5.1	0.0	8	dbSNP_134	37	2,8318		0,2,4158	yes	missense	RP1L1	NM_178857.5	64	0,71,6062	AA,AG,GG		0.024,1.7486,0.5788	benign	1493/2401	10467130	71,12195	1973	4160	6133	SO:0001583	missense	94137	exon4			GGTTGGGCCTGCG	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.4478C>T	8.37:g.10467130G>A	ENSP00000371923:p.Ala1493Val	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	3.081	-0.189007	0.06299	0.017486	2.4E-4	ENSG00000183638	ENST00000382483	T	0.03860	3.78	4.78	-5.14	0.02875	.	1.690280	0.03804	N	0.264929	T	0.01092	0.0036	N	0.14661	0.345	0.09310	N	1	B	0.26483	0.15	B	0.19946	0.027	T	0.41680	-0.9495	10	0.09338	T	0.73	-0.4613	4.2452	0.10669	0.4089:0.0:0.2703:0.3208	.	1493	A6NKC6	.	V	1493	ENSP00000371923:A1493V	ENSP00000371923:A1493V	A	-	2	0	RP1L1	10504540	0.017000	0.18338	0.000000	0.03702	0.013000	0.08279	0.131000	0.15870	-1.100000	0.03030	0.561000	0.74099	GCC	G|0.998;A|0.002	0.002	strong		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
DMKN	93099	hgsc.bcm.edu	37	19	36002710	36002710	+	Silent	SNP	C	C	A	rs4806162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002710C>A	ENST00000339686.3	-	4	866	c.690G>T	c.(688-690)acG>acT	p.T230T	DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Silent_p.T230T|DMKN_ENST00000451297.2_Silent_p.T230T|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000429837.1_Silent_p.T230T|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000447113.2_Silent_p.T230T|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000424570.2_Silent_p.T230T|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000440396.1_Silent_p.T230T|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000418261.1_Silent_p.T230T	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	230	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GTGGGGGATTCGTGCACTGTC	0.597													A|||	1641	0.327676	0.379	0.3343	5008	,	,		17037	0.4345		0.1441	False		,,,				2504	0.3323				p.T230T		Atlas-SNP	.											.	DMKN	116	.	0			c.G690T						PASS	.	A	,,,,,,	1576,2830	665.6+/-401.6	292,992,919	144.0	132.0	136.0		690,690,690,690,690,690,690	2.2	1.0	19	dbSNP_111	136	1232,7368	760.1+/-407.6	104,1024,3172	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMKN	NM_001126056.2,NM_001126057.2,NM_001126058.2,NM_001190347.1,NM_001190348.1,NM_001190349.1,NM_033317.4	,,,,,,	396,2016,4091	AA,AC,CC		14.3256,35.7694,21.59	,,,,,,	230/466,230/399,230/387,230/450,230/437,230/370,230/477	36002710	2808,10198	2203	4300	6503	SO:0001819	synonymous_variant	93099	exon4			GGGATTCGTGCAC	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.690G>T	19.37:g.36002710C>A		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	246	120	0.487805	NM_001190347	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1																																																																																			C|0.766;A|0.234	0.234	strong		0.597	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
OR5J2	282775	hgsc.bcm.edu	37	11	55944501	55944501	+	Missense_Mutation	SNP	G	G	C	rs12279899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55944501G>C	ENST00000312298.1	+	1	408	c.408G>C	c.(406-408)atG>atC	p.M136I		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	136			M -> I (in dbSNP:rs12279899).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	44	Esophageal squamous(21;0.00693)					CTGTAGCCATGTCTGATAGAA	0.453													.|||	111	0.0221645	0.0779	0.0115	5008	,	,		23867	0.0		0.0	False		,,,				2504	0.0				p.M136I		Atlas-SNP	.											.	OR5J2	98	.	0			c.G408C						PASS	.	G	ILE/MET	280,4122	156.6+/-189.7	9,262,1930	164.0	150.0	155.0		408	4.7	0.4	11	dbSNP_120	155	6,8586	4.3+/-15.6	0,6,4290	yes	missense	OR5J2	NM_001005492.1	10	9,268,6220	CC,CG,GG		0.0698,6.3607,2.201	probably-damaging	136/313	55944501	286,12708	2201	4296	6497	SO:0001583	missense	282775	exon1			AGCCATGTCTGAT	AB065595	CCDS31522.1	11q11	2012-08-09			ENSG00000174957	ENSG00000174957		"""GPCR / Class A : Olfactory receptors"""	19612	protein-coding gene	gene with protein product							Standard	NM_001005492		Approved		uc010rjb.2	Q8NH18	OTTHUMG00000166835	ENST00000312298.1:c.408G>C	11.37:g.55944501G>C	ENSP00000310788:p.Met136Ile	Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	426	193	0.453052	NM_001005492	Q6IEU5	Missense_Mutation	SNP	ENST00000312298.1	37	CCDS31522.1	44	0.020146520146520148	39	0.07926829268292683	5	0.013812154696132596	0	0.0	0	0.0	G	16.43	3.120975	0.56613	0.063607	6.98E-4	ENSG00000174957	ENST00000312298	T	0.00551	6.65	4.67	4.67	0.58626	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.00073	0.0002	M	0.70595	2.14	0.51482	D	0.999923	P	0.41313	0.745	B	0.36719	0.231	T	0.75425	-0.3322	10	0.66056	D	0.02	.	17.6944	0.88277	0.0:0.0:1.0:0.0	rs12279899;rs52802580;rs12279899	136	Q8NH18	OR5J2_HUMAN	I	136	ENSP00000310788:M136I	ENSP00000310788:M136I	M	+	3	0	OR5J2	55701077	1.000000	0.71417	0.364000	0.25888	0.028000	0.11728	6.151000	0.71806	2.350000	0.79820	0.584000	0.79450	ATG	G|0.979;C|0.021	0.021	strong		0.453	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492	
NUP88	4927	hgsc.bcm.edu	37	17	5290033	5290033	+	Silent	SNP	T	T	C	rs1071705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5290033T>C	ENST00000573584.1	-	16	2666	c.2157A>G	c.(2155-2157)aaA>aaG	p.K719K	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	719					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)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						CTTACTCCTCTTTCAGGATGG	0.398													C|||	2768	0.552716	0.3994	0.4236	5008	,	,		20862	0.8244		0.4404	False		,,,				2504	0.6871				p.K719K		Atlas-SNP	.											.	NUP88	47	.	0			c.A2157G						PASS	.	C		1852,2554	633.4+/-396.0	411,1030,762	184.0	170.0	175.0		2157	3.5	1.0	17	dbSNP_86	175	3390,5210	639.9+/-399.5	666,2058,1576	no	coding-synonymous	NUP88	NM_002532.4		1077,3088,2338	CC,CT,TT		39.4186,42.0336,40.3045		719/742	5290033	5242,7764	2203	4300	6503	SO:0001819	synonymous_variant	4927	exon16			CTCCTCTTTCAGG	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.2157A>G	17.37:g.5290033T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	173	78	0.450867	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			T|0.566;C|0.434	0.434	strong		0.398	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
ARHGEF17	9828	hgsc.bcm.edu	37	11	73078685	73078685	+	Missense_Mutation	SNP	G	G	A	rs143114785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73078685G>A	ENST00000263674.3	+	21	6402	c.6052G>A	c.(6052-6054)Gcc>Acc	p.A2018T		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	2018					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						CCGAGGCCCCGCCCCTGCCAG	0.647													G|||	42	0.00838658	0.031	0.0014	5008	,	,		16959	0.0		0.0	False		,,,				2504	0.0				p.A2018T		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G6052A						PASS	.	G	THR/ALA	112,4288	86.8+/-125.4	0,112,2088	69.0	71.0	70.0		6052	-2.7	0.0	11	dbSNP_134	70	0,8586		0,0,4293	yes	missense	ARHGEF17	NM_014786.3	58	0,112,6381	AA,AG,GG		0.0,2.5455,0.8625	benign	2018/2064	73078685	112,12874	2200	4293	6493	SO:0001583	missense	9828	exon21			GGCCCCGCCCCTG	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.6052G>A	11.37:g.73078685G>A	ENSP00000263674:p.Ala2018Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	37	CCDS8221.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	4.409	0.075520	0.08485	0.025455	0.0	ENSG00000110237	ENST00000263674	T	0.57436	0.4	5.42	-2.69	0.06022	.	0.281147	0.33753	N	0.004585	T	0.07728	0.0194	N	0.02830	-0.485	0.18873	N	0.999987	B	0.06786	0.001	B	0.06405	0.002	T	0.13124	-1.0521	10	0.15499	T	0.54	-2.6535	11.6716	0.51406	0.5979:0.0:0.4021:0.0	.	2018	Q96PE2	ARHGH_HUMAN	T	2018	ENSP00000263674:A2018T	ENSP00000263674:A2018T	A	+	1	0	ARHGEF17	72756333	0.001000	0.12720	0.004000	0.12327	0.145000	0.21501	-0.227000	0.09126	-0.943000	0.03691	-0.459000	0.05422	GCC	G|0.991;A|0.009	0.009	strong		0.647	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786	
FOXN4	121643	hgsc.bcm.edu	37	12	109717697	109717697	+	Silent	SNP	A	A	G	rs10774641	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109717697A>G	ENST00000299162.5	-	10	1437	c.1333T>C	c.(1333-1335)Ttg>Ctg	p.L445L	FOXN4_ENST00000355216.1_Silent_p.L265L	NM_213596.2	NP_998761.2	Q96NZ1	FOXN4_HUMAN	forkhead box N4	445					amacrine cell differentiation (GO:0035881)|atrioventricular canal development (GO:0036302)|heart looping (GO:0001947)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of heart contraction (GO:0008016)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(9)|ovary(2)	16						AGTGTGTCCAAGCTGAATCCC	0.577													A|||	1505	0.300519	0.1467	0.3401	5008	,	,		17925	0.2857		0.4901	False		,,,				2504	0.3006				p.L445L		Atlas-SNP	.											.	FOXN4	74	.	0			c.T1333C						PASS	.	A		797,3609	319.1+/-295.9	77,643,1483	96.0	74.0	82.0		1333	3.0	1.0	12	dbSNP_120	82	3984,4616	550.4+/-385.7	909,2166,1225	no	coding-synonymous	FOXN4	NM_213596.2		986,2809,2708	GG,GA,AA		46.3256,18.089,36.76		445/518	109717697	4781,8225	2203	4300	6503	SO:0001819	synonymous_variant	121643	exon10			TGTCCAAGCTGAA	AF425596	CCDS9126.2	12q24.12	2008-02-05			ENSG00000139445	ENSG00000139445		"""Forkhead boxes"""	21399	protein-coding gene	gene with protein product		609429					Standard	NM_213596		Approved		uc001toe.4	Q96NZ1	OTTHUMG00000152868	ENST00000299162.5:c.1333T>C	12.37:g.109717697A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_213596	Q6ZMR4|Q96NZ0	Silent	SNP	ENST00000299162.5	37	CCDS9126.2																																																																																			A|0.660;G|0.340	0.340	strong		0.577	FOXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328306.1	XM_062735	
GPR133	283383	hgsc.bcm.edu	37	12	131622735	131622735	+	Silent	SNP	T	T	C	rs7302341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:131622735T>C	ENST00000261654.5	+	24	3049	c.2490T>C	c.(2488-2490)tcT>tcC	p.S830S	GPR133_ENST00000535015.1_Silent_p.S862S|GPR133_ENST00000543617.1_Silent_p.S349S|GPR133_ENST00000376682.4_Silent_p.S516S|GPR133_ENST00000540207.1_3'UTR	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	830					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		CGAGCAGCTCTGCCCGCACCT	0.602													C|||	3325	0.663938	0.3495	0.7378	5008	,	,		16161	0.9306		0.6471	False		,,,				2504	0.7791				p.S830S		Atlas-SNP	.											.	GPR133	136	.	0			c.T2490C						PASS	.	C		1845,2561	634.3+/-396.2	381,1083,739	95.0	75.0	81.0		2490	-1.8	0.0	12	dbSNP_116	81	5396,3204	483.9+/-371.3	1691,2014,595	no	coding-synonymous	GPR133	NM_198827.3		2072,3097,1334	CC,CT,TT		37.2558,41.8747,44.3257		830/875	131622735	7241,5765	2203	4300	6503	SO:0001819	synonymous_variant	283383	exon24			CAGCTCTGCCCGC	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.2490T>C	12.37:g.131622735T>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Silent	SNP	ENST00000261654.5	37	CCDS9272.1	1458	0.6675824175824175	174	0.35365853658536583	258	0.712707182320442	531	0.9283216783216783	495	0.6530343007915568	C	5.077	0.199830	0.09652	0.418747	0.627442	ENSG00000111452	ENST00000335486	.	.	.	4.46	-1.77	0.07982	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.23232	P	0.9980725	.	.	.	.	.	.	T	0.23119	-1.0197	3	.	.	.	.	10.5216	0.44922	0.0:0.4617:0.0:0.5383	rs7302341;rs7302341	.	.	.	P	184	.	.	L	+	2	0	GPR133	130188688	0.000000	0.05858	0.008000	0.14137	0.015000	0.08874	-3.362000	0.00497	-0.786000	0.04516	-1.050000	0.02344	CTG	T|0.416;C|0.584	0.584	strong		0.602	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
AATK	9625	hgsc.bcm.edu	37	17	79095629	79095629	+	Missense_Mutation	SNP	C	C	A	rs7503604|rs386799844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79095629C>A	ENST00000326724.4	-	11	2131	c.2107G>T	c.(2107-2109)Ggc>Tgc	p.G703C	AATK_ENST00000417379.1_Missense_Mutation_p.G600C	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	703			G -> C (in dbSNP:rs7503604). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9734811}.		brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			TCAGCGTGGCCGCCCGCAGAG	0.721													A|||	2787	0.55651	0.4463	0.6772	5008	,	,		12566	0.6419		0.4911	False		,,,				2504	0.5992				p.G703C		Atlas-SNP	.											AATK_ENST00000326724,NS,carcinoma,0,2	AATK	102	2	0			c.G2107T						PASS	.	A	CYS/GLY,CYS/GLY	1514,2030		367,780,625	5.0	7.0	6.0		2107,1798	-7.1	0.0	17	dbSNP_116	6	3740,4026		1007,1726,1150	yes	missense,missense	AATK	NM_001080395.2,NM_004920.2	159,159	1374,2506,1775	AA,AC,CC		48.1586,42.7201,46.4545	benign,benign	703/1375,600/1272	79095629	5254,6056	1772	3883	5655	SO:0001583	missense	9625	exon11			CGTGGCCGCCCGC	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.2107G>T	17.37:g.79095629C>A	ENSP00000324196:p.Gly703Cys	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_001080395	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	37	CCDS45807.1	1170	0.5357142857142857	212	0.43089430894308944	229	0.6325966850828729	346	0.6048951048951049	383	0.5052770448548812	A	9.655	1.142554	0.21205	0.427201	0.481586	ENSG00000181409	ENST00000326724;ENST00000374792	T;T	0.79247	-1.11;-1.25	3.91	-7.07	0.01563	.	1.777830	0.03483	N	0.215355	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.29882	-0.9997	9	0.38643	T	0.18	.	1.6467	0.02763	0.278:0.4625:0.1:0.1595	rs7503604;rs59349021	703	Q6ZMQ8	LMTK1_HUMAN	C	703;667	ENSP00000324196:G703C;ENSP00000363924:G667C	ENSP00000324196:G703C	G	-	1	0	AATK	76710224	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.384000	0.01063	-1.190000	0.02698	-1.672000	0.00744	GGC	C|0.463;A|0.537	0.537	strong		0.721	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
FZD3	7976	hgsc.bcm.edu	37	8	28413375	28413375	+	Silent	SNP	C	C	T	rs62001924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:28413375C>T	ENST00000240093.3	+	7	2152	c.1674C>T	c.(1672-1674)acC>acT	p.T558T	FZD3_ENST00000537916.1_Silent_p.T558T	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	558					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|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)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		GAACATCCACCCATGCTTCTT	0.488													C|||	76	0.0151757	0.0575	0.0	5008	,	,		19431	0.0		0.0	False		,,,				2504	0.0				p.T558T		Atlas-SNP	.											.	FZD3	65	.	0			c.C1674T						PASS	.	C	,	204,4202	124.9+/-162.1	3,198,2002	95.0	77.0	83.0		1674,1674	0.3	1.0	8	dbSNP_129	83	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FZD3	NM_017412.3,NM_145866.1	,	3,198,6302	TT,TC,CC		0.0,4.63,1.5685	,	558/667,558/667	28413375	204,12802	2203	4300	6503	SO:0001819	synonymous_variant	7976	exon7			ATCCACCCATGCT	AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"""GPCR / Class F : Frizzled receptors"""	4041	protein-coding gene	gene with protein product		606143	"""frizzled (Drosophila) homolog 3"", ""frizzled homolog 3 (Drosophila)"", ""frizzled 3, seven transmembrane spanning receptor"", ""frizzled family receptor 3"""			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.1674C>T	8.37:g.28413375C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	100	58	0.58	NM_017412	A8K615	Silent	SNP	ENST00000240093.3	37	CCDS6069.1																																																																																			C|0.984;T|0.016	0.016	strong		0.488	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866	
NPY4R	5540	hgsc.bcm.edu	37	10	47086978	47086978	+	Silent	SNP	G	G	A	rs3740294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:47086978G>A	ENST00000395716.1	+	2	280	c.195G>A	c.(193-195)gtG>gtA	p.V65V	NPY4R_ENST00000374312.1_Silent_p.V65V			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	65					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										TGATGTGTGTGACTGTGAGGC	0.557													G|||	871	0.173922	0.1029	0.1369	5008	,	,		43421	0.3264		0.1521	False		,,,				2504	0.1616				p.V65V		Atlas-SNP	.											.	PPYR1	54	.	0			c.G195A						PASS	.	G		302,4104		0,302,1901	234.0	210.0	218.0		195	1.0	0.0	10	dbSNP_107	218	974,7626		0,974,3326	no	coding-synonymous	PPYR1	NM_005972.4		0,1276,5227	AA,AG,GG		11.3256,6.8543,9.8109		65/376	47086978	1276,11730	2203	4300	6503	SO:0001819	synonymous_variant	5540	exon3			GTGTGTGACTGTG		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"""GPCR / Class A : Neuropeptide receptors : Y"""	9329	protein-coding gene	gene with protein product		601790	"""pancreatic polypeptide receptor 1"""	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.195G>A	10.37:g.47086978G>A		Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	386	89	0.23057	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Silent	SNP	ENST00000395716.1	37	CCDS31193.1																																																																																			G|0.852;A|0.148	0.148	strong		0.557	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921132	12921132	+	Missense_Mutation	SNP	A	A	G	rs12139550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12921132A>G	ENST00000240189.2	+	4	1010	c.923A>G	c.(922-924)gAg>gGg	p.E308G		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	308			E -> G (in dbSNP:rs12139550).		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)		CTATTAGAAGAGGACTTGAAG	0.488													.|||	544	0.108626	0.1248	0.098	5008	,	,		21844	0.13		0.1074	False		,,,				2504	0.0736				p.E308G		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.A923G						PASS	.	A	GLY/GLU	609,3795	257.7+/-262.0	69,471,1662	127.0	130.0	129.0		923	-1.6	0.0	1	dbSNP_120	129	960,7634	202.8+/-246.0	78,804,3415	yes	missense	PRAMEF2	NM_023014.1	98	147,1275,5077	GG,GA,AA		11.1706,13.8283,12.0711	benign	308/475	12921132	1569,11429	2202	4297	6499	SO:0001583	missense	65122	exon4			TAGAAGAGGACTT		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.923A>G	1.37:g.12921132A>G	ENSP00000240189:p.Glu308Gly	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	249	103	0.413655	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	232	0.10622710622710622	43	0.08739837398373984	36	0.09944751381215469	62	0.10839160839160839	91	0.12005277044854881	A	3.936	-0.015216	0.07681	0.138283	0.111706	ENSG00000120952	ENST00000240189	T	0.49139	0.79	0.824	-1.65	0.08291	.	1.527710	0.04188	N	0.327753	T	0.00328	0.0010	L	0.43152	1.355	0.80722	P	0.0	B	0.32693	0.38	B	0.36567	0.228	T	0.04178	-1.0971	9	0.54805	T	0.06	.	1.4457	0.02364	0.3457:0.3043:0.0:0.35	rs12139550	308	O60811	PRAM2_HUMAN	G	308	ENSP00000240189:E308G	ENSP00000240189:E308G	E	+	2	0	PRAMEF2	12843719	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.548000	0.06048	-0.938000	0.03714	0.145000	0.16022	GAG	A|0.890;G|0.110	0.110	strong		0.488	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
INTS1	26173	hgsc.bcm.edu	37	7	1542697	1542697	+	Silent	SNP	G	G	A	rs3752714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1542697G>A	ENST00000404767.3	-	3	274	c.189C>T	c.(187-189)gcC>gcT	p.A63A	INTS1_ENST00000389470.4_Silent_p.A191A|INTS1_ENST00000493531.1_5'Flank	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	63	Poly-Ala.				inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		TGGACAACGCGGCCGCCGCAT	0.667													A|||	2933	0.585663	0.7746	0.4179	5008	,	,		15450	0.7123		0.4642	False		,,,				2504	0.4438				p.A63A		Atlas-SNP	.											INTS1,NS,carcinoma,0,1	INTS1	145	1	0			c.C189T						PASS	.			2854,1190		1030,794,198	55.0	69.0	65.0		189	-3.4	0.0	7	dbSNP_107	65	3508,4828		740,2028,1400	no	coding-synonymous	INTS1	NM_001080453.2		1770,2822,1598	AA,AG,GG		42.0825,29.4263,48.6107		63/2191	1542697	6362,6018	2022	4168	6190	SO:0001819	synonymous_variant	26173	exon3			CAACGCGGCCGCC	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.189C>T	7.37:g.1542697G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																			G|0.412;A|0.588	0.588	strong		0.667	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
TTN	7273	hgsc.bcm.edu	37	2	179586779	179586779	+	Silent	SNP	A	A	G	rs16866469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179586779A>G	ENST00000591111.1	-	76	21884	c.21660T>C	c.(21658-21660)caT>caC	p.H7220H	TTN_ENST00000589042.1_Silent_p.H7537H|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Silent_p.H6293H|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|RP11-171I2.1_ENST00000590024.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12789	Ig-like 54.				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)			CACCAGTAACATGACACTCAA	0.428													A|||	101	0.0201677	0.0749	0.0029	5008	,	,		21079	0.0		0.0	False		,,,				2504	0.0				p.H7537H		Atlas-SNP	.											.	TTN	18412	.	0			c.T22611C						PASS	.	A	,,,	195,3703		6,183,1760	229.0	217.0	221.0		,18879,,	-2.7	1.0	2	dbSNP_123	221	6,8288		0,6,4141	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	6,189,5901	GG,GA,AA		0.0723,5.0026,1.6486	,,,	,6293/33424,,	179586779	201,11991	1949	4147	6096	SO:0001819	synonymous_variant	7273	exon78			AGTAACATGACAC	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.21660T>C	2.37:g.179586779A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	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|0.982;G|0.018	0.018	strong		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
VPS8	23355	hgsc.bcm.edu	37	3	184573555	184573555	+	Silent	SNP	C	C	T	rs6443999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	127	0	0		WXS	Illumina HiSeq	Phase_I	145	77	0.531034	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	
RABGGTA	5875	hgsc.bcm.edu	37	14	24736027	24736027	+	Silent	SNP	G	G	A	rs14193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24736027G>A	ENST00000399409.3	-	14	1905	c.1422C>T	c.(1420-1422)cgC>cgT	p.R474R	RABGGTA_ENST00000216840.6_Silent_p.R474R|RABGGTA_ENST00000560777.1_Silent_p.R83R|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	244	0	0		WXS	Illumina HiSeq	Phase_I	231	97	0.419913	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	
TH	7054	hgsc.bcm.edu	37	11	2191006	2191006	+	Silent	SNP	C	C	T	rs34510659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2191006C>T	ENST00000381178.1	-	3	297	c.279G>A	c.(277-279)tcG>tcA	p.S93S	TH_ENST00000352909.3_Silent_p.S62S|TH_ENST00000333684.5_Silent_p.S66S|TH_ENST00000381175.1_Silent_p.S89S	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	93					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CCCCGGGCTCCGAGGGGACTG	0.711													C|||	122	0.024361	0.0893	0.0058	5008	,	,		13970	0.0		0.0	False		,,,				2504	0.0				p.S93S		Atlas-SNP	.											.	TH	43	.	0			c.G279A						PASS	.	C	,,	343,4043		10,323,1860	17.0	20.0	19.0		186,279,267	-1.0	0.0	11	dbSNP_126	19	6,8586		0,6,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	10,329,6150	TT,TC,CC		0.0698,7.8203,2.6892	,,	62/498,93/529,89/525	2191006	349,12629	2193	4296	6489	SO:0001819	synonymous_variant	7054	exon3			GGGCTCCGAGGGG	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.279G>A	11.37:g.2191006C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	68	40	0.588235	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			C|0.971;T|0.029	0.029	strong		0.711	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
MEGF6	1953	hgsc.bcm.edu	37	1	3418391	3418391	+	Silent	SNP	C	C	T	rs4648508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	194	0	0		WXS	Illumina HiSeq	Phase_I	251	118	0.47012	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	
OR9A2	135924	hgsc.bcm.edu	37	7	142724062	142724062	+	Missense_Mutation	SNP	C	C	T	rs9885986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142724062C>T	ENST00000350513.2	-	1	220	c.158G>A	c.(157-159)cGt>cAt	p.R53H		NM_001001658.1	NP_001001658.1	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A, member 2	53			R -> H (in dbSNP:rs9885986).			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(3)|endometrium(4)|large_intestine(1)|lung(14)|skin(3)	25	Melanoma(164;0.059)					GGACTGCAGACGTTTATCCAC	0.433													C|||	439	0.0876597	0.1384	0.0548	5008	,	,		22242	0.0377		0.0577	False		,,,				2504	0.1247				p.R53H		Atlas-SNP	.											.	OR9A2	52	.	0			c.G158A						PASS	.	C	HIS/ARG	561,3845	250.9+/-257.8	43,475,1685	131.0	134.0	133.0		158	2.3	0.1	7	dbSNP_119	133	588,8012	156.4+/-210.3	25,538,3737	no	missense	OR9A2	NM_001001658.1	29	68,1013,5422	TT,TC,CC		6.8372,12.7326,8.8344	benign	53/311	142724062	1149,11857	2203	4300	6503	SO:0001583	missense	135924	exon1			TGCAGACGTTTAT		CCDS34767.1	7q34	2014-07-10			ENSG00000179468	ENSG00000179468		"""GPCR / Class A : Olfactory receptors"""	15093	protein-coding gene	gene with protein product							Standard	NM_001001658		Approved		uc003wcc.1	Q8NGT5	OTTHUMG00000158386	ENST00000350513.2:c.158G>A	7.37:g.142724062C>T	ENSP00000316518:p.Arg53His	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	164	73	0.445122	NM_001001658	B9EH51|Q6IF71|Q8NGD9	Missense_Mutation	SNP	ENST00000350513.2	37	CCDS34767.1	171	0.0782967032967033	84	0.17073170731707318	26	0.0718232044198895	24	0.04195804195804196	37	0.048812664907651716	C	2.760	-0.258015	0.05791	0.127326	0.068372	ENSG00000179468	ENST00000350513	T	0.01139	5.28	4.13	2.31	0.28768	GPCR, rhodopsin-like superfamily (1);	1.602110	0.04617	N	0.401290	T	0.00012	0.0000	N	0.25332	0.735	0.80722	P	0.0	B	0.21452	0.056	B	0.16289	0.015	T	0.45775	-0.9238	9	0.02654	T	1	-5.82	6.0054	0.19542	0.0:0.6743:0.0:0.3257	rs9885986;rs9885986	53	Q8NGT5	OR9A2_HUMAN	H	53	ENSP00000316518:R53H	ENSP00000316518:R53H	R	-	2	0	OR9A2	142434184	0.000000	0.05858	0.055000	0.19348	0.007000	0.05969	-0.748000	0.04818	0.506000	0.28125	0.561000	0.74099	CGT	C|0.909;T|0.091	0.091	strong		0.433	OR9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350862.1		
ALPK3	57538	hgsc.bcm.edu	37	15	85402610	85402610	+	Silent	SNP	G	G	A	rs34122391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	77	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	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	
NLRP7	199713	hgsc.bcm.edu	37	19	55450746	55450746	+	Missense_Mutation	SNP	C	C	T	rs61747414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000448121.2_Missense_Mutation_p.A481T|NLRP7_ENST00000446217.1_Missense_Mutation_p.A509T|NLRP7_ENST00000328092.5_Missense_Mutation_p.A481T|NLRP7_ENST00000588756.1_Missense_Mutation_p.A481T|NLRP7_ENST00000592784.1_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						PASS	.	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	117	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	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	
NCOR2	9612	hgsc.bcm.edu	37	12	124846788	124846788	+	Missense_Mutation	SNP	G	G	C	rs11057592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124846788G>C	ENST00000405201.1	-	22	2984	c.2984C>G	c.(2983-2985)gCt>gGt	p.A995G	NCOR2_ENST00000429285.2_Missense_Mutation_p.A977G|NCOR2_ENST00000356219.3_Missense_Mutation_p.A994G|NCOR2_ENST00000397355.1_Missense_Mutation_p.A978G|NCOR2_ENST00000404621.1_Missense_Mutation_p.A977G|NCOR2_ENST00000404121.2_Missense_Mutation_p.A548G			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	995	Poly-Pro.				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)		GGCTGGGGGAGCTGGCTTGGT	0.682													G|||	117	0.0233626	0.0877	0.0014	5008	,	,		12732	0.0		0.0	False		,,,				2504	0.0				p.A995G		Atlas-SNP	.											.	NCOR2	475	.	0			c.C2984G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	304,3804		12,280,1762	9.0	13.0	12.0		2930,2930,2984	3.0	0.0	12	dbSNP_120	12	4,8366		0,4,4181	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	60,60,60	12,284,5943	CC,CG,GG		0.0478,7.4002,2.4683	possibly-damaging,possibly-damaging,possibly-damaging	977/2459,977/2505,995/2515	124846788	308,12170	2054	4185	6239	SO:0001583	missense	9612	exon24			GGGGGAGCTGGCT	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.2984C>G	12.37:g.124846788G>C	ENSP00000384018:p.Ala995Gly	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	42	16	0.380952	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	47	0.02152014652014652	46	0.09349593495934959	1	0.0027624309392265192	0	0.0	0	0.0	G	8.697	0.908871	0.17833	0.074002	4.78E-4	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.31510	2.18;2.49;2.22;2.49;2.22;2.48;1.49	4.91	3.02	0.34903	.	0.502628	0.16789	U	0.199466	T	0.00998	0.0033	L	0.44542	1.39	0.09310	N	1	P;P;P	0.51933	0.824;0.824;0.949	B;B;P	0.45881	0.3;0.3;0.496	T	0.02179	-1.1200	10	0.27082	T	0.32	-2.9071	8.1686	0.31241	0.0881:0.1576:0.7543:0.0	rs11057592	977;978;995	C9J0Q5;C9J239;C9JFD3	.;.;.	G	995;977;994;978;994;548;977;995	ENSP00000384018:A995G;ENSP00000384202:A977G;ENSP00000348551:A994G;ENSP00000380513:A978G;ENSP00000385618:A548G;ENSP00000400281:A977G;ENSP00000402808:A995G	ENSP00000348551:A994G	A	-	2	0	NCOR2	123412741	0.024000	0.19004	0.009000	0.14445	0.009000	0.06853	0.963000	0.29293	0.454000	0.26884	0.462000	0.41574	GCT	G|0.973;C|0.027	0.027	strong		0.682	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
GM2A	2760	hgsc.bcm.edu	37	5	150632832	150632832	+	Missense_Mutation	SNP	G	G	A	rs1048719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150632832G>A	ENST00000357164.3	+	1	380	c.55G>A	c.(55-57)Gcc>Acc	p.A19T		NM_000405.4|NM_001167607.1	NP_000396.2|NP_001161079.1	P17900	SAP3_HUMAN	GM2 ganglioside activator	19			A -> T (in dbSNP:rs1048719). {ECO:0000269|PubMed:10364519, ECO:0000269|PubMed:1427911, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1915857, ECO:0000269|PubMed:2753159}.		ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|learning or memory (GO:0007611)|lipid storage (GO:0019915)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	apical cortex (GO:0045179)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|mitochondrion (GO:0005739)	beta-N-acetylhexosaminidase activity (GO:0004563)|lipid transporter activity (GO:0005319)|phospholipase activator activity (GO:0016004)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|upper_aerodigestive_tract(2)	8		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCTTCTCGCGGCCCCTGCGCA	0.622													G|||	401	0.0800719	0.0174	0.0821	5008	,	,		14901	0.2014		0.0308	False		,,,				2504	0.089				p.A19T		Atlas-SNP	.											.	GM2A	24	.	0			c.G55A						PASS	.	G	THR/ALA,THR/ALA	104,4302	82.9+/-121.4	0,104,2099	55.0	56.0	55.0		55,55	0.3	0.0	5	dbSNP_86	55	253,8347	99.3+/-160.8	1,251,4048	yes	missense,missense	GM2A	NM_001167607.1,NM_000405.4	58,58	1,355,6147	AA,AG,GG		2.9419,2.3604,2.7449	benign,benign	19/187,19/194	150632832	357,12649	2203	4300	6503	SO:0001583	missense	2760	exon1			CTCGCGGCCCCTG		CCDS4313.1	5q33.1	2010-03-17	2004-05-20		ENSG00000196743	ENSG00000196743			4367	protein-coding gene	gene with protein product	"""cerebroside sulfate activator protein"", ""sphingolipid activator protein 3"""	613109	"""GM2 ganglioside activator protein"""			115863, 1915857	Standard	NM_000405		Approved	SAP-3	uc003ltr.4	P17900	OTTHUMG00000130124	ENST00000357164.3:c.55G>A	5.37:g.150632832G>A	ENSP00000349687:p.Ala19Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_001167607	B2R699|D3DQH6|Q14426|Q14428|Q6LBL5	Missense_Mutation	SNP	ENST00000357164.3	37	CCDS4313.1	185	0.08470695970695971	14	0.028455284552845527	33	0.09116022099447514	112	0.1958041958041958	26	0.03430079155672823	G	12.21	1.870050	0.33069	0.023604	0.029419	ENSG00000196743	ENST00000357164	T	0.64618	-0.11	3.26	0.34	0.15985	.	1.885850	0.02210	N	0.063101	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B;B	0.27932	0.194;0.017	B;B	0.23275	0.045;0.012	T	0.02491	-1.1151	9	0.25106	T	0.35	-26.2731	1.9241	0.03313	0.1195:0.2012:0.4727:0.2066	rs1048719;rs3188750;rs1048719	19;19	B4DQM5;P17900	.;SAP3_HUMAN	T	19	ENSP00000349687:A19T	ENSP00000349687:A19T	A	+	1	0	GM2A	150613025	0.000000	0.05858	0.000000	0.03702	0.291000	0.27294	-0.105000	0.10907	0.055000	0.16094	0.462000	0.41574	GCC	G|0.952;A|0.048	0.048	strong		0.622	GM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252432.1	NM_000405	
QRFP	347148	hgsc.bcm.edu	37	9	133768921	133768921	+	Missense_Mutation	SNP	G	G	A	rs140393161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133768921G>A	ENST00000343079.1	-	1	304	c.305C>T	c.(304-306)cCt>cTt	p.P102L		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)		CCCCGCAGCAGGGAGGAAGCC	0.642													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18404	0.0		0.0	False		,,,				2504	0.0				p.P102L		Atlas-SNP	.											.	QRFP	14	.	0			c.C305T						PASS	.	G	LEU/PRO	4,4400	6.2+/-15.9	0,4,2198	57.0	63.0	61.0		305	0.9	0.0	9	dbSNP_134	61	0,8600		0,0,4300	yes	missense	QRFP	NM_198180.1	98	0,4,6498	AA,AG,GG		0.0,0.0908,0.0308	benign	102/137	133768921	4,13000	2202	4300	6502	SO:0001583	missense	347148	exon1			GCAGCAGGGAGGA	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.305C>T	9.37:g.133768921G>A	ENSP00000345487:p.Pro102Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	105	38	0.361905	NM_198180		Missense_Mutation	SNP	ENST00000343079.1	37	CCDS6936.1	5	0.0022893772893772895	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	0	0.0	G	7.215	0.596183	0.13875	9.08E-4	0.0	ENSG00000188710	ENST00000343079	T	0.41065	1.01	4.12	0.912	0.19349	.	0.654924	0.13732	N	0.366612	T	0.19087	0.0458	L	0.37507	1.11	0.09310	N	1	B	0.14438	0.01	B	0.16289	0.015	T	0.18461	-1.0336	10	0.22109	T	0.4	-0.0237	3.2515	0.06816	0.1026:0.1401:0.4738:0.2835	.	102	P83859	OX26_HUMAN	L	102	ENSP00000345487:P102L	ENSP00000345487:P102L	P	-	2	0	QRFP	132758742	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.074000	0.11450	-0.057000	0.13199	0.313000	0.20887	CCT	G|0.999;A|0.001	0.001	strong		0.642	QRFP-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254566.1	NM_198180	
POLR2A	5430	hgsc.bcm.edu	37	17	7412349	7412349	+	Silent	SNP	G	G	A	rs2228134	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7412349G>A	ENST00000322644.6	+	21	3951	c.3552G>A	c.(3550-3552)acG>acA	p.T1184T		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1184					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				CCCAGAGCACGGTGGTGGCAG	0.547													G|||	380	0.0758786	0.2655	0.0288	5008	,	,		17738	0.0		0.001	False		,,,				2504	0.0082				p.T1184T		Atlas-SNP	.											POLR2A,colon,carcinoma,+1,1	POLR2A	157	1	0			c.G3552A						PASS	.	G		993,3413	370.3+/-319.5	115,763,1325	141.0	108.0	119.0		3552	-11.0	0.0	17	dbSNP_98	119	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous	POLR2A	NM_000937.4		115,776,5612	AA,AG,GG		0.1512,22.5374,7.7349		1184/1971	7412349	1006,12000	2203	4300	6503	SO:0001819	synonymous_variant	5430	exon21			GAGCACGGTGGTG			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.3552G>A	17.37:g.7412349G>A		Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	251	135	0.537849	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			G|0.935;A|0.065	0.065	strong		0.547	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
GOLGB1	2804	hgsc.bcm.edu	37	3	121414061	121414061	+	Missense_Mutation	SNP	C	C	T	rs1127412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	227	0	0		WXS	Illumina HiSeq	Phase_I	271	138	0.509225	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	
DAGLB	221955	hgsc.bcm.edu	37	7	6461424	6461424	+	Silent	SNP	C	C	T	rs836515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6461424C>T	ENST00000297056.6	-	9	1321	c.1152G>A	c.(1150-1152)acG>acA	p.T384T	DAGLB_ENST00000436575.1_Silent_p.T343T|DAGLB_ENST00000428902.2_Silent_p.T257T|DAGLB_ENST00000421761.2_Silent_p.T128T|DAGLB_ENST00000425398.2_Silent_p.T255T	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	384					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		CTGACAGGTCCGTAAGGACAT	0.592													C|||	388	0.077476	0.1649	0.0533	5008	,	,		13676	0.0437		0.008	False		,,,				2504	0.0828				p.T384T		Atlas-SNP	.											.	DAGLB	74	.	0			c.G1152A						PASS	.	C	,	692,3714	288.7+/-280.0	61,570,1572	190.0	120.0	144.0		765,1152	-1.5	0.6	7	dbSNP_86	144	31,8569	20.4+/-63.3	0,31,4269	no	coding-synonymous,coding-synonymous	DAGLB	NM_001142936.1,NM_139179.3	,	61,601,5841	TT,TC,CC		0.3605,15.7059,5.559	,	255/544,384/673	6461424	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	221955	exon9			CAGGTCCGTAAGG	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.1152G>A	7.37:g.6461424C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	83	47	0.566265	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Silent	SNP	ENST00000297056.6	37	CCDS5350.1																																																																																			C|0.946;T|0.054	0.054	strong		0.592	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
KRT71	112802	hgsc.bcm.edu	37	12	52946498	52946498	+	Missense_Mutation	SNP	C	C	T	rs665470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	217	0	0		WXS	Illumina HiSeq	Phase_I	232	117	0.50431	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	
RICTOR	253260	hgsc.bcm.edu	37	5	38960006	38960006	+	Silent	SNP	G	G	A	rs73751814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38960006G>A	ENST00000357387.3	-	21	1956	c.1926C>T	c.(1924-1926)ccC>ccT	p.P642P	RICTOR_ENST00000296782.5_Silent_p.P642P|RICTOR_ENST00000503698.1_5'Flank	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)					GACTTCTTTCGGGTTTCATTC	0.363													A|||	36	0.0071885	0.025	0.0043	5008	,	,		18686	0.0		0.0	False		,,,				2504	0.0				p.P642P		Atlas-SNP	.											.	RICTOR	182	.	0			c.C1926T						PASS	.	A		92,4314	817.2+/-416.3	1,90,2112	133.0	135.0	134.0		1926	-3.2	1.0	5	dbSNP_130	134	0,8600		0,0,4300	no	coding-synonymous	RICTOR	NM_152756.3		1,90,6412	AA,AG,GG		0.0,2.0881,0.7074		642/1709	38960006	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	253260	exon21			TCTTTCGGGTTTC		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.1926C>T	5.37:g.38960006G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	158	82	0.518987	NM_152756		Silent	SNP	ENST00000357387.3	37	CCDS34148.1																																																																																			G|0.993;A|0.007	0.007	strong		0.363	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
B3GNT4	79369	hgsc.bcm.edu	37	12	122691058	122691058	+	Missense_Mutation	SNP	T	T	C	rs35203505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122691058T>C	ENST00000324189.4	+	3	616	c.260T>C	c.(259-261)cTg>cCg	p.L87P	B3GNT4_ENST00000535274.1_Missense_Mutation_p.L62P|B3GNT4_ENST00000545141.1_Intron|B3GNT4_ENST00000546192.1_Missense_Mutation_p.L62P	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	87			L -> P (in dbSNP:rs35203505).		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)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		AGCGCCTCTCTGTCCCTGCCT	0.592													T|||	277	0.0553115	0.1982	0.0202	5008	,	,		16804	0.0		0.001	False		,,,				2504	0.0				p.L87P		Atlas-SNP	.											.	B3GNT4	35	.	0			c.T260C						PASS	.	T	PRO/LEU	794,3612	319.1+/-295.9	77,640,1486	236.0	227.0	230.0		260	-0.7	0.9	12	dbSNP_126	230	7,8593	5.7+/-21.5	0,7,4293	yes	missense	B3GNT4	NM_030765.2	98	77,647,5779	CC,CT,TT		0.0814,18.0209,6.1587	benign	87/379	122691058	801,12205	2203	4300	6503	SO:0001583	missense	79369	exon3			CCTCTCTGTCCCT	AB049586	CCDS9227.1	12q24	2013-02-19						"""Beta 3-glycosyltransferases"""	15683	protein-coding gene	gene with protein product		605864				11042166	Standard	NM_030765		Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000324189.4:c.260T>C	12.37:g.122691058T>C	ENSP00000319636:p.Leu87Pro	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	187	82	0.438503	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Missense_Mutation	SNP	ENST00000324189.4	37	CCDS9227.1	118	0.05402930402930403	112	0.22764227642276422	6	0.016574585635359115	0	0.0	0	0.0	T	7.052	0.564562	0.13498	0.180209	8.14E-4	ENSG00000176383	ENST00000324189;ENST00000546192;ENST00000535274	T;T;T	0.36878	1.36;1.23;1.23	4.7	-0.663	0.11410	.	0.519308	0.14506	N	0.315425	T	0.00012	0.0000	L	0.40543	1.245	0.51233	P	9.00000000000345E-5	P	0.45283	0.855	B	0.41571	0.36	T	0.15263	-1.0443	9	0.30078	T	0.28	.	1.7591	0.02988	0.1302:0.2171:0.1337:0.519	rs35203505	87	Q9C0J1	B3GN4_HUMAN	P	87;62;62	ENSP00000319636:L87P;ENSP00000438840:L62P;ENSP00000444534:L62P	ENSP00000319636:L87P	L	+	2	0	B3GNT4	121257011	0.000000	0.05858	0.850000	0.33497	0.397000	0.30659	0.008000	0.13197	0.247000	0.21414	0.533000	0.62120	CTG	T|0.944;C|0.056	0.056	strong		0.592	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765	
SLC38A3	10991	hgsc.bcm.edu	37	3	50257389	50257389	+	RNA	SNP	G	G	A	rs35742391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:50257389G>A	ENST00000420502.1	+	0	1536									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		CGGAGAAGGAGCCTGCAAGAT	0.587													G|||	581	0.116014	0.3495	0.0576	5008	,	,		19489	0.0		0.0298	False		,,,				2504	0.0501				p.E461E		Atlas-SNP	.											.	SLC38A3	22	.	0			c.G1383A						PASS	.	G		1088,2842		178,732,1055	93.0	80.0	84.0		1383	3.8	1.0	3	dbSNP_126	84	276,8014		9,258,3878	no	coding-synonymous	SLC38A3	NM_006841.4		187,990,4933	AA,AG,GG		3.3293,27.6845,11.162		461/505	50257389	1364,10856	1965	4145	6110			10991	exon15			GAAGGAGCCTGCA	U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"""Solute carriers"""	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		3.37:g.50257389G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	190	101	0.531579	NM_006841		Silent	SNP	ENST00000420502.1	37																																																																																				G|0.914;A|0.086	0.086	strong		0.587	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841	
SCTR	6344	hgsc.bcm.edu	37	2	120194673	120194673	+	IGR	SNP	G	G	A	rs114197773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:120194673G>A	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000306406.4_Missense_Mutation_p.G77D|TMEM37_ENST00000409826.1_Missense_Mutation_p.G89D	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)	AGAGACCTGGGCCAGGCCCAT	0.652													G|||	140	0.0279553	0.0976	0.0101	5008	,	,		14451	0.0		0.004	False		,,,				2504	0.0				p.G77D		Atlas-SNP	.											.	TMEM37	40	.	0			c.G230A						PASS	.	G	ASP/GLY	327,4077	168.3+/-199.2	12,303,1887	51.0	54.0	53.0		230	2.8	0.8	2	dbSNP_132	53	8,8590	6.4+/-24.3	0,8,4291	yes	missense	TMEM37	NM_183240.2	94	12,311,6178	AA,AG,GG		0.093,7.4251,2.5765	benign	77/191	120194673	335,12667	2202	4299	6501	SO:0001628	intergenic_variant	140738	exon2			ACCTGGGCCAGGC		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.120194673G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_183240	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	47	0.02152014652014652	41	0.08333333333333333	3	0.008287292817679558	0	0.0	3	0.00395778364116095	G	5.612	0.297674	0.10622	0.074251	9.3E-4	ENSG00000171227	ENST00000409826;ENST00000306406	.	.	.	4.74	2.78	0.32641	.	0.572504	0.18041	N	0.153613	T	0.01387	0.0045	L	0.29908	0.895	0.09310	N	0.99999	B	0.21606	0.058	B	0.22601	0.04	T	0.06698	-1.0812	9	0.15499	T	0.54	-3.9992	8.7558	0.34645	0.2022:0.0:0.7978:0.0	.	77	Q8WXS4	CCGL_HUMAN	D	89;77	.	ENSP00000303148:G77D	G	+	2	0	TMEM37	119911143	0.094000	0.21725	0.818000	0.32626	0.630000	0.37929	0.340000	0.19892	1.234000	0.43709	0.561000	0.74099	GGC	G|0.973;A|0.027	0.027	strong		0.652	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
SORBS2	8470	hgsc.bcm.edu	37	4	186573817	186573817	+	Splice_Site	SNP	C	C	T	rs61732192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:186573817C>T	ENST00000284776.7	-	7	842	c.333G>A	c.(331-333)ccG>ccA	p.P111P	SORBS2_ENST00000319471.9_Splice_Site_p.P197P|SORBS2_ENST00000393528.3_Splice_Site_p.P157P|SORBS2_ENST00000431808.1_Splice_Site_p.P111P|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000449407.2_Splice_Site_p.P197P|SORBS2_ENST00000448662.2_Splice_Site_p.P180P|SORBS2_ENST00000437304.2_Splice_Site_p.P290P|SORBS2_ENST00000418609.1_Splice_Site_p.P30P|SORBS2_ENST00000355634.5_Splice_Site_p.P211P	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	111	SoHo. {ECO:0000255|PROSITE- ProRule:PRU00195}.				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)		CAGACATACCCGGCTTGTGCA	0.483													C|||	82	0.0163738	0.0598	0.0043	5008	,	,		22370	0.0		0.0	False		,,,				2504	0.0				p.P290P	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											SORBS2_ENST00000448662,NS,carcinoma,-1,4	SORBS2	300	4	0			c.G870A						scavenged	.	C	,,,,,,,	224,4182	132.9+/-169.3	5,214,1984	247.0	195.0	213.0		591,591,540,870,90,90,471,333	-10.3	0.0	4	dbSNP_129	213	0,8600		0,0,4300	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,coding-synonymous-near-splice	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	,,,,,,,	5,214,6284	TT,TC,CC		0.0,5.084,1.7223	,,,,,,,	197/645,197/732,180/662,290/825,30/1005,30/493,157/667,111/1101	186573817	224,12782	2203	4300	6503	SO:0001630	splice_region_variant	8470	exon8			CATACCCGGCTTG		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.334+1G>A	4.37:g.186573817C>T		Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1	33|33	0.01510989010989011|0.01510989010989011	31|31	0.06300813008130081|0.06300813008130081	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	4.660|4.660	0.122652|0.122652	0.08931|0.08931	0.05084|0.05084	0.0|0.0	ENSG00000154556|ENSG00000154556	ENST00000438278|ENST00000445625	.|.	.|.	.|.	5.16|5.16	-10.3|-10.3	0.00346|0.00346	.|.	.|.	.|.	.|.	.|.	T|T	0.06050|0.06050	0.0157|0.0157	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43491|0.43491	-0.9388|-0.9388	4|4	.|.	.|.	.|.	-26.7084|-26.7084	3.9267|3.9267	0.09267|0.09267	0.206:0.1058:0.1231:0.5652|0.206:0.1058:0.1231:0.5652	.|.	.|.	.|.	.|.	R|Q	55|9	.|.	.|.	G|R	-|-	1|2	0|0	SORBS2|SORBS2	186810811|186810811	0.003000|0.003000	0.15002|0.15002	0.047000|0.047000	0.18901|0.18901	0.189000|0.189000	0.23516|0.23516	-1.527000|-1.527000	0.02227|0.02227	-3.174000|-3.174000	0.00224|0.00224	-0.819000|-0.819000	0.03115|0.03115	GGA|CGG	C|0.984;T|0.016	0.016	strong		0.483	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	Silent
TCEAL3	85012	hgsc.bcm.edu	37	X	102864251	102864251	+	Missense_Mutation	SNP	C	C	G	rs12009847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102864251C>G	ENST00000372628.1	+	3	617	c.259C>G	c.(259-261)Cag>Gag	p.Q87E	TCEAL3_ENST00000477014.1_Intron|TCEAL3_ENST00000243286.3_Missense_Mutation_p.Q87E|TCEAL3_ENST00000372627.5_Missense_Mutation_p.Q87E			Q969E4	TCAL3_HUMAN	transcription elongation factor A (SII)-like 3	87			Q -> E (in dbSNP:rs12009847).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	16						GCCAGCCTCCCAGGCAAAGCC	0.617													C|||	235	0.0622517	0.1679	0.0173	3775	,	,		11795	0.0		0.001	False		,,,				2504	0.0				p.Q87E		Atlas-SNP	.											.	TCEAL3	24	.	0			c.C259G						PASS	.	C	GLU/GLN,GLU/GLN	702,3133		56,485,105,1091,466	97.0	92.0	94.0		259,259	2.3	0.2	X	dbSNP_120	94	6,6722		0,5,1,2423,1871	no	missense,missense	TCEAL3	NM_001006933.1,NM_032926.2	29,29	56,490,106,3514,2337	GG,GC,G,CC,C		0.0892,18.3051,6.7026	benign,benign	87/201,87/201	102864251	708,9855	2203	4300	6503	SO:0001583	missense	85012	exon3			GCCTCCCAGGCAA	BC008703	CCDS14511.1	Xq22.2	2014-03-21			ENSG00000196507	ENSG00000196507			28247	protein-coding gene	gene with protein product						16221301	Standard	NM_032926		Approved	MGC15737, WEX8	uc004ekr.3	Q969E4	OTTHUMG00000022106	ENST00000372628.1:c.259C>G	X.37:g.102864251C>G	ENSP00000361711:p.Gln87Glu	Somatic	379	1	0.00263852		WXS	Illumina HiSeq	Phase_I	389	379	0.974293	NM_001006933	D3DXA4	Missense_Mutation	SNP	ENST00000372628.1	37	CCDS14511.1	84	0.05063291139240506	50	0.11682242990654206	2	0.0055248618784530384	0	0.0	0	0.0	C	0.004	-2.241804	0.00274	0.183051	8.92E-4	ENSG00000196507	ENST00000372628;ENST00000372627;ENST00000243286	T;T;T	0.21361	2.01;2.01;2.01	4.18	2.34	0.29019	.	0.536654	0.14096	N	0.341716	T	0.00039	0.0001	N	0.16602	0.42	0.80722	P	0.0	B	0.15141	0.012	B	0.12156	0.007	T	0.33085	-0.9882	9	0.02654	T	1	.	10.3974	0.44209	0.0:0.7424:0.2576:0.0	rs12009847;rs12009847	87	Q969E4	TCAL3_HUMAN	E	87	ENSP00000361711:Q87E;ENSP00000361710:Q87E;ENSP00000243286:Q87E	ENSP00000243286:Q87E	Q	+	1	0	TCEAL3	102750907	0.890000	0.30428	0.249000	0.24280	0.183000	0.23260	1.387000	0.34430	0.496000	0.27904	0.538000	0.68166	CAG	C|0.936;G|0.064	0.064	strong		0.617	TCEAL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057737.1	NM_032926	
TYMSOS	494514	hgsc.bcm.edu	37	18	658064	658064	+	Missense_Mutation	SNP	G	G	C	rs2853533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:658064G>C	ENST00000323813.3	-	1	276	c.184C>G	c.(184-186)Cgc>Ggc	p.R62G	TYMS_ENST00000323274.10_Intron|C18orf56_ENST00000585033.1_Missense_Mutation_p.R62G|RP11-806L2.5_ENST00000584679.1_RNA|TYMS_ENST00000323250.5_Intron|TYMS_ENST00000323224.7_Intron	NM_001012716.2	NP_001012734.2	Q8TAI1	TYMOS_HUMAN		62			R -> G (in dbSNP:rs2853533). {ECO:0000269|PubMed:15489334}.														TCAATCCTGCGAGGGAGGGGA	0.687													G|||	1698	0.339058	0.3759	0.2176	5008	,	,		13130	0.5476		0.1451	False		,,,				2504	0.3599				p.R62G		Atlas-SNP	.											.	C18orf56	2	.	0			c.C184G						PASS	.	G	GLY/ARG,	1508,2866		292,924,971	12.0	10.0	11.0		184,	1.7	0.0	18	dbSNP_100	11	1107,7425		85,937,3244	yes	missense,intron	TYMS,C18orf56	NM_001012716.2,NM_001071.2	125,	377,1861,4215	CC,CG,GG		12.9747,34.4765,20.2619	probably-damaging,	62/124,	658064	2615,10291	2187	4266	6453	SO:0001583	missense	494514	exon1			TCCTGCGAGGGAG																												ENST00000323813.3:c.184C>G	18.37:g.658064G>C	ENSP00000316465:p.Arg62Gly	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_001012716	A8K1S1	Missense_Mutation	SNP	ENST00000323813.3	37		661	0.30265567765567764	172	0.34959349593495936	70	0.19337016574585636	310	0.541958041958042	109	0.1437994722955145	G	8.524	0.869385	0.17322	0.344765	0.129747	ENSG00000176912	ENST00000323813	T	0.55930	0.49	2.65	1.7	0.24286	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.51233	P	8.399999999997299E-5	D	0.56035	0.974	P	0.51833	0.681	T	0.44221	-0.9342	8	0.87932	D	0	.	8.0251	0.30431	0.0:0.0:0.7558:0.2441	rs2853533;rs3087618;rs17852517;rs58594590;rs2853533	62	Q8TAI1	CR056_HUMAN	G	62	ENSP00000316465:R62G	ENSP00000316465:R62G	R	-	1	0	C18orf56	648064	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.132000	0.15891	0.615000	0.30124	0.555000	0.69702	CGC	G|0.684;C|0.316	0.316	strong		0.687	C18orf56-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000441199.2		
AJUBA	84962	hgsc.bcm.edu	37	14	23444247	23444247	+	Silent	SNP	G	G	A	rs10130692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23444247G>A	ENST00000262713.2	-	5	1681	c.1306C>T	c.(1306-1308)Ctg>Ttg	p.L436L	AJUBA_ENST00000397388.3_Silent_p.L19L|AJUBA_ENST00000361265.4_Silent_p.L436L|RP11-298I3.5_ENST00000555074.1_Intron	NM_032876.4	NP_116265.1	Q96IF1	AJUBA_HUMAN	ajuba LIM protein	436	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				calcium-dependent cell-cell adhesion (GO:0016339)|cellular protein localization (GO:0034613)|focal adhesion assembly (GO:0048041)|G2/M transition of mitotic cell cycle (GO:0000086)|gene silencing by miRNA (GO:0035195)|glycerophospholipid biosynthetic process (GO:0046474)|lamellipodium assembly (GO:0030032)|mitotic cell cycle (GO:0000278)|negative regulation of hippo signaling (GO:0035331)|negative regulation of kinase activity (GO:0033673)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular biosynthetic process (GO:0031328)|positive regulation of gene silencing by miRNA (GO:2000637)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein complex assembly (GO:0031334)|regulation of cell migration (GO:0030334)|regulation of cellular response to hypoxia (GO:1900037)|regulation of GTPase activity (GO:0043087)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|wound healing, spreading of epidermal cells (GO:0035313)	cell-cell junction (GO:0005911)|cytoplasmic mRNA processing body (GO:0000932)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcription factor complex (GO:0005667)	alpha-catenin binding (GO:0045294)|chromatin binding (GO:0003682)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)										ATGCCATCCAGGCACTTGTTG	0.522													G|||	201	0.0401358	0.1452	0.0101	5008	,	,		22256	0.0		0.002	False		,,,				2504	0.0				p.L436L		Atlas-SNP	.											.	.	.	.	0			c.C1306T						PASS	.	G	,	552,3854	248.7+/-256.4	46,460,1697	150.0	138.0	142.0		1306,55	4.1	1.0	14	dbSNP_119	142	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous,coding-synonymous	JUB	NM_032876.4,NM_198086.1	,	46,473,5984	AA,AG,GG		0.1512,12.5284,4.3441	,	436/539,19/122	23444247	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	84962	exon5			CATCCAGGCACTT	AK025567	CCDS9581.1, CCDS9582.1	14q11.2	2011-11-10	2011-11-10	2011-11-10	ENSG00000129474	ENSG00000129474			20250	protein-coding gene	gene with protein product		609066	"""jub, ajuba homolog (Xenopus laevis)"""	JUB		10330178	Standard	NM_032876		Approved	MGC15563	uc001whz.3	Q96IF1	OTTHUMG00000028711	ENST00000262713.2:c.1306C>T	14.37:g.23444247G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	81	49	0.604938	NM_032876	A8MX18|D3DS37	Silent	SNP	ENST00000262713.2	37	CCDS9581.1																																																																																			G|0.955;A|0.045	0.045	strong		0.522	AJUBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071685.2		
OR5L1	219437	hgsc.bcm.edu	37	11	55579182	55579182	+	Silent	SNP	A	A	G	rs139708815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55579182A>G	ENST00000333973.2	+	1	329	c.240A>G	c.(238-240)aaA>aaG	p.K80K		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, 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)	p.K80K(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TTGTGCCAAAAATGTTGGCTA	0.458																																					p.K80K		Atlas-SNP	.											OR5L1,NS,carcinoma,0,3	OR5L1	145	3	1	Substitution - coding silent(1)	pancreas(1)	c.A240G						PASS	.						234.0	216.0	222.0					11																	55579182		2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			GCCAAAAATGTTG	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.240A>G	11.37:g.55579182A>G		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	204	12	0.0588235	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			A|1.000;G|0.000	0.000	strong		0.458	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
CCNJL	79616	hgsc.bcm.edu	37	5	159707731	159707731	+	Silent	SNP	G	G	A	rs76732875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:159707731G>A	ENST00000393977.3	-	3	366	c.81C>T	c.(79-81)ccC>ccT	p.P27P	CCNJL_ENST00000505287.2_Silent_p.P72P|CCNJL_ENST00000377503.2_5'UTR|CCNJL_ENST00000257536.7_Silent_p.P27P|CCNJL_ENST00000519673.1_Silent_p.P27P|CCNJL_ENST00000541762.1_Silent_p.P26P	NM_024565.5	NP_078841.3	Q8IV13	CCNJL_HUMAN	cyclin J-like	27	Cyclin N-terminal.					nucleus (GO:0005634)				endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17	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)			CTCGGAAGGTGGGCAGCTTCA	0.672													G|||	255	0.0509185	0.1755	0.0303	5008	,	,		12548	0.0		0.002	False		,,,				2504	0.0				p.P27P		Atlas-SNP	.											.	CCNJL	36	.	0			c.C81T						PASS	.	G		625,3493		47,531,1481	20.0	27.0	25.0		81	-1.0	0.2	5	dbSNP_131	25	8,8342		0,8,4167	no	coding-synonymous	CCNJL	NM_024565.5		47,539,5648	AA,AG,GG		0.0958,15.1773,5.077		27/436	159707731	633,11835	2059	4175	6234	SO:0001819	synonymous_variant	79616	exon3			GAAGGTGGGCAGC	BC013353	CCDS4350.2	5q33.3	2008-10-31			ENSG00000135083	ENSG00000135083			25876	protein-coding gene	gene with protein product						12477932	Standard	XM_005265982		Approved	FLJ14166	uc003lyb.1	Q8IV13	OTTHUMG00000130325	ENST00000393977.3:c.81C>T	5.37:g.159707731G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_024565	Q6ZN43|Q9H7W8	Silent	SNP	ENST00000393977.3	37	CCDS4350.2																																																																																			G|0.959;A|0.041	0.041	strong		0.672	CCNJL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252674.1	NM_024565	
PSG2	5670	hgsc.bcm.edu	37	19	43585122	43585122	+	Missense_Mutation	SNP	C	C	T	rs143255979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43585122C>T	ENST00000406487.1	-	2	439	c.341G>A	c.(340-342)cGg>cAg	p.R114Q	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	114	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				TGCGTCCTCCCGGGTGACATT	0.443													C|||	222	0.0443291	0.0514	0.0043	5008	,	,		22221	0.0952		0.0	False		,,,				2504	0.0562				p.R114Q		Atlas-SNP	.											.	PSG2	84	.	0			c.G341A						PASS	.	C	GLN/ARG	209,4195		13,183,2006	102.0	104.0	103.0		341	-1.1	0.0	19	dbSNP_134	103	18,8536		0,18,4259	no	missense	PSG2	NM_031246.3	43	13,201,6265	TT,TC,CC		0.2104,4.7457,1.7518		114/336	43585122	227,12731	2202	4277	6479	SO:0001583	missense	5670	exon2			TCCTCCCGGGTGA		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.341G>A	19.37:g.43585122C>T	ENSP00000385706:p.Arg114Gln	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	308	160	0.519481	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	73	0.033424908424908424	22	0.044715447154471545	1	0.0027624309392265192	50	0.08741258741258741	0	0.0	N	0.008	-1.862315	0.00552	0.047457	0.002104	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.65732	-0.17	0.569	-1.14	0.09741	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00784	0.0026	N	0.01464	-0.85	0.09310	N	1	B;B	0.15473	0.013;0.003	B;B	0.11329	0.006;0.006	T	0.02081	-1.1217	8	0.06494	T	0.89	.	.	.	.	.	114;114	B5MCM8;P11465	.;PSG2_HUMAN	Q	114	ENSP00000385706:R114Q	ENSP00000332984:R114Q	R	-	2	0	PSG2	48276962	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	-1.551000	0.02178	-1.764000	0.01305	-1.109000	0.02080	CGG	C|0.978;T|0.022	0.022	strong		0.443	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
HLTF	6596	hgsc.bcm.edu	37	3	148768130	148768130	+	Silent	SNP	T	T	C	rs16861365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148768130T>C	ENST00000310053.5	-	15	1699	c.1506A>G	c.(1504-1506)gtA>gtG	p.V502V	HLTF_ENST00000392912.2_Silent_p.V502V|HLTF_ENST00000494055.1_Silent_p.V502V|HLTF_ENST00000465259.1_Silent_p.V501V	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	502	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AATTCAAGTGTACATCTGATT	0.289													T|||	149	0.0297524	0.1097	0.0043	5008	,	,		15001	0.0		0.001	False		,,,				2504	0.0				p.V502V		Atlas-SNP	.											.	HLTF	87	.	0			c.A1506G						PASS	.	T	,	443,3959	207.5+/-228.8	25,393,1783	64.0	66.0	65.0		1506,1506	1.6	1.0	3	dbSNP_123	65	6,8578	4.3+/-15.6	0,6,4286	no	coding-synonymous,coding-synonymous	HLTF	NM_003071.3,NM_139048.2	,	25,399,6069	CC,CT,TT		0.0699,10.0636,3.4576	,	502/1010,502/1010	148768130	449,12537	2201	4292	6493	SO:0001819	synonymous_variant	6596	exon15			CAAGTGTACATCT	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.1506A>G	3.37:g.148768130T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	161	84	0.521739	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Silent	SNP	ENST00000310053.5	37	CCDS33875.1																																																																																			T|0.956;C|0.044	0.044	strong		0.289	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
TRIM36	55521	hgsc.bcm.edu	37	5	114482847	114482847	+	Silent	SNP	T	T	C	rs12109197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:114482847T>C	ENST00000282369.3	-	3	664	c.543A>G	c.(541-543)gaA>gaG	p.E181E	TRIM36-IT1_ENST00000503723.1_RNA|TRIM36_ENST00000513154.1_Silent_p.E169E|TRIM36_ENST00000514154.1_Silent_p.E26E|TRIM36_ENST00000515104.1_5'UTR	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	181					acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		TTTTGAAGCATTCATTGCAGT	0.418													T|||	13	0.00259585	0.0098	0.0	5008	,	,		20229	0.0		0.0	False		,,,				2504	0.0				p.E181E		Atlas-SNP	.											.	TRIM36	126	.	0			c.A543G						PASS	.	T		20,4384	27.2+/-55.0	0,20,2182	144.0	141.0	142.0		543	-5.5	0.5	5	dbSNP_120	142	0,8600		0,0,4300	no	coding-synonymous	TRIM36	NM_018700.3		0,20,6482	CC,CT,TT		0.0,0.4541,0.1538		181/729	114482847	20,12984	2202	4300	6502	SO:0001819	synonymous_variant	55521	exon3			GAAGCATTCATTG	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16280	protein-coding gene	gene with protein product	"""zinc-binding protein Rbcc728"", ""tripartite motif protein 36"", ""RING finger protein 98"""	609317	"""tripartite motif-containing 36"""			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.543A>G	5.37:g.114482847T>C		Somatic	466	1	0.00214592		WXS	Illumina HiSeq	Phase_I	459	209	0.455338	NM_018700	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Silent	SNP	ENST00000282369.3	37	CCDS4115.1																																																																																			T|0.998;C|0.002	0.002	strong		0.418	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700	
DLAT	1737	hgsc.bcm.edu	37	11	111908137	111908137	+	Missense_Mutation	SNP	G	G	A	rs116125936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:111908137G>A	ENST00000280346.6	+	6	1587	c.928G>A	c.(928-930)Gaa>Aaa	p.E310K	DLAT_ENST00000537636.1_Missense_Mutation_p.E81K|DLAT_ENST00000393051.1_Intron	NM_001931.4	NP_001922.2	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase	310					cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue acetyltransferase activity (GO:0004742)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)	22		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)		TAGGCCAACCGAAGTAACAGA	0.448													G|||	24	0.00479233	0.0166	0.0029	5008	,	,		19194	0.0		0.0	False		,,,				2504	0.0				p.E310K		Atlas-SNP	.											.	DLAT	39	.	0			c.G928A						PASS	.	G	LYS/GLU	97,4305	78.3+/-116.7	0,97,2104	75.0	75.0	75.0		928	6.1	1.0	11	dbSNP_132	75	0,8594		0,0,4297	yes	missense	DLAT	NM_001931.4	56	0,97,6401	AA,AG,GG		0.0,2.2035,0.7464	benign	310/648	111908137	97,12899	2201	4297	6498	SO:0001583	missense	1737	exon6			CCAACCGAAGTAA	Y00978	CCDS8354.1	11q23.1	2008-02-05	2008-02-04		ENSG00000150768	ENSG00000150768	2.3.1.12		2896	protein-coding gene	gene with protein product	"""E2 component of pyruvate dehydrogenase complex"""	608770		DLTA		8102256	Standard	NM_001931		Approved	PDC-E2	uc001pmo.3	P10515	OTTHUMG00000133751	ENST00000280346.6:c.928G>A	11.37:g.111908137G>A	ENSP00000280346:p.Glu310Lys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	64	21	0.328125	NM_001931	Q16783|Q53EP3	Missense_Mutation	SNP	ENST00000280346.6	37	CCDS8354.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	15.75	2.925111	0.52759	0.022035	0.0	ENSG00000150768	ENST00000280346;ENST00000531306;ENST00000537636	T;T;T	0.21932	1.98;1.98;1.98	6.07	6.07	0.98685	Single hybrid motif (1);	0.512867	0.20290	N	0.095276	T	0.08179	0.0204	N	0.19112	0.55	0.40612	D	0.981685	B;B	0.21520	0.057;0.057	B;B	0.19148	0.024;0.024	T	0.16335	-1.0406	10	0.12103	T	0.63	-12.1494	20.6525	0.99598	0.0:0.0:1.0:0.0	.	310;310	Q86YI5;P10515	.;ODP2_HUMAN	K	310;142;81	ENSP00000280346:E310K;ENSP00000433432:E142K;ENSP00000442427:E81K	ENSP00000280346:E310K	E	+	1	0	DLAT	111413347	1.000000	0.71417	0.990000	0.47175	0.975000	0.68041	9.458000	0.97634	2.890000	0.99128	0.585000	0.79938	GAA	G|0.992;A|0.008	0.008	strong		0.448	DLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258167.1	NM_001931	
DTNBP1	84062	hgsc.bcm.edu	37	6	15533469	15533469	+	Splice_Site	SNP	G	G	A	rs61739410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:15533469G>A	ENST00000344537.5	-	8	840		c.e8+1		DTNBP1_ENST00000355917.3_Splice_Site|DTNBP1_ENST00000338950.5_Splice_Site|DTNBP1_ENST00000462989.2_Splice_Site	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1						actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			GCCCCCACTCGCCTCGCCGCT	0.627									Hermansky-Pudlak syndrome				G|||	140	0.0279553	0.0991	0.0086	5008	,	,		13972	0.0		0.002	False		,,,				2504	0.001				.		Atlas-SNP	.											.	DTNBP1	56	.	0			c.667+2C>T						PASS	.	G	,	389,4017	194.0+/-219.0	16,357,1830	70.0	61.0	64.0		,	1.8	0.5	6	dbSNP_129	64	6,8594	5.0+/-18.6	0,6,4294	yes	splice-5,splice-5	DTNBP1	NM_032122.4,NM_183040.2	,	16,363,6124	AA,AG,GG		0.0698,8.8289,3.0371	,	,	15533469	395,12611	2203	4300	6503	SO:0001630	splice_region_variant	84062	exon9	Familial Cancer Database	HPS, HPS1-8	CCACTCGCCTCGC	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17328	protein-coding gene	gene with protein product	"""dysbindin-1"", ""biogenesis of lysosomal organelles complex-1, subunit 8"""	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.667+1C>T	6.37:g.15533469G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_032122	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Splice_Site	SNP	ENST00000344537.5	37	CCDS4534.1	35	0.016025641025641024	30	0.06097560975609756	5	0.013812154696132596	0	0.0	0	0.0	G	4.160	0.028237	0.08054	0.088289	6.98E-4	ENSG00000047579	ENST00000344537;ENST00000462989;ENST00000355917;ENST00000397306;ENST00000509674;ENST00000511762;ENST00000338950;ENST00000543749	.	.	.	5.49	1.75	0.24633	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.453	0.32882	0.4003:0.0:0.5997:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DTNBP1	15641448	1.000000	0.71417	0.499000	0.27577	0.023000	0.10783	2.892000	0.48625	0.001000	0.14605	-0.218000	0.12543	.	G|0.969;A|0.031	0.031	strong		0.627	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122	Intron
ATAT1	79969	hgsc.bcm.edu	37	6	30610758	30610758	+	Missense_Mutation	SNP	G	G	T	rs150614928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30610758G>T	ENST00000376485.4	+	10	968	c.938G>T	c.(937-939)gGg>gTg	p.G313V	ATAT1_ENST00000376483.4_Missense_Mutation_p.G313V|ATAT1_ENST00000468713.1_Intron|ATAT1_ENST00000329992.8_Missense_Mutation_p.G313V|ATAT1_ENST00000318999.7_Missense_Mutation_p.G290V|ATAT1_ENST00000376478.2_Missense_Mutation_p.G290V|ATAT1_ENST00000319027.5_Missense_Mutation_p.G290V|ATAT1_ENST00000330083.5_Missense_Mutation_p.G301V					alpha tubulin acetyltransferase 1											cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	9						GCTGACCCTGGGGGCAGCCCA	0.602													G|||	72	0.014377	0.028	0.0144	5008	,	,		11232	0.003		0.008	False		,,,				2504	0.0143				p.G313V		Atlas-SNP	.											.	ATAT1	30	.	0			c.G938T						PASS	.	G	VAL/GLY,VAL/GLY,VAL/GLY	112,4294		0,112,2091	82.0	79.0	80.0		902,833,938	5.2	1.0	6	dbSNP_134	80	58,8542		2,54,4244	yes	missense,missense,missense	ATAT1	NM_001031722.2,NM_001190724.1,NM_024909.2	109,109,109	2,166,6335	TT,TG,GG		0.6744,2.542,1.3071	probably-damaging,probably-damaging,probably-damaging	301/410,278/289,313/334	30610758	170,12836	2203	4300	6503	SO:0001583	missense	79969	exon10			ACCCTGGGGGCAG	AK023220	CCDS4683.2, CCDS54978.1, CCDS59002.1	6p21.32	2014-06-17	2010-10-11	2010-10-11	ENSG00000137343	ENSG00000137343	2.3.1.108		21186	protein-coding gene	gene with protein product	"""alpha-tubulin N-acetyltransferase"""	615556	"""chromosome 6 open reading frame 134"""	C6orf134		20829795	Standard	NM_024909		Approved	FLJ13158, Em:AB023049.7, MEC17	uc003nqv.3	Q5SQI0	OTTHUMG00000031219	ENST00000376485.4:c.938G>T	6.37:g.30610758G>T	ENSP00000365668:p.Gly313Val	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	129	74	0.573643	NM_024909		Missense_Mutation	SNP	ENST00000376485.4	37		25	0.011446886446886446	17	0.034552845528455285	4	0.011049723756906077	2	0.0034965034965034965	2	0.002638522427440633	G	17.04	3.287865	0.59976	0.02542	0.006744	ENSG00000137343	ENST00000318999;ENST00000376485;ENST00000376478;ENST00000319027;ENST00000376483;ENST00000329992;ENST00000330083	.	.	.	5.16	5.16	0.70880	.	0.099255	0.43919	D	0.000512	T	0.45657	0.1353	L	0.54323	1.7	0.54753	D	0.999987	P;B;B;B;P;P	0.48640	0.913;0.409;0.208;0.156;0.719;0.719	B;B;B;B;B;B	0.44085	0.424;0.312;0.276;0.146;0.319;0.44	T	0.41574	-0.9501	9	0.32370	T	0.25	-15.2948	15.929	0.79646	0.0:0.0:1.0:0.0	.	278;290;301;313;290;313	B7Z4Q7;Q5SQI0-3;Q5SQI0-2;Q5SQI0;Q5SQI0-6;Q5SQI0-4	.;.;.;ATAT_HUMAN;.;.	V	290;313;290;290;313;313;301	.	ENSP00000324222:G290V	G	+	2	0	ATAT1	30718737	0.999000	0.42202	1.000000	0.80357	0.949000	0.60115	3.481000	0.53179	2.565000	0.86533	0.609000	0.83330	GGG	G|0.988;T|0.012	0.012	strong		0.602	ATAT1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076449.2	NM_024909	
MRPL47	57129	hgsc.bcm.edu	37	3	179306775	179306775	+	Missense_Mutation	SNP	C	C	T	rs10513762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:179306775C>T	ENST00000476781.1	-	7	667	c.638G>A	c.(637-639)cGt>cAt	p.R213H	MRPL47_ENST00000392659.2_Missense_Mutation_p.R103H|MRPL47_ENST00000259038.2_Missense_Mutation_p.R193H	NM_020409.2	NP_065142.2	Q9HD33	RM47_HUMAN	mitochondrial ribosomal protein L47	213			R -> H (in dbSNP:rs10513762).		translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)	p.R213H(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|stomach(1)	11	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			TCGTTTCTCACGTTCCAGTCT	0.318													C|||	600	0.119808	0.1051	0.147	5008	,	,		17645	0.1002		0.0795	False		,,,				2504	0.182				p.R213H		Atlas-SNP	.											MRPL47,NS,carcinoma,0,1	MRPL47	31	1	1	Substitution - Missense(1)	stomach(1)	c.G638A						PASS	.	C	HIS/ARG,HIS/ARG	406,4000	194.3+/-219.2	18,370,1815	46.0	49.0	48.0		638,308	-2.0	0.1	3	dbSNP_119	48	670,7930	166.5+/-218.5	24,622,3654	yes	missense,missense	MRPL47	NM_020409.2,NM_177988.1	29,29	42,992,5469	TT,TC,CC		7.7907,9.2147,8.2731	possibly-damaging,possibly-damaging	213/251,103/141	179306775	1076,11930	2203	4300	6503	SO:0001583	missense	57129	exon7			TTCTCACGTTCCA	AF285120	CCDS3232.1, CCDS3233.1	3q26.33	2012-11-14			ENSG00000136522	ENSG00000136522		"""Mitochondrial ribosomal proteins / large subunits"""	16652	protein-coding gene	gene with protein product	"""nasopharyngeal carcinoma metastasis-related 1"""	611852				11551941	Standard	NM_177988		Approved	CGI-204, NCM1	uc003fjz.3	Q9HD33	OTTHUMG00000157784	ENST00000476781.1:c.638G>A	3.37:g.179306775C>T	ENSP00000417602:p.Arg213His	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_020409	Q6XRG1|Q8N5D1	Missense_Mutation	SNP	ENST00000476781.1	37	CCDS3232.1	228	0.1043956043956044	58	0.11788617886178862	52	0.143646408839779	60	0.1048951048951049	58	0.07651715039577836	C	3.395	-0.123521	0.06795	0.092147	0.077907	ENSG00000136522	ENST00000476781;ENST00000259038;ENST00000392659	T;T;T	0.47528	1.42;1.43;0.84	5.56	-2.01	0.07410	.	0.746757	0.13039	N	0.418706	T	0.00210	0.0006	N	0.24115	0.695	0.80722	P	0.0	D;D	0.55385	0.971;0.966	B;B	0.43575	0.424;0.346	T	0.06356	-1.0831	9	0.44086	T	0.13	0.8899	4.3523	0.11162	0.4385:0.3685:0.0635:0.1296	rs10513762;rs11553296;rs59617374;rs10513762	193;213	Q9HD33-2;Q9HD33	.;RM47_HUMAN	H	213;193;103	ENSP00000417602:R213H;ENSP00000259038:R193H;ENSP00000376427:R103H	ENSP00000259038:R193H	R	-	2	0	MRPL47	180789469	0.551000	0.26497	0.066000	0.19879	0.080000	0.17528	1.085000	0.30840	-0.508000	0.06540	-0.469000	0.05056	CGT	C|0.903;T|0.097	0.097	strong		0.318	MRPL47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349623.1	NM_020409	
ERICH3	127254	hgsc.bcm.edu	37	1	75038963	75038963	+	Missense_Mutation	SNP	C	C	A	rs75061423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:75038963C>A	ENST00000326665.5	-	14	2649	c.2431G>T	c.(2431-2433)Gcg>Tcg	p.A811S	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		811	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						GGCTTCCACGCCCTCAAGGGA	0.557													c|||	122	0.024361	0.0908	0.0029	5008	,	,		17211	0.0		0.0	False		,,,				2504	0.0				p.A811S		Atlas-SNP	.											.	C1orf173	380	.	0			c.G2431T						PASS	.	C	SER/ALA	345,4061	181.2+/-209.3	12,321,1870	91.0	88.0	89.0		2431	2.6	0.0	1	dbSNP_131	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C1orf173	NM_001002912.4	99	12,322,6169	AA,AC,CC		0.0116,7.8302,2.6603	benign	811/1531	75038963	346,12660	2203	4300	6503	SO:0001583	missense	127254	exon14			TCCACGCCCTCAA																												ENST00000326665.5:c.2431G>T	1.37:g.75038963C>A	ENSP00000322609:p.Ala811Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	126	60	0.47619	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	C	12.22	1.873823	0.33069	0.078302	1.16E-4	ENSG00000178965	ENST00000326665	T	0.11604	2.76	5.54	2.6	0.31112	.	.	.	.	.	T	0.01870	0.0059	N	0.22421	0.69	0.09310	N	1	B	0.15719	0.014	B	0.15870	0.014	T	0.47686	-0.9098	9	0.15952	T	0.53	-1.3011	7.1998	0.25874	0.0:0.5789:0.2768:0.1442	.	811	Q5RHP9	CA173_HUMAN	S	811	ENSP00000322609:A811S	ENSP00000322609:A811S	A	-	1	0	C1orf173	74811551	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-0.211000	0.09332	0.701000	0.31803	0.561000	0.74099	GCG	A|0.022;C|0.978	0.022	strong		0.557	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
PACS2	23241	hgsc.bcm.edu	37	14	105848891	105848891	+	Silent	SNP	T	T	C	rs4076933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105848891T>C	ENST00000325438.8	+	14	1983	c.1479T>C	c.(1477-1479)ctT>ctC	p.L493L	PACS2_ENST00000551743.1_5'Flank|PACS2_ENST00000547217.1_Silent_p.L463L|PACS2_ENST00000458164.2_Silent_p.L497L|PACS2_ENST00000430725.2_Silent_p.L418L|PACS2_ENST00000447393.1_Silent_p.L497L			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	493			L -> S (in dbSNP:rs4076933).		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)		ACATCATCCTTGTCAACACCT	0.582													C|||	684	0.136581	0.4849	0.0202	5008	,	,		20860	0.0179		0.0	False		,,,				2504	0.0112				p.L497L		Atlas-SNP	.											.	PACS2	75	.	0			c.T1491C						PASS	.	C	,	1758,2648	645.5+/-398.2	360,1038,805	233.0	188.0	203.0		1491,1479	-9.1	0.0	14	dbSNP_108	203	14,8586	818.6+/-406.8	0,14,4286	no	coding-synonymous,coding-synonymous	PACS2	NM_001100913.2,NM_015197.3	,	360,1052,5091	CC,CT,TT		0.1628,39.9001,13.6245	,	497/894,493/890	105848891	1772,11234	2203	4300	6503	SO:0001819	synonymous_variant	23241	exon14			CATCCTTGTCAAC	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.1479T>C	14.37:g.105848891T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Silent	SNP	ENST00000325438.8	37	CCDS32168.1																																																																																			T|0.861;C|0.139	0.139	strong		0.582	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355	
ITGAV	3685	hgsc.bcm.edu	37	2	187490232	187490232	+	Silent	SNP	G	G	A	rs114767222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:187490232G>A	ENST00000261023.3	+	4	715	c.441G>A	c.(439-441)gaG>gaA	p.E147E	ITGAV_ENST00000433736.2_Silent_p.E101E|ITGAV_ENST00000374907.3_Silent_p.E147E	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	147					angiogenesis (GO:0001525)|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)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|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)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|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 alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	GGAGAACTGAGATGAAACAGG	0.403													G|||	50	0.00998403	0.034	0.0072	5008	,	,		17909	0.0		0.0	False		,,,				2504	0.0				p.E147E	Melanoma(58;108 1995 6081)	Atlas-SNP	.											.	ITGAV	124	.	0			c.G441A						PASS	.	G	,,	118,4288	88.7+/-127.4	2,114,2087	126.0	115.0	118.0		303,441,441	0.5	0.3	2	dbSNP_132	118	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGAV	NM_001144999.1,NM_001145000.1,NM_002210.3	,,	2,114,6387	AA,AG,GG		0.0,2.6782,0.9073	,,	101/1003,147/1013,147/1049	187490232	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	3685	exon4			AACTGAGATGAAA		CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"""CD molecules"", ""Integrins"""	6150	protein-coding gene	gene with protein product		193210	"""antigen identified by monoclonal antibody L230"", ""vitronectin receptor"", ""integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"""	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.441G>A	2.37:g.187490232G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_001145000	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Silent	SNP	ENST00000261023.3	37	CCDS2292.1																																																																																			G|0.992;A|0.008	0.008	strong		0.403	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210	
HTR2A	3356	hgsc.bcm.edu	37	13	47469940	47469940	+	Silent	SNP	G	G	A	rs6313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:47469940G>A	ENST00000378688.4	-	1	233	c.102C>T	c.(100-102)tcC>tcT	p.S34S	HTR2A_ENST00000543956.1_Intron|HTR2A_ENST00000542664.1_Silent_p.S34S			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	34					activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TAGCTTCTCCGGAGTTAAAGT	0.428													G|||	2210	0.441294	0.3926	0.3545	5008	,	,		21005	0.5883		0.4364	False		,,,				2504	0.4223				p.S34S		Atlas-SNP	.											.	HTR2A	98	.	0			c.C102T	GRCh37	CM960851	HTR2A	M	rs6313	PASS	.	G	,	1684,2722	510.3+/-367.5	310,1064,829	101.0	99.0	99.0		102,	-7.6	0.0	13	dbSNP_52	99	3527,5073	514.9+/-378.5	748,2031,1521	no	coding-synonymous,intron	HTR2A	NM_000621.3,NM_001165947.1	,	1058,3095,2350	AA,AG,GG		41.0116,38.2206,40.0661	,	34/472,	47469940	5211,7795	2203	4300	6503	SO:0001819	synonymous_variant	3356	exon2			TTCTCCGGAGTTA	X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5293	protein-coding gene	gene with protein product		182135	"""5-hydroxytryptamine (serotonin) receptor 2A"""	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.102C>T	13.37:g.47469940G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_000621	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Silent	SNP	ENST00000378688.4	37	CCDS9405.1																																																																																			G|0.581;A|0.419	0.419	strong		0.428	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621	
MAGEB10	139422	hgsc.bcm.edu	37	X	27839572	27839572	+	Missense_Mutation	SNP	T	T	C	rs1368769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:27839572T>C	ENST00000356790.2	+	3	394	c.149T>C	c.(148-150)tTc>tCc	p.F50S		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	50			F -> S (in dbSNP:rs1368769). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						AAGGATGTTTTCCAGAGTTCA	0.517													C|||	1304	0.34543	0.3775	0.2248	3775	,	,		13537	0.0645		0.3827	False		,,,				2504	0.2035				p.F50S		Atlas-SNP	.											.	MAGEB10	107	.	0			c.T149C						PASS	.	C	SER/PHE	1913,1920		398,834,283,399,288	57.0	49.0	52.0		149	1.5	0.0	X	dbSNP_88	52	3580,3148		693,1196,998,539,874	yes	missense	MAGEB10	NM_182506.3	155	1091,2030,1281,938,1162	CC,CT,C,TT,T		46.7895,49.9087,47.9879	benign	50/348	27839572	5493,5068	2202	4300	6502	SO:0001583	missense	139422	exon3			ATGTTTTCCAGAG		CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.149T>C	X.37:g.27839572T>C	ENSP00000368304:p.Phe50Ser	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	126	51	0.404762	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Missense_Mutation	SNP	ENST00000356790.2	37	CCDS35221.1	604	0.3640747438215793	137	0.3549222797927461	64	0.2119205298013245	25	0.04562043795620438	199	0.33728813559322035	C	0.077	-1.191488	0.01607	0.499087	0.532105	ENSG00000177689	ENST00000356790	T	0.04156	3.69	2.37	1.45	0.22620	Melanoma associated antigen, MAGE, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38585	-0.9654	8	0.02654	T	1	.	3.2031	0.06656	0.0:0.524:0.2915:0.1845	rs1368769;rs59237909;rs1368769	50	Q96LZ2	MAGBA_HUMAN	S	50	ENSP00000368304:F50S	ENSP00000368304:F50S	F	+	2	0	MAGEB10	27749493	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.595000	0.05727	0.002000	0.14630	-0.416000	0.06073	TTC	0|0.029;C|0.421	0.421	strong		0.517	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506	
OR4K15	81127	hgsc.bcm.edu	37	14	20444588	20444588	+	Missense_Mutation	SNP	T	T	C	rs2153466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20444588T>C	ENST00000305051.5	+	1	986	c.911T>C	c.(910-912)cTt>cCt	p.L304P		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	304			L -> P (in dbSNP:rs2153466). {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)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATCTTCACGCTTATTTTAAAC	0.408													C|||	1885	0.376398	0.7496	0.2017	5008	,	,		18141	0.1498		0.2435	False		,,,				2504	0.3661				p.L304P		Atlas-SNP	.											.	OR4K15	82	.	0			c.T911C						PASS	.	C	PRO/LEU	3041,1365		1040,961,202	107.0	108.0	108.0		911	4.0	0.7	14	dbSNP_96	108	2424,6176		332,1760,2208	no	missense	OR4K15	NM_001005486.1	98	1372,2721,2410	CC,CT,TT		28.186,30.9805,42.0191	benign	304/349	20444588	5465,7541	2203	4300	6503	SO:0001583	missense	81127	exon1			TCACGCTTATTTT		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.911T>C	14.37:g.20444588T>C	ENSP00000304077:p.Leu304Pro	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	235	235	1	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	696	0.31868131868131866	353	0.717479674796748	70	0.19337016574585636	81	0.14160839160839161	192	0.2532981530343008	.	0.012	-1.649809	0.00785	0.690195	0.28186	ENSG00000169488	ENST00000305051	T	0.30714	1.52	3.99	3.99	0.46301	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	N	0.000110	T	0.00012	0.0000	N	0.08118	0	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40572	-0.9556	9	0.02654	T	1	.	9.6002	0.39598	0.0:0.8945:0.0:0.1055	rs2153466;rs17276905;rs52807813;rs57272158;rs2153466	304	Q8NH41	OR4KF_HUMAN	P	304	ENSP00000304077:L304P	ENSP00000304077:L304P	L	+	2	0	OR4K15	19514428	0.958000	0.32768	0.749000	0.31150	0.194000	0.23727	4.153000	0.58118	0.895000	0.36342	-0.186000	0.12905	CTT	T|0.613;C|0.387	0.387	strong		0.408	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
TECPR1	25851	hgsc.bcm.edu	37	7	97847040	97847040	+	Silent	SNP	G	G	A	rs2279676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	71	0	0		WXS	Illumina HiSeq	Phase_I	121	66	0.545455	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	
ZNF611	81856	hgsc.bcm.edu	37	19	53209553	53209553	+	Missense_Mutation	SNP	G	G	A	rs4085566|rs34846371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53209553G>A	ENST00000319783.1	-	7	1071	c.755C>T	c.(754-756)cCc>cTc	p.P252L	ZNF611_ENST00000540744.1_Missense_Mutation_p.P252L|ZNF611_ENST00000453741.2_Missense_Mutation_p.P183L|ZNF611_ENST00000543227.1_Missense_Mutation_p.P252L|ZNF611_ENST00000602162.1_Missense_Mutation_p.P183L|ZNF611_ENST00000595798.1_Missense_Mutation_p.P183L|ZNF611_ENST00000602046.1_5'Flank	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	252			P -> I (requires 2 nucleotide substitutions; dbSNP:rs34846371). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.|P -> L (in dbSNP:rs4085566).|P -> T (in dbSNP:rs4085565).		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.P252L(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TCCTAAATGGGGTATCTGGTG	0.378													-|||	2197	0.438698	0.7012	0.3285	5008	,	,		21198	0.3681		0.4105	False		,,,				2504	0.2638				p.P252L		Atlas-SNP	.											ZNF611,NS,carcinoma,0,1	ZNF611	72	1	1	Substitution - Missense(1)	stomach(1)	c.C755T						PASS	.	A	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	2860,1546		1004,852,347	137.0	145.0	142.0		755,755,548,755	1.2	0.0	19	dbSNP_108	142	3194,5400		725,1744,1828	no	missense,missense,missense,missense	ZNF611	NM_001161499.1,NM_001161500.1,NM_001161501.1,NM_030972.3	98,98,98,98	1729,2596,2175	AA,AG,GG		37.1655,35.0885,46.5692	benign,benign,benign,benign	252/706,252/706,183/637,252/706	53209553	6054,6946	2203	4297	6500	SO:0001583	missense	81856	exon7			AAATGGGGTATCT	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.755C>T	19.37:g.53209553G>A	ENSP00000322427:p.Pro252Leu	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	193	107	0.554404	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	940	0.43040293040293043	322	0.6544715447154471	126	0.34806629834254144	215	0.3758741258741259	277	0.3654353562005277	.	5.048	0.194555	0.09599	0.649115	0.371655	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	1.2	1.2	0.21068	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.01729	-0.75	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.25328	-1.0135	8	0.59425	D	0.04	.	2.3777	0.04346	0.5844:0.0:0.1773:0.2382	rs4085566;rs58003344	252	Q8N823	ZN611_HUMAN	L	252;252;183;252	ENSP00000437616:P252L;ENSP00000439211:P252L;ENSP00000443505:P183L;ENSP00000322427:P252L	ENSP00000322427:P252L	P	-	2	0	ZNF611	57901365	0.000000	0.05858	0.025000	0.17156	0.006000	0.05464	-1.050000	0.03510	-0.303000	0.08856	-1.220000	0.01600	CCC	.	.	weak		0.378	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972	
RBCK1	10616	hgsc.bcm.edu	37	20	398175	398175	+	Missense_Mutation	SNP	G	G	C	rs143804674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:398175G>C	ENST00000356286.5	+	3	878	c.173G>C	c.(172-174)tGg>tCg	p.W58S	RBCK1_ENST00000382181.2_5'UTR|RBCK1_ENST00000353660.3_Missense_Mutation_p.W16S	NM_031229.2	NP_112506.2	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing 1	58	Interaction with IRF3.|Interaction with TAB2.|Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				negative regulation of necroptotic process (GO:0060546)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(4)	5		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)				TGCAGGCTGTGGGTGAGCGTG	0.587																																					p.W58S		Atlas-SNP	.											.	RBCK1	38	.	0			c.G173C						PASS	.	G	SER/TRP,SER/TRP	5,4401	9.9+/-24.2	0,5,2198	66.0	55.0	58.0		47,173	4.2	1.0	20	dbSNP_134	58	0,8600		0,0,4300	yes	missense,missense	RBCK1	NM_006462.4,NM_031229.2	177,177	0,5,6498	CC,CG,GG		0.0,0.1135,0.0384	benign,benign	16/469,58/511	398175	5,13001	2203	4300	6503	SO:0001583	missense	10616	exon3			GGCTGTGGGTGAG	U67322	CCDS12998.1, CCDS13000.2	20p13	2014-09-17	2006-06-28	2006-06-28	ENSG00000125826	ENSG00000125826		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, RAN-binding domain containing"""	15864	protein-coding gene	gene with protein product	"""heme-oxidized IRP2 ubiquitin ligase 1"""	610924	"""chromosome 20 open reading frame 18"""	C20orf18			Standard	NM_031229		Approved	RBCK2, XAP4, RNF54, ZRANB4, UBCE7IP3, HOIL1	uc002wdp.4	Q9BYM8	OTTHUMG00000031634	ENST00000356286.5:c.173G>C	20.37:g.398175G>C	ENSP00000348632:p.Trp58Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	94	54	0.574468	NM_031229	O95623|Q86SL2|Q96BS3|Q9BYM9	Missense_Mutation	SNP	ENST00000356286.5	37	CCDS13000.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.67|14.67	2.605738|2.605738	0.46527|0.46527	0.001135|0.001135	0.0|0.0	ENSG00000125826|ENSG00000125826	ENST00000414880|ENST00000411647;ENST00000356286;ENST00000441733;ENST00000353660;ENST00000400244;ENST00000400243	.|T;T;T;T	.|0.10477	.|2.87;2.87;2.87;2.87	5.12|5.12	4.17|4.17	0.49024|0.49024	.|Ubiquitin supergroup (1);	.|0.578121	.|0.16613	.|N	.|0.206802	T|T	0.09905|0.09905	0.0243|0.0243	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.19817	.|0.002;0.034;0.039	.|B;B;B	.|0.21708	.|0.002;0.036;0.01	T|T	0.08391|0.08391	-1.0724|-1.0724	5|10	.|0.12430	.|T	.|0.62	-21.4854|-21.4854	9.3395|9.3395	0.38071|0.38071	0.0967:0.0:0.9033:0.0|0.0967:0.0:0.9033:0.0	.|.	.|48;16;58	.|B4E0F5;Q9BYM8-3;Q9BYM8	.|.;.;HOIL1_HUMAN	R|S	91|58;58;57;16;58;99	.|ENSP00000415080:W58S;ENSP00000348632:W58S;ENSP00000387799:W57S;ENSP00000254960:W16S	.|ENSP00000254960:W16S	G|W	+|+	1|2	0|0	RBCK1|RBCK1	346175|346175	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.780000|0.780000	0.44128|0.44128	1.134000|1.134000	0.31442|0.31442	1.374000|1.374000	0.46228|0.46228	0.557000|0.557000	0.71058|0.71058	GGG|TGG	G|1.000;C|0.000	0.000	strong		0.587	RBCK1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077461.3	NM_031229	
NPFFR2	10886	hgsc.bcm.edu	37	4	73012709	73012709	+	Missense_Mutation	SNP	T	T	C	rs61733659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:73012709T>C	ENST00000308744.6	+	4	847	c.749T>C	c.(748-750)gTc>gCc	p.V250A	NPFFR2_ENST00000358749.3_Missense_Mutation_p.V148A|NPFFR2_ENST00000506359.1_3'UTR|NPFFR2_ENST00000344413.5_3'UTR|NPFFR2_ENST00000395999.1_Missense_Mutation_p.V151A	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	250					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			CAGTGTGTGGTCTACCCTTTT	0.393													T|||	47	0.00938498	0.0348	0.0014	5008	,	,		18136	0.0		0.0	False		,,,				2504	0.0				p.V250A		Atlas-SNP	.											.	NPFFR2	98	.	0			c.T749C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	122,4284	91.6+/-130.3	5,112,2086	189.0	190.0	190.0		452,749,443	5.8	1.0	4	dbSNP_129	190	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	NPFFR2	NM_001144756.1,NM_004885.2,NM_053036.2	64,64,64	5,114,6384	CC,CT,TT		0.0233,2.769,0.9534	possibly-damaging,possibly-damaging,possibly-damaging	151/424,250/523,148/421	73012709	124,12882	2203	4300	6503	SO:0001583	missense	10886	exon4			GTGTGGTCTACCC	AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"""GPCR / Class A :  Neuropeptide receptors : FF/AF"", ""GPCR / Class A : RF amide peptide receptors"""	4525	protein-coding gene	gene with protein product	"""neuropeptide FF 2"""	607449	"""G protein-coupled receptor 74"""	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.749T>C	4.37:g.73012709T>C	ENSP00000307822:p.Val250Ala	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_004885	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	37	CCDS3551.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	T	17.37	3.371957	0.61624	0.02769	2.33E-4	ENSG00000056291	ENST00000308744;ENST00000395999;ENST00000358749	T;T;T	0.38887	1.11;1.11;1.11	5.81	5.81	0.92471	GPCR, rhodopsin-like superfamily (1);	0.256399	0.27725	N	0.018102	T	0.32133	0.0819	M	0.85299	2.745	0.80722	D	1	P;D	0.55385	0.772;0.971	P;P	0.57057	0.628;0.812	T	0.60662	-0.7219	10	0.87932	D	0	.	15.8328	0.78769	0.0:0.0:0.0:1.0	rs61733659	151;250	Q9Y5X5-3;Q9Y5X5	.;NPFF2_HUMAN	A	250;151;148	ENSP00000307822:V250A;ENSP00000379321:V151A;ENSP00000351599:V148A	ENSP00000307822:V250A	V	+	2	0	NPFFR2	73231573	1.000000	0.71417	0.974000	0.42286	0.178000	0.23041	7.911000	0.87458	2.221000	0.72209	0.528000	0.53228	GTC	T|0.990;C|0.010	0.010	strong		0.393	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885	
SOWAHA	134548	hgsc.bcm.edu	37	5	132150804	132150804	+	Silent	SNP	G	G	A	rs7719416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132150804G>A	ENST00000378693.2	+	1	1772	c.1491G>A	c.(1489-1491)aaG>aaA	p.K497K	AC004775.5_ENST00000607389.1_lincRNA	NM_175873.4	NP_787069.3	Q2M3V2	SWAHA_HUMAN	sosondowah ankyrin repeat domain family member A	497																	GAGGCTTGAAGAAGTCGAGCT	0.587													G|||	151	0.0301518	0.1097	0.0086	5008	,	,		18235	0.0		0.0	False		,,,				2504	0.0				p.K497K		Atlas-SNP	.											.	.	.	.	0			c.G1491A						PASS	.	G		458,3948	214.5+/-233.7	27,404,1772	47.0	50.0	49.0		1491	4.2	1.0	5	dbSNP_116	49	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	ANKRD43	NM_175873.4		27,413,6063	AA,AG,GG		0.1047,10.3949,3.5907		497/550	132150804	467,12539	2203	4300	6503	SO:0001819	synonymous_variant	134548	exon1			CTTGAAGAAGTCG	AK090823	CCDS43361.1	5q23.3	2013-01-10	2012-01-12	2012-01-12	ENSG00000198944	ENSG00000198944		"""Ankyrin repeat domain containing"""	27033	protein-coding gene	gene with protein product			"""ankyrin repeat domain 43"""	ANKRD43		22234889	Standard	NM_175873		Approved		uc003kxw.3	Q2M3V2	OTTHUMG00000059844	ENST00000378693.2:c.1491G>A	5.37:g.132150804G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_175873	Q8NAE7	Silent	SNP	ENST00000378693.2	37	CCDS43361.1																																																																																			G|0.965;A|0.035	0.035	strong		0.587	SOWAHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133062.1	NM_175873	
LRRC36	55282	hgsc.bcm.edu	37	16	67409180	67409180	+	Missense_Mutation	SNP	G	G	A	rs8052655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67409180G>A	ENST00000329956.6	+	10	1544	c.1525G>A	c.(1525-1527)Ggt>Agt	p.G509S	LRRC36_ENST00000435835.3_Intron|LRRC36_ENST00000563189.1_Missense_Mutation_p.G388S|LRRC36_ENST00000541146.1_Silent_p.T29T|LRRC36_ENST00000290940.7_Missense_Mutation_p.G241S	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36	509			G -> S (in dbSNP:rs8052655).							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)		TAGTTTGCACGGTTTGGCTGG	0.468													G|||	1036	0.206869	0.6437	0.085	5008	,	,		15268	0.004		0.0408	False		,,,				2504	0.0828				p.G509S		Atlas-SNP	.											.	LRRC36	68	.	0			c.G1525A						PASS	.	G	SER/GLY,SER/GLY	2213,2183	589.4+/-387.1	563,1087,548	184.0	201.0	195.0		1162,1525	5.7	1.0	16	dbSNP_116	195	368,8232	121.7+/-180.7	9,350,3941	yes	missense,missense	LRRC36	NM_001161575.1,NM_018296.5	56,56	572,1437,4489	AA,AG,GG		4.2791,49.6588,19.86	probably-damaging,probably-damaging	388/634,509/755	67409180	2581,10415	2198	4300	6498	SO:0001583	missense	55282	exon10			TTGCACGGTTTGG	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.1525G>A	16.37:g.67409180G>A	ENSP00000329943:p.Gly509Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_018296	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Missense_Mutation	SNP	ENST00000329956.6	37	CCDS32467.1	381	0.17445054945054944	314	0.6382113821138211	34	0.09392265193370165	2	0.0034965034965034965	31	0.040897097625329816	G	25.1	4.603119	0.87157	0.503412	0.042791	ENSG00000159708	ENST00000329956;ENST00000290940	T;T	0.54479	2.95;0.57	5.69	5.69	0.88448	.	0.070932	0.52532	D	0.000063	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	1.0	D;D	0.89917	0.999;1.0	D;D	0.72625	0.92;0.978	T	0.51872	-0.8650	9	0.66056	D	0.02	-13.0546	15.3241	0.74147	0.0:0.0:1.0:0.0	rs8052655;rs52836757;rs8052655	388;509	Q1X8D7-2;Q1X8D7	.;LRC36_HUMAN	S	509;241	ENSP00000329943:G509S;ENSP00000290940:G241S	ENSP00000290940:G241S	G	+	1	0	LRRC36	65966681	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.268000	0.51585	2.699000	0.92147	0.591000	0.81541	GGT	G|0.790;A|0.210	0.210	strong		0.468	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296	
GNAI1	2770	hgsc.bcm.edu	37	7	79828573	79828573	+	Silent	SNP	A	A	G	rs6970347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:79828573A>G	ENST00000351004.3	+	4	709	c.336A>G	c.(334-336)ggA>ggG	p.G112G	GNAI1_ENST00000457358.2_Silent_p.G60G	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	112					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						TGCTAGCTGGAGCTGCTGAAG	0.413													A|||	92	0.0183706	0.0673	0.0043	5008	,	,		18019	0.0		0.0	False		,,,				2504	0.0				p.G112G		Atlas-SNP	.											.	GNAI1	44	.	0			c.A336G						PASS	.	A		284,4122	157.8+/-190.6	14,256,1933	116.0	110.0	112.0		336	-3.0	1.0	7	dbSNP_116	112	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	GNAI1	NM_002069.5		14,258,6231	GG,GA,AA		0.0233,6.4458,2.199		112/355	79828573	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	2770	exon4			AGCTGGAGCTGCT	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"""Gi1 protein alpha subunit"""	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.336A>G	7.37:g.79828573A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Silent	SNP	ENST00000351004.3	37	CCDS5595.1																																																																																			A|0.982;G|0.018	0.018	strong		0.413	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069	
ZC3HAV1L	92092	hgsc.bcm.edu	37	7	138713674	138713674	+	Silent	SNP	C	C	G	rs7800990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:138713674C>G	ENST00000275766.1	-	3	545	c.534G>C	c.(532-534)ctG>ctC	p.L178L		NM_080660.3	NP_542391.2	Q96H79	ZCCHL_HUMAN	zinc finger CCCH-type, antiviral 1-like	178										NS(2)|endometrium(2)|large_intestine(1)|lung(4)|skin(1)	10						AGTAGCCATACAGGGCTTCCC	0.433													G|||	185	0.0369409	0.1354	0.0072	5008	,	,		23164	0.0		0.001	False		,,,				2504	0.0				p.L178L		Atlas-SNP	.											.	ZC3HAV1L	15	.	0			c.G534C						PASS	.	G		554,3852	774.6+/-414.0	28,498,1677	71.0	69.0	70.0		534	-5.1	0.0	7	dbSNP_116	70	4,8596	819.0+/-406.8	0,4,4296	no	coding-synonymous	ZC3HAV1L	NM_080660.3		28,502,5973	GG,GC,CC		0.0465,12.5738,4.2903		178/301	138713674	558,12448	2203	4300	6503	SO:0001819	synonymous_variant	92092	exon3			GCCATACAGGGCT	BC008842	CCDS5850.1	7q34	2006-07-03	2006-07-03	2006-07-03	ENSG00000146858	ENSG00000146858			22423	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 39"""	C7orf39			Standard	NM_080660		Approved	MGC14289	uc003vum.1	Q96H79	OTTHUMG00000157229	ENST00000275766.1:c.534G>C	7.37:g.138713674C>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_080660	Q8WUD9	Silent	SNP	ENST00000275766.1	37	CCDS5850.1																																																																																			C|0.961;G|0.039	0.039	strong		0.433	ZC3HAV1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348090.1	NM_080660	
OR10G9	219870	hgsc.bcm.edu	37	11	123894329	123894329	+	Missense_Mutation	SNP	C	C	G	rs79417294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123894329C>G	ENST00000375024.1	+	1	610	c.610C>G	c.(610-612)Cta>Gta	p.L204V		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L204V(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)		GGACATTGGGCTAGTGGCCTC	0.547													G|||	436	0.0870607	0.1059	0.1556	5008	,	,		21026	0.1438		0.007	False		,,,				2504	0.0368				p.L204V		Atlas-SNP	.											OR10G9,NS,carcinoma,0,1	OR10G9	80	1	1	Substitution - Missense(1)	stomach(1)	c.C610G						PASS	.	G	VAL/LEU	399,4003	788.2+/-414.9	19,361,1821	257.0	223.0	235.0		610	-3.4	0.0	11	dbSNP_131	235	31,8567	817.8+/-406.9	0,31,4268	no	missense	OR10G9	NM_001001953.1	32	19,392,6089	GG,GC,CC		0.3605,9.0641,3.3077	benign	204/312	123894329	430,12570	2201	4299	6500	SO:0001583	missense	219870	exon1			ATTGGGCTAGTGG	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.610C>G	11.37:g.123894329C>G	ENSP00000364164:p.Leu204Val	Somatic	475	0	0		WXS	Illumina HiSeq	Phase_I	513	280	0.545809	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	213	0.09752747252747253	59	0.11991869918699187	66	0.18232044198895028	82	0.14335664335664336	6	0.0079155672823219	G	0.001	-3.230738	0.00023	0.090641	0.003605	ENSG00000236981	ENST00000375024	T	0.39229	1.09	3.48	-3.36	0.04913	GPCR, rhodopsin-like superfamily (1);	0.341004	0.21004	N	0.081809	T	0.00039	0.0001	N	0.11673	0.155	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.24584	-1.0156	9	0.09338	T	0.73	.	6.2065	0.20606	0.4767:0.2354:0.2879:0.0	.	204	Q8NGN4	O10G9_HUMAN	V	204	ENSP00000364164:L204V	ENSP00000364164:L204V	L	+	1	2	OR10G9	123399539	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	-1.446000	0.02398	-1.041000	0.03266	-2.664000	0.00146	CTA	C|0.948;G|0.052	0.052	strong		0.547	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
KRT38	8687	hgsc.bcm.edu	37	17	39594356	39594356	+	Silent	SNP	G	G	A	rs28550887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39594356G>A	ENST00000246646.3	-	6	1229	c.1230C>T	c.(1228-1230)agC>agT	p.S410S		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	410	Coil 2.|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)				TGCAGTCCTCGCTTTCCAGAA	0.542													G|||	362	0.0722843	0.2035	0.0317	5008	,	,		19974	0.0198		0.0249	False		,,,				2504	0.0266				p.S410S		Atlas-SNP	.											.	KRT38	63	.	0			c.C1230T						PASS	.	G		696,3710		73,550,1580	94.0	87.0	90.0		1230	-7.5	0.9	17	dbSNP_125	90	211,8389		4,203,4093	no	coding-synonymous	KRT38	NM_006771.3		77,753,5673	AA,AG,GG		2.4535,15.7966,6.9737		410/457	39594356	907,12099	2203	4300	6503	SO:0001819	synonymous_variant	8687	exon6			GTCCTCGCTTTCC	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.1230C>T	17.37:g.39594356G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	175	81	0.462857	NM_006771	A2RRM5|Q6A164	Silent	SNP	ENST00000246646.3	37	CCDS11392.1																																																																																			G|0.934;A|0.066	0.066	strong		0.542	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
SIRPA	140885	hgsc.bcm.edu	37	20	1895842	1895842	+	Silent	SNP	T	T	C	rs17853847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1895842T>C	ENST00000358771.4	+	2	329	c.177T>C	c.(175-177)tcT>tcC	p.S59S	SIRPA_ENST00000400068.3_Silent_p.S59S|SIRPA_ENST00000356025.3_Silent_p.S59S	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	59	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CTGCGACCTCTCTGATCCCTG	0.582													T|||	1687	0.336861	0.1982	0.3631	5008	,	,		12012	0.5506		0.2604	False		,,,				2504	0.364				p.S59S	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											.	SIRPA	83	.	0			c.T177C						PASS	.	T	,,	134,4184		5,124,2030	56.0	49.0	51.0		177,177,177	0.8	0.0	20	dbSNP_123	51	424,7940		16,392,3774	no	coding-synonymous,coding-synonymous,coding-synonymous	SIRPA	NM_001040022.1,NM_001040023.1,NM_080792.2	,,	21,516,5804	CC,CT,TT		5.0693,3.1033,4.3999	,,	59/505,59/505,59/505	1895842	558,12124	2159	4182	6341	SO:0001819	synonymous_variant	140885	exon3			GACCTCTCTGATC	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.177T>C	20.37:g.1895842T>C		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	132	9	0.0681818	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Silent	SNP	ENST00000358771.4	37	CCDS13022.1																																																																																			T|0.881;C|0.119	0.119	strong		0.582	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
FBXO41	150726	hgsc.bcm.edu	37	2	73490412	73490412	+	Silent	SNP	A	A	G	rs34363861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73490412A>G	ENST00000521871.1	-	9	2515	c.2100T>C	c.(2098-2100)caT>caC	p.H700H	FBXO41_ENST00000295133.5_Silent_p.H761H|FBXO41_ENST00000520530.2_Silent_p.H700H			Q8TF61	FBX41_HUMAN	F-box protein 41	700										breast(2)|central_nervous_system(1)|endometrium(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)	13						AAATGACCTCATGGCCCACGG	0.587													G|||	2629	0.52496	0.8502	0.4294	5008	,	,		16504	0.3849		0.4821	False		,,,				2504	0.3415				p.H700H		Atlas-SNP	.											.	FBXO41	82	.	0			c.T2100C						PASS	.	G		3063,845		1234,595,125	20.0	24.0	22.0		2100	-10.0	0.2	2	dbSNP_126	22	3941,4291		983,1975,1158	no	coding-synonymous	FBXO41	NM_001080410.2		2217,2570,1283	GG,GA,AA		47.8741,21.6223,42.3064		700/876	73490412	7004,5136	1954	4116	6070	SO:0001819	synonymous_variant	150726	exon8			GACCTCATGGCCC	AB075820	CCDS46337.1, CCDS46337.2	2p13.2	2004-08-24				ENSG00000163013		"""F-boxes /  ""other"""""	29409	protein-coding gene	gene with protein product		609108				11853319	Standard	NM_001080410		Approved	KIAA1940, Fbx41	uc021vjh.1	Q8TF61		ENST00000521871.1:c.2100T>C	2.37:g.73490412A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001080410	G3V0Z7|Q2M1V8	Silent	SNP	ENST00000521871.1	37	CCDS46337.2																																																																																			A|0.461;G|0.539	0.539	strong		0.587	FBXO41-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377381.1		
LRRC47	57470	hgsc.bcm.edu	37	1	3701663	3701663	+	Silent	SNP	T	T	C	rs2298227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3701663T>C	ENST00000378251.1	-	3	1209	c.1182A>G	c.(1180-1182)ccA>ccG	p.P394P	RP1-286D6.5_ENST00000607459.1_RNA|RN7SL574P_ENST00000581512.1_RNA	NM_020710.2	NP_065761.1	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	394							phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		TGAGGTCCTGTGGGGGCCGGG	0.602													C|||	543	0.108427	0.1452	0.1023	5008	,	,		18489	0.1111		0.1213	False		,,,				2504	0.047				p.P394P		Atlas-SNP	.											.	LRRC47	42	.	0			c.A1182G						PASS	.	C		570,3836	768.5+/-413.6	29,512,1662	53.0	52.0	52.0		1182	-9.5	0.1	1	dbSNP_100	52	926,7674	774.1+/-407.7	48,830,3422	no	coding-synonymous	LRRC47	NM_020710.2		77,1342,5084	CC,CT,TT		10.7674,12.9369,11.5024		394/584	3701663	1496,11510	2203	4300	6503	SO:0001819	synonymous_variant	57470	exon3			GTCCTGTGGGGGC	AB033011	CCDS51.1	1p36.32	2008-02-05			ENSG00000130764	ENSG00000130764			29207	protein-coding gene	gene with protein product						10574461	Standard	NM_020710		Approved	KIAA1185, RP1-286D6.3	uc001akx.1	Q8N1G4	OTTHUMG00000003506	ENST00000378251.1:c.1182A>G	1.37:g.3701663T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_020710	Q9ULN5	Silent	SNP	ENST00000378251.1	37	CCDS51.1																																																																																			T|0.882;C|0.118	0.118	strong		0.602	LRRC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009744.1	NM_020710	
TLR6	10333	hgsc.bcm.edu	37	4	38829702	38829702	+	Missense_Mutation	SNP	C	C	T	rs5743816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38829702C>T	ENST00000381950.1	-	1	1458	c.1393G>A	c.(1393-1395)Gtt>Att	p.V465I	TLR6_ENST00000436693.2_Missense_Mutation_p.V465I			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	465			V -> I (in dbSNP:rs5743816). {ECO:0000269|PubMed:21618349}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|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)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGTTTAGGAACGCTCTTTATT	0.388													c|||	159	0.0317492	0.1006	0.0029	5008	,	,		20792	0.0069		0.001	False		,,,				2504	0.0164				p.V465I		Atlas-SNP	.											.	TLR6	67	.	0			c.G1393A						PASS	.						133.0	145.0	141.0					4																	38829702		2203	4300	6503	SO:0001583	missense	10333	exon2			TAGGAACGCTCTT		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.1393G>A	4.37:g.38829702C>T	ENSP00000371376:p.Val465Ile	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	211	80	0.379147	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	37	CCDS3446.1	49	0.022435897435897436	45	0.09146341463414634	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	c	0	-2.849326	0.00066	.	.	ENSG00000174130	ENST00000436693;ENST00000381950	T;T	0.48522	0.81;0.81	5.14	2.63	0.31362	.	0.182497	0.38326	N	0.001737	T	0.00875	0.0029	N	0.16201	0.385	0.45554	P	0.0014960000000000528	B	0.02656	0.0	B	0.10450	0.005	T	0.11567	-1.0582	9	0.07325	T	0.83	.	9.4019	0.38437	0.0:0.2162:0.0:0.7838	rs5743816	465	Q9Y2C9	TLR6_HUMAN	I	465	ENSP00000389600:V465I;ENSP00000371376:V465I	ENSP00000371376:V465I	V	-	1	0	TLR6	38506097	0.066000	0.20996	0.500000	0.27589	0.056000	0.15407	0.404000	0.20999	0.787000	0.33731	-0.578000	0.04140	GTT	C|0.931;T|0.069	0.069	strong		0.388	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1		
AFAP1L2	84632	hgsc.bcm.edu	37	10	116064528	116064528	+	Missense_Mutation	SNP	G	G	A	rs73365341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116064528G>A	ENST00000304129.4	-	11	1263	c.1234C>T	c.(1234-1236)Ctc>Ttc	p.L412F	AFAP1L2_ENST00000545353.1_Missense_Mutation_p.L465F|AFAP1L2_ENST00000491814.1_5'Flank|AFAP1L2_ENST00000369271.3_Missense_Mutation_p.L412F			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	40	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	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	
OR8G5	219865	hgsc.bcm.edu	37	11	124135009	124135009	+	Missense_Mutation	SNP	G	G	A	rs2512168	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124135009G>A	ENST00000524943.2	+	1	287	c.287G>A	c.(286-288)tGt>tAt	p.C96Y	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	96						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		CCTATGTACTGTTTCCTCAGC	0.483													a|||	2196	0.438498	0.292	0.5591	5008	,	,		21549	0.5833		0.5527	False		,,,				2504	0.2843				p.C96Y	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.G287A						PASS	.	A	TYR/CYS	1386,2974		230,926,1024	135.0	116.0	123.0		287	-5.0	0.5	11	dbSNP_100	123	4624,3936		1275,2074,931	no	missense	OR8G5	NM_001005198.1	194	1505,3000,1955	AA,AG,GG		45.9813,31.789,46.517		96/347	124135009	6010,6910	2180	4280	6460	SO:0001583	missense	219865	exon1			TGTACTGTTTCCT	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.287G>A	11.37:g.124135009G>A	ENSP00000477014:p.Cys96Tyr	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	169	168	0.994083	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	37																																																																																				G|0.507;A|0.493	0.493	strong		0.483	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
OR6K6	128371	hgsc.bcm.edu	37	1	158725080	158725080	+	Missense_Mutation	SNP	C	C	T	rs16841001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158725080C>T	ENST00000368144.2	+	1	571	c.475C>T	c.(475-477)Cgt>Tgt	p.R159C		NM_001005184.1	NP_001005184.1	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K, member 6	159			R -> C (in dbSNP:rs16841001).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(17)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0378)					CAATCCACTCCGTTACCCAAC	0.468													C|||	518	0.103435	0.0431	0.1095	5008	,	,		24956	0.1667		0.1541	False		,,,				2504	0.0634				p.R159C		Atlas-SNP	.											.	OR6K6	81	.	0			c.C475T						PASS	.	C	CYS/ARG	249,4157	143.8+/-178.8	8,233,1962	131.0	109.0	116.0		475	5.5	1.0	1	dbSNP_123	116	1132,7468	233.7+/-266.9	80,972,3248	yes	missense	OR6K6	NM_001005184.1	180	88,1205,5210	TT,TC,CC		13.1628,5.6514,10.6182	benign	159/344	158725080	1381,11625	2203	4300	6503	SO:0001583	missense	128371	exon1			CCACTCCGTTACC	BK004198	CCDS30904.1	1q23.1	2012-08-09			ENSG00000180433	ENSG00000180433		"""GPCR / Class A : Olfactory receptors"""	15033	protein-coding gene	gene with protein product							Standard	NM_001005184		Approved		uc001fsw.1	Q8NGW6	OTTHUMG00000022772	ENST00000368144.2:c.475C>T	1.37:g.158725080C>T	ENSP00000357126:p.Arg159Cys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	154	87	0.564935	NM_001005184	B9EIM8|Q5VUU9|Q6IFR4	Missense_Mutation	SNP	ENST00000368144.2	37	CCDS30904.1	282	0.12912087912087913	23	0.046747967479674794	37	0.10220994475138122	100	0.17482517482517482	122	0.16094986807387862	C	14.81	2.646762	0.47258	0.056514	0.131628	ENSG00000180433	ENST00000368144	T	0.02280	4.36	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.319150	0.22869	N	0.054656	T	0.01976	0.0062	M	0.62209	1.925	0.21762	P	0.999551967	B	0.32507	0.373	B	0.26094	0.066	T	0.45673	-0.9245	9	0.56958	D	0.05	-2.2299	18.27	0.90065	0.0:1.0:0.0:0.0	rs16841001;rs52808207;rs16841001	159	Q8NGW6	OR6K6_HUMAN	C	159	ENSP00000357126:R159C	ENSP00000357126:R159C	R	+	1	0	OR6K6	156991704	0.706000	0.27856	1.000000	0.80357	0.782000	0.44232	2.968000	0.49224	2.848000	0.98002	0.655000	0.94253	CGT	C|0.885;T|0.115	0.115	strong		0.468	OR6K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059065.2	NM_001005184	
NOV	4856	hgsc.bcm.edu	37	8	120429024	120429024	+	Missense_Mutation	SNP	G	G	A	rs2279112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120429024G>A	ENST00000259526.3	+	2	352	c.125G>A	c.(124-126)cGg>cAg	p.R42Q		NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	0	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)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			TGCCCGGGCCGGTGCCCTGCG	0.716											OREG0018940	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1567	0.312899	0.5681	0.1902	5008	,	,		13266	0.1538		0.2266	False		,,,				2504	0.3078				p.R42Q		Atlas-SNP	.											.	NOV	51	.	0			c.G125A						PASS	.	A	GLN/ARG	2280,2074		634,1012,531	10.0	10.0	10.0		125	-8.4	0.0	8	dbSNP_100	10	2260,6164		358,1544,2310	no	missense	NOV	NM_002514.3	43	992,2556,2841	AA,AG,GG		26.8281,47.6344,35.5298	benign	42/358	120429024	4540,8238	2177	4212	6389	SO:0001583	missense	4856	exon2			CGGGCCGGTGCCC	X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"""nephroblastoma overexpressed gene"""			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.125G>A	8.37:g.120429024G>A	ENSP00000259526:p.Arg42Gln	Somatic	7	0	0	1503	WXS	Illumina HiSeq	Phase_I	13	7	0.538462	NM_002514		Missense_Mutation	SNP	ENST00000259526.3	37	CCDS6328.1	627	0.28708791208791207	286	0.5813008130081301	80	0.22099447513812154	95	0.1660839160839161	166	0.21899736147757257	A	11.67	1.708383	0.30322	0.523656	0.268281	ENSG00000136999	ENST00000259526	T	0.56941	0.43	5.39	-8.39	0.00969	Insulin-like growth factor-binding protein, IGFBP (3);	0.903135	0.09617	N	0.778031	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	0.30909	-0.9962	9	0.02654	T	1	1.3931	5.4903	0.16773	0.2889:0.2:0.4299:0.0812	rs2279112;rs58156952	42	P48745	NOV_HUMAN	Q	42	ENSP00000259526:R42Q	ENSP00000259526:R42Q	R	+	2	0	NOV	120498205	0.000000	0.05858	0.006000	0.13384	0.508000	0.34012	-0.773000	0.04689	-1.696000	0.01421	-0.381000	0.06696	CGG	G|0.709;A|0.291	0.291	strong		0.716	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514	
ZNF610	162963	hgsc.bcm.edu	37	19	52869534	52869534	+	Silent	SNP	G	G	A	rs162119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52869534G>A	ENST00000403906.3	+	6	1359	c.903G>A	c.(901-903)tcG>tcA	p.S301S	ZNF610_ENST00000321287.8_Silent_p.S301S|ZNF610_ENST00000601151.1_Silent_p.S258S|ZNF610_ENST00000327920.8_Silent_p.S301S	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	301					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.S301S(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		GAGAGTGTTCGGGACTTACTA	0.393													A|||	4020	0.802716	0.826	0.7911	5008	,	,		21013	0.6151		0.8966	False		,,,				2504	0.8763				p.S301S		Atlas-SNP	.											ZNF610,NS,carcinoma,0,1	ZNF610	84	1	1	Substitution - coding silent(1)	stomach(1)	c.G903A						PASS	.	A	,,,	3641,765	310.0+/-291.3	1498,645,60	53.0	49.0	50.0		903,903,774,903	1.7	0.0	19	dbSNP_79	50	7500,1100	227.8+/-263.0	3270,960,70	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF610	NM_001161425.1,NM_001161426.1,NM_001161427.1,NM_173530.2	,,,	4768,1605,130	AA,AG,GG		12.7907,17.3627,14.3395	,,,	301/463,301/463,258/420,301/463	52869534	11141,1865	2203	4300	6503	SO:0001819	synonymous_variant	162963	exon6			GTGTTCGGGACTT	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"""Zinc fingers, C2H2-type"", ""-"""	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.903G>A	19.37:g.52869534G>A		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_001161426	A8K4C3|Q86YH8|Q8NDS9	Silent	SNP	ENST00000403906.3	37	CCDS12851.1																																																																																			A|0.826;G|0.174	0.826	strong		0.393	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530	
GBP5	115362	hgsc.bcm.edu	37	1	89735229	89735229	+	Missense_Mutation	SNP	C	C	G	rs17130763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89735229C>G	ENST00000370459.3	-	2	137	c.10G>C	c.(10-12)Gag>Cag	p.E4Q	RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000343435.5_Missense_Mutation_p.E4Q			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	4	GTPase domain (Globular). {ECO:0000250}.		E -> Q (in dbSNP:rs17130763).			cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		ATGTGGATCTCTAAAGCCATG	0.443													C|||	76	0.0151757	0.053	0.0086	5008	,	,		12783	0.0		0.0	False		,,,				2504	0.0				p.E4Q		Atlas-SNP	.											.	GBP5	65	.	0			c.G10C						PASS	.	C	GLN/GLU,GLN/GLU	202,4204	125.3+/-162.5	4,194,2005	169.0	164.0	166.0		10,10	1.5	0.0	1	dbSNP_123	166	0,8600		0,0,4300	yes	missense,missense	GBP5	NM_001134486.2,NM_052942.3	29,29	4,194,6305	GG,GC,CC		0.0,4.5847,1.5531	benign,benign	4/587,4/587	89735229	202,12804	2203	4300	6503	SO:0001583	missense	115362	exon3			GGATCTCTAAAGC	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.10G>C	1.37:g.89735229C>G	ENSP00000359488:p.Glu4Gln	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	137	72	0.525547	NM_052942	B2RCE1|Q86TM5	Missense_Mutation	SNP	ENST00000370459.3	37	CCDS722.1	25	0.011446886446886446	21	0.042682926829268296	4	0.011049723756906077	0	0.0	0	0.0	C	11.40	1.626401	0.28978	0.045847	0.0	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	T;T;T	0.66099	0.36;0.36;-0.19	5.0	1.48	0.22813	.	0.954043	0.08802	N	0.891614	T	0.35008	0.0917	M	0.62154	1.92	0.09310	N	1	B	0.20052	0.041	B	0.22152	0.038	T	0.32693	-0.9897	10	0.33141	T	0.24	-0.4944	5.2406	0.15469	0.1544:0.6219:0.0:0.2237	rs17130763;rs17130763	4	Q96PP8	GBP5_HUMAN	Q	4	ENSP00000340396:E4Q;ENSP00000359488:E4Q;ENSP00000403010:E4Q	ENSP00000340396:E4Q	E	-	1	0	GBP5	89507817	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.226000	0.17776	0.521000	0.28445	0.655000	0.94253	GAG	C|0.976;G|0.024	0.024	strong		0.443	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942	
ABCA1	19	hgsc.bcm.edu	37	9	107547872	107547872	+	Silent	SNP	C	C	T	rs61741359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107547872C>T	ENST00000374736.3	-	49	6844	c.6450G>A	c.(6448-6450)ccG>ccA	p.P2150P		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	2150			P -> L (in HDLD2). {ECO:0000269|PubMed:11086027}.		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)	GCTTCAGGTCCGGGTTGGACC	0.418													C|||	57	0.0113818	0.0386	0.0072	5008	,	,		17972	0.0		0.001	False		,,,				2504	0.0				p.P2150P		Atlas-SNP	.											.	ABCA1	244	.	0			c.G6450A						PASS	.	C		172,4234	112.5+/-150.6	0,172,2031	85.0	87.0	87.0		6450	2.2	1.0	9	dbSNP_129	87	0,8600		0,0,4300	yes	coding-synonymous	ABCA1	NM_005502.3		0,172,6331	TT,TC,CC		0.0,3.9038,1.3225		2150/2262	107547872	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	19	exon49			CAGGTCCGGGTTG	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.6450G>A	9.37:g.107547872C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	54	0.760563	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			C|0.985;T|0.015	0.015	strong		0.418	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
PKD1L1	168507	hgsc.bcm.edu	37	7	47925609	47925609	+	Silent	SNP	G	G	A	rs78480673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47925609G>A	ENST00000289672.2	-	18	2930	c.2880C>T	c.(2878-2880)ctC>ctT	p.L960L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	960	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						AAATGGCACCGAGTCCCAGCG	0.488													g|||	194	0.038738	0.1377	0.0101	5008	,	,		17976	0.0		0.004	False		,,,				2504	0.001				p.L960L		Atlas-SNP	.											PKD1L1,NS,carcinoma,0,2	PKD1L1	328	2	0			c.C2880T						PASS	.	A		638,3768	272.8+/-271.0	47,544,1612	60.0	56.0	58.0		2880	-9.9	0.0	7	dbSNP_132	58	85,8515	48.1+/-107.5	1,83,4216	no	coding-synonymous	PKD1L1	NM_138295.3		48,627,5828	AA,AG,GG		0.9884,14.4803,5.559		960/2850	47925609	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon18			GGCACCGAGTCCC	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.2880C>T	7.37:g.47925609G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			G|0.951;A|0.049	0.049	strong		0.488	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
MUC17	140453	hgsc.bcm.edu	37	7	100681303	100681303	+	Silent	SNP	T	T	C	rs143516283		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100681303T>C	ENST00000306151.4	+	3	6670	c.6606T>C	c.(6604-6606)ccT>ccC	p.P2202P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2202	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)					GTTCATCTCCTACAACTTCTG	0.507																																					p.P2202P		Atlas-SNP	.											MUC17,rectum,carcinoma,0,1	MUC17	804	1	0			c.T6606C						scavenged	.						311.0	311.0	311.0					7																	100681303		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			ATCTCCTACAACT	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.6606T>C	7.37:g.100681303T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	168	13	0.077381	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			.	.	weak		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
KIAA1683	80726	hgsc.bcm.edu	37	19	18376780	18376780	+	Missense_Mutation	SNP	T	T	C	rs12462974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18376780T>C	ENST00000600328.3	-	3	1763	c.1570A>G	c.(1570-1572)Aca>Gca	p.T524A	KIAA1683_ENST00000600359.3_Missense_Mutation_p.T478A|KIAA1683_ENST00000392413.4_Missense_Mutation_p.T524A			Q9H0B3	K1683_HUMAN	KIAA1683	524			T -> A (in dbSNP:rs12462974).			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TTTGCCACTGTTGGAGAGGCC	0.617													T|||	738	0.147364	0.4297	0.1282	5008	,	,		17239	0.0129		0.0288	False		,,,				2504	0.0399				p.T524A		Atlas-SNP	.											.	KIAA1683	190	.	0			c.A1570G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	1674,2732	510.1+/-367.4	321,1032,850	74.0	68.0	70.0		1570,1432,1570	-7.2	0.0	19	dbSNP_120	70	231,8369	95.6+/-157.4	4,223,4073	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	58,58,58	325,1255,4923	CC,CT,TT		2.686,37.9936,14.6471	benign,benign,benign	524/1368,478/1135,524/1181	18376780	1905,11101	2203	4300	6503	SO:0001583	missense	80726	exon3			CCACTGTTGGAGA	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1570A>G	19.37:g.18376780T>C	ENSP00000470780:p.Thr524Ala	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	153	83	0.542484	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	278	0.12728937728937728	213	0.4329268292682927	48	0.13259668508287292	1	0.0017482517482517483	16	0.021108179419525065	T	0.160	-1.082165	0.01888	0.379936	0.02686	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634	T;T;T	0.03242	4.07;4.08;4.0	3.97	-7.21	0.01490	.	1.083510	0.07343	N	0.881096	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	0.47686	-0.9098	9	0.02654	T	1	-2.4415	0.3148	0.00294	0.2788:0.2233:0.1381:0.3598	rs12462974;rs12462974	524;524	E9PDE0;Q9H0B3	.;K1683_HUMAN	A	524;524;478	ENSP00000376213:T524A;ENSP00000352774:T524A;ENSP00000404501:T478A	ENSP00000352774:T524A	T	-	1	0	KIAA1683	18237780	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.232000	0.09055	-1.289000	0.02375	-0.337000	0.08149	ACA	T|0.861;C|0.139	0.139	strong		0.617	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
CRNKL1	51340	hgsc.bcm.edu	37	20	20033194	20033194	+	Silent	SNP	G	G	T	rs145198573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:20033194G>T	ENST00000377340.2	-	2	307	c.276C>A	c.(274-276)cgC>cgA	p.R92R	C20orf26_ENST00000245957.5_5'Flank|CRNKL1_ENST00000536226.1_5'Flank|C20orf26_ENST00000377306.1_5'Flank|C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000389656.3_5'UTR|CRNKL1_ENST00000377327.4_Silent_p.R80R	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	92					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						CGTCCTCCTTGCGGCAGCGCG	0.662													G|||	20	0.00399361	0.0151	0.0	5008	,	,		18175	0.0		0.0	False		,,,				2504	0.0				p.R92R		Atlas-SNP	.											.	CRNKL1	101	.	0			c.C276A						PASS	.	G	,	67,4339	60.5+/-97.4	0,67,2136	51.0	47.0	48.0		,276	-2.9	0.0	20	dbSNP_134	48	2,8598	1.2+/-3.3	0,2,4298	no	utr-5,coding-synonymous	C20orf26,CRNKL1	NM_015585.3,NM_016652.4	,	0,69,6434	TT,TG,GG		0.0233,1.5207,0.5305	,	,92/849	20033194	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	51340	exon2			CTCCTTGCGGCAG	AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"""SYF3 pre-mRNA-splicing factor"""	610952	"""crooked neck (Drosophila Crn homolog)-like 1"", ""Crn, crooked neck-like 1 (Drosophila)"", ""crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"""				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.276C>A	20.37:g.20033194G>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Silent	SNP	ENST00000377340.2	37	CCDS33446.1																																																																																			G|0.996;T|0.004	0.004	strong		0.662	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1		
ANKRD34B	340120	hgsc.bcm.edu	37	5	79854667	79854667	+	Missense_Mutation	SNP	A	A	G	rs147745221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79854667A>G	ENST00000338682.3	-	5	1844	c.1172T>C	c.(1171-1173)aTa>aCa	p.I391T		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	391						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	28		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		TTTCTTTCCTATAAGTGCTTT	0.463													a|||	2	0.000399361	0.0015	0.0	5008	,	,		14523	0.0		0.0	False		,,,				2504	0.0				p.I391T		Atlas-SNP	.											.	ANKRD34B	61	.	0			c.T1172C						PASS	.	G	THR/ILE	12,4394	19.1+/-41.9	0,12,2191	57.0	62.0	60.0		1172	-5.4	0.0	5	dbSNP_134	60	0,8600		0,0,4300	yes	missense	ANKRD34B	NM_001004441.2	89	0,12,6491	GG,GA,AA		0.0,0.2724,0.0923	benign	391/515	79854667	12,12994	2203	4300	6503	SO:0001583	missense	340120	exon5			TTTCCTATAAGTG		CCDS34194.1	5q14.1	2014-08-12			ENSG00000189127	ENSG00000189127		"""Ankyrin repeat domain containing"""	33736	protein-coding gene	gene with protein product							Standard	NM_001004441		Approved	DP58	uc003kgw.3	A5PLL1	OTTHUMG00000162541	ENST00000338682.3:c.1172T>C	5.37:g.79854667A>G	ENSP00000339802:p.Ile391Thr	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	57	34	0.596491	NM_001004441	B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	37	CCDS34194.1	.	.	.	.	.	.	.	.	.	.	a	4.439	0.081337	0.08533	0.002724	0.0	ENSG00000189127	ENST00000338682	T	0.20738	2.05	5.8	-5.38	0.02673	.	17.413900	0.01263	N	0.009220	T	0.17450	0.0419	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25293	-1.0136	10	0.40728	T	0.16	3.3058	10.1179	0.42603	0.5602:0.0:0.3519:0.0879	.	391	A5PLL1	AN34B_HUMAN	T	391	ENSP00000339802:I391T	ENSP00000339802:I391T	I	-	2	0	ANKRD34B	79890423	0.000000	0.05858	0.000000	0.03702	0.673000	0.39480	-0.530000	0.06179	-1.261000	0.02462	-0.976000	0.02587	ATA	A|0.999;G|0.001	0.001	strong		0.463	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441	
TXNDC2	84203	hgsc.bcm.edu	37	18	9886988	9886988	+	Missense_Mutation	SNP	C	C	T	rs34812912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9886988C>T	ENST00000306084.6	+	2	711	c.512C>T	c.(511-513)cCc>cTc	p.P171L	TXNDC2_ENST00000536353.2_Missense_Mutation_p.P104L|TXNDC2_ENST00000357775.5_Missense_Mutation_p.P104L	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	171	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						TCAGTGAAGCCCAGCCAGCCC	0.557													c|||	309	0.0617013	0.0371	0.0576	5008	,	,		21648	0.0198		0.0716	False		,,,				2504	0.1309				p.P171L		Atlas-SNP	.											.	TXNDC2	168	.	0			c.C512T						PASS	.	C	LEU/PRO,LEU/PRO	180,4226	116.3+/-154.2	3,174,2026	127.0	132.0	130.0		512,311	0.8	0.0	18	dbSNP_126	130	668,7932	167.8+/-219.5	28,612,3660	no	missense,missense	TXNDC2	NM_001098529.1,NM_032243.5	98,98	31,786,5686	TT,TC,CC		7.7674,4.0853,6.5201	possibly-damaging,possibly-damaging	171/554,104/487	9886988	848,12158	2203	4300	6503	SO:0001583	missense	84203	exon2			TGAAGCCCAGCCA	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.512C>T	18.37:g.9886988C>T	ENSP00000304908:p.Pro171Leu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	101	0.04624542124542125	12	0.024390243902439025	19	0.052486187845303865	16	0.027972027972027972	54	0.0712401055408971	c	2.562	-0.301725	0.05495	0.040853	0.077674	ENSG00000168454	ENST00000357775;ENST00000306084;ENST00000426718	T;T	0.76839	-1.05;-1.05	2.74	0.756	0.18421	.	3.088650	0.01252	N	0.008906	T	0.12475	0.0303	N	0.19112	0.55	0.09310	N	1	D	0.53312	0.959	P	0.52343	0.696	T	0.48068	-0.9067	9	.	.	.	0.7324	1.1901	0.01863	0.2273:0.4052:0.2233:0.1442	rs34812912	171	Q86VQ3	TXND2_HUMAN	L	104;171;171	ENSP00000350419:P104L;ENSP00000304908:P171L	.	P	+	2	0	TXNDC2	9876988	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.780000	0.00368	0.206000	0.20587	0.481000	0.45027	CCC	C|0.940;T|0.060	0.060	strong		0.557	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
SLC46A2	57864	hgsc.bcm.edu	37	9	115652836	115652836	+	Silent	SNP	G	G	A	rs3802492	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:115652836G>A	ENST00000374228.4	-	1	357	c.126C>T	c.(124-126)ctC>ctT	p.L42L		NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	42					negative regulation of T cell apoptotic process (GO:0070233)|regulation of T cell differentiation (GO:0045580)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(1)	18						CCTTCACCACGAGGAGTAGCC	0.677													G|||	1408	0.28115	0.3986	0.2363	5008	,	,		15844	0.0982		0.3191	False		,,,				2504	0.3037				p.L42L		Atlas-SNP	.											.	SLC46A2	30	.	0			c.C126T						PASS	.	G		1716,2690	514.7+/-368.7	349,1018,836	57.0	60.0	59.0		126	-1.1	1.0	9	dbSNP_107	59	2750,5850	437.4+/-358.6	472,1806,2022	no	coding-synonymous	SLC46A2	NM_033051.3		821,2824,2858	AA,AG,GG		31.9767,38.9469,34.338		42/476	115652836	4466,8540	2203	4300	6503	SO:0001819	synonymous_variant	57864	exon1			CACCACGAGGAGT	AF242557	CCDS6786.1	9q32	2013-05-22	2007-03-29	2007-03-29	ENSG00000119457	ENSG00000119457		"""Solute carriers"""	16055	protein-coding gene	gene with protein product		608956	"""thymic stromal co-transporter"""	TSCOT		10978518, 12826694	Standard	NM_033051		Approved	Ly110	uc004bgk.3	Q9BY10	OTTHUMG00000020513	ENST00000374228.4:c.126C>T	9.37:g.115652836G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_033051	B1ALK1|Q86VT0|Q96NE2	Silent	SNP	ENST00000374228.4	37	CCDS6786.1																																																																																			G|0.682;A|0.318	0.318	strong		0.677	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051	
ZNF835	90485	hgsc.bcm.edu	37	19	57176198	57176198	+	Silent	SNP	T	T	G	rs8108756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	82	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	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	
XKR3	150165	hgsc.bcm.edu	37	22	17288849	17288849	+	Missense_Mutation	SNP	A	A	G	rs150400922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17288849A>G	ENST00000331428.5	-	2	217	c.115T>C	c.(115-117)Ttc>Ctc	p.F39L		NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN	XK, Kell blood group complex subunit-related family, member 3	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				ACAGTTGAGAAGATAATGCTA	0.388													.|||	22	0.00439297	0.0159	0.0014	5008	,	,		19510	0.0		0.0	False		,,,				2504	0.0				p.F39L		Atlas-SNP	.											.	XKR3	51	.	0			c.T115C						PASS	.	A	LEU/PHE	71,3691		0,71,1810	115.0	110.0	112.0		115	0.5	0.0	22	dbSNP_134	112	0,8218		0,0,4109	yes	missense	XKR3	NM_175878.3	22	0,71,5919	GG,GA,AA		0.0,1.8873,0.5927	benign	39/460	17288849	71,11909	1881	4109	5990	SO:0001583	missense	150165	exon2			TTGAGAAGATAAT	AY989815	CCDS42975.1	22q11.1	2007-01-16	2006-01-12		ENSG00000172967	ENSG00000172967			28778	protein-coding gene	gene with protein product		611674	"""X Kell blood group precursor-related family, member 3"""			16431037	Standard	NM_175878		Approved	MGC57211, XTES	uc002zlv.3	Q5GH77	OTTHUMG00000143726	ENST00000331428.5:c.115T>C	22.37:g.17288849A>G	ENSP00000331704:p.Phe39Leu	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	209	94	0.449761	NM_175878	B2RPN1|Q52PG8|Q8N7E1	Missense_Mutation	SNP	ENST00000331428.5	37	CCDS42975.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	.	4.134	0.023117	0.08006	0.018873	0.0	ENSG00000172967	ENST00000331428	T	0.61859	0.07	0.539	0.539	0.17156	.	0.396682	0.23023	U	0.052823	T	0.17577	0.0422	N	0.22421	0.69	0.19775	N	0.999951	B	0.02656	0.0	B	0.01281	0.0	T	0.04090	-1.0978	10	0.13853	T	0.58	.	2.6787	0.05087	0.5696:1.0E-4:0.0:0.4304	.	39	Q5GH77	XKR3_HUMAN	L	39	ENSP00000331704:F39L	ENSP00000331704:F39L	F	-	1	0	XKR3	15668849	0.930000	0.31532	0.021000	0.16686	0.010000	0.07245	0.129000	0.15830	0.485000	0.27652	0.246000	0.17985	TTC	A|0.996;G|0.004	0.004	strong		0.388	XKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289789.1	NM_175878	
BRAF	673	hgsc.bcm.edu	37	7	140449150	140449150	+	Silent	SNP	T	T	C	rs9648696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	141	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	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	
CYP4F12	66002	hgsc.bcm.edu	37	19	15807830	15807830	+	Silent	SNP	T	T	C	rs593421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15807830T>C	ENST00000550308.1	+	13	1890	c.1510T>C	c.(1510-1512)Ttg>Ctg	p.L504L	CYP4F12_ENST00000324632.10_Silent_p.L504L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	504					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GAAGCTGGAATTGATCATGCG	0.587													C|||	1210	0.241613	0.4032	0.2421	5008	,	,		18747	0.0139		0.2763	False		,,,				2504	0.2219				p.L504L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.T1510C						PASS	.	C		1693,2711		329,1035,838	56.0	60.0	59.0		1510	-3.1	0.0	19	dbSNP_83	59	2116,6484		294,1528,2478	no	coding-synonymous	CYP4F12	NM_023944.3		623,2563,3316	CC,CT,TT		24.6047,38.4423,29.291		504/525	15807830	3809,9195	2202	4300	6502	SO:0001819	synonymous_variant	66002	exon13			CTGGAATTGATCA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1510T>C	19.37:g.15807830T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	246	149	0.605691	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			T|0.770;C|0.230	0.230	strong		0.587	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
HOGA1	112817	hgsc.bcm.edu	37	10	99371344	99371344	+	Silent	SNP	C	C	A	rs12261752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99371344C>A	ENST00000370646.4	+	7	1273	c.912C>A	c.(910-912)gcC>gcA	p.A304A	PI4K2A_ENST00000555577.1_Intron|PI4K2A_ENST00000370649.3_Intron|HOGA1_ENST00000370647.4_Silent_p.A141A	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	96	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	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	
LETM1	3954	hgsc.bcm.edu	37	4	1834666	1834666	+	Silent	SNP	T	T	C	rs140729898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1834666T>C	ENST00000302787.2	-	6	1181	c.885A>G	c.(883-885)gaA>gaG	p.E295E		NM_012318.2	NP_036450.1	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane protein 1	295	LETM1.				cristae formation (GO:0042407)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(2)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	13			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)			TCTCCCCTGTTTCCCGGATCT	0.602													C|||	58	0.0115815	0.0015	0.0159	5008	,	,		17570	0.001		0.0358	False		,,,				2504	0.0082				p.E295E		Atlas-SNP	.											.	LETM1	48	.	0			c.A885G						PASS	.	C		35,4371	822.8+/-416.5	0,35,2168	64.0	59.0	61.0		885	3.8	1.0	4	dbSNP_134	61	300,8300	805.6+/-407.3	5,290,4005	no	coding-synonymous	LETM1	NM_012318.2		5,325,6173	CC,CT,TT		3.4884,0.7944,2.5757		295/740	1834666	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	3954	exon6			CCCTGTTTCCCGG	AF061025	CCDS3355.1	4p16.3	2013-01-10			ENSG00000168924	ENSG00000168924		"""EF-hand domain containing"""	6556	protein-coding gene	gene with protein product	"""Mdm38 homolog (yeast)"""	604407				10486213	Standard	NM_012318		Approved		uc003gdv.3	O95202	OTTHUMG00000121149	ENST00000302787.2:c.885A>G	4.37:g.1834666T>C		Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	217	108	0.497696	NM_012318	B4DED2|Q9UF65	Silent	SNP	ENST00000302787.2	37	CCDS3355.1																																																																																			T|0.977;C|0.023	0.023	strong		0.602	LETM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241634.1		
C7orf55-LUC7L2	100996928	hgsc.bcm.edu	37	7	139090515	139090515	+	Silent	SNP	A	A	G	rs74758604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139090515A>G	ENST00000354926.4	+	5	846	c.492A>G	c.(490-492)gcA>gcG	p.A164A	LUC7L2_ENST00000541515.3_Silent_p.A230A|C7orf55-LUC7L2_ENST00000541170.3_Silent_p.A161A|C7orf55-LUC7L2_ENST00000263545.6_Silent_p.A163A	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough																		AAGCACGGGCAAAGAAAAGAG	0.368													A|||	80	0.0159744	0.0582	0.0029	5008	,	,		17933	0.0		0.001	False		,,,				2504	0.0				p.A230A		Atlas-SNP	.											LUC7L2,NS,carcinoma,+2,1	.	.	1	0			c.A690G						PASS	.	A		171,3519		5,161,1679	100.0	103.0	102.0		492	1.4	1.0	7	dbSNP_132	102	1,8165		0,1,4082	no	coding-synonymous	LUC7L2	NM_016019.3		5,162,5761	GG,GA,AA		0.0122,4.6341,1.4507		164/393	139090515	172,11684	1845	4083	5928	SO:0001819	synonymous_variant	100996928	exon6			ACGGGCAAAGAAA		CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.492A>G	7.37:g.139090515A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_001244584		Silent	SNP	ENST00000354926.4	37	CCDS43656.1																																																																																			A|0.981;G|0.019	0.019	strong		0.368	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2		
PCED1B	91523	hgsc.bcm.edu	37	12	47629368	47629368	+	Silent	SNP	G	G	T	rs2244818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:47629368G>T	ENST00000546455.1	+	4	1253	c.522G>T	c.(520-522)ggG>ggT	p.G174G	PCED1B_ENST00000432328.1_Silent_p.G174G|RP11-493L12.3_ENST00000547748.1_RNA			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	174							hydrolase activity (GO:0016787)										AAGTCACCGGGGGTTTTCTTC	0.602													G|||	742	0.148163	0.1846	0.1081	5008	,	,		15708	0.12		0.1759	False		,,,				2504	0.1278				p.G174G		Atlas-SNP	.											.	.	.	.	0			c.G522T						PASS	.	G		776,3630		59,658,1486	36.0	35.0	35.0		522	-4.3	0.0	12	dbSNP_100	35	1392,7208		106,1180,3014	no	coding-synonymous	FAM113B	NM_138371.1		165,1838,4500	TT,TG,GG		16.186,17.6123,16.6692		174/433	47629368	2168,10838	2203	4300	6503	SO:0001819	synonymous_variant	91523	exon2			CACCGGGGGTTTT	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.522G>T	12.37:g.47629368G>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_138371	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																			G|0.835;T|0.165	0.165	strong		0.602	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
PRTN3	5657	hgsc.bcm.edu	37	19	844020	844020	+	Missense_Mutation	SNP	G	G	A	rs351111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:844020G>A	ENST00000234347.5	+	3	401	c.355G>A	c.(355-357)Gtt>Att	p.V119I	PRTN3_ENST00000544537.2_Missense_Mutation_p.V78I	NM_002777.3	NP_002768.3	P24158	PRTN3_HUMAN	proteinase 3	119	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		V -> I (in dbSNP:rs351111). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1681549, ECO:0000269|PubMed:2377228, ECO:0000269|PubMed:2598267, ECO:0000269|PubMed:7539799, ECO:0000269|PubMed:9924693, ECO:0000269|Ref.3}.		collagen catabolic process (GO:0030574)|mature dendritic cell differentiation (GO:0097029)|negative regulation of phagocytosis (GO:0050765)|positive regulation of cell proliferation (GO:0008284)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|ovary(2)|urinary_tract(1)	4		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;0.000172)|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)		ACTGAACGACGTTCTCCTCAT	0.647													g|||	2223	0.44389	0.5333	0.4971	5008	,	,		9006	0.3512		0.4006	False		,,,				2504	0.4254				p.V119I		Atlas-SNP	.											.	PRTN3	9	.	0			c.G355A						PASS	.		ILE/VAL	2319,2083		616,1087,498	33.0	34.0	34.0		355	-3.6	0.0	19	dbSNP_79	34	3531,5067		711,2109,1479	yes	missense	PRTN3	NM_002777.3	29	1327,3196,1977	AA,AG,GG		41.0677,47.3194,45.0	benign	119/257	844020	5850,7150	2201	4299	6500	SO:0001583	missense	5657	exon3			AACGACGTTCTCC		CCDS32860.1	19p13.3	2008-07-31	2008-07-31			ENSG00000196415			9495	protein-coding gene	gene with protein product	"""myeloblastin"", ""serine proteinase, neutrophil"", ""Wegener granulomatosis autoantigen"""	177020				2258701	Standard	NM_002777		Approved	PR-3, ACPA, C-ANCA, AGP7, MBT, P29	uc002lqa.1	P24158		ENST00000234347.5:c.355G>A	19.37:g.844020G>A	ENSP00000234347:p.Val119Ile	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	137	52	0.379562	NM_002777	P15637|P18078|Q4VB08|Q4VB09|Q6LBM7|Q6LBN2|Q9UD25|Q9UQD8	Missense_Mutation	SNP	ENST00000234347.5	37	CCDS32860.1	964	0.4413919413919414	250	0.508130081300813	185	0.511049723756906	213	0.3723776223776224	316	0.41688654353562005	g	0.118	-1.128857	0.01756	0.526806	0.410677	ENSG00000196415	ENST00000234347;ENST00000544537	T	0.49139	0.79	2.73	-3.59	0.04583	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	N	0.00473	-1.45	0.80722	P	0.0	B	0.30406	0.278	B	0.28139	0.086	T	0.31475	-0.9942	8	0.02654	T	1	.	7.6584	0.28389	0.6738:0.0:0.3262:0.0	rs351111;rs600071;rs1126597;rs3181721;rs17366042;rs17400579;rs58626854;rs351111	119	P24158	PRTN3_HUMAN	I	119;78	ENSP00000234347:V119I	ENSP00000234347:V119I	V	+	1	0	PRTN3	795020	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.066000	0.03454	-0.588000	0.05882	-0.348000	0.07805	GTT	G|0.546;A|0.454	0.454	strong		0.647	PRTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457888.2	NM_002777	
PSG2	5670	hgsc.bcm.edu	37	19	43585253	43585253	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	274	6	0.0218978		WXS	Illumina HiSeq	Phase_I	292	11	0.0376712	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	
C1orf127	148345	hgsc.bcm.edu	37	1	11008102	11008102	+	Missense_Mutation	SNP	G	G	A	rs1281018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11008102G>A	ENST00000377008.4	-	11	2035	c.1589C>T	c.(1588-1590)gCg>gTg	p.A530V	C1orf127_ENST00000377004.4_Missense_Mutation_p.A697V			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	530			A -> V (in dbSNP:rs1281018).							NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TGCCAGGGGCGCTGCCAGCCT	0.622													G|||	442	0.0882588	0.2542	0.0245	5008	,	,		18073	0.0069		0.0447	False		,,,				2504	0.0378				p.A697V		Atlas-SNP	.											.	C1orf127	134	.	0			c.C2090T						PASS	.	G	VAL/ALA	809,3597	299.6+/-285.9	81,647,1475	36.0	38.0	37.0		2090	-2.0	0.0	1	dbSNP_87	37	346,8254	112.3+/-172.5	4,338,3958	yes	missense	C1orf127	NM_001170754.1	64	85,985,5433	AA,AG,GG		4.0233,18.3613,8.8805	possibly-damaging	697/824	11008102	1155,11851	2203	4300	6503	SO:0001583	missense	148345	exon12			AGGGGCGCTGCCA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1589C>T	1.37:g.11008102G>A	ENSP00000366207:p.Ala530Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		165|165	0.07554945054945054|0.07554945054945054	115|115	0.23373983739837398|0.23373983739837398	8|8	0.022099447513812154|0.022099447513812154	2|2	0.0034965034965034965|0.0034965034965034965	40|40	0.052770448548812667|0.052770448548812667	G|G	7.224|7.224	0.597877|0.597877	0.13939|0.13939	0.183613|0.183613	0.040233|0.040233	ENSG00000175262|ENSG00000175262	ENST00000377004;ENST00000377008|ENST00000418570;ENST00000520253	T;T|.	0.33865|.	1.39;1.39|.	3.9|3.9	-2.05|-2.05	0.07321|0.07321	.|.	0.523531|.	0.14669|.	N|.	0.305451|.	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	P;P;P|.	0.42961|.	0.795;0.795;0.795|.	B;B;B|.	0.31390|.	0.129;0.129;0.081|.	T|T	0.35051|0.35051	-0.9804|-0.9804	9|4	0.18276|.	T|.	0.48|.	-0.422|-0.422	0.9467|0.9467	0.01367|0.01367	0.2137:0.3268:0.2711:0.1885|0.2137:0.3268:0.2711:0.1885	rs1281018;rs1281018|rs1281018;rs1281018	548;522;530|.	B7ZLG7;Q8N9H9-2;Q8N9H9|.	.;.;CA127_HUMAN|.	V|C	697;530|532;649	ENSP00000366203:A697V;ENSP00000366207:A530V|.	ENSP00000366203:A697V|.	A|R	-|-	2|1	0|0	C1orf127|C1orf127	10930689|10930689	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.030000|0.030000	0.12068|0.12068	-2.362000|-2.362000	0.01082|0.01082	-0.266000|-0.266000	0.09339|0.09339	-0.474000|-0.474000	0.04947|0.04947	GCG|CGC	G|0.914;A|0.086	0.086	strong		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
MKRN1	23608	hgsc.bcm.edu	37	7	140158960	140158960	+	Silent	SNP	G	G	A	rs61736379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140158960G>A	ENST00000255977.2	-	4	842	c.618C>T	c.(616-618)gcC>gcT	p.A206A	MKRN1_ENST00000474576.1_Silent_p.A142A|MKRN1_ENST00000480552.1_Intron|MKRN1_ENST00000481705.1_5'Flank|MKRN1_ENST00000443720.2_Silent_p.A206A|MKRN1_ENST00000437223.2_Intron	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	206					protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					TTGTCTCCACGGCGGTTTGCT	0.537													g|||	32	0.00638978	0.0227	0.0029	5008	,	,		17416	0.0		0.0	False		,,,				2504	0.0				p.A206A		Atlas-SNP	.											.	MKRN1	35	.	0			c.C618T						PASS	.	G	,	83,4323	70.9+/-108.8	1,81,2121	133.0	130.0	131.0		618,618	-9.8	0.0	7	dbSNP_129	131	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MKRN1	NM_001145125.1,NM_013446.3	,	1,81,6421	AA,AG,GG		0.0,1.8838,0.6382	,	206/330,206/483	140158960	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	23608	exon4			CTCCACGGCGGTT	AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606		"""RING-type (C3HC4) zinc fingers"""	7112	protein-coding gene	gene with protein product		607754				10843807	Standard	NM_013446		Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.618C>T	7.37:g.140158960G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	260	125	0.480769	NM_013446	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Silent	SNP	ENST00000255977.2	37	CCDS5860.1																																																																																			G|0.993;A|0.007	0.007	strong		0.537	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446	
CROCC	9696	hgsc.bcm.edu	37	1	17250836	17250836	+	Silent	SNP	A	A	G	rs57174186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17250836A>G	ENST00000375541.5	+	3	282	c.213A>G	c.(211-213)acA>acG	p.T71T	CROCC_ENST00000467938.1_Intron	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)		TGCCGGCCACAGAGATGGCAT	0.657																																					p.T71T		Atlas-SNP	.											CROCC,NS,carcinoma,0,3	CROCC	185	3	0			c.A213G						PASS	.	G		1667,2739		0,1667,536	38.0	33.0	35.0		213	-7.0	0.0	1	dbSNP_129	35	2771,5827		0,2771,1528	no	coding-synonymous	CROCC	NM_014675.3		0,4438,2064	GG,GA,AA		32.2284,37.8348,34.128		71/2018	17250836	4438,8566	2203	4299	6502	SO:0001819	synonymous_variant	9696	exon3			GGCCACAGAGATG	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.213A>G	1.37:g.17250836A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	102	31	0.303922	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			A|0.638;G|0.362	0.362	strong		0.657	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
OVGP1	5016	hgsc.bcm.edu	37	1	111957097	111957097	+	Missense_Mutation	SNP	C	C	G	rs7825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	69	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	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	
GGT1	2678	hgsc.bcm.edu	37	22	25016311	25016311	+	Silent	SNP	G	G	A	rs183458338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25016311G>A	ENST00000400382.1	+	8	1154	c.399G>A	c.(397-399)gcG>gcA	p.A133A	GGT1_ENST00000406383.2_Silent_p.A133A|GGT1_ENST00000400380.1_Silent_p.A133A|GGT1_ENST00000400383.1_Silent_p.A133A|GGT1_ENST00000248923.4_Silent_p.A133A			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	133					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	TGTCGGTGGCGGTGCCTGGGG	0.677													a|||	198	0.0395367	0.1362	0.0187	5008	,	,		15877	0.0		0.005	False		,,,				2504	0.0				p.A133A		Atlas-SNP	.											.	GGT1	68	.	0			c.G399A						PASS	.	A	,,,	296,3406		6,284,1561	15.0	18.0	17.0		399,399,399,399	-6.7	0.0	22		17	25,8151		0,25,4063	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GGT1	NM_001032364.2,NM_001032365.2,NM_005265.2,NM_013430.2	,,,	6,309,5624	AA,AG,GG		0.3058,7.9957,2.7025	,,,	133/570,133/570,133/570,133/570	25016311	321,11557	1851	4088	5939	SO:0001819	synonymous_variant	2678	exon8			GGTGGCGGTGCCT	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.399G>A	22.37:g.25016311G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	267	137	0.513109	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Silent	SNP	ENST00000400382.1	37	CCDS42992.1																																																																																			G|0.985;A|0.015	0.015	strong		0.677	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
LRRN1	57633	hgsc.bcm.edu	37	3	3886721	3886721	+	Silent	SNP	C	C	A	rs3749350	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:3886721C>A	ENST00000319331.3	+	2	1157	c.396C>A	c.(394-396)acC>acA	p.T132T	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	132						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		ATCAGATTACCGAGATGACTG	0.428													A|||	1458	0.291134	0.4047	0.2565	5008	,	,		20305	0.4067		0.1074	False		,,,				2504	0.2321				p.T132T		Atlas-SNP	.											.	LRRN1	82	.	0			c.C396A						PASS	.	A		1584,2822	658.8+/-400.5	301,982,920	70.0	73.0	72.0		396	-11.3	0.0	3	dbSNP_107	72	1090,7510	768.9+/-407.6	67,956,3277	no	coding-synonymous	LRRN1	NM_020873.5		368,1938,4197	AA,AC,CC		12.6744,35.951,20.5597		132/717	3886721	2674,10332	2203	4300	6503	SO:0001819	synonymous_variant	57633	exon2			GATTACCGAGATG	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"""Immunoglobulin superfamily / I-set domain containing"""	20980	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 3"""					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.396C>A	3.37:g.3886721C>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	97	42	0.43299	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																			C|0.758;A|0.242	0.242	strong		0.428	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
SFRP2	6423	hgsc.bcm.edu	37	4	154709854	154709854	+	Missense_Mutation	SNP	G	G	A	rs386680891|rs4643790	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:154709854G>A	ENST00000274063.4	-	1	418	c.134C>T	c.(133-135)gCc>gTc	p.A45V		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	45	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.		A -> V (in dbSNP:rs4643790). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		bone morphogenesis (GO:0060349)|brain development (GO:0007420)|cardiac left ventricle morphogenesis (GO:0003214)|cell-cell signaling (GO:0007267)|cellular response to extracellular stimulus (GO:0031668)|cellular response to X-ray (GO:0071481)|chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|embryonic digit morphogenesis (GO:0042733)|gonad development (GO:0008406)|hematopoietic stem cell proliferation (GO:0071425)|male gonad development (GO:0008584)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dermatome development (GO:0061185)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of gene expression (GO:0010629)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-anal tail morphogenesis (GO:0036342)|regulation of stem cell division (GO:2000035)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|sclerotome development (GO:0061056)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase activator activity (GO:0061133)|fibronectin binding (GO:0001968)|integrin binding (GO:0005178)|metalloenzyme activator activity (GO:0010577)|PDZ domain binding (GO:0030165)|receptor agonist activity (GO:0048018)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	16	all_hematologic(180;0.093)	Renal(120;0.117)				CTGCAGGTTGGCAGGGATGGG	0.647													G|||	748	0.149361	0.2784	0.1066	5008	,	,		15766	0.005		0.1879	False		,,,				2504	0.1145				p.A45V		Atlas-SNP	.											SFRP2,NS,carcinoma,-1,1	SFRP2	45	1	0			c.C134T						PASS	.	G	VAL/ALA	1167,3239	379.9+/-323.5	147,873,1183	57.0	62.0	60.0		134	4.6	1.0	4	dbSNP_111	60	1580,7020	267.1+/-287.1	152,1276,2872	yes	missense	SFRP2	NM_003013.2	64	299,2149,4055	AA,AG,GG		18.3721,26.4866,21.121	possibly-damaging	45/296	154709854	2747,10259	2203	4300	6503	SO:0001583	missense	6423	exon1			AGGTTGGCAGGGA	AF017986	CCDS34082.1	4q31.3	2008-08-29			ENSG00000145423	ENSG00000145423		"""Secreted frizzled-related proteins"""	10777	protein-coding gene	gene with protein product		604157				9391078	Standard	NM_003013		Approved	SARP1, SDF-5, FRP-2	uc003inv.1	Q96HF1	OTTHUMG00000161559	ENST00000274063.4:c.134C>T	4.37:g.154709854G>A	ENSP00000274063:p.Ala45Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	46	0.410714	NM_003013	B3KQR2|O14778|Q9HAP5	Missense_Mutation	SNP	ENST00000274063.4	37	CCDS34082.1	340	0.15567765567765568	150	0.3048780487804878	46	0.1270718232044199	3	0.005244755244755245	141	0.18601583113456466	G	14.96	2.692402	0.48202	0.264866	0.183721	ENSG00000145423	ENST00000274063	T	0.72167	-0.63	4.63	4.63	0.57726	Frizzled domain (5);	0.049068	0.85682	D	0.000000	T	0.00012	0.0000	N	0.25201	0.72	0.09310	P	0.999999385125	B	0.15473	0.013	B	0.22152	0.038	T	0.05178	-1.0901	9	0.25751	T	0.34	.	17.8889	0.88865	0.0:0.0:1.0:0.0	rs4643790;rs17850362;rs4643790	45	Q96HF1	SFRP2_HUMAN	V	45	ENSP00000274063:A45V	ENSP00000274063:A45V	A	-	2	0	SFRP2	154929304	1.000000	0.71417	0.989000	0.46669	0.955000	0.61496	5.407000	0.66363	2.288000	0.76882	0.650000	0.86243	GCC	G|0.806;A|0.194	0.194	strong		0.647	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1		
MUC16	94025	hgsc.bcm.edu	37	19	9068530	9068530	+	Missense_Mutation	SNP	C	C	T	rs7250080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	218	0	0		WXS	Illumina HiSeq	Phase_I	259	138	0.532819	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	
SPAG7	9552	hgsc.bcm.edu	37	17	4863574	4863574	+	Silent	SNP	G	G	A	rs73343383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4863574G>A	ENST00000206020.3	-	4	349	c.282C>T	c.(280-282)tcC>tcT	p.S94S	SPAG7_ENST00000575142.1_Silent_p.S83S|SPAG7_ENST00000573366.1_Silent_p.S43S	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	94	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						CTTCCCCAAAGGAGAAGGATG	0.537													G|||	149	0.0297524	0.1089	0.0058	5008	,	,		18290	0.0		0.001	False		,,,				2504	0.0				p.S94S		Atlas-SNP	.											.	SPAG7	22	.	0			c.C282T						PASS	.	G		347,3719		20,307,1706	63.0	66.0	65.0		282	2.2	1.0	17	dbSNP_130	65	4,8392		0,4,4194	no	coding-synonymous	SPAG7	NM_004890.2		20,311,5900	AA,AG,GG		0.0476,8.5342,2.8166		94/228	4863574	351,12111	2033	4198	6231	SO:0001819	synonymous_variant	9552	exon4			CCCAAAGGAGAAG	AF047437	CCDS42240.1	17p13.2	2008-07-18				ENSG00000091640			11216	protein-coding gene	gene with protein product		610056				9653160	Standard	NM_004890		Approved	FSA-1, ACRP, MGC20134	uc002gae.3	O75391		ENST00000206020.3:c.282C>T	17.37:g.4863574G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	NM_004890	Q96EU5	Silent	SNP	ENST00000206020.3	37	CCDS42240.1																																																																																			G|0.978;A|0.022	0.022	strong		0.537	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890	
SLC4A5	57835	hgsc.bcm.edu	37	2	74460685	74460685	+	Silent	SNP	C	C	T	rs3796109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74460685C>T	ENST00000377634.4	-	23	2838	c.2439G>A	c.(2437-2439)acG>acA	p.T813T	SLC4A5_ENST00000423644.1_Silent_p.T813T|SLC4A5_ENST00000346834.4_Silent_p.T813T|SLC4A5_ENST00000357822.5_Silent_p.T813T|SLC4A5_ENST00000359484.4_Silent_p.T711T|SLC4A5_ENST00000377632.1_Silent_p.T813T|SLC4A5_ENST00000358683.4_Silent_p.T711T|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000394019.2_Silent_p.T813T|RP11-287D1.3_ENST00000451608.2_3'UTR					solute carrier family 4 (sodium bicarbonate cotransporter), member 5											breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						GGTCAGGCCGCGTTGGCTGAG	0.627													C|||	543	0.108427	0.1589	0.2262	5008	,	,		18172	0.1071		0.0268	False		,,,				2504	0.0419				p.T813T		Atlas-SNP	.											.	SLC4A5	215	.	0			c.G2439A						PASS	.	C	,	592,3814	254.0+/-259.7	40,512,1651	26.0	28.0	27.0		2439,2439	-8.4	0.8	2	dbSNP_107	27	261,8339	100.1+/-161.6	4,253,4043	no	coding-synonymous,coding-synonymous	SLC4A5	NM_021196.3,NM_133478.2	,	44,765,5694	TT,TC,CC		3.0349,13.4362,6.5585	,	813/1138,813/1122	74460685	853,12153	2203	4300	6503	SO:0001819	synonymous_variant	57835	exon18			AGGCCGCGTTGGC	AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"""Solute carriers"""	18168	protein-coding gene	gene with protein product		606757	"""solute carrier family 4, sodium bicarbonate cotransporter, member 5"""			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.2439G>A	2.37:g.74460685C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	24	9	0.375	NM_021196		Silent	SNP	ENST00000377634.4	37	CCDS1936.1																																																																																			C|0.917;T|0.083	0.083	strong		0.627	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3		
UGGT2	55757	hgsc.bcm.edu	37	13	96508566	96508566	+	Missense_Mutation	SNP	T	T	A	rs35123499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:96508566T>A	ENST00000376747.3	-	34	3924	c.3854A>T	c.(3853-3855)tAt>tTt	p.Y1285F		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1285	Glucosyltransferase.		Y -> F (in dbSNP:rs35123499).		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						TCGGAATCCATACTCTTTAGC	0.348													T|||	91	0.0181709	0.0666	0.0029	5008	,	,		15927	0.0		0.001	False		,,,				2504	0.0				p.Y1285F		Atlas-SNP	.											.	UGGT2	127	.	0			c.A3854T						PASS	.	T	PHE/TYR	247,4159	142.7+/-177.9	6,235,1962	112.0	119.0	116.0		3854	5.2	1.0	13	dbSNP_126	116	0,8600		0,0,4300	yes	missense	UGGT2	NM_020121.3	22	6,235,6262	AA,AT,TT		0.0,5.606,1.8991	probably-damaging	1285/1517	96508566	247,12759	2203	4300	6503	SO:0001583	missense	55757	exon34			AATCCATACTCTT	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.3854A>T	13.37:g.96508566T>A	ENSP00000365938:p.Tyr1285Phe	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	177	88	0.497175	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	T	25.9	4.680767	0.88542	0.05606	0.0	ENSG00000102595	ENST00000376747	T	0.40756	1.02	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.14614	0.0353	L	0.53671	1.685	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.41106	-0.9527	10	0.87932	D	0	-16.5421	15.0092	0.71536	0.0:0.0:0.0:1.0	rs35123499	1285	Q9NYU1	UGGG2_HUMAN	F	1285	ENSP00000365938:Y1285F	ENSP00000365938:Y1285F	Y	-	2	0	UGGT2	95306567	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	7.698000	0.84413	1.936000	0.56123	0.533000	0.62120	TAT	T|0.980;A|0.020	0.020	strong		0.348	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
KNTC1	9735	hgsc.bcm.edu	37	12	123089955	123089955	+	Missense_Mutation	SNP	C	C	T	rs7310898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123089955C>T	ENST00000333479.7	+	51	5666	c.5489C>T	c.(5488-5490)cCt>cTt	p.P1830L	KNTC1_ENST00000450485.2_Intron|KNTC1_ENST00000537348.1_Missense_Mutation_p.P255L|KNTC1_ENST00000436959.3_5'UTR	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	1830			P -> L (in dbSNP:rs7310898).		mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		TCAACAAAACCTGGTGAAGTA	0.393													C|||	196	0.0391374	0.143	0.0101	5008	,	,		16684	0.0		0.0	False		,,,				2504	0.0				p.P1830L		Atlas-SNP	.											KNTC1,caecum,carcinoma,0,1	KNTC1	182	1	0			c.C5489T						PASS	.	C	LEU/PRO	433,3323		20,393,1465	57.0	56.0	56.0		5489	3.8	0.1	12	dbSNP_116	56	4,8242		0,4,4119	yes	missense	KNTC1	NM_014708.4	98	20,397,5584	TT,TC,CC		0.0485,11.5282,3.6411	possibly-damaging	1830/2210	123089955	437,11565	1878	4123	6001	SO:0001583	missense	9735	exon51			CAAAACCTGGTGA		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.5489C>T	12.37:g.123089955C>T	ENSP00000328236:p.Pro1830Leu	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	172	71	0.412791	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	C	25.8	4.677569	0.88445	0.115282	4.85E-4	ENSG00000184445	ENST00000333479;ENST00000537348;ENST00000546125	T;T;T	0.30182	1.54;1.54;1.54	5.64	3.79	0.43588	RZZ complex, subunit KNTC1/ROD, C-terminal (1);	0.330869	0.36932	N	0.002322	T	0.00328	0.0010	L	0.44542	1.39	0.50813	P	1.0299999999996423E-4	P	0.40534	0.72	P	0.44673	0.457	T	0.09975	-1.0650	9	0.72032	D	0.01	-12.0893	11.1536	0.48473	0.1268:0.806:0.0:0.0672	rs7310898;rs52809397;rs57876510;rs7310898	1830	P50748	KNTC1_HUMAN	L	1830;255;17	ENSP00000328236:P1830L;ENSP00000443622:P255L;ENSP00000439119:P17L	ENSP00000328236:P1830L	P	+	2	0	KNTC1	121655908	0.836000	0.29430	0.093000	0.20910	0.968000	0.65278	3.480000	0.53172	1.372000	0.46190	0.650000	0.86243	CCT	C|0.962;T|0.038	0.038	strong		0.393	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
LIPN	643418	hgsc.bcm.edu	37	10	90530683	90530683	+	Missense_Mutation	SNP	C	C	T	rs114737713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90530683C>T	ENST00000404459.1	+	6	754	c.754C>T	c.(754-756)Ctc>Ttc	p.L252F		NM_001102469.1	NP_001095939.1	Q5VXI9	LIPN_HUMAN	lipase, family member N	252					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	9		Colorectal(252;0.0161)		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)		CAATAAGATACTCTGGTTGAT	0.323													C|||	76	0.0151757	0.0545	0.0043	5008	,	,		17038	0.0		0.001	False		,,,				2504	0.0				p.L252F		Atlas-SNP	.											.	LIPN	28	.	0			c.C754T						PASS	.	C	PHE/LEU	117,3509		2,113,1698	67.0	64.0	65.0		754	1.9	0.4	10	dbSNP_132	65	3,8125		0,3,4061	yes	missense	LIPN	NM_001102469.1	22	2,116,5759	TT,TC,CC		0.0369,3.2267,1.0209	benign	252/399	90530683	120,11634	1813	4064	5877	SO:0001583	missense	643418	exon6			AAGATACTCTGGT		CCDS44456.1	10q23.31	2013-09-20	2007-02-27	2007-02-27	ENSG00000204020	ENSG00000204020			23452	protein-coding gene	gene with protein product		613924	"""lipase-like, ab-hydrolase domain containing 4"""	LIPL4			Standard	NM_001102469		Approved	bA186O14.3	uc010qmw.2	Q5VXI9	OTTHUMG00000018694	ENST00000404459.1:c.754C>T	10.37:g.90530683C>T	ENSP00000383923:p.Leu252Phe	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	150	76	0.506667	NM_001102469	A7KIH9	Missense_Mutation	SNP	ENST00000404459.1	37	CCDS44456.1	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	C	6.188	0.402853	0.11696	0.032267	3.69E-4	ENSG00000204020	ENST00000404459	T	0.62232	0.04	4.86	1.85	0.25348	Alpha/beta hydrolase fold-1 (1);	0.760258	0.11368	N	0.571199	T	0.03783	0.0107	N	0.20845	0.615	0.09310	N	1	B	0.26975	0.165	B	0.25506	0.061	T	0.04635	-1.0937	10	0.10377	T	0.69	-8.2711	5.458	0.16602	0.0:0.4967:0.0:0.5032	.	252	Q5VXI9	LIPN_HUMAN	F	252	ENSP00000383923:L252F	ENSP00000383923:L252F	L	+	1	0	LIPN	90520663	0.003000	0.15002	0.412000	0.26496	0.894000	0.52154	-0.146000	0.10250	0.668000	0.31126	0.650000	0.86243	CTC	C|0.983;T|0.017	0.017	strong		0.323	LIPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049254.2	XM_926751	
ZNF518B	85460	hgsc.bcm.edu	37	4	10447848	10447848	+	Silent	SNP	T	T	G	rs10021506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:10447848T>G	ENST00000326756.3	-	3	543	c.105A>C	c.(103-105)ccA>ccC	p.P35P		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	35					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(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						CTTGTCTATTTGGCCGAGGTG	0.468													T|||	739	0.147564	0.3245	0.0403	5008	,	,		20378	0.1627		0.003	False		,,,				2504	0.1176				p.P35P		Atlas-SNP	.											.	ZNF518B	116	.	0			c.A105C						PASS	.	T		1149,3257	407.5+/-334.3	160,829,1214	230.0	194.0	207.0		105	-4.1	0.0	4	dbSNP_119	207	34,8566	24.0+/-70.4	1,32,4267	no	coding-synonymous	ZNF518B	NM_053042.2		161,861,5481	GG,GT,TT		0.3953,26.0781,9.0958		35/1075	10447848	1183,11823	2203	4300	6503	SO:0001819	synonymous_variant	85460	exon3			TCTATTTGGCCGA	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.105A>C	4.37:g.10447848T>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_053042	Q96LN8	Silent	SNP	ENST00000326756.3	37	CCDS33960.1																																																																																			T|0.883;G|0.117	0.117	strong		0.468	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
HSH2D	84941	hgsc.bcm.edu	37	19	16259623	16259623	+	Silent	SNP	C	C	T	rs8103852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16259623C>T	ENST00000253680.6	+	4	594	c.63C>T	c.(61-63)acC>acT	p.T21T	HSH2D_ENST00000588246.1_Silent_p.T21T|HSH2D_ENST00000593154.2_Silent_p.T21T|HSH2D_ENST00000397372.4_Intron			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	21					negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(2)	4						TTGTGCACACCCAGATGGGCC	0.637													C|||	617	0.123203	0.3464	0.0692	5008	,	,		14551	0.0169		0.0746	False		,,,				2504	0.0194				p.T21T		Atlas-SNP	.											.	HSH2D	16	.	0			c.C63T						PASS	.	C		1139,2703		171,797,953	50.0	58.0	56.0		63	-3.3	1.0	19	dbSNP_116	56	559,7669		19,521,3574	no	coding-synonymous	HSH2D	NM_032855.2		190,1318,4527	TT,TC,CC		6.7939,29.646,14.0679		21/353	16259623	1698,10372	1921	4114	6035	SO:0001819	synonymous_variant	84941	exon4			GCACACCCAGATG	AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684		"""SH2 domain containing"""	24920	protein-coding gene	gene with protein product		608349				11700021	Standard	NM_032855		Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000253680.6:c.63C>T	19.37:g.16259623C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_032855	B5ME72|Q6ZNG7	Silent	SNP	ENST00000253680.6	37																																																																																				C|0.891;T|0.109	0.109	strong		0.637	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855	
TBXAS1	6916	hgsc.bcm.edu	37	7	139661964	139661964	+	Missense_Mutation	SNP	C	C	G	rs4529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139661964C>G	ENST00000336425.5	+	13	1455	c.1066C>G	c.(1066-1068)Cta>Gta	p.L356V	TBXAS1_ENST00000462275.1_3'UTR|TBXAS1_ENST00000416849.2_Missense_Mutation_p.L403V|TBXAS1_ENST00000425687.1_Missense_Mutation_p.L289V|TBXAS1_ENST00000263552.6_Missense_Mutation_p.L357V|TBXAS1_ENST00000448866.1_Missense_Mutation_p.L356V|TBXAS1_ENST00000411653.1_Missense_Mutation_p.L356V|TBXAS1_ENST00000458722.1_Missense_Mutation_p.L402V|TBXAS1_ENST00000436047.2_Missense_Mutation_p.L357V|TBXAS1_ENST00000414508.2_Missense_Mutation_p.L357V			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	356			L -> V (in allele CYP5A1*5; dbSNP:rs4529). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:11465543}.		arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	TGCCACCTACCTACTGGCCAC	0.502													C|||	209	0.0417332	0.1543	0.0058	5008	,	,		18923	0.0		0.001	False		,,,				2504	0.0				p.L403V		Atlas-SNP	.											.	TBXAS1	121	.	0			c.C1207G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	512,3894	236.1+/-248.4	24,464,1715	111.0	98.0	102.0		1069,1069,1207,865,1069	4.2	1.0	7	dbSNP_52	102	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	32,32,32,32,32	24,467,6012	GG,GC,CC		0.0349,11.6205,3.9597	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	357/535,357/535,403/581,289/467,357/461	139661964	515,12491	2203	4300	6503	SO:0001583	missense	6916	exon10			ACCTACCTACTGG	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.1066C>G	7.37:g.139661964C>G	ENSP00000338087:p.Leu356Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	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		66	0.03021978021978022	62	0.12601626016260162	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	16.28	3.079361	0.55753	0.116205	3.49E-4	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000414508;ENST00000448866;ENST00000458722;ENST00000411653	T;T;T;T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	5.98	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.02533	0.0077	M	0.71920	2.185	0.80722	D	1	P;D;P;D;P;P;P	0.63880	0.937;0.993;0.85;0.992;0.878;0.923;0.923	P;D;P;P;P;P;P	0.65573	0.896;0.936;0.775;0.811;0.722;0.696;0.696	T	0.46076	-0.9217	10	0.18276	T	0.48	.	5.3733	0.16152	0.2612:0.5412:0.1263:0.0712	rs4529;rs52804680;rs57867324;rs4529	337;403;308;289;357;357;356	B4DVP1;E7EP08;B4E0M5;E7ESB5;E7EMU9;Q53F23;P24557	.;.;.;.;.;.;THAS_HUMAN	V	289;357;356;403;357;357;356;402;356	ENSP00000388736:L289V;ENSP00000263552:L357V;ENSP00000338087:L356V;ENSP00000389414:L403V;ENSP00000392361:L357V;ENSP00000392702:L357V;ENSP00000402536:L356V;ENSP00000411274:L402V;ENSP00000411326:L356V	ENSP00000263552:L357V	L	+	1	2	TBXAS1	139308433	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	2.191000	0.42640	0.826000	0.34661	0.655000	0.94253	CTA	C|0.953;G|0.047	0.047	strong		0.502	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1		
APBA2	321	hgsc.bcm.edu	37	15	29397593	29397593	+	Silent	SNP	C	C	T	rs35322773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:29397593C>T	ENST00000558402.1	+	12	2135	c.1536C>T	c.(1534-1536)atC>atT	p.I512I	APBA2_ENST00000558259.1_Silent_p.I512I|APBA2_ENST00000411764.1_Silent_p.I500I|APBA2_ENST00000558330.1_Silent_p.I500I|APBA2_ENST00000561069.1_Silent_p.I512I			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	512	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CCCAGCTCATCGCCCAGTCTA	0.657													C|||	74	0.0147764	0.0499	0.0058	5008	,	,		17739	0.001		0.003	False		,,,				2504	0.0				p.I512I		Atlas-SNP	.											.	APBA2	132	.	0			c.C1536T						PASS	.	C	,	200,4202	122.1+/-159.5	4,192,2005	57.0	44.0	49.0		1500,1536	-6.9	0.9	15	dbSNP_126	49	58,8542	36.9+/-92.0	0,58,4242	no	coding-synonymous,coding-synonymous	APBA2	NM_001130414.1,NM_005503.3	,	4,250,6247	TT,TC,CC		0.6744,4.5434,1.9843	,	500/738,512/750	29397593	258,12744	2201	4300	6501	SO:0001819	synonymous_variant	321	exon10			GCTCATCGCCCAG	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1536C>T	15.37:g.29397593C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_005503	E9PGI4|O60571|Q5XKC0	Silent	SNP	ENST00000558402.1	37	CCDS10022.1																																																																																			C|0.980;T|0.020	0.020	strong		0.657	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
NEBL	10529	hgsc.bcm.edu	37	10	21139389	21139389	+	Missense_Mutation	SNP	T	T	C	rs4025981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:21139389T>C	ENST00000377122.4	-	11	1447	c.1051A>G	c.(1051-1053)Atg>Gtg	p.M351V	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	351			M -> V (in dbSNP:rs4025981). {ECO:0000269|PubMed:11140941}.		cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.M351V(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AATTCAAGCATTGGCTTTCCC	0.318													T|||	194	0.038738	0.0053	0.0461	5008	,	,		19089	0.0268		0.0835	False		,,,				2504	0.045				p.M351V		Atlas-SNP	.											NEBL,NS,carcinoma,0,1	NEBL	199	1	1	Substitution - Missense(1)	stomach(1)	c.A1051G						PASS	.	T	,VAL/MET,	78,4328	68.7+/-106.4	0,78,2125	179.0	170.0	173.0		,1051,	4.1	0.8	10	dbSNP_108	173	717,7883	175.3+/-225.4	28,661,3611	yes	intron,missense,intron	NEBL	NM_001173484.1,NM_006393.2,NM_213569.2	,21,	28,739,5736	CC,CT,TT		8.3372,1.7703,6.1126	,benign,	,351/1015,	21139389	795,12211	2203	4300	6503	SO:0001583	missense	10529	exon11			CAAGCATTGGCTT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1051A>G	10.37:g.21139389T>C	ENSP00000366326:p.Met351Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	37	CCDS7134.1	102	0.046703296703296704	8	0.016260162601626018	20	0.055248618784530384	15	0.026223776223776224	59	0.07783641160949868	T	10.23	1.293962	0.23564	0.017703	0.083372	ENSG00000078114	ENST00000377122	T	0.04406	3.63	5.27	4.11	0.48088	.	0.150621	0.64402	D	0.000008	T	0.00384	0.0012	M	0.62209	1.925	0.80722	D	1	B	0.16396	0.017	B	0.17722	0.019	T	0.33214	-0.9877	10	0.52906	T	0.07	.	9.0093	0.36131	0.2954:0.0:0.0:0.7046	rs4025981;rs4025981	351	O76041	NEBL_HUMAN	V	351	ENSP00000366326:M351V	ENSP00000366326:M351V	M	-	1	0	NEBL	21179395	0.984000	0.35163	0.762000	0.31397	0.935000	0.57460	1.954000	0.40362	0.924000	0.37069	0.533000	0.62120	ATG	T|0.942;C|0.058	0.058	strong		0.318	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	
FAM189A1	23359	hgsc.bcm.edu	37	15	29443949	29443949	+	Silent	SNP	A	A	G	rs3764211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:29443949A>G	ENST00000261275.4	-	5	617	c.618T>C	c.(616-618)gaT>gaC	p.D206D		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	206						integral component of membrane (GO:0016021)		p.D206D(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						TCTGCAGGACATCGGAGGAGA	0.587													G|||	950	0.189696	0.407	0.1297	5008	,	,		21334	0.1875		0.0408	False		,,,				2504	0.0941				p.D206D		Atlas-SNP	.											FAM189A1,NS,carcinoma,0,1	FAM189A1	20	1	1	Substitution - coding silent(1)	stomach(1)	c.T618C						PASS	.	G		501,883		94,313,285	122.0	106.0	111.0		618	-6.7	0.1	15	dbSNP_107	111	152,3030		4,144,1443	no	coding-synonymous	FAM189A1	NM_015307.1		98,457,1728	GG,GA,AA		4.7769,36.1994,14.3014		206/540	29443949	653,3913	692	1591	2283	SO:0001819	synonymous_variant	23359	exon5			CAGGACATCGGAG		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.618T>C	15.37:g.29443949A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_015307	A0PK09	Silent	SNP	ENST00000261275.4	37	CCDS45198.1																																																																																			A|0.791;G|0.209	0.209	strong		0.587	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
ADORA1	134	hgsc.bcm.edu	37	1	203098275	203098275	+	Silent	SNP	T	T	G	rs2228079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:203098275T>G	ENST00000367236.4	+	2	1227	c.306T>G	c.(304-306)gcT>gcG	p.A102A	ADORA1_ENST00000309502.3_Silent_p.A102A|ADORA1_ENST00000367235.1_Silent_p.A102A|ADORA1_ENST00000337894.4_Silent_p.A102A|RP11-335O13.7_ENST00000421055.1_RNA	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	102					activation of MAPKK activity (GO:0000186)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cognition (GO:0050890)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood pressure (GO:0045776)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heart contraction (GO:0045822)|negative regulation of hormone secretion (GO:0046888)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of mucus secretion (GO:0070256)|negative regulation of neurotrophin production (GO:0032900)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of vasodilation (GO:0045908)|nervous system development (GO:0007399)|phagocytosis (GO:0006909)|positive regulation of blood pressure (GO:0045777)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of nucleoside transport (GO:0032244)|positive regulation of peptide secretion (GO:0002793)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of protein dephosphorylation (GO:0035307)|protein targeting to membrane (GO:0006612)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glomerular filtration (GO:0003093)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|relaxation of vascular smooth muscle (GO:0060087)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|temperature homeostasis (GO:0001659)	asymmetric synapse (GO:0032279)|axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled adenosine receptor activity (GO:0001609)|phospholipase C activity (GO:0004629)|purine nucleoside binding (GO:0001883)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(9)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25					Adenosine(DB00640)|Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Gabapentin(DB00996)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Theobromine(DB01412)|Theophylline(DB00277)	TGGCAATTGCTGTGGACCGCT	0.597													C|||	1170	0.233626	0.1036	0.2565	5008	,	,		19241	0.1448		0.338	False		,,,				2504	0.3773				p.A102A		Atlas-SNP	.											.	ADORA1	62	.	0			c.T306G						PASS	.	C	,	556,3850		36,484,1683	123.0	118.0	120.0		306,306	-5.3	0.8	1	dbSNP_120	120	2871,5729		487,1897,1916	no	coding-synonymous,coding-synonymous	ADORA1	NM_000674.2,NM_001048230.1	,	523,2381,3599	GG,GT,TT		33.3837,12.6192,26.3494	,	102/327,102/327	203098275	3427,9579	2203	4300	6503	SO:0001819	synonymous_variant	134	exon2			AATTGCTGTGGAC	BC026340	CCDS1434.1	1q32.1	2012-08-08			ENSG00000163485	ENSG00000163485		"""GPCR / Class A : Adenosine receptors"""	262	protein-coding gene	gene with protein product		102775				1662665, 2541503	Standard	NM_001048230		Approved	RDC7	uc001gzf.1	P30542	OTTHUMG00000042125	ENST00000367236.4:c.306T>G	1.37:g.203098275T>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	104	38	0.365385	NM_001048230	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Silent	SNP	ENST00000367236.4	37	CCDS1434.1																																																																																			T|0.745;G|0.255	0.255	strong		0.597	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674	
COL18A1	80781	hgsc.bcm.edu	37	21	46900670	46900670	+	Silent	SNP	C	C	T	rs112723616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46900670C>T	ENST00000359759.4	+	12	2775	c.2754C>T	c.(2752-2754)ggC>ggT	p.G918G	COL18A1_ENST00000400337.2_Silent_p.G503G|COL18A1_ENST00000355480.5_Silent_p.G683G			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	918	Triple-helical region 3 (COL3).				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)		GCCTGCCCGGCGAGCCAGGCC	0.716													C|||	68	0.0135783	0.0454	0.0115	5008	,	,		11100	0.0		0.0	False		,,,				2504	0.0				p.G683G		Atlas-SNP	.											.	COL18A1	129	.	0			c.C2049T						PASS	.	C	,	141,3665		4,133,1766	21.0	26.0	24.0		2049,1509	-8.1	0.9	21	dbSNP_132	24	1,8213		0,1,4106	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	4,134,5872	TT,TC,CC		0.0122,3.7047,1.1814	,	683/1520,503/1340	46900670	142,11878	1903	4107	6010	SO:0001819	synonymous_variant	80781	exon12			GCCCGGCGAGCCA		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.2754C>T	21.37:g.46900670C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	57	36	0.631579	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.990;T|0.010	0.010	strong		0.716	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
C1orf109	54955	hgsc.bcm.edu	37	1	38155319	38155319	+	Silent	SNP	C	C	T	rs61731880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38155319C>T	ENST00000358011.4	-	2	423	c.234G>A	c.(232-234)ctG>ctA	p.L78L	CDCA8_ENST00000373055.1_5'Flank|CDCA8_ENST00000327331.2_5'Flank|C1orf109_ENST00000464085.1_Silent_p.L78L	NM_017850.1	NP_060320.1	Q9NX04	CA109_HUMAN	chromosome 1 open reading frame 109	78										lung(2)|prostate(2)	4		Myeloproliferative disorder(586;0.0393)				CACCAGCCACCAGCTGCTTAC	0.547													C|||	196	0.0391374	0.1369	0.0202	5008	,	,		18248	0.0		0.001	False		,,,				2504	0.0				p.L78L		Atlas-SNP	.											.	C1orf109	13	.	0			c.G234A						PASS	.	C		501,3905	225.2+/-241.2	27,447,1729	93.0	99.0	97.0		234	2.7	0.5	1	dbSNP_129	97	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	C1orf109	NM_017850.1		27,450,6026	TT,TC,CC		0.0349,11.3709,3.8751		78/204	38155319	504,12502	2203	4300	6503	SO:0001819	synonymous_variant	54955	exon2			AGCCACCAGCTGC	AK000515	CCDS423.1	1p34.3	2012-06-21			ENSG00000116922	ENSG00000116922			26039	protein-coding gene	gene with protein product		614799				22548824	Standard	XM_005270979		Approved	FLJ20508	uc001cbp.3	Q9NX04	OTTHUMG00000004323	ENST00000358011.4:c.234G>A	1.37:g.38155319C>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	214	103	0.481308	NM_017850	D3DPT1|Q8WVD1	Silent	SNP	ENST00000358011.4	37	CCDS423.1																																																																																			C|0.966;T|0.034	0.034	strong		0.547	C1orf109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012486.1	NM_017850	
DPY19L3	147991	hgsc.bcm.edu	37	19	32930808	32930808	+	Missense_Mutation	SNP	G	G	A	rs139732410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:32930808G>A	ENST00000342179.5	+	8	1062	c.847G>A	c.(847-849)Gca>Aca	p.A283T	DPY19L3_ENST00000392250.2_Missense_Mutation_p.A283T|DPY19L3_ENST00000586987.1_Missense_Mutation_p.A283T	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	283						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					CATGCTGCCAGCAGTGAAGGT	0.373													G|||	12	0.00239617	0.0091	0.0	5008	,	,		17998	0.0		0.0	False		,,,				2504	0.0				p.A283T		Atlas-SNP	.											.	DPY19L3	70	.	0			c.G847A						PASS	.	G	THR/ALA,THR/ALA	31,4375	37.6+/-69.7	0,31,2172	153.0	142.0	146.0		847,847	3.5	0.1	19	dbSNP_134	146	0,8600		0,0,4300	yes	missense,missense	DPY19L3	NM_001172774.1,NM_207325.2	58,58	0,31,6472	AA,AG,GG		0.0,0.7036,0.2384	benign,benign	283/717,283/717	32930808	31,12975	2203	4300	6503	SO:0001583	missense	147991	exon8			CTGCCAGCAGTGA		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.847G>A	19.37:g.32930808G>A	ENSP00000344937:p.Ala283Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Missense_Mutation	SNP	ENST00000342179.5	37	CCDS12422.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	5.569	0.289764	0.10567	0.007036	0.0	ENSG00000178904	ENST00000392250;ENST00000319326;ENST00000342179	T;T	0.54479	0.57;0.57	5.82	3.55	0.40652	.	0.164682	0.52532	D	0.000078	T	0.13927	0.0337	N	0.03084	-0.415	0.28833	N	0.897055	B	0.09022	0.002	B	0.08055	0.003	T	0.24154	-1.0168	10	0.05525	T	0.97	-8.0566	3.27	0.06878	0.1826:0.2943:0.523:0.0	.	283	Q6ZPD9	D19L3_HUMAN	T	283	ENSP00000376081:A283T;ENSP00000344937:A283T	ENSP00000315672:A283T	A	+	1	0	DPY19L3	37622648	0.997000	0.39634	0.084000	0.20598	0.988000	0.76386	3.927000	0.56499	1.448000	0.47680	0.557000	0.71058	GCA	G|0.998;A|0.002	0.002	strong		0.373	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325	
TNFRSF11A	8792	hgsc.bcm.edu	37	18	60036547	60036547	+	Missense_Mutation	SNP	G	G	A	rs35993683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:60036547G>A	ENST00000586569.1	+	9	1435	c.1397G>A	c.(1396-1398)cGt>cAt	p.R466H	TNFRSF11A_ENST00000269485.7_Intron	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	466					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)				TCCCCAAAACGTGGACCCTTG	0.662													G|||	61	0.0121805	0.0439	0.0043	5008	,	,		18183	0.0		0.0	False		,,,				2504	0.0				p.R466H		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.G1397A						PASS	.	G	HIS/ARG	142,4260		0,142,2059	37.0	38.0	38.0		1397	-0.8	0.1	18	dbSNP_126	38	1,8587		0,1,4293	yes	missense	TNFRSF11A	NM_003839.2	29	0,143,6352	AA,AG,GG		0.0116,3.2258,1.1008	benign	466/617	60036547	143,12847	2201	4294	6495	SO:0001583	missense	8792	exon9			CAAAACGTGGACC	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.1397G>A	18.37:g.60036547G>A	ENSP00000465500:p.Arg466His	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_003839	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Missense_Mutation	SNP	ENST00000586569.1	37	CCDS11980.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	G	12.75	2.032926	0.35893	0.032258	1.16E-4	ENSG00000141655	ENST00000269485	.	.	.	5.03	-0.8	0.10897	.	3.161140	0.01102	N	0.005394	T	0.06735	0.0172	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.11155	-1.0599	8	.	.	.	0.0539	6.8356	0.23935	0.4461:0.1218:0.4321:0.0	rs35993683;rs61751991	466	Q9Y6Q6	TNR11_HUMAN	H	466	.	.	R	+	2	0	TNFRSF11A	58187527	0.037000	0.19845	0.081000	0.20488	0.362000	0.29581	-0.004000	0.12878	-0.089000	0.12484	-0.244000	0.11960	CGT	G|0.989;A|0.011	0.011	strong		0.662	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2		
SI	6476	hgsc.bcm.edu	37	3	164750325	164750325	+	Silent	SNP	A	A	G	rs140829463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:164750325A>G	ENST00000264382.3	-	24	2783	c.2721T>C	c.(2719-2721)taT>taC	p.Y907Y		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	907	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)	TAGAAGCATCATAAGTGAAAT	0.313										HNSCC(35;0.089)			A|||	2	0.000399361	0.0015	0.0	5008	,	,		14779	0.0		0.0	False		,,,				2504	0.0				p.Y907Y		Atlas-SNP	.											.	SI	500	.	0			c.T2721C						PASS	.	A		10,4394	16.8+/-37.8	0,10,2192	133.0	128.0	130.0		2721	1.2	0.3	3	dbSNP_134	130	0,8600		0,0,4300	no	coding-synonymous	SI	NM_001041.3		0,10,6492	GG,GA,AA		0.0,0.2271,0.0769		907/1828	164750325	10,12994	2202	4300	6502	SO:0001819	synonymous_variant	6476	exon24			AGCATCATAAGTG	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.2721T>C	3.37:g.164750325A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	37	CCDS3196.1																																																																																			A|0.999;G|0.001	0.001	strong		0.313	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
IFNA16	3449	hgsc.bcm.edu	37	9	21216908	21216908	+	Missense_Mutation	SNP	C	C	G	rs386733486|rs28368163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21216908C>G	ENST00000380216.1	-	1	402	c.397G>C	c.(397-399)Gcc>Ccc	p.A133P		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	133					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		TTCATCAGGGCAATCTCTTCC	0.468													G|||	130	0.0259585	0.0499	0.0216	5008	,	,		19223	0.0		0.0427	False		,,,				2504	0.0061				p.A133P		Atlas-SNP	.											.	IFNA16	27	.	0			c.G397C						PASS	.	G	PRO/ALA	68,4336		4,60,2138	197.0	191.0	193.0		397	-1.9	0.0	9	dbSNP_125	193	140,8460		7,126,4167	no	missense	IFNA16	NM_002173.2	27	11,186,6305	GG,GC,CC		1.6279,1.5441,1.5995	benign	133/190	21216908	208,12796	2202	4300	6502	SO:0001583	missense	3449	exon1			TCAGGGCAATCTC		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"""Interferons"""	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.397G>C	9.37:g.21216908C>G	ENSP00000369564:p.Ala133Pro	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	300	127	0.423333	NM_002173	Q5VV12	Missense_Mutation	SNP	ENST00000380216.1	37	CCDS34996.1	40	0.018315018315018316	11	0.022357723577235773	6	0.016574585635359115	0	0.0	23	0.030343007915567283	-	0.007	-1.990886	0.00439	0.015441	0.016279	ENSG00000147885	ENST00000380216	T	0.03301	3.98	2.62	-1.9	0.07665	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.297473	0.27749	N	0.018011	T	0.00271	0.0008	N	0.00179	-1.91	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38693	-0.9649	10	0.02654	T	1	.	7.5429	0.27748	0.196:0.6125:0.1914:0.0	rs28368163	133	P05015	IFN16_HUMAN	P	133	ENSP00000369564:A133P	ENSP00000369564:A133P	A	-	1	0	IFNA16	21206908	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-3.642000	0.00406	-0.769000	0.04620	-1.122000	0.02009	GCC	C|0.973;G|0.027	0.027	strong		0.468	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173	
PLA2G4F	255189	hgsc.bcm.edu	37	15	42434905	42434905	+	Missense_Mutation	SNP	T	T	C	rs144100358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42434905T>C	ENST00000382396.4	-	19	2236	c.2150A>G	c.(2149-2151)aAg>aGg	p.K717R	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.K719R			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	717	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)		CTCTGTCATCTTCAAGACCTG	0.607													T|||	38	0.00758786	0.028	0.0014	5008	,	,		15524	0.0		0.0	False		,,,				2504	0.0				p.K717R		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.A2150G						PASS	.	T	ARG/LYS	97,4309	78.3+/-116.7	5,87,2111	70.0	58.0	62.0		2150	3.5	1.0	15	dbSNP_134	62	1,8597	1.2+/-3.3	0,1,4298	yes	missense	PLA2G4F	NM_213600.3	26	5,88,6409	CC,CT,TT		0.0116,2.2015,0.7536	benign	717/850	42434905	98,12906	2203	4299	6502	SO:0001583	missense	255189	exon19			GTCATCTTCAAGA		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.2150A>G	15.37:g.42434905T>C	ENSP00000371833:p.Lys717Arg	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	114	67	0.587719	NM_213600	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	37	CCDS32204.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	11.00	1.510289	0.27036	0.022015	1.16E-4	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000443825	T;T	0.11821	2.74;2.74	4.69	3.53	0.40419	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.502059	0.18373	N	0.143181	T	0.02304	0.0071	N	0.12887	0.27	0.23611	N	0.997295	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.32052	-0.9921	10	0.30854	T	0.27	-12.5606	10.4046	0.44249	0.0:0.0796:0.0:0.9204	.	504;719;717	A2RRC4;C9J281;Q68DD2	.;.;PA24F_HUMAN	R	713;719;717;717	ENSP00000380442:K719R;ENSP00000371833:K717R	ENSP00000290497:K713R	K	-	2	0	PLA2G4F	40222197	0.787000	0.28750	0.998000	0.56505	0.446000	0.32137	3.246000	0.51414	0.908000	0.36671	0.482000	0.46254	AAG	T|0.992;C|0.008	0.008	strong		0.607	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
IFI30	10437	hgsc.bcm.edu	37	19	18288069	18288069	+	Silent	SNP	A	A	G	rs7125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18288069A>G	ENST00000407280.3	+	5	778	c.603A>G	c.(601-603)ccA>ccG	p.P201P	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	201					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 II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)	p.P201P(1)		endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						TCCAGCCACCACACGAGTATG	0.572													G|||	2130	0.425319	0.5825	0.4769	5008	,	,		17497	0.2103		0.5308	False		,,,				2504	0.2894				p.P201P		Atlas-SNP	.											IFI30,NS,carcinoma,0,1	IFI30	12	1	1	Substitution - coding silent(1)	stomach(1)	c.A603G						PASS	.	G		2433,1853		713,1007,423	35.0	38.0	37.0		603	-10.2	0.0	19	dbSNP_52	37	4504,4014		1247,2010,1002	no	coding-synonymous	IFI30	NM_006332.3		1960,3017,1425	GG,GA,AA		47.1237,43.2338,45.8216		201/251	18288069	6937,5867	2143	4259	6402	SO:0001819	synonymous_variant	10437	exon5			GCCACCACACGAG	J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"""gamma-interferon-inducible lysosomal thiol reductase"", ""interferon gamma-inducible protein 30 preproprotein"""	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.603A>G	19.37:g.18288069A>G		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	193	193	1	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Silent	SNP	ENST00000407280.3	37	CCDS46015.1																																																																																			A|0.525;C|0.003	.	strong		0.572	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332	
CTBP2	1488	hgsc.bcm.edu	37	10	126715075	126715075	+	Intron	SNP	T	T	C	rs3781413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:126715075T>C	ENST00000337195.5	-	3	458				CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000309035.6_Silent_p.A418A|CTBP2_ENST00000531469.1_Intron	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		AATAGGTGGCTGCCGTCTCCA	0.687													C|||	609	0.121605	0.1074	0.2896	5008	,	,		13999	0.0456		0.1352	False		,,,				2504	0.0859				p.A418A		Atlas-SNP	.											CTBP2,NS,carcinoma,0,1	CTBP2	100	1	0			c.A1254G						PASS	.	C	,,	411,3985		17,377,1804	28.0	26.0	27.0		,,1254	-6.0	0.0	10	dbSNP_107	27	1080,7510		61,958,3276	no	intron,intron,coding-synonymous	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,	78,1335,5080	CC,CT,TT		12.5728,9.3494,11.4816	,,	,,418/986	126715075	1491,11495	2198	4295	6493	SO:0001627	intron_variant	1488	exon1			GGTGGCTGCCGTC	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12490A>G	10.37:g.126715075T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Silent	SNP	ENST00000337195.5	37	CCDS7643.1																																																																																			T|0.892;C|0.108	0.108	strong		0.687	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552921	43552921	+	Silent	SNP	C	C	T	rs12452273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43552921C>T	ENST00000430334.3	-	4	601	c.468G>A	c.(466-468)cgG>cgA	p.R156R	PLEKHM1_ENST00000421073.2_Silent_p.R67R	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	156	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CCTCAGCATCCCGGAGCAGGG	0.602													C|||	412	0.0822684	0.0378	0.1556	5008	,	,		19188	0.001		0.1958	False		,,,				2504	0.0573				p.R156R		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.G468A						PASS	.	C		276,4128	141.9+/-177.2	10,256,1936	43.0	42.0	42.0		468	-4.5	0.2	17	dbSNP_120	42	1606,6992	272.0+/-289.9	155,1296,2848	no	coding-synonymous	PLEKHM1	NM_014798.2		165,1552,4784	TT,TC,CC		18.6788,6.267,14.4747		156/1057	43552921	1882,11120	2202	4299	6501	SO:0001819	synonymous_variant	9842	exon4			AGCATCCCGGAGC	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.468G>A	17.37:g.43552921C>T		Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	266	122	0.458647	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			C|0.865;T|0.135	0.135	strong		0.602	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
ZNF813	126017	hgsc.bcm.edu	37	19	53993988	53993988	+	Missense_Mutation	SNP	A	A	T	rs12460628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53993988A>T	ENST00000396403.4	+	4	630	c.502A>T	c.(502-504)Atc>Ttc	p.I168F	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	168			I -> F (in dbSNP:rs12460628).		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)	1				GBM - Glioblastoma multiforme(134;0.00619)		GGAGAAGTCTATCAACGATGC	0.393													a|||	461	0.0920527	0.0961	0.0778	5008	,	,		20520	0.12		0.0567	False		,,,				2504	0.1043				p.I168F		Atlas-SNP	.											ZNF813_ENST00000396403,NS,carcinoma,0,1	ZNF813	81	1	0			c.A502T						PASS	.	A	PHE/ILE	395,4009	180.5+/-208.7	20,355,1827	121.0	129.0	127.0		502	-1.0	0.0	19	dbSNP_120	127	466,8132	133.9+/-191.4	23,420,3856	no	missense	ZNF813	NM_001004301.3	21	43,775,5683	TT,TA,AA		5.4199,8.9691,6.6221	benign	168/618	53993988	861,12141	2202	4299	6501	SO:0001583	missense	126017	exon4			AAGTCTATCAACG	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.502A>T	19.37:g.53993988A>T	ENSP00000379684:p.Ile168Phe	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	382	191	0.5	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	183	0.08379120879120878	53	0.10772357723577236	22	0.06077348066298342	68	0.11888111888111888	40	0.052770448548812667	A	0.022	-1.413467	0.01145	0.089691	0.054199	ENSG00000198346	ENST00000468450;ENST00000396403	T;T	0.05855	3.83;3.38	0.75	-1.0	0.10196	.	.	.	.	.	T	0.00039	0.0001	N	0.00859	-1.14	0.80722	P	0.0	B	0.20671	0.047	B	0.23419	0.046	T	0.42682	-0.9437	7	0.02654	T	1	.	.	.	.	rs12460628;rs52795330;rs12460628	168	Q6ZN06	ZN813_HUMAN	F	115;168	ENSP00000419821:I115F;ENSP00000379684:I168F	ENSP00000379684:I168F	I	+	1	0	ZNF813	58685800	0.000000	0.05858	0.016000	0.15963	0.031000	0.12232	-2.256000	0.01181	-0.425000	0.07371	0.172000	0.16884	ATC	.	.	weak		0.393	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
MRPL40	64976	hgsc.bcm.edu	37	22	19423250	19423250	+	Missense_Mutation	SNP	G	G	A	rs7575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19423250G>A	ENST00000333130.3	+	4	1039	c.386G>A	c.(385-387)cGt>cAt	p.R129H	HIRA_ENST00000546308.1_Intron|MRPL40_ENST00000443660.1_3'UTR|HIRA_ENST00000541063.1_Intron	NM_003776.2	NP_003767.2	Q9NQ50	RM40_HUMAN	mitochondrial ribosomal protein L40	129			R -> H (in dbSNP:rs7575). {ECO:0000269|PubMed:9790763}.		anatomical structure morphogenesis (GO:0009653)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|upper_aerodigestive_tract(1)	2	Colorectal(54;0.0993)					CAGCAAGAGCGTAAGATGGAG	0.552													A|||	1204	0.240415	0.4629	0.1599	5008	,	,		20621	0.1369		0.1302	False		,,,				2504	0.2168				p.R129H		Atlas-SNP	.											.	MRPL40	13	.	0			c.G386A						PASS	.	A	HIS/ARG	1771,2635	645.0+/-398.1	343,1085,775	151.0	153.0	152.0		386	4.1	0.4	22	dbSNP_52	152	1071,7529	769.9+/-407.6	59,953,3288	yes	missense	MRPL40	NM_003776.2	29	402,2038,4063	AA,AG,GG		12.4535,40.1952,21.8515	benign	129/207	19423250	2842,10164	2203	4300	6503	SO:0001583	missense	64976	exon4			AAGAGCGTAAGAT	AB051624	CCDS13760.1	22q11.2	2012-09-13	2002-11-13		ENSG00000185608	ENSG00000185608		"""Mitochondrial ribosomal proteins / large subunits"""	14491	protein-coding gene	gene with protein product		605089	"""nuclear localization signal deleted in velocardiofacial syndrome"""	NLVCF		9790763, 11543634	Standard	NM_003776		Approved	MRP-L22	uc002zpg.3	Q9NQ50	OTTHUMG00000150136	ENST00000333130.3:c.386G>A	22.37:g.19423250G>A	ENSP00000333401:p.Arg129His	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	145	75	0.517241	NM_003776	B3KVZ7|O95134	Missense_Mutation	SNP	ENST00000333130.3	37	CCDS13760.1	451	0.2065018315018315	228	0.4634146341463415	63	0.17403314917127072	67	0.11713286713286714	93	0.12269129287598944	A	1.612	-0.523852	0.04141	0.401952	0.124535	ENSG00000185608	ENST00000333130	T	0.46451	0.87	5.22	4.14	0.48551	.	0.279462	0.38381	N	0.001715	T	0.00012	0.0000	N	0.00128	-2.045	0.52099	P	5.299999999996974E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45659	-0.9246	9	0.02654	T	1	-2.778	8.2618	0.31790	0.7973:0.133:0.0697:0.0	rs7575;rs3177312;rs56481519;rs57534682;rs7575	129	Q9NQ50	RM40_HUMAN	H	129	ENSP00000333401:R129H	ENSP00000333401:R129H	R	+	2	0	MRPL40	17803250	0.994000	0.37717	0.381000	0.26106	0.244000	0.25665	3.268000	0.51585	1.001000	0.39076	-0.360000	0.07572	CGT	G|0.776;A|0.224	0.224	strong		0.552	MRPL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316491.2	NM_003776	
FBXW12	285231	hgsc.bcm.edu	37	3	48420987	48420987	+	Missense_Mutation	SNP	A	A	G	rs77256337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48420987A>G	ENST00000296438.5	+	7	899	c.713A>G	c.(712-714)cAc>cGc	p.H238R	FBXW12_ENST00000415155.1_Missense_Mutation_p.H168R|FBXW12_ENST00000436231.1_Missense_Mutation_p.H81R|RN7SL321P_ENST00000581742.1_RNA|FBXW12_ENST00000445170.1_Missense_Mutation_p.H219R	NM_207102.2	NP_996985.2	Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	238										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)		GTACTTCTACACTGCTCTCCT	0.428													A|||	33	0.00658946	0.0234	0.0029	5008	,	,		24553	0.0		0.0	False		,,,				2504	0.0				p.H238R		Atlas-SNP	.											.	FBXW12	44	.	0			c.A713G						PASS	.	A	ARG/HIS,ARG/HIS,ARG/HIS	77,4329	67.6+/-105.2	1,75,2127	301.0	269.0	280.0		503,656,713	-7.2	0.0	3	dbSNP_131	280	0,8600		0,0,4300	yes	missense,missense,missense	FBXW12	NM_001159927.1,NM_001159929.1,NM_207102.2	29,29,29	1,75,6427	GG,GA,AA		0.0,1.7476,0.592	benign,benign,benign	168/395,219/446,238/465	48420987	77,12929	2203	4300	6503	SO:0001583	missense	285231	exon7			TTCTACACTGCTC	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.713A>G	3.37:g.48420987A>G	ENSP00000296438:p.His238Arg	Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	220	119	0.540909	NM_207102	E9PG36|Q494Y9|Q494Z0	Missense_Mutation	SNP	ENST00000296438.5	37	CCDS2764.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	A	1.575	-0.533025	0.04112	0.017476	0.0	ENSG00000164049	ENST00000458736;ENST00000296438;ENST00000436231;ENST00000445170;ENST00000415155	T;T;T;T	0.62232	1.62;0.04;1.62;3.52	4.03	-7.21	0.01490	WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);	1.379180	0.04600	N	0.398402	T	0.20414	0.0491	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.10870	-1.0611	10	0.16420	T	0.52	-12.9603	1.3588	0.02187	0.1804:0.1139:0.2788:0.4269	.	137;219;168;238	E9PCA2;E9PG36;Q494Z0;Q6X9E4	.;.;.;FBW12_HUMAN	R	137;238;81;219;168	ENSP00000296438:H238R;ENSP00000413866:H81R;ENSP00000406139:H219R;ENSP00000414683:H168R	ENSP00000296438:H238R	H	+	2	0	FBXW12	48395991	0.005000	0.15991	0.000000	0.03702	0.020000	0.10135	-0.149000	0.10204	-1.503000	0.01812	-1.253000	0.01494	CAC	A|0.994;G|0.006	0.006	strong		0.428	FBXW12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257505.1	NM_207102	
CRTAC1	55118	hgsc.bcm.edu	37	10	99667840	99667840	+	Silent	SNP	A	A	G	rs35333633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99667840A>G	ENST00000370597.3	-	6	1135	c.780T>C	c.(778-780)aaT>aaC	p.N260N	CRTAC1_ENST00000370591.2_Silent_p.N260N|CRTAC1_ENST00000298819.4_Silent_p.N260N	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	260						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)		GCCCATTCTCATTGTCGCAGA	0.607													G|||	285	0.0569089	0.2005	0.0231	5008	,	,		20899	0.0		0.004	False		,,,				2504	0.0				p.N260N		Atlas-SNP	.											.	CRTAC1	86	.	0			c.T780C						PASS	.	G	,	725,3681	757.9+/-412.8	68,589,1546	89.0	68.0	75.0		780,780	-2.7	1.0	10	dbSNP_126	75	7,8593	819.0+/-406.8	0,7,4293	no	coding-synonymous,coding-synonymous	CRTAC1	NM_001206528.2,NM_018058.6	,	68,596,5839	GG,GA,AA		0.0814,16.4548,5.6282	,	260/646,260/662	99667840	732,12274	2203	4300	6503	SO:0001819	synonymous_variant	55118	exon6			ATTCTCATTGTCG	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.780T>C	10.37:g.99667840A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	153	75	0.490196	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Silent	SNP	ENST00000370597.3	37	CCDS31266.1																																																																																			A|0.946;G|0.054	0.054	strong		0.607	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
EPRS	2058	hgsc.bcm.edu	37	1	220154768	220154768	+	Silent	SNP	C	C	T	rs1061160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:220154768C>T	ENST00000366923.3	-	24	3674	c.3405G>A	c.(3403-3405)caG>caA	p.Q1135Q		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1135	Proline--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	CTCTGTGTGACTGTACCCATT	0.388													C|||	1773	0.354034	0.3986	0.4294	5008	,	,		13799	0.3423		0.3101	False		,,,				2504	0.2975				p.Q1135Q		Atlas-SNP	.											.	EPRS	140	.	0			c.G3405A						PASS	.	C		1649,2757	504.9+/-366.0	329,991,883	143.0	127.0	133.0		3405	4.1	1.0	1	dbSNP_86	133	2938,5662	457.3+/-364.3	523,1892,1885	no	coding-synonymous	EPRS	NM_004446.2		852,2883,2768	TT,TC,CC		34.1628,37.4262,35.2683		1135/1513	220154768	4587,8419	2203	4300	6503	SO:0001819	synonymous_variant	2058	exon24			GTGTGACTGTACC	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"""Aminoacyl tRNA synthetases / Class I"", ""Aminoacyl tRNA synthetases / Class II"""	3418	protein-coding gene	gene with protein product	"""glutamate tRNA ligase"", ""proline tRNA ligase"""	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3405G>A	1.37:g.220154768C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Silent	SNP	ENST00000366923.3	37	CCDS31027.1																																																																																			C|0.645;T|0.355	0.355	strong		0.388	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446	
OTOF	9381	hgsc.bcm.edu	37	2	26699822	26699822	+	Silent	SNP	G	G	A	rs2272068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26699822G>A	ENST00000272371.2	-	22	2739	c.2613C>T	c.(2611-2613)ctC>ctT	p.L871L	OTOF_ENST00000339598.3_Silent_p.L124L|OTOF_ENST00000402415.3_Silent_p.L181L|OTOF_ENST00000338581.6_Silent_p.L124L|OTOF_ENST00000403946.3_Silent_p.L871L	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	871					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CGATGGAGAAGAGCAGGTCCT	0.607													G|||	287	0.0573083	0.0492	0.036	5008	,	,		7727	0.129		0.0169	False		,,,				2504	0.0511				p.L871L	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C2613T						PASS	.	G	,,,	244,4150	141.9+/-177.2	11,222,1964	76.0	62.0	67.0		372,2613,543,372	0.5	1.0	2	dbSNP_100	67	105,8483	56.4+/-117.6	1,103,4190	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	12,325,6154	AA,AG,GG		1.2226,5.553,2.6883	,,,	124/1231,871/1998,181/1308,124/1231	26699822	349,12633	2197	4294	6491	SO:0001819	synonymous_variant	9381	exon22			GGAGAAGAGCAGG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2613C>T	2.37:g.26699822G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			G|0.965;A|0.035	0.035	strong		0.607	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
TTF2	8458	hgsc.bcm.edu	37	1	117637966	117637966	+	Silent	SNP	A	A	G	rs34079217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117637966A>G	ENST00000369466.4	+	19	3056	c.3012A>G	c.(3010-3012)caA>caG	p.Q1004Q	MIR942_ENST00000401111.1_RNA	NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	1004	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		AGGCAATTCAAAGAAATTCAG	0.358													A|||	171	0.0341454	0.1263	0.0058	5008	,	,		22139	0.0		0.0	False		,,,				2504	0.0				p.Q1004Q		Atlas-SNP	.											.	TTF2	92	.	0			c.A3012G						PASS	.	A		535,3871	240.9+/-251.5	30,475,1698	133.0	136.0	135.0		3012	2.4	0.5	1	dbSNP_126	135	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	TTF2	NM_003594.3		30,481,5992	GG,GA,AA		0.0698,12.1425,4.1596		1004/1163	117637966	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	8458	exon19			AATTCAAAGAAAT	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 6"""	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.3012A>G	1.37:g.117637966A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Silent	SNP	ENST00000369466.4	37	CCDS892.1																																																																																			A|0.964;G|0.036	0.036	strong		0.358	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3		
PAPLN	89932	hgsc.bcm.edu	37	14	73716774	73716774	+	Silent	SNP	G	G	A	rs177393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000340738.5_Silent_p.T139T|PAPLN_ENST00000381166.3_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	91	0	0		WXS	Illumina HiSeq	Phase_I	121	57	0.471074	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	
CDKN1A	1026	hgsc.bcm.edu	37	6	36651971	36651971	+	Missense_Mutation	SNP	C	C	A	rs1801270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36651971C>A	ENST00000405375.1	+	2	328	c.93C>A	c.(91-93)agC>agA	p.S31R	CDKN1A_ENST00000373711.2_Missense_Mutation_p.S31R|CDKN1A_ENST00000448526.2_Missense_Mutation_p.S65R|CDKN1A_ENST00000244741.5_Missense_Mutation_p.S31R|CDKN1A_ENST00000478800.1_3'UTR	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	31			S -> R (in dbSNP:rs1801270). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7655464, ECO:0000269|Ref.8}.		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						AGCAGCTGAGCCGCGACTGTG	0.647													C|||	1283	0.25619	0.3094	0.2493	5008	,	,		18195	0.4881		0.0666	False		,,,				2504	0.1452				p.S31R		Atlas-SNP	.											.	CDKN1A	27	.	0			c.C93A	GRCh37	CM940226	CDKN1A	M	rs1801270	PASS	.	C	ARG/SER,ARG/SER,ARG/SER,ARG/SER	1057,3349	376.1+/-321.9	130,797,1276	40.0	37.0	38.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	93,93,93,93	-3.6	0.3	6	dbSNP_89	38	602,7998	157.3+/-211.0	21,560,3719	yes	missense,missense,missense,missense	CDKN1A	NM_000389.4,NM_001220777.1,NM_001220778.1,NM_078467.2	110,110,110,110	151,1357,4995	AA,AC,CC		7.0,23.99,12.7557	benign,benign,benign,benign	31/165,31/165,31/165,31/165	36651971	1659,11347	2203	4300	6503	SO:0001583	missense	1026	exon2			GCTGAGCCGCGAC	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.93C>A	6.37:g.36651971C>A	ENSP00000384849:p.Ser31Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	37	CCDS4824.1	539	0.2467948717948718	147	0.29878048780487804	80	0.22099447513812154	262	0.458041958041958	50	0.06596306068601583	C	0.006	-2.057394	0.00390	0.2399	0.07	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61	5.06	-3.6	0.04570	.	0.965863	0.08530	N	0.932136	T	0.30759	0.0775	N	0.05012	-0.13	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	0.07809	-1.0753	9	0.05351	T	0.99	-7.2889	5.3115	0.15833	0.2314:0.199:0.4908:0.0788	rs1801270;rs3176351;rs17849556;rs17851079;rs1801270	65;31;31	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	R	65;31;31;31	ENSP00000409259:S65R;ENSP00000244741:S31R;ENSP00000384849:S31R;ENSP00000362815:S31R	ENSP00000244741:S31R	S	+	3	2	CDKN1A	36759949	0.925000	0.31364	0.288000	0.24862	0.068000	0.16541	0.270000	0.18607	-0.519000	0.06444	-1.383000	0.01170	AGC	C|0.812;A|0.188	0.188	strong		0.647	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467	
ATP6V1C2	245973	hgsc.bcm.edu	37	2	10912719	10912719	+	Silent	SNP	G	G	A	rs72777388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10912719G>A	ENST00000272238.4	+	8	730	c.621G>A	c.(619-621)gtG>gtA	p.V207V	RP11-791G15.2_ENST00000606907.1_lincRNA|ATP6V1C2_ENST00000381661.3_Silent_p.V207V	NM_001039362.1	NP_001034451.1	Q8NEY4	VATC2_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2	207					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|protein dimerization activity (GO:0046983)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		CAGACATGGTGGTCCCTCGAT	0.512													G|||	622	0.124201	0.1558	0.1369	5008	,	,		21688	0.0526		0.2028	False		,,,				2504	0.0654				p.V207V	NSCLC(188;1042 2136 10807 16813 47705)	Atlas-SNP	.											.	ATP6V1C2	73	.	0			c.G621A						PASS	.	G	,	651,3755	278.4+/-274.2	45,561,1597	273.0	273.0	273.0		621,621	2.2	1.0	2	dbSNP_130	273	1774,6826	322.0+/-315.3	187,1400,2713	no	coding-synonymous,coding-synonymous	ATP6V1C2	NM_001039362.1,NM_144583.3	,	232,1961,4310	AA,AG,GG		20.6279,14.7753,18.6452	,	207/428,207/382	10912719	2425,10581	2203	4300	6503	SO:0001819	synonymous_variant	245973	exon8			CATGGTGGTCCCT	AY039759	CCDS1674.1, CCDS42653.1	2p25.1	2010-04-21	2006-01-13		ENSG00000143882	ENSG00000143882		"""ATPases / V-type"""	18264	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 42kD, V1 subunit C isoform 2"", ""ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C isoform 2"""			12384298	Standard	XR_426949		Approved	VMA5, ATP6C2	uc002ras.3	Q8NEY4	OTTHUMG00000090459	ENST00000272238.4:c.621G>A	2.37:g.10912719G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001039362	Q96EL8	Silent	SNP	ENST00000272238.4	37	CCDS42653.1																																																																																			G|0.830;A|0.170	0.170	strong		0.512	ATP6V1C2-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323555.1	NM_144583	
FMR1NB	158521	hgsc.bcm.edu	37	X	147088249	147088249	+	Missense_Mutation	SNP	C	C	T	rs764631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:147088249C>T	ENST00000370467.3	+	3	499	c.425C>T	c.(424-426)gCa>gTa	p.A142V	5S_rRNA_ENST00000364415.1_RNA	NM_152578.2	NP_689791.1	Q8N0W7	FMR1N_HUMAN	fragile X mental retardation 1 neighbor	142	P-type.		A -> V (in dbSNP:rs764631).			integral component of membrane (GO:0016021)|nucleolus (GO:0005730)				breast(2)|cervix(1)|endometrium(3)|large_intestine(7)|lung(10)|ovary(1)|skin(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					AATCAGGTGGCAAAGCCTTGT	0.368													T|||	1597	0.423046	0.2776	0.3242	3775	,	,		12246	0.5119		0.2843	False		,,,				2504	0.2076				p.A142V		Atlas-SNP	.											.	FMR1NB	51	.	0			c.C425T						PASS	.	T	VAL/ALA	1389,2446		201,781,206,650,365	173.0	161.0	165.0		425	1.4	0.0	X	dbSNP_86	165	2473,4255		331,1126,685,971,1187	yes	missense	FMR1NB	NM_152578.2	64	532,1907,891,1621,1552	TT,TC,T,CC,C		36.7568,36.219,36.5616	benign	142/256	147088249	3862,6701	2203	4300	6503	SO:0001583	missense	158521	exon3			AGGTGGCAAAGCC		CCDS14683.1	Xq28	2009-03-25			ENSG00000176988	ENSG00000176988			26372	protein-coding gene	gene with protein product	"""cancer/testis antigen 37"""					12601173	Standard	NM_152578		Approved	FLJ25736, NY-SAR-35, CT37	uc004fcm.3	Q8N0W7	OTTHUMG00000022608	ENST00000370467.3:c.425C>T	X.37:g.147088249C>T	ENSP00000359498:p.Ala142Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	91	55	0.604396	NM_152578	D3DWT3	Missense_Mutation	SNP	ENST00000370467.3	37	CCDS14683.1	754	0.45449065702230257	94	0.22926829268292684	72	0.24161073825503357	191	0.5276243093922652	154	0.24600638977635783	T	0.059	-1.228678	0.01518	0.36219	0.367568	ENSG00000176988	ENST00000370467	T	0.42131	0.98	5.32	1.43	0.22495	P-type trefoil (1);	1.766360	0.03711	N	0.250227	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41052	-0.9530	9	0.02654	T	1	-0.0411	4.4681	0.11700	0.0:0.2775:0.2036:0.5189	rs764631;rs17247066;rs52819475;rs58562508;rs764631	142	Q8N0W7	FMR1N_HUMAN	V	142	ENSP00000359498:A142V	ENSP00000359498:A142V	A	+	2	0	FMR1NB	146895941	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.590000	0.23954	-0.452000	0.07087	-2.121000	0.00349	GCA	C|0.582;0|0.015	.	strong		0.368	FMR1NB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058667.1	NM_152578	
MSL1	339287	hgsc.bcm.edu	37	17	38285681	38285681	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38285681T>C	ENST00000398532.4	+	3	1491	c.1176T>C	c.(1174-1176)tcT>tcC	p.S392S	MSL1_ENST00000579565.1_Silent_p.S129S|MSL1_ENST00000578648.1_Silent_p.S392S|MSL1_ENST00000577454.1_Silent_p.S392S	NM_001012241.1	NP_001012241.1	Q68DK7	MSL1_HUMAN	male-specific lethal 1 homolog (Drosophila)	392					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(2)	7						AGCCCCGGTCTTCAGTGGACA	0.498																																					p.S129S		Atlas-SNP	.											.	MSL1	21	.	0			c.T387C						PASS	.						52.0	54.0	54.0					17																	38285681		1834	4093	5927	SO:0001819	synonymous_variant	339287	exon4			CCGGTCTTCAGTG		CCDS45670.1	17q21.1	2011-03-21			ENSG00000188895	ENSG00000188895			27905	protein-coding gene	gene with protein product		614801				16227571, 16543150	Standard	NM_001012241		Approved	hMSL1, MSL-1, DKFZp686P24239	uc002hua.4	Q68DK7		ENST00000398532.4:c.1176T>C	17.37:g.38285681T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	95	5	0.0526316	NM_001012241	Q0VF46|Q69Z03	Silent	SNP	ENST00000398532.4	37																																																																																				.	.	none		0.498	MSL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000447409.2	NM_001012241	
RASSF7	8045	hgsc.bcm.edu	37	11	563257	563257	+	Silent	SNP	G	G	A	rs34954482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:563257G>A	ENST00000397583.3	+	4	1324	c.891G>A	c.(889-891)caG>caA	p.Q297Q	RASSF7_ENST00000431809.1_Silent_p.Q297Q|C11orf35_ENST00000329451.3_5'Flank|RASSF7_ENST00000454668.2_Silent_p.Q297Q|RASSF7_ENST00000344375.4_Silent_p.Q297Q|RASSF7_ENST00000397582.3_Silent_p.Q297Q|MIR210HG_ENST00000500447.1_lincRNA	NM_003475.3	NP_003466.1	Q02833	RASF7_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	297					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(3)	8		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGTTCATCCAGCAGACCGGGG	0.662													G|||	584	0.116613	0.1263	0.1556	5008	,	,		18575	0.1696		0.0527	False		,,,				2504	0.0869				p.Q297Q	Pancreas(184;1170 3913 7268)	Atlas-SNP	.											.	RASSF7	22	.	0			c.G891A						PASS	.	G	,,	483,3921	214.8+/-234.0	24,435,1743	27.0	29.0	28.0		891,891,891	3.2	1.0	11	dbSNP_126	28	382,8218	121.0+/-180.1	8,366,3926	no	coding-synonymous,coding-synonymous,coding-synonymous	RASSF7	NM_001143993.1,NM_001143994.1,NM_003475.3	,,	32,801,5669	AA,AG,GG		4.4419,10.9673,6.6518	,,	297/338,297/321,297/374	563257	865,12139	2202	4300	6502	SO:0001819	synonymous_variant	8045	exon4			CATCCAGCAGACC	M91083	CCDS7702.1, CCDS44505.1, CCDS44506.1	11p15.5	2008-02-22	2008-02-22	2005-09-14	ENSG00000099849	ENSG00000099849			1166	protein-coding gene	gene with protein product		143023	"""chromosome 11 open reading frame 13"""	C11orf13		1339391	Standard	NM_001143993		Approved	HRC1, HRAS1	uc001lqc.3	Q02833	OTTHUMG00000132004	ENST00000397583.3:c.891G>A	11.37:g.563257G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	155	59	0.380645	NM_001143994	G5E9N9|Q3KP41|Q3KP42	Silent	SNP	ENST00000397583.3	37	CCDS7702.1																																																																																			G|0.921;A|0.079	0.079	strong		0.662	RASSF7-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254972.2	NM_003475	
NF1	4763	hgsc.bcm.edu	37	17	29652884	29652884	+	Silent	SNP	T	T	C	rs10512435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:29652884T>C	ENST00000358273.4	+	37	5265	c.4882T>C	c.(4882-4884)Tta>Cta	p.L1628L	NF1_ENST00000581113.2_3'UTR|NF1_ENST00000356175.3_Silent_p.L1607L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1628	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		ATACCATGTCTTACTGACTTT	0.338			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			T|||	107	0.0213658	0.0802	0.0014	5008	,	,		19715	0.0		0.0	False		,,,				2504	0.0				p.L1628L		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.T4882C						PASS	.	T	,	309,4097	164.7+/-196.3	6,297,1900	116.0	112.0	113.0		4819,4882	4.6	1.0	17	dbSNP_119	113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NF1	NM_000267.3,NM_001042492.2	,	6,298,6199	CC,CT,TT		0.0116,7.0132,2.3835	,	1607/2819,1628/2840	29652884	310,12696	2203	4300	6503	SO:0001819	synonymous_variant	4763	exon37	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CATGTCTTACTGA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4882T>C	17.37:g.29652884T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																			T|0.979;C|0.021	0.021	strong		0.338	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
TRIO	7204	hgsc.bcm.edu	37	5	14291259	14291259	+	Silent	SNP	G	G	A	rs61737132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:14291259G>A	ENST00000344204.4	+	5	999	c.975G>A	c.(973-975)ctG>ctA	p.L325L	TRIO_ENST00000509967.2_Silent_p.L276L|TRIO_ENST00000537187.1_Silent_p.L325L	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	325					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)					GGCAGCATCTGCACCAGATGT	0.562													G|||	213	0.0425319	0.152	0.0173	5008	,	,		19393	0.0		0.0	False		,,,				2504	0.0				p.L325L		Atlas-SNP	.											.	TRIO	305	.	0			c.G975A						PASS	.	G		550,3856	236.8+/-248.8	36,478,1689	54.0	52.0	53.0		975	4.2	1.0	5	dbSNP_129	53	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	TRIO	NM_007118.2		36,482,5985	AA,AG,GG		0.0465,12.483,4.2596		325/3098	14291259	554,12452	2203	4300	6503	SO:0001819	synonymous_variant	7204	exon5			GCATCTGCACCAG	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.975G>A	5.37:g.14291259G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	143	63	0.440559	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																			G|0.963;A|0.037	0.037	strong		0.562	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
WDR53	348793	hgsc.bcm.edu	37	3	196281263	196281263	+	Missense_Mutation	SNP	C	C	T	rs61730533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196281263C>T	ENST00000332629.5	-	4	1463	c.896G>A	c.(895-897)gGt>gAt	p.G299D	WDR53_ENST00000433160.1_Missense_Mutation_p.G140D|WDR53_ENST00000429115.1_Missense_Mutation_p.G138D	NM_182627.1	NP_872433.1	Q7Z5U6	WDR53_HUMAN	WD repeat domain 53	299										breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	13	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		AGTATTTCCACCCTGCTTGGT	0.418													C|||	283	0.0565096	0.1997	0.0245	5008	,	,		18151	0.0		0.002	False		,,,				2504	0.0				p.G299D		Atlas-SNP	.											.	WDR53	26	.	0			c.G896A						PASS	.	C	ASP/GLY	759,3647	310.0+/-291.3	63,633,1507	290.0	249.0	263.0		896	-3.3	0.0	3	dbSNP_129	263	11,8589	8.4+/-32.0	0,11,4289	yes	missense	WDR53	NM_182627.1	94	63,644,5796	TT,TC,CC		0.1279,17.2265,5.9203	benign	299/359	196281263	770,12236	2203	4300	6503	SO:0001583	missense	348793	exon4			TTTCCACCCTGCT	BC054030	CCDS3318.1	3q29	2013-01-09			ENSG00000185798	ENSG00000185798		"""WD repeat domain containing"""	28786	protein-coding gene	gene with protein product		615110				12477932	Standard	NM_182627		Approved	MGC64882, MGC12928	uc003fwt.3	Q7Z5U6	OTTHUMG00000155572	ENST00000332629.5:c.896G>A	3.37:g.196281263C>T	ENSP00000328079:p.Gly299Asp	Somatic	523	1	0.00191205		WXS	Illumina HiSeq	Phase_I	549	259	0.471767	NM_182627	A0MNP1	Missense_Mutation	SNP	ENST00000332629.5	37	CCDS3318.1	113	0.051739926739926737	104	0.21138211382113822	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	C	0.015	-1.543285	0.00934	0.172265	0.001279	ENSG00000185798	ENST00000332629;ENST00000429115;ENST00000433160	T;T;T	0.72282	-0.64;1.94;1.94	5.67	-3.35	0.04928	.	1.642950	0.02577	N	0.098418	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.11966	-1.0566	9	0.02654	T	1	-15.4206	0.1558	0.00098	0.3118:0.235:0.2066:0.2466	.	299	Q7Z5U6	WDR53_HUMAN	D	299;138;140	ENSP00000328079:G299D;ENSP00000396668:G138D;ENSP00000410677:G140D	ENSP00000328079:G299D	G	-	2	0	WDR53	197765660	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.565000	0.05929	-0.487000	0.06735	-1.036000	0.02392	GGT	C|0.942;T|0.058	0.058	strong		0.418	WDR53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340689.1	NM_182627	
STOX1	219736	hgsc.bcm.edu	37	10	70646139	70646139	+	Missense_Mutation	SNP	G	G	A	rs7904300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70646139G>A	ENST00000298596.6	+	3	2670	c.2587G>A	c.(2587-2589)Gcc>Acc	p.A863T	STOX1_ENST00000421961.2_Missense_Mutation_p.A753T|STOX1_ENST00000399165.4_Intron|STOX1_ENST00000399169.4_Missense_Mutation_p.A863T|STOX1_ENST00000399162.2_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	863			A -> T (in dbSNP:rs7904300).			cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						CGCAAGAAAAGCCAGTTTTGA	0.423													G|||	145	0.0289537	0.1014	0.0144	5008	,	,		20639	0.0		0.001	False		,,,				2504	0.0				p.A863T		Atlas-SNP	.											.	STOX1	75	.	0			c.G2587A						PASS	.	G	,,THR/ALA,THR/ALA,THR/ALA	385,3671		22,341,1665	81.0	81.0	81.0		,,2587,2257,2587	-1.5	0.0	10	dbSNP_116	81	4,8436		0,4,4216	yes	intron,intron,missense,missense,missense	STOX1	NM_001130159.2,NM_001130160.2,NM_001130161.2,NM_001130162.2,NM_152709.4	,,58,58,58	22,345,5881	AA,AG,GG		0.0474,9.4921,3.113	,,benign,benign,benign	,,863/990,753/880,863/990	70646139	389,12107	2028	4220	6248	SO:0001583	missense	219736	exon3			AGAAAAGCCAGTT	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.2587G>A	10.37:g.70646139G>A	ENSP00000298596:p.Ala863Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	105	42	0.4	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	7.158	0.585121	0.13749	0.094921	4.74E-4	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000421961	T;T;T	0.66815	-0.23;-0.23;-0.23	6.17	-1.51	0.08664	.	0.471664	0.25324	N	0.031488	T	0.01695	0.0054	L	0.56769	1.78	0.80722	P	0.0	B	0.19445	0.036	B	0.17098	0.017	T	0.09618	-1.0666	9	0.46703	T	0.11	.	7.4728	0.27359	0.2424:0.2162:0.5415:0.0	rs7904300;rs52803686;rs7904300	863	Q6ZVD7	STOX1_HUMAN	T	863;863;753	ENSP00000382121:A863T;ENSP00000298596:A863T;ENSP00000394509:A753T	ENSP00000298596:A863T	A	+	1	0	STOX1	70316145	0.119000	0.22226	0.000000	0.03702	0.006000	0.05464	0.598000	0.24074	-0.561000	0.06094	0.655000	0.94253	GCC	G|0.968;A|0.032	0.032	strong		0.423	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
SENP7	57337	hgsc.bcm.edu	37	3	101090925	101090925	+	Missense_Mutation	SNP	C	C	A	rs115061809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101090925C>A	ENST00000394095.2	-	7	776	c.723G>T	c.(721-723)caG>caT	p.Q241H	SENP7_ENST00000314261.7_Missense_Mutation_p.Q175H|SENP7_ENST00000394091.1_Missense_Mutation_p.Q77H|SENP7_ENST00000348610.3_Missense_Mutation_p.Q208H|SENP7_ENST00000358203.3_Missense_Mutation_p.Q77H|SENP7_ENST00000394094.2_Missense_Mutation_p.Q176H	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	241						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			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						TGTGCGCAGTCTGCTTTGCAG	0.368													C|||	50	0.00998403	0.0371	0.0014	5008	,	,		13309	0.0		0.0	False		,,,				2504	0.0				p.Q241H		Atlas-SNP	.											.	SENP7	170	.	0			c.G723T						PASS	.	C	HIS/GLN,HIS/GLN	156,4250	103.8+/-142.4	4,148,2051	135.0	127.0	129.0		528,723	1.7	0.2	3	dbSNP_132	129	0,8600		0,0,4300	yes	missense,missense	SENP7	NM_001077203.1,NM_020654.3	24,24	4,148,6351	AA,AC,CC		0.0,3.5406,1.1994	possibly-damaging,possibly-damaging	176/986,241/1051	101090925	156,12850	2203	4300	6503	SO:0001583	missense	57337	exon7			CGCAGTCTGCTTT		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.723G>T	3.37:g.101090925C>A	ENSP00000377655:p.Gln241His	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	10.27	1.303827	0.23736	0.035406	0.0	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.20069	2.12;2.1;2.15;2.11;2.11;2.13	5.1	1.66	0.24008	.	0.601428	0.14885	N	0.292719	T	0.05273	0.0140	L	0.54323	1.7	0.09310	N	1	P;P;P;P	0.48503	0.911;0.846;0.797;0.694	P;P;P;B	0.47470	0.465;0.465;0.548;0.346	T	0.08743	-1.0707	10	0.87932	D	0	-0.6991	2.926	0.05784	0.2106:0.529:0.0:0.2604	.	77;175;208;241	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	H	241;176;175;77;77;208	ENSP00000377655:Q241H;ENSP00000377654:Q176H;ENSP00000313624:Q175H;ENSP00000377651:Q77H;ENSP00000350936:Q77H;ENSP00000342159:Q208H	ENSP00000313624:Q175H	Q	-	3	2	SENP7	102573615	0.220000	0.23631	0.175000	0.22980	0.007000	0.05969	0.278000	0.18753	0.606000	0.29965	0.585000	0.79938	CAG	C|0.988;A|0.012	0.012	strong		0.368	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
ABCA13	154664	hgsc.bcm.edu	37	7	48313881	48313881	+	Missense_Mutation	SNP	T	T	C	rs17712299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:48313881T>C	ENST00000435803.1	+	17	4642	c.4618T>C	c.(4618-4620)Ttt>Ctt	p.F1540L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1540			F -> L (in dbSNP:rs17712299).		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						TCCTAATCAGTTTCAAAATAT	0.303													T|||	483	0.0964457	0.143	0.0548	5008	,	,		17567	0.1498		0.0487	False		,,,				2504	0.0573				p.F1540L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T4618C						PASS	.	T	LEU/PHE	398,3212		23,352,1430	41.0	42.0	41.0		4618	5.3	0.8	7	dbSNP_123	41	468,7628		13,442,3593	yes	missense	ABCA13	NM_152701.3	22	36,794,5023	CC,CT,TT		5.7806,11.0249,7.3979	probably-damaging	1540/5059	48313881	866,10840	1805	4048	5853	SO:0001583	missense	154664	exon17			AATCAGTTTCAAA	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.4618T>C	7.37:g.48313881T>C	ENSP00000411096:p.Phe1540Leu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	239	0.10943223443223443	80	0.16260162601626016	25	0.06906077348066299	96	0.16783216783216784	38	0.05013192612137203	T	17.56	3.420584	0.62622	0.110249	0.057806	ENSG00000179869	ENST00000435803	D	0.91631	-2.88	5.28	5.28	0.74379	.	0.000000	0.48286	D	0.000187	T	0.05456	0.0144	M	0.66939	2.045	0.09310	P	1.0	D	0.69078	0.997	D	0.75020	0.985	T	0.31971	-0.9924	8	.	.	.	.	13.2284	0.59927	0.0:0.0:0.0:1.0	rs17712299;rs17712299	1540	Q86UQ4	ABCAD_HUMAN	L	1540	ENSP00000411096:F1540L	.	F	+	1	0	ABCA13	48284427	0.614000	0.27017	0.788000	0.31933	0.576000	0.36127	2.325000	0.43840	2.125000	0.65367	0.460000	0.39030	TTT	T|0.884;C|0.116	0.116	strong		0.303	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
LRRC38	126755	hgsc.bcm.edu	37	1	13802437	13802437	+	Silent	SNP	G	G	A	rs3013106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:13802437G>A	ENST00000376085.3	-	2	1216	c.762C>T	c.(760-762)tcC>tcT	p.S254S		NM_001010847.1	NP_001010847.1	Q5VT99	LRC38_HUMAN	leucine rich repeat containing 38	254					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CGGCCACACCGGAGAAAATGA	0.582													G|||	1626	0.324681	0.4221	0.2262	5008	,	,		19646	0.3879		0.2505	False		,,,				2504	0.274				p.S254S		Atlas-SNP	.											.	LRRC38	12	.	0			c.C762T						PASS	.																																			SO:0001819	synonymous_variant	126755	exon2			CACACCGGAGAAA	BC016048	CCDS53269.1	1p36.21	2008-02-05			ENSG00000162494	ENSG00000162494			27005	protein-coding gene	gene with protein product		615212				12477932	Standard	NM_001010847		Approved		uc001avb.3	Q5VT99	OTTHUMG00000007918	ENST00000376085.3:c.762C>T	1.37:g.13802437G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	NM_001010847	Q96B32	Silent	SNP	ENST00000376085.3	37	CCDS53269.1																																																																																			A|0.323;C|0.008	0.323	strong		0.582	LRRC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021793.1		
CATSPERG	57828	hgsc.bcm.edu	37	19	38834974	38834974	+	Missense_Mutation	SNP	G	G	A	rs61732182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38834974G>A	ENST00000409235.3	+	6	750	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	CATSPERG_ENST00000410018.1_Missense_Mutation_p.R212Q|CATSPERG_ENST00000215069.4_Missense_Mutation_p.R197Q	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	212					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						AAGAGAGACCGGGACAATAAC	0.537													G|||	14	0.00279553	0.0106	0.0	5008	,	,		19650	0.0		0.0	False		,,,				2504	0.0				p.R212Q		Atlas-SNP	.											.	CATSPERG	121	.	0			c.G635A						PASS	.	G	GLN/ARG	24,1360		0,24,668	133.0	116.0	121.0		635	-6.7	0.0	19	dbSNP_129	121	0,3182		0,0,1591	no	missense	CATSPERG	NM_021185.4	43	0,24,2259	AA,AG,GG		0.0,1.7341,0.5256	benign	212/1160	38834974	24,4542	692	1591	2283	SO:0001583	missense	57828	exon6			GAGACCGGGACAA	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.635G>A	19.37:g.38834974G>A	ENSP00000386962:p.Arg212Gln	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	127	69	0.543307	NM_021185	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	37	CCDS12514.2	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	2.197	-0.383886	0.04966	0.017341	0.0	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410;ENST00000215069	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	4.61	-6.69	0.01772	.	2.425480	0.01465	N	0.016055	T	0.06096	0.0158	N	0.03177	-0.4	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15350	-1.0440	10	0.27785	T	0.31	5.2025	7.9175	0.29827	0.255:0.2965:0.4485:0.0	rs61732182	212;212	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	Q	212;212;212;197	ENSP00000387057:R212Q;ENSP00000386962:R212Q;ENSP00000386950:R212Q;ENSP00000215069:R197Q	ENSP00000215069:R197Q	R	+	2	0	CATSPERG	43526814	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.727000	0.00807	-1.348000	0.02205	-1.068000	0.02270	CGG	G|0.997;A|0.003	0.003	strong		0.537	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185	
C8A	731	hgsc.bcm.edu	37	1	57378198	57378198	+	Silent	SNP	T	T	C	rs1754533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57378198T>C	ENST00000361249.3	+	10	1599	c.1503T>C	c.(1501-1503)ccT>ccC	p.P501P		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	501	EGF-like.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						GATGTGGGCCTTGCTTCAACA	0.622													C|||	684	0.136581	0.2617	0.1326	5008	,	,		17969	0.0407		0.0487	False		,,,				2504	0.1595				p.P501P		Atlas-SNP	.											.	C8A	103	.	0			c.T1503C						PASS	.	C		901,3505	740.2+/-411.2	90,721,1392	91.0	94.0	93.0		1503	2.5	1.0	1	dbSNP_89	93	407,8193	801.2+/-407.4	8,391,3901	no	coding-synonymous	C8A	NM_000562.2		98,1112,5293	CC,CT,TT		4.7326,20.4494,10.0569		501/585	57378198	1308,11698	2203	4300	6503	SO:0001819	synonymous_variant	731	exon10			TGGGCCTTGCTTC	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"""Complement system"""	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1503T>C	1.37:g.57378198T>C		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	291	143	0.491409	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Silent	SNP	ENST00000361249.3	37	CCDS606.1																																																																																			T|0.900;C|0.100	0.100	strong		0.622	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
CYP1A2	1544	hgsc.bcm.edu	37	15	75043592	75043592	+	Missense_Mutation	SNP	C	C	A	rs17861157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75043592C>A	ENST00000343932.4	+	3	957	c.894C>A	c.(892-894)agC>agA	p.S298R		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	298			S -> R (in dbSNP:rs17861157). {ECO:0000269|PubMed:15469410}.		alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|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, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""""""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"""	CTAGAGCCAGCGGCAACCTCA	0.562													C|||	120	0.0239617	0.0893	0.0029	5008	,	,		21893	0.0		0.0	False		,,,				2504	0.0				p.S298R		Atlas-SNP	.											.	CYP1A2	70	.	0			c.C894A						PASS	.	C	ARG/SER	308,4086	164.7+/-196.3	7,294,1896	138.0	110.0	120.0		894	-9.7	0.0	15	dbSNP_123	120	2,8590	2.2+/-6.3	0,2,4294	yes	missense	CYP1A2	NM_000761.3	110	7,296,6190	AA,AC,CC		0.0233,7.0096,2.3872	benign	298/517	75043592	310,12676	2197	4296	6493	SO:0001583	missense	1544	exon3			AGCCAGCGGCAAC	AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"""Cytochrome P450s"""	2596	protein-coding gene	gene with protein product		124060	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"""			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.894C>A	15.37:g.75043592C>A	ENSP00000342007:p.Ser298Arg	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Missense_Mutation	SNP	ENST00000343932.4	37	CCDS32293.1	41	0.018772893772893772	41	0.08333333333333333	0	0.0	0	0.0	0	0.0	C	12.56	1.975261	0.34848	0.070096	2.33E-4	ENSG00000140505	ENST00000343932	T	0.79653	-1.29	4.85	-9.7	0.00521	.	0.549195	0.21605	N	0.071895	T	0.06962	0.0177	L	0.27053	0.805	0.09310	N	1	B	0.31174	0.311	B	0.28784	0.094	T	0.38112	-0.9676	10	0.59425	D	0.04	.	8.7855	0.34818	0.0:0.2777:0.1818:0.5405	rs17861157;rs56991650	298	P05177-2	.	R	298	ENSP00000342007:S298R	ENSP00000342007:S298R	S	+	3	2	CYP1A2	72830645	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-4.224000	0.00271	-3.301000	0.00192	-0.369000	0.07265	AGC	C|0.973;A|0.027	0.027	strong		0.562	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761	
C15orf40	123207	hgsc.bcm.edu	37	15	83680329	83680329	+	Missense_Mutation	SNP	G	G	A	rs17361375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83680329G>A	ENST00000513601.2	-	1	38	c.31C>T	c.(31-33)Ctt>Ttt	p.L11F	C15orf40_ENST00000451195.3_Missense_Mutation_p.L11F|RP11-382A20.7_ENST00000570202.1_RNA|C15orf40_ENST00000538348.2_Missense_Mutation_p.L11F|C15orf40_ENST00000304177.5_5'UTR|RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000565712.1_Missense_Mutation_p.L11F			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40	11										large_intestine(3)|lung(2)|skin(1)	6						GTTGCCCGAAGGTGCCTCAGC	0.697											OREG0023391	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	651	0.129992	0.1566	0.2291	5008	,	,		13813	0.003		0.1918	False		,,,				2504	0.091				p.L11F		Atlas-SNP	.											.	C15orf40	18	.	0			c.C31T						PASS	.	G	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	726,3678		46,634,1522	18.0	20.0	19.0		31,31,31,31,31	-1.2	0.0	15	dbSNP_123	19	1780,6820		176,1428,2696	yes	missense,missense,missense,missense,missense	C15orf40	NM_144597.2,NM_001160116.1,NM_001160115.1,NM_001160114.1,NM_001160113.1	22,22,22,22,22	222,2062,4218	AA,AG,GG		20.6977,16.485,19.271	benign,benign,benign,benign,benign	11/154,11/150,11/168,11/154,11/168	83680329	2506,10498	2202	4300	6502	SO:0001583	missense	123207	exon1			CCCGAAGGTGCCT	BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.31C>T	15.37:g.83680329G>A	ENSP00000424666:p.Leu11Phe	Somatic	25	0	0	1223	WXS	Illumina HiSeq	Phase_I	25	17	0.68	NM_001160116	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Missense_Mutation	SNP	ENST00000513601.2	37	CCDS32312.2	290	0.13278388278388278	71	0.1443089430894309	73	0.20165745856353592	1	0.0017482517482517483	145	0.19129287598944592	G	10.89	1.479786	0.26511	0.16485	0.206977	ENSG00000169609	ENST00000538348;ENST00000451195;ENST00000513601	.	.	.	3.61	-1.25	0.09405	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.51482	P	7.900000000005125E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.36939	-0.9727	7	0.11182	T	0.66	.	3.9244	0.09257	0.2978:0.3667:0.3354:0.0	rs17361375;rs17361375	11;11;11	F8WD31;F5GX92;G5EA00	.;.;.	F	11	.	ENSP00000403987:L11F	L	-	1	0	C15orf40	81471333	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.601000	0.05687	-0.228000	0.09869	-1.717000	0.00709	CTT	G|0.855;A|0.145	0.145	strong		0.697	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597	
ABCA13	154664	hgsc.bcm.edu	37	7	48506642	48506642	+	Splice_Site	SNP	A	A	G	rs4917153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	95	42	0.442105	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
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254074	39254074	+	Missense_Mutation	SNP	G	G	T	rs78662167		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39254074G>T	ENST00000333822.4	-	1	319	c.263C>A	c.(262-264)aCc>aAc	p.T88N		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	88	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						GTGGCAGCAGGTGGGCTGGCA	0.662																																					p.T88N		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C263A						PASS	.						7.0	11.0	10.0					17																	39254074		684	1571	2255	SO:0001583	missense	728224	exon1			CAGCAGGTGGGCT	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.263C>A	17.37:g.39254074G>T	ENSP00000328444:p.Thr88Asn	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	133	19	0.142857	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	12.61	1.990330	0.35131	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01464	4.86	3.31	-6.61	0.01818	.	.	.	.	.	T	0.02848	0.0085	M	0.87547	2.89	0.09310	N	0.999995	B	0.09022	0.002	B	0.08055	0.003	T	0.35674	-0.9779	9	0.52906	T	0.07	.	2.3202	0.04208	0.2779:0.4366:0.1148:0.1707	.	88	Q9BYQ9	KRA48_HUMAN	N	88;73	ENSP00000328444:T88N	ENSP00000414561:T73N	T	-	2	0	KRTAP4-8	36507600	0.000000	0.05858	0.000000	0.03702	0.921000	0.55340	-5.373000	0.00127	-4.086000	0.00075	0.449000	0.29647	ACC	G|0.500;T|0.500	0.500	weak		0.662	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274172	39274172	+	Silent	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39274172G>T	ENST00000391413.2	-	1	434	c.396C>A	c.(394-396)ccC>ccA	p.P132P		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	132	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ggcagcaggtgggctggcagc	0.672																																					p.P132P		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,-2,2	KRTAP4-11	94	2	0			c.C396A						scavenged	.						7.0	12.0	11.0					17																	39274172		675	1578	2253	SO:0001819	synonymous_variant	653240	exon1			GCAGGTGGGCTGG	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.396C>A	17.37:g.39274172G>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	138	4	0.0289855	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.	.	none		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
C9orf173	441476	hgsc.bcm.edu	37	9	140146526	140146526	+	Silent	SNP	G	G	A	rs74822962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140146526G>A	ENST00000412566.1	+	3	351	c.342G>A	c.(340-342)ccG>ccA	p.P114P	C9orf173_ENST00000388931.3_Silent_p.P114P			Q8N7X2	CI173_HUMAN	chromosome 9 open reading frame 173	114								p.P114P(1)		kidney(1)|large_intestine(1)|lung(5)|pancreas(1)	8						TGCCGAGCCCGTCCGTACGAG	0.672													G|||	36	0.0071885	0.0257	0.0029	5008	,	,		16156	0.0		0.0	False		,,,				2504	0.0				p.P114P		Atlas-SNP	.											C9orf173,colon,carcinoma,0,1	C9orf173	19	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G342A						PASS	.	G		64,4044		0,64,1990	40.0	50.0	47.0		342	-7.8	0.0	9	dbSNP_132	47	1,8369		0,1,4184	no	coding-synonymous	C9orf173	NM_001004353.2		0,65,6174	AA,AG,GG		0.0119,1.5579,0.5209		114/309	140146526	65,12413	2054	4185	6239	SO:0001819	synonymous_variant	441476	exon3			GAGCCCGTCCGTA		CCDS48065.1, CCDS59156.1, CCDS75940.1, CCDS75941.1	9q34.3	2009-10-02			ENSG00000197768	ENSG00000197768			37285	protein-coding gene	gene with protein product							Standard	NM_001256699		Approved	FLJ40246	uc004cmk.2	Q8N7X2		ENST00000412566.1:c.342G>A	9.37:g.140146526G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	71	52	0.732394	NM_001256701	A2RU24|B7ZM72|B7ZM76|Q8NEA3	Silent	SNP	ENST00000412566.1	37	CCDS48065.1																																																																																			G|0.991;A|0.009	0.009	strong		0.672	C9orf173-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004353	
ZFC3H1	196441	hgsc.bcm.edu	37	12	72020103	72020103	+	Silent	SNP	G	G	A	rs56384440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72020103G>A	ENST00000378743.3	-	22	4612	c.4254C>T	c.(4252-4254)gaC>gaT	p.D1418D		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1418					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						CCTGCACCTCGTCCTTGGTTC	0.413													G|||	121	0.0241613	0.0862	0.0086	5008	,	,		17082	0.0		0.001	False		,,,				2504	0.0				p.D1418D		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.C4254T						PASS	.	G		253,3587		9,235,1676	185.0	176.0	179.0		4254	-7.2	0.5	12	dbSNP_129	179	3,8243		0,3,4120	no	coding-synonymous	ZFC3H1	NM_144982.4		9,238,5796	AA,AG,GG		0.0364,6.5885,2.1182		1418/1990	72020103	256,11830	1920	4123	6043	SO:0001819	synonymous_variant	196441	exon22			CACCTCGTCCTTG	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.4254C>T	12.37:g.72020103G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	147	70	0.47619	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Silent	SNP	ENST00000378743.3	37	CCDS41813.1																																																																																			A|0.013;G|0.987	0.013	strong		0.413	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
ITPKC	80271	hgsc.bcm.edu	37	19	41235120	41235120	+	Silent	SNP	A	A	G	rs10420685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41235120A>G	ENST00000263370.2	+	3	1302	c.1269A>G	c.(1267-1269)gcA>gcG	p.A423A		NM_025194.2	NP_079470.1	Q96DU7	IP3KC_HUMAN	inositol-trisphosphate 3-kinase C	423					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)			ACTTCCAGGCAGGAGAGGATG	0.537													A|||	636	0.126997	0.2088	0.0533	5008	,	,		14672	0.2252		0.0477	False		,,,				2504	0.0491				p.A423A		Atlas-SNP	.											.	ITPKC	36	.	0			c.A1269G						PASS	.	A		832,3574	319.3+/-296.1	78,676,1449	53.0	50.0	51.0		1269	-8.8	0.9	19	dbSNP_119	51	423,8177	127.2+/-185.5	10,403,3887	no	coding-synonymous	ITPKC	NM_025194.2		88,1079,5336	GG,GA,AA		4.9186,18.8833,9.6494		423/684	41235120	1255,11751	2203	4300	6503	SO:0001819	synonymous_variant	80271	exon3			CCAGGCAGGAGAG	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.1269A>G	19.37:g.41235120A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_025194	Q9UE25|Q9Y475	Silent	SNP	ENST00000263370.2	37	CCDS12563.1																																																																																			A|0.881;G|0.119	0.119	strong		0.537	ITPKC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463104.1	NM_025194	
NUDT9	53343	hgsc.bcm.edu	37	4	88344063	88344063	+	Silent	SNP	G	G	C	rs11937770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88344063G>C	ENST00000302174.4	+	1	330	c.6G>C	c.(4-6)gcG>gcC	p.A2A	NUDT9_ENST00000473942.1_Intron	NM_024047.4	NP_076952.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 9	2					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)		CGCTCATGGCGGGACGCCTCC	0.667													C|||	539	0.107628	0.3865	0.0187	5008	,	,		15327	0.001		0.003	False		,,,				2504	0.0112				p.A2A		Atlas-SNP	.											.	NUDT9	21	.	0			c.G6C						PASS	.	C	,	1471,2935	670.9+/-402.4	263,945,995	59.0	65.0	63.0		6,	1.3	0.7	4	dbSNP_120	63	20,8580	809.7+/-407.1	0,20,4280	no	coding-synonymous,intron	NUDT9	NM_024047.3,NM_198038.1	,	263,965,5275	CC,CG,GG		0.2326,33.3863,11.4639	,	2/351,	88344063	1491,11515	2203	4300	6503	SO:0001819	synonymous_variant	53343	exon1			CATGGCGGGACGC	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.6G>C	4.37:g.88344063G>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	21	20	0.952381	NM_001248011	Q8NBN1|Q8NCB9|Q8NG25	Silent	SNP	ENST00000302174.4	37	CCDS3620.1																																																																																			G|0.895;C|0.105	0.105	strong		0.667	NUDT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253035.2		
GFRAL	389400	hgsc.bcm.edu	37	6	55196587	55196587	+	Missense_Mutation	SNP	C	C	T	rs12199003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:55196587C>T	ENST00000340465.2	+	2	183	c.97C>T	c.(97-99)Cgt>Tgt	p.R33C		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	33			R -> C (in dbSNP:rs12199003).		negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			GCAATGCTTACGTGATGCAAA	0.343													C|||	2078	0.414936	0.4312	0.2594	5008	,	,		17227	0.3056		0.3728	False		,,,				2504	0.6595				p.R33C		Atlas-SNP	.											.	GFRAL	91	.	0			c.C97T						PASS	.	C	CYS/ARG	1778,2628	525.5+/-371.6	355,1068,780	110.0	100.0	104.0		97	1.1	0.0	6	dbSNP_120	104	3122,5478	475.7+/-369.2	576,1970,1754	yes	missense	GFRAL	NM_207410.2	180	931,3038,2534	TT,TC,CC		36.3023,40.3541,37.6749	benign	33/395	55196587	4900,8106	2203	4300	6503	SO:0001583	missense	389400	exon2			TGCTTACGTGATG	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 144"""	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.97C>T	6.37:g.55196587C>T	ENSP00000343636:p.Arg33Cys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_207410	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	37	CCDS4957.1	750	0.3434065934065934	207	0.42073170731707316	104	0.287292817679558	155	0.270979020979021	284	0.37467018469656993	C	4.744	0.138430	0.09083	0.403541	0.363023	ENSG00000187871	ENST00000340465	T	0.32023	1.47	4.92	1.07	0.20283	GDNF/GAS1 (1);	0.763973	0.12676	N	0.448376	T	0.04363	0.0120	N	0.08118	0	0.80722	P	0.0	P	0.40302	0.712	B	0.33042	0.157	T	0.25882	-1.0119	9	0.54805	T	0.06	-4.7752	5.4581	0.16602	0.5391:0.365:0.0959:0.0	rs12199003;rs52831854;rs57201493;rs12199003	33	Q6UXV0	GFRAL_HUMAN	C	33	ENSP00000343636:R33C	ENSP00000343636:R33C	R	+	1	0	GFRAL	55304546	0.000000	0.05858	0.006000	0.13384	0.009000	0.06853	0.179000	0.16840	-0.047000	0.13423	-0.518000	0.04402	CGT	C|0.627;T|0.373	0.373	strong		0.343	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410	
GJB4	127534	hgsc.bcm.edu	37	1	35227041	35227041	+	Silent	SNP	C	C	T	rs76188300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35227041C>T	ENST00000339480.1	+	2	556	c.186C>T	c.(184-186)aaC>aaT	p.N62N	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	62					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)				GCTGCCCCAACGTCTGCTATG	0.612													C|||	181	0.0361422	0.1293	0.013	5008	,	,		21540	0.0		0.001	False		,,,				2504	0.0				p.N62N		Atlas-SNP	.											.	GJB4	51	.	0			c.C186T						PASS	.	C		513,3893	236.5+/-248.6	25,463,1715	177.0	125.0	143.0		186	-6.0	0.8	1	dbSNP_131	143	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	GJB4	NM_153212.2		25,468,6010	TT,TC,CC		0.0581,11.6432,3.9828		62/267	35227041	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	127534	exon2			CCCCAACGTCTGC		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.186C>T	1.37:g.35227041C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	166	77	0.463855	NM_153212	B3KQ82	Silent	SNP	ENST00000339480.1	37	CCDS383.1																																																																																			C|0.964;T|0.036	0.036	strong		0.612	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
ABCB11	8647	hgsc.bcm.edu	37	2	169853220	169853220	+	Silent	SNP	G	G	A	rs11568377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:169853220G>A	ENST00000263817.6	-	6	526	c.402C>T	c.(400-402)atC>atT	p.I134I		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	134	ABC transmembrane type-1 1. {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)			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)	TTTCGCTCTCGATGTTCAGCA	0.378													A|||	331	0.0660942	0.2179	0.0202	5008	,	,		13403	0.001		0.001	False		,,,				2504	0.0276				p.I134I		Atlas-SNP	.											.	ABCB11	136	.	0			c.C402T						PASS	.	A		590,3158		41,508,1325	60.0	57.0	58.0		402	2.8	0.9	2	dbSNP_121	58	3,8211		0,3,4104	no	coding-synonymous	ABCB11	NM_003742.2		41,511,5429	AA,AG,GG		0.0365,15.7417,4.9574		134/1322	169853220	593,11369	1874	4107	5981	SO:0001819	synonymous_variant	8647	exon6			GCTCTCGATGTTC	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.402C>T	2.37:g.169853220G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	37	CCDS46444.1																																																																																			G|0.935;A|0.065	0.065	strong		0.378	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
TEKT3	64518	hgsc.bcm.edu	37	17	15234895	15234895	+	Missense_Mutation	SNP	C	C	T	rs7226363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15234895C>T	ENST00000395930.1	-	3	194	c.8G>A	c.(7-9)cGt>cAt	p.R3H	TEKT3_ENST00000338696.2_Missense_Mutation_p.R3H	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	3			R -> H (in dbSNP:rs7226363).		cilium morphogenesis (GO:0060271)|regulation of fertilization (GO:0080154)|sperm motility (GO:0030317)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				endometrium(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	23				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		ACAACCTACACGTTCCATGAT	0.403													C|||	977	0.195088	0.1513	0.1686	5008	,	,		15690	0.2212		0.2356	False		,,,				2504	0.2045				p.R3H		Atlas-SNP	.											.	TEKT3	64	.	0			c.G8A						PASS	.	C	HIS/ARG	696,3710	290.1+/-280.8	44,608,1551	71.0	67.0	68.0		8	-11.0	0.0	17	dbSNP_116	68	2077,6523	359.3+/-331.5	269,1539,2492	yes	missense	TEKT3	NM_031898.2	29	313,2147,4043	TT,TC,CC		24.1512,15.7966,21.3209	benign	3/491	15234895	2773,10233	2203	4300	6503	SO:0001583	missense	64518	exon3			CCTACACGTTCCA	AF334676	CCDS11169.1	17p12	2011-05-23			ENSG00000125409	ENSG00000125409			14293	protein-coding gene	gene with protein product		612683				11381029, 14735490	Standard	NM_031898		Approved	FLJ32828	uc002gon.3	Q9BXF9	OTTHUMG00000058965	ENST00000395930.1:c.8G>A	17.37:g.15234895C>T	ENSP00000379263:p.Arg3His	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Missense_Mutation	SNP	ENST00000395930.1	37	CCDS11169.1	436	0.19963369963369965	70	0.14227642276422764	66	0.18232044198895028	141	0.2465034965034965	159	0.20976253298153033	C	8.891	0.954112	0.18431	0.157966	0.241512	ENSG00000125409	ENST00000395930;ENST00000338696;ENST00000536146;ENST00000539316;ENST00000543896	T;T;T;T;T	0.42513	4.15;4.15;1.56;1.56;0.97	5.51	-11.0	0.00169	.	0.900938	0.09728	N	0.763471	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.28350	0.208	B	0.13407	0.009	T	0.13255	-1.0516	9	0.38643	T	0.18	0.0046	1.0096	0.01495	0.3388:0.2037:0.2856:0.1719	rs7226363;rs52810686;rs61496150;rs7226363	3	Q9BXF9	TEKT3_HUMAN	H	3	ENSP00000379263:R3H;ENSP00000343995:R3H;ENSP00000446111:R3H;ENSP00000439713:R3H;ENSP00000444180:R3H	ENSP00000343995:R3H	R	-	2	0	TEKT3	15175620	0.006000	0.16342	0.000000	0.03702	0.001000	0.01503	0.810000	0.27183	-2.238000	0.00712	-0.878000	0.02970	CGT	C|0.794;T|0.206	0.206	strong		0.403	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898	
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695612	45695612	+	Silent	SNP	C	C	T	rs1346265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45695612C>T	ENST00000305560.6	+	1	1084	c.985C>T	c.(985-987)Ctg>Ttg	p.L329L	GATM_ENST00000458245.5_5'Flank|SPATA5L1_ENST00000559860.1_Silent_p.L329L	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	329						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		GTTGACGCTGCTGGACGGCGC	0.687													C|||	803	0.160343	0.528	0.0476	5008	,	,		14072	0.0079		0.002	False		,,,				2504	0.0634				p.L329L		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.C985T						PASS	.	C		1987,2399		467,1053,673	21.0	26.0	24.0		985	1.4	1.0	15	dbSNP_88	24	12,8564		0,12,4276	no	coding-synonymous	SPATA5L1	NM_024063.2		467,1065,4949	TT,TC,CC		0.1399,45.3032,15.422		329/754	45695612	1999,10963	2193	4288	6481	SO:0001819	synonymous_variant	79029	exon1			ACGCTGCTGGACG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.985C>T	15.37:g.45695612C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Silent	SNP	ENST00000305560.6	37	CCDS10123.1																																																																																			C|0.860;T|0.140	0.140	strong		0.687	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
CYP2B6	1555	hgsc.bcm.edu	37	19	41509950	41509950	+	Silent	SNP	G	G	C	rs2279341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41509950G>C	ENST00000324071.4	+	2	223	c.216G>C	c.(214-216)ccG>ccC	p.P72P	CYP2B6_ENST00000598834.1_3'UTR|CYP2B6_ENST00000593831.1_5'UTR|CYP2B6_ENST00000330446.5_Silent_p.P32P	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	72					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)	ACCTGGGACCGAGGCCCGTGG	0.572													G|||	260	0.0519169	0.0514	0.049	5008	,	,		16735	0.0486		0.0606	False		,,,				2504	0.0491				p.P72P		Atlas-SNP	.											CYP2B6,NS,carcinoma,0,1	CYP2B6	79	1	0			c.G216C						PASS	.	G		195,4211		3,189,2011	62.0	63.0	63.0		216	-8.3	0.0	19	dbSNP_100	63	466,8130		8,450,3840	no	coding-synonymous	CYP2B6	NM_000767.4		11,639,5851	CC,CG,GG		5.4211,4.4258,5.0838		72/492	41509950	661,12341	2203	4298	6501	SO:0001819	synonymous_variant	1555	exon2			GGGACCGAGGCCC	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.216G>C	19.37:g.41509950G>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	160	67	0.41875	NM_000767	B4DWP3|Q2V565|Q9UK46	Silent	SNP	ENST00000324071.4	37	CCDS12570.1																																																																																			.	.	weak		0.572	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	
PVRL2	5819	hgsc.bcm.edu	37	19	45368805	45368805	+	Silent	SNP	C	C	T	rs34929997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45368805C>T	ENST00000252483.5	+	2	366	c.366C>T	c.(364-366)gaC>gaT	p.D122D	PVRL2_ENST00000252485.4_Silent_p.D122D	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	122	Ig-like V-type.				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)		AGCTCCAGGACGCCACGCTGG	0.662													T|||	87	0.0173722	0.0651	0.0	5008	,	,		19055	0.0		0.001	False		,,,				2504	0.0				p.D122D		Atlas-SNP	.											.	PVRL2	58	.	0			c.C366T						PASS	.	T	,	215,4179		4,207,1986	22.0	20.0	20.0		366,366	-6.6	0.3	19	dbSNP_126	20	4,8566		0,4,4281	no	coding-synonymous,coding-synonymous	PVRL2	NM_001042724.1,NM_002856.2	,	4,211,6267	TT,TC,CC		0.0467,4.893,1.6893	,	122/539,122/480	45368805	219,12745	2197	4285	6482	SO:0001819	synonymous_variant	5819	exon2			CCAGGACGCCACG	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.366C>T	19.37:g.45368805C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	33	11	0.333333	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Silent	SNP	ENST00000252483.5	37	CCDS42576.1																																																																																			C|0.980;T|0.020	0.020	strong		0.662	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856	
TTYH2	94015	hgsc.bcm.edu	37	17	72227040	72227040	+	Missense_Mutation	SNP	G	G	A	rs150215307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72227040G>A	ENST00000269346.4	+	3	390	c.316G>A	c.(316-318)Gtt>Att	p.V106I	TTYH2_ENST00000529107.1_Missense_Mutation_p.V85I	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	106						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						TGCGGTGGGCGTTGGTTTCTA	0.483													g|||	23	0.00459265	0.0159	0.0014	5008	,	,		20070	0.0		0.0	False		,,,				2504	0.001				p.V106I		Atlas-SNP	.											.	TTYH2	63	.	0			c.G316A						PASS	.	A	ILE/VAL	58,4348	56.2+/-92.4	0,58,2145	174.0	137.0	150.0		316	3.4	0.9	17	dbSNP_134	150	2,8598	1.2+/-3.3	0,2,4298	yes	missense	TTYH2	NM_032646.5	29	0,60,6443	AA,AG,GG		0.0233,1.3164,0.4613	benign	106/535	72227040	60,12946	2203	4300	6503	SO:0001583	missense	94015	exon3			GTGGGCGTTGGTT		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.316G>A	17.37:g.72227040G>A	ENSP00000269346:p.Val106Ile	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	162	59	0.364198	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	g	8.083	0.772809	0.16051	0.013164	2.33E-4	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.12984	2.63;2.63	5.35	3.38	0.38709	.	0.185685	0.46758	N	0.000263	T	0.06234	0.0161	L	0.41961	1.31	0.80722	D	1	B;B	0.33857	0.429;0.092	B;B	0.28305	0.088;0.037	T	0.24870	-1.0148	10	0.13470	T	0.59	-8.4172	7.2697	0.26250	0.3324:0.0:0.6676:0.0	.	85;106	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	I	106;85	ENSP00000269346:V106I;ENSP00000433089:V85I	ENSP00000269346:V106I	V	+	1	0	TTYH2	69738635	0.567000	0.26626	0.943000	0.38184	0.688000	0.40055	1.396000	0.34531	0.658000	0.30925	-0.119000	0.15052	GTT	G|0.995;A|0.005	0.005	strong		0.483	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
UNC5C	8633	hgsc.bcm.edu	37	4	96127869	96127869	+	Silent	SNP	T	T	G	rs2276322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:96127869T>G	ENST00000453304.1	-	11	2160	c.1812A>C	c.(1810-1812)ccA>ccC	p.P604P		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	604	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)		TGAGGACGACTGGGCGGGTGA	0.587													G|||	2647	0.528554	0.5514	0.513	5008	,	,		14806	0.3601		0.7068	False		,,,				2504	0.499				p.P604P		Atlas-SNP	.											.	UNC5C	141	.	0			c.A1812C						PASS	.	G		2397,2009	561.4+/-380.7	638,1121,444	74.0	68.0	70.0		1812	-10.6	0.1	4	dbSNP_100	70	5785,2815	441.7+/-359.9	1944,1897,459	no	coding-synonymous	UNC5C	NM_003728.3		2582,3018,903	GG,GT,TT		32.7326,45.5969,37.0906		604/932	96127869	8182,4824	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon11			GACGACTGGGCGG	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.1812A>C	4.37:g.96127869T>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			T|0.394;G|0.606	0.606	strong		0.587	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
KDM3A	55818	hgsc.bcm.edu	37	2	86709704	86709704	+	Silent	SNP	C	C	T	rs34673273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86709704C>T	ENST00000409556.1	+	19	3174	c.2809C>T	c.(2809-2811)Ctg>Ttg	p.L937L	KDM3A_ENST00000409064.1_Silent_p.L937L|KDM3A_ENST00000312912.5_Silent_p.L937L|KDM3A_ENST00000542128.1_Silent_p.L885L			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	937					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						gcccagcattctgggctttga	0.443													C|||	122	0.024361	0.09	0.0043	5008	,	,		19735	0.0		0.0	False		,,,				2504	0.0				p.L937L	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.C2809T						PASS	.	C	,	377,4029	193.3+/-218.5	18,341,1844	126.0	119.0	121.0		2809,2809	3.7	1.0	2	dbSNP_126	121	1,8599	3.0+/-9.4	0,1,4299	no	coding-synonymous,coding-synonymous	KDM3A	NM_001146688.1,NM_018433.5	,	18,342,6143	TT,TC,CC		0.0116,8.5565,2.9064	,	937/1322,937/1322	86709704	378,12628	2203	4300	6503	SO:0001819	synonymous_variant	55818	exon18			AGCATTCTGGGCT	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"""Chromatin-modifying enzymes / K-demethylases"""	20815	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 2A"""	611512	"""jumonji domain containing 1"", ""jumonji domain containing 1A"""	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.2809C>T	2.37:g.86709704C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	185	96	0.518919	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Silent	SNP	ENST00000409556.1	37	CCDS1990.1																																																																																			C|0.969;T|0.031	0.031	strong		0.443	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
DCAF6	55827	hgsc.bcm.edu	37	1	168013850	168013850	+	Missense_Mutation	SNP	T	T	C	rs11558511	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000432587.2_Missense_Mutation_p.V593A|DCAF6_ENST00000367840.3_Missense_Mutation_p.V624A	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	112	0	0		WXS	Illumina HiSeq	Phase_I	167	79	0.473054	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	
PLEKHG4	25894	hgsc.bcm.edu	37	16	67318242	67318242	+	Missense_Mutation	SNP	A	A	G	rs8044843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67318242A>G	ENST00000360461.5	+	11	4109	c.1574A>G	c.(1573-1575)gAc>gGc	p.D525G	PLEKHG4_ENST00000427155.2_Missense_Mutation_p.D525G|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.D444G|PLEKHG4_ENST00000379344.3_Missense_Mutation_p.D525G	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	525			D -> G (in dbSNP:rs8044843).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		GCTGAACTGGACCCCCCTGGG	0.657													G|||	1410	0.28155	0.7511	0.1239	5008	,	,		16673	0.0387		0.1044	False		,,,				2504	0.1912				p.D525G		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.A1574G						PASS	.	G	GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP	2684,1712		836,1012,350	21.0	26.0	24.0		1574,1574,1574,1331,1574	4.5	0.8	16	dbSNP_116	24	895,7703		55,785,3459	yes	missense,missense,missense,missense,missense	PLEKHG4	NM_001129727.1,NM_001129728.1,NM_001129729.1,NM_001129731.1,NM_015432.3	94,94,94,94,94	891,1797,3809	GG,GA,AA		10.4094,38.9445,27.5435	benign,benign,benign,benign,benign	525/1192,525/1192,525/1192,444/1111,525/1192	67318242	3579,9415	2198	4299	6497	SO:0001583	missense	25894	exon12			AACTGGACCCCCC	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.1574A>G	16.37:g.67318242A>G	ENSP00000353646:p.Asp525Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	37	CCDS32466.1	517	0.2367216117216117	374	0.7601626016260162	52	0.143646408839779	15	0.026223776223776224	76	0.10026385224274406	G	0.626	-0.819221	0.02776	0.610555	0.104094	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.09350	3.01;3.01;3.01;2.99	4.47	4.47	0.54385	.	0.000000	0.33980	N	0.004367	T	0.00012	0.0000	N	0.00138	-2.015	0.54753	P	1.7000000000044757E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18777	-1.0326	9	0.15499	T	0.54	.	8.525	0.33300	0.1053:0.0:0.8947:0.0	rs8044843;rs58013267;rs8044843	444;525	Q58EX7-2;Q58EX7	.;PKHG4_HUMAN	G	525;525;525;444	ENSP00000353646:D525G;ENSP00000401118:D525G;ENSP00000368649:D525G;ENSP00000398030:D444G	ENSP00000353646:D525G	D	+	2	0	PLEKHG4	65875743	0.515000	0.26210	0.842000	0.33263	0.070000	0.16714	0.624000	0.24462	1.116000	0.41820	-0.197000	0.12766	GAC	A|0.727;G|0.273	0.273	strong		0.657	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
MAGED2	10916	hgsc.bcm.edu	37	X	54837277	54837277	+	Missense_Mutation	SNP	G	G	C	rs12014977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54837277G>C	ENST00000375068.1	+	4	794	c.561G>C	c.(559-561)gaG>gaC	p.E187D	MAGED2_ENST00000497484.1_3'UTR|MAGED2_ENST00000375053.2_Missense_Mutation_p.E187D|MAGED2_ENST00000218439.4_Missense_Mutation_p.E187D|MAGED2_ENST00000347546.4_Missense_Mutation_p.E169D|MAGED2_ENST00000396224.1_Missense_Mutation_p.E187D|MAGED2_ENST00000375060.1_Missense_Mutation_p.E149D|MAGED2_ENST00000375058.1_Missense_Mutation_p.E187D|MAGED2_ENST00000375062.4_Missense_Mutation_p.E149D			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	187			E -> D (in dbSNP:rs12014977).			membrane (GO:0016020)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						ATGGGGAAGAGGATGGCAGCA	0.552													G|||	91	0.024106	0.0666	0.0043	3775	,	,		4773	0.0		0.0	False		,,,				2504	0.0				p.E187D		Atlas-SNP	.											.	MAGED2	74	.	0			c.G561C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU	275,3560		8,225,34,1399,537	59.0	57.0	58.0		561,561,561	2.1	1.0	X	dbSNP_120	58	4,6724		0,4,0,2424,1872	yes	missense,missense,missense	MAGED2	NM_014599.4,NM_177433.1,NM_201222.1	45,45,45	8,229,34,3823,2409	CC,CG,C,GG,G		0.0595,7.1708,2.6413	probably-damaging,probably-damaging,probably-damaging	187/607,187/607,187/607	54837277	279,10284	2203	4300	6503	SO:0001583	missense	10916	exon4			GGAAGAGGATGGC	AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"""hepatocellular carcinoma associated protein"", ""breast cancer associated gene 1"", ""melanoma-associated antigen D2"", ""hepatocellular carcinoma-associated protein HCA10"""	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.561G>C	X.37:g.54837277G>C	ENSP00000364209:p.Glu187Asp	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	196	105	0.535714	NM_201222	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Missense_Mutation	SNP	ENST00000375068.1	37	CCDS14362.1	35	0.02109704641350211	20	0.0425531914893617	1	0.0028089887640449437	0	0.0	0	0.0	G	16.72	3.200742	0.58126	0.071708	5.95E-4	ENSG00000102316	ENST00000375068;ENST00000375053;ENST00000347546;ENST00000343474;ENST00000375062;ENST00000218439;ENST00000375058;ENST00000375060;ENST00000396224	T;T;T;T;T;T;T;T;T	0.71698	1.26;1.26;3.95;-0.59;0.91;1.26;1.26;0.91;1.26	3.85	2.06	0.26882	.	0.000000	0.44097	D	0.000493	T	0.15998	0.0385	L	0.27053	0.805	0.38540	P	0.05080499999999999	D;P;D	0.61697	0.99;0.956;0.982	D;D;D	0.72982	0.979;0.931;0.952	T	0.56866	-0.7908	9	0.29301	T	0.29	.	7.4321	0.27134	0.2294:0.0:0.7706:0.0	rs12014977;rs52798808;rs12014977	169;149;187	Q9UNF1-2;Q5H907;Q9UNF1	.;.;MAGD2_HUMAN	D	187;187;131;169;149;187;187;149;187	ENSP00000364209:E187D;ENSP00000364193:E187D;ENSP00000336962:E131D;ENSP00000340290:E169D;ENSP00000364202:E149D;ENSP00000218439:E187D;ENSP00000364198:E187D;ENSP00000364200:E149D;ENSP00000379526:E187D	ENSP00000218439:E187D	E	+	3	2	MAGED2	54854002	0.885000	0.30320	1.000000	0.80357	0.993000	0.82548	-0.682000	0.05185	0.430000	0.26230	-0.192000	0.12808	GAG	G|0.973;C|0.027	0.027	strong		0.552	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599	
GPR110	266977	hgsc.bcm.edu	37	6	46977783	46977783	+	Missense_Mutation	SNP	C	C	T	rs45598235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46977783C>T	ENST00000371253.2	-	11	1603	c.1388G>A	c.(1387-1389)cGt>cAt	p.R463H	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.R266H	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	463					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						AATTAACACACGGCCTCTGAT	0.438													C|||	186	0.0371406	0.0787	0.0389	5008	,	,		20334	0.0		0.0447	False		,,,				2504	0.0102				p.R463H		Atlas-SNP	.											GPR110,NS,carcinoma,0,1	GPR110	102	1	0			c.G1388A						PASS	.	C	HIS/ARG	378,4028	190.9+/-216.7	14,350,1839	97.0	92.0	94.0		1388	-3.6	0.0	6	dbSNP_127	94	328,8272	115.3+/-175.2	7,314,3979	yes	missense	GPR110	NM_153840.2	29	21,664,5818	TT,TC,CC		3.814,8.5792,5.4283	benign	463/911	46977783	706,12300	2203	4300	6503	SO:0001583	missense	266977	exon11			AACACACGGCCTC	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.1388G>A	6.37:g.46977783C>T	ENSP00000360299:p.Arg463His	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	176	85	0.482955	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	37	CCDS34471.1	83	0.038003663003663	43	0.08739837398373984	13	0.03591160220994475	0	0.0	27	0.03562005277044855	C	8.205	0.798930	0.16397	0.085792	0.03814	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000283297	T;T	0.34472	1.37;1.36	5.2	-3.63	0.04529	.	1.386990	0.04430	N	0.369085	T	0.04588	0.0125	N	0.02202	-0.64	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28996	-1.0026	10	0.35671	T	0.21	-0.5469	6.9695	0.24640	0.0:0.2802:0.2071:0.5127	rs45598235	463	Q5T601	GP110_HUMAN	H	463;463;266	ENSP00000360299:R463H;ENSP00000283297:R266H	ENSP00000283297:R266H	R	-	2	0	GPR110	47085742	0.000000	0.05858	0.022000	0.16811	0.063000	0.16089	-0.885000	0.04161	-0.181000	0.10619	-1.467000	0.01014	CGT	C|0.952;T|0.048	0.048	strong		0.438	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
CHI3L1	1116	hgsc.bcm.edu	37	1	203152851	203152851	+	Missense_Mutation	SNP	C	C	T	rs147131854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:203152851C>T	ENST00000255409.3	-	5	508	c.383G>A	c.(382-384)cGc>cAc	p.R128H		NM_001276.2	NP_001267.2	P36222	CH3L1_HUMAN	chitinase 3-like 1 (cartilage glycoprotein-39)	128					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to tumor necrosis factor (GO:0071356)|chitin catabolic process (GO:0006032)|inflammatory response (GO:0006954)|interleukin-8 secretion (GO:0072606)|lung development (GO:0030324)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase B signaling (GO:0051897)|response to interleukin-1 (GO:0070555)|response to interleukin-6 (GO:0070741)|response to mechanical stimulus (GO:0009612)|response to tumor necrosis factor (GO:0034612)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|extracellular matrix structural constituent (GO:0005201)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.R128H(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|skin(1)	18						GCCATGGGTGCGCAGAAATGG	0.532													C|||	2	0.000399361	0.0	0.0	5008	,	,		22573	0.0		0.0	False		,,,				2504	0.002				p.R128H		Atlas-SNP	.											CHI3L1,colon,carcinoma,0,1	CHI3L1	51	1	1	Substitution - Missense(1)	large_intestine(1)	c.G383A						PASS	.	C	HIS/ARG	5,4401	9.9+/-24.2	0,5,2198	136.0	109.0	118.0		383	5.7	0.9	1	dbSNP_134	118	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CHI3L1	NM_001276.2	29	0,10,6493	TT,TC,CC		0.0581,0.1135,0.0769	probably-damaging	128/384	203152851	10,12996	2203	4300	6503	SO:0001583	missense	1116	exon5			TGGGTGCGCAGAA	BC008568	CCDS1435.1	1q32.1	2008-02-05			ENSG00000133048	ENSG00000133048			1932	protein-coding gene	gene with protein product		601525				8245017, 9244440	Standard	NM_001276		Approved	GP39, YKL40	uc001gzi.2	P36222	OTTHUMG00000042122	ENST00000255409.3:c.383G>A	1.37:g.203152851C>T	ENSP00000255409:p.Arg128His	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_001276	B2R7B0|P30923|Q8IVA4|Q96HI7	Missense_Mutation	SNP	ENST00000255409.3	37	CCDS1435.1	.	.	.	.	.	.	.	.	.	.	C	19.23	3.787628	0.70337	0.001135	5.81E-4	ENSG00000133048	ENST00000255409	T	0.07114	3.22	5.69	5.69	0.88448	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.50627	D	0.000104	T	0.35799	0.0944	M	0.87456	2.885	0.54753	D	0.999988	D	0.89917	1.0	D	0.97110	1.0	T	0.15407	-1.0438	10	0.62326	D	0.03	-35.3845	17.3057	0.87194	0.0:1.0:0.0:0.0	.	128	P36222	CH3L1_HUMAN	H	128	ENSP00000255409:R128H	ENSP00000255409:R128H	R	-	2	0	CHI3L1	201419474	1.000000	0.71417	0.910000	0.35882	0.095000	0.18619	7.061000	0.76699	2.664000	0.90586	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	strong		0.532	CHI3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100265.1	NM_001276	
MT-CO1	4512	hgsc.bcm.edu	37	M	6150	6150	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:6150G>A	ENST00000361624.2	+	1	247	c.247G>A	c.(247-249)Gtt>Att	p.V83I	MT-CO2_ENST00000361739.1_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TN_ENST00000387400.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TA_ENST00000387392.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TQ_ENST00000387372.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TW_ENST00000387382.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TK_ENST00000387421.1_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	83					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						GCAACTGACTAGTTCCCCTAA	0.463																																					p.V83I		Atlas-SNP	.											.	.	.	.	0			c.G247A						PASS	.																																			SO:0001583	missense	5742	exon1			TGACTAGTTCCCC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.247G>A	M.37:g.6150G>A	ENSP00000354499:p.Val83Ile	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	ENST00000361624	Q34770	Missense_Mutation	SNP	ENST00000361624.2	37																																																																																				.	.	none		0.463	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028	
COG6	57511	hgsc.bcm.edu	37	13	40229957	40229957	+	Missense_Mutation	SNP	T	T	A	rs3812883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:40229957T>A	ENST00000455146.3	+	1	144	c.94T>A	c.(94-96)Tgc>Agc	p.C32S	COG6_ENST00000416691.1_Missense_Mutation_p.C32S	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	32			C -> S (in dbSNP:rs3812883). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.6}.		glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		GGCGACGACCTGCAACCCGCT	0.677													A|||	2425	0.484225	0.5015	0.5879	5008	,	,		14507	0.4573		0.3767	False		,,,				2504	0.5256				p.C32S		Atlas-SNP	.											.	COG6	49	.	0			c.T94A						PASS	.	A	SER/CYS,SER/CYS	2079,2315		492,1095,610	19.0	19.0	19.0		94,94	3.0	0.0	13	dbSNP_107	19	3324,5268		694,1936,1666	yes	missense,missense	COG6	NM_001145079.1,NM_020751.2	112,112	1186,3031,2276	AA,AT,TT		38.6872,47.3145,41.6063	benign,benign	32/616,32/658	40229957	5403,7583	2197	4296	6493	SO:0001583	missense	57511	exon1			ACGACCTGCAACC	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"""Components of oligomeric golgi complex"""	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.94T>A	13.37:g.40229957T>A	ENSP00000397441:p.Cys32Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	97	55	0.56701	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	37	CCDS9370.1	1013	0.46382783882783885	249	0.5060975609756098	210	0.580110497237569	261	0.4562937062937063	293	0.3865435356200528	A	5.269	0.235062	0.09969	0.473145	0.386872	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000422759;ENST00000455146	T;T;T	0.32515	1.45;1.71;1.46	5.41	3.0	0.34707	.	0.624277	0.17468	N	0.173170	T	0.00012	0.0000	N	0.01048	-1.04	0.54753	P	1.2000000000012001E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45906	-0.9229	9	0.02654	T	1	-27.9087	2.2529	0.04048	0.5888:0.1751:0.0858:0.1503	rs3812883;rs3812883	53;32	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	S	32;63;32;32	ENSP00000403733:C32S;ENSP00000412877:C32S;ENSP00000397441:C32S	ENSP00000255468:C63S	C	+	1	0	COG6	39127957	0.980000	0.34600	0.016000	0.15963	0.004000	0.04260	2.549000	0.45803	0.056000	0.16144	-0.364000	0.07487	TGC	T|0.567;A|0.433	0.433	strong		0.677	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3		
HERC2	8924	hgsc.bcm.edu	37	15	28456220	28456220	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:28456220G>A	ENST00000261609.7	-	44	7105	c.6997C>T	c.(6997-6999)Ctc>Ttc	p.L2333F		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)		TGGTGGGAGAGCAGCGCCCGA	0.517																																					p.L2333F		Atlas-SNP	.											HERC2,NS,carcinoma,0,1	HERC2	501	1	0			c.C6997T						scavenged	.						78.0	74.0	75.0					15																	28456220		2202	4298	6500	SO:0001583	missense	8924	exon44			GGGAGAGCAGCGC	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.6997C>T	15.37:g.28456220G>A	ENSP00000261609:p.Leu2333Phe	Somatic	644	1	0.0015528		WXS	Illumina HiSeq	Phase_I	738	15	0.0203252	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.406637	0.62399	.	.	ENSG00000128731	ENST00000261609	T	0.38722	1.12	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.52549	0.1741	L	0.38175	1.15	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.36720	-0.9736	10	0.13108	T	0.6	.	18.1363	0.89620	0.0:0.0:1.0:0.0	.	2333	O95714	HERC2_HUMAN	F	2333	ENSP00000261609:L2333F	ENSP00000261609:L2333F	L	-	1	0	HERC2	26129815	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	9.652000	0.98499	2.497000	0.84241	0.561000	0.74099	CTC	.	.	weak		0.517	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
ZNF43	7594	hgsc.bcm.edu	37	19	21991663	21991663	+	Silent	SNP	A	A	G	rs61733114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21991663A>G	ENST00000354959.4	-	4	1345	c.1176T>C	c.(1174-1176)caT>caC	p.H392H	ZNF43_ENST00000595461.1_Silent_p.H386H|ZNF43_ENST00000594012.1_Silent_p.H386H|ZNF43_ENST00000598381.1_Silent_p.H386H	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	392					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		TCTTTTCAGTATGAATTTTCT	0.363													a|||	195	0.0389377	0.1392	0.0159	5008	,	,		20000	0.0		0.0	False		,,,				2504	0.0				p.H401H		Atlas-SNP	.											.	ZNF43	152	.	0			c.T1203C						PASS	.	A		469,3937	213.8+/-233.3	27,415,1761	55.0	59.0	58.0		1176	-2.5	0.0	19	dbSNP_129	58	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	ZNF43	NM_003423.2		27,423,6053	GG,GA,AA		0.093,10.6446,3.6675		392/810	21991663	477,12529	2203	4300	6503	SO:0001819	synonymous_variant	7594	exon4			TTCAGTATGAATT	X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"""Zinc fingers, C2H2-type"", ""-"""	13109	protein-coding gene	gene with protein product		603972	"""zinc finger protein 39-like 1 (KOX 27)"", ""zinc finger protein 43 (HTF6)"""	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.1176T>C	19.37:g.21991663A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_001256653	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Silent	SNP	ENST00000354959.4	37	CCDS12413.2																																																																																			A|0.968;G|0.032	0.032	strong		0.363	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423	
FAM166A	401565	hgsc.bcm.edu	37	9	140140188	140140188	+	Silent	SNP	G	G	A	rs112239130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140140188G>A	ENST00000344774.4	-	2	228	c.174C>T	c.(172-174)ccC>ccT	p.P58P	FAM166A_ENST00000388932.2_Silent_p.P58P	NM_001001710.1	NP_001001710.1	Q6J272	F166A_HUMAN	family with sequence similarity 166, member A	58						nucleus (GO:0005634)				kidney(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(2)	15						GTTTGGACATGGGGGACAGCA	0.622													G|||	33	0.00658946	0.0234	0.0029	5008	,	,		18282	0.0		0.0	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											.	FAM166A	44	.	0			c.C174T						PASS	.	G		69,4337	63.5+/-100.7	0,69,2134	55.0	58.0	57.0		174	-2.9	0.3	9	dbSNP_132	57	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	FAM166A	NM_001001710.1		0,70,6432	AA,AG,GG		0.0116,1.566,0.5383		58/318	140140188	70,12934	2203	4299	6502	SO:0001819	synonymous_variant	401565	exon2			GGACATGGGGGAC	BC132916	CCDS35186.1	9q34.3	2008-08-08			ENSG00000188163	ENSG00000188163			33818	protein-coding gene	gene with protein product							Standard	XR_245332		Approved		uc004cmi.1	Q6J272	OTTHUMG00000159545	ENST00000344774.4:c.174C>T	9.37:g.140140188G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	116	76	0.655172	NM_001001710	A6NND9|Q8N830	Silent	SNP	ENST00000344774.4	37	CCDS35186.1																																																																																			G|0.992;A|0.008	0.008	strong		0.622	FAM166A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356125.1	NM_001001710	
GPT	2875	hgsc.bcm.edu	37	8	145729727	145729727	+	Missense_Mutation	SNP	C	C	A	rs1063739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145729727C>A	ENST00000528431.1	+	2	197	c.40C>A	c.(40-42)Cat>Aat	p.H14N	GPT_ENST00000394955.2_Missense_Mutation_p.H14N			P24298	ALAT1_HUMAN	glutamic-pyruvate transaminase (alanine aminotransferase)	14			H -> N (in allele GPT*2; dbSNP:rs1063739). {ECO:0000269|PubMed:9119391, ECO:0000269|Ref.4}.		cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-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;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)		L-Alanine(DB00160)|Phenelzine(DB00780)	GGCGGTGAGGCATGGACTGAG	0.647													.|||	2167	0.432708	0.1861	0.5086	5008	,	,		20289	0.5377		0.4602	False		,,,				2504	0.5757				p.H14N		Atlas-SNP	.											GPT,NS,haematopoietic_neoplasm,-2,1	GPT	31	1	0			c.C40A						PASS	.	A	ASN/HIS	1020,3384	719.9+/-409.0	133,754,1315	101.0	98.0	99.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	40	3.9	0.1	8	dbSNP_86	99	4001,4597	597.1+/-393.7	944,2113,1242	yes	missense	GPT	NM_005309.2	68	1077,2867,2557	AA,AC,CC		46.5341,23.1608,38.6171	benign	14/497	145729727	5021,7981	2202	4299	6501	SO:0001583	missense	2875	exon1			GTGAGGCATGGAC		CCDS6430.1	8q24.3	2013-09-19			ENSG00000167701	ENSG00000167701	2.6.1.2		4552	protein-coding gene	gene with protein product		138200					Standard	NM_005309		Approved	ALT1, GPT1	uc003zdh.4	P24298	OTTHUMG00000165176	ENST00000528431.1:c.40C>A	8.37:g.145729727C>A	ENSP00000433586:p.His14Asn	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_005309	B0YJ18|D3DWM7|P78398|Q93076	Missense_Mutation	SNP	ENST00000528431.1	37	CCDS6430.1	907	0.4152930402930403	88	0.17886178861788618	195	0.5386740331491713	276	0.4825174825174825	348	0.45910290237467016	A	0.012	-1.685669	0.00745	0.231608	0.465341	ENSG00000167701	ENST00000528431;ENST00000394955	T;T	0.73152	-0.72;-0.72	5.05	3.88	0.44766	.	0.232251	0.41097	N	0.000944	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	0.43621	-0.9380	9	0.06891	T	0.86	-1.6569	5.5333	0.16997	0.7346:0.173:0.0924:0.0	rs1063739;rs56754585;rs1063739	14	P24298	ALAT1_HUMAN	N	14	ENSP00000433586:H14N;ENSP00000378408:H14N	ENSP00000378408:H14N	H	+	1	0	GPT	145700535	0.007000	0.16637	0.065000	0.19835	0.004000	0.04260	0.391000	0.20784	0.782000	0.33613	-0.382000	0.06688	CAT	A|0.384;C|0.616	0.384	strong		0.647	GPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382471.1		
USP17L22	100287513	hgsc.bcm.edu	37	4	9270328	9270328	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:9270328G>A	ENST00000511280.1	+	1	984	c.984G>A	c.(982-984)tgG>tgA	p.W328*		NM_001256863.1	NP_001243792.1	D6RA61	U17LM_HUMAN	ubiquitin specific peptidase 17-like family member 22	328	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.W328*(1)									ACGCTGGGTGGAGTTGTCACA	0.498																																					p.W328X		Atlas-SNP	.											RP11-1286E23.17,NS,carcinoma,0,1	.	.	1	1	Substitution - Nonsense(1)	breast(1)	c.G984A						scavenged	.																																			SO:0001587	stop_gained	100287441	exon1			TGGGTGGAGTTGT		CCDS59463.1	4p16.1	2012-10-09			ENSG00000248933	ENSG00000248933			44450	protein-coding gene	gene with protein product							Standard	NM_001256863		Approved			D6RA61	OTTHUMG00000160159	ENST00000511280.1:c.984G>A	4.37:g.9270328G>A	ENSP00000423115:p.Trp328*	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	977	73	0.0747185	NM_001256861		Nonsense_Mutation	SNP	ENST00000511280.1	37	CCDS59463.1	.	.	.	.	.	.	.	.	.	.	.	12.24	1.878008	0.33162	.	.	ENSG00000248933	ENST00000511280	.	.	.	0.337	0.337	0.15966	.	1.191590	0.06372	N	0.713729	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	328	.	ENSP00000423115:W328X	W	+	3	0	RP11-1286E23.17	8965445	0.289000	0.24334	0.271000	0.24616	0.094000	0.18550	0.042000	0.13949	0.444000	0.26612	0.121000	0.15741	TGG	.	.	none		0.498	USP17L22-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359427.1	NM_001256863	
CST1	1469	hgsc.bcm.edu	37	20	23731426	23731426	+	Silent	SNP	C	C	T	rs13045477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23731426C>T	ENST00000304749.2	-	1	148	c.78G>A	c.(76-78)gaG>gaA	p.E26E	CST1_ENST00000398402.1_Silent_p.E26E	NM_001898.2	NP_001889.2	P01037	CYTN_HUMAN	cystatin SN	26					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.E26E(1)		kidney(1)|large_intestine(1)|lung(8)|ovary(1)|stomach(1)|urinary_tract(1)	13	Lung NSC(19;0.0676)|all_lung(19;0.148)					TTATCCTATCCTCCTCCTTGG	0.582													.|||	1837	0.366813	0.5779	0.3343	5008	,	,		14402	0.2123		0.2465	False		,,,				2504	0.3875				p.E26E		Atlas-SNP	.											CST1,NS,carcinoma,0,1	CST1	37	1	1	Substitution - coding silent(1)	stomach(1)	c.G78A						PASS	.	C		2206,2200	589.8+/-387.2	566,1074,563	93.0	82.0	86.0		78	-0.9	0.0	20	dbSNP_121	86	2140,6460	365.2+/-333.8	274,1592,2434	no	coding-synonymous	CST1	NM_001898.2		840,2666,2997	TT,TC,CC		24.8837,49.9319,33.4153		26/142	23731426	4346,8660	2203	4300	6503	SO:0001819	synonymous_variant	1469	exon1			CCTATCCTCCTCC	M19169	CCDS13160.1	20p11.2	2008-04-15			ENSG00000170373	ENSG00000170373			2473	protein-coding gene	gene with protein product		123855					Standard	NM_001898		Approved		uc002wtp.3	P01037	OTTHUMG00000032085	ENST00000304749.2:c.78G>A	20.37:g.23731426C>T		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	170	169	0.994118	NM_001898	Q96LE6|Q9UCQ6	Silent	SNP	ENST00000304749.2	37	CCDS13160.1																																																																																			C|0.665;T|0.335	0.335	strong		0.582	CST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078351.2	NM_001898	
KRT84	3890	hgsc.bcm.edu	37	12	52774305	52774305	+	Silent	SNP	A	A	G	rs1732293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52774305A>G	ENST00000257951.3	-	7	1332	c.1266T>C	c.(1264-1266)gaT>gaC	p.D422D	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	422	Coil 2.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TGCATTTGGCATCACTGAGGG	0.632											OREG0021848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1686	0.336661	0.6369	0.3184	5008	,	,		20415	0.2004		0.2068	False		,,,				2504	0.2178				p.D422D		Atlas-SNP	.											.	KRT84	61	.	0			c.T1266C						PASS	.	G		2537,1869	537.0+/-374.6	756,1025,422	46.0	38.0	41.0		1266	-10.1	0.0	12	dbSNP_89	41	1804,6796	726.4+/-406.6	180,1444,2676	no	coding-synonymous	KRT84	NM_033045.3		936,2469,3098	GG,GA,AA		20.9767,42.4194,33.3769		422/601	52774305	4341,8665	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon7			TTTGGCATCACTG	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.1266T>C	12.37:g.52774305A>G		Somatic	111	0	0	987	WXS	Illumina HiSeq	Phase_I	112	112	1	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.682;G|0.318	0.318	strong		0.632	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
WDR31	114987	hgsc.bcm.edu	37	9	116085148	116085148	+	Silent	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116085148A>C	ENST00000374193.4	-	7	759	c.513T>G	c.(511-513)ctT>ctG	p.L171L	WDR31_ENST00000374195.3_Silent_p.L46L|WDR31_ENST00000461942.1_5'UTR|WDR31_ENST00000341761.4_Silent_p.L170L	NM_001012361.2|NM_145241.3	NP_001012361.1|NP_660284.1	Q8NA23	WDR31_HUMAN	WD repeat domain 31	171										NS(1)|large_intestine(1)|lung(2)|prostate(2)	6						CATCCCACAGAAGCAGGGTGT	0.527																																					p.L171L		Atlas-SNP	.											.	WDR31	23	.	0			c.T513G						PASS	.						124.0	104.0	111.0					9																	116085148		2203	4300	6503	SO:0001819	synonymous_variant	114987	exon7			CCACAGAAGCAGG	BC012352	CCDS6792.1, CCDS35110.1	9q33.1	2013-01-09			ENSG00000148225	ENSG00000148225		"""WD repeat domain containing"""	21421	protein-coding gene	gene with protein product	"""similar to spermatid WD-repeat protein"""						Standard	NM_145241		Approved	FLJ35921	uc004bhb.3	Q8NA23	OTTHUMG00000020525	ENST00000374193.4:c.513T>G	9.37:g.116085148A>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	195	68	0.348718	NM_001012361	Q5W0T9|Q96EG8	Silent	SNP	ENST00000374193.4	37	CCDS35110.1																																																																																			.	.	none		0.527	WDR31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053734.2	NM_145241	
KLF16	83855	hgsc.bcm.edu	37	19	1854701	1854701	+	Silent	SNP	G	G	A	rs76157530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1854701G>A	ENST00000250916.4	-	2	586	c.516C>T	c.(514-516)gaC>gaT	p.D172D	CTB-31O20.6_ENST00000592884.1_RNA|KLF16_ENST00000592313.1_5'UTR	NM_031918.3	NP_114124.1	Q9BXK1	KLF16_HUMAN	Kruppel-like factor 16	172					dopamine receptor signaling pathway (GO:0007212)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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(1)	1		Ovarian(11;1.78e-06)|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)		GGGCCAGCTCGTCGGAGCGGG	0.672													G|||	55	0.0109824	0.0401	0.0029	5008	,	,		10702	0.0		0.0	False		,,,				2504	0.0				p.D172D		Atlas-SNP	.											.	KLF16	9	.	0			c.C516T						PASS	.	G		133,4271	90.6+/-129.3	3,127,2072	35.0	39.0	37.0		516	-1.2	1.0	19	dbSNP_131	37	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KLF16	NM_031918.3		3,128,6371	AA,AG,GG		0.0116,3.02,1.0305		172/253	1854701	134,12870	2202	4300	6502	SO:0001819	synonymous_variant	83855	exon2			CAGCTCGTCGGAG	AF327440	CCDS12075.1	19p13.3	2013-10-15			ENSG00000129911	ENSG00000129911		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	16857	protein-coding gene	gene with protein product		606139				11438660	Standard	NM_031918		Approved	NSLP2, BTEB4, DRRF	uc002luc.3	Q9BXK1	OTTHUMG00000179994	ENST00000250916.4:c.516C>T	19.37:g.1854701G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_031918		Silent	SNP	ENST00000250916.4	37	CCDS12075.1																																																																																			G|0.989;A|0.011	0.011	strong		0.672	KLF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449214.1		
ABCC11	85320	hgsc.bcm.edu	37	16	48234214	48234214	+	Silent	SNP	C	C	T	rs61745566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48234214C>T	ENST00000394747.1	-	14	2404	c.2055G>A	c.(2053-2055)acG>acA	p.T685T	ABCC11_ENST00000537808.1_Silent_p.T685T|ABCC11_ENST00000356608.2_Silent_p.T685T|ABCC11_ENST00000353782.5_Silent_p.T685T|ABCC11_ENST00000394748.1_Silent_p.T685T	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	685	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|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)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CCAGGACGACCGTCTTCCCCC	0.552													C|||	108	0.0215655	0.0787	0.0043	5008	,	,		17717	0.0		0.0	False		,,,				2504	0.001				p.T685T		Atlas-SNP	.											.	ABCC11	177	.	0			c.G2055A						PASS	.	C	,,	233,4169	140.0+/-175.5	7,219,1975	114.0	98.0	104.0		2055,2055,2055	-11.4	0.0	16	dbSNP_129	104	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	7,224,6270	TT,TC,CC		0.0581,5.293,1.8305	,,	685/1383,685/1383,685/1345	48234214	238,12764	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon14			GACGACCGTCTTC	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2055G>A	16.37:g.48234214C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			C|0.980;T|0.020	0.020	strong		0.552	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
WDR19	57728	hgsc.bcm.edu	37	4	39267749	39267749	+	Missense_Mutation	SNP	G	G	A	rs16995209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39267749G>A	ENST00000399820.3	+	29	3404	c.3250G>A	c.(3250-3252)Ggc>Agc	p.G1084S	WDR19_ENST00000288634.7_Missense_Mutation_p.G924S	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	1084			G -> S (in dbSNP:rs16995209).		ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						GGAGAACGATGGCATGCCTAA	0.453													G|||	185	0.0369409	0.1301	0.0173	5008	,	,		15274	0.0		0.001	False		,,,				2504	0.0				p.G1084S		Atlas-SNP	.											.	WDR19	96	.	0			c.G3250A						PASS	.	G	SER/GLY	417,3589		21,375,1607	68.0	72.0	71.0		3250	5.4	1.0	4	dbSNP_123	71	3,8325		0,3,4161	yes	missense	WDR19	NM_025132.3	56	21,378,5768	AA,AG,GG		0.036,10.4094,3.4052	probably-damaging	1084/1343	39267749	420,11914	2003	4164	6167	SO:0001583	missense	57728	exon29			AACGATGGCATGC	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.3250G>A	4.37:g.39267749G>A	ENSP00000382717:p.Gly1084Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	161	66	0.409938	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	37	CCDS47042.1	54	0.024725274725274724	49	0.09959349593495935	5	0.013812154696132596	0	0.0	0	0.0	G	18.81	3.703584	0.68501	0.104094	3.6E-4	ENSG00000157796	ENST00000399820;ENST00000288634	T;T	0.68624	-0.34;-0.34	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.11324	0.0276	M	0.91090	3.175	0.80722	D	1	P	0.41947	0.766	P	0.47162	0.54	T	0.60662	-0.7219	10	0.52906	T	0.07	-18.5327	19.2559	0.93945	0.0:0.0:1.0:0.0	rs16995209;rs52802549;rs16995209	1084	Q8NEZ3	WDR19_HUMAN	S	1084;924	ENSP00000382717:G1084S;ENSP00000288634:G924S	ENSP00000288634:G924S	G	+	1	0	WDR19	38944144	1.000000	0.71417	0.983000	0.44433	0.048000	0.14542	9.108000	0.94275	2.539000	0.85634	0.455000	0.32223	GGC	G|0.962;A|0.038	0.038	strong		0.453	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		
PTPN1	5770	hgsc.bcm.edu	37	20	49197955	49197955	+	Silent	SNP	C	C	T	rs74607837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:49197955C>T	ENST00000371621.3	+	9	1416	c.1242C>T	c.(1240-1242)tgC>tgT	p.C414C	PTPN1_ENST00000541713.1_Silent_p.C341C	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	414					actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	TCAACATGTGCGTGGCTACGG	0.627													C|||	81	0.0161741	0.059	0.0043	5008	,	,		18745	0.0		0.0	False		,,,				2504	0.0				p.C414C		Atlas-SNP	.											.	PTPN1	36	.	0			c.C1242T						PASS	.	C		223,4183	133.7+/-170.0	6,211,1986	110.0	74.0	86.0		1242	0.4	0.8	20	dbSNP_132	86	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	PTPN1	NM_002827.2		6,215,6282	TT,TC,CC		0.0465,5.0613,1.7453		414/436	49197955	227,12779	2203	4300	6503	SO:0001819	synonymous_variant	5770	exon9			CATGTGCGTGGCT		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.1242C>T	20.37:g.49197955C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	162	81	0.5	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	37	CCDS13430.1																																																																																			C|0.980;T|0.020	0.020	strong		0.627	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2		
SLTM	79811	hgsc.bcm.edu	37	15	59179264	59179264	+	Silent	SNP	G	G	A	rs2124203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:59179264G>A	ENST00000380516.2	-	19	2832	c.2745C>T	c.(2743-2745)ggC>ggT	p.G915G	SLTM_ENST00000536328.1_Silent_p.G484G|AC025918.2_ENST00000452467.1_RNA	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	915					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)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CAGGGGGAGCGCCTCTCACAC	0.502													G|||	270	0.0539137	0.0893	0.0519	5008	,	,		17402	0.0139		0.0567	False		,,,				2504	0.046				p.G915G		Atlas-SNP	.											SLTM,colon,carcinoma,0,1	SLTM	90	1	0			c.C2745T						PASS	.	G	,	374,4010	189.5+/-215.6	16,342,1834	89.0	75.0	80.0		2691,2745	-11.1	0.0	15	dbSNP_96	80	565,8019	153.3+/-207.7	22,521,3749	no	coding-synonymous,coding-synonymous	SLTM	NM_001013843.1,NM_024755.2	,	38,863,5583	AA,AG,GG		6.582,8.531,7.2409	,	897/1017,915/1035	59179264	939,12029	2192	4292	6484	SO:0001819	synonymous_variant	79811	exon19			GGGAGCGCCTCTC	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"""RNA binding motif (RRM) containing"""	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.2745C>T	15.37:g.59179264G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_024755	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000380516.2	37	CCDS10168.2																																																																																			G|0.937;A|0.063	0.063	strong		0.502	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755	
ITGA11	22801	hgsc.bcm.edu	37	15	68609647	68609647	+	Missense_Mutation	SNP	G	G	T	rs2271725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68609647G>T	ENST00000315757.7	-	21	2757	c.2671C>A	c.(2671-2673)Caa>Aaa	p.Q891K	ITGA11_ENST00000423218.2_Missense_Mutation_p.Q891K	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	891			Q -> K (in dbSNP:rs2271725).		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)			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						TTGCAGACTTGCTTCTGGAGC	0.602													T|||	819	0.163538	0.298	0.1556	5008	,	,		17941	0.2381		0.0268	False		,,,				2504	0.0511				p.Q891K		Atlas-SNP	.											.	ITGA11	110	.	0			c.C2671A						PASS	.	T	LYS/GLN	1069,3063		133,803,1130	143.0	157.0	153.0		2671	4.8	1.0	15	dbSNP_100	153	239,8157		4,231,3963	yes	missense	ITGA11	NM_001004439.1	53	137,1034,5093	TT,TG,GG		2.8466,25.8712,10.4406	benign	891/1189	68609647	1308,11220	2066	4198	6264	SO:0001583	missense	22801	exon21			AGACTTGCTTCTG	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.2671C>A	15.37:g.68609647G>T	ENSP00000327290:p.Gln891Lys	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	142	52	0.366197	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	360	0.16483516483516483	155	0.3150406504065041	62	0.1712707182320442	126	0.2202797202797203	17	0.022427440633245383	T	0.013	-1.627285	0.00813	0.258712	0.028466	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.42900	0.96;0.96	4.79	4.79	0.61399	Integrin alpha-2 (1);	0.092215	0.64402	N	0.000001	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	0.01281	0.0;0.0	T	0.37174	-0.9717	9	0.02654	T	1	.	11.0359	0.47799	0.0:0.0:0.1564:0.8436	rs2271725;rs2271725	891;891	A8K8T0;Q9UKX5	.;ITA11_HUMAN	K	891;891;526	ENSP00000327290:Q891K;ENSP00000403392:Q891K	ENSP00000327290:Q891K	Q	-	1	0	ITGA11	66396701	1.000000	0.71417	0.999000	0.59377	0.020000	0.10135	2.735000	0.47377	0.694000	0.31654	-0.363000	0.07495	CAA	G|0.833;T|0.167	0.167	strong		0.602	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
TNRC18	84629	hgsc.bcm.edu	37	7	5391702	5391702	+	Missense_Mutation	SNP	C	C	G	rs3801048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5391702C>G	ENST00000430969.1	-	17	5566	c.5218G>C	c.(5218-5220)Gaa>Caa	p.E1740Q	TNRC18_ENST00000399537.4_Missense_Mutation_p.E1740Q	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1740							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)		TTCAGGAATTCTTCGTCTTCC	0.507													C|||	950	0.189696	0.2526	0.1844	5008	,	,		19265	0.0625		0.2147	False		,,,				2504	0.2137				p.E1740Q		Atlas-SNP	.											.	TNRC18	311	.	0			c.G5218C						PASS	.	C	GLN/GLU	779,2357		85,609,874	39.0	36.0	37.0		5218	4.0	0.0	7	dbSNP_107	37	1211,5953		101,1009,2472	yes	missense	TNRC18	NM_001080495.2	29	186,1618,3346	GG,GC,CC		16.904,24.8406,19.3204	benign	1740/2969	5391702	1990,8310	1568	3582	5150	SO:0001583	missense	84629	exon17			GGAATTCTTCGTC	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.5218G>C	7.37:g.5391702C>G	ENSP00000395538:p.Glu1740Gln	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	389	0.17811355311355312	130	0.26422764227642276	63	0.17403314917127072	30	0.05244755244755245	166	0.21899736147757257	c	14.58	2.578239	0.45902	0.248406	0.16904	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	T;T;T	0.48201	2.64;2.64;0.82	4.92	4.0	0.46444	.	0.946100	0.08634	N	0.916650	T	0.00012	0.0000	L	0.50333	1.59	0.48975	P	2.609999999999557E-4	B;B	0.20164	0.001;0.042	B;B	0.16722	0.005;0.016	T	0.14282	-1.0478	9	0.24483	T	0.36	.	14.7976	0.69889	0.0:0.8547:0.1453:0.0	rs3801048;rs10384278;rs60343046;rs3801048	795;1740	A8MSW5;O15417	.;TNC18_HUMAN	Q	1740;1740;795;230	ENSP00000382452:E1740Q;ENSP00000395538:E1740Q;ENSP00000395990:E230Q	ENSP00000382452:E1740Q	E	-	1	0	TNRC18	5358228	0.733000	0.28132	0.005000	0.12908	0.952000	0.60782	2.845000	0.48254	0.997000	0.38969	0.561000	0.74099	GAA	C|0.797;G|0.203	0.203	strong		0.507	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156085	39156085	+	Silent	SNP	G	G	T	rs386797022|rs548322379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39156085G>T	ENST00000391587.1	-	1	53	c.21C>A	c.(19-21)cgC>cgA	p.R7R		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	7	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R7R(1)		endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				CACTGCAGCTGCGAGAGGCAC	0.552													.|||	307	0.0613019	0.2216	0.0173	5008	,	,		18167	0.0		0.002	False		,,,				2504	0.0				p.R7R		Atlas-SNP	.											KRTAP3-2,rectum,carcinoma,0,1	KRTAP3-2	11	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C21A						PASS	.						65.0	75.0	72.0					17																	39156085		2203	4296	6499	SO:0001819	synonymous_variant	83897	exon1			GCAGCTGCGAGAG	AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"""Keratin associated proteins"""	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.21C>A	17.37:g.39156085G>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	174	58	0.333333	NM_031959		Silent	SNP	ENST00000391587.1	37	CCDS32644.1																																																																																			.	.	none		0.552	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257685.1		
ARHGEF28	64283	hgsc.bcm.edu	37	5	73142296	73142296	+	Missense_Mutation	SNP	C	C	T	rs2973571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:73142296C>T	ENST00000426542.2	+	11	1651	c.1631C>T	c.(1630-1632)tCg>tTg	p.S544L	ARHGEF28_ENST00000513841.1_3'UTR|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.S544L|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.S544L|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.S544L|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.S544L|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.S231L|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.S544L			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	544			S -> L (in dbSNP:rs2973571).		central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										AATCTACAGTCGAAGGTATTC	0.353													C|||	862	0.172125	0.121	0.2522	5008	,	,		18407	0.0764		0.2575	False		,,,				2504	0.1953				p.S544L		Atlas-SNP	.											.	.	.	.	0			c.C1631T						PASS	.	C	LEU/SER,LEU/SER	586,3070		53,480,1295	74.0	68.0	70.0		1631,1631	-0.9	0.0	5	dbSNP_101	70	2232,5942		319,1594,2174	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	145,145	372,2074,3469	TT,TC,CC		27.3061,16.0284,23.8208	benign,benign	544/1732,544/1706	73142296	2818,9012	1828	4087	5915	SO:0001583	missense	64283	exon12			TACAGTCGAAGGT		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.1631C>T	5.37:g.73142296C>T	ENSP00000412175:p.Ser544Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	385	0.1762820512820513	54	0.10975609756097561	91	0.2513812154696133	41	0.07167832167832168	199	0.262532981530343	C	11.38	1.623055	0.28889	0.160284	0.273061	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.10668	3.09;3.07;3.08;2.85;3.07;3.08;2.93	5.69	-0.952	0.10366	.	.	.	.	.	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B;B;B;B;B	0.17667	0.001;0.001;0.001;0.023;0.001	B;B;B;B;B	0.12156	0.001;0.001;0.001;0.007;0.002	T	0.49000	-0.8984	8	0.20046	T	0.44	.	10.3084	0.43693	0.0:0.5982:0.0:0.4018	rs2973571;rs17553106;rs52832546;rs2973571	231;544;544;544;544	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-2;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	L	544;544;544;544;544;544;231	ENSP00000296794:S544L;ENSP00000441913:S544L;ENSP00000441436:S544L;ENSP00000287898:S544L;ENSP00000411459:S544L;ENSP00000412175:S544L;ENSP00000296799:S231L	ENSP00000287898:S544L	S	+	2	0	RP11-428C6.1	73178052	0.000000	0.05858	0.008000	0.14137	0.895000	0.52256	0.016000	0.13377	-0.249000	0.09569	0.484000	0.47621	TCG	C|0.829;T|0.171	0.171	strong		0.353	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921137	12921137	+	Missense_Mutation	SNP	T	T	A	rs17039283	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	199	0	0		WXS	Illumina HiSeq	Phase_I	254	5	0.019685	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	
KRT33A	3883	hgsc.bcm.edu	37	17	39503163	39503163	+	Missense_Mutation	SNP	G	G	A	rs12937519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	210	0	0		WXS	Illumina HiSeq	Phase_I	228	217	0.951754	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	
MRO	83876	hgsc.bcm.edu	37	18	48327815	48327815	+	Silent	SNP	G	G	A	rs2276186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:48327815G>A	ENST00000428869.2	-	7	747	c.489C>T	c.(487-489)gcC>gcT	p.A163A	MRO_ENST00000588444.1_Intron|MRO_ENST00000431965.2_Intron|MRO_ENST00000587291.1_5'UTR|MRO_ENST00000256425.2_Silent_p.A163A|MRO_ENST00000436348.2_Silent_p.A177A|MRO_ENST00000398439.3_Silent_p.A163A			Q9BYG7	MSTRO_HUMAN	maestro	163						nucleolus (GO:0005730)		p.A163A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|skin(2)	10		Colorectal(6;0.0596)		Colorectal(21;0.082)		ATTTCCTCCCGGCAAAGGCAG	0.463													G|||	2151	0.429513	0.261	0.5519	5008	,	,		20552	0.3512		0.5239	False		,,,				2504	0.5542				p.A177A		Atlas-SNP	.											MRO,NS,carcinoma,0,1	MRO	36	1	1	Substitution - coding silent(1)	prostate(1)	c.C531T						PASS	.	G	,,,	1353,3053	451.2+/-349.6	207,939,1057	148.0	148.0	148.0		,,531,489	-1.2	0.9	18	dbSNP_100	148	4279,4321	575.6+/-390.3	1095,2089,1116	no	intron,intron,coding-synonymous,coding-synonymous	MRO	NM_001127174.1,NM_001127175.1,NM_001127176.1,NM_031939.3	,,,	1302,3028,2173	AA,AG,GG		49.7558,30.7081,43.3031	,,,	,,177/263,163/249	48327815	5632,7374	2203	4300	6503	SO:0001819	synonymous_variant	83876	exon5			CCTCCCGGCAAAG	AK054702	CCDS11947.1, CCDS45867.1, CCDS45868.1, CCDS45869.1	18q21	2012-12-19	2004-06-15		ENSG00000134042	ENSG00000134042		"""maestro heat-like repeat containing"""	24121	protein-coding gene	gene with protein product	"""B29 protein"", ""beside the Ma29 deletion"""	608080	"""chromosome 18 open reading frame 3"""	C18orf3		11401430	Standard	NM_031939		Approved	B29, FLJ30140	uc010dpa.3	Q9BYG7	OTTHUMG00000132692	ENST00000428869.2:c.489C>T	18.37:g.48327815G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_001127176	B7Z2I5|B7Z3B2|E9PAT5|E9PBI3|K7EKJ8|Q8N6K5	Silent	SNP	ENST00000428869.2	37	CCDS11947.1																																																																																			G|0.579;A|0.421	0.421	strong		0.463	MRO-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449478.2	NM_031939	
TNFSF14	8740	hgsc.bcm.edu	37	19	6669934	6669934	+	Silent	SNP	G	G	A	rs2291668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6669934G>A	ENST00000599359.1	-	2	528	c.147C>T	c.(145-147)gcC>gcT	p.A49A	TNFSF14_ENST00000245912.3_Intron|TNFSF14_ENST00000326176.9_Intron			O43557	TNF14_HUMAN	tumor necrosis factor (ligand) superfamily, member 14	49					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of T cell chemotaxis (GO:0010820)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|receptor binding (GO:0005102)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18						CGGCCAGCCCGGCCCCCATCA	0.662													G|||	883	0.176318	0.0983	0.2248	5008	,	,		15316	0.2788		0.1958	False		,,,				2504	0.1217				p.A49A		Atlas-SNP	.											TNFSF14,NS,carcinoma,-1,1	TNFSF14	40	1	0			c.C147T						scavenged	.	G	,	490,3916	227.8+/-242.9	27,436,1740	89.0	84.0	86.0		147,	-9.8	0.0	19	dbSNP_100	86	1362,7238	266.1+/-286.5	121,1120,3059	no	coding-synonymous,intron	TNFSF14	NM_003807.3,NM_172014.2	,	148,1556,4799	AA,AG,GG		15.8372,11.1212,14.2396	,	49/241,	6669934	1852,11154	2203	4300	6503	SO:0001819	synonymous_variant	8740	exon2			CAGCCCGGCCCCC	AF036581	CCDS12171.1, CCDS45939.1	19p13.3	2008-02-05				ENSG00000125735		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11930	protein-coding gene	gene with protein product		604520				9462508	Standard	NM_172014		Approved	LIGHT, LTg, HVEM-L, CD258	uc002mfk.2	O43557		ENST00000599359.1:c.147C>T	19.37:g.6669934G>A		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	137	69	0.50365	NM_003807	A8K7M2|C9J5H4|O75476|Q6FHA1|Q8WVF8|Q96LD2	Silent	SNP	ENST00000599359.1	37	CCDS12171.1																																																																																			G|0.841;A|0.159	0.159	strong		0.662	TNFSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457863.1		
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077765	19077765	+	Missense_Mutation	SNP	T	T	C	rs10833049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:19077765T>C	ENST00000329773.2	-	2	272	c.185A>G	c.(184-186)aAc>aGc	p.N62S		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	62			N -> S (in dbSNP:rs10833049). {ECO:0000269|PubMed:15862286, ECO:0000269|Ref.5}.		positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)	p.N62S(1)		NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						AGAGAAGGCGTTCCTGCGCAT	0.562													T|||	1595	0.31849	0.5265	0.2781	5008	,	,		17944	0.2659		0.2614	False		,,,				2504	0.1789				p.N62S	GBM(198;1966 2199 4849 37227 49954)	Atlas-SNP	.											MRGPRX2,NS,carcinoma,0,1	MRGPRX2	42	1	1	Substitution - Missense(1)	stomach(1)	c.A185G						PASS	.	T	SER/ASN	2074,2324		504,1066,629	82.0	90.0	87.0		185	1.4	0.0	11	dbSNP_120	87	2283,6303		301,1681,2311	yes	missense	MRGPRX2	NM_054030.2	46	805,2747,2940	CC,CT,TT		26.5898,47.1578,33.5567	probably-damaging	62/331	19077765	4357,8627	2199	4293	6492	SO:0001583	missense	117194	exon2			AAGGCGTTCCTGC		CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"""GPCR / Class A : Orphans"""	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.185A>G	11.37:g.19077765T>C	ENSP00000333800:p.Asn62Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_054030	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Missense_Mutation	SNP	ENST00000329773.2	37	CCDS7847.1	690	0.3159340659340659	257	0.5223577235772358	102	0.281767955801105	142	0.24825174825174826	189	0.24934036939313983	.	14.37	2.515471	0.44763	0.471578	0.265898	ENSG00000183695	ENST00000329773	T	0.09073	3.02	5.14	1.41	0.22369	GPCR, rhodopsin-like superfamily (1);	0.079983	0.52532	D	0.000064	T	0.00012	0.0000	L	0.58428	1.81	0.80722	P	0.0	D	0.56521	0.976	P	0.57283	0.817	T	0.48570	-0.9024	9	0.66056	D	0.02	.	2.9449	0.05842	0.1426:0.0803:0.1486:0.6285	rs10833049;rs52795288;rs60268974;rs10833049	62	Q96LB1	MRGX2_HUMAN	S	62	ENSP00000333800:N62S	ENSP00000333800:N62S	N	-	2	0	MRGPRX2	19034341	0.172000	0.23043	0.001000	0.08648	0.447000	0.32167	0.390000	0.20768	0.130000	0.18549	0.533000	0.62120	AAC	C|0.329;G|0.000;T|0.671	0.329	strong		0.562	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030	
LRRK2	120892	hgsc.bcm.edu	37	12	40657700	40657700	+	Missense_Mutation	SNP	C	C	G	rs7308720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:40657700C>G	ENST00000298910.7	+	14	1711	c.1653C>G	c.(1651-1653)aaC>aaG	p.N551K	LRRK2_ENST00000343742.2_Missense_Mutation_p.N551K	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	551			N -> K (in dbSNP:rs7308720). {ECO:0000269|PubMed:16172858, ECO:0000269|PubMed:16251215, ECO:0000269|PubMed:17344846, 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)				CAGCTTTGAACAGGGTATGTT	0.323													C|||	498	0.0994409	0.1278	0.1614	5008	,	,		15444	0.1042		0.0636	False		,,,				2504	0.0491				p.N551K		Atlas-SNP	.											.	LRRK2	763	.	0			c.C1653G						PASS	.	C	LYS/ASN	609,3797	265.0+/-266.4	38,533,1632	74.0	78.0	76.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1653	2.7	1.0	12	dbSNP_116	76	621,7975	159.5+/-212.8	23,575,3700	yes	missense	LRRK2	NM_198578.3	94	61,1108,5332	GG,GC,CC		7.2243,13.8221,9.4601	probably-damaging	551/2528	40657700	1230,11772	2203	4298	6501	SO:0001583	missense	120892	exon14			TTTGAACAGGGTA	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.1653C>G	12.37:g.40657700C>G	ENSP00000298910:p.Asn551Lys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	221	0.10119047619047619	65	0.13211382113821138	51	0.1408839779005525	54	0.0944055944055944	51	0.06728232189973615	C	17.76	3.468331	0.63625	0.138221	0.072243	ENSG00000188906	ENST00000416796;ENST00000343742;ENST00000298910	T;T;T	0.58210	0.35;0.35;0.35	5.9	2.69	0.31865	Armadillo-like helical (1);Armadillo-type fold (1);	0.046651	0.85682	D	0.000000	T	0.00875	0.0029	M	0.61703	1.905	0.26842	P	0.9683462	P;D	0.89917	0.884;1.0	B;D	0.71184	0.326;0.972	T	0.32188	-0.9916	9	0.54805	T	0.06	.	9.8726	0.41185	0.0:0.7425:0.0:0.2575	rs7308720;rs17490831;rs36223899;rs56469962;rs7308720	551;551	E9PC85;Q5S007	.;LRRK2_HUMAN	K	299;551;551	ENSP00000398726:N299K;ENSP00000341930:N551K;ENSP00000298910:N551K	ENSP00000298910:N551K	N	+	3	2	LRRK2	38943967	0.997000	0.39634	1.000000	0.80357	0.901000	0.52897	0.224000	0.17738	0.849000	0.35215	0.650000	0.86243	AAC	C|0.897;G|0.103	0.103	strong		0.323	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
RGS8	85397	hgsc.bcm.edu	37	1	182640864	182640864	+	5'UTR	SNP	T	T	C	rs680277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182640864T>C	ENST00000483095.2	-	0	82				RGS8_ENST00000367556.1_5'UTR|RGS8_ENST00000367557.4_5'UTR|RGS8_ENST00000258302.4_Splice_Site_p.N3S|RGS8_ENST00000491420.2_5'UTR			P57771	RGS8_HUMAN	regulator of G-protein signaling 8						positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.N3S(1)		haematopoietic_and_lymphoid_tissue(1)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	5						GGTTAAGGTGTTCTGGGGAAA	0.483													C|||	1018	0.203275	0.5083	0.147	5008	,	,		19459	0.1399		0.0408	False		,,,				2504	0.0634				p.N3S	Ovarian(189;1262 3804 41973)	Atlas-SNP	.											RGS8,NS,carcinoma,0,1	RGS8	51	1	1	Substitution - Missense(1)	stomach(1)	c.A8G						PASS	.	C	,SER/ASN	1782,2624	641.5+/-397.5	367,1048,788	171.0	173.0	173.0		,8	3.3	1.0	1	dbSNP_83	173	370,8230	802.7+/-407.3	6,358,3936	yes	utr-5,missense-near-splice	RGS8	NM_001102450.1,NM_033345.2	,46	373,1406,4724	CC,CT,TT		4.3023,40.4448,16.5462	,benign	,3/199	182640864	2152,10854	2203	4300	6503	SO:0001623	5_prime_UTR_variant	85397	exon2			AAGGTGTTCTGGG	AF297015	CCDS1349.1, CCDS41443.1	1q25	2008-07-18	2007-08-14		ENSG00000135824	ENSG00000135824		"""Regulators of G-protein signaling"""	16810	protein-coding gene	gene with protein product		607189	"""regulator of G-protein signalling 8"""			11318611	Standard	NM_001102450		Approved	MGC119067, MGC119068, MGC119069	uc001gpm.1	P57771	OTTHUMG00000035219	ENST00000483095.2:c.-176A>G	1.37:g.182640864T>C		Somatic	278	1	0.00359712		WXS	Illumina HiSeq	Phase_I	225	85	0.377778	NM_033345	B4DGL9|Q3SYD2	Missense_Mutation	SNP	ENST00000483095.2	37	CCDS41443.1	435	0.19917582417582416	255	0.5182926829268293	52	0.143646408839779	99	0.17307692307692307	29	0.03825857519788918	C	0.703	-0.790254	0.02884	0.404448	0.043023	ENSG00000135824	ENST00000258302	T	0.42513	0.97	5.28	3.34	0.38264	.	2.661080	0.01665	N	0.025301	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999996292	B	0.02656	0.0	B	0.01281	0.0	T	0.42766	-0.9432	8	0.07644	T	0.81	.	5.3712	0.16140	0.0:0.6472:0.1631:0.1897	rs680277;rs2023337;rs680277	3	P57771-2	.	S	3	ENSP00000258302:N3S	ENSP00000258302:N3S	N	-	2	0	RGS8	180907487	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	0.364000	0.20325	0.198000	0.20407	-0.213000	0.12676	AAC	T|0.817;C|0.183	0.183	strong		0.483	RGS8-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358979.1	NM_033345	
MB	4151	hgsc.bcm.edu	37	22	36007045	36007045	+	Silent	SNP	G	G	A	rs7292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36007045G>A	ENST00000397326.2	-	2	402	c.204C>T	c.(202-204)acC>acT	p.T68T	MB_ENST00000397328.1_Silent_p.T68T|MB_ENST00000406324.1_Silent_p.T68T|MB_ENST00000401702.1_Silent_p.T13T|MB_ENST00000359787.1_Silent_p.T68T	NM_005368.2	NP_005359.1	P02144	MYG_HUMAN	myoglobin	68					brown fat cell differentiation (GO:0050873)|enucleate erythrocyte differentiation (GO:0043353)|heart development (GO:0007507)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|slow-twitch skeletal muscle fiber contraction (GO:0031444)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			lung(1)	1						CGGTGAGCACGGTGGCACCAT	0.552													G|||	2826	0.564297	0.5703	0.4798	5008	,	,		21661	0.747		0.4493	False		,,,				2504	0.546				p.T68T	GBM(49;694 1113 16998 18419)|Esophageal Squamous(101;120 1973 10459 37086)	Atlas-SNP	.											.	MB	7	.	0			c.C204T						PASS	.	G	,,	2425,1981	618.2+/-393.1	678,1069,456	130.0	100.0	110.0		204,204,204	-10.6	0.0	22	dbSNP_52	110	4022,4578	556.1+/-386.8	958,2106,1236	no	coding-synonymous,coding-synonymous,coding-synonymous	MB	NM_005368.2,NM_203377.1,NM_203378.1	,,	1636,3175,1692	AA,AG,GG		46.7674,44.9614,49.5694	,,	68/155,68/155,68/155	36007045	6447,6559	2203	4300	6503	SO:0001819	synonymous_variant	4151	exon3			GAGCACGGTGGCA		CCDS13917.1	22q13.1	2012-10-02			ENSG00000198125	ENSG00000198125			6915	protein-coding gene	gene with protein product		160000				10591208, 2989088	Standard	NM_005368		Approved	PVALB	uc003anz.3	P02144	OTTHUMG00000150606	ENST00000397326.2:c.204C>T	22.37:g.36007045G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_203377	Q52H51|Q5THY7	Silent	SNP	ENST00000397326.2	37	CCDS13917.1																																																																																			G|0.474;A|0.526	0.526	strong		0.552	MB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319057.2	NM_203377	
TAGLN	6876	hgsc.bcm.edu	37	11	117075014	117075014	+	Missense_Mutation	SNP	A	A	G	rs12284316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117075014A>G	ENST00000532870.1	+	4	1686	c.545A>G	c.(544-546)aAc>aGc	p.N182S	TAGLN_ENST00000392951.4_Missense_Mutation_p.N182S|PCSK7_ENST00000529458.1_5'Flank|TAGLN_ENST00000530649.1_Missense_Mutation_p.N182S			Q01995	TAGL_HUMAN	transgelin	182			N -> S (in dbSNP:rs12284316).		epithelial cell differentiation (GO:0030855)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)				central_nervous_system(1)|large_intestine(4)|lung(1)|urinary_tract(1)	7	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;1.63e-06)|Epithelial(105;5.49e-05)|all cancers(92;0.000435)		ATGGGCAGCAACAGAGGGGCC	0.612													A|||	15	0.00299521	0.0113	0.0	5008	,	,		18601	0.0		0.0	False		,,,				2504	0.0				p.N182S		Atlas-SNP	.											.	TAGLN	17	.	0			c.A545G						PASS	.	A	SER/ASN,SER/ASN	46,4356	48.2+/-83.0	0,46,2155	80.0	83.0	82.0		545,545	4.6	1.0	11	dbSNP_120	82	0,8592		0,0,4296	yes	missense,missense	TAGLN	NM_001001522.1,NM_003186.3	46,46	0,46,6451	GG,GA,AA		0.0,1.045,0.354	probably-damaging,probably-damaging	182/202,182/202	117075014	46,12948	2201	4296	6497	SO:0001583	missense	6876	exon5			GCAGCAACAGAGG	M95787	CCDS8381.1	11q23.2	2008-07-21				ENSG00000149591			11553	protein-coding gene	gene with protein product	"""SM22-alpha"", ""transgelin variant 2"""	600818				8117285, 1520290	Standard	NM_003186		Approved	SM22, WS3-10, TAGLN1, SMCC, DKFZp686P11128	uc001pqm.3	Q01995		ENST00000532870.1:c.545A>G	11.37:g.117075014A>G	ENSP00000432282:p.Asn182Ser	Somatic	312	1	0.00320513		WXS	Illumina HiSeq	Phase_I	255	146	0.572549	NM_001001522	O15542	Missense_Mutation	SNP	ENST00000532870.1	37	CCDS8381.1	6|6	0.0027472527472527475|0.0027472527472527475	6|6	0.012195121951219513|0.012195121951219513	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	22.5|22.5	4.294103|4.294103	0.81025|0.81025	0.01045|0.01045	0.0|0.0	ENSG00000149591|ENSG00000149591	ENST00000392951;ENST00000525531;ENST00000278968;ENST00000530649;ENST00000532870|ENST00000529622	T;T;T;T;T|.	0.68331|.	-0.32;-0.32;-0.32;-0.32;-0.32|.	4.63|4.63	4.63|4.63	0.57726|0.57726	Calponin homology domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.82231|0.82231	0.4992|0.4992	H|H	0.95745|0.95745	3.715|3.715	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.71414|.	0.973|.	D|D	0.88266|0.88266	0.2926|0.2926	10|5	0.87932|.	D|.	0|.	.|.	13.0278|13.0278	0.58825|0.58825	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs12284316|rs12284316	182|.	Q01995|.	TAGL_HUMAN|.	S|A	182|132	ENSP00000376678:N182S;ENSP00000432054:N182S;ENSP00000278968:N182S;ENSP00000431941:N182S;ENSP00000432282:N182S|.	ENSP00000278968:N182S|.	N|T	+|+	2|1	0|0	TAGLN|TAGLN	116580224|116580224	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	8.709000|8.709000	0.91379|0.91379	1.954000|1.954000	0.56735|0.56735	0.402000|0.402000	0.26972|0.26972	AAC|ACA	A|0.996;G|0.004	0.004	strong		0.612	TAGLN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392864.1	NM_001001522	
ZNF853	54753	hgsc.bcm.edu	37	7	6656830	6656830	+	Missense_Mutation	SNP	G	G	A	rs2243563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6656830G>A	ENST00000457543.3	+	2	580	c.22G>A	c.(22-24)Ggg>Agg	p.G8R		NM_017560.1	NP_060030.1	P0CG23	ZN853_HUMAN	zinc finger protein 853	8			G -> R (in dbSNP:rs2243563).				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						GCCGACTCCCGGGAATCGGGG	0.637													G|||	3712	0.741214	0.823	0.683	5008	,	,		18907	0.753		0.5427	False		,,,				2504	0.864				p.G8R		Atlas-SNP	.											ZNF853_ENST00000457543,rectum,carcinoma,0,2	ZNF853	32	2	0			c.G22A						PASS	.	G	ARG/GLY	1085,299		429,227,36	24.0	31.0	29.0		22	-7.7	0.0	7	dbSNP_100	29	1749,1433		478,793,320	yes	missense	ZNF853	NM_017560.1	125	907,1020,356	AA,AG,GG		45.0346,21.604,37.9325	benign	8/660	6656830	2834,1732	692	1591	2283	SO:0001583	missense	54753	exon2			ACTCCCGGGAATC	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.22G>A	7.37:g.6656830G>A	ENSP00000455585:p.Gly8Arg	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_017560		Missense_Mutation	SNP	ENST00000457543.3	37	CCDS59048.1																																																																																			G|0.313;A|0.687	0.687	strong		0.637	ZNF853-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324169.2	NM_017560	
AKNA	80709	hgsc.bcm.edu	37	9	117110112	117110112	+	Missense_Mutation	SNP	T	T	C	rs1265891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117110112T>C	ENST00000307564.4	-	16	3451	c.3290A>G	c.(3289-3291)cAg>cGg	p.Q1097R	AKNA_ENST00000223791.3_Missense_Mutation_p.Q557R|AKNA_ENST00000374075.5_Missense_Mutation_p.Q1016R|AKNA_ENST00000374079.4_Missense_Mutation_p.Q42R|AKNA_ENST00000374088.3_Missense_Mutation_p.Q1097R|AKNA_ENST00000492875.1_5'Flank	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1097			Q -> R (in dbSNP:rs1265891).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						CTGGAGTGGCTGGTGCAGGCT	0.667													C|||	1051	0.209864	0.6891	0.0605	5008	,	,		14024	0.0526		0.003	False		,,,				2504	0.0429				p.Q1097R		Atlas-SNP	.											.	AKNA	119	.	0			c.A3290G						PASS	.	C	ARG/GLN	2091,2139		503,1085,527	15.0	15.0	15.0		3290	-3.5	0.0	9	dbSNP_87	15	21,8365		0,21,4172	no	missense	AKNA	NM_030767.4	43	503,1106,4699	CC,CT,TT		0.2504,49.4326,16.7406	benign	1097/1440	117110112	2112,10504	2115	4193	6308	SO:0001583	missense	80709	exon16			AGTGGCTGGTGCA	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3290A>G	9.37:g.117110112T>C	ENSP00000303769:p.Gln1097Arg	Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	398	0.18223443223443223	337	0.6849593495934959	27	0.07458563535911603	32	0.055944055944055944	2	0.002638522427440633	C	6.830	0.522364	0.13066	0.494326	0.002504	ENSG00000106948	ENST00000307564;ENST00000374079;ENST00000320310;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T;T	0.17370	2.74;2.28;2.74;2.51;2.74	5.44	-3.52	0.04682	.	1.042290	0.07587	N	0.921372	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	0.40459	-0.9562	9	0.02654	T	1	-2.0827	6.3932	0.21599	0.0:0.2694:0.3256:0.405	rs1265891;rs52814197;rs1265891	1097;1016	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	R	1097;42;109;1097;557;1016	ENSP00000303769:Q1097R;ENSP00000363192:Q42R;ENSP00000363201:Q1097R;ENSP00000223791:Q557R;ENSP00000363188:Q1016R	ENSP00000223791:Q557R	Q	-	2	0	AKNA	116149933	0.001000	0.12720	0.019000	0.16419	0.639000	0.38242	-0.315000	0.08081	-0.930000	0.03752	-0.726000	0.03593	CAG	T|0.754;C|0.246	0.246	strong		0.667	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
TEKT3	64518	hgsc.bcm.edu	37	17	15217535	15217535	+	Silent	SNP	C	C	T	rs144456077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15217535C>T	ENST00000395930.1	-	6	933	c.747G>A	c.(745-747)gcG>gcA	p.A249A	RNU6-799P_ENST00000363567.1_RNA|TEKT3_ENST00000338696.2_Silent_p.A249A	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	249					cilium morphogenesis (GO:0060271)|regulation of fertilization (GO:0080154)|sperm motility (GO:0030317)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				endometrium(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	23				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		CATGCTGGGACGCTCTGTTGG	0.547													C|||	20	0.00399361	0.0151	0.0	5008	,	,		21690	0.0		0.0	False		,,,				2504	0.0				p.A249A		Atlas-SNP	.											TEKT3,NS,adenocarcinoma,0,1	TEKT3	64	1	0			c.G747A						PASS	.	C		47,4359	49.6+/-84.7	0,47,2156	174.0	111.0	132.0		747	-10.9	0.0	17	dbSNP_134	132	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	TEKT3	NM_031898.2		0,51,6452	TT,TC,CC		0.0465,1.0667,0.3921		249/491	15217535	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	64518	exon6			CTGGGACGCTCTG	AF334676	CCDS11169.1	17p12	2011-05-23			ENSG00000125409	ENSG00000125409			14293	protein-coding gene	gene with protein product		612683				11381029, 14735490	Standard	NM_031898		Approved	FLJ32828	uc002gon.3	Q9BXF9	OTTHUMG00000058965	ENST00000395930.1:c.747G>A	17.37:g.15217535C>T		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	312	159	0.509615	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Silent	SNP	ENST00000395930.1	37	CCDS11169.1																																																																																			C|0.996;T|0.004	0.004	strong		0.547	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898	
ZWINT	11130	hgsc.bcm.edu	37	10	58118630	58118630	+	Missense_Mutation	SNP	T	T	C	rs2241666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:58118630T>C	ENST00000373944.3	-	6	597	c.559A>G	c.(559-561)Agg>Ggg	p.R187G	ZWINT_ENST00000395405.1_Missense_Mutation_p.R187G|ZWINT_ENST00000361148.6_Intron|ZWINT_ENST00000318387.2_Missense_Mutation_p.R67G|ZWINT_ENST00000460654.1_5'UTR			O95229	ZWINT_HUMAN	ZW10 interacting kinetochore protein	187			R -> G (in dbSNP:rs2241666). {ECO:0000269|PubMed:10806105, ECO:0000269|PubMed:15489334}.		establishment of localization in cell (GO:0051649)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|kinetochore (GO:0000776)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)	20						TGAAACACCCTGTCAAGCTCC	0.552													C|||	3816	0.761981	0.8026	0.7781	5008	,	,		18623	0.8313		0.6382	False		,,,				2504	0.7515				p.R187G		Atlas-SNP	.											.	ZWINT	39	.	0			c.A559G						PASS	.	C	,GLY/ARG,GLY/ARG	3318,1088	393.3+/-328.8	1247,824,132	125.0	123.0	124.0		,559,559	1.4	0.0	10	dbSNP_98	124	5429,3171	482.1+/-370.8	1714,2001,585	yes	intron,missense,missense	ZWINT	NM_001005413.1,NM_032997.2,NM_007057.3	,125,125	2961,2825,717	CC,CT,TT		36.8721,24.6936,32.7464	,benign,benign	,187/278,187/278	58118630	8747,4259	2203	4300	6503	SO:0001583	missense	11130	exon6			ACACCCTGTCAAG	AF067656	CCDS7249.1, CCDS31205.1	10q21-q22	2013-05-01	2013-05-01		ENSG00000122952	ENSG00000122952			13195	protein-coding gene	gene with protein product		609177	"""ZW10 interactor"""				Standard	XM_005269463		Approved	KNTC2AP	uc001jka.1	O95229	OTTHUMG00000018261	ENST00000373944.3:c.559A>G	10.37:g.58118630T>C	ENSP00000363055:p.Arg187Gly	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	269	268	0.996283	NM_007057	A6NNV6|Q0D2I3|Q9BWD0	Missense_Mutation	SNP	ENST00000373944.3	37	CCDS7249.1	1607	0.7358058608058609	374	0.7601626016260162	275	0.7596685082872928	470	0.8216783216783217	488	0.6437994722955145	C	0.045	-1.268236	0.01433	0.753064	0.631279	ENSG00000122952	ENST00000373944;ENST00000395405;ENST00000318387	T;T;T	0.48201	0.82;0.82;0.82	4.48	1.39	0.22231	.	0.919113	0.09040	N	0.857498	T	0.00012	0.0000	N	0.20401	0.57	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.35051	-0.9804	9	0.14656	T	0.56	-13.4497	7.0588	0.25113	0.0:0.3325:0.3545:0.3129	rs2241666;rs17652937;rs17856625;rs52808198;rs57541824;rs2241666	187	O95229	ZWINT_HUMAN	G	187;187;67	ENSP00000363055:R187G;ENSP00000378801:R187G;ENSP00000322850:R67G	ENSP00000322850:R67G	R	-	1	2	ZWINT	57788636	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.152000	0.16302	0.061000	0.16311	-0.821000	0.03111	AGG	C|0.704;N|0.000	0.704	strong		0.552	ZWINT-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048132.1		
TUBA3D	113457	hgsc.bcm.edu	37	2	132240298	132240298	+	Silent	SNP	C	C	T	rs138292408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:132240298C>T	ENST00000321253.6	+	5	1337	c.1230C>T	c.(1228-1230)ggC>ggT	p.G410G	MZT2A_ENST00000410036.2_5'Flank	NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	410					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		GGTACGTGGGCGAAGGCATGG	0.597													.|||	248	0.0495208	0.1785	0.0159	5008	,	,		20048	0.0		0.001	False		,,,				2504	0.0				p.G410G	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											.	TUBA3D	60	.	0			c.C1230T						PASS	.	C		728,3678	296.1+/-284.1	47,634,1522	159.0	157.0	158.0		1230	-4.8	1.0	2	dbSNP_134	158	9,8591	5.7+/-21.5	0,9,4291	no	coding-synonymous	TUBA3D	NM_080386.2		47,643,5813	TT,TC,CC		0.1047,16.5229,5.6666		410/451	132240298	737,12269	2203	4300	6503	SO:0001819	synonymous_variant	113457	exon5			CGTGGGCGAAGGC	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"""Tubulins"""	24071	protein-coding gene	gene with protein product	"""alpha-tubulin isotype H2-alpha"""					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.1230C>T	2.37:g.132240298C>T		Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	299	136	0.45485	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000321253.6	37	CCDS33290.1																																																																																			C|0.942;T|0.058	0.058	strong		0.597	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386	
GPR107	57720	hgsc.bcm.edu	37	9	132854643	132854643	+	Silent	SNP	T	T	C	rs34227818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132854643T>C	ENST00000372406.1	+	9	1353	c.846T>C	c.(844-846)caT>caC	p.H282H	GPR107_ENST00000372410.3_Silent_p.H282H|GPR107_ENST00000347136.6_Silent_p.H282H	NM_001136557.1	NP_001130029.1	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107	282						integral component of membrane (GO:0016021)				endometrium(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	11		Ovarian(14;0.000531)				TCTGGATTCATATCCTTCGAA	0.423													T|||	120	0.0239617	0.0825	0.0144	5008	,	,		15888	0.0		0.001	False		,,,				2504	0.0				p.H282H		Atlas-SNP	.											.	GPR107	30	.	0			c.T846C						PASS	.	T	,,	325,4081	173.0+/-202.9	5,315,1883	147.0	144.0	145.0		846,846,846	2.2	1.0	9	dbSNP_126	145	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	GPR107	NM_001136557.1,NM_001136558.1,NM_020960.4	,,	5,322,6176	CC,CT,TT		0.0814,7.3763,2.5527	,,	282/601,282/572,282/553	132854643	332,12674	2203	4300	6503	SO:0001819	synonymous_variant	57720	exon9			GATTCATATCCTT	AF376725	CCDS35162.1, CCDS48041.1, CCDS48042.1	9q34.2	2014-01-30			ENSG00000148358	ENSG00000148358		"""GPCR / Unclassified : 7TM orphan receptors"""	17830	protein-coding gene	gene with protein product							Standard	NM_020960		Approved	KIAA1624, RP11-88G17, FLJ20998, LUSTR1	uc004bzd.2	Q5VW38	OTTHUMG00000020804	ENST00000372406.1:c.846T>C	9.37:g.132854643T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	203	126	0.62069	NM_001136557	A6NJ53|Q2TB81|Q5JPA3|Q5VW39|Q96T26|Q9H658|Q9HCE8	Silent	SNP	ENST00000372406.1	37	CCDS48041.1																																																																																			T|0.980;C|0.020	0.020	strong		0.423	GPR107-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054643.2		
TICRR	90381	hgsc.bcm.edu	37	15	90164769	90164769	+	Silent	SNP	T	T	C	rs75934760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90164769T>C	ENST00000268138.7	+	19	3405	c.3300T>C	c.(3298-3300)ccT>ccC	p.P1100P	KIF7_ENST00000558928.1_Intron|TICRR_ENST00000560985.1_Silent_p.P1099P			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1100					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)										CGGAGGTACCTGCAGCTTACC	0.428													T|||	221	0.0441294	0.1558	0.0216	5008	,	,		19124	0.0		0.0	False		,,,				2504	0.0				p.P1100P		Atlas-SNP	.											.	.	.	.	0			c.T3300C						PASS	.	T		445,3261		33,379,1441	55.0	54.0	54.0		3300	1.5	0.0	15	dbSNP_132	54	6,8188		0,6,4091	no	coding-synonymous	C15orf42	NM_152259.3		33,385,5532	CC,CT,TT		0.0732,12.0076,3.7899		1100/1911	90164769	451,11449	1853	4097	5950	SO:0001819	synonymous_variant	90381	exon19			GGTACCTGCAGCT	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.3300T>C	15.37:g.90164769T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																			T|0.973;C|0.027	0.027	strong		0.428	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
MOGS	7841	hgsc.bcm.edu	37	2	74688884	74688884	+	Missense_Mutation	SNP	G	G	A	rs13405869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74688884G>A	ENST00000233616.4	-	4	2194	c.2032C>T	c.(2032-2034)Cgg>Tgg	p.R678W	MOGS_ENST00000452063.2_Missense_Mutation_p.R572W|MOGS_ENST00000409065.1_3'UTR|MOGS_ENST00000462443.1_5'Flank	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	678					cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						GGTTGGGGCCGACCCACCACC	0.597													G|||	133	0.0265575	0.0961	0.0086	5008	,	,		18324	0.0		0.0	False		,,,				2504	0.0				p.R678W		Atlas-SNP	.											.	MOGS	58	.	0			c.C2032T						PASS	.	G	TRP/ARG,TRP/ARG	309,3659		17,275,1692	64.0	76.0	72.0		1714,2032	-0.3	0.9	2	dbSNP_121	72	3,8293		0,3,4145	yes	missense,missense	MOGS	NM_001146158.1,NM_006302.2	101,101	17,278,5837	AA,AG,GG		0.0362,7.7873,2.544	probably-damaging,probably-damaging	572/732,678/838	74688884	312,11952	1984	4148	6132	SO:0001583	missense	7841	exon4			GGGGCCGACCCAC	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"""glucosidase I"", ""processing A-glucosidase I"""	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.2032C>T	2.37:g.74688884G>A	ENSP00000233616:p.Arg678Trp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	118	47	0.398305	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	37	CCDS42700.1	63	0.028846153846153848	59	0.11991869918699187	4	0.011049723756906077	0	0.0	0	0.0	G	8.207	0.799569	0.16397	0.077873	3.62E-4	ENSG00000115275	ENST00000233616;ENST00000452063	T;T	0.39406	1.08;1.08	5.01	-0.259	0.12971	Six-hairpin glycosidase-like (1);	0.118143	0.52532	N	0.000072	T	0.01124	0.0037	M	0.61703	1.905	0.09310	P	0.999999999995561	D	0.89917	1.0	D	0.81914	0.995	T	0.21621	-1.0240	9	0.52906	T	0.07	-11.998	8.8519	0.35206	0.0776:0.0:0.271:0.6514	rs13405869	678	Q13724	MOGS_HUMAN	W	678;572	ENSP00000233616:R678W;ENSP00000388201:R572W	ENSP00000233616:R678W	R	-	1	2	MOGS	74542392	0.955000	0.32602	0.865000	0.33974	0.148000	0.21650	0.271000	0.18626	-0.231000	0.09825	-2.140000	0.00339	CGG	G|0.980;A|0.020	0.020	strong		0.597	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302	
PCLO	27445	hgsc.bcm.edu	37	7	82764924	82764924	+	Missense_Mutation	SNP	C	C	T	rs138200846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:82764924C>T	ENST00000333891.9	-	3	2279	c.1942G>A	c.(1942-1944)Ggg>Agg	p.G648R	PCLO_ENST00000423517.2_Missense_Mutation_p.G648R	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						GCCAGATCCCCGCCTAGAGCT	0.453													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		14124	0.0		0.0	False		,,,				2504	0.0				p.G648R		Atlas-SNP	.											.	PCLO	1506	.	0			c.G1942A						PASS	.	C	ARG/GLY,ARG/GLY	88,3802		0,88,1857	57.0	57.0	57.0		1942,1942	5.3	1.0	7	dbSNP_134	57	1,8259		0,1,4129	yes	missense,missense	PCLO	NM_014510.2,NM_033026.5	125,125	0,89,5986	TT,TC,CC		0.0121,2.2622,0.7325	probably-damaging,probably-damaging	648/4936,648/5143	82764924	89,12061	1945	4130	6075	SO:0001583	missense	27445	exon3			GATCCCCGCCTAG	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.1942G>A	7.37:g.82764924C>T	ENSP00000334319:p.Gly648Arg	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	155	83	0.535484	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	C	7.181	0.589683	0.13812	0.022622	1.21E-4	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17528	2.27;2.27	5.31	5.31	0.75309	.	.	.	.	.	T	0.11153	0.0272	L	0.34521	1.04	0.25271	N	0.989512	D;D	0.69078	0.997;0.997	P;P	0.50970	0.655;0.655	T	0.04481	-1.0948	9	0.87932	D	0	.	12.3476	0.55130	0.0:0.9226:0.0:0.0774	.	648;648	Q9Y6V0-5;Q9Y6V0-6	.;.	R	594;648;648	ENSP00000334319:G648R;ENSP00000388393:G648R	ENSP00000334319:G648R	G	-	1	0	PCLO	82602860	0.380000	0.25131	0.990000	0.47175	0.708000	0.40852	2.840000	0.48215	2.485000	0.83878	0.591000	0.81541	GGG	C|0.995;T|0.005	0.005	strong		0.453	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
OCA2	4948	hgsc.bcm.edu	37	15	28211921	28211921	+	Silent	SNP	G	G	A	rs1800411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:28211921G>A	ENST00000354638.3	-	15	1706	c.1551C>T	c.(1549-1551)tgC>tgT	p.C517C	OCA2_ENST00000353809.5_Silent_p.C493C|OCA2_ENST00000382996.2_Silent_p.C517C	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	517					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)		GGAGAACAAGGCAAATCCCAA	0.493									Oculocutaneous Albinism				G|||	1823	0.364018	0.2383	0.4712	5008	,	,		20394	0.1558		0.6779	False		,,,				2504	0.3497				p.C517C		Atlas-SNP	.											OCA2,NS,carcinoma,-2,1	OCA2	173	1	0			c.C1551T						scavenged	.	G		1302,3104	439.8+/-345.8	203,896,1104	111.0	90.0	97.0		1551	4.2	0.9	15	dbSNP_89	97	6073,2527	692.7+/-404.6	2144,1785,371	no	coding-synonymous	OCA2	NM_000275.2		2347,2681,1475	AA,AG,GG		29.3837,29.5506,43.2954		517/839	28211921	7375,5631	2203	4300	6503	SO:0001819	synonymous_variant	4948	exon15	Familial Cancer Database		AACAAGGCAAATC		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.1551C>T	15.37:g.28211921G>A		Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	151	61	0.403974	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Silent	SNP	ENST00000354638.3	37	CCDS10020.1																																																																																			G|0.543;A|0.457	0.457	strong		0.493	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559849	140559849	+	Missense_Mutation	SNP	G	G	A	rs17096961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140559849G>A	ENST00000239444.2	+	1	2479	c.2234G>A	c.(2233-2235)aGc>aAc	p.S745N	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	745			S -> N (in dbSNP:rs17096961).		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)			GGCACCGGGAGCCTGTCTCAG	0.597													G|||	758	0.151358	0.2572	0.1902	5008	,	,		15316	0.0407		0.1531	False		,,,				2504	0.093				p.S745N		Atlas-SNP	.											.	PCDHB8	199	.	0			c.G2234A						PASS	.	G	ASN/SER	1039,3367	384.4+/-325.3	116,807,1280	89.0	91.0	91.0		2234	3.7	0.2	5	dbSNP_123	91	1429,7171	275.0+/-291.5	126,1177,2997	yes	missense	PCDHB8	NM_019120.3	46	242,1984,4277	AA,AG,GG		16.6163,23.5815,18.9759	benign	745/802	140559849	2468,10538	2203	4300	6503	SO:0001583	missense	56128	exon1			CCGGGAGCCTGTC	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.2234G>A	5.37:g.140559849G>A	ENSP00000239444:p.Ser745Asn	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	327	0.14972527472527472	122	0.24796747967479674	63	0.17403314917127072	26	0.045454545454545456	116	0.15303430079155672	g	11.20	1.567178	0.28003	0.235815	0.166163	ENSG00000120322	ENST00000239444	T	0.49432	0.78	4.53	3.66	0.41972	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.40933	P	0.015599999999999947	B	0.02656	0.0	B	0.04013	0.001	T	0.07597	-1.0764	8	0.66056	D	0.02	.	14.1857	0.65605	0.0:0.8474:0.1526:0.0	rs17096961;rs17844509;rs17096961	745	Q9UN66	PCDB8_HUMAN	N	745	ENSP00000239444:S745N	ENSP00000239444:S745N	S	+	2	0	PCDHB8	140540033	0.626000	0.27120	0.220000	0.23810	0.001000	0.01503	3.667000	0.54547	0.895000	0.36342	-0.241000	0.12123	AGC	G|0.827;A|0.173	0.173	strong		0.597	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
TRPM1	4308	hgsc.bcm.edu	37	15	31342744	31342744	+	Silent	SNP	C	C	T	rs1035705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31342744C>T	ENST00000256552.6	-	12	1452	c.1305G>A	c.(1303-1305)acG>acA	p.T435T	TRPM1_ENST00000542188.1_Silent_p.T452T|TRPM1_ENST00000397795.2_Silent_p.T413T	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)		TCTCCTTCTCCGTGGCTTTGC	0.542													C|||	2600	0.519169	0.1566	0.621	5008	,	,		22786	0.9435		0.5179	False		,,,				2504	0.501				p.T452T		Atlas-SNP	.											.	TRPM1	183	.	0			c.G1356A						PASS	.	C		894,2992		113,668,1162	97.0	95.0	95.0		1239	-8.4	0.1	15	dbSNP_86	95	4445,3831		1184,2077,877	no	coding-synonymous	TRPM1	NM_002420.4		1297,2745,2039	TT,TC,CC		46.2905,23.0057,43.899		413/1604	31342744	5339,6823	1943	4138	6081	SO:0001819	synonymous_variant	4308	exon11			CTTCTCCGTGGCT	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.1305G>A	15.37:g.31342744C>T		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	253	133	0.525692	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			C|0.456;T|0.544	0.544	strong		0.542	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
PSG7	5676	hgsc.bcm.edu	37	19	43433805	43433805	+	RNA	SNP	A	A	G	rs1065178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43433805A>G	ENST00000406070.2	-	0	594				PSG7_ENST00000446844.3_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)						female pregnancy (GO:0007565)	extracellular region (GO:0005576)							Prostate(69;0.00682)				CACAGGTTAAAATCACAGCCT	0.527													.|||	2229	0.445088	0.5666	0.4294	5008	,	,		18641	0.4216		0.2704	False		,,,				2504	0.4959				p.I44I		Atlas-SNP	.											.	.	.	.	0			c.T132C						PASS	.	G	,	2464,1938		733,998,470	220.0	217.0	218.0		132,498	-2.7	0.0	19	dbSNP_86	218	2421,6179		400,1621,2279	no	coding-synonymous,coding-synonymous	PSG7	NM_001206650.1,NM_002783.2	,	1133,2619,2749	GG,GA,AA		28.1512,44.0254,37.5711	,	44/298,166/420	43433805	4885,8117	2201	4300	6501			5676	exon2			GGTTAAAATCACA			19q13.2	2013-01-29	2010-02-26		ENSG00000221878	ENSG00000221878		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9524	protein-coding gene	gene with protein product		176396	"""pregnancy specific beta-1-glycoprotein 7"""				Standard	NM_002783		Approved		uc010xwl.2	Q13046	OTTHUMG00000151125		19.37:g.43433805A>G		Somatic	225	2	0.00888889		WXS	Illumina HiSeq	Phase_I	298	297	0.996644	NM_001206650	Q15232	Silent	SNP	ENST00000406070.2	37																																																																																				A|0.622;G|0.378	0.378	strong		0.527	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	NM_001206650	
UCK1	83549	hgsc.bcm.edu	37	9	134404337	134404337	+	Silent	SNP	G	G	A	rs11557925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:134404337G>A	ENST00000372215.4	-	5	690	c.597C>T	c.(595-597)tgC>tgT	p.C199C	UCK1_ENST00000459858.1_5'UTR|UCK1_ENST00000372211.3_Silent_p.C204C|UCK1_ENST00000372210.3_Silent_p.C190C|UCK1_ENST00000372208.3_Intron	NM_001261450.1|NM_001261451.1|NM_031432.2	NP_001248379.1|NP_001248380.1|NP_113620.1	Q9HA47	UCK1_HUMAN	uridine-cytidine kinase 1	199					CTP salvage (GO:0044211)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)		GTACCGGCAGGCAGAACTCCT	0.602													G|||	111	0.0221645	0.0794	0.0086	5008	,	,		17080	0.0		0.0	False		,,,				2504	0.0				p.C204C	Melanoma(42;523 1129 28385 43975 48113)	Atlas-SNP	.											.	UCK1	29	.	0			c.C612T						PASS	.	G	,	281,4125	153.7+/-187.2	8,265,1930	74.0	57.0	63.0		,597	3.7	1.0	9	dbSNP_120	63	0,8600		0,0,4300	no	intron,coding-synonymous	UCK1	NM_001135954.1,NM_031432.2	,	8,265,6230	AA,AG,GG		0.0,6.3777,2.1605	,	,199/278	134404337	281,12725	2203	4300	6503	SO:0001819	synonymous_variant	83549	exon5			CGGCAGGCAGAAC	AF237290	CCDS6944.1, CCDS48046.1, CCDS59151.1, CCDS59152.1	9q34.1	2008-02-05			ENSG00000130717	ENSG00000130717	2.7.1.48		14859	protein-coding gene	gene with protein product		609328				11306702	Standard	NM_031432		Approved	URK1, FLJ12255	uc031tfj.1	Q9HA47	OTTHUMG00000020823	ENST00000372215.4:c.597C>T	9.37:g.134404337G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_001261451	Q5JT09|Q5JT10|Q5JT12|Q5JT13|Q6IA74|Q96BJ0	Silent	SNP	ENST00000372215.4	37	CCDS6944.1																																																																																			G|0.976;A|0.024	0.024	strong		0.602	UCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054726.1	NM_031432	
ZNF17	7565	hgsc.bcm.edu	37	19	57931553	57931553	+	Silent	SNP	C	C	T	rs10417533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57931553C>T	ENST00000601808.1	+	3	906	c.693C>T	c.(691-693)tcC>tcT	p.S231S	AC004076.7_ENST00000597410.1_Intron|ZNF17_ENST00000307658.7_Silent_p.S233S	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	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)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		GGTACAACTCCGACCTTATTA	0.413													C|||	1133	0.226238	0.3449	0.2176	5008	,	,		23816	0.0794		0.2694	False		,,,				2504	0.1789				p.S231S	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.C693T						PASS	.	C		1306,3092	411.3+/-335.7	195,916,1088	87.0	89.0	89.0		693	-3.5	0.0	19	dbSNP_119	89	2171,6427	363.7+/-333.3	274,1623,2402	no	coding-synonymous	ZNF17	NM_006959.2		469,2539,3490	TT,TC,CC		25.2501,29.6953,26.7544		231/663	57931553	3477,9519	2199	4299	6498	SO:0001819	synonymous_variant	7565	exon3			CAACTCCGACCTT	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"""Zinc fingers, C2H2-type"", ""-"""	12958	protein-coding gene	gene with protein product			"""zinc finger protein 17 (HPF3, KOX 10)"""			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.693C>T	19.37:g.57931553C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Silent	SNP	ENST00000601808.1	37	CCDS42636.1																																																																																			C|0.772;T|0.228	0.228	strong		0.413	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959	
CCDC138	165055	hgsc.bcm.edu	37	2	109429277	109429277	+	Splice_Site	SNP	G	G	C	rs58170568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:109429277G>C	ENST00000295124.4	+	9	995	c.935G>C	c.(934-936)aGg>aCg	p.R312T	CCDC138_ENST00000412964.2_Splice_Site_p.R312T	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	312										endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						CTGTTGCAGAGGAAGTACGAG	0.318													G|||	31	0.0061901	0.0212	0.0043	5008	,	,		19524	0.0		0.0	False		,,,				2504	0.0				p.R312T		Atlas-SNP	.											.	CCDC138	49	.	0			c.G935C						PASS	.	G	THR/ARG	77,4329	68.1+/-105.8	1,75,2127	88.0	90.0	89.0		935	5.5	1.0	2	dbSNP_129	89	0,8598		0,0,4299	yes	missense-near-splice	CCDC138	NM_144978.1	71	1,75,6426	CC,CG,GG		0.0,1.7476,0.5921	benign	312/666	109429277	77,12927	2203	4299	6502	SO:0001630	splice_region_variant	165055	exon9			TGCAGAGGAAGTA	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.934-1G>C	2.37:g.109429277G>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	37	CCDS2080.1	14|14	0.00641025641025641|0.00641025641025641	11|11	0.022357723577235773|0.022357723577235773	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.96|13.96	2.393929|2.393929	0.42410|0.42410	0.017476|0.017476	0.0|0.0	ENSG00000163006|ENSG00000163006	ENST00000456512|ENST00000412964;ENST00000295124	.|D;D	.|0.89681	.|-2.55;-2.55	5.49|5.49	5.49|5.49	0.81192|0.81192	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.89670|0.89670	0.6782|0.6782	M|M	0.72894|0.72894	2.215|2.215	0.44798|0.44798	D|D	0.997805|0.997805	.|D;B	.|0.76494	.|0.999;0.441	.|D;B	.|0.83275	.|0.996;0.2	D|D	0.89997|0.89997	0.4112|0.4112	5|10	.|0.45353	.|T	.|0.12	.|.	18.1478|18.1478	0.89663|0.89663	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs58170568|rs58170568	.|312;312	.|Q96M89-2;Q96M89	.|.;CC138_HUMAN	R|T	209|312	.|ENSP00000411800:R312T;ENSP00000295124:R312T	.|ENSP00000295124:R312T	G|R	+|+	1|2	0|0	CCDC138|CCDC138	108795709|108795709	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.398000|0.398000	0.30690|0.30690	5.570000|5.570000	0.67398|0.67398	2.572000|2.572000	0.86782|0.86782	0.655000|0.655000	0.94253|0.94253	GGA|AGG	G|0.993;C|0.007	0.007	strong		0.318	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	Missense_Mutation
ISOC1	51015	hgsc.bcm.edu	37	5	128442644	128442644	+	Silent	SNP	T	T	C	rs3734161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:128442644T>C	ENST00000173527.5	+	4	655	c.639T>C	c.(637-639)caT>caC	p.H213H		NM_016048.2	NP_057132.2	Q96CN7	ISOC1_HUMAN	isochorismatase domain containing 1	213						extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	catalytic activity (GO:0003824)			kidney(2)|lung(7)	9		all_cancers(142;0.0813)|Prostate(80;0.0865)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.138)|OV - Ovarian serous cystadenocarcinoma(64;0.164)		ACTAGACTCATGTGTGCATCC	0.408													T|||	357	0.0712859	0.1861	0.0346	5008	,	,		20035	0.0446		0.0219	False		,,,				2504	0.0204				p.H213H		Atlas-SNP	.											.	ISOC1	26	.	0			c.T639C						PASS	.	T		608,3356		41,526,1415	99.0	94.0	96.0		639	-2.7	1.0	5	dbSNP_107	96	225,8119		1,223,3948	no	coding-synonymous	ISOC1	NM_016048.2		42,749,5363	CC,CT,TT		2.6965,15.338,6.768		213/299	128442644	833,11475	1982	4172	6154	SO:0001819	synonymous_variant	51015	exon4			GACTCATGTGTGC	AF151869	CCDS43357.1	5q22.1-q33.3	2010-03-19			ENSG00000066583	ENSG00000066583			24254	protein-coding gene	gene with protein product						10810093, 18566572	Standard	NM_016048		Approved	CGI-111	uc003kva.3	Q96CN7	OTTHUMG00000163144	ENST00000173527.5:c.639T>C	5.37:g.128442644T>C		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_016048	Q7Z770	Silent	SNP	ENST00000173527.5	37	CCDS43357.1																																																																																			T|0.931;C|0.069	0.069	strong		0.408	ISOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371826.1	NM_016048	
VWDE	221806	hgsc.bcm.edu	37	7	12409535	12409535	+	Silent	SNP	A	A	G	rs3801366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12409535A>G	ENST00000275358.3	-	12	2585	c.2397T>C	c.(2395-2397)tcT>tcC	p.S799S		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	799						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						CGGTGAGGCCAGAGGGAGTGG	0.498													A|||	801	0.159944	0.1747	0.0836	5008	,	,		19322	0.2024		0.1044	False		,,,				2504	0.2076				p.S799S		Atlas-SNP	.											.	VWDE	123	.	0			c.T2397C						PASS	.	A		249,1135		23,203,466	63.0	48.0	53.0		2397	0.8	1.0	7	dbSNP_107	53	366,2816		20,326,1245	no	coding-synonymous	VWDE	NM_001135924.1		43,529,1711	GG,GA,AA		11.5022,17.9913,13.4691		799/1591	12409535	615,3951	692	1591	2283	SO:0001819	synonymous_variant	221806	exon12			GAGGCCAGAGGGA		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.2397T>C	7.37:g.12409535A>G		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	186	87	0.467742	NM_001135924	B7ZM77|Q96SQ3	Silent	SNP	ENST00000275358.3	37	CCDS47544.1																																																																																			A|0.851;G|0.149	0.149	strong		0.498	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
CXorf57	55086	hgsc.bcm.edu	37	X	105883826	105883826	+	Missense_Mutation	SNP	T	T	G	rs5962707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:105883826T>G	ENST00000372548.4	+	10	1888	c.1779T>G	c.(1777-1779)atT>atG	p.I593M	CXorf57_ENST00000372544.2_Missense_Mutation_p.I496M|MIR548AN_ENST00000408286.2_RNA|CXorf57_ENST00000497124.1_3'UTR	NM_018015.5	NP_060485.4	Q6NSI4	CX057_HUMAN	chromosome X open reading frame 57	593			I -> M (in dbSNP:rs5962707). {ECO:0000269|PubMed:15489334}.				poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	31						GAGTAGAAATTCAAGAAAGAA	0.333													T|||	445	0.117881	0.3185	0.0346	3775	,	,		11888	0.0		0.0	False		,,,				2504	0.0				p.I593M		Atlas-SNP	.											.	CXorf57	107	.	0			c.T1779G						PASS	.	T	MET/ILE,MET/ILE	1450,2385		216,789,229,627,342	118.0	111.0	113.0		1488,1779	1.0	0.0	X	dbSNP_114	113	8,6720		0,7,1,2421,1871	yes	missense,missense	CXorf57	NM_001184782.1,NM_018015.5	10,10	216,796,230,3048,2213	GG,GT,G,TT,T		0.1189,37.8096,13.8029	benign,benign	496/759,593/856	105883826	1458,9105	2203	4300	6503	SO:0001583	missense	55086	exon10			AGAAATTCAAGAA	AK024253	CCDS14519.1, CCDS55470.1	Xq22.3	2008-02-05			ENSG00000147231	ENSG00000147231			25486	protein-coding gene	gene with protein product							Standard	NM_018015		Approved	FLJ14191, FLJ10178	uc004emi.4	Q6NSI4	OTTHUMG00000022150	ENST00000372548.4:c.1779T>G	X.37:g.105883826T>G	ENSP00000361628:p.Ile593Met	Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	419	145	0.346062	NM_018015	H7BY89|Q4G0L7|Q5JQS1|Q5JRF9|Q6PHY5|Q6PII9|Q6PJU8|Q9H7W5|Q9NWA6	Missense_Mutation	SNP	ENST00000372548.4	37	CCDS14519.1	168	0.10126582278481013	105	0.2734375	6	0.01694915254237288	0	0.0	0	0.0	T	6.656	0.489589	0.12641	0.378096	0.001189	ENSG00000147231	ENST00000372544;ENST00000372548;ENST00000421550	T;T;T	0.64618	0.88;-0.11;0.88	3.51	0.993	0.19825	.	1.046520	0.07422	N	0.894082	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.12630	0.006;0.006	B;B	0.06405	0.002;0.002	T	0.28808	-1.0032	9	0.56958	D	0.05	0.7933	3.0646	0.06210	0.0:0.141:0.2513:0.6078	rs5962707;rs52800882;rs5962707	593;593	A8K6R5;Q6NSI4	.;CX057_HUMAN	M	496;593;304	ENSP00000361623:I496M;ENSP00000361628:I593M;ENSP00000405866:I304M	ENSP00000361623:I496M	I	+	3	3	CXorf57	105770482	0.005000	0.15991	0.001000	0.08648	0.152000	0.21847	0.853000	0.27777	0.098000	0.17522	0.339000	0.21740	ATT	0|0.014;G|0.148	0.148	strong		0.333	CXorf57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057800.2	NM_018015	
FPR1	2357	hgsc.bcm.edu	37	19	52249702	52249702	+	Silent	SNP	G	G	T	rs2070746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	41	0	0		WXS	Illumina HiSeq	Phase_I	53	33	0.622642	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	
NPSR1	387129	hgsc.bcm.edu	37	7	34917759	34917759	+	Missense_Mutation	SNP	C	C	T	rs13230135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:34917759C>T	ENST00000359791.1	+	9	1225	c.1097C>T	c.(1096-1098)aCt>aTt	p.T366I	NPSR1_ENST00000531252.1_Missense_Mutation_p.T355I	NM_207173.1	NP_997056.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	0						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	TGGAAGGGTACTTGGCCAGGT	0.572													C|||	45	0.00898562	0.031	0.0043	5008	,	,		17115	0.0		0.0	False		,,,				2504	0.001				p.T366I		Atlas-SNP	.											.	NPSR1	134	.	0			c.C1097T						PASS	.	C	ILE/THR	157,4249	99.8+/-138.5	2,153,2048	76.0	60.0	65.0		1097	-1.2	0.0	7	dbSNP_121	65	3,8597	3.0+/-9.4	0,3,4297	no	missense	NPSR1	NM_207173.1	89	2,156,6345	TT,TC,CC		0.0349,3.5633,1.2302		366/378	34917759	160,12846	2203	4300	6503	SO:0001583	missense	387129	exon9			AGGGTACTTGGCC	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000359791.1:c.1097C>T	7.37:g.34917759C>T	ENSP00000352839:p.Thr366Ile	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	288	146	0.506944	NM_207173	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000359791.1	37	CCDS5443.1	17	0.007783882783882784	14	0.028455284552845527	3	0.008287292817679558	0	0.0	0	0.0	C	8.876	0.950372	0.18431	0.035633	3.49E-4	ENSG00000187258	ENST00000359791;ENST00000531252	T;T	0.72167	-0.63;-0.25	2.64	-1.25	0.09405	.	.	.	.	.	T	0.13798	0.0334	N	0.08118	0	0.09310	N	1	B;B;B	0.26975	0.165;0.003;0.003	B;B;B	0.18561	0.022;0.006;0.006	T	0.07578	-1.0765	9	0.46703	T	0.11	.	3.1688	0.06545	0.0:0.3835:0.2193:0.3971	rs13230135	300;355;366	B7ZMA2;Q6W5P4-5;Q6W5P4-4	.;.;.	I	366;355	ENSP00000352839:T366I;ENSP00000433258:T355I	ENSP00000352839:T366I	T	+	2	0	NPSR1	34884284	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.050000	0.11904	-0.336000	0.08438	-0.324000	0.08512	ACT	C|0.987;T|0.013	0.013	strong		0.572	NPSR1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216838.1	NM_207173	
SULT1A1	6817	hgsc.bcm.edu	37	16	28617413	28617413	+	Missense_Mutation	SNP	A	A	G	rs28374453		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:28617413A>G	ENST00000395607.1	-	7	1012	c.739T>C	c.(739-741)Ttc>Ctc	p.F247L	SULT1A1_ENST00000395609.1_Missense_Mutation_p.F247L|SULT1A1_ENST00000569554.1_Missense_Mutation_p.F247L|SULT1A1_ENST00000350842.4_Missense_Mutation_p.F169L|SULT1A1_ENST00000314752.7_Missense_Mutation_p.F247L	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	247					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)	p.F247L(5)|p.F169L(5)		endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	TGGTCCATGAACTCCTGGGGG	0.607																																					p.F247L		Atlas-SNP	.											SULT1A1_ENST00000350842,NS,carcinoma,0,10	SULT1A1	53	10	10	Substitution - Missense(10)	kidney(10)	c.T739C						scavenged	.						264.0	206.0	226.0					16																	28617413		2197	4300	6497	SO:0001583	missense	6817	exon6			CCATGAACTCCTG	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.739T>C	16.37:g.28617413A>G	ENSP00000378971:p.Phe247Leu	Somatic	516	0	0		WXS	Illumina HiSeq	Phase_I	271	83	0.306273	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Missense_Mutation	SNP	ENST00000395607.1	37	CCDS32420.1	56	0.02564102564102564	29	0.05894308943089431	5	0.013812154696132596	1	0.0017482517482517483	21	0.027704485488126648	a	7.042	0.562645	0.13498	.	.	ENSG00000196502	ENST00000314752;ENST00000350842;ENST00000395609;ENST00000395607	T;T;T;T	0.01548	4.78;4.78;4.78;4.78	2.17	-4.34	0.03666	Sulfotransferase domain (1);	0.865026	0.10074	N	0.719350	T	0.00144	0.0004	N	0.12920	0.275	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	0.46414	-0.9193	10	0.22109	T	0.4	.	1.793	0.03056	0.1608:0.4101:0.2253:0.2039	rs28374453	199;169;247	Q59GG0;P50225-2;P50225	.;.;ST1A1_HUMAN	L	247;169;247;247	ENSP00000321988:F247L;ENSP00000329399:F169L;ENSP00000378972:F247L;ENSP00000378971:F247L	ENSP00000321988:F247L	F	-	1	0	SULT1A1	28524914	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-3.681000	0.00394	-1.249000	0.02500	0.248000	0.18094	TTC	A|0.974;G|0.026	0.026	strong		0.607	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
NOL8	55035	hgsc.bcm.edu	37	9	95076665	95076665	+	Missense_Mutation	SNP	C	C	G	rs2236344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95076665C>G	ENST00000535387.1	-	6	2241	c.2242G>C	c.(2242-2244)Gtg>Ctg	p.V748L	NOL8_ENST00000358855.4_Missense_Mutation_p.V680L|NOL8_ENST00000442668.2_Missense_Mutation_p.V748L|NOL8_ENST00000545558.1_Missense_Mutation_p.V748L|NOL8_ENST00000542053.1_Missense_Mutation_p.V680L					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TTAGCACTCACATCTGACGAA	0.433													G|||	354	0.0706869	0.1188	0.0533	5008	,	,		21015	0.0446		0.0239	False		,,,				2504	0.093				p.V748L		Atlas-SNP	.											.	NOL8	118	.	0			c.G2242C						PASS	.	G	LEU/VAL	405,3465		18,369,1548	91.0	82.0	85.0		2242	0.8	0.0	9	dbSNP_98	85	352,7962		12,328,3817	yes	missense	NOL8	NM_017948.5	32	30,697,5365	GG,GC,CC		4.2338,10.4651,6.2131	benign	748/1168	95076665	757,11427	1935	4157	6092	SO:0001583	missense	55035	exon7			CACTCACATCTGA	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.2242G>C	9.37:g.95076665C>G	ENSP00000441300:p.Val748Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	99	56	0.565657	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	124	0.056776556776556776	67	0.13617886178861788	20	0.055248618784530384	20	0.03496503496503497	17	0.022427440633245383	G	0.058	-1.230797	0.01518	0.104651	0.042338	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	4.83	0.776	0.18532	.	1.179860	0.06090	N	0.663456	T	0.00241	0.0007	L	0.51422	1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.11203	-1.0597	9	0.23302	T	0.38	1.1273	2.3112	0.04186	0.2858:0.3908:0.195:0.1284	rs2236344;rs61437291;rs2236344	748	Q76FK4	NOL8_HUMAN	L	748;750;680;748;748;680;748	ENSP00000401177:V748L;ENSP00000351723:V680L;ENSP00000441140:V748L;ENSP00000441300:V748L;ENSP00000440709:V680L;ENSP00000414112:V748L	ENSP00000351723:V680L	V	-	1	0	NOL8	94116486	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.436000	0.06922	-0.410000	0.07542	-1.164000	0.01763	GTG	C|0.939;G|0.061	0.061	strong		0.433	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
SARDH	1757	hgsc.bcm.edu	37	9	136535746	136535746	+	Missense_Mutation	SNP	C	C	T	rs61685718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136535746C>T	ENST00000371872.4	-	19	2712	c.2455G>A	c.(2455-2457)Gca>Aca	p.A819T	SARDH_ENST00000422262.2_Missense_Mutation_p.A651T|SARDH_ENST00000371868.1_Missense_Mutation_p.A247T|SARDH_ENST00000439388.1_Missense_Mutation_p.A819T	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	819					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CGGAGGCCTGCGGCCCGCTGC	0.697													C|||	75	0.014976	0.0545	0.0043	5008	,	,		13059	0.0		0.0	False		,,,				2504	0.0				p.A819T		Atlas-SNP	.											SARDH,colon,carcinoma,0,1	SARDH	112	1	0			c.G2455A						PASS	.	C	THR/ALA,THR/ALA	197,4115		3,191,1962	11.0	11.0	11.0		2455,2455	-10.0	0.0	9	dbSNP_129	11	6,8490		0,6,4242	yes	missense,missense	SARDH	NM_001134707.1,NM_007101.3	58,58	3,197,6204	TT,TC,CC		0.0706,4.5686,1.5849	benign,benign	819/919,819/919	136535746	203,12605	2156	4248	6404	SO:0001583	missense	1757	exon19			GGCCTGCGGCCCG		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.2455G>A	9.37:g.136535746C>T	ENSP00000360938:p.Ala819Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	119	41	0.344538	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	27	0.012362637362637362	24	0.04878048780487805	3	0.008287292817679558	0	0.0	0	0.0	C	5.568	0.289698	0.10567	0.045686	7.06E-4	ENSG00000123453	ENST00000371872;ENST00000371868;ENST00000439388;ENST00000422262	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.01	-10.0	0.00425	Glycine cleavage T-protein, C-terminal barrel (1);	1.295140	0.05116	N	0.489711	T	0.12774	0.0310	N	0.11131	0.1	0.09310	N	0.999999	B;B	0.09022	0.001;0.002	B;B	0.13407	0.005;0.009	T	0.26224	-1.0109	10	0.30854	T	0.27	5.8048	0.49	0.00562	0.358:0.2261:0.1855:0.2303	rs61685718;rs61745311	819;247	Q9UL12;Q5SYV2	SARDH_HUMAN;.	T	819;247;819;651	ENSP00000360938:A819T;ENSP00000360934:A247T;ENSP00000403084:A819T;ENSP00000415537:A651T	ENSP00000360934:A247T	A	-	1	0	SARDH	135525567	0.000000	0.05858	0.000000	0.03702	0.480000	0.33159	-0.744000	0.04839	-2.619000	0.00441	-0.485000	0.04761	GCA	C|0.987;T|0.013	0.013	strong		0.697	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
FLG	2312	hgsc.bcm.edu	37	1	152281039	152281039	+	Missense_Mutation	SNP	G	G	A	rs7522925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281039G>A	ENST00000368799.1	-	3	6358	c.6323C>T	c.(6322-6324)gCg>gTg	p.A2108V	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	517	1	0.00193424		WXS	Illumina HiSeq	Phase_I	952	502	0.527311	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	
PCDHGB3	56102	hgsc.bcm.edu	37	5	140778256	140778256	+	Intron	SNP	G	G	A	rs6867460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140778256G>A	ENST00000576222.1	+	1	2546				PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAACAGGATGGTAGTAAATA	0.433													.|||	1016	0.202875	0.32	0.1902	5008	,	,		18939	0.1548		0.1024	False		,,,				2504	0.2065				p.G188S		Atlas-SNP	.											.	.	.	.	0			c.G562A						PASS	.	G	,,,,,,,,,,,SER/GLY,,SER/GLY	1172,2540		197,778,881	69.0	72.0	71.0		,,,,,,,,,,,562,,562	4.8	0.8	5	dbSNP_116	71	1005,7179		65,875,3152	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,missense	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032099.1	,,,,,,,,,,,56,,56	262,1653,4033	AA,AG,GG		12.2801,31.5733,18.3003	,,,,,,,,,,,,,	,,,,,,,,,,,188/924,,188/819	140778256	2177,9719	1856	4092	5948	SO:0001627	intron_variant	56101	exon1			CAGGATGGTAGTA	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+25880G>A	5.37:g.140778256G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_018925	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			G|0.804;A|0.196	0.196	strong		0.433	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
MAGEB2	4113	hgsc.bcm.edu	37	X	30237003	30237003	+	Silent	SNP	C	C	T	rs2074793|rs386824543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:30237003C>T	ENST00000378988.4	+	2	407	c.306C>T	c.(304-306)tcC>tcT	p.S102S		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	102										breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						CCTCAACATCCACTAAGAGCC	0.483													T|||	1221	0.323444	0.4281	0.3098	3775	,	,		15119	0.0298		0.2724	False		,,,				2504	0.1391				p.S102S		Atlas-SNP	.											.	MAGEB2	133	.	0			c.C306T						PASS	.	T		2081,1752		479,806,317,346,254	40.0	40.0	40.0		306	0.1	0.0	X	dbSNP_96	40	2654,4074		388,1148,730,892,1142	no	coding-synonymous	MAGEB2	NM_002364.4		867,1954,1047,1238,1396	TT,TC,T,CC,C		39.4471,45.7083,44.8348		102/320	30237003	4735,5826	2202	4300	6502	SO:0001819	synonymous_variant	4113	exon2			AACATCCACTAAG	AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"""DSS/AHC critical interval MAGE superfamily 6"", ""melanoma-associated antigen B2"", ""cancer/testis antigen family 3, member 2"""	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.306C>T	X.37:g.30237003C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	170	75	0.441176	NM_002364	O75860	Silent	SNP	ENST00000378988.4	37	CCDS14219.1																																																																																			C|0.599;0|0.003	.	strong		0.483	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364	
TMEM105	284186	hgsc.bcm.edu	37	17	79287477	79287477	+	Missense_Mutation	SNP	G	G	A	rs9916085	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79287477G>A	ENST00000332900.1	-	3	913	c.364C>T	c.(364-366)Cgg>Tgg	p.R122W		NM_178520.3	NP_848615.1	Q8N8V8	TM105_HUMAN	transmembrane protein 105	122			R -> W (in dbSNP:rs9916085).			integral component of membrane (GO:0016021)				NS(1)|large_intestine(3)|lung(1)|ovary(2)	7	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.0892)			CCTGCACCCCGGCCCCACAGC	0.592													G|||	494	0.0986422	0.292	0.0504	5008	,	,		14401	0.0		0.0586	False		,,,				2504	0.0143				p.R122W		Atlas-SNP	.											.	TMEM105	19	.	0			c.C364T						PASS	.	G	TRP/ARG	1170,3234	405.8+/-333.6	157,856,1189	54.0	58.0	56.0		364	0.1	0.0	17	dbSNP_119	56	421,8179	129.3+/-187.4	17,387,3896	yes	missense	TMEM105	NM_178520.3	101	174,1243,5085	AA,AG,GG		4.8953,26.5668,12.2347	possibly-damaging	122/130	79287477	1591,11413	2202	4300	6502	SO:0001583	missense	284186	exon3			CACCCCGGCCCCA	AK096111	CCDS11781.1	17q25.3	2008-04-21	2008-04-21	2008-04-21		ENSG00000185332			26794	protein-coding gene	gene with protein product							Standard	NM_178520		Approved	FLJ38792	uc002kad.2	Q8N8V8		ENST00000332900.1:c.364C>T	17.37:g.79287477G>A	ENSP00000329795:p.Arg122Trp	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	143	65	0.454545	NM_178520		Missense_Mutation	SNP	ENST00000332900.1	37	CCDS11781.1	205	0.09386446886446886	145	0.29471544715447157	13	0.03591160220994475	0	0.0	47	0.06200527704485488	G	9.289	1.050099	0.19827	0.265668	0.048953	ENSG00000185332	ENST00000332900	T	0.56444	0.46	1.16	0.114	0.14639	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.27932	0.194	B	0.09377	0.004	T	0.25433	-1.0132	8	0.87932	D	0	.	3.2835	0.06924	0.306:0.0:0.694:0.0	rs9916085;rs59672127;rs9916085	122	Q8N8V8	TM105_HUMAN	W	122	ENSP00000329795:R122W	ENSP00000329795:R122W	R	-	1	2	TMEM105	76902072	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.069000	0.11542	0.047000	0.15862	0.436000	0.28706	CGG	G|0.882;A|0.118	0.118	strong		0.592	TMEM105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439607.1	NM_178520	
OR10G7	390265	hgsc.bcm.edu	37	11	123909099	123909099	+	Missense_Mutation	SNP	G	G	T	rs59358830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909099G>T	ENST00000330487.5	-	1	618	c.610C>A	c.(610-612)Cta>Ata	p.L204I		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L204I(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		GAGGCCACTAGCCCAATATTC	0.557													C|||	356	0.0710863	0.062	0.1427	5008	,	,		21056	0.1438		0.007	False		,,,				2504	0.0235				p.L204I		Atlas-SNP	.											OR10G7,NS,carcinoma,0,1	OR10G7	103	1	1	Substitution - Missense(1)	stomach(1)	c.C610A						scavenged	.	C	ILE/LEU	223,4177		11,201,1988	237.0	208.0	218.0		610	0.2	0.0	11	dbSNP_129	218	26,8572		0,26,4273	no	missense	OR10G7	NM_001004463.1	5	11,227,6261	TT,TG,GG		0.3024,5.0682,1.9157	benign	204/312	123909099	249,12749	2200	4299	6499	SO:0001583	missense	390265	exon1			CCACTAGCCCAAT	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.610C>A	11.37:g.123909099G>T	ENSP00000329689:p.Leu204Ile	Somatic	471	5	0.0106157		WXS	Illumina HiSeq	Phase_I	426	183	0.429577	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	183	0.08379120879120878	30	0.06097560975609756	60	0.16574585635359115	87	0.1520979020979021	6	0.0079155672823219	C	0	-2.812780	0.00073	0.050682	0.003024	ENSG00000182634	ENST00000330487	T	0.39406	1.08	3.38	0.193	0.15139	GPCR, rhodopsin-like superfamily (1);	0.341004	0.21004	N	0.081809	T	0.00073	0.0002	N	0.25245	0.725	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.13202	-1.0518	9	0.32370	T	0.25	.	1.6512	0.02772	0.2543:0.1988:0.3752:0.1717	rs59358830	204	Q8NGN6	O10G7_HUMAN	I	204	ENSP00000329689:L204I	ENSP00000329689:L204I	L	-	1	2	OR10G7	123414309	0.000000	0.05858	0.003000	0.11579	0.130000	0.20726	-0.985000	0.03751	-0.335000	0.08451	-0.224000	0.12420	CTA	G|0.962;T|0.038	0.038	strong		0.557	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
SMURF2	64750	hgsc.bcm.edu	37	17	62567987	62567987	+	Silent	SNP	G	G	A	rs34788315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62567987G>A	ENST00000262435.9	-	10	1132	c.945C>T	c.(943-945)ttC>ttT	p.F315F	SMURF2_ENST00000578200.1_Intron	NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	315	WW 3. {ECO:0000255|PROSITE- ProRule:PRU00224}.				BMP signaling pathway (GO:0030509)|gene expression (GO:0010467)|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)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|SMAD binding (GO:0046332)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(4)	22	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			TATGGTCAACGAAATAAACTC	0.383													G|||	160	0.0319489	0.115	0.0115	5008	,	,		17923	0.0		0.0	False		,,,				2504	0.0				p.F315F		Atlas-SNP	.											.	SMURF2	63	.	0			c.C945T						PASS	.	G		414,3992	204.1+/-226.4	13,388,1802	118.0	106.0	110.0		945	0.8	1.0	17	dbSNP_126	110	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SMURF2	NM_022739.3		13,390,6100	AA,AG,GG		0.0233,9.3963,3.1985		315/749	62567987	416,12590	2203	4300	6503	SO:0001819	synonymous_variant	64750	exon10			GTCAACGAAATAA	AF301463	CCDS32707.1	17q22-q23	2012-10-05			ENSG00000108854	ENSG00000108854			16809	protein-coding gene	gene with protein product		605532				11016919	Standard	XM_005257585		Approved		uc002jep.1	Q9HAU4	OTTHUMG00000179189	ENST00000262435.9:c.945C>T	17.37:g.62567987G>A		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	182	92	0.505495	NM_022739	Q52LL1|Q9H260	Silent	SNP	ENST00000262435.9	37	CCDS32707.1																																																																																			G|0.964;A|0.036	0.036	strong		0.383	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739	
GPR149	344758	hgsc.bcm.edu	37	3	154146922	154146922	+	Silent	SNP	A	A	G	rs34792862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:154146922A>G	ENST00000389740.2	-	1	582	c.483T>C	c.(481-483)agT>agC	p.S161S		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	161					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AGAGCAGCAGACTGGCTGCCC	0.642													A|||	814	0.16254	0.112	0.1974	5008	,	,		14601	0.246		0.1392	False		,,,				2504	0.1442				p.S161S		Atlas-SNP	.											.	GPR149	134	.	0			c.T483C						PASS	.	A		464,3572		20,424,1574	22.0	27.0	25.0		483	-2.7	0.9	3	dbSNP_126	25	1177,7171		88,1001,3085	no	coding-synonymous	GPR149	NM_001038705.1		108,1425,4659	GG,GA,AA		14.0992,11.4965,13.251		161/732	154146922	1641,10743	2018	4174	6192	SO:0001819	synonymous_variant	344758	exon1			CAGCAGACTGGCT	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.483T>C	3.37:g.154146922A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	16	0.333333	NM_001038705		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																			A|0.841;G|0.159	0.159	strong		0.642	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
ABCC1	4363	hgsc.bcm.edu	37	16	16139714	16139714	+	Silent	SNP	T	T	C	rs35587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16139714T>C	ENST00000399410.3	+	9	1237	c.1062T>C	c.(1060-1062)aaT>aaC	p.N354N	ABCC1_ENST00000349029.5_Silent_p.N354N|ABCC1_ENST00000399408.2_Silent_p.N354N|ABCC1_ENST00000345148.5_Silent_p.N354N|ABCC1_ENST00000351154.5_Silent_p.N354N|ABCC1_ENST00000346370.5_Silent_p.N354N	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	354	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	AGTTCGTGAATGACACGAAGG	0.562											OREG0023639	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	2118	0.422923	0.711	0.3573	5008	,	,		21507	0.4415		0.3131	False		,,,				2504	0.1738				p.N354N		Atlas-SNP	.											.	ABCC1	156	.	0			c.T1062C						PASS	.	C	,,,,	2564,1580		821,922,329	47.0	51.0	50.0		1062,1062,1062,1062,1062	-6.0	0.2	16	dbSNP_76	50	2447,5985		348,1751,2117	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	1169,2673,2446	CC,CT,TT		29.0204,38.1274,39.8457	,,,,	354/1532,354/1473,354/1476,354/1417,354/1467	16139714	5011,7565	2072	4216	6288	SO:0001819	synonymous_variant	4363	exon9			CGTGAATGACACG	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.1062T>C	16.37:g.16139714T>C		Somatic	106	0	0	708	WXS	Illumina HiSeq	Phase_I	113	63	0.557522	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			T|0.576;C|0.424	0.424	strong		0.562	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
TMEM232	642987	hgsc.bcm.edu	37	5	109973902	109973902	+	Silent	SNP	T	T	G	rs1422495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:109973902T>G	ENST00000455884.2	-	5	548	c.498A>C	c.(496-498)gcA>gcC	p.A166A	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Silent_p.A166A			C9JQI7	TM232_HUMAN	transmembrane protein 232	166						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						AACATACCTTTGCTAGCTTTA	0.303													T|||	434	0.0866613	0.0756	0.1153	5008	,	,		14761	0.0903		0.0895	False		,,,				2504	0.0746				p.A166A		Atlas-SNP	.											.	TMEM232	57	.	0			c.A498C						PASS	.	T		109,1275		3,103,586	76.0	63.0	67.0		498	0.9	0.3	5	dbSNP_88	67	276,2906		14,248,1329	no	coding-synonymous	TMEM232	NM_001039763.3		17,351,1915	GG,GT,TT		8.6738,7.8757,8.4319		166/658	109973902	385,4181	692	1591	2283	SO:0001819	synonymous_variant	642987	exon5			TACCTTTGCTAGC	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.498A>C	5.37:g.109973902T>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	162	82	0.506173	NM_001039763	B4DKF4	Silent	SNP	ENST00000455884.2	37	CCDS47253.2																																																																																			T|0.910;G|0.090	0.090	strong		0.303	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
LCLAT1	253558	hgsc.bcm.edu	37	2	30863092	30863092	+	Silent	SNP	C	C	T	rs12467646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:30863092C>T	ENST00000309052.4	+	7	1061	c.852C>T	c.(850-852)caC>caT	p.H284H	LCLAT1_ENST00000491680.2_3'UTR|LCLAT1_ENST00000379509.3_Silent_p.H246H|LCLAT1_ENST00000540623.1_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	139	0	0		WXS	Illumina HiSeq	Phase_I	141	68	0.482269	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	
WIF1	11197	hgsc.bcm.edu	37	12	65514266	65514266	+	Silent	SNP	T	T	C	rs7301320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:65514266T>C	ENST00000286574.4	-	2	593	c.219A>G	c.(217-219)gcA>gcG	p.A73A		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	73	WIF. {ECO:0000255|PROSITE- ProRule:PRU00222}.				multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		TTCTCTGTTGTGCTTTTCTGA	0.363			T	HMGA2	pleomorphic salivary gland adenoma								C|||	4127	0.824081	0.7632	0.7118	5008	,	,		19699	0.999		0.7465	False		,,,				2504	0.8855				p.A73A	Esophageal Squamous(148;1595 1816 48559 49439 49664)	Atlas-SNP	.		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	WIF1	96	.	0			c.A219G						PASS	.	C		3360,1046	383.2+/-324.8	1271,818,114	140.0	144.0	143.0		219	-6.0	0.9	12	dbSNP_116	143	6363,2237	379.9+/-339.4	2330,1703,267	no	coding-synonymous	WIF1	NM_007191.4		3601,2521,381	CC,CT,TT		26.0116,23.7404,25.2422		73/380	65514266	9723,3283	2203	4300	6503	SO:0001819	synonymous_variant	11197	exon2			CTGTTGTGCTTTT	AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.219A>G	12.37:g.65514266T>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	139	64	0.460432	NM_007191	Q6UXI1|Q8WVG4	Silent	SNP	ENST00000286574.4	37	CCDS8971.1																																																																																			T|0.221;C|0.779	0.779	strong		0.363	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2		
OAF	220323	hgsc.bcm.edu	37	11	120097551	120097551	+	Silent	SNP	G	G	A	rs873058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:120097551G>A	ENST00000328965.4	+	3	906	c.393G>A	c.(391-393)gcG>gcA	p.A131A	OAF_ENST00000531220.1_Silent_p.A15A	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	131						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(5)	6		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		TGCGGCAGGCGGAGGAGGTTC	0.612													G|||	71	0.0141773	0.0507	0.0058	5008	,	,		16367	0.0		0.0	False		,,,				2504	0.0				p.A131A		Atlas-SNP	.											.	OAF	12	.	0			c.G393A						PASS	.	G		213,4193	129.0+/-165.8	5,203,1995	64.0	59.0	61.0		393	-10.4	0.6	11	dbSNP_86	61	2,8598		0,2,4298	no	coding-synonymous	OAF	NM_178507.2		5,205,6293	AA,AG,GG		0.0233,4.8343,1.6531		131/274	120097551	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	220323	exon3			GCAGGCGGAGGAG	BC047726	CCDS8430.1	11q23.3	2010-11-23			ENSG00000184232	ENSG00000184232			28752	protein-coding gene	gene with protein product						12477932	Standard	NM_178507		Approved	MGC52117	uc001pxb.3	Q86UD1	OTTHUMG00000166139	ENST00000328965.4:c.393G>A	11.37:g.120097551G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	70	45	0.642857	NM_178507		Silent	SNP	ENST00000328965.4	37	CCDS8430.1																																																																																			G|0.982;A|0.018	0.018	strong		0.612	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507	
SOWAHA	134548	hgsc.bcm.edu	37	5	132149593	132149593	+	Missense_Mutation	SNP	G	G	A	rs114865630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132149593G>A	ENST00000378693.2	+	1	561	c.280G>A	c.(280-282)Ggc>Agc	p.G94S		NM_175873.4	NP_787069.3	Q2M3V2	SWAHA_HUMAN	sosondowah ankyrin repeat domain family member A	94	Pro-rich.																CGCACCCTTCGGCCCCCCGGG	0.726													G|||	151	0.0301518	0.1097	0.0086	5008	,	,		9361	0.0		0.0	False		,,,				2504	0.0				p.G94S		Atlas-SNP	.											.	.	.	.	0			c.G280A						PASS	.	G	SER/GLY	228,2496		11,206,1145	9.0	13.0	12.0		280	-6.5	0.0	5	dbSNP_132	12	4,6042		0,4,3019	no	missense	ANKRD43	NM_175873.4	56	11,210,4164	AA,AG,GG		0.0662,8.37,2.6454	benign	94/550	132149593	232,8538	1362	3023	4385	SO:0001583	missense	134548	exon1			CCCTTCGGCCCCC	AK090823	CCDS43361.1	5q23.3	2013-01-10	2012-01-12	2012-01-12	ENSG00000198944	ENSG00000198944		"""Ankyrin repeat domain containing"""	27033	protein-coding gene	gene with protein product			"""ankyrin repeat domain 43"""	ANKRD43		22234889	Standard	NM_175873		Approved		uc003kxw.3	Q2M3V2	OTTHUMG00000059844	ENST00000378693.2:c.280G>A	5.37:g.132149593G>A	ENSP00000367965:p.Gly94Ser	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	16	12	0.75	NM_175873	Q8NAE7	Missense_Mutation	SNP	ENST00000378693.2	37	CCDS43361.1	68	0.031135531135531136	57	0.11585365853658537	11	0.03038674033149171	0	0.0	0	0.0	g	7.170	0.587390	0.13812	0.0837	6.62E-4	ENSG00000198944	ENST00000378693	T	0.35421	1.31	3.95	-6.54	0.01860	.	.	.	.	.	T	0.00210	0.0006	N	0.14661	0.345	0.80722	P	0.0	B	0.18610	0.029	B	0.08055	0.003	T	0.37753	-0.9692	8	0.06236	T	0.91	7.4965	10.6849	0.45837	0.0:0.0953:0.7015:0.2032	.	94	Q2M3V2	ANR43_HUMAN	S	94	ENSP00000367965:G94S	ENSP00000367965:G94S	G	+	1	0	ANKRD43	132177492	0.000000	0.05858	0.002000	0.10522	0.064000	0.16182	-3.229000	0.00549	-0.876000	0.04017	0.290000	0.19541	GGC	G|0.964;A|0.036	0.036	strong		0.726	SOWAHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133062.1	NM_175873	
GEMIN4	50628	hgsc.bcm.edu	37	17	648916	648916	+	Silent	SNP	T	T	C	rs12942598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:648916T>C	ENST00000319004.5	-	2	2485	c.2367A>G	c.(2365-2367)acA>acG	p.T789T	GEMIN4_ENST00000576778.1_Silent_p.T778T	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	789					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TCTCAAAAAGTGTGGCTGGCA	0.587													T|||	74	0.0147764	0.0008	0.0331	5008	,	,		19967	0.0		0.0398	False		,,,				2504	0.0102				p.T789T		Atlas-SNP	.											.	GEMIN4	116	.	0			c.A2367G						PASS	.	T		28,3812		0,28,1892	16.0	17.0	17.0		2367	-5.6	1.0	17	dbSNP_121	17	360,7860		8,344,3758	no	coding-synonymous	GEMIN4	NM_015721.2		8,372,5650	CC,CT,TT		4.3796,0.7292,3.2172		789/1059	648916	388,11672	1920	4110	6030	SO:0001819	synonymous_variant	50628	exon2			AAAAAGTGTGGCT	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.2367A>G	17.37:g.648916T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			T|0.974;C|0.026	0.026	strong		0.587	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
C17orf50	146853	hgsc.bcm.edu	37	17	34091078	34091078	+	Missense_Mutation	SNP	C	C	G	rs4795087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34091078C>G	ENST00000285023.4	+	2	98	c.66C>G	c.(64-66)gaC>gaG	p.D22E	C17orf50_ENST00000588628.1_Missense_Mutation_p.R30G|C17orf50_ENST00000586491.1_Missense_Mutation_p.D22E	NM_145272.3	NP_660315.2	Q8WW18	CQ050_HUMAN	chromosome 17 open reading frame 50	22			D -> E (in dbSNP:rs4795087).										Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGGCCgaggacgcggagcaag	0.687													G|||	1685	0.336462	0.5386	0.2392	5008	,	,		9553	0.3214		0.166	False		,,,				2504	0.3231				p.D22E		Atlas-SNP	.											.	C17orf50	4	.	0			c.C66G						PASS	.	G	GLU/ASP	1258,1838		253,752,543	10.0	15.0	13.0		66	4.2	0.1	17	dbSNP_111	13	912,5596		59,794,2401	yes	missense	C17orf50	NM_145272.3	45	312,1546,2944	GG,GC,CC		14.0135,40.6331,22.5948	benign	22/175	34091078	2170,7434	1548	3254	4802	SO:0001583	missense	146853	exon2			CGAGGACGCGGAG	BC021727	CCDS42298.1	17q12	2014-05-06			ENSG00000154768	ENSG00000270806			29581	protein-coding gene	gene with protein product							Standard	NM_145272		Approved		uc002hjx.3	Q8WW18	OTTHUMG00000188389	ENST00000285023.4:c.66C>G	17.37:g.34091078C>G	ENSP00000285023:p.Asp22Glu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_145272	Q6Q621	Missense_Mutation	SNP	ENST00000285023.4	37	CCDS42298.1	656	0.30036630036630035	248	0.5040650406504065	91	0.2513812154696133	184	0.32167832167832167	133	0.17546174142480211	G	6.960	0.546998	0.13312	0.406331	0.140135	ENSG00000154768	ENST00000285023	T	0.30448	1.53	5.16	4.15	0.48705	.	0.401992	0.18332	N	0.144463	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	0.45498	-0.9257	9	0.02654	T	1	-15.876	8.7171	0.34419	0.0:0.1646:0.6647:0.1708	rs4795087	22	Q8WW18	CQ050_HUMAN	E	22	ENSP00000285023:D22E	ENSP00000285023:D22E	D	+	3	2	C17orf50	31115191	0.289000	0.24334	0.057000	0.19452	0.345000	0.29048	0.169000	0.16641	1.181000	0.42912	-0.215000	0.12644	GAC	C|0.698;G|0.302	0.302	strong		0.687	C17orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449132.1	NM_145272	
FRYL	285527	hgsc.bcm.edu	37	4	48588742	48588742	+	Silent	SNP	C	C	T	rs34558821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:48588742C>T	ENST00000503238.1	-	16	1643	c.1644G>A	c.(1642-1644)ggG>ggA	p.G548G	FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000507711.1_Silent_p.G548G|FRYL_ENST00000537810.1_Silent_p.G548G|FRYL_ENST00000506685.1_Silent_p.G254G|FRYL_ENST00000358350.4_Silent_p.G548G			O94915	FRYL_HUMAN	FRY-like	548					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						GTTTTCTTTCCCCCCTGAAAA	0.368													C|||	2667	0.532548	0.6218	0.353	5008	,	,		14204	0.5288		0.4553	False		,,,				2504	0.6227				p.G548G		Atlas-SNP	.											.	FRYL	242	.	0			c.G1644A						PASS	.	C		2265,1367		715,835,266	90.0	85.0	87.0		1644	-3.4	1.0	4	dbSNP_126	87	3960,4190		984,1992,1099	no	coding-synonymous	FRYL	NM_015030.1		1699,2827,1365	TT,TC,CC		48.589,37.6377,47.1652		548/3014	48588742	6225,5557	1816	4075	5891	SO:0001819	synonymous_variant	285527	exon19			TCTTTCCCCCCTG	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.1644G>A	4.37:g.48588742C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	56	0.982456	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	37	CCDS43227.1																																																																																			C|0.516;T|0.484	0.484	strong		0.368	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
MBOAT1	154141	hgsc.bcm.edu	37	6	20109842	20109842	+	Missense_Mutation	SNP	T	T	C	rs2065649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:20109842T>C	ENST00000324607.7	-	12	1512	c.1348A>G	c.(1348-1350)Atc>Gtc	p.I450V	MBOAT1_ENST00000541730.1_Missense_Mutation_p.I301V	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	450			I -> V (in dbSNP:rs2065649).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			TATAAGCTGATGGTCGGTTCA	0.468													T|||	239	0.0477236	0.1641	0.0259	5008	,	,		18796	0.0		0.004	False		,,,				2504	0.0				p.I450V		Atlas-SNP	.											.	MBOAT1	48	.	0			c.A1348G						PASS	.	T	VAL/ILE	691,3715	289.5+/-280.5	54,583,1566	149.0	133.0	139.0		1348	3.0	1.0	6	dbSNP_94	139	13,8587	9.8+/-36.6	0,13,4287	yes	missense	MBOAT1	NM_001080480.1	29	54,596,5853	CC,CT,TT		0.1512,15.6832,5.4129	benign	450/496	20109842	704,12302	2203	4300	6503	SO:0001583	missense	154141	exon12			AGCTGATGGTCGG	AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197			21579	protein-coding gene	gene with protein product	"""lysophosphatidylethanolamine acyltransferase 1"""	611732	"""O-acyltransferase (membrane bound) domain containing 1"""	OACT1		18287005	Standard	NM_001080480		Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.1348A>G	6.37:g.20109842T>C	ENSP00000324944:p.Ile450Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Missense_Mutation	SNP	ENST00000324607.7	37	CCDS34346.1	75	0.034340659340659344	66	0.13414634146341464	9	0.024861878453038673	0	0.0	0	0.0	T	12.51	1.960413	0.34565	0.156832	0.001512	ENSG00000172197	ENST00000541730;ENST00000324607	T;T	0.18502	2.21;2.68	5.38	2.96	0.34315	.	0.312699	0.38548	N	0.001653	T	0.06142	0.0159	L	0.61036	1.89	0.09310	P	0.9999999999999988	B;B	0.18741	0.03;0.006	B;B	0.20577	0.03;0.003	T	0.17198	-1.0377	9	0.39692	T	0.17	-7.5096	4.338	0.11095	0.0:0.238:0.164:0.598	rs2065649;rs2065649	301;450	Q6ZNC8-2;Q6ZNC8	.;MBOA1_HUMAN	V	301;450	ENSP00000441568:I301V;ENSP00000324944:I450V	ENSP00000324944:I450V	I	-	1	0	MBOAT1	20217821	0.259000	0.24043	0.995000	0.50966	0.991000	0.79684	-0.065000	0.11617	0.409000	0.25649	0.533000	0.62120	ATC	T|0.949;C|0.051	0.051	strong		0.468	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1		
CYP4F12	66002	hgsc.bcm.edu	37	19	15784377	15784377	+	Missense_Mutation	SNP	C	C	T	rs16995376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15784377C>T	ENST00000550308.1	+	2	418	c.38C>T	c.(37-39)cCg>cTg	p.P13L	CYP4F12_ENST00000324632.10_Missense_Mutation_p.P13L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	13			P -> L (in dbSNP:rs16995376). {ECO:0000269|PubMed:11162645}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GGCCTCAGACCGGTGGCAACG	0.647													.|||	1030	0.205671	0.3139	0.2161	5008	,	,		6485	0.0109		0.2584	False		,,,				2504	0.1984				p.P13L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C38T						PASS	.	A	LEU/PRO	1513,2883		226,1061,911	57.0	62.0	60.0		38	-4.9	0.0	19	dbSNP_123	60	2065,6533		282,1501,2516	yes	missense	CYP4F12	NM_023944.3	98	508,2562,3427	TT,TC,CC		24.0172,34.4177,27.5358	benign	13/525	15784377	3578,9416	2198	4299	6497	SO:0001583	missense	66002	exon2			TCAGACCGGTGGC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.38C>T	19.37:g.15784377C>T	ENSP00000448998:p.Pro13Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	207	73	0.352657	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	477	0.2184065934065934	164	0.3333333333333333	95	0.26243093922651933	11	0.019230769230769232	207	0.27308707124010556	.	6.370	0.436299	0.12104	0.344177	0.240172	ENSG00000186204	ENST00000550308;ENST00000324632	D;D	0.92048	-2.96;-2.96	2.46	-4.92	0.03075	.	1.096560	0.07077	U	0.836348	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B;B	0.31256	0.316;0.05;0.028	B;B;B	0.26969	0.075;0.021;0.014	T	0.08166	-1.0735	9	0.27785	T	0.31	.	3.7556	0.08584	0.3401:0.2669:0.0:0.393	rs16995376;rs16995376	13;13;13	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	L	13	ENSP00000448998:P13L;ENSP00000321821:P13L	ENSP00000321821:P13L	P	+	2	0	CYP4F12	15645377	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.371000	0.00244	-2.258000	0.00694	-1.284000	0.01376	CCG	C|0.775;T|0.225	0.225	strong		0.647	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
PRR32	100130613	hgsc.bcm.edu	37	X	125955199	125955199	+	Missense_Mutation	SNP	T	T	C	rs4289953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:125955199T>C	ENST00000371125.3	+	2	658	c.578T>C	c.(577-579)aTg>aCg	p.M193T		NM_001122716.1	NP_001116188.1	B1ATL7	PRR32_HUMAN		193			M -> T (in dbSNP:rs4289953).														GGGATAGTAATGGAGGTGCCG	0.532													T|||	684	0.181192	0.1725	0.1556	3775	,	,		13426	0.247		0.0189	False		,,,				2504	0.0818				p.M193T		Atlas-SNP	.											.	.	.	.	0			c.T578C						PASS	.	T	THR/MET	262,947		21,193,27,303,148	42.0	41.0	41.0		578	4.0	0.9	X	dbSNP_111	41	40,2351		0,28,12,772,779	yes	missense	CXorf64	NM_001122716.1	81	21,221,39,1075,927	CC,CT,C,TT,T		1.6729,21.6708,8.3889	benign	193/299	125955199	302,3298	692	1591	2283	SO:0001583	missense	100130613	exon2			TAGTAATGGAGGT																												ENST00000371125.3:c.578T>C	X.37:g.125955199T>C	ENSP00000360166:p.Met193Thr	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	169	108	0.639053	NM_001122716		Missense_Mutation	SNP	ENST00000371125.3	37	CCDS48163.1	260	0.1567209162145871	54	0.12	29	0.08787878787878788	89	0.178	10	0.013440860215053764	T	14.06	2.424009	0.43020	0.216708	0.016729	ENSG00000183631	ENST00000371125	T	0.40756	1.02	4.02	4.02	0.46733	.	0.000000	0.40818	N	0.001010	T	0.00039	0.0001	L	0.34521	1.04	0.33893	P	0.362422	D	0.65815	0.995	D	0.63877	0.919	T	0.07271	-1.0781	9	0.87932	D	0	-12.8648	8.4212	0.32700	0.0:0.0:0.0:1.0	rs4289953;rs52819793;rs60946504;rs4289953	193	B1ATL7	CX064_HUMAN	T	193	ENSP00000360166:M193T	ENSP00000360166:M193T	M	+	2	0	CXorf64	125782880	1.000000	0.71417	0.894000	0.35097	0.033000	0.12548	1.364000	0.34171	1.808000	0.52836	0.486000	0.48141	ATG	0|0.026;C|0.181	0.181	strong		0.532	CXorf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058188.1		
FAAH	2166	hgsc.bcm.edu	37	1	46876488	46876488	+	Silent	SNP	G	G	C	rs74783386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46876488G>C	ENST00000243167.8	+	11	1362	c.1278G>C	c.(1276-1278)ctG>ctC	p.L426L		NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	426					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	CTGTGCAGCTGCCAAGGCTGT	0.617													C|||	42	0.00838658	0.0076	0.0	5008	,	,		18450	0.0159		0.0	False		,,,				2504	0.0164				p.L426L		Atlas-SNP	.											.	FAAH	36	.	0			c.G1278C						PASS	.	C		8,4398	825.1+/-416.5	0,8,2195	93.0	80.0	84.0		1278	1.2	1.0	1	dbSNP_131	84	4,8596	819.0+/-406.8	0,4,4296	no	coding-synonymous	FAAH	NM_001441.2		0,12,6491	CC,CG,GG		0.0465,0.1816,0.0923		426/580	46876488	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	2166	exon11			GCAGCTGCCAAGG	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.1278G>C	1.37:g.46876488G>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	176	80	0.454545	NM_001441	D3DQ19|Q52M86|Q5TDF8	Silent	SNP	ENST00000243167.8	37	CCDS535.1																																																																																			G|0.998;C|0.002	0.002	strong		0.617	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
CEACAM8	1088	hgsc.bcm.edu	37	19	43098931	43098931	+	Missense_Mutation	SNP	C	C	A	rs28367882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43098931C>A	ENST00000244336.5	-	1	151	c.50G>T	c.(49-51)gGg>gTg	p.G17V	CEACAM8_ENST00000599005.1_Missense_Mutation_p.G17V|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000594688.1_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	17			G -> V (in dbSNP:rs28367882).		immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				GAGCAGGAGCCCCTGCCAGGG	0.632													.|||	355	0.0708866	0.2542	0.0231	5008	,	,		18261	0.0		0.003	False		,,,				2504	0.0				p.G17V		Atlas-SNP	.											.	CEACAM8	44	.	0			c.G50T						PASS	.	C	VAL/GLY	873,3533	340.5+/-306.2	92,689,1422	102.0	95.0	97.0		50	-0.8	0.0	19	dbSNP_125	97	18,8582	10.5+/-38.8	0,18,4282	no	missense	CEACAM8	NM_001816.3	109	92,707,5704	AA,AC,CC		0.2093,19.8139,6.8507	possibly-damaging	17/350	43098931	891,12115	2203	4300	6503	SO:0001583	missense	1088	exon1			AGGAGCCCCTGCC	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.50G>T	19.37:g.43098931C>A	ENSP00000244336:p.Gly17Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_001816	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	37	CCDS12610.1	124	0.056776556776556776	110	0.22357723577235772	11	0.03038674033149171	0	0.0	3	0.00395778364116095	c	6.456	0.452336	0.12283	0.198139	0.002093	ENSG00000124469	ENST00000244336	T	0.21031	2.03	1.48	-0.838	0.10762	.	.	.	.	.	T	0.00012	0.0000	M	0.88704	2.975	0.80722	P	0.0	P	0.40000	0.698	P	0.46758	0.526	T	0.05716	-1.0868	8	0.72032	D	0.01	.	4.0532	0.09804	0.0:0.5677:0.0:0.4323	rs28367882;rs59229803	17	P31997	CEAM8_HUMAN	V	17	ENSP00000244336:G17V	ENSP00000244336:G17V	G	-	2	0	CEACAM8	47790771	0.000000	0.05858	0.010000	0.14722	0.009000	0.06853	0.062000	0.14389	-0.173000	0.10761	-0.671000	0.03813	GGG	C|0.939;A|0.061	0.061	strong		0.632	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
PPP4R1	9989	hgsc.bcm.edu	37	18	9562042	9562042	+	Missense_Mutation	SNP	C	C	T	rs2306134	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9562042C>T	ENST00000400556.3	-	13	1851	c.1778G>A	c.(1777-1779)aGc>aAc	p.S593N	PPP4R1_ENST00000400555.3_Missense_Mutation_p.S576N	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	593			S -> N (in dbSNP:rs2306134).		dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						GTCTGAATCGCTGTGAATATA	0.368													T|||	1391	0.277756	0.1997	0.2233	5008	,	,		20058	0.5099		0.167	False		,,,				2504	0.2965				p.S593N	Melanoma(188;1232 2082 5061 11948 35994)	Atlas-SNP	.											PPP4R1_ENST00000400556,NS,carcinoma,+1,1	PPP4R1	63	1	0			c.G1778A						PASS	.	T	ASN/SER,ASN/SER	705,3041		72,561,1240	151.0	143.0	145.0		1778,1727	3.3	0.0	18	dbSNP_100	145	1305,6899		90,1125,2887	yes	missense,missense	PPP4R1	NM_001042388.1,NM_005134.2	46,46	162,1686,4127	TT,TC,CC		15.9069,18.8201,16.8201	benign,benign	593/951,576/934	9562042	2010,9940	1873	4102	5975	SO:0001583	missense	9989	exon13			GAATCGCTGTGAA	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.1778G>A	18.37:g.9562042C>T	ENSP00000383402:p.Ser593Asn	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	153	152	0.993464	NM_001042388	Q99774|Q9UNQ7	Missense_Mutation	SNP	ENST00000400556.3	37	CCDS42412.1	595	0.2724358974358974	104	0.21138211382113822	66	0.18232044198895028	304	0.5314685314685315	121	0.15963060686015831	T	0.008	-1.931823	0.00488	0.188201	0.159069	ENSG00000154845	ENST00000400556;ENST00000400555	T;T	0.17213	2.29;2.29	5.09	3.35	0.38373	Armadillo-type fold (1);	0.275088	0.30446	N	0.009603	T	0.00012	0.0000	N	0.00197	-1.87	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40831	-0.9542	8	.	.	.	-3.6677	8.3369	0.32219	0.0:0.2124:0.0:0.7876	rs2306134;rs56617930;rs60567707;rs2306134	593;576	Q8TF05;Q8TF05-2	PP4R1_HUMAN;.	N	593;576	ENSP00000383402:S593N;ENSP00000383401:S576N	.	S	-	2	0	PPP4R1	9552042	0.968000	0.33430	0.000000	0.03702	0.018000	0.09664	0.943000	0.29030	0.098000	0.17522	-0.254000	0.11334	AGC	C|0.730;T|0.270	0.270	strong		0.368	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134	
MED22	6837	hgsc.bcm.edu	37	9	136208405	136208405	+	Missense_Mutation	SNP	C	C	T	rs145653063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136208405C>T	ENST00000491289.1	-	5	1134	c.553G>A	c.(553-555)Gcc>Acc	p.A185T	MED22_ENST00000344469.5_3'UTR|MED22_ENST00000343730.5_Missense_Mutation_p.A185T|MED22_ENST00000471524.1_5'Flank|MED22_ENST00000476080.1_3'UTR			Q15528	MED22_HUMAN	mediator complex subunit 22	185						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)		TGGGCAGGGGCTGCCACCTGT	0.677													C|||	52	0.0103834	0.0378	0.0029	5008	,	,		15147	0.0		0.0	False		,,,				2504	0.0				p.A185T		Atlas-SNP	.											.	MED22	13	.	0			c.G553A						PASS	.	C	THR/ALA,	116,4286	85.3+/-124.0	2,112,2087	22.0	26.0	25.0		553,	1.2	0.0	9	dbSNP_134	25	5,8589	3.7+/-12.6	0,5,4292	no	missense,utr-3	MED22	NM_133640.3,NM_181491.1	58,	2,117,6379	TT,TC,CC		0.0582,2.6352,0.9311	benign,	185/201,	136208405	121,12875	2201	4297	6498	SO:0001583	missense	6837	exon5			CAGGGGCTGCCAC		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.553G>A	9.37:g.136208405C>T	ENSP00000420393:p.Ala185Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	39	0.33913	NM_133640	B3KW83|B3KWX4|O76072|Q5T8U0	Missense_Mutation	SNP	ENST00000491289.1	37	CCDS6963.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	0.576	-0.838931	0.02692	0.026352	5.82E-4	ENSG00000148297	ENST00000491289;ENST00000343730	.	.	.	4.15	1.23	0.21249	.	0.579278	0.18389	N	0.142701	T	0.02418	0.0074	N	0.04880	-0.145	0.18873	N	0.999985	B	0.02656	0.0	B	0.01281	0.0	T	0.23154	-1.0196	9	0.05620	T	0.96	-4.6055	2.9823	0.05957	0.1951:0.4783:0.0:0.3266	.	185	Q15528	MED22_HUMAN	T	185	.	ENSP00000342343:A185T	A	-	1	0	MED22	135198226	0.879000	0.30193	0.041000	0.18516	0.049000	0.14656	1.605000	0.36815	0.146000	0.19002	0.563000	0.77884	GCC	C|0.989;T|0.011	0.011	strong		0.677	MED22-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054898.2	NM_133640	
GMNC	647309	hgsc.bcm.edu	37	3	190578566	190578566	+	Missense_Mutation	SNP	A	A	G	rs13075089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:190578566A>G	ENST00000442080.1	-	2	84	c.85T>C	c.(85-87)Tct>Cct	p.S29P	GMNC_ENST00000479491.1_Intron	NM_001146686.2	NP_001140158.1	A6NCL1	GEMC1_HUMAN	geminin coiled-coil domain containing	29					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication initiation (GO:0006270)	nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|endometrium(3)|skin(1)	5						TCAACACTAGATTCTGACGTT	0.498													A|||	2225	0.444289	0.4327	0.3833	5008	,	,		18611	0.4484		0.4095	False		,,,				2504	0.5348				p.S29P		Atlas-SNP	.											.	GMNC	12	.	0			c.T85C						PASS	.	A	PRO/SER	532,852		109,314,269	104.0	93.0	97.0		85	2.9	1.0	3	dbSNP_121	97	1269,1913		238,793,560	yes	missense	GMNC	NM_001146686.2	74	347,1107,829	GG,GA,AA		39.8806,38.4393,39.4437	benign	29/335	190578566	1801,2765	692	1591	2283	SO:0001583	missense	647309	exon2			CACTAGATTCTGA	BC031680	CCDS54697.1	3q28	2011-08-19	2011-08-19		ENSG00000205835	ENSG00000205835			40049	protein-coding gene	gene with protein product		614448				20383140, 20855966	Standard	NM_001146686		Approved	GEMC1	uc011bsl.1	A6NCL1	OTTHUMG00000156195	ENST00000442080.1:c.85T>C	3.37:g.190578566A>G	ENSP00000406164:p.Ser29Pro	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	130	70	0.538462	NM_001146686		Missense_Mutation	SNP	ENST00000442080.1	37	CCDS54697.1	893	0.4088827838827839	205	0.4166666666666667	141	0.38950276243093923	232	0.40559440559440557	315	0.4155672823218997	A	10.59	1.391691	0.25118	0.384393	0.398806	ENSG00000205835	ENST00000442080	.	.	.	5.41	2.91	0.33838	.	0.349592	0.27640	N	0.018470	T	0.00012	0.0000	M	0.62723	1.935	0.31069	P	0.7132769999999999	P	0.48503	0.911	P	0.55577	0.779	T	0.38478	-0.9659	8	0.44086	T	0.13	-1.1021	8.9669	0.35883	0.7036:0.0:0.0:0.2964	rs13075089;rs58186737	29	A6NCL1	GEMC1_HUMAN	P	29	.	ENSP00000406164:S29P	S	-	1	0	RP11-332P22.1	192061260	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.748000	0.26305	0.312000	0.23038	0.533000	0.62120	TCT	A|0.589;G|0.411	0.411	strong		0.498	GMNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343364.1	NM_001146686	
DOCK7	85440	hgsc.bcm.edu	37	1	63113968	63113968	+	Missense_Mutation	SNP	T	T	C	rs61743961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:63113968T>C	ENST00000340370.5	-	6	558	c.541A>G	c.(541-543)Atg>Gtg	p.M181V	DOCK7_ENST00000404627.2_Missense_Mutation_p.M181V|DOCK7_ENST00000251157.5_Missense_Mutation_p.M181V	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	181					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)	p.M181V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TCTATTGACATTGAACGTCTT	0.308													T|||	305	0.0609026	0.1233	0.0115	5008	,	,		13493	0.128		0.001	False		,,,				2504	0.0041				p.M181V		Atlas-SNP	.											DOCK7,NS,carcinoma,0,1	DOCK7	184	1	1	Substitution - Missense(1)	stomach(1)	c.A541G						PASS	.	T	VAL/MET	484,3898	203.8+/-226.2	32,420,1739	52.0	53.0	53.0		541	0.8	1.0	1	dbSNP_129	53	8,8586	5.7+/-21.5	0,8,4289	yes	missense	DOCK7	NM_033407.2	21	32,428,6028	CC,CT,TT		0.0931,11.0452,3.7916	benign	181/2110	63113968	492,12484	2191	4297	6488	SO:0001583	missense	85440	exon6			TTGACATTGAACG		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.541A>G	1.37:g.63113968T>C	ENSP00000340742:p.Met181Val	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	148	0.06776556776556776	72	0.14634146341463414	5	0.013812154696132596	71	0.12412587412587413	0	0.0	T	6.096	0.385969	0.11524	0.110452	9.31E-4	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.17213	2.72;2.71;2.29	4.53	0.823	0.18812	.	0.119887	0.85682	N	0.000000	T	0.01353	0.0044	N	0.00823	-1.155	0.21355	P	0.999717036	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0	B;B;B;B;B	0.11329	0.0;0.001;0.006;0.006;0.002	T	0.47923	-0.9079	9	0.25751	T	0.34	.	8.727	0.34476	0.0:0.2233:0.0:0.7767	.	181;181;181;181;181	Q96NI0;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3	.;.;.;.;.	V	181	ENSP00000251157:M181V;ENSP00000340742:M181V;ENSP00000384446:M181V	ENSP00000251157:M181V	M	-	1	0	DOCK7	62886556	0.997000	0.39634	0.997000	0.53966	0.990000	0.78478	1.681000	0.37618	-0.030000	0.13804	0.379000	0.24179	ATG	T|0.959;C|0.041	0.041	strong		0.308	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
CR1	1378	hgsc.bcm.edu	37	1	207782931	207782931	+	Missense_Mutation	SNP	A	A	G	rs6691117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207782931A>G	ENST00000367049.4	+	37	6193	c.6193A>G	c.(6193-6195)Atc>Gtc	p.I2065V	CR1_ENST00000367051.1_Missense_Mutation_p.I1615V|CR1_ENST00000367052.1_Missense_Mutation_p.I1615V|CR1_ENST00000367053.1_Missense_Mutation_p.I1615V|CR1_ENST00000400960.2_Missense_Mutation_p.I1615V	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1615					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						CACTGAGATCATCAGATTTAG	0.498													G|||	2471	0.493411	0.8722	0.3761	5008	,	,		19776	0.3433		0.2256	False		,,,				2504	0.4949				p.I2065V		Atlas-SNP	.											.	CR1	354	.	0			c.A6193G						PASS	.	G	VAL/ILE,VAL/ILE	2892,958		1089,714,122	36.0	37.0	37.0		4843,6193	2.5	0.0	1	dbSNP_116	37	1761,6497		162,1437,2530	yes	missense,missense	CR1	NM_000573.3,NM_000651.4	29,29	1251,2151,2652	GG,GA,AA		21.3248,24.8831,38.4291	benign,benign	1615/2040,2065/2490	207782931	4653,7455	1925	4129	6054	SO:0001583	missense	1378	exon37			GAGATCATCAGAT	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.6193A>G	1.37:g.207782931A>G	ENSP00000356016:p.Ile2065Val	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	850	0.3891941391941392	408	0.8292682926829268	135	0.3729281767955801	143	0.25	164	0.21635883905013192	G	0.017	-1.509804	0.00984	0.751169	0.213248	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17	2.54	2.54	0.30619	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.10450	0.0;0.0;0.005	T	0.38866	-0.9641	8	0.02654	T	1	.	5.5311	0.16985	0.1589:0.0:0.8411:0.0	rs6691117;rs59510794;rs6691117	1615;1615;2065	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	V	1615;1615;1615;1615;2065	ENSP00000356019:I1615V;ENSP00000356018:I1615V;ENSP00000356020:I1615V;ENSP00000383744:I1615V;ENSP00000356016:I2065V	ENSP00000356016:I2065V	I	+	1	0	CR1	205849554	0.801000	0.28930	0.004000	0.12327	0.078000	0.17371	2.671000	0.46842	0.637000	0.30526	-0.355000	0.07637	ATC	A|0.601;G|0.399	0.399	strong		0.498	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
LLGL2	3993	hgsc.bcm.edu	37	17	73566094	73566094	+	Missense_Mutation	SNP	G	G	C	rs115026154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73566094G>C	ENST00000392550.3	+	15	1749	c.1632G>C	c.(1630-1632)caG>caC	p.Q544H	LLGL2_ENST00000577200.1_Missense_Mutation_p.Q544H|LLGL2_ENST00000167462.5_Missense_Mutation_p.Q544H	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	544					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CTGTGGAGCAGGTGGAGGCCG	0.672													G|||	70	0.0139776	0.0514	0.0029	5008	,	,		15575	0.0		0.0	False		,,,				2504	0.0				p.Q544H		Atlas-SNP	.											.	LLGL2	155	.	0			c.G1632C						PASS	.	G	HIS/GLN,HIS/GLN	256,4148	140.0+/-175.5	7,242,1953	34.0	33.0	34.0		1632,1632	0.4	1.0	17	dbSNP_132	34	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	24,24	7,243,6252	CC,CG,GG		0.0116,5.8129,1.9763	benign,benign	544/1021,544/1016	73566094	257,12747	2202	4300	6502	SO:0001583	missense	3993	exon15			GGAGCAGGTGGAG	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1632G>C	17.37:g.73566094G>C	ENSP00000376333:p.Gln544His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	62	0.62	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	10.86	1.471205	0.26423	0.058129	1.16E-4	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.44083	0.93;0.93	5.2	0.448	0.16614	WD40/YVTN repeat-like-containing domain (1);	0.309685	0.35013	N	0.003504	T	0.01254	0.0041	N	0.16478	0.41	0.27032	N	0.964225	B;B;B;B;B	0.06786	0.001;0.0;0.001;0.0;0.0	B;B;B;B;B	0.10450	0.005;0.002;0.004;0.003;0.001	T	0.05484	-1.0882	10	0.17832	T	0.49	-0.9242	1.9897	0.03444	0.1345:0.225:0.353:0.2875	.	171;533;533;544;544	B4DVR9;B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;.;L2GL2_HUMAN	H	544;544;533	ENSP00000167462:Q544H;ENSP00000376333:Q544H	ENSP00000167462:Q544H	Q	+	3	2	LLGL2	71077689	0.829000	0.29322	1.000000	0.80357	0.904000	0.53231	0.044000	0.13992	0.541000	0.28827	0.549000	0.68633	CAG	G|0.977;C|0.023	0.023	strong		0.672	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
CYP4F12	66002	hgsc.bcm.edu	37	19	15794423	15794423	+	Silent	SNP	C	C	T	rs114945576|rs386807235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794423C>T	ENST00000550308.1	+	7	1148	c.768C>T	c.(766-768)ttC>ttT	p.F256F	CYP4F12_ENST00000324632.10_Silent_p.F256F	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	256					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GGCGGCGCTTCCACAGGGCCT	0.557													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20890	0.0		0.001	False		,,,				2504	0.0				p.F256F		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C768T						PASS	.						79.0	81.0	80.0					19																	15794423		2199	4295	6494	SO:0001819	synonymous_variant	66002	exon7			GCGCTTCCACAGG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.768C>T	19.37:g.15794423C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	189	52	0.275132	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			C|0.990;T|0.010	0.010	strong		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417765	105417765	+	Silent	SNP	A	A	C	rs2894636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417765A>C	ENST00000333244.5	-	7	4142	c.4023T>G	c.(4021-4023)tcT>tcG	p.S1341S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1341						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)			TGCCTGGGGCAGACACCCCGA	0.607																																					p.S1341S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T4023G						PASS	.	A		167,3493		42,83,1705	128.0	119.0	122.0		4023	-8.6	0.0	14	dbSNP_101	122	39,6505		8,23,3241	no	coding-synonymous	AHNAK2	NM_138420.2		50,106,4946	CC,CA,AA		0.596,4.5628,2.0188		1341/5796	105417765	206,9998	1830	3272	5102	SO:0001819	synonymous_variant	113146	exon7			TGGGGCAGACACC	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.4023T>G	14.37:g.105417765A>C		Somatic	389	1	0.00257069		WXS	Illumina HiSeq	Phase_I	264	263	0.996212	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.831;C|0.169	0.169	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OR2L3	391192	hgsc.bcm.edu	37	1	248224099	248224099	+	Missense_Mutation	SNP	T	T	C	rs6666048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248224099T>C	ENST00000359959.3	+	1	116	c.116T>C	c.(115-117)aTt>aCt	p.I39T	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	39			I -> T (in dbSNP:rs6666048).			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(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	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;0.0278)			ATGGCTCTAATTGGAAACCTA	0.393													t|||	943	0.188299	0.298	0.098	5008	,	,		20570	0.254		0.1461	False		,,,				2504	0.0798				p.I39T		Atlas-SNP	.											.	OR2L3	97	.	0			c.T116C						PASS	.	T	THR/ILE,	1206,3200		158,890,1155	249.0	246.0	247.0		116,	0.7	0.0	1	dbSNP_116	247	1186,7408		90,1006,3201	no	missense,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	89,	248,1896,4356	CC,CT,TT		13.8003,27.3718,18.4	benign,	39/313,	248224099	2392,10608	2203	4297	6500	SO:0001583	missense	391192	exon1			CTCTAATTGGAAA	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"""GPCR / Class A : Olfactory receptors"""	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.116T>C	1.37:g.248224099T>C	ENSP00000353044:p.Ile39Thr	Somatic	466	0	0		WXS	Illumina HiSeq	Phase_I	483	222	0.459627	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	465	0.2129120879120879	147	0.29878048780487804	37	0.10220994475138122	172	0.3006993006993007	109	0.1437994722955145	.	0	-2.828662	0.00070	0.273718	0.138003	ENSG00000198128	ENST00000359959	T	0.00472	7.19	2.05	0.726	0.18248	.	.	.	.	.	T	0.00012	0.0000	N	0.04805	-0.155	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.00341	-1.1804	8	0.12430	T	0.62	.	7.3385	0.26623	0.0:0.0:0.2246:0.7754	rs6666048;rs59835396	39	Q8NG85	OR2L3_HUMAN	T	39	ENSP00000353044:I39T	ENSP00000353044:I39T	I	+	2	0	OR2L3	246290722	0.000000	0.05858	0.006000	0.13384	0.016000	0.09150	0.425000	0.21346	0.023000	0.15187	0.379000	0.24179	ATT	.	.	weak		0.393	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
KCNMB2	10242	hgsc.bcm.edu	37	3	178560581	178560581	+	Silent	SNP	A	A	C	rs6443583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:178560581A>C	ENST00000432997.1	+	5	916	c.564A>C	c.(562-564)acA>acC	p.T188T	KCNMB2_ENST00000358316.3_Silent_p.T188T|RP11-385J1.2_ENST00000451742.1_RNA|KCNMB2_ENST00000452583.1_Silent_p.T188T|RP11-385J1.2_ENST00000425330.1_RNA|RP11-385J1.2_ENST00000432385.1_RNA|RP11-385J1.2_ENST00000437488.1_RNA|KCNMB2_ENST00000420517.2_Silent_p.T188T	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	202					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(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	TTATCCTAACAAAACTCTACA	0.458													C|||	2907	0.580471	0.9266	0.5259	5008	,	,		18160	0.2212		0.5795	False		,,,				2504	0.5225				p.T188T		Atlas-SNP	.											.	KCNMB2	35	.	0			c.A564C						PASS	.	C	,	3828,578	257.0+/-261.6	1664,500,39	103.0	96.0	99.0		564,564	2.3	1.0	3	dbSNP_116	99	5019,3581	518.1+/-379.2	1497,2025,778	no	coding-synonymous,coding-synonymous	KCNMB2	NM_005832.3,NM_181361.1	,	3161,2525,817	CC,CA,AA		41.6395,13.1185,31.9775	,	188/236,188/236	178560581	8847,4159	2203	4300	6503	SO:0001819	synonymous_variant	10242	exon6			CCTAACAAAACTC	AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584		"""Potassium channels"""	6286	protein-coding gene	gene with protein product		605214				10097176	Standard	NM_181361		Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.564A>C	3.37:g.178560581A>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_005832	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Silent	SNP	ENST00000432997.1	37	CCDS3223.1																																																																																			A|0.352;C|0.648	0.648	strong		0.458	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348251.1	NM_181361	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702169	27702169	+	Silent	SNP	C	C	T	rs6482625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	124	0	0		WXS	Illumina HiSeq	Phase_I	155	155	1	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	
GGT7	2686	hgsc.bcm.edu	37	20	33447314	33447314	+	Missense_Mutation	SNP	C	C	T	rs61319953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33447314C>T	ENST00000336431.5	-	7	990	c.946G>A	c.(946-948)Gta>Ata	p.V316I		NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	316					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						GTGCCAAGTACATCCAGCACC	0.657													C|||	177	0.0353435	0.1256	0.0159	5008	,	,		13069	0.0		0.0	False		,,,				2504	0.0				p.V316I		Atlas-SNP	.											.	GGT7	41	.	0			c.G946A						PASS	.	C	ILE/VAL	418,3988	196.0+/-220.5	16,386,1801	36.0	31.0	33.0		946	-3.3	0.0	20	dbSNP_129	33	4,8594	2.2+/-6.3	0,4,4295	yes	missense	GGT7	NM_178026.2	29	16,390,6096	TT,TC,CC		0.0465,9.4871,3.2452	benign	316/663	33447314	422,12582	2203	4299	6502	SO:0001583	missense	2686	exon7			CAAGTACATCCAG	AL049709	CCDS13242.2	20q11.22	2008-11-24	2008-03-10	2008-03-10	ENSG00000131067	ENSG00000131067		"""Gamma-glutamyltransferases"""	4259	protein-coding gene	gene with protein product		612342	"""gamma-glutamyltransferase-like 3"""	GGTL5, GGTL3		8104871, 18357469	Standard	NM_178026		Approved	D20S101, dJ18C9.2	uc002xay.3	Q9UJ14	OTTHUMG00000032314	ENST00000336431.5:c.946G>A	20.37:g.33447314C>T	ENSP00000338964:p.Val316Ile	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_178026	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Missense_Mutation	SNP	ENST00000336431.5	37	CCDS13242.2	57	0.0260989010989011	50	0.1016260162601626	7	0.019337016574585635	0	0.0	0	0.0	C	10.57	1.386090	0.25031	0.094871	4.65E-4	ENSG00000131067	ENST00000336431	T	0.06218	3.33	5.84	-3.3	0.05003	.	1.463100	0.03616	N	0.235604	T	0.00073	0.0002	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.42949	-0.9421	10	0.17369	T	0.5	-16.9643	1.2329	0.01947	0.249:0.302:0.0955:0.3535	rs61319953	316;316	A4FU32;Q9UJ14	.;GGT7_HUMAN	I	316	ENSP00000338964:V316I	ENSP00000338964:V316I	V	-	1	0	GGT7	32910975	0.000000	0.05858	0.004000	0.12327	0.858000	0.48976	-0.023000	0.12456	-0.350000	0.08262	-0.254000	0.11334	GTA	C|0.971;T|0.029	0.029	strong		0.657	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2	NM_178026	
HLX	3142	hgsc.bcm.edu	37	1	221057662	221057662	+	Silent	SNP	G	G	A	rs3738182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:221057662G>A	ENST00000366903.6	+	4	2584	c.1083G>A	c.(1081-1083)gaG>gaA	p.E361E	HLX_ENST00000549319.1_Silent_p.E147E	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	361					cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		CGGATGGCGAGCAGGACGAGA	0.667													G|||	936	0.186901	0.2572	0.1801	5008	,	,		11857	0.0942		0.1779	False		,,,				2504	0.2014				p.E361E		Atlas-SNP	.											.	HLX	67	.	0			c.G1083A						PASS	.	G		1007,3399	342.5+/-307.2	124,759,1320	34.0	35.0	35.0		1083	-2.2	0.0	1	dbSNP_107	35	1707,6893	294.6+/-302.0	151,1405,2744	no	coding-synonymous	HLX	NM_021958.3		275,2164,4064	AA,AG,GG		19.8488,22.8552,20.8673		361/489	221057662	2714,10292	2203	4300	6503	SO:0001819	synonymous_variant	3142	exon4			TGGCGAGCAGGAC	BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"""Homeoboxes / ANTP class : NKL subclass"""	4978	protein-coding gene	gene with protein product		142995	"""H2.0 (Drosophila)-like homeo box 1"", ""H2.0-like homeobox 1 (Drosophila)"", ""H2.0-like homeobox 1"""	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.1083G>A	1.37:g.221057662G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	186	91	0.489247	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Silent	SNP	ENST00000366903.6	37	CCDS1527.1																																																																																			G|0.810;A|0.190	0.190	strong		0.667	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
OR52E8	390079	hgsc.bcm.edu	37	11	5878458	5878458	+	Silent	SNP	G	G	A	rs549924845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	174	0	0		WXS	Illumina HiSeq	Phase_I	207	7	0.0338164	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	
VWA5B1	127731	hgsc.bcm.edu	37	1	20680718	20680718	+	Missense_Mutation	SNP	G	G	A	rs2072751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	214	0	0		WXS	Illumina HiSeq	Phase_I	233	100	0.429185	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	
LRP2	4036	hgsc.bcm.edu	37	2	169993977	169993977	+	Silent	SNP	C	C	T	rs34029982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:169993977C>T	ENST00000263816.3	-	76	13830	c.13545G>A	c.(13543-13545)ggG>ggA	p.G4515G		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4515					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)"""	TGGGCTGCTTCCCCATTTCCA	0.438													C|||	26	0.00519169	0.0197	0.0	5008	,	,		18764	0.0		0.0	False		,,,				2504	0.0				p.G4515G		Atlas-SNP	.											.	LRP2	751	.	0			c.G13545A						PASS	.	C		95,4311	69.2+/-107.0	0,95,2108	151.0	144.0	146.0		13545	3.6	1.0	2	dbSNP_126	146	0,8600		0,0,4300	no	coding-synonymous	LRP2	NM_004525.2		0,95,6408	TT,TC,CC		0.0,2.1562,0.7304		4515/4656	169993977	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon76			CTGCTTCCCCATT		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.13545G>A	2.37:g.169993977C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			C|0.992;T|0.008	0.008	strong		0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
ZNF467	168544	hgsc.bcm.edu	37	7	149462055	149462055	+	Silent	SNP	G	G	A	rs863021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149462055G>A	ENST00000302017.3	-	5	1949	c.1536C>T	c.(1534-1536)agC>agT	p.S512S	ZNF467_ENST00000484747.1_Intron	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	512					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|urinary_tract(1)	13	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CGTGGGGGCGGCTGCCAGTGT	0.726													G|||	330	0.0658946	0.239	0.0173	5008	,	,		8834	0.0		0.002	False		,,,				2504	0.0				p.S512S		Atlas-SNP	.											.	ZNF467	50	.	0			c.C1536T						PASS	.	G		861,3477		106,649,1414	16.0	21.0	19.0		1536	-4.4	1.0	7	dbSNP_86	19	20,8504		1,18,4243	no	coding-synonymous	ZNF467	NM_207336.1		107,667,5657	AA,AG,GG		0.2346,19.8479,6.8496		512/596	149462055	881,11981	2169	4262	6431	SO:0001819	synonymous_variant	168544	exon5			GGGGCGGCTGCCA	BC029296	CCDS5899.1	7q36.1	2013-01-08			ENSG00000181444	ENSG00000181444		"""Zinc fingers, C2H2-type"""	23154	protein-coding gene	gene with protein product		614040				12426389	Standard	NM_207336		Approved	EZI, Zfp467	uc003wgd.2	Q7Z7K2	OTTHUMG00000157883	ENST00000302017.3:c.1536C>T	7.37:g.149462055G>A		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_207336		Silent	SNP	ENST00000302017.3	37	CCDS5899.1																																																																																			G|0.947;A|0.053	0.053	strong		0.726	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349833.1	NM_207336	
NUFIP2	57532	hgsc.bcm.edu	37	17	27620934	27620934	+	Silent	SNP	G	G	A	rs1054145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27620934G>A	ENST00000225388.4	-	1	202	c.144C>T	c.(142-144)caC>caT	p.H48H	NUFIP2_ENST00000579665.1_Silent_p.H48H	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	48	His-rich.					cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			ggtgatgatggtggtggtggt	0.592													G|||	77	0.0153754	0.0522	0.0072	5008	,	,		10946	0.0		0.003	False		,,,				2504	0.0				p.H48H		Atlas-SNP	.											NUFIP2,NS,carcinoma,-2,1	NUFIP2	60	1	0			c.C144T						PASS	.	G		227,4179	135.3+/-171.4	7,213,1983	144.0	141.0	142.0		144	3.2	1.0	17	dbSNP_86	142	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous	NUFIP2	NM_020772.2		7,215,6281	AA,AG,GG		0.0233,5.1521,1.7607		48/696	27620934	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	57532	exon1			ATGATGGTGGTGG	AB037742	CCDS32600.1	17q11.1	2006-03-01				ENSG00000108256			17634	protein-coding gene	gene with protein product		609356				12837692, 16407062	Standard	NM_020772		Approved	KIAA1321, MGC117262, PIG1, 182-FIP, FIP-82, 82-FIP	uc002hdy.4	Q7Z417		ENST00000225388.4:c.144C>T	17.37:g.27620934G>A		Somatic	476	0	0		WXS	Illumina HiSeq	Phase_I	525	275	0.52381	NM_020772	A1L3A6|Q9P2M5	Silent	SNP	ENST00000225388.4	37	CCDS32600.1																																																																																			G|0.981;A|0.019	0.019	strong		0.592	NUFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447015.2	NM_020772	
CKM	1158	hgsc.bcm.edu	37	19	45815033	45815033	+	Silent	SNP	G	G	T	rs17875616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45815033G>T	ENST00000221476.3	-	5	801	c.627C>A	c.(625-627)cgC>cgA	p.R209R		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	209	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				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)			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)	CGGGCCAGTCGCGGGCCATGC	0.672													G|||	353	0.0704872	0.1256	0.0476	5008	,	,		11665	0.0		0.0736	False		,,,				2504	0.0818				p.R209R		Atlas-SNP	.											CKM,rectum,carcinoma,0,2	CKM	40	2	0			c.C627A						PASS	.	G		455,3949		21,413,1768	30.0	24.0	26.0		627	-10.4	0.1	19	dbSNP_124	26	579,8019		21,537,3741	no	coding-synonymous	CKM	NM_001824.3		42,950,5509	TT,TG,GG		6.7341,10.3315,7.9526		209/382	45815033	1034,11968	2202	4299	6501	SO:0001819	synonymous_variant	1158	exon5			CCAGTCGCGGGCC	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.627C>A	19.37:g.45815033G>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_001824	Q96QL9	Silent	SNP	ENST00000221476.3	37	CCDS12659.1																																																																																			G|0.928;T|0.072	0.072	strong		0.672	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1		
CMYA5	202333	hgsc.bcm.edu	37	5	79032562	79032562	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79032562A>G	ENST00000446378.2	+	2	8005	c.7974A>G	c.(7972-7974)gtA>gtG	p.V2658V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2658					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)		GAAATCTAGTATTAGAAAAGT	0.408																																					p.V2658V		Atlas-SNP	.											CMYA5_ENST00000446378,lower_third,carcinoma,0,2	CMYA5	643	2	0			c.A7974G						scavenged	.						48.0	48.0	48.0					5																	79032562		1831	4091	5922	SO:0001819	synonymous_variant	202333	exon2			TCTAGTATTAGAA	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.7974A>G	5.37:g.79032562A>G		Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	140	3	0.0214286	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			.	.	none		0.408	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
TEP1	7011	hgsc.bcm.edu	37	14	20852817	20852817	+	Missense_Mutation	SNP	G	G	A	rs1760903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20852817G>A	ENST00000262715.5	-	22	3203	c.3163C>T	c.(3163-3165)Cgt>Tgt	p.R1055C	TEP1_ENST00000545983.1_5'Flank|TEP1_ENST00000556935.1_Missense_Mutation_p.R947C	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1055			R -> C (in dbSNP:rs1760903). {ECO:0000269|PubMed:9020079}.		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)		GAGATCCGACGTGCGGCCTCT	0.532													A|||	3172	0.633387	0.7837	0.5994	5008	,	,		17370	0.6121		0.4573	False		,,,				2504	0.6575				p.R1055C		Atlas-SNP	.											.	TEP1	224	.	0			c.C3163T						PASS	.	A	CYS/ARG	3256,1150	407.1+/-334.1	1198,860,145	123.0	133.0	129.0		3163	3.2	0.0	14	dbSNP_89	129	3910,4690	605.4+/-394.9	877,2156,1267	yes	missense	TEP1	NM_007110.4	180	2075,3016,1412	AA,AG,GG		45.4651,26.1008,44.9024	benign	1055/2628	20852817	7166,5840	2203	4300	6503	SO:0001583	missense	7011	exon22			TCCGACGTGCGGC		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.3163C>T	14.37:g.20852817G>A	ENSP00000262715:p.Arg1055Cys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	1256	0.575091575091575	363	0.7378048780487805	203	0.5607734806629834	344	0.6013986013986014	346	0.45646437994722955	A	7.330	0.618750	0.14129	0.738992	0.454651	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.18960	2.18;2.18	5.2	3.21	0.36854	.	1.280850	0.04811	N	0.435261	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;D;B	0.60160	0.0;0.987;0.0	B;P;B	0.47705	0.0;0.555;0.0	T	0.41627	-0.9498	9	0.54805	T	0.06	-0.0704	8.3593	0.32348	0.081:0.121:0.6866:0.1114	rs1760903;rs2228028;rs52837188;rs60187020;rs1760903	947;405;1055	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	C	1055;1055;947	ENSP00000262715:R1055C;ENSP00000452574:R947C	ENSP00000262715:R1055C	R	-	1	0	TEP1	19922657	0.034000	0.19679	0.037000	0.18230	0.807000	0.45602	1.437000	0.34991	0.576000	0.29452	-1.197000	0.01672	CGT	G|0.428;A|0.572	0.572	strong		0.532	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
ANKRD17	26057	hgsc.bcm.edu	37	4	73956736	73956736	+	Silent	SNP	G	G	A	rs6855349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:73956736G>A	ENST00000358602.4	-	29	6725	c.6609C>T	c.(6607-6609)ctC>ctT	p.L2203L	ANKRD17_ENST00000330838.6_Silent_p.L1952L|ANKRD17_ENST00000509867.2_Silent_p.L2090L	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2203					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GATTGACACTGAGGACTGCAA	0.458													G|||	1762	0.351837	0.2375	0.2968	5008	,	,		20331	0.3849		0.4483	False		,,,				2504	0.4121				p.L2203L		Atlas-SNP	.											.	ANKRD17	214	.	0			c.C6609T						PASS	.	G	,	1217,3189	422.5+/-339.8	185,847,1171	134.0	141.0	139.0		6609,5856	3.7	1.0	4	dbSNP_116	139	3585,5015	519.3+/-379.4	736,2113,1451	no	coding-synonymous,coding-synonymous	ANKRD17	NM_032217.3,NM_198889.1	,	921,2960,2622	AA,AG,GG		41.686,27.6214,36.9214	,	2203/2604,1952/2353	73956736	4802,8204	2203	4300	6503	SO:0001819	synonymous_variant	26057	exon29			GACACTGAGGACT	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.6609C>T	4.37:g.73956736G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	165	76	0.460606	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	37	CCDS34004.1																																																																																			G|0.639;A|0.361	0.361	strong		0.458	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
MTTP	4547	hgsc.bcm.edu	37	4	100512919	100512919	+	Missense_Mutation	SNP	C	C	G	rs17599091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100512919C>G	ENST00000265517.5	+	6	933	c.730C>G	c.(730-732)Caa>Gaa	p.Q244E	MTTP_ENST00000511045.1_Missense_Mutation_p.Q271E|MTTP_ENST00000457717.1_Missense_Mutation_p.Q244E			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	244	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		Q -> E (in dbSNP:rs17599091). {ECO:0000269|PubMed:11792722}.		cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	GAATTTCCTACAAACCATTAA	0.303													C|||	103	0.0205671	0.0477	0.0086	5008	,	,		18429	0.0		0.0239	False		,,,				2504	0.0102				p.Q244E		Atlas-SNP	.											.	MTTP	127	.	0			c.C730G						PASS	.	C	GLU/GLN	240,4166	137.7+/-173.5	7,226,1970	65.0	64.0	64.0		730	3.5	0.6	4	dbSNP_123	64	289,8311	107.0+/-167.8	4,281,4015	yes	missense	MTTP	NM_000253.2	29	11,507,5985	GG,GC,CC		3.3605,5.4471,4.0674	benign	244/895	100512919	529,12477	2203	4300	6503	SO:0001583	missense	4547	exon7			TTCCTACAAACCA		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.730C>G	4.37:g.100512919C>G	ENSP00000265517:p.Gln244Glu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	150	60	0.4	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	49	0.022435897435897436	25	0.0508130081300813	3	0.008287292817679558	0	0.0	21	0.027704485488126648	C	0.588	-0.834158	0.02713	0.054471	0.033605	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.40225	1.04;1.04;1.04	5.53	3.47	0.39725	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.964707	0.08632	N	0.916909	T	0.05135	0.0137	L	0.38531	1.155	0.09310	N	1	B;B	0.14805	0.003;0.011	B;B	0.19148	0.008;0.024	T	0.25502	-1.0130	10	0.02654	T	1	-25.7225	7.9279	0.29885	0.3471:0.5753:0.0:0.0775	rs17599091;rs52789259	271;244	E9PBP6;P55157	.;MTP_HUMAN	E	271;244;244;244	ENSP00000427679:Q271E;ENSP00000400821:Q244E;ENSP00000265517:Q244E	ENSP00000265517:Q244E	Q	+	1	0	MTTP	100731942	0.044000	0.20184	0.609000	0.28983	0.195000	0.23768	0.419000	0.21247	1.429000	0.47314	0.650000	0.86243	CAA	C|0.964;G|0.036	0.036	strong		0.303	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
CER1	9350	hgsc.bcm.edu	37	9	14722477	14722477	+	Missense_Mutation	SNP	G	G	C	rs3747532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14722477G>C	ENST00000380911.3	-	1	238	c.194C>G	c.(193-195)gCc>gGc	p.A65G		NM_005454.2	NP_005445.1	O95813	CER1_HUMAN	cerberus 1, DAN family BMP antagonist	65			A -> G (in dbSNP:rs3747532). {ECO:0000269|PubMed:15489334}.		anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|bone mineralization (GO:0030282)|cell migration involved in gastrulation (GO:0042074)|cellular response to BMP stimulus (GO:0071773)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|growth plate cartilage chondrocyte proliferation (GO:0003419)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mesoderm development (GO:2000381)|nervous system development (GO:0007399)|sequestering of BMP in extracellular matrix (GO:0035582)|signal transduction involved in regulation of gene expression (GO:0023019)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(6)	11				GBM - Glioblastoma multiforme(50;3.16e-06)		AGGGCTGGTGGCTACAAGGTG	0.552													C|||	2060	0.411342	0.848	0.3084	5008	,	,		19119	0.127		0.3062	False		,,,				2504	0.2955				p.A65G		Atlas-SNP	.											.	CER1	41	.	0			c.C194G						PASS	.	C	GLY/ALA	3273,1133	404.9+/-333.3	1220,833,150	123.0	128.0	126.0		194	2.1	0.0	9	dbSNP_107	126	2822,5778	675.8+/-403.2	467,1888,1945	yes	missense	CER1	NM_005454.2	60	1687,2721,2095	CC,CG,GG		32.814,25.7149,46.863	benign	65/268	14722477	6095,6911	2203	4300	6503	SO:0001583	missense	9350	exon1			CTGGTGGCTACAA	AF090189	CCDS6476.1	9p23-p22	2013-02-26	2013-02-26		ENSG00000147869	ENSG00000147869			1862	protein-coding gene	gene with protein product		603777	"""cerberus 1 (Xenopus laevis) homolog (cysteine knot superfamily)"", ""cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis)"""			10049596	Standard	NM_005454		Approved	DAND4	uc003zlj.3	O95813	OTTHUMG00000021022	ENST00000380911.3:c.194C>G	9.37:g.14722477G>C	ENSP00000370297:p.Ala65Gly	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_005454	Q6ISJ1|Q6ISJ6|Q6ISQ2|Q6ISS1	Missense_Mutation	SNP	ENST00000380911.3	37	CCDS6476.1	810	0.3708791208791209	409	0.8313008130081301	115	0.31767955801104975	45	0.07867132867132867	241	0.3179419525065963	C	0	-2.649998	0.00109	0.742851	0.32814	ENSG00000147869	ENST00000380911	T	0.17370	2.28	4.89	2.06	0.26882	.	0.330918	0.26489	N	0.024081	T	0.00012	0.0000	N	0.00210	-1.845	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28235	-1.0050	9	0.02654	T	1	-2.1648	4.3035	0.10935	0.0:0.5595:0.1673:0.2732	rs3747532;rs17217056;rs52789555;rs58115487;rs3747532	65	O95813	CER1_HUMAN	G	65	ENSP00000370297:A65G	ENSP00000370297:A65G	A	-	2	0	CER1	14712477	0.008000	0.16893	0.001000	0.08648	0.003000	0.03518	0.112000	0.15479	0.375000	0.24679	-0.120000	0.15030	GCC	G|0.572;C|0.428	0.428	strong		0.552	CER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055453.1	NM_005454	
MKI67	4288	hgsc.bcm.edu	37	10	129904477	129904477	+	Missense_Mutation	SNP	C	C	T	rs11591817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129904477C>T	ENST00000368654.3	-	13	6002	c.5627G>A	c.(5626-5628)cGg>cAg	p.R1876Q	MKI67_ENST00000368653.3_Missense_Mutation_p.R1516Q	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1876	16 X 122 AA approximate repeats.		R -> Q (in dbSNP:rs11591817).		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)				TCTCTTGGGCCGTTGCTTTGT	0.468													C|||	1114	0.222444	0.3056	0.2233	5008	,	,		20557	0.2609		0.1571	False		,,,				2504	0.137				p.R1876Q		Atlas-SNP	.											.	MKI67	363	.	0			c.G5627A						PASS	.	C	GLN/ARG,GLN/ARG	1187,3219	416.5+/-337.6	157,873,1173	258.0	264.0	262.0		4547,5627	-4.3	0.0	10	dbSNP_120	262	1489,7111	283.1+/-295.9	137,1215,2948	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	43,43	294,2088,4121	TT,TC,CC		17.314,26.9405,20.5751	probably-damaging,probably-damaging	1516/2897,1876/3257	129904477	2676,10330	2203	4300	6503	SO:0001583	missense	4288	exon13			TTGGGCCGTTGCT	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.5627G>A	10.37:g.129904477C>T	ENSP00000357643:p.Arg1876Gln	Somatic	439	1	0.0022779		WXS	Illumina HiSeq	Phase_I	447	228	0.510067	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	466	0.21336996336996336	127	0.258130081300813	66	0.18232044198895028	150	0.26223776223776224	123	0.16226912928759896	C	12.64	1.999002	0.35226	0.269405	0.17314	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01963	4.53;4.53	2.66	-4.27	0.03744	.	2.427910	0.02422	N	0.082631	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;P;D	0.89917	0.019;0.493;1.0	B;B;D	0.66716	0.006;0.05;0.946	T	0.48559	-0.9025	9	0.13470	T	0.59	.	0.5944	0.00733	0.172:0.2647:0.1738:0.3895	rs11591817;rs52809288;rs58668910	1875;1516;1876	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	Q	1876;1516;1875	ENSP00000357643:R1876Q;ENSP00000357642:R1516Q	ENSP00000357642:R1516Q	R	-	2	0	MKI67	129794467	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.628000	0.00206	-0.537000	0.06290	-0.367000	0.07326	CGG	C|0.798;T|0.202	0.202	strong		0.468	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
DDX51	317781	hgsc.bcm.edu	37	12	132628281	132628281	+	Missense_Mutation	SNP	C	C	T	rs78871841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132628281C>T	ENST00000397333.3	-	2	516	c.478G>A	c.(478-480)Ggc>Agc	p.G160S	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	160					rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		AGCACCAGGCCGGGGACCAGG	0.751													c|||	254	0.0507188	0.0802	0.0043	5008	,	,		10953	0.0476		0.0219	False		,,,				2504	0.0767				p.G160S		Atlas-SNP	.											.	DDX51	33	.	0			c.G478A						PASS	.		SER/GLY	138,2788		1,136,1326	3.0	4.0	3.0		478	1.6	0.0	12	dbSNP_131	3	24,6890		0,24,3433	yes	missense	DDX51	NM_175066.3	56	1,160,4759	TT,TC,CC		0.3471,4.7163,1.6463	benign	160/667	132628281	162,9678	1463	3457	4920	SO:0001583	missense	317781	exon2			CCAGGCCGGGGAC	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"""DEAD-boxes"""	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.478G>A	12.37:g.132628281C>T	ENSP00000380495:p.Gly160Ser	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	16	6	0.375	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	37	CCDS41865.1	82	0.037545787545787544	30	0.06097560975609756	6	0.016574585635359115	26	0.045454545454545456	20	0.026385224274406333	c	0.472	-0.883980	0.02530	0.047163	0.003471	ENSG00000185163	ENST00000397333	T	0.01725	4.67	2.49	1.59	0.23543	.	0.789795	0.11401	U	0.567852	T	0.00178	0.0005	L	0.27053	0.805	0.09310	N	1	B	0.22211	0.066	B	0.09377	0.004	T	0.49504	-0.8933	10	0.13853	T	0.58	-1.4426	5.097	0.14739	0.0:0.8312:0.0:0.1688	.	160	Q8N8A6	DDX51_HUMAN	S	160	ENSP00000380495:G160S	ENSP00000380495:G160S	G	-	1	0	DDX51	131194234	0.000000	0.05858	0.012000	0.15200	0.059000	0.15707	0.104000	0.15313	0.624000	0.30286	0.479000	0.44913	GGC	C|0.962;T|0.038	0.038	strong		0.751	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
CD36	948	hgsc.bcm.edu	37	7	80300449	80300449	+	Nonsense_Mutation	SNP	T	T	G	rs3211938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:80300449T>G	ENST00000435819.1	+	13	1659	c.975T>G	c.(973-975)taT>taG	p.Y325*	CD36_ENST00000544133.1_Intron|CD36_ENST00000309881.7_Nonsense_Mutation_p.Y325*|CD36_ENST00000433696.2_Nonsense_Mutation_p.Y286*|CD36_ENST00000394788.3_Nonsense_Mutation_p.Y325*|CD36_ENST00000534394.1_Nonsense_Mutation_p.Y249*|CD36_ENST00000432207.1_Nonsense_Mutation_p.Y325*|CD36_ENST00000538969.1_Nonsense_Mutation_p.Y265*|CD36_ENST00000447544.2_Nonsense_Mutation_p.Y325*			P16671	CD36_HUMAN	CD36 molecule (thrombospondin receptor)	325					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular lipid metabolic process (GO:0044255)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to hydroperoxide (GO:0071447)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cGMP-mediated signaling (GO:0019934)|cholesterol transport (GO:0030301)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|lipoprotein transport (GO:0042953)|long-chain fatty acid import (GO:0044539)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle mediated signaling (GO:0055096)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitric oxide mediated signal transduction (GO:0007263)|phagocytosis, recognition (GO:0006910)|plasma lipoprotein particle clearance (GO:0034381)|plasma membrane long-chain fatty acid transport (GO:0015911)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood microparticle formation (GO:2000334)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of removal of superoxide radicals (GO:2000121)|response to stilbenoid (GO:0035634)|small molecule metabolic process (GO:0044281)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|lipoteichoic acid receptor activity (GO:0070892)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|thrombospondin receptor activity (GO:0070053)|transforming growth factor beta binding (GO:0050431)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(10)|large_intestine(1)|lung(6)|ovary(1)	21						GTACATCATATGGTGTGCTAG	0.363													T|||	155	0.0309505	0.1157	0.0029	5008	,	,		16040	0.0		0.0	False		,,,				2504	0.0				p.Y325X		Atlas-SNP	.											.	CD36	185	.	0			c.T975G	GRCh37	CM001647	CD36	M	rs3211938	PASS	.	T	stop/TYR,stop/TYR,stop/TYR,stop/TYR,stop/TYR	361,4045	182.6+/-210.3	16,329,1858	76.0	75.0	75.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	975,975,975,975,975	-0.8	0.5	7	dbSNP_105	75	2,8598	1.2+/-3.3	0,2,4298	yes	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	CD36	NM_000072.3,NM_001001547.2,NM_001001548.2,NM_001127443.1,NM_001127444.1	,,,,	16,331,6156	GG,GT,TT		0.0233,8.1934,2.791	,,,,	325/473,325/473,325/473,325/473,325/473	80300449	363,12643	2203	4300	6503	SO:0001587	stop_gained	948	exon8			ATCATATGGTGTG	Z32770	CCDS34673.1	7q11.2	2010-02-26	2006-03-28		ENSG00000135218	ENSG00000135218		"""CD molecules"""	1663	protein-coding gene	gene with protein product		173510	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)"""			7503937	Standard	NM_001001548		Approved	SCARB3, GPIV, FAT, GP4, GP3B	uc003uhg.4	P16671	OTTHUMG00000155383	ENST00000435819.1:c.975T>G	7.37:g.80300449T>G	ENSP00000399421:p.Tyr325*	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_001127444	D9IX66|D9IX67|D9IX68|D9IX69|Q13966|Q16093|Q8TCV7|Q9BPZ8|Q9BQC2|Q9BZM8|Q9BZN3|Q9BZN4|Q9BZN5	Nonsense_Mutation	SNP	ENST00000435819.1	37	CCDS34673.1	72	0.03296703296703297	72	0.14634146341463414	0	0.0	0	0.0	0	0.0	T	35	5.563074	0.96527	0.081934	2.33E-4	ENSG00000135218	ENST00000435819;ENST00000309881;ENST00000534394;ENST00000394788;ENST00000447544;ENST00000432207;ENST00000419819;ENST00000538969;ENST00000433696	.	.	.	5.57	-0.823	0.10815	.	0.163457	0.53938	D	0.000054	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.6549	9.8443	0.41017	0.0:0.3443:0.0:0.6557	rs3211938;rs10372565;rs17154273;rs3211938	.	.	.	X	325;325;249;325;325;325;325;265;286	.	.	Y	+	3	2	CD36	80138385	0.999000	0.42202	0.528000	0.27938	0.976000	0.68499	0.485000	0.22324	-0.378000	0.07918	0.397000	0.26171	TAT	T|0.967;G|0.033	0.033	strong		0.363	CD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339767.6	NM_001001547	
LRRC8B	23507	hgsc.bcm.edu	37	1	90049088	90049088	+	Silent	SNP	G	G	A	rs35903285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:90049088G>A	ENST00000330947.2	+	5	1239	c.879G>A	c.(877-879)gtG>gtA	p.V293V	RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000439853.1_Silent_p.V293V|LRRC8B_ENST00000358200.4_Silent_p.V293V	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	293					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)		CAGTTGATGTGCAGGCTTTTA	0.353													G|||	110	0.0219649	0.0787	0.0086	5008	,	,		22049	0.0		0.0	False		,,,				2504	0.0				p.V293V		Atlas-SNP	.											.	LRRC8B	49	.	0			c.G879A						PASS	.	G	,	315,4091	167.3+/-198.3	12,291,1900	154.0	153.0	153.0		879,879	-0.2	0.9	1	dbSNP_126	153	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	LRRC8B	NM_001134476.1,NM_015350.2	,	12,295,6196	AA,AG,GG		0.0465,7.1493,2.4527	,	293/804,293/804	90049088	319,12687	2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			TGATGTGCAGGCT	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.879G>A	1.37:g.90049088G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			G|0.976;A|0.024	0.024	strong		0.353	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350	
MROH2B	133558	hgsc.bcm.edu	37	5	40998760	40998760	+	Silent	SNP	C	C	T	rs61745464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:40998760C>T	ENST00000399564.4	-	41	5055	c.4605G>A	c.(4603-4605)ttG>ttA	p.L1535L	MROH2B_ENST00000506092.2_Silent_p.L1090L	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	1535																	ATTGGCTGGTCAAATTGAGAA	0.398													C|||	334	0.0666933	0.1831	0.0605	5008	,	,		19350	0.001		0.0348	False		,,,				2504	0.0143				p.L1535L		Atlas-SNP	.											.	.	.	.	0			c.G4605A						PASS	.	C		632,3106		60,512,1297	82.0	84.0	83.0		4605	5.0	1.0	5	dbSNP_129	83	322,7874		8,306,3784	no	coding-synonymous	HEATR7B2	NM_173489.4		68,818,5081	TT,TC,CC		3.9287,16.9074,7.994		1535/1586	40998760	954,10980	1869	4098	5967	SO:0001819	synonymous_variant	133558	exon41			GCTGGTCAAATTG		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.4605G>A	5.37:g.40998760C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Silent	SNP	ENST00000399564.4	37	CCDS47202.1																																																																																			C|0.936;T|0.064	0.064	strong		0.398	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
MYO7B	4648	hgsc.bcm.edu	37	2	128367092	128367092	+	Silent	SNP	G	G	A	rs777432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128367092G>A	ENST00000409816.2	+	22	2858	c.2826G>A	c.(2824-2826)tcG>tcA	p.S942S	MYO7B_ENST00000389524.4_Silent_p.S942S|MYO7B_ENST00000428314.1_Silent_p.S942S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	942						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		ATCTGGAATCGAAGACCCAGA	0.597													A|||	1608	0.321086	0.3661	0.2478	5008	,	,		19290	0.1319		0.3857	False		,,,				2504	0.4407				p.S942S		Atlas-SNP	.											MYO7B_ENST00000428314,colon,carcinoma,0,2	MYO7B	359	2	0			c.G2826A						PASS	.	A		1392,2710		242,908,901	36.0	42.0	40.0		2826	-6.9	0.0	2	dbSNP_86	40	2971,5405		527,1917,1744	no	coding-synonymous	MYO7B	NM_001080527.1		769,2825,2645	AA,AG,GG		35.4704,33.9347,34.9655		942/2117	128367092	4363,8115	2051	4188	6239	SO:0001819	synonymous_variant	4648	exon23			GGAATCGAAGACC		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.2826G>A	2.37:g.128367092G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	37	CCDS46405.1																																																																																			G|0.692;A|0.308	0.308	strong		0.597	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
HOMEZ	57594	hgsc.bcm.edu	37	14	23745723	23745723	+	Silent	SNP	G	G	A	rs11844797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23745723G>A	ENST00000357460.5	-	2	878	c.714C>T	c.(712-714)aaC>aaT	p.N238N	HOMEZ_ENST00000561013.1_Silent_p.N240N|HOMEZ_ENST00000431326.2_Silent_p.N240N	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	238					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)		CATGTGACTGGTTGGGACCCC	0.532													G|||	250	0.0499201	0.1853	0.0072	5008	,	,		18809	0.0		0.0	False		,,,				2504	0.0				p.N238N		Atlas-SNP	.											.	HOMEZ	80	.	0			c.C714T						PASS	.	G		638,3510		52,534,1488	76.0	79.0	78.0		714	2.2	0.0	14	dbSNP_120	78	12,8408		1,10,4199	no	coding-synonymous	HOMEZ	NM_020834.2		53,544,5687	AA,AG,GG		0.1425,15.3809,5.1719		238/551	23745723	650,11918	2074	4210	6284	SO:0001819	synonymous_variant	57594	exon2			TGACTGGTTGGGA	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.714C>T	14.37:g.23745723G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			G|0.948;A|0.052	0.052	strong		0.532	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
COL20A1	57642	hgsc.bcm.edu	37	20	61960961	61960961	+	Missense_Mutation	SNP	T	T	C	rs6011740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61960961T>C	ENST00000358894.6	+	35	3906	c.3806T>C	c.(3805-3807)aTg>aCg	p.M1269T	COL20A1_ENST00000435874.1_Missense_Mutation_p.M1282T|COL20A1_ENST00000326996.6_Missense_Mutation_p.M1301T|COL20A1_ENST00000496810.1_3'UTR|COL20A1_ENST00000422202.1_Missense_Mutation_p.M1282T	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1269					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GTTGGTCAGATGGGCAGCCCT	0.652													C|||	244	0.048722	0.1611	0.0072	5008	,	,		18080	0.0		0.0	False		,,,				2504	0.0266				p.M1269T		Atlas-SNP	.											.	COL20A1	137	.	0			c.T3806C						PASS	.	C	THR/MET	497,3519		37,423,1548	28.0	33.0	32.0		3806	-4.9	0.0	20	dbSNP_114	32	5,8331		0,5,4163	yes	missense	COL20A1	NM_020882.2	81	37,428,5711	CC,CT,TT		0.06,12.3755,4.0641	benign	1269/1285	61960961	502,11850	2008	4168	6176	SO:0001583	missense	57642	exon35			GTCAGATGGGCAG	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.3806T>C	20.37:g.61960961T>C	ENSP00000351767:p.Met1269Thr	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	72	0.03296703296703297	70	0.14227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	C	0.007	-1.963878	0.00461	0.123755	6.0E-4	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	D;D;D;D	0.85955	-2.02;-2.05;-2.02;-2.02	3.15	-4.86	0.03132	.	3.567220	0.01372	N	0.012620	T	0.00695	0.0023	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	0.27502	-1.0072	9	0.19147	T	0.46	.	1.7705	0.03010	0.1455:0.2136:0.1439:0.497	rs6011740;rs6011740	1282;1269	Q9P218-2;Q9P218	.;COKA1_HUMAN	T	1269;1301;1282;1282	ENSP00000351767:M1269T;ENSP00000323077:M1301T;ENSP00000408690:M1282T;ENSP00000414753:M1282T	ENSP00000323077:M1301T	M	+	2	0	COL20A1	61431405	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-3.643000	0.00405	-1.192000	0.02691	-0.642000	0.03964	ATG	T|0.949;C|0.051	0.051	strong		0.652	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011571	46011571	+	Silent	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011571G>T	ENST00000400368.1	-	1	815	c.795C>A	c.(793-795)ccC>ccA	p.P265P	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	265	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CGTGCTGGCAGGGGGAGGAGG	0.642																																					p.P265P		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C795A						PASS	.						118.0	120.0	119.0					21																	46011571		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			CTGGCAGGGGGAG	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.795C>A	21.37:g.46011571G>T		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	341	21	0.0615836	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.642	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
CENPE	1062	hgsc.bcm.edu	37	4	104059542	104059542	+	Missense_Mutation	SNP	G	G	A	rs2243682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:104059542G>A	ENST00000265148.3	-	39	6358	c.6269C>T	c.(6268-6270)aCg>aTg	p.T2090M	CENPE_ENST00000380026.3_Missense_Mutation_p.T1969M	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2090			T -> M (in dbSNP:rs2243682). {ECO:0000269|PubMed:1406971}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.T2090M(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CAGGCTTTCCGTAAGGTGCTG	0.393													G|||	550	0.109824	0.0197	0.1153	5008	,	,		18082	0.1409		0.2207	False		,,,				2504	0.0818				p.T2090M		Atlas-SNP	.											CENPE,NS,carcinoma,0,1	CENPE	253	1	1	Substitution - Missense(1)	stomach(1)	c.C6269T						PASS	.	G	MET/THR	182,4224	118.0+/-155.7	6,170,2027	241.0	231.0	234.0		6269	0.4	0.0	4	dbSNP_100	234	1772,6828	320.0+/-314.4	196,1380,2724	yes	missense	CENPE	NM_001813.2	81	202,1550,4751	AA,AG,GG		20.6047,4.1307,15.0238	probably-damaging	2090/2702	104059542	1954,11052	2203	4300	6503	SO:0001583	missense	1062	exon39			CTTTCCGTAAGGT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.6269C>T	4.37:g.104059542G>A	ENSP00000265148:p.Thr2090Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	324	0.14835164835164835	16	0.032520325203252036	51	0.1408839779005525	74	0.12937062937062938	183	0.24142480211081793	G	10.54	1.379672	0.24944	0.041307	0.206047	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.72394	-0.65;-0.61	4.34	0.381	0.16228	.	.	.	.	.	T	0.00039	0.0001	L	0.44542	1.39	0.80722	P	0.0	P;B	0.37398	0.593;0.297	B;B	0.22386	0.039;0.015	T	0.01401	-1.1364	8	0.45353	T	0.12	.	6.5724	0.22545	0.4583:0.0:0.5417:0.0	rs2243682;rs52801440;rs58953735;rs2243682	1969;2090	Q02224-3;Q02224	.;CENPE_HUMAN	M	2090;2090;1969	ENSP00000265148:T2090M;ENSP00000369365:T1969M	ENSP00000265148:T2090M	T	-	2	0	CENPE	104278991	0.000000	0.05858	0.002000	0.10522	0.296000	0.27459	-0.164000	0.09983	0.137000	0.18759	0.544000	0.68410	ACG	G|0.855;A|0.145	0.145	strong		0.393	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SP140L	93349	hgsc.bcm.edu	37	2	231258150	231258150	+	Missense_Mutation	SNP	C	C	T	rs7590429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231258150C>T	ENST00000415673.2	+	13	1215	c.1129C>T	c.(1129-1131)Cca>Tca	p.P377S	SP140L_ENST00000396563.4_Missense_Mutation_p.P342S|SP140L_ENST00000243810.6_Missense_Mutation_p.P377S|SP140L_ENST00000444636.1_Missense_Mutation_p.P377S	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	377			P -> S (in dbSNP:rs7590429).			nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						ACCTAATCCTCCAAGAATATA	0.353													C|||	2087	0.416733	0.4811	0.3919	5008	,	,		19709	0.2143		0.4404	False		,,,				2504	0.5317				p.P377S		Atlas-SNP	.											.	SP140L	68	.	0			c.C1129T						PASS	.	C	SER/PRO	1657,2025		374,909,558	64.0	63.0	63.0		1129	2.1	0.1	2	dbSNP_116	63	3556,4600		781,1994,1303	yes	missense	SP140L	NM_138402.4	74	1155,2903,1861	TT,TC,CC		43.5998,45.0027,44.0362	benign	377/581	231258150	5213,6625	1841	4078	5919	SO:0001583	missense	93349	exon13			AATCCTCCAAGAA	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.1129C>T	2.37:g.231258150C>T	ENSP00000397911:p.Pro377Ser	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	812	0.3717948717948718	223	0.4532520325203252	131	0.36187845303867405	133	0.23251748251748253	325	0.4287598944591029	C	8.266	0.812214	0.16537	0.450027	0.435998	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	3.94	2.13	0.27403	.	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;B	0.27625	0.183;0.089	B;B	0.32393	0.145;0.068	T	0.41645	-0.9497	8	0.38643	T	0.18	.	6.5031	0.22180	0.0:0.7764:0.0:0.2236	rs7590429;rs52792690;rs56807857;rs7590429	342;377	Q9H930-2;Q9H930-4	.;.	S	377;377;377;342	ENSP00000395195:P377S;ENSP00000397911:P377S;ENSP00000243810:P377S;ENSP00000379811:P342S	ENSP00000243810:P377S	P	+	1	0	SP140L	230966394	0.081000	0.21417	0.055000	0.19348	0.004000	0.04260	1.716000	0.37981	0.436000	0.26393	-0.966000	0.02617	CCA	C|0.605;T|0.395	0.395	strong		0.353	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
EP400	57634	hgsc.bcm.edu	37	12	132547068	132547068	+	Missense_Mutation	SNP	G	G	A	rs68030464|rs367737531|rs60930033		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132547068G>A	ENST00000333577.4	+	48	8373	c.8264G>A	c.(8263-8265)aGg>aAg	p.R2755K	EP400_ENST00000389561.2_Missense_Mutation_p.R2719K|EP400_ENST00000389562.2_Missense_Mutation_p.R2718K|EP400_ENST00000330386.6_Missense_Mutation_p.R2638K|EP400_ENST00000332482.4_Missense_Mutation_p.R2682K			Q96L91	EP400_HUMAN	E1A binding protein p400	2755	Interaction with ZNF42. {ECO:0000250}.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R2718K(2)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CAGCTTCTCAGgcagcagcag	0.567																																					p.R2719K		Atlas-SNP	.											EP400,NS,carcinoma,0,2	EP400	370	2	2	Substitution - Missense(2)	lung(2)	c.G8156A						scavenged	.						48.0	48.0	48.0					12																	132547068		2203	4300	6503	SO:0001583	missense	57634	exon47			TTCTCAGGCAGCA	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8264G>A	12.37:g.132547068G>A	ENSP00000333602:p.Arg2755Lys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	91	3	0.032967	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	G	15.46	2.840128	0.51057	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62	4.89	4.89	0.63831	.	0.266539	0.31542	N	0.007465	D	0.91264	0.7246	L	0.27053	0.805	0.26223	N	0.97913	D;D;D	0.53312	0.959;0.959;0.959	D;D;D	0.65684	0.937;0.937;0.937	D	0.84986	0.0891	10	0.29301	T	0.29	.	17.0403	0.86487	0.0:0.0:1.0:0.0	.	2719;2638;2718	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	K	2755;2719;2718;2682;2638;2719	ENSP00000333602:R2755K;ENSP00000374212:R2719K;ENSP00000374213:R2718K;ENSP00000331737:R2682K;ENSP00000330620:R2638K	ENSP00000330620:R2638K	R	+	2	0	EP400	131113021	1.000000	0.71417	0.878000	0.34440	0.286000	0.27126	5.957000	0.70323	2.236000	0.73375	0.561000	0.74099	AGG	.	.	none		0.567	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
MYH8	4626	hgsc.bcm.edu	37	17	10312792	10312792	+	Silent	SNP	C	C	T	rs73275411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10312792C>T	ENST00000403437.2	-	16	1795	c.1701G>A	c.(1699-1701)caG>caA	p.Q567Q	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	567	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						CCTTGGGCTTCTGGAAGTTGG	0.517									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				C|||	88	0.0175719	0.0666	0.0	5008	,	,		18938	0.0		0.0	False		,,,				2504	0.0				p.Q567Q		Atlas-SNP	.											.	MYH8	346	.	0			c.G1701A						PASS	.	C		288,4118	158.5+/-191.2	12,264,1927	119.0	118.0	118.0		1701	3.3	1.0	17	dbSNP_131	118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MYH8	NM_002472.2		12,265,6226	TT,TC,CC		0.0116,6.5365,2.2221		567/1938	10312792	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	4626	exon16	Familial Cancer Database	Carney Complex Variant	GGGCTTCTGGAAG		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.1701G>A	17.37:g.10312792C>T		Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	251	134	0.533865	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																			C|0.976;T|0.024	0.024	strong		0.517	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
WDFY4	57705	hgsc.bcm.edu	37	10	49998824	49998824	+	Silent	SNP	C	C	T	rs10857644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:49998824C>T	ENST00000325239.5	+	22	4146	c.4119C>T	c.(4117-4119)ggC>ggT	p.G1373G	WDFY4_ENST00000413659.2_Intron	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1373						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						ACTTCATTGGCGGGCCTGCCA	0.547													C|||	849	0.169529	0.3147	0.0922	5008	,	,		21863	0.1577		0.0924	False		,,,				2504	0.1196				p.G1373G		Atlas-SNP	.											WDFY4,colon,carcinoma,0,1	WDFY4	205	1	0			c.C4119T						scavenged	.						72.0	62.0	65.0					10																	49998824		692	1591	2283	SO:0001819	synonymous_variant	57705	exon23			CATTGGCGGGCCT	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.4119C>T	10.37:g.49998824C>T		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	160	84	0.525	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	364	0.16666666666666666	153	0.31097560975609756	40	0.11049723756906077	95	0.1660839160839161	76	0.10026385224274406	C	9.198	1.027641	0.19512	.	.	ENSG00000128815	ENST00000312002	.	.	.	5.18	-8.28	0.01013	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999985119	.	.	.	.	.	.	T	0.20605	-1.0270	3	.	.	.	.	7.56	0.27845	0.275:0.1759:0.0:0.5492	rs10857644;rs56445870;rs10857644	.	.	.	W	464	.	.	R	+	1	2	WDFY4	49668830	0.000000	0.05858	0.272000	0.24630	0.996000	0.88848	-2.359000	0.01085	-1.729000	0.01364	0.557000	0.71058	CGG	C|0.834;T|0.166	0.166	strong		0.547	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692173	31692173	+	Missense_Mutation	SNP	C	C	T	rs78165499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31692173C>T	ENST00000360542.3	-	1	434	c.181G>A	c.(181-183)Ggt>Agt	p.G61S		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	61						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GTTGGTTCACCGCAGGTCTCT	0.572													C|||	49	0.00978435	0.0325	0.0029	5008	,	,		19017	0.003		0.0	False		,,,				2504	0.001				p.G61S		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.G181A						PASS	.	C	SER/GLY	143,4263	101.2+/-139.8	1,141,2061	115.0	113.0	113.0		181	-0.3	0.0	21	dbSNP_131	113	0,8600		0,0,4300	yes	missense	KRTAP26-1	NM_203405.1	56	1,141,6361	TT,TC,CC		0.0,3.2456,1.0995	benign	61/211	31692173	143,12863	2203	4300	6503	SO:0001583	missense	388818	exon1			GTTCACCGCAGGT	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"""Keratin associated proteins"""	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.181G>A	21.37:g.31692173C>T	ENSP00000353742:p.Gly61Ser	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	196	114	0.581633	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	21	0.009615384615384616	16	0.032520325203252036	2	0.0055248618784530384	3	0.005244755244755245	0	0.0	C	5.629	0.300713	0.10678	0.032456	0.0	ENSG00000197683	ENST00000360542	T	0.03242	4.0	5.01	-0.306	0.12780	.	1.404840	0.04481	N	0.377750	T	0.00936	0.0031	N	0.19112	0.55	0.09310	N	1	B	0.21753	0.06	B	0.22753	0.041	T	0.45469	-0.9259	10	0.42905	T	0.14	2.1832	3.3195	0.07045	0.1879:0.4114:0.0:0.4007	.	61	Q6PEX3	KR261_HUMAN	S	61	ENSP00000353742:G61S	ENSP00000353742:G61S	G	-	1	0	KRTAP26-1	30614044	0.000000	0.05858	0.000000	0.03702	0.960000	0.62799	-0.293000	0.08320	0.113000	0.18004	0.655000	0.94253	GGT	C|0.988;T|0.012	0.012	strong		0.572	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405	
ZNF860	344787	hgsc.bcm.edu	37	3	32032397	32032397	+	Missense_Mutation	SNP	G	G	T	rs4955216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:32032397G>T	ENST00000360311.4	+	2	2375	c.1826G>T	c.(1825-1827)cGc>cTc	p.R609L		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	609					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						CATTCACATCGCATTAGACAT	0.398													T|||	2157	0.430711	0.7988	0.3573	5008	,	,		22192	0.3006		0.1928	False		,,,				2504	0.364				p.R609L		Atlas-SNP	.											.	ZNF860	96	.	0			c.G1826T						PASS	.	T	LEU/ARG	935,449		322,291,79	43.0	36.0	38.0		1826	0.3	0.0	3	dbSNP_111	38	610,2572		58,494,1039	no	missense	ZNF860	NM_001137674.2	102	380,785,1118	TT,TG,GG		19.1703,32.4422,33.8371	benign	609/633	32032397	1545,3021	692	1591	2283	SO:0001583	missense	344787	exon2			CACATCGCATTAG	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1826G>T	3.37:g.32032397G>T	ENSP00000373274:p.Arg609Leu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	836	0.38278388278388276	385	0.782520325203252	125	0.3453038674033149	176	0.3076923076923077	150	0.19788918205804748	T	0.004	-2.318068	0.00235	0.675578	0.191703	ENSG00000197385	ENST00000360311	T	0.06687	3.27	0.314	0.314	0.15847	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00186	-1.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09122	-1.0689	7	.	.	.	.	5.1539	0.15025	0.0:0.0:0.6429:0.357	rs4955216;rs17028702;rs52831549;rs59940424;rs4955216	609	A6NHJ4	ZN860_HUMAN	L	609	ENSP00000373274:R609L	.	R	+	2	0	ZNF860	32007401	0.275000	0.24201	0.001000	0.08648	0.001000	0.01503	1.189000	0.32114	-0.768000	0.04626	-0.930000	0.02707	CGC	G|0.644;T|0.356	0.356	strong		0.398	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
CHRNA2	1135	hgsc.bcm.edu	37	8	27324844	27324844	+	Silent	SNP	G	G	A	rs2565061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27324844G>A	ENST00000520933.2	-	4	504	c.351C>T	c.(349-351)gaC>gaT	p.D117D	CHRNA2_ENST00000407991.1_Silent_p.D117D|CHRNA2_ENST00000240132.2_Silent_p.D102D			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	117					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|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)|drug binding (GO:0008144)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	GCAGTTTGTAGTCGCTCCACT	0.547													G|||	1191	0.237819	0.2579	0.2017	5008	,	,		18862	0.4177		0.1402	False		,,,				2504	0.1513				p.D117D		Atlas-SNP	.											.	CHRNA2	48	.	0			c.C351T						PASS	.	G		1047,3359	384.4+/-325.3	116,815,1272	102.0	100.0	101.0		351	4.7	1.0	8	dbSNP_100	101	1127,7473	233.0+/-266.5	77,973,3250	no	coding-synonymous	CHRNA2	NM_000742.3		193,1788,4522	AA,AG,GG		13.1047,23.7631,16.7154		117/530	27324844	2174,10832	2203	4300	6503	SO:0001819	synonymous_variant	1135	exon5			TTTGTAGTCGCTC	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1956	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 2 (neuronal)"""	118502	"""cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"""			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.351C>T	8.37:g.27324844G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	110	42	0.381818	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Silent	SNP	ENST00000520933.2	37	CCDS6059.1																																																																																			G|0.788;A|0.212	0.212	strong		0.547	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4		
PLA1A	51365	hgsc.bcm.edu	37	3	119331874	119331874	+	Silent	SNP	C	C	T	rs2272270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119331874C>T	ENST00000273371.4	+	5	645	c.573C>T	c.(571-573)ccC>ccT	p.P191P	PLA1A_ENST00000494440.1_Silent_p.P175P|PLA1A_ENST00000488919.1_Silent_p.P18P|PLA1A_ENST00000495992.1_Silent_p.P175P	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	191					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GCCTGGACCCCGCTGGACCTG	0.582													C|||	1432	0.285942	0.3487	0.1398	5008	,	,		20434	0.4484		0.16	False		,,,				2504	0.2669				p.P191P		Atlas-SNP	.											.	PLA1A	65	.	0			c.C573T						PASS	.	C	,,	1393,3013		231,931,1041	50.0	39.0	43.0		525,54,573	-9.7	0.5	3	dbSNP_100	43	1431,7169		114,1203,2983	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA1A	NM_001206960.1,NM_001206961.1,NM_015900.3	,,	345,2134,4024	TT,TC,CC		16.6395,31.616,21.7131	,,	175/441,18/284,191/457	119331874	2824,10182	2203	4300	6503	SO:0001819	synonymous_variant	51365	exon5			GGACCCCGCTGGA	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.573C>T	3.37:g.119331874C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Silent	SNP	ENST00000273371.4	37	CCDS2991.1																																																																																			C|0.759;T|0.241	0.241	strong		0.582	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2		
PCDHB10	56126	hgsc.bcm.edu	37	5	140573508	140573508	+	Silent	SNP	C	C	G	rs112214830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140573508C>G	ENST00000239446.4	+	1	1567	c.1383C>G	c.(1381-1383)cgC>cgG	p.R461R		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	461	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(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)			TGTTCGTCCGCGAGAACAACA	0.632																																					p.R461R		Atlas-SNP	.											PCDHB10,NS,carcinoma,+2,2	PCDHB10	177	2	0			c.C1383G						scavenged	.						42.0	49.0	47.0					5																	140573508		2203	4290	6493	SO:0001819	synonymous_variant	56126	exon1			CGTCCGCGAGAAC	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.1383C>G	5.37:g.140573508C>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	174	56	0.321839	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.029;G|0.971	0.971	strong		0.632	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
E2F4	1874	hgsc.bcm.edu	37	16	67229827	67229827	+	Silent	SNP	C	C	T	rs3730404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67229827C>T	ENST00000379378.3	+	7	1010	c.951C>T	c.(949-951)agC>agT	p.S317S		NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	317	Poly-Ser.				blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		gcagcagcagcagcagcaaca	0.612													C|||	311	0.0621006	0.1762	0.0086	5008	,	,		18005	0.003		0.003	False		,,,				2504	0.0675				p.S317S		Atlas-SNP	.											.	E2F4	25	.	0			c.C951T						PASS	.	-		587,3809	256.1+/-261.0	39,509,1650	47.0	50.0	49.0		951	0.5	1.0	16	dbSNP_107	49	7,8591	3.7+/-12.6	0,7,4292	no	coding-synonymous	E2F4	NM_001950.3		39,516,5942	TT,TC,CC		0.0814,13.353,4.5713		317/414	67229827	594,12400	2198	4299	6497	SO:0001819	synonymous_variant	1874	exon7			CAGCAGCAGCAGC	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975	ENST00000379378.3:c.951C>T	16.37:g.67229827C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	115	63	0.547826	NM_001950	A6NGR8|B5BU56|Q12991|Q15328	Silent	SNP	ENST00000379378.3	37	CCDS32464.1																																																																																			C|0.949;T|0.051	0.051	strong		0.612	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604694	140604694	+	Silent	SNP	G	G	A	rs76971158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604694G>A	ENST00000239449.4	+	1	1617	c.1617G>A	c.(1615-1617)ccG>ccA	p.P539P	PCDHB14_ENST00000515856.2_Silent_p.P386P	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	539	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)|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)			GCGGGTCCCCGGCGTTGAGCA	0.672													g|||	132	0.0263578	0.0946	0.0086	5008	,	,		16525	0.0		0.001	False		,,,				2504	0.0				p.P539P	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											PCDHB14,caecum,carcinoma,0,1	PCDHB14	132	1	0			c.G1617A						PASS	.	G		301,4105		7,287,1909	51.0	57.0	55.0		1617	-4.4	0.6	5	dbSNP_131	55	4,8592		0,4,4294	no	coding-synonymous	PCDHB14	NM_018934.2		7,291,6203	AA,AG,GG		0.0465,6.8316,2.3458		539/799	140604694	305,12697	2203	4298	6501	SO:0001819	synonymous_variant	56122	exon1			GTCCCCGGCGTTG	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.1617G>A	5.37:g.140604694G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	247	119	0.481781	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			G|0.978;A|0.022	0.022	strong		0.672	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
COL1A2	1278	hgsc.bcm.edu	37	7	94027699	94027699	+	Silent	SNP	T	T	C	rs1801182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:94027699T>C	ENST00000297268.6	+	3	558	c.87T>C	c.(85-87)acT>acC	p.T29T		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	29					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)	TCTAGGAAACTGTAAGAAAGG	0.244										HNSCC(75;0.22)			T|||	1027	0.205072	0.4183	0.0562	5008	,	,		12928	0.3502		0.0189	False		,,,				2504	0.0644				p.T29T		Atlas-SNP	.											.	COL1A2	240	.	0			c.T87C						PASS	.	T		1051,2703		127,797,953	7.0	8.0	8.0		87	1.0	0.9	7	dbSNP_89	8	80,7750		2,76,3837	no	coding-synonymous	COL1A2	NM_000089.3		129,873,4790	CC,CT,TT		1.0217,27.9968,9.7635		29/1367	94027699	1131,10453	1877	3915	5792	SO:0001819	synonymous_variant	1278	exon3			GGAAACTGTAAGA	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.87T>C	7.37:g.94027699T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	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|0.823;C|0.177	0.177	strong		0.244	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
TRIM48	79097	hgsc.bcm.edu	37	11	55029787	55029787	+	Splice_Site	SNP	G	G	A	rs12799381	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55029787G>A	ENST00000417545.2	+	1	130	c.44G>A	c.(43-45)cGa>cAa	p.R15Q		NM_024114.3	NP_077019.2	Q8IWZ4	TRI48_HUMAN	tripartite motif containing 48	0						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.R15Q(1)		endometrium(13)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						AGAACCCAGCGGTGAGTGAAA	0.333													.|||	496	0.0990415	0.1505	0.049	5008	,	,		17203	0.0853		0.1113	False		,,,				2504	0.0665				p.R15Q		Atlas-SNP	.											TRIM48_ENST00000417545,caecum,carcinoma,+1,2	TRIM48	149	2	1	Substitution - Missense(1)	stomach(1)	c.G44A						PASS	.	G	GLN/ARG	205,1179		16,173,503	41.0	36.0	38.0		44	-0.8	0.0	11	dbSNP_121	38	343,2839		19,305,1267	no	missense-near-splice	TRIM48	NM_024114.3	43	35,478,1770	AA,AG,GG		10.7794,14.8121,12.0018		15/225	55029787	548,4018	692	1591	2283	SO:0001630	splice_region_variant	79097	exon1			CCCAGCGGTGAGT	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.44+1G>A	11.37:g.55029787G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	161	82	0.509317	NM_024114	Q9BUW4	Missense_Mutation	SNP	ENST00000417545.2	37	CCDS7947.2	227	0.10393772893772894	87	0.17682926829268292	22	0.06077348066298342	35	0.06118881118881119	83	0.10949868073878628	.	6.705	0.498677	0.12762	0.148121	0.107794	ENSG00000150244	ENST00000417545	T	0.73047	-0.71	0.41	-0.821	0.10822	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.11155	-1.0599	4	0.41790	T	0.15	.	.	.	.	rs12799381	.	.	.	Q	15	ENSP00000402414:R15Q	ENSP00000402414:R15Q	R	+	2	0	TRIM48	54786363	0.006000	0.16342	0.028000	0.17463	0.009000	0.06853	0.470000	0.22084	-0.494000	0.06669	-1.202000	0.01658	CGA	G|0.891;A|0.109	0.109	strong		0.333	TRIM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347088.1		Missense_Mutation
TTF2	8458	hgsc.bcm.edu	37	1	117618024	117618024	+	Missense_Mutation	SNP	G	G	C	rs17036832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117618024G>C	ENST00000369466.4	+	5	862	c.818G>C	c.(817-819)aGc>aCc	p.S273T		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	273					ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		AACTCAATAAGCAAGCCCCAG	0.473													G|||	125	0.0249601	0.09	0.0072	5008	,	,		19352	0.0		0.001	False		,,,				2504	0.0				p.S273T		Atlas-SNP	.											.	TTF2	92	.	0			c.G818C						PASS	.	G	THR/SER	262,4144	143.8+/-178.8	17,228,1958	98.0	109.0	105.0		818	-1.2	0.0	1	dbSNP_123	105	5,8595	4.3+/-15.6	0,5,4295	yes	missense	TTF2	NM_003594.3	58	17,233,6253	CC,CG,GG		0.0581,5.9464,2.0529	benign	273/1163	117618024	267,12739	2203	4300	6503	SO:0001583	missense	8458	exon5			CAATAAGCAAGCC	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 6"""	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.818G>C	1.37:g.117618024G>C	ENSP00000358478:p.Ser273Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	37	CCDS892.1	49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	G	10.55	1.380822	0.24944	0.059464	5.81E-4	ENSG00000116830	ENST00000369466	D	0.86956	-2.19	5.13	-1.21	0.09524	.	0.471757	0.18081	N	0.152313	T	0.61974	0.2390	L	0.56769	1.78	0.09310	N	1	B;B	0.20052	0.002;0.041	B;B	0.14578	0.003;0.011	T	0.48502	-0.9030	10	0.24483	T	0.36	-0.004	1.0168	0.01509	0.3182:0.2659:0.2795:0.1364	rs17036832;rs52826473;rs17036832	273;273	Q9UNY4;Q9UNY4-2	TTF2_HUMAN;.	T	273	ENSP00000358478:S273T	ENSP00000358478:S273T	S	+	2	0	TTF2	117419547	0.000000	0.05858	0.005000	0.12908	0.093000	0.18481	-0.924000	0.03996	-0.081000	0.12662	0.655000	0.94253	AGC	A|0.000;C|0.019;G|0.980	0.019	strong		0.473	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3		
NIN	51199	hgsc.bcm.edu	37	14	51204996	51204996	+	Silent	SNP	C	C	T	rs11376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:51204996C>T	ENST00000382041.3	-	27	5827	c.5637G>A	c.(5635-5637)caG>caA	p.Q1879Q	NIN_ENST00000453196.1_Silent_p.Q1879Q|NIN_ENST00000389868.3_Silent_p.Q1166Q|NIN_ENST00000324330.9_Silent_p.Q1879Q|NIN_ENST00000245441.5_Silent_p.Q1879Q|NIN_ENST00000382043.4_Silent_p.Q1166Q|NIN_ENST00000530997.2_Silent_p.Q1879Q	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1879					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					TGGATTCCAACTGACGGACCT	0.388			T	PDGFRB	MPD								T|||	2548	0.508786	0.7375	0.4092	5008	,	,		20711	0.3155		0.4851	False		,,,				2504	0.4939				p.Q1879Q		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.G5637A						PASS	.	T	,,,	3067,1339	447.1+/-348.2	1080,907,216	160.0	140.0	147.0		3498,5637,5637,5637	-11.4	0.0	14	dbSNP_52	147	4449,4151	566.0+/-388.6	1141,2167,992	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	,,,	2221,3074,1208	TT,TC,CC		48.2674,30.3904,42.2113	,,,	1166/1378,1879/2134,1879/2047,1879/2091	51204996	7516,5490	2203	4300	6503	SO:0001819	synonymous_variant	51199	exon27			TTCCAACTGACGG	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"""EF-hand domain containing"""	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.5637G>A	14.37:g.51204996C>T		Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	216	216	1	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	37	CCDS32079.1	1100	0.5036630036630036	382	0.7764227642276422	155	0.4281767955801105	188	0.32867132867132864	375	0.4947229551451187	T	2.392	-0.339670	0.05243	0.696096	0.517326	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	5.72	-11.4	0.00090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27919	P	0.9383365	.	.	.	.	.	.	T	0.03587	-1.1022	3	.	.	.	-7.271	15.2542	0.73571	0.0776:0.6719:0.0784:0.172	rs11376;rs1134126;rs3015463;rs11554814;rs17295972;rs17350344;rs17792348;rs17846102;rs17859105;rs52836159;rs61295335;rs11376	.	.	.	I	1370	.	.	V	-	1	0	NIN	50274746	0.024000	0.19004	0.001000	0.08648	0.541000	0.35023	-0.727000	0.04931	-3.046000	0.00261	-0.360000	0.07572	GTT	C|0.452;T|0.548	0.548	strong		0.388	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
NAA25	80018	hgsc.bcm.edu	37	12	112471090	112471090	+	Missense_Mutation	SNP	G	G	T	rs12298022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:112471090G>T	ENST00000261745.4	-	23	2991	c.2743C>A	c.(2743-2745)Cta>Ata	p.L915I		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	915			L -> I (in dbSNP:rs12298022).			cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						AGTGCAATTAGATGTGTTTCA	0.388													g|||	563	0.11242	0.298	0.098	5008	,	,		19040	0.0		0.0706	False		,,,				2504	0.0307				p.L915I		Atlas-SNP	.											.	NAA25	105	.	0			c.C2743A						PASS	.	G	ILE/LEU	1133,3273	404.6+/-333.2	148,837,1218	111.0	116.0	114.0		2743	5.0	1.0	12	dbSNP_120	114	629,7971	164.1+/-216.5	22,585,3693	yes	missense	NAA25	NM_024953.3	5	170,1422,4911	TT,TG,GG		7.314,25.7149,13.5476	benign	915/973	112471090	1762,11244	2203	4300	6503	SO:0001583	missense	80018	exon23			CAATTAGATGTGT	AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"""N(alpha)-acetyltransferase subunits"""	25783	protein-coding gene	gene with protein product		612755	"""chromosome 12 open reading frame 30"""	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.2743C>A	12.37:g.112471090G>T	ENSP00000261745:p.Leu915Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	106	0.972477	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	237	0.10851648351648352	147	0.29878048780487804	45	0.12430939226519337	0	0.0	45	0.059366754617414245	G	14.73	2.621707	0.46736	0.257149	0.07314	ENSG00000111300	ENST00000261745	T	0.35421	1.31	5.91	5.01	0.66863	.	0.257811	0.33916	N	0.004423	T	0.00012	0.0000	N	0.19112	0.55	0.26394	P	0.9765313	D	0.52996	0.957	P	0.44696	0.458	T	0.33929	-0.9849	9	0.40728	T	0.16	-2.1641	14.549	0.68052	0.0695:0.0:0.9305:0.0	rs12298022;rs52836486;rs57720948;rs12298022	915	Q14CX7	NAA25_HUMAN	I	915	ENSP00000261745:L915I	ENSP00000261745:L915I	L	-	1	2	NAA25	110955473	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.008000	0.49544	2.816000	0.96949	0.644000	0.83932	CTA	G|0.868;T|0.132	0.132	strong		0.388	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953	
ADAMTS8	11095	hgsc.bcm.edu	37	11	130284495	130284495	+	Silent	SNP	C	C	T	rs142963990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:130284495C>T	ENST00000257359.6	-	5	2203	c.1497G>A	c.(1495-1497)acG>acA	p.T499T		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	499	Disintegrin.				negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		GCCCGCACGGCGTGCCGTCAG	0.662													C|||	20	0.00399361	0.0151	0.0	5008	,	,		17513	0.0		0.0	False		,,,				2504	0.0				p.T499T		Atlas-SNP	.											.	ADAMTS8	172	.	0			c.G1497A						PASS	.	C		53,3979		0,53,1963	48.0	54.0	52.0		1497	-11.2	0.2	11	dbSNP_134	52	0,8342		0,0,4171	no	coding-synonymous	ADAMTS8	NM_007037.4		0,53,6134	TT,TC,CC		0.0,1.3145,0.4283		499/890	130284495	53,12321	2016	4171	6187	SO:0001819	synonymous_variant	11095	exon5			GCACGGCGTGCCG	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	224	protein-coding gene	gene with protein product		605175	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"""			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.1497G>A	11.37:g.130284495C>T		Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	271	127	0.468635	NM_007037	Q9NZS0	Silent	SNP	ENST00000257359.6	37	CCDS41732.1																																																																																			C|0.996;T|0.004	0.004	strong		0.662	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037	
TF	7018	hgsc.bcm.edu	37	3	133486988	133486988	+	Silent	SNP	C	C	T	rs7845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133486988C>T	ENST00000402696.3	+	13	2087	c.1602C>T	c.(1600-1602)taC>taT	p.Y534Y	TF_ENST00000264998.3_Silent_p.Y407Y	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	534	Transferrin-like 2. {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)	AGGGATACTACGGCTACACAG	0.448													C|||	71	0.0141773	0.0522	0.0029	5008	,	,		19620	0.0		0.0	False		,,,				2504	0.0				p.Y534Y		Atlas-SNP	.											.	TF	116	.	0			c.C1602T						PASS	.	C		174,4232	113.3+/-151.4	5,164,2034	81.0	83.0	82.0		1602	-2.4	1.0	3	dbSNP_52	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TF	NM_001063.3		5,166,6332	TT,TC,CC		0.0233,3.9492,1.3532		534/699	133486988	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon13			ATACTACGGCTAC		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.1602C>T	3.37:g.133486988C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			C|0.985;G|0.000;T|0.015	0.015	strong		0.448	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
MFSD9	84804	hgsc.bcm.edu	37	2	103334969	103334969	+	Silent	SNP	G	G	A	rs1052431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:103334969G>A	ENST00000258436.5	-	6	1378	c.1335C>T	c.(1333-1335)ggC>ggT	p.G445G	MFSD9_ENST00000496253.1_5'Flank	NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	445					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						CTAACACAGCGCCCAGGCTGG	0.552													G|||	2056	0.410543	0.295	0.3271	5008	,	,		18498	0.5714		0.3539	False		,,,				2504	0.5184				p.G445G		Atlas-SNP	.											.	MFSD9	56	.	0			c.C1335T						PASS	.	G		1245,3161	396.7+/-330.2	184,877,1142	40.0	45.0	43.0		1335	-7.6	0.0	2	dbSNP_86	43	2752,5846	404.9+/-348.3	437,1878,1984	no	coding-synonymous	MFSD9	NM_032718.3		621,2755,3126	AA,AG,GG		32.0074,28.2569,30.7367		445/475	103334969	3997,9007	2203	4299	6502	SO:0001819	synonymous_variant	84804	exon6			CACAGCGCCCAGG		CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.1335C>T	2.37:g.103334969G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_032718	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Silent	SNP	ENST00000258436.5	37	CCDS2063.1																																																																																			G|0.653;A|0.347	0.347	strong		0.552	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548026	32548026	+	Missense_Mutation	SNP	G	G	C	rs9269744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32548026G>C	ENST00000360004.5	-	5	890	c.785C>G	c.(784-786)aCa>aGa	p.T262R		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	262			T -> R (in dbSNP:rs9269744).		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						GGTATTACCTGTTGGCTGAAG	0.453										Multiple Myeloma(14;0.17)																											p.T262R		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C785G						PASS	.						32.0	37.0	35.0					6																	32548026		2089	4081	6170	SO:0001583	missense	3123	exon5			TTACCTGTTGGCT	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.785C>G	6.37:g.32548026G>C	ENSP00000353099:p.Thr262Arg	Somatic	431	0	0		WXS	Illumina HiSeq	Phase_I	330	61	0.184848	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	14.00	2.403780	0.42613	.	.	ENSG00000196126	ENST00000360004	T	0.00628	6.11	3.96	3.06	0.35304	.	0.521505	0.16081	N	0.230501	T	0.01287	0.0042	.	.	.	0.80722	D	1	B;B;D	0.89917	0.005;0.001;1.0	B;B;D	0.85130	0.012;0.012;0.997	T	0.62732	-0.6792	9	0.52906	T	0.07	.	9.6894	0.40118	0.0:0.213:0.787:0.0	rs9269744;rs17880393;rs33909504	262;262;262	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	R	262	ENSP00000353099:T262R	ENSP00000353099:T262R	T	-	2	0	HLA-DRB1	32656004	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	2.243000	0.43115	0.736000	0.32559	0.551000	0.68910	ACA	G|0.500;C|0.500	0.500	strong		0.453	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
CYP4F12	66002	hgsc.bcm.edu	37	19	15795939	15795939	+	Silent	SNP	A	A	G	rs61729075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15795939A>G	ENST00000550308.1	+	9	1427	c.1047A>G	c.(1045-1047)gaA>gaG	p.E349E	CYP4F12_ENST00000324632.10_Silent_p.E349E	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	349					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GGCACCCAGAATACCAGGAGC	0.582													.|||	99	0.0197684	0.0711	0.0058	5008	,	,		18068	0.0		0.001	False		,,,				2504	0.0				p.E349E		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A1047G						PASS	.	G		383,4023		7,369,1827	66.0	62.0	63.0		1047	-0.9	1.0	19	dbSNP_129	63	3,8597		0,3,4297	no	coding-synonymous	CYP4F12	NM_023944.3		7,372,6124	GG,GA,AA		0.0349,8.6927,2.9679		349/525	15795939	386,12620	2203	4300	6503	SO:0001819	synonymous_variant	66002	exon9			CCCAGAATACCAG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1047A>G	19.37:g.15795939A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	258	71	0.275194	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			A|0.981;G|0.019	0.019	strong		0.582	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
OSBP2	23762	hgsc.bcm.edu	37	22	31091064	31091064	+	Silent	SNP	C	C	T	rs41279967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31091064C>T	ENST00000332585.6	+	1	272	c.168C>T	c.(166-168)ccC>ccT	p.P56P	OSBP2_ENST00000382310.3_Silent_p.P56P|OSBP2_ENST00000403222.3_Intron|OSBP2_ENST00000407373.1_Intron|OSBP2_ENST00000446658.2_Silent_p.P56P	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	56					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						AGCCCCAGCCCGTGCCCGAAC	0.692													c|||	540	0.107827	0.2746	0.0735	5008	,	,		9026	0.0		0.0885	False		,,,				2504	0.0378				p.P56P		Atlas-SNP	.											.	OSBP2	52	.	0			c.C168T						PASS	.			908,3008		102,704,1152	13.0	17.0	16.0		168	-7.6	0.0	22	dbSNP_127	16	678,7630		23,632,3499	no	coding-synonymous	OSBP2	NM_030758.3		125,1336,4651	TT,TC,CC		8.1608,23.1869,12.9745		56/917	31091064	1586,10638	1958	4154	6112	SO:0001819	synonymous_variant	23762	exon1			CCAGCCCGTGCCC		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.168C>T	22.37:g.31091064C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	38	0.655172	NM_030758	B0QYG1|B4DK24|B4DKE4|B4DTR3|F5H2A3|O60396|Q0VF99|Q8NA37|Q9BY96|Q9BZF0	Silent	SNP	ENST00000332585.6	37	CCDS43002.1																																																																																			C|0.888;T|0.112	0.112	strong		0.692	OSBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321547.2	NM_030758	
ZDHHC1	29800	hgsc.bcm.edu	37	16	67440289	67440289	+	Silent	SNP	C	C	T	rs8058306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67440289C>T	ENST00000348579.2	-	3	407	c.66G>A	c.(64-66)acG>acA	p.T22T		NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	22					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		GTGCCGGTGCCGTCCACACAC	0.622													C|||	361	0.0720847	0.205	0.013	5008	,	,		17815	0.003		0.003	False		,,,				2504	0.0767				p.T22T		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.G66A						PASS	.	C		710,3678		52,606,1536	26.0	23.0	24.0		66	-9.3	0.1	16	dbSNP_116	24	11,8577		0,11,4283	no	coding-synonymous	ZDHHC1	NM_013304.2		52,617,5819	TT,TC,CC		0.1281,16.1805,5.5564		22/486	67440289	721,12255	2194	4294	6488	SO:0001819	synonymous_variant	29800	exon3			CGGTGCCGTCCAC	U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"""Zinc fingers, DHHC-type"""	17916	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 1"""	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.66G>A	16.37:g.67440289C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	161	71	0.440994	NM_013304	O15461	Silent	SNP	ENST00000348579.2	37	CCDS10836.1																																																																																			C|0.924;T|0.076	0.076	strong		0.622	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304	
MUC4	4585	hgsc.bcm.edu	37	3	195515030	195515030	+	Missense_Mutation	SNP	C	C	A	rs538504516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515030C>A	ENST00000463781.3	-	2	3880	c.3421G>T	c.(3421-3423)Gac>Tac	p.D1141Y	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D1141Y	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	608					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)		GAGGAAGTGTCGGTGACAGGA	0.572													.|||	4	0.000798722	0.0015	0.0	5008	,	,		15001	0.0		0.001	False		,,,				2504	0.001				p.D1141Y		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.G3421T						scavenged	.						8.0	6.0	7.0					3																	195515030		651	1358	2009	SO:0001583	missense	4585	exon2			AAGTGTCGGTGAC	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.3421G>T	3.37:g.195515030C>A	ENSP00000417498:p.Asp1141Tyr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	436	23	0.0527523	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	.	.	.	.	.	.	.	.	.	.	-	1.771	-0.484381	0.04383	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34859	1.34;1.34	0.663	-1.33	0.09172	.	.	.	.	.	T	0.32882	0.0844	N	0.14661	0.345	0.09310	N	1	D	0.69078	0.997	D	0.72982	0.979	T	0.19192	-1.0313	8	.	.	.	.	3.7507	0.08565	0.214:0.2493:0.5366:0.0	.	1141	E7ESK3	.	Y	1141	ENSP00000417498:D1141Y;ENSP00000420243:D1141Y	.	D	-	1	0	MUC4	196999425	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-2.687000	0.00833	-1.284000	0.02390	0.064000	0.15345	GAC	.	.	none		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ATP2A3	489	hgsc.bcm.edu	37	17	3846802	3846802	+	Silent	SNP	A	A	G	rs758641	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3846802A>G	ENST00000352011.3	-	11	1356	c.1302T>C	c.(1300-1302)taT>taC	p.Y434Y	ATP2A3_ENST00000397041.3_Silent_p.Y434Y|ATP2A3_ENST00000397043.3_Silent_p.Y434Y|ATP2A3_ENST00000309890.7_Silent_p.Y434Y|ATP2A3_ENST00000397035.3_Silent_p.Y434Y|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000359983.3_Silent_p.Y434Y			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	434					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		CCACCTTCTCATACACACCCT	0.642													G|||	1669	0.333267	0.3956	0.4582	5008	,	,		16607	0.0843		0.4563	False		,,,				2504	0.2904				p.Y434Y	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T1302C						PASS	.	G	,,,,,,	1730,2676	648.5+/-398.7	344,1042,817	132.0	118.0	123.0		1302,1302,1302,1302,1302,1302,1302	-0.9	0.9	17	dbSNP_86	123	3981,4619	600.8+/-394.3	943,2095,1262	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	1287,3137,2079	GG,GA,AA		46.2907,39.2646,43.9105	,,,,,,	434/1000,434/1053,434/1045,434/1044,434/1030,434/999,434/1030	3846802	5711,7295	2203	4300	6503	SO:0001819	synonymous_variant	489	exon11			CTTCTCATACACA		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1302T>C	17.37:g.3846802A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			A|0.605;G|0.395	0.395	strong		0.642	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
CFC1	55997	hgsc.bcm.edu	37	2	131356322	131356322	+	Missense_Mutation	SNP	C	C	T	rs201431919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131356322C>T	ENST00000259216.4	-	3	402	c.140G>A	c.(139-141)cGa>cAa	p.R47Q		NM_032545.3	NP_115934.1	P0CG37	CFC1_HUMAN	cripto, FRL-1, cryptic family 1	47					determination of left/right symmetry (GO:0007368)|gastrulation (GO:0007369)|nodal signaling pathway (GO:0038092)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nodal binding (GO:0038100)			endometrium(1)|lung(4)	5	Colorectal(110;0.1)					CGGTGACTGTCGGTGCTTCTG	0.537													c|||	372	0.0742812	0.2663	0.0259	5008	,	,		16561	0.0		0.002	False		,,,				2504	0.0				p.R47Q		Atlas-SNP	.											CFC1,fourth_ventricle,glioma,0,1	.	.	1	0			c.G140A	GRCh37	CM023185	CFC1	M		PASS	.						15.0	23.0	21.0					2																	131356322		2174	4254	6428	SO:0001583	missense	653275	exon3			GACTGTCGGTGCT	AF312769	CCDS2162.1, CCDS74573.1, CCDS74574.1	2q21.2	2014-02-04			ENSG00000136698	ENSG00000136698			18292	protein-coding gene	gene with protein product		605194	"""heterotaxy 2 (autosomal dominant)"""	HTX2		11062482, 10858660	Standard	NM_032545		Approved	CRYPTIC, HTX2	uc002tro.2	P0CG37	OTTHUMG00000131628	ENST00000259216.4:c.140G>A	2.37:g.131356322C>T	ENSP00000259216:p.Arg47Gln	Somatic	1076	0	0		WXS	Illumina HiSeq	Phase_I	797	540	0.677541	NM_001079530	B2RCY0|B9EJD3|Q53T05|Q9GZR3	Missense_Mutation	SNP	ENST00000259216.4	37	CCDS2162.1	101	0.04624542124542125	92	0.18699186991869918	9	0.024861878453038673	0	0.0	0	0.0	.	0.054	-1.241061	0.01493	.	.	ENSG00000136698	ENST00000259216	D	0.88818	-2.43	1.91	0.598	0.17512	.	0.638739	0.14771	N	0.299398	T	0.00109	0.0003	N	0.00197	-1.87	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22836	-1.0205	10	0.07030	T	0.85	-32.4582	1.7088	0.02888	0.2856:0.1859:0.0:0.5285	.	47	P0CG37	CFC1_HUMAN	Q	47	ENSP00000259216:R47Q	ENSP00000259216:R47Q	R	-	2	0	CFC1	131072792	0.006000	0.16342	0.003000	0.11579	0.092000	0.18411	0.487000	0.22356	-0.207000	0.10187	-0.665000	0.03846	CGA	C|0.969;T|0.031	0.031	strong		0.537	CFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333367.1	NM_032545	
TRIM56	81844	hgsc.bcm.edu	37	7	100731896	100731896	+	Silent	SNP	T	T	C	rs61730716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100731896T>C	ENST00000306085.6	+	3	1600	c.1303T>C	c.(1303-1305)Ttg>Ctg	p.L435L		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	435					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)					AGCCCAGACCTTGGAGGAGGA	0.602													T|||	389	0.0776757	0.2095	0.0605	5008	,	,		17188	0.001		0.0567	False		,,,				2504	0.0123				p.L435L	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.T1303C						PASS	.	T		678,3238		57,564,1337	47.0	65.0	59.0		1303	1.9	0.0	7	dbSNP_129	59	633,7631		29,575,3528	no	coding-synonymous	TRIM56	NM_030961.1		86,1139,4865	CC,CT,TT		7.6597,17.3136,10.7635		435/756	100731896	1311,10869	1958	4132	6090	SO:0001819	synonymous_variant	81844	exon3			CAGACCTTGGAGG	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.1303T>C	7.37:g.100731896T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																			T|0.922;C|0.078	0.078	strong		0.602	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961	
MSLN	10232	hgsc.bcm.edu	37	16	815593	815593	+	Missense_Mutation	SNP	G	G	C	rs115279916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:815593G>C	ENST00000382862.3	+	9	866	c.771G>C	c.(769-771)caG>caC	p.Q257H	MSLN_ENST00000566549.1_Missense_Mutation_p.Q257H|MSLN_ENST00000545450.2_Missense_Mutation_p.Q257H|MSLN_ENST00000563941.1_Missense_Mutation_p.Q257H	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	257					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)				TGCTGGGCCAGCCCATCATCC	0.706													G|||	81	0.0161741	0.059	0.0043	5008	,	,		14281	0.0		0.0	False		,,,				2504	0.0				p.Q257H		Atlas-SNP	.											.	MSLN	109	.	0			c.G771C						PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN	207,4145	119.2+/-156.9	5,197,1974	31.0	32.0	32.0		771,771,771	1.0	0.0	16	dbSNP_132	32	1,8569	1.2+/-3.3	0,1,4284	yes	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	24,24,24	5,198,6258	CC,CG,GG		0.0117,4.7564,1.6097	benign,benign,benign	257/623,257/623,257/631	815593	208,12714	2176	4285	6461	SO:0001583	missense	10232	exon10			GGGCCAGCCCATC	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.771G>C	16.37:g.815593G>C	ENSP00000372313:p.Gln257His	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	117	65	0.555556	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	G	2.785	-0.252545	0.05829	0.047564	1.17E-4	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.12569	2.67;2.67	3.03	1.03	0.20045	.	1.781050	0.03402	N	0.203448	T	0.01489	0.0048	N	0.25647	0.755	0.09310	N	1	B;B;B;B	0.15141	0.007;0.008;0.012;0.007	B;B;B;B	0.12156	0.004;0.007;0.007;0.004	T	0.30119	-0.9989	10	0.39692	T	0.17	-0.1169	4.9829	0.14175	0.2994:0.0:0.7006:0.0	.	256;257;257;257	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	H	257	ENSP00000442965:Q257H;ENSP00000372313:Q257H	ENSP00000372313:Q257H	Q	+	3	2	MSLN	755594	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.687000	0.25407	0.060000	0.16281	-0.271000	0.10264	CAG	G|0.985;C|0.015	0.015	strong		0.706	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
OR6C4	341418	hgsc.bcm.edu	37	12	55945265	55945265	+	Silent	SNP	A	A	G	rs74093226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55945265A>G	ENST00000394256.2	+	1	283	c.255A>G	c.(253-255)acA>acG	p.T85T	RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	85						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(3)|lung(5)|skin(1)	11						GCATGACAACAGGAAATAAAG	0.413													A|||	289	0.0577077	0.2095	0.0173	5008	,	,		20860	0.0		0.0	False		,,,				2504	0.0				p.T85T		Atlas-SNP	.											.	OR6C4	34	.	0			c.A255G						PASS	.	A		780,3626	300.1+/-286.2	65,650,1488	82.0	88.0	86.0		255	2.3	1.0	12	dbSNP_130	86	12,8586	7.7+/-29.5	0,12,4287	no	coding-synonymous	OR6C4	NM_001005494.1		65,662,5775	GG,GA,AA		0.1396,17.7031,6.0904		85/310	55945265	792,12212	2203	4299	6502	SO:0001819	synonymous_variant	341418	exon1			GACAACAGGAAAT	BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"""GPCR / Class A : Olfactory receptors"""	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.255A>G	12.37:g.55945265A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_001005494	A8MZG7|B2RNN2|Q6IFK1	Silent	SNP	ENST00000394256.2	37	CCDS31827.1																																																																																			A|0.951;G|0.049	0.049	strong		0.413	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1		
MUC17	140453	hgsc.bcm.edu	37	7	100678693	100678693	+	Silent	SNP	T	T	C	rs78176991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678693T>C	ENST00000306151.4	+	3	4060	c.3996T>C	c.(3994-3996)taT>taC	p.Y1332Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1332	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)					CCTCAACTTATAGTGAAGGAA	0.448																																					p.Y1332Y		Atlas-SNP	.											.	MUC17	804	.	0			c.T3996C						PASS	.						241.0	232.0	235.0					7																	100678693		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTTATAGTGAA	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.3996T>C	7.37:g.100678693T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	144	16	0.111111	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.994;C|0.006	0.006	strong		0.448	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CCAR2	57805	hgsc.bcm.edu	37	8	22473646	22473646	+	Missense_Mutation	SNP	A	A	C	rs143150726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22473646A>C	ENST00000308511.4	+	14	1979	c.1730A>C	c.(1729-1731)gAg>gCg	p.E577A	CCAR2_ENST00000389279.3_Missense_Mutation_p.E577A|RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000520861.1_Missense_Mutation_p.E252A			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	577					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										GAGAAGGAGGAGGCGGCCAAG	0.532													A|||	11	0.00219649	0.0045	0.0	5008	,	,		17062	0.003		0.0	False		,,,				2504	0.002				p.E577A		Atlas-SNP	.											.	KIAA1967	72	.	0			c.A1730C						PASS	.	A	ALA/GLU	14,4392	22.3+/-47.3	0,14,2189	91.0	87.0	88.0		1730	4.2	1.0	8	dbSNP_134	88	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KIAA1967	NM_021174.5	107	0,15,6488	CC,CA,AA		0.0116,0.3177,0.1153	probably-damaging	577/924	22473646	15,12991	2203	4300	6503	SO:0001583	missense	57805	exon14			AGGAGGAGGCGGC	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1730A>C	8.37:g.22473646A>C	ENSP00000310670:p.Glu577Ala	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	44	0.37931	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	3	0.005244755244755245	0	0.0	A	15.25	2.777147	0.49786	0.003177	1.16E-4	ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000520861	T;T;T	0.34667	1.37;1.37;1.35	5.41	4.24	0.50183	.	0.332894	0.27991	N	0.017029	T	0.16557	0.0398	N	0.19112	0.55	0.37034	D	0.896847	B;B	0.14805	0.011;0.007	B;B	0.16722	0.016;0.004	T	0.09840	-1.0656	10	0.23302	T	0.38	-22.2627	10.6868	0.45848	0.8393:0.1607:0.0:0.0	.	252;577	G3V119;Q8N163	.;K1967_HUMAN	A	577;577;252	ENSP00000310670:E577A;ENSP00000373930:E577A;ENSP00000429773:E252A	ENSP00000310670:E577A	E	+	2	0	KIAA1967	22529591	1.000000	0.71417	0.972000	0.41901	0.846000	0.48090	4.106000	0.57804	1.041000	0.40125	0.460000	0.39030	GAG	A|0.998;C|0.002	0.002	strong		0.532	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
GBE1	2632	hgsc.bcm.edu	37	3	81586149	81586149	+	Silent	SNP	G	G	A	rs2229520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:81586149G>A	ENST00000429644.2	-	13	2359	c.1716C>T	c.(1714-1716)gaC>gaT	p.D572D	GBE1_ENST00000489715.1_Silent_p.D531D	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	572					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		GAAGAAGGTCGTCGTCAGTTA	0.413									Glycogen Storage Disease, type IV				A|||	77	0.0153754	0.0552	0.0058	5008	,	,		16494	0.0		0.0	False		,,,				2504	0.0				p.D572D		Atlas-SNP	.											.	GBE1	111	.	0			c.C1716T						PASS	.	A		195,3489		3,189,1650	114.0	110.0	111.0		1716	0.1	1.0	3	dbSNP_98	111	2,8168		0,2,4083	no	coding-synonymous	GBE1	NM_000158.3		3,191,5733	AA,AG,GG		0.0245,5.2932,1.6619		572/703	81586149	197,11657	1842	4085	5927	SO:0001819	synonymous_variant	2632	exon13	Familial Cancer Database	Andersen Disease, Brancher deficiency	AAGGTCGTCGTCA		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"""glycogen branching enzyme"", ""Andersen disease"", ""glycogen storage disease type IV"""	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.1716C>T	3.37:g.81586149G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	127	49	0.385827	NM_000158	B3KWV3|Q96EN0	Silent	SNP	ENST00000429644.2	37	CCDS54612.1																																																																																			G|0.987;A|0.013	0.013	strong		0.413	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		
TRIP6	7205	hgsc.bcm.edu	37	7	100466441	100466441	+	Missense_Mutation	SNP	G	G	A	rs2075756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	156	0	0		WXS	Illumina HiSeq	Phase_I	160	93	0.58125	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	
IFT140	9742	hgsc.bcm.edu	37	16	1634225	1634225	+	Missense_Mutation	SNP	G	G	A	rs8060532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1634225G>A	ENST00000426508.2	-	11	1715	c.1352C>T	c.(1351-1353)gCc>gTc	p.A451V	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	451			A -> V (in dbSNP:rs8060532).		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)				CACCTTGGTGGCAAACACTCC	0.632													G|||	129	0.0257588	0.0961	0.0029	5008	,	,		17110	0.0		0.0	False		,,,				2504	0.0				p.A451V		Atlas-SNP	.											.	IFT140	128	.	0			c.C1352T						PASS	.	G	VAL/ALA	393,4005	194.0+/-219.0	19,355,1825	41.0	34.0	36.0		1352	1.4	0.6	16	dbSNP_116	36	2,8598	1.2+/-3.3	0,2,4298	yes	missense	IFT140	NM_014714.3	64	19,357,6123	AA,AG,GG		0.0233,8.9359,3.0389	benign	451/1463	1634225	395,12603	2199	4300	6499	SO:0001583	missense	9742	exon11			TTGGTGGCAAACA	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.1352C>T	16.37:g.1634225G>A	ENSP00000406012:p.Ala451Val	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	55	0.025183150183150184	54	0.10975609756097561	1	0.0027624309392265192	0	0.0	0	0.0	G	0.024	-1.389209	0.01185	0.089359	2.33E-4	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.58210	0.35	5.51	1.37	0.22104	.	0.719273	0.14508	N	0.315333	T	0.00754	0.0025	L	0.43923	1.385	0.26845	N	0.968287	B;B	0.18461	0.009;0.028	B;B	0.21360	0.007;0.034	T	0.08973	-1.0696	10	0.02654	T	1	.	8.7453	0.34583	0.3607:0.0:0.6392:0.0	rs8060532;rs8060532	451;176	Q96RY7;B4DR58	IF140_HUMAN;.	V	451	ENSP00000406012:A451V	ENSP00000380562:A451V	A	-	2	0	IFT140	1574226	1.000000	0.71417	0.621000	0.29145	0.082000	0.17680	4.038000	0.57318	0.105000	0.17753	-0.150000	0.13652	GCC	G|0.969;A|0.031	0.031	strong		0.632	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
PRPH2	5961	hgsc.bcm.edu	37	6	42689940	42689940	+	Missense_Mutation	SNP	G	G	A	rs61755770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42689940G>A	ENST00000230381.5	-	1	372	c.133C>T	c.(133-135)Ctc>Ttc	p.L45F		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	45			L -> F (in RP7; in combination with a null mutation of ROM1; dbSNP:rs61755770).		cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			CTCTTTCGGAGTTCAATCTTC	0.512													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		20575	0.0		0.0	False		,,,				2504	0.0				p.L45F		Atlas-SNP	.											.	PRPH2	47	.	0			c.C133T	GRCh37	CM951114	PRPH2	M	rs61755770	PASS	.	G	PHE/LEU	68,4338	61.7+/-98.7	0,68,2135	109.0	93.0	98.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	133	4.7	1.0	6	dbSNP_129	98	0,8600		0,0,4300	yes	missense	PRPH2	NM_000322.4	22	0,68,6435	AA,AG,GG		0.0,1.5433,0.5228	probably-damaging	45/347	42689940	68,12938	2203	4300	6503	SO:0001583	missense	5961	exon1			TTCGGAGTTCAAT		CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"""Tetraspanins"""	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"""retinal degeneration, slow (retinitis pigmentosa 7)"", ""retinal degeneration, slow"""	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.133C>T	6.37:g.42689940G>A	ENSP00000230381:p.Leu45Phe	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	121	68	0.561983	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	20.2	3.948475	0.73787	0.015433	0.0	ENSG00000112619	ENST00000230381	T	0.80393	-1.37	5.61	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.87845	0.6280	M	0.85859	2.78	0.58432	D	0.999991	D	0.60160	0.987	D	0.66497	0.944	D	0.87105	0.2181	10	0.40728	T	0.16	.	15.9296	0.79648	0.0:0.0:0.8645:0.1355	rs61755770	45	P23942	PRPH2_HUMAN	F	45	ENSP00000230381:L45F	ENSP00000230381:L45F	L	-	1	0	PRPH2	42797918	1.000000	0.71417	0.951000	0.38953	0.943000	0.58893	6.097000	0.71452	2.631000	0.89168	0.655000	0.94253	CTC	G|0.994;A|0.006	0.006	strong		0.512	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322	
S1PR5	53637	hgsc.bcm.edu	37	19	10625067	10625067	+	Silent	SNP	A	A	C	rs6511701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10625067A>C	ENST00000439028.3	-	2	746	c.621T>G	c.(619-621)gcT>gcG	p.A207A	S1PR5_ENST00000333430.4_Silent_p.A207A	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	207					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	GTGCACAGATAGCGGCCAGGA	0.692													C|||	4078	0.814297	0.7602	0.8386	5008	,	,		14935	0.7847		0.8022	False		,,,				2504	0.9131				p.A207A		Atlas-SNP	.											S1PR5,NS,carcinoma,0,1	S1PR5	33	1	0			c.T621G						PASS	.	C	,	3368,1028		1302,764,132	26.0	23.0	24.0		621,621	-2.1	0.3	19	dbSNP_116	24	6744,1850		2646,1452,199	no	coding-synonymous,coding-synonymous	S1PR5	NM_001166215.1,NM_030760.4	,	3948,2216,331	CC,CA,AA		21.5266,23.3849,22.1555	,	207/399,207/399	10625067	10112,2878	2198	4297	6495	SO:0001819	synonymous_variant	53637	exon2			ACAGATAGCGGCC	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	14299	protein-coding gene	gene with protein product		605146	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"""	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.621T>G	19.37:g.10625067A>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_030760	Q6NW11	Silent	SNP	ENST00000439028.3	37	CCDS12240.1																																																																																			A|0.222;C|0.778	0.778	strong		0.692	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760	
DCTN1	1639	hgsc.bcm.edu	37	2	74597937	74597937	+	Missense_Mutation	SNP	G	G	T	rs13420401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74597937G>T	ENST00000361874.3	-	10	1176	c.859C>A	c.(859-861)Ctg>Atg	p.L287M	DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000394003.3_Missense_Mutation_p.L280M|DCTN1_ENST00000409240.1_Missense_Mutation_p.L250M|DCTN1_ENST00000409438.1_Missense_Mutation_p.L153M|DCTN1_ENST00000409567.3_Missense_Mutation_p.L267M|DCTN1_ENST00000407639.2_Missense_Mutation_p.L153M|DCTN1_ENST00000409868.1_Missense_Mutation_p.L270M	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	287			L -> M (in dbSNP:rs13420401).		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						TTTGCCTCCAGCGCCTCCTTG	0.567													G|||	229	0.0457268	0.1649	0.0159	5008	,	,		21252	0.0		0.0	False		,,,				2504	0.0				p.L287M		Atlas-SNP	.											.	DCTN1	110	.	0			c.C859A						PASS	.	G	MET/LEU,MET/LEU,MET/LEU,MET/LEU,MET/LEU,MET/LEU	604,3802	264.1+/-265.8	38,528,1637	99.0	96.0	97.0		799,457,748,838,859,457	3.5	0.7	2	dbSNP_121	97	6,8594	3.7+/-12.6	0,6,4294	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	15,15,15,15,15,15	38,534,5931	TT,TG,GG		0.0698,13.7086,4.6901	benign,benign,benign,benign,benign,benign	267/1254,153/1140,250/1237,280/1272,287/1279,153/1145	74597937	610,12396	2203	4300	6503	SO:0001583	missense	1639	exon10			CCTCCAGCGCCTC		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.859C>A	2.37:g.74597937G>T	ENSP00000354791:p.Leu287Met	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	138	73	0.528986	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	85	0.03891941391941392	79	0.16056910569105692	6	0.016574585635359115	0	0.0	0	0.0	G	10.70	1.423353	0.25639	0.137086	6.98E-4	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.79845	-0.86;-1.08;-0.79;-0.79;-1.31;-1.04;-1.09	5.66	3.48	0.39840	.	0.000000	0.33792	N	0.004541	T	0.00784	0.0026	M	0.75264	2.295	0.30403	P	0.7798160000000001	B;B;B;B;P;B	0.35575	0.204;0.245;0.034;0.129;0.51;0.057	B;B;B;B;B;B	0.32624	0.049;0.049;0.007;0.043;0.149;0.015	T	0.37798	-0.9690	9	0.33940	T	0.23	-5.9903	8.5044	0.33179	0.0832:0.0:0.6425:0.2743	rs13420401;rs58339203	267;250;287;280;153;153	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	M	287;280;270;153;153;250;270;267	ENSP00000354791:L287M;ENSP00000377571:L280M;ENSP00000384844:L153M;ENSP00000387270:L153M;ENSP00000386406:L250M;ENSP00000387327:L270M;ENSP00000386843:L267M	ENSP00000354791:L287M	L	-	1	2	DCTN1	74451445	0.680000	0.27605	0.708000	0.30435	0.947000	0.59692	0.896000	0.28377	1.345000	0.45676	0.655000	0.94253	CTG	G|0.954;T|0.046	0.046	strong		0.567	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
PPP1R26	9858	hgsc.bcm.edu	37	9	138378308	138378308	+	Missense_Mutation	SNP	G	G	A	rs35142799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138378308G>A	ENST00000356818.2	+	4	2501	c.1952G>A	c.(1951-1953)gGc>gAc	p.G651D	PPP1R26_ENST00000605660.1_Missense_Mutation_p.G651D|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000401470.3_Missense_Mutation_p.G651D|PPP1R26_ENST00000605286.1_Missense_Mutation_p.G651D|PPP1R26_ENST00000604351.1_Missense_Mutation_p.G651D	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	651					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGAGGGGAGGGCACCGCCAGG	0.652													G|||	36	0.0071885	0.0272	0.0	5008	,	,		17736	0.0		0.0	False		,,,				2504	0.0				p.G651D		Atlas-SNP	.											.	.	.	.	0			c.G1952A						PASS	.	G	ASP/GLY	100,4300	73.1+/-111.1	1,98,2101	29.0	33.0	31.0		1952	0.7	0.0	9	dbSNP_126	31	0,8600		0,0,4300	no	missense	KIAA0649	NM_014811.3	94	1,98,6401	AA,AG,GG		0.0,2.2727,0.7692	benign	651/1210	138378308	100,12900	2200	4300	6500	SO:0001583	missense	9858	exon4			GGGAGGGCACCGC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.1952G>A	9.37:g.138378308G>A	ENSP00000349274:p.Gly651Asp	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	147	107	0.727891	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	3.546	-0.092690	0.07053	0.022727	0.0	ENSG00000196422	ENST00000356818	T	0.20738	2.05	4.34	0.693	0.18056	.	0.864323	0.09973	N	0.732016	T	0.07143	0.0181	L	0.29908	0.895	0.09310	N	1	B	0.16396	0.017	B	0.12156	0.007	T	0.26189	-1.0110	10	0.52906	T	0.07	-15.8819	6.8421	0.23969	0.1852:0.6278:0.187:0.0	rs35142799	651	Q5T8A7	PPR26_HUMAN	D	651	ENSP00000349274:G651D	ENSP00000349274:G651D	G	+	2	0	KIAA0649	137518129	0.060000	0.20803	0.001000	0.08648	0.006000	0.05464	1.152000	0.31663	0.249000	0.21456	0.561000	0.74099	GGC	G|0.994;A|0.006	0.006	strong		0.652	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
DNAJC13	23317	hgsc.bcm.edu	37	3	132218075	132218075	+	Missense_Mutation	SNP	C	C	T	rs61748102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:132218075C>T	ENST00000260818.6	+	37	4510	c.4262C>T	c.(4261-4263)gCg>gTg	p.A1421V		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1421					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						TTGTTGCCTGCGGCTACAGAG	0.438													C|||	64	0.0127796	0.0242	0.0101	5008	,	,		18844	0.0		0.0209	False		,,,				2504	0.0041				p.A1421V		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C4262T						PASS	.	C	VAL/ALA	112,4294	88.7+/-127.4	0,112,2091	93.0	93.0	93.0		4262	5.4	1.0	3	dbSNP_129	93	162,8438	76.0+/-138.7	1,160,4139	yes	missense	DNAJC13	NM_015268.3	64	1,272,6230	TT,TC,CC		1.8837,2.542,2.1067	probably-damaging	1421/2244	132218075	274,12732	2203	4300	6503	SO:0001583	missense	23317	exon37			TGCCTGCGGCTAC	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.4262C>T	3.37:g.132218075C>T	ENSP00000260818:p.Ala1421Val	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	148	66	0.445946	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	36	0.016483516483516484	13	0.026422764227642278	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	34	5.360586	0.95877	0.02542	0.018837	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.52754	0.65	5.42	5.42	0.78866	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.44030	0.1274	M	0.81802	2.56	0.80722	D	1	D	0.71674	0.998	P	0.56648	0.803	T	0.64698	-0.6346	10	0.72032	D	0.01	.	19.5793	0.95459	0.0:1.0:0.0:0.0	rs61748102	1421	O75165	DJC13_HUMAN	V	1421;68	ENSP00000260818:A1421V	ENSP00000260818:A1421V	A	+	2	0	DNAJC13	133700765	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	7.535000	0.82014	2.706000	0.92434	0.555000	0.69702	GCG	C|0.981;T|0.019	0.019	strong		0.438	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
PHIP	55023	hgsc.bcm.edu	37	6	79700648	79700648	+	Silent	SNP	C	C	T	rs149171291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:79700648C>T	ENST00000275034.4	-	20	2423	c.2256G>A	c.(2254-2256)agG>agA	p.R752R		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	752					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)		TCTCTTCTGACCTGTAAGTCT	0.313													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		17543	0.0		0.0	False		,,,				2504	0.0				p.R752R		Atlas-SNP	.											.	PHIP	177	.	0			c.G2256A						PASS	.	C		29,4377	35.2+/-66.4	0,29,2174	110.0	110.0	110.0		2256	-0.4	1.0	6	dbSNP_134	110	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PHIP	NM_017934.5		0,30,6472	TT,TC,CC		0.0116,0.6582,0.2307		752/1822	79700648	30,12974	2203	4299	6502	SO:0001819	synonymous_variant	55023	exon20			TTCTGACCTGTAA	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.2256G>A	6.37:g.79700648C>T		Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	220	101	0.459091	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			C|0.997;T|0.003	0.003	strong		0.313	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
MUC5B	727897	hgsc.bcm.edu	37	11	1252708	1252708	+	Silent	SNP	G	G	C	rs2735709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1252708G>C	ENST00000529681.1	+	14	1654	c.1596G>C	c.(1594-1596)ctG>ctC	p.L532L	MUC5B_ENST00000447027.1_Silent_p.L535L	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	532	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)		AGACAGGCCTGGGGCTGCAGC	0.667													c|||	2852	0.569489	0.5726	0.611	5008	,	,		15576	0.6548		0.498	False		,,,				2504	0.5215				p.L532L		Atlas-SNP	.											.	MUC5B	473	.	0			c.G1596C						PASS	.	C		2349,1667		712,925,371	22.0	25.0	24.0		1596	-5.9	0.0	11	dbSNP_100	24	4204,4172		1100,2004,1084	no	coding-synonymous	MUC5B	NM_002458.2		1812,2929,1455	CC,CG,GG		49.809,41.509,47.1191		532/5763	1252708	6553,5839	2008	4188	6196	SO:0001819	synonymous_variant	727897	exon14			AGGCCTGGGGCTG	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.1596G>C	11.37:g.1252708G>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.443;C|0.557	0.557	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
NLRC3	197358	hgsc.bcm.edu	37	16	3613239	3613239	+	RNA	SNP	C	C	T	rs8057436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3613239C>T	ENST00000301749.7	-	0	2104				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CAGTGCAACACGTTGATGGCC	0.706													C|||	189	0.0377396	0.1331	0.0144	5008	,	,		16561	0.0		0.001	False		,,,				2504	0.002				p.V567M		Atlas-SNP	.											.	NLRC3	103	.	0			c.G1699A						PASS	.	C	MET/VAL	433,3803		13,407,1698	12.0	15.0	14.0		1699	-7.5	0.0	16	dbSNP_116	14	27,8409		0,27,4191	yes	missense	NLRC3	NM_178844.2	21	13,434,5889	TT,TC,CC		0.3201,10.2219,3.6301	benign	567/1066	3613239	460,12212	2118	4218	6336			197358	exon5			GCAACACGTTGAT	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613239C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	32	20	0.625	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		69	0.03159340659340659	61	0.12398373983739837	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	2.395	-0.338967	0.05243	0.102219	0.003201	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0	5.1	-7.47	0.01365	.	0.710025	0.13675	N	0.370619	T	0.03011	0.0089	.	.	.	0.09310	N	1	B	0.23650	0.089	B	0.20577	0.03	T	0.23691	-1.0181	9	0.46703	T	0.11	.	11.4138	0.49941	0.0:0.2375:0.0978:0.6647	rs8057436;rs8057436	614	C9JLH9	.	M	567;567;567;614;549	ENSP00000301749:V567M;ENSP00000352039:V567M;ENSP00000414415:V614M;ENSP00000323897:V549M	ENSP00000301749:V567M	V	-	1	0	NLRC3	3553240	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.154000	0.00580	-1.430000	0.01985	-0.812000	0.03155	GTG	C|0.969;T|0.031	0.031	strong		0.706	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
TOMM70A	9868	hgsc.bcm.edu	37	3	100084432	100084432	+	Silent	SNP	G	G	A	rs277644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:100084432G>A	ENST00000284320.5	-	12	2251	c.1803C>T	c.(1801-1803)taC>taT	p.Y601Y		NM_014820.4	NP_055635.3	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70 homolog A (S. cerevisiae)	601					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			endometrium(11)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	32						GTTTTAATCCGTATTTCTTTG	0.438													G|||	1266	0.252796	0.3775	0.1988	5008	,	,		19620	0.5129		0.0398	False		,,,				2504	0.0736				p.Y601Y		Atlas-SNP	.											.	TOMM70A	65	.	0			c.C1803T						PASS	.	G		1359,3047	451.6+/-349.7	202,955,1046	184.0	180.0	182.0		1803	-7.2	0.4	3	dbSNP_79	182	417,8183	129.7+/-187.7	14,389,3897	no	coding-synonymous	TOMM70A	NM_014820.3		216,1344,4943	AA,AG,GG		4.8488,30.8443,13.6552		601/609	100084432	1776,11230	2203	4300	6503	SO:0001819	synonymous_variant	9868	exon12			TAATCCGTATTTC	AB018262	CCDS33807.1	3q12.2	2013-01-10	2006-04-04		ENSG00000154174	ENSG00000154174		"""Tetratricopeptide (TTC) repeat domain containing"""	11985	protein-coding gene	gene with protein product		606081	"""translocase of outer mitochondrial membrane 70 (yeast) homolog A"", ""translocase of outer mitochondrial membrane 70 homolog A (yeast)"""			10582581	Standard	NM_014820		Approved	KIAA0719	uc003dtw.3	O94826	OTTHUMG00000159065	ENST00000284320.5:c.1803C>T	3.37:g.100084432G>A		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	229	105	0.458515	NM_014820	D3DN48	Silent	SNP	ENST00000284320.5	37	CCDS33807.1																																																																																			G|0.834;A|0.166	0.166	strong		0.438	TOMM70A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353141.2		
VWA8	23078	hgsc.bcm.edu	37	13	42465713	42465713	+	Missense_Mutation	SNP	C	C	T	rs9562362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:42465713C>T	ENST00000379310.3	-	5	562	c.494G>A	c.(493-495)cGt>cAt	p.R165H	VWA8_ENST00000281496.6_Missense_Mutation_p.R165H	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	165			R -> H (in dbSNP:rs9562362).			extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										TGTGGCTGCACGAACTGCACA	0.398													C|||	1012	0.202077	0.0151	0.2954	5008	,	,		20968	0.1786		0.3171	False		,,,				2504	0.2945				p.R165H		Atlas-SNP	.											.	.	.	.	0			c.G494A						PASS	.	C	HIS/ARG,HIS/ARG	262,4144	147.3+/-181.8	4,254,1945	77.0	69.0	72.0		494,494	5.7	1.0	13	dbSNP_119	72	2737,5863	436.9+/-358.5	439,1859,2002	yes	missense,missense	KIAA0564	NM_001009814.1,NM_015058.1	29,29	443,2113,3947	TT,TC,CC		31.8256,5.9464,23.0586	probably-damaging,probably-damaging	165/1040,165/1906	42465713	2999,10007	2203	4300	6503	SO:0001583	missense	23078	exon5			GCTGCACGAACTG	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"""KIAA0564"""	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.494G>A	13.37:g.42465713C>T	ENSP00000368612:p.Arg165His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	488	0.22344322344322345	10	0.02032520325203252	114	0.3149171270718232	115	0.20104895104895104	249	0.32849604221635886	C	36	5.662997	0.96745	0.059464	0.318256	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496;ENST00000398857	T;T	0.59083	0.29;0.29	5.71	5.71	0.89125	ATPase, dynein-related, AAA domain (1);	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	M	0.92077	3.27	0.09310	P	0.999999999480994	D	0.61080	0.989	P	0.58077	0.832	T	0.00756	-1.1579	9	0.87932	D	0	.	20.2245	0.98337	0.0:1.0:0.0:0.0	rs9562362;rs17534916;rs52826154;rs60454473;rs9562362	165	A3KMH1	K0564_HUMAN	H	69;165;165;165	ENSP00000368612:R165H;ENSP00000281496:R165H	ENSP00000251030:R69H	R	-	2	0	KIAA0564	41363713	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.536000	0.82023	2.861000	0.98227	0.650000	0.86243	CGT	C|0.775;T|0.225	0.225	strong		0.398	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
DCST2	127579	hgsc.bcm.edu	37	1	155006091	155006091	+	Silent	SNP	A	A	G	rs10908453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155006091A>G	ENST00000368424.3	-	1	145	c.87T>C	c.(85-87)ggT>ggC	p.G29G	DCST1_ENST00000295542.1_5'Flank|DCST1_ENST00000368419.2_5'Flank|DCST1_ENST00000392480.1_5'Flank|DCST1_ENST00000423025.2_5'Flank|DCST2_ENST00000295536.5_Silent_p.G29G	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	29						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	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)			CCAGGGTAAAACCTCCCACGC	0.612													G|||	2999	0.598842	0.5416	0.6052	5008	,	,		18636	0.881		0.3608	False		,,,				2504	0.6258				p.G29G		Atlas-SNP	.											.	DCST2	80	.	0			c.T87C						PASS	.	G		2342,2064	566.5+/-381.9	611,1120,472	74.0	71.0	72.0		87	1.6	0.0	1	dbSNP_120	72	2997,5603	662.2+/-401.9	521,1955,1824	no	coding-synonymous	DCST2	NM_144622.2		1132,3075,2296	GG,GA,AA		34.8488,46.8452,41.0503		29/774	155006091	5339,7667	2203	4300	6503	SO:0001819	synonymous_variant	127579	exon1			GGTAAAACCTCCC	AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.87T>C	1.37:g.155006091A>G		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_144622	Q2M2R2|Q8N810|Q96M03	Silent	SNP	ENST00000368424.3	37	CCDS1082.2																																																																																			A|0.513;G|0.487	0.487	strong		0.612	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622	
EXOC5	10640	hgsc.bcm.edu	37	14	57676330	57676330	+	Silent	SNP	G	G	T	rs1804820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:57676330G>T	ENST00000413566.2	-	17	2252	c.1893C>A	c.(1891-1893)gcC>gcA	p.A631A	EXOC5_ENST00000340918.7_Silent_p.A566A	NM_006544.3	NP_006535.1	O00471	EXOC5_HUMAN	exocyst complex component 5	631					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|vesicle docking (GO:0048278)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(3)|endometrium(1)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	22						CATCACAAATGGCCAACATGC	0.403													T|||	1396	0.278754	0.8442	0.0994	5008	,	,		14307	0.0883		0.0577	False		,,,				2504	0.0654				p.A631A		Atlas-SNP	.											.	EXOC5	45	.	0			c.C1893A						PASS	.	T		2565,1267		884,797,235	115.0	104.0	108.0		1893	2.8	1.0	14	dbSNP_89	108	476,7784		13,450,3667	no	coding-synonymous	EXOC5	NM_006544.3		897,1247,3902	TT,TG,GG		5.7627,33.0637,25.1489		631/709	57676330	3041,9051	1916	4130	6046	SO:0001819	synonymous_variant	10640	exon17			ACAAATGGCCAAC	U85946	CCDS45111.1	14q22.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000070367	ENSG00000070367			10696	protein-coding gene	gene with protein product		604469	"""SEC10 (S. cerevisiae)-like 1"", ""SEC10-like 1 (S. cerevisiae)"""	SEC10L1		9119050	Standard	XM_005267272		Approved	SEC10, SEC10P	uc001xct.3	O00471	OTTHUMG00000171309	ENST00000413566.2:c.1893C>A	14.37:g.57676330G>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	163	82	0.503067	NM_006544	B2R6C5	Silent	SNP	ENST00000413566.2	37	CCDS45111.1																																																																																			G|0.765;T|0.235	0.235	strong		0.403	EXOC5-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412905.1	NM_006544	
PKD1L2	114780	hgsc.bcm.edu	37	16	81232426	81232426	+	RNA	SNP	A	A	C	rs9934856	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81232426A>C	ENST00000525539.1	-	0	1383				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						CCAAGCTCCAAATGGTCAGAA	0.557													A|||	101	0.0201677	0.0734	0.0058	5008	,	,		20314	0.0		0.0	False		,,,				2504	0.0				p.L462V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T1384G						PASS	.	A	VAL/LEU,VAL/LEU	224,3784		6,212,1786	128.0	131.0	130.0		1384,1384	-7.3	0.0	16	dbSNP_119	130	0,8340		0,0,4170	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	32,32	6,212,5956	CC,CA,AA		0.0,5.5888,1.8141	benign,benign	462/992,462/2460	81232426	224,12124	2004	4170	6174			114780	exon7			GCTCCAAATGGTC	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.81232426A>C		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	203	111	0.546798	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	A	2.456	-0.325238	0.05350	0.055888	0.0	ENSG00000166473	ENST00000337114	T	0.01304	5.03	4.77	-7.3	0.01446	Egg jelly receptor, REJ-like (1);	0.379301	0.24776	N	0.035687	T	0.00144	0.0004	.	.	.	0.09310	N	1	B;B	0.15473	0.013;0.001	B;B	0.19666	0.026;0.002	T	0.44498	-0.9324	9	0.23302	T	0.38	-1.4298	11.0124	0.47669	0.1809:0.5054:0.3137:0.0	rs9934856;rs52821211;rs56414767;rs9934856	462;462	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	V	462	ENSP00000337397:L462V	ENSP00000337397:L462V	L	-	1	2	PKD1L2	79789927	0.000000	0.05858	0.001000	0.08648	0.041000	0.13682	-0.318000	0.08050	-1.278000	0.02408	-1.249000	0.01516	TTG	A|0.984;C|0.016;G|0.000	0.016	strong		0.557	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
DSG1	1828	hgsc.bcm.edu	37	18	28919794	28919794	+	Missense_Mutation	SNP	C	C	A	rs8091117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28919794C>A	ENST00000257192.4	+	11	1705	c.1493C>A	c.(1492-1494)aCt>aAt	p.T498N		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	498			T -> N (in dbSNP:rs8091117).		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)			GAGCCGAACACTAAAATTACT	0.348													C|||	1119	0.223442	0.5113	0.1182	5008	,	,		16069	0.0645		0.0905	False		,,,				2504	0.2096				p.T498N		Atlas-SNP	.											.	DSG1	176	.	0			c.C1493A						PASS	.	C	ASN/THR	1872,2534	540.7+/-375.6	391,1090,722	105.0	105.0	105.0		1493	-1.9	0.0	18	dbSNP_116	105	624,7976	162.3+/-215.1	30,564,3706	yes	missense	DSG1	NM_001942.2	65	421,1654,4428	AA,AC,CC		7.2558,42.4875,19.1911	benign	498/1050	28919794	2496,10510	2203	4300	6503	SO:0001583	missense	1828	exon11			CGAACACTAAAAT	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.1493C>A	18.37:g.28919794C>A	ENSP00000257192:p.Thr498Asn	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	383	0.17536630036630035	247	0.5020325203252033	44	0.12154696132596685	34	0.05944055944055944	58	0.07651715039577836	C	1.831	-0.469873	0.04445	0.424875	0.072558	ENSG00000134760	ENST00000257192	T	0.57595	0.39	3.29	-1.94	0.07571	Cadherin (1);	0.894418	0.09631	N	0.776187	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	0.48186	-0.9057	9	0.18276	T	0.48	.	7.7511	0.28898	0.1709:0.3254:0.5036:0.0	rs8091117;rs56989750;rs8091117	498	Q02413	DSG1_HUMAN	N	498	ENSP00000257192:T498N	ENSP00000257192:T498N	T	+	2	0	DSG1	27173792	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.296000	0.08287	-0.473000	0.06871	-0.233000	0.12211	ACT	C|0.806;A|0.194	0.194	strong		0.348	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
OR1F1	4992	hgsc.bcm.edu	37	16	3254622	3254622	+	Missense_Mutation	SNP	G	G	A	rs8045183	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3254622G>A	ENST00000304646.2	+	1	376	c.376G>A	c.(376-378)Gtg>Atg	p.V126M	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	126			V -> M (in dbSNP:rs8045183).		signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(2)|lung(7)	11						CTTTGTCGCCGTGTGCCACCC	0.502													g|||	159	0.0317492	0.115	0.0086	5008	,	,		24960	0.0		0.001	False		,,,				2504	0.0				p.V126M		Atlas-SNP	.											.	OR1F1	36	.	0			c.G376A						PASS	.	A	MET/VAL	402,3992	199.4+/-223.0	11,380,1806	220.0	175.0	190.0		376	-6.7	0.0	16	dbSNP_116	190	7,8593	5.7+/-21.5	0,7,4293	no	missense	OR1F1	NM_012360.1	21	11,387,6099	AA,AG,GG		0.0814,9.1488,3.1476	possibly-damaging	126/313	3254622	409,12585	2197	4300	6497	SO:0001583	missense	4992	exon1			GTCGCCGTGTGCC	Y14442	CCDS10496.1	16p13.3	2012-08-09			ENSG00000168124	ENSG00000168124		"""GPCR / Class A : Olfactory receptors"""	8194	protein-coding gene	gene with protein product		603232		OR1F4, OR1F6, OR1F7, OR1F8, OR1F9, OR1F5, OR1F10, OR1F13P		9288094, 9500546	Standard	NM_012360		Approved	Olfmf, OR16-36, OR16-37, OR16-88, OR16-89, OR16-90, OLFMF, OR3-145	uc010uwu.2	O43749	OTTHUMG00000133153	ENST00000304646.2:c.376G>A	16.37:g.3254622G>A	ENSP00000305424:p.Val126Met	Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	250	126	0.504	NM_012360	O15246|Q6IFL5	Missense_Mutation	SNP	ENST00000304646.2	37	CCDS10496.1	68	0.031135531135531136	65	0.13211382113821138	3	0.008287292817679558	0	0.0	0	0.0	G	13.94	2.388405	0.42308	0.091488	8.14E-4	ENSG00000168124	ENST00000304646	T	0.49432	0.78	5.27	-6.68	0.01778	GPCR, rhodopsin-like superfamily (1);	0.893841	0.09289	N	0.822529	T	0.00695	0.0023	M	0.72118	2.19	0.80722	P	0.0	D	0.55800	0.973	P	0.51135	0.66	T	0.48714	-0.9011	9	0.87932	D	0	.	10.8187	0.46591	0.7188:0.1085:0.1727:0.0	rs8045183;rs52799876;rs8045183	126	O43749	OR1F1_HUMAN	M	126	ENSP00000305424:V126M	ENSP00000305424:V126M	V	+	1	0	OR1F1	3194623	0.418000	0.25440	0.000000	0.03702	0.630000	0.37929	0.957000	0.29215	-1.050000	0.03230	0.393000	0.25936	GTG	G|0.966;A|0.034	0.034	strong		0.502	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1		
NQO2	4835	hgsc.bcm.edu	37	6	3010298	3010298	+	Missense_Mutation	SNP	A	A	G	rs28383623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:3010298A>G	ENST00000338130.2	+	6	759	c.47A>G	c.(46-48)aAg>aGg	p.K16R	NQO2_ENST00000606474.1_3'UTR|NQO2_ENST00000380455.4_Missense_Mutation_p.K16R|NQO2_ENST00000380441.1_Missense_Mutation_p.K16R|NQO2_ENST00000380430.1_Missense_Mutation_p.K16R|NQO2_ENST00000380454.4_Missense_Mutation_p.K16R			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	16			K -> R (in dbSNP:rs28383623). {ECO:0000269|Ref.4}.		memory (GO:0007613)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	dihydronicotinamide riboside quinone reductase activity (GO:0001512)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADPH dehydrogenase (quinone) activity (GO:0008753)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Dabigatran etexilate(DB06695)|Flavin adenine dinucleotide(DB03147)|Melatonin(DB01065)|Menadione(DB00170)|Primaquine(DB01087)	CAGGAACCCAAGTCTTTCAAC	0.443													G|||	153	0.0305511	0.0582	0.0288	5008	,	,		18599	0.002		0.0497	False		,,,				2504	0.0041				p.K16R		Atlas-SNP	.											.	NQO2	21	.	0			c.A47G						PASS	.	G	ARG/LYS	237,4169	804.9+/-415.8	4,229,1970	117.0	103.0	108.0		47	-7.5	0.0	6	dbSNP_125	108	324,8276	804.9+/-407.3	11,302,3987	yes	missense	NQO2	NM_000904.3	26	15,531,5957	GG,GA,AA		3.7674,5.379,4.3134	benign	16/232	3010298	561,12445	2203	4300	6503	SO:0001583	missense	4835	exon3			AACCCAAGTCTTT	U07736	CCDS4481.1, CCDS75388.1	6p25.2	2012-09-20	2001-11-30	2001-12-07	ENSG00000124588	ENSG00000124588	1.6.5.2		7856	protein-coding gene	gene with protein product		160998	"""NAD(P)H menadione oxidoreductase 2, dioxin-inducible"""	NMOR2		1691923	Standard	XM_005249152		Approved	QR2, DHQV, DIA6	uc003mus.2	P16083	OTTHUMG00000014130	ENST00000338130.2:c.47A>G	6.37:g.3010298A>G	ENSP00000337773:p.Lys16Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	158	77	0.487342	NM_000904	B2R492|Q5TD04	Missense_Mutation	SNP	ENST00000338130.2	37	CCDS4481.1	80	0.03663003663003663	36	0.07317073170731707	9	0.024861878453038673	0	0.0	35	0.04617414248021108	G	3.877	-0.026748	0.07589	0.05379	0.037674	ENSG00000124588	ENST00000426637;ENST00000380472;ENST00000538898;ENST00000397717;ENST00000338130;ENST00000380441;ENST00000380455;ENST00000380454;ENST00000380430	T;T;T;T;T;T;T;T	0.10005	3.12;2.92;2.92;3.12;3.12;3.12;3.12;3.12	5.63	-7.48	0.01360	Flavodoxin-like fold (1);	0.609607	0.18974	N	0.126042	T	0.00815	0.0027	N	0.05510	-0.035	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.36890	-0.9729	10	0.02654	T	1	-6.783	10.0735	0.42347	0.604:0.2762:0.1197:0.0	rs28383623;rs28383623	16;63	P16083;Q59EN2	NQO2_HUMAN;.	R	16;16;63;16;16;16;16;16;16	ENSP00000406951:K16R;ENSP00000369839:K16R;ENSP00000380829:K16R;ENSP00000337773:K16R;ENSP00000369806:K16R;ENSP00000369822:K16R;ENSP00000369821:K16R;ENSP00000369795:K16R	ENSP00000337773:K16R	K	+	2	0	NQO2	2955297	0.000000	0.05858	0.010000	0.14722	0.014000	0.08584	-1.029000	0.03585	-1.518000	0.01778	-0.213000	0.12676	AAG	A|0.960;G|0.040	0.040	strong		0.443	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1		
TSKU	25987	hgsc.bcm.edu	37	11	76507403	76507403	+	Missense_Mutation	SNP	G	G	A	rs11236938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:76507403G>A	ENST00000527881.1	+	2	1769	c.743G>A	c.(742-744)aGt>aAt	p.S248N	TSKU_ENST00000333090.4_Missense_Mutation_p.S248N			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	248			S -> N (in dbSNP:rs11236938).		anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					CTGGCGCCCAGTGGCTTCCGT	0.647													A|||	423	0.0844649	0.2201	0.0605	5008	,	,		17127	0.0556		0.0278	False		,,,				2504	0.0061				p.S248N		Atlas-SNP	.											.	TSKU	26	.	0			c.G743A						PASS	.	A	ASN/SER	828,3562		90,648,1457	51.0	57.0	55.0		743	2.1	0.0	11	dbSNP_120	55	234,8338		2,230,4054	yes	missense	TSKU	NM_015516.3	46	92,878,5511	AA,AG,GG		2.7298,18.861,8.1932	benign	248/354	76507403	1062,11900	2195	4286	6481	SO:0001583	missense	25987	exon2			CGCCCAGTGGCTT	AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"""leucine rich repeat containing 54"", ""tsukushin"", ""tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"""	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.743G>A	11.37:g.76507403G>A	ENSP00000434847:p.Ser248Asn	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	114	67	0.587719	NM_015516	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Missense_Mutation	SNP	ENST00000527881.1	37	CCDS8246.1	197	0.0902014652014652	109	0.22154471544715448	23	0.06353591160220995	40	0.06993006993006994	25	0.032981530343007916	A	2.555	-0.303289	0.05495	0.18861	0.027298	ENSG00000182704	ENST00000333090;ENST00000439807;ENST00000527881	T;T	0.56444	0.46;0.46	4.64	2.14	0.27477	.	0.967627	0.08640	N	0.915639	T	0.00039	0.0001	N	0.21324	0.655	0.80722	P	0.0	B	0.09022	0.002	B	0.17979	0.02	T	0.19063	-1.0317	9	0.23302	T	0.38	1.1007	4.8846	0.13697	0.6969:0.0:0.1656:0.1376	rs11236938;rs60587105;rs11236938	248	Q8WUA8	TSK_HUMAN	N	248;216;248	ENSP00000332668:S248N;ENSP00000434847:S248N	ENSP00000332668:S248N	S	+	2	0	TSKU	76185051	0.002000	0.14202	0.003000	0.11579	0.084000	0.17831	1.788000	0.38714	0.263000	0.21812	-0.361000	0.07541	AGT	G|0.913;A|0.087	0.087	strong		0.647	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516	
GAB4	128954	hgsc.bcm.edu	37	22	17447237	17447237	+	Silent	SNP	C	C	G	rs115898475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17447237C>G	ENST00000400588.1	-	6	1148	c.1041G>C	c.(1039-1041)gtG>gtC	p.V347V	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	347										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)				CTGACAGGCCCACAAGCGTTC	0.527													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		21894	0.0		0.0	False		,,,				2504	0.0				p.V347V		Atlas-SNP	.											.	GAB4	95	.	0			c.G1041C						PASS	.	C		72,3902		0,72,1915	26.0	28.0	28.0		1041	1.7	0.2	22	dbSNP_132	28	0,8384		0,0,4192	no	coding-synonymous	GAB4	NM_001037814.1		0,72,6107	GG,GC,CC		0.0,1.8118,0.5826		347/575	17447237	72,12286	1987	4192	6179	SO:0001819	synonymous_variant	128954	exon6			CAGGCCCACAAGC	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.1041G>C	22.37:g.17447237C>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			C|0.994;G|0.006	0.006	strong		0.527	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
TICAM2	353376	hgsc.bcm.edu	37	5	114916763	114916763	+	Missense_Mutation	SNP	C	C	T	rs113049216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:114916763C>T	ENST00000427199.2	-	2	632	c.191G>A	c.(190-192)aGc>aAc	p.S64N	TICAM2_ENST00000513729.1_5'Flank|TMED7-TICAM2_ENST00000333314.3_3'UTR|TICAM2_ENST00000408996.4_Missense_Mutation_p.S233N|TMED7-TICAM2_ENST00000282382.4_Missense_Mutation_p.S233N	NM_021649.6	NP_067681.1	Q86XR7	TCAM2_HUMAN	toll-like receptor adaptor molecule 2	64					cellular response to lipopolysaccharide (GO:0071222)|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 chemokine (C-C motif) ligand 5 production (GO:0071650)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18-mediated signaling pathway (GO:2000494)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|response to interleukin-12 (GO:0070671)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			cervix(1)|kidney(1)|lung(2)|soft_tissue(1)	5		all_cancers(142;0.0223)|all_epithelial(76;0.000869)|Prostate(80;0.0115)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;4.38e-07)|Epithelial(69;1.62e-06)|all cancers(49;6.93e-05)		CTCTTCCACGCTCTGAGCTCC	0.463													C|||	56	0.0111821	0.0408	0.0014	5008	,	,		18559	0.0		0.001	False		,,,				2504	0.0				p.S233N		Atlas-SNP	.											.	.	.	.	0			c.G698A						PASS	.	C	ASN/SER,,ASN/SER	167,4237	111.6+/-149.8	2,163,2037	289.0	294.0	293.0		698,,191	-0.3	0.0	5	dbSNP_132	293	0,8600		0,0,4300	yes	missense,utr-3,missense	TICAM2,TMED7-TICAM2	NM_001164468.2,NM_001164469.2,NM_021649.6	46,,46	2,163,6337	TT,TC,CC		0.0,3.792,1.2842	,,	233/405,,64/236	114916763	167,12837	2202	4300	6502	SO:0001583	missense	100302736	exon4			TCCACGCTCTGAG	AY232653	CCDS4119.1	5q22.3	2012-11-21			ENSG00000243414	ENSG00000243414			21354	protein-coding gene	gene with protein product		608321					Standard	NM_021649		Approved	TRAM, TICAM-2, TIRP		Q86XR7	OTTHUMG00000162905	ENST00000427199.2:c.191G>A	5.37:g.114916763C>T	ENSP00000415139:p.Ser64Asn	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	148	68	0.459459	NM_001164468	B3Y698|Q6JUT2	Missense_Mutation	SNP	ENST00000427199.2	37	CCDS4119.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	C	11.76	1.736040	0.30774	0.03792	0.0	ENSG00000243414;ENSG00000243414;ENSG00000251201	ENST00000408996;ENST00000427199;ENST00000282382	T;T	0.23348	1.91;1.91	5.14	-0.31	0.12765	.	1.924210	0.03117	N	0.163224	T	0.03739	0.0106	N	0.14661	0.345	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.14023	0.006;0.01	T	0.22277	-1.0221	10	0.21540	T	0.41	.	10.3083	0.43693	0.2337:0.2165:0.5498:0.0	.	233;64	Q6JUT2;Q86XR7	.;TCAM2_HUMAN	N	233;64;233	ENSP00000386341:S233N;ENSP00000282382:S233N	ENSP00000415139:S64N	S	-	2	0	TICAM2;TMED7-TICAM2	114944662	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.694000	0.01915	-0.079000	0.12707	0.585000	0.79938	AGC	C|0.989;T|0.011	0.011	strong		0.463	TICAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338755.1	NM_021649	
CDHR2	54825	hgsc.bcm.edu	37	5	175998246	175998246	+	Silent	SNP	T	T	C	rs17078320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:175998246T>C	ENST00000510636.1	+	6	622	c.348T>C	c.(346-348)gaT>gaC	p.D116D	CDHR2_ENST00000261944.5_Silent_p.D116D|CDHR2_ENST00000506348.1_Silent_p.D116D	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	116	Cadherin 1. {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						TTGTGGAAGATAGAAACGACA	0.512													C|||	1606	0.320687	0.3026	0.2262	5008	,	,		15205	0.4841		0.2157	False		,,,				2504	0.3517				p.D116D		Atlas-SNP	.											.	CDHR2	152	.	0			c.T348C						PASS	.	C	,	1295,3111	698.0+/-406.3	175,945,1083	99.0	82.0	88.0		348,348	2.4	1.0	5	dbSNP_123	88	1693,6907	737.6+/-407.0	154,1385,2761	no	coding-synonymous,coding-synonymous	CDHR2	NM_001171976.1,NM_017675.4	,	329,2330,3844	CC,CT,TT		19.686,29.3917,22.974	,	116/1311,116/1311	175998246	2988,10018	2203	4300	6503	SO:0001819	synonymous_variant	54825	exon6			GGAAGATAGAAAC	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.348T>C	5.37:g.175998246T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_017675	A1L3U4|A6NC80|Q9NXP8	Silent	SNP	ENST00000510636.1	37	CCDS34297.1																																																																																			T|0.732;C|0.268	0.268	strong		0.512	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
PTPLAD1	51495	hgsc.bcm.edu	37	15	65863917	65863917	+	Missense_Mutation	SNP	A	A	C	rs2279854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65863917A>C	ENST00000261875.5	+	9	971	c.805A>C	c.(805-807)Atg>Ctg	p.M269L	snoU13_ENST00000459019.1_RNA|PTPLAD1_ENST00000565299.1_Missense_Mutation_p.M307L|PTPLAD1_ENST00000568793.1_Missense_Mutation_p.M244L|PTPLAD1_ENST00000562901.1_Missense_Mutation_p.M152L|PTPLAD1_ENST00000566074.1_Missense_Mutation_p.M152L|PTPLAD1_ENST00000566511.1_Missense_Mutation_p.M152L|PTPLAD1_ENST00000442729.2_Missense_Mutation_p.M214L|PTPLAD1_ENST00000569894.1_Missense_Mutation_p.M152L	NM_016395.2	NP_057479.2	Q9P035	HACD3_HUMAN	protein tyrosine phosphatase-like A domain containing 1	269			M -> L (in dbSNP:rs2279854).		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						GTGCATTGACATGGATTGGAA	0.428													A|||	282	0.0563099	0.0915	0.0331	5008	,	,		20876	0.0427		0.0457	False		,,,				2504	0.0501				p.M269L		Atlas-SNP	.											.	PTPLAD1	23	.	0			c.A805C						PASS	.	A	LEU/MET	352,3556		13,326,1615	155.0	145.0	148.0		805	4.7	1.0	15	dbSNP_100	148	481,7819		14,453,3683	yes	missense	PTPLAD1	NM_016395.2	15	27,779,5298	CC,CA,AA		5.7952,9.0072,6.8234	benign	269/363	65863917	833,11375	1954	4150	6104	SO:0001583	missense	51495	exon9			ATTGACATGGATT		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.805A>C	15.37:g.65863917A>C	ENSP00000261875:p.Met269Leu	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	306	125	0.408497	NM_016395	A0PJA1|B4DRF4|Q280Z3|Q6PD63|Q8IUI5|Q8NC86|Q8NCB1|Q96T12|Q9NQA7	Missense_Mutation	SNP	ENST00000261875.5	37	CCDS45282.1	103	0.04716117216117216	35	0.07113821138211382	14	0.03867403314917127	24	0.04195804195804196	30	0.0395778364116095	A	13.63	2.293116	0.40594	0.090072	0.057952	ENSG00000074696	ENST00000442729;ENST00000261875	T;T	0.28069	1.63;1.63	5.83	4.66	0.58398	.	0.188681	0.56097	D	0.000028	T	0.00845	0.0028	L	0.36672	1.1	0.33734	D	0.618531	B;B	0.24823	0.112;0.021	B;B	0.29663	0.105;0.021	T	0.08391	-1.0724	10	0.10902	T	0.67	-23.838	13.2201	0.59883	0.8678:0.1322:0.0:0.0	rs2279854;rs52832145;rs59360753;rs2279854	214;269	B4DRF4;Q9P035	.;HACD3_HUMAN	L	214;269	ENSP00000392491:M214L;ENSP00000261875:M269L	ENSP00000261875:M269L	M	+	1	0	PTPLAD1	63650970	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	5.321000	0.65846	2.225000	0.72522	0.533000	0.62120	ATG	A|0.949;C|0.051	0.051	strong		0.428	PTPLAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419739.1	NM_016395	
PPAN	56342	hgsc.bcm.edu	37	19	10221804	10221804	+	Missense_Mutation	SNP	G	G	T	rs200927331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10221804G>T	ENST00000253107.7	+	12	1491	c.1385G>T	c.(1384-1386)gGc>gTc	p.G462V	PPAN-P2RY11_ENST00000393796.4_Intron|P2RY11_ENST00000321826.4_5'Flank|SNORD105B_ENST00000458770.1_RNA|PPAN_ENST00000556468.1_Intron|PPAN-P2RY11_ENST00000428358.1_Intron|PPAN_ENST00000393793.1_Missense_Mutation_p.G409V	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	462					RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|liver(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			GGTGGGCGAGGCCGGGGCCGG	0.701													G|||	6	0.00119808	0.0045	0.0	5008	,	,		11572	0.0		0.0	False		,,,				2504	0.0				p.G462V		Atlas-SNP	.											.	PPAN	43	.	0			c.G1385T						PASS	.	G	,,VAL/GLY	13,4349		0,13,2168	8.0	10.0	9.0		,,1385	2.9	0.0	19		9	0,8536		0,0,4268	no	intron,intron,missense	PPAN,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_020230.5	,,109	0,13,6436	TT,TG,GG		0.0,0.298,0.1008	,,	,,462/474	10221804	13,12885	2181	4268	6449	SO:0001583	missense	56342	exon12			GGCGAGGCCGGGG	BC033202	CCDS12225.1	19p13.2	2008-02-05	2001-11-28		ENSG00000130810	ENSG00000130810			9227	protein-coding gene	gene with protein product		607793	"""peter pan (Drosophila) homolog"""			10873382	Standard	NM_020230		Approved	SSF1, SSF2, SSF, BXDC3		Q9NQ55	OTTHUMG00000156826	ENST00000253107.7:c.1385G>T	19.37:g.10221804G>T	ENSP00000253107:p.Gly462Val	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_020230	C9J3F9|Q9BW97|Q9H170	Missense_Mutation	SNP	ENST00000253107.7	37	CCDS12225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.74|10.74	1.436723|1.436723	0.25900|0.25900	0.00298|0.00298	0.0|0.0	ENSG00000130810|ENSG00000130810	ENST00000444703|ENST00000253107;ENST00000342696;ENST00000393793	.|T;T	.|0.28454	.|1.61;1.61	3.98|3.98	2.93|2.93	0.34026|0.34026	.|.	.|.	.|.	.|.	.|.	T|T	0.24431|0.24431	0.0592|0.0592	L|L	0.29908|0.29908	0.895|0.895	0.40426|0.40426	D|D	0.979893|0.979893	.|P	.|0.52316	.|0.952	.|P	.|0.46585	.|0.521	T|T	0.02450|0.02450	-1.1157|-1.1157	5|9	.|0.36615	.|T	.|0.2	.|.	8.2265|8.2265	0.31572|0.31572	0.1174:0.0:0.8826:0.0|0.1174:0.0:0.8826:0.0	.|.	.|462	.|Q9NQ55	.|SSF1_HUMAN	S|V	197|462;449;409	.|ENSP00000253107:G462V;ENSP00000377382:G409V	.|ENSP00000253107:G462V	A|G	+|+	1|2	0|0	PPAN|PPAN	10082804|10082804	0.477000|0.477000	0.25909|0.25909	0.002000|0.002000	0.10522|0.10522	0.002000|0.002000	0.02628|0.02628	1.932000|1.932000	0.40143|0.40143	0.975000|0.975000	0.38392|0.38392	-0.258000|-0.258000	0.10820|0.10820	GCC|GGC	.	.	weak		0.701	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230	
SIRPB1	10326	hgsc.bcm.edu	37	20	1546906	1546906	+	Silent	SNP	C	C	T	rs11907593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1546906C>T	ENST00000381605.4	-	5	1156	c.1092G>A	c.(1090-1092)gcG>gcA	p.A364A	SIRPB1_ENST00000262929.5_Silent_p.A146A|SIRPB1_ENST00000381603.3_Silent_p.A147A|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	364					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						TAGGAGCCAGCGCTGCTTCTG	0.607													.|||	92	0.0183706	0.0666	0.0058	5008	,	,		16446	0.0		0.0	False		,,,				2504	0.0				p.A364A		Atlas-SNP	.											.	SIRPB1	83	.	0			c.G1092A						PASS	.	C	,	172,4234		4,164,2035	42.0	35.0	38.0		441,1092	-6.0	0.0	20	dbSNP_120	38	4,8592		0,4,4294	no	coding-synonymous,coding-synonymous	SIRPB1	NM_001083910.2,NM_006065.3	,	4,168,6329	TT,TC,CC		0.0465,3.9038,1.3536	,	147/182,364/399	1546906	176,12826	2203	4298	6501	SO:0001819	synonymous_variant	10326	exon5			AGCCAGCGCTGCT	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.1092G>A	20.37:g.1546906C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	51	0.69863	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			C|0.984;T|0.016	0.016	strong		0.607	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
EFTUD1	79631	hgsc.bcm.edu	37	15	82533686	82533686	+	Silent	SNP	T	T	G	rs11548681	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:82533686T>G	ENST00000268206.7	-	5	471	c.303A>C	c.(301-303)tcA>tcC	p.S101S	EFTUD1_ENST00000359445.3_Silent_p.S50S	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	101	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						TTGATACTTCTGAGGAAAAGT	0.418													T|||	196	0.0391374	0.0794	0.0288	5008	,	,		20495	0.0347		0.0258	False		,,,				2504	0.0102				p.S101S		Atlas-SNP	.											.	EFTUD1	74	.	0			c.A303C						PASS	.	T	,	330,3512		10,310,1601	87.0	78.0	81.0		150,303	-8.6	0.1	15	dbSNP_120	81	188,8076		6,176,3950	no	coding-synonymous,coding-synonymous	EFTUD1	NM_001040610.2,NM_024580.5	,	16,486,5551	GG,GT,TT		2.2749,8.5893,4.2789	,	50/1070,101/1121	82533686	518,11588	1921	4132	6053	SO:0001819	synonymous_variant	79631	exon5			TACTTCTGAGGAA	AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"""ribosome assembly 1 homolog (yeast)"""					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.303A>C	15.37:g.82533686T>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Silent	SNP	ENST00000268206.7	37	CCDS42071.1																																																																																			T|0.969;G|0.031	0.031	strong		0.418	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580	
DGKZ	8525	hgsc.bcm.edu	37	11	46388024	46388024	+	Missense_Mutation	SNP	G	G	A	rs11827702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46388024G>A	ENST00000454345.1	+	2	343	c.218G>A	c.(217-219)cGg>cAg	p.R73Q	DGKZ_ENST00000456247.2_Intron|DGKZ_ENST00000421244.2_Intron|DGKZ_ENST00000527911.1_Intron|DGKZ_ENST00000343674.6_Intron|DGKZ_ENST00000395574.3_Intron|DGKZ_ENST00000528615.1_Intron|DGKZ_ENST00000318201.8_Intron|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000532868.2_Intron|DGKZ_ENST00000525434.1_3'UTR	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	73					blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		TCCAGCCGCCGGCGCTCCAGC	0.701													G|||	204	0.0407348	0.1475	0.0101	5008	,	,		12532	0.0		0.001	False		,,,				2504	0.001				p.R73Q		Atlas-SNP	.											.	DGKZ	199	.	0			c.G218A						PASS	.	G	GLN/ARG,,,,,,	346,3634		8,330,1652	13.0	15.0	15.0		218,,,,,,	3.2	1.0	11	dbSNP_120	15	4,8270		0,4,4133	yes	missense,intron,intron,intron,intron,intron,intron	DGKZ	NM_001105540.1,NM_001199266.1,NM_001199267.1,NM_001199268.1,NM_003646.3,NM_201532.2,NM_201533.3	43,,,,,,	8,334,5785	AA,AG,GG		0.0483,8.6935,2.8562	possibly-damaging,,,,,,	73/1118,,,,,,	46388024	350,11904	1990	4137	6127	SO:0001583	missense	8525	exon2			GCCGCCGGCGCTC	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"""diacylglycerol kinase, zeta 104kDa"""			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.218G>A	11.37:g.46388024G>A	ENSP00000412178:p.Arg73Gln	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	44	26	0.590909	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Missense_Mutation	SNP	ENST00000454345.1	37	CCDS41640.1	68	0.031135531135531136	63	0.12804878048780488	5	0.013812154696132596	0	0.0	0	0.0	G	23.1	4.371425	0.82573	0.086935	4.83E-4	ENSG00000149091	ENST00000454345	T	0.74002	-0.8	4.15	3.15	0.36227	.	2.389100	0.02186	N	0.060943	T	0.03520	0.0101	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	P	0.61275	0.886	T	0.57745	-0.7758	10	0.72032	D	0.01	.	12.8442	0.57821	0.0:0.0:0.8362:0.1637	rs11827702	73	Q13574	DGKZ_HUMAN	Q	73	ENSP00000412178:R73Q	ENSP00000412178:R73Q	R	+	2	0	DGKZ	46344600	1.000000	0.71417	1.000000	0.80357	0.539000	0.34962	6.808000	0.75206	2.033000	0.60031	0.462000	0.41574	CGG	G|0.968;A|0.032	0.032	strong		0.701	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540	
GPR144	347088	hgsc.bcm.edu	37	9	127231765	127231765	+	Missense_Mutation	SNP	C	C	T	rs76434769|rs386738474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127231765C>T	ENST00000334810.1	+	16	2497	c.2497C>T	c.(2497-2499)Cgc>Tgc	p.R833C				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	833					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						CAGTGCCCGCCGCCGTGCCCG	0.642													C|||	88	0.0175719	0.0635	0.0058	5008	,	,		17409	0.0		0.0	False		,,,				2504	0.0				p.R833C		Atlas-SNP	.											.	GPR144	33	.	0			c.C2497T						PASS	.	C	CYS/ARG	110,1274		6,98,588	29.0	35.0	33.0		2497	4.2	1.0	9	dbSNP_131	33	1,3181		0,1,1590	yes	missense	GPR144	NM_001161808.1	180	6,99,2178	TT,TC,CC		0.0314,7.948,2.431	benign	833/964	127231765	111,4455	692	1591	2283	SO:0001583	missense	347088	exon16			GCCCGCCGCCGTG	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.2497C>T	9.37:g.127231765C>T	ENSP00000335156:p.Arg833Cys	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	143	140	0.979021	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	C	14.13	2.444880	0.43429	0.07948	3.14E-4	ENSG00000180264	ENST00000334810	T	0.40476	1.03	4.22	4.22	0.49857	GPCR, family 2-like (1);	.	.	.	.	T	0.03305	0.0096	M	0.80183	2.485	0.51767	D	0.999936	P	0.39847	0.691	B	0.38880	0.284	T	0.03017	-1.1082	9	0.52906	T	0.07	.	9.7035	0.40200	0.331:0.669:0.0:0.0	.	833	Q7Z7M1	GP144_HUMAN	C	833	ENSP00000335156:R833C	ENSP00000335156:R833C	R	+	1	0	GPR144	126271586	0.841000	0.29509	0.998000	0.56505	0.895000	0.52256	1.068000	0.30629	1.890000	0.54733	0.462000	0.41574	CGC	C|0.977;T|0.023	0.023	strong		0.642	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
TMEM176A	55365	hgsc.bcm.edu	37	7	150500832	150500832	+	Missense_Mutation	SNP	C	C	T	rs76937000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150500832C>T	ENST00000484928.1	+	5	1048	c.467C>T	c.(466-468)tCg>tTg	p.S156L	TMEM176A_ENST00000004103.3_Missense_Mutation_p.S156L|TMEM176B_ENST00000447204.2_5'Flank|TMEM176A_ENST00000461345.1_Missense_Mutation_p.S97L			Q96HP8	T176A_HUMAN	transmembrane protein 176A	156					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATCTCCAGCTCGAGTGACTGG	0.517													C|||	100	0.0199681	0.0741	0.0029	5008	,	,		18259	0.0		0.0	False		,,,				2504	0.0				p.S156L		Atlas-SNP	.											.	TMEM176A	35	.	0			c.C467T						PASS	.	C	LEU/SER	286,4120	159.6+/-192.1	11,264,1928	64.0	66.0	65.0		467	1.5	0.0	7	dbSNP_131	65	3,8597	2.2+/-6.3	0,3,4297	yes	missense	TMEM176A	NM_018487.2	145	11,267,6225	TT,TC,CC		0.0349,6.4911,2.2221	possibly-damaging	156/236	150500832	289,12717	2203	4300	6503	SO:0001583	missense	55365	exon5			CCAGCTCGAGTGA	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.467C>T	7.37:g.150500832C>T	ENSP00000417626:p.Ser156Leu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_018487	D3DX00|Q9NYC7	Missense_Mutation	SNP	ENST00000484928.1	37	CCDS5909.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	C	9.342	1.063261	0.20067	0.064911	3.49E-4	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536;ENST00000468689	T;T;T;T;T	0.12774	3.16;3.16;2.65;2.85;4.31	2.47	1.51	0.23008	.	5.604390	0.00166	N	0.000010	T	0.00936	0.0031	M	0.64997	1.995	0.09310	N	1	P	0.44627	0.839	B	0.29663	0.105	T	0.34403	-0.9830	10	0.62326	D	0.03	-1.4451	6.1594	0.20356	0.301:0.699:0.0:0.0	.	156	Q96HP8	T176A_HUMAN	L	156;156;97;108;97	ENSP00000417626:S156L;ENSP00000004103:S156L;ENSP00000420818:S97L;ENSP00000417834:S108L;ENSP00000420081:S97L	ENSP00000004103:S156L	S	+	2	0	TMEM176A	150131765	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	-0.768000	0.04715	0.569000	0.29329	0.555000	0.69702	TCG	C|0.977;T|0.023	0.023	strong		0.517	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487	
PLIN4	729359	hgsc.bcm.edu	37	19	4512934	4512934	+	Silent	SNP	A	A	G	rs199854884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512934A>G	ENST00000301286.3	-	3	995	c.996T>C	c.(994-996)aaT>aaC	p.N332N		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	332	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						CTTTGGCCACATTCATGGCAC	0.567													G|||	552	0.110224	0.3525	0.0403	5008	,	,		19461	0.0		0.0129	False		,,,				2504	0.046				p.N332N		Atlas-SNP	.											.	PLIN4	191	.	0			c.T996C						PASS	.						43.0	55.0	51.0					19																	4512934		1883	4139	6022	SO:0001819	synonymous_variant	729359	exon3			GGCCACATTCATG	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.996T>C	19.37:g.4512934A>G		Somatic	377	0	0		WXS	Illumina HiSeq	Phase_I	250	70	0.28	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			A|0.989;G|0.011	0.011	strong		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
C2orf54	79919	hgsc.bcm.edu	37	2	241834944	241834944	+	Silent	SNP	T	T	C	rs4468809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241834944T>C	ENST00000388934.4	-	1	629	c.471A>G	c.(469-471)gtA>gtG	p.V157V		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	157										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		CGATGGCTGCTACCAGCAGGT	0.607													C|||	2640	0.527157	0.7806	0.3473	5008	,	,		23599	0.4405		0.5179	False		,,,				2504	0.411				p.V157V		Atlas-SNP	.											.	C2orf54	14	.	0			c.A471G						PASS	.	C		3201,1197		1185,831,183	21.0	24.0	23.0		471	3.5	1.0	2	dbSNP_111	23	4222,4364		1072,2078,1143	no	coding-synonymous	C2orf54	NM_001085437.1		2257,2909,1326	CC,CT,TT		49.1731,27.2169,42.8296		157/448	241834944	7423,5561	2199	4293	6492	SO:0001819	synonymous_variant	79919	exon1			GGCTGCTACCAGC	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.471A>G	2.37:g.241834944T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	139	59	0.42446	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	37	CCDS42839.1																																																																																			T|0.497;C|0.503	0.503	strong		0.607	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
LDLRAD4	753	hgsc.bcm.edu	37	18	13645310	13645310	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13645310G>A	ENST00000359446.5	+	6	1043	c.575G>A	c.(574-576)cGg>cAg	p.R192Q	LDLRAD4_ENST00000585931.1_Missense_Mutation_p.R115Q|LDLRAD4_ENST00000587757.1_Missense_Mutation_p.R155Q|LDLRAD4_ENST00000592991.1_Missense_Mutation_p.R94Q|LDLRAD4_ENST00000586765.1_Missense_Mutation_p.R137Q|LDLRAD4_ENST00000399848.3_Missense_Mutation_p.R174Q|RP11-701H16.4_ENST00000588397.1_RNA|LDLRAD4_ENST00000361205.4_Missense_Mutation_p.R192Q	NM_001276251.1	NP_001263180.1	O15165	LRAD4_HUMAN	low density lipoprotein receptor class A domain containing 4	192					negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|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)	early endosome membrane (GO:0031901)|endosome (GO:0005768)|integral component of membrane (GO:0016021)	R-SMAD binding (GO:0070412)										CTGCAGCTCCGGGACCCTGAA	0.552																																					p.R174Q		Atlas-SNP	.											C18orf1_ENST00000359446,NS,carcinoma,0,2	.	.	2	0			c.G521A						scavenged	.						78.0	86.0	83.0					18																	13645310		2203	4300	6503	SO:0001583	missense	753	exon6			AGCTCCGGGACCC	AF009424, AF009428	CCDS32793.1, CCDS32794.1, CCDS32795.1, CCDS42415.1, CCDS62392.1, CCDS62393.1	18p11.21	2014-04-29	2012-10-24	2012-10-24	ENSG00000168675	ENSG00000168675			1224	protein-coding gene	gene with protein product	"""clone 22"""	606571	"""chromosome 18 open reading frame 1"""	C18orf1		9479497, 9129712, 24627487	Standard	NM_181482		Approved		uc002ksb.3	O15165	OTTHUMG00000181925	ENST00000359446.5:c.575G>A	18.37:g.13645310G>A	ENSP00000352420:p.Arg192Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	108	3	0.0277778	NM_181482	B3KNT9|E9PAY9|K7EN38|O15166|O15167|O15168|Q5U646|Q6NXP3	Missense_Mutation	SNP	ENST00000359446.5	37	CCDS32793.1	.	.	.	.	.	.	.	.	.	.	G	35	5.495195	0.96355	.	.	ENSG00000168675	ENST00000361205;ENST00000399848;ENST00000359446;ENST00000399847;ENST00000361303;ENST00000435606	T;T	0.59906	0.39;0.23	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.79458	0.4449	M	0.84683	2.71	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.993;0.996;0.993;0.996;0.998;0.996	D	0.83584	0.0119	10	0.87932	D	0	-2.3937	18.1744	0.89757	0.0:0.0:1.0:0.0	.	116;134;137;155;174;192	O15165-4;O15165-3;E9PAY9;B3KNT9;O15165-2;O15165	.;.;.;.;.;CR001_HUMAN	Q	192;174;155;137;134;116	ENSP00000354753:R192Q;ENSP00000382741:R174Q	ENSP00000352420:R155Q	R	+	2	0	C18orf1	13635310	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.480000	0.97931	2.304000	0.77564	0.655000	0.94253	CGG	.	.	none		0.552	LDLRAD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458326.1	NM_181481	
OR4A5	81318	hgsc.bcm.edu	37	11	51412370	51412370	+	Missense_Mutation	SNP	T	T	A	rs149177099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:51412370T>A	ENST00000319760.6	-	1	78	c.26A>T	c.(25-27)gAa>gTa	p.E9V		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	9						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)				GAGGACAAATTCTGTAATATT	0.423													.|||	42	0.00838658	0.0272	0.0086	5008	,	,		18603	0.0		0.0	False		,,,				2504	0.0				p.E9V		Atlas-SNP	.											OR4A5,NS,carcinoma,-1,1	OR4A5	116	1	0			c.A26T						PASS	.	T	VAL/GLU	130,4266		1,128,2069	28.0	27.0	27.0		26	2.0	0.3	11	dbSNP_134	27	6,8576		0,6,4285	no	missense	OR4A5	NM_001005272.3	121	1,134,6354	AA,AT,TT		0.0699,2.9572,1.0479	probably-damaging	9/316	51412370	136,12842	2198	4291	6489	SO:0001583	missense	81318	exon1			ACAAATTCTGTAA	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.26A>T	11.37:g.51412370T>A	ENSP00000367664:p.Glu9Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	13	0.005952380952380952	10	0.02032520325203252	3	0.008287292817679558	0	0.0	0	0.0	.	4.648	0.120435	0.08881	0.029572	6.99E-4	ENSG00000221840	ENST00000319760	T	0.01139	5.28	2.01	2.01	0.26516	.	0.000000	0.48286	D	0.000188	T	0.00845	0.0028	M	0.84511	2.7	0.09310	N	0.999991	P	0.35714	0.517	B	0.37833	0.259	T	0.24512	-1.0158	10	0.72032	D	0.01	.	7.9849	0.30205	0.0:0.0:0.0:1.0	.	9	Q8NH83	OR4A5_HUMAN	V	9	ENSP00000367664:E9V	ENSP00000367664:E9V	E	-	2	0	OR4A5	51268946	0.027000	0.19231	0.318000	0.25279	0.086000	0.17979	1.684000	0.37649	1.181000	0.42912	0.136000	0.15936	GAA	T|0.990;A|0.010	0.010	strong		0.423	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
GSK3B	2932	hgsc.bcm.edu	37	3	119720980	119720980	+	Silent	SNP	T	T	A	rs34002644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119720980T>A	ENST00000264235.8	-	2	1177	c.195A>T	c.(193-195)ggA>ggT	p.G65G	GSK3B_ENST00000316626.5_Silent_p.G65G	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	65	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	CACCAAATGATCCATTTCCAA	0.463													T|||	328	0.0654952	0.2315	0.0159	5008	,	,		14337	0.006		0.001	False		,,,				2504	0.0041				p.G65G		Atlas-SNP	.											GSK3B_ENST00000316626,colon,carcinoma,-1,2	GSK3B	119	2	0			c.A195T						PASS	.	T	,	882,3524	343.1+/-307.5	79,724,1400	244.0	229.0	234.0		195,195	0.4	1.0	3	dbSNP_126	234	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous	GSK3B	NM_001146156.1,NM_002093.3	,	79,731,5693	AA,AT,TT		0.0814,20.0182,6.8353	,	65/421,65/434	119720980	889,12117	2203	4300	6503	SO:0001819	synonymous_variant	2932	exon2			AAATGATCCATTT	BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701			4617	protein-coding gene	gene with protein product		605004				10486203	Standard	NM_002093		Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.195A>T	3.37:g.119720980T>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_002093	D3DN89|Q9BWH3|Q9UL47	Silent	SNP	ENST00000264235.8	37	CCDS54628.1																																																																																			T|0.938;A|0.062	0.062	strong		0.463	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258240.2		
NFAM1	150372	hgsc.bcm.edu	37	22	42783070	42783070	+	Silent	SNP	G	G	A	rs34963472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42783070G>A	ENST00000329021.5	-	5	715	c.678C>T	c.(676-678)cgC>cgT	p.R226R		NM_145912.5	NP_666017.1	Q8NET5	NFAM1_HUMAN	NFAT activating protein with ITAM motif 1	226	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cytokine production (GO:0001819)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of B cell differentiation (GO:0045577)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(3)	4						CCTCGGTCTCGCGGCGCTGCA	0.657													G|||	438	0.0874601	0.0666	0.183	5008	,	,		18323	0.001		0.1402	False		,,,				2504	0.0828				p.R226R		Atlas-SNP	.											.	NFAM1	12	.	0			c.C678T						PASS	.	G		389,4017	195.0+/-219.7	13,363,1827	84.0	77.0	79.0		678	-7.3	0.0	22	dbSNP_126	79	1282,7318	253.3+/-279.0	91,1100,3109	no	coding-synonymous	NFAM1	NM_145912.5		104,1463,4936	AA,AG,GG		14.907,8.8289,12.8479		226/271	42783070	1671,11335	2203	4300	6503	SO:0001819	synonymous_variant	150372	exon5			GGTCTCGCGGCGC	BC038241	CCDS14034.1	22q13.2	2005-02-01			ENSG00000235568	ENSG00000235568			29872	protein-coding gene	gene with protein product		608740				12615919	Standard	NM_145912		Approved	CNAIP	uc003bcn.4	Q8NET5	OTTHUMG00000150923	ENST00000329021.5:c.678C>T	22.37:g.42783070G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	61	37	0.606557	NM_145912	B0QYD0|Q20WL2|Q5JZ96|Q8IUY8|Q8TEM8	Silent	SNP	ENST00000329021.5	37	CCDS14034.1																																																																																			G|0.880;A|0.120	0.120	strong		0.657	NFAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320541.1	NM_145912	
ACCS	84680	hgsc.bcm.edu	37	11	44089352	44089352	+	Missense_Mutation	SNP	G	G	A	rs33952257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44089352G>A	ENST00000263776.8	+	2	609	c.175G>A	c.(175-177)Gat>Aat	p.D59N	ACCS_ENST00000533208.1_Intron|ACCS_ENST00000432284.2_Missense_Mutation_p.D59N	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	59			D -> N (in dbSNP:rs33952257).		biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						GATCTCCTCTGATACCTCCTA	0.512													G|||	1339	0.267372	0.4818	0.098	5008	,	,		1910	0.3085		0.1581	False		,,,				2504	0.1677				p.D59N	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											.	ACCS	64	.	0			c.G175A						PASS	.	G	ASN/ASP,ASN/ASP	1889,2517	543.6+/-376.3	404,1081,718	92.0	87.0	89.0		175,175	-0.4	0.1	11	dbSNP_126	89	1255,7345	251.4+/-277.9	98,1059,3143	yes	missense,missense	ACCS	NM_001127219.1,NM_032592.3	23,23	502,2140,3861	AA,AG,GG		14.593,42.8734,24.1735	benign,benign	59/502,59/502	44089352	3144,9862	2203	4300	6503	SO:0001583	missense	84680	exon2			TCCTCTGATACCT	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.175G>A	11.37:g.44089352G>A	ENSP00000263776:p.Asp59Asn	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	156	79	0.50641	NM_032592	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	37	CCDS7907.1	547	0.25045787545787546	218	0.44308943089430897	38	0.10497237569060773	179	0.3129370629370629	112	0.14775725593667546	G	8.622	0.891541	0.17613	0.428734	0.14593	ENSG00000110455	ENST00000524990;ENST00000263776;ENST00000432284;ENST00000533404	T;T;T;T	0.60040	0.98;0.22;0.98;0.88	5.37	-0.447	0.12234	Pyridoxal phosphate-dependent transferase, major domain (1);	1.373470	0.04542	N	0.388436	T	0.00012	0.0000	N	0.04043	-0.29	0.80722	P	0.0	B;B	0.17667	0.023;0.0	B;B	0.15052	0.012;0.001	T	0.35674	-0.9779	8	.	.	.	-3.0453	8.032	0.30470	0.6237:0.0:0.3763:0.0	rs33952257;rs58939098	59;59	B4E219;Q96QU6	.;1A1L1_HUMAN	N	59	ENSP00000434156:D59N;ENSP00000263776:D59N;ENSP00000391775:D59N;ENSP00000435919:D59N	.	D	+	1	0	ACCS	44045928	0.000000	0.05858	0.133000	0.22050	0.227000	0.25037	0.427000	0.21379	0.019000	0.15079	0.591000	0.81541	GAT	G|0.754;A|0.246	0.246	strong		0.512	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592	
OR5L1	219437	hgsc.bcm.edu	37	11	55579078	55579078	+	Missense_Mutation	SNP	A	A	T	rs2869020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55579078A>T	ENST00000333973.2	+	1	225	c.136A>T	c.(136-138)Att>Ttt	p.I46F		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	46			I -> F (in dbSNP:rs2869020).			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(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				CCTGGGCATGATTGCACTGAT	0.493													N|||	121	0.0241613	0.0862	0.0101	5008	,	,		19133	0.0		0.0	False		,,,				2504	0.0				p.I46F		Atlas-SNP	.											.	OR5L1	145	.	0			c.A136T						PASS	.	A	PHE/ILE	307,4093	167.3+/-198.3	16,275,1909	330.0	288.0	302.0		136	0.6	0.1	11	dbSNP_101	302	6,8586	5.7+/-21.5	0,6,4290	yes	missense	OR5L1	NM_001004738.1	21	16,281,6199	TT,TA,AA		0.0698,6.9773,2.4092	benign	46/312	55579078	313,12679	2200	4296	6496	SO:0001583	missense	219437	exon1			GGCATGATTGCAC	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.136A>T	11.37:g.55579078A>T	ENSP00000335529:p.Ile46Phe	Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	238	107	0.44958	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	43	0.019688644688644688	39	0.07926829268292683	4	0.011049723756906077	0	0.0	0	0.0	a	12.72	2.022276	0.35701	0.069773	6.98E-4	ENSG00000186117	ENST00000333973	T	0.00638	6.04	4.32	0.548	0.17208	GPCR, rhodopsin-like superfamily (1);	0.454491	0.18670	N	0.134475	T	0.00109	0.0003	M	0.84219	2.685	0.09310	N	1	B	0.29612	0.251	B	0.35039	0.194	T	0.39603	-0.9606	10	0.87932	D	0	-7.0075	8.3108	0.32071	0.6568:0.0:0.3432:0.0	rs2869020;rs52812745;rs2869020	46	Q8NGL2	OR5L1_HUMAN	F	46	ENSP00000335529:I46F	ENSP00000335529:I46F	I	+	1	0	OR5L1	55335654	0.000000	0.05858	0.057000	0.19452	0.019000	0.09904	-0.143000	0.10296	-0.167000	0.10871	0.358000	0.22013	ATT	A|0.976;T|0.024	0.024	strong		0.493	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
CRAT	1384	hgsc.bcm.edu	37	9	131860421	131860421	+	Silent	SNP	G	G	A	rs16930895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131860421G>A	ENST00000318080.2	-	11	1629	c.1335C>T	c.(1333-1335)taC>taT	p.Y445Y	RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	445					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	ATGCCTGTCCGTAGATCCTGG	0.642													G|||	198	0.0395367	0.1445	0.0086	5008	,	,		20455	0.0		0.001	False		,,,				2504	0.0				p.Y445Y		Atlas-SNP	.											.	CRAT	43	.	0			c.C1335T						PASS	.	G		605,3801	264.1+/-265.8	34,537,1632	113.0	114.0	114.0		1335	1.2	0.6	9	dbSNP_123	114	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CRAT	NM_000755.3		34,540,5929	AA,AG,GG		0.0349,13.7313,4.6748		445/627	131860421	608,12398	2203	4300	6503	SO:0001819	synonymous_variant	1384	exon11			CTGTCCGTAGATC	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"""carnitine acetyltransferase"""			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.1335C>T	9.37:g.131860421G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_000755	Q5T952|Q9BW16	Silent	SNP	ENST00000318080.2	37	CCDS6919.1	82	0.037545787545787544	77	0.1565040650406504	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	5.678	0.309678	0.10733	0.137313	3.49E-4	ENSG00000095321	ENST00000455396	.	.	.	5.65	1.21	0.21127	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	P	0.999999999693856	.	.	.	.	.	.	T	0.10706	-1.0618	3	.	.	.	-22.048	9.4792	0.38891	0.4152:0.0:0.5848:0.0	rs16930895;rs17486087;rs16930895	.	.	.	W	44	.	.	R	-	1	2	CRAT	130900242	0.002000	0.14202	0.565000	0.28409	0.678000	0.39670	-0.028000	0.12350	0.332000	0.23536	0.561000	0.74099	CGG	G|0.943;A|0.057	0.057	strong		0.642	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1		
RBM11	54033	hgsc.bcm.edu	37	21	15599354	15599354	+	Missense_Mutation	SNP	G	G	A	rs139439630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:15599354G>A	ENST00000400577.3	+	5	595	c.586G>A	c.(586-588)Gac>Aac	p.D196N	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	196					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(U) RNA binding (GO:0008266)|protein homodimerization activity (GO:0042803)			endometrium(3)|kidney(3)|lung(7)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		ACAACCAAGTGACTCTGACCT	0.468													.|||	17	0.00339457	0.0008	0.0072	5008	,	,		21404	0.0		0.0099	False		,,,				2504	0.001				p.D196N		Atlas-SNP	.											.	RBM11	41	.	0			c.G586A						PASS	.	G	ASN/ASP	9,3953		0,9,1972	326.0	307.0	313.0		586	1.9	0.1	21	dbSNP_134	313	140,8188		2,136,4026	yes	missense	RBM11	NM_144770.3	23	2,145,5998	AA,AG,GG		1.6811,0.2272,1.2124	probably-damaging	196/282	15599354	149,12141	1981	4164	6145	SO:0001583	missense	54033	exon5			CCAAGTGACTCTG	AF130358	CCDS46635.1	21q11	2013-02-12			ENSG00000185272	ENSG00000185272		"""RNA binding motif (RRM) containing"""	9897	protein-coding gene	gene with protein product						12036298	Standard	NM_144770		Approved		uc002yjo.4	P57052	OTTHUMG00000074263	ENST00000400577.3:c.586G>A	21.37:g.15599354G>A	ENSP00000383421:p.Asp196Asn	Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	361	160	0.443213	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	13	0.005952380952380952	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	9.181	1.023488	0.19433	0.002272	0.016811	ENSG00000185272	ENST00000400577	T	0.08720	3.06	1.87	1.87	0.25490	.	0.067005	0.64402	D	0.000010	T	0.03827	0.0108	N	0.08118	0	0.22926	N	0.998552	D	0.57571	0.98	P	0.61658	0.892	T	0.38308	-0.9667	10	0.17832	T	0.49	.	11.1988	0.48728	0.0:0.0:1.0:0.0	.	196	P57052	RBM11_HUMAN	N	196	ENSP00000383421:D196N	ENSP00000383421:D196N	D	+	1	0	RBM11	14521225	0.107000	0.21998	0.112000	0.21494	0.343000	0.28985	1.259000	0.32956	1.330000	0.45394	0.195000	0.17529	GAC	G|0.988;A|0.012	0.012	strong		0.468	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770	
KIF19	124602	hgsc.bcm.edu	37	17	72350412	72350412	+	Missense_Mutation	SNP	G	G	A	rs2271535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	4	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	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	
FREM1	158326	hgsc.bcm.edu	37	9	14784389	14784389	+	Missense_Mutation	SNP	G	G	A	rs41265306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14784389G>A	ENST00000380880.3	-	24	5204	c.4421C>T	c.(4420-4422)aCt>aTt	p.T1474I	FREM1_ENST00000380881.4_Missense_Mutation_p.T1475I|FREM1_ENST00000422223.2_Missense_Mutation_p.T1474I			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1474					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)		ACTGGAGACAGTCACCTTGCT	0.428													G|||	406	0.0810703	0.1604	0.085	5008	,	,		17969	0.0625		0.0139	False		,,,				2504	0.0593				p.T1474I		Atlas-SNP	.											.	FREM1	261	.	0			c.C4421T						PASS	.	G	ILE/THR	583,3237		35,513,1362	101.0	95.0	97.0		4421	4.6	0.0	9	dbSNP_127	97	140,8094		3,134,3980	yes	missense	FREM1	NM_144966.5	89	38,647,5342	AA,AG,GG		1.7003,15.2618,5.998	benign	1474/2180	14784389	723,11331	1910	4117	6027	SO:0001583	missense	158326	exon25			GAGACAGTCACCT	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.4421C>T	9.37:g.14784389G>A	ENSP00000370262:p.Thr1474Ile	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	184	0.08424908424908426	91	0.18495934959349594	35	0.09668508287292818	45	0.07867132867132867	13	0.017150395778364115	G	10.61	1.399014	0.25291	0.152618	0.017003	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.29655	1.56;1.56;1.56	5.53	4.64	0.57946	.	1.037950	0.07563	N	0.917287	T	0.00039	0.0001	N	0.16368	0.405	0.80722	P	0.0	B	0.21688	0.059	B	0.17098	0.017	T	0.18023	-1.0350	9	0.21014	T	0.42	-1.1403	12.0926	0.53736	0.1442:0.0:0.8558:0.0	rs41265306;rs61745898	1474	Q5H8C1	FREM1_HUMAN	I	1475;1474;1474	ENSP00000370263:T1475I;ENSP00000412940:T1474I;ENSP00000370262:T1474I	ENSP00000370262:T1474I	T	-	2	0	FREM1	14774389	0.013000	0.17824	0.005000	0.12908	0.670000	0.39368	1.651000	0.37302	1.469000	0.48083	0.591000	0.81541	ACT	G|0.928;A|0.072	0.072	strong		0.428	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
COL27A1	85301	hgsc.bcm.edu	37	9	116931099	116931099	+	Missense_Mutation	SNP	G	G	A	rs2241671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116931099G>A	ENST00000356083.3	+	3	1655	c.1264G>A	c.(1264-1266)Gca>Aca	p.A422T		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	422	Pro-rich.		A -> T (in dbSNP:rs2241671). {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)	p.A422T(1)		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						CTCCCGTCCCGCAGAGAAGCC	0.592													G|||	1885	0.376398	0.3041	0.317	5008	,	,		14098	0.5129		0.4304	False		,,,				2504	0.32				p.A422T		Atlas-SNP	.											COL27A1,NS,carcinoma,0,1	COL27A1	200	1	1	Substitution - Missense(1)	stomach(1)	c.G1264A						PASS	.	G	THR/ALA	1469,2937	473.3+/-356.6	230,1009,964	115.0	137.0	130.0		1264	-8.5	0.0	9	dbSNP_98	130	3717,4883	531.2+/-381.9	788,2141,1371	yes	missense	COL27A1	NM_032888.2	58	1018,3150,2335	AA,AG,GG		43.2209,33.3409,39.8739	benign	422/1861	116931099	5186,7820	2203	4300	6503	SO:0001583	missense	85301	exon3			CGTCCCGCAGAGA	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.1264G>A	9.37:g.116931099G>A	ENSP00000348385:p.Ala422Thr	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	128	90	0.703125	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	900	0.41208791208791207	154	0.3130081300813008	126	0.34806629834254144	303	0.5297202797202797	317	0.4182058047493404	G	8.990	0.977384	0.18812	0.333409	0.432209	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	D;D	0.90676	-2.45;-2.71	4.26	-8.53	0.00916	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.10296	0.0;0.003	B;B	0.06405	0.0;0.002	T	0.22871	-1.0204	8	0.02654	T	1	.	1.1229	0.01728	0.3173:0.2275:0.0884:0.3667	rs2241671;rs17207056;rs57097923;rs2241671	422;369	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	T	422;422;369;369	ENSP00000348385:A422T;ENSP00000391328:A369T	ENSP00000348385:A422T	A	+	1	0	COL27A1	115970920	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.604000	0.05667	-1.614000	0.01575	-2.761000	0.00122	GCA	G|0.596;A|0.404	0.404	strong		0.592	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
PGM2	55276	hgsc.bcm.edu	37	4	37857342	37857342	+	Silent	SNP	G	G	C	rs11554509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:37857342G>C	ENST00000381967.4	+	13	1816	c.1716G>C	c.(1714-1716)ctG>ctC	p.L572L	PGM2_ENST00000537241.1_Silent_p.L412L	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	572					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						ATGCAGAGCTGTGTGCCCCAC	0.493													G|||	862	0.172125	0.323	0.1167	5008	,	,		16436	0.1091		0.1471	False		,,,				2504	0.0982				p.L572L		Atlas-SNP	.											.	PGM2	45	.	0			c.G1716C						PASS	.	G		1271,3135	434.9+/-344.1	192,887,1124	98.0	90.0	93.0		1716	3.0	1.0	4	dbSNP_120	93	1189,7411	241.8+/-272.0	92,1005,3203	no	coding-synonymous	PGM2	NM_018290.3		284,1892,4327	CC,CG,GG		13.8256,28.847,18.9143		572/613	37857342	2460,10546	2203	4300	6503	SO:0001819	synonymous_variant	55276	exon13			AGAGCTGTGTGCC	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"""phosphopentomutase"""	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.1716G>C	4.37:g.37857342G>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Silent	SNP	ENST00000381967.4	37	CCDS3443.1																																																																																			G|0.826;C|0.174	0.174	strong		0.493	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557489	32557489	+	Missense_Mutation	SNP	A	A	T	rs199514452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32557489A>T	ENST00000360004.5	-	1	136	c.31T>A	c.(31-33)Tgc>Agc	p.C11S		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	11					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						GCTGTCATGCAGGAGCCTCCA	0.582										Multiple Myeloma(14;0.17)			A|||	371	0.0740815	0.1225	0.0389	5008	,	,		25825	0.0585		0.0417	False		,,,				2504	0.0828				p.C11S		Atlas-SNP	.											HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	0			c.T31A						PASS	.						86.0	103.0	97.0					6																	32557489		1511	2709	4220	SO:0001583	missense	3123	exon1			TCATGCAGGAGCC	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.31T>A	6.37:g.32557489A>T	ENSP00000353099:p.Cys11Ser	Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	274	23	0.0839416	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	11.88	1.772049	0.31320	.	.	ENSG00000196126	ENST00000360004	T	0.00241	8.46	4.68	2.29	0.28610	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00039	0.0001	L	0.48362	1.52	0.09310	N	1	B	0.20887	0.049	B	0.23419	0.046	T	0.38308	-0.9667	9	0.45353	T	0.12	.	3.8919	0.09122	0.7162:0.0:0.0991:0.1848	.	11	P01911	2B1F_HUMAN	S	11	ENSP00000353099:C11S	ENSP00000353099:C11S	C	-	1	0	HLA-DRB1	32665467	0.021000	0.18746	0.048000	0.18961	0.007000	0.05969	0.788000	0.26872	0.321000	0.23259	-0.530000	0.04314	TGC	A|0.864;T|0.136	0.136	strong		0.582	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
SULT1C3	442038	hgsc.bcm.edu	37	2	108875270	108875270	+	Missense_Mutation	SNP	G	G	A	rs61743196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:108875270G>A	ENST00000329106.2	+	5	607	c.607G>A	c.(607-609)Gag>Aag	p.E203K	SULT1C3_ENST00000376700.1_Missense_Mutation_p.E203K	NM_001008743.1	NP_001008743.1	Q6IMI6	ST1C3_HUMAN	sulfotransferase family, cytosolic, 1C, member 3	203					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						CCTCTTCTACGAGGATATTAA	0.453													.|||	89	0.0177716	0.0643	0.0043	5008	,	,		18204	0.0		0.001	False		,,,				2504	0.0				p.E203K		Atlas-SNP	.											.	SULT1C3	53	.	0			c.G607A						PASS	.	G	LYS/GLU	264,4142	150.7+/-184.7	7,250,1946	81.0	85.0	84.0		607	1.2	0.0	2	dbSNP_129	84	3,8597	3.0+/-9.4	0,3,4297	yes	missense	SULT1C3	NM_001008743.1	56	7,253,6243	AA,AG,GG		0.0349,5.9918,2.0529	probably-damaging	203/305	108875270	267,12739	2203	4300	6503	SO:0001583	missense	442038	exon5			TTCTACGAGGATA	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.607G>A	2.37:g.108875270G>A	ENSP00000333310:p.Glu203Lys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_001008743	Q6IMI5	Missense_Mutation	SNP	ENST00000329106.2	37	CCDS33267.1	38	0.0173992673992674	35	0.07113821138211382	3	0.008287292817679558	0	0.0	0	0.0	G	17.06	3.292897	0.60086	0.059918	3.49E-4	ENSG00000196228	ENST00000329106;ENST00000376700	T;T	0.07908	3.15;3.15	3.1	1.22	0.21188	Sulfotransferase domain (1);	0.109180	0.39909	N	0.001223	T	0.03263	0.0095	H	0.97158	3.95	0.45342	D	0.998332	D	0.89917	1.0	D	0.97110	1.0	T	0.00314	-1.1824	10	0.87932	D	0	.	7.1352	0.25525	0.1009:0.1726:0.7264:0.0	rs61743196	203	Q6IMI6	ST1C3_HUMAN	K	203	ENSP00000333310:E203K;ENSP00000365890:E203K	ENSP00000333310:E203K	E	+	1	0	SULT1C3	108241702	1.000000	0.71417	0.002000	0.10522	0.009000	0.06853	5.266000	0.65525	0.146000	0.19002	0.609000	0.83330	GAG	G|0.978;A|0.022	0.022	strong		0.453	SULT1C3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330255.1	NM_001008743	
SNX31	169166	hgsc.bcm.edu	37	8	101586133	101586133	+	Missense_Mutation	SNP	T	T	C	rs2022923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	107	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	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	
EPPK1	83481	hgsc.bcm.edu	37	8	144940462	144940462	+	Silent	SNP	G	G	A	rs56146920		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144940462G>A	ENST00000525985.1	-	2	7031	c.6960C>T	c.(6958-6960)tcC>tcT	p.S2320S				P58107	EPIPL_HUMAN	epiplakin 1	2320						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)			CCTGGAAGAGGGAGATCTGCT	0.701																																					p.S2320S		Atlas-SNP	.											.	EPPK1	199	.	0			c.C6960T						PASS	.	G		13,4351		0,13,2169	199.0	190.0	193.0		6960	-0.8	1.0	8	dbSNP_129	193	1,8519		0,1,4259	no	coding-synonymous	EPPK1	NM_031308.1		0,14,6428	AA,AG,GG		0.0117,0.2979,0.1087		2320/2420	144940462	14,12870	2182	4260	6442	SO:0001819	synonymous_variant	83481	exon1			GAAGAGGGAGATC	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.6960C>T	8.37:g.144940462G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	198	11	0.0555556	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.500;A|0.500	0.500	weak		0.701	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
OR52L1	338751	hgsc.bcm.edu	37	11	6007679	6007679	+	Missense_Mutation	SNP	C	C	T	rs61742092|rs386750238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6007679C>T	ENST00000332249.4	-	1	536	c.482G>A	c.(481-483)tGc>tAc	p.C161Y		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	161			C -> R (in dbSNP:rs4436524). {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)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATTCCGATGCACCCTATGAC	0.512													.|||	122	0.024361	0.0855	0.013	5008	,	,		23519	0.0		0.0	False		,,,				2504	0.0				p.C161Y	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											OR52L1_ENST00000332249,NS,carcinoma,-1,2	OR52L1	100	2	0			c.G482A						PASS	.	C	TYR/CYS	26,4038		3,20,2009	76.0	73.0	74.0		482	0.5	0.0	11	dbSNP_129	74	2,8378		0,2,4188	no	missense	OR52L1	NM_001005173.2	194	3,22,6197	TT,TC,CC		0.0239,0.6398,0.225	benign	161/330	6007679	28,12416	2032	4190	6222	SO:0001583	missense	338751	exon1			CCGATGCACCCTA	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"""GPCR / Class A : Olfactory receptors"""	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.482G>A	11.37:g.6007679C>T	ENSP00000330338:p.Cys161Tyr	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	160	70	0.4375	NM_001005173	B2RPA6|Q6IFK9	Missense_Mutation	SNP	ENST00000332249.4	37	CCDS44529.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	C	0.004	-2.262469	0.00262	0.006398	2.39E-4	ENSG00000183313	ENST00000332249	T	0.36520	1.25	3.85	0.545	0.17190	GPCR, rhodopsin-like superfamily (1);	0.486110	0.17495	N	0.172195	T	0.01558	0.0050	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.15867	-1.0422	10	0.18276	T	0.48	.	4.1238	0.10118	0.0:0.4045:0.2702:0.3253	.	161	Q8NGH7	O52L1_HUMAN	Y	161	ENSP00000330338:C161Y	ENSP00000330338:C161Y	C	-	2	0	OR52L1	5964255	0.000000	0.05858	0.027000	0.17364	0.006000	0.05464	-3.285000	0.00526	0.235000	0.21160	0.313000	0.20887	TGC	A|0.000;C|0.988;T|0.012	0.012	strong		0.512	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173	
DNHD1	144132	hgsc.bcm.edu	37	11	6585670	6585670	+	Silent	SNP	C	C	T	rs16915423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6585670C>T	ENST00000527990.2	+	30	10392	c.10392C>T	c.(10390-10392)gaC>gaT	p.D3464D	DNHD1_ENST00000254579.6_Silent_p.D3464D			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3464					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)		AGCTACTGGACGAGTGGTTAG	0.552													C|||	600	0.119808	0.295	0.0922	5008	,	,		21225	0.0149		0.0169	False		,,,				2504	0.1166				p.D3464D		Atlas-SNP	.											.	DNHD1	198	.	0			c.C10392T						PASS	.	C		356,1028		43,270,379	115.0	110.0	112.0		10392	-1.9	0.9	11	dbSNP_123	112	81,3101		0,81,1510	no	coding-synonymous	DNHD1	NM_144666.2		43,351,1889	TT,TC,CC		2.5456,25.7225,9.5707		3464/4754	6585670	437,4129	692	1591	2283	SO:0001819	synonymous_variant	144132	exon32			ACTGGACGAGTGG	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.10392C>T	11.37:g.6585670C>T		Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	215	110	0.511628	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			C|0.905;T|0.095	0.095	strong		0.552	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
NOP16	51491	hgsc.bcm.edu	37	5	175811133	175811133	+	3'UTR	SNP	T	T	C	rs1065212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:175811133T>C	ENST00000389158.5	-	0	1071				NOP16_ENST00000507413.1_3'UTR|NOP16_ENST00000510123.1_Missense_Mutation_p.E182G			Q9Y3C1	NOP16_HUMAN	NOP16 nucleolar protein							intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|lung(4)|ovary(1)	8						CCTGGCCAGCTCCTCTGGAGC	0.577													C|||	413	0.0824681	0.1967	0.0648	5008	,	,		16505	0.0		0.0895	False		,,,				2504	0.0184				p.E183G		Atlas-SNP	.											.	NOP16	26	.	0			c.A548G						PASS	.																																			SO:0001624	3_prime_UTR_variant	51491	exon5			GCCAGCTCCTCTG		CCDS43403.1, CCDS58991.1	5q35.2	2012-12-10	2012-12-10		ENSG00000048162	ENSG00000048162			26934	protein-coding gene	gene with protein product	"""hypothetical protein HSPC111"", ""HBV pre-S2 trans-regulated protein 3"""	612861	"""nucleolar protein 16 homolog (yeast)"", ""NOP16 nucleolar protein homolog (yeast)"""			10810093, 11042152	Standard	NM_001291308		Approved	HSPC111, HSPC185, LOC51491	uc003mee.4	Q9Y3C1	OTTHUMG00000163186	ENST00000389158.5:c.*99A>G	5.37:g.175811133T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001256539	B4DV13|D6RGD3|Q05D05|Q6IAI6|Q8IXL5	Missense_Mutation	SNP	ENST00000389158.5	37	CCDS43403.1	182	0.08333333333333333	85	0.17276422764227642	27	0.07458563535911603	0	0.0	70	0.09234828496042216	C	6.311	0.425518	0.11987	.	.	ENSG00000048162	ENST00000510123;ENST00000341213;ENST00000451293	.	.	.	4.79	-5.99	0.02213	.	1.303370	0.04934	N	0.457486	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.13176	-1.0519	7	0.31617	T	0.26	-0.0482	1.8679	0.03202	0.1976:0.0926:0.3011:0.4086	rs1065212;rs3172923;rs52812001;rs59387745;rs1065212	183;182	Q6PIM0;D6RGD3	.;.	G	182;187;183	.	ENSP00000340662:E187G	E	-	2	0	NOP16	175743739	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.202000	0.09451	-1.714000	0.01390	-4.622000	0.00004	GAG	T|0.896;C|0.104	0.104	strong		0.577	NOP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371963.1	NM_016391	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377436	49377436	+	Missense_Mutation	SNP	G	G	C	rs556052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49377436G>C	ENST00000200453.5	+	2	1215	c.946G>C	c.(946-948)Gct>Cct	p.A316P		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	316	Glu-rich.		A -> P (in dbSNP:rs556052). {ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		TGAGGTCAAGGCTTTGGGGGC	0.622													G|||	2132	0.425719	0.7761	0.3329	5008	,	,		18799	0.1151		0.336	False		,,,				2504	0.4305				p.A316P		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G946C						PASS	.	G	PRO/ALA	3190,1216	705.8+/-407.3	1158,874,171	73.0	78.0	76.0		946	1.2	0.0	19	dbSNP_83	76	2910,5690	452.5+/-363.0	490,1930,1880	yes	missense	PPP1R15A	NM_014330.3	27	1648,2804,2051	CC,CG,GG		33.8372,27.5987,46.9014	possibly-damaging	316/675	49377436	6100,6906	2203	4300	6503	SO:0001583	missense	23645	exon2			GTCAAGGCTTTGG	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.946G>C	19.37:g.49377436G>C	ENSP00000200453:p.Ala316Pro	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	805	0.3685897435897436	358	0.7276422764227642	123	0.3397790055248619	71	0.12412587412587413	253	0.3337730870712401	G	8.601	0.886951	0.17540	0.724013	0.338372	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05319	3.46	4.68	1.24	0.21308	.	1.663540	0.03882	N	0.277310	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	0.34675	-0.9819	9	0.29301	T	0.29	2.0956	7.9394	0.29950	0.147:0.1372:0.7158:0.0	rs556052;rs3170540;rs3745700;rs556052	316	O75807	PR15A_HUMAN	P	316;156;274	ENSP00000200453:A316P	ENSP00000200453:A316P	A	+	1	0	PPP1R15A	54069248	0.070000	0.21116	0.000000	0.03702	0.000000	0.00434	2.920000	0.48844	-0.076000	0.12775	-1.761000	0.00669	GCT	G|0.568;C|0.432	0.432	strong		0.622	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
ERCC5	2073	hgsc.bcm.edu	37	13	103514939	103514939	+	Silent	SNP	C	C	T	rs4150316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103514939C>T	ENST00000355739.4	+	8	2863	c.1440C>T	c.(1438-1440)caC>caT	p.H480H	ERCC5_ENST00000375954.1_5'Flank|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.R906C	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	480					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)					CACTTGTTCACGTGGGGACTG	0.493			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	180	0.0359425	0.1331	0.0043	5008	,	,		20640	0.0		0.001	False		,,,				2504	0.0				p.H934H		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.C2802T						PASS	.	C	,	495,3911	228.8+/-243.5	32,431,1740	71.0	60.0	64.0		1440,2802	-10.5	0.0	13	dbSNP_110	64	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	32,444,6027	TT,TC,CC		0.1512,11.2347,3.9059	,	480/1187,934/1641	103514939	508,12498	2203	4300	6503	SO:0001819	synonymous_variant	0	exon16	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TGTTCACGTGGGG	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.1440C>T	13.37:g.103514939C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	120	69	0.575	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			C|0.959;T|0.041	0.041	strong		0.493	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
NDRG4	65009	hgsc.bcm.edu	37	16	58542901	58542901	+	Silent	SNP	G	G	A	rs867583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58542901G>A	ENST00000570248.1	+	11	871	c.765G>A	c.(763-765)acG>acA	p.T255T	NDRG4_ENST00000563799.1_Silent_p.T273T|NDRG4_ENST00000562999.1_Silent_p.T255T|NDRG4_ENST00000566192.1_Silent_p.T255T|NDRG4_ENST00000394282.4_Silent_p.T307T|NDRG4_ENST00000356752.4_Silent_p.T285T|NDRG4_ENST00000394279.2_Silent_p.T287T|NDRG4_ENST00000258187.5_Silent_p.T287T|NDRG4_ENST00000569923.1_Silent_p.T200T|NDRG4_ENST00000568640.1_Silent_p.T273T	NM_001242835.1	NP_001229764.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	255	Poly-Thr.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						CGACCACTACGACCTTCCTGA	0.632													G|||	1797	0.358826	0.379	0.2392	5008	,	,		18235	0.5694		0.2127	False		,,,				2504	0.3497				p.T307T		Atlas-SNP	.											.	NDRG4	29	.	0			c.G921A						PASS	.	G	,,,,,,	1646,2750	501.2+/-364.9	320,1006,872	68.0	70.0	69.0		921,855,819,765,765,861,861	-7.5	0.8	16	dbSNP_86	69	1716,6884	313.1+/-311.2	163,1390,2747	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDRG4	NM_001130487.1,NM_001242833.1,NM_001242834.1,NM_001242835.1,NM_001242836.1,NM_020465.3,NM_022910.3	,,,,,,	483,2396,3619	AA,AG,GG		19.9535,37.4431,25.8695	,,,,,,	307/392,285/370,273/358,255/353,255/340,287/372,287/372	58542901	3362,9634	2198	4300	6498	SO:0001819	synonymous_variant	65009	exon13			CACTACGACCTTC	AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034			14466	protein-coding gene	gene with protein product		614463				11352569, 16408304	Standard	NM_020465		Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000570248.1:c.765G>A	16.37:g.58542901G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	NM_001130487	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	Silent	SNP	ENST00000570248.1	37	CCDS58466.1																																																																																			G|0.696;A|0.304	0.304	strong		0.632	NDRG4-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422671.2		
SAG	6295	hgsc.bcm.edu	37	2	234255548	234255548	+	Missense_Mutation	SNP	T	T	C	rs1046976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234255548T>C	ENST00000409110.1	+	16	1438	c.1208T>C	c.(1207-1209)gTt>gCt	p.V403A		NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	403			V -> A (in dbSNP:rs1046976). {ECO:0000269|PubMed:3164688, ECO:0000269|PubMed:9020843}.|V -> I (in dbSNP:rs1046974).		cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		AAGAATGACGTTGATGAGTGA	0.458													T|||	702	0.140176	0.2625	0.1095	5008	,	,		20863	0.0466		0.0855	False		,,,				2504	0.1493				p.V403A		Atlas-SNP	.											.	SAG	77	.	0			c.T1208C						PASS	.	T	ALA/VAL	928,3088		109,710,1189	90.0	96.0	94.0		1208	-8.8	0.0	2	dbSNP_86	94	693,7661		27,639,3511	yes	missense	SAG	NM_000541.4	64	136,1349,4700	CC,CT,TT		8.2954,23.1076,13.1043	benign	403/406	234255548	1621,10749	2008	4177	6185	SO:0001583	missense	6295	exon16			ATGACGTTGATGA		CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.1208T>C	2.37:g.234255548T>C	ENSP00000386444:p.Val403Ala	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_000541	A0FDN6|Q53SV3|Q99858	Missense_Mutation	SNP	ENST00000409110.1	37	CCDS46545.1	266	0.12179487179487179	143	0.29065040650406504	35	0.09668508287292818	27	0.0472027972027972	61	0.08047493403693931	t	0.955	-0.705056	0.03255	0.231076	0.082954	ENSG00000130561	ENST00000252857;ENST00000409110	T	0.06849	3.25	4.39	-8.79	0.00820	.	2.199560	0.02549	N	0.095496	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	0.42565	-0.9444	9	0.08837	T	0.75	6.8364	2.8869	0.05664	0.2015:0.3507:0.3189:0.1289	rs1046976;rs3186970;rs52808946;rs1046976	403	P10523	ARRS_HUMAN	A	403	ENSP00000386444:V403A	ENSP00000252857:V403A	V	+	2	0	SAG	233920287	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.364000	0.07583	-2.003000	0.00962	-1.569000	0.00873	GTT	T|0.869;C|0.131	0.131	strong		0.458	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1	NM_000541	
CYP3A7	1551	hgsc.bcm.edu	37	7	99317993	99317993	+	Silent	SNP	G	G	A	rs45466796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99317993G>A	ENST00000336374.2	-	4	263	c.261C>T	c.(259-261)ccC>ccT	p.P87P		NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	87					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)|oxygen binding (GO:0019825)			autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TGATCATGTCGGGATCTGTGA	0.388													G|||	111	0.0221645	0.0802	0.0072	5008	,	,		18474	0.0		0.0	False		,,,				2504	0.0				p.P87P		Atlas-SNP	.											.	CYP3A7	59	.	0			c.C261T						PASS	.	G		281,4125	156.3+/-189.4	8,265,1930	129.0	117.0	121.0		261	-2.8	0.0	7	dbSNP_127	121	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	CYP3A7	NM_000765.3		8,267,6228	AA,AG,GG		0.0233,6.3777,2.1759		87/504	99317993	283,12723	2203	4300	6503	SO:0001819	synonymous_variant	1551	exon4			CATGTCGGGATCT	AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"""Cytochrome P450s"""	2640	protein-coding gene	gene with protein product		605340	"""cytochrome P450, subfamily IIIA, polypeptide 7"""			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.261C>T	7.37:g.99317993G>A		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	299	142	0.474916	NM_000765	A4D288|Q9H241	Silent	SNP	ENST00000336374.2	37	CCDS5673.1																																																																																			G|0.983;A|0.017	0.017	strong		0.388	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1		
IFITM2	10581	hgsc.bcm.edu	37	11	309127	309127	+	Missense_Mutation	SNP	A	A	G	rs1059091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:309127A>G	ENST00000399817.4	+	2	391	c.361A>G	c.(361-363)Atc>Gtc	p.I121V	RP11-326C3.7_ENST00000526612.1_RNA|IFITM2_ENST00000602569.1_Missense_Mutation_p.I101V|IFITM2_ENST00000533141.1_Missense_Mutation_p.I101V	NM_006435.2	NP_006426.2	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2	121			I -> V (in dbSNP:rs1059091). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1906403}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(49;2e-09)|all_epithelial(84;3.36e-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;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)		CATTCTGCTCATCATCATCCC	0.577													N|||	2707	0.540535	0.5976	0.4553	5008	,	,		21628	0.6944		0.332	False		,,,				2504	0.5798				p.I121V		Atlas-SNP	.											.	IFITM2	21	.	0			c.A361G						PASS	.	G	VAL/ILE	2248,1872		615,1018,427	83.0	84.0	84.0		361	-3.8	0.0	11	dbSNP_86	84	2757,5609		453,1851,1879	yes	missense	IFITM2	NM_006435.2	29	1068,2869,2306	GG,GA,AA		32.9548,45.4369,40.0849	benign	121/133	309127	5005,7481	2060	4183	6243	SO:0001583	missense	10581	exon2			CTGCTCATCATCA	X57351	CCDS41583.1	11p15.5	2012-03-13	2012-03-13		ENSG00000185201	ENSG00000185201			5413	protein-coding gene	gene with protein product		605578	"""interferon induced transmembrane protein 2 (1-8D)"""			1906403	Standard	NM_006435		Approved	1-8D	uc001lox.4	Q01629		ENST00000399817.4:c.361A>G	11.37:g.309127A>G	ENSP00000382714:p.Ile121Val	Somatic	410	0	0		WXS	Illumina HiSeq	Phase_I	447	447	1	NM_006435	Q6FH82|Q96DA8	Missense_Mutation	SNP	ENST00000399817.4	37	CCDS41583.1	1097|1097	0.5022893772893773|0.5022893772893773	287|287	0.5833333333333334|0.5833333333333334	160|160	0.4419889502762431|0.4419889502762431	396|396	0.6923076923076923|0.6923076923076923	254|254	0.33509234828496043|0.33509234828496043	G|G	8.381|8.381	0.837569|0.837569	0.16891|0.16891	0.545631|0.545631	0.329548|0.329548	ENSG00000185201|ENSG00000185201	ENST00000327366|ENST00000533141;ENST00000399817	.|D;D	.|0.86627	.|-2.15;-2.15	2.35|2.35	-3.77|-3.77	0.04346|0.04346	.|.	1.013090|.	0.07963|.	N|.	0.982712|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.69463|0.69463	2.115|2.115	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	T|T	0.42050|0.42050	-0.9474|-0.9474	6|8	0.87932|0.35671	D|T	0|0.21	-6.1667|-6.1667	4.3203|4.3203	0.11013|0.11013	0.3671:0.0:0.4565:0.1764|0.3671:0.0:0.4565:0.1764	rs1059091;rs3168356;rs3765194;rs17845234;rs17858050;rs1059091|rs1059091;rs3168356;rs3765194;rs17845234;rs17858050;rs1059091	.|121	.|Q01629	.|IFM2_HUMAN	R|V	117|101;121	.|ENSP00000434443:I101V;ENSP00000382714:I121V	ENSP00000327996:H117R|ENSP00000382714:I121V	H|I	+|+	2|1	0|0	IFITM2|IFITM2	299127|299127	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-0.264000|-0.264000	0.08658|0.08658	-1.307000|-1.307000	0.02321|0.02321	-2.523000|-2.523000	0.00184|0.00184	CAT|ATC	A|0.607;C|0.000;G|0.393	0.393	strong		0.577	IFITM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383591.1	NM_006435	
IGF2R	3482	hgsc.bcm.edu	37	6	160464289	160464289	+	Silent	SNP	G	G	A	rs894817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	85	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	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	
ABI3	51225	hgsc.bcm.edu	37	17	47295165	47295165	+	Missense_Mutation	SNP	G	G	A	rs137924898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:47295165G>A	ENST00000225941.1	+	3	848	c.350G>A	c.(349-351)cGg>cAg	p.R117Q	ABI3_ENST00000419580.2_Missense_Mutation_p.R111Q	NM_001135186.1|NM_016428.2	NP_001128658.1|NP_057512	Q9P2A4	ABI3_HUMAN	ABI family, member 3	117					cellular component movement (GO:0006928)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	12			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			ACTGTCCAGCGGCTGCCCCCC	0.612										HNSCC(55;0.14)			G|||	11	0.00219649	0.0083	0.0	5008	,	,		13980	0.0		0.0	False		,,,				2504	0.0				p.R117Q		Atlas-SNP	.											.	ABI3	35	.	0			c.G350A						PASS	.	G	GLN/ARG,GLN/ARG	46,4360	47.5+/-82.1	0,46,2157	95.0	94.0	94.0		332,350	2.8	1.0	17	dbSNP_134	94	1,8599		0,1,4299	yes	missense,missense	ABI3	NM_001135186.1,NM_016428.2	43,43	0,47,6456	AA,AG,GG		0.0116,1.044,0.3614	possibly-damaging,possibly-damaging	111/361,117/367	47295165	47,12959	2203	4300	6503	SO:0001583	missense	51225	exon3			TCCAGCGGCTGCC	AB037886	CCDS11546.1, CCDS45725.1	17q21.3	2011-03-04	2008-09-12		ENSG00000108798	ENSG00000108798			29859	protein-coding gene	gene with protein product		606363				10978530, 11956071	Standard	NM_001135186		Approved	NESH, SSH3BP3	uc002iop.1	Q9P2A4	OTTHUMG00000161306	ENST00000225941.1:c.350G>A	17.37:g.47295165G>A	ENSP00000225941:p.Arg117Gln	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_016428	C9IZN8|Q9H0P6	Missense_Mutation	SNP	ENST00000225941.1	37	CCDS11546.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	12.92	2.082944	0.36758	0.01044	1.16E-4	ENSG00000108798	ENST00000225941;ENST00000419580	T;T	0.09911	2.93;2.97	4.92	2.85	0.33270	Abl-interactor, homeo-domain homologous domain (1);	0.258373	0.28219	N	0.016153	T	0.06325	0.0163	L	0.45581	1.43	0.43390	D	0.995501	B;B	0.11235	0.003;0.004	B;B	0.12837	0.005;0.008	T	0.16276	-1.0408	10	0.39692	T	0.17	-17.6666	5.5446	0.17057	0.1921:0.1608:0.6471:0.0	.	111;117	Q9P2A4-2;Q9P2A4	.;ABI3_HUMAN	Q	117;111	ENSP00000225941:R117Q;ENSP00000406651:R111Q	ENSP00000225941:R117Q	R	+	2	0	ABI3	44650164	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	1.567000	0.36407	0.604000	0.29930	0.555000	0.69702	CGG	G|0.997;A|0.003	0.003	strong		0.612	ABI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364475.1	NM_016428	
DSC3	1825	hgsc.bcm.edu	37	18	28586964	28586964	+	Silent	SNP	A	A	G	rs1313586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28586964A>G	ENST00000360428.4	-	12	1877	c.1797T>C	c.(1795-1797)ccT>ccC	p.P599P	DSC3_ENST00000434452.1_Silent_p.P599P	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	599	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.P599P(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			CAGGTTCATCAGGATCAACAG	0.368													G|||	2976	0.594249	0.8268	0.3833	5008	,	,		14919	0.7917		0.3121	False		,,,				2504	0.5164				p.P599P		Atlas-SNP	.											DSC3,NS,carcinoma,0,1	DSC3	225	1	1	Substitution - coding silent(1)	stomach(1)	c.T1797C						PASS	.	G	,	3339,1067	388.6+/-327.0	1275,789,139	118.0	113.0	115.0		1797,1797	-10.2	0.0	18	dbSNP_87	115	2767,5833	679.2+/-403.5	434,1899,1967	no	coding-synonymous,coding-synonymous	DSC3	NM_001941.3,NM_024423.2	,	1709,2688,2106	GG,GA,AA		32.1744,24.217,46.9476	,	599/897,599/840	28586964	6106,6900	2203	4300	6503	SO:0001819	synonymous_variant	1825	exon12			TTCATCAGGATCA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.1797T>C	18.37:g.28586964A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_024423	A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	37	CCDS32810.1																																																																																			A|0.478;G|0.521	0.521	strong		0.368	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
OR10V1	390201	hgsc.bcm.edu	37	11	59480969	59480969	+	Missense_Mutation	SNP	A	A	G	rs472177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59480969A>G	ENST00000307552.2	-	1	368	c.350T>C	c.(349-351)gTa>gCa	p.V117A	STX3_ENST00000300150.7_5'UTR	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, member 1	117			V -> A (in dbSNP:rs472177).			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)|liver(1)|lung(10)|skin(1)	16						AGCCATGACTACCAGCAGGAC	0.507													G|||	936	0.186901	0.4796	0.1787	5008	,	,		20892	0.0685		0.0636	False		,,,				2504	0.046				p.V117A		Atlas-SNP	.											.	OR10V1	40	.	0			c.T350C						PASS	.	G	ALA/VAL	1772,2630	644.2+/-398.0	356,1060,785	76.0	64.0	68.0		350	4.4	0.9	11	dbSNP_83	68	529,8061	794.8+/-407.5	20,489,3786	yes	missense	OR10V1	NM_001005324.1	64	376,1549,4571	GG,GA,AA		6.1583,40.2544,17.7109	benign	117/310	59480969	2301,10691	2201	4295	6496	SO:0001583	missense	390201	exon1			ATGACTACCAGCA	AB065807	CCDS31565.1	11q12.1	2012-08-09			ENSG00000172289	ENSG00000172289		"""GPCR / Class A : Olfactory receptors"""	15136	protein-coding gene	gene with protein product							Standard	NM_001005324		Approved		uc001nof.1	Q8NGI7	OTTHUMG00000167406	ENST00000307552.2:c.350T>C	11.37:g.59480969A>G	ENSP00000302199:p.Val117Ala	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_001005324	Q6IFD9|Q96R50	Missense_Mutation	SNP	ENST00000307552.2	37	CCDS31565.1	353	0.16163003663003664	218	0.44308943089430897	56	0.15469613259668508	28	0.04895104895104895	51	0.06728232189973615	G	0.088	-1.171484	0.01660	0.402544	0.061583	ENSG00000172289	ENST00000307552	T	0.01295	5.04	4.36	4.36	0.52297	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	N	0.000073	T	0.00012	0.0000	N	0.00230	-1.795	0.32056	P	0.5963350000000001	B	0.02656	0.0	B	0.01281	0.0	T	0.30794	-0.9966	9	0.02654	T	1	.	10.7611	0.46266	0.0938:0.0:0.9062:0.0	rs472177;rs52800483;rs60332505;rs472177	117	Q8NGI7	O10V1_HUMAN	A	117	ENSP00000302199:V117A	ENSP00000302199:V117A	V	-	2	0	OR10V1	59237545	0.261000	0.24063	0.860000	0.33809	0.525000	0.34531	2.361000	0.44160	1.227000	0.43598	-0.245000	0.11935	GTA	A|0.824;G|0.176	0.176	strong		0.507	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324	
DNAJB8	165721	hgsc.bcm.edu	37	3	128182074	128182074	+	Silent	SNP	G	G	A	rs2981026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:128182074G>A	ENST00000469083.1	-	2	2572	c.15C>T	c.(13-15)taC>taT	p.Y5Y	DNAJB8-AS1_ENST00000471626.1_RNA|DNAJB8_ENST00000319153.3_Silent_p.Y5Y			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	213	0	0		WXS	Illumina HiSeq	Phase_I	249	136	0.546185	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	
TIFA	92610	hgsc.bcm.edu	37	4	113199075	113199075	+	Silent	SNP	A	A	G	rs701759|rs386678484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:113199075A>G	ENST00000361717.3	-	2	779	c.498T>C	c.(496-498)taT>taC	p.Y166Y	TIFA_ENST00000500655.2_Silent_p.Y166Y	NM_052864.2	NP_443096.1	Q96CG3	TIFA_HUMAN	TRAF-interacting protein with forkhead-associated domain	166					I-kappaB kinase/NF-kappaB signaling (GO:0007249)					breast(2)|endometrium(1)|large_intestine(1)|lung(1)|skin(1)	6		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00172)		AGCAGAGCGAATAAGTGCCAT	0.423													A|||	3256	0.65016	0.8926	0.634	5008	,	,		18519	0.751		0.508	False		,,,				2504	0.3763				p.Y166Y		Atlas-SNP	.											.	TIFA	15	.	0			c.T498C						PASS	.	A		3697,709	757.8+/-412.8	1554,589,60	90.0	91.0	91.0		498	-11.2	0.0	4	dbSNP_86	91	4495,4105	590.0+/-392.6	1201,2093,1006	no	coding-synonymous	TIFA	NM_052864.2		2755,2682,1066	GG,GA,AA		47.7326,16.0917,37.0137		166/185	113199075	8192,4814	2203	4300	6503	SO:0001819	synonymous_variant	92610	exon2			GAGCGAATAAGTG	BC008294	CCDS34051.1	4q25	2008-03-17				ENSG00000145365			19075	protein-coding gene	gene with protein product	"""TRAF2 binding protein"", ""TRAF6 binding protein"""	609028				1179819	Standard	NM_052864		Approved	MGC20791, T2BP, T6BP, TIFAA	uc003ial.3	Q96CG3		ENST00000361717.3:c.498T>C	4.37:g.113199075A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_052864		Silent	SNP	ENST00000361717.3	37	CCDS34051.1																																																																																			A|0.344;G|0.656	0.656	strong		0.423	TIFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363647.2	NM_052864	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416685	105416685	+	Silent	SNP	C	C	G	rs2582506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416685C>G	ENST00000333244.5	-	7	5222	c.5103G>C	c.(5101-5103)ctG>ctC	p.L1701L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1701						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)			CAGTGGTCTTCAGGTCCCCCT	0.642													.|||	11	0.00219649	0.0038	0.0	5008	,	,		15282	0.001		0.0	False		,,,				2504	0.0051				p.L1701L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G5103C						PASS	.	G		2835,1023		1126,583,220	125.0	145.0	139.0		5103	0.9	0.0	14	dbSNP_100	139	5485,2699		2035,1415,642	no	coding-synonymous	AHNAK2	NM_138420.2		3161,1998,862	GG,GC,CC		32.979,26.5163,30.9085		1701/5796	105416685	8320,3722	1929	4092	6021	SO:0001819	synonymous_variant	113146	exon7			GGTCTTCAGGTCC	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.5103G>C	14.37:g.105416685C>G		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	259	258	0.996139	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.401;G|0.599	0.599	strong		0.642	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43630156	43630156	+	Silent	SNP	A	A	C	rs11559311	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43630156A>C	ENST00000236051.2	-	9	1020	c.879T>G	c.(877-879)ccT>ccG	p.P293P	EBNA1BP2_ENST00000431635.2_Silent_p.P348P	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	293					ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)	16	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTCGTTTTCCAGGTCTCTTCT	0.443													A|||	410	0.081869	0.2405	0.0605	5008	,	,		19601	0.001		0.0368	False		,,,				2504	0.0123				p.P348P		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.T1044G						PASS	.	A	,	913,3493	351.1+/-311.1	102,709,1392	176.0	155.0	162.0		1044,879	-0.3	1.0	1	dbSNP_120	162	356,8244	119.7+/-179.0	6,344,3950	no	coding-synonymous,coding-synonymous	EBNA1BP2	NM_001159936.1,NM_006824.2	,	108,1053,5342	CC,CA,AA		4.1395,20.7217,9.757	,	348/362,293/307	43630156	1269,11737	2203	4300	6503	SO:0001819	synonymous_variant	10969	exon10			TTTTCCAGGTCTC	U86602	CCDS478.1, CCDS53308.1	1p35-p33	2011-02-10	2001-11-28		ENSG00000117395	ENSG00000117395			15531	protein-coding gene	gene with protein product		614443	"""EBNA1-binding protein 2"""			10074103, 11438656	Standard	NM_001159936		Approved	NOBP, EBP2, P40	uc010ojx.2	Q99848	OTTHUMG00000007284	ENST00000236051.2:c.879T>G	1.37:g.43630156A>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	158	80	0.506329	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	37	CCDS478.1																																																																																			A|0.912;C|0.088	0.088	strong		0.443	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1		
PCDHB14	56122	hgsc.bcm.edu	37	5	140605092	140605092	+	Missense_Mutation	SNP	C	C	G	rs76671799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140605092C>G	ENST00000239449.4	+	1	2015	c.2015C>G	c.(2014-2016)cCg>cGg	p.P672R	PCDHB14_ENST00000515856.2_Missense_Mutation_p.P519R	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	672					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)			CCCTACCTGCCGCTCCCTGAG	0.692													c|||	132	0.0263578	0.0946	0.0086	5008	,	,		14125	0.0		0.001	False		,,,				2504	0.0				p.P672R	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C2015G						PASS	.	C	ARG/PRO	234,4046		6,222,1912	46.0	53.0	51.0		2015	0.6	0.5	5	dbSNP_131	51	3,8453		0,3,4225	no	missense	PCDHB14	NM_018934.2	103	6,225,6137	GG,GC,CC		0.0355,5.4673,1.8609	benign	672/799	140605092	237,12499	2140	4228	6368	SO:0001583	missense	56122	exon1			ACCTGCCGCTCCC	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.2015C>G	5.37:g.140605092C>G	ENSP00000239449:p.Pro672Arg	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	45	0.020604395604395604	42	0.08536585365853659	3	0.008287292817679558	0	0.0	0	0.0	-	12.23	1.876740	0.33162	0.054673	3.55E-4	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.51817	0.7;0.69	3.83	0.644	0.17776	.	.	.	.	.	T	0.02533	0.0077	M	0.82923	2.615	0.19945	N	0.999944	B	0.28378	0.209	B	0.30029	0.11	T	0.10177	-1.0641	9	0.39692	T	0.17	.	6.8594	0.24058	0.5742:0.2934:0.1324:0.0	.	672	Q9Y5E9	PCDBE_HUMAN	R	519;672	ENSP00000444518:P519R;ENSP00000239449:P672R	ENSP00000239449:P672R	P	+	2	0	PCDHB14	140585276	0.000000	0.05858	0.479000	0.27329	0.090000	0.18270	0.062000	0.14389	0.695000	0.31675	-0.251000	0.11542	CCG	C|0.978;G|0.022	0.022	strong		0.692	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
WNK2	65268	hgsc.bcm.edu	37	9	95993326	95993326	+	Silent	SNP	T	T	C	rs11787888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95993326T>C	ENST00000297954.4	+	3	1011	c.1011T>C	c.(1009-1011)tcT>tcC	p.S337S	WNK2_ENST00000349097.3_5'UTR|WNK2_ENST00000395477.2_Silent_p.S337S|WNK2_ENST00000427277.2_5'UTR|WNK2_ENST00000395475.2_Silent_p.S323S|WNK2_ENST00000356055.3_5'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	337	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						CAACTGGGTCTGTGAAGATTG	0.537													T|||	744	0.148562	0.0983	0.111	5008	,	,		20051	0.0843		0.1541	False		,,,				2504	0.3037				p.S337S		Atlas-SNP	.											WNK2_ENST00000297954,NS,carcinoma,+1,2	WNK2	277	2	0			c.T1011C						PASS	.	T		467,3939	221.0+/-238.3	15,437,1751	184.0	183.0	184.0		1011	-6.7	0.5	9	dbSNP_120	184	1181,7419	242.1+/-272.2	87,1007,3206	no	coding-synonymous	WNK2	NM_006648.3		102,1444,4957	CC,CT,TT		13.7326,10.5992,12.6711		337/2218	95993326	1648,11358	2203	4300	6503	SO:0001819	synonymous_variant	65268	exon3			TGGGTCTGTGAAG	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.1011T>C	9.37:g.95993326T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	214	64	0.299065	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		247	0.1130952380952381	49	0.09959349593495935	42	0.11602209944751381	38	0.06643356643356643	118	0.15567282321899736	T	10.56	1.385337	0.25031	0.105992	0.137326	ENSG00000165238	ENST00000432730	.	.	.	5.52	-6.68	0.01778	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.18840	-1.0324	3	.	.	.	.	3.2884	0.06940	0.1033:0.3687:0.2131:0.315	rs11787888;rs11787888	.	.	.	P	333	.	.	L	+	2	0	WNK2	95033147	0.000000	0.05858	0.535000	0.28026	0.976000	0.68499	-1.965000	0.01511	-1.726000	0.01370	0.533000	0.62120	CTG	T|0.881;C|0.119	0.119	strong		0.537	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
IFITM3	10410	hgsc.bcm.edu	37	11	320606	320606	+	Missense_Mutation	SNP	G	G	T	rs199749095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:320606G>T	ENST00000399808.4	-	1	444	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	RP11-326C3.14_ENST00000602809.1_lincRNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.P49T|RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.P49T|RP11-326C3.11_ENST00000508004.2_RNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	70	Interaction with SPP1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.P70T(3)		central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-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;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGGCAGCAGGGGTTCATGAAG	0.632																																					p.P70T		Atlas-SNP	.											IFITM3,caecum,carcinoma,0,13	IFITM3	132	13	3	Substitution - Missense(3)	endometrium(2)|central_nervous_system(1)	c.C208A						scavenged	.						89.0	95.0	93.0					11																	320606		2101	4210	6311	SO:0001583	missense	10410	exon1			AGCAGGGGTTCAT	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"""interferon induced transmembrane protein 3 (1-8U)"""			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.208C>A	11.37:g.320606G>T	ENSP00000382707:p.Pro70Thr	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	171	8	0.0467836	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	CCDS41585.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|G	0.076|0.076	-1.193620|-1.193620	0.01594|0.01594	.|.	.|.	ENSG00000142089|ENSG00000142089	ENST00000270031|ENST00000399808;ENST00000526811	.|T;T	.|0.78595	.|-0.94;-1.19	4.65|4.65	-9.3|-9.3	0.00649|0.00649	.|.	.|.	.|.	.|.	.|.	.|T	.|0.54447	.|0.1859	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	.|T	.|0.32375	.|-0.9909	.|9	.|0.22109	.|T	.|0.4	.|.	2.5632|2.5632	0.04777|0.04777	0.1587:0.0951:0.2785:0.4676|0.1587:0.0951:0.2785:0.4676	.|.	.|70	.|Q01628	.|IFM3_HUMAN	.|T	-1|70;49	.|ENSP00000382707:P70T;ENSP00000432108:P49T	.|ENSP00000382707:P70T	.|P	-|-	.|1	.|0	IFITM3|IFITM3	310606|310606	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.022000|0.022000	0.10575|0.10575	-1.460000|-1.460000	0.02368|0.02368	-3.272000|-3.272000	0.00199|0.00199	-2.532000|-2.532000	0.00182|0.00182	.|CCC	G|0.936;T|0.064	0.064	strong		0.632	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034	
RPGRIP1	57096	hgsc.bcm.edu	37	14	21769193	21769193	+	Missense_Mutation	SNP	C	C	A	rs1040904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21769193C>A	ENST00000400017.2	+	3	287	c.287C>A	c.(286-288)cCg>cAg	p.P96Q	RPGRIP1_ENST00000206660.6_Missense_Mutation_p.P96Q|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.P96Q|RPGRIP1_ENST00000556336.1_Missense_Mutation_p.P96Q	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	96			P -> Q (in dbSNP:rs1040904). {ECO:0000269|PubMed:18682808}.		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)		GAGGCGGCGCCGCTCTCGGAG	0.682													c|||	292	0.0583067	0.0454	0.1758	5008	,	,		11488	0.0317		0.0467	False		,,,				2504	0.0317				p.P96Q		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.C287A						PASS	.	C	GLN/PRO	204,3608		3,198,1705	27.0	32.0	31.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	287	-0.4	0.0	14	dbSNP_86	31	317,7815		5,307,3754	no	missense	RPGRIP1	NM_020366.3	76	8,505,5459	AA,AC,CC		3.8982,5.3515,4.362	benign	96/1287	21769193	521,11423	1906	4066	5972	SO:0001583	missense	57096	exon3			CGGCGCCGCTCTC	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.287C>A	14.37:g.21769193C>A	ENSP00000382895:p.Pro96Gln	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	17	13	0.764706	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	133	0.060897435897435896	28	0.056910569105691054	55	0.15193370165745856	15	0.026223776223776224	35	0.04617414248021108	c	0.034	-1.318046	0.01320	0.053515	0.038982	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	3.71	-0.434	0.12283	.	2.645290	0.01490	N	0.017026	T	0.00073	0.0002	N	0.03115	-0.41	0.58432	P	5.999999999950489E-6	B	0.13145	0.007	B	0.04013	0.001	T	0.13980	-1.0489	9	0.02654	T	1	11.8105	4.5263	0.11983	0.4152:0.3946:0.0:0.1902	rs1040904	96	Q96KN7	RPGR1_HUMAN	Q	96	ENSP00000450445:P96Q;ENSP00000451219:P96Q;ENSP00000382895:P96Q;ENSP00000206660:P96Q	ENSP00000206660:P96Q	P	+	2	0	RPGRIP1	20839033	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	0.445000	0.21677	-0.161000	0.10983	-0.556000	0.04195	CCG	C|0.941;A|0.059	0.059	strong		0.682	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
EPHA1	2041	hgsc.bcm.edu	37	7	143088592	143088592	+	Silent	SNP	G	G	A	rs56307701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143088592G>A	ENST00000275815.3	-	18	2975	c.2889C>T	c.(2887-2889)caC>caT	p.H963H	EPHA1_ENST00000458129.1_5'Flank	NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	963	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|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 cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				TGCGCTTCTGGTGCCCGGGCA	0.632													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		16965	0.0		0.0	False		,,,				2504	0.0				p.H963H		Atlas-SNP	.											.	EPHA1	193	.	0			c.C2889T						PASS	.	G		187,4219	118.4+/-156.1	3,181,2019	89.0	59.0	69.0		2889	3.4	1.0	7	dbSNP_129	69	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	EPHA1	NM_005232.4		3,185,6315	AA,AG,GG		0.0465,4.2442,1.4686		963/977	143088592	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	2041	exon18			CTTCTGGTGCCCG	M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3385	protein-coding gene	gene with protein product		179610	"""EphA1"""	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.2889C>T	7.37:g.143088592G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Silent	SNP	ENST00000275815.3	37	CCDS5884.1																																																																																			G|0.988;A|0.013	0.013	strong		0.632	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1		
NOL11	25926	hgsc.bcm.edu	37	17	65732093	65732093	+	Silent	SNP	A	A	G	rs3760227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65732093A>G	ENST00000253247.4	+	9	1123	c.1008A>G	c.(1006-1008)tcA>tcG	p.S336S	NOL11_ENST00000535137.1_Silent_p.S154S	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	336					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			GTGAAGTGTCATCATTAGCAG	0.328													A|||	436	0.0870607	0.0575	0.0937	5008	,	,		16795	0.13		0.1193	False		,,,				2504	0.045				p.S336S		Atlas-SNP	.											.	NOL11	48	.	0			c.A1008G						PASS	.	A		266,4140	149.9+/-184.0	3,260,1940	122.0	111.0	115.0		1008	-3.6	0.3	17	dbSNP_107	115	925,7675	203.4+/-246.4	56,813,3431	no	coding-synonymous	NOL11	NM_015462.3		59,1073,5371	GG,GA,AA		10.7558,6.0372,9.1573		336/720	65732093	1191,11815	2203	4300	6503	SO:0001819	synonymous_variant	25926	exon9			AGTGTCATCATTA	AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.1008A>G	17.37:g.65732093A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	187	91	0.486631	NM_015462	B7Z5V9|Q7L5S1|Q9UG18	Silent	SNP	ENST00000253247.4	37	CCDS11671.1																																																																																			A|0.903;G|0.097	0.097	strong		0.328	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462	
COL27A1	85301	hgsc.bcm.edu	37	9	117068826	117068826	+	Silent	SNP	G	G	A	rs1249762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117068826G>A	ENST00000356083.3	+	58	5356	c.4965G>A	c.(4963-4965)gtG>gtA	p.V1655V		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1655					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						ACCGGCTGGTGCTGGACCAGG	0.587											OREG0019417	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	112	0.0223642	0.0847	0.0	5008	,	,		14302	0.0		0.0	False		,,,				2504	0.0				p.V1655V		Atlas-SNP	.											.	COL27A1	200	.	0			c.G4965A						PASS	.	G		298,4108	162.9+/-194.8	12,274,1917	61.0	64.0	63.0		4965	4.4	1.0	9	dbSNP_87	63	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL27A1	NM_032888.2		12,275,6216	AA,AG,GG		0.0116,6.7635,2.2989		1655/1861	117068826	299,12707	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon58			GCTGGTGCTGGAC	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.4965G>A	9.37:g.117068826G>A		Somatic	62	0	0	1478	WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			G|0.974;A|0.026	0.026	strong		0.587	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
BIN1	274	hgsc.bcm.edu	37	2	127821207	127821207	+	Silent	SNP	G	G	A	rs1137845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:127821207G>A	ENST00000316724.5	-	9	1125	c.714C>T	c.(712-714)taC>taT	p.Y238Y	BIN1_ENST00000259238.4_Silent_p.Y207Y|BIN1_ENST00000393041.3_Silent_p.Y207Y|BIN1_ENST00000357970.3_Silent_p.Y238Y|BIN1_ENST00000351659.3_Silent_p.Y238Y|BIN1_ENST00000376113.2_Silent_p.Y207Y|BIN1_ENST00000393040.3_Silent_p.Y207Y|BIN1_ENST00000346226.3_Silent_p.Y207Y|BIN1_ENST00000348750.4_Silent_p.Y207Y|BIN1_ENST00000466111.1_5'UTR|BIN1_ENST00000409400.1_Silent_p.Y207Y|BIN1_ENST00000352848.3_Silent_p.Y207Y	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	238	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				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)		ACGTGTTGACGTAGAAACCTA	0.607													G|||	483	0.0964457	0.0227	0.1383	5008	,	,		19365	0.1508		0.0457	False		,,,				2504	0.1626				p.Y238Y		Atlas-SNP	.											.	BIN1	85	.	0			c.C714T						PASS	.	G	,,,,,,,,,	70,4336	64.7+/-102.0	0,70,2133	80.0	65.0	70.0		621,714,714,714,621,621,621,621,621,621	-9.3	0.4	2	dbSNP_86	70	248,8352	98.4+/-159.9	6,236,4058	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	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	,,,,,,,,,	6,306,6191	AA,AG,GG		2.8837,1.5887,2.445	,,,,,,,,,	207/455,238/594,238/551,238/507,207/498,207/519,207/483,207/476,207/440,207/410	127821207	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	274	exon9			GTTGACGTAGAAA	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.714C>T	2.37:g.127821207G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_139345	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			G|0.772;T|0.015	.	strong		0.607	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
DNAH5	1767	hgsc.bcm.edu	37	5	13753517	13753517	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13753517A>T	ENST00000265104.4	-	63	10801	c.10697T>A	c.(10696-10698)aTg>aAg	p.M3566K		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3566					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)					ATCAATCAACATCTCACTGAG	0.403									Kartagener syndrome																												p.M3566K		Atlas-SNP	.											DNAH5,NS,carcinoma,+1,1	DNAH5	868	1	0			c.T10697A						PASS	.						136.0	131.0	133.0					5																	13753517		2203	4300	6503	SO:0001583	missense	1767	exon63	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATCAACATCTCAC	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.10697T>A	5.37:g.13753517A>T	ENSP00000265104:p.Met3566Lys	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	216	24	0.111111	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.141563	0.77775	.	.	ENSG00000039139	ENST00000265104	T	0.25250	1.81	5.77	5.77	0.91146	.	0.087828	0.85682	D	0.000000	T	0.48314	0.1493	M	0.89478	3.035	0.80722	D	1	B	0.34290	0.447	B	0.44044	0.439	T	0.54139	-0.8338	10	0.66056	D	0.02	.	16.3948	0.83586	1.0:0.0:0.0:0.0	.	3566	Q8TE73	DYH5_HUMAN	K	3566	ENSP00000265104:M3566K	ENSP00000265104:M3566K	M	-	2	0	DNAH5	13806517	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	8.851000	0.92205	2.326000	0.78906	0.533000	0.62120	ATG	.	.	none		0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
LAMA1	284217	hgsc.bcm.edu	37	18	7043335	7043335	+	Missense_Mutation	SNP	A	A	G	rs9950267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:7043335A>G	ENST00000389658.3	-	8	1139	c.1046T>C	c.(1045-1047)tTg>tCg	p.L349S		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	349	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.		L -> S (in dbSNP:rs9950267).		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)				AGCAGTATTCAAACTTTTCTT	0.358													A|||	305	0.0609026	0.2179	0.0245	5008	,	,		18061	0.0		0.0	False		,,,				2504	0.0				p.L349S		Atlas-SNP	.											.	LAMA1	458	.	0			c.T1046C						PASS	.	A	SER/LEU	821,3585	325.6+/-299.2	69,683,1451	195.0	169.0	178.0		1046	5.8	0.1	18	dbSNP_119	178	11,8589	8.4+/-32.0	0,11,4289	yes	missense	LAMA1	NM_005559.3	145	69,694,5740	GG,GA,AA		0.1279,18.6337,6.397	probably-damaging	349/3076	7043335	832,12174	2203	4300	6503	SO:0001583	missense	284217	exon8			GTATTCAAACTTT	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.1046T>C	18.37:g.7043335A>G	ENSP00000374309:p.Leu349Ser	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	137	135	0.985401	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	96	0.04395604395604396	87	0.17682926829268292	9	0.024861878453038673	0	0.0	0	0.0	A	13.81	2.349439	0.41599	0.186337	0.001279	ENSG00000101680	ENST00000389658	T	0.20200	2.09	5.76	5.76	0.90799	EGF-like, laminin (3);	0.273866	0.29212	N	0.012820	T	0.00109	0.0003	M	0.84511	2.7	0.25975	P	0.9824494	D	0.76494	0.999	D	0.67900	0.954	T	0.00282	-1.1850	9	0.56958	D	0.05	.	16.3668	0.83335	1.0:0.0:0.0:0.0	rs9950267;rs9950267	349	P25391	LAMA1_HUMAN	S	349	ENSP00000374309:L349S	ENSP00000374309:L349S	L	-	2	0	LAMA1	7033335	0.998000	0.40836	0.125000	0.21846	0.015000	0.08874	6.262000	0.72514	2.322000	0.78497	0.528000	0.53228	TTG	A|0.939;G|0.061	0.061	strong		0.358	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
MANSC1	54682	hgsc.bcm.edu	37	12	12496086	12496086	+	Missense_Mutation	SNP	C	C	T	rs3741798	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:12496086C>T	ENST00000535902.1	-	2	726	c.163G>A	c.(163-165)Gta>Ata	p.V55I	MANSC1_ENST00000396349.3_Missense_Mutation_p.V21I			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	55	MANSC. {ECO:0000255|PROSITE- ProRule:PRU00341}.		V -> I (in dbSNP:rs3741798). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		GAAGTATATACGGGCTCATTG	0.388													C|||	401	0.0800719	0.0772	0.0879	5008	,	,		21408	0.0764		0.1163	False		,,,				2504	0.045				p.V55I		Atlas-SNP	.											.	MANSC1	38	.	0			c.G163A						PASS	.	C	ILE/VAL	415,3991	203.5+/-225.9	23,369,1811	170.0	168.0	168.0		163	-2.2	0.0	12	dbSNP_107	168	993,7607	215.0+/-254.5	51,891,3358	yes	missense	MANSC1	NM_018050.2	29	74,1260,5169	TT,TC,CC		11.5465,9.419,10.8258	benign	55/432	12496086	1408,11598	2203	4300	6503	SO:0001583	missense	54682	exon2			TATATACGGGCTC	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.163G>A	12.37:g.12496086C>T	ENSP00000438205:p.Val55Ile	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	116	65	0.560345	NM_018050	Q8NEC1|Q9NW60	Missense_Mutation	SNP	ENST00000535902.1	37	CCDS8648.1	213	0.09752747252747253	44	0.08943089430894309	35	0.09668508287292818	56	0.0979020979020979	78	0.10290237467018469	C	0.032	-1.326428	0.01309	0.09419	0.115465	ENSG00000111261	ENST00000535902;ENST00000396349;ENST00000543314	T;T;T	0.36157	1.99;1.99;1.27	5.66	-2.16	0.07080	Seven cysteines (1);Seven cysteines, N-terminal (2);	1.386070	0.05028	N	0.474172	T	0.00144	0.0004	N	0.00677	-1.265	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.32613	-0.9900	9	0.02654	T	1	-5.2156	10.6695	0.45749	0.0:0.4575:0.0:0.5425	rs3741798;rs17846030;rs17859014;rs52831774;rs60985477;rs3741798	21;55	Q9NW60;Q9H8J5	.;MANS1_HUMAN	I	55;21;55	ENSP00000438205:V55I;ENSP00000379638:V21I;ENSP00000437624:V55I	ENSP00000379638:V21I	V	-	1	0	MANSC1	12387353	0.016000	0.18221	0.037000	0.18230	0.332000	0.28634	-0.418000	0.07080	-0.402000	0.07633	-1.063000	0.02288	GTA	C|0.898;T|0.102	0.102	strong		0.388	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050	
PRKD3	23683	hgsc.bcm.edu	37	2	37505105	37505105	+	Silent	SNP	T	T	G	rs10460527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37505105T>G	ENST00000379066.1	-	9	1962	c.1200A>C	c.(1198-1200)ctA>ctC	p.L400L	PRKD3_ENST00000234179.2_Silent_p.L400L			O94806	KPCD3_HUMAN	protein kinase D3	400					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)	p.L400L(2)		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)				CAACCCTCATTAGCGGAATAT	0.363													T|||	1118	0.223243	0.2254	0.2824	5008	,	,		16392	0.3373		0.1272	False		,,,				2504	0.1595				p.L400L	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											PRKD3_ENST00000379066,NS,carcinoma,0,2	PRKD3	170	2	2	Substitution - coding silent(2)	stomach(2)	c.A1200C						PASS	.	T		918,3488	350.5+/-310.9	92,734,1377	202.0	166.0	178.0		1200	-2.9	1.0	2	dbSNP_119	178	866,7734	195.8+/-240.9	62,742,3496	no	coding-synonymous	PRKD3	NM_005813.3		154,1476,4873	GG,GT,TT		10.0698,20.8352,13.7167		400/891	37505105	1784,11222	2203	4300	6503	SO:0001819	synonymous_variant	23683	exon8			CCTCATTAGCGGA	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.1200A>C	2.37:g.37505105T>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	161	76	0.47205	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1																																																																																			T|0.827;G|0.173	0.173	strong		0.363	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	
NKX1-2	390010	hgsc.bcm.edu	37	10	126136112	126136112	+	Silent	SNP	A	A	G	rs7075981|rs386748536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:126136112A>G	ENST00000451024.3	-	2	1059	c.819T>C	c.(817-819)aaT>aaC	p.N273N	RP13-238F13.3_ENST00000604581.1_RNA|NKX1-2_ENST00000440536.2_Silent_p.N295N|RP13-238F13.5_ENST00000602332.1_lincRNA	NM_001146340.1	NP_001139812.1	Q9UD57	NKX12_HUMAN	NK1 homeobox 2	273					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)										GGAAGAGGACATTGGCCGCGG	0.741													G|||	937	0.187101	0.3154	0.1167	5008	,	,		9188	0.1012		0.173	False		,,,				2504	0.1667				p.N273N		Atlas-SNP	.											NKX1-2_ENST00000440536,NS,carcinoma,0,2	NKX1-2	6	2	0			c.T819C						PASS	.	G		385,999		58,269,365	42.0	66.0	59.0		819	2.1	1.0	10	dbSNP_116	59	438,2744		33,372,1186	no	coding-synonymous	NKX1-2	NM_001146340.1		91,641,1551	GG,GA,AA		13.7649,27.8179,18.0245		273/311	126136112	823,3743	692	1591	2283	SO:0001819	synonymous_variant	390010	exon2			GAGGACATTGGCC	CN285329	CCDS59221.1	10q26.13	2012-03-09	2007-07-09	2006-06-29		ENSG00000229544		"""Homeoboxes / ANTP class : NKL subclass"""	31652	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 121"", ""NK1 transcription factor related, locus 2 (Drosophila)"""	C10orf121		10681422	Standard	NM_001146340		Approved	bB238F13.2	uc010quf.2	Q9UD57		ENST00000451024.3:c.819T>C	10.37:g.126136112A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_001146340		Silent	SNP	ENST00000451024.3	37	CCDS59221.1																																																																																			A|0.824;G|0.176	0.176	strong		0.741	NKX1-2-001	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050861.3	XM_372331	
OR4E2	26686	hgsc.bcm.edu	37	14	22133416	22133416	+	Silent	SNP	A	A	G	rs12717305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:22133416A>G	ENST00000408935.1	+	1	120	c.120A>G	c.(118-120)tcA>tcG	p.S40S		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		TAACGCTTTCAGGGAACATTC	0.433													a|||	2360	0.471246	0.6263	0.5317	5008	,	,		21121	0.3641		0.494	False		,,,				2504	0.3057				p.S40S		Atlas-SNP	.											.	OR4E2	44	.	0			c.A120G						PASS	.	A		2404,1558		727,950,304	255.0	245.0	248.0		120	0.8	0.8	14	dbSNP_121	248	4129,4205		1048,2033,1086	no	coding-synonymous	OR4E2	NM_001001912.1		1775,2983,1390	GG,GA,AA		49.544,39.3236,46.8689		40/314	22133416	6533,5763	1981	4167	6148	SO:0001819	synonymous_variant	26686	exon1			GCTTTCAGGGAAC		CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"""GPCR / Class A : Olfactory receptors"""	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.120A>G	14.37:g.22133416A>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	170	170	1	NM_001001912	Q6IET6|Q96R62	Silent	SNP	ENST00000408935.1	37	CCDS41916.1																																																																																			A|0.520;G|0.480	0.480	strong		0.433	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1		
FRA10AC1	118924	hgsc.bcm.edu	37	10	95441272	95441272	+	Missense_Mutation	SNP	G	G	A	rs11187583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:95441272G>A	ENST00000359204.4	-	11	949	c.752C>T	c.(751-753)tCt>tTt	p.S251F	FRA10AC1_ENST00000536233.1_Missense_Mutation_p.S251F|FRA10AC1_ENST00000394100.2_Missense_Mutation_p.S251F|FRA10AC1_ENST00000371430.2_Missense_Mutation_p.S251F	NM_145246.4	NP_660289.2	Q70Z53	F10C1_HUMAN	fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1	251	Lys-rich.		S -> F (in dbSNP:rs11187583).			nucleus (GO:0005634)				NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(1)	14						TTCTGCAGAAGATAATCTGGA	0.303													G|||	409	0.0816693	0.093	0.0965	5008	,	,		15209	0.0337		0.1193	False		,,,				2504	0.0665				p.S251F		Atlas-SNP	.											FRA10AC1_ENST00000371426,colon,carcinoma,-1,2	FRA10AC1	68	2	0			c.C752T						PASS	.	G	PHE/SER	385,4019	194.0+/-219.0	18,349,1835	177.0	156.0	163.0		752	5.2	0.9	10	dbSNP_120	163	974,7624	211.0+/-251.7	65,844,3390	yes	missense	FRA10AC1	NM_145246.4	155	83,1193,5225	AA,AG,GG		11.3282,8.7421,10.4522	possibly-damaging	251/316	95441272	1359,11643	2202	4299	6501	SO:0001583	missense	118924	exon11			GCAGAAGATAATC	AK090955	CCDS7430.1	10q23.33	2014-01-28	2010-05-25	2010-05-25	ENSG00000148690	ENSG00000148690			1162	protein-coding gene	gene with protein product		608866	"""chromosome 10 open reading frame 4"""	C10orf4		15203205	Standard	NM_145246		Approved		uc001kiz.2	Q70Z53	OTTHUMG00000018776	ENST00000359204.4:c.752C>T	10.37:g.95441272G>A	ENSP00000360488:p.Ser251Phe	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_145246	C9JCR4|C9JCR5|C9JMY4|Q70Z49|Q70Z50|Q70Z51|Q70Z52|Q8N293|Q8WVH5|Q96JQ8	Missense_Mutation	SNP	ENST00000359204.4	37	CCDS7430.1	188	0.08608058608058608	42	0.08536585365853659	46	0.1270718232044199	14	0.024475524475524476	86	0.11345646437994723	G	15.10	2.734050	0.48939	0.087421	0.113282	ENSG00000148690	ENST00000359204;ENST00000536233;ENST00000371426;ENST00000371430;ENST00000394100	T;T;T;T	0.25579	1.81;1.8;1.79;1.8	5.17	5.17	0.71159	.	0.293421	0.37857	N	0.001919	T	0.00328	0.0010	L	0.59436	1.845	0.38708	P	0.04685600000000001	P	0.48407	0.91	B	0.43575	0.424	T	0.03139	-1.1068	9	0.66056	D	0.02	-3.4566	15.7456	0.77939	0.0:0.0:1.0:0.0	rs11187583;rs52826468;rs11187583	251	Q70Z53	F10C1_HUMAN	F	251	ENSP00000360488:S251F;ENSP00000438405:S251F;ENSP00000360484:S251F;ENSP00000377660:S251F	ENSP00000360488:S251F	S	-	2	0	FRA10AC1	95431262	1.000000	0.71417	0.890000	0.34922	0.831000	0.47069	4.748000	0.62148	2.572000	0.86782	0.655000	0.94253	TCT	G|0.902;A|0.098	0.098	strong		0.303	FRA10AC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049439.1	NM_145246	
BCL2A1	597	hgsc.bcm.edu	37	15	80260014	80260014	+	Intron	SNP	T	T	C	rs8026803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80260014T>C	ENST00000267953.3	-	1	747				BCL2A1_ENST00000335661.6_Silent_p.T147T	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1						extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						CCAGCATAGGTGTGTGATTGT	0.358													C|||	1950	0.389377	0.3956	0.2925	5008	,	,		18762	0.5288		0.2584	False		,,,				2504	0.4407				p.T147T		Atlas-SNP	.											.	BCL2A1	28	.	0			c.A441G						PASS	.	C	,	1147,1989		199,749,620	101.0	84.0	89.0		441,	-0.0	0.0	15	dbSNP_116	89	1841,5323		211,1419,1952	no	coding-synonymous,intron	BCL2A1	NM_001114735.1,NM_004049.3	,	410,2168,2572	CC,CT,TT		25.6979,36.5753,29.0097	,	147/164,	80260014	2988,7312	1568	3582	5150	SO:0001627	intron_variant	597	exon2			CATAGGTGTGTGA		CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.420+3027A>G	15.37:g.80260014T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Silent	SNP	ENST00000267953.3	37	CCDS10312.1																																																																																			T|0.622;C|0.378	0.378	strong		0.358	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049	
FLG	2312	hgsc.bcm.edu	37	1	152277717	152277717	+	Silent	SNP	C	C	A	rs9436066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152277717C>A	ENST00000368799.1	-	3	9680	c.9645G>T	c.(9643-9645)gtG>gtT	p.V3215V	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	512	2	0.00390625		WXS	Illumina HiSeq	Phase_I	415	414	0.99759	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	
ZNF678	339500	hgsc.bcm.edu	37	1	227842405	227842405	+	Missense_Mutation	SNP	C	C	A	rs61283390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227842405C>A	ENST00000343776.5	+	4	799	c.454C>A	c.(454-456)Ccc>Acc	p.P152T	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.P207T	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	152			P -> T (in dbSNP:rs61283390).		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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				TGGAGAGAAACCCTACAAATG	0.353													C|||	51	0.0101837	0.0371	0.0029	5008	,	,		20735	0.0		0.0	False		,,,				2504	0.0				p.P207T		Atlas-SNP	.											.	ZNF678	137	.	0			c.C619A						PASS	.	C	THR/PRO	173,4229	104.7+/-143.2	5,163,2033	56.0	65.0	62.0		619	-3.1	0.0	1	dbSNP_129	62	0,8598		0,0,4299	no	missense	ZNF678	NM_178549.3	38	5,163,6332	AA,AC,CC		0.0,3.93,1.3308	possibly-damaging	207/581	227842405	173,12827	2201	4299	6500	SO:0001583	missense	339500	exon4			GAGAAACCCTACA	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"""Zinc fingers, C2H2-type"", ""-"""	28652	protein-coding gene	gene with protein product	"""hypothetical protein MGC42493"""					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.454C>A	1.37:g.227842405C>A	ENSP00000344828:p.Pro152Thr	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	90	52	0.577778	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	C	10.34	1.322066	0.23994	0.0393	0.0	ENSG00000181450	ENST00000343776;ENST00000397097;ENST00000440339	T;T;T	0.28895	2.31;2.31;1.59	1.55	-3.11	0.05299	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16642	0.0400	M	0.78637	2.42	0.24660	N	0.993474	D	0.54964	0.969	P	0.61275	0.886	T	0.25433	-1.0132	9	0.66056	D	0.02	.	7.8273	0.29322	0.0:0.7281:0.0:0.2719	rs61283390;rs61739464	152	Q5SXM1	ZN678_HUMAN	T	152;207;207	ENSP00000344828:P152T;ENSP00000440403:P207T;ENSP00000394651:P207T	ENSP00000344828:P152T	P	+	1	0	ZNF678	225909028	0.030000	0.19436	0.000000	0.03702	0.000000	0.00434	0.807000	0.27140	-0.880000	0.03997	-0.924000	0.02725	CCC	C|0.987;A|0.013	0.013	strong		0.353	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549	
DDX27	55661	hgsc.bcm.edu	37	20	47838020	47838020	+	Missense_Mutation	SNP	C	C	T	rs114928867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47838020C>T	ENST00000371764.4	+	2	227	c.218C>T	c.(217-219)gCt>gTt	p.A73V	DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	73	Asp/Glu/Lys-rich.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CGACAAAAAGCTTTGGGGAAG	0.522													C|||	14	0.00279553	0.0106	0.0	5008	,	,		18783	0.0		0.0	False		,,,				2504	0.0				p.A73V		Atlas-SNP	.											.	DDX27	74	.	0			c.C218T						PASS	.	C	VAL/ALA	47,4359	50.2+/-85.5	0,47,2156	83.0	72.0	76.0		218	5.2	1.0	20	dbSNP_132	76	0,8600		0,0,4300	yes	missense	DDX27	NM_017895.7	64	0,47,6456	TT,TC,CC		0.0,1.0667,0.3614	benign	73/797	47838020	47,12959	2203	4300	6503	SO:0001583	missense	55661	exon2			AAAAAGCTTTGGG	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.218C>T	20.37:g.47838020C>T	ENSP00000360828:p.Ala73Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	13.11	2.138594	0.37728	0.010667	0.0	ENSG00000124228	ENST00000535160;ENST00000371764	T	0.01474	4.85	5.16	5.16	0.70880	.	0.553075	0.18353	N	0.143813	T	0.01156	0.0038	N	0.22421	0.69	0.37063	D	0.89816	B	0.24823	0.112	B	0.19148	0.024	T	0.60459	-0.7259	10	0.30078	T	0.28	-17.0082	11.1111	0.48232	0.1841:0.8159:0.0:0.0	.	73	Q96GQ7	DDX27_HUMAN	V	73	ENSP00000360828:A73V	ENSP00000360828:A73V	A	+	2	0	DDX27	47271427	0.984000	0.35163	1.000000	0.80357	0.550000	0.35303	1.360000	0.34125	2.698000	0.92095	0.561000	0.74099	GCT	C|0.997;T|0.003	0.003	strong		0.522	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		
TJP3	27134	hgsc.bcm.edu	37	19	3747910	3747910	+	Missense_Mutation	SNP	G	G	A	rs10408494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3747910G>A	ENST00000541714.2	+	19	2903	c.2441G>A	c.(2440-2442)gGc>gAc	p.G814D	TJP3_ENST00000382008.3_Missense_Mutation_p.G828D|TJP3_ENST00000539908.2_Missense_Mutation_p.G778D|TJP3_ENST00000262968.9_Missense_Mutation_p.G847D|TJP3_ENST00000587686.1_Missense_Mutation_p.G833D|TJP3_ENST00000589378.1_Missense_Mutation_p.G823D	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	814					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)		GGCGAGGGCGGCGCGTACACG	0.692													G|||	244	0.048722	0.1747	0.0187	5008	,	,		15847	0.0		0.0	False		,,,				2504	0.0				p.G823D		Atlas-SNP	.											.	TJP3	79	.	0			c.G2468A						PASS	.	G	ASP/GLY	642,3762	260.7+/-263.8	41,560,1601	36.0	32.0	33.0		2540	2.8	0.9	19	dbSNP_119	33	4,8594	3.0+/-9.4	0,4,4295	yes	missense	TJP3	NM_014428.1	94	41,564,5896	AA,AG,GG		0.0465,14.5777,4.9685	benign	847/953	3747910	646,12356	2202	4299	6501	SO:0001583	missense	27134	exon19			AGGGCGGCGCGTA	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.2441G>A	19.37:g.3747910G>A	ENSP00000439278:p.Gly814Asp	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	140	80	0.571429	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	85	0.03891941391941392	81	0.16463414634146342	4	0.011049723756906077	0	0.0	0	0.0	G	9.121	1.008881	0.19199	0.145777	4.65E-4	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.11821	2.74;2.92;2.78;2.85	2.81	2.81	0.32909	.	0.137458	0.47455	U	0.000231	T	0.00073	0.0002	M	0.62723	1.935	0.31716	P	0.638979	P;P;P;P	0.47762	0.835;0.9;0.745;0.835	B;B;B;B	0.41813	0.367;0.367;0.202;0.367	T	0.18903	-1.0322	9	0.87932	D	0	.	12.4552	0.55700	0.0:0.0:1.0:0.0	rs10408494	833;847;828;814	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	D	814;778;828;847	ENSP00000439278:G814D;ENSP00000439991:G778D;ENSP00000371438:G828D;ENSP00000262968:G847D	ENSP00000262968:G847D	G	+	2	0	TJP3	3698910	1.000000	0.71417	0.950000	0.38849	0.016000	0.09150	4.057000	0.57455	1.069000	0.40788	0.511000	0.50034	GGC	G|0.950;A|0.050	0.050	strong		0.692	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
TRIM15	89870	hgsc.bcm.edu	37	6	30139971	30139971	+	Missense_Mutation	SNP	G	G	C	rs115649931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30139971G>C	ENST00000376694.4	+	7	1712	c.1243G>C	c.(1243-1245)Gtg>Ctg	p.V415L	TRIM15_ENST00000376688.1_Intron	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	415	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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						CCCGCGCGGCGTGAGAGTCGC	0.682													G|||	26	0.00519169	0.0182	0.0029	5008	,	,		12909	0.0		0.0	False		,,,				2504	0.0				p.V415L		Atlas-SNP	.											.	TRIM15	34	.	0			c.G1243C						PASS	.	G	LEU/VAL	53,2929		0,53,1438	16.0	13.0	14.0		1243	3.7	0.0	6	dbSNP_133	14	0,5354		0,0,2677	yes	missense	TRIM15	NM_033229.2	32	0,53,4115	CC,CG,GG		0.0,1.7773,0.6358	probably-damaging	415/466	30139971	53,8283	1491	2677	4168	SO:0001583	missense	89870	exon7			CGCGGCGTGAGAG	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.1243G>C	6.37:g.30139971G>C	ENSP00000365884:p.Val415Leu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Missense_Mutation	SNP	ENST00000376694.4	37	CCDS4677.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.859376	0.32884	0.017773	0.0	ENSG00000204610	ENST00000376695;ENST00000376694	T	0.74002	-0.8	4.54	3.67	0.42095	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.39759	U	0.001266	T	0.51126	0.1656	L	0.58669	1.825	0.48087	D	0.999587	B	0.33448	0.412	B	0.32393	0.145	T	0.54702	-0.8254	10	0.45353	T	0.12	.	5.7541	0.18162	0.1022:0.0:0.7065:0.1913	.	415	Q9C019	TRI15_HUMAN	L	346;415	ENSP00000365884:V415L	ENSP00000365884:V415L	V	+	1	0	TRIM15	30247950	0.042000	0.20092	0.011000	0.14972	0.017000	0.09413	0.313000	0.19415	0.886000	0.36113	0.478000	0.44815	GTG	G|0.990;C|0.010	0.010	strong		0.682	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229	
ABCA7	10347	hgsc.bcm.edu	37	19	1052086	1052086	+	Silent	SNP	G	G	A	rs61576791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1052086G>A	ENST00000263094.6	+	22	3339	c.3108G>A	c.(3106-3108)acG>acA	p.T1036T	ABCA7_ENST00000435683.2_Silent_p.T898T|ABCA7_ENST00000433129.1_Silent_p.T1036T	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1036	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)		ACTACCTGACGCTGGTGAAGG	0.672													G|||	323	0.0644968	0.2383	0.0101	5008	,	,		10142	0.0		0.001	False		,,,				2504	0.0				p.T1036T		Atlas-SNP	.											.	ABCA7	174	.	0			c.G3108A						PASS	.			761,3593		76,609,1492	29.0	25.0	26.0		3108	-8.9	0.0	19	dbSNP_129	26	7,8557		0,7,4275	no	coding-synonymous	ABCA7	NM_019112.3		76,616,5767	AA,AG,GG		0.0817,17.4782,5.9452		1036/2147	1052086	768,12150	2177	4282	6459	SO:0001819	synonymous_variant	10347	exon22			CCTGACGCTGGTG	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.3108G>A	19.37:g.1052086G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			G|0.938;A|0.062	0.062	strong		0.672	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
PXDN	7837	hgsc.bcm.edu	37	2	1642700	1642700	+	Missense_Mutation	SNP	G	G	A	rs61747875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1642700G>A	ENST00000252804.4	-	21	4174	c.4124C>T	c.(4123-4125)aCa>aTa	p.T1375I		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1375					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)		ATCTGAGCGTGTGCTGAAGGC	0.537													G|||	52	0.0103834	0.0363	0.0043	5008	,	,		20910	0.0		0.001	False		,,,				2504	0.0				p.T1375I		Atlas-SNP	.											.	PXDN	255	.	0			c.C4124T						PASS	.	G	ILE/THR	103,4175		1,101,2037	127.0	133.0	131.0		4124	3.0	0.1	2	dbSNP_129	131	5,8483		0,5,4239	yes	missense	PXDN	NM_012293.1	89	1,106,6276	AA,AG,GG		0.0589,2.4077,0.846	benign	1375/1480	1642700	108,12658	2139	4244	6383	SO:0001583	missense	7837	exon21			GAGCGTGTGCTGA	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.4124C>T	2.37:g.1642700G>A	ENSP00000252804:p.Thr1375Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	131	53	0.40458	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	G	10.13	1.265304	0.23136	0.024077	5.89E-4	ENSG00000130508	ENST00000252804	T	0.61040	0.14	5.43	3.05	0.35203	.	0.558829	0.19914	N	0.103226	T	0.08268	0.0206	N	0.03608	-0.345	0.20074	N	0.999932	B	0.16603	0.018	B	0.15484	0.013	T	0.07693	-1.0759	10	0.41790	T	0.15	-30.0156	7.522	0.27633	0.1358:0.0:0.1542:0.71	.	1375	Q92626	PXDN_HUMAN	I	1375	ENSP00000252804:T1375I	ENSP00000252804:T1375I	T	-	2	0	PXDN	1621707	0.735000	0.28153	0.080000	0.20451	0.000000	0.00434	3.286000	0.51724	0.446000	0.26666	-1.114000	0.02060	ACA	G|0.990;A|0.010	0.010	strong		0.537	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
MAP2	4133	hgsc.bcm.edu	37	2	210559960	210559960	+	Silent	SNP	G	G	T	rs2239672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:210559960G>T	ENST00000360351.4	+	7	3572	c.3066G>T	c.(3064-3066)gtG>gtT	p.V1022V	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000447185.1_Silent_p.V1018V|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1022					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	TTAGTTCAGTGCCAGAGATAG	0.433													G|||	673	0.134385	0.1641	0.0634	5008	,	,		22183	0.1984		0.0765	False		,,,				2504	0.138				p.V1022V	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.G3066T						PASS	.	G	,,,	655,3751	277.8+/-273.9	45,565,1593	100.0	98.0	99.0		,3066,,	0.5	1.0	2	dbSNP_98	99	603,7997	159.5+/-212.8	19,565,3716	no	intron,coding-synonymous,intron,intron	MAP2	NM_001039538.1,NM_002374.3,NM_031845.2,NM_031847.2	,,,	64,1130,5309	TT,TG,GG		7.0116,14.8661,9.6725	,,,	,1022/1828,,	210559960	1258,11748	2203	4300	6503	SO:0001819	synonymous_variant	4133	exon7			TTCAGTGCCAGAG		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.3066G>T	2.37:g.210559960G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	37	CCDS2384.1																																																																																			G|0.883;T|0.117	0.117	strong		0.433	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
STRADA	92335	hgsc.bcm.edu	37	17	61787892	61787892	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61787892C>T	ENST00000336174.6	-	8	652	c.540G>A	c.(538-540)ctG>ctA	p.L180L	STRADA_ENST00000579340.1_Silent_p.L122L|STRADA_ENST00000245865.5_Silent_p.L122L|STRADA_ENST00000582137.1_Silent_p.L151L|STRADA_ENST00000580039.1_5'UTR|RP11-51F16.8_ENST00000580553.1_Intron|STRADA_ENST00000447001.3_Silent_p.L136L|STRADA_ENST00000375840.4_Silent_p.L122L|STRADA_ENST00000392950.4_Silent_p.L143L	NM_001003787.2	NP_001003787.1	Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha	180	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|protein export from nucleus (GO:0006611)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|prostate(2)	13						CGAGGGCCTTCAGCACCCCCT	0.512																																					p.L180L		Atlas-SNP	.											.	STRADA	27	.	0			c.G540A						PASS	.						109.0	90.0	97.0					17																	61787892		2203	4300	6503	SO:0001819	synonymous_variant	92335	exon8			GGCCTTCAGCACC	AF308302	CCDS11642.1, CCDS32703.1, CCDS42367.1, CCDS54156.1, CCDS58585.1	17q23.3	2014-09-04			ENSG00000266173	ENSG00000266173			30172	protein-coding gene	gene with protein product	"""STE20-like pseudokinase"""	608626				12805220, 17921699	Standard	NM_153335		Approved	NY-BR-96, LYK5, Stlk, STRAD	uc002jbm.3	Q7RTN6	OTTHUMG00000178908	ENST00000336174.6:c.540G>A	17.37:g.61787892C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_001003787	B4DDE3|B4DW17|J3KTC9|Q5JPI2|Q7Z4K9|Q8NC31|Q8NCF1|Q9H272	Silent	SNP	ENST00000336174.6	37	CCDS32703.1																																																																																			.	.	none		0.512	STRADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443894.1		
GIGYF1	64599	hgsc.bcm.edu	37	7	100285476	100285476	+	Missense_Mutation	SNP	C	C	T	rs77794375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100285476C>T	ENST00000275732.5	-	3	1405	c.196G>A	c.(196-198)Gcc>Acc	p.A66T	GIGYF1_ENST00000471340.2_5'UTR	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	66					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					AGCACCGCGGCGAACTCCTTG	0.677													C|||	836	0.166933	0.0242	0.2824	5008	,	,		9778	0.497		0.0109	False		,,,				2504	0.0982				p.A66T		Atlas-SNP	.											.	GIGYF1	113	.	0			c.G196A						PASS	.	C	THR/ALA	102,4304		0,102,2101	46.0	50.0	49.0		196	4.1	0.9	7	dbSNP_131	49	64,8534		1,62,4236	yes	missense	GIGYF1	NM_022574.4	58	1,164,6337	TT,TC,CC		0.7444,2.315,1.2765	benign	66/1036	100285476	166,12838	2203	4299	6502	SO:0001583	missense	64599	exon3			CCGCGGCGAACTC	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"""GYF domain containing 1"""	612064	"""PERQ amino acid rich, with GYF domain 1"""	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.196G>A	7.37:g.100285476C>T	ENSP00000275732:p.Ala66Thr	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	147	56	0.380952	NM_022574	Q6Y7W7|Q8WZ38	Missense_Mutation	SNP	ENST00000275732.5	37	CCDS34708.1	382	0.1749084249084249	9	0.018292682926829267	75	0.20718232044198895	288	0.5034965034965035	10	0.013192612137203167	.	15.70	2.911933	0.52439	0.02315	0.007444	ENSG00000146830	ENST00000275732	D	0.83419	-1.72	5.01	4.11	0.48088	.	0.064498	0.64402	D	0.000011	T	0.00012	0.0000	M	0.61703	1.905	0.20196	P	0.9999285618	P	0.42161	0.772	B	0.30943	0.122	T	0.45086	-0.9285	9	0.15499	T	0.54	-4.1422	12.3836	0.55322	0.1694:0.8305:0.0:0.0	.	66	O75420	PERQ1_HUMAN	T	66	ENSP00000275732:A66T	ENSP00000275732:A66T	A	-	1	0	GIGYF1	100123412	0.104000	0.21937	0.878000	0.34440	0.891000	0.51852	0.451000	0.21779	1.290000	0.44636	0.563000	0.77884	GCC	C|0.942;T|0.058	0.058	strong		0.677	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574	
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67236097	67236097	+	Missense_Mutation	SNP	A	A	T	rs1060575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	52	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	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	
ANKLE2	23141	hgsc.bcm.edu	37	12	133331459	133331459	+	Missense_Mutation	SNP	G	G	C	rs7968520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133331459G>C	ENST00000357997.5	-	2	531	c.442C>G	c.(442-444)Cag>Gag	p.Q148E	ANKLE2_ENST00000337516.5_Missense_Mutation_p.Q148E|ANKLE2_ENST00000539605.1_Missense_Mutation_p.Q86E	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	148			Q -> E (in dbSNP:rs7968520).		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)		AAACCAGCCTGATCAGTTGGG	0.527													G|||	514	0.102636	0.2481	0.1859	5008	,	,		17910	0.0		0.0487	False		,,,				2504	0.0082				p.Q148E		Atlas-SNP	.											.	ANKLE2	76	.	0			c.C442G						PASS	.	G	GLU/GLN	830,2986		109,612,1187	66.0	67.0	67.0		442	4.5	0.0	12	dbSNP_116	67	521,7735		16,489,3623	yes	missense	ANKLE2	NM_015114.1	29	125,1101,4810	CC,CG,GG		6.3106,21.7505,11.1912	benign	148/939	133331459	1351,10721	1908	4128	6036	SO:0001583	missense	23141	exon2			CAGCCTGATCAGT	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.442C>G	12.37:g.133331459G>C	ENSP00000350686:p.Gln148Glu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	37	CCDS41869.1	190	0.08699633699633699	107	0.21747967479674796	51	0.1408839779005525	0	0.0	32	0.04221635883905013	G	9.223	1.033945	0.19590	0.217505	0.063106	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000337516	T;T;T	0.29142	2.02;2.0;1.58	5.38	4.48	0.54585	.	0.880964	0.10284	N	0.693133	T	0.00012	0.0000	L	0.41027	1.25	0.80722	P	0.0	B;P	0.40875	0.174;0.731	B;B	0.31442	0.069;0.13	T	0.17107	-1.0380	9	0.12103	T	0.63	-1.4383	12.8359	0.57773	0.0771:0.0:0.9229:0.0	rs7968520;rs7968520	148;148	Q86XL3-2;Q86XL3	.;ANKL2_HUMAN	E	86;148;148	ENSP00000446268:Q86E;ENSP00000350686:Q148E;ENSP00000337651:Q148E	ENSP00000337651:Q148E	Q	-	1	0	ANKLE2	131841532	0.000000	0.05858	0.015000	0.15790	0.035000	0.12851	0.675000	0.25232	2.547000	0.85894	0.650000	0.86243	CAG	G|0.917;C|0.083	0.083	strong		0.527	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		
TBC1D32	221322	hgsc.bcm.edu	37	6	121576518	121576518	+	Missense_Mutation	SNP	C	C	G	rs201833154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:121576518C>G	ENST00000398212.2	-	17	2023	c.1974G>C	c.(1972-1974)gaG>gaC	p.E658D	TBC1D32_ENST00000275159.6_Missense_Mutation_p.E658D	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	658					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)										AATCAGAACCCTCTACTGGAG	0.289													C|||	7	0.00139776	0.0053	0.0	5008	,	,		8412	0.0		0.0	False		,,,				2504	0.0				p.E658D		Atlas-SNP	.											C6orf170,colon,carcinoma,-2,1	C6orf170	146	1	0			c.G1974C						PASS	.	C	ASP/GLU	21,3563		0,21,1771	55.0	55.0	55.0		1974	-6.1	0.0	6		55	0,8094		0,0,4047	yes	missense	C6orf170	NM_152730.4	45	0,21,5818	GG,GC,CC		0.0,0.5859,0.1798	benign	658/1258	121576518	21,11657	1792	4047	5839	SO:0001583	missense	221322	exon17			AGAACCCTCTACT	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.1974G>C	6.37:g.121576518C>G	ENSP00000381270:p.Glu658Asp	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	C	6.113	0.389161	0.11581	0.005859	0.0	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.17370	2.28;2.28	5.81	-6.14	0.02111	.	0.553654	0.18121	N	0.151042	T	0.02571	0.0078	L	0.38175	1.15	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.40701	-0.9549	10	0.22109	T	0.4	.	6.2469	0.20823	0.1049:0.2255:0.0805:0.5892	.	658;658	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	D	658	ENSP00000275159:E658D;ENSP00000381270:E658D	ENSP00000275159:E658D	E	-	3	2	C6orf170	121618217	0.000000	0.05858	0.006000	0.13384	0.982000	0.71751	-1.136000	0.03222	-1.369000	0.02147	-0.150000	0.13652	GAG	.	.	weak		0.289	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
FCRLB	127943	hgsc.bcm.edu	37	1	161697072	161697072	+	Missense_Mutation	SNP	G	G	C	rs72704099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161697072G>C	ENST00000367948.2	+	8	1116	c.901G>C	c.(901-903)Gct>Cct	p.A301P	FCRLB_ENST00000495397.1_3'UTR|FCRLB_ENST00000367945.1_Missense_Mutation_p.Q245H|FCRLB_ENST00000367944.3_Missense_Mutation_p.S259T|FCRLB_ENST00000336830.5_Missense_Mutation_p.S266T|FCRLB_ENST00000367946.3_Missense_Mutation_p.Q252H|FCRLB_ENST00000392158.1_Missense_Mutation_p.A301P			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	301					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)			CACCGCCCCAGCTCCATGGGC	0.652													G|||	1565	0.3125	0.652	0.0951	5008	,	,		10331	0.4266		0.0606	False		,,,				2504	0.1493				p.A301P		Atlas-SNP	.											FCRLB,NS,carcinoma,0,1	FCRLB	35	1	0			c.G901C						scavenged	.	G	PRO/ALA	2396,2008		660,1076,466	21.0	25.0	23.0		901	3.0	0.0	1	dbSNP_131	23	679,7917		22,635,3641	yes	missense	FCRLB	NM_001002901.2	27	682,1711,4107	CC,CG,GG		7.899,45.5949,23.6538	benign	301/427	161697072	3075,9925	2202	4298	6500	SO:0001583	missense	127943	exon6			GCCCCAGCTCCAT	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.901G>C	1.37:g.161697072G>C	ENSP00000356925:p.Ala301Pro	Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Missense_Mutation	SNP	ENST00000367948.2	37	CCDS30927.1	612|612|612	0.2802197802197802|0.2802197802197802|0.2802197802197802	302|302|302	0.6138211382113821|0.6138211382113821|0.6138211382113821	41|41|41	0.1132596685082873|0.1132596685082873|0.1132596685082873	224|224|224	0.3916083916083916|0.3916083916083916|0.3916083916083916	45|45|45	0.059366754617414245|0.059366754617414245|0.059366754617414245	G|G|G	11.35|11.35|11.35	1.611622|1.611622|1.611622	0.28712|0.28712|0.28712	0.544051|0.544051|0.544051	0.07899|0.07899|0.07899	ENSG00000162746|ENSG00000162746|ENSG00000162746	ENST00000367948;ENST00000392158|ENST00000367946;ENST00000367945|ENST00000336830;ENST00000367944	D;D|T;T|T;T	0.96200|0.02067|0.02158	-3.94;-3.94|4.47;4.48|4.42;4.44	3.97|3.97|3.97	3.04|3.04|3.04	0.35103|0.35103|0.35103	.|.|.	1.082470|.|.	0.07330|.|.	N|.|.	0.879054|.|.	T|T|T	0.00815|0.00815|0.00815	0.0027|0.0027|0.0027	N|N|N	0.24115|0.24115|0.24115	0.695|0.695|0.695	0.80722|0.80722|0.80722	P|P|P	0.0|0.0|0.0	B|B;B|P;B;B	0.02656|0.33448|0.46512	0.0|0.412;0.412|0.879;0.027;0.027	B|B;B|B;B;B	0.01281|0.31946|0.39660	0.0|0.138;0.138|0.306;0.023;0.023	T|T|T	0.56920|0.56920|0.56920	-0.7899|-0.7899|-0.7899	9|8|8	0.12103|0.45353|0.87932	T|T|D	0.63|0.12|0	.|.|.	9.4625|9.4625|9.4625	0.38794|0.38794|0.38794	0.0:0.2171:0.7829:0.0|0.0:0.2171:0.7829:0.0|0.0:0.2171:0.7829:0.0	.|.|.	301|245;252|303;259;266	Q6BAA4|Q6BAA4-5;Q6BAA4-4|Q96DP6;Q6BAA4-3;Q6BAA4-2	FCRLB_HUMAN|.;.|.;.;.	P|H|T	301|252;245|266;259	ENSP00000356925:A301P;ENSP00000375999:A301P|ENSP00000356923:Q252H;ENSP00000356922:Q245H|ENSP00000338598:S266T;ENSP00000356921:S259T	ENSP00000356925:A301P|ENSP00000356922:Q245H|ENSP00000338598:S266T	A|Q|S	+|+|+	1|3|2	0|2|0	FCRLB|FCRLB|FCRLB	159963696|159963696|159963696	0.024000|0.024000|0.024000	0.19004|0.19004|0.19004	0.001000|0.001000|0.001000	0.08648|0.08648|0.08648	0.081000|0.081000|0.081000	0.17604|0.17604|0.17604	1.639000|1.639000|1.639000	0.37176|0.37176|0.37176	0.874000|0.874000|0.874000	0.35823|0.35823|0.35823	0.442000|0.442000|0.442000	0.29010|0.29010|0.29010	GCT|CAG|AGC	G|0.770;C|0.230	0.230	strong		0.652	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378	
ZNF860	344787	hgsc.bcm.edu	37	3	32031135	32031135	+	Silent	SNP	A	A	G	rs6419811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:32031135A>G	ENST00000360311.4	+	2	1113	c.564A>G	c.(562-564)tcA>tcG	p.S188S		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	188					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						ATGCTTCCTCAGTTCTAACGT	0.358													G|||	2356	0.470447	0.7988	0.3602	5008	,	,		20726	0.4524		0.1968	False		,,,				2504	0.4049				p.S188S		Atlas-SNP	.											ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	0			c.A564G						PASS	.	G		938,446		325,288,79	58.0	44.0	48.0		564	0.3	0.0	3	dbSNP_116	48	608,2574		58,492,1041	no	coding-synonymous	ZNF860	NM_001137674.2		383,780,1120	GG,GA,AA		19.1075,32.2254,33.859		188/633	32031135	1546,3020	692	1591	2283	SO:0001819	synonymous_variant	344787	exon2			TTCCTCAGTTCTA	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.564A>G	3.37:g.32031135A>G		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	163	70	0.429448	NM_001137674	B4DFA4	Silent	SNP	ENST00000360311.4	37	CCDS46784.1																																																																																			A|0.567;G|0.433	0.433	strong		0.358	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
ZNF268	10795	hgsc.bcm.edu	37	12	133780309	133780309	+	Missense_Mutation	SNP	G	G	T	rs36127550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133780309G>T	ENST00000536435.2	+	6	2367	c.2037G>T	c.(2035-2037)ttG>ttT	p.L679F	ZNF268_ENST00000536899.2_3'UTR|ZNF268_ENST00000542986.2_3'UTR|ZNF268_ENST00000541009.2_3'UTR|ZNF268_ENST00000228289.5_Missense_Mutation_p.L679F|ZNF268_ENST00000537565.1_Missense_Mutation_p.L518F	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	679					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)	p.L679F(1)		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)		CCTTTAGTTTGAAGTCCCAGC	0.418													G|||	710	0.141773	0.0204	0.2709	5008	,	,		21719	0.1448		0.1581	False		,,,				2504	0.1943				p.L679F		Atlas-SNP	.											ZNF268,NS,carcinoma,0,1	ZNF268	71	1	1	Substitution - Missense(1)	kidney(1)	c.G2037T						PASS	.	G	PHE/LEU,PHE/LEU,,,,,,PHE/LEU,	80,1304		1,78,613	77.0	72.0	74.0		2037,1788,,,,,,2037,	-7.1	0.0	12	dbSNP_126	74	534,2648		40,454,1097	yes	missense,missense,utr-3,utr-3,utr-3,utr-3,utr-3,missense,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	22,22,,,,,,22,	41,532,1710	TT,TG,GG		16.7819,5.7803,13.4472	probably-damaging,probably-damaging,,,,,,probably-damaging,	679/948,596/865,,,,,,679/948,	133780309	614,3952	692	1591	2283	SO:0001583	missense	10795	exon6			TAGTTTGAAGTCC	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.2037G>T	12.37:g.133780309G>T	ENSP00000444412:p.Leu679Phe	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001165881	Q8TDG8|Q96RH4|Q9BZJ9	Missense_Mutation	SNP	ENST00000536435.2	37	CCDS45012.1	310	0.14194139194139194	14	0.028455284552845527	96	0.26519337016574585	79	0.1381118881118881	121	0.15963060686015831	G	6.497	0.459803	0.12342	0.057803	0.167819	ENSG00000090612	ENST00000541009;ENST00000228289;ENST00000537565;ENST00000541019	T;T	0.03951	3.75;3.75	4.28	-7.08	0.01558	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.14438	0.006;0.01	B;B	0.14023	0.005;0.01	T	0.49818	-0.8899	7	.	.	.	.	1.3194	0.02113	0.1538:0.2499:0.24:0.3563	.	679;518	Q14587;Q14587-2	ZN268_HUMAN;.	F	679;679;518;518	ENSP00000228289:L679F;ENSP00000445713:L518F	.	L	+	3	2	ZNF268	.	0.000000	0.05858	0.001000	0.08648	0.994000	0.84299	-1.190000	0.03058	-0.985000	0.03503	0.655000	0.94253	TTG	G|0.858;T|0.142	0.142	strong		0.418	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943	
RP1L1	94137	hgsc.bcm.edu	37	8	10470130	10470130	+	Missense_Mutation	SNP	C	C	T	rs79401306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10470130C>T	ENST00000382483.3	-	4	1701	c.1478G>A	c.(1477-1479)cGg>cAg	p.R493Q		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	493					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)		TCCAGCTTTCCGCTCAGCCCC	0.721													C|||	103	0.0205671	0.0764	0.0029	5008	,	,		15146	0.0		0.0	False		,,,				2504	0.0				p.R493Q		Atlas-SNP	.											.	RP1L1	453	.	0			c.G1478A						PASS	.	C	GLN/ARG	205,3593		6,193,1700	26.0	30.0	29.0		1478	-2.6	0.0	8	dbSNP_131	29	3,8241		0,3,4119	yes	missense	RP1L1	NM_178857.5	43	6,196,5819	TT,TC,CC		0.0364,5.3976,1.7273	possibly-damaging	493/2401	10470130	208,11834	1899	4122	6021	SO:0001583	missense	94137	exon4			GCTTTCCGCTCAG	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.1478G>A	8.37:g.10470130C>T	ENSP00000371923:p.Arg493Gln	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	33	11	0.333333	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	44	0.020146520146520148	44	0.08943089430894309	0	0.0	0	0.0	0	0.0	C	7.544	0.661253	0.14645	0.053976	3.64E-4	ENSG00000183638	ENST00000382483	T	0.04083	3.71	4.06	-2.57	0.06248	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	B	0.16396	0.017	B	0.04013	0.001	T	0.45190	-0.9278	9	0.41790	T	0.15	14.544	4.0305	0.09706	0.1672:0.3134:0.0:0.5194	.	493	A6NKC6	.	Q	493	ENSP00000371923:R493Q	ENSP00000371923:R493Q	R	-	2	0	RP1L1	10507540	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.619000	0.05572	-0.838000	0.04218	0.561000	0.74099	CGG	C|0.987;T|0.013	0.013	strong		0.721	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
GYPB	2994	hgsc.bcm.edu	37	4	145041720	145041720	+	Intron	SNP	A	A	G	rs7682260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:145041720A>G	ENST00000283126.7	-	1	93				GYPA_ENST00000512789.1_Intron|GYPA_ENST00000512064.1_Missense_Mutation_p.L20S|RP11-673E1.4_ENST00000506982.1_RNA|GYPA_ENST00000503627.1_Missense_Mutation_p.L20S|GYPA_ENST00000535709.1_5'UTR|GYPA_ENST00000504786.1_Missense_Mutation_p.L20S|GYPA_ENST00000324022.10_Intron|GYPA_ENST00000360771.4_Missense_Mutation_p.L20S			P06028	GLPB_HUMAN	glycophorin B (MNS blood group)							integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|skin(1)	4	all_hematologic(180;0.158)					AGTGGTACTTAATGCTGATAT	0.353													G|||	1428	0.285144	0.1944	0.3545	5008	,	,		12360	0.3125		0.2813	False		,,,				2504	0.3344				p.L20S		Atlas-SNP	.											GYPA,NS,carcinoma,0,1	GYPA	27	1	0			c.T59C						scavenged	.	G	SER/LEU	737,3513		243,251,1631	57.0	30.0	39.0		59	-3.4	0.0	4	dbSNP_116	39	1997,6329		706,585,2872	no	missense	GYPA	NM_002099.6	145	949,836,4503	GG,GA,AA		23.9851,17.3412,21.7398	benign	20/151	145041720	2734,9842	2125	4163	6288	SO:0001627	intron_variant	2993	exon2			GTACTTAATGCTG		CCDS54809.1	4q31.21	2014-09-17	2006-02-23			ENSG00000250361		"""CD molecules"", ""Blood group antigens"""	4703	protein-coding gene	gene with protein product		111740	"""glycophorin B (includes Ss blood group)"", ""glycophorin B (Ss blood group)"""	MNS			Standard	NM_002100		Approved	GPB, SS, CD235b		P06028		ENST00000283126.7:c.37+20031T>C	4.37:g.145041720A>G		Somatic	181	29	0.160221		WXS	Illumina HiSeq	Phase_I	196	30	0.153061	NM_002099	B8Q174|E2QBW7|Q0VAF4|Q58HE9|Q58HF0|Q58HF1|Q9UCH7	Missense_Mutation	SNP	ENST00000283126.7	37		.	.	.	.	.	.	.	.	.	.	G	2.787	-0.252207	0.05829	0.173412	0.239851	ENSG00000170180	ENST00000360771;ENST00000512064;ENST00000504786;ENST00000503627;ENST00000394119	T;T;T;T	0.04809	4.59;4.61;4.54;3.55	1.71	-3.42	0.04825	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.46555	-0.9183	7	0.52906	T	0.07	.	0.8306	0.01129	0.3297:0.3169:0.194:0.1595	rs7682260;rs17845377;rs17858231	20;20;20	E9PD10;E7EQF3;Q16336	.;.;.	S	20	ENSP00000354003:L20S;ENSP00000426130:L20S;ENSP00000425549:L20S;ENSP00000421243:L20S	ENSP00000354003:L20S	L	-	2	0	GYPA	145261170	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.801000	0.04550	-2.458000	0.00538	-2.395000	0.00226	TTA	A|0.519;G|0.481	0.481	strong		0.353	GYPB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002100	
CEP131	22994	hgsc.bcm.edu	37	17	79170576	79170576	+	Silent	SNP	C	C	T	rs1542961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79170576C>T	ENST00000269392.4	-	15	2080	c.1833G>A	c.(1831-1833)gcG>gcA	p.A611A	RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000450824.2_Silent_p.A608A|AZI1_ENST00000575907.1_Silent_p.A611A|AZI1_ENST00000374782.3_Silent_p.A608A	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		611					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)			GCCGGCTCAGCGCCTTCTCTG	0.701													C|||	1108	0.221246	0.2927	0.2622	5008	,	,		12663	0.0149		0.4036	False		,,,				2504	0.1207				p.A608A		Atlas-SNP	.											AZI1_ENST00000450824,NS,carcinoma,0,2	AZI1	145	2	0			c.G1824A						PASS	.	C	,	1300,3068		187,926,1071	23.0	22.0	22.0		1824,1824	0.6	0.1	17	dbSNP_88	22	3373,5197		688,1997,1600	no	coding-synonymous,coding-synonymous	AZI1	NM_001009811.2,NM_014984.2	,	875,2923,2671	TT,TC,CC		39.3582,29.7619,36.1184	,	608/1045,608/1081	79170576	4673,8265	2184	4285	6469	SO:0001819	synonymous_variant	22994	exon15			GCTCAGCGCCTTC																												ENST00000269392.4:c.1833G>A	17.37:g.79170576C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_014984	A6NHI8|B2RN11|Q96F50	Silent	SNP	ENST00000269392.4	37																																																																																				C|0.699;T|0.301	0.301	strong		0.701	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
CAPN9	10753	hgsc.bcm.edu	37	1	230895340	230895340	+	Missense_Mutation	SNP	C	C	A	rs28359608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230895340C>A	ENST00000271971.2	+	3	479	c.366C>A	c.(364-366)agC>agA	p.S122R	CAPN9_ENST00000354537.1_Missense_Mutation_p.S122R|CAPN9_ENST00000366666.2_Intron|RP11-99J16__A.2_ENST00000412344.1_RNA	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	122	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		S -> R (in dbSNP:rs28359608). {ECO:0000269|Ref.3}.		digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				AGGACCAAAGCTTTGGCCCTG	0.562													C|||	775	0.154752	0.174	0.0648	5008	,	,		17831	0.0764		0.1451	False		,,,				2504	0.2832				p.S122R		Atlas-SNP	.											.	CAPN9	116	.	0			c.C366A						PASS	.	C	ARG/SER,ARG/SER	738,3668	304.1+/-288.3	70,598,1535	54.0	52.0	53.0		366,366	-1.1	0.9	1	dbSNP_125	53	1196,7404	243.1+/-272.8	80,1036,3184	yes	missense,missense	CAPN9	NM_006615.2,NM_016452.1	110,110	150,1634,4719	AA,AC,CC		13.907,16.7499,14.8701	probably-damaging,probably-damaging	122/691,122/665	230895340	1934,11072	2203	4300	6503	SO:0001583	missense	10753	exon3			CCAAAGCTTTGGC	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.366C>A	1.37:g.230895340C>A	ENSP00000271971:p.Ser122Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	37	CCDS1586.1	293	0.13415750915750915	97	0.19715447154471544	25	0.06906077348066299	51	0.08916083916083917	120	0.158311345646438	C	14.90	2.672015	0.47781	0.167499	0.13907	ENSG00000135773	ENST00000271971;ENST00000354537	D;D	0.89196	-2.48;-2.48	5.02	-1.09	0.09904	Peptidase C2, calpain, catalytic domain (3);	0.533147	0.23962	N	0.042855	T	0.00784	0.0026	M	0.93720	3.45	0.09310	P	1.0	B;P	0.43169	0.21;0.8	B;P	0.47528	0.126;0.549	T	0.52403	-0.8580	9	0.87932	D	0	.	4.6129	0.12411	0.154:0.3686:0.0:0.4774	rs28359608;rs28359608	122;122	O14815-2;O14815	.;CAN9_HUMAN	R	122	ENSP00000271971:S122R;ENSP00000346538:S122R	ENSP00000271971:S122R	S	+	3	2	CAPN9	228961963	1.000000	0.71417	0.937000	0.37676	0.404000	0.30871	1.710000	0.37920	-0.026000	0.13895	-0.793000	0.03317	AGC	C|0.861;A|0.139	0.139	strong		0.562	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036971	33036971	+	Silent	SNP	C	C	T	rs2308928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33036971C>T	ENST00000419277.1	-	4	582	c.453G>A	c.(451-453)acG>acA	p.T151T	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Silent_p.T151T	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	151	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						TGCACAGCCACGTGACGTTGA	0.567													.|||	2198	0.438898	0.5802	0.2839	5008	,	,		19188	0.6796		0.1889	False		,,,				2504	0.3671				p.T151T		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G453A						PASS	.	C	,,	1423,1595		327,769,413	144.0	168.0	160.0		453,453,453	-2.0	0.9	6	dbSNP_126	160	960,4456		72,816,1820	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	399,1585,2233	TT,TC,CC		17.7253,47.1504,28.2547	,,	151/261,151/261,151/261	33036971	2383,6051	1509	2708	4217	SO:0001819	synonymous_variant	3113	exon3			CAGCCACGTGACG	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.453G>A	6.37:g.33036971C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1	864	0.3956043956043956	274	0.556910569105691	89	0.24585635359116023	371	0.6486013986013986	130	0.17150395778364116	C	9.336	1.061867	0.19987	0.471504	0.177253	ENSG00000231389	ENST00000437811	.	.	.	3.4	-1.99	0.07457	.	.	.	.	.	T	0.06096	0.0158	.	.	.	0.09310	P	0.9999999999999838	.	.	.	.	.	.	T	0.35649	-0.9780	3	.	.	.	.	0.2576	0.00214	0.3011:0.282:0.1489:0.2681	rs2308928;rs17850579	.	.	.	M	19	.	.	V	-	1	0	HLA-DPA1	33144949	0.000000	0.05858	0.911000	0.35937	0.725000	0.41563	-5.615000	0.00109	-0.669000	0.05289	-0.165000	0.13383	GTG	C|0.695;T|0.305	0.305	strong		0.567	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
PDP1	54704	hgsc.bcm.edu	37	8	94935623	94935623	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:94935623A>G	ENST00000297598.4	+	2	1605	c.1336A>G	c.(1336-1338)Ata>Gta	p.I446V	PDP1_ENST00000396200.3_Missense_Mutation_p.I471V|PDP1_ENST00000520728.1_Missense_Mutation_p.I446V|PDP1_ENST00000517764.1_Missense_Mutation_p.I446V	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	446					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|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)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						CCAACAGCCAATAGCTGTTGG	0.493																																					p.I471V		Atlas-SNP	.											PDP1,caecum,carcinoma,-2,1	PDP1	97	1	0			c.A1411G						PASS	.						80.0	80.0	80.0					8																	94935623		2203	4300	6503	SO:0001583	missense	54704	exon3			CAGCCAATAGCTG	AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9279	protein-coding gene	gene with protein product		605993	"""protein phosphatase 2C, magnesium-dependent, catalytic subunit"""	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.1336A>G	8.37:g.94935623A>G	ENSP00000297598:p.Ile446Val	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	221	117	0.529412	NM_001161780	B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	A	5.314	0.243239	0.10077	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000517764	T;T;T;T	0.41065	1.03;1.03;1.01;1.03	6.03	6.03	0.97812	Protein phosphatase 2C-like (3);	0.127835	0.64402	D	0.000016	T	0.16896	0.0406	N	0.02247	-0.625	0.42964	D	0.994412	B;B	0.12013	0.005;0.001	B;B	0.10450	0.005;0.005	T	0.18871	-1.0323	10	0.02654	T	1	-7.6316	12.4101	0.55461	0.86:0.14:0.0:0.0	.	497;446	B4DYX8;Q9P0J1	.;PDP1_HUMAN	V	446;446;471;446	ENSP00000297598:I446V;ENSP00000428317:I446V;ENSP00000379503:I471V;ENSP00000430380:I446V	ENSP00000297598:I446V	I	+	1	0	PDP1	95004799	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	4.348000	0.59379	2.308000	0.77769	0.533000	0.62120	ATA	.	.	none		0.493	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444	
RGS10	6001	hgsc.bcm.edu	37	10	121275099	121275099	+	Silent	SNP	G	G	A	rs11550215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:121275099G>A	ENST00000369101.3	-	3	324	c.297C>T	c.(295-297)aaC>aaT	p.N99N	RGS10_ENST00000469575.1_Intron|RGS10_ENST00000392865.1_Silent_p.N93N|RGS10_ENST00000369103.2_Silent_p.N107N			O43665	RGS10_HUMAN	regulator of G-protein signaling 10	99	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(2)|large_intestine(1)|lung(3)	6		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00105)|GBM - Glioblastoma multiforme(135;0.195)		GCCCCTCCACGTTGACCTGTG	0.552													G|||	160	0.0319489	0.0227	0.0749	5008	,	,		17708	0.001		0.0527	False		,,,				2504	0.0245				p.N107N		Atlas-SNP	.											.	RGS10	14	.	0			c.C321T						PASS	.	G	,	136,4270	98.0+/-136.7	0,136,2067	215.0	171.0	186.0		321,279	-4.1	1.0	10	dbSNP_120	186	524,8076	146.5+/-202.0	10,504,3786	no	coding-synonymous,coding-synonymous	RGS10	NM_001005339.1,NM_002925.3	,	10,640,5853	AA,AG,GG		6.093,3.0867,5.0746	,	107/182,93/168	121275099	660,12346	2203	4300	6503	SO:0001819	synonymous_variant	6001	exon4			CTCCACGTTGACC	AF045229	CCDS31294.1, CCDS41572.1	10q25	2007-08-14	2007-08-14		ENSG00000148908	ENSG00000148908		"""Regulators of G-protein signaling"""	9992	protein-coding gene	gene with protein product		602856	"""regulator of G-protein signalling 10"""			8774883	Standard	NM_002925		Approved		uc001leg.3	O43665	OTTHUMG00000019150	ENST00000369101.3:c.297C>T	10.37:g.121275099G>A		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	250	128	0.512	NM_001005339	A8K408|B1AMR8|Q6IAZ6|Q96GN0	Silent	SNP	ENST00000369101.3	37																																																																																				G|0.951;A|0.049	0.049	strong		0.552	RGS10-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050655.1	NM_002925	
EBI3	10148	hgsc.bcm.edu	37	19	4236996	4236996	+	Missense_Mutation	SNP	G	G	A	rs4740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4236996G>A	ENST00000221847.5	+	5	654	c.601G>A	c.(601-603)Gtc>Atc	p.V201I		NM_005755.2	NP_005746.2	Q14213	IL27B_HUMAN	Epstein-Barr virus induced 3	201	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs4740). {ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		cytokine-mediated signaling pathway (GO:0019221)|humoral immune response (GO:0006959)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|T-helper 1 type immune response (GO:0042088)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0336)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGTACTACGTCCAAGTGGC	0.607													g|||	2246	0.448482	0.6233	0.2738	5008	,	,		15690	0.4415		0.3052	False		,,,				2504	0.4908				p.V201I		Atlas-SNP	.											.	EBI3	15	.	0			c.G601A						PASS	.	G	ILE/VAL	2572,1834	633.1+/-396.0	752,1068,383	54.0	54.0	54.0		601	-8.9	0.0	19	dbSNP_52	54	2456,6144	401.9+/-347.3	368,1720,2212	yes	missense	EBI3	NM_005755.2	29	1120,2788,2595	AA,AG,GG		28.5581,41.6251,38.6591	benign	201/230	4236996	5028,7978	2203	4300	6503	SO:0001583	missense	10148	exon5			TACTACGTCCAAG	L08187	CCDS12123.1	19p13	2013-02-11	2008-09-12		ENSG00000105246	ENSG00000105246		"""Fibronectin type III domain containing"""	3129	protein-coding gene	gene with protein product	"""IL27 subunit"", ""IL35 subunit"""	605816				8551575	Standard	NM_005755		Approved		uc002lzu.3	Q14213		ENST00000221847.5:c.601G>A	19.37:g.4236996G>A	ENSP00000221847:p.Val201Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_005755	A0N0N2|O75269	Missense_Mutation	SNP	ENST00000221847.5	37	CCDS12123.1	889	0.40705128205128205	297	0.6036585365853658	100	0.27624309392265195	254	0.44405594405594406	238	0.31398416886543534	G	2.664	-0.279141	0.05642	0.583749	0.285581	ENSG00000105246	ENST00000221847	T	0.59083	0.29	5.41	-8.95	0.00765	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.720518	0.13155	N	0.409544	T	0.00012	0.0000	N	0.10664	0.02	0.80722	P	0.0	B	0.21753	0.06	B	0.18871	0.023	T	0.29822	-0.9999	9	0.20046	T	0.44	-22.3909	20.4741	0.99163	0.1443:0.0:0.8557:0.0	rs4740;rs82395;rs710083;rs3170371;rs3888633;rs17764870;rs57865374;rs4740	201	Q14213	IL27B_HUMAN	I	201	ENSP00000221847:V201I	ENSP00000221847:V201I	V	+	1	0	EBI3	4187996	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.447000	0.02396	-2.080000	0.00870	-1.223000	0.01593	GTC	A|0.399;C|0.003	0.399	strong		0.607	EBI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458005.1		
TSPAN18	90139	hgsc.bcm.edu	37	11	44948263	44948263	+	Silent	SNP	C	C	T	rs34695714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44948263C>T	ENST00000520358.2	+	9	1069	c.654C>T	c.(652-654)taC>taT	p.Y218Y	TSPAN18_ENST00000340160.3_Silent_p.Y218Y			Q96SJ8	TSN18_HUMAN	tetraspanin 18	218						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						TCGAGACCTACGTCTACTTGG	0.602											OREG0020922	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	129	0.0257588	0.0953	0.0043	5008	,	,		17858	0.0		0.0	False		,,,				2504	0.0				p.Y218Y		Atlas-SNP	.											TSPAN18,colon,carcinoma,+1,1	TSPAN18	38	1	0			c.C654T						PASS	.	C		320,4086	169.8+/-200.3	6,308,1889	217.0	187.0	197.0		654	-1.0	1.0	11	dbSNP_126	197	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	TSPAN18	NM_130783.4		6,310,6186	TT,TC,CC		0.0233,7.2628,2.4762		218/249	44948263	322,12682	2203	4299	6502	SO:0001819	synonymous_variant	90139	exon8			GACCTACGTCTAC	AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"""Tetraspanins"""	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.654C>T	11.37:g.44948263C>T		Somatic	107	0	0	927	WXS	Illumina HiSeq	Phase_I	124	65	0.524194	NM_130783	Q6UY44|Q8NBI9	Silent	SNP	ENST00000520358.2	37	CCDS7910.1	58	0.026556776556776556	57	0.11585365853658537	1	0.0027624309392265192	0	0.0	0	0.0	C	3.000	-0.206236	0.06180	0.072628	2.33E-4	ENSG00000157570	ENST00000518429	.	.	.	4.54	-1.0	0.10196	.	.	.	.	.	T	0.00666	0.0022	.	.	.	0.09310	P	0.9999999999999879	.	.	.	.	.	.	T	0.23511	-1.0186	3	.	.	.	.	9.8138	0.40840	0.0:0.4987:0.0:0.5013	rs34695714	.	.	.	C	222	.	.	R	+	1	0	TSPAN18	44904839	0.935000	0.31712	0.991000	0.47740	0.329000	0.28539	0.060000	0.14342	-0.186000	0.10533	0.479000	0.44913	CGT	C|0.972;T|0.028	0.028	strong		0.602	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783	
OR2T4	127074	hgsc.bcm.edu	37	1	248525071	248525071	+	Silent	SNP	T	T	C	rs28499298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248525071T>C	ENST00000366475.1	+	1	189	c.189T>C	c.(187-189)atT>atC	p.I63I		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, 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)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTGTGGTCATTTTTGTGGTTT	0.483													t|||	1734	0.346246	0.3926	0.2896	5008	,	,		21339	0.4385		0.1948	False		,,,				2504	0.3845				p.I63I		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	1	0			c.T189C						PASS	.						196.0	194.0	195.0					1																	248525071		2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			GGTCATTTTTGTG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.189T>C	1.37:g.248525071T>C		Somatic	778	2	0.00257069		WXS	Illumina HiSeq	Phase_I	695	306	0.440288	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			T|0.769;C|0.231	0.231	strong		0.483	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
ZNF737	100129842	hgsc.bcm.edu	37	19	20727932	20727932	+	Silent	SNP	G	G	A	rs33926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:20727932G>A	ENST00000427401.4	-	4	1171	c.1077C>T	c.(1075-1077)caC>caT	p.H359H		NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	359					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)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						GAATTATCTTGTGTGTAGTAA	0.393													a|||	2793	0.557708	0.5893	0.5893	5008	,	,		22316	0.6171		0.495	False		,,,				2504	0.4959				p.H359H		Atlas-SNP	.											.	ZNF737	50	.	0			c.C1077T						PASS	.	A		793,591		229,335,128	18.0	18.0	18.0		1077	-0.6	0.4	19	dbSNP_76	18	1520,1662		369,782,440	no	coding-synonymous	ZNF737	NM_001159293.1		598,1117,568	AA,AG,GG		47.7687,42.7023,49.343		359/537	20727932	2313,2253	692	1591	2283	SO:0001819	synonymous_variant	100129842	exon4			TATCTTGTGTGTA	BC015765	CCDS54238.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	32468	protein-coding gene	gene with protein product		603984					Standard	NM_001159293		Approved	ZNF102	uc002npa.3	O75373		ENST00000427401.4:c.1077C>T	19.37:g.20727932G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_001159293	C9JHM3	Silent	SNP	ENST00000427401.4	37	CCDS54238.1																																																																																			G|0.431;A|0.569	0.569	strong		0.393	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289	
PSG11	5680	hgsc.bcm.edu	37	19	43528932	43528932	+	Missense_Mutation	SNP	C	C	T	rs111739483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43528932C>T	ENST00000401740.1	-	2	444	c.341G>A	c.(340-342)cGg>cAg	p.R114Q	PSG11_ENST00000403486.1_Intron|PSG11_ENST00000320078.7_Missense_Mutation_p.R114Q|PSG11_ENST00000306322.7_Intron			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	114	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)				TGCGTCCTCCCGGGTGACATT	0.443													.|||	228	0.0455272	0.0605	0.0058	5008	,	,		20906	0.0883		0.0	False		,,,				2504	0.0562				p.R114Q		Atlas-SNP	.											.	PSG11	57	.	0			c.G341A						PASS	.	C	,GLN/ARG,	166,4230		15,136,2047	157.0	153.0	154.0		,341,	-1.9	0.0	19	dbSNP_132	154	16,8574		0,16,4279	no	intron,missense,intron	PSG11	NM_001113410.1,NM_002785.2,NM_203287.1	,43,	15,152,6326	TT,TC,CC		0.1863,3.7762,1.4015	,,	,114/336,	43528932	182,12804	2198	4295	6493	SO:0001583	missense	5680	exon2			TCCTCCCGGGTGA	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.341G>A	19.37:g.43528932C>T	ENSP00000384995:p.Arg114Gln	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	277	133	0.480144	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	79	0.036172161172161175	28	0.056910569105691054	1	0.0027624309392265192	50	0.08741258741258741	0	0.0	t	0.021	-1.424426	0.01126	0.037762	0.001863	ENSG00000243130	ENST00000320078;ENST00000401740	T;T	0.65732	-0.17;-0.17	0.929	-1.86	0.07760	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00967	0.0032	N	0.03983	-0.305	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.03202	-1.1061	9	0.07990	T	0.79	.	1.4589	0.02391	0.3155:0.2605:0.0:0.424	.	114	Q9UQ72	PSG11_HUMAN	Q	114	ENSP00000319140:R114Q;ENSP00000384995:R114Q	ENSP00000319140:R114Q	R	-	2	0	PSG11	48220772	0.000000	0.05858	0.024000	0.17045	0.008000	0.06430	-2.383000	0.01063	-1.324000	0.02272	-1.109000	0.02080	CGG	C|0.977;T|0.023	0.023	strong		0.443	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
RANBP6	26953	hgsc.bcm.edu	37	9	6015011	6015011	+	Silent	SNP	T	T	C	rs343500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:6015011T>C	ENST00000259569.5	-	1	607	c.597A>G	c.(595-597)acA>acG	p.T199T	RANBP6_ENST00000485372.1_Intron	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	199					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T199T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		TAGCGGATAATGTCCTGATTG	0.428													T|||	756	0.150958	0.3192	0.0245	5008	,	,		23481	0.2183		0.0159	False		,,,				2504	0.0828				p.T199T		Atlas-SNP	.											RANBP6,NS,carcinoma,0,1	RANBP6	127	1	1	Substitution - coding silent(1)	stomach(1)	c.A597G						PASS	.	T		1203,3203	418.9+/-338.5	159,885,1159	93.0	84.0	87.0		597	-7.2	0.9	9	dbSNP_79	87	85,8515	50.2+/-110.2	0,85,4215	no	coding-synonymous	RANBP6	NM_012416.3		159,970,5374	CC,CT,TT		0.9884,27.3037,9.9031		199/1106	6015011	1288,11718	2203	4300	6503	SO:0001819	synonymous_variant	26953	exon1			GGATAATGTCCTG	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.597A>G	9.37:g.6015011T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Silent	SNP	ENST00000259569.5	37	CCDS6467.1																																																																																			T|0.882;C|0.118	0.118	strong		0.428	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416	
UPK1A	11045	hgsc.bcm.edu	37	19	36157740	36157740	+	Missense_Mutation	SNP	C	C	T	rs61741212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	204	102	0.5	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		
ABCC12	94160	hgsc.bcm.edu	37	16	48175235	48175235	+	Missense_Mutation	SNP	G	G	T	rs16945874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48175235G>T	ENST00000311303.3	-	3	650	c.305C>A	c.(304-306)gCa>gAa	p.A102E	ABCC12_ENST00000448542.1_Missense_Mutation_p.A102E|ABCC12_ENST00000416054.1_Missense_Mutation_p.A102E	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	102			A -> E (in dbSNP:rs16945874).			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)				ACCCACCCTTGCTACCTCTTC	0.498													T|||	728	0.145367	0.4297	0.0879	5008	,	,		21622	0.0		0.0875	False		,,,				2504	0.0112				p.A102E		Atlas-SNP	.											.	ABCC12	190	.	0			c.C305A						PASS	.	T	GLU/ALA	1552,2850	668.6+/-402.0	282,988,931	110.0	98.0	102.0		305	2.9	0.1	16	dbSNP_123	102	613,7987	791.9+/-407.5	20,573,3707	yes	missense	ABCC12	NM_033226.2	107	302,1561,4638	TT,TG,GG		7.1279,35.2567,16.6513	benign	102/1360	48175235	2165,10837	2201	4300	6501	SO:0001583	missense	94160	exon3			ACCCTTGCTACCT	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.305C>A	16.37:g.48175235G>T	ENSP00000311030:p.Ala102Glu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	298	0.13644688644688643	194	0.3943089430894309	39	0.10773480662983426	0	0.0	65	0.08575197889182058	T	2.421	-0.333064	0.05278	0.352567	0.071279	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939;ENST00000416054;ENST00000527640	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.38	2.93	0.34026	ABC transporter, transmembrane domain, type 1 (1);	0.436542	0.25146	N	0.032792	T	0.00012	0.0000	L	0.28274	0.84	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.0	B;B	0.16289	0.015;0.001	T	0.41034	-0.9531	9	0.02654	T	1	.	7.8707	0.29565	0.0:0.081:0.3552:0.5638	rs16945874;rs52837329;rs59188678;rs16945874	102;102	Q96J65-2;Q96J65	.;MRP9_HUMAN	E	102	ENSP00000311030:A102E;ENSP00000401855:A102E;ENSP00000413046:A102E;ENSP00000436647:A102E	ENSP00000311030:A102E	A	-	2	0	ABCC12	46732736	0.009000	0.17119	0.085000	0.20634	0.334000	0.28698	0.911000	0.28584	0.438000	0.26450	-1.417000	0.01113	GCA	G|0.841;T|0.159	0.159	strong		0.498	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412066	105412066	+	Missense_Mutation	SNP	C	C	T	rs77154428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105412066C>T	ENST00000333244.5	-	7	9841	c.9722G>A	c.(9721-9723)cGc>cAc	p.R3241H	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3241						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)			GGGGCCCTTGCGATCTACTTT	0.607																																					p.R3241H		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-1,2	AHNAK2	719	2	0			c.G9722A						scavenged	.						130.0	94.0	105.0					14																	105412066		1876	4070	5946	SO:0001583	missense	113146	exon7			CCCTTGCGATCTA	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.9722G>A	14.37:g.105412066C>T	ENSP00000353114:p.Arg3241His	Somatic	252	3	0.0119048		WXS	Illumina HiSeq	Phase_I	368	135	0.366848	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	936	0.42857142857142855	224	0.45528455284552843	165	0.4558011049723757	168	0.2937062937062937	379	0.5	c	2.256	-0.370373	0.05069	.	.	ENSG00000185567	ENST00000333244	T	0.00678	5.87	2.75	1.55	0.23275	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.42908	0.793	B	0.23716	0.048	T	0.00004	-1.2570	8	0.25106	T	0.35	.	8.4104	0.32640	0.7997:0.2003:0.0:0.0	.	3241	Q8IVF2	AHNK2_HUMAN	H	3241	ENSP00000353114:R3241H	ENSP00000353114:R3241H	R	-	2	0	AHNAK2	104483111	0.004000	0.15560	0.001000	0.08648	0.001000	0.01503	0.432000	0.21461	0.248000	0.21435	-0.842000	0.03052	CGC	C|0.547;T|0.453	0.453	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ZNF180	7733	hgsc.bcm.edu	37	19	45001398	45001398	+	Silent	SNP	G	G	A	rs10423647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45001398G>A	ENST00000221327.4	-	2	351	c.70C>T	c.(70-72)Ctg>Ttg	p.L24L	ZNF180_ENST00000587047.1_Silent_p.A25A|ZNF180_ENST00000586637.1_5'UTR|ZNF180_ENST00000592529.1_5'UTR|ZNF180_ENST00000585514.1_5'UTR|ZNF180_ENST00000391956.4_Silent_p.L24L	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	24					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(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				CTCTCCTCCAGGCACAGCAGG	0.622													G|||	453	0.0904553	0.3275	0.0173	5008	,	,		16153	0.0		0.004	False		,,,				2504	0.0041				p.L24L	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.C70T						PASS	.	G		1089,3317	389.3+/-327.3	128,833,1242	42.0	39.0	40.0		70	2.5	0.2	19	dbSNP_119	40	10,8590	5.7+/-21.5	0,10,4290	no	coding-synonymous	ZNF180	NM_013256.3		128,843,5532	AA,AG,GG		0.1163,24.7163,8.4499		24/693	45001398	1099,11907	2203	4300	6503	SO:0001819	synonymous_variant	7733	exon2			CCTCCAGGCACAG	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.70C>T	19.37:g.45001398G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																			G|0.906;A|0.094	0.094	strong		0.622	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
CRIP1	1396	hgsc.bcm.edu	37	14	105954682	105954682	+	Silent	SNP	C	C	G	rs1128308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105954682C>G	ENST00000330233.7	+	3	1093	c.150C>G	c.(148-150)ccC>ccG	p.P50P	CRIP1_ENST00000551180.1_Missense_Mutation_p.L19V|C14orf80_ENST00000329886.7_5'Flank|C14orf80_ENST00000354560.6_5'Flank|CRIP1_ENST00000392531.3_Silent_p.P50P|C14orf80_ENST00000392522.3_5'Flank|C14orf80_ENST00000392523.4_5'Flank|CRIP1_ENST00000409393.2_Silent_p.P50P|C14orf80_ENST00000334656.7_5'Flank|C14orf80_ENST00000392527.1_5'Flank			P50238	CRIP1_HUMAN	cysteine-rich protein 1 (intestinal)	50	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell proliferation (GO:0008283)|cellular response to antibiotic (GO:0071236)|cellular response to UV-B (GO:0071493)|heart development (GO:0007507)|immune response (GO:0006955)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|prostate gland stromal morphogenesis (GO:0060741)|regulation of gene expression (GO:0010468)|response to organic substance (GO:0010033)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)	AT DNA binding (GO:0003680)|DNA binding, bending (GO:0008301)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)						Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.235)		AAGGCAAACCCTACTGCAACC	0.662													C|||	892	0.178115	0.5961	0.0663	5008	,	,		10889	0.002		0.0249	False		,,,				2504	0.0317				p.P50P		Atlas-SNP	.											.	CRIP1	1	.	0			c.C150G						PASS	.	C		2177,2227	560.5+/-380.5	572,1033,597	47.0	65.0	59.0		150	0.9	1.0	14	dbSNP_86	59	179,8421	78.9+/-141.6	0,179,4121	no	coding-synonymous	CRIP1	NM_001311.4		572,1212,4718	GG,GC,CC		2.0814,49.4323,18.1175		50/78	105954682	2356,10648	2202	4300	6502	SO:0001819	synonymous_variant	1396	exon4			CAAACCCTACTGC		CCDS10004.1	14q32.33	2004-06-18			ENSG00000213145	ENSG00000213145			2360	protein-coding gene	gene with protein product		123875				9480758	Standard	NM_001311		Approved	CRIP	uc001yri.4	P50238	OTTHUMG00000029908	ENST00000330233.7:c.150C>G	14.37:g.105954682C>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	130	72	0.553846	NM_001311	H3BPI2|Q13628|Q53XY7|Q96J34	Silent	SNP	ENST00000330233.7	37	CCDS10004.1																																																																																			C|0.834;G|0.166	0.166	strong		0.662	CRIP1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335466.2	NM_001311	
TRAPPC9	83696	hgsc.bcm.edu	37	8	140743460	140743460	+	Silent	SNP	G	G	A	rs148857575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:140743460G>A	ENST00000438773.2	-	23	3424	c.3291C>T	c.(3289-3291)tcC>tcT	p.S1097S	TRAPPC9_ENST00000389328.4_Silent_p.S1195S|TRAPPC9_ENST00000522504.1_5'UTR|TRAPPC9_ENST00000389327.3_Silent_p.S1088S	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	1097					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						CCGACTGGCCGGACGGCTGCA	0.622													G|||	12	0.00239617	0.0083	0.0014	5008	,	,		14736	0.0		0.0	False		,,,				2504	0.0				p.S1195S		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C3585T						PASS	.	G	,	30,4376	36.8+/-68.6	0,30,2173	38.0	38.0	38.0		3291,3585	-9.9	0.0	8	dbSNP_134	38	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	0,30,6473	AA,AG,GG		0.0,0.6809,0.2307	,	1097/1149,1195/1247	140743460	30,12976	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon23			CTGGCCGGACGGC	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.3291C>T	8.37:g.140743460G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	0.021	-1.421690	0.01126	0.006809	0.0	ENSG00000167632	ENST00000520857	.	.	.	4.93	-9.86	0.00473	.	.	.	.	.	T	0.35624	0.0938	.	.	.	0.38039	D	0.935405	.	.	.	.	.	.	T	0.56792	-0.7920	4	.	.	.	.	6.719	0.23321	0.0688:0.4132:0.3666:0.1514	.	.	.	.	W	941	.	.	R	-	1	2	TRAPPC9	140812642	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-3.021000	0.00642	-4.055000	0.00078	-3.274000	0.00048	CGG	G|0.998;A|0.002	0.002	strong		0.622	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
BRCA1	672	hgsc.bcm.edu	37	17	41245643	41245643	+	Silent	SNP	A	A	G	rs369373293		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41245643A>G	ENST00000357654.3	-	10	2023	c.1905T>C	c.(1903-1905)aaT>aaC	p.N635N	BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000346315.3_Silent_p.N635N|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000354071.3_Silent_p.N635N|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000493795.1_Silent_p.N588N|BRCA1_ENST00000309486.4_Silent_p.N339N|BRCA1_ENST00000471181.2_Silent_p.N635N|BRCA1_ENST00000586385.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	635					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)		ATTCAGTACAATTAGGTGGGC	0.388			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.N635N		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.T1905C						PASS	.	A	,,,,	2,4404	4.2+/-10.8	0,2,2201	94.0	92.0	93.0		1905,1764,,,1905	1.6	0.0	17		93	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	,,,,	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	,,,,	635/1864,588/1817,,,635/1885	41245643	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	672	exon10	Familial Cancer Database		AGTACAATTAGGT	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.1905T>C	17.37:g.41245643A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	136	61	0.448529	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	37	CCDS11453.1																																																																																			.	.	weak		0.388	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
TMBIM6	7009	hgsc.bcm.edu	37	12	50153060	50153060	+	Silent	SNP	A	A	G	rs12310796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50153060A>G	ENST00000267115.5	+	8	655	c.570A>G	c.(568-570)caA>caG	p.Q190Q	TMBIM6_ENST00000547798.1_Silent_p.Q153Q|TMBIM6_ENST00000423828.1_Silent_p.Q248Q|TMBIM6_ENST00000549385.1_Silent_p.Q190Q|TMBIM6_ENST00000395006.4_Silent_p.Q190Q|TMBIM6_ENST00000552699.1_Silent_p.Q248Q	NM_003217.2	NP_003208.2	P55061	BI1_HUMAN	transmembrane BAX inhibitor motif containing 6	190					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)				lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	6						TTGATACTCAACTCATTATTG	0.418													A|||	27	0.00539137	0.0204	0.0	5008	,	,		20350	0.0		0.0	False		,,,				2504	0.0				p.Q248Q		Atlas-SNP	.											.	TMBIM6	26	.	0			c.A744G						PASS	.	A	,	81,4325	69.2+/-107.0	0,81,2122	212.0	192.0	199.0		744,570	3.0	1.0	12	dbSNP_120	199	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TMBIM6	NM_001098576.1,NM_003217.2	,	0,81,6422	GG,GA,AA		0.0,1.8384,0.6228	,	248/296,190/238	50153060	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	7009	exon8			TACTCAACTCATT	X75861	CCDS31797.1, CCDS44875.1	12q13.12	2013-10-08	2008-09-17	2008-09-17	ENSG00000139644	ENSG00000139644			11723	protein-coding gene	gene with protein product	"""BAX inhibitor 1"""	600748	"""testis enhanced gene transcript"""	TEGT		8530040, 9660918	Standard	NM_001098576		Approved	BI-1, BAXI1	uc001ruy.2	P55061	OTTHUMG00000169652	ENST00000267115.5:c.570A>G	12.37:g.50153060A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_001098576	B2R5M4|F8W034|O14938|Q643A7|Q96J50	Silent	SNP	ENST00000267115.5	37	CCDS31797.1																																																																																			A|0.993;G|0.007	0.007	strong		0.418	TMBIM6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405289.1	NM_003217	
ARHGAP25	9938	hgsc.bcm.edu	37	2	69040500	69040500	+	Silent	SNP	G	G	A	rs2280310	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69040500G>A	ENST00000295381.3	+	6	1172	c.753G>A	c.(751-753)caG>caA	p.Q251Q	ARHGAP25_ENST00000409202.3_Silent_p.Q252Q|ARHGAP25_ENST00000409220.1_Silent_p.Q245Q|ARHGAP25_ENST00000497079.1_Silent_p.Q245Q|ARHGAP25_ENST00000456116.2_3'UTR|ARHGAP25_ENST00000467265.1_Silent_p.Q212Q|ARHGAP25_ENST00000409030.3_Silent_p.Q244Q|ARHGAP25_ENST00000544262.1_Silent_p.Q226Q	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	251	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)	GTPase activator activity (GO:0005096)	p.Q245Q(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CCTGGAGCCAGTACGAAGGGT	0.512													G|||	1491	0.297724	0.2927	0.3213	5008	,	,		19180	0.4425		0.1839	False		,,,				2504	0.2556				p.Q252Q		Atlas-SNP	.											ARHGAP25,NS,carcinoma,0,1	ARHGAP25	175	1	1	Substitution - coding silent(1)	stomach(1)	c.G756A						scavenged	.	G	,,,	1189,3217	416.7+/-337.7	153,883,1167	108.0	94.0	99.0		756,735,636,732	3.6	1.0	2	dbSNP_100	99	1653,6947	305.0+/-307.2	171,1311,2818	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	,,,	324,2194,3985	AA,AG,GG		19.2209,26.9859,21.8515	,,,	252/647,245/640,212/607,244/639	69040500	2842,10164	2203	4300	6503	SO:0001819	synonymous_variant	9938	exon6			GAGCCAGTACGAA	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.753G>A	2.37:g.69040500G>A		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Silent	SNP	ENST00000295381.3	37		616	0.28205128205128205	140	0.2845528455284553	112	0.30939226519337015	225	0.39335664335664333	139	0.18337730870712401	G	9.214	1.031745	0.19590	0.269859	0.192209	ENSG00000163219	ENST00000497259	.	.	.	5.73	3.62	0.41486	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38351	-0.9665	3	.	.	.	.	12.3657	0.55226	0.1637:0.0:0.8363:0.0	rs2280310;rs58055279;rs2280310	.	.	.	N	111	.	.	S	+	2	0	ARHGAP25	68894004	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	0.624000	0.24462	1.432000	0.47375	0.655000	0.94253	AGT	G|0.744;A|0.256	0.256	strong		0.512	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
PKDREJ	10343	hgsc.bcm.edu	37	22	46652929	46652929	+	Silent	SNP	G	G	A	rs6008365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	74	38	0.513514	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	
FLT3LG	2323	hgsc.bcm.edu	37	19	49977929	49977929	+	Splice_Site	SNP	A	A	G	rs75750998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49977929A>G	ENST00000594009.1	+	1	112	c.33A>G	c.(31-33)acA>acG	p.T11T	FLT3LG_ENST00000204637.2_5'UTR|FLT3LG_ENST00000595510.1_5'UTR|FLT3LG_ENST00000600429.1_Splice_Site_p.T11T|CTD-3148I10.9_ENST00000599536.1_3'UTR|FLT3LG_ENST00000597551.1_Splice_Site_p.T11T|FLT3LG_ENST00000596435.1_Splice_Site_p.T11T|FLT3LG_ENST00000344019.3_Splice_Site_p.T11T|CTD-3148I10.15_ENST00000595815.1_RNA	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand	11					embryonic hemopoiesis (GO:0035162)|lymphocyte differentiation (GO:0030098)|positive regulation of cell proliferation (GO:0008284)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|membrane (GO:0016020)	receptor binding (GO:0005102)			large_intestine(2)|lung(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	10		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		GGAGCCCAACAGTGCGTAAAC	0.612													a|||	162	0.0323482	0.1036	0.0259	5008	,	,		12436	0.0		0.007	False		,,,				2504	0.0				p.T11T		Atlas-SNP	.											.	FLT3LG	22	.	0			c.A33G						PASS	.	A	,,	347,4059	173.0+/-202.9	13,321,1869	40.0	38.0	38.0		33,33,33	-4.8	0.9	19	dbSNP_131	38	13,8585	9.8+/-36.6	0,13,4286	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	FLT3LG	NM_001204502.1,NM_001204503.1,NM_001459.3	,,	13,334,6155	GG,GA,AA		0.1512,7.8756,2.7684	,,	11/236,11/236,11/236	49977929	360,12644	2203	4299	6502	SO:0001630	splice_region_variant	2323	exon1			CCCAACAGTGCGT	U04806	CCDS12767.1, CCDS62753.1	19q13.3	2014-01-30				ENSG00000090554		"""Endogenous ligands"""	3766	protein-coding gene	gene with protein product		600007				8145851, 7824267	Standard	NM_001204502		Approved		uc010yau.2	P49771		ENST00000594009.1:c.33+1A>G	19.37:g.49977929A>G		Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	357	183	0.512605	NM_001204503	A0AVC2|B9EGH2|Q05C96	Silent	SNP	ENST00000594009.1	37	CCDS12767.1																																																																																			A|0.974;G|0.026	0.026	strong		0.612	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465305.1		Silent
PRAMEF4	400735	hgsc.bcm.edu	37	1	12939674	12939674	+	Silent	SNP	C	C	G	rs28546260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12939674C>G	ENST00000235349.5	-	4	1198	c.1128G>C	c.(1126-1128)ctG>ctC	p.L376L		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	376					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.L376L(1)		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)		AGCAGCGGCTCAGGGCAGGCA	0.498													c|||	579	0.115615	0.1362	0.1023	5008	,	,		20404	0.1399		0.1123	False		,,,				2504	0.0757				p.L376L		Atlas-SNP	.											PRAMEF4,NS,carcinoma,0,2	PRAMEF4	62	2	1	Substitution - coding silent(1)	prostate(1)	c.G1128C						scavenged	.	C		435,2561		63,309,1126	95.0	99.0	97.0		1128	1.5	0.5	1	dbSNP_130	97	620,4750		69,482,2134	no	coding-synonymous	PRAMEF4	NM_001009611.2		132,791,3260	GG,GC,CC		11.5456,14.5194,12.6106		376/479	12939674	1055,7311	1498	2685	4183	SO:0001819	synonymous_variant	400735	exon4			GCGGCTCAGGGCA		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.1128G>C	1.37:g.12939674C>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	131	44	0.335878	NM_001009611	Q5LJB5	Silent	SNP	ENST00000235349.5	37	CCDS30592.1																																																																																			C|0.879;G|0.121	0.121	strong		0.498	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
GLI3	2737	hgsc.bcm.edu	37	7	42004897	42004897	+	Silent	SNP	G	G	C	rs35448119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:42004897G>C	ENST00000395925.3	-	15	3858	c.3774C>G	c.(3772-3774)ctC>ctG	p.L1258L	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1258					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						GCTGCCTGTTGAGACAGTTCC	0.627									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				G|||	69	0.013778	0.0484	0.0072	5008	,	,		16948	0.0		0.0	False		,,,				2504	0.0				p.L1258L		Atlas-SNP	.											.	GLI3	312	.	0			c.C3774G						PASS	.	G		195,4211	123.3+/-160.7	7,181,2015	62.0	65.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3774	-9.7	0.0	7	dbSNP_126	64	0,8600		0,0,4300	no	coding-synonymous	GLI3	NM_000168.5		7,181,6315	CC,CG,GG		0.0,4.4258,1.4993		1258/1581	42004897	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	2737	exon15	Familial Cancer Database	;	CCTGTTGAGACAG		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.3774C>G	7.37:g.42004897G>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																			G|0.984;C|0.016	0.016	strong		0.627	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
KCNK12	56660	hgsc.bcm.edu	37	2	47748487	47748487	+	Silent	SNP	G	G	A	rs77883212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47748487G>A	ENST00000327876.4	-	2	1459	c.852C>T	c.(850-852)atC>atT	p.I284I	MSH2_ENST00000461394.1_Intron	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	284						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)			CGCCGAGCAGGATGAAGAGGA	0.607													G|||	48	0.00958466	0.0333	0.0058	5008	,	,		13662	0.0		0.0	False		,,,				2504	0.0				p.I284I		Atlas-SNP	.											.	KCNK12	11	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.C852T						PASS	.	G		151,4255	103.0+/-141.5	2,147,2054	57.0	54.0	55.0		852	1.5	1.0	2	dbSNP_132	55	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous	KCNK12	NM_022055.1		2,151,6349	AA,AG,GG		0.0465,3.4271,1.1919		284/431	47748487	155,12849	2203	4299	6502	SO:0001819	synonymous_variant	56660	exon2			GAGCAGGATGAAG	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.852C>T	2.37:g.47748487G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_022055		Silent	SNP	ENST00000327876.4	37	CCDS1835.1																																																																																			G|0.986;A|0.014	0.014	strong		0.607	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055	
ERN1	2081	hgsc.bcm.edu	37	17	62137893	62137893	+	Missense_Mutation	SNP	T	T	C	rs79107850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62137893T>C	ENST00000433197.3	-	11	1237	c.1142A>G	c.(1141-1143)aAc>aGc	p.N381S		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						GGGTAGATTGTTGGGAAATCT	0.473													T|||	33	0.00658946	0.0234	0.0029	5008	,	,		21401	0.0		0.0	False		,,,				2504	0.0				p.N381S		Atlas-SNP	.											.	ERN1	102	.	0			c.A1142G						PASS	.	T	SER/ASN	60,3790		1,58,1866	164.0	158.0	160.0		1142	5.3	1.0	17	dbSNP_131	160	0,8276		0,0,4138	yes	missense	ERN1	NM_001433.3	46	1,58,6004	CC,CT,TT		0.0,1.5584,0.4948	benign	381/978	62137893	60,12066	1925	4138	6063	SO:0001583	missense	2081	exon11			AGATTGTTGGGAA	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"""inositol-requiring enzyme 1"""	604033	"""ER to nucleus signalling 1"""			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.1142A>G	17.37:g.62137893T>C	ENSP00000401445:p.Asn381Ser	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	150	64	0.426667	NM_001433		Missense_Mutation	SNP	ENST00000433197.3	37	CCDS45762.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	T	8.605	0.887770	0.17540	0.015584	0.0	ENSG00000178607	ENST00000433197	T	0.58060	0.36	5.33	5.33	0.75918	.	0.150729	0.64402	D	0.000013	T	0.11110	0.0271	N	0.14661	0.345	0.30788	N	0.741199	B	0.06786	0.001	B	0.01281	0.0	T	0.16158	-1.0412	10	0.07175	T	0.84	-44.0147	8.0501	0.30572	0.0:0.1225:0.0:0.8775	.	381	O75460	ERN1_HUMAN	S	381	ENSP00000401445:N381S	ENSP00000401445:N381S	N	-	2	0	ERN1	59491625	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.120000	0.57897	2.008000	0.58898	0.379000	0.24179	AAC	T|0.990;C|0.010	0.010	strong		0.473	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433	
OC90	729330	hgsc.bcm.edu	37	8	133036743	133036743	+	Silent	SNP	A	A	G	rs11991659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133036743A>G	ENST00000443356.2	-	15	1553	c.1467T>C	c.(1465-1467)ccT>ccC	p.P489P	OC90_ENST00000603859.1_Silent_p.P473P|OC90_ENST00000254627.3_Silent_p.P473P|OC90_ENST00000262283.5_Silent_p.P685P			Q02509	OC90_HUMAN	otoconin 90	489					lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			TTCCATGAAGAGGCCCGATCC	0.577													G|||	252	0.0503195	0.174	0.013	5008	,	,		19645	0.002		0.008	False		,,,				2504	0.0031				p.P473P		Atlas-SNP	.											OC90_ENST00000262283,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,2	OC90	163	2	0			c.T1419C						PASS	.	G		470,3414		23,424,1495	23.0	26.0	25.0		1419	0.9	0.0	8	dbSNP_120	25	67,8215		1,65,4075	no	coding-synonymous	OC90	NM_001080399.2		24,489,5570	GG,GA,AA		0.809,12.1009,4.4139		473/478	133036743	537,11629	1942	4141	6083	SO:0001819	synonymous_variant	729330	exon14			ATGAAGAGGCCCG	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.1467T>C	8.37:g.133036743A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	34	20	0.588235	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				A|0.952;G|0.048	0.048	strong		0.577	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	
TNFSF8	944	hgsc.bcm.edu	37	9	117668142	117668142	+	Silent	SNP	C	C	T	rs3181195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117668142C>T	ENST00000223795.2	-	3	389	c.276G>A	c.(274-276)agG>agA	p.R92R	TNFSF8_ENST00000474301.1_5'Flank	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	92					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						TGAATGGAGCCCTTTTCAGGA	0.418													C|||	1648	0.329073	0.1974	0.5	5008	,	,		13628	0.245		0.4016	False		,,,				2504	0.3978				p.R92R		Atlas-SNP	.											TNFSF8,colon,carcinoma,-1,1	TNFSF8	34	1	0			c.G276A						PASS	.	C		1084,3322	394.7+/-329.4	135,814,1254	171.0	173.0	172.0		276	1.7	0.1	9	dbSNP_105	172	3491,5109	510.8+/-377.6	663,2165,1472	no	coding-synonymous	TNFSF8	NM_001244.2		798,2979,2726	TT,TC,CC		40.593,24.6028,35.1761		92/235	117668142	4575,8431	2203	4300	6503	SO:0001819	synonymous_variant	944	exon3			TGGAGCCCTTTTC	L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.276G>A	9.37:g.117668142C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	163	51	0.312883	NM_001252290	O43404	Silent	SNP	ENST00000223795.2	37	CCDS6810.1																																																																																			C|0.661;T|0.339	0.339	strong		0.418	TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1		
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919623	12919623	+	Silent	SNP	C	C	T	rs75838083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919623C>T	ENST00000240189.2	+	3	450	c.363C>T	c.(361-363)gcC>gcT	p.A121A		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	121					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)		GAGCCTGGGCCCTGTCCTGCT	0.552													.|||	543	0.108427	0.1256	0.098	5008	,	,		21027	0.129		0.1064	False		,,,				2504	0.0736				p.A121A		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.C363T						PASS	.	C		187,4217		46,95,2061	142.0	163.0	156.0		363	-0.3	0.0	1	dbSNP_131	156	162,8432		38,86,4173	no	coding-synonymous	PRAMEF2	NM_023014.1		84,181,6234	TT,TC,CC		1.885,4.2461,2.685		121/475	12919623	349,12649	2202	4297	6499	SO:0001819	synonymous_variant	65122	exon3			CTGGGCCCTGTCC		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.363C>T	1.37:g.12919623C>T		Somatic	341	1	0.00293255		WXS	Illumina HiSeq	Phase_I	323	152	0.470588	NM_023014		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			C|0.897;T|0.103	0.103	strong		0.552	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
TTN	7273	hgsc.bcm.edu	37	2	179610695	179610695	+	Intron	SNP	C	C	T	rs72648915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179610695C>T	ENST00000591111.1	-	46	10585				TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.V5478M|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000578746.1_RNA			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)			TTTGCTATCACAGCAAATATT	0.403													T|||	192	0.0383387	0.1399	0.0101	5008	,	,		20502	0.0		0.0	False		,,,				2504	0.0				p.V5478M		Atlas-SNP	.											.	TTN	18412	.	0			c.G16432A						PASS	.	T	,,MET/VAL,,	529,3877	774.4+/-414.0	33,463,1707	108.0	105.0	106.0		,,16432,,	-6.2	0.0	2	dbSNP_130	106	7,8593	817.5+/-406.9	0,7,4293	no	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,21,,	33,470,6000	TT,TC,CC		0.0814,12.0064,4.1212	,,,,	,,5478/5605,,	179610695	536,12470	2203	4300	6503	SO:0001627	intron_variant	7273	exon46			CTATCACAGCAAA	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.10361-4047G>A	2.37:g.179610695C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		68	0.031135531135531136	63	0.12804878048780488	5	0.013812154696132596	0	0.0	0	0.0	T	0.009	-1.801722	0.00611	0.120064	8.14E-4	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.59083	0.29	6.07	-6.15	0.02105	.	.	.	.	.	T	0.00300	0.0009	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.05550	-1.0878	8	0.25106	T	0.35	.	5.6092	0.17396	0.098:0.3526:0.417:0.1325	.	5478	Q8WZ42-6	.	M	5478;759	ENSP00000354117:V5478M	ENSP00000304714:V759M	V	-	1	0	TTN	179318940	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.290000	0.08354	-1.567000	0.01671	-1.170000	0.01741	GTG	C|0.961;T|0.039	0.039	strong		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FRMPD1	22844	hgsc.bcm.edu	37	9	37731007	37731007	+	Silent	SNP	C	C	T	rs2274324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:37731007C>T	ENST00000539465.1	+	9	1358	c.765C>T	c.(763-765)gaC>gaT	p.D255D	FRMPD1_ENST00000541302.1_Silent_p.D124D|RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Silent_p.D255D|FRMPD1_ENST00000536622.1_Silent_p.D77D			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	255	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		AGTCACATGACTACCGCTGCC	0.507													C|||	441	0.0880591	0.0688	0.0821	5008	,	,		19066	0.1885		0.0239	False		,,,				2504	0.0808				p.D255D		Atlas-SNP	.											.	FRMPD1	237	.	0			c.C765T						PASS	.	C		257,4149	149.9+/-184.0	7,243,1953	103.0	96.0	98.0		765	5.6	1.0	9	dbSNP_100	98	217,8383	92.8+/-154.8	1,215,4084	yes	coding-synonymous	FRMPD1	NM_014907.2		8,458,6037	TT,TC,CC		2.5233,5.833,3.6445		255/1579	37731007	474,12532	2203	4300	6503	SO:0001819	synonymous_variant	22844	exon9			ACATGACTACCGC	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.765C>T	9.37:g.37731007C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	132	81	0.613636	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	37	CCDS6612.1																																																																																			C|0.942;T|0.058	0.058	strong		0.507	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
CLSPN	63967	hgsc.bcm.edu	37	1	36202585	36202585	+	Missense_Mutation	SNP	G	G	A	rs35490896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36202585G>A	ENST00000318121.3	-	24	3896	c.3839C>T	c.(3838-3840)tCa>tTa	p.S1280L	CLSPN_ENST00000373220.3_Missense_Mutation_p.S1216L|CLSPN_ENST00000466308.1_5'UTR|RP11-435D7.3_ENST00000373226.2_RNA|CLSPN_ENST00000251195.5_Missense_Mutation_p.S1280L|CLSPN_ENST00000520551.1_Missense_Mutation_p.S1227L	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	1280			S -> L (in dbSNP:rs35490896).		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)				AAAGTTTCTTGAATTTCGAGG	0.468													G|||	252	0.0503195	0.0817	0.0403	5008	,	,		16455	0.001		0.0686	False		,,,				2504	0.047				p.S1280L		Atlas-SNP	.											.	CLSPN	248	.	0			c.C3839T						PASS	.	G	LEU/SER,LEU/SER	362,4044	185.3+/-212.5	15,332,1856	96.0	98.0	97.0		3647,3839	4.3	1.0	1	dbSNP_126	97	558,8042	151.2+/-206.0	22,514,3764	yes	missense,missense	CLSPN	NM_001190481.1,NM_022111.3	145,145	37,846,5620	AA,AG,GG		6.4884,8.2161,7.0737	benign,benign	1216/1276,1280/1340	36202585	920,12086	2203	4300	6503	SO:0001583	missense	63967	exon24			TTTCTTGAATTTC	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.3839C>T	1.37:g.36202585G>A	ENSP00000312995:p.Ser1280Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_022111	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	110	0.05036630036630037	39	0.07926829268292683	18	0.049723756906077346	1	0.0017482517482517483	52	0.06860158311345646	G	16.28	3.079236	0.55753	0.082161	0.064884	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551	T;T;T;T	0.27557	1.66;1.67;1.71;1.72	6.17	4.27	0.50696	.	0.342227	0.32147	N	0.006513	T	0.01353	0.0044	L	0.38531	1.155	0.28373	N	0.919928	B;B	0.13145	0.007;0.004	B;B	0.18561	0.006;0.022	T	0.03051	-1.1078	10	0.56958	D	0.05	-1.1164	12.7114	0.57092	0.1297:0.0:0.8703:0.0	rs35490896;rs61751001	1216;1280	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	L	1280;1280;1216;1227	ENSP00000251195:S1280L;ENSP00000312995:S1280L;ENSP00000362317:S1216L;ENSP00000428848:S1227L	ENSP00000251195:S1280L	S	-	2	0	CLSPN	35975172	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.342000	0.52159	0.886000	0.36113	0.655000	0.94253	TCA	G|0.935;A|0.065	0.065	strong		0.468	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111	
CAPN1	823	hgsc.bcm.edu	37	11	64981472	64981472	+	IGR	SNP	G	G	C	rs239258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	77	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	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		
IKBKE	9641	hgsc.bcm.edu	37	1	206658404	206658404	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206658404C>T	ENST00000367120.3	+	14	1871	c.1498C>T	c.(1498-1500)Cgg>Tgg	p.R500W	IKBKE_ENST00000537984.1_Missense_Mutation_p.R415W	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	500	Interaction with DDX3X.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					GTCCAGGCTGCGGACTGTGAG	0.617																																					p.R500W		Atlas-SNP	.											.	IKBKE	77	.	0			c.C1498T						PASS	.						47.0	42.0	44.0					1																	206658404		2203	4300	6503	SO:0001583	missense	9641	exon14			AGGCTGCGGACTG	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.1498C>T	1.37:g.206658404C>T	ENSP00000356087:p.Arg500Trp	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	37	CCDS30996.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070122	0.76301	.	.	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.64085	-0.08;0.08	5.24	4.32	0.51571	.	0.527792	0.20321	N	0.094636	T	0.60274	0.2256	L	0.36672	1.1	0.22961	N	0.998503	D;D	0.69078	0.991;0.997	P;P	0.50192	0.549;0.634	T	0.55611	-0.8114	10	0.66056	D	0.02	2.2858	12.7736	0.57436	0.1634:0.8366:0.0:0.0	.	415;500	Q3B754;Q14164	.;IKKE_HUMAN	W	500;415	ENSP00000356087:R500W;ENSP00000444529:R415W	ENSP00000356087:R500W	R	+	1	2	IKBKE	204725027	0.993000	0.37304	1.000000	0.80357	0.994000	0.84299	1.450000	0.35134	1.204000	0.43247	0.563000	0.77884	CGG	.	.	none		0.617	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
EDC4	23644	hgsc.bcm.edu	37	16	67911517	67911517	+	Silent	SNP	T	T	C	rs8060686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67911517T>C	ENST00000358933.5	+	6	986	c.747T>C	c.(745-747)tgT>tgC	p.C249C	AC040162.1_ENST00000408599.1_RNA|EDC4_ENST00000574770.1_3'UTR	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	249					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)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		AAGACTGCTGTGAGGAGAGCA	0.602													C|||	1637	0.326877	0.73	0.2867	5008	,	,		21883	0.0685		0.1799	False		,,,				2504	0.228				p.C249C		Atlas-SNP	.											.	EDC4	101	.	0			c.T747C						PASS	.	C		2778,1618	500.5+/-364.7	876,1026,296	75.0	79.0	78.0	http://www.ncbi.nlm.nih.gov/pubmed?term	747	1.6	1.0	16	dbSNP_116	78	1513,7087	747.6+/-407.3	164,1185,2951	yes	coding-synonymous	EDC4	NM_014329.3		1040,2211,3247	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	17.593,36.8062,33.0179		249/1402	67911517	4291,8705	2198	4300	6498	SO:0001819	synonymous_variant	23644	exon6			CTGCTGTGAGGAG	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.747T>C	16.37:g.67911517T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	109	60	0.550459	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Silent	SNP	ENST00000358933.5	37	CCDS10849.1																																																																																			T|0.669;C|0.331	0.331	strong		0.602	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329	
GTPBP3	84705	hgsc.bcm.edu	37	19	17450038	17450038	+	Silent	SNP	C	C	T	rs11880362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17450038C>T	ENST00000324894.8	+	6	839	c.771C>T	c.(769-771)ccC>ccT	p.P257P	GTPBP3_ENST00000598038.1_3'UTR|GTPBP3_ENST00000361619.5_Silent_p.P279P|GTPBP3_ENST00000358792.7_Silent_p.P289P|GTPBP3_ENST00000600625.1_Silent_p.P257P	NM_032620.3|NM_133644.3	NP_116009.2|NP_598399.2	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial)	257	TrmE-type G.				tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	18						TCACTGGACCCCCCAATGCGG	0.667													c|||	103	0.0205671	0.0726	0.0101	5008	,	,		12031	0.0		0.0	False		,,,				2504	0.0				p.P289P		Atlas-SNP	.											.	GTPBP3	40	.	0			c.C867T						PASS	.	C	,,,	288,4118		9,270,1924	20.0	22.0	21.0		771,837,771,867	-6.3	0.9	19	dbSNP_120	21	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GTPBP3	NM_001128855.2,NM_001195422.1,NM_032620.3,NM_133644.3	,,,	9,271,6223	TT,TC,CC		0.0116,6.5365,2.2221	,,,	257/472,279/515,257/493,289/525	17450038	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	84705	exon5			TGGACCCCCCAAT	AF360742	CCDS32950.1, CCDS32951.1, CCDS56088.1, CCDS59364.1	19p13.2	2008-02-05				ENSG00000130299			14880	protein-coding gene	gene with protein product		608536				1290633	Standard	NM_001128855		Approved	MSS1, THDF1, GTPBG3, MTGP1, FLJ14700	uc010xpo.2	Q969Y2		ENST00000324894.8:c.771C>T	19.37:g.17450038C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	NM_133644	A6NFH1|A6NIG5|A6NKR4|A8K7B4|B7Z4V8|Q8TCY6|Q8WUW9|Q969G4|Q9BX61	Silent	SNP	ENST00000324894.8	37	CCDS32951.1																																																																																			C|0.972;T|0.028	0.028	strong		0.667	GTPBP3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463624.1	NM_032620	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465094	39465094	+	Missense_Mutation	SNP	C	C	T	rs12453338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.																																			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	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	245	103	0.420408	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	
ENPP2	5168	hgsc.bcm.edu	37	8	120569877	120569877	+	Silent	SNP	T	T	G	rs2305129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120569877T>G	ENST00000075322.6	-	25	2534	c.2476A>C	c.(2476-2478)Agg>Cgg	p.R826R	ENPP2_ENST00000522167.1_Silent_p.R461R|ENPP2_ENST00000522826.1_Silent_p.R851R|ENPP2_ENST00000427067.2_Silent_p.R847R|ENPP2_ENST00000259486.6_Silent_p.R878R	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	826					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TCACGCACCCTAGCTGTGTGC	0.458													G|||	704	0.140575	0.2292	0.1167	5008	,	,		4696	0.1359		0.0427	False		,,,				2504	0.1431				p.R878R	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											ENPP2,larynx,carcinoma,+2,1	ENPP2	254	1	0			c.A2632C						PASS	.	G	,,	957,3449	734.9+/-410.6	105,747,1351	226.0	203.0	211.0		2476,2551,2632	5.0	1.0	8	dbSNP_100	211	337,8263	804.5+/-407.3	5,327,3968	no	coding-synonymous,coding-synonymous,coding-synonymous	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	,,	110,1074,5319	GG,GT,TT		3.9186,21.7204,9.9493	,,	826/864,851/889,878/916	120569877	1294,11712	2203	4300	6503	SO:0001819	synonymous_variant	5168	exon26			GCACCCTAGCTGT	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2476A>C	8.37:g.120569877T>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	136	55	0.404412	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			T|0.887;G|0.113	0.113	strong		0.458	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
MMEL1	79258	hgsc.bcm.edu	37	1	2535613	2535613	+	Silent	SNP	C	C	A	rs4648562	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	173	0	0		WXS	Illumina HiSeq	Phase_I	193	78	0.404145	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	
RP1L1	94137	hgsc.bcm.edu	37	8	10469817	10469817	+	Silent	SNP	G	G	A	rs6996950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10469817G>A	ENST00000382483.3	-	4	2014	c.1791C>T	c.(1789-1791)ggC>ggT	p.G597G		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	597					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)		CCTGCTCGGTGCCCTGTCCTT	0.637													A|||	3993	0.797324	0.7988	0.8372	5008	,	,		16845	0.6101		0.8757	False		,,,				2504	0.8793				p.G597G		Atlas-SNP	.											.	RP1L1	453	.	0			c.C1791T						PASS	.	A		3381,761		1375,631,65	59.0	68.0	65.0		1791	-2.2	0.0	8	dbSNP_116	65	7244,1170		3127,990,90	yes	coding-synonymous	RP1L1	NM_178857.5		4502,1621,155	AA,AG,GG		13.9054,18.3728,15.3791		597/2401	10469817	10625,1931	2071	4207	6278	SO:0001819	synonymous_variant	94137	exon4			CTCGGTGCCCTGT	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.1791C>T	8.37:g.10469817G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	88	35	0.397727	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			G|0.198;A|0.799	0.799	strong		0.637	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
KHDRBS2	202559	hgsc.bcm.edu	37	6	62442604	62442604	+	Silent	SNP	A	A	G	rs10484690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:62442604A>G	ENST00000281156.4	-	7	1154	c.876T>C	c.(874-876)taT>taC	p.Y292Y		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	292					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		TTTGGGTCGCATAGCTGTTAT	0.383													A|||	1957	0.390775	0.6218	0.3242	5008	,	,		17006	0.3046		0.2813	False		,,,				2504	0.3272				p.Y292Y		Atlas-SNP	.											.	KHDRBS2	103	.	0			c.T876C						PASS	.	A		2511,1895	629.1+/-395.2	731,1049,423	191.0	184.0	187.0		876	3.2	1.0	6	dbSNP_119	187	2637,5963	426.4+/-355.3	402,1833,2065	no	coding-synonymous	KHDRBS2	NM_152688.2		1133,2882,2488	GG,GA,AA		30.6628,43.0095,39.5817		292/350	62442604	5148,7858	2203	4300	6503	SO:0001819	synonymous_variant	202559	exon7			GGTCGCATAGCTG	BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"""Sam68-like mammalian protein 1"""	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.876T>C	6.37:g.62442604A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	178	79	0.44382	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Silent	SNP	ENST00000281156.4	37	CCDS4963.1																																																																																			A|0.601;G|0.399	0.399	strong		0.383	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688	
ZNF853	54753	hgsc.bcm.edu	37	7	6656897	6656897	+	Missense_Mutation	SNP	A	A	G	rs1806552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6656897A>G	ENST00000457543.3	+	2	647	c.89A>G	c.(88-90)cAa>cGa	p.Q30R		NM_017560.1	NP_060030.1	P0CG23	ZN853_HUMAN	zinc finger protein 853	30			Q -> R (in dbSNP:rs1806552). {ECO:0000269|Ref.2}.				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						CTGGAACTTCAATGTCTTGAG	0.622													G|||	3865	0.771765	0.9274	0.6931	5008	,	,		18650	0.7609		0.5437	False		,,,				2504	0.863				p.Q30R		Atlas-SNP	.											ZNF853_ENST00000457543,NS,carcinoma,+1,2	ZNF853	32	2	0			c.A89G						PASS	.						39.0	46.0	44.0					7																	6656897		692	1591	2283	SO:0001583	missense	54753	exon2			AACTTCAATGTCT	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.89A>G	7.37:g.6656897A>G	ENSP00000455585:p.Gln30Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_017560		Missense_Mutation	SNP	ENST00000457543.3	37	CCDS59048.1																																																																																			A|0.289;G|0.711	0.711	strong		0.622	ZNF853-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324169.2	NM_017560	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048640	33048640	+	Missense_Mutation	SNP	A	A	G	rs1042140	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33048640A>G	ENST00000418931.2	+	2	408	c.292A>G	c.(292-294)Aag>Gag	p.K98E	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.K98E|HLA-DPA1_ENST00000419277.1_5'Flank	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	98	Beta-1.		K -> E (in allele DPB1*02:01, allele DPB1*02:02, allele DPB1*02:03, allele DPB1*04:03, allele DPB1*06:01, allele DPB1*08:01, allele DPB1*08:02, allele DPB1*09:01, allele DPB1*09:02, allele DPB1*10:01, allele DPB1*11:02, allele DPB1*13:01, allele DPB1*13:02, allele DPB1*16:01, allele DPB1*16:02, allele DPB1*17:01, allele DPB1*18:02, allele DPB1*19:01, allele DPB1*20:02, allele DPB1*21:01, allele DPB1*22:01, allele DPB1*26:02, allele DPB1*29:01, allele DPB1*30:01, allele DPB1*32:01, allele DPB1*33:01, allele DPB1*37:01, allele DPB1*41:01, allele DPB1*44:01, allele DPB1*46:01, allele DPB1*47:01, allele DPB1*48:01, allele DPB1*54:01, allele DPB1*55:01, allele DPB1*58:01, allele DPB1*71:01, allele DPB1*81:01, allele DPB1*86:01, allele DPB1*88:01, allele DPB1*93:01 and allele DPB1*95:01; dbSNP:rs1042140).|K -> R (in allele DPB1*11:01, allele DPB1*15:01, allele DPB1*69:01 and allele DPB1*74:01; dbSNP:rs12722027).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CCTGGAGGAGAAGCGGGCAGT	0.687													.|||	1580	0.315495	0.3064	0.2161	5008	,	,		13279	0.4206		0.2227	False		,,,				2504	0.3855				p.K98E		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.A292G	GRCh37	CM930400	HLA-DPB1	M	rs1042140	PASS	.	A	GLU/LYS	751,2271		96,559,856	41.0	43.0	42.0		292	-8.0	0.0	6	dbSNP_86	42	1214,4202		119,976,1613	yes	missense	HLA-DPB1	NM_002121.5	56	215,1535,2469	GG,GA,AA		22.4151,24.8511,23.2875	benign	98/259	33048640	1965,6473	1511	2708	4219	SO:0001583	missense	3115	exon2			GAGGAGAAGCGGG		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.292A>G	6.37:g.33048640A>G	ENSP00000408146:p.Lys98Glu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	50	14	0.28	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	594	0.27197802197802196	128	0.2601626016260163	74	0.20441988950276244	244	0.42657342657342656	148	0.19525065963060687	A	10.03	1.240080	0.22711	0.248511	0.224151	ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835	T;T;T	0.00327	8.09;8.09;8.09	4.02	-8.04	0.01110	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);	5.998850	0.00465	N	0.000108	T	0.00039	0.0001	N	0.26162	0.8	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.28933	-1.0028	9	0.29301	T	0.29	.	8.8377	0.35121	0.1762:0.3554:0.4684:0.0	rs1042140;rs3173292;rs17221129	108;98	Q59GY1;P04440	.;DPB1_HUMAN	E	98;98;98;75	ENSP00000408146:K98E;ENSP00000439674:K98E;ENSP00000412654:K75E	ENSP00000389210:K98E	K	+	1	0	HLA-DPB1	33156618	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.374000	0.00493	-2.124000	0.00822	-1.336000	0.01259	AAG	A|0.758;C|0.000;G|0.242;T|0.000	0.242	strong		0.687	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
IGLL1	3543	hgsc.bcm.edu	37	22	23922281	23922281	+	Missense_Mutation	SNP	C	C	T	rs116760479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:23922281C>T	ENST00000330377.2	-	1	214	c.97G>A	c.(97-99)Gtg>Atg	p.V33M	KB-208E9.1_ENST00000608615.1_lincRNA|IGLL1_ENST00000249053.3_Missense_Mutation_p.V33M	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	33					immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						TGGGTTACCACGGCCAGACCC	0.721													C|||	190	0.0379393	0.0953	0.013	5008	,	,		14290	0.0		0.0119	False		,,,				2504	0.044				p.V33M		Atlas-SNP	.											.	IGLL1	27	.	0			c.G97A						PASS	.	C	MET/VAL,MET/VAL	323,4029		7,309,1860	7.0	8.0	8.0		97,97	-2.2	0.0	22	dbSNP_132	8	121,8377		0,121,4128	yes	missense,missense	IGLL1	NM_020070.2,NM_152855.1	21,21	7,430,5988	TT,TC,CC		1.4239,7.4219,3.4553	possibly-damaging,possibly-damaging	33/214,33/85	23922281	444,12406	2176	4249	6425	SO:0001583	missense	3543	exon1			TTACCACGGCCAG	X52204	CCDS13809.1, CCDS13810.1	22q11.23	2014-09-17			ENSG00000128322	ENSG00000128322		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	5870	protein-coding gene	gene with protein product		146770		IGLL		3139558, 2511029	Standard	NM_020070		Approved	IGVPB, IGL5, 14.1, CD179B	uc002zxd.3	P15814	OTTHUMG00000150673	ENST00000330377.2:c.97G>A	22.37:g.23922281C>T	ENSP00000329312:p.Val33Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	89	33	0.370787	NM_020070	Q0P681	Missense_Mutation	SNP	ENST00000330377.2	37	CCDS13809.1	45	0.020604395604395604	31	0.06300813008130081	7	0.019337016574585635	0	0.0	7	0.009234828496042216	c	0.200	-1.045357	0.01997	0.074219	0.014239	ENSG00000128322	ENST00000249053;ENST00000330377;ENST00000438703	T;T	0.00902	6.87;5.56	1.78	-2.18	0.07037	.	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.09310	N	1	B;B	0.24768	0.025;0.111	B;B	0.14023	0.01;0.01	T	0.40813	-0.9543	9	0.05721	T	0.95	.	3.5367	0.07796	0.0:0.3802:0.1991:0.4207	.	33;33	Q0P681;P15814	.;IGLL1_HUMAN	M	33	ENSP00000329312:V33M;ENSP00000403391:V33M	ENSP00000249053:V33M	V	-	1	0	IGLL1	22252281	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.444000	0.06854	-0.496000	0.06650	-2.956000	0.00083	GTG	C|0.980;T|0.020	0.020	strong		0.721	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1	NM_020070	
AHNAK2	113146	hgsc.bcm.edu	37	14	105407798	105407798	+	Missense_Mutation	SNP	T	T	C	rs4465542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105407798T>C	ENST00000333244.5	-	7	14109	c.13990A>G	c.(13990-13992)Aca>Gca	p.T4664A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4664			T -> A (in dbSNP:rs4465542). {ECO:0000269|PubMed:17974005}.			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)			ATGGGAAATGTGGAAGTCTTC	0.428													C|||	2780	0.555112	0.6437	0.5115	5008	,	,		21212	0.4117		0.5338	False		,,,				2504	0.636				p.T4664A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A13990G						PASS	.	C	ALA/THR	2580,1258		871,838,210	45.0	48.0	47.0		13990	-3.4	0.0	14	dbSNP_111	47	4456,3770		1222,2012,879	yes	missense	AHNAK2	NM_138420.2	58	2093,2850,1089	CC,CT,TT		45.8303,32.7775,41.6777	benign	4664/5796	105407798	7036,5028	1919	4113	6032	SO:0001583	missense	113146	exon7			GAAATGTGGAAGT	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.13990A>G	14.37:g.105407798T>C	ENSP00000353114:p.Thr4664Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1144	0.5238095238095238	324	0.6585365853658537	199	0.5497237569060773	219	0.38286713286713286	402	0.5303430079155673	C	0.024	-1.386842	0.01194	0.672225	0.541697	ENSG00000185567	ENST00000333244	T	0.00626	6.13	1.71	-3.43	0.04810	.	.	.	.	.	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	0.20907	-1.0261	8	0.07990	T	0.79	.	2.1446	0.03784	0.2223:0.3902:0.2581:0.1294	rs4465542;rs17232097;rs52808542;rs57895880;rs4465542	4664	Q8IVF2	AHNK2_HUMAN	A	4664	ENSP00000353114:T4664A	ENSP00000353114:T4664A	T	-	1	0	AHNAK2	104478843	0.009000	0.17119	0.000000	0.03702	0.023000	0.10783	2.491000	0.45303	-2.122000	0.00824	-1.026000	0.02426	ACA	T|0.466;C|0.534	0.534	strong		0.428	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
F5	2153	hgsc.bcm.edu	37	1	169510380	169510380	+	Silent	SNP	G	G	A	rs9287090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	530	1	0.00188679		WXS	Illumina HiSeq	Phase_I	611	311	0.509002	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	
MRPS24	64951	hgsc.bcm.edu	37	7	43906544	43906544	+	Silent	SNP	C	C	T	rs9154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:43906544C>T	ENST00000317534.5	-	4	319	c.258G>A	c.(256-258)acG>acA	p.T86T	MRPS24_ENST00000467084.1_5'UTR|URGCP-MRPS24_ENST00000603700.1_3'UTR	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	86					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.T86T(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5						CATCCTCCACCGTTCGCTCTG	0.557													C|||	248	0.0495208	0.1831	0.0058	5008	,	,		17550	0.0		0.002	False		,,,				2504	0.0				p.T86T		Atlas-SNP	.											MRPS24,colon,carcinoma,-1,2	MRPS24	9	2	1	Substitution - coding silent(1)	lung(1)	c.G258A						PASS	.	C	,	694,3712	291.0+/-281.2	51,592,1560	68.0	64.0	65.0		,258	-10.5	0.1	7	dbSNP_52	65	5,8595	4.3+/-15.6	0,5,4295	no	utr-3,coding-synonymous	MRPS24,URGCP-MRPS24	NM_001204871.1,NM_032014.2	,	51,597,5855	TT,TC,CC		0.0581,15.7512,5.3744	,	,86/168	43906544	699,12307	2203	4300	6503	SO:0001819	synonymous_variant	64951	exon4			CTCCACCGTTCGC	AB061207	CCDS5473.1	7p14	2012-09-13			ENSG00000062582	ENSG00000062582		"""Mitochondrial ribosomal proteins / small subunits"""	14510	protein-coding gene	gene with protein product		611986				8127713, 11279123	Standard	NM_032014		Approved	MRP-S24, HSPC335	uc003tit.1	Q96EL2	OTTHUMG00000023175	ENST00000317534.5:c.258G>A	7.37:g.43906544C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_032014	A4D1U9|P82668|Q96Q23|Q9P047	Silent	SNP	ENST00000317534.5	37	CCDS5473.1																																																																																			C|0.953;T|0.047	0.047	strong		0.557	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014	
EP400	57634	hgsc.bcm.edu	37	12	132547093	132547093	+	Silent	SNP	A	A	G	rs10902490|rs528214697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132547093A>G	ENST00000333577.4	+	48	8398	c.8289A>G	c.(8287-8289)caA>caG	p.Q2763Q	EP400_ENST00000389561.2_Silent_p.Q2727Q|EP400_ENST00000389562.2_Silent_p.Q2726Q|EP400_ENST00000330386.6_Silent_p.Q2646Q|EP400_ENST00000332482.4_Silent_p.Q2690Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2763	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Q2726Q(9)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcaacaacagcagcagc	0.567																																					p.Q2727Q		Atlas-SNP	.											EP400,NS,carcinoma,0,15	EP400	370	15	9	Substitution - coding silent(9)	lung(3)|kidney(2)|endometrium(2)|central_nervous_system(2)	c.A8181G						scavenged	.						25.0	29.0	28.0					12																	132547093		2173	4217	6390	SO:0001819	synonymous_variant	57634	exon47			GCAACAACAGCAG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8289A>G	12.37:g.132547093A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	118	10	0.0847458	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				A|0.500;G|0.500	0.500	weak		0.567	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
FLYWCH1	84256	hgsc.bcm.edu	37	16	2983483	2983483	+	Silent	SNP	C	C	G	rs2074362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	60	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	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	
KBTBD12	166348	hgsc.bcm.edu	37	3	127642814	127642814	+	Missense_Mutation	SNP	G	G	C	rs61268888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127642814G>C	ENST00000405109.1	+	2	1377	c.910G>C	c.(910-912)Gta>Cta	p.V304L	KBTBD12_ENST00000407609.3_Intron|KBTBD12_ENST00000343941.4_Intron|KBTBD12_ENST00000405256.1_Missense_Mutation_p.V304L			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	304										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						TTATGATCCTGTATCACGGAA	0.413													G|||	957	0.191094	0.1664	0.085	5008	,	,		17625	0.2331		0.1233	False		,,,				2504	0.3262				p.V304L		Atlas-SNP	.											.	KBTBD12	41	.	0			c.G910C						PASS	.	G	LEU/VAL	649,3191		49,551,1320	134.0	128.0	130.0		910	-1.1	0.0	3	dbSNP_129	130	1054,7168		63,928,3120	yes	missense	KBTBD12	NM_207335.2	32	112,1479,4440	CC,CG,GG		12.8193,16.901,14.1187	benign	304/624	127642814	1703,10359	1920	4111	6031	SO:0001583	missense	166348	exon1			GATCCTGTATCAC		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"""BTB/POZ domain containing"""	25731	protein-coding gene	gene with protein product			"""kelch domain containing 6"""	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.910G>C	3.37:g.127642814G>C	ENSP00000385957:p.Val304Leu	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	202	92	0.455446	NM_207335	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	37	CCDS33848.2	343	0.15705128205128205	89	0.18089430894308944	36	0.09944751381215469	122	0.21328671328671328	96	0.1266490765171504	G	2.653	-0.281515	0.05642	0.16901	0.128193	ENSG00000187715	ENST00000405109;ENST00000405256	T;T	0.66099	-0.19;-0.19	5.47	-1.1	0.09872	Kelch-type beta propeller (1);	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09058	-1.0692	8	0.33141	T	0.24	.	2.4812	0.04587	0.1929:0.1041:0.4764:0.2266	rs61268888;rs61734842	304	Q3ZCT8	KBTBC_HUMAN	L	304	ENSP00000385957:V304L;ENSP00000385879:V304L	ENSP00000385957:V304L	V	+	1	0	KBTBD12	129125504	0.000000	0.05858	0.000000	0.03702	0.971000	0.66376	0.528000	0.23002	0.062000	0.16340	-0.224000	0.12420	GTA	G|0.846;C|0.154	0.154	strong		0.413	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335	
ZBED4	9889	hgsc.bcm.edu	37	22	50280688	50280688	+	Silent	SNP	A	A	C	rs9627781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50280688A>C	ENST00000216268.5	+	2	3855	c.3378A>C	c.(3376-3378)ccA>ccC	p.P1126P		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	1126						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		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)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GCTGCCCCCCAAGCATCGTCC	0.537													A|||	286	0.0571086	0.1732	0.0173	5008	,	,		18451	0.0377		0.001	False		,,,				2504	0.0061				p.P1126P		Atlas-SNP	.											.	ZBED4	102	.	0			c.A3378C						PASS	.	A		675,3731	254.6+/-260.1	51,573,1579	50.0	48.0	49.0		3378	-10.4	0.1	22	dbSNP_119	49	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	ZBED4	NM_014838.2		51,576,5876	CC,CA,AA		0.0349,15.32,5.213		1126/1172	50280688	678,12328	2203	4300	6503	SO:0001819	synonymous_variant	9889	exon2			CCCCCCAAGCATC	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.3378A>C	22.37:g.50280688A>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Silent	SNP	ENST00000216268.5	37	CCDS33677.1																																																																																			A|0.939;C|0.061	0.061	strong		0.537	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
CYP4F12	66002	hgsc.bcm.edu	37	19	15795690	15795690	+	Missense_Mutation	SNP	G	G	C	rs61729079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15795690G>C	ENST00000550308.1	+	8	1363	c.983G>C	c.(982-984)gGa>gCa	p.G328A	CYP4F12_ENST00000324632.10_Missense_Mutation_p.G328A	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	328					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	TTCATGTTTGGAGGTGAGGGT	0.532													.|||	99	0.0197684	0.0711	0.0058	5008	,	,		18415	0.0		0.001	False		,,,				2504	0.0				p.G328A		Atlas-SNP	.											.	CYP4F12	89	.	0			c.G983C						PASS	.	G	ALA/GLY	380,4022		6,368,1827	89.0	84.0	85.0		983	-5.2	0.0	19	dbSNP_129	85	3,8597		0,3,4297	yes	missense	CYP4F12	NM_023944.3	60	6,371,6124	CC,CG,GG		0.0349,8.6324,2.9457	benign	328/525	15795690	383,12619	2201	4300	6501	SO:0001583	missense	66002	exon8			TGTTTGGAGGTGA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.983G>C	19.37:g.15795690G>C	ENSP00000448998:p.Gly328Ala	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	151	48	0.317881	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	.	0.001	-3.085659	0.00035	0.086324	3.49E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.64085	-0.08;-0.08	2.58	-5.16	0.02857	.	0.269718	0.28176	N	0.016308	T	0.01029	0.0034	N	0.02368	-0.58	0.09310	N	0.999999	B	0.02656	0.0	B	0.08055	0.003	T	0.17107	-1.0380	10	0.25106	T	0.35	.	8.4642	0.32947	0.2353:0.4491:0.3156:0.0	rs61729079	328	Q9HCS2	CP4FC_HUMAN	A	328	ENSP00000448998:G328A;ENSP00000321821:G328A	ENSP00000321821:G328A	G	+	2	0	CYP4F12	15656690	0.000000	0.05858	0.041000	0.18516	0.005000	0.04900	-1.520000	0.02241	-5.413000	0.00015	-4.134000	0.00010	GGA	G|0.981;C|0.019	0.019	strong		0.532	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
RPGR	6103	hgsc.bcm.edu	37	X	38145841	38145841	+	Intron	SNP	C	C	T	rs147388235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145841C>T	ENST00000339363.3	-	14	2688				TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000378505.2_Missense_Mutation_p.R804K|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						ttcctcccctctcccctctgt	0.572													C|||	38	0.0100662	0.0265	0.0043	3775	,	,		7854	0.0		0.0	False		,,,				2504	0.0				p.R804K		Atlas-SNP	.											.	RPGR	175	.	0			c.G2411A						PASS	.		,LYS/ARG	114,3133		2,98,12,1355,325	209.0	149.0	170.0		,2411	-0.9	0.0	X	dbSNP_134	170	3,5559		0,0,3,2116,1327	yes	intron,missense	RPGR	NM_000328.2,NM_001034853.1	,26	2,98,15,3471,1652	TT,TC,T,CC,C		0.0539,3.5109,1.3282	,benign	,804/1153	38145841	117,8692	1792	3446	5238	SO:0001627	intron_variant	6103	exon15			TCCCCTCTCCCCT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+505G>A	X.37:g.38145841C>T		Somatic	469	1	0.0021322		WXS	Illumina HiSeq	Phase_I	522	236	0.452107	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		13	0.007836045810729355	9	0.018367346938775512	3	0.008287292817679558	0	0.0	0	0.0	c	5.090	0.202211	0.09652	0.035109	5.39E-4	ENSG00000156313	ENST00000378505	T	0.02301	4.35	2.0	-0.924	0.10462	.	0.274603	0.23272	U	0.050002	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46400	-0.9194	10	0.31617	T	0.26	.	4.6346	0.12518	0.0:0.4094:0.1765:0.4141	.	804	E9PE28	.	K	804	ENSP00000367766:R804K	ENSP00000367766:R804K	R	-	2	0	RPGR	38030785	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.188000	0.17018	-0.612000	0.05701	-0.921000	0.02739	AGA	C|0.985;T|0.015	0.015	strong		0.572	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
DDX11	1663	hgsc.bcm.edu	37	12	31242869	31242869	+	Silent	SNP	G	G	A	rs201738430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:31242869G>A	ENST00000407793.2	+	9	1181	c.930G>A	c.(928-930)gaG>gaA	p.E310E	DDX11_ENST00000350437.4_Silent_p.E310E|DDX11_ENST00000228264.6_Silent_p.E284E|DDX11_ENST00000545668.1_Silent_p.E310E|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_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	759	2	0.00263505		WXS	Illumina HiSeq	Phase_I	762	74	0.0971129	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	
MICAL1	64780	hgsc.bcm.edu	37	6	109767930	109767930	+	Missense_Mutation	SNP	G	G	T	rs552227069|rs9320288|rs35260632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	261	261	1	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	
LKAAEAR1	198437	hgsc.bcm.edu	37	20	62714783	62714783	+	3'UTR	SNP	C	C	G	rs6010717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62714783C>G	ENST00000302096.4	-	0	729				OPRL1_ENST00000349451.3_5'Flank|OPRL1_ENST00000355631.4_Intron|C20orf201_ENST00000308906.2_Silent_p.A226A|OPRL1_ENST00000336866.2_Intron			Q8TD35	LKAM1_HUMAN																			CACTCTCAGTCGCCGTCACCG	0.647													C|||	3128	0.624601	0.6422	0.6628	5008	,	,		12748	0.7093		0.6531	False		,,,				2504	0.4571				p.A226A		Atlas-SNP	.											C20orf201,NS,carcinoma,0,1	C20orf201	4	1	0			c.G678C						scavenged	.	C	,,	2796,1604		875,1046,279	21.0	23.0	22.0		,678,	1.4	0.0	20	dbSNP_114	22	5362,3220		1675,2012,604	no	intron,coding-synonymous,intron	OPRL1,C20orf201	NM_000913.4,NM_001007125.1,NM_182647.2	,,	2550,3058,883	GG,GC,CC		37.5204,36.4545,37.1591	,,	,226/241,	62714783	8158,4824	2200	4291	6491	SO:0001624	3_prime_UTR_variant	198437	exon2			CTCAGTCGCCGTC																												ENST00000302096.4:c.*5G>C	20.37:g.62714783C>G		Somatic	39	1	0.025641		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_001007125	Q8N419|Q8TD36	Silent	SNP	ENST00000302096.4	37																																																																																				C|0.368;G|0.632	0.632	strong		0.647	C20orf201-002	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000080270.2		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110491840	110491840	+	Missense_Mutation	SNP	C	C	G	rs1783147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	95	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	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	
POLRMT	5442	hgsc.bcm.edu	37	19	617804	617804	+	Silent	SNP	G	G	A	rs144281668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:617804G>A	ENST00000588649.2	-	18	3552	c.3468C>T	c.(3466-3468)caC>caT	p.H1156H	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	1156	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)			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)		CATCAGCTGCGTGAGTCCAGT	0.642													g|||	3	0.000599042	0.0023	0.0	5008	,	,		11388	0.0		0.0	False		,,,				2504	0.0				p.H1156H		Atlas-SNP	.											.	POLRMT	91	.	0			c.C3468T						PASS	.	G		13,4391		0,13,2189	83.0	65.0	71.0		3468	-7.8	0.0	19	dbSNP_134	71	1,8597		0,1,4298	no	coding-synonymous	POLRMT	NM_005035.3		0,14,6487	AA,AG,GG		0.0116,0.2952,0.1077		1156/1231	617804	14,12988	2202	4299	6501	SO:0001819	synonymous_variant	5442	exon18			AGCTGCGTGAGTC		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.3468C>T	19.37:g.617804G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	139	58	0.417266	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			G|0.999;A|0.001	0.001	strong		0.642	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
USP14	9097	hgsc.bcm.edu	37	18	166819	166819	+	Splice_Site	SNP	T	T	C	rs563155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:166819T>C	ENST00000261601.7	+	3	286	c.195T>C	c.(193-195)aaT>aaC	p.N65N	USP14_ENST00000582707.1_Splice_Site_p.N65N|USP14_ENST00000400266.3_Intron|USP14_ENST00000383589.2_Intron	NM_005151.3	NP_005142.1	P54578	UBP14_HUMAN	ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)	65	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				negative regulation of endopeptidase activity (GO:0010951)|protein deubiquitination (GO:0016579)|regulation of chemotaxis (GO:0050920)|regulation of proteasomal protein catabolic process (GO:0061136)|synaptic transmission (GO:0007268)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|synapse (GO:0045202)	cysteine-type endopeptidase activity (GO:0004197)|endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)|tRNA guanylyltransferase activity (GO:0008193)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(2)	11		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				AAATAAAAAATGTAAGTATTA	0.294													T|||	774	0.154553	0.174	0.134	5008	,	,		14788	0.006		0.2117	False		,,,				2504	0.2372				p.N65N		Atlas-SNP	.											.	USP14	41	.	0			c.T195C						PASS	.	T	,	779,3627	313.3+/-293.0	67,645,1491	125.0	131.0	129.0		195,195	4.4	1.0	18	dbSNP_83	129	1914,6686	337.2+/-322.2	223,1468,2609	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	USP14	NM_001037334.1,NM_005151.3	,	290,2113,4100	CC,CT,TT		22.2558,17.6804,20.7058	,	65/460,65/495	166819	2693,10313	2203	4300	6503	SO:0001630	splice_region_variant	9097	exon3			AAAAAATGTAAGT	U30888	CCDS32780.1, CCDS32781.1	18p11.32	2006-10-06	2005-08-08			ENSG00000101557		"""Ubiquitin-specific peptidases"""	12612	protein-coding gene	gene with protein product		607274	"""ubiquitin specific protease 14 (tRNA-guanine transglycosylase)"""			12838346	Standard	NM_001037334		Approved	TGT	uc002kkf.1	P54578		ENST00000261601.7:c.195+1T>C	18.37:g.166819T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_001037334	J3QRZ5|Q53XY5	Silent	SNP	ENST00000261601.7	37	CCDS32780.1																																																																																			T|0.812;C|0.188	0.188	strong		0.294	USP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440305.3	NM_005151	Silent
SPTAN1	6709	hgsc.bcm.edu	37	9	131362361	131362361	+	Silent	SNP	T	T	C	rs945831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131362361T>C	ENST00000372731.4	+	27	3656	c.3546T>C	c.(3544-3546)gaT>gaC	p.D1182D	SPTAN1_ENST00000358161.5_Silent_p.D1182D|SPTAN1_ENST00000372739.3_Silent_p.D1182D	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1182					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						TTGAATAGGATGAAACTGATT	0.433													T|||	175	0.0349441	0.1263	0.0115	5008	,	,		18973	0.0		0.0	False		,,,				2504	0.0				p.D1182D	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.T3546C						PASS	.	T	,,	478,3928	223.3+/-239.8	28,422,1753	124.0	113.0	117.0		3546,3486,3546	6.1	1.0	9	dbSNP_86	117	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	28,430,6045	CC,CT,TT		0.093,10.8488,3.7367	,,	1182/2478,1162/2453,1182/2473	131362361	486,12520	2203	4300	6503	SO:0001819	synonymous_variant	6709	exon27			ATAGGATGAAACT	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.3546T>C	9.37:g.131362361T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	229	93	0.406114	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																			T|0.963;C|0.037	0.037	strong		0.433	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
RIF1	55183	hgsc.bcm.edu	37	2	152320501	152320501	+	Silent	SNP	T	T	C	rs7566841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152320501T>C	ENST00000243326.5	+	29	4950	c.4467T>C	c.(4465-4467)acT>acC	p.T1489T	RIF1_ENST00000444746.2_Silent_p.T1489T|RIF1_ENST00000430328.2_Silent_p.T1489T|RIF1_ENST00000428287.2_Silent_p.T1489T|RIF1_ENST00000453091.2_Silent_p.T1489T			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		ATGAGAAGACTCTTGGGGAAA	0.368													T|||	101	0.0201677	0.0734	0.0043	5008	,	,		19435	0.0		0.001	False		,,,				2504	0.0				p.T1489T		Atlas-SNP	.											.	RIF1	244	.	0			c.T4467C						PASS	.	T	,,,	213,4191		4,205,1993	57.0	65.0	62.0		4467,4467,4467,4467	1.7	0.1	2	dbSNP_116	62	1,8589		0,1,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	,,,	4,206,6287	CC,CT,TT		0.0116,4.8365,1.6469	,,,	1489/2447,1489/2447,1489/2447,1489/2473	152320501	214,12780	2202	4295	6497	SO:0001819	synonymous_variant	55183	exon30			GAAGACTCTTGGG	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.4467T>C	2.37:g.152320501T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	80	50	0.625	NM_018151	A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	37	CCDS2194.1																																																																																			T|0.981;C|0.019	0.019	strong		0.368	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
CNNM1	26507	hgsc.bcm.edu	37	10	101120671	101120671	+	Silent	SNP	G	G	A	rs61735150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101120671G>A	ENST00000356713.4	+	3	2086	c.1797G>A	c.(1795-1797)acG>acA	p.T599T	CNNM1_ENST00000446890.1_Silent_p.T528T|CNNM1_ENST00000370528.3_Silent_p.T528T|CNNM1_ENST00000370534.4_Silent_p.T234T	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	599					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)		TTTCGGACACGGAGATGCGGG	0.542													G|||	20	0.00399361	0.0144	0.0014	5008	,	,		20089	0.0		0.0	False		,,,				2504	0.0				p.T599T		Atlas-SNP	.											CNNM1_ENST00000356713,NS,carcinoma,0,2	CNNM1	101	2	0			c.G1797A						PASS	.	G		86,4320	72.5+/-110.5	0,86,2117	117.0	111.0	113.0		1797	-11.5	0.0	10	dbSNP_129	113	0,8600		0,0,4300	no	coding-synonymous	CNNM1	NM_020348.2		0,86,6417	AA,AG,GG		0.0,1.9519,0.6612		599/952	101120671	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	26507	exon3			GGACACGGAGATG	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.1797G>A	10.37:g.101120671G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	37	CCDS7478.2																																																																																			G|0.992;A|0.008	0.008	strong		0.542	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
MESP2	145873	hgsc.bcm.edu	37	15	90320000	90320000	+	Missense_Mutation	SNP	G	G	A	rs28462216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90320000G>A	ENST00000341735.3	+	1	412	c.412G>A	c.(412-414)Gtg>Atg	p.V138M	MESP2_ENST00000560219.1_Intron|MESP2_ENST00000558723.1_Intron	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	138			V -> M (in dbSNP:rs28462216).		mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|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)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			CCTATCGGCCGTGCTGGGTCT	0.736													G|||	393	0.0784744	0.2572	0.0216	5008	,	,		13798	0.0		0.002	False		,,,				2504	0.0368				p.V138M		Atlas-SNP	.											.	MESP2	20	.	0			c.G412A						PASS	.	G	MET/VAL	771,3403		58,655,1374	7.0	9.0	8.0		412	1.8	1.0	15	dbSNP_125	8	5,8363		0,5,4179	no	missense	MESP2	NM_001039958.1	21	58,660,5553	AA,AG,GG		0.0598,18.4715,6.1872	benign	138/398	90320000	776,11766	2087	4184	6271	SO:0001583	missense	145873	exon1			TCGGCCGTGCTGG		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"""Basic helix-loop-helix proteins"""	29659	protein-coding gene	gene with protein product		605195	"""mesoderm posterior 2 homolog (mouse)"""			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.412G>A	15.37:g.90320000G>A	ENSP00000342392:p.Val138Met	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_001039958	Q7RTU2	Missense_Mutation	SNP	ENST00000341735.3	37	CCDS42078.1	130	0.05952380952380952	121	0.2459349593495935	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	G	13.92	2.380200	0.42207	0.184715	5.98E-4	ENSG00000188095	ENST00000341735	D	0.88509	-2.39	3.89	1.76	0.24704	Helix-loop-helix DNA-binding (3);	.	.	.	.	T	0.00109	0.0003	L	0.55481	1.735	0.47905	P	4.5799999999995844E-4	D	0.63880	0.993	P	0.49528	0.614	T	0.00146	-1.1991	8	0.51188	T	0.08	-6.0463	11.5389	0.50655	0.0:0.6191:0.3809:0.0	rs28462216;rs60624982	138	Q0VG99	MESP2_HUMAN	M	138	ENSP00000342392:V138M	ENSP00000342392:V138M	V	+	1	0	MESP2	88121004	0.564000	0.26602	1.000000	0.80357	0.565000	0.35776	0.973000	0.29422	0.785000	0.33685	0.313000	0.20887	GTG	G|0.940;A|0.060	0.060	strong		0.736	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261	
ICE1	23379	hgsc.bcm.edu	37	5	5464237	5464237	+	Missense_Mutation	SNP	A	A	C	rs10065646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:5464237A>C	ENST00000296564.7	+	13	5012	c.4790A>C	c.(4789-4791)cAa>cCa	p.Q1597P		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1597			Q -> P (in dbSNP:rs10065646).		positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						ACAAAAACTCAAAGAAGCCAA	0.418													A|||	242	0.0483227	0.1725	0.0187	5008	,	,		20166	0.0		0.001	False		,,,				2504	0.0				p.Q1597P		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A4790C						PASS	.	A	PRO/GLN	500,3252		44,412,1420	47.0	47.0	47.0		4790	-0.5	0.0	5	dbSNP_119	47	9,8207		0,9,4099	yes	missense	KIAA0947	NM_015325.1	76	44,421,5519	CC,CA,AA		0.1095,13.3262,4.253	benign	1597/2267	5464237	509,11459	1876	4108	5984	SO:0001583	missense	23379	exon13			AAACTCAAAGAAG																												ENST00000296564.7:c.4790A>C	5.37:g.5464237A>C	ENSP00000296564:p.Gln1597Pro	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	100	0.045787545787545784	88	0.17886178861788618	12	0.03314917127071823	0	0.0	0	0.0	A	9.076	0.998101	0.19043	0.133262	0.001095	ENSG00000164151	ENST00000296564	T	0.10763	2.84	5.27	-0.478	0.12093	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15930	0.015	B	0.16722	0.016	T	0.46289	-0.9202	8	0.29301	T	0.29	0.0	7.2058	0.25907	0.3909:0.4671:0.0:0.1421	rs10065646;rs52803291;rs10065646	1597	Q9Y2F5	K0947_HUMAN	P	1597	ENSP00000296564:Q1597P	ENSP00000296564:Q1597P	Q	+	2	0	KIAA0947	5517237	0.000000	0.05858	0.000000	0.03702	0.560000	0.35617	-0.688000	0.05150	-0.319000	0.08652	0.377000	0.23210	CAA	A|0.932;C|0.068	0.068	strong		0.418	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
ADAT3	113179	hgsc.bcm.edu	37	19	1912986	1912986	+	Silent	SNP	C	C	T	rs76159002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1912986C>T	ENST00000602400.1	+	2	1120	c.892C>T	c.(892-894)Ctg>Ttg	p.L298L	ADAT3_ENST00000329478.2_Silent_p.L314L|SCAMP4_ENST00000414057.2_Intron|SCAMP4_ENST00000316097.8_Intron|SCAMP4_ENST00000409472.1_Intron			Q96EY9	ADAT3_HUMAN	adenosine deaminase, tRNA-specific 3	298					tRNA processing (GO:0008033)		hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|pancreas(1)|skin(2)	7		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)		CGCCATGGCCCTGGTGCACGC	0.697													C|||	1187	0.237021	0.3207	0.2594	5008	,	,		12444	0.2252		0.1392	False		,,,				2504	0.2209				p.L314L		Atlas-SNP	.											ADAT3,NS,haematopoietic_neoplasm,0,1	ADAT3	15	1	0			c.C940T						PASS	.	C	,	1347,3059	417.2+/-337.8	226,895,1082	61.0	54.0	56.0		,892	2.9	1.0	19	dbSNP_131	56	907,7685	191.4+/-237.6	48,811,3437	no	intron,coding-synonymous	SCAMP4,ADAT3	NM_079834.2,NM_138422.1	,	274,1706,4519	TT,TC,CC		10.5563,30.5719,17.3411	,	,298/352	1912986	2254,10744	2203	4296	6499	SO:0001819	synonymous_variant	113179	exon2			ATGGCCCTGGTGC	BC011824	CCDS12076.1, CCDS12076.2	19p13.3	2011-05-19	2011-05-19		ENSG00000213638	ENSG00000213638			25151	protein-coding gene	gene with protein product	"""tRNA-specific adenosine deaminase 3 homolog (S. cerevisiae)"""	615302	"""adenosine deaminase, tRNA-specific 3, TAD3 homolog (S. cerevisiae)"""			12457566	Standard	NM_138422		Approved	TAD3	uc002luh.4	Q96EY9	OTTHUMG00000154591	ENST00000602400.1:c.892C>T	19.37:g.1912986C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_138422		Silent	SNP	ENST00000602400.1	37																																																																																				C|0.816;T|0.184	0.184	strong		0.697	ADAT3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_138422	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38610394	38610394	+	Missense_Mutation	SNP	G	G	A	rs140119542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38610394G>A	ENST00000222345.6	+	9	3249	c.2740G>A	c.(2740-2742)Ggg>Agg	p.G914R		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	914					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)			CTGCTACTGCGGGGATGTCAT	0.532													G|||	3	0.000599042	0.0008	0.0	5008	,	,		20769	0.0		0.0	False		,,,				2504	0.002				p.G914R		Atlas-SNP	.											SIPA1L3,caecum,carcinoma,0,1	SIPA1L3	150	1	0			c.G2740A						PASS	.	G	ARG/GLY	1,4403	2.1+/-5.4	0,1,2201	98.0	108.0	105.0		2740	5.8	1.0	19	dbSNP_134	105	1,8599	1.2+/-3.3	0,1,4299	no	missense	SIPA1L3	NM_015073.1	125	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	benign	914/1782	38610394	2,13002	2202	4300	6502	SO:0001583	missense	23094	exon9			TACTGCGGGGATG	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.2740G>A	19.37:g.38610394G>A	ENSP00000222345:p.Gly914Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	8.917	0.960050	0.18507	2.27E-4	1.16E-4	ENSG00000105738	ENST00000222345	T	0.73152	-0.72	5.75	5.75	0.90469	.	0.183723	0.47852	D	0.000205	T	0.44871	0.1314	N	0.02345	-0.59	0.38997	D	0.959275	B	0.17852	0.024	B	0.14578	0.011	T	0.51725	-0.8669	10	0.02654	T	1	-42.3387	18.7237	0.91705	0.0:0.0:1.0:0.0	.	914	O60292	SI1L3_HUMAN	R	914	ENSP00000222345:G914R	ENSP00000222345:G914R	G	+	1	0	SIPA1L3	43302234	0.002000	0.14202	0.997000	0.53966	0.994000	0.84299	0.479000	0.22228	2.725000	0.93324	0.655000	0.94253	GGG	G|1.000;A|0.000	0.000	strong		0.532	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
ZNF765	91661	hgsc.bcm.edu	37	19	53911786	53911786	+	Silent	SNP	G	G	A	rs10407020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53911786G>A	ENST00000396408.3	+	4	1095	c.978G>A	c.(976-978)ccG>ccA	p.P326P	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	326					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)		GAGAGAAACCGTACAAGTGTA	0.388													.|||	296	0.0591054	0.146	0.0231	5008	,	,		23994	0.0397		0.0119	False		,,,				2504	0.0358				p.P326P		Atlas-SNP	.											.	ZNF765	61	.	0			c.G978A						PASS	.	G		554,3852	236.8+/-248.8	37,480,1686	88.0	91.0	90.0		978	-2.6	0.0	19	dbSNP_119	90	121,8479	61.0+/-122.8	2,117,4181	no	coding-synonymous	ZNF765	NM_001040185.1		39,597,5867	AA,AG,GG		1.407,12.5738,5.1899		326/524	53911786	675,12331	2203	4300	6503	SO:0001819	synonymous_variant	91661	exon4			GAAACCGTACAAG	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.978G>A	19.37:g.53911786G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Silent	SNP	ENST00000396408.3	37	CCDS46171.1																																																																																			G|0.951;A|0.049	0.049	strong		0.388	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372	
KIRREL	55243	hgsc.bcm.edu	37	1	158057633	158057633	+	Silent	SNP	C	C	G	rs36008419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158057633C>G	ENST00000359209.6	+	6	817	c.750C>G	c.(748-750)ccC>ccG	p.P250P	KIRREL_ENST00000416935.2_Silent_p.P150P|KIRREL_ENST00000360089.4_Silent_p.P86P|KIRREL_ENST00000368172.1_Silent_p.P48P|KIRREL_ENST00000392272.2_Silent_p.P147P|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	108	1	0.00925926	1790	WXS	Illumina HiSeq	Phase_I	97	97	1	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	
OR8B3	390271	hgsc.bcm.edu	37	11	124266927	124266927	+	Silent	SNP	A	A	G	rs142812088		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124266927A>G	ENST00000354597.3	-	1	337	c.321T>C	c.(319-321)ttT>ttC	p.F107F		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CAGAGATGACAAAAAAGAGAA	0.388																																					p.F107F		Atlas-SNP	.											OR8B3,NS,carcinoma,0,1	OR8B3	36	1	0			c.T321C						scavenged	.						78.0	76.0	77.0					11																	124266927		2201	4299	6500	SO:0001819	synonymous_variant	390271	exon1			GATGACAAAAAAG	AB065827	CCDS31709.1	11q24.1	2012-08-09			ENSG00000196661	ENSG00000196661		"""GPCR / Class A : Olfactory receptors"""	8472	protein-coding gene	gene with protein product							Standard	NM_001005467		Approved		uc010saj.2	Q8NGG8	OTTHUMG00000165983	ENST00000354597.3:c.321T>C	11.37:g.124266927A>G		Somatic	288	13	0.0451389		WXS	Illumina HiSeq	Phase_I	277	19	0.0685921	NM_001005467	Q6IFQ8|Q8NGH1	Silent	SNP	ENST00000354597.3	37	CCDS31709.1																																																																																			A|1.000;G|0.000	0.000	weak		0.388	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467	
ACER2	340485	hgsc.bcm.edu	37	9	19450598	19450598	+	Silent	SNP	G	G	C	rs7855739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:19450598G>C	ENST00000340967.2	+	6	818	c.792G>C	c.(790-792)ctG>ctC	p.L264L	RP11-363E7.4_ENST00000563205.1_RNA	NM_001010887.2	NP_001010887.2	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	264					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to drug (GO:0035690)|ceramide metabolic process (GO:0006672)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of protein glycosylation in Golgi (GO:0090285)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	13						TGTCCCTCCTGTGTGCCAACA	0.517													G|||	375	0.0748802	0.2579	0.0216	5008	,	,		19358	0.003		0.0	False		,,,				2504	0.0164				p.L264L		Atlas-SNP	.											.	ACER2	24	.	0			c.G792C						PASS	.	G		1024,3382	378.7+/-323.0	131,762,1310	145.0	131.0	136.0		792	-0.3	0.9	9	dbSNP_116	136	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	ACER2	NM_001010887.2		131,770,5602	CC,CG,GG		0.093,23.241,7.9348		264/276	19450598	1032,11974	2203	4300	6503	SO:0001819	synonymous_variant	340485	exon6			CCTCCTGTGTGCC	AK123581	CCDS34992.1	9p21.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000177076	ENSG00000177076	3.5.1.23	"""Alkaline ceramidase"""	23675	protein-coding gene	gene with protein product		613492	"""N-acylsphingosine amidohydrolase 3-like"""	ASAH3L		18945876	Standard	XM_005251447		Approved	FLJ41587	uc003zny.1	Q5QJU3	OTTHUMG00000019644	ENST00000340967.2:c.792G>C	9.37:g.19450598G>C		Somatic	282	1	0.0035461		WXS	Illumina HiSeq	Phase_I	330	328	0.993939	NM_001010887	A2A3R8|Q569G5|Q5VZR7|Q71RD2	Silent	SNP	ENST00000340967.2	37	CCDS34992.1																																																																																			G|0.933;C|0.067	0.067	strong		0.517	ACER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051864.1	XM_294540	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786845	75786845	+	Silent	SNP	T	T	C	rs62250105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75786845T>C	ENST00000478296.1	-	4	2055	c.1779A>G	c.(1777-1779)ggA>ggG	p.G593G	ZNF717_ENST00000422325.1_Silent_p.G643G|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Silent_p.G636G|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	636					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						AAGGTTTCTCTCCTGTGTGAG	0.438																																					p.G643G		Atlas-SNP	.											.	ZNF717	160	.	0			c.A1929G						PASS	.						35.0	39.0	38.0					3																	75786845		633	1557	2190	SO:0001819	synonymous_variant	100131827	exon5			TTTCTCTCCTGTG	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1779A>G	3.37:g.75786845T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_001128223		Silent	SNP	ENST00000478296.1	37																																																																																				T|0.250;C|0.750	0.750	strong		0.438	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
PDIA4	9601	hgsc.bcm.edu	37	7	148701245	148701245	+	Missense_Mutation	SNP	C	C	T	rs61739277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:148701245C>T	ENST00000286091.4	-	10	1811	c.1579G>A	c.(1579-1581)Gtc>Atc	p.V527I		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	527	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			ACGACCTTGACGGGTCCCTTG	0.567													C|||	47	0.00938498	0.034	0.0029	5008	,	,		12360	0.0		0.0	False		,,,				2504	0.0				p.V527I		Atlas-SNP	.											.	PDIA4	57	.	0			c.G1579A						PASS	.	C	ILE/VAL	104,4302	83.4+/-121.9	1,102,2100	167.0	152.0	157.0		1579	4.9	0.8	7	dbSNP_129	157	0,8600		0,0,4300	yes	missense	PDIA4	NM_004911.4	29	1,102,6400	TT,TC,CC		0.0,2.3604,0.7996	benign	527/646	148701245	104,12902	2203	4300	6503	SO:0001583	missense	9601	exon10			CCTTGACGGGTCC	BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"""Protein disulfide isomerases"""	30167	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 4"""			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.1579G>A	7.37:g.148701245C>T	ENSP00000286091:p.Val527Ile	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	175	78	0.445714	NM_004911	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	37	CCDS5893.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	C	15.92	2.975631	0.53720	0.023604	0.0	ENSG00000155660	ENST00000286091	T	0.26810	1.71	5.81	4.92	0.64577	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.056360	0.64402	D	0.000001	T	0.25306	0.0615	M	0.77406	2.37	0.80722	D	1	B	0.28419	0.211	B	0.40410	0.328	T	0.30268	-0.9984	10	0.72032	D	0.01	.	15.1664	0.72828	0.0:0.9316:0.0:0.0684	.	527	P13667	PDIA4_HUMAN	I	527	ENSP00000286091:V527I	ENSP00000286091:V527I	V	-	1	0	PDIA4	148332178	1.000000	0.71417	0.785000	0.31869	0.119000	0.20118	5.851000	0.69481	2.751000	0.94390	0.555000	0.69702	GTC	C|0.992;T|0.008	0.008	strong		0.567	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911	
ADAMTS19	171019	hgsc.bcm.edu	37	5	128844838	128844838	+	Silent	SNP	A	A	G	rs28630040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:128844838A>G	ENST00000274487.4	+	3	943	c.798A>G	c.(796-798)acA>acG	p.T266T	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	266						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		TGGCCATAACAGGTCACCCAC	0.393													A|||	638	0.127396	0.1747	0.1715	5008	,	,		15417	0.0883		0.0755	False		,,,				2504	0.1258				p.T266T		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.A798G						PASS	.	A		667,3739	283.4+/-277.1	54,559,1590	107.0	97.0	101.0		798	-0.7	1.0	5	dbSNP_125	101	705,7895	173.0+/-223.6	35,635,3630	no	coding-synonymous	ADAMTS19	NM_133638.3		89,1194,5220	GG,GA,AA		8.1977,15.1384,10.549		266/1208	128844838	1372,11634	2203	4300	6503	SO:0001819	synonymous_variant	171019	exon3			CATAACAGGTCAC	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17111	protein-coding gene	gene with protein product		607513	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"""			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.798A>G	5.37:g.128844838A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_133638		Silent	SNP	ENST00000274487.4	37	CCDS4146.1																																																																																			A|0.892;G|0.108	0.108	strong		0.393	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	
KANK1	23189	hgsc.bcm.edu	37	9	710966	710966	+	Missense_Mutation	SNP	G	G	A	rs7860464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:710966G>A	ENST00000382303.1	+	7	852	c.200G>A	c.(199-201)cGg>cAg	p.R67Q	KANK1_ENST00000382293.3_5'UTR|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.R67Q	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	67	Nuclear localization signal 1 (NLS 1).				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)		CAGAAGAGGCGGAAGCCGTCC	0.478													G|||	854	0.170527	0.5507	0.0648	5008	,	,		20098	0.0		0.0179	False		,,,				2504	0.0644				p.R67Q		Atlas-SNP	.											.	KANK1	231	.	0			c.G200A						PASS	.	G	GLN/ARG,	2182,2224	587.0+/-386.6	551,1080,572	105.0	89.0	95.0		200,	3.3	1.0	9	dbSNP_116	95	69,8531	39.8+/-96.3	0,69,4231	yes	missense,utr-5	KANK1	NM_015158.2,NM_153186.3	43,	551,1149,4803	AA,AG,GG		0.8023,49.5234,17.3074	probably-damaging,	67/1353,	710966	2251,10755	2203	4300	6503	SO:0001583	missense	23189	exon7			AGAGGCGGAAGCC	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.200G>A	9.37:g.710966G>A	ENSP00000371740:p.Arg67Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	307	0.14056776556776557	275	0.5589430894308943	25	0.06906077348066299	0	0.0	7	0.009234828496042216	G	13.01	2.108040	0.37242	0.495234	0.008023	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297	T;T	0.40756	1.02;1.02	6.06	3.28	0.37604	Kank N-terminal motif (1);	0.173929	0.28241	N	0.016071	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	0.999999999999951	P;P	0.35844	0.524;0.473	B;B	0.29077	0.098;0.066	T	0.45644	-0.9247	9	0.23302	T	0.38	-5.0E-4	11.2907	0.49247	0.1916:0.0:0.8084:0.0	rs7860464;rs60562236	67;67	Q5W0W1;Q14678	.;KANK1_HUMAN	Q	67	ENSP00000371740:R67Q;ENSP00000371734:R67Q	ENSP00000346479:R67Q	R	+	2	0	KANK1	700966	1.000000	0.71417	0.988000	0.46212	0.971000	0.66376	1.990000	0.40717	0.470000	0.27294	0.655000	0.94253	CGG	G|0.843;A|0.157	0.157	strong		0.478	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
PRPF8	10594	hgsc.bcm.edu	37	17	1554770	1554770	+	Silent	SNP	A	A	G	rs1802491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1554770A>G	ENST00000572621.1	-	40	6853	c.6588T>C	c.(6586-6588)caT>caC	p.H2196H	PRPF8_ENST00000575116.1_5'Flank|RILP_ENST00000301336.6_5'Flank|PRPF8_ENST00000304992.6_Silent_p.H2196H			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	2196	MPN.				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)		TGATCTTGGCATGGGTGGTGA	0.537													a|||	1150	0.229633	0.6278	0.085	5008	,	,		22442	0.0883		0.0736	False		,,,				2504	0.1002				p.H2196H		Atlas-SNP	.											.	PRPF8	169	.	0			c.T6588C						PASS	.	G		2350,2056	566.3+/-381.9	631,1088,484	120.0	108.0	112.0		6588	-1.6	1.0	17	dbSNP_89	112	530,8070	795.7+/-407.5	23,484,3793	no	coding-synonymous	PRPF8	NM_006445.3		654,1572,4277	GG,GA,AA		6.1628,46.6636,22.1436		2196/2336	1554770	2880,10126	2203	4300	6503	SO:0001819	synonymous_variant	10594	exon41			CTTGGCATGGGTG	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.6588T>C	17.37:g.1554770A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_006445	O14547|O75965	Silent	SNP	ENST00000572621.1	37	CCDS11010.1																																																																																			A|0.777;G|0.223	0.223	strong		0.537	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
ADAM32	203102	hgsc.bcm.edu	37	8	39091526	39091526	+	Silent	SNP	T	T	C	rs4515515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39091526T>C	ENST00000379907.4	+	16	1870	c.1743T>C	c.(1741-1743)acT>acC	p.T581T	ADAM32_ENST00000437682.2_Silent_p.T482T|ADAM32_ENST00000519315.1_Silent_p.T475T	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	581						integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			TATGCATAACTGTAGACTACA	0.373													T|||	1081	0.215855	0.1233	0.2133	5008	,	,		13078	0.2937		0.2396	False		,,,				2504	0.2382				p.T581T		Atlas-SNP	.											ADAM32,NS,carcinoma,0,1	ADAM32	70	1	0			c.T1743C						PASS	.	T		552,3160		55,442,1359	71.0	62.0	65.0		1743	1.0	0.0	8	dbSNP_111	65	1959,6219		244,1471,2374	no	coding-synonymous	ADAM32	NM_145004.5		299,1913,3733	CC,CT,TT		23.9545,14.8707,21.1186		581/788	39091526	2511,9379	1856	4089	5945	SO:0001819	synonymous_variant	203102	exon16			CATAACTGTAGAC	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1743T>C	8.37:g.39091526T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	117	59	0.504274	NM_145004	Q8TC42	Silent	SNP	ENST00000379907.4	37	CCDS47846.1																																																																																			T|0.781;C|0.219	0.219	strong		0.373	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
KRT72	140807	hgsc.bcm.edu	37	12	52995127	52995127	+	Missense_Mutation	SNP	C	C	T	rs61747194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52995127C>T	ENST00000537672.2	-	1	120	c.110G>A	c.(109-111)cGg>cAg	p.R37Q	KRT72_ENST00000354310.4_Missense_Mutation_p.R37Q|KRT72_ENST00000398066.3_5'UTR|KRT72_ENST00000293745.2_Missense_Mutation_p.R37Q|RP11-641A6.2_ENST00000551089.1_RNA	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	37	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		GCCCTTGACCCGGGCCCGGAA	0.726													C|||	67	0.0133786	0.0484	0.0029	5008	,	,		12331	0.0		0.001	False		,,,				2504	0.0				p.R37Q		Atlas-SNP	.											.	KRT72	70	.	0			c.G110A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	143,3439		0,143,1648	3.0	4.0	3.0		110,110,110	4.0	0.1	12	dbSNP_129	3	3,7115		0,3,3556	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	43,43,43	0,146,5204	TT,TC,CC		0.0421,3.9922,1.3645	benign,benign,benign	37/512,37/470,37/512	52995127	146,10554	1791	3559	5350	SO:0001583	missense	140807	exon1			TTGACCCGGGCCC	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.110G>A	12.37:g.52995127C>T	ENSP00000441160:p.Arg37Gln	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	29|29	0.013278388278388278|0.013278388278388278	27|27	0.054878048780487805|0.054878048780487805	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	14.43|14.43	2.532485|2.532485	0.45073|0.45073	0.039922|0.039922	4.21E-4|4.21E-4	ENSG00000170486|ENSG00000170486	ENST00000549979|ENST00000537672;ENST00000293745;ENST00000354310	.|T;T;T	.|0.75260	.|-0.92;-0.92;-0.92	4.04|4.04	4.04|4.04	0.47022|0.47022	.|.	.|0.000000	.|0.53938	.|D	.|0.000058	T|T	0.20740|0.20740	0.0499|0.0499	L|L	0.27053|0.27053	0.805|0.805	0.19575|0.19575	N|N	0.999962|0.999962	.|B;B	.|0.18610	.|0.016;0.029	.|B;B	.|0.21708	.|0.001;0.036	T|T	0.34229|0.34229	-0.9837|-0.9837	5|10	.|0.52906	.|T	.|0.07	.|.	9.2743|9.2743	0.37690|0.37690	0.1593:0.6857:0.155:0.0|0.1593:0.6857:0.155:0.0	.|.	.|37;37	.|B4DEI8;Q14CN4	.|.;K2C72_HUMAN	R|Q	23|37	.|ENSP00000441160:R37Q;ENSP00000293745:R37Q;ENSP00000346269:R37Q	.|ENSP00000293745:R37Q	G|R	-|-	1|2	0|0	KRT72|KRT72	51281394|51281394	.|.	.|.	0.107000|0.107000	0.21349|0.21349	0.130000|0.130000	0.20726|0.20726	.|.	.|.	2.543000|2.543000	0.85770|0.85770	0.561000|0.561000	0.74099|0.74099	GGG|CGG	C|0.987;T|0.013	0.013	strong		0.726	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
USP19	10869	hgsc.bcm.edu	37	3	49149020	49149020	+	Missense_Mutation	SNP	T	T	C	rs13321689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49149020T>C	ENST00000398888.2	-	20	3139	c.2821A>G	c.(2821-2823)Acc>Gcc	p.T941A	USP19_ENST00000417901.1_Missense_Mutation_p.T1044A|USP19_ENST00000434032.2_Missense_Mutation_p.T1042A|USP19_ENST00000453664.1_Missense_Mutation_p.T1032A|USP19_ENST00000398896.1_Missense_Mutation_p.T749A|USP19_ENST00000398898.2_Missense_Mutation_p.T981A|USP19_ENST00000398892.3_Missense_Mutation_p.T981A	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	941	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ATTCCACTGGTGCTGGGCACA	0.637													T|||	96	0.0191693	0.0688	0.0072	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.T1044A		Atlas-SNP	.											.	USP19	158	.	0			c.A3130G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR	283,3485		9,265,1610	27.0	29.0	29.0		3124,3130,3094,2821	4.9	1.0	3	dbSNP_121	29	6,8216		0,6,4105	yes	missense,missense,missense,missense	USP19	NM_001199160.1,NM_001199161.1,NM_001199162.1,NM_006677.2	58,58,58,58	9,271,5715	CC,CT,TT		0.073,7.5106,2.4103	benign,benign,benign,benign	1042/1420,1044/1385,1032/1373,941/1319	49149020	289,11701	1884	4111	5995	SO:0001583	missense	10869	exon21			CACTGGTGCTGGG	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.2821A>G	3.37:g.49149020T>C	ENSP00000381863:p.Thr941Ala	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	42	0.019230769230769232	37	0.07520325203252033	5	0.013812154696132596	0	0.0	0	0.0	T	2.392	-0.339698	0.05243	0.075106	7.3E-4	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.18657	2.2;2.21;2.3;2.3;2.2;2.3;2.29	6.04	4.93	0.64822	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.787862	0.12324	N	0.478992	T	0.00384	0.0012	N	0.02213	-0.635	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.003;0.001;0.0;0.001	B;B;B;B;B	0.14578	0.011;0.011;0.005;0.005;0.005	T	0.38001	-0.9681	10	0.14252	T	0.57	-11.953	5.3341	0.15947	0.0:0.0978:0.2401:0.6621	rs13321689	1042;1032;941;981;749	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	A	749;981;1044;1032;981;941;1042	ENSP00000381870:T749A;ENSP00000381872:T981A;ENSP00000395260:T1044A;ENSP00000400090:T1032A;ENSP00000381867:T981A;ENSP00000381863:T941A;ENSP00000401197:T1042A	ENSP00000381863:T941A	T	-	1	0	USP19	49124024	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.989000	0.29629	2.330000	0.79161	0.529000	0.55759	ACC	T|0.972;C|0.028	0.028	strong		0.637	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
STRC	161497	hgsc.bcm.edu	37	15	43893072	43893072	+	Silent	SNP	G	G	A	rs3097773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43893072G>A	ENST00000450892.2	-	25	4919	c.4842C>T	c.(4840-4842)ttC>ttT	p.F1614F	RNU6-554P_ENST00000410466.1_RNA|STRC_ENST00000541030.1_Silent_p.F841F	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	1614					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CAAATGACCTGAACTCCCAAC	0.552													A|||	1982	0.395767	0.7943	0.2291	5008	,	,		18022	0.4216		0.1064	False		,,,				2504	0.2464				p.F1614F		Atlas-SNP	.											.	STRC	58	.	0			c.C4842T						PASS	.	A		2942,1458	442.0+/-346.6	1020,902,278	75.0	97.0	89.0		4842	2.1	1.0	15	dbSNP_103	89	865,7729	769.3+/-407.6	55,755,3487	no	coding-synonymous	STRC	NM_153700.2		1075,1657,3765	AA,AG,GG		10.0652,33.1364,29.2981		1614/1776	43893072	3807,9187	2200	4297	6497	SO:0001819	synonymous_variant	161497	exon25			TGACCTGAACTCC	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.4842C>T	15.37:g.43893072G>A		Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	336	128	0.380952	NM_153700		Silent	SNP	ENST00000450892.2	37	CCDS10098.1																																																																																			.	.	weak		0.552	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
ZBTB37	84614	hgsc.bcm.edu	37	1	173839435	173839435	+	Silent	SNP	G	G	A	rs9425761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173839435G>A	ENST00000367701.5	+	2	263	c.72G>A	c.(70-72)caG>caA	p.Q24Q	ZBTB37_ENST00000367702.1_Silent_p.Q24Q|ZBTB37_ENST00000432989.1_Silent_p.Q24Q|GAS5_ENST00000364084.1_RNA|ZBTB37_ENST00000367704.1_Silent_p.Q24Q|ZBTB37_ENST00000427304.1_Silent_p.Q24Q			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	24					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						ATCTAAACCAGTTGCGCATGC	0.527													G|||	560	0.111821	0.4009	0.0346	5008	,	,		17279	0.0		0.006	False		,,,				2504	0.0				p.Q24Q		Atlas-SNP	.											.	ZBTB37	38	.	0			c.G72A						PASS	.	G	,	1333,3073	446.1+/-347.9	199,935,1069	79.0	73.0	75.0		72,72	3.8	1.0	1	dbSNP_119	75	31,8569	20.4+/-63.3	0,31,4269	no	coding-synonymous,coding-synonymous	ZBTB37	NM_001122770.1,NM_032522.3	,	199,966,5338	AA,AG,GG		0.3605,30.2542,10.4875	,	24/504,24/362	173839435	1364,11642	2203	4300	6503	SO:0001819	synonymous_variant	84614	exon3			AAACCAGTTGCGC	AK057310	CCDS1312.1, CCDS44278.1	1q24.2	2013-01-08			ENSG00000185278	ENSG00000185278		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	28365	protein-coding gene	gene with protein product						12477932	Standard	NM_032522		Approved	MGC2629, ZNF908	uc009wwp.1	Q5TC79	OTTHUMG00000037274	ENST00000367701.5:c.72G>A	1.37:g.173839435G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	192	89	0.463542	NM_032522	Q5TC80|Q96M87|Q9BQ88	Silent	SNP	ENST00000367701.5	37	CCDS44278.1																																																																																			G|0.875;A|0.125	0.125	strong		0.527	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522	
ABAT	18	hgsc.bcm.edu	37	16	8868776	8868776	+	Silent	SNP	C	C	A	rs1641022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:8868776C>A	ENST00000396600.2	+	13	1922	c.984C>A	c.(982-984)gtC>gtA	p.V328V	ABAT_ENST00000425191.2_Silent_p.V328V|ABAT_ENST00000569156.1_Silent_p.V328V|ABAT_ENST00000268251.8_Silent_p.V328V|ABAT_ENST00000567812.1_Silent_p.V343V	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	328					behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	TGGACGAGGTCCAGACCGGAG	0.592													C|||	1590	0.317492	0.0552	0.3429	5008	,	,		18174	0.4167		0.4374	False		,,,				2504	0.4284				p.V328V		Atlas-SNP	.											.	ABAT	46	.	0			c.C984A						PASS	.	C	,,	531,3863	240.3+/-251.1	27,477,1693	59.0	56.0	57.0		984,984,984	-1.1	1.0	16	dbSNP_89	57	3661,4939	524.1+/-380.5	782,2097,1421	no	coding-synonymous,coding-synonymous,coding-synonymous	ABAT	NM_000663.4,NM_001127448.1,NM_020686.5	,,	809,2574,3114	AA,AC,CC		42.5698,12.0847,32.261	,,	328/501,328/501,328/501	8868776	4192,8802	2197	4300	6497	SO:0001819	synonymous_variant	18	exon13			CGAGGTCCAGACC	L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	2.6.1.19		23	protein-coding gene	gene with protein product	"""4-aminobutyrate transaminase"""	137150				7721088	Standard	NM_020686		Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000396600.2:c.984C>A	16.37:g.8868776C>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_001127448	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	Silent	SNP	ENST00000396600.2	37	CCDS10534.1																																																																																			C|0.674;A|0.326	0.326	strong		0.592	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2	NM_020686	
ACSM3	6296	hgsc.bcm.edu	37	16	20802172	20802172	+	Intron	SNP	C	C	T	rs2301770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20802172C>T	ENST00000289416.5	+	10	1801				ACSM3_ENST00000450120.2_Intron|ACSM3_ENST00000567387.1_Intron|ERI2_ENST00000300005.3_Splice_Site_p.G272D	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3						cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						GAAGAAATACCCAAATTCTTG	0.453													C|||	534	0.106629	0.1263	0.0663	5008	,	,		18274	0.1329		0.0755	False		,,,				2504	0.1135				p.G272D		Atlas-SNP	.											.	ERI2	50	.	0			c.G815A						PASS	.	C	,ASP/GLY	505,3897	232.0+/-245.7	31,443,1727	97.0	105.0	103.0		,815	-0.5	0.0	16	dbSNP_100	103	604,7996	158.9+/-212.3	20,564,3716	yes	intron,missense-near-splice	ACSM3,ERI2	NM_005622.3,NM_080663.2	,94	51,1007,5443	TT,TC,CC		7.0233,11.4721,8.5295	,	,272/329	20802172	1109,11893	2201	4300	6501	SO:0001627	intron_variant	112479	exon9			AAATACCCAAATT	D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"""Acyl-CoA synthetase family"""	10522	protein-coding gene	gene with protein product		145505	"""SA (rat hypertension-associated) homolog"", ""SA hypertension-associated homolog (rat)"""	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.1326+162C>T	16.37:g.20802172C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	151	68	0.450331	NM_080663	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Missense_Mutation	SNP	ENST00000289416.5	37	CCDS10589.1	242	0.1108058608058608	67	0.13617886178861788	31	0.0856353591160221	86	0.15034965034965034	58	0.07651715039577836	C	6.413	0.444309	0.12164	0.114721	0.070233	ENSG00000196678	ENST00000300005	.	.	.	2.61	-0.5	0.12012	.	.	.	.	.	T	0.00496	0.0016	.	.	.	0.80722	P	0.0	D	0.76494	0.999	D	0.74023	0.982	T	0.12372	-1.0550	5	.	.	.	.	5.237	0.15452	0.0:0.5657:0.0:0.4343	rs2301770;rs57708260;rs2301770	272	A8K979-4	.	D	272	.	.	G	-	2	0	ERI2	20709673	0.000000	0.05858	0.000000	0.03702	0.129000	0.20672	-1.022000	0.03611	-0.080000	0.12685	0.455000	0.32223	GGC	C|0.906;T|0.094	0.094	strong		0.453	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622	
SPAG17	200162	hgsc.bcm.edu	37	1	118512719	118512719	+	Missense_Mutation	SNP	G	G	T	rs140504036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118512719G>T	ENST00000336338.5	-	46	6412	c.6347C>A	c.(6346-6348)cCa>cAa	p.P2116Q	SPAG17_ENST00000492438.1_5'Flank	NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	2116						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TGTGCTGGGTGGGGGCTGCTT	0.393													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18332	0.0		0.0	False		,,,				2504	0.0				p.P2116Q		Atlas-SNP	.											.	SPAG17	263	.	0			c.C6347A						PASS	.	G	GLN/PRO	8,4398	14.3+/-33.2	0,8,2195	141.0	139.0	140.0		6347	5.3	1.0	1	dbSNP_134	140	0,8600		0,0,4300	yes	missense	SPAG17	NM_206996.2	76	0,8,6495	TT,TG,GG		0.0,0.1816,0.0615	probably-damaging	2116/2224	118512719	8,12998	2203	4300	6503	SO:0001583	missense	200162	exon46			CTGGGTGGGGGCT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.6347C>A	1.37:g.118512719G>T	ENSP00000337804:p.Pro2116Gln	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.974497	0.74246	0.001816	0.0	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.21031	2.03	5.3	5.3	0.74995	.	0.067501	0.64402	D	0.000011	T	0.37732	0.1014	M	0.78049	2.395	0.32515	N	0.536992	D	0.67145	0.996	D	0.65573	0.936	T	0.30909	-0.9962	10	0.87932	D	0	.	15.9899	0.80197	0.0:0.0:1.0:0.0	.	2116	Q6Q759	SPG17_HUMAN	Q	2116;596	ENSP00000337804:P2116Q	ENSP00000337804:P2116Q	P	-	2	0	SPAG17	118314242	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.801000	0.69115	2.775000	0.95449	0.650000	0.86243	CCA	G|0.999;T|0.001	0.001	strong		0.393	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
DDX59	83479	hgsc.bcm.edu	37	1	200635550	200635550	+	Missense_Mutation	SNP	T	T	C	rs3795634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200635550T>C	ENST00000331314.6	-	2	532	c.319A>G	c.(319-321)Atc>Gtc	p.I107V	DDX59_ENST00000367348.3_Missense_Mutation_p.I107V|DDX59_ENST00000447706.2_Missense_Mutation_p.I107V	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	107			I -> V (in dbSNP:rs3795634).			cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						ACAACACAGATGGGTTCCCCT	0.463													C|||	1094	0.21845	0.1664	0.2392	5008	,	,		21100	0.4365		0.0696	False		,,,				2504	0.2025				p.I107V		Atlas-SNP	.											.	DDX59	117	.	0			c.A319G						PASS	.	C	VAL/ILE	639,3767	766.7+/-413.5	47,545,1611	70.0	70.0	70.0		319	4.3	0.1	1	dbSNP_107	70	535,8065	795.4+/-407.5	11,513,3776	yes	missense	DDX59	NM_001031725.4	29	58,1058,5387	CC,CT,TT		6.2209,14.503,9.0266	benign	107/620	200635550	1174,11832	2203	4300	6503	SO:0001583	missense	83479	exon2			CACAGATGGGTTC	BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"""Zinc fingers, HIT-type"", ""DEAD-boxes"""	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.319A>G	1.37:g.200635550T>C	ENSP00000330460:p.Ile107Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_001031725	Q6PJL2|Q8IVW3|Q9H0W3	Missense_Mutation	SNP	ENST00000331314.6	37	CCDS30964.1	434	0.1987179487179487	78	0.15853658536585366	67	0.1850828729281768	231	0.40384615384615385	58	0.07651715039577836	C	4.298	0.054574	0.08291	0.14503	0.062209	ENSG00000118197	ENST00000447706;ENST00000367348;ENST00000331314;ENST00000436897	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.24	4.32	0.51571	Zinc finger, HIT-type (1);	0.058799	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00960	-1.095	0.46096	P	0.0011339999999999684	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42932	-0.9422	9	0.02654	T	1	-14.6233	11.8633	0.52478	0.0:0.8574:0.0:0.1426	rs3795634;rs52791317;rs56843782;rs3795634	107;107	B7Z5N6;Q5T1V6	.;DDX59_HUMAN	V	107	ENSP00000394367:I107V;ENSP00000356317:I107V;ENSP00000330460:I107V;ENSP00000391312:I107V	ENSP00000330460:I107V	I	-	1	0	DDX59	198902173	0.984000	0.35163	0.063000	0.19743	0.742000	0.42306	2.697000	0.47060	0.620000	0.30215	-0.222000	0.12452	ATC	T|0.871;C|0.129	0.129	strong		0.463	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4	
SRGAP2	23380	hgsc.bcm.edu	37	1	206574931	206574931	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206574931G>A	ENST00000414007.1	+	4	563	c.563G>A	c.(562-564)cGc>cAc	p.R188H	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	328	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)					GACAAGCAGCGCCTCATGGAG	0.527																																					p.R174H		Atlas-SNP	.											SRGAP2_ENST00000414007,NS,carcinoma,0,3	.	.	3	0			c.G521A						scavenged	.						16.0	14.0	14.0					1																	206574931		1795	4026	5821	SO:0001583	missense	100996712	exon4			AGCAGCGCCTCAT	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.563G>A	1.37:g.206574931G>A	ENSP00000390898:p.Arg188His	Somatic	1644	1	0.000608273		WXS	Illumina HiSeq	Phase_I	1642	188	0.114495	NM_001271887		Missense_Mutation	SNP	ENST00000414007.1	37		.	.	.	.	.	.	.	.	.	.	G	28.8	4.949468	0.92660	.	.	ENSG00000163486	ENST00000414359;ENST00000414007	T	0.13778	2.56	6.02	6.02	0.97574	.	0.054744	0.64402	D	0.000001	T	0.21881	0.0527	.	.	.	0.80722	D	1.000000	D;P;B	0.60160	0.987;0.602;0.174	P;B;B	0.45474	0.482;0.107;0.02	T	0.00601	-1.1650	8	0.49607	T	0.09	.	20.5373	0.99239	0.0:0.0:1.0:0.0	.	175;328;327	B4DDU0;O75044;B7Z3G4	.;FNBP2_HUMAN;.	H	241;188	ENSP00000390898:R188H	ENSP00000390898:R188H	R	+	2	0	SRGAP2	204641554	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.558000	0.73942	2.857000	0.98124	0.650000	0.86243	CGC	.	.	none		0.527	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326	
NAT10	55226	hgsc.bcm.edu	37	11	34133767	34133767	+	Silent	SNP	G	G	A	rs36003235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34133767G>A	ENST00000257829.3	+	4	575	c.369G>A	c.(367-369)ctG>ctA	p.L123L	NAT10_ENST00000531159.2_Silent_p.L51L|NAT10_ENST00000527971.1_Silent_p.L123L	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	123						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				TGTGTGTGCTGCAGGTGGGTG	0.517													G|||	32	0.00638978	0.0219	0.0043	5008	,	,		20244	0.0		0.0	False		,,,				2504	0.0				p.L123L		Atlas-SNP	.											.	NAT10	78	.	0			c.G369A						PASS	.	G	,	49,4355	50.9+/-86.3	0,49,2153	115.0	82.0	93.0		153,369	-2.1	1.0	11	dbSNP_126	93	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous	NAT10	NM_001144030.1,NM_024662.2	,	0,50,6450	AA,AG,GG		0.0116,1.1126,0.3846	,	51/954,123/1026	34133767	50,12950	2202	4298	6500	SO:0001819	synonymous_variant	55226	exon4			TGTGCTGCAGGTG	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"""N-acetyltransferase 10"""			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.369G>A	11.37:g.34133767G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	163	77	0.472393	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Silent	SNP	ENST00000257829.3	37	CCDS7889.1																																																																																			G|0.996;A|0.004	0.004	strong		0.517	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662	
OR11H12	440153	hgsc.bcm.edu	37	14	19377881	19377881	+	Missense_Mutation	SNP	G	G	A	rs138502172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:19377881G>A	ENST00000550708.1	+	1	360	c.288G>A	c.(286-288)atG>atA	p.M96I		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	96						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)		TTCCCAAGATGTTGGTCAACT	0.403																																					p.M96I		Atlas-SNP	.											OR11H12,NS,carcinoma,0,1	OR11H12	58	1	0			c.G288A						scavenged	.						5.0	5.0	5.0					14																	19377881		1160	2711	3871	SO:0001583	missense	440153	exon1			CAAGATGTTGGTC		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.288G>A	14.37:g.19377881G>A	ENSP00000449002:p.Met96Ile	Somatic	566	3	0.00530035		WXS	Illumina HiSeq	Phase_I	599	62	0.103506	NM_001013354		Missense_Mutation	SNP	ENST00000550708.1	37	CCDS32017.1	.	.	.	.	.	.	.	.	.	.	g	11.75	1.732631	0.30684	.	.	ENSG00000257115	ENST00000550708	T	0.05513	3.43	0.585	0.585	0.17428	GPCR, rhodopsin-like superfamily (1);	0.289165	0.23960	N	0.042866	T	0.11239	0.0274	M	0.78223	2.4	0.22675	N	0.998867	P	0.51537	0.946	P	0.47528	0.549	T	0.14282	-1.0478	9	0.59425	D	0.04	.	7.1009	0.25336	1.0E-4:0.0:0.9999:0.0	.	96	B2RN74	O11HC_HUMAN	I	96	ENSP00000449002:M96I	ENSP00000449002:M96I	M	+	3	0	CR383656.1	18447881	0.814000	0.29104	0.980000	0.43619	0.268000	0.26511	0.362000	0.20284	0.619000	0.30197	0.064000	0.15345	ATG	G|0.973;A|0.027	0.027	strong		0.403	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354	
DMBT1	1755	hgsc.bcm.edu	37	10	124351954	124351954	+	Silent	SNP	G	G	A	rs4752722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:124351954G>A	ENST00000338354.3	+	20	2449	c.2343G>A	c.(2341-2343)tcG>tcA	p.S781S	DMBT1_ENST00000344338.3_Silent_p.S771S|DMBT1_ENST00000368909.3_Silent_p.S781S|DMBT1_ENST00000368955.3_Silent_p.S771S|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000368956.2_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	781	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GGGCCACGTCGGCCCCAGGAA	0.617													g|||	1864	0.372204	0.5469	0.2435	5008	,	,		17432	0.4395		0.1511	False		,,,				2504	0.3855				p.S781S	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G2343A						PASS	.	A	,,	1880,2108		461,958,575	179.0	145.0	156.0		,2343,2313	-7.7	0.0	10	dbSNP_111	156	1157,7105		170,817,3144	no	intron,coding-synonymous,coding-synonymous	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	,,	631,1775,3719	AA,AG,GG		14.0039,47.1414,24.7918	,,	,781/2414,771/2404	124351954	3037,9213	1994	4131	6125	SO:0001819	synonymous_variant	1755	exon20			CACGTCGGCCCCA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.2343G>A	10.37:g.124351954G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	154	109	0.707792	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																				G|0.732;A|0.268	0.268	strong		0.617	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163266	163266	+	Missense_Mutation	SNP	C	C	G	rs3810867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:163266C>G	ENST00000283426.6	+	11	2061	c.2011C>G	c.(2011-2013)Cgc>Ggc	p.R671G		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	671				R -> G (in Ref. 1; BAB67802). {ECO:0000305}.			Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GGAGACCCTGCGCCCAGGGCT	0.697													G|||	1920	0.383387	0.4584	0.3184	5008	,	,		13760	0.1944		0.3817	False		,,,				2504	0.5245				p.R671G		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.C2011G						PASS	.	G	GLY/ARG	1908,2468		436,1036,716	12.0	14.0	13.0		2011	-4.4	0.0	5	dbSNP_107	13	3376,5192		688,2000,1596	yes	missense	PLEKHG4B	NM_052909.3	125	1124,3036,2312	GG,GC,CC		39.4024,43.6015,40.822	benign	671/1272	163266	5284,7660	2188	4284	6472	SO:0001583	missense	153478	exon11			ACCCTGCGCCCAG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.2011C>G	5.37:g.163266C>G	ENSP00000283426:p.Arg671Gly	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	677	0.309981684981685	200	0.4065040650406504	112	0.30939226519337015	103	0.18006993006993008	262	0.34564643799472294	G	0.008	-1.917018	0.00503	0.436015	0.394024	ENSG00000153404	ENST00000283426	T	0.28255	1.62	2.91	-4.41	0.03590	.	.	.	.	.	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	0.46596	-0.9180	8	0.22109	T	0.4	.	5.3271	0.15913	0.4358:0.2652:0.2991:0.0	rs3810867;rs59972694	671	Q96PX9	PKH4B_HUMAN	G	671	ENSP00000283426:R671G	ENSP00000283426:R671G	R	+	1	0	PLEKHG4B	216266	0.000000	0.05858	0.004000	0.12327	0.022000	0.10575	-1.042000	0.03539	-1.821000	0.01213	-1.407000	0.01130	CGC	C|0.689;G|0.311	0.311	strong		0.697	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
VWDE	221806	hgsc.bcm.edu	37	7	12409263	12409263	+	Missense_Mutation	SNP	C	C	A	rs17165906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12409263C>A	ENST00000275358.3	-	12	2857	c.2669G>T	c.(2668-2670)tGc>tTc	p.C890F		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	890						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TAAATTGGGGCATTTTAATAC	0.423													C|||	786	0.156949	0.1747	0.0836	5008	,	,		18603	0.2024		0.1044	False		,,,				2504	0.1922				p.C890F		Atlas-SNP	.											.	VWDE	123	.	0			c.G2669T						PASS	.	C	PHE/CYS	242,1142		21,200,471	129.0	103.0	111.0		2669	4.8	1.0	7	dbSNP_123	111	366,2816		20,326,1245	yes	missense	VWDE	NM_001135924.1	205	41,526,1716	AA,AC,CC		11.5022,17.4855,13.3158	probably-damaging	890/1591	12409263	608,3958	692	1591	2283	SO:0001583	missense	221806	exon12			TTGGGGCATTTTA		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.2669G>T	7.37:g.12409263C>A	ENSP00000275358:p.Cys890Phe	Somatic	239	1	0.0041841		WXS	Illumina HiSeq	Phase_I	207	95	0.458937	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	340	0.15567765567765568	84	0.17073170731707318	31	0.0856353591160221	138	0.24125874125874125	87	0.11477572559366754	C	16.13	3.036632	0.54896	0.174855	0.115022	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.93488	-3.23	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.00608	0.0020	M	0.70275	2.135	0.20489	P	0.999891743	D	0.89917	1.0	D	0.87578	0.998	T	0.00000	-1.3677	9	0.87932	D	0	.	18.096	0.89490	0.0:1.0:0.0:0.0	rs17165906;rs52797888;rs17165906	890	Q8N2E2	VWDE_HUMAN	F	890;344	ENSP00000275358:C890F	ENSP00000275358:C890F	C	-	2	0	VWDE	12375788	1.000000	0.71417	0.995000	0.50966	0.254000	0.26022	7.252000	0.78309	2.512000	0.84698	0.655000	0.94253	TGC	C|0.841;A|0.159	0.159	strong		0.423	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
ADCY9	115	hgsc.bcm.edu	37	16	4016943	4016943	+	Silent	SNP	A	A	G	rs2230741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4016943A>G	ENST00000294016.3	-	11	3433	c.2895T>C	c.(2893-2895)agT>agC	p.S965S		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	965					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						GCGGCACCGAACTATTGCACG	0.607													G|||	849	0.169529	0.3835	0.0504	5008	,	,		17025	0.2371		0.0268	False		,,,				2504	0.0419				p.S965S		Atlas-SNP	.											.	ADCY9	151	.	0			c.T2895C						PASS	.	G		1328,3050		205,918,1066	39.0	45.0	43.0		2895	3.2	0.8	16	dbSNP_107	43	248,8330		8,232,4049	no	coding-synonymous	ADCY9	NM_001116.3		213,1150,5115	GG,GA,AA		2.8911,30.3335,12.1642		965/1354	4016943	1576,11380	2189	4289	6478	SO:0001819	synonymous_variant	115	exon11			CACCGAACTATTG	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.2895T>C	16.37:g.4016943A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	CCDS32382.1																																																																																			A|0.856;G|0.144	0.144	strong		0.607	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
TBC1D15	64786	hgsc.bcm.edu	37	12	72307637	72307637	+	Silent	SNP	C	C	G	rs11178983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72307637C>G	ENST00000550746.1	+	13	1447	c.1383C>G	c.(1381-1383)tcC>tcG	p.S461S	TBC1D15_ENST00000485960.2_Silent_p.S444S|TBC1D15_ENST00000548679.1_3'UTR|TBC1D15_ENST00000319106.8_Silent_p.S452S|TBC1D15_ENST00000393309.3_Silent_p.S215S	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	461	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ATTTACTTTCCCCTCTTTTAT	0.353													C|||	315	0.0628994	0.003	0.0346	5008	,	,		16596	0.0734		0.0606	False		,,,				2504	0.1554				p.S461S		Atlas-SNP	.											.	TBC1D15	99	.	0			c.C1383G						PASS	.	C	,,	81,4325	67.6+/-105.2	0,81,2122	131.0	136.0	134.0		1332,1356,1383	-6.5	0.6	12	dbSNP_120	134	661,7939	166.5+/-218.5	26,609,3665	no	coding-synonymous,coding-synonymous,coding-synonymous	TBC1D15	NM_001146213.1,NM_001146214.1,NM_022771.4	,,	26,690,5787	GG,GC,CC		7.686,1.8384,5.7051	,,	444/675,452/683,461/692	72307637	742,12264	2203	4300	6503	SO:0001819	synonymous_variant	64786	exon13			ACTTTCCCCTCTT	AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.1383C>G	12.37:g.72307637C>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_022771	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Silent	SNP	ENST00000550746.1	37	CCDS31858.1																																																																																			C|0.947;G|0.053	0.053	strong		0.353	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771	
CXorf36	79742	hgsc.bcm.edu	37	X	45051111	45051111	+	Missense_Mutation	SNP	C	C	T	rs1132201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:45051111C>T	ENST00000398000.2	-	2	457	c.383G>A	c.(382-384)aGa>aAa	p.R128K	RP11-342D14.1_ENST00000438181.1_RNA|CXorf36_ENST00000477281.1_5'UTR|RP11-342D14.1_ENST00000450527.1_RNA|CXorf36_ENST00000377934.4_Missense_Mutation_p.R128K	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	128			R -> K (in dbSNP:rs1132201). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						GGCACAGATTCTCCTGTCTGA	0.498													C|||	1659	0.43947	0.1324	0.3775	3775	,	,		13466	0.5724		0.2525	False		,,,				2504	0.3998				p.R128K		Atlas-SNP	.											.	CXorf36	53	.	0			c.G383A						PASS	.	C	LYS/ARG,LYS/ARG	774,3061		62,538,112,1032,459	89.0	84.0	86.0		383,383	2.9	1.0	X	dbSNP_86	86	2185,4543		261,1067,596,1100,1276	yes	missense,missense	CXorf36	NM_024689.2,NM_176819.3	26,26	323,1605,708,2132,1735	TT,TC,T,CC,C		32.4762,20.1825,28.0129	benign,benign	128/183,128/434	45051111	2959,7604	2203	4300	6503	SO:0001583	missense	79742	exon2			CAGATTCTCCTGT	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.383G>A	X.37:g.45051111C>T	ENSP00000381086:p.Arg128Lys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	165	79	0.478788	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Missense_Mutation	SNP	ENST00000398000.2	37	CCDS48096.1	717	0.4321880650994575	48	0.10714285714285714	80	0.29411764705882354	220	0.625	133	0.2078125	C	12.98	2.101528	0.37048	0.201825	0.324762	ENSG00000147113	ENST00000398000;ENST00000377934	T;T	0.30448	1.62;1.53	5.63	2.92	0.33932	.	0.225472	0.38897	N	0.001527	T	0.00012	0.0000	N	0.26042	0.785	0.40769	P	0.016925999999999997	B;B	0.20052	0.005;0.041	B;B	0.14578	0.006;0.011	T	0.40887	-0.9539	9	0.08599	T	0.76	.	8.5812	0.33630	0.0:0.6796:0.0:0.3204	rs1132201;rs3192766;rs17261166;rs52822123;rs56729282;rs1132201	128;128	Q9H7Y0-2;Q9H7Y0	.;CX036_HUMAN	K	128	ENSP00000381086:R128K;ENSP00000367168:R128K	ENSP00000367168:R128K	R	-	2	0	CXorf36	44936055	1.000000	0.71417	0.992000	0.48379	0.972000	0.66771	1.172000	0.31908	0.553000	0.29044	-0.191000	0.12829	AGA	0|0.013;T|0.348	0.348	strong		0.498	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689	
WDR72	256764	hgsc.bcm.edu	37	15	53907906	53907906	+	Missense_Mutation	SNP	A	A	C	rs16966320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:53907906A>C	ENST00000396328.1	-	15	2736	c.2497T>G	c.(2497-2499)Tct>Gct	p.S833A	WDR72_ENST00000557913.1_Missense_Mutation_p.S830A|WDR72_ENST00000559418.1_Missense_Mutation_p.S843A|WDR72_ENST00000360509.5_Missense_Mutation_p.S833A	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	833			S -> A (in dbSNP:rs16966320).							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)		TCATTCAAAGAAATTCCCAAA	0.348													C|||	674	0.134585	0.4349	0.0591	5008	,	,		18453	0.0		0.0408	False		,,,				2504	0.0174				p.S833A		Atlas-SNP	.											.	WDR72	177	.	0			c.T2497G						PASS	.	C	ALA/SER	1523,2861	628.2+/-395.1	278,967,947	63.0	66.0	65.0		2497	4.8	1.0	15	dbSNP_123	65	331,8249	781.9+/-407.6	5,321,3964	yes	missense	WDR72	NM_182758.2	99	283,1288,4911	CC,CA,AA		3.8578,34.74,14.3011	benign	833/1103	53907906	1854,11110	2192	4290	6482	SO:0001583	missense	256764	exon15			TCAAAGAAATTCC	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.2497T>G	15.37:g.53907906A>C	ENSP00000379619:p.Ser833Ala	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	80	33	0.4125	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	251	0.11492673992673992	200	0.4065040650406504	21	0.058011049723756904	0	0.0	30	0.0395778364116095	C	2.531	-0.308463	0.05458	0.3474	0.038578	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.32988	1.43;1.43	5.72	4.8	0.61643	.	0.152129	0.46442	N	0.000298	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	9	0.24483	T	0.36	.	7.0988	0.25325	0.1396:0.7203:0.0:0.1401	rs16966320;rs52795659;rs59442033;rs16966320	833	Q3MJ13	WDR72_HUMAN	A	833	ENSP00000379619:S833A;ENSP00000353699:S833A	ENSP00000353699:S833A	S	-	1	0	WDR72	51695198	0.201000	0.23410	0.996000	0.52242	0.198000	0.23893	0.430000	0.21428	1.439000	0.47511	-0.121000	0.15023	TCT	A|0.863;C|0.137	0.137	strong		0.348	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
ASPG	374569	hgsc.bcm.edu	37	14	104559922	104559922	+	Missense_Mutation	SNP	C	C	G	rs1744284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:104559922C>G	ENST00000551177.1	+	3	378	c.286C>G	c.(286-288)Ctt>Gtt	p.L96V	ASPG_ENST00000455920.2_Missense_Mutation_p.L96V|ASPG_ENST00000546892.2_Missense_Mutation_p.L96V	NM_001080464.2	NP_001073933.2	Q86U10	LPP60_HUMAN	asparaginase	96	Asparaginase.|Asparaginase/glutaminase. {ECO:0000255|PROSITE-ProRule:PRU01068}.		L -> V (in dbSNP:rs1744284).		asparagine metabolic process (GO:0006528)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)		1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|asparaginase activity (GO:0004067)|lysophospholipase activity (GO:0004622)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	11						GTGGGTTTGCCTTGCCCAGAC	0.642													G|||	2066	0.41254	0.6815	0.3314	5008	,	,		11004	0.3869		0.1809	False		,,,				2504	0.3712				p.L96V		Atlas-SNP	.											.	ASPG	34	.	0			c.C286G						PASS	.	G	VAL/LEU	2288,1866		607,1074,396	73.0	86.0	82.0		286	1.0	0.2	14	dbSNP_89	82	1422,6954		119,1184,2885	yes	missense	ASPG	NM_001080464.2	32	726,2258,3281	GG,GC,CC		16.9771,44.9206,29.6089	benign	96/574	104559922	3710,8820	2077	4188	6265	SO:0001583	missense	374569	exon3			GTTTGCCTTGCCC		CCDS45170.1, CCDS45170.2	14q32.33	2014-03-14	2014-03-14	2008-11-06	ENSG00000166183	ENSG00000166183	3.1.1.5, 3.5.1.1	"""Ankyrin repeat domain containing"""	20123	protein-coding gene	gene with protein product	"""60-kDa-lysophospholipase"""		"""chromosome 14 open reading frame 76"", ""asparaginase homolog (S. cerevisiae)"""	C14orf76			Standard	NM_001080464		Approved		uc001yoq.2	Q86U10		ENST00000551177.1:c.286C>G	14.37:g.104559922C>G	ENSP00000450040:p.Leu96Val	Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_001080464	B9EGQ2|Q8IV80	Missense_Mutation	SNP	ENST00000551177.1	37	CCDS45170.2	869|869	0.39789377289377287|0.39789377289377287	367|367	0.7459349593495935|0.7459349593495935	131|131	0.36187845303867405|0.36187845303867405	230|230	0.4020979020979021|0.4020979020979021	141|141	0.18601583113456466|0.18601583113456466	G|G	3.291|3.291	-0.144993|-0.144993	0.06627|0.06627	0.550794|0.550794	0.169771|0.169771	ENSG00000166183|ENSG00000166183	ENST00000551177;ENST00000299234;ENST00000546892;ENST00000455920|ENST00000551170	T;T;T|.	0.35605|.	1.3;1.3;1.3|.	3.57|3.57	1.01|1.01	0.19927|0.19927	.|.	0.120423|.	0.53938|.	N|.	0.000041|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.33792|0.33792	1.035|1.035	0.54753|0.54753	P|P	2.0000000000020002E-5|2.0000000000020002E-5	B;B;B;B|.	0.11235|.	0.004;0.0;0.0;0.001|.	B;B;B;B|.	0.15052|.	0.012;0.001;0.001;0.008|.	T|T	0.30149|0.30149	-0.9988|-0.9988	9|4	0.62326|.	D|.	0.03|.	-1.3355|-1.3355	5.606|5.606	0.17379|0.17379	0.5774:0.325:0.0976:0.0|0.5774:0.325:0.0976:0.0	rs1744284;rs1890980;rs2758760;rs56974110;rs1744284|rs1744284;rs1890980;rs2758760;rs56974110;rs1744284	96;96;96;124|.	G3V1Y8;Q86U10;Q86U10-3;E5RFC2|.	.;LPP60_HUMAN;.;.|.	V|R	96;124;96;96|32	ENSP00000450040:L96V;ENSP00000448911:L96V;ENSP00000389003:L96V|.	ENSP00000299234:L124V|.	L|P	+|+	1|2	0|0	ASPG|ASPG	103629675|103629675	0.924000|0.924000	0.31332|0.31332	0.223000|0.223000	0.23860|0.23860	0.015000|0.015000	0.08874|0.08874	2.059000|2.059000	0.41384|0.41384	-0.348000|-0.348000	0.08286|0.08286	-1.145000|-1.145000	0.01858|0.01858	CTT|CCT	C|0.634;G|0.366	0.366	strong		0.642	ASPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407005.1	NM_001080464	
TMEM102	284114	hgsc.bcm.edu	37	17	7339903	7339903	+	Missense_Mutation	SNP	C	C	G	rs76805816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7339903C>G	ENST00000323206.1	+	3	878	c.605C>G	c.(604-606)gCg>gGg	p.A202G	FGF11_ENST00000575235.1_5'Flank|RP11-104H15.7_ENST00000575310.1_RNA|FGF11_ENST00000293829.4_5'Flank|TMEM102_ENST00000396568.1_Missense_Mutation_p.A202G|RP11-104H15.9_ENST00000570444.1_RNA|RP11-104H15.8_ENST00000576615.1_RNA|RP11-104H15.10_ENST00000575331.1_RNA	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	202					apoptotic process (GO:0006915)|positive regulation of cell adhesion (GO:0045785)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				kidney(1)|lung(3)|skin(1)	5		Prostate(122;0.173)				GAGCACGAGGCGCCGGTGTCT	0.557													C|||	179	0.0357428	0.1286	0.0115	5008	,	,		18254	0.0		0.001	False		,,,				2504	0.0				p.A202G		Atlas-SNP	.											.	TMEM102	11	.	0			c.C605G						PASS	.	C	GLY/ALA	481,3925	224.3+/-240.5	32,417,1754	90.0	92.0	91.0		605	3.2	0.0	17	dbSNP_132	91	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMEM102	NM_178518.2	60	32,419,6052	GG,GC,CC		0.0233,10.9169,3.7137	possibly-damaging	202/509	7339903	483,12523	2203	4300	6503	SO:0001583	missense	284114	exon3			ACGAGGCGCCGGT	AK094197	CCDS11104.1	17p13.1	2008-04-21			ENSG00000181284	ENSG00000181284			26722	protein-coding gene	gene with protein product		613936				12477932	Standard	NM_178518		Approved	FLJ36878	uc002ggx.1	Q8N9M5	OTTHUMG00000132901	ENST00000323206.1:c.605C>G	17.37:g.7339903C>G	ENSP00000315387:p.Ala202Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	131	62	0.473282	NM_178518	D3DTP8	Missense_Mutation	SNP	ENST00000323206.1	37	CCDS11104.1	64	0.029304029304029304	59	0.11991869918699187	5	0.013812154696132596	0	0.0	0	0.0	C	9.073	0.997424	0.19043	0.109169	2.33E-4	ENSG00000181284	ENST00000323206;ENST00000396568	T;T	0.44482	0.92;0.92	5.36	3.25	0.37280	.	1.011090	0.07935	N	0.978275	T	0.00384	0.0012	N	0.14661	0.345	0.09310	N	1	B	0.20887	0.049	B	0.20384	0.029	T	0.05162	-1.0902	10	0.49607	T	0.09	-0.6557	6.9622	0.24603	0.0:0.7316:0.1752:0.0931	.	202	Q8N9M5	TM102_HUMAN	G	202	ENSP00000315387:A202G;ENSP00000379815:A202G	ENSP00000315387:A202G	A	+	2	0	TMEM102	7280627	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.442000	0.06871	1.399000	0.46721	0.655000	0.94253	GCG	C|0.967;G|0.033	0.033	strong		0.557	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518	
MAP3K19	80122	hgsc.bcm.edu	37	2	135745648	135745648	+	Missense_Mutation	SNP	G	G	A	rs113683052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:135745648G>A	ENST00000375845.3	-	7	824	c.794C>T	c.(793-795)cCg>cTg	p.P265L	MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.P282L|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.P152L|MAP3K19_ENST00000392918.3_Intron	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	265							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										TAGGGCTCCCGGAGGCTCGTT	0.448													G|||	44	0.00878594	0.031	0.0043	5008	,	,		19304	0.0		0.0	False		,,,				2504	0.0				p.P265L		Atlas-SNP	.											.	.	.	.	0			c.C794T						PASS	.	G	,LEU/PRO	119,4287	89.7+/-128.4	0,119,2084	78.0	83.0	81.0		,794	1.0	0.0	2	dbSNP_132	81	2,8598	2.2+/-6.3	0,2,4298	yes	intron,missense	YSK4	NM_001018046.1,NM_025052.3	,98	0,121,6382	AA,AG,GG		0.0233,2.7009,0.9303	,benign	,265/1329	135745648	121,12885	2203	4300	6503	SO:0001583	missense	80122	exon7			GCTCCCGGAGGCT	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.794C>T	2.37:g.135745648G>A	ENSP00000365005:p.Pro265Leu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	2.128	-0.399907	0.04865	0.027009	2.33E-4	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915	T;T;T	0.69306	-0.39;-0.39;1.98	4.72	1.02	0.19986	.	0.637582	0.12907	N	0.429241	T	0.22205	0.0535	N	0.22421	0.69	0.09310	N	0.999997	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.19386	-1.0307	10	0.52906	T	0.07	.	2.7976	0.05405	0.1402:0.0796:0.1588:0.6214	.	152;282;265	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	L	265;152;282	ENSP00000365005:P265L;ENSP00000351140:P152L;ENSP00000376647:P282L	ENSP00000351140:P152L	P	-	2	0	YSK4	135462118	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	-0.057000	0.11768	0.020000	0.15106	-0.271000	0.10264	CCG	G|0.989;A|0.011	0.011	strong		0.448	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
CLDND2	125875	hgsc.bcm.edu	37	19	51870771	51870771	+	Missense_Mutation	SNP	C	C	A	rs61737052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51870771C>A	ENST00000291715.1	-	3	795	c.370G>T	c.(370-372)Gtc>Ttc	p.V124F	CLDND2_ENST00000601435.1_Missense_Mutation_p.V124F|CTD-2616J11.11_ENST00000600067.1_Intron|CTD-2616J11.10_ENST00000595500.1_RNA|ETFB_ENST00000309244.4_5'Flank	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	124						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GAGAAGAAGACGTTGTTCTTC	0.582													C|||	269	0.0537141	0.1906	0.0245	5008	,	,		14710	0.0		0.0	False		,,,				2504	0.0				p.V124F		Atlas-SNP	.											.	CLDND2	11	.	0			c.G370T						PASS	.	C	PHE/VAL	698,3708	280.2+/-275.2	57,584,1562	72.0	73.0	73.0		370	1.1	0.3	19	dbSNP_129	73	11,8589	7.1+/-27.0	0,11,4289	yes	missense	CLDND2	NM_152353.2	50	57,595,5851	AA,AC,CC		0.1279,15.842,5.4513	possibly-damaging	124/168	51870771	709,12297	2203	4300	6503	SO:0001583	missense	125875	exon3			AGAAGACGTTGTT	BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.370G>T	19.37:g.51870771C>A	ENSP00000291715:p.Val124Phe	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	192	101	0.526042	NM_152353		Missense_Mutation	SNP	ENST00000291715.1	37	CCDS12829.1	86	0.039377289377289376	74	0.15040650406504066	12	0.03314917127071823	0	0.0	0	0.0	C	17.60	3.430878	0.62844	0.15842	0.001279	ENSG00000160318	ENST00000291715	D	0.88586	-2.4	4.63	1.11	0.20524	.	0.377447	0.18697	N	0.133682	T	0.01835	0.0058	M	0.67953	2.075	0.80722	P	0.0	P	0.50272	0.933	P	0.48982	0.597	T	0.58081	-0.7699	9	0.10636	T	0.68	-10.6815	5.0991	0.14749	0.0:0.6298:0.17:0.2002	.	124	Q8NHS1	CLDN2_HUMAN	F	124	ENSP00000291715:V124F	ENSP00000291715:V124F	V	-	1	0	CLDND2	56562583	0.348000	0.24861	0.346000	0.25655	0.864000	0.49448	0.320000	0.19540	0.362000	0.24319	0.491000	0.48974	GTC	C|0.949;A|0.051	0.051	strong		0.582	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353	
OR51L1	119682	hgsc.bcm.edu	37	11	5020542	5020542	+	Silent	SNP	A	A	T	rs368384016		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5020542A>T	ENST00000321543.1	+	1	330	c.330A>T	c.(328-330)acA>acT	p.T110T		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACACATTCACATTCCTGGAGT	0.502																																					p.T110T		Atlas-SNP	.											.	OR51L1	60	.	0			c.A330T						PASS	.	A		6,4396	11.4+/-27.6	0,6,2195	296.0	222.0	247.0		330	-0.0	1.0	11		247	0,8596		0,0,4298	no	coding-synonymous	OR51L1	NM_001004755.1		0,6,6493	TT,TA,AA		0.0,0.1363,0.0462		110/316	5020542	6,12992	2201	4298	6499	SO:0001819	synonymous_variant	119682	exon1			ATTCACATTCCTG	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"""GPCR / Class A : Olfactory receptors"""	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.330A>T	11.37:g.5020542A>T		Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	423	203	0.479905	NM_001004755	Q6IFE5	Silent	SNP	ENST00000321543.1	37	CCDS31369.1																																																																																			.	.	weak		0.502	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755	
INCENP	3619	hgsc.bcm.edu	37	11	61897542	61897542	+	Silent	SNP	G	G	A	rs145875137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61897542G>A	ENST00000394818.3	+	4	745	c.543G>A	c.(541-543)caG>caA	p.Q181Q	INCENP_ENST00000278849.4_Silent_p.Q181Q	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	181					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						ATGCTGAGCAGCATGTCACCC	0.617													G|||	13	0.00259585	0.0098	0.0	5008	,	,		16459	0.0		0.0	False		,,,				2504	0.0				p.Q181Q		Atlas-SNP	.											.	INCENP	122	.	0			c.G543A						PASS	.	G	,	50,4354	50.9+/-86.3	0,50,2152	65.0	56.0	59.0		543,543	1.8	0.0	11	dbSNP_134	59	1,8597		0,1,4298	no	coding-synonymous,coding-synonymous	INCENP	NM_001040694.1,NM_020238.2	,	0,51,6450	AA,AG,GG		0.0116,1.1353,0.3922	,	181/919,181/915	61897542	51,12951	2202	4299	6501	SO:0001819	synonymous_variant	3619	exon4			TGAGCAGCATGTC	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.543G>A	11.37:g.61897542G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_001040694	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	37	CCDS44624.1																																																																																			G|0.996;A|0.004	0.004	strong		0.617	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
PABPC1	26986	hgsc.bcm.edu	37	8	101718965	101718965	+	Missense_Mutation	SNP	G	G	A	rs62513921		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101718965G>A	ENST00000318607.5	-	11	2644	c.1516C>T	c.(1516-1518)Cgc>Tgc	p.R506C	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519004.1_Missense_Mutation_p.R461C|PABPC1_ENST00000522387.1_Missense_Mutation_p.R474C|PABPC1_ENST00000519596.1_Intron	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	506					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			GGAACGGTGCGGACAGCAGGA	0.438																																					p.R506C		Atlas-SNP	.											PABPC1,NS,carcinoma,+2,2	PABPC1	76	2	0			c.C1516T						PASS	.						62.0	58.0	59.0					8																	101718965		2203	4300	6503	SO:0001583	missense	26986	exon11			CGGTGCGGACAGC	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.1516C>T	8.37:g.101718965G>A	ENSP00000313007:p.Arg506Cys	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	221	74	0.334842	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.966636	0.53507	.	.	ENSG00000070756	ENST00000318607;ENST00000519004;ENST00000522387;ENST00000517990;ENST00000522658	T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89	5.4	4.52	0.55395	Polyadenylate-binding protein/Hyperplastic disc protein (1);	0.087768	0.45606	D	0.000353	T	0.50820	0.1638	M	0.68952	2.095	0.80722	D	1	P;B;D	0.55172	0.928;0.016;0.97	P;B;P	0.52856	0.711;0.017;0.62	T	0.54214	-0.8327	10	0.62326	D	0.03	.	9.4895	0.38951	0.0721:0.0:0.7865:0.1414	rs62513921	474;506;506	E7ERJ7;B3KT93;P11940	.;.;PABP1_HUMAN	C	506;461;474;15;53	ENSP00000313007:R506C;ENSP00000429594:R461C;ENSP00000429395:R474C;ENSP00000428030:R15C;ENSP00000428840:R53C	ENSP00000313007:R506C	R	-	1	0	PABPC1	101788141	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.013000	0.70776	1.427000	0.47276	-0.150000	0.13652	CGC	.	.	weak		0.438	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
SNTB2	6645	hgsc.bcm.edu	37	16	69221510	69221510	+	Silent	SNP	C	C	G	rs10650	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	21	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	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		
EPB41L3	23136	hgsc.bcm.edu	37	18	5416221	5416221	+	Missense_Mutation	SNP	C	C	T	rs9966357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:5416221C>T	ENST00000341928.2	-	13	2003	c.1663G>A	c.(1663-1665)Gcc>Acc	p.A555T	EPB41L3_ENST00000542652.2_Intron|EPB41L3_ENST00000400111.3_Intron|EPB41L3_ENST00000540638.2_Intron|EPB41L3_ENST00000544123.1_Intron|EPB41L3_ENST00000427684.2_Intron|EPB41L3_ENST00000542146.1_Intron|EPB41L3_ENST00000342933.3_Missense_Mutation_p.A555T	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	555	Spectrin--actin-binding. {ECO:0000255}.		A -> T (in dbSNP:rs9966357).		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						GAGTCCAAGGCGGGCTCTCCA	0.572													c|||	252	0.0503195	0.121	0.0187	5008	,	,		17646	0.0		0.0268	False		,,,				2504	0.0532				p.A555T		Atlas-SNP	.											.	EPB41L3	222	.	0			c.G1663A						PASS	.	T	THR/ALA	470,3936	220.7+/-238.1	25,420,1758	82.0	84.0	84.0		1663	-11.1	0.0	18	dbSNP_119	84	269,8331	103.3+/-164.5	7,255,4038	yes	missense	EPB41L3	NM_012307.2	58	32,675,5796	TT,TC,CC		3.1279,10.6673,5.682	benign	555/1088	5416221	739,12267	2203	4300	6503	SO:0001583	missense	23136	exon13			CCAAGGCGGGCTC	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.1663G>A	18.37:g.5416221C>T	ENSP00000343158:p.Ala555Thr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	167	87	0.520958	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	101	0.04624542124542125	72	0.14634146341463414	7	0.019337016574585635	0	0.0	22	0.029023746701846966	c	0.008	-1.930120	0.00488	0.106673	0.031279	ENSG00000082397	ENST00000341928;ENST00000342933	T;T	0.80393	-1.37;-1.37	5.55	-11.1	0.00147	.	.	.	.	.	T	0.00384	0.0012	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.04268	-1.0964	8	0.13470	T	0.59	.	6.6903	0.23167	0.3941:0.1901:0.0:0.4158	rs9966357;rs52812768;rs9966357	555	Q9Y2J2	E41L3_HUMAN	T	555	ENSP00000343158:A555T;ENSP00000341138:A555T	ENSP00000343158:A555T	A	-	1	0	EPB41L3	5406221	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.647000	0.00860	-4.798000	0.00031	-3.942000	0.00015	GCC	C|0.945;T|0.055	0.055	strong		0.572	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
MS4A6A	64231	hgsc.bcm.edu	37	11	59943082	59943082	+	Silent	SNP	C	C	T	rs138028890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59943082C>T	ENST00000530839.1	-	6	834	c.342G>A	c.(340-342)gtG>gtA	p.V114V	MS4A6A_ENST00000412309.2_Silent_p.V142V|MS4A6A_ENST00000323961.3_Silent_p.V114V|MS4A6A_ENST00000528851.1_Silent_p.V114V|MS4A6A_ENST00000426738.2_Silent_p.V69V|MS4A6A_ENST00000533023.1_Silent_p.V50V|MS4A6A_ENST00000529054.1_Silent_p.V142V|MS4A6A_ENST00000529906.1_5'Flank|MS4A6A_ENST00000420732.2_Silent_p.V114V	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	114						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGCTGCTATGCACCTGAAAGA	0.448													C|||	9	0.00179712	0.0068	0.0	5008	,	,		21254	0.0		0.0	False		,,,				2504	0.0				p.V142V		Atlas-SNP	.											.	MS4A6A	85	.	0			c.G426A						PASS	.	C	,,	26,4376	31.7+/-61.6	0,26,2175	95.0	84.0	88.0		342,342,342	-5.1	0.0	11	dbSNP_134	88	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	MS4A6A	NM_022349.2,NM_152851.1,NM_152852.1	,,	0,26,6470	TT,TC,CC		0.0,0.5906,0.2001	,,	114/226,114/179,114/249	59943082	26,12966	2201	4295	6496	SO:0001819	synonymous_variant	64231	exon6			GCTATGCACCTGA	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.342G>A	11.37:g.59943082C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	110	64	0.581818	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Silent	SNP	ENST00000530839.1	37	CCDS7981.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	1.565	-0.535705	0.04082	0.005906	0.0	ENSG00000110077	ENST00000533989	.	.	.	4.99	-5.13	0.02884	.	.	.	.	.	T	0.11196	0.0273	.	.	.	0.18873	N	0.999984	.	.	.	.	.	.	T	0.25187	-1.0139	4	.	.	.	.	0.3632	0.00367	0.2373:0.2707:0.2458:0.2462	.	.	.	.	Y	49	.	.	C	-	2	0	MS4A6A	59699658	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.770000	0.01791	-0.810000	0.04375	-0.976000	0.02587	TGC	C|0.997;T|0.003	0.003	strong		0.448	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		
SH3BP1	23616	hgsc.bcm.edu	37	22	38035851	38035851	+	Silent	SNP	A	A	G	rs13055139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38035851A>G	ENST00000357436.4	+	1	370	c.57A>G	c.(55-57)ggA>ggG	p.G19G	SH3BP1_ENST00000442465.2_Silent_p.G19G|Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000336738.5_Silent_p.G19G|SH3BP1_ENST00000599616.1_5'Flank	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	19	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)					GCAGCTTGGGACGGTGAGTGT	0.701													A|||	1094	0.21845	0.382	0.1412	5008	,	,		8162	0.2252		0.0775	False		,,,				2504	0.1902				p.G19G		Atlas-SNP	.											.	SH3BP1	41	.	0			c.A57G						PASS	.	A		998,3196		114,770,1213	6.0	8.0	7.0		57	2.9	1.0	22	dbSNP_121	7	578,7788		18,542,3623	no	coding-synonymous	SH3BP1	NM_018957.3		132,1312,4836	GG,GA,AA		6.9089,23.7959,12.5478		19/702	38035851	1576,10984	2097	4183	6280	SO:0001819	synonymous_variant	23616	exon1			CTTGGGACGGTGA		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.57A>G	22.37:g.38035851A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	109	42	0.385321	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			A|0.816;G|0.184	0.184	strong		0.701	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
SLX4	84464	hgsc.bcm.edu	37	16	3656625	3656625	+	Missense_Mutation	SNP	G	G	A	rs79842542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3656625G>A	ENST00000294008.3	-	3	1250	c.610C>T	c.(610-612)Cgc>Tgc	p.R204C		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	204	Interaction with SLX4IP, ERCC4 and MSH2.		R -> C (in dbSNP:rs79842542). {ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TGTGCTGTGCGGGGTTTGGAG	0.557								Direct reversal of damage					G|||	299	0.0597045	0.0688	0.0735	5008	,	,		19452	0.0506		0.0646	False		,,,				2504	0.0419				p.R204C		Atlas-SNP	.											SLX4,NS,carcinoma,+1,2	SLX4	173	2	0			c.C610T						scavenged	.	G	CYS/ARG	343,4051	177.6+/-206.5	9,325,1863	178.0	179.0	179.0		610	3.1	0.9	16	dbSNP_131	179	583,8017	156.6+/-210.4	15,553,3732	yes	missense	SLX4	NM_032444.2	180	24,878,5595	AA,AG,GG		6.7791,7.8061,7.1264	probably-damaging	204/1835	3656625	926,12068	2197	4300	6497	SO:0001583	missense	84464	exon3			CTGTGCGGGGTTT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.610C>T	16.37:g.3656625G>A	ENSP00000294008:p.Arg204Cys	Somatic	261	2	0.00766284		WXS	Illumina HiSeq	Phase_I	255	146	0.572549	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	133	0.060897435897435896	35	0.07113821138211382	26	0.0718232044198895	24	0.04195804195804196	48	0.0633245382585752	G	19.50	3.839913	0.71488	0.078061	0.067791	ENSG00000188827	ENST00000294008	T	0.05139	3.49	5.16	3.11	0.35812	.	0.085562	0.45606	D	0.000360	T	0.00936	0.0031	L	0.55990	1.75	0.46336	D	0.99899	D	0.89917	1.0	D	0.91635	0.999	T	0.00042	-1.2227	10	0.87932	D	0	.	12.8945	0.58091	0.0:0.0:0.6944:0.3056	.	204	Q8IY92	SLX4_HUMAN	C	204	ENSP00000294008:R204C	ENSP00000294008:R204C	R	-	1	0	SLX4	3596626	0.990000	0.36364	0.943000	0.38184	0.776000	0.43924	2.460000	0.45031	0.620000	0.30215	0.655000	0.94253	CGC	G|0.937;A|0.063	0.063	strong		0.557	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
C17orf97	400566	hgsc.bcm.edu	37	17	263645	263645	+	Silent	SNP	C	C	T	rs71369083|rs71145728		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:263645C>T	ENST00000360127.6	+	2	1027	c.1011C>T	c.(1009-1011)ccC>ccT	p.P337P	C17orf97_ENST00000571106.1_Intron|AC108004.3_ENST00000466740.2_RNA	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	367	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.									breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						GCTTCCACCCCGACCCCGAGG	0.692																																					p.P337P		Atlas-SNP	.											C17orf97_ENST00000360127,NS,carcinoma,+2,2	C17orf97	76	2	0			c.C1011T						scavenged	.																																			SO:0001819	synonymous_variant	400566	exon2			CCACCCCGACCCC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.1011C>T	17.37:g.263645C>T		Somatic	322	8	0.0248447		WXS	Illumina HiSeq	Phase_I	321	14	0.0436137	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Silent	SNP	ENST00000360127.6	37	CCDS32519.2																																																																																			C|0.981;T|0.019	0.019	strong		0.692	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79083120	79083120	+	Missense_Mutation	SNP	G	G	A	rs2127898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:79083120G>A	ENST00000388820.4	-	6	1130	c.920C>T	c.(919-921)aCg>aTg	p.T307M	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	307	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.		T -> M (in dbSNP:rs2127898). {ECO:0000269|PubMed:15489334}.		cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						TGCATGGTGCGTGATCTTTAG	0.562																																					p.T307M		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C920T						PASS	.	G	MET/THR	1260,3132	429.5+/-342.2	178,904,1114	180.0	139.0	153.0		920	2.8	1.0	15	dbSNP_96	153	2248,6338	378.4+/-338.9	317,1614,2362	no	missense	ADAMTS7	NM_014272.3	81	495,2518,3476	AA,AG,GG		26.1822,28.6885,27.0304	probably-damaging	307/1687	79083120	3508,9470	2196	4293	6489	SO:0001583	missense	11173	exon6			TGGTGCGTGATCT	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.920C>T	15.37:g.79083120G>A	ENSP00000373472:p.Thr307Met	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	135	35	0.259259	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	547	0.25045787545787546	102	0.2073170731707317	107	0.2955801104972376	163	0.28496503496503495	175	0.23087071240105542	G	16.30	3.084407	0.55861	0.286885	0.261822	ENSG00000136378	ENST00000388820;ENST00000456326	D	0.88277	-2.36	4.86	2.85	0.33270	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.129475	0.49916	D	0.000122	T	0.00039	0.0001	M	0.83483	2.645	0.26834	P	0.9685151	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.73380	0.98;0.969;0.976	T	0.00001	-1.2722	9	0.72032	D	0.01	.	7.9579	0.30053	0.092:0.1618:0.7462:0.0	rs2127898;rs17857516	307;307;307	E7EP58;A8MQ00;Q9UKP4	.;.;ATS7_HUMAN	M	307	ENSP00000373472:T307M	ENSP00000373472:T307M	T	-	2	0	ADAMTS7	76870175	1.000000	0.71417	0.964000	0.40570	0.877000	0.50540	4.633000	0.61318	1.060000	0.40578	-0.643000	0.03959	ACG	G|0.438;A|0.562	0.562	strong		0.562	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
CST7	8530	hgsc.bcm.edu	37	20	24939590	24939590	+	Silent	SNP	G	G	C	rs1056033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:24939590G>C	ENST00000480798.1	+	3	546	c.270G>C	c.(268-270)ctG>ctC	p.L90L	CST7_ENST00000376835.2_Silent_p.L112L	NM_003650.3	NP_003641.3	O76096	CYTF_HUMAN	cystatin F (leukocystatin)	90					immune response (GO:0006955)|negative regulation of endopeptidase activity (GO:0010951)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)			large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	5						AATATATGCTGGAGGTGGAAA	0.537													C|||	2963	0.591653	0.3374	0.6354	5008	,	,		19073	0.9325		0.5229	False		,,,				2504	0.6237				p.L90L		Atlas-SNP	.											.	CST7	14	.	0			c.G270C						PASS	.	C		1509,2897	675.3+/-403.1	264,981,958	117.0	109.0	112.0		270	-10.8	0.0	20	dbSNP_86	112	4243,4357	582.3+/-391.4	1043,2157,1100	no	coding-synonymous	CST7	NM_003650.3		1307,3138,2058	CC,CG,GG		49.3372,34.2488,44.2257		90/146	24939590	5752,7254	2203	4300	6503	SO:0001819	synonymous_variant	8530	exon3			TATGCTGGAGGTG	AF036342	CCDS13165.1, CCDS13165.2	20p11.21	2008-04-15			ENSG00000077984	ENSG00000077984			2479	protein-coding gene	gene with protein product		603253				9733783, 9632704	Standard	NM_003650		Approved		uc002wtx.2	O76096	OTTHUMG00000032108	ENST00000480798.1:c.270G>C	20.37:g.24939590G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_003650	Q6FH95|Q7Z4J8|Q9UED4	Silent	SNP	ENST00000480798.1	37	CCDS13165.2																																																																																			G|0.504;C|0.496	0.496	strong		0.537	CST7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078381.2	NM_003650	
CNRIP1	25927	hgsc.bcm.edu	37	2	68546449	68546449	+	Silent	SNP	G	G	A	rs13025842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:68546449G>A	ENST00000263655.3	-	1	689	c.84C>T	c.(82-84)gaC>gaT	p.D28D	CNRIP1_ENST00000481714.1_5'UTR|CNRIP1_ENST00000409559.3_Silent_p.D28D|CNRIP1_ENST00000409862.1_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	86	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	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	
RNH1	6050	hgsc.bcm.edu	37	11	499120	499120	+	Missense_Mutation	SNP	G	G	A	rs17585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:499120G>A	ENST00000534797.1	-	4	1916	c.509C>T	c.(508-510)cCg>cTg	p.P170L	RNH1_ENST00000533592.1_5'Flank|RNH1_ENST00000397614.1_Missense_Mutation_p.P170L|RNH1_ENST00000438658.2_Missense_Mutation_p.P170L|RNH1_ENST00000354420.2_Missense_Mutation_p.P170L|RNH1_ENST00000397615.2_Missense_Mutation_p.P170L|RNH1_ENST00000533410.1_Missense_Mutation_p.P170L|RNH1_ENST00000356187.5_Missense_Mutation_p.P170L|RNH1_ENST00000397604.3_Missense_Mutation_p.P170L			O60930	RNH1_HUMAN	ribonuclease/angiogenin inhibitor 1	0	RNase H. {ECO:0000255|PROSITE- ProRule:PRU00408}.				mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10		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;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTTGAAGTCCGGCTTGGCCCT	0.642													G|||	437	0.0872604	0.0756	0.0879	5008	,	,		15651	0.003		0.1352	False		,,,				2504	0.1401				p.P170L		Atlas-SNP	.											.	RNH1	24	.	0			c.C509T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	403,4003	194.3+/-219.2	14,375,1814	63.0	50.0	55.0		509,509,509,509,509,509,509,509	-2.6	0.0	11	dbSNP_63	55	1171,7429	236.1+/-268.4	90,991,3219	yes	missense,missense,missense,missense,missense,missense,missense,missense	RNH1	NM_002939.3,NM_203383.1,NM_203384.1,NM_203385.1,NM_203386.1,NM_203387.1,NM_203388.1,NM_203389.1	98,98,98,98,98,98,98,98	104,1366,5033	AA,AG,GG		13.6163,9.1466,12.1021	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	170/462,170/462,170/462,170/462,170/462,170/462,170/462,170/462	499120	1574,11432	2203	4300	6503	SO:0001583	missense	6050	exon5			AAGTCCGGCTTGG		CCDS7697.1	11p15.5	2008-02-05	2005-06-01	2005-06-01	ENSG00000023191	ENSG00000023191			10074	protein-coding gene	gene with protein product		173320	"""ribonuclease/angiogenin inhibitor"""	RNH			Standard	NM_203386		Approved	RAI	uc001lpo.1	P13489	OTTHUMG00000119086	ENST00000534797.1:c.509C>T	11.37:g.499120G>A	ENSP00000433999:p.Pro170Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_203384	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Missense_Mutation	SNP	ENST00000534797.1	37	CCDS7697.1	193	0.08836996336996338	49	0.09959349593495935	44	0.12154696132596685	3	0.005244755244755245	97	0.1279683377308707	G	15.28	2.788088	0.49997	0.091466	0.136163	ENSG00000023191	ENST00000534797;ENST00000397614;ENST00000397615;ENST00000397604;ENST00000533410;ENST00000438658;ENST00000354420;ENST00000356187;ENST00000527485;ENST00000529368;ENST00000529306	T;T;T;T;T;T;T;T;T;T;T	0.54866	1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;0.55	3.7	-2.59	0.06209	.	2.250640	0.02604	N	0.101387	T	0.00412	0.0013	M	0.61703	1.905	0.80722	P	0.0	B	0.15930	0.015	B	0.06405	0.002	T	0.11966	-1.0566	9	0.51188	T	0.08	.	1.3186	0.02112	0.176:0.2885:0.3163:0.2191	rs17585;rs17155880;rs17585	170	P13489	RINI_HUMAN	L	170	ENSP00000433999:P170L;ENSP00000380738:P170L;ENSP00000380739:P170L;ENSP00000380729:P170L;ENSP00000435594:P170L;ENSP00000416589:P170L;ENSP00000346402:P170L;ENSP00000348515:P170L;ENSP00000435748:P170L;ENSP00000435057:P170L;ENSP00000434947:P170L	ENSP00000346402:P170L	P	-	2	0	RNH1	489120	0.000000	0.05858	0.000000	0.03702	0.993000	0.82548	-0.054000	0.11826	-0.238000	0.09724	0.478000	0.44815	CCG	G|0.891;A|0.109	0.109	strong		0.642	RNH1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384301.1	NM_203389	
PDPN	10630	hgsc.bcm.edu	37	1	13910417	13910417	+	Silent	SNP	C	C	T	rs355025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:13910417C>T	ENST00000294489.6	+	1	458	c.117C>T	c.(115-117)ccC>ccT	p.P39P	PDPN_ENST00000376061.4_5'Flank|PDPN_ENST00000475043.1_5'Flank|PDPN_ENST00000513143.1_5'Flank|PDPN_ENST00000376057.4_Silent_p.P39P|PDPN_ENST00000487038.1_5'Flank|PDPN_ENST00000509009.1_5'Flank					podoplanin											endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(185;0.249)	all_lung(284;2.29e-05)|Lung NSC(185;4.37e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00969)|Colorectal(212;4.48e-06)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000347)|Kidney(185;0.00087)|KIRC - Kidney renal clear cell carcinoma(229;0.0027)|STAD - Stomach adenocarcinoma(313;0.00802)|READ - Rectum adenocarcinoma(331;0.0678)		CTCCGGCCCCCCCACCGTCGC	0.642													c|||	2820	0.563099	0.6293	0.4798	5008	,	,		11983	0.6577		0.329	False		,,,				2504	0.6759				p.P39P		Atlas-SNP	.											PDPN,NS,carcinoma,0,1	PDPN	44	1	0			c.C117T						PASS	.	C	,	2451,1947		691,1069,439	18.0	21.0	20.0		117,117	1.4	0.0	1	dbSNP_79	20	2817,5771		465,1887,1942	no	coding-synonymous,coding-synonymous	PDPN	NM_006474.4,NM_198389.2	,	1156,2956,2381	TT,TC,CC		32.8016,44.2701,40.5668	,	39/239,39/237	13910417	5268,7718	2199	4294	6493	SO:0001819	synonymous_variant	10630	exon1			GGCCCCCCCACCG	AB127958, AY194238	CCDS30602.1, CCDS41266.1, CCDS44060.1, CCDS53270.1	1p36.21	2008-02-05			ENSG00000162493	ENSG00000162493			29602	protein-coding gene	gene with protein product	"""lung type I cell membrane associated glycoprotein"""	608863				10393083, 9651190	Standard	NM_006474		Approved	T1A-2, Gp38, aggrus, GP40, PA2.26	uc001avd.3	Q86YL7	OTTHUMG00000007912	ENST00000294489.6:c.117C>T	1.37:g.13910417C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_006474		Silent	SNP	ENST00000294489.6	37	CCDS30602.1																																																																																			C|0.526;T|0.474	0.474	strong		0.642	PDPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021783.2	NM_006474	
NOS1AP	9722	hgsc.bcm.edu	37	1	162335256	162335256	+	Silent	SNP	C	C	T	rs348624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:162335256C>T	ENST00000361897.5	+	9	1404	c.1002C>T	c.(1000-1002)cgC>cgT	p.R334R	NOS1AP_ENST00000530878.1_Silent_p.R329R|RP11-565P22.6_ENST00000431696.1_Silent_p.R20R|NOS1AP_ENST00000493151.1_Silent_p.R39R	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	334					regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			CCCAGGCTCGCGTGCATCAGC	0.592													C|||	1256	0.250799	0.4342	0.2161	5008	,	,		18697	0.123		0.1193	False		,,,				2504	0.2945				p.R334R		Atlas-SNP	.											.	NOS1AP	139	.	0			c.C1002T						PASS	.	C	,,	1761,2645	521.9+/-370.6	339,1083,781	69.0	63.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	117,987,1002	-7.3	0.9	1	dbSNP_79	65	1031,7569	219.4+/-257.5	60,911,3329	no	coding-synonymous,coding-synonymous,coding-synonymous	NOS1AP	NM_001126060.1,NM_001164757.1,NM_014697.2	,,	399,1994,4110	TT,TC,CC		11.9884,39.9682,21.467	,,	39/212,329/502,334/507	162335256	2792,10214	2203	4300	6503	SO:0001819	synonymous_variant	9722	exon9			GGCTCGCGTGCAT	AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"""C-terminal PDZ domain ligand of neuronal nitric oxide synthase"""	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.1002C>T	1.37:g.162335256C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_014697	B7ZLF5|O43564|Q3T551|Q5VU95	Silent	SNP	ENST00000361897.5	37	CCDS1237.1																																																																																			C|0.779;T|0.221	0.221	strong		0.592	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697	
TAAR1	134864	hgsc.bcm.edu	37	6	132967032	132967032	+	Silent	SNP	T	T	G	rs73775159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:132967032T>G	ENST00000275216.1	-	1	110	c.111A>C	c.(109-111)acA>acC	p.T37T		NM_138327.1	NP_612200.1	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	37					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)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)	18	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)|Dextroamphetamine(DB01576)|Methamphetamine(DB01577)|Propylhexedrine(DB06714)	TGCCAACGAGTGTGGTCAGAA	0.383													T|||	59	0.0117812	0.0431	0.0029	5008	,	,		20615	0.0		0.0	False		,,,				2504	0.0				p.T37T		Atlas-SNP	.											.	TAAR1	41	.	0			c.A111C						PASS	.	T		160,4246	108.2+/-146.6	1,158,2044	168.0	165.0	166.0		111	-3.0	0.0	6	dbSNP_130	166	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	TAAR1	NM_138327.1		1,160,6342	GG,GT,TT		0.0233,3.6314,1.2456		37/340	132967032	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	134864	exon1			AACGAGTGTGGTC	AY180374	CCDS5158.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146399	ENSG00000146399		"""GPCR / Class A : Trace amine associated receptors"""	17734	protein-coding gene	gene with protein product		609333	"""trace amine receptor 1"""	TRAR1		11459929, 15718104	Standard	NM_138327		Approved	TAR1, TA1	uc003qdm.1	Q96RJ0	OTTHUMG00000015583	ENST00000275216.1:c.111A>C	6.37:g.132967032T>G		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	272	144	0.529412	NM_138327	Q2M1W5|Q3MIH8|Q5VUQ1	Silent	SNP	ENST00000275216.1	37	CCDS5158.1																																																																																			T|0.989;G|0.011	0.011	strong		0.383	TAAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042259.1	NM_138327	
SLC4A7	9497	hgsc.bcm.edu	37	3	27472936	27472936	+	Missense_Mutation	SNP	C	C	T	rs3755652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:27472936C>T	ENST00000295736.5	-	7	1046	c.976G>A	c.(976-978)Gag>Aag	p.E326K	SLC4A7_ENST00000455077.1_Intron|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000440156.1_Missense_Mutation_p.E322K|SLC4A7_ENST00000446700.1_Missense_Mutation_p.E318K|SLC4A7_ENST00000445684.1_Missense_Mutation_p.E322K|SLC4A7_ENST00000435667.2_Intron|SLC4A7_ENST00000437179.1_Intron|SLC4A7_ENST00000428386.1_Intron|SLC4A7_ENST00000425128.2_Missense_Mutation_p.E318K|SLC4A7_ENST00000454389.1_Missense_Mutation_p.E335K	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	326			E -> K (in dbSNP:rs3755652). {ECO:0000269|PubMed:10347222, ECO:0000269|Ref.4}.		auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CGCTGACTCTCTTGGGAACTT	0.542													c|||	647	0.129193	0.0461	0.1643	5008	,	,		15813	0.0565		0.2266	False		,,,				2504	0.1912				p.E326K		Atlas-SNP	.											.	SLC4A7	119	.	0			c.G976A						PASS	.	C	LYS/GLU	359,4047	184.3+/-211.7	10,339,1854	108.0	113.0	111.0		976	5.1	0.8	3	dbSNP_107	111	2159,6441	369.3+/-335.4	270,1619,2411	yes	missense	SLC4A7	NM_003615.3	56	280,1958,4265	TT,TC,CC		25.1047,8.148,19.3603	benign	326/1215	27472936	2518,10488	2203	4300	6503	SO:0001583	missense	9497	exon7			GACTCTCTTGGGA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.976G>A	3.37:g.27472936C>T	ENSP00000295736:p.Glu326Lys	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	245	124	0.506122	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	276	0.12637362637362637	21	0.042682926829268296	70	0.19337016574585636	19	0.033216783216783216	166	0.21899736147757257	c	4.815	0.151530	0.09185	0.08148	0.251047	ENSG00000033867	ENST00000295736;ENST00000454389;ENST00000440156;ENST00000446700;ENST00000445684;ENST00000425128	T;T;T;T;T;T	0.77489	-1.01;-1.02;-1.1;-1.1;-1.1;0.42	5.98	5.12	0.69794	Bicarbonate transporter, cytoplasmic (1);	0.315954	0.28284	N	0.015915	T	0.00039	0.0001	N	0.11560	0.145	0.38427	P	0.053651000000000004	B;B;B;B;B	0.15141	0.012;0.012;0.012;0.012;0.005	B;B;B;B;B	0.21917	0.037;0.037;0.037;0.037;0.025	T	0.03576	-1.1023	9	0.06757	T	0.87	.	15.793	0.78380	0.0:0.2578:0.7422:0.0	rs3755652;rs17682585;rs56593324;rs57811624;rs3755652	322;318;322;335;326	E9PFN4;E9PGC1;B5M453;E9PDL9;Q9Y6M7	.;.;.;.;S4A7_HUMAN	K	326;335;322;318;322;318	ENSP00000295736:E326K;ENSP00000390394:E335K;ENSP00000414797:E322K;ENSP00000406605:E318K;ENSP00000406804:E322K;ENSP00000401949:E318K	ENSP00000295736:E326K	E	-	1	0	SLC4A7	27447940	0.996000	0.38824	0.793000	0.32043	0.844000	0.47949	2.454000	0.44979	1.560000	0.49568	-0.191000	0.12829	GAG	C|0.843;T|0.157	0.157	strong		0.542	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
LINC00283	100874057	hgsc.bcm.edu	37	13	103398300	103398300	+	RNA	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103398300G>A	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		GATTTGACAAGCTCATTATCC	0.398																																					p.L1583F		Atlas-SNP	.											.	.	.	.	0			c.C4747T						PASS	.						298.0	234.0	254.0					13																	103398300		692	1590	2282			643677	exon4			TGACAAGCTCATT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103398300G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	227	27	0.118943	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				.	.	none		0.398	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
ZNF318	24149	hgsc.bcm.edu	37	6	43307861	43307861	+	Missense_Mutation	SNP	G	G	A	rs10948072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	128	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417102	105417102	+	Silent	SNP	T	T	C	rs2248966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417102T>C	ENST00000333244.5	-	7	4805	c.4686A>G	c.(4684-4686)ccA>ccG	p.P1562P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1562						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)			CAGGGCCCTCTGGGAGTTTCA	0.627													.|||	2785	0.55611	0.6172	0.487	5008	,	,		15082	0.374		0.5984	False		,,,				2504	0.6667				p.P1562P		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A4686G						PASS	.	T		2370,1386		807,756,315	96.0	98.0	97.0		4686	-7.6	0.0	14	dbSNP_100	97	4866,3252		1676,1514,869	no	coding-synonymous	AHNAK2	NM_138420.2		2483,2270,1184	CC,CT,TT		40.0591,36.901,39.0601		1562/5796	105417102	7236,4638	1878	4059	5937	SO:0001819	synonymous_variant	113146	exon7			GCCCTCTGGGAGT	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.4686A>G	14.37:g.105417102T>C		Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	308	302	0.980519	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			T|0.517;C|0.483	0.483	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
RNF122	79845	hgsc.bcm.edu	37	8	33408901	33408901	+	Silent	SNP	C	C	G	rs3735949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:33408901C>G	ENST00000256257.1	-	3	590	c.189G>C	c.(187-189)ctG>ctC	p.L63L		NM_024787.2	NP_079063.2	Q9H9V4	RN122_HUMAN	ring finger protein 122	63						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)		CCTGGTTCCGCAGTTTGCTGG	0.493													N|||	833	0.166334	0.416	0.0706	5008	,	,		21478	0.126		0.0268	False		,,,				2504	0.0818				p.L63L		Atlas-SNP	.											.	RNF122	17	.	0			c.G189C						PASS	.	G		1584,2822	665.8+/-401.6	297,990,916	119.0	105.0	110.0		189	2.0	1.0	8	dbSNP_107	110	327,8273	804.5+/-407.3	5,317,3978	no	coding-synonymous	RNF122	NM_024787.2		302,1307,4894	GG,GC,CC		3.8023,35.951,14.6932		63/156	33408901	1911,11095	2203	4300	6503	SO:0001819	synonymous_variant	79845	exon3			GTTCCGCAGTTTG	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.189G>C	8.37:g.33408901C>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	130	60	0.461538	NM_024787	Q52LK3	Silent	SNP	ENST00000256257.1	37	CCDS6091.1																																																																																			C|0.864;G|0.136	0.136	strong		0.493	RNF122-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376562.1	NM_024787	
ABCB10	23456	hgsc.bcm.edu	37	1	229683264	229683264	+	Silent	SNP	G	G	A	rs3738187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229683264G>A	ENST00000344517.4	-	3	945	c.903C>T	c.(901-903)tcC>tcT	p.S301S	RNA5SP78_ENST00000364622.1_RNA	NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	301	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				TGATGCCTACGGAAGCCTGGG	0.587													A|||	1515	0.302516	0.5696	0.3285	5008	,	,		18047	0.1627		0.2097	False		,,,				2504	0.1626				p.S301S		Atlas-SNP	.											.	ABCB10	71	.	0			c.C903T						PASS	.	A		2318,2088	567.3+/-382.1	594,1130,479	37.0	41.0	40.0		903	-10.7	0.0	1	dbSNP_107	40	1867,6733	726.8+/-406.6	204,1459,2637	no	coding-synonymous	ABCB10	NM_012089.2		798,2589,3116	AA,AG,GG		21.7093,47.3899,32.1775		301/739	229683264	4185,8821	2203	4300	6503	SO:0001819	synonymous_variant	23456	exon3			GCCTACGGAAGCC	U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"""ATP binding cassette transporters / subfamily B"""	41	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family B member 10, mitochondrial"", ""ATP-binding cassette transporter 10"", ""ABC transporter 10 protein"", ""mitochondrial ATP-binding cassette 2"""	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.903C>T	1.37:g.229683264G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_012089	Q13040|Q6P1Q8|Q9H3V0	Silent	SNP	ENST00000344517.4	37	CCDS1580.1																																																																																			G|0.690;A|0.310	0.310	strong		0.587	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089	
ATXN1	6310	hgsc.bcm.edu	37	6	16327909	16327909	+	Missense_Mutation	SNP	A	A	C	rs59310777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:16327909A>C	ENST00000244769.4	-	8	1569	c.633T>G	c.(631-633)caT>caG	p.H211Q	ATXN1_ENST00000436367.1_Missense_Mutation_p.H211Q	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	211	Poly-Gln.			H -> HQ (in Ref. 1; CAA55793). {ECO:0000305}.	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.H209_H211delHQH(1)		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)				gctgctgctgatgctgatgct	0.672													A|||	1334	0.266374	0.2897	0.2161	5008	,	,		12493	0.3879		0.0964	False		,,,				2504	0.32				p.H211Q		Atlas-SNP	.											ATXN1,colon,carcinoma,0,3	ATXN1	117	3	1	Deletion - In frame(1)	prostate(1)	c.T633G						PASS	.						4.0	7.0	6.0					6																	16327909		1575	3495	5070	SO:0001583	missense	6310	exon7			CTGCTGATGCTGA	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.633T>G	6.37:g.16327909A>C	ENSP00000244769:p.His211Gln	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	8	0.126984	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	369	0.16895604395604397	105	0.21341463414634146	59	0.16298342541436464	150	0.26223776223776224	55	0.07255936675461741	A	5.976	0.364085	0.11296	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.50813	0.73;0.73	.	.	.	.	.	.	.	.	T	0.08358	0.0208	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.31223	-0.9951	4	0.15952	T	0.53	.	.	.	.	rs59310777	211	P54253	ATX1_HUMAN	Q	211	ENSP00000244769:H211Q;ENSP00000416360:H211Q	ENSP00000244769:H211Q	H	-	3	2	ATXN1	16435888	0.694000	0.27738	0.023000	0.16930	0.066000	0.16364	1.537000	0.36083	0.000000	0.14550	0.000000	0.15137	CAT	A|0.830;C|0.170	0.170	strong		0.672	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
TRPM1	4308	hgsc.bcm.edu	37	15	31294343	31294343	+	Missense_Mutation	SNP	A	A	T	rs12898290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31294343A>T	ENST00000256552.6	-	28	4707	c.4560T>A	c.(4558-4560)caT>caA	p.H1520Q	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000542188.1_Missense_Mutation_p.H1537Q|TRPM1_ENST00000397795.2_Missense_Mutation_p.H1498Q	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)		ACTGCTCTTTATGCTCAGCTT	0.463													A|||	342	0.0682907	0.0772	0.049	5008	,	,		24142	0.0169		0.0616	False		,,,				2504	0.1299				p.H1537Q		Atlas-SNP	.											.	TRPM1	183	.	0			c.T4611A						PASS	.	A	GLN/HIS	309,3785		15,279,1753	237.0	222.0	227.0		4494	-10.3	0.0	15	dbSNP_121	227	469,7905		11,447,3729	yes	missense	TRPM1	NM_002420.4	24	26,726,5482	TT,TA,AA		5.6007,7.5476,6.24	benign	1498/1604	31294343	778,11690	2047	4187	6234	SO:0001583	missense	4308	exon27			CTCTTTATGCTCA	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.4560T>A	15.37:g.31294343A>T	ENSP00000256552:p.His1520Gln	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	110	0.05036630036630037	35	0.07113821138211382	25	0.06906077348066299	13	0.022727272727272728	37	0.048812664907651716	A	0.008	-1.862085	0.00552	0.075476	0.056007	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.44083	0.95;0.93;0.95	5.17	-10.3	0.00346	.	1.203080	0.06074	N	0.660635	T	0.00724	0.0024	N	0.04880	-0.145	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.16808	-1.0390	10	0.39692	T	0.17	0.2066	1.8655	0.03198	0.328:0.1892:0.3265:0.1564	rs12898290;rs52826303;rs12898290	1492;1498	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	Q	1498;1537;1520;1498	ENSP00000380897:H1498Q;ENSP00000437849:H1537Q;ENSP00000256552:H1520Q	ENSP00000256552:H1520Q	H	-	3	2	TRPM1	29081635	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-4.635000	0.00205	-4.828000	0.00030	-1.789000	0.00628	CAT	A|0.933;T|0.067	0.067	strong		0.463	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
RBM19	9904	hgsc.bcm.edu	37	12	114386639	114386639	+	Splice_Site	SNP	A	A	G	rs7966348|rs17849837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114386639A>G	ENST00000545145.2	-	10	1353	c.1275T>C	c.(1273-1275)taT>taC	p.Y425Y	RBM19_ENST00000392561.3_Splice_Site_p.Y425Y|RBM19_ENST00000261741.5_Splice_Site_p.Y425Y	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	425	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Y425Y(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					CACCCCTACCATATTTGGAGA	0.607													G|||	992	0.198083	0.3457	0.0764	5008	,	,		18272	0.1885		0.1133	False		,,,				2504	0.182				p.Y425Y		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - coding silent(1)	stomach(1)	c.T1275C						PASS	.	G	,,	1441,2965	683.3+/-404.2	253,935,1015	76.0	66.0	69.0		1275,1275,1275	0.8	0.8	12	dbSNP_116	69	887,7713	778.8+/-407.7	38,811,3451	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	291,1746,4466	GG,GA,AA		10.314,32.7054,17.8994	,,	425/961,425/961,425/961	114386639	2328,10678	2203	4300	6503	SO:0001630	splice_region_variant	9904	exon10			CCTACCATATTTG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1276+1T>C	12.37:g.114386639A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	130	82	0.630769	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			A|0.823;G|0.177	0.177	strong		0.607	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	Silent
UBR2	23304	hgsc.bcm.edu	37	6	42571346	42571346	+	Silent	SNP	A	A	T	rs16895863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42571346A>T	ENST00000372899.1	+	5	810	c.552A>T	c.(550-552)tcA>tcT	p.S184S	UBR2_ENST00000372903.2_Silent_p.S184S|UBR2_ENST00000372901.1_Silent_p.S184S	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	184					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TTCATTTATCAGAAGATGTGA	0.328													A|||	1006	0.200879	0.2352	0.183	5008	,	,		18936	0.0893		0.2366	False		,,,				2504	0.2454				p.S184S		Atlas-SNP	.											.	UBR2	134	.	0			c.A552T						PASS	.	A	,	1026,3380	375.4+/-321.6	116,794,1293	66.0	64.0	65.0		552,552	3.1	1.0	6	dbSNP_123	65	1828,6762	326.6+/-317.4	204,1420,2671	no	coding-synonymous,coding-synonymous	UBR2	NM_001184801.1,NM_015255.2	,	320,2214,3964	TT,TA,AA		21.2806,23.2864,21.9606	,	184/440,184/1756	42571346	2854,10142	2203	4295	6498	SO:0001819	synonymous_variant	23304	exon5			TTTATCAGAAGAT	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.552A>T	6.37:g.42571346A>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			A|0.793;T|0.207	0.207	strong		0.328	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
CYP4A22	284541	hgsc.bcm.edu	37	1	47607785	47607785	+	Missense_Mutation	SNP	G	G	A	rs2056900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47607785G>A	ENST00000371891.3	+	4	419	c.388G>A	c.(388-390)Ggc>Agc	p.G130S	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000371890.3_Missense_Mutation_p.G130S|CYP4A22_ENST00000294337.3_Missense_Mutation_p.G130S|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	130			G -> S (in allele CYP4A22*4, allele CYP4A22*10, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs2056900). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTTAGGGTACGGCTTGCTCCT	0.537													G|||	1684	0.336262	0.2073	0.232	5008	,	,		22904	0.5546		0.1928	False		,,,				2504	0.5072				p.G130S	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.G388A						PASS	.	G	SER/GLY	1005,3401	374.2+/-321.1	104,797,1302	100.0	83.0	89.0		388	0.7	0.1	1	dbSNP_94	89	1733,6867	316.6+/-312.8	183,1367,2750	yes	missense	CYP4A22	NM_001010969.2	56	287,2164,4052	AA,AG,GG		20.1512,22.8098,21.0518	probably-damaging	130/520	47607785	2738,10268	2203	4300	6503	SO:0001583	missense	284541	exon4			GGGTACGGCTTGC		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.388G>A	1.37:g.47607785G>A	ENSP00000360958:p.Gly130Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	128	56	0.4375	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	640	0.29304029304029305	98	0.1991869918699187	86	0.23756906077348067	315	0.5506993006993007	141	0.18601583113456466	g	18.98	3.738385	0.69304	0.228098	0.201512	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.72394	-0.65;-0.65;-0.65	1.7	0.679	0.17975	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.87328	2.875	0.22811	P	0.99870156	P;D	0.69078	0.935;0.997	B;P	0.61722	0.38;0.893	T	0.45716	-0.9242	9	0.72032	D	0.01	.	8.2754	0.31868	0.1313:0.0:0.8687:0.0	rs2056900;rs52794745;rs2056900	130;130	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	S	130	ENSP00000360957:G130S;ENSP00000360958:G130S;ENSP00000294337:G130S	ENSP00000294337:G130S	G	+	1	0	CYP4A22	47380372	1.000000	0.71417	0.118000	0.21660	0.682000	0.39822	3.218000	0.51192	0.034000	0.15491	0.195000	0.17529	GGC	G|0.768;A|0.232	0.232	strong		0.537	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
TSPAN2	10100	hgsc.bcm.edu	37	1	115604798	115604798	+	Silent	SNP	C	C	T	rs10776795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:115604798C>T	ENST00000369516.2	-	3	259	c.228G>A	c.(226-228)ggG>ggA	p.G76G	TSPAN2_ENST00000369515.2_Silent_p.G76G|TSPAN2_ENST00000369514.2_Silent_p.G76G	NM_005725.4	NP_005716.2	O60636	TSN2_HUMAN	tetraspanin 2	76					astrocyte development (GO:0014002)|axon development (GO:0061564)|brain development (GO:0007420)|inflammatory response (GO:0006954)|microglia development (GO:0014005)|myelination (GO:0042552)|oligodendrocyte differentiation (GO:0048709)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)				central_nervous_system(1)|large_intestine(4)|lung(3)|pancreas(1)|prostate(1)	10	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		CTCCGCAGCACCCGAAGAACC	0.627													C|||	1603	0.320088	0.3018	0.3343	5008	,	,		12891	0.4921		0.3012	False		,,,				2504	0.1769				p.G76G		Atlas-SNP	.											TSPAN2,NS,carcinoma,0,1	TSPAN2	37	1	0			c.G228A						PASS	.	C		1292,3114		199,894,1110	54.0	47.0	49.0		228	-4.3	1.0	1	dbSNP_120	49	2512,6082		378,1756,2163	no	coding-synonymous	TSPAN2	NM_005725.4		577,2650,3273	TT,TC,CC		29.2297,29.3236,29.2615		76/222	115604798	3804,9196	2203	4297	6500	SO:0001819	synonymous_variant	10100	exon3			GCAGCACCCGAAG	AF054839	CCDS881.1	1p13.1	2013-02-14			ENSG00000134198	ENSG00000134198		"""Tetraspanins"""	20659	protein-coding gene	gene with protein product		613133				9714763, 11739647	Standard	NM_005725		Approved	TSPAN-2, TSN2, FLJ12082	uc001eft.3	O60636	OTTHUMG00000011878	ENST00000369516.2:c.228G>A	1.37:g.115604798C>T		Somatic	323	1	0.00309598		WXS	Illumina HiSeq	Phase_I	315	145	0.460317	NM_005725	D6PTH4|Q5TET2|Q8WU05	Silent	SNP	ENST00000369516.2	37	CCDS881.1																																																																																			C|0.686;T|0.314	0.314	strong		0.627	TSPAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032828.1	NM_005725	
SPDYE4	388333	hgsc.bcm.edu	37	17	8661641	8661641	+	Silent	SNP	C	C	T	rs72848106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8661641C>T	ENST00000328794.6	-	1	236	c.60G>A	c.(58-60)acG>acA	p.T20T		NM_001128076.1	NP_001121548.1	A6NLX3	SPDE4_HUMAN	speedy/RINGO cell cycle regulator family member E4	20										breast(1)|endometrium(2)|kidney(1)	4						GGGACCGTACCGTTGTGCTAG	0.572													C|||	197	0.0393371	0.1203	0.0144	5008	,	,		17944	0.0		0.0219	False		,,,				2504	0.0061				p.T20T		Atlas-SNP	.											SPDYE4,NS,carcinoma,-1,2	SPDYE4	22	2	0			c.G60A						PASS	.	C		105,1279		5,95,592	31.0	33.0	32.0		60	-4.7	0.0	17	dbSNP_130	32	78,3104		0,78,1513	no	coding-synonymous	SPDYE4	NM_001128076.1		5,173,2105	TT,TC,CC		2.4513,7.5867,4.0079		20/238	8661641	183,4383	692	1591	2283	SO:0001819	synonymous_variant	388333	exon1			CCGTACCGTTGTG	BC146949	CCDS45609.1	17p13.1	2013-05-08	2013-05-08			ENSG00000183318		"""Speedy homologs"""	35463	protein-coding gene	gene with protein product			"""speedy homolog E4 (Xenopus laevis)"""				Standard	NM_001128076		Approved		uc010cnz.1	A6NLX3		ENST00000328794.6:c.60G>A	17.37:g.8661641C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_001128076	B2RUZ6	Silent	SNP	ENST00000328794.6	37	CCDS45609.1																																																																																			C|0.967;T|0.033	0.033	strong		0.572	SPDYE4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442494.1	NM_001128076	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48594973	48594973	+	Missense_Mutation	SNP	G	G	A	rs75706684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48594973G>A	ENST00000323776.5	+	4	673	c.511G>A	c.(511-513)Gat>Aat	p.D171N	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.D134N	NM_032133.4	NP_115509.4			MYCBP associated protein									p.D134N(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			TGACAGCTTCGATGGCAGTGA	0.512													G|||	135	0.0269569	0.0961	0.0086	5008	,	,		6764	0.0		0.002	False		,,,				2504	0.0				p.D171N		Atlas-SNP	.											MYCBPAP,NS,NS,0,1	MYCBPAP	135	1	1	Substitution - Missense(1)	pancreas(1)	c.G511A						PASS	.	G	ASN/ASP	371,4035	188.1+/-214.6	26,319,1858	68.0	68.0	68.0		511	-5.3	0.0	17	dbSNP_131	68	5,8595	3.7+/-12.6	0,5,4295	yes	missense	MYCBPAP	NM_032133.4	23	26,324,6153	AA,AG,GG		0.0581,8.4203,2.891	benign	171/985	48594973	376,12630	2203	4300	6503	SO:0001583	missense	84073	exon4			AGCTTCGATGGCA	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.511G>A	17.37:g.48594973G>A	ENSP00000323184:p.Asp171Asn	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	196	100	0.510204	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	47	0.02152014652014652	41	0.08333333333333333	4	0.011049723756906077	0	0.0	2	0.002638522427440633	G	16.50	3.139471	0.56936	0.084203	5.81E-4	ENSG00000136449	ENST00000323776;ENST00000452039;ENST00000436259	T;T	0.26957	1.72;1.7	5.6	-5.28	0.02755	.	1.777540	0.02671	N	0.108617	T	0.00724	0.0024	L	0.27053	0.805	0.09310	N	1	D;D	0.63880	0.993;0.993	P;P	0.46543	0.52;0.52	T	0.23868	-1.0176	10	0.11794	T	0.64	3.2954	0.1959	0.00139	0.2453:0.2206:0.2006:0.3335	.	134;171	Q8TBZ2;B4DZQ1	MYBPP_HUMAN;.	N	171;186;134	ENSP00000323184:D171N;ENSP00000397209:D134N	ENSP00000323184:D171N	D	+	1	0	MYCBPAP	45949972	0.000000	0.05858	0.000000	0.03702	0.636000	0.38137	0.053000	0.14184	-0.811000	0.04369	-0.219000	0.12488	GAT	G|0.970;A|0.030	0.030	strong		0.512	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
PPIG	9360	hgsc.bcm.edu	37	2	170493784	170493784	+	Silent	SNP	T	T	C	rs114584157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170493784T>C	ENST00000260970.3	+	14	2236	c.2016T>C	c.(2014-2016)aaT>aaC	p.N672N	PPIG_ENST00000448752.2_Silent_p.N672N|PPIG_ENST00000409714.3_Silent_p.N657N	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	672					protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	GTGATCATAATAGCTCAAATA	0.353													T|||	8	0.00159744	0.0061	0.0	5008	,	,		19790	0.0		0.0	False		,,,				2504	0.0				p.N672N		Atlas-SNP	.											.	PPIG	100	.	0			c.T2016C						PASS	.	T		42,4364	43.1+/-76.7	1,40,2162	70.0	74.0	73.0		2016	2.2	1.0	2	dbSNP_132	73	0,8600		0,0,4300	no	coding-synonymous	PPIG	NM_004792.2		1,40,6462	CC,CT,TT		0.0,0.9532,0.3229		672/755	170493784	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	9360	exon14			TCATAATAGCTCA	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.2016T>C	2.37:g.170493784T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	123	44	0.357724	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Silent	SNP	ENST00000260970.3	37	CCDS2235.1																																																																																			T|0.997;C|0.003	0.003	strong		0.353	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		
CHRD	8646	hgsc.bcm.edu	37	3	184099050	184099050	+	Missense_Mutation	SNP	C	C	T	rs34095724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184099050C>T	ENST00000204604.1	+	3	526	c.280C>T	c.(280-282)Cct>Tct	p.P94S	EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000545352.1_5'Flank|CHRD_ENST00000450923.1_Missense_Mutation_p.P94S|CHRD_ENST00000348986.3_Missense_Mutation_p.P94S|CHRD_ENST00000482805.1_3'UTR	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	94	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.		P -> S (in dbSNP:rs34095724).		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)			TACCAGGGGCCCTGGCAGGGT	0.657													C|||	195	0.0389377	0.093	0.0173	5008	,	,		14626	0.002		0.0378	False		,,,				2504	0.0204				p.P94S		Atlas-SNP	.											.	CHRD	149	.	0			c.C280T						PASS	.	C	SER/PRO	410,3994		18,374,1810	21.0	26.0	24.0		280	4.3	1.0	3	dbSNP_126	24	292,8302		2,288,4007	yes	missense	CHRD	NM_003741.2	74	20,662,5817	TT,TC,CC		3.3977,9.3097,5.4008	benign	94/956	184099050	702,12296	2202	4297	6499	SO:0001583	missense	8646	exon3			AGGGGCCCTGGCA	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.280C>T	3.37:g.184099050C>T	ENSP00000204604:p.Pro94Ser	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	259	135	0.521236	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	92	0.04212454212454213	53	0.10772357723577236	9	0.024861878453038673	1	0.0017482517482517483	29	0.03825857519788918	C	3.315	-0.140029	0.06669	0.093097	0.033977	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986	T;T;T	0.13307	2.83;2.6;2.61	5.18	4.3	0.51218	von Willebrand factor, type C (3);	0.242099	0.43110	D	0.000610	T	0.00144	0.0004	N	0.12182	0.205	0.80722	D	1	B;B	0.11235	0.0;0.004	B;B	0.15870	0.007;0.014	T	0.49960	-0.8883	10	0.20519	T	0.43	-8.4545	7.7367	0.28819	0.0:0.5773:0.3366:0.0861	rs34095724	94;94	E7ESX1;Q9H2X0	.;CHRD_HUMAN	S	94	ENSP00000204604:P94S;ENSP00000408972:P94S;ENSP00000334036:P94S	ENSP00000204604:P94S	P	+	1	0	CHRD	185581744	0.001000	0.12720	1.000000	0.80357	0.678000	0.39670	0.462000	0.21956	1.169000	0.42739	0.561000	0.74099	CCT	C|0.949;T|0.051	0.051	strong		0.657	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
KRTAP22-2	100288287	hgsc.bcm.edu	37	21	31962649	31962649	+	Silent	SNP	G	G	A	rs78392137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31962649G>A	ENST00000382830.2	-	1	67	c.45C>T	c.(43-45)tgC>tgT	p.C15C	KRTAP6-3_ENST00000391624.1_5'Flank	NM_001164434.1	NP_001157906.1	Q3LI68	KR222_HUMAN	keratin associated protein 22-2	15						intermediate filament (GO:0005882)											AGCCATAGCTGCAACCATAGT	0.423													G|||	55	0.0109824	0.0401	0.0029	5008	,	,		18361	0.0		0.0	False		,,,				2504	0.0				p.C15C		Atlas-SNP	.											.	KRTAP22-2	6	.	0			c.C45T						PASS	.						133.0	118.0	122.0					21																	31962649		692	1591	2283	SO:0001819	synonymous_variant	100288287	exon1			ATAGCTGCAACCA	AB096950	CCDS46641.1	21q22.11	2009-11-23			ENSG00000206106	ENSG00000206106		"""Keratin associated proteins"""	37091	protein-coding gene	gene with protein product							Standard	NM_001164434		Approved	KAP22.2	uc021wih.1	Q3LI68	OTTHUMG00000065630	ENST00000382830.2:c.45C>T	21.37:g.31962649G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	149	79	0.530201	NM_001164434		Silent	SNP	ENST00000382830.2	37	CCDS46641.1																																																																																			G|0.990;A|0.010	0.010	strong		0.423	KRTAP22-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140633.2	XM_002343740	
GGT1	2678	hgsc.bcm.edu	37	22	24984261	24984261	+	Intron	SNP	G	G	A	rs201281973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24984261G>A	ENST00000248923.4	+	1	59				FAM211B_ENST00000318753.8_Nonsense_Mutation_p.R115*|FAM211B_ENST00000495297.1_5'Flank	NM_013430.2	NP_038347.2	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1						arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	ATGAGCTGTCGGCAGATCTTG	0.617													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19843	0.0		0.0	False		,,,				2504	0.0				p.R115X		Atlas-SNP	.											C22orf36,colon,carcinoma,0,1	.	.	1	0			c.C343T						PASS	.	G	,stop/ARG	4,4270		0,4,2133	116.0	128.0	124.0		,343	-0.4	0.0	22		124	0,8470		0,0,4235	yes	intron,stop-gained	GGT1,C22orf36	NM_013430.2,NM_207644.2	,	0,4,6368	AA,AG,GG		0.0,0.0936,0.0314	,	,115/316	24984261	4,12740	2137	4235	6372	SO:0001627	intron_variant	388886	exon3			GCTGTCGGCAGAT	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000248923.4:c.-429+4485G>A	22.37:g.24984261G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	201	106	0.527363	NM_207644	Q08247|Q14404|Q8TBS1|Q9UMK1	Nonsense_Mutation	SNP	ENST00000248923.4	37	CCDS42992.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.90	2.969710	0.53614	9.36E-4	0.0	ENSG00000178026	ENST00000318753	.	.	.	3.5	-0.358	0.12575	.	0.000000	0.64402	U	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.9843	0.09509	0.3955:0.0:0.4411:0.1634	.	.	.	.	X	115	.	ENSP00000320520:R115X	R	-	1	2	C22orf36	23314261	0.993000	0.37304	0.045000	0.18777	0.635000	0.38103	0.761000	0.26489	-0.007000	0.14345	0.462000	0.41574	CGA	G|1.000;A|0.000	0.000	strong		0.617	GGT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319110.1	NM_013430	
NIPAL2	79815	hgsc.bcm.edu	37	8	99205612	99205612	+	Splice_Site	SNP	C	C	T	rs3735887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:99205612C>T	ENST00000341166.3	-	11	1323		c.e11+1		NIPAL2_ENST00000430223.2_Intron|NIPAL2_ENST00000520545.1_Intron|RNU6-914P_ENST00000516749.1_RNA	NM_024759.1	NP_079035.1	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2							integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(3)|kidney(1)|large_intestine(2)|lung(5)|stomach(1)	12						CATTCACTCACCTCCAAGCCT	0.453													T|||	2918	0.582668	0.5461	0.6427	5008	,	,		18555	0.5893		0.5	False		,,,				2504	0.6677				.		Atlas-SNP	.											.	NIPAL2	23	.	0			c.1067+1G>A						PASS	.	T		2289,2117	576.4+/-384.2	595,1099,509	195.0	188.0	191.0			3.7	0.0	8	dbSNP_107	191	4379,4221	572.2+/-389.7	1103,2173,1024	yes	splice-5	NIPAL2	NM_024759.1		1698,3272,1533	TT,TC,CC		49.0814,48.0481,48.7314			99205612	6668,6338	2203	4300	6503	SO:0001630	splice_region_variant	79815	exon12			CACTCACCTCCAA	AK024017	CCDS6278.1	8q22.2	2009-03-24		2009-03-24	ENSG00000104361	ENSG00000104361			25854	protein-coding gene	gene with protein product				NPAL2		14702039	Standard	NM_024759		Approved	FLJ13955	uc003yil.1	Q9H841	OTTHUMG00000164668	ENST00000341166.3:c.1067+1G>A	8.37:g.99205612C>T		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_024759	A2RTY8	Splice_Site	SNP	ENST00000341166.3	37	CCDS6278.1	1225	0.5608974358974359	273	0.5548780487804879	227	0.6270718232044199	341	0.5961538461538461	384	0.5065963060686016	T	10.44	1.351666	0.24512	0.519519	0.509186	ENSG00000104361	ENST00000341166	.	.	.	4.8	3.65	0.41850	.	.	.	.	.	.	.	.	.	.	.	0.44168	P	0.003025999999999973	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7832	0.23659	0.0:0.193:0.0:0.807	rs3735887;rs17286348;rs3735887	.	.	.	.	-1	.	.	.	-	.	.	NIPAL2	99274788	0.017000	0.18338	0.004000	0.12327	0.010000	0.07245	1.145000	0.31577	0.402000	0.25451	-0.360000	0.07572	.	C|0.467;T|0.533	0.533	strong		0.453	NIPAL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379677.1	NM_024759	Intron
NLRP8	126205	hgsc.bcm.edu	37	19	56459614	56459614	+	Missense_Mutation	SNP	G	G	C	rs306506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56459614G>C	ENST00000291971.3	+	1	417	c.346G>C	c.(346-348)Gta>Cta	p.V116L	NLRP8_ENST00000590542.1_Missense_Mutation_p.V116L	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	116	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.		V -> L (in dbSNP:rs306506).		neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AATGTGTGTTGTAGTCCGCAG	0.488													C|||	3640	0.726837	0.7504	0.7579	5008	,	,		16948	0.8135		0.5974	False		,,,				2504	0.7168				p.V116L		Atlas-SNP	.											.	NLRP8	225	.	0			c.G346C						PASS	.	C	LEU/VAL	3214,1192	417.6+/-338.0	1172,870,161	98.0	96.0	97.0		346	1.2	0.0	19	dbSNP_79	97	5021,3579	518.2+/-379.2	1470,2081,749	yes	missense	NLRP8	NM_176811.2	32	2642,2951,910	CC,CG,GG		41.6163,27.054,36.6831	benign	116/1049	56459614	8235,4771	2203	4300	6503	SO:0001583	missense	126205	exon1			TGTGTTGTAGTCC	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.346G>C	19.37:g.56459614G>C	ENSP00000291971:p.Val116Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	1565	0.7165750915750916	364	0.7398373983739838	262	0.7237569060773481	475	0.8304195804195804	464	0.6121372031662269	C	0.027	-1.363830	0.01235	0.72946	0.583837	ENSG00000179709	ENST00000291971	T	0.57436	0.4	2.23	1.19	0.21007	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.20605	-1.0270	8	0.30854	T	0.27	.	3.5601	0.07878	0.0:0.5745:0.2653:0.1602	rs306506;rs17644766;rs52815843;rs60294832;rs306506	116;116	Q86W28-2;Q86W28	.;NALP8_HUMAN	L	116	ENSP00000291971:V116L	ENSP00000291971:V116L	V	+	1	0	NLRP8	61151426	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.463000	0.06696	0.092000	0.17331	-0.281000	0.10026	GTA	G|0.334;C|0.665	0.665	strong		0.488	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
TENM4	26011	hgsc.bcm.edu	37	11	78437182	78437182	+	Silent	SNP	G	G	A	rs689369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:78437182G>A	ENST00000278550.7	-	23	3954	c.3492C>T	c.(3490-3492)gaC>gaT	p.D1164D		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1164					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										GCTTGGACGCGTCAATTTCAT	0.453													A|||	903	0.180312	0.2398	0.2277	5008	,	,		20862	0.1438		0.161	False		,,,				2504	0.1237				p.D1164D		Atlas-SNP	.											.	.	.	.	0			c.C3492T						PASS	.	A		810,3066		100,610,1228	317.0	307.0	310.0		3492	-1.0	1.0	11	dbSNP_83	310	1377,6895		121,1135,2880	yes	coding-synonymous	ODZ4	NM_001098816.2		221,1745,4108	AA,AG,GG		16.6465,20.8978,18.003		1164/2770	78437182	2187,9961	1938	4136	6074	SO:0001819	synonymous_variant	26011	exon23			GGACGCGTCAATT	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.3492C>T	11.37:g.78437182G>A		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	251	123	0.49004	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			G|0.814;A|0.186	0.186	strong		0.453	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
CMPK2	129607	hgsc.bcm.edu	37	2	7003680	7003680	+	Silent	SNP	T	T	C	rs77719173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:7003680T>C	ENST00000256722.5	-	2	704	c.705A>G	c.(703-705)gcA>gcG	p.A235A	CMPK2_ENST00000478738.1_5'UTR|CMPK2_ENST00000404168.1_Silent_p.A235A|CMPK2_ENST00000458098.1_Silent_p.A235A	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	235					cellular response to lipopolysaccharide (GO:0071222)|dTDP biosynthetic process (GO:0006233)|dUDP biosynthetic process (GO:0006227)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)|thymidylate kinase activity (GO:0004798)|UMP kinase activity (GO:0033862)			large_intestine(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGTCAAGCACTGCCCGGGCTT	0.478													C|||	349	0.0696885	0.2549	0.0159	5008	,	,		18590	0.0		0.0	False		,,,				2504	0.001				p.A235A		Atlas-SNP	.											.	CMPK2	30	.	0			c.A705G						PASS	.	C		758,3044		81,596,1224	98.0	98.0	98.0		705	-10.4	0.1	2	dbSNP_131	98	9,8199		0,9,4095	no	coding-synonymous	CMPK2	NM_207315.2		81,605,5319	CC,CT,TT		0.1096,19.9369,6.3863		235/450	7003680	767,11243	1901	4104	6005	SO:0001819	synonymous_variant	129607	exon2			AAGCACTGCCCGG		CCDS42648.1, CCDS58695.1, CCDS58696.1	2p25.2	2008-01-25			ENSG00000134326	ENSG00000134326	2.7.4.14		27015	protein-coding gene	gene with protein product	"""cytidylate kinase 2"""	611787				17999954	Standard	NM_207315		Approved	TYKi, UMP-CMPK2	uc002qyo.4	Q5EBM0	OTTHUMG00000151629	ENST00000256722.5:c.705A>G	2.37:g.7003680T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	141	52	0.368794	NM_001256478	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Silent	SNP	ENST00000256722.5	37	CCDS42648.1																																																																																			T|0.968;C|0.032	0.032	strong		0.478	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315	
ALG1	56052	hgsc.bcm.edu	37	16	5132586	5132586	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5132586C>G	ENST00000262374.5	+	11	1130	c.1099C>G	c.(1099-1101)Cac>Gac	p.H367D	ALG1_ENST00000588623.1_Missense_Mutation_p.H256D|ALG1_ENST00000544428.1_Missense_Mutation_p.H256D	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	367					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)	p.H367Y(1)		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)				TGTCTGTCTGCACACGTCCTC	0.597																																					p.H367D		Atlas-SNP	.											ALG1,NS,carcinoma,0,1	ALG1	35	1	1	Substitution - Missense(1)	breast(1)	c.C1099G						scavenged	.						64.0	52.0	56.0					16																	5132586		2078	3944	6022	SO:0001583	missense	56052	exon11			TGTCTGCACACGT	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.1099C>G	16.37:g.5132586C>G	ENSP00000262374:p.His367Asp	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	110	7	0.0636364	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.820699	0.90873	.	.	ENSG00000033011	ENST00000262374;ENST00000544428	T;T	0.75704	-0.96;-0.96	5.28	5.28	0.74379	Glycosyl transferase, family 1 (1);	0.000000	0.85682	D	0.000000	D	0.90307	0.6968	H	0.97240	3.965	0.80722	D	1	P;P	0.45827	0.603;0.867	P;P	0.58013	0.622;0.831	D	0.93433	0.6787	10	0.87932	D	0	-24.1817	17.5165	0.87775	0.0:1.0:0.0:0.0	.	256;367	B4DP08;Q9BT22	.;ALG1_HUMAN	D	367;256	ENSP00000262374:H367D;ENSP00000440019:H256D	ENSP00000262374:H367D	H	+	1	0	ALG1	5072587	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.492000	0.66893	2.474000	0.83562	0.555000	0.69702	CAC	.	.	none		0.597	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
RAB8A	4218	hgsc.bcm.edu	37	19	16238279	16238279	+	Silent	SNP	C	C	T	rs1043308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16238279C>T	ENST00000300935.3	+	5	630	c.357C>T	c.(355-357)ctC>ctT	p.L119L	CTD-2231E14.8_ENST00000597983.1_RNA|RAB8A_ENST00000586682.1_Silent_p.L119L	NM_005370.4	NP_005361.2	P61006	RAB8A_HUMAN	RAB8A, member RAS oncogene family	119					axonogenesis (GO:0007409)|cellular response to insulin stimulus (GO:0032869)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi vesicle fusion to target membrane (GO:0048210)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein transport (GO:0051223)|small GTPase mediated signal transduction (GO:0007264)|vesicle docking involved in exocytosis (GO:0006904)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|neuronal cell body (GO:0043025)|nonmotile primary cilium (GO:0031513)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)|recycling endosome membrane (GO:0055038)|trans-Golgi network transport vesicle (GO:0030140)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			endometrium(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	8						AGATGATACTCGGGAACAAGT	0.582													C|||	1505	0.300519	0.1831	0.379	5008	,	,		20433	0.2976		0.337	False		,,,				2504	0.3691				p.L119L		Atlas-SNP	.											.	RAB8A	19	.	0			c.C357T						PASS	.	C		962,3444	361.4+/-315.7	114,734,1355	106.0	77.0	87.0		357	-9.6	0.6	19	dbSNP_86	87	2789,5811	440.2+/-359.4	457,1875,1968	no	coding-synonymous	RAB8A	NM_005370.4		571,2609,3323	TT,TC,CC		32.4302,21.8339,28.8405		119/208	16238279	3751,9255	2203	4300	6503	SO:0001819	synonymous_variant	4218	exon5			GATACTCGGGAAC		CCDS12339.1	19p13.2-p13.1	2008-05-14	2004-01-30	2004-01-30		ENSG00000167461		"""RAB, member RAS oncogene"""	7007	protein-coding gene	gene with protein product		165040	"""mel transforming oncogene (derived from cell line NK14)"""	MEL		1886711, 8408203	Standard	NM_005370		Approved	RAB8	uc002ndn.4	P61006		ENST00000300935.3:c.357C>T	19.37:g.16238279C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	141	59	0.41844	NM_005370	B4DEK7|P24407|Q6FHV5	Silent	SNP	ENST00000300935.3	37	CCDS12339.1																																																																																			A|0.000;C|0.710;G|0.000;T|0.290	0.290	strong		0.582	RAB8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460186.1	NM_005370	
TAS1R2	80834	hgsc.bcm.edu	37	1	19166243	19166243	+	Silent	SNP	G	G	A	rs12075191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19166243G>A	ENST00000375371.3	-	6	2391	c.2370C>T	c.(2368-2370)atC>atT	p.I790I		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	790					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)	AGAGGTCCACGATGGTGACCA	0.577													g|||	423	0.0844649	0.0363	0.0231	5008	,	,		20505	0.1141		0.0557	False		,,,				2504	0.1922				p.I790I		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C2370T						PASS	.			196,4210	123.3+/-160.7	5,186,2012	120.0	91.0	101.0		2370	2.2	0.9	1	dbSNP_120	101	397,8203	126.7+/-185.1	14,369,3917	no	coding-synonymous	TAS1R2	NM_152232.2		19,555,5929	AA,AG,GG		4.6163,4.4485,4.5594		790/840	19166243	593,12413	2203	4300	6503	SO:0001819	synonymous_variant	80834	exon6			GTCCACGATGGTG		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.2370C>T	1.37:g.19166243G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	204	108	0.529412	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			G|0.950;A|0.050	0.050	strong		0.577	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
HLA-G	3135	hgsc.bcm.edu	37	6	29796327	29796327	+	Silent	SNP	C	C	T	rs1130356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29796327C>T	ENST00000360323.6	+	3	375	c.351C>T	c.(349-351)caC>caT	p.H117H	HLA-G_ENST00000428701.1_Silent_p.H117H|HLA-G_ENST00000376828.2_Silent_p.H122H|HLA-G_ENST00000376818.3_Intron|HLA-G_ENST00000376815.3_Intron			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	117	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						CAGGTTCTCACACCCTCCAGT	0.662													c|||	1253	0.2502	0.2625	0.2565	5008	,	,		13097	0.1141		0.2763	False		,,,				2504	0.3425				p.H117H		Atlas-SNP	.											.	HLA-G	90	.	0			c.C351T						PASS	.	C		823,2195		112,599,798	68.0	72.0	71.0		351	0.8	0.2	6	dbSNP_86	71	1692,3724		272,1148,1288	no	coding-synonymous	HLA-G	NM_002127.5		384,1747,2086	TT,TC,CC		31.2408,27.2697,29.8198		117/339	29796327	2515,5919	1509	2708	4217	SO:0001819	synonymous_variant	3135	exon4			TTCTCACACCCTC		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.351C>T	6.37:g.29796327C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	134	62	0.462687	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			C|0.734;T|0.266	0.266	strong		0.662	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
RNF186	54546	hgsc.bcm.edu	37	1	20141283	20141283	+	Silent	SNP	C	C	T	rs1541184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:20141283C>T	ENST00000375121.2	-	1	488	c.312G>A	c.(310-312)gcG>gcA	p.A104A	RP11-91K11.2_ENST00000454736.1_RNA	NM_019062.1	NP_061935.1	Q9NXI6	RN186_HUMAN	ring finger protein 186	104						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)		GCCCCACCACCGCCTCATGGT	0.672													C|||	760	0.151757	0.1346	0.268	5008	,	,		17074	0.1776		0.0497	False		,,,				2504	0.1708				p.A104A		Atlas-SNP	.											.	RNF186	14	.	0			c.G312A						PASS	.	C		470,3936	213.1+/-232.8	31,408,1764	40.0	45.0	43.0		312	-9.4	0.0	1	dbSNP_88	43	371,8229	117.0+/-176.6	9,353,3938	no	coding-synonymous	RNF186	NM_019062.1		40,761,5702	TT,TC,CC		4.314,10.6673,6.4662		104/228	20141283	841,12165	2203	4300	6503	SO:0001819	synonymous_variant	54546	exon1			CACCACCGCCTCA		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.312G>A	1.37:g.20141283C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	116	67	0.577586	NM_019062	Q53GE0	Silent	SNP	ENST00000375121.2	37	CCDS199.1																																																																																			C|0.912;T|0.088	0.088	strong		0.672	RNF186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007694.1	NM_019062	
MUC4	4585	hgsc.bcm.edu	37	3	195513439	195513439	+	Missense_Mutation	SNP	G	G	A	rs200271894		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513439G>A	ENST00000463781.3	-	2	5471	c.5012C>T	c.(5011-5013)tCc>tTc	p.S1671F	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1671F	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)		GGATGCTGAGGAAGTGCTGGT	0.597																																					p.S1671F		Atlas-SNP	.											.	MUC4	1505	.	0			c.C5012T						PASS	.						38.0	36.0	37.0					3																	195513439		689	1584	2273	SO:0001583	missense	4585	exon2			GCTGAGGAAGTGC	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.5012C>T	3.37:g.195513439G>A	ENSP00000417498:p.Ser1671Phe	Somatic	518	0	0		WXS	Illumina HiSeq	Phase_I	521	145	0.278311	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	.	.	.	.	.	.	.	.	.	.	-	4.292	0.053463	0.08291	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34472	1.36;1.38	0.595	-0.863	0.10669	.	.	.	.	.	T	0.18551	0.0445	N	0.19112	0.55	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.25363	-1.0134	8	.	.	.	.	5.1757	0.15133	0.2702:0.0:0.7298:0.0	.	1671	E7ESK3	.	F	1671	ENSP00000417498:S1671F;ENSP00000420243:S1671F	.	S	-	2	0	MUC4	196997834	0.019000	0.18553	0.000000	0.03702	0.009000	0.06853	1.583000	0.36579	-0.313000	0.08728	0.089000	0.15464	TCC	.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DDX53	168400	hgsc.bcm.edu	37	X	23019346	23019346	+	Missense_Mutation	SNP	G	G	T	rs5926203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:23019346G>T	ENST00000327968.5	+	1	1260	c.1172G>T	c.(1171-1173)aGg>aTg	p.R391M	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	391	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		R -> M (in dbSNP:rs5926203).			nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						CCCCAGATAAGGAAGATTTTA	0.393													T|||	1286	0.340662	0.4902	0.0793	3775	,	,		15013	0.2073		0.0915	False		,,,				2504	0.2883				p.R391M		Atlas-SNP	.											.	DDX53	76	.	0			c.G1172T						PASS	.	T	MET/ARG	2088,1747		490,813,295,329,276	140.0	140.0	140.0		1172	-2.1	0.0	X	dbSNP_114	140	818,5910		30,511,247,1887,1625	yes	missense	DDX53	NM_182699.3	91	520,1324,542,2216,1901	TT,TG,T,GG,G		12.1581,45.5541,27.5111	benign	391/632	23019346	2906,7657	2203	4300	6503	SO:0001583	missense	168400	exon1			AGATAAGGAAGAT	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"""DEAD-boxes"""	20083	protein-coding gene	gene with protein product	"""cancer associated gene"", ""cancer/testis antigen 26"""						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.1172G>T	X.37:g.23019346G>T	ENSP00000368667:p.Arg391Met	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_182699	Q0D2N2|Q6NVV4	Missense_Mutation	SNP	ENST00000327968.5	37	CCDS35214.1	444	0.26763110307414106	164	0.4823529411764706	22	0.06321839080459771	69	0.13745019920318724	52	0.07222222222222222	T	0.455	-0.892045	0.02491	0.544459	0.121581	ENSG00000184735	ENST00000327968	T	0.16196	2.36	4.03	-2.07	0.07276	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.081576	0.85682	N	0.000000	T	0.00012	0.0000	M	0.77313	2.365	0.39580	P	0.030571000000000015	B	0.02656	0.0	B	0.06405	0.002	T	0.48536	-0.9027	9	0.19590	T	0.45	-18.4477	1.365	0.02200	0.2516:0.0862:0.2724:0.3898	rs5926203;rs7065007;rs52811818;rs59571064;rs5926203	391	Q86TM3	DDX53_HUMAN	M	391	ENSP00000368667:R391M	ENSP00000368667:R391M	R	+	2	0	DDX53	22929267	1.000000	0.71417	0.002000	0.10522	0.397000	0.30659	0.907000	0.28531	-1.338000	0.02233	-1.228000	0.01579	AGG	G|0.686;0|0.012	.	strong		0.393	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699	
PCDH15	65217	hgsc.bcm.edu	37	10	55755491	55755491	+	Missense_Mutation	SNP	C	C	T	rs2135720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:55755491C>T	ENST00000320301.6	-	21	3180	c.2786G>A	c.(2785-2787)cGa>cAa	p.R929Q	PCDH15_ENST00000395438.1_Missense_Mutation_p.R929Q|PCDH15_ENST00000395430.1_Missense_Mutation_p.R929Q|PCDH15_ENST00000414778.1_Missense_Mutation_p.R934Q|PCDH15_ENST00000361849.3_Missense_Mutation_p.R929Q|PCDH15_ENST00000395432.2_Missense_Mutation_p.R892Q|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000437009.1_Missense_Mutation_p.R858Q|PCDH15_ENST00000395445.1_Missense_Mutation_p.R936Q|PCDH15_ENST00000409834.1_Missense_Mutation_p.R540Q|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373965.2_Missense_Mutation_p.R936Q|PCDH15_ENST00000373955.1_Missense_Mutation_p.R929Q|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.R907Q	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						PASS	.	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	116	0	0		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	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	
DEF8	54849	hgsc.bcm.edu	37	16	90032296	90032296	+	Silent	SNP	T	T	G	rs11861894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:90032296T>G	ENST00000268676.7	+	13	1553	c.1464T>G	c.(1462-1464)acT>acG	p.T488T	DEF8_ENST00000570182.1_Silent_p.T417T|DEF8_ENST00000569453.1_Silent_p.T427T|DEF8_ENST00000563795.1_Silent_p.T410T|DEF8_ENST00000567874.1_Silent_p.T367T|DEF8_ENST00000563594.1_Silent_p.T427T	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	488					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		ACTCCACCACTTGTCCCAAGT	0.627													G|||	806	0.160942	0.4599	0.0591	5008	,	,		17453	0.0089		0.0258	False		,,,				2504	0.1247				p.T488T		Atlas-SNP	.											.	DEF8	28	.	0			c.T1464G						PASS	.	G	,,,,,	1762,2634	642.8+/-397.7	346,1070,782	51.0	43.0	46.0		1251,1101,1281,1230,1281,1464	-6.2	0.6	16	dbSNP_120	46	253,8347	806.5+/-407.2	4,245,4051	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DEF8	NM_001242816.1,NM_001242817.1,NM_001242818.1,NM_001242819.1,NM_001242820.1,NM_207514.2	,,,,,	350,1315,4833	GG,GT,TT		2.9419,40.0819,15.5048	,,,,,	417/442,367/392,427/452,410/435,427/452,488/513	90032296	2015,10981	2198	4300	6498	SO:0001819	synonymous_variant	54849	exon13			CACCACTTGTCCC	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.1464T>G	16.37:g.90032296T>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	109	63	0.577982	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	37	CCDS10989.1																																																																																			T|0.861;G|0.139	0.139	strong		0.627	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514	
PRR21	643905	hgsc.bcm.edu	37	2	240982052	240982052	+	Silent	SNP	C	C	G	rs77588089		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240982052C>G	ENST00000408934.1	-	1	347	c.348G>C	c.(346-348)tcG>tcC	p.S116S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	116	Pro-rich.							p.S116S(2)		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						GAGGCATGGACGAAGGGCCGT	0.627																																					p.S116S		Atlas-SNP	.											PRR21,pharynx,carcinoma,0,4	PRR21	53	4	2	Substitution - coding silent(2)	upper_aerodigestive_tract(2)	c.G348C						scavenged	.						5.0	6.0	6.0					2																	240982052		1363	2884	4247	SO:0001819	synonymous_variant	643905	exon1			CATGGACGAAGGG	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.348G>C	2.37:g.240982052C>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			C|0.250;G|0.750	0.750	weak		0.627	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
IL34	146433	hgsc.bcm.edu	37	16	70690989	70690989	+	Missense_Mutation	SNP	G	G	C	rs8046424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70690989G>C	ENST00000288098.2	+	4	750	c.367G>C	c.(367-369)Gag>Cag	p.E123Q	IL34_ENST00000566361.1_Missense_Mutation_p.E98Q|IL34_ENST00000429149.2_Missense_Mutation_p.E123Q	NM_001172772.1	NP_001166243.1	Q6ZMJ4	IL34_HUMAN	interleukin 34	123			E -> Q (in dbSNP:rs8046424). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18467591}.		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						GCAGGAGGTGGAGACGCTGCT	0.607													C|||	3581	0.715056	0.9826	0.5994	5008	,	,		20344	0.6687		0.4742	False		,,,				2504	0.7311				p.E123Q		Atlas-SNP	.											.	IL34	26	.	0			c.G367C						PASS	.	C	GLN/GLU,GLN/GLU,GLN/GLU	3958,438	209.8+/-230.5	1790,378,30	115.0	84.0	94.0		364,367,367	3.0	0.1	16	dbSNP_116	94	4199,4401	583.6+/-391.6	1032,2135,1133	yes	missense,missense,missense	IL34	NM_001172771.1,NM_001172772.1,NM_152456.2	29,29,29	2822,2513,1163	CC,CG,GG		48.8256,9.9636,37.2345	benign,benign,benign	122/242,123/243,123/243	70690989	8157,4839	2198	4300	6498	SO:0001583	missense	146433	exon5			GAGGTGGAGACGC	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.367G>C	16.37:g.70690989G>C	ENSP00000288098:p.Glu123Gln	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_152456	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	Missense_Mutation	SNP	ENST00000288098.2	37	CCDS10895.1	1429	0.6543040293040293	478	0.9715447154471545	203	0.5607734806629834	397	0.6940559440559441	351	0.4630606860158311	C	10.33	1.319045	0.23994	0.900364	0.488256	ENSG00000157368	ENST00000429149;ENST00000288098	T;T	0.44083	0.93;0.93	5.18	3.04	0.35103	.	0.691102	0.13631	N	0.373759	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	0.36040	-0.9764	9	0.06365	T	0.9	-10.8047	2.4406	0.04493	0.1665:0.5233:0.1616:0.1486	rs8046424;rs17856848;rs57318770;rs8046424	122;123	Q6ZMJ4-2;Q6ZMJ4	.;IL34_HUMAN	Q	123	ENSP00000397863:E123Q;ENSP00000288098:E123Q	ENSP00000288098:E123Q	E	+	1	0	IL34	69248490	0.020000	0.18652	0.115000	0.21578	0.440000	0.31957	1.221000	0.32503	1.197000	0.43143	-0.322000	0.08575	GAG	G|0.354;C|0.646	0.646	strong		0.607	IL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268971.3	NM_152456	
TMEM198	130612	hgsc.bcm.edu	37	2	220414019	220414019	+	Silent	SNP	T	T	C	rs13023533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220414019T>C	ENST00000344458.2	+	5	1473	c.888T>C	c.(886-888)ccT>ccC	p.P296P	TMEM198_ENST00000373883.3_Silent_p.P296P|RP11-256I23.1_ENST00000596829.1_RNA|MIR3132_ENST00000581997.1_RNA			Q66K66	TM198_HUMAN	transmembrane protein 198	296	Arg-rich.				multicellular organismal development (GO:0007275)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	16		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CACCAGACCCTGCTTATCGGC	0.622													T|||	1965	0.392372	0.4077	0.5231	5008	,	,		11770	0.38		0.4592	False		,,,				2504	0.2229				p.P296P		Atlas-SNP	.											TMEM198,NS,carcinoma,0,2	TMEM198	36	2	0			c.T888C						PASS	.	T		716,3690		295,126,1782	41.0	45.0	44.0		888	-1.4	1.0	2	dbSNP_121	44	1537,7063		640,257,3403	no	coding-synonymous	TMEM198	NM_001005209.1		935,383,5185	CC,CT,TT		17.8721,16.2506,17.3228		296/361	220414019	2253,10753	2203	4300	6503	SO:0001819	synonymous_variant	130612	exon4			AGACCCTGCTTAT	BC068567	CCDS33385.1	2q35	2011-12-06			ENSG00000188760	ENSG00000188760			33704	protein-coding gene	gene with protein product							Standard	NM_001005209		Approved	MGC99813, TMEM198A	uc002vmf.3	Q66K66	OTTHUMG00000059156	ENST00000344458.2:c.888T>C	2.37:g.220414019T>C		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	202	199	0.985148	NM_001005209		Silent	SNP	ENST00000344458.2	37	CCDS33385.1																																																																																			T|0.559;C|0.441	0.441	strong		0.622	TMEM198-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131063.1	NM_001005209	
IFNA14	3448	hgsc.bcm.edu	37	9	21239578	21239578	+	Silent	SNP	C	C	T	rs141933410		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21239578C>T	ENST00000380222.2	-	1	400	c.357G>A	c.(355-357)ctG>ctA	p.L119L		NM_002172.2	NP_002163.2	P01570	IFN14_HUMAN	interferon, alpha 14	119					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)	11				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		CACAGGCTTCCAGGTCATTCA	0.448																																					p.L119L		Atlas-SNP	.											.	IFNA14	29	.	0			c.G357A						PASS	.						150.0	156.0	154.0					9																	21239578		2203	4300	6503	SO:0001819	synonymous_variant	3448	exon1			GGCTTCCAGGTCA		CCDS6501.1	9p22	2010-08-24			ENSG00000228083	ENSG00000228083		"""Interferons"""	5420	protein-coding gene	gene with protein product		147579				1385305	Standard	NM_002172		Approved	LEIF2H, IFN-alphaH	uc010mis.3	P01570	OTTHUMG00000019665	ENST00000380222.2:c.357G>A	9.37:g.21239578C>T		Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	429	43	0.100233	NM_002172	Q5VZ56|Q7M4S1	Silent	SNP	ENST00000380222.2	37	CCDS6501.1																																																																																			C|0.999;G|0.000;T|0.001	0.001	strong		0.448	IFNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051894.1	NM_002172	
ERCC5	2073	hgsc.bcm.edu	37	13	103518036	103518036	+	Silent	SNP	A	A	G	rs55686372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103518036A>G	ENST00000355739.4	+	9	3397	c.1974A>G	c.(1972-1974)caA>caG	p.Q658Q	ERCC5_ENST00000375954.1_5'UTR|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.K1084E	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	658					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)					TTGAAGTGCAAAGTGTGATTA	0.413			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				A|||	27	0.00539137	0.0197	0.0014	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0				p.Q1112Q		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.A3336G						PASS	.	A	,	74,4332	64.1+/-101.4	2,70,2131	33.0	32.0	32.0		1974,3336	-1.4	0.5	13	dbSNP_129	32	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	2,70,6431	GG,GA,AA		0.0,1.6795,0.569	,	658/1187,1112/1641	103518036	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	0	exon17	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGTGCAAAGTGTG	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.1974A>G	13.37:g.103518036A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			A|0.995;G|0.005	0.005	strong		0.413	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
MAN2B2	23324	hgsc.bcm.edu	37	4	6621677	6621677	+	Silent	SNP	C	C	G	rs147252633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6621677C>G	ENST00000285599.3	+	18	2874	c.2838C>G	c.(2836-2838)tcC>tcG	p.S946S	MAN2B2_ENST00000504248.1_Silent_p.S895S	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	946					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						CGCTGGGGTCCGTGGTGGCAG	0.652													C|||	15	0.00299521	0.0106	0.0014	5008	,	,		17764	0.0		0.0	False		,,,				2504	0.0				p.S946S		Atlas-SNP	.											.	MAN2B2	80	.	0			c.C2838G						PASS	.	C		58,4348	53.6+/-89.4	0,58,2145	50.0	55.0	53.0		2838	-0.9	0.0	4	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous	MAN2B2	NM_015274.1		0,58,6445	GG,GC,CC		0.0,1.3164,0.4459		946/1010	6621677	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	23324	exon18			GGGGTCCGTGGTG	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.2838C>G	4.37:g.6621677C>G		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	181	88	0.486188	NM_015274	Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	37	CCDS33951.1																																																																																			C|0.994;G|0.006	0.006	strong		0.652	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
ZNF469	84627	hgsc.bcm.edu	37	16	88500822	88500822	+	Missense_Mutation	SNP	C	C	G	rs77490207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88500822C>G	ENST00000437464.1	+	2	6860	c.6860C>G	c.(6859-6861)cCc>cGc	p.P2287R	ZNF469_ENST00000565624.1_Missense_Mutation_p.P2315R	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2287					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						GGAGCCCCGCCCCACACCAAC	0.682													C|||	86	0.0171725	0.0613	0.0072	5008	,	,		14649	0.0		0.0	False		,,,				2504	0.0				p.P2287R		Atlas-SNP	.											.	ZNF469	121	.	0			c.C6860G						PASS	.						6.0	11.0	10.0					16																	88500822		677	1564	2241	SO:0001583	missense	84627	exon2			CCCCGCCCCACAC	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.6860C>G	16.37:g.88500822C>G	ENSP00000402343:p.Pro2287Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	25	0.011446886446886446	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	0	0.0	C	7.590	0.670481	0.14776	.	.	ENSG00000225614	ENST00000437464	T	0.46063	0.88	4.4	2.43	0.29744	.	.	.	.	.	T	0.04182	0.0116	N	0.14661	0.345	0.09310	N	1	P	0.40476	0.718	B	0.39258	0.295	T	0.03684	-1.1013	9	0.72032	D	0.01	.	6.5162	0.22248	0.0:0.7728:0.0:0.2272	.	2287	Q96JG9	ZN469_HUMAN	R	2287	ENSP00000402343:P2287R	ENSP00000402343:P2287R	P	+	2	0	ZNF469	87028323	0.001000	0.12720	0.000000	0.03702	0.011000	0.07611	1.264000	0.33015	0.325000	0.23359	0.462000	0.41574	CCC	C|0.988;G|0.012	0.012	strong		0.682	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
BUB1B	701	hgsc.bcm.edu	37	15	40462780	40462780	+	Silent	SNP	G	G	A	rs1801389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40462780G>A	ENST00000287598.6	+	4	477	c.282G>A	c.(280-282)aaG>aaA	p.K94K	BUB1B_ENST00000560120.1_3'UTR|BUB1B_ENST00000412359.3_Silent_p.K108K	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	114	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	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		
LIFR	3977	hgsc.bcm.edu	37	5	38510768	38510768	+	Silent	SNP	T	T	C	rs141925289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38510768T>C	ENST00000263409.4	-	7	951	c.789A>G	c.(787-789)gtA>gtG	p.V263V	LIFR_ENST00000453190.2_Silent_p.V263V|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	263					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					TGTCTGAGCCTACAAGTATCA	0.348			T	PLAG1	salivary adenoma								T|||	21	0.00419329	0.0159	0.0	5008	,	,		17591	0.0		0.0	False		,,,				2504	0.0				p.V263V	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.A789G						PASS	.	T	,	38,4368	40.0+/-72.8	0,38,2165	80.0	73.0	76.0		789,789	-0.2	1.0	5	dbSNP_134	76	0,8600		0,0,4300	yes	coding-synonymous,coding-synonymous	LIFR	NM_001127671.1,NM_002310.5	,	0,38,6465	CC,CT,TT		0.0,0.8625,0.2922	,	263/1098,263/1098	38510768	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	3977	exon7			TGAGCCTACAAGT	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.789A>G	5.37:g.38510768T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	123	54	0.439024	NM_002310	Q6LCD9	Silent	SNP	ENST00000263409.4	37	CCDS3927.1																																																																																			T|0.997;C|0.003	0.003	strong		0.348	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
HLA-G	3135	hgsc.bcm.edu	37	6	29797639	29797639	+	Silent	SNP	C	C	T	rs1049033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29797639C>T	ENST00000360323.6	+	5	966	c.942C>T	c.(940-942)ggC>ggT	p.G314G	HLA-G_ENST00000428701.1_Silent_p.G314G|HLA-G_ENST00000376828.2_Silent_p.G319G|HLA-G_ENST00000376818.3_Silent_p.G222G|HLA-G_ENST00000376815.3_Silent_p.G130G			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	314					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						TCGTTGCTGGCCTGGTTGTCC	0.597													N|||	1161	0.231829	0.2504	0.245	5008	,	,		20908	0.1091		0.2555	False		,,,				2504	0.2996				p.G314G		Atlas-SNP	.											.	HLA-G	90	.	0			c.C942T						PASS	.	C		1182,3224		158,866,1179	109.0	90.0	96.0		942	-0.2	0.0	6	dbSNP_86	96	2541,6059		367,1807,2126	no	coding-synonymous	HLA-G	NM_002127.5		525,2673,3305	TT,TC,CC		29.5465,26.8271,28.6252		314/339	29797639	3723,9283	2203	4300	6503	SO:0001819	synonymous_variant	3135	exon6			TGCTGGCCTGGTT		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.942C>T	6.37:g.29797639C>T		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	295	127	0.430508	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			C|0.738;T|0.262	0.262	strong		0.597	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
MDN1	23195	hgsc.bcm.edu	37	6	90497589	90497589	+	Missense_Mutation	SNP	A	A	C	rs4707569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90497589A>C	ENST00000369393.3	-	8	1433	c.1318T>G	c.(1318-1320)Ttt>Gtt	p.F440V	MDN1_ENST00000428876.1_Missense_Mutation_p.F440V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	440			F -> V (in dbSNP:rs4707569).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GTTGCAAAAAACTGAAATCCA	0.463													A|||	771	0.153954	0.1399	0.1398	5008	,	,		17057	0.2163		0.1819	False		,,,				2504	0.09				p.F440V		Atlas-SNP	.											.	MDN1	478	.	0			c.T1318G						PASS	.	A	VAL/PHE	719,3687	292.1+/-281.9	63,593,1547	102.0	97.0	99.0		1318	4.4	1.0	6	dbSNP_111	99	1536,7064	284.2+/-296.5	142,1252,2906	yes	missense	MDN1	NM_014611.1	50	205,1845,4453	CC,CA,AA		17.8605,16.3187,17.3382	benign	440/5597	90497589	2255,10751	2203	4300	6503	SO:0001583	missense	23195	exon8			CAAAAAACTGAAA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.1318T>G	6.37:g.90497589A>C	ENSP00000358400:p.Phe440Val	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	370	0.16941391941391942	54	0.10975609756097561	45	0.12430939226519337	127	0.22202797202797203	144	0.18997361477572558	A	11.90	1.777902	0.31502	0.163187	0.178605	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.46819	0.86;0.86	5.65	4.45	0.53987	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.051750	0.85682	D	0.000000	T	0.16428	0.0395	N	0.13235	0.315	0.27005	P	0.9648156999999999	P;B	0.40000	0.698;0.036	B;B	0.40702	0.338;0.065	T	0.07009	-1.0795	9	0.51188	T	0.08	.	8.4306	0.32755	0.7872:0.0:0.2128:0.0	rs4707569;rs61658597;rs4707569	440;440	Q6ZVV6;Q9NU22	.;MDN1_HUMAN	V	440	ENSP00000358400:F440V;ENSP00000413970:F440V	ENSP00000358400:F440V	F	-	1	0	MDN1	90554310	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.988000	0.56951	1.031000	0.39867	0.460000	0.39030	TTT	A|0.832;C|0.168	0.168	strong		0.463	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37730017	37730017	+	Missense_Mutation	SNP	G	G	A	rs16887092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:37730017G>A	ENST00000330843.4	-	4	2315	c.2303C>T	c.(2302-2304)gCt>gTt	p.A768V	RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000523182.1_5'UTR	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	768			A -> V (in dbSNP:rs16887092).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			CACTTCTTCAGCTGCATCCCT	0.577													A|||	540	0.107827	0.3722	0.0418	5008	,	,		18823	0.0079		0.005	False		,,,				2504	0.0061				p.A768V		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.C2303T						PASS	.	A	VAL/ALA,	1370,3036	690.5+/-405.3	218,934,1051	87.0	89.0	88.0		2303,	-4.6	0.0	8	dbSNP_123	88	13,8587	818.7+/-406.8	0,13,4287	yes	missense,intron	RAB11FIP1	NM_001002814.2,NM_025151.4	64,	218,947,5338	AA,AG,GG		0.1512,31.094,10.6336	benign,	768/1284,	37730017	1383,11623	2203	4300	6503	SO:0001583	missense	80223	exon4			TCTTCAGCTGCAT	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.2303C>T	8.37:g.37730017G>A	ENSP00000331342:p.Ala768Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_001002814	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	37	CCDS34882.1	196	0.08974358974358974	178	0.3617886178861789	16	0.04419889502762431	0	0.0	2	0.002638522427440633	A	7.240	0.600997	0.13939	0.31094	0.001512	ENSG00000156675	ENST00000330843	T	0.09817	2.94	4.11	-4.62	0.03370	.	3.975120	0.00866	N	0.001966	T	0.00012	0.0000	N	0.12182	0.205	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46512	-0.9186	9	0.20046	T	0.44	3.6141	6.7903	0.23695	0.2589:0.0:0.5516:0.1895	rs16887092;rs52799569;rs16887092	97;768	Q67C35;Q6WKZ4	.;RFIP1_HUMAN	V	768	ENSP00000331342:A768V	ENSP00000331342:A768V	A	-	2	0	RAB11FIP1	37849175	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.799000	0.01746	-1.042000	0.03262	-0.982000	0.02568	GCT	G|0.890;A|0.110	0.110	strong		0.577	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151	
GRIN3B	116444	hgsc.bcm.edu	37	19	1003439	1003439	+	Missense_Mutation	SNP	G	G	A	rs55646937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1003439G>A	ENST00000234389.3	+	2	756	c.737G>A	c.(736-738)cGt>cAt	p.R246H	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	246					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCCCGTGCCCGTCGGGTGCTG	0.756													N|||	550	0.109824	0.084	0.0331	5008	,	,		11342	0.1954		0.0527	False		,,,				2504	0.1697				p.R246H		Atlas-SNP	.											.	GRIN3B	46	.	0			c.G737A						PASS	.		HIS/ARG	235,3467		5,225,1621	3.0	4.0	4.0		737	-2.0	0.0	19	dbSNP_129	4	245,7231		1,243,3494	no	missense	GRIN3B	NM_138690.1	29	6,468,5115	AA,AG,GG		3.2772,6.3479,4.2941	benign	246/1044	1003439	480,10698	1851	3738	5589	SO:0001583	missense	116444	exon2			GTGCCCGTCGGGT		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.737G>A	19.37:g.1003439G>A	ENSP00000234389:p.Arg246His	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	211	0.09661172161172162	48	0.0975609756097561	15	0.04143646408839779	114	0.1993006993006993	34	0.044854881266490766	g	11.38	1.621109	0.28889	0.063479	0.032772	ENSG00000116032	ENST00000234389	T	0.11604	2.76	4.05	-2.02	0.07388	.	1.415140	0.04769	N	0.427641	T	0.00012	0.0000	L	0.35341	1.055	0.80722	P	0.0	B	0.12013	0.005	B	0.04013	0.001	T	0.44651	-0.9314	9	0.41790	T	0.15	.	2.6825	0.05098	0.2767:0.1144:0.4807:0.1282	rs55646937;rs61744193	246	O60391	NMD3B_HUMAN	H	246	ENSP00000234389:R246H	ENSP00000234389:R246H	R	+	2	0	GRIN3B	954439	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.050000	0.11904	-0.106000	0.12110	-0.776000	0.03382	CGT	G|0.903;A|0.097	0.097	strong		0.756	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
ZNF30	90075	hgsc.bcm.edu	37	19	35435006	35435006	+	Missense_Mutation	SNP	G	G	A	rs1345658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35435006G>A	ENST00000601142.1	+	5	1373	c.1136G>A	c.(1135-1137)aGa>aAa	p.R379K	ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000426813.2_Missense_Mutation_p.R298K|ZNF30_ENST00000303586.7_Missense_Mutation_p.R380K|ZNF30_ENST00000439785.1_Missense_Mutation_p.R380K			P17039	ZNF30_HUMAN	zinc finger protein 30	379			R -> K (in dbSNP:rs1345658). {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)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		GAATGCGGGAGAACCTTCAGT	0.473													A|||	3267	0.652356	0.9402	0.4049	5008	,	,		24938	0.6002		0.5129	False		,,,				2504	0.636				p.R380K		Atlas-SNP	.											.	ZNF30	44	.	0			c.G1139A						PASS	.	A	LYS/ARG,LYS/ARG,LYS/ARG	3758,644	244.0+/-253.5	1612,534,55	71.0	81.0	78.0		1139,1139,1136	2.1	0.0	19	dbSNP_88	78	4065,4533	577.1+/-390.5	971,2123,1205	yes	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	26,26,26	2583,2657,1260	AA,AG,GG		47.2784,14.6297,39.8231	benign,benign,benign	380/625,380/625,379/624	35435006	7823,5177	2201	4299	6500	SO:0001583	missense	90075	exon5			GCGGGAGAACCTT	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.1136G>A	19.37:g.35435006G>A	ENSP00000469954:p.Arg379Lys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	133	0.992537	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	1374	0.6291208791208791	464	0.943089430894309	169	0.46685082872928174	358	0.6258741258741258	383	0.5052770448548812	a	0.695	-0.793153	0.02862	0.853703	0.472784	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813;ENST00000342559	T;T	0.10288	2.89;2.89	2.07	2.07	0.26955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00765	-1.205	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23013	-1.0200	8	0.02654	T	1	.	5.3836	0.16206	0.8393:0.0:0.1607:0.0	rs1345658;rs3826987;rs52837481;rs61057657;rs1345658	380;379	P17039-2;P17039	.;ZNF30_HUMAN	K	380;379;298;88	ENSP00000403441:R380K;ENSP00000416457:R298K	ENSP00000303889:R379K	R	+	2	0	ZNF30	40126846	0.966000	0.33281	0.005000	0.12908	0.001000	0.01503	2.619000	0.46401	0.080000	0.16959	-0.773000	0.03387	AGA	G|0.345;T|0.003	.	strong		0.473	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
SLC27A2	11001	hgsc.bcm.edu	37	15	50474766	50474766	+	Missense_Mutation	SNP	A	A	C	rs1648348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:50474766A>C	ENST00000267842.5	+	1	374	c.142A>C	c.(142-144)Aag>Cag	p.K48Q	SLC27A2_ENST00000380902.4_Missense_Mutation_p.K48Q	NM_003645.3	NP_003636.2	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid transporter), member 2	48			K -> Q (in dbSNP:rs1648348). {ECO:0000269|PubMed:10198260, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1, ECO:0000269|Ref.6}.		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)|very long-chain fatty acid catabolic process (GO:0042760)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of peroxisomal membrane (GO:0005779)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|fatty acid transporter activity (GO:0015245)|long-chain fatty acid-CoA ligase activity (GO:0004467)|phytanate-CoA ligase activity (GO:0050197)|pristanate-CoA ligase activity (GO:0070251)|receptor binding (GO:0005102)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)		CAGCTACGGGAAGCGGCGGCC	0.647													A|||	3070	0.613019	0.3729	0.6326	5008	,	,		13597	0.8095		0.6501	False		,,,				2504	0.683				p.K48Q		Atlas-SNP	.											.	SLC27A2	50	.	0			c.A142C						PASS	.	A	GLN/LYS,GLN/LYS	1867,2519		393,1081,719	19.0	20.0	20.0		142,142	0.7	0.0	15	dbSNP_89	20	5703,2873		1911,1881,496	yes	missense,missense	SLC27A2	NM_001159629.1,NM_003645.3	53,53	2304,2962,1215	CC,CA,AA		33.5005,42.5673,41.5985	benign,benign	48/568,48/621	50474766	7570,5392	2193	4288	6481	SO:0001583	missense	11001	exon1			TACGGGAAGCGGC	D88308	CCDS10133.1, CCDS53943.1	15q21.2	2013-05-22			ENSG00000140284	ENSG00000140284		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10996	protein-coding gene	gene with protein product		603247		FACVL1		9730624	Standard	NM_003645		Approved	FATP2, hFACVL1, VLACS, VLCS, HsT17226, ACSVL1	uc001zxw.3	O14975	OTTHUMG00000131643	ENST00000267842.5:c.142A>C	15.37:g.50474766A>C	ENSP00000267842:p.Lys48Gln	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	11	0.215686	NM_003645	A8K2J7|Q53FY6|Q6PF09	Missense_Mutation	SNP	ENST00000267842.5	37	CCDS10133.1	1413	0.646978021978022	205	0.4166666666666667	221	0.6104972375690608	471	0.8234265734265734	516	0.6807387862796834	A	1.463	-0.561990	0.03939	0.425673	0.664995	ENSG00000140284	ENST00000380902;ENST00000267842	T;T	0.60548	0.29;0.18	4.94	0.708	0.18144	.	2.094770	0.02304	N	0.071516	T	0.00012	0.0000	N	0.05280	-0.08	0.50467	P	1.2900000000004574E-4	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.45745	-0.9240	9	0.20519	T	0.43	.	13.7473	0.62883	0.6771:0.3229:0.0:0.0	rs1648348;rs17848318;rs1648348	48;48	Q6PF09;O14975	.;S27A2_HUMAN	Q	48	ENSP00000370289:K48Q;ENSP00000267842:K48Q	ENSP00000267842:K48Q	K	+	1	0	SLC27A2	48262058	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.034000	0.13776	-0.049000	0.13379	-0.249000	0.11873	AAG	A|0.412;C|0.588	0.588	strong		0.647	SLC27A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254539.2	NM_003645	
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239237783	239237783	+	Missense_Mutation	SNP	C	C	T	rs34723381	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239237783C>T	ENST00000373327.4	+	5	937	c.715C>T	c.(715-717)Cgg>Tgg	p.R239W	TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.R239W|TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.R239W	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	239	Abolishes microtubules-binding when missing.|Arg-rich.|DISC1-interaction domain.		R -> W (in dbSNP:rs34723381).		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)		caacagggagcgggacagaga	0.597													C|||	228	0.0455272	0.1611	0.0216	5008	,	,		16990	0.0		0.0	False		,,,				2504	0.0				p.R239W		Atlas-SNP	.											.	TRAF3IP1	58	.	0			c.C715T						PASS	.	C	TRP/ARG,TRP/ARG	516,3828		27,462,1683	71.0	72.0	72.0		715,715	3.2	0.1	2	dbSNP_126	72	8,8478		0,8,4235	yes	missense,missense	TRAF3IP1	NM_001139490.1,NM_015650.3	101,101	27,470,5918	TT,TC,CC		0.0943,11.8785,4.0842	probably-damaging,probably-damaging	239/626,239/692	239237783	524,12306	2172	4243	6415	SO:0001583	missense	26146	exon5			AGGGAGCGGGACA	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.715C>T	2.37:g.239237783C>T	ENSP00000362424:p.Arg239Trp	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	132	55	0.416667	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	37	CCDS33415.1	101	0.04624542124542125	91	0.18495934959349594	10	0.027624309392265192	0	0.0	0	0.0	C	15.99	2.996440	0.54147	0.118785	9.43E-4	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.15372	2.43;2.43;2.43	4.12	3.17	0.36434	.	0.811391	0.10616	N	0.653948	T	0.00073	0.0002	M	0.61703	1.905	0.46096	P	0.0011360000000000259	D;D	0.69078	0.997;0.997	P;P	0.55055	0.656;0.767	T	0.10847	-1.0612	9	0.72032	D	0.01	-4.3779	12.5493	0.56218	0.0:0.7311:0.2689:0.0	rs34723381	239;239	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	W	239	ENSP00000375851:R239W;ENSP00000362424:R239W;ENSP00000375852:R239W	ENSP00000362424:R239W	R	+	1	2	TRAF3IP1	238902522	0.112000	0.22096	0.055000	0.19348	0.014000	0.08584	0.585000	0.23879	2.023000	0.59567	0.467000	0.42956	CGG	C|0.950;T|0.050	0.050	strong		0.597	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650	
THBD	7056	hgsc.bcm.edu	37	20	23029971	23029971	+	Silent	SNP	G	G	T	rs201268201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23029971G>T	ENST00000377103.2	-	1	407	c.171C>A	c.(169-171)ggC>ggA	p.G57G		NM_000361.2	NP_000352.1	P07204	TRBM_HUMAN	thrombomodulin	57	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood coagulation (GO:0007596)|female pregnancy (GO:0007565)|leukocyte migration (GO:0050900)|negative regulation of blood coagulation (GO:0030195)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|response to cAMP (GO:0051591)|response to lipopolysaccharide (GO:0032496)|response to X-ray (GO:0010165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|large_intestine(3)|ovary(1)|skin(1)	7	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)				Drotrecogin alfa(DB00055)|Ibuprofen(DB01050)	TCATTAGGTGGCCCCGCAGTC	0.677													G|||	2	0.000399361	0.0015	0.0	5008	,	,		11359	0.0		0.0	False		,,,				2504	0.0				p.G57G		Atlas-SNP	.											.	THBD	26	.	0			c.C171A						PASS	.	G		3,4261		0,3,2129	8.0	9.0	9.0		171	1.3	1.0	20		9	0,8380		0,0,4190	no	coding-synonymous	THBD	NM_000361.2		0,3,6319	TT,TG,GG		0.0,0.0704,0.0237		57/576	23029971	3,12641	2132	4190	6322	SO:0001819	synonymous_variant	7056	exon1			TAGGTGGCCCCGC		CCDS13148.1	20p11.21	2014-09-17			ENSG00000178726	ENSG00000178726		"""CD molecules"""	11784	protein-coding gene	gene with protein product		188040					Standard	NM_000361		Approved	CD141	uc002wss.3	P07204	OTTHUMG00000032053	ENST00000377103.2:c.171C>A	20.37:g.23029971G>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	40	30	0.75	NM_000361	Q8IV29|Q9UC32	Silent	SNP	ENST00000377103.2	37	CCDS13148.1																																																																																			G|0.999;T|0.001	0.001	strong		0.677	THBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078307.2		
CSTL1	128817	hgsc.bcm.edu	37	20	23424660	23424660	+	Silent	SNP	G	G	C	rs12625959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	92	0	0		WXS	Illumina HiSeq	Phase_I	112	43	0.383929	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		
IRX4	50805	hgsc.bcm.edu	37	5	1880891	1880891	+	Missense_Mutation	SNP	C	C	T	rs2232376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:1880891C>T	ENST00000505790.1	-	4	811	c.355G>A	c.(355-357)Gct>Act	p.A119T	IRX4_ENST00000505938.1_5'UTR|IRX4_ENST00000231357.2_Missense_Mutation_p.A119T|IRX4_ENST00000513692.1_Missense_Mutation_p.A119T	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	119			A -> T (in dbSNP:rs2232376). {ECO:0000269|PubMed:15489334}.		establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		TAGGCGGCAGCGGCTGGTGCC	0.632													C|||	687	0.137181	0.2156	0.1599	5008	,	,		13055	0.0139		0.2058	False		,,,				2504	0.0716				p.A119T		Atlas-SNP	.											IRX4,colon,carcinoma,0,1	IRX4	45	1	0			c.G355A						PASS	.	C	THR/ALA	1014,3390	372.5+/-320.4	107,800,1295	71.0	75.0	74.0		355	4.0	0.0	5	dbSNP_98	74	1742,6858	315.1+/-312.1	175,1392,2733	yes	missense	IRX4	NM_016358.2	58	282,2192,4028	TT,TC,CC		20.2558,23.0245,21.1935	benign	119/520	1880891	2756,10248	2202	4300	6502	SO:0001583	missense	50805	exon3			CGGCAGCGGCTGG	AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430		"""Homeoboxes / TALE class"""	6129	protein-coding gene	gene with protein product		606199	"""iroquois homeobox protein 4"""			10625552	Standard	NM_016358		Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.355G>A	5.37:g.1880891C>T	ENSP00000423161:p.Ala119Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Missense_Mutation	SNP	ENST00000505790.1	37	CCDS3867.1	346	0.15842490842490842	112	0.22764227642276422	70	0.19337016574585636	10	0.017482517482517484	154	0.20316622691292877	C	6.313	0.425811	0.11987	0.230245	0.202558	ENSG00000113430	ENST00000231357;ENST00000505790;ENST00000513692;ENST00000511126	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.04	4.03	4.03	0.46877	.	0.359172	0.28332	N	0.015722	T	0.00012	0.0000	N	0.16478	0.41	0.29531	P	0.852752	P	0.37061	0.58	B	0.26310	0.068	T	0.10428	-1.0630	9	0.21014	T	0.42	-14.4145	14.9752	0.71267	0.0:1.0:0.0:0.0	rs2232376;rs60328712;rs2232376	119	P78413	IRX4_HUMAN	T	119	ENSP00000231357:A119T;ENSP00000423161:A119T;ENSP00000424235:A119T;ENSP00000421772:A119T	ENSP00000231357:A119T	A	-	1	0	IRX4	1933891	0.997000	0.39634	0.014000	0.15608	0.013000	0.08279	3.640000	0.54350	1.801000	0.52704	0.557000	0.71058	GCT	T|0.195;G|0.006	0.195	strong		0.632	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358	
RABGAP1L	9910	hgsc.bcm.edu	37	1	174219724	174219724	+	Missense_Mutation	SNP	A	A	G	rs7339904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:174219724A>G	ENST00000251507.4	+	6	1003	c.829A>G	c.(829-831)Agt>Ggt	p.S277G	RABGAP1L_ENST00000367689.3_5'UTR|RABGAP1L_ENST00000357444.6_Missense_Mutation_p.S240G	NM_014857.4	NP_055672.3	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	0										NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						GTTTACCTTCAGTGTCTCCTT	0.388													A|||	328	0.0654952	0.2405	0.0144	5008	,	,		16084	0.0		0.0	False		,,,				2504	0.0				p.S277G		Atlas-SNP	.											.	RABGAP1L	103	.	0			c.A829G						PASS	.	A	GLY/SER	917,3489	353.1+/-312.0	107,703,1393	141.0	138.0	139.0		829	4.7	1.0	1	dbSNP_116	139	6,8594	5.0+/-18.6	0,6,4294	yes	missense	RABGAP1L	NM_014857.4	56	107,709,5687	GG,GA,AA		0.0698,20.8125,7.0967	benign	277/816	174219724	923,12083	2203	4300	6503	SO:0001583	missense	9910	exon6			ACCTTCAGTGTCT	AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061			24663	protein-coding gene	gene with protein product		609238				10585558	Standard	NM_014857		Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000251507.4:c.829A>G	1.37:g.174219724A>G	ENSP00000251507:p.Ser277Gly	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_014857	B7ZAA4	Missense_Mutation	SNP	ENST00000251507.4	37	CCDS1314.1	137	0.06272893772893773	132	0.2682926829268293	5	0.013812154696132596	0	0.0	0	0.0	A	15.94	2.982019	0.53827	0.208125	6.98E-4	ENSG00000152061	ENST00000357444;ENST00000251507;ENST00000457696;ENST00000367692	T;T;T	0.47528	0.87;3.46;0.84	5.8	4.68	0.58851	.	0.235735	0.48767	N	0.000180	T	0.00012	0.0000	L	0.38531	1.155	0.09310	P	1.0	P;B;B	0.35328	0.495;0.017;0.372	B;B;B	0.30401	0.115;0.066;0.083	T	0.27571	-1.0070	9	0.23891	T	0.37	.	11.7008	0.51569	0.9314:0.0:0.0686:0.0	rs7339904;rs52822913;rs7339904	277;277;240	B7WPG6;Q5R372;Q5R372-2	.;RBG1L_HUMAN;.	G	240;277;277;277	ENSP00000350027:S240G;ENSP00000251507:S277G;ENSP00000403136:S277G	ENSP00000251507:S277G	S	+	1	0	RABGAP1L	172486347	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.023000	0.64084	1.044000	0.40200	0.459000	0.35465	AGT	A|0.914;G|0.086	0.086	strong		0.388	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084497.1	NM_001243765	
MAML3	55534	hgsc.bcm.edu	37	4	140640703	140640703	+	Missense_Mutation	SNP	G	G	T	rs61747885	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:140640703G>T	ENST00000509479.2	-	5	4047	c.3191C>A	c.(3190-3192)cCc>cAc	p.P1064H	MGST2_ENST00000515137.1_Intron	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					CTGTGCTGGGGGCTGGCTGAA	0.617													G|||	548	0.109425	0.0378	0.0922	5008	,	,		19107	0.1567		0.1412	False		,,,				2504	0.137				p.P1060H		Atlas-SNP	.											.	MAML3	192	.	0			c.C3179A						PASS	.	G	,,HIS/PRO	233,4165	118.0+/-155.7	5,223,1971	32.0	36.0	35.0		,,3191	4.8	1.0	4	dbSNP_129	35	1342,7250	253.9+/-279.4	104,1134,3058	yes	intron,intron,missense	MGST2,MAML3	NM_001204366.1,NM_001204367.1,NM_018717.4	,,77	109,1357,5029	TT,TG,GG		15.6192,5.2979,12.1247	,,possibly-damaging	,,1064/1139	140640703	1575,11415	2199	4296	6495	SO:0001583	missense	55534	exon6			GCTGGGGGCTGGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.3191C>A	4.37:g.140640703G>T	ENSP00000421180:p.Pro1064His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	260	0.11904761904761904	20	0.04065040650406504	47	0.1298342541436464	81	0.14160839160839161	112	0.14775725593667546	G	13.86	2.363105	0.41902	0.052979	0.156192	ENSG00000196782	ENST00000509479;ENST00000538400	T	0.24350	1.86	4.78	4.78	0.61160	.	0.642458	0.15615	N	0.253161	T	0.00144	0.0004	M	0.70595	2.14	0.09310	P	1.0	P;P	0.45348	0.856;0.856	B;B	0.40101	0.319;0.319	T	0.11743	-1.0575	9	0.44086	T	0.13	.	18.1787	0.89769	0.0:0.0:1.0:0.0	rs61747885	1064;1060	E7EVW8;Q96JK9	.;MAML3_HUMAN	H	1064;371	ENSP00000421180:P1064H	ENSP00000421180:P1064H	P	-	2	0	MAML3	140860153	1.000000	0.71417	0.995000	0.50966	0.948000	0.59901	5.774000	0.68906	2.342000	0.79632	0.591000	0.81541	CCC	G|0.877;T|0.123	0.123	strong		0.617	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
UCP3	7352	hgsc.bcm.edu	37	11	73717254	73717254	+	Silent	SNP	A	A	G	rs1800006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73717254A>G	ENST00000314032.4	-	3	849	c.297T>C	c.(295-297)taT>taC	p.Y99Y	UCP3_ENST00000348534.4_Silent_p.Y99Y|UCP3_ENST00000426995.2_Silent_p.Y99Y	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	99					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to hormone stimulus (GO:0032870)|fatty acid metabolic process (GO:0006631)|lipid metabolic process (GO:0006629)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to activity (GO:0014823)|response to cold (GO:0009409)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					TGACGGAGTCATAGAGGCCGA	0.622													G|||	1719	0.343251	0.6445	0.1556	5008	,	,		18847	0.2808		0.2416	False		,,,				2504	0.2382				p.Y99Y		Atlas-SNP	.											.	UCP3	31	.	0			c.T297C						PASS	.	G	,	2599,1801	528.9+/-372.5	772,1055,373	44.0	44.0	44.0		297,297	-7.6	0.3	11	dbSNP_89	44	2091,6495	715.0+/-406.0	256,1579,2458	no	coding-synonymous,coding-synonymous	UCP3	NM_003356.3,NM_022803.2	,	1028,2634,2831	GG,GA,AA		24.3536,40.9318,36.1158	,	99/313,99/276	73717254	4690,8296	2200	4293	6493	SO:0001819	synonymous_variant	7352	exon3			GGAGTCATAGAGG	AF001787	CCDS8229.1, CCDS44677.1	11q13.4	2013-05-22				ENSG00000175564		"""Solute carriers"""	12519	protein-coding gene	gene with protein product		602044				9480760, 9196039	Standard	NM_003356		Approved	SLC25A9	uc001our.3	P55916		ENST00000314032.4:c.297T>C	11.37:g.73717254A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_003356	O60475|Q96HL3	Silent	SNP	ENST00000314032.4	37	CCDS8229.1																																																																																			A|0.651;G|0.349	0.349	strong		0.622	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356	
KCNU1	157855	hgsc.bcm.edu	37	8	36788479	36788479	+	Missense_Mutation	SNP	A	A	G	rs16885577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	66	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	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	
RASA1	5921	hgsc.bcm.edu	37	5	86681125	86681125	+	Silent	SNP	A	A	T	rs137898246		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:86681125A>T	ENST00000274376.6	+	22	3330	c.2766A>T	c.(2764-2766)ccA>ccT	p.P922P	RASA1_ENST00000506290.1_Silent_p.P756P|RASA1_ENST00000456692.2_Silent_p.P745P|RASA1_ENST00000512763.1_Silent_p.P755P	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	922	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		CAGATTCTCCATCTCCTATTG	0.363																																					p.P922P		Atlas-SNP	.											.	RASA1	213	.	0			c.A2766T						PASS	.	A	,	5,4401	8.1+/-20.4	0,5,2198	124.0	111.0	116.0		2766,2235	-1.5	1.0	5	dbSNP_134	116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	RASA1	NM_002890.2,NM_022650.2	,	0,5,6498	TT,TA,AA		0.0,0.1135,0.0384	,	922/1048,745/871	86681125	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5921	exon22			TTCTCCATCTCCT		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	9871	protein-coding gene	gene with protein product	"""capillary malformation-arteriovenous malformation"""	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.2766A>T	5.37:g.86681125A>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	68	0.557377	NM_002890	B2R6W3|Q9UDI1	Silent	SNP	ENST00000274376.6	37	CCDS34200.1																																																																																			A|1.000;G|0.000;T|0.000	0.000	strong		0.363	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890	
MRPL47	57129	hgsc.bcm.edu	37	3	179322385	179322385	+	Missense_Mutation	SNP	A	A	C	rs2339844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:179322385A>C	ENST00000476781.1	-	1	57	c.28T>G	c.(28-30)Tgt>Ggt	p.C10G	MRPL47_ENST00000259038.2_Missense_Mutation_p.C10G|MRPL47_ENST00000392659.2_5'UTR|NDUFB5_ENST00000259037.3_5'Flank|NDUFB5_ENST00000493866.1_5'Flank|NDUFB5_ENST00000472629.1_5'Flank	NM_020409.2	NP_065142.2	Q9HD33	RM47_HUMAN	mitochondrial ribosomal protein L47	10			C -> G (in dbSNP:rs2339844).		translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|stomach(1)	11	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			ACTCTCCTACAAAGAAGGGCC	0.537													A|||	605	0.120807	0.1044	0.1455	5008	,	,		18033	0.1002		0.0795	False		,,,				2504	0.1892				p.C10G		Atlas-SNP	.											.	MRPL47	31	.	0			c.T28G						PASS	.	A	GLY/CYS,	407,3999	196.7+/-221.0	18,371,1814	81.0	86.0	84.0		28,	5.1	0.1	3	dbSNP_100	84	675,7925	165.8+/-217.9	24,627,3649	yes	missense,utr-5	MRPL47	NM_020409.2,NM_177988.1	159,	42,998,5463	CC,CA,AA		7.8488,9.2374,8.3192	benign,	10/251,	179322385	1082,11924	2203	4300	6503	SO:0001583	missense	57129	exon1			TCCTACAAAGAAG	AF285120	CCDS3232.1, CCDS3233.1	3q26.33	2012-11-14			ENSG00000136522	ENSG00000136522		"""Mitochondrial ribosomal proteins / large subunits"""	16652	protein-coding gene	gene with protein product	"""nasopharyngeal carcinoma metastasis-related 1"""	611852				11551941	Standard	NM_177988		Approved	CGI-204, NCM1	uc003fjz.3	Q9HD33	OTTHUMG00000157784	ENST00000476781.1:c.28T>G	3.37:g.179322385A>C	ENSP00000417602:p.Cys10Gly	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_020409	Q6XRG1|Q8N5D1	Missense_Mutation	SNP	ENST00000476781.1	37	CCDS3232.1	228	0.1043956043956044	58	0.11788617886178862	52	0.143646408839779	60	0.1048951048951049	58	0.07651715039577836	A	12.62	1.991639	0.35131	0.092374	0.078488	ENSG00000136522	ENST00000476781;ENST00000259038	T;T	0.39406	1.08;1.26	5.12	5.12	0.69794	.	0.060494	0.64402	D	0.000003	T	0.00300	0.0009	L	0.47716	1.5	0.09310	P	0.9999999999979553	B;B	0.12013	0.005;0.002	B;B	0.09377	0.004;0.004	T	0.04440	-1.0951	9	0.41790	T	0.15	-3.5543	11.4895	0.50373	1.0:0.0:0.0:0.0	rs2339844;rs56483537;rs58924449;rs2339844	10;10	Q9HD33-2;Q9HD33	.;RM47_HUMAN	G	10	ENSP00000417602:C10G;ENSP00000259038:C10G	ENSP00000259038:C10G	C	-	1	0	MRPL47	180805079	0.393000	0.25237	0.146000	0.22360	0.029000	0.11900	2.637000	0.46553	2.276000	0.75962	0.528000	0.53228	TGT	A|0.897;C|0.103	0.103	strong		0.537	MRPL47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349623.1	NM_020409	
SP140L	93349	hgsc.bcm.edu	37	2	231256812	231256812	+	Silent	SNP	A	A	G	rs7559665|rs386656123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231256812A>G	ENST00000415673.2	+	12	1061	c.975A>G	c.(973-975)gcA>gcG	p.A325A	SP140L_ENST00000396563.4_Silent_p.A290A|SP140L_ENST00000243810.6_Silent_p.A325A|SP140L_ENST00000444636.1_Silent_p.A325A	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	325	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						GAACCTTGGCAAAGTGTATAC	0.502													G|||	1026	0.204872	0.1997	0.2248	5008	,	,		19277	0.0685		0.3221	False		,,,				2504	0.2178				p.A325A		Atlas-SNP	.											.	SP140L	68	.	0			c.A975G						PASS	.	G		848,3146		90,668,1239	105.0	111.0	109.0		975	1.6	0.0	2	dbSNP_116	109	2560,5820		384,1792,2014	no	coding-synonymous	SP140L	NM_138402.4		474,2460,3253	GG,GA,AA		30.5489,21.2318,27.5416		325/581	231256812	3408,8966	1997	4190	6187	SO:0001819	synonymous_variant	93349	exon12			CTTGGCAAAGTGT	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.975A>G	2.37:g.231256812A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	172	83	0.482558	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Silent	SNP	ENST00000415673.2	37	CCDS46538.1																																																																																			A|0.801;G|0.199	0.199	strong		0.502	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
PPP1R9A	55607	hgsc.bcm.edu	37	7	94540416	94540416	+	Missense_Mutation	SNP	A	A	G	rs10230714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:94540416A>G	ENST00000433881.1	+	2	1523	c.991A>G	c.(991-993)Atg>Gtg	p.M331V	PPP1R9A_ENST00000340694.4_Missense_Mutation_p.M331V|PPP1R9A_ENST00000289495.5_Missense_Mutation_p.M331V|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.M331V|PPP1R9A_ENST00000424654.1_Missense_Mutation_p.M331V|PPP1R9A_ENST00000456331.2_Missense_Mutation_p.M331V			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	331			M -> V (in dbSNP:rs10230714). {ECO:0000269|PubMed:15489334}.		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)			AAGTAAGGCAATGCCAAAGTC	0.478										HNSCC(28;0.073)			A|||	999	0.199481	0.3525	0.1455	5008	,	,		21564	0.2183		0.0507	False		,,,				2504	0.1646				p.M331V		Atlas-SNP	.											.	PPP1R9A	264	.	0			c.A991G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET	1416,2990	462.1+/-353.1	234,948,1021	81.0	83.0	83.0		991,991,991,991,991	0.3	0.1	7	dbSNP_119	83	360,8240	120.4+/-179.7	4,352,3944	yes	missense,missense,missense,missense,missense	PPP1R9A	NM_001166160.1,NM_001166161.1,NM_001166162.1,NM_001166163.1,NM_017650.2	21,21,21,21,21	238,1300,4965	GG,GA,AA		4.186,32.138,13.6552	benign,benign,benign,benign,benign	331/1375,331/1297,331/1254,331/1091,331/1099	94540416	1776,11230	2203	4300	6503	SO:0001583	missense	55607	exon2			AAGGCAATGCCAA	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.991A>G	7.37:g.94540416A>G	ENSP00000398870:p.Met331Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_017650	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Missense_Mutation	SNP	ENST00000433881.1	37	CCDS34683.1	354	0.1620879120879121	161	0.32723577235772355	46	0.1270718232044199	113	0.19755244755244755	34	0.044854881266490766	A	0.011	-1.732466	0.00687	0.32138	0.04186	ENSG00000158528	ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331	D;D;D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22;-3.22;-3.22	5.44	0.326	0.15908	.	0.531499	0.21465	N	0.074100	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0	T	0.06899	-1.0801	8	.	.	.	.	5.1681	0.15096	0.5831:0.0:0.2888:0.1281	rs10230714;rs61628310;rs10230714	331;331;331;331;331	B7ZLX4;F8W7J9;E9PDX1;E9PCK6;Q9ULJ8	.;.;.;.;NEB1_HUMAN	V	331	ENSP00000405514:M331V;ENSP00000344524:M331V;ENSP00000411342:M331V;ENSP00000398870:M331V;ENSP00000289495:M331V;ENSP00000402893:M331V	.	M	+	1	0	PPP1R9A	94378352	0.105000	0.21958	0.091000	0.20842	0.104000	0.19210	0.585000	0.23879	-0.028000	0.13850	-0.256000	0.11100	ATG	A|0.847;G|0.153	0.153	strong		0.478	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160	
PRPH2	5961	hgsc.bcm.edu	37	6	42666244	42666244	+	Splice_Site	SNP	A	A	C	rs140406696		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42666244A>C	ENST00000230381.5	-	3	1069	c.830T>G	c.(829-831)gTg>gGg	p.V277G		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	277					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			TGTAATGGTCACCTGGTGGTG	0.572													A|||	1	0.000199681	0.0008	0.0	5008	,	,		19706	0.0		0.0	False		,,,				2504	0.0				p.V277G		Atlas-SNP	.											.	PRPH2	47	.	0			c.T830G						PASS	.	A	GLY/VAL	5,4401	9.9+/-24.2	0,5,2198	74.0	73.0	73.0		830	5.0	0.9	6	dbSNP_134	73	0,8600		0,0,4300	yes	missense-near-splice	PRPH2	NM_000322.4	109	0,5,6498	CC,CA,AA		0.0,0.1135,0.0384	benign	277/347	42666244	5,13001	2203	4300	6503	SO:0001630	splice_region_variant	5961	exon3			ATGGTCACCTGGT		CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"""Tetraspanins"""	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"""retinal degeneration, slow (retinitis pigmentosa 7)"", ""retinal degeneration, slow"""	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.829-1T>G	6.37:g.42666244A>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.730591	0.48939	0.001135	0.0	ENSG00000112619	ENST00000230381	D	0.81739	-1.53	5.0	5.0	0.66597	.	0.243684	0.40818	N	0.001012	T	0.74261	0.3693	L	0.46157	1.445	0.58432	D	0.999993	P	0.41673	0.759	P	0.46585	0.521	T	0.79167	-0.1915	10	0.66056	D	0.02	.	14.6991	0.69145	1.0:0.0:0.0:0.0	.	277	P23942	PRPH2_HUMAN	G	277	ENSP00000230381:V277G	ENSP00000230381:V277G	V	-	2	0	PRPH2	42774222	0.998000	0.40836	0.926000	0.36857	0.031000	0.12232	4.115000	0.57865	1.858000	0.53909	0.533000	0.62120	GTG	A|1.000;C|0.000	0.000	weak		0.572	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322	Missense_Mutation
KIAA1683	80726	hgsc.bcm.edu	37	19	18376509	18376509	+	Missense_Mutation	SNP	G	G	A	rs16982285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18376509G>A	ENST00000600328.3	-	3	2034	c.1841C>T	c.(1840-1842)gCg>gTg	p.A614V	KIAA1683_ENST00000600359.3_Missense_Mutation_p.A568V|KIAA1683_ENST00000392413.4_Missense_Mutation_p.A614V			Q9H0B3	K1683_HUMAN	KIAA1683	614			A -> V (in dbSNP:rs16982285).			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GTCTGTTTTCGCCTGTTTCTG	0.562													A|||	738	0.147364	0.4297	0.1282	5008	,	,		20460	0.0129		0.0288	False		,,,				2504	0.0399				p.A614V		Atlas-SNP	.											KIAA1683_ENST00000392413,colon,carcinoma,0,2	KIAA1683	190	2	0			c.C1841T						PASS	.	A	VAL/ALA,VAL/ALA,VAL/ALA	1675,2731	654.3+/-399.7	321,1033,849	59.0	64.0	62.0		1841,1703,1841	-7.1	0.0	19	dbSNP_123	62	231,8369	808.4+/-407.2	4,223,4073	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	64,64,64	325,1256,4922	AA,AG,GG		2.686,38.0163,14.6548	benign,benign,benign	614/1368,568/1135,614/1181	18376509	1906,11100	2203	4300	6503	SO:0001583	missense	80726	exon3			GTTTTCGCCTGTT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1841C>T	19.37:g.18376509G>A	ENSP00000470780:p.Ala614Val	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	149	66	0.442953	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	278	0.12728937728937728	213	0.4329268292682927	48	0.13259668508287292	1	0.0017482517482517483	16	0.021108179419525065	A	1.743	-0.491261	0.04322	0.380163	0.02686	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634	T;T;T	0.03717	3.9;3.9;3.83	3.81	-7.09	0.01553	.	3.072470	0.01420	N	0.014343	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	0.48502	-0.9030	9	0.20046	T	0.44	-0.0309	4.2064	0.10490	0.1471:0.3414:0.3989:0.1126	rs16982285;rs16982285	614;614	E9PDE0;Q9H0B3	.;K1683_HUMAN	V	614;614;568	ENSP00000376213:A614V;ENSP00000352774:A614V;ENSP00000404501:A568V	ENSP00000352774:A614V	A	-	2	0	KIAA1683	18237509	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.555000	0.05999	-2.263000	0.00689	-2.747000	0.00125	GCG	G|0.854;A|0.146	0.146	strong		0.562	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
PSG3	5671	hgsc.bcm.edu	37	19	43244485	43244485	+	Missense_Mutation	SNP	G	G	C	rs11880551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43244485G>C	ENST00000327495.5	-	1	236	c.52C>G	c.(52-54)Ctc>Gtc	p.L18V	PSG3_ENST00000595140.1_Missense_Mutation_p.L18V|PSG3_ENST00000490592.1_5'Flank	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	18					defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				GTGAGCAGGAGCCCCTTCCAG	0.607													.|||	1206	0.240815	0.6377	0.1484	5008	,	,		17909	0.0585		0.0795	False		,,,				2504	0.1237				p.L18V		Atlas-SNP	.											.	PSG3	82	.	0			c.C52G						PASS	.	G	VAL/LEU	1675,1347		477,721,313	116.0	135.0	128.0		52	-2.0	0.0	19	dbSNP_120	128	420,4994		11,398,2298	no	missense	PSG3	NM_021016.3	32	488,1119,2611	CC,CG,GG		7.7577,44.5731,24.834	benign	18/429	43244485	2095,6341	1511	2707	4218	SO:0001583	missense	5671	exon1			GCAGGAGCCCCTT		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.52C>G	19.37:g.43244485G>C	ENSP00000332215:p.Leu18Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	37	CCDS12611.1	437	0.2000915750915751	278	0.5650406504065041	62	0.1712707182320442	31	0.05419580419580419	66	0.0870712401055409	N	4.028	0.002732	0.07866	0.554269	0.077577	ENSG00000221826	ENST00000327495	T	0.23754	1.89	1.21	-1.99	0.07457	.	.	.	.	.	T	0.00012	0.0000	L	0.31926	0.97	0.80722	P	0.0	B	0.21606	0.058	B	0.29440	0.102	T	0.44112	-0.9349	8	0.49607	T	0.09	.	2.6346	0.04954	0.229:0.3092:0.4617:0.0	rs11880551;rs60337351	18	Q16557	PSG3_HUMAN	V	18	ENSP00000332215:L18V	ENSP00000332215:L18V	L	-	1	0	PSG3	47936325	0.006000	0.16342	0.005000	0.12908	0.090000	0.18270	-0.178000	0.09782	-0.350000	0.08262	0.121000	0.15741	CTC	G|0.782;C|0.218	0.218	strong		0.607	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016	
SLC7A3	84889	hgsc.bcm.edu	37	X	70146475	70146475	+	Missense_Mutation	SNP	G	G	C	rs6525447	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70146475G>C	ENST00000374299.3	-	10	1666	c.1522C>G	c.(1522-1524)Ctg>Gtg	p.L508V	SLC7A3_ENST00000298085.4_Missense_Mutation_p.L508V			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	508			L -> V (in dbSNP:rs6525447). {ECO:0000269|PubMed:15489334}.		amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GCAGTCCACAGCAGGTCTCCA	0.517													C|||	1513	0.400795	0.4463	0.304	3775	,	,		14389	0.3512		0.0616	False		,,,				2504	0.3027				p.L508V		Atlas-SNP	.											.	SLC7A3	76	.	0			c.C1522G						PASS	.	C	VAL/LEU,VAL/LEU	2165,1669		533,772,327,327,243	45.0	37.0	40.0		1522,1522	4.2	1.0	X	dbSNP_116	40	638,6088		31,406,170,1991,1700	yes	missense,missense	SLC7A3	NM_001048164.2,NM_032803.5	32,32	564,1178,497,2318,1943	CC,CG,C,GG,G		9.4856,43.5316,26.5436	benign,benign	508/620,508/620	70146475	2803,7757	2202	4298	6500	SO:0001583	missense	84889	exon10			TCCACAGCAGGTC	AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"""Solute carriers"""	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.1522C>G	X.37:g.70146475G>C	ENSP00000363417:p.Leu508Val	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	192	191	0.994792	NM_032803	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Missense_Mutation	SNP	ENST00000374299.3	37	CCDS14404.1	575	0.3465943339361061	149	0.4281609195402299	77	0.275	115	0.279126213592233	34	0.04607046070460705	C	0.012	-1.681666	0.00745	0.564684	0.094856	ENSG00000165349	ENST00000374299;ENST00000298085	D;D	0.87571	-2.27;-2.27	5.01	4.15	0.48705	.	0.695584	0.14611	N	0.309011	T	0.00012	0.0000	N	0.00162	-1.95	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44174	-0.9345	9	0.12430	T	0.62	.	7.8134	0.29245	0.0:0.612:0.3015:0.0866	rs6525447;rs17265153;rs17856987;rs52796906;rs6525447	508	Q8WY07	CTR3_HUMAN	V	508	ENSP00000363417:L508V;ENSP00000298085:L508V	ENSP00000298085:L508V	L	-	1	2	SLC7A3	70063200	0.000000	0.05858	0.999000	0.59377	0.016000	0.09150	-0.142000	0.10311	0.632000	0.30432	-0.252000	0.11476	CTG	0|0.018;C|0.306	0.306	strong		0.517	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803	
ZBTB9	221504	hgsc.bcm.edu	37	6	33423698	33423698	+	Missense_Mutation	SNP	C	C	G	rs9469425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33423698C>G	ENST00000395064.2	+	2	1089	c.821C>G	c.(820-822)gCc>gGc	p.A274G		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	274	Pro-rich.		A -> G (in dbSNP:rs9469425).		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)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						GAGCTTCCTGCCCCTCCTGCA	0.567													C|||	344	0.0686901	0.2534	0.013	5008	,	,		19073	0.0		0.0	False		,,,				2504	0.0				p.A274G		Atlas-SNP	.											.	ZBTB9	23	.	0			c.C821G						PASS	.	C	GLY/ALA	876,3530	338.6+/-305.4	75,726,1402	58.0	61.0	60.0		821	4.4	0.1	6	dbSNP_119	60	8,8592	6.4+/-24.3	0,8,4292	yes	missense	ZBTB9	NM_152735.3	60	75,734,5694	GG,GC,CC		0.093,19.882,6.7969	possibly-damaging	274/474	33423698	884,12122	2203	4300	6503	SO:0001583	missense	221504	exon2			TTCCTGCCCCTCC	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.821C>G	6.37:g.33423698C>G	ENSP00000378503:p.Ala274Gly	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_152735	A2AB19	Missense_Mutation	SNP	ENST00000395064.2	37	CCDS4780.1	139	0.06364468864468864	136	0.2764227642276423	3	0.008287292817679558	0	0.0	0	0.0	C	6.353	0.433225	0.12045	0.19882	9.3E-4	ENSG00000213588	ENST00000395064	T	0.07114	3.22	5.28	4.39	0.52855	.	3.470690	0.02755	U	0.117890	T	0.03095	0.0091	L	0.29908	0.895	0.54753	P	1.6000000000016E-5	B	0.24186	0.099	B	0.22601	0.04	T	0.30937	-0.9961	9	0.33940	T	0.23	.	11.5797	0.50883	0.0:0.8205:0.1795:0.0	rs9469425	274	Q96C00	ZBTB9_HUMAN	G	274	ENSP00000378503:A274G	ENSP00000378503:A274G	A	+	2	0	ZBTB9	33531676	0.051000	0.20477	0.114000	0.21550	0.988000	0.76386	1.337000	0.33862	1.419000	0.47118	0.655000	0.94253	GCC	C|0.921;G|0.079	0.079	strong		0.567	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735	
OR5B3	441608	hgsc.bcm.edu	37	11	58170342	58170342	+	Missense_Mutation	SNP	C	C	T	rs11229411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58170342C>T	ENST00000309403.2	-	1	540	c.541G>A	c.(541-543)Gca>Aca	p.A181T		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	181			A -> T (in dbSNP:rs11229411).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A181T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ACCATGACTGCTGGAATATCA	0.408													C|||	1453	0.290136	0.3533	0.2695	5008	,	,		23137	0.1448		0.3628	False		,,,				2504	0.2945				p.A181T		Atlas-SNP	.											OR5B3,NS,carcinoma,0,1	OR5B3	65	1	1	Substitution - Missense(1)	stomach(1)	c.G541A						PASS	.	C	THR/ALA	1442,2960	467.6+/-354.9	229,984,988	98.0	91.0	94.0		541	3.0	1.0	11	dbSNP_120	94	3095,5495	473.1+/-368.5	550,1995,1750	yes	missense	OR5B3	NM_001005469.1	58	779,2979,2738	TT,TC,CC		36.0303,32.7578,34.9215	possibly-damaging	181/315	58170342	4537,8455	2201	4295	6496	SO:0001583	missense	441608	exon1			TGACTGCTGGAAT	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.541G>A	11.37:g.58170342C>T	ENSP00000308270:p.Ala181Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	656	0.30036630036630035	195	0.39634146341463417	89	0.24585635359116023	95	0.1660839160839161	277	0.3654353562005277	c	13.88	2.369354	0.42003	0.327578	0.360303	ENSG00000172769	ENST00000309403	T	0.00130	8.69	4.05	3.04	0.35103	GPCR, rhodopsin-like superfamily (1);	0.146062	0.31976	N	0.006773	T	0.00012	0.0000	M	0.73962	2.25	0.46564	P	8.979999999999544E-4	D	0.56968	0.978	P	0.59825	0.864	T	0.34976	-0.9807	9	0.87932	D	0	-35.6255	10.4344	0.44426	0.0:0.6318:0.3682:0.0	rs11229411;rs61524907;rs11229411	181	Q8NH48	OR5B3_HUMAN	T	181	ENSP00000308270:A181T	ENSP00000308270:A181T	A	-	1	0	OR5B3	57926918	0.000000	0.05858	0.999000	0.59377	0.105000	0.19272	-0.039000	0.12124	2.264000	0.75181	0.650000	0.86243	GCA	C|0.676;T|0.324	0.324	strong		0.408	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
NRAP	4892	hgsc.bcm.edu	37	10	115412793	115412793	+	Silent	SNP	A	A	G	rs3737322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115412793A>G	ENST00000359988.3	-	6	715	c.471T>C	c.(469-471)taT>taC	p.Y157Y	NRAP_ENST00000369360.3_Silent_p.Y157Y|NRAP_ENST00000369358.4_Silent_p.Y157Y|NRAP_ENST00000360478.3_Silent_p.Y157Y	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		AGTCTTCTGTATATTCCTGTT	0.443													A|||	1543	0.308107	0.4887	0.2378	5008	,	,		16745	0.2173		0.2664	False		,,,				2504	0.2505				p.Y157Y		Atlas-SNP	.											.	NRAP	208	.	0			c.T471C						PASS	.	A	,	1969,2435		499,971,732	157.0	139.0	145.0		471,471	-1.3	0.2	10	dbSNP_107	145	2390,6210		336,1718,2246	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	835,2689,2978	GG,GA,AA		27.7907,44.7094,33.5205	,	157/1696,157/1731	115412793	4359,8645	2202	4300	6502	SO:0001819	synonymous_variant	4892	exon6			TTCTGTATATTCC		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.471T>C	10.37:g.115412793A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	126	54	0.428571	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			A|0.676;G|0.324	0.324	strong		0.443	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
N4BP2L2	10443	hgsc.bcm.edu	37	13	33017158	33017158	+	Missense_Mutation	SNP	G	G	T	rs17077569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33017158G>T	ENST00000504114.1	-	6	1562	c.1471C>A	c.(1471-1473)Cgt>Agt	p.R491S	N4BP2L2_ENST00000399396.3_Missense_Mutation_p.R506S|N4BP2L2_ENST00000357505.6_Missense_Mutation_p.R491S|N4BP2L2_ENST00000380121.3_5'UTR|N4BP2L2_ENST00000446957.2_Intron			Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	427					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		ACACCGATACGACTCTGTCCT	0.323													G|||	245	0.0489217	0.1543	0.0159	5008	,	,		19508	0.0		0.0219	False		,,,				2504	0.0082				p.R506S		Atlas-SNP	.											N4BP2L2_ENST00000399396,NS,carcinoma,0,3	N4BP2L2	90	3	0			c.C1516A						PASS	.	G	SER/ARG	445,3187		19,407,1390	122.0	111.0	114.0		1516	-0.2	0.0	13	dbSNP_123	114	193,7957		3,187,3885	yes	missense	N4BP2L2	NM_033111.3	110	22,594,5275	TT,TG,GG		2.3681,12.2522,5.415	benign	506/753	33017158	638,11144	1816	4075	5891	SO:0001583	missense	10443	exon7			CGATACGACTCTG	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"""phosphonoformate immuno-associated protein 5"""	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000504114.1:c.1471C>A	13.37:g.33017158G>T	ENSP00000427477:p.Arg491Ser	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	160	84	0.525	NM_033111	A3KME8	Missense_Mutation	SNP	ENST00000504114.1	37		90	0.04120879120879121	72	0.14634146341463414	6	0.016574585635359115	0	0.0	12	0.0158311345646438	G	1.068	-0.670648	0.03403	0.122522	0.023681	ENSG00000139617;ENSG00000139617;ENSG00000244754;ENSG00000244754;ENSG00000244754	ENST00000380121;ENST00000503296;ENST00000504114;ENST00000357505;ENST00000399396	.	.	.	5.45	-0.214	0.13161	.	2.318410	0.01623	N	0.023131	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.14012	0.009;0.009;0.009;0.009	B;B;B;B	0.14023	0.01;0.006;0.01;0.01	T	0.14090	-1.0485	8	0.13470	T	0.59	-0.3124	1.3036	0.02084	0.198:0.1598:0.402:0.2402	rs17077569;rs52835694;rs17077569	491;506;389;389	B4DPY1;Q92802-3;Q96KV2;Q9Y3H6	.;.;.;.	S	389;418;491;491;506	.	ENSP00000350104:R491S	R	-	1	0	N4BP2L2;RP11-298P3.4	31915158	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.165000	0.16564	-0.067000	0.12976	0.650000	0.86243	CGT	G|0.943;T|0.057	0.057	strong		0.323	N4BP2L2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000361380.1	NM_014887	
TSC22D1	8848	hgsc.bcm.edu	37	13	45148257	45148257	+	Missense_Mutation	SNP	G	G	A	rs9525983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:45148257G>A	ENST00000458659.2	-	1	2444	c.1954C>T	c.(1954-1956)Cct>Tct	p.P652S	TSC22D1_ENST00000501704.2_Intron|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	652	Gln-rich.		P -> S (in dbSNP:rs9525983).		negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		TCTGAAGCAGGATTTTGAGTC	0.502													G|||	251	0.0501198	0.0068	0.0922	5008	,	,		22808	0.001		0.1173	False		,,,				2504	0.0603				p.P652S		Atlas-SNP	.											.	TSC22D1	88	.	0			c.C1954T						PASS	.	G	SER/PRO	105,4301	81.4+/-119.9	1,103,2099	108.0	103.0	105.0		1954	1.0	0.0	13	dbSNP_119	105	1063,7537	222.2+/-259.3	71,921,3308	yes	missense	TSC22D1	NM_183422.3	74	72,1024,5407	AA,AG,GG		12.3605,2.3831,8.9805	benign	652/1074	45148257	1168,11838	2203	4300	6503	SO:0001583	missense	8848	exon1			AAGCAGGATTTTG	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.1954C>T	13.37:g.45148257G>A	ENSP00000397435:p.Pro652Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	159	83	0.522013	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	37	CCDS31966.1	115	0.052655677655677656	5	0.01016260162601626	19	0.052486187845303865	0	0.0	91	0.12005277044854881	G	0.004	-2.318264	0.00235	0.023831	0.123605	ENSG00000102804	ENST00000458659	T	0.31510	1.49	4.74	0.994	0.19832	.	0.346611	0.25065	N	0.033401	T	0.00178	0.0005	N	0.12746	0.255	0.18873	N	0.999983	B	0.06786	0.001	B	0.06405	0.002	T	0.24621	-1.0155	10	0.06099	T	0.92	.	4.4964	0.11839	0.4158:0.1625:0.4217:0.0	rs9525983;rs52835504;rs60681641;rs9525983	652	Q15714	T22D1_HUMAN	S	652	ENSP00000397435:P652S	ENSP00000397435:P652S	P	-	1	0	TSC22D1	44046257	0.770000	0.28543	0.034000	0.17996	0.868000	0.49771	0.937000	0.28951	0.239000	0.21243	-0.320000	0.08662	CCT	G|0.926;A|0.074	0.074	strong		0.502	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022	
CPA5	93979	hgsc.bcm.edu	37	7	130007381	130007381	+	Missense_Mutation	SNP	T	T	C	rs11761888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:130007381T>C	ENST00000485477.1	+	10	2136	c.1007T>C	c.(1006-1008)tTg>tCg	p.L336S	CPA5_ENST00000355388.3_Missense_Mutation_p.L336S|CPA5_ENST00000461828.1_Missense_Mutation_p.L336S|CPA5_ENST00000466363.2_Missense_Mutation_p.L336S|CPA5_ENST00000393213.3_Missense_Mutation_p.L336S|CPA5_ENST00000474905.1_Missense_Mutation_p.L336S|CPA5_ENST00000431780.2_Missense_Mutation_p.L336S			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	336			L -> S (in dbSNP:rs11761888). {ECO:0000269|PubMed:11920156, ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					TACGGCCGATTGCTGGAGCCC	0.517													C|||	1014	0.202476	0.4259	0.1225	5008	,	,		18328	0.0258		0.2048	False		,,,				2504	0.137				p.L336S		Atlas-SNP	.											.	CPA5	61	.	0			c.T1007C						PASS	.	C	SER/LEU,SER/LEU,SER/LEU	1672,2734	655.8+/-400.0	307,1058,838	124.0	118.0	120.0		1007,1007,1007	3.7	0.3	7	dbSNP_120	120	1854,6746	730.2+/-406.8	202,1450,2648	yes	missense,missense,missense	CPA5	NM_001127441.1,NM_001127442.1,NM_080385.4	145,145,145	509,2508,3486	CC,CT,TT		21.5581,37.9483,27.1106	benign,benign,benign	336/437,336/404,336/437	130007381	3526,9480	2203	4300	6503	SO:0001583	missense	93979	exon11			GCCGATTGCTGGA	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.1007T>C	7.37:g.130007381T>C	ENSP00000420237:p.Leu336Ser	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	314	144	0.458599	NM_080385	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	37	CCDS5819.1	417	0.19093406593406592	198	0.4024390243902439	46	0.1270718232044199	12	0.02097902097902098	161	0.21240105540897097	C	2.814	-0.246343	0.05867	0.379483	0.215581	ENSG00000158525	ENST00000355388;ENST00000461828;ENST00000466363;ENST00000485477;ENST00000431780;ENST00000474905;ENST00000393213	T;T;T;T;T;T;T	0.02656	4.21;4.21;4.21;4.21;4.21;4.21;4.21	5.61	3.73	0.42828	Peptidase M14, carboxypeptidase A (2);	0.780103	0.11283	N	0.580123	T	0.00012	0.0000	N	0.00053	-2.385	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40059	-0.9583	8	.	.	.	.	4.6819	0.12739	0.2065:0.5242:0.1911:0.0783	rs11761888;rs17857277;rs61540978;rs11761888	336;336	G3V0G8;Q8WXQ8	.;CBPA5_HUMAN	S	336	ENSP00000347549:L336S;ENSP00000418183:L336S;ENSP00000419025:L336S;ENSP00000420237:L336S;ENSP00000393045:L336S;ENSP00000417314:L336S;ENSP00000376907:L336S	.	L	+	2	0	CPA5	129794617	0.736000	0.28164	0.289000	0.24876	0.002000	0.02628	0.926000	0.28804	1.389000	0.46526	-0.355000	0.07637	TTG	C|0.239;T|0.761	0.239	strong		0.517	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441	
SPP1	6696	hgsc.bcm.edu	37	4	88903774	88903774	+	Missense_Mutation	SNP	G	G	A	rs7435825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88903774G>A	ENST00000395080.3	+	7	798	c.671G>A	c.(670-672)aGt>aAt	p.S224N	SPP1_ENST00000237623.7_Missense_Mutation_p.S210N|SPP1_ENST00000360804.4_Missense_Mutation_p.S197N|SPP1_ENST00000509659.1_3'UTR	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	224			S -> N (in dbSNP:rs7435825).		biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|negative regulation of collateral sprouting of intact axon in response to injury (GO:0048685)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell-substrate adhesion (GO:0010811)|response to steroid hormone (GO:0048545)|response to vitamin D (GO:0033280)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix binding (GO:0050840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		GGGAAGGACAGTTATGAAACG	0.517													G|||	253	0.0505192	0.1861	0.0101	5008	,	,		19566	0.0		0.0	False		,,,				2504	0.0				p.S237N		Atlas-SNP	.											.	SPP1	35	.	0			c.G710A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	628,3778	269.2+/-268.9	47,534,1622	158.0	145.0	149.0		629,671,590	4.0	0.6	4	dbSNP_116	149	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense	SPP1	NM_000582.2,NM_001040058.1,NM_001040060.1	46,46,46	47,538,5918	AA,AG,GG		0.0465,14.2533,4.8593	probably-damaging,probably-damaging,probably-damaging	210/301,224/315,197/288	88903774	632,12374	2203	4300	6503	SO:0001583	missense	6696	exon8			AGGACAGTTATGA		CCDS3626.1, CCDS34027.1, CCDS43250.1	4q22.1	2014-01-30	2008-07-31		ENSG00000118785	ENSG00000118785		"""Endogenous ligands"""	11255	protein-coding gene	gene with protein product	"""early T-lymphocyte activation 1"""	166490	"""osteopontin"", ""bone sialoprotein I"""	BNSP, OPN		1575754	Standard	NM_001251829		Approved	BSPI, ETA-1	uc003hra.3	P10451	OTTHUMG00000130599	ENST00000395080.3:c.671G>A	4.37:g.88903774G>A	ENSP00000378517:p.Ser224Asn	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	182	85	0.467033	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Missense_Mutation	SNP	ENST00000395080.3	37	CCDS43250.1	94	0.04304029304029304	92	0.18699186991869918	2	0.0055248618784530384	0	0.0	0	0.0	G	15.46	2.840614	0.51057	0.142533	4.65E-4	ENSG00000118785	ENST00000359072;ENST00000535912;ENST00000237623;ENST00000395080;ENST00000360804;ENST00000508233	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	4.84	3.99	0.46301	.	0.332965	0.27563	N	0.018811	T	0.00073	0.0002	L	0.61218	1.895	0.33157	P	0.453592	P;B;P;B;P	0.41366	0.747;0.003;0.594;0.006;0.594	B;B;B;B;B	0.42771	0.397;0.011;0.261;0.028;0.261	T	0.08066	-1.0740	9	0.72032	D	0.01	.	9.3187	0.37950	0.1012:0.0:0.8988:0.0	rs7435825;rs52832944;rs7435825	237;183;210;197;224	B7Z351;Q3LGB0;B2RDA1;Q567T5;P10451	.;.;.;.;OSTP_HUMAN	N	202;183;210;224;197;183	ENSP00000237623:S210N;ENSP00000378517:S224N;ENSP00000354042:S197N;ENSP00000422973:S183N	ENSP00000237623:S210N	S	+	2	0	SPP1	89122798	0.999000	0.42202	0.648000	0.29521	0.342000	0.28953	1.862000	0.39448	1.159000	0.42565	0.453000	0.30009	AGT	G|0.958;A|0.042	0.042	strong		0.517	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3		
LLGL2	3993	hgsc.bcm.edu	37	17	73566469	73566469	+	Missense_Mutation	SNP	C	C	T	rs150412778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73566469C>T	ENST00000392550.3	+	16	2032	c.1915C>T	c.(1915-1917)Cca>Tca	p.P639S	LLGL2_ENST00000577200.1_Missense_Mutation_p.P639S|LLGL2_ENST00000167462.5_Missense_Mutation_p.P639S	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	639					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CTTGGAGGGCCCACTCTCCCG	0.682													C|||	35	0.00698882	0.0265	0.0	5008	,	,		16144	0.0		0.0	False		,,,				2504	0.0				p.P639S		Atlas-SNP	.											.	LLGL2	155	.	0			c.C1915T						PASS	.	C	SER/PRO,SER/PRO	109,4289	78.3+/-116.7	1,107,2091	34.0	29.0	31.0		1915,1915	4.9	1.0	17	dbSNP_134	31	1,8591		0,1,4295	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	74,74	1,108,6386	TT,TC,CC		0.0116,2.4784,0.8468	probably-damaging,probably-damaging	639/1021,639/1016	73566469	110,12880	2199	4296	6495	SO:0001583	missense	3993	exon16			GAGGGCCCACTCT	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1915C>T	17.37:g.73566469C>T	ENSP00000376333:p.Pro639Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	104	58	0.557692	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	C	15.72	2.916820	0.52546	0.024784	1.16E-4	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.56611	0.45;0.45	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.52075	0.1712	M	0.77103	2.36	0.80722	D	1	P;D;D;D;P	0.89917	0.729;1.0;1.0;0.959;0.931	P;D;D;P;P	0.91635	0.544;0.997;0.999;0.835;0.688	T	0.70296	-0.4911	10	0.56958	D	0.05	4.4938	18.2389	0.89960	0.0:1.0:0.0:0.0	.	266;628;628;639;639	B4DVR9;B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;.;L2GL2_HUMAN	S	639;639;628	ENSP00000167462:P639S;ENSP00000376333:P639S	ENSP00000167462:P639S	P	+	1	0	LLGL2	71078064	1.000000	0.71417	0.996000	0.52242	0.660000	0.38997	7.766000	0.85320	2.314000	0.78098	0.549000	0.68633	CCA	C|0.989;T|0.011	0.011	strong		0.682	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259822	71259822	+	Missense_Mutation	SNP	A	A	G	rs10792769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71259822A>G	ENST00000528743.2	+	1	357	c.119A>G	c.(118-120)tAc>tGc	p.Y40C		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	40	8 X 4 AA repeats of C-C-X-P.		Y -> C (in dbSNP:rs10792769). {ECO:0000269|Ref.3}.		epidermis development (GO:0008544)	keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						GCACCCGTCTACTGCTGCAAG	0.662													N|||	989	0.197484	0.4062	0.1455	5008	,	,		17872	0.1329		0.1362	False		,,,				2504	0.0818				p.Y40C		Atlas-SNP	.											.	KRTAP5-9	19	.	0			c.A119G						PASS	.	G	CYS/TYR	1598,2802		316,966,918	83.0	94.0	90.0		119	1.6	0.9	11	dbSNP_120	90	1063,7525		68,927,3299	no	missense	KRTAP5-9	NM_005553.3	194	384,1893,4217	GG,GA,AA		12.3777,36.3182,20.4881	benign	40/170	71259822	2661,10327	2200	4294	6494	SO:0001583	missense	3846	exon1			CCGTCTACTGCTG	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.119A>G	11.37:g.71259822A>G	ENSP00000431443:p.Tyr40Cys	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	329	327	0.993921	NM_005553	Q14564|Q3MIP8	Missense_Mutation	SNP	ENST00000528743.2	37	CCDS53677.1	400	0.18315018315018314	178	0.3617886178861789	51	0.1408839779005525	70	0.12237762237762238	101	0.13324538258575197	N	6.676	0.493371	0.12702	0.363182	0.123777	ENSG00000254997	ENST00000528743	T	0.02579	4.24	1.57	1.57	0.23409	.	.	.	.	.	T	0.00012	0.0000	N	0.00004	-3.37	0.48236	P	3.8800000000005497E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.42982	-0.9419	8	0.02654	T	1	.	4.1148	0.10076	0.3975:0.0:0.6025:0.0	rs10792769;rs10792769	40	P26371	KRA59_HUMAN	C	40	ENSP00000431443:Y40C	ENSP00000431443:Y40C	Y	+	2	0	KRTAP5-9	70937470	0.994000	0.37717	0.931000	0.37212	0.616000	0.37450	0.754000	0.26390	0.236000	0.21180	-0.391000	0.06502	TAC	A|0.819;G|0.181	0.181	strong		0.662	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
MICA	100507436	hgsc.bcm.edu	37	6	31379802	31379802	+	Missense_Mutation	SNP	A	A	G	rs41546915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31379802A>G	ENST00000449934.2	+	4	746	c.692A>G	c.(691-693)tAt>tGt	p.Y231C	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)				TCCAGCTTCTATCCCCGGAAT	0.587													a|||	3	0.000599042	0.0023	0.0	5008	,	,		19291	0.0		0.0	False		,,,				2504	0.0				p.Y231C		Atlas-SNP	.											.	MICA	21	.	0			c.A692G						PASS	.						18.0	22.0	21.0					6																	31379802		692	1591	2283	SO:0001583	missense	100507436	exon4			GCTTCTATCCCCG	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.692A>G	6.37:g.31379802A>G	ENSP00000413079:p.Tyr231Cys	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	a	12.79	2.044981	0.36085	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.04317	3.65;3.65	2.38	-2.63	0.06133	.	1.496520	0.04824	N	0.437454	T	0.13586	0.0329	H	0.95294	3.65	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.06807	-1.0806	10	0.87932	D	0	.	3.1987	0.06643	0.4334:0.1971:0.0:0.3695	rs41546915	93;231	Q5SS58;Q96QC4	.;.	C	93;231;188;231;122	ENSP00000413079:Y231C;ENSP00000402410:Y122C	ENSP00000365394:Y231C	Y	+	2	0	MICA	31487781	0.626000	0.27120	0.004000	0.12327	0.037000	0.13140	-0.027000	0.12371	-0.196000	0.10366	0.365000	0.22127	TAT	.	.	weak		0.587	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
VWDE	221806	hgsc.bcm.edu	37	7	12433347	12433347	+	Missense_Mutation	SNP	C	C	T	rs17165995	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12433347C>T	ENST00000275358.3	-	2	304	c.116G>A	c.(115-117)cGt>cAt	p.R39H		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	39						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TGAGTCAAAACGGACACTTCT	0.458													T|||	992	0.198083	0.3956	0.1167	5008	,	,		16938	0.126		0.1123	False		,,,				2504	0.1513				p.R39H		Atlas-SNP	.											.	VWDE	123	.	0			c.G116A						PASS	.	T	HIS/ARG	489,895		86,317,289	69.0	63.0	65.0		116	2.5	0.1	7	dbSNP_123	65	399,2783		24,351,1216	yes	missense	VWDE	NM_001135924.1	29	110,668,1505	TT,TC,CC		12.5393,35.3324,19.4481	benign	39/1591	12433347	888,3678	692	1591	2283	SO:0001583	missense	221806	exon2			TCAAAACGGACAC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.116G>A	7.37:g.12433347C>T	ENSP00000275358:p.Arg39His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	432	0.1978021978021978	208	0.42276422764227645	44	0.12154696132596685	87	0.1520979020979021	93	0.12269129287598944	T	0.432	-0.902961	0.02453	0.353324	0.125393	ENSG00000146530	ENST00000275358;ENST00000541006	T	0.63744	-0.06	4.87	2.49	0.30216	.	0.808953	0.11671	N	0.540894	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	0.43589	-0.9382	9	0.27785	T	0.31	.	6.0796	0.19935	0.0:0.1447:0.1375:0.7179	rs17165995;rs52826585;rs57756323;rs17165995	39	Q8N2E2	VWDE_HUMAN	H	39	ENSP00000275358:R39H	ENSP00000275358:R39H	R	-	2	0	VWDE	12399872	0.699000	0.27786	0.095000	0.20976	0.700000	0.40528	1.139000	0.31504	0.061000	0.16311	-0.254000	0.11334	CGT	C|0.794;T|0.206	0.206	strong		0.458	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50667859	50667859	+	Silent	SNP	A	A	G	rs6010211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50667859A>G	ENST00000248846.5	-	4	1368	c.1264T>C	c.(1264-1266)Ttg>Ctg	p.L422L	TUBGCP6_ENST00000439308.2_Silent_p.L422L			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	422					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)		TTGCTGTACAAAGAGTCCAGG	0.567													A|||	297	0.0593051	0.2171	0.0144	5008	,	,		20076	0.0		0.0	False		,,,				2504	0.0				p.L422L		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.T1264C						PASS	.	A		817,3585	317.4+/-295.1	79,659,1463	78.0	57.0	64.0		1264	-2.6	0.0	22	dbSNP_114	64	0,8600		0,0,4300	no	coding-synonymous	TUBGCP6	NM_020461.3		79,659,5763	GG,GA,AA		0.0,18.5597,6.2836		422/1820	50667859	817,12185	2201	4300	6501	SO:0001819	synonymous_variant	85378	exon4			TGTACAAAGAGTC	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.1264T>C	22.37:g.50667859A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	208	86	0.413462	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																			A|0.936;G|0.064	0.064	strong		0.567	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
MICAL1	64780	hgsc.bcm.edu	37	6	109768295	109768295	+	Silent	SNP	G	G	A	rs910730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	72	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	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	
COL15A1	1306	hgsc.bcm.edu	37	9	101748356	101748356	+	Missense_Mutation	SNP	A	A	G	rs2075663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101748356A>G	ENST00000375001.3	+	3	1033	c.610A>G	c.(610-612)Atg>Gtg	p.M204V		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	204	Laminin G-like.		M -> V (in dbSNP:rs2075663). {ECO:0000269|PubMed:8307960}.		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)				TGGAATCTTCATGGGCAATGC	0.552													G|||	3019	0.602835	0.8064	0.5447	5008	,	,		18380	0.5853		0.4155	False		,,,				2504	0.5798				p.M204V		Atlas-SNP	.											.	COL15A1	211	.	0			c.A610G						PASS	.	G	VAL/MET	3291,1115		1231,829,143	32.0	34.0	34.0		610	4.3	1.0	9	dbSNP_96	34	3228,5370		616,1996,1687	yes	missense	COL15A1	NM_001855.3	21	1847,2825,1830	GG,GA,AA		37.5436,25.3064,49.8693	benign	204/1389	101748356	6519,6485	2203	4299	6502	SO:0001583	missense	1306	exon3			ATCTTCATGGGCA	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.610A>G	9.37:g.101748356A>G	ENSP00000364140:p.Met204Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	1226	0.5613553113553114	396	0.8048780487804879	172	0.47513812154696133	339	0.5926573426573427	319	0.420844327176781	G	10.07	1.249435	0.22880	0.746936	0.375436	ENSG00000204291	ENST00000375001;ENST00000536083	T	0.71222	-0.55	5.25	4.34	0.51931	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.061993	0.64402	N	0.000004	T	0.00012	0.0000	N	0.00024	-2.69	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44802	-0.9304	9	0.02654	T	1	-11.6491	8.8377	0.35121	0.08:0.0:0.7714:0.1485	rs2075663;rs2229801;rs4742754;rs17711315;rs57249290;rs4742754	204;174	P39059;B3KTP7	COFA1_HUMAN;.	V	204;174	ENSP00000364140:M204V	ENSP00000364140:M204V	M	+	1	0	COL15A1	100788177	1.000000	0.71417	0.998000	0.56505	0.703000	0.40648	4.927000	0.63440	0.704000	0.31869	-0.128000	0.14901	ATG	A|0.472;C|0.000;G|0.528	0.528	strong		0.552	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
KIF16B	55614	hgsc.bcm.edu	37	20	16352401	16352401	+	Missense_Mutation	SNP	T	T	C	rs8123195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:16352401T>C	ENST00000354981.2	-	21	3513	c.3356A>G	c.(3355-3357)aAt>aGt	p.N1119S	KIF16B_ENST00000355755.3_Missense_Mutation_p.N1119S|KIF16B_ENST00000378003.2_Missense_Mutation_p.N345S|KIF16B_ENST00000408042.1_Missense_Mutation_p.N1119S	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	1119			N -> S (in dbSNP:rs8123195).		ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						AATGTAAGCATTGATCCTGTA	0.453													T|||	292	0.0583067	0.1717	0.0274	5008	,	,		19239	0.001		0.0099	False		,,,				2504	0.0358				p.N1119S		Atlas-SNP	.											.	KIF16B	305	.	0			c.A3356G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	765,3641	311.4+/-292.0	66,633,1504	164.0	136.0	145.0		3203,3356,3356	-3.9	0.9	20	dbSNP_116	145	51,8549	32.3+/-84.9	0,51,4249	yes	missense,missense,missense	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	46,46,46	66,684,5753	CC,CT,TT		0.593,17.3627,6.274	benign,benign,benign	1068/1267,1119/1393,1119/1318	16352401	816,12190	2203	4300	6503	SO:0001583	missense	55614	exon21			TAAGCATTGATCC	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.3356A>G	20.37:g.16352401T>C	ENSP00000347076:p.Asn1119Ser	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_001199866	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	93	0.042582417582417584	81	0.16463414634146342	6	0.016574585635359115	0	0.0	6	0.0079155672823219	T	11.33	1.605795	0.28623	0.173627	0.00593	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000378003;ENST00000408042	T;T;T;T	0.72282	-0.62;-0.64;2.42;-0.64	5.8	-3.88	0.04205	.	0.422796	0.28718	N	0.014372	T	0.00178	0.0005	N	0.12471	0.22	0.42344	P	0.007653000000000021	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.12156	0.007;0.003;0.001	T	0.03403	-1.1040	9	0.24483	T	0.36	.	12.6412	0.56711	0.0:0.4037:0.0:0.5963	rs8123195;rs52832260;rs8123195	1119;1119;1119	Q96L93-2;Q96L93-6;Q96L93	.;.;KI16B_HUMAN	S	1119;1119;963;345;1119	ENSP00000347076:N1119S;ENSP00000347995:N1119S;ENSP00000367242:N345S;ENSP00000384164:N1119S	ENSP00000347076:N1119S	N	-	2	0	KIF16B	16300401	0.999000	0.42202	0.900000	0.35374	0.928000	0.56348	0.441000	0.21611	-1.084000	0.03092	-0.263000	0.10527	AAT	T|0.940;C|0.060	0.060	strong		0.453	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
SEMA5A	9037	hgsc.bcm.edu	37	5	9044674	9044674	+	Silent	SNP	G	G	A	rs11741186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:9044674G>A	ENST00000382496.5	-	22	3581	c.2916C>T	c.(2914-2916)atC>atT	p.I972I	CTD-2215L10.1_ENST00000506519.1_RNA	NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	972					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GCCCCACGGCGATCATGTGGA	0.527													G|||	198	0.0395367	0.1309	0.0115	5008	,	,		17614	0.0		0.0159	False		,,,				2504	0.001				p.I972I		Atlas-SNP	.											.	SEMA5A	236	.	0			c.C2916T						PASS	.	G		495,3911	228.1+/-243.1	23,449,1731	87.0	81.0	83.0		2916	-10.3	0.0	5	dbSNP_120	83	180,8420	82.3+/-144.9	3,174,4123	no	coding-synonymous	SEMA5A	NM_003966.2		26,623,5854	AA,AG,GG		2.093,11.2347,5.1899		972/1075	9044674	675,12331	2203	4300	6503	SO:0001819	synonymous_variant	9037	exon22			CACGGCGATCATG	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.2916C>T	5.37:g.9044674G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	52	0.553191	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																			G|0.950;A|0.050	0.050	strong		0.527	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
MACC1	346389	hgsc.bcm.edu	37	7	20198440	20198440	+	Missense_Mutation	SNP	G	G	A	rs975263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20198440G>A	ENST00000400331.5	-	5	1852	c.1544C>T	c.(1543-1545)tCg>tTg	p.S515L	MACC1_ENST00000332878.4_Missense_Mutation_p.S515L|MACC1_ENST00000589011.1_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	108	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	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	
MADCAM1	8174	hgsc.bcm.edu	37	19	498524	498524	+	Silent	SNP	A	A	G	rs2302217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:498524A>G	ENST00000215637.3	+	3	412	c.366A>G	c.(364-366)ccA>ccG	p.P122P	MADCAM1_ENST00000587541.1_Intron|MADCAM1_ENST00000382683.4_Silent_p.P27P|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Silent_p.P122P	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	122	Ig-like 2.				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)		CCGTCTCCCCAGCAGCCCTGG	0.706													G|||	3173	0.633586	0.826	0.438	5008	,	,		12677	0.753		0.4563	False		,,,				2504	0.5716				p.P122P		Atlas-SNP	.											MADCAM1,NS,carcinoma,0,1	MADCAM1	29	1	0			c.A366G						scavenged	.	G	,	3385,1019		1317,751,134	24.0	32.0	29.0		366,366	-8.3	0.0	19	dbSNP_100	29	3942,4656		931,2080,1288	no	coding-synonymous,coding-synonymous	MADCAM1	NM_130760.2,NM_130762.2	,	2248,2831,1422	GG,GA,AA		45.8479,23.1381,43.6471	,	122/383,122/296	498524	7327,5675	2202	4299	6501	SO:0001819	synonymous_variant	8174	exon3			CTCCCCAGCAGCC	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.366A>G	19.37:g.498524A>G		Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Silent	SNP	ENST00000215637.3	37	CCDS12028.1																																																																																			A|0.429;G|0.571	0.571	strong		0.706	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
SPANXD	64648	hgsc.bcm.edu	37	X	140785714	140785714	+	Missense_Mutation	SNP	C	C	G	rs5953618		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:140785714C>G	ENST00000370515.3	-	2	535	c.202G>C	c.(202-204)Gtg>Ctg	p.V68L		NM_032417.2|NM_145665.1	NP_115793.1|NP_663698.1	Q9BXN6	SPNXD_HUMAN	SPANX family, member D	68			V -> L (in dbSNP:rs5953618).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	Acute lymphoblastic leukemia(192;7.65e-05)					TGGTCATTCACCAGTTCCTCT	0.458																																					p.V68L		Atlas-SNP	.											.	.	.	.	0			c.G202C						PASS	.						243.0	201.0	215.0					X																	140785714		2202	4287	6489	SO:0001583	missense	171489	exon2			CATTCACCAGTTC	AJ457791	CCDS14675.1	Xq27.2	2014-06-19			ENSG00000196406	ENSG00000196406			14332	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 4"""	300670, 300671	"""SPANX family, member E"""	SPANXE			Standard	NM_032417		Approved	CT11.4		Q9BXN6	OTTHUMG00000022563	ENST00000370515.3:c.202G>C	X.37:g.140785714C>G	ENSP00000359546:p.Val68Leu	Somatic	633	1	0.00157978		WXS	Illumina HiSeq	Phase_I	1176	235	0.19983	NM_145665	Q5JWI1	Missense_Mutation	SNP	ENST00000370515.3	37	CCDS14675.1	.	.	.	.	.	.	.	.	.	.	N	0.016	-1.536097	0.00942	.	.	ENSG00000196406	ENST00000370515	T	0.07021	3.23	.	.	.	.	.	.	.	.	T	0.02888	0.0086	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.46162	-0.9211	6	0.05833	T	0.94	.	.	.	.	rs5953618;rs17855378;rs17855767	68	Q9BXN6	SPNXD_HUMAN	L	68	ENSP00000359546:V68L	ENSP00000359546:V68L	V	-	1	0	SPANXD	140613380	0.017000	0.18338	0.016000	0.15963	0.015000	0.08874	0.064000	0.14437	0.068000	0.16574	0.068000	0.15388	GTG	C|1.000;|0.000	.	weak		0.458	SPANXD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058598.1		
PI16	221476	hgsc.bcm.edu	37	6	36930795	36930795	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36930795A>T	ENST00000373674.3	+	5	1005	c.677A>T	c.(676-678)gAc>gTc	p.D226V	PI16_ENST00000491324.1_3'UTR	NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	226					negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GAAGCATCAGACTCTAGGAAA	0.547																																					p.D226V		Atlas-SNP	.											.	PI16	50	.	0			c.A677T						PASS	.						87.0	81.0	83.0					6																	36930795		2203	4300	6503	SO:0001583	missense	221476	exon6			CATCAGACTCTAG		CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"""microseminoprotein, beta-binding protein"""		"""protease inhibitor 16"""				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.677A>T	6.37:g.36930795A>T	ENSP00000362778:p.Asp226Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	130	54	0.415385	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	37	CCDS34440.1	.	.	.	.	.	.	.	.	.	.	A	4.768	0.142776	0.09083	.	.	ENSG00000164530	ENST00000536757;ENST00000373674;ENST00000539035	T	0.06849	3.25	4.56	-5.47	0.02600	.	1.282230	0.05284	N	0.519917	T	0.00936	0.0031	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.46176	-0.9210	10	0.35671	T	0.21	.	2.847	0.05546	0.4899:0.2078:0.1969:0.1054	.	226;226	Q6UXB8;Q6UXB8-2	PI16_HUMAN;.	V	226;226;78	ENSP00000362778:D226V	ENSP00000362778:D226V	D	+	2	0	PI16	37038773	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-1.147000	0.03188	-1.317000	0.02292	-1.155000	0.01812	GAC	.	.	none		0.547	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370	
SIGLEC12	89858	hgsc.bcm.edu	37	19	52000616	52000616	+	Missense_Mutation	SNP	T	T	C	rs28572419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52000616T>C	ENST00000291707.3	-	6	1544	c.1489A>G	c.(1489-1491)Atc>Gtc	p.I497V	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.I379V	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	497					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)		ACGAAGATGATGCAGAAGTAC	0.567													N|||	165	0.0329473	0.1203	0.0086	5008	,	,		17500	0.0		0.0	False		,,,				2504	0.0				p.I497V		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.A1489G						PASS	.	C	VAL/ILE,VAL/ILE	455,3951		24,407,1772	157.0	138.0	144.0		1135,1489	-3.4	0.0	19	dbSNP_125	144	5,8595		0,5,4295	yes	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	29,29	24,412,6067	CC,CT,TT		0.0581,10.3268,3.5368	benign,benign	379/478,497/596	52000616	460,12546	2203	4300	6503	SO:0001583	missense	89858	exon6			AGATGATGCAGAA	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.1489A>G	19.37:g.52000616T>C	ENSP00000291707:p.Ile497Val	Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	212	120	0.566038	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	.	0.004	-2.281268	0.00251	0.103268	5.81E-4	ENSG00000254521	ENST00000291707	T	0.35236	1.32	1.69	-3.38	0.04883	.	.	.	.	.	T	0.00178	0.0005	N	0.05124	-0.11	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.0;0.003	T	0.16041	-1.0416	9	0.29301	T	0.29	.	0.7952	0.01065	0.1706:0.202:0.3393:0.2881	rs28572419	497;379	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	V	497	ENSP00000291707:I497V	ENSP00000291707:I497V	I	-	1	0	SIGLEC12	56692428	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-2.840000	0.00738	-1.881000	0.01123	-0.751000	0.03497	ATC	T|0.968;C|0.032	0.032	strong		0.567	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
TBC1D15	64786	hgsc.bcm.edu	37	12	72307616	72307616	+	Silent	SNP	A	A	G	rs3759171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72307616A>G	ENST00000550746.1	+	13	1426	c.1362A>G	c.(1360-1362)caA>caG	p.Q454Q	TBC1D15_ENST00000485960.2_Silent_p.Q437Q|TBC1D15_ENST00000548679.1_3'UTR|TBC1D15_ENST00000319106.8_Silent_p.Q445Q|TBC1D15_ENST00000393309.3_Silent_p.Q208Q	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	454	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GATATGTTCAAGGAATGAGTG	0.358													G|||	3334	0.665735	0.9349	0.5634	5008	,	,		16358	0.8819		0.2674	False		,,,				2504	0.5613				p.Q454Q		Atlas-SNP	.											.	TBC1D15	99	.	0			c.A1362G						PASS	.	G	,,	3753,653	262.5+/-264.9	1611,531,61	111.0	117.0	115.0		1311,1335,1362	1.8	1.0	12	dbSNP_107	115	2365,6235	680.3+/-403.6	345,1675,2280	yes	coding-synonymous,coding-synonymous,coding-synonymous	TBC1D15	NM_001146213.1,NM_001146214.1,NM_022771.4	,,	1956,2206,2341	GG,GA,AA		27.5,14.8207,47.0398	,,	437/675,445/683,454/692	72307616	6118,6888	2203	4300	6503	SO:0001819	synonymous_variant	64786	exon13			TGTTCAAGGAATG	AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.1362A>G	12.37:g.72307616A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	50	48	0.96	NM_022771	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Silent	SNP	ENST00000550746.1	37	CCDS31858.1																																																																																			A|0.446;G|0.554	0.554	strong		0.358	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771	
UTP20	27340	hgsc.bcm.edu	37	12	101679569	101679569	+	Missense_Mutation	SNP	A	A	G	rs140064475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101679569A>G	ENST00000261637.4	+	4	410	c.236A>G	c.(235-237)aAt>aGt	p.N79S		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	79					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						CAATCATTCAATCAGTTGGTG	0.368													A|||	11	0.00219649	0.0083	0.0	5008	,	,		18123	0.0		0.0	False		,,,				2504	0.0				p.N79S		Atlas-SNP	.											.	UTP20	222	.	0			c.A236G						PASS	.	A	SER/ASN	23,4383	30.8+/-60.4	0,23,2180	99.0	99.0	99.0		236	5.6	1.0	12	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	yes	missense	UTP20	NM_014503.2	46	0,24,6479	GG,GA,AA		0.0116,0.522,0.1845	probably-damaging	79/2786	101679569	24,12982	2203	4300	6503	SO:0001583	missense	27340	exon4			CATTCAATCAGTT	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.236A>G	12.37:g.101679569A>G	ENSP00000261637:p.Asn79Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	15.61	2.883689	0.51908	0.00522	1.16E-4	ENSG00000120800	ENST00000261637	T	0.40476	1.03	5.56	5.56	0.83823	.	0.104115	0.64402	D	0.000005	T	0.48132	0.1483	L	0.57536	1.79	0.48040	D	0.999572	D	0.62365	0.991	P	0.58013	0.831	T	0.53215	-0.8470	10	0.46703	T	0.11	-26.0442	15.7176	0.77681	1.0:0.0:0.0:0.0	.	79	O75691	UTP20_HUMAN	S	79	ENSP00000261637:N79S	ENSP00000261637:N79S	N	+	2	0	UTP20	100203700	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.098000	0.76974	2.104000	0.64026	0.528000	0.53228	AAT	A|0.998;G|0.002	0.002	strong		0.368	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
CD200R1	131450	hgsc.bcm.edu	37	3	112648125	112648125	+	Silent	SNP	G	G	T	rs6438117|rs71625219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112648125G>T	ENST00000471858.1	-	3	595	c.363C>A	c.(361-363)acC>acA	p.T121T	CD200R1_ENST00000490004.1_Silent_p.T121T|CD200R1_ENST00000308611.3_Silent_p.T144T|CD200R1_ENST00000295863.4_Silent_p.T99T|CD200R1_ENST00000440122.2_Silent_p.T144T	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	121	Ig-like V-type.		P -> T (in allele 2; dbSNP:rs4596117). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15274657, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.7}.		regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TGATGGCCACGGTACGAATCT	0.448													T|||	3262	0.651358	0.7216	0.6066	5008	,	,		19604	0.7024		0.5328	False		,,,				2504	0.6575				p.T144T		Atlas-SNP	.											CD200R1_ENST00000440122,colon,carcinoma,0,2	CD200R1	91	2	0			c.C432A						PASS	.	T	,,,	1835,2571		838,159,1206	174.0	167.0	169.0		432,432,363,363	1.5	0.1	3	dbSNP_116	169	2088,6512		903,282,3115	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD200R1	NM_138806.3,NM_138939.2,NM_138940.2,NM_170780.2	,,,	1741,441,4321	TT,TG,GG		24.2791,41.6478,30.163	,,,	144/349,144/189,121/166,121/326	112648125	3923,9083	2203	4300	6503	SO:0001819	synonymous_variant	131450	exon4			GGCCACGGTACGA	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.363C>A	3.37:g.112648125G>T		Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	313	313	1	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Silent	SNP	ENST00000471858.1	37	CCDS2970.1																																																																																			GGT|0.500;TGG|0.500	.	alt		0.448	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
OTC	5009	hgsc.bcm.edu	37	X	38226603	38226603	+	Missense_Mutation	SNP	A	A	G	rs1800321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38226603A>G	ENST00000039007.4	+	2	289	c.137A>G	c.(136-138)aAa>aGa	p.K46R	TM4SF2_ENST00000465127.1_Intron|OTC_ENST00000488812.1_3'UTR	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	46			K -> R (in dbSNP:rs1800321). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2474822}.		ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	CTCACTCTAAAAAACTTTACC	0.343													A|||	695	0.184106	0.2912	0.1167	3775	,	,		12634	0.002		0.2048	False		,,,				2504	0.0215				p.K46R		Atlas-SNP	.											.	OTC	60	.	0			c.A137G						PASS	.	A	ARG/LYS	1443,2390		252,726,213,653,358	46.0	46.0	46.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	137	4.2	0.9	X	dbSNP_89	46	1623,5104		155,862,451,1411,1420	yes	missense	OTC	NM_000531.5	26	407,1588,664,2064,1778	GG,GA,G,AA,A		24.1267,37.6468,29.0341	benign	46/355	38226603	3066,7494	2202	4299	6501	SO:0001583	missense	5009	exon2			CTCTAAAAAACTT	K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.137A>G	X.37:g.38226603A>G	ENSP00000039007:p.Lys46Arg	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	254	135	0.531496	NM_000531	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Missense_Mutation	SNP	ENST00000039007.4	37	CCDS14247.1	327	0.19710669077757687	82	0.20603015075376885	39	0.11337209302325581	1	0.0017482517482517483	101	0.15256797583081572	A	11.07	1.530492	0.27387	0.376468	0.241267	ENSG00000036473	ENST00000039007	D	0.98493	-4.96	5.39	4.23	0.50019	Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding (1);	0.207551	0.49305	N	0.000150	T	0.00012	0.0000	L	0.46614	1.455	0.27994	P	0.9355521	B	0.27679	0.185	B	0.29942	0.109	T	0.00361	-1.1789	9	0.21540	T	0.41	-29.6416	9.3789	0.38301	0.9133:0.0:0.0867:0.0	rs1800321;rs60302012;rs1800321	46	P00480	OTC_HUMAN	R	46	ENSP00000039007:K46R	ENSP00000039007:K46R	K	+	2	0	OTC	38111547	1.000000	0.71417	0.909000	0.35828	0.665000	0.39181	7.119000	0.77145	0.700000	0.31782	0.345000	0.21793	AAA	A|0.721;0|0.027	.	strong		0.343	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2		
KEL	3792	hgsc.bcm.edu	37	7	142640004	142640004	+	Silent	SNP	T	T	C	rs8176039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142640004T>C	ENST00000355265.2	-	17	2373	c.1899A>G	c.(1897-1899)ttA>ttG	p.L633L		NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	633					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					CAGCATTCTCTAAGAATGTGA	0.517													C|||	353	0.0704872	0.2519	0.0274	5008	,	,		21440	0.0		0.001	False		,,,				2504	0.0				p.L633L		Atlas-SNP	.											.	KEL	128	.	0			c.A1899G						PASS	.	C		957,3449	735.8+/-410.7	105,747,1351	103.0	94.0	97.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1899	1.8	0.2	7	dbSNP_117	97	10,8590	818.3+/-406.9	0,10,4290	no	coding-synonymous	KEL	NM_000420.2		105,757,5641	CC,CT,TT		0.1163,21.7204,7.435		633/733	142640004	967,12039	2203	4300	6503	SO:0001819	synonymous_variant	3792	exon17			ATTCTCTAAGAAT	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"""CD molecules"", ""Blood group antigens"""	6308	protein-coding gene	gene with protein product		613883	"""Kell blood group"", ""Kell blood group, metalloendopeptidase"""			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1899A>G	7.37:g.142640004T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_000420	B2RBV4|Q96RS8|Q99885	Silent	SNP	ENST00000355265.2	37	CCDS34766.1																																																																																			A|0.102;C|0.060	0.060	strong		0.517	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420	
CELSR1	9620	hgsc.bcm.edu	37	22	46787697	46787697	+	Missense_Mutation	SNP	A	A	G	rs6008795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	82	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	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	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74205878	74205878	+	Silent	SNP	C	C	T	rs17782128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	115	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	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	
OLFM3	118427	hgsc.bcm.edu	37	1	102296279	102296279	+	Silent	SNP	T	T	C	rs10493973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:102296279T>C	ENST00000338858.5	-	3	380	c.381A>G	c.(379-381)aaA>aaG	p.K127K	OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000370103.4_Silent_p.K107K|OLFM3_ENST00000359814.3_Silent_p.K127K|OLFM3_ENST00000536598.1_Silent_p.K32K			Q96PB7	NOE3_HUMAN	olfactomedin 3	127					eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		TCTGCCGAAATTTTGCCTTCA	0.383													C|||	736	0.146965	0.2852	0.1081	5008	,	,		18517	0.0079		0.1779	False		,,,				2504	0.0992				p.K107K		Atlas-SNP	.											.	OLFM3	178	.	0			c.A321G						PASS	.	C		1055,3351	724.9+/-409.6	132,791,1280	207.0	199.0	202.0		321	2.5	1.0	1	dbSNP_119	202	1546,7054	746.1+/-407.3	148,1250,2902	no	coding-synonymous	OLFM3	NM_058170.2		280,2041,4182	CC,CT,TT		17.9767,23.9446,19.9985		107/459	102296279	2601,10405	2203	4300	6503	SO:0001819	synonymous_variant	118427	exon3			CCGAAATTTTGCC	AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"""optimedin"""	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.381A>G	1.37:g.102296279T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	163	80	0.490798	NM_058170	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Silent	SNP	ENST00000338858.5	37																																																																																				T|0.824;C|0.176	0.176	strong		0.383	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1		
QRICH2	84074	hgsc.bcm.edu	37	17	74290097	74290097	+	Silent	SNP	T	T	A	rs7225131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74290097T>A	ENST00000262765.5	-	4	392	c.213A>T	c.(211-213)tcA>tcT	p.S71S		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	71										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						TAAGTGTTTCTGAGCCCTGGT	0.428													T|||	2352	0.469649	0.7073	0.3098	5008	,	,		20370	0.5724		0.2753	False		,,,				2504	0.3558				p.S71S		Atlas-SNP	.											QRICH2,NS,adenoma,0,1	QRICH2	143	1	0			c.A213T						scavenged	.	T		2922,1482	654.3+/-399.7	975,972,255	63.0	71.0	69.0		213	-1.3	0.1	17	dbSNP_116	69	2487,6111	384.7+/-341.2	349,1789,2161	no	coding-synonymous	QRICH2	NM_032134.1		1324,2761,2416	AA,AT,TT		28.9253,33.6512,41.6013		71/1664	74290097	5409,7593	2202	4299	6501	SO:0001819	synonymous_variant	84074	exon4			TGTTTCTGAGCCC	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.213A>T	17.37:g.74290097T>A		Somatic	49	1	0.0204082		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																			T|0.574;A|0.426	0.426	strong		0.428	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
SEMA4D	10507	hgsc.bcm.edu	37	9	91978397	91978397	+	Missense_Mutation	SNP	C	C	T	rs13295305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:91978397C>T	ENST00000420987.1	-	19	2584	c.2138G>A	c.(2137-2139)aGg>aAg	p.R713K	SEMA4D_ENST00000455551.2_Missense_Mutation_p.R713K|SEMA4D_ENST00000343780.4_Missense_Mutation_p.R713K|SEMA4D_ENST00000339861.4_Missense_Mutation_p.R713K|SEMA4D_ENST00000420101.2_Missense_Mutation_p.R98K|SEMA4D_ENST00000469653.1_5'UTR	NM_001142287.1	NP_001135759.1	Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	0					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						AGCCACAGCCCTCCAGGCAGA	0.627													C|||	788	0.157348	0.025	0.366	5008	,	,		17146	0.2331		0.1203	False		,,,				2504	0.1483				p.R713K		Atlas-SNP	.											.	SEMA4D	81	.	0			c.G2138A						PASS	.	C	LYS/ARG	184,4222	117.5+/-155.4	5,174,2024	59.0	64.0	62.0		2138	0.8	0.5	9	dbSNP_121	62	1147,7453	235.4+/-268.0	84,979,3237	yes	missense	SEMA4D	NM_001142287.1	26	89,1153,5261	TT,TC,CC		13.3372,4.1761,10.2337		713/739	91978397	1331,11675	2203	4300	6503	SO:0001583	missense	10507	exon20			ACAGCCCTCCAGG	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000420987.1:c.2138G>A	9.37:g.91978397C>T	ENSP00000391733:p.Arg713Lys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	94	58	0.617021	NM_001142287	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000420987.1	37	CCDS47991.1	345	0.15796703296703296	21	0.042682926829268296	116	0.32044198895027626	100	0.17482517482517482	108	0.1424802110817942	C	10.11	1.260965	0.23051	0.041761	0.133372	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000420101;ENST00000455551;ENST00000343780	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	4.99	0.793	0.18632	.	0.437294	0.20662	N	0.088017	T	0.00012	0.0000	.	.	.	0.33217	P	0.44578799999999996	B	0.11235	0.004	B	0.12156	0.007	T	0.47446	-0.9117	8	0.13470	T	0.59	.	8.526	0.33304	0.0:0.6353:0.0:0.3647	rs13295305	713	Q92854-2	.	K	713;713;98;713;713	ENSP00000344923:R713K;ENSP00000391733:R713K;ENSP00000411981:R713K;ENSP00000343418:R713K	ENSP00000344923:R713K	R	-	2	0	SEMA4D	91168217	0.113000	0.22115	0.486000	0.27416	0.819000	0.46315	0.259000	0.18405	0.285000	0.22329	0.561000	0.74099	AGG	C|0.880;T|0.120	0.120	strong		0.627	SEMA4D-203	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402418.2	NM_006378	
ACKR1	2532	hgsc.bcm.edu	37	1	159175354	159175354	+	Missense_Mutation	SNP	G	G	A	rs12075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159175354G>A	ENST00000368122.2	+	2	804	c.125G>A	c.(124-126)gGt>gAt	p.G42D	DARC_ENST00000368121.2_Missense_Mutation_p.G44D|CTA-134P22.2_ENST00000609696.1_RNA|DARC_ENST00000537147.1_Missense_Mutation_p.G42D	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		42			G -> D (antigen Fy(b); dbSNP:rs12075). {ECO:0000269|PubMed:7663520, ECO:0000269|PubMed:7705836, ECO:0000269|PubMed:8248172, ECO:0000269|PubMed:9731074, ECO:0000269|PubMed:9886340}.		chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					GGAGACTATGGTGCCAACCTG	0.527													A|||	2707	0.540535	0.9811	0.5389	5008	,	,		20455	0.0774		0.6024	False		,,,				2504	0.3599				p.G44D		Atlas-SNP	.											.	DARC	76	.	0			c.G131A	GRCh37	CM950484	DARC	M	rs12075	PASS	.	A	ASP/GLY,ASP/GLY	4037,369	187.8+/-214.3	1849,339,15	95.0	87.0	90.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	131,125	-1.1	0.0	1	dbSNP_52	90	4967,3633	523.8+/-380.4	1441,2085,774	yes	missense,missense	DARC	NM_001122951.2,NM_002036.3	94,94	3290,2424,789	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	42.2442,8.3749,30.7704	benign,benign	44/339,42/337	159175354	9004,4002	2203	4300	6503	SO:0001583	missense	2532	exon1			ACTATGGTGCCAA																												ENST00000368122.2:c.125G>A	1.37:g.159175354G>A	ENSP00000357104:p.Gly42Asp	Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	201	201	1	NM_001122951	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Missense_Mutation	SNP	ENST00000368122.2	37	CCDS1183.1	1176	0.5384615384615384	474	0.9634146341463414	209	0.5773480662983426	47	0.08216783216783216	446	0.5883905013192612	A	0.168	-1.074849	0.01903	0.916251	0.577558	ENSG00000213088	ENST00000368122;ENST00000537147;ENST00000359381;ENST00000435307;ENST00000368121	T;T;T;T	0.22336	4.47;4.47;1.96;4.46	4.36	-1.07	0.09968	.	.	.	.	.	T	0.01287	0.0042	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	0.42396	-0.9454	8	0.02654	T	1	-10.5139	3.1012	0.06327	0.4283:0.0:0.1875:0.3841	rs12075;rs3171130;rs61460694;rs12075	44;42	Q5Y7A1;Q16570	.;DUFFY_HUMAN	D	42;42;42;44;44	ENSP00000357104:G42D;ENSP00000441985:G42D;ENSP00000398406:G44D;ENSP00000357103:G44D	ENSP00000352341:G42D	G	+	2	0	DARC	157441978	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.283000	0.18846	-0.484000	0.06763	-0.361000	0.07541	GGT	G|0.393;A|0.607	0.607	strong		0.527	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2		
WDR62	284403	hgsc.bcm.edu	37	19	36583692	36583692	+	Missense_Mutation	SNP	A	A	G	rs61747277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36583692A>G	ENST00000270301.7	+	19	2312	c.2312A>G	c.(2311-2313)aAg>aGg	p.K771R	WDR62_ENST00000401500.2_Missense_Mutation_p.K771R			O43379	WDR62_HUMAN	WD repeat domain 62	771					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)			ACAAATGACAAGAAGCGGAGT	0.622													A|||	92	0.0183706	0.0673	0.0029	5008	,	,		16554	0.0		0.001	False		,,,				2504	0.0				p.K771R		Atlas-SNP	.											.	WDR62	102	.	0			c.A2312G						PASS	.	A	ARG/LYS,ARG/LYS	268,4138	149.9+/-184.0	11,246,1946	72.0	75.0	74.0		2312,2312	-4.4	0.0	19	dbSNP_129	74	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	26,26	11,252,6240	GG,GA,AA		0.0698,6.0826,2.1067	benign,benign	771/1524,771/1519	36583692	274,12732	2203	4300	6503	SO:0001583	missense	284403	exon19			ATGACAAGAAGCG	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.2312A>G	19.37:g.36583692A>G	ENSP00000270301:p.Lys771Arg	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	170	76	0.447059	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	34	0.015567765567765568	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	5.908	0.351581	0.11182	0.060826	6.98E-4	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.43294	0.95;0.95	5.01	-4.44	0.03557	.	0.201397	0.41938	D	0.000797	T	0.00906	0.0030	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.18935	-1.0321	10	0.15952	T	0.53	0.0189	7.3192	0.26517	0.5771:0.1282:0.2946:0.0	rs61747277	771;771	O43379-4;O43379	.;WDR62_HUMAN	R	771	ENSP00000384792:K771R;ENSP00000270301:K771R	ENSP00000270301:K771R	K	+	2	0	WDR62	41275532	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.452000	0.07087	-0.132000	0.14878	AAG	A|0.982;G|0.018	0.018	strong		0.622	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
FLG	2312	hgsc.bcm.edu	37	1	152282899	152282899	+	Missense_Mutation	SNP	G	G	T	rs3120648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152282899G>T	ENST00000368799.1	-	3	4498	c.4463C>A	c.(4462-4464)aCc>aAc	p.T1488N	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1488	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)			TCCACGAATGGTGTCCTGACC	0.582									Ichthyosis				G|||	402	0.0802716	0.2905	0.0245	5008	,	,		21397	0.0		0.001	False		,,,				2504	0.0				p.T1488N		Atlas-SNP	.											.	FLG	900	.	0			c.C4463A						PASS	.	G	ASN/THR	1035,3371	381.1+/-324.0	111,813,1279	386.0	372.0	377.0		4463	-2.2	0.0	1	dbSNP_103	377	10,8590	7.7+/-29.5	0,10,4290	no	missense	FLG	NM_002016.1	65	111,823,5569	TT,TG,GG		0.1163,23.4907,8.0348	benign	1488/4062	152282899	1045,11961	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGAATGGTGTCCT	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.4463C>A	1.37:g.152282899G>T	ENSP00000357789:p.Thr1488Asn	Somatic	461	0	0		WXS	Illumina HiSeq	Phase_I	424	423	0.997642	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	141	0.06456043956043957	132	0.2682926829268293	9	0.024861878453038673	0	0.0	0	0.0	G	9.042	0.989984	0.18966	0.234907	0.001163	ENSG00000143631	ENST00000368799	T	0.01725	4.67	3.12	-2.23	0.06930	.	.	.	.	.	T	0.00666	0.0022	M	0.78223	2.4	0.80722	P	0.0	B	0.20052	0.041	B	0.13407	0.009	T	0.46679	-0.9174	8	0.13470	T	0.59	.	2.2485	0.04037	0.1236:0.3919:0.3103:0.1742	rs3120648;rs58109062	1488	P20930	FILA_HUMAN	N	1488	ENSP00000357789:T1488N	ENSP00000357789:T1488N	T	-	2	0	FLG	150549523	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.592000	0.05747	-0.155000	0.11098	-0.321000	0.08615	ACC	G|0.915;T|0.085	0.085	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CCDC157	550631	hgsc.bcm.edu	37	22	30772567	30772567	+	Missense_Mutation	SNP	T	T	C	rs202178544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30772567T>C	ENST00000405659.1	+	12	2801	c.2092T>C	c.(2092-2094)Tct>Cct	p.S698P	CCDC157_ENST00000338306.3_Missense_Mutation_p.S698P|RP1-130H16.16_ENST00000332468.4_RNA			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	698										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CACATCCCCATCTCGGCAGCC	0.667													T|||	6	0.00119808	0.0038	0.0014	5008	,	,		15299	0.0		0.0	False		,,,				2504	0.0				p.S698P		Atlas-SNP	.											CCDC157_ENST00000405659,bladder,carcinoma,0,4	CCDC157	86	4	0			c.T2092C						PASS	.						71.0	79.0	76.0					22																	30772567		2203	4300	6503	SO:0001583	missense	550631	exon12			TCCCCATCTCGGC	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.2092T>C	22.37:g.30772567T>C	ENSP00000385357:p.Ser698Pro	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	125	15	0.12	NM_001017437	Q0VD76|Q9BYA4	Missense_Mutation	SNP	ENST00000405659.1	37	CCDS33632.2	.	.	.	.	.	.	.	.	.	.	T	7.336	0.619980	0.14193	.	.	ENSG00000187860	ENST00000405659;ENST00000338306	T;T	0.39229	1.09;1.09	3.04	-2.83	0.05769	.	1.188910	0.06203	N	0.683596	T	0.20373	0.0490	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19549	-1.0302	10	0.25106	T	0.35	-1.9381	7.0241	0.24930	0.0:0.3799:0.0:0.6201	.	698	Q569K6	CC157_HUMAN	P	698	ENSP00000385357:S698P;ENSP00000343087:S698P	ENSP00000343087:S698P	S	+	1	0	CCDC157	29102567	0.000000	0.05858	0.008000	0.14137	0.026000	0.11368	-0.341000	0.07811	-0.707000	0.05022	-0.415000	0.06103	TCT	.	.	weak		0.667	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
TPRX1	284355	hgsc.bcm.edu	37	19	48305651	48305651	+	Missense_Mutation	SNP	G	G	A	rs62130758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	98	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	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	
OBSCN	84033	hgsc.bcm.edu	37	1	228399628	228399628	+	Silent	SNP	G	G	A	rs114375717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228399628G>A	ENST00000422127.1	+	2	188	c.144G>A	c.(142-144)caG>caA	p.Q48Q	OBSCN_ENST00000570156.2_Silent_p.Q48Q|OBSCN_ENST00000284548.11_Silent_p.Q48Q|OBSCN_ENST00000366707.4_5'UTR|C1orf145_ENST00000295012.5_Intron|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	48	Ig-like 1.				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)				AGGACCAGCAGCCGGTGGCGG	0.682													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		11232	0.0		0.0	False		,,,				2504	0.0				p.Q48Q		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G144A						PASS	.	G	,	120,3834		0,120,1857	8.0	10.0	10.0		144,144	1.5	0.9	1	dbSNP_132	10	0,8146		0,0,4073	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,120,5930	AA,AG,GG		0.0,3.0349,0.9917	,	48/7969,48/6621	228399628	120,11980	1977	4073	6050	SO:0001819	synonymous_variant	84033	exon2			CCAGCAGCCGGTG	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.144G>A	1.37:g.228399628G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	42	0.591549	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																																																																																			G|0.992;A|0.008	0.008	strong		0.682	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OR51Q1	390061	hgsc.bcm.edu	37	11	5443867	5443867	+	Missense_Mutation	SNP	C	C	T	rs10838092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5443867C>T	ENST00000300778.4	+	1	527	c.437C>T	c.(436-438)aCt>aTt	p.T146I	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	146			T -> I (in dbSNP:rs10838092). {ECO:0000269|Ref.3}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATTGGTAGAACTGGGTTAGCC	0.527													T|||	2272	0.453674	0.2799	0.3991	5008	,	,		21966	0.7024		0.3986	False		,,,				2504	0.5276				p.T146I		Atlas-SNP	.											.	OR51Q1	79	.	0			c.C437T						PASS	.	T	ILE/THR	1328,3074	693.8+/-405.7	202,924,1075	269.0	229.0	242.0		437	5.0	0.1	11	dbSNP_120	242	3372,5222	641.9+/-399.8	675,2022,1600	yes	missense	OR51Q1	NM_001004757.2	89	877,2946,2675	TT,TC,CC		39.2367,30.1681,36.165	benign	146/318	5443867	4700,8296	2201	4297	6498	SO:0001583	missense	390061	exon1			GTAGAACTGGGTT	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.437C>T	11.37:g.5443867C>T	ENSP00000300778:p.Thr146Ile	Somatic	275	2	0.00727273		WXS	Illumina HiSeq	Phase_I	226	224	0.99115	NM_001004757	B2RNN1	Missense_Mutation	SNP	ENST00000300778.4	37	CCDS31381.1	966	0.4423076923076923	139	0.28252032520325204	148	0.4088397790055249	395	0.6905594405594405	284	0.37467018469656993	T	1.308	-0.603044	0.03744	0.301681	0.392367	ENSG00000167360	ENST00000300778	T	0.34275	1.37	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.101808	0.42420	N	0.000719	T	0.00012	0.0000	N	0.00042	-2.475	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44421	-0.9329	9	0.02654	T	1	.	9.9808	0.41813	0.0:0.0807:0.0:0.9193	rs10838092;rs58812600;rs10838092	146	Q8NH59	O51Q1_HUMAN	I	146	ENSP00000300778:T146I	ENSP00000300778:T146I	T	+	2	0	OR51Q1	5400443	0.000000	0.05858	0.067000	0.19924	0.667000	0.39255	0.024000	0.13555	0.960000	0.38005	-1.531000	0.00922	ACT	C|0.602;T|0.398	0.398	strong		0.527	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
ANKRD35	148741	hgsc.bcm.edu	37	1	145561594	145561594	+	Missense_Mutation	SNP	C	C	T	rs6670984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:145561594C>T	ENST00000355594.4	+	10	1369	c.1282C>T	c.(1282-1284)Ccc>Tcc	p.P428S		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	428			P -> S (in dbSNP:rs6670984). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							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)					ACAGGGGCCACCCCAGAGCCC	0.547													C|||	2828	0.564696	0.5794	0.5043	5008	,	,		18882	0.7252		0.3797	False		,,,				2504	0.6125				p.P428S	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.C1282T						PASS	.	C	SER/PRO	2326,2080	586.9+/-386.6	613,1100,490	60.0	71.0	67.0		1282	-3.1	0.0	1	dbSNP_116	67	3163,5437	473.4+/-368.6	572,2019,1709	yes	missense	ANKRD35	NM_144698.3	74	1185,3119,2199	TT,TC,CC		36.7791,47.2084,42.2036	benign	428/1002	145561594	5489,7517	2203	4300	6503	SO:0001583	missense	148741	exon10			GGGCCACCCCAGA	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.1282C>T	1.37:g.145561594C>T	ENSP00000347802:p.Pro428Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	1154	0.5283882783882784	275	0.5589430894308943	169	0.46685082872928174	419	0.7325174825174825	291	0.3839050131926121	C	2.083	-0.410284	0.04799	0.527916	0.367791	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.64991	-0.13	5.21	-3.07	0.05363	.	1.124390	0.06867	N	0.800111	T	0.21674	0.0522	L	0.41027	1.25	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.05273	-1.0895	9	0.08837	T	0.75	0.4115	6.7985	0.23738	0.0:0.4134:0.1204:0.4661	rs6670984;rs57708309;rs6670984	428	Q8N283	ANR35_HUMAN	S	337;428	ENSP00000347802:P428S	ENSP00000347802:P428S	P	+	1	0	ANKRD35	144272951	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.280000	0.18790	-0.485000	0.06754	-0.140000	0.14226	CCC	C|0.526;T|0.474	0.474	strong		0.547	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
OR4C6	219432	hgsc.bcm.edu	37	11	55433040	55433040	+	Missense_Mutation	SNP	T	T	C	rs11230600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55433040T>C	ENST00000314259.3	+	1	427	c.398T>C	c.(397-399)aTc>aCc	p.I133T		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	133			I -> T (in dbSNP:rs11230600).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						TACACGATCATCATGAGTCCA	0.512													t|||	1267	0.252995	0.1029	0.3242	5008	,	,		18616	0.3909		0.2843	False		,,,				2504	0.2311				p.I133T		Atlas-SNP	.											.	OR4C6	114	.	0			c.T398C						PASS	.	T	THR/ILE	567,3833	254.0+/-259.7	33,501,1666	104.0	97.0	99.0		398	2.5	0.4	11	dbSNP_120	99	2291,6301	386.9+/-342.0	330,1631,2335	yes	missense	OR4C6	NM_001004704.1	89	363,2132,4001	CC,CT,TT		26.6643,12.8864,21.9982	possibly-damaging	133/310	55433040	2858,10134	2200	4296	6496	SO:0001583	missense	219432	exon1			CGATCATCATGAG	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"""GPCR / Class A : Olfactory receptors"""	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.398T>C	11.37:g.55433040T>C	ENSP00000324769:p.Ile133Thr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	146	63	0.431507	NM_001004704	B2RP11|Q6IFD2	Missense_Mutation	SNP	ENST00000314259.3	37	CCDS31506.1	605	0.27701465201465203	47	0.09552845528455285	126	0.34806629834254144	214	0.3741258741258741	218	0.287598944591029	T	11.60	1.687192	0.29962	0.128864	0.266643	ENSG00000181903	ENST00000314259	T	0.21191	2.02	3.77	2.52	0.30459	GPCR, rhodopsin-like superfamily (1);	0.189403	0.25639	N	0.029298	T	0.00012	0.0000	M	0.65320	2	0.44417	P	0.0026610000000000245	B	0.20164	0.042	B	0.27608	0.081	T	0.38972	-0.9636	9	0.59425	D	0.04	.	7.9326	0.29912	0.1838:0.0:0.0:0.8162	rs11230600;rs11230600	133	Q8NH72	OR4C6_HUMAN	T	133	ENSP00000324769:I133T	ENSP00000324769:I133T	I	+	2	0	OR4C6	55189616	0.000000	0.05858	0.449000	0.26957	0.625000	0.37756	0.307000	0.19296	1.383000	0.46405	0.438000	0.28831	ATC	T|0.759;C|0.241	0.241	strong		0.512	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704	
URB1	9875	hgsc.bcm.edu	37	21	33755787	33755787	+	Missense_Mutation	SNP	G	G	A	rs148857803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33755787G>A	ENST00000382751.3	-	4	626	c.511C>T	c.(511-513)Cat>Tat	p.H171Y		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	171						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						AAATCAAAATGGCTGCAGACG	0.572													G|||	10	0.00199681	0.0068	0.0014	5008	,	,		17128	0.0		0.0	False		,,,				2504	0.0				p.H171Y		Atlas-SNP	.											.	URB1	176	.	0			c.C511T						PASS	.	G	TYR/HIS	4,1380		0,4,688	75.0	77.0	76.0		511	3.5	1.0	21	dbSNP_134	76	5,3177		0,5,1586	yes	missense	URB1	NM_014825.2	83	0,9,2274	AA,AG,GG		0.1571,0.289,0.1971	possibly-damaging	171/2272	33755787	9,4557	692	1591	2283	SO:0001583	missense	9875	exon4			CAAAATGGCTGCA	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.511C>T	21.37:g.33755787G>A	ENSP00000372199:p.His171Tyr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	37	CCDS46645.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	G	17.51	3.407946	0.62399	0.00289	0.001571	ENSG00000142207	ENST00000382751	T	0.32515	1.45	5.34	3.46	0.39613	.	0.670476	0.15407	N	0.263997	T	0.25717	0.0626	L	0.50333	1.59	0.30481	N	0.772369	P	0.42203	0.773	P	0.48598	0.583	T	0.12785	-1.0534	10	0.19147	T	0.46	-1.1195	8.4059	0.32614	0.0838:0.0:0.7613:0.1549	.	171	O60287	NPA1P_HUMAN	Y	171	ENSP00000372199:H171Y	ENSP00000372199:H171Y	H	-	1	0	URB1	32677658	1.000000	0.71417	0.961000	0.40146	0.971000	0.66376	2.136000	0.42121	0.579000	0.29504	0.563000	0.77884	CAT	G|0.998;A|0.002	0.002	strong		0.572	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
MCM8	84515	hgsc.bcm.edu	37	20	5974265	5974265	+	Missense_Mutation	SNP	A	A	G	rs16991638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5974265A>G	ENST00000378896.3	+	18	2731	c.2354A>G	c.(2353-2355)aAc>aGc	p.N785S	MCM8_ENST00000265187.4_Missense_Mutation_p.N769S|MCM8_ENST00000378883.1_Missense_Mutation_p.N738S|MCM8_ENST00000378886.2_Missense_Mutation_p.N825S	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	785			N -> S (in dbSNP:rs16991638).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						GCTCTCAACAACGTTGCTGAA	0.358													A|||	378	0.0754792	0.1853	0.1009	5008	,	,		18096	0.001		0.0199	False		,,,				2504	0.0429				p.N785S		Atlas-SNP	.											.	MCM8	125	.	0			c.A2354G						PASS	.	A	SER/ASN,SER/ASN	703,3703	283.4+/-277.1	58,587,1558	57.0	62.0	61.0		2354,2306	0.4	1.0	20	dbSNP_123	61	181,8419	82.3+/-144.9	2,177,4121	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	46,46	60,764,5679	GG,GA,AA		2.1047,15.9555,6.7969	benign,benign	785/841,769/825	5974265	884,12122	2203	4300	6503	SO:0001583	missense	84515	exon18			TCAACAACGTTGC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.2354A>G	20.37:g.5974265A>G	ENSP00000368174:p.Asn785Ser	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	48	17	0.354167	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	128	0.05860805860805861	86	0.17479674796747968	26	0.0718232044198895	1	0.0017482517482517483	15	0.01978891820580475	A	9.100	1.003892	0.19199	0.159555	0.021047	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.02812	4.25;4.15;4.23;4.25	5.82	0.411	0.16392	.	0.769958	0.13000	N	0.421768	T	0.00012	0.0000	N	0.01576	-0.805	0.54753	P	1.3000000000040757E-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;0.0	T	0.45056	-0.9287	9	0.17832	T	0.49	-3.3433	6.6121	0.22757	0.2319:0.3374:0.4307:0.0	rs16991638;rs56419414;rs16991638	738;825;769;785	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	S	785;738;825;769	ENSP00000368174:N785S;ENSP00000368161:N738S;ENSP00000368164:N825S;ENSP00000265187:N769S	ENSP00000265187:N769S	N	+	2	0	MCM8	5922265	0.001000	0.12720	0.997000	0.53966	0.995000	0.86356	-0.073000	0.11468	0.055000	0.16094	0.533000	0.62120	AAC	A|0.934;G|0.066	0.066	strong		0.358	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
FAM83C	128876	hgsc.bcm.edu	37	20	33874720	33874720	+	Missense_Mutation	SNP	C	C	T	rs2425049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33874720C>T	ENST00000374408.3	-	4	1958	c.1862G>A	c.(1861-1863)cGg>cAg	p.R621Q	FAM83C-AS1_ENST00000429167.1_RNA|EIF6_ENST00000374443.3_5'Flank|EIF6_ENST00000462894.1_5'Flank|EIF6_ENST00000374436.3_5'Flank|EIF6_ENST00000374450.3_5'Flank	NM_178468.5	NP_848563.1	Q9BQN1	FA83C_HUMAN	family with sequence similarity 83, member C	621			R -> Q (in dbSNP:rs2425049).							central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(18;0.00252)			ATCTGGTGCCCGTCTGGCAGG	0.627													T|||	1892	0.377796	0.7474	0.1744	5008	,	,		18761	0.2232		0.2028	False		,,,				2504	0.362				p.R621Q		Atlas-SNP	.											.	FAM83C	80	.	0			c.G1862A						PASS	.	T	GLN/ARG	2773,1633	494.6+/-363.0	877,1019,307	52.0	51.0	51.0		1862	2.8	0.3	20	dbSNP_100	51	1871,6729	723.6+/-406.5	218,1435,2647	yes	missense	FAM83C	NM_178468.4	43	1095,2454,2954	TT,TC,CC		21.7558,37.0631,35.7066	benign	621/748	33874720	4644,8362	2203	4300	6503	SO:0001583	missense	128876	exon4			GGTGCCCGTCTGG	AL121753	CCDS13251.1	20q11.22	2011-04-01	2006-03-23	2006-03-23	ENSG00000125998	ENSG00000125998			16121	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 128"""	C20orf128			Standard	NM_178468		Approved	dJ614O4.7	uc021wck.1	Q9BQN1	OTTHUMG00000032332	ENST00000374408.3:c.1862G>A	20.37:g.33874720C>T	ENSP00000363529:p.Arg621Gln	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	154	154	1	NM_178468	Q14D67|Q5JWN6|Q8N276	Missense_Mutation	SNP	ENST00000374408.3	37	CCDS13251.1	699	0.32005494505494503	352	0.7154471544715447	78	0.2154696132596685	109	0.19055944055944055	160	0.21108179419525067	T	0.005	-2.132108	0.00338	0.629369	0.217558	ENSG00000125998	ENST00000374408	T	0.05580	3.42	4.0	2.85	0.33270	.	0.728390	0.11643	N	0.543528	T	0.00012	0.0000	N	0.00453	-1.485	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09100	-1.0690	9	0.15952	T	0.53	-25.7861	5.2018	0.15269	0.0:0.0977:0.1806:0.7217	rs2425049;rs3795160;rs56737880;rs2425049	621	Q9BQN1	FA83C_HUMAN	Q	621	ENSP00000363529:R621Q	ENSP00000363529:R621Q	R	-	2	0	FAM83C	33338134	0.088000	0.21588	0.334000	0.25495	0.004000	0.04260	0.401000	0.20948	0.332000	0.23536	-0.361000	0.07541	CGG	C|0.647;T|0.353	0.353	strong		0.627	FAM83C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078854.3		
POLR1A	25885	hgsc.bcm.edu	37	2	86305404	86305404	+	Missense_Mutation	SNP	T	T	C	rs35239368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86305404T>C	ENST00000263857.6	-	10	1468	c.1090A>G	c.(1090-1092)Aaa>Gaa	p.K364E	POLR1A_ENST00000409681.1_Missense_Mutation_p.K364E			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	364			K -> E (in dbSNP:rs35239368).		gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						AAAGAGTCTTTTTCCTGGAAG	0.408													T|||	658	0.13139	0.447	0.036	5008	,	,		19186	0.0		0.003	False		,,,				2504	0.0399				p.K364E		Atlas-SNP	.											.	POLR1A	137	.	0			c.A1090G						PASS	.	T	GLU/LYS	1319,2381		256,807,787	94.0	84.0	87.0		1090	1.3	1.0	2	dbSNP_126	87	12,8170		0,12,4079	yes	missense	POLR1A	NM_015425.3	56	256,819,4866	CC,CT,TT		0.1467,35.6486,11.2018	benign	364/1721	86305404	1331,10551	1850	4091	5941	SO:0001583	missense	25885	exon10			AGTCTTTTTCCTG	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1090A>G	2.37:g.86305404T>C	ENSP00000263857:p.Lys364Glu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	212	0.09706959706959707	200	0.4065040650406504	10	0.027624309392265192	0	0.0	2	0.002638522427440633	T	6.764	0.509783	0.12883	0.356486	0.001467	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.66280	-0.2;-0.2	5.22	1.33	0.21861	RNA polymerase, N-terminal (1);	1.947470	0.02022	N	0.047881	T	0.00012	0.0000	N	0.02011	-0.69	0.52501	P	4.700000000001925E-5	B;B	0.11235	0.0;0.004	B;B	0.08055	0.001;0.003	T	0.32719	-0.9896	9	0.02654	T	1	-9.8026	6.3055	0.21137	0.1469:0.0:0.4215:0.4317	rs35239368	364;364	B9ZVN9;O95602	.;RPA1_HUMAN	E	364	ENSP00000263857:K364E;ENSP00000386300:K364E	ENSP00000263857:K364E	K	-	1	0	POLR1A	86158915	0.098000	0.21812	0.985000	0.45067	0.766000	0.43426	0.898000	0.28404	0.901000	0.36495	0.459000	0.35465	AAA	T|0.930;C|0.070	0.070	strong		0.408	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
BPIFB4	149954	hgsc.bcm.edu	37	20	31671209	31671209	+	Missense_Mutation	SNP	G	G	C	rs13036385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31671209G>C	ENST00000375483.3	+	3	206	c.206G>C	c.(205-207)cGa>cCa	p.R69P		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	69						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TTCCATGTCCGAGGACCCCCC	0.498													g|||	1080	0.215655	0.1891	0.3069	5008	,	,		11957	0.1528		0.2316	False		,,,				2504	0.2352				p.R69P		Atlas-SNP	.											.	.	.	.	0			c.G206C						PASS	.		PRO/ARG	959,3447	359.4+/-314.8	119,721,1363	88.0	86.0	87.0		206	2.9	0.4	20	dbSNP_121	87	1995,6605	347.8+/-326.7	222,1551,2527	yes	missense	BPIFB4	NM_182519.2	103	341,2272,3890	CC,CG,GG		23.1977,21.7658,22.7126	probably-damaging	69/615	31671209	2954,10052	2203	4300	6503	SO:0001583	missense	149954	exon3			ATGTCCGAGGACC	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.206G>C	20.37:g.31671209G>C	ENSP00000364632:p.Arg69Pro	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	464	0.21245421245421245	78	0.15853658536585366	113	0.31215469613259667	97	0.16958041958041958	176	0.23218997361477572	g	9.146	1.014987	0.19355	0.217658	0.231977	ENSG00000186191	ENST00000375483	T	0.01538	4.79	2.89	2.89	0.33648	.	0.000000	0.28414	U	0.015427	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	8.000000000008E-6	D	0.67145	0.996	D	0.70487	0.969	T	0.57952	-0.7722	9	0.49607	T	0.09	0.036	9.3529	0.38149	0.0:0.0:1.0:0.0	rs13036385;rs52795648;rs13036385	69	P59827	BPIB4_HUMAN	P	69	ENSP00000364632:R69P	ENSP00000364632:R69P	R	+	2	0	BPIFB4	31134870	0.998000	0.40836	0.432000	0.26747	0.013000	0.08279	2.545000	0.45769	1.607000	0.50170	0.306000	0.20318	CGA	G|0.777;C|0.223	0.223	strong		0.498	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
ANKRD55	79722	hgsc.bcm.edu	37	5	55412471	55412471	+	Silent	SNP	C	C	T	rs60779428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:55412471C>T	ENST00000341048.4	-	9	1087	c.936G>A	c.(934-936)gcG>gcA	p.A312A	ANKRD55_ENST00000504958.2_Silent_p.A269A|ANKRD55_ENST00000505970.2_5'UTR|ANKRD55_ENST00000434982.2_Silent_p.A24A	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	312										breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				GTTTGACACACGCCGTGTGAC	0.468													C|||	417	0.0832668	0.233	0.0389	5008	,	,		15115	0.001		0.0497	False		,,,				2504	0.0317				p.A312A		Atlas-SNP	.											ANKRD55,NS,malignant_melanoma,-2,2	ANKRD55	70	2	0			c.G936A						PASS	.	C		958,3448	362.1+/-316.0	106,746,1351	101.0	106.0	104.0		936	-0.1	0.3	5	dbSNP_129	104	470,8130	138.7+/-195.5	10,450,3840	no	coding-synonymous	ANKRD55	NM_024669.2		116,1196,5191	TT,TC,CC		5.4651,21.7431,10.9795		312/615	55412471	1428,11578	2203	4300	6503	SO:0001819	synonymous_variant	79722	exon9			GACACACGCCGTG	AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"""Ankyrin repeat domain containing"""	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.936G>A	5.37:g.55412471C>T		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	275	135	0.490909	NM_024669	B3KVT8|Q3KP45|Q9HAD3	Silent	SNP	ENST00000341048.4	37	CCDS34161.1																																																																																			C|0.907;T|0.093	0.093	strong		0.468	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368510.4	NM_024669	
OR10G9	219870	hgsc.bcm.edu	37	11	123893745	123893745	+	Missense_Mutation	SNP	C	C	T	rs79715120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123893745C>T	ENST00000375024.1	+	1	26	c.26C>T	c.(25-27)gCg>gTg	p.A9V		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A9E(1)|p.A9V(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)		CTCGTGACAGCGTTCATCCTC	0.542													c|||	607	0.121206	0.2269	0.1643	5008	,	,		20512	0.1448		0.007	False		,,,				2504	0.0409				p.A9V		Atlas-SNP	.											OR10G9,NS,carcinoma,-1,2	OR10G9	80	2	2	Substitution - Missense(2)	lung(1)|stomach(1)	c.C26T						scavenged	.	T	VAL/ALA	738,3664	302.7+/-287.5	63,612,1526	166.0	160.0	162.0		26	0.1	0.0	11	dbSNP_131	162	31,8567	19.8+/-62.0	0,31,4268	no	missense	OR10G9	NM_001001953.1	64	63,643,5794	TT,TC,CC		0.3605,16.7651,5.9154	benign	9/312	123893745	769,12231	2201	4299	6500	SO:0001583	missense	219870	exon1			TGACAGCGTTCAT	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.26C>T	11.37:g.123893745C>T	ENSP00000364164:p.Ala9Val	Somatic	453	2	0.00441501		WXS	Illumina HiSeq	Phase_I	293	280	0.955631	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	268	0.1227106227106227	110	0.22357723577235772	69	0.19060773480662985	83	0.1451048951048951	6	0.0079155672823219	c	6.990	0.552700	0.13374	0.167651	0.003605	ENSG00000236981	ENST00000375024	T	0.01099	5.34	3.33	0.0811	0.14423	.	1.672720	0.03223	N	0.177899	T	0.00012	0.0000	N	0.03948	-0.315	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.46470	-0.9189	9	0.66056	D	0.02	.	3.9561	0.09390	0.2761:0.4281:0.0:0.2959	.	9	Q8NGN4	O10G9_HUMAN	V	9	ENSP00000364164:A9V	ENSP00000364164:A9V	A	+	2	0	OR10G9	123398955	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.570000	0.05895	-0.395000	0.07715	-4.114000	0.00011	GCG	C|0.925;T|0.075	0.075	strong		0.542	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
GNPDA1	10007	hgsc.bcm.edu	37	5	141381630	141381630	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141381630C>T	ENST00000508177.1	-	6	1592	c.834G>A	c.(832-834)gaG>gaA	p.E278E	GNPDA1_ENST00000458112.2_Silent_p.E244E|GNPDA1_ENST00000513454.1_Intron|GNPDA1_ENST00000311337.6_Silent_p.E278E|GNPDA1_ENST00000503794.1_Silent_p.E278E|GNPDA1_ENST00000500692.2_Silent_p.E278E|GNPDA1_ENST00000542860.1_Silent_p.E201E			P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1	278					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)			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)			ATTGGCTTTTCTCAGTTTCTT	0.383																																					p.E278E		Atlas-SNP	.											GNPDA1,colon,carcinoma,0,1	GNPDA1	16	1	0			c.G834A						scavenged	.						139.0	133.0	135.0					5																	141381630		2203	4300	6503	SO:0001819	synonymous_variant	10007	exon7			GCTTTTCTCAGTT	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.834G>A	5.37:g.141381630C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	131	4	0.0305344	NM_005471	B7Z3X4|D3DQE7	Silent	SNP	ENST00000508177.1	37	CCDS4272.1																																																																																			.	.	none		0.383	GNPDA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370631.1	NM_005471	
OR5D14	219436	hgsc.bcm.edu	37	11	55563738	55563738	+	Missense_Mutation	SNP	G	G	A	rs67863827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55563738G>A	ENST00000335605.1	+	1	707	c.707G>A	c.(706-708)cGc>cAc	p.R236H		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R236H(1)		breast(1)|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)				GTTAGTGGGCGCCACAAAGCC	0.458													g|||	447	0.0892572	0.1301	0.0432	5008	,	,		18674	0.0823		0.0924	False		,,,				2504	0.0706				p.R236H		Atlas-SNP	.											OR5D14,rectum,carcinoma,+1,4	OR5D14	116	4	1	Substitution - Missense(1)	stomach(1)	c.G707A						PASS	.	G	HIS/ARG	526,3874	239.6+/-250.7	35,456,1709	129.0	120.0	123.0		707	2.1	0.0	11	dbSNP_130	123	722,7870	176.0+/-226.0	31,660,3605	yes	missense	OR5D14	NM_001004735.1	29	66,1116,5314	AA,AG,GG		8.4032,11.9545,9.6059	benign	236/315	55563738	1248,11744	2200	4296	6496	SO:0001583	missense	219436	exon1			GTGGGCGCCACAA	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.707G>A	11.37:g.55563738G>A	ENSP00000334456:p.Arg236His	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	261	112	0.429119	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	196	0.08974358974358974	76	0.15447154471544716	20	0.055248618784530384	35	0.06118881118881119	65	0.08575197889182058	g	6.197	0.404439	0.11754	0.119545	0.084032	ENSG00000186113	ENST00000335605	T	0.00333	8.07	5.08	2.13	0.27403	GPCR, rhodopsin-like superfamily (1);	0.172823	0.25774	N	0.028382	T	0.00012	0.0000	M	0.79805	2.47	0.80722	P	0.0	B	0.26512	0.151	B	0.29524	0.103	T	0.36696	-0.9737	9	0.54805	T	0.06	-3.9031	5.4947	0.16795	0.2359:0.0:0.6227:0.1413	.	236	Q8NGL3	OR5DE_HUMAN	H	236	ENSP00000334456:R236H	ENSP00000334456:R236H	R	+	2	0	OR5D14	55320314	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.512000	0.02258	0.164000	0.19529	0.643000	0.83706	CGC	G|0.907;A|0.093	0.093	strong		0.458	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735	
EVC	2121	hgsc.bcm.edu	37	4	5721049	5721049	+	Silent	SNP	A	A	G	rs35870680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	155	0	0		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	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		
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552537	43552537	+	Silent	SNP	G	G	A	rs71238846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43552537G>A	ENST00000430334.3	-	4	985	c.852C>T	c.(850-852)tgC>tgT	p.C284C	PLEKHM1_ENST00000421073.2_Silent_p.C195C	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	284					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					TGGGCTCCTCGCAATGGTCTG	0.572													G|||	412	0.0822684	0.0378	0.1556	5008	,	,		18814	0.001		0.1958	False		,,,				2504	0.0573				p.C284C		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.C852T						PASS	.	G		281,4125	157.0+/-190.0	10,261,1932	50.0	47.0	48.0		852	0.9	0.5	17	dbSNP_130	48	1648,6952	303.6+/-306.5	155,1338,2807	no	coding-synonymous	PLEKHM1	NM_014798.2		165,1599,4739	AA,AG,GG		19.1628,6.3777,14.8316		284/1057	43552537	1929,11077	2203	4300	6503	SO:0001819	synonymous_variant	9842	exon4			CTCCTCGCAATGG	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.852C>T	17.37:g.43552537G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	207	97	0.468599	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			G|0.865;A|0.135	0.135	strong		0.572	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
FTH1P18	441490	hgsc.bcm.edu	37	X	37061389	37061389	+	IGR	SNP	C	C	T	rs28675922		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37061389C>T								FAM47C (31650 upstream) : PRRG1 (147138 downstream)																							TCTGGCTTCCCGACGTCATGA	0.622													t|||	1160	0.307285	0.5545	0.2262	3775	,	,		12980	0.0734		0.0726	False		,,,				2504	0.1258				p.G125R		Atlas-SNP	.											.	.	.	.	0			c.G373A						PASS	.																																			SO:0001628	intergenic_variant	441490	exon1			GCTTCCCGACGTC																													X.37:g.37061389C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_001271682		Missense_Mutation	SNP		37																																																																																				C|0.736;T|0.264	0.264	strong	0	0.622								
RBM10	8241	hgsc.bcm.edu	37	X	47041414	47041414	+	Silent	SNP	C	C	T	rs112102343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47041414C>T	ENST00000377604.3	+	16	2500	c.1758C>T	c.(1756-1758)acC>acT	p.T586T	RBM10_ENST00000345781.6_Silent_p.T509T|RBM10_ENST00000329236.7_Silent_p.T508T	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	586	Tyr-rich.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						ACCCCCAGACCGGCCTCTACT	0.602													C|||	41	0.0108609	0.028	0.0043	3775	,	,		13729	0.001		0.0	False		,,,				2504	0.0				p.T651T	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.C1953T						PASS	.		,,,,	149,3686		3,118,25,1511,546	84.0	75.0	78.0		1527,1755,1953,1758,1524	-8.1	0.9	X	dbSNP_132	78	2,6726		0,2,0,2426,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RBM10	NM_001204466.1,NM_001204467.1,NM_001204468.1,NM_005676.4,NM_152856.2	,,,,	3,120,25,3937,2418	TT,TC,T,CC,C		0.0297,3.8853,1.4295	,,,,	509/854,585/930,651/996,586/931,508/853	47041414	151,10412	2203	4300	6503	SO:0001819	synonymous_variant	8241	exon16			CCAGACCGGCCTC	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.1758C>T	X.37:g.47041414C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	144	73	0.506944	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Silent	SNP	ENST00000377604.3	37	CCDS14274.1																																																																																			C|0.986;T|0.014	0.014	strong		0.602	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	
HS3ST3B1	9953	hgsc.bcm.edu	37	17	14248345	14248345	+	Splice_Site	SNP	G	G	A	rs77608217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:14248345G>A	ENST00000360954.2	+	2	991	c.555G>A	c.(553-555)cgG>cgA	p.R185R		NM_006041.1	NP_006032.1	Q9Y662	HS3SB_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	185					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)			large_intestine(3)|lung(3)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)		CGTTTCTCAGGGACCTGATGC	0.577													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17223	0.0		0.0	False		,,,				2504	0.0				p.R185R		Atlas-SNP	.											.	HS3ST3B1	19	.	0			c.G555A						PASS	.	G		70,4336	62.9+/-100.1	1,68,2134	61.0	63.0	63.0		555	2.6	1.0	17	dbSNP_131	63	0,8600		0,0,4300	yes	coding-synonymous-near-splice	HS3ST3B1	NM_006041.1		1,68,6434	AA,AG,GG		0.0,1.5887,0.5382		185/391	14248345	70,12936	2203	4300	6503	SO:0001630	splice_region_variant	9953	exon2			TCTCAGGGACCTG	AF105377	CCDS11167.1	17p12	2007-04-02			ENSG00000125430	ENSG00000125430	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5198	protein-coding gene	gene with protein product		604058				9988767	Standard	NM_006041		Approved	3OST3B1, 30ST3B1	uc002goh.1	Q9Y662	OTTHUMG00000058810	ENST00000360954.2:c.555-1G>A	17.37:g.14248345G>A		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	290	148	0.510345	NM_006041	B3KN58|D3DTS6	Silent	SNP	ENST00000360954.2	37	CCDS11167.1																																																																																			G|0.995;A|0.005	0.005	strong		0.577	HS3ST3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129998.1	NM_006041	Silent
ANKRD36B	57730	hgsc.bcm.edu	37	2	98165911	98165911	+	RNA	SNP	T	T	C	rs1839230|rs112877086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98165911T>C	ENST00000443455.1	-	0	1558							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		ATCCTTTTTTTCTCTGGCTAT	0.308													.|||	980	0.195687	0.5703	0.1239	5008	,	,		38822	0.0069		0.1004	False		,,,				2504	0.0327				p.E483G		Atlas-SNP	.											.	.	.	.	0			c.A1448G						PASS	.						45.0	18.0	26.0					2																	98165911		1759	3782	5541			57730	exon20			TTTTTTTCTCTGG	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98165911T>C		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	14	8	0.571429	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				T|0.848;C|0.152	0.152	strong		0.308	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
C2orf54	79919	hgsc.bcm.edu	37	2	241835110	241835110	+	Missense_Mutation	SNP	G	G	A	rs146162100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241835110G>A	ENST00000388934.4	-	1	463	c.305C>T	c.(304-306)cCg>cTg	p.P102L		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	102										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)		GCCATCCTCCGGCTGGGTGGC	0.637													G|||	47	0.00938498	0.0348	0.0	5008	,	,		21036	0.0		0.0	False		,,,				2504	0.001				p.P102L		Atlas-SNP	.											.	C2orf54	14	.	0			c.C305T						PASS	.	G	LEU/PRO	108,3930		1,106,1912	39.0	43.0	42.0		305	2.0	0.0	2	dbSNP_134	42	0,8320		0,0,4160	yes	missense	C2orf54	NM_001085437.1	98	1,106,6072	AA,AG,GG		0.0,2.6746,0.8739	benign	102/448	241835110	108,12250	2019	4160	6179	SO:0001583	missense	79919	exon1			TCCTCCGGCTGGG	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.305C>T	2.37:g.241835110G>A	ENSP00000373586:p.Pro102Leu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	142	68	0.478873	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Missense_Mutation	SNP	ENST00000388934.4	37	CCDS42839.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	G	4.191	0.034120	0.08101	0.026746	0.0	ENSG00000172478	ENST00000388934;ENST00000414499;ENST00000454476	T;T;T	0.11495	2.77;2.77;2.77	4.87	2.03	0.26663	.	0.889113	0.09556	N	0.786255	T	0.01730	0.0055	L	0.40543	1.245	0.09310	N	1	B	0.18461	0.028	B	0.13407	0.009	T	0.40021	-0.9585	10	0.27082	T	0.32	4.8878	4.8735	0.13644	0.2407:0.0:0.558:0.2014	.	102	Q08AI8	CB054_HUMAN	L	102;102;92	ENSP00000373586:P102L;ENSP00000390935:P102L;ENSP00000394874:P92L	ENSP00000373586:P102L	P	-	2	0	C2orf54	241483783	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-0.397000	0.07269	0.474000	0.27392	0.561000	0.74099	CCG	G|0.990;A|0.010	0.010	strong		0.637	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
MUC17	140453	hgsc.bcm.edu	37	7	100677630	100677630	+	Missense_Mutation	SNP	C	C	T	rs78990442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677630C>T	ENST00000306151.4	+	3	2997	c.2933C>T	c.(2932-2934)cCt>cTt	p.P978L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	978	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)					ACCTCGACTCCTAGTGAAGGA	0.512													C|||	1003	0.20028	0.2678	0.0994	5008	,	,		34431	0.2282		0.1113	False		,,,				2504	0.2434				p.P978L		Atlas-SNP	.											.	MUC17	804	.	0			c.C2933T						PASS	.	C	LEU/PRO	912,3494		0,912,1291	355.0	332.0	340.0		2933	0.6	0.0	7	dbSNP_131	340	814,7786		0,814,3486	no	missense	MUC17	NM_001040105.1	98	0,1726,4777	TT,TC,CC		9.4651,20.699,13.2708	probably-damaging	978/4494	100677630	1726,11280	2203	4300	6503	SO:0001583	missense	140453	exon3			CGACTCCTAGTGA	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.2933C>T	7.37:g.100677630C>T	ENSP00000302716:p.Pro978Leu	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	259	124	0.478764	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	4.251	0.045554	0.08196	0.20699	0.094651	ENSG00000169876	ENST00000306151	T	0.03242	4.0	0.632	0.632	0.17705	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.21604	N	0.999623	D	0.76494	0.999	D	0.71184	0.972	T	0.50608	-0.8808	9	0.13853	T	0.58	.	7.1889	0.25814	0.0:0.9999:0.0:1.0E-4	.	978	Q685J3	MUC17_HUMAN	L	978	ENSP00000302716:P978L	ENSP00000302716:P978L	P	+	2	0	MUC17	100464350	0.000000	0.05858	0.013000	0.15412	0.007000	0.05969	-0.008000	0.12788	0.647000	0.30713	0.134000	0.15878	CCT	C|0.935;T|0.065	0.065	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
HBS1L	10767	hgsc.bcm.edu	37	6	135358398	135358398	+	Intron	SNP	G	G	A	rs116294454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135358398G>A	ENST00000367837.5	-	4	637				HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367822.5_Silent_p.N399N|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000314674.3_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		CAGATGACTGGTTACAAAGGT	0.408													G|||	88	0.0175719	0.0628	0.0072	5008	,	,		19700	0.0		0.0	False		,,,				2504	0.0				p.N399N		Atlas-SNP	.											.	HBS1L	75	.	0			c.C1197T						PASS	.	G	,,	48,1336		1,46,645	138.0	114.0	122.0		,1197,	3.8	0.5	6	dbSNP_132	122	2,3180		0,2,1589	no	intron,coding-synonymous,intron	HBS1L	NM_001145158.1,NM_001145207.1,NM_006620.3	,,	1,48,2234	AA,AG,GG		0.0629,3.4682,1.0951	,,	,399/633,	135358398	50,4516	692	1591	2283	SO:0001627	intron_variant	10767	exon5			TGACTGGTTACAA	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2312C>T	6.37:g.135358398G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1																																																																																			G|0.978;A|0.022	0.022	strong		0.408	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
OR52K2	119774	hgsc.bcm.edu	37	11	4471473	4471473	+	Missense_Mutation	SNP	C	C	T	rs7934336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4471473C>T	ENST00000325719.4	+	1	949	c.904C>T	c.(904-906)Cgt>Tgt	p.R302C		NM_001005172.2	NP_001005172.2	Q8NGK3	O52K2_HUMAN	olfactory receptor, family 52, subfamily K, member 2	302			R -> C (in dbSNP:rs7934336).			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)|kidney(1)|large_intestine(4)|lung(10)|skin(6)	25		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.48e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0821)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAAGCAAATCCGTGAGAGCAT	0.498													C|||	633	0.126398	0.3737	0.0706	5008	,	,		21207	0.0347		0.0298	False		,,,				2504	0.0256				p.R302C		Atlas-SNP	.											.	OR52K2	61	.	0			c.C904T						PASS	.	C	CYS/ARG	1407,2995	463.6+/-353.6	216,975,1010	96.0	92.0	94.0		904	2.2	1.0	11	dbSNP_116	94	235,8361	94.7+/-156.6	4,227,4067	yes	missense	OR52K2	NM_001005172.2	180	220,1202,5077	TT,TC,CC		2.7338,31.9627,12.6327	benign	302/315	4471473	1642,11356	2201	4298	6499	SO:0001583	missense	119774	exon1			CAAATCCGTGAGA	AB065791	CCDS31351.1	11p15.4	2012-08-09			ENSG00000181963	ENSG00000181963		"""GPCR / Class A : Olfactory receptors"""	15223	protein-coding gene	gene with protein product							Standard	NM_001005172		Approved		uc001lyz.2	Q8NGK3	OTTHUMG00000165703	ENST00000325719.4:c.904C>T	11.37:g.4471473C>T	ENSP00000318956:p.Arg302Cys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_001005172	A8MUY8|B2RP35|Q6IFK4	Missense_Mutation	SNP	ENST00000325719.4	37	CCDS31351.1	275	0.1259157509157509	206	0.4186991869918699	24	0.06629834254143646	23	0.04020979020979021	22	0.029023746701846966	C	8.510	0.866352	0.17250	0.319627	0.027338	ENSG00000181963	ENST00000325719	T	0.58358	0.34	4.16	2.24	0.28232	.	0.139494	0.32785	N	0.005660	T	0.00012	0.0000	M	0.79614	2.46	0.27898	P	0.9390894	B	0.18310	0.027	B	0.11329	0.006	T	0.25433	-1.0132	9	0.87932	D	0	.	6.7791	0.23636	0.1741:0.7276:0.0:0.0984	rs7934336;rs52810694;rs7934336	302	Q8NGK3	O52K2_HUMAN	C	302	ENSP00000318956:R302C	ENSP00000318956:R302C	R	+	1	0	OR52K2	4428049	0.817000	0.29147	0.990000	0.47175	0.395000	0.30598	2.067000	0.41461	0.387000	0.25024	0.586000	0.80456	CGT	C|0.868;T|0.132	0.132	strong		0.498	OR52K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385844.1	NM_001005172	
DNAH10	196385	hgsc.bcm.edu	37	12	124267703	124267703	+	Silent	SNP	T	T	C	rs11057355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	92	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	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		
REM1	28954	hgsc.bcm.edu	37	20	30070239	30070239	+	Silent	SNP	C	C	A	rs2233832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:30070239C>A	ENST00000201979.2	+	4	866	c.573C>A	c.(571-573)atC>atA	p.I191I		NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	191					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			TGCCCATCATCCTCGTGGGCA	0.607													C|||	711	0.141973	0.0764	0.1383	5008	,	,		20109	0.246		0.0905	False		,,,				2504	0.1789				p.I191I		Atlas-SNP	.											.	REM1	54	.	0			c.C573A						PASS	.	C		422,3984	206.5+/-228.1	21,380,1802	89.0	78.0	82.0		573	5.0	1.0	20	dbSNP_98	82	718,7882	175.6+/-225.6	27,664,3609	no	coding-synonymous	REM1	NM_014012.4		48,1044,5411	AA,AC,CC		8.3488,9.5778,8.7652		191/299	30070239	1140,11866	2203	4300	6503	SO:0001819	synonymous_variant	28954	exon4			CATCATCCTCGTG	AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"""GTPase GES"""	610388	"""RAS (RAD and GEM)-like GTP-binding"""	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.573C>A	20.37:g.30070239C>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_014012	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Silent	SNP	ENST00000201979.2	37	CCDS13181.1																																																																																			C|0.886;A|0.114	0.114	strong		0.607	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012	
MTOR	2475	hgsc.bcm.edu	37	1	11190646	11190646	+	Silent	SNP	G	G	A	rs2275527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11190646G>A	ENST00000361445.4	-	39	5629	c.5553C>T	c.(5551-5553)agC>agT	p.S1851S	MTOR_ENST00000376838.1_Silent_p.S56S|MTOR_ENST00000495435.1_5'Flank	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1851	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCTCGGCCTCGCTCTCACTGT	0.627													G|||	1145	0.228634	0.4486	0.1542	5008	,	,		17004	0.0794		0.2356	False		,,,				2504	0.1309				p.S1851S		Atlas-SNP	.											.	MTOR	327	.	0			c.C5553T						PASS	.	G		1927,2479	549.0+/-377.7	407,1113,683	107.0	88.0	95.0		5553	-5.7	0.9	1	dbSNP_100	95	2052,6548	356.5+/-330.3	249,1554,2497	no	coding-synonymous	MTOR	NM_004958.3		656,2667,3180	AA,AG,GG		23.8605,43.7358,30.5936		1851/2550	11190646	3979,9027	2203	4300	6503	SO:0001819	synonymous_variant	2475	exon39			GGCCTCGCTCTCA	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.5553C>T	1.37:g.11190646G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	171	84	0.491228	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			G|0.716;A|0.284	0.284	strong		0.627	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
NCR1	9437	hgsc.bcm.edu	37	19	55420801	55420801	+	Silent	SNP	C	C	A	rs3765013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55420801C>A	ENST00000291890.4	+	4	591	c.553C>A	c.(553-555)Cga>Aga	p.R185R	NCR1_ENST00000338835.5_Silent_p.R185R|NCR1_ENST00000594765.1_Silent_p.R185R|NCR1_ENST00000350790.5_Silent_p.R90R|NCR1_ENST00000598576.1_Silent_p.R173R|NCR1_ENST00000447255.1_Silent_p.R185R|NCR1_ENST00000357397.5_Silent_p.R78R	NM_004829.5	NP_004820.2	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	185	Ig-like 2.				cellular defense response (GO:0006968)|intracellular signal transduction (GO:0035556)|natural killer cell activation (GO:0030101)|regulation of natural killer cell mediated cytotoxicity (GO:0042269)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|SWI/SNF complex (GO:0016514)	receptor signaling protein activity (GO:0005057)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(193;0.0449)		CACAGCCCACCGAGGGACATA	0.567													.|||	2420	0.483227	0.7148	0.4236	5008	,	,		17754	0.5268		0.2286	False		,,,				2504	0.4294				p.R185R		Atlas-SNP	.											.	NCR1	60	.	0			c.C553A						PASS	.	A	,,,,	2787,1619	498.4+/-364.1	868,1051,284	84.0	82.0	82.0		553,553,268,268,553	-1.5	0.0	19	dbSNP_107	82	1935,6665	726.6+/-406.6	226,1483,2591	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCR1	NM_001145457.1,NM_001145458.1,NM_001242356.1,NM_001242357.1,NM_004829.5	,,,,	1094,2534,2875	AA,AC,CC		22.5,36.7453,36.3063	,,,,	185/304,185/288,90/210,90/193,185/305	55420801	4722,8284	2203	4300	6503	SO:0001819	synonymous_variant	9437	exon4			GCCCACCGAGGGA	AJ001383	CCDS12911.1, CCDS46181.1, CCDS46182.1, CCDS56103.1	19q13.42	2013-09-20	2002-11-13	2002-11-15	ENSG00000189430	ENSG00000189430		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6731	protein-coding gene	gene with protein product		604530	"""lymphocyte antigen 94 (mouse) homolog (activating NK-receptor; NK-p46)"""	LY94		9730896	Standard	NM_001145457		Approved	NK-p46, NKP46, CD335	uc002qib.2	O76036	OTTHUMG00000183212	ENST00000291890.4:c.553C>A	19.37:g.55420801C>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001145458	B0V3L2|B0V3L3|B0V3L4|B0V3L5|B8JL03|O76016|O76017|O76018	Silent	SNP	ENST00000291890.4	37	CCDS12911.1																																																																																			C|0.604;A|0.396	0.396	strong		0.567	NCR1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465680.1		
ZNF319	57567	hgsc.bcm.edu	37	16	58031996	58031996	+	Silent	SNP	G	G	A	rs115738968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58031996G>A	ENST00000299237.2	-	2	796	c.174C>T	c.(172-174)ccC>ccT	p.P58P	USB1_ENST00000561743.1_5'Flank	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	58	Pro-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)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8						GCTGCAGGCCGGGGTCTGGCT	0.701													G|||	42	0.00838658	0.0272	0.0058	5008	,	,		16696	0.0		0.002	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											.	ZNF319	42	.	0			c.C174T						PASS	.	G		102,4294	79.3+/-117.8	4,94,2100	33.0	36.0	35.0		174	-10.4	0.0	16	dbSNP_132	35	19,8577	13.3+/-46.6	0,19,4279	no	coding-synonymous	ZNF319	NM_020807.1		4,113,6379	AA,AG,GG		0.221,2.3203,0.9313		58/583	58031996	121,12871	2198	4298	6496	SO:0001819	synonymous_variant	57567	exon2			CAGGCCGGGGTCT	AB037809	CCDS32462.1	16q21	2013-01-08				ENSG00000166188		"""Zinc fingers, C2H2-type"""	13644	protein-coding gene	gene with protein product						10718198, 11161788	Standard	XM_005256069		Approved	KIAA1388, Zfp319	uc002emx.1	Q9P2F9		ENST00000299237.2:c.174C>T	16.37:g.58031996G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_020807	Q52LH8	Silent	SNP	ENST00000299237.2	37	CCDS32462.1																																																																																			G|0.992;A|0.008	0.008	strong		0.701	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1		
LZTS2	84445	hgsc.bcm.edu	37	10	102762439	102762439	+	Silent	SNP	C	C	T	rs142122181|rs35061268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102762439C>T	ENST00000370220.1	+	1	3207	c.144C>T	c.(142-144)caC>caT	p.H48H	LZTS2_ENST00000370223.3_Silent_p.H48H					leucine zipper, putative tumor suppressor 2											breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		CCCGCCACCACGGCCCTCCTG	0.682													C|||	6	0.00119808	0.003	0.0014	5008	,	,		16468	0.0		0.001	False		,,,				2504	0.0				p.H48H	Esophageal Squamous(8;38 437 13604 19902 37640)	Atlas-SNP	.											.	LZTS2	57	.	0			c.C144T						PASS	.	C		22,4384		0,22,2181	36.0	43.0	41.0		144	-9.3	0.0	10	dbSNP_134	41	2,8596		0,2,4297	no	coding-synonymous	LZTS2	NM_032429.2		0,24,6478	TT,TC,CC		0.0233,0.4993,0.1846		48/670	102762439	24,12980	2203	4299	6502	SO:0001819	synonymous_variant	84445	exon2			CCACCACGGCCCT	AB058716	CCDS7507.1	10q24	2004-03-18			ENSG00000107816	ENSG00000107816			29381	protein-coding gene	gene with protein product		610454				11347906, 11709705	Standard	NM_032429		Approved	KIAA1813, LAPSER1	uc001ksj.3	Q9BRK4	OTTHUMG00000018914	ENST00000370220.1:c.144C>T	10.37:g.102762439C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	122	70	0.57377	NM_032429		Silent	SNP	ENST00000370220.1	37	CCDS7507.1																																																																																			C|0.998;T|0.002	0.002	strong		0.682	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743	
C1orf127	148345	hgsc.bcm.edu	37	1	11009679	11009679	+	Splice_Site	SNP	G	G	A	rs1281013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11009679G>A	ENST00000377008.4	-	10	1236		c.e10+1		C1orf127_ENST00000377004.4_Splice_Site			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127											NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CCATAGACGTGCTTTGGCCAG	0.612													G|||	346	0.0690895	0.2035	0.0144	5008	,	,		17717	0.004		0.0427	False		,,,				2504	0.0204				.		Atlas-SNP	.											.	C1orf127	134	.	0			c.1290+2C>T						PASS	.	G		719,3679		64,591,1544	34.0	29.0	31.0			-0.6	0.0	1	dbSNP_87	31	331,8269		4,323,3973	yes	splice-5	C1orf127	NM_001170754.1		68,914,5517	AA,AG,GG		3.8488,16.3483,8.0782			11009679	1050,11948	2199	4300	6499	SO:0001630	splice_region_variant	148345	exon12			AGACGTGCTTTGG	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.789+1C>T	1.37:g.11009679G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Splice_Site	SNP	ENST00000377008.4	37		166	0.076007326007326	122	0.24796747967479674	4	0.011049723756906077	1	0.0017482517482517483	39	0.051451187335092345	G	2.596	-0.293985	0.05568	0.163483	0.038488	ENSG00000175262	ENST00000418570;ENST00000377004;ENST00000377008	.	.	.	3.68	-0.578	0.11724	.	.	.	.	.	.	.	.	.	.	.	0.51012	P	9.899999999996023E-5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.2328	0.01946	0.2149:0.1807:0.4347:0.1697	rs1281013;rs1281013	.	.	.	.	-1	.	.	.	-	.	.	C1orf127	10932266	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.106000	0.15354	-0.247000	0.09597	-0.354000	0.07668	.	G|0.907;A|0.093	0.093	strong		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	Intron
OR6P1	128366	hgsc.bcm.edu	37	1	158532908	158532908	+	Missense_Mutation	SNP	T	T	C	rs114056876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158532908T>C	ENST00000334632.1	-	1	486	c.487A>G	c.(487-489)Att>Gtt	p.I163V		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	163						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						AATTGGGAAATAAAAAGAAGC	0.493													T|||	79	0.0157748	0.0582	0.0029	5008	,	,		21050	0.0		0.0	False		,,,				2504	0.0				p.I163V		Atlas-SNP	.											.	OR6P1	47	.	0			c.A487G						PASS	.	T	VAL/ILE	76,1308		3,70,619	63.0	61.0	61.0		487	4.0	1.0	1	dbSNP_132	61	1,3181		0,1,1590	yes	missense	OR6P1	NM_001160325.1	29	3,71,2209	CC,CT,TT		0.0314,5.4913,1.6864	probably-damaging	163/318	158532908	77,4489	692	1591	2283	SO:0001583	missense	128366	exon1			GGGAAATAAAAAG	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.487A>G	1.37:g.158532908T>C	ENSP00000334721:p.Ile163Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_001160325	Q6IFR9	Missense_Mutation	SNP	ENST00000334632.1	37	CCDS53391.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	T	10.53	1.375197	0.24857	0.054913	3.14E-4	ENSG00000186440	ENST00000334632	T	0.00069	8.77	5.11	3.95	0.45737	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000248	T	0.00109	0.0003	L	0.35414	1.06	0.09310	N	1	D	0.71674	0.998	D	0.80764	0.994	T	0.41645	-0.9497	10	0.32370	T	0.25	.	6.8131	0.23814	0.0:0.0827:0.1524:0.7648	.	163	Q8NGX9	OR6P1_HUMAN	V	163	ENSP00000334721:I163V	ENSP00000334721:I163V	I	-	1	0	OR6P1	156799532	0.003000	0.15002	0.998000	0.56505	0.033000	0.12548	0.919000	0.28692	2.147000	0.66899	0.482000	0.46254	ATT	T|0.988;C|0.012	0.012	strong		0.493	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
PCDHA5	56143	hgsc.bcm.edu	37	5	140201418	140201418	+	Missense_Mutation	SNP	C	C	T	rs386692889|rs56285019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140201418C>T	ENST00000529859.1	+	1	58	c.58C>T	c.(58-60)Ctt>Ttt	p.L20F	PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.L20F|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.L20F|PCDHA1_ENST00000504120.2_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	20					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGCTTCTCCTTGCCTACTG	0.567													.|||	264	0.0527157	0.1952	0.0058	5008	,	,		14691	0.001		0.001	False		,,,				2504	0.0				p.L20F		Atlas-SNP	.											.	PCDHA5	361	.	0			c.C58T						PASS	.	C	,,,,PHE/LEU,,PHE/LEU	13,4393		4,5,2194	61.0	68.0	66.0		,,,,58,,58	2.0	0.0	5	dbSNP_129	66	0,8600		0,0,4300	yes	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,22,,22	4,5,6494	TT,TC,CC		0.0,0.2951,0.1	,,,,,,	,,,,20/937,,20/817	140201418	13,12993	2203	4300	6503	SO:0001583	missense	56143	exon1			CTTCTCCTTGCCT	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.58C>T	5.37:g.140201418C>T	ENSP00000436557:p.Leu20Phe	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	76	0.0347985347985348	73	0.1483739837398374	3	0.008287292817679558	0	0.0	0	0.0	C	2.978	-0.211037	0.06140	0.002951	0.0	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.54479	0.6;0.57;0.6	3.81	2.0	0.26442	.	.	.	.	.	T	0.00271	0.0008	L	0.52823	1.66	0.80722	P	0.0	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.08055	0.001;0.002;0.003	T	0.12889	-1.0530	8	0.11794	T	0.64	.	7.5552	0.27820	0.0:0.7302:0.0:0.2698	rs56285019;rs61730628	20;20;20	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	F	20	ENSP00000433416:L20F;ENSP00000436557:L20F;ENSP00000367366:L20F	ENSP00000367366:L20F	L	+	1	0	PCDHA5	140181602	0.000000	0.05858	0.012000	0.15200	0.358000	0.29455	-0.212000	0.09319	0.224000	0.20940	0.543000	0.68304	CTT	C|0.952;T|0.048	0.048	strong		0.567	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
DDX11	1663	hgsc.bcm.edu	37	12	31254820	31254820	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:31254820G>A	ENST00000407793.2	+	21	2357	c.2106G>A	c.(2104-2106)ggG>ggA	p.G702G	DDX11_ENST00000350437.4_Intron|DDX11_ENST00000228264.6_Silent_p.G676G|DDX11_ENST00000545668.1_Silent_p.G702G|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Silent_p.G702G	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	702					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)					TTCCTGGAGGGGTGGTCTGTT	0.622										Multiple Myeloma(12;0.14)																											p.G702G		Atlas-SNP	.											DDX11,NS,carcinoma,+2,1	DDX11	188	1	0			c.G2106A						scavenged	.						159.0	155.0	156.0					12																	31254820		1961	4141	6102	SO:0001819	synonymous_variant	1663	exon21			TGGAGGGGTGGTC	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.2106G>A	12.37:g.31254820G>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	239	4	0.0167364	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	37	CCDS44856.1																																																																																			.	.	none		0.622	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
PDE10A	10846	hgsc.bcm.edu	37	6	165801790	165801790	+	Silent	SNP	G	G	A	rs1511746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:165801790G>A	ENST00000366882.1	-	18	1933	c.1779C>T	c.(1777-1779)ctC>ctT	p.L593L	PDE10A_ENST00000354448.4_Silent_p.L593L|PDE10A_ENST00000539869.2_Silent_p.L603L			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	593					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	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)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	GACTCACCTGGAGGATGGACA	0.532													G|||	906	0.180911	0.348	0.1297	5008	,	,		15923	0.003		0.1491	False		,,,				2504	0.2076				p.L603L	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											.	PDE10A	154	.	0			c.C1809T						PASS	.	G	,	1355,3051	452.2+/-349.9	205,945,1053	145.0	123.0	130.0		1809,1779	-11.8	0.9	6	dbSNP_88	130	1249,7351	249.9+/-277.0	88,1073,3139	no	coding-synonymous,coding-synonymous	PDE10A	NM_001130690.1,NM_006661.2	,	293,2018,4192	AA,AG,GG		14.5233,30.7535,20.0215	,	603/790,593/780	165801790	2604,10402	2203	4300	6503	SO:0001819	synonymous_variant	10846	exon17			CACCTGGAGGATG	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"""Phosphodiesterases"""	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.1779C>T	6.37:g.165801790G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Silent	SNP	ENST00000366882.1	37																																																																																				G|0.806;A|0.194	0.194	strong		0.532	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1		
ARMC5	79798	hgsc.bcm.edu	37	16	31477795	31477795	+	Missense_Mutation	SNP	G	G	C	rs115611533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31477795G>C	ENST00000563544.1	+	7	2939	c.2393G>C	c.(2392-2394)gGt>gCt	p.G798A	ARMC5_ENST00000412665.2_Missense_Mutation_p.G442A|ARMC5_ENST00000408912.3_Missense_Mutation_p.G893A|ARMC5_ENST00000457010.2_3'UTR|ARMC5_ENST00000268314.4_Missense_Mutation_p.G798A|ARMC5_ENST00000538189.1_Missense_Mutation_p.G830A			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	798	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CTGTCGCCTGGTGCAGCCTGG	0.687													g|||	41	0.0081869	0.0287	0.0043	5008	,	,		16435	0.0		0.0	False		,,,				2504	0.0				p.G798A		Atlas-SNP	.											.	ARMC5	94	.	0			c.G2393C						PASS	.		ALA/GLY,	94,3996		2,90,1953	29.0	35.0	33.0		2393,	4.7	0.3	16	dbSNP_132	33	1,8347		0,1,4173	yes	missense,utr-3	ARMC5	NM_001105247.1,NM_024742.2	60,	2,91,6126	CC,CG,GG		0.012,2.2983,0.7638	benign,	798/936,	31477795	95,12343	2045	4174	6219	SO:0001583	missense	79798	exon6			CGCCTGGTGCAGC	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.2393G>C	16.37:g.31477795G>C	ENSP00000456877:p.Gly798Ala	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_001105247	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	g	0.136	-1.108013	0.01813	0.022983	1.2E-4	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000412665	T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45	5.64	4.69	0.59074	BTB/POZ-like (1);BTB/POZ fold (1);	0.393509	0.28549	N	0.014953	T	0.22244	0.0536	N	0.13235	0.315	0.09310	N	1	B;B;B;B	0.22800	0.031;0.031;0.075;0.015	B;B;B;B	0.20184	0.028;0.028;0.017;0.012	T	0.07214	-1.0784	10	0.10377	T	0.69	-26.6313	12.3369	0.55073	0.0816:0.0:0.9184:0.0	.	830;830;893;798	B4DH27;F5H156;B4DIU9;Q96C12	.;.;.;ARMC5_HUMAN	A	893;830;798;442	ENSP00000386125:G893A;ENSP00000443995:G830A;ENSP00000268314:G798A;ENSP00000400183:G442A	ENSP00000268314:G798A	G	+	2	0	ARMC5	31385296	0.704000	0.27836	0.271000	0.24616	0.056000	0.15407	4.288000	0.59007	1.389000	0.46526	0.546000	0.68486	GGT	G|0.992;C|0.008	0.008	strong		0.687	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2389793	2389793	+	Missense_Mutation	SNP	A	A	G	rs8100709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2389793A>G	ENST00000332578.3	+	1	10	c.10A>G	c.(10-12)Act>Gct	p.T4A		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	4			T -> A (in dbSNP:rs8100709).		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)		CATGGAGCCCACTGTGGCTGA	0.617													A|||	250	0.0499201	0.1815	0.0101	5008	,	,		19564	0.0		0.003	False		,,,				2504	0.0				p.T4A		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.A10G						PASS	.	A	ALA/THR	754,3652	303.2+/-287.8	55,644,1504	63.0	45.0	51.0		10	-4.2	0.0	19	dbSNP_116	51	20,8580	13.3+/-46.6	0,20,4280	yes	missense	TMPRSS9	NM_182973.1	58	55,664,5784	GG,GA,AA		0.2326,17.113,5.9511	benign	4/1060	2389793	774,12232	2203	4300	6503	SO:0001583	missense	360200	exon1			GAGCCCACTGTGG	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.10A>G	19.37:g.2389793A>G	ENSP00000330264:p.Thr4Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	84	0.038461538461538464	81	0.16463414634146342	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	2.015	-0.426184	0.04701	0.17113	0.002326	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.87256	-2.23	4.16	-4.2	0.03823	.	1.292730	0.05536	N	0.564908	T	0.00524	0.0017	N	0.11560	0.145	0.80722	P	0.0	B;B	0.09022	0.0;0.002	B;B	0.04013	0.001;0.001	T	0.07558	-1.0766	9	0.29301	T	0.29	.	12.5441	0.56188	0.2898:0.0:0.7102:0.0	rs8100709;rs52805984;rs8100709	4;4	Q7Z410;E7EMP4	TMPS9_HUMAN;.	A	4	ENSP00000330264:T4A	ENSP00000330264:T4A	T	+	1	0	TMPRSS9	2340793	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.994000	0.03716	-0.882000	0.03987	-0.432000	0.05891	ACT	A|0.948;G|0.052	0.052	strong		0.617	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
LLGL2	3993	hgsc.bcm.edu	37	17	73559453	73559453	+	Silent	SNP	C	C	T	rs139362844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73559453C>T	ENST00000392550.3	+	8	852	c.735C>T	c.(733-735)ctC>ctT	p.L245L	LLGL2_ENST00000375227.4_Silent_p.L245L|LLGL2_ENST00000578363.1_Silent_p.L245L|LLGL2_ENST00000577200.1_Silent_p.L245L|LLGL2_ENST00000167462.5_Silent_p.L245L	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	245					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			GCCGCCTGCTCGTCAGCTGTC	0.647													C|||	16	0.00319489	0.0121	0.0	5008	,	,		17901	0.0		0.0	False		,,,				2504	0.0				p.L245L		Atlas-SNP	.											.	LLGL2	155	.	0			c.C735T						PASS	.	C	,,	27,4375	30.8+/-60.4	1,25,2175	34.0	33.0	33.0		735,735,735	-7.7	0.6	17	dbSNP_134	33	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	LLGL2	NM_001015002.1,NM_001031803.1,NM_004524.2	,,	1,25,6475	TT,TC,CC		0.0,0.6134,0.2077	,,	245/357,245/1021,245/1016	73559453	27,12975	2201	4300	6501	SO:0001819	synonymous_variant	3993	exon8			CCTGCTCGTCAGC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.735C>T	17.37:g.73559453C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_001015002	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	37	CCDS32733.1																																																																																			C|0.996;T|0.004	0.004	strong		0.647	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
MACROD1	28992	hgsc.bcm.edu	37	11	63884453	63884453	+	Intron	SNP	C	C	T	rs3751120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:63884453C>T	ENST00000255681.6	-	3	584				FLRT1_ENST00000246841.3_Silent_p.R238R|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						CCAACCAGCGCATCGCCGACG	0.657													C|||	1768	0.353035	0.6014	0.1873	5008	,	,		19038	0.5377		0.0865	False		,,,				2504	0.2188				p.R238R		Atlas-SNP	.											.	FLRT1	46	.	0			c.C714T						PASS	.	C	,	2191,2211	546.4+/-377.0	556,1079,566	33.0	31.0	32.0		714,	2.5	1.0	11	dbSNP_107	32	616,7978	154.3+/-208.6	29,558,3710	no	coding-synonymous,intron	FLRT1,MACROD1	NM_013280.4,NM_014067.3	,	585,1637,4276	TT,TC,CC		7.1678,49.7728,21.599	,	238/675,	63884453	2807,10189	2201	4297	6498	SO:0001627	intron_variant	23769	exon2			CCAGCGCATCGCC	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+34257G>A	11.37:g.63884453C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			C|0.702;T|0.298	0.298	strong		0.657	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
NSUN5	55695	hgsc.bcm.edu	37	7	72717686	72717686	+	Silent	SNP	C	C	T	rs145622470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:72717686C>T	ENST00000252594.6	-	9	1212	c.1197G>A	c.(1195-1197)ccG>ccA	p.P399P	NSUN5_ENST00000438747.2_Silent_p.P399P|NSUN5_ENST00000310326.8_Silent_p.P399P|NSUN5_ENST00000428206.1_Silent_p.P361P			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	399					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)				GCTCGGCACCCGGGAACGTGC	0.642													.|||	35	0.00698882	0.025	0.0029	5008	,	,		16592	0.0		0.0	False		,,,				2504	0.0				p.P399P		Atlas-SNP	.											.	NSUN5	47	.	0			c.G1197A						PASS	.	C	,,,	92,4314		0,92,2111	49.0	48.0	48.0		1197,1083,1197,1197	-4.7	0.0	7	dbSNP_134	48	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NSUN5	NM_001168347.1,NM_001168348.1,NM_018044.3,NM_148956.2	,,,	0,92,6411	TT,TC,CC		0.0,2.0881,0.7074	,,,	399/471,361/392,399/430,399/467	72717686	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	55695	exon9			GGCACCCGGGAAC	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.1197G>A	7.37:g.72717686C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	131	70	0.534351	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Silent	SNP	ENST00000252594.6	37	CCDS5547.1																																																																																			C|0.993;T|0.007	0.007	strong		0.642	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
AHNAK2	113146	hgsc.bcm.edu	37	14	105405942	105405942	+	Silent	SNP	G	G	A	rs28454709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105405942G>A	ENST00000333244.5	-	7	15965	c.15846C>T	c.(15844-15846)ctC>ctT	p.L5282L	AHNAK2_ENST00000557457.1_Silent_p.L280L	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5282						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)			CAGCAGTGGAGAGGTGCAGCT	0.517													G|||	2779	0.554912	0.6437	0.5115	5008	,	,		20019	0.4107		0.5338	False		,,,				2504	0.636				p.L5282L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C15846T						PASS	.	G		2726,1334		924,878,228	87.0	91.0	90.0		15846	-4.9	0.0	14	dbSNP_125	90	4567,3831		1263,2041,895	no	coding-synonymous	AHNAK2	NM_138420.2		2187,2919,1123	AA,AG,GG		45.618,32.8571,41.4593		5282/5796	105405942	7293,5165	2030	4199	6229	SO:0001819	synonymous_variant	113146	exon7			AGTGGAGAGGTGC	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.15846C>T	14.37:g.105405942G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	67	65	0.970149	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.467;A|0.533	0.533	strong		0.517	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ZNF320	162967	hgsc.bcm.edu	37	19	53384197	53384197	+	Silent	SNP	A	A	G	rs61745485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53384197A>G	ENST00000595635.1	-	8	1683	c.1182T>C	c.(1180-1182)ttT>ttC	p.F394F	ZNF320_ENST00000597909.1_Intron|ZNF320_ENST00000600930.1_Intron|ZNF320_ENST00000391781.2_Silent_p.F394F	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		CTTTTGTACTAAAAACCTTGC	0.403													.|||	334	0.0666933	0.143	0.0288	5008	,	,		23267	0.0437		0.0487	False		,,,				2504	0.0327				p.F394F		Atlas-SNP	.											.	ZNF320	67	.	0			c.T1182C						PASS	.	A		569,3837		26,517,1660	91.0	87.0	88.0		1182	-0.3	0.0	19	dbSNP_129	88	353,8247		5,343,3952	no	coding-synonymous	ZNF320	NM_207333.2		31,860,5612	GG,GA,AA		4.1047,12.9142,7.089		394/510	53384197	922,12084	2203	4300	6503	SO:0001819	synonymous_variant	162967	exon4			TGTACTAAAAACC	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"""Zinc fingers, C2H2-type"", ""-"""	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.1182T>C	19.37:g.53384197A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	107	46	0.429907	NM_207333	Q8NDR6	Silent	SNP	ENST00000595635.1	37	CCDS33095.1																																																																																			A|0.933;G|0.067	0.067	strong		0.403	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333	
PUS10	150962	hgsc.bcm.edu	37	2	61188643	61188643	+	Missense_Mutation	SNP	C	C	T	rs113622721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61188643C>T	ENST00000316752.6	-	10	1090	c.829G>A	c.(829-831)Gct>Act	p.A277T	PUS10_ENST00000407787.1_Missense_Mutation_p.A277T	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	277					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			TCAAGAACAGCGCATACAGCC	0.348													C|||	87	0.0173722	0.0658	0.0	5008	,	,		19044	0.0		0.0	False		,,,				2504	0.0				p.A277T		Atlas-SNP	.											.	PUS10	49	.	0			c.G829A						PASS	.	C	THR/ALA	177,4229	114.6+/-152.6	4,169,2030	222.0	236.0	232.0		829	-2.4	1.0	2	dbSNP_132	232	4,8596	3.0+/-9.4	0,4,4296	yes	missense	PUS10	NM_144709.2	58	4,173,6326	TT,TC,CC		0.0465,4.0172,1.3917	benign	277/530	61188643	181,12825	2203	4300	6503	SO:0001583	missense	150962	exon10			GAACAGCGCATAC	AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"""coiled-coil domain containing 139"""	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.829G>A	2.37:g.61188643C>T	ENSP00000326003:p.Ala277Thr	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	235	112	0.476596	NM_144709	Q5JPJ5|Q96MI8	Missense_Mutation	SNP	ENST00000316752.6	37	CCDS1865.1	47	0.02152014652014652	47	0.09552845528455285	0	0.0	0	0.0	0	0.0	C	4.727	0.135097	0.09032	0.040172	4.65E-4	ENSG00000162927	ENST00000316752;ENST00000407787	T;T	0.38722	1.12;1.12	5.91	-2.41	0.06562	.	0.476386	0.23506	N	0.047441	T	0.00241	0.0007	N	0.00583	-1.355	0.31617	N	0.650811	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27806	-1.0063	10	0.10902	T	0.67	-7.5462	4.7823	0.13208	0.4331:0.1848:0.0:0.3822	.	277;277	A8K6R4;Q3MIT2	.;PUS10_HUMAN	T	277	ENSP00000326003:A277T;ENSP00000386074:A277T	ENSP00000326003:A277T	A	-	1	0	PUS10	61042147	0.997000	0.39634	0.991000	0.47740	0.993000	0.82548	0.379000	0.20585	-0.138000	0.11434	-0.247000	0.11927	GCT	C|0.985;T|0.015	0.015	strong		0.348	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709	
EXTL1	2134	hgsc.bcm.edu	37	1	26357656	26357656	+	Missense_Mutation	SNP	C	C	A	rs2736831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26357656C>A	ENST00000374280.3	+	5	2002	c.1135C>A	c.(1135-1137)Cac>Aac	p.H379N	EXTL1_ENST00000484339.1_3'UTR	NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	379			H -> N (in dbSNP:rs2736831). {ECO:0000269|PubMed:10480354, ECO:0000269|PubMed:10575224, ECO:0000269|PubMed:9037597}.		protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		AACATCAGCTCACCCCTCACT	0.567													C|||	2976	0.594249	0.2027	0.732	5008	,	,		18516	0.75		0.6978	False		,,,				2504	0.7587				p.H379N		Atlas-SNP	.											.	EXTL1	61	.	0			c.C1135A						PASS	.	C	ASN/HIS	1276,3130	433.7+/-343.7	198,880,1125	118.0	112.0	114.0		1135	4.7	0.0	1	dbSNP_100	114	5833,2767	679.2+/-403.5	1980,1873,447	yes	missense	EXTL1	NM_004455.2	68	2178,2753,1572	AA,AC,CC		32.1744,28.9605,45.3406	possibly-damaging	379/677	26357656	7109,5897	2203	4300	6503	SO:0001583	missense	2134	exon5			TCAGCTCACCCCT	U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"""Exostosin glycosyltransferase family"""	3515	protein-coding gene	gene with protein product	"""glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""alpha-N-acetylglucosaminyltransferase II"", ""glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase"", ""exostosin-L"""	601738	"""exostoses (multiple)-like 1"""			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.1135C>A	1.37:g.26357656C>A	ENSP00000363398:p.His379Asn	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_004455	Q6GSC1	Missense_Mutation	SNP	ENST00000374280.3	37	CCDS271.1	1339	0.6130952380952381	115	0.23373983739837398	259	0.7154696132596685	419	0.7325174825174825	546	0.7203166226912929	C	22.0	4.233153	0.79688	0.289605	0.678256	ENSG00000158008	ENST00000374280	D	0.94862	-3.54	4.7	4.7	0.59300	.	0.331675	0.27500	N	0.019092	T	0.00012	0.0000	L	0.47716	1.5	0.33240	P	0.44294900000000004	B	0.18610	0.029	B	0.14023	0.01	T	0.48525	-0.9028	9	0.30854	T	0.27	-12.1318	16.6014	0.84816	0.0:1.0:0.0:0.0	rs2736831;rs11247847;rs58001292;rs11247847	379	Q92935	EXTL1_HUMAN	N	379	ENSP00000363398:H379N	ENSP00000363398:H379N	H	+	1	0	EXTL1	26230243	0.003000	0.15002	0.038000	0.18304	0.975000	0.68041	1.294000	0.33365	2.453000	0.82957	0.561000	0.74099	CAC	C|0.442;A|0.558	0.558	strong		0.567	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455	
CRNN	49860	hgsc.bcm.edu	37	1	152382436	152382436	+	Missense_Mutation	SNP	C	C	G	rs6695830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152382436C>G	ENST00000271835.3	-	3	1184	c.1122G>C	c.(1120-1122)caG>caC	p.Q374H	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	374	Gln-rich.		Q -> H (in dbSNP:rs6695830).		response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGGTCTGTCCCTGTTCTCTAG	0.592													C|||	366	0.0730831	0.261	0.0231	5008	,	,		25184	0.0		0.005	False		,,,				2504	0.0				p.Q374H		Atlas-SNP	.											CRNN,NS,carcinoma,-2,1	CRNN	78	1	0			c.G1122C						PASS	.	C	HIS/GLN	855,3551	336.0+/-304.2	78,699,1426	171.0	145.0	154.0		1122	1.0	0.0	1	dbSNP_116	154	23,8577	16.6+/-54.9	0,23,4277	yes	missense	CRNN	NM_016190.2	24	78,722,5703	GG,GC,CC		0.2674,19.4054,6.7507	possibly-damaging	374/496	152382436	878,12128	2203	4300	6503	SO:0001583	missense	49860	exon3			CTGTCCCTGTTCT	AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"""EF-hand domain containing"""	1230	protein-coding gene	gene with protein product		611312	"""chromosome 1 open reading frame 10"""	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.1122G>C	1.37:g.152382436C>G	ENSP00000271835:p.Gln374His	Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	341	340	0.997067	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	CCDS1010.1	120	0.054945054945054944	114	0.23170731707317074	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	14.19	2.462134	0.43736	0.194054	0.002674	ENSG00000143536	ENST00000271835	T	0.05139	3.49	4.86	0.955	0.19602	.	0.889113	0.09605	N	0.779761	T	0.04182	0.0116	L	0.54323	1.7	0.80722	P	0.0	D	0.56035	0.974	P	0.49012	0.598	T	0.36286	-0.9754	9	0.62326	D	0.03	.	6.7488	0.23475	0.0:0.6177:0.0:0.3823	rs6695830;rs6695830	374	Q9UBG3	CRNN_HUMAN	H	374	ENSP00000271835:Q374H	ENSP00000271835:Q374H	Q	-	3	2	CRNN	150649060	0.361000	0.24972	0.006000	0.13384	0.150000	0.21749	0.677000	0.25262	0.018000	0.15052	-0.225000	0.12378	CAG	C|0.939;G|0.061	0.061	strong		0.592	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190	
RPP38	10557	hgsc.bcm.edu	37	10	15145917	15145917	+	Missense_Mutation	SNP	A	A	C	rs12249258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:15145917A>C	ENST00000378197.4	+	3	1118	c.604A>C	c.(604-606)Agt>Cgt	p.S202R	RPP38_ENST00000378202.5_Missense_Mutation_p.S202R|RPP38_ENST00000451677.1_Intron|NMT2_ENST00000466201.1_Intron	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	202			S -> R (in dbSNP:rs12249258).		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						CAGAGTCCCCAGTTTAAGTGT	0.463													A|||	241	0.048123	0.1725	0.013	5008	,	,		20068	0.0		0.004	False		,,,				2504	0.0				p.S202R	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.A604C						PASS	.	A	ARG/SER,ARG/SER,ARG/SER	543,3863	244.7+/-253.9	41,461,1701	68.0	69.0	69.0		604,604,604	-3.0	0.0	10	dbSNP_120	69	5,8595	3.7+/-12.6	0,5,4295	yes	missense,missense,missense	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	110,110,110	41,466,5996	CC,CA,AA		0.0581,12.3241,4.2134	benign,benign,benign	202/284,202/284,202/284	15145917	548,12458	2203	4300	6503	SO:0001583	missense	10557	exon2			GTCCCCAGTTTAA	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.604A>C	10.37:g.15145917A>C	ENSP00000367439:p.Ser202Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Missense_Mutation	SNP	ENST00000378197.4	37	CCDS7108.1	96	0.04395604395604396	86	0.17479674796747968	7	0.019337016574585635	0	0.0	3	0.00395778364116095	A	5.707	0.315044	0.10789	0.123241	5.81E-4	ENSG00000152464	ENST00000378203;ENST00000378202;ENST00000378197	T;T;T	0.10192	2.9;2.9;2.9	5.88	-2.97	0.05530	.	1.421770	0.04406	N	0.365158	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.43360	-0.9396	9	0.15952	T	0.53	-0.0859	5.4796	0.16717	0.2215:0.5329:0.1457:0.0999	rs12249258;rs52829912;rs57326558;rs12249258	202	P78345	RPP38_HUMAN	R	202	ENSP00000367445:S202R;ENSP00000367444:S202R;ENSP00000367439:S202R	ENSP00000367439:S202R	S	+	1	0	RPP38	15185923	0.000000	0.05858	0.006000	0.13384	0.561000	0.35649	-0.048000	0.11944	-0.396000	0.07703	0.482000	0.46254	AGT	A|0.946;C|0.054	0.054	strong		0.463	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414	
BPTF	2186	hgsc.bcm.edu	37	17	65919092	65919092	+	Silent	SNP	G	G	A	rs59088743	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65919092G>A	ENST00000321892.4	+	16	6133	c.6072G>A	c.(6070-6072)agG>agA	p.R2024R	BPTF_ENST00000306378.6_Silent_p.R1898R|BPTF_ENST00000424123.3_Silent_p.R1885R|BPTF_ENST00000335221.5_Silent_p.R2024R			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2024					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GGGAGATCAGGGCATTTGCTG	0.398													G|||	95	0.0189696	0.0666	0.0086	5008	,	,		18950	0.0		0.001	False		,,,				2504	0.0				p.R2024R		Atlas-SNP	.											.	BPTF	415	.	0			c.G6072A						PASS	.	G	,	247,4159	143.1+/-178.2	7,233,1963	144.0	139.0	141.0		6072,5694	3.8	1.0	17	dbSNP_129	141	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous	BPTF	NM_004459.6,NM_182641.3	,	7,241,6255	AA,AG,GG		0.093,5.606,1.9606	,	2024/2904,1898/2921	65919092	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	2186	exon16			GATCAGGGCATTT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.6072G>A	17.37:g.65919092G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	37																																																																																				G|0.981;A|0.019	0.019	strong		0.398	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
GHSR	2693	hgsc.bcm.edu	37	3	172165757	172165757	+	Silent	SNP	G	G	C	rs2232169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:172165757G>C	ENST00000241256.2	-	1	489	c.447C>G	c.(445-447)ctC>ctG	p.L149L	GHSR_ENST00000427970.1_Silent_p.L149L	NM_198407.2	NP_940799.1	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor	149					actin polymerization or depolymerization (GO:0008154)|adult feeding behavior (GO:0008343)|cellular response to insulin stimulus (GO:0032869)|decidualization (GO:0046697)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone secretion (GO:0030252)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin secretion (GO:0046676)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of appetite (GO:0032100)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of hindgut contraction (GO:0043134)|regulation of synapse assembly (GO:0051963)|response to food (GO:0032094)|response to hormone (GO:0009725)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|growth hormone secretagogue receptor activity (GO:0001616)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	33	Ovarian(172;0.00143)|Breast(254;0.197)		Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			CCTTGGCCCGGAGTGGGAAGC	0.622													C|||	158	0.0315495	0.0658	0.0231	5008	,	,		19788	0.0		0.0278	False		,,,				2504	0.0276				p.L149L	Esophageal Squamous(93;641 1401 20883 29581 34638)	Atlas-SNP	.											GHSR_ENST00000427970,NS,carcinoma,-2,1	GHSR	104	1	0			c.C447G						PASS	.	C	,	301,4105	793.5+/-415.2	7,287,1909	56.0	55.0	55.0		447,447	4.7	1.0	3	dbSNP_98	55	252,8348	806.8+/-407.2	5,242,4053	no	coding-synonymous,coding-synonymous	GHSR	NM_004122.2,NM_198407.2	,	12,529,5962	CC,CG,GG		2.9302,6.8316,4.2519	,	149/290,149/367	172165757	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	2693	exon1			GGCCCGGAGTGGG	AY429112	CCDS3218.1, CCDS46959.1	3q26.31	2012-08-08			ENSG00000121853	ENSG00000121853		"""GPCR / Class A : Ghrelin receptors"""	4267	protein-coding gene	gene with protein product		601898				8688086	Standard	NM_198407		Approved		uc003fib.2	Q92847	OTTHUMG00000156946	ENST00000241256.2:c.447C>G	3.37:g.172165757G>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	113	47	0.415929	NM_198407	Q14D12|Q6ISR8|Q92848|Q96RJ7	Silent	SNP	ENST00000241256.2	37	CCDS3218.1																																																																																			G|0.963;C|0.037	0.037	strong		0.622	GHSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346728.1	NM_004122	
CCL16	6360	hgsc.bcm.edu	37	17	34304680	34304680	+	Silent	SNP	C	C	T	rs74842203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34304680C>T	ENST00000293275.3	-	3	360	c.285G>A	c.(283-285)ttG>ttA	p.L95L		NM_004590.2	NP_004581.1	O15467	CCL16_HUMAN	chemokine (C-C motif) ligand 16	95					cell chemotaxis (GO:0060326)|cell communication (GO:0007154)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive chemotaxis (GO:0050918)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)			endometrium(1)|lung(2)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TGGTAGGCAGCAAAGGTAGGT	0.512													C|||	358	0.0714856	0.087	0.0303	5008	,	,		16505	0.0427		0.0268	False		,,,				2504	0.1554				p.L95L		Atlas-SNP	.											.	CCL16	7	.	0			c.G285A						PASS	.	C		290,4116	160.7+/-193.0	13,264,1926	216.0	188.0	197.0		285	4.9	0.0	17	dbSNP_132	197	214,8386	90.9+/-153.0	1,212,4087	no	coding-synonymous	CCL16	NM_004590.2		14,476,6013	TT,TC,CC		2.4884,6.5819,3.8751		95/121	34304680	504,12502	2203	4300	6503	SO:0001819	synonymous_variant	6360	exon3			AGGCAGCAAAGGT	AB007454	CCDS11303.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000161573	ENSG00000275152		"""Chemokine ligands"", ""Endogenous ligands"""	10614	protein-coding gene	gene with protein product		601394	"""small inducible cytokine subfamily A (Cys-Cys), member 16"""	SCYA16		8661057	Standard	NM_004590		Approved	NCC-4, SCYL4, LEC, HCC-4, LMC, LCC-1, CKb12, Mtn-1	uc002hkl.3	O15467	OTTHUMG00000188402	ENST00000293275.3:c.285G>A	17.37:g.34304680C>T		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	268	137	0.511194	NM_004590	Q4KKU0	Silent	SNP	ENST00000293275.3	37	CCDS11303.1																																																																																			C|0.959;T|0.041	0.041	strong		0.512	CCL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256579.1	NM_004590	
POM121L12	285877	hgsc.bcm.edu	37	7	53103382	53103382	+	Silent	SNP	G	G	T	rs72598685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:53103382G>T	ENST00000408890.4	+	1	34	c.18G>T	c.(16-18)ccG>ccT	p.P6P		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	6										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CTGCAGCTCCGGCCGAGTCCG	0.701													G|||	1517	0.302915	0.1392	0.2349	5008	,	,		13789	0.4325		0.2853	False		,,,				2504	0.4571				p.P6P		Atlas-SNP	.											.	POM121L12	146	.	0			c.G18T						PASS	.	G		550,3462		41,468,1497	7.0	10.0	9.0		18	-2.9	0.0	7	dbSNP_130	9	2020,6212		248,1524,2344	no	coding-synonymous	POM121L12	NM_182595.3		289,1992,3841	TT,TG,GG		24.5384,13.7089,20.9899		6/297	53103382	2570,9674	2006	4116	6122	SO:0001819	synonymous_variant	285877	exon1			AGCTCCGGCCGAG		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.18G>T	7.37:g.53103382G>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			G|0.718;T|0.282	0.282	strong		0.701	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
GRM5	2915	hgsc.bcm.edu	37	11	88337922	88337922	+	Missense_Mutation	SNP	G	G	A	rs61741175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:88337922G>A	ENST00000305447.4	-	4	1507	c.1358C>T	c.(1357-1359)aCg>aTg	p.T453M	GRM5_ENST00000418177.2_Missense_Mutation_p.T453M|GRM5_ENST00000305432.5_Missense_Mutation_p.T453M|GRM5_ENST00000393297.1_Missense_Mutation_p.T453M|GRM5_ENST00000455756.2_Missense_Mutation_p.T453M	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	453					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	GAATAGGATCGTATCTCCAGA	0.448													G|||	136	0.0271565	0.0946	0.0144	5008	,	,		20219	0.0		0.001	False		,,,				2504	0.0				p.T453M		Atlas-SNP	.											GRM5_ENST00000418177,right_upper_lobe,carcinoma,+1,2	GRM5	414	2	0			c.C1358T						PASS	.	G	MET/THR,MET/THR	352,4050	181.9+/-209.8	14,324,1863	58.0	60.0	59.0		1358,1358	2.1	1.0	11	dbSNP_129	59	2,8596	2.2+/-6.3	0,2,4297	yes	missense,missense	GRM5	NM_000842.3,NM_001143831.2	81,81	14,326,6160	AA,AG,GG		0.0233,7.9964,2.7231	benign,benign	453/1181,453/1213	88337922	354,12646	2201	4299	6500	SO:0001583	missense	2915	exon5			AGGATCGTATCTC	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4597	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 86"""	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1358C>T	11.37:g.88337922G>A	ENSP00000306138:p.Thr453Met	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_000842	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	37	CCDS44694.1	47	0.02152014652014652	43	0.08739837398373984	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	9.419	1.082463	0.20309	0.079964	2.33E-4	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61	5.77	2.13	0.27403	Extracellular ligand-binding receptor (1);	0.320592	0.41294	N	0.000913	T	0.10121	0.0248	L	0.45137	1.4	0.22479	N	0.999063	B;B	0.19935	0.04;0.002	B;B	0.15484	0.013;0.002	T	0.12041	-1.0563	9	.	.	.	.	9.7316	0.40363	0.7425:0.0:0.2575:0.0	.	453;453	P41594-2;P41594	.;GRM5_HUMAN	M	453	ENSP00000402912:T453M;ENSP00000405690:T453M;ENSP00000305905:T453M;ENSP00000306138:T453M;ENSP00000376975:T453M	.	T	-	2	0	GRM5	87977570	0.706000	0.27856	1.000000	0.80357	0.863000	0.49368	0.371000	0.20450	0.461000	0.27071	-1.721000	0.00707	ACG	G|0.972;A|0.028	0.028	strong		0.448	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842	
DNAH10	196385	hgsc.bcm.edu	37	12	124354954	124354954	+	Missense_Mutation	SNP	C	C	T	rs7977449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124354954C>T	ENST00000409039.3	+	43	7232	c.7207C>T	c.(7207-7209)Cgg>Tgg	p.R2403W		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2403			R -> W (in dbSNP:rs7977449).		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)		TGATAACAAACGGAATCAATG	0.393													C|||	118	0.0235623	0.0295	0.0086	5008	,	,		21920	0.0526		0.007	False		,,,				2504	0.0133				p.R2403W		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7207T						PASS	.	C	TRP/ARG	109,3641		3,103,1769	91.0	88.0	89.0		7207	2.2	0.0	12	dbSNP_116	89	59,8163		0,59,4052	yes	missense	DNAH10	NM_207437.3	101	3,162,5821	TT,TC,CC		0.7176,2.9067,1.4033	probably-damaging	2403/4472	124354954	168,11804	1875	4111	5986	SO:0001583	missense	196385	exon43			AACAAACGGAATC	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.7207C>T	12.37:g.124354954C>T	ENSP00000386770:p.Arg2403Trp	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	63	0.028846153846153848	19	0.03861788617886179	3	0.008287292817679558	37	0.06468531468531469	4	0.005277044854881266	C	15.02	2.709681	0.48517	0.029067	0.007176	ENSG00000197653	ENST00000409039	T	0.22945	1.93	5.21	2.23	0.28157	.	1.696560	0.05959	U	0.640214	T	0.03434	0.0099	L	0.49778	1.585	0.09310	N	1	P	0.52316	0.952	P	0.44860	0.462	T	0.13255	-1.0516	10	0.66056	D	0.02	.	8.4827	0.33052	0.5085:0.4206:0.0:0.0709	rs7977449;rs7977449	2403	Q8IVF4	DYH10_HUMAN	W	2403	ENSP00000386770:R2403W	ENSP00000386770:R2403W	R	+	1	2	DNAH10	122920907	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	0.510000	0.22723	0.571000	0.29365	0.655000	0.94253	CGG	C|0.971;T|0.029	0.029	strong		0.393	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
OR4A16	81327	hgsc.bcm.edu	37	11	55110989	55110989	+	Missense_Mutation	SNP	C	C	G	rs116541488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55110989C>G	ENST00000314721.2	+	1	363	c.313C>G	c.(313-315)Ctt>Gtt	p.L105V		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	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)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						AGAACACTTACTTGGTGGTGC	0.448													.|||	50	0.00998403	0.0333	0.0086	5008	,	,		22391	0.0		0.0	False		,,,				2504	0.0				p.L105V		Atlas-SNP	.											.	OR4A16	120	.	0			c.C313G						PASS	.	C	VAL/LEU	142,4260	100.3+/-138.9	1,140,2060	201.0	188.0	192.0		313	1.4	0.2	11	dbSNP_132	192	5,8587	5.0+/-18.6	0,5,4291	yes	missense	OR4A16	NM_001005274.1	32	1,145,6351	GG,GC,CC		0.0582,3.2258,1.1313	benign	105/329	55110989	147,12847	2201	4296	6497	SO:0001583	missense	81327	exon1			CACTTACTTGGTG	AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"""GPCR / Class A : Olfactory receptors"""	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.313C>G	11.37:g.55110989C>G	ENSP00000325128:p.Leu105Val	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	289	128	0.442907	NM_001005274	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	CCDS31499.1	16	0.007326007326007326	13	0.026422764227642278	3	0.008287292817679558	0	0.0	0	0.0	c	0.720	-0.783973	0.02907	0.032258	5.82E-4	ENSG00000181961	ENST00000314721	T	0.00700	5.82	2.57	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00356	0.0011	L	0.41079	1.255	0.09310	N	1	B	0.25007	0.116	B	0.29353	0.101	T	0.48658	-0.9016	9	0.87932	D	0	.	4.5335	0.12017	0.0:0.3127:0.0:0.6873	.	105	Q8NH70	O4A16_HUMAN	V	105	ENSP00000325128:L105V	ENSP00000325128:L105V	L	+	1	0	OR4A16	54867565	0.036000	0.19791	0.157000	0.22605	0.029000	0.11900	0.995000	0.29706	0.240000	0.21263	-0.664000	0.03847	CTT	C|0.988;G|0.012	0.012	strong		0.448	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274	
ACSM5	54988	hgsc.bcm.edu	37	16	20423000	20423000	+	Missense_Mutation	SNP	G	G	A	rs9928053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20423000G>A	ENST00000331849.4	+	2	341	c.194G>A	c.(193-195)cGg>cAg	p.R65Q	ACSM5_ENST00000575584.1_Missense_Mutation_p.R65Q	NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	65			R -> Q (in dbSNP:rs9928053).		fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						GTGTGGAGTCGGCTGGAAGAG	0.557													G|||	399	0.0796725	0.1831	0.0159	5008	,	,		19758	0.0536		0.0169	False		,,,				2504	0.0767				p.R65Q		Atlas-SNP	.											.	ACSM5	101	.	0			c.G194A						PASS	.	G	GLN/ARG	759,3647	309.1+/-290.9	63,633,1507	77.0	63.0	68.0		194	3.6	1.0	16	dbSNP_119	68	181,8419	82.3+/-144.9	3,175,4122	no	missense	ACSM5	NM_017888.2	43	66,808,5629	AA,AG,GG		2.1047,17.2265,7.2274	benign	65/580	20423000	940,12066	2203	4300	6503	SO:0001583	missense	54988	exon2			GGAGTCGGCTGGA		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.194G>A	16.37:g.20423000G>A	ENSP00000327916:p.Arg65Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	148	0.06776556776556776	91	0.18495934959349594	8	0.022099447513812154	35	0.06118881118881119	14	0.018469656992084433	G	1.799	-0.477572	0.04414	0.172265	0.021047	ENSG00000183549	ENST00000331849	T	0.50277	0.75	4.69	3.61	0.41365	.	0.245204	0.28927	N	0.013696	T	0.00039	0.0001	N	0.02315	-0.6	0.47659	P	5.140000000000144E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.20306	-1.0279	9	0.02654	T	1	-15.1236	3.7258	0.08474	0.6565:0.0:0.1821:0.1615	rs9928053;rs52796138;rs9928053	65	Q6NUN0	ACSM5_HUMAN	Q	65	ENSP00000327916:R65Q	ENSP00000327916:R65Q	R	+	2	0	ACSM5	20330501	0.000000	0.05858	1.000000	0.80357	0.749000	0.42624	0.988000	0.29616	0.826000	0.34661	-0.302000	0.09304	CGG	G|0.922;A|0.078	0.078	strong		0.557	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
DND1	373863	hgsc.bcm.edu	37	5	140051009	140051009	+	Silent	SNP	G	G	A	rs146252353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140051009G>A	ENST00000542735.1	-	4	974	c.931C>T	c.(931-933)Cta>Tta	p.L311L	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	311					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)			CGGCCATCTAGGGTCAGCACA	0.622													G|||	28	0.00559105	0.0212	0.0	5008	,	,		20864	0.0		0.0	False		,,,				2504	0.0				p.L311L		Atlas-SNP	.											.	DND1	15	.	0			c.C931T						PASS	.	G		78,4010		0,78,1966	22.0	23.0	23.0		931	-1.9	0.0	5	dbSNP_134	23	0,8094		0,0,4047	no	coding-synonymous	DND1	NM_194249.2		0,78,6013	AA,AG,GG		0.0,1.908,0.6403		311/354	140051009	78,12104	2044	4047	6091	SO:0001819	synonymous_variant	373863	exon4			CATCTAGGGTCAG	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.931C>T	5.37:g.140051009G>A		Somatic	407	0	0		WXS	Illumina HiSeq	Phase_I	406	202	0.497537	NM_194249		Silent	SNP	ENST00000542735.1	37	CCDS4236.1																																																																																			G|0.994;A|0.006	0.006	strong		0.622	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
BBS5	129880	hgsc.bcm.edu	37	2	170336102	170336102	+	Silent	SNP	C	C	G	rs10188609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170336102C>G	ENST00000295240.3	+	1	415	c.39C>G	c.(37-39)gtC>gtG	p.V13V	RP11-724O16.1_ENST00000513963.1_Silent_p.V13V|BBS5_ENST00000392663.2_Silent_p.V13V|BBS5_ENST00000554017.1_Silent_p.V13V	NM_152384.2	NP_689597.1	Q8N3I7	BBS5_HUMAN	Bardet-Biedl syndrome 5	13					cilium assembly (GO:0042384)|heart looping (GO:0001947)|melanosome transport (GO:0032402)|motile cilium assembly (GO:0044458)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphate binding (GO:0032266)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						ATCGGGATGTCCGTTTCGACC	0.637									Bardet-Biedl syndrome				C|||	233	0.0465256	0.1702	0.0115	5008	,	,		17042	0.0		0.0	False		,,,				2504	0.0				p.V13V		Atlas-SNP	.											.	BBS5	27	.	0			c.C39G						PASS	.	C		613,3793	265.3+/-266.6	56,501,1646	134.0	121.0	125.0		39	5.1	1.0	2	dbSNP_119	125	0,8600		0,0,4300	no	coding-synonymous	BBS5	NM_152384.2		56,501,5946	GG,GC,CC		0.0,13.9128,4.7132		13/342	170336102	613,12393	2203	4300	6503	SO:0001819	synonymous_variant	129880	exon1	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GGATGTCCGTTTC	AY604003	CCDS2233.1	2q31	2011-08-02			ENSG00000163093	ENSG00000163093			970	protein-coding gene	gene with protein product		603650				9888993, 10053027	Standard	NM_152384		Approved	DKFZp762I194		Q8N3I7	OTTHUMG00000132207	ENST00000295240.3:c.39C>G	2.37:g.170336102C>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_152384	D3DPC3|Q6PKN0	Silent	SNP	ENST00000295240.3	37	CCDS2233.1																																																																																			C|0.954;G|0.046	0.046	strong		0.637	BBS5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255265.2	NM_152384	
KIAA0922	23240	hgsc.bcm.edu	37	4	154478222	154478222	+	Silent	SNP	C	C	T	rs10001845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:154478222C>T	ENST00000409663.3	+	6	589	c.537C>T	c.(535-537)gtC>gtT	p.V179V	KIAA0922_ENST00000409959.3_Silent_p.V179V|KIAA0922_ENST00000440693.1_Silent_p.V179V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	179						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)				CGTATGGAGTCCTTTCCTATC	0.348													C|||	2079	0.415136	0.5144	0.4438	5008	,	,		19981	0.5169		0.1998	False		,,,				2504	0.3773				p.V179V		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C537T						PASS	.	C	,	2139,2267	575.9+/-384.1	515,1109,579	79.0	81.0	81.0		537,537	2.5	1.0	4	dbSNP_119	81	1892,6708	334.0+/-320.8	206,1480,2614	no	coding-synonymous,coding-synonymous	KIAA0922	NM_001131007.1,NM_015196.3	,	721,2589,3193	TT,TC,CC		22.0,48.5474,30.9934	,	179/1611,179/1610	154478222	4031,8975	2203	4300	6503	SO:0001819	synonymous_variant	23240	exon6			TGGAGTCCTTTCC	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.537C>T	4.37:g.154478222C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	152	53	0.348684	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																			C|0.657;T|0.343	0.343	strong		0.348	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
IMP3	55272	hgsc.bcm.edu	37	15	75932129	75932129	+	Silent	SNP	G	G	T	rs13737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75932129G>T	ENST00000314852.2	-	2	1324	c.381C>A	c.(379-381)gcC>gcA	p.A127A	CTD-2026K11.2_ENST00000564683.1_RNA|IMP3_ENST00000403490.1_Silent_p.A127A|IMP3_ENST00000565349.1_5'Flank			Q8TCT8	SPP2A_HUMAN	IMP3, U3 small nucleolar ribonucleoprotein	118	PA.				membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			large_intestine(1)	1						CAAAGGCCACGGCAGCCTGAA	0.667													G|||	1973	0.39397	0.5151	0.3876	5008	,	,		19460	0.369		0.2704	False		,,,				2504	0.3875				p.A127A		Atlas-SNP	.											IMP3,colon,carcinoma,0,1	IMP3	10	1	0			c.C381A						PASS	.	G		2100,2294	560.2+/-380.4	504,1092,601	52.0	46.0	48.0		381	-6.3	0.8	15	dbSNP_52	48	2285,6303	373.1+/-336.9	301,1683,2310	no	coding-synonymous	IMP3	NM_018285.3		805,2775,2911	TT,TG,GG		26.6069,47.7924,33.7775		127/185	75932129	4385,8597	2197	4294	6491	SO:0001819	synonymous_variant	55272	exon1			GGCCACGGCAGCC	AB051628	CCDS10282.1	15q24	2014-02-19	2014-02-19	2005-07-14	ENSG00000177971	ENSG00000177971			14497	protein-coding gene	gene with protein product		612980	"""mitochondrial ribosomal protein S4"", ""chromosome 15 open reading frame 12"", ""IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""	MRPS4, C15orf12		11543634, 12655004	Standard	NM_018285		Approved	FLJ10968, BRMS2	uc010bkl.2	Q9NV31	OTTHUMG00000142840	ENST00000314852.2:c.381C>A	15.37:g.75932129G>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_018285	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000314852.2	37	CCDS10282.1																																																																																			G|0.628;T|0.372	0.372	strong		0.667	IMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286476.1	NM_018285	
ZNF668	79759	hgsc.bcm.edu	37	16	31073244	31073244	+	Silent	SNP	C	C	A	rs34831291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31073244C>A	ENST00000538906.1	-	3	1789	c.1005G>T	c.(1003-1005)ccG>ccT	p.P335P	ZNF668_ENST00000535577.1_Silent_p.P335P|ZNF668_ENST00000539836.3_Silent_p.P358P|ZNF668_ENST00000426488.2_Silent_p.P358P|ZNF668_ENST00000300849.4_Silent_p.P335P|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000394983.2_Silent_p.P335P|ZNF668_ENST00000417110.2_Missense_Mutation_p.N144K	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	335					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						GGCACTTGAACGGCCGGTCGC	0.652													C|||	36	0.0071885	0.0242	0.0058	5008	,	,		15280	0.0		0.0	False		,,,				2504	0.0				p.P358P	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.G1074T						PASS	.	C	,,,	133,4259		3,127,2066	35.0	37.0	36.0		1005,1074,1005,1005	-11.3	0.5	16	dbSNP_126	36	1,8591		0,1,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	3,128,6361	AA,AC,CC		0.0116,3.0282,1.032	,,,	335/620,358/643,335/620,335/620	31073244	134,12850	2196	4296	6492	SO:0001819	synonymous_variant	79759	exon4			CTTGAACGGCCGG		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.1005G>T	16.37:g.31073244C>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	3.701	-0.061523	0.07317	0.030282	1.16E-4	ENSG00000232748	ENST00000417110	.	.	.	5.63	-11.3	0.00108	.	.	.	.	.	T	0.27594	0.0678	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66356	-0.5944	5	0.87932	D	0	-27.0566	5.6564	0.17644	0.17:0.1581:0.4906:0.1812	rs34831291	.	.	.	K	144	.	ENSP00000391989:N144K	N	+	3	2	AC135050.1	30980745	0.000000	0.05858	0.522000	0.27862	0.356000	0.29392	-5.729000	0.00102	-1.861000	0.01153	-1.119000	0.02030	AAC	C|0.990;A|0.010	0.010	strong		0.652	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
SETD5	55209	hgsc.bcm.edu	37	3	9490272	9490272	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9490272A>G	ENST00000406341.1	+	15	2494	c.2304A>G	c.(2302-2304)cgA>cgG	p.R768R	SETD5_ENST00000407969.1_Silent_p.R787R|SETD5_ENST00000488236.1_3'UTR|SETD5_ENST00000302463.6_Silent_p.R670R|SETD5_ENST00000402466.1_Silent_p.R670R|SETD5_ENST00000402198.1_Silent_p.R768R			Q9C0A6	SETD5_HUMAN	SET domain containing 5	768										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)		AGAGACGTCGAAGGCCCCTTC	0.448																																					p.R768R		Atlas-SNP	.											SETD5_ENST00000402198,NS,carcinoma,+1,2	SETD5	210	2	0			c.A2304G						scavenged	.						71.0	69.0	70.0					3																	9490272		1936	4143	6079	SO:0001819	synonymous_variant	55209	exon16			ACGTCGAAGGCCC	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.2304A>G	3.37:g.9490272A>G		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	219	5	0.0228311	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Silent	SNP	ENST00000406341.1	37	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	A	8.129	0.782625	0.16189	.	.	ENSG00000168137	ENST00000399686;ENST00000421188	.	.	.	5.73	3.27	0.37495	.	.	.	.	.	T	0.59183	0.2175	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52946	-0.8507	4	.	.	.	-7.7584	9.5952	0.39569	0.799:0.0:0.201:0.0	.	.	.	.	E	436;80	.	.	K	+	1	0	SETD5	9465272	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	0.798000	0.27014	0.491000	0.27793	0.533000	0.62120	AAG	.	.	none		0.448	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614	
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53720436	53720436	+	Missense_Mutation	SNP	C	C	T	rs61747071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53720436C>T	ENST00000379925.3	-	6	735	c.685G>A	c.(685-687)Gct>Act	p.A229T	RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.A229T|RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.A229T|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.A229T	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	229			A -> T (polymorphism associated with the development of retinal degeneration in individuals with ciliopathies caused by mutations in other genes; abrogates interaction with RPGR; found in patients with Leber congenital amaurosis, Senior- Loken syndrome, Joubert syndrome and Bardet-Biedl syndrome; dbSNP:rs61747071). {ECO:0000269|PubMed:19430481}.		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)				AGGATCTCAGCCAAGTGCTCT	0.373													C|||	267	0.0533147	0.1203	0.0259	5008	,	,		18515	0.001		0.0219	False		,,,				2504	0.0685				p.A229T		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.G685A						PASS	.	C	THR/ALA,THR/ALA	443,3953	214.1+/-233.5	14,415,1769	124.0	119.0	121.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	685,685	2.7	1.0	16	dbSNP_129	121	282,8318	105.0+/-166.0	4,274,4022	yes	missense,missense	RPGRIP1L	NM_001127897.1,NM_015272.2	58,58	18,689,5791	TT,TC,CC		3.2791,10.0773,5.5786	possibly-damaging,possibly-damaging	229/1236,229/1316	53720436	725,12271	2198	4300	6498	SO:0001583	missense	23322	exon6			TCTCAGCCAAGTG		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.685G>A	16.37:g.53720436C>T	ENSP00000369257:p.Ala229Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	105	65	0.619048	NM_001127897	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	85	0.03891941391941392	60	0.12195121951219512	8	0.022099447513812154	0	0.0	17	0.022427440633245383	C	11.37	1.619244	0.28801	0.100773	0.032791	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.77229	-0.89;-1.08	5.73	2.67	0.31697	.	0.836541	0.11273	N	0.581181	T	0.01320	0.0043	N	0.19112	0.55	0.34168	D	0.669435	B;B;B;B	0.12013	0.001;0.0;0.005;0.0	B;B;B;B	0.09377	0.001;0.001;0.004;0.002	T	0.14924	-1.0455	10	0.12430	T	0.62	-1.9763	5.155	0.15031	0.1364:0.5817:0.0:0.2819	rs61747071	229;229;229;229	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	T	229	ENSP00000369257:A229T;ENSP00000262135:A229T	ENSP00000262135:A229T	A	-	1	0	RPGRIP1L	52277937	0.002000	0.14202	0.995000	0.50966	0.998000	0.95712	-0.035000	0.12205	0.407000	0.25591	0.655000	0.94253	GCT	C|0.953;T|0.047	0.047	strong		0.373	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
OR4K15	81127	hgsc.bcm.edu	37	14	20444193	20444193	+	Silent	SNP	A	A	C	rs2318556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20444193A>C	ENST00000305051.5	+	1	591	c.516A>C	c.(514-516)tcA>tcC	p.S172S		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	172						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCCTCATTTCATGGTTTGTGG	0.443													C|||	1885	0.376398	0.7481	0.2017	5008	,	,		22524	0.1498		0.2435	False		,,,				2504	0.3681				p.S172S		Atlas-SNP	.											.	OR4K15	82	.	0			c.A516C						PASS	.	C		3043,1363		1041,961,201	148.0	147.0	147.0		516	-3.8	0.0	14	dbSNP_100	147	2447,6151		337,1773,2189	no	coding-synonymous	OR4K15	NM_001005486.1		1378,2734,2390	CC,CA,AA		28.4601,30.9351,42.2178		172/349	20444193	5490,7514	2203	4299	6502	SO:0001819	synonymous_variant	81127	exon1			CATTTCATGGTTT		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.516A>C	14.37:g.20444193A>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	221	220	0.995475	NM_001005486	B9EIL3|Q6IEZ4	Silent	SNP	ENST00000305051.5	37	CCDS32026.1																																																																																			A|0.619;C|0.380;G|0.001	0.380	strong		0.443	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
SERPINA1	5265	hgsc.bcm.edu	37	14	94844975	94844975	+	Silent	SNP	G	G	A	rs9630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94844975G>A	ENST00000448921.1	-	7	1640	c.1068C>T	c.(1066-1068)gcC>gcT	p.A356A	SERPINA1_ENST00000449399.3_Silent_p.A356A|SERPINA1_ENST00000393087.4_Silent_p.A356A|SERPINA1_ENST00000440909.1_Silent_p.A356A|SERPINA1_ENST00000437397.1_Silent_p.A356A|SERPINA1_ENST00000404814.4_Silent_p.A356A|SERPINA1_ENST00000393088.4_Silent_p.A356A|SERPINA1_ENST00000355814.4_Silent_p.A356A	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	356					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		CCTTATGCACGGCCTGGAGGG	0.592													G|||	50	0.00998403	0.0356	0.0043	5008	,	,		19798	0.0		0.0	False		,,,				2504	0.0				p.A356A		Atlas-SNP	.											.	SERPINA1	51	.	0			c.C1068T						PASS	.	G	,,,,,,,,,,	122,4284	90.2+/-128.9	1,120,2082	80.0	59.0	66.0		1068,1068,1068,1068,1068,1068,1068,1068,1068,1068,1068	-9.6	0.0	14	dbSNP_52	66	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,coding-synonymous,coding-synonymous,coding-synonymous	SERPINA1	NM_000295.4,NM_001002235.2,NM_001002236.2,NM_001127700.1,NM_001127701.1,NM_001127702.1,NM_001127703.1,NM_001127704.1,NM_001127705.1,NM_001127706.1,NM_001127707.1	,,,,,,,,,,	1,121,6381	AA,AG,GG		0.0116,2.769,0.9457	,,,,,,,,,,	356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419	94844975	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	5265	exon7			ATGCACGGCCTGG	X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"""Serine (or cysteine) peptidase inhibitors"""	8941	protein-coding gene	gene with protein product	"""protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"""	107400	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"""	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.1068C>T	14.37:g.94844975G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	168	82	0.488095	NM_001127701	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Silent	SNP	ENST00000448921.1	37	CCDS9925.1																																																																																			G|0.989;A|0.011	0.011	strong		0.592	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235	
PLD1	5337	hgsc.bcm.edu	37	3	171338237	171338237	+	Silent	SNP	T	T	G	rs9881788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:171338237T>G	ENST00000351298.4	-	24	2793	c.2667A>C	c.(2665-2667)gtA>gtC	p.V889V	PLD1_ENST00000340989.4_Silent_p.V889V|PLD1_ENST00000342215.6_3'UTR|PLD1_ENST00000356327.5_Silent_p.V851V	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	889	Catalytic.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	TAAGCTCAGTTACTAGGTTTC	0.328													G|||	2370	0.473243	0.7352	0.4669	5008	,	,		16128	0.3562		0.3946	False		,,,				2504	0.3252				p.V889V	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.A2667C						PASS	.	G	,	2954,1452	469.4+/-355.4	971,1012,220	131.0	126.0	128.0		2553,2667	4.6	1.0	3	dbSNP_119	128	3668,4932	622.9+/-397.4	794,2080,1426	no	coding-synonymous,coding-synonymous	PLD1	NM_001130081.2,NM_002662.4	,	1765,3092,1646	GG,GT,TT		42.6512,32.9551,49.085	,	851/1037,889/1075	171338237	6622,6384	2203	4300	6503	SO:0001819	synonymous_variant	5337	exon24			CTCAGTTACTAGG	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.2667A>C	3.37:g.171338237T>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_002662		Silent	SNP	ENST00000351298.4	37	CCDS3216.1	1034	0.4734432234432234	385	0.782520325203252	154	0.425414364640884	190	0.3321678321678322	305	0.4023746701846966	G	1.092	-0.663792	0.03428	0.670449	0.426512	ENSG00000075651	ENST00000446289	.	.	.	5.5	4.63	0.57726	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.6543	10.9251	0.47187	0.0672:0.0:0.8027:0.1301	rs9881788;rs58557066;rs9881788	.	.	.	S	152	.	.	X	-	2	2	PLD1	172820931	1.000000	0.71417	0.998000	0.56505	0.099000	0.18886	4.606000	0.61126	0.704000	0.31869	-1.392000	0.01152	TAA	T|0.504;G|0.496	0.496	strong		0.328	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
ACE	1636	hgsc.bcm.edu	37	17	61557200	61557200	+	Silent	SNP	C	C	T	rs4298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61557200C>T	ENST00000290866.4	+	4	606	c.582C>T	c.(580-582)aaC>aaT	p.N194N	ACE_ENST00000538928.1_Silent_p.N194N|ACE_ENST00000584529.1_3'UTR|ACE_ENST00000428043.1_Silent_p.N194N	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	194	Peptidase M2 1.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	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 membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	GCTGGCACAACGCTGCGGGCA	0.607													C|||	723	0.144369	0.4039	0.0807	5008	,	,		21461	0.0099		0.0835	False		,,,				2504	0.0399				p.N194N		Atlas-SNP	.											.	ACE	187	.	0			c.C582T						PASS	.	C		1486,2920	476.3+/-357.6	242,1002,959	109.0	78.0	88.0		582	-4.8	0.0	17	dbSNP_36	88	638,7962	163.6+/-216.1	18,602,3680	no	coding-synonymous	ACE	NM_000789.3		260,1604,4639	TT,TC,CC		7.4186,33.7267,16.3309		194/1307	61557200	2124,10882	2203	4300	6503	SO:0001819	synonymous_variant	1636	exon4			GCACAACGCTGCG	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.582C>T	17.37:g.61557200C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Silent	SNP	ENST00000290866.4	37	CCDS11637.1																																																																																			C|0.850;T|0.150	0.150	strong		0.607	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
PNMAL1	55228	hgsc.bcm.edu	37	19	46973693	46973693	+	Silent	SNP	C	C	T	rs73552938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46973693C>T	ENST00000313683.10	-	2	905	c.600G>A	c.(598-600)ccG>ccA	p.P200P	PNMAL1_ENST00000438932.2_Silent_p.P200P|PNMAL1_ENST00000602246.1_Intron	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	200										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)		CTGCAAGCCCCGGTTCTTTCT	0.592													C|||	99	0.0197684	0.0696	0.0101	5008	,	,		18070	0.0		0.0	False		,,,				2504	0.0				p.P200P		Atlas-SNP	.											PNMAL1_ENST00000438932,lower_third,carcinoma,-1,2	PNMAL1	87	2	0			c.G600A						scavenged	.	C	,	250,4156	143.5+/-178.5	4,242,1957	58.0	60.0	59.0		600,600	-7.7	0.0	19	dbSNP_130	59	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	PNMAL1	NM_001103149.1,NM_018215.3	,	4,244,6255	TT,TC,CC		0.0233,5.6741,1.9376	,	200/379,200/440	46973693	252,12754	2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			AAGCCCCGGTTCT	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.600G>A	19.37:g.46973693C>T		Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1	41	0.018772893772893772	38	0.07723577235772358	3	0.008287292817679558	0	0.0	0	0.0	C	4.609	0.113215	0.08831	0.056741	2.33E-4	ENSG00000182013	ENST00000417103	.	.	.	3.84	-7.67	0.01272	.	.	.	.	.	T	0.01558	0.0050	.	.	.	0.21386	N	0.99971	.	.	.	.	.	.	T	0.13845	-1.0494	5	0.46703	T	0.11	-21.5671	4.3527	0.11163	0.0894:0.1015:0.3706:0.4386	.	.	.	.	R	180	.	ENSP00000389114:G180R	G	-	1	0	PNMAL1	51665533	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-5.361000	0.00128	-3.560000	0.00141	-0.345000	0.07892	GGG	C|0.977;T|0.023	0.023	strong		0.592	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
FCRLA	84824	hgsc.bcm.edu	37	1	161681780	161681780	+	Missense_Mutation	SNP	A	A	G	rs2275603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161681780A>G	ENST00000236938.6	+	4	849	c.607A>G	c.(607-609)Agc>Ggc	p.S203G	FCRLA_ENST00000350710.3_Intron|FCRLA_ENST00000309691.6_Missense_Mutation_p.S97G|FCRLA_ENST00000367953.3_Missense_Mutation_p.S192G|FCRLA_ENST00000349527.4_Intron|FCRLA_ENST00000540926.1_Missense_Mutation_p.S192G|FCRLA_ENST00000367957.2_Missense_Mutation_p.S63G|FCRLA_ENST00000367949.2_Intron|FCRLA_ENST00000540521.1_Missense_Mutation_p.S69G|FCRLA_ENST00000294796.4_Missense_Mutation_p.S52G|FCRLA_ENST00000367959.2_Missense_Mutation_p.S209G|FCRLA_ENST00000546024.1_Missense_Mutation_p.S114G|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000367950.1_Intron	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	186	Ig-like C2-type 2.				cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			CCAAGCAGGAAGCCCCATGAC	0.522													G|||	2389	0.477037	0.764	0.4553	5008	,	,		17754	0.5734		0.2078	False		,,,				2504	0.2822				p.S209G		Atlas-SNP	.											.	FCRLA	101	.	0			c.A625G						PASS	.	G	GLY/SER,GLY/SER,GLY/SER,,GLY/SER,,GLY/SER	2903,1503	477.0+/-357.8	980,943,280	116.0	145.0	135.0		625,340,205,,187,,607	-8.4	0.0	1	dbSNP_100	135	1882,6718	726.9+/-406.6	220,1442,2638	yes	missense,missense,missense,intron,missense,intron,missense	FCRLA	NM_001184866.1,NM_001184867.1,NM_001184870.1,NM_001184871.1,NM_001184872.1,NM_001184873.1,NM_032738.3	56,56,56,,56,,56	1200,2385,2918	GG,GA,AA		21.8837,34.1126,36.7907	benign,benign,benign,,benign,,benign	209/383,114/288,69/243,,63/237,,203/377	161681780	4785,8221	2203	4300	6503	SO:0001583	missense	84824	exon5			GCAGGAAGCCCCA	AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18504	protein-coding gene	gene with protein product		606891	"""Fc receptor-like and mucin-like 1"""	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.607A>G	1.37:g.161681780A>G	ENSP00000236938:p.Ser203Gly	Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_001184866	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Missense_Mutation	SNP	ENST00000236938.6	37	CCDS30926.1	977	0.44734432234432236	357	0.725609756097561	143	0.39502762430939226	317	0.5541958041958042	160	0.21108179419525067	G	0.009	-1.843804	0.00568	0.658874	0.218837	ENSG00000132185	ENST00000236938;ENST00000367959;ENST00000546024;ENST00000540521;ENST00000540926;ENST00000367957;ENST00000309691;ENST00000294796;ENST00000367953	T;T;T;T;T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77	5.57	-8.4	0.00965	.	0.922351	0.09125	N	0.845187	T	0.02610	0.0079	L	0.41356	1.27	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.15484	0.001;0.013;0.001;0.0;0.001	T	0.46105	-0.9215	9	0.08837	T	0.75	.	20.1836	0.98210	0.8865:0.0:0.1135:0.0	rs2275603;rs60711230;rs2275603	69;63;114;209;203	F5H720;Q5VXB1;G3V1J2;A6NC03;Q7L513-9	.;.;.;.;.	G	203;209;114;69;192;63;97;52;192	ENSP00000236938:S203G;ENSP00000356936:S209G;ENSP00000439838:S114G;ENSP00000442870:S69G;ENSP00000446380:S192G;ENSP00000356934:S63G;ENSP00000309596:S97G;ENSP00000294796:S52G;ENSP00000356930:S192G	ENSP00000236938:S203G	S	+	1	0	FCRLA	159948404	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.373000	0.07494	-2.199000	0.00748	-0.930000	0.02707	AGC	A|0.595;G|0.405	0.405	strong		0.522	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738	
KIF23	9493	hgsc.bcm.edu	37	15	69709748	69709748	+	Silent	SNP	C	C	A	rs3759826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:69709748C>A	ENST00000260363.4	+	3	225	c.108C>A	c.(106-108)ggC>ggA	p.G36G	RP11-253M7.1_ENST00000560539.1_RNA|KIF23_ENST00000559279.1_Silent_p.G36G|KIF23_ENST00000395392.2_Silent_p.G36G|KIF23_ENST00000352331.4_Silent_p.G36G|RP11-253M7.1_ENST00000558617.1_RNA	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	36	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)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						GCCCACTGGGCTTTCCTGATC	0.423													C|||	676	0.134984	0.2504	0.1239	5008	,	,		17525	0.2014		0.0229	False		,,,				2504	0.0337				p.G36G		Atlas-SNP	.											.	KIF23	57	.	0			c.C108A						PASS	.	C	,	871,3527	339.1+/-305.6	80,711,1408	144.0	128.0	133.0		108,108	3.8	1.0	15	dbSNP_107	133	163,8433	76.6+/-139.3	0,163,4135	no	coding-synonymous,coding-synonymous	KIF23	NM_004856.5,NM_138555.2	,	80,874,5543	AA,AC,CC		1.8962,19.8045,7.9575	,	36/857,36/961	69709748	1034,11960	2199	4298	6497	SO:0001819	synonymous_variant	9493	exon3			ACTGGGCTTTCCT	X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"""Kinesins"""	6392	protein-coding gene	gene with protein product		605064	"""kinesin-like 5 (mitotic kinesin-like protein 1)"""	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.108C>A	15.37:g.69709748C>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_138555	Q8WVP0	Silent	SNP	ENST00000260363.4	37	CCDS32278.1																																																																																			C|0.904;A|0.096	0.096	strong		0.423	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
MUC4	4585	hgsc.bcm.edu	37	3	195513364	195513364	+	Missense_Mutation	SNP	C	C	T	rs79986529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513364C>T	ENST00000463781.3	-	2	5546	c.5087G>A	c.(5086-5088)cGt>cAt	p.R1696H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.R1696H	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)		GACAGGAAGACGGGTGGTGTC	0.597																																					p.R1696H		Atlas-SNP	.											.	MUC4	1505	.	0			c.G5087A						PASS	.						40.0	43.0	42.0					3																	195513364		689	1582	2271	SO:0001583	missense	4585	exon2			GGAAGACGGGTGG	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.5087G>A	3.37:g.195513364C>T	ENSP00000417498:p.Arg1696His	Somatic	552	0	0		WXS	Illumina HiSeq	Phase_I	443	129	0.291196	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	.	.	.	.	.	.	.	.	.	.	-	6.832	0.522620	0.13066	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.44;1.45	.	.	.	.	.	.	.	.	T	0.11367	0.0277	N	0.19112	0.55	0.80722	P	0.0	P	0.35793	0.521	B	0.08055	0.003	T	0.12451	-1.0547	6	.	.	.	.	5.3651	0.16109	1.0E-4:0.3585:0.6414:0.0	.	1696	E7ESK3	.	H	1696	ENSP00000417498:R1696H;ENSP00000420243:R1696H	.	R	-	2	0	MUC4	196997759	0.001000	0.12720	0.007000	0.13788	0.007000	0.05969	-0.253000	0.08794	-1.916000	0.01075	-1.964000	0.00472	CGT	C|0.946;G|0.002;T|0.052	0.052	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TTN	7273	hgsc.bcm.edu	37	2	179396159	179396159	+	Silent	SNP	C	C	T	rs371075036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179396159C>T	ENST00000591111.1	-	308	100484	c.100260G>A	c.(100258-100260)gcG>gcA	p.A33420A	TTN_ENST00000589042.1_Silent_p.A35061A|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000460472.2_Silent_p.A25996A|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Silent_p.A32493A|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Silent_p.A26121A|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342175.6_Silent_p.A26188A|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33420					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)			AAACAGCATACGCCTCTGTTC	0.478													C|||	2	0.000399361	0.0015	0.0	5008	,	,		22850	0.0		0.0	False		,,,				2504	0.0				p.A35061A		Atlas-SNP	.											TTN_ENST00000359218,caecum,carcinoma,-1,5	TTN	18412	5	0			c.G105183A						scavenged	.	C	,,,	12,3814		0,12,1901	118.0	117.0	117.0		77988,97479,78363,78564	-8.1	1.0	2		117	1,8257		0,1,4128	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,13,6029	TT,TC,CC		0.0121,0.3136,0.1076	,,,	25996/26927,32493/33424,26121/27052,26188/27119	179396159	13,12071	1913	4129	6042	SO:0001819	synonymous_variant	7273	exon358			AGCATACGCCTCT	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.100260G>A	2.37:g.179396159C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	96	3	0.03125	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																																																																																				.	.	weak		0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PCDHA10	56139	hgsc.bcm.edu	37	5	140237826	140237826	+	Silent	SNP	G	G	C	rs180990865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140237826G>C	ENST00000307360.5	+	1	2193	c.2193G>C	c.(2191-2193)ggG>ggC	p.G731G	PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	731					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)			GCGCATGTGGGCCGGTGAAGC	0.672													.|||	66	0.0131789	0.0492	0.0014	5008	,	,		13681	0.0		0.0	False		,,,				2504	0.0				p.G731G		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G2193C						PASS	.	G	,,,,,,,,,,,,,	90,2554		6,78,1238	32.0	32.0	32.0		,2193,,,,,,,,,,,2193,	-2.2	0.0	5		32	0,4582		0,0,2291	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron	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	,,,,,,,,,,,,,	6,78,3529	CC,CG,GG		0.0,3.4039,1.2455	,,,,,,,,,,,,,	,731/949,,,,,,,,,,,731/845,	140237826	90,7136	1322	2291	3613	SO:0001819	synonymous_variant	56139	exon1			ATGTGGGCCGGTG	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.2193G>C	5.37:g.140237826G>C		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	234	108	0.461538	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	37	CCDS54921.1																																																																																			G|0.989;C|0.011	0.011	strong		0.672	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
TBL3	10607	hgsc.bcm.edu	37	16	2025206	2025206	+	Silent	SNP	A	A	C	rs8053843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2025206A>C	ENST00000568546.1	+	8	782	c.654A>C	c.(652-654)atA>atC	p.I218I		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	218					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						GTGACAAGATATGTATCATCT	0.612													C|||	1143	0.228235	0.2905	0.2637	5008	,	,		19224	0.0427		0.2356	False		,,,				2504	0.3027				p.I218I	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.A654C						PASS	.	C		1117,3279	716.0+/-408.5	144,829,1225	95.0	101.0	99.0		654	5.4	1.0	16	dbSNP_116	99	1945,6655	724.7+/-406.5	213,1519,2568	no	coding-synonymous	TBL3	NM_006453.2		357,2348,3793	CC,CA,AA		22.6163,25.4095,23.5611		218/809	2025206	3062,9934	2198	4300	6498	SO:0001819	synonymous_variant	10607	exon8			CAAGATATGTATC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.654A>C	16.37:g.2025206A>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			A|0.782;C|0.218	0.218	strong		0.612	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
PODN	127435	hgsc.bcm.edu	37	1	53544271	53544271	+	Silent	SNP	G	G	C	rs62000444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53544271G>C	ENST00000312553.5	+	8	1240	c.1233G>C	c.(1231-1233)acG>acC	p.T411T	PODN_ENST00000395871.2_Silent_p.T269T|RP11-334A14.5_ENST00000447867.1_RNA|PODN_ENST00000371500.3_Silent_p.T392T	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	363					negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGTTGCACACGGTGCACCTGT	0.662													G|||	54	0.0107827	0.034	0.0115	5008	,	,		19751	0.0		0.001	False		,,,				2504	0.0				p.T411T		Atlas-SNP	.											.	PODN	86	.	0			c.G1233C						PASS	.	G	,,,	95,4311	76.2+/-114.5	1,93,2109	66.0	61.0	63.0		1176,1176,807,1233	-1.9	1.0	1	dbSNP_129	63	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PODN	NM_001199080.1,NM_001199081.1,NM_001199082.1,NM_153703.4	,,,	1,102,6400	CC,CG,GG		0.1047,2.1562,0.7996	,,,	392/643,392/643,269/520,411/662	53544271	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	127435	exon8			GCACACGGTGCAC	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.1233G>C	1.37:g.53544271G>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Silent	SNP	ENST00000312553.5	37	CCDS573.1																																																																																			G|0.992;C|0.008	0.008	strong		0.662	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703	
OR6C74	254783	hgsc.bcm.edu	37	12	55641075	55641075	+	Missense_Mutation	SNP	A	A	G	rs7301705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	76	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	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		
KIAA0556	23247	hgsc.bcm.edu	37	16	27763110	27763110	+	Silent	SNP	T	T	C	rs2289875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27763110T>C	ENST00000261588.4	+	17	3436	c.3417T>C	c.(3415-3417)tcT>tcC	p.S1139S		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1139						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						TATTCTATTCTGATGAGATGT	0.537													C|||	513	0.102436	0.2474	0.0274	5008	,	,		18200	0.0913		0.0229	False		,,,				2504	0.0532				p.S1139S		Atlas-SNP	.											.	KIAA0556	348	.	0			c.T3417C						PASS	.	C		884,3510	740.7+/-411.2	84,716,1397	110.0	98.0	102.0		3417	-10.0	0.0	16	dbSNP_100	102	178,8422	811.6+/-407.1	1,176,4123	no	coding-synonymous	KIAA0556	NM_015202.2		85,892,5520	CC,CT,TT		2.0698,20.1183,8.173		1139/1619	27763110	1062,11932	2197	4300	6497	SO:0001819	synonymous_variant	23247	exon17			CTATTCTGATGAG	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.3417T>C	16.37:g.27763110T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	184	82	0.445652	NM_015202	A7E2C2	Silent	SNP	ENST00000261588.4	37	CCDS32415.1																																																																																			T|0.904;C|0.096	0.096	strong		0.537	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51918112	51918112	+	Silent	SNP	A	A	G	rs3810099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51918112A>G	ENST00000339313.5	-	8	1697	c.1581T>C	c.(1579-1581)caT>caC	p.H527H	SIGLEC10_ENST00000432469.2_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000439889.2_Silent_p.H469H|SIGLEC10_ENST00000353836.5_Intron|SIGLEC10_ENST00000441969.3_Intron|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.H527H|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	527					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)		TCTGGGCCCCATGGACGTTCC	0.662													a|||	1218	0.243211	0.3835	0.1974	5008	,	,		15844	0.2113		0.1501	False		,,,				2504	0.2147				p.H527H		Atlas-SNP	.											SIGLEC12_ENST00000439889,NS,carcinoma,-1,4	SIGLEC10	112	4	0			c.T1581C						PASS	.	A	,,,,,,	1516,2890		260,996,947	55.0	65.0	61.0		1407,,,,,,1581	-9.4	0.0	19	dbSNP_107	61	1291,7309		101,1089,3110	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	,,,,,,	361,2085,4057	GG,GA,AA		15.0116,34.4076,21.5823	,,,,,,	469/640,,,,,,527/698	51918112	2807,10199	2203	4300	6503	SO:0001819	synonymous_variant	89790	exon8			GGCCCCATGGACG	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.1581T>C	19.37:g.51918112A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_033130	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			A|0.791;G|0.209	0.209	strong		0.662	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
SULT6B1	391365	hgsc.bcm.edu	37	2	37406645	37406645	+	Missense_Mutation	SNP	T	T	C	rs61737618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37406645T>C	ENST00000535679.1	-	4	484	c.485A>G	c.(484-486)tAt>tGt	p.Y162C	SULT6B1_ENST00000379149.2_Intron|SULT6B1_ENST00000260637.3_Missense_Mutation_p.Y124C|SULT6B1_ENST00000407963.1_Missense_Mutation_p.Y124C			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	162						cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				CCAAGAGCCATAGCTTGGAAT	0.378													T|||	9	0.00179712	0.0068	0.0	5008	,	,		19591	0.0		0.0	False		,,,				2504	0.0				p.Y124C		Atlas-SNP	.											.	SULT6B1	46	.	0			c.A371G						PASS	.	T	CYS/TYR	33,4373	38.4+/-70.7	0,33,2170	161.0	151.0	154.0		371	3.0	1.0	2	dbSNP_129	154	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SULT6B1	NM_001032377.1	194	0,34,6469	CC,CT,TT		0.0116,0.749,0.2614	probably-damaging	124/266	37406645	34,12972	2203	4300	6503	SO:0001583	missense	391365	exon4			GAGCCATAGCTTG	AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"""Sulfotransferases, cytosolic"""	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.485A>G	2.37:g.37406645T>C	ENSP00000444081:p.Tyr162Cys	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001032377	B2RTS7	Missense_Mutation	SNP	ENST00000535679.1	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	15.08	2.726804	0.48833	0.00749	1.16E-4	ENSG00000138068	ENST00000535679;ENST00000260637;ENST00000407963	D;D;D	0.82167	-1.58;-1.58;-1.58	4.27	3.02	0.34903	Sulfotransferase domain (1);	1.254540	0.05257	N	0.515113	D	0.86522	0.5953	M	0.73372	2.23	0.40291	D	0.9785	D	0.71674	0.998	D	0.65443	0.935	T	0.81870	-0.0734	10	0.40728	T	0.16	.	9.6717	0.40017	0.1561:0.0:0.0:0.8439	.	162	Q6IMI4	ST6B1_HUMAN	C	162;124;124	ENSP00000444081:Y162C;ENSP00000260637:Y124C;ENSP00000384950:Y124C	ENSP00000260637:Y124C	Y	-	2	0	SULT6B1	37260149	0.715000	0.27946	0.981000	0.43875	0.855000	0.48748	0.833000	0.27504	1.928000	0.55862	0.459000	0.35465	TAT	T|0.997;C|0.003	0.003	strong		0.378	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377	
NAF1	92345	hgsc.bcm.edu	37	4	164087753	164087753	+	Missense_Mutation	SNP	G	G	A	rs12331663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:164087753G>A	ENST00000274054.2	-	1	320	c.127C>T	c.(127-129)Ccg>Tcg	p.P43S	NAF1_ENST00000422287.2_Missense_Mutation_p.P43S	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	43			P -> S (in dbSNP:rs12331663).		pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				GACTGTAGCGGCGGCTGTGTC	0.657													G|||	148	0.0295527	0.1104	0.0029	5008	,	,		11685	0.0		0.0	False		,,,				2504	0.0				p.P43S		Atlas-SNP	.											.	NAF1	69	.	0			c.C127T						PASS	.	G	SER/PRO,SER/PRO	409,3655		27,355,1650	8.0	12.0	11.0		127,127	0.6	0.0	4	dbSNP_120	11	7,8217		0,7,4105	yes	missense,missense	NAF1	NM_001128931.1,NM_138386.2	74,74	27,362,5755	AA,AG,GG		0.0851,10.064,3.3854	benign,benign	43/390,43/495	164087753	416,11872	2032	4112	6144	SO:0001583	missense	92345	exon1			GTAGCGGCGGCTG		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"""nuclear assembly factor 1 homolog (S. cerevisiae)"""			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.127C>T	4.37:g.164087753G>A	ENSP00000274054:p.Pro43Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_138386	D3DP28|E9PAZ2	Missense_Mutation	SNP	ENST00000274054.2	37	CCDS3803.1	58	0.026556776556776556	56	0.11382113821138211	2	0.0055248618784530384	0	0.0	0	0.0	G	9.310	1.055342	0.19907	0.10064	8.51E-4	ENSG00000145414	ENST00000422287;ENST00000274054	T;T	0.31510	1.49;1.51	2.42	0.648	0.17801	.	0.570177	0.14188	N	0.335578	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	B;B	0.31655	0.0;0.334	B;B	0.18561	0.0;0.022	T	0.21484	-1.0244	10	0.07644	T	0.81	-0.4303	4.7772	0.13185	0.3241:0.0:0.6759:0.0	rs12331663;rs52833318;rs12331663	43;43	E9PAZ2;Q96HR8	.;NAF1_HUMAN	S	43	ENSP00000408963:P43S;ENSP00000274054:P43S	ENSP00000274054:P43S	P	-	1	0	NAF1	164307203	0.000000	0.05858	0.010000	0.14722	0.377000	0.30045	-0.380000	0.07427	0.135000	0.18707	-0.680000	0.03767	CCG	G|0.963;A|0.037	0.037	strong		0.657	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386	
OR10C1	442194	hgsc.bcm.edu	37	6	29408275	29408275	+	Missense_Mutation	SNP	C	C	A	rs2074467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29408275C>A	ENST00000444197.2	+	1	1193	c.483C>A	c.(481-483)ttC>ttA	p.F161L	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	161			F -> L (in dbSNP:rs2074467).			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)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						ACACCCCTTTCATCTTCTCTT	0.617													C|||	316	0.063099	0.152	0.0562	5008	,	,		17927	0.0456		0.0159	False		,,,				2504	0.0143				p.F161L		Atlas-SNP	.											.	OR10C1	58	.	0			c.C483A						PASS	.	C	LEU/PHE	335,2687		23,289,1199	110.0	124.0	119.0		483	1.5	1.0	6	dbSNP_96	119	93,5325		2,89,2618	yes	missense	OR10C1	NM_013941.3	22	25,378,3817	AA,AC,CC		1.7165,11.0854,5.0711	benign	161/313	29408275	428,8012	1511	2709	4220	SO:0001583	missense	442194	exon1			CCCTTTCATCTTC		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.483C>A	6.37:g.29408275C>A	ENSP00000419119:p.Phe161Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	121	55	0.454545	NM_013941	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	37	CCDS34364.1	132	0.06043956043956044	85	0.17276422764227642	17	0.04696132596685083	24	0.04195804195804196	6	0.0079155672823219	C	8.999	0.979712	0.18812	0.110854	0.017165	ENSG00000206474	ENST00000444197	T	0.00048	8.82	3.37	1.47	0.22746	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41097	D	0.000943	T	0.00039	0.0001	N	0.03917	-0.325	0.80722	P	0.0	P	0.43352	0.804	P	0.52031	0.688	T	0.12319	-1.0552	9	0.05351	T	0.99	.	7.3361	0.26611	0.0:0.6095:0.0:0.3905	rs2074467;rs17184037;rs52816876;rs2074467	161	Q96KK4	O10C1_HUMAN	L	161	ENSP00000419119:F161L	ENSP00000419119:F161L	F	+	3	2	OR10C1	29516254	0.000000	0.05858	0.993000	0.49108	0.378000	0.30076	-2.967000	0.00669	0.621000	0.30232	0.508000	0.49915	TTC	C|0.949;A|0.051	0.051	strong		0.617	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2		
PNMAL1	55228	hgsc.bcm.edu	37	19	46973315	46973315	+	Silent	SNP	G	G	A	rs61628326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46973315G>A	ENST00000313683.10	-	2	1283	c.978C>T	c.(976-978)gcC>gcT	p.A326A	PNMAL1_ENST00000438932.2_Silent_p.A326A|PNMAL1_ENST00000602246.1_Intron	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	326										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)		CTGGGCTCTCGGCTTCTGCCC	0.602													G|||	75	0.014976	0.0545	0.0043	5008	,	,		17043	0.0		0.0	False		,,,				2504	0.0				p.A326A		Atlas-SNP	.											.	PNMAL1	87	.	0			c.C978T						PASS	.	G	,	195,4211	118.0+/-155.7	8,179,2016	110.0	122.0	118.0		978,978	-7.3	0.0	19	dbSNP_129	118	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	PNMAL1	NM_001103149.1,NM_018215.3	,	8,183,6312	AA,AG,GG		0.0465,4.4258,1.5301	,	326/379,326/440	46973315	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			GCTCTCGGCTTCT	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.978C>T	19.37:g.46973315G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
SYCE3	644186	hgsc.bcm.edu	37	22	50989824	50989824	+	Silent	SNP	C	C	T	rs6009990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50989824C>T	ENST00000406915.3	-	3	164	c.117G>A	c.(115-117)gcG>gcA	p.A39A	SYCE3_ENST00000402753.1_Silent_p.A39A	NM_001123225.1	NP_001116697.1	A1L190	SYCE3_HUMAN	synaptonemal complex central element protein 3	39					positive regulation of apoptotic process (GO:0043065)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|chromosome (GO:0005694)|nucleus (GO:0005634)				endometrium(1)|kidney(1)	2						CCATCCAGGTCGCCTGCACTG	0.632													T|||	447	0.0892572	0.2383	0.0274	5008	,	,		19647	0.0109		0.0249	False		,,,				2504	0.0787				p.A39A		Atlas-SNP	.											.	SYCE3	10	.	0			c.G117A						PASS	.	T		296,1088		29,238,425	41.0	36.0	37.0		117	-7.2	0.9	22	dbSNP_114	37	81,3101		2,77,1512	no	coding-synonymous	C22orf41	NM_001123225.1		31,315,1937	TT,TC,CC		2.5456,21.3873,8.2567		39/89	50989824	377,4189	692	1591	2283	SO:0001819	synonymous_variant	644186	exon3			CCAGGTCGCCTGC		CCDS46733.1	22q13.33	2011-10-05	2011-10-05	2011-10-05	ENSG00000217442	ENSG00000217442			35245	protein-coding gene	gene with protein product	"""testis highly expressed protein 2"""	615775	"""chromosome 22 open reading frame 41"""	C22orf41		21637789	Standard	NM_001123225		Approved		uc010hbe.3	A1L190	OTTHUMG00000150273	ENST00000406915.3:c.117G>A	22.37:g.50989824C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_001123225		Silent	SNP	ENST00000406915.3	37	CCDS46733.1																																																																																			C|0.935;T|0.065	0.065	strong		0.632	SYCE3-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317660.1	NM_001123225	
PRMT7	54496	hgsc.bcm.edu	37	16	68389772	68389772	+	Silent	SNP	C	C	T	rs1131933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:68389772C>T	ENST00000339507.5	+	17	2627	c.1797C>T	c.(1795-1797)acC>acT	p.T599T	PRMT7_ENST00000441236.1_Silent_p.T549T|PRMT7_ENST00000348497.4_Silent_p.T451T|PRMT7_ENST00000449359.3_Silent_p.T549T			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	599	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		CCGAGGGCACCGTGGAGCTCA	0.677													C|||	2816	0.5623	0.5825	0.5764	5008	,	,		17878	0.7649		0.4026	False		,,,				2504	0.4806				p.T599T		Atlas-SNP	.											.	PRMT7	51	.	0			c.C1797T						PASS	.	C	,	2443,1951		678,1087,432	24.0	23.0	23.0		1647,1797	2.9	0.0	16	dbSNP_86	23	3796,4802		860,2076,1363	no	coding-synonymous,coding-synonymous	PRMT7	NM_001184824.1,NM_019023.2	,	1538,3163,1795	TT,TC,CC		44.1498,44.4015,48.0219	,	549/643,599/693	68389772	6239,6753	2197	4299	6496	SO:0001819	synonymous_variant	54496	exon17			GGGCACCGTGGAG	AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"""Protein arginine methyltransferases"""	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.1797C>T	16.37:g.68389772C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_019023	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Silent	SNP	ENST00000339507.5	37	CCDS10866.1																																																																																			C|0.488;T|0.512	0.512	strong		0.677	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	
COMMD10	51397	hgsc.bcm.edu	37	5	115428334	115428334	+	Silent	SNP	G	G	T	rs1129494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	87	0	0		WXS	Illumina HiSeq	Phase_I	98	36	0.367347	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	
CYP2A7	1549	hgsc.bcm.edu	37	19	41383217	41383217	+	Missense_Mutation	SNP	T	T	C	rs2302987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41383217T>C	ENST00000301146.4	-	7	1580	c.1039A>G	c.(1039-1041)Acc>Gcc	p.T347A	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.T296A	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	347						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)			GGCATCTTGGTCCGGTCCTCA	0.537													.|||	930	0.185703	0.2005	0.1124	5008	,	,		17445	0.2123		0.2386	False		,,,				2504	0.136				p.T347A		Atlas-SNP	.											.	CYP2A7	71	.	0			c.A1039G						PASS	.	T	ALA/THR,ALA/THR	834,3572	319.6+/-296.2	85,664,1454	113.0	92.0	99.0		1039,886	-1.2	0.2	19	dbSNP_100	99	2007,6589	346.0+/-326.0	290,1427,2581	no	missense,missense	CYP2A7	NM_000764.2,NM_030589.2	58,58	375,2091,4035	CC,CT,TT		23.3481,18.9287,21.8505	benign,benign	347/495,296/444	41383217	2841,10161	2203	4298	6501	SO:0001583	missense	1549	exon7			TCTTGGTCCGGTC	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.1039A>G	19.37:g.41383217T>C	ENSP00000301146:p.Thr347Ala	Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	273	96	0.351648	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	391	0.17902930402930403	85	0.17276422764227642	39	0.10773480662983426	104	0.18181818181818182	163	0.21503957783641162	T	0	-2.672588	0.00104	0.189287	0.233481	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.66638	-0.22;-0.22	2.18	-1.22	0.09494	.	0.614141	0.16066	N	0.231229	T	0.00012	0.0000	N	0.01091	-1.02	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.13926	-1.0491	9	0.14252	T	0.57	.	3.328	0.07074	0.1947:0.2753:0.0:0.5299	rs2302987	296;347	F8W816;P20853	.;CP2A7_HUMAN	A	347;296	ENSP00000301146:T347A;ENSP00000291764:T296A	ENSP00000291764:T296A	T	-	1	0	CYP2A7	46075057	0.000000	0.05858	0.151000	0.22473	0.217000	0.24651	-2.409000	0.01041	-0.391000	0.07763	-1.372000	0.01188	ACC	T|0.500;C|0.500	0.500	strong		0.537	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
MCF2L	23263	hgsc.bcm.edu	37	13	113739226	113739226	+	Silent	SNP	T	T	C	rs2281723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113739226T>C	ENST00000375608.3	+	20	2230	c.2172T>C	c.(2170-2172)taT>taC	p.Y724Y	MCF2L_ENST00000423482.2_Silent_p.Y692Y|MCF2L_ENST00000375604.2_Silent_p.Y751Y|MCF2L_ENST00000442652.2_Silent_p.Y724Y|MCF2L_ENST00000397030.1_Silent_p.Y727Y|MCF2L_ENST00000375601.3_Silent_p.Y698Y|MCF2L_ENST00000535094.2_Silent_p.Y694Y|MCF2L_ENST00000434480.2_Silent_p.Y700Y|MCF2L_ENST00000375597.4_Silent_p.Y692Y|MCF2L_ENST00000421756.1_Silent_p.Y698Y			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	724	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|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)				TCCAGATCTATGAGAAGTACT	0.582													c|||	562	0.11222	0.0764	0.0865	5008	,	,		17663	0.2649		0.0656	False		,,,				2504	0.0695				p.Y694Y		Atlas-SNP	.											.	MCF2L	182	.	0			c.T2082C						PASS	.	C	,	306,4100	797.5+/-415.4	10,286,1907	125.0	119.0	121.0		2082,2076	-3.1	1.0	13	dbSNP_100	121	607,7993	791.9+/-407.5	14,579,3707	yes	coding-synonymous,coding-synonymous	MCF2L	NM_001112732.2,NM_024979.4	,	24,865,5614	CC,CT,TT		7.0581,6.9451,7.0198	,	694/1126,692/1124	113739226	913,12093	2203	4300	6503	SO:0001819	synonymous_variant	23263	exon19			GATCTATGAGAAG	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.2172T>C	13.37:g.113739226T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	51	0.607143	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37		257	0.11767399267399267	43	0.08739837398373984	32	0.08839779005524862	135	0.23601398601398602	47	0.06200527704485488	C	9.298	1.052343	0.19827	0.069451	0.070581	ENSG00000126217	ENST00000397017	.	.	.	4.64	-3.09	0.05331	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2654	0.73657	0.0:0.1181:0.0:0.8819	rs2281723;rs17692545;rs2281723	.	.	.	R	355	.	.	X	+	1	0	MCF2L	112787227	0.995000	0.38212	0.975000	0.42487	0.824000	0.46624	0.321000	0.19558	-0.859000	0.04105	-0.711000	0.03637	TGA	T|0.904;C|0.096	0.096	strong		0.582	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
ISM2	145501	hgsc.bcm.edu	37	14	77950877	77950877	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:77950877C>T	ENST00000342219.4	-	3	472	c.416G>A	c.(415-417)aGg>aAg	p.R139K	ISM2_ENST00000493585.1_Missense_Mutation_p.R139K|ISM2_ENST00000393684.3_Missense_Mutation_p.R51K|ISM2_ENST00000412904.1_Intron|ISM2_ENST00000429906.1_Missense_Mutation_p.R58K	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	139						extracellular region (GO:0005576)				endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						CTCCTCTTCCCTCAGAGGCCT	0.597																																					p.R139K		Atlas-SNP	.											ISM2,NS,carcinoma,+1,1	ISM2	68	1	0			c.G416A						scavenged	.						68.0	61.0	64.0					14																	77950877		2203	4300	6503	SO:0001583	missense	145501	exon3			TCTTCCCTCAGAG	AK056709	CCDS9864.1, CCDS45143.1	14q24.3	2013-05-15	2013-05-15	2008-12-23	ENSG00000100593	ENSG00000100593			23176	protein-coding gene	gene with protein product	"""thrombospondin and AMOP containing isthmin-like 1"""	612684	"""thrombospondin, type I domain-containing 3"", ""thrombospondin, type I, domain containing 3"", ""isthmin 2 homolog (zebrafish)"""	THSD3		15194193	Standard	NM_199296		Approved	FLJ32147, TAIL1	uc001xtz.3	Q6H9L7	OTTHUMG00000158563	ENST00000342219.4:c.416G>A	14.37:g.77950877C>T	ENSP00000341490:p.Arg139Lys	Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	180	2	0.0111111	NM_199296	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Missense_Mutation	SNP	ENST00000342219.4	37	CCDS9864.1	.	.	.	.	.	.	.	.	.	.	C	2.040	-0.420366	0.04734	.	.	ENSG00000100593	ENST00000342219;ENST00000429906;ENST00000393684;ENST00000493585;ENST00000554801	T;T;T;T	0.30182	2.03;2.03;2.37;1.54	3.23	-2.0	0.07433	.	3.132790	0.01442	N	0.015158	T	0.15825	0.0381	N	0.14661	0.345	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.002	T	0.21211	-1.0252	10	0.05959	T	0.93	.	6.8075	0.23786	0.0:0.3626:0.0:0.6374	.	139;139	Q6H9L7-2;Q6H9L7	.;ISM2_HUMAN	K	139;58;51;139;58	ENSP00000341490:R139K;ENSP00000395387:R58K;ENSP00000377289:R51K;ENSP00000420452:R139K	ENSP00000341490:R139K	R	-	2	0	ISM2	77020630	0.000000	0.05858	0.000000	0.03702	0.427000	0.31564	-0.192000	0.09587	-0.264000	0.09365	-0.683000	0.03753	AGG	.	.	none		0.597	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509	
PPP6R3	55291	hgsc.bcm.edu	37	11	68377446	68377446	+	Missense_Mutation	SNP	C	C	T	rs34009811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:68377446C>T	ENST00000393800.2	+	23	2779	c.2525C>T	c.(2524-2526)gCg>gTg	p.A842V	PPP6R3_ENST00000393799.2_Missense_Mutation_p.A848V|PPP6R3_ENST00000393801.3_Missense_Mutation_p.A848V|PPP6R3_ENST00000529710.1_Missense_Mutation_p.A762V|PPP6R3_ENST00000527403.2_Missense_Mutation_p.A807V|PPP6R3_ENST00000534534.1_Missense_Mutation_p.A610V|PPP6R3_ENST00000524845.1_Missense_Mutation_p.A813V|PPP6R3_ENST00000524904.1_Missense_Mutation_p.A836V|PPP6R3_ENST00000265637.4_Missense_Mutation_p.A796V|PPP6R3_ENST00000265636.5_Missense_Mutation_p.A762V	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	842			A -> V (in dbSNP:rs34009811).		regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						ACTGCAGAGGCGAAGTGCGCG	0.607													C|||	219	0.04373	0.1604	0.0058	5008	,	,		19105	0.0		0.003	False		,,,				2504	0.0				p.A848V		Atlas-SNP	.											.	PPP6R3	159	.	0			c.C2543T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	566,3834	255.2+/-260.5	35,496,1669	89.0	80.0	83.0		2543,2525,2507,2438,2285,2285	-0.6	0.0	11	dbSNP_126	83	2,8586	2.2+/-6.3	0,2,4292	yes	missense,missense,missense,missense,missense,missense	PPP6R3	NM_001164160.1,NM_001164161.1,NM_001164162.1,NM_001164163.1,NM_001164164.1,NM_018312.4	64,64,64,64,64,64	35,498,5961	TT,TC,CC		0.0233,12.8636,4.3733	benign,benign,benign,benign,benign,benign	848/880,842/874,836/868,813/845,762/792,762/794	68377446	568,12420	2200	4294	6494	SO:0001583	missense	55291	exon24			CAGAGGCGAAGTG	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	1173	protein-coding gene	gene with protein product	"""sporulation-induced transcript 4-associated protein"""	610879	"""chromosome 11 open reading frame 23"", ""SAPS domain family, member 3"""	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.2525C>T	11.37:g.68377446C>T	ENSP00000377389:p.Ala842Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_001164160	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	37	CCDS53672.1	85|85	0.03891941391941392|0.03891941391941392	80|80	0.16260162601626016|0.16260162601626016	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	C|C	10.96|10.96	1.498149|1.498149	0.26861|0.26861	0.128636|0.128636	2.33E-4|2.33E-4	ENSG00000110075|ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000534534;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190|ENST00000530734	T;T;T;T;T;T;T;T;T;T;T|.	0.52295|.	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67|.	5.08|5.08	-0.623|-0.623	0.11556|0.11556	.|.	0.964243|.	0.08580|.	N|.	0.924730|.	T|.	0.00073|.	0.0002|.	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B;B;B|.	0.09022|.	0.001;0.0;0.002;0.001;0.002;0.001;0.001;0.001|.	B;B;B;B;B;B;B;B|.	0.11329|.	0.001;0.0;0.006;0.001;0.001;0.0;0.001;0.001|.	T|.	0.23547|.	-1.0185|.	9|.	0.30078|.	T|.	0.28|.	.|.	0.4596|0.4596	0.00514|0.00514	0.2168:0.3253:0.2173:0.2406|0.2168:0.3253:0.2173:0.2406	rs34009811;rs59254728|rs34009811;rs59254728	525;610;762;813;836;842;848;762|.	B4DYU6;E9PQP7;Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4|.	.;.;.;.;.;PP6R3_HUMAN;.;.|.	V|X	848;842;610;813;796;836;848;762;762;807;549|10	ENSP00000377388:A848V;ENSP00000377389:A842V;ENSP00000434429:A610V;ENSP00000431415:A813V;ENSP00000265637:A796V;ENSP00000433058:A836V;ENSP00000377390:A848V;ENSP00000265636:A762V;ENSP00000437329:A762V;ENSP00000433565:A807V;ENSP00000436209:A549V|.	ENSP00000265636:A762V|.	A|R	+|+	2|1	0|2	PPP6R3|PPP6R3	68134022|68134022	0.006000|0.006000	0.16342|0.16342	0.006000|0.006000	0.13384|0.13384	0.008000|0.008000	0.06430|0.06430	0.042000|0.042000	0.13949|0.13949	-0.088000|-0.088000	0.12506|0.12506	-0.459000|-0.459000	0.05422|0.05422	GCG|CGA	C|0.950;T|0.050	0.050	strong		0.607	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312	
PHF10	55274	hgsc.bcm.edu	37	6	170105725	170105725	+	Silent	SNP	T	T	C	rs4286788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170105725T>C	ENST00000339209.4	-	10	1332	c.1209A>G	c.(1207-1209)caA>caG	p.Q403Q	C6orf120_ENST00000332290.2_3'UTR|PHF10_ENST00000366780.4_Silent_p.Q401Q	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	403					nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		TATTCTCACATTGGGAGCAGT	0.353													T|||	21	0.00419329	0.0151	0.0014	5008	,	,		19342	0.0		0.0	False		,,,				2504	0.0				p.Q403Q		Atlas-SNP	.											.	PHF10	76	.	0			c.A1209G						PASS	.	T	,,	63,4343	59.3+/-96.0	0,63,2140	114.0	110.0	111.0		,1209,1203	-0.5	1.0	6	dbSNP_111	111	0,8600		0,0,4300	no	utr-3,coding-synonymous,coding-synonymous	PHF10,C6orf120	NM_001029863.1,NM_018288.3,NM_133325.2	,,	0,63,6440	CC,CT,TT		0.0,1.4299,0.4844	,,	,403/499,401/497	170105725	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	55274	exon10			CTCACATTGGGAG	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"""Zinc fingers, PHD-type"""	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.1209A>G	6.37:g.170105725T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Silent	SNP	ENST00000339209.4	37	CCDS5308.2																																																																																			T|0.995;C|0.005	0.005	strong		0.353	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288	
DPPA4	55211	hgsc.bcm.edu	37	3	109056363	109056363	+	Start_Codon_SNP	SNP	A	A	G	rs16855561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:109056363A>G	ENST00000335658.6	-	1	56	c.2T>C	c.(1-3)aTg>aCg	p.M1T	DPPA4_ENST00000478791.1_5'Flank	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	1					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						GCCTCGCAACATGCTTCCAAA	0.483													A|||	255	0.0509185	0.1641	0.0274	5008	,	,		14833	0.001		0.0169	False		,,,				2504	0.001				p.M1T		Atlas-SNP	.											.	DPPA4	56	.	0			c.T2C						PASS	.	A	THR/MET	637,3769	273.7+/-271.5	46,545,1612	120.0	101.0	107.0		2	-3.1	0.0	3	dbSNP_123	107	159,8441	76.0+/-138.7	2,155,4143	yes	missense	DPPA4	NM_018189.3	81	48,700,5755	GG,GA,AA		1.8488,14.4576,6.1203	benign	1/305	109056363	796,12210	2203	4300	6503	SO:0001582	initiator_codon_variant	55211	exon1			CGCAACATGCTTC	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.2T>C	3.37:g.109056363A>G	ENSP00000335306:p.Met1Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Missense_Mutation	SNP	ENST00000335658.6	37	CCDS33814.1	83	0.038003663003663	59	0.11991869918699187	11	0.03038674033149171	1	0.0017482517482517483	12	0.0158311345646438	A	5.437	0.265682	0.10294	0.144576	0.018488	ENSG00000121570	ENST00000335658	T	0.23348	1.91	3.85	-3.1	0.05315	.	4.070930	0.01129	U	0.005952	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15983	-1.0418	7	.	.	.	3.2593	0.8962	0.01264	0.2002:0.116:0.2402:0.4436	rs16855561;rs16855561	1;1	B7Z595;Q7L190	.;DPPA4_HUMAN	T	1	ENSP00000335306:M1T	.	M	-	2	0	DPPA4	110539053	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-0.515000	0.06290	-0.573000	0.05998	0.533000	0.62120	ATG	A|0.944;G|0.056	0.056	strong		0.483	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189	Missense_Mutation
PAK2	5062	hgsc.bcm.edu	37	3	196509577	196509577	+	Missense_Mutation	SNP	C	C	G	rs76714248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196509577C>G	ENST00000327134.3	+	2	382	c.60C>G	c.(58-60)agC>agG	p.S20R	RNU6-42P_ENST00000384165.1_RNA	NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	20					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)		GAATGAGCAGCACCATCTTTA	0.443																																					p.S20R		Atlas-SNP	.											PAK2_ENST00000327134,colon,carcinoma,0,2	PAK2	113	2	0			c.C60G						scavenged	.						123.0	129.0	127.0					3																	196509577		2203	4300	6503	SO:0001583	missense	5062	exon2			GAGCAGCACCATC	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.60C>G	3.37:g.196509577C>G	ENSP00000314067:p.Ser20Arg	Somatic	207	2	0.00966184		WXS	Illumina HiSeq	Phase_I	232	9	0.0387931	NM_002577	Q13154|Q6ISC3	Missense_Mutation	SNP	ENST00000327134.3	37	CCDS3321.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.749766	0.69533	.	.	ENSG00000180370	ENST00000327134	T	0.74737	-0.87	5.21	-3.63	0.04529	.	0.081384	0.85682	D	0.000000	D	0.83115	0.5184	M	0.78456	2.415	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.83597	0.0126	10	0.87932	D	0	.	14.4339	0.67268	0.0:0.6189:0.0:0.3811	.	20	Q13177	PAK2_HUMAN	R	20	ENSP00000314067:S20R	ENSP00000314067:S20R	S	+	3	2	PAK2	197993974	0.899000	0.30636	0.987000	0.45799	0.994000	0.84299	-0.061000	0.11693	-0.583000	0.05921	-0.290000	0.09829	AGC	C|0.991;G|0.009	0.009	strong		0.443	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
LPA	4018	hgsc.bcm.edu	37	6	161026103	161026103	+	Missense_Mutation	SNP	G	G	A	rs189364869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:161026103G>A	ENST00000316300.5	-	18	2964	c.2920C>T	c.(2920-2922)Cgg>Tgg	p.R974W	LPA_ENST00000447678.1_Missense_Mutation_p.R974W			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3482	Kringle 9. {ECO:0000255|PROSITE- ProRule:PRU00121}.				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)	GCTGGGGTCCGACTATGCGAG	0.443													G|||	4	0.000798722	0.003	0.0	5008	,	,		21608	0.0		0.0	False		,,,				2504	0.0				p.R974W		Atlas-SNP	.											.	LPA	237	.	0			c.C2920T						PASS	.	G	TRP/ARG	12,4376	17.9+/-39.9	0,12,2182	367.0	381.0	376.0		2920	0.9	0.0	6		376	0,8596		0,0,4298	no	missense	LPA	NM_005577.2	101	0,12,6480	AA,AG,GG		0.0,0.2735,0.0924	probably-damaging	974/2041	161026103	12,12972	2194	4298	6492	SO:0001583	missense	4018	exon19			GGGTCCGACTATG	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.2920C>T	6.37:g.161026103G>A	ENSP00000321334:p.Arg974Trp	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	g	7.632	0.679154	0.14907	0.002735	0.0	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.62941	-0.01;-0.01	2.16	0.902	0.19290	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.61022	0.2314	M	0.78456	2.415	0.09310	N	1	D	0.89917	1.0	D	0.77557	0.99	T	0.47911	-0.9080	9	0.36615	T	0.2	.	5.0035	0.14277	0.0:0.0:0.3278:0.6722	.	3482	P08519	APOA_HUMAN	W	974	ENSP00000321334:R974W;ENSP00000395608:R974W	ENSP00000321334:R974W	R	-	1	2	LPA	160946093	0.049000	0.20398	0.002000	0.10522	0.135000	0.20990	0.804000	0.27098	0.095000	0.17434	0.184000	0.17185	CGG	G|0.999;A|0.001	0.001	strong		0.443	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
MED12L	116931	hgsc.bcm.edu	37	3	150874033	150874033	+	Silent	SNP	T	T	C	rs61734152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150874033T>C	ENST00000474524.1	+	5	680	c.642T>C	c.(640-642)gaT>gaC	p.D214D	MED12L_ENST00000309237.4_Silent_p.D214D|MED12L_ENST00000273432.4_Silent_p.D214D|MED12L_ENST00000422248.2_Silent_p.D214D	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	214						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)			GCACGGGCGATGGCCCTGTCC	0.473													T|||	81	0.0161741	0.059	0.0029	5008	,	,		19291	0.0		0.001	False		,,,				2504	0.0				p.D214D		Atlas-SNP	.											MED12L,NS,carcinoma,+2,1	MED12L	271	1	0			c.T642C						PASS	.	T		264,4142	150.3+/-184.3	8,248,1947	113.0	106.0	109.0		642	-8.9	0.0	3	dbSNP_129	109	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	MED12L	NM_053002.4		8,252,6243	CC,CT,TT		0.0465,5.9918,2.0606		214/2146	150874033	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon5			GGGCGATGGCCCT	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.642T>C	3.37:g.150874033T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	75	27	0.36	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			T|0.983;C|0.017	0.017	strong		0.473	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
IFIH1	64135	hgsc.bcm.edu	37	2	163137871	163137871	+	Silent	SNP	C	C	G	rs12479043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:163137871C>G	ENST00000263642.2	-	7	1886	c.1491G>C	c.(1489-1491)acG>acC	p.T497T		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	497	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						TGGCTTGCTTCGTGGCCCCTC	0.393													C|||	804	0.160543	0.3245	0.3141	5008	,	,		18802	0.125		0.0109	False		,,,				2504	0.0204				p.T497T		Atlas-SNP	.											IFIH1,NS,carcinoma,0,1	IFIH1	102	1	0			c.G1491C						PASS	.	C		1383,3023	456.3+/-351.3	214,955,1034	135.0	128.0	131.0		1491	-4.5	0.0	2	dbSNP_120	131	126,8474	62.8+/-124.8	0,126,4174	no	coding-synonymous	IFIH1	NM_022168.2		214,1081,5208	GG,GC,CC		1.4651,31.389,11.6023		497/1026	163137871	1509,11497	2203	4300	6503	SO:0001819	synonymous_variant	64135	exon7			TTGCTTCGTGGCC	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.1491G>C	2.37:g.163137871C>G		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	175	108	0.617143	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Silent	SNP	ENST00000263642.2	37	CCDS2217.1																																																																																			C|0.879;G|0.121	0.121	strong		0.393	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168	
RAB40AL	282808	hgsc.bcm.edu	37	X	102192693	102192693	+	Silent	SNP	C	C	T	rs150288459		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192693C>T	ENST00000218249.5	+	1	494	c.447C>T	c.(445-447)ggC>ggT	p.G149G	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	149					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						AGCGCCTGGGCGTGACCTTCT	0.592																																					p.G149G		Atlas-SNP	.											.	RAB40AL	33	.	0			c.C447T						PASS	.						38.0	47.0	44.0					X																	102192693		2202	4300	6502	SO:0001819	synonymous_variant	282808	exon1			CCTGGGCGTGACC	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"""Ras like GTPase"""	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.447C>T	X.37:g.102192693C>T		Somatic	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	93	90	0.967742	NM_001031834	Q495H3	Silent	SNP	ENST00000218249.5	37	CCDS35353.1																																																																																			C|0.500;T|0.500	0.500	strong		0.592	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834	
KCNT2	343450	hgsc.bcm.edu	37	1	196303117	196303117	+	Silent	SNP	C	C	T	rs116401401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:196303117C>T	ENST00000294725.9	-	17	2772	c.1857G>A	c.(1855-1857)gaG>gaA	p.E619E	KCNT2_ENST00000367431.4_Silent_p.E569E|KCNT2_ENST00000451324.2_Silent_p.E230E|KCNT2_ENST00000367433.5_Silent_p.E619E|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000609185.1_Silent_p.E569E			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	619					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						CTTTGCTTCCCTCTGTAGGAA	0.393													C|||	25	0.00499201	0.0166	0.0043	5008	,	,		16218	0.0		0.0	False		,,,				2504	0.0				p.E619E		Atlas-SNP	.											.	KCNT2	243	.	0			c.G1857A						PASS	.	C		52,4354	52.3+/-87.9	0,52,2151	126.0	115.0	118.0		1857	0.6	1.0	1	dbSNP_132	118	0,8600		0,0,4300	no	coding-synonymous	KCNT2	NM_198503.2		0,52,6451	TT,TC,CC		0.0,1.1802,0.3998		619/1136	196303117	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	343450	exon17			GCTTCCCTCTGTA	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.1857G>A	1.37:g.196303117C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	37	CCDS1384.1																																																																																			C|0.995;T|0.005	0.005	strong		0.393	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503	
NRDE2	55051	hgsc.bcm.edu	37	14	90767607	90767607	+	Silent	SNP	C	C	T	rs3825661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:90767607C>T	ENST00000354366.3	-	7	1753	c.1521G>A	c.(1519-1521)gtG>gtA	p.V507V	NRDE2_ENST00000357904.3_Silent_p.V276V	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	507																	GCAGATCTTTCACGCTGTCGG	0.552													C|||	3387	0.676318	0.5673	0.6484	5008	,	,		15669	0.7976		0.671	False		,,,				2504	0.7239				p.V507V		Atlas-SNP	.											.	.	.	.	0			c.G1521A						PASS	.	C	,	2623,1783	642.4+/-397.6	804,1015,384	122.0	98.0	106.0		1521,828	4.9	0.9	14	dbSNP_107	106	6003,2597	688.2+/-404.3	2110,1783,407	no	coding-synonymous,coding-synonymous	C14orf102	NM_017970.3,NM_199043.1	,	2914,2798,791	TT,TC,CC		30.1977,40.4675,33.6768	,	507/1165,276/934	90767607	8626,4380	2203	4300	6503	SO:0001819	synonymous_variant	55051	exon7			ATCTTTCACGCTG	AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 102"""	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.1521G>A	14.37:g.90767607C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Silent	SNP	ENST00000354366.3	37	CCDS9890.1																																																																																			C|0.328;T|0.672	0.672	strong		0.552	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970	
CABYR	26256	hgsc.bcm.edu	37	18	21736486	21736486	+	Nonsense_Mutation	SNP	C	C	T	rs35554127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:21736486C>T	ENST00000399481.2	+	2	879	c.727C>T	c.(727-729)Cga>Tga	p.R243*	RP11-799B12.4_ENST00000583267.1_lincRNA|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000581397.1_Intron|CABYR_ENST00000399496.3_Intron|CABYR_ENST00000399499.1_Intron|CABYR_ENST00000415309.2_Intron			O75952	CABYR_HUMAN	calcium binding tyrosine-(Y)-phosphorylation regulated	341					epithelial cilium movement (GO:0003351)|sperm capacitation (GO:0048240)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)					GCAGTCACCACGAGTTAGTCC	0.378													C|||	71	0.0141773	0.0537	0.0	5008	,	,		21641	0.0		0.0	False		,,,				2504	0.0				p.R341X		Atlas-SNP	.											.	CABYR	51	.	0			c.C1021T						PASS	.	C	stop/ARG,,,stop/ARG,,	194,4212	118.8+/-156.5	3,188,2012	60.0	63.0	62.0		1021,,,967,,	3.4	1.0	18	dbSNP_126	62	0,8600		0,0,4300	yes	stop-gained,intron,intron,stop-gained,intron,intron	CABYR	NM_012189.2,NM_138643.1,NM_138644.1,NM_153768.1,NM_153769.1,NM_153770.1	,,,,,	3,188,6312	TT,TC,CC		0.0,4.4031,1.4916	,,,,,	341/494,,,323/476,,	21736486	194,12812	2203	4300	6503	SO:0001587	stop_gained	26256	exon4			TCACCACGAGTTA	AF088868	CCDS11881.1, CCDS11882.1, CCDS11883.1, CCDS42420.1, CCDS45840.1	18q11.2	2009-08-06	2007-11-22		ENSG00000154040	ENSG00000154040			15569	protein-coding gene	gene with protein product	"""fibrousheathin 2"", ""cancer/testis antigen 88"""	612135				11820818, 17317841, 16139264	Standard	NM_012189		Approved	FSP-2, CBP86, CT88	uc002kux.3	O75952	OTTHUMG00000037365	ENST00000399481.2:c.727C>T	18.37:g.21736486C>T	ENSP00000382404:p.Arg243*	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_012189	B2R857|Q8WXW5|Q9HAY3|Q9HAY4|Q9HAY5|Q9HCY9	Nonsense_Mutation	SNP	ENST00000399481.2	37		26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	C	23.4	4.416434	0.83449	0.044031	0.0	ENSG00000154040	ENST00000399481	.	.	.	5.31	3.39	0.38822	.	0.460245	0.20298	N	0.095093	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.8475	6.5485	0.22420	0.0:0.784:0.0:0.216	rs35554127	.	.	.	X	243	.	.	R	+	1	2	CABYR	19990484	0.415000	0.25416	0.972000	0.41901	0.862000	0.49288	0.095000	0.15127	1.466000	0.48025	0.655000	0.94253	CGA	C|0.986;T|0.014	0.014	strong		0.378	CABYR-201	KNOWN	basic	protein_coding	protein_coding		NM_153770	
MOB3A	126308	hgsc.bcm.edu	37	19	2078290	2078290	+	Silent	SNP	G	G	A	rs34483500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2078290G>A	ENST00000357066.3	-	3	649	c.270C>T	c.(268-270)gtC>gtT	p.V90V	MOB3A_ENST00000592280.1_Silent_p.V90V|MOB3A_ENST00000592143.1_Intron	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	90						intracellular (GO:0005622)	metal ion binding (GO:0046872)										CCCCCGACATGACGGGGCAGG	0.612													G|||	24	0.00479233	0.0174	0.0014	5008	,	,		16424	0.0		0.0	False		,,,				2504	0.0				p.V90V		Atlas-SNP	.											MOBKL2A,colon,carcinoma,-2,1	.	.	1	0			c.C270T						PASS	.	G		60,4346	57.4+/-93.9	1,58,2144	68.0	54.0	59.0		270	1.0	1.0	19	dbSNP_126	59	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MOB3A	NM_130807.2		1,59,6443	AA,AG,GG		0.0116,1.3618,0.469		90/218	2078290	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	126308	exon3			CGACATGACGGGG	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.270C>T	19.37:g.2078290G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	165	86	0.521212	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			G|0.994;A|0.006	0.006	strong		0.612	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
GJA4	2701	hgsc.bcm.edu	37	1	35260769	35260769	+	Missense_Mutation	SNP	C	C	T	rs1764391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	39	0	0		WXS	Illumina HiSeq	Phase_I	50	49	0.98	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	
HSD3B2	3284	hgsc.bcm.edu	37	1	119964625	119964625	+	Silent	SNP	G	G	A	rs6207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:119964625G>A	ENST00000543831.1	+	4	750	c.501G>A	c.(499-501)gcG>gcA	p.A167A	HSD3B2_ENST00000369416.3_Silent_p.A167A	NM_001166120.1	NP_001159592.1	P26439	3BHS2_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	167			A -> V (in AH2; late onset; almost normal activity; dbSNP:rs35486059). {ECO:0000269|PubMed:10599696}.		androgen biosynthetic process (GO:0006702)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(19)|ovary(2)|skin(1)	27	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	Corticotropin(DB01285)|Medroxyprogesterone Acetate(DB00603)|Trilostane(DB01108)	CTGTGCTGGCGGCTAATGGGT	0.488													G|||	15	0.00299521	0.0113	0.0	5008	,	,		19558	0.0		0.0	False		,,,				2504	0.0				p.A167A		Atlas-SNP	.											.	HSD3B2	48	.	0			c.G501A						PASS	.	G	,	41,4365		1,39,2163	77.0	77.0	77.0		501,501	-5.1	0.6	1	dbSNP_52	77	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	HSD3B2	NM_000198.3,NM_001166120.1	,	1,39,6463	AA,AG,GG		0.0,0.9305,0.3152	,	167/373,167/373	119964625	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	3284	exon4			GCTGGCGGCTAAT	BC038419	CCDS902.1	1p12	2014-06-03			ENSG00000203859	ENSG00000203859	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5218	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 2"""	613890				1363812, 19027726	Standard	NM_000198		Approved	SDR11E2	uc001eht.3	P26439	OTTHUMG00000012526	ENST00000543831.1:c.501G>A	1.37:g.119964625G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_001166120	A2RRA5|Q16010|Q53GD4|Q6AI10|Q6LDB9|Q99890|Q9UD08	Silent	SNP	ENST00000543831.1	37	CCDS902.1																																																																																			G|0.996;A|0.004	0.004	strong		0.488	HSD3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034994.1	NM_000198	
MYRIP	25924	hgsc.bcm.edu	37	3	40223771	40223771	+	Missense_Mutation	SNP	G	G	A	rs59923220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:40223771G>A	ENST00000302541.6	+	9	1276	c.934G>A	c.(934-936)Gct>Act	p.A312T	MYRIP_ENST00000539167.1_Missense_Mutation_p.A125T|MYRIP_ENST00000425621.1_Missense_Mutation_p.A312T|MYRIP_ENST00000444716.1_Missense_Mutation_p.A312T|MYRIP_ENST00000396217.3_Missense_Mutation_p.A223T|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	312	Myosin-binding.		A -> T (in dbSNP:rs59923220). {ECO:0000269|PubMed:15489334}.		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)		TCCAGTGGAGGCTCCATCGAG	0.567													G|||	391	0.0780751	0.2746	0.0346	5008	,	,		17481	0.0		0.004	False		,,,				2504	0.0				p.A312T		Atlas-SNP	.											.	MYRIP	98	.	0			c.G934A						PASS	.	G	THR/ALA	1037,3369	382.8+/-324.6	108,821,1274	76.0	77.0	77.0		934	0.8	0.1	3	dbSNP_129	77	13,8587	9.8+/-36.6	0,13,4287	yes	missense	MYRIP	NM_015460.2	58	108,834,5561	AA,AG,GG		0.1512,23.5361,8.0732	benign	312/860	40223771	1050,11956	2203	4300	6503	SO:0001583	missense	25924	exon9			GTGGAGGCTCCAT	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.934G>A	3.37:g.40223771G>A	ENSP00000301972:p.Ala312Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	140	62	0.442857	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	161	0.07371794871794872	150	0.3048780487804878	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	G	9.859	1.195685	0.22037	0.235361	0.001512	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81	5.27	0.792	0.18625	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.590955	0.16727	N	0.202020	T	0.00012	0.0000	L	0.40543	1.245	0.54753	P	1.799999999996249E-5	B;B;B	0.22080	0.064;0.001;0.003	B;B;B	0.22152	0.038;0.006;0.009	T	0.43032	-0.9416	8	.	.	.	.	6.3243	0.21234	0.2573:0.0:0.6071:0.1356	rs59923220	223;312;312	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	T	312;312;312;223;125	ENSP00000398665:A312T;ENSP00000301972:A312T;ENSP00000389323:A312T;ENSP00000379519:A223T;ENSP00000438297:A125T	.	A	+	1	0	MYRIP	40198775	0.997000	0.39634	0.096000	0.21009	0.003000	0.03518	0.665000	0.25083	0.211000	0.20683	-0.136000	0.14681	GCT	G|0.927;A|0.073	0.073	strong		0.567	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
DSC1	1823	hgsc.bcm.edu	37	18	28722103	28722103	+	Silent	SNP	T	T	C	rs2577074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28722103T>C	ENST00000257198.5	-	9	1380	c.1119A>G	c.(1117-1119)ttA>ttG	p.L373L	RP11-408H20.2_ENST00000581836.1_RNA|DSC1_ENST00000257197.3_Silent_p.L373L	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	373	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CCTTCATTCGTAAAATCTCCA	0.338													T|||	1726	0.344649	0.4085	0.3746	5008	,	,		17144	0.5655		0.2127	False		,,,				2504	0.1452				p.L373L		Atlas-SNP	.											.	DSC1	240	.	0			c.A1119G						PASS	.	T	,	1771,2635	525.1+/-371.5	357,1057,789	167.0	154.0	158.0		1119,1119	-0.0	1.0	18	dbSNP_100	158	1611,6989	300.2+/-304.8	160,1291,2849	no	coding-synonymous,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	517,2348,3638	CC,CT,TT		18.7326,40.1952,26.0034	,	373/841,373/895	28722103	3382,9624	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon9			CATTCGTAAAATC	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1119A>G	18.37:g.28722103T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	208	101	0.485577	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			T|0.690;C|0.310	0.310	strong		0.338	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
FMO2	2327	hgsc.bcm.edu	37	1	171176879	171176879	+	Silent	SNP	G	G	A	rs6671692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171176879G>A	ENST00000209929.7	+	8	1364	c.1206G>A	c.(1204-1206)gaG>gaA	p.E402E	RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Silent_p.E402E|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	401					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGCCCTCAGAGAGAACTATGA	0.313													G|||	232	0.0463259	0.1573	0.0115	5008	,	,		19971	0.0		0.001	False		,,,				2504	0.0153				p.E402E		Atlas-SNP	.											.	FMO2	66	.	0			c.G1206A						PASS	.	G		502,3904	229.4+/-244.0	26,450,1727	100.0	106.0	104.0		1206	5.8	0.5	1	dbSNP_116	104	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	FMO2	NM_001460.2		26,456,6021	AA,AG,GG		0.0698,11.3936,3.9059		402/472	171176879	508,12498	2203	4300	6503	SO:0001819	synonymous_variant	2327	exon8			CTCAGAGAGAACT	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.1206G>A	1.37:g.171176879G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	196	86	0.438776	NM_001460	Q53XR0	Silent	SNP	ENST00000209929.7	37	CCDS1293.1																																																																																			G|0.953;A|0.047	0.047	strong		0.313	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
GOT2	2806	hgsc.bcm.edu	37	16	58757683	58757683	+	Silent	SNP	A	A	G	rs257636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58757683A>G	ENST00000245206.5	-	2	341	c.213T>C	c.(211-213)aaT>aaC	p.N71N	GOT2_ENST00000434819.2_Silent_p.N71N|GOT2_ENST00000564400.1_5'UTR	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	71					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)	AAGGCTTTCCATTATCATCCC	0.498													G|||	3453	0.689497	0.8238	0.7594	5008	,	,		20246	0.6032		0.661	False		,,,				2504	0.5767				p.N71N		Atlas-SNP	.											.	GOT2	42	.	0			c.T213C						PASS	.	G		3474,922	353.1+/-312.0	1360,754,84	209.0	211.0	210.0		213	-2.0	1.0	16	dbSNP_79	210	5580,3020	466.1+/-366.7	1808,1964,528	yes	coding-synonymous	GOT2	NM_002080.2		3168,2718,612	GG,GA,AA		35.1163,20.9736,30.3324		71/431	58757683	9054,3942	2198	4300	6498	SO:0001819	synonymous_variant	2806	exon2			CTTTCCATTATCA		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.213T>C	16.37:g.58757683A>G		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	209	92	0.440191	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Silent	SNP	ENST00000245206.5	37	CCDS10801.1																																																																																			A|0.308;G|0.692	0.692	strong		0.498	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
SDK1	221935	hgsc.bcm.edu	37	7	3991479	3991479	+	Silent	SNP	A	A	G	rs6961589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:3991479A>G	ENST00000404826.2	+	7	1216	c.1077A>G	c.(1075-1077)ccA>ccG	p.P359P	SDK1_ENST00000389531.3_Silent_p.P359P	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	359	Ig-like C2-type 3.				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)		ACACCGGGCCATACGTCTGCG	0.602													G|||	341	0.0680911	0.2398	0.0303	5008	,	,		16870	0.0		0.002	False		,,,				2504	0.001				p.P359P		Atlas-SNP	.											.	SDK1	361	.	0			c.A1077G						PASS	.	G		958,3448	731.8+/-410.3	104,750,1349	52.0	52.0	52.0		1077	0.9	0.0	7	dbSNP_116	52	9,8591	817.5+/-406.9	0,9,4291	no	coding-synonymous	SDK1	NM_152744.3		104,759,5640	GG,GA,AA		0.1047,21.7431,7.435		359/2214	3991479	967,12039	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon7			CGGGCCATACGTC	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.1077A>G	7.37:g.3991479A>G		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1	110	0.05036630036630037	102	0.2073170731707317	6	0.016574585635359115	0	0.0	2	0.002638522427440633	G	0.457	-0.890886	0.02491	0.217431	0.001047	ENSG00000146555	ENST00000426596	.	.	.	4.87	0.937	0.19494	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22253	P	0.999251882	.	.	.	.	.	.	T	0.24190	-1.0167	3	.	.	.	.	3.246	0.06797	0.1411:0.2537:0.474:0.1313	rs6961589;rs17134087;rs6961589	.	.	.	R	78	.	.	H	+	2	0	SDK1	3958005	0.838000	0.29461	0.001000	0.08648	0.000000	0.00434	1.014000	0.29950	-0.265000	0.09352	-2.011000	0.00436	CAT	A|0.926;G|0.074	0.074	strong		0.602	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
POMZP3	22932	hgsc.bcm.edu	37	7	76240877	76240877	+	Missense_Mutation	SNP	A	A	T	rs73365247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:76240877A>T	ENST00000310842.4	-	6	1153	c.469T>A	c.(469-471)Tgt>Agt	p.C157S	AC004980.7_ENST00000418663.1_RNA|UPK3B_ENST00000419923.2_Intron|POMZP3_ENST00000275569.4_Intron|UPK3B_ENST00000443097.2_Intron	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	157										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				CAGCATTGACAGATGTCAGCC	0.517													a|||	295	0.0589058	0.2148	0.0144	5008	,	,		18707	0.001		0.0	False		,,,				2504	0.0				p.C157S		Atlas-SNP	.											.	POMZP3	19	.	0			c.T469A						PASS	.	A	SER/CYS,	887,3517		137,613,1452	74.0	76.0	75.0		469,	0.8	0.8	7	dbSNP_130	75	16,8566		1,14,4276	no	missense,intron	POMZP3	NM_012230.3,NM_152992.2	112,	138,627,5728	TT,TA,AA		0.1864,20.1408,6.9536	probably-damaging,	157/188,	76240877	903,12083	2202	4291	6493	SO:0001583	missense	22932	exon6			ATTGACAGATGTC	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.469T>A	7.37:g.76240877A>T	ENSP00000309233:p.Cys157Ser	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	284	110	0.387324	NM_012230	F6STJ3|Q12903|Q9BWB4	Missense_Mutation	SNP	ENST00000310842.4	37	CCDS43606.1	143|143	0.06547619047619048|0.06547619047619048	138|138	0.2804878048780488|0.2804878048780488	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	N|N	17.67|17.67	3.447194|3.447194	0.63178|0.63178	0.201408|0.201408	0.001864|0.001864	ENSG00000146707|ENSG00000146707	ENST00000310842|ENST00000441393	T|.	0.65732|.	-0.17|.	0.786|0.786	0.786|0.786	0.18590|0.18590	.|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.88310|0.88310	2.945|2.945	0.09310|0.09310	P|P	0.9999947731|0.9999947731	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.04650|0.04650	-1.0936|-1.0936	9|4	0.87932|.	D|.	0|.	.|.	3.9669|3.9669	0.09436|0.09436	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	157|.	Q6PJE2|.	POZP3_HUMAN|.	S|Q	157|93	ENSP00000309233:C157S|.	ENSP00000309233:C157S|.	C|L	-|-	1|2	0|0	POMZP3|POMZP3	76078813|76078813	1.000000|1.000000	0.71417|0.71417	0.795000|0.795000	0.32087|0.32087	0.753000|0.753000	0.42808|0.42808	2.176000|2.176000	0.42500|0.42500	0.612000|0.612000	0.30071|0.30071	0.305000|0.305000	0.20034|0.20034	TGT|CTG	A|0.957;T|0.043	0.043	strong		0.517	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341775.1	NM_012230	
FBXL17	64839	hgsc.bcm.edu	37	5	107197502	107197502	+	Silent	SNP	G	G	A	rs34990078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:107197502G>A	ENST00000542267.1	-	9	2431	c.2025C>T	c.(2023-2025)acC>acT	p.T675T	FBXL17_ENST00000359660.5_Silent_p.T277T	NM_001163315.2	NP_001156787.2	Q9UF56	FXL17_HUMAN	F-box and leucine-rich repeat protein 17	675										endometrium(1)|large_intestine(4)|lung(1)	6		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)		CCTGCAGGACGGTGCTGAAGG	0.587													G|||	778	0.155351	0.1036	0.111	5008	,	,		18355	0.1448		0.2087	False		,,,				2504	0.2127				p.T675T		Atlas-SNP	.											FBXL17_ENST00000542267,colon,carcinoma,-2,2	FBXL17	60	2	0			c.C2025T						PASS	.	G		590,3814	259.8+/-263.3	45,500,1657	127.0	92.0	104.0		2025	-8.1	1.0	5	dbSNP_126	104	1677,6923	308.0+/-308.7	166,1345,2789	no	coding-synonymous	FBXL17	NM_001163315.2		211,1845,4446	AA,AG,GG		19.5,13.3969,17.4331		675/702	107197502	2267,10737	2202	4300	6502	SO:0001819	synonymous_variant	64839	exon9			CAGGACGGTGCTG	AL133602	CCDS54886.1	5q21.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000145743	ENSG00000145743		"""F-boxes / Leucine-rich repeats"""	13615	protein-coding gene	gene with protein product		609083	"""F-box only protein 13"""	FBXO13			Standard	NM_001163315		Approved	DKFZP434C1715, Fbx13, Fbl17	uc011cvc.2	Q9UF56	OTTHUMG00000159785	ENST00000542267.1:c.2025C>T	5.37:g.107197502G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	80	47	0.5875	NM_001163315	A1A4E3	Silent	SNP	ENST00000542267.1	37	CCDS54886.1																																																																																			G|0.826;A|0.174	0.174	strong		0.587	FBXL17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
KLHL1	57626	hgsc.bcm.edu	37	13	70413291	70413291	+	Silent	SNP	A	A	G	rs41283972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:70413291A>G	ENST00000377844.4	-	6	1990	c.1231T>C	c.(1231-1233)Ttg>Ctg	p.L411L	KLHL1_ENST00000545028.1_Silent_p.L218L	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	411					actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		AGGTCAGCCAATATCTGTGAA	0.308													G|||	404	0.0806709	0.2247	0.0648	5008	,	,		17353	0.0089		0.0338	False		,,,				2504	0.0194				p.L411L		Atlas-SNP	.											.	KLHL1	164	.	0			c.T1231C						PASS	.	G		902,3502	733.7+/-410.5	91,720,1391	89.0	87.0	88.0		1231	0.1	1.0	13	dbSNP_127	88	311,8285	801.8+/-407.4	9,293,3996	no	coding-synonymous	KLHL1	NM_020866.2		100,1013,5387	GG,GA,AA		3.618,20.4814,9.3308		411/749	70413291	1213,11787	2202	4298	6500	SO:0001819	synonymous_variant	57626	exon6			CAGCCAATATCTG	AB040923	CCDS9445.1, CCDS73582.1	13q21	2013-01-30	2013-01-30		ENSG00000150361	ENSG00000150361		"""Kelch-like"", ""BTB/POZ domain containing"""	6352	protein-coding gene	gene with protein product	"""Kelch-like protein 1"", ""Mayven-related protein 2"""	605332	"""kelch (Drosophila)-like 1"", ""kelch-like 1 (Drosophila)"""			10888605	Standard	NM_020866		Approved	KIAA1490, MRP2, FLJ30047	uc001vip.3	Q9NR64	OTTHUMG00000017056	ENST00000377844.4:c.1231T>C	13.37:g.70413291A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Silent	SNP	ENST00000377844.4	37	CCDS9445.1																																																																																			A|0.919;G|0.081	0.081	strong		0.308	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866	
SBSN	374897	hgsc.bcm.edu	37	19	36018435	36018435	+	Missense_Mutation	SNP	G	G	A	rs147913080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36018435G>A	ENST00000452271.2	-	1	777	c.749C>T	c.(748-750)gCg>gTg	p.A250V	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	250	Ala/Gly/His-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GGCCTGCCCCGCAGCATGGTG	0.627													G|||	143	0.0285543	0.1044	0.0072	5008	,	,		20537	0.0		0.0	False		,,,				2504	0.0				p.A250V		Atlas-SNP	.											.	SBSN	58	.	0			c.C749T						PASS	.	G	VAL/ALA,,	148,1236		8,132,552	29.0	36.0	34.0		749,,	-5.1	0.0	19	dbSNP_134	34	0,3182		0,0,1591	no	missense,intron,intron	SBSN	NM_001166034.1,NM_001166035.1,NM_198538.3	64,,	8,132,2143	AA,AG,GG		0.0,10.6936,3.2413	benign,,	250/591,,	36018435	148,4418	692	1591	2283	SO:0001583	missense	374897	exon1			TGCCCCGCAGCAT	AY358701	CCDS12464.1, CCDS54253.1	19q13.13	2008-02-05							24950	protein-coding gene	gene with protein product		609969				12228223	Standard	NM_198538		Approved	UNQ698, HLAR698	uc002oad.2	Q6UWP8		ENST00000452271.2:c.749C>T	19.37:g.36018435G>A	ENSP00000430242:p.Ala250Val	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_001166034	A8K5J0|E9PBV3	Missense_Mutation	SNP	ENST00000452271.2	37	CCDS54253.1	50	0.022893772893772892	40	0.08130081300813008	3	0.008287292817679558	7	0.012237762237762238	0	0.0	G	10.51	1.369069	0.24771	0.106936	0.0	ENSG00000189001	ENST00000452271	T	0.48201	0.82	4.63	-5.14	0.02875	.	.	.	.	.	T	0.00580	0.0019	L	0.40543	1.245	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.16424	-1.0403	9	0.17369	T	0.5	.	7.6648	0.28423	0.3905:0.1283:0.4812:0.0	.	250	E9PBV3	.	V	250	ENSP00000430242:A250V	ENSP00000430242:A250V	A	-	2	0	SBSN	40710275	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.794000	0.01753	-0.578000	0.05959	-1.069000	0.02264	GCG	G|0.977;A|0.023	0.023	strong		0.627	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538	
QRICH2	84074	hgsc.bcm.edu	37	17	74289705	74289705	+	Missense_Mutation	SNP	A	A	G	rs6501880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74289705A>G	ENST00000262765.5	-	4	784	c.605T>C	c.(604-606)tTg>tCg	p.L202S		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	202			L -> S (in dbSNP:rs6501880).							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						GTCTCTGGCCAAGGGTAAGTC	0.522													G|||	2317	0.46266	0.6815	0.3084	5008	,	,		24481	0.5724		0.2753	False		,,,				2504	0.3558				p.L202S		Atlas-SNP	.											.	QRICH2	143	.	0			c.T605C						PASS	.	G	SER/LEU	2837,1569	489.0+/-361.4	920,997,286	132.0	101.0	111.0		605	-4.5	0.0	17	dbSNP_116	111	2486,6114	696.3+/-404.9	348,1790,2162	yes	missense	QRICH2	NM_032134.1	145	1268,2787,2448	GG,GA,AA		28.907,35.6105,40.9273	benign	202/1664	74289705	5323,7683	2203	4300	6503	SO:0001583	missense	84074	exon4			CTGGCCAAGGGTA	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.605T>C	17.37:g.74289705A>G	ENSP00000262765:p.Leu202Ser	Somatic	410	0	0		WXS	Illumina HiSeq	Phase_I	425	201	0.472941	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	971	0.44459706959706957	337	0.6849593495934959	106	0.292817679558011	332	0.5804195804195804	196	0.25857519788918204	G	3.851	-0.031778	0.07543	0.643895	0.28907	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.17691	2.26	3.69	-4.53	0.03462	.	.	.	.	.	T	0.00012	0.0000	N	0.12569	0.235	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.06405	0.001;0.002	T	0.35549	-0.9784	8	0.07813	T	0.8	.	7.1823	0.25780	0.6822:0.0:0.17:0.1478	rs6501880;rs60042941;rs6501880	202;202	B5MD94;Q9H0J4	.;QRIC2_HUMAN	S	202	ENSP00000262765:L202S	ENSP00000262765:L202S	L	-	2	0	QRICH2	71801300	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.980000	0.03770	-1.269000	0.02436	-1.945000	0.00491	TTG	A|0.564;G|0.436	0.436	strong		0.522	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
ISX	91464	hgsc.bcm.edu	37	22	35480467	35480467	+	Missense_Mutation	SNP	C	C	T	rs7291048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:35480467C>T	ENST00000308700.6	+	3	1425	c.473C>T	c.(472-474)gCc>gTc	p.A158V	ISX_ENST00000404699.2_Missense_Mutation_p.A158V	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	158			A -> V (in dbSNP:rs7291048).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						GCCAGTGTGGCCCTGCCCACA	0.552													C|||	462	0.0922524	0.2579	0.0159	5008	,	,		17641	0.0546		0.002	False		,,,				2504	0.0542				p.A158V		Atlas-SNP	.											.	ISX	62	.	0			c.C473T						PASS	.	C	VAL/ALA	966,3440	363.1+/-316.4	99,768,1336	52.0	46.0	48.0		473	1.3	0.0	22	dbSNP_116	48	15,8585	9.1+/-34.3	0,15,4285	yes	missense	ISX	NM_001008494.1	64	99,783,5621	TT,TC,CC		0.1744,21.9246,7.5427	probably-damaging	158/246	35480467	981,12025	2203	4300	6503	SO:0001583	missense	91464	exon3			GTGTGGCCCTGCC	AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"""Homeoboxes / PRD class"""	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.473C>T	22.37:g.35480467C>T	ENSP00000311492:p.Ala158Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_001008494	Q68DJ5	Missense_Mutation	SNP	ENST00000308700.6	37	CCDS33640.1	170	0.07783882783882784	133	0.2703252032520325	6	0.016574585635359115	30	0.05244755244755245	1	0.0013192612137203166	C	15.23	2.771772	0.49680	0.219246	0.001744	ENSG00000175329	ENST00000308700;ENST00000404699	D;D	0.90676	-2.71;-2.71	5.07	1.27	0.21489	.	0.944627	0.08782	N	0.894475	T	0.00039	0.0001	M	0.64997	1.995	0.80722	P	0.0	B	0.25312	0.123	B	0.19391	0.025	T	0.05500	-1.0881	9	0.25751	T	0.34	.	5.3469	0.16014	0.0:0.6004:0.1686:0.2309	rs7291048;rs52832930;rs57036230;rs7291048	158	Q2M1V0	ISX_HUMAN	V	158	ENSP00000311492:A158V;ENSP00000386037:A158V	ENSP00000311492:A158V	A	+	2	0	ISX	33810467	0.000000	0.05858	0.005000	0.12908	0.308000	0.27856	0.429000	0.21412	0.618000	0.30179	0.655000	0.94253	GCC	C|0.915;T|0.085	0.085	strong		0.552	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494	
OR2T4	127074	hgsc.bcm.edu	37	1	248525330	248525330	+	Missense_Mutation	SNP	A	A	G	rs376643959|rs56721857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248525330A>G	ENST00000366475.1	+	1	448	c.448A>G	c.(448-450)Atg>Gtg	p.M150V		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCTAGCCACCATGGCCTATGA	0.522													a|||	1358	0.271166	0.2284	0.2637	5008	,	,		19950	0.381		0.1779	False		,,,				2504	0.317				p.M150V		Atlas-SNP	.											.	OR2T4	126	.	0			c.A448G						PASS	.						179.0	174.0	176.0					1																	248525330		2203	4300	6503	SO:0001583	missense	127074	exon1			GCCACCATGGCCT	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.448A>G	1.37:g.248525330A>G	ENSP00000355431:p.Met150Val	Somatic	897	3	0.00334448		WXS	Illumina HiSeq	Phase_I	847	308	0.363636	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.455416	0.63401	.	.	ENSG00000196944	ENST00000366475	T	0.00995	5.46	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000023	T	0.05502	0.0145	M	0.91972	3.26	0.38959	D	0.958507	D	0.61080	0.989	P	0.58721	0.844	T	0.05209	-1.0899	10	0.87932	D	0	.	11.6861	0.51487	1.0:0.0:0.0:0.0	rs56721857	150	Q8NH00	OR2T4_HUMAN	V	150	ENSP00000355431:M150V	ENSP00000355431:M150V	M	+	1	0	OR2T4	246591953	1.000000	0.71417	0.636000	0.29352	0.769000	0.43574	5.832000	0.69337	1.205000	0.43262	0.397000	0.26171	ATG	A|0.878;G|0.122	0.122	strong		0.522	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
GSDMD	79792	hgsc.bcm.edu	37	8	144644405	144644405	+	Silent	SNP	G	G	A	rs11551198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144644405G>A	ENST00000526406.1	+	12	1906	c.1023G>A	c.(1021-1023)ccG>ccA	p.P341P	GSDMD_ENST00000262580.4_Silent_p.P341P|GSDMD_ENST00000533063.1_Silent_p.P389P	NM_001166237.1	NP_001159709.1	P57764	GSDMD_HUMAN	gasdermin D	341					cellular response to extracellular stimulus (GO:0031668)					breast(1)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	12						GCCTTGGGCCGGTGGAGCCCC	0.682													G|||	659	0.131589	0.1104	0.1311	5008	,	,		11253	0.0357		0.2256	False		,,,				2504	0.1626				p.P341P		Atlas-SNP	.											.	GSDMD	28	.	0			c.G1023A						PASS	.	G	,	461,3877		38,385,1746	22.0	21.0	21.0		1023,1023	-0.7	0.0	8	dbSNP_120	21	1797,6753		189,1419,2667	no	coding-synonymous,coding-synonymous	GSDMD	NM_001166237.1,NM_024736.6	,	227,1804,4413	AA,AG,GG		21.0175,10.627,17.5202	,	341/485,341/485	144644405	2258,10630	2169	4275	6444	SO:0001819	synonymous_variant	79792	exon12			TGGGCCGGTGGAG	AK096216	CCDS34956.1	8q24.3	2008-07-31	2008-07-31	2008-07-31		ENSG00000104518			25697	protein-coding gene	gene with protein product			"""gasdermin domain containing 1"""	GSDMDC1		15289881, 17350798	Standard	NM_024736		Approved	FLJ12150, DF5L	uc003yyg.3	P57764		ENST00000526406.1:c.1023G>A	8.37:g.144644405G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	NM_001166237	D3DWJ9|Q96Q98	Silent	SNP	ENST00000526406.1	37	CCDS34956.1	285	0.1304945054945055	65	0.13211382113821138	46	0.1270718232044199	14	0.024475524475524476	160	0.21108179419525067	G	3.369	-0.128730	0.06753	0.10627	0.210175	ENSG00000104518	ENST00000525208	.	.	.	4.39	-0.686	0.11324	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.24548	-1.0157	3	.	.	.	-8.7647	2.2659	0.04078	0.1647:0.124:0.4583:0.253	rs11551198	.	.	.	S	37	.	.	G	+	1	0	GSDMD	144715548	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.121000	0.15667	-0.385000	0.07833	-1.193000	0.01689	GGT	G|0.851;A|0.149	0.149	strong		0.682	GSDMD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382046.3	NM_024736	
COL20A1	57642	hgsc.bcm.edu	37	20	61959758	61959758	+	Missense_Mutation	SNP	C	C	T	rs115749294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61959758C>T	ENST00000358894.6	+	34	3789	c.3689C>T	c.(3688-3690)cCg>cTg	p.P1230L	COL20A1_ENST00000435874.1_Missense_Mutation_p.P1243L|COL20A1_ENST00000326996.6_Missense_Mutation_p.P1262L|COL20A1_ENST00000422202.1_Missense_Mutation_p.P1243L	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1230				P -> Q (in Ref. 2; AAH43183). {ECO:0000305}.	extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					AAGCTGGAGCCGGGCACTGAG	0.662													C|||	37	0.00738818	0.028	0.0	5008	,	,		15679	0.0		0.0	False		,,,				2504	0.0				p.P1230L		Atlas-SNP	.											.	COL20A1	137	.	0			c.C3689T						PASS	.	C	LEU/PRO	92,3808		1,90,1859	26.0	31.0	29.0		3689	1.2	0.0	20	dbSNP_132	29	4,8234		0,4,4115	yes	missense	COL20A1	NM_020882.2	98	1,94,5974	TT,TC,CC		0.0486,2.359,0.7909	benign	1230/1285	61959758	96,12042	1950	4119	6069	SO:0001583	missense	57642	exon34			TGGAGCCGGGCAC	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.3689C>T	20.37:g.61959758C>T	ENSP00000351767:p.Pro1230Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	131	75	0.572519	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	4.851	0.158169	0.09236	0.02359	4.86E-4	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202;ENST00000415763;ENST00000455906	D;D;D;D;D;D	0.90900	-2.22;-2.18;-2.14;-2.14;-2.75;-2.59	3.37	1.25	0.21368	.	0.343274	0.25598	N	0.029561	T	0.56848	0.2013	N	0.12746	0.255	0.09310	N	1	B;B	0.12013	0.003;0.005	B;B	0.08055	0.001;0.003	T	0.58983	-0.7539	10	0.35671	T	0.21	.	5.6298	0.17504	0.0:0.6946:0.0:0.3054	.	1243;1230	Q9P218-2;Q9P218	.;COKA1_HUMAN	L	1230;1262;1243;1243;371;226	ENSP00000351767:P1230L;ENSP00000323077:P1262L;ENSP00000408690:P1243L;ENSP00000414753:P1243L;ENSP00000410799:P371L;ENSP00000406345:P226L	ENSP00000323077:P1262L	P	+	2	0	COL20A1	61430202	0.006000	0.16342	0.001000	0.08648	0.097000	0.18754	0.478000	0.22212	0.356000	0.24157	0.313000	0.20887	CCG	C|0.995;T|0.005	0.005	strong		0.662	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
FREM1	158326	hgsc.bcm.edu	37	9	14824799	14824799	+	Silent	SNP	G	G	A	rs12236053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14824799G>A	ENST00000380880.3	-	11	2856	c.2073C>T	c.(2071-2073)agC>agT	p.S691S	FREM1_ENST00000380881.4_Silent_p.S692S|FREM1_ENST00000422223.2_Silent_p.S691S			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	151	0	0		WXS	Illumina HiSeq	Phase_I	137	75	0.547445	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	
DSG1	1828	hgsc.bcm.edu	37	18	28923906	28923906	+	Missense_Mutation	SNP	A	A	G	rs116081362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28923906A>G	ENST00000257192.4	+	13	2051	c.1839A>G	c.(1837-1839)atA>atG	p.I613M	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578119.1_RNA|DSG1_ENST00000462981.2_5'UTR|RNU6-167P_ENST00000384292.1_RNA	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	613					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)			CCACTGTCATACCACAAATAC	0.318													A|||	142	0.0283546	0.1021	0.0086	5008	,	,		15765	0.0		0.001	False		,,,				2504	0.0				p.I613M		Atlas-SNP	.											.	DSG1	176	.	0			c.A1839G						PASS	.	A	MET/ILE	385,4021	192.6+/-218.0	16,353,1834	124.0	114.0	118.0		1839	0.9	0.0	18	dbSNP_132	118	3,8593	3.0+/-9.4	0,3,4295	yes	missense	DSG1	NM_001942.2	10	16,356,6129	GG,GA,AA		0.0349,8.7381,2.9842	benign	613/1050	28923906	388,12614	2203	4298	6501	SO:0001583	missense	1828	exon13			TGTCATACCACAA	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.1839A>G	18.37:g.28923906A>G	ENSP00000257192:p.Ile613Met	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	161	73	0.453416	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	53	0.024267399267399268	49	0.09959349593495935	4	0.011049723756906077	0	0.0	0	0.0	A	7.734	0.699824	0.15106	0.087381	3.49E-4	ENSG00000134760	ENST00000257192	T	0.42513	0.97	4.98	0.91	0.19337	.	0.499779	0.18540	N	0.138233	T	0.00637	0.0021	N	0.14661	0.345	0.09310	N	0.999997	P	0.40266	0.71	P	0.45167	0.472	T	0.02533	-1.1145	10	0.37606	T	0.19	.	3.6502	0.08201	0.3746:0.2209:0.4045:0.0	.	613	Q02413	DSG1_HUMAN	M	613	ENSP00000257192:I613M	ENSP00000257192:I613M	I	+	3	3	DSG1	27177904	0.212000	0.23540	0.009000	0.14445	0.000000	0.00434	0.194000	0.17135	0.046000	0.15833	-0.291000	0.09656	ATA	A|0.967;G|0.033	0.033	strong		0.318	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
UNC13B	10497	hgsc.bcm.edu	37	9	35398900	35398900	+	Missense_Mutation	SNP	G	G	T	rs12339582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35398900G>T	ENST00000378495.3	+	32	3918	c.3696G>T	c.(3694-3696)gaG>gaT	p.E1232D	UNC13B_ENST00000481299.1_3'UTR|UNC13B_ENST00000378496.4_Missense_Mutation_p.E1232D|UNC13B_ENST00000396787.1_Missense_Mutation_p.E1244D	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1232			E -> D (in dbSNP:rs12339582).		apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GGATTGATGAGTGTGTTCGAC	0.582													G|||	153	0.0305511	0.1067	0.0043	5008	,	,		21512	0.0079		0.001	False		,,,				2504	0.0				p.E1232D		Atlas-SNP	.											.	UNC13B	153	.	0			c.G3696T						PASS	.	G	ASP/GLU	379,4027	191.9+/-217.4	16,347,1840	126.0	129.0	128.0		3696	4.1	1.0	9	dbSNP_120	128	4,8596	3.7+/-12.6	0,4,4296	yes	missense	UNC13B	NM_006377.3	45	16,351,6136	TT,TG,GG		0.0465,8.6019,2.9448	benign	1232/1592	35398900	383,12623	2203	4300	6503	SO:0001583	missense	10497	exon32			TGATGAGTGTGTT	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.3696G>T	9.37:g.35398900G>T	ENSP00000367756:p.Glu1232Asp	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	200	88	0.44	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	69	0.03159340659340659	62	0.12601626016260162	2	0.0055248618784530384	4	0.006993006993006993	1	0.0013192612137203166	G	13.61	2.288018	0.40494	0.086019	4.65E-4	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.10099	2.91;2.91;2.91	5.94	4.07	0.47477	.	0.102509	0.64402	D	0.000003	T	0.00073	0.0002	N	0.25332	0.735	0.50171	D	0.999858	B;B	0.15473	0.013;0.011	B;B	0.14023	0.009;0.01	T	0.52223	-0.8604	10	0.24483	T	0.36	-27.2563	7.8494	0.29446	0.1495:0.1355:0.715:0.0	rs12339582;rs17849224;rs12339582	1232;1232	F8W8M9;O14795	.;UN13B_HUMAN	D	1244;1232;1232;819	ENSP00000380006:E1244D;ENSP00000367756:E1232D;ENSP00000367757:E1232D	ENSP00000367756:E1232D	E	+	3	2	UNC13B	35388900	0.992000	0.36948	1.000000	0.80357	0.998000	0.95712	0.238000	0.18004	1.493000	0.48517	0.557000	0.71058	GAG	G|0.960;T|0.040	0.040	strong		0.582	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	
CCDC186	55088	hgsc.bcm.edu	37	10	115887340	115887340	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115887340T>A	ENST00000369287.3	-	14	2539	c.2273A>T	c.(2272-2274)aAg>aTg	p.K758M	C10orf118_ENST00000543782.1_Missense_Mutation_p.K356M|C10orf118_ENST00000497592.1_5'Flank	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		758										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)		CAACATGGCCTTATCTACTTG	0.433																																					p.K758M		Atlas-SNP	.											C10orf118,NS,malignant_melanoma,0,1	C10orf118	70	1	0			c.A2273T						scavenged	.						139.0	125.0	130.0					10																	115887340		2203	4300	6503	SO:0001583	missense	55088	exon14			ATGGCCTTATCTA																												ENST00000369287.3:c.2273A>T	10.37:g.115887340T>A	ENSP00000358293:p.Lys758Met	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	139	3	0.0215827	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Missense_Mutation	SNP	ENST00000369287.3	37	CCDS7587.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.1|23.1	4.378994|4.378994	0.82682|0.82682	.|.	.|.	ENSG00000165813|ENSG00000165813	ENST00000369287;ENST00000543782;ENST00000430353|ENST00000428953	T|.	0.27890|.	1.64|.	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.74137|.	0.3677|.	M|M	0.79258|0.79258	2.445|2.445	0.58432|0.58432	D|D	0.999998|0.999998	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.998;0.999|.	T|.	0.75811|.	-0.3186|.	10|.	0.62326|.	D|.	0.03|.	.|.	13.1396|13.1396	0.59428|0.59428	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	356;758|.	F6VCB7;Q7Z3E2|.	.;CJ118_HUMAN|.	M|Y	758;356;864|386	ENSP00000358293:K758M|.	ENSP00000358293:K758M|.	K|X	-|-	2|3	0|2	C10orf118|C10orf118	115877330|115877330	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	8.008000|8.008000	0.88588|0.88588	1.826000|1.826000	0.53198|0.53198	0.449000|0.449000	0.29647|0.29647	AAG|TAA	.	.	none		0.433	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1		
SLC26A9	115019	hgsc.bcm.edu	37	1	205901000	205901000	+	Silent	SNP	G	G	A	rs33943971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:205901000G>A	ENST00000367135.3	-	5	653	c.540C>T	c.(538-540)acC>acT	p.T180T	SLC26A9_ENST00000340781.4_Silent_p.T180T|SLC26A9_ENST00000367134.2_Silent_p.T180T	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	180					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			GGATGATGGCGGTGAGGCAGG	0.562													G|||	370	0.0738818	0.1664	0.0677	5008	,	,		18568	0.0		0.0805	False		,,,				2504	0.0225				p.T180T		Atlas-SNP	.											.	SLC26A9	176	.	0			c.C540T						PASS	.	G	,	708,3698	293.8+/-282.8	51,606,1546	57.0	56.0	56.0		540,540	-9.1	0.9	1	dbSNP_126	56	673,7927	169.1+/-220.5	31,611,3658	no	coding-synonymous,coding-synonymous	SLC26A9	NM_052934.3,NM_134325.2	,	82,1217,5204	AA,AG,GG		7.8256,16.069,10.6182	,	180/792,180/888	205901000	1381,11625	2203	4300	6503	SO:0001819	synonymous_variant	115019	exon5			GATGGCGGTGAGG	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"""Solute carriers"""	14469	protein-coding gene	gene with protein product	"""anion transporter/exchanger-9"""	608481	"""solute carrier family 26, member 9"""			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.540C>T	1.37:g.205901000G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	167	72	0.431138	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Silent	SNP	ENST00000367135.3	37	CCDS30990.1																																																																																			G|0.899;A|0.101	0.101	strong		0.562	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934	
LRP1B	53353	hgsc.bcm.edu	37	2	141274456	141274456	+	Splice_Site	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:141274456A>G	ENST00000389484.3	-	50	9121		c.e50+1			NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B						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)		ACAATGTCTCACCACAGTGGA	0.328										TSP Lung(27;0.18)																											.	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.8149+2T>C						PASS	.						146.0	134.0	138.0					2																	141274456		2203	4300	6503	SO:0001630	splice_region_variant	53353	exon51			TGTCTCACCACAG	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.8149+1T>C	2.37:g.141274456A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	66	12	0.181818	NM_018557	Q8WY29|Q8WY30|Q8WY31	Splice_Site	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	18.09	3.546269	0.65198	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5612	0.68136	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRP1B	140990926	1.000000	0.71417	0.994000	0.49952	0.576000	0.36127	9.278000	0.95766	1.815000	0.52974	0.460000	0.39030	.	.	.	none		0.328	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Intron
ADAMTS17	170691	hgsc.bcm.edu	37	15	100636586	100636586	+	Silent	SNP	G	G	A	rs4965583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	57	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	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	
MUC2	4583	hgsc.bcm.edu	37	11	1093362	1093362	+	Silent	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1093362C>G	ENST00000441003.2	+	30	5208	c.5181C>G	c.(5179-5181)acC>acG	p.T1727T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1694T|MUC2_ENST00000333592.6_Silent_p.T15T	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)	tctccaccaccactacggtga	0.647																																					p.T1727T		Atlas-SNP	.											.	MUC2	614	.	0			c.C5181G						PASS	.						187.0	230.0	215.0					11																	1093362		1968	3798	5766	SO:0001819	synonymous_variant	4583	exon30			CACCACCACTACG	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.5181C>G	11.37:g.1093362C>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	132	8	0.0606061	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FRMPD2	143162	hgsc.bcm.edu	37	10	49420008	49420008	+	Missense_Mutation	SNP	T	T	C	rs1864345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:49420008T>C	ENST00000374201.3	-	13	1902	c.1600A>G	c.(1600-1602)Aag>Gag	p.K534E	FRMPD2_ENST00000305531.3_Missense_Mutation_p.K509E|FRMPD2_ENST00000407470.4_Missense_Mutation_p.K502E	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	534	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		K -> E (in dbSNP:rs1864345). {ECO:0000269|PubMed:14702039}.		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)		CTCAAGAACTTCAGCTCAGCA	0.577													C|||	1414	0.282348	0.6074	0.183	5008	,	,		16139	0.0694		0.2535	False		,,,				2504	0.1626				p.K534E		Atlas-SNP	.											.	FRMPD2	157	.	0			c.A1600G						PASS	.	C	GLU/LYS	2392,2014	561.2+/-380.7	663,1066,474	101.0	88.0	92.0		1600	3.4	1.0	10	dbSNP_92	92	1870,6730	727.7+/-406.6	186,1498,2616	yes	missense	FRMPD2	NM_001018071.3	56	849,2564,3090	CC,CT,TT		21.7442,45.7104,32.7695	benign	534/1310	49420008	4262,8744	2203	4300	6503	SO:0001583	missense	143162	exon13			AGAACTTCAGCTC	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.1600A>G	10.37:g.49420008T>C	ENSP00000363317:p.Lys534Glu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	596	0.27289377289377287	307	0.6239837398373984	73	0.20165745856353592	26	0.045454545454545456	190	0.25065963060686014	C	4.384	0.070801	0.08436	0.542896	0.217442	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.78595	-1.19;-1.19;-1.19	5.28	3.39	0.38822	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	.	.	.	.	T	0.00012	0.0000	N	0.00034	-2.56	0.58432	P	9.000000000036756E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.47484	-0.9114	8	0.02654	T	1	.	8.6763	0.34181	0.0:0.6075:0.3133:0.0792	rs1864345;rs52798519;rs57169678;rs1864345	509;534;502	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	E	534;509;502	ENSP00000363317:K534E;ENSP00000307079:K509E;ENSP00000384339:K502E	ENSP00000307079:K509E	K	-	1	0	FRMPD2	49090014	1.000000	0.71417	0.998000	0.56505	0.967000	0.64934	1.490000	0.35573	0.225000	0.20959	-1.147000	0.01851	AAG	T|0.692;C|0.308	0.308	strong		0.577	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
C14orf80	283643	hgsc.bcm.edu	37	14	105958010	105958010	+	Missense_Mutation	SNP	G	G	T	rs587675709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105958010G>T	ENST00000392523.4	+	2	320	c.199G>T	c.(199-201)Ggc>Tgc	p.G67C	C14orf80_ENST00000329886.7_Missense_Mutation_p.G28C|C14orf80_ENST00000354560.6_Missense_Mutation_p.G67C|C14orf80_ENST00000551054.1_3'UTR|C14orf80_ENST00000450383.1_5'UTR|C14orf80_ENST00000392522.3_Missense_Mutation_p.G67C|C14orf80_ENST00000334656.7_Missense_Mutation_p.G26C|C14orf80_ENST00000392527.1_Missense_Mutation_p.G26C			Q86SX3	CN080_HUMAN	chromosome 14 open reading frame 80	67										central_nervous_system(1)	1		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.239)		ACTCCCTGCGGGCAACGCCTT	0.692													G|||	4	0.000798722	0.003	0.0	5008	,	,		10467	0.0		0.0	False		,,,				2504	0.0				p.G67C		Atlas-SNP	.											.	C14orf80	19	.	0			c.G199T						PASS	.						12.0	13.0	13.0					14																	105958010		692	1587	2279	SO:0001583	missense	283643	exon2			CCTGCGGGCAACG		CCDS45180.1, CCDS45181.1, CCDS45182.1, CCDS55955.1	14q32.33	2012-09-25			ENSG00000185347	ENSG00000185347			20127	protein-coding gene	gene with protein product							Standard	NM_001134875		Approved		uc001yrn.3	Q86SX3	OTTHUMG00000170426	ENST00000392523.4:c.199G>T	14.37:g.105958010G>T	ENSP00000376308:p.Gly67Cys	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	154	77	0.5	NM_001134876	B5MDG3|E9PAQ4|Q86TT3|Q86TT4|Q86TT5|Q96B41|Q9H7H4	Missense_Mutation	SNP	ENST00000392523.4	37		.	.	.	.	.	.	.	.	.	.	G	17.21	3.331819	0.60853	.	.	ENSG00000185347	ENST00000329886;ENST00000427614;ENST00000455454;ENST00000432805;ENST00000392527;ENST00000443229;ENST00000334656;ENST00000392522;ENST00000392523;ENST00000354560;ENST00000548920	.	.	.	5.35	-5.54	0.02544	.	2.792540	0.01787	N	0.032086	T	0.22820	0.0551	L	0.40543	1.245	0.09310	N	1	B;P;B;P;B	0.50272	0.002;0.933;0.007;0.932;0.015	B;B;B;B;B	0.43445	0.002;0.394;0.002;0.42;0.009	T	0.37407	-0.9707	9	0.48119	T	0.1	-2.1135	2.1586	0.03819	0.2184:0.4083:0.1687:0.2046	.	67;67;67;26;28	Q86SX3-2;E9PAQ4;Q86SX3;B5MDG3;Q86SX3-3	.;.;CN080_HUMAN;.;.	C	28;26;26;26;26;26;26;67;67;67;67	.	ENSP00000333010:G28C	G	+	1	0	C14orf80	105029055	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.058000	0.11750	-0.676000	0.05238	0.561000	0.74099	GGC	.	.	none		0.692	C14orf80-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409090.1	NM_001134875	
HIST1H3B	8358	hgsc.bcm.edu	37	6	26031962	26031962	+	Silent	SNP	G	G	A	rs34966100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26031962G>A	ENST00000244661.2	-	1	326	c.327C>T	c.(325-327)aaC>aaT	p.N109N		NM_003537.3	NP_003528.1	P68431	H31_HUMAN	histone cluster 1, H3b	109					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(10)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	25						TGGCGCAAAGGTTTGTGTCCT	0.527													G|||	176	0.0351438	0.1203	0.013	5008	,	,		18951	0.0		0.004	False		,,,				2504	0.0041				p.N109N		Atlas-SNP	.											.	HIST1H3B	59	.	0			c.C327T						PASS	.	G		396,4010	198.4+/-222.2	12,372,1819	78.0	79.0	79.0		327	4.2	1.0	6	dbSNP_126	79	55,8545	34.3+/-88.2	0,55,4245	no	coding-synonymous	HIST1H3B	NM_003537.3		12,427,6064	AA,AG,GG		0.6395,8.9877,3.4676		109/137	26031962	451,12555	2203	4300	6503	SO:0001819	synonymous_variant	8358	exon1			GCAAAGGTTTGTG	X00090	CCDS4573.1	6p22.1	2011-01-27	2006-10-11	2003-03-14	ENSG00000124693	ENSG00000274267		"""Histones / Replication-dependent"""	4776	protein-coding gene	gene with protein product		602819	"""H3 histone family, member L"", ""histone 1, H3b"""	H3FL		6647026, 9119399, 12408966	Standard	NM_003537		Approved	H3/l	uc003nfs.1	P68431	OTTHUMG00000014415	ENST00000244661.2:c.327C>T	6.37:g.26031962G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	141	59	0.41844	NM_003537	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000244661.2	37	CCDS4573.1																																																																																			G|0.966;A|0.034	0.034	strong		0.527	HIST1H3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040077.1	NM_003537	
YTHDF1	54915	hgsc.bcm.edu	37	20	61834169	61834169	+	Missense_Mutation	SNP	G	G	A	rs34379989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61834169G>A	ENST00000370339.3	-	4	1464	c.1123C>T	c.(1123-1125)Cac>Tac	p.H375Y	YTHDF1_ENST00000370334.4_Intron|YTHDF1_ENST00000370333.4_Missense_Mutation_p.H325Y	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	375							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						TTGTAGCTGTGAGCAGCCTTC	0.537													G|||	66	0.0131789	0.0477	0.0043	5008	,	,		18939	0.0		0.0	False		,,,				2504	0.0				p.H375Y		Atlas-SNP	.											.	YTHDF1	66	.	0			c.C1123T						PASS	.	G	TYR/HIS	145,4261	98.9+/-137.6	2,141,2060	87.0	89.0	88.0		1123	4.7	1.0	20	dbSNP_126	88	0,8600		0,0,4300	yes	missense	YTHDF1	NM_017798.3	83	2,141,6360	AA,AG,GG		0.0,3.291,1.1149	possibly-damaging	375/560	61834169	145,12861	2203	4300	6503	SO:0001583	missense	54915	exon4			AGCTGTGAGCAGC	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"""YTH domain family 1"""	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.1123C>T	20.37:g.61834169G>A	ENSP00000359364:p.His375Tyr	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	148	66	0.445946	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Missense_Mutation	SNP	ENST00000370339.3	37	CCDS13511.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	G	14.56	2.572951	0.45798	0.03291	0.0	ENSG00000149658	ENST00000370339;ENST00000370333;ENST00000342761	T;T	0.23147	1.92;1.92	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.09512	0.0234	M	0.63428	1.95	0.58432	D	0.999999	P	0.39696	0.683	B	0.40565	0.333	T	0.06499	-1.0823	10	0.87932	D	0	-43.1736	18.0486	0.89341	0.0:0.0:1.0:0.0	rs34379989	375	Q9BYJ9	YTHD1_HUMAN	Y	375;325;191	ENSP00000359364:H375Y;ENSP00000359358:H325Y	ENSP00000339489:H191Y	H	-	1	0	YTHDF1	61304614	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	7.661000	0.83786	2.339000	0.79563	0.591000	0.81541	CAC	G|0.991;A|0.009	0.009	strong		0.537	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798	
CDH23	64072	hgsc.bcm.edu	37	10	73558952	73558952	+	Missense_Mutation	SNP	C	C	T	rs4747195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73558952C>T	ENST00000224721.6	+	50	7159	c.7154C>T	c.(7153-7155)cCg>cTg	p.P2385L	CDH23_ENST00000398788.3_Missense_Mutation_p.P140L|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2380	Cadherin 22. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.P2385L(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						AACGGGTCCCCGCCCCGGGCA	0.592													C|||	1644	0.328275	0.2443	0.3473	5008	,	,		19778	0.5298		0.2744	False		,,,				2504	0.2761				p.P2380L		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - Missense(1)	stomach(1)	c.C7139T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	966,3058		114,738,1160	70.0	80.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	419,419,7139	5.6	1.0	10	dbSNP_111	77	2173,6145		304,1565,2290	yes	missense,missense,missense	CDH23	NM_001171933.1,NM_001171934.1,NM_022124.5	98,98,98	418,2303,3450	TT,TC,CC		26.1241,24.006,25.4335	probably-damaging,probably-damaging,probably-damaging	140/1115,140/1080,2380/3355	73558952	3139,9203	2012	4159	6171	SO:0001583	missense	64072	exon49			GGTCCCCGCCCCG	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.7154C>T	10.37:g.73558952C>T	ENSP00000224721:p.Pro2385Leu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		749	0.34294871794871795	133	0.2703252032520325	108	0.2983425414364641	300	0.5244755244755245	208	0.27440633245382584	C	22.5	4.304758	0.81247	0.24006	0.261241	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.00792	5.69	5.55	5.55	0.83447	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.82716	2.605	0.09310	P	0.99999999999995	D;D	0.89917	1.0;1.0	D;D	0.73708	0.981;0.981	T	0.53373	-0.8448	9	0.62326	D	0.03	.	19.516	0.95165	0.0:1.0:0.0:0.0	rs4747195;rs60719007;rs4747195	2380;2380	E9PEX1;Q9H251	.;CAD23_HUMAN	L	2385;2380;2383;140	ENSP00000381768:P140L	ENSP00000224721:P2385L	P	+	2	0	CDH23	73228958	1.000000	0.71417	0.994000	0.49952	0.319000	0.28217	7.786000	0.85741	2.623000	0.88846	0.655000	0.94253	CCG	C|0.668;T|0.332	0.332	strong		0.592	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
CDC14A	8556	hgsc.bcm.edu	37	1	100933576	100933576	+	Silent	SNP	T	T	C	rs17122597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100933576T>C	ENST00000336454.3	+	10	1258	c.903T>C	c.(901-903)caT>caC	p.H301H	RP5-837M10.4_ENST00000432210.1_RNA|CDC14A_ENST00000544534.1_Silent_p.H301H|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000370124.3_Silent_p.H301H|CDC14A_ENST00000361544.6_Silent_p.H301H|CDC14A_ENST00000542213.1_Silent_p.H243H	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	301	B.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		GGTTTACACATGCTGAAATAA	0.398													C|||	302	0.0603035	0.2216	0.0086	5008	,	,		20803	0.0		0.003	False		,,,				2504	0.0				p.H301H		Atlas-SNP	.											.	CDC14A	65	.	0			c.T903C						PASS	.	C	,,	894,3512	741.8+/-411.3	94,706,1403	159.0	159.0	159.0		903,903,903	-7.4	0.3	1	dbSNP_123	159	5,8595	819.1+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	94,711,5698	CC,CT,TT		0.0581,20.2905,6.9122	,,	301/595,301/624,301/384	100933576	899,12107	2203	4300	6503	SO:0001819	synonymous_variant	8556	exon10			TACACATGCTGAA	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1718	protein-coding gene	gene with protein product		603504	"""CDC10 (cell division cycle 10, S. cerevisiae, homolog)"", ""CDC14 cell division cycle 14 homolog A (S. cerevisiae)"""			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.903T>C	1.37:g.100933576T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			T|0.931;C|0.069	0.069	strong		0.398	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	
CCDC168	643677	hgsc.bcm.edu	37	13	103385309	103385309	+	Missense_Mutation	SNP	A	A	G	rs80279368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103385309A>G	ENST00000322527.2	-	1	3850	c.3851T>C	c.(3850-3852)gTt>gCt	p.V1284A		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1284																	AAATTCCAGAACACCTTCCTC	0.443													A|||	182	0.0363419	0.1339	0.0058	5008	,	,		20458	0.0		0.001	False		,,,				2504	0.0				p.V5913A		Atlas-SNP	.											.	.	.	.	0			c.T17738C						PASS	.	A	ALA/VAL	184,1200		18,148,526	178.0	136.0	149.0		17738	-1.5	0.0	13	dbSNP_132	149	6,3176		0,6,1585	yes	missense	CCDC168	NM_001146197.1	64	18,154,2111	GG,GA,AA		0.1886,13.2948,4.1612	benign	5913/7082	103385309	190,4376	692	1591	2283	SO:0001583	missense	643677	exon4			TCCAGAACACCTT		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.3851T>C	13.37:g.103385309A>G	ENSP00000320232:p.Val1284Ala	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	261	141	0.54023	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		65	0.02976190476190476	64	0.13008130081300814	1	0.0027624309392265192	0	0.0	0	0.0	A	0.487	-0.877060	0.02550	0.132948	0.001886	ENSG00000175820	ENST00000322527	T	0.03635	3.86	2.89	-1.46	0.08800	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.28713	0.22	B	0.20184	0.028	T	0.47142	-0.9140	8	0.23302	T	0.38	.	0.4721	0.00533	0.4296:0.2212:0.1341:0.2151	.	1284	Q8NDH2	CC168_HUMAN	A	1284	ENSP00000320232:V1284A	ENSP00000320232:V1284A	V	-	2	0	CCDC168	102183310	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.200000	0.09478	-0.254000	0.09500	-0.467000	0.05162	GTT	A|0.965;G|0.035	0.035	strong		0.443	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
CYP11B2	1585	hgsc.bcm.edu	37	8	143994279	143994279	+	Silent	SNP	A	A	G	rs61757295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143994279A>G	ENST00000323110.2	-	7	1146	c.1144T>C	c.(1144-1146)Ttg>Ctg	p.L382L		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	382					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	ACTCGCTCCAAAAACAGACCC	0.597									Familial Hyperaldosteronism type I				.|||	200	0.0399361	0.0416	0.0288	5008	,	,		15944	0.0546		0.0089	False		,,,				2504	0.0624				p.L382L		Atlas-SNP	.											CYP11B2,NS,carcinoma,+2,1	CYP11B2	107	1	0			c.T1144C						scavenged	.						68.0	66.0	66.0					8																	143994279		2202	4300	6502	SO:0001819	synonymous_variant	1585	exon7	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	GCTCCAAAAACAG	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"""Cytochrome P450s"""	2592	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	124080	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"""	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.1144T>C	8.37:g.143994279A>G		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	122	16	0.131148	NM_000498	B0ZBE4|Q16726	Silent	SNP	ENST00000323110.2	37	CCDS6393.1																																																																																			A|0.988;G|0.012	0.012	strong		0.597	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		
WDR72	256764	hgsc.bcm.edu	37	15	53997415	53997415	+	Missense_Mutation	SNP	G	G	T	rs142505794		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:53997415G>T	ENST00000396328.1	-	11	1357	c.1118C>A	c.(1117-1119)gCc>gAc	p.A373D	WDR72_ENST00000557913.1_Missense_Mutation_p.A370D|WDR72_ENST00000559418.1_Missense_Mutation_p.A383D|WDR72_ENST00000360509.5_Missense_Mutation_p.A373D	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	373										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)		AGTCCAGGTGGCAGTTACTGG	0.358																																					p.A373D		Atlas-SNP	.											.	WDR72	177	.	0			c.C1118A						PASS	.	G	ASP/ALA	1,4387	2.1+/-5.4	0,1,2193	61.0	62.0	61.0		1118	4.8	1.0	15	dbSNP_134	61	0,8586		0,0,4293	no	missense	WDR72	NM_182758.2	126	0,1,6486	TT,TG,GG		0.0,0.0228,0.0077	benign	373/1103	53997415	1,12973	2194	4293	6487	SO:0001583	missense	256764	exon11			CAGGTGGCAGTTA	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.1118C>A	15.37:g.53997415G>T	ENSP00000379619:p.Ala373Asp	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	38	23	0.605263	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265633	0.40095	2.28E-4	0.0	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.52295	0.67;0.67	5.75	4.84	0.62591	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.281989	0.35262	N	0.003332	T	0.33876	0.0878	N	0.14661	0.345	0.24960	N	0.991737	B	0.21606	0.058	B	0.18561	0.022	T	0.31641	-0.9936	10	0.59425	D	0.04	.	15.9329	0.79679	0.0:0.1353:0.8647:0.0	.	373	Q3MJ13	WDR72_HUMAN	D	373	ENSP00000379619:A373D;ENSP00000353699:A373D	ENSP00000353699:A373D	A	-	2	0	WDR72	51784707	0.988000	0.35896	0.997000	0.53966	0.830000	0.47004	3.442000	0.52900	1.434000	0.47414	0.460000	0.39030	GCC	G|1.000;T|0.000	0.000	weak		0.358	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
CSRNP1	64651	hgsc.bcm.edu	37	3	39184959	39184959	+	Missense_Mutation	SNP	C	C	T	rs1274958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39184959C>T	ENST00000273153.5	-	5	1534	c.1357G>A	c.(1357-1359)Gtc>Atc	p.V453I	CSRNP1_ENST00000514182.1_Missense_Mutation_p.V453I	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	453			V -> I (in dbSNP:rs1274958). {ECO:0000269|PubMed:11526492, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		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						TCATCCAGGACGCCTGATGTG	0.577													T|||	3929	0.784545	0.795	0.7709	5008	,	,		20934	0.7669		0.7694	False		,,,				2504	0.8139				p.V453I		Atlas-SNP	.											.	CSRNP1	59	.	0			c.G1357A						PASS	.	T	ILE/VAL	3547,859	337.8+/-305.0	1433,681,89	63.0	61.0	61.0		1357	0.7	0.6	3	dbSNP_87	61	6479,2121	363.9+/-333.3	2475,1529,296	yes	missense	CSRNP1	NM_033027.3	29	3908,2210,385	TT,TC,CC		24.6628,19.4961,22.9125	benign	453/590	39184959	10026,2980	2203	4300	6503	SO:0001583	missense	64651	exon5			CCAGGACGCCTGA	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.1357G>A	3.37:g.39184959C>T	ENSP00000273153:p.Val453Ile	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_033027	Q69YY5	Missense_Mutation	SNP	ENST00000273153.5	37	CCDS2682.1	1676	0.7673992673992674	388	0.7886178861788617	273	0.7541436464088398	432	0.7552447552447552	583	0.7691292875989446	T	0.017	-1.504416	0.00992	0.805039	0.753372	ENSG00000144655	ENST00000273153;ENST00000514182;ENST00000318290	T;T	0.40476	1.03;1.03	4.52	0.7	0.18099	.	0.398778	0.23949	N	0.042971	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.33929	-0.9849	9	0.02654	T	1	-17.6546	4.3409	0.11110	0.2041:0.3105:0.0:0.4854	rs1274958;rs3211112;rs17845849;rs17858820;rs17859256;rs61356983;rs1274958	453	Q96S65	CSRN1_HUMAN	I	453;453;111	ENSP00000273153:V453I;ENSP00000422532:V453I	ENSP00000273153:V453I	V	-	1	0	CSRNP1	39159963	0.004000	0.15560	0.631000	0.29282	0.483000	0.33249	-0.140000	0.10342	0.068000	0.16574	-0.254000	0.11334	GTC	T|0.767;G|0.005	0.767	strong		0.577	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027	
LAMA4	3910	hgsc.bcm.edu	37	6	112513025	112513025	+	Silent	SNP	G	G	A	rs61742228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:112513025G>A	ENST00000230538.7	-	6	928	c.531C>T	c.(529-531)ccC>ccT	p.P177P	LAMA4_ENST00000524032.1_5'UTR|LAMA4_ENST00000389463.4_Silent_p.P177P|LAMA4_ENST00000424408.2_Silent_p.P177P|LAMA4_ENST00000522006.1_Silent_p.P177P	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	177	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)		CAATGAGTAAGGGGTTTCCAT	0.393													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		21553	0.0		0.0	False		,,,				2504	0.0				p.P177P		Atlas-SNP	.											.	LAMA4	227	.	0			c.C531T						PASS	.	G	,,	188,4218	109.5+/-147.8	8,172,2023	68.0	63.0	64.0		531,531,531	4.0	1.0	6	dbSNP_129	64	2,8598		0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	,,	8,174,6321	AA,AG,GG		0.0233,4.2669,1.4609	,,	177/1824,177/1817,177/1817	112513025	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	3910	exon6			GAGTAAGGGGTTT		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.531C>T	6.37:g.112513025G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1																																																																																			G|0.985;A|0.015	0.015	strong		0.393	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
LCE2B	26239	hgsc.bcm.edu	37	1	152659392	152659392	+	Missense_Mutation	SNP	C	C	T	rs61730791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152659392C>T	ENST00000368780.3	+	2	127	c.73C>T	c.(73-75)Cca>Tca	p.P25S	LCE2B_ENST00000417924.2_Missense_Mutation_p.P25S	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	25	Cys-rich.|Pro-rich.				epidermis development (GO:0008544)|keratinization (GO:0031424)					endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	11	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCAAAATGTCCACCTAAGTG	0.572													C|||	65	0.0129792	0.0461	0.0043	5008	,	,		15748	0.0		0.001	False		,,,				2504	0.0				p.P25S		Atlas-SNP	.											.	LCE2B	40	.	0			c.C73T						PASS	.	C	SER/PRO	146,4260	102.5+/-141.1	4,138,2061	123.0	122.0	123.0		73	1.5	0.0	1	dbSNP_129	123	1,8599		0,1,4299	yes	missense	LCE2B	NM_014357.4	74	4,139,6360	TT,TC,CC		0.0116,3.3137,1.1302	benign	25/111	152659392	147,12859	2203	4300	6503	SO:0001583	missense	26239	exon2			AAATGTCCACCTA	BI670514	CCDS1020.1	1q21	2008-02-05	2004-10-11	2004-10-15	ENSG00000159455	ENSG00000159455		"""Late cornified envelopes"""	16610	protein-coding gene	gene with protein product		612610	"""small proline rich-like (epidermal differentiation complex) 1B"""	SPRL1B		11698679, 9344646	Standard	NM_014357		Approved	LEP10, XP5	uc001fai.3	O14633	OTTHUMG00000012404	ENST00000368780.3:c.73C>T	1.37:g.152659392C>T	ENSP00000357769:p.Pro25Ser	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	240	124	0.516667	NM_014357	Q5TA80	Missense_Mutation	SNP	ENST00000368780.3	37	CCDS1020.1	24	0.01098901098901099	21	0.042682926829268296	3	0.008287292817679558	0	0.0	0	0.0	C	1.661	-0.511564	0.04200	0.033137	1.16E-4	ENSG00000159455	ENST00000417924;ENST00000368780	T;T	0.03607	3.87;3.87	2.46	1.45	0.22620	.	.	.	.	.	T	0.01940	0.0061	M	0.77820	2.39	0.09310	N	1	B	0.14012	0.009	B	0.17722	0.019	T	0.40213	-0.9575	9	0.87932	D	0	.	4.1955	0.10441	0.0:0.7428:0.0:0.2572	rs61730791	25	O14633	LCE2B_HUMAN	S	25	ENSP00000414043:P25S;ENSP00000357769:P25S	ENSP00000357769:P25S	P	+	1	0	LCE2B	150926016	0.000000	0.05858	0.001000	0.08648	0.514000	0.34195	-0.555000	0.05999	0.257000	0.21650	0.313000	0.20887	CCA	C|0.986;T|0.014	0.014	strong		0.572	LCE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034524.1	NM_014357	
MAP4	4134	hgsc.bcm.edu	37	3	47958037	47958037	+	Missense_Mutation	SNP	G	G	T	rs1060407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47958037G>T	ENST00000360240.6	-	7	1798	c.1280C>A	c.(1279-1281)tCc>tAc	p.S427Y	MAP4_ENST00000395734.3_Missense_Mutation_p.S427Y|MAP4_ENST00000383737.4_Intron|MAP4_ENST00000426837.2_Missense_Mutation_p.S444Y	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	220	0	0		WXS	Illumina HiSeq	Phase_I	235	115	0.489362	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	
PROP1	5626	hgsc.bcm.edu	37	5	177421275	177421275	+	Silent	SNP	C	C	T	rs2233784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:177421275C>T	ENST00000308304.2	-	2	482	c.174G>A	c.(172-174)ccG>ccA	p.P58P		NM_006261.4	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	58					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)			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)			GTCCTCCTTGCGGGGAGAACC	0.662													c|||	125	0.0249601	0.0908	0.0072	5008	,	,		15546	0.0		0.0	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											PROP1,NS,carcinoma,-2,1	PROP1	28	1	0			c.G174A						PASS	.	T		357,4043		13,331,1856	25.0	26.0	26.0		174	-6.3	0.0	5	dbSNP_98	26	3,8597		0,3,4297	no	coding-synonymous	PROP1	NM_006261.4		13,334,6153	TT,TC,CC		0.0349,8.1136,2.7692		58/227	177421275	360,12640	2200	4300	6500	SO:0001819	synonymous_variant	5626	exon2			TCCTTGCGGGGAG	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.174G>A	5.37:g.177421275C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	131	68	0.519084	NM_006261		Silent	SNP	ENST00000308304.2	37	CCDS4430.1																																																																																			C|0.969;T|0.031	0.031	strong		0.662	PROP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253472.1	NM_006261	
FBXW9	84261	hgsc.bcm.edu	37	19	12807066	12807066	+	Silent	SNP	G	G	C	rs6511832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12807066G>C	ENST00000380339.3	-	1	366	c.330C>G	c.(328-330)ctC>ctG	p.L110L	FBXW9_ENST00000587955.1_Silent_p.L110L|FBXW9_ENST00000393261.3_Silent_p.L110L|FBXW9_ENST00000544494.1_5'UTR			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	110	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CGAGGTCGCGGAGCGCGTGGC	0.721													C|||	748	0.149361	0.534	0.0461	5008	,	,		12393	0.0		0.0099	False		,,,				2504	0.0				p.L110L		Atlas-SNP	.											.	FBXW9	30	.	0			c.C330G						PASS	.	C		1528,2426		306,916,755	10.0	14.0	13.0		330	2.8	1.0	19	dbSNP_116	13	117,8057		1,115,3971	no	coding-synonymous	FBXW9	NM_032301.2		307,1031,4726	CC,CG,GG		1.4314,38.6444,13.5637		110/459	12807066	1645,10483	1977	4087	6064	SO:0001819	synonymous_variant	84261	exon1			GTCGCGGAGCGCG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.330C>G	19.37:g.12807066G>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_032301	B3KVP7|Q9BT89	Silent	SNP	ENST00000380339.3	37																																																																																				G|0.902;C|0.098	0.098	strong		0.721	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
PPFIA1	8500	hgsc.bcm.edu	37	11	70200516	70200516	+	Missense_Mutation	SNP	C	C	T	rs139448605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:70200516C>T	ENST00000253925.7	+	17	2488	c.2273C>T	c.(2272-2274)gCg>gTg	p.A758V	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.A758V	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	758					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)			CACAAAGGGGCGCTGCACACC	0.567													C|||	50	0.00998403	0.0378	0.0	5008	,	,		15864	0.0		0.0	False		,,,				2504	0.0				p.A758V		Atlas-SNP	.											.	PPFIA1	114	.	0			c.C2273T						PASS	.	C	VAL/ALA,VAL/ALA	116,4284	88.2+/-126.9	0,116,2084	51.0	44.0	46.0		2273,2273	4.4	0.0	11	dbSNP_134	46	2,8586	1.2+/-3.3	0,2,4292	yes	missense,missense	PPFIA1	NM_003626.2,NM_177423.1	64,64	0,118,6376	TT,TC,CC		0.0233,2.6364,0.9085	benign,benign	758/1203,758/1186	70200516	118,12870	2200	4294	6494	SO:0001583	missense	8500	exon17			AAGGGGCGCTGCA	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.2273C>T	11.37:g.70200516C>T	ENSP00000253925:p.Ala758Val	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	14|14	0.00641025641025641|0.00641025641025641	14|14	0.028455284552845527|0.028455284552845527	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	14.81|14.81	2.646317|2.646317	0.47258|0.47258	0.026364|0.026364	2.33E-4|2.33E-4	ENSG00000131626|ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000544950|ENST00000528750	T;T|.	0.28255|.	1.62;1.62|.	5.36|5.36	4.45|4.45	0.53987|0.53987	.|.	0.314716|.	0.29508|.	N|.	0.011941|.	T|T	0.36580|0.36580	0.0972|0.0972	M|M	0.62723|0.62723	1.935|1.935	0.31697|0.31697	N|N	0.64121|0.64121	B;B|.	0.23377|.	0.012;0.084|.	B;B|.	0.15870|.	0.004;0.014|.	T|T	0.59920|0.59920	-0.7363|-0.7363	10|5	0.29301|.	T|.	0.29|.	.|.	14.198|14.198	0.65684|0.65684	0.0:0.9277:0.0:0.0723|0.0:0.9277:0.0:0.0723	.|.	758;758|.	Q13136;Q13136-2|.	LIPA1_HUMAN;.|.	V|C	758;758;255|201	ENSP00000253925:A758V;ENSP00000374198:A758V|.	ENSP00000253925:A758V|.	A|R	+|+	2|1	0|0	PPFIA1|PPFIA1	69878164|69878164	0.926000|0.926000	0.31397|0.31397	0.009000|0.009000	0.14445|0.14445	0.490000|0.490000	0.33462|0.33462	2.135000|2.135000	0.42112|0.42112	1.272000|1.272000	0.44329|0.44329	0.561000|0.561000	0.74099|0.74099	GCG|CGC	C|0.992;T|0.008	0.008	strong		0.567	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626	
HTT	3064	hgsc.bcm.edu	37	4	3189547	3189547	+	Missense_Mutation	SNP	C	C	A	rs363125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:3189547C>A	ENST00000355072.5	+	39	5304	c.5159C>A	c.(5158-5160)aCt>aAt	p.T1720N		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1720			T -> N (in dbSNP:rs363125).		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)		GGGGACAGTACTTCAACGCTA	0.373													A|||	947	0.189097	0.4834	0.1225	5008	,	,		20071	0.0089		0.1083	False		,,,				2504	0.1074				p.T1720N		Atlas-SNP	.											.	HTT	221	.	0			c.C5159A						PASS	.	A	ASN/THR	1484,2210		308,868,671	119.0	111.0	113.0		5159	-11.3	0.0	4	dbSNP_79	113	960,7248		44,872,3188	yes	missense	HTT	NM_002111.6	65	352,1740,3859	AA,AC,CC		11.6959,40.1733,20.5344	benign	1720/3143	3189547	2444,9458	1847	4104	5951	SO:0001583	missense	3064	exon39			ACAGTACTTCAAC	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.5159C>A	4.37:g.3189547C>A	ENSP00000347184:p.Thr1720Asn	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	362	0.16575091575091574	234	0.47560975609756095	42	0.11602209944751381	2	0.0034965034965034965	84	0.11081794195250659	A	1.789	-0.479891	0.04383	0.401733	0.116959	ENSG00000197386	ENST00000355072	T	0.04706	3.57	5.66	-11.3	0.00108	.	0.988029	0.08277	N	0.970573	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	0.48234	-0.9053	9	0.17369	T	0.5	.	8.4339	0.32775	0.177:0.4818:0.2725:0.0687	rs363125;rs363125	1720	P42858	HD_HUMAN	N	1720	ENSP00000347184:T1720N	ENSP00000347184:T1720N	T	+	2	0	HTT	3159345	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.105000	0.03323	-2.325000	0.00638	-0.256000	0.11100	ACT	C|0.812;A|0.188	0.188	strong		0.373	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
MUC4	4585	hgsc.bcm.edu	37	3	195515448	195515448	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515448T>C	ENST00000463781.3	-	2	3462	c.3003A>G	c.(3001-3003)gtA>gtG	p.V1001V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V1001V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	425	Ser-rich.				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)		GACCTGTGGATACTGAGGAAG	0.587																																					p.V1001V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,12	MUC4	1505	12	0			c.A3003G						scavenged	.						43.0	35.0	38.0					3																	195515448		2190	4257	6447	SO:0001819	synonymous_variant	4585	exon2			TGTGGATACTGAG	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.3003A>G	3.37:g.195515448T>C		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	587	10	0.0170358	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																																																																																			.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PSKH2	85481	hgsc.bcm.edu	37	8	87076651	87076651	+	Missense_Mutation	SNP	T	T	C	rs16879427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87076651T>C	ENST00000276616.2	-	2	469	c.395A>G	c.(394-396)cAa>cGa	p.Q132R	PSKH2_ENST00000517981.1_5'UTR	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	132	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Q -> R (in dbSNP:rs16879427). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			CATGTAAACTTGATCCTCAGT	0.542													C|||	503	0.100439	0.3533	0.036	5008	,	,		15987	0.0		0.005	False		,,,				2504	0.0061				p.Q132R		Atlas-SNP	.											PSKH2,right_upper_lobe,carcinoma,-1,1	PSKH2	79	1	0			c.A395G						PASS	.	C	ARG/GLN	1304,3102	697.8+/-406.3	192,920,1091	86.0	82.0	83.0		395	2.5	0.0	8	dbSNP_123	83	19,8581	818.4+/-406.9	0,19,4281	yes	missense	PSKH2	NM_033126.1	43	192,939,5372	CC,CT,TT		0.2209,29.596,10.1722	benign	132/386	87076651	1323,11683	2203	4300	6503	SO:0001583	missense	85481	exon2			TAAACTTGATCCT	AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.395A>G	8.37:g.87076651T>C	ENSP00000276616:p.Gln132Arg	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_033126	A0AV22	Missense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	186	0.08516483516483517	172	0.34959349593495936	12	0.03314917127071823	0	0.0	2	0.002638522427440633	C	0.021	-1.427937	0.01117	0.29596	0.002209	ENSG00000147613	ENST00000276616	T	0.64803	-0.12	5.22	2.46	0.29980	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.10874	0.06	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.28586	-1.0039	8	0.07175	T	0.84	.	9.205	0.37285	0.0:0.6926:0.0:0.3074	rs16879427;rs52809304;rs16879427	132	Q96QS6	KPSH2_HUMAN	R	132	ENSP00000276616:Q132R	ENSP00000276616:Q132R	Q	-	2	0	PSKH2	87145767	0.895000	0.30542	0.003000	0.11579	0.206000	0.24218	1.883000	0.39658	-0.015000	0.14150	-0.702000	0.03669	CAA	T|0.874;C|0.126	0.126	strong		0.542	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
WDR88	126248	hgsc.bcm.edu	37	19	33666345	33666345	+	Missense_Mutation	SNP	C	C	A	rs77589178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33666345C>A	ENST00000355868.3	+	11	1362	c.1286C>A	c.(1285-1287)aCc>aAc	p.T429N	CTD-2540B15.10_ENST00000590117.1_RNA|WDR88_ENST00000361680.2_3'UTR|AC008738.2_ENST00000577275.1_RNA	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	429										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					AAGAGTGACACCTCTTCTGAA	0.478													C|||	111	0.0221645	0.0832	0.0014	5008	,	,		20731	0.0		0.0	False		,,,				2504	0.0				p.T429N		Atlas-SNP	.											.	WDR88	50	.	0			c.C1286A						PASS	.	C	ASN/THR	263,4143	150.3+/-184.3	11,241,1951	179.0	171.0	174.0		1286	-5.6	0.0	19	dbSNP_131	174	0,8600		0,0,4300	yes	missense	WDR88	NM_173479.3	65	11,241,6251	AA,AC,CC		0.0,5.9691,2.0221	benign	429/473	33666345	263,12743	2203	4300	6503	SO:0001583	missense	126248	exon11			GTGACACCTCTTC	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"""WD repeat domain containing"""	26999	protein-coding gene	gene with protein product			"""PQQ repeat and WD repeat domain containing"""	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.1286C>A	19.37:g.33666345C>A	ENSP00000348129:p.Thr429Asn	Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	224	103	0.459821	NM_173479	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	37	CCDS12429.1	46	0.021062271062271064	45	0.09146341463414634	1	0.0027624309392265192	0	0.0	0	0.0	C	4.208	0.037382	0.08148	0.059691	0.0	ENSG00000166359	ENST00000355868	T	0.56941	0.43	4.92	-5.61	0.02489	.	3.589250	0.00520	N	0.000190	T	0.01189	0.0039	N	0.22421	0.69	0.09310	N	1	B	0.13594	0.008	B	0.09377	0.004	T	0.04140	-1.0974	10	0.40728	T	0.16	.	0.5128	0.00598	0.4107:0.1392:0.196:0.2542	.	429	Q6ZMY6	WDR88_HUMAN	N	429	ENSP00000348129:T429N	ENSP00000348129:T429N	T	+	2	0	WDR88	38358185	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-1.093000	0.03362	-0.598000	0.05806	-0.314000	0.08810	ACC	C|0.975;A|0.025	0.025	strong		0.478	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
RYR1	6261	hgsc.bcm.edu	37	19	38956803	38956803	+	Silent	SNP	G	G	A	rs2228069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	89	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	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		
CROCC	9696	hgsc.bcm.edu	37	1	17264939	17264939	+	Silent	SNP	T	T	C	rs4558023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17264939T>C	ENST00000375541.5	+	11	1404	c.1335T>C	c.(1333-1335)gaT>gaC	p.D445D	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin									p.D445D(1)		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)		AGACAGAGGATGGAGAGGGGC	0.632																																					p.D445D		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	1	Substitution - coding silent(1)	prostate(1)	c.T1335C						scavenged	.						19.0	16.0	17.0					1																	17264939		2178	4273	6451	SO:0001819	synonymous_variant	9696	exon11			AGAGGATGGAGAG	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.1335T>C	1.37:g.17264939T>C		Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	428	142	0.331776	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			T|0.699;C|0.301	0.301	strong		0.632	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
INCENP	3619	hgsc.bcm.edu	37	11	61908440	61908440	+	Missense_Mutation	SNP	T	T	C	rs2277283	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	201	0	0		WXS	Illumina HiSeq	Phase_I	201	95	0.472637	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	
LGALS3	3958	hgsc.bcm.edu	37	14	55604935	55604935	+	Missense_Mutation	SNP	C	C	A	rs4644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55604935C>A	ENST00000254301.9	+	3	452	c.191C>A	c.(190-192)cCt>cAt	p.P64H	LGALS3_ENST00000554715.1_Missense_Mutation_p.P64H|LGALS3_ENST00000553755.1_3'UTR	NM_002306.3	NP_002297.2	P17931	LEG3_HUMAN	lectin, galactoside-binding, soluble, 3	64	8 X 9 AA tandem repeats of Y-P-G-X(3)-P- G-A.		P -> H (in dbSNP:rs4644). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2022338, ECO:0000269|PubMed:2261464}.		eosinophil chemotaxis (GO:0048245)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|mononuclear cell migration (GO:0071674)|mRNA processing (GO:0006397)|negative regulation of endocytosis (GO:0045806)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of immunological synapse formation (GO:2000521)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell receptor signaling pathway (GO:0050860)|neutrophil chemotaxis (GO:0030593)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of mononuclear cell migration (GO:0071677)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of T cell apoptotic process (GO:0070232)|regulation of T cell proliferation (GO:0042129)|RNA splicing (GO:0008380)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)	carbohydrate binding (GO:0030246)|chemoattractant activity (GO:0042056)|IgE binding (GO:0019863)|laminin binding (GO:0043236)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|prostate(1)	3						GGCGCCTACCCTGGAGCACCT	0.692													C|||	1469	0.293331	0.2534	0.2781	5008	,	,		15154	0.1885		0.4076	False		,,,				2504	0.3487				p.P64H		Atlas-SNP	.											.	LGALS3	10	.	0			c.C191A	GRCh37	CM086193	LGALS3	M	rs4644	PASS	.	C	HIS/PRO,HIS/PRO	1015,2623		148,719,952	21.0	23.0	23.0		191,191	5.7	0.2	14	dbSNP_52	23	3240,4898		699,1842,1528	yes	missense,missense	LGALS3	NM_001177388.1,NM_002306.3	77,77	847,2561,2480	AA,AC,CC		39.8132,27.8999,36.1328	probably-damaging,probably-damaging	64/201,64/251	55604935	4255,7521	1819	4069	5888	SO:0001583	missense	3958	exon3			CCTACCCTGGAGC	M64303	CCDS41956.1	14q22.3	2014-03-19	2007-02-01		ENSG00000131981	ENSG00000131981		"""Lectins, galactoside-binding"", ""Endogenous ligands"""	6563	protein-coding gene	gene with protein product	"""galectin 3"""	153619		LGALS2		2009535, 8063692	Standard	NR_003225		Approved	MAC-2, GALIG	uc001xbr.3	P17931	OTTHUMG00000171030	ENST00000254301.9:c.191C>A	14.37:g.55604935C>A	ENSP00000254301:p.Pro64His	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	153	79	0.51634	NM_002306	B2RC38|Q16005|Q6IBA7|Q96J47	Missense_Mutation	SNP	ENST00000254301.9	37	CCDS41956.1	638	0.29212454212454214	124	0.25203252032520324	100	0.27624309392265195	101	0.17657342657342656	313	0.4129287598944591	C	12.18	1.861623	0.32884	0.278999	0.398132	ENSG00000131981	ENST00000553493;ENST00000254301;ENST00000554715	T;T;T	0.78364	-1.17;3.08;2.35	5.65	5.65	0.86999	.	0.113638	0.64402	D	0.000012	T	0.00012	0.0000	M	0.76574	2.34	0.19575	P	0.9999653885	D	0.89917	1.0	D	0.85130	0.997	T	0.00847	-1.1542	9	0.62326	D	0.03	-0.8773	16.6435	0.85138	0.0:1.0:0.0:0.0	rs4644;rs2075599;rs3181581;rs17253709;rs17854838;rs61570076;rs4644	64	P17931	LEG3_HUMAN	H	64	ENSP00000451526:P64H;ENSP00000254301:P64H;ENSP00000451381:P64H	ENSP00000254301:P64H	P	+	2	0	LGALS3	54674688	0.995000	0.38212	0.176000	0.23000	0.086000	0.17979	4.212000	0.58514	2.662000	0.90505	0.655000	0.94253	CCT	C|0.700;A|0.300	0.300	strong		0.692	LGALS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411309.1	NM_002306	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418276	105418276	+	Missense_Mutation	SNP	G	G	A	rs35374867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105418276G>A	ENST00000333244.5	-	7	3631	c.3512C>T	c.(3511-3513)cCa>cTa	p.P1171L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1171						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCCGAACGATGGCATCTTGAA	0.617													.|||	175	0.0349441	0.1286	0.0058	5008	,	,		18260	0.0		0.001	False		,,,				2504	0.0				p.P1171L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C3512T						PASS	.	G	LEU/PRO	399,3475		46,307,1584	189.0	192.0	191.0		3512	4.4	1.0	14	dbSNP_126	191	5,8237		0,5,4116	no	missense	AHNAK2	NM_138420.2	98	46,312,5700	AA,AG,GG		0.0607,10.2994,3.3344	benign	1171/5796	105418276	404,11712	1937	4121	6058	SO:0001583	missense	113146	exon7			AACGATGGCATCT	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.3512C>T	14.37:g.105418276G>A	ENSP00000353114:p.Pro1171Leu	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	303	140	0.462046	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	60	0.027472527472527472	57	0.11585365853658537	3	0.008287292817679558	0	0.0	0	0.0	g	19.11	3.763478	0.69763	0.102994	6.07E-4	ENSG00000185567	ENST00000333244	T	0.05717	3.4	4.4	4.4	0.53042	.	.	.	.	.	T	0.00552	0.0018	H	0.95712	3.71	0.49483	D	0.999799	D	0.89917	1.0	D	0.91635	0.999	T	0.06826	-1.0805	9	0.72032	D	0.01	-13.4451	16.6046	0.84825	0.0:0.0:1.0:0.0	.	1171	Q8IVF2	AHNK2_HUMAN	L	1171	ENSP00000353114:P1171L	ENSP00000353114:P1171L	P	-	2	0	AHNAK2	104489321	1.000000	0.71417	0.967000	0.41034	0.114000	0.19823	5.979000	0.70508	1.998000	0.58463	0.491000	0.48974	CCA	G|0.978;A|0.022	0.022	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
GAREM	64762	hgsc.bcm.edu	37	18	29972964	29972964	+	Silent	SNP	A	A	G	rs3786308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:29972964A>G	ENST00000269209.6	-	2	159	c.156T>C	c.(154-156)taT>taC	p.Y52Y	GAREM_ENST00000399218.4_Silent_p.Y52Y			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	52	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										GAATCAGCAGATAGTCATTTT	0.443													G|||	771	0.153954	0.23	0.0937	5008	,	,		15768	0.1657		0.1074	False		,,,				2504	0.1299				p.Y52Y		Atlas-SNP	.											.	.	.	.	0			c.T156C						PASS	.	G	,	903,3503	740.8+/-411.2	107,689,1407	139.0	117.0	125.0		156,156	3.2	1.0	18	dbSNP_107	125	806,7794	782.6+/-407.6	44,718,3538	no	coding-synonymous,coding-synonymous	FAM59A	NM_001242409.1,NM_022751.2	,	151,1407,4945	GG,GA,AA		9.3721,20.4948,13.1401	,	52/877,52/876	29972964	1709,11297	2203	4300	6503	SO:0001819	synonymous_variant	64762	exon2			CAGCAGATAGTCA	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"""Grb2-associated and regulator of Erk/MAPK"""		"""chromosome 18 open reading frame 11"", ""family with sequence similarity 59, member A"""	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.156T>C	18.37:g.29972964A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Silent	SNP	ENST00000269209.6	37	CCDS56057.1																																																																																			A|0.855;G|0.145	0.145	strong		0.443	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751	
MLXIPL	51085	hgsc.bcm.edu	37	7	73020328	73020328	+	Missense_Mutation	SNP	G	G	T	rs34922362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73020328G>T	ENST00000313375.3	-	6	779	c.732C>A	c.(730-732)gaC>gaA	p.D244E	MLXIPL_ENST00000434326.1_Intron|MLXIPL_ENST00000414749.2_Missense_Mutation_p.D244E|MLXIPL_ENST00000395189.1_Intron|MLXIPL_ENST00000354613.1_Missense_Mutation_p.D244E|MLXIPL_ENST00000429400.2_Missense_Mutation_p.D244E	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	244			D -> E (in dbSNP:rs34922362).		anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				AGCAATTGAGGTCCAGGAGCT	0.637													G|||	110	0.0219649	0.0825	0.0014	5008	,	,		17810	0.0		0.0	False		,,,				2504	0.0				p.D244E		Atlas-SNP	.											.	MLXIPL	54	.	0			c.C732A						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	239,4165		6,227,1969	33.0	32.0	32.0		732,732,732,732	1.8	1.0	7	dbSNP_126	32	0,8594		0,0,4297	yes	missense,missense,missense,missense	MLXIPL	NM_032951.2,NM_032952.2,NM_032953.2,NM_032954.2	45,45,45,45	6,227,6266	TT,TG,GG		0.0,5.4269,1.8387	benign,benign,benign,benign	244/853,244/834,244/851,244/832	73020328	239,12759	2202	4297	6499	SO:0001583	missense	51085	exon6			ATTGAGGTCCAGG	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"""carbohydrate response element binding protein"""	605678	"""Williams Beuren syndrome chromosome region 14"""	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.732C>A	7.37:g.73020328G>T	ENSP00000320886:p.Asp244Glu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Missense_Mutation	SNP	ENST00000313375.3	37	CCDS5553.1	47	0.02152014652014652	46	0.09349593495934959	1	0.0027624309392265192	0	0.0	0	0.0	G	13.57	2.277764	0.40294	0.054269	0.0	ENSG00000009950	ENST00000414749;ENST00000429400;ENST00000313375;ENST00000354613;ENST00000456640	T;T;T;T;T	0.59364	1.81;1.85;1.82;1.83;0.27	3.68	1.79	0.24919	.	0.068000	0.56097	D	0.000024	T	0.03305	0.0096	L	0.59436	1.845	0.80722	D	1	P;D;D;D	0.54207	0.941;0.965;0.965;0.965	B;P;P;P	0.47015	0.333;0.534;0.534;0.534	T	0.01432	-1.1356	10	0.87932	D	0	-11.5469	5.3046	0.15797	0.2859:0.0:0.7141:0.0	rs34922362	244;244;244;244	Q9NP71;Q9NP71-2;Q9NP71-3;Q9NP71-4	MLXPL_HUMAN;.;.;.	E	244;244;244;244;206	ENSP00000412330:D244E;ENSP00000406296:D244E;ENSP00000320886:D244E;ENSP00000346629:D244E;ENSP00000402615:D206E	ENSP00000320886:D244E	D	-	3	2	MLXIPL	72658264	1.000000	0.71417	0.986000	0.45419	0.877000	0.50540	2.652000	0.46682	0.221000	0.20879	0.313000	0.20887	GAC	G|0.978;T|0.022	0.022	strong		0.637	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951	
CTRC	11330	hgsc.bcm.edu	37	1	15767036	15767036	+	Silent	SNP	C	C	A	rs497078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:15767036C>A	ENST00000375949.4	+	3	206	c.180C>A	c.(178-180)ggC>ggA	p.G60G	CTRC_ENST00000375943.2_Intron|CTRC_ENST00000483406.1_3'UTR	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|||	90	0.0179712	0.0651	0.0058	5008	,	,		14713	0.0		0.0	False		,,,				2504	0.0				p.G60G		Atlas-SNP	.											.	CTRC	28	.	0			c.C180A						PASS	.						144.0	95.0	111.0					1																	15767036		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>A	1.37:g.15767036C>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	108	40	0.37037	NM_007272	A8K082|O00765|Q9NUH5	Silent	SNP	ENST00000375949.4	37	CCDS156.1																																																																																			A|0.000;C|0.887;T|0.113	0.000	strong		0.627	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272	
SNX7	51375	hgsc.bcm.edu	37	1	99150590	99150590	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:99150590A>G	ENST00000306121.3	+	2	339	c.330A>G	c.(328-330)atA>atG	p.I110M	SNX7_ENST00000370189.5_Missense_Mutation_p.I46M|SNX7_ENST00000529992.1_Missense_Mutation_p.I110M	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	46	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		TTACTACAATAGAAACTTTCA	0.318																																					p.I110M		Atlas-SNP	.											.	SNX7	76	.	0			c.A330G						PASS	.						80.0	73.0	75.0					1																	99150590		2203	4300	6503	SO:0001583	missense	51375	exon2			TACAATAGAAACT	AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"""Sorting nexins"""	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.330A>G	1.37:g.99150590A>G	ENSP00000304429:p.Ile110Met	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	184	95	0.516304	NM_015976	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Missense_Mutation	SNP	ENST00000306121.3	37	CCDS755.2	.	.	.	.	.	.	.	.	.	.	A	5.637	0.302207	0.10678	.	.	ENSG00000162627	ENST00000370189;ENST00000529992;ENST00000306121;ENST00000454199	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.39	0.163	0.14986	.	0.106693	0.64402	D	0.000006	T	0.09335	0.0230	N	0.02213	-0.635	0.48135	D	0.999592	P;B;B	0.44260	0.83;0.0;0.001	P;B;B	0.58210	0.835;0.007;0.019	T	0.19712	-1.0297	10	0.02654	T	1	-24.3064	4.5265	0.11983	0.2744:0.137:0.0:0.5886	.	110;110;46	E9PNL2;Q9UNH6-3;Q9UNH6-2	.;.;.	M	46;110;110;46	ENSP00000359208:I46M;ENSP00000434731:I110M;ENSP00000304429:I110M;ENSP00000388266:I46M	ENSP00000304429:I110M	I	+	3	3	SNX7	98923178	0.994000	0.37717	0.996000	0.52242	0.469000	0.32828	0.198000	0.17217	-0.237000	0.09739	-0.451000	0.05528	ATA	.	.	none		0.318	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2		
TAS1R2	80834	hgsc.bcm.edu	37	1	19166100	19166100	+	Missense_Mutation	SNP	C	C	T	rs9988418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19166100C>T	ENST00000375371.3	-	6	2534	c.2513G>A	c.(2512-2514)aGg>aAg	p.R838K		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	838			R -> K (in dbSNP:rs9988418).		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)	GCACTAGTCCCTCCTCATGGT	0.612													c|||	288	0.057508	0.1944	0.0303	5008	,	,		15986	0.001		0.003	False		,,,				2504	0.0061				p.R838K		Atlas-SNP	.											.	TAS1R2	134	.	0			c.G2513A						PASS	.		LYS/ARG	613,3793	264.1+/-265.8	43,527,1633	64.0	51.0	55.0		2513	-5.4	0.0	1	dbSNP_119	55	60,8540	35.9+/-90.5	1,58,4241	yes	missense	TAS1R2	NM_152232.2	26	44,585,5874	TT,TC,CC		0.6977,13.9128,5.1745	benign	838/840	19166100	673,12333	2203	4300	6503	SO:0001583	missense	80834	exon6			TAGTCCCTCCTCA		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.2513G>A	1.37:g.19166100C>T	ENSP00000364520:p.Arg838Lys	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	186	83	0.446237	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	91	0.041666666666666664	71	0.1443089430894309	16	0.04419889502762431	1	0.0017482517482517483	3	0.00395778364116095	C	0.013	-1.638637	0.00799	0.139128	0.006977	ENSG00000179002	ENST00000375371	D	0.87650	-2.28	5.19	-5.36	0.02689	.	0.573210	0.15415	N	0.263527	T	0.00608	0.0020	N	0.01576	-0.805	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.34279	-0.9835	9	0.02654	T	1	.	6.9586	0.24585	0.135:0.5063:0.0:0.3587	rs9988418;rs52814741;rs9988418	838	Q8TE23	TS1R2_HUMAN	K	838	ENSP00000364520:R838K	ENSP00000364520:R838K	R	-	2	0	TAS1R2	19038687	0.002000	0.14202	0.003000	0.11579	0.095000	0.18619	-0.049000	0.11924	-1.382000	0.02109	-0.364000	0.07487	AGG	C|0.950;T|0.050	0.050	strong		0.612	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
FH	2271	hgsc.bcm.edu	37	1	241663825	241663825	+	Silent	SNP	G	G	A	rs2070080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241663825G>A	ENST00000366560.3	-	9	1340	c.1302C>T	c.(1300-1302)tgC>tgT	p.C434C		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	434					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		TTCCCACCACGCAGTTTTCTG	0.438			"""Mis, N, F"""			"""lieomyomatosis, renal"""			Hereditary Leiomyomatosis and Renal Cell Cancer				G|||	183	0.0365415	0.1346	0.0072	5008	,	,		15620	0.0		0.0	False		,,,				2504	0.0				p.C434C	Melanoma(148;1573 2486 7381 46575)	Atlas-SNP	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"""E, M"""	FH,NS,carcinoma,0,1	FH	64	1	0			c.C1302T						PASS	.	G		428,3978	207.2+/-228.6	19,390,1794	135.0	129.0	131.0		1302	-10.7	0.7	1	dbSNP_96	131	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous	FH	NM_000143.3		19,395,6089	AA,AG,GG		0.0581,9.714,3.3292		434/511	241663825	433,12573	2203	4300	6503	SO:0001819	synonymous_variant	2271	exon9	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	CACCACGCAGTTT	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.1302C>T	1.37:g.241663825G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	142	68	0.478873	NM_000143	B1ANK7	Silent	SNP	ENST00000366560.3	37	CCDS1617.1																																																																																			G|0.972;A|0.028	0.028	strong		0.438	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143	
RFX8	731220	hgsc.bcm.edu	37	2	102031324	102031324	+	Missense_Mutation	SNP	T	T	G	rs6753088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102031324T>G	ENST00000376826.2	-	10	891	c.892A>C	c.(892-894)Atg>Ctg	p.M298L	RFX8_ENST00000428343.1_Missense_Mutation_p.M185L			Q6ZV50	RFX8_HUMAN	RFX family member 8, lacking RFX DNA binding domain	298					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|kidney(1)|stomach(1)	3						ACCTTAGCCATGTTGGAAAGG	0.413													t|||	64	0.0127796	0.0454	0.0043	5008	,	,		21079	0.0		0.001	False		,,,				2504	0.0				p.M185L		Atlas-SNP	.											.	RFX8	16	.	0			c.A553C						PASS	.	T	LEU/MET	61,1323		2,57,633	211.0	163.0	178.0		553	5.1	1.0	2	dbSNP_116	178	3,3179		0,3,1588	yes	missense	RFX8	NM_001145664.1	15	2,60,2221	GG,GT,TT		0.0943,4.4075,1.4017	benign	185/474	102031324	64,4502	692	1591	2283	SO:0001583	missense	731220	exon7			TAGCCATGTTGGA	AK124976	CCDS46376.1	2q11.2	2012-11-15	2012-11-15		ENSG00000196460	ENSG00000196460			37253	protein-coding gene	gene with protein product			"""regulatory factor X, 8"", ""RFX gene family member 8, lacking RFX DNA binding domain"""				Standard	NM_001145664		Approved	FLJ42986	uc010yvx.1	Q6ZV50	OTTHUMG00000130693	ENST00000376826.2:c.892A>C	2.37:g.102031324T>G	ENSP00000366022:p.Met298Leu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001145664	B4DQ32	Missense_Mutation	SNP	ENST00000376826.2	37		23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	T	10.11	1.261043	0.23051	0.044075	9.43E-4	ENSG00000196460	ENST00000376826;ENST00000428343	T;T	0.68765	-0.35;1.71	5.08	5.08	0.68730	.	.	.	.	.	T	0.32376	0.0827	N	0.24115	0.695	0.28290	N	0.923599	P	0.51147	0.942	D	0.67231	0.95	T	0.46652	-0.9176	9	0.02654	T	1	.	11.2069	0.48775	0.0:0.0:0.0:1.0	rs6753088;rs6753088	185	Q6ZV50-3	.	L	298;185	ENSP00000366022:M298L;ENSP00000401536:M185L	ENSP00000366022:M298L	M	-	1	0	RFX8	101397756	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.845000	0.55880	2.153000	0.67306	0.454000	0.30748	ATG	T|0.991;G|0.009	0.009	strong		0.413	RFX8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145664	
COG5	10466	hgsc.bcm.edu	37	7	106938740	106938740	+	Missense_Mutation	SNP	C	C	T	rs35258567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:106938740C>T	ENST00000347053.3	-	12	1303	c.1253G>A	c.(1252-1254)cGt>cAt	p.R418H	COG5_ENST00000297135.3_Missense_Mutation_p.R418H|COG5_ENST00000393603.2_Missense_Mutation_p.R418H	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	418					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						ATTATAAAGACGTAATAATTT	0.343													C|||	7	0.00139776	0.0053	0.0	5008	,	,		12763	0.0		0.0	False		,,,				2504	0.0				p.R418H		Atlas-SNP	.											COG5,colon,carcinoma,-1,1	COG5	78	1	0			c.G1253A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	15,4391	22.3+/-47.3	0,15,2188	89.0	84.0	86.0		1253,1253,1253	4.8	1.0	7	dbSNP_126	86	0,8600		0,0,4300	yes	missense,missense,missense	COG5	NM_001161520.1,NM_006348.3,NM_181733.2	29,29,29	0,15,6488	TT,TC,CC		0.0,0.3404,0.1153	probably-damaging,probably-damaging,probably-damaging	418/824,418/861,418/840	106938740	15,12991	2203	4300	6503	SO:0001583	missense	10466	exon12			TAAAGACGTAATA	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.1253G>A	7.37:g.106938740C>T	ENSP00000334703:p.Arg418His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	14.56	2.571964	0.45798	0.003404	0.0	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.71934	-0.61;-0.61;-0.61	5.68	4.8	0.61643	.	0.055380	0.64402	D	0.000001	T	0.67173	0.2865	M	0.76170	2.325	0.49687	D	0.999819	B;P	0.41366	0.203;0.747	B;B	0.31495	0.026;0.131	T	0.72191	-0.4365	10	0.56958	D	0.05	-11.5895	14.608	0.68495	0.0:0.9302:0.0:0.0698	rs35258567	418;418	Q9UP83;Q9UP83-2	COG5_HUMAN;.	H	418	ENSP00000334703:R418H;ENSP00000297135:R418H;ENSP00000377228:R418H	ENSP00000297135:R418H	R	-	2	0	COG5	106725976	1.000000	0.71417	1.000000	0.80357	0.471000	0.32888	4.194000	0.58393	1.417000	0.47077	-0.142000	0.14014	CGT	C|0.999;T|0.001	0.001	strong		0.343	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
POT1	25913	hgsc.bcm.edu	37	7	124464037	124464037	+	Silent	SNP	T	T	G	rs17147565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:124464037T>G	ENST00000357628.3	-	19	2482	c.1884A>C	c.(1882-1884)acA>acC	p.T628T	POT1_ENST00000393329.1_Silent_p.T497T	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	628					DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47						CTTCTGCAACTGTGGTGTCAA	0.363													T|||	144	0.028754	0.1044	0.0086	5008	,	,		18834	0.0		0.0	False		,,,				2504	0.0				p.T628T	Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)	Atlas-SNP	.											POT1_ENST00000357628,NS,carcinoma,-2,2	POT1	186	2	0			c.A1884C						PASS	.	T	,	448,3956	212.5+/-232.4	28,392,1782	192.0	166.0	175.0		1491,1884	-0.8	0.9	7	dbSNP_123	175	2,8592	2.2+/-6.3	0,2,4295	no	coding-synonymous,coding-synonymous	POT1	NM_001042594.1,NM_015450.2	,	28,394,6077	GG,GT,TT		0.0233,10.1726,3.4621	,	497/504,628/635	124464037	450,12548	2202	4297	6499	SO:0001819	synonymous_variant	25913	exon19			TGCAACTGTGGTG	AK022580	CCDS5793.1	7q31.33	2013-01-21	2013-01-21		ENSG00000128513	ENSG00000128513			17284	protein-coding gene	gene with protein product		606478	"""protection of telomeres 1 homolog (S. pombe)"""			11349150, 12391173	Standard	NR_003102		Approved	hPot1, DKFZp586D211	uc003vlm.3	Q9NUX5	OTTHUMG00000157194	ENST00000357628.3:c.1884A>C	7.37:g.124464037T>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	194	102	0.525773	NM_015450	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Silent	SNP	ENST00000357628.3	37	CCDS5793.1	52	0.023809523809523808	49	0.09959349593495935	3	0.008287292817679558	0	0.0	0	0.0	T	9.568	1.120153	0.20877	0.101726	2.33E-4	ENSG00000128513	ENST00000436534	.	.	.	5.95	-0.844	0.10741	.	.	.	.	.	T	0.01940	0.0061	.	.	.	0.58432	D	0.999991	.	.	.	.	.	.	T	0.02917	-1.1094	4	.	.	.	0.0241	5.3043	0.15795	0.1235:0.3184:0.0:0.5581	rs17147565;rs17147565	.	.	.	R	127	.	.	S	-	1	0	POT1	124251273	0.779000	0.28652	0.918000	0.36340	0.990000	0.78478	0.164000	0.16542	-0.092000	0.12417	0.533000	0.62120	AGT	T|0.970;G|0.030	0.030	strong		0.363	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1		
TGM3	7053	hgsc.bcm.edu	37	20	2291722	2291722	+	Missense_Mutation	SNP	A	A	C	rs6048066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2291722A>C	ENST00000381458.5	+	4	550	c.487A>C	c.(487-489)Atc>Ctc	p.I163L		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	163			I -> L (in dbSNP:rs6048066). {ECO:0000269|Ref.3}.		cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	TGCCGGCATCATCTTTGTGGG	0.458													A|||	605	0.120807	0.4304	0.0519	5008	,	,		21488	0.0		0.0	False		,,,				2504	0.0				p.I163L		Atlas-SNP	.											.	TGM3	105	.	0			c.A487C						PASS	.	A	LEU/ILE	1503,2903	479.4+/-358.5	255,993,955	158.0	148.0	151.0		487	5.7	0.5	20	dbSNP_114	151	11,8589	7.1+/-27.0	0,11,4289	yes	missense	TGM3	NM_003245.3	5	255,1004,5244	CC,CA,AA		0.1279,34.1126,11.6408	possibly-damaging	163/694	2291722	1514,11492	2203	4300	6503	SO:0001583	missense	7053	exon4			GGCATCATCTTTG	L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"""Transglutaminases"""	11779	protein-coding gene	gene with protein product	"""E polypeptide, protein-glutamine-gamma-glutamyltransferase"""	600238	"""transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.487A>C	20.37:g.2291722A>C	ENSP00000370867:p.Ile163Leu	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	169	93	0.550296	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	37	CCDS33435.1	224	0.10256410256410256	203	0.41260162601626016	19	0.052486187845303865	0	0.0	2	0.002638522427440633	A	18.58	3.653803	0.67472	0.341126	0.001279	ENSG00000125780	ENST00000381458;ENST00000420960	D	0.85171	-1.95	5.71	5.71	0.89125	.	0.243134	0.42821	D	0.000652	T	0.00012	0.0000	M	0.81179	2.53	0.20403	P	0.9999028236	P	0.48407	0.91	D	0.80764	0.994	T	0.00000	-1.2810	9	0.72032	D	0.01	.	13.9352	0.64021	1.0:0.0:0.0:0.0	rs6048066;rs7272340;rs52800893;rs6048066	163	Q08188	TGM3_HUMAN	L	163	ENSP00000370867:I163L	ENSP00000370867:I163L	I	+	1	0	TGM3	2239722	0.997000	0.39634	0.532000	0.27989	0.430000	0.31655	3.089000	0.50183	2.184000	0.69523	0.454000	0.30748	ATC	A|0.871;C|0.129	0.129	strong		0.458	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245	
PALLD	23022	hgsc.bcm.edu	37	4	169606649	169606649	+	Missense_Mutation	SNP	C	C	A	rs62333891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169606649C>A	ENST00000505667.1	+	6	1447	c.1274C>A	c.(1273-1275)aCt>aAt	p.T425N	RNU6-1336P_ENST00000383886.1_RNA|PALLD_ENST00000335742.7_Missense_Mutation_p.T43N|PALLD_ENST00000261509.6_Missense_Mutation_p.T425N|PALLD_ENST00000333488.4_Missense_Mutation_p.T302N|PALLD_ENST00000512127.1_Missense_Mutation_p.T43N			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	425					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)		CACAGTCCAACTTCATATCTC	0.403									Pancreatic Cancer, Familial Clustering of				C|||	646	0.128994	0.208	0.196	5008	,	,		19036	0.0804		0.0785	False		,,,				2504	0.0767				p.T425N	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C1274A						PASS	.	C	ASN/THR,ASN/THR,ASN/THR	807,3599	322.6+/-297.7	79,649,1475	219.0	213.0	215.0		1274,128,1274	5.8	1.0	4	dbSNP_129	215	642,7958	165.4+/-217.5	15,612,3673	yes	missense,missense,missense	PALLD	NM_001166108.1,NM_001166109.1,NM_016081.3	65,65,65	94,1261,5148	AA,AC,CC		7.4651,18.3159,11.141	probably-damaging,probably-damaging,probably-damaging	425/1124,43/778,425/1107	169606649	1449,11557	2203	4300	6503	SO:0001583	missense	23022	exon6	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GTCCAACTTCATA	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.1274C>A	4.37:g.169606649C>A	ENSP00000425556:p.Thr425Asn	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	124	52	0.419355	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	262	0.11996336996336997	78	0.15853658536585366	69	0.19060773480662985	46	0.08041958041958042	69	0.09102902374670185	C	18.88	3.716838	0.68844	0.183159	0.074651	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000508898;ENST00000333488;ENST00000504519;ENST00000512127;ENST00000513245;ENST00000503457	T;T;T;T;T;T;T;D	0.91295	-0.21;-0.27;0.06;-0.25;-0.1;-1.42;-0.2;-2.82	5.77	5.77	0.91146	.	0.000000	0.32901	U	0.005513	T	0.02494	0.0076	M	0.73598	2.24	0.28329	P	0.9218524	D;D;D	0.76494	0.998;0.997;0.999	P;P;D	0.64410	0.852;0.879;0.925	T	0.12268	-1.0554	9	0.62326	D	0.03	.	19.9947	0.97381	0.0:1.0:0.0:0.0	rs62333891	425;43;425	B7ZMM5;B3KTG2;B2RTX2	.;.;.	N	425;43;425;404;302;43;43;43;43	ENSP00000261509:T425N;ENSP00000336735:T43N;ENSP00000425556:T425N;ENSP00000423063:T404N;ENSP00000328945:T302N;ENSP00000424121:T43N;ENSP00000426947:T43N;ENSP00000424288:T43N	ENSP00000261509:T425N	T	+	2	0	PALLD	169843224	1.000000	0.71417	0.984000	0.44739	0.788000	0.44548	3.600000	0.54052	2.736000	0.93811	0.305000	0.20034	ACT	C|0.887;A|0.113	0.113	strong		0.403	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
CMYA5	202333	hgsc.bcm.edu	37	5	79031372	79031372	+	Missense_Mutation	SNP	G	G	C	rs6859595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79031372G>C	ENST00000446378.2	+	2	6815	c.6784G>C	c.(6784-6786)Gtt>Ctt	p.V2262L		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2262			V -> L (in dbSNP:rs6859595). {ECO:0000269|PubMed:15489334}.		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)		CGGTCAAAACGTTAAAGAAAA	0.343													G|||	1359	0.271366	0.5749	0.0821	5008	,	,		20192	0.3621		0.0815	False		,,,				2504	0.0971				p.V2262L		Atlas-SNP	.											.	CMYA5	643	.	0			c.G6784C						PASS	.	G	LEU/VAL	1758,1834		439,880,477	68.0	71.0	70.0		6784	-1.3	0.9	5	dbSNP_116	70	697,7435		40,617,3409	yes	missense	CMYA5	NM_153610.3	32	479,1497,3886	CC,CG,GG		8.5711,48.9421,20.94	benign	2262/4070	79031372	2455,9269	1796	4066	5862	SO:0001583	missense	202333	exon2			CAAAACGTTAAAG	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.6784G>C	5.37:g.79031372G>C	ENSP00000394770:p.Val2262Leu	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	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	620	0.2838827838827839	299	0.6077235772357723	30	0.08287292817679558	232	0.40559440559440557	59	0.07783641160949868	G	0.005	-2.236224	0.00277	0.489421	0.085711	ENSG00000164309	ENST00000446378	T	0.15017	2.46	5.74	-1.29	0.09288	.	0.951459	0.08743	N	0.900308	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47032	-0.9148	9	0.02654	T	1	.	1.4302	0.02332	0.1568:0.2929:0.3491:0.2012	rs6859595;rs17846621;rs17859711;rs57126049;rs6859595	2262	Q8N3K9	CMYA5_HUMAN	L	2262	ENSP00000394770:V2262L	ENSP00000394770:V2262L	V	+	1	0	CMYA5	79067128	0.002000	0.14202	0.943000	0.38184	0.004000	0.04260	-0.194000	0.09559	0.147000	0.19030	-1.149000	0.01842	GTT	G|0.737;C|0.263	0.263	strong		0.343	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
PRAMEF4	400735	hgsc.bcm.edu	37	1	12943200	12943200	+	Missense_Mutation	SNP	A	A	G	rs3121079		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12943200A>G	ENST00000235349.5	-	2	86	c.16T>C	c.(16-18)Tgg>Cgg	p.W6R		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	6					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)		GGTGGAGTCCAGATGCTCATC	0.557																																					p.W6R		Atlas-SNP	.											.	PRAMEF4	62	.	0			c.T16C						PASS	.						125.0	135.0	132.0					1																	12943200		2179	4285	6464	SO:0001583	missense	400735	exon2			GAGTCCAGATGCT		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.16T>C	1.37:g.12943200A>G	ENSP00000235349:p.Trp6Arg	Somatic	320	1	0.003125		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	.	.	.	.	.	.	.	.	.	.	N	0.003	-2.577187	0.00131	.	.	ENSG00000243073	ENST00000235349	T	0.04406	3.63	1.48	0.538	0.17150	.	2.863710	0.01212	N	0.007864	T	0.01870	0.0059	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40572	-0.9556	10	0.11794	T	0.64	.	4.0418	0.09755	0.4291:0.0:0.5709:0.0	rs3121079	6	O60810	PRAM4_HUMAN	R	6	ENSP00000235349:W6R	ENSP00000235349:W6R	W	-	1	0	PRAMEF4	12865787	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.845000	0.01677	-0.151000	0.11176	-0.498000	0.04607	TGG	.	.	weak		0.557	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
C3orf22	152065	hgsc.bcm.edu	37	3	126270923	126270923	+	Silent	SNP	G	G	C	rs34760151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126270923G>C	ENST00000318225.2	-	3	510	c.132C>G	c.(130-132)ccC>ccG	p.P44P		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	44										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		TGACCTCCCAGGGCTGCAGGG	0.602													G|||	481	0.0960463	0.2685	0.0403	5008	,	,		18751	0.002		0.0288	False		,,,				2504	0.0685				p.P44P		Atlas-SNP	.											.	C3orf22	17	.	0			c.C132G						PASS	.	G		894,3512	348.0+/-309.7	98,698,1407	83.0	77.0	79.0		132	-0.0	0.0	3	dbSNP_126	79	294,8306	108.0+/-168.7	6,282,4012	no	coding-synonymous	C3orf22	NM_152533.1		104,980,5419	CC,CG,GG		3.4186,20.2905,9.1342		44/142	126270923	1188,11818	2203	4300	6503	SO:0001819	synonymous_variant	152065	exon3			CTCCCAGGGCTGC		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.132C>G	3.37:g.126270923G>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_152533	B3KUS9	Silent	SNP	ENST00000318225.2	37	CCDS3040.1																																																																																			G|0.912;C|0.088	0.088	strong		0.602	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533	
PSG6	5675	hgsc.bcm.edu	37	19	43420290	43420290	+	Silent	SNP	A	A	G	rs76022539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43420290A>G	ENST00000292125.2	-	2	458	c.414T>C	c.(412-414)acT>acC	p.T138T	PSG6_ENST00000601833.1_Silent_p.T67T|PSG6_ENST00000187910.2_Silent_p.T138T|PSG6_ENST00000402603.4_Silent_p.T138T	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	138	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				ATAAGGTGACAGTGAAATATC	0.512													.|||	179	0.0357428	0.1225	0.0101	5008	,	,		19988	0.0089		0.0	False		,,,				2504	0.001				p.T138T		Atlas-SNP	.											.	PSG6	89	.	0			c.T414C						PASS	.	G	,	501,3901		35,431,1735	253.0	220.0	231.0		414,414	0.1	0.0	19	dbSNP_131	231	4,8594		0,4,4295	no	coding-synonymous,coding-synonymous	PSG6	NM_001031850.2,NM_002782.3	,	35,435,6030	GG,GA,AA		0.0465,11.3812,3.8846	,	138/425,138/436	43420290	505,12495	2201	4299	6500	SO:0001819	synonymous_variant	5675	exon2			GGTGACAGTGAAA		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.414T>C	19.37:g.43420290A>G		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	176	89	0.505682	NM_001031850	O75244|Q15224|Q15235|Q549K1	Silent	SNP	ENST00000292125.2	37	CCDS12613.1																																																																																			A|0.961;G|0.039	0.039	strong		0.512	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
KCTD7	154881	hgsc.bcm.edu	37	7	66094184	66094184	+	Silent	SNP	C	C	T	rs587780370		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:66094184C>T	ENST00000275532.3	+	1	317	c.133C>T	c.(133-135)Ctg>Ttg	p.L45L	KCTD7_ENST00000443322.1_Silent_p.L45L	NM_001167961.2|NM_153033.4	NP_001161433.1|NP_694578.1	Q96MP8	KCTD7_HUMAN	potassium channel tetramerization domain containing 7	45					cell death (GO:0008219)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						GCTGCCCCTGCTGCCACAGGA	0.776																																					p.L45L		Atlas-SNP	.											KCTD7,brain,glioma,-2,1	KCTD7	26	1	0			c.C133T						scavenged	.																																			SO:0001819	synonymous_variant	154881	exon1			CCCCTGCTGCCAC	AK056631	CCDS5534.1, CCDS55117.1	7q11.21	2014-09-17	2013-06-20		ENSG00000243335	ENSG00000243335			21957	protein-coding gene	gene with protein product		611725	"""potassium channel tetramerisation domain containing 7"""			12477932	Standard	NM_001167961		Approved	FLJ32069, EPM3, CLN14	uc003tve.3	Q96MP8	OTTHUMG00000129543	ENST00000275532.3:c.133C>T	7.37:g.66094184C>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_001167961	A4D2M4|Q8IVR0	Silent	SNP	ENST00000275532.3	37	CCDS5534.1																																																																																			.	.	none		0.776	KCTD7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251733.2	NM_153033	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249121	71249121	+	Missense_Mutation	SNP	C	C	G	rs200585722		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249121C>G	ENST00000398534.3	+	1	51	c.20C>G	c.(19-21)tCt>tGt	p.S7C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	7						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						TGTGGCTGCTCTGGAGGCTGT	0.657																																					p.S7C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.C20G						PASS	.						47.0	66.0	60.0					11																	71249121		2189	4282	6471	SO:0001583	missense	57830	exon1			GCTGCTCTGGAGG	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.20C>G	11.37:g.71249121C>G	ENSP00000420723:p.Ser7Cys	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	233	37	0.158798	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	37	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	c	3.358	-0.131059	0.06753	.	.	ENSG00000241233	ENST00000398534	T	0.01527	4.8	1.57	1.57	0.23409	.	.	.	.	.	T	0.03564	0.0102	M	0.74389	2.26	0.09310	N	1	P	0.39094	0.659	B	0.43225	0.412	T	0.34204	-0.9838	9	0.62326	D	0.03	.	3.9595	0.09404	0.0:0.775:0.0:0.225	.	7	O75690	KRA58_HUMAN	C	7	ENSP00000420723:S7C	ENSP00000420723:S7C	S	+	2	0	KRTAP5-8	70926769	0.030000	0.19436	0.804000	0.32291	0.223000	0.24884	-0.589000	0.05767	1.182000	0.42928	0.514000	0.50259	TCT	.	.	weak		0.657	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
RNF213	57674	hgsc.bcm.edu	37	17	78319136	78319136	+	Missense_Mutation	SNP	G	G	A	rs9674961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78319136G>A	ENST00000582970.1	+	29	7144	c.7001G>A	c.(7000-7002)aGt>aAt	p.S2334N	RNF213_ENST00000336301.6_Missense_Mutation_p.S407N|RNF213_ENST00000508628.2_Missense_Mutation_p.S2383N	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2334					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)	p.S407N(2)|p.S2383N(2)		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)			GATGCCATCAGTCACTTGACT	0.522													A|||	2797	0.558506	0.6528	0.4337	5008	,	,		20475	0.376		0.6879	False		,,,				2504	0.5746				p.S2334N		Atlas-SNP	.											RNF213_ENST00000411702,colon,carcinoma,0,6	RNF213	766	6	4	Substitution - Missense(4)	large_intestine(2)|stomach(2)	c.G7001A						PASS	.	A	ASN/SER	2876,1530	485.5+/-360.3	950,976,277	124.0	114.0	117.0		7148	0.9	0.0	17	dbSNP_119	117	5714,2886	452.3+/-362.9	1909,1896,495	yes	missense	RNF213	NM_020914.4	46	2859,2872,772	AA,AG,GG		33.5581,34.7254,33.9536	benign	2383/5257	78319136	8590,4416	2203	4300	6503	SO:0001583	missense	57674	exon29			CCATCAGTCACTT	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.7001G>A	17.37:g.78319136G>A	ENSP00000464087:p.Ser2334Asn	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	153	153	1	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	1244	0.5695970695970696	326	0.6626016260162602	173	0.47790055248618785	212	0.3706293706293706	533	0.7031662269129287	A	3.858	-0.030522	0.07543	0.652746	0.664419	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.21734	1.99	5.84	0.943	0.19531	.	0.670270	0.15010	N	0.285649	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	0.35025	-0.9805	9	0.07644	T	0.81	.	11.2868	0.49226	0.6123:0.0:0.3877:0.0	rs9674961;rs52799145;rs61333363;rs9674961	407	Q63HN8	RN213_HUMAN	N	2334;2383;407	ENSP00000338218:S407N	ENSP00000338218:S407N	S	+	2	0	RNF213	75933731	0.098000	0.21812	0.000000	0.03702	0.002000	0.02628	2.159000	0.42339	-0.073000	0.12842	-0.982000	0.02568	AGT	G|0.368;A|0.632	0.632	strong		0.522	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
TRIO	7204	hgsc.bcm.edu	37	5	14389469	14389469	+	Silent	SNP	C	C	T	rs7715916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:14389469C>T	ENST00000344204.4	+	25	4044	c.4020C>T	c.(4018-4020)atC>atT	p.I1340I	TRIO_ENST00000509967.2_Silent_p.I1291I|TRIO_ENST00000537187.1_Silent_p.I1340I	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1340	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)					AACTCATCATCTTCGGAAACA	0.433													C|||	549	0.109625	0.264	0.1037	5008	,	,		18889	0.0		0.0606	False		,,,				2504	0.0685				p.I1340I		Atlas-SNP	.											.	TRIO	305	.	0			c.C4020T						PASS	.	C		1061,3345	384.4+/-325.3	133,795,1275	106.0	107.0	106.0		4020	6.0	1.0	5	dbSNP_116	106	385,8215	124.6+/-183.3	10,365,3925	no	coding-synonymous	TRIO	NM_007118.2		143,1160,5200	TT,TC,CC		4.4767,24.0808,11.1179		1340/3098	14389469	1446,11560	2203	4300	6503	SO:0001819	synonymous_variant	7204	exon25			CATCATCTTCGGA	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.4020C>T	5.37:g.14389469C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																			C|0.891;T|0.109	0.109	strong		0.433	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
SLCO2A1	6578	hgsc.bcm.edu	37	3	133653566	133653566	+	Silent	SNP	G	G	A	rs72978391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133653566G>A	ENST00000310926.4	-	14	2196	c.1923C>T	c.(1921-1923)ggC>ggT	p.G641G	SLCO2A1_ENST00000493729.1_Silent_p.G565G	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	641					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	GTCAGATGAGGCCTGCCGCCT	0.557													G|||	160	0.0319489	0.112	0.0144	5008	,	,		18588	0.0		0.002	False		,,,				2504	0.0				p.G641G		Atlas-SNP	.											.	SLCO2A1	72	.	0			c.C1923T						PASS	.	G		407,3999	201.8+/-224.7	15,377,1811	121.0	103.0	109.0		1923	2.6	0.7	3	dbSNP_130	109	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	SLCO2A1	NM_005630.2		15,384,6104	AA,AG,GG		0.0814,9.2374,3.1831		641/644	133653566	414,12592	2203	4300	6503	SO:0001819	synonymous_variant	6578	exon14			GATGAGGCCTGCC		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"""Solute carriers"""	10955	protein-coding gene	gene with protein product		601460	"""solute carrier family 21 (prostaglandin transporter), member 2"", ""matrin F/G 1"""	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.1923C>T	3.37:g.133653566G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_005630	Q86V98|Q8IUN2	Silent	SNP	ENST00000310926.4	37	CCDS3084.1																																																																																			G|0.970;A|0.030	0.030	strong		0.557	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630	
KIAA0556	23247	hgsc.bcm.edu	37	16	27752135	27752135	+	Silent	SNP	C	C	T	rs12447120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27752135C>T	ENST00000261588.4	+	15	2536	c.2517C>T	c.(2515-2517)gaC>gaT	p.D839D		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	839						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						ATGACTCAGACATCTTTAACC	0.607													C|||	669	0.133586	0.2496	0.1931	5008	,	,		19590	0.001		0.162	False		,,,				2504	0.0419				p.D839D		Atlas-SNP	.											.	KIAA0556	348	.	0			c.C2517T						PASS	.	C		1055,3339	382.3+/-324.4	121,813,1263	48.0	48.0	48.0		2517	4.2	1.0	16	dbSNP_120	48	1285,7315	252.9+/-278.8	85,1115,3100	no	coding-synonymous	KIAA0556	NM_015202.2		206,1928,4363	TT,TC,CC		14.9419,24.01,18.0083		839/1619	27752135	2340,10654	2197	4300	6497	SO:0001819	synonymous_variant	23247	exon15			CTCAGACATCTTT	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.2517C>T	16.37:g.27752135C>T		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_015202	A7E2C2	Silent	SNP	ENST00000261588.4	37	CCDS32415.1																																																																																			C|0.837;T|0.163	0.163	strong		0.607	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
TAT	6898	hgsc.bcm.edu	37	16	71602665	71602665	+	Silent	SNP	C	C	T	rs16973331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71602665C>T	ENST00000355962.4	-	11	1306	c.1173G>A	c.(1171-1173)gaG>gaA	p.E391E	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	391					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	GCTCCGTGAACTCCACATCGT	0.522													C|||	189	0.0377396	0.1377	0.0101	5008	,	,		16730	0.0		0.0	False		,,,				2504	0.0				p.E391E	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.G1173A						PASS	.	C		561,3835	250.9+/-257.8	44,473,1681	84.0	70.0	75.0		1173	-0.3	1.0	16	dbSNP_123	75	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous	TAT	NM_000353.2		44,478,5976	TT,TC,CC		0.0581,12.7616,4.3552		391/455	71602665	566,12430	2198	4300	6498	SO:0001819	synonymous_variant	6898	exon11			CGTGAACTCCACA		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.1173G>A	16.37:g.71602665C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_000353	B2R8I1|D3DWS2	Silent	SNP	ENST00000355962.4	37	CCDS10903.1																																																																																			C|0.958;T|0.042	0.042	strong		0.522	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1		
LAMB4	22798	hgsc.bcm.edu	37	7	107746313	107746313	+	Silent	SNP	T	T	C	rs35265257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107746313T>C	ENST00000388781.3	-	8	902	c.819A>G	c.(817-819)gaA>gaG	p.E273E	LAMB4_ENST00000418464.1_Silent_p.E273E|LAMB4_ENST00000388780.3_Silent_p.E273E|LAMB4_ENST00000414450.2_Silent_p.E273E|LAMB4_ENST00000205386.4_Silent_p.E273E	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	273	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						TAGGGCGACATTCGCTAGCAT	0.473													T|||	101	0.0201677	0.0734	0.0058	5008	,	,		19580	0.0		0.0	False		,,,				2504	0.0				p.E273E		Atlas-SNP	.											LAMB4,right_upper_lobe,carcinoma,-1,1	LAMB4	253	1	0			c.A819G						PASS	.	T		261,4145	149.5+/-183.7	8,245,1950	120.0	105.0	110.0		819	0.9	0.2	7	dbSNP_126	110	5,8595	5.0+/-18.6	0,5,4295	no	coding-synonymous	LAMB4	NM_007356.2		8,250,6245	CC,CT,TT		0.0581,5.9237,2.0452		273/1762	107746313	266,12740	2203	4300	6503	SO:0001819	synonymous_variant	22798	exon8			GCGACATTCGCTA	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.819A>G	7.37:g.107746313T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	161	80	0.496894	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			T|0.982;C|0.018	0.018	strong		0.473	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
SERPINB7	8710	hgsc.bcm.edu	37	18	61471593	61471593	+	Silent	SNP	A	A	G	rs11873045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61471593A>G	ENST00000398019.2	+	8	1192	c.867A>G	c.(865-867)caA>caG	p.Q289Q	SERPINB7_ENST00000336429.2_Silent_p.Q289Q|SERPINB7_ENST00000546027.1_Silent_p.Q289Q|SERPINB7_ENST00000540675.1_Silent_p.Q272Q	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	289					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)				AAATGAAACAATATTTGAGAG	0.398													A|||	252	0.0503195	0.18	0.0173	5008	,	,		18557	0.0		0.002	False		,,,				2504	0.0				p.Q289Q		Atlas-SNP	.											.	SERPINB7	66	.	0			c.A867G						PASS	.	A	,	699,3707	288.4+/-279.8	52,595,1556	49.0	51.0	50.0		867,867	-1.4	0.0	18	dbSNP_120	50	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	SERPINB7	NM_001040147.1,NM_003784.2	,	52,601,5850	GG,GA,AA		0.0698,15.8647,5.4206	,	289/381,289/381	61471593	705,12301	2203	4300	6503	SO:0001819	synonymous_variant	8710	exon8			GAAACAATATTTG	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.867A>G	18.37:g.61471593A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_001261830	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Silent	SNP	ENST00000398019.2	37	CCDS11988.1																																																																																			A|0.943;G|0.057	0.057	strong		0.398	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134007.1	NM_003784	
OR2J3	442186	hgsc.bcm.edu	37	6	29080386	29080386	+	Missense_Mutation	SNP	T	T	C	rs79293918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29080386T>C	ENST00000377169.1	+	1	719	c.719T>C	c.(718-720)gTg>gCg	p.V240A		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	240						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						CTTCAGAAAGTGTTTGGAACA	0.448													T|||	116	0.0231629	0.0651	0.0101	5008	,	,		22544	0.0079		0.0119	False		,,,				2504	0.0031				p.V240A		Atlas-SNP	.											.	OR2J3	53	.	0			c.T719C						PASS	.	T	ALA/VAL	185,2355		4,177,1089	118.0	123.0	121.0		719	1.6	0.9	6	dbSNP_131	121	26,5120		0,26,2547	yes	missense	OR2J3	NM_001005216.2	64	4,203,3636	CC,CT,TT		0.5052,7.2835,2.7453	possibly-damaging	240/312	29080386	211,7475	1270	2573	3843	SO:0001583	missense	442186	exon1			AGAAAGTGTTTGG		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.719T>C	6.37:g.29080386T>C	ENSP00000366374:p.Val240Ala	Somatic	386	0	0		WXS	Illumina HiSeq	Phase_I	370	177	0.478378	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	54	0.024725274725274724	32	0.06504065040650407	6	0.016574585635359115	6	0.01048951048951049	10	0.013192612137203167	T	0.005	-2.139654	0.00335	0.072835	0.005052	ENSG00000204701	ENST00000377169	T	0.00009	9.47	2.78	1.63	0.23807	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00123	-2.06	0.40080	D	0.976121	B	0.09022	0.002	B	0.13407	0.009	T	0.00849	-1.1541	9	0.02654	T	1	.	3.5019	0.07676	0.0:0.4818:0.0:0.5182	.	240	O76001	OR2J3_HUMAN	A	240	ENSP00000366374:V240A	ENSP00000366374:V240A	V	+	2	0	OR2J3	29188365	0.981000	0.34729	0.937000	0.37676	0.020000	0.10135	1.790000	0.38734	1.268000	0.44264	0.358000	0.22013	GTG	T|0.981;C|0.019	0.019	strong		0.448	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
KREMEN2	79412	hgsc.bcm.edu	37	16	3016716	3016716	+	Missense_Mutation	SNP	C	C	G	rs111311295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3016716C>G	ENST00000303746.5	+	5	1137	c.560C>G	c.(559-561)cCc>cGc	p.P187R	KREMEN2_ENST00000572045.1_Missense_Mutation_p.P187R|KREMEN2_ENST00000575769.1_Missense_Mutation_p.P187R|KREMEN2_ENST00000571007.1_Intron|PAQR4_ENST00000293978.8_5'Flank|PKMYT1_ENST00000571102.1_5'Flank|PAQR4_ENST00000318782.8_5'Flank|PAQR4_ENST00000572687.1_5'Flank|KREMEN2_ENST00000319500.6_Missense_Mutation_p.P187R|KREMEN2_ENST00000575885.1_Intron|PAQR4_ENST00000576565.1_5'Flank			Q8NCW0	KREM2_HUMAN	kringle containing transmembrane protein 2	187	WSC. {ECO:0000255|PROSITE- ProRule:PRU00558, ECO:0000305}.			Missing (in Ref. 2; BAC11365). {ECO:0000305}.	Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|large_intestine(1)	4						CGCCTGGCCCCCGCCACCGAC	0.692																																					p.P187R		Atlas-SNP	.											.	KREMEN2	13	.	0			c.C560G						PASS	.	C	ARG/PRO,ARG/PRO	14,4368		0,14,2177	19.0	24.0	22.0		560,560	2.9	0.0	16	dbSNP_132	22	0,8584		0,0,4292	yes	missense,missense	KREMEN2	NM_024507.2,NM_172229.1	103,103	0,14,6469	GG,GC,CC		0.0,0.3195,0.108	probably-damaging,probably-damaging	187/421,187/463	3016716	14,12952	2191	4292	6483	SO:0001583	missense	79412	exon5			TGGCCCCCGCCAC	BC003533	CCDS10483.1, CCDS10484.1, CCDS58412.1, CCDS58413.1	16p13.11	2008-08-04			ENSG00000131650	ENSG00000131650			18797	protein-coding gene	gene with protein product		609899				12050670	Standard	NM_172229		Approved	MGC10791, KRM2	uc002csg.3	Q8NCW0	OTTHUMG00000128976	ENST00000303746.5:c.560C>G	16.37:g.3016716C>G	ENSP00000304422:p.Pro187Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_024507	B4DXF6|I3L2S2|Q8N2J4|Q8NCW1|Q96GL8|Q9BTP9	Missense_Mutation	SNP	ENST00000303746.5	37	CCDS10483.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.579580	0.46006	0.003195	0.0	ENSG00000131650	ENST00000303746;ENST00000319500	T;T	0.54071	0.59;0.59	4.91	2.92	0.33932	Carbohydrate-binding WSC (2);	0.151142	0.30732	N	0.008999	T	0.57242	0.2040	M	0.78285	2.405	0.30519	N	0.768604	P;P;P;P	0.37101	0.527;0.527;0.527;0.582	B;B;B;P	0.46299	0.377;0.377;0.377;0.511	T	0.60151	-0.7319	10	0.49607	T	0.09	.	5.5586	0.17131	0.0:0.6523:0.1625:0.1852	.	187;187;187;187	Q8NCW0-2;Q8NCW0-4;Q8NCW0-3;Q8NCW0	.;.;.;KREM2_HUMAN	R	187	ENSP00000304422:P187R;ENSP00000322079:P187R	ENSP00000304422:P187R	P	+	2	0	KREMEN2	2956717	0.083000	0.21467	0.035000	0.18076	0.983000	0.72400	1.656000	0.37355	1.066000	0.40716	0.456000	0.33151	CCC	C|0.999;G|0.001	0.001	strong		0.692	KREMEN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250964.2	NM_145347	
DPY19L2	283417	hgsc.bcm.edu	37	12	64062065	64062065	+	Missense_Mutation	SNP	T	T	C	rs10878075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:64062065T>C	ENST00000324472.4	-	1	292	c.109A>G	c.(109-111)Atg>Gtg	p.M37V	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	37			M -> V (in dbSNP:rs10878075). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GACTTTTCCATCTCCTCCTCT	0.642													C|||	1980	0.395367	0.4433	0.2565	5008	,	,		14843	0.5714		0.1978	False		,,,				2504	0.4509				p.M37V		Atlas-SNP	.											.	DPY19L2	97	.	0			c.A109G						PASS	.	C	VAL/MET	1659,2729		308,1043,843	28.0	36.0	34.0		109	0.6	0.0	12	dbSNP_120	34	1695,6897		179,1337,2780	no	missense	DPY19L2	NM_173812.4	21	487,2380,3623	CC,CT,TT		19.7277,37.8077,25.8398	benign	37/759	64062065	3354,9626	2194	4296	6490	SO:0001583	missense	283417	exon1			TTTCCATCTCCTC		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.109A>G	12.37:g.64062065T>C	ENSP00000315988:p.Met37Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	154	60	0.38961	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	767	0.35119047619047616	189	0.38414634146341464	99	0.27348066298342544	331	0.5786713286713286	148	0.19525065963060687	C	1.696	-0.502757	0.04261	0.378077	0.197277	ENSG00000177990	ENST00000324472;ENST00000542209	T;T	0.34072	1.38;1.99	1.61	0.65	0.17812	.	1.705710	0.04502	N	0.381454	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45086	-0.9285	8	.	.	.	.	2.3121	0.04189	0.2942:0.512:0.0:0.1938	rs10878075;rs10878075	37	Q6NUT2	D19L2_HUMAN	V	37	ENSP00000315988:M37V;ENSP00000444932:M37V	.	M	-	1	0	DPY19L2	62348332	0.000000	0.05858	0.007000	0.13788	0.027000	0.11550	-1.353000	0.02617	-0.139000	0.11414	-1.063000	0.02288	ATG	T|0.711;C|0.289	0.289	strong		0.642	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
SCFD2	152579	hgsc.bcm.edu	37	4	53740161	53740161	+	Missense_Mutation	SNP	C	C	T	rs149034746		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:53740161C>T	ENST00000401642.3	-	9	2163	c.2030G>A	c.(2029-2031)cGa>cAa	p.R677Q	SCFD2_ENST00000388940.4_Missense_Mutation_p.R632Q	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	677					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)			p.R677Q(1)		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)			TGGATGCAGTCGGTCAGTTGC	0.498																																					p.R677Q		Atlas-SNP	.											SCFD2,caecum,carcinoma,0,1	SCFD2	78	1	1	Substitution - Missense(1)	large_intestine(1)	c.G2030A						scavenged	.	C	GLN/ARG	0,4406		0,0,2203	133.0	116.0	122.0		2030	4.1	1.0	4	dbSNP_134	122	1,8599	1.2+/-3.3	0,1,4299	no	missense	SCFD2	NM_152540.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	677/685	53740161	1,13005	2203	4300	6503	SO:0001583	missense	152579	exon9			TGCAGTCGGTCAG	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.2030G>A	4.37:g.53740161C>T	ENSP00000384182:p.Arg677Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	151	3	0.0198676	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	37	CCDS33984.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.249632	0.59212	0.0	1.16E-4	ENSG00000184178	ENST00000401642;ENST00000388940	T;T	0.50813	0.73;0.8	5.04	4.13	0.48395	.	0.166521	0.36002	N	0.002860	T	0.48429	0.1499	N	0.19112	0.55	0.40204	D	0.97754	D;D	0.89917	1.0;1.0	D;P	0.67900	0.954;0.901	T	0.48422	-0.9037	10	0.49607	T	0.09	.	9.8066	0.40797	0.0:0.7778:0.1424:0.0798	.	632;677	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	Q	677;632	ENSP00000384182:R677Q;ENSP00000373592:R632Q	ENSP00000373592:R632Q	R	-	2	0	SCFD2	53434918	0.998000	0.40836	0.999000	0.59377	0.233000	0.25261	2.157000	0.42320	2.508000	0.84585	0.655000	0.94253	CGA	C|1.000;T|0.000	0.000	weak		0.498	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	
APBA3	9546	hgsc.bcm.edu	37	19	3760056	3760056	+	Silent	SNP	G	G	A	rs61729800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3760056G>A	ENST00000316757.3	-	2	407	c.207C>T	c.(205-207)ggC>ggT	p.G69G	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	69					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)		CCACCAGATCGCCTGGCAGAG	0.637													G|||	145	0.0289537	0.1067	0.0058	5008	,	,		16441	0.0		0.0	False		,,,				2504	0.0				p.G69G		Atlas-SNP	.											APBA3,colon,carcinoma,0,1	APBA3	28	1	0			c.C207T						PASS	.	G		388,4014	187.4+/-214.1	19,350,1832	46.0	47.0	47.0		207	-8.0	0.0	19	dbSNP_129	47	5,8595	2.2+/-6.3	0,5,4295	no	coding-synonymous	APBA3	NM_004886.3		19,355,6127	AA,AG,GG		0.0581,8.8142,3.0226		69/576	3760056	393,12609	2201	4300	6501	SO:0001819	synonymous_variant	9546	exon2			CAGATCGCCTGGC	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.207C>T	19.37:g.3760056G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			G|0.973;A|0.027	0.027	strong		0.637	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
PPP1R26	9858	hgsc.bcm.edu	37	9	138377657	138377657	+	Missense_Mutation	SNP	T	T	C	rs1808998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138377657T>C	ENST00000356818.2	+	4	1850	c.1301T>C	c.(1300-1302)aTg>aCg	p.M434T	PPP1R26_ENST00000605660.1_Missense_Mutation_p.M434T|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000401470.3_Missense_Mutation_p.M434T|PPP1R26_ENST00000605286.1_Missense_Mutation_p.M434T|PPP1R26_ENST00000604351.1_Missense_Mutation_p.M434T	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	434			M -> T (in dbSNP:rs1808998). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										ACCAAGACCATGGACCCTGGT	0.592													C|||	2324	0.464058	0.4183	0.5231	5008	,	,		18270	0.6825		0.2147	False		,,,				2504	0.5153				p.M434T		Atlas-SNP	.											.	.	.	.	0			c.T1301C						PASS	.	C	THR/MET	1645,2761	636.1+/-396.5	304,1037,862	33.0	37.0	36.0		1301	-2.0	0.0	9	dbSNP_92	36	1822,6778	713.3+/-405.9	201,1420,2679	yes	missense	KIAA0649	NM_014811.3	81	505,2457,3541	CC,CT,TT		21.186,37.3355,26.6569	benign	434/1210	138377657	3467,9539	2203	4300	6503	SO:0001583	missense	9858	exon4			AGACCATGGACCC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.1301T>C	9.37:g.138377657T>C	ENSP00000349274:p.Met434Thr	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	31	20	0.645161	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	908	0.4157509157509158	168	0.34146341463414637	163	0.45027624309392267	416	0.7272727272727273	161	0.21240105540897097	C	0.016	-1.520221	0.00967	0.373355	0.21186	ENSG00000196422	ENST00000356818	T	0.08102	3.13	5.06	-1.98	0.07480	.	1.322620	0.05171	N	0.499637	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39921	-0.9590	9	0.02654	T	1	0.4383	1.8933	0.03252	0.1239:0.3712:0.1217:0.3833	rs1808998;rs3748193;rs17846421;rs17859466;rs1808998	434	Q5T8A7	PPR26_HUMAN	T	434	ENSP00000349274:M434T	ENSP00000349274:M434T	M	+	2	0	KIAA0649	137517478	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.935000	0.03950	-1.293000	0.02362	-1.859000	0.00561	ATG	T|0.653;C|0.347	0.347	strong		0.592	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
CEP192	55125	hgsc.bcm.edu	37	18	13040858	13040858	+	Silent	SNP	A	A	G	rs145309087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13040858A>G	ENST00000325971.8	+	12	1644	c.51A>G	c.(49-51)ccA>ccG	p.P17P	CEP192_ENST00000506447.1_Silent_p.P613P|CEP192_ENST00000430049.2_Silent_p.P138P			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	17					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TTAGATCACCAGAGAAGAGAG	0.299													A|||	62	0.0123802	0.0439	0.0058	5008	,	,		17505	0.0		0.0	False		,,,				2504	0.0				p.P613P		Atlas-SNP	.											.	CEP192	340	.	0			c.A1839G						PASS	.	A		158,4248	105.2+/-143.6	1,156,2046	67.0	70.0	69.0		1839	0.3	1.0	18	dbSNP_134	69	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	CEP192	NM_032142.3		1,157,6342	GG,GA,AA		0.0116,3.586,1.2231		613/2538	13040858	159,12841	2203	4297	6500	SO:0001819	synonymous_variant	55125	exon14			ATCACCAGAGAAG	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.51A>G	18.37:g.13040858A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	171	90	0.526316	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	37																																																																																				A|0.987;G|0.013	0.013	strong		0.299	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
PSMF1	9491	hgsc.bcm.edu	37	20	1099523	1099523	+	Missense_Mutation	SNP	T	T	G	rs1803415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1099523T>G	ENST00000335877.6	+	1	283	c.107T>G	c.(106-108)tTc>tGc	p.F36C	PSMF1_ENST00000333082.3_Missense_Mutation_p.F36C|PSMF1_ENST00000246015.4_Missense_Mutation_p.F36C|PSMF1_ENST00000438768.2_Missense_Mutation_p.F36C|PSMF1_ENST00000381898.4_Intron	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	36	Important for homodimerization and interaction with FBXO7.		F -> C (in dbSNP:rs1803415). {ECO:0000269|PubMed:10764772, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						CACGGTTACTTCGGCTTGGGT	0.632													A|||	3655	0.729832	0.8071	0.7723	5008	,	,		15275	0.4583		0.838	False		,,,				2504	0.7638				p.F36C		Atlas-SNP	.											.	PSMF1	27	.	0			c.T107G						PASS	.	A	CYS/PHE,CYS/PHE	3576,830		1446,684,73	81.0	75.0	77.0		107,107	1.9	1.0	20	dbSNP_89	77	7131,1469		2954,1223,123	yes	missense,missense	PSMF1	NM_006814.3,NM_178578.2	205,205	4400,1907,196	GG,GT,TT		17.0814,18.8379,17.6765	benign,benign	36/272,36/272	1099523	10707,2299	2203	4300	6503	SO:0001583	missense	9491	exon1			GTTACTTCGGCTT	D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"""Proteasome (prosome, macropain) subunits"""	9571	protein-coding gene	gene with protein product	"""proteasome inhibitor hP131 subunit"""					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.107T>G	20.37:g.1099523T>G	ENSP00000338039:p.Phe36Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_006814	A0AVQ9|D3DVW3|Q9H4I1	Missense_Mutation	SNP	ENST00000335877.6	37	CCDS13010.1	1582	0.7243589743589743	407	0.8272357723577236	287	0.7928176795580111	257	0.4493006993006993	631	0.8324538258575198	A	0.455	-0.892019	0.02491	0.811621	0.829186	ENSG00000125818	ENST00000333082;ENST00000381899;ENST00000246015;ENST00000335877;ENST00000438768	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	4.26	1.94	0.25998	.	0.565491	0.15873	N	0.240441	T	0.00012	0.0000	N	0.08118	0	0.20703	P	0.999864573	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.11842	-1.0571	9	0.46703	T	0.11	-3.4805	3.0951	0.06307	0.5334:0.0:0.2865:0.1802	rs1803415;rs11557003;rs59237259;rs1803415	36;36;36	E7ER20;Q5QPM7;Q92530	.;.;PSMF1_HUMAN	C	36	ENSP00000327704:F36C;ENSP00000371324:F36C;ENSP00000246015:F36C;ENSP00000338039:F36C;ENSP00000401404:F36C	ENSP00000246015:F36C	F	+	2	0	PSMF1	1047523	0.002000	0.14202	0.981000	0.43875	0.118000	0.20060	-0.118000	0.10692	0.206000	0.20587	-0.694000	0.03704	TTC	G|0.777;N|0.000	0.777	strong		0.632	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578	
AP3B1	8546	hgsc.bcm.edu	37	5	77412011	77412011	+	Silent	SNP	A	A	G	rs42360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:77412011A>G	ENST00000255194.6	-	18	2191	c.2016T>C	c.(2014-2016)gcT>gcC	p.A672A	AP3B1_ENST00000519295.1_Silent_p.A623A	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	672					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		AAAACTTCTTAGCAGAATTCT	0.338									Hermansky-Pudlak syndrome				A|||	946	0.188898	0.2383	0.3271	5008	,	,		16072	0.0754		0.2127	False		,,,				2504	0.1166				p.A672A		Atlas-SNP	.											AP3B1,NS,carcinoma,0,1	AP3B1	94	1	0			c.T2016C						PASS	.	A		1135,3271	401.5+/-332.0	163,809,1231	87.0	91.0	89.0		2016	3.6	0.8	5	dbSNP_76	89	2013,6587	351.2+/-328.2	249,1515,2536	no	coding-synonymous	AP3B1	NM_003664.3		412,2324,3767	GG,GA,AA		23.407,25.7603,24.2042		672/1095	77412011	3148,9858	2203	4300	6503	SO:0001819	synonymous_variant	8546	exon18	Familial Cancer Database	HPS, HPS1-8	CTTCTTAGCAGAA	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.2016T>C	5.37:g.77412011A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																			A|0.776;C|0.001	.	strong		0.338	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
RNF17	56163	hgsc.bcm.edu	37	13	25374636	25374636	+	Silent	SNP	A	A	G	rs35957316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25374636A>G	ENST00000255324.5	+	13	1774	c.1722A>G	c.(1720-1722)caA>caG	p.Q574Q	RNF17_ENST00000255325.6_Silent_p.Q574Q|RNF17_ENST00000381921.1_Silent_p.Q574Q	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	574					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)		CATTAGCACAACCATGCTCAT	0.358													A|||	244	0.048722	0.1755	0.0159	5008	,	,		18152	0.0		0.001	False		,,,				2504	0.0				p.Q574Q		Atlas-SNP	.											.	RNF17	259	.	0			c.A1722G						PASS	.	A	,	649,3757	277.8+/-273.9	46,557,1600	125.0	121.0	123.0		1722,1722	0.6	0.9	13	dbSNP_126	123	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	RNF17	NM_001184993.1,NM_031277.2	,	46,569,5888	GG,GA,AA		0.1395,14.7299,5.0823	,	574/1620,574/1624	25374636	661,12345	2203	4300	6503	SO:0001819	synonymous_variant	56163	exon13			AGCACAACCATGC	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.1722A>G	13.37:g.25374636A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	37	CCDS9308.2																																																																																			A|0.952;G|0.048	0.048	strong		0.358	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
LYZL6	57151	hgsc.bcm.edu	37	17	34264859	34264859	+	Silent	SNP	A	A	G	rs2280783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34264859A>G	ENST00000585556.1	-	3	535	c.201T>C	c.(199-201)gaT>gaC	p.D67D	LYZL6_ENST00000293274.4_Silent_p.D67D|LYZL6_ENST00000492340.2_5'UTR|LYZL6_ENST00000394523.3_Silent_p.D67D			O75951	LYZL6_HUMAN	lysozyme-like 6	67					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)	p.D67D(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	12				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CAAAGCTTCCATCTGCATTTT	0.448													A|||	647	0.129193	0.2247	0.0994	5008	,	,		23330	0.0972		0.1302	False		,,,				2504	0.0532				p.D67D		Atlas-SNP	.											LYZL6,NS,carcinoma,0,1	LYZL6	18	1	1	Substitution - coding silent(1)	stomach(1)	c.T201C						PASS	.	A	,	894,3512	346.9+/-309.2	92,710,1401	103.0	101.0	101.0		201,201	-3.1	0.3	17	dbSNP_100	101	1144,7456	235.8+/-268.3	71,1002,3227	no	coding-synonymous,coding-synonymous	LYZL6	NM_001199951.1,NM_020426.2	,	163,1712,4628	GG,GA,AA		13.3023,20.2905,15.6697	,	67/149,67/149	34264859	2038,10968	2203	4300	6503	SO:0001819	synonymous_variant	57151	exon2			GCTTCCATCTGCA	AF088219, AY742214	CCDS11302.1	17q11.2	2014-04-10			ENSG00000161572	ENSG00000275722			29614	protein-coding gene	gene with protein product		612751				10213461	Standard	NM_020426		Approved	LYC1, PRO1485, TKAL754	uc002hkj.2	O75951	OTTHUMG00000188400	ENST00000585556.1:c.201T>C	17.37:g.34264859A>G		Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_020426	Q6UW30	Silent	SNP	ENST00000585556.1	37	CCDS11302.1																																																																																			A|0.847;G|0.153	0.153	strong		0.448	LYZL6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256578.2	NM_020426	
FBL	2091	hgsc.bcm.edu	37	19	40329747	40329747	+	Silent	SNP	C	C	T	rs150137200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40329747C>T	ENST00000221801.3	-	5	590	c.477G>A	c.(475-477)ccG>ccA	p.P159P	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	159					histone glutamine methylation (GO:1990258)|osteoblast differentiation (GO:0001649)|rRNA processing (GO:0006364)|snoRNA metabolic process (GO:0016074)|tRNA processing (GO:0008033)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone-glutamine methyltransferase activity (GO:1990259)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)	9	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		CCTTAGCCCCCGGTTTGATGT	0.577													C|||	12	0.00239617	0.0076	0.0	5008	,	,		20414	0.0		0.0	False		,,,				2504	0.002				p.P159P		Atlas-SNP	.											.	FBL	37	.	0			c.G477A						PASS	.	C		35,4371	40.0+/-72.8	0,35,2168	143.0	128.0	133.0		477	-9.6	0.9	19	dbSNP_134	133	0,8600		0,0,4300	no	coding-synonymous	FBL	NM_001436.3		0,35,6468	TT,TC,CC		0.0,0.7944,0.2691		159/322	40329747	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	2091	exon5			AGCCCCCGGTTTG	AC005393	CCDS12545.1	19q13.1	2010-02-17			ENSG00000105202	ENSG00000105202			3599	protein-coding gene	gene with protein product		134795				1846968, 2026646	Standard	NM_001436		Approved	RNU3IP1, FLRN, FIB	uc002omn.3	P22087		ENST00000221801.3:c.477G>A	19.37:g.40329747C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	183	81	0.442623	NM_001436	B5BUE8|O75259|Q6IAT5|Q9UPI6	Silent	SNP	ENST00000221801.3	37	CCDS12545.1																																																																																			C|0.996;T|0.004	0.004	strong		0.577	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436	
SPTBN5	51332	hgsc.bcm.edu	37	15	42171483	42171483	+	Missense_Mutation	SNP	G	G	A	rs1197682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42171483G>A	ENST00000320955.6	-	16	3384	c.3157C>T	c.(3157-3159)Cac>Tac	p.H1053Y		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1053				H -> Y (in Ref. 1; AAF65317). {ECO:0000305}.	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)		TGGAGGAAGTGGACCCTCCTC	0.642													G|||	646	0.128994	0.2163	0.0879	5008	,	,		18981	0.1954		0.0517	False		,,,				2504	0.0511				p.H1018Y		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C3052T						PASS	.	G	TYR/HIS	745,3323		60,625,1349	50.0	54.0	53.0		3052	-0.5	0.0	15	dbSNP_87	53	386,8012		11,364,3824	yes	missense	SPTBN5	NM_016642.2	83	71,989,5173	AA,AG,GG		4.5963,18.3137,9.0727	benign	1018/3640	42171483	1131,11335	2034	4199	6233	SO:0001583	missense	51332	exon16			GGAAGTGGACCCT	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.3157C>T	15.37:g.42171483G>A	ENSP00000317790:p.His1053Tyr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		275	0.1259157509157509	99	0.20121951219512196	23	0.06353591160220995	114	0.1993006993006993	39	0.051451187335092345	.	12.68	2.011168	0.35511	0.183137	0.045963	ENSG00000137877	ENST00000320955	T	0.34859	1.34	4.4	-0.479	0.12089	.	1.280010	0.05249	N	0.513514	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.22800	-1.0206	6	0.52906	T	0.07	.	5.4222	0.16405	0.4059:0.2244:0.3697:0.0	rs1197682;rs1624838;rs57712460;rs1197682	.	.	.	Y	1053	ENSP00000317790:H1053Y	ENSP00000317790:H1053Y	H	-	1	0	SPTBN5	39958775	0.224000	0.23674	0.000000	0.03702	0.488000	0.33401	0.878000	0.28126	-0.003000	0.14444	0.313000	0.20887	CAC	G|0.866;A|0.134	0.134	strong		0.642	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
CDX1	1044	hgsc.bcm.edu	37	5	149562398	149562398	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149562398G>T	ENST00000231656.8	+	2	595	c.513G>T	c.(511-513)aaG>aaT	p.K171N		NM_001804.2	NP_001795.2	P47902	CDX1_HUMAN	caudal type homeobox 1	171					anterior/posterior pattern specification (GO:0009952)|bone morphogenesis (GO:0060349)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	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 positive regulation of transcription (GO:0001205)			central_nervous_system(1)|kidney(2)|lung(1)|ovary(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGCTGGAGAAGGAGTTTCATT	0.552																																					p.K171N		Atlas-SNP	.											.	CDX1	11	.	0			c.G513T						PASS	.						139.0	140.0	140.0					5																	149562398		2203	4300	6503	SO:0001583	missense	1044	exon2			GGAGAAGGAGTTT	U51095	CCDS4304.1	5q32	2012-03-09	2007-07-09		ENSG00000113722	ENSG00000113722		"""Homeoboxes / ANTP class : HOXL subclass"""	1805	protein-coding gene	gene with protein product		600746	"""caudal type homeo box transcription factor 1"""			8530027	Standard	NM_001804		Approved		uc003lrq.3	P47902	OTTHUMG00000169772	ENST00000231656.8:c.513G>T	5.37:g.149562398G>T	ENSP00000231656:p.Lys171Asn	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	160	71	0.44375	NM_001804	Q4VAU4|Q9NYK8	Missense_Mutation	SNP	ENST00000231656.8	37	CCDS4304.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.156375	0.78114	.	.	ENSG00000113722	ENST00000231656;ENST00000377812	D	0.96491	-4.03	5.87	3.03	0.35002	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.110690	0.64402	D	0.000012	D	0.97170	0.9075	M	0.65677	2.01	0.80722	D	1	D	0.56287	0.975	D	0.67900	0.954	D	0.96399	0.9295	10	0.87932	D	0	-13.0587	11.532	0.50616	0.1832:0.0:0.8168:0.0	.	171	P47902	CDX1_HUMAN	N	171;60	ENSP00000231656:K171N	ENSP00000231656:K171N	K	+	3	2	CDX1	149542591	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.447000	0.52936	0.342000	0.23796	-0.345000	0.07892	AAG	.	.	none		0.552	CDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252328.7	NM_001804	
TRPM1	4308	hgsc.bcm.edu	37	15	31294714	31294714	+	Nonsense_Mutation	SNP	C	C	A	rs3784589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31294714C>A	ENST00000256552.6	-	28	4336	c.4189G>T	c.(4189-4191)Gaa>Taa	p.E1397*	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000542188.1_Nonsense_Mutation_p.E1414*|TRPM1_ENST00000397795.2_Nonsense_Mutation_p.E1375*	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)		GAAATAGTTTCTTCTTTTTTA	0.353													C|||	342	0.0682907	0.0772	0.049	5008	,	,		22224	0.0169		0.0616	False		,,,				2504	0.1299				p.E1414X		Atlas-SNP	.											.	TRPM1	183	.	0			c.G4240T	GRCh37	CM068094	TRPM1	M	rs3784589	PASS	.	C	stop/GLU	293,3403		15,263,1570	167.0	155.0	159.0		4123	5.1	0.0	15	dbSNP_107	159	463,7729		11,441,3644	yes	stop-gained	TRPM1	NM_002420.4		26,704,5214	AA,AC,CC		5.6519,7.9275,6.3594		1375/1604	31294714	756,11132	1848	4096	5944	SO:0001587	stop_gained	4308	exon27			TAGTTTCTTCTTT	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.4189G>T	15.37:g.31294714C>A	ENSP00000256552:p.Glu1397*	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_001252020		Nonsense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	110	0.05036630036630037	35	0.07113821138211382	25	0.06906077348066299	13	0.022727272727272728	37	0.048812664907651716	C	39	7.318356	0.98207	0.079275	0.056519	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	.	.	.	5.05	5.05	0.67936	.	1.964930	0.02312	N	0.072176	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-16.3817	11.8701	0.52515	0.0:0.9205:0.0:0.0795	rs3784589;rs52813512;rs59580223;rs3784589	.	.	.	X	1375;1414;1397;1375	.	ENSP00000256552:E1397X	E	-	1	0	TRPM1	29082006	0.979000	0.34478	0.005000	0.12908	0.223000	0.24884	2.601000	0.46249	2.341000	0.79615	0.650000	0.86243	GAA	C|0.940;A|0.060	0.060	strong		0.353	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
MRGPRE	116534	hgsc.bcm.edu	37	11	3249552	3249552	+	Missense_Mutation	SNP	C	C	T	rs4391795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:3249552C>T	ENST00000389832.5	-	2	784	c.478G>A	c.(478-480)Ggc>Agc	p.G160S	AC109309.4_ENST00000418995.2_RNA|MRGPRE_ENST00000436689.2_Missense_Mutation_p.G159S			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	30	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	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	
DIAPH2	1730	hgsc.bcm.edu	37	X	96354707	96354707	+	Silent	SNP	T	T	C	rs20387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:96354707T>C	ENST00000324765.8	+	20	2609	c.2262T>C	c.(2260-2262)caT>caC	p.H754H	DIAPH2_ENST00000373054.4_Silent_p.H750H|DIAPH2_ENST00000355827.4_Silent_p.H754H|DIAPH2_ENST00000373049.4_Silent_p.H754H|DIAPH2_ENST00000373061.3_Silent_p.H754H			O60879	DIAP2_HUMAN	diaphanous-related formin 2	754	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						TTGTGAAACATCTTCCTGAGC	0.308													T|||	17	0.00450331	0.0121	0.0014	3775	,	,		10804	0.0		0.0	False		,,,				2504	0.0				p.H754H		Atlas-SNP	.											.	DIAPH2	148	.	0			c.T2262C						PASS	.	T	,	74,3761		0,62,12,1570,559	84.0	69.0	74.0		2262,2262	0.1	0.9	X	dbSNP_67	74	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	DIAPH2	NM_006729.4,NM_007309.3	,	0,62,13,3998,2430	CC,CT,C,TT,T		0.0149,1.9296,0.71	,	754/1102,754/1097	96354707	75,10488	2203	4300	6503	SO:0001819	synonymous_variant	1730	exon20			GAAACATCTTCCT	Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"""diaphanous (Drosophila, homolog) 2"", ""diaphanous homolog 2 (Drosophila)"""			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.2262T>C	X.37:g.96354707T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	142	75	0.528169	NM_007309	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Silent	SNP	ENST00000324765.8	37	CCDS14467.1																																																																																			T|0.993;C|0.007	0.007	strong		0.308	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309	
C1orf177	163747	hgsc.bcm.edu	37	1	55277553	55277553	+	Silent	SNP	C	C	T	rs61691036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55277553C>T	ENST00000371273.3	+	5	582	c.567C>T	c.(565-567)tcC>tcT	p.S189S	C1orf177_ENST00000358193.3_Silent_p.S189S	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	189										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						GGTCTCATTCCGAGGGCCTCA	0.617													C|||	73	0.0145767	0.0522	0.0029	5008	,	,		17175	0.0		0.0	False		,,,				2504	0.002				p.S189S		Atlas-SNP	.											.	C1orf177	36	.	0			c.C567T						PASS	.	C	,	248,4158	145.0+/-179.8	10,228,1965	75.0	70.0	71.0		567,567	-0.4	0.9	1	dbSNP_129	71	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	C1orf177	NM_001110533.1,NM_152607.2	,	10,230,6263	TT,TC,CC		0.0233,5.6287,1.9222	,	189/419,189/415	55277553	250,12756	2203	4300	6503	SO:0001819	synonymous_variant	163747	exon5			TCATTCCGAGGGC	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.567C>T	1.37:g.55277553C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	214	112	0.523364	NM_001110533	B7WPL2|Q8N7Y9	Silent	SNP	ENST00000371273.3	37	CCDS44153.1																																																																																			C|0.979;T|0.021	0.021	strong		0.617	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
OR10J3	441911	hgsc.bcm.edu	37	1	159283746	159283746	+	Missense_Mutation	SNP	T	T	C	rs11265165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159283746T>C	ENST00000332217.5	-	1	703	c.704A>G	c.(703-705)cAg>cGg	p.Q235R		NM_001004467.1	NP_001004467.1	Q5JRS4	O10J3_HUMAN	olfactory receptor, family 10, subfamily J, member 3	235			Q -> R (in dbSNP:rs11265165).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(19)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	47	all_hematologic(112;0.0429)					GGCCTTCTTCTGACCTTCAGC	0.517													C|||	981	0.195887	0.1793	0.1326	5008	,	,		22333	0.4236		0.0964	False		,,,				2504	0.1309				p.Q235R		Atlas-SNP	.											OR10J3,NS,carcinoma,+1,1	OR10J3	86	1	0			c.A704G						PASS	.	C	ARG/GLN	670,3736	763.6+/-413.2	48,574,1581	154.0	133.0	140.0		704	4.4	0.1	1	dbSNP_120	140	675,7925	788.9+/-407.6	31,613,3656	yes	missense	OR10J3	NM_001004467.1	43	79,1187,5237	CC,CT,TT		7.8488,15.2065,10.3414	benign	235/330	159283746	1345,11661	2203	4300	6503	SO:0001583	missense	441911	exon1			TTCTTCTGACCTT		CCDS30909.1	1q23.2	2012-08-09		2004-03-10	ENSG00000196266	ENSG00000196266		"""GPCR / Class A : Olfactory receptors"""	14992	protein-coding gene	gene with protein product				OR10J3P			Standard	NM_001004467		Approved		uc010piu.2	Q5JRS4	OTTHUMG00000037233	ENST00000332217.5:c.704A>G	1.37:g.159283746T>C	ENSP00000331789:p.Gln235Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_001004467		Missense_Mutation	SNP	ENST00000332217.5	37	CCDS30909.1	461	0.21108058608058608	108	0.21951219512195122	41	0.1132596685082873	245	0.42832167832167833	67	0.08839050131926121	C	0.007	-1.989593	0.00439	0.152065	0.078488	ENSG00000196266	ENST00000332217	T	0.00011	9.35	5.34	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.683552	0.10890	N	0.622781	T	0.00012	0.0000	N	0.00088	-2.19	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.08806	-1.0704	9	0.02654	T	1	.	10.2643	0.43445	0.0:0.8398:0.0:0.1602	rs11265165;rs52807905;rs60024036;rs11265165	235	Q5JRS4	O10J3_HUMAN	R	235	ENSP00000331789:Q235R	ENSP00000331789:Q235R	Q	-	2	0	OR10J3	157550370	0.000000	0.05858	0.086000	0.20670	0.392000	0.30506	-0.024000	0.12435	0.835000	0.34877	-0.119000	0.15052	CAG	T|0.843;C|0.157	0.157	strong		0.517	OR10J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090629.1		
RYR2	6262	hgsc.bcm.edu	37	1	237620034	237620034	+	Splice_Site	SNP	G	G	A	rs78281932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:237620034G>A	ENST00000366574.2	+	16	1928	c.1611G>A	c.(1609-1611)ctG>ctA	p.L537L	RYR2_ENST00000542537.1_Splice_Site_p.L521L|RYR2_ENST00000360064.6_Splice_Site_p.L535L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	537					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATGAGTTGCTGGGTAAGAAGC	0.433													G|||	300	0.0599042	0.2148	0.0202	5008	,	,		18734	0.0		0.001	False		,,,				2504	0.001				p.L537L		Atlas-SNP	.											.	RYR2	1273	.	0			c.G1611A						PASS	.	G		683,3123		48,587,1268	158.0	154.0	155.0		1611	-3.0	1.0	1	dbSNP_131	155	10,8242		0,10,4116	yes	coding-synonymous-near-splice	RYR2	NM_001035.2		48,597,5384	AA,AG,GG		0.1212,17.9453,5.7472		537/4968	237620034	693,11365	1903	4126	6029	SO:0001630	splice_region_variant	6262	exon16			GTTGCTGGGTAAG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.1612+1G>A	1.37:g.237620034G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			G|0.960;A|0.040	0.040	strong		0.433	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	Silent
SARS2	54938	hgsc.bcm.edu	37	19	39410465	39410465	+	Silent	SNP	G	G	A	rs35389151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39410465G>A	ENST00000221431.6	-	7	855	c.696C>T	c.(694-696)cgC>cgT	p.R232R	SARS2_ENST00000448145.2_Silent_p.R232R|SARS2_ENST00000430193.3_Silent_p.R232R|SARS2_ENST00000598831.1_5'Flank|SARS2_ENST00000594171.1_Silent_p.R42R|SARS2_ENST00000600042.1_Silent_p.R234R|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.R302W	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	232					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CTCCAGCCCCGCGCAGGTAAT	0.652													g|||	4	0.000798722	0.0015	0.0	5008	,	,		15718	0.001		0.0	False		,,,				2504	0.001				p.R234R		Atlas-SNP	.											.	SARS2	33	.	0			c.C702T						PASS	.	G	,	23,4383	28.1+/-56.4	0,23,2180	36.0	37.0	37.0		702,696	-9.3	0.2	19	dbSNP_126	37	5,8595	5.0+/-18.6	0,5,4295	no	coding-synonymous,coding-synonymous	SARS2	NM_001145901.1,NM_017827.3	,	0,28,6475	AA,AG,GG		0.0581,0.522,0.2153	,	234/521,232/519	39410465	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	54938	exon8			AGCCCCGCGCAGG	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"""Aminoacyl tRNA synthetases / Class II"""	17697	protein-coding gene	gene with protein product	"""serine tRNA ligase 2, mitochondrial"""	612804	"""serine-tRNA ligase, mitochondrial"", ""seryl-tRNA synthetase 2"""	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.696C>T	19.37:g.39410465G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	153	80	0.522876	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	37	CCDS33017.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	g	4.214	0.038427	0.08148	0.00522	5.81E-4	ENSG00000104835	ENST00000455102	T	0.30182	1.54	4.63	-9.26	0.00662	.	.	.	.	.	T	0.11410	0.0278	.	.	.	.	.	.	.	.	.	.	.	.	T	0.17319	-1.0373	5	0.18710	T	0.47	.	9.0126	0.36150	0.6017:0.0:0.1514:0.2469	rs35389151	.	.	.	V	211	ENSP00000414954:A211V	ENSP00000414954:A211V	A	-	2	0	FBXO17	44102305	0.000000	0.05858	0.195000	0.23364	0.321000	0.28281	-4.751000	0.00190	-2.795000	0.00354	-4.032000	0.00013	GCG	G|0.997;A|0.003	0.003	strong		0.652	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827	
CFAP69	79846	hgsc.bcm.edu	37	7	89933362	89933362	+	Silent	SNP	G	G	A	rs17867249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:89933362G>A	ENST00000389297.4	+	18	2381	c.2130G>A	c.(2128-2130)gcG>gcA	p.A710A	C7orf63_ENST00000497910.1_Silent_p.A692A|C7orf63_ENST00000316089.8_Intron	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		710										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						CATCTATTGCGGTTATGGATG	0.348													G|||	605	0.120807	0.2572	0.1196	5008	,	,		14843	0.1677		0.002	False		,,,				2504	0.0112				p.A710A		Atlas-SNP	.											.	C7orf63	158	.	0			c.G2130A						PASS	.	G	,	290,1094		28,234,430	171.0	158.0	162.0		2130,2076	-3.9	1.0	7	dbSNP_123	162	12,3170		0,12,1579	no	coding-synonymous,coding-synonymous	C7orf63	NM_001039706.2,NM_001160138.1	,	28,246,2009	AA,AG,GG		0.3771,20.9538,6.6141	,	710/942,692/924	89933362	302,4264	692	1591	2283	SO:0001819	synonymous_variant	79846	exon18			TATTGCGGTTATG																												ENST00000389297.4:c.2130G>A	7.37:g.89933362G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	105	42	0.4	NM_001039706	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Silent	SNP	ENST00000389297.4	37	CCDS43613.2	284	0.13003663003663005	144	0.2926829268292683	40	0.11049723756906077	99	0.17307692307692307	1	0.0013192612137203166	G	9.140	1.013602	0.19277	0.209538	0.003771	ENSG00000105792	ENST00000412839	.	.	.	5.57	-3.86	0.04230	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999998247	.	.	.	.	.	.	T	0.41288	-0.9517	3	.	.	.	-16.1843	0.4558	0.00508	0.2662:0.1645:0.2854:0.2839	rs17867249;rs58377189;rs17867249	.	.	.	S	5	.	.	G	+	1	0	C7orf63	89771298	0.953000	0.32496	0.951000	0.38953	0.873000	0.50193	0.010000	0.13242	-0.492000	0.06687	-0.982000	0.02568	GGT	G|0.865;A|0.135	0.135	strong		0.348	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4		
SGSM1	129049	hgsc.bcm.edu	37	22	25294155	25294155	+	Missense_Mutation	SNP	A	A	C	rs6004350	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25294155A>C	ENST00000400359.4	+	20	2411	c.2404A>C	c.(2404-2406)Acg>Ccg	p.T802P	SNORD56_ENST00000362913.1_RNA|SGSM1_ENST00000400358.4_Missense_Mutation_p.T747P	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	802	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		T -> P (in dbSNP:rs6004350).			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						GAACACCCCCACGGTGCTGCG	0.627													C|||	496	0.0990415	0.3578	0.0317	5008	,	,		20487	0.0		0.001	False		,,,				2504	0.0				p.T802P		Atlas-SNP	.											SGSM1_ENST00000400359,NS,carcinoma,-1,2	SGSM1	150	2	0			c.A2404C						PASS	.	C	PRO/THR,PRO/THR,PRO/THR,PRO/THR	1165,3097		173,819,1139	52.0	64.0	60.0		2404,2239,2056,2221	0.4	0.0	22	dbSNP_114	60	10,8508		0,10,4249	yes	missense,missense,missense,missense	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	38,38,38,38	173,829,5388	CC,CA,AA		0.1174,27.3346,9.1941	benign,benign,benign,benign	802/1149,747/1094,686/1033,741/1088	25294155	1175,11605	2131	4259	6390	SO:0001583	missense	129049	exon20			ACCCCCACGGTGC	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.2404A>C	22.37:g.25294155A>C	ENSP00000383212:p.Thr802Pro	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	118	66	0.559322	NM_001039948	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	37	CCDS46674.1	169	0.07738095238095238	159	0.3231707317073171	10	0.027624309392265192	0	0.0	0	0.0	C	2.963	-0.214065	0.06101	0.273346	0.001174	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.07021	3.23;3.24	5.24	0.383	0.16239	Rab-GAP/TBC domain (2);	0.597033	0.15795	N	0.244222	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.48875	-0.8996	9	0.28530	T	0.3	-11.8193	5.2429	0.15481	0.2279:0.4713:0.2332:0.0676	rs6004350;rs52792982;rs6004350	747;802;819;802	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	P	802;747;802	ENSP00000383211:T747P;ENSP00000383212:T802P	ENSP00000383211:T747P	T	+	1	0	SGSM1	23624155	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.080000	0.14802	0.007000	0.14760	-0.187000	0.12897	ACG	A|0.872;C|0.128	0.128	strong		0.627	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
CABLES2	81928	hgsc.bcm.edu	37	20	60968596	60968596	+	Silent	SNP	A	A	G	rs1570027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60968596A>G	ENST00000279101.5	-	6	788	c.780T>C	c.(778-780)caT>caC	p.H260H		NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	260					cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCAGCAGGCCATGGCTGTCAC	0.592													A|||	1014	0.202476	0.2035	0.2666	5008	,	,		19142	0.1498		0.2336	False		,,,				2504	0.1779				p.H260H		Atlas-SNP	.											.	CABLES2	30	.	0			c.T780C						PASS	.	A		1036,3370	381.6+/-324.1	114,808,1281	119.0	117.0	117.0		780	-6.5	0.1	20	dbSNP_88	117	1917,6683	338.5+/-322.8	228,1461,2611	no	coding-synonymous	CABLES2	NM_031215.2		342,2269,3892	GG,GA,AA		22.2907,23.5134,22.7049		260/479	60968596	2953,10053	2203	4300	6503	SO:0001819	synonymous_variant	81928	exon6			CAGGCCATGGCTG	BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679			16143	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 150"""	C20orf150		12477932	Standard	NM_031215		Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.780T>C	20.37:g.60968596A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	141	75	0.531915	NM_031215	Q5JWL0|Q9BYK0	Silent	SNP	ENST00000279101.5	37	CCDS33503.1	436	0.19963369963369965	104	0.21138211382113822	102	0.281767955801105	64	0.11188811188811189	166	0.21899736147757257	A	0.144	-1.099321	0.01843	0.235134	0.222907	ENSG00000149679	ENST00000453274	.	.	.	5.15	-6.47	0.01902	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.12192	-1.0557	3	.	.	.	-24.4711	14.808	0.69971	0.4038:0.0:0.5962:0.0	rs1570027;rs1570027	.	.	.	T	54	.	.	M	-	2	0	CABLES2	60401991	0.000000	0.05858	0.058000	0.19502	0.035000	0.12851	-1.013000	0.03645	-1.179000	0.02737	-0.468000	0.05107	ATG	A|0.785;G|0.215	0.215	strong		0.592	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080027.2	XM_037265	
USP35	57558	hgsc.bcm.edu	37	11	77921013	77921013	+	Silent	SNP	A	A	G	rs78142936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77921013A>G	ENST00000529308.1	+	10	2373	c.2112A>G	c.(2110-2112)ggA>ggG	p.G704G	USP35_ENST00000530267.1_Silent_p.G272G|USP35_ENST00000526425.1_Silent_p.G435G|USP35_ENST00000530535.1_3'UTR|USP35_ENST00000441408.2_Silent_p.G290G	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	704	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)			gaggggaaggagagagggaga	0.547													A|||	394	0.0786741	0.2814	0.0231	5008	,	,		18681	0.0		0.005	False		,,,				2504	0.001				p.G704G		Atlas-SNP	.											.	USP35	179	.	0			c.A2112G						PASS	.	A		976,3208		101,774,1217	46.0	61.0	56.0		2112	0.8	0.0	11	dbSNP_131	56	25,8435		1,23,4206	no	coding-synonymous	USP35	NM_020798.2		102,797,5423	GG,GA,AA		0.2955,23.327,7.9168		704/1019	77921013	1001,11643	2092	4230	6322	SO:0001819	synonymous_variant	57558	exon10			GGAAGGAGAGAGG	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.2112A>G	11.37:g.77921013A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_020798		Silent	SNP	ENST00000529308.1	37	CCDS41693.1																																																																																			A|0.935;G|0.065	0.065	strong		0.547	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
ADAM18	8749	hgsc.bcm.edu	37	8	39581395	39581395	+	Missense_Mutation	SNP	T	T	A	rs79109719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39581395T>A	ENST00000265707.5	+	19	2191	c.2146T>A	c.(2146-2148)Tca>Aca	p.S716T	ADAM18_ENST00000523755.1_3'UTR|ADAM18_ENST00000541111.1_Missense_Mutation_p.S130T|ADAM18_ENST00000379866.1_Missense_Mutation_p.S692T	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	716					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)			AATAAGTAAATCATGTAACAG	0.308													T|||	141	0.028155	0.0998	0.0101	5008	,	,		14093	0.0		0.002	False		,,,				2504	0.0				p.S716T		Atlas-SNP	.											.	ADAM18	169	.	0			c.T2146A						PASS	.		THR/SER	403,4001	192.3+/-217.7	22,359,1821	99.0	104.0	102.0		2146	2.3	0.0	8	dbSNP_131	102	3,8591	2.2+/-6.3	0,3,4294	yes	missense	ADAM18	NM_014237.2	58	22,362,6115	AA,AT,TT		0.0349,9.1508,3.1236	benign	716/740	39581395	406,12592	2202	4297	6499	SO:0001583	missense	8749	exon19			AGTAAATCATGTA	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.2146T>A	8.37:g.39581395T>A	ENSP00000265707:p.Ser716Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	57	0.0260989010989011	51	0.10365853658536585	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	4.809	0.150384	0.09185	0.091508	3.49E-4	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000541111	D;D;D	0.93366	-3.21;-3.21;-3.21	4.77	2.32	0.28847	.	2.401010	0.01912	N	0.039915	T	0.34135	0.0887	L	0.56769	1.78	0.09310	N	1	B;B	0.22604	0.072;0.043	B;B	0.33960	0.173;0.084	T	0.61778	-0.6993	10	0.22706	T	0.39	.	5.2918	0.15731	0.0:0.0953:0.1793:0.7254	.	692;716	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	T	716;692;130	ENSP00000265707:S716T;ENSP00000369195:S692T;ENSP00000444729:S130T	ENSP00000265707:S716T	S	+	1	0	ADAM18	39700552	0.004000	0.15560	0.003000	0.11579	0.007000	0.05969	0.525000	0.22956	0.376000	0.24707	0.451000	0.29950	TCA	T|0.968;A|0.032	0.032	strong		0.308	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
CDH12	1010	hgsc.bcm.edu	37	5	22078584	22078584	+	Missense_Mutation	SNP	C	C	T	rs4371716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:22078584C>T	ENST00000382254.1	-	5	1288	c.202G>A	c.(202-204)Gtg>Atg	p.V68M	CDH12_ENST00000504376.2_Missense_Mutation_p.V68M|CDH12_ENST00000522262.1_Missense_Mutation_p.V68M	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	68	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> M (in dbSNP:rs4371716). {ECO:0000269|PubMed:7731968}.		adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TCGGAGCCCACGTATTCTTCC	0.443										HNSCC(59;0.17)			T|||	1814	0.36222	0.6755	0.2824	5008	,	,		19512	0.1438		0.2396	False		,,,				2504	0.3466				p.V68M		Atlas-SNP	.											CDH12,NS,carcinoma,+2,1	CDH12	238	1	0			c.G202A	GRCh37	CM067358	CDH12	M	rs4371716	PASS	.	T	MET/VAL	2732,1674	508.8+/-367.0	855,1022,326	102.0	102.0	102.0		202	5.5	1.0	5	dbSNP_111	102	2068,6532	718.9+/-406.2	240,1588,2472	yes	missense	CDH12	NM_004061.3	21	1095,2610,2798	TT,TC,CC		24.0465,37.9936,36.906	benign	68/795	22078584	4800,8206	2203	4300	6503	SO:0001583	missense	1010	exon5			AGCCCACGTATTC	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"""Cadherins / Major cadherins"""	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.202G>A	5.37:g.22078584C>T	ENSP00000371689:p.Val68Met	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	194	94	0.484536	NM_004061	B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	37	CCDS3890.1	707	0.32371794871794873	339	0.6890243902439024	97	0.26795580110497236	87	0.1520979020979021	184	0.24274406332453827	T	14.54	2.565803	0.45694	0.620064	0.240465	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.00013	9.26;9.26;9.26	5.5	5.5	0.81552	Cadherin (1);Cadherin-like (1);	0.039736	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00885	-1.115	0.49389	P	2.1700000000002273E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.03493	-1.1031	9	0.24483	T	0.36	.	11.5275	0.50588	0.0:0.0702:0.0:0.9298	rs4371716;rs52822851;rs57140592;rs4371716	68;68	B7Z2U6;P55289	.;CAD12_HUMAN	M	68	ENSP00000423577:V68M;ENSP00000371689:V68M;ENSP00000428786:V68M	ENSP00000371689:V68M	V	-	1	0	CDH12	22114341	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.801000	0.69115	0.931000	0.37242	-0.269000	0.10298	GTG	C|0.643;T|0.357	0.357	strong		0.443	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061	
PXDNL	137902	hgsc.bcm.edu	37	8	52325767	52325767	+	Missense_Mutation	SNP	T	T	G	rs16916207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:52325767T>G	ENST00000356297.4	-	15	1947	c.1847A>C	c.(1846-1848)gAt>gCt	p.D616A	PXDNL_ENST00000543296.1_Missense_Mutation_p.D616A	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	616			D -> A (in dbSNP:rs16916207).		hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CTGTACAGCATCAAGAATGGA	0.343													T|||	795	0.158746	0.1921	0.0793	5008	,	,		20248	0.2768		0.0865	False		,,,				2504	0.1227				p.D616A		Atlas-SNP	.											.	PXDNL	414	.	0			c.A1847C						PASS	.	T	ALA/ASP	683,3073		64,555,1259	140.0	137.0	138.0		1847	3.6	0.0	8	dbSNP_123	138	720,7538		31,658,3440	yes	missense	PXDNL	NM_144651.4	126	95,1213,4699	GG,GT,TT		8.7188,18.1842,11.678	possibly-damaging	616/1464	52325767	1403,10611	1878	4129	6007	SO:0001583	missense	137902	exon15			ACAGCATCAAGAA		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1847A>C	8.37:g.52325767T>G	ENSP00000348645:p.Asp616Ala	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	341	0.15613553113553114	94	0.1910569105691057	29	0.08011049723756906	152	0.26573426573426573	66	0.0870712401055409	T	11.16	1.557645	0.27827	0.181842	0.087188	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.64085	-0.06;-0.08	4.78	3.61	0.41365	.	.	.	.	.	T	0.00012	0.0000	L	0.44542	1.39	0.43321	P	0.004654999999999965	B	0.25563	0.129	B	0.23419	0.046	T	0.06320	-1.0833	8	0.72032	D	0.01	.	8.6127	0.33813	0.0:0.0935:0.0:0.9064	rs16916207;rs57038753;rs16916207	616	A1KZ92	PXDNL_HUMAN	A	616	ENSP00000348645:D616A;ENSP00000444865:D616A	ENSP00000348645:D616A	D	-	2	0	PXDNL	52488320	0.988000	0.35896	0.017000	0.16124	0.489000	0.33432	4.320000	0.59203	0.674000	0.31244	0.533000	0.62120	GAT	T|0.846;G|0.154	0.154	strong		0.343	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
ATP6V1E2	90423	hgsc.bcm.edu	37	2	46739683	46739683	+	Silent	SNP	A	A	G	rs17035245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:46739683A>G	ENST00000306448.4	-	2	1281	c.168T>C	c.(166-168)taT>taC	p.Y56Y	ATP6V1E2_ENST00000522587.1_Silent_p.Y56Y	NM_080653.3	NP_542384.1	Q96A05	VATE2_HUMAN	ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E2	56					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|proton-transporting two-sector ATPase complex, catalytic domain (GO:0033178)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.151)			TTTTCTCATAATACTCCATAA	0.468													A|||	134	0.0267572	0.0908	0.0187	5008	,	,		21675	0.0		0.001	False		,,,				2504	0.0				p.Y56Y		Atlas-SNP	.											.	ATP6V1E2	25	.	0			c.T168C						PASS	.	A		340,4066	178.0+/-206.8	14,312,1877	203.0	202.0	202.0		168	1.7	1.0	2	dbSNP_123	202	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	ATP6V1E2	NM_080653.3		14,319,6170	GG,GA,AA		0.0814,7.7167,2.668		56/227	46739683	347,12659	2203	4300	6503	SO:0001819	synonymous_variant	90423	exon2			CTCATAATACTCC	BC008981	CCDS1826.1	2p21	2011-02-10	2006-01-13	2002-06-21	ENSG00000250565	ENSG00000250565		"""ATPases / V-type"""	18125	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) 31kD-like 2"", ""ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E isoform 2"""	ATP6EL2, ATP6V1EL2		12036578	Standard	NM_080653		Approved	MGC9341, VMA4, ATP6E1	uc002ruy.3	Q96A05	OTTHUMG00000128819	ENST00000306448.4:c.168T>C	2.37:g.46739683A>G		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	227	120	0.528634	NM_080653		Silent	SNP	ENST00000306448.4	37	CCDS1826.1																																																																																			A|0.964;G|0.036	0.036	strong		0.468	ATP6V1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250753.1	NM_080653	
DEGS2	123099	hgsc.bcm.edu	37	14	100615707	100615707	+	Silent	SNP	G	G	A	rs113575369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:100615707G>A	ENST00000305631.5	-	2	998	c.423C>T	c.(421-423)gaC>gaT	p.D141D	DEGS2_ENST00000557117.1_5'UTR|DEGS2_ENST00000553834.1_Intron	NM_206918.2	NP_996801.2			delta(4)-desaturase, sphingolipid 2											breast(1)|lung(6)|skin(1)	8		Melanoma(154;0.212)				GCACGTCCACGTCCAGCCCGT	0.672													G|||	60	0.0119808	0.0431	0.0043	5008	,	,		16559	0.0		0.0	False		,,,				2504	0.0				p.D141D		Atlas-SNP	.											.	DEGS2	25	.	0			c.C423T						PASS	.	G		130,4272	88.7+/-127.4	1,128,2072	29.0	28.0	29.0		423	-1.0	1.0	14	dbSNP_132	29	1,8595		0,1,4297	no	coding-synonymous	DEGS2	NM_206918.2		1,129,6369	AA,AG,GG		0.0116,2.9532,1.0078		141/324	100615707	131,12867	2201	4298	6499	SO:0001819	synonymous_variant	123099	exon2			GTCCACGTCCAGC		CCDS9956.1	14q32.2	2013-09-02	2011-12-09	2004-12-14	ENSG00000168350	ENSG00000168350		"""Fatty acid desaturases"""	20113	protein-coding gene	gene with protein product	"""sphingolipid delta(4)-desaturase 2"", ""dihydroceramide desaturase 2"""	610862	"""chromosome 14 open reading frame 66"", ""degenerative spermatocyte homolog 2, lipid desaturase (Drosophila)"""	C14orf66			Standard	NM_206918		Approved	DES2, FADS8	uc001ygx.2	Q6QHC5	OTTHUMG00000171537	ENST00000305631.5:c.423C>T	14.37:g.100615707G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	119	67	0.563025	NM_206918		Silent	SNP	ENST00000305631.5	37	CCDS9956.1																																																																																			G|0.991;A|0.009	0.009	strong		0.672	DEGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414003.1	NM_206918	
OPRD1	4985	hgsc.bcm.edu	37	1	29189597	29189597	+	Silent	SNP	C	C	T	rs2234918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	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	
NFASC	23114	hgsc.bcm.edu	37	1	204966428	204966428	+	Missense_Mutation	SNP	C	C	G	rs2802808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204966428C>G	ENST00000401399.1	+	24	3112	c.2913C>G	c.(2911-2913)atC>atG	p.I971M	NFASC_ENST00000495396.1_Intron|NFASC_ENST00000338515.6_Missense_Mutation_p.I1078M|NFASC_ENST00000367169.4_Intron|NFASC_ENST00000367172.4_Missense_Mutation_p.I1078M|NFASC_ENST00000339876.6_Missense_Mutation_p.I971M|NFASC_ENST00000360049.4_Intron|NFASC_ENST00000367170.4_Intron|NFASC_ENST00000404907.1_Intron|NFASC_ENST00000539706.1_Intron|NFASC_ENST00000404076.1_Intron|NFASC_ENST00000367171.4_Missense_Mutation_p.I1063M|NFASC_ENST00000338586.6_Intron|NFASC_ENST00000513543.1_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	223	0	0		WXS	Illumina HiSeq	Phase_I	256	123	0.480469	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	
CACNA1F	778	hgsc.bcm.edu	37	X	49071964	49071964	+	Silent	SNP	A	A	G	rs2075866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49071964A>G	ENST00000376265.2	-	28	3370	c.3309T>C	c.(3307-3309)caT>caC	p.H1103H	CACNA1F_ENST00000323022.5_Silent_p.H1092H|CACNA1F_ENST00000376251.1_Silent_p.H1038H	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1103	Dihydropyridine binding. {ECO:0000250}.				axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AGATGGGGCCATGGTCCTCTG	0.522													g|||	2084	0.552053	0.6278	0.4481	3775	,	,		9881	0.5179		0.2097	False		,,,				2504	0.2147				p.H1103H		Atlas-SNP	.											.	CACNA1F	218	.	0			c.T3309C						PASS	.			2842,993		912,603,415,117,156	99.0	80.0	86.0		3309	-0.1	0.0	X	dbSNP_96	86	1971,4757		217,988,549,1223,1323	no	coding-synonymous	CACNA1F	NM_005183.2		1129,1591,964,1340,1479	GG,GA,G,AA,A		29.2955,25.8931,45.5647		1103/1978	49071964	4813,5750	2203	4300	6503	SO:0001819	synonymous_variant	778	exon28			GGGGCCATGGTCC	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.3309T>C	X.37:g.49071964A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	150	150	1	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	37	CCDS35253.1																																																																																			0|0.014;T|0.004	.	strong		0.522	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
SYDE2	84144	hgsc.bcm.edu	37	1	85666156	85666156	+	Missense_Mutation	SNP	T	T	G	rs12121540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:85666156T>G	ENST00000341460.5	-	1	573	c.524A>C	c.(523-525)cAg>cCg	p.Q175P		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	175				Q -> P (in Ref. 3; BAB14711). {ECO:0000305}.	activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		GGGGCCTTCCTGGCGGTCTCC	0.622													T|||	1525	0.304513	0.1543	0.379	5008	,	,		16400	0.4683		0.2376	False		,,,				2504	0.3548				p.Q175P		Atlas-SNP	.											.	SYDE2	135	.	0			c.A524C						PASS	.	T	PRO/GLN	628,3240		42,544,1348	54.0	57.0	56.0		524	-9.1	0.0	1	dbSNP_120	56	1975,6311		244,1487,2412	yes	missense	SYDE2	NM_032184.1	76	286,2031,3760	GG,GT,TT		23.8354,16.2358,21.4168	benign	175/1195	85666156	2603,9551	1934	4143	6077	SO:0001583	missense	84144	exon1			CCTTCCTGGCGGT	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.524A>C	1.37:g.85666156T>G	ENSP00000340594:p.Gln175Pro	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	CCDS44169.1	657	0.3008241758241758	82	0.16666666666666666	131	0.36187845303867405	278	0.486013986013986	166	0.21899736147757257	T	2.467	-0.322733	0.05350	0.162358	0.238354	ENSG00000097096	ENST00000341460	T	0.06294	3.32	5.07	-9.1	0.00714	.	0.566434	0.15454	N	0.261471	T	0.00524	0.0017	N	0.11201	0.11	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.45175	-0.9279	9	0.09843	T	0.71	.	1.9173	0.03300	0.1694:0.1286:0.2964:0.4057	rs12121540	175;175	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	P	175	ENSP00000340594:Q175P	ENSP00000340594:Q175P	Q	-	2	0	SYDE2	85438744	0.001000	0.12720	0.028000	0.17463	0.036000	0.12997	-0.785000	0.04628	-1.318000	0.02289	-1.843000	0.00578	CAG	T|0.705;G|0.295	0.295	strong		0.622	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2		
RIPPLY3	53820	hgsc.bcm.edu	37	21	38390419	38390419	+	Missense_Mutation	SNP	G	G	A	rs61735126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38390419G>A	ENST00000329553.2	+	4	695	c.485G>A	c.(484-486)cGa>cAa	p.R162Q	RIPPLY3_ENST00000485272.1_3'UTR	NM_018962.2	NP_061835.1	P57055	DSCR6_HUMAN	ripply transcriptional repressor 3	162					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pharyngeal system development (GO:0060037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)											CAAGGGCAGCGATCCTCAGGA	0.627													G|||	67	0.0133786	0.0469	0.0058	5008	,	,		16442	0.0		0.001	False		,,,				2504	0.0				p.R162Q		Atlas-SNP	.											.	DSCR6	16	.	0			c.G485A						PASS	.	G	GLN/ARG	146,4260	99.4+/-138.0	4,138,2061	47.0	46.0	46.0		485	0.1	0.0	21	dbSNP_129	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DSCR6	NM_018962.2	43	4,139,6360	AA,AG,GG		0.0116,3.3137,1.1302	probably-damaging	162/191	38390419	147,12859	2203	4300	6503	SO:0001583	missense	53820	exon4			GGCAGCGATCCTC	AB037158	CCDS13648.1	21q22.2	2013-07-23	2013-07-23	2013-06-04	ENSG00000183145	ENSG00000183145			3047	protein-coding gene	gene with protein product		609892	"""Down syndrome critical region gene 6"", ""ripply3 homolog (zebrafish)"""	DSCR6		10814524, 22354841	Standard	NM_018962		Approved			P57055	OTTHUMG00000086639	ENST00000329553.2:c.485G>A	21.37:g.38390419G>A	ENSP00000331734:p.Arg162Gln	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_018962		Missense_Mutation	SNP	ENST00000329553.2	37	CCDS13648.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	10.33	1.319066	0.23994	0.033137	1.16E-4	ENSG00000183145	ENST00000329553	.	.	.	3.52	0.127	0.14727	.	1.934300	0.03067	N	0.156638	T	0.06188	0.0160	N	0.19112	0.55	0.09310	N	1	D	0.63880	0.993	P	0.46543	0.52	T	0.12967	-1.0527	9	0.45353	T	0.12	2.0523	6.2061	0.20604	0.0:0.4264:0.3815:0.1922	rs61735126	162	P57055	DSCR6_HUMAN	Q	162	.	ENSP00000331734:R162Q	R	+	2	0	DSCR6	37312289	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.614000	0.05604	0.232000	0.21100	-0.311000	0.09066	CGA	G|0.989;A|0.011	0.011	strong		0.627	RIPPLY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194703.1		
MROH6	642475	hgsc.bcm.edu	37	8	144654693	144654693	+	Silent	SNP	G	G	C	rs4873804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144654693G>C	ENST00000398882.3	-	1	448	c.192C>G	c.(190-192)ccC>ccG	p.P64P	RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000460623.1_5'Flank|MROH6_ENST00000533679.1_5'Flank	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	64																	CTGCCTCAGAGGGGGCGGTGA	0.706													g|||	1597	0.31889	0.1067	0.415	5008	,	,		13924	0.3562		0.5239	False		,,,				2504	0.2883				p.P64P		Atlas-SNP	.											C8orf73_ENST00000398882,NS,carcinoma,0,2	.	.	2	0			c.C192G						PASS	.			651,3315		56,539,1388	16.0	20.0	19.0		192	-1.1	0.0	8	dbSNP_111	19	4348,3946		1199,1950,998	no	coding-synonymous	C8orf73	NM_001100878.1		1255,2489,2386	CC,CG,GG		47.5766,16.4145,40.7749		64/720	144654693	4999,7261	1983	4147	6130	SO:0001819	synonymous_variant	642475	exon1			CTCAGAGGGGGCG	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"""maestro heat-like repeat containing"""	27814	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 73"""	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.192C>G	8.37:g.144654693G>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_001100878	A8MWB1	Silent	SNP	ENST00000398882.3	37	CCDS47928.1																																																																																			G|0.624;C|0.376	0.376	strong		0.706	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878	
PARP15	165631	hgsc.bcm.edu	37	3	122351055	122351055	+	Missense_Mutation	SNP	G	G	A	rs34383355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122351055G>A	ENST00000464300.2	+	10	1627	c.1561G>A	c.(1561-1563)Gca>Aca	p.A521T	PARP15_ENST00000310366.4_Missense_Mutation_p.A287T|PARP15_ENST00000483793.1_Missense_Mutation_p.A326T|PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000493645.1_Missense_Mutation_p.A218T	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	521	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.		A -> T (in dbSNP:rs34383355).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		TTCTTCCTACGCAATAGAGAA	0.358													G|||	100	0.0199681	0.0734	0.0029	5008	,	,		22011	0.0		0.001	False		,,,				2504	0.0				p.A521T		Atlas-SNP	.											PARP15_ENST00000464300,NS,carcinoma,0,2	PARP15	115	2	0			c.G1561A						PASS	.	G	THR/ALA,THR/ALA	252,4154	145.7+/-180.5	6,240,1957	64.0	63.0	63.0		859,1561	-7.6	0.0	3	dbSNP_126	63	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	PARP15	NM_152615.1,NM_001113523.1	58,58	6,243,6254	AA,AG,GG		0.0349,5.7195,1.9606	benign,benign	287/445,521/679	122351055	255,12751	2203	4300	6503	SO:0001583	missense	165631	exon10			TCCTACGCAATAG	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1561G>A	3.37:g.122351055G>A	ENSP00000417214:p.Ala521Thr	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	23	15	0.652174	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	32	0.014652014652014652	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	1.319	-0.600018	0.03744	0.057195	3.49E-4	ENSG00000173200	ENST00000464300;ENST00000483793;ENST00000542823;ENST00000310366;ENST00000493645	T;T;T;T	0.12984	2.63;2.63;2.63;2.63	3.77	-7.55	0.01327	Poly(ADP-ribose) polymerase, catalytic domain (2);	.	.	.	.	T	0.00384	0.0012	N	0.01576	-0.805	0.09310	N	1	B;B;B;B;B	0.17465	0.0;0.0;0.0;0.022;0.0	B;B;B;B;B	0.10450	0.002;0.0;0.0;0.005;0.002	T	0.43376	-0.9395	9	0.13470	T	0.59	.	6.614	0.22766	0.2724:0.3821:0.3455:0.0	rs34383355;rs56885169	218;287;268;326;499	B7ZL48;Q460N3-2;F5H8I1;C9J7L3;Q460N3	.;.;.;.;PAR15_HUMAN	T	521;326;268;287;218	ENSP00000417214:A521T;ENSP00000417785:A326T;ENSP00000308436:A287T;ENSP00000419488:A218T	ENSP00000308436:A287T	A	+	1	0	PARP15	123833745	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.060000	0.14342	-1.640000	0.01525	-1.085000	0.02201	GCA	G|0.981;A|0.019	0.019	strong		0.358	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
KIF21A	55605	hgsc.bcm.edu	37	12	39734066	39734066	+	Silent	SNP	T	T	G	rs150241656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:39734066T>G	ENST00000361418.5	-	16	2226	c.2211A>C	c.(2209-2211)gcA>gcC	p.A737A	KIF21A_ENST00000361961.3_Silent_p.A724A|KIF21A_ENST00000395670.3_Silent_p.A737A|KIF21A_ENST00000544797.2_Silent_p.A724A|KIF21A_ENST00000541463.2_Silent_p.A724A			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	737					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)				CTTTTTGAGCTGCTTGAAGTC	0.363													T|||	6	0.00119808	0.0045	0.0	5008	,	,		18446	0.0		0.0	False		,,,				2504	0.0				p.A737A		Atlas-SNP	.											.	KIF21A	238	.	0			c.A2211C						PASS	.	T	,,,	31,4375	36.8+/-68.6	0,31,2172	125.0	109.0	114.0		2172,2211,2172,2172	-4.0	0.8	12	dbSNP_134	114	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF21A	NM_001173463.1,NM_001173464.1,NM_001173465.1,NM_017641.3	,,,	0,31,6470	GG,GT,TT		0.0,0.7036,0.2384	,,,	724/1638,737/1675,724/1622,724/1662	39734066	31,12971	2203	4298	6501	SO:0001819	synonymous_variant	55605	exon16			TTGAGCTGCTTGA	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.2211A>C	12.37:g.39734066T>G		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	269	136	0.505576	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Silent	SNP	ENST00000361418.5	37	CCDS53776.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	10.31	1.314750	0.23908	0.007036	0.0	ENSG00000139116	ENST00000552961	.	.	.	5.22	-4.01	0.04045	.	.	.	.	.	T	0.38665	0.1049	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40327	-0.9569	4	.	.	.	.	5.0229	0.14370	0.5061:0.2038:0.0:0.2901	.	.	.	.	P	85	.	.	Q	-	2	0	KIF21A	38020333	0.026000	0.19158	0.768000	0.31515	0.987000	0.75469	-1.450000	0.02390	-0.615000	0.05679	0.533000	0.62120	CAG	T|0.998;G|0.002	0.002	strong		0.363	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
CCT8	10694	hgsc.bcm.edu	37	21	30433876	30433876	+	Missense_Mutation	SNP	C	C	T	rs8129954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:30433876C>T	ENST00000286788.4	-	12	1431	c.1225G>A	c.(1225-1227)Gta>Ata	p.V409I	CCT8_ENST00000470450.1_5'UTR|CCT8_ENST00000540844.1_Missense_Mutation_p.V336I|CCT8_ENST00000542732.1_Missense_Mutation_p.V390I|AF129075.5_ENST00000457162.2_RNA	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	409			V -> I (in dbSNP:rs8129954).		'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						CCTCCGGGTACAAGACGTTTA	0.363													C|||	115	0.0229633	0.0809	0.0043	5008	,	,		17710	0.003		0.002	False		,,,				2504	0.0				p.V409I		Atlas-SNP	.											.	CCT8	38	.	0			c.G1225A						PASS	.	C	ILE/VAL	346,4060	179.0+/-207.6	14,318,1871	87.0	83.0	84.0		1225	4.3	1.0	21	dbSNP_116	84	3,8597	2.2+/-6.3	0,3,4297	yes	missense	CCT8	NM_006585.2	29	14,321,6168	TT,TC,CC		0.0349,7.8529,2.6834	benign	409/549	30433876	349,12657	2203	4300	6503	SO:0001583	missense	10694	exon12			CGGGTACAAGACG	Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"""Heat Shock Proteins / Chaperonins"""	1623	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 112"""	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595	ENST00000286788.4:c.1225G>A	21.37:g.30433876C>T	ENSP00000286788:p.Val409Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Missense_Mutation	SNP	ENST00000286788.4	37	CCDS33528.1	30	0.013736263736263736	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	15.31	2.797070	0.50208	0.078529	3.49E-4	ENSG00000156261	ENST00000389159;ENST00000286788;ENST00000542732;ENST00000540844	D;D;D	0.82526	-1.62;-1.62;-1.62	5.19	4.3	0.51218	.	0.194901	0.43110	D	0.000602	T	0.28067	0.0692	M	0.64260	1.97	0.44454	D	0.997383	B;B;B;B;B	0.22746	0.074;0.057;0.071;0.058;0.01	B;B;B;B;B	0.35770	0.151;0.151;0.21;0.133;0.019	T	0.66638	-0.5873	10	0.51188	T	0.08	-15.0082	15.657	0.77144	0.1381:0.8619:0.0:0.0	rs8129954;rs8129954	336;390;409;408;409	B4DQH4;B4DEM7;Q53HU0;G5E9B2;P50990	.;.;.;.;TCPQ_HUMAN	I	408;409;390;336	ENSP00000286788:V409I;ENSP00000444984:V390I;ENSP00000442730:V336I	ENSP00000286788:V409I	V	-	1	0	CCT8	29355747	1.000000	0.71417	0.994000	0.49952	0.915000	0.54546	2.928000	0.48908	1.542000	0.49330	0.650000	0.86243	GTA	C|0.973;T|0.027	0.027	strong		0.363	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1		
FBXL4	26235	hgsc.bcm.edu	37	6	99374436	99374436	+	Silent	SNP	T	T	C	rs17058965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:99374436T>C	ENST00000369244.2	-	4	857	c.429A>G	c.(427-429)ctA>ctG	p.L143L	FBXL4_ENST00000229971.1_Silent_p.L143L	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	143					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		GATAGGTTTCTAGAACATGTA	0.418													T|||	21	0.00419329	0.0151	0.0014	5008	,	,		19281	0.0		0.0	False		,,,				2504	0.0				p.L143L		Atlas-SNP	.											.	FBXL4	54	.	0			c.A429G						PASS	.	T		59,4347	57.4+/-93.9	0,59,2144	93.0	82.0	86.0		429	1.5	1.0	6	dbSNP_123	86	0,8600		0,0,4300	no	coding-synonymous	FBXL4	NM_012160.3		0,59,6444	CC,CT,TT		0.0,1.3391,0.4536		143/622	99374436	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	26235	exon3			GGTTTCTAGAACA	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"""F-boxes / Leucine-rich repeats"""	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.429A>G	6.37:g.99374436T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	157	78	0.496815	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Silent	SNP	ENST00000369244.2	37	CCDS5041.1																																																																																			T|0.996;C|0.004	0.004	strong		0.418	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2		
GABRG3	2567	hgsc.bcm.edu	37	15	27765155	27765155	+	Silent	SNP	T	T	C	rs34130136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:27765155T>C	ENST00000333743.6	+	7	1004	c.750T>C	c.(748-750)agT>agC	p.S250S	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	250					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)	TTGAATTGAGTAGAAGAATGG	0.328													T|||	50	0.00998403	0.0371	0.0014	5008	,	,		17163	0.0		0.0	False		,,,				2504	0.0				p.S250S	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.T750C						PASS	.	T		103,3561		0,103,1729	66.0	60.0	62.0		750	-0.9	1.0	15	dbSNP_126	62	1,8171		0,1,4085	no	coding-synonymous	GABRG3	NM_033223.4		0,104,5814	CC,CT,TT		0.0122,2.8111,0.8787		250/468	27765155	104,11732	1832	4086	5918	SO:0001819	synonymous_variant	2567	exon7			ATTGAGTAGAAGA		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.750T>C	15.37:g.27765155T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	36	0.428571	NM_033223	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	T	9.515	1.106645	0.20714	0.028111	1.22E-4	ENSG00000182256	ENST00000451330	.	.	.	5.35	-0.876	0.10624	.	.	.	.	.	T	0.32823	0.0842	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43909	-0.9362	4	.	.	.	.	10.5939	0.45325	0.0:0.4796:0.0:0.5204	rs34130136	.	.	.	A	13	.	.	V	+	2	0	GABRG3	25438750	0.958000	0.32768	0.995000	0.50966	0.985000	0.73830	0.034000	0.13776	-0.058000	0.13177	-0.334000	0.08254	GTA	T|0.993;C|0.007	0.007	strong		0.328	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
NLRX1	79671	hgsc.bcm.edu	37	11	119052826	119052826	+	Missense_Mutation	SNP	C	C	A	rs4245191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119052826C>A	ENST00000409109.1	+	9	2965	c.2378C>A	c.(2377-2379)gCg>gAg	p.A793E	NLRX1_ENST00000292199.2_Missense_Mutation_p.A793E|NLRX1_ENST00000409991.1_Missense_Mutation_p.A793E|NLRX1_ENST00000409265.4_Missense_Mutation_p.A793E|NLRX1_ENST00000525863.1_Missense_Mutation_p.A793E	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	793	Required for the repression of MAVS- induced interferon signaling.		A -> E (in dbSNP:rs4245191). {ECO:0000269|PubMed:12766759, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)		CCGCTGACGGCGGCAGGTGTT	0.632													C|||	3447	0.688299	0.708	0.4179	5008	,	,		18563	0.8839		0.5477	False		,,,				2504	0.7965				p.A793E		Atlas-SNP	.											.	NLRX1	128	.	0			c.C2378A						PASS	.	C	GLU/ALA,GLU/ALA	2971,1429	652.9+/-399.5	1024,923,253	124.0	118.0	120.0		2378,2378	2.9	0.0	11	dbSNP_111	120	4477,4113	565.2+/-388.4	1172,2133,990	yes	missense,missense	NLRX1	NM_024618.2,NM_170722.1	107,107	2196,3056,1243	AA,AC,CC		47.8813,32.4773,42.6636	benign,benign	793/976,793/922	119052826	7448,5542	2200	4295	6495	SO:0001583	missense	79671	exon9			TGACGGCGGCAGG	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.2378C>A	11.37:g.119052826C>A	ENSP00000387334:p.Ala793Glu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	1419	0.6497252747252747	349	0.709349593495935	166	0.4585635359116022	496	0.8671328671328671	408	0.5382585751978892	C	0.006	-2.091840	0.00364	0.675227	0.521187	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	4.78	2.91	0.33838	.	0.152719	0.40640	N	0.001049	T	0.00012	0.0000	N	0.03115	-0.41	0.54753	P	1.799999999996249E-5	B;B	0.15719	0.014;0.007	B;B	0.17979	0.02;0.006	T	0.40590	-0.9555	9	0.02654	T	1	.	6.5557	0.22460	0.1759:0.6611:0.0:0.163	rs4245191;rs17627663;rs17845376;rs17858230;rs61333211;rs4245191	793;793	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	E	793	ENSP00000386851:A793E;ENSP00000292199:A793E;ENSP00000386858:A793E;ENSP00000387334:A793E;ENSP00000433442:A793E	ENSP00000292199:A793E	A	+	2	0	NLRX1	118558036	0.979000	0.34478	0.018000	0.16275	0.003000	0.03518	2.559000	0.45888	0.628000	0.30357	0.609000	0.83330	GCG	C|0.378;A|0.622	0.622	strong		0.632	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	
LCE3C	353144	hgsc.bcm.edu	37	1	152573464	152573464	+	Missense_Mutation	SNP	G	G	A	rs148755167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152573464G>A	ENST00000333881.3	+	1	327	c.257G>A	c.(256-258)cGt>cAt	p.R86H		NM_178434.2	NP_848521.1	Q5T5A8	LCE3C_HUMAN	late cornified envelope 3C	86					keratinization (GO:0031424)					lung(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0313)|Kidney(5;0.0367)		GGCTCCTGCCGTGGCCATGGC	0.597													G|||	62	0.0123802	0.0469	0.0	5008	,	,		6910	0.0		0.0	False		,,,				2504	0.0				p.R86H		Atlas-SNP	.											.	LCE3C	3	.	0			c.G257A						PASS	.	G	HIS/ARG	128,3478		23,82,1698	32.0	32.0	32.0		257	3.1	0.5	1	dbSNP_134	32	2,5326		0,2,2662	no	missense	LCE3C	NM_178434.2	29	23,84,4360	AA,AG,GG		0.0375,3.5496,1.4551	benign	86/95	152573464	130,8804	1803	2664	4467	SO:0001583	missense	353144	exon1			CCTGCCGTGGCCA	BI670516	CCDS1015.1	1q21.3	2008-02-05		2004-10-15	ENSG00000244057	ENSG00000244057		"""Late cornified envelopes"""	16612	protein-coding gene	gene with protein product		612615	"""small proline rich-like (epidermal differentiation complex) 3A"""	SPRL3A		11698679	Standard	NM_178434		Approved	LEP15	uc001fac.2	Q5T5A8	OTTHUMG00000014403	ENST00000333881.3:c.257G>A	1.37:g.152573464G>A	ENSP00000334644:p.Arg86His	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	161	79	0.490683	NM_178434	A1L420	Missense_Mutation	SNP	ENST00000333881.3	37	CCDS1015.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	G	3.891	-0.024030	0.07634	0.035496	3.75E-4	ENSG00000244057	ENST00000333881	T	0.03524	3.9	4.01	3.08	0.35506	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.09310	N	1	B	0.18741	0.03	B	0.06405	0.002	T	0.47156	-0.9139	8	0.29301	T	0.29	.	9.3733	0.38268	0.0:0.2192:0.7808:0.0	.	86	Q5T5A8	LCE3C_HUMAN	H	86	ENSP00000334644:R86H	ENSP00000334644:R86H	R	+	2	0	LCE3C	150840088	0.520000	0.26250	0.478000	0.27316	0.166000	0.22503	1.037000	0.30241	0.858000	0.35431	0.313000	0.20887	CGT	G|0.988;A|0.012	0.012	strong		0.597	LCE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040061.2	NM_178434	
OR4X1	390113	hgsc.bcm.edu	37	11	48285424	48285424	+	Silent	SNP	A	A	G	rs713323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48285424A>G	ENST00000320048.1	+	1	12	c.12A>G	c.(10-12)acA>acG	p.T4T		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						TGGTTGCTACAAACAATGTGA	0.428													A|||	80	0.0159744	0.0575	0.0058	5008	,	,		20768	0.0		0.0	False		,,,				2504	0.0				p.T4T		Atlas-SNP	.											.	OR4X1	75	.	0			c.A12G						PASS	.	A		203,4199	125.7+/-162.9	5,193,2003	94.0	90.0	91.0		12	-1.7	0.0	11	dbSNP_86	91	0,8596		0,0,4298	no	coding-synonymous	OR4X1	NM_001004726.1		5,193,6301	GG,GA,AA		0.0,4.6115,1.5618		4/306	48285424	203,12795	2201	4298	6499	SO:0001819	synonymous_variant	390113	exon1			TGCTACAAACAAT	AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"""GPCR / Class A : Olfactory receptors"""	14854	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily X, member 1"""				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.12A>G	11.37:g.48285424A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	167	82	0.491018	NM_001004726	Q6IF74	Silent	SNP	ENST00000320048.1	37	CCDS31487.1																																																																																			A|0.982;G|0.018	0.018	strong		0.428	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726	
STX1A	6804	hgsc.bcm.edu	37	7	73122923	73122923	+	Silent	SNP	A	A	G	rs2228607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73122923A>G	ENST00000222812.3	-	3	230	c.204T>C	c.(202-204)gaT>gaC	p.D68D	STX1A_ENST00000395155.3_Silent_p.D68D|MIR4284_ENST00000578924.1_RNA|STX1A_ENST00000395154.3_Silent_p.D68D|STX1A_ENST00000395156.3_Silent_p.D68D	NM_004603.3	NP_004594.1	Q16623	STX1A_HUMAN	syntaxin 1A (brain)	68					calcium ion-dependent exocytosis (GO:0017156)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of insulin secretion (GO:0050796)|response to gravity (GO:0009629)|secretion by cell (GO:0032940)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)	actomyosin (GO:0042641)|cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synaptic vesicle membrane (GO:0030672)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)	calcium channel inhibitor activity (GO:0019855)			large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(55;0.0908)|all_lung(88;0.198)				ACTCACTCTCATCGGGGTTGG	0.632													A|||	2289	0.457069	0.5008	0.3948	5008	,	,		15594	0.4067		0.5596	False		,,,				2504	0.3885				p.D68D		Atlas-SNP	.											.	STX1A	16	.	0			c.T204C	GRCh37	CM014827	STX1A	M	rs2228607	PASS	.	A	,	2228,2178	586.6+/-386.5	564,1100,539	85.0	62.0	70.0		204,204	-6.4	0.9	7	dbSNP_98	70	4870,3730	610.7+/-395.7	1398,2074,828	no	coding-synonymous,coding-synonymous	STX1A	NM_001165903.1,NM_004603.3	,	1962,3174,1367	GG,GA,AA		43.3721,49.4326,45.4252	,	68/252,68/289	73122923	7098,5908	2203	4300	6503	SO:0001819	synonymous_variant	6804	exon3			ACTCTCATCGGGG		CCDS34655.1, CCDS55120.1	7q11.2	2008-07-18			ENSG00000106089	ENSG00000106089			11433	protein-coding gene	gene with protein product		186590		STX1		1321498	Standard	NM_001165903		Approved	HPC-1, p35-1	uc003tyx.3	Q16623	OTTHUMG00000137422	ENST00000222812.3:c.204T>C	7.37:g.73122923A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	110	41	0.372727	NM_004603	O15447|O15448|Q12936|Q75MD9|Q7Z5K3|Q9BPZ6	Silent	SNP	ENST00000222812.3	37	CCDS34655.1																																																																																			A|0.473;G|0.527	0.527	strong		0.632	STX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268422.1	NM_004603	
KCND1	3750	hgsc.bcm.edu	37	X	48820064	48820064	+	Silent	SNP	G	G	A	rs3027483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48820064G>A	ENST00000218176.3	-	6	3019	c.1722C>T	c.(1720-1722)cgC>cgT	p.R574R	KCND1_ENST00000376477.1_Silent_p.R197R	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	574					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	TGAGGCTGGAGCGGCTGTGGA	0.577													g|||	357	0.0945695	0.2602	0.0187	3775	,	,		12645	0.0		0.0	False		,,,				2504	0.0				p.R574R		Atlas-SNP	.											.	KCND1	63	.	0			c.C1722T						PASS	.			1078,2757		136,643,163,853,408	34.0	33.0	33.0		1722	4.0	1.0	X	dbSNP_102	33	5,6723		0,3,2,2425,1870	no	coding-synonymous	KCND1	NM_004979.4		136,646,165,3278,2278	AA,AG,A,GG,G		0.0743,28.1095,10.2528		574/648	48820064	1083,9480	2203	4300	6503	SO:0001819	synonymous_variant	3750	exon6			GCTGGAGCGGCTG	AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.1722C>T	X.37:g.48820064G>A		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	280	135	0.482143	NM_004979	A6NEF1|B2RCG0|O75671	Silent	SNP	ENST00000218176.3	37	CCDS14314.1																																																																																			G|0.884;A|0.116	0.116	strong		0.577	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979	
LRP2	4036	hgsc.bcm.edu	37	2	170063471	170063471	+	Silent	SNP	A	A	G	rs35114151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170063471A>G	ENST00000263816.3	-	39	7044	c.6759T>C	c.(6757-6759)gaT>gaC	p.D2253D		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2253					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)"""	TATCTAAAGAATCATCAACCC	0.448													A|||	303	0.0605032	0.115	0.013	5008	,	,		19993	0.0308		0.0308	False		,,,				2504	0.0818				p.D2253D		Atlas-SNP	.											.	LRP2	751	.	0			c.T6759C						PASS	.	A		474,3932	224.9+/-240.9	21,432,1750	145.0	144.0	144.0		6759	3.2	1.0	2	dbSNP_126	144	180,8420	82.0+/-144.6	3,174,4123	no	coding-synonymous	LRP2	NM_004525.2		24,606,5873	GG,GA,AA		2.093,10.7581,5.0284		2253/4656	170063471	654,12352	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon39			TAAAGAATCATCA		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.6759T>C	2.37:g.170063471A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	36	0.371134	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			A|0.954;G|0.046	0.046	strong		0.448	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
TLR10	81793	hgsc.bcm.edu	37	4	38776303	38776303	+	Silent	SNP	T	T	C	rs11466652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38776303T>C	ENST00000308973.4	-	4	1514	c.909A>G	c.(907-909)aaA>aaG	p.K303K	TLR10_ENST00000508334.1_Silent_p.K303K|TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000506111.1_Silent_p.K303K|TLR10_ENST00000361424.2_Silent_p.K303K	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	303					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						CATGCTCCAATTTTATAGTTC	0.343													T|||	1009	0.201478	0.3374	0.0994	5008	,	,		19962	0.122		0.1481	False		,,,				2504	0.227				p.K303K		Atlas-SNP	.											TLR10,NS,carcinoma,-2,1	TLR10	87	1	0			c.A909G						PASS	.	T	,,,,	1253,3153	423.6+/-340.2	167,919,1117	83.0	85.0	85.0		909,909,909,867,909	1.3	0.8	4	dbSNP_120	85	1200,7398	241.4+/-271.8	85,1030,3184	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	,,,,	252,1949,4301	CC,CT,TT		13.9567,28.4385,18.8634	,,,,	303/812,303/812,303/812,289/798,303/812	38776303	2453,10551	2203	4299	6502	SO:0001819	synonymous_variant	81793	exon2			CTCCAATTTTATA	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.909A>G	4.37:g.38776303T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																			T|0.814;C|0.186	0.186	strong		0.343	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201822	32201822	+	RNA	SNP	G	G	T	rs9982910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:32201822G>T	ENST00000452750.1	-	0	256							Q8IUC3	KRA71_HUMAN	keratin associated protein 7-1 (gene/pseudogene)							intermediate filament (GO:0005882)											CATAGCAGCCGCCCAGGTTGT	0.562													G|||	2458	0.490815	0.4266	0.6354	5008	,	,		18563	0.4405		0.4781	False		,,,				2504	0.5399				p.G65G		Atlas-SNP	.											.	.	.	.	0			c.C195A						PASS	.	G		607,777		141,325,226	65.0	67.0	66.0		196	3.4	0.0	21	dbSNP_119	66	1360,1822		278,804,509	no	coding-synonymous	KRTAP7-1	NM_181606.2		419,1129,735	TT,TG,GG		42.7404,43.8584,43.0793		65/88	32201822	1967,2599	692	1591	2283			337878	exon2			GCAGCCGCCCAGG	AJ457063	CCDS74780.1	21q22.1	2014-04-10	2010-03-12		ENSG00000184586	ENSG00000274749		"""Keratin associated proteins"""	18934	protein-coding gene	gene with protein product			"""keratin associated protein 7-1"""			12359730	Standard	NM_181606		Approved	KAP7.1	uc011adj.2	Q8IUC3	OTTHUMG00000188305		21.37:g.32201822G>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	209	95	0.454545	NM_181606	Q3LI56	Silent	SNP	ENST00000452750.1	37																																																																																				G|0.504;T|0.496	0.496	strong		0.562	KRTAP7-1-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000128248.3	NM_181606	
MST1L	11223	hgsc.bcm.edu	37	1	17083839	17083839	+	RNA	SNP	A	A	T	rs549455414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17083839A>T	ENST00000455405.2	-	0	749							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										AATTCCTTTCAGGACCCAGCA	0.577													.|||	182	0.0363419	0.1293	0.0159	5008	,	,		38722	0.0		0.0	False		,,,				2504	0.0				p.L653Q		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,+1,1	.	.	1	0			c.T1958A						PASS	.																																					11223	exon15			CCTTTCAGGACCC	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.17083839A>T		Somatic	420	0	0		WXS	Illumina HiSeq	Phase_I	500	151	0.302	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	13.19	2.163948	0.38217	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.32753	N	0.005696	T	0.64057	0.2564	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.67914	-0.5547	6	0.52906	T	0.07	.	5.2253	0.15391	0.9998:0.0:2.0E-4:0.0	.	653;679	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	Q	653;679	.	ENSP00000439273:L653Q	L	-	2	0	MST1P9	16956426	1.000000	0.71417	0.950000	0.38849	0.000000	0.00434	5.601000	0.67606	0.419000	0.25927	0.000000	0.15137	CTG	.	.	none		0.577	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
INADL	10207	hgsc.bcm.edu	37	1	62455982	62455982	+	Silent	SNP	G	G	A	rs6681983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62455982G>A	ENST00000371158.2	+	28	3927	c.3813G>A	c.(3811-3813)ccG>ccA	p.P1271P	INADL_ENST00000545929.1_5'UTR|INADL_ENST00000316485.6_Silent_p.P1271P|INADL_ENST00000543708.1_Silent_p.P55P	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1271	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						GAATTAACCCGGAAGGACCTG	0.433													G|||	99	0.0197684	0.0711	0.0072	5008	,	,		15469	0.0		0.0	False		,,,				2504	0.0				p.P1271P		Atlas-SNP	.											.	INADL	179	.	0			c.G3813A						PASS	.	G		187,4219	119.6+/-157.3	4,179,2020	94.0	89.0	90.0		3813	-11.7	0.0	1	dbSNP_116	90	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	INADL	NM_176877.2		4,182,6317	AA,AG,GG		0.0349,4.2442,1.4609		1271/1802	62455982	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	10207	exon28			TAACCCGGAAGGA	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.3813G>A	1.37:g.62455982G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			G|0.985;A|0.015	0.015	strong		0.433	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
SGK223	157285	hgsc.bcm.edu	37	8	8234714	8234714	+	Missense_Mutation	SNP	C	C	T	rs3896980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8234714C>T	ENST00000520004.1	-	3	1469	c.1205G>A	c.(1204-1206)cGg>cAg	p.R402Q	SGK223_ENST00000330777.4_Missense_Mutation_p.R402Q			Q86YV5	SG223_HUMAN		404							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TGTAGCCTCCCGGGGGTGGGC	0.642													C|||	2283	0.455871	0.3903	0.4366	5008	,	,		16058	0.6409		0.3052	False		,,,				2504	0.5225				p.R402Q	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G1205A						PASS	.	C	GLN/ARG	1363,2447		257,849,799	28.0	32.0	31.0		1205	1.0	0.0	8	dbSNP_108	31	2494,5700		391,1712,1994	yes	missense	SGK223	NM_001080826.1	43	648,2561,2793	TT,TC,CC		30.4369,35.7743,32.131	probably-damaging	402/1403	8234714	3857,8147	1905	4097	6002	SO:0001583	missense	0	exon2			GCCTCCCGGGGGT																												ENST00000520004.1:c.1205G>A	8.37:g.8234714C>T	ENSP00000428054:p.Arg402Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	961	0.440018315018315	202	0.4105691056910569	144	0.39779005524861877	392	0.6853146853146853	223	0.2941952506596306	C	8.815	0.936192	0.18206	0.357743	0.304369	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.57595	0.39;0.39	5.02	1.03	0.20045	.	0.467819	0.18850	N	0.129440	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	P	0.40398	0.716	B	0.22880	0.042	T	0.45862	-0.9232	9	0.35671	T	0.21	.	0.8844	0.01241	0.1558:0.3864:0.1731:0.2847	rs3896980;rs60739349	402	Q86YV5	SG223_HUMAN	Q	402	ENSP00000330930:R402Q;ENSP00000428054:R402Q	ENSP00000330930:R402Q	R	-	2	0	AC068353.1	8272124	0.000000	0.05858	0.016000	0.15963	0.307000	0.27823	0.001000	0.13038	0.644000	0.30656	-0.136000	0.14681	CGG	C|0.612;T|0.388	0.388	strong		0.642	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
MGAT1	4245	hgsc.bcm.edu	37	5	180218820	180218820	+	Silent	SNP	C	C	A	rs2070925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180218820C>A	ENST00000446023.2	-	3	1902	c.1152G>T	c.(1150-1152)gtG>gtT	p.V384V	MGAT1_ENST00000427865.2_Silent_p.V384V|MGAT1_ENST00000307826.4_Silent_p.V384V|MGAT1_ENST00000393340.3_Silent_p.V384V|MGAT1_ENST00000333055.3_Silent_p.V384V	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	384					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|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)			ACTGCACCCGCACCTCCCCCA	0.622													C|||	622	0.124201	0.1369	0.0432	5008	,	,		18103	0.1984		0.0547	False		,,,				2504	0.1595				p.V384V		Atlas-SNP	.											.	MGAT1	48	.	0			c.G1152T						PASS	.	C	,,,,	474,3932	224.9+/-240.9	29,416,1758	76.0	66.0	69.0		1152,1152,1152,1152,1152	-0.4	1.0	5	dbSNP_96	69	311,8289	112.1+/-172.3	9,293,3998	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	,,,,	38,709,5756	AA,AC,CC		3.6163,10.7581,6.0357	,,,,	384/446,384/446,384/446,384/446,384/446	180218820	785,12221	2203	4300	6503	SO:0001819	synonymous_variant	4245	exon3			CACCCGCACCTCC	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.1152G>T	5.37:g.180218820C>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Silent	SNP	ENST00000446023.2	37	CCDS4458.1																																																																																			C|0.928;A|0.072	0.072	strong		0.622	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
ARID3C	138715	hgsc.bcm.edu	37	9	34622389	34622389	+	Missense_Mutation	SNP	A	A	C	rs3808869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:34622389A>C	ENST00000378909.2	-	5	1095	c.1003T>G	c.(1003-1005)Tgc>Ggc	p.C335G	DCTN3_ENST00000378913.2_5'Flank|DCTN3_ENST00000447983.2_5'Flank|DCTN3_ENST00000378916.4_5'Flank|DCTN3_ENST00000341694.2_5'Flank|DCTN3_ENST00000259632.7_5'Flank|DCTN3_ENST00000477738.2_5'Flank	NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	335	Pro-rich.|REKLES. {ECO:0000255|PROSITE- ProRule:PRU00819}.		C -> G (in dbSNP:rs3808869).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		GGGGGCATGCAAGGTCGAGGT	0.627													C|||	3017	0.602436	0.7723	0.598	5008	,	,		16667	0.4802		0.4692	False		,,,				2504	0.6391				p.C335G		Atlas-SNP	.											.	ARID3C	33	.	0			c.T1003G						PASS	.	C	GLY/CYS	3203,1203	415.9+/-337.4	1171,861,171	45.0	47.0	46.0		1003	0.3	0.0	9	dbSNP_107	46	4398,4202	567.4+/-388.8	1127,2144,1029	yes	missense	ARID3C	NM_001017363.1	159	2298,3005,1200	CC,CA,AA		48.8605,27.3037,41.5577	benign	335/413	34622389	7601,5405	2203	4300	6503	SO:0001583	missense	138715	exon5			GCATGCAAGGTCG		CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"""-"""	21209	protein-coding gene	gene with protein product			"""AT rich interactive domain 3C (BRIGHT- like)"""				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.1003T>G	9.37:g.34622389A>C	ENSP00000368189:p.Cys335Gly	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_001017363		Missense_Mutation	SNP	ENST00000378909.2	37	CCDS35006.1	1233	0.5645604395604396	369	0.75	206	0.569060773480663	294	0.513986013986014	364	0.48021108179419525	C	0.022	-1.413812	0.01145	0.726963	0.511395	ENSG00000205143	ENST00000378909	T	0.38401	1.14	4.61	0.293	0.15742	REKLES domain (1);	0.347888	0.21170	N	0.078986	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	0.27157	-1.0082	9	0.09084	T	0.74	0.5687	4.0924	0.09975	0.2786:0.4597:0.0:0.2617	rs3808869;rs52800005;rs58670080;rs3808869	335	A6NKF2	ARI3C_HUMAN	G	335	ENSP00000368189:C335G	ENSP00000368189:C335G	C	-	1	0	ARID3C	34612389	0.000000	0.05858	0.003000	0.11579	0.980000	0.70556	-0.178000	0.09782	-0.044000	0.13491	-0.232000	0.12228	TGC	A|0.428;C|0.572	0.572	strong		0.627	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061	
EID3	493861	hgsc.bcm.edu	37	12	104698265	104698265	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:104698265C>T	ENST00000527879.1	+	1	749	c.553C>T	c.(553-555)Cga>Tga	p.R185*	TXNRD1_ENST00000354940.6_Intron|TXNRD1_ENST00000525566.1_Intron|TXNRD1_ENST00000524698.1_Intron|TXNRD1_ENST00000540716.1_Intron|TXNRD1_ENST00000378070.4_Intron|TXNRD1_ENST00000542918.1_Intron|TXNRD1_ENST00000503506.2_Intron|TXNRD1_ENST00000429002.2_Intron|TXNRD1_ENST00000388854.3_Intron|TXNRD1_ENST00000526691.1_Intron|TXNRD1_ENST00000397736.2_Intron|TXNRD1_ENST00000526390.1_Intron|TXNRD1_ENST00000529546.1_Intron	NM_001008394.2	NP_001008395.1			EP300 interacting inhibitor of differentiation 3											large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						ACCAAAGCCCCGACTTGAACA	0.428																																					p.R185X		Atlas-SNP	.											EID3,rectum,carcinoma,-1,2	EID3	28	2	0			c.C553T						scavenged	.						123.0	121.0	122.0					12																	104698265		1894	4117	6011	SO:0001587	stop_gained	493861	exon1			AAGCCCCGACTTG	BC027612	CCDS53822.1	12q23.3	2006-11-24				ENSG00000255150			32961	protein-coding gene	gene with protein product		612986				15987788, 15752197	Standard	NM_001008394		Approved	FLJ25832, NSMCE4B, NSE4B	uc001tkw.3	Q8N140		ENST00000527879.1:c.553C>T	12.37:g.104698265C>T	ENSP00000435619:p.Arg185*	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	68	2	0.0294118	NM_001008394		Nonsense_Mutation	SNP	ENST00000527879.1	37	CCDS53822.1	.	.	.	.	.	.	.	.	.	.	C	33	5.215137	0.95104	.	.	ENSG00000255150	ENST00000527879	.	.	.	4.94	4.05	0.47172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.1803	0.37138	0.0:0.902:0.0:0.098	.	.	.	.	X	185	.	ENSP00000435619:R185X	R	+	1	2	EID3	103222395	0.421000	0.25465	0.017000	0.16124	0.228000	0.25075	1.104000	0.31074	1.469000	0.48083	0.555000	0.69702	CGA	.	.	none		0.428	EID3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387034.1	NM_001008394	
MUC17	140453	hgsc.bcm.edu	37	7	100677645	100677645	+	Missense_Mutation	SNP	C	C	A	rs114262718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677645C>A	ENST00000306151.4	+	3	3012	c.2948C>A	c.(2947-2949)aCt>aAt	p.T983N		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	983	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)					GAAGGAACGACTCCATTAACA	0.512																																					p.T983N		Atlas-SNP	.											.	MUC17	804	.	0			c.C2948A						PASS	.	C	ASN/THR	294,4112	131.8+/-168.3	0,294,1909	370.0	334.0	346.0		2948	0.4	0.0	7	dbSNP_133	346	181,8419	61.0+/-122.8	0,181,4119	no	missense	MUC17	NM_001040105.1	65	0,475,6028	AA,AC,CC		2.1047,6.6727,3.6522	probably-damaging	983/4494	100677645	475,12531	2203	4300	6503	SO:0001583	missense	140453	exon3			GAACGACTCCATT	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.2948C>A	7.37:g.100677645C>A	ENSP00000302716:p.Thr983Asn	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	270	53	0.196296	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	1.988	-0.432413	0.04669	0.066727	0.021047	ENSG00000169876	ENST00000306151	T	0.02472	4.28	0.373	0.373	0.16178	.	.	.	.	.	T	0.00412	0.0013	N	0.24115	0.695	0.09310	N	1	D	0.64830	0.994	D	0.65010	0.931	T	0.50065	-0.8871	9	0.49607	T	0.09	.	6.6259	0.22828	0.0:0.9998:0.0:2.0E-4	.	983	Q685J3	MUC17_HUMAN	N	983	ENSP00000302716:T983N	ENSP00000302716:T983N	T	+	2	0	MUC17	100464365	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.193000	0.17116	0.472000	0.27344	0.134000	0.15878	ACT	C|0.936;A|0.064	0.064	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
RPA1	6117	hgsc.bcm.edu	37	17	1782957	1782957	+	Silent	SNP	C	C	T	rs2230930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	89	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	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	
STRIP2	57464	hgsc.bcm.edu	37	7	129098602	129098602	+	Missense_Mutation	SNP	G	G	A	rs571423095		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:129098602G>A	ENST00000249344.2	+	11	1364	c.1324G>A	c.(1324-1326)Gga>Aga	p.G442R	STRIP2_ENST00000435494.2_Missense_Mutation_p.G442R	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	442					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)		p.G442R(1)									CAAGTTCATCGGATTCACCCT	0.517													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17567	0.0		0.0	False		,,,				2504	0.0				p.G442R		Atlas-SNP	.											FAM40B,lymph_node,lymphoid_neoplasm,0,1	.	.	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1324A						PASS	.						110.0	95.0	100.0					7																	129098602		2203	4300	6503	SO:0001583	missense	57464	exon11			TTCATCGGATTCA	AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog B (yeast)"""		"""family with sequence similarity 40, member B"""	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.1324G>A	7.37:g.129098602G>A	ENSP00000249344:p.Gly442Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	112	45	0.401786	NM_020704	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.608630	0.87258	.	.	ENSG00000128578	ENST00000249344;ENST00000435494;ENST00000450266	T;T	0.48836	0.8;0.8	5.34	5.34	0.76211	.	0.102042	0.64402	D	0.000002	T	0.73087	0.3542	M	0.85099	2.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.76016	-0.3113	10	0.54805	T	0.06	-3.4152	18.3766	0.90437	0.0:0.0:1.0:0.0	.	442;442	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	R	442;442;113	ENSP00000249344:G442R;ENSP00000392393:G442R	ENSP00000249344:G442R	G	+	1	0	FAM40B	128885838	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.747000	0.98863	2.655000	0.90218	0.561000	0.74099	GGA	.	.	none		0.517	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336	
ANKRD53	79998	hgsc.bcm.edu	37	2	71212380	71212380	+	Silent	SNP	C	C	A	rs61732288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71212380C>A	ENST00000360589.3	+	6	1577	c.1543C>A	c.(1543-1545)Cga>Aga	p.R515R	AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000272421.6_3'UTR|ANKRD53_ENST00000457410.1_Silent_p.R481R|ANKRD53_ENST00000441349.1_3'UTR	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	515										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						GGCAGCTGTGCGATCTCATCA	0.572											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	184	0.0367412	0.1331	0.0101	5008	,	,		13411	0.0		0.001	False		,,,				2504	0.0				p.R515R		Atlas-SNP	.											.	ANKRD53	55	.	0			c.C1543A						PASS	.	C	,	182,1202		12,158,522	31.0	32.0	31.0		1543,	-0.8	0.1	2	dbSNP_129	31	2,3180		0,2,1589	no	coding-synonymous,utr-3	ANKRD53	NM_001115116.1,NM_024933.3	,	12,160,2111	AA,AC,CC		0.0629,13.1503,4.0298	,	515/531,	71212380	184,4382	692	1591	2283	SO:0001819	synonymous_variant	79998	exon6			GCTGTGCGATCTC	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"""Ankyrin repeat domain containing"""	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.1543C>A	2.37:g.71212380C>A		Somatic	134	0	0	1128	WXS	Illumina HiSeq	Phase_I	135	56	0.414815	NM_001115116	Q8IYP8	Silent	SNP	ENST00000360589.3	37	CCDS46321.1																																																																																			C|0.968;A|0.032	0.032	strong		0.572	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933	
TCF12	6938	hgsc.bcm.edu	37	15	57384061	57384061	+	Silent	SNP	A	A	G	rs34560099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:57384061A>G	ENST00000267811.5	+	5	601	c.297A>G	c.(295-297)ccA>ccG	p.P99P	TCF12_ENST00000557843.1_Silent_p.P99P|TCF12_ENST00000333725.5_Silent_p.P99P|TCF12_ENST00000452095.2_Silent_p.P95P|TCF12_ENST00000438423.2_Silent_p.P99P	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	99					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		GCTTGTCCCCAACACCTTTCA	0.423			T	TEC	extraskeletal myxoid chondrosarcoma								A|||	237	0.0473243	0.1626	0.0216	5008	,	,		18239	0.0		0.007	False		,,,				2504	0.0				p.P99P		Atlas-SNP	.		Dom	yes		15	15q21	6938	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""		M	.	TCF12	242	.	0			c.A297G						PASS	.	A	,,,	551,3833	247.8+/-255.9	35,481,1676	109.0	107.0	108.0		297,297,297,297	4.6	1.0	15	dbSNP_126	108	37,8547	25.1+/-72.6	1,35,4256	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCF12	NM_003205.3,NM_207036.1,NM_207037.1,NM_207038.1	,,,	36,516,5932	GG,GA,AA		0.431,12.5684,4.5342	,,,	99/683,99/707,99/707,99/683	57384061	588,12380	2192	4292	6484	SO:0001819	synonymous_variant	6938	exon5			GTCCCCAACACCT	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.297A>G	15.37:g.57384061A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	91	33	0.362637	NM_207036	Q7Z3D9|Q86TC1|Q86VM2	Silent	SNP	ENST00000267811.5	37	CCDS10159.1																																																																																			A|0.959;G|0.041	0.041	strong		0.423	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205	
P2RY1	5028	hgsc.bcm.edu	37	3	152554357	152554357	+	Silent	SNP	A	A	G	rs701265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:152554357A>G	ENST00000305097.3	+	1	1622	c.786A>G	c.(784-786)gtA>gtG	p.V262V	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	262					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TTTACCTGGTAATCATTGTAC	0.433													G|||	1830	0.365415	0.7852	0.2651	5008	,	,		19943	0.248		0.163	False		,,,				2504	0.1984				p.V262V		Atlas-SNP	.											.	P2RY1	49	.	0			c.A786G						PASS	.	G		2983,1423	463.6+/-353.6	1010,963,230	109.0	107.0	108.0		786	-0.1	1.0	3	dbSNP_86	108	1271,7329	760.5+/-407.6	87,1097,3116	no	coding-synonymous	P2RY1	NM_002563.2		1097,2060,3346	GG,GA,AA		14.7791,32.2969,32.708		262/374	152554357	4254,8752	2203	4300	6503	SO:0001819	synonymous_variant	5028	exon1			CCTGGTAATCATT	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.786A>G	3.37:g.152554357A>G		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	187	187	1	NM_002563		Silent	SNP	ENST00000305097.3	37	CCDS3169.1																																																																																			A|0.653;G|0.347	0.347	strong		0.433	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563	
PEX1	5189	hgsc.bcm.edu	37	7	92118654	92118654	+	Silent	SNP	G	G	A	rs34825053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:92118654G>A	ENST00000248633.4	-	23	3815	c.3720C>T	c.(3718-3720)caC>caT	p.H1240H	AC007566.10_ENST00000427458.1_RNA|AC007566.10_ENST00000441539.1_RNA|PEX1_ENST00000428214.1_Silent_p.H1183H|PEX1_ENST00000438045.1_Silent_p.H918H	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	1240					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			ATGGTCTTGTGTGACCAAGTG	0.388													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		15394	0.0		0.0	False		,,,				2504	0.0				p.H1240H		Atlas-SNP	.											.	PEX1	102	.	0			c.C3720T						PASS	.	G		71,4335	64.1+/-101.4	1,69,2133	144.0	115.0	125.0		3720	2.3	0.9	7	dbSNP_126	125	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PEX1	NM_000466.2		1,70,6432	AA,AG,GG		0.0116,1.6114,0.5536		1240/1284	92118654	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	5189	exon23			TCTTGTGTGACCA	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"""ATPases / AAA-type"""	8850	protein-coding gene	gene with protein product		602136	"""peroxisome biogenesis factor 1"", ""Zellweger syndrome 1"", ""Zellweger syndrome"""	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.3720C>T	7.37:g.92118654G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	140	61	0.435714	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	37	CCDS5627.1																																																																																			G|0.992;A|0.008	0.008	strong		0.388	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466	
OR10G7	390265	hgsc.bcm.edu	37	11	123909168	123909168	+	Missense_Mutation	SNP	G	G	A	rs150532549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909168G>A	ENST00000330487.5	-	1	549	c.541C>T	c.(541-543)Ccg>Tcg	p.P181S		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AGGATGGGCGGTGCGTCACAG	0.532																																					p.P181S		Atlas-SNP	.											OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	0			c.C541T						scavenged	.						213.0	204.0	207.0					11																	123909168		2201	4297	6498	SO:0001583	missense	390265	exon1			TGGGCGGTGCGTC	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.541C>T	11.37:g.123909168G>A	ENSP00000329689:p.Pro181Ser	Somatic	504	0	0		WXS	Illumina HiSeq	Phase_I	433	14	0.0323326	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.136481	0.37728	.	.	ENSG00000182634	ENST00000330487	T	0.00202	8.56	3.24	3.24	0.37175	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	D	0.000286	T	0.00384	0.0012	M	0.64404	1.975	0.09310	N	1	D	0.55605	0.972	D	0.65233	0.933	T	0.48559	-0.9025	10	0.62326	D	0.03	.	8.6875	0.34247	0.1098:0.0:0.8902:0.0	.	181	Q8NGN6	O10G7_HUMAN	S	181	ENSP00000329689:P181S	ENSP00000329689:P181S	P	-	1	0	OR10G7	123414378	0.000000	0.05858	0.355000	0.25773	0.884000	0.51177	0.166000	0.16583	1.826000	0.53198	0.455000	0.32223	CCG	G|0.907;A|0.093	0.093	strong		0.532	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
FLG	2312	hgsc.bcm.edu	37	1	152280864	152280864	+	Silent	SNP	A	A	G	rs2184954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152280864A>G	ENST00000368799.1	-	3	6533	c.6498T>C	c.(6496-6498)tcT>tcC	p.S2166S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	428	0	0		WXS	Illumina HiSeq	Phase_I	676	674	0.997041	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	
DNA2	1763	hgsc.bcm.edu	37	10	70225504	70225504	+	Silent	SNP	G	G	T	rs3758626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	77	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	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		
CBLC	23624	hgsc.bcm.edu	37	19	45284495	45284495	+	Missense_Mutation	SNP	C	C	T	rs114569424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45284495C>T	ENST00000270279.3	+	3	595	c.532C>T	c.(532-534)Ctc>Ttc	p.L178F	CBLC_ENST00000341505.4_Missense_Mutation_p.L178F	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	178	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|EF-hand-like.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				GTTTGAGTCCCTCCTGGGCAC	0.652			M		AML								c|||	39	0.00778754	0.0242	0.0058	5008	,	,		16049	0.0		0.0	False		,,,				2504	0.0031				p.L178F		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.C532T						PASS	.		PHE/LEU,PHE/LEU	59,4347		0,59,2144	68.0	57.0	61.0		532,532	1.7	0.0	19	dbSNP_132	61	0,8600		0,0,4300	yes	missense,missense	CBLC	NM_001130852.1,NM_012116.3	22,22	0,59,6444	TT,TC,CC		0.0,1.3391,0.4536	probably-damaging,probably-damaging	178/429,178/475	45284495	59,12947	2203	4300	6503	SO:0001583	missense	23624	exon3			GAGTCCCTCCTGG	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.532C>T	19.37:g.45284495C>T	ENSP00000270279:p.Leu178Phe	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	37	CCDS12643.1	21	0.009615384615384616	17	0.034552845528455285	4	0.011049723756906077	0	0.0	0	0.0	.	12.98	2.099594	0.37048	0.013391	0.0	ENSG00000142273	ENST00000270279;ENST00000341505	D;D	0.87256	-2.23;-2.23	3.95	1.72	0.24424	Adaptor protein Cbl, PTB domain (1);EF-hand-like domain (1);Adaptor protein Cbl, EF hand-like (1);	0.976806	0.08347	N	0.959896	T	0.74238	0.3690	L	0.57536	1.79	0.09310	N	1	D;D	0.61697	0.958;0.99	P;P	0.53549	0.682;0.729	T	0.68142	-0.5487	10	0.23891	T	0.37	-15.6691	7.2319	0.26046	0.1838:0.4585:0.3578:0.0	.	178;178	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	F	178	ENSP00000270279:L178F;ENSP00000340250:L178F	ENSP00000270279:L178F	L	+	1	0	CBLC	49976335	0.003000	0.15002	0.005000	0.12908	0.756000	0.42949	1.111000	0.31159	0.318000	0.23185	0.306000	0.20318	CTC	C|0.994;T|0.006	0.006	strong		0.652	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
ESPL1	9700	hgsc.bcm.edu	37	12	53682326	53682326	+	Silent	SNP	G	G	A	rs1110720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53682326G>A	ENST00000257934.4	+	20	4642	c.4551G>A	c.(4549-4551)ggG>ggA	p.G1517G	ESPL1_ENST00000552462.1_Silent_p.G1517G	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1517					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						CCCCAGGTGGGAAGACTCCAG	0.567											OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3232	0.645367	0.4327	0.6326	5008	,	,		17084	0.8204		0.6382	False		,,,				2504	0.7689				p.G1517G	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.G4551A						PASS	.	G		1951,2455		420,1111,672	27.0	26.0	26.0		4551	3.0	0.8	12	dbSNP_86	26	5464,3134		1747,1970,582	no	coding-synonymous	ESPL1	NM_012291.4		2167,3081,1254	AA,AG,GG		36.4503,44.2805,42.9791		1517/2121	53682326	7415,5589	2203	4299	6502	SO:0001819	synonymous_variant	9700	exon20			AGGTGGGAAGACT	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.4551G>A	12.37:g.53682326G>A		Somatic	56	0	0	994	WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_012291		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																			G|0.402;A|0.598	0.598	strong		0.567	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604419	140604419	+	Missense_Mutation	SNP	G	G	A	rs61731253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604419G>A	ENST00000239449.4	+	1	1342	c.1342G>A	c.(1342-1344)Gcc>Acc	p.A448T	PCDHB14_ENST00000515856.2_Missense_Mutation_p.A295T	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	448	Cadherin 4. {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)			CAATGACAACGCCCCCACCTT	0.582													g|||	103	0.0205671	0.0734	0.0072	5008	,	,		17391	0.0		0.001	False		,,,				2504	0.0				p.A448T	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G1342A						PASS	.	G	THR/ALA	278,4128		6,266,1931	145.0	140.0	142.0		1342	3.5	1.0	5	dbSNP_129	142	0,8600		0,0,4300	no	missense	PCDHB14	NM_018934.2	58	6,266,6231	AA,AG,GG		0.0,6.3096,2.1375	benign	448/799	140604419	278,12728	2203	4300	6503	SO:0001583	missense	56122	exon1			GACAACGCCCCCA	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.1342G>A	5.37:g.140604419G>A	ENSP00000239449:p.Ala448Thr	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	200	108	0.54	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	-	8.743	0.919419	0.17982	0.063096	0.0	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.03181	4.02;4.02	4.5	3.55	0.40652	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.00300	0.0009	M	0.75777	2.31	0.30169	N	0.801422	P	0.49559	0.925	B	0.34652	0.187	T	0.21827	-1.0234	9	0.56958	D	0.05	.	9.2019	0.37263	0.0:0.2719:0.6013:0.1268	rs61731253	448	Q9Y5E9	PCDBE_HUMAN	T	295;448	ENSP00000444518:A295T;ENSP00000239449:A448T	ENSP00000239449:A448T	A	+	1	0	PCDHB14	140584603	0.003000	0.15002	1.000000	0.80357	0.089000	0.18198	-0.272000	0.08560	2.235000	0.73313	0.556000	0.70494	GCC	G|0.979;A|0.021	0.021	strong		0.582	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
SLC4A7	9497	hgsc.bcm.edu	37	3	27490194	27490194	+	Silent	SNP	T	T	C	rs13096477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:27490194T>C	ENST00000295736.5	-	3	280	c.210A>G	c.(208-210)agA>agG	p.R70R	SLC4A7_ENST00000455077.1_Silent_p.R75R|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000440156.1_Silent_p.R79R|SLC4A7_ENST00000446700.1_Silent_p.R75R|SLC4A7_ENST00000445684.1_Silent_p.R79R|SLC4A7_ENST00000435667.2_Silent_p.R79R|SLC4A7_ENST00000437179.1_Silent_p.R75R|SLC4A7_ENST00000428386.1_Silent_p.R70R|SLC4A7_ENST00000425128.2_Silent_p.R75R|SLC4A7_ENST00000454389.1_Silent_p.R79R	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	70					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	TATCTTTTCTTCTCCGGTGGT	0.403													T|||	605	0.120807	0.034	0.1527	5008	,	,		14346	0.0565		0.2107	False		,,,				2504	0.1892				p.R75R		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A225G						PASS	.	T		300,4106	162.9+/-194.8	7,286,1910	238.0	214.0	222.0		210	0.6	1.0	3	dbSNP_121	222	1989,6611	347.9+/-326.8	221,1547,2532	no	coding-synonymous	SLC4A7	NM_003615.3		228,1833,4442	CC,CT,TT		23.1279,6.8089,17.5996		70/1215	27490194	2289,10717	2203	4300	6503	SO:0001819	synonymous_variant	9497	exon3			TTTTCTTCTCCGG	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.210A>G	3.37:g.27490194T>C		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	185	86	0.464865	NM_001258379	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			T|0.851;C|0.149	0.149	strong		0.403	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
SLC27A3	11000	hgsc.bcm.edu	37	1	153745128	153745128	+	5'Flank	SNP	G	G	C	rs6663011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153745128G>C	ENST00000368661.3	+	0	0				SLC27A3_ENST00000271857.2_5'Flank|INTS3_ENST00000435409.2_Silent_p.T945T|INTS3_ENST00000512605.1_Silent_p.T805T|INTS3_ENST00000456435.1_Silent_p.T805T|INTS3_ENST00000318967.2_Silent_p.T945T|INTS3_ENST00000476843.1_3'UTR	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3						fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TTAGCCAGACGCCAATTCTCC	0.507													C|||	771	0.153954	0.4266	0.0749	5008	,	,		19407	0.0129		0.0736	False		,,,				2504	0.0695				p.T945T		Atlas-SNP	.											INTS3,NS,carcinoma,0,1	INTS3	83	1	0			c.G2835C						scavenged	.	C		1632,2774	658.3+/-400.4	295,1042,866	47.0	50.0	49.0		2835	1.3	1.0	1	dbSNP_116	49	598,8002	791.8+/-407.5	14,570,3716	no	coding-synonymous	INTS3	NM_023015.3		309,1612,4582	CC,CG,GG		6.9535,37.0404,17.1459		945/1043	153745128	2230,10776	2203	4300	6503	SO:0001631	upstream_gene_variant	65123	exon28			CCAGACGCCAATT	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155		1.37:g.153745128G>C	Exception_encountered	Somatic	173	4	0.0231214		WXS	Illumina HiSeq	Phase_I	208	115	0.552885	NM_023015	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Silent	SNP	ENST00000368661.3	37	CCDS1053.1																																																																																			C|0.159;G|0.841;T|0.000	0.159	strong		0.507	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330	
ALG11	440138	hgsc.bcm.edu	37	13	52598668	52598668	+	Missense_Mutation	SNP	C	C	A	rs148434423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:52598668C>A	ENST00000521508.1	+	3	807	c.802C>A	c.(802-804)Cta>Ata	p.L268I	UTP14C_ENST00000521776.2_5'Flank|ALG11_ENST00000519151.1_3'UTR|ALG11_ENST00000523764.1_Intron	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	268					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)		TATTCTCTCACTATGGAAAGT	0.378													C|||	2	0.000399361	0.0015	0.0	5008	,	,		22470	0.0		0.0	False		,,,				2504	0.0				p.L268I		Atlas-SNP	.											.	ALG11	39	.	0			c.C802A						PASS	.	C	ILE/LEU	8,4398	15.5+/-35.6	0,8,2195	120.0	111.0	114.0		802	5.2	1.0	13	dbSNP_134	114	0,8600		0,0,4300	yes	missense	ALG11	NM_001004127.2	5	0,8,6495	AA,AC,CC		0.0,0.1816,0.0615	possibly-damaging	268/493	52598668	8,12998	2203	4300	6503	SO:0001583	missense	440138	exon3			CTCTCACTATGGA	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.802C>A	13.37:g.52598668C>A	ENSP00000430236:p.Leu268Ile	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	216	100	0.462963	NM_001004127	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Missense_Mutation	SNP	ENST00000521508.1	37	CCDS31977.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	12.85	2.062733	0.36373	0.001816	0.0	ENSG00000253710	ENST00000521508	T	0.80304	-1.36	6.03	5.19	0.71726	.	0.000000	0.64402	U	0.000002	T	0.81517	0.4839	L	0.50993	1.605	0.80722	D	1	D	0.57571	0.98	P	0.52309	0.695	T	0.78563	-0.2156	10	0.20519	T	0.43	.	15.3059	0.73992	0.0:0.9333:0.0:0.0667	.	268	Q2TAA5	ALG11_HUMAN	I	268	ENSP00000430236:L268I	ENSP00000430236:L268I	L	+	1	2	ALG11	51496669	0.993000	0.37304	0.970000	0.41538	0.930000	0.56654	3.054000	0.49908	1.569000	0.49696	0.557000	0.71058	CTA	C|0.999;A|0.001	0.001	strong		0.378	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127	
KLHL38	340359	hgsc.bcm.edu	37	8	124663895	124663895	+	Silent	SNP	G	G	A	rs16898689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124663895G>A	ENST00000325995.7	-	1	1295	c.1272C>T	c.(1270-1272)ccC>ccT	p.P424P	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	424										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						CAGCGACTGCGGGGTGGAGCA	0.552													G|||	916	0.182907	0.2284	0.1311	5008	,	,		21736	0.2202		0.0686	False		,,,				2504	0.2372				p.P424P		Atlas-SNP	.											.	KLHL38	81	.	0			c.C1272T						PASS	.	G		754,3296		80,594,1351	94.0	93.0	94.0		1272	-0.5	1.0	8	dbSNP_123	94	568,7802		21,526,3638	no	coding-synonymous	KLHL38	NM_001081675.2		101,1120,4989	AA,AG,GG		6.7861,18.6173,10.6441		424/582	124663895	1322,11098	2025	4185	6210	SO:0001819	synonymous_variant	340359	exon1			GACTGCGGGGTGG		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.1272C>T	8.37:g.124663895G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	37	CCDS43766.1																																																																																			G|0.857;A|0.143	0.143	strong		0.552	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
MRPS21	54460	hgsc.bcm.edu	37	1	150280550	150280550	+	Missense_Mutation	SNP	G	G	A	rs4845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150280550G>A	ENST00000369084.5	+	2	599	c.152G>A	c.(151-153)cGg>cAg	p.R51Q	MRPS21_ENST00000309092.7_Missense_Mutation_p.R51Q	NM_018997.3	NP_061870.1	P82921	RT21_HUMAN	mitochondrial ribosomal protein S21	51			R -> Q (in dbSNP:rs4845).		translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(1)|pancreas(1)	4	Lung NSC(24;5.57e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCATGCCGCCGGCGACAGAGG	0.493													G|||	440	0.0878594	0.2337	0.0519	5008	,	,		17084	0.001		0.0706	False		,,,				2504	0.0235				p.R51Q		Atlas-SNP	.											.	MRPS21	8	.	0			c.G152A						PASS	.	G	GLN/ARG,GLN/ARG	845,3561	331.2+/-301.9	72,701,1430	49.0	46.0	47.0		152,152	4.9	1.0	1	dbSNP_52	47	767,7833	182.0+/-230.6	37,693,3570	no	missense,missense	MRPS21	NM_018997.2,NM_031901.4	43,43	109,1394,5000	AA,AG,GG		8.9186,19.1784,12.3943	benign,benign	51/88,51/88	150280550	1612,11394	2203	4300	6503	SO:0001583	missense	54460	exon2			GCCGCCGGCGACA	AB051353	CCDS950.1	1q21	2012-09-13			ENSG00000187145			"""Mitochondrial ribosomal proteins / small subunits"""	14046	protein-coding gene	gene with protein product		611984					Standard	NM_031901		Approved		uc001euk.3	P82921	OTTHUMG00000012544	ENST00000369084.5:c.152G>A	1.37:g.150280550G>A	ENSP00000358080:p.Arg51Gln	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	208	112	0.538462	NM_018997	Q5TB11|Q9BST6	Missense_Mutation	SNP	ENST00000369084.5	37	CCDS950.1	197	0.0902014652014652	121	0.2459349593495935	15	0.04143646408839779	1	0.0017482517482517483	60	0.079155672823219	G	11.58	1.681805	0.29872	0.191784	0.089186	ENSG00000187145	ENST00000309092;ENST00000369084	T;T	0.32272	1.46;1.46	4.94	4.94	0.65067	.	.	.	.	.	T	0.05640	0.0148	.	.	.	0.44985	P	0.0019940000000000513	B	0.14805	0.011	B	0.15052	0.012	T	0.22977	-1.0201	7	0.07990	T	0.79	.	9.1038	0.36685	0.1625:0.0:0.8375:0.0	rs4845;rs1050856;rs3191211;rs4845	51	P82921	RT21_HUMAN	Q	51	ENSP00000312395:R51Q;ENSP00000358080:R51Q	ENSP00000312395:R51Q	R	+	2	0	MRPS21	148547174	0.084000	0.21492	0.989000	0.46669	0.988000	0.76386	1.483000	0.35497	2.572000	0.86782	0.655000	0.94253	CGG	G|0.888;A|0.112	0.112	strong		0.493	MRPS21-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035813.1	NM_018997	
DDX3X	1654	hgsc.bcm.edu	37	X	41204446	41204446	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:41204446G>C	ENST00000399959.2	+	11	1894	c.1039G>C	c.(1039-1041)Gat>Cat	p.D347H	DDX3X_ENST00000457138.2_Missense_Mutation_p.D331H|DDX3X_ENST00000542215.1_3'UTR|DDX3X_ENST00000478993.1_3'UTR|RN7SL15P_ENST00000582825.1_RNA|DDX3X_ENST00000441189.2_Intron	NM_001193416.1|NM_001193417.1|NM_001356.3	NP_001180345.1|NP_001180346.1|NP_001347.3	O00571	DDX3X_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked	347	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Interaction with GSK3B.|Necessary for interaction with XPO1.				ATP catabolic process (GO:0006200)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to osmotic stress (GO:0071470)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|mature ribosome assembly (GO:0042256)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell growth (GO:0030307)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|stress granule assembly (GO:0034063)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 5'-UTR binding (GO:0048027)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|transcription factor binding (GO:0008134)|translation initiation factor binding (GO:0031369)			NS(3)|breast(8)|central_nervous_system(36)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84						CTTGGTGTTAGATGAAGCTGA	0.393										HNSCC(61;0.18)																											p.D347H		Atlas-SNP	.											.	DDX3X	138	.	0			c.G1039C						PASS	.						145.0	134.0	137.0					X																	41204446		2102	4246	6348	SO:0001583	missense	1654	exon11			GTGTTAGATGAAG	U50553	CCDS43931.1, CCDS55404.1	Xp11.3-p11.23	2013-07-16	2013-07-16	2003-06-20	ENSG00000215301	ENSG00000215301		"""DEAD-boxes"""	2745	protein-coding gene	gene with protein product		300160	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked"""	DDX3		9381176, 9730595	Standard	NM_001193416		Approved	DBX, HLP2, DDX14	uc004dfe.3	O00571	OTTHUMG00000021369	ENST00000399959.2:c.1039G>C	X.37:g.41204446G>C	ENSP00000382840:p.Asp347His	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	131	25	0.19084	NM_001193416	A8K538|B4E3E8|O15536	Missense_Mutation	SNP	ENST00000399959.2	37	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	g	25.1	4.598675	0.87055	.	.	ENSG00000215301	ENST00000399959;ENST00000457138	T;T	0.55588	0.51;0.51	5.5	5.5	0.81552	RNA helicase, ATP-dependent, DEAD-box, conserved site (1);DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.099615	0.64402	D	0.000001	D	0.85106	0.5621	H	0.99299	4.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.997;0.997	D	0.91820	0.5466	10	0.87932	D	0	-16.0361	18.5127	0.90923	0.0:0.0:1.0:0.0	.	347;331;359;347	B4DLU5;B4E3E8;Q59GX6;O00571	.;.;.;DDX3X_HUMAN	H	347;331	ENSP00000382840:D347H;ENSP00000392494:D331H	ENSP00000382840:D347H	D	+	1	0	DDX3X	41089390	1.000000	0.71417	0.998000	0.56505	0.869000	0.49853	9.807000	0.99171	2.313000	0.78055	0.597000	0.82753	GAT	.	.	none		0.393	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388819	1388819	+	Missense_Mutation	SNP	T	T	C	rs144797159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1388819T>C	ENST00000324803.4	+	1	3480	c.520T>C	c.(520-522)Tgt>Cgt	p.C174R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	174					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)			CACGTGCCCATGTGGAGTGCC	0.677													N|||	940	0.1877	0.3328	0.1398	5008	,	,		17297	0.0992		0.0378	False		,,,				2504	0.271				p.C174R		Atlas-SNP	.											CRIPAK,NS,carcinoma,0,4	CRIPAK	185	4	0			c.T520C						PASS	.						191.0	130.0	151.0					4																	1388819		2194	4196	6390	SO:0001583	missense	285464	exon1			TGCCCATGTGGAG	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.520T>C	4.37:g.1388819T>C	ENSP00000323978:p.Cys174Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	160	20	0.125	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	2.950|2.950	-0.216975|-0.216975	0.06101|0.06101	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000324803|ENST00000382944	T|.	0.29142|.	1.58|.	1.25|1.25	-0.146|-0.146	0.13432|0.13432	Post-SET domain (1);|.	.|.	.|.	.|.	.|.	T|T	0.15825|0.15825	0.0381|0.0381	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|.	0.20052|.	0.041|.	B|.	0.11329|.	0.006|.	T|T	0.24977|0.24977	-1.0145|-1.0145	9|6	0.66056|0.27082	D|T	0.02|0.32	.|.	4.6847|4.6847	0.12752|0.12752	0.0:0.2124:0.0:0.7876|0.0:0.2124:0.0:0.7876	.|.	174|.	Q8N1N5|.	CRPAK_HUMAN|.	R|T	174|157	ENSP00000323978:C174R|.	ENSP00000323978:C174R|ENSP00000372402:M157T	C|M	+|+	1|2	0|0	CRIPAK|CRIPAK	1378819|1378819	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.014000|0.014000	0.08584|0.08584	-0.160000|-0.160000	0.10041|0.10041	-0.013000|-0.013000	0.14199|0.14199	0.102000|0.102000	0.15555|0.15555	TGT|ATG	.	.	weak		0.677	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
ITLN1	55600	hgsc.bcm.edu	37	1	160853312	160853312	+	Silent	SNP	C	C	T	rs79969862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160853312C>T	ENST00000326245.3	-	3	178	c.63G>A	c.(61-63)gaG>gaA	p.E21E	ITLN1_ENST00000487531.1_5'Flank	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	21					positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			AAGTATTAGCCTCATCTAGGG	0.463													C|||	89	0.0177716	0.0461	0.0043	5008	,	,		18185	0.0		0.0	False		,,,				2504	0.0256				p.E21E		Atlas-SNP	.											.	ITLN1	45	.	0			c.G63A						PASS	.	C		182,4224	117.1+/-155.0	5,172,2026	159.0	145.0	150.0		63	-3.0	0.0	1	dbSNP_132	150	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITLN1	NM_017625.2		5,173,6325	TT,TC,CC		0.0116,4.1307,1.407		21/314	160853312	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	55600	exon3			ATTAGCCTCATCT	AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.63G>A	1.37:g.160853312C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	149	61	0.409396	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Silent	SNP	ENST00000326245.3	37	CCDS1211.1																																																																																			C|0.984;T|0.016	0.016	strong		0.463	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625	
SPP1	6696	hgsc.bcm.edu	37	4	88902725	88902725	+	Silent	SNP	G	G	A	rs6812524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88902725G>A	ENST00000395080.3	+	6	442	c.315G>A	c.(313-315)tcG>tcA	p.S105S	SPP1_ENST00000237623.7_Silent_p.S91S|SPP1_ENST00000360804.4_Silent_p.S78S|SPP1_ENST00000509659.1_3'UTR	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	105					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|negative regulation of collateral sprouting of intact axon in response to injury (GO:0048685)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell-substrate adhesion (GO:0010811)|response to steroid hormone (GO:0048545)|response to vitamin D (GO:0033280)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix binding (GO:0050840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		CCATTGACTCGAACGACTCTG	0.458													G|||	367	0.0732827	0.2663	0.0202	5008	,	,		18848	0.0		0.001	False		,,,				2504	0.0				p.S118S		Atlas-SNP	.											.	SPP1	35	.	0			c.G354A						PASS	.	G	,,	885,3521	341.2+/-306.6	88,709,1406	310.0	286.0	294.0		273,315,234	-9.6	0.0	4	dbSNP_116	294	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	SPP1	NM_000582.2,NM_001040058.1,NM_001040060.1	,,	88,719,5696	AA,AG,GG		0.1163,20.0862,6.8814	,,	91/301,105/315,78/288	88902725	895,12111	2203	4300	6503	SO:0001819	synonymous_variant	6696	exon7			TGACTCGAACGAC		CCDS3626.1, CCDS34027.1, CCDS43250.1	4q22.1	2014-01-30	2008-07-31		ENSG00000118785	ENSG00000118785		"""Endogenous ligands"""	11255	protein-coding gene	gene with protein product	"""early T-lymphocyte activation 1"""	166490	"""osteopontin"", ""bone sialoprotein I"""	BNSP, OPN		1575754	Standard	NM_001251829		Approved	BSPI, ETA-1	uc003hra.3	P10451	OTTHUMG00000130599	ENST00000395080.3:c.315G>A	4.37:g.88902725G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	269	128	0.475836	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Silent	SNP	ENST00000395080.3	37	CCDS43250.1																																																																																			G|0.921;A|0.079	0.079	strong		0.458	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3		
MR1	3140	hgsc.bcm.edu	37	1	181019253	181019253	+	Silent	SNP	T	T	C	rs61731103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:181019253T>C	ENST00000367580.5	+	3	440	c.435T>C	c.(433-435)aaT>aaC	p.N145N	MR1_ENST00000438435.2_3'UTR|MR1_ENST00000434571.2_Silent_p.N145N|MR1_ENST00000282990.6_Silent_p.N145N|MR1_ENST00000367579.3_Intron	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	145	Alpha-2.|Ligand-binding.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	TGATCTTCAATAAAGACACCC	0.488													T|||	195	0.0389377	0.1218	0.0159	5008	,	,		21267	0.0228		0.0	False		,,,				2504	0.0				p.N145N	Colon(174;1412 1962 45296 46549 47110)	Atlas-SNP	.											.	MR1	46	.	0			c.T435C						PASS	.	T	,,,	437,3969	211.5+/-231.7	27,383,1793	125.0	115.0	119.0		,435,435,435	-1.9	0.0	1	dbSNP_129	119	6,8594	4.3+/-15.6	0,6,4294	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	MR1	NM_001194999.1,NM_001195000.1,NM_001195035.1,NM_001531.2	,,,	27,389,6087	CC,CT,TT		0.0698,9.9183,3.4061	,,,	,145/250,145/215,145/342	181019253	443,12563	2203	4300	6503	SO:0001819	synonymous_variant	3140	exon4			CTTCAATAAAGAC	AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"""Immunoglobulin superfamily / C1-set domain containing"""	4975	protein-coding gene	gene with protein product		600764	"""major histocompatibility complex, class I-like sequence"""	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.435T>C	1.37:g.181019253T>C		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	296	150	0.506757	NM_001195035	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Silent	SNP	ENST00000367580.5	37	CCDS1342.1																																																																																			T|0.967;C|0.033	0.033	strong		0.488	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531	
ZNF98	148198	hgsc.bcm.edu	37	19	22575481	22575481	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22575481C>T	ENST00000357774.5	-	4	677	c.556G>A	c.(556-558)Gaa>Aaa	p.E186K		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	186					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)				TTTTCACATTCTTTACACTTG	0.303																																					p.E186K		Atlas-SNP	.											ZNF98_ENST00000357774,caecum,carcinoma,0,2	ZNF98	230	2	0			c.G556A						scavenged	.						24.0	24.0	24.0					19																	22575481		2007	4196	6203	SO:0001583	missense	148198	exon4			CACATTCTTTACA		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.556G>A	19.37:g.22575481C>T	ENSP00000350418:p.Glu186Lys	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	309	4	0.012945	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	3.730	-0.055780	0.07362	.	.	ENSG00000197360	ENST00000357774	T	0.07327	3.2	1.28	-0.304	0.12788	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06188	0.0160	N	0.25992	0.78	0.09310	N	1	B	0.14438	0.01	B	0.22880	0.042	T	0.39941	-0.9589	9	0.35671	T	0.21	.	8.1641	0.31215	0.0:0.7501:0.2498:0.0	.	186	A6NK75	ZNF98_HUMAN	K	186	ENSP00000350418:E186K	ENSP00000350418:E186K	E	-	1	0	ZNF98	22367321	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	0.118000	0.15605	0.676000	0.31285	0.305000	0.20034	GAA	.	.	none		0.303	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
F10	2159	hgsc.bcm.edu	37	13	113798236	113798236	+	Missense_Mutation	SNP	G	G	A	rs3211783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113798236G>A	ENST00000375559.3	+	6	612	c.574G>A	c.(574-576)Ggg>Agg	p.G192R	F10_ENST00000409306.1_Missense_Mutation_p.G192R|F10_ENST00000375551.3_Missense_Mutation_p.G192R	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	192	O-glycosylated at one site.		G -> R (in dbSNP:rs3211783). {ECO:0000269|Ref.3}.		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)|positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(4)|lung(10)|pancreas(1)|stomach(1)	18	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;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Antihemophilic Factor(DB00025)|Apixaban(DB06605)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Menadione(DB00170)|Rivaroxaban(DB06228)	CAGCAGCAGCGGGGAGGCCCC	0.632													G|||	148	0.0295527	0.1089	0.0058	5008	,	,		16770	0.0		0.0	False		,,,				2504	0.0				p.G192R		Atlas-SNP	.											.	F10	53	.	0			c.G574A						PASS	.	G	ARG/GLY	378,4028	188.8+/-215.1	17,344,1842	71.0	61.0	64.0		574	0.6	0.0	13	dbSNP_105	64	4,8596	3.7+/-12.6	0,4,4296	yes	missense	F10	NM_000504.3	125	17,348,6138	AA,AG,GG		0.0465,8.5792,2.9371	benign	192/489	113798236	382,12624	2203	4300	6503	SO:0001583	missense	2159	exon6			AGCAGCGGGGAGG		CCDS9530.1	13q34	2012-10-02			ENSG00000126218	ENSG00000126218	3.4.21.6		3528	protein-coding gene	gene with protein product		613872					Standard	XM_005268298		Approved		uc001vsx.3	P00742	OTTHUMG00000017374	ENST00000375559.3:c.574G>A	13.37:g.113798236G>A	ENSP00000364709:p.Gly192Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_000504	Q14340	Missense_Mutation	SNP	ENST00000375559.3	37	CCDS9530.1	46	0.021062271062271064	45	0.09146341463414634	1	0.0027624309392265192	0	0.0	0	0.0	G	6.631	0.484887	0.12641	0.085792	4.65E-4	ENSG00000126218	ENST00000409306;ENST00000375551;ENST00000375559	D;D;D	0.95588	-3.73;-3.75;-2.9	4.72	0.594	0.17485	.	2.606730	0.01382	N	0.012940	T	0.31482	0.0798	L	0.29908	0.895	0.09310	N	1	P;P;P	0.49961	0.93;0.93;0.682	B;B;B	0.34931	0.136;0.192;0.053	T	0.74542	-0.3631	10	0.18276	T	0.48	.	4.0037	0.09592	0.4003:0.1745:0.4252:0.0	rs3211783	192;192;192	B7ZBK1;Q5JVE8;P00742	.;.;FA10_HUMAN	R	192	ENSP00000387092:G192R;ENSP00000364701:G192R;ENSP00000364709:G192R	ENSP00000364701:G192R	G	+	1	0	F10	112846237	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.422000	0.07043	0.081000	0.16988	-0.333000	0.08304	GGG	G|0.973;A|0.027	0.027	strong		0.632	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3		
PBK	55872	hgsc.bcm.edu	37	8	27668587	27668587	+	Missense_Mutation	SNP	C	C	G	rs17057901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27668587C>G	ENST00000301905.4	-	7	1123	c.660G>C	c.(658-660)gaG>gaC	p.E220D	ESCO2_ENST00000397418.2_Intron|PBK_ENST00000522944.1_Missense_Mutation_p.E231D	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> D (in dbSNP:rs17057901).		mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		TAACACCATTCTCCTCCACAG	0.428													C|||	105	0.0209665	0.0741	0.0101	5008	,	,		19638	0.0		0.0	False		,,,				2504	0.0				p.E220D		Atlas-SNP	.											.	PBK	29	.	0			c.G660C						PASS	.	C	ASP/GLU	299,4107	163.6+/-195.4	12,275,1916	134.0	114.0	121.0		660	-1.1	0.8	8	dbSNP_123	121	4,8596	3.7+/-12.6	0,4,4296	yes	missense	PBK	NM_018492.2	45	12,279,6212	GG,GC,CC		0.0465,6.7862,2.3297	benign	220/323	27668587	303,12703	2203	4300	6503	SO:0001583	missense	55872	exon7			ACCATTCTCCTCC	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"""T-LAK cell-originated protein kinase"", ""cancer/testis antigen 84"""	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.660G>C	8.37:g.27668587C>G	ENSP00000301905:p.Glu220Asp	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	139	67	0.482014	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Missense_Mutation	SNP	ENST00000301905.4	37	CCDS6063.1	31	0.014194139194139194	28	0.056910569105691054	3	0.008287292817679558	0	0.0	0	0.0	C	13.60	2.284682	0.40394	0.067862	4.65E-4	ENSG00000168078	ENST00000301905;ENST00000522944	T;T	0.33654	1.4;1.4	5.49	-1.13	0.09775	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043945	0.85682	D	0.000000	T	0.01661	0.0053	N	0.21448	0.665	0.44843	D	0.997853	B;B	0.24675	0.109;0.04	B;B	0.35312	0.2;0.075	T	0.06770	-1.0808	10	0.15066	T	0.55	-24.1822	10.3658	0.44024	0.0:0.4018:0.0:0.5982	rs17057901;rs17057901	231;220	B4DX68;Q96KB5	.;TOPK_HUMAN	D	220;231	ENSP00000301905:E220D;ENSP00000428489:E231D	ENSP00000301905:E220D	E	-	3	2	PBK	27724506	0.005000	0.15991	0.807000	0.32361	0.928000	0.56348	-0.940000	0.03929	-0.140000	0.11394	0.655000	0.94253	GAG	C|0.978;G|0.022	0.022	strong		0.428	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492	
DGKB	1607	hgsc.bcm.edu	37	7	14758273	14758273	+	Silent	SNP	C	C	T	rs1997040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:14758273C>T	ENST00000403951.2	-	6	779	c.360G>A	c.(358-360)cgG>cgA	p.R120R	DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000399322.3_Silent_p.R120R|DGKB_ENST00000407950.1_Silent_p.R113R|DGKB_ENST00000444700.2_Silent_p.R113R|DGKB_ENST00000406247.3_Silent_p.R120R|DGKB_ENST00000402815.1_Silent_p.R120R|DGKB_ENST00000258767.5_Silent_p.R120R			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	120					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						GAGAAGTAGTCCGGGGAGGGG	0.398													C|||	2534	0.50599	0.1467	0.5893	5008	,	,		15411	0.8819		0.4384	False		,,,				2504	0.6145				p.R120R		Atlas-SNP	.											.	DGKB	166	.	0			c.G360A						PASS	.	C	,	757,2935		90,577,1179	85.0	81.0	83.0		360,360	-5.6	0.2	7	dbSNP_92	83	3726,4468		833,2060,1204	no	coding-synonymous,coding-synonymous	DGKB	NM_004080.2,NM_145695.2	,	923,2637,2383	TT,TC,CC		45.4723,20.5038,37.7166	,	120/805,120/774	14758273	4483,7403	1846	4097	5943	SO:0001819	synonymous_variant	1607	exon5			AGTAGTCCGGGGA	AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"""EF-hand domain containing"""	2850	protein-coding gene	gene with protein product		604070	"""diacylglycerol kinase, beta (90kD)"""	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.360G>A	7.37:g.14758273C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	152	67	0.440789	NM_145695	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Silent	SNP	ENST00000403951.2	37	CCDS47547.1																																																																																			C|0.500;T|0.500	0.500	strong		0.398	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080	
NTSR2	23620	hgsc.bcm.edu	37	2	11800180	11800180	+	Silent	SNP	G	G	A	rs35653499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11800180G>A	ENST00000306928.5	-	3	1012	c.978C>T	c.(976-978)gaC>gaT	p.D326D		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	326					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	CAGTCCACGCGTCATCAGGTA	0.602													G|||	81	0.0161741	0.0446	0.0086	5008	,	,		21158	0.0159		0.0	False		,,,				2504	0.0				p.D326D		Atlas-SNP	.											.	NTSR2	36	.	0			c.C978T						PASS	.	G		196,4210	122.1+/-159.5	7,182,2014	105.0	89.0	95.0		978	-1.8	0.0	2	dbSNP_126	95	0,8600		0,0,4300	no	coding-synonymous	NTSR2	NM_012344.3		7,182,6314	AA,AG,GG		0.0,4.4485,1.507		326/411	11800180	196,12810	2203	4300	6503	SO:0001819	synonymous_variant	23620	exon3			CCACGCGTCATCA	Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"""GPCR / Class A : Neurotensin receptors"""	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.978C>T	2.37:g.11800180G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Silent	SNP	ENST00000306928.5	37	CCDS1681.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1		
PER3	8863	hgsc.bcm.edu	37	1	7887499	7887499	+	Missense_Mutation	SNP	T	T	G	rs35899625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:7887499T>G	ENST00000361923.2	+	17	2661	c.2486T>G	c.(2485-2487)tTg>tGg	p.L829W	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.L837W	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	829	Pro-rich.				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)		GGGCTGCCCTTGTCCGAGGGC	0.592													T|||	12	0.00239617	0.0083	0.0014	5008	,	,		17848	0.0		0.0	False		,,,				2504	0.0				p.L829W		Atlas-SNP	.											.	PER3	95	.	0			c.T2486G						PASS	.	T	TRP/LEU	46,4360	48.2+/-83.0	1,44,2158	104.0	104.0	104.0		2486	-1.6	0.0	1	dbSNP_126	104	0,8600		0,0,4300	yes	missense	PER3	NM_016831.1	61	1,44,6458	GG,GT,TT		0.0,1.044,0.3537	possibly-damaging	829/1202	7887499	46,12960	2203	4300	6503	SO:0001583	missense	8863	exon17			TGCCCTTGTCCGA	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.2486T>G	1.37:g.7887499T>G	ENSP00000355031:p.Leu829Trp	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	207	116	0.560386	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	T	14.56	2.570910	0.45798	0.01044	0.0	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.11063	2.81;2.81	3.82	-1.61	0.08399	.	2.355770	0.02257	N	0.067230	T	0.10981	0.0268	N	0.14661	0.345	0.09310	N	1	D;D;D;D	0.60575	0.979;0.983;0.988;0.979	P;P;P;P	0.62089	0.793;0.842;0.898;0.793	T	0.32666	-0.9898	10	0.38643	T	0.18	.	9.3251	0.37988	0.0:0.4119:0.0:0.5881	rs35899625	829;837;837;829	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	W	837;829;40	ENSP00000366755:L837W;ENSP00000355031:L829W	ENSP00000355031:L829W	L	+	2	0	PER3	7810086	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.331000	0.07914	-0.204000	0.10235	-0.337000	0.08149	TTG	T|0.995;G|0.005	0.005	strong		0.592	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
C2CD3	26005	hgsc.bcm.edu	37	11	73789332	73789332	+	Silent	SNP	C	C	T	rs75137555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73789332C>T	ENST00000334126.7	-	23	4657	c.4431G>A	c.(4429-4431)agG>agA	p.R1477R	C2CD3_ENST00000313663.7_Silent_p.R1477R			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1477					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GTGATGGGCCCCTGGTGACTT	0.488													C|||	74	0.0147764	0.0363	0.0029	5008	,	,		20003	0.0069		0.0129	False		,,,				2504	0.0041				p.R1477R		Atlas-SNP	.											.	C2CD3	288	.	0			c.G4431A						PASS	.	C		199,4201	123.3+/-160.7	4,191,2005	128.0	114.0	119.0		4431	3.5	0.8	11	dbSNP_132	119	97,8489	54.4+/-115.2	1,95,4197	no	coding-synonymous	C2CD3	NM_015531.4		5,286,6202	TT,TC,CC		1.1297,4.5227,2.2794		1477/1964	73789332	296,12690	2200	4293	6493	SO:0001819	synonymous_variant	26005	exon23			TGGGCCCCTGGTG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.4431G>A	11.37:g.73789332C>T		Somatic	397	0	0		WXS	Illumina HiSeq	Phase_I	431	230	0.533643	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Silent	SNP	ENST00000334126.7	37																																																																																				C|0.979;T|0.021	0.021	strong		0.488	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
MMP27	64066	hgsc.bcm.edu	37	11	102576382	102576382	+	Missense_Mutation	SNP	G	G	A	rs12099177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:102576382G>A	ENST00000260229.4	-	1	155	c.64C>T	c.(64-66)Cgg>Tgg	p.R22W		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	22			R -> W (in dbSNP:rs12099177).		collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R22W(1)		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)	TCCGTCATCCGGACTAAGGGA	0.363													G|||	844	0.16853	0.1687	0.1455	5008	,	,		19020	0.2996		0.0666	False		,,,				2504	0.1544				p.R22W		Atlas-SNP	.											MMP27,NS,carcinoma,0,1	MMP27	84	1	1	Substitution - Missense(1)	stomach(1)	c.C64T						PASS	.	G	TRP/ARG	741,3665	301.0+/-286.6	67,607,1529	99.0	106.0	104.0		64	0.5	0.0	11	dbSNP_120	104	550,8048	150.4+/-205.3	15,520,3764	yes	missense	MMP27	NM_022122.2	101	82,1127,5293	AA,AG,GG		6.3968,16.818,9.9277	possibly-damaging	22/514	102576382	1291,11713	2203	4299	6502	SO:0001583	missense	64066	exon1			TCATCCGGACTAA	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.64C>T	11.37:g.102576382G>A	ENSP00000260229:p.Arg22Trp	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	123	46	0.373984	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	340	0.15567765567765568	93	0.18902439024390244	43	0.11878453038674033	161	0.28146853146853146	43	0.05672823218997362	G	10.72	1.429129	0.25726	0.16818	0.063968	ENSG00000137675	ENST00000260229	T	0.36520	1.25	4.98	0.533	0.17121	.	1.468070	0.05201	U	0.505000	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.21606	0.058	B	0.20384	0.029	T	0.33548	-0.9864	9	0.66056	D	0.02	.	3.9186	0.09234	0.0821:0.1352:0.4882:0.2945	rs12099177;rs60819172;rs12099177	22	Q9H306	MMP27_HUMAN	W	22	ENSP00000260229:R22W	ENSP00000260229:R22W	R	-	1	2	MMP27	102081592	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	1.091000	0.30915	0.330000	0.23485	0.655000	0.94253	CGG	G|0.882;A|0.118	0.118	strong		0.363	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
DSP	1832	hgsc.bcm.edu	37	6	7576569	7576569	+	Silent	SNP	T	T	C	rs146407262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7576569T>C	ENST00000379802.3	+	19	3014	c.2673T>C	c.(2671-2673)taT>taC	p.Y891Y	DSP_ENST00000418664.2_Silent_p.Y891Y	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	891	Globular 1.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			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)		TGAGGAATTATCGTGATAACT	0.383													T|||	35	0.00698882	0.0257	0.0014	5008	,	,		18556	0.0		0.0	False		,,,				2504	0.0				p.Y891Y		Atlas-SNP	.											.	DSP	306	.	0			c.T2673C						PASS	.	T	,	100,4306	79.9+/-118.3	1,98,2104	107.0	110.0	109.0		2673,2673	-6.6	0.9	6	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DSP	NM_001008844.1,NM_004415.2	,	1,98,6404	CC,CT,TT		0.0,2.2696,0.7689	,	891/2273,891/2872	7576569	100,12906	2203	4300	6503	SO:0001819	synonymous_variant	1832	exon19			GAATTATCGTGAT	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.2673T>C	6.37:g.7576569T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																			T|0.991;C|0.009	0.009	strong		0.383	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
SLC26A8	116369	hgsc.bcm.edu	37	6	35923246	35923246	+	Missense_Mutation	SNP	T	T	C	rs2295852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	181	0	0		WXS	Illumina HiSeq	Phase_I	174	83	0.477012	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		
DHTKD1	55526	hgsc.bcm.edu	37	10	12160868	12160868	+	Silent	SNP	C	C	T	rs12769375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:12160868C>T	ENST00000263035.4	+	15	2585	c.2523C>T	c.(2521-2523)ttC>ttT	p.F841F	U6_ENST00000606801.1_RNA	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	841					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			TCTGCCCCTTCCCGTTGGATT	0.448													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		17605	0.0		0.0	False		,,,				2504	0.0				p.F841F		Atlas-SNP	.											.	DHTKD1	104	.	0			c.C2523T						PASS	.	C		153,4253	104.7+/-143.2	4,145,2054	146.0	143.0	144.0		2523	3.2	1.0	10	dbSNP_121	144	0,8600		0,0,4300	no	coding-synonymous	DHTKD1	NM_018706.5		4,145,6354	TT,TC,CC		0.0,3.4725,1.1764		841/920	12160868	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	55526	exon15			CCCCTTCCCGTTG	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2523C>T	10.37:g.12160868C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Silent	SNP	ENST00000263035.4	37	CCDS7087.1																																																																																			C|0.985;T|0.015	0.015	strong		0.448	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706	
FLG	2312	hgsc.bcm.edu	37	1	152281304	152281304	+	Missense_Mutation	SNP	A	A	C	rs7512857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281304A>C	ENST00000368799.1	-	3	6093	c.6058T>G	c.(6058-6060)Tca>Gca	p.S2020A	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2020	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)			CCAATGCCTGAGTGTCTGGAG	0.547									Ichthyosis																												p.S2020A		Atlas-SNP	.											.	FLG	900	.	0			c.T6058G						PASS	.	A	ALA/SER	1440,2966		0,1440,763	635.0	522.0	560.0		6058	1.1	0.0	1	dbSNP_116	560	1143,7457		0,1143,3157	no	missense	FLG	NM_002016.1	99	0,2583,3920	CC,CA,AA		13.2907,32.6827,19.8601	probably-damaging	2020/4062	152281304	2583,10423	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGCCTGAGTGTCT	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.6058T>G	1.37:g.152281304A>C	ENSP00000357789:p.Ser2020Ala	Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	512	230	0.449219	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	a	6.327	0.428418	0.11987	0.326827	0.132907	ENSG00000143631	ENST00000368799	T	0.08807	3.05	3.79	1.13	0.20643	.	.	.	.	.	T	0.07999	0.0200	M	0.68952	2.095	0.09310	N	1	D	0.71674	0.998	D	0.64776	0.929	T	0.14868	-1.0457	9	0.35671	T	0.21	.	2.8858	0.05661	0.5641:0.2519:0.184:0.0	rs7512857;rs7512857	2020	P20930	FILA_HUMAN	A	2020	ENSP00000357789:S2020A	ENSP00000357789:S2020A	S	-	1	0	FLG	150547928	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.391000	0.20784	0.103000	0.17682	0.477000	0.44152	TCA	A|0.968;C|0.032	0.032	strong		0.547	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ZP4	57829	hgsc.bcm.edu	37	1	238053226	238053226	+	Missense_Mutation	SNP	G	G	A	rs34370253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:238053226G>A	ENST00000366570.4	-	3	499	c.341C>T	c.(340-342)gCg>gTg	p.A114V	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	114			A -> V (in dbSNP:rs34370253).		acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GTGTTCAGCCGCGCCTGCTCC	0.567													G|||	154	0.0307508	0.1089	0.013	5008	,	,		19719	0.0		0.001	False		,,,				2504	0.0				p.A114V	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											ZP4,caecum,carcinoma,0,1	ZP4	161	1	0			c.C341T						PASS	.	G	VAL/ALA	386,4020	194.0+/-219.0	14,358,1831	199.0	206.0	203.0		341	-6.6	0.0	1	dbSNP_126	203	6,8594	4.3+/-15.6	0,6,4294	yes	missense	ZP4	NM_021186.3	64	14,364,6125	AA,AG,GG		0.0698,8.7608,3.014	benign	114/541	238053226	392,12614	2203	4300	6503	SO:0001583	missense	57829	exon3			TCAGCCGCGCCTG	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.341C>T	1.37:g.238053226G>A	ENSP00000355529:p.Ala114Val	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	172	84	0.488372	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	0.052	-1.248697	0.01469	0.087608	6.98E-4	ENSG00000116996	ENST00000366570	T	0.74632	-0.86	4.37	-6.58	0.01836	.	0.845246	0.10705	N	0.643569	T	0.00875	0.0029	N	0.11201	0.11	0.09310	N	1	B	0.17667	0.023	B	0.10450	0.005	T	0.13522	-1.0506	10	0.02654	T	1	0.4495	3.7495	0.08561	0.5715:0.1196:0.1878:0.1212	rs34370253	114	Q12836	ZP4_HUMAN	V	114	ENSP00000355529:A114V	ENSP00000355529:A114V	A	-	2	0	ZP4	236119849	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.059000	0.11731	-2.021000	0.00939	-2.828000	0.00107	GCG	G|0.972;A|0.028	0.028	strong		0.567	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
ZFPM2	23414	hgsc.bcm.edu	37	8	106814086	106814086	+	Silent	SNP	T	T	C	rs16873732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:106814086T>C	ENST00000407775.2	+	8	2026	c.1776T>C	c.(1774-1776)ccT>ccC	p.P592P	ZFPM2_ENST00000520492.1_Silent_p.P460P|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000521622.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000509144.2_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000520433.1_RNA|ZFPM2_ENST00000517361.1_Silent_p.P460P|ZFPM2_ENST00000378472.4_Silent_p.P323P|RP11-152P17.2_ENST00000520594.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	592					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			AAAAGATGCCTGAAGCTTTGA	0.458													T|||	332	0.0662939	0.1717	0.0403	5008	,	,		20006	0.0069		0.0268	False		,,,				2504	0.044				p.P592P		Atlas-SNP	.											.	ZFPM2	219	.	0			c.T1776C						PASS	.	T		493,3419		33,427,1496	130.0	132.0	131.0		1776	-6.5	1.0	8	dbSNP_123	131	191,8113		2,187,3963	no	coding-synonymous	ZFPM2	NM_012082.3		35,614,5459	CC,CT,TT		2.3001,12.6022,5.5992		592/1152	106814086	684,11532	1956	4152	6108	SO:0001819	synonymous_variant	23414	exon8			GATGCCTGAAGCT	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.1776T>C	8.37:g.106814086T>C		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	153	80	0.522876	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Silent	SNP	ENST00000407775.2	37	CCDS47908.1																																																																																			T|0.939;C|0.061	0.061	strong		0.458	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
PSG8	440533	hgsc.bcm.edu	37	19	43268242	43268242	+	Missense_Mutation	SNP	C	C	T	rs76352186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43268242C>T	ENST00000306511.4	-	2	353	c.256G>A	c.(256-258)Ggt>Agt	p.G86S	PSG8_ENST00000406636.3_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.G86S|PSG8_ENST00000401467.2_Missense_Mutation_p.G86S	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	86	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)				ATTATTTGACCGTCTACTACA	0.433													.|||	285	0.0569089	0.1952	0.0202	5008	,	,		22232	0.0		0.006	False		,,,				2504	0.0072				p.G86S		Atlas-SNP	.											.	PSG8	101	.	0			c.G256A						PASS	.	T	SER/GLY,,SER/GLY	772,3634	311.9+/-292.3	84,604,1515	248.0	265.0	259.0		256,,256	-2.7	0.0	19	dbSNP_131	259	131,8467	67.3+/-129.8	1,129,4169	no	missense,intron,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	56,,56	85,733,5684	TT,TC,CC		1.5236,17.5216,6.944	benign,,benign	86/420,,86/427	43268242	903,12101	2203	4299	6502	SO:0001583	missense	440533	exon2			TTTGACCGTCTAC	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.256G>A	19.37:g.43268242C>T	ENSP00000305005:p.Gly86Ser	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	233	98	0.420601	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	126	0.057692307692307696	112	0.22764227642276422	8	0.022099447513812154	0	0.0	6	0.0079155672823219	c	0.005	-2.167646	0.00315	0.175216	0.015236	ENSG00000124467	ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.63913	-0.07;-0.07;-0.07	1.35	-2.7	0.06004	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.15975	0.35	0.80722	P	0.0	B;B;B;B;B	0.20780	0.002;0.003;0.048;0.001;0.001	B;B;B;B;B	0.23018	0.004;0.011;0.043;0.005;0.009	T	0.06303	-1.0834	8	0.08599	T	0.76	.	5.2757	0.15649	0.0:0.4599:0.1655:0.3746	.	86;86;86;86;86	B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.;.	S	86	ENSP00000385869:G86S;ENSP00000386090:G86S;ENSP00000305005:G86S	ENSP00000305005:G86S	G	-	1	0	PSG8	47960082	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.991000	0.01478	-3.700000	0.00119	-2.741000	0.00127	GGT	C|0.936;T|0.064	0.064	strong		0.433	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
ARHGEF28	64283	hgsc.bcm.edu	37	5	73163831	73163831	+	Silent	SNP	C	C	T	rs2931423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:73163831C>T	ENST00000426542.2	+	18	2303	c.2283C>T	c.(2281-2283)ggC>ggT	p.G761G	ARHGEF28_ENST00000296799.4_Silent_p.G448G|ARHGEF28_ENST00000287898.5_Silent_p.G761G|ARHGEF28_ENST00000437974.1_Silent_p.G761G|ARHGEF28_ENST00000296794.6_Silent_p.G761G|ARHGEF28_ENST00000513042.2_Silent_p.G761G|ARHGEF28_ENST00000545377.1_Silent_p.G761G			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	761					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GTGTTCCAGGCACCACCTTGG	0.537													C|||	1115	0.222644	0.177	0.3631	5008	,	,		20460	0.1389		0.3012	False		,,,				2504	0.1902				p.G761G		Atlas-SNP	.											.	.	.	.	0			c.C2283T						PASS	.	C	,	795,3125		85,625,1250	100.0	95.0	97.0		2283,2283	-1.7	0.1	5	dbSNP_101	97	2594,5698		409,1776,1961	no	coding-synonymous,coding-synonymous	RGNEF	NM_001080479.2,NM_001177693.1	,	494,2401,3211	TT,TC,CC		31.2832,20.2806,27.7514	,	761/1732,761/1706	73163831	3389,8823	1960	4146	6106	SO:0001819	synonymous_variant	64283	exon19			TCCAGGCACCACC		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2283C>T	5.37:g.73163831C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																			C|0.759;T|0.241	0.241	strong		0.537	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
KCNA7	3743	hgsc.bcm.edu	37	19	49575304	49575304	+	Missense_Mutation	SNP	G	G	A	rs77059600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49575304G>A	ENST00000221444.1	-	1	894	c.539C>T	c.(538-540)gCa>gTa	p.A180V		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	180				A -> V (in Ref. 3; AAX11186). {ECO:0000305}.	protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	GGCTGCGGCTGCAGCAGCAAG	0.687													A|||	709	0.141573	0.2837	0.1398	5008	,	,		8486	0.0486		0.0885	False		,,,				2504	0.1012				p.A180V	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											KCNA7,rectum,carcinoma,0,1	KCNA7	30	1	0			c.C539T						scavenged	.	A	VAL/ALA	883,3133		82,719,1207	7.0	9.0	8.0		539	1.8	0.0	19	dbSNP_131	8	658,7272		33,592,3340	no	missense	KCNA7	NM_031886.2	64	115,1311,4547	AA,AG,GG		8.2976,21.9871,12.8997	benign	180/457	49575304	1541,10405	2008	3965	5973	SO:0001583	missense	3743	exon1			GCGGCTGCAGCAG	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.539C>T	19.37:g.49575304G>A	ENSP00000221444:p.Ala180Val	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_031886	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	37	CCDS12755.1	322	0.14743589743589744	158	0.32113821138211385	62	0.1712707182320442	34	0.05944055944055944	68	0.08970976253298153	A	9.871	1.198847	0.22121	0.219871	0.082976	ENSG00000104848	ENST00000221444	D	0.97620	-4.46	4.28	1.79	0.24919	.	3.155100	0.01167	N	0.006767	T	0.00012	0.0000	N	0.03224	-0.385	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.55503	-0.8131	9	0.27785	T	0.31	.	4.3707	0.11246	0.4332:0.237:0.3298:0.0	.	180	Q96RP8	KCNA7_HUMAN	V	180	ENSP00000221444:A180V	ENSP00000221444:A180V	A	-	2	0	KCNA7	54267116	0.034000	0.19679	0.006000	0.13384	0.002000	0.02628	-0.536000	0.06135	0.175000	0.19841	-0.504000	0.04507	GCA	G|0.847;A|0.153	0.153	strong		0.687	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886	
OR5L1	219437	hgsc.bcm.edu	37	11	55579102	55579102	+	Missense_Mutation	SNP	C	C	T	rs34961497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55579102C>T	ENST00000333973.2	+	1	249	c.160C>T	c.(160-162)Cgg>Tgg	p.R54W		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	54			R -> W (in dbSNP:rs34961497).			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(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				GGTCAGCTCTCGGCTCCACAC	0.468													N|||	448	0.0894569	0.1309	0.0432	5008	,	,		20175	0.0813		0.0924	False		,,,				2504	0.0716				p.R54W		Atlas-SNP	.											OR5L1,NS,carcinoma,-1,1	OR5L1	145	1	0			c.C160T						PASS	.	C	TRP/ARG	518,3882	235.5+/-248.0	32,454,1714	311.0	273.0	286.0		160	-4.8	0.0	11	dbSNP_126	286	716,7876	175.0+/-225.2	26,664,3606	no	missense	OR5L1	NM_001004738.1	101	58,1118,5320	TT,TC,CC		8.3333,11.7727,9.4982	probably-damaging	54/312	55579102	1234,11758	2200	4296	6496	SO:0001583	missense	219437	exon1			AGCTCTCGGCTCC	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.160C>T	11.37:g.55579102C>T	ENSP00000335529:p.Arg54Trp	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	276	131	0.474638	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	199	0.09111721611721611	78	0.15853658536585366	20	0.055248618784530384	36	0.06293706293706294	65	0.08575197889182058	c	14.43	2.533746	0.45073	0.117727	0.083333	ENSG00000186117	ENST00000333973	T	0.01152	5.26	4.32	-4.81	0.03180	GPCR, rhodopsin-like superfamily (1);	1.504320	0.04361	N	0.357399	T	0.00012	0.0000	M	0.87097	2.86	0.80722	P	0.0	D	0.59767	0.986	P	0.46339	0.513	T	0.33979	-0.9847	9	0.87932	D	0	9.4321	9.3255	0.37990	0.4691:0.2081:0.3227:0.0	rs34961497;rs61998195	54	Q8NGL2	OR5L1_HUMAN	W	54	ENSP00000335529:R54W	ENSP00000335529:R54W	R	+	1	2	OR5L1	55335678	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.488000	0.06497	-0.824000	0.04295	-0.575000	0.04146	CGG	C|0.907;T|0.093	0.093	strong		0.468	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418938	105418938	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105418938C>T	ENST00000333244.5	-	7	2969	c.2850G>A	c.(2848-2850)gcG>gcA	p.A950A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	950						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)			CTGTCACTTCCGCCTTGGGGC	0.617																																					p.A950A		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,-1,1	AHNAK2	719	1	0			c.G2850A						scavenged	.						139.0	163.0	156.0					14																	105418938		1929	4116	6045	SO:0001819	synonymous_variant	113146	exon7			CACTTCCGCCTTG	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.2850G>A	14.37:g.105418938C>T		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	287	5	0.0174216	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.	.	none		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MROH7	374977	hgsc.bcm.edu	37	1	55119289	55119289	+	Silent	SNP	G	G	C	rs9332417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55119289G>C	ENST00000421030.2	+	3	975	c.690G>C	c.(688-690)ctG>ctC	p.L230L	MROH7_ENST00000409996.1_Intron|MROH7-TTC4_ENST00000414150.2_Silent_p.L230L|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000395690.2_Silent_p.L230L|MROH7_ENST00000545244.1_Intron|MROH7_ENST00000339553.5_Silent_p.L230L|MROH7_ENST00000454855.2_Intron	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	230						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											AGCTGAACCTGAATGTAGCTC	0.453													G|||	2106	0.420527	0.2716	0.4063	5008	,	,		21481	0.5208		0.5944	False		,,,				2504	0.3497				p.L230L		Atlas-SNP	.											.	.	.	.	0			c.G690C						PASS	.	G		1415,2433		258,899,767	67.0	63.0	64.0		690	1.2	0.0	1	dbSNP_119	64	4876,3394		1435,2006,694	no	coding-synonymous	HEATR8	NM_001039464.2		1693,2905,1461	CC,CG,GG		41.0399,36.7723,48.0855		230/1324	55119289	6291,5827	1924	4135	6059	SO:0001819	synonymous_variant	374977	exon3			GAACCTGAATGTA	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.690G>C	1.37:g.55119289G>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	144	64	0.444444	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	37	CCDS41342.2																																																																																			G|0.547;C|0.453	0.453	strong		0.453	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
WDR11	55717	hgsc.bcm.edu	37	10	122649481	122649481	+	Missense_Mutation	SNP	C	C	T	rs150399543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:122649481C>T	ENST00000263461.6	+	18	2549	c.2303C>T	c.(2302-2304)gCa>gTa	p.A768V	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						AAATTAATAGCAATGTACAAT	0.393													C|||	12	0.00239617	0.0091	0.0	5008	,	,		15112	0.0		0.0	False		,,,				2504	0.0				p.A768V		Atlas-SNP	.											WDR11,NS,carcinoma,-1,1	WDR11	95	1	0			c.C2303T						PASS	.	C	VAL/ALA	30,4376	23.3+/-48.9	0,30,2173	114.0	108.0	110.0		2303	5.5	1.0	10	dbSNP_134	110	0,8600		0,0,4300	yes	missense	WDR11	NM_018117.11	64	0,30,6473	TT,TC,CC		0.0,0.6809,0.2307	benign	768/1225	122649481	30,12976	2203	4300	6503	SO:0001583	missense	55717	exon18			TAATAGCAATGTA	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.2303C>T	10.37:g.122649481C>T	ENSP00000263461:p.Ala768Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	37	CCDS7619.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	c	9.054	0.992836	0.18966	0.006809	0.0	ENSG00000120008	ENST00000263461	T	0.50001	0.76	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);	0.184844	0.49916	D	0.000125	T	0.11024	0.0269	N	0.00648	-1.295	0.44477	D	0.99741	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.30357	-0.9981	10	0.02654	T	1	-9.4036	13.0155	0.58754	0.0:0.9262:0.0:0.0738	.	768;768;59;297	Q9BZH6;B2RCJ6;Q9NWV7;Q659C9	WDR11_HUMAN;.;.;.	V	768	ENSP00000263461:A768V	ENSP00000263461:A768V	A	+	2	0	WDR11	122639471	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.417000	0.66423	2.733000	0.93635	0.655000	0.94253	GCA	C|0.997;T|0.003	0.003	strong		0.393	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
UPK3A	7380	hgsc.bcm.edu	37	22	45685002	45685002	+	Silent	SNP	A	A	G	rs1135360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45685002A>G	ENST00000216211.4	+	4	581	c.549A>G	c.(547-549)tcA>tcG	p.S183S	UPK3A_ENST00000396082.2_Intron	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	183					cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CCCTGTGGTCAGACCCCATCC	0.597													a|||	3327	0.664337	0.9032	0.5749	5008	,	,		17504	0.6954		0.4324	False		,,,				2504	0.6115				p.S183S		Atlas-SNP	.											.	UPK3A	14	.	0			c.A549G						PASS	.	G	,	3660,746	755.5+/-412.6	1512,636,55	90.0	82.0	85.0		,549	-9.6	0.2	22	dbSNP_86	85	3551,5049	516.0+/-378.7	737,2077,1486	no	intron,coding-synonymous	UPK3A	NM_001167574.1,NM_006953.3	,	2249,2713,1541	GG,GA,AA		41.2907,16.9315,44.5564	,	,183/288	45685002	7211,5795	2203	4300	6503	SO:0001819	synonymous_variant	7380	exon4			GTGGTCAGACCCC	AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"""uroplakin 3"""	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.549A>G	22.37:g.45685002A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Silent	SNP	ENST00000216211.4	37	CCDS14064.1																																																																																			A|0.413;G|0.587	0.587	strong		0.597	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953	
BAZ2B	29994	hgsc.bcm.edu	37	2	160287443	160287443	+	Missense_Mutation	SNP	A	A	C	rs200904019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160287443A>C	ENST00000392783.2	-	10	2620	c.2125T>G	c.(2125-2127)Tgt>Ggt	p.C709G	BAZ2B_ENST00000392782.1_Missense_Mutation_p.C707G|BAZ2B_ENST00000343439.5_Intron|BAZ2B_ENST00000355831.2_Missense_Mutation_p.C709G	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	709					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)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						GATTCAGAACATAAGGCAGCA	0.453													A|||	6	0.00119808	0.0045	0.0	5008	,	,		18357	0.0		0.0	False		,,,				2504	0.0				p.C709G		Atlas-SNP	.											.	BAZ2B	196	.	0			c.T2125G						PASS	.	A	GLY/CYS	20,3846		0,20,1913	145.0	144.0	144.0		2125	5.7	1.0	2		144	0,8272		0,0,4136	yes	missense	BAZ2B	NM_013450.2	159	0,20,6049	CC,CA,AA		0.0,0.5173,0.1648	probably-damaging	709/2169	160287443	20,12118	1933	4136	6069	SO:0001583	missense	29994	exon10			CAGAACATAAGGC	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.2125T>G	2.37:g.160287443A>C	ENSP00000376534:p.Cys709Gly	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	162	70	0.432099	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	3	0.005244755244755245	0	0.0	A	14.89	2.670797	0.47781	0.005173	0.0	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831	T;T;T	0.21191	2.02;2.02;2.02	5.71	5.71	0.89125	.	0.000000	0.40222	U	0.001146	T	0.27063	0.0663	L	0.32530	0.975	0.80722	D	1	D;D;D	0.71674	0.996;0.978;0.998	P;D;D	0.75484	0.889;0.922;0.986	T	0.02398	-1.1165	10	0.25751	T	0.34	-8.1218	15.968	0.79987	1.0:0.0:0.0:0.0	.	513;707;709	Q9UIF8-4;Q9UIF8-5;Q9UIF8	.;.;BAZ2B_HUMAN	G	707;709;709	ENSP00000376533:C707G;ENSP00000376534:C709G;ENSP00000348087:C709G	ENSP00000348087:C709G	C	-	1	0	BAZ2B	159995689	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.327000	0.52045	2.175000	0.68902	0.523000	0.50628	TGT	A|0.998;C|0.002	0.002	strong		0.453	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
ADAMTS7	11173	hgsc.bcm.edu	37	15	79065509	79065509	+	Missense_Mutation	SNP	T	T	C	rs146076001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:79065509T>C	ENST00000388820.4	-	14	2257	c.2047A>G	c.(2047-2049)Atg>Gtg	p.M683V	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	683	Cys-rich.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CGGTCCTCCATAGCACCGGAG	0.677													T|||	3	0.000599042	0.0023	0.0	5008	,	,		9782	0.0		0.0	False		,,,				2504	0.0				p.M683V		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.A2047G						PASS	.	T	VAL/MET	3,4287		0,3,2142	15.0	14.0	15.0		2047	-4.2	0.1	15	dbSNP_134	15	0,8154		0,0,4077	no	missense	ADAMTS7	NM_014272.3	21	0,3,6219	CC,CT,TT		0.0,0.0699,0.0241	benign	683/1687	79065509	3,12441	2145	4077	6222	SO:0001583	missense	11173	exon14			CCTCCATAGCACC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.2047A>G	15.37:g.79065509T>C	ENSP00000373472:p.Met683Val	Somatic	461	1	0.0021692		WXS	Illumina HiSeq	Phase_I	783	340	0.434227	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	T	0.018	-1.480661	0.01027	6.99E-4	0.0	ENSG00000136378	ENST00000388820	T	0.68025	-0.3	3.75	-4.16	0.03869	.	0.686315	0.12999	N	0.421839	T	0.22282	0.0537	N	0.00347	-1.61	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43621	-0.9380	10	0.02654	T	1	.	10.8048	0.46512	0.0:0.4278:0.0:0.5722	.	683;683	A8MQ00;Q9UKP4	.;ATS7_HUMAN	V	683	ENSP00000373472:M683V	ENSP00000373472:M683V	M	-	1	0	ADAMTS7	76852564	0.000000	0.05858	0.065000	0.19835	0.592000	0.36648	0.103000	0.15292	-0.746000	0.04766	0.386000	0.25728	ATG	T|1.000;C|0.000	0.000	weak		0.677	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
WDFY4	57705	hgsc.bcm.edu	37	10	49933974	49933974	+	Missense_Mutation	SNP	T	T	C	rs7072606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:49933974T>C	ENST00000325239.5	+	5	667	c.640T>C	c.(640-642)Tca>Cca	p.S214P	WDFY4_ENST00000413659.2_Missense_Mutation_p.S214P|WDFY4_ENST00000360890.2_Missense_Mutation_p.S214P	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	214			S -> P (in dbSNP:rs7072606). {ECO:0000269|PubMed:14702039}.			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						GGGACTCCTCTCAGGAAGTGA	0.512													T|||	702	0.140176	0.1452	0.1081	5008	,	,		21362	0.1835		0.0825	False		,,,				2504	0.1708				p.S214P		Atlas-SNP	.											.	WDFY4	205	.	0			c.T640C						PASS	.	T	PRO/SER	171,1213		13,145,534	83.0	77.0	79.0		640	-1.1	0.0	10	dbSNP_116	79	234,2948		7,220,1364	yes	missense	WDFY4	NM_020945.1	74	20,365,1898	CC,CT,TT		7.3539,12.3555,8.8699	possibly-damaging	214/3185	49933974	405,4161	692	1591	2283	SO:0001583	missense	57705	exon6			CTCCTCTCAGGAA	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.640T>C	10.37:g.49933974T>C	ENSP00000320563:p.Ser214Pro	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	290	0.13278388278388278	77	0.1565040650406504	43	0.11878453038674033	107	0.18706293706293706	63	0.08311345646437995	T	10.69	1.421290	0.25639	0.123555	0.073539	ENSG00000128815	ENST00000360890;ENST00000454161;ENST00000426033;ENST00000325239;ENST00000413659	T;T;T	0.51574	0.7;1.54;1.54	5.84	-1.14	0.09741	.	.	.	.	.	T	0.00039	0.0001	M	0.68317	2.08	0.80722	P	0.0	P;P	0.44090	0.475;0.826	B;B	0.35353	0.099;0.201	T	0.04781	-1.0927	8	0.44086	T	0.13	.	1.374	0.02216	0.216:0.1591:0.3855:0.2395	rs7072606;rs60440997;rs7072606	214;214	Q6ZS81;Q6ZS81-2	WDFY4_HUMAN;.	P	214;223;214;214;214	ENSP00000354141:S214P;ENSP00000320563:S214P;ENSP00000403789:S214P	ENSP00000320563:S214P	S	+	1	0	WDFY4	49603980	0.002000	0.14202	0.005000	0.12908	0.033000	0.12548	-0.123000	0.10611	0.108000	0.17862	-0.379000	0.06801	TCA	T|0.865;C|0.135	0.135	strong		0.512	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
KMO	8564	hgsc.bcm.edu	37	1	241712134	241712134	+	Silent	SNP	C	C	T	rs11556464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241712134C>T	ENST00000366559.4	+	2	371	c.60C>T	c.(58-60)ggC>ggT	p.G20G	KMO_ENST00000484628.1_3'UTR|KMO_ENST00000366557.4_Silent_p.G20G|KMO_ENST00000366558.3_Silent_p.G20G	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)											NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			tCTAGGTTGGCTCATTACAAG	0.348													C|||	1869	0.373203	0.528	0.4236	5008	,	,		15923	0.2788		0.3042	False		,,,				2504	0.2965				p.G20G		Atlas-SNP	.											.	KMO	69	.	0			c.C60T						PASS	.	C		2194,2212	583.2+/-385.8	540,1114,549	66.0	68.0	68.0		60	3.0	1.0	1	dbSNP_120	68	2833,5767	443.9+/-360.5	465,1903,1932	no	coding-synonymous	KMO	NM_003679.3		1005,3017,2481	TT,TC,CC		32.9419,49.7957,38.6514		20/487	241712134	5027,7979	2203	4300	6503	SO:0001819	synonymous_variant	8564	exon2			GGTTGGCTCATTA	AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	1.14.13.9		6381	protein-coding gene	gene with protein product		603538				9237672	Standard	NM_003679		Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.60C>T	1.37:g.241712134C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	15	5	0.333333	NM_003679		Silent	SNP	ENST00000366559.4	37	CCDS1618.1																																																																																			C|0.616;T|0.384	0.384	strong		0.348	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095612.1	NM_003679	
SMTN	6525	hgsc.bcm.edu	37	22	31492781	31492781	+	Missense_Mutation	SNP	C	C	T	rs34292278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31492781C>T	ENST00000347557.2	+	14	2142	c.1924C>T	c.(1924-1926)Cgc>Tgc	p.R642C	SMTN_ENST00000358743.1_Missense_Mutation_p.R642C|SMTN_ENST00000404574.1_Intron|SMTN_ENST00000333137.7_Missense_Mutation_p.R642C	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	642			R -> C (in dbSNP:rs34292278).		muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						AGGGGAGGGGCGCGGCAACAC	0.682																																					p.R727C		Atlas-SNP	.											.	SMTN	219	.	0			c.C2179T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	942,3464	329.9+/-301.2	98,746,1359	38.0	42.0	41.0		2179,2092,1924,1924,1924	4.5	0.9	22	dbSNP_126	41	4,8596	3.0+/-9.4	0,4,4296	no	missense,missense,missense,missense,missense	SMTN	NM_001207017.1,NM_001207018.1,NM_006932.4,NM_134269.2,NM_134270.2	180,180,180,180,180	98,750,5655	TT,TC,CC		0.0465,21.3799,7.2736	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	727/1003,698/972,642/918,642/916,642/941	31492781	946,12060	2203	4300	6503	SO:0001583	missense	6525	exon15			GAGGGGCGCGGCA	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.1924C>T	22.37:g.31492781C>T	ENSP00000328635:p.Arg642Cys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_001207017	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	37	CCDS13886.1	122	0.055860805860805864	115	0.23373983739837398	7	0.019337016574585635	0	0.0	0	0.0	C	14.45	2.540054	0.45176	0.213799	4.65E-4	ENSG00000183963	ENST00000358743;ENST00000347557;ENST00000333137;ENST00000329852;ENST00000404496	T;T;T	0.71579	-0.19;-0.58;-0.58	4.51	4.51	0.55191	.	0.508313	0.14906	N	0.291527	T	0.00073	0.0002	L	0.43152	1.355	0.24841	P	0.9924638	D;D;D;D;D;D	0.76494	0.998;0.999;0.999;0.998;0.997;0.999	P;P;P;P;P;P	0.62382	0.634;0.8;0.8;0.708;0.632;0.901	T	0.06716	-1.0811	9	0.87932	D	0	-0.0587	11.2158	0.48825	0.3184:0.6816:0.0:0.0	rs34292278;rs60483618	698;727;665;642;642;642	E7ETT8;B4E229;B5MC56;E7EWD0;P53814;P53814-5	.;.;.;.;SMTN_HUMAN;.	C	642;642;642;640;665	ENSP00000351593:R642C;ENSP00000328635:R642C;ENSP00000329532:R642C	ENSP00000329393:R640C	R	+	1	0	SMTN	29822781	0.932000	0.31603	0.905000	0.35620	0.034000	0.12701	2.597000	0.46214	2.237000	0.73441	0.456000	0.33151	CGC	C|0.929;T|0.071	0.071	strong		0.682	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197614	39197614	+	Silent	SNP	G	G	A	rs141856614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39197614G>A	ENST00000306271.4	-	1	99	c.36C>T	c.(34-36)ccC>ccT	p.P12P		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	12			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)			TGGAGCAGCTGGGAAATCCAC	0.587													g|||	501	0.10004	0.1846	0.1138	5008	,	,		15385	0.1419		0.0169	False		,,,				2504	0.0184				p.P12P		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.C36T						PASS	.						48.0	56.0	53.0					17																	39197614		1952	4163	6115	SO:0001819	synonymous_variant	81851	exon1			GCAGCTGGGAAAT	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.36C>T	17.37:g.39197614G>A		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	197	54	0.274112	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			G|0.935;A|0.065	0.065	strong		0.587	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
EPS8L3	79574	hgsc.bcm.edu	37	1	110301260	110301260	+	Missense_Mutation	SNP	C	C	T	rs6693815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110301260C>T	ENST00000361965.4	-	7	593	c.487G>A	c.(487-489)Ggc>Agc	p.G163S	RP4-735C1.4_ENST00000431955.1_RNA|EPS8L3_ENST00000494151.1_5'UTR|EPS8L3_ENST00000369805.3_Missense_Mutation_p.G164S|EPS8L3_ENST00000361852.4_Missense_Mutation_p.G163S	NM_133181.3	NP_573444.2	Q8TE67	ES8L3_HUMAN	EPS8-like 3	163			G -> S (in dbSNP:rs6693815). {ECO:0000269|PubMed:12620401}.			cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	32		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		CTGTCCTGGCCTGGCTGAAGG	0.607													C|||	1585	0.316494	0.7239	0.2248	5008	,	,		17602	0.0556		0.1918	False		,,,				2504	0.228				p.G164S		Atlas-SNP	.											.	EPS8L3	73	.	0			c.G490A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	2703,1703	649.4+/-398.9	828,1047,328	52.0	52.0	52.0		487,487,490	-2.2	0.0	1	dbSNP_116	52	1891,6709	335.0+/-321.2	194,1503,2603	yes	missense,missense,missense	EPS8L3	NM_024526.3,NM_133181.3,NM_139053.2	56,56,56	1022,2550,2931	TT,TC,CC		21.9884,38.6518,35.3222	benign,benign,benign	163/564,163/594,164/595	110301260	4594,8412	2203	4300	6503	SO:0001583	missense	79574	exon7			CCTGGCCTGGCTG	AK025175	CCDS813.1, CCDS814.1, CCDS815.1	1p13.2	2008-02-05			ENSG00000198758	ENSG00000198758			21297	protein-coding gene	gene with protein product		614989				12620401	Standard	NM_139053		Approved	FLJ21522, MGC16817	uc001dyq.2	Q8TE67	OTTHUMG00000011651	ENST00000361965.4:c.487G>A	1.37:g.110301260C>T	ENSP00000355255:p.Gly163Ser	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_139053	A8K833|Q5T8Q6|Q5T8Q7|Q5T8Q8|Q96E47|Q9H719	Missense_Mutation	SNP	ENST00000361965.4	37	CCDS814.1	637	0.2916666666666667	351	0.7134146341463414	85	0.23480662983425415	39	0.06818181818181818	162	0.21372031662269128	C	13.57	2.277964	0.40294	0.613482	0.219884	ENSG00000198758	ENST00000361852;ENST00000369805;ENST00000361965	T;T;T	0.59772	2.6;0.24;0.25	5.51	-2.18	0.07037	.	1.692000	0.02443	N	0.084779	T	0.07188	0.0182	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B	0.15473	0.003;0.013;0.001;0.002	B;B;B;B	0.09377	0.001;0.004;0.001;0.004	T	0.07271	-1.0781	9	0.08837	T	0.75	-0.8016	1.3281	0.02129	0.1439:0.3222:0.1401:0.3938	rs6693815;rs6693815	163;163;163;164	A8K2J6;Q8TE67-2;Q8TE67;Q8TE67-3	.;.;ES8L3_HUMAN;.	S	163;164;163	ENSP00000354551:G163S;ENSP00000358820:G164S;ENSP00000355255:G163S	ENSP00000354551:G163S	G	-	1	0	EPS8L3	110102783	0.000000	0.05858	0.003000	0.11579	0.498000	0.33706	-0.846000	0.04336	-0.055000	0.13244	0.655000	0.94253	GGC	C|0.668;T|0.332	0.332	strong		0.607	EPS8L3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032234.1	NM_024526	
OPN1LW	5956	hgsc.bcm.edu	37	X	153418535	153418535	+	Missense_Mutation	SNP	A	A	G	rs145009674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153418535A>G	ENST00000369951.4	+	3	592	c.532A>G	c.(532-534)Atc>Gtc	p.I178V	OPN1LW_ENST00000463296.1_3'UTR	NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	178					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)					CTTCTCCTGGATCTGGTCTGC	0.577													A|||	138	0.0365563	0.053	0.0202	3775	,	,		13379	0.0188		0.0109	False		,,,				2504	0.0245				p.I178V		Atlas-SNP	.											.	OPN1LW	87	.	0			c.A532G	GRCh37	CM890024	OPN1LW	M	rs145009674	PASS	.	A	VAL/ILE	134,3668		8,91,27,1531,515	242.0	144.0	178.0		532	-5.9	0.8	X	dbSNP_134	178	84,6298		11,33,29,2333,1599	no	missense	OPN1LW	NM_020061.4	29	19,124,56,3864,2114	GG,GA,G,AA,A		1.3162,3.5245,2.1406	benign	178/365	153418535	218,9966	2172	4005	6177	SO:0001583	missense	5956	exon3			TCCTGGATCTGGT	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.532A>G	X.37:g.153418535A>G	ENSP00000358967:p.Ile178Val	Somatic	430	1	0.00232558		WXS	Illumina HiSeq	Phase_I	912	287	0.314693	NM_020061		Missense_Mutation	SNP	ENST00000369951.4	37	CCDS14742.1	36	0.0216998191681736	15	0.030612244897959183	6	0.016666666666666666	9	0.015734265734265736	10	0.013227513227513227	A	0.006	-2.074522	0.00379	0.035245	0.013162	ENSG00000102076	ENST00000369951;ENST00000442922	T;T	0.37058	1.22;1.22	4.4	-5.92	0.02261	GPCR, rhodopsin-like superfamily (1);	0.592885	0.17274	N	0.180253	T	0.01695	0.0054	N	0.00504	-1.425	0.23700	N	0.997078	B	0.06786	0.001	B	0.09377	0.004	T	0.13926	-1.0491	10	0.02654	T	1	.	16.9735	0.86306	0.2531:0.0:0.7469:0.0	.	178	P04000	OPSR_HUMAN	V	178;41	ENSP00000358967:I178V;ENSP00000402493:I41V	ENSP00000358967:I178V	I	+	1	0	OPN1LW	153071729	0.000000	0.05858	0.847000	0.33407	0.049000	0.14656	-3.389000	0.00488	-1.404000	0.02050	-1.591000	0.00844	ATC	.	.	weak		0.577	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061	
ACSS1	84532	hgsc.bcm.edu	37	20	25038484	25038484	+	Silent	SNP	G	G	A	rs66817095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:25038484G>A	ENST00000323482.4	-	1	334	c.255C>T	c.(253-255)acC>acT	p.T85T	ACSS1_ENST00000376726.3_Silent_p.T85T|ACSS1_ENST00000432802.2_Silent_p.T85T	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	85					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)	TGTGGTAGGGGGTGTCCCACA	0.662																																					p.T85T		Atlas-SNP	.											.	ACSS1	46	.	0			c.C255T						PASS	.						42.0	47.0	45.0					20																	25038484		2203	4300	6503	SO:0001819	synonymous_variant	84532	exon1			GTAGGGGGTGTCC		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.255C>T	20.37:g.25038484G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																			G|0.845;T|0.155	.	alt		0.662	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
ADCY2	108	hgsc.bcm.edu	37	5	7690872	7690872	+	Silent	SNP	G	G	A	rs10079813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:7690872G>A	ENST00000338316.4	+	5	878	c.789G>A	c.(787-789)agG>agA	p.R263R	ADCY2_ENST00000537121.1_Silent_p.R83R|ADCY2_ENST00000513693.1_3'UTR	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	263					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						TCATCCAGAGGCTGCAGGGCC	0.567													G|||	98	0.0195687	0.0741	0.0	5008	,	,		15611	0.0		0.0	False		,,,				2504	0.0				p.R263R		Atlas-SNP	.											.	ADCY2	337	.	0			c.G789A						PASS	.	G		292,4114	159.6+/-192.1	7,278,1918	70.0	66.0	67.0		789	1.9	1.0	5	dbSNP_119	67	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ADCY2	NM_020546.2		7,281,6215	AA,AG,GG		0.0349,6.6273,2.2682		263/1092	7690872	295,12711	2203	4300	6503	SO:0001819	synonymous_variant	108	exon5			CCAGAGGCTGCAG	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.789G>A	5.37:g.7690872G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																			G|0.976;A|0.024	0.024	strong		0.567	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
RIMS2	9699	hgsc.bcm.edu	37	8	104897606	104897606	+	Missense_Mutation	SNP	C	C	G	rs146399863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104897606C>G	ENST00000436393.2	+	2	354	c.113C>G	c.(112-114)gCt>gGt	p.A38G	RIMS2_ENST00000262231.10_Missense_Mutation_p.A68G|RIMS2_ENST00000522174.1_3'UTR|RIMS2_ENST00000507740.1_Missense_Mutation_p.A68G|RIMS2_ENST00000406091.3_Missense_Mutation_p.A260G			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	291	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TCACAGTATGCTACTTCGGAT	0.398										HNSCC(12;0.0054)			C|||	2	0.000399361	0.0015	0.0	5008	,	,		21790	0.0		0.0	False		,,,				2504	0.0				p.A260G		Atlas-SNP	.											.	RIMS2	1357	.	0			c.C779G						PASS	.	C	GLY/ALA,GLY/ALA	6,3780		0,6,1887	92.0	83.0	86.0		779,203	4.4	1.0	8	dbSNP_134	86	0,8240		0,0,4120	yes	missense,missense	RIMS2	NM_001100117.2,NM_014677.4	60,60	0,6,6007	GG,GC,CC		0.0,0.1585,0.0499	benign,benign	260/1350,68/1164	104897606	6,12020	1893	4120	6013	SO:0001583	missense	9699	exon4			AGTATGCTACTTC	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.113C>G	8.37:g.104897606C>G	ENSP00000390665:p.Ala38Gly	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	14.15	2.450412	0.43531	0.001585	0.0	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.37584	1.19;1.19;2.19;2.26;2.25;2.18;2.62	5.31	4.42	0.53409	.	.	.	.	.	T	0.41419	0.1158	L	0.51422	1.61	0.80722	D	1	B;P;P;P;P	0.45902	0.278;0.676;0.868;0.694;0.559	B;B;P;B;B	0.48141	0.248;0.273;0.568;0.332;0.361	T	0.31138	-0.9954	9	0.54805	T	0.06	.	12.9673	0.58492	0.0:0.9206:0.0:0.0794	.	291;38;68;68;260	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	G	260;291;260;291;68;68;68;68;38	ENSP00000427018:A260G;ENSP00000384892:A260G;ENSP00000425205:A68G;ENSP00000262231:A68G;ENSP00000423559:A68G;ENSP00000386228:A68G;ENSP00000390665:A38G	ENSP00000262231:A68G	A	+	2	0	RIMS2	104966782	1.000000	0.71417	0.973000	0.42090	0.970000	0.65996	4.441000	0.59981	1.204000	0.43247	0.460000	0.39030	GCT	C|0.999;G|0.001	0.001	strong		0.398	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117	
DPP6	1804	hgsc.bcm.edu	37	7	154672646	154672646	+	Silent	SNP	T	T	C	rs3817522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:154672646T>C	ENST00000377770.3	+	21	2268	c.2127T>C	c.(2125-2127)ttT>ttC	p.F709F	DPP6_ENST00000332007.3_Silent_p.F647F|DPP6_ENST00000404039.1_Silent_p.F645F|DPP6_ENST00000427557.1_Silent_p.F602F			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	709					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TGGCCGTGTTTGGGAAGGTGA	0.552													t|||	1327	0.264976	0.4902	0.3963	5008	,	,		16029	0.1002		0.1879	False		,,,				2504	0.1166				p.F709F	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.T2127C						PASS	.	T	,,	1773,2469		377,1019,725	99.0	109.0	106.0		1581,1500,1500	-2.1	1.0	7	dbSNP_107	106	1514,6950		133,1248,2851	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	510,2267,3576	CC,CT,TT		17.8875,41.7963,25.8697	,,	527/684,500/657,500/657	154672646	3287,9419	2121	4232	6353	SO:0001819	synonymous_variant	1804	exon21			CGTGTTTGGGAAG	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"""dipeptidylpeptidase VI"", ""dipeptidylpeptidase 6"""			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.2127T>C	7.37:g.154672646T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				T|0.742;C|0.258	0.258	strong		0.552	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
TANK	10010	hgsc.bcm.edu	37	2	162088034	162088034	+	Missense_Mutation	SNP	C	C	T	rs2229759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:162088034C>T	ENST00000392749.2	+	7	1312	c.1073C>T	c.(1072-1074)cCg>cTg	p.P358L	TANK_ENST00000402568.1_Intron|TANK_ENST00000406287.1_Intron|AC009299.2_ENST00000445372.1_RNA|AC009299.2_ENST00000421122.2_RNA|TANK_ENST00000405852.1_Missense_Mutation_p.P358L|TANK_ENST00000259075.2_Missense_Mutation_p.P358L	NM_001199135.1	NP_001186064.1	Q92844	TANK_HUMAN	TRAF family member-associated NFKB activator	358			P -> L (in dbSNP:rs2229759).		I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)	21						CTCGATTCCCCGGGAAAAGCA	0.433													C|||	128	0.0255591	0.0938	0.0058	5008	,	,		19086	0.0		0.0	False		,,,				2504	0.0				p.P358L		Atlas-SNP	.											TANK,NS,carcinoma,-1,1	TANK	35	1	0			c.C1073T						PASS	.	C	LEU/PRO,LEU/PRO	230,4176	129.8+/-166.5	4,222,1977	45.0	45.0	45.0		1073,1073	5.6	1.0	2	dbSNP_98	45	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense	TANK	NM_001199135.1,NM_004180.2	98,98	4,225,6273	TT,TC,CC		0.0349,5.2202,1.7918	probably-damaging,probably-damaging	358/426,358/426	162088034	233,12771	2203	4299	6502	SO:0001583	missense	10010	exon7			ATTCCCCGGGAAA	U59863	CCDS2215.1, CCDS46436.1	2q24-q31	2008-02-05			ENSG00000136560	ENSG00000136560			11562	protein-coding gene	gene with protein product		603893		TRAF2		8710854, 8855313	Standard	NM_004180		Approved	I-TRAF	uc002ubr.2	Q92844	OTTHUMG00000132037	ENST00000392749.2:c.1073C>T	2.37:g.162088034C>T	ENSP00000376505:p.Pro358Leu	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_004180	D3DPB5|Q7Z4J6|Q92885	Missense_Mutation	SNP	ENST00000392749.2	37	CCDS2215.1	49	0.022435897435897436	47	0.09552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	16.38	3.106713	0.56291	0.052202	3.49E-4	ENSG00000136560	ENST00000259075;ENST00000392749;ENST00000405852;ENST00000437623;ENST00000439442	T;T;T;T;T	0.35973	1.68;1.68;1.29;1.28;1.61	5.57	5.57	0.84162	.	0.280521	0.34460	N	0.003944	T	0.01489	0.0048	L	0.59436	1.845	0.80722	D	1	D	0.63046	0.992	P	0.48454	0.578	T	0.00126	-1.2021	10	0.87932	D	0	-5.8187	15.5156	0.75822	0.1389:0.8611:0.0:0.0	rs2229759;rs35125118	358	Q92844	TANK_HUMAN	L	358;358;358;249;113	ENSP00000259075:P358L;ENSP00000376505:P358L;ENSP00000385487:P358L;ENSP00000412556:P249L;ENSP00000387439:P113L	ENSP00000259075:P358L	P	+	2	0	TANK	161796280	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	3.944000	0.56629	2.784000	0.95788	0.585000	0.79938	CCG	C|0.977;T|0.023	0.023	strong		0.433	TANK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324232.1	NM_133484	
MUC4	4585	hgsc.bcm.edu	37	3	195512117	195512117	+	Missense_Mutation	SNP	C	C	G	rs200655750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512117C>G	ENST00000463781.3	-	2	6793	c.6334G>C	c.(6334-6336)Gct>Cct	p.A2112P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2112P	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		TCATGAAGAGCGGTGGCGTGA	0.567																																					p.A2112P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G6334C						scavenged	.						73.0	62.0	65.0					3																	195512117		691	1589	2280	SO:0001583	missense	4585	exon2			GAAGAGCGGTGGC	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.6334G>C	3.37:g.195512117C>G	ENSP00000417498:p.Ala2112Pro	Somatic	685	5	0.00729927		WXS	Illumina HiSeq	Phase_I	331	85	0.256798	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	7.400	0.632537	0.14322	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.43688	0.94;0.97	.	.	.	.	.	.	.	.	T	0.11750	0.0286	N	0.02539	-0.55	0.19575	N	0.999964	B	0.27316	0.175	B	0.12156	0.007	T	0.15263	-1.0443	7	.	.	.	.	2.7487	0.05274	0.0:0.2996:0.4009:0.2994	.	2112	E7ESK3	.	P	2112	ENSP00000417498:A2112P;ENSP00000420243:A2112P	.	A	-	1	0	MUC4	196996512	.	.	0.012000	0.15200	0.011000	0.07611	.	.	-2.075000	0.00876	-2.332000	0.00249	GCT	C|0.939;G|0.061	0.061	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SH3BP4	23677	hgsc.bcm.edu	37	2	235949920	235949920	+	Silent	SNP	A	A	G	rs3731645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:235949920A>G	ENST00000409212.1	+	4	1014	c.507A>G	c.(505-507)ccA>ccG	p.P169P	SH3BP4_ENST00000344528.4_Silent_p.P169P|SH3BP4_ENST00000392011.2_Silent_p.P169P			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	169					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)	p.P169P(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		AGACCAATCCATTTCTGAATG	0.502													G|||	1657	0.330871	0.4002	0.3372	5008	,	,		21045	0.4127		0.0915	False		,,,				2504	0.3947				p.P169P		Atlas-SNP	.											SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	1	Substitution - coding silent(1)	stomach(1)	c.A507G						PASS	.	G		1615,2791	662.3+/-401.0	311,993,899	114.0	115.0	115.0		507	-11.2	0.0	2	dbSNP_107	115	895,7705	778.2+/-407.7	44,807,3449	no	coding-synonymous	SH3BP4	NM_014521.2		355,1800,4348	GG,GA,AA		10.407,36.6546,19.2988		169/964	235949920	2510,10496	2203	4300	6503	SO:0001819	synonymous_variant	23677	exon4			CAATCCATTTCTG	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.507A>G	2.37:g.235949920A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	CCDS2513.1																																																																																			A|0.760;G|0.240	0.240	strong		0.502	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
XAB2	56949	hgsc.bcm.edu	37	19	7684502	7684502	+	Silent	SNP	G	G	A	rs4134869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7684502G>A	ENST00000358368.4	-	19	2575	c.2538C>T	c.(2536-2538)gcC>gcT	p.A846A	XAB2_ENST00000534844.1_Silent_p.A843A	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	846					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CAAACACTGCGGCTGGCACGC	0.647								Direct reversal of damage;Nucleotide excision repair (NER)					g|||	196	0.0391374	0.1415	0.0115	5008	,	,		8459	0.001		0.0	False		,,,				2504	0.0				p.A846A		Atlas-SNP	.											.	XAB2	69	.	0			c.C2538T						PASS	.			613,3789		55,503,1643	26.0	24.0	25.0		2538	-7.2	0.1	19	dbSNP_108	25	4,8592		0,4,4294	no	coding-synonymous	XAB2	NM_020196.2		55,507,5937	AA,AG,GG		0.0465,13.9255,4.7469		846/856	7684502	617,12381	2201	4298	6499	SO:0001819	synonymous_variant	56949	exon19			CACTGCGGCTGGC	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.2538C>T	19.37:g.7684502G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	161	78	0.484472	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	37	CCDS32892.1																																																																																			G|0.944;A|0.056	0.056	strong		0.647	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
BMPER	168667	hgsc.bcm.edu	37	7	33946464	33946464	+	Silent	SNP	C	C	T	rs112068976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:33946464C>T	ENST00000297161.2	+	3	542	c.168C>T	c.(166-168)gtC>gtT	p.V56V	BMPER_ENST00000426693.1_Silent_p.V56V	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	56	VWFC 1. {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						AAGGTGAAGTCCTCCAGATTC	0.378													C|||	4	0.000798722	0.003	0.0	5008	,	,		18193	0.0		0.0	False		,,,				2504	0.0				p.V56V		Atlas-SNP	.											BMPER,NS,carcinoma,+1,1	BMPER	131	1	0			c.C168T						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	142.0	130.0	134.0		168	-6.9	0.3	7	dbSNP_132	134	0,8600		0,0,4300	no	coding-synonymous	BMPER	NM_133468.3		0,15,6488	TT,TC,CC		0.0,0.3404,0.1153		56/686	33946464	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	168667	exon3			TGAAGTCCTCCAG		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.168C>T	7.37:g.33946464C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	37	CCDS5442.1																																																																																			C|0.999;T|0.001	0.001	strong		0.378	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
ARID4B	51742	hgsc.bcm.edu	37	1	235392546	235392546	+	Splice_Site	SNP	T	T	C	rs17846600|rs12731746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235392546T>C	ENST00000264183.3	-	11	1394	c.897A>G	c.(895-897)gaA>gaG	p.E299E	ARID4B_ENST00000366603.2_Splice_Site_p.E299E|ARID4B_ENST00000349213.3_Splice_Site_p.E299E	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	299	Glu-rich.				histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TTTCACTTACTTCTTCTTCAC	0.348													C|||	2247	0.448682	0.4342	0.5086	5008	,	,		17805	0.251		0.4791	False		,,,				2504	0.5982				p.E299E		Atlas-SNP	.											.	ARID4B	142	.	0			c.A897G						PASS	.	C	,,	2060,2346	605.0+/-390.5	474,1112,617	95.0	88.0	90.0		897,897,897	4.0	1.0	1	dbSNP_121	90	3983,4617	598.5+/-393.9	920,2143,1237	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ARID4B	NM_001206794.1,NM_016374.5,NM_031371.3	,,	1394,3255,1854	CC,CT,TT		46.314,46.7544,46.4632	,,	299/1313,299/1313,299/1227	235392546	6043,6963	2203	4300	6503	SO:0001630	splice_region_variant	51742	exon11			ACTTACTTCTTCT	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.897+1A>G	1.37:g.235392546T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Silent	SNP	ENST00000264183.3	37	CCDS31061.1																																																																																			T|0.545;C|0.455	0.455	strong		0.348	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	Silent
CHD1	1105	hgsc.bcm.edu	37	5	98199204	98199204	+	Silent	SNP	C	C	T	rs161941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:98199204C>T	ENST00000284049.3	-	31	4484	c.4335G>A	c.(4333-4335)gaG>gaA	p.E1445E	CHD1_ENST00000511067.1_5'UTR	NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1445					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	GTCTAGTATGCTCTAGTTGTT	0.338													T|||	1484	0.296326	0.6082	0.2363	5008	,	,		15783	0.0427		0.2903	False		,,,				2504	0.1851				p.E1445E		Atlas-SNP	.											.	CHD1	137	.	0			c.G4335A						PASS	.	T		2367,2037	559.5+/-380.2	652,1063,487	96.0	102.0	100.0		4335	-6.7	0.8	5	dbSNP_79	100	2469,6129	692.1+/-404.6	355,1759,2185	no	coding-synonymous	CHD1	NM_001270.2		1007,2822,2672	TT,TC,CC		28.716,46.2534,37.1943		1445/1711	98199204	4836,8166	2202	4299	6501	SO:0001819	synonymous_variant	1105	exon31			AGTATGCTCTAGT	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.4335G>A	5.37:g.98199204C>T		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_001270	Q17RZ3	Silent	SNP	ENST00000284049.3	37	CCDS34204.1																																																																																			C|0.658;T|0.342	0.342	strong		0.338	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
LRRC14	9684	hgsc.bcm.edu	37	8	145742879	145742879	+	5'Flank	SNP	T	T	C	rs2306386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145742879T>C	ENST00000292524.1	+	0	0				RECQL4_ENST00000532237.1_5'UTR|RECQL4_ENST00000428558.2_Silent_p.E44E|LRRC14_ENST00000529022.1_5'Flank	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-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;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GAGTGCGGTATTCCCGGTAGA	0.786													C|||	2880	0.57508	0.618	0.6282	5008	,	,		8649	0.5238		0.4891	False		,,,				2504	0.6207				p.E44E		Atlas-SNP	.											.	RECQL4	75	.	0			c.A132G						PASS	.	C		2027,1165		681,665,250	5.0	7.0	6.0		132	1.0	0.6	8	dbSNP_100	6	3861,3639		1088,1685,977	no	coding-synonymous	RECQL4	NM_004260.3		1769,2350,1227	CC,CT,TT		48.52,36.4975,44.9308		44/1209	145742879	5888,4804	1596	3750	5346	SO:0001631	upstream_gene_variant	9401	exon3			GCGGTATTCCCGG	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		8.37:g.145742879T>C	Exception_encountered	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_004260	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			T|0.468;C|0.532	0.532	strong		0.786	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
FCRL6	343413	hgsc.bcm.edu	37	1	159785425	159785425	+	Missense_Mutation	SNP	A	A	G	rs4443889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159785425A>G	ENST00000368106.3	+	10	1280	c.1279A>G	c.(1279-1281)Agc>Ggc	p.S427G	FCRL6_ENST00000339348.5_3'UTR|FCRL6_ENST00000321935.6_3'UTR	NM_001004310.2	NP_001004310.2	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6	427			S -> G (in dbSNP:rs4443889).			external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.S427G(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)					AGAACCCCTTAGCGACTGTGA	0.547													.|||	1268	0.253195	0.4622	0.2334	5008	,	,		19157	0.1716		0.2018	False		,,,				2504	0.1217				p.S427G		Atlas-SNP	.											FCRL6,NS,carcinoma,0,1	FCRL6	61	1	1	Substitution - Missense(1)	stomach(1)	c.A1279G						PASS	.	G	GLY/SER	1921,2485	624.3+/-394.3	426,1069,708	87.0	88.0	88.0		1279	2.0	0.0	1	dbSNP_111	88	1704,6896	737.8+/-407.0	168,1368,2764	yes	missense	FCRL6	NM_001004310.2	56	594,2437,3472	GG,GA,AA		19.814,43.5996,27.8718	benign	427/435	159785425	3625,9381	2203	4300	6503	SO:0001583	missense	343413	exon10			CCCCTTAGCGACT	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.1279A>G	1.37:g.159785425A>G	ENSP00000357086:p.Ser427Gly	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001004310	A1KXW6|A2A4D6|Q6DN73|Q6XRC3|Q6ZNI1	Missense_Mutation	SNP	ENST00000368106.3	37	CCDS30912.1	556	0.25457875457875456	207	0.42073170731707316	92	0.2541436464088398	112	0.1958041958041958	145	0.19129287598944592	G	0.023	-1.396496	0.01175	0.435996	0.19814	ENSG00000181036	ENST00000368106	T	0.01221	5.15	3.87	2.01	0.26516	.	.	.	.	.	T	0.00210	0.0006	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33752	-0.9856	8	0.02654	T	1	.	6.1235	0.20165	0.3226:0.0:0.6774:0.0	rs4443889;rs59806834;rs4443889	427	Q6DN72	FCRL6_HUMAN	G	427	ENSP00000357086:S427G	ENSP00000357086:S427G	S	+	1	0	FCRL6	158052049	0.001000	0.12720	0.000000	0.03702	0.017000	0.09413	0.391000	0.20784	0.244000	0.21351	-0.320000	0.08662	AGC	A|0.725;G|0.275	0.275	strong		0.547	FCRL6-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276853.1	NM_001004310	
SYNE3	161176	hgsc.bcm.edu	37	14	95906023	95906023	+	Silent	SNP	G	G	A	rs17828632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95906023G>A	ENST00000334258.5	-	12	2186	c.2172C>T	c.(2170-2172)gcC>gcT	p.A724A	SYNE3_ENST00000554873.1_Silent_p.A481A|SYNE3_ENST00000557275.1_Silent_p.A724A	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	724					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						CCTGCACCACGGCAGCACCCT	0.637													G|||	629	0.125599	0.0756	0.0865	5008	,	,		19100	0.1677		0.0944	False		,,,				2504	0.2096				p.A724A		Atlas-SNP	.											.	SYNE3	130	.	0			c.C2172T						PASS	.	G		376,4030	191.6+/-217.2	19,338,1846	50.0	52.0	51.0		2172	-4.1	0.0	14	dbSNP_123	51	1136,7464	235.4+/-268.0	79,978,3243	no	coding-synonymous	C14orf49	NM_152592.3		98,1316,5089	AA,AG,GG		13.2093,8.5338,11.6254		724/976	95906023	1512,11494	2203	4300	6503	SO:0001819	synonymous_variant	161176	exon12			CACCACGGCAGCA	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.2172C>T	14.37:g.95906023G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	79	29	0.367089	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	37	CCDS9935.1																																																																																			G|0.883;A|0.117	0.117	strong		0.637	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
MEIOB	254528	hgsc.bcm.edu	37	16	1894912	1894912	+	Silent	SNP	C	C	T	rs9806826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1894912C>T	ENST00000397344.3	-	10	1025	c.831G>A	c.(829-831)acG>acA	p.T277T	MEIOB_ENST00000452149.2_Silent_p.T277T|LA16c-429E7.1_ENST00000570247.1_RNA|MEIOB_ENST00000325962.3_Silent_p.T277T|MEIOB_ENST00000470044.1_Silent_p.T70T|MEIOB_ENST00000412554.2_Silent_p.T277T	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	277					double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										CCAGAACATTCGTTTCTTTAT	0.279													T|||	1854	0.370208	0.3548	0.3242	5008	,	,		17509	0.4246		0.3141	False		,,,				2504	0.4254				p.T277T		Atlas-SNP	.											C16orf73_ENST00000412554,NS,carcinoma,-1,2	.	.	2	0			c.G831A						PASS	.	T	,	1467,2921	665.6+/-401.6	242,983,969	50.0	51.0	50.0		831,831	0.8	0.0	16	dbSNP_119	50	2459,6107	685.3+/-404.0	374,1711,2198	no	coding-synonymous,coding-synonymous	C16orf73	NM_001163560.2,NM_152764.2	,	616,2694,3167	TT,TC,CC		28.7065,33.4321,30.3072	,	277/472,277/443	1894912	3926,9028	2194	4283	6477	SO:0001819	synonymous_variant	254528	exon10			AACATTCGTTTCT	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 73"""	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.831G>A	16.37:g.1894912C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	209	86	0.411483	NM_001163560	B1AK39|C9J0S1|Q96RY0	Silent	SNP	ENST00000397344.3	37	CCDS10449.2																																																																																			C|0.681;T|0.319	0.319	strong		0.279	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764	
BAI2	576	hgsc.bcm.edu	37	1	32196647	32196647	+	Silent	SNP	C	C	G	rs909001|rs35020949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:32196647C>G	ENST00000373658.3	-	29	4475	c.4134G>C	c.(4132-4134)ccG>ccC	p.P1378P	BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000257070.4_Silent_p.P1345P|BAI2_ENST00000398542.1_Silent_p.P1278P|BAI2_ENST00000398538.1_Silent_p.P1366P|BAI2_ENST00000527361.1_Silent_p.P1345P|BAI2_ENST00000373655.2_Silent_p.P1378P|BAI2_ENST00000440175.2_Silent_p.P987P|BAI2_ENST00000398547.1_Silent_p.P1311P|BAI2_ENST00000398556.3_Silent_p.P1293P	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1378					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GGGTCCCCTCCGGCCGGGCCC	0.711													G|||	1930	0.385383	0.7579	0.2594	5008	,	,		12912	0.2331		0.159	False		,,,				2504	0.3609				p.P1378P		Atlas-SNP	.											.	BAI2	128	.	0			c.G4134C						PASS	.	G		2507,1833		741,1025,404	8.0	11.0	10.0		4134	-10.9	0.0	1	dbSNP_86	10	1364,7136		119,1126,3005	no	coding-synonymous	BAI2	NM_001703.2		860,2151,3409	GG,GC,CC		16.0471,42.235,30.148		1378/1586	32196647	3871,8969	2170	4250	6420	SO:0001819	synonymous_variant	576	exon29			CCCCTCCGGCCGG	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.4134G>C	1.37:g.32196647C>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	37	CCDS346.2																																																																																			C|0.675;G|0.325	0.325	strong		0.711	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
FREM2	341640	hgsc.bcm.edu	37	13	39264690	39264690	+	Missense_Mutation	SNP	T	T	C	rs2496425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39264690T>C	ENST00000280481.7	+	1	3425	c.3209T>C	c.(3208-3210)tTt>tCt	p.F1070S		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1070			F -> S (in dbSNP:rs2496425).		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)		CCAGAAATCTTTGTAGGTGAA	0.413													C|||	2410	0.48123	0.8381	0.4496	5008	,	,		21289	0.4177		0.2624	False		,,,				2504	0.3119				p.F1070S		Atlas-SNP	.											FREM2,colon,carcinoma,0,1	FREM2	385	1	0			c.T3209C	GRCh37	CM065186	FREM2	M	rs2496425	PASS	.	C	SER/PHE	3315,1091	395.4+/-329.6	1247,821,135	105.0	106.0	106.0		3209	6.1	1.0	13	dbSNP_100	106	2360,6240	702.8+/-405.3	325,1710,2265	yes	missense	FREM2	NM_207361.4	155	1572,2531,2400	CC,CT,TT		27.4419,24.7617,43.6337	benign	1070/3170	39264690	5675,7331	2203	4300	6503	SO:0001583	missense	341640	exon1			AAATCTTTGTAGG	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.3209T>C	13.37:g.39264690T>C	ENSP00000280481:p.Phe1070Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	104	43	0.413462	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	998	0.45695970695970695	403	0.8191056910569106	151	0.4171270718232044	245	0.42832167832167833	199	0.262532981530343	C	0.013	-1.615018	0.00835	0.752383	0.274419	ENSG00000150893	ENST00000280481	T	0.39229	1.09	6.07	6.07	0.98685	.	0.283692	0.41001	N	0.000966	T	0.00012	0.0000	N	0.21545	0.675	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27839	-1.0062	9	0.11794	T	0.64	.	10.1398	0.42728	0.0:0.8123:0.0:0.1877	rs2496425;rs17304515;rs57839593;rs2496425	1070	Q5SZK8	FREM2_HUMAN	S	1070	ENSP00000280481:F1070S	ENSP00000280481:F1070S	F	+	2	0	FREM2	38162690	0.000000	0.05858	0.989000	0.46669	0.624000	0.37722	0.928000	0.28831	1.598000	0.50083	-0.128000	0.14901	TTT	T|0.546;C|0.454	0.454	strong		0.413	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
FCGBP	8857	hgsc.bcm.edu	37	19	40364397	40364397	+	Missense_Mutation	SNP	C	C	T	rs148917660		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40364397C>T	ENST00000221347.6	-	31	14252	c.14245G>A	c.(14245-14247)Ggt>Agt	p.G4749S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4749	TIL 11.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CAGGAGTCACCGCAGAGCTCA	0.647													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14509	0.0		0.0	False		,,,				2504	0.0				p.G4749S		Atlas-SNP	.											.	FCGBP	416	.	0			c.G14245A						PASS	.	C	SER/GLY	28,4376		0,28,2174	36.0	35.0	35.0		14245	4.1	0.0	19	dbSNP_134	35	0,8600		0,0,4300	no	missense	FCGBP	NM_003890.2	56	0,28,6474	TT,TC,CC		0.0,0.6358,0.2153	probably-damaging	4749/5406	40364397	28,12976	2202	4300	6502	SO:0001583	missense	8857	exon31			AGTCACCGCAGAG	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.14245G>A	19.37:g.40364397C>T	ENSP00000221347:p.Gly4749Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.577576	0.28180	0.006358	0.0	ENSG00000090920	ENST00000221347	T	0.77750	-1.12	5.14	4.1	0.47936	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	0.072904	0.53938	U	0.000047	T	0.59932	0.2230	M	0.66439	2.03	0.09310	N	1	P	0.40731	0.728	B	0.30495	0.116	T	0.58645	-0.7600	10	0.06891	T	0.86	.	12.6598	0.56808	0.0:0.9183:0.0:0.0817	.	4749	Q9Y6R7	FCGBP_HUMAN	S	4749	ENSP00000221347:G4749S	ENSP00000221347:G4749S	G	-	1	0	FCGBP	45056237	0.096000	0.21769	0.026000	0.17262	0.357000	0.29423	2.708000	0.47152	1.312000	0.45043	0.313000	0.20887	GGT	C|0.997;T|0.003	0.003	strong		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PTPRN2	5799	hgsc.bcm.edu	37	7	157959794	157959794	+	Missense_Mutation	SNP	T	T	C	rs73745196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157959794T>C	ENST00000389418.4	-	6	748	c.739A>G	c.(739-741)Agt>Ggt	p.S247G	PTPRN2_ENST00000409483.1_Missense_Mutation_p.S209G|PTPRN2_ENST00000389416.4_Missense_Mutation_p.S230G|PTPRN2_ENST00000389413.3_Missense_Mutation_p.S247G|PTPRN2_ENST00000404321.2_Missense_Mutation_p.S270G	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	247				S -> G (in Ref. 2; CAA69880). {ECO:0000305}.	negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCATAGGCACTGAGGGCCGCC	0.662													C|||	100	0.0199681	0.0688	0.0086	5008	,	,		16162	0.0		0.003	False		,,,				2504	0.0				p.S247G		Atlas-SNP	.											.	PTPRN2	243	.	0			c.A739G						PASS	.		GLY/SER,GLY/SER,GLY/SER	297,4109	770.2+/-413.7	12,273,1918	27.0	23.0	25.0		739,688,739	-0.8	0.0	7	dbSNP_130	25	0,8600		0,0,4300	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	56,56,56	12,273,6218	CC,CT,TT		0.0,6.7408,2.2836	benign,benign,benign	247/1016,230/999,247/987	157959794	297,12709	2203	4300	6503	SO:0001583	missense	5799	exon6			AGGCACTGAGGGC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.739A>G	7.37:g.157959794T>C	ENSP00000374069:p.Ser247Gly	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	49	0.022435897435897436	42	0.08536585365853659	4	0.011049723756906077	0	0.0	3	0.00395778364116095	C	0.036	-1.306812	0.01353	0.067408	0.0	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02916	4.12;4.13;4.12;4.12;4.11	4.59	-0.828	0.10799	.	0.484707	0.13807	N	0.361341	T	0.00073	0.0002	N	0.04203	-0.255	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.48080	-0.9066	10	0.19147	T	0.46	.	10.525	0.44943	0.0:0.1914:0.0:0.8086	.	270;209;247;230;247	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	G	209;247;230;247;270	ENSP00000387114:S209G;ENSP00000374064:S247G;ENSP00000374067:S230G;ENSP00000374069:S247G;ENSP00000385464:S270G	ENSP00000374064:S247G	S	-	1	0	PTPRN2	157652555	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.189000	0.09629	-0.624000	0.05611	-1.071000	0.02255	AGT	T|0.974;C|0.026	0.026	strong		0.662	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
DEPDC7	91614	hgsc.bcm.edu	37	11	33053107	33053107	+	Silent	SNP	C	C	T	rs966191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:33053107C>T	ENST00000241051.3	+	5	1058	c.966C>T	c.(964-966)gaC>gaT	p.D322D	DEPDC7_ENST00000311388.3_Silent_p.D313D	NM_001077242.1	NP_001070710.1	Q96QD5	DEPD7_HUMAN	DEP domain containing 7	322					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						ACTTATCTGACGTTCATAATG	0.373													C|||	1987	0.396765	0.4402	0.4553	5008	,	,		21448	0.4236		0.4105	False		,,,				2504	0.2546				p.D322D		Atlas-SNP	.											.	DEPDC7	94	.	0			c.C966T						PASS	.	C	,	1578,2102		331,916,593	88.0	83.0	85.0		966,939	-4.4	0.9	11	dbSNP_86	85	3291,4905		676,1939,1483	no	coding-synonymous,coding-synonymous	DEPDC7	NM_001077242.1,NM_139160.2	,	1007,2855,2076	TT,TC,CC		40.1537,42.8804,40.9987	,	322/512,313/503	33053107	4869,7007	1840	4098	5938	SO:0001819	synonymous_variant	91614	exon5			ATCTGACGTTCAT		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.966C>T	11.37:g.33053107C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_001077242	G5E941|Q8N602|Q8NCU9|Q9UGK5	Silent	SNP	ENST00000241051.3	37	CCDS41632.1																																																																																			C|0.588;T|0.412	0.412	strong		0.373	DEPDC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388655.1	NM_139160	
ACO1	48	hgsc.bcm.edu	37	9	32425910	32425910	+	Silent	SNP	A	A	G	rs3780473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:32425910A>G	ENST00000309951.6	+	11	1401	c.1263A>G	c.(1261-1263)gaA>gaG	p.E421E	ACO1_ENST00000379923.1_Silent_p.E421E|ACO1_ENST00000541043.1_Silent_p.E322E	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	421					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)		ATAACACTGAATTCACCCTTG	0.393													A|||	1772	0.353834	0.2632	0.3386	5008	,	,		17408	0.5516		0.336	False		,,,				2504	0.3016				p.E421E		Atlas-SNP	.											.	ACO1	149	.	0			c.A1263G						PASS	.	A		1204,3202	417.8+/-338.1	167,870,1166	142.0	110.0	121.0		1263	0.7	1.0	9	dbSNP_107	121	3048,5552	468.5+/-367.3	566,1916,1818	no	coding-synonymous	ACO1	NM_002197.2		733,2786,2984	GG,GA,AA		35.4419,27.3264,32.6926		421/890	32425910	4252,8754	2203	4300	6503	SO:0001819	synonymous_variant	48	exon11			CACTGAATTCACC	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.1263A>G	9.37:g.32425910A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	126	60	0.47619	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	37	CCDS6525.1																																																																																			G|0.346;N|0.000	0.346	strong		0.393	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	
PSPH	5723	hgsc.bcm.edu	37	7	56088789	56088789	+	Silent	SNP	G	G	A	rs199851385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:56088789G>A	ENST00000395471.3	-	4	922	c.117C>T	c.(115-117)ggC>ggT	p.G39G	PSPH_ENST00000275605.3_Silent_p.G39G|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	39					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CGTCCTCAACGCCACAGATTT	0.423																																					p.G39G		Atlas-SNP	.											.	PSPH	23	.	0			c.C117T						PASS	.						152.0	117.0	129.0					7																	56088789		2203	4300	6503	SO:0001819	synonymous_variant	5723	exon4			CTCAACGCCACAG	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.117C>T	7.37:g.56088789G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	231	67	0.290043	NM_004577	B2RCR5|Q7Z3S5	Silent	SNP	ENST00000395471.3	37	CCDS5522.1																																																																																			G|0.750;A|0.250	0.250	strong		0.423	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
TCHH	7062	hgsc.bcm.edu	37	1	152082320	152082320	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152082320T>C	ENST00000368804.1	-	2	3372	c.3373A>G	c.(3373-3375)Aga>Gga	p.R1125G		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1125	10 X 30 AA tandem repeats.				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)			cgttcctctctcagcagctgc	0.612																																					p.R1125G		Atlas-SNP	.											TCHH,NS,carcinoma,0,5	TCHH	275	5	0			c.A3373G						scavenged	.						93.0	94.0	94.0					1																	152082320		1979	4139	6118	SO:0001583	missense	7062	exon3			CCTCTCTCAGCAG	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.3373A>G	1.37:g.152082320T>C	ENSP00000357794:p.Arg1125Gly	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	292	12	0.0410959	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	T	5.521	0.281051	0.10458	.	.	ENSG00000159450	ENST00000368804	T	0.06849	3.25	2.38	1.02	0.19986	.	.	.	.	.	T	0.04407	0.0121	L	0.29908	0.895	0.09310	N	1	D	0.58268	0.982	P	0.59171	0.853	T	0.40590	-0.9555	9	0.28530	T	0.3	.	5.1512	0.15011	0.0:0.0:0.3026:0.6974	.	1125	Q07283	TRHY_HUMAN	G	1125	ENSP00000357794:R1125G	ENSP00000357794:R1125G	R	-	1	2	TCHH	150348944	0.001000	0.12720	0.006000	0.13384	0.018000	0.09664	1.171000	0.31896	0.940000	0.37473	0.379000	0.24179	AGA	.	.	none		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16843708	16843708	+	Missense_Mutation	SNP	T	T	A	rs74811083|rs376630110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16843708T>A	ENST00000261652.2	-	4	575	c.563A>T	c.(562-564)aAg>aTg	p.K188M	TNFRSF13B_ENST00000579315.1_Intron|TNFRSF13B_ENST00000583789.1_Missense_Mutation_p.K142M|TNFRSF13B_ENST00000437538.2_Missense_Mutation_p.K142M|TNFRSF13B_ENST00000581616.2_5'Flank	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	188					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						ATCCCCCCTCTTCTTGAGGAA	0.647									IgA Deficiency, Selective				.|||	74	0.0147764	0.053	0.0058	5008	,	,		15377	0.0		0.0	False		,,,				2504	0.0				p.K188M		Atlas-SNP	.											.	TNFRSF13B	34	.	0			c.A563T						PASS	.	T	MET/LYS	217,4189	132.1+/-168.6	3,211,1989	73.0	74.0	74.0		563	2.4	0.8	17	dbSNP_131	74	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TNFRSF13B	NM_012452.2	95	3,212,6288	AA,AT,TT		0.0116,4.9251,1.6761	benign	188/294	16843708	218,12788	2203	4300	6503	SO:0001583	missense	23495	exon4	Familial Cancer Database	IGAD1, IGAD2	CCCCTCTTCTTGA	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.563A>T	17.37:g.16843708T>A	ENSP00000261652:p.Lys188Met	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	94	58	0.617021	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Missense_Mutation	SNP	ENST00000261652.2	37	CCDS11181.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	t	3.080	-0.189246	0.06299	0.049251	1.16E-4	ENSG00000240505	ENST00000437538;ENST00000261652	D;D	0.94417	-3.42;-3.38	3.43	2.43	0.29744	.	0.227067	0.28778	N	0.014167	T	0.70527	0.3234	L	0.39898	1.24	0.28171	N	0.928553	P;P	0.49447	0.924;0.875	P;B	0.47981	0.563;0.36	T	0.77109	-0.2709	10	0.87932	D	0	-20.7502	6.3592	0.21419	0.0:0.8441:0.0:0.1559	.	142;188	O14836-2;O14836	.;TR13B_HUMAN	M	142;188	ENSP00000413453:K142M;ENSP00000261652:K188M	ENSP00000261652:K188M	K	-	2	0	TNFRSF13B	16784433	0.992000	0.36948	0.846000	0.33378	0.143000	0.21401	0.653000	0.24902	0.520000	0.28426	-0.477000	0.04895	AAG	T|0.985;A|0.015	0.015	strong		0.647	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2		
BPIFA3	128861	hgsc.bcm.edu	37	20	31812206	31812206	+	Missense_Mutation	SNP	A	A	G	rs112731808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31812206A>G	ENST00000375454.3	+	3	534	c.324A>G	c.(322-324)atA>atG	p.I108M	BPIFA3_ENST00000490499.1_3'UTR|BPIFA3_ENST00000375452.3_Intron	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	108						extracellular region (GO:0005576)	lipid binding (GO:0008289)										GGATCCAGATATCATTCCATA	0.483													G|||	99	0.0197684	0.0446	0.0072	5008	,	,		20967	0.0308		0.004	False		,,,				2504	0.0				p.I108M		Atlas-SNP	.											.	.	.	.	0			c.A324G						PASS	.	G	,MET/ILE	187,4219	809.5+/-416.0	5,177,2021	173.0	153.0	160.0		,324	3.4	0.6	20	dbSNP_132	160	13,8587	818.7+/-406.8	0,13,4287	yes	intron,missense	BPIFA3	NM_001042439.1,NM_178466.3	,10	5,190,6308	GG,GA,AA		0.1512,4.2442,1.5378	,benign	,108/255	31812206	200,12806	2203	4300	6503	SO:0001583	missense	128861	exon3			CCAGATATCATTC		CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"""BPI fold containing"""	16204	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 71"""	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.324A>G	20.37:g.31812206A>G	ENSP00000364603:p.Ile108Met	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	190	94	0.494737	NM_178466	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	37	CCDS13216.2	55	0.025183150183150184	28	0.056910569105691054	3	0.008287292817679558	20	0.03496503496503497	4	0.005277044854881266	G	0.006	-2.099179	0.00360	0.042442	0.001512	ENSG00000131059	ENST00000375454	T	0.04970	3.52	4.35	3.41	0.39046	.	0.313773	0.27986	N	0.017055	T	0.00300	0.0009	N	0.01168	-0.975	0.43841	D	0.996421	B	0.02656	0.0	B	0.04013	0.001	T	0.55016	-0.8206	10	0.30854	T	0.27	-4.1596	7.0156	0.24887	0.2026:0.0:0.7974:0.0	.	108	Q9BQP9	BPIA3_HUMAN	M	108	ENSP00000364603:I108M	ENSP00000364603:I108M	I	+	3	3	BPIFA3	31275867	0.997000	0.39634	0.603000	0.28903	0.084000	0.17831	1.446000	0.35090	0.804000	0.34136	-0.213000	0.12676	ATA	A|0.983;G|0.017	0.017	strong		0.483	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037419	33037419	+	Splice_Site	SNP	G	G	A	rs17850584|rs1126543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33037419G>A	ENST00000419277.1	-	3	474	c.345C>T	c.(343-345)aaC>aaT	p.N115N	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Splice_Site_p.N115N	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	115	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						AGGGCGTACCGTTGGTGGCCT	0.542													.|||	2200	0.439297	0.5809	0.2853	5008	,	,		19932	0.6796		0.1889	False		,,,				2504	0.3671				p.N115N		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C345T						PASS	.	A	,,	1387,1633		327,733,450	137.0	126.0	130.0		345,345,345	-3.5	0.0	6	dbSNP_86	130	942,4476		70,802,1837	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	397,1535,2287	AA,AG,GG		17.3865,45.9272,27.6013	,,	115/261,115/261,115/261	33037419	2329,6109	1510	2709	4219	SO:0001630	splice_region_variant	3113	exon2			CGTACCGTTGGTG	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.346+1C>T	6.37:g.33037419G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1																																																																																			G|0.700;A|0.300	0.300	strong		0.542	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	Silent
MUC17	140453	hgsc.bcm.edu	37	7	100678932	100678932	+	Missense_Mutation	SNP	A	A	G	rs114941002		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678932A>G	ENST00000306151.4	+	3	4299	c.4235A>G	c.(4234-4236)gAg>gGg	p.E1412G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1412	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)					GTCAGTTCTGAGGCTAGCACC	0.502																																					p.E1412G		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.A4235G						scavenged	.						272.0	277.0	275.0					7																	100678932		2203	4300	6503	SO:0001583	missense	140453	exon3			GTTCTGAGGCTAG	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.4235A>G	7.37:g.100678932A>G	ENSP00000302716:p.Glu1412Gly	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	147	10	0.0680272	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	1.916	-0.449416	0.04572	.	.	ENSG00000169876	ENST00000306151	T	0.02737	4.18	0.838	-0.578	0.11724	.	.	.	.	.	T	0.01592	0.0051	N	0.17082	0.46	0.09310	N	1	B	0.27765	0.188	B	0.19946	0.027	T	0.48502	-0.9030	9	0.23891	T	0.37	.	3.0434	0.06146	0.6909:0.0:0.3091:0.0	.	1412	Q685J3	MUC17_HUMAN	G	1412	ENSP00000302716:E1412G	ENSP00000302716:E1412G	E	+	2	0	MUC17	100465652	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.362000	0.07602	-0.153000	0.11137	0.113000	0.15668	GAG	.	.	weak		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
KIAA1211	57482	hgsc.bcm.edu	37	4	57181995	57181995	+	Missense_Mutation	SNP	C	C	T	rs3796547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57181995C>T	ENST00000504228.1	+	6	2432	c.2327C>T	c.(2326-2328)tCg>tTg	p.S776L	KIAA1211_ENST00000264229.6_Missense_Mutation_p.S776L|KIAA1211_ENST00000541073.1_Missense_Mutation_p.S769L			Q6ZU35	K1211_HUMAN	KIAA1211	776			S -> L (in dbSNP:rs3796547). {ECO:0000269|PubMed:14702039}.					p.S776L(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)					CCGGAGAAGTCGGAGATGCAC	0.597													C|||	1212	0.242013	0.1997	0.2334	5008	,	,		14559	0.254		0.34	False		,,,				2504	0.1922				p.S776L		Atlas-SNP	.											KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	1	Substitution - Missense(1)	stomach(1)	c.C2327T						PASS	.	C	LEU/SER	878,3072		96,686,1193	62.0	76.0	72.0		2327	-5.8	0.0	4	dbSNP_107	72	2849,5455		497,1855,1800	yes	missense	KIAA1211	NM_020722.1	145	593,2541,2993	TT,TC,CC		34.3088,22.2278,30.4146	benign	776/1234	57181995	3727,8527	1975	4152	6127	SO:0001583	missense	57482	exon8			AGAAGTCGGAGAT	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.2327C>T	4.37:g.57181995C>T	ENSP00000423366:p.Ser776Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	575	0.2632783882783883	84	0.17073170731707318	92	0.2541436464088398	144	0.2517482517482518	255	0.33641160949868076	C	10.70	1.425095	0.25639	0.222278	0.343088	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.10668	2.85;2.85;2.85	4.79	-5.82	0.02333	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.20887	0.049;0.049	B;B	0.12156	0.007;0.007	T	0.48670	-0.9015	8	0.10111	T	0.7	0.6006	10.3039	0.43670	0.0975:0.5901:0.0:0.3124	rs3796547;rs17490484;rs58264499;rs3796547	769;776	F5H1N7;Q6ZU35	.;K1211_HUMAN	L	776;776;769;686	ENSP00000264229:S776L;ENSP00000423366:S776L;ENSP00000444006:S769L	ENSP00000264229:S776L	S	+	2	0	KIAA1211	56876752	0.000000	0.05858	0.000000	0.03702	0.197000	0.23852	-0.293000	0.08320	-1.173000	0.02758	-0.367000	0.07326	TCG	C|0.728;T|0.272	0.272	strong		0.597	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238671609	238671609	+	Missense_Mutation	SNP	A	A	G	rs2001301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238671609A>G	ENST00000392000.4	+	11	1370	c.1253A>G	c.(1252-1254)aAc>aGc	p.N418S	LRRFIP1_ENST00000244815.5_Missense_Mutation_p.N394S|LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000289175.6_Missense_Mutation_p.N362S	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	418			N -> S (in dbSNP:rs2001301).		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)		GATGGTGGGAACCACACAGAG	0.517													G|||	741	0.147963	0.3238	0.0893	5008	,	,		21343	0.1369		0.0348	False		,,,				2504	0.0798				p.N418S		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.A1253G						PASS	.	G	,,SER/ASN,SER/ASN,SER/ASN	1329,3077	690.4+/-405.3	222,885,1096	87.0	94.0	91.0		,,1253,1085,1181	-4.1	0.0	2	dbSNP_92	91	248,8352	807.3+/-407.2	4,240,4056	no	intron,intron,missense,missense,missense	LRRFIP1	NM_001137550.1,NM_001137551.1,NM_001137552.1,NM_001137553.1,NM_004735.3	,,46,46,46	226,1125,5152	GG,GA,AA		2.8837,30.1634,12.1252	,,benign,benign,benign	,,418/809,362/753,394/785	238671609	1577,11429	2203	4300	6503	SO:0001583	missense	9208	exon11			GTGGGAACCACAC	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.1253A>G	2.37:g.238671609A>G	ENSP00000375857:p.Asn418Ser	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	273	144	0.527473	NM_001137552	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	37	CCDS46552.1	322	0.14743589743589744	179	0.3638211382113821	31	0.0856353591160221	92	0.16083916083916083	20	0.026385224274406333	G	0.920	-0.716117	0.03206	0.301634	0.028837	ENSG00000124831	ENST00000289175;ENST00000244815;ENST00000392000	T;T;T	0.10099	2.91;2.91;2.91	3.77	-4.12	0.03916	.	3.320190	0.00357	N	0.000035	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.46303	-0.9201	9	0.17832	T	0.49	-2.541	7.8022	0.29180	0.4565:0.2013:0.3422:0.0	rs2001301;rs11546349	362;418;394	Q32MZ4-3;Q32MZ4;Q32MZ4-2	.;LRRF1_HUMAN;.	S	362;394;418	ENSP00000289175:N362S;ENSP00000244815:N394S;ENSP00000375857:N418S	ENSP00000244815:N394S	N	+	2	0	LRRFIP1	238336348	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.951000	0.03885	-1.756000	0.01318	-4.001000	0.00013	AAC	A|0.873;G|0.127	0.127	strong		0.517	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
SRMS	6725	hgsc.bcm.edu	37	20	62173561	62173561	+	Missense_Mutation	SNP	C	C	G	rs310657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62173561C>G	ENST00000217188.1	-	5	941	c.901G>C	c.(901-903)Gtc>Ctc	p.V301L		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	301	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> L (in dbSNP:rs310657). {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)			AGTTCCGTGACGATGTACACA	0.677													C|||	579	0.115615	0.3608	0.0576	5008	,	,		16696	0.0139		0.0258	False		,,,				2504	0.0225				p.V301L		Atlas-SNP	.											SRMS,NS,carcinoma,+2,1	SRMS	48	1	0			c.G901C						PASS	.	C	LEU/VAL	1389,3009	452.2+/-349.9	215,959,1025	96.0	76.0	83.0		901	4.6	1.0	20	dbSNP_79	83	166,8434	77.5+/-140.1	0,166,4134	yes	missense	SRMS	NM_080823.2	32	215,1125,5159	GG,GC,CC		1.9302,31.5825,11.9634	probably-damaging	301/489	62173561	1555,11443	2199	4300	6499	SO:0001583	missense	6725	exon5			CCGTGACGATGTA		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.901G>C	20.37:g.62173561C>G	ENSP00000217188:p.Val301Leu	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	193	192	0.994819	NM_080823		Missense_Mutation	SNP	ENST00000217188.1	37	CCDS13525.1	235	0.10760073260073261	192	0.3902439024390244	16	0.04419889502762431	10	0.017482517482517484	17	0.022427440633245383	C	17.54	3.416230	0.62511	0.315825	0.019302	ENSG00000125508	ENST00000217188	D	0.87179	-2.22	4.62	4.62	0.57501	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.124501	0.35936	N	0.002882	T	0.00012	0.0000	L	0.53780	1.695	0.31636	P	0.648475	B	0.33549	0.417	P	0.45377	0.478	T	0.01706	-1.1291	9	0.87932	D	0	.	12.0155	0.53311	0.0:0.9126:0.0:0.0873	rs310657;rs311541;rs1757734;rs58635261;rs310657	301	Q9H3Y6	SRMS_HUMAN	L	301	ENSP00000217188:V301L	ENSP00000217188:V301L	V	-	1	0	SRMS	61644005	1.000000	0.71417	1.000000	0.80357	0.211000	0.24417	1.512000	0.35812	2.120000	0.65058	0.561000	0.74099	GTC	C|0.889;G|0.111	0.111	strong		0.677	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39306004	39306004	+	Missense_Mutation	SNP	A	A	G	rs238829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39306004A>G	ENST00000343246.4	-	1	50	c.16T>C	c.(16-18)Tgt>Cgt	p.C6R		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	6	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].		C -> R (in dbSNP:rs238829).		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)			ACAGAGCCACAACAGGAGCTG	0.592													A|||	189	0.0377396	0.1377	0.0101	5008	,	,		18094	0.0		0.0	False		,,,				2504	0.0				p.C6R		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.T16C						PASS	.	A	ARG/CYS	502,3898		31,440,1729	34.0	36.0	35.0		16	4.2	1.0	17	dbSNP_79	35	1,8595		0,1,4297	yes	missense	KRTAP4-5	NM_033188.3	180	31,441,6026	GG,GA,AA		0.0116,11.4091,3.8704	probably-damaging	6/182	39306004	503,12493	2200	4298	6498	SO:0001583	missense	85289	exon1			AGCCACAACAGGA	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.16T>C	17.37:g.39306004A>G	ENSP00000340546:p.Cys6Arg	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	346	153	0.442197	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	76	0.0347985347985348	70	0.14227642276422764	6	0.016574585635359115	0	0.0	0	0.0	.	8.628	0.892905	0.17613	0.114091	1.16E-4	ENSG00000198271	ENST00000343246	T	0.03065	4.06	4.25	4.25	0.50352	.	0.000000	0.40385	U	0.001109	T	0.00178	0.0005	H	0.94698	3.57	0.21325	P	0.999724217	D	0.59767	0.986	P	0.61800	0.894	T	0.04178	-1.0971	9	0.87932	D	0	.	11.6139	0.51078	1.0:0.0:0.0:0.0	rs238829;rs52814152;rs238829	6	Q9BYR2	KRA45_HUMAN	R	6	ENSP00000340546:C6R	ENSP00000340546:C6R	C	-	1	0	KRTAP4-5	36559530	0.995000	0.38212	1.000000	0.80357	0.017000	0.09413	1.548000	0.36201	1.900000	0.55004	0.533000	0.62120	TGT	A|0.962;G|0.038	0.038	strong		0.592	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
MYO5A	4644	hgsc.bcm.edu	37	15	52652174	52652174	+	Silent	SNP	T	T	C	rs13329278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52652174T>C	ENST00000399231.3	-	25	3657	c.3414A>G	c.(3412-3414)tcA>tcG	p.S1138S	MYO5A_ENST00000399233.2_Silent_p.S1138S|MYO5A_ENST00000553916.1_Silent_p.S1138S|MYO5A_ENST00000358212.6_Silent_p.S1138S|MYO5A_ENST00000356338.6_Silent_p.S1138S	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1138					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)		CCTCTGTCCTTGATGGAATGT	0.433													C|||	679	0.135583	0.4032	0.0274	5008	,	,		19263	0.0367		0.003	False		,,,				2504	0.089				p.S1138S		Atlas-SNP	.											.	MYO5A	145	.	0			c.A3414G						PASS	.	C	,	1198,2684		184,830,927	77.0	74.0	75.0		3414,3414	-6.4	0.0	15	dbSNP_121	75	38,8274		0,38,4118	no	coding-synonymous,coding-synonymous	MYO5A	NM_000259.3,NM_001142495.1	,	184,868,5045	CC,CT,TT		0.4572,30.8604,10.1361	,	1138/1856,1138/1829	52652174	1236,10958	1941	4156	6097	SO:0001819	synonymous_variant	4644	exon25			TGTCCTTGATGGA		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.3414A>G	15.37:g.52652174T>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	208	104	0.5	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	37	CCDS42037.1																																																																																			T|0.887;C|0.113	0.113	strong		0.433	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
OR1L1	26737	hgsc.bcm.edu	37	9	125424277	125424277	+	Missense_Mutation	SNP	A	A	G	rs70157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125424277A>G	ENST00000373686.1	+	1	433	c.433A>G	c.(433-435)Agt>Ggt	p.S145G	OR1L1_ENST00000309623.1_Missense_Mutation_p.S95G			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	145			S -> G (in dbSNP:rs70157). {ECO:0000269|PubMed:14983052, 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)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17						CATCTCTTACAGTGAGTGTCT	0.428													.|||	649	0.129593	0.4713	0.036	5008	,	,		24856	0.0		0.001	False		,,,				2504	0.0				p.S95G		Atlas-SNP	.											.	OR1L1	54	.	0			c.A283G						PASS	.	G	GLY/SER	1689,2717	654.4+/-399.7	329,1031,843	202.0	199.0	200.0		283	1.1	0.0	9	dbSNP_79	200	10,8590	818.9+/-406.8	0,10,4290	yes	missense	OR1L1	NM_001005236.3	56	329,1041,5133	GG,GA,AA		0.1163,38.3341,13.0632	benign	95/311	125424277	1699,11307	2203	4300	6503	SO:0001583	missense	26737	exon1			TCTTACAGTGAGT		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.433A>G	9.37:g.125424277A>G	ENSP00000362790:p.Ser145Gly	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	180	114	0.633333	NM_001005236	Q5T7Z3|Q6IFN2	Missense_Mutation	SNP	ENST00000373686.1	37		228	0.1043956043956044	217	0.4410569105691057	11	0.03038674033149171	0	0.0	0	0.0	G	2.229	-0.376473	0.05000	0.383341	0.001163	ENSG00000173679	ENST00000373686;ENST00000309623	T;T	0.00402	7.56;7.56	3.11	1.14	0.20703	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.11756	0.17	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.22941	-1.0202	8	0.46703	T	0.11	.	1.3175	0.02110	0.2108:0.169:0.4474:0.1728	rs70157;rs700052;rs56487442;rs70157	145	Q8NH94	OR1L1_HUMAN	G	145;95	ENSP00000362790:S145G;ENSP00000310773:S95G	ENSP00000310773:S95G	S	+	1	0	OR1L1	124464098	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-3.542000	0.00436	-0.119000	0.11830	-0.642000	0.03964	AGT	A|0.860;G|0.140	0.140	strong		0.428	OR1L1-201	KNOWN	basic	protein_coding	protein_coding			
PRSS1	5644	hgsc.bcm.edu	37	7	142460752	142460752	+	Missense_Mutation	SNP	C	C	G	rs140793689		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142460752C>G	ENST00000311737.7	+	5	631	c.625C>G	c.(625-627)Cag>Gag	p.Q209E	PRSS1_ENST00000486171.1_Missense_Mutation_p.Q223E	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	209	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	CTGCAATGGACAGCTCCAAGG	0.498																																					p.Q209E		Atlas-SNP	.											PRSS1,NS,carcinoma,-2,2	PRSS1	68	2	0			c.C625G						scavenged	.						81.0	82.0	82.0					7																	142460752		2203	4300	6503	SO:0001583	missense	5644	exon5			AATGGACAGCTCC	M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.625C>G	7.37:g.142460752C>G	ENSP00000308720:p.Gln209Glu	Somatic	383	2	0.00522193		WXS	Illumina HiSeq	Phase_I	424	10	0.0235849	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Missense_Mutation	SNP	ENST00000311737.7	37	CCDS5872.1	.	.	.	.	.	.	.	.	.	.	C	0.001	-3.193364	0.00026	.	.	ENSG00000204983	ENST00000486171;ENST00000311737;ENST00000529243	D;D	0.92752	-3.1;-3.1	3.18	-6.37	0.01963	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.378699	0.32671	N	0.005798	T	0.78142	0.4237	N	0.11818	0.18	0.23758	N	0.996928	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.003	T	0.62539	-0.6833	10	0.02654	T	1	.	15.6905	0.77446	0.0827:0.7314:0.186:0.0	.	223;209	E7EQ64;P07477	.;TRY1_HUMAN	E	223;209;199	ENSP00000417854:Q223E;ENSP00000308720:Q209E	ENSP00000308720:Q209E	Q	+	1	0	PRSS1	142140326	0.000000	0.05858	0.024000	0.17045	0.003000	0.03518	-1.756000	0.01813	-1.839000	0.01186	0.195000	0.17529	CAG	.	.	weak		0.498	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		
SEMA6C	10500	hgsc.bcm.edu	37	1	151112483	151112483	+	Missense_Mutation	SNP	T	T	C	rs75185260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151112483T>C	ENST00000341697.3	-	4	1893	c.202A>G	c.(202-204)Acc>Gcc	p.T68A				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	68	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|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)			CGGTTCAAGGTCAGGAATCTC	0.572													T|||	308	0.0615016	0.1195	0.0159	5008	,	,		20742	0.0278		0.0219	False		,,,				2504	0.091				p.T68A		Atlas-SNP	.											.	SEMA6C	70	.	0			c.A202G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	398,4008	198.4+/-222.2	10,378,1815	87.0	61.0	70.0		202,202,202	4.8	1.0	1	dbSNP_132	70	188,8412	82.9+/-145.4	0,188,4112	yes	missense,missense,missense	SEMA6C	NM_001178061.1,NM_001178062.1,NM_030913.4	58,58,58	10,566,5927	CC,CT,TT		2.186,9.0331,4.5056	possibly-damaging,possibly-damaging,possibly-damaging	68/963,68/923,68/931	151112483	586,12420	2203	4300	6503	SO:0001583	missense	10500	exon4			TCAAGGTCAGGAA	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"""Semaphorins"""	10740	protein-coding gene	gene with protein product	"""m-Sema Y2"""	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.202A>G	1.37:g.151112483T>C	ENSP00000344148:p.Thr68Ala	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	106	39	0.367925	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	37	CCDS984.1	100	0.045787545787545784	64	0.13008130081300814	7	0.019337016574585635	10	0.017482517482517484	19	0.025065963060686015	T	15.11	2.735203	0.48939	0.090331	0.02186	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697;ENST00000392792	T;T;T;T	0.17854	2.25;2.45;2.26;2.25	4.77	4.77	0.60923	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (3);	0.297335	0.34828	N	0.003657	T	0.05181	0.0138	N	0.14661	0.345	0.29327	N	0.866961	B;P;B;P	0.42456	0.229;0.739;0.192;0.78	B;B;B;B	0.43301	0.193;0.291;0.122;0.415	T	0.15578	-1.0432	10	0.42905	T	0.14	.	10.595	0.45331	0.0:0.0:0.0:1.0	.	68;68;68;68	B4DZD4;Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;.;SEM6C_HUMAN	A	68	ENSP00000357910:T68A;ENSP00000357908:T68A;ENSP00000357909:T68A;ENSP00000344148:T68A	ENSP00000344148:T68A	T	-	1	0	SEMA6C	149379107	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.894000	0.39768	2.016000	0.59253	0.459000	0.35465	ACC	T|0.953;C|0.047	0.047	strong		0.572	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913	
KMT2C	58508	hgsc.bcm.edu	37	7	151932990	151932990	+	Missense_Mutation	SNP	C	C	T	rs76844681		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151932990C>T	ENST00000262189.6	-	16	2899	c.2681G>A	c.(2680-2682)cGg>cAg	p.R894Q	KMT2C_ENST00000355193.2_Missense_Mutation_p.R894Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	894					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)										TCGAGGTCTCCGCTTTCCTGG	0.502																																					p.R894Q		Atlas-SNP	.											MLL3_ENST00000355193,NS,malignant_melanoma,+1,4	MLL3	1564	4	0			c.G2681A						scavenged	.						33.0	34.0	33.0					7																	151932990		2202	4295	6497	SO:0001583	missense	58508	exon16			GGTCTCCGCTTTC	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.2681G>A	7.37:g.151932990C>T	ENSP00000262189:p.Arg894Gln	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	182	9	0.0494506	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.710284	0.89018	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.89485	-2.5;-2.52	5.1	5.1	0.69264	.	0.000000	0.42294	D	0.000721	D	0.93314	0.7869	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	D	0.93742	0.7051	10	0.66056	D	0.02	.	17.0444	0.86498	0.0:1.0:0.0:0.0	.	894	Q8NEZ4	MLL3_HUMAN	Q	894	ENSP00000262189:R894Q;ENSP00000347325:R894Q	ENSP00000262189:R894Q	R	-	2	0	MLL3	151563923	1.000000	0.71417	0.996000	0.52242	0.951000	0.60555	7.268000	0.78473	2.530000	0.85305	0.650000	0.86243	CGG	C|0.999;T|0.001	0.001	weak		0.502	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
NTN4	59277	hgsc.bcm.edu	37	12	96077312	96077312	+	Silent	SNP	C	C	T	rs17851048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:96077312C>T	ENST00000343702.4	-	6	1804	c.1356G>A	c.(1354-1356)gcG>gcA	p.A452A	NTN4_ENST00000538383.1_Silent_p.A415A|NTN4_ENST00000553059.1_Silent_p.A452A|NTN4_ENST00000344911.4_Silent_p.A415A	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	452					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						CACAGCTCCCCGCACAGTCAC	0.557													C|||	585	0.116813	0.0197	0.2104	5008	,	,		20137	0.0		0.2952	False		,,,				2504	0.1186				p.A452A		Atlas-SNP	.											.	NTN4	67	.	0			c.G1356A						PASS	.	C		244,4162	142.3+/-177.5	12,220,1971	96.0	80.0	85.0		1356	-11.5	0.0	12	dbSNP_123	85	2345,6255	390.2+/-343.2	313,1719,2268	no	coding-synonymous	NTN4	NM_021229.3		325,1939,4239	TT,TC,CC		27.2674,5.5379,19.9062		452/629	96077312	2589,10417	2203	4300	6503	SO:0001819	synonymous_variant	59277	exon6			GCTCCCCGCACAG	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.1356G>A	12.37:g.96077312C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_021229	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Silent	SNP	ENST00000343702.4	37	CCDS9054.1																																																																																			C|0.819;T|0.181	0.181	strong		0.557	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229	
LHX3	8022	hgsc.bcm.edu	37	9	139096782	139096782	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139096782C>T	ENST00000371748.5	-	1	173	c.77G>A	c.(76-78)cGg>cAg	p.R26Q	LHX3_ENST00000371746.3_5'Flank	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	26					inner ear development (GO:0048839)|lung development (GO:0030324)|medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|placenta development (GO:0001890)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron cell fate specification (GO:0021520)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Myeloproliferative disorder(178;0.0511)		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)		GGGCTTACCCCGAGTCCCGCC	0.721																																					p.R26Q		Atlas-SNP	.											.	LHX3	23	.	0			c.G77A						PASS	.						15.0	16.0	15.0					9																	139096782		2173	4271	6444	SO:0001583	missense	8022	exon1			TTACCCCGAGTCC	AF096169	CCDS6994.1, CCDS6995.1	9q34.3	2011-06-20			ENSG00000107187	ENSG00000107187		"""Homeoboxes / LIM class"""	6595	protein-coding gene	gene with protein product		600577				10598593, 10717474	Standard	NM_178138		Approved		uc004cgz.3	Q9UBR4	OTTHUMG00000020924	ENST00000371748.5:c.77G>A	9.37:g.139096782C>T	ENSP00000360813:p.Arg26Gln	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_178138	Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Missense_Mutation	SNP	ENST00000371748.5	37	CCDS6994.1	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.571243	0.00895	.	.	ENSG00000107187	ENST00000371748	D	0.87729	-2.29	2.48	-3.37	0.04898	.	.	.	.	.	T	0.68805	0.3041	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55503	-0.8131	9	0.08599	T	0.76	.	5.7854	0.18331	0.0:0.2132:0.172:0.6149	.	26	Q9UBR4	LHX3_HUMAN	Q	26	ENSP00000360813:R26Q	ENSP00000360813:R26Q	R	-	2	0	LHX3	138236603	0.000000	0.05858	0.000000	0.03702	0.239000	0.25481	-1.334000	0.02665	-0.951000	0.03654	-0.350000	0.07774	CGG	.	.	none		0.721	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3		
FSHB	2488	hgsc.bcm.edu	37	11	30255185	30255185	+	Silent	SNP	C	C	T	rs6169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:30255185C>T	ENST00000417547.1	+	3	267	c.228C>T	c.(226-228)taC>taT	p.Y76Y	FSHB_ENST00000533718.1_Silent_p.Y76Y|FSHB_ENST00000254122.3_Silent_p.Y76Y	NM_001018080.1	NP_001018090.1	P01225	FSHB_HUMAN	follicle stimulating hormone, beta polypeptide	76					cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|female pregnancy (GO:0007565)|follicle-stimulating hormone signaling pathway (GO:0042699)|peptide hormone processing (GO:0016486)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone biosynthetic process (GO:0006701)|regulation of osteoclast differentiation (GO:0045670)|Sertoli cell proliferation (GO:0060011)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	12						AACTGGTATACGAAACAGTGA	0.498													T|||	3079	0.614816	0.7572	0.5317	5008	,	,		18146	0.6696		0.4503	False		,,,				2504	0.5941				p.Y76Y		Atlas-SNP	.											.	FSHB	28	.	0			c.C228T						PASS	.	T	,	3124,1280	437.6+/-345.0	1100,924,178	107.0	94.0	99.0		228,228	-8.5	0.5	11	dbSNP_52	99	3747,4851	617.0+/-396.6	825,2097,1377	no	coding-synonymous,coding-synonymous	FSHB	NM_000510.2,NM_001018080.1	,	1925,3021,1555	TT,TC,CC		43.5799,29.0645,47.1543	,	76/130,76/130	30255185	6871,6131	2202	4299	6501	SO:0001819	synonymous_variant	2488	exon3			GGTATACGAAACA		CCDS7868.1	11p13	2013-02-26				ENSG00000131808		"""Endogenous ligands"""	3964	protein-coding gene	gene with protein product	"""follitropin, beta chain"", ""follicle-stimulating hormone beta subunit"""	136530				2885163, 3151250	Standard	NM_000510		Approved		uc001msm.3	P01225		ENST00000417547.1:c.228C>T	11.37:g.30255185C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_000510	A2TF08|A5JVV3|Q14D61	Silent	SNP	ENST00000417547.1	37	CCDS7868.1																																																																																			C|0.436;T|0.564	0.564	strong		0.498	FSHB-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389757.1	NM_000510	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2929392	2929392	+	Silent	SNP	G	G	A	rs55904912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2929392G>A	ENST00000254695.8	+	20	1932	c.1842G>A	c.(1840-1842)ccG>ccA	p.P614P	RAP1GAP2_ENST00000540393.2_Silent_p.P595P|RAP1GAP2_ENST00000366401.4_Silent_p.P599P|RAP1GAP2_ENST00000542807.1_Silent_p.P614P	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	614	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)	p.P614P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CCAGCTCTCCGGAAATCTGCC	0.577													G|||	2146	0.428514	0.2451	0.4986	5008	,	,		16508	0.5466		0.4066	False		,,,				2504	0.5276				p.P614P		Atlas-SNP	.											RAP1GAP2_ENST00000254695,NS,carcinoma,0,2	RAP1GAP2	90	2	1	Substitution - coding silent(1)	stomach(1)	c.G1842A						scavenged	.	G	,	1082,2966		152,778,1094	45.0	48.0	47.0		1797,1842	-7.4	1.0	17	dbSNP_129	47	3415,4945		687,2041,1452	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	839,2819,2546	AA,AG,GG		40.8493,26.7292,36.2427	,	599/716,614/731	2929392	4497,7911	2024	4180	6204	SO:0001819	synonymous_variant	23108	exon20			CTCTCCGGAAATC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1842G>A	17.37:g.2929392G>A		Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	269	123	0.457249	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			G|0.579;A|0.421	0.421	strong		0.577	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
TMEM89	440955	hgsc.bcm.edu	37	3	48659009	48659009	+	Missense_Mutation	SNP	G	G	T	rs9834639	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48659009G>T	ENST00000330862.3	-	1	279	c.181C>A	c.(181-183)Cct>Act	p.P61T		NM_001008269.1	NP_001008270.1	A2RUT3	TMM89_HUMAN	transmembrane protein 89	61			P -> T (in dbSNP:rs9834639).			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)		CTTGCTCCAGGGCCCAGCCAG	0.652													G|||	549	0.109625	0.2685	0.0937	5008	,	,		14325	0.0228		0.0825	False		,,,				2504	0.0235				p.P61T		Atlas-SNP	.											.	TMEM89	10	.	0			c.C181A						PASS	.	G	THR/PRO	1030,3376	355.6+/-313.1	110,810,1283	54.0	47.0	49.0		181	2.8	0.9	3	dbSNP_119	49	653,7947	157.7+/-211.4	32,589,3679	yes	missense	TMEM89	NM_001008269.1	38	142,1399,4962	TT,TG,GG		7.593,23.3772,12.9402	possibly-damaging	61/160	48659009	1683,11323	2203	4300	6503	SO:0001583	missense	440955	exon1			CTCCAGGGCCCAG	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.181C>A	3.37:g.48659009G>T	ENSP00000329557:p.Pro61Thr	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	178	80	0.449438	NM_001008269		Missense_Mutation	SNP	ENST00000330862.3	37	CCDS33751.1	236	0.10805860805860806	123	0.25	31	0.0856353591160221	19	0.033216783216783216	63	0.08311345646437995	G	12.61	1.990025	0.35131	0.233772	0.07593	ENSG00000183396	ENST00000330862	T	0.41400	1.0	4.7	2.84	0.33178	.	0.841083	0.09976	N	0.731570	T	0.00012	0.0000	N	0.22421	0.69	0.43517	P	0.004214999999999969	B	0.21452	0.056	B	0.20384	0.029	T	0.17899	-1.0354	9	0.59425	D	0.04	-4.1779	7.6057	0.28101	0.0:0.1817:0.6301:0.1883	rs9834639;rs58298641;rs9834639	61	A2RUT3	TMM89_HUMAN	T	61	ENSP00000329557:P61T	ENSP00000329557:P61T	P	-	1	0	TMEM89	48634013	0.989000	0.36119	0.922000	0.36590	0.007000	0.05969	1.725000	0.38074	0.547000	0.28938	0.462000	0.41574	CCT	G|0.878;T|0.122	0.122	strong		0.652	TMEM89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345046.1	NM_001008269	
POM121L2	94026	hgsc.bcm.edu	37	6	27277716	27277716	+	Missense_Mutation	SNP	A	A	T	rs61736082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27277716A>T	ENST00000444565.1	-	1	2233	c.2234T>A	c.(2233-2235)aTc>aAc	p.I745N	POM121L2_ENST00000377451.2_Missense_Mutation_p.I681N	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	745										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						CAGGTTGGAGATGCTGGGGGT	0.547													A|||	151	0.0301518	0.0983	0.0159	5008	,	,		20168	0.001		0.005	False		,,,				2504	0.0041				p.I745N		Atlas-SNP	.											.	POM121L2	61	.	0			c.T2234A						PASS	.	A	ASN/ILE	119,1265		4,111,577	60.0	58.0	58.0		2234	-7.9	0.0	6	dbSNP_129	58	38,3144		0,38,1553	yes	missense	POM121L2	NM_033482.3	149	4,149,2130	TT,TA,AA		1.1942,8.5983,3.4385	benign	745/1036	27277716	157,4409	692	1591	2283	SO:0001583	missense	94026	exon1			TTGGAGATGCTGG	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.2234T>A	6.37:g.27277716A>T	ENSP00000392726:p.Ile745Asn	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	161	79	0.490683	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	58	0.026556776556776556	46	0.09349593495934959	6	0.016574585635359115	1	0.0017482517482517483	5	0.006596306068601583	A	6.160	0.397724	0.11696	0.085983	0.011942	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.14893	2.47;2.47	3.95	-7.89	0.01174	.	2.196470	0.02896	N	0.134806	T	0.02083	0.0065	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35549	-0.9784	10	0.17369	T	0.5	.	0.5556	0.00670	0.1881:0.2896:0.1786:0.3437	rs61736082	745	C9J1I7	.	N	681;745	ENSP00000366671:I681N;ENSP00000392726:I745N	ENSP00000366671:I681N	I	-	2	0	POM121L2	27385695	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.893000	0.04127	-1.522000	0.01769	0.254000	0.18369	ATC	A|0.952;T|0.048	0.048	strong		0.547	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
ARSG	22901	hgsc.bcm.edu	37	17	66397521	66397521	+	Silent	SNP	C	C	T	rs62638719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66397521C>T	ENST00000448504.2	+	11	2029	c.1233C>T	c.(1231-1233)agC>agT	p.S411S	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Silent_p.S247S	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	411					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)			ACCCCAACAGCGGGGCAGCTG	0.557													C|||	11	0.00219649	0.0083	0.0	5008	,	,		19346	0.0		0.0	False		,,,				2504	0.0				p.S411S		Atlas-SNP	.											ARSG,NS,carcinoma,+1,1	ARSG	55	1	0			c.C1233T						PASS	.	C		65,4341	60.5+/-97.4	0,65,2138	90.0	90.0	90.0		1233	-10.0	0.1	17	dbSNP_129	90	0,8600		0,0,4300	no	coding-synonymous	ARSG	NM_014960.3		0,65,6438	TT,TC,CC		0.0,1.4753,0.4998		411/526	66397521	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	22901	exon11			CAACAGCGGGGCA	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.1233C>T	17.37:g.66397521C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	173	105	0.606936	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	37	CCDS11676.1																																																																																			C|0.996;T|0.004	0.004	strong		0.557	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
ITGBL1	9358	hgsc.bcm.edu	37	13	102227872	102227872	+	Silent	SNP	C	C	T	rs3916912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:102227872C>T	ENST00000376180.3	+	4	780	c.561C>T	c.(559-561)gaC>gaT	p.D187D	ITGBL1_ENST00000376162.3_Silent_p.D94D|ITGBL1_ENST00000545560.2_Silent_p.D46D	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	187	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)				breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AATGCATAGACGATGAAACAG	0.348													C|||	665	0.132788	0.2587	0.1081	5008	,	,		17994	0.001		0.1809	False		,,,				2504	0.0665				p.D187D		Atlas-SNP	.											.	ITGBL1	83	.	0			c.C561T						PASS	.	C		953,3453	363.1+/-316.4	102,749,1352	231.0	215.0	221.0		561	-0.7	1.0	13	dbSNP_108	221	1533,7067	289.7+/-299.4	149,1235,2916	no	coding-synonymous	ITGBL1	NM_004791.1		251,1984,4268	TT,TC,CC		17.8256,21.6296,19.1143		187/495	102227872	2486,10520	2203	4300	6503	SO:0001819	synonymous_variant	9358	exon4			CATAGACGATGAA	AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"""ten integrin EGF-like repeat domains protein"", ""ITGBL1, integrin beta-like 1"""	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.561C>T	13.37:g.102227872C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	146	76	0.520548	NM_004791	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Silent	SNP	ENST00000376180.3	37	CCDS9499.1																																																																																			C|0.831;T|0.169	0.169	strong		0.348	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791	
ABCC2	1244	hgsc.bcm.edu	37	10	101611294	101611294	+	Missense_Mutation	SNP	G	G	A	rs8187710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101611294G>A	ENST00000370449.4	+	32	4657	c.4544G>A	c.(4543-4545)tGc>tAc	p.C1515Y		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1515	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		C -> Y (in dbSNP:rs8187710). {ECO:0000269|PubMed:22290738, ECO:0000269|Ref.2}.		cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	ATTATAGAGTGCGGCAGCCCT	0.418													A|||	340	0.0678914	0.1619	0.0548	5008	,	,		14647	0.0		0.0706	False		,,,				2504	0.0174				p.C1515Y		Atlas-SNP	.											ABCC2,NS,carcinoma,-1,1	ABCC2	160	1	0			c.G4544A						scavenged	.		TYR/CYS	692,3714	761.2+/-413.0	60,572,1571	117.0	117.0	117.0		4544	2.0	0.9	10	dbSNP_123	117	533,8067	795.7+/-407.5	14,505,3781	yes	missense	ABCC2	NM_000392.3	194	74,1077,5352	AA,AG,GG		6.1977,15.7059,9.4187	benign	1515/1546	101611294	1225,11781	2203	4300	6503	SO:0001583	missense	1244	exon32			TAGAGTGCGGCAG	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.4544G>A	10.37:g.101611294G>A	ENSP00000359478:p.Cys1515Tyr	Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	152	0.0695970695970696	84	0.17073170731707318	22	0.06077348066298342	0	0.0	46	0.06068601583113457	A	8.691	0.907406	0.17833	0.157059	0.061977	ENSG00000023839	ENST00000370449	T	0.65549	-0.16	4.58	1.96	0.26148	ABC transporter-like (1);	0.109437	0.64402	N	0.000005	T	0.00073	0.0002	N	0.02334	-0.595	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06991	-1.0796	9	0.15952	T	0.53	-1.6801	4.8001	0.13292	0.3743:0.0:0.0982:0.5274	rs8187710;rs17222568;rs52804507;rs58135906;rs8187710	1515	Q92887	MRP2_HUMAN	Y	1515	ENSP00000359478:C1515Y	ENSP00000359478:C1515Y	C	+	2	0	ABCC2	101601284	0.174000	0.23070	0.931000	0.37212	0.717000	0.41224	0.593000	0.23999	0.241000	0.21283	-0.361000	0.07541	TGC	G|0.752;A|0.248	0.248	strong		0.418	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
PLBD1	79887	hgsc.bcm.edu	37	12	14656768	14656768	+	Missense_Mutation	SNP	G	G	C	rs1600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:14656768G>C	ENST00000240617.5	-	11	2252	c.1600C>G	c.(1600-1602)Cca>Gca	p.P534A		NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	534			P -> A (in dbSNP:rs1600). {ECO:0000269|PubMed:15489334}.		glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						TAGACCTCTGGCATGCCCTGA	0.413													G|||	2572	0.513578	0.6437	0.5778	5008	,	,		16482	0.38		0.4573	False		,,,				2504	0.4877				p.P534A		Atlas-SNP	.											.	PLBD1	36	.	0			c.C1600G						PASS	.	G	ALA/PRO	2761,1645	659.2+/-400.5	865,1031,307	126.0	121.0	123.0		1600	5.0	1.0	12	dbSNP_36	123	4021,4579	556.1+/-386.8	934,2153,1213	yes	missense	PLBD1	NM_024829.5	27	1799,3184,1520	CC,CG,GG		46.7558,37.3355,47.8548	probably-damaging	534/554	14656768	6782,6224	2203	4300	6503	SO:0001583	missense	79887	exon11			CCTCTGGCATGCC	BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"""PLB homolog 1 (Dictyostelium)"""					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.1600C>G	12.37:g.14656768G>C	ENSP00000240617:p.Pro534Ala	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	186	185	0.994624	NM_024829	A8K4E9|Q9BVV3|Q9H625	Missense_Mutation	SNP	ENST00000240617.5	37	CCDS31751.1	1077	0.49313186813186816	318	0.6463414634146342	192	0.5303867403314917	216	0.3776223776223776	351	0.4630606860158311	G	24.1	4.492333	0.84962	0.626645	0.467558	ENSG00000121316	ENST00000240617	T	0.24350	1.86	5.86	4.97	0.65823	.	0.049601	0.85682	N	0.000000	T	0.00012	0.0000	M	0.94021	3.485	0.09310	P	0.99999827061	D	0.89917	1.0	D	0.83275	0.996	T	0.46233	-0.9206	9	0.72032	D	0.01	-14.3777	15.8105	0.78561	0.0:0.1351:0.8649:0.0	rs1600;rs3168592;rs3789995;rs17844869;rs17855851;rs17857584;rs1600	534	Q6P4A8	PLBL1_HUMAN	A	534	ENSP00000240617:P534A	ENSP00000240617:P534A	P	-	1	0	PLBD1	14548035	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	9.434000	0.97515	1.613000	0.50231	-0.172000	0.13284	CCA	G|0.490;C|0.510	0.510	strong		0.413	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829	
IGF2R	3482	hgsc.bcm.edu	37	6	160448324	160448324	+	Missense_Mutation	SNP	C	C	G	rs8191754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160448324C>G	ENST00000356956.1	+	6	902	c.754C>G	c.(754-756)Ctg>Gtg	p.L252V		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	252			L -> V (in dbSNP:rs8191754). {ECO:0000269|Ref.5}.		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)	CCGGGACGGACTGAAGCTGGT	0.612													C|||	803	0.160343	0.1498	0.0533	5008	,	,		18426	0.2202		0.1481	False		,,,				2504	0.2014				p.L252V		Atlas-SNP	.											.	IGF2R	251	.	0			c.C754G						PASS	.	C	VAL/LEU	614,3792	262.2+/-264.8	37,540,1626	34.0	33.0	33.0		754	4.3	0.5	6	dbSNP_117	33	1126,7472	229.1+/-263.9	62,1002,3235	yes	missense	IGF2R	NM_000876.2	32	99,1542,4861	GG,GC,CC		13.0961,13.9355,13.3805	possibly-damaging	252/2492	160448324	1740,11264	2203	4299	6502	SO:0001583	missense	3482	exon6			GACGGACTGAAGC	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.754C>G	6.37:g.160448324C>G	ENSP00000349437:p.Leu252Val	Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	226	125	0.553097	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	310	0.14194139194139194	58	0.11788617886178862	17	0.04696132596685083	113	0.19755244755244755	122	0.16094986807387862	C	16.39	3.110100	0.56398	0.139355	0.130961	ENSG00000197081	ENST00000356956	T	0.02301	4.35	5.22	4.34	0.51931	Mannose-6-phosphate receptor, binding (1);	0.066396	0.64402	D	0.000008	T	0.06188	0.0160	M	0.88842	2.985	0.20638	P	0.999879852	P	0.46142	0.873	P	0.54499	0.754	T	0.00247	-1.1881	9	0.59425	D	0.04	-10.0413	11.8459	0.52385	0.0:0.9188:0.0:0.0812	rs8191754;rs17847669;rs8191754	252	P11717	MPRI_HUMAN	V	252	ENSP00000349437:L252V	ENSP00000349437:L252V	L	+	1	2	IGF2R	160368314	0.989000	0.36119	0.548000	0.28192	0.525000	0.34531	2.893000	0.48633	2.577000	0.86979	0.655000	0.94253	CTG	C|0.862;G|0.138	0.138	strong		0.612	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
NOVA1	4857	hgsc.bcm.edu	37	14	26917826	26917826	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:26917826A>G	ENST00000539517.2	-	5	1180	c.863T>C	c.(862-864)cTa>cCa	p.L288P	NOVA1_ENST00000465357.2_Missense_Mutation_p.L264P|NOVA1_ENST00000267422.7_Missense_Mutation_p.L166P	NM_002515.2	NP_002506.2	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	291	Ala-rich.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		ATGTCCTAATAGCCCTGCAGC	0.498																																					p.L288P		Atlas-SNP	.											NOVA1,NS,carcinoma,-1,1	NOVA1	146	1	0			c.T863C						scavenged	.						84.0	79.0	80.0					14																	26917826		2203	4300	6503	SO:0001583	missense	4857	exon5			CCTAATAGCCCTG	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000539517.2:c.863T>C	14.37:g.26917826A>G	ENSP00000438875:p.Leu288Pro	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	143	2	0.013986	NM_002515	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000539517.2	37	CCDS32061.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.349631	0.41599	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000267422;ENST00000449198	T;T;T;T	0.35421	1.39;1.34;1.35;1.31	5.93	5.93	0.95920	.	0.218253	0.31589	N	0.007393	T	0.50188	0.1601	L	0.38838	1.175	0.80722	D	1	D;D;D	0.71674	0.998;0.995;0.997	D;D;D	0.80764	0.991;0.986;0.994	T	0.38779	-0.9645	10	0.31617	T	0.26	-5.5399	16.3756	0.83387	1.0:0.0:0.0:0.0	.	291;264;288	P51513;D3DS81;P51513-4	NOVA1_HUMAN;.;.	P	264;288;166;247	ENSP00000447391:L264P;ENSP00000438875:L288P;ENSP00000267422:L166P;ENSP00000408914:L247P	ENSP00000267422:L166P	L	-	2	0	NOVA1	25987666	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.297000	0.96120	2.270000	0.75569	0.460000	0.39030	CTA	.	.	none		0.498	NOVA1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000073261.3	NM_006491	
NR5A1	2516	hgsc.bcm.edu	37	9	127262864	127262864	+	Silent	SNP	C	C	T	rs1110062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127262864C>T	ENST00000373588.4	-	4	571	c.375G>A	c.(373-375)ccG>ccA	p.P125P		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	125					adrenal gland development (GO:0030325)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|hormone metabolic process (GO:0042445)|intracellular receptor signaling pathway (GO:0030522)|luteinization (GO:0001553)|maintenance of protein location in nucleus (GO:0051457)|male gonad development (GO:0008584)|multicellular organismal aging (GO:0010259)|negative regulation of female gonad development (GO:2000195)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|primary sex determination (GO:0007538)|regulation of steroid biosynthetic process (GO:0050810)|tissue development (GO:0009888)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)	2						GCACCCCCATCGGGGGCCCTG	0.682													C|||	436	0.0870607	0.3154	0.0245	5008	,	,		12705	0.002		0.0	False		,,,				2504	0.0				p.P125P		Atlas-SNP	.											.	NR5A1	32	.	0			c.G375A						PASS	.	C		1188,3052		158,872,1090	19.0	22.0	21.0		375	-9.1	0.0	9	dbSNP_86	21	9,8255		0,9,4123	no	coding-synonymous	NR5A1	NM_004959.4		158,881,5213	TT,TC,CC		0.1089,28.0189,9.5729		125/462	127262864	1197,11307	2120	4132	6252	SO:0001819	synonymous_variant	2516	exon4			CCCCATCGGGGGC	D88155	CCDS6856.1	9q33	2013-01-16			ENSG00000136931	ENSG00000136931		"""Nuclear hormone receptors"""	7983	protein-coding gene	gene with protein product		184757		FTZF1		7789992	Standard	NM_004959		Approved	FTZ1, SF-1, ELP, AD4BP	uc004boo.1	Q13285	OTTHUMG00000020655	ENST00000373588.4:c.375G>A	9.37:g.127262864C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_004959	O15196|Q5T6F5	Silent	SNP	ENST00000373588.4	37	CCDS6856.1																																																																																			C|0.948;T|0.052	0.052	strong		0.682	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959	
LLGL2	3993	hgsc.bcm.edu	37	17	73567846	73567846	+	Missense_Mutation	SNP	C	C	T	rs1661715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73567846C>T	ENST00000392550.3	+	18	2392	c.2275C>T	c.(2275-2277)Cct>Tct	p.P759S	LLGL2_ENST00000577200.1_Missense_Mutation_p.P759S|LLGL2_ENST00000167462.5_Missense_Mutation_p.P759S	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	759			P -> S (in dbSNP:rs1661715). {ECO:0000269|PubMed:15489334}.		cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			AATGGATGAGCCTGTGCGGGC	0.697													C|||	1552	0.309904	0.5915	0.2435	5008	,	,		17459	0.1508		0.2823	False		,,,				2504	0.1687				p.P759S		Atlas-SNP	.											LLGL2_ENST00000167462,rectum,carcinoma,0,6	LLGL2	155	6	0			c.C2275T						PASS	.	C	SER/PRO,SER/PRO	2440,1962		693,1054,454	29.0	31.0	30.0		2275,2275	4.4	0.8	17	dbSNP_89	30	2542,6054		397,1748,2153	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	74,74	1090,2802,2607	TT,TC,CC		29.5719,44.5706,38.329	benign,benign	759/1021,759/1016	73567846	4982,8016	2201	4298	6499	SO:0001583	missense	3993	exon18			GATGAGCCTGTGC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2275C>T	17.37:g.73567846C>T	ENSP00000376333:p.Pro759Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	711	0.32554945054945056	322	0.6544715447154471	87	0.24033149171270718	81	0.14160839160839161	221	0.29155672823219	C	12.78	2.039977	0.35989	0.554294	0.295719	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.08008	3.14;3.26	5.4	4.41	0.53225	.	0.209202	0.51477	D	0.000100	T	0.00012	0.0000	L	0.57536	1.79	0.27633	P	0.947969	B;P;B;B	0.36789	0.434;0.57;0.01;0.003	B;B;B;B	0.39904	0.166;0.313;0.015;0.004	T	0.06516	-1.0822	9	0.33141	T	0.24	-0.6264	10.9596	0.47376	0.1462:0.713:0.1408:0.0	rs1661715;rs17855941;rs60583153;rs1661715	748;748;759;759	B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;L2GL2_HUMAN	S	759;759;748	ENSP00000167462:P759S;ENSP00000376333:P759S	ENSP00000167462:P759S	P	+	1	0	LLGL2	71079441	0.854000	0.29725	0.840000	0.33206	0.932000	0.56968	2.448000	0.44926	1.245000	0.43885	0.549000	0.68633	CCT	C|0.622;T|0.378	0.378	strong		0.697	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
CYP4A22	284541	hgsc.bcm.edu	37	1	47611598	47611598	+	Missense_Mutation	SNP	T	T	C	rs2405599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47611598T>C	ENST00000371891.3	+	10	1314	c.1283T>C	c.(1282-1284)cTa>cCa	p.L428P	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000371890.3_Missense_Mutation_p.L330P|CYP4A22_ENST00000294337.3_Missense_Mutation_p.L428P|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	428			L -> P (in allele CYP4A22*6, allele CYP4A22*9, allele CYP4A22*10, allele CYP4A22*12, allele CYP4A22*13 and allele CYP4A22*15; dbSNP:rs2405599). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGGCCCAACCTAGAGGTATGT	0.512													C|||	1882	0.375799	0.2239	0.2896	5008	,	,		21691	0.6141		0.2237	False		,,,				2504	0.5532				p.L428P	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.T1283C						PASS	.	C	PRO/LEU	1117,3289		132,853,1218	290.0	284.0	286.0		1283	0.6	0.7	1	dbSNP_100	286	1931,6669		221,1489,2590	no	missense	CYP4A22	NM_001010969.2	98	353,2342,3808	CC,CT,TT		22.4535,25.3518,23.4353	benign	428/520	47611598	3048,9958	2203	4300	6503	SO:0001583	missense	284541	exon10			CCAACCTAGAGGT		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.1283T>C	1.37:g.47611598T>C	ENSP00000360958:p.Leu428Pro	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	276	140	0.507246	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	683	0.31272893772893773	97	0.19715447154471544	91	0.2513812154696133	335	0.5856643356643356	160	0.21108179419525067	N	0.023	-1.394920	0.01175	0.253518	0.224535	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.27890	1.64;1.64;1.64	1.59	0.642	0.17765	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00001	-3.695	0.30109	P	0.806743	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.0	T	0.44221	-0.9342	9	0.02654	T	1	.	5.7987	0.18401	0.0:0.6711:0.0:0.3289	rs2405599;rs59295354	330;428	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	P	330;428;428	ENSP00000360957:L330P;ENSP00000360958:L428P;ENSP00000294337:L428P	ENSP00000294337:L428P	L	+	2	0	CYP4A22	47384185	1.000000	0.71417	0.722000	0.30670	0.190000	0.23558	3.694000	0.54742	-0.120000	0.11809	-1.033000	0.02402	CTA	T|0.740;C|0.260	0.260	strong		0.512	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
SFXN2	118980	hgsc.bcm.edu	37	10	104486489	104486489	+	Silent	SNP	C	C	T	rs35153373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:104486489C>T	ENST00000369893.5	+	2	263	c.96C>T	c.(94-96)gaC>gaT	p.D32D	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	32					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		ACATCACGGACCCCCGCACTG	0.597													C|||	98	0.0195687	0.0719	0.0043	5008	,	,		19104	0.0		0.0	False		,,,				2504	0.0				p.D32D		Atlas-SNP	.											.	SFXN2	40	.	0			c.C96T						PASS	.	C		273,4133	153.3+/-186.9	5,263,1935	91.0	90.0	90.0		96	1.1	1.0	10	dbSNP_126	90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SFXN2	NM_178858.4		5,264,6234	TT,TC,CC		0.0116,6.1961,2.1067		32/323	104486489	274,12732	2203	4300	6503	SO:0001819	synonymous_variant	118980	exon2			CACGGACCCCCGC	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.96C>T	10.37:g.104486489C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	156	77	0.49359	NM_178858	Q5JSM6	Silent	SNP	ENST00000369893.5	37	CCDS7539.1																																																																																			C|0.980;T|0.020	0.020	strong		0.597	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359	
OR10H2	26538	hgsc.bcm.edu	37	19	15839081	15839081	+	Silent	SNP	C	C	T	rs2067083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15839081C>T	ENST00000305899.3	+	1	248	c.228C>T	c.(226-228)gcC>gcT	p.A76A		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	76						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					ACACCGTGGCCATCATCCCGC	0.617													C|||	1287	0.256989	0.4198	0.2709	5008	,	,		23430	0.0119		0.3111	False		,,,				2504	0.2239				p.A76A		Atlas-SNP	.											.	OR10H2	59	.	0			c.C228T						PASS	.	C		1763,2643		337,1089,777	149.0	122.0	131.0		228	2.3	0.8	19	dbSNP_96	131	2449,6151		356,1737,2207	no	coding-synonymous	OR10H2	NM_013939.2		693,2826,2984	TT,TC,CC		28.4767,40.0136,32.3851		76/316	15839081	4212,8794	2203	4300	6503	SO:0001819	synonymous_variant	26538	exon1			CGTGGCCATCATC	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.228C>T	19.37:g.15839081C>T		Somatic	437	1	0.00228833		WXS	Illumina HiSeq	Phase_I	426	168	0.394366	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			C|0.708;T|0.292	0.292	strong		0.617	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
IMMT	10989	hgsc.bcm.edu	37	2	86385812	86385812	+	Silent	SNP	T	T	C	rs2228352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86385812T>C	ENST00000410111.3	-	10	1452	c.1065A>G	c.(1063-1065)gtA>gtG	p.V355V	Y_RNA_ENST00000363371.1_RNA|IMMT_ENST00000254636.5_Silent_p.V256V|IMMT_ENST00000449247.2_Silent_p.V344V|IMMT_ENST00000490238.1_5'UTR|IMMT_ENST00000409051.2_Silent_p.V308V|IMMT_ENST00000442664.2_Silent_p.V354V	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	355					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GATACTGAGATACAACCTTAG	0.433													T|||	224	0.0447284	0.1331	0.0115	5008	,	,		20269	0.0		0.001	False		,,,				2504	0.0399				p.V355V		Atlas-SNP	.											.	IMMT	65	.	0			c.A1065G						PASS	.	T	,,	366,3392		15,336,1528	60.0	55.0	56.0		1062,1032,1065	-7.7	0.7	2	dbSNP_98	56	3,8249		0,3,4123	no	coding-synonymous,coding-synonymous,coding-synonymous	IMMT	NM_001100169.1,NM_001100170.1,NM_006839.2	,,	15,339,5651	CC,CT,TT		0.0364,9.7392,3.0724	,,	354/758,344/748,355/759	86385812	369,11641	1879	4126	6005	SO:0001819	synonymous_variant	10989	exon10			CTGAGATACAACC	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"""mitofilin"", ""mitochondrial inner membrane organizing system 2"""	600378	"""inner membrane protein, mitochondrial (mitofilin)"""			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.1065A>G	2.37:g.86385812T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	117	50	0.42735	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Silent	SNP	ENST00000410111.3	37	CCDS46355.1	56	0.02564102564102564	51	0.10365853658536585	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	T	9.781	1.175415	0.21704	0.097392	3.64E-4	ENSG00000132305	ENST00000419070	.	.	.	5.76	-7.73	0.01245	.	.	.	.	.	T	0.01940	0.0061	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49011	-0.8983	4	.	.	.	-18.6743	10.0221	0.42048	0.0:0.2774:0.1707:0.5519	rs2228352;rs2228352	.	.	.	V	210	.	.	I	-	1	0	IMMT	86239323	0.003000	0.15002	0.651000	0.29564	0.993000	0.82548	-1.546000	0.02188	-1.085000	0.03088	-0.256000	0.11100	ATC	T|0.968;C|0.032	0.032	strong		0.433	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839	
ASPG	374569	hgsc.bcm.edu	37	14	104559852	104559852	+	Silent	SNP	T	T	C	rs941953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:104559852T>C	ENST00000551177.1	+	3	308	c.216T>C	c.(214-216)atT>atC	p.I72I	ASPG_ENST00000455920.2_Silent_p.I72I|ASPG_ENST00000546892.2_Silent_p.I72I	NM_001080464.2	NP_001073933.2	Q86U10	LPP60_HUMAN	asparaginase	72	Asparaginase.|Asparaginase/glutaminase. {ECO:0000255|PROSITE-ProRule:PRU01068}.				asparagine metabolic process (GO:0006528)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)		1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|asparaginase activity (GO:0004067)|lysophospholipase activity (GO:0004622)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	11						ACCAGAGGATTCTCTACACCG	0.622													C|||	2067	0.41274	0.6823	0.3314	5008	,	,		13262	0.3869		0.1809	False		,,,				2504	0.3712				p.I72I		Atlas-SNP	.											.	ASPG	34	.	0			c.T216C						PASS	.	C		2280,1854		606,1068,393	69.0	81.0	77.0		216	1.6	0.8	14	dbSNP_86	77	1413,6957		119,1175,2891	no	coding-synonymous	ASPG	NM_001080464.2		725,2243,3284	CC,CT,TT		16.8817,44.8476,29.5345		72/574	104559852	3693,8811	2067	4185	6252	SO:0001819	synonymous_variant	374569	exon3			GAGGATTCTCTAC		CCDS45170.1, CCDS45170.2	14q32.33	2014-03-14	2014-03-14	2008-11-06	ENSG00000166183	ENSG00000166183	3.1.1.5, 3.5.1.1	"""Ankyrin repeat domain containing"""	20123	protein-coding gene	gene with protein product	"""60-kDa-lysophospholipase"""		"""chromosome 14 open reading frame 76"", ""asparaginase homolog (S. cerevisiae)"""	C14orf76			Standard	NM_001080464		Approved		uc001yoq.2	Q86U10		ENST00000551177.1:c.216T>C	14.37:g.104559852T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001080464	B9EGQ2|Q8IV80	Silent	SNP	ENST00000551177.1	37	CCDS45170.2	788	0.3608058608058608	317	0.6443089430894309	126	0.34806629834254144	218	0.3811188811188811	127	0.16754617414248021	C	2.774	-0.255089	0.05829	0.551524	0.168817	ENSG00000166183	ENST00000551170	.	.	.	3.57	1.64	0.23874	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19575	P	0.9999653784	.	.	.	.	.	.	T	0.39820	-0.9595	3	.	.	.	-22.8141	3.8673	0.09021	0.1665:0.4251:0.0:0.4083	rs941953;rs1744283;rs59940089;rs941953	.	.	.	P	9	.	.	S	+	1	0	ASPG	103629605	0.001000	0.12720	0.761000	0.31378	0.086000	0.17979	-0.340000	0.07821	0.172000	0.19760	-1.140000	0.01884	TCT	T|0.625;C|0.375	0.375	strong		0.622	ASPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407005.1	NM_001080464	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18656225	18656225	+	Silent	SNP	G	G	A	rs11044142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18656225G>A	ENST00000266497.5	+	21	2942	c.2904G>A	c.(2902-2904)caG>caA	p.Q968Q	PIK3C2G_ENST00000433979.1_Silent_p.Q968Q|PIK3C2G_ENST00000538779.1_Silent_p.Q1009Q			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	968	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				GATTGGTGCAGATGGTACCTG	0.403													G|||	804	0.160543	0.3744	0.1254	5008	,	,		16910	0.0		0.1789	False		,,,				2504	0.0429				p.Q968Q		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.G2904A						PASS	.	G		1162,2554		193,776,889	92.0	88.0	89.0		2904	3.0	1.0	12	dbSNP_120	89	1401,6805		115,1171,2817	no	coding-synonymous	PIK3C2G	NM_004570.4		308,1947,3706	AA,AG,GG		17.0729,31.2702,21.4981		968/1446	18656225	2563,9359	1858	4103	5961	SO:0001819	synonymous_variant	5288	exon22			GGTGCAGATGGTA	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2904G>A	12.37:g.18656225G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	131	57	0.435115	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																			G|0.842;A|0.158	0.158	strong		0.403	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
MIIP	60672	hgsc.bcm.edu	37	1	12082334	12082334	+	Missense_Mutation	SNP	A	A	T	rs11553925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12082334A>T	ENST00000235332.4	+	3	466	c.297A>T	c.(295-297)aaA>aaT	p.K99N	MIIP_ENST00000466860.1_3'UTR|Y_RNA_ENST00000365591.1_RNA|MIIP_ENST00000436478.2_Missense_Mutation_p.K99N	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein	99			K -> N (in dbSNP:rs11553925). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15867349}.							autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						CACCTGCCAAATGCCAGCACC	0.701													A|||	812	0.162141	0.1762	0.1398	5008	,	,		18127	0.0685		0.2515	False		,,,				2504	0.1636				p.K99N		Atlas-SNP	.											MIIP,brain,glioma,0,1	MIIP	34	1	0			c.A297T						PASS	.	A	ASN/LYS	744,3662	280.2+/-275.2	61,622,1520	45.0	49.0	48.0		297	-1.2	0.0	1	dbSNP_120	48	2149,6443	336.4+/-321.9	276,1597,2423	yes	missense	MIIP	NM_021933.3	94	337,2219,3943	TT,TA,AA		25.0116,16.8861,22.2573	possibly-damaging	99/389	12082334	2893,10105	2203	4296	6499	SO:0001583	missense	60672	exon3			TGCCAAATGCCAG	AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"""invasion inhibitory protein 45"""	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.297A>T	1.37:g.12082334A>T	ENSP00000235332:p.Lys99Asn	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	139	70	0.503597	NM_021933	C0KL22|Q96HU6|Q9H839|Q9HA00	Missense_Mutation	SNP	ENST00000235332.4	37	CCDS143.1	346	0.15842490842490842	81	0.16463414634146342	51	0.1408839779005525	21	0.03671328671328671	193	0.2546174142480211	A	20.4	3.982609	0.74474	0.168861	0.250116	ENSG00000116691	ENST00000235332;ENST00000436478	T;T	0.21543	2.0;2.0	4.49	-1.21	0.09524	.	1.829550	0.02773	N	0.119944	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	P	0.52316	0.952	P	0.51701	0.677	T	0.13469	-1.0508	9	0.41790	T	0.15	-0.001	8.0747	0.30710	0.4922:0.0:0.5077:0.0	rs11553925;rs17856239;rs61368770	99	Q5JXC2	MIIP_HUMAN	N	99	ENSP00000235332:K99N;ENSP00000392417:K99N	ENSP00000235332:K99N	K	+	3	2	MIIP	12004921	0.000000	0.05858	0.000000	0.03702	0.740000	0.42216	-0.465000	0.06680	-0.287000	0.09064	-0.285000	0.09966	AAA	A|0.799;T|0.201	0.201	strong		0.701	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933	
SVIL	6840	hgsc.bcm.edu	37	10	29779847	29779847	+	Missense_Mutation	SNP	A	A	C	rs199726033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:29779847A>C	ENST00000355867.4	-	22	4873	c.4121T>G	c.(4120-4122)cTc>cGc	p.L1374R	SVIL_ENST00000538146.1_Missense_Mutation_p.L166R|SVIL_ENST00000375398.2_Missense_Mutation_p.L1374R|SVIL_ENST00000375400.3_Missense_Mutation_p.L948R|SVIL_ENST00000535393.1_Missense_Mutation_p.L288R	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1374					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.L1374R(2)		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)				TTCCTGAAGGAGATCTTCTCT	0.522																																					p.L1374R		Atlas-SNP	.											SVIL,NS,carcinoma,0,4	SVIL	226	4	2	Substitution - Missense(2)	stomach(1)|central_nervous_system(1)	c.T4121G						PASS	.						61.0	64.0	63.0					10																	29779847		2203	4297	6500	SO:0001583	missense	6840	exon22			TGAAGGAGATCTT	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.4121T>G	10.37:g.29779847A>C	ENSP00000348128:p.Leu1374Arg	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	240	50	0.208333	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.079593	0.55753	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;D	0.86164	2.23;2.3;2.3;2.07;-2.08	4.08	4.08	0.47627	.	0.052248	0.85682	D	0.000000	D	0.91402	0.7287	M	0.68952	2.095	0.43583	D	0.995928	P;D;D;P	0.62365	0.947;0.986;0.991;0.884	P;D;D;P	0.64506	0.789;0.921;0.926;0.507	D	0.92348	0.5887	10	0.87932	D	0	-17.1694	13.2793	0.60205	1.0:0.0:0.0:0.0	.	288;166;948;1374	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	R	948;1374;1374;288;328;166	ENSP00000364549:L948R;ENSP00000364547:L1374R;ENSP00000348128:L1374R;ENSP00000445472:L288R;ENSP00000440343:L166R	ENSP00000348128:L1374R	L	-	2	0	SVIL	29819853	1.000000	0.71417	0.983000	0.44433	0.278000	0.26855	8.642000	0.91036	1.714000	0.51371	0.397000	0.26171	CTC	A|0.783;C|0.217	0.217	strong		0.522	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
COL28A1	340267	hgsc.bcm.edu	37	7	7545691	7545691	+	Missense_Mutation	SNP	G	G	C	rs10486176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:7545691G>C	ENST00000399429.3	-	11	1120	c.980C>G	c.(979-981)aCt>aGt	p.T327S		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	327	Collagen-like 2.		T -> S (in dbSNP:rs10486176).		cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TGGAGGTCCAGTAATTCCCTG	0.483													C|||	716	0.142971	0.1188	0.1527	5008	,	,		18641	0.1696		0.1173	False		,,,				2504	0.1677				p.T327S		Atlas-SNP	.											.	COL28A1	113	.	0			c.C980G						PASS	.	C	SER/THR	450,3270		28,394,1438	88.0	86.0	86.0		980	1.7	0.7	7	dbSNP_119	86	956,7240		58,840,3200	yes	missense	COL28A1	NM_001037763.2	58	86,1234,4638	CC,CG,GG		11.6642,12.0968,11.7993	benign	327/1126	7545691	1406,10510	1860	4098	5958	SO:0001583	missense	340267	exon11			GGTCCAGTAATTC	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.980C>G	7.37:g.7545691G>C	ENSP00000382356:p.Thr327Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	137	58	0.423358	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	283	0.1295787545787546	52	0.10569105691056911	60	0.16574585635359115	86	0.15034965034965034	85	0.11213720316622691	C	0.072	-1.201327	0.01581	0.120968	0.116642	ENSG00000215018	ENST00000399429;ENST00000399419	D	0.93189	-3.18	4.52	1.68	0.24146	.	0.955778	0.08549	N	0.929345	T	0.01320	0.0043	L	0.35288	1.05	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40813	-0.9543	9	0.13853	T	0.58	0.0743	5.235	0.15441	0.0:0.4599:0.3515:0.1886	rs10486176;rs10486176	327	Q2UY09	COSA1_HUMAN	S	327	ENSP00000382356:T327S	ENSP00000382347:T327S	T	-	2	0	COL28A1	7512216	0.781000	0.28676	0.665000	0.29768	0.811000	0.45836	0.520000	0.22878	0.010000	0.14839	-0.215000	0.12644	ACT	G|0.869;C|0.131	0.131	strong		0.483	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
MST1L	11223	hgsc.bcm.edu	37	1	17086976	17086976	+	RNA	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17086976G>A	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										TCCGGAGCGTGGGCATGTACC	0.607																																					p.P116P		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,-2,2	.	.	2	0			c.C348T						PASS	.																																					11223	exon4			GAGCGTGGGCATG	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.17086976G>A		Somatic	396	0	0		WXS	Illumina HiSeq	Phase_I	491	53	0.107943	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				.	.	none		0.607	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
LAMC2	3918	hgsc.bcm.edu	37	1	183184650	183184650	+	Missense_Mutation	SNP	G	G	C	rs12065473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:183184650G>C	ENST00000264144.4	+	3	396	c.331G>C	c.(331-333)Gcc>Ccc	p.A111P	LAMC2_ENST00000493293.1_Missense_Mutation_p.A111P	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	111	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.		A -> P (in dbSNP:rs12065473).		cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						TGTGACAGGAGCCAGATGCGA	0.547													G|||	160	0.0319489	0.1135	0.013	5008	,	,		19074	0.0		0.001	False		,,,				2504	0.0				p.A111P		Atlas-SNP	.											.	LAMC2	113	.	0			c.G331C						PASS	.	G	PRO/ALA,PRO/ALA	484,3922	226.9+/-242.2	23,438,1742	124.0	110.0	115.0		331,331	2.0	0.7	1	dbSNP_120	115	7,8593	5.0+/-18.6	0,7,4293	yes	missense,missense	LAMC2	NM_005562.2,NM_018891.2	27,27	23,445,6035	CC,CG,GG		0.0814,10.985,3.7752	benign,benign	111/1194,111/1112	183184650	491,12515	2203	4300	6503	SO:0001583	missense	3918	exon3			ACAGGAGCCAGAT	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.331G>C	1.37:g.183184650G>C	ENSP00000264144:p.Ala111Pro	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	173	77	0.445087	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	37	CCDS1352.1	51	0.023351648351648352	46	0.09349593495934959	5	0.013812154696132596	0	0.0	0	0.0	G	16.35	3.099112	0.56183	0.10985	8.14E-4	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.61392	0.11;0.11	4.97	2.0	0.26442	EGF-like, laminin (4);Growth factor, receptor (1);	0.621389	0.16329	N	0.219195	T	0.00637	0.0021	N	0.05230	-0.09	0.27001	N	0.964914	B;B	0.26041	0.14;0.034	B;B	0.31495	0.131;0.039	T	0.04678	-1.0934	10	0.30854	T	0.27	.	5.6168	0.17436	0.2342:0.148:0.6178:0.0	rs12065473;rs52806764;rs12065473	111;111	Q13753;Q13753-2	LAMC2_HUMAN;.	P	111	ENSP00000432063:A111P;ENSP00000264144:A111P	ENSP00000264144:A111P	A	+	1	0	LAMC2	181451273	0.946000	0.32159	0.668000	0.29813	0.953000	0.61014	1.823000	0.39062	0.139000	0.18822	-0.137000	0.14449	GCC	G|0.963;C|0.037	0.037	strong		0.547	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656479	46656479	+	Missense_Mutation	SNP	A	A	G	rs6519993	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	91	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	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	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642827	1642827	+	Missense_Mutation	SNP	G	G	C	rs374921824|rs541987207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1642827G>C	ENST00000399682.1	-	1	541	c.497C>G	c.(496-498)tCc>tGc	p.S166C		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACCTGAGGAGGAGCAGCAGGG	0.607													g|||	148	0.0295527	0.056	0.0187	5008	,	,		15114	0.0188		0.0229	False		,,,				2504	0.0194				p.S166C		Atlas-SNP	.											KRTAP5-4,colon,carcinoma,0,3	KRTAP5-4	78	3	0			c.C497G						scavenged	.						22.0	35.0	31.0					11																	1642827		692	1590	2282	SO:0001583	missense	387267	exon1			GAGGAGGAGCAGC	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.497C>G	11.37:g.1642827G>C	ENSP00000382590:p.Ser166Cys	Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	206	9	0.0436893	NM_001012709		Missense_Mutation	SNP	ENST00000399682.1	37		.	.	.	.	.	.	.	.	.	.	G	2.402	-0.337333	0.05278	.	.	ENSG00000241598	ENST00000399682	T	0.00792	5.69	0.891	-0.0782	0.13716	.	.	.	.	.	T	0.00468	0.0015	N	0.02960	-0.455	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.45056	-0.9287	9	0.51188	T	0.08	.	6.6433	0.22921	0.0:0.5966:0.4034:0.0	.	226	Q6L8H1	KRA54_HUMAN	C	166	ENSP00000382590:S166C	ENSP00000382590:S166C	S	-	2	0	KRTAP5-4	1599403	0.001000	0.12720	0.007000	0.13788	0.001000	0.01503	-0.354000	0.07681	-0.014000	0.14175	-1.289000	0.01358	TCC	.	.	none		0.607	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
PADI4	23569	hgsc.bcm.edu	37	1	17668508	17668508	+	Silent	SNP	C	C	T	rs16825565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17668508C>T	ENST00000375448.4	+	7	749	c.723C>T	c.(721-723)ccC>ccT	p.P241P	AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	241					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	TGATGGTCCCCGGTGGAAAGC	0.602													C|||	74	0.0147764	0.0537	0.0043	5008	,	,		17108	0.0		0.0	False		,,,				2504	0.0				p.P241P		Atlas-SNP	.											.	PADI4	70	.	0			c.C723T						PASS	.	C		190,4216	119.6+/-157.3	6,178,2019	85.0	78.0	81.0		723	-9.9	0.0	1	dbSNP_123	81	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	PADI4	NM_012387.2		6,180,6317	TT,TC,CC		0.0233,4.3123,1.4762		241/664	17668508	192,12814	2203	4300	6503	SO:0001819	synonymous_variant	23569	exon7			GGTCCCCGGTGGA	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"""Peptidyl arginine deiminases"""	18368	protein-coding gene	gene with protein product		605347	"""peptidyl arginine deiminase, type V"""	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.723C>T	1.37:g.17668508C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	122	54	0.442623	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Silent	SNP	ENST00000375448.4	37	CCDS180.1																																																																																			C|0.984;T|0.016	0.016	strong		0.602	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
LAIR1	3903	hgsc.bcm.edu	37	19	54871664	54871664	+	Missense_Mutation	SNP	G	G	C	rs74463408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54871664G>C	ENST00000391742.2	-	4	532	c.380C>G	c.(379-381)cCg>cGg	p.P127R	LAIR1_ENST00000463489.1_5'UTR|LAIR1_ENST00000313038.6_Missense_Mutation_p.P120R|LAIR1_ENST00000391743.3_Missense_Mutation_p.P109R|LAIR1_ENST00000348231.4_Intron|LAIR1_ENST00000474878.1_Intron|LAIR1_ENST00000434277.2_Missense_Mutation_p.P126R			Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like receptor 1	127					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(4)|prostate(1)|stomach(3)	26	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)		CGGGGAGTCCGGGCCTCCAGA	0.627													G|||	778	0.155351	0.0802	0.1153	5008	,	,		16464	0.2877		0.1402	False		,,,				2504	0.1646				p.P127R		Atlas-SNP	.											LAIR1,colon,carcinoma,+1,2	LAIR1	44	2	0			c.C380G						PASS	.	G	ARG/PRO,	321,4057		25,271,1893	53.0	57.0	56.0		380,	-2.3	0.0	19	dbSNP_131	56	986,7610		79,828,3391	no	missense,intron	LAIR1	NM_002287.3,NM_021706.2	103,	104,1099,5284	CC,CG,GG		11.4705,7.3321,10.074	benign,	127/288,	54871664	1307,11667	2189	4298	6487	SO:0001583	missense	3903	exon4			GAGTCCGGGCCTC	AF013249	CCDS12891.1, CCDS12892.1, CCDS74448.1, CCDS74449.1, CCDS74450.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167613	ENSG00000167613		"""Leukocyte-associated Ig like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6477	protein-coding gene	gene with protein product		602992	"""leukocyte-associated Ig-like receptor 1"""			9285412	Standard	XM_005258924		Approved	CD305	uc002qfk.1	Q6GTX8	OTTHUMG00000065545	ENST00000391742.2:c.380C>G	19.37:g.54871664G>C	ENSP00000375622:p.Pro127Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	256	78	0.304688	NM_002287		Missense_Mutation	SNP	ENST00000391742.2	37	CCDS12891.1	333	0.15247252747252749	42	0.08536585365853659	49	0.13535911602209943	146	0.25524475524475526	96	0.1266490765171504	.	5.214	0.224908	0.09916	0.073321	0.114705	ENSG00000167613	ENST00000391743;ENST00000391742;ENST00000434277;ENST00000313038;ENST00000444687	T;T;T;T;T	0.64085	6.72;6.74;6.76;6.73;-0.08	1.88	-2.29	0.06805	.	.	.	.	.	T	0.00012	0.0000	N	0.25485	0.75	0.80722	P	0.0	P;B;B;P	0.45715	0.516;0.034;0.054;0.865	B;B;B;P	0.47206	0.25;0.015;0.02;0.541	T	0.02546	-1.1143	8	0.37606	T	0.19	.	2.177	0.03865	0.4243:0.0:0.3314:0.2443	rs35781676	127;109;126;127	Q6GTX8-4;A8MZ84;D3YTC8;Q6GTX8	.;.;.;LAIR1_HUMAN	R	109;127;126;120;17	ENSP00000375623:P109R;ENSP00000375622:P127R;ENSP00000391003:P126R;ENSP00000319204:P120R;ENSP00000392722:P17R	ENSP00000319204:P120R	P	-	2	0	LAIR1	59563476	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.372000	0.20467	-0.603000	0.05767	-1.129000	0.01985	CCG	G|0.886;C|0.114	0.114	strong		0.627	LAIR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140506.1		
NOD1	10392	hgsc.bcm.edu	37	7	30496382	30496382	+	Silent	SNP	G	G	C	rs2075818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30496382G>C	ENST00000222823.4	-	4	681	c.156C>G	c.(154-156)gcC>gcG	p.A52A	NOD1_ENST00000423334.2_Silent_p.A52A	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	52	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|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)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|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 cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|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 tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|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)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						CCGCATCTTCGGCCGAGAAGT	0.547													G|||	1849	0.369209	0.5166	0.1902	5008	,	,		18461	0.3859		0.2326	False		,,,				2504	0.4202				p.A52A		Atlas-SNP	.											.	NOD1	79	.	0			c.C156G						PASS	.	G		2093,2313	573.3+/-383.5	502,1089,612	126.0	112.0	116.0		156	-11.6	0.0	7	dbSNP_96	116	2137,6463	367.3+/-334.7	284,1569,2447	no	coding-synonymous	NOD1	NM_006092.2		786,2658,3059	CC,CG,GG		24.8488,47.5034,32.5235		52/954	30496382	4230,8776	2203	4300	6503	SO:0001819	synonymous_variant	10392	exon4			ATCTTCGGCCGAG	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.156C>G	7.37:g.30496382G>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	175	97	0.554286	NM_006092	B4DTU3|Q549U4|Q8IWF5	Silent	SNP	ENST00000222823.4	37	CCDS5427.1																																																																																			G|0.683;C|0.317	0.317	strong		0.547	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
SHANK1	50944	hgsc.bcm.edu	37	19	51172526	51172526	+	Missense_Mutation	SNP	G	G	C	rs41275782	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51172526G>C	ENST00000293441.1	-	22	2709	c.2691C>G	c.(2689-2691)gaC>gaG	p.D897E	SYT3_ENST00000544769.1_5'Flank|SHANK1_ENST00000391814.1_Missense_Mutation_p.D905E|SHANK1_ENST00000359082.3_Missense_Mutation_p.D888E|SHANK1_ENST00000391813.1_Missense_Mutation_p.D284E	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	897					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|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)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		GGTAAGGTCTGTCATCTTCTG	0.622											OREG0025642	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	409	0.0816693	0.1051	0.0375	5008	,	,		11380	0.1052		0.0457	False		,,,				2504	0.0941				p.D897E		Atlas-SNP	.											.	SHANK1	210	.	0			c.C2691G						PASS	.	G	GLU/ASP	505,3897		41,423,1737	20.0	17.0	18.0		2691	-2.5	1.0	19	dbSNP_127	18	318,8280		7,304,3988	yes	missense	SHANK1	NM_016148.2	45	48,727,5725	CC,CG,GG		3.6985,11.4721,6.3308	benign	897/2162	51172526	823,12177	2201	4299	6500	SO:0001583	missense	50944	exon22			AGGTCTGTCATCT	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	15474	protein-coding gene	gene with protein product	"""somatostatin receptor-interacting protein"""	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.2691C>G	19.37:g.51172526G>C	ENSP00000293441:p.Asp897Glu	Somatic	109	0	0	975	WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	37	CCDS12799.1	162	0.07417582417582418	62	0.12601626016260162	17	0.04696132596685083	53	0.09265734265734266	30	0.0395778364116095	G	14.51	2.558043	0.45590	0.114721	0.036985	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	T;T;T;T	0.32753	1.53;1.94;1.51;1.44	3.77	-2.55	0.06288	.	0.391477	0.21289	U	0.077011	T	0.00073	0.0002	N	0.01197	-0.965	0.42303	P	0.007816000000000045	B;B	0.26195	0.128;0.144	B;B	0.36504	0.043;0.226	T	0.19811	-1.0294	9	0.06625	T	0.88	.	4.6593	0.12634	0.4079:0.2917:0.3005:0.0	rs41275782	897;284	Q9Y566;Q9Y566-2	SHAN1_HUMAN;.	E	897;284;888;905	ENSP00000293441:D897E;ENSP00000375689:D284E;ENSP00000351984:D888E;ENSP00000375690:D905E	ENSP00000293441:D897E	D	-	3	2	SHANK1	55864338	0.015000	0.18098	0.961000	0.40146	0.980000	0.70556	-1.393000	0.02521	-0.641000	0.05487	0.549000	0.68633	GAC	G|0.936;C|0.064	0.064	strong		0.622	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148	
LILRB3	11025	hgsc.bcm.edu	37	19	54725913	54725913	+	Missense_Mutation	SNP	C	C	T	rs199822090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54725913C>T	ENST00000391750.1	-	5	581	c.445G>A	c.(445-447)Gga>Aga	p.G149R	LILRA6_ENST00000391735.3_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000245620.9_Missense_Mutation_p.G149R|LILRB3_ENST00000407860.2_Missense_Mutation_p.G149R|LILRB3_ENST00000346401.6_Missense_Mutation_p.G149R|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000424807.1_Missense_Mutation_p.G149R|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	149	Ig-like C2-type 2.			G -> R (in Ref. 2; AAB87667). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGTGATATCCCTTCTGTGAG	0.597													.|||	783	0.15635	0.3411	0.1715	5008	,	,		12077	0.002		0.1362	False		,,,				2504	0.0757				p.G149R		Atlas-SNP	.											.	LILRB3	67	.	0			c.G445A						PASS	.						23.0	15.0	18.0					19																	54725913		2079	3867	5946	SO:0001583	missense	11025	exon4			GATATCCCTTCTG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.445G>A	19.37:g.54725913C>T	ENSP00000375630:p.Gly149Arg	Somatic	491	0	0		WXS	Illumina HiSeq	Phase_I	544	115	0.211397	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	6.911	0.537697	0.13188	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000445347	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76;5.76	2.87	-5.75	0.02384	Immunoglobulin-like fold (1);	2.192950	0.01626	N	0.023278	T	0.07683	0.0193	L	0.37800	1.135	0.80722	P	0.0	B;B;P;P;P	0.41546	0.218;0.08;0.555;0.754;0.68	B;B;B;B;B	0.39094	0.271;0.132;0.29;0.049;0.209	T	0.17258	-1.0375	9	0.41790	T	0.15	.	1.2731	0.02025	0.1365:0.1909:0.2699:0.4027	.	149;149;149;149;149	B5MCX0;F8WD89;O75022-2;O75022;O75022-3	.;.;.;LIRB3_HUMAN;.	R	149	ENSP00000375630:G149R;ENSP00000412771:G149R;ENSP00000345184:G149R;ENSP00000245620:G149R;ENSP00000384274:G149R;ENSP00000388199:G149R	ENSP00000245620:G149R	G	-	1	0	LILRB3	59417725	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.520000	0.00951	-1.631000	0.01543	-0.510000	0.04470	GGA	C|0.931;T|0.069	0.069	strong		0.597	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3686676	3686676	+	Missense_Mutation	SNP	C	C	G	rs35953127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3686676C>G	ENST00000344754.4	-	3	420	c.421G>C	c.(421-423)Gtg>Ctg	p.V141L	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.V141L	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	141	Ig-like C2-type 1.		V -> L (in dbSNP:rs35953127).		cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						ATGGTGGGCACCCTGGGCTCC	0.627													C|||	212	0.0423323	0.1551	0.0101	5008	,	,		17587	0.0		0.0	False		,,,				2504	0.0				p.V141L		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.G421C						PASS	.	C	LEU/VAL	534,3872	236.5+/-248.6	30,474,1699	47.0	51.0	49.0		421	-4.2	0.0	20	dbSNP_126	49	7,8593	4.3+/-15.6	0,7,4293	yes	missense	SIGLEC1	NM_023068.3	32	30,481,5992	GG,GC,CC		0.0814,12.1198,4.1596	benign	141/1710	3686676	541,12465	2203	4300	6503	SO:0001583	missense	6614	exon3			TGGGCACCCTGGG	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.421G>C	20.37:g.3686676C>G	ENSP00000341141:p.Val141Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	37	CCDS13060.1	55	0.025183150183150184	51	0.10365853658536585	4	0.011049723756906077	0	0.0	0	0.0	C	9.310	1.055241	0.19907	0.121198	8.14E-4	ENSG00000088827	ENST00000344754;ENST00000202578	D;D	0.86030	-2.06;-2.06	5.14	-4.16	0.03869	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.833960	0.01625	N	0.023240	T	0.03390	0.0098	L	0.36672	1.1	0.09310	N	1	B;B;B	0.11235	0.004;0.002;0.004	B;B;B	0.12156	0.007;0.002;0.004	T	0.35500	-0.9786	10	0.15952	T	0.53	.	5.3212	0.15881	0.0:0.2732:0.2779:0.4489	rs35953127;rs57549161	141;141;141	Q9BZZ2-2;Q9BZZ2;Q9BZZ2-3	.;SN_HUMAN;.	L	141	ENSP00000341141:V141L;ENSP00000202578:V141L	ENSP00000202578:V141L	V	-	1	0	SIGLEC1	3634676	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.094000	0.11094	-0.384000	0.07845	0.563000	0.77884	GTG	C|0.957;G|0.043	0.043	strong		0.627	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
ADH1B	125	hgsc.bcm.edu	37	4	100237169	100237169	+	Silent	SNP	C	C	T	rs139645116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100237169C>T	ENST00000305046.8	-	5	520	c.453G>A	c.(451-453)acG>acA	p.T151T	ADH1B_ENST00000394887.3_Silent_p.T111T|ADH1B_ENST00000504498.1_5'Flank			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	151					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	CATCCACCACCGTGTACTGGG	0.582													.|||	13	0.00259585	0.0098	0.0	5008	,	,		18733	0.0		0.0	False		,,,				2504	0.0				p.T151T		Atlas-SNP	.											.	ADH1B	68	.	0			c.G453A						PASS	.	C		31,4375	36.0+/-67.5	0,31,2172	131.0	118.0	122.0		453	-7.9	0.1	4	dbSNP_134	122	0,8600		0,0,4300	no	coding-synonymous	ADH1B	NM_000668.4		0,31,6472	TT,TC,CC		0.0,0.7036,0.2384		151/376	100237169	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	125	exon5			CACCACCGTGTAC	AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"""Alcohol dehydrogenases"""	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.453G>A	4.37:g.100237169C>T		Somatic	317	1	0.00315457		WXS	Illumina HiSeq	Phase_I	286	137	0.479021	NM_000668	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	ENST00000305046.8	37	CCDS34033.1																																																																																			C|0.998;T|0.002	0.002	strong		0.582	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668	
TRAPPC3L	100128327	hgsc.bcm.edu	37	6	116818225	116818225	+	Silent	SNP	C	C	T	rs114678052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116818225C>T	ENST00000368602.3	-	5	533	c.438G>A	c.(436-438)gcG>gcA	p.A146A	TRAPPC3L_ENST00000356128.4_Silent_p.A62A|RP11-259P20.1_ENST00000420595.2_RNA	NM_001139444.2	NP_001132916.1	Q5T215	TPC3L_HUMAN	trafficking protein particle complex 3-like	146					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)											TAACATCAGCCGCCAAATGAA	0.333													A|||	240	0.0479233	0.171	0.0101	5008	,	,		17317	0.0		0.007	False		,,,				2504	0.0				p.A146A		Atlas-SNP	.											.	BET3L	18	.	0			c.G438A						PASS	.						110.0	85.0	93.0					6																	116818225		692	1591	2283	SO:0001819	synonymous_variant	100128327	exon5			ATCAGCCGCCAAA	AK002042	CCDS47468.1	6q22.31	2013-05-01	2013-05-01	2013-05-01	ENSG00000173626	ENSG00000173626			21090	protein-coding gene	gene with protein product		614137	"""BET3 like (S. cerevisiae)"""	BET3L		21525244	Standard	NM_001139444		Approved	bA259P20.2, FLJ11180		Q5T215	OTTHUMG00000015440	ENST00000368602.3:c.438G>A	6.37:g.116818225C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001139444	Q5T213|Q5T214	Silent	SNP	ENST00000368602.3	37	CCDS47468.1																																																																																			C|0.968;T|0.032	0.032	strong		0.333	TRAPPC3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000101701.1	XM_166322	
LRP11	84918	hgsc.bcm.edu	37	6	150158486	150158486	+	Missense_Mutation	SNP	A	A	G	rs375299752		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:150158486A>G	ENST00000239367.2	-	4	1032	c.1027T>C	c.(1027-1029)Ttc>Ctc	p.F343L	LRP11_ENST00000546019.1_Missense_Mutation_p.F88L|LRP11_ENST00000463728.1_5'Flank	NM_032832.5	NP_116221.3	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein 11	343	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				cervix(1)|kidney(5)|large_intestine(1)|lung(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		TTCTGGCAGAAGTCTTCATCA	0.517																																					p.F343L		Atlas-SNP	.											.	LRP11	27	.	0			c.T1027C						PASS	.	A	LEU/PHE	2,4404	4.2+/-10.8	0,2,2201	122.0	101.0	108.0		1027	5.3	0.9	6		108	0,8600		0,0,4300	no	missense	LRP11	NM_032832.5	22	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	probably-damaging	343/501	150158486	2,13004	2203	4300	6503	SO:0001583	missense	84918	exon4			GGCAGAAGTCTTC	AK027641	CCDS5220.1	6q24.3	2013-02-27			ENSG00000120256	ENSG00000120256		"""Low density lipoprotein receptors"""	16936	protein-coding gene	gene with protein product							Standard	NM_032832		Approved	bA350J20.3, MANSC3	uc003qng.2	Q86VZ4	OTTHUMG00000015801	ENST00000239367.2:c.1027T>C	6.37:g.150158486A>G	ENSP00000239367:p.Phe343Leu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	107	41	0.383178	NM_032832	Q5VYC0|Q96SN6	Missense_Mutation	SNP	ENST00000239367.2	37	CCDS5220.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.958758	0.92726	4.54E-4	0.0	ENSG00000120256	ENST00000239367;ENST00000546019	D;D	0.95272	-3.66;-3.66	5.32	5.32	0.75619	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.93416	0.7900	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94587	0.7784	10	0.51188	T	0.08	-22.8051	14.5589	0.68120	1.0:0.0:0.0:0.0	.	343	Q86VZ4	LRP11_HUMAN	L	343;88	ENSP00000239367:F343L;ENSP00000440196:F88L	ENSP00000239367:F343L	F	-	1	0	LRP11	150200179	1.000000	0.71417	0.923000	0.36655	0.767000	0.43475	8.118000	0.89577	2.134000	0.65973	0.455000	0.32223	TTC	.	.	weak		0.517	LRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042664.1	NM_032832	
CR1L	1379	hgsc.bcm.edu	37	1	207890892	207890892	+	Missense_Mutation	SNP	G	G	A	rs116455739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207890892G>A	ENST00000508064.2	+	11	1558	c.1498G>A	c.(1498-1500)Gta>Ata	p.V500I		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	500	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TGGAAAAGAAGTATCTTACAC	0.478													a|||	149	0.0297524	0.003	0.0317	5008	,	,		17826	0.005		0.0547	False		,,,				2504	0.0644				p.V500I		Atlas-SNP	.											.	CR1L	97	.	0			c.G1498A						PASS	.	G	ILE/VAL	40,3744		0,40,1852	125.0	118.0	121.0		1498	-5.7	0.0	1	dbSNP_132	121	510,7700		19,472,3614	no	missense	CR1L	NM_175710.1	29	19,512,5466	AA,AG,GG		6.2119,1.0571,4.5856	benign	500/570	207890892	550,11444	1892	4105	5997	SO:0001583	missense	1379	exon11			AAAGAAGTATCTT	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1498G>A	1.37:g.207890892G>A	ENSP00000421736:p.Val500Ile	Somatic	325	1	0.00307692		WXS	Illumina HiSeq	Phase_I	306	137	0.447712	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	43	0.019688644688644688	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	36	0.047493403693931395	.	8.823	0.937939	0.18206	0.010571	0.062119	ENSG00000197721	ENST00000508064	T	0.68331	-0.32	3.01	-5.66	0.02451	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.10035	0.0246	L	0.42632	1.34	0.09310	N	1	B	0.02656	0.0	B	0.23716	0.048	T	0.23583	-1.0184	9	0.16896	T	0.51	.	8.581	0.33628	0.4874:0.0:0.5126:0.0	.	500	Q2VPA4	CR1L_HUMAN	I	500	ENSP00000421736:V500I	ENSP00000421736:V500I	V	+	1	0	CR1L	205957515	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-3.849000	0.00351	-1.208000	0.02634	-0.704000	0.03662	GTA	G|0.972;A|0.028	0.028	strong		0.478	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
GSAP	54103	hgsc.bcm.edu	37	7	76950686	76950686	+	Missense_Mutation	SNP	C	C	A	rs17151689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:76950686C>A	ENST00000257626.7	-	25	2036	c.1958G>T	c.(1957-1959)tGg>tTg	p.W653L	GSAP_ENST00000440473.1_5'UTR|GSAP_ENST00000441833.2_Intron	NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	653			W -> L (in dbSNP:rs17151689).		positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										ATGTTTCCTCCAATTGGTTTC	0.453													C|||	398	0.0794728	0.1203	0.0432	5008	,	,		21400	0.0724		0.0368	False		,,,				2504	0.1012				p.W653L		Atlas-SNP	.											PION,NS,carcinoma,-1,1	PION	74	1	0			c.G1958T						PASS	.	C	LEU/TRP	395,3545		20,355,1595	122.0	119.0	120.0		1958	5.6	1.0	7	dbSNP_123	120	371,7945		7,357,3794	yes	missense	PION	NM_017439.3	61	27,712,5389	AA,AC,CC		4.4613,10.0254,6.25	probably-damaging	653/855	76950686	766,11490	1970	4158	6128	SO:0001583	missense	54103	exon25			TTCCTCCAATTGG		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"""pigeon homolog (Drosophila)"""	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.1958G>T	7.37:g.76950686C>A	ENSP00000257626:p.Trp653Leu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	195	103	0.528205	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Missense_Mutation	SNP	ENST00000257626.7	37	CCDS34672.2	153	0.07005494505494506	57	0.11585365853658537	18	0.049723756906077346	50	0.08741258741258741	28	0.036939313984168866	C	15.79	2.935996	0.52972	0.100254	0.044613	ENSG00000186088	ENST00000257626;ENST00000415112	T;T	0.29142	1.58;1.58	5.56	5.56	0.83823	.	0.061038	0.64402	D	0.000001	T	0.00906	0.0030	M	0.69823	2.125	0.09310	P	1.0	D	0.58620	0.983	P	0.54544	0.755	T	0.00928	-1.1511	9	0.72032	D	0.01	.	16.8033	0.85619	0.0:1.0:0.0:0.0	rs17151689;rs17151689	653	A4D1B5	GSAP_HUMAN	L	653;106	ENSP00000257626:W653L;ENSP00000396230:W106L	ENSP00000257626:W653L	W	-	2	0	PION	76788622	1.000000	0.71417	0.992000	0.48379	0.634000	0.38068	4.639000	0.61361	2.777000	0.95525	0.591000	0.81541	TGG	C|0.925;A|0.075	0.075	strong		0.453	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
ABCC6	368	hgsc.bcm.edu	37	16	16291983	16291983	+	Silent	SNP	A	A	G	rs9930886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	126	0	0		WXS	Illumina HiSeq	Phase_I	144	68	0.472222	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		
PLIN4	729359	hgsc.bcm.edu	37	19	4511757	4511757	+	Missense_Mutation	SNP	C	C	T	rs74627313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4511757C>T	ENST00000301286.3	-	3	2172	c.2173G>A	c.(2173-2175)Ggt>Agt	p.G725S		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	725	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						TTCGCAGCACCGGTCACCCCA	0.587													C|||	268	0.0535144	0.1914	0.0159	5008	,	,		29873	0.002		0.002	False		,,,				2504	0.0				p.G725S		Atlas-SNP	.											.	PLIN4	191	.	0			c.G2173A						PASS	.	C	SER/GLY	582,3526		2,578,1474	169.0	161.0	164.0		2173	0.9	0.0	19	dbSNP_131	164	6,8366		0,6,4180	no	missense	PLIN4	NM_001080400.1	56	2,584,5654	TT,TC,CC		0.0717,14.1675,4.7115	benign	725/1358	4511757	588,11892	2054	4186	6240	SO:0001583	missense	729359	exon3			CAGCACCGGTCAC	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.2173G>A	19.37:g.4511757C>T	ENSP00000301286:p.Gly725Ser	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	455	108	0.237363	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	91	0.041666666666666664	83	0.16869918699186992	3	0.008287292817679558	2	0.0034965034965034965	3	0.00395778364116095	C	9.531	1.110845	0.20714	0.141675	7.17E-4	ENSG00000167676	ENST00000301286	T	0.06849	3.25	4.26	0.951	0.19579	.	0.000000	0.43579	U	0.000560	T	0.00039	0.0001	M	0.71206	2.165	0.09310	N	1	D	0.61080	0.989	B	0.43155	0.41	T	0.37267	-0.9713	10	0.52906	T	0.07	-19.0077	8.739	0.34545	0.0:0.7398:0.0:0.2602	.	725	Q96Q06	PLIN4_HUMAN	S	725	ENSP00000301286:G725S	ENSP00000301286:G725S	G	-	1	0	PLIN4	4462757	0.000000	0.05858	0.006000	0.13384	0.001000	0.01503	-0.818000	0.04467	0.799000	0.34018	-0.974000	0.02594	GGT	C|0.967;T|0.033	0.033	strong		0.587	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
WDR59	79726	hgsc.bcm.edu	37	16	74943471	74943471	+	Missense_Mutation	SNP	T	T	C	rs61734551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:74943471T>C	ENST00000262144.6	-	16	1700	c.1570A>G	c.(1570-1572)Acg>Gcg	p.T524A		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	524										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						CCGTAAGCCGTGGTCACCCGC	0.547													T|||	66	0.0131789	0.0484	0.0029	5008	,	,		16262	0.0		0.0	False		,,,				2504	0.0				p.T524A		Atlas-SNP	.											.	WDR59	66	.	0			c.A1570G						PASS	.	T	ALA/THR	124,4272	92.5+/-131.2	0,124,2074	89.0	95.0	93.0		1570	4.8	1.0	16	dbSNP_129	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	WDR59	NM_030581.3	58	0,126,6372	CC,CT,TT		0.0233,2.8207,0.9695	benign	524/975	74943471	126,12870	2198	4300	6498	SO:0001583	missense	79726	exon16			AAGCCGTGGTCAC	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.1570A>G	16.37:g.74943471T>C	ENSP00000262144:p.Thr524Ala	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Missense_Mutation	SNP	ENST00000262144.6	37	CCDS32488.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	T	10.57	1.388491	0.25118	0.028207	2.33E-4	ENSG00000103091	ENST00000262144	T	0.67698	-0.28	5.86	4.76	0.60689	.	0.137136	0.64402	D	0.000005	T	0.14313	0.0346	N	0.08118	0	0.34596	D	0.715995	B	0.12013	0.005	B	0.14023	0.01	T	0.30794	-0.9966	10	0.08381	T	0.77	-12.4732	13.1941	0.59728	0.0:0.0:0.1332:0.8668	.	524	Q6PJI9	WDR59_HUMAN	A	524	ENSP00000262144:T524A	ENSP00000262144:T524A	T	-	1	0	WDR59	73500972	1.000000	0.71417	0.997000	0.53966	0.015000	0.08874	5.542000	0.67218	1.129000	0.42072	-0.323000	0.08544	ACG	T|0.988;C|0.012	0.012	strong		0.547	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581	
OR6P1	128366	hgsc.bcm.edu	37	1	158532605	158532605	+	Missense_Mutation	SNP	C	C	A	rs115786820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158532605C>A	ENST00000334632.1	-	1	789	c.790G>T	c.(790-792)Gcc>Tcc	p.A264S		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	264						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						GTGTACATGGCCCGGGGCCGT	0.512													C|||	79	0.0157748	0.0582	0.0029	5008	,	,		20887	0.0		0.0	False		,,,				2504	0.0				p.A264S		Atlas-SNP	.											.	OR6P1	47	.	0			c.G790T						PASS	.	C	SER/ALA	76,1308		3,70,619	157.0	127.0	136.0		790	4.0	1.0	1	dbSNP_132	136	1,3181		0,1,1590	yes	missense	OR6P1	NM_001160325.1	99	3,71,2209	AA,AC,CC		0.0314,5.4913,1.6864	probably-damaging	264/318	158532605	77,4489	692	1591	2283	SO:0001583	missense	128366	exon1			ACATGGCCCGGGG	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.790G>T	1.37:g.158532605C>A	ENSP00000334721:p.Ala264Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	175	87	0.497143	NM_001160325	Q6IFR9	Missense_Mutation	SNP	ENST00000334632.1	37	CCDS53391.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	C	10.32	1.317865	0.23994	0.054913	3.14E-4	ENSG00000186440	ENST00000334632	T	0.00019	9.06	4.91	3.95	0.45737	GPCR, rhodopsin-like superfamily (1);	0.168012	0.28006	N	0.016962	T	0.00039	0.0001	N	0.03253	-0.375	0.09310	N	1	D	0.57571	0.98	P	0.54346	0.749	T	0.38134	-0.9675	10	0.02654	T	1	.	7.4127	0.27025	0.1677:0.7458:0.0:0.0864	.	264	Q8NGX9	OR6P1_HUMAN	S	264	ENSP00000334721:A264S	ENSP00000334721:A264S	A	-	1	0	OR6P1	156799229	0.000000	0.05858	0.966000	0.40874	0.008000	0.06430	-0.210000	0.09345	2.551000	0.86045	0.591000	0.81541	GCC	C|0.987;A|0.013	0.013	strong		0.512	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
HLA-G	3135	hgsc.bcm.edu	37	6	29795657	29795657	+	Silent	SNP	G	G	A	rs1630185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29795657G>A	ENST00000360323.6	+	1	60	c.36G>A	c.(34-36)ctG>ctA	p.L12L	HLA-G_ENST00000376818.3_Silent_p.L12L|HLA-G_ENST00000428701.1_Silent_p.L12L|HLA-G_ENST00000376828.2_Silent_p.L17L|HLA-G_ENST00000376815.3_Silent_p.L12L			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	12					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						TCTTCCTGCTGCTCTCGGGGG	0.706													g|||	2726	0.544329	0.5083	0.4654	5008	,	,		13560	0.6032		0.4324	False		,,,				2504	0.7035				p.L12L		Atlas-SNP	.											.	HLA-G	90	.	0			c.G36A						PASS	.	G		1538,1484		393,752,366	38.0	43.0	41.0		36	0.6	0.3	6	dbSNP_89	41	2507,2911		597,1313,799	no	coding-synonymous	HLA-G	NM_002127.5		990,2065,1165	AA,AG,GG		46.2717,49.1066,47.9265		12/339	29795657	4045,4395	1511	2709	4220	SO:0001819	synonymous_variant	3135	exon2			CCTGCTGCTCTCG		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.36G>A	6.37:g.29795657G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	184	80	0.434783	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			G|0.518;A|0.482	0.482	strong		0.706	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
CYP4F12	66002	hgsc.bcm.edu	37	19	15794425	15794425	+	Missense_Mutation	SNP	A	A	G	rs116788636|rs386807235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794425A>G	ENST00000550308.1	+	7	1150	c.770A>G	c.(769-771)cAc>cGc	p.H257R	CYP4F12_ENST00000324632.10_Missense_Mutation_p.H257R	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	257					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CGGCGCTTCCACAGGGCCTGC	0.547													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20966	0.0		0.001	False		,,,				2504	0.0				p.H257R		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A770G						PASS	.	A	ARG/HIS	173,4223		0,173,2025	79.0	81.0	80.0		770	-4.9	0.1	19	dbSNP_132	80	1,8589		0,1,4294	no	missense	CYP4F12	NM_023944.3	29	0,174,6319	GG,GA,AA		0.0116,3.9354,1.3399	benign	257/525	15794425	174,12812	2198	4295	6493	SO:0001583	missense	66002	exon7			GCTTCCACAGGGC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.770A>G	19.37:g.15794425A>G	ENSP00000448998:p.His257Arg	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	184	49	0.266304	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	20	0.009157509157509158	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	0.001	-3.865349	0.00003	0.039354	1.16E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.67865	-0.29;-0.29	2.47	-4.94	0.03057	.	1.089430	0.07278	N	0.870346	T	0.05090	0.0136	N	0.00368	-1.59	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11542	-1.0583	10	0.02654	T	1	.	5.3926	0.16251	0.2262:0.0:0.5255:0.2483	.	257	Q9HCS2	CP4FC_HUMAN	R	257	ENSP00000448998:H257R;ENSP00000321821:H257R	ENSP00000321821:H257R	H	+	2	0	CYP4F12	15655425	0.000000	0.05858	0.056000	0.19401	0.005000	0.04900	-0.089000	0.11180	-1.586000	0.01632	-4.406000	0.00006	CAC	A|0.990;G|0.010	0.010	strong		0.547	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
FHAD1	114827	hgsc.bcm.edu	37	1	15668319	15668319	+	Missense_Mutation	SNP	G	G	A	rs12126178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:15668319G>A	ENST00000375998.4	+	14	1994	c.1994G>A	c.(1993-1995)cGa>cAa	p.R665Q	FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000417793.1_Missense_Mutation_p.R665Q|FHAD1_ENST00000358897.4_Missense_Mutation_p.R665Q|RP3-467K16.2_ENST00000428747.1_RNA|FHAD1_ENST00000375999.3_Missense_Mutation_p.R665Q			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	665								p.R665Q(1)|p.E380K(1)		skin(1)|stomach(1)	2						GAAGCTGAACGAGGAGAGGCT	0.493													G|||	250	0.0499201	0.1036	0.0447	5008	,	,		19553	0.0		0.0477	False		,,,				2504	0.0348				p.R665Q		Atlas-SNP	.											FHAD1_ENST00000375999,NS,carcinoma,0,2	FHAD1	78	2	2	Substitution - Missense(2)	stomach(2)	c.G1994A						scavenged	.	G	GLN/ARG	146,1238		10,126,556	115.0	105.0	108.0		1994	-3.3	0.0	1	dbSNP_120	108	220,2962		4,212,1375	yes	missense	FHAD1	NM_052929.1	43	14,338,1931	AA,AG,GG		6.9139,10.5491,8.0158	benign	665/1413	15668319	366,4200	692	1591	2283	SO:0001583	missense	114827	exon15			CTGAACGAGGAGA	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.1994G>A	1.37:g.15668319G>A	ENSP00000365166:p.Arg665Gln	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	182	90	0.494505	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		112	0.05128205128205128	57	0.11585365853658537	19	0.052486187845303865	0	0.0	36	0.047493403693931395	G	3.210	-0.161861	0.06502	0.105491	0.069139	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998	D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94	4.49	-3.3	0.05003	.	3.151500	0.01328	N	0.011174	T	0.01695	0.0054	N	0.03608	-0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.36407	-0.9749	9	0.14252	T	0.57	8.5824	2.6167	0.04906	0.1772:0.4109:0.2724:0.1395	rs12126178;rs52808140;rs59045252;rs12126178	665	B1AJZ9	FHAD1_HUMAN	Q	665	ENSP00000351770:R665Q;ENSP00000407615:R665Q;ENSP00000365167:R665Q;ENSP00000365166:R665Q	ENSP00000351770:R665Q	R	+	2	0	FHAD1	15540906	0.000000	0.05858	0.007000	0.13788	0.100000	0.18952	-2.620000	0.00879	-0.479000	0.06813	-1.355000	0.01225	CGA	G|0.930;A|0.070	0.070	strong		0.493	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
SLC22A16	85413	hgsc.bcm.edu	37	6	110778128	110778128	+	Missense_Mutation	SNP	T	T	C	rs714368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:110778128T>C	ENST00000368919.3	-	2	212	c.146A>G	c.(145-147)cAt>cGt	p.H49R	SLC22A16_ENST00000461487.1_5'UTR|SLC22A16_ENST00000439654.1_Missense_Mutation_p.H49R|SLC22A16_ENST00000330550.4_Missense_Mutation_p.H47R|SLC22A16_ENST00000456137.2_Missense_Mutation_p.H49R	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	49			H -> R (in dbSNP:rs714368).		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)	GCAGACATGATGAGGGGTGAC	0.493													t|||	1572	0.313898	0.3888	0.2406	5008	,	,		17832	0.4097		0.2207	False		,,,				2504	0.2618				p.H49R		Atlas-SNP	.											.	SLC22A16	81	.	0			c.A146G						PASS	.	T	ARG/HIS	1600,2806	496.9+/-363.7	281,1038,884	65.0	68.0	67.0		146	-3.1	0.0	6	dbSNP_86	67	1917,6683	340.3+/-323.5	180,1557,2563	yes	missense	SLC22A16	NM_033125.2	29	461,2595,3447	CC,CT,TT		22.2907,36.3141,27.0414	benign	49/578	110778128	3517,9489	2203	4300	6503	SO:0001583	missense	85413	exon2			ACATGATGAGGGG		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.146A>G	6.37:g.110778128T>C	ENSP00000357915:p.His49Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	94	38	0.404255	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	667	0.30540293040293043	172	0.34959349593495936	93	0.2569060773480663	245	0.42832167832167833	157	0.20712401055408972	t	8.623	0.891879	0.17613	0.363141	0.222907	ENSG00000004809	ENST00000368919;ENST00000330550;ENST00000439654;ENST00000437378;ENST00000456137;ENST00000424139	D;T;D;T;D;T	0.82167	-1.58;-0.08;-1.58;-0.08;-1.58;-0.08	4.63	-3.12	0.05282	.	1.299300	0.05397	N	0.540040	T	0.41373	0.1156	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	0.03453	-1.1035	9	0.27082	T	0.32	.	10.625	0.45502	0.0:0.284:0.0:0.716	rs714368;rs52825948;rs60832844;rs714368	49;47	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	R	49;47;49;6;49;6	ENSP00000357915:H49R;ENSP00000328583:H47R;ENSP00000408799:H49R;ENSP00000416310:H6R;ENSP00000402111:H49R;ENSP00000401007:H6R	ENSP00000328583:H47R	H	-	2	0	SLC22A16	110884821	0.013000	0.17824	0.000000	0.03702	0.002000	0.02628	0.856000	0.27818	-0.837000	0.04223	-1.875000	0.00549	CAT	T|0.701;C|0.299	0.299	strong		0.493	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
FAM129C	199786	hgsc.bcm.edu	37	19	17638141	17638141	+	Missense_Mutation	SNP	G	G	A	rs73504235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17638141G>A	ENST00000335393.4	+	2	223	c.85G>A	c.(85-87)Gac>Aac	p.D29N	FAM129C_ENST00000599164.1_5'UTR|FAM129C_ENST00000300971.2_Missense_Mutation_p.D29N|FAM129C_ENST00000599124.1_5'UTR|FAM129C_ENST00000601861.1_5'UTR|FAM129C_ENST00000597887.1_3'UTR|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000595684.1_Missense_Mutation_p.D29N|FAM129C_ENST00000600871.1_5'UTR|FAM129C_ENST00000332386.5_Missense_Mutation_p.D29N|FAM129C_ENST00000352727.3_Missense_Mutation_p.D29N	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	29										autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						CCCGGGAGACGACAGCAGCAT	0.687													G|||	46	0.0091853	0.0348	0.0	5008	,	,		11779	0.0		0.0	False		,,,				2504	0.0				p.D29N		Atlas-SNP	.											.	FAM129C	110	.	0			c.G85A						PASS	.	G	ASN/ASP,ASN/ASP	96,3940		1,94,1923	26.0	21.0	23.0		85,85	-6.0	0.0	19	dbSNP_130	23	3,7943		0,3,3970	yes	missense,missense	FAM129C	NM_001098524.1,NM_173544.4	23,23	1,97,5893	AA,AG,GG		0.0378,2.3786,0.8262	benign,benign	29/652,29/698	17638141	99,11883	2018	3973	5991	SO:0001583	missense	199786	exon2			GGAGACGACAGCA	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.85G>A	19.37:g.17638141G>A	ENSP00000335040:p.Asp29Asn	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	221	221	1	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	7.241	0.601307	0.13939	0.023786	3.78E-4	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000300971	T;T;T;T	0.26518	1.92;2.05;1.73;1.75	3.01	-6.03	0.02185	.	1.713730	0.03912	N	0.282032	T	0.04318	0.0119	N	0.08118	0	0.18873	N	0.999985	B;B	0.10296	0.003;0.003	B;B	0.01281	0.0;0.0	T	0.16100	-1.0414	10	0.14656	T	0.56	.	1.1511	0.01786	0.4056:0.0975:0.15:0.3469	.	29;29	Q86XR2;Q86XR2-3	NIBL2_HUMAN;.	N	29	ENSP00000335040:D29N;ENSP00000333447:D29N;ENSP00000341067:D29N;ENSP00000300971:D29N	ENSP00000300971:D29N	D	+	1	0	FAM129C	17499141	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-4.173000	0.00280	-3.604000	0.00133	-0.339000	0.08088	GAC	G|0.990;A|0.010	0.010	strong		0.687	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
FOXC1	2296	hgsc.bcm.edu	37	6	1611085	1611085	+	Silent	SNP	C	C	T	rs2230096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:1611085C>T	ENST00000380874.2	+	1	405	c.405C>T	c.(403-405)tgC>tgT	p.C135C		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	135					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		TCAACGAGTGCTTCGTCAAGG	0.602													c|||	160	0.0319489	0.115	0.0101	5008	,	,		11123	0.0		0.001	False		,,,				2504	0.0				p.C135C	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.C405T						PASS	.	C		454,3952	215.1+/-234.2	26,402,1775	85.0	94.0	91.0		405	3.7	1.0	6	dbSNP_98	91	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	FOXC1	NM_001453.2		26,406,6071	TT,TC,CC		0.0465,10.3041,3.5215		135/554	1611085	458,12548	2203	4300	6503	SO:0001819	synonymous_variant	2296	exon1			CGAGTGCTTCGTC	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"""Forkhead boxes"""	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.405C>T	6.37:g.1611085C>T		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	295	130	0.440678	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Silent	SNP	ENST00000380874.2	37	CCDS4473.1																																																																																			C|0.970;T|0.030	0.030	strong		0.602	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1		
SLC22A14	9389	hgsc.bcm.edu	37	3	38347851	38347851	+	Missense_Mutation	SNP	A	A	G	rs2073714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38347851A>G	ENST00000273173.4	+	1	425	c.334A>G	c.(334-336)Aaa>Gaa	p.K112E	RNU6-235P_ENST00000362644.1_RNA|SLC22A14_ENST00000448498.1_Missense_Mutation_p.K112E	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	112			K -> E (in dbSNP:rs2073714).		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)		CCACCTGTCCAAAGCTGAGCA	0.522													G|||	376	0.0750799	0.0726	0.0605	5008	,	,		22352	0.1617		0.0596	False		,,,				2504	0.0153				p.K112E		Atlas-SNP	.											SLC22A14,NS,carcinoma,0,1	SLC22A14	64	1	0			c.A334G						PASS	.	G	GLU/LYS	319,4087	796.9+/-415.4	14,291,1898	112.0	103.0	106.0		334	3.3	0.0	3	dbSNP_96	106	404,8196	801.0+/-407.4	12,380,3908	yes	missense	SLC22A14	NM_004803.3	56	26,671,5806	GG,GA,AA		4.6977,7.2401,5.559	benign	112/595	38347851	723,12283	2203	4300	6503	SO:0001583	missense	9389	exon1			CTGTCCAAAGCTG	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.334A>G	3.37:g.38347851A>G	ENSP00000273173:p.Lys112Glu	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	167	100	0.598802	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	197	0.0902014652014652	42	0.08536585365853659	19	0.052486187845303865	85	0.1486013986013986	51	0.06728232189973615	G	0.005	-2.124684	0.00342	0.072401	0.046977	ENSG00000144671	ENST00000448498;ENST00000423219;ENST00000273173	T;T	0.34275	1.37;1.37	5.5	3.35	0.38373	.	1.064140	0.07446	N	0.898203	T	0.00039	0.0001	N	0.00088	-2.19	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24083	-1.0170	9	0.02654	T	1	.	9.9749	0.41777	0.2802:0.0:0.7198:0.0	rs2073714;rs56645827;rs2073714	112	Q9Y267	S22AE_HUMAN	E	112	ENSP00000396283:K112E;ENSP00000273173:K112E	ENSP00000273173:K112E	K	+	1	0	SLC22A14	38322855	0.000000	0.05858	0.002000	0.10522	0.012000	0.07955	0.093000	0.15086	0.822000	0.34565	-0.733000	0.03571	AAA	A|0.927;G|0.073	0.073	strong		0.522	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803	
PROSER1	80209	hgsc.bcm.edu	37	13	39603498	39603498	+	Silent	SNP	G	G	A	rs61737582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39603498G>A	ENST00000352251.3	-	4	1028	c.195C>T	c.(193-195)gtC>gtT	p.V65V	PROSER1_ENST00000350125.3_Silent_p.V43V	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	65																	CTGTTGGCTGGACAGCCACCA	0.318													G|||	457	0.091254	0.0855	0.1095	5008	,	,		15384	0.0903		0.0586	False		,,,				2504	0.1207				p.V65V		Atlas-SNP	.											C13orf23,NS,carcinoma,-2,1	.	.	1	0			c.C195T						PASS	.	G	,	214,3394		4,206,1594	72.0	71.0	71.0		195,129	-0.0	1.0	13	dbSNP_129	71	525,7617		16,493,3562	no	coding-synonymous,coding-synonymous	PROSER1	NM_025138.3,NM_170719.2	,	20,699,5156	AA,AG,GG		6.448,5.9313,6.2894	,	65/945,43/923	39603498	739,11011	1804	4071	5875	SO:0001819	synonymous_variant	80209	exon4			TGGCTGGACAGCC	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.195C>T	13.37:g.39603498G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	119	83	0.697479	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																			G|0.921;A|0.079	0.079	strong		0.318	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
WDR66	144406	hgsc.bcm.edu	37	12	122413196	122413196	+	Missense_Mutation	SNP	T	T	C	rs77422261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122413196T>C	ENST00000288912.4	+	18	3672	c.2818T>C	c.(2818-2820)Ttc>Ctc	p.F940L		NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	940							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)		CTTGACCCCATTCTATGGTCT	0.473													T|||	564	0.11262	0.121	0.0159	5008	,	,		19501	0.2321		0.0239	False		,,,				2504	0.138				p.F940L	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.T2818C						PASS	.	T	LEU/PHE	461,3795		25,411,1692	97.0	103.0	101.0		2818	5.5	1.0	12	dbSNP_131	101	205,8269		3,199,4035	yes	missense	WDR66	NM_144668.5	22	28,610,5727	CC,CT,TT		2.4192,10.8318,5.2317	probably-damaging	940/1150	122413196	666,12064	2128	4237	6365	SO:0001583	missense	144406	exon18			ACCCCATTCTATG	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.2818T>C	12.37:g.122413196T>C	ENSP00000288912:p.Phe940Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	167	99	0.592814	NM_144668	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	210	0.09615384615384616	63	0.12804878048780488	5	0.013812154696132596	123	0.21503496503496503	19	0.025065963060686015	T	28.0	4.880242	0.91740	0.108318	0.024192	ENSG00000158023	ENST00000288912	T	0.08546	3.08	5.47	5.47	0.80525	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.63169	1.94	0.09310	P	1.0	P	0.45283	0.855	P	0.48304	0.573	T	0.18304	-1.0341	9	0.87932	D	0	.	15.5686	0.76313	0.0:0.0:0.0:1.0	.	940	Q8TBY9	WDR66_HUMAN	L	940	ENSP00000288912:F940L	ENSP00000288912:F940L	F	+	1	0	WDR66	120897579	1.000000	0.71417	0.957000	0.39632	0.984000	0.73092	6.242000	0.72376	2.083000	0.62718	0.460000	0.39030	TTC	T|0.928;C|0.072	0.072	strong		0.473	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
FBXO34	55030	hgsc.bcm.edu	37	14	55818517	55818517	+	Missense_Mutation	SNP	T	T	A	rs1045002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55818517T>A	ENST00000313833.4	+	2	1654	c.1409T>A	c.(1408-1410)aTt>aAt	p.I470N	FBXO34_ENST00000440021.1_Missense_Mutation_p.I470N	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	470			I -> N (in dbSNP:rs1045002). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.					p.I470N(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						CAGCCTTCCATTTTAAACTCC	0.423													A|||	1661	0.331669	0.2322	0.3098	5008	,	,		20331	0.3185		0.4245	False		,,,				2504	0.3998				p.I470N		Atlas-SNP	.											FBXO34,NS,carcinoma,0,1	FBXO34	61	1	1	Substitution - Missense(1)	stomach(1)	c.T1409A						PASS	.	A	ASN/ILE,ASN/ILE	1147,3259	713.6+/-408.3	154,839,1210	115.0	112.0	113.0		1409,1409	-0.8	0.0	14	dbSNP_86	113	3621,4979	624.3+/-397.6	780,2061,1459	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	149,149	934,2900,2669	AA,AT,TT		42.1047,26.0327,36.66	benign,benign	470/712,470/712	55818517	4768,8238	2203	4300	6503	SO:0001583	missense	55030	exon2			CTTCCATTTTAAA	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1409T>A	14.37:g.55818517T>A	ENSP00000313159:p.Ile470Asn	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	223	126	0.565022	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	748	0.3424908424908425	118	0.23983739837398374	116	0.32044198895027626	191	0.3339160839160839	323	0.4261213720316623	A	0.013	-1.642727	0.00792	0.260327	0.421047	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.16457	2.34;2.34	5.48	-0.84	0.10755	.	1.461070	0.04686	N	0.413270	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.12837	0.008	T	0.48139	-0.9061	9	0.15499	T	0.54	-0.416	4.9015	0.13777	0.1197:0.4841:0.1548:0.2414	rs1045002;rs3168901;rs3742568;rs17674186;rs60147901;rs1045002	470	Q9NWN3	FBX34_HUMAN	N	470	ENSP00000313159:I470N;ENSP00000394117:I470N	ENSP00000313159:I470N	I	+	2	0	FBXO34	54888270	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.270000	0.08584	-0.639000	0.05502	-1.546000	0.00904	ATT	A|0.366;N|0.000	0.366	strong		0.423	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
LCE2B	26239	hgsc.bcm.edu	37	1	152659471	152659471	+	Missense_Mutation	SNP	T	T	G	rs3737859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152659471T>G	ENST00000368780.3	+	2	206	c.152T>G	c.(151-153)aTc>aGc	p.I51S	LCE2B_ENST00000417924.2_Missense_Mutation_p.I51S	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	51	Cys-rich.		I -> S (in dbSNP:rs3737859).		epidermis development (GO:0008544)|keratinization (GO:0031424)			p.I51S(1)		endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	11	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTGGTCCCATCTCTGGGGGC	0.637													G|||	1033	0.20627	0.3071	0.1556	5008	,	,		14305	0.2946		0.0875	False		,,,				2504	0.137				p.I51S		Atlas-SNP	.											LCE2B,NS,carcinoma,0,1	LCE2B	40	1	1	Substitution - Missense(1)	stomach(1)	c.T152G						PASS	.	G	SER/ILE	1263,3143	701.8+/-406.8	184,895,1124	126.0	139.0	135.0		152	2.4	1.0	1	dbSNP_107	135	700,7900	787.6+/-407.6	35,630,3635	no	missense	LCE2B	NM_014357.4	142	219,1525,4759	GG,GT,TT		8.1395,28.6655,15.093	benign	51/111	152659471	1963,11043	2203	4300	6503	SO:0001583	missense	26239	exon2			GTCCCATCTCTGG	BI670514	CCDS1020.1	1q21	2008-02-05	2004-10-11	2004-10-15	ENSG00000159455	ENSG00000159455		"""Late cornified envelopes"""	16610	protein-coding gene	gene with protein product		612610	"""small proline rich-like (epidermal differentiation complex) 1B"""	SPRL1B		11698679, 9344646	Standard	NM_014357		Approved	LEP10, XP5	uc001fai.3	O14633	OTTHUMG00000012404	ENST00000368780.3:c.152T>G	1.37:g.152659471T>G	ENSP00000357769:p.Ile51Ser	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	269	141	0.524164	NM_014357	Q5TA80	Missense_Mutation	SNP	ENST00000368780.3	37	CCDS1020.1	424	0.19413919413919414	142	0.2886178861788618	42	0.11602209944751381	170	0.2972027972027972	70	0.09234828496042216	G	1.573	-0.533501	0.04082	0.286655	0.081395	ENSG00000159455	ENST00000417924;ENST00000368780	T;T	0.03152	4.03;4.03	2.37	2.37	0.29283	.	.	.	.	.	T	0.00241	0.0007	N	0.00170	-1.935	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.34004	-0.9846	8	0.07325	T	0.83	.	6.1109	0.20100	0.0:0.0:0.6964:0.3036	rs3737859;rs52809414;rs3737859	51	O14633	LCE2B_HUMAN	S	51	ENSP00000414043:I51S;ENSP00000357769:I51S	ENSP00000357769:I51S	I	+	2	0	LCE2B	150926095	0.359000	0.24955	0.981000	0.43875	0.019000	0.09904	0.875000	0.28079	0.211000	0.20683	-0.648000	0.03929	ATC	T|0.841;G|0.159	0.159	strong		0.637	LCE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034524.1	NM_014357	
TMCC1	23023	hgsc.bcm.edu	37	3	129546664	129546664	+	Silent	SNP	C	C	T	rs72987361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129546664C>T	ENST00000393238.3	-	3	898	c.558G>A	c.(556-558)gaG>gaA	p.E186E	TMCC1_ENST00000426664.2_Silent_p.E72E	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	186						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						CAGTTCCCTCCTCTCCTGGTA	0.463													C|||	409	0.0816693	0.1793	0.0648	5008	,	,		17916	0.003		0.0775	False		,,,				2504	0.047				p.E186E		Atlas-SNP	.											.	TMCC1	105	.	0			c.G558A						PASS	.	C	,	687,3719	286.6+/-278.8	50,587,1566	42.0	44.0	44.0		558,216	-1.8	1.0	3	dbSNP_130	44	677,7923	168.8+/-220.3	21,635,3644	no	coding-synonymous,coding-synonymous	TMCC1	NM_001017395.3,NM_001128224.2	,	71,1222,5210	TT,TC,CC		7.8721,15.5924,10.4875	,	186/654,72/540	129546664	1364,11642	2203	4300	6503	SO:0001819	synonymous_variant	23023	exon3			TCCCTCCTCTCCT	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"""Transmembrane and coiled-coil domain containing"""	29116	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 1"""			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.558G>A	3.37:g.129546664C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Silent	SNP	ENST00000393238.3	37	CCDS33855.1																																																																																			C|0.897;T|0.103	0.103	strong		0.463	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008	
DAB2	1601	hgsc.bcm.edu	37	5	39377132	39377132	+	Missense_Mutation	SNP	G	G	A	rs700241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:39377132G>A	ENST00000320816.6	-	12	2224	c.1757C>T	c.(1756-1758)aCa>aTa	p.T586I	DAB2_ENST00000545653.1_Missense_Mutation_p.T565I|DAB2_ENST00000509337.1_Missense_Mutation_p.T565I|DAB2_ENST00000339788.6_Missense_Mutation_p.T368I	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	586			T -> I (in dbSNP:rs700241).		activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			AGGGCTTGTTGTTGACCAAGC	0.552											OREG0016586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	264	0.0527157	0.1286	0.0259	5008	,	,		18845	0.0427		0.0129	False		,,,				2504	0.0204				p.T586I		Atlas-SNP	.											.	DAB2	124	.	0			c.C1757T						PASS	.	G	ILE/THR	534,3872	243.1+/-252.9	30,474,1699	80.0	92.0	88.0		1757	4.7	0.2	5	dbSNP_86	88	108,8492	58.3+/-119.8	0,108,4192	yes	missense	DAB2	NM_001343.3	89	30,582,5891	AA,AG,GG		1.2558,12.1198,4.9362	benign	586/771	39377132	642,12364	2203	4300	6503	SO:0001583	missense	1601	exon12			CTTGTTGTTGACC	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1757C>T	5.37:g.39377132G>A	ENSP00000313391:p.Thr586Ile	Somatic	162	0	0	885	WXS	Illumina HiSeq	Phase_I	154	65	0.422078	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	CCDS34149.1	96	0.04395604395604396	63	0.12804878048780488	8	0.022099447513812154	18	0.03146853146853147	7	0.009234828496042216	G	8.484	0.860372	0.17178	0.121198	0.012558	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.37058	1.25;1.24;1.22;1.22	5.57	4.69	0.59074	.	0.803378	0.11503	N	0.557461	T	0.00210	0.0006	N	0.08118	0	0.80722	P	0.0	B;B	0.20164	0.042;0.041	B;B	0.20384	0.013;0.029	T	0.04140	-1.0974	9	0.34782	T	0.22	-2.617	8.2215	0.31543	0.0801:0.0:0.6714:0.2485	rs700241;rs1661851;rs3733800;rs52816384;rs61460036;rs700241	586;565	P98082;P98082-3	DAB2_HUMAN;.	I	586;368;565;565	ENSP00000313391:T586I;ENSP00000345508:T368I;ENSP00000439919:T565I;ENSP00000426245:T565I	ENSP00000313391:T586I	T	-	2	0	DAB2	39412889	0.729000	0.28090	0.180000	0.23079	0.366000	0.29705	2.656000	0.46716	2.617000	0.88574	0.655000	0.94253	ACA	G|0.945;A|0.055	0.055	strong		0.552	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343	
MEP1B	4225	hgsc.bcm.edu	37	18	29788107	29788107	+	Silent	SNP	G	G	A	rs4799640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:29788107G>A	ENST00000269202.6	+	9	839	c.792G>A	c.(790-792)tcG>tcA	p.S264S	MEP1B_ENST00000581447.1_Silent_p.S264S	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	264	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TTATGGACTCGTGCAGTTTTG	0.408													G|||	1154	0.230431	0.2814	0.1902	5008	,	,		19138	0.126		0.2207	False		,,,				2504	0.3078				p.S264S		Atlas-SNP	.											.	MEP1B	54	.	0			c.G792A						PASS	.	G		1006,2760		141,724,1018	220.0	213.0	215.0		792	-10.8	0.3	18	dbSNP_111	215	2010,6240		255,1500,2370	no	coding-synonymous	MEP1B	NM_005925.2		396,2224,3388	AA,AG,GG		24.3636,26.7127,25.0999		264/702	29788107	3016,9000	1883	4125	6008	SO:0001819	synonymous_variant	4225	exon9			GGACTCGTGCAGT	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.792G>A	18.37:g.29788107G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	174	77	0.442529	NM_005925	B7ZM35|B9EGL6|Q670J1	Silent	SNP	ENST00000269202.6	37	CCDS45846.1																																																																																			G|0.778;A|0.222	0.222	strong		0.408	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
COQ3	51805	hgsc.bcm.edu	37	6	99825348	99825348	+	Missense_Mutation	SNP	T	T	C	rs11548336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:99825348T>C	ENST00000254759.3	-	4	424	c.400A>G	c.(400-402)Aaa>Gaa	p.K134E	COQ3_ENST00000479163.1_5'UTR|COQ3_ENST00000369240.1_5'Flank|COQ3_ENST00000369242.1_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	45	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	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	
COL10A1	1300	hgsc.bcm.edu	37	6	116441646	116441646	+	Missense_Mutation	SNP	C	C	G	rs2228547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116441646C>G	ENST00000327673.4	-	2	2040	c.1633G>C	c.(1633-1635)Ggg>Cgg	p.G545R	NT5DC1_ENST00000319550.4_Intron|AL121963.1_ENST00000430695.1_5'Flank|COL10A1_ENST00000243222.4_Missense_Mutation_p.G545R			Q03692	COAA1_HUMAN	collagen, type X, alpha 1	545	Nonhelical region (NC1).		G -> R (in dbSNP:rs2228547). {ECO:0000269|PubMed:15880705, ECO:0000269|PubMed:7607655}.		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)		CCTGTTACCCCCTGGTTGGCA	0.483													C|||	1070	0.213658	0.2806	0.1138	5008	,	,		19584	0.249		0.1243	False		,,,				2504	0.2495				p.G545R		Atlas-SNP	.											.	COL10A1	51	.	0			c.G1633C						PASS	.	C	ARG/GLY,	1113,3293	382.3+/-324.4	153,807,1243	59.0	66.0	64.0		1633,	4.8	1.0	6	dbSNP_98	64	980,7620	209.6+/-250.7	53,874,3373	yes	missense,intron	COL10A1,NT5DC1	NM_000493.3,NM_152729.2	125,	206,1681,4616	GG,GC,CC		11.3953,25.261,16.0926	probably-damaging,	545/681,	116441646	2093,10913	2203	4300	6503	SO:0001583	missense	1300	exon3			TTACCCCCTGGTT		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.1633G>C	6.37:g.116441646C>G	ENSP00000327368:p.Gly545Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_000493	A1L4P2	Missense_Mutation	SNP	ENST00000327673.4	37	CCDS5105.1	398	0.18223443223443223	128	0.2601626016260163	37	0.10220994475138122	137	0.2395104895104895	96	0.1266490765171504	C	12.35	1.911885	0.33721	0.25261	0.113953	ENSG00000123500	ENST00000243222;ENST00000327673	D;D	0.90197	-2.63;-2.63	4.8	4.8	0.61643	Complement C1q protein (1);	0.345327	0.30365	N	0.009787	D	0.90765	0.7101	M	0.73962	2.25	0.30961	P	0.7236929999999999	D	0.54397	0.966	P	0.49665	0.618	D	0.91736	0.5400	9	0.54805	T	0.06	.	16.4072	0.83684	0.0:1.0:0.0:0.0	rs2228547;rs52792905;rs57710620;rs2228547	545	Q03692	COAA1_HUMAN	R	545	ENSP00000243222:G545R;ENSP00000327368:G545R	ENSP00000243222:G545R	G	-	1	0	COL10A1	116548339	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	4.152000	0.58111	2.362000	0.80069	0.561000	0.74099	GGG	C|0.838;G|0.162	0.162	strong		0.483	COL10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041926.1		
ZNF107	51427	hgsc.bcm.edu	37	7	64168641	64168641	+	Silent	SNP	A	A	G	rs73363327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:64168641A>G	ENST00000395391.1	+	4	3334	c.1959A>G	c.(1957-1959)agA>agG	p.R653R	ZNF107_ENST00000423627.1_Silent_p.R653R|ZNF107_ENST00000344930.3_Silent_p.R653R			Q9UII5	ZN107_HUMAN	zinc finger protein 107	653					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				CCCTTAATAGACATAAGATAA	0.363													a|||	131	0.0261581	0.0983	0.0014	5008	,	,		18481	0.0		0.0	False		,,,				2504	0.0				p.R653R		Atlas-SNP	.											.	ZNF107	107	.	0			c.A1959G						PASS	.	A	,	297,4075		9,279,1898	30.0	34.0	33.0		1959,1959	-0.3	0.1	7	dbSNP_131	33	3,8583		0,3,4290	no	coding-synonymous,coding-synonymous	ZNF107	NM_001013746.1,NM_016220.3	,	9,282,6188	GG,GA,AA		0.0349,6.7932,2.3152	,	653/784,653/784	64168641	300,12658	2186	4293	6479	SO:0001819	synonymous_variant	51427	exon7			TAATAGACATAAG	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"""Zinc fingers, C2H2-type"""	12887	protein-coding gene	gene with protein product		603989	"""zinc finger protein 588"", ""zinc finger protein 107 (Y8)"""	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.1959A>G	7.37:g.64168641A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	25	9	0.36	NM_016220		Silent	SNP	ENST00000395391.1	37	CCDS5527.1																																																																																			A|0.985;G|0.015	0.015	strong		0.363	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220	
KSR2	283455	hgsc.bcm.edu	37	12	117993064	117993064	+	Silent	SNP	C	C	T	rs7955803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117993064C>T	ENST00000339824.5	-	9	2155	c.1428G>A	c.(1426-1428)ccG>ccA	p.P476P	KSR2_ENST00000425217.1_Silent_p.P447P|KSR2_ENST00000545002.1_5'UTR|KSR2_ENST00000302438.5_Silent_p.P173P			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	476					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGATGTCACACGGAACGGACT	0.488													C|||	1264	0.252396	0.2799	0.2003	5008	,	,		20620	0.1587		0.2684	False		,,,				2504	0.3323				p.P447P		Atlas-SNP	.											.	KSR2	208	.	0			c.G1341A						PASS	.	C		1045,2909		143,759,1075	130.0	135.0	134.0		1341	-10.2	0.3	12	dbSNP_116	134	2125,6185		286,1553,2316	no	coding-synonymous	KSR2	NM_173598.4		429,2312,3391	TT,TC,CC		25.5716,26.4289,25.848		447/922	117993064	3170,9094	1977	4155	6132	SO:0001819	synonymous_variant	283455	exon9			GTCACACGGAACG	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.1428G>A	12.37:g.117993064C>T		Somatic	294	1	0.00340136		WXS	Illumina HiSeq	Phase_I	327	159	0.486239	NM_173598	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	37																																																																																				C|0.758;T|0.242	0.242	strong		0.488	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598	
TRIM16L	147166	hgsc.bcm.edu	37	17	18634541	18634541	+	Silent	SNP	C	C	T	rs8073459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18634541C>T	ENST00000449552.2	+	5	1844	c.360C>T	c.(358-360)tcC>tcT	p.S120S	TRIM16L_ENST00000395671.4_Silent_p.S120S|TRIM16L_ENST00000572555.1_Silent_p.S120S|TRIM16L_ENST00000395672.2_Silent_p.S120S|TRIM16L_ENST00000414850.2_Intron|TRIM16L_ENST00000571708.1_Silent_p.S120S|TRIM16L_ENST00000395902.3_Silent_p.S174S			Q309B1	TR16L_HUMAN	tripartite motif containing 16-like	120						cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)	9						AGGAGTTTTCCAAGGAAGGTG	0.458													.|||	360	0.071885	0.0961	0.049	5008	,	,		16707	0.003		0.0815	False		,,,				2504	0.1166				p.S120S		Atlas-SNP	.											.	TRIM16L	15	.	0			c.C360T						PASS	.	C		422,3982	206.2+/-227.9	19,384,1799	110.0	104.0	106.0		360	3.3	0.9	17	dbSNP_116	106	708,7892	174.5+/-224.7	28,652,3620	no	coding-synonymous	TRIM16L	NM_001037330.1		47,1036,5419	TT,TC,CC		8.2326,9.5822,8.6896		120/349	18634541	1130,11874	2202	4300	6502	SO:0001819	synonymous_variant	147166	exon3			GTTTTCCAAGGAA	DQ232882	CCDS32588.1	17p11.2	2011-02-10	2011-01-25		ENSG00000108448	ENSG00000108448			32670	protein-coding gene	gene with protein product			"""tripartite motif-containing 16-like"""				Standard	XM_005256479		Approved	TRIM70	uc002gui.1	Q309B1	OTTHUMG00000059050	ENST00000449552.2:c.360C>T	17.37:g.18634541C>T		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	235	110	0.468085	NM_001037330	A0PK10|B2RUW6|B4DQK2|B4DWQ8	Silent	SNP	ENST00000449552.2	37	CCDS32588.1																																																																																			C|0.920;T|0.080	0.080	strong		0.458	TRIM16L-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130670.3	NM_001037330	
SLC47A2	146802	hgsc.bcm.edu	37	17	19608773	19608773	+	Silent	SNP	G	G	A	rs4925042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19608773G>A	ENST00000325411.5	-	10	1043	c.993C>T	c.(991-993)taC>taT	p.Y331Y	SLC47A2_ENST00000350657.5_Silent_p.Y295Y|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	331					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	TGGCCACCTCGTAGATGACAG	0.652													G|||	2136	0.426518	0.3949	0.4409	5008	,	,		12732	0.6081		0.2972	False		,,,				2504	0.4049				p.Y331Y		Atlas-SNP	.											.	SLC47A2	61	.	0			c.C993T						PASS	.	G	,	1849,2557	518.1+/-369.6	408,1033,762	57.0	48.0	51.0		885,993	-6.1	0.5	17	dbSNP_111	51	2637,5963	410.3+/-350.1	411,1815,2074	yes	coding-synonymous,coding-synonymous	SLC47A2	NM_001099646.1,NM_152908.3	,	819,2848,2836	AA,AG,GG		30.6628,41.9655,34.4918	,	295/567,331/603	19608773	4486,8520	2203	4300	6503	SO:0001819	synonymous_variant	146802	exon10			CACCTCGTAGATG	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.993C>T	17.37:g.19608773G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Silent	SNP	ENST00000325411.5	37	CCDS11211.1																																																																																			G|0.622;A|0.378	0.378	strong		0.652	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
HELZ2	85441	hgsc.bcm.edu	37	20	62200929	62200929	+	Silent	SNP	G	G	A	rs6089925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62200929G>A	ENST00000467148.1	-	4	729	c.660C>T	c.(658-660)taC>taT	p.Y220Y	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	220					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)										CACCCCGTGCGTAGAGCCGGC	0.677													G|||	931	0.185903	0.4304	0.1383	5008	,	,		15912	0.0317		0.0676	False		,,,				2504	0.1697				p.Y220Y		Atlas-SNP	.											.	.	.	.	0			c.C660T						PASS	.	G		1525,2809		274,977,916	12.0	13.0	13.0		660	-4.7	0.0	20	dbSNP_114	13	621,7927		23,575,3676	no	coding-synonymous	PRIC285	NM_001037335.2		297,1552,4592	AA,AG,GG		7.2649,35.1869,16.6589		220/2650	62200929	2146,10736	2167	4274	6441	SO:0001819	synonymous_variant	85441	exon5			CCGTGCGTAGAGC	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.660C>T	20.37:g.62200929G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	73	43	0.589041	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			G|0.847;A|0.153	0.153	strong		0.677	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
PSG11	5680	hgsc.bcm.edu	37	19	43519442	43519442	+	Missense_Mutation	SNP	T	T	C	rs10414166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43519442T>C	ENST00000401740.1	-	4	893	c.790A>G	c.(790-792)Aac>Gac	p.N264D	PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000403486.1_Missense_Mutation_p.N142D|PSG11_ENST00000320078.7_Missense_Mutation_p.N264D|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	127	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	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	
DNAH10	196385	hgsc.bcm.edu	37	12	124274474	124274474	+	Splice_Site	SNP	A	A	G	rs10846559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	100	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	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
PPFIBP2	8495	hgsc.bcm.edu	37	11	7673029	7673029	+	Missense_Mutation	SNP	T	T	C	rs77873429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7673029T>C	ENST00000299492.4	+	23	2778	c.2390T>C	c.(2389-2391)aTg>aCg	p.M797T	PPFIBP2_ENST00000533792.1_Missense_Mutation_p.M639T|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.M685T|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.M654T	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	797					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CGAGAGAAAATGGCCTCACCA	0.597													T|||	471	0.0940495	0.2708	0.0476	5008	,	,		19476	0.0149		0.004	False		,,,				2504	0.0624				p.M797T		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.T2390C						PASS	.	T	THR/MET	1144,3258	408.0+/-334.4	146,852,1203	134.0	129.0	130.0		2390	5.8	1.0	11	dbSNP_131	130	40,8552	27.4+/-76.7	0,40,4256	yes	missense	PPFIBP2	NM_003621.2	81	146,892,5459	CC,CT,TT		0.4655,25.9882,9.1119	benign	797/877	7673029	1184,11810	2201	4296	6497	SO:0001583	missense	8495	exon23			AGAAAATGGCCTC	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.2390T>C	11.37:g.7673029T>C	ENSP00000299492:p.Met797Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	59	17	0.288136	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	160	0.07326007326007326	129	0.2621951219512195	15	0.04143646408839779	13	0.022727272727272728	3	0.00395778364116095	T	7.418	0.636121	0.14386	0.259882	0.004655	ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	T;T;T;T	0.29655	1.98;1.57;1.98;1.56	5.77	5.77	0.91146	.	0.127954	0.53938	D	0.000047	T	0.00012	0.0000	L	0.38531	1.155	0.25772	P	0.984823	B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0;0.0	B;B;B;B;B;B	0.06405	0.001;0.001;0.002;0.001;0.002;0.001	T	0.31861	-0.9928	9	0.18276	T	0.48	-17.2519	14.3292	0.66541	0.0:0.0:0.0:1.0	.	685;685;720;639;654;797	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	T	797;138;639;720;685;654	ENSP00000299492:M797T;ENSP00000436498:M639T;ENSP00000435469:M685T;ENSP00000437321:M654T	ENSP00000299492:M797T	M	+	2	0	PPFIBP2	7629605	1.000000	0.71417	0.994000	0.49952	0.142000	0.21351	2.644000	0.46613	2.326000	0.78906	0.533000	0.62120	ATG	T|0.914;C|0.086	0.086	strong		0.597	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
VWA5A	4013	hgsc.bcm.edu	37	11	123989383	123989383	+	Missense_Mutation	SNP	G	G	A	rs35215239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123989383G>A	ENST00000456829.2	+	6	864	c.613G>A	c.(613-615)Gag>Aag	p.E205K	VWA5A_ENST00000360334.4_Missense_Mutation_p.E205K|VWA5A_ENST00000392748.1_Missense_Mutation_p.E205K|VWA5A_ENST00000361352.5_Missense_Mutation_p.E205K|VWA5A_ENST00000392744.4_Missense_Mutation_p.E221K|VWA5A_ENST00000449321.1_Missense_Mutation_p.E205K	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	205			E -> K (in dbSNP:rs35215239).					p.E205*(1)		autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						GAGTCCTACCGAGTACCTAGG	0.517													G|||	109	0.0217652	0.0809	0.0029	5008	,	,		20475	0.0		0.0	False		,,,				2504	0.0				p.E205K		Atlas-SNP	.											VWA5A,larynx,carcinoma,0,1	VWA5A	102	1	1	Substitution - Nonsense(1)	upper_aerodigestive_tract(1)	c.G613A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	253,4149	145.7+/-180.5	8,237,1956	90.0	82.0	85.0		613,613,613	-2.8	0.0	11	dbSNP_126	85	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense,missense	VWA5A	NM_001130142.1,NM_014622.4,NM_198315.2	56,56,56	8,240,6252	AA,AG,GG		0.0349,5.7474,1.9692	benign,benign,benign	205/787,205/787,205/416	123989383	256,12744	2201	4299	6500	SO:0001583	missense	4013	exon5			CCTACCGAGTACC	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.613G>A	11.37:g.123989383G>A	ENSP00000407726:p.Glu205Lys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	78	28	0.358974	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	CCDS8444.1	40	0.018315018315018316	39	0.07926829268292683	1	0.0027624309392265192	0	0.0	0	0.0	G	7.535	0.659528	0.14645	0.057474	3.49E-4	ENSG00000110002	ENST00000456829;ENST00000360334;ENST00000392748;ENST00000524524;ENST00000530025;ENST00000361352;ENST00000449321;ENST00000392744	T;T;T;T;T;T	0.22743	3.78;1.94;3.78;2.28;2.28;2.27	5.6	-2.84	0.05751	.	0.832622	0.11287	N	0.579757	T	0.00608	0.0020	L	0.52364	1.645	0.09310	N	1	B;B	0.31859	0.091;0.343	B;B	0.24269	0.023;0.052	T	0.30736	-0.9968	10	0.08599	T	0.76	-11.1706	6.7445	0.23454	0.2766:0.318:0.4054:0.0	rs35215239	221;205	B4DHS6;O00534	.;VMA5A_HUMAN	K	205;205;205;205;205;205;205;221	ENSP00000407726:E205K;ENSP00000353485:E205K;ENSP00000376504:E205K;ENSP00000355070:E205K;ENSP00000404683:E205K;ENSP00000376501:E221K	ENSP00000353485:E205K	E	+	1	0	VWA5A	123494593	0.001000	0.12720	0.003000	0.11579	0.055000	0.15305	-0.395000	0.07287	-0.184000	0.10567	-0.315000	0.08773	GAG	G|0.978;A|0.022	0.022	strong		0.517	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011526	46011526	+	Silent	SNP	T	T	A	rs371768583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011526T>A	ENST00000400368.1	-	1	860	c.840A>T	c.(838-840)acA>acT	p.T280T	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	280	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.T280T(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						GGCAGCATGATGTGGAAGCCC	0.652													.|||	5	0.000998403	0.0008	0.0	5008	,	,		22429	0.001		0.0	False		,,,				2504	0.0031				p.T280T		Atlas-SNP	.											KRTAP10-6,NS,carcinoma,0,2	KRTAP10-6	57	2	1	Substitution - coding silent(1)	kidney(1)	c.A840T						scavenged	.						106.0	110.0	109.0					21																	46011526		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			GCATGATGTGGAA	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.840A>T	21.37:g.46011526T>A		Somatic	245	2	0.00816326		WXS	Illumina HiSeq	Phase_I	300	34	0.113333	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	weak		0.652	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
GLCE	26035	hgsc.bcm.edu	37	15	69561181	69561181	+	Silent	SNP	T	T	C	rs56045514	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:69561181T>C	ENST00000261858.2	+	5	1680	c.1452T>C	c.(1450-1452)caT>caC	p.H484H	GLCE_ENST00000559420.2_Silent_p.H420H	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	484					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						CTGAGCAGCATGGAGTTAAAG	0.353													T|||	323	0.0644968	0.2383	0.0086	5008	,	,		21803	0.0		0.002	False		,,,				2504	0.0				p.H484H		Atlas-SNP	.											.	GLCE	48	.	0			c.T1452C						PASS	.	T		685,3715	279.6+/-274.9	68,549,1583	58.0	65.0	62.0		1452	-6.6	0.8	15	dbSNP_129	62	5,8591	3.7+/-12.6	0,5,4293	no	coding-synonymous	GLCE	NM_015554.1		68,554,5876	CC,CT,TT		0.0582,15.5682,5.3093		484/618	69561181	690,12306	2200	4298	6498	SO:0001819	synonymous_variant	26035	exon5			GCAGCATGGAGTT	AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"""heparan sulfate epimerase"""	612134	"""D-glucuronyl C5-epimerase"", ""UDP-glucuronic acid epimerase"""			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.1452T>C	15.37:g.69561181T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_015554	Q6GUQ2	Silent	SNP	ENST00000261858.2	37	CCDS32277.1																																																																																			T|0.951;C|0.049	0.049	strong		0.353	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626767	140626767	+	Silent	SNP	C	C	T	rs3096081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	227	0	0		WXS	Illumina HiSeq	Phase_I	239	237	0.991632	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	
PABPC1	26986	hgsc.bcm.edu	37	8	101718932	101718932	+	Missense_Mutation	SNP	C	C	G	rs62513920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101718932C>G	ENST00000318607.5	-	11	2677	c.1549G>C	c.(1549-1551)Gtt>Ctt	p.V517L	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519004.1_Missense_Mutation_p.V472L|PABPC1_ENST00000522387.1_Missense_Mutation_p.V485L|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	517					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			GGATTGCGAACTCCTGCAGCA	0.448																																					p.V517L		Atlas-SNP	.											.	PABPC1	76	.	0			c.G1549C						PASS	.						85.0	81.0	82.0					8																	101718932		2203	4300	6503	SO:0001583	missense	26986	exon11			TGCGAACTCCTGC	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.1549G>C	8.37:g.101718932C>G	ENSP00000313007:p.Val517Leu	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	258	72	0.27907	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	32|32|32	5.122361|5.122361|5.122361	0.94429|0.94429|0.94429	.|.|.	.|.|.	ENSG00000070756|ENSG00000070756|ENSG00000070756	ENST00000520868;ENST00000517403|ENST00000519596|ENST00000318607;ENST00000519004;ENST00000522387;ENST00000517990;ENST00000522658	.|.|T;T;T;T;T	.|.|0.41065	.|.|1.01;1.01;1.01;1.01;1.01	5.3|5.3|5.3	5.3|5.3|5.3	0.74995|0.74995|0.74995	.|.|Polyadenylate-binding protein/Hyperplastic disc protein (1);	.|.|0.099482	.|.|0.42294	.|.|D	.|.|0.000734	T|T|T	0.44159|0.44159|0.44159	0.1280|0.1280|0.1280	M|M|M	0.62088|0.62088|0.62088	1.915|1.915|1.915	0.58432|0.58432|0.58432	D|D|D	0.999999|0.999999|0.999999	.|.|B;B;B	.|.|0.02656	.|.|0.0;0.0;0.0	.|.|B;B;B	.|.|0.08055	.|.|0.003;0.003;0.001	T|T|T	0.29058|0.29058|0.29058	-1.0024|-1.0024|-1.0024	5|5|10	.|.|0.27082	.|.|T	.|.|0.32	.|.|.	19.3206|19.3206|19.3206	0.94237|0.94237|0.94237	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs62513920|rs62513920|rs62513920	.|.|485;517;517	.|.|E7ERJ7;B3KT93;P11940	.|.|.;.;PABP1_HUMAN	D|T|L	49;169|254|517;472;485;26;64	.|.|ENSP00000313007:V517L;ENSP00000429594:V472L;ENSP00000429395:V485L;ENSP00000428030:V26L;ENSP00000428840:V64L	.|.|ENSP00000313007:V517L	E|S|V	-|-|-	3|2|1	2|0|0	PABPC1|PABPC1|PABPC1	101788108|101788108|101788108	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.994000|0.994000|0.994000	0.49952|0.49952|0.49952	0.990000|0.990000|0.990000	0.78478|0.78478|0.78478	7.233000|7.233000|7.233000	0.78125|0.78125|0.78125	2.658000|2.658000|2.658000	0.90341|0.90341|0.90341	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GAG|AGT|GTT	C|0.811;G|0.188	0.188	strong		0.448	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1628992	1628992	+	Silent	SNP	G	G	A	rs60210378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1628992G>A	ENST00000399685.1	-	1	701	c.624C>T	c.(622-624)ggC>ggT	p.G208G		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	208	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		atgacccacagcctgaggagc	0.617													g|||	2309	0.461062	0.4939	0.4467	5008	,	,		17035	0.3879		0.5239	False		,,,				2504	0.4376				p.G208G		Atlas-SNP	.											KRTAP5-3,NS,carcinoma,0,1	KRTAP5-3	33	1	0			c.C624T						PASS	.						111.0	121.0	118.0					11																	1628992		2201	4295	6496	SO:0001819	synonymous_variant	387266	exon1			CCCACAGCCTGAG	AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"""Keratin associated proteins"""	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.624C>T	11.37:g.1628992G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	191	186	0.973822	NM_001012708	Q6PL44|Q701N3	Silent	SNP	ENST00000399685.1	37	CCDS41591.1																																																																																			G|0.561;A|0.439	0.439	strong		0.617	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1		
SUFU	51684	hgsc.bcm.edu	37	10	104386934	104386934	+	Silent	SNP	T	T	C	rs17114803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:104386934T>C	ENST00000369902.3	+	11	1465	c.1299T>C	c.(1297-1299)atT>atC	p.I433I		NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	433					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|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)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		CTTCACAGATTCTGTTGACCG	0.398			"""D, F, S"""		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation				T|||	1232	0.246006	0.2277	0.2378	5008	,	,		20545	0.4335		0.0934	False		,,,				2504	0.2403				p.I433I		Atlas-SNP	.	yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	.	SUFU	44	.	0			c.T1299C						PASS	.	T		954,3452	362.1+/-316.0	97,760,1346	169.0	169.0	169.0		1299	2.2	1.0	10	dbSNP_123	169	717,7883	175.5+/-225.5	26,665,3609	no	coding-synonymous	SUFU	NM_016169.3		123,1425,4955	CC,CT,TT		8.3372,21.6523,12.8479		433/485	104386934	1671,11335	2203	4300	6503	SO:0001819	synonymous_variant	51684	exon11	Familial Cancer Database		ACAGATTCTGTTG	AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.1299T>C	10.37:g.104386934T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_016169	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Silent	SNP	ENST00000369902.3	37	CCDS7537.1																																																																																			T|0.814;C|0.186	0.186	strong		0.398	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050089.1	NM_016169	
IL12RB1	3594	hgsc.bcm.edu	37	19	18180451	18180451	+	Missense_Mutation	SNP	A	A	G	rs375947	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18180451A>G	ENST00000600835.2	-	11	1392	c.1094T>C	c.(1093-1095)aTg>aCg	p.M365T	IL12RB1_ENST00000593993.2_Missense_Mutation_p.M365T			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	365	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		M -> T (in dbSNP:rs375947). {ECO:0000269|Ref.3}.		cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						GCAATACGTCATGCTCTGAGC	0.607													G|||	1345	0.26857	0.2368	0.1758	5008	,	,		18923	0.376		0.3131	False		,,,				2504	0.2209				p.M365T		Atlas-SNP	.											.	IL12RB1	92	.	0			c.T1094C	GRCh37	CM030470	IL12RB1	M	rs375947	PASS	.	G	THR/MET	1071,3079		140,791,1144	84.0	92.0	89.0		1094	-4.5	0.0	19	dbSNP_80	89	2613,5793		401,1811,1991	yes	missense	IL12RB1	NM_005535.1	81	541,2602,3135	GG,GA,AA		31.0849,25.8072,29.3406	benign	365/663	18180451	3684,8872	2075	4203	6278	SO:0001583	missense	3594	exon10			TACGTCATGCTCT	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.1094T>C	19.37:g.18180451A>G	ENSP00000470788:p.Met365Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_005535	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	ENST00000600835.2	37	CCDS54232.1	630	0.28846153846153844	112	0.22764227642276422	75	0.20718232044198895	206	0.36013986013986016	237	0.31266490765171506	G	1.841	-0.467325	0.04476	0.258072	0.310849	ENSG00000096996	ENST00000430026	T	0.79352	-1.26	4.0	-4.51	0.03483	Long hematopoietin receptor, Gp130 family 2, conserved site (1);	0.655827	0.13905	N	0.354671	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	0.09015	-1.0694	9	0.07325	T	0.83	-0.4671	5.8474	0.18673	0.5975:0.0:0.2565:0.1459	rs375947;rs2230366;rs17711020;rs17882709;rs52802164;rs58231425;rs375947	365;365	P42701-2;P42701	.;I12R1_HUMAN	T	365	ENSP00000403103:M365T	ENSP00000403103:M365T	M	-	2	0	IL12RB1	18041451	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.948000	0.03897	-0.781000	0.04548	-0.441000	0.05720	ATG	A|0.701;G|0.299	0.299	strong		0.607	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
PSG5	5673	hgsc.bcm.edu	37	19	43690506	43690506	+	Missense_Mutation	SNP	G	G	C	rs8107936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43690506G>C	ENST00000366175.3	-	1	182	c.52C>G	c.(52-54)Ctc>Gtc	p.L18V	PSG5_ENST00000599812.1_Missense_Mutation_p.L18V|PSG5_ENST00000401992.1_5'UTR|PSG5_ENST00000342951.6_Missense_Mutation_p.L18V|PSG5_ENST00000407568.1_Missense_Mutation_p.L18V|PSG5_ENST00000407356.1_Missense_Mutation_p.L18V|PSG5_ENST00000404580.1_Missense_Mutation_p.L18V			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	18			L -> V (in dbSNP:rs8107936). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1922019, ECO:0000269|PubMed:2735907, ECO:0000269|PubMed:2789512}.		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				GTGAGCAGGAGCCCCTTCCAG	0.582													G|||	3659	0.730631	0.7481	0.5749	5008	,	,		18212	0.9762		0.6123	False		,,,				2504	0.6861				p.L18V		Atlas-SNP	.											PSG5,rectum,carcinoma,0,1	PSG5	58	1	0			c.C52G						scavenged	.	G	VAL/LEU,VAL/LEU	3185,1221		1179,827,197	91.0	91.0	91.0		52,52	0.3	0.0	19	dbSNP_116	91	5160,3426		1603,1954,736	no	missense,missense	PSG5	NM_001130014.1,NM_002781.3	32,32	2782,2781,933	CC,CG,GG		39.9022,27.7122,35.7682	benign,benign	18/336,18/336	43690506	8345,4647	2203	4293	6496	SO:0001583	missense	5673	exon1			GCAGGAGCCCCTT		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.52C>G	19.37:g.43690506G>C	ENSP00000382334:p.Leu18Val	Somatic	30	1	0.0333333		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_002781	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	1393	0.6378205128205128	289	0.5873983739837398	177	0.4889502762430939	518	0.9055944055944056	409	0.5395778364116095	N	3.655	-0.070693	0.07228	0.722878	0.600978	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000407568;ENST00000342951;ENST00000404580;ENST00000401992	T;T;T;T;T	0.01665	5.01;5.01;4.7;5.01;4.99	1.41	0.325	0.15903	.	.	.	.	.	T	0.00012	0.0000	L	0.33753	1.03	0.80722	P	0.0	B;B	0.29671	0.254;0.14	B;B	0.43575	0.424;0.35	T	0.02639	-1.1130	8	0.49607	T	0.09	.	3.7117	0.08423	0.2559:0.0:0.7441:0.0	rs8107936;rs11549987;rs17856401;rs59769041	18;18	E9PC55;Q15238	.;PSG5_HUMAN	V	18	ENSP00000382334:L18V;ENSP00000386008:L18V;ENSP00000386053:L18V;ENSP00000344413:L18V;ENSP00000385250:L18V	ENSP00000344413:L18V	L	-	1	0	PSG5	48382346	0.117000	0.22190	0.003000	0.11579	0.030000	0.12068	0.008000	0.13197	0.166000	0.19597	0.184000	0.17185	CTC	G|0.373;C|0.627	0.627	strong		0.582	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
CIPC	85457	hgsc.bcm.edu	37	14	77580068	77580068	+	Missense_Mutation	SNP	A	A	G	rs759593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:77580068A>G	ENST00000361786.2	+	4	924	c.607A>G	c.(607-609)Acc>Gcc	p.T203A	RP11-463C8.4_ENST00000557752.1_Intron	NM_033426.2	NP_219494.2	Q9C0C6	CIPC_HUMAN		203			T -> A (in dbSNP:rs759593).		negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(2)|lung(4)|prostate(3)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		CAGTGAGCCAACCAAGGCTGG	0.577													A|||	257	0.0513179	0.1573	0.0144	5008	,	,		20070	0.0317		0.005	False		,,,				2504	0.002				p.T203A		Atlas-SNP	.											.	KIAA1737	26	.	0			c.A607G						PASS	.	A	ALA/THR	600,3806	260.1+/-263.5	43,514,1646	48.0	49.0	49.0		607	0.9	0.0	14	dbSNP_86	49	17,8583	12.6+/-44.7	0,17,4283	yes	missense	KIAA1737	NM_033426.2	58	43,531,5929	GG,GA,AA		0.1977,13.6178,4.744	benign	203/400	77580068	617,12389	2203	4300	6503	SO:0001583	missense	85457	exon4			GAGCCAACCAAGG																												ENST00000361786.2:c.607A>G	14.37:g.77580068A>G	ENSP00000355319:p.Thr203Ala	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_033426	B2RCI1|Q8N389|Q8NDZ1	Missense_Mutation	SNP	ENST00000361786.2	37	CCDS9855.1	112	0.05128205128205128	72	0.14634146341463414	8	0.022099447513812154	30	0.05244755244755245	2	0.002638522427440633	A	6.650	0.488393	0.12641	0.136178	0.001977	ENSG00000198894	ENST00000361786	T	0.29142	1.58	5.29	0.933	0.19471	.	0.719349	0.14224	N	0.333230	T	0.00073	0.0002	L	0.31294	0.92	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.31336	-0.9947	9	0.14252	T	0.57	-18.6661	3.6726	0.08280	0.6344:0.0:0.2094:0.1562	rs759593;rs52803926;rs759593	203;105	Q9C0C6;B3KU75	K1737_HUMAN;.	A	203	ENSP00000355319:T203A	ENSP00000355319:T203A	T	+	1	0	KIAA1737	76649821	0.004000	0.15560	0.044000	0.18714	0.901000	0.52897	0.646000	0.24797	-0.073000	0.12842	0.374000	0.22700	ACC	A|0.953;G|0.047	0.047	strong		0.577	KIAA1737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414278.1		
RELN	5649	hgsc.bcm.edu	37	7	103124265	103124265	+	Missense_Mutation	SNP	A	A	G	rs150638029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103124265A>G	ENST00000428762.1	-	62	10175	c.10016T>C	c.(10015-10017)aTg>aCg	p.M3339T	RELN_ENST00000343529.5_Missense_Mutation_p.M3339T|RELN_ENST00000473945.1_5'UTR|RN7SKP86_ENST00000410454.1_RNA|CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000424685.2_Missense_Mutation_p.M3339T	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	3339					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)		CGTCTGCGACATGCTCCCAAT	0.453																																					p.M3339T	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T10016C						PASS	.	A	THR/MET,THR/MET	2,4404	4.2+/-10.8	0,2,2201	106.0	99.0	101.0		10016,10016	2.9	0.0	7	dbSNP_134	101	0,8600		0,0,4300	no	missense,missense	RELN	NM_005045.3,NM_173054.2	81,81	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	benign,benign	3339/3461,3339/3459	103124265	2,13004	2203	4300	6503	SO:0001583	missense	5649	exon62			TGCGACATGCTCC		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.10016T>C	7.37:g.103124265A>G	ENSP00000392423:p.Met3339Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	A	3.338	-0.135242	0.06711	4.54E-4	0.0	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000424828;ENST00000448171	T;T;T	0.20463	2.07;2.07;2.07	5.64	2.87	0.33458	.	0.695276	0.14403	N	0.321778	T	0.08403	0.0209	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39354	-0.9618	10	0.17832	T	0.49	.	8.0051	0.30321	0.4314:0.0:0.5686:0.0	.	3339;3339	P78509-2;P78509	.;RELN_HUMAN	T	3339;3339;3339;856;3339	ENSP00000392423:M3339T;ENSP00000345694:M3339T;ENSP00000388446:M3339T	ENSP00000345694:M3339T	M	-	2	0	RELN	102911501	0.017000	0.18338	0.013000	0.15412	0.558000	0.35554	1.440000	0.35024	0.327000	0.23409	-1.055000	0.02315	ATG	A|1.000;G|0.000	0.000	strong		0.453	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
SLC28A1	9154	hgsc.bcm.edu	37	15	85448796	85448796	+	Silent	SNP	A	A	T	rs8187755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85448796A>T	ENST00000286749.3	+	7	720	c.630A>T	c.(628-630)ggA>ggT	p.G210G	SLC28A1_ENST00000394573.1_Silent_p.G210G|SLC28A1_ENST00000537624.1_Silent_p.G210G|SLC28A1_ENST00000538177.1_Silent_p.G210G|SLC28A1_ENST00000537216.1_Silent_p.G210G|SLC28A1_ENST00000537703.1_Silent_p.G132G			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	210					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)	TGTCTTGGGGACTTGGACTGC	0.587													A|||	156	0.0311502	0.1142	0.0072	5008	,	,		19535	0.0		0.0	False		,,,				2504	0.0				p.G210G		Atlas-SNP	.											SLC28A1_ENST00000537624,NS,carcinoma,+1,2	SLC28A1	118	2	0			c.A630T						scavenged	.	A		404,4002	200.8+/-224.0	20,364,1819	215.0	172.0	186.0		630	1.1	1.0	15	dbSNP_123	186	3,8595	2.2+/-6.3	0,3,4296	no	coding-synonymous	SLC28A1	NM_004213.3		20,367,6115	TT,TA,AA		0.0349,9.1693,3.1298		210/650	85448796	407,12597	2203	4299	6502	SO:0001819	synonymous_variant	9154	exon8			TTGGGGACTTGGA	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.630A>T	15.37:g.85448796A>T		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	198	74	0.373737	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	37	CCDS10334.1																																																																																			A|0.973;T|0.027	0.027	strong		0.587	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
TTC32	130502	hgsc.bcm.edu	37	2	20101487	20101487	+	Silent	SNP	G	G	A	rs2304589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20101487G>A	ENST00000333610.3	-	1	260	c.129C>T	c.(127-129)tcC>tcT	p.S43S	TTC32_ENST00000402414.1_Silent_p.S43S|RP11-79O8.1_ENST00000607190.1_lincRNA	NM_001008237.1	NP_001008238.1	Q5I0X7	TTC32_HUMAN	tetratricopeptide repeat domain 32	43										kidney(2)|large_intestine(1)|lung(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTCGTCGCTGGAGGCCGCGC	0.637													g|||	1411	0.281749	0.208	0.2305	5008	,	,		16050	0.4028		0.175	False		,,,				2504	0.4029				p.S43S		Atlas-SNP	.											.	TTC32	13	.	0			c.C129T						PASS	.	A		904,3502	349.8+/-310.5	102,700,1401	57.0	58.0	58.0		129	-8.4	0.0	2	dbSNP_100	58	1392,7208	269.4+/-288.4	127,1138,3035	no	coding-synonymous	TTC32	NM_001008237.1		229,1838,4436	AA,AG,GG		16.186,20.5175,17.6534		43/152	20101487	2296,10710	2203	4300	6503	SO:0001819	synonymous_variant	130502	exon1			GTCGCTGGAGGCC	BC057850	CCDS33151.1	2p24.1	2013-01-10			ENSG00000183891	ENSG00000183891		"""Tetratricopeptide (TTC) repeat domain containing"""	32954	protein-coding gene	gene with protein product							Standard	NM_001008237		Approved		uc002rdg.3	Q5I0X7	OTTHUMG00000151776	ENST00000333610.3:c.129C>T	2.37:g.20101487G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_001008237		Silent	SNP	ENST00000333610.3	37	CCDS33151.1																																																																																			G|0.740;A|0.260	0.260	strong		0.637	TTC32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323868.1	NM_001008237	
CCDC102A	92922	hgsc.bcm.edu	37	16	57552088	57552088	+	Silent	SNP	T	T	C	rs28756858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57552088T>C	ENST00000258214.2	-	6	1386	c.1140A>G	c.(1138-1140)gcA>gcG	p.A380A		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	380										endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						CTCCGACCTGTGCCCGCAGCT	0.701													T|||	1078	0.215256	0.413	0.1585	5008	,	,		15230	0.0288		0.2445	False		,,,				2504	0.1503				p.A380A		Atlas-SNP	.											.	CCDC102A	22	.	0			c.A1140G						PASS	.	T		1718,2678		343,1032,823	50.0	63.0	58.0		1140	-6.6	0.8	16	dbSNP_125	58	2031,6563		240,1551,2506	no	coding-synonymous	CCDC102A	NM_033212.3		583,2583,3329	CC,CT,TT		23.6328,39.081,28.8607		380/551	57552088	3749,9241	2198	4297	6495	SO:0001819	synonymous_variant	92922	exon6			GACCTGTGCCCGC	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.1140A>G	16.37:g.57552088T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	49	30	0.612245	NM_033212	Q9BT74	Silent	SNP	ENST00000258214.2	37	CCDS10784.1																																																																																			A|0.000;C|0.268;T|0.732	0.268	strong		0.701	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212	
HIST1H2AB	8335	hgsc.bcm.edu	37	6	26033641	26033641	+	Silent	SNP	G	G	A	rs2230654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26033641G>A	ENST00000259791.2	-	1	155	c.156C>T	c.(154-156)ctC>ctT	p.L52L	HIST1H3B_ENST00000244661.2_5'Flank	NM_003513.2	NP_003504.2	P04908	H2A1B_HUMAN	histone cluster 1, H2ab	52						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						GCACCGCCGCGAGATACACCG	0.657													G|||	975	0.194688	0.3472	0.1556	5008	,	,		14712	0.0734		0.1352	False		,,,				2504	0.2025				p.L52L		Atlas-SNP	.											.	HIST1H2AB	18	.	0			c.C156T						PASS	.	G		1364,3042		223,918,1062	34.0	40.0	38.0		156	0.7	1.0	6	dbSNP_98	38	1335,7263		109,1117,3073	no	coding-synonymous	HIST1H2AB	NM_003513.2		332,2035,4135	AA,AG,GG		15.5269,30.9578,20.7552		52/131	26033641	2699,10305	2203	4299	6502	SO:0001819	synonymous_variant	8335	exon1			CGCCGCGAGATAC	X00089	CCDS4574.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000137259	ENSG00000278463		"""Histones / Replication-dependent"""	4734	protein-coding gene	gene with protein product		602795	"""H2A histone family, member M"", ""histone 1, H2ab"""	H2AFM		9439656, 9119399, 12408966	Standard	NM_003513		Approved	H2A/m	uc003nft.1	P04908	OTTHUMG00000014420	ENST00000259791.2:c.156C>T	6.37:g.26033641G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	226	125	0.553097	NM_003513	P28001|Q76P63	Silent	SNP	ENST00000259791.2	37	CCDS4574.1																																																																																			G|0.810;A|0.190	0.190	strong		0.657	HIST1H2AB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040082.1	NM_003513	
EPHB3	2049	hgsc.bcm.edu	37	3	184290348	184290348	+	Silent	SNP	G	G	A	rs9862375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184290348G>A	ENST00000330394.2	+	3	692	c.240G>A	c.(238-240)gtG>gtA	p.V80V	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	80	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			CATACCAGGTGTGTAATGTGC	0.547													G|||	288	0.057508	0.0877	0.072	5008	,	,		19487	0.0		0.1074	False		,,,				2504	0.0143				p.V80V		Atlas-SNP	.											.	EPHB3	114	.	0			c.G240A						PASS	.	G		379,4027	189.9+/-215.9	20,339,1844	65.0	60.0	62.0		240	5.5	1.0	3	dbSNP_119	62	837,7763	191.8+/-238.0	49,739,3512	no	coding-synonymous	EPHB3	NM_004443.3		69,1078,5356	AA,AG,GG		9.7326,8.6019,9.3495		80/999	184290348	1216,11790	2203	4300	6503	SO:0001819	synonymous_variant	2049	exon3			CCAGGTGTGTAAT	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.240G>A	3.37:g.184290348G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			G|0.918;A|0.082	0.082	strong		0.547	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
SGCA	6442	hgsc.bcm.edu	37	17	48247689	48247689	+	Silent	SNP	C	C	T	rs1801191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48247689C>T	ENST00000262018.3	+	7	969	c.933C>T	c.(931-933)gtC>gtT	p.V311V	SGCA_ENST00000543315.1_Intron|HILS1_ENST00000504307.1_RNA|SGCA_ENST00000513942.1_Intron|SGCA_ENST00000344627.6_Intron	NM_000023.2	NP_000014.1	Q16586	SGCA_HUMAN	sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein)	311					muscle contraction (GO:0006936)|muscle organ development (GO:0007517)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						TGGCCTATGTCATGTGCTGCC	0.632													C|||	394	0.0786741	0.236	0.0288	5008	,	,		20676	0.0079		0.0457	False		,,,				2504	0.0082				p.V311V		Atlas-SNP	.											.	SGCA	35	.	0			c.C933T						PASS	.	C	,	874,3532	341.8+/-306.9	85,704,1414	98.0	86.0	90.0		933,	2.7	0.9	17	dbSNP_89	90	358,8242	120.2+/-179.5	5,348,3947	no	coding-synonymous,intron	SGCA	NM_000023.2,NM_001135697.1	,	90,1052,5361	TT,TC,CC		4.1628,19.8366,9.4726	,	311/388,	48247689	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	6442	exon7			CTATGTCATGTGC	L34355	CCDS32679.1, CCDS45729.1	17q21	2014-09-17	2002-08-29		ENSG00000108823	ENSG00000108823			10805	protein-coding gene	gene with protein product	"""50kD DAG"", ""Sarcoglycan, alpha (50kD dystrophin-associated glycoprotein; adhalin)"", ""adhalin (limb girdle muscular dystrophy 2D)"""	600119	"""sarcoglycan, alpha (50kD dystrophin-associated glycoprotein)"""	ADL		7937874	Standard	NM_000023		Approved	SCARMD1, LGMD2D, adhalin, DMDA2, A2	uc002iqi.3	Q16586	OTTHUMG00000162024	ENST00000262018.3:c.933C>T	17.37:g.48247689C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	154	74	0.480519	NM_000023	A6NEB8|A8K3K7|Q13710|Q13712	Silent	SNP	ENST00000262018.3	37	CCDS32679.1	149	0.06822344322344322	98	0.1991869918699187	9	0.024861878453038673	8	0.013986013986013986	34	0.044854881266490766	C	10.64	1.407907	0.25378	0.198366	0.041628	ENSG00000108823	ENST00000504073	.	.	.	5.8	2.68	0.31781	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06625	-1.0816	3	.	.	.	-14.6598	9.1601	0.37016	0.0:0.6906:0.0:0.3094	rs1801191;rs1801191	.	.	.	Y	84	.	.	H	+	1	0	SGCA	45602688	1.000000	0.71417	0.897000	0.35233	0.977000	0.68977	1.725000	0.38074	0.349000	0.23975	-0.136000	0.14681	CAT	C|0.911;T|0.089	0.089	strong		0.632	SGCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366841.1	NM_000023	
PLXND1	23129	hgsc.bcm.edu	37	3	129291499	129291499	+	Silent	SNP	G	G	A	rs2285368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129291499G>A	ENST00000324093.4	-	15	3208	c.3030C>T	c.(3028-3030)tcC>tcT	p.S1010S	PLXND1_ENST00000393239.1_Silent_p.S1010S	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1010	IPT/TIG 2.				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						CCTGGAGCTCGGAGCCTACAT	0.627													G|||	726	0.144968	0.3427	0.0504	5008	,	,		17501	0.1042		0.0388	False		,,,				2504	0.0961				p.S1010S	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C3030T						PASS	.	G		1331,3075	433.9+/-343.8	207,917,1079	53.0	49.0	50.0		3030	-4.2	0.9	3	dbSNP_100	50	301,8299	107.4+/-168.2	8,285,4007	no	coding-synonymous	PLXND1	NM_015103.2		215,1202,5086	AA,AG,GG		3.5,30.2088,12.5481		1010/1926	129291499	1632,11374	2203	4300	6503	SO:0001819	synonymous_variant	23129	exon15			GAGCTCGGAGCCT	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.3030C>T	3.37:g.129291499G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	205	116	0.565854	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			G|0.865;A|0.135	0.135	strong		0.627	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
SLC28A1	9154	hgsc.bcm.edu	37	15	85478573	85478573	+	Silent	SNP	C	C	A	rs8187779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85478573C>A	ENST00000286749.3	+	14	1495	c.1405C>A	c.(1405-1407)Cgg>Agg	p.R469R	SLC28A1_ENST00000394573.1_Silent_p.R469R|SLC28A1_ENST00000537624.1_Silent_p.R469R|SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000537216.1_Silent_p.R469R			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	469					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)	CTACATCCTGCGGCCTGTAGC	0.607													C|||	34	0.00678914	0.0227	0.0043	5008	,	,		20483	0.0		0.001	False		,,,				2504	0.0				p.R469R		Atlas-SNP	.											SLC28A1,colon,carcinoma,-1,1	SLC28A1	118	1	0			c.C1405A						scavenged	.	C		79,4327	68.7+/-106.4	2,75,2126	110.0	88.0	95.0		1405	2.2	1.0	15	dbSNP_123	95	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous	SLC28A1	NM_004213.3		2,79,6421	AA,AC,CC		0.0465,1.793,0.6383		469/650	85478573	83,12921	2203	4299	6502	SO:0001819	synonymous_variant	9154	exon15			ATCCTGCGGCCTG	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.1405C>A	15.37:g.85478573C>A		Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	142	77	0.542253	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	37	CCDS10334.1																																																																																			C|0.995;A|0.005	0.005	strong		0.607	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
SCO1	6341	hgsc.bcm.edu	37	17	10600653	10600653	+	Missense_Mutation	SNP	G	G	A	rs1802083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10600653G>A	ENST00000255390.5	-	1	232	c.172C>T	c.(172-174)Cct>Tct	p.P58S	SCO1_ENST00000582053.1_Intron|ADPRM_ENST00000379774.4_5'Flank|SCO1_ENST00000577427.1_Missense_Mutation_p.P58S	NM_004589.2	NP_004580.1	O75880	SCO1_HUMAN	SCO1 cytochrome c oxidase assembly protein	58			P -> S (in dbSNP:rs1802083).		cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|generation of precursor metabolites and energy (GO:0006091)|respiratory chain complex IV assembly (GO:0008535)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)	copper ion binding (GO:0005507)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|urinary_tract(1)	10						CAATAGCCAGGGCGCCCCGAG	0.726													G|||	309	0.0617013	0.2216	0.0159	5008	,	,		10465	0.0		0.005	False		,,,				2504	0.0				p.P58S	Melanoma(128;591 1731 19711 31891 44645)	Atlas-SNP	.											.	SCO1	24	.	0			c.C172T						PASS	.	G	SER/PRO	629,3663		35,559,1552	6.0	7.0	7.0		172	1.7	0.0	17	dbSNP_89	7	11,8423		0,11,4206	no	missense	SCO1	NM_004589.2	74	35,570,5758	AA,AG,GG		0.1304,14.6552,5.0291	benign	58/302	10600653	640,12086	2146	4217	6363	SO:0001583	missense	6341	exon1			AGCCAGGGCGCCC	AF026852	CCDS11158.1	17p13.1	2012-10-15	2012-10-15		ENSG00000133028	ENSG00000133028		"""Mitochondrial respiratory chain complex assembly factors"""	10603	protein-coding gene	gene with protein product		603644	"""SCO (cytochrome oxidase deficient, yeast) homolog 1"", ""SCO cytochrome oxidase deficient homolog 1 (yeast)"""	SCOD1		9878253	Standard	NM_004589		Approved		uc002gmr.4	O75880	OTTHUMG00000130364	ENST00000255390.5:c.172C>T	17.37:g.10600653G>A	ENSP00000255390:p.Pro58Ser	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_004589	B2RDM0	Missense_Mutation	SNP	ENST00000255390.5	37	CCDS11158.1	110	0.05036630036630037	99	0.20121951219512196	9	0.024861878453038673	0	0.0	2	0.002638522427440633	G	10.34	1.324239	0.24080	0.146552	0.001304	ENSG00000133028	ENST00000255390;ENST00000396047	D	0.84873	-1.91	3.87	1.72	0.24424	.	0.533478	0.16696	N	0.203334	T	0.00178	0.0005	N	0.14661	0.345	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.03184	-1.1063	9	0.12430	T	0.62	-1.1139	10.6528	0.45657	0.0:0.4881:0.5119:0.0	rs1802083	58;58	A8MY34;O75880	.;SCO1_HUMAN	S	58	ENSP00000255390:P58S	ENSP00000255390:P58S	P	-	1	0	SCO1	10541378	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.044000	0.03532	0.504000	0.28082	-0.171000	0.13296	CCT	G|0.948;A|0.052	0.052	strong		0.726	SCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252729.2	NM_004589	
LCE1C	353133	hgsc.bcm.edu	37	1	152777877	152777877	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152777877G>A	ENST00000607093.1	-	1	77	c.78C>T	c.(76-78)acC>acT	p.T26T	LCE1C_ENST00000368768.1_Silent_p.T26T			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	26	Pro-rich.				keratinization (GO:0031424)					NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1)	9	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gacactttggggTGgggcact	0.647																																					p.T26T		Atlas-SNP	.											.	LCE1C	40	.	0			c.C78T						PASS	.						45.0	46.0	46.0					1																	152777877		2203	4300	6503	SO:0001819	synonymous_variant	353133	exon2			CTTTGGGGTGGGG		CCDS1026.1	1q21.3	2008-02-05			ENSG00000197084	ENSG00000197084		"""Late cornified envelopes"""	29464	protein-coding gene	gene with protein product		612605				11698679	Standard	NM_001276331		Approved	LEP3	uc001fap.1	Q5T751	OTTHUMG00000012445	ENST00000607093.1:c.78C>T	1.37:g.152777877G>A		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	409	29	0.0709046	NM_178351		Silent	SNP	ENST00000607093.1	37	CCDS1026.1																																																																																			.	.	none		0.647	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351	
TDRD5	163589	hgsc.bcm.edu	37	1	179562740	179562740	+	Missense_Mutation	SNP	G	G	C	rs61310274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179562740G>C	ENST00000367614.1	+	3	737	c.378G>C	c.(376-378)agG>agC	p.R126S	RP11-545A16.4_ENST00000567150.1_RNA|TDRD5_ENST00000294848.8_Missense_Mutation_p.R126S|TDRD5_ENST00000444136.1_Missense_Mutation_p.R126S	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	126				R -> S (in Ref. 3; AAI30533/AAI44059). {ECO:0000305}.	DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						ACCGAGGAAGGGTTGCCCCTA	0.453													G|||	1541	0.307708	0.0877	0.4092	5008	,	,		20589	0.371		0.3897	False		,,,				2504	0.3834				p.R126S		Atlas-SNP	.											TDRD5,NS,neuroblastoma,+1,1	TDRD5	149	1	0			c.G378C						PASS	.	G	SER/ARG,SER/ARG,SER/ARG,SER/ARG	658,3748	279.6+/-274.9	54,550,1599	167.0	155.0	159.0		378,378,378,378	2.6	1.0	1	dbSNP_129	159	3124,5476	477.0+/-369.5	555,2014,1731	yes	missense,missense,missense,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_173533.3	110,110,110,110	609,2564,3330	CC,CG,GG		36.3256,14.9342,29.0789	probably-damaging,probably-damaging,probably-damaging,probably-damaging	126/1036,126/1036,126/982,126/982	179562740	3782,9224	2203	4300	6503	SO:0001583	missense	163589	exon3			AGGAAGGGTTGCC	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.378G>C	1.37:g.179562740G>C	ENSP00000356586:p.Arg126Ser	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	325	159	0.489231	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	725	0.33195970695970695	46	0.09349593495934959	153	0.42265193370165743	236	0.4125874125874126	290	0.38258575197889183	G	18.60	3.658717	0.67586	0.149342	0.363256	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.12879	2.64;2.64;2.78	5.59	2.58	0.30949	.	0.200944	0.41194	D	0.000923	T	0.00012	0.0000	L	0.27053	0.805	0.31208	P	0.6990000000000001	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.986	T	0.46162	-0.9211	9	0.30854	T	0.27	-0.0298	7.1341	0.25519	0.3841:0.0:0.6159:0.0	rs61310274	126;126	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	S	126	ENSP00000356586:R126S;ENSP00000294848:R126S;ENSP00000406052:R126S	ENSP00000294848:R126S	R	+	3	2	TDRD5	177829363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.835000	0.27531	0.625000	0.30304	0.655000	0.94253	AGG	G|0.693;C|0.307	0.307	strong		0.453	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
ITGA11	22801	hgsc.bcm.edu	37	15	68605169	68605169	+	Missense_Mutation	SNP	G	G	A	rs4777035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68605169G>A	ENST00000315757.7	-	24	3001	c.2915C>T	c.(2914-2916)cCc>cTc	p.P972L	ITGA11_ENST00000423218.2_Missense_Mutation_p.P972L	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	972			P -> L (in dbSNP:rs4777035). {ECO:0000269|PubMed:10464311, ECO:0000269|PubMed:10486209, ECO:0000269|Ref.4}.		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)			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						CGAGCTGTTGGGCTTGACCTC	0.607													G|||	3588	0.716454	0.5371	0.7262	5008	,	,		17729	0.9375		0.5885	False		,,,				2504	0.8558				p.P972L		Atlas-SNP	.											.	ITGA11	110	.	0			c.C2915T						PASS	.	G	LEU/PRO	2300,1844		662,976,434	74.0	76.0	75.0		2915	5.0	1.0	15	dbSNP_111	75	5124,3314		1574,1976,669	yes	missense	ITGA11	NM_001004439.1	98	2236,2952,1103	AA,AG,GG		39.2747,44.4981,40.9951	benign	972/1189	68605169	7424,5158	2072	4219	6291	SO:0001583	missense	22801	exon24			CTGTTGGGCTTGA	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.2915C>T	15.37:g.68605169G>A	ENSP00000327290:p.Pro972Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	131	45	0.343511	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	1503	0.6881868131868132	266	0.540650406504065	250	0.6906077348066298	536	0.9370629370629371	451	0.5949868073878628	G	17.60	3.430253	0.62844	0.555019	0.607253	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.41758	0.99;0.99	4.97	4.97	0.65823	Integrin alpha-2 (1);	0.459305	0.25478	N	0.030394	T	0.00012	0.0000	L	0.50333	1.59	0.21147	P	0.999779471	P;B	0.44478	0.836;0.273	P;B	0.56216	0.794;0.16	T	0.05225	-1.0898	9	0.36615	T	0.2	.	16.8179	0.85738	0.0:0.0:1.0:0.0	rs4777035;rs52836241;rs56600365;rs59029828;rs4777035	972;972	A8K8T0;Q9UKX5	.;ITA11_HUMAN	L	972;972;607	ENSP00000327290:P972L;ENSP00000403392:P972L	ENSP00000327290:P972L	P	-	2	0	ITGA11	66392223	1.000000	0.71417	1.000000	0.80357	0.768000	0.43524	7.333000	0.79214	2.307000	0.77673	0.561000	0.74099	CCC	G|0.313;A|0.686	0.686	strong		0.607	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
HIST1H3I	8354	hgsc.bcm.edu	37	6	27839746	27839746	+	Silent	SNP	T	T	C	rs200956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27839746T>C	ENST00000328488.2	-	1	353	c.348A>G	c.(346-348)aaA>aaG	p.K116K		NM_003533.2	NP_003524.1	P68431	H31_HUMAN	histone cluster 1, H3i	116					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TAGTGACGCGTTTGGCGTGAA	0.572													C|||	1273	0.254193	0.4758	0.2305	5008	,	,		18092	0.1389		0.1511	False		,,,				2504	0.1963				p.K116K		Atlas-SNP	.											.	HIST1H3I	28	.	0			c.A348G						PASS	.	C		1856,2550	634.1+/-396.1	405,1046,752	125.0	136.0	133.0		348	2.3	1.0	6	dbSNP_79	133	1396,7204	754.3+/-407.5	114,1168,3018	no	coding-synonymous	HIST1H3I	NM_003533.2		519,2214,3770	CC,CT,TT		16.2326,42.1244,25.0038		116/137	27839746	3252,9754	2203	4300	6503	SO:0001819	synonymous_variant	8354	exon1			GACGCGTTTGGCG	X83550	CCDS4636.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000182572	ENSG00000275379		"""Histones / Replication-dependent"""	4771	protein-coding gene	gene with protein product		602814	"""H3 histone family, member F"", ""histone 1, H3i"""	H3FF		9031620, 9439656, 12408966	Standard	NM_003533		Approved	H3/f, H3.f	uc003njy.3	P68431	OTTHUMG00000016184	ENST00000328488.2:c.348A>G	6.37:g.27839746T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	160	85	0.53125	NM_003533	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000328488.2	37	CCDS4636.1																																																																																			A|0.004;C|0.245	0.245	strong		0.572	HIST1H3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043452.1	NM_003533	
TEP1	7011	hgsc.bcm.edu	37	14	20852267	20852267	+	Missense_Mutation	SNP	C	C	T	rs2228041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20852267C>T	ENST00000262715.5	-	24	3504	c.3464G>A	c.(3463-3465)cGg>cAg	p.R1155Q	TEP1_ENST00000556935.1_Missense_Mutation_p.R1047Q|TEP1_ENST00000545983.1_5'Flank	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1155			R -> Q (in dbSNP:rs2228041). {ECO:0000269|PubMed:9020079}.		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)		CAGCATCAGCCGTTGCACTGT	0.642													T|||	168	0.0335463	0.003	0.0303	5008	,	,		19333	0.0		0.0686	False		,,,				2504	0.0757				p.R1155Q		Atlas-SNP	.											.	TEP1	224	.	0			c.G3464A						PASS	.	T	GLN/ARG	50,4356	819.6+/-416.4	0,50,2153	58.0	58.0	58.0		3464	0.6	0.2	14	dbSNP_98	58	531,8069	793.4+/-407.5	19,493,3788	yes	missense	TEP1	NM_007110.4	43	19,543,5941	TT,TC,CC		6.1744,1.1348,4.4672	benign	1155/2628	20852267	581,12425	2203	4300	6503	SO:0001583	missense	7011	exon24			ATCAGCCGTTGCA		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.3464G>A	14.37:g.20852267C>T	ENSP00000262715:p.Arg1155Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	50	0.617284	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	70	0.03205128205128205	0	0.0	9	0.024861878453038673	0	0.0	61	0.08047493403693931	T	0.017	-1.496953	0.01001	0.011348	0.061744	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.81247	-1.47;-1.47	5.62	0.586	0.17434	.	0.480048	0.22293	N	0.061978	T	0.02533	0.0077	N	0.00483	-1.445	0.09310	P	0.9999999653158	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.27365	-1.0076	9	0.02654	T	1	-3.1745	4.1841	0.10390	0.1522:0.3376:0.0:0.5102	rs2228041;rs17211369;rs52824344;rs2228041	1047;505;1155	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	Q	1155;1155;1047	ENSP00000262715:R1155Q;ENSP00000452574:R1047Q	ENSP00000262715:R1155Q	R	-	2	0	TEP1	19922107	0.303000	0.24463	0.188000	0.23233	0.086000	0.17979	0.476000	0.22180	-0.147000	0.11254	-1.062000	0.02293	CGG	C|0.957;T|0.043	0.043	strong		0.642	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
ZFP69	339559	hgsc.bcm.edu	37	1	40960619	40960619	+	Missense_Mutation	SNP	G	G	A	rs41301076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:40960619G>A	ENST00000372706.1	+	6	1475	c.469G>A	c.(469-471)Gag>Aag	p.E157K	RP11-656D10.3_ENST00000450713.1_RNA|ZFP69_ENST00000372705.3_Missense_Mutation_p.E157K			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	157					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										AGAAACCATTGAGTCAACTGC	0.328													G|||	236	0.0471246	0.1203	0.0331	5008	,	,		13274	0.0		0.0437	False		,,,				2504	0.0102				p.E157K		Atlas-SNP	.											.	.	.	.	0			c.G469A						PASS	.	G	LYS/GLU	429,3973	183.3+/-210.9	18,393,1790	53.0	56.0	55.0		469	0.8	0.0	1	dbSNP_127	55	385,8209	121.1+/-180.3	17,351,3929	yes	missense	ZNF642	NM_198494.2	56	35,744,5719	AA,AG,GG		4.4799,9.7456,6.2635	benign	157/527	40960619	814,12182	2201	4297	6498	SO:0001583	missense	339559	exon6			ACCATTGAGTCAA	AK122618	CCDS30686.1	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187815	ENSG00000187815		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	24708	protein-coding gene	gene with protein product	"""ZFP69 zinc finger protein A"""		"""zinc finger protein 642"""	ZNF642			Standard	XM_005270808		Approved	ZKSCAN23A, FLJ16030, ZFP69A, ZSCAN54A	uc001cfo.3	Q49AA0	OTTHUMG00000007303	ENST00000372706.1:c.469G>A	1.37:g.40960619G>A	ENSP00000361791:p.Glu157Lys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_198494	Q5SWM5|Q6ZWK8	Missense_Mutation	SNP	ENST00000372706.1	37	CCDS30686.1	112	0.05128205128205128	67	0.13617886178861788	15	0.04143646408839779	0	0.0	30	0.0395778364116095	G	0.511	-0.866482	0.02590	0.097456	0.044799	ENSG00000187815	ENST00000372706;ENST00000372705	T;T	0.05258	3.47;3.47	4.31	0.762	0.18454	.	1.171190	0.06555	N	0.745795	T	0.00039	0.0001	N	0.21508	0.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47222	-0.9134	9	0.12766	T	0.61	0.6711	7.2687	0.26244	0.2769:0.0:0.7231:0.0	rs41301076	157	Q49AA0	ZN642_HUMAN	K	157	ENSP00000361791:E157K;ENSP00000361790:E157K	ENSP00000361790:E157K	E	+	1	0	ZNF642	40733206	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.310000	0.19356	0.137000	0.18759	0.467000	0.42956	GAG	G|0.946;A|0.054	0.054	strong		0.328	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494	
TTLL6	284076	hgsc.bcm.edu	37	17	46894377	46894377	+	Missense_Mutation	SNP	A	A	C	rs3959442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:46894377A>C	ENST00000393382.3	-	1	199	c.58T>G	c.(58-60)Tgg>Ggg	p.W20G	TTLL6_ENST00000470462.2_5'UTR	NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CTGCTAGTCCAGCTTGCAACC	0.667													A|||	1360	0.271565	0.3434	0.4063	5008	,	,		12670	0.1875		0.2664	False		,,,				2504	0.1708				p.W20G		Atlas-SNP	.											.	TTLL6	113	.	0			c.T58G						PASS	.	A	GLY/TRP	456,928		79,298,315	40.0	51.0	48.0		58	-0.6	0.0	17	dbSNP_108	48	862,2320		120,622,849	yes	missense	TTLL6	NM_001130918.1	184	199,920,1164	CC,CA,AA		27.0899,32.948,28.8655		20/892	46894377	1318,3248	692	1591	2283	SO:0001583	missense	284076	exon1			TAGTCCAGCTTGC	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"""Tubulin tyrosine ligase-like family"""	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.58T>G	17.37:g.46894377A>C	ENSP00000377043:p.Trp20Gly	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	25	9	0.36	NM_001130918		Missense_Mutation	SNP	ENST00000393382.3	37	CCDS45724.1	606	0.2774725274725275	163	0.3313008130081301	145	0.4005524861878453	95	0.1660839160839161	203	0.2678100263852243	A	0.930	-0.713124	0.03206	0.32948	0.270899	ENSG00000170703	ENST00000440941;ENST00000418322	.	.	.	4.19	-0.634	0.11516	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	.	.	.	.	.	.	T	0.47509	-0.9112	5	0.29301	T	0.29	.	5.1484	0.14996	0.5233:0.3665:0.0:0.1101	rs3959442	.	.	.	G	20;22	.	ENSP00000403514:W22G	W	-	1	0	TTLL6	44249376	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.112000	0.10791	-0.138000	0.11434	-0.294000	0.09567	TGG	T|0.000;G|0.000;C|0.278;A|0.721	0.278	strong		0.667	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623	
NLRC3	197358	hgsc.bcm.edu	37	16	3613690	3613690	+	RNA	SNP	G	G	A	rs144685315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3613690G>A	ENST00000301749.7	-	0	1653				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGTCTTGCTCGTAAAACACGT	0.602													G|||	11	0.00219649	0.0083	0.0	5008	,	,		20370	0.0		0.0	False		,,,				2504	0.0				p.Y416Y		Atlas-SNP	.											.	NLRC3	103	.	0			c.C1248T						PASS	.	G		28,4006		0,28,1989	62.0	62.0	62.0		1248	-6.6	0.9	16	dbSNP_134	62	0,8352		0,0,4176	no	coding-synonymous	NLRC3	NM_178844.2		0,28,6165	AA,AG,GG		0.0,0.6941,0.2261		416/1066	3613690	28,12358	2017	4176	6193			197358	exon5			TTGCTCGTAAAAC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613690G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	37																																																																																				G|0.999;A|0.001	0.001	strong		0.602	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48602933	48602933	+	Missense_Mutation	SNP	T	T	C	rs2307282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48602933T>C	ENST00000599921.1	-	5	799	c.442A>G	c.(442-444)Aga>Gga	p.R148G	PLA2G4C_ENST00000599111.1_Missense_Mutation_p.R158G|PLA2G4C_ENST00000413144.2_Missense_Mutation_p.R148G|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.R148G			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	148	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		R -> G (in dbSNP:rs2307282). {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)		CTTACTTCTCTGGTTTGCTTA	0.527													T|||	221	0.0441294	0.1566	0.013	5008	,	,		17533	0.0		0.0	False		,,,				2504	0.0051				p.R158G		Atlas-SNP	.											PLA2G4C,middle_lobe,carcinoma,+1,1	PLA2G4C	76	1	0			c.A472G						PASS	.	T	GLY/ARG,GLY/ARG,GLY/ARG	504,3902	234.6+/-247.4	33,438,1732	102.0	98.0	99.0		472,442,442	0.8	0.4	19	dbSNP_100	99	13,8587	8.4+/-32.0	0,13,4287	yes	missense,missense,missense	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	125,125,125	33,451,6019	CC,CT,TT		0.1512,11.4389,3.9751	probably-damaging,probably-damaging,probably-damaging	158/552,148/528,148/542	48602933	517,12489	2203	4300	6503	SO:0001583	missense	8605	exon5			CTTCTCTGGTTTG	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.442A>G	19.37:g.48602933T>C	ENSP00000469473:p.Arg148Gly	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	T	16.81	3.226912	0.58668	0.114389	0.001512	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.03920	3.76;3.76	3.17	0.779	0.18550	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.158082	0.39985	U	0.001218	T	0.00039	0.0001	N	0.05487	-0.04	0.26973	N	0.965549	D;D;D	0.63046	0.992;0.992;0.992	D;D;D	0.63192	0.912;0.912;0.912	T	0.44143	-0.9347	10	0.15499	T	0.54	-15.3518	7.5148	0.27593	0.0:0.0:0.4963:0.5037	rs2307282;rs52815563;rs56435935;rs2307282	158;148;148	B4DI40;Q8WWC5;Q9UP65	.;.;PA24C_HUMAN	G	148	ENSP00000346228:R148G;ENSP00000400036:R148G	ENSP00000346228:R148G	R	-	1	2	PLA2G4C	53294745	0.937000	0.31787	0.417000	0.26559	0.668000	0.39293	0.459000	0.21908	-0.144000	0.11314	0.338000	0.21704	AGA	T|0.956;C|0.044	0.044	strong		0.527	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
BIRC6	57448	hgsc.bcm.edu	37	2	32673884	32673884	+	Silent	SNP	A	A	G	rs150651833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32673884A>G	ENST00000421745.2	+	22	4640	c.4506A>G	c.(4504-4506)ccA>ccG	p.P1502P		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1502					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					ATAGCTCACCATTTGATCCAG	0.318													A|||	9	0.00179712	0.0061	0.0014	5008	,	,		14704	0.0		0.0	False		,,,				2504	0.0				p.P1502P	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A4506G						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	120.0	123.0	122.0		4506	-3.2	1.0	2	dbSNP_134	122	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	BIRC6	NM_016252.3		0,28,6475	GG,GA,AA		0.0465,0.5447,0.2153		1502/4858	32673884	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	57448	exon22			CTCACCATTTGAT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.4506A>G	2.37:g.32673884A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			A|0.998;G|0.002	0.002	strong		0.318	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
PTGES	9536	hgsc.bcm.edu	37	9	132510960	132510960	+	Silent	SNP	G	G	A	rs3205181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132510960G>A	ENST00000340607.4	-	2	217	c.183C>T	c.(181-183)agC>agT	p.S61S	PTGES_ENST00000481476.1_5'UTR	NM_004878.4	NP_004869.1	O14684	PTGES_HUMAN	prostaglandin E synthase	61					acute inflammatory response (GO:0002526)|arachidonic acid metabolic process (GO:0019369)|chronic inflammatory response (GO:0002544)|cyclooxygenase pathway (GO:0019371)|negative regulation of cell proliferation (GO:0008285)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|response to calcium ion (GO:0051592)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)	glutathione binding (GO:0043295)|prostaglandin-E synthase activity (GO:0050220)			lung(1)|skin(1)	2		Ovarian(14;0.00556)				CGTCGGGGTCGCTCCTGCAAT	0.607													G|||	132	0.0263578	0.093	0.0115	5008	,	,		16751	0.0		0.001	False		,,,				2504	0.0				p.S61S		Atlas-SNP	.											.	PTGES	7	.	0			c.C183T						PASS	.	G		367,4039	185.7+/-212.7	14,339,1850	49.0	42.0	44.0		183	-12.2	0.0	9	dbSNP_105	44	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	PTGES	NM_004878.4		14,345,6144	AA,AG,GG		0.0698,8.3296,2.8679		61/153	132510960	373,12633	2203	4300	6503	SO:0001819	synonymous_variant	9536	exon2			GGGGTCGCTCCTG	AF010316	CCDS6927.1	9q34.3	2008-07-21			ENSG00000148344	ENSG00000148344			9599	protein-coding gene	gene with protein product	"""microsomal glutathione S-transferase 1-like 1"", ""tumor protein p53 inducible protein 12"", ""p53-induced gene 12"", ""microsomal prostaglandin E synthase-1"", ""glutathione S-transferase 1-like 1"", ""MGST1-like 1"""	605172		MGST1L1		9305847, 10091672	Standard	NM_004878		Approved	MGST-IV, PIG12, MGST1-L1, TP53I12	uc004byi.3	O14684	OTTHUMG00000020791	ENST00000340607.4:c.183C>T	9.37:g.132510960G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	71	48	0.676056	NM_004878	O14900|Q5SZC0	Silent	SNP	ENST00000340607.4	37	CCDS6927.1																																																																																			G|0.969;A|0.031	0.031	strong		0.607	PTGES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054599.2	NM_004878	
TOM1	10043	hgsc.bcm.edu	37	22	35713931	35713931	+	Silent	SNP	C	C	T	rs57755951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:35713931C>T	ENST00000449058.2	+	2	239	c.114C>T	c.(112-114)gaC>gaT	p.D38D	TOM1_ENST00000425375.1_Silent_p.D38D|TOM1_ENST00000447733.1_Silent_p.D5D|TOM1_ENST00000382034.5_5'UTR|TOM1_ENST00000411850.1_Silent_p.D38D|TOM1_ENST00000436462.2_Missense_Mutation_p.T17I	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	38	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	clathrin binding (GO:0030276)			NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						AGATCTGCGACATCATCAACG	0.597													C|||	80	0.0159744	0.0582	0.0043	5008	,	,		20039	0.0		0.0	False		,,,				2504	0.0				p.D38D		Atlas-SNP	.											.	TOM1	43	.	0			c.C114T						PASS	.	C	,,,	211,4195	130.2+/-166.9	8,195,2000	107.0	106.0	106.0		15,114,114,114	5.4	1.0	22	dbSNP_129	106	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TOM1	NM_001135729.1,NM_001135730.1,NM_001135732.1,NM_005488.2	,,,	8,197,6298	TT,TC,CC		0.0233,4.7889,1.6377	,,,	5/461,38/448,38/494,38/493	35713931	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	10043	exon2			CTGCGACATCATC	AJ006973	CCDS13913.1, CCDS46696.1, CCDS46697.1, CCDS46698.1	22q13.1	2011-01-31	2001-11-28		ENSG00000100284	ENSG00000100284			11982	protein-coding gene	gene with protein product		604700	"""target of myb1 (chicken) homolog"""			10329004, 15047686	Standard	NM_005488		Approved		uc003anp.3	O60784	OTTHUMG00000150958	ENST00000449058.2:c.114C>T	22.37:g.35713931C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	197	94	0.477157	NM_001135732	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Silent	SNP	ENST00000449058.2	37	CCDS13913.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	13.28	2.189681	0.38707	0.047889	2.33E-4	ENSG00000100284	ENST00000436462	T	0.21361	2.01	5.36	5.36	0.76844	.	.	.	.	.	T	0.01695	0.0054	.	.	.	0.80722	D	1	D	0.53312	0.959	B	0.43623	0.425	T	0.08351	-1.0726	8	0.02654	T	1	-30.6633	12.4314	0.55575	0.0:0.9231:0.0:0.0769	rs57755951	17	E7EPD0	.	I	17	ENSP00000402556:T17I	ENSP00000402556:T17I	T	+	2	0	TOM1	34043931	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.017000	0.57167	2.502000	0.84385	0.561000	0.74099	ACA	C|0.982;T|0.018	0.018	strong		0.597	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488	
IVL	3713	hgsc.bcm.edu	37	1	152883608	152883608	+	Silent	SNP	G	G	A	rs7545413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152883608G>A	ENST00000368764.3	+	2	1399	c.1335G>A	c.(1333-1335)caG>caA	p.Q445Q	IVL_ENST00000392667.2_Silent_p.Q299Q			P07476	INVO_HUMAN	involucrin	445	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ATCTGGAGCAGCAGCAGGGGC	0.632													g|||	2065	0.41234	0.6808	0.2997	5008	,	,		19909	0.5615		0.1083	False		,,,				2504	0.2883				p.Q445Q		Atlas-SNP	.											.	IVL	100	.	0			c.G1335A						PASS	.	G		2399,1957		689,1021,468	22.0	26.0	25.0		1335	2.2	0.0	1	dbSNP_116	25	760,7786		39,682,3552	no	coding-synonymous	IVL	NM_005547.2		728,1703,4020	AA,AG,GG		8.893,44.9265,24.4846		445/586	152883608	3159,9743	2178	4273	6451	SO:0001819	synonymous_variant	3713	exon2			GGAGCAGCAGCAG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1335G>A	1.37:g.152883608G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	190	186	0.978947	NM_005547	Q5T7P4	Silent	SNP	ENST00000368764.3	37	CCDS1030.1																																																																																			G|0.664;A|0.336	0.336	strong		0.632	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
PLEKHG7	440107	hgsc.bcm.edu	37	12	93147907	93147907	+	Silent	SNP	A	A	T	rs9669519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:93147907A>T	ENST00000344636.3	+	6	541	c.357A>T	c.(355-357)ccA>ccT	p.P119P		NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	119	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						TCCACGTGCCAGAGCTGCTAG	0.502													T|||	3269	0.652756	0.5847	0.7017	5008	,	,		20403	0.8919		0.4861	False		,,,				2504	0.635				p.P119P		Atlas-SNP	.											.	PLEKHG7	38	.	0			c.A357T						PASS	.	T		2457,1949	553.3+/-378.7	687,1083,433	104.0	93.0	97.0		357	0.1	1.0	12	dbSNP_119	97	4211,4389	582.8+/-391.5	1035,2141,1124	no	coding-synonymous	PLEKHG7	NM_001004330.2		1722,3224,1557	TT,TA,AA		48.9651,44.2351,48.7314		119/380	93147907	6668,6338	2203	4300	6503	SO:0001819	synonymous_variant	440107	exon6			CGTGCCAGAGCTG	AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"""Pleckstrin homology (PH) domain containing"""	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.357A>T	12.37:g.93147907A>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_001004330	B2RNR7	Silent	SNP	ENST00000344636.3	37	CCDS31873.1																																																																																			A|0.440;T|0.560	0.560	strong		0.502	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330	
PDGFRL	5157	hgsc.bcm.edu	37	8	17434813	17434813	+	Missense_Mutation	SNP	G	G	A	rs114432448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17434813G>A	ENST00000541323.1	+	2	497	c.52G>A	c.(52-54)Gat>Aat	p.D18N	PDGFRL_ENST00000251630.6_Missense_Mutation_p.D18N|PDGFRL_ENST00000398074.3_Missense_Mutation_p.D18N	NM_006207.2	NP_006198.1	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like	18					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)		AGCGCTGGAGGATGGTGAGTG	0.677											OREG0018579	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	61	0.0121805	0.0431	0.0058	5008	,	,		10540	0.0		0.0	False		,,,				2504	0.0				p.D18N		Atlas-SNP	.											.	PDGFRL	27	.	0			c.G52A						PASS	.	G	ASN/ASP	171,4235	109.5+/-147.8	4,163,2036	54.0	51.0	52.0		52	0.6	0.7	8	dbSNP_132	52	0,8600		0,0,4300	yes	missense	PDGFRL	NM_006207.2	23	4,163,6336	AA,AG,GG		0.0,3.8811,1.3148	benign	18/376	17434813	171,12835	2203	4300	6503	SO:0001583	missense	5157	exon2			CTGGAGGATGGTG	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.52G>A	8.37:g.17434813G>A	ENSP00000444211:p.Asp18Asn	Somatic	152	0	0	718	WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_006207	A8K085|Q6FH04	Missense_Mutation	SNP	ENST00000541323.1	37	CCDS6003.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	G	3.726	-0.056629	0.07362	0.038811	0.0	ENSG00000104213	ENST00000251630;ENST00000541323;ENST00000398074	T;T;T	0.32023	1.47;1.47;1.47	3.59	0.567	0.17325	.	0.436898	0.23854	N	0.043902	T	0.02848	0.0085	N	0.22421	0.69	0.27009	N	0.964738	B	0.02656	0.0	B	0.01281	0.0	T	0.20538	-1.0272	10	0.09843	T	0.71	-12.0401	3.4884	0.07629	0.388:0.1982:0.4137:0.0	.	18	Q15198	PGFRL_HUMAN	N	18	ENSP00000251630:D18N;ENSP00000444211:D18N;ENSP00000381149:D18N	ENSP00000251630:D18N	D	+	1	0	PDGFRL	17479098	0.860000	0.29831	0.667000	0.29798	0.381000	0.30169	0.234000	0.17930	0.097000	0.17492	0.462000	0.41574	GAT	G|0.987;A|0.013	0.013	strong		0.677	PDGFRL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253366.3	NM_006207	
HKDC1	80201	hgsc.bcm.edu	37	10	70980243	70980243	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70980243C>A	ENST00000354624.5	+	1	185	c.52C>A	c.(52-54)Cag>Aag	p.Q18K	HKDC1_ENST00000395086.2_Missense_Mutation_p.Q18K|RP11-227H15.4_ENST00000450995.1_RNA	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	18	Hexokinase type-1 1.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						GAAGGAGGACCAGATCAAGAA	0.468																																					p.Q18K		Atlas-SNP	.											.	HKDC1	98	.	0			c.C52A						PASS	.						81.0	76.0	78.0					10																	70980243		2203	4300	6503	SO:0001583	missense	80201	exon1			GAGGACCAGATCA		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.52C>A	10.37:g.70980243C>A	ENSP00000346643:p.Gln18Lys	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.270551	0.59540	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.98968	-5.28;-5.28	5.44	5.44	0.79542	Hexokinase, N-terminal (1);	0.149729	0.47093	D	0.000250	D	0.98232	0.9415	M	0.86740	2.835	0.54753	D	0.99998	B	0.14438	0.01	B	0.20184	0.028	D	0.98393	1.0564	10	0.25106	T	0.35	-10.1756	19.279	0.94044	0.0:1.0:0.0:0.0	.	18	Q2TB90	HKDC1_HUMAN	K	18	ENSP00000346643:Q18K;ENSP00000378521:Q18K	ENSP00000346643:Q18K	Q	+	1	0	HKDC1	70650249	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.339000	0.79282	2.554000	0.86153	0.655000	0.94253	CAG	.	.	none		0.468	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130	
GRIN2B	2904	hgsc.bcm.edu	37	12	13717508	13717508	+	Silent	SNP	G	G	A	rs1806201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:13717508G>A	ENST00000609686.1	-	13	2873	c.2664C>T	c.(2662-2664)acC>acT	p.T888T		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	888				T -> P (in Ref. 5; AAA69920/AAA74930). {ECO:0000305}.	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)	TCATGGTTGCGGTGGGGGAGT	0.572													G|||	1519	0.303315	0.0703	0.3213	5008	,	,		19555	0.5208		0.2783	False		,,,				2504	0.407				p.T888T		Atlas-SNP	.											GRIN2B,NS,carcinoma,0,2	GRIN2B	303	2	0			c.C2664T	GRCh37	CM074898	GRIN2B	M	rs1806201	PASS	.	G		476,3930	220.7+/-238.1	32,412,1759	127.0	114.0	118.0		2664	-10.6	0.4	12	dbSNP_92	118	2357,6243	381.0+/-339.9	345,1667,2288	no	coding-synonymous	GRIN2B	NM_000834.3		377,2079,4047	AA,AG,GG		27.407,10.8034,21.7823		888/1485	13717508	2833,10173	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon13			GGTTGCGGTGGGG		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.2664C>T	12.37:g.13717508G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	139	52	0.374101	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			G|0.746;A|0.254	0.254	strong		0.572	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
RFX7	64864	hgsc.bcm.edu	37	15	56387142	56387142	+	Silent	SNP	G	G	A	rs34361729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56387142G>A	ENST00000559447.2	-	9	2764	c.2493C>T	c.(2491-2493)caC>caT	p.H831H	RFX7_ENST00000422057.1_Silent_p.H831H|RFX7_ENST00000317318.6_Silent_p.H928H|RFX7_ENST00000423270.1_Silent_p.H928H			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	831					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TGCTGGAAGTGTGAGATGACA	0.502													G|||	617	0.123203	0.1051	0.0836	5008	,	,		18677	0.1002		0.1491	False		,,,				2504	0.1728				p.H928H		Atlas-SNP	.											RFX7_ENST00000423270,NS,carcinoma,-1,2	RFX7	170	2	0			c.C2784T						PASS	.	G		387,3783		24,339,1722	104.0	113.0	110.0		2784	-6.1	0.1	15	dbSNP_126	110	1122,7304		78,966,3169	no	coding-synonymous	RFX7	NM_022841.5		102,1305,4891	AA,AG,GG		13.3159,9.2806,11.98		928/1461	56387142	1509,11087	2085	4213	6298	SO:0001819	synonymous_variant	64864	exon9			GGAAGTGTGAGAT			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.2493C>T	15.37:g.56387142G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	98	56	0.571429	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																				G|0.879;A|0.121	0.121	strong		0.502	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
RELN	5649	hgsc.bcm.edu	37	7	103292224	103292224	+	Silent	SNP	T	T	C	rs2072403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103292224T>C	ENST00000428762.1	-	15	1935	c.1776A>G	c.(1774-1776)gaA>gaG	p.E592E	RELN_ENST00000343529.5_Silent_p.E592E|RELN_ENST00000424685.2_Silent_p.E592E	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	592					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)		TGGTAGAAAATTCCAAGCTGA	0.458													C|||	603	0.120407	0.2209	0.111	5008	,	,		16673	0.1429		0.0567	False		,,,				2504	0.0337				p.E592E	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											RELN,NS,malignant_melanoma,-2,1	RELN	593	1	0			c.A1776G						scavenged	.	C	,	794,3612	750.5+/-412.1	80,634,1489	61.0	50.0	54.0		1776,1776	1.5	1.0	7	dbSNP_96	54	423,8177	800.0+/-407.4	10,403,3887	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	90,1037,5376	CC,CT,TT		4.9186,18.0209,9.3572	,	592/3461,592/3459	103292224	1217,11789	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon15			AGAAAATTCCAAG		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.1776A>G	7.37:g.103292224T>C		Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			T|0.899;C|0.101	0.101	strong		0.458	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
CMYA5	202333	hgsc.bcm.edu	37	5	79029383	79029383	+	Missense_Mutation	SNP	T	T	G	rs1428224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79029383T>G	ENST00000446378.2	+	2	4826	c.4795T>G	c.(4795-4797)Tct>Gct	p.S1599A		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1599			S -> A (in dbSNP:rs1428224).		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)		AGTGGAGGTATCTTCTACAGC	0.453													T|||	1383	0.276158	0.5915	0.085	5008	,	,		19423	0.3621		0.0815	False		,,,				2504	0.0971				p.S1599A		Atlas-SNP	.											.	CMYA5	643	.	0			c.T4795G						PASS	.	T	ALA/SER	1895,1867		479,937,465	121.0	122.0	121.0		4795	-2.7	0.0	5	dbSNP_88	121	714,7522		39,636,3443	yes	missense	CMYA5	NM_153610.3	99	518,1573,3908	GG,GT,TT		8.6693,49.6279,21.7453	possibly-damaging	1599/4070	79029383	2609,9389	1881	4118	5999	SO:0001583	missense	202333	exon2			GAGGTATCTTCTA	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.4795T>G	5.37:g.79029383T>G	ENSP00000394770:p.Ser1599Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	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	626	0.2866300366300366	304	0.6178861788617886	31	0.0856353591160221	232	0.40559440559440557	59	0.07783641160949868	T	12.08	1.829387	0.32329	0.503721	0.086693	ENSG00000164309	ENST00000446378	T	0.06371	3.31	4.78	-2.73	0.05950	.	0.990258	0.08208	N	0.981160	T	0.00012	0.0000	L	0.47190	1.495	0.80722	P	0.0	B	0.14438	0.01	B	0.12156	0.007	T	0.47249	-0.9132	9	0.06891	T	0.86	.	0.0836	0.00034	0.3081:0.2046:0.1595:0.3278	rs1428224;rs16877138;rs59088137;rs1428224	1599	Q8N3K9	CMYA5_HUMAN	A	1599	ENSP00000394770:S1599A	ENSP00000394770:S1599A	S	+	1	0	CMYA5	79065139	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.102000	0.10956	-0.059000	0.13154	-0.316000	0.08728	TCT	T|0.702;G|0.298	0.298	strong		0.453	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
PODNL1	79883	hgsc.bcm.edu	37	19	14043843	14043843	+	Missense_Mutation	SNP	C	C	T	rs80103045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14043843C>T	ENST00000339560.5	-	8	1487	c.1214G>A	c.(1213-1215)cGc>cAc	p.R405H	PODNL1_ENST00000254320.3_Missense_Mutation_p.R323H|PODNL1_ENST00000538371.2_Missense_Mutation_p.R403H|PODNL1_ENST00000538517.2_Missense_Mutation_p.R314H	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	405	Leu-rich.					proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			ACGCAACCGGCGGAAGGCCCG	0.711													C|||	153	0.0305511	0.1074	0.0029	5008	,	,		15309	0.0		0.001	False		,,,				2504	0.0082				p.R405H		Atlas-SNP	.											.	PODNL1	27	.	0			c.G1214A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	318,3856		6,306,1775	6.0	7.0	7.0		1208,941,1214	3.8	0.9	19	dbSNP_131	7	17,8171		0,17,4077	yes	missense,missense,missense	PODNL1	NM_001146254.1,NM_001146255.1,NM_024825.3	29,29,29	6,323,5852	TT,TC,CC		0.2076,7.6186,2.7099	probably-damaging,probably-damaging,probably-damaging	403/511,314/422,405/513	14043843	335,12027	2087	4094	6181	SO:0001583	missense	79883	exon8			AACCGGCGGAAGG	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.1214G>A	19.37:g.14043843C>T	ENSP00000345175:p.Arg405His	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_024825	B7Z564|Q9H5G9	Missense_Mutation	SNP	ENST00000339560.5	37	CCDS12300.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	13.68	2.309090	0.40895	0.076186	0.002076	ENSG00000132000	ENST00000538371;ENST00000538517;ENST00000339560;ENST00000545071;ENST00000254320	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	4.79	3.76	0.43208	.	0.451987	0.18547	N	0.138005	T	0.02267	0.0070	N	0.16066	0.365	0.26971	N	0.965586	B;B;B;B	0.29037	0.046;0.231;0.113;0.224	B;B;B;B	0.33690	0.046;0.115;0.052;0.168	T	0.04400	-1.0954	10	0.51188	T	0.08	.	10.0503	0.42212	0.0:0.9024:0.0:0.0976	.	403;323;314;405	F5H7F9;B7Z3M0;G3V1J6;Q6PEZ8	.;.;.;PONL1_HUMAN	H	403;314;405;255;323	ENSP00000442553:R403H;ENSP00000440080:R314H;ENSP00000345175:R405H;ENSP00000254320:R323H	ENSP00000254320:R323H	R	-	2	0	PODNL1	13904843	0.997000	0.39634	0.903000	0.35520	0.313000	0.28021	2.510000	0.45468	1.015000	0.39444	0.453000	0.30009	CGC	C|0.980;T|0.020	0.020	strong		0.711	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825	
LILRB3	11025	hgsc.bcm.edu	37	19	54726237	54726237	+	Missense_Mutation	SNP	C	C	G	rs138323850		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54726237C>G	ENST00000391750.1	-	4	404	c.268G>C	c.(268-270)Gag>Cag	p.E90Q	LILRA6_ENST00000391735.3_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000245620.9_Missense_Mutation_p.E90Q|LILRB3_ENST00000407860.2_Intron|LILRB3_ENST00000346401.6_Missense_Mutation_p.E90Q|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000424807.1_Missense_Mutation_p.E90Q|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	90	Ig-like C2-type 1.		E -> Q (in dbSNP:rs1052963). {ECO:0000269|PubMed:9548455}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.E90Q(1)		endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCATGGTGCTCTGTCATGGAT	0.557																																					p.E90Q		Atlas-SNP	.											LILRB3,NS,carcinoma,0,1	LILRB3	67	1	1	Substitution - Missense(1)	prostate(1)	c.G268C						scavenged	.						87.0	123.0	111.0					19																	54726237		2019	4025	6044	SO:0001583	missense	11025	exon3			GGTGCTCTGTCAT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.268G>C	19.37:g.54726237C>G	ENSP00000375630:p.Glu90Gln	Somatic	1123	0	0		WXS	Illumina HiSeq	Phase_I	427	14	0.0327869	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	G	0.767	-0.767250	0.02974	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000445347	T;T;T;T;T	0.13196	2.61;2.61;2.61;2.61;2.61	3.08	-6.17	0.02091	Immunoglobulin-like fold (1);	2.768340	0.01040	N	0.004297	T	0.09818	0.0241	L	0.39245	1.2	0.09310	N	1	B;B	0.22800	0.037;0.075	B;B	0.27608	0.002;0.081	T	0.31806	-0.9930	10	0.12103	T	0.63	.	3.0186	0.06067	0.1961:0.2034:0.4352:0.1653	.	90;90	O75022;O75022-3	LIRB3_HUMAN;.	Q	90	ENSP00000375630:E90Q;ENSP00000412771:E90Q;ENSP00000345184:E90Q;ENSP00000245620:E90Q;ENSP00000388199:E90Q	ENSP00000245620:E90Q	E	-	1	0	LILRB3	59418049	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.048000	0.00156	-2.865000	0.00325	-0.957000	0.02645	GAG	C|0.333;G|0.667	0.667	strong		0.557	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
WFDC8	90199	hgsc.bcm.edu	37	20	44184375	44184375	+	Missense_Mutation	SNP	T	T	C	rs2250860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44184375T>C	ENST00000357199.4	-	4	488	c.410A>G	c.(409-411)aAt>aGt	p.N137S	WFDC8_ENST00000289953.2_Missense_Mutation_p.N137S	NM_181510.2	NP_852611.2	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8	137	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.		N -> S (in dbSNP:rs2250860). {ECO:0000269|PubMed:12206714}.			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			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)				GGCATCCTCATTTAAGAAGTT	0.438													C|||	1419	0.283347	0.3707	0.3444	5008	,	,		19547	0.0585		0.4016	False		,,,				2504	0.2321				p.N137S		Atlas-SNP	.											.	WFDC8	28	.	0			c.A410G						PASS	.	C	SER/ASN,SER/ASN	1650,2756	658.8+/-400.5	297,1056,850	136.0	120.0	126.0		410,410	-4.4	0.0	20	dbSNP_100	126	3568,5032	628.9+/-398.2	770,2028,1502	yes	missense,missense	WFDC8	NM_130896.2,NM_181510.2	46,46	1067,3084,2352	CC,CT,TT		41.4884,37.4489,40.1199	benign,benign	137/242,137/242	44184375	5218,7788	2203	4300	6503	SO:0001583	missense	90199	exon4			TCCTCATTTAAGA	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.410A>G	20.37:g.44184375T>C	ENSP00000361735:p.Asn137Ser	Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	188	188	1	NM_181510	E1P623|Q5TDV2|Q96A34	Missense_Mutation	SNP	ENST00000357199.4	37	CCDS13361.1	634	0.2902930402930403	172	0.34959349593495936	131	0.36187845303867405	27	0.0472027972027972	304	0.40105540897097625	C	0.065	-1.215450	0.01542	0.374489	0.414884	ENSG00000158901	ENST00000357199;ENST00000289953	T;T	0.51325	0.71;0.71	4.26	-4.39	0.03611	Proteinase inhibitor I2, Kunitz metazoa (6);Proteinase inhibitor I2, Kunitz, conserved site (1);	0.838014	0.10808	N	0.631962	T	0.00012	0.0000	N	0.00387	-1.565	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.21690	-1.0238	9	0.02654	T	1	.	6.9775	0.24683	0.0:0.2021:0.3888:0.4091	rs2250860;rs17348584;rs58854739;rs2250860	137	Q8IUA0	WFDC8_HUMAN	S	137	ENSP00000361735:N137S;ENSP00000289953:N137S	ENSP00000289953:N137S	N	-	2	0	WFDC8	43617789	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.703000	0.01900	-1.210000	0.02627	-0.119000	0.15052	AAT	T|0.663;C|0.337	0.337	strong		0.438	WFDC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106958.1		
CSF2	1437	hgsc.bcm.edu	37	5	131411460	131411460	+	Missense_Mutation	SNP	T	T	C	rs25882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:131411460T>C	ENST00000296871.2	+	4	384	c.350T>C	c.(349-351)aTt>aCt	p.I117T		NM_000758.3	NP_000749.2	P04141	CSF2_HUMAN	colony stimulating factor 2 (granulocyte-macrophage)	117			I -> T (in dbSNP:rs25882). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6, ECO:0000269|Ref.9}.		cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|embryonic placenta development (GO:0001892)|epithelial fluid transport (GO:0042045)|immune response (GO:0006955)|macrophage activation (GO:0042116)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cytolysis (GO:0045918)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of podosome assembly (GO:0071803)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	granulocyte macrophage colony-stimulating factor receptor binding (GO:0005129)			skin(1)	1		all_cancers(142;4.28e-07)|all_lung(232;2.81e-05)|Lung NSC(810;0.000693)|Lung SC(612;0.122)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCAACCCAGATTATCACCTTT	0.463													T|||	1752	0.34984	0.3169	0.2709	5008	,	,		15704	0.622		0.2465	False		,,,				2504	0.2761				p.I117T		Atlas-SNP	.											.	CSF2	2	.	0			c.T350C	GRCh37	CM004548	CSF2	M	rs25882	PASS	.	T	THR/ILE	1407,2999	458.4+/-352.0	236,935,1032	110.0	131.0	124.0		350	-1.5	0.0	5	dbSNP_76	124	1824,6776	326.6+/-317.4	190,1444,2666	yes	missense	CSF2	NM_000758.2	89	426,2379,3698	CC,CT,TT		21.2093,31.9337,24.8424	benign	117/145	131411460	3231,9775	2203	4300	6503	SO:0001583	missense	1437	exon4			CCCAGATTATCAC	M11734	CCDS4150.1	5q23-q31	2012-10-02			ENSG00000164400	ENSG00000164400			2434	protein-coding gene	gene with protein product	"""sargramostim"", ""molgramostin"", ""granulocyte-macrophage colony stimulating factor"""	138960				3898082, 2999978	Standard	NM_000758		Approved	GM-CSF, GMCSF	uc003kwf.4	P04141	OTTHUMG00000059637	ENST00000296871.2:c.350T>C	5.37:g.131411460T>C	ENSP00000296871:p.Ile117Thr	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_000758	Q14CE8|Q2VPI8|Q8NFI6	Missense_Mutation	SNP	ENST00000296871.2	37	CCDS4150.1	808	0.36996336996337	160	0.3252032520325203	92	0.2541436464088398	362	0.6328671328671329	194	0.2559366754617414	T	10.95	1.494396	0.26774	0.319337	0.212093	ENSG00000164400	ENST00000296871	T	0.31247	1.5	4.69	-1.53	0.08611	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.952780	0.02234	N	0.065127	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.45308	-0.9270	9	0.15066	T	0.55	3.7898	2.6539	0.05007	0.3322:0.2445:0.0:0.4234	rs25882;rs630043;rs1126706;rs1801712;rs2229043;rs3181894;rs3854262;rs17414791;rs52812898;rs25882	117	P04141	CSF2_HUMAN	T	117	ENSP00000296871:I117T	ENSP00000296871:I117T	I	+	2	0	CSF2	131439359	0.000000	0.05858	0.000000	0.03702	0.969000	0.65631	-0.458000	0.06737	-0.195000	0.10382	0.482000	0.46254	ATT	C|0.319;N|0.000	0.319	strong		0.463	CSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132636.2	NM_000758	
ST6GAL2	84620	hgsc.bcm.edu	37	2	107460162	107460162	+	Missense_Mutation	SNP	G	G	A	rs80079355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:107460162G>A	ENST00000409382.3	-	2	882	c.272C>T	c.(271-273)gCg>gTg	p.A91V	ST6GAL2_ENST00000361686.4_Missense_Mutation_p.A91V|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000409087.3_Missense_Mutation_p.A91V	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	91					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						TCCAGGCCCCGCATGAAAGGA	0.622													G|||	254	0.0507188	0.1755	0.0216	5008	,	,		14128	0.005		0.002	False		,,,				2504	0.0				p.A91V		Atlas-SNP	.											ST6GAL2,rectum,carcinoma,0,1	ST6GAL2	159	1	0			c.C272T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	611,3739		41,529,1605	30.0	36.0	34.0		272,272,272	-1.4	0.0	2	dbSNP_131	34	18,8526		0,18,4254	yes	missense,missense,missense	ST6GAL2	NM_001142351.1,NM_001142352.1,NM_032528.2	64,64,64	41,547,5859	AA,AG,GG		0.2107,14.046,4.8782	benign,benign,benign	91/530,91/467,91/530	107460162	629,12265	2175	4272	6447	SO:0001583	missense	84620	exon2			GGCCCCGCATGAA	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.272C>T	2.37:g.107460162G>A	ENSP00000386942:p.Ala91Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	37	CCDS2073.1	106	0.048534798534798536	91	0.18495934959349594	8	0.022099447513812154	6	0.01048951048951049	1	0.0013192612137203166	G	10.52	1.374099	0.24857	0.14046	0.002107	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.29655	2.56;2.56;1.56	5.35	-1.35	0.09114	.	1.615520	0.03144	N	0.166966	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B	0.20261	0.043;0.001	B;B	0.08055	0.003;0.001	T	0.13124	-1.0521	9	0.05525	T	0.97	-0.9807	5.443	0.16519	0.3548:0.2384:0.4068:0.0	.	91;91	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	V	91	ENSP00000355273:A91V;ENSP00000386942:A91V;ENSP00000387332:A91V	ENSP00000355273:A91V	A	-	2	0	ST6GAL2	106826594	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.979000	0.03774	-0.003000	0.14444	-0.150000	0.13652	GCG	G|0.962;A|0.038	0.038	strong		0.622	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
SLC5A5	6528	hgsc.bcm.edu	37	19	17988794	17988794	+	Silent	SNP	C	C	T	rs35209536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17988794C>T	ENST00000222248.3	+	7	1208	c.861C>T	c.(859-861)gtC>gtT	p.V287V		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	287					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						TCAACCAGGTCGGCCTGTTCC	0.632													C|||	97	0.019369	0.0703	0.0058	5008	,	,		18147	0.0		0.0	False		,,,				2504	0.0				p.V287V	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.C861T						PASS	.	C		255,4151	148.4+/-182.8	10,235,1958	104.0	75.0	85.0		861	0.3	1.0	19	dbSNP_126	85	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC5A5	NM_000453.2		10,236,6257	TT,TC,CC		0.0116,5.7876,1.9683		287/644	17988794	256,12750	2203	4300	6503	SO:0001819	synonymous_variant	6528	exon7			CCAGGTCGGCCTG		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"""Solute carriers"""	11040	protein-coding gene	gene with protein product		601843	"""solute carrier family 5 (sodium iodide symporter), member 5"""			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.861C>T	19.37:g.17988794C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_000453	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	37	CCDS12368.1																																																																																			C|0.982;T|0.018	0.018	strong		0.632	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1		
TAS2R43	259289	hgsc.bcm.edu	37	12	11244194	11244194	+	Missense_Mutation	SNP	T	T	C	rs71443637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11244194T>C	ENST00000531678.1	-	1	718	c.635A>G	c.(634-636)cAt>cGt	p.H212R	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	212				H -> R (in Ref. 1; AAM19328, 3; AAU21145 and 5; AAI17424). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TCCTTTACCATGGAGCTGCAT	0.408													.|||	3114	0.621805	0.0998	0.7104	5008	,	,		13446	0.9425		0.7525	False		,,,				2504	0.7996				p.H212R		Atlas-SNP	.											TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	0			c.A635G						PASS	.						123.0	99.0	107.0					12																	11244194		2155	4165	6320	SO:0001583	missense	259289	exon1			TTACCATGGAGCT	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.635A>G	12.37:g.11244194T>C	ENSP00000431719:p.His212Arg	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	173	139	0.803468	NM_176884	P59546|Q645X4	Missense_Mutation	SNP	ENST00000531678.1	37	CCDS53749.1	949	0.43452380952380953	28	0.056910569105691054	163	0.45027624309392267	439	0.7674825174825175	319	0.420844327176781	-	2.129	-0.399500	0.04865	.	.	ENSG00000255374	ENST00000531678	T	0.00737	5.76	1.45	-1.32	0.09201	.	.	.	.	.	T	0.00012	0.0000	M	0.86178	2.8	0.80722	P	0.0	.	.	.	.	.	.	T	0.07028	-1.0794	6	0.52906	T	0.07	.	4.3248	0.11034	0.0:0.4339:0.0:0.5661	.	.	.	.	R	212	ENSP00000431719:H212R	ENSP00000431719:H212R	H	-	2	0	TAS2R43	11135461	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.381000	0.07417	-0.374000	0.07967	-1.273000	0.01405	CAT	T|0.599;C|0.401	0.401	strong		0.408	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
EPHX1	2052	hgsc.bcm.edu	37	1	226026406	226026406	+	Missense_Mutation	SNP	A	A	G	rs2234922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226026406A>G	ENST00000366837.4	+	4	612	c.416A>G	c.(415-417)cAt>cGt	p.H139R	EPHX1_ENST00000272167.5_Missense_Mutation_p.H139R|RP11-285F7.2_ENST00000424332.1_RNA	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	139			H -> R (in allele EPHX1*4; 62% of wild type enzyme activity; dbSNP:rs2234922). {ECO:0000269|PubMed:11058921, ECO:0000269|PubMed:12173035, ECO:0000269|PubMed:7516776, ECO:0000269|Ref.8}.		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)			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)					CCCGCAGGCCATACCCCGAAG	0.607													G|||	1079	0.215455	0.3533	0.1427	5008	,	,		16264	0.1181		0.164	False		,,,				2504	0.2342				p.H139R		Atlas-SNP	.											.	EPHX1	57	.	0			c.A416G	GRCh37	CM024366	EPHX1	M	rs2234922	PASS	.	G	ARG/HIS,ARG/HIS	1484,2922	677.4+/-403.4	250,984,969	88.0	97.0	94.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	416,416	2.5	0.0	1	dbSNP_98	94	1763,6837	734.5+/-406.9	191,1381,2728	yes	missense,missense	EPHX1	NM_000120.3,NM_001136018.2	29,29	441,2365,3697	GG,GA,AA		20.5,33.6813,24.9654	benign,benign	139/456,139/456	226026406	3247,9759	2203	4300	6503	SO:0001583	missense	2052	exon4			CAGGCCATACCCC	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.416A>G	1.37:g.226026406A>G	ENSP00000355802:p.His139Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	114	65	0.570175	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Missense_Mutation	SNP	ENST00000366837.4	37	CCDS1547.1	404	0.184981684981685	165	0.3353658536585366	50	0.13812154696132597	62	0.10839160839160839	127	0.16754617414248021	G	0.008	-1.918526	0.00498	0.336813	0.205	ENSG00000143819	ENST00000445856;ENST00000272167;ENST00000366837	T;T;T	0.03524	3.9;3.9;3.9	5.83	2.55	0.30701	Epoxide hydrolase, N-terminal (1);	0.550791	0.21311	N	0.076624	T	0.00012	0.0000	N	0.00841	-1.15	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40478	-0.9561	9	0.12430	T	0.62	-11.8523	7.654	0.28365	0.5145:0.0:0.4855:0.0	rs2234922;rs59975602;rs2234922	139	P07099	HYEP_HUMAN	R	139	ENSP00000398491:H139R;ENSP00000272167:H139R;ENSP00000355802:H139R	ENSP00000272167:H139R	H	+	2	0	EPHX1	224093029	0.002000	0.14202	0.004000	0.12327	0.035000	0.12851	0.819000	0.27308	0.379000	0.24794	-0.227000	0.12334	CAT	A|0.779;G|0.221	0.221	strong		0.607	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
ACOX2	8309	hgsc.bcm.edu	37	3	58512285	58512285	+	Silent	SNP	T	T	C	rs13097249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:58512285T>C	ENST00000302819.5	-	10	1545	c.1254A>G	c.(1252-1254)tcA>tcG	p.S418S	ACOX2_ENST00000459701.2_Silent_p.S404S	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	418					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		CACTCAGCTTTGAGTAGCCAT	0.587													T|||	245	0.0489217	0.1362	0.0317	5008	,	,		19019	0.0		0.0338	False		,,,				2504	0.0092				p.S418S		Atlas-SNP	.											.	ACOX2	53	.	0			c.A1254G						PASS	.	T		503,3903	231.4+/-245.2	22,459,1722	85.0	71.0	75.0		1254	-8.8	0.4	3	dbSNP_121	75	390,8210	126.2+/-184.7	8,374,3918	no	coding-synonymous	ACOX2	NM_003500.3		30,833,5640	CC,CT,TT		4.5349,11.4163,6.8661		418/682	58512285	893,12113	2203	4300	6503	SO:0001819	synonymous_variant	8309	exon10			CAGCTTTGAGTAG	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.1254A>G	3.37:g.58512285T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	186	76	0.408602	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			T|0.932;C|0.068	0.068	strong		0.587	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
SMG6	23293	hgsc.bcm.edu	37	17	2203462	2203462	+	Silent	SNP	T	T	C	rs140746531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2203462T>C	ENST00000263073.6	-	2	635	c.585A>G	c.(583-585)ccA>ccG	p.P195P	SMG6_ENST00000544865.1_Silent_p.P164P	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	195	Interaction with telomeric DNA.				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						CAGCCCTGTCTGGTTTATTCG	0.512													T|||	3	0.000599042	0.0023	0.0	5008	,	,		17852	0.0		0.0	False		,,,				2504	0.0				p.P195P	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A585G						PASS	.	T	,	6,4400	12.9+/-30.5	0,6,2197	249.0	270.0	263.0		492,585	0.1	0.3	17	dbSNP_134	263	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SMG6	NM_001170957.1,NM_017575.4	,	0,6,6497	CC,CT,TT		0.0,0.1362,0.0461	,	164/1389,195/1420	2203462	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	23293	exon2			CCTGTCTGGTTTA	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.585A>G	17.37:g.2203462T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	37	CCDS11016.1																																																																																			T|1.000;C|0.000	0.000	strong		0.512	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549464	32549464	+	Silent	SNP	T	T	C	rs78767604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32549464T>C	ENST00000360004.5	-	3	627	c.522A>G	c.(520-522)acA>acG	p.T174T		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	174	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						GGATCAGGCCTGTGGACACCA	0.547										Multiple Myeloma(14;0.17)																											p.T174T		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.A522G						PASS	.						130.0	149.0	142.0					6																	32549464		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon3			CAGGCCTGTGGAC	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.522A>G	6.37:g.32549464T>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	340	92	0.270588	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			T|0.855;C|0.145	0.145	strong		0.547	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
POU5F1B	5462	hgsc.bcm.edu	37	8	128428592	128428592	+	Missense_Mutation	SNP	G	G	A	rs140000439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:128428592G>A	ENST00000465342.2	+	2	1638	c.481G>A	c.(481-483)Gga>Aga	p.G161R	POU5F1B_ENST00000391675.1_Missense_Mutation_p.G161R|CASC8_ENST00000523825.1_RNA|CASC8_ENST00000502082.1_RNA|CASC8_ENST00000501396.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	161	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|prostate(1)|urinary_tract(1)	3						GATCACCCTGGGATATACACA	0.522													g|||	78	0.0155751	0.053	0.0115	5008	,	,		17902	0.0		0.0	False		,,,				2504	0.0				p.G161R		Atlas-SNP	.											.	POU5F1B	32	.	0			c.G481A						PASS	.	G	ARG/GLY	73,1311		2,69,621	47.0	54.0	52.0		481	1.1	0.8	8	dbSNP_134	52	0,3182		0,0,1591	no	missense	POU5F1B	NM_001159542.1	125	2,69,2212	AA,AG,GG		0.0,5.2746,1.5988	probably-damaging	161/360	128428592	73,4493	692	1591	2283	SO:0001583	missense	5462	exon1			ACCCTGGGATATA	AF268615	CCDS55274.1	8q24.21	2011-06-20	2009-04-15	2009-04-15	ENSG00000212993	ENSG00000212993		"""Homeoboxes / POU class"""	9223	protein-coding gene	gene with protein product		615739	"""POU domain class 5, transcription factor 1 pseudogene 1"", ""POU class 5 homeobox 1 pseudogene 1"""	OTF3P1, POU5F1P1		1408763	Standard	NM_001159542		Approved	OTF3C	uc003ysf.3	Q06416	OTTHUMG00000157807	ENST00000465342.2:c.481G>A	8.37:g.128428592G>A	ENSP00000419298:p.Gly161Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	161	81	0.503106	NM_001159542	D5K9S4|D5K9S9|D5K9T0|D5K9T1|D5K9T3|D5K9U3|D5K9U6|D5K9V4|D5K9V6|D5K9W0|D5K9W2|D5K9W7|D5K9X2|D5K9X3|D5K9X5|D5K9X8|D5K9X9|E9LRB1|E9LRB2|E9LRH5|E9LRH6|E9LRH7|E9LRK4|E9LRK5|E9LRK7|E9LRK8|E9LRM7|E9LRM9|E9LRN2|E9LRN4|E9LRN5|E9LRP8|E9LRQ0|E9LRQ2|E9LRQ3|E9LRQ4|E9LRQ5|E9LRS3|Q2VIK6|Q9BZV7|Q9BZV9	Missense_Mutation	SNP	ENST00000465342.2	37	CCDS55274.1	32	0.014652014652014652	28	0.056910569105691054	4	0.011049723756906077	0	0.0	0	0.0	G	23.4	4.412629	0.83340	0.052746	0.0	ENSG00000212993	ENST00000465342;ENST00000391675	T;T	0.77877	-1.13;-1.13	1.14	1.14	0.20703	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.40144	N	0.001164	T	0.50137	0.1598	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74328	-0.3701	10	0.87932	D	0	.	8.3083	0.32055	0.0:0.0:1.0:0.0	.	161	Q06416	P5F1B_HUMAN	R	161	ENSP00000419298:G161R;ENSP00000375557:G161R	ENSP00000375557:G161R	G	+	1	0	POU5F1B	128497774	1.000000	0.71417	0.759000	0.31340	0.727000	0.41649	6.555000	0.73928	0.968000	0.38212	0.134000	0.15878	GGA	G|0.985;A|0.015	0.015	strong		0.522	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542	
MMAB	326625	hgsc.bcm.edu	37	12	110011230	110011230	+	Missense_Mutation	SNP	C	C	T	rs10774775|rs36013132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:110011230C>T	ENST00000545712.2	-	1	449	c.56G>A	c.(55-57)cGc>cAc	p.R19H	MVK_ENST00000539696.1_5'Flank|MMAB_ENST00000266839.5_5'UTR|MVK_ENST00000539575.1_5'Flank|MVK_ENST00000541384.1_5'Flank|MVK_ENST00000228510.3_5'Flank|MVK_ENST00000392727.3_5'Flank|MMAB_ENST00000540016.1_Missense_Mutation_p.R19H|MVK_ENST00000535044.1_3'UTR	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	49	0	0		WXS	Illumina HiSeq	Phase_I	77	49	0.636364	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		
SLITRK2	84631	hgsc.bcm.edu	37	X	144904252	144904252	+	Silent	SNP	G	G	A	rs3810704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:144904252G>A	ENST00000370490.1	+	1	4564	c.309G>A	c.(307-309)acG>acA	p.T103T	SLITRK2_ENST00000447897.2_Silent_p.T103T|SLITRK2_ENST00000413937.2_Silent_p.T103T|SLITRK2_ENST00000434188.2_Silent_p.T103T|SLITRK2_ENST00000428560.2_Silent_p.T103T			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	103					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					AGATCCGAACGGGGGCATTCA	0.483													G|||	592	0.156821	0.1407	0.0591	3775	,	,		14738	0.0407		0.1412	False		,,,				2504	0.1861				p.T103T		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G309A						PASS	.	G	,,,,,,,	719,3116		63,494,99,1075,472	72.0	63.0	66.0		309,309,309,309,309,309,309,309	-9.8	0.0	X	dbSNP_107	66	1124,5604		56,670,342,1702,1530	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLITRK2	NM_001144003.2,NM_001144004.2,NM_001144005.2,NM_001144006.2,NM_001144008.2,NM_001144009.2,NM_001144010.2,NM_032539.4	,,,,,,,	119,1164,441,2777,2002	AA,AG,A,GG,G		16.7063,18.7484,17.4477	,,,,,,,	103/846,103/846,103/846,103/846,103/846,103/846,103/846,103/846	144904252	1843,8720	2203	4300	6503	SO:0001819	synonymous_variant	84631	exon5			CCGAACGGGGGCA	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.309G>A	X.37:g.144904252G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																			G|0.836;A|0.164	0.164	strong		0.483	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
SYNPO2L	79933	hgsc.bcm.edu	37	10	75407887	75407887	+	Missense_Mutation	SNP	G	G	T	rs57006992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:75407887G>T	ENST00000394810.2	-	4	1672	c.1523C>A	c.(1522-1524)cCc>cAc	p.P508H	SYNPO2L_ENST00000372873.4_Missense_Mutation_p.P284H	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	508	Pro-rich.		P -> H (in dbSNP:rs57006992).			cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					AGACAAGAAGGGGGGTGGGGC	0.667													G|||	383	0.0764776	0.2511	0.0346	5008	,	,		12697	0.0089		0.007	False		,,,				2504	0.0112				p.P508H		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.C1523A						PASS	.	G	HIS/PRO,HIS/PRO	846,3216		60,726,1245	6.0	9.0	8.0		1523,851	4.4	0.7	10	dbSNP_129	8	51,7955		2,47,3954	yes	missense,missense	SYNPO2L	NM_001114133.1,NM_024875.3	77,77	62,773,5199	TT,TG,GG		0.637,20.8272,7.4329	probably-damaging,probably-damaging	508/978,284/754	75407887	897,11171	2031	4003	6034	SO:0001583	missense	79933	exon4			AAGAAGGGGGGTG	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.1523C>A	10.37:g.75407887G>T	ENSP00000378289:p.Pro508His	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_001114133	A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	37	CCDS44438.1	144	0.06593406593406594	115	0.23373983739837398	16	0.04419889502762431	7	0.012237762237762238	6	0.0079155672823219	G	12.87	2.067278	0.36470	0.208272	0.00637	ENSG00000166317	ENST00000372873;ENST00000372872;ENST00000394810	T;T;T	0.35048	1.85;1.33;2.16	5.31	4.41	0.53225	.	0.264551	0.37715	N	0.001977	T	0.00012	0.0000	L	0.40543	1.245	0.22066	P	0.999386352	B;B	0.33171	0.278;0.4	B;B	0.36464	0.07;0.225	T	0.15578	-1.0432	9	0.62326	D	0.03	-5.2926	15.6046	0.76652	0.0:0.0:0.8615:0.1385	rs57006992	508;284	Q9H987;Q9H987-2	SYP2L_HUMAN;.	H	284;508;508	ENSP00000361964:P284H;ENSP00000361963:P508H;ENSP00000378289:P508H	ENSP00000361963:P508H	P	-	2	0	SYNPO2L	75077893	0.994000	0.37717	0.666000	0.29783	0.768000	0.43524	2.544000	0.45761	1.474000	0.48178	-0.268000	0.10319	CCC	G|0.933;T|0.067	0.067	strong		0.667	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
C10orf90	118611	hgsc.bcm.edu	37	10	128193368	128193368	+	Missense_Mutation	SNP	C	C	T	rs11245008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:128193368C>T	ENST00000284694.7	-	3	521	c.401G>A	c.(400-402)cGc>cAc	p.R134H	C10orf90_ENST00000356858.3_Missense_Mutation_p.R87H|C10orf90_ENST00000544758.1_Missense_Mutation_p.R231H|C10orf90_ENST00000454341.1_Missense_Mutation_p.R134H|C10orf90_ENST00000392694.1_Missense_Mutation_p.R87H|C10orf90_ENST00000368674.1_5'UTR	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	134	Required for interaction with HDAC1. {ECO:0000250}.		R -> H (in dbSNP:rs11245008).		mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		AAACCCTCTGCGGGGGCCCCC	0.672											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1077	0.215056	0.4592	0.1599	5008	,	,		14007	0.129		0.1153	False		,,,				2504	0.1155				p.R134H		Atlas-SNP	.											.	C10orf90	121	.	0			c.G401A						PASS	.	C	HIS/ARG	1634,2730		321,992,869	28.0	33.0	32.0		401	-9.9	0.0	10	dbSNP_120	32	1103,7457		75,953,3252	yes	missense	C10orf90	NM_001004298.2	29	396,1945,4121	TT,TC,CC		12.8855,37.4427,21.1777	benign	134/700	128193368	2737,10187	2182	4280	6462	SO:0001583	missense	118611	exon3			CCTCTGCGGGGGC	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"""fragile-site associated tumor suppressor"""					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.401G>A	10.37:g.128193368C>T	ENSP00000284694:p.Arg134His	Somatic	105	0	0	1563	WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	37	CCDS31310.1	449	0.20558608058608058	217	0.4410569105691057	59	0.16298342541436464	85	0.1486013986013986	88	0.11609498680738786	C	9.636	1.137739	0.21123	0.374427	0.128855	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.26810	2.01;2.01;2.03;2.02;1.71	4.97	-9.93	0.00452	.	1.535690	0.03830	N	0.268998	T	0.00012	0.0000	N	0.04636	-0.2	0.80722	P	0.0	B;B;B;B;B	0.18741	0.003;0.008;0.03;0.008;0.008	B;B;B;B;B	0.14578	0.003;0.002;0.011;0.003;0.003	T	0.31052	-0.9957	9	0.30078	T	0.28	-0.0577	11.4554	0.50179	0.0:0.2321:0.1567:0.6112	rs11245008;rs60449744;rs11245008	231;231;87;134;134	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	H	87;134;134;231;134;87;87	ENSP00000284694:R134H;ENSP00000398786:R134H;ENSP00000444369:R231H;ENSP00000405995:R134H;ENSP00000376459:R87H	ENSP00000284694:R134H	R	-	2	0	C10orf90	128183358	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-2.225000	0.01212	-3.872000	0.00096	-1.421000	0.01109	CGC	C|0.781;T|0.219	0.219	strong		0.672	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
LRP1B	53353	hgsc.bcm.edu	37	2	141625346	141625346	+	Silent	SNP	T	T	C	rs79054985	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:141625346T>C	ENST00000389484.3	-	27	5363	c.4392A>G	c.(4390-4392)cgA>cgG	p.R1464R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1464					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)		ATTCATGACCTCGGATGATTT	0.403										TSP Lung(27;0.18)			T|||	172	0.034345	0.1203	0.013	5008	,	,		14463	0.004		0.0	False		,,,				2504	0.0				p.R1464R	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A4392G						PASS	.	T		506,3900	228.8+/-243.5	35,436,1732	119.0	120.0	119.0		4392	-6.3	0.8	2	dbSNP_132	119	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	LRP1B	NM_018557.2		35,440,6028	CC,CT,TT		0.0465,11.4843,3.9213		1464/4600	141625346	510,12496	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon27			ATGACCTCGGATG	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.4392A>G	2.37:g.141625346T>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	175	87	0.497143	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			T|0.965;C|0.035	0.035	strong		0.403	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
SYCP2	10388	hgsc.bcm.edu	37	20	58441612	58441612	+	Silent	SNP	C	C	T	rs58905758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58441612C>T	ENST00000357552.3	-	40	4383	c.4158G>A	c.(4156-4158)acG>acA	p.T1386T	SYCP2_ENST00000371001.2_Silent_p.T1386T			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	1386					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			TCCAAGACTGCGTAGTAAAAT	0.318													C|||	87	0.0173722	0.0635	0.0029	5008	,	,		15377	0.0		0.001	False		,,,				2504	0.0				p.T1386T		Atlas-SNP	.											.	SYCP2	204	.	0			c.G4158A						PASS	.	C		199,4207	122.5+/-159.9	4,191,2008	85.0	87.0	86.0		4158	-2.6	0.1	20	dbSNP_129	86	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	SYCP2	NM_014258.2		4,193,6304	TT,TC,CC		0.0233,4.5166,1.5459		1386/1531	58441612	201,12801	2203	4298	6501	SO:0001819	synonymous_variant	10388	exon39			AGACTGCGTAGTA	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.4158G>A	20.37:g.58441612C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	47	29	0.617021	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Silent	SNP	ENST00000357552.3	37	CCDS13482.1																																																																																			C|0.983;T|0.017	0.017	strong		0.318	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057952	46057952	+	Silent	SNP	C	C	A	rs74701761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057952C>A	ENST00000380095.1	+	1	680	c.618C>A	c.(616-618)gtC>gtA	p.V206V	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	206	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						GCGTGCCCGTCCCCTCCTGCG	0.706													C|||	103	0.0205671	0.0756	0.0043	5008	,	,		19027	0.0		0.0	False		,,,				2504	0.0				p.V206V		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C618A						PASS	.						91.0	95.0	94.0					21																	46057952		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			GCCCGTCCCCTCC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.618C>A	21.37:g.46057952C>A		Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	473	113	0.238901	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.982;A|0.018	0.018	strong		0.706	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
SNX29	92017	hgsc.bcm.edu	37	16	12162969	12162969	+	Silent	SNP	A	A	G	rs1641843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:12162969A>G	ENST00000566228.1	+	10	1368	c.1299A>G	c.(1297-1299)ccA>ccG	p.P433P	SNX29_ENST00000306030.3_Silent_p.P48P|SNX29_ENST00000323433.4_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	98	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	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		
RAD21L1	642636	hgsc.bcm.edu	37	20	1224774	1224774	+	Missense_Mutation	SNP	A	A	C	rs17717241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1224774A>C	ENST00000409241.1	+	11	1361	c.1268A>C	c.(1267-1269)cAt>cCt	p.H423P	RAD21L1_ENST00000402452.1_Missense_Mutation_p.H423P|RAD21L1_ENST00000381882.2_Missense_Mutation_p.H423P	NM_001136566.2	NP_001130038.2	Q9H4I0	RD21L_HUMAN	RAD21-like 1 (S. pombe)	423			H -> P (in dbSNP:rs17717241).		attachment of telomeric heterochromatin to nuclear envelope (GO:0070197)|chromosome segregation (GO:0007059)|double-strand break repair via homologous recombination (GO:0000724)|fertilization (GO:0009566)|linear element assembly (GO:0030999)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleus (GO:0005634)				NS(1)|breast(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	7						GGATCTCAGCATAGCTCTCAT	0.353													A|||	298	0.0595048	0.0787	0.0836	5008	,	,		17319	0.0159		0.0964	False		,,,				2504	0.0235				p.H423P		Atlas-SNP	.											.	RAD21L1	51	.	0			c.A1268C						PASS	.	A	PRO/HIS	127,1257		8,111,573	135.0	116.0	122.0		1268	3.6	0.0	20	dbSNP_123	122	271,2911		10,251,1330	yes	missense	RAD21L1	NM_001136566.2	77	18,362,1903	CC,CA,AA		8.5167,9.1763,8.7166	benign	423/557	1224774	398,4168	692	1591	2283	SO:0001583	missense	642636	exon11			CTCAGCATAGCTC	AL031665	CCDS46568.1	20p13	2011-08-12			ENSG00000244588	ENSG00000244588			16271	protein-coding gene	gene with protein product							Standard	NM_001136566		Approved	dJ545L17.2, RAD21L	uc010gab.1	Q9H4I0	OTTHUMG00000031664	ENST00000409241.1:c.1268A>C	20.37:g.1224774A>C	ENSP00000386414:p.His423Pro	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_001136566	B2RXL0|B7ZBB1|B7ZW76|Q5W0X5	Missense_Mutation	SNP	ENST00000409241.1	37	CCDS46568.1	158	0.07234432234432235	49	0.09959349593495935	29	0.08011049723756906	8	0.013986013986013986	72	0.09498680738786279	A	0.874	-0.731023	0.03135	0.091763	0.085167	ENSG00000244588	ENST00000402452;ENST00000409241;ENST00000381882	T;T;T	0.62639	0.01;0.09;0.01	5.5	3.56	0.40772	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.80722	P	0.0	B	0.21309	0.054	B	0.08055	0.003	T	0.07028	-1.0794	8	0.30854	T	0.27	.	7.6764	0.28488	0.191:0.0:0.809:0.0	rs17717241;rs52834781;rs61377268;rs17717241	423	Q9H4I0	RD21L_HUMAN	P	423	ENSP00000385925:H423P;ENSP00000386414:H423P;ENSP00000371306:H423P	ENSP00000371306:H423P	H	+	2	0	RAD21L1	1172774	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.307000	0.19296	0.865000	0.35603	-0.242000	0.12053	CAT	A|0.928;C|0.072	0.072	strong		0.353	RAD21L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334022.1		
CIDEC	63924	hgsc.bcm.edu	37	3	9918861	9918861	+	Silent	SNP	C	C	A	rs456168	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9918861C>A	ENST00000336832.2	-	3	235	c.96G>T	c.(94-96)ctG>ctT	p.L32L	CIDEC_ENST00000443115.1_Silent_p.L32L|CIDEC_ENST00000383817.1_Silent_p.L32L|CIDEC_ENST00000455015.1_Intron|CIDEC_ENST00000430427.1_Silent_p.L32L|CIDEC_ENST00000423850.1_Intron	NM_001199552.1|NM_001199623.1|NM_022094.3	NP_001186481.1|NP_001186552.1|NP_071377.2	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	32					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|lipid particle organization (GO:0034389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	8	Medulloblastoma(99;0.227)					TGGGCTCCGACAGCAGCTGCT	0.647													C|||	1569	0.313299	0.4962	0.3458	5008	,	,		18973	0.248		0.1998	False		,,,				2504	0.227				p.L45L		Atlas-SNP	.											CIDEC,NS,carcinoma,0,1	CIDEC	22	1	0			c.G135T						PASS	.	C	,,,	1785,2463		385,1015,724	27.0	27.0	27.0		96,96,135,96	4.2	0.0	3	dbSNP_80	27	1568,6736		155,1258,2739	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIDEC	NM_001199551.1,NM_001199552.1,NM_001199623.1,NM_022094.3	,,,	540,2273,3463	AA,AC,CC		18.8825,42.0198,26.7129	,,,	32/249,32/239,45/252,32/239	9918861	3353,9199	2124	4152	6276	SO:0001819	synonymous_variant	63924	exon3			CTCCGACAGCAGC		CCDS2587.1, CCDS56239.1, CCDS74897.1	3p25	2004-07-26			ENSG00000187288	ENSG00000187288			24229	protein-coding gene	gene with protein product		612120				12429024	Standard	NM_001199623		Approved	CIDE-3, FLJ20871, Fsp27	uc021wsw.1	Q96AQ7	OTTHUMG00000128522	ENST00000336832.2:c.96G>T	3.37:g.9918861C>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	99	39	0.393939	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Silent	SNP	ENST00000336832.2	37	CCDS2587.1																																																																																			C|0.678;A|0.322	0.322	strong		0.647	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094	
IRF3	3661	hgsc.bcm.edu	37	19	50162909	50162909	+	Missense_Mutation	SNP	C	C	G	rs7251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50162909C>G	ENST00000597198.1	-	8	1661	c.1280G>C	c.(1279-1281)aGc>aCc	p.S427T	IRF3_ENST00000599144.1_Missense_Mutation_p.S281T|IRF3_ENST00000600911.1_Missense_Mutation_p.E388D|IRF3_ENST00000599223.1_Missense_Mutation_p.S300T|IRF3_ENST00000596822.1_Missense_Mutation_p.E115D|IRF3_ENST00000598808.1_Missense_Mutation_p.S281T|IRF3_ENST00000600022.1_Missense_Mutation_p.S154T|IRF3_ENST00000377139.3_Missense_Mutation_p.S427T|IRF3_ENST00000593922.1_Missense_Mutation_p.S281T|IRF3_ENST00000601291.1_Missense_Mutation_p.E432D|IRF3_ENST00000377135.4_Missense_Mutation_p.S300T|IRF3_ENST00000309877.7_Missense_Mutation_p.S427T|IRF3_ENST00000599680.1_5'UTR|IRF3_ENST00000596765.1_Missense_Mutation_p.S154T			Q14653	IRF3_HUMAN	interferon regulatory factor 3	427			S -> T (in dbSNP:rs7251). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dsRNA (GO:0071359)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage apoptotic process (GO:0071888)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of interferon-beta biosynthetic process (GO:0045358)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|programmed necrotic cell death (GO:0097300)|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)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)	p.S427T(1)		breast(1)|large_intestine(2)|lung(4)|ovary(2)|stomach(1)	10		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.02)		GAGGGCTCAGCTCTCCCCAGG	0.587													G|||	2427	0.484625	0.708	0.4409	5008	,	,		17387	0.3571		0.333	False		,,,				2504	0.501				p.E432D		Atlas-SNP	.											IRF3,NS,carcinoma,0,1	IRF3	27	1	1	Substitution - Missense(1)	stomach(1)	c.G1296C						PASS	.	G	ASP/GLU,THR/SER,THR/SER,THR/SER,THR/SER,THR/SER,THR/SER,THR/SER	2920,1484	467.0+/-354.7	986,948,268	108.0	91.0	97.0		1296,1175,899,842,842,461,461,1280	-1.1	0.0	19	dbSNP_52	97	2715,5879	670.6+/-402.8	431,1853,2013	yes	missense,missense,missense,missense,missense,missense,missense,missense	IRF3	NM_001197122.1,NM_001197123.1,NM_001197124.1,NM_001197125.1,NM_001197126.1,NM_001197127.1,NM_001197128.1,NM_001571.5	45,58,58,58,58,58,58,58	1417,2801,2281	GG,GC,CC		31.5918,33.6966,43.3528	benign,benign,benign,benign,benign,benign,benign,benign	432/453,392/393,300/301,281/282,281/282,154/155,154/155,427/428	50162909	5635,7363	2202	4297	6499	SO:0001583	missense	3661	exon8			GCTCAGCTCTCCC		CCDS12775.1, CCDS56099.1, CCDS59407.1, CCDS59408.1, CCDS59409.1	19q13.3-q13.4	2008-07-16				ENSG00000126456			6118	protein-coding gene	gene with protein product		603734				8524823	Standard	NM_001571		Approved		uc002pow.3	Q14653		ENST00000597198.1:c.1280G>C	19.37:g.50162909C>G	ENSP00000469113:p.Ser427Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001197122	A8K7L2|B2RAZ3|Q5FBY1|Q5FBY2|Q5FBY4|Q7Z5G6	Missense_Mutation	SNP	ENST00000597198.1	37	CCDS12775.1	971	0.44459706959706957	355	0.7215447154471545	153	0.42265193370165743	220	0.38461538461538464	243	0.32058047493403696	G	0.062	-1.221020	0.01530	0.663034	0.315918	ENSG00000126456	ENST00000377139;ENST00000309877;ENST00000377135	D;D;D	0.96554	-4.05;-4.05;-3.94	4.25	-1.13	0.09775	SMAD/FHA domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.40695	P	0.017568999999999946	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31779	-0.9931	8	0.02654	T	1	.	4.4658	0.11689	0.3207:0.3403:0.3389:0.0	rs7251;rs17713;rs3170560;rs12976242;rs17856307;rs59032938;rs7251	427;300	Q14653;Q5FBY1	IRF3_HUMAN;.	T	427;427;300	ENSP00000366344:S427T;ENSP00000310127:S427T;ENSP00000366339:S300T	ENSP00000310127:S427T	S	-	2	0	IRF3	54854721	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.481000	0.06552	-0.168000	0.10853	-0.225000	0.12378	AGC	C|0.546;G|0.454	0.454	strong		0.587	IRF3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465962.1	NM_001571	
SLC36A3	285641	hgsc.bcm.edu	37	5	150666843	150666843	+	Silent	SNP	A	A	G	rs6579846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	128	0	0		WXS	Illumina HiSeq	Phase_I	183	96	0.52459	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	
DNMT3A	1788	hgsc.bcm.edu	37	2	25469502	25469502	+	Silent	SNP	C	C	T	rs2276598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:25469502C>T	ENST00000264709.3	-	10	1603	c.1266G>A	c.(1264-1266)ctG>ctA	p.L422L	DNMT3A_ENST00000402667.1_Silent_p.L199L|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000321117.5_Silent_p.L422L|DNMT3A_ENST00000380746.4_Silent_p.L233L	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	422					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGGTGGCTCCAGGCCCTTAG	0.622			"""Mis, F, N, S"""		AML								c|||	1121	0.223842	0.3162	0.1556	5008	,	,		18289	0.3204		0.1541	False		,,,				2504	0.1196				p.L422L		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.G1266A						PASS	.	T	,,	1301,3097		189,923,1087	37.0	38.0	38.0		1266,699,1266	2.4	1.0	2	dbSNP_100	38	1355,7207		110,1135,3036	no	coding-synonymous,coding-synonymous,coding-synonymous	DNMT3A	NM_022552.3,NM_153759.2,NM_175629.1	,,	299,2058,4123	TT,TC,CC		15.8257,29.5816,20.4938	,,	422/913,233/724,422/913	25469502	2656,10304	2199	4281	6480	SO:0001819	synonymous_variant	1788	exon10			TGGCTCCAGGCCC		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1266G>A	2.37:g.25469502C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Silent	SNP	ENST00000264709.3	37	CCDS33157.1																																																																																			C|0.792;T|0.208	0.208	strong		0.622	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	
COLEC12	81035	hgsc.bcm.edu	37	18	334994	334994	+	Missense_Mutation	SNP	A	A	G	rs2305025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:334994A>G	ENST00000400256.3	-	6	1771	c.1564T>C	c.(1564-1566)Tcc>Ccc	p.S522P		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	522	Collagen-like 2.		S -> P (in dbSNP:rs2305025). {ECO:0000269|PubMed:11162630, ECO:0000269|PubMed:11564734, ECO:0000269|PubMed:12601552, ECO:0000269|PubMed:12761161, ECO:0000269|PubMed:15489334}.		carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				TCCCCACTGGAGCCCTGAGGG	0.711													G|||	3131	0.6252	0.615	0.572	5008	,	,		13662	0.7907		0.6103	False		,,,				2504	0.5215				p.S522P		Atlas-SNP	.											COLEC12,NS,carcinoma,0,1	COLEC12	121	1	0			c.T1564C						PASS	.	G	PRO/SER	2658,1608		875,908,350	11.0	14.0	13.0		1564	2.8	0.9	18	dbSNP_100	13	5211,3233		1660,1891,671	no	missense	COLEC12	NM_130386.2	74	2535,2799,1021	GG,GA,AA		38.2875,37.6934,38.0881	benign	522/743	334994	7869,4841	2133	4222	6355	SO:0001583	missense	81035	exon6			CACTGGAGCCCTG	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"""Collectins"""	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.1564T>C	18.37:g.334994A>G	ENSP00000383115:p.Ser522Pro	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	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		
NKX2-5	1482	hgsc.bcm.edu	37	5	172662014	172662014	+	Missense_Mutation	SNP	G	G	A	rs28936670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:172662014G>A	ENST00000329198.4	-	1	346	c.73C>T	c.(73-75)Cgc>Tgc	p.R25C	NKX2-5_ENST00000424406.2_Missense_Mutation_p.R25C|NKX2-5_ENST00000521848.1_Missense_Mutation_p.R25C	NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	25			R -> C (in ASD7, TOF, CHNG5 and HLHS2; exhibits significant functional impairment with reduction of transactivation properties and dominant- negative effect; the mutant protein activity on the DIO2, TG and TPO promoters is significantly impaired; dbSNP:rs28936670). {ECO:0000269|PubMed:10587520, ECO:0000269|PubMed:11714651, ECO:0000269|PubMed:14607454, ECO:0000269|PubMed:15342699, ECO:0000269|PubMed:15810002, ECO:0000269|PubMed:16418214}.		adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|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 via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GCCAGGCTGCGCTGCTGCTGT	0.672													G|||	51	0.0101837	0.0363	0.0029	5008	,	,		12104	0.0		0.001	False		,,,				2504	0.0				p.R25C	Esophageal Squamous(72;810 1219 2387 13420 44943)	Atlas-SNP	.											.	NKX2-5	42	.	0			c.C73T	GRCh37	CM993125	NKX2-5	M	rs28936670	PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	115,4231		0,115,2058	20.0	25.0	23.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	73,73,73	3.9	1.0	5	dbSNP_125	23	8,8528		0,8,4260	yes	missense,missense,missense	NKX2-5	NM_001166175.1,NM_001166176.1,NM_004387.3	180,180,180	0,123,6318	AA,AG,GG		0.0937,2.6461,0.9548	probably-damaging,probably-damaging,probably-damaging	25/113,25/152,25/325	172662014	123,12759	2173	4268	6441	SO:0001583	missense	1482	exon1			GGCTGCGCTGCTG	AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"""Homeoboxes / ANTP class : NKL subclass"""	2488	protein-coding gene	gene with protein product	"""tinman paralog (Drosophila)"""	600584	"""cardiac-specific homeo box"", ""NK2 transcription factor related, locus 5 (Drosophila)"""	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.73C>T	5.37:g.172662014G>A	ENSP00000327758:p.Arg25Cys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	157	77	0.490446	NM_004387	A8K3K0|B4DNB6|E9PBU6	Missense_Mutation	SNP	ENST00000329198.4	37	CCDS4387.1	10	0.004578754578754579	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	17.06	3.293107	0.60086	0.026461	9.37E-4	ENSG00000183072	ENST00000329198;ENST00000424406;ENST00000521848;ENST00000517440	D;D;D;D	0.90385	-2.66;-2.53;-2.6;-2.55	4.76	3.89	0.44902	.	0.491101	0.15624	N	0.252757	T	0.66157	0.2761	L	0.40543	1.245	0.38768	A	0.954489	B;B;B	0.29646	0.253;0.089;0.002	B;B;B	0.21546	0.035;0.008;0.001	T	0.76594	-0.2902	9	0.56958	D	0.05	.	3.5512	0.07847	0.0824:0.2014:0.467:0.2492	rs28936670	25;25;25	B4DNB6;E5RH49;P52952	.;.;NKX25_HUMAN	C	25	ENSP00000327758:R25C;ENSP00000395378:R25C;ENSP00000427906:R25C;ENSP00000429905:R25C	ENSP00000327758:R25C	R	-	1	0	NKX2-5	172594620	0.992000	0.36948	0.993000	0.49108	0.842000	0.47809	1.185000	0.32065	1.118000	0.41863	0.462000	0.41574	CGC	G|0.993;A|0.007	0.007	strong		0.672	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2		
AGMO	392636	hgsc.bcm.edu	37	7	15458186	15458186	+	Silent	SNP	T	T	C	rs28635514	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:15458186T>C	ENST00000342526.3	-	5	775	c.606A>G	c.(604-606)acA>acG	p.T202T		NM_001004320.1	NP_001004320.1	Q6ZNB7	ALKMO_HUMAN	alkylglycerol monooxygenase	202					ether lipid metabolic process (GO:0046485)|fatty acid biosynthetic process (GO:0006633)|membrane lipid metabolic process (GO:0006643)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glyceryl-ether monooxygenase activity (GO:0050479)|iron ion binding (GO:0005506)			breast(1)|kidney(1)|large_intestine(6)|liver(1)|lung(30)|prostate(1)|skin(2)	42						GTTTTACCTCTGTATGGATCC	0.353													T|||	303	0.0605032	0.1566	0.0605	5008	,	,		13011	0.0		0.0288	False		,,,				2504	0.0256				p.T202T		Atlas-SNP	.											.	AGMO	98	.	0			c.A606G						PASS	.	T		525,3869		31,463,1703	32.0	38.0	36.0		606	-0.5	1.0	7	dbSNP_125	36	324,8250		9,306,3972	no	coding-synonymous	AGMO	NM_001004320.1		40,769,5675	CC,CT,TT		3.7789,11.9481,6.5469		202/446	15458186	849,12119	2197	4287	6484	SO:0001819	synonymous_variant	392636	exon5			TACCTCTGTATGG		CCDS34604.1	7p21.1	2013-03-04	2011-01-31	2011-01-31	ENSG00000187546	ENSG00000187546	1.14.16.5	"""Fatty acid hydroxylase domain containing"""	33784	protein-coding gene	gene with protein product		613738	"""transmembrane protein 195"""	TMEM195		20643956	Standard	NM_001004320		Approved	FLJ16237	uc003stb.1	Q6ZNB7	OTTHUMG00000152387	ENST00000342526.3:c.606A>G	7.37:g.15458186T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_001004320	A4D114|A6NCH5	Silent	SNP	ENST00000342526.3	37	CCDS34604.1																																																																																			T|0.943;C|0.057	0.057	strong		0.353	AGMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326049.2	NM_001004320	
ZNF813	126017	hgsc.bcm.edu	37	19	53994178	53994178	+	Missense_Mutation	SNP	G	G	A	rs10421308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53994178G>A	ENST00000396403.4	+	4	820	c.692G>A	c.(691-693)aGg>aAg	p.R231K	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	231			R -> K (in dbSNP:rs10421308).		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.R231K(1)		large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		TCACTCTTAAGGAAACATCAA	0.368													.|||	459	0.0916534	0.0946	0.0778	5008	,	,		21536	0.12		0.0567	False		,,,				2504	0.1043				p.R231K		Atlas-SNP	.											ZNF813_ENST00000396403,NS,carcinoma,0,1	ZNF813	81	1	1	Substitution - Missense(1)	stomach(1)	c.G692A						PASS	.	G	LYS/ARG	374,4022	173.4+/-203.2	18,338,1842	71.0	75.0	74.0		692	-0.9	0.0	19	dbSNP_119	74	468,8130	132.6+/-190.3	23,422,3854	no	missense	ZNF813	NM_001004301.3	26	41,760,5696	AA,AG,GG		5.4431,8.5077,6.4799	benign	231/618	53994178	842,12152	2198	4299	6497	SO:0001583	missense	126017	exon4			TCTTAAGGAAACA	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.692G>A	19.37:g.53994178G>A	ENSP00000379684:p.Arg231Lys	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	157	75	0.477707	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	182	0.08333333333333333	52	0.10569105691056911	22	0.06077348066298342	68	0.11888111888111888	40	0.052770448548812667	G	0.101	-1.152221	0.01700	0.085077	0.054431	ENSG00000198346	ENST00000396403	T	0.20200	2.09	1.0	-0.918	0.10482	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00109	0.0003	N	0.01742	-0.745	0.80722	P	0.0	B	0.22211	0.066	B	0.26416	0.069	T	0.41734	-0.9492	8	0.19147	T	0.46	.	3.8116	0.08799	0.7133:0.0:0.2866:0.0	rs10421308;rs17305122;rs10421308	231	Q6ZN06	ZN813_HUMAN	K	231	ENSP00000379684:R231K	ENSP00000379684:R231K	R	+	2	0	ZNF813	58685990	0.000000	0.05858	0.001000	0.08648	0.084000	0.17831	-6.679000	0.00057	-0.397000	0.07691	0.205000	0.17691	AGG	G|0.911;A|0.089	0.089	strong		0.368	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178634672	178634672	+	Missense_Mutation	SNP	C	C	T	rs398829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:178634672C>T	ENST00000251582.7	-	4	834	c.733G>A	c.(733-735)Gtc>Atc	p.V245I	ADAMTS2_ENST00000274609.5_Missense_Mutation_p.V245I	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	245			V -> I (in dbSNP:rs398829).		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)		TCCTCTAGGACGCCCAGGGCG	0.657													C|||	2163	0.431909	0.4054	0.2565	5008	,	,		15058	0.6349		0.2763	False		,,,				2504	0.5429				p.V245I		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.G733A						PASS	.	C	ILE/VAL,ILE/VAL	1674,2732	508.4+/-367.0	314,1046,843	90.0	78.0	82.0		733,733	1.2	0.4	5	dbSNP_80	82	2555,6045	415.5+/-351.8	378,1799,2123	yes	missense,missense	ADAMTS2	NM_014244.4,NM_021599.2	29,29	692,2845,2966	TT,TC,CC		29.7093,37.9936,32.5158	benign,benign	245/1212,245/567	178634672	4229,8777	2203	4300	6503	SO:0001583	missense	9509	exon4			CTAGGACGCCCAG	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.733G>A	5.37:g.178634672C>T	ENSP00000251582:p.Val245Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_021599		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	867	0.39697802197802196	198	0.4024390243902439	99	0.27348066298342544	368	0.6433566433566433	202	0.26649076517150394	C	3.478	-0.106590	0.06924	0.379936	0.297093	ENSG00000087116	ENST00000251582;ENST00000274609	T;T	0.59772	0.28;0.24	5.34	1.18	0.20946	.	0.836897	0.09859	N	0.746428	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.001	T	0.46925	-0.9156	9	0.18276	T	0.48	.	6.6881	0.23156	0.0:0.5061:0.1613:0.3326	rs398829;rs3733917;rs61577946;rs398829	245;245	O95450-2;O95450	.;ATS2_HUMAN	I	245	ENSP00000251582:V245I;ENSP00000274609:V245I	ENSP00000251582:V245I	V	-	1	0	ADAMTS2	178567278	0.000000	0.05858	0.426000	0.26672	0.034000	0.12701	-0.564000	0.05936	0.250000	0.21479	0.561000	0.74099	GTC	C|0.635;T|0.365	0.365	strong		0.657	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
MKKS	8195	hgsc.bcm.edu	37	20	10394046	10394046	+	Silent	SNP	G	G	A	rs16991547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:10394046G>A	ENST00000347364.3	-	3	879	c.117C>T	c.(115-117)ccC>ccT	p.P39P	MKKS_ENST00000399054.2_Silent_p.P39P	NM_170784.2	NP_740754.1	Q9NPJ1	MKKS_HUMAN	McKusick-Kaufman syndrome	39					artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|chaperone-mediated protein complex assembly (GO:0051131)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|determination of left/right symmetry (GO:0007368)|fat cell differentiation (GO:0045444)|gonad development (GO:0008406)|heart development (GO:0007507)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of multicellular organism growth (GO:0040018)|protein folding (GO:0006457)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sensory perception of smell (GO:0007608)|social behavior (GO:0035176)|spermatid development (GO:0007286)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)|unfolded protein binding (GO:0051082)	p.P39P(1)		kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|stomach(2)	16						GCCTACCTGAGGGGCCATAGC	0.478													A|||	1194	0.238419	0.3744	0.1268	5008	,	,		19525	0.2579		0.0895	False		,,,				2504	0.2669				p.P39P	Melanoma(79;1979 2212 6640)	Atlas-SNP	.											MKKS,NS,carcinoma,0,1	MKKS	35	1	1	Substitution - coding silent(1)	stomach(1)	c.C117T						PASS	.	A	,	1360,3046	691.1+/-405.3	212,936,1055	150.0	130.0	137.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	117,117	-1.4	0.2	20	dbSNP_123	137	969,7631	774.1+/-407.7	65,839,3396	no	coding-synonymous,coding-synonymous	MKKS	NM_018848.2,NM_170784.1	,	277,1775,4451	AA,AG,GG		11.2674,30.867,17.9071	,	39/571,39/571	10394046	2329,10677	2203	4300	6503	SO:0001819	synonymous_variant	8195	exon3			ACCTGAGGGGCCA	AF221993	CCDS13111.1	20p12	2013-01-08			ENSG00000125863	ENSG00000125863		"""Heat Shock Proteins / Chaperonins"""	7108	protein-coding gene	gene with protein product		604896		BBS6		9467007	Standard	NR_072977		Approved		uc002wnu.2	Q9NPJ1	OTTHUMG00000031868	ENST00000347364.3:c.117C>T	20.37:g.10394046G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_170784	A8K7B0|D3DW18	Silent	SNP	ENST00000347364.3	37	CCDS13111.1																																																																																			G|0.800;A|0.200	0.200	strong		0.478	MKKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077991.3		
DDX26B	203522	hgsc.bcm.edu	37	X	134713861	134713861	+	Silent	SNP	C	C	T	rs2298302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:134713861C>T	ENST00000370752.4	+	15	2491	c.2157C>T	c.(2155-2157)gaC>gaT	p.D719D	DDX26B_ENST00000481908.1_3'UTR	NM_182540.4	NP_872346.3	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26B	719										large_intestine(1)|lung(8)	9	Acute lymphoblastic leukemia(192;6.56e-05)					CTCTGTCTGACGACTTCACAA	0.448													C|||	455	0.12053	0.1952	0.0231	3775	,	,		15332	0.0694		0.0139	False		,,,				2504	0.0992				p.D719D		Atlas-SNP	.											.	DDX26B	130	.	0			c.C2157T						PASS	.	C		922,2913		103,586,130,943,441	80.0	72.0	75.0		2157	-4.2	0.1	X	dbSNP_100	75	157,6571		3,101,50,2324,1822	no	coding-synonymous	DDX26B	NM_182540.4		106,687,180,3267,2263	TT,TC,T,CC,C		2.3335,24.0417,10.2149		719/862	134713861	1079,9484	2203	4300	6503	SO:0001819	synonymous_variant	203522	exon15			GTCTGACGACTTC	AK096544	CCDS35401.1	Xq26	2008-02-05			ENSG00000165359	ENSG00000165359		"""DEAD-boxes"""	27334	protein-coding gene	gene with protein product							Standard	NM_182540		Approved	FLJ41215	uc004eyw.4	Q5JSJ4	OTTHUMG00000022484	ENST00000370752.4:c.2157C>T	X.37:g.134713861C>T		Somatic	427	1	0.00234192		WXS	Illumina HiSeq	Phase_I	503	499	0.992048	NM_182540	Q5CZA2|Q6IPS3|Q6ZTU5|Q6ZWE4	Silent	SNP	ENST00000370752.4	37	CCDS35401.1																																																																																			C|0.893;0|0.003	.	strong		0.448	DDX26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058420.1	NM_182540	
ATAD3A	55210	hgsc.bcm.edu	37	1	1458915	1458915	+	Missense_Mutation	SNP	C	C	T	rs113107431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1458915C>T	ENST00000378755.5	+	9	1169	c.1075C>T	c.(1075-1077)Ccc>Tcc	p.P359S	ATAD3A_ENST00000536055.1_Missense_Mutation_p.P232S|ATAD3A_ENST00000378756.3_Missense_Mutation_p.P311S	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	359					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)			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)		CCTCAGTCGACCCCAGGACGC	0.706													c|||	108	0.0215655	0.0756	0.0115	5008	,	,		12132	0.0		0.0	False		,,,				2504	0.0				p.P359S		Atlas-SNP	.											.	ATAD3A	35	.	0			c.C1075T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	341,4065	171.6+/-201.8	11,319,1873	48.0	47.0	47.0		931,694,1075	4.8	0.8	1	dbSNP_132	47	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	ATAD3A	NM_001170535.1,NM_001170536.1,NM_018188.3	74,74,74	11,321,6171	TT,TC,CC		0.0233,7.7394,2.6372	benign,benign,benign	311/587,232/508,359/635	1458915	343,12663	2203	4300	6503	SO:0001583	missense	55210	exon9			AGTCGACCCCAGG	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.1075C>T	1.37:g.1458915C>T	ENSP00000368030:p.Pro359Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	181	102	0.563536	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Missense_Mutation	SNP	ENST00000378755.5	37	CCDS31.1	55|55	0.025183150183150184|0.025183150183150184	49|49	0.09959349593495935|0.09959349593495935	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	0|0	0.0|0.0	c|c	9.414|9.414	1.081264|1.081264	0.20309|0.20309	0.077394|0.077394	2.33E-4|2.33E-4	ENSG00000197785|ENSG00000197785	ENST00000378756;ENST00000378755;ENST00000536055|ENST00000339113	D;D;D|.	0.94723|.	-3.25;-3.12;-3.5|.	4.8|4.8	4.8|4.8	0.61643|0.61643	.|.	0.325455|.	0.33895|.	N|.	0.004457|.	T|T	0.01835|0.01835	0.0058|0.0058	L|L	0.41906|0.41906	1.305|1.305	0.34198|0.34198	D|D	0.672866|0.672866	B;B|.	0.28439|.	0.047;0.212|.	B;B|.	0.22601|.	0.027;0.04|.	T|T	0.30416|0.30416	-0.9979|-0.9979	10|5	0.33940|.	T|.	0.23|.	.|.	8.613|8.613	0.33815|0.33815	0.1587:0.665:0.1764:0.0|0.1587:0.665:0.1764:0.0	.|.	311;359|.	D2K8Q1;Q9NVI7|.	.;ATD3A_HUMAN|.	S|I	311;359;232|296	ENSP00000368031:P311S;ENSP00000368030:P359S;ENSP00000439290:P232S|.	ENSP00000368030:P359S|.	P|T	+|+	1|2	0|0	ATAD3A|ATAD3A	1448778|1448778	1.000000|1.000000	0.71417|0.71417	0.842000|0.842000	0.33263|0.33263	0.047000|0.047000	0.14425|0.14425	3.205000|3.205000	0.51090|0.51090	2.220000|2.220000	0.72140|0.72140	0.556000|0.556000	0.70494|0.70494	CCC|ACC	C|0.972;T|0.028	0.028	strong		0.706	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188	
PABPC1	26986	hgsc.bcm.edu	37	8	101719201	101719201	+	Missense_Mutation	SNP	A	A	G	rs72681439		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101719201A>G	ENST00000318607.5	-	10	2489	c.1361T>C	c.(1360-1362)aTc>aCc	p.I454T	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519004.1_Missense_Mutation_p.I409T|PABPC1_ENST00000522387.1_Missense_Mutation_p.I422T|PABPC1_ENST00000519596.1_Intron	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	454					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			AGCTGGGCGGATAGCACCGGG	0.433																																					p.I454T		Atlas-SNP	.											PABPC1,bladder,carcinoma,+1,1	PABPC1	76	1	0			c.T1361C						scavenged	.						72.0	69.0	70.0					8																	101719201		2203	4300	6503	SO:0001583	missense	26986	exon10			GGGCGGATAGCAC	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.1361T>C	8.37:g.101719201A>G	ENSP00000313007:p.Ile454Thr	Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	89	19	0.213483	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.57|17.57	3.422927|3.422927	0.62733|0.62733	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000519004;ENST00000522387;ENST00000522658|ENST00000517403	T;T;T;T|.	0.50548|.	1.64;1.55;2.61;0.74|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.000000|.	0.64402|.	D|.	0.000004|.	T|T	0.63558|0.63558	0.2521|0.2521	L|L	0.47016|0.47016	1.485|1.485	0.46654|0.46654	D|D	0.999149|0.999149	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.09377|.	0.001;0.004;0.002|.	T|T	0.60424|0.60424	-0.7266|-0.7266	9|5	.|.	.|.	.|.	.|.	16.1251|16.1251	0.81386|0.81386	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	422;454;454|.	E7ERJ7;B3KT93;P11940|.	.;.;PABP1_HUMAN|.	T|P	454;409;422;1|107	ENSP00000313007:I454T;ENSP00000429594:I409T;ENSP00000429395:I422T;ENSP00000428840:I1T|.	.|.	I|S	-|-	2|1	0|0	PABPC1|PABPC1	101788377|101788377	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.628000|8.628000	0.90979|0.90979	2.272000|2.272000	0.75746|0.75746	0.528000|0.528000	0.53228|0.53228	ATC|TCC	A|0.500;G|0.500	0.500	strong		0.433	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
HMHA1	23526	hgsc.bcm.edu	37	19	1077985	1077985	+	Missense_Mutation	SNP	A	A	G	rs7251797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1077985A>G	ENST00000313093.2	+	11	1546	c.1315A>G	c.(1315-1317)Agc>Ggc	p.S439G	HMHA1_ENST00000586866.1_Missense_Mutation_p.S443G|HMHA1_ENST00000590214.1_Missense_Mutation_p.S466G|HMHA1_ENST00000536472.1_Missense_Mutation_p.S279G|HMHA1_ENST00000543365.1_Missense_Mutation_p.S322G|HMHA1_ENST00000590577.1_Missense_Mutation_p.S74G|HMHA1_ENST00000539243.2_Missense_Mutation_p.S455G	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	439			S -> G (in dbSNP:rs7251797). {ECO:0000269|Ref.5}.		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)		GGGAGCAGGCAGCACGGCCAC	0.697													a|||	2337	0.466653	0.7549	0.4164	5008	,	,		12275	0.3343		0.3449	False		,,,				2504	0.3742				p.S455G		Atlas-SNP	.											.	HMHA1	78	.	0			c.A1363G						PASS	.		GLY/SER	2792,1450		950,892,279	20.0	20.0	20.0		1315	1.2	0.0	19	dbSNP_116	20	3012,5402		595,1822,1790	no	missense	HMHA1	NM_012292.2	56	1545,2714,2069	GG,GA,AA		35.7975,34.182,45.8597	benign	439/1137	1077985	5804,6852	2121	4207	6328	SO:0001583	missense	23526	exon11			GCAGGCAGCACGG	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.1315A>G	19.37:g.1077985A>G	ENSP00000316772:p.Ser439Gly	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	174	172	0.988506	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	37	CCDS32863.1	978	0.4478021978021978	348	0.7073170731707317	152	0.4198895027624309	211	0.3688811188811189	267	0.35224274406332456	a	0.150	-1.092908	0.01858	0.65818	0.357975	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000544746;ENST00000536472;ENST00000412039;ENST00000543365	T;T;T;T	0.23754	1.92;1.92;1.95;1.89	4.64	1.24	0.21308	.	0.464711	0.23760	N	0.044839	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.08055	0.003;0.002;0.002;0.001	T	0.22977	-1.0201	9	0.23891	T	0.37	-6.9205	6.9125	0.24342	0.6836:0.0:0.3164:0.0	rs7251797;rs17855955;rs61184148;rs7251797	279;455;322;439	F5H4A3;F6QP70;F5H1R4;Q92619	.;.;.;HMHA1_HUMAN	G	455;439;439;279;433;322	ENSP00000439601:S455G;ENSP00000316772:S439G;ENSP00000445109:S279G;ENSP00000438979:S322G	ENSP00000316772:S439G	S	+	1	0	HMHA1	1028985	1.000000	0.71417	0.000000	0.03702	0.001000	0.01503	1.998000	0.40796	-0.124000	0.11724	-0.419000	0.06015	AGC	A|0.534;G|0.466	0.466	strong		0.697	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
PCNXL2	80003	hgsc.bcm.edu	37	1	233388242	233388242	+	Silent	SNP	A	A	G	rs6682865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:233388242A>G	ENST00000258229.9	-	7	2220	c.1986T>C	c.(1984-1986)ttT>ttC	p.F662F	PCNXL2_ENST00000430153.1_5'UTR	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	662						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)				TATTGCCCTGAAAACTTAACA	0.368													G|||	173	0.0345447	0.0749	0.013	5008	,	,		19108	0.0139		0.0149	False		,,,				2504	0.0368				p.F662F		Atlas-SNP	.											.	PCNXL2	204	.	0			c.T1986C						PASS	.	G		246,3400		7,232,1584	105.0	99.0	101.0		1986	2.5	1.0	1	dbSNP_116	101	82,8088		0,82,4003	no	coding-synonymous	PCNXL2	NM_014801.3		7,314,5587	GG,GA,AA		1.0037,6.7471,2.7759		662/2138	233388242	328,11488	1823	4085	5908	SO:0001819	synonymous_variant	80003	exon7			GCCCTGAAAACTT	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.1986T>C	1.37:g.233388242A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	160	80	0.5	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Silent	SNP	ENST00000258229.9	37	CCDS44335.1																																																																																			A|0.968;G|0.032	0.032	strong		0.368	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
LILRB3	11025	hgsc.bcm.edu	37	19	54722250	54722250	+	Missense_Mutation	SNP	T	T	C	rs1132610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54722250T>C	ENST00000391750.1	-	12	1709	c.1573A>G	c.(1573-1575)Agg>Ggg	p.R525G	LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.R525G|LILRB3_ENST00000407860.2_Missense_Mutation_p.R542G|LILRB3_ENST00000346401.6_Missense_Mutation_p.R537G|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.R525G|LILRB3_ENST00000424807.1_Missense_Mutation_p.R525G|LILRA6_ENST00000440558.2_Missense_Mutation_p.R525G|LILRA6_ENST00000270464.5_Missense_Mutation_p.R525G			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	525				R -> G (in Ref. 2; AAB87667). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AGCTCCACCCTGTCCTCAGAC	0.617													.|||	740	0.147764	0.3525	0.1354	5008	,	,		18421	0.002		0.1103	False		,,,				2504	0.0685				p.R525G		Atlas-SNP	.											LILRB3,colon,carcinoma,+2,1	LILRB3	67	1	0			c.A1573G						PASS	.	G	GLY/ARG,GLY/ARG	1383,3023		239,905,1059	119.0	102.0	108.0		1573,1573	-0.3	0.0	19	dbSNP_86	108	1039,7561		58,923,3319	yes	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	125,125	297,1828,4378	CC,CT,TT		12.0814,31.389,18.6222	benign,benign	525/633,525/632	54722250	2422,10584	2203	4300	6503	SO:0001583	missense	11025	exon11			CCACCCTGTCCTC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1573A>G	19.37:g.54722250T>C	ENSP00000375630:p.Arg525Gly	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	268	127	0.473881	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	294	0.1346153846153846	176	0.35772357723577236	42	0.11602209944751381	2	0.0034965034965034965	74	0.09762532981530343	G	0.006	-2.043597	0.00398	0.31389	0.120814	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00454	7.49;7.49;7.36;7.47;7.32;7.48;7.49;7.49	3.11	-0.331	0.12679	.	.	.	.	.	T	0.00012	0.0000	N	0.00221	-1.82	0.80722	P	0.0	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001;0.0;0.0	B;B;B;B;B;B;B	0.12156	0.0;0.001;0.0;0.007;0.003;0.001;0.001	T	0.25047	-1.0143	8	0.02654	T	1	.	4.2725	0.10794	0.0:0.4068:0.3677:0.2255	rs1132610;rs3193489;rs52834610;rs58789613	542;525;525;537;542;525;525	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	G	525;525;537;525;542;525;525;525	ENSP00000375630:R525G;ENSP00000412771:R525G;ENSP00000345184:R537G;ENSP00000245620:R525G;ENSP00000384274:R542G;ENSP00000390120:R525G;ENSP00000270464:R525G;ENSP00000411227:R525G	ENSP00000270464:R525G	R	-	1	2	LILRB3;LILRA6	59414062	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.023000	0.01438	-0.189000	0.10482	-3.810000	0.00019	AGG	T|0.826;C|0.174	0.174	strong		0.617	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
MUC4	4585	hgsc.bcm.edu	37	3	195509113	195509113	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509113G>A	ENST00000463781.3	-	2	9797	c.9338C>T	c.(9337-9339)gCa>gTa	p.A3113V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3113V	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)		ACCTGTGGATGCTGAGGAAGG	0.587																																					p.A3113V		Atlas-SNP	.											.	MUC4	1505	.	0			c.C9338T						PASS	.																																			SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	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.9338C>T	3.37:g.195509113G>A	ENSP00000417498:p.Ala3113Val	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	313	60	0.191693	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	1.513	-0.549035	0.04024	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.49;1.5	.	.	.	.	.	.	.	.	T	0.12220	0.0297	N	0.19112	0.55	0.09310	N	1	P	0.42584	0.784	B	0.31686	0.134	T	0.15549	-1.0433	7	.	.	.	.	3.8973	0.09144	0.0:0.0:0.5926:0.4074	.	2985	E7ESK3	.	V	3113	ENSP00000417498:A3113V;ENSP00000420243:A3113V	.	A	-	2	0	MUC4	196993892	0.000000	0.05858	0.006000	0.13384	0.000000	0.00434	-1.817000	0.01719	-0.889000	0.03950	0.000000	0.15137	GCA	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PRDM16	63976	hgsc.bcm.edu	37	1	3322139	3322139	+	Silent	SNP	C	C	T	rs61745281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3322139C>T	ENST00000270722.5	+	8	1162	c.1113C>T	c.(1111-1113)tgC>tgT	p.C371C	PRDM16_ENST00000441472.2_Silent_p.C371C|PRDM16_ENST00000378398.3_Silent_p.C372C|PRDM16_ENST00000514189.1_Silent_p.C372C|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000442529.2_Silent_p.C371C|PRDM16_ENST00000378391.2_Silent_p.C371C|PRDM16_ENST00000511072.1_Silent_p.C372C			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	371					brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|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)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GCCCCGACTGCGGGAAGACCT	0.657			T	EVI1	"""MDS, AML"""								c|||	139	0.0277556	0.0998	0.0101	5008	,	,		14941	0.0		0.0	False		,,,				2504	0.0				p.C371C		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C1113T						PASS	.	C	,	363,4035		14,335,1850	41.0	48.0	46.0		1113,1113	-4.0	1.0	1	dbSNP_129	46	6,8576		0,6,4285	no	coding-synonymous,coding-synonymous	PRDM16	NM_022114.3,NM_199454.2	,	14,341,6135	TT,TC,CC		0.0699,8.2538,2.8428	,	371/1277,371/1258	3322139	369,12611	2199	4291	6490	SO:0001819	synonymous_variant	63976	exon8			CGACTGCGGGAAG	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.1113C>T	1.37:g.3322139C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																			C|0.984;T|0.016	0.016	strong		0.657	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
NDUFS1	4719	hgsc.bcm.edu	37	2	207012483	207012483	+	Silent	SNP	A	A	G	rs11548670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:207012483A>G	ENST00000233190.6	-	6	680	c.414T>C	c.(412-414)gaT>gaC	p.D138D	NDUFS1_ENST00000455934.2_Silent_p.D152D|NDUFS1_ENST00000423725.1_Silent_p.D81D|NDUFS1_ENST00000449699.1_Silent_p.D138D|NDUFS1_ENST00000432169.1_Silent_p.D27D|NDUFS1_ENST00000440274.1_Silent_p.D102D|NDUFS1_ENST00000457011.1_Silent_p.D22D	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	138					apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ATACCTGCAGATCACATTCAC	0.358													A|||	329	0.0656949	0.1067	0.0288	5008	,	,		17593	0.0476		0.0408	False		,,,				2504	0.0808				p.D152D		Atlas-SNP	.											.	NDUFS1	82	.	0			c.T456C						PASS	.	A	,,,,	463,3943	222.6+/-239.4	26,411,1766	103.0	97.0	99.0		306,81,243,456,414	4.8	1.0	2	dbSNP_120	99	264,8336	101.6+/-162.9	6,252,4042	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDUFS1	NM_001199981.1,NM_001199982.1,NM_001199983.1,NM_001199984.1,NM_005006.6	,,,,	32,663,5808	GG,GA,AA		3.0698,10.5084,5.5897	,,,,	102/692,27/617,81/671,152/742,138/728	207012483	727,12279	2203	4300	6503	SO:0001819	synonymous_variant	4719	exon6			CTGCAGATCACAT		CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7707	protein-coding gene	gene with protein product	"""complex I 75kDa subunit"", ""NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"""	157655	"""NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"""			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.414T>C	2.37:g.207012483A>G		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	148	60	0.405405	NM_001199984	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Silent	SNP	ENST00000233190.6	37	CCDS2366.1																																																																																			A|0.946;G|0.054	0.054	strong		0.358	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006	
OR2L8	391190	hgsc.bcm.edu	37	1	248112546	248112546	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248112546C>T	ENST00000357191.3	+	1	387	c.387C>T	c.(385-387)ctC>ctT	p.L129L	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	129						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			GCTTTCCTCTCCACTATCTCA	0.443																																					p.L129L		Atlas-SNP	.											OR2L8,NS,carcinoma,0,1	OR2L8	92	1	0			c.C387T						scavenged	.						298.0	260.0	273.0					1																	248112546		2203	4300	6503	SO:0001819	synonymous_variant	391190	exon1			TCCTCTCCACTAT	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"""GPCR / Class A : Olfactory receptors"""	15014	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily L, member 8"""				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.387C>T	1.37:g.248112546C>T		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	338	32	0.0946746	NM_001001963	Q6IF03	Silent	SNP	ENST00000357191.3	37	CCDS31101.1																																																																																			.	.	none		0.443	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2		
PROKR2	128674	hgsc.bcm.edu	37	20	5283316	5283316	+	Silent	SNP	G	G	C	rs3746683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5283316G>C	ENST00000217270.3	-	2	524	c.525C>G	c.(523-525)gcC>gcG	p.A175A	PROKR2_ENST00000546004.1_Silent_p.A175A	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	175					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						TCCAGACCAAGGCGATCAGGA	0.493										HNSCC(71;0.22)			G|||	493	0.0984425	0.1195	0.0793	5008	,	,		23135	0.0377		0.1362	False		,,,				2504	0.1074				p.A175A		Atlas-SNP	.											PROKR2,caecum,carcinoma,-2,3	PROKR2	90	3	0			c.C525G						PASS	.	G		548,3858	248.7+/-256.4	41,466,1696	140.0	146.0	144.0		525	-7.7	0.2	20	dbSNP_107	144	996,7604	215.6+/-254.9	60,876,3364	no	coding-synonymous	PROKR2	NM_144773.2		101,1342,5060	CC,CG,GG		11.5814,12.4376,11.8714		175/385	5283316	1544,11462	2203	4300	6503	SO:0001819	synonymous_variant	128674	exon2			GACCAAGGCGATC	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.525C>G	20.37:g.5283316G>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_144773	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Silent	SNP	ENST00000217270.3	37	CCDS13089.1																																																																																			G|0.887;C|0.113	0.113	strong		0.493	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773	
SPATA9	83890	hgsc.bcm.edu	37	5	95011166	95011166	+	Missense_Mutation	SNP	G	G	A	rs140676515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:95011166G>A	ENST00000274432.8	-	3	469	c.328C>T	c.(328-330)Cgt>Tgt	p.R110C	SPATA9_ENST00000395899.3_Missense_Mutation_p.R110C|RFESD_ENST00000508206.1_Intron|SPATA9_ENST00000477047.2_5'UTR	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	110					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)	7		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)		CTCAGCAGACGACCAGATATG	0.433													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18649	0.0		0.0	False		,,,				2504	0.0				p.R110C		Atlas-SNP	.											SPATA9,NS,carcinoma,+1,1	SPATA9	17	1	0			c.C328T						scavenged	.	G	CYS/ARG	29,4377	35.2+/-66.4	0,29,2174	133.0	113.0	120.0		328	3.9	0.0	5	dbSNP_134	120	0,8600		0,0,4300	yes	missense	SPATA9	NM_031952.3	180	0,29,6474	AA,AG,GG		0.0,0.6582,0.223	probably-damaging	110/255	95011166	29,12977	2203	4300	6503	SO:0001583	missense	83890	exon3			GCAGACGACCAGA	AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.328C>T	5.37:g.95011166G>A	ENSP00000274432:p.Arg110Cys	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	137	63	0.459854	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Missense_Mutation	SNP	ENST00000274432.8	37	CCDS4076.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	12.73	2.024694	0.35701	0.006582	0.0	ENSG00000145757	ENST00000274432;ENST00000395899	T	0.31510	1.49	4.76	3.88	0.44766	.	0.000000	0.51477	D	0.000082	T	0.26448	0.0646	L	0.27053	0.805	0.19300	N	0.999974	D	0.67145	0.996	P	0.57371	0.819	T	0.05818	-1.0862	10	0.87932	D	0	-8.0846	10.6281	0.45519	0.0:0.0:0.8093:0.1907	.	110	Q9BWV2	SPAT9_HUMAN	C	110	ENSP00000274432:R110C	ENSP00000274432:R110C	R	-	1	0	SPATA9	95036922	0.074000	0.21230	0.029000	0.17559	0.011000	0.07611	1.948000	0.40303	1.329000	0.45376	0.655000	0.94253	CGT	G|0.998;A|0.002	0.002	strong		0.433	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952	
OR8K5	219453	hgsc.bcm.edu	37	11	55927591	55927591	+	Missense_Mutation	SNP	A	A	G	rs2512938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55927591A>G	ENST00000313447.1	-	1	202	c.203T>C	c.(202-204)tTt>tCt	p.F68S		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	68			F -> S (in dbSNP:rs2512938).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				AAGATCAACAAAAGCCAAATG	0.398													.|||	111	0.0221645	0.0779	0.0115	5008	,	,		21695	0.0		0.0	False		,,,				2504	0.0				p.F68S		Atlas-SNP	.											.	OR8K5	82	.	0			c.T203C						PASS	.	A	SER/PHE	280,4122	155.9+/-189.0	9,262,1930	110.0	109.0	109.0		203	2.7	0.9	11	dbSNP_100	109	6,8586	4.3+/-15.6	0,6,4290	yes	missense	OR8K5	NM_001004058.2	155	9,268,6220	GG,GA,AA		0.0698,6.3607,2.201	possibly-damaging	68/308	55927591	286,12708	2201	4296	6497	SO:0001583	missense	219453	exon1			TCAACAAAAGCCA	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"""GPCR / Class A : Olfactory receptors"""	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.203T>C	11.37:g.55927591A>G	ENSP00000323853:p.Phe68Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_001004058	Q6IFB5	Missense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	44	0.020146520146520148	39	0.07926829268292683	5	0.013812154696132596	0	0.0	0	0.0	A	11.51	1.659357	0.29515	0.063607	6.98E-4	ENSG00000181752	ENST00000313447	T	0.01005	5.45	3.87	2.69	0.31865	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00178	0.0005	M	0.79475	2.455	0.23834	N	0.996718	D	0.56746	0.977	P	0.47744	0.556	T	0.48559	-0.9025	9	0.72032	D	0.01	.	8.9967	0.36057	0.8337:0.0:0.0:0.1663	rs2512938;rs56484064;rs2512938	68	Q8NH50	OR8K5_HUMAN	S	68	ENSP00000323853:F68S	ENSP00000323853:F68S	F	-	2	0	OR8K5	55684167	0.082000	0.21442	0.937000	0.37676	0.050000	0.14768	3.809000	0.55606	0.621000	0.30232	-0.555000	0.04198	TTT	A|0.974;G|0.026	0.026	strong		0.398	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058	
WDR73	84942	hgsc.bcm.edu	37	15	85188839	85188839	+	Missense_Mutation	SNP	C	C	T	rs11073619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85188839C>T	ENST00000434634.2	-	7	806	c.746G>A	c.(745-747)cGt>cAt	p.R249H	WDR73_ENST00000398528.3_5'UTR	NM_032856.2	NP_116245.2	Q6P4I2	WDR73_HUMAN	WD repeat domain 73	249			R -> H (in dbSNP:rs11073619).							cervix(1)|large_intestine(1)|lung(1)	3						AAGACAAAGACGCCCATCTGA	0.627													C|||	408	0.0814696	0.1097	0.1902	5008	,	,		16265	0.002		0.1074	False		,,,				2504	0.0215				p.R249H		Atlas-SNP	.											.	WDR73	15	.	0			c.G746A						PASS	.	C	HIS/ARG	441,3489		29,383,1553	25.0	30.0	29.0		746	2.2	0.9	15	dbSNP_120	29	781,7523		38,705,3409	yes	missense	WDR73	NM_032856.2	29	67,1088,4962	TT,TC,CC		9.4051,11.2214,9.9886	benign	249/379	85188839	1222,11012	1965	4152	6117	SO:0001583	missense	84942	exon7			CAAAGACGCCCAT	AK027200	CCDS45339.1	15q25.2	2013-01-09				ENSG00000177082		"""WD repeat domain containing"""	25928	protein-coding gene	gene with protein product						12477932	Standard	NM_032856		Approved	FLJ14888, HSPC264	uc002bkw.2	Q6P4I2		ENST00000434634.2:c.746G>A	15.37:g.85188839C>T	ENSP00000387982:p.Arg249His	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_032856	Q96JZ1|Q9P0B7	Missense_Mutation	SNP	ENST00000434634.2	37	CCDS45339.1	218	0.09981684981684982	71	0.1443089430894309	58	0.16022099447513813	2	0.0034965034965034965	87	0.11477572559366754	C	2.708	-0.269511	0.05716	0.112214	0.094051	ENSG00000177082	ENST00000398528;ENST00000434634	T	0.29397	1.57	5.8	2.21	0.28008	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.634443	0.17879	N	0.158934	T	0.00039	0.0001	N	0.01352	-0.895	0.47153	P	6.690000000000307E-4	B	0.06786	0.001	B	0.04013	0.001	T	0.32561	-0.9902	9	0.23302	T	0.38	-17.6382	6.6191	0.22792	0.1385:0.0823:0.0:0.7792	rs11073619;rs52820653;rs58160077;rs11073619	249	Q6P4I2	WDR73_HUMAN	H	257;249	ENSP00000387982:R249H	ENSP00000381539:R257H	R	-	2	0	WDR73	82989843	0.891000	0.30450	0.864000	0.33941	0.138000	0.21146	0.344000	0.19962	0.111000	0.17947	-1.110000	0.02074	CGT	C|0.903;T|0.097	0.097	strong		0.627	WDR73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418195.1	NM_032856	
GSTO2	119391	hgsc.bcm.edu	37	10	106058940	106058940	+	Silent	SNP	C	C	T	rs157078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:106058940C>T	ENST00000338595.2	+	7	950	c.630C>T	c.(628-630)gaC>gaT	p.D210D	GSTO2_ENST00000369707.2_Silent_p.D182D|GSTO2_ENST00000450629.2_Silent_p.D176D|GSTO2_ENST00000429569.2_Missense_Mutation_p.P113S	NM_183239.1	NP_899062.1	Q9H4Y5	GSTO2_HUMAN	glutathione S-transferase omega 2	210	GST C-terminal.				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)			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)	TGAAGTGGGACCCCACAGTCT	0.522													C|||	247	0.0493211	0.1823	0.0086	5008	,	,		16782	0.0		0.0	False		,,,				2504	0.0				p.D210D		Atlas-SNP	.											.	GSTO2	23	.	0			c.C630T						PASS	.	C	,,,	643,3763	276.0+/-272.9	61,521,1621	104.0	100.0	101.0		528,546,444,630	4.1	1.0	10	dbSNP_79	101	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GSTO2	NM_001191013.1,NM_001191014.1,NM_001191015.1,NM_183239.1	,,,	61,523,5919	TT,TC,CC		0.0233,14.5937,4.9592	,,,	176/210,182/216,148/182,210/244	106058940	645,12361	2203	4300	6503	SO:0001819	synonymous_variant	119391	exon7			GTGGGACCCCACA	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.630C>T	10.37:g.106058940C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	130	61	0.469231	NM_183239	A8K771|B4DJW6|E7ESD6|Q49TW5|Q5GM70|Q5JU15|Q86WP3	Silent	SNP	ENST00000338595.2	37	CCDS7556.1	76	0.0347985347985348	71	0.1443089430894309	5	0.013812154696132596	0	0.0	0	0.0	C	13.14	2.149018	0.37923	0.145937	2.33E-4	ENSG00000065621	ENST00000429569	T	0.13901	2.55	5.9	4.06	0.47325	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.24759	N	0.992935	B	0.12630	0.006	B	0.11329	0.006	T	0.36553	-0.9743	8	0.33141	T	0.24	-34.5724	8.1478	0.31121	0.0:0.8242:0.0:0.1758	rs157078;rs545826;rs157078	113	B4DML4	.	S	113	ENSP00000407381:P113S	ENSP00000407381:P113S	P	+	1	0	GSTO2	106048930	1.000000	0.71417	1.000000	0.80357	0.528000	0.34623	0.617000	0.24359	1.501000	0.48654	0.563000	0.77884	CCC	C|0.952;T|0.048	0.048	strong		0.522	GSTO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050210.2	NM_183239	
PRR21	643905	hgsc.bcm.edu	37	2	240982200	240982200	+	Missense_Mutation	SNP	C	C	T	rs114958540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240982200C>T	ENST00000408934.1	-	1	199	c.200G>A	c.(199-201)tGt>tAt	p.C67Y		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	67	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						GGTGAAGGGACATGGGTGAAG	0.607													N|||	410	0.081869	0.0651	0.0605	5008	,	,		14426	0.1677		0.0666	False		,,,				2504	0.047				p.C67Y		Atlas-SNP	.											PRR21,NS,carcinoma,+1,2	PRR21	53	2	0			c.G200A						scavenged	.						136.0	123.0	127.0					2																	240982200		2202	4300	6502	SO:0001583	missense	643905	exon1			AAGGGACATGGGT	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.200G>A	2.37:g.240982200C>T	ENSP00000386166:p.Cys67Tyr	Somatic	147	2	0.0136054		WXS	Illumina HiSeq	Phase_I	170	10	0.0588235	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	N	2.358	-0.347289	0.05208	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13420	2.59;2.59	1.46	-2.3	0.06785	.	.	.	.	.	T	0.05731	0.0150	N	0.08118	0	0.09310	N	1	B	0.21071	0.051	B	0.15870	0.014	T	0.43637	-0.9379	9	0.19590	T	0.45	.	8.228	0.31582	0.0:0.7349:0.0:0.2651	.	67	Q8WXC7	PRR21_HUMAN	Y	67	ENSP00000386166:C67Y;ENSP00000418240:C67Y	ENSP00000386166:C67Y	C	-	2	0	PRR21	240630873	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.852000	0.04308	-0.717000	0.04955	-1.756000	0.00673	TGT	C|0.980;T|0.019	0.019	strong		0.607	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
AIM1	202	hgsc.bcm.edu	37	6	106960447	106960447	+	Silent	SNP	G	G	A	rs11152999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:106960447G>A	ENST00000369066.3	+	1	718	c.231G>A	c.(229-231)gaG>gaA	p.E77E		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		CGAGCCCAGAGTCCAAGCCCA	0.677													G|||	1274	0.254393	0.1135	0.3026	5008	,	,		14075	0.4395		0.166	False		,,,				2504	0.3108				p.E77E		Atlas-SNP	.											.	AIM1	161	.	0			c.G231A						PASS	.	G		504,3782		37,430,1676	10.0	11.0	11.0		231	2.7	0.0	6	dbSNP_120	11	1197,7241		91,1015,3113	no	coding-synonymous	AIM1	NM_001624.2		128,1445,4789	AA,AG,GG		14.1858,11.7592,13.3684		77/1724	106960447	1701,11023	2143	4219	6362	SO:0001819	synonymous_variant	202	exon1			CCCAGAGTCCAAG	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.231G>A	6.37:g.106960447G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_001624	Q6P2P0|Q9BTM3	Silent	SNP	ENST00000369066.3	37	CCDS34506.1																																																																																			G|0.804;A|0.196	0.196	strong		0.677	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
CYP4F12	66002	hgsc.bcm.edu	37	19	15794470	15794470	+	Missense_Mutation	SNP	G	G	A	rs150943202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794470G>A	ENST00000550308.1	+	7	1195	c.815G>A	c.(814-816)cGg>cAg	p.R272Q	CYP4F12_ENST00000324632.10_Missense_Mutation_p.R272Q	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	272					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GCTGTCATCCGGGAGCGGCGT	0.542													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20675	0.0		0.001	False		,,,				2504	0.0				p.R272Q		Atlas-SNP	.											CYP4F12,NS,haematopoietic_neoplasm,+1,1	CYP4F12	89	1	0			c.G815A						PASS	.	G	GLN/ARG	240,4156		0,240,1958	93.0	94.0	94.0		815	0.3	1.0	19	dbSNP_134	94	2,8594		0,2,4296	yes	missense	CYP4F12	NM_023944.3	43	0,242,6254	AA,AG,GG		0.0233,5.4595,1.8627	benign	272/525	15794470	242,12750	2198	4298	6496	SO:0001583	missense	66002	exon7			TCATCCGGGAGCG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.815G>A	19.37:g.15794470G>A	ENSP00000448998:p.Arg272Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	155	36	0.232258	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	.	0.017	-1.504706	0.00992	0.054595	2.33E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.67523	-0.27;-0.27	2.46	0.278	0.15673	.	0.278314	0.28877	N	0.013843	T	0.05456	0.0144	N	0.02751	-0.505	0.24533	N	0.994106	B	0.02656	0.0	B	0.04013	0.001	T	0.14531	-1.0469	10	0.02654	T	1	.	5.8094	0.18457	0.7285:0.0:0.2715:0.0	.	272	Q9HCS2	CP4FC_HUMAN	Q	272	ENSP00000448998:R272Q;ENSP00000321821:R272Q	ENSP00000321821:R272Q	R	+	2	0	CYP4F12	15655470	1.000000	0.71417	0.993000	0.49108	0.356000	0.29392	1.185000	0.32065	-0.008000	0.14320	-0.475000	0.04921	CGG	G|0.989;A|0.011	0.011	strong		0.542	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
CPA5	93979	hgsc.bcm.edu	37	7	129986338	129986338	+	Silent	SNP	C	C	T	rs6973851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:129986338C>T	ENST00000485477.1	+	2	1141	c.12C>T	c.(10-12)acC>acT	p.T4T	CPA5_ENST00000355388.3_Silent_p.T4T|snoU13_ENST00000459205.1_RNA|CPA5_ENST00000466363.2_Silent_p.T4T|CPA5_ENST00000461828.1_Silent_p.T4T|CPA5_ENST00000393213.3_Silent_p.T4T|CPA5_ENST00000474905.1_Silent_p.T4T|CPA5_ENST00000431780.2_Silent_p.T4T			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	4						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					TGCAGGGCACCCCTGGAGGCG	0.622													C|||	2972	0.59345	0.6467	0.6484	5008	,	,		18970	0.5347		0.5845	False		,,,				2504	0.5521				p.T4T		Atlas-SNP	.											.	CPA5	61	.	0			c.C12T						PASS	.	C	,,	2812,1594	662.3+/-401.0	900,1012,291	66.0	72.0	70.0		12,12,12	1.6	0.0	7	dbSNP_116	70	4989,3611	624.1+/-397.5	1444,2101,755	no	coding-synonymous,coding-synonymous,coding-synonymous	CPA5	NM_001127441.1,NM_001127442.1,NM_080385.4	,,	2344,3113,1046	TT,TC,CC		41.9884,36.1779,40.02	,,	4/437,4/404,4/437	129986338	7801,5205	2203	4300	6503	SO:0001819	synonymous_variant	93979	exon3			GGGCACCCCTGGA	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.12C>T	7.37:g.129986338C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_080385	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Silent	SNP	ENST00000485477.1	37	CCDS5819.1																																																																																			C|0.418;T|0.582	0.582	strong		0.622	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441	
NPHP4	261734	hgsc.bcm.edu	37	1	5926507	5926507	+	Silent	SNP	T	T	C	rs555164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:5926507T>C	ENST00000378156.4	-	26	3835	c.3570A>G	c.(3568-3570)gaA>gaG	p.E1190E	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	1190					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.E1190E(2)		NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		TGTCCCGTGGTTCCCCGGGGC	0.562													C|||	1601	0.319688	0.1619	0.379	5008	,	,		17616	0.2837		0.4135	False		,,,				2504	0.4315				p.E1190E		Atlas-SNP	.											NPHP4,NS,carcinoma,0,1	NPHP4	119	1	2	Substitution - coding silent(2)	prostate(2)	c.A3570G						PASS	.	C		768,3102		79,610,1246	32.0	34.0	33.0		3570	3.2	1.0	1	dbSNP_83	33	3460,4784		760,1940,1422	no	coding-synonymous	NPHP4	NM_015102.3		839,2550,2668	CC,CT,TT		41.9699,19.845,34.9018		1190/1427	5926507	4228,7886	1935	4122	6057	SO:0001819	synonymous_variant	261734	exon26			CCGTGGTTCCCCG	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.3570A>G	1.37:g.5926507T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	139	49	0.352518	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																			T|0.698;C|0.302	0.302	strong		0.562	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
PCDHGA8	9708	hgsc.bcm.edu	37	5	140773388	140773388	+	Silent	SNP	G	G	T	rs370400807|rs2240700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140773388G>T	ENST00000398604.2	+	1	1008	c.1008G>T	c.(1006-1008)tcG>tcT	p.S336S	PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	336	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)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTCATTTCGGTGGAAGATG	0.398													.|||	1012	0.202077	0.3169	0.1902	5008	,	,		18441	0.1548		0.1014	False		,,,				2504	0.2076				p.S336S		Atlas-SNP	.											PCDHGA8,caecum,carcinoma,+1,3	PCDHGA8	146	3	0			c.G1008T						PASS	.	G	,,,,,,,,,,,,	1171,2545		190,791,877	146.0	149.0	148.0		,1008,,,,,,,,,,,1008	-10.6	0.1	5	dbSNP_98	148	1005,7203		63,879,3162	yes	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,,,,,,,,,,,,	253,1670,4039	TT,TG,GG		12.2442,31.5124,18.2489	,,,,,,,,,,,,	,336/821,,,,,,,,,,,336/933	140773388	2176,9748	1858	4104	5962	SO:0001819	synonymous_variant	9708	exon1			CATTTCGGTGGAA	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.1008G>T	5.37:g.140773388G>T		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	246	95	0.386179	NM_014004	A7MCZ4|O15039	Silent	SNP	ENST00000398604.2	37	CCDS47291.1																																																																																			G|0.805;T|0.195	0.195	strong		0.398	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
ENTPD5	957	hgsc.bcm.edu	37	14	74454675	74454675	+	Missense_Mutation	SNP	C	C	G	rs60372237	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74454675C>G	ENST00000334696.6	-	4	450	c.131G>C	c.(130-132)aGc>aCc	p.S44T	ENTPD5_ENST00000557325.1_Missense_Mutation_p.S44T|ENTPD5_ENST00000556242.1_Missense_Mutation_p.S44T|ENTPD5_ENST00000554664.1_5'Flank	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	44					'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)		GGTGCTGGCGCTGACATTGAT	0.493													C|||	17	0.00339457	0.0129	0.0	5008	,	,		18640	0.0		0.0	False		,,,				2504	0.0				p.S44T		Atlas-SNP	.											.	ENTPD5	26	.	0			c.G131C						PASS	.	C	THR/SER	21,4385	28.1+/-56.4	0,21,2182	115.0	100.0	105.0		131	5.2	1.0	14	dbSNP_129	105	0,8600		0,0,4300	yes	missense	ENTPD5	NM_001249.2	58	0,21,6482	GG,GC,CC		0.0,0.4766,0.1615	benign	44/429	74454675	21,12985	2203	4300	6503	SO:0001583	missense	957	exon4			CTGGCGCTGACAT	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.131G>C	14.37:g.74454675C>G	ENSP00000335246:p.Ser44Thr	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_001249	A1L4C5|Q96RX0	Missense_Mutation	SNP	ENST00000334696.6	37	CCDS9825.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	13.72	2.320324	0.41096	0.004766	0.0	ENSG00000187097	ENST00000557325;ENST00000334696;ENST00000553284;ENST00000556242	T;T;T	0.30714	2.26;2.52;1.52	5.2	5.2	0.72013	.	0.672949	0.15537	N	0.257193	T	0.09291	0.0229	N	0.19112	0.55	0.24994	N	0.991512	B;B	0.22146	0.065;0.053	B;B	0.18561	0.022;0.013	T	0.11446	-1.0587	10	0.13470	T	0.59	-12.6302	10.8164	0.46578	0.0:0.9069:0.0:0.0931	rs60372237	44;44	O75356;G3V4I0	ENTP5_HUMAN;.	T	44	ENSP00000451810:S44T;ENSP00000335246:S44T;ENSP00000451591:S44T	ENSP00000335246:S44T	S	-	2	0	ENTPD5	73524428	0.858000	0.29795	1.000000	0.80357	0.972000	0.66771	1.528000	0.35985	2.708000	0.92522	0.551000	0.68910	AGC	C|0.997;G|0.003	0.003	strong		0.493	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249	
RARS2	57038	hgsc.bcm.edu	37	6	88224164	88224164	+	Silent	SNP	T	T	C	rs8802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88224164T>C	ENST00000369536.5	-	20	1749	c.1704A>G	c.(1702-1704)aaA>aaG	p.K568K		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	568					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)		TTCCAAGAAGTTTCATTCCAT	0.333													T|||	661	0.131989	0.1604	0.1441	5008	,	,		18114	0.1468		0.1014	False		,,,				2504	0.1012				p.K568K		Atlas-SNP	.											.	RARS2	61	.	0			c.A1704G						PASS	.	T		723,3683	299.0+/-285.6	60,603,1540	64.0	67.0	66.0		1704	3.2	1.0	6	dbSNP_52	66	800,7800	185.7+/-233.4	30,740,3530	no	coding-synonymous	RARS2	NM_020320.3		90,1343,5070	CC,CT,TT		9.3023,16.4094,11.71		568/579	88224164	1523,11483	2203	4300	6503	SO:0001819	synonymous_variant	57038	exon20			AAGAAGTTTCATT	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.1704A>G	6.37:g.88224164T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	180	94	0.522222	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Silent	SNP	ENST00000369536.5	37	CCDS5011.1																																																																																			T|0.871;C|0.129	0.129	strong		0.333	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
SSH2	85464	hgsc.bcm.edu	37	17	27959903	27959903	+	Missense_Mutation	SNP	G	G	A	rs2289629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27959903G>A	ENST00000269033.3	-	15	2379	c.2228C>T	c.(2227-2229)tCg>tTg	p.S743L	SSH2_ENST00000540801.1_Missense_Mutation_p.S770L|RP11-68I3.2_ENST00000581474.1_RNA	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	743			S -> L (in dbSNP:rs2289629).		actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	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)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGCATTTTCCGAGTGAGACTG	0.403													G|||	925	0.184704	0.1044	0.2983	5008	,	,		22841	0.0764		0.335	False		,,,				2504	0.1697				p.S743L		Atlas-SNP	.											.	SSH2	107	.	0			c.C2228T						PASS	.	G	LEU/SER	680,3726	284.9+/-277.9	48,584,1571	71.0	65.0	67.0		2228	4.1	1.0	17	dbSNP_100	67	2861,5739	448.8+/-361.9	484,1893,1923	yes	missense	SSH2	NM_033389.2	145	532,2477,3494	AA,AG,GG		33.2674,15.4335,27.2259	benign	743/1424	27959903	3541,9465	2203	4300	6503	SO:0001583	missense	85464	exon15			TTTTCCGAGTGAG	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30580	protein-coding gene	gene with protein product		606779	"""slingshot homolog 2 (Drosophila)"""			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.2228C>T	17.37:g.27959903G>A	ENSP00000269033:p.Ser743Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	37	CCDS11253.1	432	0.1978021978021978	50	0.1016260162601626	108	0.2983425414364641	35	0.06118881118881119	239	0.3153034300791557	G	14.83	2.653224	0.47362	0.154335	0.332674	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.54675	0.56;0.56	6.08	4.1	0.47936	.	0.456816	0.22979	N	0.053336	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	0.9999999999999972	B;B	0.26081	0.141;0.087	B;B	0.20184	0.028;0.013	T	0.09530	-1.0670	9	0.48119	T	0.1	-1.9919	17.9574	0.89073	0.0645:0.0:0.9355:0.0	rs2289629;rs17766954;rs52836060;rs59862381;rs2289629	770;743	F5H527;Q76I76	.;SSH2_HUMAN	L	743;770	ENSP00000269033:S743L;ENSP00000444743:S770L	ENSP00000269033:S743L	S	-	2	0	SSH2	24984029	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.615000	0.54167	0.907000	0.36646	-0.940000	0.02684	TCG	G|0.775;A|0.225	0.225	strong		0.403	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389	
PARP12	64761	hgsc.bcm.edu	37	7	139746793	139746793	+	Missense_Mutation	SNP	C	C	T	rs34111764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139746793C>T	ENST00000263549.3	-	5	1750	c.877G>A	c.(877-879)Gtt>Att	p.V293I		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	293			V -> I (in dbSNP:rs34111764).			nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					TGGAAATGAACTCTATGGCAC	0.433													C|||	490	0.0978435	0.298	0.0375	5008	,	,		20477	0.0		0.0408	False		,,,				2504	0.0297				p.V293I		Atlas-SNP	.											.	PARP12	59	.	0			c.G877A						PASS	.	C	ILE/VAL	1162,3244	412.4+/-336.1	165,832,1206	118.0	105.0	110.0		877	3.7	0.7	7	dbSNP_126	110	383,8217	124.1+/-182.9	13,357,3930	yes	missense	PARP12	NM_022750.2	29	178,1189,5136	TT,TC,CC		4.4535,26.3731,11.8791	possibly-damaging	293/702	139746793	1545,11461	2203	4300	6503	SO:0001583	missense	64761	exon5			AATGAACTCTATG	AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	21919	protein-coding gene	gene with protein product		612481	"""zinc finger CCCH-type domain containing 1"""	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.877G>A	7.37:g.139746793C>T	ENSP00000263549:p.Val293Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_022750	Q9H610|Q9NP36|Q9NTI3	Missense_Mutation	SNP	ENST00000263549.3	37	CCDS5857.1	166	0.076007326007326	127	0.258130081300813	11	0.03038674033149171	0	0.0	28	0.036939313984168866	C	9.431	1.085463	0.20390	0.263731	0.044535	ENSG00000059378	ENST00000263549	T	0.07114	3.22	5.56	3.67	0.42095	WWE domain (1);Zinc finger, CCCH-type (2);	0.355683	0.29846	N	0.011057	T	0.00012	0.0000	L	0.53561	1.675	0.52099	P	5.599999999994498E-5	P	0.40360	0.714	B	0.39027	0.288	T	0.50145	-0.8862	9	0.25106	T	0.35	.	9.9843	0.41832	0.0:0.7508:0.0:0.2492	rs34111764	293	Q9H0J9	PAR12_HUMAN	I	293	ENSP00000263549:V293I	ENSP00000263549:V293I	V	-	1	0	PARP12	139393262	0.991000	0.36638	0.727000	0.30756	0.195000	0.23768	2.699000	0.47077	0.756000	0.33013	-0.390000	0.06520	GTT	C|0.893;T|0.107	0.107	strong		0.433	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750	
OR13C5	138799	hgsc.bcm.edu	37	9	107361451	107361451	+	Silent	SNP	G	G	A	rs376107801|rs201540433|rs377523807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361451G>A	ENST00000374779.2	-	1	337	c.244C>T	c.(244-246)Cta>Tta	p.L82L		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AAGCTCACTAGCGTGGAGGGA	0.512													A|||	3407	0.680312	0.761	0.5937	5008	,	,		19219	0.9573		0.4225	False		,,,				2504	0.6125				p.L82L		Atlas-SNP	.											.	OR13C5	60	.	0			c.C244T						PASS	.																																			SO:0001819	synonymous_variant	138799	exon1			TCACTAGCGTGGA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.244C>T	9.37:g.107361451G>A		Somatic	757	0	0		WXS	Illumina HiSeq	Phase_I	713	296	0.415147	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			.	.	weak		0.512	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
APEH	327	hgsc.bcm.edu	37	3	49721606	49721606	+	IGR	SNP	G	G	A	rs138238101		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49721606G>A	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Missense_Mutation_p.P678L|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.P664L(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCAGGCAAGTGGGCCCCCGTA	0.562																																					p.P678L		Atlas-SNP	.											MST1,caecum,carcinoma,0,1	MST1	84	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2033T						scavenged	.						27.0	25.0	25.0					3																	49721606		2203	4300	6503	SO:0001628	intergenic_variant	4485	exon18			GCAAGTGGGCCCC	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49721606G>A		Somatic	547	23	0.0420475		WXS	Illumina HiSeq	Phase_I	587	55	0.0936968	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.778691	0.90195	.	.	ENSG00000173531	ENST00000449682	D	0.98684	-5.07	5.44	5.44	0.79542	.	0.000000	0.42053	D	0.000775	D	0.99579	0.9848	H	0.98849	4.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97649	1.0153	10	0.87932	D	0	.	19.2477	0.93909	0.0:0.0:1.0:0.0	.	678	G3XAK1	.	L	678	ENSP00000414287:P678L	ENSP00000414287:P678L	P	-	2	0	MST1	49696610	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.295000	0.96095	2.544000	0.85801	0.655000	0.94253	CCA	.	.	weak		0.562	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
FAM83B	222584	hgsc.bcm.edu	37	6	54806379	54806379	+	Silent	SNP	A	A	G	rs17678648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:54806379A>G	ENST00000306858.7	+	5	2726	c.2610A>G	c.(2608-2610)ccA>ccG	p.P870P	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	870										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					CACCTTCTCCAGGTCCAGTTG	0.433													A|||	148	0.0295527	0.0219	0.0389	5008	,	,		20220	0.0		0.0557	False		,,,				2504	0.0368				p.P870P		Atlas-SNP	.											.	FAM83B	186	.	0			c.A2610G						PASS	.	A		118,4288	86.8+/-125.4	1,116,2086	61.0	58.0	59.0		2610	1.8	0.0	6	dbSNP_123	59	546,8054	148.5+/-203.7	15,516,3769	no	coding-synonymous	FAM83B	NM_001010872.1		16,632,5855	GG,GA,AA		6.3488,2.6782,5.1053		870/1012	54806379	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	222584	exon5			TTCTCCAGGTCCA	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.2610A>G	6.37:g.54806379A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_001010872	Q2M1P3|Q96DQ2	Silent	SNP	ENST00000306858.7	37	CCDS34479.1																																																																																			A|0.956;G|0.044	0.044	strong		0.433	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
EEFSEC	60678	hgsc.bcm.edu	37	3	127872506	127872506	+	Silent	SNP	C	C	T	rs11711710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127872506C>T	ENST00000254730.6	+	1	210	c.156C>T	c.(154-156)ggC>ggT	p.G52G	EEFSEC_ENST00000483457.1_Silent_p.G52G|RUVBL1_ENST00000464873.1_5'UTR	NM_021937.3	NP_068756.2	P57772	SELB_HUMAN	eukaryotic elongation factor, selenocysteine-tRNA-specific	52	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				selenocysteine incorporation (GO:0001514)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)|translation elongation factor activity (GO:0003746)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)	25						TCGATCTGGGCTTCTCGTGCT	0.726													C|||	682	0.136182	0.2315	0.134	5008	,	,		11740	0.0069		0.1143	False		,,,				2504	0.1646				p.G52G		Atlas-SNP	.											.	EEFSEC	53	.	0			c.C156T						PASS	.	C		880,3484		96,688,1398	11.0	14.0	13.0		156	4.3	1.0	3	dbSNP_120	13	1010,7520		57,896,3312	no	coding-synonymous	EEFSEC	NM_021937.3		153,1584,4710	TT,TC,CC		11.8406,20.165,14.658		52/597	127872506	1890,11004	2182	4265	6447	SO:0001819	synonymous_variant	60678	exon1			TCTGGGCTTCTCG		CCDS33849.1	3q21.3	2007-05-25			ENSG00000132394	ENSG00000132394			24614	protein-coding gene	gene with protein product	"""elongation factor for selenoprotein translation"""	607695				10970870, 15229221	Standard	XM_005247696		Approved	SELB, EFSEC	uc003eki.3	P57772	OTTHUMG00000159659	ENST00000254730.6:c.156C>T	3.37:g.127872506C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_021937	Q96HZ6	Silent	SNP	ENST00000254730.6	37	CCDS33849.1																																																																																			C|0.866;T|0.134	0.134	strong		0.726	EEFSEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356738.2	NM_021937	
DLG1	1739	hgsc.bcm.edu	37	3	196842831	196842831	+	Silent	SNP	A	A	G	rs79212676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196842831A>G	ENST00000419354.1	-	14	1795	c.1509T>C	c.(1507-1509)agT>agC	p.S503S	DLG1_ENST00000448528.2_Silent_p.S503S|DLG1_ENST00000314062.3_Silent_p.S452S|DLG1_ENST00000422288.1_Silent_p.S452S|DLG1_ENST00000452595.1_Silent_p.S387S|DLG1_ENST00000450955.1_Silent_p.S470S|DLG1_ENST00000392382.2_Silent_p.S470S|DLG1_ENST00000357674.4_Silent_p.S470S|DLG1_ENST00000443183.1_Silent_p.S387S|DLG1_ENST00000346964.2_Silent_p.S503S			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	503	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		TGAGCTCTCCACTTAGATCAG	0.408													A|||	40	0.00798722	0.0265	0.0072	5008	,	,		16788	0.0		0.0	False		,,,				2504	0.0				p.S503S		Atlas-SNP	.											.	DLG1	120	.	0			c.T1509C						PASS	.	A	,,,,	118,4288	88.7+/-127.4	1,116,2086	119.0	114.0	116.0		1509,1410,1161,1161,1509	3.2	1.0	3	dbSNP_131	116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLG1	NM_001098424.1,NM_001204386.1,NM_001204387.1,NM_001204388.1,NM_004087.2	,,,,	1,116,6386	GG,GA,AA		0.0,2.6782,0.9073	,,,,	503/905,470/893,387/801,387/789,503/927	196842831	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	1739	exon14			CTCTCCACTTAGA	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"""discs large homolog 1"", ""presynaptic protein SAP97"", ""synapse-associated protein 97"""	601014	"""discs, large (Drosophila) homolog 1"""			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.1509T>C	3.37:g.196842831A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	195	88	0.451282	NM_001098424	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Silent	SNP	ENST00000419354.1	37	CCDS43194.1																																																																																			A|0.990;G|0.010	0.010	strong		0.408	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087	
SMARCAL1	50485	hgsc.bcm.edu	37	2	217315787	217315787	+	Splice_Site	SNP	T	T	C	rs2066527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:217315787T>C	ENST00000357276.4	+	12	2400	c.2070T>C	c.(2068-2070)acT>acC	p.T690T	SMARCAL1_ENST00000358207.5_Splice_Site_p.T690T	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	690					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		AGGACAAAACTGTGAGTCCAG	0.527									Schimke Immuno-Osseous Dysplasia				T|||	423	0.0844649	0.0431	0.0476	5008	,	,		20873	0.0079		0.1044	False		,,,				2504	0.2249				p.T690T		Atlas-SNP	.											SMARCAL1,NS,carcinoma,0,1	SMARCAL1	93	1	0			c.T2070C						PASS	.	T	,	214,4192	123.7+/-161.0	10,194,1999	34.0	36.0	35.0		2070,2070	-3.5	0.9	2	dbSNP_98	35	1086,7514	222.0+/-259.2	63,960,3277	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	SMARCAL1	NM_001127207.1,NM_014140.3	,	73,1154,5276	CC,CT,TT		12.6279,4.857,9.9954	,	690/955,690/955	217315787	1300,11706	2203	4300	6503	SO:0001630	splice_region_variant	50485	exon12	Familial Cancer Database	SIOD	CAAAACTGTGAGT	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"""HepA-related protein"", ""ATP-driven annealing helicase"""	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.2070+1T>C	2.37:g.217315787T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Silent	SNP	ENST00000357276.4	37	CCDS2403.1																																																																																			T|0.912;C|0.088	0.088	strong		0.527	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2		Silent
ALOX15B	247	hgsc.bcm.edu	37	17	7951149	7951149	+	Silent	SNP	C	C	T	rs9904554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7951149C>T	ENST00000380183.4	+	13	1906	c.1767C>T	c.(1765-1767)ggC>ggT	p.G589G	ALOX15B_ENST00000380173.2_Silent_p.G560G|ALOX15B_ENST00000573359.1_Silent_p.G515G|ALOX15B_ENST00000572022.1_Silent_p.G577G	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	589	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)	p.G589G(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						CATGCGAGGGCTTCATAGCCA	0.592													C|||	600	0.119808	0.3033	0.0389	5008	,	,		19701	0.12		0.0139	False		,,,				2504	0.0378				p.G589G		Atlas-SNP	.											ALOX15B,NS,carcinoma,0,1	ALOX15B	66	1	1	Substitution - coding silent(1)	stomach(1)	c.C1767T						PASS	.	C	,,	1119,3287	401.3+/-331.9	144,831,1228	94.0	79.0	84.0		1680,1545,1767	-2.7	0.1	17	dbSNP_119	84	110,8490	58.7+/-120.3	0,110,4190	no	coding-synonymous,coding-synonymous,coding-synonymous	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	,,	144,941,5418	TT,TC,CC		1.2791,25.3972,9.4495	,,	560/648,515/603,589/677	7951149	1229,11777	2203	4300	6503	SO:0001819	synonymous_variant	247	exon13			CGAGGGCTTCATA	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1767C>T	17.37:g.7951149C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Silent	SNP	ENST00000380183.4	37	CCDS11128.1																																																																																			C|0.899;T|0.101	0.101	strong		0.592	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
SLC18A1	6570	hgsc.bcm.edu	37	8	20036827	20036827	+	Missense_Mutation	SNP	C	C	G	rs2270637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:20036827C>G	ENST00000276373.5	-	3	559	c.293G>C	c.(292-294)aGt>aCt	p.S98T	SLC18A1_ENST00000437980.1_Missense_Mutation_p.S98T|SLC18A1_ENST00000265808.7_Missense_Mutation_p.S98T|SLC18A1_ENST00000440926.1_Missense_Mutation_p.S98T|SLC18A1_ENST00000519026.1_Missense_Mutation_p.S98T|SLC18A1_ENST00000381608.4_Missense_Mutation_p.S98T	NM_003053.3	NP_003044.1	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 1	98			S -> T (in dbSNP:rs2270637).		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)			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)	TGCTATTCCACTAGGTACGCT	0.517													C|||	953	0.190296	0.233	0.1499	5008	,	,		18977	0.1448		0.1889	False		,,,				2504	0.2096				p.S98T		Atlas-SNP	.											SLC18A1,colon,carcinoma,0,1	SLC18A1	68	1	0			c.G293C						PASS	.	C	THR/SER,THR/SER,THR/SER,THR/SER	978,3428	366.4+/-317.8	111,756,1336	169.0	112.0	131.0		293,293,293,293	-5.8	0.0	8	dbSNP_100	131	1640,6960	303.7+/-306.6	153,1334,2813	yes	missense,missense,missense,missense	SLC18A1	NM_001135691.2,NM_001142324.1,NM_001142325.1,NM_003053.3	58,58,58,58	264,2090,4149	GG,GC,CC		19.0698,22.197,20.1292	benign,benign,benign,benign	98/526,98/494,98/473,98/526	20036827	2618,10388	2203	4300	6503	SO:0001583	missense	6570	exon4			ATTCCACTAGGTA		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.293G>C	8.37:g.20036827C>G	ENSP00000276373:p.Ser98Thr	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	195	93	0.476923	NM_001142324	E9PDJ5|Q9BRE4	Missense_Mutation	SNP	ENST00000276373.5	37	CCDS6013.1	413	0.1891025641025641	113	0.22967479674796748	49	0.13535911602209943	103	0.18006993006993008	148	0.19525065963060687	C	4.515	0.095568	0.08681	0.22197	0.190698	ENSG00000036565	ENST00000265808;ENST00000276373;ENST00000440926;ENST00000437980;ENST00000519026;ENST00000381608;ENST00000522513	T;T;T;T;T;T;T	0.04454	3.9;3.91;3.91;3.9;3.9;3.9;3.62	5.95	-5.81	0.02340	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.659160	0.02116	N	0.055177	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.21225	0.0;0.053;0.033	B;B;B	0.27170	0.01;0.056;0.077	T	0.46624	-0.9178	9	0.17832	T	0.49	14.038	3.2589	0.06842	0.1298:0.2963:0.0947:0.4792	rs2270637;rs17215794;rs17840572;rs2270637	98;98;98	E9PB33;E9PDJ5;P54219	.;.;VMAT1_HUMAN	T	98	ENSP00000265808:S98T;ENSP00000276373:S98T;ENSP00000387549:S98T;ENSP00000413361:S98T;ENSP00000429664:S98T;ENSP00000371021:S98T;ENSP00000428999:S98T	ENSP00000265808:S98T	S	-	2	0	SLC18A1	20081107	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.746000	0.04829	-0.799000	0.04439	-0.880000	0.02959	AGT	C|0.796;G|0.204	0.204	strong		0.517	SLC18A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214106.1		
MRPS11	64963	hgsc.bcm.edu	37	15	89010976	89010976	+	Missense_Mutation	SNP	C	C	T	rs16941904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89010976C>T	ENST00000325844.4	+	1	293	c.28C>T	c.(28-30)Cgg>Tgg	p.R10W	MRPL46_ENST00000312475.4_5'Flank|MRPS11_ENST00000557974.1_3'UTR|MRPS11_ENST00000353598.6_Missense_Mutation_p.R10W|MRPL46_ENST00000559538.1_5'Flank	NM_022839.3	NP_073750.2	P82912	RT11_HUMAN	mitochondrial ribosomal protein S11	10			R -> W (in dbSNP:rs16941904).		DNA damage response, detection of DNA damage (GO:0042769)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(3)	3	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			CGCGGGGTCGCGGTTCCTGCG	0.627													T|||	389	0.0776757	0.2663	0.0187	5008	,	,		15222	0.006		0.001	False		,,,				2504	0.0174				p.R10W		Atlas-SNP	.											.	MRPS11	14	.	0			c.C28T						PASS	.	T	TRP/ARG,TRP/ARG	1023,3379	726.5+/-409.7	129,765,1307	57.0	59.0	58.0		28,28	0.1	0.0	15	dbSNP_123	58	8,8590	818.7+/-406.8	0,8,4291	yes	missense,missense	MRPS11	NM_022839.3,NM_176805.2	101,101	129,773,5598	TT,TC,CC		0.093,23.2394,7.9308	benign,benign	10/195,10/162	89010976	1031,11969	2201	4299	6500	SO:0001583	missense	64963	exon1			GGGTCGCGGTTCC	AB051349	CCDS10342.1, CCDS10343.1	15q25	2012-09-13			ENSG00000181991	ENSG00000181991		"""Mitochondrial ribosomal proteins / small subunits"""	14050	protein-coding gene	gene with protein product	"""cervical cancer proto-oncogene 2"""	611977				11402041	Standard	NM_022839		Approved	FLJ23406, HCC-2, FLJ22512	uc002bml.3	P82912	OTTHUMG00000148678	ENST00000325844.4:c.28C>T	15.37:g.89010976C>T	ENSP00000317376:p.Arg10Trp	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	118	69	0.584746	NM_176805	B2RD52|Q969D7|Q96GI3|Q9BYC3	Missense_Mutation	SNP	ENST00000325844.4	37	CCDS10342.1	129	0.059065934065934064	120	0.24390243902439024	7	0.019337016574585635	2	0.0034965034965034965	0	0.0	T	11.34	1.611080	0.28712	0.232394	9.3E-4	ENSG00000181991	ENST00000325844;ENST00000353598	T;T	0.32023	1.47;1.59	4.87	0.116	0.14647	.	0.702183	0.13884	N	0.356082	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41610	-0.9499	9	0.02654	T	1	5.0E-4	9.0595	0.36425	0.0:0.5518:0.0:0.4482	rs16941904;rs61652389	10;10;10	P82912-2;P82912-3;P82912	.;.;RT11_HUMAN	W	10	ENSP00000317376:R10W;ENSP00000318054:R10W	ENSP00000317376:R10W	R	+	1	2	MRPS11	86811980	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.789000	0.04609	-0.101000	0.12219	-0.254000	0.11334	CGG	C|0.929;T|0.071	0.071	strong		0.627	MRPS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309067.2	NM_022839	
PABPC3	5042	hgsc.bcm.edu	37	13	25671759	25671759	+	Missense_Mutation	SNP	C	C	T	rs115121649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25671759C>T	ENST00000281589.3	+	1	1460	c.1423C>T	c.(1423-1425)Cgt>Tgt	p.R475C		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	475					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		GTCAACGCAGCGTGTTGCTAA	0.532																																					p.R475C		Atlas-SNP	.											PABPC3,NS,carcinoma,-1,1	PABPC3	129	1	0			c.C1423T						scavenged	.						93.0	84.0	87.0					13																	25671759		2203	4300	6503	SO:0001583	missense	5042	exon1			ACGCAGCGTGTTG	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1423C>T	13.37:g.25671759C>T	ENSP00000281589:p.Arg475Cys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	116	5	0.0431034	NM_030979	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	C	7.042	0.562727	0.13498	.	.	ENSG00000151846	ENST00000281589	T	0.29142	1.58	0.875	-1.75	0.08031	.	0.000000	0.48767	U	0.000176	T	0.32346	0.0826	M	0.86740	2.835	0.52501	D	0.999952	B	0.11235	0.004	B	0.06405	0.002	T	0.03750	-1.1007	10	0.48119	T	0.1	.	6.6426	0.22917	0.0:0.732:0.0:0.268	.	475	Q9H361	PABP3_HUMAN	C	475	ENSP00000281589:R475C	ENSP00000281589:R475C	R	+	1	0	PABPC3	24569759	1.000000	0.71417	0.869000	0.34112	0.045000	0.14185	1.663000	0.37429	-0.898000	0.03906	-1.305000	0.01319	CGT	C|0.879;T|0.122	0.122	strong		0.532	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
PDZD8	118987	hgsc.bcm.edu	37	10	119133968	119133968	+	Silent	SNP	G	G	C	rs3814230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:119133968G>C	ENST00000334464.5	-	1	1010	c.771C>G	c.(769-771)tcC>tcG	p.S257S		NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	257					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)		CTTCAAACTGGGAGCGCACCT	0.577													G|||	1548	0.309105	0.3782	0.2392	5008	,	,		18250	0.4415		0.1501	False		,,,				2504	0.2924				p.S257S		Atlas-SNP	.											.	PDZD8	85	.	0			c.C771G						PASS	.	G		1491,2915	475.5+/-357.3	242,1007,954	59.0	62.0	61.0		771	-1.7	1.0	10	dbSNP_107	61	1330,7270	261.2+/-283.7	101,1128,3071	no	coding-synonymous	PDZD8	NM_173791.3		343,2135,4025	CC,CG,GG		15.4651,33.8402,21.69		257/1155	119133968	2821,10185	2203	4300	6503	SO:0001819	synonymous_variant	118987	exon1			AAACTGGGAGCGC	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.771C>G	10.37:g.119133968G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Silent	SNP	ENST00000334464.5	37	CCDS7600.1																																																																																			G|0.766;C|0.234	0.234	strong		0.577	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791	
FAM83E	54854	hgsc.bcm.edu	37	19	49116359	49116359	+	Missense_Mutation	SNP	T	T	C	rs447802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49116359T>C	ENST00000263266.3	-	1	460	c.271A>G	c.(271-273)Acc>Gcc	p.T91A	FAM83E_ENST00000595110.1_5'Flank	NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	91			T -> A (in dbSNP:rs447802). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		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;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		TCCACATCGGTGGTGGTGGCT	0.682													C|||	2759	0.550919	0.7277	0.4986	5008	,	,		12886	0.7431		0.2614	False		,,,				2504	0.4489				p.T91A		Atlas-SNP	.											FAM83E,NS,carcinoma,0,2	FAM83E	34	2	0			c.A271G						scavenged	.						12.0	21.0	18.0					19																	49116359		2090	4216	6306	SO:0001583	missense	54854	exon1			CATCGGTGGTGGT	AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523			25972	protein-coding gene	gene with protein product							Standard	NM_017708		Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.271A>G	19.37:g.49116359T>C	ENSP00000263266:p.Thr91Ala	Somatic	138	3	0.0217391		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_017708	Q9NXK1	Missense_Mutation	SNP	ENST00000263266.3	37	CCDS42587.1	1077	0.49313186813186816	343	0.6971544715447154	160	0.4419889502762431	389	0.6800699300699301	185	0.24406332453825857	C	2.961	-0.214627	0.06101	.	.	ENSG00000105523	ENST00000263266	T	0.10668	2.85	3.79	-5.7	0.02421	.	1.732010	0.03225	N	0.178172	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.42565	-0.9444	9	0.02654	T	1	-0.2116	10.3255	0.43790	0.0:0.5744:0.1163:0.3093	rs447802;rs52796733;rs447802	91	Q2M2I3	FA83E_HUMAN	A	91	ENSP00000263266:T91A	ENSP00000263266:T91A	T	-	1	0	FAM83E	53808171	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.799000	0.01746	-1.443000	0.01953	-1.874000	0.00550	ACC	T|0.521;C|0.479	0.479	strong		0.682	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
C1orf95	375057	hgsc.bcm.edu	37	1	226785102	226785102	+	Intron	SNP	A	A	G	rs73098850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226785102A>G	ENST00000366788.3	+	2	487				C1orf95_ENST00000366789.4_Intron	NM_001003665.3	NP_001003665.1	Q69YW2	STUM_HUMAN	chromosome 1 open reading frame 95							integral component of membrane (GO:0016021)				large_intestine(1)|lung(4)|ovary(3)	8	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)		CGTTCCCTGTATTTTCCCACG	0.468													A|||	272	0.0543131	0.1914	0.0245	5008	,	,		21325	0.0		0.001	False		,,,				2504	0.001				.		Atlas-SNP	.											.	C1orf95	16	.	0			c.383-2A>G						PASS	.	A		248,1136		22,204,466	354.0	286.0	306.0			-2.8	0.0	1	dbSNP_130	306	0,3182		0,0,1591	yes	intron	C1orf95	NM_001003665.3		22,204,2057	GG,GA,AA		0.0,17.9191,5.4314			226785102	248,4318	692	1591	2283	SO:0001627	intron_variant	375057	exon3			CCCTGTATTTTCC	AF035308	CCDS31044.1	1q42.12	2012-06-26			ENSG00000203685	ENSG00000203685			30491	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001003665		Approved	DKFZp761P211	uc021pjw.1	Q69YW2	OTTHUMG00000037583	ENST00000366788.3:c.382+420A>G	1.37:g.226785102A>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	205	101	0.492683	NM_001003665	A6NGL2	Splice_Site	SNP	ENST00000366788.3	37	CCDS31044.1																																																																																			A|0.961;G|0.039	0.039	strong		0.468	C1orf95-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091634.1	NM_001003665	
AGPAT1	10554	hgsc.bcm.edu	37	6	32139186	32139186	+	Missense_Mutation	SNP	G	G	A	rs11964847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32139186G>A	ENST00000395499.1	-	2	667	c.88C>T	c.(88-90)Ccc>Tcc	p.P30S	AGPAT1_ENST00000375104.2_Missense_Mutation_p.P30S|PPT2-EGFL8_ENST00000422437.1_3'UTR|AGPAT1_ENST00000395496.1_Missense_Mutation_p.P30S|AGPAT1_ENST00000375107.3_Missense_Mutation_p.P30S|AGPAT1_ENST00000336984.6_Missense_Mutation_p.P30S|AGPAT1_ENST00000490711.1_5'UTR|AGPAT1_ENST00000412465.2_5'UTR|AGPAT1_ENST00000395497.1_Missense_Mutation_p.P30S			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	30			P -> S (in dbSNP:rs11964847).		CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cellular metabolic process (GO:0031325)|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)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			central_nervous_system(1)|large_intestine(3)|lung(6)|ovary(2)	12						TTGGCACTGGGGCTGCAGAAC	0.597													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		19885	0.0		0.0	False		,,,				2504	0.0				p.P30S		Atlas-SNP	.											AGPAT1,NS,carcinoma,+1,1	AGPAT1	22	1	0			c.C88T						PASS	.	G	SER/PRO,SER/PRO	15,3007		0,15,1496	90.0	69.0	76.0		88,88	2.0	1.0	6	dbSNP_120	76	0,5418		0,0,2709	yes	missense,missense	AGPAT1	NM_006411.3,NM_032741.4	74,74	0,15,4205	AA,AG,GG		0.0,0.4964,0.1777	benign,benign	30/284,30/284	32139186	15,8425	1511	2709	4220	SO:0001583	missense	10554	exon2			CACTGGGGCTGCA	U56417	CCDS4744.1	6p21.3	2013-02-05	2013-02-05		ENSG00000204310	ENSG00000204310	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	324	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, alpha"""	603099	"""1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)"""			9461603, 9291118	Standard	NM_032741		Approved	LPAAT-alpha	uc003oae.3	Q99943	OTTHUMG00000031210	ENST00000395499.1:c.88C>T	6.37:g.32139186G>A	ENSP00000378877:p.Pro30Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_006411	A2BFI5|Q5BL03	Missense_Mutation	SNP	ENST00000395499.1	37	CCDS4744.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	4.129	0.022157	0.08006	0.004964	0.0	ENSG00000204310	ENST00000395496;ENST00000375107;ENST00000395499;ENST00000375104;ENST00000395497;ENST00000336984	T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92	5.11	1.98	0.26296	.	0.468866	0.25546	N	0.029922	T	0.04092	0.0114	N	0.01705	-0.755	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30001	-0.9993	10	0.09590	T	0.72	-13.782	2.9511	0.05862	0.1065:0.3516:0.3918:0.1502	rs11964847;rs11964847	30	Q99943	PLCA_HUMAN	S	30	ENSP00000378874:P30S;ENSP00000364248:P30S;ENSP00000378877:P30S;ENSP00000364245:P30S;ENSP00000378875:P30S;ENSP00000337463:P30S	ENSP00000337463:P30S	P	-	1	0	AGPAT1	32247164	0.970000	0.33590	1.000000	0.80357	0.998000	0.95712	0.297000	0.19101	1.132000	0.42129	0.561000	0.74099	CCC	G|0.995;A|0.005	0.005	strong		0.597	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411	
MGAM	8972	hgsc.bcm.edu	37	7	141759274	141759274	+	Silent	SNP	T	T	C	rs2960758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141759274T>C	ENST00000549489.2	+	32	3917	c.3822T>C	c.(3820-3822)gaT>gaC	p.D1274D	MGAM_ENST00000475668.2_Silent_p.D1274D	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1274	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)	TCCCGCAGGATGTGCAGTACT	0.562													N|||	1101	0.219848	0.1785	0.3862	5008	,	,		18252	0.0099		0.3777	False		,,,				2504	0.2117				p.D1274D		Atlas-SNP	.											.	MGAM	767	.	0			c.T3822C						PASS	.						33.0	29.0	31.0					7																	141759274		2002	4150	6152	SO:0001819	synonymous_variant	8972	exon32			GCAGGATGTGCAG	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.3822T>C	7.37:g.141759274T>C		Somatic	338	1	0.00295858		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			C|1.000;|0.000	1.000	weak		0.562	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
CDRT1	374286	hgsc.bcm.edu	37	17	15510888	15510888	+	Splice_Site	SNP	G	G	A	rs62070401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15510888G>A	ENST00000395906.3	-	6	1231	c.1232C>T	c.(1231-1233)aCg>aTg	p.T411M	RP11-385D13.1_ENST00000455584.2_Splice_Site_p.T721M	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	411										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)		CAGTACCTACGTGTCAGAGAG	0.493													G|||	1466	0.292732	0.264	0.2767	5008	,	,		18548	0.4514		0.1511	False		,,,				2504	0.3252				p.T411M		Atlas-SNP	.											.	CDRT1	83	.	0			c.C1232T						PASS	.	G	MET/THR	1085,3321	390.3+/-327.6	143,799,1261	68.0	65.0	66.0		1232	-4.1	0.8	17	dbSNP_129	66	1459,7141	275.3+/-291.7	127,1205,2968	no	missense-near-splice	CDRT1	NM_006382.3	81	270,2004,4229	AA,AG,GG		16.9651,24.6255,19.5602	possibly-damaging	411/753	15510888	2544,10462	2203	4300	6503	SO:0001630	splice_region_variant	374286	exon6			ACCTACGTGTCAG	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.1232+1C>T	17.37:g.15510888G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	254	98	0.385827	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	570|570	0.260989010989011|0.260989010989011	100|100	0.2032520325203252|0.2032520325203252	86|86	0.23756906077348067|0.23756906077348067	256|256	0.44755244755244755|0.44755244755244755	128|128	0.16886543535620052|0.16886543535620052	G|G	9.414|9.414	1.081185|1.081185	0.20309|0.20309	0.246255|0.246255	0.169651|0.169651	ENSG00000251537|ENSG00000251537	ENST00000455584|ENST00000261644;ENST00000395906	.|T	.|0.58940	.|0.3	4.99|4.99	-4.14|-4.14	0.03892|0.03892	.|WD40 repeat-like-containing domain (1);	.|0.395907	.|0.18373	.|U	.|0.143193	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.51422|0.51422	1.61|1.61	0.09310|0.09310	P|P	0.99999999077601|0.99999999077601	.|D;B	.|0.56521	.|0.976;0.203	.|B;B	.|0.42959	.|0.403;0.029	T|T	0.32955|0.32955	-0.9887|-0.9887	4|8	.|.	.|.	.|.	.|.	6.6345|6.6345	0.22875|0.22875	0.5699:0.138:0.2921:0.0|0.5699:0.138:0.2921:0.0	rs62070401|rs62070401	.|411;735	.|O95170;Q59EB2	.|CDRT1_HUMAN;.	C|M	736|441;411	.|ENSP00000379242:T411M	.|.	R|T	-|-	1|2	0|0	RP11-385D13.1|RP11-385D13.1	15451613|15451613	0.231000|0.231000	0.23751|0.23751	0.832000|0.832000	0.32986|0.32986	0.010000|0.010000	0.07245|0.07245	-0.782000|-0.782000	0.04643|0.04643	-0.694000|-0.694000	0.05113|0.05113	-1.259000|-1.259000	0.01468|0.01468	CGT|ACG	G|0.754;A|0.246	0.246	strong		0.493	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	Missense_Mutation
VPS13A	23230	hgsc.bcm.edu	37	9	79929004	79929004	+	Missense_Mutation	SNP	C	C	T	rs140993797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79929004C>T	ENST00000360280.3	+	36	4471	c.4211C>T	c.(4210-4212)aCc>aTc	p.T1404I	VPS13A_ENST00000423463.2_3'UTR|VPS13A_ENST00000376634.4_Missense_Mutation_p.T1404I|VPS13A_ENST00000357409.5_Missense_Mutation_p.T1404I|VPS13A_ENST00000376636.3_Missense_Mutation_p.T1365I	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1404					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						GATGATCTCACCATGGTGCTG	0.388																																					p.T1404I		Atlas-SNP	.											.	VPS13A	735	.	0			c.C4211T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR,ILE/THR	3,4403	6.2+/-15.9	0,3,2200	115.0	86.0	96.0		4094,4211,4211,4211	4.5	1.0	9	dbSNP_134	96	0,8600		0,0,4300	yes	missense,missense,missense,missense	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	89,89,89,89	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign,benign,benign,benign	1365/3136,1404/3070,1404/3096,1404/3175	79929004	3,13003	2203	4300	6503	SO:0001583	missense	23230	exon36			ATCTCACCATGGT	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.4211C>T	9.37:g.79929004C>T	ENSP00000353422:p.Thr1404Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	94	62	0.659574	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.782618	0.49891	6.81E-4	0.0	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.47528	1.02;0.84;0.93;1.02	5.44	4.53	0.55603	.	0.285219	0.33290	N	0.005074	T	0.38799	0.1054	L	0.29908	0.895	0.80722	D	1	B;B;B;B	0.22414	0.002;0.019;0.069;0.033	B;B;B;B	0.27715	0.008;0.027;0.082;0.06	T	0.17930	-1.0353	10	0.37606	T	0.19	.	14.5567	0.68106	0.0:0.9276:0.0:0.0724	.	1365;1404;1404;1404	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	I	1404;1365;1404;1404	ENSP00000365821:T1404I;ENSP00000365823:T1365I;ENSP00000353422:T1404I;ENSP00000349985:T1404I	ENSP00000349985:T1404I	T	+	2	0	VPS13A	79118824	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.410000	0.44592	1.399000	0.46721	0.650000	0.86243	ACC	C|1.000;T|0.000	0.000	strong		0.388	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
LRRC8E	80131	hgsc.bcm.edu	37	19	7963949	7963949	+	Missense_Mutation	SNP	A	A	G	rs386806520|rs2042919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7963949A>G	ENST00000306708.6	+	3	643	c.542A>G	c.(541-543)gAa>gGa	p.E181G	AC010336.1_ENST00000539278.1_3'UTR	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	181			E -> G (in dbSNP:rs2042919).		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						GCAGCCACCGAACGGGCTGCG	0.642													G|||	1166	0.232827	0.323	0.183	5008	,	,		17165	0.2292		0.2425	False		,,,				2504	0.1401				p.E181G		Atlas-SNP	.											.	LRRC8E	67	.	0			c.A542G						PASS	.	G	GLY/GLU	1068,3336		204,660,1338	30.0	38.0	36.0		542	4.1	0.0	19	dbSNP_94	36	2087,6509		274,1539,2485	no	missense	LRRC8E	NM_025061.3	98	478,2199,3823	GG,GA,AA		24.2787,24.2507,24.2692	benign	181/797	7963949	3155,9845	2202	4298	6500	SO:0001583	missense	80131	exon4			CCACCGAACGGGC		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.542A>G	19.37:g.7963949A>G	ENSP00000306524:p.Glu181Gly	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Missense_Mutation	SNP	ENST00000306708.6	37	CCDS12189.1	546	0.25	173	0.3516260162601626	63	0.17403314917127072	132	0.23076923076923078	178	0.23482849604221637	G	0.069	-1.206104	0.01568	0.242507	0.242787	ENSG00000171017	ENST00000306708	T	0.27890	1.64	5.19	4.14	0.48551	.	0.468333	0.23620	N	0.046258	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P	0.40875	0.731	B	0.36464	0.225	T	0.46638	-0.9177	9	0.22109	T	0.4	.	5.5225	0.16941	0.171:0.1642:0.6648:0.0	rs2042919;rs3745380;rs60626324	181	Q6NSJ5	LRC8E_HUMAN	G	181	ENSP00000306524:E181G	ENSP00000306524:E181G	E	+	2	0	LRRC8E	7869949	0.001000	0.12720	0.009000	0.14445	0.002000	0.02628	1.315000	0.33608	0.785000	0.33685	-0.802000	0.03209	GAA	A|0.759;G|0.241	0.241	strong		0.642	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
MYO18B	84700	hgsc.bcm.edu	37	22	26247456	26247456	+	Silent	SNP	G	G	A	rs5996988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26247456G>A	ENST00000407587.2	+	21	3967	c.3798G>A	c.(3796-3798)ggG>ggA	p.G1266G	MYO18B_ENST00000536101.1_Silent_p.G1265G|MYO18B_ENST00000335473.7_Silent_p.G1265G			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1265	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						ACCACATGGGGCTCACTCGCT	0.572													G|||	1212	0.242013	0.171	0.3559	5008	,	,		18680	0.0833		0.3946	False		,,,				2504	0.2638				p.G1265G		Atlas-SNP	.											MYO18B,NS,carcinoma,0,1	MYO18B	322	1	0			c.G3795A						PASS	.	G		861,3479		87,687,1396	31.0	32.0	32.0		3795	-0.6	1.0	22	dbSNP_114	32	3217,5271		641,1935,1668	no	coding-synonymous	MYO18B	NM_032608.5		728,2622,3064	AA,AG,GG		37.9006,19.8387,31.7898		1265/2568	26247456	4078,8750	2170	4244	6414	SO:0001819	synonymous_variant	84700	exon21			CATGGGGCTCACT	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.3798G>A	22.37:g.26247456G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				G|0.748;A|0.252	0.252	strong		0.572	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
XDH	7498	hgsc.bcm.edu	37	2	31598339	31598339	+	Silent	SNP	G	G	C	rs45612839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31598339G>C	ENST00000379416.3	-	15	1557	c.1509C>G	c.(1507-1509)ggC>ggG	p.G503G		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	503					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)	AGTCCACCATGCCACCAGGGG	0.602													G|||	314	0.0626997	0.2277	0.0159	5008	,	,		17654	0.0		0.002	False		,,,				2504	0.0				p.G503G	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.C1509G						PASS	.	G		857,3549	338.1+/-305.1	72,713,1418	86.0	80.0	82.0		1509	2.4	1.0	2	dbSNP_127	82	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	XDH	NM_000379.3		72,720,5711	CC,CG,GG		0.0814,19.4507,6.6431		503/1334	31598339	864,12142	2203	4300	6503	SO:0001819	synonymous_variant	7498	exon15			CACCATGCCACCA	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.1509C>G	2.37:g.31598339G>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			G|0.936;C|0.064	0.064	strong		0.602	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
PTGFRN	5738	hgsc.bcm.edu	37	1	117527444	117527444	+	Silent	SNP	C	C	T	rs17036676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117527444C>T	ENST00000393203.2	+	8	2457	c.2310C>T	c.(2308-2310)cgC>cgT	p.R770R		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	770	Ig-like C2-type 6.				lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		GCCTGGAGCGCGTGAGTGTGC	0.587													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		21854	0.0		0.0	False		,,,				2504	0.0				p.R770R		Atlas-SNP	.											PTGFRN,NS,chondrosarcoma,+1,1	PTGFRN	91	1	0			c.C2310T						PASS	.	C		60,4346	56.2+/-92.4	1,58,2144	219.0	170.0	187.0		2310	-11.2	0.0	1	dbSNP_123	187	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PTGFRN	NM_020440.2		1,60,6442	TT,TC,CC		0.0233,1.3618,0.4767		770/880	117527444	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	5738	exon8			GGAGCGCGTGAGT	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9601	protein-coding gene	gene with protein product		601204	"""prostaglandin F2 receptor negative regulator"""			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.2310C>T	1.37:g.117527444C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	193	94	0.487047	NM_020440	Q5VVU9|Q8N2K6	Silent	SNP	ENST00000393203.2	37	CCDS890.1																																																																																			C|0.994;T|0.006	0.006	strong		0.587	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
NRG2	9542	hgsc.bcm.edu	37	5	139422232	139422232	+	Silent	SNP	G	G	A	rs144634106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:139422232G>A	ENST00000361474.1	-	1	647	c.423C>T	c.(421-423)gcC>gcT	p.A141A	NRG2_ENST00000541337.1_Silent_p.A141A|NRG2_ENST00000394770.1_Silent_p.A141A|NRG2_ENST00000289409.4_Silent_p.A141A|NRG2_ENST00000545385.1_Silent_p.A141A|NRG2_ENST00000289422.7_Silent_p.A141A|NRG2_ENST00000358522.3_Silent_p.A141A	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	141					embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAGCCGCCGGCTGGGACCA	0.697													G|||	134	0.0267572	0.0272	0.0403	5008	,	,		7889	0.0		0.0616	False		,,,				2504	0.0082				p.A141A		Atlas-SNP	.											.	NRG2	69	.	0			c.C423T						PASS	.	G	,,,,	145,4055		4,137,1959	6.0	8.0	7.0		423,423,423,423,423	-0.9	1.0	5	dbSNP_134	7	503,7855		16,471,3692	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRG2	NM_001184935.1,NM_004883.2,NM_013981.3,NM_013982.2,NM_013983.2	,,,,	20,608,5651	AA,AG,GG		6.0182,3.4524,5.1601	,,,,	141/785,141/851,141/845,141/859,141/853	139422232	648,11910	2100	4179	6279	SO:0001819	synonymous_variant	9542	exon1			GCCGCCGGCTGGG		CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"""Immunoglobulin superfamily / I-set domain containing"""	7998	protein-coding gene	gene with protein product	"""neural- and thymus-derived activator for ErbB kinases"", ""divergent of neuregulin-1"""	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.423C>T	5.37:g.139422232G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	48	30	0.625	NM_013982		Silent	SNP	ENST00000361474.1	37	CCDS4217.1																																																																																			G|0.965;A|0.035	0.035	strong		0.697	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982	
MMAB	326625	hgsc.bcm.edu	37	12	110011229	110011229	+	Silent	SNP	G	G	T	rs10774774|rs36013132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:110011229G>T	ENST00000545712.2	-	1	450	c.57C>A	c.(55-57)cgC>cgA	p.R19R	MVK_ENST00000539696.1_5'Flank|MMAB_ENST00000266839.5_5'UTR|MVK_ENST00000539575.1_5'Flank|MVK_ENST00000541384.1_5'Flank|MVK_ENST00000228510.3_5'Flank|MVK_ENST00000392727.3_5'Flank|MMAB_ENST00000540016.1_Silent_p.R19R|MVK_ENST00000535044.1_3'UTR	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	48	0	0		WXS	Illumina HiSeq	Phase_I	78	49	0.628205	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		
TCOF1	6949	hgsc.bcm.edu	37	5	149755845	149755845	+	Silent	SNP	A	A	G	rs34796297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149755845A>G	ENST00000504761.2	+	13	2094	c.2094A>G	c.(2092-2094)gaA>gaG	p.E698E	TCOF1_ENST00000394269.3_Silent_p.E698E|TCOF1_ENST00000451292.1_Silent_p.E698E|TCOF1_ENST00000445265.2_Silent_p.E621E|TCOF1_ENST00000513346.1_Silent_p.E698E|TCOF1_ENST00000323668.7_Silent_p.E621E|TCOF1_ENST00000439160.2_Silent_p.E698E|TCOF1_ENST00000377797.3_Silent_p.E698E			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	698					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCAGTGAGGAATCAGATAGTG	0.602													A|||	111	0.0221645	0.0787	0.0086	5008	,	,		18022	0.0		0.001	False		,,,				2504	0.0				p.E698E		Atlas-SNP	.											.	TCOF1	154	.	0			c.A2094G						PASS	.	A	,,,,,	268,4128		13,242,1943	119.0	142.0	134.0		1863,2094,2094,2094,1863,2094	1.1	0.3	5	dbSNP_126	134	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	,,,,,	13,242,6238	GG,GA,AA		0.0,6.0965,2.0638	,,,,,	621/1412,698/959,698/1489,698/1452,621/1413,698/1451	149755845	268,12718	2198	4295	6493	SO:0001819	synonymous_variant	6949	exon13			TGAGGAATCAGAT		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.2094A>G	5.37:g.149755845A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Silent	SNP	ENST00000504761.2	37	CCDS54936.1																																																																																			A|0.984;G|0.016	0.016	strong		0.602	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
PKDCC	91461	hgsc.bcm.edu	37	2	42275819	42275819	+	Silent	SNP	T	T	C	rs11897440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	41	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	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		
FLG	2312	hgsc.bcm.edu	37	1	152277575	152277575	+	Missense_Mutation	SNP	C	C	T	rs79771385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152277575C>T	ENST00000368799.1	-	3	9822	c.9787G>A	c.(9787-9789)Ggt>Agt	p.G3263S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3263	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)			TGCCCGTGACCGGCTCTGTCT	0.587									Ichthyosis				C|||	190	0.0379393	0.1362	0.013	5008	,	,		19484	0.0		0.001	False		,,,				2504	0.0				p.G3263S		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.G9787A						scavenged	.	C	SER/GLY	459,3947	218.1+/-236.3	22,415,1766	256.0	260.0	259.0		9787	-5.6	0.0	1	dbSNP_131	259	10,8590	7.7+/-29.5	0,10,4290	no	missense	FLG	NM_002016.1	56	22,425,6056	TT,TC,CC		0.1163,10.4176,3.606	probably-damaging	3263/4062	152277575	469,12537	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGTGACCGGCTCT	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.9787G>A	1.37:g.152277575C>T	ENSP00000357789:p.Gly3263Ser	Somatic	509	3	0.00589391		WXS	Illumina HiSeq	Phase_I	570	281	0.492982	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	66	0.03021978021978022	62	0.12601626016260162	4	0.011049723756906077	0	0.0	0	0.0	c	10.64	1.407204	0.25378	0.104176	0.001163	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.01092	5.35	2.8	-5.6	0.02497	.	.	.	.	.	T	0.00328	0.0010	L	0.32530	0.975	0.80722	P	0.0	P	0.52061	0.95	P	0.45428	0.48	T	0.35425	-0.9789	8	0.14656	T	0.56	.	4.5119	0.11915	0.0:0.2393:0.3104:0.4503	.	3263	P20930	FILA_HUMAN	S	3263;201	ENSP00000357789:G3263S	ENSP00000357786:G201S	G	-	1	0	FLG	150544199	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-4.225000	0.00270	-1.835000	0.01191	-1.316000	0.01300	GGT	C|0.959;T|0.041	0.041	strong		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LCE3D	84648	hgsc.bcm.edu	37	1	152552311	152552311	+	Silent	SNP	G	G	A	rs149516289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152552311G>A	ENST00000368787.3	-	2	158	c.102C>T	c.(100-102)tcC>tcT	p.S34S		NM_032563.1	NP_115952.1	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	34					keratinization (GO:0031424)					breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		CACAGCCAGAGGAAGCTGGAG	0.662													G|||	43	0.00858626	0.0325	0.0	5008	,	,		16707	0.0		0.0	False		,,,				2504	0.0				p.S34S		Atlas-SNP	.											.	LCE3D	28	.	0			c.C102T						PASS	.	G		102,4304	81.4+/-119.9	2,98,2103	75.0	83.0	81.0		102	-1.4	0.1	1	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous	LCE3D	NM_032563.1		2,98,6403	AA,AG,GG		0.0,2.315,0.7843		34/93	152552311	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	84648	exon2			GCCAGAGGAAGCT	BI670519	CCDS1014.1	1q21	2008-02-05	2004-05-21	2004-10-15	ENSG00000163202	ENSG00000163202		"""Late cornified envelopes"""	16615	protein-coding gene	gene with protein product		612616	"""small proline rich-like (epidermal differentiation complex) 6B"""	SPRL6B, SPRL6A		11698679	Standard	NM_032563		Approved	LEP16	uc001fab.3	Q9BYE3	OTTHUMG00000012384	ENST00000368787.3:c.102C>T	1.37:g.152552311G>A		Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	263	137	0.520913	NM_032563	Q3MIL1	Silent	SNP	ENST00000368787.3	37	CCDS1014.1																																																																																			G|0.992;A|0.008	0.008	strong		0.662	LCE3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034504.1	NM_032563	
TSC2	7249	hgsc.bcm.edu	37	16	2136866	2136866	+	Silent	SNP	C	C	T	rs35534817|rs137854272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2136866C>T	ENST00000219476.3	+	38	5613	c.4983C>T	c.(4981-4983)acC>acT	p.T1661T	TSC2_ENST00000382538.6_Silent_p.T1546T|TSC2_ENST00000439673.2_Silent_p.T1558T|TSC2_ENST00000353929.4_Silent_p.T1618T|TSC2_ENST00000568454.1_Silent_p.T1605T|TSC2_ENST00000401874.2_Silent_p.T1594T|TSC2_ENST00000350773.4_Silent_p.T1638T	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1661	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)				AGCTTGGCACCATCAAGGTGA	0.617			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				C|||	136	0.0271565	0.0983	0.0086	5008	,	,		20370	0.0		0.0	False		,,,				2504	0.0				p.T1661T		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	.	TSC2	364	.	0			c.C4983T						PASS	.	C	,,	297,4081		11,275,1903	53.0	39.0	44.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4983,4782,4914	5.2	1.0	16	dbSNP_126	44	3,8571		0,3,4284	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	,,	11,278,6187	TT,TC,CC		0.035,6.7839,2.3162	,,	1661/1808,1594/1741,1638/1785	2136866	300,12652	2189	4287	6476	SO:0001819	synonymous_variant	7249	exon38	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TGGCACCATCAAG	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.4983C>T	16.37:g.2136866C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																			C|0.975;T|0.025	0.025	strong		0.617	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
MICALL1	85377	hgsc.bcm.edu	37	22	38323700	38323700	+	Missense_Mutation	SNP	C	C	T	rs2272829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	88	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	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	
SAG	6295	hgsc.bcm.edu	37	2	234229320	234229320	+	Missense_Mutation	SNP	A	A	G	rs7565275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234229320A>G	ENST00000409110.1	+	5	456	c.226A>G	c.(226-228)Att>Gtt	p.I76V	SAG_ENST00000461532.1_3'UTR|SAG_ENST00000449594.2_5'UTR	NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	76			I -> V (in dbSNP:rs7565275). {ECO:0000269|PubMed:7670478, ECO:0000269|PubMed:9501883}.		cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		CCAAGAGGACATTGACGTGAT	0.617													A|||	373	0.0744808	0.1142	0.0403	5008	,	,		19037	0.0298		0.0517	False		,,,				2504	0.1145				p.I76V		Atlas-SNP	.											.	SAG	77	.	0			c.A226G						PASS	.	A	VAL/ILE	388,3848		22,344,1752	35.0	38.0	37.0		226	4.5	1.0	2	dbSNP_116	37	437,8091		11,415,3838	yes	missense	SAG	NM_000541.4	29	33,759,5590	GG,GA,AA		5.1243,9.1596,6.4635	benign	76/406	234229320	825,11939	2118	4264	6382	SO:0001583	missense	6295	exon5			GAGGACATTGACG		CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.226A>G	2.37:g.234229320A>G	ENSP00000386444:p.Ile76Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_000541	A0FDN6|Q53SV3|Q99858	Missense_Mutation	SNP	ENST00000409110.1	37	CCDS46545.1	131	0.059981684981684984	60	0.12195121951219512	13	0.03591160220994475	16	0.027972027972027972	42	0.055408970976253295	A	14.54	2.565381	0.45694	0.091596	0.051243	ENSG00000130561	ENST00000252857;ENST00000447536;ENST00000409110	T;T	0.29397	1.57;1.57	4.46	4.46	0.54185	Arrestin, N-terminal (1);Immunoglobulin E-set (1);Arrestin-like, N-terminal (1);Arrestin, conserved site (1);	0.143283	0.64402	D	0.000006	T	0.00784	0.0026	L	0.50919	1.6	0.09310	P	1.0	P	0.41159	0.74	P	0.56612	0.802	T	0.04400	-1.0954	9	0.51188	T	0.08	-30.9562	14.2245	0.65850	1.0:0.0:0.0:0.0	rs7565275;rs7565275	76	P10523	ARRS_HUMAN	V	76	ENSP00000408937:I76V;ENSP00000386444:I76V	ENSP00000252857:I76V	I	+	1	0	SAG	233894059	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	2.276000	0.43408	2.003000	0.58678	0.533000	0.62120	ATT	A|0.937;G|0.063	0.063	strong		0.617	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1	NM_000541	
COG4	25839	hgsc.bcm.edu	37	16	70546234	70546234	+	Silent	SNP	G	G	A	rs3762171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70546234G>A	ENST00000323786.5	-	5	667	c.646C>T	c.(646-648)Ctg>Ttg	p.L216L	COG4_ENST00000393612.4_Silent_p.L212L|COG4_ENST00000564653.1_Silent_p.I173I	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	212					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				ACCTGGGGCAGATCACCTTCC	0.507													G|||	2355	0.470248	0.2859	0.415	5008	,	,		23036	0.5813		0.4175	False		,,,				2504	0.6984				p.L216L		Atlas-SNP	.											.	COG4	64	.	0			c.C646T						PASS	.	G	,	1313,3083	440.8+/-346.1	195,923,1080	96.0	84.0	88.0		646,646	2.4	1.0	16	dbSNP_107	88	3649,4951	524.2+/-380.5	788,2073,1439	no	coding-synonymous,coding-synonymous	COG4	NM_001195139.1,NM_015386.2	,	983,2996,2519	AA,AG,GG		42.4302,29.8681,38.181	,	216/769,216/790	70546234	4962,8034	2198	4300	6498	SO:0001819	synonymous_variant	25839	exon5			GGGGCAGATCACC	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"""Components of oligomeric golgi complex"""	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.646C>T	16.37:g.70546234G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	202	201	0.995049	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Silent	SNP	ENST00000323786.5	37	CCDS10892.2																																																																																			G|0.578;A|0.422	0.422	strong		0.507	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3		
LY75	4065	hgsc.bcm.edu	37	2	160676350	160676350	+	Missense_Mutation	SNP	T	T	C	rs17827158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160676350T>C	ENST00000263636.4	-	29	4067	c.4040A>G	c.(4039-4041)aAg>aGg	p.K1347R	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.K1347R|LY75_ENST00000554112.1_Missense_Mutation_p.K1347R|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.K1347R|LY75_ENST00000553424.1_Missense_Mutation_p.K1347R	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1347	C-type lectin 8. {ECO:0000255|PROSITE- ProRule:PRU00040}.		K -> R (in dbSNP:rs17827158).		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)		AGCCAAAAACTTCTCATTTTT	0.363													T|||	365	0.0728834	0.0567	0.0807	5008	,	,		17662	0.0079		0.1044	False		,,,				2504	0.1237				p.K1347R		Atlas-SNP	.											.	LY75	151	.	0			c.A4040G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	309,4097	162.9+/-194.8	17,275,1911	81.0	86.0	84.0		4040,4040,4040	2.0	0.1	2	dbSNP_123	84	901,7699	202.1+/-245.5	52,797,3451	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	26,26,26	69,1072,5362	CC,CT,TT		10.4767,7.0132,9.3034	benign,benign,benign	1347/1874,1347/1818,1347/1723	160676350	1210,11796	2203	4300	6503	SO:0001583	missense	4065	exon29			AAAAACTTCTCAT	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.4040A>G	2.37:g.160676350T>C	ENSP00000263636:p.Lys1347Arg	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	174	67	0.385057	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	161	0.07371794871794872	38	0.07723577235772358	45	0.12430939226519337	3	0.005244755244755245	75	0.09894459102902374	T	8.685	0.905974	0.17760	0.070132	0.104767	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15	5.65	1.98	0.26296	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	.	.	.	.	T	0.00073	0.0002	L	0.32530	0.975	0.80722	P	0.0	B;B;B	0.11235	0.003;0.004;0.004	B;B;B	0.14023	0.009;0.01;0.006	T	0.42916	-0.9423	8	0.15952	T	0.53	-4.5352	1.4096	0.02288	0.1352:0.206:0.1403:0.5185	rs17827158;rs52833817;rs17827158	1347;1347;1347	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	R	1347	ENSP00000451511:K1347R;ENSP00000451446:K1347R;ENSP00000263636:K1347R;ENSP00000423463:K1347R;ENSP00000421035:K1347R	ENSP00000423463:K1347R	K	-	2	0	LY75;LY75-CD302	160384596	0.000000	0.05858	0.114000	0.21550	0.746000	0.42486	0.646000	0.24797	0.403000	0.25479	0.482000	0.46254	AAG	T|0.915;C|0.085	0.085	strong		0.363	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
MSMP	692094	hgsc.bcm.edu	37	9	35754052	35754052	+	Missense_Mutation	SNP	C	C	T	rs189235807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35754052C>T	ENST00000436428.2	-	1	214	c.75G>A	c.(73-75)atG>atA	p.M25I	RGP1_ENST00000378078.4_3'UTR|MSMP_ENST00000414286.1_Intron|RP11-112J3.15_ENST00000425499.2_RNA	NM_001044264.2	NP_001037729.1	Q1L6U9	MSMP_HUMAN	microseminoprotein, prostate associated	25						cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(2)|kidney(1)|lung(3)|prostate(3)	9						GGAGTAGAGACATCACCAAGC	0.577													C|||	11	0.00219649	0.0076	0.0	5008	,	,		19648	0.0		0.0	False		,,,				2504	0.001				p.M25I		Atlas-SNP	.											.	MSMP	15	.	0			c.G75A						PASS	.	C	ILE/MET	14,4138		0,14,2062	158.0	168.0	165.0		75	-7.9	0.5	9		165	0,8454		0,0,4227	yes	missense	MSMP	NM_001044264.2	10	0,14,6289	TT,TC,CC		0.0,0.3372,0.1111	benign	25/140	35754052	14,12592	2076	4227	6303	SO:0001583	missense	692094	exon1			TAGAGACATCACC	DQ012170	CCDS43797.1	9p13.3	2012-10-02			ENSG00000215183	ENSG00000215183			29663	protein-coding gene	gene with protein product		612191				17338636	Standard	NM_001044264		Approved	PC-3, PSMP	uc003zyb.2	Q1L6U9	OTTHUMG00000019882	ENST00000436428.2:c.75G>A	9.37:g.35754052C>T	ENSP00000419194:p.Met25Ile	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	139	63	0.453237	NM_001044264		Missense_Mutation	SNP	ENST00000436428.2	37	CCDS43797.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	8.661	0.900498	0.17686	0.003372	0.0	ENSG00000215183	ENST00000436428	T	0.40476	1.03	5.92	-7.93	0.01156	.	1.391910	0.05859	N	0.622637	T	0.12050	0.0293	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20907	-1.0261	10	0.08599	T;T	0.76;0.76	.	4.3929	0.11350	0.1292:0.1236:0.4683:0.2788	.	25	Q1L6U9	MSMP_HUMAN	I	25	ENSP00000419194:M25I	ENSP00000419194:M25I;ENSP00000419194:M25I	M	-	3	0	MSMP	35744052	0.000000	0.05858	0.494000	0.27515	0.988000	0.76386	-3.267000	0.00533	-0.951000	0.03654	-0.140000	0.14226	ATG	C|1.000;T|0.000	0.000	strong		0.577	MSMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052384.2	NM_001044264	
C5	727	hgsc.bcm.edu	37	9	123800218	123800218	+	Missense_Mutation	SNP	C	C	T	rs17216529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:123800218C>T	ENST00000223642.1	-	4	462	c.433G>A	c.(433-435)Gtt>Att	p.V145I		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	145			V -> I (in dbSNP:rs17216529). {ECO:0000269|Ref.2}.		activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	AACGAATAAACTCTAACTTTT	0.249													C|||	734	0.146565	0.3124	0.0504	5008	,	,		15211	0.1845		0.0696	False		,,,				2504	0.0307				p.V145I		Atlas-SNP	.											.	C5	124	.	0			c.G433A						PASS	.	C	ILE/VAL	991,3401		108,775,1313	21.0	22.0	22.0		433	3.5	1.0	9	dbSNP_123	22	612,7928		29,554,3687	yes	missense	C5	NM_001735.2	29	137,1329,5000	TT,TC,CC		7.1663,22.5638,12.3956	possibly-damaging	145/1677	123800218	1603,11329	2196	4270	6466	SO:0001583	missense	727	exon4			AATAAACTCTAAC	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.433G>A	9.37:g.123800218C>T	ENSP00000223642:p.Val145Ile	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	152	48	0.315789	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	330	0.1510989010989011	155	0.3150406504065041	18	0.049723756906077346	103	0.18006993006993008	54	0.0712401055408971	C	16.12	3.033935	0.54896	0.225638	0.071663	ENSG00000106804	ENST00000223642;ENST00000430906	T	0.74106	-0.81	5.44	3.48	0.39840	Alpha-2-macroglobulin, N-terminal (1);	0.063724	0.64402	D	0.000006	T	0.00012	0.0000	L	0.36672	1.1	0.24814	P	0.99262246	P;P	0.48407	0.821;0.91	P;P	0.46237	0.461;0.508	T	0.05852	-1.0860	9	0.40728	T	0.16	.	9.9544	0.41657	0.0:0.784:0.1389:0.0771	rs17216529	216;145	Q59GS8;P01031	.;CO5_HUMAN	I	145;216	ENSP00000223642:V145I	ENSP00000223642:V145I	V	-	1	0	C5	122840039	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.460000	0.53028	1.444000	0.47605	0.650000	0.86243	GTT	C|0.880;T|0.120	0.120	strong		0.249	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
KRT39	390792	hgsc.bcm.edu	37	17	39114962	39114962	+	Missense_Mutation	SNP	C	C	T	rs7213256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	140	0	0		WXS	Illumina HiSeq	Phase_I	145	55	0.37931	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	
KCNAB1	7881	hgsc.bcm.edu	37	3	155838488	155838488	+	Missense_Mutation	SNP	G	G	C	rs67167156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:155838488G>C	ENST00000490337.1	+	1	152	c.88G>C	c.(88-90)Ggg>Cgg	p.G30R	KCNAB1_ENST00000389636.5_Missense_Mutation_p.G30R	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	30					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TTCTGTAGCAGGGAAAGACAA	0.547													G|||	90	0.0179712	0.0666	0.0029	5008	,	,		19474	0.0		0.0	False		,,,				2504	0.0				p.G30R		Atlas-SNP	.											.	KCNAB1	176	.	0			c.G88C						PASS	.	G	ARG/GLY	235,4171	139.6+/-175.2	6,223,1974	86.0	94.0	92.0		88	-2.0	0.0	3	dbSNP_130	92	2,8598	1.2+/-3.3	0,2,4298	yes	missense	KCNAB1	NM_172160.2	125	6,225,6272	CC,CG,GG		0.0233,5.3336,1.8222	benign	30/420	155838488	237,12769	2203	4300	6503	SO:0001583	missense	7881	exon1			GTAGCAGGGAAAG	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"""Potassium channels"", ""Aldo-keto reductases"""	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.88G>C	3.37:g.155838488G>C	ENSP00000419952:p.Gly30Arg	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	99	61	0.616162	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	37	CCDS3174.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	G	11.35	1.613207	0.28712	0.053336	2.33E-4	ENSG00000169282	ENST00000490337;ENST00000389636	T;T	0.10960	3.21;2.82	5.47	-1.96	0.07525	.	.	.	.	.	T	0.00608	0.0020	N	0.08118	0	0.09310	N	0.999998	B;B	0.19583	0.037;0.01	B;B	0.15870	0.014;0.014	T	0.37731	-0.9693	9	0.59425	D	0.04	-10.322	11.9133	0.52751	0.8314:0.0:0.1686:0.0	.	30;30	B7Z8E5;Q14722	.;KCAB1_HUMAN	R	30	ENSP00000419952:G30R;ENSP00000374287:G30R	ENSP00000374287:G30R	G	+	1	0	KCNAB1	157321182	0.884000	0.30299	0.000000	0.03702	0.802000	0.45316	0.538000	0.23160	-0.249000	0.09569	0.557000	0.71058	GGG	G|0.981;C|0.019	0.019	strong		0.547	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471	
LRP2	4036	hgsc.bcm.edu	37	2	170092395	170092395	+	Silent	SNP	A	A	G	rs2229267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170092395A>G	ENST00000263816.3	-	29	5160	c.4875T>C	c.(4873-4875)tgT>tgC	p.C1625C		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1625					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)"""	CATTATAATCACAAAAGTCCA	0.433													A|||	2310	0.461262	0.7088	0.4697	5008	,	,		18625	0.4058		0.2634	False		,,,				2504	0.3814				p.C1625C		Atlas-SNP	.											.	LRP2	751	.	0			c.T4875C						PASS	.	A		2843,1563	668.4+/-402.0	933,977,293	133.0	122.0	126.0		4875	3.0	1.0	2	dbSNP_98	126	2073,6527	359.4+/-331.5	261,1551,2488	no	coding-synonymous	LRP2	NM_004525.2		1194,2528,2781	GG,GA,AA		24.1047,35.4744,37.7979		1625/4656	170092395	4916,8090	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon29			ATAATCACAAAAG		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.4875T>C	2.37:g.170092395A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			T|0.095;G|0.314	0.314	strong		0.433	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
SPTB	6710	hgsc.bcm.edu	37	14	65216120	65216120	+	Silent	SNP	C	C	T	rs57421986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:65216120C>T	ENST00000556626.1	-	36	7033	c.6891G>A	c.(6889-6891)gcG>gcA	p.A2297A	SPTB_ENST00000342835.4_5'UTR|SPTB_ENST00000389722.3_Silent_p.A2297A			P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	0					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)		GCAGGCTCTGCGCCTTGACGC	0.632													C|||	523	0.104433	0.2421	0.0346	5008	,	,		13049	0.0317		0.0775	False		,,,				2504	0.0706				p.A2297A		Atlas-SNP	.											.	SPTB	378	.	0			c.G6891A						PASS	.	C		979,3427	354.6+/-312.7	114,751,1338	56.0	50.0	52.0		6891	-9.5	0.4	14	dbSNP_129	52	509,8091	139.8+/-196.4	16,477,3807	no	coding-synonymous	SPTB	NM_001024858.2		130,1228,5145	TT,TC,CC		5.9186,22.2197,11.4409		2297/2329	65216120	1488,11518	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon35			GCTCTGCGCCTTG		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		ENST00000556626.1:c.6891G>A	14.37:g.65216120C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	70	40	0.571429	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000556626.1	37	CCDS32099.1																																																																																			A|0.000;C|0.891;T|0.108	0.108	strong		0.632	SPTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414076.1		
RSBN1L	222194	hgsc.bcm.edu	37	7	77365770	77365770	+	Silent	SNP	A	A	G	rs3764824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:77365770A>G	ENST00000334955.8	+	2	657	c.630A>G	c.(628-630)gaA>gaG	p.E210E	RSBN1L_ENST00000445288.1_5'UTR	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	210	Lys-rich.					nucleus (GO:0005634)				central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						aagaaaaagaaagagaaaaaa	0.249													G|||	2892	0.577476	0.8979	0.4481	5008	,	,		15634	0.3095		0.5219	False		,,,				2504	0.5695				p.E210E		Atlas-SNP	.											.	RSBN1L	74	.	0			c.A630G						PASS	.	G		2886,600		1200,486,57	51.0	53.0	53.0		630	2.8	1.0	7	dbSNP_107	53	4049,3933		1084,1881,1026	no	coding-synonymous	RSBN1L	NM_198467.2		2284,2367,1083	GG,GA,AA		49.2734,17.2117,39.5274		210/847	77365770	6935,4533	1743	3991	5734	SO:0001819	synonymous_variant	222194	exon2			AAAAGAAAGAGAA	AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.630A>G	7.37:g.77365770A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_198467	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Silent	SNP	ENST00000334955.8	37	CCDS43607.1																																																																																			A|0.466;G|0.534	0.534	strong		0.249	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467	
PRODH2	58510	hgsc.bcm.edu	37	19	36298022	36298022	+	Splice_Site	SNP	T	T	C	rs73594420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	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
NOTCH1	4851	hgsc.bcm.edu	37	9	139391636	139391636	+	Silent	SNP	G	G	A	rs2229974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139391636G>A	ENST00000277541.6	-	34	6630	c.6555C>T	c.(6553-6555)gaC>gaT	p.D2185D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2185					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K2182fs*61(1)|p.S2163_T2283del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		AGCCCTTGCCGTCCTGGGACT	0.662			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3481	0.695088	0.6278	0.6542	5008	,	,		16337	0.9494		0.5775	False		,,,				2504	0.6738				p.D2185D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.C6555T						PASS	.	G		2777,1589		891,995,297	47.0	54.0	52.0		6555	-0.8	1.0	9	dbSNP_98	52	4726,3816		1319,2088,864	no	coding-synonymous	NOTCH1	NM_017617.3		2210,3083,1161	AA,AG,GG		44.6734,36.3949,41.8733		2185/2556	139391636	7503,5405	2183	4271	6454	SO:0001819	synonymous_variant	4851	exon34			CTTGCCGTCCTGG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6555C>T	9.37:g.139391636G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	133	77	0.578947	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.341;A|0.659	0.659	strong		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
GPR146	115330	hgsc.bcm.edu	37	7	1097183	1097183	+	Missense_Mutation	SNP	G	G	A	rs11761941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1097183G>A	ENST00000397095.1	+	2	255	c.32G>A	c.(31-33)gGg>gAg	p.G11E	C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000397098.3_Intron|GPR146_ENST00000297468.3_Missense_Mutation_p.G11E|C7orf50_ENST00000397100.2_Intron|RP11-449P15.1_ENST00000549241.1_RNA			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	11						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		AACGGCACAGGGCTGGTGGAG	0.677													G|||	345	0.0688898	0.0204	0.0821	5008	,	,		17500	0.0		0.1262	False		,,,				2504	0.137				p.G11E		Atlas-SNP	.											.	GPR146	20	.	0			c.G32A						PASS	.		,,,GLU/GLY	204,4192		2,200,1996	29.0	28.0	28.0		,,,32	-2.5	0.0	7	dbSNP_120	28	1342,7256		105,1132,3062	yes	intron,intron,intron,missense	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,98	107,1332,5058	AA,AG,GG		15.6083,4.6406,11.8978	,,,benign	,,,11/334	1097183	1546,11448	2198	4299	6497	SO:0001583	missense	115330	exon1			GCACAGGGCTGGT	BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"""GPCR / Class A : Orphans"""	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.32G>A	7.37:g.1097183G>A	ENSP00000380283:p.Gly11Glu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	150	79	0.526667	NM_138445	Q86SP5	Missense_Mutation	SNP	ENST00000397095.1	37	CCDS5321.1	143	0.06547619047619048	10	0.02032520325203252	31	0.0856353591160221	0	0.0	102	0.1345646437994723	G	0.662	-0.805227	0.02819	0.046406	0.156083	ENSG00000164849	ENST00000444847;ENST00000397095;ENST00000427680;ENST00000297468	T;T;T	0.36340	1.26;1.26;1.26	5.12	-2.48	0.06423	.	0.771901	0.12341	N	0.477461	T	0.00073	0.0002	L	0.34521	1.04	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.25117	-1.0141	9	0.06625	T	0.88	-6.8234	0.5541	0.00668	0.3465:0.1291:0.2796:0.2448	rs11761941	11	Q96CH1	GP146_HUMAN	E	11	ENSP00000410743:G11E;ENSP00000380283:G11E;ENSP00000297468:G11E	ENSP00000297468:G11E	G	+	2	0	GPR146	1063709	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.135000	0.15952	-0.364000	0.08088	0.561000	0.74099	GGG	G|0.903;A|0.097	0.097	strong		0.677	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
MPDZ	8777	hgsc.bcm.edu	37	9	13223570	13223570	+	Splice_Site	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:13223570C>T	ENST00000319217.7	-	5	780	c.533G>A	c.(532-534)aGa>aAa	p.R178K	MPDZ_ENST00000541718.1_Splice_Site_p.R178K|MPDZ_ENST00000546205.1_Splice_Site_p.R178K|MPDZ_ENST00000536827.1_Splice_Site_p.R178K|MPDZ_ENST00000381015.4_Splice_Site_p.R178K|MPDZ_ENST00000447879.1_Splice_Site_p.R178K|MPDZ_ENST00000381022.2_Splice_Site_p.R178K	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	178	PDZ 1. {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)	p.R178I(2)		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)		ACCATCTCACCTATGGGCCAC	0.423																																					p.R178K		Atlas-SNP	.											MPDZ_ENST00000541718,NS,carcinoma,0,2	MPDZ	324	2	2	Substitution - Missense(2)	endometrium(2)	c.G533A						scavenged	.						95.0	94.0	94.0					9																	13223570		1865	4107	5972	SO:0001630	splice_region_variant	8777	exon5			TCTCACCTATGGG	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.533+1G>A	9.37:g.13223570C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	228	5	0.0219298	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	C	14.02	2.410736	0.42817	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68;1.68;1.68	6.08	6.08	0.98989	.	0.131207	0.34853	N	0.003629	T	0.25419	0.0618	L	0.35723	1.085	0.80722	D	1	B;B;B	0.16603	0.018;0.007;0.007	B;B;B	0.19391	0.025;0.01;0.01	T	0.04855	-1.0922	9	.	.	.	.	20.6721	0.99693	0.0:1.0:0.0:0.0	.	178;178;178	B7ZMI4;O75970-3;O75970-2	.;.;.	K	178	ENSP00000320006:R178K;ENSP00000439807:R178K;ENSP00000370410:R178K;ENSP00000444151:R178K;ENSP00000415208:R178K;ENSP00000370403:R178K;ENSP00000446358:R178K	.	R	-	2	0	MPDZ	13213570	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	5.760000	0.68793	2.894000	0.99253	0.591000	0.81541	AGA	.	.	none		0.423	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	Missense_Mutation
HECW2	57520	hgsc.bcm.edu	37	2	197087061	197087061	+	Silent	SNP	T	T	C	rs16847486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:197087061T>C	ENST00000260983.3	-	24	4202	c.4020A>G	c.(4018-4020)ctA>ctG	p.L1340L	HECW2_ENST00000409111.1_Silent_p.L984L	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1340	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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						TCAGGTCACATAGACTAAGAT	0.388													T|||	140	0.0279553	0.0976	0.0159	5008	,	,		21341	0.0		0.0	False		,,,				2504	0.0				p.L1340L		Atlas-SNP	.											.	HECW2	239	.	0			c.A4020G						PASS	.	T		443,3963	214.8+/-234.0	23,397,1783	120.0	104.0	110.0		4020	-1.3	0.8	2	dbSNP_123	110	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	HECW2	NM_020760.1		23,407,6073	CC,CT,TT		0.1163,10.0545,3.483		1340/1573	197087061	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	57520	exon24			GTCACATAGACTA	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.4020A>G	2.37:g.197087061T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	55	0.591398	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Silent	SNP	ENST00000260983.3	37	CCDS33354.1																																																																																			T|0.965;C|0.035	0.035	strong		0.388	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760	
RYR1	6261	hgsc.bcm.edu	37	19	38964275	38964275	+	Missense_Mutation	SNP	A	A	G	rs34694816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38964275A>G	ENST00000359596.3	+	28	4024	c.4024A>G	c.(4024-4026)Agc>Ggc	p.S1342G	RYR1_ENST00000360985.3_Missense_Mutation_p.S1342G|RYR1_ENST00000355481.4_Missense_Mutation_p.S1342G			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1342	6 X approximate repeats.		S -> G (in dbSNP:rs34694816). {ECO:0000269|PubMed:19191329}.		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)	TGGGGGCTGGAGCGAGGCAGA	0.741													G|||	271	0.0541134	0.1936	0.0187	5008	,	,		12448	0.0		0.002	False		,,,				2504	0.0				p.S1342G		Atlas-SNP	.											.	RYR1	708	.	0			c.A4024G						PASS	.	G	GLY/SER,GLY/SER	450,3742		20,410,1666	6.0	8.0	7.0		4024,4024	4.0	1.0	19	dbSNP_126	7	5,8089		0,5,4042	yes	missense,missense	RYR1	NM_000540.2,NM_001042723.1	56,56	20,415,5708	GG,GA,AA		0.0618,10.7347,3.7034	benign,benign	1342/5039,1342/5034	38964275	455,11831	2096	4047	6143	SO:0001583	missense	6261	exon28			GGCTGGAGCGAGG	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.4024A>G	19.37:g.38964275A>G	ENSP00000352608:p.Ser1342Gly	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	114	0.0521978021978022	104	0.21138211382113822	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	G	9.860	1.196031	0.22037	0.107347	6.18E-4	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96745	-4.11;-4.11;-4.11	5.07	4.03	0.46877	.	0.085426	0.46758	N	0.000270	T	0.00440	0.0014	N	0.08118	0	0.51012	P	9.199999999998099E-5	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.47355	-0.9124	9	0.20519	T	0.43	.	8.5434	0.33406	0.1826:0.0:0.8174:0.0	rs34694816	1342;1342	P21817-2;P21817	.;RYR1_HUMAN	G	1342	ENSP00000352608:S1342G;ENSP00000347667:S1342G;ENSP00000354254:S1342G	ENSP00000347667:S1342G	S	+	1	0	RYR1	43656115	1.000000	0.71417	0.983000	0.44433	0.196000	0.23810	4.468000	0.60162	1.142000	0.42291	-0.355000	0.07637	AGC	A|0.949;G|0.051	0.051	strong		0.741	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26422993	26422993	+	Silent	SNP	C	C	T	rs7290069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26422993C>T	ENST00000407587.2	+	43	7225	c.7056C>T	c.(7054-7056)tgC>tgT	p.C2352C	MYO18B_ENST00000536101.1_Silent_p.C2351C|MYO18B_ENST00000335473.7_Silent_p.C2351C			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2351						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TCAGTTCCTGCGAGTCCCTCT	0.567													C|||	172	0.034345	0.1256	0.0072	5008	,	,		19058	0.001		0.0	False		,,,				2504	0.0				p.C2351C		Atlas-SNP	.											MYO18B,NS,carcinoma,+2,1	MYO18B	322	1	0			c.C7053T						PASS	.	C		437,3431		26,385,1523	79.0	88.0	85.0		7053	-0.2	1.0	22	dbSNP_116	85	3,8269		0,3,4133	no	coding-synonymous	MYO18B	NM_032608.5		26,388,5656	TT,TC,CC		0.0363,11.2978,3.6244		2351/2568	26422993	440,11700	1934	4136	6070	SO:0001819	synonymous_variant	84700	exon43			TTCCTGCGAGTCC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7056C>T	22.37:g.26422993C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37		65	0.02976190476190476	63	0.12804878048780488	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	8.758	0.922959	0.18056	0.112978	3.63E-4	ENSG00000133454	ENST00000543971	.	.	.	4.89	-0.211	0.13172	.	.	.	.	.	T	0.00496	0.0016	.	.	.	0.09310	P	0.9999999999999841	.	.	.	.	.	.	T	0.17961	-1.0352	3	.	.	.	.	9.1903	0.37195	0.0:0.5439:0.0:0.4561	rs7290069	.	.	.	V	301	.	.	A	+	2	0	MYO18B	24752993	0.125000	0.22332	0.988000	0.46212	0.824000	0.46624	-1.147000	0.03188	0.125000	0.18397	0.462000	0.41574	GCG	C|0.968;T|0.032	0.032	strong		0.567	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
S100A2	6273	hgsc.bcm.edu	37	1	153534027	153534027	+	Missense_Mutation	SNP	C	C	T	rs1047325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153534027C>T	ENST00000368708.3	-	3	554	c.182G>A	c.(181-183)aGc>aAc	p.S61N	S100A2_ENST00000497140.1_Missense_Mutation_p.S28N|S100A2_ENST00000368707.4_3'UTR|S100A2_ENST00000368710.1_Missense_Mutation_p.S61N|S100A2_ENST00000487430.2_Missense_Mutation_p.S61N|S100A2_ENST00000368709.1_Missense_Mutation_p.S61N	NM_005978.3	NP_005969.1	P29034	S10A2_HUMAN	S100 calcium binding protein A2	62	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				endothelial cell migration (GO:0043542)		calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5	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)		Olopatadine(DB00768)	CTCATCCAGGCTGCCCATCAG	0.537													T|||	757	0.151158	0.4463	0.0821	5008	,	,		21128	0.0109		0.0527	False		,,,				2504	0.047				p.S61N		Atlas-SNP	.											.	S100A2	14	.	0			c.G182A						PASS	.	T	ASN/SER	1775,2631	643.4+/-397.8	363,1049,791	235.0	219.0	224.0		182	-4.6	0.0	1	dbSNP_86	224	441,8159	799.7+/-407.4	15,411,3874	yes	missense	S100A2	NM_005978.3	46	378,1460,4665	TT,TC,CC		5.1279,40.286,17.0383	benign	61/98	153534027	2216,10790	2203	4300	6503	SO:0001583	missense	6273	exon3			TCCAGGCTGCCCA	BC002829	CCDS1044.1	1q21	2013-01-10	2001-11-28		ENSG00000196754	ENSG00000196754		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	10492	protein-coding gene	gene with protein product		176993	"""S100 calcium-binding protein A2"""	S100L		8341667	Standard	NM_005978		Approved	CAN19	uc001fcb.3	P29034	OTTHUMG00000035031	ENST00000368708.3:c.182G>A	1.37:g.153534027C>T	ENSP00000357697:p.Ser61Asn	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	250	248	0.992	NM_005978	O00266|Q3KRB9|Q5RHS8|Q9BU83	Missense_Mutation	SNP	ENST00000368708.3	37	CCDS1044.1	274	0.12545787545787546	208	0.42276422764227645	30	0.08287292817679558	4	0.006993006993006993	32	0.04221635883905013	T	5.767	0.325859	0.10900	0.40286	0.051279	ENSG00000196754	ENST00000368708;ENST00000368710;ENST00000368709;ENST00000368707	T;T;T	0.14266	2.52;2.52;2.52	4.77	-4.58	0.03410	S100/Calbindin-D9k, conserved site (1);EF-hand-like domain (1);	0.948424	0.08683	N	0.909215	T	0.01940	0.0061	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43940	-0.9360	8	0.44086	T	0.13	.	1.7661	0.03002	0.1195:0.308:0.2454:0.3271	rs1047325;rs3174843;rs52793522;rs56586255;rs60177723;rs1047325	62	P29034	S10A2_HUMAN	N	61;61;61;102	ENSP00000357697:S61N;ENSP00000357699:S61N;ENSP00000357698:S61N	ENSP00000357696:S102N	S	-	2	0	S100A2	151800651	0.019000	0.18553	0.000000	0.03702	0.286000	0.27126	0.583000	0.23849	-1.416000	0.02019	-0.254000	0.11334	AGC	C|0.841;T|0.159	0.159	strong		0.537	S100A2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084789.1	NM_005978	
PLXNB2	23654	hgsc.bcm.edu	37	22	50716068	50716068	+	Silent	SNP	C	C	T	rs11547732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50716068C>T	ENST00000449103.1	-	33	5288	c.5148G>A	c.(5146-5148)gcG>gcA	p.A1716A	PLXNB2_ENST00000359337.4_Silent_p.A1716A			O15031	PLXB2_HUMAN	plexin B2	1716					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)		TGAAGGTCTGCGCGATGACTG	0.632													C|||	471	0.0940495	0.3374	0.0303	5008	,	,		16203	0.0		0.004	False		,,,				2504	0.0				p.A1716A		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G5148A						PASS	.	C		1148,3132		141,866,1133	60.0	66.0	64.0		5148	-7.9	0.0	22	dbSNP_120	64	10,8510		0,10,4250	no	coding-synonymous	PLXNB2	NM_012401.3		141,876,5383	TT,TC,CC		0.1174,26.8224,9.0469		1716/1839	50716068	1158,11642	2140	4260	6400	SO:0001819	synonymous_variant	23654	exon33			GGTCTGCGCGATG		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.5148G>A	22.37:g.50716068C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1	161	0.07371794871794872	147	0.29878048780487804	13	0.03591160220994475	0	0.0	1	0.0013192612137203166	C	0.034	-1.315528	0.01331	0.268224	0.001174	ENSG00000196576	ENST00000399964	.	.	.	3.94	-7.87	0.01183	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999955255	.	.	.	.	.	.	T	0.48937	-0.8990	4	0.87932	D	0	.	3.99	0.09533	0.1301:0.3253:0.341:0.2036	rs11547732	.	.	.	H	346	.	ENSP00000382845:R346H	R	-	2	0	PLXNB2	49058195	0.000000	0.05858	0.009000	0.14445	0.067000	0.16453	-3.257000	0.00537	-6.532000	0.00003	-2.734000	0.00129	CGC	T|0.048;G|0.000;C|0.952;A|0.000	0.048	strong		0.632	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
EPPIN	57119	hgsc.bcm.edu	37	20	44174306	44174306	+	Silent	SNP	G	G	A	rs374858005		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44174306G>A	ENST00000354280.4	-	2	261	c.195C>T	c.(193-195)tgC>tgT	p.C65C	EPPIN_ENST00000409554.1_Silent_p.C65C|EPPIN_ENST00000336443.3_Silent_p.C49C|EPPIN_ENST00000555685.1_Silent_p.C65C|EPPIN-WFDC6_ENST00000504988.1_Silent_p.C65C	NM_020398.3	NP_065131.1	O95925	EPPI_HUMAN	epididymal peptidase inhibitor	65	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.				defense response to bacterium (GO:0042742)|negative regulation of peptidase activity (GO:0010466)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										ATTTTTTTCCGCAGCTGAAGA	0.453													G|||	1	0.000199681	0.0	0.0	5008	,	,		20884	0.0		0.0	False		,,,				2504	0.001				p.C65C		Atlas-SNP	.											.	.	.	.	0			c.C195T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	320.0	284.0	296.0		195,195	-3.6	0.9	20		296	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SPINLW1,SPINLW1-WFDC6	NM_001198986.1,NM_020398.3	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	65/180,65/134	44174306	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	100526773	exon2			TTTTCCGCAGCTG	AF286370	CCDS13359.1	20q13.12	2014-01-21	2012-08-22	2012-08-22	ENSG00000101448	ENSG00000101448		"""WAP four-disulfide core domain containing"""	15932	protein-coding gene	gene with protein product	"""epididymal protease inhibitor"", ""cancer/testis antigen 72"""	609031	"""serine protease inhibitor-like, with Kunitz and WAP domains 1 (eppin)"", ""serine peptidase inhibitor-like, with Kunitz and WAP domains 1 (eppin)"""	SPINLW1		11404006, 12206714	Standard	NM_020398		Approved	EPPIN1, EPPIN2, EPPIN3, dJ461P17.2, WAP7, WFDC7, CT71		O95925	OTTHUMG00000032588	ENST00000354280.4:c.195C>T	20.37:g.44174306G>A		Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	278	132	0.47482	NM_001198986	A6PVD6|Q86TP9|Q96SD7|Q9HD30	Silent	SNP	ENST00000354280.4	37	CCDS13359.1																																																																																			.	.	weak		0.453	EPPIN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079467.4		
NRXN1	9378	hgsc.bcm.edu	37	2	51254901	51254901	+	Silent	SNP	G	G	A	rs1045874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:51254901G>A	ENST00000406316.2	-	2	1987	c.511C>T	c.(511-513)Ctg>Ttg	p.L171L	NRXN1_ENST00000406859.3_Silent_p.L171L|NRXN1_ENST00000405472.3_Silent_p.L171L|NRXN1_ENST00000405581.1_Silent_p.L171L|NRXN1_ENST00000402717.3_Silent_p.L171L|NRXN1_ENST00000401669.2_Silent_p.L171L|NRXN1_ENST00000404971.1_Silent_p.L171L	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	171	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ACCGAGGCCAGGGTGAGCTTG	0.677													G|||	1067	0.213059	0.4841	0.0663	5008	,	,		13008	0.1151		0.0736	False		,,,				2504	0.1953				p.L171L		Atlas-SNP	.											NRXN1_ENST00000536085,NS,carcinoma,0,3	NRXN1	1118	3	0			c.C511T						PASS	.	G	,	1545,2567		281,983,792	25.0	30.0	28.0		511,511	2.8	1.0	2	dbSNP_86	28	625,7733		33,559,3587	no	coding-synonymous,coding-synonymous	NRXN1	NM_001135659.1,NM_004801.4	,	314,1542,4379	AA,AG,GG		7.4779,37.573,17.4018	,	171/1548,171/1478	51254901	2170,10300	2056	4179	6235	SO:0001819	synonymous_variant	9378	exon2			AGGCCAGGGTGAG	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.511C>T	2.37:g.51254901G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	143	73	0.51049	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			G|0.853;A|0.147	0.147	strong		0.677	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
HDLBP	3069	hgsc.bcm.edu	37	2	242173247	242173247	+	Silent	SNP	G	G	A	rs2230359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242173247G>A	ENST00000391975.1	-	24	3503	c.3276C>T	c.(3274-3276)gaC>gaT	p.D1092D	HDLBP_ENST00000391976.2_Silent_p.D1092D|HDLBP_ENST00000310931.4_Silent_p.D1092D|HDLBP_ENST00000427183.2_Silent_p.D1059D	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1092	KH 13. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		GGTTCCCATCGTCCTTATCAG	0.522													G|||	619	0.123602	0.4365	0.0418	5008	,	,		20045	0.0		0.003	False		,,,				2504	0.0102				p.D1092D		Atlas-SNP	.											.	HDLBP	118	.	0			c.C3276T						PASS	.	G	,	1641,2765	504.2+/-365.8	296,1049,858	146.0	130.0	135.0		3276,3276	-10.6	0.0	2	dbSNP_98	135	27,8573	18.5+/-59.3	0,27,4273	no	coding-synonymous,coding-synonymous	HDLBP	NM_005336.4,NM_203346.3	,	296,1076,5131	AA,AG,GG		0.314,37.2447,12.8249	,	1092/1269,1092/1269	242173247	1668,11338	2203	4300	6503	SO:0001819	synonymous_variant	3069	exon24			CCCATCGTCCTTA		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"""vigilin"""	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.3276C>T	2.37:g.242173247G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	137	135	0.985401	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Silent	SNP	ENST00000391975.1	37	CCDS2547.1																																																																																			T|0.032;G|0.738;C|0.133;A|0.097	0.097	strong		0.522	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
AP3D1	8943	hgsc.bcm.edu	37	19	2116616	2116616	+	Silent	SNP	T	T	C	rs73512353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2116616T>C	ENST00000345016.5	-	17	2220	c.1989A>G	c.(1987-1989)gaA>gaG	p.E663E	AP3D1_ENST00000355272.6_Silent_p.E663E|AP3D1_ENST00000350812.6_Silent_p.E494E|AP3D1_ENST00000356926.4_Silent_p.E572E	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	663					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		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)		GAGCCAGCTCTTCCTCGTCCG	0.692													T|||	38	0.00758786	0.0265	0.0043	5008	,	,		15549	0.0		0.0	False		,,,				2504	0.0				p.E663E		Atlas-SNP	.											.	AP3D1	81	.	0			c.A1989G						PASS	.	T	,	64,4056		1,62,1997	15.0	17.0	16.0		1716,1989	2.8	1.0	19	dbSNP_130	16	0,8376		0,0,4188	no	coding-synonymous,coding-synonymous	AP3D1	NM_001077523.1,NM_003938.5	,	1,62,6185	CC,CT,TT		0.0,1.5534,0.5122	,	572/1113,663/1154	2116616	64,12432	2060	4188	6248	SO:0001819	synonymous_variant	8943	exon17			CAGCTCTTCCTCG	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.1989A>G	19.37:g.2116616T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Silent	SNP	ENST00000345016.5	37	CCDS42459.1																																																																																			T|0.992;C|0.008	0.008	strong		0.692	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
WDR81	124997	hgsc.bcm.edu	37	17	1630992	1630992	+	Silent	SNP	G	G	A	rs9912287|rs587780502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1630992G>A	ENST00000409644.1	+	1	2739	c.2739G>A	c.(2737-2739)ctG>ctA	p.L913L	WDR81_ENST00000545662.1_5'Flank|WDR81_ENST00000446363.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000419248.1_Intron|WDR81_ENST00000309182.5_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	913					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)		GCGCGGTGCTGAAGGACATCA	0.617													G|||	1232	0.246006	0.239	0.2061	5008	,	,		19324	0.1845		0.1948	False		,,,				2504	0.3998				p.L913L		Atlas-SNP	.											.	WDR81	180	.	0			c.G2739A						PASS	.	G	,,,	318,1066		38,242,412	56.0	54.0	54.0		,2739,,	2.7	0.8	17	dbSNP_119	54	689,2493		64,561,966	no	intron,coding-synonymous,intron,intron	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	102,803,1378	AA,AG,GG		21.653,22.9769,22.0543	,,,	,913/1942,,	1630992	1007,3559	692	1591	2283	SO:0001819	synonymous_variant	124997	exon1			GGTGCTGAAGGAC	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.2739G>A	17.37:g.1630992G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	62	0.462687	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			G|0.790;A|0.208	0.208	strong		0.617	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
LGALS9	3965	hgsc.bcm.edu	37	17	25970633	25970633	+	Missense_Mutation	SNP	G	G	A	rs361497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:25970633G>A	ENST00000395473.2	+	5	1995	c.527G>A	c.(526-528)gGg>gAg	p.G176E	LGALS9_ENST00000302228.5_Intron|LGALS9_ENST00000313648.6_Intron|LGALS9_ENST00000413914.2_Missense_Mutation_p.G119E|LGALS9_ENST00000310394.5_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	535	1	0.00186916		WXS	Illumina HiSeq	Phase_I	558	250	0.448029	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	
FRAS1	80144	hgsc.bcm.edu	37	4	79447763	79447763	+	Missense_Mutation	SNP	T	T	C	rs34670941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79447763T>C	ENST00000264895.6	+	70	11317	c.10877T>C	c.(10876-10878)gTt>gCt	p.V3626A		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3622					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						CAGCCATGGGTTGACCCAGGA	0.478													T|||	728	0.145367	0.1755	0.0865	5008	,	,		22507	0.2272		0.1093	False		,,,				2504	0.0992				p.V3626A		Atlas-SNP	.											.	FRAS1	779	.	0			c.T10877C						PASS	.	T	ALA/VAL	652,3336		46,560,1388	50.0	53.0	52.0		10877	-0.8	0.0	4	dbSNP_126	52	832,7504		38,756,3374	yes	missense	FRAS1	NM_025074.6	64	84,1316,4762	CC,CT,TT		9.9808,16.349,12.0415	benign	3626/4013	79447763	1484,10840	1994	4168	6162	SO:0001583	missense	80144	exon70			CATGGGTTGACCC	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.10877T>C	4.37:g.79447763T>C	ENSP00000264895:p.Val3626Ala	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	289	132	0.456747	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	342	0.1565934065934066	96	0.1951219512195122	32	0.08839779005524862	128	0.22377622377622378	86	0.11345646437994723	T	5.318	0.243937	0.10077	0.16349	0.099808	ENSG00000138759	ENST00000264895	T	0.11063	2.81	5.75	-0.78	0.10969	.	1.100870	0.06846	N	0.796502	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	0.48246	-0.9052	9	0.15952	T	0.53	.	11.2992	0.49295	0.0:0.406:0.0:0.594	rs34670941	3626	E9PHH6	.	A	3626	ENSP00000264895:V3626A	ENSP00000264895:V3626A	V	+	2	0	FRAS1	79666787	0.000000	0.05858	0.003000	0.11579	0.368000	0.29767	0.372000	0.20467	-0.331000	0.08501	0.397000	0.26171	GTT	T|0.854;C|0.146	0.146	strong		0.478	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TEKT1	83659	hgsc.bcm.edu	37	17	6733672	6733672	+	Silent	SNP	T	T	C	rs8078571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:6733672T>C	ENST00000338694.2	-	2	153	c.24A>G	c.(22-24)ccA>ccG	p.P8P	TEKT1_ENST00000535086.1_5'UTR	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	8						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.P8P(1)		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)				GGAACTTGGGTGGAGGTTGTA	0.433													C|||	3029	0.604832	0.9047	0.4323	5008	,	,		18050	0.5615		0.4632	False		,,,				2504	0.5123				p.P8P		Atlas-SNP	.											TEKT1,NS,carcinoma,0,1	TEKT1	49	1	1	Substitution - coding silent(1)	stomach(1)	c.A24G						PASS	.	C		3617,789	317.4+/-295.1	1492,633,78	77.0	70.0	72.0		24	-9.8	0.0	17	dbSNP_116	72	4021,4579	598.6+/-393.9	964,2093,1243	no	coding-synonymous	TEKT1	NM_053285.1		2456,2726,1321	CC,CT,TT		46.7558,17.9074,41.2733		8/419	6733672	7638,5368	2203	4300	6503	SO:0001819	synonymous_variant	83659	exon2			CTTGGGTGGAGGT		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.24A>G	17.37:g.6733672T>C		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	220	220	1	NM_053285	D3DTM7	Silent	SNP	ENST00000338694.2	37	CCDS11083.1																																																																																			T|0.415;C|0.585	0.585	strong		0.433	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285	
MRPS2	51116	hgsc.bcm.edu	37	9	138395969	138395969	+	Missense_Mutation	SNP	A	A	G	rs3748199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138395969A>G	ENST00000371785.1	+	5	1090	c.881A>G	c.(880-882)cAt>cGt	p.H294R	C9orf116_ENST00000371791.1_5'Flank|RP11-426A6.5_ENST00000415062.1_RNA|MRPS2_ENST00000241600.5_Missense_Mutation_p.H294R			Q9Y399	RT02_HUMAN	mitochondrial ribosomal protein S2	294			H -> R (in dbSNP:rs3748199).		translation (GO:0006412)	mitochondrion (GO:0005739)|small ribosomal subunit (GO:0015935)	structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(1)|prostate(2)|urinary_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.46e-53)|Epithelial(140;2.04e-47)|all cancers(34;1.23e-42)		GACATGAGCCATTCCCTGTGA	0.637													G|||	783	0.15635	0.3608	0.0807	5008	,	,		18075	0.0685		0.0606	False		,,,				2504	0.1227				p.H294R		Atlas-SNP	.											.	MRPS2	17	.	0			c.A881G						PASS	.	G	ARG/HIS	1293,3103		202,889,1107	20.0	21.0	21.0		881	-6.4	0.0	9	dbSNP_107	21	527,8071		18,491,3790	yes	missense	MRPS2	NM_016034.3	29	220,1380,4897	GG,GA,AA		6.1293,29.4131,14.0065	benign	294/297	138395969	1820,11174	2198	4299	6497	SO:0001583	missense	51116	exon4			TGAGCCATTCCCT	AB051627	CCDS6990.1	9q34	2012-09-13			ENSG00000122140	ENSG00000122140		"""Mitochondrial ribosomal proteins / small subunits"""	14495	protein-coding gene	gene with protein product		611971					Standard	NM_016034		Approved	CGI-91	uc004cfv.5	Q9Y399	OTTHUMG00000020910	ENST00000371785.1:c.881A>G	9.37:g.138395969A>G	ENSP00000360850:p.His294Arg	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_016034	Q5T899|Q9BSQ4	Missense_Mutation	SNP	ENST00000371785.1	37	CCDS6990.1	255	0.11675824175824176	154	0.3130081300813008	27	0.07458563535911603	26	0.045454545454545456	48	0.0633245382585752	G	0.005	-2.214476	0.00289	0.294131	0.061293	ENSG00000122140	ENST00000371785;ENST00000241600	T;T	0.24723	1.84;1.84	3.21	-6.41	0.01938	.	1.900150	0.03877	N	0.276508	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	0.31251	-0.9950	9	0.06494	T	0.89	0.3993	9.5981	0.39587	0.245:0.3254:0.4296:0.0	rs3748199;rs60286354;rs3748199	294	Q9Y399	RT02_HUMAN	R	294	ENSP00000360850:H294R;ENSP00000241600:H294R	ENSP00000241600:H294R	H	+	2	0	MRPS2	137535790	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-3.560000	0.00431	-3.340000	0.00183	-1.400000	0.01143	CAT	A|0.868;G|0.132	0.132	strong		0.637	MRPS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054998.1		
LILRB4	11006	hgsc.bcm.edu	37	19	55179364	55179364	+	Missense_Mutation	SNP	A	A	G	rs1048801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55179364A>G	ENST00000391736.1	+	14	1556	c.1241A>G	c.(1240-1242)cAg>cGg	p.Q414R	LILRB4_ENST00000270452.2_Missense_Mutation_p.Q414R|LILRB4_ENST00000391733.3_Missense_Mutation_p.Q415R|LILRB4_ENST00000391734.3_Missense_Mutation_p.Q361R|LILRB4_ENST00000430952.2_Missense_Mutation_p.Q413R	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	414			Q -> R (in dbSNP:rs1048801). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9548455}.		immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		ACCTACGCCCAGCTGCACAGC	0.647													A|||	1888	0.376997	0.4803	0.3818	5008	,	,		15595	0.3155		0.327	False		,,,				2504	0.3487				p.Q414R		Atlas-SNP	.											LILRB4,NS,carcinoma,-1,1	LILRB4	86	1	0			c.A1241G						PASS	.	A	ARG/GLN,ARG/GLN	1972,2434	555.8+/-379.4	476,1020,707	84.0	88.0	87.0		1238,1241	1.0	0.0	19	dbSNP_86	87	3210,5390	484.2+/-371.3	578,2054,1668	no	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	43,43	1054,3074,2375	GG,GA,AA		37.3256,44.7571,39.8431	possibly-damaging,possibly-damaging	413/448,414/449	55179364	5182,7824	2203	4300	6503	SO:0001583	missense	11006	exon12			ACGCCCAGCTGCA	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1241A>G	19.37:g.55179364A>G	ENSP00000375616:p.Gln414Arg	Somatic	349	1	0.00286533		WXS	Illumina HiSeq	Phase_I	390	371	0.951282	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	788	0.3608058608058608	225	0.4573170731707317	144	0.39779005524861877	171	0.29895104895104896	248	0.32717678100263853	A	10.65	1.410687	0.25465	0.447571	0.373256	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733	T;T;T;T;T	0.01084	5.36;5.36;5.37;6.51;5.37	2.07	0.983	0.19767	.	.	.	.	.	T	0.00012	0.0000	M	0.86864	2.845	0.80722	P	0.0	D;D;D;D	0.65815	0.992;0.995;0.985;0.963	P;P;P;P	0.56563	0.584;0.763;0.801;0.543	T	0.46048	-0.9219	8	0.51188	T	0.08	.	3.8581	0.08984	0.7937:0.0:0.2063:0.0	rs1048801;rs3177732;rs3188849;rs11574595;rs16985517;rs17845809;rs17858774;rs52795380;rs59824494	361;415;413;414	A8MUE1;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	R	414;414;413;361;415	ENSP00000375616:Q414R;ENSP00000270452:Q414R;ENSP00000408995:Q413R;ENSP00000375614:Q361R;ENSP00000375613:Q415R	ENSP00000270452:Q414R	Q	+	2	0	LILRB4	59871176	0.111000	0.22076	0.032000	0.17829	0.331000	0.28603	1.012000	0.29924	0.089000	0.17243	0.334000	0.21626	CAG	A|0.608;G|0.392	0.392	strong		0.647	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
EEF1D	1936	hgsc.bcm.edu	37	8	144671489	144671489	+	Intron	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144671489G>C	ENST00000529272.1	-	2	397				EEF1D_ENST00000395119.3_Intron|EEF1D_ENST00000531621.1_Intron|EEF1D_ENST00000528610.1_Intron|EEF1D_ENST00000532400.1_Intron|EEF1D_ENST00000526838.1_Intron|EEF1D_ENST00000532741.1_Missense_Mutation_p.P305A|EEF1D_ENST00000419152.2_Intron|EEF1D_ENST00000524624.1_Intron|EEF1D_ENST00000317198.6_Intron|EEF1D_ENST00000442189.2_Missense_Mutation_p.P255A|EEF1D_ENST00000423316.2_Missense_Mutation_p.P255A			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	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)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			TTCCCTGGGGGATGGCCGTCA	0.697																																					p.P255A		Atlas-SNP	.											.	EEF1D	48	.	0			c.C763G						PASS	.						5.0	7.0	6.0					8																	144671489		2037	4109	6146	SO:0001627	intron_variant	1936	exon3			CTGGGGGATGGCC	AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.4-2470C>G	8.37:g.144671489G>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	64	25	0.390625	NM_001130053	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	37	CCDS6405.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.470797	0.43942	.	.	ENSG00000104529	ENST00000532741;ENST00000442189;ENST00000423316;ENST00000356793;ENST00000337369;ENST00000526710;ENST00000531281	.	.	.	4.4	4.4	0.53042	.	0.309039	0.29940	N	0.010803	T	0.51312	0.1667	L	0.44542	1.39	0.80722	D	1	P;P;P	0.50528	0.894;0.894;0.936	B;B;P	0.50405	0.437;0.437;0.64	T	0.50381	-0.8835	9	0.45353	T	0.12	.	9.8627	0.41125	0.0939:0.0:0.9061:0.0	.	255;305;255	D3DWK1;E9PRY8;P29692-2	.;.;.	A	305;255;255;207;255;255;255	.	ENSP00000338323:P255A	P	-	1	0	EEF1D	144742632	1.000000	0.71417	0.988000	0.46212	0.875000	0.50365	3.368000	0.52357	2.277000	0.76020	0.561000	0.74099	CCC	.	.	none		0.697	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378	
TEKT4	150483	hgsc.bcm.edu	37	2	95537501	95537501	+	Silent	SNP	C	C	T	rs11889464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:95537501C>T	ENST00000295201.4	+	1	314	c.177C>T	c.(175-177)cgC>cgT	p.R59R	AC097374.2_ENST00000568768.1_RNA|TEKT4_ENST00000427593.2_Silent_p.R59R	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	59					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						TCGCCGACCGCGACCAGTCGG	0.692													.|||	485	0.096845	0.2927	0.0432	5008	,	,		16314	0.0228		0.0308	False		,,,				2504	0.0143				p.R59R		Atlas-SNP	.											.	TEKT4	72	.	0			c.C177T						PASS	.	C		1106,3222		135,836,1193	25.0	30.0	29.0		177	1.0	1.0	2	dbSNP_120	29	250,8154		3,244,3955	no	coding-synonymous	TEKT4	NM_144705.2		138,1080,5148	TT,TC,CC		2.9748,25.5545,10.6503		59/436	95537501	1356,11376	2164	4202	6366	SO:0001819	synonymous_variant	150483	exon1			CGACCGCGACCAG	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.177C>T	2.37:g.95537501C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_144705		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																			C|0.897;T|0.103	0.103	strong		0.692	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
MAP2	4133	hgsc.bcm.edu	37	2	210558162	210558162	+	Missense_Mutation	SNP	G	G	A	rs741006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:210558162G>A	ENST00000360351.4	+	7	1774	c.1268G>A	c.(1267-1269)aGg>aAg	p.R423K	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.R419K|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	423			R -> K (in dbSNP:rs741006).		axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	GTGCAGCAAAGGGATACTTTC	0.418													A|||	822	0.164137	0.2746	0.0692	5008	,	,		19500	0.1974		0.0765	False		,,,				2504	0.138				p.R423K	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.G1268A						PASS	.	A	,LYS/ARG,,	1090,3316	712.4+/-408.1	145,800,1258	89.0	91.0	90.0		,1268,,	0.5	0.0	2	dbSNP_86	90	599,8001	788.3+/-407.6	19,561,3720	yes	intron,missense,intron,intron	MAP2	NM_001039538.1,NM_002374.3,NM_031845.2,NM_031847.2	,26,,	164,1361,4978	AA,AG,GG		6.9651,24.739,12.9863	,benign,,	,423/1828,,	210558162	1689,11317	2203	4300	6503	SO:0001583	missense	4133	exon7			AGCAAAGGGATAC		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.1268G>A	2.37:g.210558162G>A	ENSP00000353508:p.Arg423Lys	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	210	110	0.52381	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	311	0.1423992673992674	119	0.241869918699187	28	0.07734806629834254	109	0.19055944055944055	55	0.07255936675461741	A	0	-2.587322	0.00128	0.24739	0.069651	ENSG00000078018	ENST00000360351;ENST00000445941;ENST00000447185	T;T;T	0.14391	2.51;2.51;2.51	5.8	0.492	0.16872	MAP2/Tau projection (1);	0.451737	0.22705	N	0.056642	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35624	-0.9781	9	0.02654	T	1	-4.1355	2.293	0.04143	0.5161:0.2401:0.1286:0.1152	rs741006;rs59017203;rs741006	419;423	P11137-3;P11137	.;MAP2_HUMAN	K	423;505;419	ENSP00000353508:R423K;ENSP00000409969:R505K;ENSP00000392164:R419K	ENSP00000353508:R423K	R	+	2	0	MAP2	210266407	0.945000	0.32115	0.000000	0.03702	0.003000	0.03518	0.818000	0.27295	-0.412000	0.07519	-0.269000	0.10298	AGG	G|0.850;A|0.150	0.150	strong		0.418	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
MUC4	4585	hgsc.bcm.edu	37	3	195515122	195515122	+	Missense_Mutation	SNP	G	G	C	rs202171964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515122G>C	ENST00000463781.3	-	2	3788	c.3329C>G	c.(3328-3330)aCt>aGt	p.T1110S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1110S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	541					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)		TACTGAGGAAGTGTCGGTGAC	0.572													.|||	134	0.0267572	0.0477	0.0303	5008	,	,		17642	0.0		0.0427	False		,,,				2504	0.0072				p.T1110S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C3329G						PASS	.						11.0	7.0	8.0					3																	195515122		661	1494	2155	SO:0001583	missense	4585	exon2			GAGGAAGTGTCGG	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.3329C>G	3.37:g.195515122G>C	ENSP00000417498:p.Thr1110Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	353	101	0.286119	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	.	.	.	.	.	.	.	.	.	.	-	4.996	0.185039	0.09495	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.42;1.42	0.814	-1.27	0.09347	.	.	.	.	.	T	0.16642	0.0400	N	0.19112	0.55	0.80722	P	0.0	P	0.50943	0.94	B	0.42625	0.393	T	0.26538	-1.0100	7	.	.	.	.	5.9156	0.19053	0.0:0.0:0.6694:0.3305	.	1110	E7ESK3	.	S	1110	ENSP00000417498:T1110S;ENSP00000420243:T1110S	.	T	-	2	0	MUC4	196999517	0.000000	0.05858	0.000000	0.03702	0.296000	0.27459	-0.322000	0.08007	-0.275000	0.09219	0.064000	0.15345	ACT	G|0.949;C|0.052	0.052	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PIBF1	10464	hgsc.bcm.edu	37	13	73369642	73369642	+	Missense_Mutation	SNP	A	A	G	rs1372000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	80	0	0		WXS	Illumina HiSeq	Phase_I	145	144	0.993103	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	
GABBR2	9568	hgsc.bcm.edu	37	9	101068580	101068580	+	Silent	SNP	G	G	A	rs2304389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101068580G>A	ENST00000259455.2	-	15	2511	c.2052C>T	c.(2050-2052)ccC>ccT	p.P684P		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	684					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	CGTTGAGTGCGGGGATGCTGA	0.557													G|||	970	0.19369	0.1815	0.2061	5008	,	,		19497	0.1925		0.17	False		,,,				2504	0.227				p.P684P		Atlas-SNP	.											GABBR2,NS,malignant_melanoma,-1,1	GABBR2	126	1	0			c.C2052T						PASS	.	G		737,3669	303.2+/-287.8	63,611,1529	119.0	80.0	93.0		2052	-10.3	0.1	9	dbSNP_100	93	1427,7173	273.0+/-290.4	122,1183,2995	no	coding-synonymous	GABBR2	NM_005458.7		185,1794,4524	AA,AG,GG		16.593,16.7272,16.6385		684/942	101068580	2164,10842	2203	4300	6503	SO:0001819	synonymous_variant	9568	exon15			GAGTGCGGGGATG	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.2052C>T	9.37:g.101068580G>A		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	290	93	0.32069	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Silent	SNP	ENST00000259455.2	37	CCDS6736.1																																																																																			G|0.831;A|0.169	0.169	strong		0.557	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
CDC27	996	hgsc.bcm.edu	37	17	45214661	45214661	+	Silent	SNP	G	G	A	rs111322439		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45214661G>A	ENST00000066544.3	-	14	1863	c.1770C>T	c.(1768-1770)ttC>ttT	p.F590F	CDC27_ENST00000531206.1_Silent_p.F596F|CDC27_ENST00000446365.2_Silent_p.F529F|CDC27_ENST00000527547.1_Silent_p.F589F	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	590					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAGCTCTCTGGAAGAATTTAA	0.383																																					p.F596F		Atlas-SNP	.											CDC27_ENST00000531206,rectum,carcinoma,0,4	CDC27	337	4	0			c.C1788T						scavenged	.						58.0	61.0	60.0					17																	45214661		2203	4300	6503	SO:0001819	synonymous_variant	996	exon14			TCTCTGGAAGAAT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1770C>T	17.37:g.45214661G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	23	5	0.217391	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																			G|0.500;A|0.500	0.500	weak		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
COL6A3	1293	hgsc.bcm.edu	37	2	238289842	238289842	+	Missense_Mutation	SNP	G	G	A	rs34741387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238289842G>A	ENST00000295550.4	-	5	2065	c.1613C>T	c.(1612-1614)aCg>aTg	p.T538M	COL6A3_ENST00000472056.1_Missense_Mutation_p.T131M|COL6A3_ENST00000409809.1_Missense_Mutation_p.T332M|COL6A3_ENST00000346358.4_Missense_Mutation_p.T538M|COL6A3_ENST00000392003.2_Missense_Mutation_p.T131M|COL6A3_ENST00000347401.3_Missense_Mutation_p.T337M|COL6A3_ENST00000353578.4_Missense_Mutation_p.T332M|COL6A3_ENST00000392004.3_Missense_Mutation_p.T332M	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	538	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.		T -> M (in dbSNP:rs34741387).		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)	p.T538K(1)|p.T332K(1)		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)		GGCTGAACTCGTGAATAGGTT	0.552													G|||	44	0.00878594	0.031	0.0043	5008	,	,		18735	0.0		0.0	False		,,,				2504	0.0				p.T538M		Atlas-SNP	.											.	COL6A3	608	.	2	Substitution - Missense(2)	lung(2)	c.C1613T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	115,4291	85.3+/-124.0	1,113,2089	69.0	80.0	76.0		1613,392,995,392,995	3.6	0.5	2	dbSNP_126	76	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,missense	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	81,81,81,81,81	1,114,6388	AA,AG,GG		0.0116,2.6101,0.8919	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	538/3178,131/1037,332/1238,131/2571,332/2972	238289842	116,12890	2203	4300	6503	SO:0001583	missense	1293	exon5			GAACTCGTGAATA	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.1613C>T	2.37:g.238289842G>A	ENSP00000295550:p.Thr538Met	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	11.65	1.702027	0.30232	0.026101	1.16E-4	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	D;D;D;D;D;D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8	5.6	3.62	0.41486	von Willebrand factor, type A (3);	0.360229	0.23277	N	0.049959	T	0.80964	0.4725	M	0.87547	2.89	0.24906	N	0.992072	D;D;D;D;D;D	0.89917	0.999;1.0;0.984;0.998;1.0;0.994	D;D;P;D;D;P	0.79784	0.916;0.993;0.87;0.964;0.99;0.88	T	0.77525	-0.2555	10	0.51188	T	0.08	.	12.068	0.53598	0.0695:0.0:0.8014:0.129	rs34741387	538;131;131;332;332;538	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	M	538;337;332;131;332;538;332;131;538	ENSP00000295550:T538M;ENSP00000315609:T337M;ENSP00000315873:T332M;ENSP00000418285:T131M;ENSP00000386844:T332M;ENSP00000295546:T538M;ENSP00000375861:T332M;ENSP00000375860:T131M;ENSP00000389539:T538M	ENSP00000295550:T538M	T	-	2	0	COL6A3	237954581	0.193000	0.23313	0.484000	0.27391	0.010000	0.07245	0.549000	0.23329	1.366000	0.46076	0.655000	0.94253	ACG	G|0.991;A|0.009	0.009	strong		0.552	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
PAPOLB	56903	hgsc.bcm.edu	37	7	4900095	4900095	+	Silent	SNP	A	A	G	rs1553960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	262	0	0		WXS	Illumina HiSeq	Phase_I	252	126	0.5	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	
ELF4	2000	hgsc.bcm.edu	37	X	129201179	129201179	+	Silent	SNP	C	C	T	rs2181440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:129201179C>T	ENST00000308167.5	-	9	1888	c.1509G>A	c.(1507-1509)acG>acA	p.T503T	ELF4_ENST00000335997.7_Silent_p.T503T	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)											breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						CCCCTGTGACCGTGGGTGGCG	0.657			T	ERG	AML								c|||	772	0.204503	0.0348	0.317	3775	,	,		12362	0.1002		0.2286	False		,,,				2504	0.1789				p.T503T		Atlas-SNP	.		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	.	ELF4	67	.	0			c.G1509A						PASS	.		,	273,3558		10,215,38,1406,531	24.0	26.0	25.0		1509,1509	-7.2	0.0	X	dbSNP_96	25	1731,4977		158,919,496,1348,1362	no	coding-synonymous,coding-synonymous	ELF4	NM_001127197.1,NM_001421.3	,	168,1134,534,2754,1893	TT,TC,T,CC,C		25.805,7.1261,19.0151	,	503/664,503/664	129201179	2004,8535	2200	4283	6483	SO:0001819	synonymous_variant	2000	exon9			TGTGACCGTGGGT	U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.1509G>A	X.37:g.129201179C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	108	72	0.666667	NM_001421		Silent	SNP	ENST00000308167.5	37	CCDS14617.1																																																																																			C|0.813;T|0.187	0.187	strong		0.657	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421	
DHRS11	79154	hgsc.bcm.edu	37	17	34958531	34958531	+	IGR	SNP	C	C	T	rs60978234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34958531C>T	ENST00000251312.5	+	0	1598				MRM1_ENST00000250156.7_Missense_Mutation_p.P98S|MRM1_ENST00000585770.1_5'UTR	NM_024308.3	NP_077284.2	Q6UWP2	DHR11_HUMAN	dehydrogenase/reductase (SDR family) member 11							extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(4)	5						GCGGGACATTCCAGTTCTGCG	0.701													C|||	23	0.00459265	0.0166	0.0	5008	,	,		15249	0.0		0.001	False		,,,				2504	0.0				p.P98S		Atlas-SNP	.											MRM1,NS,haematopoietic_neoplasm,-2,1	MRM1	19	1	0			c.C292T						PASS	.	C	SER/PRO	68,4320		1,66,2127	22.0	26.0	24.0		292	4.9	1.0	17	dbSNP_129	24	0,8576		0,0,4288	yes	missense	MRM1	NM_024864.3	74	1,66,6415	TT,TC,CC		0.0,1.5497,0.5245	probably-damaging	98/354	34958531	68,12896	2194	4288	6482	SO:0001628	intergenic_variant	79922	exon1			GACATTCCAGTTC		CCDS11315.2	17q12	2014-05-06			ENSG00000108272	ENSG00000278535		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	28639	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 24C, member 1"""					12975309, 19027726	Standard	NM_024308		Approved	MGC4172, SDR24C1	uc002hnd.3	Q6UWP2	OTTHUMG00000188442		17.37:g.34958531C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	21	8	0.380952	NM_024864	B2RDZ3|Q9BUC7|Q9H674	Missense_Mutation	SNP	ENST00000251312.5	37	CCDS11315.2	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	14.72	2.620552	0.46736	0.015497	0.0	ENSG00000129282	ENST00000250156	T	0.28666	1.6	4.9	4.9	0.64082	RNA 2-O ribose methyltransferase, substrate binding (2);	0.065831	0.64402	D	0.000006	T	0.21509	0.0518	M	0.69463	2.115	0.80722	D	1	B	0.32968	0.392	B	0.42062	0.374	T	0.07139	-1.0788	10	0.07175	T	0.84	-13.0363	15.1676	0.72840	0.0:1.0:0.0:0.0	rs60978234	98	Q6IN84	MRM1_HUMAN	S	98	ENSP00000250156:P98S	ENSP00000250156:P98S	P	+	1	0	MRM1	32032644	0.845000	0.29573	0.969000	0.41365	0.561000	0.35649	3.772000	0.55325	2.423000	0.82170	0.555000	0.69702	CCA	C|0.993;T|0.007	0.007	strong		0.701	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308	
TEX14	56155	hgsc.bcm.edu	37	17	56690848	56690848	+	Silent	SNP	T	T	C	rs8077548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56690848T>C	ENST00000240361.8	-	9	1042	c.957A>G	c.(955-957)ctA>ctG	p.L319L	TEX14_ENST00000349033.5_Silent_p.L313L|TEX14_ENST00000389934.3_Silent_p.L313L			Q8IWB6	TEX14_HUMAN	testis expressed 14	319	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	p.L313L(1)|p.L319L(1)		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)					GGGTTTTCTCTAGGTCCTGGG	0.502													T|||	1169	0.233427	0.3328	0.0663	5008	,	,		17596	0.3036		0.0726	False		,,,				2504	0.3108				p.L319L		Atlas-SNP	.											TEX14_ENST00000240361,NS,carcinoma,0,2	TEX14	343	2	2	Substitution - coding silent(2)	stomach(2)	c.A957G						scavenged	.	T	,,	1205,3201	421.5+/-339.4	161,883,1159	162.0	139.0	147.0		957,939,939	2.5	1.0	17	dbSNP_116	147	564,8036	152.7+/-207.2	19,526,3755	no	coding-synonymous,coding-synonymous,coding-synonymous	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	,,	180,1409,4914	CC,CT,TT		6.5581,27.3491,13.6014	,,	319/1498,313/1452,313/1492	56690848	1769,11237	2203	4300	6503	SO:0001819	synonymous_variant	56155	exon9			TTTCTCTAGGTCC	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.957A>G	17.37:g.56690848T>C		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	149	68	0.456376	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Silent	SNP	ENST00000240361.8	37	CCDS56042.1																																																																																			T|0.835;C|0.165	0.165	strong		0.502	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
ZSCAN18	65982	hgsc.bcm.edu	37	19	58597611	58597611	+	Missense_Mutation	SNP	G	G	C	rs147947490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58597611G>C	ENST00000240727.6	-	6	1167	c.768C>G	c.(766-768)gaC>gaG	p.D256E	ZSCAN18_ENST00000600404.1_Missense_Mutation_p.D312E|ZSCAN18_ENST00000421612.2_Missense_Mutation_p.D121E|ZSCAN18_ENST00000601144.1_Missense_Mutation_p.D256E	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	256					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)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|skin(3)	19		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		TGGAGGCAGCGTCAGGCTGGG	0.542													G|||	25	0.00499201	0.0174	0.0014	5008	,	,		17998	0.0		0.001	False		,,,				2504	0.0				p.D312E		Atlas-SNP	.											.	ZSCAN18	104	.	0			c.C936G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	74,4332	65.3+/-102.7	1,72,2130	74.0	64.0	67.0		936,768,363,768	-1.3	0.0	19	dbSNP_134	67	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,missense	ZSCAN18	NM_001145542.1,NM_001145543.1,NM_001145544.1,NM_023926.4	45,45,45,45	1,74,6428	CC,CG,GG		0.0233,1.6795,0.5843	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	312/567,256/511,121/375,256/511	58597611	76,12930	2203	4300	6503	SO:0001583	missense	65982	exon6			GGCAGCGTCAGGC	AY280799, AY279352	CCDS12971.1, CCDS46214.1, CCDS46215.1	19q13.43	2013-01-09	2007-02-20	2007-02-20		ENSG00000121413		"""-"", ""Zinc fingers, C2H2-type"""	21037	protein-coding gene	gene with protein product			"""zinc finger protein 447"""	ZNF447			Standard	NM_001145542		Approved	FLJ12895	uc010yht.1	Q8TBC5		ENST00000240727.6:c.768C>G	19.37:g.58597611G>C	ENSP00000240727:p.Asp256Glu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_001145542	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	Missense_Mutation	SNP	ENST00000240727.6	37	CCDS12971.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	12.06	1.825940	0.32237	0.016795	2.33E-4	ENSG00000121413	ENST00000433686;ENST00000240727;ENST00000421612	T;T	0.02197	4.64;4.4	3.3	-1.28	0.09318	.	0.195954	0.25233	N	0.032148	T	0.00845	0.0028	N	0.14661	0.345	0.09310	N	1	D;D;D;P	0.56521	0.976;0.976;0.972;0.953	P;P;P;B	0.48270	0.506;0.506;0.572;0.369	T	0.52990	-0.8501	10	0.28530	T	0.3	-5.2194	7.362	0.26752	0.4923:0.0:0.5077:0.0	.	312;121;256;256	B4DG23;E9PBI0;Q8TBC5-2;Q8TBC5	.;.;.;ZSC18_HUMAN	E	312;256;121	ENSP00000240727:D256E;ENSP00000392653:D121E	ENSP00000240727:D256E	D	-	3	2	ZSCAN18	63289423	0.065000	0.20965	0.014000	0.15608	0.577000	0.36160	0.093000	0.15086	-0.370000	0.08016	-0.291000	0.09656	GAC	G|0.993;C|0.007	0.007	strong		0.542	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926	
YARS2	51067	hgsc.bcm.edu	37	12	32908518	32908518	+	Silent	SNP	G	G	A	rs11539444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:32908518G>A	ENST00000324868.8	-	1	318	c.291C>T	c.(289-291)ggC>ggT	p.G97G		NM_001040436.2	NP_001035526.1	Q9Y2Z4	SYYM_HUMAN	tyrosyl-tRNA synthetase 2, mitochondrial	97					gene expression (GO:0010467)|mitochondrial tyrosyl-tRNA aminoacylation (GO:0070184)|translation (GO:0006412)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)|tyrosine binding (GO:0072545)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	16	Lung NSC(5;2.43e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)				L-Tyrosine(DB00135)	AATGAAACAGGCCCAGCAGCG	0.637											OREG0021729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	636	0.126997	0.177	0.0937	5008	,	,		16417	0.0833		0.162	False		,,,				2504	0.092				p.G97G		Atlas-SNP	.											.	YARS2	33	.	0			c.C291T						PASS	.	G		724,3682	295.6+/-283.7	58,608,1537	45.0	49.0	48.0		291	1.9	1.0	12	dbSNP_120	48	1249,7351	248.9+/-276.4	104,1041,3155	no	coding-synonymous	YARS2	NM_001040436.2		162,1649,4692	AA,AG,GG		14.5233,16.4321,15.1699		97/478	32908518	1973,11033	2203	4300	6503	SO:0001819	synonymous_variant	51067	exon1			AAACAGGCCCAGC	AF132939	CCDS31770.1	12p11.21	2014-03-19	2007-02-23		ENSG00000139131	ENSG00000139131	6.1.1.1	"""Aminoacyl tRNA synthetases / Class I"""	24249	protein-coding gene	gene with protein product	"""tyrosine tRNA ligase 2, mitochondrial"""	610957				15779907, 15840810	Standard	NM_001040436		Approved	FLJ13995, CGI-04, mt-TyrRS	uc001rli.3	Q9Y2Z4	OTTHUMG00000169454	ENST00000324868.8:c.291C>T	12.37:g.32908518G>A		Somatic	79	0	0	836	WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_001040436	D3DUW8|Q9H817	Silent	SNP	ENST00000324868.8	37	CCDS31770.1																																																																																			G|0.854;A|0.146	0.146	strong		0.637	YARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404153.1	NM_015936	
CDC5L	988	hgsc.bcm.edu	37	6	44413463	44413463	+	Silent	SNP	T	T	A	rs2273666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	147	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	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		
SP140	11262	hgsc.bcm.edu	37	2	231118041	231118041	+	Missense_Mutation	SNP	A	A	C	rs3820975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231118041A>C	ENST00000392045.3	+	11	1182	c.1068A>C	c.(1066-1068)ttA>ttC	p.L356F	SP140_ENST00000417495.3_Intron|SP140_ENST00000343805.6_Intron|SP140_ENST00000350136.5_Intron|SP140_ENST00000486687.2_Missense_Mutation_p.L280F|SP140_ENST00000420434.3_Missense_Mutation_p.L356F	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	356			L -> F (in dbSNP:rs3820975).	LSA -> FST (in Ref. 1; AAB18617). {ECO:0000305}.	defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|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)		TTTCTTGTTTATCTGCAGAGA	0.473													a|||	617	0.123203	0.1815	0.1081	5008	,	,		19243	0.0952		0.1332	False		,,,				2504	0.0736				p.L356F		Atlas-SNP	.											.	SP140	121	.	0			c.A1068C						PASS	.	C	PHE/LEU	635,3141		55,525,1308	150.0	135.0	140.0		1068	1.7	0.0	2	dbSNP_107	140	1092,7140		84,924,3108	yes	missense	SP140	NM_007237.4	22	139,1449,4416	CC,CA,AA		13.2653,16.8167,14.3821	benign	356/868	231118041	1727,10281	1888	4116	6004	SO:0001583	missense	11262	exon11			TTGTTTATCTGCA	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"""Zinc fingers, PHD-type"""	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.1068A>C	2.37:g.231118041A>C	ENSP00000375899:p.Leu356Phe	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	179	80	0.446927	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	CCDS42831.1	280	0.1282051282051282	96	0.1951219512195122	40	0.11049723756906077	50	0.08741258741258741	94	0.12401055408970976	a	0.090	-1.168032	0.01660	0.168167	0.132653	ENSG00000079263	ENST00000486687;ENST00000392045;ENST00000420434	T;T;T	0.59772	0.24;0.52;0.56	2.55	1.67	0.24075	.	.	.	.	.	T	0.00039	0.0001	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	0.16394	-1.0404	8	0.09338	T	0.73	.	3.289	0.06942	0.2553:0.6001:0.0:0.1446	rs3820975;rs52809113;rs3820975	356;356	E7EUR5;Q13342	.;LY10_HUMAN	F	280;356;356	ENSP00000440107:L280F;ENSP00000375899:L356F;ENSP00000398210:L356F	ENSP00000375899:L356F	L	+	3	2	SP140	230826285	0.001000	0.12720	0.008000	0.14137	0.003000	0.03518	0.332000	0.19751	0.189000	0.20188	-0.290000	0.09829	TTA	A|0.867;C|0.133	0.133	strong		0.473	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237	
GATA2	2624	hgsc.bcm.edu	37	3	128204951	128204951	+	Missense_Mutation	SNP	C	C	T	rs2335052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:128204951C>T	ENST00000341105.2	-	3	821	c.490G>A	c.(490-492)Gcc>Acc	p.A164T	GATA2_ENST00000430265.2_Missense_Mutation_p.A164T|GATA2_ENST00000487848.1_Missense_Mutation_p.A164T	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	164			A -> T (in dbSNP:rs2335052). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		blood coagulation (GO:0007596)|cell differentiation in hindbrain (GO:0021533)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|definitive hemopoiesis (GO:0060216)|embryonic placenta development (GO:0001892)|eosinophil fate commitment (GO:0035854)|GABAergic neuron differentiation (GO:0097154)|homeostasis of number of cells within a tissue (GO:0048873)|inner ear morphogenesis (GO:0042472)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of phagocytosis (GO:0050766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of forebrain neuron differentiation (GO:2000977)|regulation of histone acetylation (GO:0035065)|semicircular canal development (GO:0060872)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|ventral spinal cord interneuron differentiation (GO:0021514)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|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)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(58)|kidney(2)|large_intestine(3)|lung(9)|prostate(3)|skin(1)|urinary_tract(1)	79				GBM - Glioblastoma multiforme(114;0.173)		CCAGAGTGGGCTGCTGTAGGG	0.672			Mis		AML(CML blast transformation)								C|||	1166	0.232827	0.2156	0.2406	5008	,	,		13545	0.378		0.1829	False		,,,				2504	0.1524				p.A164T		Atlas-SNP	.		Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	GATA2,colon,carcinoma,0,2	GATA2	122	2	0			c.G490A	GRCh37	CM066570	GATA2	M	rs2335052	PASS	.	C	THR/ALA,THR/ALA,THR/ALA	736,3670	293.0+/-282.3	66,604,1533	41.0	39.0	40.0		490,490,490	1.8	0.9	3	dbSNP_100	40	1395,7205	258.7+/-282.2	122,1151,3027	yes	missense,missense,missense	GATA2	NM_001145661.1,NM_001145662.1,NM_032638.4	58,58,58	188,1755,4560	TT,TC,CC		16.2209,16.7045,16.3847	benign,benign,benign	164/481,164/467,164/481	128204951	2131,10875	2203	4300	6503	SO:0001583	missense	2624	exon3			AGTGGGCTGCTGT	AF169253	CCDS3049.1, CCDS46903.1	3q21	2014-09-17	2001-11-28		ENSG00000179348	ENSG00000179348		"""GATA zinc finger domain containing"""	4171	protein-coding gene	gene with protein product		137295	"""GATA-binding protein 2"""			1714909	Standard	NM_032638		Approved	NFE1B	uc003eko.2	P23769	OTTHUMG00000159689	ENST00000341105.2:c.490G>A	3.37:g.128204951C>T	ENSP00000345681:p.Ala164Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	152	83	0.546053	NM_001145662	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	529	0.24221611721611722	101	0.20528455284552846	81	0.22375690607734808	212	0.3706293706293706	135	0.17810026385224276	C	11.98	1.801096	0.31869	0.167045	0.162209	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848	D;D;D	0.97303	-4.32;-4.33;-4.32	3.9	1.83	0.25207	.	0.333921	0.33875	N	0.004464	T	0.00012	0.0000	N	0.04724	-0.175	0.34725	P	0.270903	B;B	0.15473	0.013;0.001	B;B	0.19391	0.025;0.002	T	0.10086	-1.0645	9	0.21540	T	0.41	-13.4507	9.5554	0.39334	0.0:0.5805:0.4195:0.0	rs2335052;rs4343643;rs17465403;rs60980469;rs2335052	164;164	P23769-2;P23769	.;GATA2_HUMAN	T	164	ENSP00000345681:A164T;ENSP00000400259:A164T;ENSP00000417074:A164T	ENSP00000345681:A164T	A	-	1	0	GATA2	129687641	0.824000	0.29247	0.899000	0.35326	0.973000	0.67179	0.622000	0.24433	0.911000	0.36747	0.484000	0.47621	GCC	C|0.800;T|0.200	0.200	strong		0.672	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638	
CEP85	64793	hgsc.bcm.edu	37	1	26596080	26596080	+	Missense_Mutation	SNP	G	G	A	rs7550997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26596080G>A	ENST00000252992.4	+	9	1755	c.1624G>A	c.(1624-1626)Gca>Aca	p.A542T	CEP85_ENST00000469609.1_3'UTR|CEP85_ENST00000451429.2_Missense_Mutation_p.A491T	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	542			A -> T (in dbSNP:rs7550997).			centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						GCAGAGAGAAGCAGAATTCTC	0.502													G|||	648	0.129393	0.2027	0.1052	5008	,	,		16924	0.0228		0.1889	False		,,,				2504	0.0961				p.A542T		Atlas-SNP	.											.	CEP85	61	.	0			c.G1624A						PASS	.	G	THR/ALA	701,3705	292.4+/-282.0	60,581,1562	59.0	57.0	58.0		1624	3.1	1.0	1	dbSNP_116	58	1432,7168	273.7+/-290.8	110,1212,2978	yes	missense	CEP85	NM_022778.2	58	170,1793,4540	AA,AG,GG		16.6512,15.9101,16.4001	benign	542/763	26596080	2133,10873	2203	4300	6503	SO:0001583	missense	64793	exon9			AGAGAAGCAGAAT	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"""coiled-coil domain containing 21"""	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.1624G>A	1.37:g.26596080G>A	ENSP00000252992:p.Ala542Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	68	24	0.352941	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Missense_Mutation	SNP	ENST00000252992.4	37	CCDS277.1	287	0.13141025641025642	80	0.16260162601626016	41	0.1132596685082873	12	0.02097902097902098	154	0.20316622691292877	G	8.915	0.959619	0.18507	0.159101	0.166512	ENSG00000130695	ENST00000451429;ENST00000252992	T;T	0.10960	2.82;2.82	5.06	3.11	0.35812	.	0.570233	0.20173	N	0.097692	T	0.00012	0.0000	L	0.36672	1.1	0.44946	P	0.0020320000000000338	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.002	T	0.36261	-0.9755	9	0.27785	T	0.31	-2.0585	5.216	0.15342	0.193:0.2319:0.5751:0.0	rs7550997;rs17257183;rs35972494;rs59910526;rs7550997	491;542;542	F8W7K4;Q6P2H3;Q6P2H3-2	.;CEP85_HUMAN;.	T	491;542	ENSP00000417002:A491T;ENSP00000252992:A542T	ENSP00000252992:A542T	A	+	1	0	CEP85	26468667	0.981000	0.34729	1.000000	0.80357	0.126000	0.20510	0.154000	0.16343	1.365000	0.46057	0.561000	0.74099	GCA	G|0.849;A|0.151	0.151	strong		0.502	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778	
LGALS3	3958	hgsc.bcm.edu	37	14	55611839	55611839	+	Missense_Mutation	SNP	A	A	T	rs11125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55611839A>T	ENST00000254301.9	+	6	864	c.603A>T	c.(601-603)caA>caT	p.Q201H		NM_002306.3	NP_002297.2	P17931	LEG3_HUMAN	lectin, galactoside-binding, soluble, 3	201	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				eosinophil chemotaxis (GO:0048245)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|mononuclear cell migration (GO:0071674)|mRNA processing (GO:0006397)|negative regulation of endocytosis (GO:0045806)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of immunological synapse formation (GO:2000521)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell receptor signaling pathway (GO:0050860)|neutrophil chemotaxis (GO:0030593)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of mononuclear cell migration (GO:0071677)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of T cell apoptotic process (GO:0070232)|regulation of T cell proliferation (GO:0042129)|RNA splicing (GO:0008380)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)	carbohydrate binding (GO:0030246)|chemoattractant activity (GO:0042056)|IgE binding (GO:0019863)|laminin binding (GO:0043236)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|prostate(1)	3						TTCAGATACAAGTACTGGTTG	0.373													A|||	231	0.0461262	0.0008	0.0793	5008	,	,		19985	0.006		0.0785	False		,,,				2504	0.092				p.Q201H		Atlas-SNP	.											.	LGALS3	10	.	0			c.A603T						PASS	.	A	,HIS/GLN	53,3809		0,53,1878	130.0	127.0	128.0		,603	2.4	1.0	14	dbSNP_52	128	636,7638		21,594,3522	yes	intron,missense	LGALS3	NM_001177388.1,NM_002306.3	,24	21,647,5400	TT,TA,AA		7.6867,1.3723,5.6773	,probably-damaging	,201/251	55611839	689,11447	1931	4137	6068	SO:0001583	missense	3958	exon6			GATACAAGTACTG	M64303	CCDS41956.1	14q22.3	2014-03-19	2007-02-01		ENSG00000131981	ENSG00000131981		"""Lectins, galactoside-binding"", ""Endogenous ligands"""	6563	protein-coding gene	gene with protein product	"""galectin 3"""	153619		LGALS2		2009535, 8063692	Standard	NR_003225		Approved	MAC-2, GALIG	uc001xbr.3	P17931	OTTHUMG00000171030	ENST00000254301.9:c.603A>T	14.37:g.55611839A>T	ENSP00000254301:p.Gln201His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	107	59	0.551402	NM_002306	B2RC38|Q16005|Q6IBA7|Q96J47	Missense_Mutation	SNP	ENST00000254301.9	37	CCDS41956.1	94	0.04304029304029304	1	0.0020325203252032522	37	0.10220994475138122	2	0.0034965034965034965	54	0.0712401055408971	A	13.59	2.282691	0.40394	0.013723	0.076867	ENSG00000131981	ENST00000254301	T	0.05786	3.39	6.02	2.37	0.29283	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.217575	0.48767	D	0.000171	T	0.00384	0.0012	L	0.58669	1.825	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.03750	-1.1007	10	0.34782	T	0.22	-8.9608	8.3987	0.32572	0.709:0.0:0.291:0.0	rs11125;rs1126860;rs3182151;rs11538650;rs17295916;rs17354346	201	P17931	LEG3_HUMAN	H	201	ENSP00000254301:Q201H	ENSP00000254301:Q201H	Q	+	3	2	LGALS3	54681592	0.963000	0.33076	0.971000	0.41717	0.019000	0.09904	0.091000	0.15046	0.491000	0.27793	0.533000	0.62120	CAA	A|0.943;T|0.057	0.057	strong		0.373	LGALS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411309.1	NM_002306	
ATRAID	51374	hgsc.bcm.edu	37	2	27439751	27439751	+	Missense_Mutation	SNP	G	G	T	rs7437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27439751G>T	ENST00000606999.1	+	7	683	c.625G>T	c.(625-627)Gcc>Tcc	p.A209S	CAD_ENST00000403525.1_5'Flank|CAD_ENST00000264705.4_5'Flank|ATRAID_ENST00000405489.3_Missense_Mutation_p.A151S|ATRAID_ENST00000380171.3_Missense_Mutation_p.A264S	NM_001170795.1	NP_001164266.1	Q6UW56	ARAID_HUMAN	all-trans retinoic acid-induced differentiation factor	209			A -> S (in dbSNP:rs7437). {ECO:0000269|Ref.1}.		cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)											GATTCTGGGAGCCACCACTCT	0.498													T|||	281	0.0561102	0.1082	0.0389	5008	,	,		17936	0.001		0.0507	False		,,,				2504	0.0603				p.A264S		Atlas-SNP	.											.	.	.	.	0			c.G790T						PASS	.	T	SER/ALA,SER/ALA,SER/ALA	453,3953	784.6+/-414.7	25,403,1775	145.0	123.0	130.0		625,451,790	4.4	1.0	2	dbSNP_52	130	418,8182	800.8+/-407.4	14,390,3896	yes	missense,missense,missense	C2orf28	NM_001170795.1,NM_016085.4,NM_080592.3	99,99,99	39,793,5671	TT,TG,GG		4.8605,10.2814,6.6969	benign,benign,benign	209/230,151/172,264/285	27439751	871,12135	2203	4300	6503	SO:0001583	missense	51374	exon7			CTGGGAGCCACCA	BC021237	CCDS1741.1, CCDS46243.1, CCDS62877.1	2p23.3	2012-08-01	2012-07-30	2012-07-30	ENSG00000138085	ENSG00000138085			24090	protein-coding gene	gene with protein product	"""apoptosis-related protein 3"""		"""chromosome 2 open reading frame 28"""	C2orf28		17524364, 21723284	Standard	NM_016085		Approved	HSPC013, p18, APR3	uc002rjf.3	Q6UW56	OTTHUMG00000128405	ENST00000606999.1:c.625G>T	2.37:g.27439751G>T	ENSP00000476080:p.Ala209Ser	Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	268	127	0.473881	NM_080592	A8C1S2|A8K779|Q96FF6|Q96RT2|Q9Y2R7|Q9Y5L7	Missense_Mutation	SNP	ENST00000606999.1	37		101	0.04624542124542125	48	0.0975609756097561	18	0.049723756906077346	1	0.0017482517482517483	34	0.044854881266490766	T	10.75	1.439545	0.25900	0.102814	0.048605	ENSG00000138085	ENST00000380171;ENST00000405489	T;T	0.47869	0.83;0.92	5.58	4.38	0.52667	.	0.224065	0.46145	N	0.000306	T	0.00328	0.0010	N	0.00621	-1.32	0.19300	N	0.999977	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26950	-1.0088	10	0.02654	T	1	-12.0644	4.9742	0.14133	0.2286:0.0:0.1592:0.6122	rs7437;rs1044272;rs3171996;rs7437	209;264	Q6UW56;Q6UW56-3	APR3_HUMAN;.	S	264;151	ENSP00000369518:A264S;ENSP00000384033:A151S	ENSP00000369518:A264S	A	+	1	0	C2orf28	27293255	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	0.898000	0.28404	0.948000	0.37687	-0.363000	0.07495	GCC	G|0.940;T|0.060	0.060	strong		0.498	ATRAID-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470709.1	NM_016085	
RRS1	23212	hgsc.bcm.edu	37	8	67341378	67341378	+	Silent	SNP	G	G	A	rs3739334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:67341378G>A	ENST00000320270.2	+	1	116	c.12G>A	c.(10-12)caG>caA	p.Q4Q	RP11-346I3.4_ENST00000499642.1_lincRNA	NM_015169.3	NP_055984.1	Q15050	RRS1_HUMAN	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	4					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)			TGGAGGGCCAGAGCGTGGAGG	0.607											OREG0018806	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	614	0.122604	0.1369	0.219	5008	,	,		15531	0.1548		0.0398	False		,,,				2504	0.0869				p.Q4Q		Atlas-SNP	.											.	RRS1	13	.	0			c.G12A						PASS	.	G		577,3829	249.0+/-256.6	35,507,1661	55.0	50.0	52.0		12	-1.1	0.0	8	dbSNP_107	52	277,8323	104.0+/-165.0	5,267,4028	no	coding-synonymous	RRS1	NM_015169.3		40,774,5689	AA,AG,GG		3.2209,13.0958,6.5662		4/366	67341378	854,12152	2203	4300	6503	SO:0001819	synonymous_variant	23212	exon1			GGGCCAGAGCGTG	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.12G>A	8.37:g.67341378G>A		Somatic	142	0	0	1098	WXS	Illumina HiSeq	Phase_I	151	89	0.589404	NM_015169	Q9BUX8	Silent	SNP	ENST00000320270.2	37	CCDS6189.1																																																																																			G|0.919;A|0.081	0.081	strong		0.607	RRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380126.1	NM_015169	
GEN1	348654	hgsc.bcm.edu	37	2	17962117	17962117	+	Silent	SNP	T	T	A	rs61762986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:17962117T>A	ENST00000381254.2	+	14	1852	c.1638T>A	c.(1636-1638)tcT>tcA	p.S546S	GEN1_ENST00000317402.7_Silent_p.S546S|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	546					DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AGTTCATGTCTTCTCTAAGAC	0.363								Homologous recombination					T|||	50	0.00998403	0.0121	0.0216	5008	,	,		18882	0.0		0.0189	False		,,,				2504	0.0				p.S546S		Atlas-SNP	.											.	GEN1	79	.	0			c.T1638A						PASS	.	T	,	64,4342	61.1+/-98.1	1,62,2140	82.0	77.0	79.0		1638,1638	0.0	0.7	2	dbSNP_129	79	126,8474	64.2+/-126.4	4,118,4178	no	coding-synonymous,coding-synonymous	GEN1	NM_001130009.1,NM_182625.3	,	5,180,6318	AA,AT,TT		1.4651,1.4526,1.4609	,	546/909,546/909	17962117	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	348654	exon14			CATGTCTTCTCTA	AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"""Holliday junction resolvase"""	612449	"""Gen endonuclease homolog 1 (Drosophila)"""			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.1638T>A	2.37:g.17962117T>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_182625	Q17RS9|Q6ZN37	Silent	SNP	ENST00000381254.2	37	CCDS1691.1																																																																																			T|0.987;A|0.013	0.013	strong		0.363	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625	
DPY19L2	283417	hgsc.bcm.edu	37	12	64062052	64062052	+	Missense_Mutation	SNP	G	G	A	rs10878074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:64062052G>A	ENST00000324472.4	-	1	305	c.122C>T	c.(121-123)gCc>gTc	p.A41V	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	41			A -> V (in dbSNP:rs10878074). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GCCGCCTAGGGCCGACTTTTC	0.657													G|||	1979	0.395168	0.4425	0.2565	5008	,	,		14964	0.5714		0.1978	False		,,,				2504	0.4509				p.A41V		Atlas-SNP	.											.	DPY19L2	97	.	0			c.C122T						PASS	.	G	VAL/ALA	1679,2717		309,1061,828	32.0	41.0	38.0		122	-0.6	0.0	12	dbSNP_120	38	1704,6888		179,1346,2771	yes	missense	DPY19L2	NM_173812.4	64	488,2407,3599	AA,AG,GG		19.8324,38.1938,26.0471	benign	41/759	64062052	3383,9605	2198	4296	6494	SO:0001583	missense	283417	exon1			CCTAGGGCCGACT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.122C>T	12.37:g.64062052G>A	ENSP00000315988:p.Ala41Val	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	166	68	0.409639	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	766	0.3507326007326007	189	0.38414634146341464	99	0.27348066298342544	330	0.5769230769230769	148	0.19525065963060687	G	4.869	0.161472	0.09287	0.381938	0.198324	ENSG00000177990	ENST00000324472;ENST00000542209	T;T	0.39787	1.06;1.82	1.61	-0.623	0.11556	.	0.555051	0.14868	N	0.293715	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	1.0000000000287557E-6	B	0.10296	0.003	B	0.04013	0.001	T	0.44937	-0.9295	8	.	.	.	.	2.4499	0.04516	0.2454:0.3274:0.4272:0.0	rs10878074	41	Q6NUT2	D19L2_HUMAN	V	41	ENSP00000315988:A41V;ENSP00000444932:A41V	.	A	-	2	0	DPY19L2	62348319	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.946000	0.29069	-0.190000	0.10465	0.195000	0.17529	GCC	G|0.718;A|0.282	0.282	strong		0.657	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
PKDREJ	10343	hgsc.bcm.edu	37	22	46654323	46654323	+	Silent	SNP	G	G	A	rs6007740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	93	0	0		WXS	Illumina HiSeq	Phase_I	118	49	0.415254	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	
SCG3	29106	hgsc.bcm.edu	37	15	51984362	51984362	+	Missense_Mutation	SNP	A	A	G	rs35664837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51984362A>G	ENST00000220478.3	+	7	1100	c.697A>G	c.(697-699)Atg>Gtg	p.M233V	SCG3_ENST00000542355.2_Start_Codon_SNP_p.M1V|RP11-313P18.2_ENST00000559918.1_lincRNA	NM_013243.3	NP_037375.2	Q8WXD2	SCG3_HUMAN	secretogranin III	233			M -> V (in dbSNP:rs35664837).		blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				all cancers(107;0.00488)		GGAGACTCCAATGGCAGCAAT	0.378													A|||	335	0.066893	0.2421	0.0202	5008	,	,		20943	0.0		0.001	False		,,,				2504	0.0				p.M233V		Atlas-SNP	.											.	SCG3	50	.	0			c.A697G						PASS	.	A	VAL/MET,VAL/MET	858,3532	331.5+/-302.0	92,674,1429	82.0	84.0	83.0		1,697	-0.2	0.9	15	dbSNP_126	83	16,8570	10.5+/-38.8	0,16,4277	yes	missense,missense	SCG3	NM_001165257.1,NM_013243.3	21,21	92,690,5706	GG,GA,AA		0.1863,19.5444,6.7355	benign,benign	1/237,233/469	51984362	874,12102	2195	4293	6488	SO:0001583	missense	29106	exon7			ACTCCAATGGCAG	AF078851	CCDS10142.1, CCDS53947.1	15q21.2	2013-09-23			ENSG00000104112	ENSG00000104112			13707	protein-coding gene	gene with protein product		611796				2053134, 8825061	Standard	NM_013243		Approved	SGIII, FLJ90833	uc002abh.3	Q8WXD2	OTTHUMG00000131748	ENST00000220478.3:c.697A>G	15.37:g.51984362A>G	ENSP00000220478:p.Met233Val	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	56	16	0.285714	NM_013243	A8K2B0|B3KQP6|B4DK99|F5H3R8|Q96C83|Q96GE8|Q9Y6G7	Missense_Mutation	SNP	ENST00000220478.3	37	CCDS10142.1	101	0.04624542124542125	95	0.19308943089430894	6	0.016574585635359115	0	0.0	0	0.0	A	5.337	0.247417	0.10130	0.195444	0.001863	ENSG00000104112	ENST00000220478;ENST00000542355	T;T	0.41065	2.01;1.01	5.85	-0.205	0.13196	.	0.938701	0.09229	N	0.830880	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	0.25813	-1.0121	9	0.37606	T	0.19	-10.026	5.4541	0.16580	0.5035:0.1668:0.3297:0.0	rs35664837	233	Q8WXD2	SCG3_HUMAN	V	233;1	ENSP00000220478:M233V;ENSP00000445205:M1V	ENSP00000220478:M233V	M	+	1	0	SCG3	49771654	0.017000	0.18338	0.902000	0.35471	0.919000	0.55068	1.154000	0.31688	-0.055000	0.13244	-0.441000	0.05720	ATG	A|0.935;G|0.065	0.065	strong		0.378	SCG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254670.2	NM_013243	
MCTP2	55784	hgsc.bcm.edu	37	15	94945719	94945719	+	Intron	SNP	G	G	T	rs7178698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:94945719G>T	ENST00000357742.4	+	16	2085				MCTP2_ENST00000331706.4_Missense_Mutation_p.R285L|MCTP2_ENST00000557742.1_Missense_Mutation_p.R285L|MCTP2_ENST00000451018.3_Intron	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2						calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			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)			ATTCAGCACCGCAAAGAGGAA	0.378													T|||	3107	0.620407	0.5499	0.6484	5008	,	,		19751	0.5089		0.8131	False		,,,				2504	0.6125				p.R285L		Atlas-SNP	.											.	MCTP2	122	.	0			c.G854T						PASS	.	T	,LEU/ARG,	761,611		210,341,135	147.0	116.0	126.0		,854,	-2.4	0.0	15	dbSNP_116	126	2566,612		1037,492,60	yes	intron,missense,intron	MCTP2	NM_001159643.1,NM_001159644.1,NM_018349.3	,102,	1247,833,195	TT,TG,GG		19.2574,44.5335,26.8791	,,	,285/307,	94945719	3327,1223	686	1589	2275	SO:0001627	intron_variant	55784	exon10			AGCACCGCAAAGA	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.2085+471G>T	15.37:g.94945719G>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	155	68	0.43871	NM_001159644	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	37	CCDS32338.1	1421	0.6506410256410257	256	0.5203252032520326	250	0.6906077348066298	291	0.5087412587412588	624	0.8232189973614775	T	5.565	0.289024	0.10513	0.554665	0.807426	ENSG00000140563	ENST00000331706	T	0.64260	-0.09	4.39	-2.44	0.06502	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35375	-0.9791	7	0.11485	T	0.65	.	3.8968	0.09143	0.3508:0.0:0.3439:0.3053	rs7178698;rs57280670;rs7178698	285	Q6DN12-4	.	L	285	ENSP00000329646:R285L	ENSP00000329646:R285L	R	+	2	0	MCTP2	92746723	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.547000	0.06055	-0.821000	0.04312	-1.962000	0.00476	CGC	G|0.358;T|0.642	0.642	strong		0.378	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	
SYCE3	644186	hgsc.bcm.edu	37	22	50989678	50989678	+	Missense_Mutation	SNP	A	A	G	rs6009989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50989678A>G	ENST00000406915.3	-	3	310	c.263T>C	c.(262-264)cTg>cCg	p.L88P	SYCE3_ENST00000402753.1_Missense_Mutation_p.L88P	NM_001123225.1	NP_001116697.1	A1L190	SYCE3_HUMAN	synaptonemal complex central element protein 3	88			L -> P (in dbSNP:rs6009989).		positive regulation of apoptotic process (GO:0043065)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|chromosome (GO:0005694)|nucleus (GO:0005634)				endometrium(1)|kidney(1)	2						TGGGGCCTACAGCCTTTGCTT	0.592													G|||	475	0.0948482	0.2496	0.0461	5008	,	,		18860	0.0109		0.0249	False		,,,				2504	0.0787				p.L88P		Atlas-SNP	.											.	SYCE3	10	.	0			c.T263C						PASS	.	G	PRO/LEU	304,1080		32,240,420	53.0	57.0	56.0		263	1.7	0.0	22	dbSNP_114	56	81,3101		2,77,1512	yes	missense	C22orf41	NM_001123225.1	98	34,317,1932	GG,GA,AA		2.5456,21.9653,8.4319	benign	88/89	50989678	385,4181	692	1591	2283	SO:0001583	missense	644186	exon3			GCCTACAGCCTTT		CCDS46733.1	22q13.33	2011-10-05	2011-10-05	2011-10-05	ENSG00000217442	ENSG00000217442			35245	protein-coding gene	gene with protein product	"""testis highly expressed protein 2"""	615775	"""chromosome 22 open reading frame 41"""	C22orf41		21637789	Standard	NM_001123225		Approved		uc010hbe.3	A1L190	OTTHUMG00000150273	ENST00000406915.3:c.263T>C	22.37:g.50989678A>G	ENSP00000385480:p.Leu88Pro	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	148	76	0.513514	NM_001123225		Missense_Mutation	SNP	ENST00000406915.3	37	CCDS46733.1	139	0.06364468864468864	103	0.20934959349593496	14	0.03867403314917127	3	0.005244755244755245	19	0.025065963060686015	G	6.598	0.478680	0.12521	0.219653	0.025456	ENSG00000217442	ENST00000406915;ENST00000402753	T;T	0.51817	0.69;0.69	5.34	1.72	0.24424	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07083	-1.0791	7	0.87932	D	0	.	7.998	0.30280	0.1286:0.0:0.5095:0.3618	rs6009989;rs7290339;rs52822093;rs6009989	88	A1L190	SYCE3_HUMAN	P	88	ENSP00000385480:L88P;ENSP00000385122:L88P	ENSP00000385122:L88P	L	-	2	0	C22orf41	49336544	0.185000	0.23213	0.003000	0.11579	0.002000	0.02628	0.248000	0.18198	0.116000	0.18110	-1.464000	0.01018	CTG	A|0.933;G|0.067	0.067	strong		0.592	SYCE3-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317660.1	NM_001123225	
MUC4	4585	hgsc.bcm.edu	37	3	195506462	195506462	+	Missense_Mutation	SNP	G	G	C	rs547195540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195506462G>C	ENST00000463781.3	-	2	12448	c.11989C>G	c.(11989-11991)Cac>Gac	p.H3997D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3997D	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)		GGGGTGGCGTGACCTGTGGAT	0.602													.|||	35	0.00698882	0.0227	0.0	5008	,	,		9048	0.003		0.002	False		,,,				2504	0.0				p.H3997D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+2,2	MUC4	1505	2	0			c.C11989G						PASS	.						12.0	9.0	10.0					3																	195506462		664	1461	2125	SO:0001583	missense	4585	exon2			TGGCGTGACCTGT	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.11989C>G	3.37:g.195506462G>C	ENSP00000417498:p.His3997Asp	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	2.909	-0.225781	0.06022	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.41;1.5	0.764	-0.498	0.12019	.	0.000000	0.25267	N	0.031920	T	0.15003	0.0362	N	0.19112	0.55	0.09310	N	1	B	0.14805	0.011	B	0.21546	0.035	T	0.21827	-1.0234	9	.	.	.	.	5.621	0.17457	0.0:0.0:0.6825:0.3174	.	3869	E7ESK3	.	D	3997	ENSP00000417498:H3997D;ENSP00000420243:H3997D	.	H	-	1	0	MUC4	196991241	0.000000	0.05858	0.001000	0.08648	0.189000	0.23516	-0.901000	0.04093	-0.142000	0.11354	0.064000	0.15345	CAC	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SDK1	221935	hgsc.bcm.edu	37	7	4116697	4116697	+	Silent	SNP	G	G	A	rs61735695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:4116697G>A	ENST00000404826.2	+	21	3217	c.3078G>A	c.(3076-3078)acG>acA	p.T1026T	SDK1_ENST00000389531.3_Silent_p.T1026T	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1026	Fibronectin type-III 4. {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)		TGAACAGCACGACGCACGAGT	0.567													G|||	56	0.0111821	0.0408	0.0029	5008	,	,		21381	0.0		0.0	False		,,,				2504	0.0				p.T1026T		Atlas-SNP	.											SDK1,NS,carcinoma,+1,2	SDK1	361	2	0			c.G3078A						PASS	.	G		134,4272	96.7+/-135.4	2,130,2071	171.0	132.0	145.0		3078	-6.5	0.0	7	dbSNP_129	145	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SDK1	NM_152744.3		2,131,6370	AA,AG,GG		0.0116,3.0413,1.038		1026/2214	4116697	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon21			CAGCACGACGCAC	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.3078G>A	7.37:g.4116697G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			G|0.990;A|0.010	0.010	strong		0.567	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
DAAM1	23002	hgsc.bcm.edu	37	14	59821936	59821936	+	Silent	SNP	C	C	T	rs61755340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:59821936C>T	ENST00000395125.1	+	20	2463	c.2440C>T	c.(2440-2442)Ctg>Ttg	p.L814L	DAAM1_ENST00000351081.1_Silent_p.L814L|DAAM1_ENST00000360909.3_Silent_p.L804L|DAAM1_ENST00000553966.1_Intron	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	814	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				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)		CAAGCAGTTGCTGGAGGTGGT	0.383													C|||	61	0.0121805	0.0446	0.0029	5008	,	,		23182	0.0		0.0	False		,,,				2504	0.0				p.L814L		Atlas-SNP	.											.	DAAM1	95	.	0			c.C2440T						PASS	.	C		90,4316	73.6+/-111.7	1,88,2114	188.0	176.0	180.0		2440	0.6	0.8	14	dbSNP_129	180	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	DAAM1	NM_014992.1		1,92,6410	TT,TC,CC		0.0465,2.0427,0.7227		814/1079	59821936	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon20			CAGTTGCTGGAGG	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.2440C>T	14.37:g.59821936C>T		Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	280	126	0.45	NM_014992	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			C|0.993;T|0.007	0.007	strong		0.383	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
PPAT	5471	hgsc.bcm.edu	37	4	57268328	57268328	+	Silent	SNP	T	T	C	rs2271924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57268328T>C	ENST00000264220.2	-	6	818	c.681A>G	c.(679-681)acA>acG	p.T227T	PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	227	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)			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)	CCCATCCTTCTGTTTCTGATG	0.318													T|||	629	0.125599	0.1067	0.0634	5008	,	,		15735	0.2381		0.0974	False		,,,				2504	0.1084				p.T227T		Atlas-SNP	.											.	PPAT	41	.	0			c.A681G						PASS	.	T		406,4000	201.1+/-224.2	21,364,1818	101.0	103.0	102.0		681	-10.7	0.4	4	dbSNP_100	102	633,7961	163.0+/-215.7	28,577,3692	no	coding-synonymous	PPAT	NM_002703.4		49,941,5510	CC,CT,TT		7.3656,9.2147,7.9923		227/518	57268328	1039,11961	2203	4297	6500	SO:0001819	synonymous_variant	5471	exon6			TCCTTCTGTTTCT		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.681A>G	4.37:g.57268328T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	88	51	0.579545	NM_002703		Silent	SNP	ENST00000264220.2	37	CCDS3505.1																																																																																			T|0.907;C|0.093	0.093	strong		0.318	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703	
RPRD1B	58490	hgsc.bcm.edu	37	20	36668874	36668874	+	Silent	SNP	G	G	A	rs2273353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36668874G>A	ENST00000373433.4	+	2	591	c.189G>A	c.(187-189)gcG>gcA	p.A63A		NM_021215.3	NP_067038.1	Q9NQG5	RPR1B_HUMAN	regulation of nuclear pre-mRNA domain containing 1B	63	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.				dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle process (GO:0010564)|transcription, DNA-templated (GO:0006351)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)	12						TGTATTTAGCGAATGATGTCA	0.323													G|||	1456	0.290735	0.4962	0.134	5008	,	,		18769	0.2163		0.164	False		,,,				2504	0.3313				p.A63A		Atlas-SNP	.											RPRD1B,NS,carcinoma,+1,2	RPRD1B	25	2	0			c.G189A						scavenged	.	G		1909,2495	546.1+/-377.0	425,1059,718	153.0	149.0	150.0		189	-10.3	0.4	20	dbSNP_100	150	1413,7187	269.8+/-288.6	113,1187,3000	no	coding-synonymous	RPRD1B	NM_021215.3		538,2246,3718	AA,AG,GG		16.4302,43.347,25.546		63/327	36668874	3322,9682	2202	4300	6502	SO:0001819	synonymous_variant	58490	exon2			TTTAGCGAATGAT	AL109823	CCDS13301.1	20q11.21-q12	2012-02-09	2008-08-15	2008-07-28	ENSG00000101413	ENSG00000101413			16209	protein-coding gene	gene with protein product		614694	"""chromosome 20 open reading frame 77"""	C20orf77		22231121	Standard	NM_021215		Approved	dJ1057B20.2, DKFZp434P0735, CREPT, FLJ44520, NET60	uc002xho.4	Q9NQG5	OTTHUMG00000032434	ENST00000373433.4:c.189G>A	20.37:g.36668874G>A		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	NM_021215	Q1WDE7|Q6PKF4	Silent	SNP	ENST00000373433.4	37	CCDS13301.1																																																																																			G|0.747;A|0.253	0.253	strong		0.323	RPRD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079142.2	NM_021215	
EBF1	1879	hgsc.bcm.edu	37	5	158204425	158204425	+	Silent	SNP	A	A	G	rs1368298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:158204425A>G	ENST00000313708.6	-	10	1314	c.1032T>C	c.(1030-1032)taT>taC	p.Y344Y	EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000517373.1_Silent_p.Y336Y|EBF1_ENST00000380654.4_Silent_p.Y313Y	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	344	IPT/TIG.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y344Y(1)	HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCTTACCTGTATAAATGAATC	0.458			T	HMGA2	lipoma								G|||	2972	0.59345	0.854	0.6138	5008	,	,		19972	0.6151		0.4513	False		,,,				2504	0.3507				p.Y344Y		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	EBF1,NS,carcinoma,0,1	EBF1	110	1	1	Substitution - coding silent(1)	prostate(1)	c.T1032C						PASS	.	G		3494,912	350.3+/-310.7	1407,680,116	157.0	143.0	148.0		1032	1.9	1.0	5	dbSNP_88	148	3828,4772	610.7+/-395.7	870,2088,1342	no	coding-synonymous	EBF1	NM_024007.3		2277,2768,1458	GG,GA,AA		44.5116,20.699,43.7029		344/592	158204425	7322,5684	2203	4300	6503	SO:0001819	synonymous_variant	1879	exon10			ACCTGTATAAATG	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"""early B-cell factor"""	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1032T>C	5.37:g.158204425A>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	204	203	0.995098	NM_024007	Q8IW11	Silent	SNP	ENST00000313708.6	37	CCDS4343.1																																																																																			A|0.408;G|0.592	0.592	strong		0.458	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007	
FAM47C	442444	hgsc.bcm.edu	37	X	37028127	37028127	+	Silent	SNP	A	A	G	rs73631164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37028127A>G	ENST00000358047.3	+	1	1696	c.1644A>G	c.(1642-1644)ccA>ccG	p.P548P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	548										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						ATCTCCGCCCAGAGCCTCCTG	0.612													-|||	1420	0.376159	0.6589	0.245	3775	,	,		12948	0.0982		0.0785	False		,,,				2504	0.2055				p.P548P		Atlas-SNP	.											.	FAM47C	267	.	0			c.A1644G						PASS	.	A		2974,859		997,539,441,95,130	61.0	67.0	65.0		1644	-3.3	0.0	X	dbSNP_130	65	782,5946		26,498,232,1904,1640	no	coding-synonymous	FAM47C	NM_001013736.2		1023,1037,673,1999,1770	GG,GA,G,AA,A		11.6231,22.4106,35.5648		548/1036	37028127	3756,6805	2202	4300	6502	SO:0001819	synonymous_variant	442444	exon1			CCGCCCAGAGCCT	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.1644A>G	X.37:g.37028127A>G		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	207	199	0.961353	NM_001013736	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																			A|0.644;G|0.356	0.356	strong		0.612	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
FLT4	2324	hgsc.bcm.edu	37	5	180043439	180043439	+	Silent	SNP	G	G	A	rs56127961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180043439G>A	ENST00000261937.6	-	23	3225	c.3147C>T	c.(3145-3147)gaC>gaT	p.D1049D	FLT4_ENST00000393347.3_Silent_p.D1049D|FLT4_ENST00000502649.1_Silent_p.D1049D	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1049	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> N (in dbSNP:rs56310180). {ECO:0000269|PubMed:17344846}.		blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCTTCACCACGTCGCTTTCCG	0.622													G|||	72	0.014377	0.053	0.0014	5008	,	,		19924	0.001		0.0	False		,,,				2504	0.0				p.D1049D	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C3147T						PASS	.	G	,	183,4223	116.7+/-154.6	5,173,2025	126.0	115.0	118.0		3147,3147	-5.8	0.4	5	dbSNP_129	118	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FLT4	NM_002020.4,NM_182925.4	,	5,173,6325	AA,AG,GG		0.0,4.1534,1.407	,	1049/1299,1049/1364	180043439	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	2324	exon23			CACCACGTCGCTT	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.3147C>T	5.37:g.180043439G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	193	94	0.487047	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																			G|0.982;A|0.018	0.018	strong		0.622	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
GOLGA7	51125	hgsc.bcm.edu	37	8	41355096	41355096	+	Silent	SNP	C	C	T	rs17656952	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:41355096C>T	ENST00000357743.4	+	2	381	c.180C>T	c.(178-180)ctC>ctT	p.L60L	GOLGA7_ENST00000405786.2_Silent_p.L60L|GOLGA7_ENST00000518270.1_Silent_p.L60L|GOLGA7_ENST00000520817.1_Silent_p.L60L	NM_001002296.1	NP_001002296.1	Q7Z5G4	GOGA7_HUMAN	golgin A7	60					Golgi to plasma membrane protein transport (GO:0043001)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)				breast(1)|large_intestine(1)	2	Ovarian(28;0.014)|Colorectal(14;0.0234)|Lung SC(25;0.211)	all_lung(54;0.000771)|Lung NSC(58;0.0031)|Hepatocellular(245;0.014)|Esophageal squamous(32;0.0559)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00596)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)			CAGAGAAGCTCGGCGGCCAGT	0.368													C|||	465	0.0928514	0.1165	0.1297	5008	,	,		19845	0.0		0.1471	False		,,,				2504	0.0746				p.L60L		Atlas-SNP	.											.	GOLGA7	10	.	0			c.C180T						PASS	.	C	,,	628,3778	272.5+/-270.8	46,536,1621	152.0	160.0	157.0		180,180,180	-2.6	1.0	8	dbSNP_123	157	1260,7340	253.0+/-278.9	81,1098,3121	no	coding-synonymous,coding-synonymous,coding-synonymous	GOLGA7	NM_001002296.1,NM_001174124.1,NM_016099.2	,,	127,1634,4742	TT,TC,CC		14.6512,14.2533,14.5164	,,	60/138,60/135,60/138	41355096	1888,11118	2203	4300	6503	SO:0001819	synonymous_variant	51125	exon2			GAAGCTCGGCGGC	AF125102	CCDS34887.1, CCDS55226.1	8p11.21	2011-10-25	2010-02-12		ENSG00000147533	ENSG00000147533			24876	protein-coding gene	gene with protein product		609453	"""golgi autoantigen, golgin subfamily a, 7"""			11042152	Standard	NM_001174124		Approved	GCP16, HSPC041, GOLGA3AP1, GOLGA7A	uc003xnu.3	Q7Z5G4	OTTHUMG00000164077	ENST00000357743.4:c.180C>T	8.37:g.41355096C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	64	22	0.34375	NM_001002296	D3DSX9|J3KQ24|Q96EQ4|Q9P1S0|Q9Y5U7	Silent	SNP	ENST00000357743.4	37	CCDS34887.1																																																																																			C|0.876;T|0.124	0.124	strong		0.368	GOLGA7-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377142.1	NM_016099	
TEKT4	150483	hgsc.bcm.edu	37	2	95537572	95537572	+	Missense_Mutation	SNP	C	C	T	rs4854235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	12	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	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	
ADAM12	8038	hgsc.bcm.edu	37	10	127824167	127824167	+	Silent	SNP	C	C	T	rs12098586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:127824167C>T	ENST00000368679.4	-	5	720	c.411G>A	c.(409-411)acG>acA	p.T137T	ADAM12_ENST00000368676.4_Silent_p.T137T	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	137					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)		GACCAGAACACGTGCTGAGAC	0.498													c|||	207	0.0413339	0.1415	0.0259	5008	,	,		19767	0.0		0.002	False		,,,				2504	0.0				p.T137T		Atlas-SNP	.											.	ADAM12	388	.	0			c.G411A						PASS	.	C	,	514,3892	237.4+/-249.2	33,448,1722	161.0	120.0	134.0		411,411	-6.5	0.9	10	dbSNP_120	134	24,8576	17.9+/-57.8	0,24,4276	no	coding-synonymous,coding-synonymous	ADAM12	NM_003474.4,NM_021641.3	,	33,472,5998	TT,TC,CC		0.2791,11.6659,4.1366	,	137/910,137/739	127824167	538,12468	2203	4300	6503	SO:0001819	synonymous_variant	8038	exon5			AGAACACGTGCTG	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.411G>A	10.37:g.127824167C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Silent	SNP	ENST00000368679.4	37	CCDS7653.1																																																																																			C|0.960;T|0.040	0.040	strong		0.498	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		
ZNF366	167465	hgsc.bcm.edu	37	5	71739602	71739602	+	Missense_Mutation	SNP	G	G	C	rs13188519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71739602G>C	ENST00000318442.5	-	5	2706	c.2216C>G	c.(2215-2217)gCa>gGa	p.A739G	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	739	Interaction with CTBP1.|Interaction with NRIP1.		A -> G (in dbSNP:rs13188519).		negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TAAAAGCACTGCTTGTTTTTC	0.388													G|||	363	0.072484	0.0605	0.0389	5008	,	,		18997	0.0714		0.0964	False		,,,				2504	0.089				p.A739G		Atlas-SNP	.											.	ZNF366	108	.	0			c.C2216G						PASS	.	G	GLY/ALA	259,4117		4,251,1933	46.0	52.0	50.0		2216	5.9	1.0	5	dbSNP_121	50	927,7669		45,837,3416	yes	missense	ZNF366	NM_152625.1	60	49,1088,5349	CC,CG,GG		10.7841,5.9186,9.1428	benign	739/745	71739602	1186,11786	2188	4298	6486	SO:0001583	missense	167465	exon5			AGCACTGCTTGTT	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.2216C>G	5.37:g.71739602G>C	ENSP00000313158:p.Ala739Gly	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	35	0.364583	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	37	CCDS4015.1	140	0.0641025641025641	30	0.06097560975609756	13	0.03591160220994475	20	0.03496503496503497	77	0.10158311345646438	G	16.77	3.215688	0.58452	0.059186	0.107841	ENSG00000178175	ENST00000318442	T	0.10288	2.89	5.87	5.87	0.94306	.	0.171581	0.41605	D	0.000860	T	0.00210	0.0006	L	0.29908	0.895	0.33098	D	0.538779	P	0.36282	0.546	B	0.32149	0.141	T	0.05386	-1.0888	10	0.59425	D	0.04	-6.1181	16.1124	0.81273	0.0:0.0:0.8657:0.1343	rs13188519;rs52832178;rs13188519	739	Q8N895	ZN366_HUMAN	G	739	ENSP00000313158:A739G	ENSP00000313158:A739G	A	-	2	0	ZNF366	71775358	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.660000	0.61511	2.941000	0.99782	0.655000	0.94253	GCA	G|0.916;C|0.084	0.084	strong		0.388	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
SIK2	23235	hgsc.bcm.edu	37	11	111594520	111594520	+	Silent	SNP	G	G	A	rs75997369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:111594520G>A	ENST00000304987.3	+	15	2621	c.2448G>A	c.(2446-2448)acG>acA	p.T816T		NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	816					insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						CTCTGCCCACGCAGCTACAGC	0.637													G|||	9	0.00179712	0.0068	0.0	5008	,	,		10597	0.0		0.0	False		,,,				2504	0.0				p.T816T		Atlas-SNP	.											.	SIK2	89	.	0			c.G2448A						PASS	.	G		48,4354	49.6+/-84.7	0,48,2153	64.0	72.0	69.0		2448	-8.7	0.0	11	dbSNP_131	69	0,8594		0,0,4297	no	coding-synonymous	SIK2	NM_015191.1		0,48,6450	AA,AG,GG		0.0,1.0904,0.3693		816/927	111594520	48,12948	2201	4297	6498	SO:0001819	synonymous_variant	23235	exon15			GCCCACGCAGCTA	AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"""SNF1-like kinase 2"""	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.2448G>A	11.37:g.111594520G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	57	36	0.631579	NM_015191	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Silent	SNP	ENST00000304987.3	37	CCDS8347.1																																																																																			G|0.997;A|0.003	0.003	strong		0.637	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191	
PPM1H	57460	hgsc.bcm.edu	37	12	63083521	63083521	+	Silent	SNP	G	G	A	rs11174604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:63083521G>A	ENST00000228705.6	-	8	1503	c.1203C>T	c.(1201-1203)gaC>gaT	p.D401D	PPM1H_ENST00000551214.1_5'UTR	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	401	PP2C-like.						phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		AGATGTTGGAGTCATGCACCT	0.463													G|||	848	0.169329	0.3185	0.062	5008	,	,		20407	0.1101		0.0924	False		,,,				2504	0.184				p.D401D		Atlas-SNP	.											PPM1H,NS,carcinoma,-2,1	PPM1H	42	1	0			c.C1203T						PASS	.	G		1073,2747		158,757,995	97.0	97.0	97.0		1203	3.9	1.0	12	dbSNP_120	97	688,7612		28,632,3490	no	coding-synonymous	PPM1H	NM_020700.1		186,1389,4485	AA,AG,GG		8.2892,28.089,14.5297		401/515	63083521	1761,10359	1910	4150	6060	SO:0001819	synonymous_variant	57460	exon8			GTTGGAGTCATGC	AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	18583	protein-coding gene	gene with protein product	"""neurite extension-related protein phosphatase related to PP2C"""		"""ras homolog gene family, member C like 1"", ""protein phosphatase 1H (PP2C domain containing)"""	ARHCL1			Standard	NM_020700		Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.1203C>T	12.37:g.63083521G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	143	84	0.587413	NM_020700	B1Q2A9|B2RXG4|Q6PI86	Silent	SNP	ENST00000228705.6	37	CCDS44934.1																																																																																			G|0.858;A|0.141	0.141	strong		0.463	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700	
DYSF	8291	hgsc.bcm.edu	37	2	71838661	71838661	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71838661G>A	ENST00000258104.3	+	38	4349	c.4072G>A	c.(4072-4074)Gtg>Atg	p.V1358M	DYSF_ENST00000429174.2_Missense_Mutation_p.V1358M|DYSF_ENST00000410041.1_Missense_Mutation_p.V1376M|DYSF_ENST00000394120.2_Missense_Mutation_p.V1359M|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409651.1_Missense_Mutation_p.V1390M|DYSF_ENST00000409744.1_Missense_Mutation_p.V1345M|DYSF_ENST00000409762.1_Missense_Mutation_p.V1375M|DYSF_ENST00000409582.3_Missense_Mutation_p.V1375M|DYSF_ENST00000413539.2_Missense_Mutation_p.V1389M|DYSF_ENST00000410020.3_Missense_Mutation_p.V1376M|DYSF_ENST00000409366.1_Missense_Mutation_p.V1359M	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1358	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CCCCAGCCTCGTGGTAGAGTG	0.567																																					p.V1390M		Atlas-SNP	.											DYSF_ENST00000410020,NS,carcinoma,0,2	DYSF	536	2	0			c.G4168A						PASS	.						58.0	57.0	57.0					2																	71838661		2203	4300	6503	SO:0001583	missense	8291	exon39			AGCCTCGTGGTAG	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.4072G>A	2.37:g.71838661G>A	ENSP00000258104:p.Val1358Met	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.054472	0.55218	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64	5.54	4.65	0.58169	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.213647	0.42548	D	0.000687	D	0.86053	0.5841	L	0.54323	1.7	0.32057	N	0.596244	D;D;D;D;D;D;P;P;B;P;B;P;P;D;P	0.71674	0.984;0.998;0.998;0.995;0.995;0.995;0.851;0.773;0.415;0.769;0.077;0.46;0.769;0.995;0.807	P;P;P;P;P;D;P;P;B;B;B;B;B;P;P	0.66497	0.843;0.855;0.9;0.9;0.9;0.944;0.554;0.684;0.433;0.433;0.087;0.238;0.433;0.855;0.569	D	0.85452	0.1161	10	0.40728	T	0.16	-21.6668	8.921	0.35612	0.1689:0.0:0.8311:0.0	.	101;1390;1376;1359;1345;1376;1345;1375;1344;1389;1375;1358;1344;1359;1358	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	M	1389;1375;1375;1358;1358;1390;1359;1345;1359;1376;1376	ENSP00000407046:V1389M;ENSP00000387137:V1375M;ENSP00000386547:V1375M;ENSP00000398305:V1358M;ENSP00000258104:V1358M;ENSP00000386683:V1390M;ENSP00000377678:V1359M;ENSP00000386285:V1345M;ENSP00000386512:V1359M;ENSP00000386881:V1376M;ENSP00000386617:V1376M	ENSP00000258104:V1358M	V	+	1	0	DYSF	71692169	0.054000	0.20591	0.944000	0.38274	0.395000	0.30598	0.451000	0.21779	2.623000	0.88846	0.561000	0.74099	GTG	.	.	none		0.567	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
KSR1	8844	hgsc.bcm.edu	37	17	25932816	25932816	+	Silent	SNP	G	G	A	rs55938675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:25932816G>A	ENST00000319524.6	+	15	2037	c.2037G>A	c.(2035-2037)ccG>ccA	p.P679P	KSR1_ENST00000268763.6_Silent_p.P542P|KSR1_ENST00000509603.2_Silent_p.P657P|KSR1_ENST00000398988.3_Silent_p.P542P			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	679	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		GCATGAACCCGCCCCACCTGG	0.587													G|||	247	0.0493211	0.1641	0.0259	5008	,	,		14332	0.0		0.0109	False		,,,				2504	0.001				p.P542P	Esophageal Squamous(88;1120 1336 6324 10502 16832)	Atlas-SNP	.											.	KSR1	151	.	0			c.G1626A						PASS	.	G		433,3459		23,387,1536	17.0	17.0	17.0		1626	-10.9	0.1	17	dbSNP_129	17	40,8172		0,40,4066	no	coding-synonymous	KSR1	NM_014238.1		23,427,5602	AA,AG,GG		0.4871,11.1254,3.9078		542/763	25932816	473,11631	1946	4106	6052	SO:0001819	synonymous_variant	8844	exon15			GAACCCGCCCCAC	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.2037G>A	17.37:g.25932816G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	148	81	0.547297	NM_014238	F8WEA9|H7BYU0|Q13476	Silent	SNP	ENST00000319524.6	37		95	0.043498168498168496	79	0.16056910569105692	9	0.024861878453038673	0	0.0	7	0.009234828496042216	G	7.486	0.649577	0.14516	0.111254	0.004871	ENSG00000141068	ENST00000398988	.	.	.	5.46	-10.9	0.00192	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.99999999999997	.	.	.	.	.	.	T	0.02553	-1.1142	3	.	.	.	.	3.8317	0.08877	0.1879:0.2877:0.0681:0.4563	rs55938675	.	.	.	T	393	.	.	A	+	1	0	KSR1	22956943	0.000000	0.05858	0.052000	0.19188	0.964000	0.63967	-4.383000	0.00243	-4.020000	0.00081	-1.333000	0.01266	GCC	G|0.964;A|0.036	0.036	strong		0.587	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238	
ASTN2	23245	hgsc.bcm.edu	37	9	119739015	119739015	+	Silent	SNP	G	G	A	rs10983437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	96	0	0		WXS	Illumina HiSeq	Phase_I	141	102	0.723404	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	
TNRC6A	27327	hgsc.bcm.edu	37	16	24802204	24802204	+	Silent	SNP	C	C	T	rs113288384		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24802204C>T	ENST00000395799.3	+	6	2370	c.2241C>T	c.(2239-2241)gaC>gaT	p.D747D	TNRC6A_ENST00000315183.7_Silent_p.D747D	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	747	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.|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)			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)		GAAAGACTGACAATGGGACAG	0.473													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20045	0.0		0.0	False		,,,				2504	0.0				p.D747D		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C2241T						PASS	.	C		2,4392	4.2+/-10.8	0,2,2195	53.0	55.0	55.0		2241	3.9	1.0	16	dbSNP_132	55	0,8600		0,0,4300	no	coding-synonymous	TNRC6A	NM_014494.2		0,2,6495	TT,TC,CC		0.0,0.0455,0.0154		747/1963	24802204	2,12992	2197	4300	6497	SO:0001819	synonymous_variant	27327	exon6			GACTGACAATGGG	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.2241C>T	16.37:g.24802204C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2																																																																																			C|0.999;T|0.001	0.001	strong		0.473	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
PTPRS	5802	hgsc.bcm.edu	37	19	5210762	5210762	+	Silent	SNP	G	G	A	rs1143699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5210762G>A	ENST00000587303.1	-	33	5388	c.5289C>T	c.(5287-5289)gaC>gaT	p.D1763D	PTPRS_ENST00000262963.6_Silent_p.D1743D|PTPRS_ENST00000372412.4_Silent_p.D1764D|PTPRS_ENST00000348075.2_Silent_p.D1725D|PTPRS_ENST00000353284.2_Silent_p.D1316D|PTPRS_ENST00000592099.1_Silent_p.D1316D|PTPRS_ENST00000588012.1_Silent_p.D1725D|PTPRS_ENST00000357368.4_Silent_p.D1763D|PTPRS_ENST00000588552.1_5'UTR			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1763	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			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)	TGCGCCAGAAGTCTTCCGTGG	0.662													G|||	504	0.100639	0.2216	0.0807	5008	,	,		18976	0.0		0.0994	False		,,,				2504	0.0562				p.D1763D		Atlas-SNP	.											.	PTPRS	169	.	0			c.C5289T						PASS	.	G	,,,	819,3587	325.0+/-298.9	87,645,1471	98.0	77.0	84.0		5289,3948,5175,3960	-2.7	1.0	19	dbSNP_86	84	875,7725	197.5+/-242.1	46,783,3471	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRS	NM_002850.3,NM_130853.2,NM_130854.2,NM_130855.2	,,,	133,1428,4942	AA,AG,GG		10.1744,18.5883,13.0248	,,,	1763/1949,1316/1502,1725/1911,1320/1506	5210762	1694,11312	2203	4300	6503	SO:0001819	synonymous_variant	5802	exon34			CCAGAAGTCTTCC	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.5289C>T	19.37:g.5210762G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																			G|0.874;A|0.126	0.126	strong		0.662	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
ZNF474	133923	hgsc.bcm.edu	37	5	121487954	121487954	+	Missense_Mutation	SNP	G	G	A	rs116158782	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:121487954G>A	ENST00000296600.4	+	2	652	c.269G>A	c.(268-270)cGc>cAc	p.R90H	CTC-441N14.2_ENST00000504829.1_RNA|ZNF474_ENST00000514925.1_Intron|CTC-441N14.1_ENST00000505209.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	90							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		ATCCCGGCCCGCAGGCCTGGA	0.493													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		17011	0.0		0.0	False		,,,				2504	0.0				p.R90H		Atlas-SNP	.											.	ZNF474	43	.	0			c.G269A						PASS	.	G	HIS/ARG	146,4260	102.1+/-140.7	3,140,2060	76.0	86.0	82.0		269	4.7	1.0	5	dbSNP_132	82	5,8593	4.3+/-15.6	0,5,4294	yes	missense	ZNF474	NM_207317.1	29	3,145,6354	AA,AG,GG		0.0582,3.3137,1.1612	probably-damaging	90/365	121487954	151,12853	2203	4299	6502	SO:0001583	missense	133923	exon2			CGGCCCGCAGGCC	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"""Zinc fingers, C2H2-type"""	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.269G>A	5.37:g.121487954G>A	ENSP00000296600:p.Arg90His	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	128	56	0.4375	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	G	15.38	2.817454	0.50633	0.033137	5.82E-4	ENSG00000164185	ENST00000296600	T	0.50001	0.76	5.58	4.66	0.58398	.	0.157757	0.33980	N	0.004370	T	0.19525	0.0469	L	0.36672	1.1	0.36400	D	0.863073	D	0.89917	1.0	D	0.73708	0.981	T	0.55010	-0.8207	10	0.62326	D	0.03	-6.5368	15.9342	0.79688	0.0:0.135:0.865:0.0	.	90	Q6S9Z5	ZN474_HUMAN	H	90	ENSP00000296600:R90H	ENSP00000296600:R90H	R	+	2	0	ZNF474	121515853	0.999000	0.42202	1.000000	0.80357	0.102000	0.19082	1.797000	0.38804	2.624000	0.88883	0.655000	0.94253	CGC	G|0.988;A|0.012	0.012	strong		0.493	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317	
MTOR	2475	hgsc.bcm.edu	37	1	11181327	11181327	+	Silent	SNP	C	C	T	rs11121691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11181327C>T	ENST00000361445.4	-	49	6985	c.6909G>A	c.(6907-6909)ctG>ctA	p.L2303L	MTOR_ENST00000376838.1_Silent_p.L508L	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2303	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TTTTCAGCCACAGCAGCTTGG	0.587													C|||	1105	0.220647	0.4365	0.1542	5008	,	,		17412	0.0565		0.2356	False		,,,				2504	0.1299				p.L2303L		Atlas-SNP	.											.	MTOR	327	.	0			c.G6909A						PASS	.	C		1875,2531	541.3+/-375.7	383,1109,711	80.0	68.0	72.0		6909	3.9	1.0	1	dbSNP_120	72	2054,6546	356.9+/-330.5	249,1556,2495	no	coding-synonymous	MTOR	NM_004958.3		632,2665,3206	TT,TC,CC		23.8837,42.5556,30.2091		2303/2550	11181327	3929,9077	2203	4300	6503	SO:0001819	synonymous_variant	2475	exon49			CAGCCACAGCAGC	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6909G>A	1.37:g.11181327C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	101	40	0.39604	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			C|0.721;T|0.279	0.279	strong		0.587	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
LILRB3	11025	hgsc.bcm.edu	37	19	54721272	54721272	+	Missense_Mutation	SNP	C	C	T	rs114189491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54721272C>T	ENST00000391750.1	-	13	1801	c.1665G>A	c.(1663-1665)atG>atA	p.M555I	LILRB3_ENST00000245620.9_Missense_Mutation_p.M556I|LILRB3_ENST00000407860.2_Missense_Mutation_p.M572I|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000346401.6_Missense_Mutation_p.M567I|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.M556I|LILRB3_ENST00000424807.1_Missense_Mutation_p.M555I|LILRA6_ENST00000440558.2_Missense_Mutation_p.M555I|LILRA6_ENST00000270464.5_Missense_Mutation_p.M556I			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	555					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GAGGAGAGGCCATTTCTCTCC	0.577													.|||	174	0.0347444	0.1293	0.0043	5008	,	,		17886	0.0		0.0	False		,,,				2504	0.0				p.M556I		Atlas-SNP	.											.	LILRB3	67	.	0			c.G1668A						PASS	.	C	ILE/MET,ILE/MET	451,3953	216.4+/-235.1	26,399,1777	130.0	130.0	130.0		1668,1665	-0.9	0.0	19	dbSNP_132	130	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	10,10	26,402,6074	TT,TC,CC		0.0349,10.2407,3.4912	benign,benign	556/633,555/632	54721272	454,12550	2202	4300	6502	SO:0001583	missense	11025	exon12			AGAGGCCATTTCT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1665G>A	19.37:g.54721272C>T	ENSP00000375630:p.Met555Ile	Somatic	602	0	0		WXS	Illumina HiSeq	Phase_I	418	208	0.497608	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	63	0.028846153846153848	62	0.12601626016260162	1	0.0027624309392265192	0	0.0	0	0.0	C	12.21	1.870077	0.33069	0.102407	3.49E-4	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00477	7.16;7.16;7.14;7.17;7.14;7.16;7.16;7.18	2.45	-0.895	0.10560	.	.	.	.	.	T	0.00012	0.0000	L	0.50919	1.6	0.09310	N	1	D;B;B;B;B;B;P	0.56287	0.975;0.39;0.197;0.121;0.014;0.006;0.78	D;B;B;B;B;B;P	0.65684	0.937;0.026;0.109;0.015;0.002;0.001;0.458	T	0.55179	-0.8181	9	0.54805	T	0.06	.	2.7524	0.05284	0.0:0.4373:0.2613:0.3014	.	572;555;556;567;572;555;556	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	I	555;555;567;556;572;555;556;556	ENSP00000375630:M555I;ENSP00000412771:M555I;ENSP00000345184:M567I;ENSP00000245620:M556I;ENSP00000384274:M572I;ENSP00000390120:M555I;ENSP00000270464:M556I;ENSP00000411227:M556I	ENSP00000270464:M556I	M	-	3	0	LILRB3;LILRA6	59413084	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.049000	0.11924	-0.089000	0.12484	0.121000	0.15741	ATG	C|0.961;T|0.039	0.039	strong		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
ASPSCR1	79058	hgsc.bcm.edu	37	17	79943475	79943475	+	Silent	SNP	A	A	G	rs4796860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79943475A>G	ENST00000306739.4	+	4	463	c.366A>G	c.(364-366)ccA>ccG	p.P122P	ASPSCR1_ENST00000306729.7_Silent_p.P122P|ASPSCR1_ENST00000580534.1_Silent_p.P45P|ASPSCR1_ENST00000581647.1_Silent_p.P122P	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	122					glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GCCATTTTCCACAGATCAGGT	0.582			T	TFE3	alveolar soft part sarcoma								A|||	55	0.0109824	0.0401	0.0029	5008	,	,		19456	0.0		0.0	False		,,,				2504	0.0				p.P122P		Atlas-SNP	.		Dom	yes		17	17q25	79058	"""alveolar soft part sarcoma chromosome region, candidate 1"""		M	.	ASPSCR1	27	.	0			c.A366G						PASS	.	A		235,4171	136.9+/-172.8	5,225,1973	77.0	68.0	71.0		366	1.8	1.0	17	dbSNP_111	71	0,8600		0,0,4300	yes	coding-synonymous	ASPSCR1	NM_024083.2		5,225,6273	GG,GA,AA		0.0,5.3336,1.8069		122/554	79943475	235,12771	2203	4300	6503	SO:0001819	synonymous_variant	79058	exon4			TTTTCCACAGATC	AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"""UBX domain containing"""	13825	protein-coding gene	gene with protein product	"""UBX domain protein 9"""	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.366A>G	17.37:g.79943475A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	178	82	0.460674	NM_001251888	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Silent	SNP	ENST00000306739.4	37	CCDS11796.1																																																																																			A|0.983;G|0.017	0.017	strong		0.582	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083	
CELSR1	9620	hgsc.bcm.edu	37	22	46760037	46760037	+	Missense_Mutation	SNP	G	G	A	rs375307146|rs6008777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46760037G>A	ENST00000262738.3	-	34	8890	c.8891C>T	c.(8890-8892)tCg>tTg	p.S2964L		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2964			S -> L (in NTD; shows reduced protein localization to the cell membrane; dbSNP:rs6008777). {ECO:0000269|PubMed:22095531}.		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)		AGACGTGCGCGAGGATGTGGG	0.682													G|||	116	0.0231629	0.0832	0.0086	5008	,	,		14793	0.0		0.0	False		,,,				2504	0.0				p.S2964L		Atlas-SNP	.											CELSR1,colon,carcinoma,+1,1	CELSR1	242	1	0			c.C8891T						PASS	.	G	LEU/SER	399,4005	190.2+/-216.2	29,341,1832	40.0	46.0	44.0		8891	4.8	0.1	22	dbSNP_114	44	4,8594	3.0+/-9.4	0,4,4295	yes	missense	CELSR1	NM_014246.1	145	29,345,6127	AA,AG,GG		0.0465,9.0599,3.0995	probably-damaging	2964/3015	46760037	403,12599	2202	4299	6501	SO:0001583	missense	9620	exon34			GTGCGCGAGGATG	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.8891C>T	22.37:g.46760037G>A	ENSP00000262738:p.Ser2964Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	159	85	0.534591	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	G	14.11	2.438063	0.43326	0.090599	4.65E-4	ENSG00000075275	ENST00000262738	T	0.71579	-0.58	4.85	4.85	0.62838	.	0.000000	0.36374	U	0.002632	T	0.11367	0.0277	M	0.74258	2.255	0.37738	D	0.925504	D	0.67145	0.996	P	0.47786	0.557	T	0.57046	-0.7878	10	0.33141	T	0.24	.	17.569	0.87930	0.0:0.0:1.0:0.0	rs6008777	2964	Q9NYQ6	CELR1_HUMAN	L	2964	ENSP00000262738:S2964L	ENSP00000262738:S2964L	S	-	2	0	CELSR1	45138701	0.994000	0.37717	0.060000	0.19600	0.011000	0.07611	3.602000	0.54066	2.211000	0.71520	0.563000	0.77884	TCG	G|0.971;A|0.029	0.029	strong		0.682	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
DDX20	11218	hgsc.bcm.edu	37	1	112309123	112309123	+	Missense_Mutation	SNP	C	C	A	rs197414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:112309123C>A	ENST00000369702.4	+	11	2697	c.2077C>A	c.(2077-2079)Cgt>Agt	p.R693S	DDX20_ENST00000475700.1_Missense_Mutation_p.R301S	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	693			R -> S (in dbSNP:rs197414).		ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGTGGATGATCGTATTTCTTT	0.433													C|||	831	0.165935	0.4274	0.0965	5008	,	,		20348	0.003		0.1252	False		,,,				2504	0.0716				p.R693S		Atlas-SNP	.											.	DDX20	50	.	0			c.C2077A	GRCh37	CM086198	DDX20	M	rs197414	PASS	.	C	SER/ARG	1627,2779	487.6+/-361.0	296,1035,872	79.0	82.0	81.0		2077	4.1	0.5	1	dbSNP_79	81	1099,7499	228.6+/-263.6	69,961,3269	yes	missense	DDX20	NM_007204.4	110	365,1996,4141	AA,AC,CC		12.782,36.9269,20.9628	benign	693/825	112309123	2726,10278	2203	4299	6502	SO:0001583	missense	11218	exon11			GATGATCGTATTT	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2077C>A	1.37:g.112309123C>A	ENSP00000358716:p.Arg693Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	338	0.15476190476190477	213	0.4329268292682927	30	0.08287292817679558	0	0.0	95	0.12532981530343007	C	4.758	0.140947	0.09083	0.369269	0.12782	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.31247	1.5;2.06	5.0	4.09	0.47781	.	2.687950	0.00649	N	0.000558	T	0.09247	0.0228	N	0.22421	0.69	0.09310	P	0.9999999999930954	B;B	0.12630	0.006;0.002	B;B	0.12837	0.008;0.005	T	0.11891	-1.0569	8	.	.	.	-0.8902	8.3507	0.32301	0.1541:0.7669:0.0:0.079	rs197414;rs665164;rs742792;rs52835282;rs57983595;rs197414	301;693	E9PJ60;Q9UHI6	.;DDX20_HUMAN	S	693;301	ENSP00000358716:R693S;ENSP00000435660:R301S	.	R	+	1	0	DDX20	112110646	0.005000	0.15991	0.498000	0.27564	0.024000	0.10985	1.194000	0.32174	1.476000	0.48215	0.655000	0.94253	CGT	C|0.846;A|0.154	0.154	strong		0.433	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
RBM19	9904	hgsc.bcm.edu	37	12	114383651	114383651	+	Silent	SNP	C	C	T	rs12321179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114383651C>T	ENST00000545145.2	-	13	1686	c.1608G>A	c.(1606-1608)aaG>aaA	p.K536K	RBM19_ENST00000392561.3_Silent_p.K536K|RBM19_ENST00000261741.5_Silent_p.K536K	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	536					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K536K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					ACACTTGACTCTTGGTGGCGT	0.552													C|||	994	0.198482	0.3472	0.0764	5008	,	,		22010	0.1885		0.1133	False		,,,				2504	0.182				p.K536K		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - coding silent(1)	stomach(1)	c.G1608A						PASS	.	C	,,	1440,2966	466.0+/-354.4	254,932,1017	161.0	119.0	133.0		1608,1608,1608	3.8	1.0	12	dbSNP_120	133	887,7713	199.4+/-243.5	39,809,3452	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	293,1741,4469	TT,TC,CC		10.314,32.6827,17.8917	,,	536/961,536/961,536/961	114383651	2327,10679	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon13			TTGACTCTTGGTG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1608G>A	12.37:g.114383651C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			C|0.823;T|0.177	0.177	strong		0.552	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
UBB	7314	hgsc.bcm.edu	37	17	16285404	16285404	+	Silent	SNP	C	C	T	rs9908960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16285404C>T	ENST00000395837.1	+	2	364	c.183C>T	c.(181-183)atC>atT	p.I61I	UBB_ENST00000302182.3_Silent_p.I61I|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000535788.1_Silent_p.I61I|UBB_ENST00000578649.1_Intron|UBB_ENST00000395839.1_Silent_p.I61I	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	61	Ubiquitin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|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)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|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)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|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 epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|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)|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 transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|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)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		ACTACAACATCCAGAAGGAGT	0.562													C|||	308	0.0615016	0.1619	0.0648	5008	,	,		22409	0.0198		0.0109	False		,,,				2504	0.0184				p.I61I	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											.	UBB	30	.	0			c.C183T						PASS	.	C		599,3807	262.5+/-264.9	39,521,1643	78.0	77.0	78.0		183	3.1	1.0	17	dbSNP_119	78	122,8478	63.1+/-125.2	0,122,4178	no	coding-synonymous	UBB	NM_018955.2		39,643,5821	TT,TC,CC		1.4186,13.5951,5.5436		61/230	16285404	721,12285	2203	4300	6503	SO:0001819	synonymous_variant	7314	exon2			CAACATCCAGAAG		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.183C>T	17.37:g.16285404C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	179	82	0.458101	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			C|0.947;T|0.053	0.053	strong		0.562	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
MYO9B	4650	hgsc.bcm.edu	37	19	17316782	17316782	+	Missense_Mutation	SNP	T	T	C	rs7248508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17316782T>C	ENST00000594824.1	+	32	5225	c.5078T>C	c.(5077-5079)gTt>gCt	p.V1693A	CTD-3032J10.3_ENST00000601929.1_RNA|MYO9B_ENST00000595618.1_Missense_Mutation_p.V1693A|MYO9B_ENST00000397274.2_Missense_Mutation_p.V1693A			Q13459	MYO9B_HUMAN	myosin IXB	1693	Tail.			V -> A (in Ref. 1; AAC50402). {ECO:0000305}.	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						GAGCCAGGCGTTGAGCCTGGC	0.667													C|||	3163	0.631589	0.708	0.6772	5008	,	,		12871	0.746		0.3917	False		,,,				2504	0.6247				p.V1693A		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	0			c.T5078C						PASS	.	C	ALA/VAL,ALA/VAL	2660,1460		885,890,285	21.0	27.0	25.0		5078,5078	4.7	0.0	19	dbSNP_116	25	3346,5022		710,1926,1548	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	64,64	1595,2816,1833	CC,CT,TT		39.9857,35.4369,48.0942	benign,benign	1693/2023,1693/2158	17316782	6006,6482	2060	4184	6244	SO:0001583	missense	4650	exon32			CAGGCGTTGAGCC		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.5078T>C	19.37:g.17316782T>C	ENSP00000471367:p.Val1693Ala	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		1311	0.6002747252747253	331	0.6727642276422764	232	0.6408839779005525	445	0.777972027972028	303	0.3997361477572559	C	2.673	-0.277158	0.05679	0.645631	0.399857	ENSG00000099331	ENST00000397274;ENST00000319396	D	0.84442	-1.85	4.74	4.74	0.60224	.	0.234317	0.29676	N	0.011484	T	0.00012	0.0000	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	0.41142	-0.9525	9	0.05959	T	0.93	.	10.8777	0.46921	0.0:0.9112:0.0:0.0888	rs7248508;rs11545735;rs7248508	1693;1693;1699	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	A	1693;38	ENSP00000380444:V1693A	ENSP00000314032:V38A	V	+	2	0	MYO9B	17177782	0.001000	0.12720	0.039000	0.18376	0.005000	0.04900	1.204000	0.32296	1.136000	0.42199	-0.215000	0.12644	GTT	T|0.406;C|0.594	0.594	strong		0.667	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
ZNF99	7652	hgsc.bcm.edu	37	19	22952111	22952111	+	Missense_Mutation	SNP	A	A	G	rs34726149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22952111A>G	ENST00000596209.1	-	2	109	c.19T>C	c.(19-21)Tgg>Cgg	p.W7R	ZNF99_ENST00000397104.3_Missense_Mutation_p.W28R	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	7	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		W -> R (in dbSNP:rs34726149).		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.W28R(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GTCACATCCCAAAATGTCAAC	0.393													G|||	1089	0.217452	0.4198	0.1326	5008	,	,		15615	0.1756		0.1372	False		,,,				2504	0.1299				p.W7R		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	1	1	Substitution - Missense(1)	stomach(1)	c.T19C						PASS	.	G	ARG/TRP	1654,2736		299,1056,840	70.0	76.0	74.0		82	-2.1	0.0	19	dbSNP_126	74	1041,7557		70,901,3328	no	missense	ZNF99	NM_001080409.2	101	369,1957,4168	GG,GA,AA		12.1075,37.6765,20.7499	benign	28/912	22952111	2695,10293	2195	4299	6494	SO:0001583	missense	7652	exon2			CATCCCAAAATGT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.19T>C	19.37:g.22952111A>G	ENSP00000472969:p.Trp7Arg	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	460	0.21062271062271062	205	0.4166666666666667	55	0.15193370165745856	105	0.18356643356643357	95	0.12532981530343007	N	0	-2.657345	0.00108	0.376765	0.121075	ENSG00000213973	ENST00000397104	T	0.01527	4.8	1.04	-2.08	0.07254	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	N	0.00018	-2.82	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47262	-0.9131	8	0.05436	T	0.98	.	2.9505	0.05860	0.2153:0.0:0.2594:0.5253	rs34726149;rs62120120	28	A8MXY4	ZNF99_HUMAN	R	28	ENSP00000380293:W28R	ENSP00000380293:W28R	W	-	1	0	ZNF99	22743951	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.162000	0.03141	-4.685000	0.00036	-4.816000	0.00003	TGG	A|0.809;G|0.191	0.191	strong		0.393	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
KIAA0922	23240	hgsc.bcm.edu	37	4	154504741	154504741	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:154504741A>G	ENST00000409663.3	+	11	1029	c.977A>G	c.(976-978)gAt>gGt	p.D326G	KIAA0922_ENST00000409959.3_Missense_Mutation_p.D326G|KIAA0922_ENST00000440693.1_Missense_Mutation_p.D326G	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	326						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)				TCACAGAGAGATGCTCTGTCT	0.373																																					p.D326G		Atlas-SNP	.											KIAA0922,colon,carcinoma,+1,1	KIAA0922	214	1	0			c.A977G						scavenged	.						115.0	114.0	114.0					4																	154504741		2203	4300	6503	SO:0001583	missense	23240	exon11			AGAGAGATGCTCT	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.977A>G	4.37:g.154504741A>G	ENSP00000386574:p.Asp326Gly	Somatic	457	1	0.00218818		WXS	Illumina HiSeq	Phase_I	481	5	0.010395	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	A	9.195	1.026899	0.19512	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.20069	2.33;2.1;2.34;2.1	5.78	3.3	0.37823	.	0.551000	0.21224	N	0.078088	T	0.12561	0.0305	N	0.24115	0.695	0.09310	N	1	B;B;B	0.14805	0.005;0.008;0.011	B;B;B	0.16289	0.004;0.014;0.015	T	0.21449	-1.0245	10	0.45353	T	0.12	-1.261	5.5611	0.17144	0.7067:0.1461:0.1472:0.0	.	326;326;326	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	G	326;326;326;187	ENSP00000386574:D326G;ENSP00000409663:D326G;ENSP00000386787:D326G;ENSP00000240487:D187G	ENSP00000240487:D187G	D	+	2	0	KIAA0922	154724191	0.156000	0.22821	0.006000	0.13384	0.912000	0.54170	1.713000	0.37951	0.444000	0.26612	0.533000	0.62120	GAT	.	.	none		0.373	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
VAV3	10451	hgsc.bcm.edu	37	1	108138961	108138961	+	Silent	SNP	T	T	C	rs17229705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:108138961T>C	ENST00000370056.4	-	25	2497	c.2223A>G	c.(2221-2223)gaA>gaG	p.E741E	VAV3_ENST00000527011.1_Silent_p.E741E|VAV3_ENST00000415432.2_Silent_p.E181E|VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000544443.1_Silent_p.E145E	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	741	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.|Sufficient for interaction with ROS1.				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)		ACTCCACAAGTTCCTTTGGAA	0.378													T|||	184	0.0367412	0.0333	0.0418	5008	,	,		19543	0.002		0.0557	False		,,,				2504	0.0542				p.E741E		Atlas-SNP	.											.	VAV3	176	.	0			c.A2223G						PASS	.	T	,	165,4241	109.9+/-148.2	3,159,2041	109.0	104.0	105.0		543,2223	1.9	1.0	1	dbSNP_123	105	522,8078	146.0+/-201.7	14,494,3792	no	coding-synonymous,coding-synonymous	VAV3	NM_001079874.1,NM_006113.4	,	17,653,5833	CC,CT,TT		6.0698,3.7449,5.2822	,	181/288,741/848	108138961	687,12319	2203	4300	6503	SO:0001819	synonymous_variant	10451	exon25			CACAAGTTCCTTT	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.2223A>G	1.37:g.108138961T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	143	63	0.440559	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Silent	SNP	ENST00000370056.4	37	CCDS785.1																																																																																			T|0.950;C|0.050	0.050	strong		0.378	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
PLEKHG4	25894	hgsc.bcm.edu	37	16	67316234	67316234	+	Missense_Mutation	SNP	C	C	T	rs11860295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67316234C>T	ENST00000360461.5	+	8	3770	c.1235C>T	c.(1234-1236)aCc>aTc	p.T412I	PLEKHG4_ENST00000379344.3_Missense_Mutation_p.T412I|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.T412I|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.T331I	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	412			T -> I (in dbSNP:rs11860295).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CCAGAGGTGACCCTGAGCCCA	0.612													C|||	1222	0.24401	0.6944	0.1023	5008	,	,		17531	0.003		0.0716	False		,,,				2504	0.1616				p.T412I		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.C1235T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR,ILE/THR,ILE/THR	2454,1942	587.9+/-386.8	685,1084,429	25.0	28.0	27.0		1235,1235,1235,992,1235	3.2	1.0	16	dbSNP_120	27	644,7954	158.8+/-212.2	24,596,3679	yes	missense,missense,missense,missense,missense	PLEKHG4	NM_001129727.1,NM_001129728.1,NM_001129729.1,NM_001129731.1,NM_015432.3	89,89,89,89,89	709,1680,4108	TT,TC,CC		7.4901,44.1765,23.8418	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	412/1192,412/1192,412/1192,331/1111,412/1192	67316234	3098,9896	2198	4299	6497	SO:0001583	missense	25894	exon9			AGGTGACCCTGAG	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.1235C>T	16.37:g.67316234C>T	ENSP00000353646:p.Thr412Ile	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	35	0.686275	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	37	CCDS32466.1	446	0.2042124542124542	346	0.7032520325203252	42	0.11602209944751381	2	0.0034965034965034965	56	0.07387862796833773	C	13.83	2.352781	0.41700	0.558235	0.074901	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.10005	2.92;2.92;2.92;2.93	5.55	3.24	0.37175	.	.	.	.	.	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	D;B	0.53462	0.96;0.267	P;B	0.51229	0.663;0.086	T	0.04153	-1.0973	8	0.35671	T	0.21	.	8.5159	0.33246	0.0:0.7949:0.0:0.2051	rs11860295;rs52814135;rs58234933;rs11860295	331;412	Q58EX7-2;Q58EX7	.;PKHG4_HUMAN	I	412;412;412;331	ENSP00000353646:T412I;ENSP00000401118:T412I;ENSP00000368649:T412I;ENSP00000398030:T331I	ENSP00000353646:T412I	T	+	2	0	PLEKHG4	65873735	0.002000	0.14202	1.000000	0.80357	0.940000	0.58332	0.009000	0.13219	1.342000	0.45619	0.655000	0.94253	ACC	C|0.752;T|0.248	0.248	strong		0.612	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
GANC	2595	hgsc.bcm.edu	37	15	42631928	42631928	+	Silent	SNP	T	T	C	rs36023127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42631928T>C	ENST00000318010.8	+	17	2145	c.1905T>C	c.(1903-1905)gcT>gcC	p.A635A		NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	635					carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)	p.A635A(1)		breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	GGTACCAGGCTGGAGCCTACC	0.567													C|||	473	0.0944489	0.1399	0.062	5008	,	,		15919	0.002		0.0845	False		,,,				2504	0.1616				p.A635A		Atlas-SNP	.											GANC,brain,glioma,0,1	GANC	57	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.T1905C						scavenged	.	C		615,3791	769.5+/-413.7	45,525,1633	88.0	84.0	86.0		1905	-12.1	0.1	15	dbSNP_126	86	695,7903	787.5+/-407.6	32,631,3636	no	coding-synonymous	GANC	NM_198141.2		77,1156,5269	CC,CT,TT		8.0833,13.9582,10.0738		635/915	42631928	1310,11694	2203	4299	6502	SO:0001819	synonymous_variant	2595	exon17			CCAGGCTGGAGCC	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.1905T>C	15.37:g.42631928T>C		Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Silent	SNP	ENST00000318010.8	37	CCDS10084.1																																																																																			T|0.910;C|0.090	0.090	strong		0.567	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
TEX15	56154	hgsc.bcm.edu	37	8	30704725	30704725	+	Silent	SNP	C	C	T	rs62000451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:30704725C>T	ENST00000256246.2	-	1	1883	c.1809G>A	c.(1807-1809)caG>caA	p.Q603Q	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	603					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		CACTAGCTATCTGTATTGCAG	0.388													C|||	743	0.148363	0.2973	0.0677	5008	,	,		20299	0.0575		0.0626	False		,,,				2504	0.1861				p.Q603Q		Atlas-SNP	.											.	TEX15	350	.	0			c.G1809A						PASS	.	C		1135,3271	404.6+/-333.2	137,861,1205	121.0	114.0	116.0		1809	-1.6	0.0	8	dbSNP_129	116	445,8155	133.9+/-191.4	10,425,3865	no	coding-synonymous	TEX15	NM_031271.3		147,1286,5070	TT,TC,CC		5.1744,25.7603,12.1482		603/2790	30704725	1580,11426	2203	4300	6503	SO:0001819	synonymous_variant	56154	exon1			AGCTATCTGTATT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.1809G>A	8.37:g.30704725C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_031271		Silent	SNP	ENST00000256246.2	37	CCDS6080.1																																																																																			C|0.886;T|0.114	0.114	strong		0.388	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
DYRK4	8798	hgsc.bcm.edu	37	12	4702173	4702173	+	Silent	SNP	C	C	T	rs2240763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:4702173C>T	ENST00000540757.2	+	4	284	c.124C>T	c.(124-126)Cta>Tta	p.L42L	DYRK4_ENST00000543431.1_Silent_p.L42L|DYRK4_ENST00000010132.5_Silent_p.L42L	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	42						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			CACAGAGGCCCTAAAGCTTTT	0.507													C|||	698	0.139377	0.1657	0.0303	5008	,	,		18264	0.2639		0.0239	False		,,,				2504	0.1718				p.L42L		Atlas-SNP	.											DYRK4,NS,carcinoma,-2,1	DYRK4	75	1	0			c.C124T						PASS	.	C		664,3742	276.0+/-272.9	54,556,1593	73.0	79.0	77.0		124	3.7	1.0	12	dbSNP_98	77	270,8330	100.6+/-161.9	5,260,4035	no	coding-synonymous	DYRK4	NM_003845.1		59,816,5628	TT,TC,CC		3.1395,15.0704,7.1813		42/521	4702173	934,12072	2203	4300	6503	SO:0001819	synonymous_variant	8798	exon4			GAGGCCCTAAAGC	Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.124C>T	12.37:g.4702173C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_003845	A8K8F7|Q8NEF2|Q92631	Silent	SNP	ENST00000540757.2	37	CCDS8530.1																																																																																			C|0.897;T|0.103	0.103	strong		0.507	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398780.2		
BBS12	166379	hgsc.bcm.edu	37	4	123663098	123663098	+	Silent	SNP	A	A	G	rs17006077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:123663098A>G	ENST00000314218.3	+	2	244	c.51A>G	c.(49-51)caA>caG	p.Q17Q	BBS12_ENST00000542236.1_Silent_p.Q17Q	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	17					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TGGGACTTCAACAACTTTCAT	0.338									Bardet-Biedl syndrome				A|||	342	0.0682907	0.2398	0.0303	5008	,	,		20228	0.002		0.002	False		,,,				2504	0.0				p.Q17Q		Atlas-SNP	.											.	BBS12	63	.	0			c.A51G						PASS	.	A	,	919,3487	351.8+/-311.4	93,733,1377	88.0	87.0	87.0		51,51	-3.9	0.9	4	dbSNP_123	87	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	93,752,5658	GG,GA,AA		0.2209,20.8579,7.2121	,	17/711,17/711	123663098	938,12068	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	ACTTCAACAACTT	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.51A>G	4.37:g.123663098A>G		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	326	162	0.496933	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			A|0.927;G|0.073	0.073	strong		0.338	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
CIB4	130106	hgsc.bcm.edu	37	2	26805761	26805761	+	Silent	SNP	C	C	T	rs7595964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26805761C>T	ENST00000288861.4	-	6	512	c.459G>A	c.(457-459)ctG>ctA	p.L153L	CIB4_ENST00000405346.3_5'UTR	NM_001029881.1	NP_001025052.1	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4	153	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTCATTGTCCAGATCCGACT	0.542													C|||	237	0.0473243	0.1483	0.0231	5008	,	,		21713	0.0		0.001	False		,,,				2504	0.0245				p.L153L		Atlas-SNP	.											.	CIB4	15	.	0			c.G459A						PASS	.	C		564,3842	251.8+/-258.4	33,498,1672	128.0	102.0	110.0		459	4.6	1.0	2	dbSNP_116	110	24,8576	17.3+/-56.4	0,24,4276	no	coding-synonymous	CIB4	NM_001029881.1		33,522,5948	TT,TC,CC		0.2791,12.8007,4.521		153/186	26805761	588,12418	2203	4300	6503	SO:0001819	synonymous_variant	130106	exon6			ATTGTCCAGATCC		CCDS33160.1	2p23.3	2013-01-10			ENSG00000157884	ENSG00000157884		"""EF-hand domain containing"""	33703	protein-coding gene	gene with protein product		610646				15574431	Standard	NM_001029881		Approved		uc002rhm.3	A0PJX0	OTTHUMG00000151993	ENST00000288861.4:c.459G>A	2.37:g.26805761C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_001029881	B2RU18	Silent	SNP	ENST00000288861.4	37	CCDS33160.1																																																																																			C|0.951;T|0.049	0.049	strong		0.542	CIB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324709.1		
PRKCH	5583	hgsc.bcm.edu	37	14	61857969	61857969	+	Silent	SNP	A	A	G	rs2230499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:61857969A>G	ENST00000332981.5	+	2	775	c.390A>G	c.(388-390)gtA>gtG	p.V130V	PRKCH_ENST00000555082.1_5'UTR	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	130					blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		AGGGGAAAGTATTTGTGGTAA	0.348													A|||	1390	0.277556	0.4955	0.1873	5008	,	,		17836	0.248		0.163	False		,,,				2504	0.1953				p.V130V	Melanoma(135;863 1779 8064 14443 26348)	Atlas-SNP	.											.	PRKCH	89	.	0			c.A390G						PASS	.	A		1787,2619	523.9+/-371.2	364,1059,780	86.0	84.0	85.0		390	-2.9	1.0	14	dbSNP_107	85	1375,7225	265.8+/-286.4	103,1169,3028	no	coding-synonymous	PRKCH	NM_006255.3		467,2228,3808	GG,GA,AA		15.9884,40.5583,24.3119		130/684	61857969	3162,9844	2203	4300	6503	SO:0001819	synonymous_variant	5583	exon2			GAAAGTATTTGTG	M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.390A>G	14.37:g.61857969A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_006255	B4DJN5|Q16246|Q8NE03	Silent	SNP	ENST00000332981.5	37	CCDS9752.1																																																																																			A|0.743;G|0.257	0.257	strong		0.348	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255	
CLCA4	22802	hgsc.bcm.edu	37	1	87012929	87012929	+	Missense_Mutation	SNP	C	C	T	rs2231580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87012929C>T	ENST00000370563.3	+	1	169	c.127C>T	c.(127-129)Cca>Tca	p.P43S	CLCA4_ENST00000263723.5_5'UTR	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	43			P -> S (in dbSNP:rs2231580).		chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		TCCTAGTGTGCCAGAAGATGA	0.289													C|||	197	0.0393371	0.143	0.0115	5008	,	,		17655	0.0		0.0	False		,,,				2504	0.0				p.P43S		Atlas-SNP	.											.	CLCA4	131	.	0			c.C127T						PASS	.	C	SER/PRO	430,3208		15,400,1404	112.0	103.0	106.0		127	2.5	0.9	1	dbSNP_98	106	1,8149		0,1,4074	yes	missense	CLCA4	NM_012128.3	74	15,401,5478	TT,TC,CC		0.0123,11.8197,3.6563	benign	43/920	87012929	431,11357	1819	4075	5894	SO:0001583	missense	22802	exon1			AGTGTGCCAGAAG	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.127C>T	1.37:g.87012929C>T	ENSP00000359594:p.Pro43Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	94	50	0.531915	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Missense_Mutation	SNP	ENST00000370563.3	37	CCDS41355.1	71	0.03250915750915751	67	0.13617886178861788	4	0.011049723756906077	0	0.0	0	0.0	C	13.02	2.111801	0.37242	0.118197	1.23E-4	ENSG00000016602	ENST00000370563	T	0.15487	2.42	5.51	2.51	0.30379	Chloride channel calcium-activated (1);	0.460669	0.22684	N	0.056907	T	0.11324	0.0276	L	0.50993	1.605	0.80722	D	1	P	0.40534	0.72	P	0.53102	0.718	T	0.17961	-1.0352	10	0.34782	T	0.22	-0.5846	2.8316	0.05502	0.1469:0.5502:0.1426:0.1603	rs2231580;rs52821083;rs60157342;rs2231580	43	Q14CN2	CLCA4_HUMAN	S	43	ENSP00000359594:P43S	ENSP00000359594:P43S	P	+	1	0	CLCA4	86785517	0.986000	0.35501	0.942000	0.38095	0.500000	0.33767	0.870000	0.28010	0.336000	0.23639	0.655000	0.94253	CCA	C|0.971;T|0.029	0.029	strong		0.289	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
CDH26	60437	hgsc.bcm.edu	37	20	58571064	58571064	+	Missense_Mutation	SNP	G	G	T	rs194998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58571064G>T	ENST00000244047.5	+	12	2154	c.1843G>T	c.(1843-1845)Gtg>Ttg	p.V615L	CDH26_ENST00000350849.6_5'Flank|CDH26_ENST00000244049.3_5'Flank|CDH26_ENST00000348616.4_Missense_Mutation_p.V615L|CDH26_ENST00000497614.1_3'UTR			Q8IXH8	CAD26_HUMAN	cadherin 26	615			V -> L (in dbSNP:rs194998).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			GGGGCTTCATGTGGGGGCCCT	0.582													G|||	162	0.0323482	0.1203	0.0029	5008	,	,		17976	0.0		0.001	False		,,,				2504	0.0				p.V615L		Atlas-SNP	.											.	CDH26	229	.	0			c.G1843T						PASS	.	G	LEU/VAL	509,3897	234.6+/-247.4	28,453,1722	107.0	90.0	95.0		1843	-7.2	0.0	20	dbSNP_79	95	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CDH26	NM_177980.2	32	28,457,6018	TT,TG,GG		0.0465,11.5524,3.9443	benign	615/833	58571064	513,12493	2203	4300	6503	SO:0001583	missense	60437	exon12			CTTCATGTGGGGG	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"""Cadherins / Major cadherins"""	15902	protein-coding gene	gene with protein product			"""cadherin-like 26"""				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.1843G>T	20.37:g.58571064G>T	ENSP00000244047:p.Val615Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	37		59|59	0.027014652014652016|0.027014652014652016	58|58	0.11788617886178862|0.11788617886178862	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	10.78|10.78	1.446421|1.446421	0.25987|0.25987	0.115524|0.115524	4.65E-4|4.65E-4	ENSG00000124215|ENSG00000124215	ENST00000370991|ENST00000244047;ENST00000348616	.|T;T	.|0.58358	.|0.34;0.44	4.2|4.2	-7.21|-7.21	0.01490|0.01490	.|.	.|3.738960	.|0.00633	.|N	.|0.000487	T|T	0.00384|0.00384	0.0012|0.0012	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|B;B	.|0.32071	.|0.2;0.355	.|B;B	.|0.29716	.|0.048;0.106	T|T	0.15549|0.15549	-1.0433|-1.0433	5|10	.|0.06099	.|T	.|0.92	.|.	2.1968|2.1968	0.03913|0.03913	0.1448:0.3231:0.2971:0.235|0.1448:0.3231:0.2971:0.235	rs194998;rs52815481;rs194998|rs194998;rs52815481;rs194998	.|615;615	.|Q8IXH8;Q8IXH8-4	.|CAD26_HUMAN;.	I|L	206|615	.|ENSP00000244047:V615L;ENSP00000339390:V615L	.|ENSP00000244047:V615L	M|V	+|+	3|1	0|0	CDH26|CDH26	58004459|58004459	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.826000|-0.826000	0.04429|0.04429	-1.730000|-1.730000	0.01362|0.01362	-0.136000|-0.136000	0.14681|0.14681	ATG|GTG	A|0.001;C|0.008	.	strong		0.582	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	
SLC14A1	6563	hgsc.bcm.edu	37	18	43307338	43307338	+	Intron	SNP	C	C	A	rs11877086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:43307338C>A	ENST00000321925.4	+	2	211				RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000589700.1_5'Flank|SLC14A1_ENST00000436407.3_Silent_p.G34G|SLC14A1_ENST00000402943.2_Intron|SLC14A1_ENST00000415427.3_Silent_p.G34G|SLC14A1_ENST00000502059.2_5'UTR|SLC14A1_ENST00000535474.1_Intron|SLC14A1_ENST00000586142.1_5'Flank	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)						transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						CGCGCAGAGGCATCGCCCGGC	0.607													C|||	2016	0.402556	0.1853	0.5115	5008	,	,		18400	0.5198		0.5099	False		,,,				2504	0.3875				p.G34G		Atlas-SNP	.											.	SLC14A1	84	.	0			c.C102A						PASS	.	C	,,,	293,1091		28,237,427	51.0	50.0	50.0		102,,102,	2.3	0.1	18	dbSNP_120	50	1563,1619		398,767,426	no	coding-synonymous,utr-5,coding-synonymous,intron	SLC14A1	NM_001128588.3,NM_001146036.2,NM_001146037.1,NM_015865.6	,,,	426,1004,853	AA,AC,CC		49.1201,21.1705,40.6483	,,,	34/446,,34/446,	43307338	1856,2710	692	1591	2283	SO:0001627	intron_variant	6563	exon1			CAGAGGCATCGCC	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"""Blood group antigens"", ""Solute carriers"""	10918	protein-coding gene	gene with protein product		613868	"""Kidd blood group"", ""solute carrier family 14 (urea transporter), member 1"""	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.-22+2360C>A	18.37:g.43307338C>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Silent	SNP	ENST00000321925.4	37	CCDS11925.1																																																																																			C|0.566;A|0.434	0.434	strong		0.607	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865	
DNAH10	196385	hgsc.bcm.edu	37	12	124409630	124409630	+	Missense_Mutation	SNP	G	G	T	rs74845458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124409630G>T	ENST00000409039.3	+	67	11471	c.11446G>T	c.(11446-11448)Gtc>Ttc	p.V3816F	CCDC92_ENST00000544798.1_Intron|RP11-380L11.4_ENST00000602952.1_RNA	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3816					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)		GCAGTTTCCCGTCCCCTTGGG	0.473													T|||	327	0.0652955	0.2322	0.0231	5008	,	,		20433	0.0		0.003	False		,,,				2504	0.001				p.V3816F		Atlas-SNP	.											DNAH10_same_name,NS,carcinoma,0,2	DNAH10	888	2	0			c.G11446T						PASS	.	T	PHE/VAL	709,3179		59,591,1294	174.0	167.0	170.0		11446	1.5	0.3	12	dbSNP_131	170	39,8265		1,37,4114	yes	missense	DNAH10	NM_207437.3	50	60,628,5408	TT,TG,GG		0.4697,18.2356,6.1352	benign	3816/4472	124409630	748,11444	1944	4152	6096	SO:0001583	missense	196385	exon67			TTTCCCGTCCCCT	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.11446G>T	12.37:g.124409630G>T	ENSP00000386770:p.Val3816Phe	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	282	136	0.482269	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	113	0.051739926739926737	100	0.2032520325203252	11	0.03038674033149171	0	0.0	2	0.002638522427440633	T	0.013	-1.642308	0.00799	0.182356	0.004697	ENSG00000197653	ENST00000409039	T	0.09538	2.97	5.45	1.5	0.22942	Dynein heavy chain (1);	0.344630	0.30085	N	0.010460	T	0.00012	0.0000	N	0.00277	-1.72	0.19945	P	0.9999460444	B	0.02656	0.0	B	0.01281	0.0	T	0.40308	-0.9570	9	0.12430	T	0.62	.	2.5158	0.04667	0.11:0.1927:0.1142:0.5831	.	3816	Q8IVF4	DYH10_HUMAN	F	3816	ENSP00000386770:V3816F	ENSP00000386770:V3816F	V	+	1	0	DNAH10	122975583	0.935000	0.31712	0.251000	0.24312	0.009000	0.06853	1.289000	0.33307	0.040000	0.15660	-1.401000	0.01141	GTC	G|0.958;T|0.042	0.042	strong		0.473	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
PRKAG3	53632	hgsc.bcm.edu	37	2	219691801	219691801	+	Missense_Mutation	SNP	G	G	A	rs33985460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219691801G>A	ENST00000529249.1	-	10	1333	c.1018C>T	c.(1018-1020)Cgg>Tgg	p.R340W	PRKAG3_ENST00000545803.1_Missense_Mutation_p.R156W|PRKAG3_ENST00000392098.3_Silent_p.P324P|PRKAG3_ENST00000439262.2_Missense_Mutation_p.R315W			Q9UGI9	AAKG3_HUMAN	protein kinase, AMP-activated, gamma 3 non-catalytic subunit	340	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.		R -> Q. {ECO:0000269|PubMed:17878938}.|R -> W (in dbSNP:rs33985460). {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)	AAGGAGGGCCGGGGCAGCAGG	0.607													G|||	154	0.0307508	0.0038	0.0432	5008	,	,		18697	0.0		0.0606	False		,,,				2504	0.0593				p.R340W		Atlas-SNP	.											.	PRKAG3	47	.	0			c.C1018T						PASS	.	G	TRP/ARG	53,4353	54.2+/-90.2	0,53,2150	92.0	96.0	95.0		1018	3.8	1.0	2	dbSNP_126	95	493,8107	142.5+/-198.7	10,473,3817	yes	missense	PRKAG3	NM_017431.2	101	10,526,5967	AA,AG,GG		5.7326,1.2029,4.1981	possibly-damaging	340/490	219691801	546,12460	2203	4300	6503	SO:0001583	missense	53632	exon10			AGGGCCGGGGCAG	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.1018C>T	2.37:g.219691801G>A	ENSP00000436068:p.Arg340Trp	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	176	82	0.465909	NM_017431	Q4QQG8|Q4V779|Q9NRL1	Missense_Mutation	SNP	ENST00000529249.1	37	CCDS2424.1	60	0.027472527472527472	3	0.006097560975609756	10	0.027624309392265192	0	0.0	47	0.06200527704485488	G	22.0	4.227310	0.79576	0.012029	0.057326	ENSG00000115592	ENST00000439262;ENST00000545803;ENST00000529249	D;D;D	0.88046	-1.64;-2.33;-1.63	5.77	3.79	0.43588	Cystathionine beta-synthase, core (1);	0.342203	0.34046	N	0.004318	T	0.49525	0.1562	L	0.38175	1.15	0.80722	D	1	D	0.64830	0.994	P	0.53360	0.724	T	0.74396	-0.3679	10	0.62326	D	0.03	-7.7995	13.4251	0.61020	0.0:0.0:0.5987:0.4013	rs33985460	340	Q9UGI9	AAKG3_HUMAN	W	315;156;340	ENSP00000397133:R315W;ENSP00000444536:R156W;ENSP00000436068:R340W	ENSP00000233944:R340W	R	-	1	2	PRKAG3	219400045	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.596000	0.61055	1.440000	0.47531	0.655000	0.94253	CGG	G|0.961;A|0.039	0.039	strong		0.607	PRKAG3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385992.1		
FRG2B	441581	hgsc.bcm.edu	37	10	135440203	135440203	+	Missense_Mutation	SNP	A	A	T	rs200661929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135440203A>T	ENST00000425520.1	-	1	96	c.44T>A	c.(43-45)aTc>aAc	p.I15N	FRG2B_ENST00000443774.1_Missense_Mutation_p.I15N	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	15						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		GGAGCACTGGATGGAGGAGCA	0.507													.|||	867	0.173123	0.1437	0.1254	5008	,	,		19912	0.2411		0.0885	False		,,,				2504	0.2638				p.I15N		Atlas-SNP	.											FRG2B,NS,haematopoietic_neoplasm,0,1	FRG2B	47	1	0			c.T44A						scavenged	.	A	ASN/ILE	303,4103		0,303,1900	227.0	254.0	245.0		44	0.1	0.0	10		245	380,8220		0,380,3920	no	missense	FRG2B	NM_001080998.1	149	0,683,5820	TT,TA,AA		4.4186,6.877,5.2514	benign	15/279	135440203	683,12323	2203	4300	6503	SO:0001583	missense	441581	exon1			CACTGGATGGAGG	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.44T>A	10.37:g.135440203A>T	ENSP00000401310:p.Ile15Asn	Somatic	1248	0	0		WXS	Illumina HiSeq	Phase_I	1297	230	0.177332	NM_001080998	Q5VSQ1	Missense_Mutation	SNP	ENST00000425520.1	37	CCDS44502.1	.	.	.	.	.	.	.	.	.	.	.	3.902	-0.021862	0.07634	0.06877	0.044186	ENSG00000225899	ENST00000443774;ENST00000425520	T;T	0.44881	0.91;0.91	0.109	0.109	0.14578	.	2.975530	0.01571	N	0.020585	T	0.01905	0.0060	N	0.14661	0.345	0.09310	N	1	B	0.31859	0.343	B	0.24155	0.051	T	0.14227	-1.0480	9	0.87932	D	0	1.8074	.	.	.	.	15	Q96QU4	FRG2B_HUMAN	N	15	ENSP00000408343:I15N;ENSP00000401310:I15N	ENSP00000401310:I15N	I	-	2	0	FRG2B	135290193	0.957000	0.32711	0.030000	0.17652	0.030000	0.12068	0.803000	0.27083	0.156000	0.19299	0.155000	0.16302	ATC	A|0.986;T|0.014	0.014	strong		0.507	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
SACS	26278	hgsc.bcm.edu	37	13	23929189	23929189	+	Missense_Mutation	SNP	C	C	G	rs190617851		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23929189C>G	ENST00000382292.3	-	7	1835	c.1562G>C	c.(1561-1563)aGc>aCc	p.S521T	SACS_ENST00000402364.1_5'UTR|SACS_ENST00000382298.3_Missense_Mutation_p.S521T|SACS_ENST00000476776.1_5'Flank			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	521					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GAAATCAGAGCTCTTTTCCAT	0.458													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20393	0.0		0.0	False		,,,				2504	0.0				p.S521T		Atlas-SNP	.											.	SACS	871	.	0			c.G1562C						PASS	.	C	THR/SER	1,4405	2.1+/-5.4	0,1,2202	77.0	85.0	82.0		1562	2.3	0.0	13		82	0,8600		0,0,4300	no	missense	SACS	NM_014363.4	58	0,1,6502	GG,GC,CC		0.0,0.0227,0.0077	benign	521/4580	23929189	1,13005	2203	4300	6503	SO:0001583	missense	26278	exon8			TCAGAGCTCTTTT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.1562G>C	13.37:g.23929189C>G	ENSP00000371729:p.Ser521Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	12.48|12.48	1.950654|1.950654	0.34377|0.34377	2.27E-4|2.27E-4	0.0|0.0	ENSG00000151835|ENSG00000151835	ENST00000455470|ENST00000382292;ENST00000382298;ENST00000423156	.|T;T;T	.|0.21191	.|2.02;2.02;2.02	5.48|5.48	2.34|2.34	0.29019|0.29019	.|.	.|0.444341	.|0.27384	.|N	.|0.019604	T|T	0.11495|0.11495	0.0280|0.0280	L|L	0.34521|0.34521	1.04|1.04	0.26264|0.26264	N|N	0.978528|0.978528	.|B;B;B	.|0.31625	.|0.332;0.332;0.0	.|B;B;B	.|0.30572	.|0.075;0.117;0.002	T|T	0.24190|0.24190	-1.0167|-1.0167	5|10	.|0.14656	.|T	.|0.56	.|.	3.6068|3.6068	0.08045|0.08045	0.0:0.2101:0.4786:0.3113|0.0:0.2101:0.4786:0.3113	.|.	.|420;308;521	.|B2REB1;E9PAL4;Q9NZJ4	.|.;.;SACS_HUMAN	D|T	420|521;521;145	.|ENSP00000371729:S521T;ENSP00000371735:S521T;ENSP00000390925:S145T	.|ENSP00000371729:S521T	E|S	-|-	3|2	2|0	SACS|SACS	22827189|22827189	0.968000|0.968000	0.33430|0.33430	0.001000|0.001000	0.08648|0.08648	0.923000|0.923000	0.55619|0.55619	1.379000|1.379000	0.34340|0.34340	0.259000|0.259000	0.21709|0.21709	0.561000|0.561000	0.74099|0.74099	GAG|AGC	C|1.000;G|0.000	0.000	strong		0.458	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
MPG	4350	hgsc.bcm.edu	37	16	129654	129654	+	Silent	SNP	C	C	T	rs710081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:129654C>T	ENST00000219431.4	+	3	501	c.270C>T	c.(268-270)ttC>ttT	p.F90F	MPG_ENST00000475280.1_3'UTR|MPG_ENST00000397817.1_Silent_p.F73F	NM_002434.3	NP_002425.2	P29372	3MG_HUMAN	N-methylpurine-DNA glycosylase	90					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)	alkylbase DNA N-glycosylase activity (GO:0003905)|damaged DNA binding (GO:0003684)|DNA-3-methyladenine glycosylase activity (GO:0008725)|DNA-3-methylguanine glycosylase activity (GO:0052822)|DNA-7-methyladenine glycosylase activity (GO:0052821)|DNA-7-methylguanine glycosylase activity (GO:0043916)	p.F90F(1)		endometrium(4)|kidney(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)				GGTTGGAGTTCTTCGACCAGC	0.622								Base excision repair (BER), DNA glycosylases					N|||	1249	0.249401	0.6203	0.1484	5008	,	,		17330	0.1091		0.0119	False		,,,				2504	0.2086				p.F90F		Atlas-SNP	.											MPG,NS,carcinoma,0,1	MPG	26	1	1	Substitution - coding silent(1)	stomach(1)	c.C270T						PASS	.		,,	2097,2247		526,1045,601	20.0	26.0	24.0		255,219,270	-1.0	0.4	16	dbSNP_98	24	91,8463		2,87,4188	no	coding-synonymous,coding-synonymous,coding-synonymous	MPG	NM_001015052.1,NM_001015054.1,NM_002434.2	,,	528,1132,4789	TT,TC,CC		1.0638,48.2735,16.9639	,,	85/294,73/282,90/299	129654	2188,10710	2172	4277	6449	SO:0001819	synonymous_variant	4350	exon3			GGAGTTCTTCGAC		CCDS32345.1, CCDS32346.1, CCDS42087.1	16p13.3	2008-07-29			ENSG00000103152	ENSG00000103152	3.2.2.21		7211	protein-coding gene	gene with protein product	"""alkyladenine DNA glycosylase"""	156565				1874728	Standard	NM_002434		Approved	MDG	uc002cfo.4	P29372	OTTHUMG00000047887	ENST00000219431.4:c.270C>T	16.37:g.129654C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_002434	G5E9E2|Q13770|Q15275|Q15961|Q5J9I4|Q96BZ6|Q96S33|Q9NNX5	Silent	SNP	ENST00000219431.4	37	CCDS32346.1																																																																																			C|0.762;T|0.238	0.238	strong		0.622	MPG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109121.4		
FCGR3A	2214	hgsc.bcm.edu	37	1	161518297	161518297	+	Missense_Mutation	SNP	G	G	T	rs52820103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161518297G>T	ENST00000436743.1	-	4	387	c.233C>A	c.(232-234)gCt>gAt	p.A78D	FCGR3A_ENST00000443193.1_Missense_Mutation_p.A113D|RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000540048.1_Missense_Mutation_p.A78D|FCGR3A_ENST00000367969.3_Missense_Mutation_p.A114D|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)	78	Ig-like C2-type 1.				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)	GACTGTGGCAGCGTCAATGAA	0.547																																					p.A114D		Atlas-SNP	.											FCGR3A,NS,carcinoma,-1,1	FCGR3A	38	1	0			c.C341A						PASS	.	G	ASP/ALA,ASP/ALA,ASP/ALA,ASP/ALA,ASP/ALA	55,4351	49.6+/-84.7	1,53,2149	297.0	276.0	283.0		230,233,233,338,341	-8.9	0.0	1	dbSNP_128	283	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	FCGR3A	NM_001127596.1,NM_001127595.1,NM_001127593.1,NM_001127592.1,NM_000569.6	126,126,126,126,126	1,53,6449	TT,TG,GG		0.0,1.2483,0.4229	benign,benign,benign,benign,benign	77/254,78/255,78/255,113/290,114/291	161518297	55,12951	2203	4300	6503	SO:0001583	missense	2214	exon3			GTGGCAGCGTCAA	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.233C>A	1.37:g.161518297G>T	ENSP00000416607:p.Ala78Asp	Somatic	638	0	0		WXS	Illumina HiSeq	Phase_I	770	215	0.279221	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.332|3.332	-0.136371|-0.136371	0.06711|0.06711	0.012483|0.012483	0.0|0.0	ENSG00000203747|ENSG00000203747	ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048;ENST00000442336|ENST00000426740	T;T;T;T;T;T|.	0.07216|.	3.21;3.21;3.21;3.21;3.21;3.21|.	4.43|4.43	-8.86|-8.86	0.00795|0.00795	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	2.422050|.	0.01662|.	N|.	0.025162|.	T|T	0.04003|0.04003	0.0112|0.0112	N|N	0.12746|0.12746	0.255|0.255	0.09310|0.09310	N|N	1|1	B;B;B|.	0.12013|.	0.0;0.0;0.005|.	B;B;B|.	0.09377|.	0.002;0.002;0.004|.	T|T	0.10382|0.10382	-1.0632|-1.0632	10|5	0.30854|.	T|.	0.27|.	.|.	7.9762|7.9762	0.30155|0.30155	0.0652:0.155:0.1371:0.6428|0.0652:0.155:0.1371:0.6428	rs52820103|rs52820103	78;113;78|.	P08637;E9PG94;Q9UPY7|.	FCG3A_HUMAN;.;.|.	D|M	114;113;78;78;78;77|95	ENSP00000356946:A114D;ENSP00000392047:A113D;ENSP00000416607:A78D;ENSP00000356944:A78D;ENSP00000444971:A78D;ENSP00000396567:A77D|.	ENSP00000356944:A78D|.	A|L	-|-	2|1	0|2	FCGR3A|FCGR3A	159784921|159784921	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.930000|-1.930000	0.01557|0.01557	-3.913000|-3.913000	0.00092|0.00092	-0.467000|-0.467000	0.05162|0.05162	GCT|CTG	G|0.994;T|0.006	0.006	strong		0.547	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
CCDC88C	440193	hgsc.bcm.edu	37	14	91744348	91744348	+	Missense_Mutation	SNP	C	C	T	rs114849211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91744348C>T	ENST00000389857.6	-	29	5062	c.4976G>A	c.(4975-4977)cGg>cAg	p.R1659Q	CCDC88C_ENST00000331194.7_Missense_Mutation_p.R183Q	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1659					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)	p.R1659Q(2)|p.R183Q(1)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				CGAGCAGGGCCGCACTCCGAC	0.677													C|||	52	0.0103834	0.0386	0.0014	5008	,	,		17086	0.0		0.0	False		,,,				2504	0.0				p.R1659Q		Atlas-SNP	.											KIAA1509,caecum,carcinoma,-1,6	CCDC88C	192	6	3	Substitution - Missense(3)	urinary_tract(3)	c.G4976A						PASS	.	C	GLN/ARG	103,3867		0,103,1882	12.0	15.0	14.0		4976	4.5	0.2	14	dbSNP_132	14	1,8315		0,1,4157	yes	missense	CCDC88C	NM_001080414.3	43	0,104,6039	TT,TC,CC		0.012,2.5945,0.8465	probably-damaging	1659/2029	91744348	104,12182	1985	4158	6143	SO:0001583	missense	440193	exon29			CAGGGCCGCACTC		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.4976G>A	14.37:g.91744348C>T	ENSP00000374507:p.Arg1659Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	103	57	0.553398	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	16.75	3.209248	0.58343	0.025945	1.2E-4	ENSG00000015133	ENST00000389857;ENST00000427583;ENST00000331194	T;T	0.55930	2.19;0.49	5.55	4.47	0.54385	.	0.000000	0.47455	U	0.000221	T	0.40423	0.1116	L	0.54323	1.7	0.09310	N	0.999999	D;P;P	0.89917	1.0;0.812;0.812	D;B;B	0.80764	0.994;0.141;0.141	T	0.44757	-0.9307	10	0.72032	D	0.01	-41.3463	9.9503	0.41634	0.0:0.8456:0.0:0.1544	.	1659;183;109	Q9P219;Q9P219-2;Q9P219-3	DAPLE_HUMAN;.;.	Q	1659;183;183	ENSP00000374507:R1659Q;ENSP00000330332:R183Q	ENSP00000330332:R183Q	R	-	2	0	CCDC88C	90814101	0.903000	0.30736	0.169000	0.22859	0.580000	0.36256	2.140000	0.42159	2.608000	0.88229	0.462000	0.41574	CGG	C|0.994;T|0.006	0.006	strong		0.677	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
WNT4	54361	hgsc.bcm.edu	37	1	22446768	22446768	+	Silent	SNP	G	G	A	rs34228276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:22446768G>A	ENST00000290167.6	-	5	874	c.831C>T	c.(829-831)ccC>ccT	p.P277P	WNT4_ENST00000542383.1_Silent_p.P222P	NM_030761.4	NP_110388.2	P56705	WNT4_HUMAN	wingless-type MMTV integration site family, member 4	277			P -> L (in dbSNP:rs34228276).		adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to starvation (GO:0009267)|cellular response to transforming growth factor beta stimulus (GO:0071560)|embryonic epithelial tube formation (GO:0001838)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization to plasma membrane (GO:0090002)|female gonad development (GO:0008585)|female sex determination (GO:0030237)|immature T cell proliferation in thymus (GO:0033080)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|mammary gland epithelium development (GO:0061180)|mesenchymal to epithelial transition (GO:0060231)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric nephron morphogenesis (GO:0072273)|metanephric tubule formation (GO:0072174)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell migration (GO:0030336)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of gene expression (GO:0010629)|negative regulation of male gonad development (GO:2000019)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of testicular blood vessel morphogenesis (GO:0061369)|negative regulation of testosterone biosynthetic process (GO:2000225)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of wound healing (GO:0061045)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via MAPK cascade (GO:0038030)|oocyte development (GO:0048599)|paramesonephric duct development (GO:0061205)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cortisol biosynthetic process (GO:2000066)|positive regulation of dermatome development (GO:0061184)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of meiosis (GO:0045836)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|protein palmitoylation (GO:0018345)|regulation of cell-cell adhesion (GO:0022407)|renal vesicle formation (GO:0072033)|renal vesicle induction (GO:0072034)|smooth muscle cell differentiation (GO:0051145)|somatotropin secreting cell differentiation (GO:0060126)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|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)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	8		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-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;9.02e-26)|Colorectal(126;1.71e-07)|COAD - Colon adenocarcinoma(152;1.17e-05)|GBM - Glioblastoma multiforme(114;2.01e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000568)|KIRC - Kidney renal clear cell carcinoma(1967;0.00277)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CACAGAAGTCGGGGCTAGGCT	0.647													G|||	117	0.0233626	0.0582	0.0173	5008	,	,		19089	0.003		0.0229	False		,,,				2504	0.002				p.P277P		Atlas-SNP	.											.	WNT4	33	.	0			c.C831T						PASS	.	G		288,4118	158.9+/-191.5	8,272,1923	121.0	102.0	108.0		831	-6.9	0.9	1	dbSNP_126	108	180,8420	82.0+/-144.6	0,180,4120	no	coding-synonymous	WNT4	NM_030761.4		8,452,6043	AA,AG,GG		2.093,6.5365,3.5983		277/352	22446768	468,12538	2203	4300	6503	SO:0001819	synonymous_variant	54361	exon5			GAAGTCGGGGCTA	AL031281	CCDS223.1	1p36.23-p35.1	2013-02-28			ENSG00000162552	ENSG00000162552		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12783	protein-coding gene	gene with protein product		603490				8168088	Standard	NM_030761		Approved	WNT-4	uc001bfs.4	P56705	OTTHUMG00000002894	ENST00000290167.6:c.831C>T	1.37:g.22446768G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	204	103	0.504902	NM_030761	B4DJF9|Q5TZQ0|Q96T81|Q9BXF5|Q9H1J8|Q9UJM2	Silent	SNP	ENST00000290167.6	37	CCDS223.1																																																																																			G|0.968;A|0.032	0.032	strong		0.647	WNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008088.2		
ZNF469	84627	hgsc.bcm.edu	37	16	88504483	88504483	+	Silent	SNP	C	C	G	rs375672779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88504483C>G	ENST00000437464.1	+	2	10521	c.10521C>G	c.(10519-10521)acC>acG	p.T3507T	ZNF469_ENST00000565624.1_Silent_p.T3535T	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	3507					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						ACCCCGTGACCCACCCGATCA	0.647													C|||	5	0.000998403	0.0038	0.0	5008	,	,		14786	0.0		0.0	False		,,,				2504	0.0				p.T3507T		Atlas-SNP	.											.	ZNF469	121	.	0			c.C10521G						PASS	.	C		6,1378		0,6,686	53.0	61.0	59.0		10521	1.2	0.0	16		59	0,3182		0,0,1591	no	coding-synonymous	ZNF469	NM_001127464.1		0,6,2277	GG,GC,CC		0.0,0.4335,0.1314		3507/3926	88504483	6,4560	692	1591	2283	SO:0001819	synonymous_variant	84627	exon2			CGTGACCCACCCG	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.10521C>G	16.37:g.88504483C>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	50	0.617284	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			.	.	weak		0.647	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
RP1L1	94137	hgsc.bcm.edu	37	8	10464465	10464465	+	Silent	SNP	G	G	A	rs112520779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10464465G>A	ENST00000382483.3	-	4	7366	c.7143C>T	c.(7141-7143)ctC>ctT	p.L2381L		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2461					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)		CAGTGGGGGCGAGACTTCCGA	0.547													G|||	14	0.00279553	0.0106	0.0	5008	,	,		17836	0.0		0.0	False		,,,				2504	0.0				p.L2381L		Atlas-SNP	.											RP1L1,NS,carcinoma,-2,1	RP1L1	453	1	0			c.C7143T						PASS	.	G		26,3806		0,26,1890	109.0	115.0	113.0		7143	-6.4	0.0	8	dbSNP_132	113	0,8232		0,0,4116	no	coding-synonymous	RP1L1	NM_178857.5		0,26,6006	AA,AG,GG		0.0,0.6785,0.2155		2381/2401	10464465	26,12038	1916	4116	6032	SO:0001819	synonymous_variant	94137	exon4			GGGGGCGAGACTT	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.7143C>T	8.37:g.10464465G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	65	43	0.661538	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			A|0.002;G|0.998;T|0.000	0.002	strong		0.547	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
BTNL8	79908	hgsc.bcm.edu	37	5	180335743	180335743	+	Silent	SNP	C	C	T	rs112784813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180335743C>T	ENST00000340184.4	+	2	413	c.207C>T	c.(205-207)gaC>gaT	p.D69D	BTNL8_ENST00000505126.1_5'Flank|BTNL8_ENST00000231229.4_Silent_p.D69D|BTNL8_ENST00000400707.3_Intron|Y_RNA_ENST00000410920.1_RNA|BTNL8_ENST00000511704.1_Intron|BTNL8_ENST00000508408.1_Silent_p.D69D|BTNL8_ENST00000533815.2_5'Flank	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	69	Ig-like V-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCTACAGGGACGGGAAGGACC	0.537													C|||	806	0.160942	0.4614	0.0447	5008	,	,		19209	0.0992		0.006	False		,,,				2504	0.0603				p.D69D		Atlas-SNP	.											.	BTNL8	114	.	0			c.C207T						PASS	.	C	,,,,	1810,2596	531.1+/-373.1	389,1032,782	170.0	166.0	167.0		207,,207,,207	-5.5	0.0	5	dbSNP_132	167	36,8564	24.0+/-70.4	0,36,4264	no	coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_024850.2	,,,,	389,1068,5046	TT,TC,CC		0.4186,41.0803,14.1934	,,,,	69/501,,69/341,,69/348	180335743	1846,11160	2203	4300	6503	SO:0001819	synonymous_variant	79908	exon2			CAGGGACGGGAAG	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.207C>T	5.37:g.180335743C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	163	163	1	NM_001159708	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Silent	SNP	ENST00000340184.4	37	CCDS43413.1																																																																																			C|0.866;T|0.134	0.134	strong		0.537	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
MT-ND4	4538	hgsc.bcm.edu	37	M	11959	11959	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11959A>G	ENST00000361381.2	+	1	1200	c.1200A>G	c.(1198-1200)atA>atG	p.I400M	MT-TS2_ENST00000387449.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	400					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						GGACTCAACATACTAGTCACA	0.453																																					p.M400M		Atlas-SNP	.											.	.	.	.	0			c.A1200G						PASS	.																																			SO:0001583	missense	0	exon1			CAACATACTAGTC			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1200A>G	M.37:g.11959A>G	ENSP00000354961:p.Ile400Met	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	9	8	0.888889	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.453	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
TTN	7273	hgsc.bcm.edu	37	2	179434516	179434516	+	Missense_Mutation	SNP	C	C	T	rs3813243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179434516C>T	ENST00000591111.1	-	276	71644	c.71420G>A	c.(71419-71421)aGt>aAt	p.S23807N	TTN_ENST00000342175.6_Missense_Mutation_p.S16575N|TTN_ENST00000359218.5_Missense_Mutation_p.S16508N|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S16383N|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S25448N|TTN_ENST00000342992.6_Missense_Mutation_p.S22880N|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23807	Fibronectin type-III 73. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> N. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCACCAACACTCACATCACA	0.368													C|||	397	0.0792732	0.0855	0.0418	5008	,	,		21664	0.1736		0.0328	False		,,,				2504	0.0481				p.S25448N		Atlas-SNP	.											.	TTN	18412	.	0			c.G76343A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER,ASN/SER	241,3527		8,225,1651	146.0	131.0	135.0		49148,68639,49523,49724	5.9	1.0	2	dbSNP_107	135	167,8095		4,159,3968	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	46,46,46,46	12,384,5619	TT,TC,CC		2.0213,6.396,3.3915	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	16383/26927,22880/33424,16508/27052,16575/27119	179434516	408,11622	1884	4131	6015	SO:0001583	missense	7273	exon326			CCAACACTCACAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.71420G>A	2.37:g.179434516C>T	ENSP00000465570:p.Ser23807Asn	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	40	0.588235	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		177	0.08104395604395605	37	0.07520325203252033	16	0.04419889502762431	101	0.17657342657342656	23	0.030343007915567283	C	12.11	1.839419	0.32513	0.06396	0.020213	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	5.92	5.92	0.95590	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00073	0.0002	N	0.17800	0.525	0.28382	P	0.9194971	P;P;P;P	0.43231	0.801;0.801;0.801;0.684	B;B;B;B	0.38106	0.265;0.265;0.265;0.197	T	0.03095	-1.1073	8	0.87932	D	0	.	20.3081	0.98638	0.0:1.0:0.0:0.0	rs3813243;rs52789452;rs3813243	16383;16508;16575;23807	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	22880;16383;16575;16508;16381	ENSP00000343764:S22880N;ENSP00000434586:S16383N;ENSP00000340554:S16575N;ENSP00000352154:S16508N	ENSP00000340554:S16575N	S	-	2	0	TTN	179142762	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.542000	0.53625	2.795000	0.96236	0.655000	0.94253	AGT	C|0.918;T|0.082	0.082	strong		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MUC17	140453	hgsc.bcm.edu	37	7	100678481	100678481	+	Missense_Mutation	SNP	A	A	T	rs73168389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678481A>T	ENST00000306151.4	+	3	3848	c.3784A>T	c.(3784-3786)Acc>Tcc	p.T1262S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1262	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)					CTCTCCTACAACCGCTGAAGG	0.527																																					p.T1262S		Atlas-SNP	.											.	MUC17	804	.	0			c.A3784T						PASS	.	T	SER/THR	586,3820		0,586,1617	284.0	275.0	278.0		3784	-0.9	0.0	7	dbSNP_130	278	392,8208		0,392,3908	no	missense	MUC17	NM_001040105.1	58	0,978,5525	TT,TA,AA		4.5581,13.3,7.5196	probably-damaging	1262/4494	100678481	978,12028	2203	4300	6503	SO:0001583	missense	140453	exon3			CCTACAACCGCTG	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.3784A>T	7.37:g.100678481A>T	ENSP00000302716:p.Thr1262Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	133	22	0.165414	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	0.067	-1.210490	0.01555	0.133	0.045581	ENSG00000169876	ENST00000306151	T	0.02323	4.34	0.438	-0.877	0.10621	.	.	.	.	.	T	0.00039	0.0001	N	0.14661	0.345	0.09310	N	1	D	0.55385	0.971	B	0.42188	0.379	T	0.20538	-1.0272	8	0.06494	T	0.89	.	.	.	.	.	1262	Q685J3	MUC17_HUMAN	S	1262	ENSP00000302716:T1262S	ENSP00000302716:T1262S	T	+	1	0	MUC17	100465201	0.001000	0.12720	0.002000	0.10522	0.004000	0.04260	-1.637000	0.02015	-1.145000	0.02858	-1.640000	0.00773	ACC	A|0.973;T|0.027	0.027	strong		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FUCA2	2519	hgsc.bcm.edu	37	6	143823112	143823112	+	Missense_Mutation	SNP	G	G	A	rs3762001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:143823112G>A	ENST00000002165.6	-	5	1166	c.1111C>T	c.(1111-1113)Cat>Tat	p.H371Y	FUCA2_ENST00000367585.1_5'UTR|RP1-20N2.6_ENST00000415586.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|RP1-20N2.6_ENST00000589489.1_RNA|RP1-20N2.6_ENST00000591189.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA|FUCA2_ENST00000438118.2_3'UTR|RP1-20N2.6_ENST00000593045.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000593175.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	371			H -> Y (in dbSNP:rs3762001). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743}.		fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		CGCCAGGTATGGGTTTCATAA	0.428													G|||	852	0.170128	0.1233	0.1484	5008	,	,		15192	0.1696		0.2247	False		,,,				2504	0.1933				p.H371Y		Atlas-SNP	.											FUCA2,NS,carcinoma,0,1	FUCA2	28	1	0			c.C1111T						PASS	.	G	TYR/HIS	676,3730	286.3+/-278.7	52,572,1579	108.0	108.0	108.0		1111	-1.4	0.0	6	dbSNP_107	108	1934,6666	342.2+/-324.4	213,1508,2579	yes	missense	FUCA2	NM_032020.4	83	265,2080,4158	AA,AG,GG		22.4884,15.3427,20.0677	benign	371/468	143823112	2610,10396	2203	4300	6503	SO:0001583	missense	2519	exon5			AGGTATGGGTTTC	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1111C>T	6.37:g.143823112G>A	ENSP00000002165:p.His371Tyr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	398	0.18223443223443223	71	0.1443089430894309	47	0.1298342541436464	104	0.18181818181818182	176	0.23218997361477572	G	9.312	1.055759	0.19907	0.153427	0.224884	ENSG00000001036	ENST00000002165;ENST00000451668	T;T	0.70045	0.56;-0.45	5.98	-1.41	0.08941	.	0.825483	0.11409	N	0.566960	T	0.31451	0.0797	L	0.29908	0.895	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.12863	-1.0531	9	0.59425	D	0.04	-0.0053	8.8493	0.35190	0.134:0.0:0.3068:0.5592	rs3762001;rs17854673;rs17857722;rs52815197;rs61174998;rs3762001	50;371	Q7Z6V2;Q9BTY2	.;FUCO2_HUMAN	Y	371;50	ENSP00000002165:H371Y;ENSP00000398119:H50Y	ENSP00000002165:H371Y	H	-	1	0	FUCA2	143864805	0.556000	0.26538	0.001000	0.08648	0.726000	0.41606	1.172000	0.31908	-0.144000	0.11314	0.650000	0.86243	CAT	G|0.804;A|0.196	0.196	strong		0.428	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
PTPN13	5783	hgsc.bcm.edu	37	4	87696470	87696470	+	Silent	SNP	A	A	G	rs12507034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:87696470A>G	ENST00000411767.2	+	34	5718	c.5655A>G	c.(5653-5655)acA>acG	p.T1885T	PTPN13_ENST00000427191.2_Silent_p.T1866T|PTPN13_ENST00000436978.1_Silent_p.T1890T|PTPN13_ENST00000511467.1_Silent_p.T1890T|PTPN13_ENST00000316707.6_Silent_p.T1694T			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1885	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CGGACATAACACTAACGTGCA	0.383													A|||	353	0.0704872	0.1074	0.0677	5008	,	,		19265	0.0079		0.1143	False		,,,				2504	0.0419				p.T1890T		Atlas-SNP	.											.	PTPN13	203	.	0			c.A5670G						PASS	.	A	,,,	372,3362		19,334,1514	83.0	76.0	78.0		5598,5655,5082,5670	-0.6	0.0	4	dbSNP_120	78	996,7220		61,874,3173	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	,,,	80,1208,4687	GG,GA,AA		12.1227,9.9625,11.4477	,,,	1866/2467,1885/2486,1694/2295,1890/2491	87696470	1368,10582	1867	4108	5975	SO:0001819	synonymous_variant	5783	exon34			CATAACACTAACG		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.5655A>G	4.37:g.87696470A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	164	74	0.451219	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			A|0.906;G|0.094	0.094	strong		0.383	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
GOLT1A	127845	hgsc.bcm.edu	37	1	204172096	204172096	+	Silent	SNP	G	G	A	rs6689607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204172096G>A	ENST00000308302.3	-	2	230	c.45C>T	c.(43-45)acC>acT	p.T15T	GOLT1A_ENST00000475517.1_5'Flank	NM_198447.1	NP_940849.1			golgi transport 1A											kidney(1)|lung(2)|urinary_tract(1)	4	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.244)			TGCCGAAACCGGTGATCCCCA	0.562													G|||	456	0.0910543	0.2352	0.0836	5008	,	,		18927	0.006		0.0517	False		,,,				2504	0.0297				p.T15T		Atlas-SNP	.											GOLT1A,caecum,carcinoma,0,1	GOLT1A	15	1	0			c.C45T						PASS	.	G		972,3434	365.1+/-317.3	122,728,1353	103.0	90.0	94.0		45	-11.3	0.2	1	dbSNP_116	94	470,8130	139.8+/-196.4	8,454,3838	no	coding-synonymous	GOLT1A	NM_198447.1		130,1182,5191	AA,AG,GG		5.4651,22.0608,11.0872		15/133	204172096	1442,11564	2203	4300	6503	SO:0001819	synonymous_variant	127845	exon2			GAAACCGGTGATC	BC058832	CCDS1443.1	1q32.1	2010-06-24	2010-06-24		ENSG00000174567	ENSG00000174567			24766	protein-coding gene	gene with protein product			"""golgi transport 1 homolog A (S. cerevisiae)"""			12477932	Standard	NM_198447		Approved	FLJ42654, CGI-141, YMR292W, GOT1, MGC62027	uc001has.1	Q6ZVE7	OTTHUMG00000036056	ENST00000308302.3:c.45C>T	1.37:g.204172096G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	194	99	0.510309	NM_198447		Silent	SNP	ENST00000308302.3	37	CCDS1443.1																																																																																			G|0.898;A|0.102	0.102	strong		0.562	GOLT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087887.1	NM_198447	
ROBO1	6091	hgsc.bcm.edu	37	3	79174619	79174619	+	Silent	SNP	C	C	T	rs139237706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:79174619C>T	ENST00000464233.1	-	3	272	c.159G>A	c.(157-159)tcG>tcA	p.S53S		NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	53					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)		TATAGCCCAGCGAATTGTCAT	0.488													C|||	6	0.00119808	0.003	0.0014	5008	,	,		17914	0.0		0.0	False		,,,				2504	0.001				p.S53S		Atlas-SNP	.											.	ROBO1	833	.	0			c.G159A						PASS	.	C		11,3935		0,11,1962	139.0	134.0	135.0		159	5.4	1.0	3	dbSNP_134	135	0,8292		0,0,4146	no	coding-synonymous	ROBO1	NM_002941.3		0,11,6108	TT,TC,CC		0.0,0.2788,0.0899		53/1652	79174619	11,12227	1973	4146	6119	SO:0001819	synonymous_variant	6091	exon3			GCCCAGCGAATTG	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.159G>A	3.37:g.79174619C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	195	94	0.482051	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																			C|0.998;T|0.002	0.002	strong		0.488	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
KANK3	256949	hgsc.bcm.edu	37	19	8399272	8399272	+	Silent	SNP	G	G	A	rs8106699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8399272G>A	ENST00000593649.1	-	4	1424	c.1359C>T	c.(1357-1359)gaC>gaT	p.D453D	KANK3_ENST00000330915.3_Silent_p.D453D			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	453										breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						CAGGTGTGCCGTCTCTCTTCT	0.622													G|||	650	0.129792	0.2413	0.1239	5008	,	,		16175	0.0327		0.1153	False		,,,				2504	0.0982				p.D453D		Atlas-SNP	.											.	KANK3	35	.	0			c.C1359T						PASS	.	G		923,3483	351.3+/-311.2	89,745,1369	55.0	54.0	54.0		1359	-4.9	0.0	19	dbSNP_116	54	972,7626	212.0+/-252.4	67,838,3394	no	coding-synonymous	KANK3	NM_198471.2		156,1583,4763	AA,AG,GG		11.305,20.9487,14.5724		453/822	8399272	1895,11109	2203	4299	6502	SO:0001819	synonymous_variant	256949	exon4			TGTGCCGTCTCTC	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.1359C>T	19.37:g.8399272G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	Silent	SNP	ENST00000593649.1	37																																																																																				G|0.859;A|0.141	0.141	strong		0.622	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102466430	102466430	+	Silent	SNP	G	G	A	rs34690489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102466430G>A	ENST00000360184.4	+	17	4073	c.3909G>A	c.(3907-3909)gcG>gcA	p.A1303A		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1303	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						CCAAGGAGGCGCTGGAATTGA	0.567													g|||	57	0.0113818	0.028	0.0159	5008	,	,		19910	0.0		0.008	False		,,,				2504	0.001				p.A1303A		Atlas-SNP	.											DYNC1H1,colon,carcinoma,+1,1	DYNC1H1	395	1	0			c.G3909A						PASS	.			111,4295	85.3+/-124.0	3,105,2095	104.0	93.0	97.0		3909	-10.9	0.5	14	dbSNP_126	97	97,8503	53.1+/-113.8	2,93,4205	no	coding-synonymous	DYNC1H1	NM_001376.4		5,198,6300	AA,AG,GG		1.1279,2.5193,1.5993		1303/4647	102466430	208,12798	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon17			GGAGGCGCTGGAA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.3909G>A	14.37:g.102466430G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			G|0.984;A|0.016	0.016	strong		0.567	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
ALDH1L2	160428	hgsc.bcm.edu	37	12	105434467	105434467	+	Silent	SNP	C	C	T	rs11112330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	94	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	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	
SPEN	23013	hgsc.bcm.edu	37	1	16260916	16260916	+	Silent	SNP	C	C	T	rs848211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16260916C>T	ENST00000375759.3	+	11	8385	c.8181C>T	c.(8179-8181)gcC>gcT	p.A2727A		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2727	Interaction with RBPSUH. {ECO:0000250}.				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)		CAGTCAATGCCGCTGCGAGTG	0.592													C|||	607	0.121206	0.0212	0.2406	5008	,	,		19485	0.2232		0.0984	False		,,,				2504	0.09				p.A2727A		Atlas-SNP	.											SPEN,NS,carcinoma,+1,1	SPEN	374	1	0			c.C8181T						PASS	.	C		189,4217	119.2+/-156.9	6,177,2020	79.0	75.0	76.0		8181	-5.5	0.0	1	dbSNP_86	76	870,7730	197.6+/-242.2	47,776,3477	no	coding-synonymous	SPEN	NM_015001.2		53,953,5497	TT,TC,CC		10.1163,4.2896,8.1424		2727/3665	16260916	1059,11947	2203	4300	6503	SO:0001819	synonymous_variant	23013	exon11			CAATGCCGCTGCG		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.8181C>T	1.37:g.16260916C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	69	25	0.362319	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	37	CCDS164.1																																																																																			C|0.897;T|0.103	0.103	strong		0.592	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
TGM6	343641	hgsc.bcm.edu	37	20	2411118	2411118	+	Missense_Mutation	SNP	T	T	A	rs142406714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2411118T>A	ENST00000202625.2	+	11	1766	c.1705T>A	c.(1705-1707)Tac>Aac	p.Y569N	TGM6_ENST00000381423.1_Missense_Mutation_p.Y569N	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	569					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	TACAATATCTTACTCTAAGTA	0.458													T|||	3	0.000599042	0.0023	0.0	5008	,	,		19164	0.0		0.0	False		,,,				2504	0.0				p.Y569N		Atlas-SNP	.											.	TGM6	126	.	0			c.T1705A						PASS	.	T	ASN/TYR	5,4401	9.9+/-24.2	0,5,2198	92.0	87.0	88.0		1705	5.9	1.0	20	dbSNP_134	88	0,8600		0,0,4300	yes	missense	TGM6	NM_198994.2	143	0,5,6498	AA,AT,TT		0.0,0.1135,0.0384	probably-damaging	569/707	2411118	5,13001	2203	4300	6503	SO:0001583	missense	343641	exon11			ATATCTTACTCTA	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1705T>A	20.37:g.2411118T>A	ENSP00000202625:p.Tyr569Asn	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	70	41	0.585714	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Missense_Mutation	SNP	ENST00000202625.2	37	CCDS13025.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.069978	0.76301	0.001135	0.0	ENSG00000166948	ENST00000202625;ENST00000381423	T;T	0.71341	-0.56;-0.56	5.88	5.88	0.94601	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.203565	0.43919	D	0.000512	D	0.84428	0.5470	M	0.83384	2.64	0.43846	D	0.996433	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	D	0.86612	0.1873	10	0.87932	D	0	-31.5353	12.6797	0.56914	0.0:0.0:0.0:1.0	.	569;569	O95932-2;O95932	.;TGM3L_HUMAN	N	569	ENSP00000202625:Y569N;ENSP00000370831:Y569N	ENSP00000202625:Y569N	Y	+	1	0	TGM6	2359118	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	4.493000	0.60341	2.242000	0.73789	0.533000	0.62120	TAC	T|1.000;A|0.000	0.000	weak		0.458	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
OR9K2	441639	hgsc.bcm.edu	37	12	55524314	55524314	+	Silent	SNP	T	T	C	rs7137261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	124	0	0		WXS	Illumina HiSeq	Phase_I	156	87	0.557692	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		
RFC5	5985	hgsc.bcm.edu	37	12	118465820	118465820	+	Silent	SNP	T	T	C	rs5745873	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:118465820T>C	ENST00000454402.2	+	9	974	c.856T>C	c.(856-858)Ttg>Ctg	p.L286L	RFC5_ENST00000543153.1_3'UTR|RFC5_ENST00000229043.3_Silent_p.L201L|RFC5_ENST00000392542.2_Silent_p.L265L	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	286					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGAGATACACTTGTTTGTGCA	0.458													T|||	474	0.0946486	0.2489	0.0461	5008	,	,		17914	0.0		0.0964	False		,,,				2504	0.0164				p.L286L		Atlas-SNP	.											.	RFC5	35	.	0			c.T856C						PASS	.	T	,,,	993,3413	370.8+/-319.7	114,765,1324	122.0	112.0	115.0		601,847,856,793	-1.5	1.0	12	dbSNP_114	115	696,7904	172.2+/-222.9	21,654,3625	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RFC5	NM_001130112.2,NM_001206801.1,NM_007370.5,NM_181578.3	,,,	135,1419,4949	CC,CT,TT		8.093,22.5374,12.9863	,,,	201/256,283/338,286/341,265/320	118465820	1689,11317	2203	4300	6503	SO:0001819	synonymous_variant	5985	exon9			ATACACTTGTTTG		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"""ATPases / AAA-type"""	9973	protein-coding gene	gene with protein product		600407	"""replication factor C (activator 1) 5 (36.5kD)"""			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.856T>C	12.37:g.118465820T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	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	
UBR4	23352	hgsc.bcm.edu	37	1	19500830	19500830	+	Missense_Mutation	SNP	T	T	G	rs143098074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19500830T>G	ENST00000375254.3	-	22	2992	c.2965A>C	c.(2965-2967)Aag>Cag	p.K989Q	UBR4_ENST00000375226.2_Missense_Mutation_p.K989Q|UBR4_ENST00000375267.2_Missense_Mutation_p.K989Q|UBR4_ENST00000375217.2_Missense_Mutation_p.K989Q	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	989					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)			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)		GTTACATTCTTGTTTTCCTTT	0.423													T|||	9	0.00179712	0.0068	0.0	5008	,	,		19353	0.0		0.0	False		,,,				2504	0.0				p.K989Q		Atlas-SNP	.											.	UBR4	415	.	0			c.A2965C						PASS	.	T	GLN/LYS	7,4399	12.9+/-30.5	0,7,2196	155.0	131.0	139.0		2965	5.8	1.0	1	dbSNP_134	139	0,8600		0,0,4300	yes	missense	UBR4	NM_020765.2	53	0,7,6496	GG,GT,TT		0.0,0.1589,0.0538	benign	989/5184	19500830	7,12999	2203	4300	6503	SO:0001583	missense	23352	exon22			CATTCTTGTTTTC	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.2965A>C	1.37:g.19500830T>G	ENSP00000364403:p.Lys989Gln	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	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	.	.	.	.	.	.	.	.	.	.	T	16.68	3.189502	0.57909	0.001589	0.0	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.25912	1.78;1.78;1.78;1.77	5.76	5.76	0.90799	.	0.104877	0.64402	D	0.000006	T	0.21921	0.0528	L	0.36672	1.1	0.80722	D	1	P	0.34522	0.455	B	0.31869	0.137	T	0.02885	-1.1098	10	0.29301	T	0.29	.	15.7251	0.77751	0.0:0.0:0.0:1.0	.	989	Q5T4S7	UBR4_HUMAN	Q	989;989;989;989;205	ENSP00000364403:K989Q;ENSP00000364416:K989Q;ENSP00000364365:K989Q;ENSP00000364374:K989Q	ENSP00000364365:K989Q	K	-	1	0	UBR4	19373417	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.368000	0.79567	2.197000	0.70478	0.533000	0.62120	AAG	T|0.999;G|0.001	0.001	strong		0.423	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
DEFA3	1668	hgsc.bcm.edu	37	8	6873603	6873603	+	Missense_Mutation	SNP	T	T	G	rs145076681		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:6873603T>G	ENST00000327857.2	-	3	285	c.194A>C	c.(193-195)gAc>gCc	p.D65A	DEFA1B_ENST00000535841.1_Intron	NM_005217.3	NP_005208.1	P59666	DEF3_HUMAN	defensin, alpha 3, neutrophil-specific	65					antibacterial humoral response (GO:0019731)|defense response to fungus (GO:0050832)|defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular estrogen receptor signaling pathway (GO:0030520)|killing of cells of other organism (GO:0031640)	azurophil granule lumen (GO:0035578)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.D65A(1)		endometrium(1)|prostate(2)	3				COAD - Colon adenocarcinoma(149;0.0561)|READ - Rectum adenocarcinoma(644;0.118)		GCAATAGCAGTCCATGTTTTT	0.498																																					p.D65A		Atlas-SNP	.											DEFA3,NS,carcinoma,0,1	DEFA3	7	1	1	Substitution - Missense(1)	prostate(1)	c.A194C						scavenged	.						156.0	118.0	130.0					8																	6873603		1957	4128	6085	SO:0001583	missense	1668	exon3			TAGCAGTCCATGT	M23281	CCDS5962.1	8p23.1	2009-08-05			ENSG00000239839	ENSG00000239839		"""Defensins, alpha"""	2762	protein-coding gene	gene with protein product		604522		DEF3		8477861, 17214878, 15944200	Standard	NM_005217		Approved	HNP-3		P59666	OTTHUMG00000090381	ENST00000327857.2:c.194A>C	8.37:g.6873603T>G	ENSP00000328359:p.Asp65Ala	Somatic	689	28	0.0406386		WXS	Illumina HiSeq	Phase_I	696	29	0.0416667	NM_005217	P11479|Q14125	Missense_Mutation	SNP	ENST00000327857.2	37	CCDS5962.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.042516	0.00402	.	.	ENSG00000239839	ENST00000327857	T	0.41400	1.0	1.01	-2.03	0.07365	.	.	.	.	.	T	0.15046	0.0363	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24154	-1.0168	7	0.08179	T	0.78	.	0.1742	0.00116	0.3008:0.2168:0.2655:0.217	.	65	P59666	DEF3_HUMAN	A	65	ENSP00000328359:D65A	ENSP00000328359:D65A	D	-	2	0	DEFA3	6861013	0.002000	0.14202	0.000000	0.03702	0.011000	0.07611	-0.189000	0.09629	-1.937000	0.01047	-0.806000	0.03193	GAC	T|0.167;G|0.833	0.833	strong		0.498	DEFA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206753.2	NM_005217	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350674	50350674	+	Silent	SNP	T	T	C	rs3747282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:50350674T>C	ENST00000289292.7	-	6	3751	c.3468A>G	c.(3466-3468)gaA>gaG	p.E1156E	SHROOM4_ENST00000460112.3_Silent_p.E1040E|SHROOM4_ENST00000376020.2_Silent_p.E1156E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1156	Glu-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)	p.E1156E(1)		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)					GCAGctcctcttcctcctcct	0.557													T|||	1132	0.299868	0.1921	0.1758	3775	,	,		12102	0.2034		0.2266	False		,,,				2504	0.3303				p.E1156E		Atlas-SNP	.											.	SHROOM4	171	.	1	Substitution - coding silent(1)	skin(1)	c.A3468G						PASS	.	T		997,2838		119,604,155,909,416	31.0	27.0	28.0		3468	-1.4	0.5	X	dbSNP_107	28	2283,4445		295,1064,629,1069,1243	no	coding-synonymous	SHROOM4	NM_020717.3		414,1668,784,1978,1659	CC,CT,C,TT,T		33.9328,25.9974,31.0518		1156/1494	50350674	3280,7283	2203	4300	6503	SO:0001819	synonymous_variant	57477	exon6			CTCCTCTTCCTCC	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.3468A>G	X.37:g.50350674T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_020717	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	37	CCDS35277.1																																																																																			T|0.703;C|0.297	0.297	strong		0.557	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
MINOS1	440574	hgsc.bcm.edu	37	1	19950062	19950062	+	Silent	SNP	T	T	C	rs1737428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19950062T>C	ENST00000322753.6	+	3	263	c.207T>C	c.(205-207)caT>caC	p.H69H	MINOS1-NBL1_ENST00000602662.1_Intron|MINOS1_ENST00000486890.1_3'UTR	NM_001032363.3|NM_001204082.1|NM_001204083.1	NP_001027535.1|NP_001191011.1|NP_001191012.1	Q5TGZ0	MIC10_HUMAN	mitochondrial inner membrane organizing system 1	69						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)											ATCTTCTACATGGAAAATATG	0.383													C|||	1731	0.345647	0.705	0.2032	5008	,	,		19847	0.1419		0.2346	False		,,,				2504	0.2853				p.H69H		Atlas-SNP	.											.	.	.	.	0			c.T207C						PASS	.	C	,,,,	2865,1541	484.9+/-360.2	929,1007,267	119.0	116.0	117.0		207,159,207,,	0.9	1.0	1	dbSNP_89	117	1739,6861	736.3+/-407.0	208,1323,2769	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron	MINOS1,C1orf151-NBL1	NM_001032363.3,NM_001204082.1,NM_001204083.1,NM_001204088.1,NM_001204089.1	,,,,	1137,2330,3036	CC,CT,TT		20.2209,34.975,35.399	,,,,	69/79,53/63,69/141,,	19950062	4604,8402	2203	4300	6503	SO:0001819	synonymous_variant	440574	exon3			TCTACATGGAAAA	AK094318	CCDS30620.1, CCDS72719.1	1p36.13	2013-10-11	2011-10-04	2011-10-04	ENSG00000173436	ENSG00000173436			32068	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 151"""	C1orf151		21944719	Standard	NM_001032363		Approved	RP5-1056L3.2, FLJ36999, MIO10	uc021ohu.1	Q5TGZ0	OTTHUMG00000002712	ENST00000322753.6:c.207T>C	1.37:g.19950062T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	37	0.536232	NM_001032363	Q96G68	Silent	SNP	ENST00000322753.6	37	CCDS30620.1																																																																																			T|0.661;C|0.339	0.339	strong		0.383	MINOS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007697.2	NM_001032363	
ZNF841	284371	hgsc.bcm.edu	37	19	52568422	52568422	+	Missense_Mutation	SNP	T	T	G	rs61743893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52568422T>G	ENST00000426391.2	-	5	2916	c.2365A>C	c.(2365-2367)Aca>Cca	p.T789P	ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000389534.4_Missense_Mutation_p.T905P|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000359973.2_Missense_Mutation_p.T481P|ZNF841_ENST00000594295.1_Missense_Mutation_p.T905P			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	789					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(4)|kidney(3)|lung(3)	11						AGTTTAGTTGTAAGGTTCTCT	0.368													T|||	365	0.0728834	0.2057	0.0375	5008	,	,		20962	0.0079		0.0408	False		,,,				2504	0.0184				p.T905P		Atlas-SNP	.											.	ZNF841	183	.	0			c.A2713C						PASS	.	T	PRO/THR	250,1134		18,214,460	273.0	226.0	240.0		2713	0.4	0.0	19	dbSNP_129	240	79,3103		0,79,1512	yes	missense	ZNF841	NM_001136499.1	38	18,293,1972	GG,GT,TT		2.4827,18.0636,7.2054	possibly-damaging	905/925	52568422	329,4237	692	1591	2283	SO:0001583	missense	284371	exon7			TAGTTGTAAGGTT	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.2365A>C	19.37:g.52568422T>G	ENSP00000415453:p.Thr789Pro	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	246	135	0.548781	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	37		149	0.06822344322344322	99	0.20121951219512196	21	0.058011049723756904	2	0.0034965034965034965	27	0.03562005277044855	T	8.292	0.817953	0.16607	0.180636	0.024827	ENSG00000197608	ENST00000389534;ENST00000426391;ENST00000359973	T;T;T	0.08634	3.46;3.29;3.07	1.54	0.423	0.16463	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.52501	P	4.700000000001925E-5	D;D;P	0.53462	0.96;0.96;0.932	P;B;B	0.53912	0.737;0.354;0.193	T	0.44406	-0.9330	8	0.87932	D	0	.	2.1328	0.03754	0.4255:0.1776:0.0:0.3968	rs61743893	905;481;789	Q6ZN19-3;Q6ZN19-2;Q6ZN19	.;.;ZN841_HUMAN	P	905;789;481	ENSP00000374185:T905P;ENSP00000415453:T789P;ENSP00000353060:T481P	ENSP00000353060:T481P	T	-	1	0	ZNF841	57260234	0.000000	0.05858	0.006000	0.13384	0.201000	0.24016	-0.294000	0.08309	-0.101000	0.12219	0.260000	0.18958	ACA	T|0.938;G|0.062	0.062	strong		0.368	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155	
ALDH1B1	219	hgsc.bcm.edu	37	9	38396002	38396002	+	Missense_Mutation	SNP	C	C	T	rs2228093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:38396002C>T	ENST00000377698.3	+	2	410	c.257C>T	c.(256-258)gCc>gTc	p.A86V		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	86			A -> V (in allele ALDHA1B1*2; dbSNP:rs2228093). {ECO:0000269|PubMed:8244338}.		carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)			NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		GCCCGGGAAGCCTTCCGCCTG	0.667													C|||	1154	0.230431	0.0809	0.2853	5008	,	,		17003	0.3929		0.1511	False		,,,				2504	0.3078				p.A86V		Atlas-SNP	.											ALDH1B1,NS,carcinoma,+1,1	ALDH1B1	50	1	0			c.C257T						PASS	.	C	VAL/ALA	472,3934	222.6+/-239.4	27,418,1758	64.0	68.0	67.0		257	5.5	1.0	9	dbSNP_98	67	1143,7457	235.1+/-267.8	82,979,3239	yes	missense	ALDH1B1	NM_000692.4	64	109,1397,4997	TT,TC,CC		13.2907,10.7127,12.4173	probably-damaging	86/518	38396002	1615,11391	2203	4300	6503	SO:0001583	missense	219	exon2			GGGAAGCCTTCCG	M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"""Aldehyde dehydrogenases"""	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.257C>T	9.37:g.38396002C>T	ENSP00000366927:p.Ala86Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_000692	B2R8F0|Q8WX76|Q9BV45	Missense_Mutation	SNP	ENST00000377698.3	37	CCDS6615.1	487	0.222985347985348	53	0.10772357723577236	92	0.2541436464088398	226	0.3951048951048951	116	0.15303430079155672	C	27.7	4.856835	0.91433	0.107127	0.132907	ENSG00000137124	ENST00000377698	T	0.26518	1.73	5.51	5.51	0.81932	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.64402	D	0.000010	T	0.00012	0.0000	M	0.89904	3.07	0.09310	P	0.999999663107	D	0.89917	1.0	D	0.83275	0.996	T	0.24764	-1.0151	9	0.87932	D	0	.	16.9009	0.86113	0.0:1.0:0.0:0.0	rs2228093;rs2228093	86	P30837	AL1B1_HUMAN	V	86	ENSP00000366927:A86V	ENSP00000366927:A86V	A	+	2	0	ALDH1B1	38386002	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.201000	0.77847	2.598000	0.87819	0.650000	0.86243	GCC	C|0.831;A|0.001	.	strong		0.667	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1		
OR10X1	128367	hgsc.bcm.edu	37	1	158549420	158549420	+	Silent	SNP	C	C	T	rs863361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	142	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	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	
EIF2AK2	5610	hgsc.bcm.edu	37	2	37353464	37353464	+	Silent	SNP	A	A	G	rs2307478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37353464A>G	ENST00000233057.4	-	11	1198	c.876T>C	c.(874-876)acT>acC	p.T292T	EIF2AK2_ENST00000395127.2_Silent_p.T292T|EIF2AK2_ENST00000405334.1_Intron	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2	292	Interaction with TRAF5.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|evasion or tolerance by virus of host immune response (GO:0030683)|innate immune response (GO:0045087)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production (GO:0001819)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of hematopoietic progenitor cell differentiation (GO:1901532)|regulation of hematopoietic stem cell differentiation (GO:1902036)|regulation of hematopoietic stem cell proliferation (GO:1902033)|regulation of NLRP3 inflammasome complex assembly (GO:1900225)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)	22		all_hematologic(82;0.248)				TAATAACGTAAGTCTTTCCGT	0.313													A|||	82	0.0163738	0.0613	0.0014	5008	,	,		17810	0.0		0.0	False		,,,				2504	0.0				p.T292T		Atlas-SNP	.											.	EIF2AK2	54	.	0			c.T876C						PASS	.	A	,,	237,4169	141.1+/-176.5	6,225,1972	95.0	93.0	93.0		876,,876	-2.7	0.0	2	dbSNP_100	93	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,intron,coding-synonymous	EIF2AK2	NM_001135651.1,NM_001135652.1,NM_002759.2	,,	6,226,6270	GG,GA,AA		0.0116,5.379,1.8302	,,	292/552,,292/552	37353464	238,12766	2203	4299	6502	SO:0001819	synonymous_variant	5610	exon11			AACGTAAGTCTTT	BC057805	CCDS1786.1, CCDS46259.1	2p22-p21	2014-06-12	2005-01-19	2005-01-19	ENSG00000055332	ENSG00000055332			9437	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 83"""	176871	"""protein kinase, interferon-inducible double stranded RNA dependent"""	PRKR		1351683	Standard	NM_001135651		Approved	PKR, EIF2AK1, PPP1R83	uc010fac.3	P19525	OTTHUMG00000100962	ENST00000233057.4:c.876T>C	2.37:g.37353464A>G		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	152	79	0.519737	NM_001135651	A8K3P0|D6W584|E9PC80|Q52M43|Q7Z6F6|Q9UIR4	Silent	SNP	ENST00000233057.4	37	CCDS1786.1																																																																																			A|0.985;G|0.015	0.015	strong		0.313	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	NM_002759	
CMTR1	23070	hgsc.bcm.edu	37	6	37426429	37426429	+	Silent	SNP	T	T	C	rs35608753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:37426429T>C	ENST00000373451.4	+	9	983	c.819T>C	c.(817-819)ttT>ttC	p.F273F		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	273	RrmJ-type SAM-dependent 2'-O-MTase. {ECO:0000255|PROSITE-ProRule:PRU00945}.				7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)										TTCTGTACTTTGCTGATGTCT	0.527													T|||	46	0.0091853	0.031	0.0072	5008	,	,		19737	0.0		0.0	False		,,,				2504	0.0				p.F273F		Atlas-SNP	.											.	FTSJD2	64	.	0			c.T819C						PASS	.	T		196,4210	122.5+/-159.9	3,190,2010	87.0	77.0	80.0		819	3.5	1.0	6	dbSNP_126	80	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FTSJD2	NM_015050.2		3,191,6309	CC,CT,TT		0.0116,4.4485,1.5147		273/836	37426429	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	23070	exon9			GTACTTTGCTGAT	BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"""G patch domain containing"""	21077	protein-coding gene	gene with protein product			"""KIAA0082"", ""FtsJ methyltransferase domain containing 2"""	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.819T>C	6.37:g.37426429T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	156	67	0.429487	NM_015050	A8K949|Q14670|Q96FJ9	Silent	SNP	ENST00000373451.4	37	CCDS4835.1																																																																																			T|0.986;C|0.014	0.014	strong		0.527	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050	
ZNF142	7701	hgsc.bcm.edu	37	2	219508988	219508988	+	Missense_Mutation	SNP	T	T	C	rs3770214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219508988T>C	ENST00000449707.1	-	8	2672	c.2251A>G	c.(2251-2253)Agt>Ggt	p.S751G	ZNF142_ENST00000411696.2_Missense_Mutation_p.S751G	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	751			S -> G (in dbSNP:rs3770214). {ECO:0000269|PubMed:9039502}.		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(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		TCTTCAGCACTCAAGTCAGAA	0.517													C|||	3830	0.764776	0.8139	0.6614	5008	,	,		19851	0.9425		0.6223	False		,,,				2504	0.7352				p.S751G	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.A2251G						PASS	.	C	GLY/SER	3033,767		1204,625,71	81.0	82.0	82.0		2251	1.4	0.2	2	dbSNP_107	82	5115,3135		1614,1887,624	yes	missense	ZNF142	NM_001105537.1	56	2818,2512,695	CC,CT,TT		38.0,20.1842,32.3817	benign	751/1688	219508988	8148,3902	1900	4125	6025	SO:0001583	missense	7701	exon8			CAGCACTCAAGTC	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"""Zinc fingers, C2H2-type"""	12927	protein-coding gene	gene with protein product		604083	"""zinc finger protein 142 (clone pHZ-49)"""				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.2251A>G	2.37:g.219508988T>C	ENSP00000408643:p.Ser751Gly	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	314	313	0.996815	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	37	CCDS42817.1	1632	0.7472527472527473	376	0.7642276422764228	245	0.6767955801104972	536	0.9370629370629371	475	0.6266490765171504	C	0.015	-1.542824	0.00934	0.798158	0.62	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.10860	2.83;2.83	5.22	1.43	0.22495	.	1.094520	0.06675	N	0.766992	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	0.13522	-1.0506	9	0.12103	T	0.63	-17.9691	5.8407	0.18633	0.0:0.4854:0.1291:0.3855	rs3770214;rs17573037;rs52805913;rs59219307;rs3770214	751;588	P52746;A8MWU9	ZN142_HUMAN;.	G	751	ENSP00000408643:S751G;ENSP00000398798:S751G	ENSP00000398798:S751G	S	-	1	0	ZNF142	219217232	0.000000	0.05858	0.199000	0.23439	0.549000	0.35272	0.037000	0.13840	-0.103000	0.12175	-0.733000	0.03571	AGT	C|0.742;N|0.000	0.742	strong		0.517	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
VCAN	1462	hgsc.bcm.edu	37	5	82834299	82834299	+	Missense_Mutation	SNP	G	G	A	rs188703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82834299G>A	ENST00000265077.3	+	8	6042	c.5477G>A	c.(5476-5478)cGt>cAt	p.R1826H	VCAN_ENST00000343200.5_Missense_Mutation_p.R839H|VCAN-AS1_ENST00000513899.1_RNA|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1826	GAG-beta.		R -> H (in dbSNP:rs188703).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	ACTCTCCCACGTAGTCCTGCC	0.483													G|||	1795	0.358427	0.3449	0.4611	5008	,	,		16825	0.3234		0.4254	False		,,,				2504	0.271				p.R1826H		Atlas-SNP	.											VCAN,NS,carcinoma,-1,1	VCAN	498	1	0			c.G5477A						scavenged	.	G	,HIS/ARG,,HIS/ARG	1549,2857	445.5+/-347.7	261,1027,915	69.0	77.0	74.0		,2516,,5477	0.2	0.0	5	dbSNP_79	74	3441,5159	478.3+/-369.9	704,2033,1563	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,29,,29	965,3060,2478	AA,AG,GG		40.0116,35.1566,38.3669	,benign,,benign	,839/2410,,1826/3397	82834299	4990,8016	2203	4300	6503	SO:0001583	missense	1462	exon8			TCCCACGTAGTCC	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.5477G>A	5.37:g.82834299G>A	ENSP00000265077:p.Arg1826His	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	832	0.38095238095238093	139	0.28252032520325204	169	0.46685082872928174	203	0.3548951048951049	321	0.4234828496042216	G	12.50	1.956712	0.34565	0.351566	0.400116	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.84660	-1.85;-1.88;3.27	5.82	0.253	0.15551	.	0.983187	0.08317	N	0.964443	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.31931	0.347;0.235	B;B	0.27170	0.077;0.035	T	0.21415	-1.0246	9	0.49607	T	0.09	.	2.0501	0.03569	0.1803:0.1061:0.4634:0.2501	rs188703;rs309558;rs479344;rs52807291;rs60541692;rs188703	839;1826	P13611-2;P13611	.;CSPG2_HUMAN	H	1826;839;839	ENSP00000265077:R1826H;ENSP00000340062:R839H;ENSP00000426251:R839H	ENSP00000265077:R1826H	R	+	2	0	VCAN	82870055	0.003000	0.15002	0.001000	0.08648	0.027000	0.11550	0.786000	0.26844	0.328000	0.23435	0.655000	0.94253	CGT	G|0.623;A|0.377	0.377	strong		0.483	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
ANKRD40	91369	hgsc.bcm.edu	37	17	48774319	48774319	+	Silent	SNP	G	G	A	rs3815378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48774319G>A	ENST00000285243.6	-	4	1211	c.942C>T	c.(940-942)ccC>ccT	p.P314P	RP11-294J22.6_ENST00000574246.1_RNA|Y_RNA_ENST00000364470.1_RNA	NM_052855.3	NP_443087.1	Q6AI12	ANR40_HUMAN	ankyrin repeat domain 40	314										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11			BRCA - Breast invasive adenocarcinoma(22;2.03e-09)			ACAGAGTATTGGGTAACTTTC	0.438													G|||	215	0.0429313	0.0908	0.0807	5008	,	,		19551	0.0327		0.002	False		,,,				2504	0.0041				p.P314P		Atlas-SNP	.											.	ANKRD40	35	.	0			c.C942T						PASS	.	G		367,4039	187.8+/-214.3	12,343,1848	133.0	128.0	130.0		942	3.4	1.0	17	dbSNP_107	130	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	ANKRD40	NM_052855.3		12,356,6135	AA,AG,GG		0.1512,8.3296,2.9217		314/369	48774319	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	91369	exon4			AGTATTGGGTAAC	BC012978	CCDS11572.1	17q21.33	2013-01-10			ENSG00000154945	ENSG00000154945		"""Ankyrin repeat domain containing"""	28233	protein-coding gene	gene with protein product						12477932	Standard	NM_052855		Approved	MGC15396	uc002iso.3	Q6AI12	OTTHUMG00000162255	ENST00000285243.6:c.942C>T	17.37:g.48774319G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	115	44	0.382609	NM_052855	Q96E32	Silent	SNP	ENST00000285243.6	37	CCDS11572.1																																																																																			G|0.963;A|0.037	0.037	strong		0.438	ANKRD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368201.2	NM_052855	
PDZD2	23037	hgsc.bcm.edu	37	5	32000302	32000302	+	Silent	SNP	C	C	T	rs372606333		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32000302C>T	ENST00000438447.1	+	5	1567	c.1179C>T	c.(1177-1179)gtC>gtT	p.V393V	PDZD2_ENST00000282493.3_Silent_p.V393V			O15018	PDZD2_HUMAN	PDZ domain containing 2	393	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						ATTTACTGGTCGGGCTCTCCC	0.527																																					p.V393V		Atlas-SNP	.											PDZD2,NS,carcinoma,+2,1	PDZD2	306	1	0			c.C1179T						scavenged	.	C		1,4405	2.1+/-5.4	0,1,2202	117.0	109.0	112.0		1179	-7.1	0.4	5		112	0,8600		0,0,4300	no	coding-synonymous	PDZD2	NM_178140.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		393/2840	32000302	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23037	exon4			ACTGGTCGGGCTC	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.1179C>T	5.37:g.32000302C>T		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	289	5	0.017301	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			.	.	weak		0.527	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
HOMEZ	57594	hgsc.bcm.edu	37	14	23744829	23744829	+	Silent	SNP	C	C	T	rs79723196|rs35076736|rs67447855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23744829C>T	ENST00000357460.5	-	2	1772	c.1608G>A	c.(1606-1608)gaG>gaA	p.E536E	HOMEZ_ENST00000561013.1_Silent_p.E538E|HOMEZ_ENST00000431326.2_Silent_p.E538E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	536	Glu-rich.				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)		catcatcttcctcctcctcct	0.483													C|||	22	0.00439297	0.0045	0.0058	5008	,	,		18800	0.001		0.0099	False		,,,				2504	0.001				p.E536E		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G1608A						PASS	.						32.0	32.0	32.0					14																	23744829		2132	4146	6278	SO:0001819	synonymous_variant	57594	exon2			ATCTTCCTCCTCC	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.1608G>A	14.37:g.23744829C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	112	16	0.142857	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			.	.	weak		0.483	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
FUCA1	2517	hgsc.bcm.edu	37	1	24189740	24189740	+	Silent	SNP	G	G	A	rs541724746		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24189740G>A	ENST00000374479.3	-	3	553	c.546C>T	c.(544-546)taC>taT	p.Y182Y		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	182					fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		AGAGTGAGTGGTATAGTCCAT	0.358													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17635	0.0		0.0	False		,,,				2504	0.0				p.Y182Y		Atlas-SNP	.											.	FUCA1	24	.	0			c.C546T						PASS	.						94.0	88.0	90.0					1																	24189740		2203	4300	6503	SO:0001819	synonymous_variant	2517	exon3			TGAGTGGTATAGT	BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.546C>T	1.37:g.24189740G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_000147	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Silent	SNP	ENST00000374479.3	37	CCDS244.2																																																																																			.	.	none		0.358	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580958	140580958	+	Silent	SNP	C	C	A	rs74949746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140580958C>A	ENST00000354757.3	+	1	1611	c.1611C>A	c.(1609-1611)ggC>ggA	p.G537G	PCDHB11_ENST00000536699.1_Silent_p.G172G	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	537	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGACCGCGGCTCCCCGGCTT	0.672													C|||	58	0.0115815	0.0431	0.0014	5008	,	,		16231	0.0		0.0	False		,,,				2504	0.0				p.G537G		Atlas-SNP	.											PCDHB11,right_upper_lobe,carcinoma,+2,2	PCDHB11	162	2	0			c.C1611A						PASS	.	C		154,4250	103.4+/-141.9	4,146,2052	38.0	51.0	47.0		1611	-2.2	0.0	5	dbSNP_131	47	0,8598		0,0,4299	no	coding-synonymous	PCDHB11	NM_018931.2		4,146,6351	AA,AC,CC		0.0,3.4968,1.1844		537/798	140580958	154,12848	2202	4299	6501	SO:0001819	synonymous_variant	56125	exon1			CCGCGGCTCCCCG	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.1611C>A	5.37:g.140580958C>A		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	433	213	0.491917	NM_018931	B4DSF7|Q2M223	Silent	SNP	ENST00000354757.3	37	CCDS4253.1																																																																																			C|0.991;A|0.009	0.009	strong		0.672	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
RREB1	6239	hgsc.bcm.edu	37	6	7231280	7231280	+	Missense_Mutation	SNP	T	T	C	rs115093903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7231280T>C	ENST00000349384.6	+	10	3262	c.2948T>C	c.(2947-2949)tTg>tCg	p.L983S	RREB1_ENST00000379938.2_Missense_Mutation_p.L983S|RREB1_ENST00000379933.3_Missense_Mutation_p.L983S|RREB1_ENST00000334984.6_Missense_Mutation_p.L983S	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	983	Pro-rich.				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)				CCTGTAACTTTGGGGCCCAGC	0.692													T|||	74	0.0147764	0.0545	0.0029	5008	,	,		12856	0.0		0.0	False		,,,				2504	0.0				p.L983S		Atlas-SNP	.											.	RREB1	242	.	0			c.T2948C						PASS	.	T	SER/LEU,SER/LEU,SER/LEU,SER/LEU	180,4222		4,172,2025	18.0	21.0	20.0		2948,2948,2948,2948	3.3	0.0	6	dbSNP_132	20	0,8600		0,0,4300	no	missense,missense,missense,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	145,145,145,145	4,172,6325	CC,CT,TT		0.0,4.0891,1.3844	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	983/1688,983/1743,983/1477,983/1688	7231280	180,12822	2201	4300	6501	SO:0001583	missense	6239	exon10			TAACTTTGGGGCC	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.2948T>C	6.37:g.7231280T>C	ENSP00000305560:p.Leu983Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	T	12.76	2.034987	0.35893	0.040891	0.0	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.11495	2.89;2.85;2.89;2.77	5.74	3.35	0.38373	.	0.784404	0.10919	N	0.619695	T	0.03095	0.0091	L	0.43152	1.355	0.09310	N	1	B;B;B	0.32245	0.277;0.361;0.038	B;B;B	0.32289	0.143;0.107;0.037	T	0.46105	-0.9215	10	0.22109	T	0.4	-0.1912	8.4336	0.32773	0.0:0.1663:0.0:0.8337	.	983;983;983	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	S	983	ENSP00000369265:L983S;ENSP00000369270:L983S;ENSP00000305560:L983S;ENSP00000335574:L983S	ENSP00000335574:L983S	L	+	2	0	RREB1	7176279	0.264000	0.24093	0.003000	0.11579	0.012000	0.07955	1.900000	0.39828	0.442000	0.26555	0.533000	0.62120	TTG	T|0.989;C|0.011	0.011	strong		0.692	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
OR10G4	390264	hgsc.bcm.edu	37	11	123886681	123886681	+	Missense_Mutation	SNP	A	A	G	rs1893766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123886681A>G	ENST00000320891.4	+	1	400	c.400A>G	c.(400-402)Atg>Gtg	p.M134V		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	134			M -> V (in dbSNP:rs1893766).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		GTACACCAGCATGATGAGTGG	0.537																																					p.M134V		Atlas-SNP	.											OR10G4,NS,malignant_melanoma,-2,2	OR10G4	77	2	0			c.A400G						PASS	.	A	VAL/MET	1654,2750		223,1208,771	196.0	182.0	187.0		400	-3.9	0.2	11	dbSNP_92	187	3900,4698		857,2186,1256	no	missense	OR10G4	NM_001004462.1	21	1080,3394,2027	GG,GA,AA		45.3594,37.5568,42.7165	benign	134/312	123886681	5554,7448	2202	4299	6501	SO:0001583	missense	390264	exon1			ACCAGCATGATGA	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.400A>G	11.37:g.123886681A>G	ENSP00000325076:p.Met134Val	Somatic	1152	2	0.00173611		WXS	Illumina HiSeq	Phase_I	902	204	0.226164	NM_001004462	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	927	0.42445054945054944	192	0.3902439024390244	189	0.5220994475138122	220	0.38461538461538464	326	0.43007915567282323	a	0.221	-1.028595	0.02045	0.375568	0.453594	ENSG00000254737	ENST00000320891	T	0.01279	5.06	3.16	-3.86	0.04230	GPCR, rhodopsin-like superfamily (1);	0.915557	0.09172	N	0.838708	T	0.00012	0.0000	N	0.01128	-1	0.58432	P	2.9999999999752447E-6	B	0.09022	0.002	B	0.10450	0.005	T	0.20874	-1.0262	9	0.45353	T	0.12	.	6.5828	0.22605	0.2978:0.4717:0.0:0.2305	rs1893766;rs17128175	134	Q8NGN3	O10G4_HUMAN	V	134	ENSP00000325076:M134V	ENSP00000325076:M134V	M	+	1	0	OR10G4	123391891	0.000000	0.05858	0.173000	0.22940	0.146000	0.21551	-2.459000	0.01000	-0.897000	0.03910	-0.492000	0.04666	ATG	A|0.567;G|0.433	0.433	strong		0.537	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
MORC1	27136	hgsc.bcm.edu	37	3	108754260	108754260	+	Silent	SNP	A	A	G	rs3762696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108754260A>G	ENST00000483760.1	-	15	1429	c.1386T>C	c.(1384-1386)gaT>gaC	p.D462D	MORC1_ENST00000232603.5_Silent_p.D462D					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						GTTTCTCCACATCGATGTCAT	0.294													G|||	1804	0.360224	0.5136	0.2939	5008	,	,		14763	0.1101		0.4324	False		,,,				2504	0.3834				p.D462D		Atlas-SNP	.											.	MORC1	211	.	0			c.T1386C						PASS	.	G		2321,2085	571.8+/-383.2	621,1079,503	100.0	95.0	97.0		1386	-4.3	0.0	3	dbSNP_107	97	3640,4960	623.5+/-397.5	785,2070,1445	no	coding-synonymous	MORC1	NM_014429.3		1406,3149,1948	GG,GA,AA		42.3256,47.3218,45.8327		462/985	108754260	5961,7045	2203	4300	6503	SO:0001819	synonymous_variant	27136	exon15			CTCCACATCGATG	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.1386T>C	3.37:g.108754260A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_014429		Silent	SNP	ENST00000483760.1	37																																																																																				G|0.422;A|0.578	0.422	strong		0.294	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
SPTA1	6708	hgsc.bcm.edu	37	1	158612236	158612236	+	Missense_Mutation	SNP	A	A	G	rs863931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	387	1	0.00258398		WXS	Illumina HiSeq	Phase_I	407	186	0.457002	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	
EMR2	30817	hgsc.bcm.edu	37	19	14877820	14877820	+	Missense_Mutation	SNP	G	G	A	rs12976493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14877820G>A	ENST00000315576.3	-	6	908	c.457C>T	c.(457-459)Ctc>Ttc	p.L153F	EMR2_ENST00000392965.3_Missense_Mutation_p.L153F|EMR2_ENST00000392967.2_Missense_Mutation_p.L153F|EMR2_ENST00000392964.3_5'UTR|EMR2_ENST00000346057.1_Missense_Mutation_p.L153F|EMR2_ENST00000595839.1_Intron|EMR2_ENST00000596991.2_Missense_Mutation_p.L153F|EMR2_ENST00000601345.1_Missense_Mutation_p.L153F|EMR2_ENST00000353876.1_Intron|EMR2_ENST00000353005.1_Intron|EMR2_ENST00000599423.1_5'Flank|EMR2_ENST00000594294.1_Missense_Mutation_p.L153F|EMR2_ENST00000594076.1_Intron	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	153	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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						TCAGGTTTGAGCTTGAAGCCA	0.597													G|||	2024	0.404153	0.5749	0.4366	5008	,	,		12315	0.3373		0.4473	False		,,,				2504	0.1748				p.L153F		Atlas-SNP	.											EMR2,larynx,carcinoma,+2,1	EMR2	99	1	0			c.C457T						scavenged	.						58.0	59.0	59.0					19																	14877820		1523	3365	4888	SO:0001583	missense	30817	exon5			GTTTGAGCTTGAA	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.457C>T	19.37:g.14877820G>A	ENSP00000319883:p.Leu153Phe	Somatic	63	2	0.031746		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_001271052	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	767	0.35119047619047616	232	0.4715447154471545	141	0.38950276243093923	148	0.25874125874125875	246	0.3245382585751979	G	0.014	-1.577939	0.00879	.	.	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000360222;ENST00000392965;ENST00000392962	D;D;T;D;D	0.88741	-2.42;-2.42;-1.42;-2.42;-2.42	3.06	-6.11	0.02131	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	L	0.48218	1.51	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.10450	0.001;0.002;0.002;0.005	T	0.15954	-1.0419	8	0.09843	T	0.71	.	6.3278	0.21253	0.607:0.0:0.2568:0.1362	rs12976493	153;153;153;153	E7ESD7;Q9UHX3-3;Q9UHX3;Q9UHX3-2	.;.;EMR2_HUMAN;.	F	153	ENSP00000319883:L153F;ENSP00000376694:L153F;ENSP00000263380:L153F;ENSP00000376692:L153F;ENSP00000376689:L153F	ENSP00000319883:L153F	L	-	1	0	EMR2	14738820	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.324000	0.07986	-1.716000	0.01387	-1.973000	0.00462	CTC	A|1.000;|0.000	1.000	weak		0.597	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2		
PSG1	5669	hgsc.bcm.edu	37	19	43382368	43382368	+	Missense_Mutation	SNP	T	T	G	rs707745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43382368T>G	ENST00000436291.2	-	2	243	c.127A>C	c.(127-129)Acc>Ccc	p.T43P	PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000403380.3_Missense_Mutation_p.T43P|PSG1_ENST00000244296.2_Missense_Mutation_p.T43P|PSG1_ENST00000595124.1_Missense_Mutation_p.T43P|PSG1_ENST00000595356.1_Missense_Mutation_p.T43P|PSG1_ENST00000312439.6_Missense_Mutation_p.T43P	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	43	Ig-like V-type.		T -> P (in dbSNP:rs707745).	EPT -> QPP (in Ref. 4, 5 and 6). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				GAAACTTTGGTTGGCTCGGCT	0.483													.|||	2165	0.432308	0.5325	0.4222	5008	,	,		18196	0.4276		0.2505	False		,,,				2504	0.4959				p.T43P		Atlas-SNP	.											.	PSG1	196	.	0			c.A127C						PASS	.	G	PRO/THR,PRO/THR,PRO/THR	2120,2286		620,880,703	150.0	170.0	163.0		127,127,127	-1.0	0.0	19	dbSNP_86	163	1996,6602		325,1346,2628	no	missense,missense,missense	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	38,38,38	945,2226,3331	GG,GT,TT		23.2147,48.1162,31.6518	,,	43/420,43/418,43/427	43382368	4116,8888	2203	4299	6502	SO:0001583	missense	5669	exon2			CTTTGGTTGGCTC		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.127A>C	19.37:g.43382368T>G	ENSP00000413041:p.Thr43Pro	Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	344	316	0.918605	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	0.132	-1.112920	0.01799	0.481162	0.232147	ENSG00000231924	ENST00000270059;ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	1.46	-1.02	0.10135	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.05414	-0.055	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	0.11329	0.006;0.0;0.001;0.004;0.001;0.001;0.002;0.001	T	0.34477	-0.9827	8	0.02654	T	1	.	2.9451	0.05843	0.1663:0.0:0.4037:0.43	rs707745;rs3199303;rs16976235;rs52790147;rs57621156;rs707745	43;43;43;43;43;43;43;43	O75238;P11464-4;G5E9F7;P11464;P11464-3;Q9UPK8;O75237;P11464-2	.;.;.;PSG1_HUMAN;.;.;.;.	P	43	ENSP00000413041:T43P;ENSP00000385386:T43P;ENSP00000308970:T43P;ENSP00000244296:T43P	ENSP00000244296:T43P	T	-	1	0	PSG1	48074208	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.721000	0.01870	-0.760000	0.04677	-3.567000	0.00029	ACC	T|0.708;G|0.292	0.292	strong		0.483	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
ARMC12	221481	hgsc.bcm.edu	37	6	35705059	35705059	+	Intron	SNP	G	G	A	rs56183341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35705059G>A	ENST00000373866.3	+	1	185				ARMC12_ENST00000373869.3_Intron|ARMC12_ENST00000288065.2_Silent_p.P58P|RP3-510O8.4_ENST00000452048.1_RNA			Q5T9G4	ARM12_HUMAN	armadillo repeat containing 12							nucleus (GO:0005634)											GTGAGTGTCCGGGCCCTGGGG	0.612											OREG0017379	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	43	0.00858626	0.0295	0.0014	5008	,	,		19230	0.0		0.0	False		,,,				2504	0.0031				p.P58P		Atlas-SNP	.											.	.	.	.	0			c.G174A						PASS	.	G		106,4300	81.9+/-120.4	1,104,2098	68.0	64.0	65.0		174	-0.4	0.0	6	dbSNP_129	65	0,8600		0,0,4300	no	coding-synonymous	C6orf81	NM_145028.3		1,104,6398	AA,AG,GG		0.0,2.4058,0.815		58/368	35705059	106,12900	2203	4300	6503	SO:0001627	intron_variant	221481	exon1			GTGTCCGGGCCCT	AK058119	CCDS4809.1, CCDS69093.1, CCDS69094.1	6p21.31	2013-02-14	2011-12-14	2011-12-14	ENSG00000157343	ENSG00000157343		"""Armadillo repeat containing"""	21099	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 81"""	C6orf81			Standard	XM_005248920		Approved	FLJ25390	uc003ola.3	Q5T9G4	OTTHUMG00000014577	ENST00000373866.3:c.163+11G>A	6.37:g.35705059G>A		Somatic	116	0	0	857	WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_145028	Q8NEB2|Q96LL8	Silent	SNP	ENST00000373866.3	37																																																																																				G|0.992;A|0.008	0.008	strong		0.612	ARMC12-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040311.2	NM_145028	
GRIN3B	116444	hgsc.bcm.edu	37	19	1008704	1008704	+	Missense_Mutation	SNP	G	G	A	rs61744375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1008704G>A	ENST00000234389.3	+	7	2573	c.2554G>A	c.(2554-2556)Gag>Aag	p.E852K		NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	852					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CTCGCTGGGCGAGCACGCCTT	0.697													g|||	151	0.0301518	0.1059	0.0144	5008	,	,		11084	0.0		0.001	False		,,,				2504	0.0				p.E852K		Atlas-SNP	.											.	GRIN3B	46	.	0			c.G2554A						PASS	.	G	LYS/GLU	422,3978	195.3+/-220.0	23,376,1801	35.0	30.0	31.0		2554	3.8	1.0	19	dbSNP_129	31	0,8596		0,0,4298	yes	missense	GRIN3B	NM_138690.1	56	23,376,6099	AA,AG,GG		0.0,9.5909,3.2472	probably-damaging	852/1044	1008704	422,12574	2200	4298	6498	SO:0001583	missense	116444	exon7			CTGGGCGAGCACG		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.2554G>A	19.37:g.1008704G>A	ENSP00000234389:p.Glu852Lys	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	38	26	0.684211	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	58	0.026556776556776556	52	0.10569105691056911	6	0.016574585635359115	0	0.0	0	0.0	G	31	5.090219	0.94149	0.095909	0.0	ENSG00000116032	ENST00000234389	T	0.24350	1.86	3.78	3.78	0.43462	.	0.000000	0.85682	U	0.000000	T	0.01222	0.0040	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.00609	-1.1646	10	0.87932	D	0	.	14.2074	0.65744	0.0:0.0:1.0:0.0	rs61744375	852	O60391	NMD3B_HUMAN	K	852	ENSP00000234389:E852K	ENSP00000234389:E852K	E	+	1	0	GRIN3B	959704	1.000000	0.71417	0.982000	0.44146	0.976000	0.68499	9.163000	0.94750	1.661000	0.50771	0.462000	0.41574	GAG	G|0.965;A|0.035	0.035	strong		0.697	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
RBM15	64783	hgsc.bcm.edu	37	1	110884493	110884493	+	Silent	SNP	T	T	C	rs61745292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110884493T>C	ENST00000369784.3	+	1	3366	c.2466T>C	c.(2464-2466)acT>acC	p.T822T	RBM15_ENST00000602849.1_Silent_p.T822T|RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000487146.2_Silent_p.T822T	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	822	SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		AGGGTTCAACTGGAGGCAAAG	0.517			T	MKL1	acute megakaryocytic leukemia								T|||	146	0.0291534	0.1051	0.0086	5008	,	,		19970	0.0		0.001	False		,,,				2504	0.0				p.T822T		Atlas-SNP	.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	RBM15	93	.	0			c.T2466C						PASS	.	T	,	324,4082	171.2+/-201.5	12,300,1891	79.0	77.0	78.0		2466,2466	-0.2	1.0	1	dbSNP_129	78	9,8591	5.7+/-21.5	0,9,4291	no	coding-synonymous,coding-synonymous	RBM15	NM_001201545.1,NM_022768.4	,	12,309,6182	CC,CT,TT		0.1047,7.3536,2.5604	,	822/970,822/978	110884493	333,12673	2203	4300	6503	SO:0001819	synonymous_variant	64783	exon1			TTCAACTGGAGGC	AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"""RNA binding motif (RRM) containing"""	14959	protein-coding gene	gene with protein product	"""one twenty-two"""	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.2466T>C	1.37:g.110884493T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	140	60	0.428571	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Silent	SNP	ENST00000369784.3	37	CCDS822.1																																																																																			T|0.974;C|0.026	0.026	strong		0.517	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768	
C2CD4D	100191040	hgsc.bcm.edu	37	1	151810486	151810486	+	Missense_Mutation	SNP	G	G	A	rs188475396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151810486G>A	ENST00000454109.1	-	2	1565	c.980C>T	c.(979-981)aCg>aTg	p.T327M		NM_001136003.1	NP_001129475.1	B7Z1M9	C2D4D_HUMAN	C2 calcium-dependent domain containing 4D	327										skin(1)	1						AATGAGGGGCGTCTCGCACTC	0.721													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		11347	0.0		0.0	False		,,,				2504	0.0				p.T327M		Atlas-SNP	.											.	C2CD4D	3	.	0			c.C980T						PASS	.	G	MET/THR	38,1346		0,38,654	27.0	35.0	33.0		980	1.5	1.0	1		33	0,3182		0,0,1591	yes	missense	C2CD4D	NM_001136003.1	81	0,38,2245	AA,AG,GG		0.0,2.7457,0.8322	probably-damaging	327/354	151810486	38,4528	692	1591	2283	SO:0001583	missense	100191040	exon2			AGGGGCGTCTCGC	BC171843	CCDS44224.1	1q21.3	2012-07-02			ENSG00000225556	ENSG00000225556			37210	protein-coding gene	gene with protein product	"""family with sequence similarity 148, member D"""						Standard	NM_001136003		Approved	FAM148D	uc010pdq.1	B7Z1M9	OTTHUMG00000167218	ENST00000454109.1:c.980C>T	1.37:g.151810486G>A	ENSP00000389554:p.Thr327Met	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_001136003	B2RXG8	Missense_Mutation	SNP	ENST00000454109.1	37	CCDS44224.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	G	14.96	2.692350	0.48202	0.027457	0.0	ENSG00000225556	ENST00000454109	T	0.39592	1.07	3.44	1.53	0.23141	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.07098	0.0180	N	0.08118	0	0.25420	N	0.988275	B	0.22211	0.066	B	0.09377	0.004	T	0.32561	-0.9902	9	0.38643	T	0.18	.	5.4754	0.16692	0.377:0.0:0.623:0.0	.	327	B7Z1M9	C2D4D_HUMAN	M	327	ENSP00000389554:T327M	ENSP00000389554:T327M	T	-	2	0	C2CD4D	150077110	0.981000	0.34729	0.986000	0.45419	0.885000	0.51271	2.379000	0.44318	0.179000	0.19938	0.462000	0.41574	ACG	G|0.994;A|0.006	0.006	strong		0.721	C2CD4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393778.1	NM_001136003	
CFAP61	26074	hgsc.bcm.edu	37	20	20340872	20340872	+	Missense_Mutation	SNP	A	A	G	rs75487354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:20340872A>G	ENST00000245957.5	+	27	3608	c.3532A>G	c.(3532-3534)Ata>Gta	p.I1178V	C20orf26_ENST00000377309.2_3'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		1178										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)		TCTTCCTTCCATAGAGCAGTT	0.418											OREG0025807	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	68	0.0135783	0.0507	0.0014	5008	,	,		18359	0.0		0.0	False		,,,				2504	0.0				p.I1178V		Atlas-SNP	.											.	C20orf26	188	.	0			c.A3532G						PASS	.		VAL/ILE	217,4189	131.4+/-167.9	6,205,1992	144.0	155.0	151.0		3532	0.1	0.7	20	dbSNP_131	151	5,8595	3.7+/-12.6	0,5,4295	yes	missense	C20orf26	NM_015585.3	29	6,210,6287	GG,GA,AA		0.0581,4.9251,1.7069	benign	1178/1238	20340872	222,12784	2203	4300	6503	SO:0001583	missense	26074	exon27			CCTTCCATAGAGC																												ENST00000245957.5:c.3532A>G	20.37:g.20340872A>G	ENSP00000245957:p.Ile1178Val	Somatic	63	0	0	740	WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	a	7.203	0.593934	0.13875	0.049251	5.81E-4	ENSG00000089101	ENST00000343997;ENST00000389655;ENST00000245957	T	0.09255	3.0	5.09	0.0811	0.14423	.	0.335985	0.22190	N	0.063396	T	0.00695	0.0023	N	0.19112	0.55	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.48043	-0.9069	10	0.17369	T	0.5	.	2.2354	0.04007	0.5253:0.1361:0.0764:0.2623	.	1178	Q8NHU2	CT026_HUMAN	V	1118;1144;1178	ENSP00000245957:I1178V	ENSP00000245957:I1178V	I	+	1	0	C20orf26	20288872	0.027000	0.19231	0.727000	0.30756	0.085000	0.17905	-0.093000	0.11111	0.028000	0.15324	0.441000	0.28932	ATA	A|0.984;G|0.016	0.016	strong		0.418	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
ABCC5	10057	hgsc.bcm.edu	37	3	183696387	183696387	+	Silent	SNP	G	G	A	rs1053386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183696387G>A	ENST00000334444.6	-	9	1440	c.1200C>T	c.(1198-1200)agC>agT	p.S400S	ABCC5_ENST00000492216.1_5'UTR|ABCC5_ENST00000265586.6_Silent_p.S400S	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	400	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.			S -> G (in Ref. 1; AAD04169). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|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)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	CCACAGTGATGCTCTGGAAGT	0.488													G|||	455	0.0908546	0.3321	0.0216	5008	,	,		19202	0.0		0.001	False		,,,				2504	0.0				p.S400S		Atlas-SNP	.											.	ABCC5	142	.	0			c.C1200T						PASS	.	G		1053,3073		142,769,1152	91.0	108.0	103.0		1200	2.9	1.0	3	dbSNP_86	103	6,8404		0,6,4199	no	coding-synonymous	ABCC5	NM_005688.2		142,775,5351	AA,AG,GG		0.0713,25.5211,8.4477		400/1438	183696387	1059,11477	2063	4205	6268	SO:0001819	synonymous_variant	10057	exon9			AGTGATGCTCTGG	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.1200C>T	3.37:g.183696387G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																			G|0.913;A|0.087	0.087	strong		0.488	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
UNC5D	137970	hgsc.bcm.edu	37	8	35583692	35583692	+	Silent	SNP	T	T	C	rs6983275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:35583692T>C	ENST00000404895.2	+	10	1654	c.1326T>C	c.(1324-1326)tcT>tcC	p.S442S	UNC5D_ENST00000287272.2_Silent_p.S373S|UNC5D_ENST00000420357.1_Silent_p.S375S|UNC5D_ENST00000416672.1_Silent_p.S447S|UNC5D_ENST00000453357.2_Silent_p.S437S|UNC5D_ENST00000449677.1_Silent_p.S18S	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	442					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		TCCTGAATTCTGCCATGCAGC	0.488													C|||	1036	0.206869	0.5015	0.1499	5008	,	,		19125	0.1002		0.0199	False		,,,				2504	0.1513				p.S442S		Atlas-SNP	.											.	UNC5D	393	.	0			c.T1326C						PASS	.	C		1848,2558	624.3+/-394.3	371,1106,726	63.0	65.0	65.0		1326	0.8	1.0	8	dbSNP_116	65	147,8453	795.8+/-407.5	3,141,4156	no	coding-synonymous	UNC5D	NM_080872.2		374,1247,4882	CC,CT,TT		1.7093,41.9428,15.3391		442/954	35583692	1995,11011	2203	4300	6503	SO:0001819	synonymous_variant	137970	exon10			GAATTCTGCCATG	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"""Immunoglobulin superfamily / I-set domain containing"""	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.1326T>C	8.37:g.35583692T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_080872	Q8WYP7	Silent	SNP	ENST00000404895.2	37	CCDS6093.2																																																																																			T|0.826;C|0.174	0.174	strong		0.488	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2		
FCGBP	8857	hgsc.bcm.edu	37	19	40399508	40399508	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40399508C>T	ENST00000221347.6	-	13	6194	c.6187G>A	c.(6187-6189)Ggc>Agc	p.G2063S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2063						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)			GGCTGGCAGCCGTGCTGGCCG	0.657																																					p.G2063S		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.G6187A						scavenged	.						1.0	1.0	1.0					19																	40399508		183	426	609	SO:0001583	missense	8857	exon13			GGCAGCCGTGCTG	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.6187G>A	19.37:g.40399508C>T	ENSP00000221347:p.Gly2063Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	138	28	0.202899	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.485186	0.44147	.	.	ENSG00000090920	ENST00000221347	T	0.05025	3.51	3.01	3.01	0.34805	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.20170	0.0485	M	0.77103	2.36	0.31064	N	0.713759	D	0.76494	0.999	D	0.66196	0.942	T	0.07868	-1.0750	9	0.14656	T	0.56	.	12.9123	0.58187	0.0:1.0:0.0:0.0	.	2063	Q9Y6R7	FCGBP_HUMAN	S	2063	ENSP00000221347:G2063S	ENSP00000221347:G2063S	G	-	1	0	FCGBP	45091348	0.935000	0.31712	0.871000	0.34182	0.831000	0.47069	-0.229000	0.09098	1.536000	0.49237	0.298000	0.19748	GGC	.	.	weak		0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
MYLK	4638	hgsc.bcm.edu	37	3	123419573	123419573	+	Missense_Mutation	SNP	G	G	T	rs3732487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:123419573G>T	ENST00000475616.1	-	15	2741	c.2742C>A	c.(2740-2742)gaC>gaA	p.D914E	MYLK_ENST00000359169.1_Missense_Mutation_p.D914E|MYLK_ENST00000360304.3_Missense_Mutation_p.D914E|MYLK_ENST00000346322.5_Missense_Mutation_p.D845E|MYLK_ENST00000510775.1_5'Flank|MYLK_ENST00000360772.3_Missense_Mutation_p.D914E			Q15746	MYLK_HUMAN	myosin light chain kinase	914	5 X 28 AA approximate tandem repeats.		D -> E (in dbSNP:rs3732487).		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)		TCTCCTTCAGGTCGTCTTCCG	0.582													G|||	1132	0.226038	0.1513	0.0418	5008	,	,		16707	0.5496		0.0338	False		,,,				2504	0.3221				p.D914E		Atlas-SNP	.											.	MYLK	224	.	0			c.C2742A						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	504,3902	232.0+/-245.7	27,450,1726	94.0	82.0	86.0		2742,2535,2742,2535	-0.8	1.0	3	dbSNP_107	86	148,8452	73.2+/-135.9	2,144,4154	yes	missense,missense,missense,missense	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	45,45,45,45	29,594,5880	TT,TG,GG		1.7209,11.4389,5.0131	benign,benign,benign,benign	914/1915,845/1846,914/1864,845/1795	123419573	652,12354	2203	4300	6503	SO:0001583	missense	4638	exon18			CTTCAGGTCGTCT	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.2742C>A	3.37:g.123419573G>T	ENSP00000418335:p.Asp914Glu	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	161	86	0.534162	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	432	0.1978021978021978	84	0.17073170731707318	17	0.04696132596685083	300	0.5244755244755245	31	0.040897097625329816	G	4.440	0.081456	0.08533	0.114389	0.017209	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.65178	-0.14;-0.12;-0.14;-0.1;-0.12	4.99	-0.822	0.10819	.	.	.	.	.	T	0.00012	0.0000	N	0.17800	0.525	0.36349	P	0.14003699999999997	B;B;B;B;B	0.15141	0.012;0.005;0.005;0.012;0.007	B;B;B;B;B	0.17979	0.02;0.014;0.014;0.013;0.009	T	0.47195	-0.9136	8	0.14656	T	0.56	.	0.0266	0.00004	0.3147:0.2044:0.1863:0.2946	rs3732487;rs57412209;rs3732487	914;845;914;845;914	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	E	914;914;914;845;914	ENSP00000354004:D914E;ENSP00000353452:D914E;ENSP00000352088:D914E;ENSP00000320622:D845E;ENSP00000418335:D914E	ENSP00000320622:D845E	D	-	3	2	MYLK	124902263	0.870000	0.30015	0.991000	0.47740	0.412000	0.31113	0.078000	0.14761	0.137000	0.18759	-0.258000	0.10820	GAC	G|0.879;T|0.121	0.121	strong		0.582	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
PTGFRN	5738	hgsc.bcm.edu	37	1	117484581	117484581	+	Silent	SNP	C	C	T	rs77895792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117484581C>T	ENST00000393203.2	+	2	441	c.294C>T	c.(292-294)gcC>gcT	p.A98A		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	98	Ig-like C2-type 1.				lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		GGCGGACTGCCAACGACGCCG	0.592													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		17326	0.0		0.0	False		,,,				2504	0.0				p.A98A		Atlas-SNP	.											.	PTGFRN	91	.	0			c.C294T						PASS	.	C		46,4360	46.7+/-81.2	0,46,2157	85.0	79.0	81.0		294	4.2	1.0	1	dbSNP_131	81	0,8600		0,0,4300	no	coding-synonymous	PTGFRN	NM_020440.2		0,46,6457	TT,TC,CC		0.0,1.044,0.3537		98/880	117484581	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	5738	exon2			GACTGCCAACGAC	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9601	protein-coding gene	gene with protein product		601204	"""prostaglandin F2 receptor negative regulator"""			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.294C>T	1.37:g.117484581C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	199	100	0.502513	NM_020440	Q5VVU9|Q8N2K6	Silent	SNP	ENST00000393203.2	37	CCDS890.1																																																																																			C|0.995;T|0.005	0.005	strong		0.592	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
IVL	3713	hgsc.bcm.edu	37	1	152883680	152883680	+	Silent	SNP	A	A	G	rs7535306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152883680A>G	ENST00000368764.3	+	2	1471	c.1407A>G	c.(1405-1407)caA>caG	p.Q469Q	IVL_ENST00000392667.2_Silent_p.Q323Q			P07476	INVO_HUMAN	involucrin	469	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGAGAAGCAACTGGAGCTCC	0.617													G|||	2071	0.413538	0.6808	0.2997	5008	,	,		18638	0.5615		0.1083	False		,,,				2504	0.2945				p.Q469Q		Atlas-SNP	.											IVL,NS,lymphoid_neoplasm,+1,1	IVL	100	1	0			c.A1407G						PASS	.	G		2401,1947		681,1039,454	42.0	50.0	48.0		1407	-4.9	0.0	1	dbSNP_116	48	752,7780		41,670,3555	yes	coding-synonymous	IVL	NM_005547.2		722,1709,4009	GG,GA,AA		8.8139,44.7792,24.4798		469/586	152883680	3153,9727	2174	4266	6440	SO:0001819	synonymous_variant	3713	exon2			GAAGCAACTGGAG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1407A>G	1.37:g.152883680A>G		Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	213	211	0.99061	NM_005547	Q5T7P4	Silent	SNP	ENST00000368764.3	37	CCDS1030.1																																																																																			A|0.667;G|0.333	0.333	strong		0.617	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
WBP1	23559	hgsc.bcm.edu	37	2	74687550	74687550	+	Silent	SNP	T	T	C	rs8469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74687550T>C	ENST00000233615.2	+	4	826	c.552T>C	c.(550-552)ccT>ccC	p.P184P	WBP1_ENST00000494741.1_3'UTR|MOGS_ENST00000462443.1_5'Flank|WBP1_ENST00000393972.3_Silent_p.P218P|WBP1_ENST00000409737.1_Silent_p.P181P	NM_012477.3	NP_036609.1	Q96G27	WBP1_HUMAN	WW domain binding protein 1	184							WW domain binding (GO:0050699)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	8						GTGCCCCCCCTCATCAGGAGG	0.612													T|||	2625	0.524161	0.8275	0.3156	5008	,	,		15618	0.8214		0.1581	False		,,,				2504	0.3323				p.P184P		Atlas-SNP	.											.	WBP1	35	.	0			c.T552C						PASS	.	T		3085,1321		1140,805,258	52.0	70.0	64.0		552	2.0	1.0	2	dbSNP_52	64	1125,7473		88,949,3262	no	coding-synonymous	WBP1	NM_012477.3		1228,1754,3520	CC,CT,TT		13.0844,29.9818,32.3747		184/270	74687550	4210,8794	2203	4299	6502	SO:0001819	synonymous_variant	23559	exon4			CCCCCCTCATCAG	U79457	CCDS1943.1	2p12	2012-04-20			ENSG00000239779	ENSG00000239779			12737	protein-coding gene	gene with protein product		606961				7644498	Standard	NM_012477		Approved	WBP-1	uc002slj.2	Q96G27	OTTHUMG00000129958	ENST00000233615.2:c.552T>C	2.37:g.74687550T>C		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	302	302	1	NM_012477	B2RE02|O95637	Silent	SNP	ENST00000233615.2	37	CCDS1943.1																																																																																			T|0.633;C|0.367	0.367	strong		0.612	WBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252221.2	NM_012477	
SLC12A9	56996	hgsc.bcm.edu	37	7	100456506	100456506	+	Silent	SNP	C	C	T	rs78261122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100456506C>T	ENST00000354161.3	+	6	932	c.807C>T	c.(805-807)agC>agT	p.S269S	SLC12A9_ENST00000540482.1_Silent_p.S269S|SLC12A9_ENST00000415287.1_Silent_p.S180S|SLC12A9_ENST00000275729.3_Silent_p.S180S|SLC12A9_ENST00000428758.1_Silent_p.S269S	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	269				S -> N (in Ref. 1; AAF88060). {ECO:0000305}.	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)					ATTTTGCCAGCGTCTTTGCTG	0.587													C|||	32	0.00638978	0.0242	0.0	5008	,	,		19182	0.0		0.0	False		,,,				2504	0.0				p.S269S		Atlas-SNP	.											.	SLC12A9	81	.	0			c.C807T						PASS	.	C		102,4304	80.9+/-119.3	3,96,2104	99.0	77.0	84.0		807	-2.4	1.0	7	dbSNP_132	84	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	SLC12A9	NM_020246.2		3,99,6401	TT,TC,CC		0.0349,2.315,0.8073		269/915	100456506	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	56996	exon6			TGCCAGCGTCTTT	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.807C>T	7.37:g.100456506C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	196	90	0.459184	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1																																																																																			C|0.994;T|0.006	0.006	strong		0.587	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
ECE2	9718	hgsc.bcm.edu	37	3	184005719	184005719	+	Missense_Mutation	SNP	G	G	A	rs35875049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184005719G>A	ENST00000402825.3	+	11	1712	c.1712G>A	c.(1711-1713)cGg>cAg	p.R571Q	EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000404464.3_Missense_Mutation_p.R453Q|ECE2_ENST00000357474.5_Missense_Mutation_p.R499Q|ECE2_ENST00000359140.4_Missense_Mutation_p.R424Q	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	571	Endothelin-converting enzyme 2 region.		R -> Q (in dbSNP:rs35875049).		brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACGTTTGACCGGCAAAGCAAA	0.483													G|||	185	0.0369409	0.1346	0.0101	5008	,	,		19271	0.0		0.0	False		,,,				2504	0.0				p.R571Q		Atlas-SNP	.											ECE2_ENST00000402825,colon,carcinoma,0,3	ECE2	303	3	0			c.G1712A						scavenged	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	421,3985	206.5+/-228.1	19,383,1801	78.0	70.0	73.0		1271,1496,1358,1712	4.1	1.0	3	dbSNP_126	73	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	ECE2	NM_001037324.2,NM_001100120.1,NM_001100121.1,NM_014693.3	43,43,43,43	19,386,6098	AA,AG,GG		0.0349,9.5552,3.26	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	424/737,499/812,453/766,571/884	184005719	424,12582	2203	4300	6503	SO:0001583	missense	9718	exon11			TTGACCGGCAAAG	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.1712G>A	3.37:g.184005719G>A	ENSP00000384223:p.Arg571Gln	Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	37	CCDS3256.2	76	0.0347985347985348	73	0.1483739837398374	3	0.008287292817679558	0	0.0	0	0.0	G	10.80	1.452917	0.26161	0.095552	3.49E-4	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	T;T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.79;-0.79	4.95	4.07	0.47477	Peptidase M13 (1);Metallopeptidase, catalytic domain (1);	0.167177	0.42682	N	0.000677	T	0.00300	0.0009	N	0.04203	-0.255	0.31828	P	0.62512	B;B;B;B;B;B;B	0.32829	0.028;0.134;0.386;0.009;0.334;0.11;0.307	B;B;B;B;B;B;B	0.26416	0.028;0.041;0.064;0.003;0.038;0.024;0.069	T	0.08330	-1.0727	9	0.18276	T	0.48	-16.4724	8.5975	0.33725	0.1774:0.0:0.8226:0.0	rs35875049	173;424;442;453;499;424;571	B4DHU4;B4DKF3;B4DF19;O60344-2;O60344-5;O60344-3;O60344	.;.;.;.;.;.;ECE2_HUMAN	Q	571;424;453;499;445	ENSP00000384223:R571Q;ENSP00000352052:R424Q;ENSP00000385846:R453Q;ENSP00000350066:R499Q;ENSP00000398444:R445Q	ENSP00000350066:R499Q	R	+	2	0	ECE2	185488413	0.996000	0.38824	1.000000	0.80357	0.786000	0.44442	2.550000	0.45811	1.078000	0.41014	-0.140000	0.14226	CGG	G|0.967;A|0.033	0.033	strong		0.483	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
ABCA2	20	hgsc.bcm.edu	37	9	139911983	139911983	+	Silent	SNP	T	T	G	rs12348881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139911983T>G	ENST00000371605.3	-	16	2517	c.2370A>C	c.(2368-2370)gcA>gcC	p.A790A	ABCA2_ENST00000265662.5_Silent_p.A791A|ABCA2_ENST00000341511.6_Silent_p.A791A|ABCA2_ENST00000492260.1_5'Flank			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	790					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CCGCGTAGACTGCCAGGAAGA	0.607													G|||	523	0.104433	0.1853	0.0994	5008	,	,		18298	0.0337		0.1074	False		,,,				2504	0.0685				p.A821A		Atlas-SNP	.											.	ABCA2	113	.	0			c.A2463C						PASS	.	G	,	821,3489		92,637,1426	57.0	66.0	63.0		2373,2463	-8.2	0.3	9	dbSNP_120	63	831,7649		38,755,3447	yes	coding-synonymous,coding-synonymous	ABCA2	NM_001606.4,NM_212533.2	,	130,1392,4873	GG,GT,TT		9.7995,19.0487,12.9163	,	791/2437,821/2467	139911983	1652,11138	2155	4240	6395	SO:0001819	synonymous_variant	20	exon17			GTAGACTGCCAGG	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.2370A>C	9.37:g.139911983T>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	39	0.65	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	37																																																																																				T|0.905;G|0.095	0.095	strong		0.607	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	
INO80D	54891	hgsc.bcm.edu	37	2	206892933	206892933	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:206892933A>G	ENST00000403263.1	-	6	1604	c.1200T>C	c.(1198-1200)caT>caC	p.H400H	Y_RNA_ENST00000384656.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	400					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						TCCTAAACGTATGCCGGCATT	0.507																																					p.H400H		Atlas-SNP	.											INO80D,colon,carcinoma,-2,1	INO80D	134	1	0			c.T1200C						scavenged	.						68.0	65.0	66.0					2																	206892933		1897	4122	6019	SO:0001819	synonymous_variant	54891	exon6			AAACGTATGCCGG		CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"""INO80 complex subunits"""	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.1200T>C	2.37:g.206892933A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	125	3	0.024	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Silent	SNP	ENST00000403263.1	37	CCDS46500.1																																																																																			.	.	none		0.507	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	
ANKRD13B	124930	hgsc.bcm.edu	37	17	27939427	27939427	+	Silent	SNP	G	G	C	rs147156385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27939427G>C	ENST00000394859.3	+	12	1420	c.1266G>C	c.(1264-1266)ccG>ccC	p.P422P	RP11-68I3.2_ENST00000581474.1_RNA	NM_152345.4	NP_689558.4	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	422						endosome (GO:0005768)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	16						CAGAAATCCCGATCTTCCACA	0.637													G|||	9	0.00179712	0.0068	0.0	5008	,	,		12004	0.0		0.0	False		,,,				2504	0.0				p.P422P		Atlas-SNP	.											ANKRD13B,NS,carcinoma,0,1	ANKRD13B	39	1	0			c.G1266C						PASS	.	G		31,4373		0,31,2171	45.0	45.0	45.0		1266	-0.6	1.0	17	dbSNP_134	45	2,8596		0,2,4297	no	coding-synonymous	ANKRD13B	NM_152345.4		0,33,6468	CC,CG,GG		0.0233,0.7039,0.2538		422/627	27939427	33,12969	2202	4299	6501	SO:0001819	synonymous_variant	124930	exon12			AATCCCGATCTTC	AK092673	CCDS11251.1	17q11.2	2013-01-10			ENSG00000198720	ENSG00000198720		"""Ankyrin repeat domain containing"""	26363	protein-coding gene	gene with protein product		615124					Standard	NM_152345		Approved	FLJ25555	uc002hei.3	Q86YJ7	OTTHUMG00000132731	ENST00000394859.3:c.1266G>C	17.37:g.27939427G>C		Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	213	104	0.488263	NM_152345	Q8N7S9	Silent	SNP	ENST00000394859.3	37	CCDS11251.1																																																																																			G|0.998;C|0.002	0.002	strong		0.637	ANKRD13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256077.1	NM_152345	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244725	11244725	+	Missense_Mutation	SNP	C	C	G	rs68157013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11244725C>G	ENST00000531678.1	-	1	187	c.104G>C	c.(103-105)tGg>tCg	p.W35S	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	35				W -> S (in Ref. 1; AAM19328, 3; AAU21145 and 5; AAI17424). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TCTCTTGAACCACTCAATGGA	0.383													.|||	3113	0.621605	0.0976	0.7118	5008	,	,		11851	0.9425		0.7525	False		,,,				2504	0.8006				p.W35S		Atlas-SNP	.											TAS2R46_ENST00000422992,NS,carcinoma,0,4	TAS2R43	19	4	0			c.G104C						PASS	.						45.0	39.0	41.0					12																	11244725		1858	3572	5430	SO:0001583	missense	259289	exon1			TTGAACCACTCAA	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.104G>C	12.37:g.11244725C>G	ENSP00000431719:p.Trp35Ser	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	220	201	0.913636	NM_176884	P59546|Q645X4	Missense_Mutation	SNP	ENST00000531678.1	37	CCDS53749.1	926	0.423992673992674	31	0.06300813008130081	161	0.4447513812154696	418	0.7307692307692307	316	0.41688654353562005	-	1.291	-0.607724	0.03717	.	.	ENSG00000255374	ENST00000531678	T	0.01113	5.32	1.97	0.939	0.19506	.	.	.	.	.	T	0.00012	0.0000	H	0.97051	3.93	0.30802	P	0.739796	.	.	.	.	.	.	T	0.26573	-1.0099	6	0.72032	D	0.01	.	5.2922	0.15733	0.3385:0.6615:0.0:0.0	.	.	.	.	S	35	ENSP00000431719:W35S	ENSP00000431719:W35S	W	-	2	0	TAS2R43	11135992	0.155000	0.22806	0.246000	0.24233	0.092000	0.18411	1.065000	0.30592	0.107000	0.17824	0.184000	0.17185	TGG	C|0.597;G|0.403	0.403	strong		0.383	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
MT-ND4	4538	hgsc.bcm.edu	37	M	11887	11887	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11887G>A	ENST00000361381.2	+	1	1128	c.1128G>A	c.(1126-1128)ctG>ctA	p.L376L	MT-TS2_ENST00000387449.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	376					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						ATTAACCTACTGGGAGAACTC	0.458																																					p.L376L		Atlas-SNP	.											.	.	.	.	0			c.G1128A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CCTACTGGGAGAA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1128G>A	M.37:g.11887G>A		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.458	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
PHKB	5257	hgsc.bcm.edu	37	16	47697618	47697618	+	Missense_Mutation	SNP	A	A	G	rs16945474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:47697618A>G	ENST00000323584.5	+	24	2333	c.2309A>G	c.(2308-2310)tAt>tGt	p.Y770C	PHKB_ENST00000299167.8_Missense_Mutation_p.Y770C|PHKB_ENST00000566044.1_Missense_Mutation_p.Y763C|PHKB_ENST00000455779.1_Missense_Mutation_p.Y763C	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	770	Calmodulin-binding. {ECO:0000255}.		Y -> C (in dbSNP:rs16945474). {ECO:0000269|PubMed:12825073, ECO:0000269|PubMed:9326319}.		carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				GAGAGAGTCTATAGAAGAGCT	0.333													A|||	324	0.0646965	0.1649	0.0375	5008	,	,		18074	0.0149		0.0368	False		,,,				2504	0.0286				p.Y770C		Atlas-SNP	.											PHKB_ENST00000323584,NS,carcinoma,0,3	PHKB	298	3	0			c.A2309G	GRCh37	CM031328	PHKB	M	rs16945474	PASS	.	A	CYS/TYR,CYS/TYR	671,3731	285.2+/-278.0	50,571,1580	227.0	204.0	212.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2309,2288	5.7	1.0	16	dbSNP_123	212	375,8225	123.1+/-182.0	9,357,3934	yes	missense,missense	PHKB	NM_000293.2,NM_001031835.2	194,194	59,928,5514	GG,GA,AA		4.3605,15.2431,8.0449	possibly-damaging,possibly-damaging	770/1094,763/1087	47697618	1046,11956	2201	4300	6501	SO:0001583	missense	5257	exon24			GAGTCTATAGAAG		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.2309A>G	16.37:g.47697618A>G	ENSP00000313504:p.Tyr770Cys	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	234	108	0.461538	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	37	CCDS10729.1	129	0.059065934065934064	80	0.16260162601626016	18	0.049723756906077346	4	0.006993006993006993	27	0.03562005277044855	A	20.4	3.992193	0.74703	0.152431	0.043605	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.91407	-2.84;-2.84	5.73	5.73	0.89815	Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	T	0.04497	0.0123	M	0.78223	2.4	0.09310	P	0.99999999996013	B;P	0.48350	0.413;0.909	P;B	0.46479	0.518;0.425	T	0.40478	-0.9561	9	0.54805	T	0.06	-23.0012	16.0152	0.80434	1.0:0.0:0.0:0.0	rs16945474;rs52820357;rs16945474	770;763	Q93100;Q93100-4	KPBB_HUMAN;.	C	763;763;770	ENSP00000414345:Y763C;ENSP00000313504:Y770C	ENSP00000299167:Y763C	Y	+	2	0	PHKB	46255119	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.569000	0.90744	2.180000	0.69256	0.533000	0.62120	TAT	A|0.929;G|0.071	0.071	strong		0.333	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1		
BEGAIN	57596	hgsc.bcm.edu	37	14	101010204	101010204	+	Silent	SNP	T	T	C	rs4073549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101010204T>C	ENST00000355173.2	-	5	413	c.342A>G	c.(340-342)tcA>tcG	p.S114S	BEGAIN_ENST00000556751.1_Silent_p.S50S|BEGAIN_ENST00000554747.1_5'Flank|BEGAIN_ENST00000443071.2_Silent_p.S114S	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	114						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				CGTTGTCCTCTGACAGCTTGT	0.587													.|||	434	0.0866613	0.261	0.0216	5008	,	,		21801	0.0655		0.0	False		,,,				2504	0.0082				p.S114S	NSCLC(159;1889 2010 9965 27479 40101)	Atlas-SNP	.											.	BEGAIN	32	.	0			c.A342G						PASS	.		,	983,3423	726.9+/-409.8	131,721,1351	154.0	85.0	108.0		342,342	-5.2	0.9	14	dbSNP_108	108	12,8588	815.8+/-407.0	0,12,4288	no	coding-synonymous,coding-synonymous	BEGAIN	NM_001159531.1,NM_020836.3	,	131,733,5639	CC,CT,TT		0.1395,22.3105,7.6503	,	114/594,114/594	101010204	995,12011	2203	4300	6503	SO:0001819	synonymous_variant	57596	exon5			GTCCTCTGACAGC	BC002607	CCDS9962.1	14q32.2	2012-12-07	2012-12-07			ENSG00000183092			24163	protein-coding gene	gene with protein product			"""brain-enriched guanylate kinase-associated homolog (rat)"""			10819331	Standard	NM_020836		Approved	KIAA1446	uc010txa.2	Q9BUH8		ENST00000355173.2:c.342A>G	14.37:g.101010204T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_020836	Q9NPU3|Q9P282	Silent	SNP	ENST00000355173.2	37	CCDS9962.1																																																																																			T|0.915;C|0.085	0.085	strong		0.587	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836	
PCDHA7	56141	hgsc.bcm.edu	37	5	140216125	140216125	+	Silent	SNP	G	G	A	rs61730621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140216125G>A	ENST00000525929.1	+	1	2157	c.2157G>A	c.(2155-2157)acG>acA	p.T719T	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000378125.3_Silent_p.T719T|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	719					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)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGTACACGGCGTTGCGGT	0.612													.|||	74	0.0147764	0.0552	0.0014	5008	,	,		18171	0.0		0.0	False		,,,				2504	0.0				p.T719T	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.G2157A						PASS	.	G	,,,,,,,,,	237,4169	140.8+/-176.2	15,207,1981	103.0	87.0	92.0		,,,,,,2157,,,2157	-3.3	0.4	5	dbSNP_129	92	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,coding-synonymous	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_031411.1,NM_031849.1,NM_031852.1	,,,,,,,,,	15,208,6280	AA,AG,GG		0.0116,5.379,1.8299	,,,,,,,,,	,,,,,,719/938,,,719/790	140216125	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	56141	exon1			GTACACGGCGTTG	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"""Cadherins / Protocadherins : Clustered"""	8673	other	complex locus constituent	"""KIAA0345-like 7"", ""ortholog to mouse CNR4"""	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.2157G>A	5.37:g.140216125G>A		Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	338	183	0.54142	NM_031852	O75282	Silent	SNP	ENST00000525929.1	37	CCDS54918.1																																																																																			G|0.982;A|0.018	0.018	strong		0.612	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910	
NOD2	64127	hgsc.bcm.edu	37	16	50746191	50746191	+	Missense_Mutation	SNP	G	G	A	rs5743279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50746191G>A	ENST00000300589.2	+	4	2474	c.2369G>A	c.(2368-2370)cGg>cAg	p.R790Q	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	790			R -> Q (in dbSNP:rs5743279).		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)	p.R790L(1)		cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CAGCACCTCCGGCGGCCCGTG	0.607													G|||	51	0.0101837	0.0371	0.0029	5008	,	,		21469	0.0		0.0	False		,,,				2504	0.0				p.R790Q		Atlas-SNP	.											NOD2,colon,carcinoma,+1,2	NOD2	118	2	1	Substitution - Missense(1)	lung(1)	c.G2369A						PASS	.	G	GLN/ARG	149,4247	101.2+/-139.8	2,145,2051	95.0	88.0	90.0		2369	-0.2	1.0	16	dbSNP_114	90	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NOD2	NM_022162.1	43	2,146,6350	AA,AG,GG		0.0116,3.3894,1.1542	benign	790/1041	50746191	150,12846	2198	4300	6498	SO:0001583	missense	64127	exon4			ACCTCCGGCGGCC	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.2369G>A	16.37:g.50746191G>A	ENSP00000300589:p.Arg790Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	125	67	0.536	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	G	0.038	-1.298744	0.01364	0.033894	1.16E-4	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.51817	0.69	5.3	-0.17	0.13335	.	0.234851	0.28983	N	0.013509	T	0.09774	0.0240	N	0.21194	0.64	0.09310	N	1	B;B;B	0.27166	0.002;0.17;0.039	B;B;B	0.19391	0.001;0.025;0.003	T	0.10042	-1.0647	10	0.20519	T	0.43	.	8.9611	0.35847	0.5027:0.0:0.4973:0.0	rs5743279;rs5743279	574;763;790	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	Q	763;790	ENSP00000300589:R790Q	ENSP00000300589:R790Q	R	+	2	0	NOD2	49303692	0.000000	0.05858	0.988000	0.46212	0.065000	0.16274	0.196000	0.17176	0.076000	0.16826	-0.254000	0.11334	CGG	G|0.989;A|0.011	0.011	strong		0.607	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
SLC37A3	84255	hgsc.bcm.edu	37	7	140048445	140048445	+	Silent	SNP	G	G	A	rs73472776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140048445G>A	ENST00000326232.9	-	10	1208	c.1005C>T	c.(1003-1005)taC>taT	p.Y335Y	SLC37A3_ENST00000429996.2_3'UTR|SLC37A3_ENST00000447932.2_Silent_p.Y335Y|SLC37A3_ENST00000340308.3_Silent_p.Y335Y	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	335					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					CTCCAACGTCGTACCAAATGG	0.443													G|||	156	0.0311502	0.1104	0.0144	5008	,	,		17310	0.0		0.0	False		,,,				2504	0.0				p.Y335Y	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.C1005T						PASS	.	G	,	461,3945	220.4+/-237.8	24,413,1766	129.0	119.0	123.0		1005,1005	2.0	1.0	7	dbSNP_130	123	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	SLC37A3	NM_032295.2,NM_207113.1	,	24,416,6063	AA,AG,GG		0.0349,10.463,3.5676	,	335/444,335/495	140048445	464,12542	2203	4300	6503	SO:0001819	synonymous_variant	84255	exon10			AACGTCGTACCAA	AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"""Solute carriers"""	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.1005C>T	7.37:g.140048445G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Silent	SNP	ENST00000326232.9	37	CCDS5859.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	G	8.221	0.802514	0.16397	0.10463	3.49E-4	ENSG00000157800	ENST00000485734;ENST00000485861	.	.	.	5.26	2.05	0.26809	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00386	-1.1772	4	.	.	.	-14.7147	6.5083	0.22208	0.4561:0.0:0.5439:0.0	.	.	.	.	M	114;172	.	.	T	-	2	0	SLC37A3	139694914	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	0.648000	0.24828	0.613000	0.30089	0.462000	0.41574	ACG	G|0.961;A|0.039	0.039	strong		0.443	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295	
TBC1D24	57465	hgsc.bcm.edu	37	16	2546356	2546356	+	Silent	SNP	T	T	C	rs13339237	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2546356T>C	ENST00000293970.5	+	2	340	c.207T>C	c.(205-207)ccT>ccC	p.P69P	TBC1D24_ENST00000434757.2_Silent_p.P69P|RP11-20I23.1_ENST00000564543.1_Silent_p.P69P|TBC1D24_ENST00000567020.1_Silent_p.P69P	NM_001199107.1	NP_001186036.1	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	69	Rab-GAP TBC.				neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|terminal bouton (GO:0043195)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(4)|large_intestine(3)|lung(4)	13						CGGTCACGCCTGACGCCAGCG	0.672													C|||	326	0.0650958	0.2322	0.0231	5008	,	,		18489	0.0		0.003	False		,,,				2504	0.0				p.P69P		Atlas-SNP	.											.	TBC1D24	35	.	0			c.T207C						PASS	.	C	,	748,3566		62,624,1471	45.0	55.0	52.0		207,207	-11.2	0.0	16	dbSNP_121	52	18,8500		0,18,4241	no	coding-synonymous,coding-synonymous	TBC1D24	NM_001199107.1,NM_020705.2	,	62,642,5712	CC,CT,TT		0.2113,17.3389,5.9695	,	69/560,69/554	2546356	766,12066	2157	4259	6416	SO:0001819	synonymous_variant	57465	exon2			CACGCCTGACGCC	AB032997	CCDS42107.1, CCDS55980.1	16p13.3	2014-05-07				ENSG00000162065			29203	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 6"""	613577	"""deafness, autosomal recessive 86"""	DFNB86		10574461, 24387994, 24729539	Standard	NM_001199107		Approved	KIAA1171, TLDC6, DFNA65	uc002cql.3	Q9ULP9		ENST00000293970.5:c.207T>C	16.37:g.2546356T>C		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001199107	A0JNW3|B9A6M6|Q2KJ08	Silent	SNP	ENST00000293970.5	37	CCDS55980.1																																																																																			T|0.941;C|0.059	0.059	strong		0.672	TBC1D24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000435637.1	NM_020705	
CCDC107	203260	hgsc.bcm.edu	37	9	35661088	35661088	+	Silent	SNP	G	G	A	rs10441686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35661088G>A	ENST00000426546.2	+	5	822	c.756G>A	c.(754-756)agG>agA	p.R252R	ARHGEF39_ENST00000378387.3_3'UTR|ARHGEF39_ENST00000378395.2_3'UTR|CCDC107_ENST00000327351.2_3'UTR|CCDC107_ENST00000421582.2_3'UTR|CCDC107_ENST00000378409.3_Silent_p.R225R|CCDC107_ENST00000378406.1_3'UTR|CCDC107_ENST00000378407.3_3'UTR|ARHGEF39_ENST00000490970.1_5'Flank|ARHGEF39_ENST00000343259.3_3'UTR	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	252						integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TACGGAGAAGGTGCAGCCAGG	0.572													G|||	357	0.0712859	0.1982	0.0216	5008	,	,		19466	0.0139		0.0328	False		,,,				2504	0.0337				p.R252R		Atlas-SNP	.											.	CCDC107	12	.	0			c.G756A						PASS	.	G	,,,,	694,3712	290.7+/-281.1	47,600,1556	63.0	64.0	64.0		675,,,,756	0.4	1.0	9	dbSNP_119	64	229,8371	93.8+/-155.7	2,225,4073	no	coding-synonymous,utr-3,utr-3,utr-3,coding-synonymous	C9orf100,CCDC107	NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2,NM_174923.2	,,,,	49,825,5629	AA,AG,GG		2.6628,15.7512,7.0967	,,,,	225/257,,,,252/284	35661088	923,12083	2203	4300	6503	SO:0001819	synonymous_variant	203260	exon5			GAGAAGGTGCAGC	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.756G>A	9.37:g.35661088G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	134	64	0.477612	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Silent	SNP	ENST00000426546.2	37	CCDS6583.1																																																																																			G|0.925;A|0.075	0.075	strong		0.572	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923	
ABL1	25	hgsc.bcm.edu	37	9	133759546	133759546	+	Silent	SNP	G	G	A	rs34717358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133759546G>A	ENST00000318560.5	+	11	2250	c.1869G>A	c.(1867-1869)gaG>gaA	p.E623E		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	623					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)	CCTTCCGGGAGATGGACGGCC	0.602			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								G|||	116	0.0231629	0.0613	0.0245	5008	,	,		16665	0.0		0.0179	False		,,,				2504	0.0				p.E642E		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.G1926A						PASS	.	G	,	232,4174		6,220,1977	46.0	56.0	52.0		1869,1926	4.7	1.0	9	dbSNP_126	52	145,8455		0,145,4155	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	6,365,6132	AA,AG,GG		1.686,5.2655,2.8987	,	623/1131,642/1150	133759546	377,12629	2203	4300	6503	SO:0001819	synonymous_variant	25	exon11			CCGGGAGATGGAC	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.1869G>A	9.37:g.133759546G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	80	63	0.7875	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			G|0.971;A|0.029	0.029	strong		0.602	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
MUC6	4588	hgsc.bcm.edu	37	11	1017575	1017575	+	Silent	SNP	C	C	T	rs76222533		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017575C>T	ENST00000421673.2	-	31	5276	c.5226G>A	c.(5224-5226)acG>acA	p.T1742T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1742	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			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)		AGGTTTTGGCCGTGCTAAATG	0.537													-|||	1	0.000199681	0.0	0.0014	5008	,	,		39036	0.0		0.0	False		,,,				2504	0.0				p.T1742T		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	0			c.G5226A						scavenged	.						697.0	677.0	684.0					11																	1017575		2190	4282	6472	SO:0001819	synonymous_variant	4588	exon31			TTTGGCCGTGCTA	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.5226G>A	11.37:g.1017575C>T		Somatic	983	92	0.093591		WXS	Illumina HiSeq	Phase_I	1148	138	0.120209	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			C|0.500;T|0.500	0.500	strong		0.537	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
VAT1L	57687	hgsc.bcm.edu	37	16	78011559	78011559	+	Silent	SNP	C	C	T	rs3751769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:78011559C>T	ENST00000302536.2	+	9	1380	c.1227C>T	c.(1225-1227)agC>agT	p.S409S		NM_020927.1	NP_065978.1	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport 1-like	409							oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(10)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24						AGGGAGACAGCGAGAACAAGG	0.512													C|||	653	0.130391	0.2776	0.0865	5008	,	,		19747	0.0357		0.0845	False		,,,				2504	0.1074				p.S409S		Atlas-SNP	.											.	VAT1L	68	.	0			c.C1227T						PASS	.	C		1059,3337	385.1+/-325.6	128,803,1267	175.0	132.0	146.0		1227	-9.9	0.4	16	dbSNP_107	146	709,7891	172.5+/-223.2	27,655,3618	no	coding-synonymous	VAT1L	NM_020927.1		155,1458,4885	TT,TC,CC		8.2442,24.0901,13.6042		409/420	78011559	1768,11228	2198	4300	6498	SO:0001819	synonymous_variant	57687	exon9			AGACAGCGAGAAC	AB046796	CCDS32492.1	16q23.1	2014-09-09	2013-08-23		ENSG00000171724	ENSG00000171724			29315	protein-coding gene	gene with protein product			"""vesicle amine transport protein 1 homolog (T. californica)-like"""			10997877	Standard	NM_020927		Approved	KIAA1576	uc002ffg.1	Q9HCJ6	OTTHUMG00000176845	ENST00000302536.2:c.1227C>T	16.37:g.78011559C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	156	81	0.519231	NM_020927	Q8IYW8	Silent	SNP	ENST00000302536.2	37	CCDS32492.1																																																																																			C|0.873;T|0.127	0.127	strong		0.512	VAT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434010.1	NM_020927	
GPR179	440435	hgsc.bcm.edu	37	17	36487060	36487060	+	Missense_Mutation	SNP	C	C	T	rs78470373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36487060C>T	ENST00000342292.4	-	11	2412	c.2392G>A	c.(2392-2394)Gcc>Acc	p.A798T	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	798					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GTTCGAGAGGCCTTCTTGGCC	0.652													C|||	53	0.0105831	0.0386	0.0029	5008	,	,		15168	0.0		0.0	False		,,,				2504	0.0				p.A798T		Atlas-SNP	.											.	GPR179	170	.	0			c.G2392A						PASS	.	C	THR/ALA	133,3827		3,127,1850	10.0	12.0	11.0		2392	4.3	0.8	17	dbSNP_131	11	1,8293		0,1,4146	no	missense	GPR179	NM_001004334.2	58	3,128,5996	TT,TC,CC		0.0121,3.3586,1.0935	benign	798/2368	36487060	134,12120	1980	4147	6127	SO:0001583	missense	440435	exon11			GAGAGGCCTTCTT		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.2392G>A	17.37:g.36487060C>T	ENSP00000345060:p.Ala798Thr	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	C	11.74	1.727989	0.30593	0.033586	1.21E-4	ENSG00000188888	ENST00000342292	T	0.54071	0.59	5.3	4.34	0.51931	.	1.005240	0.08006	N	0.989502	T	0.22859	0.0552	L	0.44542	1.39	0.31348	N	0.682852	B	0.26195	0.144	B	0.18263	0.021	T	0.31558	-0.9939	10	0.27785	T	0.31	-0.0366	12.8987	0.58113	0.0:0.9207:0.0:0.0793	.	798	Q6PRD1	GP179_HUMAN	T	798	ENSP00000345060:A798T	ENSP00000345060:A798T	A	-	1	0	GPR179	33740586	0.007000	0.16637	0.813000	0.32504	0.033000	0.12548	1.245000	0.32790	1.469000	0.48083	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.652	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
CLDND2	125875	hgsc.bcm.edu	37	19	51871157	51871157	+	Missense_Mutation	SNP	G	G	A	rs74538792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51871157G>A	ENST00000291715.1	-	2	718	c.293C>T	c.(292-294)gCc>gTc	p.A98V	CTD-2616J11.11_ENST00000600067.1_Missense_Mutation_p.A33V|ETFB_ENST00000309244.4_5'Flank|CLDND2_ENST00000601435.1_Missense_Mutation_p.A98V|CTD-2616J11.10_ENST00000595500.1_RNA	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	98						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GAAGAGGAAGGCGCTCGTGGT	0.721													G|||	174	0.0347444	0.1195	0.0202	5008	,	,		12598	0.001		0.001	False		,,,				2504	0.0				p.A98V		Atlas-SNP	.											.	CLDND2	11	.	0			c.C293T						PASS	.	G	VAL/ALA	394,3980		20,354,1813	18.0	21.0	20.0		293	-2.1	0.0	19	dbSNP_131	20	6,8554		0,6,4274	yes	missense	CLDND2	NM_152353.2	64	20,360,6087	AA,AG,GG		0.0701,9.0078,3.0926	benign	98/168	51871157	400,12534	2187	4280	6467	SO:0001583	missense	125875	exon2			AGGAAGGCGCTCG	BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.293C>T	19.37:g.51871157G>A	ENSP00000291715:p.Ala98Val	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_152353		Missense_Mutation	SNP	ENST00000291715.1	37	CCDS12829.1	59	0.027014652014652016	49	0.09959349593495935	10	0.027624309392265192	0	0.0	0	0.0	G	13.11	2.139648	0.37728	0.090078	7.01E-4	ENSG00000160318	ENST00000291715	D	0.88046	-2.33	4.69	-2.13	0.07144	.	2.567250	0.01253	N	0.008934	T	0.08758	0.0217	L	0.31664	0.95	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.49844	-0.8896	10	0.09590	T	0.72	-3.6824	5.168	0.15096	0.4412:0.164:0.3948:0.0	.	98	Q8NHS1	CLDN2_HUMAN	V	98	ENSP00000291715:A98V	ENSP00000291715:A98V	A	-	2	0	CLDND2	56562969	0.000000	0.05858	0.000000	0.03702	0.107000	0.19398	-0.512000	0.06313	-0.169000	0.10834	0.561000	0.74099	GCC	G|0.968;A|0.032	0.032	strong		0.721	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353	
SPRTN	83932	hgsc.bcm.edu	37	1	231487133	231487133	+	Silent	SNP	G	G	A	rs73116379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:231487133G>A	ENST00000295050.7	+	4	870	c.534G>A	c.(532-534)ccG>ccA	p.P178P	SPRTN_ENST00000008440.9_Silent_p.P135P|SPRTN_ENST00000469904.1_3'UTR|SPRTN_ENST00000391858.4_Silent_p.P178P	NM_001010984.2|NM_032018.5	NP_001010984.1|NP_114407.3	Q9H040	SPRTN_HUMAN	SprT-like N-terminal domain	178	SprT-like.				cellular response to DNA damage stimulus (GO:0006974)|positive regulation of protein ubiquitination (GO:0031398)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|ubiquitin binding (GO:0043130)										ACAGGCCACCGTATTACGGCT	0.512													G|||	76	0.0151757	0.053	0.0072	5008	,	,		14878	0.0		0.001	False		,,,				2504	0.0				p.P178P		Atlas-SNP	.											.	.	.	.	0			c.G534A						PASS	.	G	,	218,4188	131.4+/-167.9	7,204,1992	68.0	67.0	68.0		534,534	-11.5	0.0	1	dbSNP_130	68	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	C1orf124	NM_001010984.1,NM_032018.4	,	7,207,6289	AA,AG,GG		0.0349,4.9478,1.6992	,	178/251,178/490	231487133	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	83932	exon4			GCCACCGTATTAC	AL512744	CCDS1594.1, CCDS31054.1, CCDS58066.1	1q42.12-q43	2013-01-30	2012-06-18	2012-06-18	ENSG00000010072	ENSG00000010072			25356	protein-coding gene	gene with protein product	"""SprT-like domain at the N terminus"", ""DNA damage-targeting VCP (p97) adaptor"""		"""chromosome 1 open reading frame 124"""	C1orf124		22681887	Standard	NM_032018		Approved	DKFZP547N043, Spartan, DVC1	uc001hur.4	Q9H040	OTTHUMG00000038022	ENST00000295050.7:c.534G>A	1.37:g.231487133G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_032018	B1AKT0|B5MEF7|Q5TE78|Q6UWW6|Q96BC5|Q96KA0	Silent	SNP	ENST00000295050.7	37	CCDS1594.1																																																																																			G|0.983;A|0.017	0.017	strong		0.512	SPRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092858.1	NM_032018	
PASD1	139135	hgsc.bcm.edu	37	X	150840185	150840185	+	Silent	SNP	T	T	C	rs6627174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:150840185T>C	ENST00000370357.4	+	13	1616	c.1371T>C	c.(1369-1371)ggT>ggC	p.G457G		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	457						nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					GTTTCTGTGGTTTATCTTTAT	0.478													T|||	1488	0.394172	0.062	0.2939	3775	,	,		15542	0.6448		0.164	False		,,,				2504	0.3957				p.G457G		Atlas-SNP	.											.	PASD1	286	.	0			c.T1371C						PASS	.	T		405,3430		17,316,55,1299,516	122.0	106.0	111.0		1371	-1.9	0.0	X	dbSNP_116	111	1495,5233		113,850,419,1465,1453	no	coding-synonymous	PASD1	NM_173493.2		130,1166,474,2764,1969	CC,CT,C,TT,T		22.2206,10.5606,17.9873		457/774	150840185	1900,8663	2203	4300	6503	SO:0001819	synonymous_variant	139135	exon13			CTGTGGTTTATCT	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.1371T>C	X.37:g.150840185T>C		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	184	115	0.625	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Silent	SNP	ENST00000370357.4	37	CCDS35431.1																																																																																			0|0.003;C|0.271	0.271	strong		0.478	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493	
TFAP2A	7020	hgsc.bcm.edu	37	6	10398707	10398707	+	Silent	SNP	G	G	A	rs3734391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10398707G>A	ENST00000482890.1	-	8	1609	c.1257C>T	c.(1255-1257)aaC>aaT	p.N419N	TFAP2A_ENST00000497266.1_5'Flank|TFAP2A_ENST00000379613.3_Silent_p.N421N|TFAP2A_ENST00000379604.2_Silent_p.N419N|TFAP2A_ENST00000379608.3_Silent_p.N413N|TFAP2A_ENST00000319516.4_Silent_p.N415N			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	419					anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|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 neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|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 (GO:0000982)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				CCGTGTGGCTGTTGGGGTTGT	0.627													G|||	445	0.0888578	0.084	0.0951	5008	,	,		12859	0.0308		0.1521	False		,,,				2504	0.0859				p.N419N		Atlas-SNP	.											.	TFAP2A	129	.	0			c.C1257T						PASS	.	G	,,	384,4022	193.0+/-218.2	12,360,1831	318.0	331.0	327.0		1239,1245,1257	5.4	1.0	6	dbSNP_107	327	1231,7369	247.1+/-275.3	93,1045,3162	no	coding-synonymous,coding-synonymous,coding-synonymous	TFAP2A	NM_001032280.2,NM_001042425.1,NM_003220.2	,,	105,1405,4993	AA,AG,GG		14.314,8.7154,12.4173	,,	413/432,415/434,419/438	10398707	1615,11391	2203	4300	6503	SO:0001819	synonymous_variant	7020	exon7			GTGGCTGTTGGGG	X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"""transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"""	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.1257C>T	6.37:g.10398707G>A		Somatic	354	1	0.00282486		WXS	Illumina HiSeq	Phase_I	442	196	0.443439	NM_003220	Q13777|Q5TAV5|Q8N1C6	Silent	SNP	ENST00000482890.1	37	CCDS4510.1																																																																																			G|0.883;A|0.117	0.117	strong		0.627	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220	
FAM210B	116151	hgsc.bcm.edu	37	20	54941268	54941268	+	Silent	SNP	G	G	A	rs6099116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:54941268G>A	ENST00000371384.3	+	3	595	c.504G>A	c.(502-504)acG>acA	p.T168T		NM_080821.2	NP_543011.2	Q96KR6	F210B_HUMAN	family with sequence similarity 210, member B	168	DUF1279.					integral component of membrane (GO:0016021)											TCAGCATTACGCTAGTCTCTG	0.453													G|||	548	0.109425	0.3835	0.0274	5008	,	,		17731	0.001		0.008	False		,,,				2504	0.0133				p.T168T		Atlas-SNP	.											.	.	.	.	0			c.G504A						PASS	.	G		1433,2973	467.6+/-354.9	239,955,1009	138.0	131.0	134.0		504	-0.7	0.0	20	dbSNP_114	134	76,8524	45.8+/-104.6	2,72,4226	no	coding-synonymous	C20orf108	NM_080821.2		241,1027,5235	AA,AG,GG		0.8837,32.5238,11.6023		168/193	54941268	1509,11497	2203	4300	6503	SO:0001819	synonymous_variant	116151	exon3			CATTACGCTAGTC	AL121914	CCDS13450.1	20q13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000124098	ENSG00000124098			16102	protein-coding gene	gene with protein product	"""hypothetical protein LOC116151"""		"""chromosome 20 open reading frame 108"""	C20orf108		11780052	Standard	NM_080821		Approved	dJ1167H4.1, DKFZP434A1114	uc002xxc.3	Q96KR6	OTTHUMG00000032793	ENST00000371384.3:c.504G>A	20.37:g.54941268G>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	264	127	0.481061	NM_080821	B2RBQ9|E1P5Y7|Q8WVN2|Q9BYL6|Q9H418	Silent	SNP	ENST00000371384.3	37	CCDS13450.1																																																																																			G|0.885;A|0.115	0.115	strong		0.453	FAM210B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079800.2	NM_080821	
DICER1	23405	hgsc.bcm.edu	37	14	95572111	95572111	+	Silent	SNP	A	A	C	rs12018992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95572111A>C	ENST00000526495.1	-	21	3288	c.2997T>G	c.(2995-2997)ctT>ctG	p.L999L	DICER1_ENST00000556045.1_5'UTR|DICER1_ENST00000393063.1_Silent_p.L999L|DICER1_ENST00000527414.1_Silent_p.L999L|DICER1_ENST00000343455.3_Silent_p.L999L|DICER1_ENST00000541352.1_Silent_p.L999L			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	999	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		GAGGTGTCAAAAGATTAAGTC	0.383			"""Mis F, N"""		"""sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"""	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome				A|||	99	0.0197684	0.0711	0.0072	5008	,	,		19488	0.0		0.0	False		,,,				2504	0.0				p.L999L		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"""dicer 1, ribonuclease type III """		"""E, M, O"""	.	DICER1	181	.	0			c.T2997G						PASS	.	A	,,	252,4154	141.9+/-177.2	11,230,1962	62.0	62.0	62.0		2997,2997,2997	4.2	1.0	14	dbSNP_120	62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	DICER1	NM_001195573.1,NM_030621.3,NM_177438.2	,,	11,231,6261	CC,CA,AA		0.0116,5.7195,1.9453	,,	999/1830,999/1923,999/1923	95572111	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	23405	exon20	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	TGTCAAAAGATTA	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"""dicer 1, double-stranded RNA-specific endoribonuclease"""	606241	"""Dicer1, Dcr-1 homolog (Drosophila)"", ""multinodular goitre 1"""	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.2997T>G	14.37:g.95572111A>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	115	47	0.408696	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Silent	SNP	ENST00000526495.1	37	CCDS9931.1																																																																																			A|0.977;C|0.023	0.023	strong		0.383	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1		
ENPP2	5168	hgsc.bcm.edu	37	8	120594802	120594802	+	Silent	SNP	A	A	G	rs4871364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120594802A>G	ENST00000075322.6	-	18	1642	c.1584T>C	c.(1582-1584)caT>caC	p.H528H	ENPP2_ENST00000522826.1_Silent_p.H528H|ENPP2_ENST00000259486.6_Silent_p.H580H|ENPP2_ENST00000427067.2_Silent_p.H524H|ENPP2_ENST00000522167.1_Silent_p.H167H	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	528					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TCAAACTTCCATGGGTCCCAT	0.423													A|||	1329	0.265375	0.5227	0.1499	5008	,	,		18881	0.1389		0.174	False		,,,				2504	0.2239				p.H580H	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.T1740C						PASS	.	A	,,	2179,2227	585.1+/-386.2	529,1121,553	159.0	163.0	161.0		1584,1584,1740	1.2	1.0	8	dbSNP_111	161	1559,7041	293.6+/-301.5	122,1315,2863	no	coding-synonymous,coding-synonymous,coding-synonymous	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	,,	651,2436,3416	GG,GA,AA		18.1279,49.4553,28.7406	,,	528/864,528/889,580/916	120594802	3738,9268	2203	4300	6503	SO:0001819	synonymous_variant	5168	exon19			ACTTCCATGGGTC	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.1584T>C	8.37:g.120594802A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			A|0.735;G|0.265	0.265	strong		0.423	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
MUC17	140453	hgsc.bcm.edu	37	7	100677586	100677586	+	Silent	SNP	A	A	G	rs189731103		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677586A>G	ENST00000306151.4	+	3	2953	c.2889A>G	c.(2887-2889)tcA>tcG	p.S963S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	963	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)					AAGCCACTTCATCTCCTACAA	0.527																																					p.S963S		Atlas-SNP	.											.	MUC17	804	.	0			c.A2889G						PASS	.	A		626,3780		0,626,1577	329.0	308.0	316.0		2889	-0.7	0.0	7	dbSNP_134	316	572,8028		0,572,3728	no	coding-synonymous	MUC17	NM_001040105.1		0,1198,5305	GG,GA,AA		6.6512,14.2079,9.2111		963/4494	100677586	1198,11808	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CACTTCATCTCCT	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.2889A>G	7.37:g.100677586A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	227	46	0.202643	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			A|0.999;G|0.001	0.001	weak		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MUC6	4588	hgsc.bcm.edu	37	11	1017068	1017068	+	Silent	SNP	C	C	T	rs78992004		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017068C>T	ENST00000421673.2	-	31	5783	c.5733G>A	c.(5731-5733)acG>acA	p.T1911T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1911	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			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)		AAGTTTTGGCCGTGCTAAATG	0.552																																					p.T1911T		Atlas-SNP	.											MUC6,NS,carcinoma,-1,1	MUC6	408	1	0			c.G5733A						scavenged	.																																			SO:0001819	synonymous_variant	4588	exon31			TTTGGCCGTGCTA	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.5733G>A	11.37:g.1017068C>T		Somatic	930	100	0.107527		WXS	Illumina HiSeq	Phase_I	1028	143	0.139105	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			C|0.500;T|0.500	0.500	weak		0.552	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ZNF233	353355	hgsc.bcm.edu	37	19	44778799	44778799	+	Silent	SNP	G	G	A	rs386809645|rs2884016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44778799G>A	ENST00000391958.2	+	5	2113	c.1986G>A	c.(1984-1986)ttG>ttA	p.L662L	ZNF233_ENST00000334152.1_Silent_p.L644L|ZNF235_ENST00000589799.1_Intron|ZNF233_ENST00000592581.1_3'UTR	NM_181756.2	NP_861421.2	A6NK53	ZN233_HUMAN	zinc finger protein 233	662					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|skin(3)|urinary_tract(1)	20		Prostate(69;0.0435)|all_neural(266;0.226)				AGAGTTCGTTGTCTTCAGATT	0.413													G|||	954	0.190495	0.2103	0.2824	5008	,	,		19009	0.2579		0.1203	False		,,,				2504	0.1012				p.L662L		Atlas-SNP	.											.	ZNF233	73	.	0			c.G1986A						PASS	.						69.0	77.0	74.0					19																	44778799		2203	4300	6503	SO:0001819	synonymous_variant	353355	exon5			TTCGTTGTCTTCA	AY166792	CCDS33047.1	19q13.31	2013-01-08				ENSG00000159915		"""Zinc fingers, C2H2-type"", ""-"""	30946	protein-coding gene	gene with protein product						12743021	Standard	NM_001207005		Approved	FLJ38032	uc021uvi.1	A6NK53		ENST00000391958.2:c.1986G>A	19.37:g.44778799G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_001207005	B2RN78|B2RN79|Q86WL8	Silent	SNP	ENST00000391958.2	37	CCDS33047.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.544947	0.27652	.	.	ENSG00000159915	ENST00000280305	.	.	.	4.19	0.75	0.18387	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999988	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.1825	0.25780	0.4734:0.0:0.5266:0.0	rs2884016;rs61035088;rs2884016	.	.	.	.	-1	.	.	.	+	.	.	ZNF233	49470639	0.000000	0.05858	0.173000	0.22940	0.965000	0.64279	-0.077000	0.11394	0.346000	0.23899	0.609000	0.83330	.	G|0.901;A|0.099	0.099	strong		0.413	ZNF233-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460737.1	NM_181756	
PEAR1	375033	hgsc.bcm.edu	37	1	156878737	156878737	+	Silent	SNP	T	T	C	rs6671392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	90	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	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	
SLIT3	6586	hgsc.bcm.edu	37	5	168098235	168098235	+	Silent	SNP	A	A	G	rs2277933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:168098235A>G	ENST00000519560.1	-	34	4514	c.4095T>C	c.(4093-4095)gaT>gaC	p.D1365D	SLIT3_ENST00000332966.8_Silent_p.D1372D|SLIT3_ENST00000404867.3_Silent_p.D1365D	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1365	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)			GGGCCTCCTGATCGCAGAGTG	0.687													G|||	1618	0.323083	0.4705	0.3934	5008	,	,		16999	0.3274		0.2435	False		,,,				2504	0.1513				p.D1372D	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.T4116C						PASS	.	G		1943,2455		408,1127,664	24.0	25.0	24.0		4095	4.6	1.0	5	dbSNP_100	24	2006,6582		247,1512,2535	no	coding-synonymous	SLIT3	NM_003062.2		655,2639,3199	GG,GA,AA		23.3582,44.1792,30.4097		1365/1524	168098235	3949,9037	2199	4294	6493	SO:0001819	synonymous_variant	6586	exon34			CTCCTGATCGCAG	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.4095T>C	5.37:g.168098235A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	85	26	0.305882	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																			A|0.689;G|0.311	0.311	strong		0.687	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
C1orf106	55765	hgsc.bcm.edu	37	1	200860731	200860731	+	Silent	SNP	G	G	A	rs141245080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200860731G>A	ENST00000367342.4	+	1	263	c.63G>A	c.(61-63)cgG>cgA	p.R21R		NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	21										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						GGGAGGCTCGGGGGGAGGGAA	0.622													G|||	43	0.00858626	0.0303	0.0029	5008	,	,		15948	0.0		0.001	False		,,,				2504	0.0				p.R35R		Atlas-SNP	.											.	C1orf106	59	.	0			c.G105A						PASS	.	G		142,4264	94.8+/-133.5	3,136,2064	25.0	29.0	27.0		63	1.5	0.0	1	dbSNP_134	27	1,8599		0,1,4299	no	coding-synonymous	C1orf106	NM_018265.3		3,137,6363	AA,AG,GG		0.0116,3.2229,1.0995		21/664	200860731	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	55765	exon1			GGCTCGGGGGGAG	AK001763	CCDS44292.1	1q32.1	2011-02-15			ENSG00000163362	ENSG00000163362			25599	protein-coding gene	gene with protein product						14702039	Standard	NM_018265		Approved	FLJ10901	uc001gvo.4	Q3KP66	OTTHUMG00000035789	ENST00000367342.4:c.63G>A	1.37:g.200860731G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	188	106	0.56383	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Silent	SNP	ENST00000367342.4	37																																																																																				A|0.008;C|0.001;G|0.991	0.008	strong		0.622	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265	
PCDHGA2	56113	hgsc.bcm.edu	37	5	140719294	140719294	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140719294G>A	ENST00000394576.2	+	1	756	c.756G>A	c.(754-756)ccG>ccA	p.P252P	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	252	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)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAAGCATTCCGGAGAATACGC	0.552																																					p.P252P		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.G756A						PASS	.						74.0	77.0	76.0					5																	140719294		2203	4300	6503	SO:0001819	synonymous_variant	56113	exon1			CATTCCGGAGAAT	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.756G>A	5.37:g.140719294G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_018915	Q52LL6|Q9Y5D5	Silent	SNP	ENST00000394576.2	37	CCDS47289.1																																																																																			.	.	none		0.552	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411700	105411700	+	Missense_Mutation	SNP	A	A	G	rs4264326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105411700A>G	ENST00000333244.5	-	7	10207	c.10088T>C	c.(10087-10089)gTg>gCg	p.V3363A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3363			V -> A (in dbSNP:rs4264326).			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)		p.V3363A(1)		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)			CTCCAGGTCCACAGAAGGGAG	0.662													.|||	2822	0.563498	0.6762	0.513	5008	,	,		18019	0.4137		0.5338	False		,,,				2504	0.6319				p.V3363A		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,2	AHNAK2	719	2	1	Substitution - Missense(1)	prostate(1)	c.T10088C						PASS	.	G	ALA/VAL	2793,1165		993,807,179	122.0	132.0	129.0		10088	3.1	0.0	14	dbSNP_111	129	4513,3781		1239,2035,873	no	missense	AHNAK2	NM_138420.2	64	2232,2842,1052	GG,GA,AA		45.5872,29.4341,40.3689	benign	3363/5796	105411700	7306,4946	1979	4147	6126	SO:0001583	missense	113146	exon7			AGGTCCACAGAAG	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.10088T>C	14.37:g.105411700A>G	ENSP00000353114:p.Val3363Ala	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	248	247	0.995968	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1182	0.5412087912087912	357	0.725609756097561	201	0.5552486187845304	225	0.39335664335664333	399	0.5263852242744064	N	0.218	-1.031006	0.02029	0.705659	0.544128	ENSG00000185567	ENST00000333244	T	0.01159	5.25	4.12	3.13	0.36017	.	2587.460000	0.00357	N	0.000031	T	0.00012	0.0000	N	0.02345	-0.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17868	-1.0355	9	0.07990	T	0.79	.	5.2812	0.15676	0.2694:0.0:0.7306:0.0	rs4264326	3363	Q8IVF2	AHNK2_HUMAN	A	3363	ENSP00000353114:V3363A	ENSP00000353114:V3363A	V	-	2	0	AHNAK2	104482745	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-1.238000	0.02919	0.977000	0.38444	-0.320000	0.08662	GTG	A|0.454;G|0.546	0.546	strong		0.662	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
PREPL	9581	hgsc.bcm.edu	37	2	44550528	44550528	+	Missense_Mutation	SNP	T	T	C	rs75128515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44550528T>C	ENST00000409936.1	-	12	2206	c.1769A>G	c.(1768-1770)aAc>aGc	p.N590S	PREPL_ENST00000409957.1_Missense_Mutation_p.N501S|PREPL_ENST00000541738.1_Missense_Mutation_p.N501S|PREPL_ENST00000378520.3_Missense_Mutation_p.N524S|PREPL_ENST00000409272.1_Missense_Mutation_p.N590S|PREPL_ENST00000378511.3_Missense_Mutation_p.N528S|PREPL_ENST00000409411.1_Missense_Mutation_p.N501S|PREPL_ENST00000260648.6_Missense_Mutation_p.N590S|PREPL_ENST00000410081.1_Missense_Mutation_p.N590S	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	590						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CATCATGGTGTTGAGAACATC	0.348													T|||	50	0.00998403	0.0363	0.0029	5008	,	,		17612	0.0		0.0	False		,,,				2504	0.0				p.N590S		Atlas-SNP	.											.	PREPL	69	.	0			c.A1769G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	146,4260	103.0+/-141.5	2,142,2059	115.0	103.0	107.0		1583,1571,1769,1769,1502,1502,1769	4.2	1.0	2	dbSNP_131	107	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense,missense,missense,missense,missense,missense	PREPL	NM_001042385.2,NM_001042386.2,NM_001171603.1,NM_001171606.1,NM_001171613.1,NM_001171617.1,NM_006036.4	46,46,46,46,46,46,46	2,144,6357	CC,CT,TT		0.0233,3.3137,1.1379	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	528/666,524/662,590/728,590/728,501/639,501/639,590/728	44550528	148,12858	2203	4300	6503	SO:0001583	missense	9581	exon12			ATGGTGTTGAGAA	AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.1769A>G	2.37:g.44550528T>C	ENSP00000386543:p.Asn590Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	136	68	0.5	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Missense_Mutation	SNP	ENST00000409936.1	37	CCDS33190.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	T	17.70	3.454601	0.63290	0.033137	2.33E-4	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511	T;T;T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6	5.3	4.15	0.48705	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.105776	0.64402	D	0.000005	T	0.16342	0.0393	L	0.49778	1.585	0.40476	D	0.980399	D;B;B	0.61697	0.99;0.302;0.374	D;B;B	0.72982	0.979;0.162;0.383	T	0.05699	-1.0869	10	0.52906	T	0.07	-17.8051	10.6101	0.45417	0.0:0.0754:0.0:0.9246	.	528;524;590	Q4J6C6-3;Q4J6C6-2;Q4J6C6	.;.;PPCEL_HUMAN	S	501;501;501;590;590;590;590;524;528	ENSP00000439626:N501S;ENSP00000387095:N501S;ENSP00000387241:N501S;ENSP00000386543:N590S;ENSP00000260648:N590S;ENSP00000386909:N590S;ENSP00000386509:N590S;ENSP00000367781:N524S;ENSP00000367772:N528S	ENSP00000260648:N590S	N	-	2	0	PREPL	44404032	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.187000	0.58344	0.864000	0.35578	0.533000	0.62120	AAC	T|0.987;C|0.013	0.013	strong		0.348	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036	
TBX4	9496	hgsc.bcm.edu	37	17	59557600	59557600	+	Missense_Mutation	SNP	C	C	T	rs3744438	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	99	95	0.959596	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	
CYP4B1	1580	hgsc.bcm.edu	37	1	47283814	47283814	+	Silent	SNP	T	T	C	rs74072926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47283814T>C	ENST00000271153.4	+	11	1317	c.1281T>C	c.(1279-1281)tcT>tcC	p.S427S	CYP4B1_ENST00000371919.4_Silent_p.S413S|CYP4B1_ENST00000371923.4_Silent_p.S428S|CYP4B1_ENST00000452782.2_Silent_p.S265S			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	427					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	TCTTTGACTCTCTGCGCTTTT	0.577													T|||	24	0.00479233	0.0166	0.0029	5008	,	,		20927	0.0		0.0	False		,,,				2504	0.0				p.S428S		Atlas-SNP	.											CYP4B1,bladder,carcinoma,+1,2	CYP4B1	81	2	0			c.T1284C						PASS	.	T	,	36,4370	42.3+/-75.8	0,36,2167	147.0	136.0	140.0		1281,1284	-4.7	0.8	1	dbSNP_130	140	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous	CYP4B1	NM_000779.3,NM_001099772.1	,	0,38,6465	CC,CT,TT		0.0233,0.8171,0.2922	,	427/512,428/513	47283814	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	1580	exon11			TGACTCTCTGCGC	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"""Cytochrome P450s"""	2644	protein-coding gene	gene with protein product		124075	"""cytochrome P450, subfamily IVB, polypeptide 1"""				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.1281T>C	1.37:g.47283814T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	187	95	0.508021	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Silent	SNP	ENST00000271153.4	37	CCDS542.1																																																																																			T|0.995;C|0.005	0.005	strong		0.577	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779	
KIAA1324	57535	hgsc.bcm.edu	37	1	109656946	109656946	+	Silent	SNP	T	T	C	rs667524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109656946T>C	ENST00000369939.3	+	1	324	c.141T>C	c.(139-141)caT>caC	p.H47H	C1orf194_ENST00000369949.4_5'Flank|KIAA1324_ENST00000529753.1_Silent_p.H47H|C1orf194_ENST00000369948.3_5'Flank|C1orf194_ENST00000369945.3_5'Flank	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	47					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		CGGAGCTTCATGCCTGCAAAG	0.637													C|||	2690	0.537141	0.7511	0.4841	5008	,	,		15146	0.4812		0.3718	False		,,,				2504	0.5133				p.H47H		Atlas-SNP	.											.	KIAA1324	77	.	0			c.T141C						PASS	.	C		2967,1439		986,995,222	20.0	22.0	22.0		141	4.4	1.0	1	dbSNP_83	22	3079,5515		586,1907,1804	no	coding-synonymous	KIAA1324	NM_020775.3		1572,2902,2026	CC,CT,TT		35.8273,32.66,46.5077		47/1014	109656946	6046,6954	2203	4297	6500	SO:0001819	synonymous_variant	57535	exon1			GCTTCATGCCTGC	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"""estrogen induced gene 121"""	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.141T>C	1.37:g.109656946T>C		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	225	224	0.995556	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	37	CCDS794.1																																																																																			T|0.512;C|0.488	0.488	strong		0.637	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	
CCT2	10576	hgsc.bcm.edu	37	12	69986788	69986788	+	Silent	SNP	A	A	G	rs1043434	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:69986788A>G	ENST00000299300.6	+	9	971	c.783A>G	c.(781-783)acA>acG	p.T261T	CCT2_ENST00000543146.2_Silent_p.T214T|CCT2_ENST00000544368.2_Silent_p.T261T	NM_006431.2	NP_006422.1	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2 (beta)	261					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(1)	24	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			TTGACTCTACAGCAAAGGTTG	0.363													A|||	1086	0.216853	0.084	0.1888	5008	,	,		19934	0.3026		0.2565	False		,,,				2504	0.2873				p.T261T		Atlas-SNP	.											.	CCT2	49	.	0			c.A783G						PASS	.	A	,	459,3947	218.1+/-236.3	20,419,1764	81.0	82.0	82.0		642,783	4.6	1.0	12	dbSNP_86	82	1954,6646	345.9+/-325.9	204,1546,2550	no	coding-synonymous,coding-synonymous	CCT2	NM_001198842.1,NM_006431.2	,	224,1965,4314	GG,GA,AA		22.7209,10.4176,18.553	,	214/489,261/536	69986788	2413,10593	2203	4300	6503	SO:0001819	synonymous_variant	10576	exon9			CTCTACAGCAAAG	AF026293	CCDS8991.1, CCDS55843.1	12q14	2011-09-02						"""Heat Shock Proteins / Chaperonins"""	1615	protein-coding gene	gene with protein product		605139				9819444	Standard	NM_001198842		Approved	Cctb	uc001svb.1	P78371	OTTHUMG00000169383	ENST00000299300.6:c.783A>G	12.37:g.69986788A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_006431	A8K402|B5BTY7|B7Z243|B7Z7K4|B7ZAT2|Q14D36|Q6IAT3	Silent	SNP	ENST00000299300.6	37	CCDS8991.1																																																																																			A|0.800;G|0.200	0.200	strong		0.363	CCT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403818.1	NM_006431	
OPRK1	4986	hgsc.bcm.edu	37	8	54142157	54142157	+	Silent	SNP	T	T	C	rs702764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:54142157T>C	ENST00000265572.3	-	4	1140	c.843A>G	c.(841-843)gcA>gcG	p.A281A	OPRK1_ENST00000524278.1_Silent_p.A192A|OPRK1_ENST00000520287.1_Silent_p.A281A|RP11-162D9.3_ENST00000524425.1_RNA	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	281					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)			NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CGACGAAGACTGCCACCACCA	0.567													C|||	1225	0.244609	0.5416	0.2709	5008	,	,		19584	0.0764		0.1402	False		,,,				2504	0.1053				p.A281A		Atlas-SNP	.											.	OPRK1	90	.	0			c.A843G						PASS	.	C		2062,2344	608.8+/-391.2	485,1092,626	73.0	77.0	76.0		843	-11.6	0.0	8	dbSNP_86	76	1219,7381	762.7+/-407.6	101,1017,3182	no	coding-synonymous	OPRK1	NM_000912.3		586,2109,3808	CC,CT,TT		14.1744,46.7998,25.2268		281/381	54142157	3281,9725	2203	4300	6503	SO:0001819	synonymous_variant	4986	exon4			GAAGACTGCCACC		CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"""GPCR / Class A : Opioid receptors"""	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.843A>G	8.37:g.54142157T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_000912	E5RHC9|Q499G4	Silent	SNP	ENST00000265572.3	37	CCDS6152.1																																																																																			T|0.752;C|0.248	0.248	strong		0.567	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1		
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33053577	33053577	+	Missense_Mutation	SNP	G	G	A	rs9276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33053577G>A	ENST00000418931.2	+	4	784	c.668G>A	c.(667-669)cGg>cAg	p.R223Q		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	223	Connecting peptide.		R -> Q (in allele DPB1*01:01; dbSNP:rs9276).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GATTCTGCCCGGAGTAAGACA	0.562													.|||	688	0.13738	0.4062	0.0432	5008	,	,		19674	0.006		0.0437	False		,,,				2504	0.0726				p.R223Q		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.G668A						PASS	.	G	GLN/ARG	1369,3037	452.6+/-350.1	212,945,1046	110.0	93.0	99.0		668	1.8	0.2	6	dbSNP_52	99	449,8151	135.4+/-192.6	10,429,3861	yes	missense	HLA-DPB1	NM_002121.5	43	222,1374,4907	AA,AG,GG		5.2209,31.0713,13.9782	benign	223/259	33053577	1818,11188	2203	4300	6503	SO:0001583	missense	3115	exon4			CTGCCCGGAGTAA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.668G>A	6.37:g.33053577G>A	ENSP00000408146:p.Arg223Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	249|249	0.11401098901098901|0.11401098901098901	202|202	0.4105691056910569|0.4105691056910569	15|15	0.04143646408839779|0.04143646408839779	0|0	0.0|0.0	32|32	0.04221635883905013|0.04221635883905013	G|G	2.126|2.126	-0.400228|-0.400228	0.04865|0.04865	0.310713|0.310713	0.052209|0.052209	ENSG00000223865|ENSG00000223865	ENST00000416804|ENST00000418931;ENST00000411942;ENST00000422592;ENST00000428835	.|T;T	.|0.00651	.|6.11;5.97	4.03|4.03	1.79|1.79	0.24919|0.24919	.|Immunoglobulin-like fold (1);	.|1.004450	.|0.08019	.|N	.|0.991660	T|T	0.00178|0.00178	0.0005|0.0005	L|L	0.31420|0.31420	0.93|0.93	0.33673|0.33673	P|P	0.388849|0.388849	.|B;B;B	.|0.22604	.|0.072;0.013;0.013	.|B;B;B	.|0.17722	.|0.019;0.012;0.007	T|T	0.33523|0.33523	-0.9865|-0.9865	4|9	.|0.02654	.|T	.|1	.|.	4.6833|4.6833	0.12745|0.12745	0.4318:0.0:0.5682:0.0|0.4318:0.0:0.5682:0.0	rs9276;rs1126683;rs3179771;rs3203622;rs17851012;rs52801282|rs9276;rs1126683;rs3179771;rs3203622;rs17851012;rs52801282	.|189;233;223	.|A2ALJ6;Q59GY1;P04440	.|.;.;DPB1_HUMAN	R|Q	190|223;193;34;200	.|ENSP00000408146:R223Q;ENSP00000412654:R200Q	.|ENSP00000389210:R193Q	G|R	+|+	1|2	0|0	HLA-DPB1|HLA-DPB1	33161555|33161555	0.001000|0.001000	0.12720|0.12720	0.159000|0.159000	0.22649|0.22649	0.823000|0.823000	0.46562|0.46562	-0.160000|-0.160000	0.10041|0.10041	0.298000|0.298000	0.22638|0.22638	0.643000|0.643000	0.83706|0.83706	GGA|CGG	A|0.132;C|0.000;G|0.868;T|0.000	0.132	strong		0.562	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
TOX3	27324	hgsc.bcm.edu	37	16	52478206	52478206	+	Silent	SNP	C	C	T	rs3743796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	89	55	0.617977	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	
LAMC3	10319	hgsc.bcm.edu	37	9	133951230	133951230	+	Silent	SNP	C	C	T	rs3818800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133951230C>T	ENST00000361069.4	+	21	3640	c.3507C>T	c.(3505-3507)acC>acT	p.T1169T	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1169	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)		ACAGAGACACCGCCACCAAGA	0.622													C|||	911	0.181909	0.3782	0.0965	5008	,	,		17905	0.1558		0.0666	False		,,,				2504	0.1227				p.T1169T		Atlas-SNP	.											.	LAMC3	167	.	0			c.C3507T						PASS	.	C		1340,3066	420.4+/-339.0	219,902,1082	45.0	39.0	41.0		3507	-10.2	0.0	9	dbSNP_107	41	579,8021	149.8+/-204.8	20,539,3741	no	coding-synonymous	LAMC3	NM_006059.3		239,1441,4823	TT,TC,CC		6.7326,30.4131,14.7547		1169/1576	133951230	1919,11087	2203	4300	6503	SO:0001819	synonymous_variant	10319	exon21			AGACACCGCCACC	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.3507C>T	9.37:g.133951230C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																			C|0.830;T|0.170	0.170	strong		0.622	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
RTL1	388015	hgsc.bcm.edu	37	14	101347090	101347090	+	Missense_Mutation	SNP	C	C	T	rs73349352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101347090C>T	ENST00000534062.1	-	1	4094	c.4036G>A	c.(4036-4038)Gaa>Aaa	p.E1346K	MIR433_ENST00000384837.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	1346					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						GGCAGCTCTTCTAGCCTTGCC	0.627													C|||	213	0.0425319	0.1536	0.0144	5008	,	,		14165	0.0		0.0	False		,,,				2504	0.0				p.E1346K		Atlas-SNP	.											.	RTL1	120	.	0			c.G4036A						PASS	.						32.0	32.0	32.0					14																	101347090		692	1591	2283	SO:0001583	missense	388015	exon1			GCTCTTCTAGCCT		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.4036G>A	14.37:g.101347090C>T	ENSP00000435342:p.Glu1346Lys	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	173	86	0.49711	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	37	CCDS53910.1	73	0.033424908424908424	70	0.14227642276422764	3	0.008287292817679558	0	0.0	0	0.0	C	12.39	1.924506	0.34002	.	.	ENSG00000254656	ENST00000534062	T	0.28255	1.62	3.29	0.236	0.15471	.	.	.	.	.	T	0.00144	0.0004	N	0.24115	0.695	0.80722	P	0.0	B	0.34103	0.437	B	0.24541	0.054	T	0.09552	-1.0669	8	0.87932	D	0	.	10.9898	0.47543	0.0:0.4239:0.5761:0.0	.	1346	E9PKS8	.	K	1346	ENSP00000435342:E1346K	ENSP00000435342:E1346K	E	-	1	0	RTL1	100416843	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.458000	0.06737	0.044000	0.15775	-0.222000	0.12452	GAA	C|0.966;T|0.034	0.034	strong		0.627	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
TRPV1	7442	hgsc.bcm.edu	37	17	3475490	3475490	+	Silent	SNP	C	C	T	rs877610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3475490C>T	ENST00000571088.1	-	14	2370	c.2157G>A	c.(2155-2157)aaG>aaA	p.K719K	TRPV1_ENST00000174621.6_Silent_p.K717K|TRPV1_ENST00000310522.5_Silent_p.K659K|TRPV1_ENST00000576351.1_Silent_p.K709K|TRPV1_ENST00000399756.4_Silent_p.K719K|SHPK_ENST00000572705.1_Silent_p.K719K|TRPV1_ENST00000425167.2_Silent_p.K730K|TRPV1_ENST00000399759.3_Silent_p.K719K	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	719					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	AGCGGAAGGCCTTCCTCATGC	0.587													C|||	349	0.0696885	0.152	0.0159	5008	,	,		21078	0.0407		0.0388	False		,,,				2504	0.0583				p.K719K	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.G2157A						PASS	.	C	,,,	578,3618		34,510,1554	69.0	72.0	71.0		2157,2157,2157,2157	2.0	1.0	17	dbSNP_86	71	439,8021		13,413,3804	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	,,,	47,923,5358	TT,TC,CC		5.1891,13.775,8.0357	,,,	719/840,719/840,719/840,719/840	3475490	1017,11639	2098	4230	6328	SO:0001819	synonymous_variant	7442	exon14			GAAGGCCTTCCTC	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.2157G>A	17.37:g.3475490C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Silent	SNP	ENST00000571088.1	37	CCDS45576.1																																																																																			C|0.927;T|0.073	0.073	strong		0.587	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
CACNA1B	774	hgsc.bcm.edu	37	9	140952690	140952690	+	Silent	SNP	G	G	A	rs2229950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140952690G>A	ENST00000371372.1	+	28	4441	c.4296G>A	c.(4294-4296)ctG>ctA	p.L1432L	CACNA1B_ENST00000277549.5_Silent_p.L628L|CACNA1B_ENST00000371357.1_Silent_p.L1433L|CACNA1B_ENST00000277551.2_Silent_p.L1432L|CACNA1B_ENST00000371363.1_Silent_p.L1432L|CACNA1B_ENST00000371355.4_Silent_p.L1433L	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1432					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	AATGCAGCCTGGAGAAGAACG	0.537													G|||	1000	0.199681	0.5166	0.0432	5008	,	,		23336	0.1855		0.0149	False		,,,				2504	0.0869				p.L1432L		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G4296A						PASS	.	G		1758,2596		385,988,804	195.0	191.0	192.0		4296	3.2	1.0	9	dbSNP_98	192	63,8465		0,63,4201	no	coding-synonymous	CACNA1B	NM_000718.3		385,1051,5005	AA,AG,GG		0.7387,40.3767,14.136		1432/2340	140952690	1821,11061	2177	4264	6441	SO:0001819	synonymous_variant	774	exon28			CAGCCTGGAGAAG	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.4296G>A	9.37:g.140952690G>A		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_001243812	B1AQK5	Silent	SNP	ENST00000371372.1	37	CCDS59522.1																																																																																			G|0.843;A|0.157	0.157	strong		0.537	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
PCDH11X	27328	hgsc.bcm.edu	37	X	91090533	91090533	+	Silent	SNP	C	C	T	rs56704613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:91090533C>T	ENST00000373094.1	+	1	875	c.30C>T	c.(28-30)ttC>ttT	p.F10F	PCDH11X_ENST00000395337.2_Silent_p.F10F|PCDH11X_ENST00000361724.1_Silent_p.F10F|PCDH11X_ENST00000406881.1_Silent_p.F10F|PCDH11X_ENST00000504220.2_Silent_p.F10F|PCDH11X_ENST00000361655.2_Silent_p.F10F|PCDH11X_ENST00000298274.8_Silent_p.F10F|PCDH11X_ENST00000373097.1_Silent_p.F10F|PCDH11X_ENST00000373088.1_Silent_p.F10F	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	10					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						CGTACATTTTCGCGGTCCTGC	0.488													C|||	266	0.0704636	0.1868	0.0245	3775	,	,		12350	0.0		0.002	False		,,,				2504	0.0				p.F10F	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.C30T						PASS	.	C	,,,,,,,	788,3047		66,529,127,1037,444	131.0	105.0	114.0		30,30,30,30,30,30,30,30	1.0	1.0	X	dbSNP_129	114	5,6723		0,4,1,2424,1871	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PCDH11X	NM_001168360.1,NM_001168361.1,NM_001168362.1,NM_001168363.1,NM_014522.1,NM_032967.2,NM_032968.3,NM_032969.3	,,,,,,,	66,533,128,3461,2315	TT,TC,T,CC,C		0.0743,20.5476,7.5073	,,,,,,,	10/1340,10/1066,10/1311,10/1330,10/1022,10/1026,10/1348,10/1338	91090533	793,9770	2203	4300	6503	SO:0001819	synonymous_variant	27328	exon1			CATTTTCGCGGTC	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.30C>T	X.37:g.91090533C>T		Somatic	517	0	0		WXS	Illumina HiSeq	Phase_I	479	477	0.995825	NM_001168363	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Silent	SNP	ENST00000373094.1	37	CCDS14461.1																																																																																			C|0.922;T|0.078	0.078	strong		0.488	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969	
DDX11	1663	hgsc.bcm.edu	37	12	31250875	31250875	+	Missense_Mutation	SNP	G	G	C	rs145461857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:31250875G>C	ENST00000407793.2	+	18	2070	c.1819G>C	c.(1819-1821)Gcc>Ccc	p.A607P	DDX11_ENST00000350437.4_Missense_Mutation_p.A607P|DDX11_ENST00000545668.1_Missense_Mutation_p.A607P|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Missense_Mutation_p.A607P|DDX11_ENST00000228264.6_Missense_Mutation_p.A581P|DDX11_ENST00000539673.1_3'UTR	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	607					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.A607P(2)		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)					TGTGCACTTTGCCCAAGTGGT	0.582										Multiple Myeloma(12;0.14)																											p.A607P		Atlas-SNP	.											DDX11_ENST00000407793,NS,haematopoietic_neoplasm,0,6	DDX11	188	6	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1819C						scavenged	.						62.0	66.0	64.0					12																	31250875		2202	4297	6499	SO:0001583	missense	1663	exon18			CACTTTGCCCAAG	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.1819G>C	12.37:g.31250875G>C	ENSP00000384703:p.Ala607Pro	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	385	48	0.124675	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.836789	0.50951	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000404673;ENST00000228264;ENST00000545668;ENST00000350437	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	3.23	2.32	0.28847	.	0.107907	0.64402	D	0.000006	T	0.51787	0.1695	M	0.85299	2.745	0.80722	D	1	D;D;D;D	0.69078	0.988;0.997;0.989;0.988	P;D;D;P	0.66084	0.868;0.921;0.941;0.868	T	0.50118	-0.8865	10	0.41790	T	0.15	.	8.4401	0.32810	0.1232:0.0:0.8768:0.0	.	581;607;607;607	Q96FC9-3;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	P	607;607;332;581;607;607	ENSP00000443426:A607P;ENSP00000384703:A607P;ENSP00000228264:A581P;ENSP00000440402:A607P;ENSP00000309965:A607P	ENSP00000228264:A581P	A	+	1	0	DDX11	31142142	1.000000	0.71417	0.993000	0.49108	0.638000	0.38207	5.546000	0.67243	0.536000	0.28733	0.505000	0.49811	GCC	.	.	weak		0.582	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
CD1E	913	hgsc.bcm.edu	37	1	158326645	158326645	+	Missense_Mutation	SNP	G	G	A	rs61734680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158326645G>A	ENST00000368167.3	+	6	1365	c.1126G>A	c.(1126-1128)Gta>Ata	p.V376I	CD1E_ENST00000368163.3_Missense_Mutation_p.V309I|CD1E_ENST00000368164.3_3'UTR|CD1E_ENST00000368154.1_Missense_Mutation_p.V132I|CD1E_ENST00000368160.3_Missense_Mutation_p.V364I|CD1E_ENST00000368161.3_3'UTR|CD1E_ENST00000444681.2_Missense_Mutation_p.V277I|CD1E_ENST00000368166.3_Missense_Mutation_p.V175I|CD1E_ENST00000368157.1_Missense_Mutation_p.V120I|CD1E_ENST00000452291.2_Missense_Mutation_p.V187I|CD1E_ENST00000368155.3_Missense_Mutation_p.V219I|CD1E_ENST00000368165.3_Missense_Mutation_p.V286I|CD1E_ENST00000368156.1_Missense_Mutation_p.V274I	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	376					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)					CAAAAACAGAGTATTGAAGAA	0.438													G|||	198	0.0395367	0.1483	0.0029	5008	,	,		17554	0.0		0.0	False		,,,				2504	0.0				p.V376I		Atlas-SNP	.											.	CD1E	129	.	0			c.G1126A						PASS	.	G	ILE/VAL,,ILE/VAL,ILE/VAL,,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	507,3337		39,429,1454	111.0	108.0	109.0		1090,,925,523,,856,655,358,559,394,829,820,1126	-7.8	0.0	1	dbSNP_129	109	6,8242		0,6,4118	yes	missense,utr-3,missense,missense,utr-3,missense,missense,missense,missense,missense,missense,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	29,,29,29,,29,29,29,29,29,29,29,29	39,435,5572	AA,AG,GG		0.0727,13.1894,4.2425	benign,,benign,benign,,benign,benign,benign,benign,benign,benign,benign,benign	364/377,,309/322,175/188,,286/299,219/232,120/133,187/200,132/145,277/290,274/287,376/389	158326645	513,11579	1922	4124	6046	SO:0001583	missense	913	exon6			AACAGAGTATTGA	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.1126G>A	1.37:g.158326645G>A	ENSP00000357149:p.Val376Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_030893	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	66	0.03021978021978022	65	0.13211382113821138	1	0.0027624309392265192	0	0.0	0	0.0	G	7.949	0.744370	0.15710	0.131894	7.27E-4	ENSG00000158488	ENST00000444681;ENST00000368167;ENST00000452291;ENST00000368165;ENST00000368166;ENST00000368163;ENST00000368157;ENST00000368160;ENST00000368156;ENST00000368155;ENST00000368154	T;T;T;T;T;T;T;T;T;T;T	0.48522	5.17;4.63;3.37;3.4;3.55;3.38;0.81;4.72;3.58;3.47;0.81	3.9	-7.8	0.01214	.	1.447200	0.04683	N	0.412624	T	0.05686	0.0149	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B;B;B;P;B;B	0.42078	0.002;0.009;0.0;0.001;0.001;0.001;0.003;0.77;0.003;0.0	B;B;B;B;B;B;B;B;B;B	0.38712	0.0;0.004;0.0;0.001;0.001;0.0;0.001;0.28;0.002;0.0	T	0.14476	-1.0471	10	0.30078	T	0.28	-0.168	2.001	0.03467	0.2855:0.3958:0.1205:0.1982	rs61734680	277;286;219;175;364;376;187;132;274;309	E7EP01;P15812-5;P15812-7;P15812-9;P15812-2;P15812;P15812-8;P15812-11;P15812-6;P15812-4	.;.;.;.;.;CD1E_HUMAN;.;.;.;.	I	277;376;187;286;175;309;120;364;274;219;132	ENSP00000402906:V277I;ENSP00000357149:V376I;ENSP00000416228:V187I;ENSP00000357147:V286I;ENSP00000357148:V175I;ENSP00000357145:V309I;ENSP00000357139:V120I;ENSP00000357142:V364I;ENSP00000357138:V274I;ENSP00000357137:V219I;ENSP00000357136:V132I	ENSP00000357136:V132I	V	+	1	0	CD1E	156593269	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	-0.133000	0.10451	-1.713000	0.01392	-2.501000	0.00191	GTA	G|0.978;A|0.022	0.022	strong		0.438	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893	
NPY2R	4887	hgsc.bcm.edu	37	4	156135250	156135250	+	Silent	SNP	C	C	T	rs2342674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:156135250C>T	ENST00000329476.3	+	2	648	c.159C>T	c.(157-159)ctC>ctT	p.L53L	NPY2R_ENST00000506608.1_Silent_p.L53L	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	53					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)	AAGTTGTTCTCATATTGGCCT	0.468													C|||	144	0.028754	0.1067	0.0043	5008	,	,		21334	0.0		0.0	False		,,,				2504	0.0				p.L53L		Atlas-SNP	.											.	NPY2R	87	.	0			c.C159T						PASS	.	C		400,4006	199.1+/-222.7	17,366,1820	213.0	198.0	203.0		159	1.6	0.9	4	dbSNP_100	203	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NPY2R	NM_000910.2		17,368,6118	TT,TC,CC		0.0233,9.0785,3.0909		53/382	156135250	402,12604	2203	4300	6503	SO:0001819	synonymous_variant	4887	exon2			TGTTCTCATATTG	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.159C>T	4.37:g.156135250C>T		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	272	133	0.488971	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Silent	SNP	ENST00000329476.3	37	CCDS3791.1																																																																																			C|0.967;T|0.033	0.033	strong		0.468	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910	
ADAMTS9	56999	hgsc.bcm.edu	37	3	64672474	64672474	+	Missense_Mutation	SNP	A	A	T	rs36115950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:64672474A>T	ENST00000498707.1	-	2	628	c.286T>A	c.(286-288)Tcc>Acc	p.S96T	ADAMTS9-AS2_ENST00000474768.1_RNA|ADAMTS9_ENST00000459780.1_Missense_Mutation_p.S96T|ADAMTS9_ENST00000295903.4_Missense_Mutation_p.S96T|ADAMTS9-AS2_ENST00000481312.1_RNA|ADAMTS9-AS2_ENST00000460833.1_RNA|ADAMTS9-AS2_ENST00000485174.1_RNA	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	96	Poly-Ser.		S -> P (in dbSNP:rs36115950). {ECO:0000269|PubMed:12514189}.|S -> T (in dbSNP:rs36115950).		glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		TGCGCCTGggaggaggtagag	0.562													A|||	632	0.126198	0.2504	0.1916	5008	,	,		16654	0.0734		0.0328	False		,,,				2504	0.0624				p.S96T		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.T286A						PASS	.	A	THR/SER	1007,3399	373.7+/-320.9	117,773,1313	60.0	52.0	55.0		286	0.9	1.0	3	dbSNP_126	55	290,8310	107.8+/-168.5	3,284,4013	yes	missense	ADAMTS9	NM_182920.1	58	120,1057,5326	TT,TA,AA		3.3721,22.8552,9.9723	benign	96/1936	64672474	1297,11709	2203	4300	6503	SO:0001583	missense	56999	exon2			CCTGGGAGGAGGT	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.286T>A	3.37:g.64672474A>T	ENSP00000418735:p.Ser96Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	184	79	0.429348	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	37	CCDS2903.1	265	0.12133699633699634	115	0.23373983739837398	63	0.17403314917127072	58	0.10139860139860139	29	0.03825857519788918	A	5.460	0.269907	0.10349	0.228552	0.033721	ENSG00000163638	ENST00000295903;ENST00000498707;ENST00000459780	T;T;T	0.06768	3.26;3.26;3.26	4.89	0.91	0.19337	Peptidase M12B, propeptide (1);	0.268793	0.30630	N	0.009215	T	0.00012	0.0000	L	0.34521	1.04	0.39638	P	0.029722000000000026	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.12837	0.008;0.008;0.008	T	0.46978	-0.9152	9	0.20046	T	0.44	.	1.8888	0.03243	0.4205:0.2564:0.0751:0.2479	rs36115950	96;96;96	B7ZVX9;Q9P2N4-2;Q9P2N4	.;.;ATS9_HUMAN	T	96	ENSP00000295903:S96T;ENSP00000418735:S96T;ENSP00000419217:S96T	ENSP00000295903:S96T	S	-	1	0	ADAMTS9	64647514	0.961000	0.32948	0.975000	0.42487	0.966000	0.64601	-0.265000	0.08644	-0.010000	0.14271	0.402000	0.26972	TCC	A|0.886;T|0.114	0.114	strong		0.562	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
REV1	51455	hgsc.bcm.edu	37	2	100055158	100055158	+	Missense_Mutation	SNP	T	T	C	rs3087399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:100055158T>C	ENST00000258428.3	-	6	1346	c.1118A>G	c.(1117-1119)aAt>aGt	p.N373S	REV1_ENST00000465835.1_5'UTR|REV1_ENST00000393445.3_Missense_Mutation_p.N373S	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	373			N -> S (in dbSNP:rs3087399).		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						TTGTAGGGTATTGACAAACTC	0.368								Direct reversal of damage					.|||	841	0.167931	0.2859	0.0576	5008	,	,		18937	0.0536		0.1193	False		,,,				2504	0.2546				p.N373S		Atlas-SNP	.											.	REV1	100	.	0			c.A1118G						PASS	.	T	SER/ASN,SER/ASN	1125,3281	399.5+/-331.2	136,853,1214	97.0	103.0	101.0		1118,1118	-0.6	0.8	2	dbSNP_102	101	1028,7572	220.6+/-258.3	59,910,3331	yes	missense,missense	REV1	NM_001037872.1,NM_016316.2	46,46	195,1763,4545	CC,CT,TT		11.9535,25.5334,16.5539	benign,benign	373/1251,373/1252	100055158	2153,10853	2203	4300	6503	SO:0001583	missense	51455	exon6			AGGGTATTGACAA	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.1118A>G	2.37:g.100055158T>C	ENSP00000258428:p.Asn373Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	121	57	0.471074	NM_001037872	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	290	0.13278388278388278	150	0.3048780487804878	20	0.055248618784530384	16	0.027972027972027972	104	0.13720316622691292	T	9.343	1.063410	0.20067	0.255334	0.119535	ENSG00000135945	ENST00000393445;ENST00000258428;ENST00000450415	T;T;T	0.53423	1.55;1.56;0.62	5.99	-0.648	0.11464	.	0.214602	0.56097	N	0.000031	T	0.00012	0.0000	L	0.49350	1.555	0.22918	P	0.99856913	B;B;B	0.22414	0.069;0.001;0.036	B;B;B	0.28991	0.086;0.008;0.097	T	0.34204	-0.9838	9	0.11485	T	0.65	.	10.7703	0.46319	0.0:0.3803:0.0:0.6197	rs3087399;rs52791165;rs57440453;rs3087399	352;373;373	Q9UBZ9-3;Q9UBZ9;Q9UBZ9-2	.;REV1_HUMAN;.	S	373;373;11	ENSP00000377091:N373S;ENSP00000258428:N373S;ENSP00000414875:N11S	ENSP00000258428:N373S	N	-	2	0	REV1	99421590	1.000000	0.71417	0.794000	0.32065	0.977000	0.68977	1.404000	0.34623	-0.321000	0.08627	-0.250000	0.11733	AAT	T|0.866;C|0.134	0.134	strong		0.368	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	
CPO	130749	hgsc.bcm.edu	37	2	207827220	207827220	+	Missense_Mutation	SNP	G	G	A	rs62617140	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	158	0	0		WXS	Illumina HiSeq	Phase_I	148	68	0.459459	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	
OR10H3	26532	hgsc.bcm.edu	37	19	15853150	15853150	+	Silent	SNP	C	C	T	rs16980824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15853150C>T	ENST00000305892.1	+	1	948	c.948C>T	c.(946-948)tcC>tcT	p.S316S		NM_013938.1	NP_039226.1	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H, member 3	316						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						CTCTAAGCTCCTAATGGCCAG	0.413													c|||	1309	0.261382	0.4327	0.2752	5008	,	,		21513	0.0119		0.3131	False		,,,				2504	0.2239				p.S316S		Atlas-SNP	.											.	OR10H3	53	.	0			c.C948T						PASS	.	C		1780,2620		371,1038,791	54.0	58.0	56.0		948	-1.8	0.0	19	dbSNP_123	56	2454,6142		373,1708,2217	no	coding-synonymous	OR10H3	NM_013938.1		744,2746,3008	TT,TC,CC		28.5482,40.4545,32.5793		316/317	15853150	4234,8762	2200	4298	6498	SO:0001819	synonymous_variant	26532	exon1			AAGCTCCTAATGG		CCDS12334.1	19p13.1	2012-08-09				ENSG00000171936		"""GPCR / Class A : Olfactory receptors"""	8174	protein-coding gene	gene with protein product							Standard	NM_013938		Approved		uc010xoq.2	O60404		ENST00000305892.1:c.948C>T	19.37:g.15853150C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_013938	Q2HIZ3|Q6IFQ0	Silent	SNP	ENST00000305892.1	37	CCDS12334.1																																																																																			C|0.720;T|0.280	0.280	strong		0.413	OR10H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460918.1		
OR10H4	126541	hgsc.bcm.edu	37	19	16060021	16060021	+	Silent	SNP	C	C	T	rs16980821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16060021C>T	ENST00000322107.1	+	1	204	c.204C>T	c.(202-204)tcC>tcT	p.S68S		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	68						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(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						GCACCCTCTCCGTCTCTGAGA	0.512													.|||	1210	0.241613	0.4629	0.1772	5008	,	,		22980	0.0526		0.2644	False		,,,				2504	0.1595				p.S68S		Atlas-SNP	.											.	OR10H4	48	.	0			c.C204T						PASS	.	C		1849,2557	537.5+/-374.7	384,1081,738	425.0	392.0	403.0		204	0.1	0.6	19	dbSNP_123	403	2050,6550	357.3+/-330.7	236,1578,2486	no	coding-synonymous	OR10H4	NM_001004465.1		620,2659,3224	TT,TC,CC		23.8372,41.9655,29.9785		68/317	16060021	3899,9107	2203	4300	6503	SO:0001819	synonymous_variant	126541	exon1			CCTCTCCGTCTCT	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"""GPCR / Class A : Olfactory receptors"""	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.204C>T	19.37:g.16060021C>T		Somatic	370	0	0		WXS	Illumina HiSeq	Phase_I	372	372	1	NM_001004465	Q6IFJ2|Q96R57	Silent	SNP	ENST00000322107.1	37	CCDS32941.1																																																																																			C|0.723;T|0.277	0.277	strong		0.512	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548534	32548534	+	Missense_Mutation	SNP	C	C	T	rs71547382		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32548534C>T	ENST00000360004.5	-	4	857	c.752G>A	c.(751-753)aGg>aAg	p.R251K		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	251					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						TTTCTGATTCCTGAAGTAGAT	0.537										Multiple Myeloma(14;0.17)																											p.R251K		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G752A						PASS	.																																			SO:0001583	missense	3123	exon4			TGATTCCTGAAGT	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.752G>A	6.37:g.32548534C>T	ENSP00000353099:p.Arg251Lys	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	439	28	0.0637813	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	12.57	1.976489	0.34848	.	.	ENSG00000196126	ENST00000360004	T	0.00635	6.06	3.98	1.66	0.24008	.	0.334220	0.32578	N	0.005907	T	0.00241	0.0007	L	0.33710	1.025	0.28819	N	0.897785	B;B;B	0.18166	0.026;0.026;0.0	B;B;B	0.17979	0.02;0.02;0.001	T	0.44757	-0.9307	10	0.38643	T	0.18	.	6.6584	0.23000	0.0:0.6946:0.0:0.3054	.	251;251;251	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	K	251	ENSP00000353099:R251K	ENSP00000353099:R251K	R	-	2	0	HLA-DRB1	32656512	0.000000	0.05858	0.929000	0.37066	0.845000	0.48019	-0.186000	0.09670	0.802000	0.34089	0.453000	0.30009	AGG	C|1.000;|0.000	.	weak		0.537	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
VIPR2	7434	hgsc.bcm.edu	37	7	158896517	158896517	+	Silent	SNP	G	G	A	rs2270313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:158896517G>A	ENST00000262178.2	-	4	473	c.288C>T	c.(286-288)gaC>gaT	p.D96D	VIPR2_ENST00000402066.1_Silent_p.D237D	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	96					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		CTGACCATCCGTCACTCGTAC	0.507													G|||	1206	0.240815	0.3185	0.1873	5008	,	,		20770	0.1974		0.2485	False		,,,				2504	0.2106				p.D96D	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.C288T						PASS	.	G		1334,3072	447.9+/-348.5	214,906,1083	235.0	192.0	206.0		288	-7.6	0.2	7	dbSNP_100	206	1995,6605	350.5+/-327.9	225,1545,2530	no	coding-synonymous	VIPR2	NM_003382.4		439,2451,3613	AA,AG,GG		23.1977,30.2769,25.5959		96/439	158896517	3329,9677	2203	4300	6503	SO:0001819	synonymous_variant	7434	exon4			CCATCCGTCACTC	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12695	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 2"""	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.288C>T	7.37:g.158896517G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	37	CCDS5950.1	560	0.2564102564102564	169	0.3434959349593496	76	0.20994475138121546	127	0.22202797202797203	188	0.24802110817941952	G	0.289	-0.981342	0.02197	0.302769	0.231977	ENSG00000106018	ENST00000418475	.	.	.	5.0	-7.55	0.01327	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21841	P	0.999511805	.	.	.	.	.	.	T	0.24621	-1.0155	3	.	.	.	.	9.5043	0.39037	0.7778:0.0:0.1167:0.1054	rs2270313;rs2270313	.	.	.	W	92	.	.	R	-	1	2	VIPR2	158589278	0.647000	0.27304	0.188000	0.23233	0.014000	0.08584	-0.332000	0.07904	-1.063000	0.03177	-1.012000	0.02466	CGG	G|0.750;A|0.250	0.250	strong		0.507	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382	
SLC35G3	146861	hgsc.bcm.edu	37	17	33520904	33520904	+	Silent	SNP	G	G	A	rs61753879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33520904G>A	ENST00000297307.5	-	1	508	c.423C>T	c.(421-423)tgC>tgT	p.C141C	RP11-799D4.2_ENST00000590144.1_RNA	NM_152462.2	NP_689675.1	Q8N808	S35G3_HUMAN	solute carrier family 35, member G3	141	EamA 1.					integral component of membrane (GO:0016021)											GGACGGCGGAGCAGACGGTGG	0.582													G|||	87	0.0173722	0.0635	0.0043	5008	,	,		19375	0.0		0.0	False		,,,				2504	0.0				p.C141C		Atlas-SNP	.											.	.	.	.	0			c.C423T						PASS	.	G		259,4147	148.4+/-182.8	5,249,1949	163.0	154.0	157.0		423		0.3	17	dbSNP_129	157	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC35G3	NM_152462.2		5,250,6248	AA,AG,GG		0.0116,5.8783,1.9991		141/339	33520904	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	146861	exon1			GGCGGAGCAGACG	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.423C>T	17.37:g.33520904G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	211	104	0.492891	NM_152462	B9EGE9	Silent	SNP	ENST00000297307.5	37	CCDS11293.1																																																																																			G|0.977;A|0.023	0.023	strong		0.582	SLC35G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256445.2	NM_152462	
OR4F6	390648	hgsc.bcm.edu	37	15	102346030	102346030	+	Silent	SNP	G	G	A	rs401632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:102346030G>A	ENST00000328882.4	+	1	129	c.108G>A	c.(106-108)gtG>gtA	p.V36V		NM_001005326.1	NP_001005326.1	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F, member 6	36						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(1)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	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)			TGTTCTATGTGTCAAGCCTGA	0.498													g|||	235	0.0469249	0.1732	0.0086	5008	,	,		20248	0.0		0.0	False		,,,				2504	0.0				p.V36V		Atlas-SNP	.											.	OR4F6	45	.	0			c.G108A						PASS	.	G		769,3637		68,633,1502	254.0	233.0	240.0		108	0.4	0.1	15	dbSNP_80	240	23,8577		0,23,4277	no	coding-synonymous	OR4F6	NM_001005326.1		68,656,5779	AA,AG,GG		0.2674,17.4535,6.0895		36/313	102346030	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	390648	exon1			CTATGTGTCAAGC	AC025234	CCDS32341.1	15q26.3	2014-02-19	2002-02-28		ENSG00000184140	ENSG00000184140		"""GPCR / Class A : Olfactory receptors"""	15372	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily F, member 12"""	OR4F12			Standard	NM_001005326		Approved		uc010utr.2	Q8NGB9	OTTHUMG00000172267	ENST00000328882.4:c.108G>A	15.37:g.102346030G>A		Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	279	135	0.483871	NM_001005326	B9EH28|Q6IF95	Silent	SNP	ENST00000328882.4	37	CCDS32341.1																																																																																			G|0.944;A|0.056	0.056	strong		0.498	OR4F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417593.1		
NBPF10	100132406	hgsc.bcm.edu	37	1	145296510	145296510	+	Silent	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:145296510C>G	ENST00000342960.5	+	3	467	c.432C>G	c.(430-432)ctC>ctG	p.L144L	NBPF10_ENST00000369338.1_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	144						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			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)		GGCAGGACCTCCAAGAACAGC	0.592																																					p.L144L		Atlas-SNP	.											NBPF10,right_lower_lobe,carcinoma,0,1	NBPF10	221	1	0			c.C432G						scavenged	.																																			SO:0001819	synonymous_variant	100132406	exon3			GGACCTCCAAGAA	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.432C>G	1.37:g.145296510C>G		Somatic	323	3	0.00928793		WXS	Illumina HiSeq	Phase_I	391	18	0.0460358	NM_001039703	Q5RHC0|Q9NWN6	Silent	SNP	ENST00000342960.5	37	CCDS53355.1																																																																																			.	.	none		0.592	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
TNFSF10	8743	hgsc.bcm.edu	37	3	172224303	172224303	+	Silent	SNP	A	A	G	rs1131532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:172224303A>G	ENST00000241261.2	-	5	947	c.825T>C	c.(823-825)ttT>ttC	p.F275F	TNFSF10_ENST00000420541.2_3'UTR	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	275					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			AAAAGGCCCCAAAAAAACTGG	0.358													G|||	3344	0.667732	0.77	0.5576	5008	,	,		19172	0.619		0.6909	False		,,,				2504	0.6339				p.F275F		Atlas-SNP	.											.	TNFSF10	30	.	0			c.T825C						PASS	.	G	,	3455,951	360.1+/-315.1	1348,759,96	57.0	56.0	56.0		,825	-7.3	0.4	3	dbSNP_86	56	5811,2789	433.6+/-357.5	1946,1919,435	no	utr-3,coding-synonymous	TNFSF10	NM_001190942.1,NM_003810.3	,	3294,2678,531	GG,GA,AA		32.4302,21.5842,28.756	,	,275/282	172224303	9266,3740	2203	4300	6503	SO:0001819	synonymous_variant	8743	exon5			GGCCCCAAAAAAA	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.825T>C	3.37:g.172224303A>G		Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	269	269	1	NM_003810	A1Y9B3	Silent	SNP	ENST00000241261.2	37	CCDS3219.1																																																																																			G|0.691;C|0.000;A|0.309	0.691	strong		0.358	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1		
SPDYA	245711	hgsc.bcm.edu	37	2	29063342	29063342	+	3'UTR	SNP	T	T	C	rs6747208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29063342T>C	ENST00000462832.1	+	0	1756				SPDYA_ENST00000334056.5_Intron|SPDYA_ENST00000379579.4_Intron					speedy/RINGO cell cycle regulator family member A											cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(172;0.155)					GAAGGTATGATTTAGTAATAT	0.373													T|||	36	0.0071885	0.0272	0.0	5008	,	,		19472	0.0		0.0	False		,,,				2504	0.0				p.I286T		Atlas-SNP	.											.	SPDYA	41	.	0			c.T857C						PASS	.	T	THR/ILE,,	85,4321	68.7+/-106.4	0,85,2118	69.0	68.0	69.0		857,,	1.7	0.9	2	dbSNP_116	69	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron,intron	SPDYA	NM_001008779.1,NM_001142634.1,NM_182756.3	89,,	0,86,6417	CC,CT,TT		0.0116,1.9292,0.6612	,,	286/287,,	29063342	86,12920	2203	4300	6503	SO:0001624	3_prime_UTR_variant	245711	exon5			GTATGATTTAGTA	AA424209	CCDS1767.2	2p23	2013-05-08	2013-05-08	2006-03-31	ENSG00000163806	ENSG00000163806		"""Speedy homologs"""	30613	protein-coding gene	gene with protein product		614029	"""speedy homolog 1 (Drosophila)"", ""speedy homolog A (Xenopus laevis)"""	SPDY1		11980914, 12839962, 15611625	Standard	NM_182756		Approved	SPY1, Ringo3	uc002rmk.3	Q5MJ70	OTTHUMG00000074041	ENST00000462832.1:c.*1753T>C	2.37:g.29063342T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_001008779		Missense_Mutation	SNP	ENST00000462832.1	37																																																																																				T|0.993;C|0.007	0.007	strong		0.373	SPDYA-003	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000157172.2	NM_182756	
GPRC6A	222545	hgsc.bcm.edu	37	6	117130561	117130561	+	Silent	SNP	T	T	G	rs76688215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117130561T>G	ENST00000310357.3	-	2	435	c.414A>C	c.(412-414)ccA>ccC	p.P138P	GPRC6A_ENST00000368549.3_Silent_p.P138P|GPRC6A_ENST00000530250.1_Silent_p.P138P	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	138					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		CCTTAACTCTTGGCATGTAGC	0.443													T|||	76	0.0151757	0.0545	0.0029	5008	,	,		19458	0.0		0.002	False		,,,				2504	0.0				p.P138P		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A414C						PASS	.	T		161,4245	109.9+/-148.2	3,155,2045	96.0	91.0	93.0		414	0.9	1.0	6	dbSNP_132	93	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	GPRC6A	NM_148963.2		3,159,6341	GG,GT,TT		0.0465,3.6541,1.2686		138/927	117130561	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	222545	exon2			AACTCTTGGCATG	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.414A>C	6.37:g.117130561T>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			T|0.984;G|0.016	0.016	strong		0.443	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
MYO10	4651	hgsc.bcm.edu	37	5	16673800	16673800	+	Silent	SNP	G	G	A	rs3188408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16673800G>A	ENST00000513610.1	-	36	5617	c.5163C>T	c.(5161-5163)acC>acT	p.T1721T	MYO10_ENST00000505695.1_Silent_p.T1060T|MYO10_ENST00000274203.9_Silent_p.T1078T|MYO10_ENST00000427430.2_Silent_p.T1078T|MYO10_ENST00000515803.1_Silent_p.T1060T	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1721	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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						CCTCCCCAGCGGTGGTGTGGG	0.537													G|||	151	0.0301518	0.1074	0.0058	5008	,	,		16446	0.0		0.001	False		,,,				2504	0.0041				p.T1721T		Atlas-SNP	.											.	MYO10	198	.	0			c.C5163T						PASS	.	G		383,3691		24,335,1678	50.0	52.0	51.0		5163	-10.6	0.2	5	dbSNP_105	51	3,8375		0,3,4186	no	coding-synonymous	MYO10	NM_012334.2		24,338,5864	AA,AG,GG		0.0358,9.4011,3.0999		1721/2059	16673800	386,12066	2037	4189	6226	SO:0001819	synonymous_variant	4651	exon36			CCCAGCGGTGGTG	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.5163C>T	5.37:g.16673800G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			G|0.980;A|0.020	0.020	strong		0.537	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
DNAH17	8632	hgsc.bcm.edu	37	17	76528591	76528591	+	Silent	SNP	C	C	T	rs11868065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76528591C>T	ENST00000585328.1	-	20	3202	c.3078G>A	c.(3076-3078)ccG>ccA	p.P1026P	DNAH17_ENST00000389840.5_Silent_p.P1029P|RN7SL454P_ENST00000492744.2_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1029	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)			CCAGGGTGGGCGGTGTCTTGG	0.552													C|||	2307	0.460663	0.5008	0.4193	5008	,	,		18466	0.4167		0.5348	False		,,,				2504	0.4049				p.P1029P		Atlas-SNP	.											.	DNAH17	347	.	0			c.G3087A						PASS	.	C		2074,2050		529,1016,517	35.0	39.0	38.0		3087	-8.0	0.0	17	dbSNP_120	38	4501,3869		1207,2087,891	no	coding-synonymous	DNAH17	NM_173628.3		1736,3103,1408	TT,TC,CC		46.2246,49.709,47.3747		1029/4463	76528591	6575,5919	2062	4185	6247	SO:0001819	synonymous_variant	8632	exon20			GGTGGGCGGTGTC	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.3078G>A	17.37:g.76528591C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	114	111	0.973684	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				C|0.509;T|0.491	0.491	strong		0.552	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
FAM9A	171482	hgsc.bcm.edu	37	X	8764370	8764370	+	Missense_Mutation	SNP	C	C	T	rs148031370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:8764370C>T	ENST00000543214.1	-	6	562	c.427G>A	c.(427-429)Gca>Aca	p.A143T	FAM9A_ENST00000381003.3_Missense_Mutation_p.A143T	NM_001171186.1	NP_001164657.1	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	143						nucleus (GO:0005634)				endometrium(11)|kidney(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	18		Hepatocellular(5;0.219)				CTGTAAGCTGCTTTATCTATT	0.294													c|||	11	0.00291391	0.0	0.0	3775	,	,		13462	0.0		0.0099	False		,,,				2504	0.001				p.A143T		Atlas-SNP	.											.	FAM9A	57	.	0			c.G427A						PASS	.	T	THR/ALA,THR/ALA	2,3833		0,2,0,1630,571	163.0	125.0	138.0		427,427	-0.3	0.0	X	dbSNP_134	138	35,6691		0,24,11,2404,1859	yes	missense,missense	FAM9A	NM_001171186.1,NM_174951.3	58,58	0,26,11,4034,2430	TT,TC,T,CC,C		0.5204,0.0522,0.3503	possibly-damaging,possibly-damaging	143/333,143/333	8764370	37,10524	2203	4298	6501	SO:0001583	missense	171482	exon6			AAGCTGCTTTATC		CCDS14131.1	Xp22.32	2012-11-29			ENSG00000183304	ENSG00000183304			18403	protein-coding gene	gene with protein product	"""testis expressed 39A"""	300477					Standard	NM_174951		Approved	TEX39A	uc004csg.3	Q8IZU1	OTTHUMG00000021110	ENST00000543214.1:c.427G>A	X.37:g.8764370C>T	ENSP00000440163:p.Ala143Thr	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	140	65	0.464286	NM_174951	B7ZLH5|Q2M2D1	Missense_Mutation	SNP	ENST00000543214.1	37	CCDS14131.1	8	0.004822182037371911	0	0.0	0	0.0	0	0.0	6	0.007957559681697613	c	5.235	0.228805	0.09916	5.22E-4	0.005204	ENSG00000183304	ENST00000381003;ENST00000543214	.	.	.	0.678	-0.327	0.12694	.	.	.	.	.	T	0.21307	0.0513	N	0.22421	0.69	0.09310	N	1	D	0.58620	0.983	P	0.53861	0.736	T	0.17379	-1.0371	7	0.14656	T	0.56	.	.	.	.	.	143	Q8IZU1	FAM9A_HUMAN	T	143	.	ENSP00000370391:A143T	A	-	1	0	FAM9A	8724370	0.971000	0.33674	0.000000	0.03702	0.005000	0.04900	0.178000	0.16820	-0.205000	0.10219	0.458000	0.33432	GCA	C|0.996;T|0.004	0.004	strong		0.294	FAM9A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055697.1	NM_174951	
UBB	7314	hgsc.bcm.edu	37	17	16285542	16285542	+	Silent	SNP	G	G	A	rs17052364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16285542G>A	ENST00000395837.1	+	2	502	c.321G>A	c.(319-321)caG>caA	p.Q107Q	UBB_ENST00000302182.3_Silent_p.Q107Q|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000535788.1_Intron|UBB_ENST00000578649.1_Intron|UBB_ENST00000395839.1_Silent_p.Q107Q	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	107	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|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)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|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)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|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 epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|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)|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 transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|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)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)		p.Q107Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		CCAAGATCCAGGATAAAGAAG	0.537																																					p.Q107Q	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,NS,carcinoma,0,1	UBB	30	1	1	Substitution - coding silent(1)	lung(1)	c.G321A						scavenged	.						114.0	110.0	112.0					17																	16285542		2203	4300	6503	SO:0001819	synonymous_variant	7314	exon2			GATCCAGGATAAA		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.321G>A	17.37:g.16285542G>A		Somatic	267	2	0.00749064		WXS	Illumina HiSeq	Phase_I	281	6	0.0213523	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			G|0.540;A|0.460	0.460	strong		0.537	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
ANK3	288	hgsc.bcm.edu	37	10	61830256	61830256	+	Silent	SNP	T	T	C	rs61732400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:61830256T>C	ENST00000280772.2	-	37	10574	c.10383A>G	c.(10381-10383)caA>caG	p.Q3461Q	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3461					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						CAAGTTTACTTTGGCTAAAAG	0.438													T|||	159	0.0317492	0.1135	0.0115	5008	,	,		21138	0.001		0.0	False		,,,				2504	0.0				p.Q3461Q		Atlas-SNP	.											.	ANK3	703	.	0			c.A10383G						PASS	.	T	,,,	449,3957	215.1+/-234.2	19,411,1773	83.0	80.0	81.0		,,,10383	-2.4	1.0	10	dbSNP_129	81	6,8594	4.3+/-15.6	0,6,4294	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	19,417,6067	CC,CT,TT		0.0698,10.1906,3.4984	,,,	,,,3461/4378	61830256	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			TTTACTTTGGCTA	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.10383A>G	10.37:g.61830256T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			T|0.970;C|0.030	0.030	strong		0.438	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
TSHR	7253	hgsc.bcm.edu	37	14	81562998	81562998	+	Silent	SNP	T	T	C	rs2075179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:81562998T>C	ENST00000541158.2	+	8	883	c.561T>C	c.(559-561)aaT>aaC	p.N187N	TSHR_ENST00000342443.6_Silent_p.N187N|TSHR_ENST00000554263.1_Silent_p.N187N|TSHR_ENST00000554435.1_Silent_p.N187N|TSHR_ENST00000298171.2_Silent_p.N187N			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	187					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)	p.N187N(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	TGTACAACAATGGCTTTACTT	0.443			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism						C|||	1503	0.30012	0.5953	0.1427	5008	,	,		20379	0.3036		0.1292	False		,,,				2504	0.1851				p.N187N		Atlas-SNP	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	TSHR_ENST00000554435,NS,carcinoma,+2,3	TSHR	462	3	1	Substitution - coding silent(1)	stomach(1)	c.T561C						PASS	.	C	,,	2341,2065	569.7+/-382.7	625,1091,487	154.0	126.0	135.0		561,561,561	0.9	1.0	14	dbSNP_96	135	1167,7433	765.0+/-407.6	78,1011,3211	no	coding-synonymous,coding-synonymous,coding-synonymous	TSHR	NM_000369.2,NM_001018036.2,NM_001142626.2	,,	703,2102,3698	CC,CT,TT		13.5698,46.8679,26.9722	,,	187/765,187/254,187/275	81562998	3508,9498	2203	4300	6503	SO:0001819	synonymous_variant	7253	exon7			CAACAATGGCTTT	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"""GPCR / Class A : Gonadotropin and TSH receptors"""	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.561T>C	14.37:g.81562998T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	138	73	0.528986	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Silent	SNP	ENST00000541158.2	37	CCDS9872.1																																																																																			T|0.711;C|0.289	0.289	strong		0.443	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369	
SLC26A9	115019	hgsc.bcm.edu	37	1	205884274	205884274	+	3'UTR	SNP	T	T	C	rs6669481	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:205884274T>C	ENST00000367135.3	-	0	2700				SLC26A9_ENST00000340781.4_Missense_Mutation_p.R804G|SLC26A9_ENST00000367134.2_Missense_Mutation_p.R804G	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9						anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			CTCTCACTCCTGTAAGGGTAG	0.632													T|||	772	0.154153	0.4523	0.0879	5008	,	,		18467	0.0		0.1004	False		,,,				2504	0.0123				p.R804G		Atlas-SNP	.											.	SLC26A9	176	.	0			c.A2410G						PASS	.	T	,GLY/ARG	1764,2642	521.9+/-370.6	366,1032,805	53.0	56.0	55.0		,2410	0.7	0.0	1	dbSNP_116	55	829,7771	191.4+/-237.6	34,761,3505	yes	utr-3,missense	SLC26A9	NM_052934.3,NM_134325.2	,125	400,1793,4310	CC,CT,TT		9.6395,40.0363,19.937	,benign	,804/888	205884274	2593,10413	2203	4300	6503	SO:0001624	3_prime_UTR_variant	115019	exon22			CACTCCTGTAAGG	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"""Solute carriers"""	14469	protein-coding gene	gene with protein product	"""anion transporter/exchanger-9"""	608481	"""solute carrier family 26, member 9"""			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.*211A>G	1.37:g.205884274T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	146	81	0.554795	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	37	CCDS30990.1	326	0.14926739926739926	214	0.4349593495934959	39	0.10773480662983426	0	0.0	73	0.09630606860158311	T	9.562	1.118803	0.20877	0.400363	0.096395	ENSG00000174502	ENST00000340781;ENST00000367134	D;D	0.93712	-3.27;-3.27	3.33	0.714	0.18180	.	3.958980	0.00589	N	0.000351	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.09022	0.0;0.002	B;B	0.10450	0.0;0.005	T	0.34428	-0.9829	9	0.44086	T	0.13	.	3.4704	0.07565	0.0:0.1357:0.2316:0.6328	rs6669481;rs52795600;rs59281091;rs6669481	804;51	B1AVM8;Q8NAY2	.;.	G	804	ENSP00000341682:R804G;ENSP00000356102:R804G	ENSP00000341682:R804G	R	-	1	2	SLC26A9	204150897	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.462000	0.21956	-0.210000	0.10140	0.379000	0.24179	AGG	T|0.807;C|0.193	0.193	strong		0.632	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934	
GGCX	2677	hgsc.bcm.edu	37	2	85780536	85780536	+	Missense_Mutation	SNP	C	C	T	rs699664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85780536C>T	ENST00000233838.4	-	8	1054	c.974G>A	c.(973-975)cGa>cAa	p.R325Q	GGCX_ENST00000473665.1_5'UTR|GGCX_ENST00000430215.3_Missense_Mutation_p.R268Q	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	325			R -> Q (in dbSNP:rs699664). {ECO:0000269|PubMed:1749935}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	TTGCAACCTTCGGGGGCAGTA	0.597													T|||	1892	0.377796	0.6626	0.2695	5008	,	,		17272	0.3095		0.3668	False		,,,				2504	0.1513				p.R325Q		Atlas-SNP	.											.	GGCX	44	.	0			c.G974A	GRCh37	CM073086	GGCX	M	rs699664	PASS	.	T	GLN/ARG,GLN/ARG	2648,1758	516.2+/-369.1	807,1034,362	62.0	70.0	67.0		974,803	-0.8	0.1	2	dbSNP_86	67	2804,5796	672.2+/-402.9	469,1866,1965	yes	missense,missense	GGCX	NM_000821.5,NM_001142269.2	43,43	1276,2900,2327	TT,TC,CC		32.6047,39.9001,41.9191	benign,benign	325/759,268/702	85780536	5452,7554	2203	4300	6503	SO:0001583	missense	2677	exon8			AACCTTCGGGGGC		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.974G>A	2.37:g.85780536C>T	ENSP00000233838:p.Arg325Gln	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	154	66	0.428571	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Missense_Mutation	SNP	ENST00000233838.4	37	CCDS1978.1	906	0.41483516483516486	340	0.6910569105691057	106	0.292817679558011	188	0.32867132867132864	272	0.35883905013192613	T	0.271	-0.992796	0.02162	0.600999	0.326047	ENSG00000115486	ENST00000233838;ENST00000430215	D;D	0.92249	-3.0;-3.0	5.64	-0.842	0.10748	.	1.025530	0.07686	N	0.937884	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B;B	0.13145	0.007;0.003	B;B	0.09377	0.004;0.002	T	0.40251	-0.9573	9	0.10902	T	0.67	0.4177	1.9336	0.03332	0.1363:0.3536:0.1402:0.3698	rs699664;rs17617541;rs52835631;rs699664	268;325	E9PEE1;P38435	.;VKGC_HUMAN	Q	325;268	ENSP00000233838:R325Q;ENSP00000408045:R268Q	ENSP00000233838:R325Q	R	-	2	0	GGCX	85634047	0.000000	0.05858	0.123000	0.21794	0.094000	0.18550	-0.117000	0.10708	-0.152000	0.11156	-1.170000	0.01741	CGA	C|0.580;T|0.420	0.420	strong		0.597	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
LSS	4047	hgsc.bcm.edu	37	21	47614443	47614443	+	Silent	SNP	A	A	G	rs2254522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47614443A>G	ENST00000397728.3	-	20	2028	c.1950T>C	c.(1948-1950)caT>caC	p.H650H	LSS_ENST00000457828.2_Silent_p.H570H|LSS_ENST00000356396.4_Silent_p.H650H|LSS_ENST00000522411.1_Silent_p.H639H|AP001468.1_ENST00000594486.1_5'Flank	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	650					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)					AGCATGTGTTATGGATCTGGG	0.622													G|||	1695	0.338458	0.3253	0.2637	5008	,	,		20984	0.5655		0.1958	False		,,,				2504	0.3221				p.H650H	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.T1950C						PASS	.	G	,,,	1379,3027	687.5+/-404.9	223,933,1047	98.0	78.0	85.0		1950,1917,1710,1950	1.2	1.0	21	dbSNP_100	85	1740,6860	735.0+/-406.9	167,1406,2727	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	,,,	390,2339,3774	GG,GA,AA		20.2326,31.2982,23.9812	,,,	650/733,639/722,570/653,650/733	47614443	3119,9887	2203	4300	6503	SO:0001819	synonymous_variant	4047	exon20			TGTGTTATGGATC	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.1950T>C	21.37:g.47614443A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Silent	SNP	ENST00000397728.3	37	CCDS13733.1	703	0.3218864468864469	126	0.25609756097560976	76	0.20994475138121546	347	0.6066433566433567	154	0.20316622691292877	G	5.699	0.313580	0.10789	0.312982	0.202326	ENSG00000160285	ENST00000419093	.	.	.	5.07	1.21	0.21127	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999816	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.0859	0.36581	0.3764:0.0:0.6236:0.0	rs2254522;rs2254522	.	.	.	Q	18	.	.	X	-	1	0	LSS	46438871	1.000000	0.71417	0.967000	0.41034	0.432000	0.31715	2.487000	0.45268	-0.190000	0.10465	-0.726000	0.03593	TAA	A|0.712;C|0.002	.	strong		0.622	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
AP2A2	161	hgsc.bcm.edu	37	11	993907	993907	+	Silent	SNP	C	C	G	rs11538725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:993907C>G	ENST00000448903.2	+	13	1845	c.1704C>G	c.(1702-1704)ctC>ctG	p.L568L	AP2A2_ENST00000534328.1_Intron|AP2A2_ENST00000332231.5_Silent_p.L569L	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	568					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACAGCCAGCTCAGGAACGCAG	0.657													g|||	924	0.184505	0.295	0.0533	5008	,	,		17321	0.2976		0.0885	False		,,,				2504	0.1104				p.L569L		Atlas-SNP	.											.	AP2A2	50	.	0			c.C1707G						PASS	.	G	,	1015,3335		116,783,1276	27.0	30.0	29.0		1707,1704	1.0	0.2	11	dbSNP_120	29	675,7879		26,623,3628	yes	coding-synonymous,coding-synonymous	AP2A2	NM_001242837.1,NM_012305.3	,	142,1406,4904	GG,GC,CC		7.891,23.3333,13.0967	,	569/941,568/940	993907	1690,11214	2175	4277	6452	SO:0001819	synonymous_variant	161	exon13			CCAGCTCAGGAAC	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"""alpha-adaptin C; Huntingtin interacting protein J"", ""adaptin, alpha B"", ""clathrin-associated/assembly/adaptor protein, large, alpha 2"""	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.1704C>G	11.37:g.993907C>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_001242837	O75403|Q53ET1|Q96SI8	Silent	SNP	ENST00000448903.2	37	CCDS44512.1																																																																																			C|0.832;G|0.168	0.168	strong		0.657	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305	
GHRHR	2692	hgsc.bcm.edu	37	7	31011677	31011677	+	Silent	SNP	C	C	T	rs740336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:31011677C>T	ENST00000326139.2	+	6	610	c.564C>T	c.(562-564)caC>caT	p.H188H	GHRHR_ENST00000409316.1_Missense_Mutation_p.T6I|GHRHR_ENST00000461424.1_3'UTR|GHRHR_ENST00000409904.3_Silent_p.H124H	NM_000823.3	NP_000814.2	Q02643	GHRHR_HUMAN	growth hormone releasing hormone receptor	188					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP-mediated signaling (GO:0019933)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|determination of adult lifespan (GO:0008340)|growth hormone secretion (GO:0030252)|hormone metabolic process (GO:0042445)|lactation (GO:0007595)|multicellular organismal reproductive process (GO:0048609)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of intracellular steroid hormone receptor signaling pathway (GO:0033143)|regulation of protein metabolic process (GO:0051246)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|somatotropin secreting cell development (GO:0060133)|water homeostasis (GO:0030104)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nuclear matrix (GO:0016363)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	G-protein coupled receptor activity (GO:0004930)|growth factor binding (GO:0019838)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35					Sermorelin(DB00010)|Tesamorelin(DB08869)	CCCTTTTCCACAGCGACGACA	0.587													C|||	299	0.0597045	0.1301	0.0231	5008	,	,		18976	0.005		0.0239	False		,,,				2504	0.0838				p.H188H		Atlas-SNP	.											.	GHRHR	55	.	0			c.C564T						PASS	.	C		487,3919	229.8+/-244.2	26,435,1742	109.0	80.0	90.0		564	-6.8	0.0	7	dbSNP_86	90	191,8409	85.0+/-147.5	1,189,4110	no	coding-synonymous	GHRHR	NM_000823.3		27,624,5852	TT,TC,CC		2.2209,11.0531,5.213		188/424	31011677	678,12328	2203	4300	6503	SO:0001819	synonymous_variant	2692	exon6			TTTCCACAGCGAC		CCDS5432.1	7p14	2012-08-10			ENSG00000106128	ENSG00000106128		"""GPCR / Class B : Glucagon receptors"""	4266	protein-coding gene	gene with protein product		139191				7680413, 7514564	Standard	NM_000823		Approved		uc003tbx.3	Q02643	OTTHUMG00000152801	ENST00000326139.2:c.564C>T	7.37:g.31011677C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_000823	Q99863	Silent	SNP	ENST00000326139.2	37	CCDS5432.1	96	0.04395604395604396	65	0.13211382113821138	11	0.03038674033149171	1	0.0017482517482517483	19	0.025065963060686015	C	9.268	1.044992	0.19748	0.110531	0.022209	ENSG00000106128	ENST00000409316	.	.	.	4.57	-6.82	0.01698	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.50632	P	1.2000000000000899E-4	B	0.28933	0.228	B	0.20955	0.032	T	0.18650	-1.0330	6	0.87932	D	0	.	1.8357	0.03139	0.2142:0.1391:0.3996:0.2471	rs740336;rs9718454;rs56649853;rs740336	6	Q9HB43	.	I	6	.	ENSP00000386602:T6I	T	+	2	0	GHRHR	30978202	0.000000	0.05858	0.000000	0.03702	0.148000	0.21650	-3.064000	0.00622	-1.131000	0.02910	0.561000	0.74099	ACA	C|0.943;T|0.057	0.057	strong		0.587	GHRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327967.2		
NT5C1B	93034	hgsc.bcm.edu	37	2	18768850	18768850	+	Silent	SNP	A	A	G	rs16985306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:18768850A>G	ENST00000359846.2	-	2	116	c.39T>C	c.(37-39)ccT>ccC	p.P13P	NT5C1B_ENST00000460052.1_5'UTR|NT5C1B_ENST00000304081.4_Silent_p.P13P|NT5C1B-RDH14_ENST00000532967.1_Silent_p.P13P|NT5C1B_ENST00000600945.1_Silent_p.P13P	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	13					nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				ACCTCATTCCAGGCTCATTCT	0.373													G|||	1595	0.31849	0.6649	0.3199	5008	,	,		16749	0.1151		0.1998	False		,,,				2504	0.181				p.P13P		Atlas-SNP	.											.	NT5C1B	72	.	0			c.T39C						PASS	.	G	,,,,,,	2590,1816	528.9+/-372.5	756,1078,369	138.0	138.0	138.0		39,39,39,39,39,39,39	-6.2	0.0	2	dbSNP_123	138	1792,6808	732.1+/-406.8	196,1400,2704	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NT5C1B,NT5C1B-RDH14	NM_001002006.2,NM_001199086.1,NM_001199087.1,NM_001199088.1,NM_001199103.1,NM_001199104.1,NM_033253.3	,,,,,,	952,2478,3073	GG,GA,AA		20.8372,41.2165,33.6921	,,,,,,	13/611,13/594,13/628,13/613,13/651,13/603,13/551	18768850	4382,8624	2203	4300	6503	SO:0001819	synonymous_variant	93034	exon2			CATTCCAGGCTCA	AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.39T>C	2.37:g.18768850A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_001199088	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Silent	SNP	ENST00000359846.2	37	CCDS33150.1																																																																																			A|0.677;G|0.323	0.323	strong		0.373	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1		
NLRC3	197358	hgsc.bcm.edu	37	16	3594296	3594296	+	RNA	SNP	C	C	T	rs35402060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3594296C>T	ENST00000301749.7	-	0	3210				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|LA16c-390H2.4_ENST00000573820.1_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCACCGCACACGCTCCGTCAT	0.597													C|||	292	0.0583067	0.059	0.072	5008	,	,		17948	0.0556		0.0636	False		,,,				2504	0.045				p.A935A		Atlas-SNP	.											.	NLRC3	103	.	0			c.G2805A						PASS	.	C		259,3945		8,243,1851	72.0	78.0	76.0		2806	-10.3	0.0	16	dbSNP_126	76	558,7900		14,530,3685	yes	coding-synonymous	NLRC3	NM_178844.2		22,773,5536	TT,TC,CC		6.5973,6.1608,6.4524		935/1066	3594296	817,11845	2102	4229	6331			197358	exon17			CGCACACGCTCCG	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3594296C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	37																																																																																				C|0.947;T|0.053	0.053	strong		0.597	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
SERPINA6	866	hgsc.bcm.edu	37	14	94772429	94772429	+	Silent	SNP	G	G	A	rs2228543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94772429G>A	ENST00000341584.3	-	4	1157	c.1011C>T	c.(1009-1011)gaC>gaT	p.D337D		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	337					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	TCAGCTGGGCGTCCTGGGTGA	0.468													G|||	770	0.153754	0.3343	0.0965	5008	,	,		22300	0.0069		0.1531	False		,,,				2504	0.1022				p.D337D		Atlas-SNP	.											SERPINA6_ENST00000341584,NS,carcinoma,-2,2	SERPINA6	102	2	0			c.C1011T						PASS	.	G		1457,2949	470.7+/-355.8	247,963,993	136.0	122.0	127.0		1011	-4.2	0.0	14	dbSNP_98	127	1226,7374	246.9+/-275.2	86,1054,3160	no	coding-synonymous	SERPINA6	NM_001756.3		333,2017,4153	AA,AG,GG		14.2558,33.0685,20.6289		337/406	94772429	2683,10323	2203	4300	6503	SO:0001819	synonymous_variant	866	exon4			CTGGGCGTCCTGG	J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"""Serine (or cysteine) peptidase inhibitors"""	1540	protein-coding gene	gene with protein product	"""corticosteroid binding globulin"", ""transcortin"""	122500	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"""	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.1011C>T	14.37:g.94772429G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_001756	A8K456|Q7Z2Q9	Silent	SNP	ENST00000341584.3	37	CCDS9924.1																																																																																			G|0.677;T|0.043	.	strong		0.468	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756	
TOX3	27324	hgsc.bcm.edu	37	16	52484317	52484317	+	Missense_Mutation	SNP	C	C	T	rs114182621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:52484317C>T	ENST00000219746.9	-	4	834	c.550G>A	c.(550-552)Gcc>Acc	p.A184T	TOX3_ENST00000407228.3_Missense_Mutation_p.A179T	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	184					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)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						CCCAACTGGGCGCTGAGCTGA	0.582													C|||	28	0.00559105	0.0189	0.0029	5008	,	,		17831	0.001		0.0	False		,,,				2504	0.0				p.A184T		Atlas-SNP	.											.	TOX3	121	.	0			c.G550A						PASS	.	C	THR/ALA,THR/ALA	74,4182		2,70,2056	150.0	158.0	155.0		550,535	3.8	1.0	16	dbSNP_132	155	0,8480		0,0,4240	yes	missense,missense	TOX3	NM_001080430.2,NM_001146188.1	58,58	2,70,6296	TT,TC,CC		0.0,1.7387,0.581	probably-damaging,probably-damaging	184/577,179/572	52484317	74,12662	2128	4240	6368	SO:0001583	missense	27324	exon4			ACTGGGCGCTGAG	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.550G>A	16.37:g.52484317C>T	ENSP00000219746:p.Ala184Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	140	70	0.5	NM_001080430	B4DRD0|B5MCW4	Missense_Mutation	SNP	ENST00000219746.9	37	CCDS54009.1	15	0.006868131868131868	13	0.026422764227642278	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	13.54	2.267516	0.40095	0.017387	0.0	ENSG00000103460	ENST00000219746;ENST00000407228	T;T	0.11495	2.77;2.77	5.71	3.77	0.43336	.	0.129794	0.49916	D	0.000134	T	0.04588	0.0125	M	0.68593	2.085	0.45025	D	0.998041	B;B	0.17268	0.008;0.021	B;B	0.06405	0.002;0.002	T	0.02411	-1.1163	10	0.72032	D	0.01	.	11.9513	0.52956	0.0:0.8601:0.0:0.1399	.	179;184	B4DRD0;O15405	.;TOX3_HUMAN	T	184;179	ENSP00000219746:A184T;ENSP00000385705:A179T	ENSP00000219746:A184T	A	-	1	0	TOX3	51041818	1.000000	0.71417	0.992000	0.48379	0.014000	0.08584	3.357000	0.52277	0.763000	0.33175	0.563000	0.77884	GCC	C|0.992;T|0.008	0.008	strong		0.582	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037	
CUBN	8029	hgsc.bcm.edu	37	10	17152994	17152994	+	Silent	SNP	G	G	A	rs1801223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:17152994G>A	ENST00000377833.4	-	9	1004	c.939C>T	c.(937-939)aaC>aaT	p.N313N		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	313	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AACAGCCGCCGTTATTTATCT	0.473													G|||	1076	0.214856	0.1944	0.2262	5008	,	,		16541	0.25		0.2584	False		,,,				2504	0.1534				p.N313N		Atlas-SNP	.											.	CUBN	515	.	0			c.C939T						PASS	.	G		956,3450	361.4+/-315.7	109,738,1356	95.0	92.0	93.0		939	-0.5	0.9	10	dbSNP_89	93	1607,6993	299.3+/-304.4	157,1293,2850	no	coding-synonymous	CUBN	NM_001081.3		266,2031,4206	AA,AG,GG		18.686,21.6977,19.7063		313/3624	17152994	2563,10443	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon9			GCCGCCGTTATTT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.939C>T	10.37:g.17152994G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			G|0.680;T|0.036	.	strong		0.473	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
ZNF800	168850	hgsc.bcm.edu	37	7	127026184	127026184	+	Silent	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:127026184A>C	ENST00000393313.1	-	3	678	c.87T>G	c.(85-87)ccT>ccG	p.P29P	ZNF800_ENST00000393312.1_Silent_p.P29P|ZNF800_ENST00000265827.3_Silent_p.P29P			Q2TB10	ZN800_HUMAN	zinc finger protein 800	29					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(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						GTAACAAAGGAGGATCTCCAG	0.343																																					p.P29P		Atlas-SNP	.											.	ZNF800	78	.	0			c.T87G						PASS	.						110.0	104.0	106.0					7																	127026184		2203	4300	6503	SO:0001819	synonymous_variant	168850	exon3			CAAAGGAGGATCT	AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"""Zinc fingers, C2H2-type"""	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.87T>G	7.37:g.127026184A>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_176814	Q9HBN0	Silent	SNP	ENST00000393313.1	37	CCDS5795.1																																																																																			.	.	none		0.343	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814	
PLIN4	729359	hgsc.bcm.edu	37	19	4512534	4512534	+	Missense_Mutation	SNP	C	C	T	rs61730732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512534C>T	ENST00000301286.3	-	3	1395	c.1396G>A	c.(1396-1398)Gcc>Acc	p.A466T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	466	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						GCCCCTTTGGCCACATTCGCA	0.597													C|||	45	0.00898562	0.0333	0.0014	5008	,	,		22756	0.0		0.0	False		,,,				2504	0.0				p.A466T		Atlas-SNP	.											.	PLIN4	191	.	0			c.G1396A						PASS	.	C	THR/ALA	146,3788		3,140,1824	114.0	122.0	119.0		1396	5.0	1.0	19	dbSNP_129	119	0,8308		0,0,4154	yes	missense	PLIN4	NM_001080400.1	58	3,140,5978	TT,TC,CC		0.0,3.7112,1.1926	possibly-damaging	466/1358	4512534	146,12096	1967	4154	6121	SO:0001583	missense	729359	exon3			CTTTGGCCACATT	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.1396G>A	19.37:g.4512534C>T	ENSP00000301286:p.Ala466Thr	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	227	100	0.440529	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	C	17.51	3.406822	0.62399	0.037112	0.0	ENSG00000167676	ENST00000301286	T	0.09350	2.99	4.99	4.99	0.66335	.	0.000000	0.52532	D	0.000078	T	0.08670	0.0215	M	0.86573	2.825	0.34738	D	0.730428	D	0.61080	0.989	P	0.56474	0.799	T	0.37619	-0.9698	10	0.30854	T	0.27	-55.3504	15.8081	0.78531	0.0:1.0:0.0:0.0	.	466	Q96Q06	PLIN4_HUMAN	T	466	ENSP00000301286:A466T	ENSP00000301286:A466T	A	-	1	0	PLIN4	4463534	0.165000	0.22948	0.996000	0.52242	0.008000	0.06430	1.816000	0.38992	2.342000	0.79632	0.549000	0.68633	GCC	C|0.991;T|0.009	0.009	strong		0.597	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259818	71259818	+	Missense_Mutation	SNP	G	G	A	rs146869772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71259818G>A	ENST00000528743.2	+	1	353	c.115G>A	c.(115-117)Gtc>Atc	p.V39I		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	39	8 X 4 AA repeats of C-C-X-P.				epidermis development (GO:0008544)	keratin filament (GO:0045095)		p.V39I(1)		kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						CTGTGCACCCGTCTACTGCTG	0.667													g|||	10	0.00199681	0.0068	0.0014	5008	,	,		17781	0.0		0.0	False		,,,				2504	0.0				p.V39I		Atlas-SNP	.											KRTAP5-9,caecum,carcinoma,0,1	KRTAP5-9	19	1	1	Substitution - Missense(1)	large_intestine(1)	c.G115A						PASS	.	G	ILE/VAL	37,4363		0,37,2163	80.0	91.0	87.0		115	1.6	0.0	11	dbSNP_134	87	0,8588		0,0,4294	no	missense	KRTAP5-9	NM_005553.3	29	0,37,6457	AA,AG,GG		0.0,0.8409,0.2849	possibly-damaging	39/170	71259818	37,12951	2200	4294	6494	SO:0001583	missense	3846	exon1			GCACCCGTCTACT	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.115G>A	11.37:g.71259818G>A	ENSP00000431443:p.Val39Ile	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	324	145	0.447531	NM_005553	Q14564|Q3MIP8	Missense_Mutation	SNP	ENST00000528743.2	37	CCDS53677.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	N	4.044	0.005754	0.07866	0.008409	0.0	ENSG00000254997	ENST00000528743	T	0.03745	3.82	1.57	1.57	0.23409	.	.	.	.	.	T	0.04003	0.0112	L	0.42487	1.325	0.09310	N	1	P	0.51537	0.946	P	0.50270	0.636	T	0.38067	-0.9678	9	0.49607	T	0.09	.	6.6099	0.22745	0.0:0.0:1.0:0.0	.	39	P26371	KRA59_HUMAN	I	39	ENSP00000431443:V39I	ENSP00000431443:V39I	V	+	1	0	KRTAP5-9	70937466	0.000000	0.05858	0.015000	0.15790	0.167000	0.22549	-0.373000	0.07494	1.189000	0.43028	0.442000	0.29010	GTC	G|0.999;A|0.001	0.001	strong		0.667	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
FAM149A	25854	hgsc.bcm.edu	37	4	187088170	187088170	+	Missense_Mutation	SNP	G	G	A	rs141044925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187088170G>A	ENST00000356371.5	+	12	2086	c.2086G>A	c.(2086-2088)Ggt>Agt	p.G696S	FAM149A_ENST00000503432.1_Missense_Mutation_p.G405S|FAM149A_ENST00000227065.4_Missense_Mutation_p.G405S|FAM149A_ENST00000502970.1_Missense_Mutation_p.G405S|FAM149A_ENST00000514153.1_Missense_Mutation_p.G405S|FAM149A_ENST00000389354.5_Missense_Mutation_p.G405S			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	696										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)		CATGCCTGACGGTACAGAACG	0.468													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		17105	0.0		0.0	False		,,,				2504	0.0				p.G405S		Atlas-SNP	.											.	FAM149A	52	.	0			c.G1213A						PASS	.	G	SER/GLY,SER/GLY	64,4342	59.3+/-96.0	0,64,2139	91.0	85.0	87.0		1213,1213	-3.5	0.0	4	dbSNP_134	87	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	56,56	0,66,6437	AA,AG,GG		0.0233,1.4526,0.5075	benign,benign	405/483,405/483	187088170	66,12940	2203	4300	6503	SO:0001583	missense	25854	exon11			CCTGACGGTACAG	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.2086G>A	4.37:g.187088170G>A	ENSP00000348732:p.Gly696Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	129	51	0.395349	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		9|9	0.004120879120879121|0.004120879120879121	8|8	0.016260162601626018|0.016260162601626018	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	2.916|2.916	-0.224222|-0.224222	0.06061|0.06061	0.014526|0.014526	2.33E-4|2.33E-4	ENSG00000109794|ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354|ENST00000512271	T;T;T;T;T;T|.	0.10005|.	2.92;2.94;2.92;2.92;2.92;2.92|.	5.72|5.72	-3.45|-3.45	0.04781|0.04781	.|.	0.347222|.	0.34268|.	N|.	0.004119|.	T|T	0.02047|0.02047	0.0064|0.0064	N|N	0.00500|0.00500	-1.43|-1.43	0.09310|0.09310	N|N	1|1	B;B|.	0.28880|.	0.226;0.085|.	B;B|.	0.16722|.	0.016;0.007|.	T|T	0.35895|0.35895	-0.9770|-0.9770	10|5	0.05620|.	T|.	0.96|.	-2.9758|-2.9758	1.239|1.239	0.01959|0.01959	0.3995:0.2553:0.2218:0.1234|0.3995:0.2553:0.2218:0.1234	.|.	696;696|.	A5PLN7-3;A5PLN7|.	.;F149A_HUMAN|.	S|Q	405;696;405;405;405;405|82	ENSP00000426835:G405S;ENSP00000348732:G696S;ENSP00000227065:G405S;ENSP00000427155:G405S;ENSP00000424380:G405S;ENSP00000374005:G405S|.	ENSP00000227065:G405S|.	G|R	+|+	1|2	0|0	FAM149A|FAM149A	187325164|187325164	0.000000|0.000000	0.05858|0.05858	0.023000|0.023000	0.16930|0.16930	0.003000|0.003000	0.03518|0.03518	0.194000|0.194000	0.17135|0.17135	-0.400000|-0.400000	0.07656|0.07656	-0.469000|-0.469000	0.05056|0.05056	GGT|CGG	G|0.995;A|0.005	0.005	strong		0.468	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37480797	37480797	+	Silent	SNP	C	C	T	rs2111833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37480797C>T	ENST00000346753.3	-	9	1199	c.1083G>A	c.(1081-1083)tcG>tcA	p.S361S	TMPRSS6_ENST00000406856.1_Silent_p.S352S|TMPRSS6_ENST00000442782.2_Silent_p.S361S|TMPRSS6_ENST00000381792.2_Silent_p.S352S|TMPRSS6_ENST00000406725.1_Silent_p.S352S|RP5-1170K4.7_ENST00000414203.2_RNA	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	134	0	0		WXS	Illumina HiSeq	Phase_I	117	50	0.42735	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	
TEKT2	27285	hgsc.bcm.edu	37	1	36551495	36551495	+	Missense_Mutation	SNP	T	T	C	rs419653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36551495T>C	ENST00000207457.3	+	4	468	c.341T>C	c.(340-342)aTt>aCt	p.I114T	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	114			I -> T (in dbSNP:rs419653).		cell projection organization (GO:0030030)|inner dynein arm assembly (GO:0036159)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)|skin(2)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GATGTGGCCATTGAGTGCCTG	0.587													T|||	65	0.0129792	0.0484	0.0014	5008	,	,		19232	0.0		0.0	False		,,,				2504	0.0				p.I114T		Atlas-SNP	.											.	TEKT2	32	.	0			c.T341C						PASS	.	T	THR/ILE	134,4272	95.7+/-134.4	5,124,2074	58.0	53.0	55.0		341	5.8	0.7	1	dbSNP_80	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TEKT2	NM_014466.2	89	5,125,6373	CC,CT,TT		0.0116,3.0413,1.038	benign	114/431	36551495	135,12871	2203	4300	6503	SO:0001583	missense	27285	exon4			TGGCCATTGAGTG	AB033823	CCDS401.1	1p34.3	2008-02-05			ENSG00000092850	ENSG00000092850			11725	protein-coding gene	gene with protein product		608953				12029069, 11751288	Standard	NM_014466		Approved	TEKTB1	uc001bzr.3	Q9UIF3	OTTHUMG00000007629	ENST00000207457.3:c.341T>C	1.37:g.36551495T>C	ENSP00000207457:p.Ile114Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	160	65	0.40625	NM_014466	A6NIS6|O60638	Missense_Mutation	SNP	ENST00000207457.3	37	CCDS401.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	T	11.29	1.595161	0.28445	0.030413	1.16E-4	ENSG00000092850	ENST00000207457	T	0.02177	4.41	5.79	5.79	0.91817	.	0.454845	0.25833	N	0.028007	T	0.00468	0.0015	N	0.12182	0.205	0.33226	D	0.55525	B	0.23990	0.095	B	0.23574	0.047	T	0.49969	-0.8882	10	0.14252	T	0.57	.	16.1354	0.81481	0.0:0.0:0.0:1.0	rs419653;rs419653	114	Q9UIF3	TEKT2_HUMAN	T	114	ENSP00000207457:I114T	ENSP00000207457:I114T	I	+	2	0	TEKT2	36324082	0.589000	0.26807	0.652000	0.29579	0.988000	0.76386	1.835000	0.39181	2.207000	0.71202	0.533000	0.62120	ATT	T|0.990;C|0.010	0.010	strong		0.587	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466	
COL14A1	7373	hgsc.bcm.edu	37	8	121259862	121259862	+	Silent	SNP	G	G	A	rs2305605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:121259862G>A	ENST00000297848.3	+	21	2760	c.2490G>A	c.(2488-2490)tcG>tcA	p.S830S	COL14A1_ENST00000309791.4_Silent_p.S830S|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000247781.3_Silent_p.S735S	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			TACCATCCTCGGGGCCCCAGA	0.463													G|||	857	0.171126	0.0764	0.2147	5008	,	,		15153	0.4107		0.0258	False		,,,				2504	0.1708				p.S830S		Atlas-SNP	.											.	COL14A1	292	.	0			c.G2490A						PASS	.	G		313,4093	166.9+/-198.0	16,281,1906	59.0	55.0	56.0		2490	-1.8	0.2	8	dbSNP_100	56	301,8299	109.6+/-170.1	3,295,4002	no	coding-synonymous	COL14A1	NM_021110.1		19,576,5908	AA,AG,GG		3.5,7.1039,4.7209		830/1797	121259862	614,12392	2203	4300	6503	SO:0001819	synonymous_variant	7373	exon21			ATCCTCGGGGCCC		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.2490G>A	8.37:g.121259862G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	64	38	0.59375	NM_021110		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																			G|0.897;A|0.103	0.103	strong		0.463	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
STAB2	55576	hgsc.bcm.edu	37	12	104123911	104123911	+	Silent	SNP	C	C	T	rs10778281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	49	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	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		
NEU2	4759	hgsc.bcm.edu	37	2	233899377	233899377	+	Silent	SNP	C	C	T	rs2233394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233899377C>T	ENST00000233840.3	+	2	753	c.753C>T	c.(751-753)gaC>gaT	p.D251D		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	251					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	GCACCAATGACGGGCTTGATT	0.667													C|||	940	0.1877	0.2738	0.2637	5008	,	,		17388	0.123		0.0845	False		,,,				2504	0.1902				p.D251D		Atlas-SNP	.											.	NEU2	42	.	0			c.C753T						PASS	.	C		1121,3283	379.2+/-323.2	144,833,1225	27.0	28.0	27.0		753	-3.5	0.0	2	dbSNP_98	27	898,7700	193.5+/-239.2	42,814,3443	no	coding-synonymous	NEU2	NM_005383.2		186,1647,4668	TT,TC,CC		10.4443,25.4541,15.5284		251/381	233899377	2019,10983	2202	4299	6501	SO:0001819	synonymous_variant	4759	exon2			CAATGACGGGCTT	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"""N-acetyl-alpha-neuraminidase 2"""	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.753C>T	2.37:g.233899377C>T		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	226	119	0.526549	NM_005383	Q3KNW4|Q6NTB4	Silent	SNP	ENST00000233840.3	37	CCDS2501.1																																																																																			C|0.833;T|0.167	0.167	strong		0.667	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383	
GATA4	2626	hgsc.bcm.edu	37	8	11614559	11614559	+	Silent	SNP	A	A	G	rs112435835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11614559A>G	ENST00000335135.4	+	6	1671	c.1113A>G	c.(1111-1113)tcA>tcG	p.S371S	GATA4_ENST00000528712.1_Silent_p.S165S|GATA4_ENST00000532059.1_Silent_p.S372S	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	371					atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		CTGGCCTGTCATCTCACTACG	0.662													A|||	51	0.0101837	0.0371	0.0029	5008	,	,		20298	0.0		0.0	False		,,,				2504	0.0				p.S371S		Atlas-SNP	.											.	GATA4	29	.	0			c.A1113G						PASS	.	A		94,4312	76.8+/-115.0	2,90,2111	90.0	70.0	76.0		1113	-11.7	0.0	8	dbSNP_132	76	0,8600		0,0,4300	no	coding-synonymous	GATA4	NM_002052.3		2,90,6411	GG,GA,AA		0.0,2.1335,0.7227		371/443	11614559	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	2626	exon6			CCTGTCATCTCAC	AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574		"""GATA zinc finger domain containing"""	4173	protein-coding gene	gene with protein product		600576	"""GATA-binding protein 4"""			7665171	Standard	NM_002052		Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.1113A>G	8.37:g.11614559A>G		Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	259	132	0.509652	NM_002052	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	Silent	SNP	ENST00000335135.4	37	CCDS5983.1																																																																																			A|0.993;G|0.007	0.007	strong		0.662	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207587.2	NM_002052	
C6orf57	135154	hgsc.bcm.edu	37	6	71289189	71289189	+	Missense_Mutation	SNP	A	A	G	rs1048886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71289189A>G	ENST00000370474.3	+	2	161	c.137A>G	c.(136-138)cAg>cGg	p.Q46R		NM_145267.2	NP_660310.2	Q5VUM1	SDHF4_HUMAN	chromosome 6 open reading frame 57	46			Q -> R (in dbSNP:rs1048886).		innate immune response (GO:0045087)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)				kidney(1)|lung(1)|skin(1)	3						CTTGTCAAACAGTCCCTTAAG	0.403													A|||	992	0.198083	0.3192	0.2161	5008	,	,		14511	0.0833		0.175	False		,,,				2504	0.1636				p.Q46R		Atlas-SNP	.											.	C6orf57	13	.	0			c.A137G						PASS	.	A	ARG/GLN	1319,3087	444.5+/-347.4	207,905,1091	112.0	111.0	111.0	http://www.ncbi.nlm.nih.gov/pubmed?term	137	4.6	0.1	6	dbSNP_86	111	1468,7132	281.2+/-294.9	141,1186,2973	yes	missense	C6orf57	NM_145267.2	43	348,2091,4064	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	17.0698,29.9365,21.4286	probably-damaging	46/109	71289189	2787,10219	2203	4300	6503	SO:0001583	missense	135154	exon2			TCAAACAGTCCCT	BC018085	CCDS4972.1	6q12	2011-12-13			ENSG00000154079	ENSG00000154079			20957	protein-coding gene	gene with protein product							Standard	NM_145267		Approved		uc003pfq.1	Q5VUM1	OTTHUMG00000014992	ENST00000370474.3:c.137A>G	6.37:g.71289189A>G	ENSP00000359505:p.Gln46Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_145267	E1P532	Missense_Mutation	SNP	ENST00000370474.3	37	CCDS4972.1	447	0.20467032967032966	165	0.3353658536585366	78	0.2154696132596685	63	0.11013986013986014	141	0.18601583113456466	A	10.53	1.375636	0.24857	0.299365	0.170698	ENSG00000154079	ENST00000370474	T	0.31247	1.5	5.82	4.64	0.57946	.	0.101718	0.64402	D	0.000002	T	0.21307	0.0513	M	0.72894	2.215	0.47511	P	5.519999999999969E-4	B	0.27910	0.193	B	0.34536	0.185	T	0.08229	-1.0732	9	0.54805	T	0.06	-6.9699	10.8459	0.46743	0.8415:0.1584:0.0:0.0	rs1048886;rs3188927;rs56527910;rs61433581;rs1048886	46	Q5VUM1	CF057_HUMAN	R	46	ENSP00000359505:Q46R	ENSP00000359505:Q46R	Q	+	2	0	C6orf57	71345910	0.926000	0.31397	0.062000	0.19696	0.196000	0.23810	4.409000	0.59768	0.989000	0.38761	0.472000	0.43445	CAG	A|0.787;G|0.213	0.213	strong		0.403	C6orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041140.1	NM_145267	
DLC1	10395	hgsc.bcm.edu	37	8	13357331	13357331	+	Missense_Mutation	SNP	C	C	T	rs35173269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:13357331C>T	ENST00000276297.4	-	2	659	c.250G>A	c.(250-252)Gat>Aat	p.D84N	DLC1_ENST00000316609.5_Missense_Mutation_p.D84N|DLC1_ENST00000511869.1_Missense_Mutation_p.D84N	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	84					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						TCGTCCACATCCTTTGAAAGA	0.453													C|||	62	0.0123802	0.0454	0.0014	5008	,	,		20510	0.0		0.001	False		,,,				2504	0.0				p.D84N		Atlas-SNP	.											.	DLC1	411	.	0			c.G250A						PASS	.	C	ASN/ASP,ASN/ASP	215,4191	132.1+/-168.6	8,199,1996	224.0	226.0	226.0		250,250	4.7	0.1	8	dbSNP_126	226	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	DLC1	NM_024767.3,NM_182643.2	23,23	8,202,6293	TT,TC,CC		0.0349,4.8797,1.6761	benign,benign	84/464,84/1529	13357331	218,12788	2203	4300	6503	SO:0001583	missense	10395	exon2			CCACATCCTTTGA	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.250G>A	8.37:g.13357331C>T	ENSP00000276297:p.Asp84Asn	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	20	0.009157509157509158	19	0.03861788617886179	0	0.0	0	0.0	1	0.0013192612137203166	C	11.29	1.596099	0.28445	0.048797	3.49E-4	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	T;T;T	0.32753	1.44;1.44;1.44	5.55	4.68	0.58851	.	0.542075	0.15368	N	0.266008	T	0.03136	0.0092	N	0.14661	0.345	0.21147	N	0.99977	B;B;B	0.22211	0.039;0.066;0.039	B;B;B	0.24006	0.032;0.05;0.023	T	0.10291	-1.0636	10	0.72032	D	0.01	.	10.6747	0.45778	0.0:0.8543:0.0:0.1457	rs35173269;rs61757613	84;84;84	E9PF76;Q96QB1-3;Q96QB1	.;.;RHG07_HUMAN	N	84	ENSP00000276297:D84N;ENSP00000321034:D84N;ENSP00000425878:D84N	ENSP00000276297:D84N	D	-	1	0	DLC1	13401702	1.000000	0.71417	0.145000	0.22337	0.066000	0.16364	3.124000	0.50461	1.500000	0.48636	0.655000	0.94253	GAT	C|0.981;T|0.019	0.019	strong		0.453	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
SLC2A4	6517	hgsc.bcm.edu	37	17	7187123	7187123	+	Silent	SNP	T	T	C	rs5435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7187123T>C	ENST00000317370.8	+	4	658	c.390T>C	c.(388-390)aaT>aaC	p.N130N	RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000424875.2_Silent_p.N120N|SLC2A4_ENST00000571308.1_Silent_p.N130N	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	130					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						GCCTGGCCAATGCTGCTGCCT	0.602													C|||	3493	0.697484	0.913	0.6081	5008	,	,		19792	0.625		0.6064	False		,,,				2504	0.638				p.N130N		Atlas-SNP	.											.	SLC2A4	44	.	0			c.T390C						PASS	.	C		3716,690	288.1+/-279.7	1576,564,63	68.0	61.0	63.0		390	-11.5	0.0	17	dbSNP_52	63	5363,3237	487.6+/-372.2	1696,1971,633	no	coding-synonymous	SLC2A4	NM_001042.2		3272,2535,696	CC,CT,TT		37.6395,15.6605,30.1938		130/510	7187123	9079,3927	2203	4300	6503	SO:0001819	synonymous_variant	6517	exon4			GGCCAATGCTGCT	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.390T>C	17.37:g.7187123T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_001042	Q05BQ3|Q14CX2	Silent	SNP	ENST00000317370.8	37	CCDS11097.1																																																																																			C|0.701;N|0.001	0.701	strong		0.602	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3		
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458893	39458893	+	Missense_Mutation	SNP	G	G	A	rs758741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	88	0	0		WXS	Illumina HiSeq	Phase_I	114	47	0.412281	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		
PSG1	5669	hgsc.bcm.edu	37	19	43382374	43382374	+	Missense_Mutation	SNP	C	C	G	rs707744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43382374C>G	ENST00000436291.2	-	2	237	c.121G>C	c.(121-123)Gag>Cag	p.E41Q	PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000403380.3_Missense_Mutation_p.E41Q|PSG1_ENST00000244296.2_Missense_Mutation_p.E41Q|PSG1_ENST00000595124.1_Missense_Mutation_p.E41Q|PSG1_ENST00000595356.1_Missense_Mutation_p.E41Q|PSG1_ENST00000312439.6_Missense_Mutation_p.E41Q	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	41	Ig-like V-type.		E -> Q (in dbSNP:rs707744).	EPT -> QPP (in Ref. 4, 5 and 6). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TTGGTTGGCTCGGCTTCAATC	0.473													.|||	2124	0.424121	0.503	0.4207	5008	,	,		18131	0.4276		0.2505	False		,,,				2504	0.4949				p.E41Q		Atlas-SNP	.											.	PSG1	196	.	0			c.G121C						PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU	2154,2252		582,990,631	147.0	166.0	160.0		121,121,121	-1.2	0.0	19	dbSNP_86	160	2121,6477		320,1481,2498	no	missense,missense,missense	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	29,29,29	902,2471,3129	GG,GC,CC		24.6685,48.8879,32.8745	,,	41/420,41/418,41/427	43382374	4275,8729	2203	4299	6502	SO:0001583	missense	5669	exon2			TTGGCTCGGCTTC		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.121G>C	19.37:g.43382374C>G	ENSP00000413041:p.Glu41Gln	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	336	129	0.383929	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	0.484	-0.878652	0.02550	0.488879	0.246685	ENSG00000231924	ENST00000270059;ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	1.46	-1.17	0.09648	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00061	-2.33	0.80722	P	0.0	B;B;B;B;B;B;B;B	0.11235	0.004;0.0;0.0;0.0;0.0;0.001;0.003;0.0	B;B;B;B;B;B;B;B	0.13407	0.008;0.003;0.001;0.004;0.003;0.007;0.009;0.004	T	0.43988	-0.9357	8	0.22706	T	0.39	.	4.7175	0.12903	0.0:0.5961:0.2282:0.1757	rs707744;rs3205494;rs16976238;rs61289360	41;41;41;41;41;41;41;41	O75238;P11464-4;G5E9F7;P11464;P11464-3;Q9UPK8;O75237;P11464-2	.;.;.;PSG1_HUMAN;.;.;.;.	Q	41	ENSP00000413041:E41Q;ENSP00000385386:E41Q;ENSP00000308970:E41Q;ENSP00000244296:E41Q	ENSP00000244296:E41Q	E	-	1	0	PSG1	48074214	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	-0.330000	0.07925	-0.696000	0.05098	-1.122000	0.02009	GAG	C|0.695;G|0.305	0.305	strong		0.473	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
TMEM150A	129303	hgsc.bcm.edu	37	2	85826721	85826721	+	Silent	SNP	G	G	A	rs11891495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85826721G>A	ENST00000409668.1	-	6	968	c.501C>T	c.(499-501)acC>acT	p.T167T	TMEM150A_ENST00000334462.5_Silent_p.T167T|TMEM150A_ENST00000306353.3_Silent_p.T114T			Q86TG1	T150A_HUMAN	transmembrane protein 150A	167					catabolic process (GO:0009056)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|lung(1)|skin(1)	7						CCAGCGGGGCGGTGGCCCCTT	0.617													G|||	880	0.175719	0.1369	0.1801	5008	,	,		20935	0.0823		0.2535	False		,,,				2504	0.2413				p.T167T		Atlas-SNP	.											.	TMEM150A	15	.	0			c.C501T						PASS	.	G		645,3761	274.9+/-272.2	42,561,1600	70.0	67.0	68.0		501	-10.2	0.1	2	dbSNP_120	68	2184,6416	372.2+/-336.6	267,1650,2383	no	coding-synonymous	TMEM150A	NM_001031738.2		309,2211,3983	AA,AG,GG		25.3953,14.6391,21.7515		167/272	85826721	2829,10177	2203	4300	6503	SO:0001819	synonymous_variant	129303	exon7			CGGGGCGGTGGCC	AK098152	CCDS33233.1	2p11.2	2009-06-12	2009-06-12	2009-06-12	ENSG00000168890	ENSG00000168890			24677	protein-coding gene	gene with protein product			"""transmembrane protein 150"""	TMEM150		10858565	Standard	NM_001031738		Approved	TM6P1, FLJ90024	uc002spy.2	Q86TG1	OTTHUMG00000130168	ENST00000409668.1:c.501C>T	2.37:g.85826721G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	241	115	0.477178	NM_001031738	A8K764|B7WPQ9|D6W5L2|Q8N2R6	Silent	SNP	ENST00000409668.1	37	CCDS33233.1																																																																																			G|0.810;A|0.190	0.190	strong		0.617	TMEM150A-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329474.1	NM_153342	
IFNA6	3443	hgsc.bcm.edu	37	9	21350487	21350487	+	Silent	SNP	G	G	A	rs61736258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21350487G>A	ENST00000380210.1	-	1	890	c.400C>T	c.(400-402)Ctg>Ttg	p.L134L		NM_021002.2	NP_066282.1	P05013	IFNA6_HUMAN	interferon, alpha 6	134					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(3)|lung(7)|skin(1)	11				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		TCATTCATCAGGGGAGTCCCT	0.498													G|||	124	0.0247604	0.09	0.0072	5008	,	,		20965	0.0		0.0	False		,,,				2504	0.0				p.L134L		Atlas-SNP	.											.	IFNA6	27	.	0			c.C400T						PASS	.	G		351,4055	181.2+/-209.3	15,321,1867	200.0	202.0	202.0		400	0.6	0.0	9	dbSNP_129	202	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	IFNA6	NM_021002.2		15,323,6165	AA,AG,GG		0.0233,7.9664,2.7141		134/190	21350487	353,12653	2203	4300	6503	SO:0001819	synonymous_variant	3443	exon1			TCATCAGGGGAGT		CCDS6504.1	9p22	2010-12-10			ENSG00000120235	ENSG00000120235		"""Interferons"""	5427	protein-coding gene	gene with protein product		147566				1385305	Standard	NM_021002		Approved	IFN-alphaK	uc011lni.2	P05013	OTTHUMG00000019676	ENST00000380210.1:c.400C>T	9.37:g.21350487G>A		Somatic	371	0	0		WXS	Illumina HiSeq	Phase_I	361	179	0.495845	NM_021002	Q5VYQ1	Silent	SNP	ENST00000380210.1	37	CCDS6504.1																																																																																			G|0.971;A|0.029	0.029	strong		0.498	IFNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051905.1	NM_021002	
MCTP2	55784	hgsc.bcm.edu	37	15	95019926	95019926	+	Splice_Site	SNP	C	C	T	rs386786753|rs79112132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:95019926C>T	ENST00000357742.4	+	21	2472	c.2472C>T	c.(2470-2472)ggC>ggT	p.G824G	MCTP2_ENST00000449432.3_3'UTR|MCTP2_ENST00000451018.3_Splice_Site_p.G769G	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	824					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			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)			ATTTTTCAGGCATAAATAAAT	0.348													C|||	436	0.0870607	0.146	0.0245	5008	,	,		17988	0.0575		0.0229	False		,,,				2504	0.1483				p.G824G		Atlas-SNP	.											.	MCTP2	122	.	0			c.C2472T						PASS	.	C	,	486,3908	188.5+/-214.9	26,434,1737	73.0	77.0	76.0		2307,2472	3.9	1.0	15	dbSNP_131	76	52,8544	31.2+/-83.2	0,52,4246	no	coding-synonymous-near-splice,coding-synonymous-near-splice	MCTP2	NM_001159643.1,NM_018349.3	,	26,486,5983	TT,TC,CC		0.6049,11.0605,4.1416	,	769/824,824/879	95019926	538,12452	2197	4298	6495	SO:0001630	splice_region_variant	55784	exon21			TTCAGGCATAAAT	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.2471-1C>T	15.37:g.95019926C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_018349	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	37	CCDS32338.1																																																																																			C|0.953;T|0.047	0.047	strong		0.348	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	Silent
TG	7038	hgsc.bcm.edu	37	8	133981760	133981760	+	Missense_Mutation	SNP	T	T	C	rs56230101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133981760T>C	ENST00000220616.4	+	32	5961	c.5921T>C	c.(5920-5922)aTg>aCg	p.M1974T	TG_ENST00000377869.1_Missense_Mutation_p.M1917T|TG_ENST00000542445.1_Missense_Mutation_p.M344T|TG_ENST00000519543.1_Missense_Mutation_p.M128T	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1974			M -> T (in dbSNP:rs56230101).		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)		CAAAAACTGATGGGGATATCC	0.343													T|||	626	0.125	0.3306	0.0735	5008	,	,		17457	0.001		0.0736	False		,,,				2504	0.0644				p.M1974T		Atlas-SNP	.											.	TG	416	.	0			c.T5921C						PASS	.	T	THR/MET	1278,3128	433.3+/-343.5	195,888,1120	103.0	113.0	110.0		5921	-0.1	0.0	8	dbSNP_129	110	633,7967	163.0+/-215.7	25,583,3692	yes	missense	TG	NM_003235.4	81	220,1471,4812	CC,CT,TT		7.3605,29.0059,14.6932	benign	1974/2769	133981760	1911,11095	2203	4300	6503	SO:0001583	missense	7038	exon32			AACTGATGGGGAT	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.5921T>C	8.37:g.133981760T>C	ENSP00000220616:p.Met1974Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	266	0.12179487179487179	177	0.3597560975609756	32	0.08839779005524862	0	0.0	57	0.07519788918205805	T	0.004	-2.254346	0.00265	0.290059	0.073605	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	T;T;T;T	0.64438	0.13;0.14;-0.08;-0.1	5.53	-0.0779	0.13716	.	0.983060	0.08309	N	0.965734	T	0.00012	0.0000	N	0.01352	-0.895	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	0.26155	-1.0111	9	0.02654	T	1	.	5.7219	0.17992	0.0:0.4479:0.284:0.2681	rs56230101;rs61750469	128;344;1974	E7EVM0;F5GWW5;P01266	.;.;THYG_HUMAN	T	1917;780;1974;344;128	ENSP00000367100:M1917T;ENSP00000220616:M1974T;ENSP00000441693:M344T;ENSP00000430430:M128T	ENSP00000220616:M1974T	M	+	2	0	TG	134050942	0.000000	0.05858	0.008000	0.14137	0.600000	0.36913	-0.633000	0.05483	0.011000	0.14865	-0.479000	0.04858	ATG	T|0.869;C|0.131	0.131	strong		0.343	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
MIA2	117153	hgsc.bcm.edu	37	14	39717002	39717002	+	Silent	SNP	A	A	G	rs17109049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:39717002A>G	ENST00000280082.3	+	4	1423	c.1224A>G	c.(1222-1224)gcA>gcG	p.A408A	MIA2_ENST00000556784.1_Silent_p.A407A|RP11-407N17.3_ENST00000553728.1_Silent_p.A408A	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	408					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		ATGGTGGGGCAGATGAACATG	0.333													A|||	380	0.0758786	0.2769	0.0202	5008	,	,		18395	0.0		0.0	False		,,,				2504	0.0				p.A408A		Atlas-SNP	.											.	MIA2	82	.	0			c.A1224G						PASS	.	A		1093,3313	385.1+/-325.6	116,861,1226	74.0	79.0	77.0		1224	3.1	0.0	14	dbSNP_123	77	11,8589	7.7+/-29.5	0,11,4289	no	coding-synonymous	MIA2	NM_054024.3		116,872,5515	GG,GA,AA		0.1279,24.8071,8.4884		408/655	39717002	1104,11902	2203	4300	6503	SO:0001819	synonymous_variant	117153	exon4			TGGGGCAGATGAA	BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.1224A>G	14.37:g.39717002A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_054024	A1L4H0|Q9H6C1	Silent	SNP	ENST00000280082.3	37	CCDS9672.1																																																																																			A|0.921;G|0.079	0.079	strong		0.333	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024	
EHHADH	1962	hgsc.bcm.edu	37	3	184922267	184922267	+	Missense_Mutation	SNP	T	T	C	rs115754857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184922267T>C	ENST00000231887.3	-	6	922	c.847A>G	c.(847-849)Act>Gct	p.T283A	EHHADH_ENST00000456310.1_Missense_Mutation_p.T187A	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	283	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CCGGAGGGAGTTGACCACTTA	0.488													T|||	82	0.0163738	0.0605	0.0029	5008	,	,		21681	0.0		0.0	False		,,,				2504	0.0				p.T283A		Atlas-SNP	.											.	EHHADH	73	.	0			c.A847G						PASS	.	T	ALA/THR,ALA/THR	170,4236	112.1+/-150.2	3,164,2036	121.0	118.0	119.0		559,847	1.6	0.4	3	dbSNP_132	119	0,8600		0,0,4300	yes	missense,missense	EHHADH	NM_001166415.1,NM_001966.3	58,58	3,164,6336	CC,CT,TT		0.0,3.8584,1.3071	benign,benign	187/628,283/724	184922267	170,12836	2203	4300	6503	SO:0001583	missense	1962	exon6			AGGGAGTTGACCA	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"""enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"""	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.847A>G	3.37:g.184922267T>C	ENSP00000231887:p.Thr283Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	56	21	0.375	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	T	7.470	0.646535	0.14451	0.038584	0.0	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.74526	-0.44;-0.85	5.53	1.61	0.23674	.	0.442567	0.26761	N	0.022621	T	0.21674	0.0522	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.15492	-1.0435	10	0.35671	T	0.21	-3.3999	1.5805	0.02633	0.1344:0.1596:0.1395:0.5665	.	283	Q08426	ECHP_HUMAN	A	283;283;187	ENSP00000231887:T283A;ENSP00000387746:T187A	ENSP00000231887:T283A	T	-	1	0	EHHADH	186404961	0.100000	0.21855	0.382000	0.26119	0.937000	0.57800	1.287000	0.33284	0.035000	0.15519	-0.309000	0.09137	ACT	T|0.986;C|0.014	0.014	strong		0.488	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1		
AADACL3	126767	hgsc.bcm.edu	37	1	12785494	12785494	+	Missense_Mutation	SNP	G	G	T	rs7513079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12785494G>T	ENST00000359318.5	+	4	789	c.584G>T	c.(583-585)tGt>tTt	p.C195F	AADACL3_ENST00000332530.3_Missense_Mutation_p.C125F	NM_001103170.1	NP_001096640.1	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3	195			C -> F (in dbSNP:rs7513079). {ECO:0000269|PubMed:14702039}.				hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	15	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		ATCTGCTACTGTTTTTTTCAA	0.458													G|||	3417	0.682308	0.4849	0.7752	5008	,	,		20711	0.7798		0.7296	False		,,,				2504	0.7342				p.C195F		Atlas-SNP	.											.	AADACL3	84	.	0			c.G584T						PASS	.	G	PHE/CYS,PHE/CYS	1942,1766		519,904,431	148.0	137.0	140.0		374,584	5.3	0.5	1	dbSNP_116	140	5994,2194		2181,1632,281	yes	missense,missense	AADACL3	NM_001103169.1,NM_001103170.1	205,205	2700,2536,712	TT,TG,GG		26.7953,47.6268,33.2885	benign,benign	125/281,195/351	12785494	7936,3960	1854	4094	5948	SO:0001583	missense	126767	exon4			GCTACTGTTTTTT		CCDS41253.1	1p36.21	2014-07-17			ENSG00000188984	ENSG00000188984			32037	protein-coding gene	gene with protein product							Standard	XM_006710337		Approved	OTTHUMG00000001887	uc009vnn.1	Q5VUY0	OTTHUMG00000001887	ENST00000359318.5:c.584G>T	1.37:g.12785494G>T	ENSP00000352268:p.Cys195Phe	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_001103170	B3KXR9|Q5VUY1	Missense_Mutation	SNP	ENST00000359318.5	37	CCDS41253.1	1529	0.700091575091575	238	0.483739837398374	272	0.7513812154696132	457	0.798951048951049	562	0.741424802110818	G	4.099	0.016412	0.07959	0.523732	0.732047	ENSG00000188984	ENST00000332530;ENST00000359318	T;T	0.06849	3.25;3.52	5.35	5.35	0.76521	.	0.108387	0.64402	N	0.000004	T	0.00012	0.0000	N	0.04275	-0.24	0.58432	P	1.0000000000287557E-6	B;B	0.25719	0.132;0.017	B;B	0.36244	0.22;0.037	T	0.39165	-0.9627	9	0.02654	T	1	-17.2471	5.3591	0.16077	0.1565:0.0:0.6728:0.1707	rs7513079;rs60105455;rs7513079	195;125	Q5VUY0;Q5VUY0-2	ADCL3_HUMAN;.	F	125;195	ENSP00000333352:C125F;ENSP00000352268:C195F	ENSP00000333352:C125F	C	+	2	0	AADACL3	12708081	0.093000	0.21703	0.464000	0.27143	0.038000	0.13279	1.327000	0.33746	2.504000	0.84457	0.484000	0.47621	TGT	G|0.302;N|0.001	.	strong		0.458	AADACL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005324.2	NM_001103170	
CDRT1	374286	hgsc.bcm.edu	37	17	15498181	15498181	+	Silent	SNP	A	A	G	rs12601532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15498181A>G	ENST00000395906.3	-	10	1727	c.1728T>C	c.(1726-1728)gcT>gcC	p.A576A	RP11-385D13.1_ENST00000455584.2_Silent_p.A886A|CDRT1_ENST00000354433.3_Silent_p.A76A|CDRT1_ENST00000583965.1_Intron	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	576										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)		GGCATTTCACAGCTCCCTCGT	0.532													G|||	1837	0.366813	0.4697	0.3545	5008	,	,		17968	0.3899		0.2356	False		,,,				2504	0.3476				p.A576A		Atlas-SNP	.											.	CDRT1	83	.	0			c.T1728C						PASS	.	G		1590,2816		461,668,1074	88.0	105.0	99.0		1728	-11.0	0.0	17	dbSNP_120	99	1673,6927		269,1135,2896	no	coding-synonymous	CDRT1	NM_006382.3		730,1803,3970	GG,GA,AA		19.4535,36.0872,25.0884		576/753	15498181	3263,9743	2203	4300	6503	SO:0001819	synonymous_variant	374286	exon10			TTTCACAGCTCCC	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.1728T>C	17.37:g.15498181A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	198	195	0.984848	NM_006382	O43848|O95611	Silent	SNP	ENST00000395906.3	37	CCDS45619.1	654	0.29945054945054944	174	0.35365853658536583	109	0.3011049723756906	204	0.35664335664335667	167	0.22031662269129287	G	1.934	-0.445217	0.04604	0.360872	0.194535	ENSG00000251537	ENST00000455584	.	.	.	5.51	-11.0	0.00169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20563	P	0.99988422	.	.	.	.	.	.	T	0.07347	-1.0777	3	.	.	.	.	6.3925	0.21595	0.3997:0.0791:0.4302:0.091	rs12601532	.	.	.	P	901	.	.	L	-	2	0	RP11-385D13.1	15438906	0.000000	0.05858	0.011000	0.14972	0.235000	0.25334	-3.535000	0.00439	-3.489000	0.00153	-1.922000	0.00515	CTG	A|0.715;G|0.285	0.285	strong		0.532	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
FAM111A	63901	hgsc.bcm.edu	37	11	58919813	58919813	+	Silent	SNP	A	A	G	rs10896928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58919813A>G	ENST00000528737.1	+	5	3490	c.672A>G	c.(670-672)gcA>gcG	p.A224A	FAM111A_ENST00000361723.3_Silent_p.A224A|FAM111A_ENST00000420244.1_Silent_p.A224A|FAM111A_ENST00000531147.1_Silent_p.A224A|FAM111A_ENST00000533703.1_Silent_p.A224A			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	224					defense response to virus (GO:0051607)|DNA replication (GO:0006260)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				TCAAGGATGCACTGTGCAAGG	0.408													G|||	1408	0.28115	0.3971	0.2507	5008	,	,		20950	0.2917		0.2028	False		,,,				2504	0.2157				p.A224A		Atlas-SNP	.											.	FAM111A	57	.	0			c.A672G						PASS	.	G	,,,,	1481,2921	677.6+/-403.4	255,971,975	122.0	122.0	122.0		672,672,672,672,672	-4.8	0.0	11	dbSNP_120	122	1826,6764	731.4+/-406.8	201,1424,2670	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FAM111A	NM_001142519.1,NM_001142520.1,NM_001142521.1,NM_022074.3,NM_198847.2	,,,,	456,2395,3645	GG,GA,AA		21.2573,33.6438,25.4541	,,,,	224/612,224/612,224/612,224/612,224/612	58919813	3307,9685	2201	4295	6496	SO:0001819	synonymous_variant	63901	exon5			GGATGCACTGTGC	AK092953	CCDS7973.1	11q12.1	2014-03-13				ENSG00000166801			24725	protein-coding gene	gene with protein product		615292				11572484, 23996431, 23684011	Standard	NM_022074		Approved	FLJ22794, KIAA1895	uc001nnq.3	Q96PZ2		ENST00000528737.1:c.672A>G	11.37:g.58919813A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_001142520	A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Silent	SNP	ENST00000528737.1	37	CCDS7973.1																																																																																			A|0.739;G|0.261	0.261	strong		0.408	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074	
ESPNL	339768	hgsc.bcm.edu	37	2	239010719	239010719	+	Silent	SNP	T	T	C	rs36066915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239010719T>C	ENST00000343063.3	+	2	695	c.432T>C	c.(430-432)gcT>gcC	p.A144A	ESPNL_ENST00000409169.1_Silent_p.A144A	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	144										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)		TGCACCACGCTGCCGTCAGTG	0.706													C|||	3051	0.609225	0.5635	0.5692	5008	,	,		13875	0.5903		0.6988	False		,,,				2504	0.6268				p.A144A		Atlas-SNP	.											.	ESPNL	63	.	0			c.T432C						PASS	.	C		2656,1670		873,910,380	9.0	11.0	10.0		432	-9.2	0.0	2	dbSNP_126	10	5553,2921		1889,1775,573	no	coding-synonymous	ESPNL	NM_194312.2		2762,2685,953	CC,CT,TT		34.4701,38.6038,35.8672		144/1006	239010719	8209,4591	2163	4237	6400	SO:0001819	synonymous_variant	339768	exon2			CCACGCTGCCGTC	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.432T>C	2.37:g.239010719T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			T|0.377;C|0.623	0.623	strong		0.706	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
AHNAK2	113146	hgsc.bcm.edu	37	14	105410411	105410411	+	Missense_Mutation	SNP	C	C	T	rs11160825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105410411C>T	ENST00000333244.5	-	7	11496	c.11377G>A	c.(11377-11379)Gac>Aac	p.D3793N	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3793			D -> N (in dbSNP:rs11160825).			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)			ACATCCTTGTCGGCCAGGGAC	0.582													.|||	2753	0.54972	0.6263	0.513	5008	,	,		20636	0.4087		0.5348	False		,,,				2504	0.6329				p.D3793N		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G11377A						PASS	.	C	ASN/ASP	2639,1357		869,901,228	222.0	222.0	222.0		11377	1.4	0.0	14	dbSNP_120	222	4517,3807		1234,2049,879	no	missense	AHNAK2	NM_138420.2	23	2103,2950,1107	TT,TC,CC		45.7352,33.959,41.9156	possibly-damaging	3793/5796	105410411	7156,5164	1998	4162	6160	SO:0001583	missense	113146	exon7			CCTTGTCGGCCAG	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.11377G>A	14.37:g.105410411C>T	ENSP00000353114:p.Asp3793Asn	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	252	250	0.992063	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1124	0.5146520146520146	309	0.6280487804878049	198	0.5469613259668509	215	0.3758741258741259	402	0.5303430079155673	c	10.26	1.302009	0.23736	0.66041	0.542648	ENSG00000185567	ENST00000333244	T	0.01821	4.62	4.3	1.37	0.22104	.	0.737133	0.10693	N	0.644947	T	0.00012	0.0000	M	0.84683	2.71	0.80722	P	0.0	P	0.42871	0.792	B	0.31191	0.125	T	0.08513	-1.0718	9	0.29301	T	0.29	.	6.6598	0.23009	0.0:0.5148:0.3818:0.1034	rs11160825	3793	Q8IVF2	AHNK2_HUMAN	N	3793	ENSP00000353114:D3793N	ENSP00000353114:D3793N	D	-	1	0	AHNAK2	104481456	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.050000	0.14120	-0.025000	0.13918	-1.582000	0.00854	GAC	C|0.480;T|0.520	0.520	strong		0.582	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MRPS24	64951	hgsc.bcm.edu	37	7	43908661	43908661	+	Silent	SNP	G	G	T	rs17854882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:43908661G>T	ENST00000317534.5	-	3	182	c.121C>A	c.(121-123)Cga>Aga	p.R41R	MRPS24_ENST00000467084.1_5'UTR|URGCP-MRPS24_ENST00000603700.1_Missense_Mutation_p.P86Q	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	41					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5						ACGCGTACTCGGGCCGCCCGG	0.647													G|||	150	0.0299521	0.112	0.0014	5008	,	,		10791	0.0		0.001	False		,,,				2504	0.0				p.P86Q		Atlas-SNP	.											.	.	.	.	0			c.C257A						PASS	.	G	GLN/PRO,	422,3984	205.8+/-227.6	21,380,1802	58.0	53.0	55.0		257,121	2.7	0.9	7	dbSNP_123	55	3,8597	3.0+/-9.4	0,3,4297	yes	missense,coding-synonymous	MRPS24,URGCP-MRPS24	NM_001204871.1,NM_032014.2	76,	21,383,6099	TT,TG,GG		0.0349,9.5778,3.2677	,	86/111,41/168	43908661	425,12581	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			GTACTCGGGCCGC	AB061207	CCDS5473.1	7p14	2012-09-13			ENSG00000062582	ENSG00000062582		"""Mitochondrial ribosomal proteins / small subunits"""	14510	protein-coding gene	gene with protein product		611986				8127713, 11279123	Standard	NM_032014		Approved	MRP-S24, HSPC335	uc003tit.1	Q96EL2	OTTHUMG00000023175	ENST00000317534.5:c.121C>A	7.37:g.43908661G>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	151	73	0.483444	NM_001204871	A4D1U9|P82668|Q96Q23|Q9P047	Missense_Mutation	SNP	ENST00000317534.5	37	CCDS5473.1																																																																																			G|0.971;T|0.029	0.029	strong		0.647	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014	
ZNF285	26974	hgsc.bcm.edu	37	19	44891554	44891554	+	Missense_Mutation	SNP	T	T	C	rs61358479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44891554T>C	ENST00000330997.4	-	4	917	c.853A>G	c.(853-855)Aag>Gag	p.K285E	ZNF285_ENST00000591679.1_Missense_Mutation_p.K292E|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Missense_Mutation_p.K285E	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	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						TAGGGAGTCTTGCCAGAGTGA	0.433													C|||	353	0.0704872	0.2148	0.0418	5008	,	,		19663	0.003		0.005	False		,,,				2504	0.0327				p.K285E		Atlas-SNP	.											.	ZNF285	86	.	0			c.A853G						PASS	.	C	GLU/LYS	709,3681		42,625,1528	80.0	94.0	90.0		853	1.8	0.0	19	dbSNP_129	90	39,8553		1,37,4258	no	missense	ZNF285	NM_152354.3	56	43,662,5786	CC,CT,TT		0.4539,16.1503,5.7618		285/591	44891554	748,12234	2195	4296	6491	SO:0001583	missense	26974	exon4			GAGTCTTGCCAGA	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.853A>G	19.37:g.44891554T>C	ENSP00000333595:p.Lys285Glu	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	103	40	0.38835	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	149	0.06822344322344322	115	0.23373983739837398	21	0.058011049723756904	1	0.0017482517482517483	12	0.0158311345646438	C	0.110	-1.139808	0.01728	0.161503	0.004539	ENSG00000062370	ENST00000544719;ENST00000330997	T;T	0.16196	2.36;5.01	2.85	1.75	0.24633	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00300	-1.685	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43245	-0.9403	8	0.02654	T	1	.	5.1318	0.14915	0.2029:0.6759:0.0:0.1211	rs61358479	309;285	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	E	308;285	ENSP00000439431:K308E;ENSP00000333595:K285E	ENSP00000333595:K285E	K	-	1	0	ZNF285	49583394	.	.	0.000000	0.03702	0.001000	0.01503	.	.	0.087000	0.17167	-0.380000	0.06706	AAG	T|0.952;C|0.048	0.048	strong		0.433	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
CCDC102B	79839	hgsc.bcm.edu	37	18	66678182	66678182	+	Missense_Mutation	SNP	C	C	A	rs17080065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:66678182C>A	ENST00000360242.5	+	7	1392	c.1275C>A	c.(1273-1275)aaC>aaA	p.N425K	CCDC102B_ENST00000584156.1_Missense_Mutation_p.N425K|CCDC102B_ENST00000319445.6_Missense_Mutation_p.N425K	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	425			N -> K (in dbSNP:rs17080065).							breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				AATTACTGAACCTTCAACATG	0.323													C|||	129	0.0257588	0.093	0.0086	5008	,	,		17732	0.0		0.0	False		,,,				2504	0.0				p.N425K		Atlas-SNP	.											.	CCDC102B	92	.	0			c.C1275A						PASS	.	C	LYS/ASN,LYS/ASN	354,4052	155.5+/-188.7	19,316,1868	62.0	60.0	60.0		1275,1275	-3.1	0.0	18	dbSNP_123	60	3,8597	1.2+/-3.3	0,3,4297	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	94,94	19,319,6165	AA,AC,CC		0.0349,8.0345,2.7449	benign,benign	425/514,425/514	66678182	357,12649	2203	4300	6503	SO:0001583	missense	79839	exon9			ACTGAACCTTCAA	AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 14"", ""aminoacylase 1-like"""	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.1275C>A	18.37:g.66678182C>A	ENSP00000353377:p.Asn425Lys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	C	5.485	0.274466	0.10403	0.080345	3.49E-4	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.11169	2.8;2.8	5.4	-3.11	0.05299	.	1.868220	0.02591	N	0.099920	T	0.00241	0.0007	N	0.22421	0.69	0.34315	D	0.685947	B	0.26400	0.148	B	0.24394	0.053	T	0.37572	-0.9700	10	0.10902	T	0.67	1.3033	1.8352	0.03138	0.4717:0.2442:0.0991:0.185	rs17080065;rs58253666;rs17080065	425	Q68D86	C102B_HUMAN	K	425	ENSP00000316237:N425K;ENSP00000353377:N425K	ENSP00000316237:N425K	N	+	3	2	CCDC102B	64829162	0.005000	0.15991	0.007000	0.13788	0.610000	0.37248	-1.893000	0.01609	-0.763000	0.04658	-0.355000	0.07637	AAC	C|0.972;A|0.028	0.028	strong		0.323	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
ACKR3	57007	hgsc.bcm.edu	37	2	237489796	237489796	+	Missense_Mutation	SNP	G	G	A	rs35095494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:237489796G>A	ENST00000272928.3	+	2	998	c.688G>A	c.(688-690)Gtc>Atc	p.V230I		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	230					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)										CATTATCGCTGTCTTCTACTT	0.572													G|||	59	0.0117812	0.0431	0.0029	5008	,	,		21400	0.0		0.0	False		,,,				2504	0.0				p.V230I		Atlas-SNP	.											.	CXCR7	72	.	0			c.G688A						PASS	.	G	ILE/VAL	212,4194	128.6+/-165.4	5,202,1996	103.0	88.0	93.0		688	0.6	0.3	2	dbSNP_126	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CXCR7	NM_020311.2	29	5,204,6294	AA,AG,GG		0.0233,4.8116,1.6454	benign	230/363	237489796	214,12792	2203	4300	6503	SO:0001583	missense	57007	exon2			ATCGCTGTCTTCT	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.688G>A	2.37:g.237489796G>A	ENSP00000272928:p.Val230Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	172	90	0.523256	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	37	CCDS2516.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	G	6.438	0.448991	0.12223	0.048116	2.33E-4	ENSG00000144476	ENST00000272928	T	0.37235	1.21	5.7	0.629	0.17687	GPCR, rhodopsin-like superfamily (1);	0.285365	0.33346	N	0.005017	T	0.02807	0.0084	N	0.25245	0.725	0.26027	N	0.981791	B	0.09022	0.002	B	0.14023	0.01	T	0.12142	-1.0559	9	.	.	.	.	5.5847	0.17267	0.3325:0.2292:0.4382:0.0	rs35095494	230	P25106	CXCR7_HUMAN	I	230	ENSP00000272928:V230I	.	V	+	1	0	CXCR7	237154535	0.001000	0.12720	0.276000	0.24689	0.421000	0.31385	-0.112000	0.10791	0.052000	0.16007	-0.140000	0.14226	GTC	G|0.984;A|0.016	0.016	strong		0.572	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311	
GSTA2	2939	hgsc.bcm.edu	37	6	52615415	52615415	+	Missense_Mutation	SNP	T	T	G	rs6577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	153	0	0		WXS	Illumina HiSeq	Phase_I	154	154	1	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	
COL27A1	85301	hgsc.bcm.edu	37	9	116931737	116931737	+	Silent	SNP	C	C	T	rs2808771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	22	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	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	
GPR148	344561	hgsc.bcm.edu	37	2	131487691	131487691	+	Missense_Mutation	SNP	C	C	T	rs143265147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131487691C>T	ENST00000309926.4	+	1	1049	c.967C>T	c.(967-969)Cgc>Tgc	p.R323C		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	323						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					GTACCTGCTCCGCTACCGGCA	0.577													.|||	23	0.00459265	0.0144	0.0043	5008	,	,		20324	0.0		0.001	False		,,,				2504	0.0				p.R323C		Atlas-SNP	.											GPR148,NS,carcinoma,0,1	GPR148	54	1	0			c.C967T						PASS	.	C	CYS/ARG	56,4350		1,54,2148	60.0	51.0	54.0		967	-4.1	0.0	2	dbSNP_134	54	1,8599		0,1,4299	yes	missense	GPR148	NM_207364.2	180	1,55,6447	TT,TC,CC		0.0116,1.271,0.4383	benign	323/348	131487691	57,12949	2203	4300	6503	SO:0001583	missense	344561	exon1			CTGCTCCGCTACC	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"""GPCR / Class A : Orphans"""	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.967C>T	2.37:g.131487691C>T	ENSP00000308908:p.Arg323Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	37	CCDS2163.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	.	8.765	0.924629	0.18056	0.01271	1.16E-4	ENSG00000173302	ENST00000309926	T	0.40476	1.03	3.49	-4.14	0.03892	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	U	0.000284	T	0.13586	0.0329	L	0.27053	0.805	0.32198	N	0.578142	B	0.18741	0.03	B	0.13407	0.009	T	0.01810	-1.1269	10	0.52906	T	0.07	-10.4178	0.3322	0.00320	0.2767:0.2483:0.1305:0.3444	.	323	Q8TDV2	GP148_HUMAN	C	323	ENSP00000308908:R323C	ENSP00000308908:R323C	R	+	1	0	GPR148	131204161	0.959000	0.32827	0.000000	0.03702	0.359000	0.29487	-0.164000	0.09983	-0.512000	0.06505	-0.261000	0.10672	CGC	C|0.996;T|0.004	0.004	strong		0.577	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092	
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24251659	24251659	+	Splice_Site	SNP	T	T	C	rs7007084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24251659T>C	ENST00000256412.4	+	4	582	c.362T>C	c.(361-363)aTg>aCg	p.M121T	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000522298.1_Splice_Site_p.M42T|ADAMDEC1_ENST00000538205.1_Splice_Site_p.M42T	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	121			M -> T (in dbSNP:rs7007084).		immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		CCTGAGAACATGGTAGGGTCC	0.423													T|||	133	0.0265575	0.0968	0.0072	5008	,	,		18292	0.0		0.0	False		,,,				2504	0.0				p.M121T	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.T362C						PASS	.	T	THR/MET,THR/MET,THR/MET	391,4015	191.6+/-217.2	21,349,1833	72.0	68.0	69.0		125,125,362	-0.3	0.2	8	dbSNP_116	69	3,8597	3.0+/-9.4	0,3,4297	yes	missense-near-splice,missense-near-splice,missense-near-splice	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	81,81,81	21,352,6130	CC,CT,TT		0.0349,8.8743,3.0294	benign,benign,benign	42/392,42/392,121/471	24251659	394,12612	2203	4300	6503	SO:0001630	splice_region_variant	27299	exon4			AGAACATGGTAGG	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.363+1T>C	8.37:g.24251659T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	49	0.022435897435897436	46	0.09349593495934959	3	0.008287292817679558	0	0.0	0	0.0	T	0.640	-0.813614	0.02798	0.088743	3.49E-4	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.05139	3.49;3.49;3.49	5.46	-0.309	0.12769	Peptidase M12B, propeptide (1);	0.592394	0.17862	N	0.159489	T	0.00144	0.0004	N	0.17872	0.535	0.09310	N	0.999996	B	0.11235	0.004	B	0.08055	0.003	T	0.43718	-0.9374	10	0.37606	T	0.19	-3.7358	1.3321	0.02137	0.3046:0.0864:0.1576:0.4513	rs7007084;rs52800945;rs7007084	121	O15204	ADEC1_HUMAN	T	121;42;42	ENSP00000256412:M121T;ENSP00000442592:M42T;ENSP00000428993:M42T	ENSP00000256412:M121T	M	+	2	0	ADAMDEC1	24307604	0.195000	0.23338	0.163000	0.22734	0.026000	0.11368	0.147000	0.16202	0.072000	0.16694	-0.371000	0.07208	ATG	T|0.967;C|0.033	0.033	strong		0.423	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	Missense_Mutation
TEX11	56159	hgsc.bcm.edu	37	X	70073159	70073159	+	Missense_Mutation	SNP	T	T	C	rs6525433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70073159T>C	ENST00000395889.2	-	7	544	c.389A>G	c.(388-390)aAa>aGa	p.K130R	TEX11_ENST00000374333.2_Missense_Mutation_p.K115R|TEX11_ENST00000344304.3_Missense_Mutation_p.K130R	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	130			K -> R (in dbSNP:rs6525433).		chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					CAACCATTCTTTTCCTATTCT	0.343													C|||	1007	0.266755	0.3139	0.1628	3775	,	,		12931	0.2351		0.004	False		,,,				2504	0.2434				p.K130R		Atlas-SNP	.											.	TEX11	132	.	0			c.A389G						PASS	.	C	ARG/LYS,ARG/LYS	1391,2444		199,766,227,667,344	59.0	52.0	55.0		389,344	0.6	0.2	X	dbSNP_116	55	63,6663		1,41,20,2385,1852	yes	missense,missense	TEX11	NM_001003811.1,NM_031276.2	26,26	200,807,247,3052,2196	CC,CT,C,TT,T		0.9367,36.2712,13.7676	benign,benign	130/941,115/926	70073159	1454,9107	2203	4299	6502	SO:0001583	missense	56159	exon7			CATTCTTTTCCTA	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"""testis expressed sequence 11"""			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.389A>G	X.37:g.70073159T>C	ENSP00000379226:p.Lys130Arg	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	154	84	0.545455	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	37	CCDS35323.1	343	0.20675105485232068	93	0.24345549738219896	38	0.11728395061728394	78	0.1703056768558952	2	0.0026455026455026454	t	0.004	-2.307809	0.00240	0.362712	0.009367	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000344304	T;T;T	0.32515	1.45;1.46;1.46	4.67	0.552	0.17230	Tetratricopeptide-like helical (1);	0.195124	0.44097	N	0.000482	T	0.00012	0.0000	L	0.28192	0.835	0.58432	P	1.0000000000287557E-6	B;B	0.10296	0.003;0.002	B;B	0.14578	0.011;0.005	T	0.48399	-0.9039	8	.	.	.	-9.5849	5.2184	0.15356	0.1379:0.1763:0.0:0.6859	rs6525433;rs52823269;rs57911929;rs6525433	115;130	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	R	115;130;130	ENSP00000363453:K115R;ENSP00000379226:K130R;ENSP00000340995:K130R	.	K	-	2	0	TEX11	69989884	0.993000	0.37304	0.217000	0.23759	0.001000	0.01503	0.343000	0.19944	-0.323000	0.08602	-1.201000	0.01664	AAA	0|0.003;C|0.200	0.200	strong		0.343	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1		
CCT8L2	150160	hgsc.bcm.edu	37	22	17072347	17072347	+	Nonsense_Mutation	SNP	C	C	T	rs139948519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17072347C>T	ENST00000359963.3	-	1	1353	c.1094G>A	c.(1093-1095)tGg>tAg	p.W365*		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	365					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				TGTACATTCCCATTCAAATAC	0.612													c|||	113	0.0225639	0.0598	0.0029	5008	,	,		18689	0.0		0.002	False		,,,				2504	0.0307				p.W365X		Atlas-SNP	.											.	CCT8L2	150	.	0			c.G1094A						PASS	.	C	stop/TRP	301,4105	164.7+/-196.3	7,287,1909	88.0	83.0	85.0		1094	2.0	0.2	22	dbSNP_134	85	28,8572	19.2+/-60.6	0,28,4272	no	stop-gained	CCT8L2	NM_014406.4		7,315,6181	TT,TC,CC		0.3256,6.8316,2.5296		365/558	17072347	329,12677	2203	4300	6503	SO:0001587	stop_gained	150160	exon1			CATTCCCATTCAA	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.1094G>A	22.37:g.17072347C>T	ENSP00000353048:p.Trp365*	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_014406	A4QPH3|Q9UJS3	Nonsense_Mutation	SNP	ENST00000359963.3	37	CCDS13738.1	29	0.013278388278388278	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	c	18.96	3.734449	0.69189	0.068316	0.003256	ENSG00000198445	ENST00000359963	.	.	.	1.98	1.98	0.26296	.	0.261754	0.21132	U	0.079635	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-8.0904	7.4423	0.27190	0.0:1.0:0.0:0.0	.	.	.	.	X	365	.	ENSP00000353048:W365X	W	-	2	0	CCT8L2	15452347	0.722000	0.28017	0.224000	0.23877	0.129000	0.20672	1.546000	0.36179	1.115000	0.41800	0.379000	0.24179	TGG	C|0.982;T|0.018	0.018	strong		0.612	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1		
TTC24	164118	hgsc.bcm.edu	37	1	156555577	156555577	+	Missense_Mutation	SNP	C	C	T	rs147693801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156555577C>T	ENST00000368237.3	+	8	1529	c.1529C>T	c.(1528-1530)aCg>aTg	p.T510M	AL365181.1_ENST00000581084.1_RNA|TTC24_ENST00000368236.3_Missense_Mutation_p.T510M|TTC24_ENST00000478081.1_3'UTR			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	510										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ACCAAGCACACGCCCTGCAGA	0.517													C|||	55	0.0109824	0.0393	0.0029	5008	,	,		20692	0.0		0.001	False		,,,				2504	0.0				p.T510M		Atlas-SNP	.											TTC24,right_upper_lobe,carcinoma,-1,1	TTC24	46	1	0			c.C1529T						PASS	.	C	MET/THR	122,4138		3,116,2011	117.0	119.0	118.0		1529	-0.6	0.0	1	dbSNP_134	118	0,8462		0,0,4231	yes	missense	TTC24	NM_001105669.2	81	3,116,6242	TT,TC,CC		0.0,2.8638,0.959	benign	510/583	156555577	122,12600	2130	4231	6361	SO:0001583	missense	164118	exon9			AGCACACGCCCTG		CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"""Tetratricopeptide (TTC) repeat domain containing"""	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.1529C>T	1.37:g.156555577C>T	ENSP00000357220:p.Thr510Met	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	155	65	0.419355	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	13|13	0.005952380952380952|0.005952380952380952	12|12	0.024390243902439025|0.024390243902439025	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	4.199|4.199	0.035700|0.035700	0.08148|0.08148	0.028638|0.028638	0.0|0.0	ENSG00000187862|ENSG00000187862	ENST00000340086|ENST00000368236;ENST00000368237	.|T;T	.|0.26223	.|1.75;1.75	3.22|3.22	-0.612|-0.612	0.11597|0.11597	.|.	.|17.220800	.|0.00397	.|N	.|0.000056	T|T	0.03915|0.03915	0.0110|0.0110	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.01281	.|0.0	T|T	0.29971|0.29971	-0.9994|-0.9994	5|10	.|0.48119	.|T	.|0.1	.|.	3.0131|3.0131	0.06051|0.06051	0.0:0.2819:0.2328:0.4852|0.0:0.2819:0.2328:0.4852	.|.	.|510	.|A2A3L6	.|TTC24_HUMAN	C|M	283|510	.|ENSP00000357219:T510M;ENSP00000357220:T510M	.|ENSP00000357219:T510M	R|T	+|+	1|2	0|0	TTC24|TTC24	154822201|154822201	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.015000|0.015000	0.08874|0.08874	0.040000|0.040000	0.13905|0.13905	-0.118000|-0.118000	0.11851|0.11851	-0.379000|-0.379000	0.06801|0.06801	CGC|ACG	C|0.994;T|0.006	0.006	strong		0.517	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384	
U2SURP	23350	hgsc.bcm.edu	37	3	142747230	142747230	+	Silent	SNP	G	G	A	rs80238215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:142747230G>A	ENST00000473835.2	+	15	1518	c.1428G>A	c.(1426-1428)aaG>aaA	p.K476K	U2SURP_ENST00000493598.2_Silent_p.K475K|U2SURP_ENST00000397933.2_Silent_p.K67K	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	476					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						ATAGGTGGAAGCTTTATTCTA	0.313													G|||	35	0.00698882	0.0234	0.0058	5008	,	,		15948	0.0		0.0	False		,,,				2504	0.0				p.K476K		Atlas-SNP	.											.	U2SURP	66	.	0			c.G1428A						PASS	.	G		61,3529		1,59,1735	74.0	70.0	71.0		1428	2.0	1.0	3	dbSNP_132	71	0,8136		0,0,4068	no	coding-synonymous	U2SURP	NM_001080415.1		1,59,5803	AA,AG,GG		0.0,1.6992,0.5202		476/1030	142747230	61,11665	1795	4068	5863	SO:0001819	synonymous_variant	23350	exon15			GTGGAAGCTTTAT	BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"""RNA binding motif (RRM) containing"""	30855	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein a"", ""Ser/Arg-rich domain protein, 140 kDa"", ""U2 associated SR140 protein"""					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.1428G>A	3.37:g.142747230G>A		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	184	85	0.461957	NM_001080415	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Silent	SNP	ENST00000473835.2	37	CCDS46928.1																																																																																			G|0.991;A|0.009	0.009	strong		0.313	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415	
HTR3E	285242	hgsc.bcm.edu	37	3	183824398	183824398	+	Missense_Mutation	SNP	G	G	A	rs13324468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183824398G>A	ENST00000415389.2	+	9	1754	c.1288G>A	c.(1288-1290)Gcg>Acg	p.A430T	HTR3E-AS1_ENST00000431427.1_RNA|HTR3E_ENST00000440596.2_Missense_Mutation_p.A456T|HTR3E_ENST00000425359.2_Missense_Mutation_p.A415T|HTR3E_ENST00000436361.2_Missense_Mutation_p.A430T|HTR3E_ENST00000335304.2_Missense_Mutation_p.A445T	NM_001256613.1|NM_198313.2	NP_001243542.1|NP_938055.1	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine (serotonin) receptor 3E, ionotropic	430			A -> T (in dbSNP:rs13324468).		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)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	40	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	GTTCAGCCACGCGATGGACGC	0.607													G|||	210	0.0419329	0.1543	0.0086	5008	,	,		18903	0.0		0.0	False		,,,				2504	0.0				p.A456T	Melanoma(7;227 727 6634 44770)	Atlas-SNP	.											.	HTR3E	65	.	0			c.G1366A						PASS	.	G	THR/ALA	520,3886	239.0+/-250.2	27,466,1710	171.0	152.0	158.0		1333	-5.5	0.0	3	dbSNP_121	158	5,8595	4.3+/-15.6	0,5,4295	no	missense	HTR3E	NM_182589.2	58	27,471,6005	AA,AG,GG		0.0581,11.8021,4.0366	benign	445/472	183824398	525,12481	2203	4300	6503	SO:0001583	missense	285242	exon7			AGCCACGCGATGG	AY159813	CCDS3251.1, CCDS58868.1, CCDS58869.1, CCDS58870.1, CCDS58871.1	3q27	2012-05-22	2012-02-03		ENSG00000186038	ENSG00000186038		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24005	protein-coding gene	gene with protein product		610123	"""5-hydroxytryptamine (serotonin) receptor 3, family member E"""			12801637, 15157181	Standard	NM_001256613		Approved		uc010hxr.3	A5X5Y0	OTTHUMG00000156857	ENST00000415389.2:c.1288G>A	3.37:g.183824398G>A	ENSP00000401444:p.Ala430Thr	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	283	146	0.515901	NM_001256614	A8IKD7|E9PGF1|Q495G1|Q495G3|Q6V706|Q6V707|Q7Z6B2	Missense_Mutation	SNP	ENST00000415389.2	37	CCDS58868.1	109	0.04990842490842491	104	0.21138211382113822	5	0.013812154696132596	0	0.0	0	0.0	g	4.180	0.031992	0.08101	0.118021	5.81E-4	ENSG00000186038	ENST00000415389;ENST00000425359;ENST00000335304;ENST00000436361;ENST00000440596	D;D;D;D;D	0.81908	-1.55;-1.55;-1.55;-1.55;-1.55	4.07	-5.5	0.02576	Neurotransmitter-gated ion-channel transmembrane domain (1);	2.871980	0.03018	N	0.150396	T	0.00109	0.0003	N	0.04043	-0.29	0.80722	P	0.0	B;B;B;B;B	0.12013	0.001;0.0;0.005;0.001;0.001	B;B;B;B;B	0.11329	0.005;0.004;0.006;0.002;0.002	T	0.10019	-1.0648	9	0.49607	T	0.09	.	7.9969	0.30273	0.2122:0.3113:0.4765:0.0	rs13324468;rs56491361;rs13324468	456;430;430;445;415	E9PGF1;A5X5Y0;A5X5Y0-4;A5X5Y0-3;A5X5Y0-2	.;5HT3E_HUMAN;.;.;.	T	430;415;445;430;456	ENSP00000401444:A430T;ENSP00000401900:A415T;ENSP00000335511:A445T;ENSP00000395833:A430T;ENSP00000406050:A456T	ENSP00000335511:A445T	A	+	1	0	HTR3E	185307092	0.000000	0.05858	0.038000	0.18304	0.020000	0.10135	0.081000	0.14823	-1.048000	0.03238	-2.223000	0.00295	GCG	G|0.941;A|0.059	0.059	strong		0.607	HTR3E-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346284.1	NM_182589	
LARGE	9215	hgsc.bcm.edu	37	22	33679238	33679238	+	Silent	SNP	T	T	C	rs11913417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:33679238T>C	ENST00000354992.2	-	14	2398	c.1827A>G	c.(1825-1827)tcA>tcG	p.S609S	LARGE_ENST00000397394.2_Silent_p.S609S|LARGE_ENST00000402320.1_Silent_p.S557S|LARGE_ENST00000437602.2_Intron|LARGE_ENST00000452586.2_Silent_p.S408S|LARGE_ENST00000337431.2_Silent_p.S557S	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	609					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				ACTCCGCTTTTGACTTGGGGA	0.547													C|||	182	0.0363419	0.0756	0.0086	5008	,	,		19914	0.005		0.004	False		,,,				2504	0.0685				p.S609S	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											.	LARGE	98	.	0			c.A1827G						PASS	.	C	,	280,4126	800.8+/-415.6	9,262,1932	138.0	119.0	126.0		1827,1827	-10.8	0.0	22	dbSNP_120	126	44,8556	817.3+/-406.9	0,44,4256	no	coding-synonymous,coding-synonymous	LARGE	NM_004737.4,NM_133642.3	,	9,306,6188	CC,CT,TT		0.5116,6.355,2.4912	,	609/757,609/757	33679238	324,12682	2203	4300	6503	SO:0001819	synonymous_variant	9215	exon14			CGCTTTTGACTTG	AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1827A>G	22.37:g.33679238T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	152	88	0.578947	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	37	CCDS13912.1																																																																																			T|0.970;C|0.030	0.030	strong		0.547	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642	
ZFP69B	65243	hgsc.bcm.edu	37	1	40928145	40928145	+	Silent	SNP	G	G	A	rs61740805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:40928145G>A	ENST00000411995.2	+	6	864	c.489G>A	c.(487-489)tcG>tcA	p.S163S	ZFP69B_ENST00000361584.3_Silent_p.S61S|RP1-228H13.5_ENST00000565390.1_RNA|ZFP69B_ENST00000484445.1_3'UTR	NM_023070.2	NP_075558.2	Q9UJL9	ZF69B_HUMAN	ZFP69 zinc finger protein B	163					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)										ATGATATTTCGTGGGAAGAAC	0.338													G|||	173	0.0345447	0.0635	0.0303	5008	,	,		19910	0.0		0.0557	False		,,,				2504	0.0123				p.S163S		Atlas-SNP	.											ZNF643_ENST00000411995,NS,carcinoma,+1,4	.	.	4	0			c.G489A						PASS	.	G		256,4150		10,236,1957	121.0	133.0	129.0		489	-6.8	0.0	1	dbSNP_129	129	472,8128		14,444,3842	no	coding-synonymous	ZNF643	NM_023070.2		24,680,5799	AA,AG,GG		5.4884,5.8103,5.5974		163/535	40928145	728,12278	2203	4300	6503	SO:0001819	synonymous_variant	65243	exon5			TATTTCGTGGGAA	BC017498	CCDS452.1, CCDS452.2	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187801	ENSG00000187801		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	28053	protein-coding gene	gene with protein product			"""zinc finger protein 643"""	ZNF643			Standard	NM_023070		Approved	ZKSCAN23B, FLJ34293, ZSCAN54B	uc001cfn.2	Q9UJL9	OTTHUMG00000007302	ENST00000411995.2:c.489G>A	1.37:g.40928145G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_023070	Q5QPL4	Silent	SNP	ENST00000411995.2	37	CCDS452.2																																																																																			G|0.950;A|0.050	0.050	strong		0.338	ZFP69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019078.2	NM_023070	
SPTB	6710	hgsc.bcm.edu	37	14	65241228	65241228	+	Silent	SNP	A	A	G	rs229592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:65241228A>G	ENST00000389721.5	-	23	4892	c.4860T>C	c.(4858-4860)atT>atC	p.I1620I	SPTB_ENST00000542895.1_Silent_p.I1620I|SPTB_ENST00000556626.1_Silent_p.I1620I|SPTB_ENST00000389720.3_Silent_p.I1620I|SPTB_ENST00000389722.3_Silent_p.I1620I	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1620					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)		TCAGCATCACAATGGCGCCCT	0.642													G|||	2396	0.478435	0.848	0.3242	5008	,	,		17956	0.4563		0.2664	False		,,,				2504	0.3292				p.I1620I		Atlas-SNP	.											.	SPTB	378	.	0			c.T4860C						PASS	.	G	,	3180,1186		1187,806,190	18.0	16.0	17.0		4860,4860	-3.9	0.9	14	dbSNP_79	17	1988,6522		256,1476,2523	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	1443,2282,2713	GG,GA,AA		23.3608,27.1645,40.1367	,	1620/2138,1620/2329	65241228	5168,7708	2183	4255	6438	SO:0001819	synonymous_variant	6710	exon23			CATCACAATGGCG		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.4860T>C	14.37:g.65241228A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	127	64	0.503937	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			A|0.516;G|0.484	0.484	strong		0.642	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
CBL	867	hgsc.bcm.edu	37	11	119170480	119170480	+	Missense_Mutation	SNP	G	G	A	rs17122769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119170480G>A	ENST00000264033.4	+	16	3086	c.2710G>A	c.(2710-2712)Gta>Ata	p.V904I		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	904	Interaction with CD2AP.		V -> I (in dbSNP:rs17122769).		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)			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)		TCCTGCCCATGTAGCTACCTA	0.493			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies				G|||	30	0.00599042	0.0219	0.0014	5008	,	,		21109	0.0		0.0	False		,,,				2504	0.0				p.V904I		Atlas-SNP	.		"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.G2710A						PASS	.	G	ILE/VAL	65,4333	61.1+/-98.1	0,65,2134	239.0	244.0	242.0		2710	4.9	0.1	11	dbSNP_123	242	2,8588	2.2+/-6.3	0,2,4293	yes	missense	CBL	NM_005188.2	29	0,67,6427	AA,AG,GG		0.0233,1.4779,0.5159	benign	904/907	119170480	67,12921	2199	4295	6494	SO:0001583	missense	867	exon16	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	GCCCATGTAGCTA	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.2710G>A	11.37:g.119170480G>A	ENSP00000264033:p.Val904Ile	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_005188	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	11.37	1.617349	0.28801	0.014779	2.33E-4	ENSG00000110395	ENST00000264033	T	0.78816	-1.21	5.8	4.89	0.63831	.	0.120265	0.56097	D	0.000027	T	0.49372	0.1553	N	0.03115	-0.41	0.44677	D	0.997661	B	0.12013	0.005	B	0.14023	0.01	T	0.50499	-0.8821	10	0.30854	T	0.27	-23.714	14.7175	0.69280	0.0692:0.0:0.9308:0.0	rs17122769;rs52793379;rs17122769	904	P22681	CBL_HUMAN	I	904	ENSP00000264033:V904I	ENSP00000264033:V904I	V	+	1	0	CBL	118675690	0.997000	0.39634	0.064000	0.19789	0.936000	0.57629	2.667000	0.46808	1.461000	0.47929	0.655000	0.94253	GTA	G|0.993;A|0.007	0.007	strong		0.493	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	
MUC17	140453	hgsc.bcm.edu	37	7	100679254	100679254	+	Missense_Mutation	SNP	A	A	G	rs199808245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100679254A>G	ENST00000306151.4	+	3	4621	c.4557A>G	c.(4555-4557)atA>atG	p.I1519M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1519	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)					TAACAAGTATACCTGTCAGCA	0.478																																					p.I1519M		Atlas-SNP	.											.	MUC17	804	.	0			c.A4557G						PASS	.						232.0	210.0	217.0					7																	100679254		2203	4300	6503	SO:0001583	missense	140453	exon3			AAGTATACCTGTC	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.4557A>G	7.37:g.100679254A>G	ENSP00000302716:p.Ile1519Met	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	155	26	0.167742	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.915578	0.00503	.	.	ENSG00000169876	ENST00000306151	T	0.02216	4.39	0.364	-0.728	0.11162	.	.	.	.	.	T	0.01320	0.0043	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49173	-0.8967	8	0.46703	T	0.11	.	.	.	.	.	1519	Q685J3	MUC17_HUMAN	M	1519	ENSP00000302716:I1519M	ENSP00000302716:I1519M	I	+	3	3	MUC17	100465974	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.763000	0.00784	-2.226000	0.00723	-1.550000	0.00899	ATA	A|0.955;G|0.045	0.045	strong		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MAP2K3	5606	hgsc.bcm.edu	37	17	21203907	21203907	+	Silent	SNP	T	T	C	rs73311539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	155	0	0		WXS	Illumina HiSeq	Phase_I	172	63	0.366279	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	
ZYG11A	440590	hgsc.bcm.edu	37	1	53326421	53326421	+	Missense_Mutation	SNP	A	A	G	rs61744306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53326421A>G	ENST00000371528.1	+	4	1175	c.1027A>G	c.(1027-1029)Atg>Gtg	p.M343V	ZYG11A_ENST00000371532.1_Start_Codon_SNP_p.M1V	NM_001004339.2	NP_001004339.2	Q6WRX3	ZY11A_HUMAN	zyg-11 family member A, cell cycle regulator	343										breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|skin(1)	10						AGGAGCCAGTATGAGTCAGAT	0.423													A|||	69	0.013778	0.0303	0.0231	5008	,	,		17868	0.0		0.0109	False		,,,				2504	0.002				p.M343V		Atlas-SNP	.											.	ZYG11A	46	.	0			c.A1027G						PASS	.	A	VAL/MET	32,1352		0,32,660	114.0	96.0	102.0		1027	-0.3	0.9	1	dbSNP_129	102	18,3164		0,18,1573	yes	missense	ZYG11A	NM_001004339.2	21	0,50,2233	GG,GA,AA		0.5657,2.3121,1.0951	benign	343/760	53326421	50,4516	692	1591	2283	SO:0001583	missense	440590	exon4			GCCAGTATGAGTC		CCDS44148.1	1p32.3	2013-01-17	2012-12-10		ENSG00000203995	ENSG00000203995		"""ZYG11 cell cycle regulator family"""	32058	protein-coding gene	gene with protein product			"""zyg-11 homolog A (C. elegans)"""				Standard	NM_001004339		Approved	ZYG11	uc001cuk.2	Q6WRX3	OTTHUMG00000008923	ENST00000371528.1:c.1027A>G	1.37:g.53326421A>G	ENSP00000360583:p.Met343Val	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	246	103	0.418699	NM_001004339	A6NCK5	Missense_Mutation	SNP	ENST00000371528.1	37	CCDS44148.1	31	0.014194139194139194	13	0.026422764227642278	12	0.03314917127071823	0	0.0	6	0.0079155672823219	A	9.069	0.996332	0.19043	0.023121	0.005657	ENSG00000203995	ENST00000371532;ENST00000371528	T;T	0.05025	3.51;3.51	4.89	-0.281	0.12882	.	0.423208	0.27787	N	0.017844	T	0.00967	0.0032	N	0.22421	0.69	0.25986	N	0.982306	B	0.02656	0.0	B	0.04013	0.001	T	0.43814	-0.9368	10	0.14656	T	0.56	-1.518	3.1939	0.06626	0.2766:0.0:0.3675:0.3559	rs61744306	343	Q6WRX3	ZY11A_HUMAN	V	1;343	ENSP00000360587:M1V;ENSP00000360583:M343V	ENSP00000360583:M343V	M	+	1	0	ZYG11A	53099009	1.000000	0.71417	0.936000	0.37596	0.987000	0.75469	1.184000	0.32053	0.032000	0.15435	0.459000	0.35465	ATG	A|0.983;G|0.017	0.017	strong		0.423	ZYG11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024856.3	NM_001004339	
CCDC157	550631	hgsc.bcm.edu	37	22	30762140	30762140	+	Missense_Mutation	SNP	G	G	A	rs740223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30762140G>A	ENST00000405659.1	+	3	860	c.151G>A	c.(151-153)Gac>Aac	p.D51N	CCDC157_ENST00000338306.3_Missense_Mutation_p.D51N|CCDC157_ENST00000399824.2_Missense_Mutation_p.D51N			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	51			D -> N (in dbSNP:rs740223).							central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CTGTGACCTCGACATGGTGGC	0.647													G|||	797	0.159145	0.1415	0.1571	5008	,	,		20656	0.1468		0.2694	False		,,,				2504	0.0838				p.D51N		Atlas-SNP	.											.	CCDC157	86	.	0			c.G151A						PASS	.	G	ASN/ASP	667,3739	282.5+/-276.6	55,557,1591	154.0	135.0	142.0		151	5.2	1.0	22	dbSNP_86	142	2204,6396	375.9+/-337.9	287,1630,2383	no	missense	CCDC157	NM_001017437.2	23	342,2187,3974	AA,AG,GG		25.6279,15.1384,22.0744	probably-damaging	51/753	30762140	2871,10135	2203	4300	6503	SO:0001583	missense	550631	exon3			GACCTCGACATGG	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.151G>A	22.37:g.30762140G>A	ENSP00000385357:p.Asp51Asn	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_001017437	Q0VD76|Q9BYA4	Missense_Mutation	SNP	ENST00000405659.1	37	CCDS33632.2	381	0.17445054945054944	70	0.14227642276422764	57	0.1574585635359116	71	0.12412587412587413	183	0.24142480211081793	G	35	5.588928	0.96590	0.151384	0.256279	ENSG00000187860	ENST00000399824;ENST00000405659;ENST00000338306;ENST00000445005;ENST00000430839	T;T;T;T;T	0.54479	0.57;1.46;1.46;1.09;1.09	5.25	5.25	0.73442	.	.	.	.	.	T	0.00039	0.0001	M	0.61703	1.905	0.09310	P	1.0	D	0.89917	1.0	D	0.97110	1.0	T	0.00076	-1.2119	8	0.41790	T	0.15	-20.5084	17.3819	0.87407	0.0:0.0:1.0:0.0	rs740223;rs13055115;rs17736500;rs52830809;rs740223	51	Q569K6	CC157_HUMAN	N	51	ENSP00000382720:D51N;ENSP00000385357:D51N;ENSP00000343087:D51N;ENSP00000387491:D51N;ENSP00000401837:D51N	ENSP00000343087:D51N	D	+	1	0	CCDC157	29092140	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.060000	0.93907	2.613000	0.88420	0.455000	0.32223	GAC	G|0.814;A|0.186	0.186	strong		0.647	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
MRPL23	6150	hgsc.bcm.edu	37	11	1977552	1977552	+	Missense_Mutation	SNP	G	G	A	rs12812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1977552G>A	ENST00000397298.3	+	5	449	c.364G>A	c.(364-366)Gct>Act	p.A122T	MRPL23_ENST00000381519.1_Missense_Mutation_p.A122T|MRPL23_ENST00000397294.3_Intron|MRPL23_ENST00000397297.3_Intron|MRPL23_ENST00000381514.3_Intron	NM_021134.3	NP_066957.3	Q16540	RM23_HUMAN	mitochondrial ribosomal protein L23	122			A -> T (in dbSNP:rs12812). {ECO:0000269|PubMed:11543634}.		translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(1)|ovary(1)	4		all_epithelial(84;6.24e-05)|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;0.0026)|Lung(200;0.0171)|LUSC - Lung squamous cell carcinoma(625;0.0842)		TGAAGGCAGCGCTGCCGACGA	0.647													G|||	715	0.142772	0.0121	0.2032	5008	,	,		12924	0.1389		0.169	False		,,,				2504	0.2536				p.A122T		Atlas-SNP	.											MRPL23,NS,carcinoma,0,1	MRPL23	14	1	0			c.G364A						PASS	.	G	THR/ALA	203,4199	126.1+/-163.2	4,195,2002	83.0	83.0	83.0		364	-6.5	0.0	11	dbSNP_52	83	1296,7302	255.4+/-280.3	91,1114,3094	yes	missense	MRPL23	NM_021134.3	58	95,1309,5096	AA,AG,GG		15.0733,4.6115,11.5308	benign	122/154	1977552	1499,11501	2201	4299	6500	SO:0001583	missense	6150	exon5			GGCAGCGCTGCCG	AB051340	CCDS31336.1	11p15.5	2012-09-13			ENSG00000214026	ENSG00000214026		"""Mitochondrial ribosomal proteins / large subunits"""	10322	protein-coding gene	gene with protein product		600789		RPL23L		8541832	Standard	NM_021134		Approved	L23MRP	uc001lux.3	Q16540	OTTHUMG00000012476	ENST00000397298.3:c.364G>A	11.37:g.1977552G>A	ENSP00000380466:p.Ala122Thr	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_021134	A8MT29|Q96Q71	Missense_Mutation	SNP	ENST00000397298.3	37	CCDS31336.1	318	0.14560439560439561	13	0.026422764227642278	68	0.1878453038674033	88	0.15384615384615385	149	0.19656992084432717	G	5.460	0.269875	0.10349	0.046115	0.150733	ENSG00000214026	ENST00000397298;ENST00000381519	T;T	0.14266	2.52;2.52	3.24	-6.48	0.01896	.	.	.	.	.	T	0.00012	0.0000	N	0.11560	0.145	0.50813	P	1.0900000000002574E-4	B	0.06786	0.001	B	0.01281	0.0	T	0.31943	-0.9925	8	0.15499	T	0.54	.	3.0296	0.06102	0.2037:0.1638:0.4707:0.1619	rs12812;rs217212;rs3168309;rs12812	122	Q16540	RM23_HUMAN	T	122	ENSP00000380466:A122T;ENSP00000370930:A122T	ENSP00000370930:A122T	A	+	1	0	MRPL23	1934128	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.103000	0.03329	-3.533000	0.00145	-2.560000	0.00174	GCT	G|0.874;A|0.126	0.126	strong		0.647	MRPL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034765.2	NM_021134	
OR6C74	254783	hgsc.bcm.edu	37	12	55641328	55641328	+	Missense_Mutation	SNP	G	G	A	rs6581025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55641328G>A	ENST00000343870.4	+	1	347	c.257G>A	c.(256-258)gGt>gAt	p.G86D		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	86			G -> D (in dbSNP:rs6581025).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	12						ATGGCAACAGGTGATAAGACC	0.398													G|||	1140	0.227636	0.1248	0.2291	5008	,	,		20270	0.1141		0.333	False		,,,				2504	0.3742				p.G86D		Atlas-SNP	.											.	OR6C74	52	.	0			c.G257A						PASS	.	G	ASP/GLY	692,3714	288.7+/-280.0	48,596,1559	198.0	200.0	199.0		257	4.5	0.2	12	dbSNP_116	199	2717,5883	433.8+/-357.5	426,1865,2009	yes	missense	OR6C74	NM_001005490.1	94	474,2461,3568	AA,AG,GG		31.593,15.7059,26.211	probably-damaging	86/313	55641328	3409,9597	2203	4300	6503	SO:0001583	missense	254783	exon1			CAACAGGTGATAA		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.257G>A	12.37:g.55641328G>A	ENSP00000342836:p.Gly86Asp	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	189	71	0.375661	NM_001005490		Missense_Mutation	SNP	ENST00000343870.4	37	CCDS31816.1	478	0.21886446886446886	66	0.13414634146341464	95	0.26243093922651933	70	0.12237762237762238	247	0.3258575197889182	g	13.46	2.244713	0.39697	0.157059	0.31593	ENSG00000197706	ENST00000343870	T	0.02787	4.16	5.36	4.47	0.54385	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000062	T	0.00012	0.0000	L	0.47016	1.485	0.80722	P	0.0	P	0.36465	0.554	B	0.38458	0.274	T	0.50783	-0.8787	9	0.87932	D	0	.	9.0034	0.36097	0.2317:0.0:0.7683:0.0	rs6581025;rs17442303;rs6581025	86	A6NCV1	O6C74_HUMAN	D	86	ENSP00000342836:G86D	ENSP00000342836:G86D	G	+	2	0	OR6C74	53927595	0.000000	0.05858	0.204000	0.23530	0.953000	0.61014	0.584000	0.23864	1.371000	0.46172	0.551000	0.68910	GGT	G|0.760;A|0.240	0.240	strong		0.398	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1		
CAND2	23066	hgsc.bcm.edu	37	3	12858028	12858028	+	Missense_Mutation	SNP	T	T	C	rs3732675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:12858028T>C	ENST00000456430.2	+	10	1638	c.1597T>C	c.(1597-1599)Tct>Cct	p.S533P	CAND2_ENST00000295989.5_Missense_Mutation_p.S440P	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	533			S -> P (in dbSNP:rs3732675).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TGTGGCTGACTCTTTCTACAA	0.637													C|||	3025	0.604034	0.9584	0.4914	5008	,	,		18601	0.4365		0.6243	False		,,,				2504	0.3569				p.S533P	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											CAND2_ENST00000456430,NS,carcinoma,0,2	CAND2	138	2	0			c.T1597C						PASS	.	C	PRO/SER,PRO/SER	3700,460		1648,404,28	39.0	44.0	43.0		1597,1318	4.2	1.0	3	dbSNP_107	43	4931,3475		1439,2053,711	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	74,74	3087,2457,739	CC,CT,TT		41.3395,11.0577,31.3147	benign,benign	533/1237,440/1120	12858028	8631,3935	2080	4203	6283	SO:0001583	missense	23066	exon10			GCTGACTCTTTCT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1597T>C	3.37:g.12858028T>C	ENSP00000387641:p.Ser533Pro	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1331	0.6094322344322345	468	0.9512195121951219	173	0.47790055248618785	226	0.3951048951048951	464	0.6121372031662269	C	1.795	-0.478506	0.04414	0.889423	0.586605	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.63744	-0.06;-0.06	5.12	4.25	0.50352	Armadillo-like helical (1);Armadillo-type fold (1);	0.204228	0.42682	N	0.000667	T	0.00012	0.0000	N	0.01086	-1.025	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42103	-0.9471	9	0.02654	T	1	-27.0988	7.3268	0.26560	0.0:0.7304:0.0:0.2696	rs3732675;rs17825071;rs60814914;rs3732675	533;440	O75155;O75155-2	CAND2_HUMAN;.	P	440;533	ENSP00000295989:S440P;ENSP00000387641:S533P	ENSP00000295989:S440P	S	+	1	0	CAND2	12833028	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	1.701000	0.37825	0.577000	0.29470	-0.215000	0.12644	TCT	C|0.609;G|0.000;T|0.391	0.609	strong		0.637	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
OR7E24	26648	hgsc.bcm.edu	37	19	9362343	9362343	+	Silent	SNP	C	C	T	rs2240927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9362343C>T	ENST00000456448.1	+	1	738	c.624C>T	c.(622-624)tcC>tcT	p.S208S		NM_001079935.1	NP_001073404.1	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E, member 24	208						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(8)|ovary(1)|prostate(1)|skin(2)	16						TTAGGTGTTCCGACACCTTCA	0.408													t|||	2663	0.531749	0.8548	0.3833	5008	,	,		21220	0.5377		0.2833	False		,,,				2504	0.4499				p.S208S		Atlas-SNP	.											.	OR7E24	48	.	0			c.C624T						PASS	.	T		2752,1092		990,772,160	57.0	58.0	57.0		624	-0.5	0.0	19	dbSNP_98	57	2129,6153		270,1589,2282	no	coding-synonymous	OR7E24	NM_001079935.1		1260,2361,2442	TT,TC,CC		25.7064,28.4079,40.2524		208/340	9362343	4881,7245	1922	4141	6063	SO:0001819	synonymous_variant	26648	exon1			GTGTTCCGACACC	Y10529	CCDS45955.1	19p13.2	2012-08-09	2004-03-04	2004-03-05		ENSG00000237521		"""GPCR / Class A : Olfactory receptors"""	8396	protein-coding gene	gene with protein product			"""olfactory receptor, family 7, subfamily E, member 24 pseudogene"""	OR7E24P		9268701	Standard	NM_001079935		Approved	OR19-8, HSHT2, OR7E24Q	uc002mlb.1	Q6IFN5		ENST00000456448.1:c.624C>T	19.37:g.9362343C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001079935	B9EJD9|Q9UPJ1	Silent	SNP	ENST00000456448.1	37	CCDS45955.1																																																																																			C|0.488;T|0.512	0.512	strong		0.408	OR7E24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449006.1		
DKC1	1736	hgsc.bcm.edu	37	X	154004584	154004584	+	Silent	SNP	C	C	T	rs1127051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:154004584C>T	ENST00000369550.5	+	14	1671	c.1461C>T	c.(1459-1461)gcC>gcT	p.A487A	SNORA56_ENST00000383966.1_RNA	NM_001142463.1|NM_001363.3	NP_001135935.1|NP_001354.1	O60832	DKC1_HUMAN	dyskeratosis congenita 1, dyskerin	487	Nuclear and nucleolar localization.				cell proliferation (GO:0008283)|pseudouridine synthesis (GO:0001522)|RNA processing (GO:0006396)|rRNA processing (GO:0006364)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)|telomerase activity (GO:0003720)			breast(2)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)	15	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					AGAGCGGGGCCGAGCCTGGAG	0.532									Congenital Dyskeratosis				C|||	233	0.0617219	0.093	0.0346	3775	,	,		14744	0.0337		0.0487	False		,,,				2504	0.0031				p.A487A		Atlas-SNP	.											.	DKC1	41	.	0			c.C1461T						PASS	.	C	,	479,3354		30,351,68,1251,501	55.0	46.0	49.0		1446,1461	0.6	0.0	X	dbSNP_86	49	458,6267		16,299,127,2113,1742	no	coding-synonymous,coding-synonymous	DKC1	NM_001142463.1,NM_001363.3	,	46,650,195,3364,2243	TT,TC,T,CC,C		6.8104,12.4967,8.8748	,	482/510,487/515	154004584	937,9621	2201	4297	6498	SO:0001819	synonymous_variant	1736	exon14	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	CGGGGCCGAGCCT	AJ224481	CCDS14761.1, CCDS76062.1	Xq28	2014-09-17			ENSG00000130826	ENSG00000130826			2890	protein-coding gene	gene with protein product		300126		DKC		9590285, 9888995	Standard	NM_001142463		Approved	XAP101, dyskerin, NAP57, NOLA4	uc004fmm.3	O60832	OTTHUMG00000024242	ENST00000369550.5:c.1461C>T	X.37:g.154004584C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	144	96	0.666667	NM_001363	F5BSB3|O43845|Q96G67|Q9Y505	Silent	SNP	ENST00000369550.5	37	CCDS14761.1																																																																																			C|0.921;T|0.079	0.079	strong		0.532	DKC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061180.5	NM_001363	
EIF3K	27335	hgsc.bcm.edu	37	19	39125677	39125677	+	Missense_Mutation	SNP	G	G	A	rs138580388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39125677G>A	ENST00000538434.1	+	6	518	c.283G>A	c.(283-285)Gac>Aac	p.D95N	EIF3K_ENST00000592558.1_Missense_Mutation_p.D156N|EIF3K_ENST00000248342.4_Missense_Mutation_p.D182N|EIF3K_ENST00000588934.1_Intron|EIF3K_ENST00000593149.1_Missense_Mutation_p.D95N|EIF3K_ENST00000545173.2_Missense_Mutation_p.D182N					eukaryotic translation initiation factor 3, subunit K										EIF3K/CYP39A1(2)	central_nervous_system(1)|endometrium(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CTGGAGTGCCGACGAGTCGGG	0.542											OREG0025450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	12	0.00239617	0.0091	0.0	5008	,	,		18892	0.0		0.0	False		,,,				2504	0.0				p.D182N		Atlas-SNP	.											.	EIF3K	22	.	0			c.G544A						PASS	.	G	ASN/ASP	25,4381	31.7+/-61.6	0,25,2178	89.0	80.0	83.0		544	3.2	0.1	19	dbSNP_134	83	0,8600		0,0,4300	yes	missense	EIF3K	NM_013234.2	23	0,25,6478	AA,AG,GG		0.0,0.5674,0.1922	benign	182/219	39125677	25,12981	2203	4300	6503	SO:0001583	missense	27335	exon7			AGTGCCGACGAGT	AB019392	CCDS12517.1, CCDS74360.1	19q13.2	2012-05-28	2007-07-27	2007-07-27	ENSG00000178982	ENSG00000178982			24656	protein-coding gene	gene with protein product		609596	"""eukaryotic translation initiation factor 3, subunit 12"""	EIF3S12		11042152, 14519125	Standard	XM_006723147		Approved	eIF3k, PRO1474, HSPC029, PTD001, PLAC-24, M9, ARG134	uc002oiz.1	Q9UBQ5		ENST00000538434.1:c.283G>A	19.37:g.39125677G>A	ENSP00000440999:p.Asp95Asn	Somatic	70	0	0	883	WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_013234		Missense_Mutation	SNP	ENST00000538434.1	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	5.726	0.318348	0.10845	0.005674	0.0	ENSG00000178982	ENST00000248342;ENST00000538434;ENST00000545173	.	.	.	5.36	3.2	0.36748	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.062209	0.64402	D	0.000005	T	0.18676	0.0448	N	0.25201	0.72	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.14504	-1.0470	9	0.87932	D	0	-16.4366	5.4949	0.16797	0.1755:0.0:0.661:0.1635	.	95;182;182	B4DQ48;B7ZAM9;Q9UBQ5	.;.;EIF3K_HUMAN	N	182;95;182	.	ENSP00000248342:D182N	D	+	1	0	EIF3K	43817517	0.010000	0.17322	0.080000	0.20451	0.512000	0.34134	0.612000	0.24283	1.397000	0.46682	0.549000	0.68633	GAC	G|0.998;A|0.002	0.002	strong		0.542	EIF3K-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000453409.1	NM_013234	
LRWD1	222229	hgsc.bcm.edu	37	7	102106459	102106459	+	Silent	SNP	G	G	A	rs146433593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:102106459G>A	ENST00000292616.5	+	2	428	c.276G>A	c.(274-276)aaG>aaA	p.K92K	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	92					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						AGTTCCCCAAGCTCGAGGAAC	0.637													G|||	18	0.00359425	0.0136	0.0	5008	,	,		19209	0.0		0.0	False		,,,				2504	0.0				p.K92K		Atlas-SNP	.											.	LRWD1	41	.	0			c.G276A						PASS	.	G		59,4347	57.4+/-93.9	0,59,2144	46.0	45.0	45.0		276	-5.5	0.0	7	dbSNP_134	45	0,8600		0,0,4300	no	coding-synonymous	LRWD1	NM_152892.1		0,59,6444	AA,AG,GG		0.0,1.3391,0.4536		92/648	102106459	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	222229	exon2			CCCCAAGCTCGAG	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.276G>A	7.37:g.102106459G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1																																																																																			G|0.995;A|0.005	0.005	strong		0.637	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
ZNF611	81856	hgsc.bcm.edu	37	19	53219140	53219140	+	Missense_Mutation	SNP	C	C	T	rs146379839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53219140C>T	ENST00000319783.1	-	5	324	c.8G>A	c.(7-9)cGt>cAt	p.R3H	ZNF611_ENST00000540744.1_Missense_Mutation_p.R3H|ZNF611_ENST00000453741.2_De_novo_Start_OutOfFrame|ZNF611_ENST00000596702.1_Missense_Mutation_p.R3H|ZNF611_ENST00000543227.1_Missense_Mutation_p.R3H|ZNF611_ENST00000602162.1_Intron|ZNF611_ENST00000595798.1_De_novo_Start_OutOfFrame|ZNF611_ENST00000600943.1_Missense_Mutation_p.R3H	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	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(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TGCTTCCTCACGTAACATGAG	0.428													-|||	5	0.000998403	0.003	0.0	5008	,	,		22412	0.001		0.0	False		,,,				2504	0.0				p.R3H		Atlas-SNP	.											.	ZNF611	72	.	0			c.G8A						PASS	.	C	HIS/ARG,HIS/ARG,,HIS/ARG	4,3018		0,4,1507	186.0	202.0	196.0		8,8,,8	-2.1	0.0	19	dbSNP_134	196	1,5417		0,1,2708	no	missense,missense,utr-5,missense	ZNF611	NM_001161499.1,NM_001161500.1,NM_001161501.1,NM_030972.3	29,29,,29	0,5,4215	TT,TC,CC		0.0185,0.1324,0.0592	benign,benign,,benign	3/706,3/706,,3/706	53219140	5,8435	1511	2709	4220	SO:0001583	missense	81856	exon5			TCCTCACGTAACA	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.8G>A	19.37:g.53219140C>T	ENSP00000322427:p.Arg3His	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	.	7.679	0.688533	0.14973	0.001324	1.85E-4	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000319783	T;T;T	0.08282	3.11;3.11;3.11	1.87	-2.06	0.07298	.	.	.	.	.	T	0.05044	0.0135	L	0.29908	0.895	0.18873	N	0.999986	B	0.02656	0.0	B	0.01281	0.0	T	0.41520	-0.9504	9	0.33141	T	0.24	.	2.9174	0.05757	0.361:0.2646:0.3743:0.0	.	3	Q8N823	ZN611_HUMAN	H	3	ENSP00000437616:R3H;ENSP00000439211:R3H;ENSP00000322427:R3H	ENSP00000322427:R3H	R	-	2	0	ZNF611	57910952	0.000000	0.05858	0.000000	0.03702	0.491000	0.33493	-0.868000	0.04236	-0.407000	0.07576	0.298000	0.19748	CGT	C|0.999;T|0.001	0.001	strong		0.428	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972	
MND1	84057	hgsc.bcm.edu	37	4	154276856	154276856	+	Silent	SNP	A	A	G	rs10471075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:154276856A>G	ENST00000504860.1	+	2	118	c.75A>G	c.(73-75)aaA>aaG	p.K25K	MND1_ENST00000503967.1_3'UTR|MND1_ENST00000240488.3_Silent_p.K40K					meiotic nuclear divisions 1 homolog (S. cerevisiae)											large_intestine(2)|lung(1)	3	all_hematologic(180;0.093)					CCAAAGAGAAAGGCATTAGTA	0.308													A|||	477	0.0952476	0.177	0.0519	5008	,	,		15463	0.0149		0.0328	False		,,,				2504	0.1626				p.K40K		Atlas-SNP	.											.	MND1	18	.	0			c.A120G						PASS	.	A		622,3782	248.4+/-256.2	48,526,1628	54.0	59.0	57.0		120	5.7	1.0	4	dbSNP_119	57	344,8248	112.3+/-172.5	6,332,3958	no	coding-synonymous	MND1	NM_032117.2		54,858,5586	GG,GA,AA		4.0037,14.1235,7.4331		40/206	154276856	966,12030	2202	4296	6498	SO:0001819	synonymous_variant	84057	exon3			AGAGAAAGGCATT	AY028916	CCDS3782.1, CCDS75202.1	4q31.3	2008-02-05			ENSG00000121211	ENSG00000121211			24839	protein-coding gene	gene with protein product		611422				11940665	Standard	NM_032117		Approved	GAJ	uc003ink.2	Q9BWT6	OTTHUMG00000161523	ENST00000504860.1:c.75A>G	4.37:g.154276856A>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_001253861		Silent	SNP	ENST00000504860.1	37																																																																																				A|0.926;G|0.074	0.074	strong		0.308	MND1-002	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365195.1	NM_032117	
ZSWIM1	90204	hgsc.bcm.edu	37	20	44511627	44511627	+	Silent	SNP	C	C	T	rs11086984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44511627C>T	ENST00000372523.1	+	2	491	c.396C>T	c.(394-396)ttC>ttT	p.F132F	ZSWIM1_ENST00000372520.1_Silent_p.F132F	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	132						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13		Myeloproliferative disorder(115;0.028)				TCCAAGTATTCAAGAAGTTTA	0.542													C|||	210	0.0419329	0.0227	0.0735	5008	,	,		21210	0.001		0.1064	False		,,,				2504	0.0215				p.F132F		Atlas-SNP	.											.	ZSWIM1	35	.	0			c.C396T						PASS	.	C		181,4225	116.7+/-154.6	5,171,2027	112.0	103.0	106.0		396	4.4	1.0	20	dbSNP_120	106	896,7704	200.3+/-244.1	49,798,3453	no	coding-synonymous	ZSWIM1	NM_080603.4		54,969,5480	TT,TC,CC		10.4186,4.108,8.2808		132/486	44511627	1077,11929	2203	4300	6503	SO:0001819	synonymous_variant	90204	exon2			AGTATTCAAGAAG	AL008726	CCDS13382.2	20q13.12	2013-09-20	2003-12-17	2003-12-19	ENSG00000168612	ENSG00000168612		"""Zinc fingers, SWIM-type"""	16155	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 162"""	C20orf162			Standard	NM_080603		Approved	dJ337O18.5	uc010ghi.3	Q9BR11	OTTHUMG00000074023	ENST00000372523.1:c.396C>T	20.37:g.44511627C>T		Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	198	109	0.550505	NM_080603	Q5JZH2|Q9BR12|Q9BV30	Silent	SNP	ENST00000372523.1	37	CCDS13382.2																																																																																			C|0.930;T|0.070	0.070	strong		0.542	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603	
MYOM1	8736	hgsc.bcm.edu	37	18	3173964	3173964	+	Silent	SNP	G	G	A	rs2230163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3173964G>A	ENST00000356443.4	-	8	1479	c.1146C>T	c.(1144-1146)caC>caT	p.H382H	MYOM1_ENST00000400569.3_Silent_p.H382H|MYOM1_ENST00000261606.7_Silent_p.H382H	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	382					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						AAGCCCCAGCGTGGAAGCGAG	0.408													A|||	1583	0.316094	0.4002	0.2262	5008	,	,		16674	0.2669		0.3062	False		,,,				2504	0.3272				p.H382H		Atlas-SNP	.											.	MYOM1	192	.	0			c.C1146T						PASS	.	A	,	1462,2268		303,856,706	82.0	78.0	79.0		1146,1146	-0.4	0.0	18	dbSNP_98	79	2593,5621		417,1759,1931	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	720,2615,2637	AA,AG,GG		31.5681,39.1957,33.9501	,	382/1686,382/1590	3173964	4055,7889	1865	4107	5972	SO:0001819	synonymous_variant	8736	exon8			CCCAGCGTGGAAG	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.1146C>T	18.37:g.3173964G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			T|0.130;G|0.427;C|0.268;A|0.175	0.175	strong		0.408	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
CHTF18	63922	hgsc.bcm.edu	37	16	842972	842972	+	Missense_Mutation	SNP	C	C	G	rs534605273		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:842972C>G	ENST00000262315.9	+	13	1642	c.1579C>G	c.(1579-1581)Ctg>Gtg	p.L527V	CHTF18_ENST00000317063.6_Intron|CHTF18_ENST00000455171.2_Missense_Mutation_p.L555V	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	527					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)				CCAGGTCTCCCTGCGGCAGGG	0.657													c|||	1	0.000199681	0.0008	0.0	5008	,	,		14564	0.0		0.0	False		,,,				2504	0.0				p.L527V		Atlas-SNP	.											.	CHTF18	52	.	0			c.C1579G						PASS	.						9.0	12.0	11.0					16																	842972		1892	4037	5929	SO:0001583	missense	63922	exon13			GTCTCCCTGCGGC	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.1579C>G	16.37:g.842972C>G	ENSP00000262315:p.Leu527Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	c	2.016	-0.425888	0.04701	.	.	ENSG00000127586	ENST00000455171;ENST00000262315	T;T	0.17370	2.28;2.28	4.9	0.103	0.14526	.	.	.	.	.	T	0.09949	0.0244	L	0.38838	1.175	0.25065	N	0.991037	B;B	0.29909	0.261;0.172	B;B	0.26202	0.067;0.03	T	0.31251	-0.9950	9	0.31617	T	0.26	.	1.2554	0.01990	0.1656:0.3096:0.3219:0.2029	.	555;527	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	V	555;527	ENSP00000406252:L555V;ENSP00000262315:L527V	ENSP00000262315:L527V	L	+	1	2	CHTF18	782973	0.000000	0.05858	0.502000	0.27614	0.443000	0.32047	-0.035000	0.12205	0.474000	0.27392	0.556000	0.70494	CTG	.	.	none		0.657	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
CPM	1368	hgsc.bcm.edu	37	12	69252715	69252715	+	Silent	SNP	A	A	G	rs1143653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:69252715A>G	ENST00000551568.1	-	8	1137	c.1077T>C	c.(1075-1077)tcT>tcC	p.S359S	CPM_ENST00000338356.3_Silent_p.S359S|CPM_ENST00000546373.1_Silent_p.S359S	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	359					anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			TTATTATATAAGACCCAGGCA	0.328													G|||	907	0.18111	0.323	0.2075	5008	,	,		12922	0.0139		0.2117	False		,,,				2504	0.1115				p.S359S		Atlas-SNP	.											.	CPM	30	.	0			c.T1077C						PASS	.	G	,,	1311,3095	692.4+/-405.5	193,925,1085	79.0	78.0	78.0		1077,1077,1077	0.9	0.7	12	dbSNP_86	78	1780,6818	729.6+/-406.7	194,1392,2713	no	coding-synonymous,coding-synonymous,coding-synonymous	CPM	NM_001005502.2,NM_001874.4,NM_198320.3	,,	387,2317,3798	GG,GA,AA		20.7025,29.7549,23.7696	,,	359/444,359/444,359/444	69252715	3091,9913	2203	4299	6502	SO:0001819	synonymous_variant	1368	exon8			TATATAAGACCCA	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"""renal carboxypeptidase"", ""urinary carboxypeptidase B"""	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.1077T>C	12.37:g.69252715A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_001005502	B2R800|Q9H2K9	Silent	SNP	ENST00000551568.1	37	CCDS8987.1	369	0.16895604395604397	135	0.27439024390243905	69	0.19060773480662985	8	0.013986013986013986	157	0.20712401055408972	G	7.668	0.686302	0.14973	0.297549	0.207025	ENSG00000135678	ENST00000551897	.	.	.	5.38	0.945	0.19543	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999906543	.	.	.	.	.	.	T	0.36212	-0.9757	3	.	.	.	-6.6564	1.4215	0.02313	0.2953:0.1051:0.3859:0.2137	rs1143653;rs17225048;rs17362456;rs60210122;rs17225048	.	.	.	P	162	.	.	L	-	2	0	CPM	67538982	0.910000	0.30920	0.683000	0.30040	0.966000	0.64601	-0.043000	0.12043	0.023000	0.15187	-0.374000	0.07098	CTT	T|0.153;G|0.175;C|0.041;A|0.631	0.175	strong		0.328	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320	
GPRC6A	222545	hgsc.bcm.edu	37	6	117114025	117114025	+	Silent	SNP	G	G	A	rs6901250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117114025G>A	ENST00000310357.3	-	6	2082	c.2061C>T	c.(2059-2061)gcC>gcT	p.A687A	GPRC6A_ENST00000368549.3_Silent_p.A616A|GPRC6A_ENST00000530250.1_Silent_p.A512A	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	687					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A687A(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		CAAAGCTGAAGGCTAGCAAAA	0.418													G|||	1607	0.320887	0.1989	0.3703	5008	,	,		21337	0.5228		0.3082	False		,,,				2504	0.2556				p.A687A		Atlas-SNP	.											GPRC6A,NS,carcinoma,0,2	GPRC6A	152	2	1	Substitution - coding silent(1)	stomach(1)	c.C2061T						scavenged	.	G		917,3489	351.8+/-311.4	94,729,1380	78.0	75.0	76.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2061	0.6	1.0	6	dbSNP_116	76	2836,5764	446.8+/-361.4	457,1922,1921	yes	coding-synonymous	GPRC6A	NM_148963.2		551,2651,3301	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	32.9767,20.8125,28.8559		687/927	117114025	3753,9253	2203	4300	6503	SO:0001819	synonymous_variant	222545	exon6			GCTGAAGGCTAGC	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2061C>T	6.37:g.117114025G>A		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			G|0.686;A|0.314	0.314	strong		0.418	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
ASAH1	427	hgsc.bcm.edu	37	8	17927327	17927327	+	Missense_Mutation	SNP	T	T	C	rs1049874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17927327T>C	ENST00000262097.6	-	4	588	c.277A>G	c.(277-279)Att>Gtt	p.I93V	ASAH1_ENST00000417108.2_Missense_Mutation_p.I28V|ASAH1_ENST00000381733.4_Missense_Mutation_p.I109V|ASAH1_ENST00000520781.1_Missense_Mutation_p.I93V|ASAH1_ENST00000314146.10_Intron|ASAH1_ENST00000520051.1_5'Flank	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	93			I -> V (in dbSNP:rs1049874). {ECO:0000269|PubMed:10993717, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8955159, ECO:0000269|Ref.2}.		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)		ACCTGCATAATTTTTCCACTT	0.279													T|||	2106	0.420527	0.2496	0.5735	5008	,	,		17684	0.372		0.4771	False		,,,				2504	0.5348				p.I109V		Atlas-SNP	.											.	ASAH1	71	.	0			c.A325G						PASS	.	T	,VAL/ILE,VAL/ILE	1253,3151	420.8+/-339.2	194,865,1143	92.0	88.0	89.0		,325,277	-10.5	0.0	8	dbSNP_86	89	4229,4369	566.5+/-388.7	1034,2161,1104	yes	intron,missense,missense	ASAH1	NM_001127505.1,NM_004315.4,NM_177924.3	,29,29	1228,3026,2247	CC,CT,TT		49.1859,28.4514,42.1627	,benign,benign	,109/412,93/396	17927327	5482,7520	2202	4299	6501	SO:0001583	missense	427	exon4			GCATAATTTTTCC	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	ENST00000262097.6:c.277A>G	8.37:g.17927327T>C	ENSP00000262097:p.Ile93Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_004315	E9PDS0|Q6W898|Q96AS2	Missense_Mutation	SNP	ENST00000262097.6	37	CCDS6006.1	927	0.42445054945054944	148	0.3008130081300813	219	0.6049723756906077	204	0.35664335664335667	356	0.46965699208443273	T	0.084	-1.179147	0.01633	0.284514	0.491859	ENSG00000104763	ENST00000262097;ENST00000381733;ENST00000520781;ENST00000417108	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.23	-10.5	0.00291	.	0.816289	0.11418	N	0.566080	T	0.00012	0.0000	N	0.16307	0.4	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.26155	-1.0111	9	0.12766	T	0.61	-4.3637	4.1802	0.10370	0.0758:0.3291:0.3039:0.2912	rs1049874;rs1049881;rs1804721;rs3174002;rs17416580;rs17856504;rs52833760;rs59209829;rs1049874	109;93;93	Q13510-2;E7EMM4;Q13510	.;.;ASAH1_HUMAN	V	93;109;93;28	ENSP00000262097:I93V;ENSP00000371152:I109V;ENSP00000427751:I93V;ENSP00000394125:I28V	ENSP00000262097:I93V	I	-	1	0	ASAH1	17971607	0.001000	0.12720	0.002000	0.10522	0.310000	0.27922	-1.936000	0.01549	-3.229000	0.00210	-0.804000	0.03201	ATT	T|0.579;C|0.421	0.421	strong		0.279	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	
ZC3H18	124245	hgsc.bcm.edu	37	16	88643806	88643806	+	Missense_Mutation	SNP	C	C	G	rs114866066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88643806C>G	ENST00000301011.5	+	2	475	c.275C>G	c.(274-276)cCg>cGg	p.P92R	ZC3H18_ENST00000452588.2_Missense_Mutation_p.P92R	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	92						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		AGCCGGGGCCCGACCAGCTCC	0.622													C|||	5	0.000998403	0.0038	0.0	5008	,	,		18131	0.0		0.0	False		,,,				2504	0.0				p.P92R	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.C275G						PASS	.	C	ARG/PRO	22,4372	27.2+/-55.0	0,22,2175	29.0	33.0	32.0		275	3.4	0.8	16	dbSNP_132	32	0,8600		0,0,4300	yes	missense	ZC3H18	NM_144604.3	103	0,22,6475	GG,GC,CC		0.0,0.5007,0.1693	benign	92/954	88643806	22,12972	2197	4300	6497	SO:0001583	missense	124245	exon2			GGGGCCCGACCAG	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.275C>G	16.37:g.88643806C>G	ENSP00000301011:p.Pro92Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	37	CCDS10967.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	6.042	0.376025	0.11466	0.005007	0.0	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588	T;T	0.30448	1.53;1.56	5.57	3.36	0.38483	.	0.366727	0.28908	N	0.013743	T	0.13243	0.0321	L	0.36672	1.1	0.09310	N	1	B;B	0.27416	0.178;0.178	B;B	0.28916	0.096;0.096	T	0.11179	-1.0598	10	0.18276	T	0.48	-21.7543	2.9583	0.05884	0.5017:0.3387:0.0:0.1595	.	92;92	E7ERS3;Q86VM9	.;ZCH18_HUMAN	R	92	ENSP00000301011:P92R;ENSP00000416951:P92R	ENSP00000289509:P92R	P	+	2	0	ZC3H18	87171307	0.247000	0.23920	0.778000	0.31720	0.046000	0.14306	0.728000	0.26013	1.310000	0.45006	0.561000	0.74099	CCG	C|0.999;G|0.001	0.001	strong		0.622	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604	
MKI67	4288	hgsc.bcm.edu	37	10	129904474	129904474	+	Missense_Mutation	SNP	G	G	A	rs61738284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129904474G>A	ENST00000368654.3	-	13	6005	c.5630C>T	c.(5629-5631)cCc>cTc	p.P1877L	MKI67_ENST00000368653.3_Missense_Mutation_p.P1517L	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1877	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GCTTCTCTTGGGCCGTTGCTT	0.468													G|||	515	0.102835	0.0666	0.1556	5008	,	,		20450	0.1359		0.0785	False		,,,				2504	0.1053				p.P1877L		Atlas-SNP	.											.	MKI67	363	.	0			c.C5630T						PASS	.	G	LEU/PRO,LEU/PRO	295,4111	161.8+/-193.9	11,273,1919	257.0	262.0	260.0		4550,5630	-4.0	0.0	10	dbSNP_129	260	771,7829	183.7+/-231.9	39,693,3568	no	missense,missense	MKI67	NM_001145966.1,NM_002417.4	98,98	50,966,5487	AA,AG,GG		8.9651,6.6954,8.1962	probably-damaging,probably-damaging	1517/2897,1877/3257	129904474	1066,11940	2203	4300	6503	SO:0001583	missense	4288	exon13			CTCTTGGGCCGTT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.5630C>T	10.37:g.129904474G>A	ENSP00000357643:p.Pro1877Leu	Somatic	432	1	0.00231481		WXS	Illumina HiSeq	Phase_I	448	226	0.504464	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	209	0.09569597069597069	33	0.06707317073170732	39	0.10773480662983426	79	0.1381118881118881	58	0.07651715039577836	G	7.574	0.667296	0.14710	0.066954	0.089651	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02158	4.42;4.42	3.01	-4.0	0.04057	.	2.514200	0.02262	N	0.067604	T	0.00012	0.0000	N	0.17800	0.525	0.80722	P	0.0	B;B;B	0.29232	0.008;0.118;0.238	B;B;B	0.33890	0.014;0.172;0.085	T	0.43114	-0.9411	9	0.25106	T	0.35	.	4.3421	0.11115	0.3141:0.3137:0.3722:0.0	rs61738284	1876;1517;1877	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	L	1877;1517;1876	ENSP00000357643:P1877L;ENSP00000357642:P1517L	ENSP00000357642:P1517L	P	-	2	0	MKI67	129794464	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.347000	0.07750	-1.098000	0.03038	-0.291000	0.09656	CCC	G|0.915;A|0.085	0.085	strong		0.468	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
ZNF518B	85460	hgsc.bcm.edu	37	4	10447640	10447640	+	Missense_Mutation	SNP	A	A	G	rs10016702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	97	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	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	
KLHL24	54800	hgsc.bcm.edu	37	3	183368216	183368216	+	Silent	SNP	A	A	T	rs3755648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183368216A>T	ENST00000454652.2	+	4	458	c.72A>T	c.(70-72)cgA>cgT	p.R24R	KLHL24_ENST00000242810.6_Silent_p.R24R|KLHL24_ENST00000476808.1_Silent_p.R24R	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24	24						cell projection (GO:0042995)|cytoplasm (GO:0005737)		p.R24R(1)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			CAACTAAGCGAAAAGTTTTTG	0.403													T|||	1755	0.350439	0.5144	0.2795	5008	,	,		17517	0.4355		0.2654	False		,,,				2504	0.1789				p.R24R		Atlas-SNP	.											KLHL24,caecum,carcinoma,+1,2	KLHL24	56	2	1	Substitution - coding silent(1)	stomach(1)	c.A72T						PASS	.	T		2126,2280	578.7+/-384.7	527,1072,604	63.0	67.0	66.0		72	-3.2	1.0	3	dbSNP_107	66	2370,6230	697.6+/-405.0	339,1692,2269	no	coding-synonymous	KLHL24	NM_017644.3		866,2764,2873	TT,TA,AA		27.5581,48.2524,34.5687		24/601	183368216	4496,8510	2203	4300	6503	SO:0001819	synonymous_variant	54800	exon3			TAAGCGAAAAGTT		CCDS3246.1	3q27.1	2013-02-22	2013-02-22		ENSG00000114796	ENSG00000114796		"""Kelch-like"", ""BTB/POZ domain containing"""	25947	protein-coding gene	gene with protein product		611295	"""kelch-like 24 (Drosophila)"""				Standard	XM_005247552		Approved	DRE1, FLJ20059	uc003flv.3	Q6TFL4	OTTHUMG00000156911	ENST00000454652.2:c.72A>T	3.37:g.183368216A>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	150	62	0.413333	NM_017644	A5PLN8|Q9H620|Q9NXT9	Silent	SNP	ENST00000454652.2	37	CCDS3246.1																																																																																			A|0.647;T|0.353	0.353	strong		0.403	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	NM_017644	
ETV7	51513	hgsc.bcm.edu	37	6	36339176	36339176	+	Missense_Mutation	SNP	C	C	T	rs34306145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36339176C>T	ENST00000340181.4	-	5	836	c.595G>A	c.(595-597)Ggc>Agc	p.G199S	ETV7_ENST00000538992.1_Missense_Mutation_p.G48S|ETV7_ENST00000373737.4_Intron|ETV7_ENST00000373738.1_Missense_Mutation_p.G144S|ETV7_ENST00000339796.5_Missense_Mutation_p.G199S	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	199			G -> S (in dbSNP:rs34306145).		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						GTCCTGCAGCCGAGCTCTGCA	0.637													C|||	60	0.0119808	0.0446	0.0	5008	,	,		18231	0.0		0.0	False		,,,				2504	0.001				p.G199S		Atlas-SNP	.											.	ETV7	31	.	0			c.G595A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY,,SER/GLY,SER/GLY,SER/GLY,SER/GLY	155,4251	98.5+/-137.1	4,147,2052	48.0	42.0	44.0		595,430,418,,430,352,142,595	-4.3	0.0	6	dbSNP_126	44	0,8600		0,0,4300	yes	missense,missense,missense,intron,missense,missense,missense,missense	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	56,56,56,,56,56,56,56	4,147,6352	TT,TC,CC		0.0,3.5179,1.1918	benign,benign,benign,,benign,benign,benign,benign	199/318,144/287,140/283,,144/263,118/261,48/191,199/342	36339176	155,12851	2203	4300	6503	SO:0001583	missense	51513	exon5			TGCAGCCGAGCTC	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.595G>A	6.37:g.36339176C>T	ENSP00000341843:p.Gly199Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Missense_Mutation	SNP	ENST00000340181.4	37	CCDS4819.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	6.332	0.429441	0.11987	0.035179	0.0	ENSG00000010030	ENST00000339796;ENST00000340181;ENST00000373738;ENST00000538992	T;T;T;T	0.13307	2.6;2.6;2.6;2.6	3.49	-4.27	0.03744	.	1.429630	0.04667	N	0.409962	T	0.03739	0.0106	N	0.17082	0.46	0.09310	N	1	B;D;B;P;B	0.69078	0.101;0.997;0.012;0.708;0.229	B;P;B;B;B	0.52481	0.056;0.7;0.017;0.087;0.014	T	0.25152	-1.0140	10	0.09084	T	0.74	.	11.3935	0.49827	0.0:0.3082:0.0:0.6918	rs34306145	140;144;199;144;199	Q9Y603-2;Q9Y603-4;Q9Y603;Q9Y603-6;Q9Y603-5	.;.;ETV7_HUMAN;.;.	S	199;199;144;48	ENSP00000342260:G199S;ENSP00000341843:G199S;ENSP00000362843:G144S;ENSP00000440592:G48S	ENSP00000342260:G199S	G	-	1	0	ETV7	36447154	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.280000	0.08468	-1.429000	0.01987	-2.010000	0.00438	GGC	C|0.987;T|0.013	0.013	strong		0.637	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135	
GJD2	57369	hgsc.bcm.edu	37	15	35044940	35044940	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:35044940G>A	ENST00000290374.4	-	2	1181	c.705C>T	c.(703-705)ccC>ccT	p.P235P	RP11-814P5.1_ENST00000558707.1_RNA|RP11-814P5.1_ENST00000503496.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	235					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)	p.P235P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		CCTTGATGCAGGGGTAGCGGT	0.478																																					p.P235P		Atlas-SNP	.											GJD2,NS,carcinoma,0,1	GJD2	49	1	1	Substitution - coding silent(1)	lung(1)	c.C705T						scavenged	.						113.0	89.0	97.0					15																	35044940		2201	4298	6499	SO:0001819	synonymous_variant	57369	exon2			GATGCAGGGGTAG	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.705C>T	15.37:g.35044940G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	194	3	0.0154639	NM_020660	Q2M241|Q9P2R0	Silent	SNP	ENST00000290374.4	37	CCDS10040.1																																																																																			.	.	none		0.478	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2		
ZNF658	26149	hgsc.bcm.edu	37	9	40774091	40774091	+	Missense_Mutation	SNP	C	C	T	rs79262629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:40774091C>T	ENST00000602553.1	-	5	1478	c.1184G>A	c.(1183-1185)cGg>cAg	p.R395Q	ZNF658_ENST00000377626.3_Missense_Mutation_p.R395Q|ZNF658_ENST00000441795.1_Missense_Mutation_p.R393Q			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GTGTGCTTTCCGGTAAAAGGA	0.393													C|||	70	0.0139776	0.0522	0.0	5008	,	,		20923	0.001		0.0	False		,,,				2504	0.0				p.R395Q		Atlas-SNP	.											ZNF658,lower_third,carcinoma,-1,1	ZNF658	100	1	0			c.G1184A						scavenged	.	C	GLN/ARG	152,4254	103.4+/-141.9	2,148,2053	218.0	217.0	218.0		1184	-0.9	0.0	9	dbSNP_131	218	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZNF658	NM_033160.5	43	2,150,6351	TT,TC,CC		0.0233,3.4498,1.1841	benign	395/1060	40774091	154,12852	2203	4300	6503	SO:0001583	missense	26149	exon5			GCTTTCCGGTAAA	AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"""Zinc fingers, C2H2-type"", ""-"""	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.1184G>A	9.37:g.40774091C>T	ENSP00000473484:p.Arg395Gln	Somatic	532	2	0.0037594		WXS	Illumina HiSeq	Phase_I	543	183	0.337017	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Missense_Mutation	SNP	ENST00000602553.1	37	CCDS35023.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	c	0.018	-1.473237	0.01044	0.034498	2.33E-4	ENSG00000196409	ENST00000441795;ENST00000377626	T;T	0.14893	2.47;2.47	1.8	-0.939	0.10408	Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00936	0.0031	N	0.01473	-0.845	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41805	-0.9488	9	0.07990	T	0.79	.	5.7522	0.18152	0.0:0.5247:0.0:0.4753	.	395;395	Q5TYW1-2;Q5TYW1	.;ZN658_HUMAN	Q	393;395	ENSP00000408462:R393Q;ENSP00000366853:R395Q	ENSP00000366853:R395Q	R	-	2	0	ZNF658	40764091	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	-0.970000	0.03810	-0.174000	0.10743	-0.820000	0.03113	CGG	C|0.990;T|0.010	0.010	strong		0.393	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160	
ITIH5	80760	hgsc.bcm.edu	37	10	7605067	7605067	+	Missense_Mutation	SNP	C	C	T	rs3824658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:7605067C>T	ENST00000446830.2	-	15	2909	c.2150G>A	c.(2149-2151)cGg>cAg	p.R717Q	ITIH5_ENST00000298441.6_Silent_p.P722P|ITIH5_ENST00000256861.6_Silent_p.P936P|ITIH5_ENST00000397146.2_Intron			Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	936					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						GGACATTCCCCGGCCAAGTGT	0.542													C|||	2863	0.571685	0.407	0.6225	5008	,	,		19488	0.5179		0.7694	False		,,,				2504	0.6104				p.R936Q		Atlas-SNP	.											.	ITIH5	343	.	0			c.G2807A						PASS	.	C	GLN/ARG,GLN/ARG	2047,2359	564.0+/-381.3	455,1137,611	185.0	178.0	180.0		2808,2166	-6.9	0.0	10	dbSNP_107	180	6597,2003	721.9+/-406.4	2523,1551,226	no	missense,missense	ITIH5	NM_030569.6,NM_032817.5	43,43	2978,2688,837	TT,TC,CC		23.2907,46.4594,33.5384	,	936/943,722/729	7605067	8644,4362	2203	4300	6503	SO:0001583	missense	80760	exon15			ATTCCCCGGCCAA			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000446830.2:c.2150G>A	10.37:g.7605067C>T	ENSP00000387969:p.Arg717Gln	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	192	98	0.510417	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000446830.2	37		1294	0.5924908424908425	205	0.4166666666666667	244	0.6740331491712708	259	0.4527972027972028	586	0.7730870712401056	C	10.17	1.276540	0.23307	0.464594	0.767093	ENSG00000123243	ENST00000446830	T	0.01787	4.64	4.72	-6.94	0.01633	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.14924	-1.0455	5	0.20046	T	0.44	-0.6082	2.0444	0.03557	0.1645:0.3936:0.2346:0.2073	rs3824658;rs59732486;rs3824658	.	.	.	Q	717	ENSP00000387969:R717Q	ENSP00000387969:R717Q	R	-	2	0	ITIH5	7645073	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.061000	0.03472	-1.075000	0.03129	-1.036000	0.02392	CGG	C|0.373;T|0.627	0.627	strong		0.542	ITIH5-203	KNOWN	basic	protein_coding	protein_coding		NM_030569	
MTA1	9112	hgsc.bcm.edu	37	14	105931109	105931109	+	Silent	SNP	C	C	T	rs36015555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105931109C>T	ENST00000331320.7	+	15	1657	c.1443C>T	c.(1441-1443)atC>atT	p.I481I	MTA1_ENST00000406191.1_Silent_p.I481I|MTA1_ENST00000435036.2_Silent_p.I17I|MTA1_ENST00000405646.1_Silent_p.I464I	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	481					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)			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)		TGACGCGGATCGCCCGGCGCC	0.672													C|||	257	0.0513179	0.1884	0.0115	5008	,	,		16374	0.0		0.0	False		,,,				2504	0.0				p.I481I		Atlas-SNP	.											.	MTA1	61	.	0			c.C1443T						PASS	.	C	,	712,3684		67,578,1553	32.0	28.0	29.0		,1443	-1.1	0.9	14	dbSNP_126	29	7,8587		0,7,4290	no	utr-3,coding-synonymous	MTA1	NM_001203258.1,NM_004689.3	,	67,585,5843	TT,TC,CC		0.0815,16.1965,5.535	,	,481/716	105931109	719,12271	2198	4297	6495	SO:0001819	synonymous_variant	9112	exon15			GCGGATCGCCCGG	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.1443C>T	14.37:g.105931109C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	60	39	0.65	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Silent	SNP	ENST00000331320.7	37	CCDS32169.1																																																																																			C|0.947;T|0.053	0.053	strong		0.672	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15		
SRMS	6725	hgsc.bcm.edu	37	20	62172281	62172281	+	Missense_Mutation	SNP	C	C	T	rs310655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	55	0	0		WXS	Illumina HiSeq	Phase_I	89	86	0.966292	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	
POLH	5429	hgsc.bcm.edu	37	6	43582091	43582091	+	Missense_Mutation	SNP	A	A	T	rs6941583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43582091A>T	ENST00000372236.4	+	11	2234	c.1939A>T	c.(1939-1941)Atg>Ttg	p.M647L	POLH_ENST00000535400.1_Missense_Mutation_p.M585L|POLH_ENST00000372226.1_3'UTR	NM_006502.2	NP_006493.1	O75417	DPOLQ_HUMAN	polymerase (DNA directed), eta	0					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)			breast(4)|endometrium(5)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			GGTATGGGATATGCCAGAACA	0.502								DNA polymerases (catalytic subunits)	Xeroderma Pigmentosum				A|||	645	0.128794	0.3487	0.0476	5008	,	,		18344	0.0308		0.0358	False		,,,				2504	0.0859				p.M647L		Atlas-SNP	.											.	POLH	54	.	0			c.A1939T						PASS	.	A	LEU/MET	1343,3063	447.5+/-348.4	213,917,1073	151.0	156.0	155.0		1939	5.7	1.0	6	dbSNP_116	155	265,8335	101.9+/-163.1	3,259,4038	yes	missense	POLH	NM_006502.2	15	216,1176,5111	TT,TA,AA		3.0814,30.4812,12.3635	benign	647/714	43582091	1608,11398	2203	4300	6503	SO:0001583	missense	5429	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TGGGATATGCCAG	AB024313	CCDS4902.1	6p21	2014-09-17			ENSG00000170734	ENSG00000170734			9181	protein-coding gene	gene with protein product		603968				10385124, 10398605	Standard	NM_006502		Approved	RAD30A, XP-V	uc003ovq.4	Q9Y253	OTTHUMG00000014743	ENST00000372236.4:c.1939A>T	6.37:g.43582091A>T	ENSP00000361310:p.Met647Leu	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	187	77	0.411765	NM_006502	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000372236.4	37	CCDS4902.1	246	0.11263736263736264	182	0.3699186991869919	14	0.03867403314917127	26	0.045454545454545456	24	0.0316622691292876	A	9.080	0.999151	0.19121	0.304812	0.030814	ENSG00000170734	ENST00000372236;ENST00000535400	T;T	0.58940	0.42;0.3	5.73	5.73	0.89815	.	0.126867	0.64402	D	0.000001	T	0.25082	0.0609	L	0.52011	1.625	0.09310	P	0.9999999999999809	B;B	0.22346	0.068;0.03	B;B	0.18561	0.022;0.006	T	0.10359	-1.0633	9	0.07990	T	0.79	-30.6674	6.7209	0.23330	0.6592:0.135:0.0:0.2058	rs6941583;rs6941583	585;647	B4DG64;Q9Y253	.;POLH_HUMAN	L	647;585	ENSP00000361310:M647L;ENSP00000442102:M585L	ENSP00000361310:M647L	M	+	1	0	POLH	43690069	0.997000	0.39634	0.996000	0.52242	0.949000	0.60115	2.921000	0.48852	2.302000	0.77476	0.533000	0.62120	ATG	A|0.875;T|0.125	0.125	strong		0.502	POLH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040666.1	NM_006502	
TRIP11	9321	hgsc.bcm.edu	37	14	92474136	92474136	+	Missense_Mutation	SNP	C	C	T	rs372171033		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:92474136C>T	ENST00000267622.4	-	10	1748	c.1375G>A	c.(1375-1377)Gct>Act	p.A459T		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	459					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TCTCTTGTAGCTGTACTTTTA	0.303			T	PDGFRB	AML								c|||	1	0.000199681	0.0008	0.0	5008	,	,		19781	0.0		0.0	False		,,,				2504	0.0				p.A459T	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.G1375A						PASS	.	C	THR/ALA	5,4399	9.9+/-24.2	0,5,2197	105.0	97.0	100.0		1375	-3.3	0.0	14		100	0,8598		0,0,4299	no	missense	TRIP11	NM_004239.3	58	0,5,6496	TT,TC,CC		0.0,0.1135,0.0385	benign	459/1980	92474136	5,12997	2202	4299	6501	SO:0001583	missense	9321	exon10			TTGTAGCTGTACT	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.1375G>A	14.37:g.92474136C>T	ENSP00000267622:p.Ala459Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.257|4.257	0.046773|0.046773	0.08243|0.08243	0.001135|0.001135	0.0|0.0	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.64438|.	-0.1|.	5.85|5.85	-3.26|-3.26	0.05064|0.05064	.|.	1.114810|.	0.06492|.	N|.	0.734730|.	T|T	0.19846|0.19846	0.0477|0.0477	N|N	0.16656|0.16656	0.425|0.425	0.09310|0.09310	N|N	1|1	B;B|.	0.13594|.	0.003;0.008|.	B;B|.	0.13407|.	0.004;0.009|.	T|T	0.33007|0.33007	-0.9885|-0.9885	10|5	0.14252|.	T|.	0.57|.	.|.	7.9021|7.9021	0.29740|0.29740	0.1338:0.334:0.0:0.5322|0.1338:0.334:0.0:0.5322	.|.	195;459|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	T|N	459;195|174	ENSP00000267622:A459T|.	ENSP00000267622:A459T|.	A|S	-|-	1|2	0|0	TRIP11|TRIP11	91543889|91543889	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.220000|0.220000	0.24768|0.24768	-0.819000|-0.819000	0.04462|0.04462	-0.445000|-0.445000	0.07159|0.07159	0.561000|0.561000	0.74099|0.74099	GCT|AGC	.	.	weak		0.303	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
GCN1L1	10985	hgsc.bcm.edu	37	12	120591143	120591143	+	Silent	SNP	A	A	G	rs12312562	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:120591143A>G	ENST00000300648.6	-	33	3948	c.3936T>C	c.(3934-3936)taT>taC	p.Y1312Y	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1312					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)					GCACAGCATCATAGCTGGCAT	0.557													G|||	1712	0.341853	0.5053	0.1441	5008	,	,		21235	0.5546		0.1551	False		,,,				2504	0.2342				p.Y1312Y		Atlas-SNP	.											GCN1L1,colon,carcinoma,0,1	GCN1L1	207	1	0			c.T3936C						PASS	.	G		1762,2454		393,976,739	71.0	78.0	76.0		3936	-12.2	0.0	12	dbSNP_120	76	1258,7180		118,1022,3079	no	coding-synonymous	GCN1L1	NM_006836.1		511,1998,3818	GG,GA,AA		14.9087,41.7932,23.866		1312/2672	120591143	3020,9634	2108	4219	6327	SO:0001819	synonymous_variant	10985	exon33			AGCATCATAGCTG	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.3936T>C	12.37:g.120591143A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																			A|0.657;G|0.343	0.343	strong		0.557	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
FLG	2312	hgsc.bcm.edu	37	1	152284457	152284457	+	Missense_Mutation	SNP	T	T	A	rs376429887|rs3120652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284457T>A	ENST00000368799.1	-	3	2940	c.2905A>T	c.(2905-2907)Aac>Tac	p.N969Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	969	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)			CCACGATGGTTTCTGGAAGCA	0.582									Ichthyosis				T|||	297	0.0593051	0.2141	0.0187	5008	,	,		21442	0.0		0.001	False		,,,				2504	0.0				p.N969Y		Atlas-SNP	.											.	FLG	900	.	0			c.A2905T						PASS	.	T	TYR/ASN	721,3685	260.4+/-263.7	46,629,1528	236.0	238.0	237.0		2905	-6.0	0.0	1	dbSNP_103	237	9,8591	7.1+/-27.0	0,9,4291	no	missense	FLG	NM_002016.1	143	46,638,5819	AA,AT,TT		0.1047,16.364,5.6128	possibly-damaging	969/4062	152284457	730,12276	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GATGGTTTCTGGA	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.2905A>T	1.37:g.152284457T>A	ENSP00000357789:p.Asn969Tyr	Somatic	446	0	0		WXS	Illumina HiSeq	Phase_I	538	214	0.39777	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	83	0.038003663003663	78	0.15853658536585366	5	0.013812154696132596	0	0.0	0	0.0	t	2.680	-0.275489	0.05679	0.16364	0.001047	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.01647	4.71	3.01	-6.01	0.02199	.	.	.	.	.	T	0.00724	0.0024	M	0.68317	2.08	0.80722	P	0.0	P	0.39831	0.69	B	0.34093	0.175	T	0.03433	-1.1037	8	0.59425	D	0.04	.	8.703	0.34338	0.0:0.0998:0.6558:0.2444	.	969	P20930	FILA_HUMAN	Y	969;176	ENSP00000357789:N969Y	ENSP00000357789:N969Y	N	-	1	0	FLG	150551081	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.749000	0.01824	-1.940000	0.01043	-0.641000	0.03968	AAC	T|0.942;A|0.058	0.058	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SPG7	6687	hgsc.bcm.edu	37	16	89623301	89623301	+	Missense_Mutation	SNP	A	A	G	rs35749032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89623301A>G	ENST00000268704.2	+	17	2203	c.2188A>G	c.(2188-2190)Aac>Gac	p.N730D	SPG7_ENST00000565891.1_3'UTR	NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	730			N -> D (in dbSNP:rs35749032). {ECO:0000269|PubMed:16534102}.		anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		CTAGCTGGCAAACGCCCTTCT	0.562													A|||	85	0.0169728	0.062	0.0043	5008	,	,		19441	0.0		0.0	False		,,,				2504	0.0				p.N730D		Atlas-SNP	.											.	SPG7	75	.	0			c.A2188G						PASS	.	A	ASP/ASN	203,4193	123.3+/-160.7	7,189,2002	111.0	110.0	110.0		2188	4.5	0.0	16	dbSNP_126	110	1,8595		0,1,4297	yes	missense	SPG7	NM_003119.2	23	7,190,6299	GG,GA,AA		0.0116,4.6178,1.5702	benign	730/796	89623301	204,12788	2198	4298	6496	SO:0001583	missense	6687	exon17			CTGGCAAACGCCC	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"""ATPases / AAA-type"""	11237	protein-coding gene	gene with protein product	"""paraplegin"""	602783	"""cell matrix adhesion regulator"""	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.2188A>G	16.37:g.89623301A>G	ENSP00000268704:p.Asn730Asp	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_003119	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	37	CCDS10977.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	A	7.955	0.745801	0.15710	0.046178	1.16E-4	ENSG00000197912	ENST00000268704	D	0.84370	-1.84	5.59	4.49	0.54785	Peptidase M41 (1);Peptidase M41, FtsH (2);	0.304067	0.39687	N	0.001298	T	0.25121	0.0610	N	0.12746	0.255	0.36713	D	0.880754	B	0.06786	0.001	B	0.09377	0.004	T	0.55250	-0.8170	10	0.36615	T	0.2	-6.0E-4	10.7824	0.46386	0.9228:0.0:0.0772:0.0	rs35749032	730	Q9UQ90	SPG7_HUMAN	D	730	ENSP00000268704:N730D	ENSP00000268704:N730D	N	+	1	0	SPG7	88150802	0.057000	0.20700	0.002000	0.10522	0.321000	0.28281	1.649000	0.37281	0.925000	0.37094	0.460000	0.39030	AAC	A|0.982;G|0.018	0.018	strong		0.562	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119	
KLHL23	151230	hgsc.bcm.edu	37	2	170592709	170592709	+	Silent	SNP	A	A	G	rs2288331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170592709A>G	ENST00000392647.2	+	2	1429	c.1185A>G	c.(1183-1185)aaA>aaG	p.K395K	KLHL23_ENST00000602521.1_Intron|KLHL23_ENST00000272797.4_Silent_p.K395K	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	395										breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						TAAAAGAGAAATGGATTCCTA	0.413													A|||	783	0.15635	0.1831	0.1369	5008	,	,		20251	0.1766		0.1581	False		,,,				2504	0.1115				p.K395K		Atlas-SNP	.											.	KLHL23	52	.	0			c.A1185G						PASS	.	A	,	677,3729	284.3+/-277.5	58,561,1584	95.0	102.0	100.0		1185,1185	-2.5	1.0	2	dbSNP_100	100	1393,7207	267.5+/-287.3	126,1141,3033	no	coding-synonymous,coding-synonymous	KLHL23,PHOSPHO2-KLHL23	NM_001199290.1,NM_144711.5	,	184,1702,4617	GG,GA,AA		16.1977,15.3654,15.9157	,	395/559,395/559	170592709	2070,10936	2203	4300	6503	SO:0001819	synonymous_variant	151230	exon2			AGAGAAATGGATT	BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160		"""Kelch-like"", ""BTB/POZ domain containing"""	27506	protein-coding gene	gene with protein product			"""kelch-like 23 (Drosophila)"""				Standard	NM_144711		Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000392647.2:c.1185A>G	2.37:g.170592709A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_144711	Q8N9B9|Q96FT8	Silent	SNP	ENST00000392647.2	37	CCDS2236.1																																																																																			A|0.835;G|0.165	0.165	strong		0.413	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711	
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39190830	39190830	+	Missense_Mutation	SNP	C	C	T	rs62622849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39190830C>T	ENST00000344363.5	-	1	277	c.244G>A	c.(244-246)Gga>Aga	p.G82R		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	92			Missing (in allele KAP1.9). {ECO:0000269|PubMed:12228244}.			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCCAGTTCCGCAGGAGCTG	0.622													c|||	535	0.106829	0.1891	0.1167	5008	,	,		19249	0.1627		0.0159	False		,,,				2504	0.0245				p.G82R		Atlas-SNP	.											.	KRTAP1-3	18	.	0			c.G244A						PASS	.	C	ARG/GLY	578,3410		38,502,1454	29.0	33.0	32.0		244	1.9	0.0	17	dbSNP_129	32	120,8216		6,108,4054	no	missense	KRTAP1-3	NM_030966.1	125	44,610,5508	TT,TC,CC		1.4395,14.4935,5.6637	benign	82/168	39190830	698,11626	1994	4168	6162	SO:0001583	missense	81850	exon1			CAGTTCCGCAGGA	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"""Keratin associated proteins"""	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.244G>A	17.37:g.39190830C>T	ENSP00000344420:p.Gly82Arg	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_030966	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	245	0.11217948717948718	103	0.20934959349593496	31	0.0856353591160221	99	0.17307692307692307	12	0.0158311345646438	C	0.345	-0.948215	0.02304	0.144935	0.014395	ENSG00000221880	ENST00000344363	T	0.29397	1.57	3.98	1.86	0.25419	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.18863	0.031	B	0.12156	0.007	T	0.38286	-0.9668	7	0.13853	T	0.58	.	5.4908	0.16774	0.0:0.601:0.2804:0.1186	rs62622849	92	Q8IUG1	KRA13_HUMAN	R	82	ENSP00000344420:G82R	ENSP00000344420:G82R	G	-	1	0	KRTAP1-3	36444356	0.985000	0.35326	0.002000	0.10522	0.017000	0.09413	-0.586000	0.05787	0.389000	0.25086	-0.126000	0.14955	GGA	C|0.888;T|0.112	0.112	strong		0.622	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1		
RPAP1	26015	hgsc.bcm.edu	37	15	41815063	41815063	+	Missense_Mutation	SNP	C	C	T	rs61748721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41815063C>T	ENST00000304330.4	-	19	2758	c.2642G>A	c.(2641-2643)cGt>cAt	p.R881H	RPAP1_ENST00000561603.1_Missense_Mutation_p.R881H	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	881	Leu-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CAGACTGAGACGGGGGCAGCC	0.632													C|||	177	0.0353435	0.1324	0.0029	5008	,	,		16841	0.0		0.0	False		,,,				2504	0.0				p.R881H		Atlas-SNP	.											.	RPAP1	111	.	0			c.G2642A						PASS	.	C	HIS/ARG	531,3875	241.5+/-251.9	29,473,1701	56.0	50.0	52.0		2642	-1.3	0.0	15	dbSNP_129	52	3,8597	2.2+/-6.3	0,3,4297	yes	missense	RPAP1	NM_015540.2	29	29,476,5998	TT,TC,CC		0.0349,12.0517,4.1058	benign	881/1394	41815063	534,12472	2203	4300	6503	SO:0001583	missense	26015	exon19			CTGAGACGGGGGC	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.2642G>A	15.37:g.41815063C>T	ENSP00000306123:p.Arg881His	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	60	0.027472527472527472	59	0.11991869918699187	1	0.0027624309392265192	0	0.0	0	0.0	C	10.52	1.373816	0.24857	0.120517	3.49E-4	ENSG00000103932	ENST00000304330	T	0.11930	2.73	5.27	-1.3	0.09259	.	0.689147	0.15432	N	0.262677	T	0.00109	0.0003	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36986	-0.9725	10	0.41790	T	0.15	-23.5071	5.7717	0.18257	0.0626:0.3333:0.3812:0.2229	.	881	Q9BWH6	RPAP1_HUMAN	H	881	ENSP00000306123:R881H	ENSP00000306123:R881H	R	-	2	0	RPAP1	39602355	0.005000	0.15991	0.000000	0.03702	0.660000	0.38997	0.344000	0.19962	-0.381000	0.07882	-1.067000	0.02272	CGT	C|0.958;T|0.042	0.042	strong		0.632	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
PKD1L2	114780	hgsc.bcm.edu	37	16	81208473	81208473	+	RNA	SNP	G	G	T	rs115666278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81208473G>T	ENST00000527937.1	-	0	511				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000531391.1_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						CTCTGACACGGCAGCCTGGAA	0.557													G|||	302	0.0603035	0.2186	0.0187	5008	,	,		19807	0.0		0.0	False		,,,				2504	0.0				p.A877D		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2630A						PASS	.	G	ASP/ALA,ASP/ALA	829,3309		91,647,1331	66.0	64.0	65.0		2630,2630	-1.8	0.0	16	dbSNP_132	65	8,8426		0,8,4209	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	126,126	91,655,5540	TT,TG,GG		0.0949,20.0338,6.6577	possibly-damaging,possibly-damaging	877/992,877/2460	81208473	837,11735	2069	4217	6286			114780	exon16			GACACGGCAGCCT	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.81208473G>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		126|126	0.057692307692307696|0.057692307692307696	121|121	0.2459349593495935|0.2459349593495935	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.39|13.39	2.221594|2.221594	0.39300|0.39300	0.200338|0.200338	9.49E-4|9.49E-4	ENSG00000166473|ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937|ENST00000526632	T;T;T|.	0.57107|.	0.42;0.42;0.42|.	4.55|4.55	-1.81|-1.81	0.07882|0.07882	Egg jelly receptor, REJ-like (1);|.	1.422600|.	0.04339|.	N|.	0.353783|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	P;P;B|.	0.37636|.	0.513;0.603;0.009|.	B;B;B|.	0.40009|.	0.299;0.316;0.009|.	T|.	0.29458|.	-1.0011|.	8|.	0.66056|.	D|.	0.02|.	-0.6932|-0.6932	8.1615|8.1615	0.31201|0.31201	0.6442:0.0:0.3558:0.0|0.6442:0.0:0.3558:0.0	.|.	133;877;877|.	Q7Z442-6;Q7Z442-3;Q7Z442|.	.;.;PK1L2_HUMAN|.	D|X	192;877;133|404	ENSP00000436309:A192D;ENSP00000337397:A877D;ENSP00000432818:A133D|.	ENSP00000337397:A877D|.	A|C	-|-	2|3	0|2	PKD1L2|PKD1L2	79765974|79765974	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.081000|0.081000	0.17604|0.17604	0.031000|0.031000	0.13710|0.13710	-0.115000|-0.115000	0.11915|0.11915	0.555000|0.555000	0.69702|0.69702	GCC|TGC	G|0.963;T|0.037	0.037	strong		0.557	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
NLRP6	171389	hgsc.bcm.edu	37	11	284299	284299	+	Silent	SNP	A	A	G	rs7108261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:284299A>G	ENST00000312165.5	+	6	2271	c.2271A>G	c.(2269-2271)gcA>gcG	p.A757A	NLRP6_ENST00000534750.1_Silent_p.A756A	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	757					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	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;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		CAGCCCCCGCACTGACGGAGC	0.637													G|||	862	0.172125	0.6165	0.062	5008	,	,		17322	0.0		0.004	False		,,,				2504	0.0				p.A757A		Atlas-SNP	.											NALP6,NS,carcinoma,+1,1	NLRP6	4	1	0			c.A2271G						scavenged	.	G		2265,2141	587.2+/-386.6	600,1065,538	41.0	43.0	42.0		2271	-0.8	0.0	11	dbSNP_116	42	25,8575	14.6+/-50.1	0,25,4275	yes	coding-synonymous	NLRP6	NM_138329.1		600,1090,4813	GG,GA,AA		0.2907,48.5928,17.6073		757/893	284299	2290,10716	2203	4300	6503	SO:0001819	synonymous_variant	171389	exon6			CCCCGCACTGACG	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.2271A>G	11.37:g.284299A>G		Somatic	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	37	CCDS7693.1																																																																																			A|0.837;G|0.163	0.163	strong		0.637	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
COPG1	22820	hgsc.bcm.edu	37	3	128984409	128984409	+	Silent	SNP	G	G	A	rs78889622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:128984409G>A	ENST00000314797.6	+	14	1346	c.1242G>A	c.(1240-1242)aaG>aaA	p.K414K		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	414					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)										TTGAGTATAAGCGCGCTATCG	0.517													G|||	150	0.0299521	0.1036	0.0173	5008	,	,		21492	0.0		0.001	False		,,,				2504	0.0				p.K414K		Atlas-SNP	.											.	.	.	.	0			c.G1242A						PASS	.	G		378,4028	191.9+/-217.4	11,356,1836	175.0	158.0	164.0		1242	4.1	1.0	3	dbSNP_131	164	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	COPG	NM_016128.3		11,363,6129	AA,AG,GG		0.0814,8.5792,2.9602		414/875	128984409	385,12621	2203	4300	6503	SO:0001819	synonymous_variant	22820	exon14			GTATAAGCGCGCT	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.1242G>A	3.37:g.128984409G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_016128	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	37	CCDS33851.1																																																																																			G|0.973;A|0.027	0.027	strong		0.517	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128	
MIS18BP1	55320	hgsc.bcm.edu	37	14	45693648	45693648	+	Silent	SNP	G	G	A	rs35223850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45693648G>A	ENST00000310806.4	-	11	2600	c.2142C>T	c.(2140-2142)tgC>tgT	p.C714C		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	714					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)			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						CACGTTCATCGCAATCTTCCT	0.343													G|||	138	0.0275559	0.0325	0.0159	5008	,	,		19114	0.0		0.0686	False		,,,				2504	0.0153				p.C714C		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.C2142T						PASS	.	G		154,4252	106.5+/-144.9	0,154,2049	69.0	70.0	69.0		2142	0.4	0.0	14	dbSNP_126	69	517,8083	144.5+/-200.4	17,483,3800	no	coding-synonymous	MIS18BP1	NM_018353.4		17,637,5849	AA,AG,GG		6.0116,3.4952,5.1592		714/1133	45693648	671,12335	2203	4300	6503	SO:0001819	synonymous_variant	55320	exon11			TTCATCGCAATCT	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.2142C>T	14.37:g.45693648G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Silent	SNP	ENST00000310806.4	37	CCDS9684.1																																																																																			G|0.954;A|0.046	0.046	strong		0.343	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2		
KIAA1731	85459	hgsc.bcm.edu	37	11	93460264	93460264	+	Missense_Mutation	SNP	C	C	G	rs61740994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:93460264C>G	ENST00000325212.6	+	24	6784	c.6622C>G	c.(6622-6624)Cag>Gag	p.Q2208E	KIAA1731_ENST00000531700.1_Missense_Mutation_p.Q388E|KIAA1731_ENST00000411936.1_Missense_Mutation_p.Q2208E|KIAA1731_ENST00000344196.4_Missense_Mutation_p.Q388E			Q9C0D2	K1731_HUMAN	KIAA1731	2208						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)				CATGAAAAATCAGAACTATCC	0.368													C|||	38	0.00758786	0.0287	0.0	5008	,	,		19790	0.0		0.0	False		,,,				2504	0.0				p.Q2208E		Atlas-SNP	.											.	KIAA1731	173	.	0			c.C6622G						PASS	.	C	GLU/GLN	18,1366		0,18,674	56.0	46.0	49.0		6622	2.3	0.8	11	dbSNP_129	49	0,3182		0,0,1591	yes	missense	KIAA1731	NM_033395.1	29	0,18,2265	GG,GC,CC		0.0,1.3006,0.3942	benign	2208/2602	93460264	18,4548	692	1591	2283	SO:0001583	missense	85459	exon24			AAAAATCAGAACT	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.6622C>G	11.37:g.93460264C>G	ENSP00000316681:p.Gln2208Glu	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	160	83	0.51875	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	37	CCDS44708.1	23	0.010531135531135532	7	0.014227642276422764	3	0.008287292817679558	7	0.012237762237762238	6	0.0079155672823219	C	4.054	0.007826	0.07866	0.013006	0.0	ENSG00000166004	ENST00000325212;ENST00000411936;ENST00000344196;ENST00000531700;ENST00000531404;ENST00000529185	T;T	0.09163	3.02;3.01	5.61	2.34	0.29019	.	.	.	.	.	T	0.09423	0.0232	L	0.48642	1.525	0.09310	N	0.999992	B;B;B	0.15930	0.006;0.015;0.006	B;B;B	0.16722	0.011;0.016;0.011	T	0.23332	-1.0191	9	0.72032	D	0.01	.	15.8875	0.79261	0.0:0.6088:0.3912:0.0	rs61740994	2208;2208;388	Q9C0D2;Q9C0D2-3;Q9C0D2-2	K1731_HUMAN;.;.	E	2208;2208;388;388;220;74	ENSP00000316681:Q2208E;ENSP00000406505:Q2208E	ENSP00000316681:Q2208E	Q	+	1	0	KIAA1731	93099912	0.004000	0.15560	0.849000	0.33467	0.253000	0.25986	0.239000	0.18023	0.665000	0.31066	0.585000	0.79938	CAG	C|0.989;G|0.011	0.011	strong		0.368	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
TP53BP2	7159	hgsc.bcm.edu	37	1	223984072	223984072	+	Silent	SNP	G	G	A	rs141654811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:223984072G>A	ENST00000343537.7	-	13	2460	c.2169C>T	c.(2167-2169)gaC>gaT	p.D723D	TP53BP2_ENST00000391878.2_Silent_p.D594D|TP53BP2_ENST00000391879.2_5'UTR|TP53BP2_ENST00000498843.1_5'UTR	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	717					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)		AGGCTTCTAGGTCAGCATCAC	0.438																																					p.D723D		Atlas-SNP	.											.	TP53BP2	144	.	0			c.C2169T						PASS	.	G	,	0,4406		0,0,2203	142.0	137.0	139.0		2169,1782	2.8	0.8	1	dbSNP_134	139	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	TP53BP2	NM_001031685.2,NM_005426.2	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	723/1135,594/1006	223984072	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7159	exon13			TTCTAGGTCAGCA	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.2169C>T	1.37:g.223984072G>A		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	247	112	0.453441	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Silent	SNP	ENST00000343537.7	37	CCDS44319.1																																																																																			G|1.000;A|0.000	0.000	strong		0.438	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426	
TSPO	706	hgsc.bcm.edu	37	22	43558972	43558972	+	Silent	SNP	G	G	A	rs41371752|rs6972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:43558972G>A	ENST00000396265.3	+	3	379	c.204G>A	c.(202-204)gcG>gcA	p.A68A	TSPO_ENST00000583777.1_Missense_Mutation_p.R58H|TSPO_ENST00000337554.3_Missense_Mutation_p.R162H|TSPO_ENST00000329563.4_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	80	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	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	
RNF152	220441	hgsc.bcm.edu	37	18	59483514	59483514	+	Silent	SNP	A	A	G	rs9319985	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:59483514A>G	ENST00000312828.3	-	2	1282	c.183T>C	c.(181-183)ccT>ccC	p.P61P		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	61					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				AGAAGCCGGGAGGCAGCTTGG	0.622													G|||	1087	0.217053	0.3343	0.1931	5008	,	,		18490	0.0992		0.2515	False		,,,				2504	0.1616				p.P61P		Atlas-SNP	.											RNF152,caecum,carcinoma,0,1	RNF152	37	1	0			c.T183C						scavenged	.	G		1328,3078	683.5+/-404.3	196,936,1071	55.0	59.0	57.0		183	3.2	1.0	18	dbSNP_119	57	2059,6541	709.6+/-405.7	252,1555,2493	no	coding-synonymous	RNF152	NM_173557.2		448,2491,3564	GG,GA,AA		23.9419,30.1407,26.0418		61/204	59483514	3387,9619	2203	4300	6503	SO:0001819	synonymous_variant	220441	exon2			GCCGGGAGGCAGC	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"""RING-type (C3HC4) zinc fingers"""	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.183T>C	18.37:g.59483514A>G		Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	80	80	1	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	
LRPPRC	10128	hgsc.bcm.edu	37	2	44175293	44175293	+	Silent	SNP	G	G	A	rs35881858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44175293G>A	ENST00000260665.7	-	18	1945	c.1888C>T	c.(1888-1890)Ctg>Ttg	p.L630L		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	630					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TAGCTTTCCAGGAGATTACGA	0.358													G|||	126	0.0251597	0.0923	0.0043	5008	,	,		15884	0.0		0.001	False		,,,				2504	0.0				p.L630L		Atlas-SNP	.											.	LRPPRC	105	.	0			c.C1888T						PASS	.	G		269,4135	149.2+/-183.4	6,257,1939	94.0	99.0	97.0		1888	3.8	0.8	2	dbSNP_126	97	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	LRPPRC	NM_133259.3		6,260,6236	AA,AG,GG		0.0349,6.1081,2.0917		630/1395	44175293	272,12732	2202	4300	6502	SO:0001819	synonymous_variant	10128	exon18			TTTCCAGGAGATT	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1888C>T	2.37:g.44175293G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	53	19	0.358491	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			G|0.983;A|0.017	0.017	strong		0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
TJP1	7082	hgsc.bcm.edu	37	15	30012209	30012209	+	Silent	SNP	A	A	C	rs376115263		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:30012209A>C	ENST00000346128.6	-	20	3249	c.2775T>G	c.(2773-2775)gcT>gcG	p.A925A	TJP1_ENST00000400011.2_Intron|TJP1_ENST00000545208.2_Intron|TJP1_ENST00000356107.6_Silent_p.A925A	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	925					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		CTGGAGATGAAGCTTCTGCTT	0.353																																					p.A925A	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.T2775G						PASS	.	A	,	3,3687		0,3,1842	125.0	115.0	118.0		2775,	4.2	1.0	15		118	0,8186		0,0,4093	no	coding-synonymous,intron	TJP1	NM_003257.3,NM_175610.2	,	0,3,5935	CC,CA,AA		0.0,0.0813,0.0253	,	925/1749,	30012209	3,11873	1845	4093	5938	SO:0001819	synonymous_variant	7082	exon20			AGATGAAGCTTCT		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"""zona occludens 1"", ""tight junction protein ZO-1"""	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.2775T>G	15.37:g.30012209A>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Silent	SNP	ENST00000346128.6	37	CCDS42007.1																																																																																			.	.	weak		0.353	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257	
FUT7	2529	hgsc.bcm.edu	37	9	139925459	139925459	+	Silent	SNP	G	G	A	rs11145973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139925459G>A	ENST00000314412.6	-	2	1750	c.732C>T	c.(730-732)aaC>aaT	p.N244N	ABCA2_ENST00000265662.5_5'Flank|ABCA2_ENST00000371605.3_5'Flank|C9orf139_ENST00000314330.2_Intron|ABCA2_ENST00000341511.6_5'Flank|ABCA2_ENST00000492260.1_5'Flank	NM_004479.3	NP_004470.1	Q11130	FUT7_HUMAN	fucosyltransferase 7 (alpha (1,3) fucosyltransferase)	244					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)		CCACCAGTGCGTTGCGCCAGA	0.627													g|||	24	0.00479233	0.0166	0.0	5008	,	,		17645	0.0		0.001	False		,,,				2504	0.001				p.N244N		Atlas-SNP	.											.	FUT7	24	.	0			c.C732T						PASS	.		,	89,4317	67.0+/-104.6	2,85,2116	88.0	104.0	99.0		732,	-1.4	0.9	9	dbSNP_120	99	0,8598		0,0,4299	no	coding-synonymous,intron	FUT7,C9orf139	NM_004479.3,NM_207511.1	,	2,85,6415	AA,AG,GG		0.0,2.02,0.6844	,	244/343,	139925459	89,12915	2203	4299	6502	SO:0001819	synonymous_variant	2529	exon2			CAGTGCGTTGCGC	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.732C>T	9.37:g.139925459G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	71	0.72449	NM_004479	B2R7U7|Q6DK54	Silent	SNP	ENST00000314412.6	37	CCDS7022.1																																																																																			G|0.993;A|0.007	0.007	strong		0.627	FUT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055220.1	NM_004479	
ANO2	57101	hgsc.bcm.edu	37	12	5841733	5841733	+	Missense_Mutation	SNP	A	A	C	rs1860961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:5841733A>C	ENST00000356134.5	-	16	1572	c.1501T>G	c.(1501-1503)Tct>Gct	p.S501A	ANO2_ENST00000538154.1_5'UTR|ANO2_ENST00000327087.8_Missense_Mutation_p.S500A|ANO2_ENST00000546188.1_Missense_Mutation_p.S501A	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	505					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.S501A(1)		central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						TGGACAGCAGACTGGTTGCTC	0.453													A|||	686	0.136981	0.2383	0.1311	5008	,	,		22847	0.1161		0.0746	False		,,,				2504	0.09				p.S500A		Atlas-SNP	.											ANO2,NS,carcinoma,0,1	ANO2	309	1	1	Substitution - Missense(1)	stomach(1)	c.T1498G						PASS	.	A	ALA/SER	872,3206		96,680,1263	128.0	124.0	125.0		1498	3.7	1.0	12	dbSNP_92	125	678,7696		35,608,3544	yes	missense	ANO2	NM_020373.2	99	131,1288,4807	CC,CA,AA		8.0965,21.383,12.4478	benign	500/999	5841733	1550,10902	2039	4187	6226	SO:0001583	missense	57101	exon15			CAGCAGACTGGTT	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.1501T>G	12.37:g.5841733A>C	ENSP00000348453:p.Ser501Ala	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	170	90	0.529412	NM_020373	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		270	0.12362637362637363	118	0.23983739837398374	35	0.09668508287292818	71	0.12412587412587413	46	0.06068601583113457	A	8.258	0.810552	0.16537	0.21383	0.080965	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277;ENST00000545860	T;T;T;T	0.65549	-0.16;-0.16;-0.16;0.68	4.84	3.66	0.41972	.	0.660666	0.15622	N	0.252809	T	0.00012	0.0000	N	0.04508	-0.205	0.48975	P	2.6199999999998447E-4	B	0.18741	0.03	B	0.15052	0.012	T	0.11203	-1.0597	9	0.09590	T	0.72	.	7.3722	0.26808	0.8984:0.0:0.1016:0.0	rs1860961;rs57832099;rs1860961	500	Q9NQ90-3	.	A	500;501;501;505;60	ENSP00000314048:S500A;ENSP00000348453:S501A;ENSP00000440981:S501A;ENSP00000443813:S60A	ENSP00000314048:S500A	S	-	1	0	ANO2	5711994	0.999000	0.42202	0.984000	0.44739	0.589000	0.36550	1.064000	0.30579	2.027000	0.59764	0.533000	0.62120	TCT	A|0.870;C|0.130	0.130	strong		0.453	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
ZNF443	10224	hgsc.bcm.edu	37	19	12541141	12541141	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12541141C>T	ENST00000301547.5	-	4	2042	c.1845G>A	c.(1843-1845)ccG>ccA	p.P615P	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	615					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						TACATTCATACGGGTTCTCTC	0.403																																					p.P615P		Atlas-SNP	.											ZNF443,lower_third,carcinoma,-1,1	ZNF443	63	1	0			c.G1845A						scavenged	.						62.0	67.0	65.0					19																	12541141		2197	4290	6487	SO:0001819	synonymous_variant	10224	exon4			TTCATACGGGTTC	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1845G>A	19.37:g.12541141C>T		Somatic	244	3	0.0122951		WXS	Illumina HiSeq	Phase_I	252	4	0.015873	NM_005815		Silent	SNP	ENST00000301547.5	37	CCDS32918.1																																																																																			.	.	none		0.403	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249458	71249458	+	Silent	SNP	T	T	C	rs372455775		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249458T>C	ENST00000398534.3	+	1	388	c.357T>C	c.(355-357)tgT>tgC	p.C119C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	119	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						AGTCCAGCTGTTGTAAGCCCT	0.607																																					p.C119C		Atlas-SNP	.											KRTAP5-8,NS,carcinoma,0,1	KRTAP5-8	28	1	0			c.T357C						scavenged	.						174.0	186.0	182.0					11																	71249458		2200	4294	6494	SO:0001819	synonymous_variant	57830	exon1			CAGCTGTTGTAAG	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.357T>C	11.37:g.71249458T>C		Somatic	181	6	0.0331492		WXS	Illumina HiSeq	Phase_I	235	9	0.0382979	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																			.	.	weak		0.607	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
CLEC2L	154790	hgsc.bcm.edu	37	7	139225215	139225215	+	Silent	SNP	T	T	C	rs112553913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139225215T>C	ENST00000422142.2	+	3	486	c.414T>C	c.(412-414)atT>atC	p.I138I		NM_001080511.2	NP_001073980.2	P0C7M8	CLC2L_HUMAN	C-type lectin domain family 2, member L	138	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(1)|kidney(2)|lung(1)	5	Melanoma(164;0.233)					TGGCTGTGATTCAGAGCCAGA	0.592													T|||	149	0.0297524	0.1097	0.0014	5008	,	,		17539	0.0		0.003	False		,,,				2504	0.0				p.I138I		Atlas-SNP	.											.	CLEC2L	14	.	0			c.T414C						PASS	.	T		311,3699		9,293,1703	13.0	17.0	16.0		414	-4.7	1.0	7	dbSNP_132	16	7,8351		0,7,4172	no	coding-synonymous	CLEC2L	NM_001080511.2		9,300,5875	CC,CT,TT		0.0838,7.7556,2.5712		138/215	139225215	318,12050	2005	4179	6184	SO:0001819	synonymous_variant	154790	exon3			TGTGATTCAGAGC	AK057548	CCDS47724.1	7q34	2011-05-18			ENSG00000236279	ENSG00000236279		"""C-type lectin domain containing"""	21969	protein-coding gene	gene with protein product							Standard	NM_001080511		Approved	FLJ32986	uc010lnd.3	P0C7M8	OTTHUMG00000164900	ENST00000422142.2:c.414T>C	7.37:g.139225215T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	126	67	0.531746	NM_001080511		Silent	SNP	ENST00000422142.2	37	CCDS47724.1	60	0.027472527472527472	58	0.11788617886178862	0	0.0	0	0.0	2	0.002638522427440633	T	9.732	1.162489	0.21538	0.077556	8.38E-4	ENSG00000236279	ENST00000521281	.	.	.	4.81	-4.68	0.03309	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33599	-0.9862	4	.	.	.	-13.0213	11.495	0.50402	0.0:0.2389:0.0:0.7611	.	.	.	.	S	62	.	.	F	+	2	0	CLEC2L	138875755	0.368000	0.25031	0.986000	0.45419	0.949000	0.60115	-1.179000	0.03090	-0.764000	0.04651	-0.376000	0.06991	TTC	T|0.972;C|0.028	0.028	strong		0.592	CLEC2L-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380878.1	NM_001080511	
CYTH2	9266	hgsc.bcm.edu	37	19	48977189	48977189	+	Silent	SNP	C	C	T	rs28582663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48977189C>T	ENST00000452733.2	+	6	938	c.462C>T	c.(460-462)ccC>ccT	p.P154P	CYTH2_ENST00000427476.1_Silent_p.P154P			Q99418	CYH2_HUMAN	cytohesin 2	154	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|inositol 1,4,5 trisphosphate binding (GO:0070679)|lipid binding (GO:0008289)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						TTCGCCTACCCGGAGAGGCCC	0.607													C|||	61	0.0121805	0.0431	0.0043	5008	,	,		16544	0.0		0.0	False		,,,				2504	0.001				p.P154P		Atlas-SNP	.											.	CYTH2	33	.	0			c.C462T						PASS	.	C	,	193,4213	123.3+/-160.7	1,191,2011	48.0	47.0	47.0		462,462	-7.4	0.9	19	dbSNP_125	47	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CYTH2	NM_004228.6,NM_017457.5	,	1,192,6310	TT,TC,CC		0.0116,4.3804,1.4916	,	154/400,154/401	48977189	194,12812	2203	4300	6503	SO:0001819	synonymous_variant	9266	exon6			CCTACCCGGAGAG	X99753	CCDS12722.1	19q13.32	2014-05-02	2008-08-14	2008-08-14	ENSG00000105443	ENSG00000105443		"""Pleckstrin homology (PH) domain containing"""	9502	protein-coding gene	gene with protein product		602488	"""pleckstrin homology, Sec7 and coiled/coil domains 2 (cytohesin-2)"", ""pleckstrin homology, Sec7 and coiled-coil domains 2"""	PSCD2L, PSCD2		8706128, 8945478, 20525696	Standard	NM_004228		Approved	CTS18.1, Sec7p-L, ARNO, Sec7p-like, cytohesin-2	uc002pjj.4	Q99418	OTTHUMG00000150245	ENST00000452733.2:c.462C>T	19.37:g.48977189C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_017457	A8K8P0|Q8IXY9|Q92958	Silent	SNP	ENST00000452733.2	37	CCDS12722.1																																																																																			C|0.982;T|0.018	0.018	strong		0.607	CYTH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317060.1	NM_004228	
HHLA2	11148	hgsc.bcm.edu	37	3	108072298	108072298	+	Missense_Mutation	SNP	T	T	C	rs6779254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108072298T>C	ENST00000357759.5	+	4	503	c.89T>C	c.(88-90)aTt>aCt	p.I30T	HHLA2_ENST00000467761.1_Missense_Mutation_p.I30T|HHLA2_ENST00000489514.2_Missense_Mutation_p.I30T|HHLA2_ENST00000491820.1_Missense_Mutation_p.I30T|HHLA2_ENST00000467562.1_Intron	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	30			I -> T (in dbSNP:rs6779254).		positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						GCTTTCTTCATTTATGTTCCT	0.388													C|||	2957	0.590455	0.7867	0.5965	5008	,	,		21742	0.2093		0.6839	False		,,,				2504	0.6176				p.I30T		Atlas-SNP	.											.	HHLA2	95	.	0			c.T89C						PASS	.	C	THR/ILE	2852,874		1095,662,106	27.0	25.0	26.0		89	-7.7	0.0	3	dbSNP_116	26	5532,2642		1862,1808,417	yes	missense	HHLA2	NM_007072.2	89	2957,2470,523	CC,CT,TT		32.322,23.4568,29.5462	possibly-damaging	30/415	108072298	8384,3516	1863	4087	5950	SO:0001583	missense	11148	exon4			TCTTCATTTATGT	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.89T>C	3.37:g.108072298T>C	ENSP00000350402:p.Ile30Thr	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Missense_Mutation	SNP	ENST00000357759.5	37	CCDS46883.1	1221	0.5590659340659341	379	0.7703252032520326	233	0.643646408839779	99	0.17307692307692307	510	0.6728232189973615	C	0.745	-0.775062	0.02951	0.765432	0.67678	ENSG00000114455	ENST00000463019;ENST00000491820;ENST00000482430;ENST00000462629;ENST00000357759;ENST00000467761;ENST00000489514	T;T;T;T;T;T;T	0.43294	2.53;5.01;2.53;0.95;5.01;5.01;5.01	5.38	-7.67	0.01272	.	2.455510	0.02244	N	0.066036	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	0.38714	-0.9648	9	0.52906	T	0.07	7.4029	1.5999	0.02672	0.4293:0.1699:0.2333:0.1675	rs6779254;rs17182503;rs60107127;rs6779254	30;30	C9J7D0;Q9UM44	.;HHLA2_HUMAN	T	30	ENSP00000419940:I30T;ENSP00000418284:I30T;ENSP00000418174:I30T;ENSP00000419911:I30T;ENSP00000350402:I30T;ENSP00000419207:I30T;ENSP00000417856:I30T	ENSP00000350402:I30T	I	+	2	0	HHLA2	109554988	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.268000	0.01169	-1.645000	0.01515	-1.779000	0.00650	ATT	T|0.430;C|0.570	0.570	strong		0.388	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072	
ADORA3	140	hgsc.bcm.edu	37	1	112045709	112045709	+	Missense_Mutation	SNP	G	G	C	rs77883500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:112045709G>C	ENST00000241356.4	-	1	673	c.268C>G	c.(268-270)Ctg>Gtg	p.L90V	ADORA3_ENST00000486342.1_5'UTR|ADORA3_ENST00000369717.4_Intron|ADORA3_ENST00000369716.4_Missense_Mutation_p.L90V	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	90					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	AAGATAAGCAGTAGGCAAGTC	0.552													G|||	86	0.0171725	0.0613	0.0058	5008	,	,		21547	0.0		0.001	False		,,,				2504	0.0				p.L90V		Atlas-SNP	.											.	ADORA3	104	.	0			c.C268G						PASS	.	G	VAL/LEU,,VAL/LEU	184,4222	117.5+/-155.4	2,180,2021	84.0	64.0	70.0		268,,268	1.1	0.7	1	dbSNP_131	70	1,8599		0,1,4299	yes	missense,intron,missense	ADORA3	NM_000677.3,NM_001081976.1,NM_020683.6	32,,32	2,181,6320	CC,CG,GG		0.0116,4.1761,1.4224	benign,,benign	90/319,,90/348	112045709	185,12821	2203	4300	6503	SO:0001583	missense	140	exon1			TAAGCAGTAGGCA	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"""GPCR / Class A : Adenosine receptors"", ""Immunoglobulin superfamily / V-set domain containing"""	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.268C>G	1.37:g.112045709G>C	ENSP00000241356:p.Leu90Val	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	291	135	0.463918	NM_020683	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000241356.4	37	CCDS839.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	4.114	0.019297	0.08006	0.041761	1.16E-4	ENSG00000121933	ENST00000369716;ENST00000241356	T;T	0.37235	1.21;1.21	5.26	1.07	0.20283	GPCR, rhodopsin-like superfamily (1);	0.645763	0.12883	N	0.431230	T	0.05777	0.0151	N	0.05510	-0.035	0.22292	N	0.999222	B;B	0.21381	0.055;0.004	B;B	0.24394	0.053;0.012	T	0.45101	-0.9284	10	0.10377	T	0.69	-1.0214	11.5274	0.50588	0.0:0.1113:0.3199:0.5688	.	90;90	P33765;P33765-2	AA3R_HUMAN;.	V	90	ENSP00000358730:L90V;ENSP00000241356:L90V	ENSP00000241356:L90V	L	-	1	2	ADORA3	111847232	0.001000	0.12720	0.667000	0.29798	0.701000	0.40568	-0.483000	0.06536	0.013000	0.14918	0.561000	0.74099	CTG	G|0.985;C|0.015	0.015	strong		0.552	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683	
ZFC3H1	196441	hgsc.bcm.edu	37	12	72008421	72008421	+	Missense_Mutation	SNP	T	T	C	rs11541286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72008421T>C	ENST00000378743.3	-	30	5778	c.5420A>G	c.(5419-5421)aAa>aGa	p.K1807R		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1807			K -> R (in dbSNP:rs11541286).		RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AGTAAAAAATTTGAATTCTTG	0.333													T|||	207	0.0413339	0.0113	0.0562	5008	,	,		15627	0.003		0.0606	False		,,,				2504	0.091				p.K1807R		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.A5420G						PASS	.	T	ARG/LYS	73,3539		1,71,1734	111.0	112.0	112.0		5420	0.0	1.0	12	dbSNP_120	112	615,7523		17,581,3471	yes	missense	ZFC3H1	NM_144982.4	26	18,652,5205	CC,CT,TT		7.5571,2.021,5.8553	probably-damaging	1807/1990	72008421	688,11062	1806	4069	5875	SO:0001583	missense	196441	exon30			AAAAATTTGAATT	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.5420A>G	12.37:g.72008421T>C	ENSP00000368017:p.Lys1807Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	76	0.0347985347985348	3	0.006097560975609756	24	0.06629834254143646	1	0.0017482517482517483	48	0.0633245382585752	T	12.11	1.840561	0.32513	0.02021	0.075571	ENSG00000133858	ENST00000378743	T	0.34072	1.38	5.35	0.0229	0.14135	.	0.161807	0.53938	N	0.000047	T	0.00998	0.0033	L	0.27053	0.805	0.80722	D	1	B	0.15141	0.012	B	0.12156	0.007	T	0.08310	-1.0728	10	0.48119	T	0.1	.	5.3631	0.16099	0.1189:0.2036:0.0:0.6775	rs11541286;rs52822945;rs59889096;rs11541286	1807	O60293	ZC3H1_HUMAN	R	1807	ENSP00000368017:K1807R	ENSP00000368017:K1807R	K	-	2	0	ZFC3H1	70294688	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	0.659000	0.24994	-0.238000	0.09724	0.455000	0.32223	AAA	T|0.956;C|0.044	0.044	strong		0.333	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
CROCC	9696	hgsc.bcm.edu	37	1	17264920	17264920	+	Missense_Mutation	SNP	C	C	T	rs4463721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17264920C>T	ENST00000375541.5	+	11	1385	c.1316C>T	c.(1315-1317)gCg>gTg	p.A439V	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin									p.A439V(3)		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)		CAGGAGCAGGCGGCCCTGGAG	0.617																																					p.A439V		Atlas-SNP	.											CROCC,NS,carcinoma,0,3	CROCC	185	3	3	Substitution - Missense(3)	prostate(3)	c.C1316T						scavenged	.						19.0	16.0	17.0					1																	17264920		2174	4263	6437	SO:0001583	missense	9696	exon11			AGCAGGCGGCCCT	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.1316C>T	1.37:g.17264920C>T	ENSP00000364691:p.Ala439Val	Somatic	293	1	0.00341297		WXS	Illumina HiSeq	Phase_I	464	145	0.3125	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	628	0.2875457875457875	134	0.27235772357723576	93	0.2569060773480663	201	0.3513986013986014	200	0.2638522427440633	C	12.64	1.997905	0.35226	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.12465	2.68	4.81	4.81	0.61882	.	.	.	.	.	T	0.00012	0.0000	L	0.41573	1.285	0.24969	N	0.991679	B;B;P	0.39022	0.003;0.017;0.655	B;B;B	0.31751	0.002;0.003;0.135	T	0.48525	-0.9028	9	0.12103	T	0.63	.	10.9447	0.47294	0.187:0.813:0.0:0.0	rs4463721;rs59602954	302;302;439	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	V	439;320	ENSP00000364691:A439V	ENSP00000364691:A439V	A	+	2	0	CROCC	17137507	0.006000	0.16342	0.535000	0.28026	0.666000	0.39218	-0.113000	0.10774	2.374000	0.81015	0.561000	0.74099	GCG	C|0.713;T|0.287	0.287	strong		0.617	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
MT-CYB	4519	hgsc.bcm.edu	37	M	15139	15139	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:15139T>C	ENST00000361789.2	+	1	393	c.393T>C	c.(391-393)taT>taC	p.Y131Y	MT-TT_ENST00000387460.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	131					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						TTCATAGGCTATGTCCTCCCG	0.458											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.Y131Y		Atlas-SNP	.											.	.	.	.	0			c.T393C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			AGGCTATGTCCTC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.393T>C	M.37:g.15139T>C		Somatic	15	0	0	585	WXS	Illumina HiSeq	Phase_I	17	17	1	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Silent	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.458	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
CBLC	23624	hgsc.bcm.edu	37	19	45281375	45281375	+	Missense_Mutation	SNP	C	C	T	rs115775900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45281375C>T	ENST00000270279.3	+	1	250	c.187C>T	c.(187-189)Cgg>Tgg	p.R63W	CBLC_ENST00000341505.4_Missense_Mutation_p.R63W	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	63	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				CCATTCTcggcgggcggccgg	0.711			M		AML								c|||	64	0.0127796	0.0454	0.0043	5008	,	,		8428	0.0		0.0	False		,,,				2504	0.001				p.R63W		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.C187T						PASS	.		TRP/ARG,TRP/ARG	85,3747		1,83,1832	8.0	11.0	10.0		187,187	-2.5	0.0	19	dbSNP_132	10	1,7799		0,1,3899	yes	missense,missense	CBLC	NM_001130852.1,NM_012116.3	101,101	1,84,5731	TT,TC,CC		0.0128,2.2182,0.7393	probably-damaging,probably-damaging	63/429,63/475	45281375	86,11546	1916	3900	5816	SO:0001583	missense	23624	exon1			TCTCGGCGGGCGG	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.187C>T	19.37:g.45281375C>T	ENSP00000270279:p.Arg63Trp	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	10	8	0.8	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	37	CCDS12643.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	.	16.25	3.071238	0.55646	0.022182	1.28E-4	ENSG00000142273	ENST00000270279;ENST00000341505	T;T	0.76968	-1.06;-1.06	3.35	-2.49	0.06403	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.588184	0.13455	N	0.386611	T	0.40272	0.1110	M	0.65975	2.015	0.09310	N	1	D;D	0.71674	0.998;0.998	P;P	0.62491	0.903;0.756	T	0.63506	-0.6622	10	0.87932	D	0	-6.6255	10.0273	0.42079	0.6988:0.3012:0.0:0.0	.	63;63	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	W	63	ENSP00000270279:R63W;ENSP00000340250:R63W	ENSP00000270279:R63W	R	+	1	2	CBLC	49973215	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.696000	0.05104	-0.081000	0.12662	0.556000	0.70494	CGG	C|0.983;T|0.017	0.017	strong		0.711	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
ETNK2	55224	hgsc.bcm.edu	37	1	204109238	204109238	+	Missense_Mutation	SNP	G	G	A	rs565275436		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204109238G>A	ENST00000367202.4	-	5	943	c.793C>T	c.(793-795)Cgg>Tgg	p.R265W	RP11-74C13.3_ENST00000433869.1_RNA|ETNK2_ENST00000367199.2_Missense_Mutation_p.R196W|ETNK2_ENST00000477125.1_5'UTR|ETNK2_ENST00000367197.1_5'UTR|ETNK2_ENST00000367201.3_Missense_Mutation_p.R265W|ETNK2_ENST00000367198.2_Missense_Mutation_p.R87W	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	265					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|placenta development (GO:0001890)|post-embryonic development (GO:0009791)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)			breast(1)|central_nervous_system(1)|large_intestine(4)|ovary(1)	7	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			TCAATGAACCGCACGTGACCT	0.488													G|||	1	0.000199681	0.0008	0.0	5008	,	,		22874	0.0		0.0	False		,,,				2504	0.0				p.R265W		Atlas-SNP	.											ETNK2_ENST00000367202,NS,carcinoma,0,2	ETNK2	48	2	0			c.C793T						PASS	.						152.0	134.0	140.0					1																	204109238		2203	4300	6503	SO:0001583	missense	55224	exon5			TGAACCGCACGTG	AK001623	CCDS1442.2, CCDS73006.1	1q32.1	2008-02-05			ENSG00000143845	ENSG00000143845			25575	protein-coding gene	gene with protein product		609859				12477932	Standard	XM_005245302		Approved	FLJ10761, EKI2	uc001hao.4	Q9NVF9	OTTHUMG00000036061	ENST00000367202.4:c.793C>T	1.37:g.204109238G>A	ENSP00000356170:p.Arg265Trp	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_018208	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Missense_Mutation	SNP	ENST00000367202.4	37	CCDS1442.2	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910054	0.52439	.	.	ENSG00000143845	ENST00000367201;ENST00000367202;ENST00000367199;ENST00000455266;ENST00000367198;ENST00000422699;ENST00000452983;ENST00000444817	T;T;T;T;T;T;T	0.58652	0.32;0.32;0.32;0.32;0.32;0.32;0.32	5.4	1.99	0.26369	Protein kinase-like domain (1);Choline/ethanolamine kinase (1);	0.207171	0.44097	D	0.000494	T	0.71281	0.3321	M	0.82323	2.585	0.40505	D	0.98068	D;D;D	0.89917	0.995;0.996;1.0	P;P;P	0.62014	0.663;0.773;0.897	T	0.73398	-0.3995	10	0.62326	D	0.03	-8.4891	9.3644	0.38215	0.0756:0.0:0.6588:0.2656	.	224;265;265	Q9NVF9-3;Q9NVF9;Q9NVF9-2	.;EKI2_HUMAN;.	W	265;265;196;131;87;131;122;111	ENSP00000356169:R265W;ENSP00000356170:R265W;ENSP00000356167:R196W;ENSP00000356166:R87W;ENSP00000405497:R131W;ENSP00000398091:R122W;ENSP00000406241:R111W	ENSP00000356166:R87W	R	-	1	2	ETNK2	202375861	0.148000	0.22702	0.308000	0.25141	0.327000	0.28475	2.116000	0.41930	0.590000	0.29694	0.650000	0.86243	CGG	.	.	none		0.488	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208	
OTOF	9381	hgsc.bcm.edu	37	2	26688662	26688662	+	Silent	SNP	C	C	T	rs2272071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26688662C>T	ENST00000272371.2	-	38	4803	c.4677G>A	c.(4675-4677)gtG>gtA	p.V1559V	OTOF_ENST00000338581.6_Silent_p.V792V|OTOF_ENST00000403946.3_Silent_p.V1559V|OTOF_ENST00000402415.3_Silent_p.V869V|OTOF_ENST00000339598.3_Silent_p.V792V	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1559	C2 4. {ECO:0000255|PROSITE- ProRule:PRU00041}.				membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)	p.V1559V(1)|p.V792V(1)		NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATACACAGCCACCGTCAGCA	0.582													C|||	309	0.0617013	0.0681	0.0375	5008	,	,		18878	0.126		0.0159	False		,,,				2504	0.0511				p.V1559V	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											OTOF_ENST00000361394,NS,carcinoma,0,2	OTOF	524	2	2	Substitution - coding silent(2)	stomach(2)	c.G4677A						PASS	.	C	,,,	290,4116	160.3+/-192.7	15,260,1928	118.0	100.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2376,4677,2607,2376	1.4	1.0	2	dbSNP_100	106	106,8494	57.2+/-118.5	1,104,4195	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	16,364,6123	TT,TC,CC		1.2326,6.5819,3.0447	,,,	792/1231,1559/1998,869/1308,792/1231	26688662	396,12610	2203	4300	6503	SO:0001819	synonymous_variant	9381	exon38			CACAGCCACCGTC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.4677G>A	2.37:g.26688662C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	194	104	0.536082	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			C|0.951;T|0.049	0.049	strong		0.582	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
COL1A2	1278	hgsc.bcm.edu	37	7	94028386	94028386	+	Missense_Mutation	SNP	G	G	A	rs139528613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:94028386G>A	ENST00000297268.6	+	4	593	c.122G>A	c.(121-123)cGt>cAt	p.R41H		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	41					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)	p.R41L(1)	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)	AGAGGACCACGTGGAGAAAGG	0.373										HNSCC(75;0.22)			G|||	15	0.00299521	0.0113	0.0	5008	,	,		15654	0.0		0.0	False		,,,				2504	0.0				p.R41H		Atlas-SNP	.											.	COL1A2	240	.	1	Substitution - Missense(1)	lung(1)	c.G122A						PASS	.	G	HIS/ARG	54,4352	54.2+/-90.2	0,54,2149	125.0	124.0	125.0		122	5.8	1.0	7	dbSNP_134	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	COL1A2	NM_000089.3	29	0,55,6448	AA,AG,GG		0.0116,1.2256,0.4229	probably-damaging	41/1367	94028386	55,12951	2203	4300	6503	SO:0001583	missense	1278	exon4			GACCACGTGGAGA	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.122G>A	7.37:g.94028386G>A	ENSP00000297268:p.Arg41His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	19.99	3.928117	0.73327	0.012256	1.16E-4	ENSG00000164692	ENST00000297268	D	0.93712	-3.27	5.85	5.85	0.93711	.	.	.	.	.	D	0.93350	0.7880	L	0.55103	1.725	0.43430	D	0.995594	D;D	0.69078	0.997;0.994	D;P	0.63033	0.91;0.727	D	0.93121	0.6525	9	0.72032	D	0.01	.	14.6939	0.69107	0.071:0.0:0.929:0.0	.	41;41	B4DTF5;P08123	.;CO1A2_HUMAN	H	41	ENSP00000297268:R41H	ENSP00000297268:R41H	R	+	2	0	COL1A2	93866322	0.971000	0.33674	1.000000	0.80357	0.993000	0.82548	2.827000	0.48112	2.941000	0.99782	0.655000	0.94253	CGT	G|0.996;A|0.004	0.004	strong		0.373	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
RETSAT	54884	hgsc.bcm.edu	37	2	85570440	85570440	+	Silent	SNP	G	G	A	rs150706527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85570440G>A	ENST00000295802.4	-	11	1870	c.1758C>T	c.(1756-1758)gcC>gcT	p.A586A	RETSAT_ENST00000263854.6_3'UTR|RETSAT_ENST00000457495.2_Silent_p.A525A|RETSAT_ENST00000475624.2_5'Flank	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	586					oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	GCTTCAGGATGGCGCTGCTGC	0.552													G|||	17	0.00339457	0.0129	0.0	5008	,	,		32923	0.0		0.0	False		,,,				2504	0.0				p.A586A		Atlas-SNP	.											RETSAT,NS,carcinoma,-2,1	RETSAT	56	1	0			c.C1758T						PASS	.	G		51,4355	50.9+/-86.3	0,51,2152	81.0	84.0	83.0		1758	1.9	1.0	2	dbSNP_134	83	0,8600		0,0,4300	no	coding-synonymous	RETSAT	NM_017750.3		0,51,6452	AA,AG,GG		0.0,1.1575,0.3921		586/611	85570440	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	54884	exon11			CAGGATGGCGCTG	AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	1.3.99.23		25991	protein-coding gene	gene with protein product						12975309, 15358783	Standard	NM_017750		Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.1758C>T	2.37:g.85570440G>A		Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	328	73	0.222561	NM_017750	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Silent	SNP	ENST00000295802.4	37	CCDS1972.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	7.937	0.741884	0.15642	0.011575	0.0	ENSG00000042445	ENST00000449375	.	.	.	4.89	1.86	0.25419	.	.	.	.	.	T	0.38134	0.1029	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21655	-1.0239	4	.	.	.	-15.1159	4.0777	0.09912	0.1989:0.0:0.6169:0.1842	.	.	.	.	L	375	.	.	P	-	2	0	RETSAT	85423951	0.882000	0.30256	0.993000	0.49108	0.657000	0.38888	0.224000	0.17738	0.579000	0.29504	0.462000	0.41574	CCA	G|0.996;A|0.004	0.004	strong		0.552	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750	
DHX9	1660	hgsc.bcm.edu	37	1	182827297	182827297	+	Silent	SNP	G	G	A	rs73063095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182827297G>A	ENST00000367549.3	+	8	842	c.732G>A	c.(730-732)ctG>ctA	p.L244L		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	244	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.|Interaction with BRCA1.|Interaction with CREBBP.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						CCTGTGCCCTGTCACTTGTCA	0.408													G|||	104	0.0207668	0.0741	0.0072	5008	,	,		20027	0.001		0.0	False		,,,				2504	0.0				p.L244L	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G732A						PASS	.	G		243,3731		8,227,1752	100.0	95.0	97.0		732	1.1	1.0	1	dbSNP_130	97	0,8354		0,0,4177	no	coding-synonymous	DHX9	NM_001357.4		8,227,5929	AA,AG,GG		0.0,6.1147,1.9711		244/1271	182827297	243,12085	1987	4177	6164	SO:0001819	synonymous_variant	1660	exon8			TGCCCTGTCACTT	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.732G>A	1.37:g.182827297G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	173	76	0.439306	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Silent	SNP	ENST00000367549.3	37	CCDS41444.1																																																																																			G|0.986;A|0.014	0.014	strong		0.408	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
ATP10B	23120	hgsc.bcm.edu	37	5	159992751	159992751	+	Silent	SNP	A	A	G	rs4921150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:159992751A>G	ENST00000327245.5	-	26	4941	c.4095T>C	c.(4093-4095)acT>acC	p.T1365T		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1365					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTGGGTGGTGAGTTGGTCGAG	0.532													G|||	719	0.14357	0.2935	0.1023	5008	,	,		14517	0.0119		0.0954	False		,,,				2504	0.1554				p.T1365T		Atlas-SNP	.											ATP10B,colon,carcinoma,0,1	ATP10B	201	1	0			c.T4095C						scavenged	.	G		935,2933		114,707,1113	103.0	114.0	111.0		4095	3.8	0.0	5	dbSNP_111	111	982,7304		62,858,3223	no	coding-synonymous	ATP10B	NM_025153.2		176,1565,4336	GG,GA,AA		11.8513,24.1727,15.7726		1365/1462	159992751	1917,10237	1934	4143	6077	SO:0001819	synonymous_variant	23120	exon26			GTGGTGAGTTGGT	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.4095T>C	5.37:g.159992751A>G		Somatic	142	7	0.0492958		WXS	Illumina HiSeq	Phase_I	161	73	0.453416	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	37	CCDS43394.1																																																																																			A|0.867;G|0.133	0.133	strong		0.532	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153	
GALNT9	50614	hgsc.bcm.edu	37	12	132681664	132681664	+	Silent	SNP	G	G	A	rs111344752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132681664G>A	ENST00000328957.8	-	11	1799	c.1800C>T	c.(1798-1800)caC>caT	p.H600H	GALNT9_ENST00000397325.2_Silent_p.H234H|GALNT9_ENST00000535228.1_Silent_p.H351H|GALNT9_ENST00000541995.1_Silent_p.H234H	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	600	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)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		AGTGCCGTGCGTGTTTGATCC	0.642													g|||	68	0.0135783	0.0499	0.0014	5008	,	,		15532	0.0		0.0	False		,,,				2504	0.001				p.H600H	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.C1800T						PASS	.		,	176,3898		3,170,1864	85.0	100.0	95.0		723,702	-6.2	0.0	12	dbSNP_132	95	0,8376		0,0,4188	no	coding-synonymous,coding-synonymous	GALNT9	NM_001122636.1.dup,NM_021808.3	,	3,170,6052	AA,AG,GG		0.0,4.3201,1.4137	,	241/245,234/238	132681664	176,12274	2037	4188	6225	SO:0001819	synonymous_variant	50614	exon11			CCGTGCGTGTTTG	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.1800C>T	12.37:g.132681664G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	37		20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	g	0.018	-1.482667	0.01027	0.043201	0.0	ENSG00000182870	ENST00000411988	.	.	.	4.45	-6.24	0.02046	.	.	.	.	.	T	0.09905	0.0243	.	.	.	0.30680	N	0.752399	.	.	.	.	.	.	T	0.35375	-0.9791	4	.	.	.	.	8.9918	0.36028	0.5625:0.0:0.3379:0.0995	.	.	.	.	C	373	.	.	R	-	1	0	GALNT9	131247617	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.994000	0.03716	-1.273000	0.02424	-1.585000	0.00851	CGC	G|0.990;A|0.010	0.010	strong		0.642	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	
ADAM21	8747	hgsc.bcm.edu	37	14	70924696	70924696	+	Silent	SNP	G	G	A	rs77892318|rs386778613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:70924696G>A	ENST00000603540.1	+	2	738	c.480G>A	c.(478-480)aaG>aaA	p.K160K	ADAM21_ENST00000267499.3_Silent_p.K160K|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	160					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)	p.K160K(1)		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)		TGGTTTATAAGATAAACAGTA	0.423													G|||	1254	0.250399	0.3026	0.1297	5008	,	,		18930	0.496		0.1173	False		,,,				2504	0.1493				p.K160K		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	1	Substitution - coding silent(1)	stomach(1)	c.G480A						PASS	.						39.0	48.0	45.0					14																	70924696		2133	4291	6424	SO:0001819	synonymous_variant	8747	exon2			TTATAAGATAAAC	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.480G>A	14.37:g.70924696G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	83	21	0.253012	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			G|0.946;A|0.054	0.054	strong		0.423	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
EPB41	2035	hgsc.bcm.edu	37	1	29391505	29391505	+	Silent	SNP	G	G	A	rs79677225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:29391505G>A	ENST00000343067.4	+	16	2146	c.2019G>A	c.(2017-2019)aaG>aaA	p.K673K	EPB41_ENST00000373797.1_Silent_p.K659K|EPB41_ENST00000373798.1_Silent_p.K673K|EPB41_ENST00000349460.4_Silent_p.K450K|EPB41_ENST00000398863.2_Silent_p.K619K|EPB41_ENST00000356093.2_Silent_p.K640K|EPB41_ENST00000347529.3_Silent_p.K584K|EPB41_ENST00000373800.3_Silent_p.K431K	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	673	Spectrin--actin-binding.				actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		ATTTAGACAAGAGTCAAGAGG	0.433													G|||	46	0.0091853	0.0325	0.0043	5008	,	,		19618	0.0		0.0	False		,,,				2504	0.0				p.K673K		Atlas-SNP	.											.	EPB41	118	.	0			c.G2019A						PASS	.	G	,,,,,	99,4307	79.3+/-117.8	2,95,2106	98.0	92.0	94.0		2019,1977,1230,1293,1350,1752	-0.5	1.0	1	dbSNP_132	94	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EPB41	NM_001166005.1,NM_001166006.1,NM_001166007.1,NM_004437.3,NM_203342.2,NM_203343.2	,,,,,	2,95,6406	AA,AG,GG		0.0,2.2469,0.7612	,,,,,	673/865,659/721,410/602,431/589,450/642,584/776	29391505	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	2035	exon16			AGACAAGAGTCAA	BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023			3377	protein-coding gene	gene with protein product		130500	"""elliptocytosis 1, RH-linked"""	EL1			Standard	NM_001166005		Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.2019G>A	1.37:g.29391505G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_001166005	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	Silent	SNP	ENST00000343067.4	37	CCDS53288.1																																																																																			G|0.991;A|0.009	0.009	strong		0.433	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010312.1	NM_203342	
ATP7B	540	hgsc.bcm.edu	37	13	52520435	52520435	+	Silent	SNP	C	C	T	rs1801248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:52520435C>T	ENST00000242839.4	-	13	3201	c.3045G>A	c.(3043-3045)ctG>ctA	p.L1015L	ATP7B_ENST00000400366.3_Silent_p.L904L|ATP7B_ENST00000448424.2_Silent_p.L937L|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000417240.2_Silent_p.L287L|ATP7B_ENST00000400370.3_Silent_p.L585L|ATP7B_ENST00000418097.2_Intron|ATP7B_ENST00000344297.5_Silent_p.L808L	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1015					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)	GCGCCATCTCCAGGGGCTTGC	0.597									Wilson disease				C|||	62	0.0123802	0.0	0.0274	5008	,	,		18934	0.0		0.0348	False		,,,				2504	0.0082				p.L1015L		Atlas-SNP	.											.	ATP7B	123	.	0			c.G3045A						PASS	.	C	,	31,3955		0,31,1962	18.0	21.0	20.0		3045,2424	2.3	1.0	13	dbSNP_89	20	333,8009		8,317,3846	no	coding-synonymous,coding-synonymous	ATP7B	NM_000053.3,NM_001005918.2	,	8,348,5808	TT,TC,CC		3.9918,0.7777,2.9526	,	1015/1466,808/1259	52520435	364,11964	1993	4171	6164	SO:0001819	synonymous_variant	540	exon13	Familial Cancer Database		CATCTCCAGGGGC	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.3045G>A	13.37:g.52520435C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Silent	SNP	ENST00000242839.4	37	CCDS41892.1																																																																																			C|0.984;T|0.016	0.016	strong		0.597	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053	
OR52K2	119774	hgsc.bcm.edu	37	11	4471276	4471276	+	Missense_Mutation	SNP	G	G	A	rs331537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4471276G>A	ENST00000325719.4	+	1	752	c.707G>A	c.(706-708)cGc>cAc	p.R236H		NM_001005172.2	NP_001005172.2	Q8NGK3	O52K2_HUMAN	olfactory receptor, family 52, subfamily K, member 2	236			R -> H (in dbSNP:rs331537). {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)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|skin(6)	25		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.48e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0821)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGGAGGCCCGCTACAAGGCA	0.488													G|||	1116	0.222843	0.7239	0.0879	5008	,	,		22301	0.0347		0.0318	False		,,,				2504	0.0317				p.R236H		Atlas-SNP	.											.	OR52K2	61	.	0			c.G707A						PASS	.	G	HIS/ARG	2604,1798	641.6+/-397.5	782,1040,379	268.0	228.0	242.0		707	4.0	1.0	11	dbSNP_79	242	268,8328	101.6+/-162.9	4,260,4034	yes	missense	OR52K2	NM_001005172.2	29	786,1300,4413	AA,AG,GG		3.1177,40.8451,22.0957	benign	236/315	4471276	2872,10126	2201	4298	6499	SO:0001583	missense	119774	exon1			AGGCCCGCTACAA	AB065791	CCDS31351.1	11p15.4	2012-08-09			ENSG00000181963	ENSG00000181963		"""GPCR / Class A : Olfactory receptors"""	15223	protein-coding gene	gene with protein product							Standard	NM_001005172		Approved		uc001lyz.2	Q8NGK3	OTTHUMG00000165703	ENST00000325719.4:c.707G>A	11.37:g.4471276G>A	ENSP00000318956:p.Arg236His	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	253	128	0.505929	NM_001005172	A8MUY8|B2RP35|Q6IFK4	Missense_Mutation	SNP	ENST00000325719.4	37	CCDS31351.1	439	0.20100732600732601	363	0.7378048780487805	29	0.08011049723756906	23	0.04020979020979021	24	0.0316622691292876	G	11.70	1.718104	0.30503	0.591549	0.031177	ENSG00000181963	ENST00000325719	T	0.00333	8.07	4.02	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.140701	0.30126	N	0.010342	T	0.00012	0.0000	M	0.86740	2.835	0.48185	P	3.990000000000382E-4	B	0.18968	0.032	B	0.19391	0.025	T	0.36962	-0.9726	9	0.87932	D	0	.	9.6637	0.39972	0.1047:0.0:0.8953:0.0	rs331537;rs59989102;rs331537	236	Q8NGK3	O52K2_HUMAN	H	236	ENSP00000318956:R236H	ENSP00000318956:R236H	R	+	2	0	OR52K2	4427852	0.001000	0.12720	0.999000	0.59377	0.879000	0.50718	0.949000	0.29109	2.082000	0.62665	0.485000	0.47835	CGC	G|0.792;A|0.208	0.208	strong		0.488	OR52K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385844.1	NM_001005172	
RAB17	64284	hgsc.bcm.edu	37	2	238483751	238483751	+	Missense_Mutation	SNP	T	T	C	rs34311889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238483751T>C	ENST00000264601.3	-	6	1179	c.550A>G	c.(550-552)Agc>Ggc	p.S184G	RAB17_ENST00000538644.1_Missense_Mutation_p.S57G|RAB17_ENST00000409822.1_Missense_Mutation_p.S57G|RAB17_ENST00000409576.1_Intron	NM_022449.3	NP_071894.1	Q9H0T7	RAB17_HUMAN	RAB17, member RAS oncogene family	184			S -> G (in dbSNP:rs34311889).		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)		TCCTCGTCGCTTCTCTGCAGT	0.662													C|||	625	0.1248	0.4418	0.0389	5008	,	,		17887	0.0		0.004	False		,,,				2504	0.0102				p.S184G	Colon(56;987 1029 6466 13943 27336)	Atlas-SNP	.											.	RAB17	17	.	0			c.A550G						PASS	.	C	GLY/SER	1649,2757	643.8+/-397.9	313,1023,867	35.0	38.0	37.0		550	-0.0	0.0	2	dbSNP_126	37	25,8575	811.2+/-407.1	0,25,4275	yes	missense	RAB17	NM_022449.3	56	313,1048,5142	CC,CT,TT		0.2907,37.4262,12.871	benign	184/213	238483751	1674,11332	2203	4300	6503	SO:0001583	missense	64284	exon6			CGTCGCTTCTCTG	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.550A>G	2.37:g.238483751T>C	ENSP00000264601:p.Ser184Gly	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	147	75	0.510204	NM_022449	Q53QV6|Q6IA73|Q6PJZ0|Q9BVU1|Q9H9U9	Missense_Mutation	SNP	ENST00000264601.3	37	CCDS2520.1	225	0.10302197802197802	207	0.42073170731707316	17	0.04696132596685083	0	0.0	1	0.0013192612137203166	C	9.138	1.013111	0.19277	0.374262	0.002907	ENSG00000124839	ENST00000264601;ENST00000538644;ENST00000409822	T;T;T	0.79845	-1.31;-1.31;-1.31	3.05	-0.00717	0.14010	.	1.882310	0.03405	N	0.203850	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	0.11036	-1.0604	9	0.27082	T	0.32	-11.7524	6.8837	0.24187	0.0:0.352:0.5348:0.1132	rs34311889	184	Q9H0T7	RAB17_HUMAN	G	184;57;57	ENSP00000264601:S184G;ENSP00000443461:S57G;ENSP00000386589:S57G	ENSP00000264601:S184G	S	-	1	0	RAB17	238148490	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.027000	0.12371	-0.272000	0.09259	-1.103000	0.02113	AGC	T|0.884;C|0.116	0.116	strong		0.662	RAB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257084.2		
MUC5B	727897	hgsc.bcm.edu	37	11	1269835	1269835	+	Missense_Mutation	SNP	G	G	A	rs2943521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1269835G>A	ENST00000529681.1	+	31	11783	c.11725G>A	c.(11725-11727)Gtc>Atc	p.V3909I	MUC5B_ENST00000447027.1_Missense_Mutation_p.V3912I|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3909	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			V -> I (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)		CCCCTCCTCCGTCCCGGGGAC	0.652													A|||	2311	0.461462	0.3185	0.5418	5008	,	,		14910	0.6567		0.4205	False		,,,				2504	0.4387				p.V3909I		Atlas-SNP	.											.	MUC5B	473	.	0			c.G11725A						PASS	.						90.0	102.0	98.0					11																	1269835		2055	4169	6224	SO:0001583	missense	727897	exon31			TCCTCCGTCCCGG	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.11725G>A	11.37:g.1269835G>A	ENSP00000436812:p.Val3909Ile	Somatic	476	1	0.00210084		WXS	Illumina HiSeq	Phase_I	474	234	0.493671	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	797	0.3649267399267399	99	0.20121951219512196	132	0.36464088397790057	322	0.5629370629370629	244	0.32189973614775724	A	4.241	0.043603	0.08196	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17528	2.27;2.46	3.11	-6.22	0.02058	.	.	.	.	.	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.51317	-0.8721	8	0.87932	D	0	.	1.5831	0.02638	0.1585:0.328:0.222:0.2914	rs59902608	4437;3912	A7Y9J9;E9PBJ0	.;.	I	3909;3912;3853;3814	ENSP00000436812:V3909I;ENSP00000415793:V3912I	ENSP00000343037:V3853I	V	+	1	0	MUC5B	1226411	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.108000	0.15396	-4.491000	0.00046	-0.848000	0.03037	GTC	G|0.614;A|0.386	0.386	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
PPP6R3	55291	hgsc.bcm.edu	37	11	68341661	68341661	+	Silent	SNP	C	C	A	rs114505709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:68341661C>A	ENST00000393800.2	+	13	1682	c.1428C>A	c.(1426-1428)ccC>ccA	p.P476P	PPP6R3_ENST00000393799.2_Silent_p.P476P|PPP6R3_ENST00000527403.2_Silent_p.P476P|PPP6R3_ENST00000393801.3_Silent_p.P476P|PPP6R3_ENST00000529710.1_Silent_p.P425P|PPP6R3_ENST00000534534.1_Silent_p.P244P|PPP6R3_ENST00000524845.1_Silent_p.P476P|PPP6R3_ENST00000524904.1_Silent_p.P476P|PPP6R3_ENST00000265637.4_Silent_p.P476P|PPP6R3_ENST00000265636.5_Silent_p.P425P	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	476					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						ACAAGGGCCCCAACAGTGCAT	0.448													C|||	37	0.00738818	0.025	0.0029	5008	,	,		20069	0.0		0.002	False		,,,				2504	0.0				p.P476P		Atlas-SNP	.											.	PPP6R3	159	.	0			c.C1428A						PASS	.	C	,,,,,	105,4295	80.9+/-119.3	3,99,2098	143.0	122.0	129.0		1428,1428,1428,1428,1275,1275	0.1	1.0	11	dbSNP_132	129	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP6R3	NM_001164160.1,NM_001164161.1,NM_001164162.1,NM_001164163.1,NM_001164164.1,NM_018312.4	,,,,,	3,99,6392	AA,AC,CC		0.0,2.3864,0.8084	,,,,,	476/880,476/874,476/868,476/845,425/792,425/794	68341661	105,12883	2200	4294	6494	SO:0001819	synonymous_variant	55291	exon13			GGGCCCCAACAGT	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	1173	protein-coding gene	gene with protein product	"""sporulation-induced transcript 4-associated protein"""	610879	"""chromosome 11 open reading frame 23"", ""SAPS domain family, member 3"""	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.1428C>A	11.37:g.68341661C>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	68	23	0.338235	NM_001164162	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Silent	SNP	ENST00000393800.2	37	CCDS53672.1																																																																																			C|0.991;A|0.009	0.009	strong		0.448	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28338298	28338298	+	Missense_Mutation	SNP	C	C	G	rs457947	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:28338298C>G	ENST00000284987.5	-	1	534	c.413G>C	c.(412-414)gGt>gCt	p.G138A		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	138			G -> A (in dbSNP:rs457947). {ECO:0000269|PubMed:10438522, ECO:0000269|PubMed:15489334}.		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						GCGGGGACTACCGTCCACTGT	0.662													C|||	701	0.139976	0.2489	0.17	5008	,	,		14671	0.004		0.1332	False		,,,				2504	0.1186				p.G138A	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.G413C						PASS	.	C	ALA/GLY	1025,3381		112,801,1290	28.0	26.0	27.0		413	4.6	1.0	21	dbSNP_80	27	1407,7191		127,1153,3019	yes	missense	ADAMTS5	NM_007038.3	60	239,1954,4309	GG,GC,CC		16.3643,23.2637,18.7019	possibly-damaging	138/931	28338298	2432,10572	2203	4299	6502	SO:0001583	missense	11096	exon1			GGACTACCGTCCA	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.413G>C	21.37:g.28338298C>G	ENSP00000284987:p.Gly138Ala	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	294	0.1346153846153846	119	0.241869918699187	62	0.1712707182320442	1	0.0017482517482517483	112	0.14775725593667546	C	10.96	1.499434	0.26861	0.232637	0.163643	ENSG00000154736	ENST00000284987	T	0.09723	2.95	4.57	4.57	0.56435	Peptidase M12B, propeptide (1);	0.163396	0.44097	D	0.000487	T	0.00012	0.0000	L	0.45228	1.405	0.31486	P	0.666612	P	0.47604	0.898	P	0.49192	0.602	T	0.51748	-0.8666	9	0.26408	T	0.33	.	12.9996	0.58667	0.0:0.8377:0.1623:0.0	rs457947	138	Q9UNA0	ATS5_HUMAN	A	138	ENSP00000284987:G138A	ENSP00000284987:G138A	G	-	2	0	ADAMTS5	27260169	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	3.780000	0.55386	2.344000	0.79699	0.563000	0.77884	GGT	C|0.834;G|0.166	0.166	strong		0.662	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
OAS3	4940	hgsc.bcm.edu	37	12	113376388	113376388	+	Missense_Mutation	SNP	G	G	A	rs1859330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113376388G>A	ENST00000228928.7	+	1	232	c.53G>A	c.(52-54)aGg>aAg	p.R18K	OAS3_ENST00000548514.1_Missense_Mutation_p.R18K|RP1-71H24.1_ENST00000552784.1_RNA|OAS3_ENST00000551007.1_Missense_Mutation_p.R18K|OAS3_ENST00000546638.1_3'UTR	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	18	OAS domain 1.		R -> K (in dbSNP:rs1859330). {ECO:0000269|PubMed:11280764}.|R -> M (in dbSNP:rs1859330).|R -> T (in dbSNP:rs1859330).		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						GTGGCCAGAAGGCTGCAGCCG	0.736													G|||	3321	0.663139	0.5537	0.7219	5008	,	,		14015	0.749		0.6302	False		,,,				2504	0.7147				p.R18K		Atlas-SNP	.											.	OAS3	63	.	0			c.G53A						PASS	.	G	LYS/ARG	2114,1456		650,814,321	12.0	14.0	13.0		53	-1.2	0.0	12	dbSNP_92	13	5068,2900		1682,1704,598	yes	missense	OAS3	NM_006187.2	26	2332,2518,919	AA,AG,GG		36.3956,40.7843,37.7535	benign	18/1088	113376388	7182,4356	1785	3984	5769	SO:0001583	missense	4940	exon1			CCAGAAGGCTGCA	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.53G>A	12.37:g.113376388G>A	ENSP00000228928:p.Arg18Lys	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	1496	0.684981684981685	306	0.6219512195121951	252	0.6961325966850829	452	0.7902097902097902	486	0.6411609498680739	G	12.70	2.016575	0.35606	0.592157	0.636044	ENSG00000111331	ENST00000228928;ENST00000551007;ENST00000548514;ENST00000323881	T;T;T	0.08193	3.12;3.12;3.12	3.11	-1.2	0.09554	2-5-oligoadenylate synthetase, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.58432	P	8.000000000008E-6	B;B;B	0.30824	0.015;0.296;0.24	B;B;B	0.26416	0.005;0.069;0.047	T	0.07539	-1.0767	8	0.44086	T	0.13	.	3.2965	0.06968	0.4057:0.2121:0.3821:0.0	rs1859330;rs3815176;rs56927475;rs1859330	18;18;18	Q9Y6K5;F8VS35;F8VWK9	OAS3_HUMAN;.;.	K	18	ENSP00000228928:R18K;ENSP00000449299:R18K;ENSP00000448388:R18K	ENSP00000228928:R18K	R	+	2	0	OAS3	111860771	0.008000	0.16893	0.023000	0.16930	0.003000	0.03518	-0.030000	0.12308	-0.125000	0.11703	-0.339000	0.08088	AGG	G|0.326;A|0.674	0.674	strong		0.736	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
UGT2A1	10941	hgsc.bcm.edu	37	4	70505162	70505162	+	Intron	SNP	G	G	A	rs28404221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:70505162G>A	ENST00000503640.1	-	1	771				UGT2A2_ENST00000457664.2_Missense_Mutation_p.A66V|UGT2A1_ENST00000514019.1_Missense_Mutation_p.A267V|UGT2A1_ENST00000286604.4_Intron|UGT2A1_ENST00000512704.1_Intron	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus						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						GAATAGAGTTGCTGATGAAGC	0.353													G|||	236	0.0471246	0.0461	0.0259	5008	,	,		18175	0.0734		0.0298	False		,,,				2504	0.0542				p.A267V		Atlas-SNP	.											.	UGT2A1	131	.	0			c.C800T						PASS	.	G	VAL/ALA,	192,3534		10,172,1681	128.0	128.0	128.0		197,	0.6	1.0	4	dbSNP_125	128	282,7900		9,264,3818	yes	missense,intron	UGT2A1,UGT2A2	NM_001105677.2,NM_006798.2	64,	19,436,5499	AA,AG,GG		3.4466,5.153,3.9805	,	66/537,	70505162	474,11434	1863	4091	5954	SO:0001627	intron_variant	10941	exon3			AGAGTTGCTGATG	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.715+7485C>T	4.37:g.70505162G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	128	52	0.40625	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	99	0.04532967032967033	26	0.052845528455284556	14	0.03867403314917127	39	0.06818181818181818	20	0.026385224274406333	G	9.389	1.075007	0.20227	0.05153	0.034466	ENSG00000173610	ENST00000457664;ENST00000514019	T;T	0.61627	0.09;0.17	5.85	0.643	0.17770	.	.	.	.	.	T	0.04907	0.0132	L	0.42632	1.34	.	.	.	B;B	0.27971	0.041;0.196	B;B	0.27380	0.038;0.079	T	0.27157	-1.0082	8	0.12103	T	0.63	.	11.1222	0.48298	0.0:0.104:0.4657:0.4303	rs28404221	267;66	E9PDM7;Q9Y4X1-2	.;.	V	66;267	ENSP00000387888:A66V;ENSP00000425497:A267V	ENSP00000387888:A66V	A	-	2	0	UGT2A1	70539751	0.001000	0.12720	0.976000	0.42696	0.952000	0.60782	1.072000	0.30678	0.331000	0.23511	0.585000	0.79938	GCA	G|0.956;A|0.044	0.044	strong		0.353	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
FLG	2312	hgsc.bcm.edu	37	1	152284382	152284382	+	Missense_Mutation	SNP	C	C	T	rs149595328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284382C>T	ENST00000368799.1	-	3	3015	c.2980G>A	c.(2980-2982)Ggt>Agt	p.G994S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	994	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.G994C(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)			TGCCCGTGACCGGCTCTGTCT	0.577									Ichthyosis				T|||	23	0.00459265	0.0166	0.0014	5008	,	,		20620	0.0		0.0	False		,,,				2504	0.0				p.G994S		Atlas-SNP	.											FLG,NS,carcinoma,+1,2	FLG	900	2	1	Substitution - Missense(1)	lung(1)	c.G2980A						PASS	.	C	SER/GLY	62,4344	820.7+/-416.4	0,62,2141	242.0	245.0	244.0		2980	-0.6	0.0	1	dbSNP_134	244	0,8600		0,0,4300	no	missense	FLG	NM_002016.1	56	0,62,6441	TT,TC,CC		0.0,1.4072,0.4767	benign	994/4062	152284382	62,12944	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGTGACCGGCTCT	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.2980G>A	1.37:g.152284382C>T	ENSP00000357789:p.Gly994Ser	Somatic	581	0	0		WXS	Illumina HiSeq	Phase_I	674	50	0.074184	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	t	7.940	0.742605	0.15642	0.014072	0.0	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.00649	5.98	2.34	-0.615	0.11587	.	.	.	.	.	T	0.00144	0.0004	L	0.32530	0.975	0.09310	N	1	B	0.29232	0.238	B	0.12156	0.007	T	0.28713	-1.0035	9	0.06625	T	0.88	.	5.25	0.15517	0.0:0.5849:0.0:0.4151	.	994	P20930	FILA_HUMAN	S	994;201	ENSP00000357789:G994S	ENSP00000357789:G994S	G	-	1	0	FLG	150551006	0.000000	0.05858	0.001000	0.08648	0.126000	0.20510	-0.003000	0.12901	0.047000	0.15862	0.291000	0.19559	GGT	C|0.995;T|0.005	0.005	strong		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CRISP3	10321	hgsc.bcm.edu	37	6	49701523	49701523	+	Missense_Mutation	SNP	A	A	G	rs495335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49701523A>G	ENST00000393666.1	-	4	322	c.316T>C	c.(316-318)Tcc>Ccc	p.S106P	CRISP3_ENST00000433368.2_Missense_Mutation_p.S129P|CRISP3_ENST00000263045.4_Missense_Mutation_p.S119P|CRISP3_ENST00000371159.4_Missense_Mutation_p.S137P|CRISP3_ENST00000423399.2_Missense_Mutation_p.S16P			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	106	SCP.		S -> P (in dbSNP:rs495335). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		defense response (GO:0006952)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|specific granule (GO:0042581)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|skin(6)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			CATGAGCTGGAGGCACTTGAC	0.433													G|||	3381	0.67512	0.7383	0.7594	5008	,	,		18918	0.5476		0.6948	False		,,,				2504	0.6411				p.S129P		Atlas-SNP	.											.	CRISP3	67	.	0			c.T385C						PASS	.	G	PRO/SER,PRO/SER	3280,1126	401.5+/-332.0	1205,870,128	149.0	139.0	142.0		385,355	5.1	0.0	6	dbSNP_83	142	5784,2816	445.5+/-361.0	1947,1890,463	yes	missense,missense	CRISP3	NM_001190986.1,NM_006061.2	74,74	3152,2760,591	GG,GA,AA		32.7442,25.5561,30.3091	benign,benign	129/269,119/259	49701523	9064,3942	2203	4300	6503	SO:0001583	missense	10321	exon5			AGCTGGAGGCACT	X94323	CCDS4929.1, CCDS4929.2, CCDS55019.1	6p12.3	2008-02-05			ENSG00000096006	ENSG00000096006			16904	protein-coding gene	gene with protein product						8665901, 12223513	Standard	NM_006061		Approved	SGP28, CRISP-3, CRS3, dJ442L6.3, Aeg2	uc003ozs.3	P54108	OTTHUMG00000014823	ENST00000393666.1:c.316T>C	6.37:g.49701523A>G	ENSP00000377274:p.Ser106Pro	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	119	66	0.554622	NM_001190986	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Missense_Mutation	SNP	ENST00000393666.1	37		1478	0.6767399267399268	372	0.7560975609756098	273	0.7541436464088398	310	0.541958041958042	523	0.6899736147757256	G	1.963	-0.438361	0.04636	0.744439	0.672558	ENSG00000096006	ENST00000263045;ENST00000433368;ENST00000393666;ENST00000423399;ENST00000371159;ENST00000354620	T;T;T;T;T;T	0.44881	3.06;3.06;3.06;0.91;3.06;3.06	5.1	5.1	0.69264	CAP domain (3);	0.182430	0.34291	N	0.004100	T	0.03305	0.0096	N	0.00500	-1.43	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35101	-0.9802	9	0.02654	T	1	.	9.8183	0.40867	0.0963:0.0:0.9037:0.0	rs495335;rs1771237;rs13192493;rs16879714;rs52821725;rs495335	106	P54108	CRIS3_HUMAN	P	119;129;106;16;137;129	ENSP00000263045:S119P;ENSP00000389026:S129P;ENSP00000377274:S106P;ENSP00000410469:S16P;ENSP00000360201:S137P;ENSP00000346636:S129P	ENSP00000263045:S119P	S	-	1	0	CRISP3	49809482	0.021000	0.18746	0.003000	0.11579	0.001000	0.01503	1.944000	0.40263	1.156000	0.42514	-0.197000	0.12766	TCC	A|0.322;G|0.678	0.678	strong		0.433	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061	
UBC	7316	hgsc.bcm.edu	37	12	125396377	125396377	+	Silent	SNP	A	A	G	rs16918544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125396377A>G	ENST00000538617.1	-	4	1117	c.801T>C	c.(799-801)gaT>gaC	p.D267D	UBC_ENST00000546120.1_Silent_p.D571D|UBC_ENST00000536661.1_5'Flank|UBC_ENST00000339647.5_Silent_p.D647D|UBC_ENST00000536769.1_Silent_p.D647D			P0CG48	UBC_HUMAN	ubiquitin C	647	Ubiquitin-like 4. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|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)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|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)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|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 epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|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)|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 transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|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)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)	p.D647D(1)		breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		ACCTCTGCTGATCAGGAGGGA	0.527													G|||	133	0.0265575	0.0802	0.0072	5008	,	,		21561	0.0179		0.002	False		,,,				2504	0.002				p.D647D		Atlas-SNP	.											UBC,NS,carcinoma,0,1	UBC	79	1	1	Substitution - coding silent(1)	prostate(1)	c.T1941C						PASS	.	G		321,4085	792.1+/-415.1	17,287,1899	190.0	177.0	182.0		1941	3.4	1.0	12	dbSNP_123	182	27,8573	818.0+/-406.9	0,27,4273	no	coding-synonymous	UBC	NM_021009.5		17,314,6172	GG,GA,AA		0.314,7.2855,2.6757		647/686	125396377	348,12658	2203	4300	6503	SO:0001819	synonymous_variant	7316	exon2			CTGCTGATCAGGA		CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"""polyubiquitin-C"""	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000538617.1:c.801T>C	12.37:g.125396377A>G		Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	341	172	0.504399	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000538617.1	37																																																																																				A|0.976;G|0.024	0.024	strong		0.527	UBC-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000400179.1	NM_021009	
SYNE2	23224	hgsc.bcm.edu	37	14	64604634	64604634	+	Silent	SNP	T	T	C	rs8007874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64604634T>C	ENST00000344113.4	+	79	14988	c.14776T>C	c.(14776-14778)Ttg>Ctg	p.L4926L	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.L1560L|SYNE2_ENST00000357395.3_Silent_p.L1311L|SYNE2_ENST00000394768.2_Silent_p.L1311L|SYNE2_ENST00000554584.1_Silent_p.L4843L|SYNE2_ENST00000358025.3_Silent_p.L4926L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4926					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)		AGAGCAGTGGTTGTCCCTGAA	0.512													T|||	228	0.0455272	0.1687	0.0072	5008	,	,		16544	0.0		0.0	False		,,,				2504	0.0				p.L4926L		Atlas-SNP	.											.	SYNE2	577	.	0			c.T14776C						PASS	.	T	,	577,3829	255.5+/-260.7	39,499,1665	83.0	73.0	76.0		14776,14776	-3.5	1.0	14	dbSNP_116	76	6,8594	3.0+/-9.4	0,6,4294	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	39,505,5959	CC,CT,TT		0.0698,13.0958,4.4825	,	4926/6886,4926/6908	64604634	583,12423	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon79			CAGTGGTTGTCCC	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.14776T>C	14.37:g.64604634T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			T|0.941;C|0.059	0.059	strong		0.512	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2389813	2389813	+	Silent	SNP	C	C	T	rs8100380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2389813C>T	ENST00000332578.3	+	1	30	c.30C>T	c.(28-30)ctC>ctT	p.L10L		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	10					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)		ACGTACACCTCGTGCCCAGGA	0.632													C|||	247	0.0493211	0.1793	0.0101	5008	,	,		18167	0.0		0.003	False		,,,				2504	0.0				p.L10L		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C30T						PASS	.	C		753,3653	306.3+/-289.4	56,641,1506	76.0	55.0	62.0		30	-4.5	0.0	19	dbSNP_116	62	20,8580	13.3+/-46.6	0,20,4280	no	coding-synonymous	TMPRSS9	NM_182973.1		56,661,5786	TT,TC,CC		0.2326,17.0903,5.9434		10/1060	2389813	773,12233	2203	4300	6503	SO:0001819	synonymous_variant	360200	exon1			ACACCTCGTGCCC	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.30C>T	19.37:g.2389813C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			C|0.948;T|0.052	0.052	strong		0.632	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
MEF2D	4209	hgsc.bcm.edu	37	1	156450719	156450719	+	Silent	SNP	G	G	A	rs1185700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156450719G>A	ENST00000348159.4	-	4	783	c.303C>T	c.(301-303)ccC>ccT	p.P101P	MEF2D_ENST00000340875.5_Intron|MEF2D_ENST00000360595.3_Silent_p.P101P|MEF2D_ENST00000368240.2_Silent_p.P101P|MEF2D_ENST00000353795.3_Intron|MEF2D_ENST00000464356.2_Intron	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	101					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCTCCCCGTCGGGCTCGGGGC	0.677											OREG0013874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1165	0.232628	0.1808	0.2983	5008	,	,		14474	0.245		0.2386	False		,,,				2504	0.2372				p.P101P		Atlas-SNP	.											.	MEF2D	43	.	0			c.C303T						PASS	.	G		932,3472	332.3+/-302.4	90,752,1360	74.0	84.0	81.0		303	-7.7	0.8	1	dbSNP_87	81	1987,6611	330.6+/-319.3	245,1497,2557	no	coding-synonymous	MEF2D	NM_005920.2		335,2249,3917	AA,AG,GG		23.11,21.1626,22.4504		101/522	156450719	2919,10083	2202	4299	6501	SO:0001819	synonymous_variant	4209	exon4			CCCGTCGGGCTCG	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"""Myocyte enhancer factors"""	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.303C>T	1.37:g.156450719G>A		Somatic	95	0	0	1778	WXS	Illumina HiSeq	Phase_I	110	54	0.490909	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Silent	SNP	ENST00000348159.4	37	CCDS1143.1																																																																																			G|0.766;A|0.234	0.234	strong		0.677	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920	
APOL5	80831	hgsc.bcm.edu	37	22	36124860	36124860	+	Missense_Mutation	SNP	C	C	G	rs2076673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36124860C>G	ENST00000249044.2	+	4	1217	c.1217C>G	c.(1216-1218)tCt>tGt	p.S406C		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	406			S -> C (in dbSNP:rs2076673).		lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|skin(2)|urinary_tract(1)	19						AGGACAGTCTCTGCCCCAAGG	0.627													C|||	1813	0.362021	0.2292	0.2291	5008	,	,		14719	0.5942		0.2942	False		,,,				2504	0.4663				p.S406C		Atlas-SNP	.											.	APOL5	45	.	0			c.C1217G						PASS	.	C	CYS/SER	951,3455	361.9+/-315.9	108,735,1360	84.0	75.0	78.0		1217	0.9	0.0	22	dbSNP_96	78	2703,5897	434.0+/-357.6	445,1813,2042	yes	missense	APOL5	NM_030642.1	112	553,2548,3402	GG,GC,CC		31.4302,21.5842,28.0947	probably-damaging	406/434	36124860	3654,9352	2203	4300	6503	SO:0001583	missense	80831	exon4			CAGTCTCTGCCCC	AY014878	CCDS13920.1	22q12.3	2013-01-24			ENSG00000128313	ENSG00000128313		"""Apolipoproteins"""	14869	protein-coding gene	gene with protein product		607255				11374903	Standard	NM_030642		Approved	APOLV	uc003aof.3	Q9BWW9	OTTHUMG00000150588	ENST00000249044.2:c.1217C>G	22.37:g.36124860C>G	ENSP00000249044:p.Ser406Cys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	105	56	0.533333	NM_030642	Q5TFL9|Q9UGW5	Missense_Mutation	SNP	ENST00000249044.2	37	CCDS13920.1	760	0.34798534798534797	119	0.241869918699187	88	0.2430939226519337	336	0.5874125874125874	217	0.2862796833773087	C	11.68	1.710932	0.30322	0.215842	0.314302	ENSG00000128313	ENST00000249044	T	0.05199	3.48	1.95	0.921	0.19403	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.71674	0.998	D	0.67725	0.953	T	0.40720	-0.9548	8	0.87932	D	0	.	4.2875	0.10862	0.0:0.7956:0.0:0.2044	rs2076673;rs2076673	406	Q9BWW9	APOL5_HUMAN	C	406	ENSP00000249044:S406C	ENSP00000249044:S406C	S	+	2	0	APOL5	34454806	0.011000	0.17503	0.008000	0.14137	0.089000	0.18198	-0.128000	0.10531	0.387000	0.25024	0.195000	0.17529	TCT	C|0.692;G|0.308	0.308	strong		0.627	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
RNF207	388591	hgsc.bcm.edu	37	1	6269021	6269021	+	Silent	SNP	C	C	T	rs114798118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6269021C>T	ENST00000377939.4	+	4	532	c.405C>T	c.(403-405)cgC>cgT	p.R135R	RNF207_ENST00000377948.2_5'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	135						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		ACCGAGCACGCATGTTCGCGC	0.701													C|||	517	0.103235	0.2481	0.0562	5008	,	,		9459	0.0476		0.0417	False		,,,				2504	0.0613				p.R135R		Atlas-SNP	.											.	RNF207	45	.	0			c.C405T						PASS	.	C		586,2932		27,532,1200	5.0	7.0	6.0		405	0.6	1.0	1	dbSNP_132	6	228,6972		4,220,3376	no	coding-synonymous	RNF207	NM_207396.2		31,752,4576	TT,TC,CC		3.1667,16.6572,7.5947		135/635	6269021	814,9904	1759	3600	5359	SO:0001819	synonymous_variant	388591	exon4			AGCACGCATGTTC	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.405C>T	1.37:g.6269021C>T		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Silent	SNP	ENST00000377939.4	37	CCDS59.2																																																																																			C|0.894;T|0.106	0.106	strong		0.701	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
METTL5	29081	hgsc.bcm.edu	37	2	170681093	170681093	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170681093C>T	ENST00000260953.5	-	1	331	c.15G>A	c.(13-15)agG>agA	p.R5R	METTL5_ENST00000410097.1_Silent_p.R5R|METTL5_ENST00000392640.2_Silent_p.R5R|UBR3_ENST00000272793.5_5'Flank|METTL5_ENST00000409340.1_Silent_p.R5R|METTL5_ENST00000409965.1_Silent_p.R5R|METTL5_ENST00000409837.1_Silent_p.R5R|UBR3_ENST00000418381.1_5'Flank|METTL5_ENST00000308099.3_Silent_p.R5R	NM_014168.2	NP_054887.2	Q9NRN9	METL5_HUMAN	methyltransferase like 5	5							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|large_intestine(5)|lung(1)|prostate(1)	10						GTTCCTTAAGCCTTACTTTCT	0.458											OREG0015052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R5R		Atlas-SNP	.											METTL5,NS,carcinoma,0,1	METTL5	24	1	0			c.G15A						scavenged	.						186.0	183.0	184.0					2																	170681093		2203	4300	6503	SO:0001819	synonymous_variant	29081	exon1			CTTAAGCCTTACT	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.15G>A	2.37:g.170681093C>T		Somatic	271	0	0	1887	WXS	Illumina HiSeq	Phase_I	261	3	0.0114943	NM_014168	D3DPC9|Q9NVX1	Silent	SNP	ENST00000260953.5	37	CCDS33320.1																																																																																			.	.	none		0.458	METTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333957.1	NM_014168	
PTGES	9536	hgsc.bcm.edu	37	9	132515247	132515247	+	Silent	SNP	G	G	A	rs11792431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132515247G>A	ENST00000340607.4	-	1	79	c.45C>T	c.(43-45)gcC>gcT	p.A15A	PTGES_ENST00000481476.1_5'UTR	NM_004878.4	NP_004869.1	O14684	PTGES_HUMAN	prostaglandin E synthase	15					acute inflammatory response (GO:0002526)|arachidonic acid metabolic process (GO:0019369)|chronic inflammatory response (GO:0002544)|cyclooxygenase pathway (GO:0019371)|negative regulation of cell proliferation (GO:0008285)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|response to calcium ion (GO:0051592)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)	glutathione binding (GO:0043295)|prostaglandin-E synthase activity (GO:0050220)			lung(1)|skin(1)	2		Ovarian(14;0.00556)				AGAGCAGGAAGGCCGGGAGGG	0.637													G|||	438	0.0874601	0.211	0.049	5008	,	,		17159	0.0169		0.0596	False		,,,				2504	0.0491				p.A15A		Atlas-SNP	.											.	PTGES	7	.	0			c.C45T						PASS	.	G		784,3622	306.0+/-289.3	63,658,1482	56.0	59.0	58.0		45	3.6	1.0	9	dbSNP_120	58	559,8041	150.6+/-205.5	6,547,3747	no	coding-synonymous	PTGES	NM_004878.4		69,1205,5229	AA,AG,GG		6.5,17.7939,10.326		15/153	132515247	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	9536	exon1			CAGGAAGGCCGGG	AF010316	CCDS6927.1	9q34.3	2008-07-21			ENSG00000148344	ENSG00000148344			9599	protein-coding gene	gene with protein product	"""microsomal glutathione S-transferase 1-like 1"", ""tumor protein p53 inducible protein 12"", ""p53-induced gene 12"", ""microsomal prostaglandin E synthase-1"", ""glutathione S-transferase 1-like 1"", ""MGST1-like 1"""	605172		MGST1L1		9305847, 10091672	Standard	NM_004878		Approved	MGST-IV, PIG12, MGST1-L1, TP53I12	uc004byi.3	O14684	OTTHUMG00000020791	ENST00000340607.4:c.45C>T	9.37:g.132515247G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_004878	O14900|Q5SZC0	Silent	SNP	ENST00000340607.4	37	CCDS6927.1																																																																																			G|0.905;A|0.095	0.095	strong		0.637	PTGES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054599.2	NM_004878	
CD101	9398	hgsc.bcm.edu	37	1	117552560	117552560	+	Silent	SNP	T	T	C	rs7554376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117552560T>C	ENST00000256652.4	+	2	190	c.132T>C	c.(130-132)aaT>aaC	p.N44N	CD101_ENST00000369470.1_Silent_p.N44N	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	44	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TTGGCTGCAATGTAACTGGCC	0.502													T|||	333	0.0664936	0.1573	0.0591	5008	,	,		20033	0.0		0.0606	False		,,,				2504	0.0235				p.N44N		Atlas-SNP	.											.	CD101	95	.	0			c.T132C						PASS	.	T		685,3721	287.5+/-279.3	45,595,1563	104.0	94.0	98.0		132	-11.6	0.0	1	dbSNP_116	98	582,8018	155.2+/-209.3	26,530,3744	no	coding-synonymous	CD101	NM_004258.3		71,1125,5307	CC,CT,TT		6.7674,15.547,9.7417		44/1022	117552560	1267,11739	2203	4300	6503	SO:0001819	synonymous_variant	9398	exon2			CTGCAATGTAACT	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.132T>C	1.37:g.117552560T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_001256109	Q15856	Silent	SNP	ENST00000256652.4	37	CCDS891.1																																																																																			T|0.915;C|0.085	0.085	strong		0.502	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
P2RY4	5030	hgsc.bcm.edu	37	X	69478749	69478749	+	Silent	SNP	G	G	T	rs3829708	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:69478749G>T	ENST00000374519.2	-	1	905	c.726C>A	c.(724-726)cgC>cgA	p.R242R		NM_002565.3	NP_002556.1	P51582	P2RY4_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 4	242					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|transepithelial chloride transport (GO:0030321)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|uridine nucleotide receptor activity (GO:0015065)|UTP-activated nucleotide receptor activity (GO:0045030)			cervix(2)|endometrium(2)|large_intestine(8)|lung(6)	18						TGCGGAGAGAGCGGAGGCGAG	0.577													G|||	654	0.173245	0.1089	0.0749	3775	,	,		13522	0.2808		0.0388	False		,,,				2504	0.1391				p.R242R		Atlas-SNP	.											.	P2RY4	39	.	0			c.C726A						PASS	.	G		445,3390		24,334,63,1274,508	74.0	64.0	67.0		726	-2.5	0.9	X	dbSNP_107	67	394,6334		7,256,124,2165,1748	no	coding-synonymous	P2RY4	NM_002565.3		31,590,187,3439,2256	TT,TG,T,GG,G		5.8561,11.6037,7.9428		242/366	69478749	839,9724	2203	4300	6503	SO:0001819	synonymous_variant	5030	exon1			GAGAGAGCGGAGG	X91852	CCDS14398.1	Xq13	2012-08-08			ENSG00000186912	ENSG00000186912		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8542	protein-coding gene	gene with protein product		300038				8537336	Standard	NM_002565		Approved	NRU, P2Y4, UNR, P2P	uc004dxz.1	P51582	OTTHUMG00000021769	ENST00000374519.2:c.726C>A	X.37:g.69478749G>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_002565	Q4VBB7|Q4VBB8|Q502W2|Q5JT22	Silent	SNP	ENST00000374519.2	37	CCDS14398.1																																																																																			G|0.866;0|0.003	.	strong		0.577	P2RY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057058.2	NM_002565	
ZNF813	126017	hgsc.bcm.edu	37	19	53989945	53989945	+	Silent	SNP	G	G	A	rs34008652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53989945G>A	ENST00000396403.4	+	3	203	c.75G>A	c.(73-75)ctG>ctA	p.L25L	ZNF813_ENST00000396421.4_Silent_p.L25L	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	25	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)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		GGAAATGCCTGGACCCTGCTC	0.473																																					p.L25L		Atlas-SNP	.											.	ZNF813	81	.	0			c.G75A						PASS	.						59.0	65.0	63.0					19																	53989945		2192	4259	6451	SO:0001819	synonymous_variant	126017	exon3			ATGCCTGGACCCT	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.75G>A	19.37:g.53989945G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	86	18	0.209302	NM_001004301		Silent	SNP	ENST00000396403.4	37	CCDS46172.1																																																																																			G|0.500;A|0.500	0.500	strong		0.473	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
PRTG	283659	hgsc.bcm.edu	37	15	55970041	55970041	+	Silent	SNP	A	A	G	rs11854213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55970041A>G	ENST00000389286.4	-	8	1382	c.1335T>C	c.(1333-1335)aaT>aaC	p.N445N	RP11-420M1.2_ENST00000561155.1_RNA	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)		CTTTGTCTGAATTATAAAGTG	0.408													A|||	1210	0.241613	0.298	0.1225	5008	,	,		15648	0.4038		0.0964	False		,,,				2504	0.2321				p.N445N		Atlas-SNP	.											.	PRTG	110	.	0			c.T1335C						PASS	.	A		1026,2692		150,726,983	123.0	116.0	118.0		1335	-0.2	1.0	15	dbSNP_120	118	786,7406		45,696,3355	no	coding-synonymous	PRTG	NM_173814.4		195,1422,4338	GG,GA,AA		9.5947,27.5955,15.2141		445/1151	55970041	1812,10098	1859	4096	5955	SO:0001819	synonymous_variant	283659	exon8			GTCTGAATTATAA	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.1335T>C	15.37:g.55970041A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_173814		Silent	SNP	ENST00000389286.4	37	CCDS42040.1																																																																																			A|0.787;G|0.213	0.213	strong		0.408	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
KIAA0825	285600	hgsc.bcm.edu	37	5	93859799	93859799	+	Missense_Mutation	SNP	T	T	C	rs2044909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:93859799T>C	ENST00000329378.7	-	4	385	c.136A>G	c.(136-138)Aaa>Gaa	p.K46E	KIAA0825_ENST00000427991.2_Missense_Mutation_p.K46E|KIAA0825_ENST00000513200.3_Missense_Mutation_p.K46E|KIAA0825_ENST00000312498.7_Missense_Mutation_p.K46E	NM_173665.2	NP_775936.1	Q8IV33	K0825_HUMAN	KIAA0825	46			K -> E (in dbSNP:rs2044909).							breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						ATGCAATGTTTTATGCTATAA	0.343													C|||	576	0.115016	0.4191	0.0259	5008	,	,		16738	0.0		0.002	False		,,,				2504	0.002				p.K46E		Atlas-SNP	.											.	KIAA0825	172	.	0			c.A136G						PASS	.	C	GLU/LYS,GLU/LYS	1537,2869	660.6+/-400.8	289,959,955	83.0	81.0	82.0		136,136	3.3	1.0	5	dbSNP_94	82	18,8580	815.0+/-407.0	0,18,4281	yes	missense,missense	KIAA0825	NM_001145678.1,NM_173665.2	56,56	289,977,5236	CC,CT,TT		0.2094,34.8842,11.9579	benign,benign	46/1276,46/325	93859799	1555,11449	2203	4299	6502	SO:0001583	missense	285600	exon4			AATGTTTTATGCT	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 36"""	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000329378.7:c.136A>G	5.37:g.93859799T>C	ENSP00000331385:p.Lys46Glu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_173665	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000329378.7	37	CCDS4070.1	212	0.09706959706959707	201	0.40853658536585363	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	C	3.832	-0.035545	0.07497	0.348842	0.002094	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498;ENST00000329378	T;T;T;T	0.33438	1.46;1.46;1.41;1.5	5.19	3.27	0.37495	.	0.594717	0.18816	N	0.130398	T	0.00012	0.0000	N	0.00500	-1.43	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46275	-0.9203	9	0.02654	T	1	.	7.5589	0.27839	0.0:0.7066:0.1384:0.155	rs2044909;rs52823349;rs60449612;rs2044909	46;46	Q8IV33;Q8IV33-2	K0825_HUMAN;.	E	46	ENSP00000424618:K46E;ENSP00000400288:K46E;ENSP00000312205:K46E;ENSP00000331385:K46E	ENSP00000312205:K46E	K	-	1	0	KIAA0825	93885555	0.953000	0.32496	1.000000	0.80357	0.948000	0.59901	0.824000	0.27379	1.339000	0.45563	-0.128000	0.14901	AAA	T|0.874;C|0.126	0.126	strong		0.343	KIAA0825-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371180.2	NM_173665	
CEP104	9731	hgsc.bcm.edu	37	1	3745924	3745924	+	Missense_Mutation	SNP	G	G	A	rs2275831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3745924G>A	ENST00000378230.3	-	15	2381	c.2057C>T	c.(2056-2058)gCg>gTg	p.A686V	CEP104_ENST00000460038.1_5'Flank	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	686			A -> V (in dbSNP:rs2275831).			centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						TTCTGTAGCCGCTTTTCTCCG	0.378													G|||	1054	0.210463	0.0802	0.1311	5008	,	,		17124	0.5208		0.0557	False		,,,				2504	0.2822				p.A686V		Atlas-SNP	.											.	CEP104	79	.	0			c.C2057T						PASS	.	G	VAL/ALA	389,4017	191.9+/-217.4	24,341,1838	51.0	54.0	53.0		2057	4.4	0.8	1	dbSNP_100	53	397,8203	126.2+/-184.7	9,379,3912	yes	missense	CEP104	NM_014704.3	64	33,720,5750	AA,AG,GG		4.6163,8.8289,6.0434	benign	686/926	3745924	786,12220	2203	4300	6503	SO:0001583	missense	9731	exon15			GTAGCCGCTTTTC	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"""glycine, glutamate, thienylcyclohexylpiperidine binding protein"""		"""KIAA0562"""	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.2057C>T	1.37:g.3745924G>A	ENSP00000367476:p.Ala686Val	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	37	CCDS30571.1	431	0.19734432234432234	43	0.08739837398373984	55	0.15193370165745856	289	0.5052447552447552	44	0.05804749340369393	G	7.460	0.644553	0.14451	0.088289	0.046163	ENSG00000116198	ENST00000378230	T	0.39997	1.05	5.32	4.39	0.52855	.	0.370796	0.27595	N	0.018662	T	0.00012	0.0000	L	0.38531	1.155	0.09310	P	0.9999999999980493	B	0.21821	0.061	B	0.17722	0.019	T	0.46884	-0.9159	9	0.28530	T	0.3	.	7.1488	0.25597	0.0889:0.0:0.7414:0.1696	rs2275831;rs52804137;rs56515208;rs56685513;rs2275831	686	O60308	CE104_HUMAN	V	686	ENSP00000367476:A686V	ENSP00000367476:A686V	A	-	2	0	CEP104	3735784	1.000000	0.71417	0.824000	0.32777	0.607000	0.37147	2.063000	0.41423	1.208000	0.43306	0.591000	0.81541	GCG	G|0.873;A|0.127	0.127	strong		0.378	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704	
CAMKK2	10645	hgsc.bcm.edu	37	12	121701681	121701681	+	Silent	SNP	G	G	A	rs2230776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121701681G>A	ENST00000324774.5	-	6	1515	c.687C>T	c.(685-687)ccC>ccT	p.P229P	CAMKK2_ENST00000412367.2_Silent_p.P229P|CAMKK2_ENST00000392473.2_Silent_p.P229P|CAMKK2_ENST00000404169.3_Silent_p.P229P|CAMKK2_ENST00000347034.2_Silent_p.P229P|CAMKK2_ENST00000402834.4_Silent_p.P229P|CAMKK2_ENST00000392474.2_Silent_p.P229P|CAMKK2_ENST00000538733.1_Silent_p.P229P|CAMKK2_ENST00000337174.3_Silent_p.P229P|CAMKK2_ENST00000535524.1_Intron|CAMKK2_ENST00000446440.2_Silent_p.P229P	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	229	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)					CCTGCTCAATGGGGCCCCTGG	0.612													G|||	498	0.0994409	0.0552	0.0793	5008	,	,		16720	0.2669		0.0765	False		,,,				2504	0.0245				p.P229P		Atlas-SNP	.											.	CAMKK2	87	.	0			c.C687T						PASS	.	G	,,,,,,	246,4160	143.1+/-178.2	6,234,1963	46.0	44.0	45.0		687,687,687,687,687,687,687	3.1	1.0	12	dbSNP_98	45	686,7914	170.3+/-221.5	23,640,3637	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMKK2	NM_006549.3,NM_153499.2,NM_153500.1,NM_172214.2,NM_172215.2,NM_172216.1,NM_172226.2	,,,,,,	29,874,5600	AA,AG,GG		7.9767,5.5833,7.1659	,,,,,,	229/589,229/542,229/499,229/534,229/491,229/546,229/542	121701681	932,12074	2203	4300	6503	SO:0001819	synonymous_variant	10645	exon6			CTCAATGGGGCCC	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.687C>T	12.37:g.121701681G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_153500	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Silent	SNP	ENST00000324774.5	37	CCDS9216.1																																																																																			G|0.911;A|0.089	0.089	strong		0.612	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	
CENPQ	55166	hgsc.bcm.edu	37	6	49459978	49459978	+	Missense_Mutation	SNP	A	A	G	rs2501968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49459978A>G	ENST00000335783.3	+	9	891	c.797A>G	c.(796-798)gAt>gGt	p.D266G		NM_018132.3	NP_060602.2	Q7L2Z9	CENPQ_HUMAN	centromere protein Q	266			D -> G (in dbSNP:rs2501968).		CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(4)|ovary(2)|prostate(1)	11	Lung NSC(77;0.0128)					AAGAAACTGGATGCATCTTAA	0.318													A|||	2399	0.479034	0.4085	0.67	5008	,	,		16849	0.5794		0.4334	False		,,,				2504	0.3824				p.D266G		Atlas-SNP	.											CENPQ,colon,carcinoma,0,2	CENPQ	23	2	0			c.A797G						PASS	.	A	GLY/ASP	1823,2583	529.5+/-372.7	366,1091,746	78.0	77.0	78.0		797	4.2	0.4	6	dbSNP_100	78	3511,5089	508.5+/-377.1	718,2075,1507	yes	missense	CENPQ	NM_018132.3	94	1084,3166,2253	GG,GA,AA		40.8256,41.3754,41.0118	benign	266/269	49459978	5334,7672	2203	4300	6503	SO:0001583	missense	55166	exon9			AACTGGATGCATC	AK001407	CCDS4925.1	6p12.3	2013-11-05	2006-06-15	2006-06-15	ENSG00000031691	ENSG00000031691			21347	protein-coding gene	gene with protein product		611506	"""chromosome 6 open reading frame 139"""	C6orf139		16622420, 16622419	Standard	NM_018132		Approved	FLJ10545, CENP-Q	uc003ozh.1	Q7L2Z9	OTTHUMG00000014815	ENST00000335783.3:c.797A>G	6.37:g.49459978A>G	ENSP00000337289:p.Asp266Gly	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	45	11	0.244444	NM_018132	A8KAF1|Q6IN61|Q9NVS5	Missense_Mutation	SNP	ENST00000335783.3	37	CCDS4925.1	1090	0.4990842490842491	201	0.40853658536585363	225	0.6215469613259669	361	0.6311188811188811	303	0.3997361477572559	A	11.95	1.790577	0.31685	0.413754	0.408256	ENSG00000031691	ENST00000335783;ENST00000371200	T	0.55413	0.52	5.4	4.24	0.50183	.	0.288766	0.37304	N	0.002153	T	0.33876	0.0878	M	0.67953	2.075	0.39877	P	0.02641199999999999	B	0.20671	0.047	B	0.27796	0.083	T	0.35176	-0.9799	9	0.66056	D	0.02	-10.7583	8.0688	0.30676	0.9099:0.0:0.0901:0.0	rs2501968;rs3209643;rs3823209;rs52825404;rs57701029;rs2501968	266	Q7L2Z9	CENPQ_HUMAN	G	266	ENSP00000337289:D266G	ENSP00000337289:D266G	D	+	2	0	CENPQ	49567937	0.998000	0.40836	0.363000	0.25875	0.417000	0.31264	2.228000	0.42981	1.067000	0.40740	0.524000	0.50904	GAT	A|0.545;C|0.003	.	strong		0.318	CENPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040855.2	NM_018132	
PCDH12	51294	hgsc.bcm.edu	37	5	141329059	141329059	+	Missense_Mutation	SNP	T	T	G	rs61737141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141329059T>G	ENST00000231484.3	-	3	4278	c.3068A>C	c.(3067-3069)gAg>gCg	p.E1023A	AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1023					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)			AGAGAGGTCCTCTTCAGGATC	0.562													T|||	32	0.00638978	0.0242	0.0	5008	,	,		18789	0.0		0.0	False		,,,				2504	0.0				p.E1023A		Atlas-SNP	.											.	PCDH12	133	.	0			c.A3068C						PASS	.	T	ALA/GLU	125,4281	93.0+/-131.7	3,119,2081	159.0	152.0	154.0		3068	3.3	1.0	5	dbSNP_129	154	0,8600		0,0,4300	yes	missense	PCDH12	NM_016580.2	107	3,119,6381	GG,GT,TT		0.0,2.837,0.9611	possibly-damaging	1023/1185	141329059	125,12881	2203	4300	6503	SO:0001583	missense	51294	exon3			AGGTCCTCTTCAG	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.3068A>C	5.37:g.141329059T>G	ENSP00000231484:p.Glu1023Ala	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	94	52	0.553191	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	T	14.87	2.663251	0.47572	0.02837	0.0	ENSG00000113555	ENST00000231484	T	0.52754	0.65	5.8	3.34	0.38264	.	0.387701	0.27739	N	0.018060	T	0.15609	0.0376	L	0.57536	1.79	0.26311	N	0.977823	B	0.29716	0.255	B	0.26614	0.071	T	0.06716	-1.0811	10	0.33141	T	0.24	.	5.3998	0.16288	0.1828:0.0:0.1684:0.6488	.	1023	Q9NPG4	PCD12_HUMAN	A	1023	ENSP00000231484:E1023A	ENSP00000231484:E1023A	E	-	2	0	PCDH12	141309243	0.960000	0.32886	1.000000	0.80357	0.985000	0.73830	1.632000	0.37102	2.224000	0.72417	0.533000	0.62120	GAG	T|0.989;G|0.011	0.011	strong		0.562	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
LRCH3	84859	hgsc.bcm.edu	37	3	197579466	197579466	+	Missense_Mutation	SNP	C	C	T	rs36078463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:197579466C>T	ENST00000425562.2	+	13	1565	c.1565C>T	c.(1564-1566)cCg>cTg	p.P522L	LRCH3_ENST00000536618.1_Missense_Mutation_p.P117L|LRCH3_ENST00000334859.4_Missense_Mutation_p.P522L|LRCH3_ENST00000441090.2_Missense_Mutation_p.P368L|LRCH3_ENST00000414675.2_Missense_Mutation_p.P494L|LRCH3_ENST00000438796.2_Missense_Mutation_p.P522L			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	522			P -> L (in dbSNP:rs36078463).			cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		AAACAGCACCCGCTCCTAGAT	0.383													C|||	527	0.105232	0.115	0.0447	5008	,	,		16705	0.1835		0.0746	False		,,,				2504	0.0859				p.P522L		Atlas-SNP	.											.	LRCH3	96	.	0			c.C1565T						PASS	.	C	LEU/PRO	471,3935	223.3+/-239.8	20,431,1752	155.0	159.0	158.0		1565	2.7	0.0	3	dbSNP_126	158	633,7967	164.3+/-216.7	21,591,3688	yes	missense	LRCH3	NM_032773.2	98	41,1022,5440	TT,TC,CC		7.3605,10.69,8.4884	benign	522/713	197579466	1104,11902	2203	4300	6503	SO:0001583	missense	84859	exon13			AGCACCCGCTCCT	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1565C>T	3.37:g.197579466C>T	ENSP00000393579:p.Pro522Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_032773	B4E0T7|Q96FP9|Q9NT52	Missense_Mutation	SNP	ENST00000425562.2	37		213	0.09752747252747253	49	0.09959349593495935	17	0.04696132596685083	89	0.1555944055944056	58	0.07651715039577836	C	3.629	-0.076024	0.07184	0.1069	0.073605	ENSG00000186001	ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562;ENST00000536618;ENST00000452660;ENST00000433298	T;T;T;T;T;T;T;T	0.46063	2.13;1.5;2.02;2.38;2.15;0.88;0.95;0.96	5.67	2.74	0.32292	.	0.319926	0.28448	N	0.015311	T	0.00073	0.0002	N	0.17082	0.46	0.80722	P	0.0	B;B;B;B;B	0.14438	0.006;0.005;0.01;0.003;0.005	B;B;B;B;B	0.16289	0.004;0.002;0.015;0.003;0.004	T	0.06972	-1.0797	9	0.48119	T	0.1	0.3333	3.8877	0.09105	0.1691:0.5802:0.1634:0.0873	rs36078463	368;494;522;522;522	E9PD99;B4E0T7;Q96II8-2;Q96II8;Q96II8-3	.;.;.;LRCH3_HUMAN;.	L	522;368;494;522;522;117;33;19	ENSP00000399751:P522L;ENSP00000394609:P368L;ENSP00000394965:P494L;ENSP00000334375:P522L;ENSP00000393579:P522L;ENSP00000439083:P117L;ENSP00000395309:P33L;ENSP00000400164:P19L	ENSP00000334375:P522L	P	+	2	0	LRCH3	199063863	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.499000	0.22546	0.740000	0.32651	0.650000	0.86243	CCG	C|0.913;T|0.087	0.087	strong		0.383	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773	
AKAP4	8852	hgsc.bcm.edu	37	X	49957346	49957346	+	Missense_Mutation	SNP	G	G	C	rs12012704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49957346G>C	ENST00000376056.2	-	5	2141	c.1991C>G	c.(1990-1992)gCg>gGg	p.A664G	AKAP4_ENST00000376064.3_Missense_Mutation_p.A664G|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Missense_Mutation_p.A290G|AKAP4_ENST00000358526.2_Missense_Mutation_p.A673G					A kinase (PRKA) anchor protein 4											NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					TTGTTCTTCCGCTTTGTCAGA	0.468													C|||	239	0.0633113	0.1755	0.0086	3775	,	,		17339	0.0		0.001	False		,,,				2504	0.0				p.A673G		Atlas-SNP	.											.	AKAP4	131	.	0			c.C2018G						PASS	.		GLY/ALA,GLY/ALA	758,3077		55,528,120,1049,451	128.0	89.0	102.0		2018,1991	-0.2	0.0	X	dbSNP_120	102	3,6725		0,3,0,2425,1872	yes	missense,missense	AKAP4	NM_003886.2,NM_139289.1	60,60	55,531,120,3474,2323	CC,CG,C,GG,G		0.0446,19.7653,7.2044	benign,benign	673/855,664/846	49957346	761,9802	2203	4300	6503	SO:0001583	missense	8852	exon5			TCTTCCGCTTTGT	AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"""A-kinase anchor proteins"""	374	protein-coding gene	gene with protein product	"""A-kinase anchor protein 82 kDa"", ""testis-specific gene HI"", ""protein kinase A anchoring protein 4"", ""cancer/testis antigen 99"""	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.1991C>G	X.37:g.49957346G>C	ENSP00000365224:p.Ala664Gly	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	185	98	0.52973	NM_003886		Missense_Mutation	SNP	ENST00000376056.2	37	CCDS14330.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.398309	0.00198	0.197653	4.46E-4	ENSG00000147081	ENST00000376056;ENST00000376058;ENST00000358526;ENST00000376064	T;T;T;T	0.07216	3.21;3.21;3.21;3.21	4.02	-0.234	0.13074	A-kinase anchor 110kDa, C-terminal (1);	1.817120	0.03350	N	0.196131	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B;B	0.11235	0.0;0.004	B;B	0.10450	0.0;0.005	T	0.41270	-0.9518	8	.	.	.	.	2.4569	0.04532	0.4695:0.2774:0.1517:0.1014	rs12012704;rs52831575;rs58361299;rs12012704	673;290	Q5JQC9;A6ND82	AKAP4_HUMAN;.	G	664;290;673;664	ENSP00000365224:A664G;ENSP00000365226:A290G;ENSP00000351327:A673G;ENSP00000365232:A664G	.	A	-	2	0	AKAP4	49844086	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.017000	0.03630	-0.823000	0.04301	-1.207000	0.01640	GCG	A|0.000;C|0.063;G|0.936	0.063	strong		0.468	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886	
ZNF257	113835	hgsc.bcm.edu	37	19	22256358	22256358	+	Missense_Mutation	SNP	A	A	G	rs73930397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22256358A>G	ENST00000594947.1	+	3	362	c.218A>G	c.(217-219)aAa>aGa	p.K73R	ZNF257_ENST00000600162.1_Missense_Mutation_p.K73R	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	73	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)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				ATGGTAGCCAAACCCCCAGGT	0.443													A|||	224	0.0447284	0.1634	0.0115	5008	,	,		15865	0.0		0.0	False		,,,				2504	0.0				p.K73R		Atlas-SNP	.											.	ZNF257	156	.	0			c.A218G						PASS	.	A	ARG/LYS	735,3671	295.3+/-283.6	61,613,1529	125.0	136.0	132.0		218	-1.7	0.2	19	dbSNP_130	132	8,8592	6.4+/-24.3	0,8,4292	yes	missense	ZNF257	NM_033468.2	26	61,621,5821	GG,GA,AA		0.093,16.6818,5.7127	benign	73/564	22256358	743,12263	2203	4300	6503	SO:0001583	missense	113835	exon3			TAGCCAAACCCCC	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"""Zinc fingers, C2H2-type"", ""-"""	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.218A>G	19.37:g.22256358A>G	ENSP00000470209:p.Lys73Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_033468	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	87	0.03983516483516483	83	0.16869918699186992	4	0.011049723756906077	0	0.0	0	0.0	A	0.702	-0.790515	0.02884	0.166818	9.3E-4	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	0.86	-1.72	0.08107	Krueppel-associated box (1);	.	.	.	.	T	0.00039	0.0001	N	0.04508	-0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.24297	-1.0164	7	0.30854	T	0.27	.	2.1458	0.03787	0.3751:0.3325:0.2924:0.0	.	73	Q9Y2Q1	ZN257_HUMAN	R	73	.	ENSP00000380312:K73R	K	+	2	0	ZNF257	22048198	0.000000	0.05858	0.249000	0.24280	0.256000	0.26092	-0.441000	0.06879	-1.510000	0.01796	-1.552000	0.00895	AAA	A|0.967;G|0.033	0.033	strong		0.443	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1		
DHX58	79132	hgsc.bcm.edu	37	17	40255812	40255812	+	Missense_Mutation	SNP	C	C	T	rs2074160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40255812C>T	ENST00000251642.3	-	12	1790	c.1568G>A	c.(1567-1569)cGg>cAg	p.R523Q		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	523	Repressor domain.		R -> Q (in dbSNP:rs2074160).		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CTGCAGATCCCGGATCTGGGG	0.612													C|||	685	0.136781	0.3086	0.0231	5008	,	,		18710	0.1667		0.0239	False		,,,				2504	0.0706				p.R523Q		Atlas-SNP	.											.	DHX58	39	.	0			c.G1568A						PASS	.	C	GLN/ARG	1225,3181		167,891,1145	33.0	32.0	32.0		1568	-5.6	0.1	17	dbSNP_96	32	165,8435		2,161,4137	yes	missense	DHX58	NM_024119.2	43	169,1052,5282	TT,TC,CC		1.9186,27.803,10.6874	benign	523/679	40255812	1390,11616	2203	4300	6503	SO:0001583	missense	79132	exon12			AGATCCCGGATCT	BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"""RNA helicase LGP2"""	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.1568G>A	17.37:g.40255812C>T	ENSP00000251642:p.Arg523Gln	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	45	26	0.577778	NM_024119	Q9HAM6	Missense_Mutation	SNP	ENST00000251642.3	37	CCDS11416.1	255	0.11675824175824176	159	0.3231707317073171	6	0.016574585635359115	76	0.13286713286713286	14	0.018469656992084433	C	5.340	0.248132	0.10130	0.27803	0.019186	ENSG00000108771	ENST00000251642	T	0.04551	3.6	5.62	-5.56	0.02529	.	1.612920	0.03016	N	0.150031	T	0.00012	0.0000	N	0.16066	0.365	0.80722	P	0.0	B;B	0.14438	0.006;0.01	B;B	0.06405	0.002;0.002	T	0.48525	-0.9028	9	0.11182	T	0.66	.	7.5574	0.27833	0.134:0.3672:0.0:0.4988	rs2074160;rs52795470;rs2074160	516;523	B7Z455;Q96C10	.;DHX58_HUMAN	Q	523	ENSP00000251642:R523Q	ENSP00000251642:R523Q	R	-	2	0	DHX58	37509338	0.000000	0.05858	0.079000	0.20413	0.553000	0.35397	-2.754000	0.00790	-0.693000	0.05121	-0.749000	0.03505	CGG	C|0.886;T|0.114	0.114	strong		0.612	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119	
IMPA2	3613	hgsc.bcm.edu	37	18	12009913	12009913	+	Missense_Mutation	SNP	G	G	A	rs16976948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:12009913G>A	ENST00000269159.3	+	3	504	c.262G>A	c.(262-264)Gcc>Acc	p.A88T	IMPA2_ENST00000588927.1_5'UTR|IMPA2_ENST00000589238.1_5'UTR|IMPA2_ENST00000588752.1_3'UTR	NM_014214.2	NP_055029.1	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	88			A -> T (in dbSNP:rs16976948).		inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)|stomach(2)|urinary_tract(1)	12					Lithium(DB01356)	GGCTTCTGGGGCCAAGTGTGT	0.562													G|||	89	0.0177716	0.0605	0.0115	5008	,	,		16273	0.0		0.001	False		,,,				2504	0.0				p.A88T		Atlas-SNP	.											.	IMPA2	27	.	0			c.G262A						PASS	.	G	THR/ALA	260,4146	149.2+/-183.4	4,252,1947	123.0	122.0	122.0		262	3.5	1.0	18	dbSNP_123	122	1,8599	1.2+/-3.3	0,1,4299	yes	missense	IMPA2	NM_014214.2	58	4,253,6246	AA,AG,GG		0.0116,5.901,2.0068	benign	88/289	12009913	261,12745	2203	4300	6503	SO:0001583	missense	3613	exon3			TCTGGGGCCAAGT	AF014398	CCDS11855.1	18p11.2	2008-03-18			ENSG00000141401	ENSG00000141401	3.1.3.25		6051	protein-coding gene	gene with protein product		605922				9322233	Standard	NM_014214		Approved		uc002kqp.2	O14732	OTTHUMG00000131693	ENST00000269159.3:c.262G>A	18.37:g.12009913G>A	ENSP00000269159:p.Ala88Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_014214	B0YJ29|Q9UJT3	Missense_Mutation	SNP	ENST00000269159.3	37	CCDS11855.1	39	0.017857142857142856	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	12.73	2.024554	0.35701	0.05901	1.16E-4	ENSG00000141401	ENST00000269159	T	0.52057	0.68	5.48	3.53	0.40419	.	0.385345	0.27181	N	0.020543	T	0.01940	0.0061	N	0.05259	-0.085	0.80722	D	1	B	0.11235	0.004	B	0.12837	0.008	T	0.02115	-1.1211	10	0.34782	T	0.22	-15.8924	11.554	0.50737	0.0:0.0:0.4818:0.5182	rs16976948;rs16976948	88	O14732	IMPA2_HUMAN	T	88	ENSP00000269159:A88T	ENSP00000269159:A88T	A	+	1	0	IMPA2	11999913	1.000000	0.71417	0.997000	0.53966	0.929000	0.56500	4.218000	0.58554	1.274000	0.44362	0.491000	0.48974	GCC	G|0.979;A|0.021	0.021	strong		0.562	IMPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254601.1		
CACNG1	786	hgsc.bcm.edu	37	17	65052343	65052343	+	Missense_Mutation	SNP	C	C	T	rs371885900		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65052343C>T	ENST00000226021.3	+	4	696	c.625C>T	c.(625-627)Cgg>Tgg	p.R209W		NM_000727.3	NP_000718.1	Q06432	CCG1_HUMAN	calcium channel, voltage-dependent, gamma subunit 1	209					muscle contraction (GO:0006936)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transport (GO:0006810)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|large_intestine(2)|lung(2)|prostate(1)|skin(2)	8	all_cancers(12;1.04e-10)|Breast(2;1.45e-16)|all_epithelial(3;4.81e-12)				Diltiazem(DB00343)|Fluspirilene(DB04842)|Ibutilide(DB00308)|Lercanidipine(DB00528)|Magnesium Sulfate(DB00653)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TCGAATGCCCCGGAACCCATG	0.632																																					p.R209W		Atlas-SNP	.											CACNG1,colon,carcinoma,0,1	CACNG1	24	1	0			c.C625T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	127.0	105.0	112.0		625	5.0	1.0	17		112	1,8599	1.2+/-3.3	0,1,4299	no	missense	CACNG1	NM_000727.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	209/223	65052343	1,13005	2203	4300	6503	SO:0001583	missense	786	exon4			ATGCCCCGGAACC	L07738	CCDS11668.1	17q24	2008-05-02				ENSG00000108878		"""Calcium channel subunits"""	1405	protein-coding gene	gene with protein product		114209		CACNLG		8395940	Standard	NM_000727		Approved		uc002jfu.3	Q06432		ENST00000226021.3:c.625C>T	17.37:g.65052343C>T	ENSP00000226021:p.Arg209Trp	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	NM_000727	B2R9N3|Q14D59	Missense_Mutation	SNP	ENST00000226021.3	37	CCDS11668.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.657308	0.67586	0.0	1.16E-4	ENSG00000108878	ENST00000226021	T	0.46819	0.86	5.0	5.0	0.66597	.	0.508381	0.19982	N	0.101758	T	0.48150	0.1484	M	0.70595	2.14	0.29089	N	0.882193	D	0.61697	0.99	B	0.43623	0.425	T	0.53151	-0.8479	10	0.30078	T	0.28	-13.263	12.7164	0.57117	0.1643:0.8357:0.0:0.0	.	209	Q06432	CCG1_HUMAN	W	209	ENSP00000226021:R209W	ENSP00000226021:R209W	R	+	1	2	CACNG1	62482805	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.173000	0.42472	2.482000	0.83794	0.462000	0.41574	CGG	.	.	weak		0.632	CACNG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447039.1		
FAM135B	51059	hgsc.bcm.edu	37	8	139149406	139149406	+	Silent	SNP	G	G	A	rs6577876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	102	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	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	
AKNAD1	254268	hgsc.bcm.edu	37	1	109394564	109394564	+	Silent	SNP	T	T	C	rs17030016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109394564T>C	ENST00000370001.3	-	2	991	c.723A>G	c.(721-723)gcA>gcG	p.A241A	AKNAD1_ENST00000369995.3_Silent_p.A241A|AKNAD1_ENST00000369994.1_Silent_p.A241A|AKNAD1_ENST00000357393.4_Intron	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	241						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						TGCCTGAATTTGCTTTTTCAG	0.388													T|||	383	0.0764776	0.1127	0.0663	5008	,	,		19243	0.0407		0.0537	False		,,,				2504	0.0951				p.A241A		Atlas-SNP	.											.	AKNAD1	83	.	0			c.A723G						PASS	.	T		515,3891	237.4+/-249.2	32,451,1720	154.0	152.0	152.0		723	0.2	0.0	1	dbSNP_123	152	332,8268	116.3+/-176.0	5,322,3973	no	coding-synonymous	AKNAD1	NM_152763.3		37,773,5693	CC,CT,TT		3.8605,11.6886,6.5124		241/837	109394564	847,12159	2203	4300	6503	SO:0001819	synonymous_variant	254268	exon2			TGAATTTGCTTTT	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.723A>G	1.37:g.109394564T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	111	59	0.531532	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Silent	SNP	ENST00000370001.3	37	CCDS791.2																																																																																			T|0.935;C|0.065	0.065	strong		0.388	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324410	39324410	+	Silent	SNP	G	G	A	rs73985507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324410G>A	ENST00000391356.2	-	1	14	c.15C>T	c.(13-15)tgC>tgT	p.C5C		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	5					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)			CAGAGCCACAGCAGGAGCTGA	0.592													A|||	519	0.103634	0.3759	0.0288	5008	,	,		16931	0.0		0.002	False		,,,				2504	0.0				p.C5C		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.C15T						PASS	.	A		1379,2993		223,933,1030	29.0	31.0	30.0		15	-1.4	0.9	17	dbSNP_130	30	5,8573		0,5,4284	no	coding-synonymous	KRTAP4-3	NM_033187.1		223,938,5314	AA,AG,GG		0.0583,31.5416,10.6873		5/196	39324410	1384,11566	2186	4289	6475	SO:0001819	synonymous_variant	85290	exon1			GCCACAGCAGGAG	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.15C>T	17.37:g.39324410G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	211	211	1	NM_033187		Silent	SNP	ENST00000391356.2	37	CCDS42331.1																																																																																			G|0.944;A|0.056	0.056	strong		0.592	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
VCAN	1462	hgsc.bcm.edu	37	5	82835724	82835724	+	Missense_Mutation	SNP	T	T	A	rs160278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82835724T>A	ENST00000265077.3	+	8	7467	c.6902T>A	c.(6901-6903)tTt>tAt	p.F2301Y	VCAN_ENST00000343200.5_Missense_Mutation_p.F1314Y|VCAN-AS1_ENST00000513899.1_RNA|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2301	GAG-beta.		F -> Y (in dbSNP:rs160278).		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)	ATTGAAGACTTTAACAGAATG	0.373													C|||	2346	0.46845	0.5091	0.5231	5008	,	,		21996	0.3919		0.5199	False		,,,				2504	0.4008				p.F2301Y		Atlas-SNP	.											.	VCAN	498	.	0			c.T6902A						PASS	.	C	,TYR/PHE,,TYR/PHE	2200,2206		547,1106,550	103.0	102.0	102.0		,3941,,6902	3.6	0.0	5	dbSNP_79	102	4244,4356		1065,2114,1121	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,22,,22	1612,3220,1671	AA,AT,TT		49.3488,49.9319,49.5464	,benign,,benign	,1314/2410,,2301/3397	82835724	6444,6562	2203	4300	6503	SO:0001583	missense	1462	exon8			AAGACTTTAACAG	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.6902T>A	5.37:g.82835724T>A	ENSP00000265077:p.Phe2301Tyr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	37	0.377551	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	1058	0.48443223443223443	235	0.47764227642276424	192	0.5303867403314917	239	0.4178321678321678	392	0.5171503957783641	C	0.004	-2.279707	0.00254	0.499319	0.493488	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.16597	2.33;2.33	6.07	3.61	0.41365	.	1.149720	0.06303	N	0.701319	T	0.00012	0.0000	N	0.11427	0.14	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44406	-0.9330	9	0.02654	T	1	.	6.6224	0.22810	0.4935:0.1278:0.0:0.3787	rs160278;rs310483;rs568397;rs871868;rs3734095;rs3844744;rs52819818;rs160278	1314;2301	P13611-2;P13611	.;CSPG2_HUMAN	Y	2301;1314	ENSP00000265077:F2301Y;ENSP00000340062:F1314Y	ENSP00000265077:F2301Y	F	+	2	0	VCAN	82871480	0.002000	0.14202	0.001000	0.08648	0.003000	0.03518	0.374000	0.20501	0.527000	0.28560	-1.150000	0.01838	TTT	T|0.507;G|0.000;N|0.000;A|0.493	0.493	strong		0.373	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
CCL4L2	388372	hgsc.bcm.edu	37	17	34641448	34641448	+	Splice_Site	SNP	A	A	G	rs184899362		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34641448A>G	ENST00000394465.2	+	3	508		c.e3-1		TBC1D3C_ENST00000308078.7_Intron|CCL4L2_ENST00000339270.6_Splice_Site|TBC1D3H_ENST00000400684.4_Intron|TBC1D3H_ENST00000535446.1_Intron|TBC1D3C_ENST00000451448.2_Intron|CCL4L2_ENST00000482104.1_3'UTR			Q8NHW4	CC4L_HUMAN	chemokine (C-C motif) ligand 4-like 2						cell chemotaxis (GO:0060326)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)		p.?(1)		endometrium(1)	1		Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTTGTTCTACAGATTCCAAAC	0.522																																					.		Atlas-SNP	.											CCL4L2,NS,carcinoma,0,1	.	.	1	1	Unknown(1)	endometrium(1)	c.192-2A>G						scavenged	.						219.0	152.0	175.0					17																	34641448		2159	4154	6313	SO:0001630	splice_region_variant	9560	exon3			TTCTACAGATTCC			17q12	2005-08-09			ENSG00000197262			"""Chemokine ligands"""	24066	protein-coding gene	gene with protein product		603782				15028295	Standard	NM_001291468		Approved		uc010cuj.3	Q8NHW4	OTTHUMG00000133066	ENST00000394465.2:c.192-1A>G	17.37:g.34641448A>G		Somatic	871	0	0		WXS	Illumina HiSeq	Phase_I	334	28	0.0838323	NM_001001435	B2RUZ3|B7ZMA8|Q50EM1|Q50EM2|Q50EM3|Q50EM4|Q50EM5|Q50EM6|Q50EM7|Q50EM8|Q569J2|Q6NSB0	Splice_Site	SNP	ENST00000394465.2	37	CCDS11311.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	N	11.83	1.756201	0.31137	.	.	ENSG00000197262	ENST00000394465;ENST00000339270	.	.	.	3.1	3.1	0.35709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.8193	0.29278	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCL4L2	31665561	1.000000	0.71417	0.994000	0.49952	0.682000	0.39822	4.719000	0.61937	1.074000	0.40909	0.344000	0.21773	.	G|1.000;|0.000	1.000	weak		0.522	CCL4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256699.1	NM_207007	Intron
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28219661	28219661	+	Missense_Mutation	SNP	G	G	A	rs9986596	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28219661G>A	ENST00000377294.2	-	1	341	c.98C>T	c.(97-99)tCc>tTc	p.S33F	ZKSCAN4_ENST00000423974.2_Intron	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	33			S -> F (in dbSNP:rs9986596).		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)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CGTCAAGGCGGAGGCTTCCTC	0.667													G|||	698	0.139377	0.2179	0.1225	5008	,	,		14031	0.128		0.1143	False		,,,				2504	0.0828				p.S33F		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.C98T						PASS	.	G	PHE/SER	953,3425		113,727,1349	44.0	49.0	47.0		98	-0.4	0.0	6	dbSNP_119	47	1180,7360		100,980,3190	yes	missense	ZKSCAN4	NM_019110.3	155	213,1707,4539	AA,AG,GG		13.8173,21.7679,16.5118	benign	33/546	28219661	2133,10785	2189	4270	6459	SO:0001583	missense	387032	exon1			AAGGCGGAGGCTT	AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13854	protein-coding gene	gene with protein product		611643	"""zinc finger protein 307"", ""zinc finger protein 427"""	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.98C>T	6.37:g.28219661G>A	ENSP00000366509:p.Ser33Phe	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_019110	B2RE32|Q5U7L4	Missense_Mutation	SNP	ENST00000377294.2	37	CCDS4647.1	310	0.14194139194139194	97	0.19715447154471544	44	0.12154696132596685	79	0.1381118881118881	90	0.11873350923482849	G	10.35	1.325696	0.24080	0.217679	0.138173	ENSG00000187626	ENST00000377294	T	0.05786	3.39	4.61	-0.381	0.12485	.	.	.	.	.	T	0.00875	0.0029	N	0.19112	0.55	0.58432	P	4.000000000004E-6	B	0.12630	0.006	B	0.10450	0.005	T	0.47799	-0.9089	8	0.10111	T	0.7	.	3.8039	0.08768	0.0885:0.1234:0.4709:0.3172	rs9986596	33	Q969J2	ZKSC4_HUMAN	F	33	ENSP00000366509:S33F	ENSP00000366509:S33F	S	-	2	0	ZKSCAN4	28327640	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	0.730000	0.26043	0.092000	0.17331	0.563000	0.77884	TCC	G|0.842;A|0.158	0.158	strong		0.667	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110	
ALOX5AP	241	hgsc.bcm.edu	37	13	31309719	31309719	+	5'UTR	SNP	C	C	T	rs17245407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:31309719C>T	ENST00000380490.3	+	0	75					NM_001204406.1|NM_001629.3	NP_001191335.1|NP_001620.2	P20292	AL5AP_HUMAN	arachidonate 5-lipoxygenase-activating protein						arachidonic acid metabolic process (GO:0019369)|cellular response to calcium ion (GO:0071277)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|positive regulation of acute inflammatory response (GO:0002675)|protein homotrimerization (GO:0070207)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	arachidonic acid binding (GO:0050544)|enzyme activator activity (GO:0008047)|protein N-terminus binding (GO:0047485)			endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)	4		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0187)|Epithelial(112;0.0803)|OV - Ovarian serous cystadenocarcinoma(117;0.0864)		CAGAGCAGTCCTCTCTGGGGA	0.517													C|||	146	0.0291534	0.1082	0.0043	5008	,	,		17333	0.0		0.0	False		,,,				2504	0.0				p.L50F		Atlas-SNP	.											.	ALOX5AP	12	.	0			c.C148T						PASS	.	C	PHE/LEU,	437,3969	211.2+/-231.4	20,397,1786	126.0	100.0	109.0		148,	1.0	0.0	13	dbSNP_123	109	1,8599	1.2+/-3.3	0,1,4299	yes	missense,utr-5	ALOX5AP	NM_001204406.1,NM_001629.3	22,	20,398,6085	TT,TC,CC		0.0116,9.9183,3.3677	,	50/219,	31309719	438,12568	2203	4300	6503	SO:0001623	5_prime_UTR_variant	241	exon2			GCAGTCCTCTCTG	AH001462	CCDS9337.1, CCDS73558.1	13q12	2008-07-18			ENSG00000132965	ENSG00000132965			436	protein-coding gene	gene with protein product	"""five-lipoxygenase activating protein"", ""MK-886-binding protein"""	603700				1673682, 10036194	Standard	NM_001629		Approved	FLAP	uc010tdr.2	P20292	OTTHUMG00000016677	ENST00000380490.3:c.-24C>T	13.37:g.31309719C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	127	75	0.590551	NM_001204406	Q5VV04	Missense_Mutation	SNP	ENST00000380490.3	37	CCDS9337.1																																																																																			C|0.968;T|0.032	0.032	strong		0.517	ALOX5AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044372.1	NM_001629	
ACAD8	27034	hgsc.bcm.edu	37	11	134131033	134131033	+	Silent	SNP	C	C	T	rs36115758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134131033C>T	ENST00000281182.4	+	7	907	c.801C>T	c.(799-801)ctC>ctT	p.L267L	ACAD8_ENST00000537423.1_Silent_p.L190L|ACAD8_ENST00000374752.4_Silent_p.L140L|ACAD8_ENST00000543332.1_Silent_p.L169L|ACAD8_ENST00000524547.1_3'UTR	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	267					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	AGGGCTTCCTCATTGCCGTGA	0.597													C|||	41	0.0081869	0.0287	0.0043	5008	,	,		18819	0.0		0.0	False		,,,				2504	0.0				p.L267L	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.C801T						PASS	.	C		84,4318	71.4+/-109.4	1,82,2118	68.0	65.0	66.0		801	0.9	1.0	11	dbSNP_126	66	0,8594		0,0,4297	no	coding-synonymous	ACAD8	NM_014384.2		1,82,6415	TT,TC,CC		0.0,1.9082,0.6464		267/416	134131033	84,12912	2201	4297	6498	SO:0001819	synonymous_variant	27034	exon7			CTTCCTCATTGCC	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"""acyl-Coenzyme A dehydrogenase family, member 8"""			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.801C>T	11.37:g.134131033C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Silent	SNP	ENST00000281182.4	37	CCDS8498.1																																																																																			C|0.993;T|0.007	0.007	strong		0.597	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384	
OR2AE1	81392	hgsc.bcm.edu	37	7	99474427	99474427	+	Missense_Mutation	SNP	A	A	G	rs2572023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99474427A>G	ENST00000316368.2	-	1	253	c.230T>C	c.(229-231)aTc>aCc	p.I77T		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	77			I -> T (in dbSNP:rs2572023).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					CTTCAGGATGATTGTGGAGAC	0.483													G|||	2781	0.555312	0.9107	0.4251	5008	,	,		23726	0.2907		0.4851	False		,,,				2504	0.5123				p.I77T		Atlas-SNP	.											.	OR2AE1	32	.	0			c.T230C						PASS	.	G	THR/ILE	3687,719	296.7+/-284.4	1546,595,62	114.0	97.0	103.0		230	0.8	0.1	7	dbSNP_100	103	4489,4111	562.2+/-387.9	1165,2159,976	yes	missense	OR2AE1	NM_001005276.1	89	2711,2754,1038	GG,GA,AA		47.8023,16.3187,37.1367	benign	77/324	99474427	8176,4830	2203	4300	6503	SO:0001583	missense	81392	exon1			AGGATGATTGTGG	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"""GPCR / Class A : Olfactory receptors"""	15087	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily AE, member 2"""	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.230T>C	7.37:g.99474427A>G	ENSP00000313936:p.Ile77Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_001005276	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	1152	0.5274725274725275	455	0.9247967479674797	171	0.4723756906077348	148	0.25874125874125875	378	0.49868073878627966	G	0.001	-3.109683	0.00032	0.836813	0.521977	ENSG00000244623	ENST00000316368	T	0.01139	5.28	3.63	0.807	0.18714	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41396	N	0.000891	T	0.00012	0.0000	N	0.04669	-0.19	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28554	-1.0040	9	0.02654	T	1	.	7.1689	0.25706	0.5367:0.0:0.4633:0.0	rs2572023;rs17277317;rs58768647;rs2572023	77	Q8NHA4	O2AE1_HUMAN	T	77	ENSP00000313936:I77T	ENSP00000313936:I77T	I	-	2	0	OR2AE1	99312363	0.000000	0.05858	0.126000	0.21872	0.014000	0.08584	-0.121000	0.10643	-0.055000	0.13244	-0.299000	0.09455	ATC	G|0.588;N|0.000	0.588	strong		0.483	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1		
RTN4RL1	146760	hgsc.bcm.edu	37	17	1840079	1840079	+	Missense_Mutation	SNP	C	C	T	rs143202933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1840079C>T	ENST00000331238.6	-	2	1516	c.1037G>A	c.(1036-1038)cGg>cAg	p.R346Q		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1											breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						GTGGCCGGGCCGGGGGCCGTG	0.687													C|||	14	0.00279553	0.0	0.0014	5008	,	,		13824	0.0		0.007	False		,,,				2504	0.0061				p.R346Q	GBM(68;949 1139 14865 32798 38342)	Atlas-SNP	.											.	RTN4RL1	21	.	0			c.G1037A						PASS	.	C	GLN/ARG	2,3884		0,2,1941	16.0	19.0	18.0		1037	4.2	0.9	17	dbSNP_134	18	25,8203		0,25,4089	yes	missense	RTN4RL1	NM_178568.2	43	0,27,6030	TT,TC,CC		0.3038,0.0515,0.2229	benign	346/442	1840079	27,12087	1943	4114	6057	SO:0001583	missense	146760	exon2			CCGGGCCGGGGGC	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.1037G>A	17.37:g.1840079C>T	ENSP00000330631:p.Arg346Gln	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	158	71	0.449367	NM_178568		Missense_Mutation	SNP	ENST00000331238.6	37	CCDS45569.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	6.698	0.497343	0.12762	5.15E-4	0.003038	ENSG00000185924	ENST00000331238	T	0.61980	0.06	4.17	4.17	0.49024	.	0.000000	0.33670	N	0.004666	T	0.57989	0.2091	L	0.54323	1.7	0.44042	D	0.996779	D	0.63880	0.993	P	0.53146	0.719	T	0.60601	-0.7231	10	0.12103	T	0.63	.	16.5187	0.84308	0.0:1.0:0.0:0.0	.	346	Q86UN2	R4RL1_HUMAN	Q	346	ENSP00000330631:R346Q	ENSP00000330631:R346Q	R	-	2	0	RTN4RL1	1786829	0.997000	0.39634	0.889000	0.34880	0.009000	0.06853	2.063000	0.41423	1.883000	0.54544	0.549000	0.68633	CGG	C|0.997;T|0.003	0.003	strong		0.687	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	NM_178568	
OBSCN	84033	hgsc.bcm.edu	37	1	228526011	228526011	+	Silent	SNP	C	C	T	rs11577699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228526011C>T	ENST00000422127.1	+	68	17066	c.17022C>T	c.(17020-17022)gcC>gcT	p.A5674A	OBSCN_ENST00000284548.11_Silent_p.A5674A|OBSCN_ENST00000570156.2_Silent_p.A6631A|OBSCN_ENST00000366709.4_Silent_p.A2793A|OBSCN_ENST00000366707.4_Silent_p.A3308A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5674					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)				AGTGGGGGGCCGCTGAGGCCC	0.642													C|||	589	0.117612	0.1006	0.1916	5008	,	,		16460	0.1091		0.1372	False		,,,				2504	0.0767				p.A6631A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C19893T						PASS	.	C	,	525,3273		33,459,1407	20.0	26.0	24.0		17022,17022	-2.2	0.0	1	dbSNP_120	24	1296,6918		99,1098,2910	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	132,1557,4317	TT,TC,CC		15.7779,13.8231,15.1598	,	5674/7969,5674/6621	228526011	1821,10191	1899	4107	6006	SO:0001819	synonymous_variant	84033	exon79			GGGGGCCGCTGAG	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.17022C>T	1.37:g.228526011C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	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	273	0.125	40	0.08130081300813008	71	0.19613259668508287	54	0.0944055944055944	108	0.1424802110817942	C	4.625	0.116119	0.08831	0.138231	0.157779	ENSG00000154358	ENST00000441106	.	.	.	4.59	-2.15	0.07102	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.53688	P	2.4000000000024002E-5	.	.	.	.	.	.	T	0.24083	-1.0170	3	.	.	.	.	5.2594	0.15565	0.3755:0.2927:0.0:0.3318	rs11577699	.	.	.	C	290	.	.	R	+	1	0	OBSCN	226592634	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.668000	0.05268	-1.045000	0.03250	-1.579000	0.00862	CGC	C|0.879;T|0.121	0.121	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OR2H2	7932	hgsc.bcm.edu	37	6	29555778	29555778	+	Silent	SNP	A	A	G	rs2235698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	265	128	0.483019	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		
OR5B2	390190	hgsc.bcm.edu	37	11	58190112	58190112	+	Missense_Mutation	SNP	A	A	G	rs10466659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	103	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	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	
SLC4A4	8671	hgsc.bcm.edu	37	4	72338467	72338467	+	Silent	SNP	C	C	T	rs35169468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:72338467C>T	ENST00000264485.5	+	14	1800	c.1683C>T	c.(1681-1683)tcC>tcT	p.S561S	SLC4A4_ENST00000512686.1_Silent_p.S517S|SLC4A4_ENST00000351898.6_Silent_p.S561S|SLC4A4_ENST00000340595.3_Silent_p.S517S|SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000425175.1_Silent_p.S561S	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	561					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	GCCTGTGGTCCGCCTTCCTAT	0.433													C|||	81	0.0161741	0.0446	0.0072	5008	,	,		17363	0.0		0.0	False		,,,				2504	0.0174				p.S561S		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C1683T						PASS	.	C	,,	161,4245	110.8+/-149.0	2,157,2044	175.0	173.0	174.0		1683,1683,1551	-3.7	1.0	4	dbSNP_126	174	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A4	NM_001098484.2,NM_001134742.1,NM_003759.3	,,	2,159,6342	TT,TC,CC		0.0233,3.6541,1.2533	,,	561/1080,561/1095,517/1036	72338467	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	8671	exon14			GTGGTCCGCCTTC	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.1683C>T	4.37:g.72338467C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	124	52	0.419355	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Silent	SNP	ENST00000264485.5	37	CCDS43236.1																																																																																			C|0.988;T|0.012	0.012	strong		0.433	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
CDH23	64072	hgsc.bcm.edu	37	10	73466709	73466709	+	Silent	SNP	T	T	C	rs10823829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73466709T>C	ENST00000224721.6	+	25	3029	c.3024T>C	c.(3022-3024)tcT>tcC	p.S1008S	CDH23_ENST00000299366.7_Silent_p.S1048S	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1003	Cadherin 10. {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						ACAATGTGTCTGTGTCCGAGG	0.637													C|||	1039	0.207468	0.4062	0.1513	5008	,	,		19342	0.2698		0.0348	False		,,,				2504	0.092				p.S1003S		Atlas-SNP	.											.	CDH23	365	.	0			c.T3009C						PASS	.	C	,,	1436,2890		225,986,952	43.0	54.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3009,3009,3009	-4.1	0.7	10	dbSNP_120	51	277,8211		5,267,3972	no	coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_022124.5	,,	230,1253,4924	CC,CT,TT		3.2634,33.1946,13.3682	,,	1003/1382,1003/1062,1003/3355	73466709	1713,11101	2163	4244	6407	SO:0001819	synonymous_variant	64072	exon25			TGTGTCTGTGTCC	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.3024T>C	10.37:g.73466709T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	144	142	0.986111	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				T|0.793;C|0.207	0.207	strong		0.637	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
SEMA4A	64218	hgsc.bcm.edu	37	1	156146218	156146218	+	Silent	SNP	C	C	T	rs12401573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156146218C>T	ENST00000368285.3	+	15	1983	c.1716C>T	c.(1714-1716)ccC>ccT	p.P572P	SEMA4A_ENST00000368282.1_Silent_p.P572P|SEMA4A_ENST00000355014.2_Silent_p.P572P|SEMA4A_ENST00000368284.1_Silent_p.P440P|SEMA4A_ENST00000368286.2_Silent_p.P440P	NM_001193300.1|NM_022367.3	NP_001180229.1|NP_071762.2	Q9H3S1	SEM4A_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	572					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|regulation of cell shape (GO:0008360)|regulation of endothelial cell migration (GO:0010594)|semaphorin-plexin signaling pathway (GO:0071526)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|ovary(2)|skin(2)	5	Hepatocellular(266;0.158)					TGGCTGTCCCCAACTCCATCC	0.522													c|||	2158	0.430911	0.3949	0.5231	5008	,	,		17757	0.2321		0.6044	False		,,,				2504	0.4407				p.P572P		Atlas-SNP	.											.	SEMA4A	75	.	0			c.C1716T						PASS	.	T	,,,	1860,2546	538.7+/-375.1	401,1058,744	51.0	51.0	51.0		1716,1716,1320,1716	1.9	1.0	1	dbSNP_120	51	5056,3544	629.7+/-398.3	1488,2080,732	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEMA4A	NM_001193300.1,NM_001193301.1,NM_001193302.1,NM_022367.3	,,,	1889,3138,1476	TT,TC,CC		41.2093,42.2152,46.8245	,,,	572/762,572/762,440/630,572/762	156146218	6916,6090	2203	4300	6503	SO:0001819	synonymous_variant	64218	exon15			TGTCCCCAACTCC	AK022416	CCDS1132.1, CCDS53378.1	1q22	2014-01-28			ENSG00000196189	ENSG00000196189		"""Semaphorins"""	10729	protein-coding gene	gene with protein product		607292		SEMAB		7748561	Standard	NM_022367		Approved	SemB, FLJ12287, CORD10	uc009wrq.3	Q9H3S1	OTTHUMG00000014042	ENST00000368285.3:c.1716C>T	1.37:g.156146218C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_001193300	B2RDH8|B3KR76|Q5TCI5|Q5TCJ6|Q8WUA9	Silent	SNP	ENST00000368285.3	37	CCDS1132.1																																																																																			C|0.508;T|0.492	0.492	strong		0.522	SEMA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039484.2	NM_022367	
OR10G8	219869	hgsc.bcm.edu	37	11	123900916	123900916	+	Missense_Mutation	SNP	C	C	T	rs75240316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123900916C>T	ENST00000431524.1	+	1	620	c.587C>T	c.(586-588)aCt>aTt	p.T196I		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	196						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T196I(1)		breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		GCCATAGAGACTGTCATTTTT	0.527													T|||	357	0.0712859	0.0514	0.1427	5008	,	,		22238	0.1448		0.007	False		,,,				2504	0.0378				p.T196I		Atlas-SNP	.											OR10G8,NS,carcinoma,-1,2	OR10G8	132	2	1	Substitution - Missense(1)	stomach(1)	c.C587T						PASS	.	T	ILE/THR	192,4210	808.3+/-415.9	4,184,2013	208.0	183.0	191.0		587	1.6	0.7	11	dbSNP_131	191	24,8574	818.2+/-406.9	0,24,4275	yes	missense	OR10G8	NM_001004464.1	89	4,208,6288	TT,TC,CC		0.2791,4.3617,1.6615	benign	196/312	123900916	216,12784	2201	4299	6500	SO:0001583	missense	219869	exon1			TAGAGACTGTCAT	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"""GPCR / Class A : Olfactory receptors"""	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.587C>T	11.37:g.123900916C>T	ENSP00000389072:p.Thr196Ile	Somatic	416	0	0		WXS	Illumina HiSeq	Phase_I	410	211	0.514634	NM_001004464	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	174	0.07967032967032966	25	0.0508130081300813	60	0.16574585635359115	83	0.1451048951048951	6	0.0079155672823219	T	0.591	-0.833010	0.02713	0.043617	0.002791	ENSG00000234560	ENST00000431524	T	0.00039	8.85	2.91	1.62	0.23740	GPCR, rhodopsin-like superfamily (1);	0.682035	0.13235	N	0.403307	T	0.00012	0.0000	N	0.11023	0.085	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.00288	-1.1845	9	0.29301	T	0.29	.	4.9639	0.14080	0.1614:0.1026:0.0:0.736	.	196	Q8NGN5	O10G8_HUMAN	I	196	ENSP00000389072:T196I	ENSP00000389072:T196I	T	+	2	0	OR10G8	123406126	0.000000	0.05858	0.658000	0.29665	0.004000	0.04260	0.882000	0.28186	0.328000	0.23435	-0.381000	0.06696	ACT	C|0.966;T|0.034	0.034	strong		0.527	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464	
NRF1	4899	hgsc.bcm.edu	37	7	129297332	129297332	+	Silent	SNP	T	T	G	rs1882094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:129297332T>G	ENST00000393232.1	+	2	258	c.141T>G	c.(139-141)tcT>tcG	p.S47S	NRF1_ENST00000311967.2_Silent_p.S47S|NRF1_ENST00000393231.3_Silent_p.S47S|NRF1_ENST00000539636.1_5'UTR|NRF1_ENST00000353868.4_Silent_p.S47S|NRF1_ENST00000223190.4_Silent_p.S47S|NRF1_ENST00000393230.2_Silent_p.S47S	NM_005011.3	NP_005002.3	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	47	Asp/Glu-rich (acidic).|Dimerization.				cellular lipid metabolic process (GO:0044255)|generation of precursor metabolites and energy (GO:0006091)|mitochondrion organization (GO:0007005)|organ regeneration (GO:0031100)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	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(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	24						CGCCTTCTTCTCCCGAGGACA	0.512																																					p.S47S		Atlas-SNP	.											NRF1,NS,adenoma,0,1	NRF1	40	1	0			c.T141G						PASS	.	T	,	2992,1414	686.2+/-404.7	1016,960,227	127.0	108.0	114.0		141,141	-0.5	1.0	7	dbSNP_92	114	2533,6067	412.5+/-350.8	383,1767,2150	no	coding-synonymous,coding-synonymous	NRF1	NM_001040110.1,NM_005011.3	,	1399,2727,2377	GG,GT,TT		29.4535,32.0926,42.4804	,	47/504,47/504	129297332	5525,7481	2203	4300	6503	SO:0001819	synonymous_variant	4899	exon2			TTCTTCTCCCGAG	L22454	CCDS5813.2	7q32	2008-07-18			ENSG00000106459	ENSG00000106459			7996	protein-coding gene	gene with protein product	"""alpha palindromic-binding protein"""	600879				2584221	Standard	NM_005011		Approved	EWG, ALPHA-PAL	uc003voz.3	Q16656	OTTHUMG00000143736	ENST00000393232.1:c.141T>G	7.37:g.129297332T>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_005011	A8K4C6|B4DDV6|Q15305|Q96AN2	Silent	SNP	ENST00000393232.1	37	CCDS5813.2																																																																																			T|0.531;G|0.469	0.469	strong		0.512	NRF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289813.1	NM_001040110	
AKNAD1	254268	hgsc.bcm.edu	37	1	109363232	109363232	+	Silent	SNP	T	T	C	rs1333130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109363232T>C	ENST00000370001.3	-	14	2452	c.2184A>G	c.(2182-2184)aaA>aaG	p.K728K	AKNAD1_ENST00000477908.1_5'Flank	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	728						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						AACAGATCCGTTTGGGTTTTA	0.328													T|||	1935	0.386382	0.2617	0.3919	5008	,	,		5833	0.6974		0.2565	False		,,,				2504	0.364				p.K728K		Atlas-SNP	.											.	AKNAD1	83	.	0			c.A2184G						PASS	.	T		1216,3190	414.6+/-336.9	178,860,1165	89.0	93.0	92.0		2184	2.9	0.0	1	dbSNP_88	92	1983,6617	345.0+/-325.6	220,1543,2537	no	coding-synonymous	AKNAD1	NM_152763.3		398,2403,3702	CC,CT,TT		23.0581,27.5987,24.5963		728/837	109363232	3199,9807	2203	4300	6503	SO:0001819	synonymous_variant	254268	exon14			GATCCGTTTGGGT	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.2184A>G	1.37:g.109363232T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Silent	SNP	ENST00000370001.3	37	CCDS791.2																																																																																			T|0.694;C|0.306	0.306	strong		0.328	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
ADAM33	80332	hgsc.bcm.edu	37	20	3650234	3650234	+	Missense_Mutation	SNP	A	A	G	rs2280091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3650234A>G	ENST00000356518.2	-	20	2532	c.2291T>C	c.(2290-2292)aTg>aCg	p.M764T	ADAM33_ENST00000379861.4_Missense_Mutation_p.M764T|ADAM33_ENST00000350009.2_Missense_Mutation_p.M738T|ADAM33_ENST00000466620.1_5'UTR	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	764			M -> T (in dbSNP:rs2280091). {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						GCCCAACTCCATGGGGTGAAC	0.647													A|||	672	0.134185	0.1354	0.0836	5008	,	,		15976	0.12		0.1421	False		,,,				2504	0.1748				p.M764T		Atlas-SNP	.											.	ADAM33	76	.	0			c.T2291C						PASS	.	A	THR/MET,THR/MET	595,3809		38,519,1645	21.0	21.0	21.0		2291,2213	1.2	0.0	20	dbSNP_100	21	1146,7446		83,980,3233	yes	missense,missense	ADAM33	NM_025220.2,NM_153202.1	81,81	121,1499,4878	GG,GA,AA		13.338,13.5104,13.3964	benign,benign	764/814,738/788	3650234	1741,11255	2202	4296	6498	SO:0001583	missense	80332	exon20			AACTCCATGGGGT	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.2291T>C	20.37:g.3650234A>G	ENSP00000348912:p.Met764Thr	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	141	71	0.503546	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Missense_Mutation	SNP	ENST00000356518.2	37	CCDS13058.1	310	0.14194139194139194	93	0.18902439024390244	38	0.10497237569060773	66	0.11538461538461539	113	0.14907651715039577	A	5.802	0.332217	0.10956	0.135104	0.13338	ENSG00000149451	ENST00000356518;ENST00000379861;ENST00000350009;ENST00000439201	T;T;T	0.01438	4.9;4.89;4.92	3.57	1.16	0.20824	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B;B;P	0.40083	0.131;0.081;0.081;0.702	B;B;B;B	0.34180	0.033;0.015;0.015;0.177	T	0.43829	-0.9367	8	0.14656	T	0.56	.	5.1534	0.15021	0.7179:0.0:0.2821:0.0	rs2280091;rs17548865;rs2280091	738;764;764;644	Q9BZ11-2;Q9BZ11;A2A2L3;Q08AM2	.;ADA33_HUMAN;.;.	T	764;764;738;644	ENSP00000348912:M764T;ENSP00000369190:M764T;ENSP00000322550:M738T	ENSP00000322550:M738T	M	-	2	0	ADAM33	3598234	0.001000	0.12720	0.001000	0.08648	0.007000	0.05969	0.812000	0.27211	0.209000	0.20645	-0.366000	0.07423	ATG	A|0.871;G|0.129	0.129	strong		0.647	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220	
LUZP1	7798	hgsc.bcm.edu	37	1	23419806	23419806	+	Missense_Mutation	SNP	A	A	C	rs12091554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23419806A>C	ENST00000302291.4	-	4	1750	c.949T>G	c.(949-951)Tcc>Gcc	p.S317A	LUZP1_ENST00000418342.1_Missense_Mutation_p.S317A|LUZP1_ENST00000314174.5_Missense_Mutation_p.S317A|LUZP1_ENST00000374623.3_Missense_Mutation_p.S317A			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	317			S -> A (in dbSNP:rs12091554).		artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		TTATTTTTGGACTTCATTTTC	0.338													C|||	242	0.0483227	0.1702	0.0245	5008	,	,		21716	0.0		0.0	False		,,,				2504	0.0				p.S317A		Atlas-SNP	.											.	LUZP1	83	.	0			c.T949G						PASS	.	C	ALA/SER,ALA/SER	637,3769	765.9+/-413.4	65,507,1631	164.0	156.0	159.0		949,949	5.2	1.0	1	dbSNP_120	159	12,8588	818.3+/-406.9	0,12,4288	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	99,99	65,519,5919	CC,CA,AA		0.1395,14.4576,4.99	benign,benign	317/1077,317/1077	23419806	649,12357	2203	4300	6503	SO:0001583	missense	7798	exon4			TTTTGGACTTCAT	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.949T>G	1.37:g.23419806A>C	ENSP00000303758:p.Ser317Ala	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	169	79	0.467456	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	82	0.037545787545787544	73	0.1483739837398374	9	0.024861878453038673	0	0.0	0	0.0	C	1.368	-0.586747	0.03827	0.144576	0.001395	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.12361	2.92;2.92;2.92;2.69	6.08	5.16	0.70880	.	0.000000	0.48286	N	0.000191	T	0.00039	0.0001	N	0.00729	-1.24	0.47065	P	6.960000000000299E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.34453	-0.9828	9	0.11485	T	0.65	.	10.4106	0.44291	0.1361:0.7953:0.0:0.0686	rs12091554;rs52806883;rs12091554	317;317	Q86V48-2;Q86V48	.;LUZP1_HUMAN	A	317	ENSP00000393460:S317A;ENSP00000363752:S317A;ENSP00000303758:S317A;ENSP00000313705:S317A	ENSP00000303758:S317A	S	-	1	0	LUZP1	23292393	1.000000	0.71417	1.000000	0.80357	0.771000	0.43674	3.887000	0.56197	1.603000	0.50134	-0.121000	0.15023	TCC	A|0.952;C|0.048	0.048	strong		0.338	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631	
MNT	4335	hgsc.bcm.edu	37	17	2290222	2290222	+	Silent	SNP	G	G	A	rs61733100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2290222G>A	ENST00000174618.4	-	6	2127	c.1722C>T	c.(1720-1722)ttC>ttT	p.F574F	MNT_ENST00000575374.1_5'Flank|RP1-59D14.1_ENST00000571775.1_RNA	NM_020310.2	NP_064706.1	Q99583	MNT_HUMAN	MAX network transcriptional repressor	574					cell aging (GO:0007569)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cell cycle (GO:0051726)|transcription from RNA polymerase II promoter (GO:0006366)	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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			endometrium(4)|large_intestine(5)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	12				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		TGCTGACTGGGAAGGAGGGCA	0.662													G|||	169	0.033746	0.0613	0.0346	5008	,	,		13082	0.0		0.0527	False		,,,				2504	0.0112				p.F574F		Atlas-SNP	.											.	MNT	35	.	0			c.C1722T						PASS	.	G		251,4137		8,235,1951	26.0	21.0	23.0		1722	2.9	1.0	17	dbSNP_129	23	386,8210		4,378,3916	no	coding-synonymous	MNT	NM_020310.2		12,613,5867	AA,AG,GG		4.4905,5.7201,4.906		574/583	2290222	637,12347	2194	4298	6492	SO:0001819	synonymous_variant	4335	exon6			GACTGGGAAGGAG	Y13444	CCDS11018.1	17p13.3	2013-11-15	2013-11-15		ENSG00000070444	ENSG00000070444		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	7188	protein-coding gene	gene with protein product	"""myc antagonist"", ""Max-interacting protein"""	603039	"""MAX binding protein"", ""MNT, MAX dimerization protein"""			9598315	Standard	NM_020310		Approved	ROX, MXD6, MAD6, bHLHd3	uc002fur.3	Q99583	OTTHUMG00000090603	ENST00000174618.4:c.1722C>T	17.37:g.2290222G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	163	95	0.582822	NM_020310	A8K6D1|D3DTI7|Q1ED38	Silent	SNP	ENST00000174618.4	37	CCDS11018.1																																																																																			G|0.953;A|0.047	0.047	strong		0.662	MNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207158.1	NM_020310	
MYO9B	4650	hgsc.bcm.edu	37	19	17312992	17312992	+	Silent	SNP	C	C	T	rs2305765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17312992C>T	ENST00000594824.1	+	28	4863	c.4716C>T	c.(4714-4716)gtC>gtT	p.V1572V	MYO9B_ENST00000595618.1_Silent_p.V1572V|MYO9B_ENST00000397274.2_Silent_p.V1572V			Q13459	MYO9B_HUMAN	myosin IXB	1572	Tail.				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						ACCAGATCGTCGTCAGCAACC	0.577													C|||	3007	0.600439	0.5991	0.6729	5008	,	,		21436	0.746		0.3897	False		,,,				2504	0.6176				p.V1572V		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,+2,2	MYO9B	264	2	0			c.C4716T						PASS	.	C	,	2172,1850		592,988,431	50.0	53.0	52.0		4716,4716	-9.0	0.7	19	dbSNP_100	52	3313,5069		672,1969,1550	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	1264,2957,1981	TT,TC,CC		39.5252,45.997,44.2196	,	1572/2023,1572/2158	17312992	5485,6919	2011	4191	6202	SO:0001819	synonymous_variant	4650	exon28			GATCGTCGTCAGC		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.4716C>T	19.37:g.17312992C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				C|0.436;T|0.564	0.564	strong		0.577	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
PCSK5	5125	hgsc.bcm.edu	37	9	78942956	78942956	+	Silent	SNP	A	A	G	rs2259969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:78942956A>G	ENST00000545128.1	+	32	4828	c.4290A>G	c.(4288-4290)tcA>tcG	p.S1430S		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1430	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						CCTGCTCATCATCTGGGACCT	0.607													G|||	2566	0.51238	0.7156	0.451	5008	,	,		18048	0.2123		0.6024	False		,,,				2504	0.498				p.S1430S		Atlas-SNP	.											.	PCSK5	329	.	0			c.A4290G						PASS	.	G		1177,575		406,365,105	394.0	337.0	355.0		4290	-10.4	0.0	9	dbSNP_100	355	2349,1633		705,939,347	no	coding-synonymous	PCSK5	NM_001190482.1		1111,1304,452	GG,GA,AA		41.0095,32.8196,38.5072		1430/1861	78942956	3526,2208	876	1991	2867	SO:0001819	synonymous_variant	5125	exon32			CTCATCATCTGGG		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.4290A>G	9.37:g.78942956A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	168	118	0.702381	NM_001190482	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			A|0.492;G|0.508	0.508	strong		0.607	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SH3BP4	23677	hgsc.bcm.edu	37	2	235949877	235949877	+	Missense_Mutation	SNP	T	T	C	rs3731644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:235949877T>C	ENST00000409212.1	+	4	971	c.464T>C	c.(463-465)aTg>aCg	p.M155T	SH3BP4_ENST00000344528.4_Missense_Mutation_p.M155T|SH3BP4_ENST00000392011.2_Missense_Mutation_p.M155T			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	155			M -> T (in dbSNP:rs3731644). {ECO:0000269|PubMed:16325581}.		cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)	p.M155T(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		CCAGGCAGAATGTACAGTAAT	0.507													C|||	1711	0.341653	0.4002	0.4092	5008	,	,		20531	0.4117		0.0964	False		,,,				2504	0.3947				p.M155T		Atlas-SNP	.											SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	1	Substitution - Missense(1)	stomach(1)	c.T464C						PASS	.	C	THR/MET	1622,2784	661.5+/-400.9	314,994,895	100.0	103.0	102.0		464	2.5	0.0	2	dbSNP_107	102	950,7650	775.6+/-407.7	49,852,3399	yes	missense	SH3BP4	NM_014521.2	81	363,1846,4294	CC,CT,TT		11.0465,36.8134,19.7755	benign	155/964	235949877	2572,10434	2203	4300	6503	SO:0001583	missense	23677	exon4			GCAGAATGTACAG	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.464T>C	2.37:g.235949877T>C	ENSP00000386862:p.Met155Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	37	CCDS2513.1	660	0.3021978021978022	200	0.4065040650406504	130	0.35911602209944754	253	0.4423076923076923	77	0.10158311345646438	C	3.825	-0.036980	0.07497	0.368134	0.110465	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000409212;ENST00000344528;ENST00000446904	T;T;T;T	0.24350	3.06;3.06;3.06;1.86	5.35	2.53	0.30540	.	1.323390	0.04695	N	0.414885	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	0.46317	-0.9200	9	0.12103	T	0.63	-17.0704	3.1836	0.06593	0.1268:0.4588:0.2683:0.1461	rs3731644;rs52831227;rs61554763;rs3731644	155;155	A8K594;Q9P0V3	.;SH3B4_HUMAN	T	155	ENSP00000375867:M155T;ENSP00000386862:M155T;ENSP00000340237:M155T;ENSP00000415391:M155T	ENSP00000340237:M155T	M	+	2	0	SH3BP4	235614616	0.004000	0.15560	0.000000	0.03702	0.198000	0.23893	1.295000	0.33377	-0.001000	0.14495	-0.761000	0.03458	ATG	T|0.747;C|0.253	0.253	strong		0.507	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
DYX1C1	161582	hgsc.bcm.edu	37	15	55790414	55790414	+	Missense_Mutation	SNP	G	G	T	rs16976354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55790414G>T	ENST00000321149.3	-	2	481	c.114C>A	c.(112-114)aaC>aaA	p.N38K	DYX1C1_ENST00000380679.1_Missense_Mutation_p.N38K|DYX1C1_ENST00000448430.2_Missense_Mutation_p.N38K|DYX1C1_ENST00000457155.2_Missense_Mutation_p.N38K|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000348518.3_Missense_Mutation_p.N38K	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	38	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.|Mediates interaction with ESR1 and STUB1.		N -> K (in dbSNP:rs16976354).		cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		CCTTCAGATAGTTTTCCGTGC	0.562													G|||	311	0.0621006	0.2262	0.0159	5008	,	,		16045	0.0		0.001	False		,,,				2504	0.0				p.N38K		Atlas-SNP	.											.	DYX1C1	54	.	0			c.C114A						PASS	.	G	LYS/ASN,LYS/ASN,LYS/ASN	849,3537	325.3+/-299.0	72,705,1416	45.0	42.0	43.0		114,114,114	-1.6	0.1	15	dbSNP_123	43	0,8582		0,0,4291	yes	missense,missense,missense	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	94,94,94	72,705,5707	TT,TG,GG		0.0,19.357,6.5469	benign,benign,benign	38/377,38/382,38/421	55790414	849,12119	2193	4291	6484	SO:0001583	missense	161582	exon2			CAGATAGTTTTCC		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.114C>A	15.37:g.55790414G>T	ENSP00000323275:p.Asn38Lys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	132	53	0.401515	NM_001033560	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	103	0.04716117216117216	97	0.19715447154471544	6	0.016574585635359115	0	0.0	0	0.0	G	12.94	2.089312	0.36855	0.19357	0.0	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63	4.82	-1.59	0.08453	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	1.338300	0.05207	U	0.506081	T	0.00012	0.0000	L	0.41573	1.285	0.58432	P	9.000000000036756E-6	B;B;P	0.44044	0.307;0.109;0.825	B;B;B	0.39217	0.117;0.122;0.294	T	0.26224	-1.0109	9	0.07813	T	0.8	.	5.7047	0.17901	0.459:0.2611:0.2799:0.0	rs16976354;rs52829594;rs58871707;rs16976354	38;38;38	Q8WXU2-3;Q8WXU2;Q8WXU2-2	.;DYXC1_HUMAN;.	K	38	ENSP00000403412:N38K;ENSP00000370054:N38K;ENSP00000402640:N38K;ENSP00000323275:N38K;ENSP00000299561:N38K	ENSP00000323275:N38K	N	-	3	2	DYX1C1	53577706	0.085000	0.21516	0.131000	0.22000	0.920000	0.55202	0.021000	0.13489	0.043000	0.15746	0.655000	0.94253	AAC	G|0.928;T|0.072	0.072	strong		0.562	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
NPR3	4883	hgsc.bcm.edu	37	5	32712119	32712119	+	Silent	SNP	T	T	C	rs6859964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32712119T>C	ENST00000265074.8	+	1	580	c.237T>C	c.(235-237)gcT>gcC	p.A79A	NPR3_ENST00000415685.2_Intron|NPR3_ENST00000415167.2_Silent_p.A79A|NPR3_ENST00000434067.2_Intron	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3	79					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	TCGAGTATGCTCTGCGCAGCG	0.642													T|||	226	0.0451278	0.1679	0.0043	5008	,	,		14376	0.0		0.001	False		,,,				2504	0.0				p.A79A		Atlas-SNP	.											.	NPR3	65	.	0			c.T237C						PASS	.	T	,,	522,3402		36,450,1476	25.0	30.0	28.0		237,237,	1.2	1.0	5	dbSNP_116	28	2,8314		0,2,4156	no	coding-synonymous,coding-synonymous,intron	NPR3	NM_000908.3,NM_001204375.1,NM_001204376.1	,,	36,452,5632	CC,CT,TT		0.0241,13.3028,4.281	,,	79/541,79/542,	32712119	524,11716	1962	4158	6120	SO:0001819	synonymous_variant	4883	exon1			GTATGCTCTGCGC		CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"""guanylate cyclase C"""	108962	"""chromosome 5 open reading frame 23"", ""atrionatriuretic peptide receptor C"", ""natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)"", ""natriuretic peptide receptor C"""	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.237T>C	5.37:g.32712119T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_000908	A2RRD1|B4DT84|E7EPG9	Silent	SNP	ENST00000265074.8	37	CCDS56357.1																																																																																			T|0.956;C|0.044	0.044	strong		0.642	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908	
CFAP43	80217	hgsc.bcm.edu	37	10	105906077	105906077	+	Missense_Mutation	SNP	T	T	C	rs369682196		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105906077T>C	ENST00000357060.3	-	30	3914	c.3799A>G	c.(3799-3801)Aga>Gga	p.R1267G	WDR96_ENST00000428666.1_Intron	NM_025145.5	NP_079421.5														NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGGTCTTCTCTAGATTTCCGA	0.418																																					p.R1267G		Atlas-SNP	.											WDR96,NS,carcinoma,+1,1	WDR96	183	1	0			c.A3799G						PASS	.	T	GLY/ARG	1,4405	2.1+/-5.4	0,1,2202	139.0	125.0	130.0		3799	3.5	0.0	10		130	0,8600		0,0,4300	no	missense	WDR96	NM_025145.5	125	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	1267/1666	105906077	1,13005	2203	4300	6503	SO:0001583	missense	80217	exon30			CTTCTCTAGATTT																												ENST00000357060.3:c.3799A>G	10.37:g.105906077T>C	ENSP00000349568:p.Arg1267Gly	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	167	85	0.508982	NM_025145		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.	.	.	.	.	.	.	.	.	.	T	7.040	0.562289	0.13498	2.27E-4	0.0	ENSG00000197748	ENST00000357060	T	0.14640	2.49	6.07	3.55	0.40652	.	0.466125	0.21837	N	0.068397	T	0.15132	0.0365	M	0.63428	1.95	0.09310	N	1	P	0.43094	0.799	B	0.36092	0.217	T	0.08973	-1.0696	10	0.51188	T	0.08	.	13.497	0.61432	0.0:0.0:0.2551:0.7449	.	1267	Q8NDM7	WDR96_HUMAN	G	1267	ENSP00000349568:R1267G	ENSP00000349568:R1267G	R	-	1	2	WDR96	105896067	0.005000	0.15991	0.036000	0.18154	0.021000	0.10359	1.590000	0.36654	1.078000	0.41014	0.533000	0.62120	AGA	.	.	none		0.418	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CCNI	10983	hgsc.bcm.edu	37	4	77976374	77976374	+	Missense_Mutation	SNP	C	C	T	rs4252903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77976374C>T	ENST00000237654.4	-	6	1195	c.619G>A	c.(619-621)Gtt>Att	p.V207I	CCNI_ENST00000537948.1_Missense_Mutation_p.V193I|CCNI_ENST00000504697.1_5'Flank	NM_006835.2	NP_006826.1	Q14094	CCNI_HUMAN	cyclin I	207			V -> I (in dbSNP:rs4252903). {ECO:0000269|Ref.4}.		regulation of cell cycle (GO:0051726)|spermatogenesis (GO:0007283)					NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9						TCCAGACTAACCATGGCCAGA	0.438													C|||	38	0.00758786	0.0287	0.0	5008	,	,		16139	0.0		0.0	False		,,,				2504	0.0				p.V207I		Atlas-SNP	.											.	CCNI	22	.	0			c.G619A						PASS	.	C	ILE/VAL	99,4307	79.3+/-117.8	2,95,2106	113.0	101.0	105.0		619	2.2	1.0	4	dbSNP_111	105	1,8599		0,1,4299	yes	missense	CCNI	NM_006835.2	29	2,96,6405	TT,TC,CC		0.0116,2.2469,0.7689	benign	207/378	77976374	100,12906	2203	4300	6503	SO:0001583	missense	10983	exon6			GACTAACCATGGC	D50310	CCDS3580.1	4q21.1	2014-07-03			ENSG00000118816	ENSG00000118816			1595	protein-coding gene	gene with protein product						7493655	Standard	NM_006835		Approved	CCNI1	uc003hkm.3	Q14094	OTTHUMG00000130106	ENST00000237654.4:c.619G>A	4.37:g.77976374C>T	ENSP00000237654:p.Val207Ile	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	220	102	0.463636	NM_006835	B2R6M0|B7Z6X4	Missense_Mutation	SNP	ENST00000237654.4	37	CCDS3580.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	5.722	0.317763	0.10845	0.022469	1.16E-4	ENSG00000118816	ENST00000237654;ENST00000537948	T;T	0.13657	2.57;2.57	5.87	2.22	0.28083	Cyclin-like (1);	0.328648	0.36268	N	0.002681	T	0.02083	0.0065	N	0.04959	-0.14	0.37675	D	0.92327	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.36335	-0.9752	10	0.07030	T	0.85	-3.5062	6.2538	0.20861	0.0:0.6096:0.1228:0.2676	rs4252903;rs52822018;rs4252903	193;207	B7Z6X4;Q14094	.;CCNI_HUMAN	I	207;193	ENSP00000237654:V207I;ENSP00000441001:V193I	ENSP00000237654:V207I	V	-	1	0	CCNI	78195398	0.993000	0.37304	1.000000	0.80357	0.993000	0.82548	0.319000	0.19522	0.484000	0.27630	0.655000	0.94253	GTT	C|0.992;T|0.008	0.008	strong		0.438	CCNI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252412.2	NM_006835	
EPHA2	1969	hgsc.bcm.edu	37	1	16459745	16459745	+	Silent	SNP	G	G	A	rs10907223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16459745G>A	ENST00000358432.5	-	11	2137	c.1983C>T	c.(1981-1983)ctC>ctT	p.L661L		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	661	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)	CGGCCTCGCCGAGGAAGTCCA	0.607													g|||	965	0.192692	0.4849	0.0793	5008	,	,		17582	0.1071		0.0477	False		,,,				2504	0.1155				p.L661L		Atlas-SNP	.											.	EPHA2	102	.	0			c.C1983T						PASS	.	C		1770,2636	523.3+/-371.0	363,1044,796	87.0	80.0	82.0		1983	-1.5	1.0	1	dbSNP_120	82	328,8272	114.0+/-174.0	8,312,3980	no	coding-synonymous	EPHA2	NM_004431.3		371,1356,4776	AA,AG,GG		3.814,40.1725,16.131		661/977	16459745	2098,10908	2203	4300	6503	SO:0001819	synonymous_variant	1969	exon11			CTCGCCGAGGAAG	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.1983C>T	1.37:g.16459745G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	144	73	0.506944	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																			G|0.827;A|0.173	0.173	strong		0.607	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
TTN	7273	hgsc.bcm.edu	37	2	179416659	179416659	+	Missense_Mutation	SNP	C	C	T	rs11887722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179416659C>T	ENST00000591111.1	-	285	86269	c.86045G>A	c.(86044-86046)aGg>aAg	p.R28682K	TTN_ENST00000342175.6_Missense_Mutation_p.R21450K|TTN_ENST00000359218.5_Missense_Mutation_p.R21383K|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R21258K|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R30323K|TTN_ENST00000342992.6_Missense_Mutation_p.R27755K|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28682					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)			ACCAGGAATCCTGAACTGGTG	0.448													C|||	180	0.0359425	0.1271	0.0159	5008	,	,		22703	0.0		0.001	False		,,,				2504	0.0				p.R30323K		Atlas-SNP	.											.	TTN	18412	.	0			c.G90968A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	418,3824		24,370,1727	132.0	141.0	138.0		64349,64148,83264,63773	5.8	1.0	2	dbSNP_120	138	8,8456		0,8,4224	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	26,26,26,26	24,378,5951	TT,TC,CC		0.0945,9.8538,3.3527	benign,benign,benign,benign	21450/27119,21383/27052,27755/33424,21258/26927	179416659	426,12280	2121	4232	6353	SO:0001583	missense	7273	exon335			GGAATCCTGAACT	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.86045G>A	2.37:g.179416659C>T	ENSP00000465570:p.Arg28682Lys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	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		86	0.039377289377289376	78	0.15853658536585366	8	0.022099447513812154	0	0.0	0	0.0	C	13.17	2.157290	0.38119	0.098538	9.45E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62105	0.05;0.29;0.27;0.26	5.76	5.76	0.90799	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.21933	P	0.999463905	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.03184	-1.1063	8	0.87932	D	0	.	12.6943	0.56994	0.0:0.8821:0.0:0.1179	rs11887722;rs52822649;rs11887722	21258;21383;21450;28682	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	27755;21258;21450;21383;21255	ENSP00000343764:R27755K;ENSP00000434586:R21258K;ENSP00000340554:R21450K;ENSP00000352154:R21383K	ENSP00000340554:R21450K	R	-	2	0	TTN	179124905	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.947000	0.40293	2.719000	0.93026	0.655000	0.94253	AGG	C|0.949;T|0.051	0.051	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ENAM	10117	hgsc.bcm.edu	37	4	71509431	71509431	+	Missense_Mutation	SNP	G	G	A	rs3796704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71509431G>A	ENST00000396073.3	+	9	2569	c.2288G>A	c.(2287-2289)cGg>cAg	p.R763Q	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	763			R -> Q (in dbSNP:rs3796704). {ECO:0000269|PubMed:18245370}.		amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			TTTCCTTCACGGAATTCCTGG	0.448													G|||	690	0.13778	0.3752	0.1009	5008	,	,		18406	0.0228		0.0487	False		,,,				2504	0.0532				p.R763Q		Atlas-SNP	.											ENAM_ENST00000396073,colon,carcinoma,0,2	ENAM	140	2	0			c.G2288A						PASS	.	G	GLN/ARG	1419,2987	437.0+/-344.8	224,971,1008	59.0	61.0	60.0		2288	3.3	0.7	4	dbSNP_107	60	372,8228	120.2+/-179.5	4,364,3932	yes	missense	ENAM	NM_031889.2	43	228,1335,4940	AA,AG,GG		4.3256,32.2061,13.7706	possibly-damaging	763/1143	71509431	1791,11215	2203	4300	6503	SO:0001583	missense	10117	exon9			CTTCACGGAATTC	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.2288G>A	4.37:g.71509431G>A	ENSP00000379383:p.Arg763Gln	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	263	0.12042124542124542	184	0.37398373983739835	36	0.09944751381215469	5	0.008741258741258742	38	0.05013192612137203	G	7.816	0.716652	0.15306	0.322061	0.043256	ENSG00000132464	ENST00000396073	T	0.29655	1.56	6.01	3.3	0.37823	.	0.647706	0.14651	N	0.306584	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	5.999999999950489E-6	B	0.09022	0.002	B	0.09377	0.004	T	0.47289	-0.9129	9	0.25106	T	0.35	2.8238	8.4383	0.32799	0.0788:0.2935:0.6277:0.0	rs3796704;rs52801525;rs3796704	763	Q9NRM1	ENAM_HUMAN	Q	763	ENSP00000379383:R763Q	ENSP00000379383:R763Q	R	+	2	0	ENAM	71728295	0.901000	0.30685	0.718000	0.30602	0.066000	0.16364	2.499000	0.45372	0.403000	0.25479	-0.947000	0.02670	CGG	G|0.873;A|0.127	0.127	strong		0.448	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889	
MST1L	11223	hgsc.bcm.edu	37	1	17083797	17083797	+	RNA	SNP	C	C	T	rs564582425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17083797C>T	ENST00000455405.2	-	0	791							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GGCTGGCCAGCGCGACCTTGT	0.567													.|||	219	0.04373	0.1543	0.0216	5008	,	,		29509	0.0		0.0	False		,,,				2504	0.0				p.R667H		Atlas-SNP	.											.	.	.	.	0			c.G2000A						PASS	.																																					11223	exon15			GGCCAGCGCGACC	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.17083797C>T		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	339	162	0.477876	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	6.905	0.536454	0.13188	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.563499	0.14822	N	0.296388	T	0.26376	0.0644	.	.	.	.	.	.	B;B	0.19935	0.04;0.003	B;B	0.11329	0.006;0.003	T	0.18840	-1.0324	6	0.51188	T	0.08	.	2.9647	0.05903	0.0:0.6115:0.0:0.3885	.	667;693	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	H	667;693	.	ENSP00000439273:R667H	R	-	2	0	MST1P9	16956384	0.999000	0.42202	0.921000	0.36526	0.000000	0.00434	2.097000	0.41748	0.502000	0.28037	0.000000	0.15137	CGC	.	.	none		0.567	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
ADAM21	8747	hgsc.bcm.edu	37	14	70924693	70924693	+	Silent	SNP	T	T	C	rs45480894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:70924693T>C	ENST00000603540.1	+	2	735	c.477T>C	c.(475-477)taT>taC	p.Y159Y	ADAM21_ENST00000267499.3_Silent_p.Y159Y|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	159					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)	p.Y159Y(1)		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)		ACCTGGTTTATAAGATAAACA	0.423													T|||	1281	0.255791	0.3094	0.1326	5008	,	,		18949	0.505		0.1203	False		,,,				2504	0.1534				p.Y159Y		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	1	Substitution - coding silent(1)	stomach(1)	c.T477C						PASS	.	T		72,4182		15,42,2070	39.0	48.0	45.0		477	2.6	0.1	14	dbSNP_127	45	13,8573		1,11,4281	no	coding-synonymous	ADAM21	NM_003813.3		16,53,6351	CC,CT,TT		0.1514,1.6925,0.662		159/723	70924693	85,12755	2127	4293	6420	SO:0001819	synonymous_variant	8747	exon2			GGTTTATAAGATA	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.477T>C	14.37:g.70924693T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	81	19	0.234568	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			T|0.945;C|0.055	0.055	strong		0.423	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
TRPV1	7442	hgsc.bcm.edu	37	17	3480910	3480910	+	Silent	SNP	A	A	G	rs34378673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3480910A>G	ENST00000571088.1	-	11	1908	c.1695T>C	c.(1693-1695)taT>taC	p.Y565Y	TRPV1_ENST00000174621.6_Silent_p.Y563Y|RP11-235E17.3_ENST00000573568.1_RNA|TRPV1_ENST00000310522.5_Silent_p.Y505Y|TRPV1_ENST00000576351.1_Silent_p.Y555Y|TRPV1_ENST00000399756.4_Silent_p.Y565Y|SHPK_ENST00000572705.1_Silent_p.Y565Y|TRPV1_ENST00000425167.2_Silent_p.Y576Y|TRPV1_ENST00000399759.3_Silent_p.Y565Y	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	565					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	TCATGACGGCATAGATGCCCA	0.587													G|||	401	0.0800719	0.171	0.0159	5008	,	,		19318	0.0417		0.0398	False		,,,				2504	0.0838				p.Y565Y	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.T1695C						PASS	.	G	,,,	632,3334		42,548,1393	37.0	41.0	40.0		1695,1695,1695,1695	-7.9	0.1	17	dbSNP_126	40	436,7842		15,406,3718	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	,,,	57,954,5111	GG,GA,AA		5.267,15.9355,8.7226	,,,	565/840,565/840,565/840,565/840	3480910	1068,11176	1983	4139	6122	SO:0001819	synonymous_variant	7442	exon11			GACGGCATAGATG	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.1695T>C	17.37:g.3480910A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Silent	SNP	ENST00000571088.1	37	CCDS45576.1																																																																																			A|0.934;G|0.066	0.066	strong		0.587	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
EBI3	10148	hgsc.bcm.edu	37	19	4237067	4237067	+	Silent	SNP	A	A	G	rs4905	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4237067A>G	ENST00000221847.5	+	5	725	c.672A>G	c.(670-672)acA>acG	p.T224T		NM_005755.2	NP_005746.2	Q14213	IL27B_HUMAN	Epstein-Barr virus induced 3	224	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|humoral immune response (GO:0006959)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|T-helper 1 type immune response (GO:0042088)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0336)|STAD - Stomach adenocarcinoma(1328;0.18)		CCACTGCCACAATGAGCCTGG	0.657													G|||	2308	0.460863	0.6679	0.2767	5008	,	,		15560	0.4435		0.3052	False		,,,				2504	0.4898				p.T224T		Atlas-SNP	.											.	EBI3	15	.	0			c.A672G						PASS	.	G		2725,1681	481.7+/-359.2	844,1037,322	40.0	40.0	40.0		672	-7.3	0.0	19	dbSNP_52	40	2457,6143	665.9+/-402.3	372,1713,2215	no	coding-synonymous	EBI3	NM_005755.2		1216,2750,2537	GG,GA,AA		28.5698,38.1525,39.8431		224/230	4237067	5182,7824	2203	4300	6503	SO:0001819	synonymous_variant	10148	exon5			TGCCACAATGAGC	L08187	CCDS12123.1	19p13	2013-02-11	2008-09-12		ENSG00000105246	ENSG00000105246		"""Fibronectin type III domain containing"""	3129	protein-coding gene	gene with protein product	"""IL27 subunit"", ""IL35 subunit"""	605816				8551575	Standard	NM_005755		Approved		uc002lzu.3	Q14213		ENST00000221847.5:c.672A>G	19.37:g.4237067A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_005755	A0N0N2|O75269	Silent	SNP	ENST00000221847.5	37	CCDS12123.1																																																																																			A|0.585;G|0.415	0.415	strong		0.657	EBI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458005.1		
TENM1	10178	hgsc.bcm.edu	37	X	123838882	123838882	+	Silent	SNP	C	C	T	rs138596900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:123838882C>T	ENST00000371130.3	-	5	1059	c.996G>A	c.(994-996)ttG>ttA	p.L332L	TENM1_ENST00000422452.2_Silent_p.L332L	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	332					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)										AGGCTAGTAACAAGGCCAAAG	0.453													C|||	71	0.0188079	0.0514	0.0043	3775	,	,		14198	0.0		0.0	False		,,,				2504	0.0				p.L332L		Atlas-SNP	.											.	.	.	.	0			c.G996A						PASS	.	C	,,	212,3623		5,173,29,1454,542	163.0	146.0	152.0		996,996,996	5.7	1.0	X	dbSNP_134	152	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	5,173,29,3882,2414	TT,TC,T,CC,C		0.0,5.528,2.007	,,	332/2733,332/2732,332/2726	123838882	212,10351	2203	4300	6503	SO:0001819	synonymous_variant	10178	exon5			TAGTAACAAGGCC	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.996G>A	X.37:g.123838882C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	128	40	0.3125	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			C|0.979;T|0.021	0.021	strong		0.453	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
PRAMEF4	400735	hgsc.bcm.edu	37	1	12939664	12939664	+	Missense_Mutation	SNP	A	A	T	rs28452936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12939664A>T	ENST00000235349.5	-	4	1208	c.1138T>A	c.(1138-1140)Ttt>Att	p.F380I		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	380					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.F380I(1)		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)		TTGAGCTCAAAGCAGCGGCTC	0.507													a|||	579	0.115615	0.1362	0.1023	5008	,	,		20417	0.1399		0.1123	False		,,,				2504	0.0757				p.F380I		Atlas-SNP	.											PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	1	1	Substitution - Missense(1)	prostate(1)	c.T1138A						scavenged	.	T	ILE/PHE	433,2563		63,307,1128	87.0	90.0	89.0		1138	-1.9	0.0	1	dbSNP_131	89	614,4742		68,478,2132	no	missense	PRAMEF4	NM_001009611.2	21	131,785,3260	TT,TA,AA		11.4638,14.4526,12.5359	probably-damaging	380/479	12939664	1047,7305	1498	2678	4176	SO:0001583	missense	400735	exon4			GCTCAAAGCAGCG		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.1138T>A	1.37:g.12939664A>T	ENSP00000235349:p.Phe380Ile	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	142	50	0.352113	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	269	0.12316849816849818	54	0.10975609756097561	44	0.12154696132596685	70	0.12237762237762238	101	0.13324538258575197	A	8.167	0.790796	0.16258	0.144526	0.114638	ENSG00000243073	ENST00000235349	T	0.09817	2.94	1.48	-1.9	0.07665	.	1.401010	0.04101	N	0.312866	T	0.00073	0.0002	L	0.35723	1.085	0.80722	P	0.0	B	0.11235	0.004	B	0.09377	0.004	T	0.40534	-0.9558	9	0.52906	T	0.07	.	2.3209	0.04211	0.4402:0.2822:0.0:0.2776	.	380	O60810	PRAM4_HUMAN	I	380	ENSP00000235349:F380I	ENSP00000235349:F380I	F	-	1	0	PRAMEF4	12862251	0.000000	0.05858	0.002000	0.10522	0.024000	0.10985	-1.237000	0.02922	-0.479000	0.06813	0.329000	0.21502	TTT	A|0.881;T|0.119	0.119	strong		0.507	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
AVPR2	554	hgsc.bcm.edu	37	X	153171993	153171993	+	Silent	SNP	A	A	G	rs5201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153171993A>G	ENST00000358927.2	+	4	1136	c.927A>G	c.(925-927)ctA>ctG	p.L309L	AVPR2_ENST00000370049.1_3'UTR|ARHGAP4_ENST00000467421.1_5'Flank|AVPR2_ENST00000337474.5_Silent_p.L309L			P30518	V2R_HUMAN	arginine vasopressin receptor 2	309			L -> P (in XNDI). {ECO:0000269|PubMed:9452109}.|L -> R (in XNDI).		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|excretion (GO:0007588)|hemostasis (GO:0007599)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-gamma production (GO:0032609)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of systemic arterial blood pressure (GO:0003084)|response to cytokine (GO:0034097)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	vasopressin receptor activity (GO:0005000)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	26	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)				Conivaptan(DB00872)|Desmopressin(DB00035)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	CCTTTGTGCTACTCATGTTGC	0.612													G|||	2599	0.688477	0.711	0.487	3775	,	,		14121	0.5446		0.2425	False		,,,				2504	0.5399				p.L309L		Atlas-SNP	.											.	AVPR2	43	.	0			c.A927G						PASS	.	G	,	3287,548		1199,389,500,44,71	160.0	139.0	146.0		927,	3.4	1.0	X	dbSNP_52	146	2018,4710		209,998,602,1221,1270	no	coding-synonymous,utr-3	AVPR2	NM_000054.4,NM_001146151.1	,	1408,1387,1102,1265,1341	GG,GA,G,AA,A		29.9941,14.2894,49.7775	,	309/372,	153171993	5305,5258	2203	4300	6503	SO:0001819	synonymous_variant	554	exon3			TGTGCTACTCATG	Z11687	CCDS14735.1, CCDS55539.1	Xq28	2014-09-17	2008-08-01		ENSG00000126895	ENSG00000126895		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	897	protein-coding gene	gene with protein product	"""nephrogenic diabetes insipidus"""	300538		DIR3, DIR		1324225	Standard	NM_000054		Approved	V2R	uc004fjh.4	P30518	OTTHUMG00000024227	ENST00000358927.2:c.927A>G	X.37:g.153171993A>G		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	199	199	1	NM_000054	C5HF20|O43192|Q3MJD3|Q9UCV9	Silent	SNP	ENST00000358927.2	37	CCDS14735.1	993	0.5985533453887885	242	0.8120805369127517	123	0.45555555555555555	212	0.572972972972973	130	0.2006172839506173	g	4.708	0.131710	0.08981	0.857106	0.299941	ENSG00000126895	ENST00000430697	T	0.41758	0.99	4.3	3.44	0.39384	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09885	-1.0654	5	0.66056	D	0.02	-19.7909	5.1929	0.15218	0.1993:0.284:0.5167:0.0	rs5201;rs2228584;rs5201	.	.	.	C	280	ENSP00000393513:Y280C	ENSP00000393513:Y280C	Y	+	2	0	AVPR2	152825187	0.974000	0.33945	1.000000	0.80357	0.185000	0.23345	0.989000	0.29629	0.258000	0.21686	-1.480000	0.00990	TAC	A|0.412;0|0.001	.	strong		0.612	AVPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061127.2		
CD3EAP	10849	hgsc.bcm.edu	37	19	45912406	45912406	+	Missense_Mutation	SNP	G	G	A	rs2336219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45912406G>A	ENST00000309424.3	+	3	1668	c.1180G>A	c.(1180-1182)Gat>Aat	p.D394N	ERCC1_ENST00000588738.1_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.D396N|ERCC1_ENST00000423698.2_3'UTR|PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000300853.3_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	394			D -> N (in dbSNP:rs2336219).		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)		AAAACAGCAAGATGCCACAGT	0.577													A|||	1415	0.282548	0.298	0.219	5008	,	,		17482	0.4613		0.1322	False		,,,				2504	0.2771				p.D394N		Atlas-SNP	.											.	CD3EAP	27	.	0			c.G1180A						PASS	.	A	,,ASN/ASP	1113,3281		150,813,1234	57.0	70.0	65.0		,,1180	-2.1	0.0	19	dbSNP_100	65	1133,7443		77,979,3232	yes	utr-3,utr-3,missense	ERCC1,CD3EAP	NM_001166049.1,NM_001983.3,NM_012099.1	,,23	227,1792,4466	AA,AG,GG		13.2113,25.33,17.3169	,,benign	,,394/511	45912406	2246,10724	2197	4288	6485	SO:0001583	missense	10849	exon3			CAGCAAGATGCCA	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.1180G>A	19.37:g.45912406G>A	ENSP00000310966:p.Asp394Asn	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	562	0.2573260073260073	125	0.2540650406504065	70	0.19337016574585636	259	0.4527972027972028	108	0.1424802110817942	A	2.513	-0.312418	0.05422	0.2533	0.132113	ENSG00000117877	ENST00000309424	T	0.11712	2.75	5.46	-2.07	0.07276	.	1.771500	0.03042	N	0.153457	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	0.45716	-0.9242	9	0.02654	T	1	0.0578	10.4878	0.44733	0.1931:0.1532:0.6537:0.0	rs2336219;rs61002808;rs2336219	396;394	O15446-2;O15446	.;RPA34_HUMAN	N	394	ENSP00000310966:D394N	ENSP00000310966:D394N	D	+	1	0	CD3EAP	50604246	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.647000	0.05397	-0.620000	0.05641	-0.361000	0.07541	GAT	G|0.767;A|0.233	0.233	strong		0.577	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
PGAM2	5224	hgsc.bcm.edu	37	7	44104913	44104913	+	Silent	SNP	G	G	A	rs111656877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44104913G>A	ENST00000297283.3	-	1	273	c.216C>T	c.(214-216)gaC>gaT	p.D72D	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	72					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						GGTCCGTGCCGTCCAGGATGG	0.627													G|||	52	0.0103834	0.0371	0.0029	5008	,	,		17290	0.0		0.0	False		,,,				2504	0.001				p.D72D		Atlas-SNP	.											.	PGAM2	20	.	0			c.C216T						PASS	.	G		218,4188	131.4+/-167.9	7,204,1992	93.0	78.0	83.0		216	-11.9	0.0	7	dbSNP_132	83	0,8600		0,0,4300	no	coding-synonymous	PGAM2	NM_000290.3		7,204,6292	AA,AG,GG		0.0,4.9478,1.6761		72/254	44104913	218,12788	2203	4300	6503	SO:0001819	synonymous_variant	5224	exon1			CGTGCCGTCCAGG		CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.216C>T	7.37:g.44104913G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	121	57	0.471074	NM_000290		Silent	SNP	ENST00000297283.3	37	CCDS34624.1																																																																																			G|0.984;A|0.016	0.016	strong		0.627	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1		
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2911352	2911352	+	Silent	SNP	C	C	T	rs36016465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2911352C>T	ENST00000254695.8	+	17	1497	c.1407C>T	c.(1405-1407)caC>caT	p.H469H	RAP1GAP2_ENST00000540393.2_Silent_p.H450H|RAP1GAP2_ENST00000542807.1_Silent_p.H469H|RAP1GAP2_ENST00000366401.4_Silent_p.H454H	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	469					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						ATGAGCTCCACGCCCACACAC	0.597													C|||	77	0.0153754	0.056	0.0029	5008	,	,		18125	0.0		0.001	False		,,,				2504	0.0				p.H469H		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.C1407T						PASS	.	C	,	139,3993		2,135,1929	63.0	69.0	67.0		1362,1407	-9.6	0.0	17	dbSNP_126	67	2,8384		0,2,4191	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	2,137,6120	TT,TC,CC		0.0238,3.364,1.1264	,	454/716,469/731	2911352	141,12377	2066	4193	6259	SO:0001819	synonymous_variant	23108	exon17			GCTCCACGCCCAC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1407C>T	17.37:g.2911352C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	128	72	0.5625	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			C|0.988;T|0.012	0.012	strong		0.597	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
DNAJA3	9093	hgsc.bcm.edu	37	16	4492415	4492415	+	Silent	SNP	C	C	T	rs141270066		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4492415C>T	ENST00000262375.6	+	5	854	c.777C>T	c.(775-777)tcC>tcT	p.S259S	DNAJA3_ENST00000431375.2_Silent_p.S106S|DNAJA3_ENST00000355296.4_Silent_p.S259S	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	259					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						GTGGCGGCTCCGGCATGGTAA	0.607													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17409	0.0		0.0	False		,,,				2504	0.0				p.S259S		Atlas-SNP	.											.	DNAJA3	52	.	0			c.C777T						PASS	.	C	,	1,4393		0,1,2196	50.0	44.0	46.0		777,777	-11.2	0.1	16	dbSNP_134	46	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DNAJA3	NM_001135110.2,NM_005147.5	,	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	,	259/454,259/481	4492415	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	9093	exon5			CGGCTCCGGCATG	AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"""Heat shock proteins / DNAJ (HSP40)"""	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.777C>T	16.37:g.4492415C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_001135110	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Silent	SNP	ENST00000262375.6	37	CCDS10515.1																																																																																			C|1.000;T|0.000	0.000	weak		0.607	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251633.1		
PCDHGA5	56110	hgsc.bcm.edu	37	5	140745333	140745333	+	Missense_Mutation	SNP	C	C	T	rs6882138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140745333C>T	ENST00000518069.1	+	1	1436	c.1436C>T	c.(1435-1437)cCc>cTc	p.P479L	PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	479	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)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCCATGACCCCGACAGCGGC	0.537													.|||	255	0.0509185	0.1641	0.013	5008	,	,		17824	0.0		0.0258	False		,,,				2504	0.0031				p.P479L		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.C1436T						PASS	.	C	,,,,LEU/PRO,,,LEU/PRO	502,3502		36,430,1536	130.0	142.0	138.0		,,,,1436,,,1436	4.3	0.8	5	dbSNP_116	138	141,8241		1,139,4051	yes	intron,intron,intron,intron,missense,intron,intron,missense	PCDHGB2,PCDHGB1,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018922.2,NM_018923.2,NM_032054.1	,,,,98,,,98	37,569,5587	TT,TC,CC		1.6822,12.5375,5.1913	,,,,,,,	,,,,479/932,,,479/814	140745333	643,11743	2002	4191	6193	SO:0001583	missense	56110	exon1			ATGACCCCGACAG	AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"""Cadherins / Protocadherins : Clustered"""	8703	other	protocadherin	"""cadherin ME3"""	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.1436C>T	5.37:g.140745333C>T	ENSP00000429834:p.Pro479Leu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_032054	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	37	CCDS54925.1	100	0.045787545787545784	73	0.1483739837398374	6	0.016574585635359115	0	0.0	21	0.027704485488126648	.	5.692	0.312222	0.10789	0.125375	0.016822	ENSG00000253485	ENST00000518069	T	0.01505	4.82	5.18	4.29	0.51040	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.37750	1.13	0.09310	N	0.999999	B;B	0.20988	0.04;0.05	B;B	0.26310	0.041;0.068	T	0.50355	-0.8838	9	0.56958	D	0.05	.	12.7075	0.57070	0.2994:0.7006:0.0:0.0	rs6882138;rs6882138	479;479	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	L	479	ENSP00000429834:P479L	ENSP00000429834:P479L	P	+	2	0	PCDHGA5	140725517	0.000000	0.05858	0.830000	0.32933	0.029000	0.11900	1.073000	0.30691	1.267000	0.44247	0.563000	0.77884	CCC	C|0.944;T|0.056	0.056	strong		0.537	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918	
ARHGEF15	22899	hgsc.bcm.edu	37	17	8216468	8216468	+	Missense_Mutation	SNP	T	T	C	rs871841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8216468T>C	ENST00000361926.3	+	3	940	c.830T>C	c.(829-831)cTc>cCc	p.L277P	ARHGEF15_ENST00000421050.1_Missense_Mutation_p.L277P	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	277			L -> P (in dbSNP:rs871841). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		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						CTCCTGCCACTCCTCAAGCCT	0.597													C|||	3110	0.621006	0.7186	0.6758	5008	,	,		16306	0.7431		0.4761	False		,,,				2504	0.4734				p.L277P		Atlas-SNP	.											.	ARHGEF15	97	.	0			c.T830C						PASS	.	C	PRO/LEU,PRO/LEU	3027,1379	454.9+/-350.8	1050,927,226	68.0	61.0	63.0		830,830	5.1	1.0	17	dbSNP_86	63	4301,4299	576.5+/-390.4	1084,2133,1083	yes	missense,missense	ARHGEF15	NM_025014.1,NM_173728.3	98,98	2134,3060,1309	CC,CT,TT		49.9884,31.2982,43.6568	benign,benign	277/842,277/842	8216468	7328,5678	2203	4300	6503	SO:0001583	missense	22899	exon3			TGCCACTCCTCAA	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.830T>C	17.37:g.8216468T>C	ENSP00000355026:p.Leu277Pro	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	75	43	0.573333	NM_025014	A8K6G1|Q8N449|Q9H8B4	Missense_Mutation	SNP	ENST00000361926.3	37	CCDS11139.1	1362	0.6236263736263736	357	0.725609756097561	226	0.6243093922651933	424	0.7412587412587412	355	0.4683377308707124	C	7.148	0.583117	0.13749	0.687018	0.500116	ENSG00000198844	ENST00000361926;ENST00000421050	T;T	0.34472	1.36;1.36	5.13	5.13	0.70059	.	0.074351	0.52532	N	0.000070	T	0.00012	0.0000	N	0.01352	-0.895	0.33021	P	0.47108799999999995	B	0.02656	0.0	B	0.01281	0.0	T	0.38757	-0.9646	9	0.02654	T	1	-19.8928	9.6731	0.40023	0.0:0.9064:0.0:0.0936	rs871841;rs3815647;rs17806556;rs17846188;rs17859203;rs52789349;rs56785551;rs871841	277	O94989	ARHGF_HUMAN	P	277	ENSP00000355026:L277P;ENSP00000412505:L277P	ENSP00000355026:L277P	L	+	2	0	ARHGEF15	8157193	0.382000	0.25148	0.995000	0.50966	0.130000	0.20726	1.477000	0.35431	1.409000	0.46915	-0.215000	0.12644	CTC	T|0.398;G|0.003	.	strong		0.597	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728	
CUL9	23113	hgsc.bcm.edu	37	6	43152366	43152366	+	Silent	SNP	C	C	A	rs41274928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43152366C>A	ENST00000252050.4	+	2	402	c.318C>A	c.(316-318)ggC>ggA	p.G106G	CUL9_ENST00000372647.2_Silent_p.G106G|CUL9_ENST00000354495.3_Silent_p.G106G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	106					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						ATCCAGGAGGCCTGGATGAAG	0.607													C|||	248	0.0495208	0.1112	0.0288	5008	,	,		20915	0.003		0.0288	False		,,,				2504	0.0501				p.G106G		Atlas-SNP	.											.	CUL9	248	.	0			c.C318A						PASS	.	C		459,3947	217.1+/-235.6	32,395,1776	89.0	96.0	94.0		318	0.7	1.0	6	dbSNP_127	94	267,8333	101.9+/-163.1	2,263,4035	no	coding-synonymous	CUL9	NM_015089.2		34,658,5811	AA,AC,CC		3.1047,10.4176,5.582		106/2518	43152366	726,12280	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon2			AGGAGGCCTGGAT	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.318C>A	6.37:g.43152366C>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	184	95	0.516304	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.948;A|0.052	0.052	strong		0.607	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
HMGXB3	22993	hgsc.bcm.edu	37	5	149404213	149404213	+	Missense_Mutation	SNP	G	G	T	rs115942845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149404213G>T	ENST00000502717.1	+	7	1894	c.1430G>T	c.(1429-1431)aGt>aTt	p.S477I	HMGXB3_ENST00000503427.1_Missense_Mutation_p.S445I	NM_014983.2	NP_055798	Q12766	HMGX3_HUMAN	HMG box domain containing 3	723					phosphorylation (GO:0016310)	nucleus (GO:0005634)	DNA binding (GO:0003677)|kinase activity (GO:0016301)			central_nervous_system(1)|endometrium(3)|kidney(3)|skin(2)	9						AGTACCTCCAGTCCACTCCCT	0.483													G|||	21	0.00419329	0.0159	0.0	5008	,	,		19720	0.0		0.0	False		,,,				2504	0.0				p.S477I		Atlas-SNP	.											.	HMGXB3	31	.	0			c.G1430T						PASS	.	G	ILE/SER	15,1369		0,15,677	51.0	51.0	51.0		1430	-0.2	0.1	5	dbSNP_132	51	2,3180		0,2,1589	yes	missense	HMGXB3	NM_014983.2	142	0,17,2266	TT,TG,GG		0.0629,1.0838,0.3723	possibly-damaging	477/1293	149404213	17,4549	692	1591	2283	SO:0001583	missense	22993	exon7			CCTCCAGTCCACT	D83778	CCDS54935.1	5q33.1	2011-07-01		2009-01-05	ENSG00000113716	ENSG00000113716		"""High mobility group / Non-canonical"""	28982	protein-coding gene	gene with protein product				HMGX3		8724849	Standard	NM_014983		Approved	SMF, KIAA0194	uc003lrk.4	Q12766	OTTHUMG00000163493	ENST00000502717.1:c.1430G>T	5.37:g.149404213G>T	ENSP00000421917:p.Ser477Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_014983	G5E9Y4|Q86UG3|Q9UMF4	Missense_Mutation	SNP	ENST00000502717.1	37	CCDS54935.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	G	9.220	1.033161	0.19590	0.010838	6.29E-4	ENSG00000113716	ENST00000503427;ENST00000502717	.	.	.	5.94	-0.254	0.12992	.	0.898615	0.10134	N	0.711723	T	0.16428	0.0395	L	0.47716	1.5	0.09310	N	1	B	0.24823	0.112	B	0.22386	0.039	T	0.33445	-0.9868	9	0.87932	D	0	-0.0037	1.2728	0.02025	0.1957:0.217:0.3649:0.2223	.	723	Q12766	HMGX3_HUMAN	I	445;477	.	ENSP00000421917:S477I	S	+	2	0	HMGXB3	149384406	0.040000	0.19996	0.095000	0.20976	0.343000	0.28985	0.365000	0.20348	-0.110000	0.12022	-0.188000	0.12872	AGT	G|0.995;T|0.005	0.005	strong		0.483	HMGXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373771.1	XM_001717202	
NLRP7	199713	hgsc.bcm.edu	37	19	55451083	55451083	+	Silent	SNP	A	A	G	rs1654636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55451083A>G	ENST00000590030.1	-	3	1144	c.1104T>C	c.(1102-1104)atT>atC	p.I368I	NLRP7_ENST00000448121.2_Silent_p.I368I|NLRP7_ENST00000588756.1_Silent_p.I368I|NLRP7_ENST00000328092.5_Silent_p.I368I|NLRP7_ENST00000592784.1_Silent_p.I368I|NLRP7_ENST00000446217.1_Silent_p.I396I|NLRP7_ENST00000340844.2_Silent_p.I368I			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	368	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)		TCGTGCACACAATCCAGCACA	0.642													.|||	123	0.0245607	0.0666	0.0202	5008	,	,		16521	0.002		0.0189	False		,,,				2504	0.0				p.I368I		Atlas-SNP	.											NLRP7_ENST00000328092,NS,carcinoma,-2,2	NLRP7	411	2	0			c.T1104C						scavenged	.						37.0	40.0	39.0					19																	55451083		2201	4299	6500	SO:0001819	synonymous_variant	199713	exon4			GCACACAATCCAG	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.1104T>C	19.37:g.55451083A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	94	18	0.191489	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			A|0.949;G|0.051	0.051	strong		0.642	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
VWA3A	146177	hgsc.bcm.edu	37	16	22137603	22137603	+	Missense_Mutation	SNP	G	G	A	rs55732851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:22137603G>A	ENST00000389398.5	+	17	1733	c.1637G>A	c.(1636-1638)tGt>tAt	p.C546Y	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	546	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					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)		AACAAGGACTGTTTCAACCTC	0.537													g|||	466	0.0930511	0.1914	0.0793	5008	,	,		17791	0.0506		0.0626	False		,,,				2504	0.045				p.C546Y		Atlas-SNP	.											.	VWA3A	115	.	0			c.G1637A						PASS	.	G	TYR/CYS	671,3365		57,557,1404	111.0	112.0	112.0		1637	-9.9	0.0	16	dbSNP_129	112	640,7712		27,586,3563	yes	missense	VWA3A	NM_173615.3	194	84,1143,4967	AA,AG,GG		7.6628,16.6254,10.5828	benign	546/1185	22137603	1311,11077	2018	4176	6194	SO:0001583	missense	146177	exon17			AGGACTGTTTCAA	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.1637G>A	16.37:g.22137603G>A	ENSP00000374049:p.Cys546Tyr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	144	67	0.465278	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	210	0.09615384615384616	112	0.22764227642276422	32	0.08839779005524862	20	0.03496503496503497	46	0.06068601583113457	g	0.004	-2.287083	0.00248	0.166254	0.076628	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.20881	2.04	4.97	-9.94	0.00449	.	1.202480	0.05532	N	0.564148	T	0.00012	0.0000	N	0.13043	0.29	0.31162	P	0.704214	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30621	-0.9972	9	0.02654	T	1	.	0.4202	0.00455	0.2611:0.259:0.242:0.2379	rs55732851	546;170	A6NCI4;A6NCI4-2	VWA3A_HUMAN;.	Y	546;169	ENSP00000374049:C546Y	ENSP00000299840:C169Y	C	+	2	0	VWA3A	22045104	0.002000	0.14202	0.033000	0.17914	0.491000	0.33493	-1.206000	0.03011	-2.453000	0.00541	-2.230000	0.00291	TGT	G|0.908;A|0.092	0.092	strong		0.537	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29910581	29910581	+	Missense_Mutation	SNP	C	C	A	rs386698550|rs1059423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29910581C>A	ENST00000396634.1	+	4	462	c.121C>A	c.(121-123)Cgc>Agc	p.R41S	HLA-A_ENST00000376809.5_Missense_Mutation_p.R41S|HLA-A_ENST00000376802.2_Missense_Mutation_p.R41S|HLA-A_ENST00000376806.5_Missense_Mutation_p.R41S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	41	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						CCGGCCCGGCCGCGGGGAGCC	0.716									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|||	623	0.124401	0.2368	0.1225	5008	,	,		14373	0.1042		0.0577	False		,,,				2504	0.0634				p.R41S		Atlas-SNP	.											.	HLA-A	89	.	0			c.C121A						PASS	.						19.0	18.0	18.0					6																	29910581		2193	4286	6479	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCCGGCCGCGGGG	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.121C>A	6.37:g.29910581C>A	ENSP00000379873:p.Arg41Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	93	20	0.215054	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	241	0.11034798534798534	120	0.24390243902439024	40	0.11049723756906077	51	0.08916083916083917	30	0.0395778364116095	.	10.33	1.321091	0.23994	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00009	9.53;9.53;9.53;9.53	3.4	1.48	0.22813	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	1.343590	0.05838	U	0.618791	T	0.00073	0.0002	M	0.92738	3.34	0.80722	P	0.0	P;B;B;B	0.35456	0.502;0.0;0.0;0.376	B;B;B;B	0.39840	0.311;0.004;0.004;0.201	T	0.26815	-1.0092	9	0.87932	D	0	.	4.4868	0.11794	0.2164:0.6608:0.0:0.1228	rs1059423;rs2230967;rs3200107;rs16896583;rs17423964;rs41547420	41;41;41;41	P13746;Q5SRN7;Q5SRN5;P04439	1A11_HUMAN;.;.;1A03_HUMAN	S	41	ENSP00000379873:R41S;ENSP00000366002:R41S;ENSP00000366005:R41S;ENSP00000365998:R41S	ENSP00000348012:R41S	R	+	1	0	HLA-A	30018560	0.003000	0.15002	0.087000	0.20705	0.517000	0.34286	0.736000	0.26130	0.232000	0.21100	0.478000	0.44815	CGC	A|0.089;C|0.911	0.089	strong		0.716	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744456	31744456	+	Missense_Mutation	SNP	G	G	A	rs16986753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31744456G>A	ENST00000399889.2	-	1	101	c.76C>T	c.(76-78)Cgt>Tgt	p.R26C		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	26			R -> C (in dbSNP:rs16986753).			intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						GAAAAGCCACGTGAGGATGCT	0.562													A|||	26	0.00519169	0.0189	0.0014	5008	,	,		19332	0.0		0.0	False		,,,				2504	0.0				p.R26C		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.C76T						PASS	.	A	CYS/ARG	99,4307	816.6+/-416.3	1,97,2105	134.0	119.0	124.0		76	2.0	0.1	21	dbSNP_123	124	1,8599	819.2+/-406.8	0,1,4299	no	missense	KRTAP13-2	NM_181621.3	180	1,98,6404	AA,AG,GG		0.0116,2.2469,0.7689	benign	26/176	31744456	100,12906	2203	4300	6503	SO:0001583	missense	337959	exon1			AGCCACGTGAGGA	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"""Keratin associated proteins"""	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.76C>T	21.37:g.31744456G>A	ENSP00000382777:p.Arg26Cys	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	247	116	0.469636	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	A	0.003	-2.531073	0.00145	0.022469	1.16E-4	ENSG00000182816	ENST00000399889	T	0.02974	4.09	4.64	2.01	0.26516	.	0.321942	0.22259	N	0.062423	T	0.00241	0.0007	N	0.00337	-1.62	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.43877	-0.9364	10	0.02654	T	1	.	1.3696	0.02208	0.5367:0.1853:0.0995:0.1786	rs16986753;rs52808457;rs16986753	26	Q52LG2	KR132_HUMAN	C	26	ENSP00000382777:R26C	ENSP00000382777:R26C	R	-	1	0	KRTAP13-2	30666327	0.992000	0.36948	0.144000	0.22314	0.017000	0.09413	1.031000	0.30165	0.330000	0.23485	-1.228000	0.01579	CGT	G|0.989;A|0.011	0.011	strong		0.562	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1		
THSD4	79875	hgsc.bcm.edu	37	15	72040774	72040774	+	Silent	SNP	C	C	T	rs1872056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:72040774C>T	ENST00000355327.3	+	14	2390	c.2256C>T	c.(2254-2256)tgC>tgT	p.C752C	THSD4_ENST00000567838.1_3'UTR|THSD4_ENST00000357769.4_Silent_p.C392C|THSD4_ENST00000261862.6_Silent_p.C752C			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	752	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						CGGTGCCCTGCGGCGTGGGAC	0.562													C|||	998	0.199281	0.3086	0.147	5008	,	,		19695	0.0823		0.2644	False		,,,				2504	0.1421				p.C752C		Atlas-SNP	.											.	THSD4	75	.	0			c.C2256T						PASS	.	C		1281,3079		190,901,1089	121.0	135.0	130.0		2256	-8.4	0.6	15	dbSNP_92	130	2145,6401		312,1521,2440	no	coding-synonymous	THSD4	NM_024817.2		502,2422,3529	TT,TC,CC		25.0995,29.3807,26.5458		752/1019	72040774	3426,9480	2180	4273	6453	SO:0001819	synonymous_variant	79875	exon13			GCCCTGCGGCGTG	AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.2256C>T	15.37:g.72040774C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	230	230	1	NM_024817	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Silent	SNP	ENST00000355327.3	37	CCDS10238.2																																																																																			C|0.782;T|0.218	0.218	strong		0.562	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817	
OC90	729330	hgsc.bcm.edu	37	8	133053909	133053909	+	Silent	SNP	G	G	C	rs115883855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133053909G>C	ENST00000443356.2	-	5	293	c.207C>G	c.(205-207)gtC>gtG	p.V69V	OC90_ENST00000603859.1_Silent_p.V69V|OC90_ENST00000254627.3_Silent_p.V69V|OC90_ENST00000262283.5_Silent_p.V265V			Q02509	OC90_HUMAN	otoconin 90	69					lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			AATTGGTGAAGACAGCCTGCA	0.577													G|||	53	0.0105831	0.0386	0.0029	5008	,	,		17110	0.0		0.0	False		,,,				2504	0.0				p.V69V		Atlas-SNP	.											OC90_ENST00000262283,caecum,carcinoma,0,2	OC90	163	2	0			c.C207G						PASS	.	G		121,3849		1,119,1865	33.0	33.0	33.0		207	2.8	1.0	8	dbSNP_132	33	0,8330		0,0,4165	no	coding-synonymous	OC90	NM_001080399.2		1,119,6030	CC,CG,GG		0.0,3.0479,0.9837		69/478	133053909	121,12179	1985	4165	6150	SO:0001819	synonymous_variant	729330	exon5			GGTGAAGACAGCC	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.207C>G	8.37:g.133053909G>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	139	70	0.503597	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				G|0.989;C|0.011	0.011	strong		0.577	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	
PRB1	5542	hgsc.bcm.edu	37	12	11506749	11506749	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11506749T>C	ENST00000500254.2	-	3	325	c.288A>G	c.(286-288)aaA>aaG	p.K96K	PRB1_ENST00000546254.1_Silent_p.K96K|PRB1_ENST00000545626.1_Silent_p.K96K	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1	35	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].		Missing (in allele M).			extracellular region (GO:0005576)		p.K96K(1)		NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			GTCCTTGTGGTTTTCCTGGAG	0.607																																					p.K96K		Atlas-SNP	.											PRB1,NS,carcinoma,0,1	PRB1	33	1	1	Substitution - coding silent(1)	lung(1)	c.A288G						scavenged	.						177.0	223.0	208.0					12																	11506749		2161	4271	6432	SO:0001819	synonymous_variant	5542	exon3			TTGTGGTTTTCCT		CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.288A>G	12.37:g.11506749T>C		Somatic	104	2	0.0192308		WXS	Illumina HiSeq	Phase_I	489	150	0.306748	NM_199353	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Silent	SNP	ENST00000500254.2	37	CCDS8642.1																																																																																			.	.	none		0.607	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039	
TRPM2	7226	hgsc.bcm.edu	37	21	45817713	45817713	+	Silent	SNP	G	G	A	rs45622331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45817713G>A	ENST00000397928.1	+	13	2461	c.2016G>A	c.(2014-2016)tcG>tcA	p.S672S	TRPM2_ENST00000300482.5_Silent_p.S672S|TRPM2_ENST00000300481.9_Silent_p.S652S|TRPM2_ENST00000397932.2_Silent_p.S672S|TRPM2_ENST00000498430.1_3'UTR	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	672					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						CGGACAGCTCGGAGGAGATGC	0.652													G|||	295	0.0589058	0.1672	0.062	5008	,	,		19503	0.0298		0.001	False		,,,				2504	0.0				p.S672S		Atlas-SNP	.											.	TRPM2	196	.	0			c.G2016A						PASS	.	G		556,3844	245.0+/-254.1	31,494,1675	75.0	60.0	65.0		2016	-9.3	0.5	21	dbSNP_127	65	7,8581	5.0+/-18.6	0,7,4287	no	coding-synonymous	TRPM2	NM_003307.3		31,501,5962	AA,AG,GG		0.0815,12.6364,4.3348		672/1504	45817713	563,12425	2200	4294	6494	SO:0001819	synonymous_variant	7226	exon13			CAGCTCGGAGGAG	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2016G>A	21.37:g.45817713G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	156	81	0.519231	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																			G|0.947;A|0.053	0.053	strong		0.652	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
MLANA	2315	hgsc.bcm.edu	37	9	5892525	5892525	+	Silent	SNP	C	C	T	rs2233178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5892525C>T	ENST00000381477.3	+	2	211	c.51C>T	c.(49-51)caC>caT	p.H17H	MLANA_ENST00000381471.1_Silent_p.H17H|snoU13_ENST00000459519.1_RNA|MLANA_ENST00000381476.1_Silent_p.H17H	NM_005511.1	NP_005502.1	Q16655	MAR1_HUMAN	melan-A	17						endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|melanosome (GO:0042470)|trans-Golgi network (GO:0005802)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	8		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(1;1.15e-06)|Lung(218;0.103)		AGAAGGGGCACGGCCACTCTT	0.532													C|||	797	0.159145	0.3888	0.0648	5008	,	,		20715	0.0298		0.0596	False		,,,				2504	0.1513				p.H17H		Atlas-SNP	.											.	MLANA	16	.	0			c.C51T						PASS	.	C		1393,3013	460.0+/-352.4	202,989,1012	104.0	84.0	91.0		51	-6.5	0.0	9	dbSNP_98	91	349,8251	117.4+/-177.0	9,331,3960	no	coding-synonymous	MLANA	NM_005511.1		211,1320,4972	TT,TC,CC		4.0581,31.616,13.3938		17/119	5892525	1742,11264	2203	4300	6503	SO:0001819	synonymous_variant	2315	exon2			GGGGCACGGCCAC		CCDS6466.1	9p24.1	2008-02-05			ENSG00000120215	ENSG00000120215			7124	protein-coding gene	gene with protein product		605513					Standard	NM_005511		Approved	MART1	uc003zjo.1	Q16655	OTTHUMG00000019510	ENST00000381477.3:c.51C>T	9.37:g.5892525C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_005511	Q6ICU4	Silent	SNP	ENST00000381477.3	37	CCDS6466.1																																																																																			C|0.863;T|0.137	0.137	strong		0.532	MLANA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051643.1		
FAM83F	113828	hgsc.bcm.edu	37	22	40417820	40417820	+	Missense_Mutation	SNP	A	A	G	rs5995794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:40417820A>G	ENST00000333407.6	+	4	1400	c.1306A>G	c.(1306-1308)Agg>Ggg	p.R436G	FAM83F_ENST00000473717.1_Missense_Mutation_p.R268G	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	436			R -> G (in dbSNP:rs5995794).							breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						CGCCCCCGCCAGGCGCTTCAG	0.657													A|||	1358	0.271166	0.3359	0.1585	5008	,	,		14624	0.0863		0.2863	False		,,,				2504	0.4387				p.R436G		Atlas-SNP	.											FAM83F,NS,carcinoma,0,1	FAM83F	29	1	0			c.A1306G						PASS	.	A	GLY/ARG	1193,3207		184,825,1191	18.0	22.0	21.0		1306	2.7	0.9	22	dbSNP_114	21	2403,6191		332,1739,2226	yes	missense	FAM83F	NM_138435.2	125	516,2564,3417	GG,GA,AA		27.9614,27.1136,27.6743	possibly-damaging	436/501	40417820	3596,9398	2200	4297	6497	SO:0001583	missense	113828	exon4			CCCGCCAGGCGCT		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.1306A>G	22.37:g.40417820A>G	ENSP00000330432:p.Arg436Gly	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	37	CCDS14000.2	500	0.22893772893772893	165	0.3353658536585366	62	0.1712707182320442	43	0.07517482517482517	230	0.3034300791556728	A	7.297	0.612217	0.14066	0.271136	0.279614	ENSG00000133477	ENST00000333407	T	0.10099	2.91	3.79	2.72	0.32119	.	0.560877	0.14341	N	0.325730	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.22276	0.067	B	0.19391	0.025	T	0.46091	-0.9216	9	0.42905	T	0.14	-11.3454	8.8472	0.35177	0.8099:0.1901:0.0:0.0	rs5995794;rs5995794	436	Q8NEG4	FA83F_HUMAN	G	436	ENSP00000330432:R436G	ENSP00000330432:R436G	R	+	1	2	FAM83F	38747766	0.996000	0.38824	0.875000	0.34327	0.027000	0.11550	3.639000	0.54339	0.478000	0.27488	0.374000	0.22700	AGG	A|0.766;G|0.234	0.234	strong		0.657	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
TAF2	6873	hgsc.bcm.edu	37	8	120793332	120793332	+	Silent	SNP	T	T	C	rs28619538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120793332T>C	ENST00000378164.2	-	17	2512	c.2214A>G	c.(2212-2214)acA>acG	p.T738T		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	738					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TAAAGTTGTTTGTTTTCACAA	0.348													T|||	117	0.0233626	0.0825	0.0086	5008	,	,		16206	0.0		0.002	False		,,,				2504	0.0				p.T738T		Atlas-SNP	.											.	TAF2	204	.	0			c.A2214G						PASS	.	T		271,4135	152.9+/-186.6	5,261,1937	79.0	84.0	82.0		2214	2.8	1.0	8	dbSNP_125	82	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	TAF2	NM_003184.3		5,296,6202	CC,CT,TT		0.407,6.1507,2.3528		738/1200	120793332	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	6873	exon17			GTTGTTTGTTTTC	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2214A>G	8.37:g.120793332T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	62	36	0.580645	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Silent	SNP	ENST00000378164.2	37	CCDS34937.1																																																																																			T|0.977;C|0.023	0.023	strong		0.348	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
TLR10	81793	hgsc.bcm.edu	37	4	38777173	38777173	+	Silent	SNP	A	A	T	rs10856838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38777173A>T	ENST00000308973.4	-	4	644	c.39T>A	c.(37-39)atT>atA	p.I13I	TLR10_ENST00000508334.1_Silent_p.I13I|TLR10_ENST00000506111.1_Silent_p.I13I|TLR10_ENST00000361424.2_Silent_p.I13I|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	13					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						CTGTCATAACAATACTACAAA	0.403													A|||	1657	0.330871	0.5053	0.2723	5008	,	,		16858	0.2302		0.1909	False		,,,				2504	0.3845				p.I13I		Atlas-SNP	.											.	TLR10	87	.	0			c.T39A						PASS	.	A	,,,,	2028,2378	563.5+/-381.2	466,1096,641	68.0	68.0	68.0		39,39,39,,39	2.6	0.0	4	dbSNP_120	68	1423,7177	273.5+/-290.7	129,1165,3006	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-5,coding-synonymous	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	,,,,	595,2261,3647	TT,TA,AA		16.5465,46.0281,26.5339	,,,,	13/812,13/812,13/812,,13/812	38777173	3451,9555	2203	4300	6503	SO:0001819	synonymous_variant	81793	exon2			CATAACAATACTA	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.39T>A	4.37:g.38777173A>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																			A|0.721;T|0.279	0.279	strong		0.403	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
PDZD2	23037	hgsc.bcm.edu	37	5	32093079	32093079	+	Silent	SNP	A	A	G	rs16889443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32093079A>G	ENST00000438447.1	+	21	8182	c.7794A>G	c.(7792-7794)ggA>ggG	p.G2598G	PDZD2_ENST00000282493.3_Silent_p.G2598G			O15018	PDZD2_HUMAN	PDZ domain containing 2	2598					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CGTCAGTGGGATCGAAATCTA	0.408													G|||	425	0.0848642	0.3064	0.0259	5008	,	,		18742	0.0		0.002	False		,,,				2504	0.0				p.G2598G		Atlas-SNP	.											.	PDZD2	306	.	0			c.A7794G						PASS	.	G		925,3481	737.3+/-410.9	104,717,1382	83.0	84.0	84.0		7794	1.9	0.1	5	dbSNP_123	84	6,8594	818.6+/-406.8	0,6,4294	no	coding-synonymous	PDZD2	NM_178140.2		104,723,5676	GG,GA,AA		0.0698,20.9941,7.1582		2598/2840	32093079	931,12075	2203	4300	6503	SO:0001819	synonymous_variant	23037	exon20			AGTGGGATCGAAA	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.7794A>G	5.37:g.32093079A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	194	100	0.515464	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			A|0.932;G|0.068	0.068	strong		0.408	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417774	105417774	+	Silent	SNP	G	G	A	rs2013228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417774G>A	ENST00000333244.5	-	7	4133	c.4014C>T	c.(4012-4014)ttC>ttT	p.F1338F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1338						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)			CAGACACCCCGAACGACGGCA	0.612													.|||	1956	0.390575	0.5726	0.3213	5008	,	,		14015	0.2986		0.2505	False		,,,				2504	0.4325				p.F1338F		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4014T						PASS	.	G		1920,1726		696,528,599	143.0	125.0	132.0		4014	-8.2	0.0	14	dbSNP_92	132	1647,4939		654,339,2300	no	coding-synonymous	AHNAK2	NM_138420.2		1350,867,2899	AA,AG,GG		25.0076,47.3396,34.8612		1338/5796	105417774	3567,6665	1823	3293	5116	SO:0001819	synonymous_variant	113146	exon7			CACCCCGAACGAC	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.4014C>T	14.37:g.105417774G>A		Somatic	378	0	0		WXS	Illumina HiSeq	Phase_I	263	263	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.700;A|0.300	0.300	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
JRK	8629	hgsc.bcm.edu	37	8	143746722	143746722	+	RNA	SNP	G	G	A	rs60195180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746722G>A	ENST00000507178.2	-	0	1088							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)				ccttataggcgacgggcaggt	0.577													G|||	63	0.0125799	0.0469	0.0014	5008	,	,		18089	0.0		0.0	False		,,,				2504	0.0				p.V252V		Atlas-SNP	.											.	.	.	.	0			c.C756T						PASS	.	G	,	90,2688		0,90,1299	13.0	15.0	14.0		756,756	-7.2	0.0	8	dbSNP_129	14	3,5557		0,3,2777	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	0,93,4076	AA,AG,GG		0.054,3.2397,1.1154	,	252/557,252/569	143746722	93,8245	1389	2780	4169			8629	exon2			ATAGGCGACGGGC	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.143746722G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				G|0.992;A|0.008	0.008	strong		0.577	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
EXD3	54932	hgsc.bcm.edu	37	9	140201604	140201604	+	Missense_Mutation	SNP	C	C	T	rs28685844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140201604C>T	ENST00000340951.4	-	22	2624	c.2429G>A	c.(2428-2430)cGg>cAg	p.R810Q	EXD3_ENST00000342129.4_Missense_Mutation_p.R448Q	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CAGCTGCAGCCGGGTGCCGTC	0.697													C|||	240	0.0479233	0.0204	0.0101	5008	,	,		12927	0.1458		0.008	False		,,,				2504	0.0521				p.R810Q		Atlas-SNP	.											EXD3_ENST00000340951,NS,carcinoma,0,1	EXD3	86	1	0			c.G2429A						scavenged	.	C	GLN/ARG	72,3920		0,72,1924	11.0	14.0	13.0		2429	-4.0	0.0	9	dbSNP_125	13	51,8271		1,49,4111	no	missense	EXD3	NM_017820.3	43	1,121,6035	TT,TC,CC		0.6128,1.8036,0.9989	benign	810/877	140201604	123,12191	1996	4161	6157	SO:0001583	missense	54932	exon22			TGCAGCCGGGTGC		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.2429G>A	9.37:g.140201604C>T	ENSP00000340474:p.Arg810Gln	Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	111	87	0.783784	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	94	0.04304029304029304	14	0.028455284552845527	2	0.0055248618784530384	72	0.1258741258741259	6	0.0079155672823219	C	12.91	2.080318	0.36662	0.018036	0.006128	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.64260	-0.09;0.63	4.42	-3.99	0.04069	.	.	.	.	.	T	0.00468	0.0015	L	0.43923	1.385	0.80722	P	0.0	B;B	0.27910	0.107;0.193	B;B	0.19946	0.027;0.014	T	0.05784	-1.0864	8	0.25106	T	0.35	.	1.0757	0.01632	0.2167:0.1659:0.3759:0.2415	rs28685844;rs28685844	448;810	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	Q	448;810	ENSP00000343705:R448Q;ENSP00000340474:R810Q	ENSP00000340474:R810Q	R	-	2	0	EXD3	139321425	0.270000	0.24152	0.000000	0.03702	0.001000	0.01503	-0.364000	0.07583	-0.596000	0.05821	-0.291000	0.09656	CGG	C|0.957;T|0.043	0.043	strong		0.697	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
ADRBK1	156	hgsc.bcm.edu	37	11	67052322	67052322	+	Silent	SNP	C	C	T	rs115867067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67052322C>T	ENST00000308595.5	+	19	1949	c.1659C>T	c.(1657-1659)taC>taT	p.Y553Y	ADRBK1_ENST00000527176.1_3'UTR|ADRBK1_ENST00000526285.1_Intron	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	553					activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	CCTCAGACTACGCCCTGGGCA	0.587													C|||	66	0.0131789	0.0484	0.0029	5008	,	,		15108	0.0		0.0	False		,,,				2504	0.0				p.Y553Y		Atlas-SNP	.											.	ADRBK1	51	.	0			c.C1659T						PASS	.	C		168,4230	108.2+/-146.6	4,160,2035	77.0	56.0	63.0		1659	1.0	1.0	11	dbSNP_132	63	1,8589		0,1,4294	no	coding-synonymous	ADRBK1	NM_001619.3		4,161,6329	TT,TC,CC		0.0116,3.8199,1.3012		553/690	67052322	169,12819	2199	4295	6494	SO:0001819	synonymous_variant	156	exon19			AGACTACGCCCTG	X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"""Pleckstrin homology (PH) domain containing"""	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.1659C>T	11.37:g.67052322C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	76	25	0.328947	NM_001619	B0ZBE1|Q13837|Q6GTT3	Silent	SNP	ENST00000308595.5	37	CCDS8156.1																																																																																			C|0.987;T|0.013	0.013	strong		0.587	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619	
CNGB3	54714	hgsc.bcm.edu	37	8	87588248	87588248	+	Silent	SNP	T	T	C	rs3735970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87588248T>C	ENST00000320005.5	-	18	2261	c.2214A>G	c.(2212-2214)gaA>gaG	p.E738E		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	738					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						TATCTTTAtcttcattttctt	0.363													T|||	412	0.0822684	0.0696	0.085	5008	,	,		18686	0.1022		0.0885	False		,,,				2504	0.0706				p.E738E		Atlas-SNP	.											.	CNGB3	176	.	0			c.A2214G						PASS	.	T		302,4104	146.1+/-180.8	11,280,1912	199.0	202.0	201.0		2214	2.8	0.2	8	dbSNP_107	201	718,7882	162.7+/-215.4	32,654,3614	no	coding-synonymous	CNGB3	NM_019098.4		43,934,5526	CC,CT,TT		8.3488,6.8543,7.8425		738/810	87588248	1020,11986	2203	4300	6503	SO:0001819	synonymous_variant	54714	exon18			TTTATCTTCATTT	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2153	protein-coding gene	gene with protein product		605080	"""achromatopsia (rod monochromacy) 3"", ""achromatopsia (rod monochromacy) 1"""	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.2214A>G	8.37:g.87588248T>C		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	304	165	0.542763	NM_019098	C9JA51|Q9NRE9	Silent	SNP	ENST00000320005.5	37	CCDS6244.1																																																																																			T|0.918;C|0.082	0.082	strong		0.363	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098	
RAI1	10743	hgsc.bcm.edu	37	17	17700792	17700792	+	Silent	SNP	C	C	T	rs35686634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17700792C>T	ENST00000353383.1	+	3	4999	c.4530C>T	c.(4528-4530)ccC>ccT	p.P1510P	RAI1_ENST00000261641.6_Silent_p.P1510P	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1510					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CCTCCCAGCCCCCGGAGGGCA	0.657													C|||	366	0.0730831	0.1906	0.0331	5008	,	,		13919	0.0069		0.0567	False		,,,				2504	0.0276				p.P1510P		Atlas-SNP	.											.	RAI1	121	.	0			c.C4530T						PASS	.	C		764,3640	272.5+/-270.8	67,630,1505	30.0	38.0	35.0		4530	0.6	0.0	17	dbSNP_126	35	510,8090	137.1+/-194.1	18,474,3808	no	coding-synonymous	RAI1	NM_030665.3		85,1104,5313	TT,TC,CC		5.9302,17.3479,9.797		1510/1907	17700792	1274,11730	2202	4300	6502	SO:0001819	synonymous_variant	10743	exon3			CCAGCCCCCGGAG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.4530C>T	17.37:g.17700792C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	123	49	0.398374	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			C|0.916;T|0.084	0.084	strong		0.657	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
C17orf82	388407	hgsc.bcm.edu	37	17	59489787	59489787	+	Missense_Mutation	SNP	G	G	C	rs58036240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:59489787G>C	ENST00000335108.2	+	1	676	c.451G>C	c.(451-453)Gcc>Ccc	p.A151P	RP11-332H18.4_ENST00000592009.1_RNA	NM_203425.1	NP_982249	Q86X59	CQ082_HUMAN	chromosome 17 open reading frame 82	151										cervix(1)|lung(1)	2						TGACGGCCGCGCCTGGTTTCC	0.682											OREG0024630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	529	0.105631	0.3343	0.0403	5008	,	,		13249	0.0486		0.0	False		,,,				2504	0.0102				p.A151P		Atlas-SNP	.											.	C17orf82	16	.	0			c.G451C						PASS	.	G	PRO/ALA	962,3398		105,752,1323	10.0	14.0	13.0		451	-1.0	0.0	17	dbSNP_129	13	5,8567		0,5,4281	yes	missense	C17orf82	NM_203425.1	27	105,757,5604	CC,CG,GG		0.0583,22.0642,7.4776	benign	151/252	59489787	967,11965	2180	4286	6466	SO:0001583	missense	388407	exon1			GGCCGCGCCTGGT	BC046200	CCDS11628.1	17q23.2	2012-10-23			ENSG00000187013	ENSG00000187013			32699	protein-coding gene	gene with protein product							Standard	NM_203425		Approved		uc002izh.1	Q86X59	OTTHUMG00000180077	ENST00000335108.2:c.451G>C	17.37:g.59489787G>C	ENSP00000335229:p.Ala151Pro	Somatic	45	0	0	1038	WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_203425		Missense_Mutation	SNP	ENST00000335108.2	37	CCDS11628.1	169	0.07738095238095238	126	0.25609756097560976	19	0.052486187845303865	24	0.04195804195804196	0	0.0	G	13.49	2.252399	0.39797	0.220642	5.83E-4	ENSG00000187013	ENST00000335108	T	0.55930	0.49	3.85	-0.977	0.10282	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.21381	0.055	B	0.22753	0.041	T	0.21965	-1.0230	8	0.87932	D	0	.	3.7563	0.08586	0.0973:0.3496:0.414:0.1391	rs58036240	151	Q86X59	CQ082_HUMAN	P	151	ENSP00000335229:A151P	ENSP00000335229:A151P	A	+	1	0	C17orf82	56844569	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.694000	0.01915	-0.227000	0.09884	-0.537000	0.04273	GCC	G|0.930;C|0.070	0.070	strong		0.682	C17orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449646.1	NM_203425	
JARID2	3720	hgsc.bcm.edu	37	6	15517415	15517415	+	Silent	SNP	C	C	T	rs11970076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:15517415C>T	ENST00000341776.2	+	17	3718	c.3474C>T	c.(3472-3474)gtC>gtT	p.V1158V	JARID2_ENST00000397311.3_Silent_p.V986V	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1158					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				ACGAAAACGTCGTGTTCTGTC	0.597													C|||	80	0.0159744	0.0575	0.0043	5008	,	,		17419	0.0		0.001	False		,,,				2504	0.0				p.V1158V		Atlas-SNP	.											.	JARID2	135	.	0			c.C3474T						PASS	.	C		229,4177	134.1+/-170.4	6,217,1980	179.0	140.0	153.0		3474	-3.5	1.0	6	dbSNP_120	153	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	JARID2	NM_004973.2		6,220,6277	TT,TC,CC		0.0349,5.1975,1.7838		1158/1247	15517415	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	3720	exon17			AAACGTCGTGTTC	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.3474C>T	6.37:g.15517415C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	136	74	0.544118	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	37	CCDS4533.1																																																																																			C|0.983;T|0.017	0.017	strong		0.597	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
HSD11B2	3291	hgsc.bcm.edu	37	16	67469733	67469733	+	Silent	SNP	C	C	A	rs5479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67469733C>A	ENST00000326152.5	+	2	600	c.468C>A	c.(466-468)acC>acA	p.T156T	ATP6V0D1_ENST00000567694.1_5'Flank|HSD11B2_ENST00000567684.2_3'UTR	NM_000196.3	NP_000187.3	P80365	DHI2_HUMAN	hydroxysteroid (11-beta) dehydrogenase 2	156					female pregnancy (GO:0007565)|glucocorticoid biosynthetic process (GO:0006704)|regulation of blood volume by renal aldosterone (GO:0002017)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)	11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity (GO:0003845)|NAD binding (GO:0051287)|steroid binding (GO:0005496)			breast(1)|endometrium(1)|liver(2)|lung(3)|upper_aerodigestive_tract(1)	8		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0401)|Epithelial(162;0.0891)		AGGCCCACACCACCAGCACCG	0.622													C|||	464	0.0926518	0.233	0.0504	5008	,	,		20001	0.003		0.0368	False		,,,				2504	0.0828				p.T156T		Atlas-SNP	.											.	HSD11B2	13	.	0			c.C468A	GRCh37	CM057710	HSD11B2	M	rs5479	PASS	.	C		833,3563	323.7+/-298.2	89,655,1454	47.0	40.0	42.0		468	-1.0	0.9	16	dbSNP_52	42	351,8249	117.6+/-177.1	9,333,3958	no	coding-synonymous	HSD11B2	NM_000196.3		98,988,5412	AA,AC,CC		4.0814,18.949,9.1105		156/406	67469733	1184,11812	2198	4300	6498	SO:0001819	synonymous_variant	3291	exon2			CCACACCACCAGC	U14631	CCDS10837.1	16q22	2011-09-14			ENSG00000176387	ENSG00000176387	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5209	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 9C, member 3"""	614232				7859916, 8611140, 19027726	Standard	NM_000196		Approved	SDR9C3	uc002etd.3	P80365	OTTHUMG00000137507	ENST00000326152.5:c.468C>A	16.37:g.67469733C>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_000196	A7LB28|C5HTY7|Q13194|Q6P2G9|Q8N439|Q96QN8|Q9UC50|Q9UC51|Q9UCW5|Q9UCW6|Q9UCW7|Q9UCW8	Silent	SNP	ENST00000326152.5	37	CCDS10837.1																																																																																			C|0.902;A|0.098	0.098	strong		0.622	HSD11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268826.3	NM_000196	
ZNF582	147948	hgsc.bcm.edu	37	19	56901457	56901457	+	Missense_Mutation	SNP	C	C	T	rs61743722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56901457C>T	ENST00000301310.4	-	4	303	c.145G>A	c.(145-147)Gtt>Att	p.V49I	AC006116.12_ENST00000589671.1_RNA|ZNF582_ENST00000586929.1_Missense_Mutation_p.V49I	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	49	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		GGTTTGGAAACGGCAAGACCT	0.542													C|||	133	0.0265575	0.093	0.0144	5008	,	,		17157	0.0		0.0	False		,,,				2504	0.0				p.V49I	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.G145A						PASS	.	C	ILE/VAL	389,4017	196.7+/-221.0	18,353,1832	91.0	86.0	88.0		145	-9.4	0.0	19	dbSNP_129	88	2,8598		0,2,4298	yes	missense	ZNF582	NM_144690.1	29	18,355,6130	TT,TC,CC		0.0233,8.8289,3.0063	benign	49/518	56901457	391,12615	2203	4300	6503	SO:0001583	missense	147948	exon4			TGGAAACGGCAAG	AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"""Zinc fingers, C2H2-type"", ""-"""	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.145G>A	19.37:g.56901457C>T	ENSP00000301310:p.Val49Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Missense_Mutation	SNP	ENST00000301310.4	37	CCDS33121.1	52	0.023809523809523808	46	0.09349593495934959	6	0.016574585635359115	0	0.0	0	0.0	C	6.754	0.507989	0.12883	0.088289	2.33E-4	ENSG00000018869	ENST00000301310	T	0.00808	5.67	4.82	-9.39	0.00619	Krueppel-associated box (3);	.	.	.	.	T	0.00039	0.0001	N	0.05012	-0.13	0.28889	N	0.893944	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47459	-0.9116	9	0.06757	T	0.87	.	15.7899	0.78345	0.1051:0.7097:0.0:0.1853	.	49;80	Q96NG8;B4DQZ9	ZN582_HUMAN;.	I	49	ENSP00000301310:V49I	ENSP00000301310:V49I	V	-	1	0	ZNF582	61593269	0.000000	0.05858	0.000000	0.03702	0.945000	0.59286	-3.092000	0.00608	-2.299000	0.00659	-0.238000	0.12139	GTT	C|0.972;T|0.028	0.028	strong		0.542	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690	
LMLN	89782	hgsc.bcm.edu	37	3	197712759	197712759	+	Silent	SNP	T	T	C	rs7373242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:197712759T>C	ENST00000330198.4	+	8	949	c.927T>C	c.(925-927)taT>taC	p.Y309Y	LMLN_ENST00000332636.5_Silent_p.Y257Y|LMLN_ENST00000420910.2_Silent_p.Y309Y|LMLN_ENST00000482695.1_Silent_p.Y257Y	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	309					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		CTTTTAATTATAGGTATTTTT	0.378													T|||	1052	0.210064	0.5204	0.1023	5008	,	,		17831	0.0109		0.1173	False		,,,				2504	0.1677				p.Y309Y		Atlas-SNP	.											.	LMLN	53	.	0			c.T927C						PASS	.	T	,	1994,2412	558.9+/-380.1	448,1098,657	75.0	73.0	73.0		927,927	-1.2	1.0	3	dbSNP_116	73	947,7653	207.3+/-249.1	38,871,3391	no	coding-synonymous,coding-synonymous	LMLN	NM_001136049.2,NM_033029.3	,	486,1969,4048	CC,CT,TT		11.0116,45.2565,22.6126	,	309/693,309/656	197712759	2941,10065	2203	4300	6503	SO:0001819	synonymous_variant	89782	exon8			TAATTATAGGTAT	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.927T>C	3.37:g.197712759T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	103	58	0.563107	NM_001136049	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Silent	SNP	ENST00000330198.4	37	CCDS3332.1																																																																																			T|0.785;C|0.215	0.215	strong		0.378	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029	
PLK2	10769	hgsc.bcm.edu	37	5	57753116	57753116	+	Silent	SNP	C	C	T	rs17710502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:57753116C>T	ENST00000274289.3	-	7	1200	c.900G>A	c.(898-900)ccG>ccA	p.P300P	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	300	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		GCAATGAGGACGGCATTGTAT	0.433													C|||	607	0.121206	0.202	0.2017	5008	,	,		18580	0.001		0.1292	False		,,,				2504	0.0706				p.P300P		Atlas-SNP	.											.	PLK2	71	.	0			c.G900A						PASS	.	C		814,3592	323.2+/-298.0	90,634,1479	86.0	82.0	83.0		900	-4.1	1.0	5	dbSNP_123	83	960,7640	209.4+/-250.6	55,850,3395	no	coding-synonymous	PLK2	NM_006622.2		145,1484,4874	TT,TC,CC		11.1628,18.4748,13.6399		300/686	57753116	1774,11232	2203	4300	6503	SO:0001819	synonymous_variant	10769	exon7			TGAGGACGGCATT		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.900G>A	5.37:g.57753116C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	37	CCDS3974.1																																																																																			C|0.868;T|0.132	0.132	strong		0.433	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622	
TTC8	123016	hgsc.bcm.edu	37	14	89343670	89343670	+	Silent	SNP	G	G	C	rs142073418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:89343670G>C	ENST00000345383.5	+	14	1518	c.1434G>C	c.(1432-1434)gcG>gcC	p.A478A	TTC8_ENST00000346301.4_Silent_p.A448A|TTC8_ENST00000358622.5_Silent_p.A290A|TTC8_ENST00000338104.6_Silent_p.A504A|TTC8_ENST00000380656.2_Silent_p.A488A|TTC8_ENST00000354441.6_Silent_p.A223A|TTC8_ENST00000536576.1_Silent_p.A249A	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	514					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						ATGTTGCTGCGCAGAAGTCTG	0.378													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		15836	0.0		0.002	False		,,,				2504	0.0031				p.A488A		Atlas-SNP	.											TTC8,NS,carcinoma,+2,1	TTC8	42	1	0			c.G1464C						PASS	.	G	,,	6,4400	11.4+/-27.6	0,6,2197	81.0	71.0	74.0		1464,1434,1344	-0.1	1.0	14	dbSNP_134	74	45,8555	27.4+/-76.7	0,45,4255	no	coding-synonymous,coding-synonymous,coding-synonymous	TTC8	NM_144596.2,NM_198309.2,NM_198310.2	,,	0,51,6452	CC,CG,GG		0.5233,0.1362,0.3921	,,	488/516,478/506,448/476	89343670	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	123016	exon15			TGCTGCGCAGAAG	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"""Tetratricopeptide (TTC) repeat domain containing"""	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.1434G>C	14.37:g.89343670G>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	120	54	0.45	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Silent	SNP	ENST00000345383.5	37	CCDS9885.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	8.459	0.854948	0.17106	0.001362	0.005233	ENSG00000165533	ENST00000554686	.	.	.	5.4	-0.12	0.13539	.	.	.	.	.	T	0.34687	0.0906	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19031	-1.0318	4	.	.	.	-15.2774	2.8711	0.05617	0.4346:0.0675:0.1193:0.3786	.	.	.	.	P	410	.	.	R	+	2	0	TTC8	88413423	0.828000	0.29307	0.998000	0.56505	0.891000	0.51852	-0.119000	0.10676	0.094000	0.17404	-0.384000	0.06662	CGC	G|0.997;C|0.003	0.003	strong		0.378	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596	
ATXN1	6310	hgsc.bcm.edu	37	6	16327912	16327912	+	Missense_Mutation	SNP	C	C	A	rs369629396|rs368218879		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:16327912C>A	ENST00000244769.4	-	8	1566	c.630G>T	c.(628-630)caG>caT	p.Q210H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q210H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	210	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.H209_H211delHQH(1)		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)				gctgctgatgctgatgctgct	0.667																																					p.Q210H		Atlas-SNP	.											ATXN1,colon,carcinoma,0,2	ATXN1	117	2	1	Deletion - In frame(1)	prostate(1)	c.G630T						scavenged	.						5.0	8.0	7.0					6																	16327912		1576	3508	5084	SO:0001583	missense	6310	exon7			CTGATGCTGATGC	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.630G>T	6.37:g.16327912C>A	ENSP00000244769:p.Gln210His	Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	67	8	0.119403	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	C	4.990	0.183769	0.09495	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.50001	0.76;0.76	.	.	.	.	.	.	.	.	T	0.07413	0.0187	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.37709	-0.9694	5	0.15952	T	0.53	.	.	.	.	.	210	P54253	ATX1_HUMAN	H	210	ENSP00000244769:Q210H;ENSP00000416360:Q210H	ENSP00000244769:Q210H	Q	-	3	2	ATXN1	16435891	0.501000	0.26099	0.020000	0.16555	0.059000	0.15707	0.066000	0.14489	0.000000	0.14550	0.000000	0.15137	CAG	.	.	weak		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
POLM	27434	hgsc.bcm.edu	37	7	44116207	44116207	+	Missense_Mutation	SNP	C	C	A	rs28382653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44116207C>A	ENST00000242248.5	-	6	837	c.736G>T	c.(736-738)Gtc>Ttc	p.V246F	POLM_ENST00000335195.6_Missense_Mutation_p.V246F|POLM_ENST00000492971.1_5'UTR|POLM_ENST00000395831.3_Intron	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	246			V -> F (in dbSNP:rs28382653). {ECO:0000269|Ref.3}.		DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(3)|skin(2)	22						TTCACACCGACCCCGAAGATC	0.607								DNA polymerases (catalytic subunits)					C|||	52	0.0103834	0.0378	0.0029	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.V246F		Atlas-SNP	.											.	POLM	50	.	0			c.G736T						PASS	.	C	PHE/VAL	220,4186	132.5+/-169.0	7,206,1990	97.0	92.0	94.0		736	5.7	1.0	7	dbSNP_125	94	0,8600		0,0,4300	yes	missense	POLM	NM_013284.2	50	7,206,6290	AA,AC,CC		0.0,4.9932,1.6915	probably-damaging	246/495	44116207	220,12786	2203	4300	6503	SO:0001583	missense	27434	exon6			CACCGACCCCGAA	AF176097	CCDS34625.1, CCDS64635.1, CCDS64636.1	7p13	2012-05-18			ENSG00000122678	ENSG00000122678		"""DNA polymerases"""	9185	protein-coding gene	gene with protein product	"""Pol iota"""	606344				10982892	Standard	XM_005249708		Approved	Tdt-N	uc003tjt.3	Q9NP87	OTTHUMG00000155353	ENST00000242248.5:c.736G>T	7.37:g.44116207C>A	ENSP00000242248:p.Val246Phe	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Missense_Mutation	SNP	ENST00000242248.5	37	CCDS34625.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	C	18.48	3.633258	0.67015	0.049932	0.0	ENSG00000122678	ENST00000335195;ENST00000242248	T;T	0.59502	0.26;0.26	5.68	5.68	0.88126	DNA-directed DNA polymerase X (1);DNA polymerase lambda, fingers domain (2);	.	.	.	.	T	0.40272	0.1110	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.994;1.0	T	0.68066	-0.5507	9	0.87932	D	0	.	15.2786	0.73764	0.0:1.0:0.0:0.0	rs28382653	246;246	Q6P5X8;Q9NP87	.;DPOLM_HUMAN	F	246	ENSP00000335141:V246F;ENSP00000242248:V246F	ENSP00000242248:V246F	V	-	1	0	POLM	44082732	0.998000	0.40836	0.995000	0.50966	0.809000	0.45718	4.994000	0.63901	2.672000	0.90937	0.650000	0.86243	GTC	C|0.983;A|0.017	0.017	strong		0.607	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284	
FYCO1	79443	hgsc.bcm.edu	37	3	46009620	46009620	+	Silent	SNP	C	C	T	rs34147726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46009620C>T	ENST00000296137.2	-	8	1411	c.1206G>A	c.(1204-1206)gaG>gaA	p.E402E	FYCO1_ENST00000535325.1_Silent_p.E402E	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	402					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)		TCTCCCCTAGCTCCTGCATCT	0.572													C|||	489	0.0976438	0.354	0.0303	5008	,	,		19633	0.0		0.0	False		,,,				2504	0.0				p.E402E		Atlas-SNP	.											.	FYCO1	115	.	0			c.G1206A						PASS	.	C		1328,3078	445.1+/-347.6	201,926,1076	195.0	195.0	195.0		1206	2.8	0.9	3	dbSNP_126	195	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous	FYCO1	NM_024513.2		201,939,5363	TT,TC,CC		0.1512,30.1407,10.3106		402/1479	46009620	1341,11665	2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			CCCTAGCTCCTGC	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.1206G>A	3.37:g.46009620C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	139	59	0.42446	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																			C|0.907;T|0.093	0.093	strong		0.572	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
DHRS4L1	728635	hgsc.bcm.edu	37	14	24507003	24507003	+	RNA	SNP	A	A	C	rs28599797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24507003A>C	ENST00000558293.1	+	0	176					NR_102693.1																						CCCACGTGGTAGTCAGCCGCC	0.637													T|||	1608	0.321086	0.5908	0.2118	5008	,	,		16879	0.3641		0.0994	False		,,,				2504	0.2178				p.V60V		Atlas-SNP	.											.	.	.	.	0			c.A180C						PASS	.	T		2332,2074		618,1096,489	32.0	34.0	33.0		180	-5.3	0.5	14	dbSNP_125	33	912,7688		49,814,3437	no	coding-synonymous	DHRS4L1	NM_001082488.1		667,1910,3926	CC,CA,AA		10.6047,47.0722,24.9423		60/282	24507003	3244,9762	2203	4300	6503			728635	exon2			CGTGGTAGTCAGC																													14.37:g.24507003A>C		Somatic	283	1	0.00353357		WXS	Illumina HiSeq	Phase_I	317	169	0.533123	NM_001082488		Silent	SNP	ENST00000558293.1	37																																																																																				A|0.751;C|0.249	0.249	strong		0.637	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1		
CTBS	1486	hgsc.bcm.edu	37	1	85040069	85040069	+	Silent	SNP	G	G	A	rs2911592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	21	0	0		WXS	Illumina HiSeq	Phase_I	20	12	0.6	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	
RHBG	57127	hgsc.bcm.edu	37	1	156354367	156354367	+	Silent	SNP	A	A	G	rs6668857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156354367A>G	ENST00000368249.1	+	9	1322	c.1284A>G	c.(1282-1284)gcA>gcG	p.A428A	RHBG_ENST00000494874.1_3'UTR|RHBG_ENST00000255013.3_Silent_p.A359A|RHBG_ENST00000368246.2_Missense_Mutation_p.H427R|RHBG_ENST00000400992.2_Silent_p.A396A	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	428					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GACTCCCAGCACTACGAGGAC	0.617											OREG0013871	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3671	0.733027	0.8956	0.6686	5008	,	,		18513	0.8978		0.5149	False		,,,				2504	0.6135				p.H428R		Atlas-SNP	.											.	RHBG	133	.	0			c.A1283G						PASS	.	G	ARG/HIS	3441,611		1456,529,41	62.0	75.0	71.0		1284	5.9	1.0	1	dbSNP_116	71	4424,3942		1201,2022,960	no	missense	RHBG	NM_020407.3	29	2657,2551,1001	GG,GA,AA		47.1193,15.079,36.6645	benign	428/459	156354367	7865,4553	2026	4183	6209	SO:0001819	synonymous_variant	57127	exon10			CCCAGCACTACGA	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.1284A>G	1.37:g.156354367A>G		Somatic	142	0	0	1777	WXS	Illumina HiSeq	Phase_I	140	138	0.985714	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		1580	0.7234432234432234	445	0.9044715447154471	238	0.6574585635359116	503	0.8793706293706294	394	0.5197889182058048	G	17.33	3.362164	0.61403	0.84921	0.528807	ENSG00000132677	ENST00000368246	T	0.18174	2.23	5.94	5.94	0.96194	.	.	.	.	.	T	0.20088	0.0483	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.07751	-1.0756	5	0.87932	D	0	-24.589	11.3531	0.49600	0.083:0.0:0.917:0.0	rs6668857;rs17383530;rs17855291;rs59799121;rs6668857	.	.	.	R	427	ENSP00000357229:H427R	ENSP00000357229:H427R	H	+	2	0	RHBG	154620991	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	4.067000	0.57527	1.545000	0.49373	-0.215000	0.12644	CAC	A|0.291;G|0.709	0.709	strong		0.617	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
MICA	100507436	hgsc.bcm.edu	37	6	31379109	31379109	+	Missense_Mutation	SNP	G	G	A	rs1051794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31379109G>A	ENST00000449934.2	+	3	640	c.586G>A	c.(586-588)Gaa>Aaa	p.E196K	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)				GCGATATCTAGAATCCGGCGT	0.532													g|||	1826	0.364617	0.4796	0.4049	5008	,	,		21041	0.2996		0.3141	False		,,,				2504	0.2996				p.E196K		Atlas-SNP	.											.	MICA	21	.	0			c.G586A						PASS	.	G	LYS/GLU	580,804		132,316,244	98.0	87.0	91.0		586	-0.8	0.0	6	dbSNP_86	91	919,2263		126,667,798	yes	missense	MICA	NM_001177519.1	56	258,983,1042	AA,AG,GG		28.8812,41.9075,32.8296	benign	196/333	31379109	1499,3067	692	1591	2283	SO:0001583	missense	100507436	exon3			TATCTAGAATCCG	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.586G>A	6.37:g.31379109G>A	ENSP00000413079:p.Glu196Lys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	799	0.3658424908424908	227	0.4613821138211382	169	0.46685082872928174	160	0.27972027972027974	243	0.32058047493403696	N	4.401	0.074063	0.08485	0.419075	0.288812	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934	T	0.00864	5.6	1.31	-0.805	0.10879	.	3.050000	0.01394	N	0.013352	T	0.00271	0.0008	.	.	.	0.80722	P	0.0	B;B	0.12013	0.004;0.005	B;B	0.20577	0.012;0.03	T	0.47071	-0.9145	8	0.32370	T	0.25	.	2.9805	0.05952	0.2051:0.2819:0.5129:0.0	rs1051794;rs3192171;rs3819267;rs9266809;rs17417510;rs17845519;rs17858409;rs17883860;rs59858174;rs1051794	58;196	Q5SS58;Q96QC4	.;.	K	58;196;153;196	ENSP00000413079:E196K	ENSP00000365394:E196K	E	+	1	0	MICA	31487088	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.226000	0.09139	-0.322000	0.08615	-1.206000	0.01644	GAA	G|0.642;A|0.358	0.358	strong		0.532	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
MUC17	140453	hgsc.bcm.edu	37	7	100684550	100684550	+	Missense_Mutation	SNP	A	A	G	rs35090328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100684550A>G	ENST00000306151.4	+	3	9917	c.9853A>G	c.(9853-9855)Agt>Ggt	p.S3285G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3285	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)					TCCATTAACAAGTATGCCTGT	0.507													A|||	483	0.0964457	0.1188	0.0764	5008	,	,		28559	0.0615		0.1133	False		,,,				2504	0.0992				p.S3285G		Atlas-SNP	.											.	MUC17	804	.	0			c.A9853G						PASS	.	A	GLY/SER	470,3936		9,452,1742	342.0	338.0	339.0		9853	-2.2	0.0	7	dbSNP_126	339	950,7650		23,904,3373	no	missense	MUC17	NM_001040105.1	56	32,1356,5115	GG,GA,AA		11.0465,10.6673,10.918	possibly-damaging	3285/4494	100684550	1420,11586	2203	4300	6503	SO:0001583	missense	140453	exon3			TTAACAAGTATGC	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.9853A>G	7.37:g.100684550A>G	ENSP00000302716:p.Ser3285Gly	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	159	73	0.459119	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	180	0.08241758241758242	39	0.07926829268292683	31	0.0856353591160221	28	0.04895104895104895	82	0.10817941952506596	a	3.445	-0.113248	0.06881	0.106673	0.110465	ENSG00000169876	ENST00000306151	T	0.02579	4.24	1.46	-2.19	0.07015	.	.	.	.	.	T	0.00039	0.0001	N	0.03608	-0.345	0.09310	N	1	P	0.37985	0.613	B	0.37047	0.24	T	0.43212	-0.9405	9	0.20519	T	0.43	.	2.3573	0.04299	0.342:0.0:0.4041:0.2539	rs35090328;rs58812832	3285	Q685J3	MUC17_HUMAN	G	3285	ENSP00000302716:S3285G	ENSP00000302716:S3285G	S	+	1	0	MUC17	100471270	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.627000	0.05521	-0.483000	0.06772	0.165000	0.16767	AGT	A|0.904;G|0.096	0.096	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CDK11A	728642	hgsc.bcm.edu	37	1	1638925	1638925	+	Missense_Mutation	SNP	C	C	T	rs200982240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1638925C>T	ENST00000378633.1	-	11	1256	c.1177G>A	c.(1177-1179)Gac>Aac	p.D393N	CDK11A_ENST00000404249.3_Missense_Mutation_p.D390N|CDK11A_ENST00000378635.3_3'UTR|CDK11A_ENST00000357760.2_Missense_Mutation_p.D389N|CDK11A_ENST00000495016.1_5'Flank|CDK11A_ENST00000378638.2_Missense_Mutation_p.D356N|CDK11A_ENST00000356200.3_Missense_Mutation_p.D356N|CDK11A_ENST00000358779.5_Missense_Mutation_p.D380N|RP1-283E3.8_ENST00000598846.1_RNA			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	393					apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						GGCACATAGTCGCCCTCTGTC	0.652													-|||	1141	0.227835	0.4455	0.1138	5008	,	,		16575	0.2083		0.0636	False		,,,				2504	0.2035				p.D390N	Pancreas(186;965 2119 30274 40311 50569)	Atlas-SNP	.											CDK11B,caecum,carcinoma,0,2	CDK11A	38	2	0			c.G1168A						PASS	.	C	ASN/ASP,ASN/ASP	1529,2493		338,853,820	43.0	56.0	52.0		1168,1138	2.9	0.7	1	dbSNP_134	52	443,7837		32,379,3729	no	missense,missense	CDK11A	NM_024011.2,NM_033529.2	23,23	370,1232,4549	TT,TC,CC		5.3502,38.0159,16.0299	,	390/781,380/771	1638925	1972,10330	2011	4140	6151	SO:0001583	missense	728642	exon11			CATAGTCGCCCTC	AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128		"""Cyclin-dependent kinases"""	1730	protein-coding gene	gene with protein product		116951	"""cell division cycle 2-like 2"", ""cell division cycle 2-like 2 (PITSLRE proteins)"""	CDC2L3, CDC2L2		7920654, 9750192, 19884882	Standard	NM_033529		Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000378633.1:c.1177G>A	1.37:g.1638925C>T	ENSP00000367900:p.Asp393Asn	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	268	114	0.425373	NM_024011	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	Missense_Mutation	SNP	ENST00000378633.1	37		.	.	.	.	.	.	.	.	.	.	-	7.765	0.706297	0.15239	0.380159	0.053502	ENSG00000008128	ENST00000356200;ENST00000404249;ENST00000357760;ENST00000358779;ENST00000378633;ENST00000378638;ENST00000378630	T;T;T;T;T;T	0.05382	3.45;3.45;3.45;3.45;3.45;3.45	2.94	2.94	0.34122	.	0.322147	0.35870	N	0.002921	T	0.00012	0.0000	N	0.12182	0.205	0.09310	P	0.9999999999999996	B;B	0.15141	0.012;0.012	B;B	0.06405	0.002;0.002	T	0.49163	-0.8968	9	0.20046	T	0.44	.	13.0052	0.58701	0.0:1.0:0.0:0.0	.	390;380	Q9UQ88-2;Q9UQ88-4	.;.	N	356;390;389;380;393;356;356	ENSP00000348529:D356N;ENSP00000384442:D390N;ENSP00000350403:D389N;ENSP00000351629:D380N;ENSP00000367900:D393N;ENSP00000367905:D356N	ENSP00000348529:D356N	D	-	1	0	CDK11A	1628785	0.998000	0.40836	0.722000	0.30670	0.381000	0.30169	3.683000	0.54663	1.503000	0.48686	0.423000	0.28283	GAC	C|0.960;T|0.040	0.040	strong		0.652	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011	
KIAA1804	84451	hgsc.bcm.edu	37	1	233489682	233489682	+	Silent	SNP	G	G	A	rs56268427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:233489682G>A	ENST00000366624.3	+	3	1377	c.1116G>A	c.(1114-1116)ccG>ccA	p.P372P	MLK4_ENST00000366623.3_Silent_p.P372P	NM_032435.2	NP_115811.2																					GCCCTGAGCCGTTTGCCAAGC	0.468													G|||	255	0.0509185	0.1823	0.0173	5008	,	,		18556	0.0		0.002	False		,,,				2504	0.0				p.P372P		Atlas-SNP	.											.	KIAA1804	129	.	0			c.G1116A						PASS	.	G		698,3708	291.0+/-281.2	53,592,1558	126.0	110.0	116.0		1116	-9.8	0.1	1	dbSNP_129	116	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	KIAA1804	NM_032435.2		53,599,5851	AA,AG,GG		0.0814,15.842,5.4206		372/1037	233489682	705,12301	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGAGCCGTTTGCC																												ENST00000366624.3:c.1116G>A	1.37:g.233489682G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	212	107	0.504717	NM_032435		Silent	SNP	ENST00000366624.3	37	CCDS1598.1																																																																																			G|0.951;A|0.049	0.049	strong		0.468	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
ZSWIM1	90204	hgsc.bcm.edu	37	20	44512013	44512013	+	Missense_Mutation	SNP	C	C	G	rs115926000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44512013C>G	ENST00000372523.1	+	2	877	c.782C>G	c.(781-783)aCc>aGc	p.T261S	ZSWIM1_ENST00000372520.1_Missense_Mutation_p.T261S	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	261						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13		Myeloproliferative disorder(115;0.028)				CTCGAGGTCACCACCCACATC	0.562													C|||	11	0.00219649	0.0068	0.0	5008	,	,		20333	0.0		0.002	False		,,,				2504	0.0				p.T261S		Atlas-SNP	.											.	ZSWIM1	35	.	0			c.C782G						PASS	.	C	SER/THR	31,4375	37.6+/-69.7	0,31,2172	110.0	94.0	99.0		782	3.1	1.0	20	dbSNP_132	99	4,8596	3.7+/-12.6	0,4,4296	yes	missense	ZSWIM1	NM_080603.4	58	0,35,6468	GG,GC,CC		0.0465,0.7036,0.2691	benign	261/486	44512013	35,12971	2203	4300	6503	SO:0001583	missense	90204	exon2			AGGTCACCACCCA	AL008726	CCDS13382.2	20q13.12	2013-09-20	2003-12-17	2003-12-19	ENSG00000168612	ENSG00000168612		"""Zinc fingers, SWIM-type"""	16155	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 162"""	C20orf162			Standard	NM_080603		Approved	dJ337O18.5	uc010ghi.3	Q9BR11	OTTHUMG00000074023	ENST00000372523.1:c.782C>G	20.37:g.44512013C>G	ENSP00000361601:p.Thr261Ser	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	203	106	0.522168	NM_080603	Q5JZH2|Q9BR12|Q9BV30	Missense_Mutation	SNP	ENST00000372523.1	37	CCDS13382.2	4	0.0018315018315018315	3	0.006097560975609756	0	0.0	0	0.0	1	0.0013192612137203166	C	12.19	1.864270	0.32977	0.007036	4.65E-4	ENSG00000168612	ENST00000372523;ENST00000372520	T;T	0.24151	1.87;1.87	5.13	3.11	0.35812	.	0.437391	0.18795	U	0.130955	T	0.09905	0.0243	N	0.24115	0.695	0.19300	N	0.999977	B	0.30482	0.281	B	0.30029	0.11	T	0.26744	-1.0094	10	0.10902	T	0.67	-20.7697	8.035	0.30486	0.0:0.6753:0.0:0.3247	.	261	Q9BR11	ZSWM1_HUMAN	S	261	ENSP00000361601:T261S;ENSP00000361598:T261S	ENSP00000361598:T261S	T	+	2	0	ZSWIM1	43945420	0.268000	0.24133	0.996000	0.52242	0.990000	0.78478	0.495000	0.22483	0.669000	0.31146	0.555000	0.69702	ACC	C|0.998;G|0.002	0.002	strong		0.562	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603	
DHRS4L1	728635	hgsc.bcm.edu	37	14	24507010	24507010	+	RNA	SNP	C	C	A	rs12587718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	289	0	0		WXS	Illumina HiSeq	Phase_I	325	179	0.550769	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		
RBM46	166863	hgsc.bcm.edu	37	4	155720349	155720349	+	Silent	SNP	C	C	A	rs12651031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155720349C>A	ENST00000281722.3	+	4	1270	c.1035C>A	c.(1033-1035)ggC>ggA	p.G345G	RBM46_ENST00000510397.1_Silent_p.G345G|RBM46_ENST00000514866.1_Silent_p.G345G	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	345							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				AAACTCTAGGCAAGCTGCCAA	0.428													C|||	693	0.138379	0.3041	0.0476	5008	,	,		18198	0.1736		0.0338	False		,,,				2504	0.0501				p.G345G		Atlas-SNP	.											.	RBM46	76	.	0			c.C1035A						PASS	.	C		1211,3195	411.9+/-335.9	165,881,1157	76.0	80.0	79.0		1035	1.3	1.0	4	dbSNP_120	79	221,8379	91.6+/-153.7	2,217,4081	no	coding-synonymous	RBM46	NM_144979.3		167,1098,5238	AA,AC,CC		2.5698,27.4852,11.0103		345/534	155720349	1432,11574	2203	4300	6503	SO:0001819	synonymous_variant	166863	exon4			TCTAGGCAAGCTG	BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"""RNA binding motif (RRM) containing"""	28401	protein-coding gene	gene with protein product	"""cancer/testis antigen 68"""					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.1035C>A	4.37:g.155720349C>A		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	266	143	0.537594	NM_144979	B3KWU8|B4DZ27	Silent	SNP	ENST00000281722.3	37	CCDS3790.1																																																																																			C|0.880;A|0.120	0.120	strong		0.428	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979	
ITGAE	3682	hgsc.bcm.edu	37	17	3631241	3631241	+	Missense_Mutation	SNP	A	A	G	rs2976230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3631241A>G	ENST00000263087.4	-	26	3154	c.3056T>C	c.(3055-3057)gTa>gCa	p.V1019A	ITGAE_ENST00000571185.1_5'UTR|CTD-3195I5.4_ENST00000575043.1_RNA	NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	1019			V -> A (in dbSNP:rs2976230). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8119947}.		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)		CTTCACTGCTACAACCTGGAG	0.428													A|||	1411	0.281749	0.6513	0.2061	5008	,	,		20622	0.0476		0.2396	False		,,,				2504	0.1207				p.V1019A	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.T3056C						PASS	.	A	ALA/VAL	2478,1928	625.4+/-394.5	700,1078,425	123.0	119.0	120.0		3056	3.2	0.0	17	dbSNP_101	120	1912,6688	338.9+/-322.9	237,1438,2625	yes	missense	ITGAE	NM_002208.4	64	937,2516,3050	GG,GA,AA		22.2326,43.7585,33.7537	benign	1019/1180	3631241	4390,8616	2203	4300	6503	SO:0001583	missense	3682	exon26			ACTGCTACAACCT	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.3056T>C	17.37:g.3631241A>G	ENSP00000263087:p.Val1019Ala	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	219	125	0.570776	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	602	0.27564102564102566	317	0.6443089430894309	80	0.22099447513812154	24	0.04195804195804196	181	0.23878627968337732	A	7.129	0.579584	0.13686	0.562415	0.222326	ENSG00000083457	ENST00000263087	T	0.48836	0.8	5.39	3.19	0.36642	Integrin alpha-2 (1);	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	P	0.38280	0.625	B	0.37508	0.252	T	0.42032	-0.9475	8	0.41790	T	0.15	.	7.2351	0.26066	0.7444:0.0:0.2556:0.0	rs2976230;rs60211921;rs2976230	1019	P38570	ITAE_HUMAN	A	1019	ENSP00000263087:V1019A	ENSP00000263087:V1019A	V	-	2	0	ITGAE	3577990	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	1.346000	0.33964	0.450000	0.26774	-0.264000	0.10439	GTA	A|0.678;G|0.322	0.322	strong		0.428	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
NEIL2	252969	hgsc.bcm.edu	37	8	11643731	11643731	+	Silent	SNP	G	G	A	rs113110839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11643731G>A	ENST00000284503.6	+	5	1547	c.948G>A	c.(946-948)ccG>ccA	p.P316P	NEIL2_ENST00000436750.3_Silent_p.P316P|NEIL2_ENST00000455213.2_Silent_p.P316P|NEIL2_ENST00000403422.3_Silent_p.P255P|NEIL2_ENST00000528323.1_Silent_p.P200P	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	316					base-excision repair (GO:0006284)|nucleotide-excision repair (GO:0006289)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		GGTGGTGCCCGCAGTGCCAGC	0.612								Base excision repair (BER), DNA glycosylases					G|||	23	0.00459265	0.0166	0.0014	5008	,	,		17965	0.0		0.0	False		,,,				2504	0.0				p.P316P		Atlas-SNP	.											.	NEIL2	14	.	0			c.G948A						PASS	.	G	,,,	42,4362		0,42,2160	23.0	21.0	22.0		948,765,600,948	-10.7	0.2	8	dbSNP_132	22	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEIL2	NM_001135746.1,NM_001135747.1,NM_001135748.1,NM_145043.2	,,,	0,42,6459	AA,AG,GG		0.0,0.9537,0.323	,,,	316/333,255/272,200/217,316/333	11643731	42,12960	2202	4299	6501	SO:0001819	synonymous_variant	252969	exon5			GTGCCCGCAGTGC	AK056206	CCDS5984.1, CCDS47802.1, CCDS47803.1	8p23.1	2010-04-27	2010-04-27		ENSG00000154328	ENSG00000154328			18956	protein-coding gene	gene with protein product		608933	"""nei like 2 (E. coli)"""			12097317, 17686777	Standard	NM_145043		Approved	NEH2, FLJ31644, MGC2832, MGC4505	uc003wue.2	Q969S2	OTTHUMG00000090753	ENST00000284503.6:c.948G>A	8.37:g.11643731G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	235	126	0.53617	NM_001135746	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Silent	SNP	ENST00000284503.6	37	CCDS5984.1																																																																																			G|0.996;A|0.004	0.004	strong		0.612	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043	
OR10Z1	128368	hgsc.bcm.edu	37	1	158576394	158576394	+	Missense_Mutation	SNP	C	C	A	rs116792162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158576394C>A	ENST00000361284.1	+	1	166	c.166C>A	c.(166-168)Cac>Aac	p.H56N		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	56						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					TAGCCATCTGCACACCCCCAT	0.512													C|||	36	0.0071885	0.0265	0.0014	5008	,	,		20596	0.0		0.0	False		,,,				2504	0.0				p.H56N		Atlas-SNP	.											OR10Z1,right_upper_lobe,carcinoma,-1,1	OR10Z1	99	1	0			c.C166A						PASS	.	C	ASN/HIS	101,4305	79.9+/-118.3	1,99,2103	257.0	247.0	251.0		166	5.4	0.9	1	dbSNP_132	251	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR10Z1	NM_001004478.1	68	1,100,6402	AA,AC,CC		0.0116,2.2923,0.7843	probably-damaging	56/314	158576394	102,12904	2203	4300	6503	SO:0001583	missense	128368	exon1			CATCTGCACACCC	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.166C>A	1.37:g.158576394C>A	ENSP00000354707:p.His56Asn	Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	368	182	0.494565	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	16.63	3.176489	0.57692	0.022923	1.16E-4	ENSG00000198967	ENST00000361284	T	0.15952	2.38	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43579	D	0.000544	T	0.42449	0.1203	M	0.92268	3.29	0.34002	D	0.650477	D	0.76494	0.999	D	0.79108	0.992	T	0.56312	-0.8000	10	0.66056	D	0.02	.	13.5532	0.61745	0.1563:0.8437:0.0:0.0	.	56	Q8NGY1	O10Z1_HUMAN	N	56	ENSP00000354707:H56N	ENSP00000354707:H56N	H	+	1	0	OR10Z1	156843018	0.443000	0.25641	0.927000	0.36925	0.716000	0.41182	1.115000	0.31209	2.783000	0.95769	0.655000	0.94253	CAC	C|0.992;A|0.008	0.008	strong		0.512	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478	
STAMBP	10617	hgsc.bcm.edu	37	2	74057995	74057995	+	Silent	SNP	T	T	C	rs919629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74057995T>C	ENST00000394070.2	+	2	515	c.12T>C	c.(10-12)caT>caC	p.H4H	STAMBP_ENST00000394073.1_Silent_p.H4H|STAMBP_ENST00000536064.1_Silent_p.H4H|STAMBP_ENST00000339566.3_Silent_p.H4H|STAMBP_ENST00000409707.1_Silent_p.H4H	NM_213622.2	NP_998787.1	O95630	STABP_HUMAN	STAM binding protein	4	Interaction with CHMP3.				JAK-STAT cascade (GO:0007259)|mitotic cytokinesis (GO:0000281)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of cell proliferation (GO:0008284)|protein deubiquitination (GO:0016579)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	18						TGTCTGACCATGGAGATGTGA	0.532													T|||	625	0.1248	0.3116	0.1369	5008	,	,		20104	0.0734		0.0179	False		,,,				2504	0.0266				p.H4H		Atlas-SNP	.											.	STAMBP	37	.	0			c.T12C						PASS	.	T	,,	1163,3243	406.0+/-333.7	148,867,1188	45.0	46.0	46.0		12,12,12	3.7	1.0	2	dbSNP_86	46	158,8442	74.8+/-137.4	0,158,4142	no	coding-synonymous,coding-synonymous,coding-synonymous	STAMBP	NM_006463.4,NM_201647.2,NM_213622.2	,,	148,1025,5330	CC,CT,TT		1.8372,26.3958,10.1569	,,	4/425,4/425,4/425	74057995	1321,11685	2203	4300	6503	SO:0001819	synonymous_variant	10617	exon3			TGACCATGGAGAT	BC007682	CCDS1929.1	2p24.3-p24.1	2008-02-05			ENSG00000124356	ENSG00000124356			16950	protein-coding gene	gene with protein product		606247				10383417	Standard	NM_006463		Approved	AMSH	uc002sjs.3	O95630	OTTHUMG00000129817	ENST00000394070.2:c.12T>C	2.37:g.74057995T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_006463	B5M0B6|D6W5H7|Q3MJE7	Silent	SNP	ENST00000394070.2	37	CCDS1929.1																																																																																			T|0.896;C|0.104	0.104	strong		0.532	STAMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252048.2	NM_006463	
MUC17	140453	hgsc.bcm.edu	37	7	100678622	100678622	+	Missense_Mutation	SNP	G	G	A	rs77299546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678622G>A	ENST00000306151.4	+	3	3989	c.3925G>A	c.(3925-3927)Gtg>Atg	p.V1309M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1309	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)					TAAAGGTCCTGTGGTCACTTC	0.448																																					p.V1309M		Atlas-SNP	.											.	MUC17	804	.	0			c.G3925A						PASS	.						236.0	226.0	229.0					7																	100678622		2203	4300	6503	SO:0001583	missense	140453	exon3			GGTCCTGTGGTCA	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.3925G>A	7.37:g.100678622G>A	ENSP00000302716:p.Val1309Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	138	22	0.15942	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.174	-1.068527	0.01934	.	.	ENSG00000169876	ENST00000306151	T	0.02763	4.17	0.471	-0.621	0.11564	.	.	.	.	.	T	0.04272	0.0118	L	0.29908	0.895	0.09310	N	1	D	0.54964	0.969	P	0.55667	0.781	T	0.44143	-0.9347	8	0.33940	T	0.23	.	.	.	.	.	1309	Q685J3	MUC17_HUMAN	M	1309	ENSP00000302716:V1309M	ENSP00000302716:V1309M	V	+	1	0	MUC17	100465342	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.596000	0.05720	-0.241000	0.09681	-1.379000	0.01178	GTG	G|0.936;A|0.064	0.064	strong		0.448	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CAPN14	440854	hgsc.bcm.edu	37	2	31411184	31411184	+	Splice_Site	SNP	C	C	A	rs1465972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31411184C>A	ENST00000403897.3	-	14	1671	c.1530G>T	c.(1528-1530)aaG>aaT	p.K510N	CAPN14_ENST00000444918.2_Splice_Site_p.K510N	NM_001145122.1	NP_001138594.1	A8MX76	CAN14_HUMAN	calpain 14	510	Linker.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)	p.K510N(1)		NS(1)|endometrium(2)|prostate(1)|skin(1)|stomach(2)	7						GACTACTCACCTTTGAGAAGA	0.463													C|||	1654	0.330272	0.5908	0.389	5008	,	,		21271	0.1558		0.1899	False		,,,				2504	0.2607				p.K510N		Atlas-SNP	.											CAPN14,NS,carcinoma,0,1	CAPN14	36	1	1	Substitution - Missense(1)	stomach(1)	c.G1530T						PASS	.	C	ASN/LYS	716,668		183,350,159	88.0	97.0	95.0		1530	3.3	0.2	2	dbSNP_88	95	530,2652		50,430,1111	yes	missense-near-splice	CAPN14	NM_001145122.1	94	233,780,1270	AA,AC,CC		16.6562,48.2659,27.2887	possibly-damaging	510/685	31411184	1246,3320	692	1591	2283	SO:0001630	splice_region_variant	440854	exon14			ACTCACCTTTGAG	AC015980	CCDS46254.1	2p23.1-p21	2013-01-10			ENSG00000214711	ENSG00000214711		"""EF-hand domain containing"""	16664	protein-coding gene	gene with protein product		610229				11675017	Standard	NM_001145122		Approved		uc010yms.2	A8MX76	OTTHUMG00000152039	ENST00000403897.3:c.1530+1G>T	2.37:g.31411184C>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_001145122	B3KRU9	Missense_Mutation	SNP	ENST00000403897.3	37	CCDS46254.1	648	0.2967032967032967	273	0.5548780487804879	131	0.36187845303867405	94	0.16433566433566432	150	0.19788918205804748	C	10.43	1.349387	0.24426	0.517341	0.166562	ENSG00000214711	ENST00000444918;ENST00000403897	D;D	0.87334	-2.24;-2.24	4.16	3.26	0.37387	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.37244	P	0.09373900000000002	B;P	0.44429	0.18;0.835	B;B	0.42798	0.112;0.398	T	0.44190	-0.9344	7	.	.	.	.	11.0223	0.47726	0.0:0.8103:0.1897:0.0	rs1465972;rs52798796;rs57316229;rs1465972	510;334	A8MX76;A8MX76-2	CAN14_HUMAN;.	N	510	ENSP00000398670:K510N;ENSP00000385247:K510N	.	K	-	3	2	CAPN14	31264688	1.000000	0.71417	0.214000	0.23707	0.017000	0.09413	3.590000	0.53979	0.702000	0.31825	0.655000	0.94253	AAG	C|0.704;A|0.296	0.296	strong		0.463	CAPN14-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325010.1	NM_001145122	Missense_Mutation
MUC5B	727897	hgsc.bcm.edu	37	11	1271429	1271429	+	Missense_Mutation	SNP	C	C	T	rs2943516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1271429C>T	ENST00000529681.1	+	31	13377	c.13319C>T	c.(13318-13320)cCg>cTg	p.P4440L	MUC5B_ENST00000447027.1_Missense_Mutation_p.P4443L|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4440	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.		P -> L (in dbSNP:rs2943516). {ECO:0000269|PubMed:9013550}.		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)		ACGGCCACCCCGTCCTCCACC	0.682													-|||	2339	0.467053	0.3222	0.5476	5008	,	,		18729	0.6518		0.4423	False		,,,				2504	0.4407				p.P4440L		Atlas-SNP	.											.	MUC5B	473	.	0			c.C13319T						PASS	.	C	LEU/PRO	1253,2885		195,863,1011	105.0	124.0	118.0		13319	-0.1	0.0	11	dbSNP_101	118	3605,4779		799,2007,1386	no	missense	MUC5B	NM_002458.2	98	994,2870,2397	TT,TC,CC		42.9986,30.2803,38.7957	benign	4440/5763	1271429	4858,7664	2069	4192	6261	SO:0001583	missense	727897	exon31			CCACCCCGTCCTC	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.13319C>T	11.37:g.1271429C>T	ENSP00000436812:p.Pro4440Leu	Somatic	443	1	0.00225734		WXS	Illumina HiSeq	Phase_I	470	208	0.442553	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	1045	0.4784798534798535	151	0.30691056910569103	181	0.5	386	0.6748251748251748	327	0.4313984168865435	-	5.129	0.209405	0.09757	0.302803	0.429986	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000535652	T;T	0.17854	2.25;2.44	2.45	-0.0467	0.13846	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B;B	0.31931	0.347;0.347	B;B	0.13407	0.005;0.009	T	0.29336	-1.0015	8	0.87932	D	0	.	4.2572	0.10722	0.0:0.5967:0.2354:0.1679	rs2943516	4913;4443	A7Y9J9;E9PBJ0	.;.	L	4440;4443;4384;4290;219	ENSP00000436812:P4440L;ENSP00000415793:P4443L	ENSP00000343037:P4384L	P	+	2	0	MUC5B	1228005	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.119000	0.15626	0.155000	0.19261	0.298000	0.19748	CCG	C|0.521;T|0.479	0.479	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
NCKAP5	344148	hgsc.bcm.edu	37	2	133887676	133887676	+	Missense_Mutation	SNP	T	T	C	rs35356262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:133887676T>C	ENST00000409261.1	-	6	588	c.215A>G	c.(214-216)aAg>aGg	p.K72R	NCKAP5_ENST00000405974.3_Missense_Mutation_p.K72R|NCKAP5_ENST00000317721.6_Missense_Mutation_p.K72R|NCKAP5_ENST00000409213.1_Missense_Mutation_p.K72R	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	72										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						ATGTATCAGCTTCTCATGCTA	0.403													T|||	6	0.00119808	0.0045	0.0	5008	,	,		20515	0.0		0.0	False		,,,				2504	0.0				p.K72R		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A215G						PASS	.	T	ARG/LYS,ARG/LYS	25,3761		0,25,1868	69.0	65.0	66.0		215,215	3.8	1.0	2	dbSNP_126	66	0,8236		0,0,4118	yes	missense,missense	NCKAP5	NM_207363.2,NM_207481.3	26,26	0,25,5986	CC,CT,TT		0.0,0.6603,0.208	probably-damaging,probably-damaging	72/1910,72/591	133887676	25,11997	1893	4118	6011	SO:0001583	missense	344148	exon6			ATCAGCTTCTCAT	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.215A>G	2.37:g.133887676T>C	ENSP00000387128:p.Lys72Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	2|2	9.157509157509158E-4|9.157509157509158E-4	2|2	0.0040650406504065045|0.0040650406504065045	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	T|T	22.4|22.4	4.279946|4.279946	0.80692|0.80692	0.006603|0.006603	0.0|0.0	ENSG00000176771|ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661;ENST00000542834|ENST00000427594	T;T;T;T|.	0.51817|.	2.68;0.69;2.68;0.69|.	6.17|6.17	3.85|3.85	0.44370|0.44370	.|.	.|.	.|.	.|.	.|.	T|T	0.19765|0.19765	0.0475|0.0475	L|L	0.27053|0.27053	0.805|0.805	0.24242|0.24242	N|N	0.995352|0.995352	B;B;B;D|.	0.58620|.	0.006;0.063;0.126;0.983|.	B;B;B;P|.	0.56865|.	0.005;0.033;0.074;0.808|.	T|T	0.14952|0.14952	-1.0454|-1.0454	9|5	0.66056|.	D|.	0.02|.	.|.	7.094|7.094	0.25299|0.25299	0.0:0.1686:0.0:0.8314|0.0:0.1686:0.0:0.8314	rs35356262|rs35356262	72;47;72;72|.	F5GYX5;O14513-3;O14513-2;O14513|.	.;.;.;NCKP5_HUMAN|.	R|G	72;72;72;72;72;47|68	ENSP00000387128:K72R;ENSP00000386952:K72R;ENSP00000380603:K72R;ENSP00000385692:K72R|.	ENSP00000380603:K72R|.	K|S	-|-	2|1	0|0	NCKAP5|NCKAP5	133604146|133604146	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	3.758000|3.758000	0.55220|0.55220	1.163000|1.163000	0.42636|0.42636	0.533000|0.533000	0.62120|0.62120	AAG|AGC	T|0.999;C|0.001	0.001	strong		0.403	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
KIAA0922	23240	hgsc.bcm.edu	37	4	154523373	154523373	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:154523373C>T	ENST00000409663.3	+	22	2385	c.2333C>T	c.(2332-2334)cCt>cTt	p.P778L	KIAA0922_ENST00000409959.3_Missense_Mutation_p.P779L|KIAA0922_ENST00000440693.1_Missense_Mutation_p.P695L	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	778						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)				GGACCTCTTCCTATAACTGTT	0.353																																					p.P779L		Atlas-SNP	.											KIAA0922_ENST00000409959,NS,malignant_melanoma,0,2	KIAA0922	214	2	0			c.C2336T						scavenged	.						95.0	97.0	97.0					4																	154523373		2203	4300	6503	SO:0001583	missense	23240	exon22			CTCTTCCTATAAC	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.2333C>T	4.37:g.154523373C>T	ENSP00000386574:p.Pro778Leu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	135	2	0.0148148	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	C	22.3	4.277864	0.80692	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.26067	2.01;1.76;2.0;1.77	5.81	4.94	0.65067	.	0.103125	0.64402	D	0.000002	T	0.55561	0.1928	M	0.85859	2.78	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.982	D;D;P	0.68621	0.925;0.959;0.798	T	0.64786	-0.6325	10	0.72032	D	0.01	-9.503	16.5544	0.84482	0.0:0.8693:0.1307:0.0	.	695;779;778	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	L	778;695;779;556	ENSP00000386574:P778L;ENSP00000409663:P695L;ENSP00000386787:P779L;ENSP00000240487:P556L	ENSP00000240487:P556L	P	+	2	0	KIAA0922	154742823	1.000000	0.71417	0.895000	0.35142	0.804000	0.45430	5.641000	0.67881	1.384000	0.46424	0.655000	0.94253	CCT	.	.	none		0.353	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
MAGEA8	4107	hgsc.bcm.edu	37	X	149013963	149013963	+	Missense_Mutation	SNP	C	C	T	rs12010332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:149013963C>T	ENST00000542674.1	+	3	1438	c.917C>T	c.(916-918)tCc>tTc	p.S306F	MAGEA8_ENST00000535454.1_Missense_Mutation_p.S306F|MAGEA8_ENST00000286482.1_Missense_Mutation_p.S306F	NM_001166401.1	NP_001159873.1	P43361	MAGA8_HUMAN	melanoma antigen family A, 8	306	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		S -> F (in dbSNP:rs12010332).							NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(12)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)					TCCTACCCATCCCTGCATGAA	0.572													c|||	182	0.0482119	0.1248	0.0144	3775	,	,		15794	0.004		0.002	False		,,,				2504	0.001				p.S306F		Atlas-SNP	.											.	MAGEA8	40	.	0			c.C917T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER	568,3267		39,405,85,1188,486	92.0	88.0	89.0		917,917,917	0.7	0.0	X	dbSNP_120	89	8,6718		0,6,2,2422,1868	yes	missense,missense,missense	MAGEA8	NM_001166400.1,NM_001166401.1,NM_005364.4	155,155,155	39,411,87,3610,2354	TT,TC,T,CC,C		0.1189,14.811,5.454	probably-damaging,probably-damaging,probably-damaging	306/319,306/319,306/319	149013963	576,9985	2203	4298	6501	SO:0001583	missense	4107	exon3			ACCCATCCCTGCA		CCDS14692.1	Xq28	2009-03-13			ENSG00000156009	ENSG00000156009			6806	protein-coding gene	gene with protein product	"""MAGE-8 antigen"", ""cancer/testis antigen family 1, member 8"""	300341		MAGE8		8575766	Standard	NM_005364		Approved	MGC2182, CT1.8	uc004fdw.2	P43361	OTTHUMG00000022635	ENST00000542674.1:c.917C>T	X.37:g.149013963C>T	ENSP00000443776:p.Ser306Phe	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	293	293	1	NM_005364	Q9BUN9	Missense_Mutation	SNP	ENST00000542674.1	37	CCDS14692.1	72	0.0433996383363472	47	0.10262008733624454	3	0.008426966292134831	1	0.0017482517482517483	1	0.0013192612137203166	.	3.559	-0.090020	0.07053	0.14811	0.001189	ENSG00000156009	ENST00000535454;ENST00000542674;ENST00000286482	T;T;T	0.01871	4.59;4.59;4.59	0.68	0.68	0.17980	.	5.208330	0.00397	N	0.000056	T	0.00039	0.0001	L	0.59967	1.855	0.80722	P	0.0	D	0.71674	0.998	P	0.57679	0.825	T	0.48210	-0.9055	8	0.08837	T	0.75	.	.	.	.	rs12010332;rs52806623;rs12010332	306	P43361	MAGA8_HUMAN	F	306	ENSP00000438293:S306F;ENSP00000443776:S306F;ENSP00000286482:S306F	ENSP00000286482:S306F	S	+	2	0	MAGEA8	148774621	0.000000	0.05858	0.001000	0.08648	0.501000	0.33797	-0.990000	0.03732	0.588000	0.29660	0.190000	0.17370	TCC	C|0.947;T|0.053	0.053	strong		0.572	MAGEA8-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058728.1	NM_005364	
ZNF500	26048	hgsc.bcm.edu	37	16	4810583	4810583	+	Missense_Mutation	SNP	C	C	T	rs151148153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4810583C>T	ENST00000219478.6	-	5	969	c.670G>A	c.(670-672)Gtg>Atg	p.V224M	ZNF500_ENST00000545009.1_Missense_Mutation_p.V224M			O60304	ZN500_HUMAN	zinc finger protein 500	224	KRAB.				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						TCCAAGTTCACGGGCACCTGC	0.632													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		20443	0.0		0.0	False		,,,				2504	0.0				p.V224M		Atlas-SNP	.											.	ZNF500	45	.	0			c.G670A						PASS	.	C	MET/VAL	65,4329	61.1+/-98.1	0,65,2132	96.0	79.0	85.0		670	3.2	0.1	16	dbSNP_134	85	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ZNF500	NM_021646.1	21	0,71,6426	TT,TC,CC		0.0698,1.4793,0.5464	possibly-damaging	224/481	4810583	71,12923	2197	4300	6497	SO:0001583	missense	26048	exon5			AGTTCACGGGCAC	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.670G>A	16.37:g.4810583C>T	ENSP00000219478:p.Val224Met	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_021646	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Missense_Mutation	SNP	ENST00000219478.6	37	CCDS32383.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	14.40	2.524884	0.44969	0.014793	6.98E-4	ENSG00000103199	ENST00000545009;ENST00000219478	T;T	0.05925	3.37;3.37	3.16	3.16	0.36331	Krueppel-associated box (3);	.	.	.	.	T	0.11495	0.0280	L	0.51853	1.615	0.21445	N	0.99968	D;D	0.76494	0.995;0.999	P;P	0.61874	0.82;0.895	T	0.04165	-1.0972	9	0.48119	T	0.1	.	12.1628	0.54113	0.0:1.0:0.0:0.0	.	224;224	B4DNN9;O60304	.;ZN500_HUMAN	M	224	ENSP00000445714:V224M;ENSP00000219478:V224M	ENSP00000219478:V224M	V	-	1	0	ZNF500	4750584	0.000000	0.05858	0.066000	0.19879	0.003000	0.03518	0.802000	0.27069	1.785000	0.52413	0.655000	0.94253	GTG	C|0.995;T|0.005	0.005	strong		0.632	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507	
ZNF594	84622	hgsc.bcm.edu	37	17	5085758	5085758	+	Silent	SNP	G	G	A	rs144567321		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085758G>A	ENST00000399604.4	-	1	1934	c.1794C>T	c.(1792-1794)tgC>tgT	p.C598C	ZNF594_ENST00000575779.1_Silent_p.C598C			Q96JF6	ZN594_HUMAN	zinc finger protein 594	598					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.C598C(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CACATTCTTTGCATTCATATG	0.413																																					p.C598C		Atlas-SNP	.											ZNF594,colon,carcinoma,-2,3	ZNF594	89	3	1	Substitution - coding silent(1)	ovary(1)	c.C1794T						PASS	.						163.0	165.0	165.0					17																	5085758		2036	4211	6247	SO:0001819	synonymous_variant	84622	exon2			TTCTTTGCATTCA	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.1794C>T	17.37:g.5085758G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	92	16	0.173913	NM_032530	Q6RFS0	Silent	SNP	ENST00000399604.4	37	CCDS42241.1																																																																																			G|0.994;A|0.006	0.006	strong		0.413	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
AADACL3	126767	hgsc.bcm.edu	37	1	12779618	12779618	+	Missense_Mutation	SNP	T	T	C	rs3010877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12779618T>C	ENST00000359318.5	+	2	344	c.139T>C	c.(139-141)Tcc>Ccc	p.S47P	AADACL3_ENST00000332530.3_Intron	NM_001103170.1	NP_001096640.1	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3	47			S -> P (in dbSNP:rs3010877).				hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	15	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		GCTGTACCAATCCAAGGCATC	0.517													C|||	4247	0.848043	0.9228	0.879	5008	,	,		18666	0.7817		0.826	False		,,,				2504	0.816				p.S47P		Atlas-SNP	.											.	AADACL3	84	.	0			c.T139C						PASS	.	C	,PRO/SER	3656,336		1670,316,10	105.0	110.0	109.0		,139	4.4	0.4	1	dbSNP_101	109	6915,1421		2853,1209,106	yes	intron,missense	AADACL3	NM_001103169.1,NM_001103170.1	,74	4523,1525,116	CC,CT,TT		17.0465,8.4168,14.2521	,benign	,47/351	12779618	10571,1757	1996	4168	6164	SO:0001583	missense	126767	exon2			TACCAATCCAAGG		CCDS41253.1	1p36.21	2014-07-17			ENSG00000188984	ENSG00000188984			32037	protein-coding gene	gene with protein product							Standard	XM_006710337		Approved	OTTHUMG00000001887	uc009vnn.1	Q5VUY0	OTTHUMG00000001887	ENST00000359318.5:c.139T>C	1.37:g.12779618T>C	ENSP00000352268:p.Ser47Pro	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	145	142	0.97931	NM_001103170	B3KXR9|Q5VUY1	Missense_Mutation	SNP	ENST00000359318.5	37	CCDS41253.1	1860	0.8516483516483516	451	0.9166666666666666	316	0.8729281767955801	463	0.8094405594405595	630	0.8311345646437994	C	0.175	-1.067753	0.01934	0.915832	0.829535	ENSG00000188984	ENST00000359318	T	0.02656	4.21	4.44	4.44	0.53790	.	0.055747	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00026	-2.67	0.58432	P	9.99999999995449E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.24083	-1.0170	9	0.02654	T	1	-17.4213	9.7469	0.40453	0.0:0.9025:0.0:0.0975	rs3010877;rs52820652;rs59887427;rs3010877	47	Q5VUY0	ADCL3_HUMAN	P	47	ENSP00000352268:S47P	ENSP00000352268:S47P	S	+	1	0	AADACL3	12702205	0.996000	0.38824	0.397000	0.26308	0.034000	0.12701	2.226000	0.42963	1.108000	0.41662	-0.320000	0.08662	TCC	T|0.150;C|0.850	0.850	strong		0.517	AADACL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005324.2	NM_001103170	
EMR1	2015	hgsc.bcm.edu	37	19	6901891	6901891	+	Missense_Mutation	SNP	G	G	A	rs897738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6901891G>A	ENST00000312053.4	+	6	557	c.520G>A	c.(520-522)Gat>Aat	p.D174N	EMR1_ENST00000381407.5_Intron|EMR1_ENST00000250572.8_Missense_Mutation_p.D174N|EMR1_ENST00000450315.3_Intron|EMR1_ENST00000601198.1_3'UTR|EMR1_ENST00000381404.4_Missense_Mutation_p.D122N	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	174	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		D -> N (in dbSNP:rs897738). {ECO:0000269|PubMed:7601460}.		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)					TTCAGACGTGGATGAATGTGC	0.438													g|||	2170	0.433307	0.6664	0.4193	5008	,	,		22002	0.4563		0.2396	False		,,,				2504	0.3037				p.D174N		Atlas-SNP	.											.	EMR1	153	.	0			c.G520A						PASS	.	G	ASN/ASP	2595,1811	640.0+/-397.2	780,1035,388	265.0	277.0	273.0		520	1.8	0.4	19	dbSNP_86	273	2211,6389	375.5+/-337.8	290,1631,2379	yes	missense	EMR1	NM_001974.3	23	1070,2666,2767	AA,AG,GG		25.7093,41.103,36.9522	possibly-damaging	174/887	6901891	4806,8200	2203	4300	6503	SO:0001583	missense	2015	exon6			GACGTGGATGAAT	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.520G>A	19.37:g.6901891G>A	ENSP00000311545:p.Asp174Asn	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	919	0.4207875457875458	318	0.6463414634146342	137	0.3784530386740331	284	0.4965034965034965	180	0.23746701846965698	G	5.882	0.346823	0.11126	0.58897	0.257093	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572	D;D;D	0.94280	-3.39;-3.39;-3.39	3.97	1.81	0.25067	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	N	0.20483	0.58	0.09310	P	0.99999999865625	B;B;B	0.19073	0.004;0.028;0.033	B;B;B	0.20577	0.006;0.027;0.03	T	0.45498	-0.9257	8	0.18276	T	0.48	.	7.0917	0.25287	0.223:0.0:0.777:0.0	rs897738;rs2228535;rs52838339;rs58854526;rs897738	174;122;174	Q14246-2;E9PD45;Q14246	.;.;EMR1_HUMAN	N	174;174;122;174	ENSP00000311545:D174N;ENSP00000370811:D122N;ENSP00000250572:D174N	ENSP00000250572:D174N	D	+	1	0	EMR1	6852891	0.889000	0.30405	0.388000	0.26195	0.002000	0.02628	0.319000	0.19522	0.170000	0.19704	-0.343000	0.07986	GAT	G|0.597;T|0.003	.	strong		0.438	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
COMMD8	54951	hgsc.bcm.edu	37	4	47462210	47462210	+	Missense_Mutation	SNP	A	A	C	rs114141818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:47462210A>C	ENST00000381571.4	-	2	240	c.173T>G	c.(172-174)aTt>aGt	p.I58S		NM_017845.3	NP_060315.1	Q9NX08	COMD8_HUMAN	COMM domain containing 8	58										large_intestine(2)|lung(5)|prostate(1)	8						AAATTTGGCAATATCTTCTAA	0.353													a|||	64	0.0127796	0.0469	0.0029	5008	,	,		16655	0.0		0.0	False		,,,				2504	0.0				p.I58S		Atlas-SNP	.											.	COMMD8	15	.	0			c.T173G						PASS	.	G	SER/ILE	201,4205	126.1+/-163.2	3,195,2005	104.0	106.0	106.0		173	1.7	0.0	4	dbSNP_132	106	2,8598		0,2,4298	yes	missense	COMMD8	NM_017845.3	142	3,197,6303	CC,CA,AA		0.0233,4.562,1.5608	benign	58/184	47462210	203,12803	2203	4300	6503	SO:0001583	missense	54951	exon2			TTGGCAATATCTT	AY542163	CCDS3475.1	4p12	2008-02-05			ENSG00000169019	ENSG00000169019			26036	protein-coding gene	gene with protein product						15799966	Standard	NM_017845		Approved	FLJ20502	uc003gxi.3	Q9NX08	OTTHUMG00000099435	ENST00000381571.4:c.173T>G	4.37:g.47462210A>C	ENSP00000370984:p.Ile58Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_017845	Q8WUR4|Q9HC15	Missense_Mutation	SNP	ENST00000381571.4	37	CCDS3475.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	a	1.694	-0.503300	0.04261	0.04562	2.33E-4	ENSG00000169019	ENST00000381571	T	0.11277	2.79	5.57	1.71	0.24356	.	0.431904	0.26832	N	0.022272	T	0.01189	0.0039	L	0.35723	1.085	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.28933	-1.0028	10	0.44086	T	0.13	-30.318	8.7378	0.34539	0.6292:0.0:0.3708:0.0	.	58	Q9NX08	COMD8_HUMAN	S	58	ENSP00000370984:I58S	ENSP00000370984:I58S	I	-	2	0	COMMD8	47156967	0.102000	0.21896	0.018000	0.16275	0.009000	0.06853	1.363000	0.34159	0.090000	0.17273	-0.253000	0.11424	ATT	A|0.985;C|0.015	0.015	strong		0.353	COMMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216898.2	NM_017845	
TMCO3	55002	hgsc.bcm.edu	37	13	114152755	114152755	+	Silent	SNP	C	C	T	rs2260218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114152755C>T	ENST00000434316.2	+	3	902	c.543C>T	c.(541-543)gaC>gaT	p.D181D	TMCO3_ENST00000375391.1_Silent_p.D181D|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	181						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			CCATGCTTGACGAGATTCTTG	0.398													.|||	1019	0.203474	0.4092	0.1369	5008	,	,		19525	0.1488		0.1292	False		,,,				2504	0.1053				p.D181D		Atlas-SNP	.											.	TMCO3	77	.	0			c.C543T						PASS	.	C		1511,2895	481.5+/-359.1	256,999,948	133.0	130.0	131.0		543	-3.9	0.0	13	dbSNP_100	131	1089,7511	226.6+/-262.3	62,965,3273	no	coding-synonymous	TMCO3	NM_017905.4		318,1964,4221	TT,TC,CC		12.6628,34.2941,19.9908		181/678	114152755	2600,10406	2203	4300	6503	SO:0001819	synonymous_variant	55002	exon3			GCTTGACGAGATT	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.543C>T	13.37:g.114152755C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																			C|0.795;T|0.205	0.205	strong		0.398	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
SLC6A5	9152	hgsc.bcm.edu	37	11	20622975	20622975	+	Missense_Mutation	SNP	G	G	A	rs1443547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:20622975G>A	ENST00000525748.1	+	2	577	c.304G>A	c.(304-306)Ggc>Agc	p.G102S		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	102			G -> S (in dbSNP:rs1443547). {ECO:0000269|PubMed:10381548}.		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)	AGAGGCGCAAGGCGCGCAGGC	0.701													G|||	2032	0.405751	0.447	0.3804	5008	,	,		14053	0.3651		0.3847	False		,,,				2504	0.4315				p.G102S		Atlas-SNP	.											.	SLC6A5	151	.	0			c.G304A						PASS	.	G	SER/GLY	1916,2474		441,1034,720	16.0	19.0	18.0		304	-4.0	0.0	11	dbSNP_88	18	2871,5697		529,1813,1942	no	missense	SLC6A5	NM_004211.3	56	970,2847,2662	AA,AG,GG		33.5084,43.6446,36.9424	benign	102/798	20622975	4787,8171	2195	4284	6479	SO:0001583	missense	9152	exon2			GCGCAAGGCGCGC	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.304G>A	11.37:g.20622975G>A	ENSP00000434364:p.Gly102Ser	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_004211	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	806	0.36904761904761907	202	0.4105691056910569	126	0.34806629834254144	201	0.3513986013986014	277	0.3654353562005277	G	1.537	-0.542827	0.04053	0.436446	0.335084	ENSG00000165970	ENST00000525748	T	0.70631	-0.5	5.37	-3.96	0.04106	.	1.669100	0.02954	N	0.142135	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.13176	-1.0519	9	0.07175	T	0.84	.	6.8887	0.24216	0.5281:0.227:0.2449:0.0	rs1443547;rs1443547	102	Q9Y345	SC6A5_HUMAN	S	102	ENSP00000434364:G102S	ENSP00000298923:G102S	G	+	1	0	SLC6A5	20579551	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	-0.675000	0.05227	-0.904000	0.03876	0.462000	0.41574	GGC	G|0.607;A|0.393	0.393	strong		0.701	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
FJX1	24147	hgsc.bcm.edu	37	11	35641428	35641428	+	Missense_Mutation	SNP	G	G	A	rs12286850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:35641428G>A	ENST00000317811.4	+	1	1694	c.1244G>A	c.(1243-1245)cGc>cAc	p.R415H	FJX1_ENST00000532914.1_3'UTR	NM_014344.3	NP_055159.2	Q86VR8	FJX1_HUMAN	four jointed box 1 (Drosophila)	415			R -> H (in dbSNP:rs12286850).		retina layer formation (GO:0010842)	extracellular space (GO:0005615)				lung(1)|urinary_tract(1)	2	all_cancers(35;0.177)|all_lung(20;0.0238)|Lung NSC(22;0.0494)|all_epithelial(35;0.0739)	all_hematologic(20;0.107)				CTGCTACAGCGCCGCCTCGAC	0.667													G|||	358	0.0714856	0.2617	0.0159	5008	,	,		13330	0.0		0.001	False		,,,				2504	0.0				p.R415H	Melanoma(161;10 2587 27165 47356)	Atlas-SNP	.											.	FJX1	32	.	0			c.G1244A						PASS	.	G	HIS/ARG	717,3093		68,581,1256	6.0	7.0	7.0		1244	4.3	1.0	11	dbSNP_120	7	9,8147		0,9,4069	yes	missense	FJX1	NM_014344.3	29	68,590,5325	AA,AG,GG		0.1103,18.8189,6.0672	probably-damaging	415/438	35641428	726,11240	1905	4078	5983	SO:0001583	missense	24147	exon1			TACAGCGCCGCCT	AJ245599	CCDS44570.1	11p13	2012-05-18				ENSG00000179431			17166	protein-coding gene	gene with protein product	"""putative secreted ligand homologous to fjx1"""	612206				7647465, 10072791	Standard	NM_014344		Approved	FLJ22416, FLJ25593	uc001mwh.3	Q86VR8		ENST00000317811.4:c.1244G>A	11.37:g.35641428G>A	ENSP00000400223:p.Arg415His	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	NM_014344	B2RCA9|Q9UGK6	Missense_Mutation	SNP	ENST00000317811.4	37	CCDS44570.1	124	0.056776556776556776	118	0.23983739837398374	6	0.016574585635359115	0	0.0	0	0.0	G	13.12	2.141657	0.37825	0.188189	0.001103	ENSG00000179431	ENST00000317811	T	0.80480	-1.38	5.21	4.29	0.51040	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.35833	P	0.174551	B	0.11235	0.004	B	0.08055	0.003	T	0.03354	-1.1045	8	0.51188	T	0.08	-3.1322	7.4212	0.27073	0.1565:0.1395:0.7039:0.0	rs12286850	415	Q86VR8	FJX1_HUMAN	H	415	ENSP00000400223:R415H	ENSP00000400223:R415H	R	+	2	0	FJX1	35598004	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.527000	0.45615	1.184000	0.42957	0.555000	0.69702	CGC	G|0.908;A|0.092	0.092	strong		0.667	FJX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389078.1	NM_014344	
SP110	3431	hgsc.bcm.edu	37	2	231065630	231065630	+	Missense_Mutation	SNP	G	G	A	rs59573011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231065630G>A	ENST00000358662.4	-	10	1178	c.1100C>T	c.(1099-1101)aCg>aTg	p.T367M	SP110_ENST00000486146.2_5'Flank|SP110_ENST00000258381.6_Missense_Mutation_p.T367M|SP110_ENST00000338556.3_Missense_Mutation_p.T69M|SP110_ENST00000540870.1_Missense_Mutation_p.T373M|SP110_ENST00000258382.5_Missense_Mutation_p.T367M|SP110_ENST00000392048.3_Missense_Mutation_p.T365M	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	367			T -> M (in dbSNP:rs59573011). {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)		TGTACTAGGCGTCTTCTGGGA	0.443													G|||	83	0.0165735	0.0598	0.0058	5008	,	,		18713	0.0		0.0	False		,,,				2504	0.0				p.T373M		Atlas-SNP	.											.	SP110	105	.	0			c.C1118T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	231,4175	137.7+/-173.5	9,213,1981	228.0	200.0	210.0		1118,1100,1100,1100	-0.6	0.0	2	dbSNP_129	210	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	81,81,81,81	9,215,6279	AA,AG,GG		0.0233,5.2429,1.7915	probably-damaging,probably-damaging,probably-damaging,probably-damaging	373/556,367/690,367/550,367/714	231065630	233,12773	2203	4300	6503	SO:0001583	missense	3431	exon11			CTAGGCGTCTTCT	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.1100C>T	2.37:g.231065630G>A	ENSP00000351488:p.Thr367Met	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	196	86	0.438776	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	G	12.50	1.957341	0.34565	0.052429	2.33E-4	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000338556	T;T;T;T;T;T	0.65364	1.07;0.92;-0.15;-0.15;-0.15;2.46	2.49	-0.633	0.11519	.	.	.	.	.	T	0.11580	0.0282	N	0.22421	0.69	0.09310	N	1	D;D;D;D;P	0.67145	0.985;0.996;0.985;0.994;0.512	P;P;P;B;B	0.48030	0.541;0.564;0.541;0.389;0.047	T	0.10730	-1.0617	9	0.51188	T	0.08	.	2.8987	0.05699	0.3085:0.2426:0.4489:0.0	rs59573011	365;69;373;367;367	G5E9C0;E7ER70;F5H1M1;Q9HB58;Q9HB58-6	.;.;.;SP110_HUMAN;.	M	367;367;365;367;373;69	ENSP00000258381:T367M;ENSP00000351488:T367M;ENSP00000375902:T365M;ENSP00000258382:T367M;ENSP00000439558:T373M;ENSP00000344049:T69M	ENSP00000258381:T367M	T	-	2	0	SP110	230773874	0.014000	0.17966	0.025000	0.17156	0.009000	0.06853	-0.059000	0.11731	-0.148000	0.11234	0.557000	0.71058	ACG	G|0.980;A|0.020	0.020	strong		0.443	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
ZNF106	64397	hgsc.bcm.edu	37	15	42740369	42740369	+	Silent	SNP	C	C	T	rs3742996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42740369C>T	ENST00000263805.4	-	3	3293	c.2967G>A	c.(2965-2967)gcG>gcA	p.A989A	ZNF106_ENST00000565380.1_Silent_p.A217A|ZNF106_ENST00000565611.1_Silent_p.A174A	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	989					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)										AACTGGAGATCGCAAGGGCTG	0.493													C|||	641	0.127995	0.1793	0.2579	5008	,	,		19406	0.1012		0.0109	False		,,,				2504	0.1145				p.A989A		Atlas-SNP	.											.	ZFP106	117	.	0			c.G2967A						PASS	.	C		673,3733	284.6+/-277.7	55,563,1585	168.0	159.0	162.0		2967	-4.8	0.0	15	dbSNP_107	162	98,8500	54.4+/-115.2	1,96,4202	no	coding-synonymous	ZFP106	NM_022473.1		56,659,5787	TT,TC,CC		1.1398,15.2746,5.9289		989/1884	42740369	771,12233	2203	4299	6502	SO:0001819	synonymous_variant	64397	exon3			GGAGATCGCAAGG	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.2967G>A	15.37:g.42740369C>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	213	110	0.516432	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Silent	SNP	ENST00000263805.4	37	CCDS32208.1																																																																																			C|0.911;T|0.089	0.089	strong		0.493	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
TP53BP1	7158	hgsc.bcm.edu	37	15	43762196	43762196	+	Missense_Mutation	SNP	C	C	T	rs689647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43762196C>T	ENST00000263801.3	-	11	1486	c.1234G>A	c.(1234-1236)Ggt>Agt	p.G412S	TP53BP1_ENST00000450115.2_Missense_Mutation_p.G417S|TP53BP1_ENST00000382039.3_Missense_Mutation_p.G417S|TP53BP1_ENST00000382044.4_Missense_Mutation_p.G417S	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	412			G -> S (in dbSNP:rs689647). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.4}.		cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|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)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		ACTGGTTCACCACTTTGAAGT	0.458								Other conserved DNA damage response genes					C|||	1915	0.382388	0.7511	0.2205	5008	,	,		16848	0.3869		0.1093	False		,,,				2504	0.2751				p.G417S		Atlas-SNP	.											.	TP53BP1	157	.	0			c.G1249A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	2774,1628	659.9+/-400.6	882,1010,309	158.0	151.0	153.0		1249,1249,1234	5.3	0.5	15	dbSNP_83	153	971,7625	211.3+/-251.9	59,853,3386	yes	missense,missense,missense	TP53BP1	NM_001141979.1,NM_001141980.1,NM_005657.2	56,56,56	941,1863,3695	TT,TC,CC		11.296,36.9832,28.8121	benign,benign,benign	417/1976,417/1978,412/1973	43762196	3745,9253	2201	4298	6499	SO:0001583	missense	7158	exon11			GTTCACCACTTTG	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"""tumor protein p53-binding protein, 1"""			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.1234G>A	15.37:g.43762196C>T	ENSP00000263801:p.Gly412Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	771	0.35302197802197804	361	0.733739837398374	79	0.21823204419889503	255	0.4458041958041958	76	0.10026385224274406	C	12.26	1.883283	0.33255	0.630168	0.11296	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.09163	3.83;3.83;3.82;3.83;3.01	5.31	5.31	0.75309	.	0.144833	0.43110	D	0.000615	T	0.00012	0.0000	N	0.08118	0	0.52099	P	5.699999999997374E-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	0.14924	-1.0455	9	0.13470	T	0.59	-6.2677	15.7083	0.77602	0.0:1.0:0.0:0.0	rs689647;rs52823918;rs57881989;rs689647	417;412;417;417	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	S	412;417;417;417;417	ENSP00000263801:G412S;ENSP00000371475:G417S;ENSP00000371470:G417S;ENSP00000393497:G417S;ENSP00000388028:G417S	ENSP00000263801:G412S	G	-	1	0	TP53BP1	41549488	0.003000	0.15002	0.530000	0.27963	0.130000	0.20726	1.139000	0.31504	2.479000	0.83701	0.563000	0.77884	GGT	C|0.671;N|0.000	.	strong		0.458	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
LHFP	10186	hgsc.bcm.edu	37	13	40175311	40175311	+	Silent	SNP	G	G	A	rs34616166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:40175311G>A	ENST00000379589.3	-	2	505	c.43C>T	c.(43-45)Ctg>Ttg	p.L15L	LHFP_ENST00000495922.1_5'Flank	NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	15						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)		HMGA2/LHFP(2)	breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		AGAAAAGACAGCAAAGCCCAG	0.537			T	HMGA2	lipoma								G|||	341	0.0680911	0.2466	0.0159	5008	,	,		20157	0.0		0.004	False		,,,				2504	0.0				p.L15L		Atlas-SNP	.		Dom	yes		13	13q12	10186	lipoma HMGIC fusion partner		M	.	LHFP	31	.	0			c.C43T						PASS	.	G		827,3579	318.0+/-295.4	77,673,1453	66.0	59.0	61.0		43	5.4	1.0	13	dbSNP_126	61	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	LHFP	NM_005780.2		77,683,5743	AA,AG,GG		0.1163,18.7699,6.4355		15/201	40175311	837,12169	2203	4300	6503	SO:0001819	synonymous_variant	10186	exon2			AAGACAGCAAAGC	AF098807	CCDS9369.1	13q12	2008-07-18			ENSG00000183722	ENSG00000183722			6586	protein-coding gene	gene with protein product		606710				10329012	Standard	NM_005780		Approved	MGC22429	uc001uxf.3	Q9Y693	OTTHUMG00000016767	ENST00000379589.3:c.43C>T	13.37:g.40175311G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	123	70	0.569106	NM_005780	B2R7M2|Q53FC0|Q96SH5	Silent	SNP	ENST00000379589.3	37	CCDS9369.1																																																																																			G|0.941;A|0.059	0.059	strong		0.537	LHFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044619.1	NM_005780	
OR4K15	81127	hgsc.bcm.edu	37	14	20444607	20444607	+	Missense_Mutation	SNP	C	C	G	rs10135467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20444607C>G	ENST00000305051.5	+	1	1005	c.930C>G	c.(928-930)atC>atG	p.I310M		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	310			I -> M (in dbSNP:rs10135467). {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)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ACCCTGTAATCTACACGCTAA	0.398													C|||	1099	0.219449	0.2186	0.1715	5008	,	,		17634	0.123		0.2227	False		,,,				2504	0.3507				p.I310M		Atlas-SNP	.											.	OR4K15	82	.	0			c.C930G						PASS	.	C	MET/ILE	1057,3347		121,815,1266	96.0	95.0	96.0		930	-0.4	0.9	14	dbSNP_119	96	2284,6316		289,1706,2305	no	missense	OR4K15	NM_001005486.1	10	410,2521,3571	GG,GC,CC		26.5581,24.0009,25.6921	probably-damaging	310/349	20444607	3341,9663	2202	4300	6502	SO:0001583	missense	81127	exon1			TGTAATCTACACG		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.930C>G	14.37:g.20444607C>G	ENSP00000304077:p.Ile310Met	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	209	207	0.990431	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	402	0.18406593406593408	97	0.19715447154471544	65	0.17955801104972377	66	0.11538461538461539	174	0.22955145118733508	.	12.66	2.004692	0.35320	0.240009	0.265581	ENSG00000169488	ENST00000305051	T	0.57273	0.41	3.69	-0.451	0.12214	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000087	T	0.00012	0.0000	M	0.72353	2.195	0.38036	P	0.064697	D	0.89917	1.0	D	0.76575	0.988	T	0.06716	-1.0811	9	0.87932	D	0	.	3.7838	0.08692	0.171:0.5187:0.0:0.3104	rs10135467;rs17276912;rs10135467	310	Q8NH41	OR4KF_HUMAN	M	310	ENSP00000304077:I310M	ENSP00000304077:I310M	I	+	3	3	OR4K15	19514447	0.070000	0.21116	0.927000	0.36925	0.707000	0.40811	-0.927000	0.03984	-0.217000	0.10033	0.591000	0.81541	ATC	C|0.770;G|0.230	0.230	strong		0.398	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
URB2	9816	hgsc.bcm.edu	37	1	229787055	229787055	+	Missense_Mutation	SNP	G	G	A	rs41310553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	121	0	0		WXS	Illumina HiSeq	Phase_I	115	63	0.547826	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	
PCDHA13	56136	hgsc.bcm.edu	37	5	140264091	140264091	+	Silent	SNP	G	G	C	rs10076265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140264091G>C	ENST00000289272.2	+	1	2238	c.2238G>C	c.(2236-2238)ggG>ggC	p.G746G	PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA13_ENST00000409494.1_Silent_p.G746G|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	746	6 X 4 AA repeats of P-X-X-P.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCGGCAGGGAGTTGGTCGT	0.677													g|||	74	0.0147764	0.053	0.0058	5008	,	,		14743	0.0		0.0	False		,,,				2504	0.0				p.G746G	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											PCDHA13,colon,carcinoma,+2,1	PCDHA13	213	1	0			c.G2238C						PASS	.	G	,,,,,,,,,,,,,,,,	248,4158	136.5+/-172.5	6,236,1961	48.0	53.0	52.0		,,,,2238,,,,,,,,,,,,2238	2.8	1.0	5	dbSNP_119	52	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031865.1	,,,,,,,,,,,,,,,,	6,237,6260	CC,CG,GG		0.0116,5.6287,1.9145	,,,,,,,,,,,,,,,,	,,,,746/951,,,,,,,,,,,,746/808	140264091	249,12757	2203	4300	6503	SO:0001819	synonymous_variant	56136	exon1			GGCAGGGAGTTGG	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"""Cadherins / Protocadherins : Clustered"""	8667	other	complex locus constituent	"""KIAA0345-like 1"", ""ortholog of mouse CNR5"""	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.2238G>C	5.37:g.140264091G>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	159	83	0.522013	NM_031865	O75277	Silent	SNP	ENST00000289272.2	37	CCDS4240.1																																																																																			G|0.982;C|0.018	0.018	strong		0.677	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904	
VCPIP1	80124	hgsc.bcm.edu	37	8	67577670	67577670	+	Silent	SNP	G	G	A	rs3808602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:67577670G>A	ENST00000310421.4	-	1	1782	c.1524C>T	c.(1522-1524)taC>taT	p.Y508Y	C8orf44_ENST00000521889.1_5'Flank|C8orf44_ENST00000519561.1_5'Flank|C8orf44-SGK3_ENST00000519289.1_5'Flank	NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	508					endoplasmic reticulum membrane fusion (GO:0016320)|Golgi reassembly (GO:0090168)|mitotic nuclear division (GO:0007067)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	ubiquitin-specific protease activity (GO:0004843)			breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			AGGGAAAGCTGTAATTTTTGT	0.418													A|||	725	0.144768	0.4319	0.0562	5008	,	,		22571	0.0218		0.0318	False		,,,				2504	0.0624				p.Y508Y	NSCLC(179;265 2915 6144 43644)	Atlas-SNP	.											.	VCPIP1	110	.	0			c.C1524T						PASS	.	A		1619,2787	661.7+/-400.9	298,1023,882	163.0	173.0	169.0		1524	-1.3	1.0	8	dbSNP_107	169	194,8406	810.8+/-407.1	1,192,4107	no	coding-synonymous	VCPIP1	NM_025054.4		299,1215,4989	AA,AG,GG		2.2558,36.7453,13.9397		508/1223	67577670	1813,11193	2203	4300	6503	SO:0001819	synonymous_variant	80124	exon1			AAAGCTGTAATTT	AB058753	CCDS6192.1	8q13	2014-02-24			ENSG00000175073	ENSG00000175073		"""OTU domain containing"""	30897	protein-coding gene	gene with protein product		611745				11347906, 12509440	Standard	NM_025054		Approved	VCIP135, KIAA1850, FLJ23132, DUBA3	uc003xwn.3	Q96JH7	OTTHUMG00000164560	ENST00000310421.4:c.1524C>T	8.37:g.67577670G>A		Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	262	117	0.446565	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Silent	SNP	ENST00000310421.4	37	CCDS6192.1																																																																																			G|0.858;A|0.142	0.142	strong		0.418	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1		
AFAP1	60312	hgsc.bcm.edu	37	4	7783172	7783172	+	Intron	SNP	G	G	A	rs77207711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:7783172G>A	ENST00000360265.4	-	12	1765				AFAP1_ENST00000382543.3_Silent_p.Y571Y|AFAP1_ENST00000420658.1_Silent_p.Y571Y|AFAP1_ENST00000358461.2_Intron|AFAP1_ENST00000513842.1_5'UTR|AFAP1-AS1_ENST00000608442.1_RNA			Q8N556	AFAP1_HUMAN	actin filament associated protein 1							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						CGGAGGCAGGGTATTTGTAAT	0.527													G|||	762	0.152157	0.2307	0.1499	5008	,	,		18893	0.0853		0.1133	False		,,,				2504	0.1564				p.Y571Y		Atlas-SNP	.											.	AFAP1	93	.	0			c.C1713T						PASS	.	G	,	290,1094		26,238,428	117.0	113.0	114.0		1713,	2.4	0.2	4	dbSNP_132	114	384,2798		21,342,1228	no	coding-synonymous,intron	AFAP1	NM_001134647.1,NM_198595.2	,	47,580,1656	AA,AG,GG		12.0679,20.9538,14.7613	,	571/815,	7783172	674,3892	692	1591	2283	SO:0001627	intron_variant	60312	exon13			GGCAGGGTATTTG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1531-2569C>T	4.37:g.7783172G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	217	96	0.442396	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	37	CCDS3397.1																																																																																			G|0.870;A|0.130	0.130	strong		0.527	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
AMBN	258	hgsc.bcm.edu	37	4	71472426	71472426	+	Silent	SNP	A	A	G	rs7680880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	270	0	0		WXS	Illumina HiSeq	Phase_I	282	161	0.570922	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	
TDG	6996	hgsc.bcm.edu	37	12	104373829	104373829	+	Silent	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:104373829C>A	ENST00000392872.3	+	3	621	c.387C>A	c.(385-387)acC>acA	p.T129T	TDG_ENST00000542036.1_5'UTR|TDG_ENST00000544861.1_5'UTR|TDG_ENST00000266775.9_Silent_p.T125T	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	129					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)	p.T129T(1)		large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		ATATTTTGACCTTCAATCTGG	0.358								Base excision repair (BER), DNA glycosylases																													p.T129T		Atlas-SNP	.											TDG,pharynx,carcinoma,0,1	TDG	43	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C387A						PASS	.						48.0	47.0	47.0					12																	104373829		2203	4300	6503	SO:0001819	synonymous_variant	6996	exon3			TTTGACCTTCAAT	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.387C>A	12.37:g.104373829C>A		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	284	35	0.123239	NM_003211	Q8IUZ6|Q8IZM3	Silent	SNP	ENST00000392872.3	37	CCDS9095.1																																																																																			.	.	weak		0.358	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
MDC1	9656	hgsc.bcm.edu	37	6	30680562	30680562	+	Missense_Mutation	SNP	G	G	A	rs28986465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30680562G>A	ENST00000376406.3	-	5	1804	c.1157C>T	c.(1156-1158)cCa>cTa	p.P386L	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Missense_Mutation_p.P386L|MDC1_ENST00000494654.1_5'Flank	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	386	Required for nuclear localization (NLS1).		P -> L (in dbSNP:rs28986465). {ECO:0000269|PubMed:16702430}.		DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						GACAGCCTGTGGGGCCTTGCC	0.552								Other conserved DNA damage response genes					G|||	317	0.0632987	0.1324	0.0504	5008	,	,		21523	0.0645		0.0189	False		,,,				2504	0.0235				p.P386L		Atlas-SNP	.											.	MDC1	218	.	0			c.C1157T						PASS	.	G	LEU/PRO	328,2692		22,284,1204	77.0	83.0	81.0		1157	2.2	0.0	6	dbSNP_125	81	92,5326		0,92,2617	yes	missense	MDC1	NM_014641.2	98	22,376,3821	AA,AG,GG		1.698,10.8609,4.9775	possibly-damaging	386/2090	30680562	420,8018	1510	2709	4219	SO:0001583	missense	9656	exon5			GCCTGTGGGGCCT	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.1157C>T	6.37:g.30680562G>A	ENSP00000365588:p.Pro386Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	142	0.06501831501831502	63	0.12804878048780488	19	0.052486187845303865	49	0.08566433566433566	11	0.014511873350923483	G	7.656	0.683988	0.14907	0.108609	0.01698	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.03124	4.15;4.04	5.19	2.19	0.27852	.	0.728871	0.11291	N	0.579298	T	0.00815	0.0027	N	0.16478	0.41	0.80722	P	0.0	B;B;B;B	0.22683	0.073;0.073;0.011;0.009	B;B;B;B	0.25884	0.064;0.064;0.01;0.016	T	0.47711	-0.9096	9	0.40728	T	0.16	-0.0123	3.3808	0.07254	0.0936:0.1625:0.5568:0.1872	rs28986465;rs28986465	386;258;386;386	Q14676-2;B4DYH4;Q14676;Q14676-4	.;.;MDC1_HUMAN;.	L	386;386;386;258	ENSP00000365588:P386L;ENSP00000365587:P386L	ENSP00000365587:P386L	P	-	2	0	MDC1	30788541	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	0.122000	0.15687	0.674000	0.31244	0.561000	0.74099	CCA	G|0.939;A|0.061	0.061	strong		0.552	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
ZNF578	147660	hgsc.bcm.edu	37	19	53014492	53014492	+	Silent	SNP	T	T	A	rs145508251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53014492T>A	ENST00000421239.2	+	6	1102	c.858T>A	c.(856-858)ccT>ccA	p.P286P	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	286					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GTGAGAAACCTTACAAGTGTA	0.378													T|||	51	0.0101837	0.0363	0.0029	5008	,	,		24259	0.0		0.001	False		,,,				2504	0.0				p.P286P		Atlas-SNP	.											.	.	.	.	0			c.T858A						PASS	.	T		92,4314		0,92,2111	111.0	115.0	114.0		858	-0.1	0.3	19	dbSNP_134	114	8,8590		0,8,4291	no	coding-synonymous	ZNF578	NM_001099694.1		0,100,6402	AA,AT,TT		0.093,2.0881,0.769		286/591	53014492	100,12904	2203	4299	6502	SO:0001819	synonymous_variant	147660	exon6			GAAACCTTACAAG	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.858T>A	19.37:g.53014492T>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	153	68	0.444444	NM_001099694	B4DR51|I3L1Y6	Silent	SNP	ENST00000421239.2	37	CCDS54310.1																																																																																			T|0.993;A|0.007	0.007	strong		0.378	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
PCDHGA4	56111	hgsc.bcm.edu	37	5	140736328	140736328	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140736328G>A	ENST00000571252.1	+	1	1561	c.1561G>A	c.(1561-1563)Gac>Aac	p.D521N	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	521	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGCTCCTTCGACTATGAGCA	0.527																																					p.D521N		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.G1561A						PASS	.						131.0	140.0	137.0					5																	140736328		2131	4270	6401	SO:0001583	missense	56111	exon1			TCCTTCGACTATG	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1561G>A	5.37:g.140736328G>A	ENSP00000458570:p.Asp521Asn	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	142	73	0.514085	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			.	.	none		0.527	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
KRT37	8688	hgsc.bcm.edu	37	17	39577215	39577215	+	Missense_Mutation	SNP	G	G	A	rs8071814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39577215G>A	ENST00000225550.3	-	7	1264	c.1265C>T	c.(1264-1266)aCg>aTg	p.T422M	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	422	Tail.		T -> M (in dbSNP:rs8071814).			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)				GGAGGCAGGCGTGGAACAGGG	0.542													G|||	224	0.0447284	0.0424	0.0331	5008	,	,		20870	0.0496		0.0775	False		,,,				2504	0.0174				p.T422M		Atlas-SNP	.											.	KRT37	61	.	0			c.C1265T						PASS	.	G	MET/THR	186,4220	120.0+/-157.7	5,176,2022	70.0	72.0	71.0		1265	4.1	0.0	17	dbSNP_116	71	748,7852	179.8+/-228.8	28,692,3580	yes	missense	KRT37	NM_003770.4	81	33,868,5602	AA,AG,GG		8.6977,4.2215,7.1813	probably-damaging	422/450	39577215	934,12072	2203	4300	6503	SO:0001583	missense	8688	exon7			GCAGGCGTGGAAC	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.1265C>T	17.37:g.39577215G>A	ENSP00000225550:p.Thr422Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	132	0.06043956043956044	21	0.042682926829268296	15	0.04143646408839779	31	0.05419580419580419	65	0.08575197889182058	G	16.13	3.036359	0.54896	0.042215	0.086977	ENSG00000108417	ENST00000225550	D	0.82984	-1.67	5.06	4.07	0.47477	.	0.000000	0.50627	D	0.000102	T	0.13970	0.0338	N	0.08118	0	0.09310	N	1	D	0.89917	1.0	D	0.63192	0.912	T	0.49184	-0.8966	10	0.72032	D	0.01	.	9.8836	0.41249	0.0979:0.0:0.9021:0.0	rs8071814;rs17737054;rs8071814	422	O76014	KRT37_HUMAN	M	422	ENSP00000225550:T422M	ENSP00000225550:T422M	T	-	2	0	KRT37	36830741	0.003000	0.15002	0.008000	0.14137	0.092000	0.18411	0.548000	0.23314	1.084000	0.41184	0.655000	0.94253	ACG	G|0.935;A|0.065	0.065	strong		0.542	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
C17orf77	146723	hgsc.bcm.edu	37	17	72588806	72588806	+	Nonsense_Mutation	SNP	C	C	A	rs545652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72588806C>A	ENST00000392620.1	+	3	983	c.621C>A	c.(619-621)tgC>tgA	p.C207*	CD300LD_ENST00000375352.1_5'Flank|C17orf77_ENST00000328023.2_Nonsense_Mutation_p.C207*	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	207						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						AAAGCCCATGCCCCAGGCTTC	0.607													C|||	1120	0.223642	0.5189	0.1441	5008	,	,		19490	0.0476		0.1392	False		,,,				2504	0.1493				p.C207X		Atlas-SNP	.											C17orf77,colon,carcinoma,0,1	C17orf77	31	1	0			c.C621A						PASS	.	C	stop/CYS	1969,2437	555.4+/-379.2	435,1099,669	79.0	80.0	79.0		621	2.4	0.0	17	dbSNP_83	79	1485,7115	280.5+/-294.5	138,1209,2953	yes	stop-gained	C17orf77	NM_152460.2		573,2308,3622	AA,AC,CC		17.2674,44.6891,26.557		207/244	72588806	3454,9552	2203	4300	6503	SO:0001587	stop_gained	146723	exon3			CCCATGCCCCAGG		CCDS32721.1	17q25.1	2006-01-16			ENSG00000182352	ENSG00000182352			26480	protein-coding gene	gene with protein product							Standard	NM_152460		Approved	FLJ31882	uc002jla.1	Q96MU5	OTTHUMG00000067611	ENST00000392620.1:c.621C>A	17.37:g.72588806C>A	ENSP00000376396:p.Cys207*	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_152460		Nonsense_Mutation	SNP	ENST00000392620.1	37	CCDS32721.1	453	0.20741758241758243	256	0.5203252032520326	67	0.1850828729281768	22	0.038461538461538464	108	0.1424802110817942	C	22.9	4.351629	0.82132	0.446891	0.172674	ENSG00000182352	ENST00000392620;ENST00000328023	.	.	.	2.38	2.38	0.29361	.	.	.	.	.	.	.	.	.	.	.	0.37000	P	0.10478399999999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3461	0.32275	0.0:1.0:0.0:0.0	rs545652;rs545652	.	.	.	X	207	.	.	C	+	3	2	C17orf77	70100401	0.000000	0.05858	0.007000	0.13788	0.031000	0.12232	-0.036000	0.12185	1.642000	0.50584	0.511000	0.50034	TGC	C|0.751;A|0.249	0.249	strong		0.607	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460	
SAMD4B	55095	hgsc.bcm.edu	37	19	39873877	39873877	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39873877A>G	ENST00000314471.6	+	15	3037	c.2002A>G	c.(2002-2004)Atc>Gtc	p.I668V	SAMD4B_ENST00000596368.1_Intron|SAMD4B_ENST00000598913.1_Missense_Mutation_p.I668V	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	668					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(5)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(2)	15	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			TGACCTGGAGATCAATCCCAC	0.577																																					p.I668V		Atlas-SNP	.											SAMD4B,NS,carcinoma,0,2	SAMD4B	48	2	0			c.A2002G						PASS	.						169.0	131.0	144.0					19																	39873877		2203	4300	6503	SO:0001583	missense	55095	exon15			CTGGAGATCAATC		CCDS33020.1	19q13.2	2013-01-10				ENSG00000179134		"""Sterile alpha motif (SAM) domain containing"""	25492	protein-coding gene	gene with protein product	"""smaug homolog B (Drosophila)"""					16221671	Standard	XM_005259029		Approved	FLJ10211, MGC99832, SMGB, hSmaug2	uc002olb.3	Q5PRF9		ENST00000314471.6:c.2002A>G	19.37:g.39873877A>G	ENSP00000317224:p.Ile668Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	160	76	0.475	NM_018028	A5Z0M6|Q6P194	Missense_Mutation	SNP	ENST00000314471.6	37	CCDS33020.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.187852	0.78789	.	.	ENSG00000179134	ENST00000314471	.	.	.	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000001	T	0.63379	0.2506	L	0.43152	1.355	0.43846	D	0.996437	P;P	0.43314	0.803;0.803	P;P	0.55824	0.785;0.785	T	0.66559	-0.5893	9	0.87932	D	0	.	11.256	0.49054	1.0:0.0:0.0:0.0	.	668;668	Q5PRF9;A5Z0M6	SMAG2_HUMAN;.	V	668	.	ENSP00000317224:I668V	I	+	1	0	SAMD4B	44565717	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	8.422000	0.90262	1.774000	0.52232	0.240000	0.17902	ATC	.	.	none		0.577	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028	
SLFN12	55106	hgsc.bcm.edu	37	17	33738752	33738752	+	Missense_Mutation	SNP	A	A	G	rs12946189	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33738752A>G	ENST00000394562.1	-	6	1865	c.1342T>C	c.(1342-1344)Tcc>Ccc	p.S448P	SLFN12_ENST00000460530.1_5'UTR|SLFN12_ENST00000452764.3_Missense_Mutation_p.S448P|SLFN12_ENST00000304905.5_Missense_Mutation_p.S448P|RP11-686D22.8_ENST00000587012.1_RNA			Q8IYM2	SLN12_HUMAN	schlafen family member 12	448			S -> P (in dbSNP:rs12946189).				ATP binding (GO:0005524)	p.S448P(1)		breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTGTCCTGGGAAATCAGAAGA	0.483													A|||	195	0.0389377	0.115	0.0086	5008	,	,		17332	0.0317		0.002	False		,,,				2504	0.0031				p.S448P		Atlas-SNP	.											SLFN12,NS,malignant_melanoma,+1,3	SLFN12	56	3	1	Substitution - Missense(1)	stomach(1)	c.T1342C						PASS	.	A	PRO/SER	412,3994	198.4+/-222.2	24,364,1815	105.0	105.0	105.0		1342	-6.4	0.0	17	dbSNP_121	105	21,8579	15.3+/-51.7	0,21,4279	no	missense	SLFN12	NM_018042.3	74	24,385,6094	GG,GA,AA		0.2442,9.3509,3.3292	possibly-damaging	448/579	33738752	433,12573	2203	4300	6503	SO:0001583	missense	55106	exon4			CCTGGGAAATCAG	AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.1342T>C	17.37:g.33738752A>G	ENSP00000378063:p.Ser448Pro	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	274	123	0.448905	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	110	0.05036630036630037	73	0.1483739837398374	7	0.019337016574585635	26	0.045454545454545456	4	0.005277044854881266	A	13.88	2.370181	0.42003	0.093509	0.002442	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764	T;T;T	0.04758	3.56;3.56;3.56	3.22	-6.44	0.01920	.	.	.	.	.	T	0.00039	0.0001	L	0.56769	1.78	0.80722	P	0.0	B	0.12630	0.006	B	0.06405	0.002	T	0.22695	-1.0209	8	0.72032	D	0.01	.	7.355	0.26714	0.1242:0.6183:0.1547:0.1028	rs12946189;rs52808777;rs12946189	448	Q8IYM2	SLN12_HUMAN	P	448	ENSP00000378063:S448P;ENSP00000302077:S448P;ENSP00000394903:S448P	ENSP00000302077:S448P	S	-	1	0	SLFN12	30762865	0.000000	0.05858	0.006000	0.13384	0.704000	0.40688	-1.754000	0.01816	-3.604000	0.00133	0.438000	0.28831	TCC	A|0.962;G|0.038	0.038	strong		0.483	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042	
FRMD7	90167	hgsc.bcm.edu	37	X	131212512	131212512	+	Silent	SNP	A	A	G	rs5977623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:131212512A>G	ENST00000298542.4	-	12	1708	c.1533T>C	c.(1531-1533)atT>atC	p.I511I	FRMD7_ENST00000370879.1_Silent_p.I391I|FRMD7_ENST00000464296.1_Silent_p.I496I	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	511					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)		p.I511I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					CCTCTGCTCTAATTGGGGACC	0.488													G|||	984	0.260662	0.3578	0.0821	3775	,	,		13740	0.0843		0.2276	False		,,,				2504	0.1431				p.I511I		Atlas-SNP	.											.	FRMD7	69	.	1	Substitution - coding silent(1)	prostate(1)	c.T1533C						PASS	.	G		1689,2146		313,807,256,512,315	139.0	136.0	137.0		1533	1.1	0.4	X	dbSNP_114	137	2072,4656		243,1011,575,1174,1297	no	coding-synonymous	FRMD7	NM_194277.2		556,1818,831,1686,1612	GG,GA,G,AA,A		30.7967,44.0417,35.6054		511/715	131212512	3761,6802	2203	4300	6503	SO:0001819	synonymous_variant	90167	exon12			TGCTCTAATTGGG	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1533T>C	X.37:g.131212512A>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	207	88	0.425121	NM_194277	C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	37	CCDS35397.1																																																																																			A|0.670;0|0.003	.	strong		0.488	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277	
OPN1LW	5956	hgsc.bcm.edu	37	X	153418514	153418514	+	Missense_Mutation	SNP	G	G	A	rs60549689		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153418514G>A	ENST00000369951.4	+	3	571	c.511G>A	c.(511-513)Gtg>Atg	p.V171M	OPN1LW_ENST00000463296.1_3'UTR	NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	171					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)					GCTGGCCATCGTGGGCATTGC	0.577													g|||	749	0.198411	0.2428	0.0749	3775	,	,		13519	0.1042		0.0527	False		,,,				2504	0.2229				p.V171M		Atlas-SNP	.											.	OPN1LW	87	.	0			c.G511A	GRCh37	CM890023	OPN1LW	X	rs79866052	PASS	.	A	MET/VAL	1109,2697		169,622,149,839,397	227.0	140.0	170.0		511	-1.1	0.0	X	dbSNP_131	170	490,5882		63,244,120,2064,1510	no	missense	OPN1LW	NM_020061.4	21	232,866,269,2903,1907	AA,AG,A,GG,G		7.6899,29.1382,15.7104	benign	171/365	153418514	1599,8579	2176	4001	6177	SO:0001583	missense	5956	exon3			GCCATCGTGGGCA	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.511G>A	X.37:g.153418514G>A	ENSP00000358967:p.Val171Met	Somatic	468	0	0		WXS	Illumina HiSeq	Phase_I	1100	325	0.295455	NM_020061		Missense_Mutation	SNP	ENST00000369951.4	37	CCDS14742.1	214	0.1289933694996986	85	0.195852534562212	18	0.05084745762711865	41	0.07454545454545454	22	0.030303030303030304	g	4.615	0.114219	0.08831	0.291382	0.076899	ENSG00000102076	ENST00000369951;ENST00000442922	T;T	0.74209	-0.82;-0.82	4.57	-1.07	0.09968	GPCR, rhodopsin-like superfamily (1);	1.027880	0.07705	N	0.941117	T	0.00012	0.0000	N	0.04994	-0.135	0.80722	P	0.0	P	0.36249	0.545	B	0.26202	0.067	T	0.01323	-1.1385	9	0.02654	T	1	.	2.3707	0.04330	0.3991:0.1172:0.3634:0.1204	.	171	P04000	OPSR_HUMAN	M	171;34	ENSP00000358967:V171M;ENSP00000402493:V34M	ENSP00000358967:V171M	V	+	1	0	OPN1LW	153071708	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	0.307000	0.19296	-0.538000	0.06281	-2.704000	0.00135	GTG	G|0.870;A|0.130	0.130	strong		0.577	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061	
MT-ND5	4540	hgsc.bcm.edu	37	M	13650	13650	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:13650C>T	ENST00000361567.2	+	1	1314	c.1314C>T	c.(1312-1314)ccC>ccT	p.P438P	MT-TT_ENST00000387460.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	438					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CCTCGCTTCCCCACCCTTACT	0.478																																					p.P438P		Atlas-SNP	.											.	.	.	.	0			c.C1314T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CTTCCCCACCCTT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1314C>T	M.37:g.13650C>T		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.478	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
TRIM31	11074	hgsc.bcm.edu	37	6	30071357	30071357	+	Silent	SNP	G	G	A	rs17194258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30071357G>A	ENST00000376734.3	-	9	1359	c.1234C>T	c.(1234-1236)Ctg>Ttg	p.L412L	TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000540829.1_Silent_p.L412L|TRIM31_ENST00000485864.1_5'Flank	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	412					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						ATCGCTGTCAGCCACTCACTC	0.547													G|||	78	0.0155751	0.0371	0.0173	5008	,	,		18691	0.002		0.006	False		,,,				2504	0.0092				p.L412L		Atlas-SNP	.											TRIM31,right_upper_lobe,carcinoma,+2,1	TRIM31	40	1	0			c.C1234T						PASS	.	G		96,2922		2,92,1415	132.0	141.0	138.0		1234	0.6	0.0	6	dbSNP_123	138	45,5373		0,45,2664	no	coding-synonymous	TRIM31	NM_007028.3		2,137,4079	AA,AG,GG		0.8306,3.1809,1.6714		412/426	30071357	141,8295	1509	2709	4218	SO:0001819	synonymous_variant	11074	exon9			CTGTCAGCCACTC	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.1234C>T	6.37:g.30071357G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			G|0.980;A|0.020	0.020	strong		0.547	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
IL4I1	259307	hgsc.bcm.edu	37	19	50393269	50393269	+	Silent	SNP	A	A	G	rs56359967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50393269A>G	ENST00000391826.2	-	8	1504	c.1362T>C	c.(1360-1362)ttT>ttC	p.F454F	MIR4750_ENST00000584564.1_RNA|IL4I1_ENST00000595948.1_Silent_p.F476F|IL4I1_ENST00000341114.3_Silent_p.F476F	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	454						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	GCTGTACCACAAAGCCACCCT	0.667											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	659	0.131589	0.1566	0.1945	5008	,	,		15075	0.1885		0.0169	False		,,,				2504	0.1125				p.F476F		Atlas-SNP	.											.	IL4I1	50	.	0			c.T1428C						PASS	.	G	,	545,3703		28,489,1607	22.0	9.0	13.0		1362,1428	2.1	1.0	19	dbSNP_129	13	178,8150		4,170,3990	no	coding-synonymous,coding-synonymous	IL4I1	NM_152899.1,NM_172374.1	,	32,659,5597	GG,GA,AA		2.1374,12.8296,5.749	,	454/568,476/590	50393269	723,11853	2124	4164	6288	SO:0001819	synonymous_variant	259307	exon10			TACCACAAAGCCA	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.1362T>C	19.37:g.50393269A>G		Somatic	37	0	0	969	WXS	Illumina HiSeq	Phase_I	47	16	0.340426	NM_172374	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Silent	SNP	ENST00000391826.2	37	CCDS12787.1																																																																																			A|0.881;G|0.119	0.119	strong		0.667	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1		
ACOX1	51	hgsc.bcm.edu	37	17	73949540	73949540	+	Missense_Mutation	SNP	G	G	C	rs1135640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73949540G>C	ENST00000301608.4	-	7	996	c.936C>G	c.(934-936)atC>atG	p.I312M	ACOX1_ENST00000537812.1_Missense_Mutation_p.I274M|ACOX1_ENST00000591857.1_5'Flank|ACOX1_ENST00000293217.5_Missense_Mutation_p.I312M	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	312			I -> M (in dbSNP:rs1135640). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:8040306, ECO:0000269|PubMed:8117268}.		alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	ACCCTGGCTTGATTTCAGACT	0.507													G|||	2758	0.550719	0.1589	0.6729	5008	,	,		19337	0.7877		0.6402	False		,,,				2504	0.6575				p.I312M		Atlas-SNP	.											.	ACOX1	85	.	0			c.C936G						PASS	.	G	MET/ILE,MET/ILE,MET/ILE	1034,3372	380.4+/-323.7	122,790,1291	106.0	87.0	94.0		822,936,936	5.2	1.0	17	dbSNP_86	94	5582,3018	663.4+/-402.1	1825,1932,543	yes	missense,missense,missense	ACOX1	NM_001185039.1,NM_004035.6,NM_007292.5	10,10,10	1947,2722,1834	CC,CG,GG		35.093,23.468,49.1312	benign,benign,benign	274/623,312/661,312/661	73949540	6616,6390	2203	4300	6503	SO:0001583	missense	51	exon7			TGGCTTGATTTCA	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"""acyl-Coenzyme A oxidase 1, palmitoyl"""			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.936C>G	17.37:g.73949540G>C	ENSP00000301608:p.Ile312Met	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	216	101	0.467593	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	37	CCDS11735.1	1251	0.5728021978021978	85	0.17276422764227642	229	0.6325966850828729	433	0.756993006993007	504	0.6649076517150396	G	13.17	2.156848	0.38119	0.23468	0.64907	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.70282	-0.47;-0.47;-0.47	6.17	5.2	0.72013	Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.200754	0.50627	D	0.000111	T	0.00012	0.0000	L	0.28458	0.855	0.23351	P	0.99785757	B;B;B;B	0.13145	0.003;0.0;0.0;0.007	B;B;B;B	0.09377	0.004;0.004;0.002;0.004	T	0.47086	-0.9144	9	0.35671	T	0.21	-22.5782	7.546	0.27768	0.0666:0.167:0.6551:0.1114	rs1135640;rs1137582;rs3198449;rs3201363;rs11550765;rs17420148;rs17583121;rs17850378;rs17850653;rs52804397;rs56586913;rs1137582	244;274;312;312	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	M	312;312;274;312;244	ENSP00000301608:I312M;ENSP00000293217:I312M;ENSP00000441257:I274M	ENSP00000293217:I312M	I	-	3	3	ACOX1	71461135	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.086000	0.30853	2.941000	0.99782	0.655000	0.94253	ATC	G|0.477;C|0.523	0.523	strong		0.507	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1		
GAD1	2571	hgsc.bcm.edu	37	2	171713564	171713564	+	Silent	SNP	C	C	T	rs769392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:171713564C>T	ENST00000358196.3	+	15	2000	c.1450C>T	c.(1450-1452)Ctg>Ttg	p.L484L		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	484					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CAACAAATGCCTGGAACTGGC	0.418													C|||	213	0.0425319	0.1505	0.0202	5008	,	,		19163	0.0		0.0	False		,,,				2504	0.0				p.L484L		Atlas-SNP	.											.	GAD1	79	.	0			c.C1450T						PASS	.	C		566,3840	254.3+/-259.9	31,504,1668	162.0	175.0	171.0		1450	1.6	1.0	2	dbSNP_98	171	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GAD1	NM_000817.2		31,507,5965	TT,TC,CC		0.0349,12.8461,4.3749		484/595	171713564	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	2571	exon15			AAATGCCTGGAAC		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1450C>T	2.37:g.171713564C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Silent	SNP	ENST00000358196.3	37	CCDS2239.1																																																																																			C|0.959;T|0.041	0.041	strong		0.418	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
NEUROG3	50674	hgsc.bcm.edu	37	10	71332480	71332480	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:71332480C>T	ENST00000242462.4	-	2	349	c.320G>A	c.(319-321)cGc>cAc	p.R107H		NM_020999.3	NP_066279.2	Q9Y4Z2	NGN3_HUMAN	neurogenin 3	107	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.		R -> S (in DIAR4; attenuated NEUROG3 function in vivo). {ECO:0000269|PubMed:16855267}.		central nervous system development (GO:0007417)|endocrine pancreas development (GO:0031018)|epithelial cell differentiation (GO:0030855)|forebrain development (GO:0030900)|hindbrain development (GO:0030902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|peripheral nervous system development (GO:0007422)|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 dendrite morphogenesis (GO:0048814)|spinal cord development (GO:0021510)|transdifferentiation (GO:0060290)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|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)|transcription coactivator activity (GO:0003713)			endometrium(4)|large_intestine(2)|lung(6)|prostate(1)	13						CAGGACACCGCGCAGGGCGTC	0.627																																					p.R107H		Atlas-SNP	.											NEUROG3,NS,carcinoma,+1,1	NEUROG3	33	1	0			c.G320A						scavenged	.						96.0	66.0	76.0					10																	71332480		2203	4300	6503	SO:0001583	missense	50674	exon2			ACACCGCGCAGGG	AJ133776	CCDS31212.1	10q21.3	2013-05-21			ENSG00000122859	ENSG00000122859		"""Basic helix-loop-helix proteins"""	13806	protein-coding gene	gene with protein product		604882				9000438, 10677506	Standard	NM_020999		Approved	Atoh5, Math4B, ngn3, bHLHa7	uc001jpp.3	Q9Y4Z2	OTTHUMG00000018391	ENST00000242462.4:c.320G>A	10.37:g.71332480C>T	ENSP00000242462:p.Arg107His	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	275	3	0.0109091	NM_020999	Q5VVI0|Q6DJX6|Q9BY24	Missense_Mutation	SNP	ENST00000242462.4	37	CCDS31212.1	.	.	.	.	.	.	.	.	.	.	C	32	5.182012	0.94885	.	.	ENSG00000122859	ENST00000242462	D	0.98717	-5.09	4.53	4.53	0.55603	Helix-loop-helix DNA-binding (5);	0.000000	0.40640	N	0.001046	D	0.99435	0.9800	H	0.96633	3.855	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98206	1.0470	10	0.87932	D	0	-21.6233	15.9925	0.80217	0.0:1.0:0.0:0.0	.	107	Q9Y4Z2	NGN3_HUMAN	H	107	ENSP00000242462:R107H	ENSP00000242462:R107H	R	-	2	0	NEUROG3	71002486	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	7.516000	0.81772	2.307000	0.77673	0.591000	0.81541	CGC	.	.	none		0.627	NEUROG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048464.1	NM_020999	
ERO1LB	56605	hgsc.bcm.edu	37	1	236381833	236381833	+	Silent	SNP	A	A	G	rs11811758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:236381833A>G	ENST00000354619.5	-	16	1588	c.1387T>C	c.(1387-1389)Tta>Cta	p.L463L	GPR137B_ENST00000477559.1_Intron	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	463					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)	CTGTGTTGTAATAAGACTTTA	0.318													A|||	231	0.0461262	0.1626	0.0216	5008	,	,		15266	0.0		0.001	False		,,,				2504	0.0				p.L463L		Atlas-SNP	.											.	ERO1LB	48	.	0			c.T1387C						PASS	.	A		620,3778	261.0+/-264.0	45,530,1624	57.0	63.0	61.0		1387	-4.8	0.8	1	dbSNP_120	61	8,8554	6.4+/-24.3	0,8,4273	no	coding-synonymous	ERO1LB	NM_019891.3		45,538,5897	GG,GA,AA		0.0934,14.0973,4.8457		463/468	236381833	628,12332	2199	4281	6480	SO:0001819	synonymous_variant	56605	exon16			GTTGTAATAAGAC	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.1387T>C	1.37:g.236381833A>G		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	216	121	0.560185	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Silent	SNP	ENST00000354619.5	37	CCDS31064.1																																																																																			A|0.961;G|0.039	0.039	strong		0.318	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891	
PPP1R3F	89801	hgsc.bcm.edu	37	X	49126714	49126714	+	Silent	SNP	C	C	T	rs111938103		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49126714C>T	ENST00000055335.6	+	1	398	c.382C>T	c.(382-384)Ctg>Ttg	p.L128L	LL0XNC01-7P3.1_ENST00000602455.1_lincRNA|PPP1R3F_ENST00000438316.1_Intron|PPP1R3F_ENST00000466508.1_Intron|PPP1R3F_ENST00000495799.1_Intron	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	128	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					GCCGGGCCGTCTGGAGCGCTT	0.761													c|||	321	0.0850331	0.2254	0.0231	3775	,	,		6517	0.0		0.0	False		,,,				2504	0.0072				p.L128L		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.C382T						PASS	.		,	536,2408		20,412,84,850,296	3.0	3.0	3.0		,382	3.3	1.0	X	dbSNP_132	3	4,5429		0,3,1,2043,1340	no	intron,coding-synonymous	PPP1R3F	NM_001184745.1,NM_033215.4	,	20,415,85,2893,1636	TT,TC,T,CC,C		0.0736,18.2065,6.4462	,	,128/800	49126714	540,7837	1662	3387	5049	SO:0001819	synonymous_variant	89801	exon1			GGCCGTCTGGAGC		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14944	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3F"""			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.382C>T	X.37:g.49126714C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	16	14	0.875	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Silent	SNP	ENST00000055335.6	37	CCDS35254.1																																																																																			C|0.941;T|0.059	0.059	strong		0.761	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
GXYLT2	727936	hgsc.bcm.edu	37	3	72971414	72971414	+	Silent	SNP	A	A	G	rs61741329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:72971414A>G	ENST00000389617.4	+	3	689	c.528A>G	c.(526-528)acA>acG	p.T176T		NM_001080393.1	NP_001073862.1	A0PJZ3	GXLT2_HUMAN	glucoside xylosyltransferase 2	176					O-glycan processing (GO:0016266)	integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	18						ACCCCATCACATTTTCTGTTG	0.448													A|||	177	0.0353435	0.1256	0.0159	5008	,	,		18993	0.0		0.0	False		,,,				2504	0.0				p.T176T		Atlas-SNP	.											.	GXYLT2	43	.	0			c.A528G						PASS	.	A		362,3352		19,324,1514	210.0	215.0	213.0		528	-2.9	1.0	3	dbSNP_129	213	4,8206		0,4,4101	no	coding-synonymous	GXYLT2	NM_001080393.1		19,328,5615	GG,GA,AA		0.0487,9.7469,3.0694		176/444	72971414	366,11558	1857	4105	5962	SO:0001819	synonymous_variant	727936	exon3			CATCACATTTTCT	AC098481	CCDS46870.1	3p13	2013-02-22	2009-11-17	2009-11-17	ENSG00000172986	ENSG00000172986		"""Glycosyltransferase family 8 domain containing"""	33383	protein-coding gene	gene with protein product		613322	"""glycosyltransferase 8 domain containing 4"""	GLT8D4		19940119	Standard	NM_001080393		Approved		uc003dpg.3	A0PJZ3	OTTHUMG00000158815	ENST00000389617.4:c.528A>G	3.37:g.72971414A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	131	60	0.458015	NM_001080393		Silent	SNP	ENST00000389617.4	37	CCDS46870.1																																																																																			A|0.976;G|0.024	0.024	strong		0.448	GXYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352318.1	NM_001080393	
PLEC	5339	hgsc.bcm.edu	37	8	145004185	145004185	+	Silent	SNP	C	C	T	rs78012434	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145004185C>T	ENST00000322810.4	-	22	3238	c.3069G>A	c.(3067-3069)ttG>ttA	p.L1023L	PLEC_ENST00000345136.3_Silent_p.L886L|PLEC_ENST00000398774.2_Silent_p.L854L|PLEC_ENST00000356346.3_Silent_p.L872L|PLEC_ENST00000527096.1_Silent_p.L909L|PLEC_ENST00000357649.2_Silent_p.L890L|PLEC_ENST00000354589.3_Silent_p.L886L|PLEC_ENST00000354958.2_Silent_p.L864L|PLEC_ENST00000436759.2_Silent_p.L913L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1023	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TGTCCACGTGCAACTGGTGCC	0.697													C|||	326	0.0650958	0.2284	0.0317	5008	,	,		16413	0.0		0.002	False		,,,				2504	0.0				p.L1023L		Atlas-SNP	.											.	PLEC	1144	.	0			c.G3069A						PASS	.	C	,,,,,,,	823,3569		84,655,1457	26.0	34.0	31.0		2739,2616,2592,3069,2562,2658,2670,2658	-0.4	1.0	8	dbSNP_132	31	20,8550		0,20,4265	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	,,,,,,,	84,675,5722	TT,TC,CC		0.2334,18.7386,6.5036	,,,,,,,	913/4575,872/4534,864/4526,1023/4685,854/4516,886/4548,890/4552,886/4548	145004185	843,12119	2196	4285	6481	SO:0001819	synonymous_variant	5339	exon22			CACGTGCAACTGG	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.3069G>A	8.37:g.145004185C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			C|0.963;T|0.037	0.037	strong		0.697	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
TAF4B	6875	hgsc.bcm.edu	37	18	23873463	23873463	+	Silent	SNP	T	T	C	rs1677016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:23873463T>C	ENST00000269142.5	+	9	2798	c.1800T>C	c.(1798-1800)aaT>aaC	p.N600N	TAF4B_ENST00000578121.1_Silent_p.N605N|TAF4B_ENST00000400466.2_Silent_p.N600N	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	600					gene expression (GO:0010467)|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)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			CTCAGAAAAATAGAATAAAAG	0.284													T|||	2544	0.507987	0.093	0.5461	5008	,	,		15568	0.7996		0.5696	False		,,,				2504	0.6779				p.N600N		Atlas-SNP	.											TAF4B,NS,carcinoma,+1,1	TAF4B	71	1	0			c.T1800C						PASS	.	T		635,2935		62,511,1212	40.0	38.0	39.0		1800	-0.6	1.0	18	dbSNP_89	39	4680,3428		1350,1980,724	no	coding-synonymous	TAF4B	NM_005640.1		1412,2491,1936	CC,CT,TT		42.2792,17.7871,45.5129		600/863	23873463	5315,6363	1785	4054	5839	SO:0001819	synonymous_variant	6875	exon9			GAAAAATAGAATA	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1800T>C	18.37:g.23873463T>C		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	236	126	0.533898	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	37	CCDS42421.1																																																																																			T|0.474;C|0.526	0.526	strong		0.284	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
TTC39B	158219	hgsc.bcm.edu	37	9	15191209	15191209	+	Silent	SNP	A	A	G	rs74818741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:15191209A>G	ENST00000512701.2	-	10	1011	c.975T>C	c.(973-975)ttT>ttC	p.F325F	TTC39B_ENST00000541445.1_3'UTR|TTC39B_ENST00000507993.1_Silent_p.F160F|TTC39B_ENST00000355694.2_Silent_p.F259F|TTC39B_ENST00000380850.4_Silent_p.F325F|TTC39B_ENST00000297615.5_Silent_p.F256F|TTC39B_ENST00000507285.1_Silent_p.F160F			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	325										NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						AAAATCCAATAAATTCTAGTA	0.323													A|||	137	0.0273562	0.1014	0.0043	5008	,	,		17741	0.0		0.0	False		,,,				2504	0.0				p.F325F		Atlas-SNP	.											.	TTC39B	83	.	0			c.T975C						PASS	.	A	,,,,	346,4060	176.9+/-206.0	13,320,1870	69.0	73.0	72.0		969,975,768,480,975	1.3	1.0	9	dbSNP_132	72	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTC39B	NM_001168339.1,NM_001168340.1,NM_001168341.1,NM_001168342.1,NM_152574.2	,,,,	13,321,6168	GG,GA,AA		0.0116,7.8529,2.6684	,,,,	323/681,325/670,256/614,160/518,325/683	15191209	347,12657	2203	4299	6502	SO:0001819	synonymous_variant	158219	exon10			TCCAATAAATTCT	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.975T>C	9.37:g.15191209A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_001168340	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Silent	SNP	ENST00000512701.2	37	CCDS6477.2																																																																																			A|0.969;G|0.031	0.031	strong		0.323	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574	
ADRB2	154	hgsc.bcm.edu	37	5	148206440	148206440	+	Missense_Mutation	SNP	G	G	A	rs1042713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	101	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	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	
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238461	71238461	+	Missense_Mutation	SNP	G	G	A	rs200128074		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71238461G>A	ENST00000398536.4	+	1	149	c.115G>A	c.(115-117)Gtc>Atc	p.V39I		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	39	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						CTGTGTGCCCGTCTGCTGCTG	0.687																																					p.V39I		Atlas-SNP	.											.	KRTAP5-7	23	.	0			c.G115A						PASS	.	G	ILE/VAL	5,4395		0,5,2195	71.0	93.0	86.0		115	1.8	0.7	11		86	13,8569		0,13,4278	no	missense	KRTAP5-7	NM_001012503.1	29	0,18,6473	AA,AG,GG		0.1515,0.1136,0.1387	possibly-damaging	39/166	71238461	18,12964	2200	4291	6491	SO:0001583	missense	440050	exon1			GTGCCCGTCTGCT	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"""Keratin associated proteins"""	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.115G>A	11.37:g.71238461G>A	ENSP00000417330:p.Val39Ile	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	365	19	0.0520548	NM_001012503	B2RNM3|Q701N5	Missense_Mutation	SNP	ENST00000398536.4	37	CCDS41682.1	.	.	.	.	.	.	.	.	.	.	N	8.822	0.937856	0.18206	0.001136	0.001515	ENSG00000244411	ENST00000398536	T	0.01484	4.84	1.8	1.8	0.24995	.	.	.	.	.	T	0.01320	0.0043	L	0.38838	1.175	0.09310	N	0.999992	P	0.51537	0.946	B	0.30782	0.12	T	0.53528	-0.8426	9	0.41790	T	0.15	.	7.1256	0.25469	0.0:0.0:1.0:0.0	.	39	Q6L8G8	KRA57_HUMAN	I	39	ENSP00000417330:V39I	ENSP00000417330:V39I	V	+	1	0	KRTAP5-7	70916109	1.000000	0.71417	0.723000	0.30687	0.465000	0.32709	2.993000	0.49425	1.345000	0.45676	0.281000	0.19383	GTC	G|0.999;A|0.001	0.001	weak		0.687	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1		
CHSY1	22856	hgsc.bcm.edu	37	15	101718097	101718097	+	Silent	SNP	C	C	G	rs28364839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:101718097C>G	ENST00000254190.3	-	3	2380	c.1905G>C	c.(1903-1905)gtG>gtC	p.V635V	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	635					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)			CTGTAGTAAACACGAGGTCGA	0.448													C|||	1206	0.240815	0.4644	0.1527	5008	,	,		20757	0.0347		0.2256	False		,,,				2504	0.229				p.V635V		Atlas-SNP	.											.	CHSY1	60	.	0			c.G1905C						PASS	.	C		1824,2582	534.4+/-373.9	388,1048,767	69.0	67.0	68.0		1905	2.8	1.0	15	dbSNP_125	68	2053,6547	352.9+/-328.9	235,1583,2482	no	coding-synonymous	CHSY1	NM_014918.4		623,2631,3249	GG,GC,CC		23.8721,41.3981,29.8093		635/803	101718097	3877,9129	2203	4300	6503	SO:0001819	synonymous_variant	22856	exon3			AGTAAACACGAGG	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.1905G>C	15.37:g.101718097C>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Silent	SNP	ENST00000254190.3	37	CCDS10390.1																																																																																			C|0.724;G|0.276	0.276	strong		0.448	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918	
FAM208A	23272	hgsc.bcm.edu	37	3	56667213	56667213	+	Silent	SNP	T	T	C	rs34828128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:56667213T>C	ENST00000493960.2	-	18	3616	c.3606A>G	c.(3604-3606)caA>caG	p.Q1202Q	FAM208A_ENST00000355628.5_Silent_p.Q1141Q|FAM208A_ENST00000431842.2_Silent_p.Q765Q	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1202							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						AAAGAGCTGGTTGAGCAGAAA	0.353													T|||	31	0.0061901	0.0	0.0101	5008	,	,		18670	0.0		0.0149	False		,,,				2504	0.0092				p.Q1202Q		Atlas-SNP	.											.	FAM208A	113	.	0			c.A3606G						PASS	.	T	,	17,4389	24.3+/-50.5	0,17,2186	114.0	116.0	115.0		3606,2295	-1.5	1.0	3	dbSNP_126	115	154,8446	73.8+/-136.5	3,148,4149	no	coding-synonymous,coding-synonymous	FAM208A	NM_001112736.1,NM_015224.3	,	3,165,6335	CC,CT,TT		1.7907,0.3858,1.3148	,	1202/1513,765/1234	56667213	171,12835	2203	4300	6503	SO:0001819	synonymous_variant	23272	exon18			AGCTGGTTGAGCA	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.3606A>G	3.37:g.56667213T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	156	68	0.435897	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Silent	SNP	ENST00000493960.2	37	CCDS46853.1																																																																																			T|0.987;C|0.013	0.013	strong		0.353	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
TADA2A	6871	hgsc.bcm.edu	37	17	35771468	35771468	+	Missense_Mutation	SNP	C	C	T	rs7211875|rs112855394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:35771468C>T	ENST00000394395.2	+	2	189	c.16C>T	c.(16-18)Ccc>Tcc	p.P6S	TADA2A_ENST00000586023.1_Missense_Mutation_p.P6S|TADA2A_ENST00000225396.6_Missense_Mutation_p.P6S|TADA2A_ENST00000417170.1_Missense_Mutation_p.P6S|RP11-378E13.4_ENST00000590364.1_RNA	NM_001166105.1	NP_001159577.1	O75478	TAD2A_HUMAN	transcriptional adaptor 2A	6			P -> S (in dbSNP:rs7211875). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8552087, ECO:0000269|Ref.2}.		chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)|skin(1)	13						CCGTTTGGGTCCCTTTAGCAG	0.473													T|||	4281	0.854832	0.9539	0.8761	5008	,	,		18736	0.7391		0.83	False		,,,				2504	0.8507				p.P6S		Atlas-SNP	.											.	TADA2A	91	.	0			c.C16T						PASS	.	T	SER/PRO,SER/PRO,SER/PRO	4105,301	166.2+/-197.5	1910,285,8	141.0	131.0	135.0		16,16,16	4.8	1.0	17	dbSNP_116	135	7381,1219	247.2+/-275.4	3173,1035,92	yes	missense,missense,missense	TADA2A	NM_001166105.1,NM_001488.3,NM_133439.2	74,74,74	5083,1320,100	TT,TC,CC		14.1744,6.8316,11.6869	benign,benign,benign	6/444,6/444,6/306	35771468	11486,1520	2203	4300	6503	SO:0001583	missense	6871	exon2			TTGGGTCCCTTTA	AK022767	CCDS11319.1, CCDS45656.1	17q12-q21	2014-04-10	2009-10-02	2009-10-02	ENSG00000108264	ENSG00000276234			11531	protein-coding gene	gene with protein product		602276	"""transcriptional adaptor 2 (ADA2 homolog, yeast)-like"""	TADA2L		8552087	Standard	XM_006722043		Approved	ADA2, hADA2, ADA2A	uc002hnt.3	O75478	OTTHUMG00000188469	ENST00000394395.2:c.16C>T	17.37:g.35771468C>T	ENSP00000377918:p.Pro6Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001488	A8MVD0|B3KMU9|Q9BVJ0|Q9UCW2|Q9UP49	Missense_Mutation	SNP	ENST00000394395.2	37	CCDS11319.1	1844	0.8443223443223443	472	0.959349593495935	317	0.8756906077348067	428	0.7482517482517482	627	0.8271767810026385	T	3.765	-0.048816	0.07407	0.931684	0.858256	ENSG00000108264	ENST00000394395;ENST00000225396;ENST00000417170	T;T;T	0.26957	2.15;2.15;1.7	4.79	4.79	0.61399	.	0.113042	0.64402	N	0.000006	T	0.00012	0.0000	N	0.03115	-0.41	0.51012	P	9.499999999995623E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41378	-0.9512	9	0.02654	T	1	15.1675	7.4762	0.27378	0.0:0.0969:0.0:0.9031	rs7211875;rs17138764;rs17856035;rs17856372;rs52814727;rs56878335;rs7211875	6;6	O75478-2;O75478	.;TAD2A_HUMAN	S	6	ENSP00000377918:P6S;ENSP00000225396:P6S;ENSP00000406699:P6S	ENSP00000225396:P6S	P	+	1	0	TADA2A	32845581	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.970000	0.40520	0.986000	0.38683	-0.368000	0.07277	CCC	C|0.135;N|0.000	.	strong		0.473	TADA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256677.3	NM_001488	
ENTPD2	954	hgsc.bcm.edu	37	9	139943112	139943112	+	Silent	SNP	A	A	G	rs17853460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139943112A>G	ENST00000355097.2	-	9	1532	c.1485T>C	c.(1483-1485)atT>atC	p.I495I	ENTPD2_ENST00000460614.1_5'UTR|NPDC1_ENST00000488145.1_5'Flank|NPDC1_ENST00000371601.4_5'Flank|ENTPD2_ENST00000312665.5_Silent_p.I472I	NM_001246.3|NM_203468.2	NP_001237.1|NP_982293.1	Q9Y5L3	ENTP2_HUMAN	ectonucleoside triphosphate diphosphohydrolase 2	495					G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|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)|lung(5)|prostate(1)|skin(2)|urinary_tract(3)	12	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		TCGGCCCCTAAATGGTGCTTG	0.682													A|||	1152	0.230032	0.0855	0.3156	5008	,	,		5420	0.3522		0.2266	False		,,,				2504	0.2423				p.I495I		Atlas-SNP	.											.	ENTPD2	30	.	0			c.T1485C						PASS	.	A	,	512,3836		40,432,1702	12.0	12.0	12.0		1416,1485	2.7	0.1	9	dbSNP_123	12	1832,6718		191,1450,2634	no	coding-synonymous,coding-synonymous	ENTPD2	NM_001246.2,NM_203468.1	,	231,1882,4336	GG,GA,AA		21.4269,11.7755,18.1734	,	472/473,495/496	139943112	2344,10554	2174	4275	6449	SO:0001819	synonymous_variant	954	exon9			CCCCTAAATGGTG	U91510	CCDS7025.1, CCDS7026.1	9q34	2008-07-21			ENSG00000054179	ENSG00000054179			3364	protein-coding gene	gene with protein product	"""CD39-like-1"", ""ecto-ATPase"""	602012		CD39L1		9271669	Standard	NM_203468		Approved	NTPDase-2	uc004ckw.2	Q9Y5L3	OTTHUMG00000020953	ENST00000355097.2:c.1485T>C	9.37:g.139943112A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	89	58	0.651685	NM_203468	O15464|Q5SPY6|Q5SPY7	Silent	SNP	ENST00000355097.2	37	CCDS7026.1																																																																																			A|0.802;G|0.198	0.198	strong		0.682	ENTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055169.1	NM_203468	
CACNA1S	779	hgsc.bcm.edu	37	1	201058428	201058428	+	Silent	SNP	G	G	A	rs61734621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201058428G>A	ENST00000362061.3	-	6	1084	c.858C>T	c.(856-858)taC>taT	p.Y286Y	CACNA1S_ENST00000367338.3_Silent_p.Y286Y	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	286					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)	TAATGCACTGGTACACGGTGA	0.607													G|||	79	0.0157748	0.056	0.0058	5008	,	,		19962	0.0		0.0	False		,,,				2504	0.001				p.Y286Y		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C858T						PASS	.	G		217,4189	134.9+/-171.1	6,205,1992	104.0	83.0	90.0		858	3.9	1.0	1	dbSNP_129	90	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	CACNA1S	NM_000069.2		6,220,6277	AA,AG,GG		0.1744,4.9251,1.7838		286/1874	201058428	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	779	exon6			GCACTGGTACACG	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.858C>T	1.37:g.201058428G>A		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	261	125	0.478927	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			G|0.984;A|0.016	0.016	strong		0.607	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
SNAPC2	6618	hgsc.bcm.edu	37	19	7987428	7987428	+	Missense_Mutation	SNP	C	C	T	rs116635738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7987428C>T	ENST00000221573.6	+	5	835	c.784C>T	c.(784-786)Cgc>Tgc	p.R262C	SNAPC2_ENST00000597584.1_Missense_Mutation_p.R25C	NM_003083.3	NP_003074.1	Q13487	SNPC2_HUMAN	small nuclear RNA activating complex, polypeptide 2, 45kDa	262					gene expression (GO:0010467)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6						GACGTACCTACGCCTGACAGC	0.657													C|||	54	0.0107827	0.0356	0.0072	5008	,	,		16883	0.0		0.0	False		,,,				2504	0.002				p.R262C		Atlas-SNP	.											SNAPC2,colon,carcinoma,0,1	SNAPC2	20	1	0			c.C784T						PASS	.	C	CYS/ARG	140,4266	100.3+/-138.9	1,138,2064	71.0	70.0	70.0		784	2.2	0.0	19	dbSNP_132	70	4,8596	3.0+/-9.4	0,4,4296	yes	missense	SNAPC2	NM_003083.3	180	1,142,6360	TT,TC,CC		0.0465,3.1775,1.1072	possibly-damaging	262/335	7987428	144,12862	2203	4300	6503	SO:0001583	missense	6618	exon5			TACCTACGCCTGA	U44898	CCDS12190.1	19p13	2008-07-22	2002-08-29			ENSG00000104976			11135	protein-coding gene	gene with protein product		605076	"""small nuclear RNA activating complex, polypeptide 2, 45kD"""			8633057	Standard	NM_003083		Approved	SNAP45, PTFdelta	uc002miw.2	Q13487		ENST00000221573.6:c.784C>T	19.37:g.7987428C>T	ENSP00000221573:p.Arg262Cys	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_003083	B2RBZ6|D6W663|Q13486	Missense_Mutation	SNP	ENST00000221573.6	37	CCDS12190.1	19	0.0086996336996337	16	0.032520325203252036	3	0.008287292817679558	0	0.0	0	0.0	c	14.33	2.503755	0.44558	0.031775	4.65E-4	ENSG00000104976	ENST00000221573	T	0.48836	0.8	4.44	2.15	0.27550	.	1.239960	0.05573	N	0.571328	T	0.19287	0.0463	N	0.22421	0.69	0.09310	N	1	D	0.67145	0.996	P	0.48227	0.571	T	0.30966	-0.9960	10	0.72032	D	0.01	-0.7906	8.8971	0.35472	0.4346:0.5654:0.0:0.0	.	262	Q13487	SNPC2_HUMAN	C	262	ENSP00000221573:R262C	ENSP00000221573:R262C	R	+	1	0	SNAPC2	7893428	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.478000	0.22212	1.074000	0.40909	-0.509000	0.04479	CGC	C|0.991;T|0.009	0.009	strong		0.657	SNAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461358.1	NM_003083	
CFI	3426	hgsc.bcm.edu	37	4	110681527	110681527	+	Missense_Mutation	SNP	C	C	T	rs112534524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:110681527C>T	ENST00000394634.2	-	6	989	c.782G>A	c.(781-783)gGc>gAc	p.G261D	CFI_ENST00000394635.3_Missense_Mutation_p.G261D|CFI_ENST00000512148.1_Missense_Mutation_p.G261D	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	261	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		GAAGCCTTTGCCTTGGCATGC	0.413													C|||	2	0.000399361	0.0	0.0	5008	,	,		19374	0.0		0.002	False		,,,				2504	0.0				p.G261D		Atlas-SNP	.											.	CFI	59	.	0			c.G782A	GRCh37	CM071595	CFI	M	rs112534524	PASS	.	C	ASP/GLY	5,4401	9.9+/-24.2	0,5,2198	127.0	113.0	117.0		782	2.2	0.0	4	dbSNP_132	117	17,8583	12.6+/-44.7	0,17,4283	yes	missense	CFI	NM_000204.3	94	0,22,6481	TT,TC,CC		0.1977,0.1135,0.1692	possibly-damaging	261/584	110681527	22,12984	2203	4300	6503	SO:0001583	missense	3426	exon6			CCTTTGCCTTGGC	J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"""Complement system"""	5394	protein-coding gene	gene with protein product	"""Konglutinogen-activating factor"", ""C3b-inactivator"""	217030	"""I factor (complement)"""	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.782G>A	4.37:g.110681527C>T	ENSP00000378130:p.Gly261Asp	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	134	49	0.365672	NM_000204	O60442	Missense_Mutation	SNP	ENST00000394634.2	37	CCDS34049.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	10.82	1.457707	0.26161	0.001135	0.001977	ENSG00000205403	ENST00000394635;ENST00000394634;ENST00000540104;ENST00000512148;ENST00000536228	D;D;D	0.95272	-3.66;-3.66;-3.66	5.92	2.15	0.27550	.	0.579484	0.20634	N	0.088529	D	0.86251	0.5888	N	0.12471	0.22	0.09310	N	1	B;B;B	0.22800	0.074;0.036;0.075	B;B;B	0.28465	0.09;0.029;0.081	T	0.76713	-0.2858	10	0.44086	T	0.13	-6.4257	5.5586	0.17131	0.0:0.5559:0.1361:0.3081	.	261;261;261	E7ETH0;G3XAM2;P05156	.;.;CFAI_HUMAN	D	261;261;261;261;243	ENSP00000378131:G261D;ENSP00000378130:G261D;ENSP00000427438:G261D	ENSP00000378130:G261D	G	-	2	0	CFI	110900976	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	-0.052000	0.11865	0.424000	0.26061	0.655000	0.94253	GGC	C|0.998;G|0.000;T|0.002	0.002	strong		0.413	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204	
CPN1	1369	hgsc.bcm.edu	37	10	101824954	101824954	+	Silent	SNP	G	G	A	rs3750717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101824954G>A	ENST00000370418.3	-	4	1001	c.750C>T	c.(748-750)ctC>ctT	p.L250L		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	250	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)		CCTTCTGGAAGAGCTTGTCGT	0.607													A|||	287	0.0573083	0.1097	0.0144	5008	,	,		15395	0.0516		0.0139	False		,,,				2504	0.0675				p.L250L		Atlas-SNP	.											.	CPN1	62	.	0			c.C750T						PASS	.			469,3937	741.6+/-411.3	23,423,1757	50.0	54.0	53.0		750	-4.0	1.0	10	dbSNP_107	53	139,8461	778.9+/-407.7	0,139,4161	no	coding-synonymous	CPN1	NM_001308.2		23,562,5918	AA,AG,GG		1.6163,10.6446,4.6748		250/459	101824954	608,12398	2203	4300	6503	SO:0001819	synonymous_variant	1369	exon4			CTGGAAGAGCTTG	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.750C>T	10.37:g.101824954G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	37	CCDS7486.1																																																																																			G|0.957;A|0.043	0.043	strong		0.607	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414238	105414238	+	Missense_Mutation	SNP	C	C	A	rs60754080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105414238C>A	ENST00000333244.5	-	7	7669	c.7550G>T	c.(7549-7551)gGg>gTg	p.G2517V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2517						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)			GGAGAGGCTCCCGTCGGCCTC	0.617													.|||	2405	0.480232	0.5779	0.3804	5008	,	,		16801	0.3194		0.5099	False		,,,				2504	0.5542				p.G2517V		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,-1,1	AHNAK2	719	1	0			c.G7550T						PASS	.	A	VAL/GLY	2313,1507		750,813,347	120.0	138.0	132.0		7550	0.3	0.0	14	dbSNP_129	132	4319,3903		1144,2031,936	no	missense	AHNAK2	NM_138420.2	109	1894,2844,1283	AA,AC,CC		47.4702,39.4503,44.9261	benign	2517/5796	105414238	6632,5410	1910	4111	6021	SO:0001583	missense	113146	exon7			AGGCTCCCGTCGG	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.7550G>T	14.37:g.105414238C>A	ENSP00000353114:p.Gly2517Val	Somatic	279	1	0.00358423		WXS	Illumina HiSeq	Phase_I	283	282	0.996466	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	853	0.39056776556776557	232	0.4715447154471545	132	0.36464088397790057	158	0.2762237762237762	331	0.4366754617414248	a	0.016	-1.527230	0.00959	0.605497	0.525298	ENSG00000185567	ENST00000333244	T	0.02103	4.45	2.87	0.322	0.15888	.	.	.	.	.	T	0.00012	0.0000	N	0.00025	-2.685	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.12426	-1.0548	8	0.26408	T	0.33	.	4.5201	0.11956	0.6385:0.1657:0.1958:0.0	rs61996035	2517	Q8IVF2	AHNK2_HUMAN	V	2517	ENSP00000353114:G2517V	ENSP00000353114:G2517V	G	-	2	0	AHNAK2	104485283	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.177000	0.16801	-0.362000	0.08113	-0.855000	0.03028	GGG	C|0.609;A|0.391	0.391	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68938185	68938185	+	Missense_Mutation	SNP	C	C	T	rs1438391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:68938185C>T	ENST00000356291.2	-	5	429	c.370G>A	c.(370-372)Gat>Aat	p.D124N	UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	124	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.		D -> N (in dbSNP:rs1438391).			extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						ATAAGAATATCCACACCTTGT	0.303													C|||	190	0.0379393	0.1301	0.0216	5008	,	,		12334	0.0		0.003	False		,,,				2504	0.0				p.D124N		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.G370A						PASS	.	C	ASN/ASP	471,3935	220.0+/-237.6	24,423,1756	89.0	89.0	89.0		370	3.6	0.0	4	dbSNP_88	89	35,8565	22.8+/-68.1	0,35,4265	yes	missense	TMPRSS11F	NM_207407.2	23	24,458,6021	TT,TC,CC		0.407,10.69,3.8905	benign	124/439	68938185	506,12500	2203	4300	6503	SO:0001583	missense	389208	exon5			GAATATCCACACC	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.370G>A	4.37:g.68938185C>T	ENSP00000348639:p.Asp124Asn	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	70	0.03205128205128205	61	0.12398373983739837	9	0.024861878453038673	0	0.0	0	0.0	C	1.216	-0.628370	0.03610	0.1069	0.00407	ENSG00000198092	ENST00000356291	T	0.37235	1.21	6.07	3.63	0.41609	SEA (3);	0.702903	0.13299	N	0.398399	T	0.00144	0.0004	N	0.01048	-1.04	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	9	0.12103	T	0.63	.	5.8211	0.18528	0.0:0.0872:0.1681:0.7447	rs1438391;rs1438391	124	Q6ZWK6	TM11F_HUMAN	N	124	ENSP00000348639:D124N	ENSP00000348639:D124N	D	-	1	0	TMPRSS11F	68620780	0.556000	0.26538	0.016000	0.15963	0.005000	0.04900	1.049000	0.30392	0.514000	0.28300	-0.302000	0.09304	GAT	C|0.960;T|0.040	0.040	strong		0.303	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	
ZNF600	162966	hgsc.bcm.edu	37	19	53270623	53270623	+	Missense_Mutation	SNP	G	G	C	rs79890896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53270623G>C	ENST00000338230.3	-	3	653	c.386C>G	c.(385-387)cCt>cGt	p.P129R		NM_198457.2	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	129					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(2)|kidney(4)|large_intestine(9)|liver(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		TTGGGGCCTAGGAGAAATTCT	0.378													-|||	321	0.0640974	0.2133	0.0245	5008	,	,		19263	0.0089		0.0109	False		,,,				2504	0.002				p.P129R	Esophageal Squamous(196;1235 2112 2375 33339 34207)	Atlas-SNP	.											ZNF600,colon,carcinoma,0,1	ZNF600	75	1	0			c.C386G						PASS	.	C	ARG/PRO	781,3625		72,637,1494	118.0	124.0	122.0		386	-2.2	0.0	19	dbSNP_131	122	116,8484		1,114,4185	yes	missense	ZNF600	NM_198457.2	103	73,751,5679	CC,CG,GG		1.3488,17.7258,6.8968	benign	129/723	53270623	897,12109	2203	4300	6503	SO:0001583	missense	162966	exon3			GGCCTAGGAGAAA	U52096	CCDS12856.1	19q13.42	2013-01-08				ENSG00000189190		"""Zinc fingers, C2H2-type"""	30951	protein-coding gene	gene with protein product						12576331	Standard	NM_198457		Approved	KR-ZNF1, DKFZp686F06123	uc002qab.4	Q6ZNG1		ENST00000338230.3:c.386C>G	19.37:g.53270623G>C	ENSP00000344791:p.Pro129Arg	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	167	80	0.479042	NM_198457	Q6MZR0	Missense_Mutation	SNP	ENST00000338230.3	37	CCDS12856.1	129	0.059065934065934064	100	0.2032520325203252	14	0.03867403314917127	6	0.01048951048951049	9	0.011873350923482849	.	0.012	-1.650134	0.00785	0.177258	0.013488	ENSG00000189190	ENST00000338230	T	0.07908	3.15	1.08	-2.17	0.07059	.	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38308	-0.9667	8	0.56958	D	0.05	.	5.1689	0.15099	0.1704:0.3728:0.4569:0.0	.	129	Q6ZNG1	ZN600_HUMAN	R	129	ENSP00000344791:P129R	ENSP00000344791:P129R	P	-	2	0	ZNF600	57962435	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.338000	0.19858	-2.412000	0.00570	-1.123000	0.02005	CCT	G|0.938;C|0.062	0.062	strong		0.378	ZNF600-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463093.1	NM_198457	
FAM198A	729085	hgsc.bcm.edu	37	3	43097765	43097765	+	Missense_Mutation	SNP	G	G	A	rs3732858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:43097765G>A	ENST00000430121.2	+	5	1710	c.1615G>A	c.(1615-1617)Ggc>Agc	p.G539S		NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	539				G -> S (in Ref. 3; CAB55980). {ECO:0000305}.		extracellular region (GO:0005576)				endometrium(1)	1						GGAAAGCCAAGGCGGAGCCCA	0.582													G|||	832	0.166134	0.028	0.1556	5008	,	,		18124	0.1498		0.166	False		,,,				2504	0.3773				p.G539S		Atlas-SNP	.											.	FAM198A	23	.	0			c.G1615A						PASS	.	G	SER/GLY	85,1299		4,77,611	60.0	60.0	60.0		1615	5.2	0.9	3	dbSNP_107	60	524,2658		41,442,1108	yes	missense	FAM198A	NM_001129908.2	56	45,519,1719	AA,AG,GG		16.4676,6.1416,13.3377	probably-damaging	539/576	43097765	609,3957	692	1591	2283	SO:0001583	missense	729085	exon5			AGCCAAGGCGGAG	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.1615G>A	3.37:g.43097765G>A	ENSP00000407301:p.Gly539Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_001129908	B3KR48	Missense_Mutation	SNP	ENST00000430121.2	37	CCDS46808.1	292	0.1336996336996337	18	0.036585365853658534	50	0.13812154696132597	88	0.15384615384615385	136	0.17941952506596306	G	27.0	4.791646	0.90367	0.061416	0.164676	ENSG00000144649	ENST00000488863;ENST00000430121	T;T	0.38401	1.14;1.14	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.00241	0.0007	M	0.83953	2.67	0.21553	P	0.999644051	D	0.89917	1.0	D	0.79784	0.993	T	0.00391	-1.1769	9	0.72032	D	0.01	-12.1499	17.7129	0.88327	0.0:0.0:1.0:0.0	rs3732858;rs17391329;rs3732858	539	Q9UFP1	F198A_HUMAN	S	110;539	ENSP00000439905:G110S;ENSP00000407301:G539S	ENSP00000273146:G539S	G	+	1	0	FAM198A	43072769	1.000000	0.71417	0.917000	0.36280	0.590000	0.36582	8.544000	0.90654	2.583000	0.87209	0.561000	0.74099	GGC	G|0.865;A|0.135	0.135	strong		0.582	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
FRAS1	80144	hgsc.bcm.edu	37	4	79229302	79229302	+	Silent	SNP	A	A	G	rs345528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79229302A>G	ENST00000325942.6	+	15	2057	c.1617A>G	c.(1615-1617)agA>agG	p.R539R	FRAS1_ENST00000264895.6_Silent_p.R539R|FRAS1_ENST00000264899.6_Silent_p.R539R	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	539					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						ACGTGCTGAGAGATGGCGGCT	0.577													A|||	677	0.135184	0.4387	0.0447	5008	,	,		16917	0.0377		0.003	False		,,,				2504	0.0256				p.R539R		Atlas-SNP	.											.	FRAS1	779	.	0			c.A1617G						PASS	.	A	,	1476,2842		246,984,929	73.0	81.0	78.0		1617,1617	-3.0	0.5	4	dbSNP_79	78	62,8448		1,60,4194	no	coding-synonymous,coding-synonymous	FRAS1	NM_001166133.1,NM_025074.6	,	247,1044,5123	GG,GA,AA		0.7286,34.1825,11.9894	,	539/1977,539/4013	79229302	1538,11290	2159	4255	6414	SO:0001819	synonymous_variant	80144	exon15			GCTGAGAGATGGC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1617A>G	4.37:g.79229302A>G		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	247	244	0.987854	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	37	CCDS54772.1	256|256	0.11721611721611722|0.11721611721611722	215|215	0.4369918699186992|0.4369918699186992	18|18	0.049723756906077346|0.049723756906077346	22|22	0.038461538461538464|0.038461538461538464	1|1	0.0013192612137203166|0.0013192612137203166	A|A	0.991|0.991	-0.694105|-0.694105	0.03303|0.03303	0.341825|0.341825	0.007286|0.007286	ENSG00000138759|ENSG00000138759	ENST00000502446|ENST00000508900	.|T	.|0.46451	.|0.87	5.57|5.57	-3.05|-3.05	0.05396|0.05396	.|.	.|0.189453	.|0.47455	.|D	.|0.000233	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.23515|0.23515	P|P	0.99751295|0.99751295	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.37798|0.37798	-0.9690|-0.9690	3|5	.|.	.|.	.|.	.|.	12.555|12.555	0.56248|0.56248	0.4432:0.0:0.5568:0.0|0.4432:0.0:0.5568:0.0	rs345528;rs57052525;rs345528|rs345528;rs57052525;rs345528	.|.	.|.	.|.	G|G	468|382	.|ENSP00000423809:R382G	.|.	E|R	+|+	2|1	0|2	FRAS1|FRAS1	79448326|79448326	1.000000|1.000000	0.71417|0.71417	0.521000|0.521000	0.27850|0.27850	0.014000|0.014000	0.08584|0.08584	0.688000|0.688000	0.25422|0.25422	-0.646000|-0.646000	0.05452|0.05452	-0.462000|-0.462000	0.05337|0.05337	GAG|AGA	A|0.864;G|0.136	0.136	strong		0.577	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
OTOGL	283310	hgsc.bcm.edu	37	12	80750659	80750659	+	Missense_Mutation	SNP	G	G	A	rs11836060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:80750659G>A	ENST00000547103.1	+	48	5927	c.5921G>A	c.(5920-5922)cGa>cAa	p.R1974Q	OTOGL_ENST00000458043.2_Missense_Mutation_p.R1986Q|OTOGL_ENST00000546620.1_Missense_Mutation_p.R5Q			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1974	Cys-rich.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						ATTCAAGTTCGACAGGAAGAA	0.348													A|||	859	0.171526	0.1838	0.2075	5008	,	,		13699	0.0506		0.1819	False		,,,				2504	0.2434				p.R1986Q		Atlas-SNP	.											.	OTOGL	235	.	0			c.G5957A						PASS	.	A	GLN/ARG	823,3583	747.6+/-411.9	74,675,1454	110.0	98.0	102.0		5957	4.1	1.0	12	dbSNP_120	102	1690,6910	738.1+/-407.0	170,1350,2780	yes	missense	OTOGL	NM_173591.3	43	244,2025,4234	AA,AG,GG		19.6512,18.6791,19.3219	benign	1986/2345	80750659	2513,10493	2203	4300	6503	SO:0001583	missense	283310	exon48			AAGTTCGACAGGA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5921G>A	12.37:g.80750659G>A	ENSP00000447211:p.Arg1974Gln	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	183	104	0.568306	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		324|324	0.14835164835164835|0.14835164835164835	86|86	0.17479674796747968|0.17479674796747968	75|75	0.20718232044198895|0.20718232044198895	27|27	0.0472027972027972|0.0472027972027972	136|136	0.17941952506596306|0.17941952506596306	A|A	13.96|13.96	2.393127|2.393127	0.42410|0.42410	0.186791|0.186791	0.196512|0.196512	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182	.|T;T;T;T	.|0.28454	.|1.61;1.61;1.61;1.61	5.36|5.36	4.06|4.06	0.47325|0.47325	.|.	.|0.264710	.|0.30244	.|N	.|0.010074	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.13168|0.13168	0.305|0.305	0.48830|0.48830	P|P	2.9000000000001247E-4|2.9000000000001247E-4	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.37641|0.37641	-0.9697|-0.9697	4|9	.|0.15952	.|T	.|0.53	.|.	7.6258|7.6258	0.28212|0.28212	0.7196:0.0:0.2804:0.0|0.7196:0.0:0.2804:0.0	rs11836060;rs17309026;rs52804264;rs60470781;rs11836060|rs11836060;rs17309026;rs52804264;rs60470781;rs11836060	.|351	.|Q3ZCN5	.|OTOGL_HUMAN	N|Q	429|1974;1986;5;3	.|ENSP00000447211:R1974Q;ENSP00000400895:R1986Q;ENSP00000449094:R5Q;ENSP00000449641:R3Q	.|ENSP00000400895:R1986Q	D|R	+|+	1|2	0|0	OTOGL|OTOGL	79274790|79274790	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.988000|0.988000	0.76386|0.76386	3.251000|3.251000	0.51453|0.51453	0.253000|0.253000	0.21552|0.21552	-0.381000|-0.381000	0.06696|0.06696	GAC|CGA	G|0.823;A|0.177	0.177	strong		0.348	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
ZNF609	23060	hgsc.bcm.edu	37	15	64967654	64967654	+	Silent	SNP	C	C	T	rs16948170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:64967654C>T	ENST00000326648.3	+	4	2729	c.2601C>T	c.(2599-2601)gcC>gcT	p.A867A		NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	867						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CAAAGGACGCCGAACAGTTGG	0.483													T|||	638	0.127396	0.3396	0.0519	5008	,	,		20467	0.001		0.0696	False		,,,				2504	0.0838				p.A867A		Atlas-SNP	.											.	ZNF609	106	.	0			c.C2601T						PASS	.	T		1283,3123	694.0+/-405.8	180,923,1100	76.0	82.0	80.0		2601	-8.2	0.3	15	dbSNP_123	80	559,8039	791.4+/-407.5	25,509,3765	no	coding-synonymous	ZNF609	NM_015042.1		205,1432,4865	TT,TC,CC		6.5015,29.1194,14.1649		867/1412	64967654	1842,11162	2203	4299	6502	SO:0001819	synonymous_variant	23060	exon4			GGACGCCGAACAG	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"""Zinc fingers, C2H2-type"""	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.2601C>T	15.37:g.64967654C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_015042	Q0D2I2	Silent	SNP	ENST00000326648.3	37	CCDS32270.1																																																																																			C|0.871;T|0.129	0.129	strong		0.483	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833	
RASA3	22821	hgsc.bcm.edu	37	13	114773022	114773022	+	Missense_Mutation	SNP	C	C	T	rs74116414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114773022C>T	ENST00000334062.7	-	18	1850	c.1729G>A	c.(1729-1731)Gtg>Atg	p.V577M	RASA3_ENST00000389544.4_Missense_Mutation_p.V545M	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	577	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)			TCTTTAAGCACGATGGGCTGC	0.562													N|||	129	0.0257588	0.0923	0.0101	5008	,	,		20382	0.0		0.0	False		,,,				2504	0.0				p.V577M		Atlas-SNP	.											.	RASA3	83	.	0			c.G1729A						PASS	.	C	MET/VAL	302,4100	162.5+/-194.5	14,274,1913	141.0	102.0	115.0		1729	0.1	1.0	13	dbSNP_130	115	5,8593	3.7+/-12.6	0,5,4294	yes	missense	RASA3	NM_007368.2	21	14,279,6207	TT,TC,CC		0.0582,6.8605,2.3615	benign	577/835	114773022	307,12693	2201	4299	6500	SO:0001583	missense	22821	exon18			TAAGCACGATGGG		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.1729G>A	13.37:g.114773022C>T	ENSP00000335029:p.Val577Met	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	37	CCDS32016.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	C	13.21	2.168248	0.38315	0.068605	5.82E-4	ENSG00000185989	ENST00000334062;ENST00000389544	D;D	0.94650	-3.48;-3.48	4.43	0.0618	0.14342	Rho GTPase activation protein (1);Pleckstrin homology-type (1);Pleckstrin homology domain (2);Ras GTPase-activating protein (1);	0.117907	0.56097	D	0.000028	T	0.59293	0.2183	M	0.76170	2.325	0.80722	D	1	B	0.14012	0.009	B	0.35688	0.208	T	0.72232	-0.4353	9	.	.	.	.	3.085	0.06275	0.2028:0.1354:0.5245:0.1373	.	577	Q14644	RASA3_HUMAN	M	577;545	ENSP00000335029:V577M;ENSP00000374195:V545M	.	V	-	1	0	RASA3	113791124	1.000000	0.71417	0.999000	0.59377	0.169000	0.22640	0.524000	0.22940	0.107000	0.17824	-0.928000	0.02712	GTG	C|0.976;T|0.024	0.024	strong		0.562	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368	
DSP	1832	hgsc.bcm.edu	37	6	7585795	7585795	+	Missense_Mutation	SNP	C	C	A	rs34884895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7585795C>A	ENST00000379802.3	+	24	8641	c.8300C>A	c.(8299-8301)aCc>aAc	p.T2767N	DSP_ENST00000418664.2_Missense_Mutation_p.T2168N	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2767	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)		CTGCAAGACACCAGCAGCTAT	0.512													C|||	35	0.00698882	0.0257	0.0014	5008	,	,		807	0.0		0.0	False		,,,				2504	0.0				p.T2767N		Atlas-SNP	.											.	DSP	306	.	0			c.C8300A						PASS	.	C	ASN/THR,ASN/THR	100,4306	79.3+/-117.8	1,98,2104	70.0	80.0	77.0		6503,8300	2.2	1.0	6	dbSNP_126	77	0,8600		0,0,4300	yes	missense,missense	DSP	NM_001008844.1,NM_004415.2	65,65	1,98,6404	AA,AC,CC		0.0,2.2696,0.7689	possibly-damaging,possibly-damaging	2168/2273,2767/2872	7585795	100,12906	2203	4300	6503	SO:0001583	missense	1832	exon24			AAGACACCAGCAG	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.8300C>A	6.37:g.7585795C>A	ENSP00000369129:p.Thr2767Asn	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	15.09	2.730333	0.48939	0.022696	0.0	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.73258	-0.73;-0.73	5.49	2.23	0.28157	.	0.171164	0.41396	D	0.000892	T	0.64283	0.2584	L	0.60455	1.87	0.22292	N	0.999227	D;P	0.67145	0.996;0.899	D;P	0.68483	0.958;0.689	T	0.57562	-0.7790	10	0.26408	T	0.33	.	8.2741	0.31862	0.0:0.6483:0.0:0.3517	rs34884895	2215;2767	Q4LE79;P15924	.;DESP_HUMAN	N	2767;2168	ENSP00000369129:T2767N;ENSP00000396591:T2168N	ENSP00000369129:T2767N	T	+	2	0	DSP	7530794	0.206000	0.23470	1.000000	0.80357	0.997000	0.91878	0.743000	0.26231	0.204000	0.20548	0.561000	0.74099	ACC	C|0.991;A|0.009	0.009	strong		0.512	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
IFT74	80173	hgsc.bcm.edu	37	9	27062721	27062721	+	Missense_Mutation	SNP	C	C	T	rs3429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:27062721C>T	ENST00000443698.1	+	20	1961	c.1790C>T	c.(1789-1791)aCc>aTc	p.T597I	IFT74_ENST00000433700.1_Missense_Mutation_p.T597I|IFT74_ENST00000380062.5_Missense_Mutation_p.T597I	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	597			T -> I (in dbSNP:rs3429). {ECO:0000269|PubMed:14702039}.		cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|keratinocyte development (GO:0003334)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|nucleus (GO:0005634)	beta-tubulin binding (GO:0048487)|chromatin binding (GO:0003682)			endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		TTACATAGCACCAGCGGAAAC	0.393													C|||	527	0.105232	0.0408	0.0706	5008	,	,		15575	0.0308		0.1441	False		,,,				2504	0.2536				p.T597I		Atlas-SNP	.											.	IFT74	46	.	0			c.C1790T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR	192,3546		5,182,1682	96.0	88.0	90.0		1790,1790,1790	3.9	0.0	9	dbSNP_36	90	1046,7146		67,912,3117	yes	missense,missense,missense	IFT74	NM_001099222.1,NM_001099223.1,NM_025103.2	89,89,89	72,1094,4799	TT,TC,CC		12.7686,5.1364,10.3772	benign,benign,benign	597/601,597/601,597/601	27062721	1238,10692	1869	4096	5965	SO:0001583	missense	80173	exon20			ATAGCACCAGCGG	AK023707	CCDS43793.1, CCDS47955.1	9p21.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000096872	ENSG00000096872		"""Intraflagellar transport homologs"""	21424	protein-coding gene	gene with protein product	"""capillary morphogenesis protein 1"""	608040	"""coiled-coil domain containing 2"", ""intraflagellar transport 74 homolog (Chlamydomonas)"""	CCDC2		11683410	Standard	NM_001099223		Approved	CMG1, CMG-1, FLJ22621	uc003zqg.4	Q96LB3	OTTHUMG00000021028	ENST00000443698.1:c.1790C>T	9.37:g.27062721C>T	ENSP00000404122:p.Thr597Ile	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_001099222	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	Missense_Mutation	SNP	ENST00000443698.1	37	CCDS43793.1	172	0.07875457875457875	21	0.042682926829268296	29	0.08011049723756906	18	0.03146853146853147	104	0.13720316622691292	C	11.59	1.684685	0.29872	0.051364	0.127686	ENSG00000096872	ENST00000433700;ENST00000443698;ENST00000380062	T;T;T	0.12039	2.72;2.72;2.72	5.9	3.87	0.44632	.	0.421653	0.24162	N	0.040969	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.22983	0.078	B	0.29785	0.107	T	0.26292	-1.0107	9	0.52906	T	0.07	-0.7514	8.2372	0.31634	0.0:0.6095:0.3013:0.0893	rs3429;rs3739543;rs17641379;rs52824285;rs3429	597	Q96LB3	IFT74_HUMAN	I	597	ENSP00000389224:T597I;ENSP00000404122:T597I;ENSP00000369402:T597I	ENSP00000369402:T597I	T	+	2	0	IFT74	27052721	0.902000	0.30710	0.026000	0.17262	0.675000	0.39556	1.796000	0.38794	0.641000	0.30601	0.650000	0.86243	ACC	C|0.900;T|0.100	0.100	strong		0.393	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055476.2	NM_025103	
CD3G	917	hgsc.bcm.edu	37	11	118221349	118221349	+	Silent	SNP	T	T	C	rs71469175|rs3753059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118221349T>C	ENST00000532917.1	+	4	458	c.390T>C	c.(388-390)gcT>gcC	p.A130A	CD3G_ENST00000532903.1_3'UTR|CD3G_ENST00000392883.2_Intron	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN	CD3g molecule, gamma (CD3-TCR complex)	130					cell surface receptor signaling pathway (GO:0007166)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|regulation of immune response (GO:0050776)|regulation of lymphocyte apoptotic process (GO:0070228)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|receptor signaling complex scaffold activity (GO:0030159)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	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)	Muromonab(DB00075)	TCGTCCTTGCTGTTGGGGTCT	0.478													T|||	1484	0.296326	0.1611	0.1095	5008	,	,		19810	0.5119		0.1789	False		,,,				2504	0.5102				p.A130A		Atlas-SNP	.											.	CD3G	31	.	0			c.T390C						PASS	.	T		12,4388		5,2,2193	193.0	167.0	176.0		390	2.2	1.0	11	dbSNP_107	176	21,8571		6,9,4281	no	coding-synonymous	CD3G	NM_000073.2		11,11,6474	CC,CT,TT		0.2444,0.2727,0.254		130/183	118221349	33,12959	2200	4296	6496	SO:0001819	synonymous_variant	917	exon4			CCTTGCTGTTGGG	X60491	CCDS8395.1	11q23	2014-09-17	2006-03-28		ENSG00000160654	ENSG00000160654		"""CD molecules"""	1675	protein-coding gene	gene with protein product		186740	"""CD3g antigen, gamma polypeptide (TiT3 complex)"""				Standard	NM_000073		Approved		uc001psu.2	P09693	OTTHUMG00000166971	ENST00000532917.1:c.390T>C	11.37:g.118221349T>C		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	197	104	0.527919	NM_000073	Q2HIZ6	Silent	SNP	ENST00000532917.1	37	CCDS8395.1																																																																																			CT|0.500;TG|0.500	.	alt		0.478	CD3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392135.1	NM_000073	
AKT1	207	hgsc.bcm.edu	37	14	105238783	105238783	+	Silent	SNP	G	G	A	rs11555434	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105238783G>A	ENST00000554581.1	-	11	2659	c.1179C>T	c.(1177-1179)ggC>ggT	p.G393G	AKT1_ENST00000555528.1_Silent_p.G393G|AKT1_ENST00000554848.1_Silent_p.G393G|AKT1_ENST00000407796.2_Silent_p.G393G|AKT1_ENST00000402615.2_Silent_p.G393G|AKT1_ENST00000554192.1_Silent_p.G80G|AKT1_ENST00000555458.1_Silent_p.G88G|AKT1_ENST00000554585.1_5'UTR|AKT1_ENST00000349310.3_Silent_p.G393G|RP11-982M15.2_ENST00000557223.1_RNA|AKT1_ENST00000544168.1_Silent_p.G331G			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	393	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)	CGGAGCCCCCGCCAAGCCTGC	0.642		1	Mis		"""breast, colorectal, ovarian, NSCLC"""								g|||	44	0.00878594	0.0325	0.0014	5008	,	,		18738	0.0		0.0	False		,,,				2504	0.0				p.G393G		Atlas-SNP	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.C1179T						PASS	.		,,	113,4291	81.4+/-119.9	5,103,2094	65.0	48.0	54.0		1179,1179,1179	-6.1	0.5	14	dbSNP_120	54	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	AKT1	NM_001014431.1,NM_001014432.1,NM_005163.2	,,	5,107,6390	AA,AG,GG		0.0465,2.5658,0.8997	,,	393/481,393/481,393/481	105238783	117,12887	2202	4300	6502	SO:0001819	synonymous_variant	207	exon12			GCCCCCGCCAAGC	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.1179C>T	14.37:g.105238783G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	130	60	0.461538	NM_005163	B2RAM5|B7Z5R1|Q9BWB6	Silent	SNP	ENST00000554581.1	37	CCDS9994.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163	
OBSCN	84033	hgsc.bcm.edu	37	1	228496014	228496014	+	Silent	SNP	G	G	A	rs876180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228496014G>A	ENST00000422127.1	+	47	12713	c.12669G>A	c.(12667-12669)acG>acA	p.T4223T	OBSCN_ENST00000284548.11_Silent_p.T4223T|OBSCN_ENST00000570156.2_Silent_p.T5180T|OBSCN_ENST00000366709.4_Silent_p.T1342T|OBSCN_ENST00000366707.4_Silent_p.T1857T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4223	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)				AGGGCGTGACGCCCGAGGACG	0.637													G|||	1067	0.213059	0.32	0.2781	5008	,	,		18436	0.1825		0.161	False		,,,				2504	0.1074				p.T5180T		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	0			c.G15540A						PASS	.	G	,	1355,2893		229,897,998	36.0	40.0	39.0		12669,12669	-12.1	0.0	1	dbSNP_86	39	1498,6956		141,1216,2870	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	370,2113,3868	AA,AG,GG		17.7194,31.8974,22.461	,	4223/7969,4223/6621	228496014	2853,9849	2124	4227	6351	SO:0001819	synonymous_variant	84033	exon58			CGTGACGCCCGAG	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.12669G>A	1.37:g.228496014G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	131	75	0.572519	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																																																																																			G|0.776;A|0.224	0.224	strong		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SIAE	54414	hgsc.bcm.edu	37	11	124539273	124539273	+	Missense_Mutation	SNP	T	T	C	rs12282107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124539273T>C	ENST00000263593.3	-	2	384	c.212A>G	c.(211-213)aAa>aGa	p.K71R	SIAE_ENST00000545756.1_Missense_Mutation_p.K36R|SIAE_ENST00000525730.1_5'Flank			Q9HAT2	SIAE_HUMAN	sialic acid acetylesterase	71			K -> R (in dbSNP:rs12282107). {ECO:0000269|PubMed:20555325}.		carbohydrate metabolic process (GO:0005975)|regulation of immune system process (GO:0002682)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	sialate O-acetylesterase activity (GO:0001681)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	15	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;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)		ACTGGTCACTTTCTTCATGAT	0.532											OREG0021460	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	523	0.104433	0.2769	0.0231	5008	,	,		19951	0.1032		0.002	False		,,,				2504	0.0358				p.K71R		Atlas-SNP	.											.	SIAE	37	.	0			c.A212G						PASS	.	T	ARG/LYS,ARG/LYS	973,3429	367.1+/-318.1	103,767,1331	241.0	189.0	207.0		107,212	4.3	1.0	11	dbSNP_120	207	17,8581	11.9+/-42.8	0,17,4282	yes	missense,missense	SIAE	NM_001199922.1,NM_170601.4	26,26	103,784,5613	CC,CT,TT		0.1977,22.1036,7.6154	possibly-damaging,possibly-damaging	36/489,71/524	124539273	990,12010	2201	4299	6500	SO:0001583	missense	54414	exon2			GTCACTTTCTTCA	AF300796	CCDS8449.1, CCDS55795.1	11q24	2005-12-15	2005-12-15	2005-12-15		ENSG00000110013			18187	protein-coding gene	gene with protein product	"""sialic acid-specific acetylesterase II"""	610079	"""Ysg2 homolog (mouse)"""	YSG2		10464298	Standard	NM_001199922		Approved	CSE-C, MGC87009, LSE	uc001qan.3	Q9HAT2		ENST00000263593.3:c.212A>G	11.37:g.124539273T>C	ENSP00000263593:p.Lys71Arg	Somatic	172	0	0	1535	WXS	Illumina HiSeq	Phase_I	152	97	0.638158	NM_170601	B3KPB0|Q8IUT9|Q9HAU7|Q9NT71	Missense_Mutation	SNP	ENST00000263593.3	37	CCDS8449.1	198	0.09065934065934066	116	0.23577235772357724	9	0.024861878453038673	72	0.1258741258741259	1	0.0013192612137203166	T	14.31	2.497558	0.44455	0.221036	0.001977	ENSG00000110013	ENST00000263593;ENST00000545756	D;D	0.84516	-1.86;-1.83	5.4	4.28	0.50868	.	0.312791	0.34531	N	0.003890	T	0.00109	0.0003	L	0.60904	1.88	0.28952	P	0.890324	B;B	0.25441	0.126;0.077	B;B	0.34138	0.176;0.053	T	0.09574	-1.0668	9	0.34782	T	0.22	.	10.1847	0.42991	0.0:0.0787:0.0:0.9213	rs12282107;rs52803899;rs56529430;rs56940230;rs12282107	36;71	Q9HAT2-2;Q9HAT2	.;SIAE_HUMAN	R	71;36	ENSP00000263593:K71R;ENSP00000437877:K36R	ENSP00000263593:K71R	K	-	2	0	SIAE	124044483	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.232000	0.51302	1.082000	0.41137	0.533000	0.62120	AAA	T|0.906;C|0.094	0.094	strong		0.532	SIAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387070.1	NM_170601	
ZNF407	55628	hgsc.bcm.edu	37	18	72344553	72344553	+	Silent	SNP	G	G	A	rs7227391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:72344553G>A	ENST00000299687.5	+	1	1578	c.1578G>A	c.(1576-1578)acG>acA	p.T526T	ZNF407_ENST00000582337.1_Silent_p.T526T|ZNF407_ENST00000309902.6_Silent_p.T526T|ZNF407_ENST00000577538.1_Silent_p.T526T	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	526					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GCTCTCAGACGTTGTGTGCTT	0.542													G|||	341	0.0680911	0.112	0.0663	5008	,	,		19719	0.003		0.1064	False		,,,				2504	0.0378				p.T526T		Atlas-SNP	.											.	ZNF407	231	.	0			c.G1578A						PASS	.	G	,,	401,3607		17,367,1620	138.0	147.0	144.0		1578,1578,1578	3.0	0.0	18	dbSNP_116	144	1159,7179		87,985,3097	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	104,1352,4717	AA,AG,GG		13.9002,10.005,12.6357	,,	526/1816,526/1661,526/2249	72344553	1560,10786	2004	4169	6173	SO:0001819	synonymous_variant	55628	exon1			TCAGACGTTGTGT	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1578G>A	18.37:g.72344553G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	130	67	0.515385	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			G|0.907;A|0.093	0.093	strong		0.542	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
PDCD2	5134	hgsc.bcm.edu	37	6	170892759	170892759	+	Silent	SNP	T	T	A	rs73258640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170892759T>A	ENST00000541970.1	-	2	438	c.360A>T	c.(358-360)acA>acT	p.T120T	PDCD2_ENST00000443345.2_Silent_p.T87T|PDCD2_ENST00000537445.1_Silent_p.T87T|PDCD2_ENST00000392090.2_Silent_p.T87T|PDCD2_ENST00000542896.1_Silent_p.T120T|PDCD2_ENST00000453163.2_Silent_p.T120T	NM_001199462.1|NM_002598.3	NP_001186391.1|NP_002589.2	Q16342	PDCD2_HUMAN	programmed cell death 2	120					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(5)	9		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)		CTGATTCTCCTGTTTCTGGGG	0.433													.|||	61	0.0121805	0.0439	0.0029	5008	,	,		17113	0.0		0.001	False		,,,				2504	0.0				p.T120T	Colon(60;1476 1726 39478)	Atlas-SNP	.											.	PDCD2	13	.	0			c.A360T						PASS	.	T	,,,,,	162,4244		5,152,2046	63.0	62.0	62.0		360,261,261,261,360,360	-2.4	0.0	6	dbSNP_130	62	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDCD2	NM_001199461.1,NM_001199462.1,NM_001199463.1,NM_001199464.1,NM_002598.3,NM_144781.2	,,,,,	5,152,6346	AA,AT,TT		0.0,3.6768,1.2456	,,,,,	120/222,87/312,87/196,87/189,120/345,120/229	170892759	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	5134	exon2			TTCTCCTGTTTCT	AJ420535	CCDS5316.1, CCDS47521.1, CCDS56460.1, CCDS56461.1, CCDS56462.1, CCDS75557.1	6q27	2008-02-05			ENSG00000071994	ENSG00000071994		"""Zinc fingers, MYND-type"""	8762	protein-coding gene	gene with protein product		600866				7606924	Standard	NM_002598		Approved	ZMYND7, RP8	uc003qxw.3	Q16342	OTTHUMG00000016083	ENST00000541970.1:c.360A>T	6.37:g.170892759T>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_002598	E9PCU7|F5GYS7|Q58HM9|Q58HN0|Q9UH12	Silent	SNP	ENST00000541970.1	37	CCDS5316.1																																																																																			T|0.985;A|0.015	0.015	strong		0.433	PDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043269.2	NM_002598	
CAMSAP3	57662	hgsc.bcm.edu	37	19	7682862	7682862	+	Silent	SNP	C	C	G	rs4134883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7682862C>G	ENST00000160298.4	+	17	3770	c.3669C>G	c.(3667-3669)gtC>gtG	p.V1223V	CAMSAP3_ENST00000446248.2_Silent_p.V1250V	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	1223	CKK. {ECO:0000255|PROSITE- ProRule:PRU00841}.				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						CCATGAGCGTCGATGCCTTCA	0.642													C|||	194	0.038738	0.1407	0.0115	5008	,	,		15396	0.0		0.0	False		,,,				2504	0.0				p.V1250V		Atlas-SNP	.											.	CAMSAP3	131	.	0			c.C3750G						PASS	.	C	,	540,3516		43,454,1531	52.0	59.0	57.0		3750,3669	0.3	1.0	19	dbSNP_108	57	2,8342		0,2,4170	no	coding-synonymous,coding-synonymous	CAMSAP3	NM_001080429.2,NM_020902.1	,	43,456,5701	GG,GC,CC		0.024,13.3136,4.371	,	1250/1277,1223/1250	7682862	542,11858	2028	4172	6200	SO:0001819	synonymous_variant	57662	exon19			GAGCGTCGATGCC	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.3669C>G	19.37:g.7682862C>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	96	42	0.4375	NM_001080429	Q8NDF1	Silent	SNP	ENST00000160298.4	37	CCDS42489.1																																																																																			C|0.969;G|0.031	0.031	strong		0.642	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362	
FOXO3	2309	hgsc.bcm.edu	37	6	108882570	108882570	+	Silent	SNP	C	C	T	rs11757217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:108882570C>T	ENST00000343882.6	+	2	463	c.159C>T	c.(157-159)gcC>gcT	p.A53A	FOXO3_ENST00000406360.1_Silent_p.A53A	NM_201559.2	NP_963853.1	O43524	FOXO3_HUMAN	forkhead box O3	53					antral ovarian follicle growth (GO:0001547)|cellular response to oxidative stress (GO:0034599)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|initiation of primordial ovarian follicle growth (GO:0001544)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|ovulation from ovarian follicle (GO:0001542)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of erythrocyte differentiation (GO:0045648)|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)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(5)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		AGACGGCCGCCGACTCCATGA	0.731													C|||	923	0.184305	0.3147	0.2133	5008	,	,		10040	0.0526		0.1829	False		,,,				2504	0.1247				p.A53A		Atlas-SNP	.											FOXO3,brain,glioma,0,4	FOXO3	67	4	0			c.C159T						scavenged	.						3.0	3.0	3.0					6																	108882570		1560	3279	4839	SO:0001819	synonymous_variant	2309	exon1			GGCCGCCGACTCC	AF032886	CCDS5068.1	6q21	2008-09-08	2007-05-02	2007-05-02	ENSG00000118689	ENSG00000118689		"""Forkhead boxes"""	3821	protein-coding gene	gene with protein product		602681		FKHRL1, FOXO3A		9479491	Standard	NM_001455		Approved	AF6q21, FOXO2	uc003psm.2	O43524	OTTHUMG00000015327	ENST00000343882.6:c.159C>T	6.37:g.108882570C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	38	10	0.263158	NM_001455	B4DVZ6|E1P5E6|O15171|Q5T2I7|Q9BZ04	Silent	SNP	ENST00000343882.6	37	CCDS5068.1																																																																																			.	.	weak		0.731	FOXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041722.2		
ITPR2	3709	hgsc.bcm.edu	37	12	26868289	26868289	+	Silent	SNP	C	C	T	rs2230383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26868289C>T	ENST00000381340.3	-	8	1214	c.798G>A	c.(796-798)acG>acA	p.T266T		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	266	Inositol 1,4,5-trisphosphate binding. {ECO:0000250}.|MIR 3. {ECO:0000255|PROSITE- ProRule:PRU00131}.				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)	GGCGCAAGGTCGTACGAAGGA	0.363													C|||	388	0.077476	0.2534	0.0317	5008	,	,		18208	0.0		0.0159	False		,,,				2504	0.0153				p.T266T		Atlas-SNP	.											.	ITPR2	270	.	0			c.G798A						PASS	.	C		821,2933		100,621,1156	145.0	144.0	144.0		798	-4.6	1.0	12	dbSNP_98	144	153,8055		1,151,3952	no	coding-synonymous	ITPR2	NM_002223.2		101,772,5108	TT,TC,CC		1.864,21.87,8.1425		266/2702	26868289	974,10988	1877	4104	5981	SO:0001819	synonymous_variant	3709	exon8			CAAGGTCGTACGA	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.798G>A	12.37:g.26868289C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			C|0.931;T|0.069	0.069	strong		0.363	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
IFNA10	3446	hgsc.bcm.edu	37	9	21206916	21206916	+	Missense_Mutation	SNP	T	T	A	rs28368145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21206916T>A	ENST00000357374.2	-	1	226	c.181A>T	c.(181-183)Atc>Ttc	p.I61F		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	61					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		TCCTGGGGGATTCGGAAATCA	0.512													a|||	200	0.0399361	0.1021	0.0231	5008	,	,		19409	0.0		0.0427	False		,,,				2504	0.0061				p.I61F		Atlas-SNP	.											.	IFNA10	29	.	0			c.A181T						PASS	.	A	PHE/ILE	44,4342		9,26,2158	112.0	119.0	116.0		181	2.5	0.0	9	dbSNP_125	116	39,8555		4,31,4262	no	missense	IFNA10	NM_002171.1	21	13,57,6420	AA,AT,TT		0.4538,1.0032,0.6394	benign	61/190	21206916	83,12897	2193	4297	6490	SO:0001583	missense	3446	exon1			GGGGGATTCGGAA		CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"""Interferons"""	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.181A>T	9.37:g.21206916T>A	ENSP00000369566:p.Ile61Phe	Somatic	342	1	0.00292398		WXS	Illumina HiSeq	Phase_I	330	329	0.99697	NM_002171	Q5VV13	Missense_Mutation	SNP	ENST00000357374.2	37	CCDS6499.1	55	0.025183150183150184	27	0.054878048780487805	6	0.016574585635359115	0	0.0	22	0.029023746701846966	-	0.057	-1.233059	0.01505	0.010032	0.004538	ENSG00000186803	ENST00000357374	T	0.02837	4.14	3.65	2.49	0.30216	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.056184	0.64402	N	0.000001	T	0.00109	0.0003	N	0.00048	-2.425	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42699	-0.9436	10	0.02654	T	1	.	3.9452	0.09346	0.7108:0.0:0.106:0.1831	rs28368145	61	P01566	IFN10_HUMAN	F	61	ENSP00000369566:I61F	ENSP00000369566:I61F	I	-	1	0	IFNA10	21196916	0.255000	0.24002	0.001000	0.08648	0.043000	0.13939	0.546000	0.23284	0.019000	0.15079	-0.476000	0.04901	ATC	T|0.962;A|0.038	0.038	strong		0.512	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171	
MMP11	4320	hgsc.bcm.edu	37	22	24124471	24124471	+	Silent	SNP	C	C	A	rs28382569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24124471C>A	ENST00000215743.3	+	7	1186	c.1134C>A	c.(1132-1134)acC>acA	p.T378T	AP000349.1_ENST00000598975.1_Missense_Mutation_p.R248L	NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	378					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	cacccctcaccgagctGGGCC	0.632													C|||	54	0.0107827	0.0371	0.0029	5008	,	,		18519	0.0		0.003	False		,,,				2504	0.0				p.T378T		Atlas-SNP	.											.	MMP11	53	.	0			c.C1134A						PASS	.	C		168,4238	112.1+/-150.2	5,158,2040	59.0	57.0	58.0		1134	-2.9	0.6	22	dbSNP_125	58	0,8600		0,0,4300	no	coding-synonymous	MMP11	NM_005940.3		5,158,6340	AA,AC,CC		0.0,3.813,1.2917		378/489	24124471	168,12838	2203	4300	6503	SO:0001819	synonymous_variant	4320	exon7			CCTCACCGAGCTG		CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"""matrix metalloproteinase 11 (stromelysin 3)"""	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.1134C>A	22.37:g.24124471C>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Silent	SNP	ENST00000215743.3	37	CCDS13816.1																																																																																			A|0.014;C|0.986	0.014	strong		0.632	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940	
PRTG	283659	hgsc.bcm.edu	37	15	55972797	55972797	+	Missense_Mutation	SNP	T	T	C	rs16976466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55972797T>C	ENST00000389286.4	-	5	753	c.706A>G	c.(706-708)Aca>Gca	p.T236A	RP11-420M1.2_ENST00000561155.1_RNA	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)		GCTATAATTGTTGGTGTGTGG	0.353													T|||	1111	0.221845	0.2988	0.1009	5008	,	,		13043	0.3214		0.0974	False		,,,				2504	0.229				p.T236A		Atlas-SNP	.											.	PRTG	110	.	0			c.A706G						PASS	.	T	ALA/THR	1024,2680		152,720,980	172.0	161.0	165.0		706	0.2	0.9	15	dbSNP_123	165	806,7394		42,722,3336	yes	missense	PRTG	NM_173814.4	58	194,1442,4316	CC,CT,TT		9.8293,27.6458,15.373	benign	236/1151	55972797	1830,10074	1852	4100	5952	SO:0001583	missense	283659	exon5			TAATTGTTGGTGT	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.706A>G	15.37:g.55972797T>C	ENSP00000373937:p.Thr236Ala	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	174	173	0.994253	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	423	0.1936813186813187	135	0.27439024390243905	44	0.12154696132596685	170	0.2972027972027972	74	0.09762532981530343	T	10.54	1.379977	0.24944	0.276458	0.098293	ENSG00000166450	ENST00000389286	T	0.66460	-0.21	5.42	0.203	0.15195	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.382139	0.28647	N	0.014605	T	0.00012	0.0000	L	0.33753	1.03	0.54753	P	1.8999999999991246E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.17715	-1.0360	9	0.12430	T	0.62	-3.5581	6.225	0.20703	0.147:0.4944:0.0:0.3586	rs16976466;rs52831048;rs56497285;rs16976466	236	Q2VWP7	PRTG_HUMAN	A	236	ENSP00000373937:T236A	ENSP00000373937:T236A	T	-	1	0	PRTG	53760089	0.014000	0.17966	0.943000	0.38184	0.750000	0.42670	0.139000	0.16036	0.014000	0.14944	0.377000	0.23210	ACA	C|0.201;N|0.000	0.201	strong		0.353	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
HIST1H4C	8364	hgsc.bcm.edu	37	6	26104280	26104280	+	Silent	SNP	T	T	C	rs2229768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	97	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	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	
SRP68	6730	hgsc.bcm.edu	37	17	74036544	74036544	+	Missense_Mutation	SNP	C	C	T	rs75353721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74036544C>T	ENST00000307877.2	-	15	1773	c.1612G>A	c.(1612-1614)Gct>Act	p.A538T	SRP68_ENST00000602720.1_Missense_Mutation_p.A199T|SRP68_ENST00000542536.2_5'UTR|SRP68_ENST00000355113.5_Missense_Mutation_p.A437T|SRP68_ENST00000539137.1_Missense_Mutation_p.A500T	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	538					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						GTTTGATGAGCGTCGTTTGCA	0.438													C|||	43	0.00858626	0.0295	0.0043	5008	,	,		21078	0.001		0.0	False		,,,				2504	0.0				p.A538T		Atlas-SNP	.											SRP68,colon,carcinoma,+2,1	SRP68	61	1	0			c.G1612A						scavenged	.	C	THR/ALA	73,4333	66.4+/-103.9	2,69,2132	150.0	125.0	134.0		1612	-4.7	0.0	17	dbSNP_131	134	0,8600		0,0,4300	yes	missense	SRP68	NM_014230.2	58	2,69,6432	TT,TC,CC		0.0,1.6568,0.5613	benign	538/628	74036544	73,12933	2203	4300	6503	SO:0001583	missense	6730	exon15			GATGAGCGTCGTT	AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"""signal recognition particle 68kD"""			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.1612G>A	17.37:g.74036544C>T	ENSP00000312066:p.Ala538Thr	Somatic	225	2	0.00888889		WXS	Illumina HiSeq	Phase_I	246	127	0.51626	NM_014230	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Missense_Mutation	SNP	ENST00000307877.2	37	CCDS11738.1	14	0.00641025641025641	12	0.024390243902439025	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	2.222	-0.378212	0.05000	0.016568	0.0	ENSG00000167881	ENST00000411758;ENST00000539137;ENST00000542536;ENST00000307877;ENST00000304220;ENST00000355113	.	.	.	6.07	-4.7	0.03288	.	1.163030	0.05794	N	0.610958	T	0.07143	0.0181	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.04013	0.001;0.001	T	0.17440	-1.0369	9	0.14656	T	0.56	-0.5259	0.5188	0.00608	0.2244:0.2613:0.1636:0.3507	.	500;538	G3V1U4;Q9UHB9	.;SRP68_HUMAN	T	278;500;199;538;507;437	.	ENSP00000307756:A507T	A	-	1	0	SRP68	71548139	0.023000	0.18921	0.001000	0.08648	0.069000	0.16628	-0.142000	0.10311	-0.743000	0.04784	-0.266000	0.10368	GCT	C|0.993;T|0.007	0.007	strong		0.438	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230	
ZNF844	284391	hgsc.bcm.edu	37	19	12186148	12186148	+	Silent	SNP	T	T	C	rs10424893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12186148T>C	ENST00000439326.3	+	4	388	c.213T>C	c.(211-213)gtT>gtC	p.V71V	ZNF844_ENST00000441304.2_Missense_Mutation_p.L51S	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	71	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)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						GAGAGAGAGTTGATGAAAATA	0.333													.|||	1421	0.283746	0.7035	0.1455	5008	,	,		15619	0.0863		0.161	False		,,,				2504	0.1442				p.V71V		Atlas-SNP	.											ZNF844,NS,NS,+2,1	ZNF844	69	1	0			c.T213C						scavenged	.	C		839,545		256,327,109	64.0	61.0	62.0		213	-0.9	0.0	19	dbSNP_119	62	416,2766		25,366,1200	no	coding-synonymous	ZNF844	NM_001136501.1		281,693,1309	CC,CT,TT		13.0735,39.3786,27.4858		71/667	12186148	1255,3311	692	1591	2283	SO:0001819	synonymous_variant	284391	exon4			GAGAGTTGATGAA	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.213T>C	19.37:g.12186148T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_001136501	Q5JPI8	Silent	SNP	ENST00000439326.3	37	CCDS45985.1	553	0.2532051282051282	319	0.6483739837398373	53	0.1464088397790055	54	0.0944055944055944	127	0.16754617414248021	t	0.777	-0.763841	0.02996	0.606214	0.130735	ENSG00000223547	ENST00000441304	T	0.01821	4.62	1.56	-0.936	0.10419	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.04551	-1.0943	5	0.45353	T	0.12	.	3.1725	0.06558	0.3397:0.4089:0.0:0.2514	rs10424893;rs10424893	.	.	.	S	51	ENSP00000402097:L51S	ENSP00000402097:L51S	L	+	2	0	ZNF844	12047148	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.757000	0.04772	-0.637000	0.05516	-1.222000	0.01597	TTG	T|0.725;C|0.275	0.275	strong		0.333	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
VWF	7450	hgsc.bcm.edu	37	12	6138575	6138575	+	Missense_Mutation	SNP	C	C	T	rs141087261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6138575C>T	ENST00000261405.5	-	22	3154	c.2900G>A	c.(2899-2901)gGc>gAc	p.G967D		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	967	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GAGGGCTTTGCCCAGCAGCAG	0.547													C|||	47	0.00938498	0.0325	0.0058	5008	,	,		20111	0.0		0.0	False		,,,				2504	0.0				p.G967D		Atlas-SNP	.											.	VWF	338	.	0			c.G2900A						PASS	.	C	ASP/GLY	109,4297	84.8+/-123.5	2,105,2096	140.0	125.0	130.0		2900	3.7	0.9	12	dbSNP_134	130	0,8600		0,0,4300	yes	missense	VWF	NM_000552.3	94	2,105,6396	TT,TC,CC		0.0,2.4739,0.8381	benign	967/2814	6138575	109,12897	2203	4300	6503	SO:0001583	missense	7450	exon22			GCTTTGCCCAGCA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2900G>A	12.37:g.6138575C>T	ENSP00000261405:p.Gly967Asp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	131	74	0.564885	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	C	18.66	3.671977	0.67928	0.024739	0.0	ENSG00000110799	ENST00000261405	T	0.61040	0.14	4.58	3.69	0.42338	von Willebrand factor, type D domain (3);	0.382429	0.19030	N	0.124571	T	0.38081	0.1027	L	0.36672	1.1	0.80722	D	1	D	0.52996	0.957	P	0.61800	0.894	T	0.50759	-0.8790	10	0.42905	T	0.14	.	11.8305	0.52293	0.0:0.9149:0.0:0.0851	.	967	P04275	VWF_HUMAN	D	967	ENSP00000261405:G967D	ENSP00000261405:G967D	G	-	2	0	VWF	6008836	1.000000	0.71417	0.913000	0.36048	0.642000	0.38348	5.586000	0.67503	1.152000	0.42452	0.484000	0.47621	GGC	C|0.992;T|0.008	0.008	strong		0.547	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
TNS1	7145	hgsc.bcm.edu	37	2	218683139	218683139	+	Missense_Mutation	SNP	G	G	A	rs34291329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218683139G>A	ENST00000171887.4	-	24	4056	c.3604C>T	c.(3604-3606)Ccc>Tcc	p.P1202S	TNS1_ENST00000419504.1_Missense_Mutation_p.P1189S|TNS1_ENST00000430930.1_Missense_Mutation_p.P1181S	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1202					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)		GCCATGCTGGGATTGATGGCC	0.652													G|||	332	0.0662939	0.0514	0.0591	5008	,	,		16428	0.0169		0.0934	False		,,,				2504	0.1145				p.P1202S		Atlas-SNP	.											.	TNS1	251	.	0			c.C3604T						PASS	.	G	SER/PRO	208,4198	124.9+/-162.1	9,190,2004	53.0	55.0	54.0		3604	1.8	0.4	2	dbSNP_126	54	654,7946	161.9+/-214.7	27,600,3673	yes	missense	TNS1	NM_022648.4	74	36,790,5677	AA,AG,GG		7.6047,4.7208,6.6277	benign	1202/1736	218683139	862,12144	2203	4300	6503	SO:0001583	missense	7145	exon24			TGCTGGGATTGAT	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.3604C>T	2.37:g.218683139G>A	ENSP00000171887:p.Pro1202Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	77	30	0.38961	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	119	0.05448717948717949	9	0.018292682926829267	24	0.06629834254143646	12	0.02097902097902098	74	0.09762532981530343	G	2.490	-0.317753	0.05386	0.047208	0.076047	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;T;D;D	0.91011	-2.76;2.24;-2.77;-2.77	4.61	1.8	0.24995	.	0.745176	0.12454	N	0.467518	T	0.13372	0.0324	L	0.43152	1.355	0.09310	P	0.9999999999958005	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.52749	-0.8534	9	0.10636	T	0.68	.	4.9661	0.14091	0.1568:0.0:0.4276:0.4157	rs34291329	1202;1181;1189	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	S	1202;340;1189;1181	ENSP00000171887:P1202S;ENSP00000394171:P340S;ENSP00000408724:P1189S;ENSP00000406016:P1181S	ENSP00000171887:P1202S	P	-	1	0	TNS1	218391384	0.275000	0.24201	0.363000	0.25875	0.806000	0.45545	0.330000	0.19715	0.190000	0.20209	0.563000	0.77884	CCC	G|0.932;A|0.068	0.068	strong		0.652	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
LILRB2	10288	hgsc.bcm.edu	37	19	54782395	54782395	+	Missense_Mutation	SNP	A	A	G	rs7246737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782395A>G	ENST00000391749.4	-	7	1248	c.977T>C	c.(976-978)tTc>tCc	p.F326S	LILRB2_ENST00000391748.1_Missense_Mutation_p.F326S|LILRB2_ENST00000391746.1_Missense_Mutation_p.F326S|LILRB2_ENST00000434421.1_Missense_Mutation_p.F210S|LILRB2_ENST00000314446.5_Missense_Mutation_p.F326S|LILRB2_ENST00000471216.1_5'Flank	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	326			F -> S (in dbSNP:rs7246737).		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)		CACTGAGATGAAGGGTGTGCC	0.612													.|||	687	0.137181	0.4614	0.0447	5008	,	,		16285	0.0288		0.003	False		,,,				2504	0.0143				p.F326S		Atlas-SNP	.											.	LILRB2	94	.	0			c.T977C						PASS	.	G	SER/PHE,SER/PHE	145,4021		12,121,1950	45.0	59.0	55.0		977,977	1.5	0.0	19	dbSNP_116	55	0,8600		0,0,4300	no	missense,missense	LILRB2	NM_001080978.2,NM_005874.3	155,155	12,121,6250	GG,GA,AA		0.0,3.4806,1.1358	benign,benign	326/598,326/599	54782395	145,12621	2083	4300	6383	SO:0001583	missense	10288	exon7			GAGATGAAGGGTG	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.977T>C	19.37:g.54782395A>G	ENSP00000375629:p.Phe326Ser	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	191	76	0.397906	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	124	0.056776556776556776	111	0.22560975609756098	7	0.019337016574585635	6	0.01048951048951049	0	0.0	G	0.008	-1.910647	0.00508	0.034806	0.0	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.02369	4.32;4.32;4.32;4.32;4.32	2.54	1.45	0.22620	Immunoglobulin-like fold (1);	0.659026	0.12624	N	0.452790	T	0.00012	0.0000	N	0.00066	-2.3	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.11329	0.003;0.003;0.006	T	0.42949	-0.9421	9	0.02654	T	1	.	8.398	0.32568	0.1497:0.0:0.8503:0.0	rs7246737;rs57030336;rs7246737	326;343;326	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	S	326;326;326;326;210	ENSP00000375628:F326S;ENSP00000319960:F326S;ENSP00000375629:F326S;ENSP00000375626:F326S;ENSP00000410117:F210S	ENSP00000319960:F326S	F	-	2	0	LILRB2	59474207	0.000000	0.05858	0.049000	0.19019	0.003000	0.03518	-0.147000	0.10234	-0.001000	0.14495	-1.847000	0.00572	TTC	A|0.971;G|0.029	0.029	strong		0.612	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
HSD17B4	3295	hgsc.bcm.edu	37	5	118877660	118877660	+	Missense_Mutation	SNP	A	A	G	rs28943594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118877660A>G	ENST00000256216.6	+	24	2315	c.2182A>G	c.(2182-2184)Atg>Gtg	p.M728V	HSD17B4_ENST00000515320.1_Missense_Mutation_p.M710V|HSD17B4_ENST00000522415.1_3'UTR|HSD17B4_ENST00000414835.2_Missense_Mutation_p.M588V|HSD17B4_ENST00000509514.1_Missense_Mutation_p.M466V|HSD17B4_ENST00000510025.1_Missense_Mutation_p.M704V|HSD17B4_ENST00000504811.1_Missense_Mutation_p.M753V|HSD17B4_ENST00000513628.1_Missense_Mutation_p.M591V	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	728	SCP2.		M -> V (in dbSNP:rs28943594).		alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		GAAACTTCAGATGATTCTTAA	0.423													A|||	167	0.0333466	0.1218	0.0043	5008	,	,		15072	0.0		0.001	False		,,,				2504	0.002				p.M753V	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.A2257G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	405,3999	198.4+/-222.2	21,363,1818	65.0	64.0	64.0		2182,2257,2128	3.5	1.0	5	dbSNP_125	64	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense,missense	HSD17B4	NM_000414.3,NM_001199291.1,NM_001199292.1	21,21,21	21,377,6104	GG,GA,AA		0.1628,9.1962,3.2221	benign,benign,benign	728/737,753/762,710/719	118877660	419,12585	2202	4300	6502	SO:0001583	missense	3295	exon25			CTTCAGATGATTC		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.2182A>G	5.37:g.118877660A>G	ENSP00000256216:p.Met728Val	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	172	87	0.505814	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Missense_Mutation	SNP	ENST00000256216.6	37	CCDS4126.1	67	0.030677655677655676	64	0.13008130081300814	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	11.01	1.512125	0.27036	0.091962	0.001628	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628;ENST00000509514	T;T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01;2.01	5.94	3.46	0.39613	SCP2 sterol-binding domain (2);	0.276882	0.46145	D	0.000301	T	0.00144	0.0004	N	0.21282	0.65	0.31931	P	0.612166	B;B;B;B;B	0.11235	0.004;0.0;0.0;0.001;0.0	B;B;B;B;B	0.10450	0.003;0.003;0.005;0.001;0.003	T	0.29671	-1.0004	8	.	.	.	-10.0531	8.5921	0.33693	0.7361:0.1351:0.0:0.1288	rs28943594	753;710;704;466;728	F5HE57;E9PB82;E7EWE5;E7EPL9;P51659	.;.;.;.;DHB4_HUMAN	V	728;710;704;753;588;591;466	ENSP00000256216:M728V;ENSP00000424613:M710V;ENSP00000424940:M704V;ENSP00000420914:M753V;ENSP00000411960:M588V;ENSP00000425993:M591V;ENSP00000426272:M466V	.	M	+	1	0	HSD17B4	118905559	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.250000	0.58772	0.446000	0.26666	0.455000	0.32223	ATG	A|0.967;G|0.033	0.033	strong		0.423	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	
SPATA13	221178	hgsc.bcm.edu	37	13	24797913	24797913	+	Intron	SNP	C	C	T	rs1220546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:24797913C>T	ENST00000382095.4	+	2	185				RP11-307N16.6_ENST00000382141.4_Silent_p.D282D|SPATA13_ENST00000382108.3_Silent_p.D282D|SPATA13_ENST00000424834.2_Silent_p.D282D	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						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)	p.D282D(2)		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)		CGGCCCATGACGCACGGGTAC	0.567													C|||	1315	0.26258	0.1097	0.196	5008	,	,		19459	0.4405		0.2942	False		,,,				2504	0.3006				p.D282D		Atlas-SNP	.											.	SPATA13	92	.	2	Substitution - coding silent(2)	endometrium(2)	c.C846T						PASS	.	C	,	205,1179		17,171,504	72.0	65.0	67.0		846,	-9.2	0.0	13	dbSNP_87	67	988,2194		154,680,757	no	coding-synonymous,intron	SPATA13	NM_001166271.1,NM_153023.2	,	171,851,1261	TT,TC,CC		31.0497,14.8121,26.1279	,	282/1278,	24797913	1193,3373	692	1591	2283	SO:0001627	intron_variant	221178	exon2			CCATGACGCACGG	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.-222-25702C>T	13.37:g.24797913C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	37	CCDS9305.1	610	0.2793040293040293	64	0.13008130081300814	76	0.20994475138121546	240	0.4195804195804196	230	0.3034300791556728	C	3.895	-0.023136	0.07634	0.148121	0.310497	ENSG00000182957	ENST00000424834	.	.	.	4.62	-9.24	0.00669	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.21484	-1.0244	3	.	.	.	.	2.1055	0.03690	0.4112:0.2767:0.1656:0.1465	rs1220546;rs17365668;rs56504932;rs60383945;rs1220546	.	.	.	C	320	.	.	R	+	1	0	SPATA13	23695913	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.827000	0.00746	-3.430000	0.00165	-1.555000	0.00892	CGC	C|0.720;T|0.280	0.280	strong		0.567	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
NUGGC	389643	hgsc.bcm.edu	37	8	27925220	27925220	+	Silent	SNP	A	A	G	rs114951850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27925220A>G	ENST00000413272.2	-	6	664	c.522T>C	c.(520-522)caT>caC	p.H174H	NUGGC_ENST00000341513.6_Silent_p.H174H	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	174					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)										CCTCCGTCCTATGCAGGAGTT	0.547													A|||	104	0.0207668	0.0756	0.0058	5008	,	,		18753	0.0		0.0	False		,,,				2504	0.0				p.H174H		Atlas-SNP	.											.	.	.	.	0			c.T522C						PASS	.	A		193,3875		6,181,1847	68.0	69.0	69.0		522	-2.4	0.0	8	dbSNP_132	69	5,8431		0,5,4213	no	coding-synonymous	C8orf80	NM_001010906.1		6,186,6060	GG,GA,AA		0.0593,4.7443,1.5835		174/797	27925220	198,12306	2034	4218	6252	SO:0001819	synonymous_variant	389643	exon6			CGTCCTATGCAGG	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.522T>C	8.37:g.27925220A>G		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	247	130	0.526316	NM_001010906	Q6ZP73	Silent	SNP	ENST00000413272.2	37	CCDS47833.1																																																																																			A|0.985;G|0.015	0.015	strong		0.547	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
CACNA2D4	93589	hgsc.bcm.edu	37	12	1955786	1955786	+	Silent	SNP	G	G	A	rs11836202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:1955786G>A	ENST00000382722.5	-	24	2678	c.2316C>T	c.(2314-2316)ttC>ttT	p.F772F	CACNA2D4_ENST00000539048.2_5'UTR|CACNA2D4_ENST00000585708.1_Silent_p.F708F|CACNA2D4_ENST00000587995.1_Silent_p.F747F|CACNA2D4_ENST00000586184.1_Silent_p.F772F|CACNA2D4_ENST00000585732.1_Silent_p.F633F|CACNA2D4_ENST00000588077.1_Silent_p.F708F	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	772					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		CGGAGCCCACGAACAAGCTGC	0.647													G|||	894	0.178514	0.087	0.1354	5008	,	,		17398	0.4206		0.0139	False		,,,				2504	0.2526				p.F772F	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.C2316T						PASS	.	G		301,3811		8,285,1763	41.0	48.0	46.0		2316	-0.2	1.0	12	dbSNP_120	46	135,8249		2,131,4059	no	coding-synonymous	CACNA2D4	NM_172364.4		10,416,5822	AA,AG,GG		1.6102,7.32,3.4891		772/1138	1955786	436,12060	2056	4192	6248	SO:0001819	synonymous_variant	93589	exon24			GCCCACGAACAAG	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.2316C>T	12.37:g.1955786G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	55	35	0.636364	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Silent	SNP	ENST00000382722.5	37	CCDS44785.1																																																																																			G|0.860;A|0.140	0.140	strong		0.647	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
SYNE3	161176	hgsc.bcm.edu	37	14	95923644	95923644	+	Missense_Mutation	SNP	C	C	T	rs74082143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95923644C>T	ENST00000334258.5	-	4	673	c.659G>A	c.(658-660)cGg>cAg	p.R220Q	SYNE3_ENST00000554873.1_5'Flank|SYNE3_ENST00000557275.1_Missense_Mutation_p.R220Q|SYNE3_ENST00000553340.1_Missense_Mutation_p.R220Q	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	220					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						CTCATGCTCCCGGGCCACCTG	0.622													C|||	57	0.0113818	0.0416	0.0029	5008	,	,		15755	0.0		0.0	False		,,,				2504	0.0				p.R220Q		Atlas-SNP	.											.	SYNE3	130	.	0			c.G659A						PASS	.	C	GLN/ARG	164,4242	110.8+/-149.0	4,156,2043	172.0	146.0	155.0		659	-9.7	0.2	14	dbSNP_130	155	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C14orf49	NM_152592.3	43	4,157,6342	TT,TC,CC		0.0116,3.7222,1.2686	benign	220/976	95923644	165,12841	2203	4300	6503	SO:0001583	missense	161176	exon4			TGCTCCCGGGCCA	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.659G>A	14.37:g.95923644C>T	ENSP00000334308:p.Arg220Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	C	8.880	0.951469	0.18431	0.037222	1.16E-4	ENSG00000176438	ENST00000334258;ENST00000557275;ENST00000553340	T;T;T	0.08634	3.67;3.67;3.07	5.59	-9.72	0.00515	.	1.176260	0.06544	N	0.743757	T	0.00784	0.0026	N	0.12471	0.22	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.46428	-0.9192	10	0.16420	T	0.52	-9.6805	10.7358	0.46124	0.0756:0.1571:0.0:0.7673	.	220;220;220	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	Q	220	ENSP00000334308:R220Q;ENSP00000450562:R220Q;ENSP00000450774:R220Q	ENSP00000334308:R220Q	R	-	2	0	C14orf49	94993397	0.009000	0.17119	0.165000	0.22776	0.027000	0.11550	0.063000	0.14410	-1.210000	0.02627	-0.263000	0.10527	CGG	C|0.989;T|0.011	0.011	strong		0.622	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
DUSP27	92235	hgsc.bcm.edu	37	1	167095881	167095881	+	Missense_Mutation	SNP	G	G	A	rs3795605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167095881G>A	ENST00000361200.2	+	6	1679	c.1513G>A	c.(1513-1515)Gca>Aca	p.A505T	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.A505T|DUSP27_ENST00000271385.5_Missense_Mutation_p.A505T			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	505			A -> T (in dbSNP:rs3795605).		protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						AGAGGAGGCGGCAGACAGGAG	0.602													G|||	1649	0.329273	0.2716	0.2003	5008	,	,		17544	0.7431		0.168	False		,,,				2504	0.2382				p.A505T		Atlas-SNP	.											.	DUSP27	235	.	0			c.G1513A						PASS	.	G	THR/ALA	1135,3271	404.2+/-333.0	155,825,1223	54.0	50.0	51.0		1513	-1.0	0.0	1	dbSNP_107	51	1464,7136	276.8+/-292.5	115,1234,2951	yes	missense	DUSP27	NM_001080426.1	58	270,2059,4174	AA,AG,GG		17.0233,25.7603,19.9831	benign	505/1159	167095881	2599,10407	2203	4300	6503	SO:0001583	missense	92235	exon5			GAGGCGGCAGACA	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1513G>A	1.37:g.167095881G>A	ENSP00000354483:p.Ala505Thr	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	211	99	0.469194	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	770	0.3525641025641026	138	0.2804878048780488	74	0.20441988950276244	435	0.7604895104895105	123	0.16226912928759896	G	6.531	0.466291	0.12402	0.257603	0.170233	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03035	4.07;4.07;4.07	1.3	-0.985	0.10256	.	1.384540	0.05035	N	0.475240	T	0.00845	0.0028	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.48670	-0.9015	9	0.42905	T	0.14	-1.7175	3.7835	0.08690	0.5587:0.0:0.4413:0.0	rs3795605;rs52789985;rs58508566;rs3795605	505	Q5VZP5	DUS27_HUMAN	T	505	ENSP00000354483:A505T;ENSP00000271385:A505T;ENSP00000404874:A505T	ENSP00000271385:A505T	A	+	1	0	DUSP27	165362505	0.142000	0.22610	0.008000	0.14137	0.008000	0.06430	0.659000	0.24994	-0.155000	0.11098	-0.148000	0.13756	GCA	G|0.731;A|0.269	0.269	strong		0.602	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
SIRPA	140885	hgsc.bcm.edu	37	20	1896059	1896059	+	Missense_Mutation	SNP	G	G	A	rs386811663|rs115287948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1896059G>A	ENST00000358771.4	+	2	546	c.394G>A	c.(394-396)Gtg>Atg	p.V132M	SIRPA_ENST00000356025.3_Missense_Mutation_p.V132M|SIRPA_ENST00000400068.3_Missense_Mutation_p.V132M	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	132	Ig-like V-type.		V -> T (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CCCCGATGACGTGGAGTTTAA	0.527													G|||	2050	0.409345	0.2761	0.4222	5008	,	,		15841	0.625		0.3171	False		,,,				2504	0.453				p.V132M	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,caecum,carcinoma,0,2	SIRPA	83	2	0			c.G394A						PASS	.						108.0	93.0	98.0					20																	1896059		2198	4290	6488	SO:0001583	missense	140885	exon3			GATGACGTGGAGT	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.394G>A	20.37:g.1896059G>A	ENSP00000351621:p.Val132Met	Somatic	461	0	0		WXS	Illumina HiSeq	Phase_I	272	44	0.161765	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	G	9.326	1.059262	0.19987	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.64991	-0.13;-0.13;-0.13	5.11	-2.28	0.06826	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	2.497550	0.01234	N	0.008420	T	0.49558	0.1564	L	0.28192	0.835	0.80722	P	0.0	B;B;B	0.27765	0.084;0.005;0.188	B;B;B	0.27887	0.057;0.01;0.084	T	0.39702	-0.9601	9	0.33141	T	0.24	.	9.8059	0.40792	0.7439:0.0:0.2561:0.0	.	112;132;132	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	M	132	ENSP00000382941:V132M;ENSP00000348307:V132M;ENSP00000351621:V132M	ENSP00000348307:V132M	V	+	1	0	SIRPA	1844059	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.421000	0.07053	-0.198000	0.10333	-1.101000	0.02118	GTG	G|0.679;A|0.321	0.321	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
IRS4	8471	hgsc.bcm.edu	37	X	107979437	107979437	+	Silent	SNP	G	G	A	rs73253702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:107979437G>A	ENST00000372129.2	-	1	214	c.138C>T	c.(136-138)acC>acT	p.T46T	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	46					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						AAGACGACCCGGTCCCAATGA	0.657													g|||	188	0.0498013	0.0514	0.0576	3775	,	,		8094	0.002		0.0408	False		,,,				2504	0.0378				p.T46T		Atlas-SNP	.											.	IRS4	253	.	0			c.C138T						PASS	.			269,3555		10,211,38,1409,526	24.0	26.0	25.0		138	1.1	1.0	X	dbSNP_130	25	386,6312		9,251,117,2164,1733	no	coding-synonymous	IRS4	NM_003604.2		19,462,155,3573,2259	AA,AG,A,GG,G		5.7629,7.0345,6.2251		46/1258	107979437	655,9867	2194	4274	6468	SO:0001819	synonymous_variant	8471	exon1			CGACCCGGTCCCA	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.138C>T	X.37:g.107979437G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	143	97	0.678322	NM_003604		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																			G|0.942;A|0.058	0.058	strong		0.657	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
PIP4K2A	5305	hgsc.bcm.edu	37	10	22830842	22830842	+	Silent	SNP	C	C	T	rs61731109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:22830842C>T	ENST00000376573.4	-	8	1155	c.927G>A	c.(925-927)ccG>ccA	p.P309P	PIP4K2A_ENST00000545335.1_Silent_p.P250P|PIP4K2A_ENST00000323883.7_Silent_p.P169P	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	309	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						GGGTTCCCACCGGGTGGGTGC	0.592													C|||	98	0.0195687	0.0522	0.0101	5008	,	,		18503	0.0		0.0149	False		,,,				2504	0.0072				p.P309P		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.G927A						PASS	.	C		217,4189	133.7+/-170.0	6,205,1992	79.0	73.0	75.0		927	-12.1	0.0	10	dbSNP_129	75	110,8490	58.3+/-119.8	1,108,4191	no	coding-synonymous	PIP4K2A	NM_005028.4		7,313,6183	TT,TC,CC		1.2791,4.9251,2.5142		309/407	22830842	327,12679	2203	4300	6503	SO:0001819	synonymous_variant	5305	exon8			TCCCACCGGGTGG	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"""phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"""	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.927G>A	10.37:g.22830842C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Silent	SNP	ENST00000376573.4	37	CCDS7141.1																																																																																			C|0.976;T|0.024	0.024	strong		0.592	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028	
MDC1	9656	hgsc.bcm.edu	37	6	30668374	30668374	+	Silent	SNP	G	G	A	rs9468812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30668374G>A	ENST00000376406.3	-	15	6785	c.6138C>T	c.(6136-6138)ttC>ttT	p.F2046F	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Silent_p.F1782F	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	2046	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Required for nuclear localization (NLS2).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						AGCAATGAGGGAAGTCCTGAG	0.542								Other conserved DNA damage response genes					G|||	234	0.0467252	0.1278	0.0432	5008	,	,		16633	0.0208		0.0129	False		,,,				2504	0.001				p.F2046F		Atlas-SNP	.											.	MDC1	218	.	0			c.C6138T						PASS	.	G		320,2702		21,278,1212	114.0	107.0	109.0		6138	-4.1	0.0	6	dbSNP_119	109	63,5355		0,63,2646	no	coding-synonymous	MDC1	NM_014641.2		21,341,3858	AA,AG,GG		1.1628,10.589,4.5379		2046/2090	30668374	383,8057	1511	2709	4220	SO:0001819	synonymous_variant	9656	exon15			ATGAGGGAAGTCC	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.6138C>T	6.37:g.30668374G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	37	CCDS34384.1																																																																																			G|0.958;A|0.042	0.042	strong		0.542	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
SMPDL3B	27293	hgsc.bcm.edu	37	1	28285123	28285123	+	Missense_Mutation	SNP	G	G	A	rs34560878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:28285123G>A	ENST00000373894.3	+	8	1333	c.1142G>A	c.(1141-1143)cGc>cAc	p.R381H	XKR8_ENST00000373884.5_5'Flank|RP11-460I13.2_ENST00000448015.1_RNA|SMPDL3B_ENST00000549094.1_Missense_Mutation_p.R333H	NM_014474.2	NP_055289.2	Q92485	ASM3B_HUMAN	sphingomyelin phosphodiesterase, acid-like 3B	381			R -> H (in dbSNP:rs34560878).		sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	16		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)		GTGCTGGACCGCATCGCTGGC	0.642													G|||	73	0.0145767	0.0507	0.0086	5008	,	,		19689	0.0		0.0	False		,,,				2504	0.0				p.R381H		Atlas-SNP	.											.	SMPDL3B	54	.	0			c.G1142A						PASS	.	G	HIS/ARG	188,4218	120.0+/-157.7	4,180,2019	69.0	64.0	65.0		1142	-1.2	0.0	1	dbSNP_126	65	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SMPDL3B	NM_014474.2	29	4,181,6318	AA,AG,GG		0.0116,4.2669,1.4532	benign	381/456	28285123	189,12817	2203	4300	6503	SO:0001583	missense	27293	exon8			TGGACCGCATCGC	Y08134	CCDS30655.1, CCDS30656.1	1p35.3	2008-02-05			ENSG00000130768	ENSG00000130768			21416	protein-coding gene	gene with protein product							Standard	NM_014474		Approved	ASML3B	uc001bpg.3	Q92485	OTTHUMG00000003910	ENST00000373894.3:c.1142G>A	1.37:g.28285123G>A	ENSP00000363001:p.Arg381His	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	173	86	0.49711	NM_014474	B7ZB35|Q5T0Z0|Q96CB7	Missense_Mutation	SNP	ENST00000373894.3	37	CCDS30655.1	19	0.0086996336996337	15	0.03048780487804878	4	0.011049723756906077	0	0.0	0	0.0	G	11.15	1.553282	0.27739	0.042669	1.16E-4	ENSG00000130768	ENST00000373894;ENST00000549094	D;D	0.90732	-2.72;-2.72	5.09	-1.23	0.09465	.	0.392324	0.27043	N	0.021217	T	0.65491	0.2696	M	0.73962	2.25	0.20074	N	0.999932	B;B	0.20887	0.049;0.029	B;B	0.17098	0.017;0.007	T	0.71331	-0.4625	10	0.52906	T	0.07	-4.737	5.5703	0.17192	0.488:0.0:0.3824:0.1296	rs34560878	333;381	F8VWW8;Q92485	.;ASM3B_HUMAN	H	381;333	ENSP00000363001:R381H;ENSP00000449450:R333H	ENSP00000363001:R381H	R	+	2	0	SMPDL3B	28157710	0.916000	0.31088	0.009000	0.14445	0.001000	0.01503	0.985000	0.29578	-0.071000	0.12886	-1.288000	0.01363	CGC	G|0.986;A|0.014	0.014	strong		0.642	SMPDL3B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011170.1	NM_014474	
BPIFB1	92747	hgsc.bcm.edu	37	20	31877770	31877770	+	Missense_Mutation	SNP	C	C	T	rs114635109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31877770C>T	ENST00000253354.1	+	4	498	c.337C>T	c.(337-339)Ccc>Tcc	p.P113S		NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	113					innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										AGTCAAGATCCCCCTGGACAT	0.582													C|||	45	0.00898562	0.0318	0.0029	5008	,	,		19004	0.0		0.001	False		,,,				2504	0.0				p.P113S		Atlas-SNP	.											.	.	.	.	0			c.C337T						PASS	.	C	SER/PRO	170,4236	111.6+/-149.8	4,162,2037	124.0	95.0	105.0		337	5.4	1.0	20	dbSNP_132	105	1,8599	1.2+/-3.3	0,1,4299	yes	missense	BPIFB1	NM_033197.2	74	4,163,6336	TT,TC,CC		0.0116,3.8584,1.3148	probably-damaging	113/485	31877770	171,12835	2203	4300	6503	SO:0001583	missense	92747	exon4			AAGATCCCCCTGG	BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"""BPI fold containing"""	16108	protein-coding gene	gene with protein product	"""von Ebner minor salivary gland protein"""		"""chromosome 20 open reading frame 114"""	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.337C>T	20.37:g.31877770C>T	ENSP00000253354:p.Pro113Ser	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	112	63	0.5625	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	37	CCDS13218.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	19.64	3.865475	0.71949	0.038584	1.16E-4	ENSG00000125999	ENST00000423645;ENST00000253354	T;T	0.06142	3.34;3.7	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000008	T	0.06645	0.0170	M	0.80847	2.515	0.39655	D	0.970525	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00099	-1.2067	10	0.38643	T	0.18	-35.2487	15.0609	0.71951	0.0:1.0:0.0:0.0	.	113;113	B2R7Z6;Q8TDL5	.;BPIB1_HUMAN	S	113	ENSP00000390471:P113S;ENSP00000253354:P113S	ENSP00000253354:P113S	P	+	1	0	BPIFB1	31341431	0.958000	0.32768	0.987000	0.45799	0.713000	0.41058	3.494000	0.53273	2.722000	0.93159	0.655000	0.94253	CCC	C|0.988;T|0.012	0.012	strong		0.582	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197	
FAM107A	11170	hgsc.bcm.edu	37	3	58552329	58552329	+	Missense_Mutation	SNP	C	C	G	rs11539086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:58552329C>G	ENST00000394481.1	-	5	979	c.421G>C	c.(421-423)Gag>Cag	p.E141Q	FAM107A_ENST00000464064.1_3'UTR|FAM107A_ENST00000447756.2_Missense_Mutation_p.E169Q|FAM107A_ENST00000474531.1_Missense_Mutation_p.E172Q|FAM107A_ENST00000360997.2_Missense_Mutation_p.E141Q	NM_001282713.1|NM_007177.2	NP_001269642.1|NP_009108.1	O95990	F107A_HUMAN	family with sequence similarity 107, member A	141			E -> Q (in dbSNP:rs11539086).		regulation of cell growth (GO:0001558)	neuron projection (GO:0043005)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)		AGCTCTCTCTCTTCGCTGGTC	0.602													C|||	545	0.108826	0.2579	0.1095	5008	,	,		17509	0.004		0.0736	False		,,,				2504	0.0511				p.E141Q		Atlas-SNP	.											.	FAM107A	33	.	0			c.G421C						PASS	.	C	GLN/GLU,GLN/GLU	982,3424	367.8+/-318.4	121,740,1342	67.0	72.0	70.0		421,421	5.1	0.1	3	dbSNP_120	70	568,8032	153.0+/-207.5	23,522,3755	yes	missense,missense	FAM107A	NM_001076778.1,NM_007177.2	29,29	144,1262,5097	GG,GC,CC		6.6047,22.2878,11.9176	probably-damaging,probably-damaging	141/145,141/145	58552329	1550,11456	2203	4300	6503	SO:0001583	missense	11170	exon4			CTCTCTCTTCGCT	AF089854	CCDS2892.1, CCDS63672.1, CCDS63673.1	3p14.2	2006-02-03			ENSG00000168309	ENSG00000168309			30827	protein-coding gene	gene with protein product		608295				10564580, 10702698	Standard	XM_005264835		Approved	DRR1, TU3A	uc003dkn.3	O95990	OTTHUMG00000159159	ENST00000394481.1:c.421G>C	3.37:g.58552329C>G	ENSP00000377991:p.Glu141Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	68	23	0.338235	NM_001076778	B3KNQ4|B7ZAY5|J3KR61|Q96NH4	Missense_Mutation	SNP	ENST00000394481.1	37	CCDS2892.1	211	0.09661172161172162	117	0.23780487804878048	36	0.09944751381215469	5	0.008741258741258742	53	0.06992084432717678	C	20.0	3.929709	0.73327	0.222878	0.066047	ENSG00000168309	ENST00000360997;ENST00000394481;ENST00000474531;ENST00000447756	T;T;T;T	0.38722	1.24;1.24;1.12;1.18	5.07	5.07	0.68467	.	0.103252	0.64402	D	0.000004	T	0.00039	0.0001	L	0.45581	1.43	0.20074	P	0.9999392385	B;B;D	0.71674	0.001;0.016;0.998	B;B;D	0.75484	0.006;0.009;0.986	T	0.00244	-1.1883	9	0.38643	T	0.18	-21.1537	18.4214	0.90591	0.0:1.0:0.0:0.0	rs11539086;rs56558641;rs11539086	169;172;141	B7ZAY5;B3KNQ4;O95990	.;.;F107A_HUMAN	Q	141;141;172;169	ENSP00000354270:E141Q;ENSP00000377991:E141Q;ENSP00000419124:E172Q;ENSP00000400858:E169Q	ENSP00000354270:E141Q	E	-	1	0	FAM107A	58527369	1.000000	0.71417	0.119000	0.21687	0.109000	0.19521	4.727000	0.61993	2.509000	0.84616	0.563000	0.77884	GAG	C|0.892;G|0.108	0.108	strong		0.602	FAM107A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353585.1	NM_007177	
NOS2	4843	hgsc.bcm.edu	37	17	26107840	26107840	+	Silent	SNP	G	G	A	rs34719207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26107840G>A	ENST00000313735.6	-	9	1190	c.957C>T	c.(955-957)ttC>ttT	p.F319F		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	319					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GTGGGATTTCGAAGAGCTCAG	0.607													G|||	22	0.00439297	0.0151	0.0014	5008	,	,		19507	0.0		0.001	False		,,,				2504	0.0				p.F319F		Atlas-SNP	.											.	NOS2	113	.	0			c.C957T						PASS	.	G		50,4356	50.9+/-86.3	0,50,2153	80.0	70.0	73.0		957	-11.0	0.1	17	dbSNP_126	73	0,8600		0,0,4300	no	coding-synonymous	NOS2	NM_000625.4		0,50,6453	AA,AG,GG		0.0,1.1348,0.3844		319/1154	26107840	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	4843	exon9			GATTTCGAAGAGC	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.957C>T	17.37:g.26107840G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																			G|0.996;A|0.004	0.004	strong		0.607	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
DCDC2B	149069	hgsc.bcm.edu	37	1	32677370	32677370	+	Silent	SNP	C	C	T	rs182464428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:32677370C>T	ENST00000409358.1	+	3	327	c.327C>T	c.(325-327)ccC>ccT	p.P109P		NM_001099434.1	NP_001092904.1	A2VCK2	DCD2B_HUMAN	doublecortin domain containing 2B	109					intracellular signal transduction (GO:0035556)					breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				AGGGTCCTCCCGTGACTCGCC	0.617													C|||	5	0.000998403	0.0038	0.0	5008	,	,		15943	0.0		0.0	False		,,,				2504	0.0				p.P109P		Atlas-SNP	.											.	DCDC2B	24	.	0			c.C327T						PASS	.	C		18,4196		0,18,2089	36.0	38.0	38.0		327	-6.6	0.0	1		38	0,8482		0,0,4241	no	coding-synonymous	DCDC2B	NM_001099434.1		0,18,6330	TT,TC,CC		0.0,0.4271,0.1418		109/350	32677370	18,12678	2107	4241	6348	SO:0001819	synonymous_variant	149069	exon3			TCCTCCCGTGACT	BC128073	CCDS44100.1	1p35.1	2008-05-13			ENSG00000222046	ENSG00000222046			32576	protein-coding gene	gene with protein product							Standard	NM_001099434		Approved		uc001bun.2	A2VCK2	OTTHUMG00000005741	ENST00000409358.1:c.327C>T	1.37:g.32677370C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_001099434	B7ZBC6	Silent	SNP	ENST00000409358.1	37	CCDS44100.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	DCDC2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328293.1	XM_940631	
ENPP4	22875	hgsc.bcm.edu	37	6	46108916	46108916	+	Silent	SNP	C	C	G	rs9472696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46108916C>G	ENST00000321037.4	+	3	1184	c.954C>G	c.(952-954)gcC>gcG	p.A318A		NM_014936.4	NP_055751.1	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative)	318					blood coagulation (GO:0007596)|positive regulation of blood coagulation (GO:0030194)|purine ribonucleoside catabolic process (GO:0046130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	18						TTTTGGTTGCCGATGAAGGCT	0.333													C|||	468	0.0934505	0.1339	0.0576	5008	,	,		17451	0.1716		0.0656	False		,,,				2504	0.0123				p.A318A		Atlas-SNP	.											.	ENPP4	44	.	0			c.C954G						PASS	.	C		607,3799	264.7+/-266.2	50,507,1646	92.0	83.0	86.0		954	-0.6	1.0	6	dbSNP_119	86	586,8008	155.4+/-209.4	15,556,3726	no	coding-synonymous	ENPP4	NM_014936.4		65,1063,5372	GG,GC,CC		6.8187,13.7767,9.1769		318/454	46108916	1193,11807	2203	4297	6500	SO:0001819	synonymous_variant	22875	exon3			GGTTGCCGATGAA	AB020686	CCDS34468.1	6p12.3	2010-06-24	2010-06-24		ENSG00000001561	ENSG00000001561			3359	protein-coding gene	gene with protein product						11027689	Standard	NM_014936		Approved	NPP4, KIAA0879	uc003oxy.3	Q9Y6X5	OTTHUMG00000014779	ENST00000321037.4:c.954C>G	6.37:g.46108916C>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	99	32	0.323232	NM_014936	A8K5G1|Q7L2N1	Silent	SNP	ENST00000321037.4	37	CCDS34468.1																																																																																			C|0.901;G|0.099	0.099	strong		0.333	ENPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040777.2		
CBL	867	hgsc.bcm.edu	37	11	119170362	119170362	+	Silent	SNP	C	C	T	rs1893177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119170362C>T	ENST00000264033.4	+	16	2968	c.2592C>T	c.(2590-2592)ctC>ctT	p.L864L		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	864	Interaction with CD2AP.|UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				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)			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)		TCGAGAACCTCATGAGTCAGG	0.537			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies				C|||	172	0.034345	0.1203	0.0187	5008	,	,		19424	0.0		0.0	False		,,,				2504	0.0				p.L864L		Atlas-SNP	.		"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.C2592T						PASS	.	C		478,3920	224.9+/-240.9	22,434,1743	217.0	217.0	217.0		2592	4.7	1.0	11	dbSNP_92	217	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	CBL	NM_005188.2		22,435,6037	TT,TC,CC		0.0116,10.8686,3.688		864/907	119170362	479,12509	2199	4295	6494	SO:0001819	synonymous_variant	867	exon16	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	GAACCTCATGAGT	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.2592C>T	11.37:g.119170362C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	79	47	0.594937	NM_005188	A3KMP8	Silent	SNP	ENST00000264033.4	37	CCDS8418.1																																																																																			C|0.948;T|0.052	0.052	strong		0.537	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	
LOXL1	4016	hgsc.bcm.edu	37	15	74219582	74219582	+	Missense_Mutation	SNP	G	G	A	rs3825942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:74219582G>A	ENST00000261921.7	+	1	784	c.458G>A	c.(457-459)gGc>gAc	p.G153D	LOXL1-AS1_ENST00000567257.1_RNA|LOXL1-AS1_ENST00000566675.1_RNA|LOXL1-AS1_ENST00000567644.1_RNA|LOXL1-AS1_ENST00000568087.1_RNA|LOXL1-AS1_ENST00000564194.1_RNA|LOXL1-AS1_ENST00000564963.1_RNA|LOXL1-AS1_ENST00000568229.1_RNA|LOXL1-AS1_ENST00000565416.1_RNA|LOXL1-AS1_ENST00000562130.1_RNA|LOXL1-AS1_ENST00000565756.1_RNA|LOXL1-AS1_ENST00000562739.1_RNA|LOXL1-AS1_ENST00000562965.1_RNA	NM_005576.2	NP_005567.2	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1	153			G -> D (associated with exfoliation syndrome in the presence of L-141; dbSNP:rs3825942). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17690259}.		extracellular matrix organization (GO:0030198)|oxidation-reduction process (GO:0055114)|protein deamination (GO:0018277)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor (GO:0016641)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						CGGCACGGGGGCTCCGCCTCC	0.731													G|||	1240	0.247604	0.41	0.1686	5008	,	,		5995	0.1399		0.1769	False		,,,				2504	0.2679				p.G153D		Atlas-SNP	.											.	LOXL1	25	.	0			c.G458A	GRCh37	CM074330	LOXL1	M	rs3825942	PASS	.	G	ASP/GLY	1563,2767		299,965,901	20.0	25.0	24.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	458	3.2	1.0	15	dbSNP_107	24	1231,7241		106,1019,3111	no	missense	LOXL1	NM_005576.2	94	405,1984,4012	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.5302,36.097,21.8247	possibly-damaging	153/575	74219582	2794,10008	2165	4236	6401	SO:0001583	missense	4016	exon1			ACGGGGGCTCCGC	L21186	CCDS10253.1	15q24-q25	2008-07-18			ENSG00000129038	ENSG00000129038			6665	protein-coding gene	gene with protein product		153456				7689553	Standard	NM_005576		Approved	LOXL, LOL	uc002awc.1	Q08397	OTTHUMG00000137595	ENST00000261921.7:c.458G>A	15.37:g.74219582G>A	ENSP00000261921:p.Gly153Asp	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_005576	Q6NUL3|Q96BW7	Missense_Mutation	SNP	ENST00000261921.7	37	CCDS10253.1	491	0.22481684981684982	203	0.41260162601626016	71	0.19613259668508287	78	0.13636363636363635	139	0.18337730870712401	G	18.67	3.673592	0.67928	0.36097	0.145302	ENSG00000129038	ENST00000261921;ENST00000395162	T	0.32988	1.43	4.1	3.17	0.36434	.	0.201537	0.31936	N	0.006833	T	0.00012	0.0000	L	0.40543	1.245	0.25425	P	0.9882311	B	0.06786	0.001	B	0.06405	0.002	T	0.44003	-0.9356	9	0.36615	T	0.2	.	5.5084	0.16866	0.2367:0.0:0.7633:0.0	rs3825942;rs3825942	153	Q08397	LOXL1_HUMAN	D	153;15	ENSP00000261921:G153D	ENSP00000261921:G153D	G	+	2	0	LOXL1	72006635	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.700000	0.47085	1.818000	0.53035	0.448000	0.29417	GGC	G|0.767;A|0.233	0.233	strong		0.731	LOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268995.2	NM_005576	
GGT5	2687	hgsc.bcm.edu	37	22	24622124	24622124	+	Silent	SNP	G	G	A	rs73879043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24622124G>A	ENST00000327365.4	-	8	1565	c.1149C>T	c.(1147-1149)ggC>ggT	p.G383G	GGT5_ENST00000398292.3_Silent_p.G383G|GGT5_ENST00000418439.2_Silent_p.G306G|GGT5_ENST00000263112.7_Silent_p.G351G	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	383					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						CTGTCCCGTGGCCCCAGGCCT	0.687													G|||	101	0.0201677	0.0711	0.0101	5008	,	,		14159	0.0		0.0	False		,,,				2504	0.0				p.G383G		Atlas-SNP	.											.	GGT5	61	.	0			c.C1149T						PASS	.	G	,,	236,4170	131.8+/-168.3	6,224,1973	30.0	32.0	31.0		1149,1053,1149	1.6	0.1	22	dbSNP_130	31	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	GGT5	NM_001099781.1,NM_001099782.1,NM_004121.2	,,	6,224,6271	AA,AG,GG		0.0,5.3563,1.8151	,,	383/588,351/555,383/587	24622124	236,12766	2203	4298	6501	SO:0001819	synonymous_variant	2687	exon8			CCCGTGGCCCCAG	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"""Gamma-glutamyltransferases"""	4260	protein-coding gene	gene with protein product		137168	"""gamma-glutamyltransferase-like activity 1"""	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.1149C>T	22.37:g.24622124G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Silent	SNP	ENST00000327365.4	37	CCDS13825.1																																																																																			G|0.981;A|0.019	0.019	strong		0.687	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121	
JAG1	182	hgsc.bcm.edu	37	20	10620386	10620386	+	Silent	SNP	A	A	G	rs1051419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:10620386A>G	ENST00000254958.5	-	26	3932	c.3417T>C	c.(3415-3417)taT>taC	p.Y1139Y	JAG1_ENST00000423891.2_Silent_p.Y980Y	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	1139					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)	p.Y1139Y(1)		biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						TCTTGTTCTCATAATCCTTGA	0.483									Alagille Syndrome				G|||	3569	0.71266	0.9289	0.6326	5008	,	,		19004	0.494		0.6481	False		,,,				2504	0.7689				p.Y1139Y		Atlas-SNP	.											JAG1_ENST00000254958,NS,carcinoma,0,1	JAG1	213	1	1	Substitution - coding silent(1)	stomach(1)	c.T3417C						PASS	.	G		3962,444	214.8+/-234.0	1781,400,22	149.0	147.0	148.0		3417	-1.1	1.0	20	dbSNP_86	148	5496,3104	474.2+/-368.8	1737,2022,541	no	coding-synonymous	JAG1	NM_000214.2		3518,2422,563	GG,GA,AA		36.093,10.0772,27.2797		1139/1219	10620386	9458,3548	2203	4300	6503	SO:0001819	synonymous_variant	182	exon26	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GTTCTCATAATCC	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.3417T>C	20.37:g.10620386A>G		Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	330	329	0.99697	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			G|0.694;C|0.000;A|0.306	0.694	strong		0.483	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
RASAL3	64926	hgsc.bcm.edu	37	19	15569378	15569378	+	Missense_Mutation	SNP	G	G	C	rs58123634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15569378G>C	ENST00000343625.7	-	7	836	c.751C>G	c.(751-753)Ctg>Gtg	p.L251V	RASAL3_ENST00000608577.1_5'Flank	NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	251	PH.		L -> V (in dbSNP:rs58123634).		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						CTGGGGTGCAGTGGCCAGATC	0.642													G|||	194	0.038738	0.0522	0.0231	5008	,	,		11687	0.005		0.0447	False		,,,				2504	0.0603				p.L251V		Atlas-SNP	.											.	RASAL3	49	.	0			c.C751G						PASS	.	G	VAL/LEU	213,3981		2,209,1886	40.0	45.0	44.0		751	3.4	1.0	19	dbSNP_129	44	409,8041		12,385,3828	yes	missense	RASAL3	NM_022904.1	32	14,594,5714	CC,CG,GG		4.8402,5.0787,4.9193	benign	251/1012	15569378	622,12022	2097	4225	6322	SO:0001583	missense	64926	exon7			GGTGCAGTGGCCA		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.751C>G	19.37:g.15569378G>C	ENSP00000341905:p.Leu251Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	144	65	0.451389	NM_022904	Q8N2T9|Q9H735	Missense_Mutation	SNP	ENST00000343625.7	37	CCDS46006.1	64	0.029304029304029304	21	0.042682926829268296	7	0.019337016574585635	1	0.0017482517482517483	35	0.04617414248021108	G	10.35	1.325523	0.24080	0.050787	0.048402	ENSG00000105122	ENST00000343625	D	0.93366	-3.21	4.47	3.42	0.39159	Pleckstrin homology domain (1);	0.000000	0.26948	U	0.021700	T	0.49236	0.1545	N	0.11106	0.095	0.32241	N	0.572703	P	0.38473	0.633	B	0.36845	0.234	T	0.73375	-0.4002	10	0.07990	T	0.79	.	10.2251	0.43220	0.1003:0.0:0.8997:0.0	rs58123634	251	Q86YV0	RASL3_HUMAN	V	251	ENSP00000341905:L251V	ENSP00000341905:L251V	L	-	1	2	RASAL3	15430378	0.006000	0.16342	0.969000	0.41365	0.571000	0.35966	0.013000	0.13310	0.874000	0.35823	0.491000	0.48974	CTG	G|0.967;C|0.033	0.033	strong		0.642	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904	
ESPL1	9700	hgsc.bcm.edu	37	12	53680135	53680135	+	Silent	SNP	C	C	T	rs61741367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53680135C>T	ENST00000257934.4	+	18	3706	c.3615C>T	c.(3613-3615)tcC>tcT	p.S1205S	ESPL1_ENST00000552462.1_Silent_p.S1205S	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1205					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TCCAAGCTTCCCTGAATCATA	0.582													C|||	180	0.0359425	0.1316	0.0086	5008	,	,		17444	0.0		0.0	False		,,,				2504	0.0				p.S1205S	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C3615T						PASS	.	C		503,3903	233.3+/-246.5	36,431,1736	79.0	87.0	84.0		3615	0.4	0.3	12	dbSNP_129	84	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	ESPL1	NM_012291.4		36,438,6029	TT,TC,CC		0.0814,11.4163,3.9213		1205/2121	53680135	510,12496	2203	4300	6503	SO:0001819	synonymous_variant	9700	exon18			AGCTTCCCTGAAT	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.3615C>T	12.37:g.53680135C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_012291		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																			C|0.957;T|0.043	0.043	strong		0.582	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
VTI1B	10490	hgsc.bcm.edu	37	14	68141105	68141105	+	Silent	SNP	C	C	T	rs2234510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:68141105C>T	ENST00000554659.1	-	1	443	c.102G>A	c.(100-102)ggG>ggA	p.G34G	RP11-1012A1.4_ENST00000553306.1_Intron|RP11-1012A1.4_ENST00000554493.1_Intron	NM_006370.2	NP_006361.1	Q9UEU0	VTI1B_HUMAN	vesicle transport through interaction with t-SNAREs 1B	34					cell proliferation (GO:0008283)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021)	SNARE binding (GO:0000149)			endometrium(1)|large_intestine(2)|stomach(1)|upper_aerodigestive_tract(1)	5				all cancers(60;0.000344)|OV - Ovarian serous cystadenocarcinoma(108;0.00212)|BRCA - Breast invasive adenocarcinoma(234;0.00941)		TCCCCGCCGTCCCCAGCAGCC	0.697													C|||	150	0.0299521	0.1097	0.0072	5008	,	,		8683	0.0		0.0	False		,,,				2504	0.0				p.G34G		Atlas-SNP	.											.	VTI1B	15	.	0			c.G102A						PASS	.	C		347,3945		9,329,1808	8.0	9.0	9.0		102	0.4	0.4	14	dbSNP_98	9	1,8419		0,1,4209	no	coding-synonymous	VTI1B	NM_006370.2		9,330,6017	TT,TC,CC		0.0119,8.0848,2.7376		34/233	68141105	348,12364	2146	4210	6356	SO:0001819	synonymous_variant	10490	exon1			CGCCGTCCCCAGC	AF060902	CCDS9786.1	14q23.3	2012-12-10	2012-12-10		ENSG00000100568	ENSG00000100568			17793	protein-coding gene	gene with protein product		603207	"""vesicle transport through interaction with t-SNAREs homolog 1B (yeast)"""			9636656, 9446565	Standard	NM_006370		Approved	VTI2	uc001xjt.3	Q9UEU0	OTTHUMG00000171251	ENST00000554659.1:c.102G>A	14.37:g.68141105C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_006370	O43547|Q96J28	Silent	SNP	ENST00000554659.1	37	CCDS9786.1																																																																																			C|0.973;T|0.027	0.027	strong		0.697	VTI1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412558.2		
ZBED4	9889	hgsc.bcm.edu	37	22	50278588	50278588	+	Silent	SNP	C	C	T	rs61731526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50278588C>T	ENST00000216268.5	+	2	1755	c.1278C>T	c.(1276-1278)tcC>tcT	p.S426S		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	426						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		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)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		CCTCGGCGTCCTCTCCTGAGA	0.532													C|||	23	0.00459265	0.0159	0.0029	5008	,	,		19928	0.0		0.0	False		,,,				2504	0.0				p.S426S		Atlas-SNP	.											.	ZBED4	102	.	0			c.C1278T						PASS	.	C		44,4362	40.8+/-73.8	0,44,2159	59.0	63.0	62.0		1278	-0.5	0.3	22	dbSNP_129	62	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZBED4	NM_014838.2		0,46,6457	TT,TC,CC		0.0233,0.9986,0.3537		426/1172	50278588	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	9889	exon2			GGCGTCCTCTCCT	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.1278C>T	22.37:g.50278588C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	55	19	0.345455	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Silent	SNP	ENST00000216268.5	37	CCDS33677.1																																																																																			C|0.996;T|0.004	0.004	strong		0.532	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
IP6K3	117283	hgsc.bcm.edu	37	6	33694659	33694659	+	Silent	SNP	G	G	A	rs34252064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33694659G>A	ENST00000293756.4	-	4	764	c.438C>T	c.(436-438)tcC>tcT	p.S146S	IP6K3_ENST00000451316.1_Silent_p.S146S	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	146					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						GGTGGGGCTCGGACCTCAGAA	0.647													G|||	453	0.0904553	0.2912	0.0317	5008	,	,		17666	0.001		0.0398	False		,,,				2504	0.0051				p.S146S		Atlas-SNP	.											.	IP6K3	52	.	0			c.C438T						PASS	.	G	,	1010,3396	376.1+/-321.9	114,782,1307	73.0	73.0	73.0		438,438	1.1	1.0	6	dbSNP_126	73	384,8216	125.0+/-183.6	12,360,3928	no	coding-synonymous,coding-synonymous	IP6K3	NM_001142883.1,NM_054111.4	,	126,1142,5235	AA,AG,GG		4.4651,22.9233,10.7181	,	146/411,146/411	33694659	1394,11612	2203	4300	6503	SO:0001819	synonymous_variant	117283	exon5			GGGCTCGGACCTC	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"""inositol hexaphosphate kinase 3"""	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.438C>T	6.37:g.33694659G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	124	68	0.548387	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	37	CCDS34435.1																																																																																			G|0.901;A|0.099	0.099	strong		0.647	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111	
OPRK1	4986	hgsc.bcm.edu	37	8	54147470	54147470	+	Silent	SNP	G	G	A	rs7815824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:54147470G>A	ENST00000265572.3	-	3	756	c.459C>T	c.(457-459)agC>agT	p.S153S	OPRK1_ENST00000524278.1_Silent_p.S64S|OPRK1_ENST00000520287.1_Silent_p.S153S|RP11-162D9.3_ENST00000524425.1_RNA	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	153					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)			NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	AGCGGTCCACGCTCATCATGG	0.488													G|||	318	0.0634984	0.1815	0.0389	5008	,	,		21237	0.0188		0.0298	False		,,,				2504	0.002				p.S153S		Atlas-SNP	.											.	OPRK1	90	.	0			c.C459T						PASS	.	G		691,3715	290.4+/-280.9	50,591,1562	131.0	105.0	114.0		459	-6.4	0.8	8	dbSNP_116	114	295,8305	108.0+/-168.7	5,285,4010	no	coding-synonymous	OPRK1	NM_000912.3		55,876,5572	AA,AG,GG		3.4302,15.6832,7.5811		153/381	54147470	986,12020	2203	4300	6503	SO:0001819	synonymous_variant	4986	exon3			GTCCACGCTCATC		CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"""GPCR / Class A : Opioid receptors"""	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.459C>T	8.37:g.54147470G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_000912	E5RHC9|Q499G4	Silent	SNP	ENST00000265572.3	37	CCDS6152.1																																																																																			G|0.927;A|0.073	0.073	strong		0.488	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1		
ZNF844	284391	hgsc.bcm.edu	37	19	12186611	12186611	+	Missense_Mutation	SNP	A	A	G	rs7259684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12186611A>G	ENST00000439326.3	+	4	851	c.676A>G	c.(676-678)Aaa>Gaa	p.K226E	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	226			K -> E (in dbSNP:rs7259684).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						GAAACCATATAAATGTAAACA	0.373													.|||	825	0.164736	0.413	0.0663	5008	,	,		21878	0.0665		0.0825	False		,,,				2504	0.0849				p.K226E		Atlas-SNP	.											.	ZNF844	69	.	0			c.A676G						PASS	.	G	GLU/LYS	492,892		95,302,295	40.0	37.0	38.0		676	-1.7	0.0	19	dbSNP_116	38	236,2946		6,224,1361	no	missense	ZNF844	NM_001136501.1	56	101,526,1656	GG,GA,AA		7.4167,35.5491,15.9439	benign	226/667	12186611	728,3838	692	1591	2283	SO:0001583	missense	284391	exon4			CCATATAAATGTA	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.676A>G	19.37:g.12186611A>G	ENSP00000392024:p.Lys226Glu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	323	0.1478937728937729	190	0.3861788617886179	27	0.07458563535911603	40	0.06993006993006994	66	0.0870712401055409	a	0.261	-0.999373	0.02128	0.355491	0.074167	ENSG00000223547	ENST00000439326;ENST00000541708;ENST00000535505;ENST00000550826	T;T	0.16196	3.1;2.36	2.31	-1.72	0.08107	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);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	0.44452	-0.9327	8	0.02654	T	1	.	8.289	0.31946	0.5789:0.0:0.4211:0.0	rs7259684;rs7259684	226	Q08AG5	ZN844_HUMAN	E	226;226;201;69	ENSP00000392024:K226E;ENSP00000448588:K69E	ENSP00000392024:K226E	K	+	1	0	ZNF844	12047611	0.000000	0.05858	0.002000	0.10522	0.421000	0.31385	-5.762000	0.00100	-1.016000	0.03371	-0.971000	0.02607	AAA	A|0.854;G|0.146	0.146	strong		0.373	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
ZNF264	9422	hgsc.bcm.edu	37	19	57723182	57723182	+	Silent	SNP	C	C	T	rs61730346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57723182C>T	ENST00000263095.6	+	4	1131	c.717C>T	c.(715-717)acC>acT	p.T239T	ZNF264_ENST00000536056.1_Silent_p.T239T	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	239					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)		GTGGGAAAACCTTTATTAAGA	0.448													.|||	48	0.00958466	0.0356	0.0	5008	,	,		21386	0.0		0.001	False		,,,				2504	0.0				p.T239T		Atlas-SNP	.											.	ZNF264	65	.	0			c.C717T						PASS	.	C		120,4286	89.2+/-127.9	2,116,2085	97.0	96.0	96.0		717	-2.4	0.0	19	dbSNP_129	96	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF264	NM_003417.4		2,118,6383	TT,TC,CC		0.0233,2.7236,0.938		239/628	57723182	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	9422	exon4			GAAAACCTTTATT	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.717C>T	19.37:g.57723182C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_003417	A8K8Y9|Q9P1V0	Silent	SNP	ENST00000263095.6	37	CCDS33127.1																																																																																			C|0.990;T|0.010	0.010	strong		0.448	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1		
KIAA0141	9812	hgsc.bcm.edu	37	5	141309752	141309752	+	Missense_Mutation	SNP	A	A	G	rs76602789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141309752A>G	ENST00000432126.2	+	7	801	c.667A>G	c.(667-669)Aaa>Gaa	p.K223E	KIAA0141_ENST00000194118.4_Missense_Mutation_p.K223E	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	223					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAACAAGATAAATCAAAAAC	0.458													A|||	87	0.0173722	0.062	0.0058	5008	,	,		20345	0.0		0.001	False		,,,				2504	0.0				p.K223E		Atlas-SNP	.											.	KIAA0141	44	.	0			c.A667G						PASS	.	A	GLU/LYS,GLU/LYS	218,4188	133.3+/-169.7	5,208,1990	66.0	69.0	68.0		667,667	-0.9	0.0	5	dbSNP_131	68	0,8600		0,0,4300	yes	missense,missense	KIAA0141	NM_001142603.1,NM_014773.3	56,56	5,208,6290	GG,GA,AA		0.0,4.9478,1.6761	benign,benign	223/516,223/516	141309752	218,12788	2203	4300	6503	SO:0001583	missense	9812	exon7			CAAGATAAATCAA	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.667A>G	5.37:g.141309752A>G	ENSP00000396225:p.Lys223Glu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	141	77	0.546099	NM_001142603	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	31	0.014194139194139194	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	9.978	1.227280	0.22542	0.049478	0.0	ENSG00000081791	ENST00000432126;ENST00000194118;ENST00000508751	T;T;T	0.18657	2.68;2.68;2.2	4.73	-0.912	0.10504	.	0.760161	0.12637	N	0.451616	T	0.01124	0.0037	L	0.28504	0.86	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35076	-0.9803	10	0.15499	T	0.54	-1.7713	6.5704	0.22535	0.4334:0.4756:0.0911:0.0	.	223	Q14154	DELE_HUMAN	E	223	ENSP00000396225:K223E;ENSP00000194118:K223E;ENSP00000422686:K223E	ENSP00000194118:K223E	K	+	1	0	KIAA0141	141289936	0.000000	0.05858	0.001000	0.08648	0.447000	0.32167	0.211000	0.17474	-0.014000	0.14175	0.254000	0.18369	AAA	A|0.980;G|0.020	0.020	strong		0.458	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
GANAB	23193	hgsc.bcm.edu	37	11	62396263	62396263	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62396263G>A	ENST00000356638.3	-	17	2174	c.2158C>T	c.(2158-2160)Cgg>Tgg	p.R720W	GANAB_ENST00000540933.1_Missense_Mutation_p.R623W|GANAB_ENST00000534779.1_Missense_Mutation_p.R628W|GANAB_ENST00000346178.4_Missense_Mutation_p.R742W	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	720					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 lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	ATGCCTTCCCGATGGGCCTGA	0.527																																					p.R742W	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											GANAB_ENST00000346178,NS,carcinoma,+1,3	GANAB	110	3	0			c.C2224T						scavenged	.						157.0	143.0	148.0					11																	62396263		2202	4299	6501	SO:0001583	missense	23193	exon18			CTTCCCGATGGGC	AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.2158C>T	11.37:g.62396263G>A	ENSP00000349053:p.Arg720Trp	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	163	3	0.0184049	NM_198335	A6NC20|Q8WTS9|Q9P0X0	Missense_Mutation	SNP	ENST00000356638.3	37	CCDS8026.1	.	.	.	.	.	.	.	.	.	.	G	17.43	3.386672	0.61956	.	.	ENSG00000089597	ENST00000346178;ENST00000356638;ENST00000534779;ENST00000540933	D;D;D;D	0.91740	-2.9;-2.9;-2.9;-2.9	5.1	3.16	0.36331	Glycoside hydrolase, superfamily (1);	0.442370	0.23183	N	0.050981	D	0.94624	0.8267	M	0.85299	2.745	0.33291	D	0.563592	D;D;D;D	0.64830	0.978;0.978;0.994;0.986	P;P;P;P	0.55303	0.773;0.773;0.773;0.663	D	0.95989	0.8984	10	0.62326	D	0.03	-1.6549	12.3479	0.55132	0.0:0.0:0.697:0.303	.	606;628;720;742	B4DIW2;E9PKU7;Q14697;Q14697-2	.;.;GANAB_HUMAN;.	W	742;720;628;623	ENSP00000340466:R742W;ENSP00000349053:R720W;ENSP00000435306:R628W;ENSP00000442962:R623W	ENSP00000340466:R742W	R	-	1	2	GANAB	62152839	0.557000	0.26546	0.323000	0.25347	0.757000	0.42996	0.856000	0.27818	0.794000	0.33899	0.561000	0.74099	CGG	.	.	none		0.527	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334	
PIAS4	51588	hgsc.bcm.edu	37	19	4012971	4012971	+	Silent	SNP	C	C	T	rs61729790	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4012971C>T	ENST00000262971.2	+	2	193	c.78C>T	c.(76-78)ttC>ttT	p.F26F		NM_015897.2	NP_056981.2	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	26	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186, ECO:0000305}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(3)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCTGGGTTTCGTGGGCCGGA	0.562													c|||	507	0.101238	0.3699	0.0245	5008	,	,		15489	0.0		0.001	False		,,,				2504	0.0				p.F26F		Atlas-SNP	.											.	PIAS4	40	.	0			c.C78T						PASS	.	T		1226,3180	424.2+/-340.4	166,894,1143	115.0	110.0	112.0		78	-8.9	0.1	19	dbSNP_129	112	11,8589	7.1+/-27.0	0,11,4289	no	coding-synonymous	PIAS4	NM_015897.2		166,905,5432	TT,TC,CC		0.1279,27.8257,9.511		26/511	4012971	1237,11769	2203	4300	6503	SO:0001819	synonymous_variant	51588	exon2			GGGTTTCGTGGGC	AF077952	CCDS12118.1	19p13.3	2011-10-11						"""Zinc fingers, MIZ-type"""	17002	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 6"""	605989				9724754	Standard	NM_015897		Approved	Piasg, PIASY, FLJ12419, ZMIZ6	uc002lzg.3	Q8N2W9		ENST00000262971.2:c.78C>T	19.37:g.4012971C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	163	163	1	NM_015897	O75926|Q96G19|Q9UN16	Silent	SNP	ENST00000262971.2	37	CCDS12118.1																																																																																			C|0.910;T|0.090	0.090	strong		0.562	PIAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457496.1	NM_015897	
CDHR2	54825	hgsc.bcm.edu	37	5	176011968	176011968	+	Missense_Mutation	SNP	G	G	A	rs114527399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176011968G>A	ENST00000510636.1	+	19	2960	c.2686G>A	c.(2686-2688)Gcc>Acc	p.A896T	CDHR2_ENST00000261944.5_Missense_Mutation_p.A896T|CDHR2_ENST00000506348.1_Missense_Mutation_p.A896T	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	896	Cadherin 8. {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						GGTTGTGCGGGCCTGTGACCT	0.627													G|||	9	0.00179712	0.0068	0.0	5008	,	,		19273	0.0		0.0	False		,,,				2504	0.0				p.A896T		Atlas-SNP	.											.	CDHR2	152	.	0			c.G2686A						PASS	.	G	THR/ALA,THR/ALA	29,4319		0,29,2145	29.0	25.0	26.0		2686,2686	5.4	1.0	5	dbSNP_132	26	0,8520		0,0,4260	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	58,58	0,29,6405	AA,AG,GG		0.0,0.667,0.2254	probably-damaging,probably-damaging	896/1311,896/1311	176011968	29,12839	2174	4260	6434	SO:0001583	missense	54825	exon19			GTGCGGGCCTGTG	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.2686G>A	5.37:g.176011968G>A	ENSP00000424565:p.Ala896Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	21.9	4.219121	0.79464	0.00667	0.0	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.75589	-0.95;-0.95;-0.95	5.42	5.42	0.78866	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.86493	0.5946	H	0.95611	3.695	0.42064	D	0.991178	D	0.62365	0.991	P	0.59595	0.86	D	0.90838	0.4721	9	0.62326	D	0.03	-45.3354	19.2279	0.93824	0.0:0.0:1.0:0.0	.	896	Q9BYE9	CDHR2_HUMAN	T	896	ENSP00000424565:A896T;ENSP00000261944:A896T;ENSP00000421078:A896T	ENSP00000261944:A896T	A	+	1	0	CDHR2	175944574	1.000000	0.71417	0.999000	0.59377	0.304000	0.27724	7.214000	0.77958	2.547000	0.85894	0.549000	0.68633	GCC	G|0.996;A|0.004	0.004	strong		0.627	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
MXD3	83463	hgsc.bcm.edu	37	5	176734945	176734945	+	Missense_Mutation	SNP	C	C	A	rs35691394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176734945C>A	ENST00000439742.2	-	5	820	c.342G>T	c.(340-342)caG>caT	p.Q114H	MXD3_ENST00000427908.2_Missense_Mutation_p.Q114H|MXD3_ENST00000423571.2_Missense_Mutation_p.Q114H|MXD3_ENST00000513063.1_Missense_Mutation_p.Q114H	NM_031300.3	NP_112590.1	Q9BW11	MAD3_HUMAN	MAX dimerization protein 3	114			Q -> H (in dbSNP:rs35691394).		negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)			GTCGGGCCCGCTGCTCCTGAT	0.711													C|||	7	0.00139776	0.0053	0.0	5008	,	,		15589	0.0		0.0	False		,,,				2504	0.0				p.Q114H		Atlas-SNP	.											.	MXD3	13	.	0			c.G342T						PASS	.	C	HIS/GLN,HIS/GLN	29,4071		0,29,2021	5.0	6.0	5.0		342,342	4.1	1.0	5	dbSNP_126	5	1,8135		0,1,4067	no	missense,missense	MXD3	NM_001142935.1,NM_031300.3	24,24	0,30,6088	AA,AC,CC		0.0123,0.7073,0.2452	possibly-damaging,possibly-damaging	114/194,114/207	176734945	30,12206	2050	4068	6118	SO:0001583	missense	83463	exon5			GGCCCGCTGCTCC	BC000745	CCDS4416.1, CCDS47347.1	5q35.3	2013-03-20			ENSG00000213347	ENSG00000213347		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	14008	protein-coding gene	gene with protein product		609450					Standard	NM_031300		Approved	MAD3, bHLHc13	uc003mgb.2	Q9BW11	OTTHUMG00000130854	ENST00000439742.2:c.342G>T	5.37:g.176734945C>A	ENSP00000401867:p.Gln114His	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_001142935	B4E0J1|Q53HK1|Q7Z4Y0|Q8NDJ7|Q96ME3	Missense_Mutation	SNP	ENST00000439742.2	37	CCDS4416.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	19.48	3.835342	0.71373	0.007073	1.23E-4	ENSG00000213347	ENST00000427908;ENST00000423571;ENST00000439742;ENST00000303165;ENST00000513063;ENST00000513169;ENST00000502529	D;D;D;D;T;T	0.88975	-2.45;-2.45;-2.45;-2.45;0.88;0.9	5.0	4.13	0.48395	Helix-loop-helix DNA-binding (3);	0.422928	0.25416	N	0.030831	D	0.87249	0.6130	L	0.44542	1.39	0.33730	D	0.618086	D;D;D;D	0.71674	0.998;0.989;0.981;0.99	P;P;P;P	0.62560	0.904;0.769;0.687;0.825	D	0.90640	0.4574	10	0.59425	D	0.04	-0.452	10.1788	0.42955	0.0:0.8454:0.0:0.1546	rs35691394	114;105;114;114	Q9BW11-3;F8W9D2;Q9BW11;B4E0J1	.;.;MAD3_HUMAN;.	H	114;114;114;105;114;31;104	ENSP00000416921:Q114H;ENSP00000389716:Q114H;ENSP00000401867:Q114H;ENSP00000421463:Q114H;ENSP00000427104:Q31H;ENSP00000425029:Q104H	ENSP00000307720:Q105H	Q	-	3	2	MXD3	176667551	0.001000	0.12720	0.979000	0.43373	0.681000	0.39784	1.288000	0.33296	1.226000	0.43582	0.561000	0.74099	CAG	C|0.997;A|0.003	0.003	strong		0.711	MXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253427.1		
FLG	2312	hgsc.bcm.edu	37	1	152276889	152276889	+	Silent	SNP	A	A	G	rs3126067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276889A>G	ENST00000368799.1	-	3	10508	c.10473T>C	c.(10471-10473)aaT>aaC	p.N3491N	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	417	2	0.00479616		WXS	Illumina HiSeq	Phase_I	413	406	0.983051	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	
LRP1B	53353	hgsc.bcm.edu	37	2	141130695	141130695	+	Silent	SNP	C	C	T	rs16843864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:141130695C>T	ENST00000389484.3	-	69	11621	c.10650G>A	c.(10648-10650)gaG>gaA	p.E3550E		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3550	LDL-receptor class A 26. {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)		AACAACTTGTCTCACAATTTC	0.343										TSP Lung(27;0.18)			T|||	528	0.105431	0.2005	0.0951	5008	,	,		16259	0.0159		0.1233	False		,,,				2504	0.0583				p.E3550E	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G10650A						PASS	.	T		853,3551	744.8+/-411.6	72,709,1421	117.0	109.0	112.0		10650	3.1	0.8	2	dbSNP_123	112	1112,7488	766.9+/-407.6	67,978,3255	no	coding-synonymous	LRP1B	NM_018557.2		139,1687,4676	TT,TC,CC		12.9302,19.3688,15.1107		3550/4600	141130695	1965,11039	2202	4300	6502	SO:0001819	synonymous_variant	53353	exon69			ACTTGTCTCACAA	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.10650G>A	2.37:g.141130695C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			C|0.863;T|0.137	0.137	strong		0.343	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
CXorf30	645090	hgsc.bcm.edu	37	X	36385156	36385156	+	Silent	SNP	A	A	G	rs6632593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:36385156A>G	ENST00000378657.4	+	16	2085	c.1437A>G	c.(1435-1437)gaA>gaG	p.E479E	RP11-87M18.2_ENST00000455438.2_RNA	NM_001098843.4	NP_001092313.2	A6PW82	CX030_HUMAN	chromosome X open reading frame 30	479										breast(1)|lung(2)|stomach(1)	4						TCGCTACTGAACCTGATACGG	0.353													g|||	619	0.163974	0.0855	0.1066	3775	,	,		12734	0.1726		0.0616	False		,,,				2504	0.2004				p.E479E		Atlas-SNP	.											.	CXorf30	76	.	0			c.A1437G						PASS	.			127,1082		4,107,12,406,163	306.0	226.0	250.0		1437	-4.3	0.0	X	dbSNP_116	250	162,2227		7,92,56,700,735	no	coding-synonymous	CXorf30	NM_001098843.3		11,199,68,1106,898	GG,GA,G,AA,A		6.7811,10.5045,8.0322		479/634	36385156	289,3309	692	1590	2282	SO:0001819	synonymous_variant	645090	exon17			TACTGAACCTGAT		CCDS55396.1	Xp21.1	2014-08-07			ENSG00000205081	ENSG00000205081			27298	protein-coding gene	gene with protein product							Standard	NM_001098843		Approved		uc011mkc.3	A6PW82	OTTHUMG00000021353	ENST00000378657.4:c.1437A>G	X.37:g.36385156A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	133	71	0.533835	NM_001098843		Silent	SNP	ENST00000378657.4	37	CCDS55396.1																																																																																			A|0.841;G|0.159	0.159	strong		0.353	CXorf30-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NP_001092313	
EXOC4	60412	hgsc.bcm.edu	37	7	133682285	133682285	+	Silent	SNP	C	C	T	rs34608222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:133682285C>T	ENST00000253861.4	+	15	2276	c.2247C>T	c.(2245-2247)ctC>ctT	p.L749L	EXOC4_ENST00000545148.1_Silent_p.L359L|EXOC4_ENST00000541309.1_Silent_p.L37L|EXOC4_ENST00000539845.1_Silent_p.L648L	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	749					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)				ACACGGATCTCCCCCCAGTGT	0.458													C|||	62	0.0123802	0.0439	0.0043	5008	,	,		19403	0.0		0.001	False		,,,				2504	0.0				p.L749L		Atlas-SNP	.											.	EXOC4	118	.	0			c.C2247T						PASS	.	C		209,4197	126.6+/-163.6	9,191,2003	141.0	114.0	123.0		2247	-2.3	0.6	7	dbSNP_126	123	0,8600		0,0,4300	no	coding-synonymous	EXOC4	NM_021807.3		9,191,6303	TT,TC,CC		0.0,4.7435,1.607		749/975	133682285	209,12797	2203	4300	6503	SO:0001819	synonymous_variant	60412	exon15			GGATCTCCCCCCA	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.2247C>T	7.37:g.133682285C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	37	CCDS5829.1																																																																																			C|0.986;T|0.014	0.014	strong		0.458	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
SPSB1	80176	hgsc.bcm.edu	37	1	9416151	9416151	+	Silent	SNP	G	G	A	rs9435243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9416151G>A	ENST00000328089.6	+	2	542	c.201G>A	c.(199-201)gtG>gtA	p.V67V	SPSB1_ENST00000377399.2_Silent_p.V67V|SPSB1_ENST00000357898.3_Silent_p.V67V	NM_025106.3	NP_079382.2	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box containing 1	67	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(2)|lung(5)|prostate(2)	13	all_lung(157;0.194)	all_epithelial(116;4.38e-15)|all_lung(118;0.000156)|Lung NSC(185;0.000446)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.72e-07)|COAD - Colon adenocarcinoma(227;9.12e-05)|Kidney(185;0.000296)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00193)|BRCA - Breast invasive adenocarcinoma(304;0.00202)|READ - Rectum adenocarcinoma(331;0.0419)		ATGTCTTTGTGAAGGAGGACG	0.582													G|||	1299	0.259385	0.2368	0.3401	5008	,	,		20489	0.2748		0.1998	False		,,,				2504	0.2781				p.V67V		Atlas-SNP	.											.	SPSB1	22	.	0			c.G201A						PASS	.	G		1056,3350	387.7+/-326.6	147,762,1294	174.0	169.0	170.0		201	2.2	1.0	1	dbSNP_119	170	1998,6602	350.7+/-328.0	230,1538,2532	no	coding-synonymous	SPSB1	NM_025106.3		377,2300,3826	AA,AG,GG		23.2326,23.9673,23.4815		67/274	9416151	3054,9952	2203	4300	6503	SO:0001819	synonymous_variant	80176	exon2			CTTTGTGAAGGAG		CCDS102.1	1p36.22	2008-02-05			ENSG00000171621	ENSG00000171621			30628	protein-coding gene	gene with protein product		611657				15713673, 12076535	Standard	NM_025106		Approved	SSB-1	uc010oae.2	Q96BD6	OTTHUMG00000001279	ENST00000328089.6:c.201G>A	1.37:g.9416151G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_025106	A2A275|Q59FA1|Q5TIH9|Q9BRY9|Q9H6C5	Silent	SNP	ENST00000328089.6	37	CCDS102.1																																																																																			G|0.765;A|0.235	0.235	strong		0.582	SPSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003727.2	NM_025106	
MRPL19	9801	hgsc.bcm.edu	37	2	75874015	75874015	+	Missense_Mutation	SNP	C	C	G	rs11552948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:75874015C>G	ENST00000393909.2	+	1	107	c.82C>G	c.(82-84)Ccg>Gcg	p.P28A	MRPL19_ENST00000358788.6_Missense_Mutation_p.P28A|MRPL19_ENST00000409374.1_Missense_Mutation_p.P28A	NM_014763.3	NP_055578.2	P49406	RM19_HUMAN	mitochondrial ribosomal protein L19	28					translation (GO:0006412)	mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(6)	8						TCTGCTCCCCCCGCCGGCCTC	0.667													C|||	141	0.028155	0.0605	0.0058	5008	,	,		14162	0.0		0.0219	False		,,,				2504	0.0358				p.P28A		Atlas-SNP	.											.	MRPL19	21	.	0			c.C82G						PASS	.	C	ALA/PRO	163,3473		0,163,1655	7.0	9.0	8.0		82	-0.1	0.0	2	dbSNP_120	8	126,7928		2,122,3903	yes	missense	MRPL19	NM_014763.3	27	2,285,5558	GG,GC,CC		1.5644,4.4829,2.4722	benign	28/293	75874015	289,11401	1818	4027	5845	SO:0001583	missense	9801	exon1			CTCCCCCCGCCGG	AB051621	CCDS1960.2	2p11.1-q11.2	2012-09-13			ENSG00000115364	ENSG00000115364		"""Mitochondrial ribosomal proteins / large subunits"""	14052	protein-coding gene	gene with protein product	"""39S ribosomal protein L19"""	611832				11543634, 17309879	Standard	XM_006712155		Approved	MRP-L15, RPML15, KIAA0104, RLX1	uc002snl.3	P49406	OTTHUMG00000129990	ENST00000393909.2:c.82C>G	2.37:g.75874015C>G	ENSP00000377486:p.Pro28Ala	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	266	134	0.503759	NM_014763	Q53TX9|Q96Q52	Missense_Mutation	SNP	ENST00000393909.2	37	CCDS1960.2	47	0.02152014652014652	26	0.052845528455284556	4	0.011049723756906077	0	0.0	17	0.022427440633245383	C	0.017	-1.489919	0.01018	0.044829	0.015644	ENSG00000115364	ENST00000393909;ENST00000409374	.	.	.	3.8	-0.134	0.13481	.	1.150850	0.06366	N	0.712679	T	0.00906	0.0030	N	0.00347	-1.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30060	-0.9991	9	0.02654	T	1	0.0141	4.5961	0.12330	0.2059:0.3526:0.4415:0.0	rs11552948	28	P49406	RM19_HUMAN	A	28	.	ENSP00000351639:P28A	P	+	1	0	MRPL19	75727523	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.266000	0.18534	-0.036000	0.13669	-0.896000	0.02909	CCG	C|0.980;G|0.020	0.020	strong		0.667	MRPL19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252256.1	NM_014763	
MMP8	4317	hgsc.bcm.edu	37	11	102584104	102584104	+	Missense_Mutation	SNP	T	T	G	rs35866072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:102584104T>G	ENST00000236826.3	-	10	1477	c.1379A>C	c.(1378-1380)aAa>aCa	p.K460T		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	460			K -> T (in dbSNP:rs35866072). {ECO:0000269|Ref.2}.		collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	GTTAAGCCATTTATTGCCTCT	0.378													T|||	442	0.0882588	0.2224	0.0591	5008	,	,		20837	0.0089		0.0437	False		,,,				2504	0.0552				p.K460T		Atlas-SNP	.											.	MMP8	68	.	0			c.A1379C						PASS	.	T	THR/LYS	879,3527	341.2+/-306.6	90,699,1414	194.0	170.0	178.0		1379	-8.0	0.0	11	dbSNP_126	178	461,8137	137.6+/-194.5	14,433,3852	yes	missense	MMP8	NM_002424.2	78	104,1132,5266	GG,GT,TT		5.3617,19.9501,10.3045	benign	460/468	102584104	1340,11664	2203	4299	6502	SO:0001583	missense	4317	exon10			AGCCATTTATTGC	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.1379A>C	11.37:g.102584104T>G	ENSP00000236826:p.Lys460Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_002424	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	176	0.08058608058608059	122	0.24796747967479674	20	0.055248618784530384	3	0.005244755244755245	31	0.040897097625329816	T	6.566	0.472756	0.12461	0.199501	0.053617	ENSG00000118113	ENST00000236826	T	0.13657	2.57	5.59	-8.0	0.01126	Hemopexin/matrixin (2);	.	.	.	.	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B;B	0.11235	0.004;0.002	B;B	0.14023	0.01;0.01	T	0.46857	-0.9161	8	0.37606	T	0.19	.	3.8104	0.08795	0.147:0.5539:0.0895:0.2096	rs35866072;rs59529121;rs61751463	460;460	A8K9E4;P22894	.;MMP8_HUMAN	T	460	ENSP00000236826:K460T	ENSP00000236826:K460T	K	-	2	0	MMP8	102089314	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	-0.226000	0.09139	-1.793000	0.01258	-0.371000	0.07208	AAA	T|0.907;G|0.093	0.093	strong		0.378	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
OR8G5	219865	hgsc.bcm.edu	37	11	124135438	124135438	+	Missense_Mutation	SNP	G	G	A	rs2512167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124135438G>A	ENST00000524943.2	+	1	716	c.716G>A	c.(715-717)gGa>gAa	p.G239E	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		ATCTTTAGTGGAATTAACATC	0.413													g|||	2196	0.438498	0.292	0.5591	5008	,	,		21705	0.5833		0.5527	False		,,,				2504	0.2843				p.G239E	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.G716A						PASS	.	G	GLU/GLY	1372,2772		230,912,930	139.0	139.0	139.0		716	-3.2	0.0	11	dbSNP_100	139	4623,3849		1268,2087,881	yes	missense	OR8G5	NM_001005198.1	98	1498,2999,1811	AA,AG,GG		45.432,33.1081,47.519		239/347	124135438	5995,6621	2072	4236	6308	SO:0001583	missense	219865	exon1			TTAGTGGAATTAA	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.716G>A	11.37:g.124135438G>A	ENSP00000477014:p.Gly239Glu	Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	238	238	1	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	37																																																																																				G|0.522;N|0.001	.	strong		0.413	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
ITIH4	3700	hgsc.bcm.edu	37	3	52853480	52853480	+	Missense_Mutation	SNP	T	T	A	rs2276814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52853480T>A	ENST00000266041.4	-	17	2102	c.2006A>T	c.(2005-2007)cAa>cTa	p.Q669L	ITIH4_ENST00000434759.3_3'UTR|ITIH4_ENST00000467462.1_5'Flank|ITIH4_ENST00000485816.1_Missense_Mutation_p.Q674L|ITIH4_ENST00000346281.5_Missense_Mutation_p.Q639L|ITIH4_ENST00000406595.1_Missense_Mutation_p.Q639L|RP5-966M1.6_ENST00000468472.1_3'UTR	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	669	Proline-rich (PRR) potential bioactive peptide.		Q -> L (in dbSNP:rs2276814).		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)		GAGTCCAAGTTGCCTGGAGCT	0.597													T|||	855	0.170727	0.4191	0.0476	5008	,	,		18470	0.0129		0.001	False		,,,				2504	0.2597				p.Q669L		Atlas-SNP	.											.	ITIH4	74	.	0			c.A2006T						PASS	.	T	LEU/GLN,LEU/GLN	1506,2900	480.3+/-358.8	250,1006,947	108.0	114.0	112.0		1916,2006	-3.1	0.0	3	dbSNP_100	112	15,8585	9.8+/-36.6	0,15,4285	yes	missense,missense	ITIH4	NM_001166449.1,NM_002218.4	113,113	250,1021,5232	AA,AT,TT		0.1744,34.1807,11.6946	benign,benign	639/901,669/931	52853480	1521,11485	2203	4300	6503	SO:0001583	missense	3700	exon17			CCAAGTTGCCTGG	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.2006A>T	3.37:g.52853480T>A	ENSP00000266041:p.Gln669Leu	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	254	124	0.488189	NM_002218	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Missense_Mutation	SNP	ENST00000266041.4	37	CCDS2865.1	217	0.09935897435897435	196	0.3983739837398374	11	0.03038674033149171	9	0.015734265734265736	1	0.0013192612137203166	T	0.014	-1.594575	0.00857	0.341807	0.001744	ENSG00000055955	ENST00000266041;ENST00000346281;ENST00000485816;ENST00000406595;ENST00000538421	T;T;T;T	0.01422	4.95;4.91;4.97;4.98	1.54	-3.08	0.05347	.	83.853200	0.00166	N	0.000000	T	0.00012	0.0000	N	0.01048	-1.04	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;0.001;0.0;0.0	T	0.45026	-0.9289	9	0.25106	T	0.35	0.7824	2.4753	0.04575	0.3815:0.0:0.3681:0.2504	rs2276814;rs52795352;rs59485826;rs2276814	639;674;669;639	E9PGN5;B7ZKJ8;Q14624;Q14624-2	.;.;ITIH4_HUMAN;.	L	669;639;674;639;627	ENSP00000266041:Q669L;ENSP00000340520:Q639L;ENSP00000417824:Q674L;ENSP00000384425:Q639L	ENSP00000266041:Q669L	Q	-	2	0	ITIH4	52828520	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.025000	0.12413	-1.104000	0.03015	-0.695000	0.03696	CAA	T|0.888;A|0.112	0.112	strong		0.597	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
SLC13A3	64849	hgsc.bcm.edu	37	20	45194904	45194904	+	Silent	SNP	C	C	G	rs202391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:45194904C>G	ENST00000279027.4	-	11	1476	c.1458G>C	c.(1456-1458)gcG>gcC	p.A486A	SLC13A3_ENST00000472148.1_Silent_p.A404A|SLC13A3_ENST00000413164.2_Silent_p.A436A|SLC13A3_ENST00000495082.1_Silent_p.A439A|SLC13A3_ENST00000396360.1_Silent_p.A404A|SLC13A3_ENST00000290317.5_Silent_p.A439A|SLC13A3_ENST00000435032.1_Silent_p.A71A	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	486					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	TGATGATGGTCGCCGTGTTGC	0.612													G|||	987	0.197085	0.3313	0.1153	5008	,	,		15426	0.1885		0.1392	False		,,,				2504	0.1421				p.A486A		Atlas-SNP	.											.	SLC13A3	88	.	0			c.G1458C						PASS	.	G	,,,,	1342,3064	690.9+/-405.3	215,912,1076	94.0	96.0	95.0		1317,1308,1212,1164,1458	3.3	1.0	20	dbSNP_79	95	1203,7397	762.2+/-407.6	85,1033,3182	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC13A3	NM_001011554.2,NM_001193339.1,NM_001193340.1,NM_001193342.1,NM_022829.5	,,,,	300,1945,4258	GG,GC,CC		13.9884,30.4585,19.5679	,,,,	439/556,436/553,404/521,388/505,486/603	45194904	2545,10461	2203	4300	6503	SO:0001819	synonymous_variant	64849	exon11			GATGGTCGCCGTG	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"""Solute carriers"""	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1458G>C	20.37:g.45194904C>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Silent	SNP	ENST00000279027.4	37	CCDS13400.1																																																																																			C|0.801;G|0.199	0.199	strong		0.612	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2		
PASK	23178	hgsc.bcm.edu	37	2	242062162	242062162	+	Silent	SNP	C	C	T	rs2302050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242062162C>T	ENST00000405260.1	-	12	3755	c.3057G>A	c.(3055-3057)aaG>aaA	p.K1019K	PASK_ENST00000234040.4_Silent_p.K1019K|PASK_ENST00000539818.1_Silent_p.K803K|PASK_ENST00000544142.1_Silent_p.K833K|PASK_ENST00000403638.3_Silent_p.K1019K|PASK_ENST00000358649.4_Silent_p.K1019K	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	1019	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		TGTTTTTTTCCTTGTCCACAG	0.597													C|||	1476	0.294728	0.4811	0.2464	5008	,	,		18407	0.4405		0.0964	False		,,,				2504	0.1309				p.K1019K		Atlas-SNP	.											.	PASK	230	.	0			c.G3057A						PASS	.	C		1823,2583	529.0+/-372.6	406,1011,786	84.0	92.0	89.0		3057	2.7	0.3	2	dbSNP_100	89	752,7848	178.3+/-227.7	30,692,3578	no	coding-synonymous	PASK	NM_015148.2		436,1703,4364	TT,TC,CC		8.7442,41.3754,19.7986		1019/1324	242062162	2575,10431	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon12			TTTTTCCTTGTCC	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.3057G>A	2.37:g.242062162C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			C|0.755;T|0.245	0.245	strong		0.597	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
IFITM2	10581	hgsc.bcm.edu	37	11	308314	308314	+	Missense_Mutation	SNP	T	T	C	rs14408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:308314T>C	ENST00000399817.4	+	1	152	c.122T>C	c.(121-123)aTg>aCg	p.M41T	IFITM2_ENST00000533141.1_Missense_Mutation_p.M21T|RP11-326C3.7_ENST00000526612.1_RNA|IFITM2_ENST00000602569.1_Missense_Mutation_p.M21T	NM_006435.2	NP_006426.2	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2	41			M -> T (in dbSNP:rs14408). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1906403}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(49;2e-09)|all_epithelial(84;3.36e-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;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)		GCTCCCCCGATGTCCACCGTG	0.607													t|||	3531	0.705072	0.7617	0.6657	5008	,	,		14037	0.9593		0.3787	False		,,,				2504	0.7301				p.M41T		Atlas-SNP	.											IFITM2,rectum,carcinoma,0,1	IFITM2	21	1	0			c.T122C						PASS	.	T	THR/MET	2520,1396		857,806,295	63.0	88.0	80.0		122	-2.8	0.0	11	dbSNP_52	80	3019,5275		590,1839,1718	no	missense	IFITM2	NM_006435.2	81	1447,2645,2013	CC,CT,TT		36.3998,35.6486,45.3645	benign	41/133	308314	5539,6671	1958	4147	6105	SO:0001583	missense	10581	exon1			CCCCGATGTCCAC	X57351	CCDS41583.1	11p15.5	2012-03-13	2012-03-13		ENSG00000185201	ENSG00000185201			5413	protein-coding gene	gene with protein product		605578	"""interferon induced transmembrane protein 2 (1-8D)"""			1906403	Standard	NM_006435		Approved	1-8D	uc001lox.4	Q01629		ENST00000399817.4:c.122T>C	11.37:g.308314T>C	ENSP00000382714:p.Met41Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_006435	Q6FH82|Q96DA8	Missense_Mutation	SNP	ENST00000399817.4	37	CCDS41583.1	1298	0.5943223443223443	337	0.6849593495934959	199	0.5497237569060773	523	0.9143356643356644	239	0.3153034300791557	T	0.004	-2.266536	0.00259	0.643514	0.363998	ENSG00000185201	ENST00000533141;ENST00000399817;ENST00000327366	T;T	0.76709	-1.04;-0.8	2.59	-2.76	0.05896	.	1.327100	0.06148	N	0.673694	T	0.00012	0.0000	N	0.00010	-3.02	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45644	-0.9247	9	0.02654	T	1	2.4836	3.407	0.07344	0.3221:0.496:0.0:0.1819	rs14408;rs3179090;rs17850538;rs58885107;rs14408	41	Q01629	IFM2_HUMAN	T	21;41;41	ENSP00000434443:M21T;ENSP00000382714:M41T	ENSP00000327996:M41T	M	+	2	0	IFITM2	298314	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-2.620000	0.00879	-0.998000	0.03446	-3.056000	0.00068	ATG	.	.	weak		0.607	IFITM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383591.1	NM_006435	
MUC17	140453	hgsc.bcm.edu	37	7	100680438	100680438	+	Missense_Mutation	SNP	G	G	C	rs112926140		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100680438G>C	ENST00000306151.4	+	3	5805	c.5741G>C	c.(5740-5742)aGc>aCc	p.S1914T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1914	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)					GCTGACGGTAGCAGCATGCCA	0.493																																					p.S1914T		Atlas-SNP	.											MUC17,right_upper_lobe,carcinoma,+1,1	MUC17	804	1	0			c.G5741C						scavenged	.						249.0	250.0	250.0					7																	100680438		2203	4300	6503	SO:0001583	missense	140453	exon3			ACGGTAGCAGCAT	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.5741G>C	7.37:g.100680438G>C	ENSP00000302716:p.Ser1914Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	136	5	0.0367647	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.074	-1.195664	0.01594	.	.	ENSG00000169876	ENST00000306151	T	0.02498	4.27	1.18	-2.36	0.06663	.	.	.	.	.	T	0.00998	0.0033	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41610	-0.9499	9	0.02654	T	1	.	1.2251	0.01932	0.1506:0.3181:0.2997:0.2316	.	1914	Q685J3	MUC17_HUMAN	T	1914	ENSP00000302716:S1914T	ENSP00000302716:S1914T	S	+	2	0	MUC17	100467158	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	-0.876000	0.04201	-3.962000	0.00087	-1.848000	0.00571	AGC	A|0.001;G|0.999	.	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ZNF285	26974	hgsc.bcm.edu	37	19	44891126	44891126	+	Silent	SNP	T	T	A	rs553045966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44891126T>A	ENST00000330997.4	-	4	1345	c.1281A>T	c.(1279-1281)ccA>ccT	p.P427P	ZNF285_ENST00000591679.1_Silent_p.P434P|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Silent_p.P427P	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	427					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.P427P(1)		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						CACACCTATATGGTTTCTCCC	0.483																																					p.P427P		Atlas-SNP	.											ZNF285,NS,carcinoma,0,1	ZNF285	86	1	1	Substitution - coding silent(1)	prostate(1)	c.A1281T						scavenged	.						62.0	59.0	60.0					19																	44891126		2203	4300	6503	SO:0001819	synonymous_variant	26974	exon4			CCTATATGGTTTC	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.1281A>T	19.37:g.44891126T>A		Somatic	85	2	0.0235294		WXS	Illumina HiSeq	Phase_I	86	2	0.0232558	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Silent	SNP	ENST00000330997.4	37	CCDS12638.1																																																																																			.	.	none		0.483	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
ZRANB2	9406	hgsc.bcm.edu	37	1	71538191	71538191	+	Silent	SNP	A	A	G	rs11556475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:71538191A>G	ENST00000370920.3	-	5	643	c.342T>C	c.(340-342)taT>taC	p.Y114Y	ZRANB2_ENST00000254821.6_Silent_p.Y114Y	NM_203350.2	NP_976225.1	O95218	ZRAB2_HUMAN	zinc finger, RAN-binding domain containing 2	114					mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|stomach(1)	15						CTCTTTCTATATATTCAACAT	0.284													A|||	355	0.0708866	0.1589	0.0692	5008	,	,		15666	0.0		0.0855	False		,,,				2504	0.0112				p.Y114Y		Atlas-SNP	.											.	ZRANB2	75	.	0			c.T342C						PASS	.	A	,	691,3711	287.5+/-279.3	42,607,1552	65.0	69.0	68.0		342,342	0.3	1.0	1	dbSNP_120	68	725,7857	176.2+/-226.1	36,653,3602	no	coding-synonymous,coding-synonymous	ZRANB2	NM_005455.4,NM_203350.2	,	78,1260,5154	GG,GA,AA		8.4479,15.6974,10.9057	,	114/321,114/331	71538191	1416,11568	2201	4291	6492	SO:0001819	synonymous_variant	9406	exon5			TTCTATATATTCA	AF065391	CCDS659.1, CCDS660.1	1p31	2008-02-05	2006-06-28	2006-06-28	ENSG00000132485	ENSG00000132485		"""Zinc fingers, RAN-binding domain containing"""	13058	protein-coding gene	gene with protein product		604347	"""zinc finger protein 265"""	ZNF265		9931435	Standard	NM_005455		Approved	ZIS, ZIS1, ZIS2	uc001dft.3	O95218	OTTHUMG00000009660	ENST00000370920.3:c.342T>C	1.37:g.71538191A>G		Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	324	153	0.472222	NM_203350	D3DQ75|Q53GS3|Q59F92|Q5VV33|Q5VV34|Q8IXN6|Q9UP63	Silent	SNP	ENST00000370920.3	37	CCDS659.1																																																																																			A|0.898;G|0.102	0.102	strong		0.284	ZRANB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026636.1	NM_203350	
CD33	945	hgsc.bcm.edu	37	19	51738920	51738920	+	Missense_Mutation	SNP	T	T	C	rs61736475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51738920T>C	ENST00000262262.4	+	6	934	c.913T>C	c.(913-915)Tca>Cca	p.S305P	CD33_ENST00000421133.2_Missense_Mutation_p.S178P|CD33_ENST00000391796.3_Missense_Mutation_p.S305P|CD33_ENST00000436584.2_Missense_Mutation_p.S178P	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	305					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	TACCACAGGGTCAGCCTCCCC	0.597													N|||	525	0.104832	0.3472	0.0533	5008	,	,		16396	0.002		0.0179	False		,,,				2504	0.0092				p.S305P		Atlas-SNP	.											.	CD33	55	.	0			c.T913C						PASS	.	C	PRO/SER,PRO/SER,PRO/SER	1299,3107	688.3+/-405.0	196,907,1100	78.0	68.0	71.0		532,913,913	-5.7	0.0	19	dbSNP_129	71	197,8403	802.2+/-407.3	7,183,4110	yes	missense,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	74,74,74	203,1090,5210	CC,CT,TT		2.2907,29.4825,11.5024	benign,benign,benign	178/238,305/311,305/365	51738920	1496,11510	2203	4300	6503	SO:0001583	missense	945	exon6			ACAGGGTCAGCCT	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.913T>C	19.37:g.51738920T>C	ENSP00000262262:p.Ser305Pro	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	186	0.08516483516483517	150	0.3048780487804878	23	0.06353591160220995	2	0.0034965034965034965	11	0.014511873350923483	C	0.048	-1.260470	0.01445	0.294825	0.022907	ENSG00000105383	ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796	T;T;T;T	0.38401	1.14;2.31;1.31;2.21	3.79	-5.74	0.02391	.	.	.	.	.	T	0.00012	0.0000	N	0.01751	-0.74	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	0.40869	-0.9540	8	0.20519	T	0.43	.	5.2162	0.15344	0.5563:0.1886:0.0:0.2551	rs61736475	178;305;305	C9JEN7;F8WAL2;P20138	.;.;CD33_HUMAN	P	178;305;178;305	ENSP00000403331:S178P;ENSP00000262262:S305P;ENSP00000410126:S178P;ENSP00000375673:S305P	ENSP00000262262:S305P	S	+	1	0	CD33	56430732	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.791000	0.00767	-1.363000	0.02164	-0.213000	0.12676	TCA	T|0.895;C|0.105	0.105	strong		0.597	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
MME	4311	hgsc.bcm.edu	37	3	154802114	154802114	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:154802114A>G	ENST00000460393.1	+	2	278	c.158A>G	c.(157-159)gAt>gGt	p.D53G	MME_ENST00000382989.3_Missense_Mutation_p.D53G|MME_ENST00000360490.2_Missense_Mutation_p.D53G|MME_ENST00000493237.1_Missense_Mutation_p.D53G|MME_ENST00000492661.1_Missense_Mutation_p.D53G|MME_ENST00000462745.1_Missense_Mutation_p.D53G	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	53					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)	GCAACCTACGATGGTGAGTTA	0.468																																					p.D53G		Atlas-SNP	.											MME,NS,carcinoma,+1,1	MME	133	1	0			c.A158G						scavenged	.						117.0	108.0	111.0					3																	154802114		2203	4300	6503	SO:0001583	missense	4311	exon2			CCTACGATGGTGA		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.158A>G	3.37:g.154802114A>G	ENSP00000418525:p.Asp53Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	92	3	0.0326087	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	A	13.28	2.191233	0.38707	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000481828;ENST00000382989;ENST00000462745;ENST00000493237;ENST00000360490;ENST00000491026;ENST00000473730;ENST00000462837	D;D;D;D;D;D;D;D;D	0.92446	-1.61;-1.61;-1.96;-1.61;-1.61;-1.61;-3.04;-3.04;-2.63	5.24	5.24	0.73138	.	1.331950	0.06575	U	0.749290	D	0.87140	0.6103	L	0.34521	1.04	0.43283	D	0.995259	P	0.36483	0.555	B	0.24848	0.056	T	0.76027	-0.3109	10	0.30854	T	0.27	-31.3554	13.6699	0.62418	1.0:0.0:0.0:0.0	.	53	P08473	NEP_HUMAN	G	53	ENSP00000420389:D53G;ENSP00000418525:D53G;ENSP00000420101:D53G;ENSP00000419653:D53G;ENSP00000417079:D53G;ENSP00000353679:D53G;ENSP00000418791:D53G;ENSP00000420542:D53G;ENSP00000417595:D53G	ENSP00000353679:D53G	D	+	2	0	MME	156284808	1.000000	0.71417	0.948000	0.38648	0.440000	0.31957	4.766000	0.62279	2.109000	0.64355	0.460000	0.39030	GAT	.	.	none		0.468	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902	
RASGRF2	5924	hgsc.bcm.edu	37	5	80419576	80419576	+	Silent	SNP	A	A	C	rs34593336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80419576A>C	ENST00000265080.4	+	16	2653	c.2586A>C	c.(2584-2586)cgA>cgC	p.R862R		NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	862					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)			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)		TCCGCTATCGACAGCCTGGAG	0.517													C|||	370	0.0738818	0.2655	0.0259	5008	,	,		17367	0.0		0.001	False		,,,				2504	0.0				p.R862R		Atlas-SNP	.											.	RASGRF2	165	.	0			c.A2586C						PASS	.	C		1107,3299	718.5+/-408.8	144,819,1240	72.0	62.0	65.0		2586	2.0	1.0	5	dbSNP_126	65	27,8573	818.0+/-406.9	1,25,4274	no	coding-synonymous	RASGRF2	NM_006909.1		145,844,5514	CC,CA,AA		0.314,25.1248,8.7191		862/1238	80419576	1134,11872	2203	4300	6503	SO:0001819	synonymous_variant	5924	exon16			CTATCGACAGCCT	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.2586A>C	5.37:g.80419576A>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	123	60	0.487805	NM_006909	B9EG89|Q9UK56	Silent	SNP	ENST00000265080.4	37	CCDS4052.1																																																																																			A|0.922;C|0.078	0.078	strong		0.517	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909	
MIB2	142678	hgsc.bcm.edu	37	1	1562536	1562536	+	Silent	SNP	G	G	A	rs11544452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1562536G>A	ENST00000357210.4	+	11	1713	c.1497G>A	c.(1495-1497)gcG>gcA	p.A499A	MIB2_ENST00000360522.4_Silent_p.A464A|MIB2_ENST00000378708.1_Silent_p.A405A|MIB2_ENST00000378712.1_Silent_p.A376A|MIB2_ENST00000505820.2_Silent_p.A556A|MIB2_ENST00000518681.1_Silent_p.A491A|MIB2_ENST00000355826.5_Silent_p.A542A|MIB2_ENST00000520777.1_Silent_p.A552A|MIB2_ENST00000504599.1_Silent_p.A455A|MIB2_ENST00000378710.3_Silent_p.A463A	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	499					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)		TGGAGGTGGCGCTGGGTAACG	0.687													.|||	707	0.141174	0.0061	0.2896	5008	,	,		13564	0.1746		0.1362	False		,,,				2504	0.1892				p.A556A		Atlas-SNP	.											.	MIB2	62	.	0			c.G1668A						PASS	.	G	,,,,	105,3907		3,99,1904	13.0	18.0	16.0		1656,1626,1473,1128,1668	-9.1	0.3	1	dbSNP_120	16	1011,7311		45,921,3195	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MIB2	NM_001170686.1,NM_001170687.1,NM_001170688.1,NM_001170689.1,NM_080875.2	,,,,	48,1020,5099	AA,AG,GG		12.1485,2.6171,9.0482	,,,,	552/1067,542/1057,491/1006,376/754,556/1071	1562536	1116,11218	2006	4161	6167	SO:0001819	synonymous_variant	142678	exon11			GGTGGCGCTGGGT	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.1497G>A	1.37:g.1562536G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	118	67	0.567797	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	Silent	SNP	ENST00000357210.4	37		305	0.13965201465201466	4	0.008130081300813009	75	0.20718232044198895	114	0.1993006993006993	112	0.14775725593667546	G	3.666	-0.068494	0.07228	0.026171	0.121485	ENSG00000197530	ENST00000514234	T	0.53640	0.61	4.59	-9.07	0.00724	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999995995	.	.	.	.	.	.	T	0.06110	-1.0845	6	0.87932	D	0	-18.8304	2.0692	0.03609	0.2581:0.3798:0.0945:0.2676	rs11544452	.	.	.	T	315	ENSP00000427680:A315T	ENSP00000427680:A315T	A	+	1	0	MIB2	1552399	0.000000	0.05858	0.254000	0.24359	0.884000	0.51177	-2.937000	0.00685	-1.519000	0.01775	0.455000	0.32223	GCT	G|0.860;A|0.140	0.140	strong		0.687	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875	
NUP133	55746	hgsc.bcm.edu	37	1	229622162	229622162	+	Silent	SNP	A	A	G	rs1065675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229622162A>G	ENST00000261396.3	-	11	1547	c.1456T>C	c.(1456-1458)Ttg>Ctg	p.L486L	NUP133_ENST00000537506.1_Silent_p.L470L	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	486					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 organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|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)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.L486L(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GACCCTTCCAAGTCTTCTGCC	0.378													G|||	1521	0.303714	0.5809	0.3285	5008	,	,		19446	0.1607		0.2097	False		,,,				2504	0.1554				p.L486L		Atlas-SNP	.											NUP133,NS,carcinoma,0,1	NUP133	111	1	1	Substitution - coding silent(1)	stomach(1)	c.T1456C						PASS	.	G		2316,2090	569.8+/-382.7	600,1116,487	105.0	110.0	108.0		1456	-1.6	0.1	1	dbSNP_86	108	1864,6736	729.8+/-406.7	201,1462,2637	no	coding-synonymous	NUP133	NM_018230.2		801,2578,3124	GG,GA,AA		21.6744,47.4353,32.139		486/1157	229622162	4180,8826	2203	4300	6503	SO:0001819	synonymous_variant	55746	exon11			CTTCCAAGTCTTC		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1456T>C	1.37:g.229622162A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	37	CCDS1579.1																																																																																			A|0.690;G|0.310	0.310	strong		0.378	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
BLM	641	hgsc.bcm.edu	37	15	91346923	91346923	+	Silent	SNP	C	C	A	rs2227934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91346923C>A	ENST00000355112.3	+	18	3649	c.3531C>A	c.(3529-3531)gcC>gcA	p.A1177A	BLM_ENST00000560509.1_Intron|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1177					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			GAAATAAAGCCCAAACTGTAC	0.313			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome				C|||	667	0.133187	0.1309	0.1052	5008	,	,		18805	0.1875		0.165	False		,,,				2504	0.0675				p.A1177A		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.C3531A						PASS	.	C		546,3850	246.2+/-254.9	28,490,1680	88.0	86.0	87.0		3531	1.2	0.3	15	dbSNP_98	87	1568,7028	291.1+/-300.1	142,1284,2872	no	coding-synonymous	BLM	NM_000057.2		170,1774,4552	AA,AC,CC		18.241,12.4204,16.2716		1177/1418	91346923	2114,10878	2198	4298	6496	SO:0001819	synonymous_variant	641	exon18	Familial Cancer Database		TAAAGCCCAAACT	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3531C>A	15.37:g.91346923C>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	37	CCDS10363.1																																																																																			C|0.848;A|0.152	0.152	strong		0.313	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
SPAG7	9552	hgsc.bcm.edu	37	17	4863540	4863540	+	Missense_Mutation	SNP	T	T	C	rs73343382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4863540T>C	ENST00000206020.3	-	4	383	c.316A>G	c.(316-318)Atc>Gtc	p.I106V	SPAG7_ENST00000575142.1_Missense_Mutation_p.I95V|SPAG7_ENST00000573366.1_Missense_Mutation_p.I55V	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	106	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						TTTTTGAAGATCATGACATAG	0.488													T|||	154	0.0307508	0.1127	0.0058	5008	,	,		19237	0.0		0.001	False		,,,				2504	0.0				p.I106V		Atlas-SNP	.											.	SPAG7	22	.	0			c.A316G						PASS	.	T	VAL/ILE	363,3671		20,323,1674	75.0	79.0	78.0		316	5.3	1.0	17	dbSNP_130	78	4,8376		0,4,4186	yes	missense	SPAG7	NM_004890.2	29	20,327,5860	CC,CT,TT		0.0477,8.9985,2.9563	benign	106/228	4863540	367,12047	2017	4190	6207	SO:0001583	missense	9552	exon4			TGAAGATCATGAC	AF047437	CCDS42240.1	17p13.2	2008-07-18				ENSG00000091640			11216	protein-coding gene	gene with protein product		610056				9653160	Standard	NM_004890		Approved	FSA-1, ACRP, MGC20134	uc002gae.3	O75391		ENST00000206020.3:c.316A>G	17.37:g.4863540T>C	ENSP00000206020:p.Ile106Val	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	183	95	0.519126	NM_004890	Q96EU5	Missense_Mutation	SNP	ENST00000206020.3	37	CCDS42240.1	46	0.021062271062271064	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	0.871	-0.732127	0.03135	0.089985	4.77E-4	ENSG00000091640	ENST00000206020	T	0.43688	0.94	5.3	5.3	0.74995	Single-stranded nucleic acid binding R3H (3);	0.117351	0.56097	D	0.000028	T	0.00967	0.0032	N	0.25789	0.76	0.41244	D	0.986669	B	0.10296	0.003	B	0.12837	0.008	T	0.02610	-1.1134	10	0.02654	T	1	-4.764	13.2379	0.59979	0.0:0.0:0.0:1.0	.	106	O75391	SPAG7_HUMAN	V	106	ENSP00000206020:I106V	ENSP00000206020:I106V	I	-	1	0	SPAG7	4804263	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.809000	0.38922	2.225000	0.72522	0.533000	0.62120	ATC	T|0.978;C|0.022	0.022	strong		0.488	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890	
TOPBP1	11073	hgsc.bcm.edu	37	3	133327457	133327457	+	Silent	SNP	T	T	C	rs1051772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	121	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	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	
PKD1L1	168507	hgsc.bcm.edu	37	7	47924233	47924233	+	Silent	SNP	G	G	A	rs79566365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47924233G>A	ENST00000289672.2	-	19	3278	c.3228C>T	c.(3226-3228)gaC>gaT	p.D1076D		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1076	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						CTTCTTGAATGTCACTGTAAT	0.448													A|||	194	0.038738	0.1377	0.0101	5008	,	,		20921	0.0		0.004	False		,,,				2504	0.001				p.D1076D		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C3228T						PASS	.	A		641,3765	767.0+/-413.5	47,547,1609	147.0	131.0	136.0		3228	-4.3	0.0	7	dbSNP_132	136	85,8515	815.6+/-407.0	1,83,4216	no	coding-synonymous	PKD1L1	NM_138295.3		48,630,5825	AA,AG,GG		0.9884,14.5483,5.582		1076/2850	47924233	726,12280	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon19			TTGAATGTCACTG	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.3228C>T	7.37:g.47924233G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	92	36	0.391304	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			G|0.951;A|0.049	0.049	strong		0.448	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
C6orf195	154386	hgsc.bcm.edu	37	6	2624053	2624053	+	Missense_Mutation	SNP	T	T	A	rs17135340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:2624053T>A	ENST00000296847.3	-	3	527	c.4A>T	c.(4-6)Atc>Ttc	p.I2F		NM_152554.2	NP_689767.2	Q96MT4	CF195_HUMAN	chromosome 6 open reading frame 195	2			I -> F (in dbSNP:rs17135340). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							cervix(1)|endometrium(1)|lung(2)|skin(1)	5	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				AGTGGATAGATCATCAGGGAC	0.458													T|||	757	0.151158	0.0613	0.1182	5008	,	,		21846	0.2679		0.1909	False		,,,				2504	0.135				p.I2F		Atlas-SNP	.											.	C6orf195	10	.	0			c.A4T						PASS	.	T	PHE/ILE	312,3514		15,282,1616	39.0	39.0	39.0		4	-2.3	0.0	6	dbSNP_123	39	1642,6620		167,1308,2656	yes	missense	C6orf195	NM_152554.2	21	182,1590,4272	AA,AT,TT		19.8741,8.1547,16.1648	possibly-damaging	2/128	2624053	1954,10134	1913	4131	6044	SO:0001583	missense	154386	exon3			GATAGATCATCAG	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.4A>T	6.37:g.2624053T>A	ENSP00000296847:p.Ile2Phe	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	106	59	0.556604	NM_152554	Q3SY08|Q3SY09|Q3SY10|Q5TAW4	Missense_Mutation	SNP	ENST00000296847.3	37	CCDS43416.1	389	0.17811355311355312	26	0.052845528455284556	51	0.1408839779005525	156	0.2727272727272727	156	0.20580474934036938	T	2.746	-0.261142	0.05791	0.081547	0.198741	ENSG00000164385	ENST00000296847	T	0.38401	1.14	1.14	-2.28	0.06826	.	.	.	.	.	T	0.03695	0.0105	N	0.08118	0	0.80722	P	0.0	P	0.42078	0.77	B	0.27262	0.078	T	0.25916	-1.0118	8	0.87932	D	0	.	2.3353	0.04246	0.0:0.2349:0.2998:0.4653	rs17135340;rs52801339;rs17135340	2	Q96MT4	CF195_HUMAN	F	2	ENSP00000296847:I2F	ENSP00000296847:I2F	I	-	1	0	C6orf195	2569052	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-1.464000	0.02359	-0.811000	0.04369	0.402000	0.26972	ATC	A|0.169;N|0.000	0.169	strong		0.458	C6orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039633.1	NM_152554	
SMG6	23293	hgsc.bcm.edu	37	17	2186100	2186100	+	Silent	SNP	C	C	T	rs749240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2186100C>T	ENST00000263073.6	-	8	2552	c.2502G>A	c.(2500-2502)caG>caA	p.Q834Q	SMG6_ENST00000544865.1_Silent_p.Q803Q	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	834					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						CTTTCCGCCACTGGTCAGGGC	0.502													T|||	2135	0.426318	0.6914	0.3573	5008	,	,		22864	0.2371		0.3618	False		,,,				2504	0.3783				p.Q834Q	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.G2502A						PASS	.	T	,	2686,1720	517.8+/-369.5	821,1044,338	126.0	119.0	121.0		2409,2502	-10.5	0.2	17	dbSNP_86	121	3004,5596	664.9+/-402.2	542,1920,1838	no	coding-synonymous,coding-synonymous	SMG6	NM_001170957.1,NM_017575.4	,	1363,2964,2176	TT,TC,CC		34.9302,39.0377,43.749	,	803/1389,834/1420	2186100	5690,7316	2203	4300	6503	SO:0001819	synonymous_variant	23293	exon8			CCGCCACTGGTCA	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.2502G>A	17.37:g.2186100C>T		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	276	274	0.992754	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	37	CCDS11016.1																																																																																			C|0.573;N|0.001	.	strong		0.502	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
DBNDD2	55861	hgsc.bcm.edu	37	20	44038574	44038574	+	Missense_Mutation	SNP	A	A	G	rs17856031|rs1127497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44038574A>G	ENST00000372720.3	+	4	805	c.574A>G	c.(574-576)Atg>Gtg	p.M192V	TP53TG5_ENST00000494455.1_5'Flank|DBNDD2_ENST00000372712.2_Missense_Mutation_p.M94V|DBNDD2_ENST00000372710.3_Missense_Mutation_p.M196V|DBNDD2_ENST00000372722.3_3'UTR|DBNDD2_ENST00000372723.3_Missense_Mutation_p.M94V|DBNDD2_ENST00000357275.2_Missense_Mutation_p.M94V|SYS1-DBNDD2_ENST00000452133.1_3'UTR|DBNDD2_ENST00000360981.4_Missense_Mutation_p.M94V|DBNDD2_ENST00000372717.1_3'UTR|SYS1-DBNDD2_ENST00000475242.1_3'UTR	NM_018478.3	NP_060948.3	Q9BQY9	DBND2_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 2	192				M -> V (in Ref. 1; AAF67656, 2; AAM77463, 3; BAA91235, 6; EAW75854/EAW75848 and 7; AAH12818/AAH01105). {ECO:0000305}.	negative regulation of protein kinase activity (GO:0006469)	cytoplasm (GO:0005737)				breast(1)|lung(2)	3		Myeloproliferative disorder(115;0.0122)				CTGGGCAGGGATGGACAACCA	0.547													G|||	3812	0.761182	0.9039	0.7738	5008	,	,		16863	0.5109		0.7803	False		,,,				2504	0.7975				p.M196V		Atlas-SNP	.											.	DBNDD2	30	.	0			c.A586G						PASS	.	G	VAL/MET,,VAL/MET,,VAL/MET,,VAL/MET,VAL/MET,VAL/MET	2963,343		1327,309,17	29.0	33.0	32.0		280,,280,,586,,280,280,574	2.6	1.0	20	dbSNP_86	32	5434,1304		2200,1034,135	yes	missense,utr-3,missense,utr-3,missense,utr-3,missense,missense,missense	DBNDD2	NM_001048221.2,NM_001048222.2,NM_001048223.2,NM_001048224.2,NM_001048225.2,NM_001048226.2,NM_001197139.1,NM_001197140.1,NM_018478.3	21,,21,,21,,21,21,21	3527,1343,152	GG,GA,AA		19.3529,10.3751,16.3978	benign,,benign,,benign,,benign,benign,benign	94/162,,94/162,,196/264,,94/162,94/162,192/260	44038574	8397,1647	1653	3369	5022	SO:0001583	missense	55861	exon3			GCAGGGATGGACA	AF220191	CCDS42880.1, CCDS42881.1, CCDS56193.1, CCDS56194.1	20q13.12	2007-07-23	2006-04-04	2006-04-04	ENSG00000244274	ENSG00000244274			15881	protein-coding gene	gene with protein product		611453	"""chromosome 20 open reading frame 35"""	C20orf35			Standard	NM_001048225		Approved	HSMNP1	uc002xof.3	Q9BQY9	OTTHUMG00000032576	ENST00000372720.3:c.574A>G	20.37:g.44038574A>G	ENSP00000361805:p.Met192Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_001048225	Q331S6|Q5QPV4|Q5QPV6|Q9BQZ0|Q9BVL1|Q9H1F6|Q9NWZ0|Q9NY07|Q9NZ31	Missense_Mutation	SNP	ENST00000372720.3	37	CCDS56193.1	1609	0.7367216117216118	445	0.9044715447154471	277	0.7651933701657458	289	0.5052447552447552	598	0.7889182058047494	G	11.60	1.685725	0.29962	0.896249	0.806471	ENSG00000244274	ENST00000372723;ENST00000357275;ENST00000372720;ENST00000360981;ENST00000372712;ENST00000372710	T;T;T;T;T;T	0.28069	1.69;1.69;1.65;1.69;1.69;1.63	5.63	2.6	0.31112	.	0.423208	0.22782	N	0.055701	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	0.18903	-1.0322	9	0.15952	T	0.53	.	6.8441	0.23979	0.1488:0.2697:0.5815:0.0	rs1127497;rs2243553;rs3183556;rs11541739;rs17435039;rs52823093;rs1127497	192	Q9BQY9	DBND2_HUMAN	V	94;94;192;94;94;196	ENSP00000361808:M94V;ENSP00000349822:M94V;ENSP00000361805:M192V;ENSP00000354250:M94V;ENSP00000361797:M94V;ENSP00000361795:M196V	ENSP00000349822:M94V	M	+	1	0	DBNDD2	43471988	0.498000	0.26075	0.977000	0.42913	0.741000	0.42261	0.144000	0.16135	0.058000	0.16222	-0.279000	0.10071	ATG	A|0.252;G|0.748	0.748	strong		0.547	DBNDD2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079438.1	NM_018478	
ASB16	92591	hgsc.bcm.edu	37	17	42248205	42248205	+	Silent	SNP	C	C	T	rs56265171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42248205C>T	ENST00000293414.1	+	1	132	c.48C>T	c.(46-48)ctC>ctT	p.L16L		NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	16					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TGCGCTCTCTCCGCCTGCAGC	0.697													C|||	168	0.0335463	0.1203	0.0115	5008	,	,		15859	0.0		0.001	False		,,,				2504	0.0				p.L16L		Atlas-SNP	.											.	ASB16	34	.	0			c.C48T						PASS	.	C		417,3989	196.4+/-220.7	17,383,1803	36.0	34.0	35.0		48	1.8	1.0	17	dbSNP_129	35	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	ASB16	NM_080863.4		17,388,6098	TT,TC,CC		0.0581,9.4644,3.2447		16/454	42248205	422,12584	2203	4300	6503	SO:0001819	synonymous_variant	92591	exon1			CTCTCTCCGCCTG	AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"""Ankyrin repeat domain containing"""	19768	protein-coding gene	gene with protein product		615056	"""ankyrin repeat and SOCS box-containing 16"""			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.48C>T	17.37:g.42248205C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	190	103	0.542105	NM_080863	B2RBC0|Q8WXK0	Silent	SNP	ENST00000293414.1	37	CCDS11478.1																																																																																			C|0.967;T|0.033	0.033	strong		0.697	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1		
FREM1	158326	hgsc.bcm.edu	37	9	14824088	14824088	+	Missense_Mutation	SNP	T	T	C	rs7864984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14824088T>C	ENST00000380880.3	-	12	2887	c.2104A>G	c.(2104-2106)Atg>Gtg	p.M702V	FREM1_ENST00000380881.4_Missense_Mutation_p.M703V|FREM1_ENST00000422223.2_Missense_Mutation_p.M702V			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	702					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)		CTGTCCACCATAAATAATTTC	0.393													T|||	185	0.0369409	0.1309	0.0086	5008	,	,		20998	0.0		0.004	False		,,,				2504	0.002				p.M702V		Atlas-SNP	.											.	FREM1	261	.	0			c.A2104G						PASS	.	T	VAL/MET	360,3416		13,334,1541	63.0	60.0	61.0		2104	0.8	0.8	9	dbSNP_116	61	16,8218		0,16,4101	yes	missense	FREM1	NM_144966.5	21	13,350,5642	CC,CT,TT		0.1943,9.5339,3.1307	benign	702/2180	14824088	376,11634	1888	4117	6005	SO:0001583	missense	158326	exon13			CCACCATAAATAA	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.2104A>G	9.37:g.14824088T>C	ENSP00000370262:p.Met702Val	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	55	0.025183150183150184	51	0.10365853658536585	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	T	7.670	0.686751	0.14973	0.095339	0.001943	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.25414	1.8;1.8;1.8	5.83	0.775	0.18527	.	0.246267	0.48767	D	0.000171	T	0.00580	0.0019	M	0.71581	2.175	0.28563	N	0.911019	B	0.22211	0.066	B	0.17098	0.017	T	0.20538	-1.0272	10	0.17832	T	0.49	-9.8199	8.6558	0.34062	0.1862:0.0:0.3315:0.4823	rs7864984;rs57027040;rs7864984	702	Q5H8C1	FREM1_HUMAN	V	703;702;702	ENSP00000370263:M703V;ENSP00000412940:M702V;ENSP00000370262:M702V	ENSP00000370257:M705V	M	-	1	0	FREM1	14814088	0.995000	0.38212	0.842000	0.33263	0.462000	0.32619	0.335000	0.19806	-0.394000	0.07727	-3.035000	0.00072	ATG	T|0.978;C|0.022	0.022	strong		0.393	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
NLN	57486	hgsc.bcm.edu	37	5	65054587	65054587	+	Missense_Mutation	SNP	G	G	A	rs34339013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:65054587G>A	ENST00000380985.5	+	2	413	c.235G>A	c.(235-237)Ggt>Agt	p.G79S	NLN_ENST00000502464.1_Intron	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	79			G -> S (in dbSNP:rs34339013).			mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		TGGAATGCTCGGTATTGAGGA	0.423													G|||	132	0.0263578	0.093	0.0115	5008	,	,		16846	0.0		0.001	False		,,,				2504	0.0				p.G79S		Atlas-SNP	.											.	NLN	51	.	0			c.G235A						PASS	.	G	SER/GLY	321,4085	171.9+/-202.1	14,293,1896	138.0	122.0	128.0		235	-1.6	0.0	5	dbSNP_126	128	0,8600		0,0,4300	yes	missense	NLN	NM_020726.4	56	14,293,6196	AA,AG,GG		0.0,7.2855,2.4681	benign	79/705	65054587	321,12685	2203	4300	6503	SO:0001583	missense	57486	exon2			ATGCTCGGTATTG	AJ300837	CCDS3989.1	5q12.3	2008-02-05	2005-03-31		ENSG00000123213	ENSG00000123213	3.4.24.16		16058	protein-coding gene	gene with protein product		611530	"""angiotensin binding protein"""	AGTBP		10574462	Standard	NM_020726		Approved	KIAA1226	uc003juf.3	Q9BYT8	OTTHUMG00000097803	ENST00000380985.5:c.235G>A	5.37:g.65054587G>A	ENSP00000370372:p.Gly79Ser	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_020726	Q9ULJ4	Missense_Mutation	SNP	ENST00000380985.5	37	CCDS3989.1	32	0.014652014652014652	27	0.054878048780487805	5	0.013812154696132596	0	0.0	0	0.0	G	8.053	0.766380	0.15983	0.072855	0.0	ENSG00000123213	ENST00000380985;ENST00000340159	T	0.06933	3.24	5.5	-1.6	0.08426	Neurolysin/Thimet oligopeptidase, N-terminal (1);	0.775582	0.12614	N	0.453646	T	0.00241	0.0007	N	0.01352	-0.895	0.09310	N	0.999999	B;B	0.27679	0.001;0.185	B;B	0.14578	0.001;0.011	T	0.44862	-0.9300	10	0.20519	T	0.43	-0.0913	12.5135	0.56019	0.3907:0.0:0.6093:0.0	rs34339013	79;79	Q9BYT8;Q9BQD0	NEUL_HUMAN;.	S	79	ENSP00000370372:G79S	ENSP00000339283:G79S	G	+	1	0	NLN	65090343	0.024000	0.19004	0.001000	0.08648	0.784000	0.44337	0.931000	0.28871	-0.729000	0.04875	-0.880000	0.02959	GGT	G|0.973;A|0.027	0.027	strong		0.423	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1271321	1271321	+	Missense_Mutation	SNP	C	C	G	rs2943517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1271321C>G	ENST00000529681.1	+	31	13269	c.13211C>G	c.(13210-13212)gCc>gGc	p.A4404G	MUC5B_ENST00000447027.1_Missense_Mutation_p.A4407G|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4404	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.		A -> G (in dbSNP:rs2943517). {ECO:0000269|PubMed:9013550}.		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)		ACAACTGCAGCCACTGGCCCC	0.647													-|||	2263	0.451877	0.3071	0.5447	5008	,	,		17919	0.629		0.4195	False		,,,				2504	0.4325				p.A4404G		Atlas-SNP	.											MUC5B,caecum,carcinoma,+1,2	MUC5B	473	2	0			c.C13211G						PASS	.						51.0	64.0	60.0					11																	1271321		1918	4115	6033	SO:0001583	missense	727897	exon31			CTGCAGCCACTGG	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.13211C>G	11.37:g.1271321C>G	ENSP00000436812:p.Ala4404Gly	Somatic	345	0	0		WXS	Illumina HiSeq	Phase_I	353	185	0.524079	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	-	4.216	0.038984	0.08148	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000535652	T;T	0.17370	2.28;2.47	2.36	-0.666	0.11399	.	.	.	.	.	T	0.18215	0.0437	L	0.54323	1.7	0.80722	P	0.0	P;P	0.51933	0.86;0.949	B;P	0.46825	0.431;0.528	T	0.20605	-1.0270	8	0.87932	D	0	.	5.3307	0.15930	0.0:0.5875:0.0:0.4125	rs2943517	4877;4407	A7Y9J9;E9PBJ0	.;.	G	4404;4407;4348;4254;183	ENSP00000436812:A4404G;ENSP00000415793:A4407G	ENSP00000343037:A4348G	A	+	2	0	MUC5B	1227897	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.172000	0.09868	-0.552000	0.06167	-0.706000	0.03657	GCC	C|0.633;G|0.367	0.367	strong		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
TEX38	374973	hgsc.bcm.edu	37	1	47138819	47138819	+	Missense_Mutation	SNP	T	T	G	rs614486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47138819T>G	ENST00000334122.4	+	2	419	c.312T>G	c.(310-312)gaT>gaG	p.D104E	TEX38_ENST00000569393.1_Missense_Mutation_p.D158E|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14-AS1_ENST00000418985.1_RNA|ATPAF1_ENST00000525633.1_Intron|TEX38_ENST00000564373.1_Missense_Mutation_p.D50E|EFCAB14_ENST00000544071.1_Intron|TEX38_ENST00000415500.1_Missense_Mutation_p.D28E	NM_001145474.2	NP_001138946.1	Q6PEX7	TEX38_HUMAN	testis expressed 38	104			D -> E (in dbSNP:rs614486). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)											TTCTGTGGGATTTGGACATCC	0.612													G|||	2701	0.539337	0.6513	0.4625	5008	,	,		19138	0.7996		0.3121	False		,,,				2504	0.408				p.D104E		Atlas-SNP	.											.	.	.	.	0			c.T312G						PASS	.	G	GLU/ASP	817,567		235,347,110	69.0	70.0	70.0		312	1.4	0.1	1	dbSNP_83	70	868,2314		102,664,825	yes	missense	ATPAF1-AS1	NM_001145474.2	45	337,1011,935	GG,GT,TT		27.2784,40.9682,36.9032	benign	104/207	47138819	1685,2881	692	1591	2283	SO:0001583	missense	374973	exon2			GTGGGATTTGGAC		CCDS57999.1, CCDS72780.1, CCDS72781.1	1p33	2012-10-12	2012-10-12	2012-10-12	ENSG00000186118	ENSG00000186118			29589	protein-coding gene	gene with protein product	"""testis highly expressed protein 4"""		"""chromosome 1 open reading frame 223"", ""ATPAF1 antisense RNA 1 (non-protein coding)"", ""ATPAF1 antisense RNA 1"""	C1orf223, ATPAF1-AS1		12477932	Standard	XM_005270845		Approved	LOC374973, THEG4	uc001cqj.3	Q6PEX7	OTTHUMG00000007991	ENST00000334122.4:c.312T>G	1.37:g.47138819T>G	ENSP00000455854:p.Asp104Glu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_001145474	A1A4F8	Missense_Mutation	SNP	ENST00000334122.4	37	CCDS57999.1																																																																																			T|0.461;G|0.539	0.539	strong		0.612	TEX38-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000021929.2	NM_001145474	
KLHL33	123103	hgsc.bcm.edu	37	14	20898058	20898058	+	Silent	SNP	G	G	C	rs79604136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20898058G>C	ENST00000344581.4	-	2	999	c.777C>G	c.(775-777)ccC>ccG	p.P259P		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	259												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)		GGAAGCGTCCGGGGGCAGGCA	0.627													G|||	210	0.0419329	0.0575	0.0288	5008	,	,		18544	0.0813		0.0189	False		,,,				2504	0.0133				p.P259P		Atlas-SNP	.											.	KLHL33	37	.	0			c.C777G						PASS	.	G		77,1307		4,69,619	36.0	42.0	40.0		777	-9.6	0.9	14	dbSNP_132	40	58,3124		1,56,1534	no	coding-synonymous	KLHL33	NM_001109997.2		5,125,2153	CC,CG,GG		1.8228,5.5636,2.9566		259/534	20898058	135,4431	692	1591	2283	SO:0001819	synonymous_variant	123103	exon2			GCGTCCGGGGGCA		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.777C>G	14.37:g.20898058G>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_001109997		Silent	SNP	ENST00000344581.4	37	CCDS53882.1																																																																																			G|0.970;C|0.030	0.030	strong		0.627	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
EPHB1	2047	hgsc.bcm.edu	37	3	134670524	134670524	+	Silent	SNP	C	C	T	rs7644369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:134670524C>T	ENST00000398015.3	+	3	805	c.435C>T	c.(433-435)agC>agT	p.S145S	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	145	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				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						CAGATGAGAGCTTCTCCCAGG	0.498													C|||	2411	0.48143	0.6377	0.5692	5008	,	,		19990	0.2123		0.4394	False		,,,				2504	0.5286				p.S145S		Atlas-SNP	.											.	EPHB1	519	.	0			c.C435T						PASS	.	C		2277,1677		699,879,399	154.0	152.0	153.0		435	4.6	1.0	3	dbSNP_116	153	3757,4657		844,2069,1294	no	coding-synonymous	EPHB1	NM_004441.4		1543,2948,1693	TT,TC,CC		44.6518,42.4127,48.7872		145/985	134670524	6034,6334	1977	4207	6184	SO:0001819	synonymous_variant	2047	exon3			TGAGAGCTTCTCC	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.435C>T	3.37:g.134670524C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	202	200	0.990099	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Silent	SNP	ENST00000398015.3	37	CCDS46921.1																																																																																			C|0.559;T|0.441	0.441	strong		0.498	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
UACA	55075	hgsc.bcm.edu	37	15	70957106	70957106	+	Silent	SNP	A	A	G	rs78551559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70957106A>G	ENST00000322954.6	-	17	4193	c.4008T>C	c.(4006-4008)aaT>aaC	p.N1336N	UACA_ENST00000539319.1_Silent_p.N1227N|UACA_ENST00000379983.2_Silent_p.N1323N|UACA_ENST00000560441.1_Silent_p.N1321N	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1336					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						GGGAAAGGCCATTGAGTGCCT	0.413													A|||	83	0.0165735	0.0605	0.0043	5008	,	,		17428	0.0		0.0	False		,,,				2504	0.0				p.N1336N		Atlas-SNP	.											.	UACA	235	.	0			c.T4008C						PASS	.	A	,	203,4195	126.6+/-163.6	3,197,1999	150.0	127.0	135.0		3969,4008	-4.9	0.0	15	dbSNP_132	135	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	3,198,6296	GG,GA,AA		0.0116,4.6157,1.57	,	1323/1404,1336/1417	70957106	204,12790	2199	4298	6497	SO:0001819	synonymous_variant	55075	exon17			AAGGCCATTGAGT	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.4008T>C	15.37:g.70957106A>G		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	203	101	0.497537	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			A|0.983;G|0.017	0.017	strong		0.413	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
LAMB4	22798	hgsc.bcm.edu	37	7	107743664	107743664	+	Silent	SNP	A	A	G	rs402113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107743664A>G	ENST00000388781.3	-	10	1088	c.1005T>C	c.(1003-1005)aaT>aaC	p.N335N	LAMB4_ENST00000414450.2_Silent_p.N335N|LAMB4_ENST00000418464.1_Silent_p.N335N|LAMB4_ENST00000388780.3_Silent_p.N335N|LAMB4_ENST00000205386.4_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	39	0	0		WXS	Illumina HiSeq	Phase_I	37	24	0.648649	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	
MISP	126353	hgsc.bcm.edu	37	19	757483	757483	+	Silent	SNP	G	G	A	rs35484463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:757483G>A	ENST00000215582.6	+	2	640	c.537G>A	c.(535-537)acG>acA	p.T179T		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	179					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CTCGGTCCACGCCCCTGGAGG	0.652													G|||	94	0.01877	0.0681	0.0058	5008	,	,		16831	0.0		0.0	False		,,,				2504	0.0				p.T179T		Atlas-SNP	.											.	C19orf21	56	.	0			c.G537A						PASS	.	G		220,4166		7,206,1980	19.0	23.0	22.0		537	-5.4	0.0	19	dbSNP_126	22	1,8587		0,1,4293	no	coding-synonymous	C19orf21	NM_173481.2		7,207,6273	AA,AG,GG		0.0116,5.016,1.7034		179/680	757483	221,12753	2193	4294	6487	SO:0001819	synonymous_variant	126353	exon2			GTCCACGCCCCTG	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"""mitotic interactor and substrate of Plk1"""	615289	"""chromosome 19 open reading frame 21"""	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.537G>A	19.37:g.757483G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_173481		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			G|0.982;A|0.018	0.018	strong		0.652	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481	
RTN4IP1	84816	hgsc.bcm.edu	37	6	107019880	107019880	+	Silent	SNP	A	A	G	rs9486410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:107019880A>G	ENST00000369063.3	-	9	1647	c.1182T>C	c.(1180-1182)aaT>aaC	p.N394N	RTN4IP1_ENST00000498091.1_5'UTR|RTN4IP1_ENST00000539449.1_3'UTR	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	394						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		TTTAAACAACATTAATTACAG	0.383													G|||	929	0.185503	0.3011	0.1081	5008	,	,		19931	0.1696		0.1561	False		,,,				2504	0.1309				p.N394N		Atlas-SNP	.											RTN4IP1,NS,carcinoma,-2,1	RTN4IP1	31	1	0			c.T1182C						PASS	.	G		1228,3178	706.5+/-407.4	171,886,1146	111.0	105.0	107.0		1182	-0.6	0.0	6	dbSNP_119	107	981,7619	773.9+/-407.7	54,873,3373	no	coding-synonymous	RTN4IP1	NM_032730.4		225,1759,4519	GG,GA,AA		11.407,27.8711,16.9845		394/397	107019880	2209,10797	2203	4300	6503	SO:0001819	synonymous_variant	84816	exon9			AACAACATTAATT	AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.1182T>C	6.37:g.107019880A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	119	44	0.369748	NM_032730	Q8N9B3|Q8WZ66|Q9BRA4	Silent	SNP	ENST00000369063.3	37	CCDS5056.1																																																																																			A|0.834;G|0.166	0.166	strong		0.383	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1		
LRCH1	23143	hgsc.bcm.edu	37	13	47127813	47127813	+	Silent	SNP	C	C	T	rs45540131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:47127813C>T	ENST00000389798.3	+	1	479	c.282C>T	c.(280-282)caC>caT	p.H94H	LRCH1_ENST00000311191.6_Silent_p.H94H|LRCH1_ENST00000389797.3_Silent_p.H94H	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	94										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		CCCCCGGGCACGACCTCTCGG	0.687													C|||	751	0.14996	0.2088	0.1268	5008	,	,		13588	0.1905		0.1054	False		,,,				2504	0.091				p.H94H		Atlas-SNP	.											.	LRCH1	104	.	0			c.C282T						PASS	.	C	,,	674,3346		53,568,1389	10.0	9.0	10.0		282,282,282	-1.9	0.8	13	dbSNP_127	10	825,7211		52,721,3245	no	coding-synonymous,coding-synonymous,coding-synonymous	LRCH1	NM_001164211.1,NM_001164213.1,NM_015116.2	,,	105,1289,4634	TT,TC,CC		10.2663,16.7662,12.4336	,,	94/764,94/697,94/729	47127813	1499,10557	2010	4018	6028	SO:0001819	synonymous_variant	23143	exon1			CGGGCACGACCTC	AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"""calponin homology (CH) domain containing 1"""	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.282C>T	13.37:g.47127813C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_015116	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Silent	SNP	ENST00000389798.3	37	CCDS31972.1																																																																																			C|0.861;T|0.139	0.139	strong		0.687	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116	
SIGLEC9	27180	hgsc.bcm.edu	37	19	51630485	51630485	+	Missense_Mutation	SNP	C	C	A	rs273688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51630485C>A	ENST00000250360.3	+	4	1014	c.947C>A	c.(946-948)gCt>gAt	p.A316D	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.A316D	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	316	Ig-like C2-type 2.		A -> D (in dbSNP:rs273688).		cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		AGGGATGCAGCTGAATTCACC	0.637													.|||	529	0.105631	0.3805	0.0331	5008	,	,		20814	0.0		0.0	False		,,,				2504	0.0031				p.A316D		Atlas-SNP	.											SIGLEC9,NS,carcinoma,+1,1	SIGLEC9	85	1	0			c.C947A						PASS	.	A	ASP/ALA,ASP/ALA	1473,2933		252,969,982	41.0	40.0	40.0		947,947	-0.0	0.0	19	dbSNP_79	40	11,8589		0,11,4289	no	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	126,126	252,980,5271	AA,AC,CC		0.1279,33.4317,11.4101	benign,benign	316/480,316/464	51630485	1484,11522	2203	4300	6503	SO:0001583	missense	27180	exon4			ATGCAGCTGAATT	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.947C>A	19.37:g.51630485C>A	ENSP00000250360:p.Ala316Asp	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	196	0.08974358974358974	183	0.3719512195121951	13	0.03591160220994475	0	0.0	0	0.0	.	6.207	0.406368	0.11754	0.334317	0.001279	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.12255	2.7;2.7	2.3	-0.0215	0.13951	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.635768	0.12920	N	0.428257	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.16166	0.016	B	0.12156	0.007	T	0.46665	-0.9175	9	0.72032	D	0.01	.	5.4292	0.16444	0.1485:0.2067:0.6448:0.0	rs273688;rs60086561;rs273688	316	Q9Y336	SIGL9_HUMAN	D	316	ENSP00000413861:A316D;ENSP00000250360:A316D	ENSP00000250360:A316D	A	+	2	0	SIGLEC9	56322297	0.018000	0.18449	0.000000	0.03702	0.001000	0.01503	0.516000	0.22817	-0.622000	0.05626	-3.343000	0.00043	GCT	C|0.895;A|0.105	0.105	strong		0.637	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441	
C2orf16	84226	hgsc.bcm.edu	37	2	27801403	27801403	+	Missense_Mutation	SNP	C	C	G	rs1919125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27801403C>G	ENST00000408964.2	+	1	2015	c.1964C>G	c.(1963-1965)aCt>aGt	p.T655S		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	655			T -> S (in dbSNP:rs1919125).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					AGTCCATGTACTCAAGTGAAG	0.393													T|||	3303	0.659545	0.7368	0.6888	5008	,	,		21823	0.8462		0.498	False		,,,				2504	0.5082				p.T655S		Atlas-SNP	.											.	C2orf16	357	.	0			c.C1964G						PASS	.	T	SER/THR	2616,1152		902,812,170	97.0	95.0	95.0		1964	-0.7	0.0	2	dbSNP_92	95	4085,4151		1029,2027,1062	yes	missense	C2orf16	NM_032266.3	58	1931,2839,1232	GG,GC,CC		49.5993,30.5732,44.1769	benign	655/1985	27801403	6701,5303	1884	4118	6002	SO:0001583	missense	84226	exon1			CATGTACTCAAGT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.1964C>G	2.37:g.27801403C>G	ENSP00000386190:p.Thr655Ser	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	301	301	1	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	1448	0.663003663003663	359	0.7296747967479674	229	0.6325966850828729	490	0.8566433566433567	370	0.48812664907651715	T	0.082	-1.181599	0.01633	0.694268	0.495993	ENSG00000221843	ENST00000408964	T	0.05649	3.41	4.27	-0.677	0.11357	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.12218	-1.0556	8	0.10377	T	0.69	.	5.683	0.17786	0.0:0.2722:0.5177:0.2101	rs1919125;rs17756208;rs60093522;rs1919125	655	Q68DN1	CB016_HUMAN	S	655	ENSP00000386190:T655S	ENSP00000386190:T655S	T	+	2	0	C2orf16	27654907	0.001000	0.12720	0.040000	0.18447	0.033000	0.12548	-0.497000	0.06428	-0.356000	0.08187	-1.482000	0.00985	ACT	C|0.375;G|0.625	0.625	strong		0.393	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
SIAE	54414	hgsc.bcm.edu	37	11	124524627	124524627	+	Silent	SNP	A	A	G	rs1942663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124524627A>G	ENST00000263593.3	-	4	640	c.468T>C	c.(466-468)tcT>tcC	p.S156S	SIAE_ENST00000545756.1_Silent_p.S121S			Q9HAT2	SIAE_HUMAN	sialic acid acetylesterase	156					carbohydrate metabolic process (GO:0005975)|regulation of immune system process (GO:0002682)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	sialate O-acetylesterase activity (GO:0001681)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	15	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;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)		TGGGAGAGACAGAGAGGATGC	0.488													G|||	1035	0.206669	0.6278	0.0706	5008	,	,		21719	0.1022		0.0209	False		,,,				2504	0.0327				p.S156S		Atlas-SNP	.											SIAE,scalp,malignant_melanoma,-1,2	SIAE	37	2	0			c.T468C						scavenged	.	G	,	2276,2126	578.5+/-384.7	604,1068,529	154.0	150.0	151.0		363,468	-11.4	0.0	11	dbSNP_92	151	201,8397	810.4+/-407.1	1,199,4099	no	coding-synonymous,coding-synonymous	SIAE	NM_001199922.1,NM_170601.4	,	605,1267,4628	GG,GA,AA		2.3378,48.2962,19.0538	,	121/489,156/524	124524627	2477,10523	2201	4299	6500	SO:0001819	synonymous_variant	54414	exon4			AGAGACAGAGAGG	AF300796	CCDS8449.1, CCDS55795.1	11q24	2005-12-15	2005-12-15	2005-12-15		ENSG00000110013			18187	protein-coding gene	gene with protein product	"""sialic acid-specific acetylesterase II"""	610079	"""Ysg2 homolog (mouse)"""	YSG2		10464298	Standard	NM_001199922		Approved	CSE-C, MGC87009, LSE	uc001qan.3	Q9HAT2		ENST00000263593.3:c.468T>C	11.37:g.124524627A>G		Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_170601	B3KPB0|Q8IUT9|Q9HAU7|Q9NT71	Silent	SNP	ENST00000263593.3	37	CCDS8449.1																																																																																			A|0.804;G|0.196	0.196	strong		0.488	SIAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387070.1	NM_170601	
SLC2A11	66035	hgsc.bcm.edu	37	22	24226890	24226890	+	Missense_Mutation	SNP	G	G	A	rs60699980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24226890G>A	ENST00000345044.6	+	12	1613	c.1345G>A	c.(1345-1347)Gcc>Acc	p.A449T	SLC2A11_ENST00000398356.2_Missense_Mutation_p.A456T|SLC2A11_ENST00000316185.8_Missense_Mutation_p.A452T|AP000350.10_ENST00000433835.3_Intron			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	449					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						TGTCTGTGGGGCCATCTACAC	0.542													G|||	149	0.0297524	0.062	0.0418	5008	,	,		19200	0.0		0.0318	False		,,,				2504	0.0061				p.A456T		Atlas-SNP	.											.	SLC2A11	32	.	0			c.G1366A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	206,4200	127.4+/-164.3	5,196,2002	191.0	173.0	179.0		1345,1354,1366	1.1	0.0	22	dbSNP_129	179	247,8353	97.5+/-159.1	2,243,4055	yes	missense,missense,missense	SLC2A11	NM_001024938.2,NM_001024939.2,NM_030807.3	58,58,58	7,439,6057	AA,AG,GG		2.8721,4.6754,3.483	probably-damaging,probably-damaging,probably-damaging	449/497,452/500,456/504	24226890	453,12553	2203	4300	6503	SO:0001583	missense	66035	exon13			TGTGGGGCCATCT	AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"""Solute carriers"""	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.1345G>A	22.37:g.24226890G>A	ENSP00000342542:p.Ala449Thr	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	234	109	0.465812	NM_030807	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Missense_Mutation	SNP	ENST00000345044.6	37	CCDS46673.1	74|74	0.03388278388278388|0.03388278388278388	37|37	0.07520325203252033|0.07520325203252033	15|15	0.04143646408839779|0.04143646408839779	0|0	0.0|0.0	22|22	0.029023746701846966|0.029023746701846966	G|G	15.77|15.77	2.930418|2.930418	0.52866|0.52866	0.046754|0.046754	0.028721|0.028721	ENSG00000133460|ENSG00000133460	ENST00000345044;ENST00000398356;ENST00000316185|ENST00000407566	T;T;T|.	0.73258|.	-0.73;-0.73;-0.73|.	3.25|3.25	1.12|1.12	0.20585|0.20585	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.243635|.	0.40302|.	N|.	0.001125|.	T|T	0.04137|0.04137	0.0115|0.0115	L|L	0.41492|0.41492	1.28|1.28	0.33433|0.33433	D|D	0.581396|0.581396	D;B;D|.	0.67145|.	0.996;0.236;0.996|.	D;B;D|.	0.70487|.	0.948;0.374;0.969|.	T|T	0.43032|0.43032	-0.9416|-0.9416	10|6	0.16420|0.62326	T|D	0.52|0.03	.|.	8.7562|8.7562	0.34648|0.34648	0.2007:0.0:0.7993:0.0|0.2007:0.0:0.7993:0.0	rs60699980|rs60699980	452;449;456|.	Q9BYW1-3;Q9BYW1;E9PH55|.	.;GTR11_HUMAN;.|.	T|D	449;456;452|455	ENSP00000342542:A449T;ENSP00000381399:A456T;ENSP00000326748:A452T|.	ENSP00000326748:A452T|ENSP00000386027:G455D	A|G	+|+	1|2	0|0	SLC2A11|SLC2A11	22556890|22556890	0.998000|0.998000	0.40836|0.40836	0.013000|0.013000	0.15412|0.15412	0.954000|0.954000	0.61252|0.61252	4.259000|4.259000	0.58828|0.58828	0.407000|0.407000	0.25591|0.25591	-0.216000|-0.216000	0.12614|0.12614	GCC|GGC	G|0.966;A|0.034	0.034	strong		0.542	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807	
C2orf16	84226	hgsc.bcm.edu	37	2	27801739	27801739	+	Missense_Mutation	SNP	T	T	C	rs13416968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27801739T>C	ENST00000408964.2	+	1	2351	c.2300T>C	c.(2299-2301)aTa>aCa	p.I767T		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	767			I -> T (in dbSNP:rs13416968).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GCTTTGGATATAAAAAACCCT	0.408													T|||	55	0.0109824	0.0378	0.0043	5008	,	,		19518	0.0		0.002	False		,,,				2504	0.0				p.I767T		Atlas-SNP	.											.	C2orf16	357	.	0			c.T2300C						PASS	.	T	THR/ILE	113,3507		3,107,1700	138.0	136.0	137.0		2300	2.4	0.6	2	dbSNP_121	137	2,8150		0,2,4074	yes	missense	C2orf16	NM_032266.3	89	3,109,5774	CC,CT,TT		0.0245,3.1215,0.9769	probably-damaging	767/1985	27801739	115,11657	1810	4076	5886	SO:0001583	missense	84226	exon1			TGGATATAAAAAA	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.2300T>C	2.37:g.27801739T>C	ENSP00000386190:p.Ile767Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	219	104	0.474886	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	21	0.009615384615384616	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	3.675	-0.066708	0.07273	0.031215	2.45E-4	ENSG00000221843	ENST00000408964	T	0.09723	2.95	4.83	2.41	0.29592	.	.	.	.	.	T	0.01353	0.0044	N	0.24115	0.695	0.09310	N	1	B	0.24368	0.102	B	0.18561	0.022	T	0.38802	-0.9644	9	0.37606	T	0.19	.	4.9147	0.13840	0.0:0.0967:0.1882:0.7151	rs13416968;rs13416968	767	Q68DN1	CB016_HUMAN	T	767	ENSP00000386190:I767T	ENSP00000386190:I767T	I	+	2	0	C2orf16	27655243	0.169000	0.23002	0.607000	0.28956	0.030000	0.12068	0.133000	0.15912	0.420000	0.25954	-0.488000	0.04728	ATA	T|0.986;C|0.014	0.014	strong		0.408	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
EVL	51466	hgsc.bcm.edu	37	14	100563868	100563868	+	Silent	SNP	G	G	A	rs35006525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:100563868G>A	ENST00000402714.2	+	3	829	c.225G>A	c.(223-225)acG>acA	p.T75T	EVL_ENST00000392920.3_Silent_p.T77T|EVL_ENST00000555048.1_3'UTR|EVL_ENST00000544450.2_Silent_p.T81T			Q9UI08	EVL_HUMAN	Enah/Vasp-like	75	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin filament organization (GO:0007015)|actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of stress fiber assembly (GO:0051496)|protein homotetramerization (GO:0051289)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	profilin binding (GO:0005522)|SH3 domain binding (GO:0017124)			cervix(1)|large_intestine(5)|lung(3)|ovary(3)|urinary_tract(2)	14		Melanoma(154;0.152)				ATCAGGCCACGCCAACCTTCC	0.458													G|||	74	0.0147764	0.0545	0.0029	5008	,	,		21124	0.0		0.0	False		,,,				2504	0.0				p.T77T		Atlas-SNP	.											.	EVL	42	.	0			c.G231A						PASS	.	G		217,4189	131.0+/-167.6	6,205,1992	89.0	81.0	84.0		231	-9.0	0.8	14	dbSNP_126	84	0,8600		0,0,4300	no	coding-synonymous	EVL	NM_016337.2		6,205,6292	AA,AG,GG		0.0,4.9251,1.6685		77/419	100563868	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	51466	exon3			GGCCACGCCAACC	AF112209	CCDS9955.1	14q32.2	2014-08-13			ENSG00000196405	ENSG00000196405			20234	protein-coding gene	gene with protein product						10945997, 10993894	Standard	NM_016337		Approved	RNB6	uc001ygu.3	Q9UI08	OTTHUMG00000171530	ENST00000402714.2:c.225G>A	14.37:g.100563868G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	93	51	0.548387	NM_016337	A8K105|O95884|Q7Z522|Q8TBV1|Q9UF25|Q9UIC2	Silent	SNP	ENST00000402714.2	37																																																																																				G|0.986;A|0.014	0.014	strong		0.458	EVL-006	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000413958.1		
CES5A	221223	hgsc.bcm.edu	37	16	55880534	55880534	+	Silent	SNP	G	G	C	rs11860488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:55880534G>C	ENST00000290567.9	-	13	1678	c.1557C>G	c.(1555-1557)ctC>ctG	p.L519L	CES5A_ENST00000521992.1_Silent_p.L548L|CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000518005.1_Silent_p.L413L|CES5A_ENST00000319165.9_Silent_p.L469L|CES5A_ENST00000520435.1_Silent_p.L489L	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	519						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						AGTCCAGCTGGAGGTACTGCT	0.532													C|||	1533	0.30611	0.4327	0.1873	5008	,	,		16694	0.2817		0.2783	False		,,,				2504	0.273				p.L548L		Atlas-SNP	.											.	CES5A	206	.	0			c.C1644G						PASS	.	C	,,	1885,2511		397,1091,710	205.0	202.0	203.0		1557,1644,1407	3.5	0.8	16	dbSNP_120	203	2083,6517		262,1559,2479	yes	coding-synonymous,coding-synonymous,coding-synonymous	CES5A	NM_001143685.1,NM_001190158.1,NM_145024.2	,,	659,2650,3189	CC,CG,GG		24.2209,42.8799,30.5325	,,	519/576,548/605,469/526	55880534	3968,9028	2198	4300	6498	SO:0001819	synonymous_variant	221223	exon14			CAGCTGGAGGTAC	AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"""Carboxylesterases"""	26459	protein-coding gene	gene with protein product			"""carboxylesterase 7"""	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1557C>G	16.37:g.55880534G>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	161	92	0.571429	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Silent	SNP	ENST00000290567.9	37	CCDS45490.1																																																																																			G|0.695;C|0.305	0.305	strong		0.532	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	
CAMK2N2	94032	hgsc.bcm.edu	37	3	183978936	183978936	+	Silent	SNP	G	G	A	rs75699255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183978936G>A	ENST00000296238.3	-	1	315	c.138C>T	c.(136-138)ccC>ccT	p.P46P	EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000402825.3_Intron	NM_033259.2	NP_150284.1	Q96S95	CK2N2_HUMAN	calcium/calmodulin-dependent protein kinase II inhibitor 2	46	Inhibitory domain. {ECO:0000250}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium-dependent protein kinase inhibitor activity (GO:0008427)					all_cancers(143;1.09e-10)|Ovarian(172;0.0339)		Epithelial(37;2.51e-33)|OV - Ovarian serous cystadenocarcinoma(80;5.69e-22)			GGCCCAGCTTGGGGGGTCGCT	0.736													G|||	200	0.0399361	0.146	0.0101	5008	,	,		8663	0.0		0.0	False		,,,				2504	0.0				p.P46P		Atlas-SNP	.											.	CAMK2N2	2	.	0			c.C138T						PASS	.	G	,	416,3990		19,378,1806	18.0	21.0	20.0		,138	-0.8	1.0	3	dbSNP_132	20	3,8597		0,3,4297	no	intron,coding-synonymous	ECE2,CAMK2N2	NM_014693.3,NM_033259.2	,	19,381,6103	AA,AG,GG		0.0349,9.4417,3.2216	,	,46/80	183978936	419,12587	2203	4300	6503	SO:0001819	synonymous_variant	94032	exon1			CAGCTTGGGGGGT	AY037149	CCDS3257.1	3q27.1	2006-03-27			ENSG00000163888	ENSG00000163888			24197	protein-coding gene	gene with protein product		608721				11444830, 9724800	Standard	NM_033259		Approved	CaM-KIIN	uc003fnj.1	Q96S95	OTTHUMG00000156821	ENST00000296238.3:c.138C>T	3.37:g.183978936G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	50	31	0.62	NM_033259		Silent	SNP	ENST00000296238.3	37	CCDS3257.1																																																																																			G|0.962;A|0.038	0.038	strong		0.736	CAMK2N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346010.1	NM_033259	
MT-ND4	4538	hgsc.bcm.edu	37	M	10793	10793	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10793C>T	ENST00000361381.2	+	1	34	c.34C>T	c.(34-36)Cta>Tta	p.L12L	MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	12					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						CAATTATATTACTACCACTGA	0.378																																					p.L12L		Atlas-SNP	.											.	.	.	.	0			c.C34T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ATATTACTACCAC			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.34C>T	M.37:g.10793C>T		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.378	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
BCR	613	hgsc.bcm.edu	37	22	23651650	23651650	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:23651650A>G	ENST00000305877.8	+	17	3803	c.3052A>G	c.(3052-3054)Acc>Gcc	p.T1018A	BCR_ENST00000359540.3_Missense_Mutation_p.T974A	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	1018					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)	CTGGCAGCGCACCGTCATCGC	0.607			T	"""ABL1,  FGFR1, JAK2 """	"""CML, ALL, AML"""																																p.T1018A		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	BCR,NS,carcinoma,0,1	BCR	74	1	0			c.A3052G						scavenged	.						33.0	25.0	28.0					22																	23651650		2201	4300	6501	SO:0001583	missense	613	exon17			CAGCGCACCGTCA		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.3052A>G	22.37:g.23651650A>G	ENSP00000303507:p.Thr1018Ala	Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	294	108	0.367347	NM_004327	P78501|Q12842|Q4LE80|Q6NZI3	Missense_Mutation	SNP	ENST00000305877.8	37	CCDS13806.1	.	.	.	.	.	.	.	.	.	.	A	7.060	0.566244	0.13560	.	.	ENSG00000186716	ENST00000305877;ENST00000359540;ENST00000334149	T;T	0.39787	1.06;1.8	4.7	2.52	0.30459	C2 calcium/lipid-binding domain, CaLB (1);	0.051625	0.85682	D	0.000000	T	0.28067	0.0692	L	0.44542	1.39	0.80722	D	1	B;B;B	0.22909	0.077;0.059;0.077	B;B;B	0.26614	0.071;0.039;0.044	T	0.04203	-1.0969	10	0.12430	T	0.62	.	4.6914	0.12783	0.6936:0.0:0.1642:0.1422	.	607;974;1018	B4E065;P11274-2;P11274	.;.;BCR_HUMAN	A	1018;974;683	ENSP00000303507:T1018A;ENSP00000352535:T974A	ENSP00000303507:T1018A	T	+	1	0	BCR	21981650	1.000000	0.71417	0.512000	0.27736	0.011000	0.07611	4.359000	0.59449	0.765000	0.33221	-0.991000	0.02546	ACC	A|0.500;G|0.500	0.500	weak		0.607	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327	
CERS3	204219	hgsc.bcm.edu	37	15	101041921	101041921	+	Missense_Mutation	SNP	T	T	C	rs60405735	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:101041921T>C	ENST00000394113.1	-	5	824	c.134A>G	c.(133-135)tAt>tGt	p.Y45C	CERS3_ENST00000538112.2_Missense_Mutation_p.Y45C|CERS3_ENST00000284382.4_Missense_Mutation_p.Y45C|CERS3_ENST00000560944.1_Intron			Q8IU89	CERS3_HUMAN	ceramide synthase 3	45			Y -> C (in dbSNP:rs60405735).		ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|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)										GAGAAAAGCATATGGAATTGT	0.383													T|||	561	0.112021	0.292	0.036	5008	,	,		20588	0.0119		0.0507	False		,,,				2504	0.089				p.Y45C		Atlas-SNP	.											.	.	.	.	0			c.A134G						PASS	.	T	CYS/TYR	1105,3301	397.6+/-330.5	136,833,1234	102.0	89.0	93.0		134	-7.7	0.0	15	dbSNP_129	93	528,8072	147.9+/-203.2	17,494,3789	yes	missense	CERS3	NM_178842.3	194	153,1327,5023	CC,CT,TT		6.1395,25.0794,12.5557	benign	45/384	101041921	1633,11373	2203	4300	6503	SO:0001583	missense	204219	exon4			AAAGCATATGGAA		CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"""Homeoboxes / CERS class"""	23752	protein-coding gene	gene with protein product		615276	"""LAG1 longevity assurance homolog 3 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 3"""	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.134A>G	15.37:g.101041921T>C	ENSP00000377672:p.Tyr45Cys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_178842	Q8NE64|Q8NEN6	Missense_Mutation	SNP	ENST00000394113.1	37	CCDS10384.1	195	0.08928571428571429	130	0.26422764227642276	15	0.04143646408839779	5	0.008741258741258742	45	0.059366754617414245	T	10.35	1.327124	0.24080	0.250794	0.061395	ENSG00000154227	ENST00000284382;ENST00000394113;ENST00000538112	T;T	0.69926	-0.44;-0.44	5.49	-7.72	0.01250	.	0.617290	0.17774	N	0.162475	T	0.00012	0.0000	M	0.71296	2.17	0.49299	P	2.2999999999995246E-4	B	0.09022	0.002	B	0.06405	0.002	T	0.07888	-1.0749	9	0.56958	D	0.05	-0.038	5.2062	0.15293	0.314:0.3799:0.0:0.3061	rs60405735;rs62619254	45	Q8IU89	CERS3_HUMAN	C	45;56;45	ENSP00000284382:Y45C;ENSP00000437640:Y45C	ENSP00000284382:Y45C	Y	-	2	0	CERS3	98859444	0.992000	0.36948	0.007000	0.13788	0.722000	0.41435	0.336000	0.19823	-1.463000	0.01904	-0.924000	0.02725	TAT	T|0.888;C|0.112	0.112	strong		0.383	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842	
NUP133	55746	hgsc.bcm.edu	37	1	229631734	229631734	+	Missense_Mutation	SNP	T	T	C	rs11805194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229631734T>C	ENST00000261396.3	-	7	971	c.880A>G	c.(880-882)Atc>Gtc	p.I294V	NUP133_ENST00000537506.1_Missense_Mutation_p.I278V	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	294			I -> V (in dbSNP:rs11805194).		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 organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|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)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.I294V(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				CATTTACTGATGTTTGAACTC	0.368													T|||	1062	0.212061	0.2617	0.3012	5008	,	,		18607	0.1577		0.2068	False		,,,				2504	0.1431				p.I294V		Atlas-SNP	.											NUP133,NS,carcinoma,0,1	NUP133	111	1	1	Substitution - Missense(1)	stomach(1)	c.A880G						PASS	.	T	VAL/ILE	1097,3309	392.1+/-328.4	134,829,1240	104.0	100.0	101.0		880	1.7	1.0	1	dbSNP_120	101	1818,6782	324.6+/-316.5	191,1436,2673	yes	missense	NUP133	NM_018230.2	29	325,2265,3913	CC,CT,TT		21.1395,24.8979,22.4127	benign	294/1157	229631734	2915,10091	2203	4300	6503	SO:0001583	missense	55746	exon7			TACTGATGTTTGA		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.880A>G	1.37:g.229631734T>C	ENSP00000261396:p.Ile294Val	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	451	0.2065018315018315	122	0.24796747967479674	93	0.2569060773480663	80	0.13986013986013987	156	0.20580474934036938	T	12.64	1.999786	0.35320	0.248979	0.211395	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.60424	0.19;0.19;0.19	5.57	1.67	0.24075	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.164275	0.52532	D	0.000067	T	0.00012	0.0000	L	0.41236	1.265	0.31397	P	0.677155	B	0.06786	0.001	B	0.06405	0.002	T	0.11155	-1.0599	9	0.30854	T	0.27	-22.3481	3.4333	0.07436	0.0942:0.1504:0.1651:0.5903	rs11805194;rs17756650;rs52814082;rs61334161;rs11805194	294	Q8WUM0	NU133_HUMAN	V	294;294;294;278	ENSP00000261396:I294V;ENSP00000355640:I294V;ENSP00000443496:I278V	ENSP00000261396:I294V	I	-	1	0	NUP133	227698357	0.960000	0.32886	0.982000	0.44146	0.917000	0.54804	0.306000	0.19279	0.408000	0.25621	0.528000	0.53228	ATC	C|0.213;N|0.000	0.213	strong		0.368	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
TTC3	7267	hgsc.bcm.edu	37	21	38512956	38512956	+	Silent	SNP	A	A	G	rs1133001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38512956A>G	ENST00000399017.2	+	20	4502	c.1755A>G	c.(1753-1755)gtA>gtG	p.V585V	TTC3_ENST00000540756.1_Silent_p.V275V|TTC3_ENST00000355666.1_Silent_p.V585V|TTC3_ENST00000354749.2_Silent_p.V585V|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	585					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TTGGAAAAGTATATTTGAAAA	0.358													A|||	2964	0.591853	0.6445	0.6282	5008	,	,		15700	0.6032		0.4642	False		,,,				2504	0.6145				p.V585V	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	1	Unknown(1)	skin(1)	c.A1755G						PASS	.	A	,	2766,1640	657.1+/-400.2	869,1028,306	92.0	91.0	91.0		1755,1755	-6.1	1.0	21	dbSNP_86	91	3848,4752	540.8+/-383.9	896,2056,1348	no	coding-synonymous,coding-synonymous	TTC3	NM_001001894.1,NM_003316.3	,	1765,3084,1654	GG,GA,AA		44.7442,37.222,49.1465	,	585/2026,585/2026	38512956	6614,6392	2203	4300	6503	SO:0001819	synonymous_variant	7267	exon20			AAAAGTATATTTG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.1755A>G	21.37:g.38512956A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1																																																																																			A|0.475;G|0.525	0.525	strong		0.358	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
KIF19	124602	hgsc.bcm.edu	37	17	72350362	72350362	+	Silent	SNP	G	G	A	rs72852235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72350362G>A	ENST00000389916.4	+	18	2508	c.2370G>A	c.(2368-2370)tcG>tcA	p.S790S	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	790					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						GGCGGCGCTCGCGGGCCCTGG	0.682													G|||	1277	0.254992	0.1051	0.3012	5008	,	,		14395	0.3452		0.2803	False		,,,				2504	0.3057				p.S790S		Atlas-SNP	.											KIF19,NS,carcinoma,0,1	KIF19	102	1	0			c.G2370A						PASS	.	G		461,3551		32,397,1577	35.0	46.0	42.0		2370	-10.1	0.3	17	dbSNP_130	42	2350,5960		329,1692,2134	no	coding-synonymous	KIF19	NM_153209.3		361,2089,3711	AA,AG,GG		28.2792,11.4905,22.8129		790/999	72350362	2811,9511	2006	4155	6161	SO:0001819	synonymous_variant	124602	exon18			GCGCTCGCGGGCC	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.2370G>A	17.37:g.72350362G>A		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			G|0.736;A|0.264	0.264	strong		0.682	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
OXCT2	64064	hgsc.bcm.edu	37	1	40236074	40236074	+	Missense_Mutation	SNP	A	A	C	rs230321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:40236074A>C	ENST00000327582.5	-	1	946	c.854T>G	c.(853-855)cTg>cGg	p.L285R	BMP8B_ENST00000372827.3_Intron|BMP8B_ENST00000397360.2_Intron	NM_022120.1	NP_071403.1	Q9BYC2	SCOT2_HUMAN	3-oxoacid CoA transferase 2	285			L -> R (in dbSNP:rs230321).		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)	TTCCTCTTTCAGGATCGTTAA	0.517											OREG0013400	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L285R		Atlas-SNP	.											.	OXCT2	12	.	0			c.T854G						PASS	.						66.0	95.0	85.0					1																	40236074		2185	4292	6477	SO:0001583	missense	64064	exon1			TCTTTCAGGATCG	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.854T>G	1.37:g.40236074A>C	ENSP00000361914:p.Leu285Arg	Somatic	247	0	0	891	WXS	Illumina HiSeq	Phase_I	73	73	1	NM_022120	B2RBB4|Q5QPK4|Q8NHR1|Q9H1I4	Missense_Mutation	SNP	ENST00000327582.5	37	CCDS445.1	478	0.21886446886446886	165	0.3353658536585366	83	0.2292817679558011	65	0.11363636363636363	165	0.21767810026385223	c	0.015	-1.566349	0.00903	.	.	ENSG00000198754	ENST00000327582	T	0.78707	-1.2	2.58	-2.11	0.07187	.	0.524948	0.19120	N	0.122206	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	0.06409	-1.0828	8	0.02654	T	1	.	3.2824	0.06920	0.4418:0.2322:0.0:0.3259	rs230321;rs7554008	285;285	B3KS89;Q9BYC2	.;SCOT2_HUMAN	R	285	ENSP00000361914:L285R	ENSP00000361914:L285R	L	-	2	0	OXCT2	40008661	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.376000	0.07465	-0.958000	0.03622	-1.167000	0.01749	CTG	A|0.750;C|0.250	0.250	weak		0.517	OXCT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025656.1	NM_022120	
CCP110	9738	hgsc.bcm.edu	37	16	19547357	19547357	+	Silent	SNP	A	A	G	rs10492785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19547357A>G	ENST00000381396.5	+	4	613	c.366A>G	c.(364-366)acA>acG	p.T122T	CCP110_ENST00000396208.2_Silent_p.T122T|CCP110_ENST00000396212.2_Silent_p.T122T	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	122	CEP97 binding.				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)		p.T122T(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						TTCCTGCTACATTTCCAAATA	0.393													A|||	1088	0.217252	0.2474	0.2536	5008	,	,		16203	0.3849		0.0746	False		,,,				2504	0.1247				p.T122T		Atlas-SNP	.											CCP110,NS,carcinoma,0,1	CCP110	57	1	1	Substitution - coding silent(1)	stomach(1)	c.A366G						PASS	.	A	,	929,3465	356.4+/-313.5	86,757,1354	76.0	76.0	76.0		366,366	-1.9	0.0	16	dbSNP_119	76	559,8041	151.9+/-206.6	15,529,3756	no	coding-synonymous,coding-synonymous	CCP110	NM_001199022.1,NM_014711.4	,	101,1286,5110	GG,GA,AA		6.5,21.1425,11.4514	,	122/1013,122/992	19547357	1488,11506	2197	4300	6497	SO:0001819	synonymous_variant	9738	exon4			TGCTACATTTCCA	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.366A>G	16.37:g.19547357A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	156	65	0.416667	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Silent	SNP	ENST00000381396.5	37	CCDS55992.1																																																																																			A|0.802;G|0.198	0.198	strong		0.393	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
LLGL2	3993	hgsc.bcm.edu	37	17	73570718	73570718	+	Silent	SNP	C	C	G	rs1126939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73570718C>G	ENST00000392550.3	+	25	3141	c.3024C>G	c.(3022-3024)gcC>gcG	p.A1008A	LLGL2_ENST00000577200.1_Silent_p.A1008A|LLGL2_ENST00000167462.5_Missense_Mutation_p.P994R	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	1008					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CACATCGAGCCGCCGTGGGGT	0.677													G|||	1579	0.315296	0.6112	0.245	5008	,	,		13176	0.1508		0.2823	False		,,,				2504	0.1687				p.P994R		Atlas-SNP	.											.	LLGL2	155	.	0			c.C2981G						PASS	.	G	,ARG/PRO	2545,1861		755,1035,413	23.0	27.0	26.0		3024,2981	0.0	0.0	17	dbSNP_86	26	2533,6067		399,1735,2166	yes	coding-synonymous,missense	LLGL2	NM_001031803.1,NM_004524.2	,103	1154,2770,2579	GG,GC,CC		29.4535,42.2379,39.0435	,	1008/1021,994/1016	73570718	5078,7928	2203	4300	6503	SO:0001819	synonymous_variant	3993	exon24			TCGAGCCGCCGTG	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.3024C>G	17.37:g.73570718C>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	723	0.33104395604395603	334	0.6788617886178862	88	0.2430939226519337	81	0.14160839160839161	220	0.29023746701846964	G	8.672	0.903015	0.17760	0.577621	0.294535	ENSG00000073350	ENST00000167462;ENST00000545227	T	0.04917	3.53	4.66	0.0224	0.14133	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15896	-1.0421	7	0.87932	D	0	0.7107	4.422	0.11484	0.3008:0.3105:0.3886:0.0	rs1126939;rs1671017;rs3211300;rs11554115;rs17846684;rs17859783;rs61184994;rs1126939	983;994	G3V1I9;Q6P1M3-2	.;.	R	994;983	ENSP00000167462:P994R	ENSP00000167462:P994R	P	+	2	0	LLGL2	71082313	0.000000	0.05858	0.000000	0.03702	0.271000	0.26615	-0.116000	0.10724	-0.271000	0.09272	-0.293000	0.09583	CCG	C|0.621;G|0.379	0.379	strong		0.677	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
ARAP1	116985	hgsc.bcm.edu	37	11	72403832	72403832	+	Splice_Site	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:72403832T>C	ENST00000393609.3	-	30	4157		c.e30-2		ARAP1-AS1_ENST00000542022.1_RNA|ARAP1_ENST00000334211.8_Splice_Site|ARAP1_ENST00000426523.1_Intron|ARAP1_ENST00000393605.3_Splice_Site|ARAP1_ENST00000429686.1_Intron|ARAP1_ENST00000495878.1_Intron|ARAP1_ENST00000455638.2_Intron|ARAP1_ENST00000359373.5_Intron	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1						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						CCTCTGGCTCTGTTTGATAGA	0.587																																					.	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.3220-2A>G						PASS	.						46.0	46.0	46.0					11																	72403832		2200	4293	6493	SO:0001630	splice_region_variant	116985	exon29			TGGCTCTGTTTGA	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.3955-2A>G	11.37:g.72403832T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_015242	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Splice_Site	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.491402	0.64074	.	.	ENSG00000186635	ENST00000393605;ENST00000334211;ENST00000393609	.	.	.	5.73	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4138	0.32659	0.1738:0.0:0.0:0.8262	.	.	.	.	.	-1	.	.	.	-	.	.	ARAP1	72081480	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.927000	0.40094	2.184000	0.69523	0.448000	0.29417	.	.	.	none		0.587	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	Intron
MYO9B	4650	hgsc.bcm.edu	37	19	17273893	17273893	+	Silent	SNP	G	G	T	rs7256689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17273893G>T	ENST00000594824.1	+	10	1779	c.1632G>T	c.(1630-1632)ctG>ctT	p.L544L	CTD-3032J10.2_ENST00000597216.1_RNA|MYO9B_ENST00000595618.1_Silent_p.L544L|MYO9B_ENST00000397274.2_Silent_p.L544L|CTD-3032J10.2_ENST00000599360.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	544	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						ATGAGCAGCTGCAGTATTACT	0.468													A|||	3747	0.748203	0.9629	0.7406	5008	,	,		20340	0.7312		0.6501	False		,,,				2504	0.5818				p.L544L		Atlas-SNP	.											.	MYO9B	264	.	0			c.G1632T						PASS	.	A	,	3671,333		1689,293,20	62.0	57.0	59.0		1632,1632	-10.1	0.2	19	dbSNP_116	59	5548,2876		1808,1932,472	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	3497,2225,492	TT,TG,GG		34.1406,8.3167,25.8207	,	544/2023,544/2158	17273893	9219,3209	2002	4212	6214	SO:0001819	synonymous_variant	4650	exon10			GCAGCTGCAGTAT		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.1632G>T	19.37:g.17273893G>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				G|0.238;T|0.762	0.762	strong		0.468	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
GOLGA8B	440270	hgsc.bcm.edu	37	15	34825091	34825091	+	Missense_Mutation	SNP	T	T	A	rs200439797		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34825091T>A	ENST00000342314.5	-	3	338	c.241A>T	c.(241-243)Agg>Tgg	p.R81W	GOLGA8A_ENST00000543376.1_Intron|GOLGA8B_ENST00000267731.7_Missense_Mutation_p.R81W|GOLGA8B_ENST00000438958.2_Missense_Mutation_p.R111W	NM_001023567.4	NP_001018861.3	A8MQT2	GOG8B_HUMAN	golgin A8 family, member B	81						Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(1)	1		all_lung(180;2.78e-08)		all cancers(64;8.27e-19)|GBM - Glioblastoma multiforme(113;6.98e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TTTATGGACCTCGAGTTCAGG	0.552																																					p.R81W		Atlas-SNP	.											GOLGA8B_ENST00000267731,right_upper_lobe,carcinoma,+1,2	GOLGA8B	7	2	0			c.A241T						scavenged	.						34.0	19.0	24.0					15																	34825091		686	1359	2045	SO:0001583	missense	440270	exon3			TGGACCTCGAGTT	AF164622	CCDS45211.1	15q14	2011-10-25	2010-02-12		ENSG00000215252	ENSG00000215252			31973	protein-coding gene	gene with protein product		609619	"""golgi autoantigen, golgin subfamily a, 8B"""				Standard	NM_001023567		Approved		uc001ziq.3	A8MQT2	OTTHUMG00000129549	ENST00000342314.5:c.241A>T	15.37:g.34825091T>A	ENSP00000343064:p.Arg81Trp	Somatic	1385	0	0		WXS	Illumina HiSeq	Phase_I	1873	467	0.249333	NM_001023567	A6NLZ2|O94937|Q2M3S9|Q9NZG8|Q9NZW0|Q9NZW3	Missense_Mutation	SNP	ENST00000342314.5	37	CCDS45211.1	.	.	.	.	.	.	.	.	.	.	t	13.59	2.284070	0.40394	.	.	ENSG00000215252	ENST00000342314;ENST00000267731;ENST00000438958	T;T;T	0.22743	1.94;1.94;2.5	1.55	0.322	0.15888	.	.	.	.	.	T	0.34745	0.0908	M	0.66939	2.045	0.21355	N	0.999712	D	0.67145	0.996	D	0.64687	0.928	T	0.13575	-1.0504	9	0.66056	D	0.02	.	3.6826	0.08316	0.3389:0.0:0.0:0.6611	.	81	A8MQT2	GOG8B_HUMAN	W	81;81;111	ENSP00000343064:R81W;ENSP00000267731:R81W;ENSP00000400063:R111W	ENSP00000267731:R81W	R	-	1	2	GOLGA8B	32612383	1.000000	0.71417	0.371000	0.25978	0.004000	0.04260	4.296000	0.59055	0.067000	0.16545	-1.078000	0.02229	AGG	T|0.998;A|0.002	0.002	weak		0.552	GOLGA8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251739.2	NM_001023567	
LILRA6	79168	hgsc.bcm.edu	37	19	54744183	54744183	+	Missense_Mutation	SNP	A	A	G	rs76090367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54744183A>G	ENST00000396365.2	-	6	1264	c.1225T>C	c.(1225-1227)Ttc>Ctc	p.F409L	LILRA6_ENST00000419410.2_Missense_Mutation_p.F409L|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000245621.5_Missense_Mutation_p.F409L|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	409					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				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)		TCACTGGGGAAAGACAGCAGG	0.622																																					p.F409L		Atlas-SNP	.											LILRA6,nipple,malignant_melanoma,+1,1	LILRA6	75	1	0			c.T1225C						scavenged	.						96.0	134.0	121.0					19																	54744183		2197	4300	6497	SO:0001583	missense	79168	exon6			TGGGGAAAGACAG	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.1225T>C	19.37:g.54744183A>G	ENSP00000379651:p.Phe409Leu	Somatic	333	1	0.003003		WXS	Illumina HiSeq	Phase_I	290	63	0.217241	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	A	0.020	-1.439570	0.01098	.	.	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.00686	5.85;5.85;5.85	2.71	-3.11	0.05299	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	12.755800	0.00166	N	0.000006	T	0.00440	0.0014	N	0.05031	-0.125	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	0.46219	-0.9207	10	0.11485	T	0.65	.	0.5921	0.00730	0.2526:0.1884:0.3669:0.1921	.	409;409;409	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	L	409	ENSP00000411227:F409L;ENSP00000379651:F409L;ENSP00000245621:F409L	ENSP00000245621:F409L	F	-	1	0	LILRA6	59435995	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.313000	0.08103	-0.667000	0.05303	-3.230000	0.00052	TTC	A|0.989;G|0.011	0.011	strong		0.622	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
TRH	7200	hgsc.bcm.edu	37	3	129694681	129694681	+	Missense_Mutation	SNP	C	C	G	rs5658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129694681C>G	ENST00000302649.3	+	2	549	c.22C>G	c.(22-24)Ctc>Gtc	p.L8V	TRH_ENST00000507066.1_Missense_Mutation_p.L8V	NM_007117.3	NP_009048.1	P20396	TRH_HUMAN	thyrotropin-releasing hormone	8			L -> V (in dbSNP:rs5658).		adult walking behavior (GO:0007628)|cell-cell signaling (GO:0007267)|eating behavior (GO:0042755)|histamine metabolic process (GO:0001692)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of feeding behavior (GO:2000252)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of insulin secretion (GO:0032024)|response to cold (GO:0009409)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	thyrotropin-releasing hormone activity (GO:0008437)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)	14						TTGGTTGCTGCTCGCTCTGGC	0.701													C|||	1122	0.224042	0.239	0.2911	5008	,	,		13936	0.3631		0.0785	False		,,,				2504	0.1626				p.L8V	Esophageal Squamous(60;321 1330 17401 41911)	Atlas-SNP	.											.	TRH	30	.	0			c.C22G						PASS	.	C	VAL/LEU	869,3421		88,693,1364	14.0	14.0	14.0		22	2.2	0.6	3	dbSNP_52	14	669,7731		34,601,3565	yes	missense	TRH	NM_007117.3	32	122,1294,4929	GG,GC,CC		7.9643,20.2564,12.1198	probably-damaging	8/243	129694681	1538,11152	2145	4200	6345	SO:0001583	missense	7200	exon2			TTGCTGCTCGCTC		CCDS3066.1	3q13.3-q21	2013-02-28				ENSG00000170893		"""Endogenous ligands"""	12298	protein-coding gene	gene with protein product	"""prothyroliberin"""	613879				2126343, 1900134	Standard	NM_007117		Approved		uc003enc.4	P20396		ENST00000302649.3:c.22C>G	3.37:g.129694681C>G	ENSP00000303452:p.Leu8Val	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	210	102	0.485714	NM_007117	B2R8R1|Q2TB83	Missense_Mutation	SNP	ENST00000302649.3	37	CCDS3066.1	477	0.2184065934065934	107	0.21747967479674796	98	0.27071823204419887	207	0.3618881118881119	65	0.08575197889182058	C	11.99	1.802842	0.31869	0.202564	0.079643	ENSG00000170893	ENST00000302649;ENST00000507066	T;T	0.52295	0.67;0.67	4.07	2.22	0.28083	.	0.633406	0.15283	N	0.270578	T	0.00012	0.0000	M	0.63428	1.95	0.36832	P	0.11303300000000005	P	0.41624	0.757	B	0.37451	0.25	T	0.34625	-0.9821	9	0.35671	T	0.21	-5.7178	7.1873	0.25806	0.1939:0.6187:0.1874:0.0	rs5658;rs1619517;rs56706099;rs5658	8	P20396	TRH_HUMAN	V	8	ENSP00000303452:L8V;ENSP00000426522:L8V	ENSP00000303452:L8V	L	+	1	0	TRH	131177371	0.996000	0.38824	0.559000	0.28332	0.156000	0.22039	1.533000	0.36040	0.452000	0.26830	-0.314000	0.08810	CTC	C|0.839;G|0.161	0.161	strong		0.701	TRH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356592.1	NM_007117	
KLK8	11202	hgsc.bcm.edu	37	19	51504415	51504415	+	Silent	SNP	G	G	C	rs34542531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51504415G>C	ENST00000600767.1	-	3	498	c.9C>G	c.(7-9)cgC>cgG	p.R3R	CTB-147C22.9_ENST00000594512.1_RNA|KLK8_ENST00000291726.7_Silent_p.R3R|KLK8_ENST00000347619.4_Silent_p.R3R|KLK8_ENST00000598195.1_5'Flank|KLK8_ENST00000320838.5_Silent_p.R3R|KLK8_ENST00000391806.2_Silent_p.R3R|KLK8_ENST00000593490.1_Silent_p.R3R|KLK9_ENST00000376832.4_3'UTR|KLK9_ENST00000250366.6_3'UTR			O60259	KLK8_HUMAN	kallikrein-related peptidase 8	3					cell death (GO:0008219)|keratinocyte proliferation (GO:0043616)|memory (GO:0007613)|negative regulation of axon regeneration (GO:0048681)|negative regulation of myelination (GO:0031642)|neuron projection morphogenesis (GO:0048812)|regulation of synapse organization (GO:0050807)|response to wounding (GO:0009611)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(8)|prostate(1)	15		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.0033)|GBM - Glioblastoma multiforme(134;0.00888)		GAGGTCGGGGGCGTCCCATGG	0.662													G|||	116	0.0231629	0.0348	0.0259	5008	,	,		15317	0.002		0.0219	False		,,,				2504	0.0286				p.R3R		Atlas-SNP	.											.	KLK8	46	.	0			c.C9G						PASS	.	G	,,,	143,4263	88.7+/-127.4	2,139,2062	34.0	29.0	31.0		9,9,9,9	-0.7	0.0	19	dbSNP_126	31	133,8467	57.5+/-118.9	0,133,4167	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KLK8	NM_007196.2,NM_144505.1,NM_144506.1,NM_144507.1	,,,	2,272,6229	CC,CG,GG		1.5465,3.2456,2.1221	,,,	3/261,3/306,3/120,3/33	51504415	276,12730	2203	4300	6503	SO:0001819	synonymous_variant	11202	exon2			TCGGGGGCGTCCC	AB008390	CCDS12813.1, CCDS12814.1, CCDS12815.1, CCDS42600.1, CCDS74433.1	19q13	2011-09-07	2006-10-27			ENSG00000129455		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6369	protein-coding gene	gene with protein product		605644	"""kallikrein 8 (neuropsin/ovasin)"""	PRSS19		10102990, 9714609, 16800724, 16800723	Standard	NM_144505		Approved	HNP, TADG14, neuropsin, ovasin	uc002pur.1	O60259		ENST00000600767.1:c.9C>G	19.37:g.51504415G>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_144505	Q5V9X1|Q5V9X2|Q8IW69|Q9HCB3|Q9NR68|Q9NR69|Q9UIL9|Q9UQ47	Silent	SNP	ENST00000600767.1	37	CCDS12813.1																																																																																			G|0.975;C|0.025	0.025	strong		0.662	KLK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465032.2	NM_007196	
ZFP91	80829	hgsc.bcm.edu	37	11	58378424	58378424	+	Splice_Site	SNP	A	A	G	rs8373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	24	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	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
LRRK1	79705	hgsc.bcm.edu	37	15	101606084	101606084	+	Silent	SNP	G	G	A	rs116529941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:101606084G>A	ENST00000388948.3	+	32	5801	c.5442G>A	c.(5440-5442)gcG>gcA	p.A1814A	LRRK1_ENST00000532145.1_3'UTR|RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Silent_p.A1811A	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)			ACTCCATCGCGGACGTGAGCA	0.622													G|||	6	0.00119808	0.0045	0.0	5008	,	,		17606	0.0		0.0	False		,,,				2504	0.0				p.A1814A		Atlas-SNP	.											.	LRRK1	310	.	0			c.G5442A						PASS	.	G		10,4162		0,10,2076	61.0	69.0	66.0		5442	-11.0	0.0	15	dbSNP_132	66	0,8430		0,0,4215	no	coding-synonymous	LRRK1	NM_024652.3		0,10,6291	AA,AG,GG		0.0,0.2397,0.0794		1814/2016	101606084	10,12592	2086	4215	6301	SO:0001819	synonymous_variant	79705	exon32			CATCGCGGACGTG	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.5442G>A	15.37:g.101606084G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	136	75	0.551471	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			G|0.997;A|0.003	0.003	strong		0.622	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
SGK223	157285	hgsc.bcm.edu	37	8	8234192	8234192	+	Missense_Mutation	SNP	G	G	C	rs4840953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8234192G>C	ENST00000520004.1	-	3	1991	c.1727C>G	c.(1726-1728)tCt>tGt	p.S576C	SGK223_ENST00000330777.4_Missense_Mutation_p.S576C			Q86YV5	SG223_HUMAN		578							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCTGCCGCCAGAGCTCCCATC	0.652													G|||	2276	0.454473	0.3918	0.4323	5008	,	,		16373	0.6409		0.3022	False		,,,				2504	0.5194				p.S576C	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1727G						PASS	.	G	CYS/SER	1306,2738		222,862,938	21.0	25.0	24.0		1727	1.9	0.0	8	dbSNP_111	24	2304,5992		322,1660,2166	yes	missense	SGK223	NM_001080826.1	112	544,2522,3104	CC,CG,GG		27.7724,32.2948,29.2545	benign	576/1403	8234192	3610,8730	2022	4148	6170	SO:0001583	missense	0	exon2			CCGCCAGAGCTCC																												ENST00000520004.1:c.1727C>G	8.37:g.8234192G>C	ENSP00000428054:p.Ser576Cys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	28	0.5	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	950	0.434981684981685	201	0.40853658536585363	142	0.39226519337016574	389	0.6800699300699301	218	0.287598944591029	G	10.25	1.297067	0.23650	0.322948	0.277724	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.59083	0.29;0.29	4.92	1.93	0.25924	.	2.545670	0.01254	N	0.008962	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.47169	-0.9138	9	0.38643	T	0.18	.	4.1097	0.10053	0.0811:0.2388:0.4682:0.212	rs4840953;rs52796687;rs59893685;rs4840953	576	Q86YV5	SG223_HUMAN	C	576	ENSP00000330930:S576C;ENSP00000428054:S576C	ENSP00000330930:S576C	S	-	2	0	AC068353.1	8271602	0.000000	0.05858	0.016000	0.15963	0.045000	0.14185	0.024000	0.13555	1.199000	0.43173	0.655000	0.94253	TCT	G|0.602;C|0.398	0.398	strong		0.652	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
DMD	1756	hgsc.bcm.edu	37	X	31893307	31893307	+	Missense_Mutation	SNP	T	T	G	rs1800275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:31893307T>G	ENST00000357033.4	-	48	7302	c.7096A>C	c.(7096-7098)Aag>Cag	p.K2366Q	DMD_ENST00000378677.2_Missense_Mutation_p.K2362Q|DMD_ENST00000378707.3_5'UTR|DMD_ENST00000541735.1_5'UTR|DMD_ENST00000474231.1_5'UTR|DMD_ENST00000343523.2_5'UTR|DMD_ENST00000359836.1_5'UTR	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	2366			K -> Q (in dbSNP:rs1800275). {ECO:0000269|PubMed:12359139, ECO:0000269|PubMed:3282674}.|Missing (in DMD).		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)				TTCCCTACCTTAACGTCAAAT	0.313													T|||	692	0.183311	0.1135	0.3314	3775	,	,		12761	0.0774		0.1581	False		,,,				2504	0.0767				.		Atlas-SNP	.											.	DMD	2127	.	0			c.7083+1A>C						PASS	.	T	GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS,,,,,	696,3137		61,474,100,1096,471	68.0	50.0	56.0		7072,7096,6727,7084,6727,3073,3064,,,,,	5.2	1.0	X	dbSNP_89	56	1465,5262		133,789,410,1506,1461	yes	missense,missense,missense,missense,missense,missense,missense,utr-5,utr-5,utr-5,utr-5,utr-5	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3,NM_004011.3,NM_004012.3,NM_004013.2,NM_004020.3,NM_004021.2,NM_004022.2,NM_004023.2	53,53,53,53,53,53,53,,,,,	194,1263,510,2602,1932	GG,GT,G,TT,T		21.7779,18.1581,20.464	benign,benign,benign,benign,benign,benign,benign,,,,,	2358/3678,2366/3686,2243/3563,2362/3682,2243/3563,1025/2345,1022/2342,,,,,	31893307	2161,8399	2202	4299	6501	SO:0001583	missense	1756	exon49			CTACCTTAACGTC	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.7096A>C	X.37:g.31893307T>G	ENSP00000354923:p.Lys2366Gln	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	178	83	0.466292	NM_004009	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Splice_Site	SNP	ENST00000357033.4	37	CCDS14233.1	337|337	0.20313441832429174|0.20313441832429174	46|46	0.09871244635193133|0.09871244635193133	77|77	0.25496688741721857|0.25496688741721857	31|31	0.05740740740740741|0.05740740740740741	86|86	0.12609970674486803|0.12609970674486803	T|T	15.07|15.07	2.722967|2.722967	0.48728|0.48728	0.181581|0.181581	0.217779|0.217779	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280|ENST00000465285	T;T;T|.	0.36699|.	1.24;1.24;1.24|.	5.18|5.18	5.18|5.18	0.71444|0.71444	.|.	0.000000|.	0.38778|.	U|.	0.001577|.	T|.	0.00012|.	0.0000|.	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	P|P	1.0|1.0	D;D;D;D;D|.	0.76494|.	0.999;0.998;0.998;0.998;0.998|.	D;D;D;D;D|.	0.80764|.	0.994;0.987;0.987;0.981;0.981|.	T|.	0.25152|.	-1.0140|.	9|.	0.24483|.	T|.	0.36|.	.|.	12.9094|12.9094	0.58171|0.58171	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs3198408|rs3198408	2358;2366;2362;1025;1022|.	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6|.	.;DMD_HUMAN;.;.;.|.	Q|S	2358;1025;1022;62;2362;2366;2366;2243|94	ENSP00000350765:K62Q;ENSP00000367948:K2362Q;ENSP00000354923:K2366Q|.	ENSP00000354923:K2366Q|.	K|X	-|-	1|2	0|2	DMD|DMD	31803228|31803228	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.725000|0.725000	0.41563|0.41563	2.455000|2.455000	0.44988|0.44988	1.830000|1.830000	0.53286|0.53286	0.486000|0.486000	0.48141|0.48141	AAG|TAA	T|0.809;0|0.003	.	strong		0.313	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
MAGEC3	139081	hgsc.bcm.edu	37	X	140967165	140967165	+	Missense_Mutation	SNP	T	T	C	rs372869684|rs11095909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:140967165T>C	ENST00000298296.1	+	3	463	c.463T>C	c.(463-465)Tcc>Ccc	p.S155P	MAGEC3_ENST00000448920.1_5'Flank|MAGEC3_ENST00000536088.1_5'Flank|MAGEC3_ENST00000443323.2_5'Flank	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	155			S -> P (in dbSNP:rs11095909).							NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					CTACACCCTTTCCCTTCCTGC	0.572													C|||	1658	0.439205	0.5348	0.3458	3775	,	,		10239	0.3651		0.0676	False		,,,				2504	0.2812				p.S155P		Atlas-SNP	.											.	MAGEC3	228	.	0			c.T463C						PASS	.	C	PRO/SER	2201,1453		686,544,285,357,195	37.0	32.0	33.0		463	-1.4	0.0	X	dbSNP_120	33	564,6162		18,376,152,2034,1718	yes	missense	MAGEC3	NM_138702.1	74	704,920,437,2391,1913	CC,CT,C,TT,T		8.3854,39.7646,26.6378	benign	155/644	140967165	2765,7615	2067	4298	6365	SO:0001583	missense	139081	exon3			ACCCTTTCCCTTC	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.463T>C	X.37:g.140967165T>C	ENSP00000298296:p.Ser155Pro	Somatic	421	1	0.0023753		WXS	Illumina HiSeq	Phase_I	458	457	0.997817	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	594	0.35804701627486435	178	0.5028248587570622	77	0.2532894736842105	130	0.29545454545454547	37	0.05096418732782369	C	0.009	-1.811288	0.00600	0.602354	0.083854	ENSG00000165509	ENST00000298296	T	0.06528	3.29	0.994	-1.44	0.08856	.	.	.	.	.	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	0.34054	-0.9844	8	0.20519	T	0.43	.	0.3624	0.00366	0.2444:0.308:0.2421:0.2055	rs11095909	155	Q8TD91	MAGC3_HUMAN	P	155	ENSP00000298296:S155P	ENSP00000298296:S155P	S	+	1	0	MAGEC3	140794831	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.198000	0.01239	-1.544000	0.01721	-2.375000	0.00234	TCC	T|0.639;C|0.361	0.361	strong		0.572	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
VPS8	23355	hgsc.bcm.edu	37	3	184550501	184550501	+	Missense_Mutation	SNP	A	A	G	rs9830734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184550501A>G	ENST00000437079.3	+	4	418	c.247A>G	c.(247-249)Att>Gtt	p.I83V	VPS8_ENST00000287546.4_Missense_Mutation_p.I83V|VPS8_ENST00000446204.2_Missense_Mutation_p.I83V|VPS8_ENST00000424463.2_Missense_Mutation_p.I83V|VPS8_ENST00000436792.2_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	182	0	0		WXS	Illumina HiSeq	Phase_I	172	78	0.453488	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	
RBM19	9904	hgsc.bcm.edu	37	12	114397192	114397192	+	Silent	SNP	C	C	T	rs140397506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114397192C>T	ENST00000545145.2	-	5	474	c.396G>A	c.(394-396)gaG>gaA	p.E132E	RBM19_ENST00000261741.5_Silent_p.E132E|RBM19_ENST00000392561.3_Silent_p.E132E	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	132					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)					ACTCCTGGAACTCTGTATCCT	0.597													C|||	26	0.00519169	0.0	0.0115	5008	,	,		17548	0.0		0.0169	False		,,,				2504	0.001				p.E132E		Atlas-SNP	.											.	RBM19	117	.	0			c.G396A						PASS	.	C	,,	17,4389	24.3+/-50.5	0,17,2186	63.0	67.0	66.0		396,396,396	2.4	1.0	12	dbSNP_134	66	139,8461	69.0+/-131.5	0,139,4161	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	0,156,6347	TT,TC,CC		1.6163,0.3858,1.1994	,,	132/961,132/961,132/961	114397192	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon5			CTGGAACTCTGTA	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.396G>A	12.37:g.114397192C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	113	63	0.557522	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			C|0.989;T|0.011	0.011	strong		0.597	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
SCN11A	11280	hgsc.bcm.edu	37	3	38945560	38945560	+	Silent	SNP	A	A	G	rs4073113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38945560A>G	ENST00000302328.3	-	12	1836	c.1638T>C	c.(1636-1638)tgT>tgC	p.C546C	SCN11A_ENST00000444237.2_Silent_p.C546C|SCN11A_ENST00000456224.3_Silent_p.C546C|SCN11A_ENST00000450244.1_Silent_p.C546C	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	546					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)	GGTTTTCTCCACAAGGGAGAC	0.507													G|||	3067	0.61242	0.4864	0.6888	5008	,	,		19281	0.6369		0.6471	False		,,,				2504	0.6677				p.C546C		Atlas-SNP	.											.	SCN11A	296	.	0			c.T1638C						PASS	.	G		2306,2100	575.0+/-383.9	590,1126,487	131.0	110.0	117.0		1638	-0.8	1.0	3	dbSNP_108	117	5594,3006	463.5+/-366.0	1832,1930,538	no	coding-synonymous	SCN11A	NM_014139.2		2422,3056,1025	GG,GA,AA		34.9535,47.6623,39.2588		546/1792	38945560	7900,5106	2203	4300	6503	SO:0001819	synonymous_variant	11280	exon12			TTCTCCACAAGGG	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.1638T>C	3.37:g.38945560A>G		Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	37	CCDS33737.1																																																																																			A|0.397;G|0.603	0.603	strong		0.507	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
TMEM200A	114801	hgsc.bcm.edu	37	6	130761957	130761957	+	Silent	SNP	A	A	G	rs3813359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:130761957A>G	ENST00000296978.3	+	3	1261	c.390A>G	c.(388-390)ccA>ccG	p.P130P	TMEM200A_ENST00000545622.1_Silent_p.P130P|TMEM200A_ENST00000392429.1_Silent_p.P130P	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	130						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TGCTTGGCCCATTCACCATGG	0.413													A|||	1396	0.278754	0.3699	0.2017	5008	,	,		20896	0.3413		0.1412	False		,,,				2504	0.2873				p.P130P		Atlas-SNP	.											.	TMEM200A	108	.	0			c.A390G						PASS	.	A		1590,2816	495.0+/-363.1	300,990,913	91.0	79.0	83.0		390	-5.3	0.9	6	dbSNP_107	83	1179,7421	240.4+/-271.1	74,1031,3195	no	coding-synonymous	TMEM200A	NM_052913.2		374,2021,4108	GG,GA,AA		13.7093,36.0872,21.2902		130/492	130761957	2769,10237	2203	4300	6503	SO:0001819	synonymous_variant	114801	exon3			TGGCCCATTCACC	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"""KIAA1913"""	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.390A>G	6.37:g.130761957A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_001258277	Q96PX5	Silent	SNP	ENST00000296978.3	37	CCDS5140.1																																																																																			A|0.770;G|0.230	0.230	strong		0.413	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913	
PFN4	375189	hgsc.bcm.edu	37	2	24344060	24344060	+	Silent	SNP	T	T	G	rs33913065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:24344060T>G	ENST00000313213.4	-	3	599	c.228A>C	c.(226-228)gcA>gcC	p.A76A	PFN4_ENST00000465360.1_5'UTR|FAM228B_ENST00000420135.2_5'Flank|FAM228B_ENST00000407625.1_5'Flank	NM_199346.1	NP_955378.1	Q8NHR9	PROF4_HUMAN	profilin family, member 4	76					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)					AATATTCATCTGCCCGGACAC	0.423													T|||	742	0.148163	0.084	0.1282	5008	,	,		19302	0.1071		0.2177	False		,,,				2504	0.2198				p.A76A		Atlas-SNP	.											.	PFN4	16	.	0			c.A228C						PASS	.	T		533,3873	239.6+/-250.7	30,473,1700	138.0	140.0	139.0		228	-1.0	1.0	2	dbSNP_126	139	1665,6935	306.5+/-307.9	157,1351,2792	no	coding-synonymous	PFN4	NM_199346.1		187,1824,4492	GG,GT,TT		19.3605,12.0971,16.8999		76/130	24344060	2198,10808	2203	4300	6503	SO:0001819	synonymous_variant	375189	exon3			TTCATCTGCCCGG	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.228A>C	2.37:g.24344060T>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	121	62	0.512397	NM_199346	Q53TL9	Silent	SNP	ENST00000313213.4	37	CCDS1709.1																																																																																			T|0.834;G|0.166	0.166	strong		0.423	PFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207617.2	NM_199346	
ZNF790	388536	hgsc.bcm.edu	37	19	37310344	37310344	+	Missense_Mutation	SNP	T	T	C	rs3745775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	55	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	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	
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186195	39186195	+	Missense_Mutation	SNP	C	C	T	rs386797029|rs141392271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39186195C>T	ENST00000377747.4	-	1	161	c.136G>A	c.(136-138)Ggc>Agc	p.G46S	KRTAP1-5_ENST00000361883.5_5'Flank	NM_001257305.1	NP_001244234.1	P0C5Y4	KRA14_HUMAN	keratin associated protein 1-4	46						keratin filament (GO:0045095)				lung(1)	1						TGGCCATAGCCAATGCCACCA	0.642													c|||	535	0.106829	0.1891	0.1167	5008	,	,		18090	0.1627		0.0159	False		,,,				2504	0.0245				p.G46S		Atlas-SNP	.											.	KRTAP1-4	4	.	0			c.G136A						PASS	.																																			SO:0001583	missense	728255	exon1			CATAGCCAATGCC	AC007455	CCDS58548.1	17q21.2	2010-06-22			ENSG00000204887	ENSG00000204887		"""Keratin associated proteins"""	18904	protein-coding gene	gene with protein product		608821					Standard	NM_001257305		Approved	KAP1.4	uc031raf.1	P0C5Y4	OTTHUMG00000133631	ENST00000377747.4:c.136G>A	17.37:g.39186195C>T	ENSP00000366976:p.Gly46Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_001257305	A6NJ92	Missense_Mutation	SNP	ENST00000377747.4	37	CCDS58548.1	222	0.10164835164835165	97	0.19715447154471544	27	0.07458563535911603	86	0.15034965034965034	12	0.0158311345646438	C	10.51	1.371800	0.24857	.	.	ENSG00000204887	ENST00000377747	T	0.45668	0.89	4.76	-5.96	0.02234	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.25467	-1.0131	5	0.02654	T	1	.	13.5045	0.61477	0.0:0.3078:0.0:0.6922	.	.	.	.	S	46	ENSP00000366976:G46S	ENSP00000366976:G46S	G	-	1	0	KRTAP1-4	36439721	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.076000	0.11412	-1.462000	0.01907	-1.851000	0.00568	GGC	C|0.898;T|0.102	0.102	strong		0.642	KRTAP1-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257776.3		
FAM71A	149647	hgsc.bcm.edu	37	1	212798977	212798977	+	Missense_Mutation	SNP	A	A	G	rs3122712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:212798977A>G	ENST00000294829.3	+	1	1189	c.758A>G	c.(757-759)aAt>aGt	p.N253S	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	253			N -> S (in dbSNP:rs3122712).			nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		AAACCCACTAATGTGCTCAAT	0.542													A|||	1267	0.252995	0.4554	0.196	5008	,	,		21770	0.0804		0.2634	False		,,,				2504	0.1871				p.N253S		Atlas-SNP	.											.	FAM71A	87	.	0			c.A758G						PASS	.	A	SER/ASN	1918,2488	547.8+/-377.4	413,1092,698	104.0	112.0	109.0		758	-0.8	0.0	1	dbSNP_103	109	2509,6091	411.1+/-350.4	382,1745,2173	yes	missense	FAM71A	NM_153606.3	46	795,2837,2871	GG,GA,AA		29.1744,43.5315,34.0381	benign	253/595	212798977	4427,8579	2203	4300	6503	SO:0001583	missense	149647	exon1			CCACTAATGTGCT		CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.758A>G	1.37:g.212798977A>G	ENSP00000294829:p.Asn253Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_153606	Q5VTZ1	Missense_Mutation	SNP	ENST00000294829.3	37	CCDS1507.1	569	0.26053113553113555	227	0.4613821138211382	87	0.24033149171270718	55	0.09615384615384616	200	0.2638522427440633	A	4.402	0.074306	0.08485	0.435315	0.291744	ENSG00000162771	ENST00000294829;ENST00000545975	T	0.03272	3.99	3.69	-0.822	0.10819	.	.	.	.	.	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.38134	-0.9675	8	0.08837	T	0.75	1.1457	1.7677	0.03005	0.2223:0.3327:0.3224:0.1226	rs3122712;rs52808176;rs56594967;rs59779974;rs3122712	253	Q8IYT1	FA71A_HUMAN	S	253;28	ENSP00000294829:N253S	ENSP00000294829:N253S	N	+	2	0	FAM71A	210865600	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	-0.003000	0.12901	-0.271000	0.09272	-0.290000	0.09829	AAT	A|0.697;G|0.303	0.303	strong		0.542	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606	
VWF	7450	hgsc.bcm.edu	37	12	6174423	6174423	+	Silent	SNP	T	T	A	rs1800375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6174423T>A	ENST00000261405.5	-	11	1427	c.1173A>T	c.(1171-1173)acA>acT	p.T391T		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	391	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.T391T(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GTGATTGACCTGTGACAAGGC	0.552													T|||	1357	0.270966	0.5076	0.1297	5008	,	,		21004	0.247		0.1213	False		,,,				2504	0.2301				p.T391T		Atlas-SNP	.											VWF,NS,carcinoma,0,1	VWF	338	1	1	Substitution - coding silent(1)	stomach(1)	c.A1173T						PASS	.	T		2055,2351	564.0+/-381.3	506,1043,654	83.0	78.0	80.0		1173	-5.9	0.6	12	dbSNP_89	80	1092,7508	227.8+/-263.0	76,940,3284	no	coding-synonymous	VWF	NM_000552.3		582,1983,3938	AA,AT,TT		12.6977,46.6409,24.1965		391/2814	6174423	3147,9859	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon11			TTGACCTGTGACA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.1173A>T	12.37:g.6174423T>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			T|0.770;A|0.230	0.230	strong		0.552	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
KRT3	3850	hgsc.bcm.edu	37	12	53189446	53189446	+	Silent	SNP	C	C	T	rs117364830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	178	0	0		WXS	Illumina HiSeq	Phase_I	184	24	0.130435	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	
LRRC8E	80131	hgsc.bcm.edu	37	19	7965669	7965669	+	Silent	SNP	C	C	T	rs3745385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7965669C>T	ENST00000306708.6	+	3	2363	c.2262C>T	c.(2260-2262)ggC>ggT	p.G754G	AC010336.1_ENST00000539278.1_5'UTR|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	754					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						AGCTCAAAGGCAACCGCTTAG	0.652													C|||	228	0.0455272	0.1029	0.0086	5008	,	,		16095	0.0823		0.0	False		,,,				2504	0.0031				p.G754G		Atlas-SNP	.											.	LRRC8E	67	.	0			c.C2262T						PASS	.	C		407,3999		17,373,1813	35.0	40.0	38.0		2262	-1.9	1.0	19	dbSNP_107	38	8,8592		0,8,4292	no	coding-synonymous	LRRC8E	NM_025061.3		17,381,6105	TT,TC,CC		0.093,9.2374,3.1908		754/797	7965669	415,12591	2203	4300	6503	SO:0001819	synonymous_variant	80131	exon4			CAAAGGCAACCGC		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.2262C>T	19.37:g.7965669C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	162	89	0.549383	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Silent	SNP	ENST00000306708.6	37	CCDS12189.1																																																																																			C|0.956;T|0.044	0.044	strong		0.652	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
ACSS2	55902	hgsc.bcm.edu	37	20	33513983	33513983	+	Missense_Mutation	SNP	G	G	C	rs45486997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33513983G>C	ENST00000360596.2	+	16	2013	c.1802G>C	c.(1801-1803)gGc>gCc	p.G601A	ACSS2_ENST00000336325.4_Missense_Mutation_p.G551A|ACSS2_ENST00000476922.1_Intron|ACSS2_ENST00000253382.5_Missense_Mutation_p.G614A	NM_018677.3	NP_061147.1	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2	601					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|lipid biosynthetic process (GO:0008610)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(9)	21					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GCTGTGGTGGGCCACCCTCAT	0.557													G|||	190	0.0379393	0.1316	0.0231	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.G614A		Atlas-SNP	.											.	ACSS2	75	.	0			c.G1841C						PASS	.	G	ALA/GLY,ALA/GLY,ALA/GLY	487,3919	224.3+/-240.5	27,433,1743	138.0	105.0	116.0		1841,1517,1802	4.3	0.9	20	dbSNP_127	116	17,8583	11.9+/-42.8	0,17,4283	yes	missense,missense,missense	ACSS2	NM_001076552.2,NM_001242393.1,NM_018677.3	60,60,60	27,450,6026	CC,CG,GG		0.1977,11.0531,3.8751	benign,benign,benign	614/715,506/607,601/702	33513983	504,12502	2203	4300	6503	SO:0001583	missense	55902	exon17			TGGTGGGCCACCC	AF263614	CCDS13243.1, CCDS42868.1, CCDS42868.2	20q11.22	2012-07-13	2005-09-08	2005-09-08	ENSG00000131069	ENSG00000131069	6.2.1.1	"""Acyl-CoA synthetase family"""	15814	protein-coding gene	gene with protein product		605832	"""acetyl-Coenzyme A synthetase 2 (ADP forming)"""	ACAS2		10843999	Standard	NM_018677		Approved	ACS, ACSA, AceCS, dJ1161H23.1	uc010gey.2	Q9NR19	OTTHUMG00000032317	ENST00000360596.2:c.1802G>C	20.37:g.33513983G>C	ENSP00000353804:p.Gly601Ala	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	182	95	0.521978	NM_001076552	A6NE90|Q5QPH2|Q5QPH3|Q8N238|Q96EL0|Q9NQP7|Q9UJ15	Missense_Mutation	SNP	ENST00000360596.2	37	CCDS13243.1	57	0.0260989010989011	50	0.1016260162601626	7	0.019337016574585635	0	0.0	0	0.0	G	15.09	2.729599	0.48833	0.110531	0.001977	ENSG00000131069	ENST00000336325;ENST00000360596;ENST00000374693;ENST00000542204;ENST00000253382	T;T;T	0.62941	-0.01;-0.01;-0.01	5.25	4.29	0.51040	.	0.241356	0.49305	N	0.000155	T	0.02083	0.0065	L	0.53780	1.695	0.51012	D	0.9999	B;B	0.10296	0.001;0.003	B;B	0.12156	0.007;0.007	T	0.15983	-1.0418	10	0.87932	D	0	-12.1309	15.8996	0.79362	0.0:0.1355:0.8645:0.0	rs45486997;rs60500786	614;601	Q5QPH3;Q9NR19	.;ACSA_HUMAN	A	551;601;599;309;614	ENSP00000337190:G551A;ENSP00000353804:G601A;ENSP00000253382:G614A	ENSP00000253382:G614A	G	+	2	0	ACSS2	32977644	1.000000	0.71417	0.898000	0.35279	0.962000	0.63368	7.711000	0.84669	1.417000	0.47077	0.563000	0.77884	GGC	G|0.968;C|0.032	0.032	strong		0.557	ACSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078823.3	NM_018677	
FAT1	2195	hgsc.bcm.edu	37	4	187557863	187557863	+	Missense_Mutation	SNP	G	G	A	rs60068521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187557863G>A	ENST00000441802.2	-	5	4057	c.3848C>T	c.(3847-3849)cCc>cTc	p.P1283L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1283	Cadherin 11. {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						TTCTGCATTGGGGCCCTCATC	0.502										HNSCC(5;0.00058)			G|||	6	0.00119808	0.0045	0.0	5008	,	,		15954	0.0		0.0	False		,,,				2504	0.0				p.P1283L	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C3848T						PASS	.	G	LEU/PRO	4,3800		0,4,1898	224.0	226.0	225.0		3848	5.0	1.0	4	dbSNP_129	225	0,8238		0,0,4119	yes	missense	FAT1	NM_005245.3	98	0,4,6017	AA,AG,GG		0.0,0.1052,0.0332	benign	1283/4589	187557863	4,12038	1902	4119	6021	SO:0001583	missense	2195	exon5			GCATTGGGGCCCT	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.3848C>T	4.37:g.187557863G>A	ENSP00000406229:p.Pro1283Leu	Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	300	155	0.516667	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	15.34	2.804208	0.50315	0.001052	0.0	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.54071	0.59	4.99	4.99	0.66335	Cadherin (4);Cadherin-like (1);	0.172618	0.52532	D	0.000077	T	0.61999	0.2392	L	0.41415	1.275	0.80722	D	1	D	0.67145	0.996	D	0.63957	0.92	T	0.54906	-0.8223	10	0.22109	T	0.4	.	18.4667	0.90758	0.0:0.0:1.0:0.0	rs60068521	1283	Q14517	FAT1_HUMAN	L	1283	ENSP00000406229:P1283L	ENSP00000260147:P1283L	P	-	2	0	FAT1	187794857	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	9.657000	0.98554	2.599000	0.87857	0.561000	0.74099	CCC	G|0.999;A|0.001	0.001	strong		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ADAM7	8756	hgsc.bcm.edu	37	8	24349482	24349482	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24349482G>A	ENST00000175238.6	+	14	1506	c.1423G>A	c.(1423-1425)Ggc>Agc	p.G475S	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM7_ENST00000520720.1_Missense_Mutation_p.G247S|ADAM7_ENST00000380789.1_Missense_Mutation_p.G475S|RP11-561E1.1_ENST00000519364.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	475	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		GATGTGCACTGGCCACTCGCC	0.463																																					p.G475S		Atlas-SNP	.											ADAM7,colon,carcinoma,-2,1	ADAM7	165	1	0			c.G1423A						PASS	.																																			SO:0001583	missense	8756	exon14			TGCACTGGCCACT	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.1423G>A	8.37:g.24349482G>A	ENSP00000175238:p.Gly475Ser	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.891293	0.91889	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.57107	0.42;0.42;0.42	5.78	5.78	0.91487	Blood coagulation inhibitor, Disintegrin (6);	0.000000	0.56097	D	0.000026	D	0.83889	0.5352	H	0.98487	4.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89755	0.3943	10	0.87932	D	0	.	17.5062	0.87746	0.0:0.0:1.0:0.0	.	247;475	E5RK87;Q9H2U9	.;ADAM7_HUMAN	S	475;475;247;290	ENSP00000175238:G475S;ENSP00000370166:G475S;ENSP00000430400:G247S	ENSP00000175238:G475S	G	+	1	0	ADAM7	24405372	1.000000	0.71417	0.997000	0.53966	0.784000	0.44337	7.643000	0.83403	2.749000	0.94314	0.655000	0.94253	GGC	.	.	none		0.463	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
GBP4	115361	hgsc.bcm.edu	37	1	89655783	89655783	+	Missense_Mutation	SNP	T	T	C	rs1831240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89655783T>C	ENST00000355754.6	-	7	1232	c.1135A>G	c.(1135-1137)Att>Gtt	p.I379V		NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	379			I -> V (in dbSNP:rs1831240).			cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		AAGACTGCAATGGCTTCCCTC	0.522													T|||	380	0.0758786	0.2738	0.0231	5008	,	,		19044	0.0		0.002	False		,,,				2504	0.0				p.I379V		Atlas-SNP	.											GBP4,colon,carcinoma,0,1	GBP4	89	1	0			c.A1135G						PASS	.	T	VAL/ILE	1026,3380	378.3+/-322.8	120,786,1297	105.0	99.0	101.0		1135	2.8	0.6	1	dbSNP_92	101	12,8588	8.4+/-32.0	0,12,4288	no	missense	GBP4	NM_052941.4	29	120,798,5585	CC,CT,TT		0.1395,23.2864,7.9809	benign	379/641	89655783	1038,11968	2203	4300	6503	SO:0001583	missense	115361	exon7			CTGCAATGGCTTC	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1135A>G	1.37:g.89655783T>C	ENSP00000359490:p.Ile379Val	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	281	145	0.516014	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Missense_Mutation	SNP	ENST00000355754.6	37	CCDS721.1	124	0.056776556776556776	115	0.23373983739837398	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	T	6.625	0.483667	0.12581	0.232864	0.001395	ENSG00000162654	ENST00000355754	T	0.02067	4.47	5.07	2.78	0.32641	Guanylate-binding protein, C-terminal (3);	0.361979	0.28589	N	0.014812	T	0.01523	0.0049	M	0.82323	2.585	0.52099	P	5.8000000000002494E-5	B	0.21225	0.053	B	0.22753	0.041	T	0.29761	-1.0001	9	0.35671	T	0.21	.	7.8039	0.29191	0.0:0.1723:0.0:0.8277	rs1831240;rs1831240	379	Q96PP9	GBP4_HUMAN	V	379	ENSP00000359490:I379V	ENSP00000359490:I379V	I	-	1	0	GBP4	89428371	0.289000	0.24334	0.596000	0.28811	0.060000	0.15804	0.162000	0.16501	0.508000	0.28173	-0.250000	0.11733	ATT	T|1.000;|0.000	.	weak		0.522	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
MUT	4594	hgsc.bcm.edu	37	6	49409599	49409599	+	Missense_Mutation	SNP	G	G	A	rs140727018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49409599G>A	ENST00000274813.3	-	10	1889	c.1762C>T	c.(1762-1764)Cgc>Tgc	p.R588C		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	588					cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AATTCCTGGCGATATGCTCCA	0.388													G|||	2	0.000399361	0.0015	0.0	5008	,	,		10715	0.0		0.0	False		,,,				2504	0.0				p.R588C		Atlas-SNP	.											.	MUT	70	.	0			c.C1762T						PASS	.	G	CYS/ARG	16,4390	23.3+/-48.9	0,16,2187	231.0	210.0	217.0		1762	4.7	1.0	6	dbSNP_134	217	0,8600		0,0,4300	yes	missense	MUT	NM_000255.3	180	0,16,6487	AA,AG,GG		0.0,0.3631,0.123	probably-damaging	588/751	49409599	16,12990	2203	4300	6503	SO:0001583	missense	4594	exon10			CCTGGCGATATGC		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"""methylmalonyl Coenzyme A mutase"""			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1762C>T	6.37:g.49409599G>A	ENSP00000274813:p.Arg588Cys	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	256	134	0.523438	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Missense_Mutation	SNP	ENST00000274813.3	37	CCDS4924.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	22.7	4.329566	0.81690	0.003631	0.0	ENSG00000146085	ENST00000274813;ENST00000540138	D	0.95069	-3.6	5.59	4.72	0.59763	Cobalamin (vitamin B12)-binding (2);	0.000000	0.85682	D	0.000000	D	0.96156	0.8747	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	D	0.96378	0.9279	10	0.59425	D	0.04	-20.2086	15.0369	0.71754	0.0:0.0:0.8569:0.1431	.	588	P22033	MUTA_HUMAN	C	588;35	ENSP00000274813:R588C	ENSP00000274813:R588C	R	-	1	0	MUT	49517558	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.507000	0.81676	1.345000	0.45676	0.585000	0.79938	CGC	G|0.999;A|0.001	0.001	strong		0.388	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1		
OR2T12	127064	hgsc.bcm.edu	37	1	248458718	248458718	+	Missense_Mutation	SNP	T	T	C	rs79635253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248458718T>C	ENST00000317996.1	-	1	162	c.163A>G	c.(163-165)Agg>Ggg	p.R55G		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	55						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)			TACATGGGCCTGTGGAGCCGG	0.527													-|||	151	0.0301518	0.0915	0.0144	5008	,	,		12875	0.001		0.0169	False		,,,				2504	0.002				p.R55G		Atlas-SNP	.											.	OR2T12	113	.	0			c.A163G						PASS	.	T	GLY/ARG	443,3963	195.7+/-220.2	54,335,1814	81.0	65.0	70.0		163	1.5	0.2	1	dbSNP_131	70	170,8426	69.0+/-131.5	10,150,4138	no	missense	OR2T12	NM_001004692.1	125	64,485,5952	CC,CT,TT		1.9777,10.0545,4.7147	benign	55/321	248458718	613,12389	2203	4298	6501	SO:0001583	missense	127064	exon1			TGGGCCTGTGGAG	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.163A>G	1.37:g.248458718T>C	ENSP00000324583:p.Arg55Gly	Somatic	491	1	0.00203666		WXS	Illumina HiSeq	Phase_I	530	345	0.650943	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	82	0.037545787545787544	51	0.10365853658536585	8	0.022099447513812154	0	0.0	23	0.030343007915567283	t	9.783	1.175918	0.21704	0.100545	0.019777	ENSG00000177201	ENST00000317996	T	0.00384	7.6	1.55	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36303	U	0.002679	T	0.00012	0.0000	L	0.52011	1.625	0.09310	N	0.999998	B	0.12013	0.005	B	0.14023	0.01	T	0.51371	-0.8714	10	0.87932	D	0	.	4.983	0.14176	0.2683:0.0:0.0:0.7317	.	55	Q8NG77	O2T12_HUMAN	G	55	ENSP00000324583:R55G	ENSP00000324583:R55G	R	-	1	2	OR2T12	246525341	0.001000	0.12720	0.159000	0.22649	0.174000	0.22865	-0.039000	0.12124	0.540000	0.28808	0.147000	0.16070	AGG	T|0.961;C|0.039	0.039	strong		0.527	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
PCYOX1L	78991	hgsc.bcm.edu	37	5	148747678	148747678	+	Missense_Mutation	SNP	G	G	A	rs35552800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:148747678G>A	ENST00000274569.4	+	6	1008	c.946G>A	c.(946-948)Gca>Aca	p.A316T	PCYOX1L_ENST00000514349.1_Missense_Mutation_p.A226T	NM_024028.3	NP_076933.3	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like	316			A -> T (in dbSNP:rs35552800).		prenylcysteine catabolic process (GO:0030328)	extracellular region (GO:0005576)|membrane (GO:0016020)	prenylcysteine oxidase activity (GO:0001735)			breast(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTAACCTTTGCAGGCTTCCA	0.572											OREG0016912	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	177	0.0353435	0.121	0.0014	5008	,	,		18388	0.0		0.0119	False		,,,				2504	0.0041				p.A316T	Ovarian(62;1136 1477 27277 27495)	Atlas-SNP	.											.	PCYOX1L	32	.	0			c.G946A						PASS	.	G	THR/ALA	429,3977	209.5+/-230.2	26,377,1800	154.0	150.0	152.0		946	3.7	1.0	5	dbSNP_126	152	90,8510	50.6+/-110.7	0,90,4210	yes	missense	PCYOX1L	NM_024028.3	58	26,467,6010	AA,AG,GG		1.0465,9.7367,3.9905	benign	316/495	148747678	519,12487	2203	4300	6503	SO:0001583	missense	78991	exon6			ACCTTTGCAGGCT		CCDS4296.1	5q33.1	2008-02-05			ENSG00000145882	ENSG00000145882			28477	protein-coding gene	gene with protein product						12477932	Standard	NM_024028		Approved	MGC3265	uc003lqk.2	Q8NBM8	OTTHUMG00000130052	ENST00000274569.4:c.946G>A	5.37:g.148747678G>A	ENSP00000274569:p.Ala316Thr	Somatic	144	0	0	1719	WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_024028	Q7Z4S2|Q8NCY5|Q8NF69|Q9BTE8|Q9BWS3	Missense_Mutation	SNP	ENST00000274569.4	37	CCDS4296.1	53	0.024267399267399268	42	0.08536585365853659	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	G	3.849	-0.032166	0.07543	0.097367	0.010465	ENSG00000145882	ENST00000274569;ENST00000514349	T;T	0.14391	2.99;2.51	5.53	3.7	0.42460	Prenylcysteine lyase (1);	0.363998	0.31721	N	0.007174	T	0.00144	0.0004	N	0.00841	-1.15	0.18873	N	0.999984	B;B;B	0.12013	0.0;0.0;0.005	B;B;B	0.14578	0.002;0.002;0.011	T	0.42932	-0.9422	10	0.14252	T	0.57	-4.3953	10.8265	0.46635	0.0741:0.4234:0.5025:0.0	rs35552800;rs59241704	198;226;316	B3KXF9;E7EVZ5;Q8NBM8	.;.;PCYXL_HUMAN	T	316;226	ENSP00000274569:A316T;ENSP00000428512:A226T	ENSP00000274569:A316T	A	+	1	0	PCYOX1L	148727871	0.013000	0.17824	1.000000	0.80357	0.211000	0.24417	0.795000	0.26972	1.286000	0.44565	0.561000	0.74099	GCA	G|0.965;A|0.035	0.035	strong		0.572	PCYOX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252331.2	NM_024028	
TATDN3	128387	hgsc.bcm.edu	37	1	212965284	212965284	+	Silent	SNP	C	C	G	rs61736926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:212965284C>G	ENST00000366974.4	+	1	115	c.21C>G	c.(19-21)ggC>ggG	p.G7G	NSL1_ENST00000473995.1_5'Flank|NSL1_ENST00000366977.3_5'Flank|TATDN3_ENST00000366973.4_Silent_p.G7G|TATDN3_ENST00000526641.1_Silent_p.G7G|TATDN3_ENST00000526997.1_Silent_p.G7G|NSL1_ENST00000366978.1_5'Flank|TATDN3_ENST00000532324.1_Silent_p.G7G|NSL1_ENST00000366976.1_5'Flank|TATDN3_ENST00000530441.1_Silent_p.G7G|NSL1_ENST00000366975.6_5'Flank|TATDN3_ENST00000531963.1_Silent_p.G7G|NSL1_ENST00000422588.2_5'Flank	NM_001042552.2|NM_001042553.2|NM_001146169.1|NM_001146171.1	NP_001036017.1|NP_001036018.1|NP_001139641.1|NP_001139643.1	Q17R31	TATD3_HUMAN	TatD DNase domain containing 3	7					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00699)|all cancers(67;0.0118)|GBM - Glioblastoma multiforme(131;0.0801)|Epithelial(68;0.104)		CTGGCGTAGGCTTGGTGGACT	0.672													G|||	1141	0.227835	0.3986	0.1196	5008	,	,		12998	0.1538		0.1541	False		,,,				2504	0.226				p.G7G		Atlas-SNP	.											TATDN3,NS,carcinoma,0,1	TATDN3	23	1	0			c.C21G						scavenged	.	G	,,,,	1595,2809	626.1+/-394.7	296,1003,903	25.0	31.0	29.0		21,21,21,21,21	-3.6	0.0	1	dbSNP_129	29	1321,7279	727.2+/-406.6	101,1119,3080	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TATDN3	NM_001042552.2,NM_001042553.2,NM_001146169.1,NM_001146170.1,NM_001146171.1	,,,,	397,2122,3983	GG,GC,CC		15.3605,36.2171,22.4239	,,,,	7/275,7/274,7/241,7/254,7/282	212965284	2916,10088	2202	4300	6502	SO:0001819	synonymous_variant	128387	exon1			CGTAGGCTTGGTG	AL832248	CCDS31019.1, CCDS41465.1, CCDS53475.1, CCDS53476.1, CCDS53477.1	1q32.3	2008-02-05			ENSG00000203705	ENSG00000203705			27010	protein-coding gene	gene with protein product							Standard	NM_001042552		Approved		uc001hjo.2	Q17R31	OTTHUMG00000036805	ENST00000366974.4:c.21C>G	1.37:g.212965284C>G		Somatic	172	4	0.0232558		WXS	Illumina HiSeq	Phase_I	201	115	0.572139	NM_001146170	A6NGS3|B7Z1C1|B7Z978|B7ZLQ6|E9PJE5|E9PNH3|G3V151|Q4G0L1	Silent	SNP	ENST00000366974.4	37	CCDS31019.1	469	0.21474358974358973	216	0.43902439024390244	48	0.13259668508287292	89	0.1555944055944056	116	0.15303430079155672	G	7.215	0.596217	0.13875	0.362171	0.153605	ENSG00000203705	ENST00000488246	.	.	.	5.24	-3.62	0.04543	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.52501	P	4.199999999998649E-5	.	.	.	.	.	.	T	0.42548	-0.9445	3	.	.	.	-9.0778	9.1104	0.36723	0.064:0.5664:0.1779:0.1917	rs61736926	.	.	.	V	7	.	.	L	+	1	0	TATDN3	211031907	0.029000	0.19370	0.004000	0.12327	0.043000	0.13939	-0.132000	0.10467	-0.757000	0.04697	-2.997000	0.00077	CTT	C|0.772;G|0.228	0.228	strong		0.672	TATDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089396.2	XM_375838	
OR5L1	219437	hgsc.bcm.edu	37	11	55579801	55579801	+	Missense_Mutation	SNP	T	T	C	rs12790505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55579801T>C	ENST00000333973.2	+	1	948	c.859T>C	c.(859-861)Tct>Cct	p.S287P		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	287			S -> P (in dbSNP:rs12790505).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S287P(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TATGCTGAACTCTGTGATCTA	0.433													N|||	525	0.104832	0.1884	0.0461	5008	,	,		15985	0.0813		0.0924	False		,,,				2504	0.0706				p.S287P		Atlas-SNP	.											OR5L1,NS,carcinoma,0,1	OR5L1	145	1	1	Substitution - Missense(1)	stomach(1)	c.T859C						PASS	.	C	PRO/SER	669,3731		63,543,1594	56.0	54.0	55.0		859	4.1	0.9	11	dbSNP_121	55	726,7866		32,662,3602	yes	missense	OR5L1	NM_001004738.1	74	95,1205,5196	CC,CT,TT		8.4497,15.2045,10.7374	benign	287/312	55579801	1395,11597	2200	4296	6496	SO:0001583	missense	219437	exon1			CTGAACTCTGTGA	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.859T>C	11.37:g.55579801T>C	ENSP00000335529:p.Ser287Pro	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	175	79	0.451429	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	213	0.09752747252747253	92	0.18699186991869918	21	0.058011049723756904	35	0.06118881118881119	65	0.08575197889182058	N	0.453	-0.892792	0.02491	0.152045	0.084497	ENSG00000186117	ENST00000333973	T	0.14516	2.5	4.12	4.12	0.48240	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	N	0.000079	T	0.00012	0.0000	N	0.00001	-3.64	0.49213	P	2.4000000000001798E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.37663	-0.9696	9	0.02654	T	1	-51.3685	11.1525	0.48466	0.0:0.9065:0.0:0.0935	rs12790505;rs52821601;rs12790505	287	Q8NGL2	OR5L1_HUMAN	P	287	ENSP00000335529:S287P	ENSP00000335529:S287P	S	+	1	0	OR5L1	55336377	0.997000	0.39634	0.884000	0.34674	0.299000	0.27559	3.578000	0.53892	0.738000	0.32606	-0.984000	0.02558	TCT	T|0.888;C|0.112	0.112	strong		0.433	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
FAM151A	338094	hgsc.bcm.edu	37	1	55075334	55075334	+	Silent	SNP	G	G	A	rs201640566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55075334G>A	ENST00000302250.2	-	8	1525	c.1365C>T	c.(1363-1365)ccC>ccT	p.P455P	ACOT11_ENST00000371316.3_Intron|FAM151A_ENST00000371304.2_Intron|ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_3'UTR	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	455						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						CCACATGGCCGGGGACCGAAA	0.642													g|||	2	0.000399361	0.0008	0.0014	5008	,	,		18259	0.0		0.0	False		,,,				2504	0.0				p.P455P		Atlas-SNP	.											.	FAM151A	58	.	0			c.C1365T						PASS	.						32.0	35.0	34.0					1																	55075334		2202	4300	6502	SO:0001819	synonymous_variant	338094	exon8			ATGGCCGGGGACC	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.1365C>T	1.37:g.55075334G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Silent	SNP	ENST00000302250.2	37	CCDS594.1																																																																																			G|1.000;A|0.000	0.000	strong		0.642	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782	
LILRB3	11025	hgsc.bcm.edu	37	19	54721320	54721320	+	Missense_Mutation	SNP	C	C	G	rs1053002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54721320C>G	ENST00000391750.1	-	13	1753	c.1617G>C	c.(1615-1617)caG>caC	p.Q539H	LILRB3_ENST00000424807.1_Missense_Mutation_p.Q539H|LILRA6_ENST00000419410.2_Missense_Mutation_p.Q540H|LILRA6_ENST00000270464.5_Missense_Mutation_p.Q540H|LILRB3_ENST00000346401.6_Missense_Mutation_p.Q551H|LILRB3_ENST00000245620.9_Missense_Mutation_p.Q540H|LILRB3_ENST00000469273.1_5'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.Q556H|LILRA6_ENST00000440558.2_Missense_Mutation_p.Q539H|LILRA6_ENST00000391735.3_3'UTR			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	539			Q -> H (in dbSNP:rs1053002). {ECO:0000269|PubMed:9548455}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACGTCACTGCCTGGGGGTCTT	0.577																																					p.Q540H		Atlas-SNP	.											LILRB3,NS,carcinoma,-2,1	LILRB3	67	1	0			c.G1620C						PASS	.						97.0	102.0	100.0					19																	54721320		2202	4300	6502	SO:0001583	missense	11025	exon12			CACTGCCTGGGGG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1617G>C	19.37:g.54721320C>G	ENSP00000375630:p.Gln539His	Somatic	610	0	0		WXS	Illumina HiSeq	Phase_I	447	115	0.257271	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	256	0.11721611721611722	140	0.2845528455284553	37	0.10220994475138122	3	0.005244755244755245	76	0.10026385224274406	C	6.747	0.506690	0.12883	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00531	6.77;6.77;6.79;6.78;6.84;6.76;6.77;6.79	2.47	-2.73	0.05950	.	.	.	.	.	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	B;D;B;B;D;D;D	0.76494	0.095;0.988;0.226;0.004;0.967;0.999;0.994	B;P;B;B;P;P;D	0.68765	0.028;0.816;0.068;0.007;0.77;0.894;0.96	T	0.51403	-0.8710	8	0.59425	D	0.04	.	2.8244	0.05481	0.2046:0.4038:0.0:0.3916	rs1053002;rs3193491	556;539;540;551;556;539;540	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	H	539;539;551;540;556;539;540;540	ENSP00000375630:Q539H;ENSP00000412771:Q539H;ENSP00000345184:Q551H;ENSP00000245620:Q540H;ENSP00000384274:Q556H;ENSP00000390120:Q539H;ENSP00000270464:Q540H;ENSP00000411227:Q540H	ENSP00000270464:Q540H	Q	-	3	2	LILRB3;LILRA6	59413132	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.903000	0.04084	-0.478000	0.06823	0.413000	0.27773	CAG	C|0.891;G|0.109	0.109	strong		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
OR2T27	403239	hgsc.bcm.edu	37	1	248813421	248813421	+	Silent	SNP	G	G	A	rs200410497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813421G>A	ENST00000344889.3	-	1	764	c.765C>T	c.(763-765)gcC>gcT	p.A255A		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATGTGTACATGGCAGCCCCAT	0.527													G|||	320	0.0638978	0.2292	0.0231	5008	,	,		17935	0.0		0.001	False		,,,				2504	0.0				p.A255A		Atlas-SNP	.											.	OR2T27	52	.	0			c.C765T						PASS	.	G		669,3711		76,517,1597	39.0	30.0	33.0		765	0.1	0.0	1	dbSNP_134	33	6,8522		0,6,4258	no	coding-synonymous	OR2T27	NM_001001824.1		76,523,5855	AA,AG,GG		0.0704,15.274,5.2293		255/318	248813421	675,12233	2190	4264	6454	SO:0001819	synonymous_variant	403239	exon1			GTACATGGCAGCC		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.765C>T	1.37:g.248813421G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	154	69	0.448052	NM_001001824		Silent	SNP	ENST00000344889.3	37	CCDS31124.1																																																																																			G|0.969;A|0.031	0.031	strong		0.527	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
IRF7	3665	hgsc.bcm.edu	37	11	614367	614367	+	Silent	SNP	T	T	C	rs11246214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:614367T>C	ENST00000397574.2	-	6	855	c.486A>G	c.(484-486)acA>acG	p.T162T	IRF7_ENST00000525445.1_Silent_p.T56T|IRF7_ENST00000397562.3_Intron|IRF7_ENST00000330243.5_Silent_p.T175T|IRF7_ENST00000397570.1_Silent_p.T162T|IRF7_ENST00000348655.6_Silent_p.T162T|IRF7_ENST00000397566.1_Silent_p.T175T	NM_001572.3	NP_001563.2	Q92985	IRF7_HUMAN	interferon regulatory factor 7	162					cellular response to DNA damage stimulus (GO:0006974)|cytokine-mediated signaling pathway (GO:0019221)|establishment of viral latency (GO:0019043)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-alpha production (GO:0032607)|interferon-beta production (GO:0032608)|interferon-gamma-mediated signaling pathway (GO:0060333)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|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)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of adaptive immune response (GO:0002819)|regulation of immune response (GO:0050776)|regulation of monocyte differentiation (GO:0045655)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|regulation of MyD88-independent toll-like receptor signaling pathway (GO:0034127)|regulation of type I interferon production (GO:0032479)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;7.68e-28)|Epithelial(43;7.44e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;6.96e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTCCAGCATGTGTGTGTGCCA	0.662													t|||	200	0.0399361	0.0772	0.0375	5008	,	,		15192	0.001		0.0527	False		,,,				2504	0.0184				p.T175T		Atlas-SNP	.											.	IRF7	23	.	0			c.A525G						PASS	.		,,	233,4147	129.8+/-166.5	8,217,1965	32.0	32.0	32.0		486,486,525	-2.5	0.0	11	dbSNP_120	32	405,8189	118.3+/-177.8	12,381,3904	no	coding-synonymous,coding-synonymous,coding-synonymous	IRF7	NM_001572.3,NM_004029.2,NM_004031.2	,,	20,598,5869	CC,CT,TT		4.7126,5.3196,4.9175	,,	162/504,162/475,175/517	614367	638,12336	2190	4297	6487	SO:0001819	synonymous_variant	3665	exon4			AGCATGTGTGTGT	U53830	CCDS7703.1, CCDS7704.1, CCDS7705.1	11p15.5	2005-10-10			ENSG00000185507	ENSG00000185507			6122	protein-coding gene	gene with protein product		605047					Standard	XM_005252906		Approved		uc001lqh.3	Q92985	OTTHUMG00000132019	ENST00000397574.2:c.486A>G	11.37:g.614367T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_004031	B9EGL3|O00331|O00332|O00333|O75924|Q9UE79	Silent	SNP	ENST00000397574.2	37	CCDS7703.1																																																																																			T|0.956;C|0.044	0.044	strong		0.662	IRF7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255026.1	NM_001572	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33393583	33393583	+	Silent	SNP	C	C	T	rs73402305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33393583C>T	ENST00000418600.2	+	3	299	c.198C>T	c.(196-198)ccC>ccT	p.P66P	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Silent_p.P66P	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	66					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						AGATACACCCCCTACTGATCC	0.697													c|||	259	0.0517173	0.1921	0.0058	5008	,	,		9030	0.0		0.001	False		,,,				2504	0.0				p.P66P		Atlas-SNP	.											SYNGAP1_ENST00000293748,NS,carcinoma,+2,2	SYNGAP1	202	2	0			c.C198T						PASS	.	C		653,3753	259.8+/-263.3	41,571,1591	47.0	40.0	43.0		198	0.8	1.0	6	dbSNP_131	43	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	SYNGAP1	NM_006772.2		41,579,5883	TT,TC,CC		0.093,14.8207,5.0823		66/1344	33393583	661,12345	2203	4300	6503	SO:0001819	synonymous_variant	8831	exon3			ACACCCCCTACTG	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.198C>T	6.37:g.33393583C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	168	77	0.458333	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			C|0.937;T|0.063	0.063	strong		0.697	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
NBAS	51594	hgsc.bcm.edu	37	2	15358939	15358939	+	Missense_Mutation	SNP	A	A	C	rs114448506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:15358939A>C	ENST00000281513.5	-	48	6415	c.6390T>G	c.(6388-6390)ttT>ttG	p.F2130L	NBAS_ENST00000441750.1_Missense_Mutation_p.F2010L	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2130					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CTTCAGTTCTAAAGAACACGA	0.517													A|||	12	0.00239617	0.0091	0.0	5008	,	,		19280	0.0		0.0	False		,,,				2504	0.0				p.F2130L		Atlas-SNP	.											.	NBAS	246	.	0			c.T6390G						PASS	.	A	LEU/PHE	37,4369	42.3+/-75.8	0,37,2166	68.0	73.0	71.0		6390	-4.2	0.0	2	dbSNP_132	71	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NBAS	NM_015909.2	22	0,38,6465	CC,CA,AA		0.0116,0.8398,0.2922	possibly-damaging	2130/2372	15358939	38,12968	2203	4300	6503	SO:0001583	missense	51594	exon48			AGTTCTAAAGAAC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.6390T>G	2.37:g.15358939A>C	ENSP00000281513:p.Phe2130Leu	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	238	127	0.533613	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	5|5	0.0022893772893772895|0.0022893772893772895	5|5	0.01016260162601626|0.01016260162601626	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	14.99|14.99	2.699080|2.699080	0.48307|0.48307	0.008398|0.008398	1.16E-4|1.16E-4	ENSG00000151779|ENSG00000151779	ENST00000441750;ENST00000281513|ENST00000442506	T;T|.	0.09255|.	3.0;3.17|.	5.63|5.63	-4.15|-4.15	0.03881|0.03881	.|.	0.248251|.	0.47455|.	D|.	0.000222|.	T|.	0.55752|.	0.1940|.	M|M	0.65498|0.65498	2.005|2.005	0.32809|0.32809	D|D	0.501197|0.501197	P;B|.	0.43231|.	0.801;0.397|.	P;B|.	0.44811|.	0.461;0.176|.	T|.	0.65405|.	-0.6176|.	10|.	0.87932|.	D|.	0|.	.|.	16.982|16.982	0.86331|0.86331	0.1405:0.0:0.8595:0.0|0.1405:0.0:0.8595:0.0	.|.	2010;2130|.	A2RRP1-2;A2RRP1|.	.;NBAS_HUMAN|.	L|X	2010;2130|1178	ENSP00000413201:F2010L;ENSP00000281513:F2130L|.	ENSP00000281513:F2130L|.	F|L	-|-	3|2	2|0	NBAS|NBAS	15276390|15276390	0.998000|0.998000	0.40836|0.40836	0.001000|0.001000	0.08648|0.08648	0.824000|0.824000	0.46624|0.46624	1.102000|1.102000	0.31050|0.31050	-1.413000|-1.413000	0.02027|0.02027	-0.326000|-0.326000	0.08463|0.08463	TTT|TTA	A|0.997;C|0.003	0.003	strong		0.517	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
SPEF2	79925	hgsc.bcm.edu	37	5	35692775	35692775	+	Missense_Mutation	SNP	T	T	A	rs7710284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:35692775T>A	ENST00000356031.3	+	12	2002	c.1848T>A	c.(1846-1848)aaT>aaA	p.N616K	SPEF2_ENST00000509059.1_Missense_Mutation_p.N616K|SPEF2_ENST00000440995.2_Missense_Mutation_p.N616K|CTD-2113L7.1_ENST00000510433.1_RNA	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	616			N -> K (in dbSNP:rs7710284).		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)			TTCAGAAAAATGATGAAGAAG	0.378													A|||	1788	0.357029	0.6195	0.2622	5008	,	,		15916	0.4067		0.1312	False		,,,				2504	0.2505				p.N616K		Atlas-SNP	.											.	SPEF2	324	.	0			c.T1848A						PASS	.	A	LYS/ASN	2023,1663		556,911,376	97.0	99.0	98.0		1848	-3.6	0.0	5	dbSNP_116	98	1069,7103		64,941,3081	yes	missense	SPEF2	NM_024867.3	94	620,1852,3457	AA,AT,TT		13.0813,45.1167,26.0752	benign	616/1823	35692775	3092,8766	1843	4086	5929	SO:0001583	missense	79925	exon12			GAAAAATGATGAA	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.1848T>A	5.37:g.35692775T>A	ENSP00000348314:p.Asn616Lys	Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	231	114	0.493506	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	734	0.3360805860805861	315	0.6402439024390244	79	0.21823204419889503	231	0.40384615384615385	109	0.1437994722955145	A	3.896	-0.023008	0.07634	0.548833	0.130813	ENSG00000152582	ENST00000356031;ENST00000509059;ENST00000440995;ENST00000504054	T;T;T;T	0.28454	3.43;3.3;3.37;1.61	5.59	-3.6	0.04570	.	0.995051	0.08146	N	0.990813	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	0.43048	-0.9415	9	0.15499	T	0.54	.	4.3977	0.11370	0.2594:0.0:0.2409:0.4998	rs7710284;rs17734895;rs56484158;rs7710284	616;616;616	D6REZ4;Q9C093-2;Q9C093	.;.;SPEF2_HUMAN	K	616;616;616;127	ENSP00000348314:N616K;ENSP00000421593:N616K;ENSP00000412125:N616K;ENSP00000421744:N127K	ENSP00000348314:N616K	N	+	3	2	SPEF2	35728532	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.388000	0.07352	-1.373000	0.02134	-1.539000	0.00912	AAT	T|0.679;A|0.321	0.321	strong		0.378	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
MASTL	84930	hgsc.bcm.edu	37	10	27459670	27459670	+	Silent	SNP	C	C	T	rs1981296	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:27459670C>T	ENST00000375940.4	+	8	1839	c.1782C>T	c.(1780-1782)atC>atT	p.I594I	MASTL_ENST00000342386.6_Silent_p.I594I|MASTL_ENST00000375946.4_Silent_p.I594I|MASTL_ENST00000477034.1_3'UTR			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	594	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						ATAGAAGCATCAAAGAATCCT	0.358													C|||	2527	0.504593	0.5234	0.5231	5008	,	,		16535	0.4375		0.6024	False		,,,				2504	0.4346				p.I594I		Atlas-SNP	.											.	MASTL	81	.	0			c.C1782T						PASS	.	C	,,	2428,1978	590.6+/-387.4	663,1102,438	34.0	35.0	35.0		1782,1782,1782	-0.8	0.9	10	dbSNP_92	35	5587,3013	633.7+/-398.8	1807,1973,520	no	coding-synonymous,coding-synonymous,coding-synonymous	MASTL	NM_001172303.1,NM_001172304.1,NM_032844.3	,,	2470,3075,958	TT,TC,CC		35.0349,44.8933,38.3746	,,	594/880,594/841,594/879	27459670	8015,4991	2203	4300	6503	SO:0001819	synonymous_variant	84930	exon8			AAGCATCAAAGAA	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.1782C>T	10.37:g.27459670C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Silent	SNP	ENST00000375940.4	37	CCDS53502.1																																																																																			C|0.431;T|0.569	0.569	strong		0.358	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844	
ADH1B	125	hgsc.bcm.edu	37	4	100235053	100235053	+	Silent	SNP	A	A	G	rs1789882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100235053A>G	ENST00000305046.8	-	6	820	c.753T>C	c.(751-753)atT>atC	p.I251I	ADH1B_ENST00000394887.3_Silent_p.I211I			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	251					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	GCACTTCCTGAATGGGTTTCT	0.463													.|||	4155	0.829673	0.7943	0.8213	5008	,	,		17736	0.9157		0.8559	False		,,,				2504	0.7679				p.I251I		Atlas-SNP	.											.	ADH1B	68	.	0			c.T753C						PASS	.	G		3356,1050	376.6+/-322.1	1284,788,131	202.0	202.0	202.0		753	2.0	0.7	4	dbSNP_89	202	7143,1437	271.2+/-289.4	2991,1161,138	no	coding-synonymous	ADH1B	NM_000668.4		4275,1949,269	GG,GA,AA		16.7483,23.8311,19.1514		251/376	100235053	10499,2487	2203	4290	6493	SO:0001819	synonymous_variant	125	exon6			TTCCTGAATGGGT	AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"""Alcohol dehydrogenases"""	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.753T>C	4.37:g.100235053A>G		Somatic	535	0	0		WXS	Illumina HiSeq	Phase_I	528	510	0.965909	NM_000668	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	ENST00000305046.8	37	CCDS34033.1																																																																																			A|0.177;G|0.823	0.823	strong		0.463	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144952255	144952255	+	Missense_Mutation	SNP	G	G	C	rs148545794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144952255G>C	ENST00000369354.3	-	4	653	c.464C>G	c.(463-465)cCa>cGa	p.P155R	PDE4DIP_ENST00000369356.4_Missense_Mutation_p.P155R|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.P292R|PDE4DIP_ENST00000369347.4_Missense_Mutation_p.P155R|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.P155R|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.P292R|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.P292R|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.P155R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.P221R			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	155					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)		CTGGTCTCCTGGTACATCTTC	0.547			T	PDGFRB	MPD																																p.P292R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C875G						PASS	.						56.0	59.0	58.0					1																	144952255		2203	4296	6499	SO:0001583	missense	9659	exon7			TCTCCTGGTACAT	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.464C>G	1.37:g.144952255G>C	ENSP00000358360:p.Pro155Arg	Somatic	1436	0	0		WXS	Illumina HiSeq	Phase_I	1786	461	0.258119	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	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933328	0.34096	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000530078;ENST00000534536;ENST00000369347;ENST00000369348;ENST00000533259	T;T;T;T;T;T;T;T;T;T;T	0.35421	4.7;4.77;4.77;4.79;4.78;3.8;3.81;2.1;2.1;3.05;1.31	4.54	-0.00175	0.14033	.	.	.	.	.	T	0.11367	0.0277	L	0.35723	1.085	0.09310	N	1	B;B;B	0.25351	0.0;0.124;0.002	B;B;B	0.24848	0.003;0.056;0.007	T	0.33317	-0.9873	9	0.72032	D	0.01	.	7.3155	0.26498	0.0:0.1574:0.3594:0.4832	.	155;221;155	Q5VU43-7;Q5VU43-3;Q5VU43	.;.;MYOME_HUMAN	R	221;155;155;292;292;155;155;221;158;155;292;78	ENSP00000327209:P221R;ENSP00000358360:P155R;ENSP00000358363:P155R;ENSP00000435654:P292R;ENSP00000358366:P292R;ENSP00000358357:P155R;ENSP00000358355:P155R;ENSP00000435920:P158R;ENSP00000358353:P155R;ENSP00000358354:P292R;ENSP00000437202:P78R	ENSP00000327209:P221R	P	-	2	0	PDE4DIP	143663612	0.000000	0.05858	0.000000	0.03702	0.852000	0.48524	0.166000	0.16583	-0.161000	0.10983	0.561000	0.74099	CCA	.	.	weak		0.547	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
MKI67	4288	hgsc.bcm.edu	37	10	129901946	129901946	+	Missense_Mutation	SNP	T	T	G	rs1050767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129901946T>G	ENST00000368654.3	-	13	8533	c.8158A>C	c.(8158-8160)Aca>Cca	p.T2720P	MKI67_ENST00000368653.3_Missense_Mutation_p.T2360P	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2720	16 X 122 AA approximate repeats.		T -> P (in dbSNP:rs1050767).		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)				TGCCTCTTTGTGCTTGCTGTG	0.488													T|||	1113	0.222244	0.3056	0.2233	5008	,	,		21121	0.2599		0.1571	False		,,,				2504	0.137				p.T2720P		Atlas-SNP	.											MKI67,NS,carcinoma,+2,1	MKI67	363	1	0			c.A8158C						scavenged	.	T	PRO/THR,PRO/THR	1190,3216	416.7+/-337.7	157,876,1170	122.0	113.0	116.0		7078,8158	-0.4	0.0	10	dbSNP_86	116	1489,7111	282.8+/-295.8	137,1215,2948	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	38,38	294,2091,4118	GG,GT,TT		17.314,27.0086,20.5982	possibly-damaging,possibly-damaging	2360/2897,2720/3257	129901946	2679,10327	2203	4300	6503	SO:0001583	missense	4288	exon13			TCTTTGTGCTTGC	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.8158A>C	10.37:g.129901946T>G	ENSP00000357643:p.Thr2720Pro	Somatic	231	2	0.00865801		WXS	Illumina HiSeq	Phase_I	255	111	0.435294	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	466	0.21336996336996336	127	0.258130081300813	66	0.18232044198895028	150	0.26223776223776224	123	0.16226912928759896	T	12.94	2.087836	0.36855	0.270086	0.17314	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02682	4.2;4.2	3.71	-0.381	0.12485	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P;D;D	0.62365	0.952;0.991;0.985	P;P;P	0.57057	0.529;0.791;0.812	T	0.51458	-0.8703	8	0.30854	T	0.27	.	3.2228	0.06721	0.4951:0.1273:0.0:0.3777	rs1050767;rs52803075;rs61581411;rs1050767	2719;2360;2720	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	P	2720;2360;2719	ENSP00000357643:T2720P;ENSP00000357642:T2360P	ENSP00000357642:T2360P	T	-	1	0	MKI67	129791936	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.422000	0.07043	-0.169000	0.10834	0.533000	0.62120	ACA	T|0.794;G|0.206	0.206	strong		0.488	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
ESD	2098	hgsc.bcm.edu	37	13	47354101	47354101	+	Missense_Mutation	SNP	C	C	T	rs9778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:47354101C>T	ENST00000378720.3	-	8	751	c.569G>A	c.(568-570)gGa>gAa	p.G190E	ESD_ENST00000495654.1_5'UTR|ESD_ENST00000378697.1_Missense_Mutation_p.G161E	NM_001984.1	NP_001975.1	P10768	ESTD_HUMAN	esterase D	190			G -> E (in allele ESD*2; dbSNP:rs9778). {ECO:0000269|PubMed:12721789, ECO:0000269|PubMed:7907313}.		formaldehyde catabolic process (GO:0046294)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carboxylic ester hydrolase activity (GO:0052689)|hydrolase activity, acting on ester bonds (GO:0016788)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)|S-formylglutathione hydrolase activity (GO:0018738)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	9		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)	TCCCAAATATCCACTAAAGGC	0.358													C|||	962	0.192093	0.0855	0.1383	5008	,	,		10141	0.4206		0.0775	False		,,,				2504	0.2566				p.G190E		Atlas-SNP	.											.	ESD	23	.	0			c.G569A						PASS	.	C	GLU/GLY	350,4056	181.5+/-209.5	10,330,1863	106.0	104.0	105.0		569	4.4	1.0	13	dbSNP_52	105	914,7686	202.1+/-245.5	42,830,3428	yes	missense	ESD	NM_001984.1	98	52,1160,5291	TT,TC,CC		10.6279,7.9437,9.7186	benign	190/283	47354101	1264,11742	2203	4300	6503	SO:0001583	missense	2098	exon8			AAATATCCACTAA	M13450	CCDS9404.1	13q14.1-q14.2	2014-05-13	2010-05-07		ENSG00000139684	ENSG00000139684	3.1.2.12		3465	protein-coding gene	gene with protein product	"""S-formylglutathione hydrolase"""	133280	"""esterase D/formylglutathione hydrolase"""				Standard	NM_001984		Approved		uc001vbn.3	P10768	OTTHUMG00000016878	ENST00000378720.3:c.569G>A	13.37:g.47354101C>T	ENSP00000367992:p.Gly190Glu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	80	31	0.3875	NM_001984	Q5TBU8|Q5TBV0|Q5TBV2|Q9BVJ2	Missense_Mutation	SNP	ENST00000378720.3	37	CCDS9404.1	380|380	0.17399267399267399|0.17399267399267399	51|51	0.10365853658536585|0.10365853658536585	54|54	0.14917127071823205|0.14917127071823205	226|226	0.3951048951048951|0.3951048951048951	49|49	0.06464379947229551|0.06464379947229551	C|C	20.9|20.9	4.071880|4.071880	0.76301|0.76301	0.079437|0.079437	0.106279|0.106279	ENSG00000139684|ENSG00000139684	ENST00000412582|ENST00000378720;ENST00000378697	.|T;T	.|0.31510	.|1.49;1.49	6.16|6.16	4.42|4.42	0.53409|0.53409	.|.	.|0.155857	.|0.56097	.|N	.|0.000026	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.82517|0.82517	2.595|2.595	0.09310|0.09310	P|P	0.9999999635137|0.9999999635137	.|P	.|0.39737	.|0.685	.|B	.|0.39503	.|0.301	T|T	0.39502|0.39502	-0.9611|-0.9611	4|9	.|0.46703	.|T	.|0.11	-6.916|-6.916	10.9038|10.9038	0.47067|0.47067	0.0:0.7987:0.1311:0.0702|0.0:0.7987:0.1311:0.0702	rs9778;rs1051064;rs3191448;rs8192894;rs17342262;rs17353977;rs52797294;rs57577491;rs8192894|rs9778;rs1051064;rs3191448;rs8192894;rs17342262;rs17353977;rs52797294;rs57577491;rs8192894	.|190	.|P10768	.|ESTD_HUMAN	N|E	138|190;161	.|ENSP00000367992:G190E;ENSP00000367969:G161E	.|ENSP00000367969:G161E	D|G	-|-	1|2	0|0	ESD|ESD	46252102|46252102	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.997000|0.997000	0.91878|0.91878	4.842000|4.842000	0.62831|0.62831	0.912000|0.912000	0.36772|0.36772	0.650000|0.650000	0.86243|0.86243	GAT|GGA	T|0.140;G|0.000;C|0.859	0.140	strong		0.358	ESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044826.1		
FAM83G	644815	hgsc.bcm.edu	37	17	18874720	18874720	+	Silent	SNP	C	C	G	rs916823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18874720C>G	ENST00000388995.6	-	6	2647	c.2424G>C	c.(2422-2424)tcG>tcC	p.S808S	SLC5A10_ENST00000395645.3_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395647.2_Intron|FAM83G_ENST00000345041.4_Silent_p.S808S|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000317977.6_Intron|FAM83G_ENST00000585154.2_Silent_p.S808S|SLC5A10_ENST00000395642.1_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	808					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						GTTTAGAATCCGATGAGGCCC	0.617													G|||	3377	0.674321	0.7587	0.6844	5008	,	,		17660	0.6329		0.5855	False		,,,				2504	0.6871				p.S808S		Atlas-SNP	.											.	FAM83G	51	.	0			c.G2424C						PASS	.	G	,,	3108,1144		1159,790,177	54.0	66.0	62.0		2424,,	-11.1	0.0	17	dbSNP_86	62	4850,3600		1419,2012,794	no	coding-synonymous,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	,,	2578,2802,971	GG,GC,CC		42.6036,26.905,37.3484	,,	808/824,,	18874720	7958,4744	2126	4225	6351	SO:0001819	synonymous_variant	644815	exon6			AGAATCCGATGAG	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.2424G>C	17.37:g.18874720C>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001039999	Q3KQZ4|Q6ZW60	Silent	SNP	ENST00000388995.6	37	CCDS42276.1																																																																																			C|0.359;G|0.641	0.641	strong		0.617	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
IFNAR1	3454	hgsc.bcm.edu	37	21	34713317	34713317	+	Silent	SNP	T	T	C	rs9981753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:34713317T>C	ENST00000270139.3	+	3	365	c.213T>C	c.(211-213)gaT>gaC	p.D71D	IFNAR1_ENST00000442357.2_Silent_p.D71D|IFNAR1_ENST00000416947.2_Silent_p.D2D	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	71	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""""""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)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	CTGGGATGGATAATTGGATAA	0.284													T|||	95	0.0189696	0.0658	0.0072	5008	,	,		17150	0.0		0.003	False		,,,				2504	0.0				p.D71D	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											.	IFNAR1	44	.	0			c.T213C						PASS	.	T		244,4162	132.1+/-168.6	6,232,1965	55.0	59.0	58.0		213	3.1	0.0	21	dbSNP_119	58	14,8582	9.8+/-36.6	0,14,4284	no	coding-synonymous	IFNAR1	NM_000629.2		6,246,6249	CC,CT,TT		0.1629,5.5379,1.9843		71/558	34713317	258,12744	2203	4298	6501	SO:0001819	synonymous_variant	3454	exon3			GATGGATAATTGG		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"""Interferons"""	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.213T>C	21.37:g.34713317T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Silent	SNP	ENST00000270139.3	37	CCDS13624.1																																																																																			T|0.986;C|0.014	0.014	strong		0.284	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		
TRPM1	4308	hgsc.bcm.edu	37	15	31294773	31294773	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31294773C>T	ENST00000256552.6	-	28	4277	c.4130G>A	c.(4129-4131)gGt>gAt	p.G1377D	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Missense_Mutation_p.G1355D|TRPM1_ENST00000542188.1_Missense_Mutation_p.G1394D	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)		AATATCTGGACCTAATTTTGA	0.393																																					p.G1394D		Atlas-SNP	.											.	TRPM1	183	.	0			c.G4181A						PASS	.						160.0	153.0	155.0					15																	31294773		1917	4138	6055	SO:0001583	missense	4308	exon27			TCTGGACCTAATT	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.4130G>A	15.37:g.31294773C>T	ENSP00000256552:p.Gly1377Asp	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	C	4.656	0.121910	0.08931	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.52526	0.67;0.66;0.68	4.81	2.63	0.31362	.	0.300372	0.27851	N	0.017600	T	0.26919	0.0659	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.10132	-1.0643	10	0.52906	T	0.07	-6.7074	5.797	0.18392	0.1392:0.6449:0.1355:0.0804	.	1349;1355	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	D	1355;1394;1377;1355	ENSP00000380897:G1355D;ENSP00000437849:G1394D;ENSP00000256552:G1377D	ENSP00000256552:G1377D	G	-	2	0	TRPM1	29082065	0.035000	0.19736	0.093000	0.20910	0.043000	0.13939	0.395000	0.20850	2.201000	0.70794	0.650000	0.86243	GGT	.	.	none		0.393	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
MCMBP	79892	hgsc.bcm.edu	37	10	121602830	121602830	+	Silent	SNP	G	G	A	rs34297798	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:121602830G>A	ENST00000360003.3	-	9	1105	c.936C>T	c.(934-936)gcC>gcT	p.A312A	MCMBP_ENST00000466047.1_5'UTR|MCMBP_ENST00000369077.3_Silent_p.A312A	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	312					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)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						GCAACTTCTGGGCTAAGATCA	0.483													G|||	44	0.00878594	0.0303	0.0058	5008	,	,		20195	0.0		0.0	False		,,,				2504	0.0				p.A312A		Atlas-SNP	.											.	MCMBP	49	.	0			c.C936T						PASS	.	G		113,4293	86.8+/-125.4	0,113,2090	289.0	228.0	249.0		936	-1.7	1.0	10	dbSNP_126	249	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	MCMBP	NM_024834.2		0,117,6386	AA,AG,GG		0.0465,2.5647,0.8996		312/643	121602830	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	79892	exon9			CTTCTGGGCTAAG	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	ENST00000360003.3:c.936C>T	10.37:g.121602830G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	214	111	0.518692	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	37	CCDS7617.1																																																																																			G|0.990;A|0.010	0.010	strong		0.483	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
MUC17	140453	hgsc.bcm.edu	37	7	100677816	100677816	+	Missense_Mutation	SNP	G	G	A	rs77671499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677816G>A	ENST00000306151.4	+	3	3183	c.3119G>A	c.(3118-3120)gGa>gAa	p.G1040E		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1040	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)					CCTAGTGAAGGAAGCACTCCA	0.517																																					p.G1040E		Atlas-SNP	.											.	MUC17	804	.	0			c.G3119A						PASS	.	G	GLU/GLY	370,4036		0,370,1833	518.0	404.0	442.0		3119	-1.0	0.0	7	dbSNP_131	442	596,8004		0,596,3704	no	missense	MUC17	NM_001040105.1	98	0,966,5537	AA,AG,GG		6.9302,8.3976,7.4273	benign	1040/4494	100677816	966,12040	2203	4300	6503	SO:0001583	missense	140453	exon3			GTGAAGGAAGCAC	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.3119G>A	7.37:g.100677816G>A	ENSP00000302716:p.Gly1040Glu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	294	71	0.241497	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.823	-0.748080	0.03065	0.083976	0.069302	ENSG00000169876	ENST00000306151	T	0.03553	3.89	0.481	-0.962	0.10333	.	.	.	.	.	T	0.00178	0.0005	L	0.29908	0.895	0.09310	N	1	B	0.20261	0.043	B	0.08055	0.003	T	0.48031	-0.9070	9	0.08381	T	0.77	.	6.1942	0.20540	0.0:0.6044:0.3955:0.0	.	1040	Q685J3	MUC17_HUMAN	E	1040	ENSP00000302716:G1040E	ENSP00000302716:G1040E	G	+	2	0	MUC17	100464536	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.771000	0.04699	-0.577000	0.05967	0.134000	0.15878	GGA	G|0.981;A|0.019	0.019	strong		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
LRRN4	164312	hgsc.bcm.edu	37	20	6032882	6032882	+	Silent	SNP	C	C	T	rs6053858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:6032882C>T	ENST00000378858.4	-	2	788	c.564G>A	c.(562-564)ggG>ggA	p.G188G		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	188					long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	27						CGGCGATGCCCCCCTGGGCTC	0.716													C|||	462	0.0922524	0.3298	0.036	5008	,	,		13542	0.0		0.0	False		,,,				2504	0.001				p.G188G		Atlas-SNP	.											.	LRRN4	54	.	0			c.G564A						PASS	.	C		963,3055		99,765,1145	6.0	5.0	5.0		564	-6.5	0.0	20	dbSNP_114	5	20,7954		1,18,3968	no	coding-synonymous	LRRN4	NM_152611.3		100,783,5113	TT,TC,CC		0.2508,23.9671,8.1971		188/741	6032882	983,11009	2009	3987	5996	SO:0001819	synonymous_variant	164312	exon2			GATGCCCCCCTGG	AL118505	CCDS13097.1	20p12.3	2013-02-11	2008-05-20	2008-05-20	ENSG00000125872	ENSG00000125872		"""Fibronectin type III domain containing"""	16208	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 75"""	C20orf75		15870286	Standard	NM_152611		Approved	dJ1056H1.1, NLRR4	uc002wmo.3	Q8WUT4	OTTHUMG00000031825	ENST00000378858.4:c.564G>A	20.37:g.6032882C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	19	9	0.473684	NM_152611	A8K258|Q5JWV6|Q9H419	Silent	SNP	ENST00000378858.4	37	CCDS13097.1																																																																																			C|0.909;T|0.091	0.091	strong		0.716	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611	
SHPRH	257218	hgsc.bcm.edu	37	6	146276280	146276280	+	Missense_Mutation	SNP	C	C	T	rs182151362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:146276280C>T	ENST00000367505.2	-	2	443	c.179G>A	c.(178-180)aGt>aAt	p.S60N	SHPRH_ENST00000275233.7_Missense_Mutation_p.S60N|SHPRH_ENST00000367503.3_Missense_Mutation_p.S60N|SHPRH_ENST00000438092.2_Missense_Mutation_p.S60N			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	60					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TTCCTTTAGACTATCACTTAG	0.408													C|||	22	0.00439297	0.0144	0.0014	5008	,	,		18451	0.0		0.002	False		,,,				2504	0.0				p.S60N		Atlas-SNP	.											.	SHPRH	169	.	0			c.G179A						PASS	.	C	ASN/SER,ASN/SER	53,3687		0,53,1817	106.0	97.0	100.0		179,179	1.9	0.0	6		100	4,8210		0,4,4103	yes	missense,missense	SHPRH	NM_001042683.2,NM_173082.3	46,46	0,57,5920	TT,TC,CC		0.0487,1.4171,0.4768	benign,benign	60/1684,60/1660	146276280	57,11897	1870	4107	5977	SO:0001583	missense	257218	exon2			TTTAGACTATCAC	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.179G>A	6.37:g.146276280C>T	ENSP00000356475:p.Ser60Asn	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	4.394	0.072688	0.08436	0.014171	4.87E-4	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.66	1.9	0.25705	.	0.291823	0.32068	N	0.006636	T	0.34250	0.0891	L	0.50333	1.59	0.09310	N	1	B;B	0.31548	0.22;0.328	B;B	0.32864	0.073;0.154	T	0.21690	-1.0238	10	0.49607	T	0.09	0.0517	8.8158	0.34996	0.0:0.6472:0.0:0.3528	.	60;60	Q149N8;Q149N8-4	SHPRH_HUMAN;.	N	60	ENSP00000356475:S60N;ENSP00000356473:S60N;ENSP00000412797:S60N;ENSP00000275233:S60N	ENSP00000275233:S60N	S	-	2	0	SHPRH	146317973	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.321000	0.19558	0.332000	0.23536	-0.136000	0.14681	AGT	C|0.998;T|0.002	0.002	strong		0.408	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
CCDC88C	440193	hgsc.bcm.edu	37	14	91739873	91739873	+	Missense_Mutation	SNP	A	A	G	rs7145583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91739873A>G	ENST00000389857.6	-	30	5269	c.5183T>C	c.(5182-5184)tTt>tCt	p.F1728S	CCDC88C_ENST00000331194.7_Missense_Mutation_p.F252S	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1728					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GGGGGCCACAAAGTTGGTGGG	0.622													A|||	28	0.00559105	0.0189	0.0043	5008	,	,		16431	0.0		0.0	False		,,,				2504	0.0				p.F1728S		Atlas-SNP	.											.	CCDC88C	192	.	0			c.T5183C						PASS	.	A	SER/PHE	63,3873		1,61,1906	29.0	33.0	32.0		5183	3.5	0.8	14	dbSNP_116	32	1,8255		0,1,4127	yes	missense	CCDC88C	NM_001080414.3	155	1,62,6033	GG,GA,AA		0.0121,1.6006,0.5249	benign	1728/2029	91739873	64,12128	1968	4128	6096	SO:0001583	missense	440193	exon30			GCCACAAAGTTGG		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.5183T>C	14.37:g.91739873A>G	ENSP00000374507:p.Phe1728Ser	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	A	7.279	0.608712	0.14066	0.016006	1.21E-4	ENSG00000015133	ENST00000389857;ENST00000427583;ENST00000331194	T;T	0.47528	2.39;0.84	4.7	3.52	0.40303	.	0.410931	0.18701	U	0.133580	T	0.25644	0.0624	M	0.64997	1.995	0.27192	N	0.960401	B;B;B	0.32160	0.242;0.231;0.358	B;B;B	0.33042	0.154;0.157;0.157	T	0.17410	-1.0370	10	0.30078	T	0.28	0.4499	6.9029	0.24293	0.6516:0.1293:0.0:0.2191	rs7145583	1728;252;178	Q9P219;Q9P219-2;Q9P219-3	DAPLE_HUMAN;.;.	S	1728;252;252	ENSP00000374507:F1728S;ENSP00000330332:F252S	ENSP00000330332:F252S	F	-	2	0	CCDC88C	90809626	0.999000	0.42202	0.816000	0.32577	0.093000	0.18481	2.620000	0.46410	0.630000	0.30394	0.377000	0.23210	TTT	A|0.997;G|0.003	0.003	strong		0.622	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
NPHP4	261734	hgsc.bcm.edu	37	1	5965824	5965824	+	Missense_Mutation	SNP	G	G	C	rs12093500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:5965824G>C	ENST00000378156.4	-	14	1896	c.1631C>G	c.(1630-1632)gCc>gGc	p.A544G	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	544			A -> G (in dbSNP:rs12093500). {ECO:0000269|PubMed:15776426}.		actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GGAGATACCGGCCTCCAACGG	0.572													C|||	127	0.0253594	0.0877	0.0115	5008	,	,		18214	0.0		0.003	False		,,,				2504	0.0				p.A544G		Atlas-SNP	.											.	NPHP4	119	.	0			c.C1631G						PASS	.	C	GLY/ALA	306,3584		10,286,1649	28.0	31.0	30.0		1631	4.5	0.3	1	dbSNP_120	30	14,8254		0,14,4120	yes	missense	NPHP4	NM_015102.3	60	10,300,5769	CC,CG,GG		0.1693,7.8663,2.632	benign	544/1427	5965824	320,11838	1945	4134	6079	SO:0001583	missense	261734	exon14			ATACCGGCCTCCA	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.1631C>G	1.37:g.5965824G>C	ENSP00000367398:p.Ala544Gly	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	132	64	0.484848	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	39	0.017857142857142856	30	0.06097560975609756	6	0.016574585635359115	0	0.0	3	0.00395778364116095	C	0.007	-1.936935	0.00484	0.078663	0.001693	ENSG00000131697	ENST00000378156	D	0.87334	-2.24	5.42	4.5	0.54988	.	0.527792	0.18448	N	0.140932	T	0.08626	0.0214	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06643	-1.0815	10	0.10377	T	0.69	.	16.1591	0.81686	0.0:0.6272:0.3728:0.0	rs12093500;rs61332996;rs12093500	544	O75161	NPHP4_HUMAN	G	544	ENSP00000367398:A544G	ENSP00000367398:A544G	A	-	2	0	NPHP4	5888411	.	.	0.285000	0.24819	0.013000	0.08279	.	.	0.644000	0.30656	-0.216000	0.12614	GCC	G|0.980;C|0.020	0.020	strong		0.572	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
DSCAM	1826	hgsc.bcm.edu	37	21	41455854	41455854	+	Silent	SNP	G	G	A	rs2297263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:41455854G>A	ENST00000400454.1	-	24	4689	c.4212C>T	c.(4210-4212)aaC>aaT	p.N1404N		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1404	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)				AGCTGCCCCCGTTGTCTCCAG	0.458													G|||	386	0.0770767	0.1036	0.0259	5008	,	,		17446	0.1548		0.0527	False		,,,				2504	0.0225				p.N1404N	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C4212T						PASS	.	G		379,3389		25,329,1530	70.0	68.0	69.0		4212	-10.9	0.1	21	dbSNP_100	69	408,7840		9,390,3725	no	coding-synonymous	DSCAM	NM_001389.3		34,719,5255	AA,AG,GG		4.9467,10.0584,6.5496		1404/2013	41455854	787,11229	1884	4124	6008	SO:0001819	synonymous_variant	1826	exon24			GCCCCCGTTGTCT	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.4212C>T	21.37:g.41455854G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_001271534	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																			G|0.935;A|0.065	0.065	strong		0.458	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
OR5I1	10798	hgsc.bcm.edu	37	11	55703523	55703523	+	Silent	SNP	G	G	A	rs11231594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55703523G>A	ENST00000301532.3	-	1	353	c.354C>T	c.(352-354)gcC>gcT	p.A118A		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	118					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						AGGCCATGGCGGCCAGGATGA	0.433													G|||	121	0.0241613	0.0862	0.0101	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.A118A		Atlas-SNP	.											.	OR5I1	110	.	0			c.C354T						PASS	.	G		304,4098	162.9+/-194.8	16,272,1913	52.0	55.0	54.0		354	-2.7	0.3	11	dbSNP_120	54	6,8578	5.7+/-21.5	0,6,4286	no	coding-synonymous	OR5I1	NM_006637.1		16,278,6199	AA,AG,GG		0.0699,6.906,2.3872		118/315	55703523	310,12676	2201	4292	6493	SO:0001819	synonymous_variant	10798	exon1			CATGGCGGCCAGG	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.354C>T	11.37:g.55703523G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_006637	Q6IEU4	Silent	SNP	ENST00000301532.3	37	CCDS7949.1																																																																																			G|0.974;A|0.026	0.026	strong		0.433	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
PALLD	23022	hgsc.bcm.edu	37	4	169433327	169433327	+	Missense_Mutation	SNP	G	G	A	rs397718410|rs373066707|rs7671781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169433327G>A	ENST00000505667.1	+	2	845	c.672G>A	c.(670-672)atG>atA	p.M224I	PALLD_ENST00000333488.4_Missense_Mutation_p.M101I|PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000261509.6_Missense_Mutation_p.M224I			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	224			M -> I (in dbSNP:rs7671781).|M -> T (in dbSNP:rs7655494). {ECO:0000269|PubMed:14702039}.		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)		AGAGCCCTATGGAAGACCAAG	0.582									Pancreatic Cancer, Familial Clustering of				G|||	1200	0.239617	0.2368	0.1844	5008	,	,		17181	0.1935		0.33	False		,,,				2504	0.2372				p.M224I	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.G672A						PASS	.	G	ILE/MET,ILE/MET	1065,3341		151,763,1289	101.0	105.0	104.0		672,672	-10.8	0.0	4	dbSNP_116	104	2624,5976		460,1704,2136	yes	missense,missense	PALLD	NM_001166108.1,NM_016081.3	10,10	611,2467,3425	AA,AG,GG		30.5116,24.1716,28.3638	benign,benign	224/1124,224/1107	169433327	3689,9317	2203	4300	6503	SO:0001583	missense	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	CCCTATGGAAGAC	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.672G>A	4.37:g.169433327G>A	ENSP00000425556:p.Met224Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	447	0.20467032967032966	89	0.18089430894308944	68	0.1878453038674033	84	0.14685314685314685	206	0.2717678100263852	G	10.73	1.433994	0.25813	0.241716	0.305116	ENSG00000129116	ENST00000261509;ENST00000505667;ENST00000508898;ENST00000333488	T;T;T;T	0.61742	0.18;0.46;0.08;0.18	5.41	-10.8	0.00216	.	0.307711	0.17926	N	0.157333	T	0.00012	0.0000	N	0.08118	0	0.53688	P	2.6999999999999247E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08576	-1.0715	9	0.13853	T	0.58	.	2.9803	0.05951	0.2733:0.4205:0.1616:0.1446	rs7671781	224;224	B7ZMM5;B2RTX2	.;.	I	224;224;203;101	ENSP00000261509:M224I;ENSP00000425556:M224I;ENSP00000423063:M203I;ENSP00000328945:M101I	ENSP00000261509:M224I	M	+	3	0	PALLD	169669902	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.466000	0.00229	-4.316000	0.00057	-0.918000	0.02743	ATG	G|0.733;A|0.267	0.267	strong		0.582	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
SCO1	6341	hgsc.bcm.edu	37	17	10595250	10595250	+	Silent	SNP	T	T	C	rs2271228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10595250T>C	ENST00000255390.5	-	4	654	c.594A>G	c.(592-594)ccA>ccG	p.P198P	SCO1_ENST00000577427.1_Silent_p.P167P|SCO1_ENST00000582053.1_5'Flank	NM_004589.2	NP_004580.1	O75880	SCO1_HUMAN	SCO1 cytochrome c oxidase assembly protein	198					cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|generation of precursor metabolites and energy (GO:0006091)|respiratory chain complex IV assembly (GO:0008535)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)	copper ion binding (GO:0005507)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|urinary_tract(1)	10						TGATGAAAAGTGGAGTTAGAT	0.358													T|||	249	0.0497204	0.1679	0.0072	5008	,	,		21532	0.0169		0.003	False		,,,				2504	0.002				p.P198P	Melanoma(128;591 1731 19711 31891 44645)	Atlas-SNP	.											SCO1,NS,carcinoma,-1,1	SCO1	24	1	0			c.A594G						scavenged	.	T		567,3839	253.4+/-259.3	36,495,1672	112.0	109.0	110.0		594	-2.1	1.0	17	dbSNP_100	110	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	SCO1	NM_004589.2		36,500,5967	CC,CT,TT		0.0581,12.8688,4.398		198/302	10595250	572,12434	2203	4300	6503	SO:0001819	synonymous_variant	6341	exon4			GAAAAGTGGAGTT	AF026852	CCDS11158.1	17p13.1	2012-10-15	2012-10-15		ENSG00000133028	ENSG00000133028		"""Mitochondrial respiratory chain complex assembly factors"""	10603	protein-coding gene	gene with protein product		603644	"""SCO (cytochrome oxidase deficient, yeast) homolog 1"", ""SCO cytochrome oxidase deficient homolog 1 (yeast)"""	SCOD1		9878253	Standard	NM_004589		Approved		uc002gmr.4	O75880	OTTHUMG00000130364	ENST00000255390.5:c.594A>G	17.37:g.10595250T>C		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	143	59	0.412587	NM_004589	B2RDM0	Silent	SNP	ENST00000255390.5	37	CCDS11158.1																																																																																			T|0.961;C|0.039	0.039	strong		0.358	SCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252729.2	NM_004589	
LPCAT3	10162	hgsc.bcm.edu	37	12	7090193	7090193	+	Missense_Mutation	SNP	A	A	G	rs1984564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	129	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	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	
ZNF407	55628	hgsc.bcm.edu	37	18	72344509	72344509	+	Missense_Mutation	SNP	G	G	A	rs7227263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:72344509G>A	ENST00000299687.5	+	1	1534	c.1534G>A	c.(1534-1536)Ggg>Agg	p.G512R	ZNF407_ENST00000582337.1_Missense_Mutation_p.G512R|ZNF407_ENST00000309902.6_Missense_Mutation_p.G512R|ZNF407_ENST00000577538.1_Missense_Mutation_p.G512R	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	512			G -> R (in dbSNP:rs7227263).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TCCGGACTCCGGGCTGCATTC	0.562													G|||	339	0.0676917	0.112	0.0663	5008	,	,		18648	0.001		0.1064	False		,,,				2504	0.0378				p.G512R		Atlas-SNP	.											.	ZNF407	231	.	0			c.G1534A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY	404,3640		17,370,1635	85.0	93.0	90.0		1534,1534,1534	-9.6	0.0	18	dbSNP_116	90	1156,7212		87,982,3115	yes	missense,missense,missense	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	125,125,125	104,1352,4750	AA,AG,GG		13.8145,9.9901,12.5685	benign,benign,benign	512/1816,512/1661,512/2249	72344509	1560,10852	2022	4184	6206	SO:0001583	missense	55628	exon1			GACTCCGGGCTGC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1534G>A	18.37:g.72344509G>A	ENSP00000299687:p.Gly512Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	56	0.57732	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	173	0.07921245421245421	59	0.11991869918699187	26	0.0718232044198895	0	0.0	88	0.11609498680738786	G	8.956	0.969380	0.18659	0.099901	0.138145	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.08984	3.03;3.44	5.78	-9.59	0.00556	.	0.000000	0.18108	U	0.151444	T	0.00039	0.0001	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.01281	0.0;0.0;0.0	T	0.40059	-0.9583	9	0.27785	T	0.31	.	5.3187	0.15870	0.1757:0.2898:0.4351:0.0994	rs7227263;rs57563446;rs7227263	512;512;512	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	R	512	ENSP00000299687:G512R;ENSP00000310359:G512R	ENSP00000299687:G512R	G	+	1	0	ZNF407	70473497	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.751000	0.04803	-0.515000	0.06479	-0.806000	0.03193	GGG	G|0.910;A|0.090	0.090	strong		0.562	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
CCNB1	891	hgsc.bcm.edu	37	5	68471232	68471232	+	Silent	SNP	C	C	T	rs2069439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68471232C>T	ENST00000256442.5	+	7	1204	c.951C>T	c.(949-951)gtC>gtT	p.V317V	snoU13_ENST00000459230.1_RNA	NM_031966.3	NP_114172.1	P14635	CCNB1_HUMAN	cyclin B1	317					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to iron(III) ion (GO:0071283)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle checkpoint (GO:0071174)|mitotic spindle stabilization (GO:0043148)|negative regulation of gene expression (GO:0010629)|negative regulation of protein phosphorylation (GO:0001933)|oocyte maturation (GO:0001556)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of chromosome condensation (GO:0060623)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to DDT (GO:0046680)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|spermatogenesis (GO:0007283)|tissue regeneration (GO:0042246)|ventricular cardiac muscle cell development (GO:0055015)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase activity (GO:0016301)|patched binding (GO:0005113)|protein kinase binding (GO:0019901)			large_intestine(2)|lung(5)|skin(1)	8		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		AGGTTGATGTCGAGCAACATA	0.393													C|||	4	0.000798722	0.003	0.0	5008	,	,		20276	0.0		0.0	False		,,,				2504	0.0				p.V317V		Atlas-SNP	.											CCNB1,NS,carcinoma,+1,1	CCNB1	36	1	0			c.C951T						PASS	.	C		26,4380	33.5+/-64.1	0,26,2177	156.0	145.0	149.0		951	-7.2	0.9	5	dbSNP_96	149	0,8600		0,0,4300	no	coding-synonymous	CCNB1	NM_031966.2		0,26,6477	TT,TC,CC		0.0,0.5901,0.1999		317/434	68471232	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	891	exon7			TGATGTCGAGCAA	U22364	CCDS3997.1	5q12	2008-07-18			ENSG00000134057	ENSG00000134057			1579	protein-coding gene	gene with protein product	"""G2/mitotic-specific cyclin B1"""	123836		CCNB		1386342	Standard	NM_031966		Approved		uc003jvm.3	P14635	OTTHUMG00000097817	ENST00000256442.5:c.951C>T	5.37:g.68471232C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	125	47	0.376	NM_031966	A8K066|Q5TZP9	Silent	SNP	ENST00000256442.5	37	CCDS3997.1																																																																																			C|0.998;T|0.002	0.002	strong		0.393	CCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215084.1	NM_031966	
OR2H1	26716	hgsc.bcm.edu	37	6	29429733	29429733	+	Missense_Mutation	SNP	G	G	A	rs61732185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29429733G>A	ENST00000377136.1	+	4	652	c.187G>A	c.(187-189)Gac>Aac	p.D63N	OR2H1_ENST00000442615.1_Missense_Mutation_p.D63N|OR2H1_ENST00000377132.1_Missense_Mutation_p.D63N|OR2H1_ENST00000377133.1_Missense_Mutation_p.D63N|OR2H1_ENST00000396792.2_Missense_Mutation_p.D63N|OR2H1_ENST00000473369.1_Intron			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	63			D -> N (in allele 6M1-16*02; dbSNP:rs61732185). {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)			large_intestine(5)|lung(12)	17						TTTCCTCTCTGACCTCTCCTT	0.532													G|||	174	0.0347444	0.1044	0.013	5008	,	,		20350	0.0119		0.0119	False		,,,				2504	0.0031				p.D63N		Atlas-SNP	.											.	OR2H1	38	.	0			c.G187A						PASS	.	G	ASN/ASP	301,2721		17,267,1227	137.0	134.0	135.0		187	0.4	1.0	6	dbSNP_129	135	33,5385		0,33,2676	yes	missense	OR2H1	NM_030883.3	23	17,300,3903	AA,AG,GG		0.6091,9.9603,3.9573	benign	63/317	29429733	334,8106	1511	2709	4220	SO:0001583	missense	26716	exon3			CTCTCTGACCTCT	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.187G>A	6.37:g.29429733G>A	ENSP00000366340:p.Asp63Asn	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	303	143	0.471947	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	88	0.040293040293040296	60	0.12195121951219512	8	0.022099447513812154	10	0.017482517482517484	10	0.013192612137203167	G	1.564	-0.535865	0.04082	0.099603	0.006091	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.00940	5.52;5.52;5.52;5.52;5.52	2.88	0.407	0.16371	GPCR, rhodopsin-like superfamily (1);	0.156786	0.30126	N	0.010354	T	0.00039	0.0001	N	0.00003	-3.425	0.24176	N	0.995605	B	0.02656	0.0	B	0.01281	0.0	T	0.12604	-1.0541	10	0.02654	T	1	.	4.2744	0.10802	0.6269:0.1713:0.2018:0.0	rs61732185	63	Q9GZK4	OR2H1_HUMAN	N	63	ENSP00000366340:D63N;ENSP00000366337:D63N;ENSP00000393254:D63N;ENSP00000366336:D63N;ENSP00000380010:D63N	ENSP00000366336:D63N	D	+	1	0	OR2H1	29537712	0.036000	0.19791	0.986000	0.45419	0.919000	0.55068	1.592000	0.36676	0.072000	0.16694	-0.354000	0.07668	GAC	G|0.964;A|0.036	0.036	strong		0.532	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
OR10G9	219870	hgsc.bcm.edu	37	11	123893801	123893801	+	Missense_Mutation	SNP	A	A	G	rs74791330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123893801A>G	ENST00000375024.1	+	1	82	c.82A>G	c.(82-84)Atc>Gtc	p.I28V		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I28V(3)		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)		ACTCTTTGGAATCTTCCTGGT	0.572																																					p.I28V		Atlas-SNP	.											OR10G9,NS,haematopoietic_neoplasm,0,3	OR10G9	80	3	3	Substitution - Missense(3)	lung(1)|stomach(1)|skin(1)	c.A82G						scavenged	.						200.0	185.0	190.0					11																	123893801		2201	4299	6500	SO:0001583	missense	219870	exon1			TTTGGAATCTTCC	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.82A>G	11.37:g.123893801A>G	ENSP00000364164:p.Ile28Val	Somatic	526	1	0.00190114		WXS	Illumina HiSeq	Phase_I	394	52	0.13198	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	G	0.717	-0.785033	0.02907	.	.	ENSG00000236981	ENST00000375024	T	0.03035	4.07	3.33	-6.67	0.01783	.	0.824866	0.10366	N	0.683403	T	0.01189	0.0039	N	0.04655	-0.195	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39035	-0.9633	10	0.02654	T	1	.	4.5432	0.12067	0.1864:0.3395:0.3804:0.0938	.	28	Q8NGN4	O10G9_HUMAN	V	28	ENSP00000364164:I28V	ENSP00000364164:I28V	I	+	1	0	OR10G9	123399011	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.504000	0.00224	-2.845000	0.00333	-2.883000	0.00097	ATC	A|0.814;G|0.186	0.186	strong		0.572	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
DUSP13	51207	hgsc.bcm.edu	37	10	76854463	76854463	+	Missense_Mutation	SNP	G	G	C	rs16931996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76854463G>C	ENST00000472493.2	-	4	646	c.568C>G	c.(568-570)Cga>Gga	p.R190G	DUSP13_ENST00000491677.2_Missense_Mutation_p.R319G|DUSP13_ENST00000607131.1_Missense_Mutation_p.R283G|DUSP13_ENST00000372702.3_3'UTR|DUSP13_ENST00000478873.2_Missense_Mutation_p.R326G|DUSP13_ENST00000372700.3_Missense_Mutation_p.R240G|DUSP13_ENST00000605915.1_Missense_Mutation_p.R212G|DUSP13_ENST00000464872.1_Missense_Mutation_p.R139G	NM_016364.3	NP_057448.3	Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	190			R -> G (in dbSNP:rs16931996).		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)					CGCCCCAGTCGGTTGTCCAGA	0.642													G|||	149	0.0297524	0.1082	0.0072	5008	,	,		17269	0.0		0.001	False		,,,				2504	0.0				p.R283G	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											.	DUSP13	82	.	0			c.C847G						PASS	.	G	,GLY/ARG,GLY/ARG,GLY/ARG	462,3944	213.8+/-233.3	24,414,1765	47.0	45.0	46.0		,718,847,568	3.6	1.0	10	dbSNP_123	46	3,8597	3.0+/-9.4	0,3,4297	yes	utr-3,missense,missense,missense	DUSP13	NM_001007271.1,NM_001007272.1,NM_001007273.1,NM_016364.3	,125,125,125	24,417,6062	CC,CG,GG		0.0349,10.4857,3.5753	,probably-damaging,probably-damaging,probably-damaging	,240/249,283/292,190/199	76854463	465,12541	2203	4300	6503	SO:0001583	missense	51207	exon6			CCAGTCGGTTGTC	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.568C>G	10.37:g.76854463G>C	ENSP00000444580:p.Arg190Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	56	35	0.625	NM_001007273	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Missense_Mutation	SNP	ENST00000472493.2	37	CCDS7346.1	59	0.027014652014652016	55	0.11178861788617886	4	0.011049723756906077	0	0.0	0	0.0	G	19.55	3.847958	0.71603	0.104857	3.49E-4	ENSG00000079393	ENST00000308475;ENST00000472493;ENST00000491677;ENST00000372698;ENST00000464872;ENST00000372700	T;T;T;T;T	0.61627	0.09;0.09;0.09;0.09;0.09	5.52	3.61	0.41365	Dual specificity phosphatase, subgroup, catalytic domain (2);	0.557970	0.19913	N	0.103241	T	0.03564	0.0102	M	0.74647	2.275	0.34897	D	0.74614	P;D;B	0.54772	0.556;0.968;0.157	B;P;B	0.54706	0.248;0.759;0.146	T	0.53500	-0.8430	10	0.49607	T	0.09	-3.9628	14.5469	0.68038	0.0:0.0:0.61:0.39	rs16931996;rs52804188;rs16931996	240;319;190	Q9UII6-4;F2Z2C4;Q9UII6	.;.;DUS13_HUMAN	G	190;190;319;283;139;240	ENSP00000311051:R190G;ENSP00000444580:R190G;ENSP00000436312:R319G;ENSP00000434041:R139G;ENSP00000361785:R240G	ENSP00000311051:R190G	R	-	1	2	DUSP13	76524469	0.947000	0.32204	1.000000	0.80357	0.987000	0.75469	1.817000	0.39002	0.635000	0.30488	-0.169000	0.13324	CGA	G|0.956;C|0.044	0.044	strong		0.642	DUSP13-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048786.3		
KIAA0141	9812	hgsc.bcm.edu	37	5	141307833	141307833	+	Missense_Mutation	SNP	T	T	C	rs10036567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141307833T>C	ENST00000432126.2	+	4	516	c.382T>C	c.(382-384)Ttc>Ctc	p.F128L	KIAA0141_ENST00000194118.4_Missense_Mutation_p.F128L	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	128			F -> L (in dbSNP:rs10036567).		extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACCGTTTCTTCTCATCTCC	0.627													C|||	789	0.157548	0.3835	0.0749	5008	,	,		18906	0.0099		0.0865	False		,,,				2504	0.136				p.F128L		Atlas-SNP	.											.	KIAA0141	44	.	0			c.T382C						PASS	.	C	LEU/PHE,LEU/PHE	1445,2961	682.2+/-404.1	235,975,993	104.0	98.0	100.0		382,382	4.8	0.8	5	dbSNP_119	100	722,7878	786.4+/-407.6	26,670,3604	yes	missense,missense	KIAA0141	NM_001142603.1,NM_014773.3	22,22	261,1645,4597	CC,CT,TT		8.3953,32.7962,16.6615	benign,benign	128/516,128/516	141307833	2167,10839	2203	4300	6503	SO:0001583	missense	9812	exon4			CGTTTCTTCTCAT	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.382T>C	5.37:g.141307833T>C	ENSP00000396225:p.Phe128Leu	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	150	76	0.506667	NM_001142603	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	290	0.13278388278388278	191	0.3882113821138211	32	0.08839779005524862	7	0.012237762237762238	60	0.079155672823219	C	2.862	-0.235939	0.05944	0.327962	0.083953	ENSG00000081791	ENST00000432126;ENST00000194118;ENST00000508751	T;T;T	0.14766	2.96;2.96;2.48	5.62	4.75	0.60458	.	0.352416	0.26297	N	0.025200	T	0.00012	0.0000	N	0.00170	-1.935	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45293	-0.9271	9	0.02654	T	1	-7.1069	9.4807	0.38900	0.0:0.8348:0.0:0.1652	rs10036567;rs52831480;rs56547810;rs59311928;rs10036567	128	Q14154	DELE_HUMAN	L	128	ENSP00000396225:F128L;ENSP00000194118:F128L;ENSP00000422686:F128L	ENSP00000194118:F128L	F	+	1	0	KIAA0141	141288017	0.924000	0.31332	0.756000	0.31282	0.471000	0.32888	1.118000	0.31246	0.856000	0.35383	-0.227000	0.12334	TTC	T|0.836;C|0.164	0.164	strong		0.627	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
TACR1	6869	hgsc.bcm.edu	37	2	75276649	75276649	+	Silent	SNP	C	C	T	rs34117315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:75276649C>T	ENST00000305249.5	-	5	1899	c.1134G>A	c.(1132-1134)tcG>tcA	p.S378S		NM_001058.3	NP_001049.1	P25103	NK1R_HUMAN	tachykinin receptor 1	378					acute inflammatory response (GO:0002526)|aggressive behavior (GO:0002118)|angiotensin-mediated drinking behavior (GO:0003051)|associative learning (GO:0008306)|behavioral response to pain (GO:0048266)|detection of abiotic stimulus (GO:0009582)|eating behavior (GO:0042755)|inflammatory response (GO:0006954)|long-term memory (GO:0007616)|operant conditioning (GO:0035106)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of action potential (GO:0045760)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of ossification (GO:0045778)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of saliva secretion (GO:0046878)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|positive regulation of vasoconstriction (GO:0045907)|regulation of smooth muscle cell migration (GO:0014910)|regulation of smooth muscle cell proliferation (GO:0048660)|response to auditory stimulus (GO:0010996)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to heat (GO:0009408)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to ozone (GO:0010193)|response to progesterone (GO:0032570)|smooth muscle contraction involved in micturition (GO:0060083)|sperm ejaculation (GO:0042713)|tachykinin receptor signaling pathway (GO:0007217)	cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance P receptor activity (GO:0016496)|tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(8)|ovary(1)|skin(1)	24					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)	GGTCCAGGGACGAGGGTGTGG	0.612													C|||	299	0.0597045	0.1309	0.0144	5008	,	,		18568	0.0565		0.001	False		,,,				2504	0.0593				p.S378S	Pancreas(64;62 1268 3653 14826 43765)	Atlas-SNP	.											TACR1,colon,carcinoma,-1,5	TACR1	62	5	0			c.G1134A						PASS	.	C		407,3999	201.8+/-224.7	12,383,1808	116.0	114.0	115.0		1134	-9.6	0.0	2	dbSNP_126	115	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	TACR1	NM_001058.3		12,390,6101	TT,TC,CC		0.0814,9.2374,3.1831		378/408	75276649	414,12592	2203	4300	6503	SO:0001819	synonymous_variant	6869	exon5			CAGGGACGAGGGT	M76675	CCDS1958.1, CCDS46345.1	2p13.1-p12	2012-08-08			ENSG00000115353	ENSG00000115353		"""GPCR / Class A : Tachykinin receptors"""	11526	protein-coding gene	gene with protein product		162323		TAC1R		1657150	Standard	NM_001058		Approved	SPR, NK1R, NKIR	uc002sng.2	P25103	OTTHUMG00000129973	ENST00000305249.5:c.1134G>A	2.37:g.75276649C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	220	108	0.490909	NM_001058	A8K150	Silent	SNP	ENST00000305249.5	37	CCDS1958.1																																																																																			C|0.957;T|0.043	0.043	strong		0.612	TACR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252239.3	NM_001058	
EGLN2	112398	hgsc.bcm.edu	37	19	41307170	41307170	+	Silent	SNP	G	G	A	rs2545763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41307170G>A	ENST00000593726.1	+	1	1721	c.693G>A	c.(691-693)ccG>ccA	p.P231P	EGLN2_ENST00000594140.1_5'Flank|RAB4B-EGLN2_ENST00000594136.1_3'UTR|CTC-490E21.12_ENST00000601627.1_5'Flank|EGLN2_ENST00000406058.2_Silent_p.P231P|EGLN2_ENST00000303961.4_Silent_p.P231P			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	231	Beta(2)beta(3) 'finger-like' loop.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|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)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	GGGCGATCCCGCCGCGCAGCA	0.687													G|||	522	0.104233	0.1074	0.0461	5008	,	,		17303	0.2579		0.0447	False		,,,				2504	0.044				p.P231P		Atlas-SNP	.											EGLN2,NS,carcinoma,0,1	EGLN2	31	1	0			c.G693A						PASS	.	G	,	415,3991	190.9+/-216.7	20,375,1808	47.0	45.0	45.0		693,693	-8.1	0.7	19	dbSNP_100	45	385,8213	119.9+/-179.2	8,369,3922	no	coding-synonymous,coding-synonymous	EGLN2	NM_053046.3,NM_080732.3	,	28,744,5730	AA,AG,GG		4.4778,9.419,6.152	,	231/408,231/408	41307170	800,12204	2203	4299	6502	SO:0001819	synonymous_variant	112398	exon2			GATCCCGCCGCGC	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"""HIF prolyl hydroxylase 1"""	606424	"""EGL nine (C.elegans) homolog 2"", ""egl nine homolog 2 (C. elegans)"""				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.693G>A	19.37:g.41307170G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Silent	SNP	ENST00000593726.1	37	CCDS12567.1																																																																																			G|0.911;A|0.089	0.089	strong		0.687	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1		
OR10C1	442194	hgsc.bcm.edu	37	6	29408278	29408278	+	Silent	SNP	C	C	T	rs17184044	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29408278C>T	ENST00000444197.2	+	1	1196	c.486C>T	c.(484-486)atC>atT	p.I162I	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	162						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)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CCCCTTTCATCTTCTCTTTGC	0.607													C|||	265	0.0529153	0.121	0.0432	5008	,	,		17863	0.0456		0.0149	False		,,,				2504	0.0143				p.I162I		Atlas-SNP	.											.	OR10C1	58	.	0			c.C486T						PASS	.	C		262,2760		15,232,1264	112.0	126.0	121.0		486	2.5	1.0	6	dbSNP_123	121	88,5330		1,86,2622	no	coding-synonymous	OR10C1	NM_013941.3		16,318,3886	TT,TC,CC		1.6242,8.6698,4.1469		162/313	29408278	350,8090	1511	2709	4220	SO:0001819	synonymous_variant	442194	exon1			TTTCATCTTCTCT		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.486C>T	6.37:g.29408278C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	NM_013941	Q5SUN7|Q96R18	Silent	SNP	ENST00000444197.2	37	CCDS34364.1																																																																																			C|0.956;T|0.044	0.044	strong		0.607	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2		
NLN	57486	hgsc.bcm.edu	37	5	65108215	65108215	+	Silent	SNP	A	A	G	rs2254485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:65108215A>G	ENST00000380985.5	+	12	2155	c.1977A>G	c.(1975-1977)ccA>ccG	p.P659P	NLN_ENST00000502464.1_Silent_p.P555P	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	659						mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		TAATGAATCCAGAGGTATAGT	0.333													N|||	3503	0.699481	0.8828	0.6066	5008	,	,		16157	0.5665		0.675	False		,,,				2504	0.68				p.P659P		Atlas-SNP	.											.	NLN	51	.	0			c.A1977G						PASS	.	G		3844,562		1680,484,39	75.0	82.0	79.0		1977	3.0	1.0	5	dbSNP_100	79	6051,2549		2101,1849,350	no	coding-synonymous	NLN	NM_020726.4		3781,2333,389	GG,GA,AA		29.6395,12.7553,23.9197		659/705	65108215	9895,3111	2203	4300	6503	SO:0001819	synonymous_variant	57486	exon12			GAATCCAGAGGTA	AJ300837	CCDS3989.1	5q12.3	2008-02-05	2005-03-31		ENSG00000123213	ENSG00000123213	3.4.24.16		16058	protein-coding gene	gene with protein product		611530	"""angiotensin binding protein"""	AGTBP		10574462	Standard	NM_020726		Approved	KIAA1226	uc003juf.3	Q9BYT8	OTTHUMG00000097803	ENST00000380985.5:c.1977A>G	5.37:g.65108215A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_020726	Q9ULJ4	Silent	SNP	ENST00000380985.5	37	CCDS3989.1	1477	0.6762820512820513	418	0.8495934959349594	229	0.6325966850828729	308	0.5384615384615384	522	0.6886543535620053	N	7.749	0.702850	0.15172	0.872447	0.703605	ENSG00000123213	ENST00000509935	.	.	.	5.37	2.96	0.34315	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.15037	-1.0451	3	.	.	.	-12.087	6.3845	0.21554	0.6947:0.0:0.1929:0.1124	rs2254485;rs56518529;rs59473118;rs2254485	.	.	.	G	256	.	.	R	+	1	2	NLN	65143971	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	1.334000	0.33827	0.141000	0.18875	-1.195000	0.01675	AGA	A|0.272;G|0.728	0.728	strong		0.333	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1		
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305774	39305774	+	Missense_Mutation	SNP	C	C	G	rs137947981		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305774C>G	ENST00000343246.4	-	1	280	c.246G>C	c.(244-246)caG>caC	p.Q82H		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	82	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.Q82H(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			agcaggtggtctggcagcagc	0.652																																					p.Q82H		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	1	1	Substitution - Missense(1)	lung(1)	c.G246C						PASS	.						14.0	21.0	19.0					17																	39305774		2102	4215	6317	SO:0001583	missense	85289	exon1			GGTGGTCTGGCAG	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.246G>C	17.37:g.39305774C>G	ENSP00000340546:p.Gln82His	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	86	50	0.581395	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	6.243	0.412973	0.11812	.	.	ENSG00000198271	ENST00000343246	T	0.00594	6.33	2.03	-0.354	0.12591	.	.	.	.	.	T	0.01320	0.0043	M	0.79693	2.465	0.09310	N	1	B	0.21147	0.052	B	0.35182	0.197	T	0.25950	-1.0117	9	0.45353	T	0.12	.	12.081	0.53671	0.0:0.7361:0.2639:0.0	.	87	Q9BYR2	KRA45_HUMAN	H	82	ENSP00000340546:Q82H	ENSP00000340546:Q82H	Q	-	3	2	KRTAP4-5	36559300	0.000000	0.05858	0.005000	0.12908	0.001000	0.01503	-3.389000	0.00488	-0.371000	0.08004	-1.872000	0.00552	CAG	.	.	weak		0.652	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
WDFY4	57705	hgsc.bcm.edu	37	10	49984879	49984879	+	Missense_Mutation	SNP	C	C	T	rs76547526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:49984879C>T	ENST00000325239.5	+	15	2975	c.2948C>T	c.(2947-2949)cCg>cTg	p.P983L	WDFY4_ENST00000413659.2_Missense_Mutation_p.P983L	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	983						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						ACACAGGCCCCGCAGCCCTTG	0.642													C|||	79	0.0157748	0.0522	0.0115	5008	,	,		15744	0.0		0.001	False		,,,				2504	0.001				p.P983L		Atlas-SNP	.											.	WDFY4	205	.	0			c.C2948T						PASS	.	C	LEU/PRO	56,1328		1,54,637	20.0	19.0	20.0		2948	-8.1	0.0	10	dbSNP_132	20	5,3177		0,5,1586	yes	missense	WDFY4	NM_020945.1	98	1,59,2223	TT,TC,CC		0.1571,4.0462,1.336	benign	983/3185	49984879	61,4505	692	1591	2283	SO:0001583	missense	57705	exon16			AGGCCCCGCAGCC	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.2948C>T	10.37:g.49984879C>T	ENSP00000320563:p.Pro983Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	25	0.011446886446886446	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	0	0.0	C	10.44	1.349541	0.24426	0.040462	0.001571	ENSG00000128815	ENST00000454161;ENST00000426033;ENST00000325239;ENST00000413659	T;T	0.55234	0.53;1.56	4.97	-8.11	0.01082	.	.	.	.	.	T	0.01765	0.0056	N	0.00583	-1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15206	-1.0445	8	.	.	.	.	3.6296	0.08126	0.1173:0.3616:0.3583:0.1628	.	983	Q6ZS81	WDFY4_HUMAN	L	992;983;983;983	ENSP00000320563:P983L;ENSP00000403789:P983L	.	P	+	2	0	WDFY4	49654885	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.111000	0.01333	-0.982000	0.03515	-0.238000	0.12139	CCG	C|0.988;T|0.012	0.012	strong		0.642	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
PTPRN2	5799	hgsc.bcm.edu	37	7	157985149	157985149	+	Missense_Mutation	SNP	C	C	G	rs3800855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157985149C>G	ENST00000389418.4	-	5	428	c.419G>C	c.(418-420)aGt>aCt	p.S140T	PTPRN2_ENST00000409483.1_Missense_Mutation_p.S102T|PTPRN2_ENST00000389416.4_Missense_Mutation_p.S123T|PTPRN2_ENST00000389413.3_Missense_Mutation_p.S140T|PTPRN2_ENST00000404321.2_Missense_Mutation_p.S163T	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	140			S -> T (in dbSNP:rs3800855). {ECO:0000269|Ref.4}.		negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCCCTCCCGACTGTACCTCCT	0.632													C|||	1224	0.244409	0.3752	0.1945	5008	,	,		15910	0.1944		0.169	False		,,,				2504	0.2321				p.S140T		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G419C						PASS	.		THR/SER,THR/SER,THR/SER	1508,2898	454.9+/-350.8	273,962,968	51.0	60.0	57.0		419,368,419	1.4	0.0	7	dbSNP_107	57	1280,7320	243.1+/-272.8	91,1098,3111	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	58,58,58	364,2060,4079	GG,GC,CC		14.8837,34.2261,21.4363	possibly-damaging,possibly-damaging,possibly-damaging	140/1016,123/999,140/987	157985149	2788,10218	2203	4300	6503	SO:0001583	missense	5799	exon5			TCCCGACTGTACC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.419G>C	7.37:g.157985149C>G	ENSP00000374069:p.Ser140Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	103	59	0.572816	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	509	0.23305860805860806	188	0.3821138211382114	66	0.18232044198895028	128	0.22377622377622378	127	0.16754617414248021	C	5.064	0.197429	0.09652	0.342261	0.148837	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.03524	3.94;3.9;3.95;3.97;3.96	4.17	1.36	0.22044	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001	B;B;B;B;B	0.09377	0.004;0.001;0.004;0.002;0.002	T	0.42816	-0.9429	8	0.12430	T	0.62	.	3.8043	0.08771	0.0:0.5724:0.2059:0.2217	rs3800855;rs10346808;rs17847434;rs3800855	163;102;140;123;140	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	T	102;140;123;140;163	ENSP00000387114:S102T;ENSP00000374064:S140T;ENSP00000374067:S123T;ENSP00000374069:S140T;ENSP00000385464:S163T	ENSP00000374064:S140T	S	-	2	0	PTPRN2	157677910	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.673000	0.05239	0.488000	0.27723	-0.189000	0.12847	AGT	C|0.780;G|0.220	0.220	strong		0.632	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26272270	26272270	+	Missense_Mutation	SNP	A	A	G	rs695633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26272270A>G	ENST00000407587.2	+	24	4367	c.4198A>G	c.(4198-4200)Att>Gtt	p.I1400V	MYO18B_ENST00000536101.1_Missense_Mutation_p.I1399V|MYO18B_ENST00000335473.7_Missense_Mutation_p.I1399V			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1399						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TAGTGCCACCATTGGAACTGA	0.582													A|||	180	0.0359425	0.1316	0.0086	5008	,	,		16872	0.0		0.0	False		,,,				2504	0.0				p.I1399V		Atlas-SNP	.											.	MYO18B	322	.	0			c.A4195G						PASS	.	A	VAL/ILE	447,3717		25,397,1660	37.0	42.0	40.0		4195	-8.4	0.0	22	dbSNP_83	40	11,8423		0,11,4206	yes	missense	MYO18B	NM_032608.5	29	25,408,5866	GG,GA,AA		0.1304,10.7349,3.6355	benign	1399/2568	26272270	458,12140	2082	4217	6299	SO:0001583	missense	84700	exon24			GCCACCATTGGAA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.4198A>G	22.37:g.26272270A>G	ENSP00000386096:p.Ile1400Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		55	0.025183150183150184	51	0.10365853658536585	4	0.011049723756906077	0	0.0	0	0.0	A	5.587	0.293142	0.10567	0.107349	0.001304	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86297	-2.08;-2.08;-2.1	4.83	-8.43	0.00953	.	0.552403	0.17941	N	0.156858	T	0.05364	0.0142	M	0.63428	1.95	0.80722	P	0.0	B;B;B;B	0.17268	0.007;0.007;0.021;0.013	B;B;B;B	0.14023	0.01;0.004;0.009;0.01	T	0.45906	-0.9229	9	0.37606	T	0.19	.	0.9513	0.01376	0.2422:0.331:0.22:0.2068	rs695633;rs695633	912;1399;1400;1399	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	V	1399;1399;1400	ENSP00000441229:I1399V;ENSP00000334563:I1399V;ENSP00000386096:I1400V	ENSP00000334563:I1399V	I	+	1	0	MYO18B	24602270	0.000000	0.05858	0.000000	0.03702	0.935000	0.57460	-1.506000	0.02271	-1.625000	0.01554	0.528000	0.53228	ATT	A|0.967;G|0.033	0.033	strong		0.582	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
BBS12	166379	hgsc.bcm.edu	37	4	123664333	123664333	+	Missense_Mutation	SNP	G	G	C	rs7665271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:123664333G>C	ENST00000314218.3	+	2	1479	c.1286G>C	c.(1285-1287)aGt>aCt	p.S429T	BBS12_ENST00000542236.1_Missense_Mutation_p.S429T	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	429			S -> T (in dbSNP:rs7665271).		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TGTATAAACAGTAAGCGGTTG	0.453									Bardet-Biedl syndrome				G|||	186	0.0371406	0.1301	0.0173	5008	,	,		20575	0.0		0.002	False		,,,				2504	0.0				p.S429T		Atlas-SNP	.											.	BBS12	63	.	0			c.G1286C						PASS	.	G	THR/SER,THR/SER	451,3955	215.5+/-234.4	21,409,1773	75.0	79.0	78.0		1286,1286	-0.6	0.0	4	dbSNP_116	78	12,8588	9.1+/-34.3	0,12,4288	yes	missense,missense	BBS12	NM_001178007.1,NM_152618.2	58,58	21,421,6061	CC,CG,GG		0.1395,10.236,3.5599	possibly-damaging,possibly-damaging	429/711,429/711	123664333	463,12543	2203	4300	6503	SO:0001583	missense	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TAAACAGTAAGCG	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1286G>C	4.37:g.123664333G>C	ENSP00000319062:p.Ser429Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	37	CCDS3728.1	75	0.034340659340659344	65	0.13211382113821138	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	G	0.004	-2.356069	0.00217	0.10236	0.001395	ENSG00000181004	ENST00000314218;ENST00000542236	T;T	0.79033	-1.23;-1.23	5.58	-0.599	0.11645	.	0.533090	0.21899	N	0.067461	T	0.01627	0.0052	M	0.67953	2.075	0.80722	P	0.0	B	0.18461	0.028	B	0.15052	0.012	T	0.21177	-1.0253	9	0.38643	T	0.18	-14.2272	7.1191	0.25433	0.2915:0.3132:0.3953:0.0	rs7665271;rs7665271	429	Q6ZW61	BBS12_HUMAN	T	429	ENSP00000319062:S429T;ENSP00000438273:S429T	ENSP00000319062:S429T	S	+	2	0	BBS12	123883783	0.005000	0.15991	0.000000	0.03702	0.013000	0.08279	0.239000	0.18023	-0.537000	0.06290	-0.157000	0.13467	AGT	G|0.959;C|0.041	0.041	strong		0.453	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
DYRK2	8445	hgsc.bcm.edu	37	12	68052166	68052166	+	Silent	SNP	C	C	T	rs56178357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:68052166C>T	ENST00000344096.3	+	3	1892	c.1479C>T	c.(1477-1479)agC>agT	p.S493S	RP11-335O4.3_ENST00000425371.2_RNA|DYRK2_ENST00000393555.3_Silent_p.S420S	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	493	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)		CACCGGAGAGCAGAGAGTGGG	0.572													C|||	538	0.107428	0.382	0.0447	5008	,	,		19022	0.0		0.002	False		,,,				2504	0.0				p.S493S		Atlas-SNP	.											.	DYRK2	63	.	0			c.C1479T						PASS	.	C	,	1334,3072	442.3+/-346.6	195,944,1064	59.0	62.0	61.0		1260,1479	5.2	1.0	12	dbSNP_129	61	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous,coding-synonymous	DYRK2	NM_003583.3,NM_006482.2	,	195,953,5355	TT,TC,CC		0.1047,30.2769,10.326	,	420/529,493/602	68052166	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	8445	exon3			GGAGAGCAGAGAG	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.1479C>T	12.37:g.68052166C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	170	85	0.5	NM_006482	B2R9V9|Q9BRB5	Silent	SNP	ENST00000344096.3	37	CCDS8978.1																																																																																			C|0.909;T|0.091	0.091	strong		0.572	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
PRR22	163154	hgsc.bcm.edu	37	19	5783905	5783905	+	Missense_Mutation	SNP	G	G	A	rs3745640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5783905G>A	ENST00000419421.2	-	3	457	c.353C>T	c.(352-354)cCt>cTt	p.P118L		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	118	Pro-rich.		P -> L (in dbSNP:rs3745640).							endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GTAGGGCTGAGGCTCCAGGAG	0.706													G|||	1540	0.307508	0.3147	0.1859	5008	,	,		10380	0.5437		0.165	False		,,,				2504	0.2873				p.P118L		Atlas-SNP	.											.	PRR22	25	.	0			c.C353T						PASS	.	G	LEU/PRO	990,3048		90,810,1119	4.0	6.0	5.0		353	4.5	0.4	19	dbSNP_107	5	1119,7019		66,987,3016	yes	missense	PRR22	NM_001134316.1	98	156,1797,4135	AA,AG,GG		13.7503,24.5171,17.321	possibly-damaging	118/423	5783905	2109,10067	2019	4069	6088	SO:0001583	missense	163154	exon3			GGCTGAGGCTCCA	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.353C>T	19.37:g.5783905G>A	ENSP00000407653:p.Pro118Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_001134316	E9PB31	Missense_Mutation	SNP	ENST00000419421.2	37	CCDS45933.1	638	0.29212454212454214	154	0.3130081300813008	75	0.20718232044198895	282	0.493006993006993	127	0.16754617414248021	G	19.20	3.782414	0.70222	0.245171	0.137503	ENSG00000212123	ENST00000419421	T	0.45668	0.89	4.51	4.51	0.55191	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.28455	P	0.9161476	P;D	0.57571	0.944;0.98	P;P	0.51806	0.548;0.68	T	0.48790	-0.9004	8	0.72032	D	0.01	-9.3203	14.7247	0.69336	0.0:0.0:1.0:0.0	rs3745640;rs3745640	118;116	E9PB31;Q8IZ63	.;PRR22_HUMAN	L	118	ENSP00000407653:P118L	ENSP00000407653:P118L	P	-	2	0	PRR22	5734905	0.736000	0.28164	0.388000	0.26195	0.756000	0.42949	5.938000	0.70170	2.338000	0.79540	0.436000	0.28706	CCT	G|0.702;A|0.298	0.298	strong		0.706	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
OR1J2	26740	hgsc.bcm.edu	37	9	125274015	125274015	+	Missense_Mutation	SNP	C	C	T	rs150890302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125274015C>T	ENST00000335302.5	+	1	935	c.935C>T	c.(934-936)tCt>tTt	p.S312F		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						ACATTTTTCTCTTGGTGACAT	0.378													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		20140	0.0		0.0	False		,,,				2504	0.0				p.S312F		Atlas-SNP	.											.	OR1J2	64	.	0			c.C935T						PASS	.	C	PHE/SER	35,4371	29.0+/-57.7	0,35,2168	39.0	42.0	41.0		935	-0.7	0.0	9	dbSNP_134	41	0,8600		0,0,4300	yes	missense	OR1J2	NM_054107.1	155	0,35,6468	TT,TC,CC		0.0,0.7944,0.2691	benign	312/314	125274015	35,12971	2203	4300	6503	SO:0001583	missense	26740	exon1			TTTTCTCTTGGTG		CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"""GPCR / Class A : Olfactory receptors"""	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.935C>T	9.37:g.125274015C>T	ENSP00000335575:p.Ser312Phe	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	96	36	0.375	NM_054107	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Missense_Mutation	SNP	ENST00000335302.5	37	CCDS35121.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.26	1.301654	0.23736	0.007944	0.0	ENSG00000197233	ENST00000335302	T	0.01505	4.82	4.67	-0.71	0.11234	.	2.214490	0.02811	U	0.124264	T	0.00845	0.0028	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.47114	-0.9142	10	0.52906	T	0.07	.	1.4467	0.02366	0.1417:0.3067:0.138:0.4137	.	312	Q8NGS2	OR1J2_HUMAN	F	312	ENSP00000335575:S312F	ENSP00000335575:S312F	S	+	2	0	OR1J2	124313836	0.000000	0.05858	0.000000	0.03702	0.120000	0.20174	-1.098000	0.03346	0.218000	0.20820	0.632000	0.83419	TCT	C|0.998;T|0.002	0.002	strong		0.378	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1		
MAN1C1	57134	hgsc.bcm.edu	37	1	25944741	25944741	+	Silent	SNP	T	T	C	rs11247857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:25944741T>C	ENST00000374332.4	+	1	783	c.453T>C	c.(451-453)cgT>cgC	p.R151R	MAN1C1_ENST00000263979.3_5'UTR	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	151					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		TCCGGAGCCGTCTCCGCCACC	0.672													C|||	1202	0.240016	0.5719	0.2061	5008	,	,		13186	0.2133		0.0089	False		,,,				2504	0.0808				p.R151R		Atlas-SNP	.											.	MAN1C1	48	.	0			c.T453C						PASS	.	C		1432,2228		281,870,679	12.0	10.0	11.0		453	1.6	1.0	1	dbSNP_120	11	50,7478		2,46,3716	no	coding-synonymous	MAN1C1	NM_020379.2		283,916,4395	CC,CT,TT		0.6642,39.1257,13.2463		151/631	25944741	1482,9706	1830	3764	5594	SO:0001819	synonymous_variant	57134	exon1			GAGCCGTCTCCGC	AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.453T>C	1.37:g.25944741T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_020379	A6NNE2|B2RNP2|Q9Y545	Silent	SNP	ENST00000374332.4	37	CCDS265.1																																																																																			T|0.815;C|0.185	0.185	strong		0.672	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379	
PPP2R3B	28227	hgsc.bcm.edu	37	X	295231	295231	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:295231A>G	ENST00000390665.3	-	13	1617	c.1599T>C	c.(1597-1599)ccT>ccC	p.P533P		NM_013239.4	NP_037371.2	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'', beta	533					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)				TCTGCTCCACAGGGCTGAGCT	0.682													A|||	2776	0.554313	0.8411	0.4337	5008	,	,		13211	0.5655		0.4344	False		,,,				2504	0.364				p.P533P		Atlas-SNP	.											.	PPP2R3B	43	.	0			c.T1599C						PASS	.	A		3401,971		1346,709,131	18.0	20.0	20.0		1599	-0.5	0.8	X	dbSNP_134	20	3531,5019		737,2057,1481	no	coding-synonymous	PPP2R3B	NM_013239.4		2083,2766,1612	GG,GA,AA		41.2982,22.2095,46.3551		533/576	295231	6932,5990	2186	4275	6461	SO:0001819	synonymous_variant	28227	exon13			CTCCACAGGGCTG	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.1599T>C	X.37:g.295231A>G		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_013239	Q6P4G9|Q7RTT1|Q96H01	Silent	SNP	ENST00000390665.3	37	CCDS14104.1																																																																																			A|0.446;G|0.554	0.554	strong		0.682	PPP2R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055577.2	NM_013239	
DOCK2	1794	hgsc.bcm.edu	37	5	169116304	169116304	+	Silent	SNP	T	T	A	rs189140579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:169116304T>A	ENST00000256935.8	+	9	890	c.810T>A	c.(808-810)atT>atA	p.I270I		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	270					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)			CTAAGGAGATTGAGATGCTCA	0.537																																					p.I270I		Atlas-SNP	.											DOCK2,caecum,carcinoma,+2,1	DOCK2	389	1	0			c.T810A						PASS	.						147.0	125.0	133.0					5																	169116304		2203	4300	6503	SO:0001819	synonymous_variant	1794	exon9			GGAGATTGAGATG	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.810T>A	5.37:g.169116304T>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			T|1.000;C|0.000	.	alt		0.537	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
USP49	25862	hgsc.bcm.edu	37	6	41774340	41774340	+	Missense_Mutation	SNP	G	G	T	rs111948785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41774340G>T	ENST00000394253.3	-	3	711	c.382C>A	c.(382-384)Ctg>Atg	p.L128M	USP49_ENST00000373009.3_Missense_Mutation_p.L128M|USP49_ENST00000297229.2_Missense_Mutation_p.L128M|USP49_ENST00000373006.1_Missense_Mutation_p.L128M|USP49_ENST00000373010.1_Missense_Mutation_p.L128M			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	128					histone H2B conserved C-terminal lysine deubiquitination (GO:0035616)|mRNA splicing, via spliceosome (GO:0000398)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)|skin(2)	23	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CGCTGCGGCAGGACCACGTCC	0.687													G|||	81	0.0161741	0.0537	0.0072	5008	,	,		12628	0.0		0.001	False		,,,				2504	0.0041				p.L128M		Atlas-SNP	.											.	USP49	58	.	0			c.C382A						PASS	.	G	MET/LEU	222,4184		6,210,1987	23.0	24.0	23.0		382	4.6	0.1	6	dbSNP_132	23	14,8582		0,14,4284	yes	missense	USP49	NM_018561.3	15	6,224,6271	TT,TG,GG		0.1629,5.0386,1.8151	benign	128/641	41774340	236,12766	2203	4298	6501	SO:0001583	missense	25862	exon4			GCGGCAGGACCAC	AJ586139	CCDS4861.1, CCDS69111.1	6p12.1	2008-02-05	2005-08-08		ENSG00000164663	ENSG00000164663		"""Ubiquitin-specific peptidases"""	20078	protein-coding gene	gene with protein product			"""ubiquitin specific protease 49"""			14715245	Standard	NM_018561		Approved	MGC20741	uc003ori.3	Q70CQ1	OTTHUMG00000014688	ENST00000394253.3:c.382C>A	6.37:g.41774340G>T	ENSP00000377797:p.Leu128Met	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_018561	Q5T3D9|Q5T3E0|Q96CK4	Missense_Mutation	SNP	ENST00000394253.3	37		.	.	.	.	.	.	.	.	.	.	G	9.151	1.016215	0.19355	0.050386	0.001629	ENSG00000164663	ENST00000394253;ENST00000373010;ENST00000373009;ENST00000373006;ENST00000297229	T;T;T;T;T	0.06933	3.72;3.24;3.72;3.5;3.5	4.6	4.6	0.57074	.	0.851504	0.10514	N	0.665818	T	0.01905	0.0060	N	0.12182	0.205	0.09310	N	1	B	0.13594	0.008	B	0.16722	0.016	T	0.44513	-0.9323	10	0.33940	T	0.23	-1.5488	10.2169	0.43173	0.0:0.0:0.7493:0.2507	.	128	Q70CQ1-2	.	M	128	ENSP00000377797:L128M;ENSP00000362101:L128M;ENSP00000362100:L128M;ENSP00000362097:L128M;ENSP00000297229:L128M	ENSP00000297229:L128M	L	-	1	2	USP49	41882318	0.566000	0.26618	0.076000	0.20297	0.974000	0.67602	2.655000	0.46707	2.376000	0.81061	0.655000	0.94253	CTG	A|0.000;G|0.986;T|0.014	0.014	strong		0.687	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000316513.3	NM_018561	
WDR60	55112	hgsc.bcm.edu	37	7	158672619	158672619	+	Missense_Mutation	SNP	A	A	G	rs2788478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:158672619A>G	ENST00000407559.3	+	5	976	c.818A>G	c.(817-819)cAa>cGa	p.Q273R		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	273			Q -> R (in dbSNP:rs2788478).		cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		GAGAGGCACCAAAGCAACGTG	0.438													G|||	2873	0.573682	0.7368	0.4294	5008	,	,		19248	0.7212		0.3837	False		,,,				2504	0.499				p.Q273R		Atlas-SNP	.											.	WDR60	94	.	0			c.A818G						PASS	.		ARG/GLN	2463,1307		809,845,231	73.0	77.0	76.0		818	0.8	0.0	7	dbSNP_100	76	3004,5188		552,1900,1644	yes	missense	WDR60	NM_018051.4	43	1361,2745,1875	GG,GA,AA		36.6699,34.6684,45.7031	benign	273/1067	158672619	5467,6495	1885	4096	5981	SO:0001583	missense	55112	exon5			GGCACCAAAGCAA		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"""WD repeat domain containing"""	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.818A>G	7.37:g.158672619A>G	ENSP00000384290:p.Gln273Arg	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	167	93	0.556886	NM_018051	Q9NW58	Missense_Mutation	SNP	ENST00000407559.3	37	CCDS47757.1	1191	0.5453296703296703	354	0.7195121951219512	155	0.4281767955801105	394	0.6888111888111889	288	0.37994722955145116	G	0.033	-1.322301	0.01320	0.653316	0.366699	ENSG00000126870	ENST00000407559	T	0.18016	2.24	4.73	0.795	0.18643	.	0.669254	0.12904	N	0.429496	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	0.36841	-0.9731	9	0.02654	T	1	0.3405	5.0153	0.14333	0.3597:0.1489:0.4914:0.0	rs2788478;rs9654723;rs10349453;rs52836646;rs56855193;rs2788478	273	Q8WVS4	WDR60_HUMAN	R	273	ENSP00000384290:Q273R	ENSP00000384290:Q273R	Q	+	2	0	WDR60	158365380	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	0.042000	0.13949	-0.043000	0.13513	-0.726000	0.03593	CAA	A|0.435;G|0.565	0.565	strong		0.438	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051	
THBS1	7057	hgsc.bcm.edu	37	15	39880358	39880358	+	Silent	SNP	C	C	T	rs2228261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39880358C>T	ENST00000260356.5	+	9	1575	c.1410C>T	c.(1408-1410)aaC>aaT	p.N470N		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	470	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.N470N(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CCCAGATGAACGGGAAACCCT	0.597													C|||	1336	0.266773	0.4493	0.1383	5008	,	,		20241	0.2897		0.1312	False		,,,				2504	0.227				p.N470N		Atlas-SNP	.											THBS1,NS,carcinoma,0,1	THBS1	106	1	1	Substitution - coding silent(1)	stomach(1)	c.C1410T						PASS	.	C		1702,2698	513.4+/-368.3	331,1040,829	83.0	78.0	80.0		1410	-12.0	0.0	15	dbSNP_98	80	1130,7464	232.5+/-266.1	64,1002,3231	no	coding-synonymous	THBS1	NM_003246.2		395,2042,4060	TT,TC,CC		13.1487,38.6818,21.7947		470/1171	39880358	2832,10162	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon9			GATGAACGGGAAA		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1410C>T	15.37:g.39880358C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.766;T|0.234	0.234	strong		0.597	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
CPAMD8	27151	hgsc.bcm.edu	37	19	17113083	17113083	+	Missense_Mutation	SNP	G	G	A	rs10426545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17113083G>A	ENST00000443236.1	-	9	923	c.892C>T	c.(892-894)Cgg>Tgg	p.R298W	CPAMD8_ENST00000388925.4_Missense_Mutation_p.R251W	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	251						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						CACCTGGCCCGCACAGTGCCT	0.607													N|||	120	0.0239617	0.0885	0.0043	5008	,	,		16334	0.0		0.0	False		,,,				2504	0.0				p.R298W		Atlas-SNP	.											CPAMD8,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	CPAMD8	192	1	0			c.C892T						scavenged	.	G	TRP/ARG	332,3516		18,296,1610	21.0	22.0	22.0		892	1.5	0.0	19	dbSNP_119	22	13,8241		0,13,4114	no	missense	CPAMD8	NM_015692.2	101	18,309,5724	AA,AG,GG		0.1575,8.6279,2.8508	probably-damaging	298/1933	17113083	345,11757	1924	4127	6051	SO:0001583	missense	27151	exon9			TGGCCCGCACAGT	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.892C>T	19.37:g.17113083G>A	ENSP00000402505:p.Arg298Trp	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	128	52	0.40625	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	N	15.04	2.714927	0.48622	0.086279	0.001575	ENSG00000160111	ENST00000291440;ENST00000388925	T;T	0.12039	2.72;2.72	2.61	1.51	0.23008	.	1.430970	0.04807	U	0.434632	T	0.00496	0.0016	L	0.46157	1.445	0.31995	N	0.604078	D	0.59357	0.985	B	0.40534	0.332	T	0.29610	-1.0006	10	0.59425	D	0.04	.	8.4214	0.32703	0.0:0.0:0.5788:0.4212	rs10426545;rs10426545	251	Q8IZJ3	CPMD8_HUMAN	W	298;251	ENSP00000291440:R298W;ENSP00000373577:R251W	ENSP00000291440:R298W	R	-	1	2	CPAMD8	16974083	0.962000	0.33011	0.047000	0.18901	0.941000	0.58515	1.586000	0.36611	0.217000	0.20800	0.466000	0.42574	CGG	G|0.982;A|0.018	0.018	strong		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
CAPN14	440854	hgsc.bcm.edu	37	2	31420143	31420143	+	Missense_Mutation	SNP	C	C	T	rs72797147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31420143C>T	ENST00000403897.3	-	8	988	c.847G>A	c.(847-849)Gtg>Atg	p.V283M	CAPN14_ENST00000444918.2_Missense_Mutation_p.V283M	NM_001145122.1	NP_001138594.1	A8MX76	CAN14_HUMAN	calpain 14	283	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|endometrium(2)|prostate(1)|skin(1)|stomach(2)	7						TTCCATTCCACCTTTCCCCAG	0.512													C|||	118	0.0235623	0.0113	0.0317	5008	,	,		21044	0.0159		0.0268	False		,,,				2504	0.0389				p.V283M		Atlas-SNP	.											.	CAPN14	36	.	0			c.G847A						PASS	.	C	MET/VAL	16,1368		0,16,676	220.0	193.0	201.0		847	1.4	0.0	2	dbSNP_130	201	64,3118		0,64,1527	yes	missense	CAPN14	NM_001145122.1	21	0,80,2203	TT,TC,CC		2.0113,1.1561,1.7521	probably-damaging	283/685	31420143	80,4486	692	1591	2283	SO:0001583	missense	440854	exon8			ATTCCACCTTTCC	AC015980	CCDS46254.1	2p23.1-p21	2013-01-10			ENSG00000214711	ENSG00000214711		"""EF-hand domain containing"""	16664	protein-coding gene	gene with protein product		610229				11675017	Standard	NM_001145122		Approved		uc010yms.2	A8MX76	OTTHUMG00000152039	ENST00000403897.3:c.847G>A	2.37:g.31420143C>T	ENSP00000385247:p.Val283Met	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	240	116	0.483333	NM_001145122	B3KRU9	Missense_Mutation	SNP	ENST00000403897.3	37	CCDS46254.1	39	0.017857142857142856	5	0.01016260162601626	9	0.024861878453038673	6	0.01048951048951049	19	0.025065963060686015	C	11.62	1.693779	0.30052	0.011561	0.020113	ENSG00000214711	ENST00000444918;ENST00000403897	D;D	0.88741	-2.42;-2.42	3.29	1.42	0.22433	Peptidase C2, calpain, catalytic domain (3);	0.581708	0.15357	U	0.266619	T	0.81569	0.4850	M	0.79011	2.435	0.20764	N	0.999857	D;D	0.61697	0.99;0.96	P;P	0.58172	0.834;0.788	T	0.77544	-0.2548	10	0.87932	D	0	.	6.2976	0.21095	0.0:0.4533:0.0:0.5467	.	283;107	A8MX76;A8MX76-2	CAN14_HUMAN;.	M	283	ENSP00000398670:V283M;ENSP00000385247:V283M	ENSP00000385247:V283M	V	-	1	0	CAPN14	31273647	0.996000	0.38824	0.010000	0.14722	0.209000	0.24338	2.145000	0.42207	0.079000	0.16929	0.462000	0.41574	GTG	C|0.982;T|0.018	0.018	strong		0.512	CAPN14-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325010.1	NM_001145122	
RPL6	6128	hgsc.bcm.edu	37	12	112843105	112843105	+	Missense_Mutation	SNP	T	T	C	rs141161168	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:112843105T>C	ENST00000424576.2	-	7	975	c.790A>G	c.(790-792)Att>Gtt	p.I264V	RPL6_ENST00000202773.9_Missense_Mutation_p.I264V	NM_001024662.1	NP_001019833.1	Q02878	RL6_HUMAN	ribosomal protein L6	264				AVDSQILPKIKAIPQLQ -> LWTHKFYQKSKLFLSSS (in Ref. 1; CAA49188). {ECO:0000305}.	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)|regulation of transcription, DNA-templated (GO:0006355)|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)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|large_intestine(6)|lung(3)	10						AGCTGAGGAATAGCTTTGATT	0.363													T|||	3	0.000599042	0.0023	0.0	5008	,	,		18604	0.0		0.0	False		,,,				2504	0.0				p.I264V		Atlas-SNP	.											.	RPL6	20	.	0			c.A790G						PASS	.	T	VAL/ILE,VAL/ILE	12,4366		0,12,2177	20.0	22.0	22.0		790,790	-1.2	0.0	12	dbSNP_134	22	0,8470		0,0,4235	no	missense,missense	RPL6	NM_000970.3,NM_001024662.1	29,29	0,12,6412	CC,CT,TT		0.0,0.2741,0.0934	benign,benign	264/289,264/289	112843105	12,12836	2189	4235	6424	SO:0001583	missense	6128	exon7			GAGGAATAGCTTT	X69391	CCDS9162.1	12q24.13	2014-06-05				ENSG00000089009		"""L ribosomal proteins"""	10362	protein-coding gene	gene with protein product		603703		TXREB1		8479925, 8457378	Standard	XM_005253920		Approved	TAXREB107, L6	uc001ttv.3	Q02878		ENST00000424576.2:c.790A>G	12.37:g.112843105T>C	ENSP00000403172:p.Ile264Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_001024662	Q2M3Q3|Q8WW97	Missense_Mutation	SNP	ENST00000424576.2	37	CCDS9162.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	4.047	0.006419	0.07866	0.002741	0.0	ENSG00000089009	ENST00000202773;ENST00000424576;ENST00000549923	T;T	0.28069	1.63;1.63	5.15	-1.17	0.09648	.	0.242260	0.41294	N	0.000912	T	0.09423	0.0232	N	0.01656	-0.775	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34054	-0.9844	10	0.10902	T	0.67	.	12.53	0.56109	0.0:0.4627:0.0:0.5373	.	264	Q02878	RL6_HUMAN	V	264;264;204	ENSP00000202773:I264V;ENSP00000403172:I264V	ENSP00000202773:I264V	I	-	1	0	RPL6	111327488	0.025000	0.19082	0.010000	0.14722	0.906000	0.53458	0.202000	0.17295	-0.480000	0.06803	-1.431000	0.01090	ATT	T|1.000;C|0.000	0.000	strong		0.363	RPL6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405422.1		
MYBBP1A	10514	hgsc.bcm.edu	37	17	4448324	4448324	+	Silent	SNP	C	C	T	rs9910964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4448324C>T	ENST00000254718.4	-	17	2613	c.2307G>A	c.(2305-2307)gcG>gcA	p.A769A	MYBBP1A_ENST00000381556.2_Silent_p.A769A			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	769	Glu-rich.				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						CACTCACCAGCGCCTTCCCAG	0.711													C|||	363	0.072484	0.2572	0.0231	5008	,	,		4471	0.0		0.007	False		,,,				2504	0.0				p.A769A		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G2307A						PASS	.	C	,	821,3251		77,667,1292	88.0	62.0	71.0		2307,2307	-1.9	1.0	17	dbSNP_119	71	16,7960		0,16,3972	yes	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	77,683,5264	TT,TC,CC		0.2006,20.1621,6.9472	,	769/1333,769/1329	4448324	837,11211	2036	3988	6024	SO:0001819	synonymous_variant	10514	exon17			CACCAGCGCCTTC	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.2307G>A	17.37:g.4448324C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			C|0.916;T|0.084	0.084	strong		0.711	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
CX3CR1	1524	hgsc.bcm.edu	37	3	39307256	39307256	+	Missense_Mutation	SNP	C	C	T	rs3732379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39307256C>T	ENST00000541347.1	-	2	984	c.745G>A	c.(745-747)Gtt>Att	p.V249I	CX3CR1_ENST00000399220.2_Missense_Mutation_p.V249I|CX3CR1_ENST00000542107.1_Missense_Mutation_p.V249I|CX3CR1_ENST00000358309.3_Missense_Mutation_p.V281I	NM_001171171.1	NP_001164642.1	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	249			V -> I (common polymorphism in Caucasian population; associated with a markedly reduced risk of acute coronary artery disease; associated with higher risk of developing ARMD12; chemotaxis of monocytes of individuals with homozygous Ile-249 and Met-280 genotypes is impaired in the presence of bound CX3CR1 protein; dbSNP:rs3732379). {ECO:0000269|PubMed:10731151, ECO:0000269|PubMed:11264153, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15208270, ECO:0000269|Ref.6}.		cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cerebral cortex cell migration (GO:0021795)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|macrophage chemotaxis (GO:0048246)|microglial cell activation involved in immune response (GO:0002282)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|response to wounding (GO:0009611)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|neuronal cell body membrane (GO:0032809)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-X3-C chemokine receptor activity (GO:0016495)|chemokine receptor activity (GO:0004950)			endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)		AAAATCATAACGTTGTAGGGT	0.483													C|||	723	0.144369	0.0893	0.2378	5008	,	,		22318	0.0278		0.2853	False		,,,				2504	0.1278				p.V281I		Atlas-SNP	.											.	CX3CR1	91	.	0			c.G841A	GRCh37	CM000504	CX3CR1	M	rs3732379	PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	515,3329		36,443,1443	112.0	115.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	745,745,841,745	-2.3	0.0	3	dbSNP_107	114	2281,5975		311,1659,2158	yes	missense,missense,missense,missense	CX3CR1	NM_001171171.1,NM_001171172.1,NM_001171174.1,NM_001337.3	29,29,29,29	347,2102,3601	TT,TC,CC		27.6284,13.3975,23.1074	benign,benign,benign,benign	249/356,249/356,281/388,249/356	39307256	2796,9304	1922	4128	6050	SO:0001583	missense	1524	exon2			TCATAACGTTGTA	BC028078	CCDS43069.1, CCDS54571.1	3p21.3	2012-08-08	2002-08-22		ENSG00000168329	ENSG00000168329		"""GPCR / Class A : Chemokine receptors : C-X-3-C motif"""	2558	protein-coding gene	gene with protein product		601470	"""chemokine (C-X3-C) receptor 1"""	GPR13, CMKBRL1		9726990, 7646814	Standard	NM_001171171		Approved	CMKDR1, V28, CCRL1	uc021wwc.1	P49238	OTTHUMG00000156249	ENST00000541347.1:c.745G>A	3.37:g.39307256C>T	ENSP00000439140:p.Val249Ile	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	170	76	0.447059	NM_001171174	A0N0N6|B2R5Z4|J3KP17	Missense_Mutation	SNP	ENST00000541347.1	37	CCDS43069.1	380	0.17399267399267399	55	0.11178861788617886	93	0.2569060773480663	20	0.03496503496503497	212	0.2796833773087071	C	0.008	-1.863526	0.00552	0.133975	0.276284	ENSG00000168329	ENST00000399220;ENST00000538756;ENST00000358309;ENST00000541347;ENST00000542107	T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4	5.77	-2.32	0.06745	GPCR, rhodopsin-like superfamily (1);	0.526611	0.21488	N	0.073733	T	0.00012	0.0000	N	0.10733	0.035	0.80722	P	0.0	B	0.19073	0.033	B	0.17433	0.018	T	0.11299	-1.0593	9	0.02654	T	1	.	12.3125	0.54935	0.0:0.3682:0.0:0.6318	rs3732379;rs17792918;rs52808794;rs59717546;rs3732379	249	P49238	CX3C1_HUMAN	I	249;257;281;249;249	ENSP00000382166:V249I;ENSP00000351059:V281I;ENSP00000439140:V249I;ENSP00000444928:V249I	ENSP00000351059:V281I	V	-	1	0	CX3CR1	39282260	0.000000	0.05858	0.000000	0.03702	0.225000	0.24961	-1.393000	0.02521	-0.555000	0.06142	-0.794000	0.03295	GTT	C|0.832;T|0.168	0.168	strong		0.483	CX3CR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343613.1	NM_001337	
HELZ2	85441	hgsc.bcm.edu	37	20	62197370	62197370	+	Silent	SNP	G	G	A	rs34830600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62197370G>A	ENST00000467148.1	-	8	2874	c.2805C>T	c.(2803-2805)tgC>tgT	p.C935C	HELZ2_ENST00000427522.2_Silent_p.C366C	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	935	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)										GCCGCTCCACGCACTCACGGA	0.701													G|||	944	0.188498	0.438	0.1383	5008	,	,		17201	0.0317		0.0676	False		,,,				2504	0.1728				p.C935C		Atlas-SNP	.											.	.	.	.	0			c.C2805T						PASS	.	G	,	1573,2777		291,991,893	17.0	16.0	16.0		2805,1098	-2.1	0.1	20	dbSNP_126	16	633,7943		22,589,3677	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	313,1580,4570	AA,AG,GG		7.3811,36.1609,17.0664	,	935/2650,366/2081	62197370	2206,10720	2175	4288	6463	SO:0001819	synonymous_variant	85441	exon9			CTCCACGCACTCA	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.2805C>T	20.37:g.62197370G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			G|0.827;A|0.173	0.173	strong		0.701	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
GLTSCR1	29998	hgsc.bcm.edu	37	19	48182859	48182859	+	Silent	SNP	G	G	A	rs60219834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48182859G>A	ENST00000396720.3	+	6	626	c.432G>A	c.(430-432)acG>acA	p.T144T	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	144										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)		CAGGCCCGACGGGCGCTGGAG	0.741													G|||	283	0.0565096	0.1997	0.0245	5008	,	,		10296	0.0		0.002	False		,,,				2504	0.0				p.T144T		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G432A						PASS	.						8.0	10.0	9.0					19																	48182859		677	1571	2248	SO:0001819	synonymous_variant	29998	exon6			CCCGACGGGCGCT	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.432G>A	19.37:g.48182859G>A		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	37	CCDS46134.1																																																																																			G|0.943;A|0.057	0.057	strong		0.741	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711	
VCAN	1462	hgsc.bcm.edu	37	5	82833145	82833145	+	Silent	SNP	G	G	A	rs2548541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82833145G>A	ENST00000265077.3	+	8	4888	c.4323G>A	c.(4321-4323)caG>caA	p.Q1441Q	VCAN_ENST00000343200.5_Silent_p.Q454Q|VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1441	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CACCTTCTCAGAATTTCTCGG	0.453																																					p.Q1441Q		Atlas-SNP	.											.	VCAN	498	.	0			c.G4323A						PASS	.	A	,,,	3493,913	350.5+/-310.9	1395,703,105	77.0	80.0	79.0		,1362,,4323	-7.8	0.2	5	dbSNP_100	79	5248,3352	497.6+/-374.5	1577,2094,629	no	intron,coding-synonymous,intron,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	2972,2797,734	AA,AG,GG		38.9767,20.7217,32.7926	,,,	,454/2410,,1441/3397	82833145	8741,4265	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			TTCTCAGAATTTC	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.4323G>A	5.37:g.82833145G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			G|0.316;A|0.684	0.684	strong		0.453	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
CFAP46	54777	hgsc.bcm.edu	37	10	134672609	134672609	+	Missense_Mutation	SNP	C	C	T	rs73391295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134672609C>T	ENST00000368586.5	-	38	5441	c.5341G>A	c.(5341-5343)Gtt>Att	p.V1781I	TTC40_ENST00000263170.5_5'Flank	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TTTACGTCAACACAATTCTCT	0.507													c|||	604	0.120607	0.3427	0.0375	5008	,	,		19727	0.0179		0.0119	False		,,,				2504	0.0971				p.V1781I		Atlas-SNP	.											.	TTC40	100	.	0			c.G5341A						PASS	.																																			SO:0001583	missense	54777	exon38			CGTCAACACAATT																												ENST00000368586.5:c.5341G>A	10.37:g.134672609C>T	ENSP00000357575:p.Val1781Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	142	78	0.549296	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	205	0.09386446886446886	172	0.34959349593495936	12	0.03314917127071823	12	0.02097902097902098	9	0.011873350923482849	c	7.517	0.655778	0.14580	.	.	ENSG00000171811	ENST00000368586	T	0.10192	2.9	4.17	2.29	0.28610	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.45056	-0.9287	6	0.07482	T	0.82	.	6.5641	0.22503	0.0:0.7767:0.0:0.2233	.	.	.	.	I	1781	ENSP00000357575:V1781I	ENSP00000357575:V1781I	V	-	1	0	C10orf93	134522599	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.645000	0.24782	0.527000	0.28560	-0.150000	0.13652	GTT	C|0.924;T|0.076	0.076	strong		0.507	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
ALMS1	7840	hgsc.bcm.edu	37	2	73676315	73676315	+	Silent	SNP	A	A	G	rs76266696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73676315A>G	ENST00000264448.6	+	8	2769	c.2658A>G	c.(2656-2658)gtA>gtG	p.V886V	ALMS1_ENST00000377715.1_Silent_p.V886V|ALMS1_ENST00000409009.1_Silent_p.V844V	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	886	34 X 47 AA approximate tandem repeat.				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						CTCTGAAAGTATCAATTGTTC	0.463													A|||	39	0.00778754	0.028	0.0029	5008	,	,		20537	0.0		0.0	False		,,,				2504	0.0				p.V886V		Atlas-SNP	.											.	ALMS1	384	.	0			c.A2658G						PASS	.	A		90,3660		1,88,1786	98.0	102.0	101.0		2658	-0.3	0.0	2	dbSNP_132	101	2,8196		0,2,4097	no	coding-synonymous	ALMS1	NM_015120.4		1,90,5883	GG,GA,AA		0.0244,2.4,0.77		886/4168	73676315	92,11856	1875	4099	5974	SO:0001819	synonymous_variant	7840	exon8			GAAAGTATCAATT	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.2658A>G	2.37:g.73676315A>G		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	264	128	0.484848	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			A|0.994;G|0.006	0.006	strong		0.463	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
DDX11	1663	hgsc.bcm.edu	37	12	31256615	31256615	+	Missense_Mutation	SNP	C	C	A	rs3893680		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:31256615C>A	ENST00000407793.2	+	26	2887	c.2636C>A	c.(2635-2637)cCg>cAg	p.P879Q	DDX11_ENST00000545668.1_Missense_Mutation_p.P879Q|DDX11_ENST00000350437.4_Missense_Mutation_p.R831S|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Missense_Mutation_p.R881S|DDX11_ENST00000228264.6_Missense_Mutation_p.R855S	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	879					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)					GATCCGAGCCCGTGTGGAGGT	0.607										Multiple Myeloma(12;0.14)																											p.R881S		Atlas-SNP	.											DDX11,lower_third,carcinoma,-2,1	DDX11	188	1	0			c.C2641A						scavenged	.						71.0	79.0	77.0					12																	31256615		2203	4300	6503	SO:0001583	missense	1663	exon26			CGAGCCCGTGTGG	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.2636C>A	12.37:g.31256615C>A	ENSP00000384703:p.Pro879Gln	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	256	10	0.0390625	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.916|1.916	-0.449442|-0.449442	0.04572|0.04572	.|.	.|.	ENSG00000013573|ENSG00000013573	ENST00000407793;ENST00000545668|ENST00000542838;ENST00000228264;ENST00000350437	T;T|T;T;T	0.71341|0.80123	-0.56;-0.56|-1.34;-1.25;-1.06	3.14|3.14	2.24|2.24	0.28232|0.28232	.|.	.|1.099370	.|0.07030	.|N	.|0.828301	T|T	0.63070|0.63070	0.2480|0.2480	N|N	0.20986|0.20986	0.625|0.625	0.80722|0.80722	D|D	1|1	B|B;B;B	0.26845|0.21452	0.161|0.056;0.056;0.056	B|B;B;B	0.19391|0.24394	0.025|0.053;0.049;0.053	T|T	0.55927|0.55927	-0.8063|-0.8063	9|10	0.87932|0.02654	D|T	0|1	.|.	3.6922|3.6922	0.08350|0.08350	0.2415:0.6231:0.0:0.1355|0.2415:0.6231:0.0:0.1355	rs3893680|rs3893680	879|855;831;881	Q96FC9|Q96FC9-3;Q96FC9-4;Q96FC9-2	DDX11_HUMAN|.;.;.	Q|S	879|881;855;831	ENSP00000384703:P879Q;ENSP00000440402:P879Q|ENSP00000443426:R881S;ENSP00000228264:R855S;ENSP00000309965:R831S	ENSP00000384703:P879Q|ENSP00000228264:R855S	P|R	+|+	2|1	0|0	DDX11|DDX11	31147882|31147882	0.998000|0.998000	0.40836|0.40836	0.986000|0.986000	0.45419|0.45419	0.053000|0.053000	0.15095|0.15095	1.393000|1.393000	0.34497|0.34497	0.518000|0.518000	0.28383|0.28383	0.430000|0.430000	0.28490|0.28490	CCG|CGT	.	.	weak		0.607	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
ZNF536	9745	hgsc.bcm.edu	37	19	31039357	31039357	+	Missense_Mutation	SNP	C	C	A	rs61741995	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:31039357C>A	ENST00000355537.3	+	4	2978	c.2831C>A	c.(2830-2832)cCc>cAc	p.P944H		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	944					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)					CTGGCTGACCCCCCTTCCATG	0.522													C|||	77	0.0153754	0.0545	0.0072	5008	,	,		17880	0.0		0.0	False		,,,				2504	0.0				p.P944H		Atlas-SNP	.											.	ZNF536	424	.	0			c.C2831A						PASS	.	C	HIS/PRO	239,4167	141.5+/-176.9	7,225,1971	132.0	143.0	139.0		2831	3.3	0.0	19	dbSNP_129	139	16,8584	11.2+/-40.8	0,16,4284	yes	missense	ZNF536	NM_014717.1	77	7,241,6255	AA,AC,CC		0.186,5.4244,1.9606	benign	944/1301	31039357	255,12751	2203	4300	6503	SO:0001583	missense	9745	exon4			CTGACCCCCCTTC		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.2831C>A	19.37:g.31039357C>A	ENSP00000347730:p.Pro944His	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	30	18	0.6	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	3.103	-0.184365	0.06340	0.054244	0.00186	ENSG00000198597	ENST00000355537	T	0.08634	3.07	5.69	3.34	0.38264	.	0.451539	0.25613	N	0.029467	T	0.00784	0.0026	N	0.24115	0.695	0.09310	N	1	P;P	0.36495	0.556;0.556	B;B	0.34038	0.174;0.174	T	0.38824	-0.9643	10	0.46703	T	0.11	-2.4559	7.0172	0.24895	0.0:0.6863:0.1357:0.178	rs61741995	944;944	A7E228;O15090	.;ZN536_HUMAN	H	944	ENSP00000347730:P944H	ENSP00000347730:P944H	P	+	2	0	ZNF536	35731197	0.090000	0.21635	0.000000	0.03702	0.954000	0.61252	0.907000	0.28531	0.576000	0.29452	0.491000	0.48974	CCC	C|0.982;A|0.018	0.018	strong		0.522	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
SCAMP5	192683	hgsc.bcm.edu	37	15	75305040	75305040	+	Silent	SNP	A	A	G	rs7174129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75305040A>G	ENST00000361900.6	+	4	237	c.30A>G	c.(28-30)ccA>ccG	p.P10P	SCAMP5_ENST00000565923.1_3'UTR|SCAMP5_ENST00000425597.3_Silent_p.P10P|SCAMP5_ENST00000545456.1_5'UTR|SCAMP5_ENST00000562212.1_Silent_p.P10P	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	10					exocytosis (GO:0006887)|negative regulation of endocytosis (GO:0045806)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of cytokine secretion (GO:0050715)|protein transport (GO:0015031)|response to endoplasmic reticulum stress (GO:0034976)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)|trans-Golgi network membrane (GO:0032588)				large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	5						ACTTCCCACCATTGCCCAAAT	0.517													A|||	1625	0.324481	0.4357	0.1499	5008	,	,		19471	0.4077		0.0865	False		,,,				2504	0.4571				p.P10P		Atlas-SNP	.											.	SCAMP5	34	.	0			c.A30G						PASS	.	A	,,	1498,2626		279,940,843	97.0	103.0	101.0		30,30,30	-10.7	0.0	15	dbSNP_116	101	607,7809		26,555,3627	no	coding-synonymous,coding-synonymous,coding-synonymous	SCAMP5	NM_001178111.1,NM_001178112.1,NM_138967.3	,,	305,1495,4470	GG,GA,AA		7.2125,36.324,16.7863	,,	10/236,10/236,10/236	75305040	2105,10435	2062	4208	6270	SO:0001819	synonymous_variant	192683	exon4			CCCACCATTGCCC	AL833230	CCDS45306.1	15q24.2	2014-05-20			ENSG00000198794	ENSG00000198794		"""Secretory carrier membrane proteins"""	30386	protein-coding gene	gene with protein product		613766				12477932	Standard	NM_001178111		Approved	MGC24969	uc002azk.2	Q8TAC9	OTTHUMG00000172704	ENST00000361900.6:c.30A>G	15.37:g.75305040A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Silent	SNP	ENST00000361900.6	37	CCDS45306.1																																																																																			A|0.735;G|0.265	0.265	strong		0.517	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967	
CACNG6	59285	hgsc.bcm.edu	37	19	54501527	54501527	+	Silent	SNP	G	G	A	rs34604090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	66	0	0		WXS	Illumina HiSeq	Phase_I	58	18	0.310345	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		
TUBA1B	10376	hgsc.bcm.edu	37	12	49522238	49522238	+	Missense_Mutation	SNP	A	A	T	rs199895521		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49522238A>T	ENST00000336023.5	-	4	953	c.859T>A	c.(859-861)Tct>Act	p.S287T	RP11-386G11.10_ENST00000548149.1_RNA|RP11-386G11.10_ENST00000547712.1_RNA|RP11-386G11.10_ENST00000552893.1_RNA|RP11-386G11.10_ENST00000547387.1_RNA	NM_006082.2	NP_006073.2	P68363	TBA1B_HUMAN	tubulin, alpha 1b	287					'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						TCTGCTACAGAAAGCTGTTCA	0.527																																					p.S287T		Atlas-SNP	.											TUBA1B,bladder,carcinoma,0,1	TUBA1B	24	1	0			c.T859A						scavenged	.						14.0	16.0	15.0					12																	49522238		2165	4231	6396	SO:0001583	missense	10376	exon4			CTACAGAAAGCTG	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.859T>A	12.37:g.49522238A>T	ENSP00000336799:p.Ser287Thr	Somatic	516	0	0		WXS	Illumina HiSeq	Phase_I	694	183	0.263689	NM_006082	P04687|P05209|Q27I68|Q8WU19	Missense_Mutation	SNP	ENST00000336023.5	37	CCDS31792.1	.	.	.	.	.	.	.	.	.	.	a	10.92	1.487232	0.26686	.	.	ENSG00000123416	ENST00000336023	D	0.83591	-1.74	5.41	4.26	0.50523	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.139910	0.28146	U	0.016435	T	0.73063	0.3539	L	0.34521	1.04	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.64854	-0.6309	10	0.29301	T	0.29	.	10.4421	0.44472	0.9218:0.0:0.0782:0.0	.	287	P68363	TBA1B_HUMAN	T	287	ENSP00000336799:S287T	ENSP00000336799:S287T	S	-	1	0	TUBA1B	47808505	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.845000	0.69437	0.908000	0.36671	0.524000	0.50904	TCT	A|0.998;T|0.002	0.002	weak		0.527	TUBA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409005.1	NM_006082	
ESPNL	339768	hgsc.bcm.edu	37	2	239040343	239040343	+	Silent	SNP	G	G	A	rs73102311	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239040343G>A	ENST00000343063.3	+	9	3251	c.2988G>A	c.(2986-2988)aaG>aaA	p.K996K	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409169.1_Silent_p.K952K|ESPNL_ENST00000409506.1_Silent_p.K628K	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	996										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGAAGGAGAAGGAAGCTGAGA	0.547													G|||	429	0.0856629	0.0923	0.062	5008	,	,		19468	0.0546		0.0915	False		,,,				2504	0.1196				p.K996K		Atlas-SNP	.											.	ESPNL	63	.	0			c.G2988A						PASS	.	G		379,4025	183.3+/-210.9	17,345,1840	70.0	75.0	74.0		2988	-4.2	0.9	2	dbSNP_130	74	763,7837	181.0+/-229.8	35,693,3572	no	coding-synonymous	ESPNL	NM_194312.2		52,1038,5412	AA,AG,GG		8.8721,8.6058,8.7819		996/1006	239040343	1142,11862	2202	4300	6502	SO:0001819	synonymous_variant	339768	exon9			GGAGAAGGAAGCT	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2988G>A	2.37:g.239040343G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			G|0.914;A|0.086	0.086	strong		0.547	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
OR52J3	119679	hgsc.bcm.edu	37	11	5068137	5068137	+	Missense_Mutation	SNP	G	G	A	rs2500017	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5068137G>A	ENST00000380370.1	+	1	382	c.382G>A	c.(382-384)Gtc>Atc	p.V128I		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	128			V -> I (in dbSNP:rs2500017). {ECO:0000269|PubMed:14983052, ECO:0000269|Ref.1, ECO:0000269|Ref.3}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTATGTGGCCGTCTGTGCTCC	0.483													A|||	2442	0.48762	0.5915	0.4971	5008	,	,		20351	0.2619		0.508	False		,,,				2504	0.5521				p.V128I		Atlas-SNP	.											.	OR52J3	77	.	0			c.G382A						PASS	.	A	ILE/VAL	2444,1958	553.0+/-378.7	688,1068,445	176.0	117.0	137.0		382	4.2	0.9	11	dbSNP_100	137	4303,4293	576.3+/-390.4	1068,2167,1063	yes	missense	OR52J3	NM_001001916.2	29	1756,3235,1508	AA,AG,GG		49.9418,44.4798,48.092	benign	128/312	5068137	6747,6251	2201	4298	6499	SO:0001583	missense	119679	exon1			GTGGCCGTCTGTG	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.382G>A	11.37:g.5068137G>A	ENSP00000369728:p.Val128Ile	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	269	130	0.483271	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	995	0.4555860805860806	290	0.5894308943089431	170	0.4696132596685083	149	0.26048951048951047	386	0.5092348284960422	A	0.017	-1.494256	0.01009	0.555202	0.500582	ENSG00000205495	ENST00000380370	T	0.26518	1.73	4.19	4.19	0.49359	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	N	0.000211	T	0.00012	0.0000	N	0.00038	-2.52	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.46373	-0.9196	9	0.02654	T	1	.	8.6796	0.34201	0.9077:0.0:0.0923:0.0	rs2500017;rs17350722;rs52791516;rs60675916;rs2500017	128	Q8NH60	O52J3_HUMAN	I	128	ENSP00000369728:V128I	ENSP00000369728:V128I	V	+	1	0	OR52J3	5024713	0.985000	0.35326	0.891000	0.34965	0.100000	0.18952	2.872000	0.48467	0.651000	0.30788	-0.254000	0.11334	GTC	G|0.493;A|0.507	0.507	strong		0.483	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
SV2B	9899	hgsc.bcm.edu	37	15	91803567	91803567	+	Silent	SNP	A	A	G	rs16945475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91803567A>G	ENST00000394232.1	+	6	1406	c.936A>G	c.(934-936)gaA>gaG	p.E312E	SV2B_ENST00000330276.4_Silent_p.E312E|SV2B_ENST00000545111.2_Silent_p.E161E	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	312					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			AACATGATGAAGCCTGGATGA	0.463													A|||	450	0.0898562	0.295	0.0375	5008	,	,		19770	0.0		0.0308	False		,,,				2504	0.0031				p.E312E		Atlas-SNP	.											.	SV2B	98	.	0			c.A936G						PASS	.	A	,	1173,3223	412.2+/-336.0	169,835,1194	154.0	156.0	155.0		483,936	1.0	1.0	15	dbSNP_123	155	314,8282	111.6+/-171.8	6,302,3990	no	coding-synonymous,coding-synonymous	SV2B	NM_001167580.1,NM_014848.4	,	175,1137,5184	GG,GA,AA		3.6529,26.6833,11.4455	,	161/533,312/684	91803567	1487,11505	2198	4298	6496	SO:0001819	synonymous_variant	9899	exon7			TGATGAAGCCTGG	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.936A>G	15.37:g.91803567A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	37	CCDS10370.1																																																																																			A|0.900;G|0.100	0.100	strong		0.463	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
OR51Q1	390061	hgsc.bcm.edu	37	11	5443893	5443893	+	Missense_Mutation	SNP	G	G	A	rs10838094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5443893G>A	ENST00000300778.4	+	1	553	c.463G>A	c.(463-465)Gtt>Att	p.V155I	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	155			V -> I (in dbSNP:rs10838094).	CCV -> RCI (in Ref. 3; BAC05778). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGCTGCTGTGTTCTGGCGGT	0.522													G|||	2272	0.453674	0.2799	0.3991	5008	,	,		20719	0.7024		0.3986	False		,,,				2504	0.5276				p.V155I		Atlas-SNP	.											.	OR51Q1	79	.	0			c.G463A						PASS	.	G	ILE/VAL	1319,3083	444.3+/-347.3	202,915,1084	256.0	221.0	233.0		463	2.0	0.9	11	dbSNP_120	233	3371,5223	499.2+/-374.9	675,2021,1601	yes	missense	OR51Q1	NM_001004757.2	29	877,2936,2685	AA,AG,GG		39.225,29.9637,36.088	benign	155/318	5443893	4690,8306	2201	4297	6498	SO:0001583	missense	390061	exon1			TGCTGTGTTCTGG	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.463G>A	11.37:g.5443893G>A	ENSP00000300778:p.Val155Ile	Somatic	297	2	0.00673401		WXS	Illumina HiSeq	Phase_I	236	233	0.987288	NM_001004757	B2RNN1	Missense_Mutation	SNP	ENST00000300778.4	37	CCDS31381.1	966	0.4423076923076923	139	0.28252032520325204	148	0.4088397790055249	395	0.6905594405594405	284	0.37467018469656993	G	1.521	-0.547012	0.04024	0.299637	0.39225	ENSG00000167360	ENST00000300778	T	0.36699	1.24	5.0	1.97	0.26223	GPCR, rhodopsin-like superfamily (1);	0.540328	0.16655	N	0.205041	T	0.00012	0.0000	N	0.13098	0.295	0.80722	P	0.0	B	0.19817	0.039	B	0.22386	0.039	T	0.32929	-0.9888	9	0.22109	T	0.4	.	6.2064	0.20606	0.1572:0.0:0.6211:0.2218	rs10838094;rs58915254;rs10838094	155	Q8NH59	O51Q1_HUMAN	I	155	ENSP00000300778:V155I	ENSP00000300778:V155I	V	+	1	0	OR51Q1	5400469	0.000000	0.05858	0.938000	0.37757	0.060000	0.15804	-1.229000	0.02945	0.734000	0.32515	-0.579000	0.04138	GTT	G|0.611;A|0.389	0.389	strong		0.522	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
DNHD1	144132	hgsc.bcm.edu	37	11	6569896	6569896	+	Missense_Mutation	SNP	G	G	A	rs11606889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6569896G>A	ENST00000527990.2	+	22	7120	c.7120G>A	c.(7120-7122)Gtg>Atg	p.V2374M	DNHD1_ENST00000254579.6_Missense_Mutation_p.V2374M			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2374					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)		CTTGTATGTGGTGGACCTGCT	0.522													G|||	636	0.126997	0.0832	0.1729	5008	,	,		19672	0.0228		0.1829	False		,,,				2504	0.2035				p.V2374M		Atlas-SNP	.											.	DNHD1	198	.	0			c.G7120A						PASS	.	G	MET/VAL	136,1248		8,120,564	59.0	52.0	54.0		7120	4.9	1.0	11	dbSNP_120	54	619,2563		51,517,1023	yes	missense	DNHD1	NM_144666.2	21	59,637,1587	AA,AG,GG		19.4532,9.8266,16.5353	probably-damaging	2374/4754	6569896	755,3811	692	1591	2283	SO:0001583	missense	144132	exon24			TATGTGGTGGACC	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.7120G>A	11.37:g.6569896G>A	ENSP00000436180:p.Val2374Met	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	253	0.11584249084249085	47	0.09552845528455285	50	0.13812154696132597	18	0.03146853146853147	138	0.1820580474934037	G	15.97	2.988476	0.53934	0.098266	0.194532	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.29397	1.57;1.57	5.96	4.95	0.65309	.	.	.	.	.	T	0.00039	0.0001	N	0.14661	0.345	0.39708	P	0.028714000000000017	D	0.63046	0.992	P	0.58077	0.832	T	0.06006	-1.0851	8	0.22706	T	0.39	.	9.6269	0.39757	0.1245:0.0:0.8755:0.0	rs11606889;rs58131910;rs11606889	2374	Q96M86	DNHD1_HUMAN	M	2374	ENSP00000254579:V2374M;ENSP00000436180:V2374M	ENSP00000254579:V2374M	V	+	1	0	DNHD1	6526472	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.820000	0.39032	2.813000	0.96785	0.655000	0.94253	GTG	G|0.887;A|0.113	0.113	strong		0.522	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
NLRX1	79671	hgsc.bcm.edu	37	11	119043656	119043656	+	Missense_Mutation	SNP	C	C	T	rs643423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119043656C>T	ENST00000409109.1	+	4	774	c.187C>T	c.(187-189)Ccc>Tcc	p.P63S	NLRX1_ENST00000292199.2_Missense_Mutation_p.P63S|NLRX1_ENST00000474751.2_3'UTR|NLRX1_ENST00000409991.1_Missense_Mutation_p.P63S|NLRX1_ENST00000409265.4_Missense_Mutation_p.P63S|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	78	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	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	
TAS2R41	259287	hgsc.bcm.edu	37	7	143175154	143175154	+	Silent	SNP	G	G	A	rs1404635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143175154G>A	ENST00000408916.1	+	1	189	c.189G>A	c.(187-189)acG>acA	p.T63T	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	63					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					TGGTTGGGACGGTGCACAACT	0.572													G|||	1057	0.211062	0.0219	0.2695	5008	,	,		15922	0.2956		0.2535	False		,,,				2504	0.2945				p.T63T		Atlas-SNP	.											.	TAS2R41	43	.	0			c.G189A						PASS	.	G		234,3884		10,214,1835	125.0	125.0	125.0		189	4.9	0.1	7	dbSNP_88	125	2283,6107		311,1661,2223	no	coding-synonymous	TAS2R41	NM_176883.2		321,1875,4058	AA,AG,GG		27.211,5.6824,20.1231		63/308	143175154	2517,9991	2059	4195	6254	SO:0001819	synonymous_variant	259287	exon1			TGGGACGGTGCAC	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.189G>A	7.37:g.143175154G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	196	81	0.413265	NM_176883	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Silent	SNP	ENST00000408916.1	37	CCDS43663.1																																																																																			G|0.772;A|0.228	0.228	strong		0.572	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1		
ABCA1	19	hgsc.bcm.edu	37	9	107591272	107591272	+	Silent	SNP	G	G	T	rs2853579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107591272G>T	ENST00000374736.3	-	15	2434	c.2040C>A	c.(2038-2040)atC>atA	p.I680I	ABCA1_ENST00000494467.1_5'UTR	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	680					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)	TAAACCAGAGGATGCTGTTGT	0.532													G|||	1698	0.339058	0.4607	0.2075	5008	,	,		21588	0.6855		0.1213	False		,,,				2504	0.135				p.I680I		Atlas-SNP	.											ABCA1,NS,adenoma,0,1	ABCA1	244	1	0			c.C2040A						PASS	.	G		1831,2575	535.3+/-374.2	404,1023,776	144.0	112.0	123.0		2040	6.0	1.0	9	dbSNP_100	123	1084,7516	226.5+/-262.2	66,952,3282	no	coding-synonymous	ABCA1	NM_005502.3		470,1975,4058	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	12.6047,41.557,22.4127		680/2262	107591272	2915,10091	2203	4300	6503	SO:0001819	synonymous_variant	19	exon15			CCAGAGGATGCTG	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.2040C>A	9.37:g.107591272G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	120	77	0.641667	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			G|0.593;T|0.233	0.233	strong		0.532	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
PCDHGA1	56114	hgsc.bcm.edu	37	5	140712210	140712210	+	Silent	SNP	G	G	T	rs62378403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140712210G>T	ENST00000517417.1	+	1	1959	c.1959G>T	c.(1957-1959)ccG>ccT	p.P653P	PCDHGA1_ENST00000378105.3_Silent_p.P653P	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	653	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCAGCCCCCGCTCTCCGCCA	0.697													g|||	1021	0.203874	0.2474	0.2032	5008	,	,		14206	0.2401		0.1372	False		,,,				2504	0.1769				p.P653P		Atlas-SNP	.											PCDHGA1_ENST00000517417,NS,carcinoma,0,2	PCDHGA1	397	2	0			c.G1959T						PASS	.	T	,	312,4048		33,246,1901	31.0	41.0	37.0		1959,1959	-0.2	1.0	5	dbSNP_129	37	439,8145		44,351,3897	no	coding-synonymous,coding-synonymous	PCDHGA1	NM_018912.2,NM_031993.1	,	77,597,5798	TT,TG,GG		5.1142,7.156,5.8019	,	653/932,653/824	140712210	751,12193	2180	4292	6472	SO:0001819	synonymous_variant	56114	exon1			GCCCCCGCTCTCC	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1959G>T	5.37:g.140712210G>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	57	0.564356	NM_018912	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	37	CCDS54922.1																																																																																			G|0.826;T|0.174	0.174	strong		0.697	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912	
CCAR2	57805	hgsc.bcm.edu	37	8	22476717	22476717	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22476717C>T	ENST00000308511.4	+	20	2825	c.2576C>T	c.(2575-2577)gCa>gTa	p.A859V	BIN3_ENST00000519335.1_5'Flank|CCAR2_ENST00000389279.3_Missense_Mutation_p.A859V|RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000520861.1_Missense_Mutation_p.A534V			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	859	Interaction with NR1D1. {ECO:0000269|PubMed:23398316}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										ACGCTGGCGGCAGAGATGCAG	0.642																																					p.A859V		Atlas-SNP	.											.	KIAA1967	72	.	0			c.C2576T						PASS	.						16.0	16.0	16.0					8																	22476717		2197	4296	6493	SO:0001583	missense	57805	exon20			TGGCGGCAGAGAT	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.2576C>T	8.37:g.22476717C>T	ENSP00000310670:p.Ala859Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.81|14.81	2.646522|2.646522	0.47258|0.47258	.|.	.|.	ENSG00000158941|ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000520861|ENST00000520738	T;T;T|.	0.00453|.	7.33;7.33;7.33|.	5.44|5.44	4.57|4.57	0.56435|0.56435	.|.	0.147376|.	0.43260|.	D|.	0.000594|.	T|.	0.30916|.	0.0780|.	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.0|.	B;B|.	0.09377|.	0.004;0.001|.	T|.	0.19160|.	-1.0314|.	10|.	0.36615|.	T|.	0.2|.	-8.609|-8.609	9.9844|9.9844	0.41832|0.41832	0.0:0.9094:0.0:0.0906|0.0:0.9094:0.0:0.0906	.|.	534;859|.	G3V119;Q8N163|.	.;K1967_HUMAN|.	V|X	859;859;534|551	ENSP00000310670:A859V;ENSP00000373930:A859V;ENSP00000429773:A534V|.	ENSP00000310670:A859V|.	A|Q	+|+	2|1	0|0	KIAA1967|KIAA1967	22532662|22532662	0.011000|0.011000	0.17503|0.17503	0.022000|0.022000	0.16811|0.16811	0.782000|0.782000	0.44232|0.44232	1.737000|1.737000	0.38197|0.38197	1.534000|1.534000	0.49203|0.49203	0.655000|0.655000	0.94253|0.94253	GCA|CAG	.	.	none		0.642	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
AKAP12	9590	hgsc.bcm.edu	37	6	151673589	151673589	+	Missense_Mutation	SNP	G	G	A	rs12201388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:151673589G>A	ENST00000253332.1	+	3	4252	c.4063G>A	c.(4063-4065)Gaa>Aaa	p.E1355K	AKAP12_ENST00000402676.2_Missense_Mutation_p.E1355K|AKAP12_ENST00000359755.5_Missense_Mutation_p.E1250K|AKAP12_ENST00000354675.6_Missense_Mutation_p.E1257K			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1355			E -> K (in dbSNP:rs12201388). {ECO:0000269|PubMed:17974005}.		G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		CCATGTGAATGAAGAGAAGCT	0.502													G|||	526	0.105032	0.149	0.0821	5008	,	,		22107	0.0099		0.0905	False		,,,				2504	0.1748				p.E1355K	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.G4063A						PASS	.	G	LYS/GLU,LYS/GLU	623,3783	268.9+/-268.7	47,529,1627	95.0	83.0	87.0		4063,3769	3.3	0.0	6	dbSNP_120	87	774,7826	180.0+/-229.1	31,712,3557	yes	missense,missense	AKAP12	NM_005100.3,NM_144497.2	56,56	78,1241,5184	AA,AG,GG		9.0,14.1398,10.7412	probably-damaging,probably-damaging	1355/1783,1257/1685	151673589	1397,11609	2203	4300	6503	SO:0001583	missense	9590	exon4			GTGAATGAAGAGA	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.4063G>A	6.37:g.151673589G>A	ENSP00000253332:p.Glu1355Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	103	40	0.38835	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	165	0.07554945054945054	61	0.12398373983739837	29	0.08011049723756906	8	0.013986013986013986	67	0.08839050131926121	G	17.70	3.454013	0.63290	0.141398	0.09	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.12039	2.72;2.72;2.76;2.76	4.21	3.33	0.38152	.	0.252728	0.20854	N	0.084466	T	0.04092	0.0114	L	0.34521	1.04	0.80722	P	0.0	B;B;B	0.33044	0.395;0.395;0.275	B;B;B	0.30105	0.111;0.111;0.051	T	0.34950	-0.9808	9	0.25106	T	0.35	.	11.7204	0.51678	0.0942:0.0:0.9058:0.0	rs12201388;rs52829259;rs56832525;rs12201388	1250;1257;1355	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	K	1355;1355;1257;1250	ENSP00000384537:E1355K;ENSP00000253332:E1355K;ENSP00000346702:E1257K;ENSP00000352794:E1250K	ENSP00000253332:E1355K	E	+	1	0	AKAP12	151715282	0.506000	0.26139	0.027000	0.17364	0.011000	0.07611	1.413000	0.34725	2.348000	0.79779	0.557000	0.71058	GAA	G|0.902;A|0.098	0.098	strong		0.502	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
ALKBH7	84266	hgsc.bcm.edu	37	19	6374229	6374229	+	Silent	SNP	C	C	A	rs116186903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6374229C>A	ENST00000245812.3	+	2	608	c.220C>A	c.(220-222)Cga>Aga	p.R74R	ALKBH7_ENST00000599849.1_Silent_p.R13R|ALKBH7_ENST00000596657.1_5'UTR	NM_032306.3	NP_115682.1	Q9BT30	ALKB7_HUMAN	alkB, alkylation repair homolog 7 (E. coli)	74					cellular response to DNA damage stimulus (GO:0006974)|fatty acid metabolic process (GO:0006631)|regulation of lipid storage (GO:0010883)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)	mitochondrial matrix (GO:0005759)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						CCACGGCTTCCGAGAGACAGA	0.657													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		15595	0.0		0.0	False		,,,				2504	0.0				p.R74R		Atlas-SNP	.											.	ALKBH7	18	.	0			c.C220A						PASS	.	C		78,4322		1,76,2123	29.0	32.0	31.0		220	3.6	1.0	19	dbSNP_132	31	0,8590		0,0,4295	no	coding-synonymous	ALKBH7	NM_032306.3		1,76,6418	AA,AC,CC		0.0,1.7727,0.6005		74/222	6374229	78,12912	2200	4295	6495	SO:0001819	synonymous_variant	84266	exon2			GGCTTCCGAGAGA	AY427650	CCDS12163.1	19p13.3	2008-02-05	2006-02-09	2006-02-09		ENSG00000125652		"""Alkylation repair homologs"""	21306	protein-coding gene	gene with protein product		613305	"""spermatogenesis associated 11"""	SPATA11		12477932	Standard	NM_032306		Approved	MGC10974	uc002meo.2	Q9BT30		ENST00000245812.3:c.220C>A	19.37:g.6374229C>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	67	43	0.641791	NM_032306	B2R4U9|Q53FF3	Silent	SNP	ENST00000245812.3	37	CCDS12163.1																																																																																			C|0.994;A|0.006	0.006	strong		0.657	ALKBH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453036.1	NM_032306	
RABEP1	9135	hgsc.bcm.edu	37	17	5284698	5284698	+	Silent	SNP	A	A	G	rs1143206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5284698A>G	ENST00000546142.2	+	17	2572	c.2385A>G	c.(2383-2385)caA>caG	p.Q795Q	NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000537505.1_Silent_p.Q752Q|RABEP1_ENST00000408982.2_Silent_p.Q762Q|RABEP1_ENST00000341923.6_Silent_p.Q762Q|RABEP1_ENST00000262477.6_Silent_p.Q795Q			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	795					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						CCGTTGAACAACTAATGTTTG	0.368													A|||	2765	0.552117	0.3964	0.4251	5008	,	,		22136	0.8254		0.4394	False		,,,				2504	0.6871				p.Q795Q		Atlas-SNP	.											.	RABEP1	59	.	0			c.A2385G						PASS	.	A	,	1519,2169		324,871,649	77.0	76.0	76.0		2286,2385	-2.4	1.0	17	dbSNP_86	76	3199,4981		620,1959,1511	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	944,2830,2160	GG,GA,AA		39.1076,41.1876,39.754	,	762/830,795/863	5284698	4718,7150	1844	4090	5934	SO:0001819	synonymous_variant	9135	exon17			TGAACAACTAATG	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2385A>G	17.37:g.5284698A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			A|0.519;G|0.481	0.481	strong		0.368	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
PLXNB3	5365	hgsc.bcm.edu	37	X	153036957	153036957	+	Silent	SNP	C	C	T	rs17091287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153036957C>T	ENST00000361971.5	+	14	2478	c.2364C>T	c.(2362-2364)tgC>tgT	p.C788C	PLXNB3_ENST00000538776.1_Silent_p.C441C|PLXNB3_ENST00000538282.1_Silent_p.C398C|PLXNB3_ENST00000538966.1_Silent_p.C811C|PLXNB3_ENST00000538543.1_Intron	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	788	PSI 3.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					TGTACGACTGCGCCATGGGCC	0.687													C|||	272	0.072053	0.1982	0.013	3775	,	,		10689	0.0		0.001	False		,,,				2504	0.0				p.C811C		Atlas-SNP	.											.	PLXNB3	208	.	0			c.C2433T						PASS	.	C	,	938,2882		100,604,134,926,426	36.0	35.0	35.0		2433,2364	-1.0	0.0	X	dbSNP_123	35	3,6716		0,1,2,2425,1865	no	coding-synonymous,coding-synonymous	PLXNB3	NM_001163257.1,NM_005393.2	,	100,605,136,3351,2291	TT,TC,T,CC,C		0.0446,24.555,8.9287	,	811/1933,788/1910	153036957	941,9598	2190	4293	6483	SO:0001819	synonymous_variant	5365	exon15			CGACTGCGCCATG	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.2364C>T	X.37:g.153036957C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	166	63	0.379518	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Silent	SNP	ENST00000361971.5	37	CCDS14729.1																																																																																			C|0.915;0|0.004	.	strong		0.687	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
MAATS1	89876	hgsc.bcm.edu	37	3	119449165	119449165	+	Missense_Mutation	SNP	C	C	G	rs9819218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119449165C>G	ENST00000273390.5	+	8	1036	c.959C>G	c.(958-960)tCt>tGt	p.S320C		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	320			S -> C (in dbSNP:rs9819218).			mitochondrion (GO:0005739)											GCCCGGTGGTCTAAACTGCAG	0.443													C|||	68	0.0135783	0.0507	0.0014	5008	,	,		19022	0.0		0.0	False		,,,				2504	0.0				p.S320C		Atlas-SNP	.											.	.	.	.	0			c.C959G						PASS	.	C	CYS/SER	201,4205	126.1+/-163.2	3,195,2005	197.0	200.0	199.0		959	0.0	0.7	3	dbSNP_119	199	4,8596	1.2+/-3.3	1,2,4297	yes	missense	C3orf15	NM_033364.3	112	4,197,6302	GG,GC,CC		0.0465,4.562,1.5762	benign	320/768	119449165	205,12801	2203	4300	6503	SO:0001583	missense	89876	exon8			GGTGGTCTAAACT	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.959C>G	3.37:g.119449165C>G	ENSP00000273390:p.Ser320Cys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	C	10.39	1.336987	0.24253	0.04562	4.65E-4	ENSG00000183833	ENST00000273390	T	0.24723	1.84	5.2	0.0316	0.14171	.	0.702681	0.14937	N	0.289762	T	0.02649	0.0080	L	0.43152	1.355	0.09310	N	1	B;B;B;B;B	0.20887	0.049;0.016;0.02;0.006;0.005	B;B;B;B;B	0.28232	0.087;0.032;0.036;0.009;0.004	T	0.21552	-1.0242	10	0.45353	T	0.12	-11.3776	1.5557	0.02584	0.26:0.3334:0.2513:0.1553	rs9819218;rs56635541;rs9819218	320;81;258;320;320	Q7Z4T9;Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	AAT1_HUMAN;.;.;.;.	C	320	ENSP00000273390:S320C	ENSP00000273390:S320C	S	+	2	0	C3orf15	120931855	0.002000	0.14202	0.668000	0.29813	0.882000	0.50991	0.021000	0.13489	0.001000	0.14605	-0.259000	0.10710	TCT	C|0.982;G|0.018	0.018	strong		0.443	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
PRR21	643905	hgsc.bcm.edu	37	2	240982312	240982312	+	Missense_Mutation	SNP	G	G	A	rs115609219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240982312G>A	ENST00000408934.1	-	1	87	c.88C>T	c.(88-90)Cac>Tac	p.H30Y		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	30										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						GATGAGCCGTGGGGGAAGAGC	0.577													N|||	311	0.0621006	0.0431	0.1311	5008	,	,		21476	0.005		0.0258	False		,,,				2504	0.135				p.H30Y		Atlas-SNP	.											PRR21,NS,carcinoma,0,2	PRR21	53	2	0			c.C88T						scavenged	.		TYR/HIS	166,4232		5,156,2038	101.0	89.0	93.0		88	-1.3	0.0	2	dbSNP_132	93	355,8245		4,347,3949	yes	missense	PRR21	NM_001080835.1	83	9,503,5987	AA,AG,GG		4.1279,3.7744,4.0083	possibly-damaging	30/390	240982312	521,12477	2199	4300	6499	SO:0001583	missense	643905	exon1			AGCCGTGGGGGAA	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.88C>T	2.37:g.240982312G>A	ENSP00000386166:p.His30Tyr	Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	123	47	0.382114	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	77	0.035256410256410256	23	0.046747967479674794	32	0.08839779005524862	1	0.0017482517482517483	21	0.027704485488126648	N	0.004	-2.279643	0.00254	0.037744	0.041279	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.26518	1.73;1.73	0.656	-1.31	0.09230	.	.	.	.	.	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	P	0.46020	0.871	B	0.28385	0.089	T	0.23511	-1.0186	9	0.87932	D	0	.	1.8377	0.03143	0.2596:0.0:0.3871:0.3533	.	30	Q8WXC7	PRR21_HUMAN	Y	30	ENSP00000386166:H30Y;ENSP00000418240:H30Y	ENSP00000386166:H30Y	H	-	1	0	PRR21	240630985	0.970000	0.33590	0.000000	0.03702	0.000000	0.00434	2.083000	0.41615	-0.502000	0.06596	-0.599000	0.04106	CAC	G|0.965;A|0.035	0.035	strong		0.577	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
TAL1	6886	hgsc.bcm.edu	37	1	47685569	47685569	+	Silent	SNP	G	G	A	rs144117146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47685569G>A	ENST00000294339.3	-	4	1395	c.819C>T	c.(817-819)ggC>ggT	p.G273G	TAL1_ENST00000371883.3_Silent_p.G275G|TAL1_ENST00000459729.1_5'UTR|TAL1_ENST00000371884.2_Silent_p.G273G	NM_003189.2	NP_003180.1	P17542	TAL1_HUMAN	T-cell acute lymphocytic leukemia 1	273	Poly-Gly.				angiogenesis (GO:0001525)|astrocyte fate commitment (GO:0060018)|basophil differentiation (GO:0030221)|cell fate commitment (GO:0045165)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|hemangioblast cell differentiation (GO:0060217)|hematopoietic stem cell differentiation (GO:0060218)|hemopoiesis (GO:0030097)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|platelet formation (GO:0030220)|positive regulation of cell division (GO:0051781)|positive regulation of chromatin assembly or disassembly (GO:0045799)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell proliferation (GO:0042127)|regulation of mast cell differentiation (GO:0060375)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord association neuron differentiation (GO:0021527)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|E-box binding (GO:0070888)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			haematopoietic_and_lymphoid_tissue(1)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	15						GGGGCGCGccgccccctcccc	0.697			T	"""TRD@, SIL"""	lymphoblastic leukemia/biphasic								G|||	255	0.0509185	0.0908	0.0346	5008	,	,		5200	0.004		0.0378	False		,,,				2504	0.0706				p.G273G		Atlas-SNP	.		Dom	yes		1	1p32	6886	T-cell acute lymphocytic leukemia 1 (SCL)		L	.	TAL1	31	.	0			c.C819T						PASS	.	G		300,3940		11,278,1831	8.0	10.0	10.0		819	-1.9	0.1	1	dbSNP_134	10	310,8078		6,298,3890	no	coding-synonymous	TAL1	NM_003189.2		17,576,5721	AA,AG,GG		3.6958,7.0755,4.8305		273/332	47685569	610,12018	2120	4194	6314	SO:0001819	synonymous_variant	6886	exon4			CGCGCCGCCCCCT	M29038	CCDS547.1	1p32	2013-05-21	2001-12-04		ENSG00000162367	ENSG00000162367		"""Basic helix-loop-helix proteins"""	11556	protein-coding gene	gene with protein product		187040		TCL5		2740341	Standard	NM_001287347		Approved	SCL, bHLHa17	uc009vyq.2	P17542	OTTHUMG00000007847	ENST00000294339.3:c.819C>T	1.37:g.47685569G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	109	61	0.559633	NM_003189	D3DQ24	Silent	SNP	ENST00000294339.3	37	CCDS547.1																																																																																			G|0.959;A|0.041	0.041	strong		0.697	TAL1-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021640.1	NM_003189	
NBPF7	343505	hgsc.bcm.edu	37	1	120378657	120378657	+	IGR	SNP	G	G	A	rs6684816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120378657G>A								REG4 (24374 upstream) : ADAM30 (57498 downstream)																							CTTTGGAATTGGAGTGTTCGC	0.443													g|||	111	0.0221645	0.0756	0.0086	5008	,	,		21408	0.0		0.004	False		,,,				2504	0.001				p.S363S		Atlas-SNP	.											.	NBPF7	46	.	0			c.C1089T						PASS	.	G		224,3620		5,214,1703	107.0	105.0	105.0		1089	-1.0	0.0	1	dbSNP_116	105	45,8253		1,43,4105	no	coding-synonymous	NBPF7	NM_001047980.1		6,257,5808	AA,AG,GG		0.5423,5.8273,2.2155		363/422	120378657	269,11873	1922	4149	6071	SO:0001628	intergenic_variant	343505	exon7			GGAATTGGAGTGT																													1.37:g.120378657G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	202	96	0.475248	NM_001047980		Silent	SNP		37																																																																																				A|0.016;G|0.984	0.016	strong	0	0.443								
FUT3	2525	hgsc.bcm.edu	37	19	5843784	5843784	+	Missense_Mutation	SNP	A	A	T	rs3894326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5843784A>T	ENST00000303225.6	-	3	1701	c.1067T>A	c.(1066-1068)aTa>aAa	p.I356K	FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000589620.1_Missense_Mutation_p.I356K|FUT3_ENST00000589918.1_Missense_Mutation_p.I356K|FUT3_ENST00000458379.2_Missense_Mutation_p.I356K	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	356			I -> K (in Le(-); less than 10% reduction in activity; dbSNP:rs3894326). {ECO:0000269|PubMed:7961897, ECO:0000269|PubMed:8063716, ECO:0000269|PubMed:8801770}.		cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						CCAAGCCGCTATGCTGCGCAC	0.642													A|||	482	0.096246	0.0408	0.0504	5008	,	,		17784	0.1478		0.0726	False		,,,				2504	0.1748				p.I356K	Esophageal Squamous(82;745 1728 24593 44831)	Atlas-SNP	.											.	FUT3	30	.	0			c.T1067A	GRCh37	CM940793	FUT3	M	rs3894326	PASS	.	A	LYS/ILE,LYS/ILE,LYS/ILE,LYS/ILE	148,4258	102.1+/-140.7	2,144,2057	58.0	62.0	61.0		1067,1067,1067,1067	2.2	0.2	19	dbSNP_108	61	622,7978	159.1+/-212.4	22,578,3700	no	missense,missense,missense,missense	FUT3	NM_000149.3,NM_001097639.1,NM_001097640.1,NM_001097641.1	102,102,102,102	24,722,5757	TT,TA,AA		7.2326,3.3591,5.9203	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	356/362,356/362,356/362,356/362	5843784	770,12236	2203	4300	6503	SO:0001583	missense	2525	exon3			GCCGCTATGCTGC		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"""CD molecules"", ""Blood group antigens"", ""Fucosyltransferases"""	4014	protein-coding gene	gene with protein product		111100	"""fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"""	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.1067T>A	19.37:g.5843784A>T	ENSP00000305603:p.Ile356Lys	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	196	91	0.464286	NM_001097640	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	CCDS12153.1	138	0.06318681318681318	23	0.046747967479674794	13	0.03591160220994475	43	0.07517482517482517	59	0.07783641160949868	A	18.27	3.586525	0.66105	0.033591	0.072326	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.26373	1.74;1.74	2.2	2.2	0.27929	.	1.042650	0.07702	U	0.940582	T	0.05960	0.0155	M	0.91818	3.245	0.42393	D	0.992534	D;P;P;P	0.57899	0.981;0.953;0.953;0.953	D;P;P;P	0.65773	0.938;0.864;0.864;0.864	T	0.17592	-1.0364	10	0.72032	D	0.01	.	8.2938	0.31973	1.0:0.0:0.0:0.0	rs3894326	356;356;356;356	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	K	356	ENSP00000305603:I356K;ENSP00000416443:I356K	ENSP00000305603:I356K	I	-	2	0	FUT3	5794784	0.004000	0.15560	0.214000	0.23707	0.450000	0.32258	1.993000	0.40747	0.959000	0.37980	0.163000	0.16589	ATA	A|0.935;T|0.065	0.065	strong		0.642	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149	
ESPNL	339768	hgsc.bcm.edu	37	2	239039183	239039183	+	Missense_Mutation	SNP	G	G	A	rs73102303	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239039183G>A	ENST00000343063.3	+	9	2091	c.1828G>A	c.(1828-1830)Gtg>Atg	p.V610M	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409169.1_Missense_Mutation_p.V566M|ESPNL_ENST00000409506.1_Missense_Mutation_p.V242M	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	610				V -> M (in Ref. 1; BAC85884 and 3; AAH42051). {ECO:0000305}.						endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GCTGAAGGGCGTGCATGGGCT	0.711													G|||	658	0.13139	0.2413	0.085	5008	,	,		16293	0.0526		0.1113	False		,,,				2504	0.1176				p.V610M		Atlas-SNP	.											ESPNL,NS,carcinoma,0,1	ESPNL	63	1	0			c.G1828A						PASS	.	G	MET/VAL	862,3504		81,700,1402	10.0	11.0	11.0		1828	-2.3	0.3	2	dbSNP_130	11	920,7564		49,822,3371	yes	missense	ESPNL	NM_194312.2	21	130,1522,4773	AA,AG,GG		10.8439,19.7435,13.8677	benign	610/1006	239039183	1782,11068	2183	4242	6425	SO:0001583	missense	339768	exon9			AAGGGCGTGCATG	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.1828G>A	2.37:g.239039183G>A	ENSP00000339115:p.Val610Met	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	249	0.11401098901098901	97	0.19715447154471544	35	0.09668508287292818	41	0.07167832167832168	76	0.10026385224274406	G	0.031	-1.332649	0.01298	0.197435	0.108439	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.63580	-0.05;1.04;0.61	3.78	-2.26	0.06867	.	0.423150	0.21191	N	0.078648	T	0.00039	0.0001	N	0.05124	-0.11	0.80722	P	0.0	B;B	0.33494	0.414;0.291	B;B	0.20384	0.029;0.013	T	0.19031	-1.0318	9	0.19147	T	0.46	-12.2189	9.0509	0.36376	0.6378:0.0:0.3622:0.0	.	566;610	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	M	610;566;242	ENSP00000339115:V610M;ENSP00000386577:V566M;ENSP00000386579:V242M	ENSP00000339115:V610M	V	+	1	0	ESPNL	238703922	0.016000	0.18221	0.297000	0.24988	0.220000	0.24768	-0.513000	0.06305	-0.396000	0.07703	0.205000	0.17691	GTG	G|0.871;A|0.129	0.129	strong		0.711	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230300	23230300	+	Missense_Mutation	SNP	C	C	T	rs382768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:23230300C>T	ENST00000526893.1	+	1	341	c.67C>T	c.(67-69)Cgc>Tgc	p.R23C	IGLL5_ENST00000531372.1_Missense_Mutation_p.R23C|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.R23C	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	23						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TCCCAGGCAGCGCTGGCCCCT	0.672													C|||	379	0.0756789	0.2027	0.0476	5008	,	,		12770	0.0		0.0348	False		,,,				2504	0.044				p.R23C		Atlas-SNP	.											.	IGLL5	26	.	0			c.C67T						PASS	.																																			SO:0001583	missense	100423062	exon1			AGGCAGCGCTGGC	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.67C>T	22.37:g.23230300C>T	ENSP00000431254:p.Arg23Cys	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	172	80	0.465116	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	115	0.052655677655677656	76	0.15447154471544716	14	0.03867403314917127	0	0.0	25	0.032981530343007916	C	7.897	0.733599	0.15574	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00569	6.52;6.52	3.25	-6.5	0.01884	.	.	.	.	.	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	0.44452	-0.9327	8	0.62326	D	0.03	.	3.5729	0.07923	0.1077:0.2861:0.1068:0.4995	rs382768	23	B9A064	IGLL5_HUMAN	C	23	ENSP00000436353:R23C;ENSP00000431254:R23C	ENSP00000431254:R23C	R	+	1	0	IGLL5	21560300	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.259000	0.00536	-2.722000	0.00388	-1.790000	0.00627	CGC	C|0.947;T|0.053	0.053	strong		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
POLR3H	171568	hgsc.bcm.edu	37	22	41926757	41926757	+	Silent	SNP	G	G	A	rs35463585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:41926757G>A	ENST00000355209.4	-	5	838	c.495C>T	c.(493-495)ccC>ccT	p.P165P	POLR3H_ENST00000407461.1_Silent_p.P165P|POLR3H_ENST00000337566.5_Silent_p.P136P|POLR3H_ENST00000396504.2_Silent_p.P165P|POLR3H_ENST00000420561.1_5'Flank	NM_001018050.2	NP_001018060.1	Q9Y535	RPC8_HUMAN	polymerase (RNA) III (DNA directed) polypeptide H (22.9kD)	165					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|nucleobase-containing compound metabolic process (GO:0006139)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|lung(5)|skin(1)|urinary_tract(1)	8						CTGCTGAGCTGGGCCCTGTGG	0.607													G|||	130	0.0259585	0.0862	0.0086	5008	,	,		18194	0.0		0.002	False		,,,				2504	0.0082				p.P165P		Atlas-SNP	.											.	POLR3H	30	.	0			c.C495T						PASS	.	G	,,	276,4130	152.5+/-186.2	8,260,1935	98.0	82.0	88.0		495,408,495	4.7	1.0	22	dbSNP_126	88	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	POLR3H	NM_001018050.2,NM_001018052.2,NM_138338.3	,,	8,267,6228	AA,AG,GG		0.0814,6.2642,2.1759	,,	165/205,136/176,165/205	41926757	283,12723	2203	4300	6503	SO:0001819	synonymous_variant	171568	exon5			TGAGCTGGGCCCT	AB051452	CCDS14018.1, CCDS33651.1	22q13	2013-01-21			ENSG00000100413	ENSG00000100413		"""RNA polymerase subunits"""	30349	protein-coding gene	gene with protein product						11258795, 12391170	Standard	XR_244356		Approved	RPC8, KIAA1665	uc003baf.3	Q9Y535	OTTHUMG00000150971	ENST00000355209.4:c.495C>T	22.37:g.41926757G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	161	82	0.509317	NM_001018050	B0QYH9|Q5M7Y8|Q96AE3|Q9BY95	Silent	SNP	ENST00000355209.4	37	CCDS14018.1																																																																																			G|0.976;A|0.024	0.024	strong		0.607	POLR3H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320701.1	NM_138338	
LETM1	3954	hgsc.bcm.edu	37	4	1843324	1843324	+	Missense_Mutation	SNP	C	C	T	rs116753949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1843324C>T	ENST00000302787.2	-	3	640	c.344G>A	c.(343-345)cGc>cAc	p.R115H		NM_012318.2	NP_036450.1	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane protein 1	115					cristae formation (GO:0042407)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(2)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	13			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)			CGAGTCATCGCGAACAGGGCG	0.597													C|||	102	0.0203674	0.0045	0.0375	5008	,	,		18502	0.001		0.0557	False		,,,				2504	0.0133				p.R115H		Atlas-SNP	.											.	LETM1	48	.	0			c.G344A						PASS	.	C	HIS/ARG	55,4351	53.6+/-89.4	0,55,2148	83.0	85.0	84.0		344	2.0	0.0	4	dbSNP_132	84	570,8030	154.0+/-208.3	18,534,3748	yes	missense	LETM1	NM_012318.2	29	18,589,5896	TT,TC,CC		6.6279,1.2483,4.8055	possibly-damaging	115/740	1843324	625,12381	2203	4300	6503	SO:0001583	missense	3954	exon3			TCATCGCGAACAG	AF061025	CCDS3355.1	4p16.3	2013-01-10			ENSG00000168924	ENSG00000168924		"""EF-hand domain containing"""	6556	protein-coding gene	gene with protein product	"""Mdm38 homolog (yeast)"""	604407				10486213	Standard	NM_012318		Approved		uc003gdv.3	O95202	OTTHUMG00000121149	ENST00000302787.2:c.344G>A	4.37:g.1843324C>T	ENSP00000305653:p.Arg115His	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_012318	B4DED2|Q9UF65	Missense_Mutation	SNP	ENST00000302787.2	37	CCDS3355.1	54	0.024725274725274724	4	0.008130081300813009	13	0.03591160220994475	1	0.0017482517482517483	36	0.047493403693931395	C	10.19	1.280899	0.23392	0.012483	0.066279	ENSG00000168924	ENST00000302787;ENST00000417150	.	.	.	4.75	2.04	0.26737	.	1.715750	0.02455	N	0.085976	T	0.02267	0.0070	L	0.29908	0.895	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.06405	0.002;0.0	T	0.06643	-1.0815	9	0.13108	T	0.6	-0.6397	3.6478	0.08191	0.171:0.4396:0.0:0.3893	.	115;115	O95202-3;O95202	.;LETM1_HUMAN	H	115;75	.	ENSP00000305653:R115H	R	-	2	0	LETM1	1813122	0.000000	0.05858	0.004000	0.12327	0.084000	0.17831	0.233000	0.17911	0.632000	0.30432	0.563000	0.77884	CGC	C|0.957;T|0.043	0.043	strong		0.597	LETM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241634.1		
OR5H15	403274	hgsc.bcm.edu	37	3	97887902	97887902	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:97887902A>G	ENST00000356526.2	+	1	359	c.359A>G	c.(358-360)tAt>tGt	p.Y120C		NM_001005515.1	NP_001005515.1	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H, member 15	120						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y120F(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(2)|stomach(1)	35						ACAATGGCATATGATCGCTAT	0.378																																					p.Y120C		Atlas-SNP	.											OR5H15,NS,carcinoma,0,1	OR5H15	70	1	1	Substitution - Missense(1)	lung(1)	c.A359G						scavenged	.						85.0	86.0	85.0					3																	97887902		2203	4298	6501	SO:0001583	missense	403274	exon1			TGGCATATGATCG		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.359A>G	3.37:g.97887902A>G	ENSP00000373195:p.Tyr120Cys	Somatic	467	4	0.00856531		WXS	Illumina HiSeq	Phase_I	481	16	0.033264	NM_001005515		Missense_Mutation	SNP	ENST00000356526.2	37	CCDS33799.1	.	.	.	.	.	.	.	.	.	.	-	4.696	0.129471	0.08981	.	.	ENSG00000233412	ENST00000356526;ENST00000454529	T	0.01347	4.99	2.48	2.48	0.30137	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42821	D	0.000649	T	0.03348	0.0097	M	0.92122	3.275	0.23727	N	0.997002	P	0.36577	0.558	B	0.30782	0.12	T	0.22068	-1.0227	10	0.87932	D	0	.	8.4982	0.33141	1.0:0.0:0.0:0.0	.	120	A6NDH6	O5H15_HUMAN	C	120	ENSP00000373195:Y120C	ENSP00000373195:Y120C	Y	+	2	0	OR5H15	99370592	1.000000	0.71417	0.988000	0.46212	0.119000	0.20118	2.521000	0.45563	1.138000	0.42230	0.155000	0.16302	TAT	.	.	none		0.378	OR5H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359109.1		
C12orf5	57103	hgsc.bcm.edu	37	12	4459032	4459032	+	Silent	SNP	G	G	A	rs7309402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	149	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	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	
OR1E2	8388	hgsc.bcm.edu	37	17	3336697	3336697	+	Missense_Mutation	SNP	G	G	A	rs77501388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3336697G>A	ENST00000248384.1	-	1	438	c.439C>T	c.(439-441)Ccc>Tcc	p.P147S		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	147					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						CAGAGCATGGGGCTCATGATG	0.567													G|||	120	0.0239617	0.0885	0.0043	5008	,	,		19503	0.0		0.0	False		,,,				2504	0.0				p.P147S		Atlas-SNP	.											OR1E2,right_upper_lobe,carcinoma,+1,1	OR1E2	25	1	0			c.C439T						PASS	.																																			SO:0001583	missense	8388	exon1			GCATGGGGCTCAT	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"""GPCR / Class A : Olfactory receptors"""	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.439C>T	17.37:g.3336697G>A	ENSP00000248384:p.Pro147Ser	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	230	98	0.426087	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	37	CCDS11026.1	45	0.020604395604395604	45	0.09146341463414634	0	0.0	0	0.0	0	0.0	G	9.675	1.147752	0.21288	.	.	ENSG00000127780	ENST00000248384;ENST00000454364	T	0.05649	3.41	5.47	4.51	0.55191	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000009	T	0.00144	0.0004	N	0.08118	0	0.09310	N	0.999998	B	0.31077	0.307	B	0.27608	0.081	T	0.45862	-0.9232	10	0.62326	D	0.03	.	6.8412	0.23963	0.0829:0.0:0.6588:0.2582	.	147	P47887	OR1E2_HUMAN	S	147;137	ENSP00000248384:P147S	ENSP00000248384:P147S	P	-	1	0	OR1E2	3283447	0.000000	0.05858	0.943000	0.38184	0.313000	0.28021	-0.200000	0.09478	1.550000	0.49438	0.650000	0.86243	CCC	G|0.987;A|0.013	0.013	strong		0.567	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1		
SALL1	6299	hgsc.bcm.edu	37	16	51173823	51173823	+	Silent	SNP	G	G	A	rs61740811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:51173823G>A	ENST00000251020.4	-	2	2343	c.2310C>T	c.(2308-2310)atC>atT	p.I770I	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.I673I|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	770					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TCTTCTGGCAGATGGGGCAGG	0.567													G|||	201	0.0401358	0.1392	0.0231	5008	,	,		19398	0.0		0.001	False		,,,				2504	0.0				p.I770I	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C2310T						PASS	.	G	,	539,3857	246.8+/-255.3	25,489,1684	86.0	90.0	89.0		2019,2310	4.2	1.0	16	dbSNP_129	89	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	SALL1	NM_001127892.1,NM_002968.2	,	25,493,5980	AA,AG,GG		0.0465,12.2611,4.1782	,	673/1228,770/1325	51173823	543,12453	2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			CTGGCAGATGGGG	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.2310C>T	16.37:g.51173823G>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	228	114	0.5	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																			G|0.957;A|0.043	0.043	strong		0.567	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
LIPF	8513	hgsc.bcm.edu	37	10	90433345	90433345	+	Splice_Site	SNP	T	T	A	rs6586145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90433345T>A	ENST00000238983.4	+	7	716	c.670T>A	c.(670-672)Ttt>Att	p.F224I	LIPF_ENST00000355843.2_Splice_Site_p.F201I|LIPF_ENST00000394375.3_Splice_Site_p.F234I|LIPF_ENST00000608620.1_Splice_Site_p.F191I	NM_004190.3	NP_004181.1	P07098	LIPG_HUMAN	lipase, gastric	224			F -> I (in dbSNP:rs6586145). {ECO:0000269|Ref.4}.		lipid catabolic process (GO:0016042)|malate metabolic process (GO:0006108)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)	lipid binding (GO:0008289)|malate dehydrogenase activity (GO:0016615)|triglyceride lipase activity (GO:0004806)			NS(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(6)	13		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)	Orlistat(DB01083)	TATTTTTCAGTTTATATTTGG	0.373													A|||	669	0.133586	0.2753	0.0793	5008	,	,		19782	0.1419		0.0626	False		,,,				2504	0.045				p.F234I		Atlas-SNP	.											.	LIPF	62	.	0			c.T700A						PASS	.	A	ILE/PHE,ILE/PHE,ILE/PHE,ILE/PHE	1077,3327	722.4+/-409.3	140,797,1265	148.0	154.0	152.0		571,700,601,670	-10.6	0.0	10	dbSNP_116	152	701,7895	787.3+/-407.6	27,647,3624	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	LIPF	NM_001198828.1,NM_001198829.1,NM_001198830.1,NM_004190.3	21,21,21,21	167,1444,4889	AA,AT,TT		8.155,24.455,13.6769	benign,benign,benign,benign	191/366,234/409,201/376,224/399	90433345	1778,11222	2202	4298	6500	SO:0001630	splice_region_variant	8513	exon8			TTTCAGTTTATAT	X05997	CCDS7389.1, CCDS55718.1, CCDS55719.1, CCDS65896.1	10q23	2005-10-30			ENSG00000182333	ENSG00000182333	3.1.1.3		6622	protein-coding gene	gene with protein product		601980				3304425, 9186906	Standard	NM_004190		Approved	HGL, HLAL	uc010qmt.2	P07098	OTTHUMG00000018695	ENST00000238983.4:c.670-1T>A	10.37:g.90433345T>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	140	74	0.528571	NM_001198829	B7Z723|F5H1P4|Q2M1P6|Q5VXI7|Q5VXI8|Q658L8	Missense_Mutation	SNP	ENST00000238983.4	37	CCDS7389.1	261	0.11950549450549451	115	0.23373983739837398	37	0.10220994475138122	63	0.11013986013986014	46	0.06068601583113457	A	12.75	2.031527	0.35797	0.24455	0.08155	ENSG00000182333	ENST00000394375;ENST00000238983;ENST00000355843	T;T;T	0.70631	-0.5;-0.5;-0.5	5.32	-10.6	0.00265	Alpha/beta hydrolase fold-1 (1);	1.890000	0.02357	N	0.076489	T	0.00012	0.0000	N	0.01874	-0.695	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	0.02450	-1.1157	8	.	.	.	-0.8645	6.7281	0.23369	0.1059:0.4165:0.3392:0.1384	rs6586145;rs17287100;rs52816421;rs6586145	191;234;201;224	Q5VXI8;F5H1P4;Q658L8;P07098	.;.;.;LIPG_HUMAN	I	234;224;191	ENSP00000377900:F234I;ENSP00000238983:F224I;ENSP00000348101:F191I	.	F	+	1	0	LIPF	90423325	0.000000	0.05858	0.000000	0.03702	0.447000	0.32167	-3.313000	0.00516	-3.715000	0.00116	-0.257000	0.10917	TTT	T|0.872;A|0.128	0.128	strong		0.373	LIPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049256.1		Missense_Mutation
HSD17B11	51170	hgsc.bcm.edu	37	4	88293887	88293887	+	Silent	SNP	G	G	A	rs6531985	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88293887G>A	ENST00000358290.4	-	4	846	c.531C>T	c.(529-531)gtC>gtT	p.V177V	HSD17B11_ENST00000507518.1_5'UTR|HSD17B11_ENST00000507286.1_Silent_p.V133V	NM_016245.3	NP_057329.2	Q8NBQ5	DHB11_HUMAN	hydroxysteroid (17-beta) dehydrogenase 11	177					androgen catabolic process (GO:0006710)|steroid biosynthetic process (GO:0006694)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|lipid particle (GO:0005811)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|steroid dehydrogenase activity (GO:0016229)			cervix(1)|endometrium(4)|kidney(2)|lung(2)|ovary(2)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000339)		AGGGGACCGAGACATGTCCAG	0.413													A|||	1429	0.285343	0.5764	0.2882	5008	,	,		14982	0.005		0.327	False		,,,				2504	0.136				p.V177V		Atlas-SNP	.											.	HSD17B11	28	.	0			c.C531T						PASS	.	A		2371,2035	564.7+/-381.5	634,1103,466	159.0	130.0	140.0		531	-8.2	0.0	4	dbSNP_116	140	2700,5900	682.1+/-403.8	406,1888,2006	no	coding-synonymous	HSD17B11	NM_016245.3		1040,2991,2472	AA,AG,GG		31.3953,46.187,38.9897		177/301	88293887	5071,7935	2203	4300	6503	SO:0001819	synonymous_variant	51170	exon4			GACCGAGACATGT	AF126780	CCDS3619.1	4q22.1	2011-09-20	2006-11-22	2006-11-22	ENSG00000198189	ENSG00000198189	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	22960	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 2"", ""short chain dehydrogenase/reductase family 16C, member 2"""	612831	"""dehydrogenase/reductase (SDR family) member 8"""	DHRS8		11165019, 12697717, 19027726	Standard	XM_006714232		Approved	RetSDR2, 17-BETA-HSD11, 17-BETA-HSDXI, PAN1B, SDR16C2	uc003hqp.2	Q8NBQ5	OTTHUMG00000130594	ENST00000358290.4:c.531C>T	4.37:g.88293887G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_016245	Q96HF6|Q9UKU4	Silent	SNP	ENST00000358290.4	37	CCDS3619.1																																																																																			G|0.645;A|0.355	0.355	strong		0.413	HSD17B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253041.1	NM_016245	
HCN4	10021	hgsc.bcm.edu	37	15	73617723	73617723	+	Silent	SNP	G	G	T	rs141966309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:73617723G>T	ENST00000261917.3	-	5	2646	c.1653C>A	c.(1651-1653)atC>atA	p.I551I		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	551					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)		AGTAGTCGTGGATGCGCTGCC	0.647													g|||	7	0.00139776	0.0053	0.0	5008	,	,		16066	0.0		0.0	False		,,,				2504	0.0				p.I551I		Atlas-SNP	.											.	HCN4	150	.	0			c.C1653A						PASS	.	G		23,4373	30.8+/-60.4	1,21,2176	107.0	111.0	110.0		1653	3.3	1.0	15	dbSNP_134	110	0,8594		0,0,4297	no	coding-synonymous	HCN4	NM_005477.2		1,21,6473	TT,TG,GG		0.0,0.5232,0.1771		551/1204	73617723	23,12967	2198	4297	6495	SO:0001819	synonymous_variant	10021	exon5			GTCGTGGATGCGC	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.1653C>A	15.37:g.73617723G>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	196	94	0.479592	NM_005477	Q9UMQ7	Silent	SNP	ENST00000261917.3	37	CCDS10248.1																																																																																			G|0.998;T|0.002	0.002	strong		0.647	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
LRRK1	79705	hgsc.bcm.edu	37	15	101591923	101591923	+	Silent	SNP	A	A	G	rs4965778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:101591923A>G	ENST00000388948.3	+	24	3806	c.3447A>G	c.(3445-3447)acA>acG	p.T1149T	RP11-505E24.3_ENST00000558979.1_RNA|RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Silent_p.T1146T	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)			TAGCCCTGACAGCCACAGAGA	0.637													G|||	2259	0.451078	0.1316	0.598	5008	,	,		19178	0.8006		0.4145	False		,,,				2504	0.456				p.T1149T		Atlas-SNP	.											.	LRRK1	310	.	0			c.A3447G						PASS	.	G		641,3507		40,561,1473	49.0	50.0	50.0		3447	-7.1	0.5	15	dbSNP_111	50	3258,5170		603,2052,1559	no	coding-synonymous	LRRK1	NM_024652.3		643,2613,3032	GG,GA,AA		38.6569,15.4532,31.0035		1149/2016	101591923	3899,8677	2074	4214	6288	SO:0001819	synonymous_variant	79705	exon24			CCTGACAGCCACA	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.3447A>G	15.37:g.101591923A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			A|0.548;G|0.452	0.452	strong		0.637	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
TRPM6	140803	hgsc.bcm.edu	37	9	77407636	77407636	+	Silent	SNP	C	C	T	rs4145894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:77407636C>T	ENST00000360774.1	-	19	2679	c.2442G>A	c.(2440-2442)caG>caA	p.Q814Q	TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000451710.3_Silent_p.Q814Q|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Silent_p.Q809Q|TRPM6_ENST00000361255.3_Silent_p.Q809Q|TRPM6_ENST00000376864.4_Silent_p.Q814Q	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	814					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						AACCAAAATGCTGATTTTCAT	0.373													C|||	1344	0.268371	0.0144	0.3919	5008	,	,		17055	0.5149		0.1769	False		,,,				2504	0.364				p.Q814Q		Atlas-SNP	.											.	TRPM6	377	.	0			c.G2442A						PASS	.	C	,,	186,4220	119.6+/-157.3	1,184,2018	149.0	124.0	133.0		2427,2427,2442	0.2	0.9	9	dbSNP_110	133	1571,7029	293.1+/-301.2	146,1279,2875	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	147,1463,4893	TT,TC,CC		18.2674,4.2215,13.5091	,,	809/2018,809/2018,814/2023	77407636	1757,11249	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon19			AAAATGCTGATTT	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.2442G>A	9.37:g.77407636C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	144	56	0.388889	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																			C|0.819;T|0.181	0.181	strong		0.373	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
ABTB2	25841	hgsc.bcm.edu	37	11	34176262	34176262	+	Missense_Mutation	SNP	T	T	C	rs2473928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34176262T>C	ENST00000435224.2	-	15	3176	c.2752A>G	c.(2752-2754)Act>Gct	p.T918A	ABTB2_ENST00000298992.2_Missense_Mutation_p.T732A	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	918			T -> A (in dbSNP:rs2473928).		cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				AGGATGTCAGTGGTGGGGATC	0.602													C|||	142	0.0283546	0.1044	0.0058	5008	,	,		20312	0.0		0.0	False		,,,				2504	0.0				p.T918A		Atlas-SNP	.											.	ABTB2	101	.	0			c.A2752G						PASS	.	C	ALA/THR	328,4076	796.1+/-415.3	14,300,1888	153.0	134.0	140.0		2752	-0.4	0.0	11	dbSNP_100	140	3,8593	819.0+/-406.8	0,3,4295	yes	missense	ABTB2	NM_145804.2	58	14,303,6183	CC,CT,TT		0.0349,7.4478,2.5462	benign	918/1026	34176262	331,12669	2202	4298	6500	SO:0001583	missense	25841	exon15			TGTCAGTGGTGGG	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.2752A>G	11.37:g.34176262T>C	ENSP00000410157:p.Thr918Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	122	69	0.565574	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Missense_Mutation	SNP	ENST00000435224.2	37	CCDS7890.2	41	0.018772893772893772	40	0.08130081300813008	1	0.0027624309392265192	0	0.0	0	0.0	C	0.013	-1.626374	0.00813	0.074478	3.49E-4	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.65732	-0.17;-0.17	4.79	-0.445	0.12242	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.385085	0.29178	N	0.012911	T	0.02012	0.0063	N	0.20807	0.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07481	-1.0770	10	0.02654	T	1	-15.8719	6.5214	0.22277	0.1139:0.4201:0.0:0.466	rs2473928;rs16925228;rs52811333;rs2473928	732	Q8N961	ABTB2_HUMAN	A	918;732	ENSP00000410157:T918A;ENSP00000298992:T732A	ENSP00000298992:T732A	T	-	1	0	ABTB2	34132838	0.000000	0.05858	0.016000	0.15963	0.433000	0.31745	-0.763000	0.04740	-0.594000	0.05836	-2.820000	0.00109	ACT	T|0.973;C|0.027	0.027	strong		0.602	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804	
IL1RL1	9173	hgsc.bcm.edu	37	2	102957136	102957136	+	Missense_Mutation	SNP	C	C	T	rs114797672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102957136C>T	ENST00000233954.1	+	5	729	c.458C>T	c.(457-459)gCt>gTt	p.A153V	IL1RL1_ENST00000311734.2_Missense_Mutation_p.A153V|IL1RL1_ENST00000393393.3_Missense_Mutation_p.A153V|IL1RL1_ENST00000404917.2_Missense_Mutation_p.A36V|IL1RL1_ENST00000409584.1_Missense_Mutation_p.A153V	NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1	153	Ig-like C2-type 2.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of macrophage activation (GO:0043032)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|interleukin-1 receptor activity (GO:0004908)|interleukin-33 receptor activity (GO:0002114)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(3)|urinary_tract(1)	16						AATTGTCAGGCTCTTCAAGGA	0.373													c|||	20	0.00399361	0.0136	0.0029	5008	,	,		17359	0.0		0.0	False		,,,				2504	0.0				p.A153V		Atlas-SNP	.											.	IL1RL1	114	.	0			c.C458T						PASS	.	C	VAL/ALA,VAL/ALA	92,4314	75.7+/-113.9	1,90,2112	125.0	121.0	122.0		458,458	1.9	0.4	2	dbSNP_132	122	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	IL1RL1	NM_003856.2,NM_016232.4	64,64	1,91,6411	TT,TC,CC		0.0116,2.0881,0.7151	benign,benign	153/329,153/557	102957136	93,12913	2203	4300	6503	SO:0001583	missense	9173	exon5			GTCAGGCTCTTCA	D12764	CCDS2057.1, CCDS2058.1, CCDS74548.1	2q12	2013-01-29			ENSG00000115602	ENSG00000115602		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5998	protein-coding gene	gene with protein product	"""homolog of mouse growth stimulation-expressed"""	601203				1482686, 10191101, 16286016	Standard	NM_016232		Approved	ST2, FIT-1, ST2L, ST2V, DER4, T1, IL33R	uc002tbu.1	Q01638	OTTHUMG00000130782	ENST00000233954.1:c.458C>T	2.37:g.102957136C>T	ENSP00000233954:p.Ala153Val	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	268	128	0.477612	NM_016232	A8K6B3|B4E0I3|Q53TU7|Q8NEJ3|Q9ULV7|Q9UQ44	Missense_Mutation	SNP	ENST00000233954.1	37	CCDS2057.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	10.58	1.390800	0.25118	0.020881	1.16E-4	ENSG00000115602	ENST00000233954;ENST00000393393;ENST00000404917;ENST00000311734;ENST00000409584	T;T;T;T;T	0.12774	2.65;2.65;2.65;2.65;2.65	5.07	1.88	0.25563	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.784816	0.11927	N	0.516068	T	0.03136	0.0092	N	0.11560	0.145	0.29045	N	0.884885	B;B;B	0.22480	0.07;0.056;0.034	B;B;B	0.27262	0.078;0.046;0.034	T	0.40117	-0.9580	10	0.28530	T	0.3	.	5.6013	0.17355	0.1466:0.6513:0.0:0.2021	.	36;153;153	B4E0I3;Q01638-2;Q01638	.;.;ILRL1_HUMAN	V	153;153;36;153;153	ENSP00000233954:A153V;ENSP00000377052:A153V;ENSP00000384822:A36V;ENSP00000310371:A153V;ENSP00000386618:A153V	ENSP00000233954:A153V	A	+	2	0	IL1RL1	102323568	0.043000	0.20138	0.398000	0.26321	0.905000	0.53344	0.083000	0.14871	0.044000	0.15775	0.563000	0.77884	GCT	C|0.992;T|0.008	0.008	strong		0.373	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253296.1	NM_016232	
STRN3	29966	hgsc.bcm.edu	37	14	31364948	31364948	+	Missense_Mutation	SNP	A	A	G	rs114922597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:31364948A>G	ENST00000357479.5	-	17	2340	c.2144T>C	c.(2143-2145)aTg>aCg	p.M715T	STRN3_ENST00000355683.5_Missense_Mutation_p.M631T	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	715					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)		AGAATGGATCATTTTACCTAA	0.333													A|||	40	0.00798722	0.0287	0.0029	5008	,	,		19925	0.0		0.0	False		,,,				2504	0.0				p.M715T		Atlas-SNP	.											.	STRN3	117	.	0			c.T2144C						PASS	.	A	THR/MET,THR/MET	117,4289	89.7+/-128.4	2,113,2088	63.0	58.0	60.0		2144,1892	4.6	1.0	14	dbSNP_132	60	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	STRN3	NM_001083893.1,NM_014574.3	81,81	2,115,6386	GG,GA,AA		0.0233,2.6555,0.915	benign,benign	715/798,631/714	31364948	119,12887	2203	4300	6503	SO:0001583	missense	29966	exon17			TGGATCATTTTAC		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.2144T>C	14.37:g.31364948A>G	ENSP00000350071:p.Met715Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	54	0.402985	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Missense_Mutation	SNP	ENST00000357479.5	37	CCDS41938.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	A	10.37	1.331773	0.24167	0.026555	2.33E-4	ENSG00000196792	ENST00000355683;ENST00000357479	T;T	0.59502	0.26;0.26	5.77	4.64	0.57946	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.332419	0.39985	N	0.001209	T	0.12518	0.0304	N	0.04090	-0.28	0.37999	D	0.934155	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.11275	-1.0594	10	0.46703	T	0.11	0.4649	7.2945	0.26385	0.7812:0.1462:0.0726:0.0	.	631;715	Q13033-2;Q13033	.;STRN3_HUMAN	T	631;715	ENSP00000347909:M631T;ENSP00000350071:M715T	ENSP00000347909:M631T	M	-	2	0	STRN3	30434699	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.949000	0.49074	2.204000	0.70986	0.383000	0.25322	ATG	A|0.990;G|0.010	0.010	strong		0.333	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
VNN1	8876	hgsc.bcm.edu	37	6	133004281	133004281	+	Nonstop_Mutation	SNP	A	A	G	rs61729583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133004281A>G	ENST00000367928.4	-	7	1553	c.1540T>C	c.(1540-1542)Tag>Cag	p.*514Q		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	0					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)		TCAATATTCTACCAACTTAAT	0.333													A|||	148	0.0295527	0.1082	0.0058	5008	,	,		16408	0.0		0.001	False		,,,				2504	0.0				p.X514Q		Atlas-SNP	.											.	VNN1	69	.	0			c.T1540C						PASS	.	A	GLN/stop	395,4011	196.7+/-221.0	18,359,1826	94.0	89.0	90.0		1540	4.7	0.9	6	dbSNP_129	90	4,8596	3.0+/-9.4	0,4,4296	yes	stop-lost	VNN1	NM_004666.2		18,363,6122	GG,GA,AA		0.0465,8.965,3.0678		514/514	133004281	399,12607	2203	4300	6503	SO:0001578	stop_lost	8876	exon7			TATTCTACCAACT	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.1540T>C	6.37:g.133004281A>G	ENSP00000356905:p.*514Gluext*13	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	A	10.88	1.475064	0.26511	0.08965	4.65E-4	ENSG00000112299	ENST00000367928	.	.	.	5.86	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.1002	0.36664	0.917:0.0:0.083:0.0	.	.	.	.	Q	514	.	.	X	-	1	0	VNN1	133045974	0.003000	0.15002	0.944000	0.38274	0.058000	0.15608	1.546000	0.36179	2.237000	0.73441	0.528000	0.53228	TAG	A|0.971;G|0.029	0.029	strong		0.333	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
SLC16A6	9120	hgsc.bcm.edu	37	17	66270082	66270082	+	Missense_Mutation	SNP	A	A	G	rs35397826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66270082A>G	ENST00000327268.4	-	4	526	c.362T>C	c.(361-363)aTc>aCc	p.I121T	ARSG_ENST00000448504.2_Intron|SLC16A6_ENST00000580666.1_Missense_Mutation_p.I121T	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	121			I -> T (in dbSNP:rs35397826).		monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	GATGATGCCGATGGCGACGTA	0.498													A|||	584	0.116613	0.087	0.111	5008	,	,		17538	0.1438		0.1113	False		,,,				2504	0.138				p.I121T		Atlas-SNP	.											.	SLC16A6	56	.	0			c.T362C						PASS	.	A	THR/ILE,THR/ILE,	435,3971	210.8+/-231.2	15,405,1783	90.0	80.0	83.0		362,362,	5.8	0.0	17	dbSNP_126	83	1066,7534	225.4+/-261.5	67,932,3301	yes	missense,missense,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	89,89,	82,1337,5084	GG,GA,AA		12.3953,9.8729,11.5408	benign,benign,	121/524,121/524,	66270082	1501,11505	2203	4300	6503	SO:0001583	missense	9120	exon4			ATGCCGATGGCGA	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"""Solute carriers"""	10927	protein-coding gene	gene with protein product		603880	"""solute carrier family 16 (monocarboxylic acid transporters), member 6"", ""solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"""			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.362T>C	17.37:g.66270082A>G	ENSP00000319991:p.Ile121Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_001174166	Q6P1X3	Missense_Mutation	SNP	ENST00000327268.4	37	CCDS11675.1	257	0.11767399267399267	46	0.09349593495934959	38	0.10497237569060773	85	0.1486013986013986	88	0.11609498680738786	A	11.15	1.553362	0.27739	0.098729	0.123953	ENSG00000108932	ENST00000327268	T	0.58506	0.33	5.8	5.8	0.92144	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.464996	0.21957	N	0.066649	T	0.00468	0.0015	M	0.64567	1.98	0.22581	P	0.99896116	B	0.19073	0.033	B	0.25759	0.063	T	0.10847	-1.0612	9	0.34782	T	0.22	.	15.3361	0.74255	1.0:0.0:0.0:0.0	rs35397826;rs62087131;rs35397826	121	O15403	MOT7_HUMAN	T	121	ENSP00000319991:I121T	ENSP00000319991:I121T	I	-	2	0	SLC16A6	63781677	1.000000	0.71417	0.006000	0.13384	0.018000	0.09664	5.833000	0.69349	2.209000	0.71365	0.533000	0.62120	ATC	A|0.883;G|0.117	0.117	strong		0.498	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694	
NLRP4	147945	hgsc.bcm.edu	37	19	56369095	56369095	+	Silent	SNP	C	C	T	rs147356242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56369095C>T	ENST00000301295.6	+	3	758	c.336C>T	c.(334-336)tcC>tcT	p.S112S	NLRP4_ENST00000346986.5_Silent_p.S112S|NLRP4_ENST00000587891.1_Silent_p.S37S	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	112					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)		GCTTATGGTCCAGCAAGTCTG	0.473													C|||	26	0.00519169	0.0189	0.0014	5008	,	,		19927	0.0		0.0	False		,,,				2504	0.0				p.S112S		Atlas-SNP	.											.	NLRP4	331	.	0			c.C336T						PASS	.	C		58,4348	57.4+/-93.9	0,58,2145	114.0	106.0	109.0		336	2.4	0.0	19	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous	NLRP4	NM_134444.4		0,58,6445	TT,TC,CC		0.0,1.3164,0.4459		112/995	56369095	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			ATGGTCCAGCAAG	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.336C>T	19.37:g.56369095C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.994;T|0.006	0.006	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
INPPL1	3636	hgsc.bcm.edu	37	11	71941212	71941212	+	Silent	SNP	A	A	G	rs2276048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71941212A>G	ENST00000298229.2	+	9	1191	c.987A>G	c.(985-987)tcA>tcG	p.S329S	INPPL1_ENST00000541756.1_Silent_p.S87S|INPPL1_ENST00000538751.1_Silent_p.S87S	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	329					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TTGGGAAGTCACAGAAGTTCA	0.617													G|||	1814	0.36222	0.5121	0.2622	5008	,	,		20209	0.3403		0.2087	False		,,,				2504	0.411				p.S329S		Atlas-SNP	.											.	INPPL1	120	.	0			c.A987G						PASS	.	G		2147,2253		531,1085,584	67.0	65.0	66.0		987	-10.8	0.7	11	dbSNP_100	66	1493,7093		121,1251,2921	no	coding-synonymous	INPPL1	NM_001567.3		652,2336,3505	GG,GA,AA		17.3888,48.7955,28.0302		329/1259	71941212	3640,9346	2200	4293	6493	SO:0001819	synonymous_variant	3636	exon9			GAAGTCACAGAAG	Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"""Sterile alpha motif (SAM) domain containing"", ""SH2 domain containing"""	6080	protein-coding gene	gene with protein product	"""51C protein"""	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.987A>G	11.37:g.71941212A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001567	B2RTX5|Q13577|Q13578	Silent	SNP	ENST00000298229.2	37	CCDS8213.1																																																																																			G|0.306;A|0.694	0.306	strong		0.617	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567	
PRF1	5551	hgsc.bcm.edu	37	10	72358577	72358577	+	Silent	SNP	G	G	A	rs885822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72358577G>A	ENST00000441259.1	-	3	1060	c.900C>T	c.(898-900)caC>caT	p.H300H	PRF1_ENST00000373209.2_Silent_p.H300H	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	300	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CCACTTCCGAGTGGCGCTCCC	0.612			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				A|||	3485	0.695887	0.8381	0.6427	5008	,	,		19157	0.7341		0.5885	False		,,,				2504	0.6125				p.H300H		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.C900T						PASS	.	A	,	3504,902	348.7+/-310.1	1397,710,96	182.0	125.0	144.0		900,900	-11.7	0.0	10	dbSNP_86	144	5111,3489	509.6+/-377.3	1534,2043,723	no	coding-synonymous,coding-synonymous	PRF1	NM_001083116.1,NM_005041.4	,	2931,2753,819	AA,AG,GG		40.5698,20.4721,33.7613	,	300/556,300/556	72358577	8615,4391	2203	4300	6503	SO:0001819	synonymous_variant	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TTCCGAGTGGCGC	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.900C>T	10.37:g.72358577G>A		Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	272	122	0.448529	NM_001083116	B2R6X4|Q59F57|Q86WX7	Silent	SNP	ENST00000441259.1	37	CCDS7305.1																																																																																			G|0.316;A|0.684	0.684	strong		0.612	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
CD3EAP	10849	hgsc.bcm.edu	37	19	45912343	45912343	+	Missense_Mutation	SNP	A	A	G	rs762562	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45912343A>G	ENST00000309424.3	+	3	1605	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	ERCC1_ENST00000588738.1_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.K375E|ERCC1_ENST00000423698.2_3'UTR|PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000300853.3_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	373			K -> E (in dbSNP:rs762562).		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)		AGAAGGAGCGAAGCCTCAGGC	0.617													G|||	1436	0.286741	0.3109	0.2233	5008	,	,		16994	0.4613		0.1322	False		,,,				2504	0.2781				p.K373E		Atlas-SNP	.											CD3EAP,NS,carcinoma,0,1	CD3EAP	27	1	0			c.A1117G						PASS	.	G	,,GLU/LYS	1183,3221		168,847,1187	39.0	48.0	45.0		,,1117	1.6	0.0	19	dbSNP_86	45	1150,7450		79,992,3229	yes	utr-3,utr-3,missense	ERCC1,CD3EAP	NM_001166049.1,NM_001983.3,NM_012099.1	,,56	247,1839,4416	GG,GA,AA		13.3721,26.8619,17.9406	,,benign	,,373/511	45912343	2333,10671	2202	4300	6502	SO:0001583	missense	10849	exon3			GGAGCGAAGCCTC	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.1117A>G	19.37:g.45912343A>G	ENSP00000310966:p.Lys373Glu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	570	0.260989010989011	131	0.266260162601626	72	0.19889502762430938	259	0.4527972027972028	108	0.1424802110817942	G	1.401	-0.578050	0.03854	0.268619	0.133721	ENSG00000117877	ENST00000309424	T	0.09911	2.93	5.4	1.59	0.23543	.	0.794983	0.10950	N	0.616167	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	0.47071	-0.9145	9	0.02654	T	1	-2.1051	5.1222	0.14865	0.3446:0.1515:0.5039:0.0	rs762562;rs56437955;rs60195558;rs762562	375;373	O15446-2;O15446	.;RPA34_HUMAN	E	373	ENSP00000310966:K373E	ENSP00000310966:K373E	K	+	1	0	CD3EAP	50604183	0.005000	0.15991	0.000000	0.03702	0.013000	0.08279	0.970000	0.29383	0.267000	0.21916	-0.215000	0.12644	AAG	A|0.774;G|0.226	0.226	strong		0.617	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
PRKCA	5578	hgsc.bcm.edu	37	17	64785022	64785022	+	Silent	SNP	G	G	A	rs2228945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:64785022G>A	ENST00000413366.3	+	16	1805	c.1779G>A	c.(1777-1779)gaG>gaA	p.E593E	MIR634_ENST00000385208.1_RNA	NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	593	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|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 inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)	p.E593E(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	ACGTGAGAGAGCATGCCTTCT	0.537													A|||	844	0.16853	0.3336	0.1398	5008	,	,		19158	0.1607		0.0805	False		,,,				2504	0.0644				p.E593E		Atlas-SNP	.											PRKCA,colon,carcinoma,0,3	PRKCA	82	3	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G1779A						PASS	.	A		1404,3002	686.6+/-404.7	227,950,1026	90.0	86.0	87.0		1779	-2.1	0.9	17	dbSNP_98	87	655,7945	790.0+/-407.6	31,593,3676	no	coding-synonymous	PRKCA	NM_002737.2		258,1543,4702	AA,AG,GG		7.6163,31.8656,15.8312		593/673	64785022	2059,10947	2203	4300	6503	SO:0001819	synonymous_variant	5578	exon16			GAGAGAGCATGCC		CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.1779G>A	17.37:g.64785022G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_002737	B5BU22|Q15137|Q32M72|Q96RE4	Silent	SNP	ENST00000413366.3	37	CCDS11664.1																																																																																			G|0.855;A|0.145	0.145	strong		0.537	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1		
DNASE2B	58511	hgsc.bcm.edu	37	1	84880380	84880380	+	Silent	SNP	T	T	C	rs3768250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:84880380T>C	ENST00000370665.3	+	6	948	c.915T>C	c.(913-915)caT>caC	p.H305H	DNASE2B_ENST00000370662.3_Silent_p.H97H	NM_021233.2	NP_067056.2	Q8WZ79	DNS2B_HUMAN	deoxyribonuclease II beta	305					apoptotic DNA fragmentation (GO:0006309)	extracellular region (GO:0005576)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)			endometrium(1)|lung(4)|skin(1)	6				all cancers(265;0.00303)|Epithelial(280;0.0112)|OV - Ovarian serous cystadenocarcinoma(397;0.0808)		ATCAAGATCATGCCAAGTGGT	0.413													T|||	1622	0.323882	0.2065	0.3573	5008	,	,		20886	0.4554		0.334	False		,,,				2504	0.3129				p.H305H	Pancreas(54;788 1175 11852 16034 30034)	Atlas-SNP	.											.	DNASE2B	40	.	0			c.T915C						PASS	.	T	,	1037,3369	383.2+/-324.8	123,791,1289	62.0	60.0	60.0		915,291	3.0	1.0	1	dbSNP_107	60	3033,5567	466.5+/-366.8	548,1937,1815	no	coding-synonymous,coding-synonymous	DNASE2B	NM_021233.2,NM_058248.1	,	671,2728,3104	CC,CT,TT		35.2674,23.5361,31.2932	,	305/362,97/154	84880380	4070,8936	2203	4300	6503	SO:0001819	synonymous_variant	58511	exon6			AGATCATGCCAAG	AF274571	CCDS694.1, CCDS44167.1	1p22.3	2008-02-05			ENSG00000137976	ENSG00000137976			28875	protein-coding gene	gene with protein product		608057				12594037, 11376952	Standard	NM_021233		Approved	DLAD	uc001djt.1	Q8WZ79	OTTHUMG00000009860	ENST00000370665.3:c.915T>C	1.37:g.84880380T>C		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	206	98	0.475728	NM_021233	Q5VXD0|Q5VXD1|Q8WZ80|Q9NQW3	Silent	SNP	ENST00000370665.3	37	CCDS44167.1																																																																																			T|0.679;C|0.321	0.321	strong		0.413	DNASE2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027248.1	NM_021233	
GIMAP6	474344	hgsc.bcm.edu	37	7	150324976	150324976	+	Missense_Mutation	SNP	T	T	C	rs11977216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150324976T>C	ENST00000328902.5	-	3	926	c.710A>G	c.(709-711)cAa>cGa	p.Q237R	GIMAP6_ENST00000493969.1_3'UTR	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	237	AIG1-type G.		Q -> R (in dbSNP:rs11977216).			cytosol (GO:0005829)	GTP binding (GO:0005525)			endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTGGGTATATTGGTAAGCCTT	0.512													T|||	163	0.0325479	0.1203	0.0058	5008	,	,		23011	0.0		0.0	False		,,,				2504	0.0				p.Q307R		Atlas-SNP	.											.	GIMAP6	60	.	0			c.A920G						PASS	.	T	ARG/GLN	479,3927	224.9+/-240.9	27,425,1751	164.0	152.0	156.0		710	-0.0	0.0	7	dbSNP_120	156	4,8596	3.7+/-12.6	0,4,4296	yes	missense	GIMAP6	NM_024711.5	43	27,429,6047	CC,CT,TT		0.0465,10.8715,3.7137	benign	237/293	150324976	483,12523	2203	4300	6503	SO:0001583	missense	474344	exon3			GTATATTGGTAAG	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"""GTPases, IMAP"""	21918	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 6"""					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.710A>G	7.37:g.150324976T>C	ENSP00000330374:p.Gln237Arg	Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	290	128	0.441379	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	CCDS34778.1	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	T	2.860	-0.236349	0.05944	0.108715	4.65E-4	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.05199	3.48	4.05	-0.00736	0.14009	AIG1 (1);	0.847263	0.10486	N	0.668996	T	0.00073	0.0002	N	0.04994	-0.135	0.09310	N	0.999999	B;B	0.18013	0.002;0.025	B;B	0.18263	0.021;0.018	T	0.47923	-0.9079	10	0.11794	T	0.64	.	3.0119	0.06047	0.3789:0.1102:0.0:0.5109	rs11977216;rs52790742;rs56467483;rs58007032;rs11977216	237;157	Q6P9H5;Q6P9H5-2	GIMA6_HUMAN;.	R	237;298	ENSP00000330374:Q237R	ENSP00000330374:Q237R	Q	-	2	0	GIMAP6	149955909	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.176000	0.09811	-0.160000	0.11002	-0.336000	0.08194	CAA	T|0.964;C|0.036	0.036	strong		0.512	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711	
MUC6	4588	hgsc.bcm.edu	37	11	1017945	1017945	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017945A>G	ENST00000421673.2	-	31	4906	c.4856T>C	c.(4855-4857)tTc>tCc	p.F1619S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1619	Approximate repeats.|Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			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)		AGAGGTGGAGAAAGGTGGAAC	0.542																																					p.F1619S		Atlas-SNP	.											.	MUC6	408	.	0			c.T4856C						PASS	.																																			SO:0001583	missense	4588	exon31			GTGGAGAAAGGTG	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.4856T>C	11.37:g.1017945A>G	ENSP00000406861:p.Phe1619Ser	Somatic	1032	0	0		WXS	Illumina HiSeq	Phase_I	1212	49	0.040429	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	A	0.026	-1.375208	0.01214	.	.	ENSG00000184956	ENST00000421673	T	0.19669	2.13	2.39	-1.65	0.08291	.	.	.	.	.	T	0.14227	0.0344	L	0.41710	1.295	0.09310	N	1	B	0.29341	0.242	B	0.35931	0.214	T	0.39860	-0.9593	9	0.06625	T	0.88	.	6.4604	0.21954	0.6729:0.0:0.3271:0.0	.	1619	Q6W4X9	MUC6_HUMAN	S	1619	ENSP00000406861:F1619S	ENSP00000406861:F1619S	F	-	2	0	MUC6	1007945	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.579000	0.05834	-0.502000	0.06596	-0.917000	0.02746	TTC	.	.	none		0.542	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ABCB5	340273	hgsc.bcm.edu	37	7	20784910	20784910	+	Missense_Mutation	SNP	T	T	C	rs60197951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20784910T>C	ENST00000404938.2	+	26	3930	c.3278T>C	c.(3277-3279)aTa>aCa	p.I1093T	ABCB5_ENST00000258738.6_Missense_Mutation_p.I648T	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	1093	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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						CGTTCCCAAATAGCAATCGTT	0.458													T|||	75	0.014976	0.0484	0.0101	5008	,	,		19479	0.0		0.003	False		,,,				2504	0.001				p.I1093T		Atlas-SNP	.											.	ABCB5	357	.	0			c.T3278C						PASS	.	T	THR/ILE,THR/ILE	247,4159	144.2+/-179.2	7,233,1963	152.0	140.0	144.0		3278,1943	0.3	0.9	7	dbSNP_129	144	30,8570	21.6+/-65.8	0,30,4270	yes	missense,missense	ABCB5	NM_001163941.1,NM_178559.5	89,89	7,263,6233	CC,CT,TT		0.3488,5.606,2.1298	benign,benign	1093/1258,648/813	20784910	277,12729	2203	4300	6503	SO:0001583	missense	340273	exon26			CCCAAATAGCAAT	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.3278T>C	7.37:g.20784910T>C	ENSP00000384881:p.Ile1093Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	37	0.01694139194139194	31	0.06300813008130081	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	11.16	1.557490	0.27827	0.05606	0.003488	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.95137	-3.62;-3.62	5.32	0.314	0.15847	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.178795	0.35235	N	0.003360	T	0.63248	0.2495	L	0.46670	1.46	0.28541	N	0.912097	B;B	0.18863	0.031;0.006	B;B	0.32724	0.151;0.021	T	0.76756	-0.2842	10	0.59425	D	0.04	.	8.784	0.34809	0.0:0.321:0.0:0.679	rs60197951;rs61732048	1093;648	A7BKA4;Q2M3G0	.;ABCB5_HUMAN	T	1093;648	ENSP00000384881:I1093T;ENSP00000258738:I648T	ENSP00000258738:I648T	I	+	2	0	ABCB5	20751435	1.000000	0.71417	0.942000	0.38095	0.504000	0.33889	4.131000	0.57970	0.095000	0.17434	-0.250000	0.11733	ATA	T|0.981;C|0.019	0.019	strong		0.458	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417503	105417503	+	Missense_Mutation	SNP	G	G	T	rs146582718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417503G>T	ENST00000333244.5	-	7	4404	c.4285C>A	c.(4285-4287)Cct>Act	p.P1429T	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1429						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)			TCTATTTCAGGGCCCTTGAGG	0.612													.|||	321	0.0640974	0.2307	0.0159	5008	,	,		12778	0.0		0.005	False		,,,				2504	0.0				p.P1429T		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4285A						PASS	.	G	THR/PRO	721,2755		187,347,1204	98.0	74.0	83.0		4285	3.9	0.1	14	dbSNP_134	83	22,5768		3,16,2876	no	missense	AHNAK2	NM_138420.2	38	190,363,4080	TT,TG,GG		0.38,20.7422,8.0186	probably-damaging	1429/5796	105417503	743,8523	1738	2895	4633	SO:0001583	missense	113146	exon7			TTTCAGGGCCCTT	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.4285C>A	14.37:g.105417503G>T	ENSP00000353114:p.Pro1429Thr	Somatic	389	0	0		WXS	Illumina HiSeq	Phase_I	411	406	0.987835	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	102	0.046703296703296704	99	0.20121951219512196	3	0.008287292817679558	0	0.0	0	0.0	g	11.78	1.742050	0.30865	0.207422	0.0038	ENSG00000185567	ENST00000333244	T	0.02656	4.21	3.87	3.87	0.44632	.	.	.	.	.	T	0.00012	0.0000	M	0.93328	3.405	0.38700	P	0.047036999999999995	D	0.89917	1.0	D	0.77557	0.99	T	0.06607	-1.0817	8	0.40728	T	0.16	-26.1992	9.0134	0.36155	0.1094:0.0:0.8906:0.0	.	1429	Q8IVF2	AHNK2_HUMAN	T	1429	ENSP00000353114:P1429T	ENSP00000353114:P1429T	P	-	1	0	AHNAK2	104488548	0.998000	0.40836	0.081000	0.20488	0.012000	0.07955	2.751000	0.47508	1.727000	0.51537	0.306000	0.20318	CCT	G|0.962;T|0.038	0.038	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
PLCH1	23007	hgsc.bcm.edu	37	3	155314034	155314034	+	Silent	SNP	A	A	G	rs359569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:155314034A>G	ENST00000340059.7	-	2	176	c.177T>C	c.(175-177)agT>agC	p.S59S	PLCH1_ENST00000460012.1_Silent_p.S41S|PLCH1_ENST00000414191.1_Silent_p.S41S|PLCH1_ENST00000494598.1_Silent_p.S59S|PLCH1_ENST00000334686.6_Silent_p.S41S|PLCH1_ENST00000447496.2_Silent_p.S59S	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	59	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.S41S(1)		NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TTGCCTTCTCACTCTTCCTAG	0.483													G|||	2301	0.459465	0.4002	0.5519	5008	,	,		16578	0.2768		0.7416	False		,,,				2504	0.3722				p.S59S		Atlas-SNP	.											PLCH1,NS,carcinoma,0,1	PLCH1	406	1	1	Substitution - coding silent(1)	prostate(1)	c.T177C						PASS	.	G	,,	2078,2328	606.6+/-390.8	493,1092,618	175.0	182.0	180.0		177,177,123	-1.5	0.8	3	dbSNP_79	180	6161,2439	401.6+/-347.2	2210,1741,349	no	coding-synonymous,coding-synonymous,coding-synonymous	PLCH1	NM_001130960.1,NM_001130961.1,NM_014996.2	,,	2703,2833,967	GG,GA,AA		28.3605,47.163,36.6523	,,	59/1694,59/1003,41/1656	155314034	8239,4767	2203	4300	6503	SO:0001819	synonymous_variant	23007	exon2			CTTCTCACTCTTC	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.177T>C	3.37:g.155314034A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	69	43	0.623188	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Silent	SNP	ENST00000340059.7	37	CCDS46939.1																																																																																			A|0.426;G|0.574	0.574	strong		0.483	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
SLC7A9	11136	hgsc.bcm.edu	37	19	33333179	33333179	+	Silent	SNP	C	C	T	rs111630604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33333179C>T	ENST00000023064.4	-	11	1310	c.1119G>A	c.(1117-1119)tcG>tcA	p.S373S	SLC7A9_ENST00000590341.1_Silent_p.S373S|SLC7A9_ENST00000587772.1_Silent_p.S373S	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	373					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	AATTGACTAACGAGTTTATGT	0.393													C|||	50	0.00998403	0.0325	0.0086	5008	,	,		19257	0.0		0.0	False		,,,				2504	0.001				p.S373S	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											SLC7A9,NS,carcinoma,-1,3	SLC7A9	78	3	0			c.G1119A						PASS	.	C	,	144,4262	102.1+/-140.7	5,134,2064	114.0	108.0	110.0		1119,1119	-11.4	0.0	19	dbSNP_132	110	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC7A9	NM_001126335.1,NM_014270.4	,	5,134,6364	TT,TC,CC		0.0,3.2683,1.1072	,	373/488,373/488	33333179	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	11136	exon11			GACTAACGAGTTT	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"""Solute carriers"""	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.1119G>A	19.37:g.33333179C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001243036	B2R9A6	Silent	SNP	ENST00000023064.4	37	CCDS12425.1																																																																																			C|0.987;T|0.013	0.013	strong		0.393	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
PCDHB14	56122	hgsc.bcm.edu	37	5	140605078	140605078	+	Silent	SNP	C	C	T	rs2907322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	36	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	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	
TMEM223	79064	hgsc.bcm.edu	37	11	62559301	62559301	+	Missense_Mutation	SNP	C	C	T	rs2956139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62559301C>T	ENST00000307366.7	-	1	192	c.166G>A	c.(166-168)Ggc>Agc	p.G56S	TMEM223_ENST00000527073.1_5'Flank|TMEM223_ENST00000525631.1_Missense_Mutation_p.G56S|NXF1_ENST00000533048.1_5'Flank	NM_001080501.2	NP_001073970.1	A0PJW6	TM223_HUMAN	transmembrane protein 223	56						integral component of membrane (GO:0016021)											CAGAAGACGCCCTGGCCCGCG	0.672													C|||	121	0.0241613	0.0855	0.0086	5008	,	,		14072	0.0		0.002	False		,,,				2504	0.0				p.G56S		Atlas-SNP	.											.	TMEM223	22	.	0			c.G166A						PASS	.	C	SER/GLY	221,3653		5,211,1721	17.0	26.0	23.0		166	5.0	1.0	11	dbSNP_101	23	2,8218		0,2,4108	yes	missense	TMEM223	NM_001080501.2	56	5,213,5829	TT,TC,CC		0.0243,5.7047,1.8439	benign	56/203	62559301	223,11871	1937	4110	6047	SO:0001583	missense	79064	exon1			AGACGCCCTGGCC		CCDS44628.1	11q12.3	2008-12-08				ENSG00000168569			28464	protein-coding gene	gene with protein product							Standard	NM_001080501		Approved	MGC3196	uc001nve.2	A0PJW6		ENST00000307366.7:c.166G>A	11.37:g.62559301C>T	ENSP00000303987:p.Gly56Ser	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_001080501	Q504S0|Q86YD4|Q8WUC5|Q96HG0	Missense_Mutation	SNP	ENST00000307366.7	37	CCDS44628.1	57|57	0.0260989010989011|0.0260989010989011	53|53	0.10772357723577236|0.10772357723577236	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	21.4|21.4	4.141694|4.141694	0.77775|0.77775	0.057047|0.057047	2.43E-4|2.43E-4	ENSG00000168569|ENSG00000168569	ENST00000528367|ENST00000525631;ENST00000307366	.|T;T	.|0.41758	.|0.99;0.99	5.94|5.94	5.02|5.02	0.67125|0.67125	.|.	0.275955|0.275955	0.35407|0.35407	N|N	0.003221|0.003221	T|T	0.00608|0.00608	0.0020|0.0020	L|L	0.34521|0.34521	1.04|1.04	0.35563|0.35563	D|D	0.804871|0.804871	.|B	.|0.30281	.|0.275	.|B	.|0.28916	.|0.096	T|T	0.09952|0.09952	-1.0651|-1.0651	6|9	.|.	.|.	.|.	-15.5835|-15.5835	13.3061|13.3061	0.60352|0.60352	0.0:0.9227:0.0:0.0773|0.0:0.9227:0.0:0.0773	rs2956139|rs2956139	.|56	.|A0PJW6	.|TM223_HUMAN	E|S	55|56	.|ENSP00000436670:G56S;ENSP00000303987:G56S	.|.	G|G	-|-	2|1	0|0	TMEM223|TMEM223	62315877|62315877	0.994000|0.994000	0.37717|0.37717	1.000000|1.000000	0.80357|0.80357	0.887000|0.887000	0.51463|0.51463	1.735000|1.735000	0.38176|0.38176	1.499000|1.499000	0.48617|0.48617	0.561000|0.561000	0.74099|0.74099	GGG|GGC	C|0.973;T|0.027	0.027	strong		0.672	TMEM223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395674.1		
POPDC2	64091	hgsc.bcm.edu	37	3	119379186	119379186	+	Missense_Mutation	SNP	C	C	T	rs4688023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119379186C>T	ENST00000264231.3	-	1	251	c.85G>A	c.(85-87)Gtc>Atc	p.V29I	POPDC2_ENST00000474523.1_Intron|POPDC2_ENST00000538678.1_Missense_Mutation_p.V29I|POPDC2_ENST00000493094.1_Missense_Mutation_p.V29I|POPDC2_ENST00000468801.1_Missense_Mutation_p.V29I	NM_022135.2	NP_071418.2	Q9HBU9	POPD2_HUMAN	popeye domain containing 2	29			V -> I (in dbSNP:rs4688023).		regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sinoatrial node cell development (GO:0060931)	integral component of membrane (GO:0016021)	cAMP binding (GO:0030552)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.242)		AGGTGGTAGACAGCCCCTTCC	0.557													C|||	2012	0.401757	0.2935	0.4611	5008	,	,		15446	0.3323		0.4304	False		,,,				2504	0.5481				p.V29I		Atlas-SNP	.											.	POPDC2	36	.	0			c.G85A						PASS	.	C	ILE/VAL	1404,3002	459.6+/-352.3	226,952,1025	89.0	83.0	85.0		85	-5.6	0.5	3	dbSNP_111	85	3806,4794	537.6+/-383.2	840,2126,1334	yes	missense	POPDC2	NM_022135.2	29	1066,3078,2359	TT,TC,CC		44.2558,31.8656,40.0584	benign	29/365	119379186	5210,7796	2203	4300	6503	SO:0001583	missense	64091	exon1			GGTAGACAGCCCC	AF204173	CCDS2992.1	3q13.33	2004-01-15			ENSG00000121577	ENSG00000121577			17648	protein-coding gene	gene with protein product		605823				10882522	Standard	NM_022135		Approved	POP2	uc031sbc.1	Q9HBU9	OTTHUMG00000159438	ENST00000264231.3:c.85G>A	3.37:g.119379186C>T	ENSP00000264231:p.Val29Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_022135	Q86UE7	Missense_Mutation	SNP	ENST00000264231.3	37	CCDS2992.1	820	0.37545787545787546	130	0.26422764227642276	170	0.4696132596685083	197	0.34440559440559443	323	0.4261213720316623	C	1.924	-0.447524	0.04572	0.318656	0.442558	ENSG00000121577	ENST00000264231;ENST00000493094;ENST00000468801;ENST00000538678	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.66	-5.63	0.02474	.	1.223450	0.05589	N	0.574411	T	0.00012	0.0000	N	0.25060	0.705	0.40670	P	0.017796000000000034	B;B	0.18166	0.026;0.009	B;B	0.16289	0.015;0.01	T	0.42050	-0.9474	9	0.06236	T	0.91	.	10.9218	0.47169	0.1494:0.2332:0.5606:0.0568	rs4688023;rs52810037;rs59425816;rs4688023	29;29	Q9HBU9-2;Q9HBU9	.;POPD2_HUMAN	I	29	ENSP00000264231:V29I;ENSP00000417250:V29I;ENSP00000420715:V29I;ENSP00000438271:V29I	ENSP00000264231:V29I	V	-	1	0	POPDC2	120861876	0.000000	0.05858	0.478000	0.27316	0.573000	0.36030	-0.433000	0.06948	-0.985000	0.03503	-0.309000	0.09137	GTC	C|0.615;T|0.385	0.385	strong		0.557	POPDC2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355378.1	NM_022135	
CR1	1378	hgsc.bcm.edu	37	1	207782889	207782889	+	Missense_Mutation	SNP	A	A	G	rs17047661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207782889A>G	ENST00000367049.4	+	37	6151	c.6151A>G	c.(6151-6153)Aga>Gga	p.R2051G	RP11-78B10.2_ENST00000597497.1_RNA|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367051.1_Missense_Mutation_p.R1601G|CR1_ENST00000367052.1_Missense_Mutation_p.R1601G|CR1_ENST00000367053.1_Missense_Mutation_p.R1601G|CR1_ENST00000400960.2_Missense_Mutation_p.R1601G	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1601					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						AAATGCAATTAGAGTACCAGG	0.468													a|||	984	0.196486	0.7103	0.0519	5008	,	,		19576	0.0		0.0089	False		,,,				2504	0.0				p.R2051G		Atlas-SNP	.											.	CR1	354	.	0			c.A6151G	GRCh37	CM015242	CR1	M	rs17047661	PASS	.	C	GLY/ARG,GLY/ARG	2160,1626		630,900,363	59.0	58.0	58.0		4801,6151	-2.0	0.0	1	dbSNP_123	58	27,8203		0,27,4088	yes	missense,missense	CR1	NM_000573.3,NM_000651.4	125,125	630,927,4451	GG,GA,AA		0.3281,42.9477,18.2007	probably-damaging,probably-damaging	1601/2040,2051/2490	207782889	2187,9829	1893	4115	6008	SO:0001583	missense	1378	exon37			GCAATTAGAGTAC	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.6151A>G	1.37:g.207782889A>G	ENSP00000356016:p.Arg2051Gly	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	152	77	0.506579	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	333	0.15247252747252749	314	0.6382113821138211	17	0.04696132596685083	0	0.0	2	0.002638522427440633	a	8.718	0.913598	0.17907	0.570523	0.003281	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;1.62;-0.11	2.54	-2.03	0.07365	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	M	0.80422	2.495	0.80722	P	0.0	B;D;D	0.59767	0.257;0.982;0.986	B;D;P	0.69479	0.069;0.964;0.79	T	0.47222	-0.9134	8	0.23891	T	0.37	.	4.646	0.12572	0.3825:0.4843:0.1331:0.0	rs17047661;rs52836690;rs17047661	1601;1601;2051	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	G	1601;1601;1601;1601;1151;2051	ENSP00000356019:R1601G;ENSP00000356018:R1601G;ENSP00000356020:R1601G;ENSP00000383744:R1601G;ENSP00000436139:R1151G;ENSP00000356016:R2051G	ENSP00000356016:R2051G	R	+	1	2	CR1	205849512	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.157000	0.10085	-0.445000	0.07159	-0.525000	0.04345	AGA	A|0.769;G|0.231	0.231	strong		0.468	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
CAPN3	825	hgsc.bcm.edu	37	15	42680058	42680058	+	Silent	SNP	T	T	C	rs17593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42680058T>C	ENST00000397163.3	+	4	825	c.606T>C	c.(604-606)agT>agC	p.S202S	CAPN3_ENST00000356316.3_Silent_p.S115S|CAPN3_ENST00000349748.3_Silent_p.S202S|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000357568.3_Silent_p.S202S|CAPN3_ENST00000318023.7_Silent_p.S202S	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	202	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		Missing (in LGMD2A). {ECO:0000269|PubMed:9452114}.		apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AGTTCTGGAGTGCTCTGCTGG	0.498													C|||	321	0.0640974	0.2095	0.0159	5008	,	,		22401	0.0		0.0089	False		,,,				2504	0.0245				p.S202S		Atlas-SNP	.											.	CAPN3	172	.	0			c.T606C						PASS	.	C	,,	698,3708	761.2+/-413.0	49,600,1554	192.0	164.0	174.0		606,606,606	-4.9	0.8	15	dbSNP_63	174	38,8560	817.5+/-406.9	0,38,4261	no	coding-synonymous,coding-synonymous,coding-synonymous	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1	,,	49,638,5815	CC,CT,TT		0.442,15.842,5.6598	,,	202/822,202/816,202/730	42680058	736,12268	2203	4299	6502	SO:0001819	synonymous_variant	825	exon4			CTGGAGTGCTCTG	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"""EF-hand domain containing"""	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.606T>C	15.37:g.42680058T>C		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	163	163	1	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																			T|0.944;C|0.056	0.056	strong		0.498	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		
ZC4H2	55906	hgsc.bcm.edu	37	X	64139051	64139051	+	Silent	SNP	T	T	C	rs6524946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:64139051T>C	ENST00000374839.3	-	4	538	c.432A>G	c.(430-432)acA>acG	p.T144T	ZC4H2_ENST00000545618.1_Silent_p.T139T|ZC4H2_ENST00000488608.1_5'UTR|ZC4H2_ENST00000337990.2_Silent_p.T121T|ZC4H2_ENST00000447788.2_Intron	NM_018684.3	NP_061154.1	Q9NQZ6	ZC4H2_HUMAN	zinc finger, C4H2 domain containing	144					nervous system development (GO:0007399)|neuromuscular junction development (GO:0007528)|spinal cord motor neuron differentiation (GO:0021522)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	metal ion binding (GO:0046872)			endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						CCTGAGGTTCTGTCTGCCATT	0.547													C|||	354	0.0937748	0.2549	0.0245	3775	,	,		13414	0.0		0.0	False		,,,				2504	0.0				p.T144T		Atlas-SNP	.											.	ZC4H2	64	.	0			c.A432G						PASS	.	C	,,	1115,2720		134,678,169,820,402	60.0	51.0	54.0		363,,432	-4.2	0.3	X	dbSNP_116	54	4,6724		0,2,2,2426,1870	no	coding-synonymous,intron,coding-synonymous	ZC4H2	NM_001178032.2,NM_001178033.2,NM_018684.3	,,	134,680,171,3246,2272	CC,CT,C,TT,T		0.0595,29.0743,10.5936	,,	121/202,,144/225	64139051	1119,9444	2203	4300	6503	SO:0001819	synonymous_variant	55906	exon4			AGGTTCTGTCTGC	AF270491	CCDS14380.1, CCDS55431.1, CCDS55432.1	Xq11.1	2013-07-23	2008-10-01	2008-10-01	ENSG00000126970	ENSG00000126970		"""Zinc fingers"""	24931	protein-coding gene	gene with protein product		300897	"""KIAA1166"", ""Wieacker-Wolff syndrome"""	KIAA1166, WWS		10574461, 12097419, 23623388	Standard	NM_018684		Approved	HCA127	uc004dvu.3	Q9NQZ6	OTTHUMG00000021712	ENST00000374839.3:c.432A>G	X.37:g.64139051T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	NM_018684	B2RDC2|B3KVZ5|B4DED0|E7EM74|G3V1L3|Q53H73|Q5JTF9|Q9H9C3|Q9H9H7|Q9ULQ4	Silent	SNP	ENST00000374839.3	37	CCDS14380.1																																																																																			T|0.894;C|0.106	0.106	strong		0.547	ZC4H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056958.1	NM_018684	
ZNF155	7711	hgsc.bcm.edu	37	19	44496070	44496070	+	Silent	SNP	A	A	G	rs431509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44496070A>G	ENST00000270014.2	+	4	347	c.219A>G	c.(217-219)caA>caG	p.Q73Q	ZNF155_ENST00000407951.2_Silent_p.Q84Q|ZNF155_ENST00000590615.1_Silent_p.Q73Q	NM_001260487.1|NM_198089.2	NP_001247416|NP_932355	Q12901	ZN155_HUMAN	zinc finger protein 155	73	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	15		Prostate(69;0.0352)				CAGCAACCCAAAGAGAAGGGA	0.478													A|||	2257	0.450679	0.5575	0.4942	5008	,	,		21633	0.5466		0.2893	False		,,,				2504	0.3425				p.Q84Q	NSCLC(61;554 1277 20909 42067 42312)	Atlas-SNP	.											.	ZNF155	30	.	0			c.A252G						PASS	.	A	,	2295,2111	601.2+/-389.7	607,1081,515	149.0	149.0	149.0		219,219	-2.0	0.1	19	dbSNP_80	149	2443,6157	403.2+/-347.7	355,1733,2212	no	coding-synonymous,coding-synonymous	ZNF155	NM_003445.2,NM_198089.1	,	962,2814,2727	GG,GA,AA		28.407,47.9119,36.4293	,	73/539,73/539	44496070	4738,8268	2203	4300	6503	SO:0001819	synonymous_variant	7711	exon5			AACCCAAAGAGAA	U09852	CCDS12634.1, CCDS58668.1	19q13.2-q13.32	2013-01-08	2006-08-22			ENSG00000204920		"""Zinc fingers, C2H2-type"", ""-"""	12940	protein-coding gene	gene with protein product		604086	"""zinc finger protein 155 (pHZ-96)"""			7557990	Standard	NM_001260486		Approved	pHZ-96	uc010xwt.2	Q12901		ENST00000270014.2:c.219A>G	19.37:g.44496070A>G		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_001260488	A2BDE6|B2RB63|B4DM95|J3KQ08|Q6AZZ8|Q9UIE1|Q9UK14	Silent	SNP	ENST00000270014.2	37	CCDS12634.1																																																																																			A|0.624;G|0.376	0.376	strong		0.478	ZNF155-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460074.1	NM_003445	
DLST	1743	hgsc.bcm.edu	37	14	75367807	75367807	+	Silent	SNP	C	C	T	rs20578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:75367807C>T	ENST00000334220.4	+	14	1159	c.1098C>T	c.(1096-1098)ggC>ggT	p.G366G	DLST_ENST00000334212.6_Silent_p.G280G	NM_001933.4	NP_001924.2	P36957	ODO2_HUMAN	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	366					cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|generation of precursor metabolites and energy (GO:0006091)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|oxoglutarate dehydrogenase complex (GO:0045252)	dihydrolipoyllysine-residue succinyltransferase activity (GO:0004149)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00698)		ATATGGATGGCGGTACCTTCA	0.458													C|||	1423	0.284145	0.3404	0.2349	5008	,	,		20960	0.2202		0.2962	False		,,,				2504	0.2965				p.G366G		Atlas-SNP	.											.	DLST	42	.	0			c.C1098T						PASS	.	C		1500,2906	479.2+/-358.4	262,976,965	151.0	145.0	147.0		1098	-6.7	0.8	14	dbSNP_67	147	2653,5947	428.1+/-355.8	420,1813,2067	no	coding-synonymous	DLST	NM_001933.4		682,2789,3032	TT,TC,CC		30.8488,34.0445,31.9314		366/454	75367807	4153,8853	2203	4300	6503	SO:0001819	synonymous_variant	1743	exon14			GGATGGCGGTACC		CCDS9833.1	14q23.1	2008-08-11			ENSG00000119689	ENSG00000119689	2.3.1.61		2911	protein-coding gene	gene with protein product		126063		DLTS		8009371	Standard	NM_001933		Approved		uc001xqv.2	P36957		ENST00000334220.4:c.1098C>T	14.37:g.75367807C>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	211	117	0.554502	NM_001933	B7Z5W8|E7ESY5|Q7LDY7|Q9BQ32	Silent	SNP	ENST00000334220.4	37	CCDS9833.1																																																																																			C|0.690;T|0.310	0.310	strong		0.458	DLST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413637.1		
MYOM2	9172	hgsc.bcm.edu	37	8	2088697	2088697	+	Missense_Mutation	SNP	G	G	C	rs34735757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2088697G>C	ENST00000262113.4	+	33	3993	c.3852G>C	c.(3850-3852)gaG>gaC	p.E1284D	MYOM2_ENST00000523438.1_Missense_Mutation_p.E709D|MYOM2_ENST00000520298.1_3'UTR	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1284			E -> D (in dbSNP:rs34735757).		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)		GGAGTGAAGAGATGGCTTGGC	0.458													G|||	55	0.0109824	0.0386	0.0043	5008	,	,		15452	0.001		0.0	False		,,,				2504	0.0				p.E1284D		Atlas-SNP	.											.	MYOM2	251	.	0			c.G3852C						PASS	.	G	ASP/GLU	155,4251	106.9+/-145.3	1,153,2049	121.0	116.0	118.0		3852	-1.4	0.7	8	dbSNP_126	118	1,8599		0,1,4299	yes	missense	MYOM2	NM_003970.2	45	1,154,6348	CC,CG,GG		0.0116,3.5179,1.1994	benign	1284/1466	2088697	156,12850	2203	4300	6503	SO:0001583	missense	9172	exon33			TGAAGAGATGGCT		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.3852G>C	8.37:g.2088697G>C	ENSP00000262113:p.Glu1284Asp	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	11.14	1.551354	0.27739	0.035179	1.16E-4	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.34667	1.35;1.35	5.02	-1.4	0.08968	Immunoglobulin-like fold (1);	0.345909	0.29473	N	0.012055	T	0.03739	0.0106	L	0.28556	0.865	0.29986	N	0.817304	B	0.06786	0.001	B	0.06405	0.002	T	0.06285	-1.0835	10	0.24483	T	0.36	.	0.3472	0.00343	0.231:0.2232:0.1729:0.373	rs34735757	1284	P54296	MYOM2_HUMAN	D	1284;709	ENSP00000262113:E1284D;ENSP00000428396:E709D	ENSP00000262113:E1284D	E	+	3	2	MYOM2	2076104	0.995000	0.38212	0.652000	0.29579	0.922000	0.55478	0.369000	0.20416	-0.371000	0.08004	0.655000	0.94253	GAG	G|0.986;C|0.014	0.014	strong		0.458	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18775810	18775810	+	Missense_Mutation	SNP	C	C	A	rs934472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:18775810C>A	ENST00000380548.4	+	18	2806	c.2467C>A	c.(2467-2469)Ctc>Atc	p.L823I		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	823	TSP type-1 7. {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)		GAAAACCGGCCTCTCAACGGT	0.552													A|||	2182	0.435703	0.3661	0.3458	5008	,	,		17341	0.4603		0.4573	False		,,,				2504	0.546				p.L823I		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.C2467A						PASS	.	A	ILE/LEU	1484,2464		304,876,794	57.0	63.0	61.0		2467	1.6	0.2	9	dbSNP_86	61	4032,4286		980,2072,1107	yes	missense	ADAMTSL1	NM_001040272.5	5	1284,2948,1901	AA,AC,CC		48.4732,37.5887,44.9698	benign	823/1763	18775810	5516,6750	1974	4159	6133	SO:0001583	missense	92949	exon18			ACCGGCCTCTCAA	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.2467C>A	9.37:g.18775810C>A	ENSP00000369921:p.Leu823Ile	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	115	61	0.530435	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	949	0.43452380952380953	203	0.41260162601626016	124	0.3425414364640884	269	0.47027972027972026	353	0.4656992084432718	A	0.303	-0.972880	0.02215	0.375887	0.484732	ENSG00000178031	ENST00000380548	T	0.62788	-0.0	5.81	1.61	0.23674	.	0.695701	0.08080	U	1.000000	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40664	-0.9551	9	0.33940	T	0.23	.	7.6219	0.28189	0.2166:0.4528:0.3306:0.0	rs934472;rs56660150;rs934472	823	Q8N6G6	ATL1_HUMAN	I	823	ENSP00000369921:L823I	ENSP00000369921:L823I	L	+	1	0	ADAMTSL1	18765810	0.000000	0.05858	0.207000	0.23584	0.001000	0.01503	-0.163000	0.09997	-0.183000	0.10585	-1.217000	0.01609	CTC	C|0.566;A|0.434	0.434	strong		0.552	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
GPRASP2	114928	hgsc.bcm.edu	37	X	101971960	101971960	+	Silent	SNP	C	C	T	rs112000579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101971960C>T	ENST00000535209.1	+	4	2994	c.2163C>T	c.(2161-2163)tcC>tcT	p.S721S	GPRASP2_ENST00000543253.1_Silent_p.S721S|GPRASP2_ENST00000332262.5_Silent_p.S721S			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	721						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						ACTATATGTCCGGGTTTCTCT	0.418													.|||	60	0.015894	0.0378	0.0014	3775	,	,		13898	0.0		0.007	False		,,,				2504	0.002				p.S721S		Atlas-SNP	.											.	GPRASP2	89	.	0			c.C2163T						PASS	.	C	,,,,,	148,3687		2,116,28,1514,543	105.0	94.0	98.0		2163,2163,2163,2163,2163,2163	-3.7	0.4	X	dbSNP_132	98	62,6666		0,50,12,2378,1860	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPRASP2,ARMCX5-GPRASP2	NM_001004051.3,NM_001184874.2,NM_001184875.2,NM_001184876.2,NM_001199818.1,NM_138437.5	,,,,,	2,166,40,3892,2403	TT,TC,T,CC,C		0.9215,3.8592,1.9881	,,,,,	721/839,721/839,721/839,721/839,721/839,721/839	101971960	210,10353	2203	4300	6503	SO:0001819	synonymous_variant	114928	exon4			TATGTCCGGGTTT	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"""Armadillo repeat containing"""	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.2163C>T	X.37:g.101971960C>T		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	274	93	0.339416	NM_138437	D3DXA0|Q8NAB4	Silent	SNP	ENST00000535209.1	37	CCDS14501.1																																																																																			C|0.981;T|0.019	0.019	strong		0.418	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
CFAP69	79846	hgsc.bcm.edu	37	7	89906609	89906609	+	Silent	SNP	C	C	T	rs3761805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	120	0	0		WXS	Illumina HiSeq	Phase_I	141	63	0.446809	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		
ZNF556	80032	hgsc.bcm.edu	37	19	2877365	2877365	+	Missense_Mutation	SNP	C	C	T	rs10421121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2877365C>T	ENST00000307635.2	+	4	496	c.409C>T	c.(409-411)Cgc>Tgc	p.R137C	ZNF556_ENST00000586426.1_Missense_Mutation_p.R136C	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	137			R -> C (in dbSNP:rs10421121).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGTCATCTGCGCAAGAATTG	0.423													C|||	492	0.0982428	0.2663	0.0692	5008	,	,		21015	0.001		0.0656	False		,,,				2504	0.0256				p.R137C		Atlas-SNP	.											.	ZNF556	73	.	0			c.C409T						PASS	.	C	CYS/ARG	1125,3281	402.2+/-332.3	141,843,1219	130.0	112.0	118.0		409	-1.8	0.0	19	dbSNP_119	118	497,8103	143.6+/-199.6	15,467,3818	yes	missense	ZNF556	NM_024967.1	180	156,1310,5037	TT,TC,CC		5.7791,25.5334,12.4712	benign	137/457	2877365	1622,11384	2203	4300	6503	SO:0001583	missense	80032	exon4			CATCTGCGCAAGA	BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"""Zinc fingers, C2H2-type"", ""-"""	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.409C>T	19.37:g.2877365C>T	ENSP00000302603:p.Arg137Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_024967	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	37	CCDS12097.1	186	0.08516483516483517	115	0.23373983739837398	27	0.07458563535911603	1	0.0017482517482517483	43	0.05672823218997362	C	11.41	1.631765	0.29068	0.255334	0.057791	ENSG00000172000	ENST00000307635	T	0.06142	3.34	1.95	-1.8	0.07907	.	.	.	.	.	T	0.00012	0.0000	L	0.39245	1.2	0.80722	P	0.0	P	0.46952	0.887	B	0.23419	0.046	T	0.48559	-0.9025	8	0.87932	D	0	.	6.0856	0.19964	0.0:0.6044:0.0:0.3956	rs10421121;rs10421121	137	Q9HAH1	ZN556_HUMAN	C	137	ENSP00000302603:R137C	ENSP00000302603:R137C	R	+	1	0	ZNF556	2828365	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.315000	0.08081	-0.540000	0.06265	-0.501000	0.04562	CGC	C|0.889;T|0.111	0.111	strong		0.423	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967	
MT-ND1	4535	hgsc.bcm.edu	37	M	3594	3594	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:3594C>T	ENST00000361390.2	+	1	288	c.288C>T	c.(286-288)gtC>gtT	p.V96V	MT-TN_ENST00000387400.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-TM_ENST00000387377.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TA_ENST00000387392.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TF_ENST00000387314.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-ND2_ENST00000361453.3_5'Flank			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	96					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AACCCCCTGGTCAACCTCAAC	0.542																																					p.V96V		Atlas-SNP	.											.	.	.	.	0			c.C288T						PASS	.																																			SO:0001819	synonymous_variant	10625	exon1			CCTGGTCAACCTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.288C>T	M.37:g.3594C>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	ENST00000361390	C0JKH6|Q37523	Silent	SNP	ENST00000361390.2	37																																																																																				.	.	none		0.542	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
ARHGEF16	27237	hgsc.bcm.edu	37	1	3397062	3397062	+	Missense_Mutation	SNP	G	G	A	rs56309807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3397062G>A	ENST00000378378.4	+	15	2446	c.2041G>A	c.(2041-2043)Gag>Aag	p.E681K	ARHGEF16_ENST00000378371.2_Missense_Mutation_p.E393K|ARHGEF16_ENST00000378373.1_Missense_Mutation_p.E393K|ARHGEF16_ENST00000413250.2_Missense_Mutation_p.E385K	NM_014448.3	NP_055263.2	Q5VV41	ARHGG_HUMAN	Rho guanine nucleotide exchange factor (GEF) 16	681	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.		E -> K (in dbSNP:rs56309807).		activation of Cdc42 GTPase activity (GO:0032864)|activation of Rac GTPase activity (GO:0032863)|apoptotic signaling pathway (GO:0097190)|cell chemotaxis (GO:0060326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	PDZ domain binding (GO:0030165)|receptor tyrosine kinase binding (GO:0030971)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			lung(6)|ovary(1)	7	all_cancers(77;0.00276)|all_epithelial(69;0.00102)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.101)	all_epithelial(116;7.14e-21)|all_lung(118;2.24e-08)|Lung NSC(185;3.55e-06)|Breast(487;0.000765)|Renal(390;0.00121)|Hepatocellular(190;0.0046)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.211)		Epithelial(90;8.62e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.62e-22)|GBM - Glioblastoma multiforme(42;2.49e-12)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000681)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		ATGGTTCCCCGAGGACTTTGC	0.677													G|||	96	0.0191693	0.0318	0.0245	5008	,	,		17786	0.0		0.0368	False		,,,				2504	0.0				p.E681K		Atlas-SNP	.											.	ARHGEF16	76	.	0			c.G2041A						PASS	.	G	LYS/GLU	132,4272	92.5+/-131.2	3,126,2073	56.0	50.0	52.0		2041	4.1	1.0	1	dbSNP_129	52	197,8399	84.8+/-147.2	2,193,4103	yes	missense	ARHGEF16	NM_014448.3	56	5,319,6176	AA,AG,GG		2.2918,2.9973,2.5308	benign	681/710	3397062	329,12671	2202	4298	6500	SO:0001583	missense	27237	exon15			TTCCCCGAGGACT	D89016	CCDS46.2	1p36.3	2013-01-10	2010-04-13		ENSG00000130762	ENSG00000130762		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	15515	protein-coding gene	gene with protein product	"""putative neuroblastoma protein"""						Standard	NM_014448		Approved	NBR, GEF16	uc001akg.4	Q5VV41	OTTHUMG00000000625	ENST00000378378.4:c.2041G>A	1.37:g.3397062G>A	ENSP00000367629:p.Glu681Lys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	38	22	0.578947	NM_014448	Q86TF0|Q99434	Missense_Mutation	SNP	ENST00000378378.4	37	CCDS46.2	61	0.027930402930402932	22	0.044715447154471545	12	0.03314917127071823	0	0.0	27	0.03562005277044855	G	6.140	0.394127	0.11638	0.029973	0.022918	ENSG00000130762	ENST00000378378;ENST00000378373;ENST00000378371;ENST00000413250	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.06	4.14	0.48551	Src homology-3 domain (3);	0.128564	0.52532	D	0.000067	T	0.09905	0.0243	L	0.31526	0.94	0.41321	D	0.987175	B;B	0.27765	0.188;0.188	B;B	0.29862	0.108;0.067	T	0.03034	-1.1080	10	0.07325	T	0.83	-26.4072	14.8718	0.70462	0.0:0.3416:0.6584:0.0	rs56309807;rs61759243	385;681	B4DJM7;Q5VV41	.;ARHGG_HUMAN	K	681;393;393;385	ENSP00000367629:E681K;ENSP00000367624:E393K;ENSP00000367622:E393K;ENSP00000408887:E385K	ENSP00000367622:E393K	E	+	1	0	ARHGEF16	3386922	0.998000	0.40836	0.989000	0.46669	0.256000	0.26092	2.935000	0.48963	1.129000	0.42072	-0.467000	0.05162	GAG	G|0.974;A|0.026	0.026	strong		0.677	ARHGEF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001515.1	NM_014448	
SLC38A8	146167	hgsc.bcm.edu	37	16	84056442	84056442	+	Missense_Mutation	SNP	G	G	C	rs11861325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84056442G>C	ENST00000299709.3	-	6	742	c.743C>G	c.(742-744)tCc>tGc	p.S248C		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	248					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						GGCCCAGTGGGAGAGGCTCCG	0.617													G|||	179	0.0357428	0.1271	0.0115	5008	,	,		17454	0.0		0.001	False		,,,				2504	0.002				p.S248C		Atlas-SNP	.											.	SLC38A8	60	.	0			c.C743G						PASS	.	G	CYS/SER	463,3937	217.1+/-235.6	27,409,1764	84.0	67.0	73.0		743	1.0	0.0	16	dbSNP_120	73	4,8596	3.0+/-9.4	0,4,4296	yes	missense	SLC38A8	NM_001080442.1	112	27,413,6060	CC,CG,GG		0.0465,10.5227,3.5923	probably-damaging	248/436	84056442	467,12533	2200	4300	6500	SO:0001583	missense	146167	exon6			CAGTGGGAGAGGC		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.743C>G	16.37:g.84056442G>C	ENSP00000299709:p.Ser248Cys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_001080442		Missense_Mutation	SNP	ENST00000299709.3	37	CCDS32495.1	71	0.03250915750915751	65	0.13211382113821138	6	0.016574585635359115	0	0.0	0	0.0	G	9.359	1.067547	0.20067	0.105227	4.65E-4	ENSG00000166558	ENST00000299709	T	0.02421	4.3	5.37	0.968	0.19680	.	0.403682	0.28322	N	0.015761	T	0.00109	0.0003	M	0.67953	2.075	0.43114	D	0.994829	D	0.65815	0.995	P	0.61800	0.894	T	0.12344	-1.0551	10	0.62326	D	0.03	.	10.254	0.43385	0.0736:0.4038:0.5226:0.0	rs11861325	248	A6NNN8	S38A8_HUMAN	C	248	ENSP00000299709:S248C	ENSP00000299709:S248C	S	-	2	0	SLC38A8	82613943	0.961000	0.32948	0.019000	0.16419	0.034000	0.12701	4.054000	0.57434	-0.033000	0.13736	0.549000	0.68633	TCC	G|0.961;C|0.039	0.039	strong		0.617	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18649057	18649057	+	Missense_Mutation	SNP	C	C	T	rs12312266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18649057C>T	ENST00000266497.5	+	19	2770	c.2732C>T	c.(2731-2733)cCg>cTg	p.P911L	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.P911L|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.P952L			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	911			P -> L (in dbSNP:rs12312266). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9878262, ECO:0000269|Ref.3}.		chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				AATGCTAATCCGATGGGCAAA	0.323													C|||	1875	0.374401	0.5008	0.366	5008	,	,		18017	0.3046		0.2425	False		,,,				2504	0.4172				p.P911L		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.C2732T						PASS	.	C	LEU/PRO	1621,2027		369,883,572	103.0	89.0	94.0		2732	4.4	1.0	12	dbSNP_120	94	1837,6305		236,1365,2470	yes	missense	PIK3C2G	NM_004570.4	98	605,2248,3042	TT,TC,CC		22.562,44.4353,29.3299	probably-damaging	911/1446	18649057	3458,8332	1824	4071	5895	SO:0001583	missense	5288	exon20			CTAATCCGATGGG	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2732C>T	12.37:g.18649057C>T	ENSP00000266497:p.Pro911Leu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	703	0.3218864468864469	218	0.44308943089430897	129	0.356353591160221	178	0.3111888111888112	178	0.23482849604221637	C	24.1	4.498890	0.85069	0.444353	0.22562	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	D;D;D	0.81908	-1.55;-1.55;-1.55	4.37	4.37	0.52481	Protein kinase-like domain (1);	0.071120	0.56097	D	0.000035	T	0.00012	0.0000	M	0.78456	2.415	0.09310	P	0.99999999684936	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.94	T	0.00768	-1.1574	9	0.59425	D	0.04	-16.2062	16.7234	0.85416	0.0:1.0:0.0:0.0	rs12312266;rs17847799;rs52825188;rs58825824;rs12312266	952;911	F5H369;O75747	.;P3C2G_HUMAN	L	911;911;952	ENSP00000404845:P911L;ENSP00000266497:P911L;ENSP00000445381:P952L	ENSP00000266497:P911L	P	+	2	0	PIK3C2G	18540324	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.384000	0.66225	2.724000	0.93272	0.650000	0.86243	CCG	C|0.665;N|0.000	.	strong		0.323	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
SLC44A4	80736	hgsc.bcm.edu	37	6	31838713	31838713	+	Silent	SNP	G	G	A	rs494620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31838713G>A	ENST00000229729.6	-	10	833	c.813C>T	c.(811-813)taC>taT	p.Y271Y	SLC44A4_ENST00000544672.1_Silent_p.Y195Y|SLC44A4_ENST00000375562.4_Silent_p.Y229Y	NM_025257.2	NP_079533.2	Q53GD3	CTL4_HUMAN	solute carrier family 44, member 4	271					acetylcholine biosynthetic process (GO:0008292)|acetylcholine secretion (GO:0061526)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of cell growth (GO:0030307)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(1)|urinary_tract(2)	35					Choline(DB00122)	AGTAGATGCCGTATGCCAGCA	0.617													G|||	2157	0.430711	0.4319	0.4683	5008	,	,		18737	0.4206		0.4513	False		,,,				2504	0.3916				p.Y271Y		Atlas-SNP	.											.	SLC44A4	67	.	0			c.C813T						PASS	.	G	,,	1287,1735		275,737,499	59.0	46.0	51.0	http://www.ncbi.nlm.nih.gov/pubmed?term	687,585,813	-2.5	0.9	6	dbSNP_83	51	2241,3177		472,1297,940	yes	coding-synonymous,coding-synonymous,coding-synonymous	SLC44A4	NM_001178044.1,NM_001178045.1,NM_025257.2	,,	747,2034,1439	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	41.3621,42.5877,41.8009	,,	229/669,195/635,271/711	31838713	3528,4912	1511	2709	4220	SO:0001819	synonymous_variant	80736	exon10			GATGCCGTATGCC	AF134726	CCDS4724.2, CCDS54989.1, CCDS54990.1	6p21.3	2014-02-17	2005-09-06	2005-09-06	ENSG00000204385	ENSG00000204385		"""Solute carriers"""	13941	protein-coding gene	gene with protein product		606107	"""chromosome 6 open reading frame 29"""	C6orf29		10677542, 15715662, 24379411	Standard	NM_025257		Approved	NG22, CTL4, FLJ14491, TPPT	uc010jti.3	Q53GD3	OTTHUMG00000031133	ENST00000229729.6:c.813C>T	6.37:g.31838713G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_025257	A2BED3|B0UXX8|B0UZY8|B4DU94|B4DWM2|E9PEK7|Q5JP84|Q5JQ93|Q658S8|Q6UX89|Q8TEW4|Q96C58|Q96K59|Q9Y332	Silent	SNP	ENST00000229729.6	37	CCDS4724.2																																																																																			G|0.559;A|0.441	0.441	strong		0.617	SLC44A4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076234.3		
MUC4	4585	hgsc.bcm.edu	37	3	195515161	195515161	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515161G>T	ENST00000463781.3	-	2	3749	c.3290C>A	c.(3289-3291)gCa>gAa	p.A1097E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1097E	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	529					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.A1097V(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)		ACCTGTGGATGCTGAGGAAGT	0.572																																					p.A1097E		Atlas-SNP	.											MUC4_ENST00000463781,trunk,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	skin(2)	c.C3290A						scavenged	.						15.0	11.0	12.0					3																	195515161		674	1566	2240	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	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.3290C>A	3.37:g.195515161G>T	ENSP00000417498:p.Ala1097Glu	Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	369	4	0.0108401	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	.	.	.	.	.	.	.	.	.	.	-	2.884	-0.231264	0.05983	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.47;1.46	0.706	-1.41	0.08941	.	.	.	.	.	T	0.23806	0.0576	N	0.19112	0.55	0.09310	N	1	D	0.55385	0.971	P	0.55749	0.783	T	0.24548	-1.0157	8	.	.	.	.	0.3496	0.00346	0.3512:0.1907:0.2672:0.1909	.	1097	E7ESK3	.	E	1097	ENSP00000417498:A1097E;ENSP00000420243:A1097E	.	A	-	2	0	MUC4	196999556	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-4.344000	0.00249	-3.280000	0.00197	-2.092000	0.00371	GCA	.	.	none		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZFP42	132625	hgsc.bcm.edu	37	4	188924450	188924450	+	Silent	SNP	A	A	G	rs61731386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:188924450A>G	ENST00000326866.4	+	4	897	c.489A>G	c.(487-489)tcA>tcG	p.S163S	ZFP42_ENST00000509524.1_Silent_p.S163S	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	163					female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		TTGACCTATCAGATCCTAAAC	0.453													A|||	187	0.0373403	0.1362	0.0086	5008	,	,		17571	0.0		0.001	False		,,,				2504	0.0				p.S163S		Atlas-SNP	.											.	ZFP42	87	.	0			c.A489G						PASS	.	A		449,3957	202.5+/-225.2	25,399,1779	103.0	116.0	112.0		489	-1.9	0.0	4	dbSNP_129	112	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZFP42	NM_174900.3		25,401,6077	GG,GA,AA		0.0233,10.1906,3.4676		163/311	188924450	451,12555	2203	4300	6503	SO:0001819	synonymous_variant	132625	exon4			CCTATCAGATCCT	AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059		"""Zinc fingers, C2H2-type"""	30949	protein-coding gene	gene with protein product		614572	"""zinc finger protein 42 homolog (mouse)"", ""zinc finger protein 42"""			12110702	Standard	NM_174900		Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.489A>G	4.37:g.188924450A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	60	37	0.616667	NM_174900	D3DP65|Q8WXE2	Silent	SNP	ENST00000326866.4	37	CCDS3849.1																																																																																			A|0.972;G|0.028	0.028	strong		0.453	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900	
MRC1	4360	hgsc.bcm.edu	37	10	18122716	18122716	+	Silent	SNP	A	A	G	rs111490411		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:18122716A>G	ENST00000239761.3	+	4	829	c.726A>G	c.(724-726)caA>caG	p.Q242Q		NM_002438.2	NP_002429.1	P22897	MRC1_HUMAN	mannose receptor, C type 1	242	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.				receptor-mediated endocytosis (GO:0006898)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	mannose binding (GO:0005537)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|kidney(1)|lung(2)|prostate(1)|urinary_tract(1)	6						CGTGGCACCAAGCGAGGAAAA	0.468																																					p.Q242Q	GBM(115;1153 1594 28187 28781 35884)	Atlas-SNP	.											.	MRC1	13	.	0			c.G726G						PASS	.	G		250,2932		90,70,1431	90.0	79.0	83.0		726	2.6	1.0	10	dbSNP_132	83	1642,5476		728,186,2645	no	coding-synonymous	MRC1	NM_002438.2		818,256,4076	GG,GA,AA		23.0683,7.8567,18.3689		242/1457	18122716	1892,8408	1591	3559	5150	SO:0001819	synonymous_variant	4360	exon4			GCACCAAGCGAGG	J05550	CCDS7123.1, CCDS7123.2	10p13	2014-04-10			ENSG00000120586	ENSG00000260314		"""CD molecules"", ""C-type lectin domain containing"""	7228	protein-coding gene	gene with protein product		153618	"""mannose receptor, C type 1-like 1"""	MRC1L1		1294118	Standard	NM_002438		Approved	CLEC13D, CD206, bA541I19.1, CLEC13DL	uc031ptj.1	P22897	OTTHUMG00000174646	ENST00000239761.3:c.726A>G	10.37:g.18122716A>G		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_002438	A5PKW3|Q5VSJ2|Q5VSK2	Silent	SNP	ENST00000239761.3	37	CCDS7123.1																																																																																			A|0.250;G|0.750	0.750	weak		0.468	MRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047057.1	NM_002438	
CLASP1	23332	hgsc.bcm.edu	37	2	122216419	122216419	+	Silent	SNP	A	A	G	rs2304560	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:122216419A>G	ENST00000263710.4	-	13	1700	c.1311T>C	c.(1309-1311)atT>atC	p.I437I	CLASP1_ENST00000455322.2_Silent_p.I437I|CLASP1_ENST00000541377.1_Silent_p.I437I|CLASP1_ENST00000545861.1_Silent_p.I205I|CLASP1_ENST00000430234.1_5'Flank|CLASP1_ENST00000409078.3_Silent_p.I437I|CLASP1_ENST00000397587.3_Silent_p.I437I|CLASP1_ENST00000541859.1_Silent_p.I206I	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	437					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)					TACTTACCCGAATAATTAACC	0.338													A|||	1277	0.254992	0.5968	0.1369	5008	,	,		17301	0.131		0.0656	False		,,,				2504	0.1994				p.I437I		Atlas-SNP	.											.	CLASP1	135	.	0			c.T1311C						PASS	.	A	,,,	1798,1880		431,936,472	71.0	71.0	71.0		1311,1311,1311,1311	0.4	1.0	2	dbSNP_100	71	622,7570		15,592,3489	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLASP1	NM_001142273.1,NM_001142274.1,NM_001207051.1,NM_015282.2	,,,	446,1528,3961	GG,GA,AA		7.5928,48.8853,20.3875	,,,	437/1480,437/1472,437/1478,437/1539	122216419	2420,9450	1839	4096	5935	SO:0001819	synonymous_variant	23332	exon13			TACCCGAATAATT	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.1311T>C	2.37:g.122216419A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001207051	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Silent	SNP	ENST00000263710.4	37																																																																																				A|0.779;G|0.221	0.221	strong		0.338	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282	
FLG	2312	hgsc.bcm.edu	37	1	152280736	152280736	+	Missense_Mutation	SNP	T	T	C	rs66977240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152280736T>C	ENST00000368799.1	-	3	6661	c.6626A>G	c.(6625-6627)cAt>cGt	p.H2209R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	451	0	0		WXS	Illumina HiSeq	Phase_I	657	218	0.331811	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	
WNK4	65266	hgsc.bcm.edu	37	17	40946913	40946913	+	Missense_Mutation	SNP	C	C	T	rs56226218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40946913C>T	ENST00000246914.5	+	14	2495	c.2474C>T	c.(2473-2475)cCa>cTa	p.P825L		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	825					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CCCATTTCCCCAGGTCCCATC	0.577													C|||	140	0.0279553	0.1021	0.0072	5008	,	,		15756	0.0		0.0	False		,,,				2504	0.0				p.P825L	Esophageal Squamous(6;201 374 4964 23855 42828)	Atlas-SNP	.											.	WNK4	182	.	0			c.C2474T						PASS	.	C	LEU/PRO	391,4015	196.4+/-220.7	17,357,1829	135.0	123.0	127.0		2474	4.6	0.9	17	dbSNP_129	127	1,8599	1.2+/-3.3	0,1,4299	yes	missense	WNK4	NM_032387.4	98	17,358,6128	TT,TC,CC		0.0116,8.8743,3.014	benign	825/1244	40946913	392,12614	2203	4300	6503	SO:0001583	missense	65266	exon14			TTTCCCCAGGTCC	AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.2474C>T	17.37:g.40946913C>T	ENSP00000246914:p.Pro825Leu	Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	279	145	0.519713	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Missense_Mutation	SNP	ENST00000246914.5	37	CCDS11439.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	12.50	1.956295	0.34565	0.088743	1.16E-4	ENSG00000126562	ENST00000246914;ENST00000316085	T	0.73363	-0.74	5.58	4.59	0.56863	.	0.143817	0.32301	N	0.006288	T	0.04588	0.0125	L	0.29908	0.895	0.47659	D	0.999481	B;B;B	0.32653	0.379;0.261;0.006	B;B;B	0.28553	0.091;0.042;0.012	T	0.14587	-1.0467	10	0.51188	T	0.08	-4.1586	8.3488	0.32290	0.1564:0.7652:0.0:0.0784	rs56226218;rs61755625	825;825;825	Q96J92-3;B0LPI0;Q96J92	.;.;WNK4_HUMAN	L	825;597	ENSP00000246914:P825L	ENSP00000246914:P825L	P	+	2	0	WNK4	38200439	0.989000	0.36119	0.913000	0.36048	0.211000	0.24417	3.653000	0.54446	1.444000	0.47605	0.591000	0.81541	CCA	C|0.974;T|0.026	0.026	strong		0.577	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
CDC25C	995	hgsc.bcm.edu	37	5	137665323	137665323	+	Missense_Mutation	SNP	G	G	A	rs3734166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:137665323G>A	ENST00000323760.6	-	3	486	c.208C>T	c.(208-210)Cgt>Tgt	p.R70C	CDC25C_ENST00000514555.1_Missense_Mutation_p.R70C|CDC25C_ENST00000356505.3_Missense_Mutation_p.R70C|CDC25C_ENST00000357274.3_Intron|CDC25C_ENST00000348983.3_Intron|CDC25C_ENST00000415130.2_Intron|CDC25C_ENST00000513970.1_Missense_Mutation_p.R70C	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	70			R -> C (in dbSNP:rs3734166). {ECO:0000269|PubMed:11139144, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2195549}.		cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)			endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			TCGAGGCAACGTTTTGGGGTT	0.398													G|||	1954	0.390176	0.4773	0.2983	5008	,	,		19081	0.6101		0.3072	False		,,,				2504	0.1963				p.R70C		Atlas-SNP	.											.	CDC25C	37	.	0			c.C208T						PASS	.	G	CYS/ARG,	1964,2442	553.9+/-378.9	435,1094,674	124.0	119.0	121.0		208,	-1.0	1.0	5	dbSNP_107	121	2388,6212	396.6+/-345.4	337,1714,2249	yes	missense,intron	CDC25C	NM_001790.3,NM_022809.2	180,	772,2808,2923	AA,AG,GG		27.7674,44.5756,33.4615	benign,	70/474,	137665323	4352,8654	2203	4300	6503	SO:0001583	missense	995	exon3			GGCAACGTTTTGG	M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1727	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 60"""	157680	"""cell division cycle 25C"", ""cell division cycle 25 homolog C (S. cerevisiae)"", ""cell division cycle 25 homolog C (S. pombe)"""	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.208C>T	5.37:g.137665323G>A	ENSP00000321656:p.Arg70Cys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	37	CCDS4202.1	889	0.40705128205128205	230	0.46747967479674796	96	0.26519337016574585	333	0.5821678321678322	230	0.3034300791556728	G	12.56	1.973598	0.34848	0.445756	0.277674	ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000513970;ENST00000534892;ENST00000514555;ENST00000503022;ENST00000510119	T;T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64;1.64	4.4	-0.963	0.10330	.	0.512067	0.18564	N	0.137526	T	0.00012	0.0000	N	0.04297	-0.235	0.09310	P	0.999999838467	B;B;B;B	0.14012	0.009;0.005;0.001;0.003	B;B;B;B	0.06405	0.002;0.001;0.001;0.001	T	0.42599	-0.9442	9	0.37606	T	0.19	0.0708	7.8092	0.29221	0.6152:0.0:0.3848:0.0	rs3734166;rs17851708;rs57255403;rs3734166	87;87;70;70	G3V1P6;B4DX61;P30307-2;P30307	.;.;.;MPIP3_HUMAN	C	70;70;70;87;70;70;87	ENSP00000321656:R70C;ENSP00000348898:R70C;ENSP00000424795:R70C;ENSP00000425470:R70C;ENSP00000427251:R70C;ENSP00000427105:R87C	ENSP00000321656:R70C	R	-	1	0	CDC25C	137693222	0.513000	0.26194	0.993000	0.49108	0.961000	0.63080	-0.842000	0.04354	-0.138000	0.11434	0.563000	0.77884	CGT	A|0.359;C|0.003	0.359	strong		0.398	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1		
HELZ2	85441	hgsc.bcm.edu	37	20	62198713	62198713	+	Silent	SNP	G	G	A	rs3810490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62198713G>A	ENST00000467148.1	-	6	2067	c.1998C>T	c.(1996-1998)atC>atT	p.I666I	HELZ2_ENST00000427522.2_Silent_p.I97I|HELZ2_ENST00000479540.1_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	666	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)										CCGCCTCATCGATGAGAATGT	0.697													G|||	899	0.179513	0.4054	0.1369	5008	,	,		15559	0.0317		0.0666	False		,,,				2504	0.1728				p.I666I		Atlas-SNP	.											.	.	.	.	0			c.C1998T						PASS	.	G	,	1404,2904		233,938,983	14.0	17.0	16.0		1998,291	-7.9	0.7	20	dbSNP_107	16	611,7903		15,581,3661	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	248,1519,4644	AA,AG,GG		7.1764,32.5905,15.7152	,	666/2650,97/2081	62198713	2015,10807	2154	4257	6411	SO:0001819	synonymous_variant	85441	exon7			CTCATCGATGAGA	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.1998C>T	20.37:g.62198713G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			G|0.846;A|0.154	0.154	strong		0.697	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
GABRR1	2569	hgsc.bcm.edu	37	6	89926962	89926962	+	Missense_Mutation	SNP	T	T	C	rs1186902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:89926962T>C	ENST00000454853.2	-	1	190	c.80A>G	c.(79-81)cAc>cGc	p.H27R	GABRR1_ENST00000435811.1_Missense_Mutation_p.H27R|GABRR1_ENST00000481493.1_5'UTR|GABRR1_ENST00000369451.3_Intron	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	206	0	0		WXS	Illumina HiSeq	Phase_I	207	113	0.545894	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		
HS1BP3	64342	hgsc.bcm.edu	37	2	20838318	20838318	+	Silent	SNP	G	G	A	rs3796064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20838318G>A	ENST00000304031.3	-	4	526	c.501C>T	c.(499-501)ttC>ttT	p.F167F	HS1BP3_ENST00000402541.1_Silent_p.F167F	NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	167							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAAAAAGTCGAAAGCCTCTT	0.587													G|||	1798	0.359026	0.2292	0.3055	5008	,	,		19367	0.5565		0.2763	False		,,,				2504	0.454				p.F167F		Atlas-SNP	.											.	HS1BP3	33	.	0			c.C501T						PASS	.	G		985,3421	367.3+/-318.2	117,751,1335	155.0	141.0	146.0		501	-8.4	0.8	2	dbSNP_107	146	2254,6346	381.0+/-339.9	298,1658,2344	no	coding-synonymous	HS1BP3	NM_022460.3		415,2409,3679	AA,AG,GG		26.2093,22.3559,24.9039		167/393	20838318	3239,9767	2203	4300	6503	SO:0001819	synonymous_variant	64342	exon4			AAAGTCGAAAGCC		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.501C>T	2.37:g.20838318G>A		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	337	163	0.48368	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	37	CCDS1700.1																																																																																			G|0.702;A|0.298	0.298	strong		0.587	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
MATN2	4147	hgsc.bcm.edu	37	8	98991223	98991223	+	Silent	SNP	A	A	G	rs1869608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:98991223A>G	ENST00000520016.1	+	5	1192	c.1068A>G	c.(1066-1068)aaA>aaG	p.K356K	MATN2_ENST00000254898.5_Silent_p.K356K|MATN2_ENST00000522025.2_Silent_p.K72K|MATN2_ENST00000524308.1_Silent_p.K356K|MATN2_ENST00000521689.1_Silent_p.K356K			O00339	MATN2_HUMAN	matrilin 2	356	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.		K -> E (in dbSNP:rs1869609). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			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)			ACCCAGATAAAAAAACGTGCA	0.433													A|||	1240	0.247604	0.3343	0.3156	5008	,	,		20904	0.1667		0.1322	False		,,,				2504	0.2843				p.K356K		Atlas-SNP	.											.	MATN2	165	.	0			c.A1068G						PASS	.	A	,	1136,2982		161,814,1084	109.0	104.0	106.0		1068,1068	-1.5	0.1	8	dbSNP_92	106	1402,7024		118,1166,2929	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	279,1980,4013	GG,GA,AA		16.639,27.5862,20.2328	,	356/957,356/938	98991223	2538,10006	2059	4213	6272	SO:0001819	synonymous_variant	4147	exon6			AGATAAAAAAACG	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.1068A>G	8.37:g.98991223A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	493	0.22573260073260074	185	0.37601626016260165	98	0.27071823204419887	100	0.17482517482517482	110	0.14511873350923482	A	5.448	0.267698	0.10294	0.275862	0.16639	ENSG00000132561	ENST00000518154;ENST00000521041	D;D	0.96491	-4.03;-4.03	5.49	-1.46	0.08800	.	0.398494	0.23838	N	0.044079	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999800825	.	.	.	.	.	.	T	0.00538	-1.1682	6	0.31617	T	0.26	-2.6418	10.083	0.42401	0.6016:0.0:0.3984:0.0	rs1869608;rs1869608	.	.	.	E	139;111	ENSP00000429622:K139E;ENSP00000430396:K111E	ENSP00000429622:K139E	K	+	1	0	MATN2	99060399	0.023000	0.18921	0.136000	0.22124	0.578000	0.36192	0.039000	0.13884	-0.503000	0.06586	0.533000	0.62120	AAA	A|0.775;G|0.225	0.225	strong		0.433	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
H6PD	9563	hgsc.bcm.edu	37	1	9324571	9324571	+	Silent	SNP	T	T	C	rs9434742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	139	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	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	
RFPL4A	342931	hgsc.bcm.edu	37	19	56274214	56274214	+	Silent	SNP	G	G	T	rs114470138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56274214G>T	ENST00000434937.2	+	3	708	c.537G>T	c.(535-537)gtG>gtT	p.V179V		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	179	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						GGAAGATTGTGCTTTCTTCAG	0.562													G|||	149	0.0297524	0.0658	0.0389	5008	,	,		20714	0.0		0.0239	False		,,,				2504	0.0112				p.V179V		Atlas-SNP	.											.	RFPL4A	8	.	0			c.G537T						PASS	.						76.0	61.0	66.0					19																	56274214		685	1535	2220	SO:0001819	synonymous_variant	342931	exon3			GATTGTGCTTTCT		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.537G>T	19.37:g.56274214G>T		Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	547	213	0.389397	NM_001145014		Silent	SNP	ENST00000434937.2	37	CCDS46201.1																																																																																			G|0.970;T|0.030	0.030	strong		0.562	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384184.1	XM_292796	
PIGN	23556	hgsc.bcm.edu	37	18	59821843	59821843	+	Missense_Mutation	SNP	T	T	C	rs17069506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:59821843T>C	ENST00000357637.5	-	7	899	c.484A>G	c.(484-486)Aaa>Gaa	p.K162E	PIGN_ENST00000400334.3_Missense_Mutation_p.K162E	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	162			K -> E (in dbSNP:rs17069506).		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)				TCCTCTCTTTTAGCATCATAA	0.303													T|||	327	0.0652955	0.0825	0.0389	5008	,	,		16581	0.0724		0.0467	False		,,,				2504	0.0726				p.K162E		Atlas-SNP	.											.	PIGN	62	.	0			c.A484G						PASS	.	T	GLU/LYS,GLU/LYS	273,3391		9,255,1568	142.0	136.0	138.0		484,484	-2.9	0.0	18	dbSNP_123	138	331,7837		6,319,3759	yes	missense,missense	PIGN	NM_012327.5,NM_176787.4	56,56	15,574,5327	CC,CT,TT		4.0524,7.4509,5.1048	benign,benign	162/932,162/932	59821843	604,11228	1832	4084	5916	SO:0001583	missense	23556	exon7			CTCTTTTAGCATC	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.484A>G	18.37:g.59821843T>C	ENSP00000350263:p.Lys162Glu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Missense_Mutation	SNP	ENST00000357637.5	37	CCDS45879.1	125	0.05723443223443223	37	0.07520325203252033	18	0.049723756906077346	42	0.07342657342657342	28	0.036939313984168866	T	0.987	-0.695342	0.03303	0.074509	0.040524	ENSG00000197563	ENST00000357637;ENST00000400334	T;T	0.27720	1.65;1.65	5.85	-2.88	0.05682	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.586428	0.18563	N	0.137575	T	0.00210	0.0006	N	0.00025	-2.675	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.0	T	0.33137	-0.9880	9	.	.	.	2.542	1.8886	0.03243	0.1166:0.2771:0.3274:0.2789	rs17069506;rs52830051;rs17069506	162;162	B2RCI8;O95427	.;PIGN_HUMAN	E	162	ENSP00000350263:K162E;ENSP00000383188:K162E	.	K	-	1	0	PIGN	57972823	0.000000	0.05858	0.000000	0.03702	0.583000	0.36354	0.014000	0.13333	-0.998000	0.03446	0.533000	0.62120	AAA	T|0.938;C|0.062	0.062	strong		0.303	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
HADHB	3032	hgsc.bcm.edu	37	2	26505745	26505745	+	Silent	SNP	G	G	A	rs7572240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26505745G>A	ENST00000317799.5	+	11	1070	c.966G>A	c.(964-966)gcG>gcA	p.A322A	HADHB_ENST00000494615.1_3'UTR|HADHB_ENST00000405867.3_Silent_p.A199A|HADHB_ENST00000545822.1_Silent_p.A300A|HADHB_ENST00000537713.1_Silent_p.A307A	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	322					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)					TAATCATGGCGGAGGAAAAGG	0.388													g|||	101	0.0201677	0.0726	0.0043	5008	,	,		18252	0.0		0.002	False		,,,				2504	0.0				p.A322A		Atlas-SNP	.											.	HADHB	50	.	0			c.G966A						PASS	.	G		268,4138	151.0+/-185.0	6,256,1941	91.0	87.0	89.0		966	-8.4	0.7	2	dbSNP_116	89	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	HADHB	NM_000183.2		6,260,6237	AA,AG,GG		0.0465,6.0826,2.0913		322/475	26505745	272,12734	2203	4300	6503	SO:0001819	synonymous_variant	3032	exon11			CATGGCGGAGGAA		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.966G>A	2.37:g.26505745G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Silent	SNP	ENST00000317799.5	37	CCDS1722.1																																																																																			G|0.982;A|0.018	0.018	strong		0.388	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183	
CD3EAP	10849	hgsc.bcm.edu	37	19	45912002	45912002	+	Missense_Mutation	SNP	A	A	C	rs735482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45912002A>C	ENST00000309424.3	+	3	1264	c.776A>C	c.(775-777)aAa>aCa	p.K259T	ERCC1_ENST00000588738.1_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.K261T|ERCC1_ENST00000423698.2_3'UTR|PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000300853.3_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	259			K -> T (in dbSNP:rs735482).		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)		CCCAAAGGGAAAGAAACCTTC	0.547													C|||	1436	0.286741	0.3109	0.2233	5008	,	,		15739	0.4613		0.1322	False		,,,				2504	0.2781				p.K259T		Atlas-SNP	.											.	CD3EAP	27	.	0			c.A776C						PASS	.	C	,,THR/LYS	1193,3213	689.1+/-405.1	169,855,1179	67.0	70.0	69.0		,,776	-1.8	0.0	19	dbSNP_86	69	1160,7440	741.9+/-407.2	81,998,3221	yes	utr-3,utr-3,missense	ERCC1,CD3EAP	NM_001166049.1,NM_001983.3,NM_012099.1	,,78	250,1853,4400	CC,CA,AA		13.4884,27.0767,18.0917	,,benign	,,259/511	45912002	2353,10653	2203	4300	6503	SO:0001583	missense	10849	exon3			AAGGGAAAGAAAC	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.776A>C	19.37:g.45912002A>C	ENSP00000310966:p.Lys259Thr	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	570	0.260989010989011	131	0.266260162601626	72	0.19889502762430938	259	0.4527972027972028	108	0.1424802110817942	C	8.088	0.773935	0.16051	0.270767	0.134884	ENSG00000117877	ENST00000309424	T	0.11495	2.77	5.06	-1.76	0.08006	.	0.717583	0.12315	N	0.479769	T	0.00012	0.0000	N	0.00621	-1.32	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42749	-0.9433	9	0.14656	T	0.56	0.2029	1.8433	0.03154	0.1195:0.3621:0.259:0.2595	rs735482;rs61340218;rs735482	261;259	O15446-2;O15446	.;RPA34_HUMAN	T	259	ENSP00000310966:K259T	ENSP00000310966:K259T	K	+	2	0	CD3EAP	50603842	0.006000	0.16342	0.007000	0.13788	0.245000	0.25701	0.192000	0.17096	-0.095000	0.12351	-0.217000	0.12591	AAA	A|0.771;C|0.229	0.229	strong		0.547	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
GOLM1	51280	hgsc.bcm.edu	37	9	88650332	88650332	+	Missense_Mutation	SNP	C	C	G	rs61741197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:88650332C>G	ENST00000388712.3	-	8	1134	c.966G>C	c.(964-966)caG>caC	p.Q322H	GOLM1_ENST00000257504.6_5'Flank|GOLM1_ENST00000388711.3_Missense_Mutation_p.Q322H	NM_016548.3	NP_057632.2	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	322					nucleus organization (GO:0006997)|regulation of lipid metabolic process (GO:0019216)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17						GGATGACAAGCTGGTCTCGCT	0.652											OREG0019278	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	249	0.0497204	0.1823	0.0115	5008	,	,		15263	0.0		0.0	False		,,,				2504	0.0				p.Q322H		Atlas-SNP	.											.	GOLM1	36	.	0			c.G966C						PASS	.	C	HIS/GLN,HIS/GLN	673,3733	284.6+/-277.7	59,555,1589	76.0	84.0	81.0		966,966	2.7	1.0	9	dbSNP_129	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	GOLM1	NM_016548.3,NM_177937.2	24,24	59,556,5888	GG,GC,CC		0.0116,15.2746,5.1822	possibly-damaging,possibly-damaging	322/402,322/402	88650332	674,12332	2203	4300	6503	SO:0001583	missense	51280	exon8			GACAAGCTGGTCT	AF236056	CCDS35054.1	9q21.33	2012-12-13	2007-07-30	2007-07-30	ENSG00000135052	ENSG00000135052			15451	protein-coding gene	gene with protein product		606804	"""golgi phosphoprotein 2"", ""chromosome 9 open reading frame 155"""	GOLPH2, C9orf155		10831838, 18953438, 22542941	Standard	NM_016548		Approved	GP73, FLJ23608, bA379P1.3	uc004aol.3	Q8NBJ4	OTTHUMG00000020130	ENST00000388712.3:c.966G>C	9.37:g.88650332C>G	ENSP00000373364:p.Gln322His	Somatic	93	0	0	1261	WXS	Illumina HiSeq	Phase_I	104	71	0.682692	NM_016548	Q6IAF4|Q9NRB9	Missense_Mutation	SNP	ENST00000388712.3	37	CCDS35054.1	90	0.04120879120879121	84	0.17073170731707318	6	0.016574585635359115	0	0.0	0	0.0	C	11.23	1.576207	0.28092	0.152746	1.16E-4	ENSG00000135052	ENST00000388712;ENST00000388711	T;T	0.47177	0.85;0.85	4.54	2.7	0.31948	.	0.524964	0.19303	N	0.117587	T	0.00241	0.0007	L	0.56769	1.78	0.33372	P	0.42634399999999995	D	0.64830	0.994	D	0.64321	0.924	T	0.06625	-1.0816	9	0.40728	T	0.16	-0.0466	6.3297	0.21262	0.0:0.7825:0.0:0.2175	rs61741197	322	Q8NBJ4	GOLM1_HUMAN	H	322	ENSP00000373364:Q322H;ENSP00000373363:Q322H	ENSP00000373363:Q322H	Q	-	3	2	GOLM1	87840152	1.000000	0.71417	0.997000	0.53966	0.445000	0.32107	1.172000	0.31908	1.282000	0.44496	0.462000	0.41574	CAG	C|0.947;G|0.053	0.053	strong		0.652	GOLM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052904.2	NM_177937	
KRT73	319101	hgsc.bcm.edu	37	12	53011955	53011955	+	Silent	SNP	G	G	A	rs61736102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53011955G>A	ENST00000305748.3	-	1	388	c.354C>T	c.(352-354)aaC>aaT	p.N118N	RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	118	Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCAGCTCCACGTTCAGGGGTG	0.592													G|||	1004	0.200479	0.152	0.1023	5008	,	,		16598	0.4454		0.1471	False		,,,				2504	0.138				p.N118N		Atlas-SNP	.											.	KRT73	101	.	0			c.C354T						PASS	.	G		675,3731	285.2+/-278.0	54,567,1582	124.0	125.0	125.0		354	-1.9	1.0	12	dbSNP_129	125	1284,7316	254.1+/-279.5	96,1092,3112	no	coding-synonymous	KRT73	NM_175068.2		150,1659,4694	AA,AG,GG		14.9302,15.32,15.0623		118/541	53011955	1959,11047	2203	4300	6503	SO:0001819	synonymous_variant	319101	exon1			CTCCACGTTCAGG	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.354C>T	12.37:g.53011955G>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	214	214	1	NM_175068	Q32MB2	Silent	SNP	ENST00000305748.3	37	CCDS8834.1																																																																																			G|0.827;A|0.173	0.173	strong		0.592	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
HDAC4	9759	hgsc.bcm.edu	37	2	240003873	240003873	+	Silent	SNP	G	G	A	rs10168964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240003873G>A	ENST00000345617.3	-	21	3353	c.2562C>T	c.(2560-2562)gaC>gaT	p.D854D	HDAC4_ENST00000543185.1_Silent_p.D438D	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	854	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GGACGCTGGGGTCGCTGTAGA	0.587													G|||	381	0.0760783	0.2799	0.0159	5008	,	,		15695	0.0		0.0	False		,,,				2504	0.0				p.D854D		Atlas-SNP	.											.	HDAC4	127	.	0			c.C2562T						PASS	.	G		1088,3318	396.7+/-330.2	134,820,1249	172.0	156.0	161.0		2562	3.0	1.0	2	dbSNP_119	161	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	HDAC4	NM_006037.3		134,826,5543	AA,AG,GG		0.0698,24.6936,8.4115		854/1085	240003873	1094,11912	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon21			GCTGGGGTCGCTG	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.2562C>T	2.37:g.240003873G>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	326	324	0.993865	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.924;A|0.076	0.076	strong		0.587	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
ATR	545	hgsc.bcm.edu	37	3	142222245	142222245	+	Silent	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:142222245C>A	ENST00000350721.4	-	30	5368	c.5247G>T	c.(5245-5247)ctG>ctT	p.L1749L	ATR_ENST00000383101.3_Silent_p.L1685L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1749	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TAACAGTAGACAGCTGACCAA	0.294								Other conserved DNA damage response genes																													p.L1749L		Atlas-SNP	.											ATR,colon,carcinoma,-1,1	ATR	285	1	0			c.G5247T						scavenged	.						56.0	54.0	55.0					3																	142222245		2203	4296	6499	SO:0001819	synonymous_variant	545	exon30			AGTAGACAGCTGA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5247G>T	3.37:g.142222245C>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	234	4	0.017094	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1																																																																																			.	.	none		0.294	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186254	39186254	+	Missense_Mutation	SNP	T	T	G	rs575093773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39186254T>G	ENST00000377747.4	-	1	102	c.77A>C	c.(76-78)cAg>cCg	p.Q26P	KRTAP1-5_ENST00000361883.5_5'Flank	NM_001257305.1	NP_001244234.1	P0C5Y4	KRA14_HUMAN	keratin associated protein 1-4	26						keratin filament (GO:0045095)				lung(1)	1						GCAGCTTGGCTGGCAGCAGCT	0.627													t|||	25	0.00499201	0.0189	0.0	5008	,	,		17746	0.0		0.0	False		,,,				2504	0.0				p.Q26P		Atlas-SNP	.											.	KRTAP1-4	4	.	0			c.A77C						PASS	.																																			SO:0001583	missense	728255	exon1			CTTGGCTGGCAGC	AC007455	CCDS58548.1	17q21.2	2010-06-22			ENSG00000204887	ENSG00000204887		"""Keratin associated proteins"""	18904	protein-coding gene	gene with protein product		608821					Standard	NM_001257305		Approved	KAP1.4	uc031raf.1	P0C5Y4	OTTHUMG00000133631	ENST00000377747.4:c.77A>C	17.37:g.39186254T>G	ENSP00000366976:p.Gln26Pro	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	137	68	0.49635	NM_001257305	A6NJ92	Missense_Mutation	SNP	ENST00000377747.4	37	CCDS58548.1	.	.	.	.	.	.	.	.	.	.	T	9.987	1.229625	0.22542	.	.	ENSG00000204887	ENST00000377747	T	0.35789	1.29	4.07	4.07	0.47477	.	0.000000	0.38778	N	0.001578	T	0.44891	0.1315	.	.	.	.	.	.	.	.	.	.	.	.	T	0.61043	-0.7142	6	0.66056	D	0.02	.	9.7179	0.40284	0.0:0.0:0.0:1.0	.	.	.	.	P	26	ENSP00000366976:Q26P	ENSP00000366976:Q26P	Q	-	2	0	KRTAP1-4	36439780	1.000000	0.71417	0.822000	0.32727	0.016000	0.09150	1.181000	0.32017	2.072000	0.62099	0.533000	0.62120	CAG	.	.	none		0.627	KRTAP1-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257776.3		
OR52H1	390067	hgsc.bcm.edu	37	11	5566460	5566460	+	Silent	SNP	G	G	A	rs115541630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5566460G>A	ENST00000322653.4	-	1	319	c.294C>T	c.(292-294)cgC>cgT	p.R98R	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	98						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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGTGATTTCGCGAGCCCCTA	0.468													G|||	61	0.0121805	0.0439	0.0043	5008	,	,		22055	0.0		0.0	False		,,,				2504	0.0				p.R98R		Atlas-SNP	.											OR52H1,NS,carcinoma,0,1	OR52H1	46	1	0			c.C294T						PASS	.	G		242,4160	142.7+/-177.9	6,230,1965	73.0	70.0	71.0		294	-9.5	0.0	11	dbSNP_132	71	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	OR52H1	NM_001005289.1		6,231,6261	AA,AG,GG		0.0116,5.4975,1.8698		98/321	5566460	243,12753	2201	4297	6498	SO:0001819	synonymous_variant	390067	exon1			GATTTCGCGAGCC	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.294C>T	11.37:g.5566460G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_001005289	B9EH26|Q6IF79	Silent	SNP	ENST00000322653.4	37	CCDS31386.1																																																																																			G|0.983;A|0.017	0.017	strong		0.468	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
GUCA1C	9626	hgsc.bcm.edu	37	3	108639423	108639423	+	Missense_Mutation	SNP	C	C	T	rs2715687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108639423C>T	ENST00000261047.3	-	2	346	c.214G>A	c.(214-216)Gtt>Att	p.V72I	GUCA1C_ENST00000393963.3_Missense_Mutation_p.V72I|GUCA1C_ENST00000471108.1_Missense_Mutation_p.V72I	NM_005459.3	NP_005450.3	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C	72	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		V -> I (in dbSNP:rs2715687). {ECO:0000269|PubMed:10037746}.		phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(2)|large_intestine(1)|liver(1)|lung(8)|pancreas(1)|skin(1)	14						AAAAAGTCAACAAATCCATCC	0.303													T|||	3113	0.621605	0.7057	0.6268	5008	,	,		18843	0.379		0.7237	False		,,,				2504	0.6493				p.V72I	NSCLC(157;1360 1999 30631 40189 44208)	Atlas-SNP	.											.	GUCA1C	39	.	0			c.G214A						PASS	.	T	ILE/VAL	3123,1283	423.4+/-340.1	1094,935,174	51.0	49.0	50.0		214	4.0	1.0	3	dbSNP_100	50	6030,2562	408.7+/-349.6	2127,1776,393	yes	missense	GUCA1C	NM_005459.3	29	3221,2711,567	TT,TC,CC		29.8184,29.1194,29.5815	benign	72/210	108639423	9153,3845	2203	4296	6499	SO:0001583	missense	9626	exon2			AGTCAACAAATCC	AF110002	CCDS2954.1	3q13.1	2013-01-10			ENSG00000138472	ENSG00000138472		"""EF-hand domain containing"""	4680	protein-coding gene	gene with protein product	"""guanylyl cyclase-activating protein 3"""	605128				10037746, 11860507	Standard	NM_005459		Approved	GCAP3	uc003dxj.2	O95843	OTTHUMG00000159204	ENST00000261047.3:c.214G>A	3.37:g.108639423C>T	ENSP00000261047:p.Val72Ile	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	205	204	0.995122	NM_005459	O95844|Q9UNM0	Missense_Mutation	SNP	ENST00000261047.3	37	CCDS2954.1	1347	0.6167582417582418	347	0.7052845528455285	233	0.643646408839779	205	0.3583916083916084	562	0.741424802110818	T	1.402	-0.577954	0.03854	0.708806	0.701816	ENSG00000138472	ENST00000393963;ENST00000261047;ENST00000471108	T;T;T	0.76186	-1.0;-1.0;-1.0	5.17	4.0	0.46444	EF-hand-like domain (1);	0.101830	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00608	-1.33	0.52501	P	4.999999999999449E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46582	-0.9181	9	0.02654	T	1	.	8.2139	0.31499	0.0:0.1685:0.0:0.8315	rs2715687;rs3749284;rs52812479;rs61275317;rs2715687	72;72	C9JNI2;O95843	.;GUC1C_HUMAN	I	72	ENSP00000377535:V72I;ENSP00000261047:V72I;ENSP00000417761:V72I	ENSP00000261047:V72I	V	-	1	0	GUCA1C	110122113	1.000000	0.71417	0.998000	0.56505	0.624000	0.37722	4.443000	0.59994	0.302000	0.22762	-0.332000	0.08345	GTT	C|0.337;T|0.662	0.662	strong		0.303	GUCA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353819.1	NM_005459	
ADCY10	55811	hgsc.bcm.edu	37	1	167825485	167825485	+	Missense_Mutation	SNP	T	T	C	rs2071921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167825485T>C	ENST00000367851.4	-	17	2273	c.2089A>G	c.(2089-2091)Att>Gtt	p.I697V	ADCY10_ENST00000367848.1_Missense_Mutation_p.I605V|ADCY10_ENST00000545172.1_Missense_Mutation_p.I544V	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	697			I -> V (in dbSNP:rs2071921). {ECO:0000269|PubMed:11423534, ECO:0000269|PubMed:11932268, ECO:0000269|PubMed:12609998}.		cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						ACTGCACCAATGACAATGTAG	0.458													t|||	2527	0.504593	0.4599	0.5749	5008	,	,		19993	0.7113		0.4105	False		,,,				2504	0.3988				p.I697V		Atlas-SNP	.											.	ADCY10	175	.	0			c.A2089G						PASS	.	T	VAL/ILE,VAL/ILE	2032,2374	563.4+/-381.2	471,1090,642	303.0	255.0	271.0		1630,2089	-2.4	0.0	1	dbSNP_96	271	3436,5164	506.2+/-376.5	692,2052,1556	yes	missense,missense	ADCY10	NM_001167749.1,NM_018417.4	29,29	1163,3142,2198	CC,CT,TT		39.9535,46.1189,42.0421	benign,benign	544/1458,697/1611	167825485	5468,7538	2203	4300	6503	SO:0001583	missense	55811	exon17			CACCAATGACAAT	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"""Adenylate cyclases"""	21285	protein-coding gene	gene with protein product	"""soluble adenylyl cyclase"", ""Hypercalciuria, absorptive, 2"""	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.2089A>G	1.37:g.167825485T>C	ENSP00000356825:p.Ile697Val	Somatic	282	1	0.0035461		WXS	Illumina HiSeq	Phase_I	222	222	1	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	
FAM117A	81558	hgsc.bcm.edu	37	17	47788755	47788755	+	Silent	SNP	G	G	A	rs34759387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:47788755G>A	ENST00000240364.2	-	8	1303	c.1224C>T	c.(1222-1224)ccC>ccT	p.P408P	FAM117A_ENST00000513602.1_Silent_p.P136P|RP11-613C6.2_ENST00000512720.1_RNA	NM_030802.3	NP_110429.1	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A	408	Pro-rich.									haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	17						CCGGGGGAAGGGGAGATCCCG	0.657													G|||	330	0.0658946	0.0726	0.1037	5008	,	,		16378	0.0456		0.0606	False		,,,				2504	0.0562				p.P408P		Atlas-SNP	.											.	FAM117A	45	.	0			c.C1224T						PASS	.	G		265,4141	148.0+/-182.4	7,251,1945	31.0	35.0	34.0		1224	-7.4	0.0	17	dbSNP_126	34	349,8251	116.1+/-175.8	5,339,3956	no	coding-synonymous	FAM117A	NM_030802.3		12,590,5901	AA,AG,GG		4.0581,6.0145,4.7209		408/454	47788755	614,12392	2203	4300	6503	SO:0001819	synonymous_variant	81558	exon8			GGGAAGGGGAGAT	BC037572	CCDS11553.1	17q21.33	2006-04-26				ENSG00000121104			24179	protein-coding gene	gene with protein product	"""C/EBP induced protein"""					12477932	Standard	NM_030802		Approved		uc002ipk.3	Q9C073		ENST00000240364.2:c.1224C>T	17.37:g.47788755G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	50	18	0.36	NM_030802	B7Z7Q3	Silent	SNP	ENST00000240364.2	37	CCDS11553.1																																																																																			G|0.946;A|0.054	0.054	strong		0.657	FAM117A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365736.1	NM_030802	
FGD6	55785	hgsc.bcm.edu	37	12	95502303	95502303	+	Silent	SNP	G	G	A	rs11107896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	145	0	0		WXS	Illumina HiSeq	Phase_I	150	85	0.566667	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	
DRD5	1816	hgsc.bcm.edu	37	4	9783971	9783971	+	Silent	SNP	C	C	T	rs113695344		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:9783971C>T	ENST00000304374.2	+	1	714	c.318C>T	c.(316-318)taC>taT	p.Y106Y		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	106					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)	TGGCCGGTTACTGGCCCTTTG	0.602																																					p.Y106Y		Atlas-SNP	.											DRD5,rectum,carcinoma,0,1	DRD5	119	1	0			c.C318T						scavenged	.						50.0	48.0	49.0					4																	9783971		2203	4300	6503	SO:0001819	synonymous_variant	1816	exon1			CGGTTACTGGCCC	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.318C>T	4.37:g.9783971C>T		Somatic	133	5	0.037594		WXS	Illumina HiSeq	Phase_I	146	10	0.0684932	NM_000798	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																			C|0.500;T|0.500	0.500	weak		0.602	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
PCDHB14	56122	hgsc.bcm.edu	37	5	140604641	140604641	+	Missense_Mutation	SNP	G	G	C	rs142548755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604641G>C	ENST00000239449.4	+	1	1564	c.1564G>C	c.(1564-1566)Gag>Cag	p.E522Q	PCDHB14_ENST00000515856.2_Missense_Mutation_p.E369Q	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	522	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)|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)			GCTGGACTACGAGGCCCTACA	0.687													g|||	27	0.00539137	0.0204	0.0	5008	,	,		16691	0.0		0.0	False		,,,				2504	0.0				p.E522Q	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G1564C						PASS	.	G	GLN/GLU	69,4337		0,69,2134	86.0	91.0	90.0		1564	4.2	1.0	5	dbSNP_134	90	0,8600		0,0,4300	no	missense	PCDHB14	NM_018934.2	29	0,69,6434	CC,CG,GG		0.0,1.566,0.5305	probably-damaging	522/799	140604641	69,12937	2203	4300	6503	SO:0001583	missense	56122	exon1			GACTACGAGGCCC	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.1564G>C	5.37:g.140604641G>C	ENSP00000239449:p.Glu522Gln	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	281	137	0.487544	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	-	20.7	4.042145	0.75732	0.01566	0.0	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.72942	-0.7;-0.7	4.15	4.15	0.48705	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.81917	0.4924	H	0.96048	3.76	0.45634	D	0.998568	D	0.89917	1.0	D	0.97110	1.0	D	0.89840	0.4002	9	0.87932	D	0	.	16.4819	0.84160	0.0:0.0:1.0:0.0	.	522	Q9Y5E9	PCDBE_HUMAN	Q	369;522	ENSP00000444518:E369Q;ENSP00000239449:E522Q	ENSP00000239449:E522Q	E	+	1	0	PCDHB14	140584825	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	7.687000	0.84139	2.048000	0.60808	0.556000	0.70494	GAG	G|0.994;C|0.006	0.006	strong		0.687	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
PXYLP1	92370	hgsc.bcm.edu	37	3	141006162	141006162	+	Silent	SNP	G	G	A	rs34601454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141006162G>A	ENST00000286353.4	+	5	509	c.372G>A	c.(370-372)ccG>ccA	p.P124P	ACPL2_ENST00000504264.1_Silent_p.P107P|ACPL2_ENST00000508812.1_Silent_p.P115P|ACPL2_ENST00000393007.1_Silent_p.P108P|ACPL2_ENST00000502783.1_Silent_p.P86P|ACPL2_ENST00000393010.2_Silent_p.P124P|RP11-438D8.2_ENST00000507698.1_RNA	NM_001037172.1|NM_001282728.1	NP_001032249.1|NP_001269657.1	Q8TE99	PXYP1_HUMAN		124						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)			endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(2)	23						CTAGGAAACCGTATCACCCAA	0.473													G|||	162	0.0323482	0.1157	0.013	5008	,	,		20337	0.0		0.0	False		,,,				2504	0.0				p.P124P		Atlas-SNP	.											.	ACPL2	50	.	0			c.G372A						PASS	.	G	,	377,4029	189.9+/-215.9	16,345,1842	151.0	158.0	155.0		372,372	-11.3	0.0	3	dbSNP_126	155	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	ACPL2	NM_001037172.1,NM_152282.3	,	16,348,6139	AA,AG,GG		0.0349,8.5565,2.9217	,	124/481,124/481	141006162	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	92370	exon7			GAAACCGTATCAC																												ENST00000286353.4:c.372G>A	3.37:g.141006162G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_152282	D3DNF5|Q49AJ2|W0TR04	Silent	SNP	ENST00000286353.4	37	CCDS3116.1																																																																																			G|0.969;A|0.031	0.031	strong		0.473	ACPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359533.2		
PARVB	29780	hgsc.bcm.edu	37	22	44495953	44495953	+	Missense_Mutation	SNP	A	A	G	rs56194750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44495953A>G	ENST00000338758.7	+	3	286	c.223A>G	c.(223-225)Atg>Gtg	p.M75V	PARVB_ENST00000404989.1_Missense_Mutation_p.M38V|PARVB_ENST00000406477.3_Missense_Mutation_p.M108V|PARVB_ENST00000477795.1_3'UTR	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	75					actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				GGAGCGCACGATGATTGACCC	0.572													A|||	3	0.000599042	0.0	0.0014	5008	,	,		18925	0.0		0.002	False		,,,				2504	0.0				p.M108V		Atlas-SNP	.											.	PARVB	44	.	0			c.A322G						PASS	.	A	VAL/MET,VAL/MET	4,4402	8.1+/-20.4	0,4,2199	123.0	100.0	108.0		322,223	3.5	0.9	22	dbSNP_129	108	35,8565	23.4+/-69.3	0,35,4265	yes	missense,missense	PARVB	NM_001003828.2,NM_013327.4	21,21	0,39,6464	GG,GA,AA		0.407,0.0908,0.2999	benign,benign	108/398,75/365	44495953	39,12967	2203	4300	6503	SO:0001583	missense	29780	exon4			CGCACGATGATTG	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.223A>G	22.37:g.44495953A>G	ENSP00000342492:p.Met75Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	37	CCDS14056.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	12.33	1.905546	0.33628	9.08E-4	0.00407	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000402876;ENST00000444029;ENST00000404989	T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37	4.5	3.45	0.39498	Calponin homology domain (1);	0.131379	0.64402	N	0.000001	T	0.31513	0.0799	L	0.52905	1.665	0.47511	D	0.999442	B;B;B;B	0.16166	0.005;0.001;0.003;0.016	B;B;B;B	0.23018	0.006;0.005;0.008;0.043	T	0.07908	-1.0748	10	0.40728	T	0.16	-2.8779	7.5657	0.27876	0.8909:0.0:0.1091:0.0	rs56194750	75;38;75;108	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	V	108;75;75;73;38	ENSP00000384515:M108V;ENSP00000342492:M75V;ENSP00000385331:M75V;ENSP00000393758:M73V;ENSP00000384353:M38V	ENSP00000342492:M75V	M	+	1	0	PARVB	42827286	1.000000	0.71417	0.919000	0.36401	0.989000	0.77384	4.938000	0.63519	0.585000	0.29608	0.460000	0.39030	ATG	A|0.997;G|0.003	0.003	strong		0.572	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828	
DNAH3	55567	hgsc.bcm.edu	37	16	21042391	21042391	+	Silent	SNP	G	G	A	rs114086288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:21042391G>A	ENST00000261383.3	-	37	5414	c.5415C>T	c.(5413-5415)aaC>aaT	p.N1805N	DNAH3_ENST00000415178.1_Silent_p.N1805N	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1805	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CCAGAACAGTGTTCATATTTT	0.378													G|||	55	0.0109824	0.0401	0.0014	5008	,	,		20518	0.0		0.001	False		,,,				2504	0.0				p.N1805N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.C5415T						PASS	.	G		133,4269	96.7+/-135.4	3,127,2071	103.0	96.0	98.0		5415	4.7	1.0	16	dbSNP_132	98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DNAH3	NM_017539.1		3,128,6370	AA,AG,GG		0.0116,3.0214,1.0306		1805/4117	21042391	134,12868	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon37			AACAGTGTTCATA	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.5415C>T	16.37:g.21042391G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			G|0.989;A|0.011	0.011	strong		0.378	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
CCDC105	126402	hgsc.bcm.edu	37	19	15133762	15133762	+	Missense_Mutation	SNP	G	G	C	rs8111625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15133762G>C	ENST00000292574.3	+	7	1413	c.1331G>C	c.(1330-1332)aGc>aCc	p.S444T		NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	444			S -> T (in dbSNP:rs8111625). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						AAGAACCTCAGCTGGGGCCTC	0.637													c|||	4306	0.859824	0.9501	0.8545	5008	,	,		16246	0.9077		0.8091	False		,,,				2504	0.7444				p.S444T		Atlas-SNP	.											.	CCDC105	53	.	0			c.G1331C						PASS	.		THR/SER	4049,355	172.3+/-202.3	1872,305,25	53.0	39.0	43.0		1331	0.8	0.0	19	dbSNP_116	43	7084,1516	272.4+/-290.1	2932,1220,148	yes	missense	CCDC105	NM_173482.2	58	4804,1525,173	CC,CG,GG		17.6279,8.0609,14.3879	benign	444/500	15133762	11133,1871	2202	4300	6502	SO:0001583	missense	126402	exon7			ACCTCAGCTGGGG	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.1331G>C	19.37:g.15133762G>C	ENSP00000292574:p.Ser444Thr	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	180	78	0.433333	NM_173482	Q8N7T5|Q8NDL5	Missense_Mutation	SNP	ENST00000292574.3	37	CCDS12322.1	1909	0.8740842490842491	472	0.959349593495935	316	0.8729281767955801	514	0.8986013986013986	607	0.8007915567282322	c	0.281	-0.986297	0.02180	0.919391	0.823721	ENSG00000160994	ENST00000292574	T	0.02421	4.3	4.12	0.78	0.18556	.	1.370820	0.04721	N	0.419319	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	0.16217	-1.0410	9	0.12766	T	0.61	-0.0194	3.9165	0.09225	0.0:0.5107:0.1793:0.31	rs8111625;rs17855586;rs8111625	444	Q8IYK2	CC105_HUMAN	T	444	ENSP00000292574:S444T	ENSP00000292574:S444T	S	+	2	0	CCDC105	14994762	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.122000	0.15687	-0.064000	0.13043	-0.345000	0.07892	AGC	G|0.132;C|0.868	0.868	strong		0.637	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482	
APOBEC3A	200315	hgsc.bcm.edu	37	22	39357634	39357634	+	Silent	SNP	A	A	G	rs2294363		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39357634A>G	ENST00000402255.1	+	4	621	c.417A>G	c.(415-417)gcA>gcG	p.A139A	APOBEC3A_ENST00000249116.2_Silent_p.A139A			P31941	ABC3A_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A	139					cellular response to xenobiotic stimulus (GO:0071466)|clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine (GO:0044356)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(2)|ovary(1)|skin(1)	5	Melanoma(58;0.04)					ATAAGGAGGCACTGCAAATGC	0.577																																					p.A139A		Atlas-SNP	.											.	APOBEC3A	20	.	0			c.A417G						PASS	.						38.0	49.0	46.0					22																	39357634		1812	3940	5752	SO:0001819	synonymous_variant	200315	exon3			GGAGGCACTGCAA	U03891	CCDS13981.1	22q13.1-q13.2	2014-01-28			ENSG00000128383	ENSG00000128383		"""Apolipoprotein B mRNA editing enzymes"""	17343	protein-coding gene	gene with protein product	"""phorbolin I"""	607109				11863358, 10469298	Standard	NM_145699		Approved	ARP3, PHRBN		P31941	OTTHUMG00000151004	ENST00000402255.1:c.417A>G	22.37:g.39357634A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_145699	A0AVM1|Q12807|Q5JZ93|Q9UH18	Silent	SNP	ENST00000402255.1	37	CCDS13981.1																																																																																			A|0.167;G|0.833	0.833	weak		0.577	APOBEC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320915.2	NM_145699	
CLDN8	9073	hgsc.bcm.edu	37	21	31587859	31587859	+	Missense_Mutation	SNP	T	T	C	rs685967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31587859T>C	ENST00000399899.1	-	1	532	c.385A>G	c.(385-387)Acg>Gcg	p.T129A	CLDN8_ENST00000286809.1_Missense_Mutation_p.T129A	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	129			T -> A (in dbSNP:rs685967).		calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|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)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						ACCATGCCCGTGATGATGAAG	0.502													T|||	415	0.0828674	0.1997	0.0447	5008	,	,		20250	0.0069		0.0427	False		,,,				2504	0.0716				p.T129A		Atlas-SNP	.											CLDN8,NS,adenocarcinoma,+2,1	CLDN8	40	1	0			c.A385G						PASS	.	T	ALA/THR	690,3716	288.1+/-279.7	52,586,1565	96.0	86.0	90.0		385	3.7	0.8	21	dbSNP_83	90	413,8187	129.0+/-187.1	8,397,3895	yes	missense	CLDN8	NM_199328.2	58	60,983,5460	CC,CT,TT		4.8023,15.6605,8.4807	benign	129/226	31587859	1103,11903	2203	4300	6503	SO:0001583	missense	9073	exon1			TGCCCGTGATGAT	AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284		"""Claudins"""	2050	protein-coding gene	gene with protein product		611231				9892664	Standard	NM_199328		Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.385A>G	21.37:g.31587859T>C	ENSP00000382783:p.Thr129Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_199328	D3DSE3|Q53EX7	Missense_Mutation	SNP	ENST00000399899.1	37	CCDS13587.1	132	0.06043956043956044	84	0.17073170731707318	17	0.04696132596685083	3	0.005244755244755245	28	0.036939313984168866	T	0.003	-2.413555	0.00191	0.156605	0.048023	ENSG00000156284	ENST00000399899;ENST00000286809;ENST00000536721	D;D	0.86627	-2.15;-2.15	4.84	3.65	0.41850	.	0.365369	0.28521	N	0.015059	T	0.00552	0.0018	N	0.12443	0.215	0.80722	P	0.0	B	0.24576	0.106	B	0.38056	0.264	T	0.30679	-0.9970	9	0.02654	T	1	.	9.126	0.36816	0.3995:0.0:0.0:0.6005	rs685967;rs52813142;rs685967	129	P56748	CLD8_HUMAN	A	129	ENSP00000382783:T129A;ENSP00000286809:T129A	ENSP00000286809:T129A	T	-	1	0	CLDN8	30509730	0.039000	0.19947	0.754000	0.31244	0.273000	0.26683	0.263000	0.18478	0.946000	0.37632	0.528000	0.53228	ACG	T|0.908;C|0.092	0.092	strong		0.502	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	NM_199328	
MANBA	4126	hgsc.bcm.edu	37	4	103645082	103645082	+	Silent	SNP	C	C	T	rs6857760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:103645082C>T	ENST00000226578.4	-	3	414	c.315G>A	c.(313-315)acG>acA	p.T105T	MANBA_ENST00000505239.1_Silent_p.T105T	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	105					cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)			cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		TTTTTGAAACCGTATCCACTC	0.274													T|||	540	0.107827	0.3752	0.0202	5008	,	,		17866	0.001		0.0219	False		,,,				2504	0.0072				p.T105T		Atlas-SNP	.											.	MANBA	78	.	0			c.G315A						PASS	.	T		1229,3175	695.6+/-406.0	183,863,1156	61.0	63.0	62.0		315	-6.0	0.0	4	dbSNP_116	62	151,8449	807.0+/-407.2	3,145,4152	no	coding-synonymous	MANBA	NM_005908.3		186,1008,5308	TT,TC,CC		1.7558,27.9064,10.6121		105/880	103645082	1380,11624	2202	4300	6502	SO:0001819	synonymous_variant	4126	exon3			TGAAACCGTATCC		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.315G>A	4.37:g.103645082C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	192	78	0.40625	NM_005908	Q96BC3|Q9NYX9	Silent	SNP	ENST00000226578.4	37	CCDS3658.1																																																																																			C|0.893;T|0.107	0.107	strong		0.274	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
ARHGAP33	115703	hgsc.bcm.edu	37	19	36278470	36278470	+	Silent	SNP	C	C	G	rs231235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36278470C>G	ENST00000007510.4	+	21	3147	c.3003C>G	c.(3001-3003)gcC>gcG	p.A1001A	ARHGAP33_ENST00000378944.5_Intron|AC002398.5_ENST00000433059.1_lincRNA|ARHGAP33_ENST00000314737.5_Silent_p.A840A			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	1001					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						AGGTCAGTGCCCAGCTCAGGG	0.662													C|||	2678	0.534744	0.6551	0.5879	5008	,	,		13735	0.627		0.3688	False		,,,				2504	0.41				p.A840A		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.C2520G						PASS	.	C	,	2644,1732		812,1020,356	16.0	20.0	19.0		,2520	2.6	1.0	19	dbSNP_79	19	3095,5441		619,1857,1792	no	intron,coding-synonymous	ARHGAP33	NM_001172630.1,NM_052948.3	,	1431,2877,2148	GG,GC,CC		36.2582,39.5795,44.447	,	,840/1127	36278470	5739,7173	2188	4268	6456	SO:0001819	synonymous_variant	115703	exon21			CAGTGCCCAGCTC	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.3003C>G	19.37:g.36278470C>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Silent	SNP	ENST00000007510.4	37																																																																																				C|0.531;G|0.469	0.469	strong		0.662	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
ATAD5	79915	hgsc.bcm.edu	37	17	29159404	29159404	+	Silent	SNP	G	G	C	rs999796|rs372459410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:29159404G>C	ENST00000321990.4	+	1	417	c.39G>C	c.(37-39)ccG>ccC	p.P13P	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	13					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				CAGCTGCTCCGCCTCCCGTGA	0.627													C|||	1441	0.28774	0.5681	0.2305	5008	,	,		16614	0.1349		0.1173	False		,,,				2504	0.2822				p.P13P		Atlas-SNP	.											ATAD5,NS,carcinoma,0,1	ATAD5	150	1	0			c.G39C						PASS	.	C		2118,2288	595.7+/-388.5	507,1104,592	67.0	73.0	71.0		39	2.8	1.0	17	dbSNP_86	71	961,7639	773.6+/-407.7	45,871,3384	yes	coding-synonymous	ATAD5	NM_024857.3		552,1975,3976	CC,CG,GG		11.1744,48.0708,23.6737		13/1845	29159404	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	79915	exon1			TGCTCCGCCTCCC		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.39G>C	17.37:g.29159404G>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																			G|0.765;C|0.235	0.235	strong		0.627	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
PRR30	339779	hgsc.bcm.edu	37	2	27361049	27361049	+	Missense_Mutation	SNP	G	G	C	rs61739485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27361049G>C	ENST00000335524.3	-	3	674	c.149C>G	c.(148-150)cCg>cGg	p.P50R		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		50	Pro-rich.									cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGAAGAGAACGGTGGTTGAGA	0.592													G|||	118	0.0235623	0.0817	0.0115	5008	,	,		18470	0.0		0.002	False		,,,				2504	0.0				p.P50R		Atlas-SNP	.											.	C2orf53	45	.	0			c.C149G						PASS	.	G	ARG/PRO	269,4137	150.3+/-184.3	10,249,1944	99.0	90.0	93.0		149	0.8	0.0	2	dbSNP_129	93	3,8597	3.0+/-9.4	0,3,4297	yes	missense	C2orf53	NM_178553.3	103	10,252,6241	CC,CG,GG		0.0349,6.1053,2.0913	benign	50/413	27361049	272,12734	2203	4300	6503	SO:0001583	missense	339779	exon3			GAGAACGGTGGTT																												ENST00000335524.3:c.149C>G	2.37:g.27361049G>C	ENSP00000335017:p.Pro50Arg	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	144	50	0.347222	NM_178553	Q86UE2	Missense_Mutation	SNP	ENST00000335524.3	37	CCDS1739.1	29	0.013278388278388278	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	8.058	0.767521	0.15983	0.061053	3.49E-4	ENSG00000186143	ENST00000335524	T	0.48522	0.81	3.88	0.835	0.18886	.	.	.	.	.	T	0.04227	0.0117	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.09015	-1.0694	9	0.56958	D	0.05	-0.0394	8.7685	0.34717	0.0:0.256:0.5932:0.1508	rs61739485	50	Q53SZ7	CB053_HUMAN	R	50	ENSP00000335017:P50R	ENSP00000335017:P50R	P	-	2	0	C2orf53	27214553	0.014000	0.17966	0.000000	0.03702	0.002000	0.02628	1.283000	0.33237	-0.082000	0.12640	0.561000	0.74099	CCG	G|0.972;C|0.028	0.028	strong		0.592	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1		
SPANXN4	441525	hgsc.bcm.edu	37	X	142121876	142121876	+	Missense_Mutation	SNP	A	A	T	rs10482390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:142121876A>T	ENST00000446864.1	+	2	241	c.144A>T	c.(142-144)aaA>aaT	p.K48N	SPANXN4_ENST00000370504.3_Missense_Mutation_p.K47N	NM_001009613.2	NP_001009613.1	Q5MJ08	SPXN4_HUMAN	SPANX family, member N4	48			K -> N (in dbSNP:rs10482390). {ECO:0000269|PubMed:16251457}.							endometrium(2)|large_intestine(2)|lung(3)|ovary(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					AAAAAGCAAAATATCCAACAT	0.403													A|||	182	0.0482119	0.1293	0.0159	3775	,	,		14555	0.0		0.0	False		,,,				2504	0.0				p.K48N		Atlas-SNP	.											.	SPANXN4	10	.	0			c.A144T						PASS	.	A	ASN/LYS	399,2760		17,299,66,984,493	44.0	39.0	41.0		144	-0.5	0.0	X	dbSNP_119	41	2,6400		0,2,0,2317,1764	yes	missense	SPANXN4	NM_001009613.2	94	17,301,66,3301,2257	TT,TA,T,AA,A		0.0312,12.6306,4.1941	possibly-damaging	48/100	142121876	401,9160	1859	4083	5942	SO:0001583	missense	441525	exon2			AGCAAAATATCCA	DQ336126	CCDS48178.1	Xq27.3	2009-03-25			ENSG00000189326	ENSG00000189326			33177	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 9"""	300667				14973187, 17012309	Standard	NM_001009613		Approved	SPANX-N4, CT11.9	uc004fbv.4	Q5MJ08	OTTHUMG00000022575	ENST00000446864.1:c.144A>T	X.37:g.142121876A>T	ENSP00000405210:p.Lys48Asn	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	245	151	0.616327	NM_001009613	Q0ZNK6|Q5W0S6	Missense_Mutation	SNP	ENST00000446864.1	37	CCDS48178.1	53	0.031946955997588906	31	0.06768558951965066	5	0.013812154696132596	0	0.0	0	0.0	A	12.64	1.999016	0.35226	0.126306	3.12E-4	ENSG00000189326	ENST00000446864;ENST00000370504	T;T	0.06218	3.33;3.33	0.775	-0.534	0.11883	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.80722	P	0.0	D	0.56521	0.976	P	0.50537	0.643	T	0.27157	-1.0082	6	0.62326	D	0.03	.	.	.	.	rs10482390;rs52795720;rs10482390	48	Q5MJ08	SPXN4_HUMAN	N	48;47	ENSP00000405210:K48N;ENSP00000359535:K47N	ENSP00000359535:K47N	K	+	3	2	SPANXN4	141949542	0.016000	0.18221	0.000000	0.03702	0.469000	0.32828	0.555000	0.23422	-0.266000	0.09339	0.158000	0.16466	AAA	A|0.920;0|0.042	.	strong		0.403	SPANXN4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377539.1	NM_001009613	
PIEZO1	9780	hgsc.bcm.edu	37	16	88793156	88793156	+	Silent	SNP	G	G	A	rs376432833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88793156G>A	ENST00000301015.9	-	25	3912	c.3666C>T	c.(3664-3666)aaC>aaT	p.N1222N		NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1222					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						TGACGGTGACGTTGTACAGAA	0.682													G|||	2	0.000399361	0.0015	0.0	5008	,	,		13543	0.0		0.0	False		,,,				2504	0.0				p.N1222N		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C3666T						PASS	.						46.0	44.0	45.0					16																	88793156		692	1589	2281	SO:0001819	synonymous_variant	9780	exon25			GGTGACGTTGTAC	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.3666C>T	16.37:g.88793156G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	.	.	.	.	.	.	.	.	.	.	G	9.795	1.178913	0.21787	.	.	ENSG00000103335	ENST00000451779	.	.	.	4.51	-4.22	0.03800	.	.	.	.	.	T	0.49440	0.1557	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45026	-0.9289	4	.	.	.	-35.03	6.9812	0.24704	0.4239:0.1109:0.4652:0.0	.	.	.	.	C	1168	.	.	R	-	1	0	FAM38A	87320657	0.145000	0.22656	0.883000	0.34634	0.954000	0.61252	-0.542000	0.06091	-1.093000	0.03058	-0.424000	0.05967	CGT	.	.	weak		0.682	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
CFH	3075	hgsc.bcm.edu	37	1	196706659	196706659	+	Missense_Mutation	SNP	C	C	A	rs114743644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:196706659C>A	ENST00000367429.4	+	17	2891	c.2651C>A	c.(2650-2652)tCc>tAc	p.S884Y		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	884	Sushi 15. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						ATTAATTCATCCAGGTCTTCA	0.338													C|||	4	0.000798722	0.0023	0.0014	5008	,	,		13290	0.0		0.0	False		,,,				2504	0.0				p.S884Y		Atlas-SNP	.											.	CFH	251	.	0			c.C2651A						PASS	.	C	TYR/SER	13,4393		0,13,2190	72.0	68.0	70.0		2651	3.6	0.0	1	dbSNP_133	70	0,8600		0,0,4300	yes	missense	CFH	NM_000186.3	144	0,13,6490	AA,AC,CC		0.0,0.2951,0.1	probably-damaging	884/1232	196706659	13,12993	2203	4300	6503	SO:0001583	missense	3075	exon17			ATTCATCCAGGTC	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2651C>A	1.37:g.196706659C>A	ENSP00000356399:p.Ser884Tyr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	13.20	2.165002	0.38217	0.002951	0.0	ENSG00000000971	ENST00000367429	T	0.64438	-0.1	5.52	3.61	0.41365	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.50837	0.1639	M	0.67625	2.065	0.09310	N	0.999999	P	0.39250	0.665	B	0.35727	0.209	T	0.42032	-0.9475	9	0.07482	T	0.82	.	6.1966	0.20553	0.1744:0.6935:0.0:0.1321	.	884	P08603	CFAH_HUMAN	Y	884	ENSP00000356399:S884Y	ENSP00000356399:S884Y	S	+	2	0	CFH	194973282	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.262000	0.18460	1.455000	0.47813	0.650000	0.86243	TCC	C|0.999;A|0.001	0.001	strong		0.338	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
KCNH1	3756	hgsc.bcm.edu	37	1	210857145	210857145	+	Silent	SNP	C	C	T	rs112047226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:210857145C>T	ENST00000271751.4	-	11	2475	c.2448G>A	c.(2446-2448)gcG>gcA	p.A816A	KCNH1_ENST00000367007.4_Silent_p.A789A			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	816					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		CGGACCCTGGCGCCTGTAGCT	0.662													C|||	50	0.00998403	0.034	0.0072	5008	,	,		16634	0.0		0.0	False		,,,				2504	0.0				p.A816A		Atlas-SNP	.											KCNH1,colon,carcinoma,-1,1	KCNH1	199	1	0			c.G2448A						PASS	.	C	,	127,4279	89.7+/-128.4	3,121,2079	44.0	50.0	48.0		2367,2448	-9.5	0.0	1	dbSNP_132	48	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KCNH1	NM_002238.3,NM_172362.2	,	3,121,6379	TT,TC,CC		0.0,2.8824,0.9765	,	789/963,816/990	210857145	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	3756	exon11			CCCTGGCGCCTGT	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.2448G>A	1.37:g.210857145C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_172362	B1AQ26|O76035|Q14CL3	Silent	SNP	ENST00000271751.4	37	CCDS1496.1																																																																																			C|0.987;T|0.013	0.013	strong		0.662	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
ZNF80	7634	hgsc.bcm.edu	37	3	113955890	113955890	+	Missense_Mutation	SNP	C	C	T	rs112412956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113955890C>T	ENST00000482457.2	-	1	535	c.32G>A	c.(31-33)gGt>gAt	p.G11D	RP11-553L6.2_ENST00000493033.1_RNA|RP11-553L6.2_ENST00000481773.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	11					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)				CAGACCATCACCTGTCCCCAA	0.522													c|||	73	0.0145767	0.053	0.0043	5008	,	,		21555	0.0		0.0	False		,,,				2504	0.0				p.G11D	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.G32A						PASS	.	T	ASP/GLY	188,4218	120.8+/-158.4	5,178,2020	111.0	111.0	111.0		32	-0.9	0.0	3	dbSNP_132	111	0,8600		0,0,4300	yes	missense	ZNF80	NM_007136.3	94	5,178,6320	TT,TC,CC		0.0,4.2669,1.4455	benign	11/274	113955890	188,12818	2203	4300	6503	SO:0001583	missense	7634	exon1			CCATCACCTGTCC	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.32G>A	3.37:g.113955890C>T	ENSP00000417192:p.Gly11Asp	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	153	78	0.509804	NM_007136	Q6NSW4|Q6NT14	Missense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	28	0.01282051282051282	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	0	0.0	c	0.052	-1.246531	0.01481	0.042669	0.0	ENSG00000174255	ENST00000482457	T	0.20463	2.07	2.88	-0.868	0.10652	.	.	.	.	.	T	0.01254	0.0041	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29119	-1.0022	9	0.87932	D	0	.	3.3265	0.07068	0.1783:0.2377:0.0:0.5841	.	11	P51504	ZNF80_HUMAN	D	11	ENSP00000417192:G11D	ENSP00000309812:G11D	G	-	2	0	ZNF80	115438580	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.250000	0.02885	-0.172000	0.10779	-2.079000	0.00380	GGT	C|0.987;T|0.013	0.013	strong		0.522	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
CA9	768	hgsc.bcm.edu	37	9	35674101	35674101	+	Silent	SNP	T	T	C	rs113003874|rs12553173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35674101T>C	ENST00000378357.4	+	1	249	c.145T>C	c.(145-147)Ttg>Ctg	p.L49L	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	49	Proteoglycan-like (PG).				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	GGATTCCCCCTTGGGAGGAGG	0.627													C|||	1032	0.20607	0.4251	0.1037	5008	,	,		18753	0.1726		0.1362	False		,,,				2504	0.089				p.L49L		Atlas-SNP	.											.	CA9	48	.	0			c.T145C						PASS	.	C		1627,2779	650.2+/-399.0	314,999,890	53.0	51.0	51.0		145	-7.4	0.0	9	dbSNP_120	51	1138,7462	759.5+/-407.6	81,976,3243	no	coding-synonymous	CA9	NM_001216.2		395,1975,4133	CC,CT,TT		13.2326,36.9269,21.2594		49/460	35674101	2765,10241	2203	4300	6503	SO:0001819	synonymous_variant	768	exon1			TCCCCCTTGGGAG	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.145T>C	9.37:g.35674101T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001216	Q5T4R1	Silent	SNP	ENST00000378357.4	37	CCDS6585.1																																																																																			T|0.791;C|0.209	0.209	strong		0.627	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
BIRC6	57448	hgsc.bcm.edu	37	2	32740349	32740349	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32740349G>C	ENST00000421745.2	+	55	10995	c.10861G>C	c.(10861-10863)Gaa>Caa	p.E3621Q		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3621					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.E3621Q(1)|p.E3593Q(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TCAATCTCCTGAAGCTATTAA	0.408																																					p.E3621Q	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,NS,carcinoma,0,2	BIRC6	838	2	2	Substitution - Missense(2)	lung(2)	c.G10861C						scavenged	.						107.0	106.0	106.0					2																	32740349		2203	4300	6503	SO:0001583	missense	57448	exon55			TCTCCTGAAGCTA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.10861G>C	2.37:g.32740349G>C	ENSP00000393596:p.Glu3621Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	89	2	0.0224719	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	11.31	1.602473	0.28534	.	.	ENSG00000115760	ENST00000421745	T	0.74106	-0.81	5.44	5.44	0.79542	.	0.128654	0.53938	D	0.000043	T	0.64864	0.2637	L	0.31294	0.92	0.45946	D	0.998779	B	0.14438	0.01	B	0.08055	0.003	T	0.59005	-0.7535	10	0.17369	T	0.5	.	19.2679	0.93997	0.0:0.0:1.0:0.0	.	3621	Q9NR09	BIRC6_HUMAN	Q	3621	ENSP00000393596:E3621Q	ENSP00000393596:E3621Q	E	+	1	0	BIRC6	32593853	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.662000	0.83803	2.563000	0.86464	0.585000	0.79938	GAA	.	.	none		0.408	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
Unknown	0	hgsc.bcm.edu	37	7	63679733	63679733	+	IGR	SNP	A	A	G	rs10270226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	244	123	0.504098	NM_001159524		Missense_Mutation	SNP		37																																																																																				A|0.311;G|0.689	0.689	strong	0	0.323								
CDC16	8881	hgsc.bcm.edu	37	13	115004914	115004914	+	Silent	SNP	C	C	T	rs2296971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:115004914C>T	ENST00000356221.3	+	5	438	c.330C>T	c.(328-330)gaC>gaT	p.D110D	CDC16_ENST00000375308.1_Silent_p.D16D|CDC16_ENST00000252457.5_Silent_p.D109D|CDC16_ENST00000252458.6_Silent_p.D16D|CDC16_ENST00000375312.3_Silent_p.D16D|CDC16_ENST00000375310.1_Silent_p.D16D|CDC16_ENST00000360383.3_Silent_p.D110D			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	76	0	0		WXS	Illumina HiSeq	Phase_I	91	34	0.373626	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	
ZSWIM6	57688	hgsc.bcm.edu	37	5	60628411	60628411	+	Silent	SNP	G	G	T	rs75429795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:60628411G>T	ENST00000252744.5	+	1	312	c.312G>T	c.(310-312)ccG>ccT	p.P104P		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	104	Gly-rich.				neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						TCCCGGAGCCGGTGCAGCGCC	0.711													G|||	510	0.101837	0.0802	0.1037	5008	,	,		2584	0.0724		0.1431	False		,,,				2504	0.1176				p.P104P		Atlas-SNP	.											.	ZSWIM6	51	.	0			c.G312T						PASS	.						6.0	11.0	9.0					5																	60628411		679	1570	2249	SO:0001819	synonymous_variant	57688	exon1			GGAGCCGGTGCAG	BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449		"""Zinc fingers, SWIM-type"""	29316	protein-coding gene	gene with protein product		615951				10997877, 16427614	Standard	NM_020928		Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.312G>T	5.37:g.60628411G>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_020928		Silent	SNP	ENST00000252744.5	37	CCDS47215.1																																																																																			G|0.881;T|0.119	0.119	strong		0.711	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368710.1	NM_020928	
MUC17	140453	hgsc.bcm.edu	37	7	100679809	100679809	+	Silent	SNP	C	C	T	rs71525815|rs4992074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100679809C>T	ENST00000306151.4	+	3	5176	c.5112C>T	c.(5110-5112)agC>agT	p.S1704S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1704	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)					CGGTGGCCAGCTCTGCAATCA	0.483													T|||	1178	0.235224	0.3396	0.1023	5008	,	,		24513	0.253		0.1213	False		,,,				2504	0.2873				p.S1704S		Atlas-SNP	.											.	MUC17	804	.	0			c.C5112T						PASS	.	T		1324,3082	695.5+/-405.9	207,910,1086	188.0	203.0	198.0		5112	-1.2	0.0	7	dbSNP_113	198	999,7601	773.3+/-407.7	57,885,3358	no	coding-synonymous	MUC17	NM_001040105.1		264,1795,4444	TT,TC,CC		11.6163,30.0499,17.861		1704/4494	100679809	2323,10683	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			GGCCAGCTCTGCA	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.5112C>T	7.37:g.100679809C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	46	0.4	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			C|0.823;T|0.177	0.177	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CSMD3	114788	hgsc.bcm.edu	37	8	113275878	113275878	+	Silent	SNP	C	C	T	rs16883323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:113275878C>T	ENST00000297405.5	-	61	10096	c.9852G>A	c.(9850-9852)ccG>ccA	p.P3284P	CSMD3_ENST00000343508.3_Silent_p.P3244P|CSMD3_ENST00000352409.3_Silent_p.P3214P|CSMD3_ENST00000455883.2_Silent_p.P3115P	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3284	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.					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						GTAAGCACTGCGGTACTTCAC	0.398										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			C|||	180	0.0359425	0.1324	0.0072	5008	,	,		16096	0.0		0.0	False		,,,				2504	0.0				p.P3284P		Atlas-SNP	.											CSMD3_ENST00000343508,caecum,carcinoma,0,4	CSMD3	2325	4	0			c.G9852A						PASS	.	C	,,	438,3968	208.8+/-229.8	21,396,1786	86.0	72.0	77.0		9345,9852,9732	-2.2	1.0	8	dbSNP_123	77	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	21,401,6081	TT,TC,CC		0.0581,9.941,3.4061	,,	3115/3539,3284/3708,3244/3668	113275878	443,12563	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon61			GCACTGCGGTACT	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.9852G>A	8.37:g.113275878C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			C|0.969;T|0.031	0.031	strong		0.398	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
APOBEC4	403314	hgsc.bcm.edu	37	1	183617311	183617311	+	Silent	SNP	T	T	A	rs10911392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:183617311T>A	ENST00000308641.4	-	2	877	c.606A>T	c.(604-606)atA>atT	p.I202I	RGL1_ENST00000536277.1_Intron|APOBEC4_ENST00000481562.1_Intron|RGL1_ENST00000304685.4_Intron	NM_203454.2	NP_982279.1	Q8WW27	ABEC4_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	202					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						AGACACCACTTATAAAGCTGT	0.502													A|||	555	0.110823	0.239	0.0418	5008	,	,		21442	0.1091		0.0318	False		,,,				2504	0.0695				p.I202I		Atlas-SNP	.											.	APOBEC4	45	.	0			c.A606T						PASS	.	A	,	880,3526	742.9+/-411.4	81,718,1404	65.0	68.0	67.0		,606	-2.9	0.0	1	dbSNP_120	67	242,8358	808.6+/-407.2	1,240,4059	yes	intron,coding-synonymous	RGL1,APOBEC4	NM_015149.3,NM_203454.2	,	82,958,5463	AA,AT,TT		2.814,19.9728,8.6268	,	,202/368	183617311	1122,11884	2203	4300	6503	SO:0001819	synonymous_variant	403314	exon2			ACCACTTATAAAG	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.606A>T	1.37:g.183617311T>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	115	45	0.391304	NM_203454	Q8N7F6	Silent	SNP	ENST00000308641.4	37	CCDS1358.1																																																																																			T|0.917;A|0.083	0.083	strong		0.502	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454	
OR5L2	26338	hgsc.bcm.edu	37	11	55595012	55595012	+	Silent	SNP	A	A	T	rs35645945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55595012A>T	ENST00000378397.1	+	1	318	c.318A>T	c.(316-318)acA>acT	p.T106T		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	106						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)				TGTTTTGCACATGTGGAGTCA	0.483										HNSCC(27;0.073)																											p.T106T		Atlas-SNP	.											.	OR5L2	135	.	0			c.A318T						PASS	.						187.0	175.0	179.0					11																	55595012		2199	4295	6494	SO:0001819	synonymous_variant	26338	exon1			TTGCACATGTGGA	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.318A>T	11.37:g.55595012A>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	129	54	0.418605	NM_001004739	Q6IF66|Q96RB2	Silent	SNP	ENST00000378397.1	37	CCDS31511.1																																																																																			A|0.934;T|0.066	0.066	strong		0.483	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
WDR90	197335	hgsc.bcm.edu	37	16	709001	709001	+	Missense_Mutation	SNP	C	C	A	rs4984906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:709001C>A	ENST00000293879.4	+	24	3001	c.3001C>A	c.(3001-3003)Cct>Act	p.P1001T	LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Missense_Mutation_p.P1001T			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1001			P -> T (in dbSNP:rs4984906). {ECO:0000269|PubMed:14702039}.							endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				TGTCCTGGCCCCTACTGAGAG	0.647													G|||	3523	0.703474	0.9024	0.6052	5008	,	,		16851	0.9802		0.3718	False		,,,				2504	0.5603				p.P1001T		Atlas-SNP	.											.	WDR90	107	.	0			c.C3001A						PASS	.	G	THR/PRO	3390,816		1376,638,89	81.0	100.0	94.0		3001	-9.6	0.0	16	dbSNP_111	94	3087,5335		584,1919,1708	yes	missense	WDR90	NM_145294.4	38	1960,2557,1797	AA,AC,CC		36.654,19.4009,48.7092	benign	1001/1749	709001	6477,6151	2103	4211	6314	SO:0001583	missense	197335	exon24			CTGGCCCCTACTG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.3001C>A	16.37:g.709001C>A	ENSP00000293879:p.Pro1001Thr	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	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	
KIF9	64147	hgsc.bcm.edu	37	3	47286320	47286320	+	Missense_Mutation	SNP	T	T	C	rs115610071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47286320T>C	ENST00000265529.3	-	16	2155	c.1475A>G	c.(1474-1476)aAg>aGg	p.K492R	KIF9_ENST00000452770.2_Missense_Mutation_p.K492R|KIF9_ENST00000444589.2_Missense_Mutation_p.K492R|KIF9_ENST00000487440.1_5'UTR|KIF9-AS1_ENST00000429315.3_RNA|KIF9_ENST00000352910.4_Missense_Mutation_p.K399R|KIF9_ENST00000335044.2_Missense_Mutation_p.K492R			Q9HAQ2	KIF9_HUMAN	kinesin family member 9	492					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle disassembly (GO:1903008)|regulation of podosome assembly (GO:0071801)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|podosome (GO:0002102)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein dimerization activity (GO:0046983)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(15)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)	34		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CTTGGCTTTCTTCCCAGGTTT	0.567													T|||	19	0.00379393	0.0	0.0086	5008	,	,		19521	0.001		0.008	False		,,,				2504	0.0041				p.K492R	Colon(44;962 1147 15977 24541)	Atlas-SNP	.											.	KIF9	59	.	0			c.A1475G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	7,4399	12.9+/-30.5	0,7,2196	177.0	149.0	158.0		1475,1475,1475	4.7	1.0	3	dbSNP_132	158	103,8497	56.4+/-117.6	2,99,4199	yes	missense,missense,missense	KIF9	NM_001134878.1,NM_022342.4,NM_182902.3	26,26,26	2,106,6395	CC,CT,TT		1.1977,0.1589,0.8458	benign,benign,benign	492/791,492/726,492/791	47286320	110,12896	2203	4300	6503	SO:0001583	missense	64147	exon15			GCTTTCTTCCCAG	AF311212	CCDS2751.1, CCDS2752.1	3p21.31	2008-03-03			ENSG00000088727	ENSG00000088727		"""Kinesins"""	16666	protein-coding gene	gene with protein product		607910				11483511	Standard	NM_022342		Approved	MGC104186	uc003cqx.3	Q9HAQ2	OTTHUMG00000133512	ENST00000265529.3:c.1475A>G	3.37:g.47286320T>C	ENSP00000265529:p.Lys492Arg	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_182902	Q86Z28|Q9H8A4	Missense_Mutation	SNP	ENST00000265529.3	37	CCDS2752.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	T	8.708	0.911321	0.17833	0.001589	0.011977	ENSG00000088727	ENST00000335044;ENST00000265529;ENST00000444589;ENST00000452770;ENST00000352910	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	4.65	4.65	0.58169	.	0.263417	0.32372	N	0.006192	T	0.19208	0.0461	N	0.16478	0.41	0.24963	N	0.991717	P;B	0.38020	0.615;0.373	B;B	0.34779	0.189;0.051	T	0.07849	-1.0751	10	0.23302	T	0.38	.	7.0449	0.25040	0.0:0.0998:0.0:0.9002	.	492;492	Q9HAQ2-2;Q9HAQ2	.;KIF9_HUMAN	R	492;492;492;492;399	ENSP00000333942:K492R;ENSP00000265529:K492R;ENSP00000414987:K492R;ENSP00000391100:K492R;ENSP00000292334:K399R	ENSP00000265529:K492R	K	-	2	0	KIF9	47261324	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	2.914000	0.48797	2.095000	0.63458	0.528000	0.53228	AAG	T|0.992;C|0.008	0.008	strong		0.567	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257475.2		
THAP4	51078	hgsc.bcm.edu	37	2	242572693	242572693	+	Silent	SNP	C	C	T	rs147500721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242572693C>T	ENST00000407315.1	-	2	1310	c.879G>A	c.(877-879)ccG>ccA	p.P293P		NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	293							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)		AAGGCTTCTGCGGTGTCGCGG	0.657													C|||	46	0.0091853	0.0325	0.0029	5008	,	,		15917	0.0		0.001	False		,,,				2504	0.0				p.P293P		Atlas-SNP	.											.	THAP4	27	.	0			c.G879A						PASS	.	C		190,4216	121.7+/-159.2	5,180,2018	74.0	80.0	78.0		879	-11.0	0.2	2	dbSNP_134	78	0,8592		0,0,4296	no	coding-synonymous	THAP4	NM_015963.5		5,180,6314	TT,TC,CC		0.0,4.3123,1.4618		293/578	242572693	190,12808	2203	4296	6499	SO:0001819	synonymous_variant	51078	exon2			CTTCTGCGGTGTC	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.879G>A	2.37:g.242572693C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_015963	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Silent	SNP	ENST00000407315.1	37	CCDS2551.1																																																																																			C|0.985;T|0.015	0.015	strong		0.657	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963	
SPPL2A	84888	hgsc.bcm.edu	37	15	51023216	51023216	+	Silent	SNP	G	G	C	rs76947817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51023216G>C	ENST00000261854.5	-	10	1309	c.1035C>G	c.(1033-1035)ggC>ggG	p.G345G		NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	345					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)		GGAGGAGAAGGCCTAGAAGTA	0.313													G|||	86	0.0171725	0.0635	0.0029	5008	,	,		15019	0.0		0.0	False		,,,				2504	0.0				p.G345G	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.C1035G						PASS	.	G		240,4152	134.5+/-170.7	6,228,1962	64.0	60.0	61.0		1035	1.6	1.0	15	dbSNP_131	61	1,8575	1.2+/-3.3	0,1,4287	no	coding-synonymous	SPPL2A	NM_032802.3		6,229,6249	CC,CG,GG		0.0117,5.4645,1.8584		345/521	51023216	241,12727	2196	4288	6484	SO:0001819	synonymous_variant	84888	exon10			GAGAAGGCCTAGA		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.1035C>G	15.37:g.51023216G>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	214	104	0.485981	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000261854.5	37	CCDS10138.1																																																																																			G|0.977;C|0.023	0.023	strong		0.313	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802	
SENP6	26054	hgsc.bcm.edu	37	6	76373002	76373002	+	Silent	SNP	G	G	A	rs16886792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:76373002G>A	ENST00000447266.2	+	9	1240	c.762G>A	c.(760-762)acG>acA	p.T254T	SENP6_ENST00000327284.8_Silent_p.T247T|SENP6_ENST00000370014.3_Silent_p.T254T|SENP6_ENST00000370010.2_Silent_p.T247T	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	254					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				TATTAAGAACGTCAATTCATC	0.353													G|||	71	0.0141773	0.053	0.0014	5008	,	,		17025	0.0		0.0	False		,,,				2504	0.0				p.T254T		Atlas-SNP	.											.	SENP6	189	.	0			c.G762A						PASS	.	G	,	190,3488		6,178,1655	108.0	102.0	104.0		741,762	-6.3	1.0	6	dbSNP_123	104	2,8180		0,2,4089	no	coding-synonymous,coding-synonymous	SENP6	NM_001100409.1,NM_015571.2	,	6,180,5744	AA,AG,GG		0.0244,5.1659,1.6189	,	247/1106,254/1113	76373002	192,11668	1839	4091	5930	SO:0001819	synonymous_variant	26054	exon9			AAGAACGTCAATT		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.762G>A	6.37:g.76373002G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Silent	SNP	ENST00000447266.2	37	CCDS47454.1																																																																																			G|0.985;A|0.015	0.015	strong		0.353	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
ABCB9	23457	hgsc.bcm.edu	37	12	123466304	123466304	+	5'Flank	SNP	A	A	G	rs74758272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123466304A>G	ENST00000542678.1	-	0	0				ARL6IP4_ENST00000392435.2_Missense_Mutation_p.K220R|ARL6IP4_ENST00000439686.2_Missense_Mutation_p.K108R|ARL6IP4_ENST00000412505.2_Missense_Mutation_p.K97R|ARL6IP4_ENST00000315580.5_Missense_Mutation_p.K239R|RP11-197N18.2_ENST00000540866.2_RNA|ARL6IP4_ENST00000453766.2_Missense_Mutation_p.K231R|ARL6IP4_ENST00000357866.4_Missense_Mutation_p.K108R|ARL6IP4_ENST00000426960.2_Missense_Mutation_p.K97R|ARL6IP4_ENST00000543566.1_Missense_Mutation_p.K220R|ARL6IP4_ENST00000454885.2_Missense_Mutation_p.K105R			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9						peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		aagaagaagaagaagaggaag	0.577													A|||	546	0.109026	0.3941	0.0346	5008	,	,		19865	0.0		0.001	False		,,,				2504	0.0				p.K239R	Ovarian(49;786 1333 9175 38236)	Atlas-SNP	.											.	ARL6IP4	14	.	0			c.A716G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	1308,3046		202,904,1071	26.0	27.0	27.0		692,659,659,716	2.6	1.0	12	dbSNP_131	27	23,8529		0,23,4253	yes	missense,missense,missense,missense	ARL6IP4	NM_001002251.1,NM_001002252.1,NM_016638.2,NM_018694.2	26,26,26,26	202,927,5324	GG,GA,AA		0.2689,30.0413,10.313	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	231/353,220/339,220/342,239/361	123466304	1331,11575	2177	4276	6453	SO:0001631	upstream_gene_variant	51329	exon3			AGAAGAAGAAGAG	U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"""ATP binding cassette transporters / subfamily B"""	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78			12.37:g.123466304A>G	Exception_encountered	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_018694	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	193	0.08836996336996338	184	0.37398373983739835	9	0.024861878453038673	0	0.0	0	0.0	A	12.68	2.010868	0.35511	0.300413	0.002689	ENSG00000182196	ENST00000544323;ENST00000543566;ENST00000315580;ENST00000542099;ENST00000392435;ENST00000413381;ENST00000426960;ENST00000453766;ENST00000454885;ENST00000412505;ENST00000439686;ENST00000456762;ENST00000357866	T;T;T;T;T;T;T;T;T;T;T;T;T	0.53857	1.22;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.69;0.6;0.6;0.69	4.96	2.59	0.31030	.	0.666484	0.15025	N	0.284816	T	0.00012	0.0000	L	0.56769	1.78	0.28457	P	0.9160855999999999	B;B;P;P;P;P	0.39326	0.026;0.021;0.617;0.668;0.467;0.617	B;B;B;B;B;B	0.40444	0.027;0.016;0.221;0.329;0.167;0.221	T	0.34850	-0.9812	9	0.27785	T	0.31	.	4.0754	0.09901	0.6128:0.0:0.2434:0.1437	.	105;231;220;220;239;231	B3V0L1;Q66PJ3-5;Q66PJ3-4;B3V0L0;Q66PJ3;Q66PJ3-2	.;.;.;.;AR6P4_HUMAN;.	R	220;220;239;228;220;108;97;231;105;97;108;98;108	ENSP00000445309:K220R;ENSP00000442718:K220R;ENSP00000313422:K239R;ENSP00000442200:K228R;ENSP00000376230:K220R;ENSP00000441406:K108R;ENSP00000406036:K97R;ENSP00000414847:K231R;ENSP00000396723:K105R;ENSP00000413132:K97R;ENSP00000396365:K108R;ENSP00000391598:K98R;ENSP00000350532:K108R	ENSP00000313422:K239R	K	+	2	0	ARL6IP4	122032257	1.000000	0.71417	0.994000	0.49952	0.062000	0.15995	1.400000	0.34577	0.336000	0.23639	0.397000	0.26171	AAG	A|0.880;G|0.120	0.120	strong		0.577	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624	
PREPL	9581	hgsc.bcm.edu	37	2	44571008	44571008	+	Silent	SNP	A	A	T	rs72875319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44571008A>T	ENST00000409936.1	-	5	929	c.492T>A	c.(490-492)gcT>gcA	p.A164A	PREPL_ENST00000409957.1_Silent_p.A75A|PREPL_ENST00000541738.1_Silent_p.A75A|PREPL_ENST00000378520.3_Silent_p.A164A|PREPL_ENST00000540817.1_5'UTR|PREPL_ENST00000409272.1_Silent_p.A164A|PREPL_ENST00000378511.3_Silent_p.A164A|PREPL_ENST00000409411.1_Silent_p.A75A|PREPL_ENST00000260648.6_Silent_p.A164A|PREPL_ENST00000410081.1_Silent_p.A164A	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	164						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TTTCATCTGGAGCAACTCTGA	0.363													A|||	190	0.0379393	0.1309	0.0231	5008	,	,		16552	0.0		0.001	False		,,,				2504	0.0				p.A164A		Atlas-SNP	.											.	PREPL	69	.	0			c.T492A						PASS	.	A	,,,,,,	487,3919	228.8+/-243.5	28,431,1744	110.0	113.0	112.0		492,492,492,492,225,225,492	4.5	1.0	2	dbSNP_130	112	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PREPL	NM_001042385.2,NM_001042386.2,NM_001171603.1,NM_001171606.1,NM_001171613.1,NM_001171617.1,NM_006036.4	,,,,,,	28,433,6042	TT,TA,AA		0.0233,11.0531,3.7598	,,,,,,	164/666,164/662,164/728,164/728,75/639,75/639,164/728	44571008	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	9581	exon5			ATCTGGAGCAACT	AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.492T>A	2.37:g.44571008A>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	114	50	0.438596	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Silent	SNP	ENST00000409936.1	37	CCDS33190.1																																																																																			A|0.966;T|0.034	0.034	strong		0.363	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036	
PLG	5340	hgsc.bcm.edu	37	6	161139857	161139857	+	Silent	SNP	A	A	G	rs13231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:161139857A>G	ENST00000308192.9	+	9	1146	c.1083A>G	c.(1081-1083)caA>caG	p.Q361Q		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	361				Q -> E (in Ref. 7; AA sequence and 9; AA sequence). {ECO:0000305}.	blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CCACGGAACAATTGGCTCCCA	0.498													G|||	683	0.136382	0.1452	0.1744	5008	,	,		17688	0.0		0.2922	False		,,,				2504	0.0777				p.Q361Q		Atlas-SNP	.											.	PLG	150	.	0			c.A1083G						PASS	.	G		777,3629	752.2+/-412.3	59,659,1485	76.0	72.0	73.0		1083	-8.7	0.0	6	dbSNP_52	73	2587,6013	689.3+/-404.3	365,1857,2078	no	coding-synonymous	PLG	NM_000301.3		424,2516,3563	GG,GA,AA		30.0814,17.635,25.865		361/811	161139857	3364,9642	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon9			GGAACAATTGGCT	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1083A>G	6.37:g.161139857A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			A|0.787;G|0.213	0.213	strong		0.498	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
OR2T3	343173	hgsc.bcm.edu	37	1	248637381	248637381	+	Missense_Mutation	SNP	G	G	A	rs139789199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248637381G>A	ENST00000359594.2	+	1	755	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GAAGGCCTTGGCCACCTGCTC	0.562																																					p.A244T		Atlas-SNP	.											OR2T3,NS,carcinoma,0,3	OR2T3	79	3	0			c.G730A						PASS	.	G	THR/ALA	108,4298	63.5+/-100.7	4,100,2099	200.0	168.0	179.0		730	-4.7	0.0	1	dbSNP_134	179	4,8596	3.0+/-9.4	0,4,4296	no	missense	OR2T3	NM_001005495.1	58	4,104,6395	AA,AG,GG		0.0465,2.4512,0.8611	benign	244/319	248637381	112,12894	2203	4300	6503	SO:0001583	missense	343173	exon1			GCCTTGGCCACCT		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.730G>A	1.37:g.248637381G>A	ENSP00000352604:p.Ala244Thr	Somatic	658	1	0.00151976		WXS	Illumina HiSeq	Phase_I	839	152	0.181168	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	56	0.02564102564102564	16	0.032520325203252036	7	0.019337016574585635	21	0.03671328671328671	12	0.0158311345646438	g	8.134	0.783767	0.16189	0.024512	4.65E-4	ENSG00000196539	ENST00000359594	T	0.00063	8.78	2.37	-4.74	0.03249	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	L	0.32530	0.975	0.09310	N	1	B	0.29531	0.247	B	0.37888	0.26	T	0.02167	-1.1202	9	0.27082	T	0.32	.	3.8534	0.08965	0.2803:0.0:0.43:0.2897	.	244	Q8NH03	OR2T3_HUMAN	T	244	ENSP00000352604:A244T	ENSP00000352604:A244T	A	+	1	0	OR2T3	246704004	0.000000	0.05858	0.001000	0.08648	0.247000	0.25773	-1.692000	0.01918	-1.238000	0.02535	0.186000	0.17326	GCC	G|0.987;A|0.013	0.013	strong		0.562	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
ITIH4	3700	hgsc.bcm.edu	37	3	52860876	52860876	+	Silent	SNP	G	G	A	rs143427404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52860876G>A	ENST00000266041.4	-	4	546	c.450C>T	c.(448-450)ctC>ctT	p.L150L	ITIH4_ENST00000434759.3_Silent_p.L62L|ITIH4_ENST00000485816.1_Silent_p.L150L|ITIH4_ENST00000346281.5_Silent_p.L150L|ITIH4_ENST00000406595.1_Silent_p.L150L|RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4-AS1_ENST00000478366.1_RNA	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	150					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)		AACGCCGCTTGAGCAGCTCCT	0.612													G|||	10	0.00199681	0.0	0.0058	5008	,	,		19934	0.0		0.006	False		,,,				2504	0.0				p.L150L		Atlas-SNP	.											ITIH4,NS,carcinoma,-2,1	ITIH4	74	1	0			c.C450T						PASS	.	G	,	10,4396	16.8+/-37.8	0,10,2193	68.0	66.0	67.0		450,450	-0.1	0.1	3	dbSNP_134	67	96,8504	53.6+/-114.3	1,94,4205	no	coding-synonymous,coding-synonymous	ITIH4	NM_001166449.1,NM_002218.4	,	1,104,6398	AA,AG,GG		1.1163,0.227,0.815	,	150/901,150/931	52860876	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	3700	exon4			CCGCTTGAGCAGC	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.450C>T	3.37:g.52860876G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_001166449	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Silent	SNP	ENST00000266041.4	37	CCDS2865.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	6.946	0.544330	0.13312	0.00227	0.011163	ENSG00000055955	ENST00000441637	.	.	.	5.4	-0.0456	0.13850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-29.1602	9.2513	0.37557	0.0785:0.6437:0.1828:0.095	.	.	.	.	X	20	.	.	Q	-	1	0	ITIH4	52835916	0.000000	0.05858	0.113000	0.21522	0.757000	0.42996	-0.468000	0.06656	-0.013000	0.14199	0.561000	0.74099	CAA	G|0.995;A|0.005	0.005	strong		0.612	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
PSG2	5670	hgsc.bcm.edu	37	19	43585334	43585334	+	Silent	SNP	T	T	G	rs79582550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43585334T>G	ENST00000406487.1	-	2	227	c.129A>C	c.(127-129)ccA>ccC	p.P43P	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	43	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.P43P(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)				CGGAAACTTTTGGTGGCTGGG	0.488																																					p.P43P		Atlas-SNP	.											PSG2,NS,carcinoma,-1,2	PSG2	84	2	2	Substitution - coding silent(2)	lung(2)	c.A129C						scavenged	.						171.0	168.0	169.0					19																	43585334		2203	4299	6502	SO:0001819	synonymous_variant	5670	exon2			AACTTTTGGTGGC		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.129A>C	19.37:g.43585334T>G		Somatic	376	1	0.00265957		WXS	Illumina HiSeq	Phase_I	462	63	0.136364	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			T|0.944;G|0.056	0.056	strong		0.488	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
BLM	641	hgsc.bcm.edu	37	15	91337479	91337479	+	Silent	SNP	G	G	A	rs2227933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91337479G>A	ENST00000355112.3	+	16	3220	c.3102G>A	c.(3100-3102)acG>acA	p.T1034T	BLM_ENST00000560509.1_Silent_p.T1034T|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1034					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			AAAATATAACGGAATGCAGGA	0.338			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome				G|||	757	0.151158	0.1974	0.1124	5008	,	,		13066	0.1855		0.165	False		,,,				2504	0.0665				p.T1034T		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.G3102A						PASS	.	G		833,3563	328.8+/-300.7	79,675,1444	104.0	106.0	106.0		3102	-8.5	0.9	15	dbSNP_98	106	1564,7028	292.0+/-300.6	141,1282,2873	no	coding-synonymous	BLM	NM_000057.2		220,1957,4317	AA,AG,GG		18.203,18.949,18.4555		1034/1418	91337479	2397,10591	2198	4296	6494	SO:0001819	synonymous_variant	641	exon16	Familial Cancer Database		TATAACGGAATGC	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3102G>A	15.37:g.91337479G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	235	90	0.382979	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	37	CCDS10363.1																																																																																			A|0.170;G|0.830	0.170	strong		0.338	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
DTX2	113878	hgsc.bcm.edu	37	7	76132805	76132805	+	Silent	SNP	C	C	G	rs73703182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:76132805C>G	ENST00000324432.5	+	10	1962	c.1452C>G	c.(1450-1452)ccC>ccG	p.P484P	DTX2_ENST00000413936.2_Silent_p.P484P|DTX2_ENST00000446600.1_Silent_p.P393P|DTX2_ENST00000446820.2_Silent_p.P437P|DTX2_ENST00000307569.8_Silent_p.P437P|DTX2_ENST00000430490.2_Silent_p.P484P	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	484					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						GGACCCAGCCCCAGGGAAAGA	0.572													.|||	88	0.0175719	0.0651	0.0029	5008	,	,		18601	0.0		0.0	False		,,,				2504	0.0				p.P484P		Atlas-SNP	.											.	DTX2	64	.	0			c.C1452G						PASS	.	C	,,,	241,4159		11,219,1970	70.0	66.0	67.0		1452,1452,1311,1452	3.0	1.0	7	dbSNP_130	67	2,8592		0,2,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	11,221,6265	GG,GC,CC		0.0233,5.4773,1.8701	,,,	484/623,484/623,437/576,484/623	76132805	243,12751	2200	4297	6497	SO:0001819	synonymous_variant	113878	exon9			CCAGCCCCAGGGA		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.1452C>G	7.37:g.76132805C>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	173	95	0.549133	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			C|0.977;G|0.023	0.023	strong		0.572	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
KANK2	25959	hgsc.bcm.edu	37	19	11289307	11289307	+	Missense_Mutation	SNP	C	C	T	rs149142528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11289307C>T	ENST00000586659.1	-	5	1653	c.1339G>A	c.(1339-1341)Gtg>Atg	p.V447M	KANK2_ENST00000589894.1_Missense_Mutation_p.V447M|KANK2_ENST00000355150.5_Missense_Mutation_p.V447M|KANK2_ENST00000589359.1_Missense_Mutation_p.V447M|KANK2_ENST00000432929.2_Missense_Mutation_p.V447M			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	447					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TGGGTGGGCACTCGGCCTGTG	0.672													C|||	79	0.0157748	0.0575	0.0043	5008	,	,		12124	0.0		0.0	False		,,,				2504	0.0				p.V447M		Atlas-SNP	.											.	KANK2	47	.	0			c.G1339A						PASS	.	C	MET/VAL,MET/VAL	197,4209	123.7+/-161.0	4,189,2010	42.0	44.0	43.0		1339,1339	1.1	0.0	19	dbSNP_134	43	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	21,21	4,193,6306	TT,TC,CC		0.0465,4.4712,1.5454	benign,benign	447/852,447/860	11289307	201,12805	2203	4300	6503	SO:0001583	missense	25959	exon3			TGGGCACTCGGCC	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	29300	protein-coding gene	gene with protein product		614610	"""matrix-remodelling associated 3"", ""ankyrin repeat domain 25"""	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.1339G>A	19.37:g.11289307C>T	ENSP00000465650:p.Val447Met	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	C	9.193	1.026620	0.19512	0.044712	4.65E-4	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.37411	1.2;1.2	3.5	1.14	0.20703	.	2.220440	0.02225	N	0.064340	T	0.06050	0.0157	L	0.42245	1.32	0.09310	N	1	B;B	0.28512	0.214;0.001	B;B	0.22753	0.041;0.006	T	0.12142	-1.0559	10	0.46703	T	0.11	-28.0739	7.049	0.25063	0.1975:0.6112:0.1913:0.0	.	447;447	Q63ZY3;Q63ZY3-2	KANK2_HUMAN;.	M	447	ENSP00000395650:V447M;ENSP00000347276:V447M	ENSP00000347276:V447M	V	-	1	0	KANK2	11150307	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.164000	0.09983	0.241000	0.21283	0.467000	0.42956	GTG	C|0.987;T|0.013	0.013	strong		0.672	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
NCKAP1	10787	hgsc.bcm.edu	37	2	183847598	183847598	+	Missense_Mutation	SNP	G	G	A	rs557066776		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:183847598G>A	ENST00000361354.4	-	12	1531	c.1159C>T	c.(1159-1161)Cgt>Tgt	p.R387C	NCKAP1_ENST00000360982.2_Missense_Mutation_p.R393C	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	387					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TCTGCATGACGAAGTAGCCAG	0.308													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19349	0.0		0.0	False		,,,				2504	0.0				p.R393C		Atlas-SNP	.											NCKAP1,colon,carcinoma,+1,1	NCKAP1	105	1	0			c.C1177T						scavenged	.						46.0	46.0	46.0					2																	183847598		2203	4300	6503	SO:0001583	missense	10787	exon13			CATGACGAAGTAG	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.1159C>T	2.37:g.183847598G>A	ENSP00000355348:p.Arg387Cys	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	213	4	0.0187793	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Missense_Mutation	SNP	ENST00000361354.4	37	CCDS2287.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.674779	0.88445	.	.	ENSG00000061676	ENST00000361354;ENST00000360982	T;T	0.39056	1.1;1.1	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.70640	0.3247	M	0.87758	2.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.74850	-0.3524	10	0.52906	T	0.07	-10.267	18.95	0.92638	0.0:0.0:1.0:0.0	.	387;393	Q9Y2A7;Q9Y2A7-2	NCKP1_HUMAN;.	C	387;393	ENSP00000355348:R387C;ENSP00000354251:R393C	ENSP00000354251:R393C	R	-	1	0	NCKAP1	183555843	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.668000	0.83897	2.485000	0.83878	0.655000	0.94253	CGT	.	.	none		0.308	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842	
CAPN1	823	hgsc.bcm.edu	37	11	64981853	64981853	+	IGR	SNP	G	G	T	rs239259	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64981853G>T	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)		CCGTCTACATGGCCGGGGTGC	0.667													G|||	1489	0.297324	0.1082	0.268	5008	,	,		14644	0.3889		0.4115	False		,,,				2504	0.362				p.M146I		Atlas-SNP	.											SLC22A20,NS,carcinoma,0,4	SLC22A20	36	4	0			c.G438T						PASS	.	G	ILE/MET	617,3463		55,507,1478	30.0	34.0	33.0		438	4.5	1.0	11	dbSNP_79	33	3571,4793		742,2087,1353	yes	missense	SLC22A20	NM_001004326.4	10	797,2594,2831	TT,TG,GG		42.6949,15.1225,33.6548	probably-damaging	146/350	64981853	4188,8256	2040	4182	6222	SO:0001628	intergenic_variant	440044	exon2			CTACATGGCCGGG	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.64981853G>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_001004326	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			G|0.667;T|0.333	0.333	strong		0.667	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
NQO2	4835	hgsc.bcm.edu	37	6	3017138	3017138	+	Silent	SNP	C	C	T	rs1130428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:3017138C>T	ENST00000338130.2	+	9	1150	c.438C>T	c.(436-438)tcC>tcT	p.S146S	NQO2_ENST00000380455.4_Silent_p.S146S|NQO2_ENST00000380454.4_Silent_p.S108S|NQO2_ENST00000380441.1_Silent_p.S108S|NQO2_ENST00000380430.1_Silent_p.S146S			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	146					memory (GO:0007613)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	dihydronicotinamide riboside quinone reductase activity (GO:0001512)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADPH dehydrogenase (quinone) activity (GO:0008753)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Dabigatran etexilate(DB06695)|Flavin adenine dinucleotide(DB03147)|Melatonin(DB01065)|Menadione(DB00170)|Primaquine(DB01087)	CGCTCCTTTCCGTAACCACGG	0.552													c|||	155	0.0309505	0.0613	0.0288	5008	,	,		19744	0.0		0.0497	False		,,,				2504	0.0041				p.S146S		Atlas-SNP	.											.	NQO2	21	.	0			c.C438T						PASS	.	T		239,4167	140.4+/-175.9	5,229,1969	130.0	99.0	110.0		438	-10.8	0.0	6	dbSNP_86	110	324,8276	113.9+/-173.9	11,302,3987	no	coding-synonymous	NQO2	NM_000904.3		16,531,5956	TT,TC,CC		3.7674,5.4244,4.3288		146/232	3017138	563,12443	2203	4300	6503	SO:0001819	synonymous_variant	4835	exon6			CCTTTCCGTAACC	U07736	CCDS4481.1, CCDS75388.1	6p25.2	2012-09-20	2001-11-30	2001-12-07	ENSG00000124588	ENSG00000124588	1.6.5.2		7856	protein-coding gene	gene with protein product		160998	"""NAD(P)H menadione oxidoreductase 2, dioxin-inducible"""	NMOR2		1691923	Standard	XM_005249152		Approved	QR2, DHQV, DIA6	uc003mus.2	P16083	OTTHUMG00000014130	ENST00000338130.2:c.438C>T	6.37:g.3017138C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	55	32	0.581818	NM_000904	B2R492|Q5TD04	Silent	SNP	ENST00000338130.2	37	CCDS4481.1																																																																																			C|0.960;T|0.040	0.040	strong		0.552	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1		
KIF3C	3797	hgsc.bcm.edu	37	2	26177198	26177198	+	Silent	SNP	A	A	G	rs17047211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26177198A>G	ENST00000264712.3	-	4	2406	c.1827T>C	c.(1825-1827)taT>taC	p.Y609Y	KIF3C_ENST00000405914.1_Silent_p.Y609Y|KIF3C_ENST00000496378.1_5'Flank	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	609					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCACGCGGATATACTCATCAT	0.627													G|||	703	0.140375	0.2685	0.121	5008	,	,		17832	0.001		0.1481	False		,,,				2504	0.1166				p.Y609Y		Atlas-SNP	.											.	KIF3C	79	.	0			c.T1827C						PASS	.	G		1108,3298	718.5+/-408.8	137,834,1232	91.0	70.0	77.0		1827	4.1	1.0	2	dbSNP_123	77	1347,7253	756.2+/-407.5	112,1123,3065	no	coding-synonymous	KIF3C	NM_002254.6		249,1957,4297	GG,GA,AA		15.6628,25.1475,18.8759		609/794	26177198	2455,10551	2203	4300	6503	SO:0001819	synonymous_variant	3797	exon4			GCGGATATACTCA		CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731		"""Kinesins"""	6321	protein-coding gene	gene with protein product		602845				9480755	Standard	NM_002254		Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000264712.3:c.1827T>C	2.37:g.26177198A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_002254	O43544|Q4ZG18|Q53SX5|Q562F7	Silent	SNP	ENST00000264712.3	37	CCDS1719.1																																																																																			A|0.828;G|0.172	0.172	strong		0.627	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1		
TTN	7273	hgsc.bcm.edu	37	2	179435337	179435337	+	Silent	SNP	T	T	G	rs6732060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179435337T>G	ENST00000591111.1	-	276	70823	c.70599A>C	c.(70597-70599)gcA>gcC	p.A23533A	TTN_ENST00000342175.6_Silent_p.A16301A|TTN_ENST00000359218.5_Silent_p.A16234A|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Silent_p.A16109A|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Silent_p.A25174A|TTN_ENST00000342992.6_Silent_p.A22606A|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23533	Ig-like 119.				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)			CGACACGTACTGCATCTTTTA	0.438													T|||	717	0.143171	0.2405	0.1801	5008	,	,		22705	0.0258		0.0527	False		,,,				2504	0.1994				p.A25174A		Atlas-SNP	.											.	TTN	18412	.	0			c.A75522C						PASS	.	T	,,,	826,3038		99,628,1205	125.0	114.0	117.0		48327,67818,48702,48903	1.9	0.6	2	dbSNP_116	117	270,7992		9,252,3870	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	108,880,5075	GG,GT,TT		3.268,21.3768,9.0384	,,,	16109/26927,22606/33424,16234/27052,16301/27119	179435337	1096,11030	1932	4131	6063	SO:0001819	synonymous_variant	7273	exon326			ACGTACTGCATCT	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.70599A>C	2.37:g.179435337T>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	168	72	0.428571	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|0.892;G|0.108	0.108	strong		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179605843	179605843	+	Silent	SNP	G	G	A	rs55895721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179605843G>A	ENST00000591111.1	-	46	11390	c.11166C>T	c.(11164-11166)ccC>ccT	p.P3722P	TTN_ENST00000342175.6_Silent_p.P3868P|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Silent_p.P3801P|TTN_ENST00000460472.2_Silent_p.P3676P|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000589042.1_Silent_p.P4039P|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33762					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)			TTGCTTTGCAGGGGGTATCAG	0.502													G|||	120	0.0239617	0.0877	0.0058	5008	,	,		19060	0.0		0.0	False		,,,				2504	0.0				p.P4039P		Atlas-SNP	.											.	TTN	18412	.	0			c.C12117T						PASS	.	G	,,,	221,3551		9,203,1674	127.0	126.0	126.0		11028,,11403,11604	-0.9	0.0	2	dbSNP_129	126	7,8233		0,7,4113	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	9,210,5787	AA,AG,GG		0.085,5.859,1.8981	,,,	3676/26927,,3801/27052,3868/27119	179605843	228,11784	1886	4120	6006	SO:0001819	synonymous_variant	7273	exon48			TTTGCAGGGGGTA	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.11166C>T	2.37:g.179605843G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	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|0.981;A|0.019	0.019	strong		0.502	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZPBP2	124626	hgsc.bcm.edu	37	17	38027824	38027824	+	Missense_Mutation	SNP	G	G	A	rs35829084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38027824G>A	ENST00000348931.4	+	4	543	c.352G>A	c.(352-354)Gca>Aca	p.A118T	ZPBP2_ENST00000584588.1_Missense_Mutation_p.A118T|ZPBP2_ENST00000377940.3_Missense_Mutation_p.A96T	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	118			A -> T (in dbSNP:rs35829084).		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)			GACTGTTAAAGCAGAAACTCA	0.318													G|||	148	0.0295527	0.1089	0.0058	5008	,	,		16323	0.0		0.0	False		,,,				2504	0.0				p.A118T		Atlas-SNP	.											.	ZPBP2	33	.	0			c.G352A						PASS	.	G	THR/ALA,THR/ALA	382,4024	189.9+/-215.9	25,332,1846	77.0	80.0	79.0		286,352	4.4	1.0	17	dbSNP_126	79	3,8589	2.2+/-6.3	0,3,4293	yes	missense,missense	ZPBP2	NM_198844.2,NM_199321.2	58,58	25,335,6139	AA,AG,GG		0.0349,8.67,2.962	probably-damaging,probably-damaging	96/317,118/339	38027824	385,12613	2203	4296	6499	SO:0001583	missense	124626	exon4			GTTAAAGCAGAAA	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.352G>A	17.37:g.38027824G>A	ENSP00000335384:p.Ala118Thr	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	154	85	0.551948	NM_199321	A8K8L8|Q6X783|Q86XL5	Missense_Mutation	SNP	ENST00000348931.4	37	CCDS11352.1	57	0.0260989010989011	55	0.11178861788617886	2	0.0055248618784530384	0	0.0	0	0.0	G	9.022	0.985096	0.18889	0.0867	3.49E-4	ENSG00000186075	ENST00000348931;ENST00000377940	T;T	0.55760	0.5;0.5	5.36	4.39	0.52855	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.455087	0.21308	N	0.076697	T	0.00784	0.0026	L	0.39898	1.24	0.22226	N	0.999272	B;B	0.26635	0.112;0.155	B;B	0.20955	0.029;0.032	T	0.00904	-1.1520	10	0.27785	T	0.31	-4.4881	6.3234	0.21231	0.2041:0.0:0.7959:0.0	rs35829084	96;118	Q6X784-2;Q6X784	.;ZPBP2_HUMAN	T	118;96	ENSP00000335384:A118T;ENSP00000367174:A96T	ENSP00000335384:A118T	A	+	1	0	ZPBP2	35281350	0.997000	0.39634	0.995000	0.50966	0.248000	0.25809	2.785000	0.47782	2.506000	0.84524	0.460000	0.39030	GCA	G|0.968;A|0.032	0.032	strong		0.318	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844	
SLC27A5	10998	hgsc.bcm.edu	37	19	59023213	59023213	+	Missense_Mutation	SNP	A	A	C	rs146147877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:59023213A>C	ENST00000263093.2	-	1	219	c.110T>G	c.(109-111)cTg>cGg	p.L37R	SLC27A5_ENST00000601355.1_Missense_Mutation_p.L37R	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	37					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		GGGATCCCCCAGGAGCCAGCG	0.687													A|||	24	0.00479233	0.0182	0.0	5008	,	,		17742	0.0		0.0	False		,,,				2504	0.0				p.L37R		Atlas-SNP	.											.	SLC27A5	58	.	0			c.T110G						PASS	.	A	ARG/LEU	53,4285		0,53,2116	8.0	9.0	9.0		110	4.3	1.0	19	dbSNP_134	9	0,8524		0,0,4262	yes	missense	SLC27A5	NM_012254.2	102	0,53,6378	CC,CA,AA		0.0,1.2218,0.4121	probably-damaging	37/691	59023213	53,12809	2169	4262	6431	SO:0001583	missense	10998	exon1			TCCCCCAGGAGCC	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.110T>G	19.37:g.59023213A>C	ENSP00000263093:p.Leu37Arg	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	a	14.75	2.628307	0.46944	0.012218	0.0	ENSG00000083807	ENST00000263093	T	0.59638	0.25	4.31	4.31	0.51392	.	0.334193	0.17602	N	0.168398	T	0.48241	0.1489	M	0.62723	1.935	0.37946	D	0.932495	D	0.58620	0.983	P	0.53401	0.725	T	0.66368	-0.5941	10	0.87932	D	0	-16.4075	10.4112	0.44294	1.0:0.0:0.0:0.0	.	37	Q9Y2P5	S27A5_HUMAN	R	37	ENSP00000263093:L37R	ENSP00000263093:L37R	L	-	2	0	SLC27A5	63715025	1.000000	0.71417	0.975000	0.42487	0.133000	0.20885	3.179000	0.50887	1.889000	0.54706	0.374000	0.22700	CTG	A|0.995;C|0.005	0.005	strong		0.687	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
UPF2	26019	hgsc.bcm.edu	37	10	12071397	12071397	+	Silent	SNP	G	G	A	rs11257490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:12071397G>A	ENST00000356352.2	-	2	965	c.492C>T	c.(490-492)ctC>ctT	p.L164L	UPF2_ENST00000357604.5_Silent_p.L164L|UPF2_ENST00000397053.2_Silent_p.L164L			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	164					gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				AACTTGAGTCGAGGCGGCTGA	0.403													A|||	1311	0.261781	0.2814	0.2507	5008	,	,		16409	0.4435		0.161	False		,,,				2504	0.1595				p.L164L		Atlas-SNP	.											.	UPF2	111	.	0			c.C492T						PASS	.	A	,	1166,3240	703.9+/-407.1	145,876,1182	102.0	111.0	108.0		492,492	-3.3	1.0	10	dbSNP_120	108	1443,7157	746.8+/-407.3	132,1179,2989	no	coding-synonymous,coding-synonymous	UPF2	NM_015542.2,NM_080599.1	,	277,2055,4171	AA,AG,GG		16.7791,26.4639,20.06	,	164/1273,164/1273	12071397	2609,10397	2203	4300	6503	SO:0001819	synonymous_variant	26019	exon3			TGAGTCGAGGCGG	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"""smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.492C>T	10.37:g.12071397G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	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		
LMNA	4000	hgsc.bcm.edu	37	1	156106185	156106185	+	Silent	SNP	T	T	C	rs505058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156106185T>C	ENST00000368300.4	+	7	1550	c.1338T>C	c.(1336-1338)gaT>gaC	p.D446D	LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000368301.2_Silent_p.D446D|LMNA_ENST00000473598.2_Silent_p.D347D|LMNA_ENST00000361308.4_Silent_p.D446D|LMNA_ENST00000368299.3_Silent_p.D446D|LMNA_ENST00000347559.2_Silent_p.D446D|LMNA_ENST00000392353.3_Silent_p.D365D|LMNA_ENST00000368297.1_Silent_p.D365D|LMNA_ENST00000448611.2_Silent_p.D334D	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	446	LTD.|Tail.		D -> V (in EDMD2). {ECO:0000269|PubMed:14684700}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					AGGAGGTGGATGAGGAGGGCA	0.602									Werner syndrome;Hutchinson-Gilford Progeria Syndrome				C|||	1248	0.249201	0.7247	0.098	5008	,	,		20622	0.0228		0.0865	False		,,,				2504	0.1145				p.D446D		Atlas-SNP	.											.	LMNA	31	.	0			c.T1338C						PASS	.	C	,,	2650,1756	492.7+/-362.5	782,1086,335	47.0	53.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1338,1338,1338	-5.0	0.9	1	dbSNP_83	51	653,7939	763.3+/-407.6	21,611,3664	yes	coding-synonymous,coding-synonymous,coding-synonymous	LMNA	NM_005572.3,NM_170707.2,NM_170708.2	,,	803,1697,3999	CC,CT,TT		7.6001,39.8547,25.4116	,,	446/573,446/665,446/635	156106185	3303,9695	2203	4296	6499	SO:0001819	synonymous_variant	4000	exon7	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	GGTGGATGAGGAG	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"""Intermediate filaments type V, lamins"""	6636	protein-coding gene	gene with protein product		150330	"""cardiomyopathy, dilated 1A (autosomal dominant)"", ""limb girdle muscular dystrophy 1B (autosomal dominant)"", ""progeria 1 (Hutchinson-Gilford type)"", ""lamin A/C-like 1"""	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1338T>C	1.37:g.156106185T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	37	CCDS1129.1	469	0.21474358974358973	347	0.7052845528455285	44	0.12154696132596685	10	0.017482517482517484	68	0.08970976253298153	C	10.16	1.275065	0.23307	0.601453	0.076001	ENSG00000160789	ENST00000292302	.	.	.	5.74	-5.0	0.03001	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4921	0.84205	0.0:0.2176:0.0:0.7824	rs505058;rs17847243;rs58351647;rs505058	.	.	.	.	-1	.	.	.	+	.	.	LMNA	154372809	0.110000	0.22057	0.908000	0.35775	0.984000	0.73092	-0.362000	0.07602	-1.095000	0.03050	-0.733000	0.03571	.	T|0.729;G|0.001	.	strong		0.602	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	
OR51Q1	390061	hgsc.bcm.edu	37	11	5444136	5444136	+	Nonsense_Mutation	SNP	C	C	T	rs2647574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5444136C>T	ENST00000300778.4	+	1	796	c.706C>T	c.(706-708)Cga>Tga	p.R236*	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGGGCTGAGCGACTCCGTGC	0.483													C|||	2273	0.453874	0.2799	0.4006	5008	,	,		20965	0.7024		0.3986	False		,,,				2504	0.5276				p.R236X		Atlas-SNP	.											.	OR51Q1	79	.	0			c.C706T						PASS	.	C	stop/ARG	1332,3070	447.3+/-348.3	203,926,1072	135.0	114.0	121.0		706	-10.0	0.0	11	dbSNP_100	121	3372,5222	499.5+/-375.0	676,2020,1601	yes	stop-gained	OR51Q1	NM_001004757.2		879,2946,2673	TT,TC,CC		39.2367,30.259,36.1958		236/318	5444136	4704,8292	2201	4297	6498	SO:0001587	stop_gained	390061	exon1			GCTGAGCGACTCC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.706C>T	11.37:g.5444136C>T	ENSP00000300778:p.Arg236*	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	137	136	0.992701	NM_001004757	B2RNN1	Nonsense_Mutation	SNP	ENST00000300778.4	37	CCDS31381.1	966	0.4423076923076923	139	0.28252032520325204	148	0.4088397790055249	395	0.6905594405594405	284	0.37467018469656993	C	9.017	0.983956	0.18889	0.30259	0.392367	ENSG00000167360	ENST00000300778	.	.	.	5.0	-9.99	0.00435	.	0.244803	0.27388	N	0.019593	.	.	.	.	.	.	0.09310	P	0.99999999896276	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	26.1186	0.99996	0.1626:0.8374:0.0:0.0	rs2647574;rs52806938;rs58830716;rs2647574	.	.	.	X	236	.	ENSP00000300778:R236X	R	+	1	2	OR51Q1	5400712	0.000000	0.05858	0.000000	0.03702	0.120000	0.20174	-6.681000	0.00057	-1.753000	0.01323	-1.378000	0.01179	CGA	C|0.603;T|0.397	0.397	strong		0.483	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
C17orf64	124773	hgsc.bcm.edu	37	17	58506748	58506748	+	Missense_Mutation	SNP	C	C	T	rs57928695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:58506748C>T	ENST00000269127.4	+	5	539	c.455C>T	c.(454-456)cCg>cTg	p.P152L		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	152										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			TCGGATGCGCCGGAGAGGTCC	0.607													C|||	710	0.141773	0.5068	0.0519	5008	,	,		18332	0.0		0.004	False		,,,				2504	0.0				p.P152L		Atlas-SNP	.											.	C17orf64	19	.	0			c.C455T						PASS	.	C	LEU/PRO	1696,2710	493.1+/-362.6	345,1006,852	34.0	36.0	35.0		455	1.6	0.0	17	dbSNP_129	35	14,8586	9.8+/-36.6	0,14,4286	yes	missense	C17orf64	NM_181707.2	98	345,1020,5138	TT,TC,CC		0.1628,38.493,13.1478	probably-damaging	152/237	58506748	1710,11296	2203	4300	6503	SO:0001583	missense	124773	exon5			ATGCGCCGGAGAG	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.455C>T	17.37:g.58506748C>T	ENSP00000269127:p.Pro152Leu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	147	75	0.510204	NM_181707	Q8IY87	Missense_Mutation	SNP	ENST00000269127.4	37	CCDS32698.2	255	0.11675824175824176	237	0.4817073170731707	15	0.04143646408839779	0	0.0	3	0.00395778364116095	C	9.889	1.203580	0.22121	0.38493	0.001628	ENSG00000141371	ENST00000269127	.	.	.	4.82	1.65	0.23941	.	0.420949	0.20436	N	0.092377	T	0.00012	0.0000	M	0.70595	2.14	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.35201	-0.9798	8	0.51188	T	0.08	-4.574	4.2009	0.10466	0.1819:0.6217:0.0:0.1964	rs57928695;rs61745732	152	Q86WR6	CQ064_HUMAN	L	152	.	ENSP00000269127:P152L	P	+	2	0	C17orf64	55861530	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.833000	0.04396	0.094000	0.17404	0.561000	0.74099	CCG	C|0.882;T|0.118	0.118	strong		0.607	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707	
MT-ND5	4540	hgsc.bcm.edu	37	M	13260	13260	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:13260T>C	ENST00000361567.2	+	1	924	c.924T>C	c.(922-924)agT>agC	p.S308S	MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	308					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TCCACTTCAAGTCAACTAGGA	0.443																																					p.S308S		Atlas-SNP	.											.	.	.	.	0			c.T924C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TTCAAGTCAACTA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.924T>C	M.37:g.13260T>C		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.443	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
MAST2	23139	hgsc.bcm.edu	37	1	46496368	46496368	+	Silent	SNP	C	C	T	rs376559790		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46496368C>T	ENST00000361297.2	+	22	2926	c.2643C>T	c.(2641-2643)gaC>gaT	p.D881D	MAST2_ENST00000372009.2_Silent_p.D811D	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)					AGAAGGAGGACCATTCAGATG	0.642																																					p.D881D		Atlas-SNP	.											.	MAST2	136	.	0			c.C2643T						PASS	.						21.0	24.0	23.0					1																	46496368		2045	4187	6232	SO:0001819	synonymous_variant	23139	exon22			GGAGGACCATTCA	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.2643C>T	1.37:g.46496368C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	119	5	0.0420168	NM_015112		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																			.	.	none		0.642	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
PTCD3	55037	hgsc.bcm.edu	37	2	86344237	86344237	+	Silent	SNP	A	A	G	rs3764948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86344237A>G	ENST00000254630.7	+	6	435	c.369A>G	c.(367-369)tcA>tcG	p.S123S	PTCD3_ENST00000409277.3_Silent_p.S123S|PTCD3_ENST00000465560.1_3'UTR	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	123					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						TTATTAATTCATACCCCAAAT	0.294													a|||	487	0.0972444	0.1331	0.0187	5008	,	,		17141	0.1845		0.0298	False		,,,				2504	0.0838				p.S123S		Atlas-SNP	.											.	PTCD3	51	.	0			c.A369G						PASS	.	G		460,3944	206.5+/-228.1	21,418,1763	54.0	55.0	54.0		369	1.2	0.7	2	dbSNP_107	54	267,8327	102.1+/-163.3	5,257,4035	no	coding-synonymous	PTCD3	NM_017952.5		26,675,5798	GG,GA,AA		3.1068,10.445,5.5932		123/690	86344237	727,12271	2202	4297	6499	SO:0001819	synonymous_variant	55037	exon6			TAATTCATACCCC		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.369A>G	2.37:g.86344237A>G		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	196	97	0.494898	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Silent	SNP	ENST00000254630.7	37	CCDS33235.1																																																																																			A|0.939;G|0.061	0.061	strong		0.294	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952	
TCHH	7062	hgsc.bcm.edu	37	1	152082304	152082304	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152082304T>G	ENST00000368804.1	-	2	3388	c.3389A>C	c.(3388-3390)aAg>aCg	p.K1130T		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1130	10 X 30 AA tandem repeats.				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)			gcgccttctcttctcccgttc	0.612																																					p.K1130T		Atlas-SNP	.											TCHH,NS,malignant_melanoma,0,1	TCHH	275	1	0			c.A3389C						scavenged	.						92.0	93.0	92.0					1																	152082304		1979	4147	6126	SO:0001583	missense	7062	exon3			CTTCTCTTCTCCC	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.3389A>C	1.37:g.152082304T>G	ENSP00000357794:p.Lys1130Thr	Somatic	215	2	0.00930233		WXS	Illumina HiSeq	Phase_I	289	13	0.0449827	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	T	6.052	0.377976	0.11466	.	.	ENSG00000159450	ENST00000368804	T	0.05925	3.37	2.57	-0.117	0.13551	.	.	.	.	.	T	0.00845	0.0028	L	0.27053	0.805	0.09310	N	1	P	0.43477	0.808	B	0.33799	0.17	T	0.41787	-0.9489	9	0.13108	T	0.6	.	2.8858	0.05661	0.0:0.3012:0.2466:0.4522	.	1130	Q07283	TRHY_HUMAN	T	1130	ENSP00000357794:K1130T	ENSP00000357794:K1130T	K	-	2	0	TCHH	150348928	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.337000	0.07852	-0.279000	0.09167	0.379000	0.24179	AAG	.	.	none		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
PTPRQ	374462	hgsc.bcm.edu	37	12	81007527	81007527	+	Missense_Mutation	SNP	T	T	C	rs7963963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:81007527T>C	ENST00000266688.5	+	34	5063	c.5063T>C	c.(5062-5064)aTt>aCt	p.I1688T				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1734	Fibronectin type-III 18. {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.I1688T(1)		breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						GCTGTCCAGATTCACAACCTC	0.378													T|||	377	0.0752796	0.2451	0.0274	5008	,	,		16074	0.0		0.0258	False		,,,				2504	0.0082				p.I1520T		Atlas-SNP	.											PTPRQ,NS,carcinoma,0,1	PTPRQ	119	1	1	Substitution - Missense(1)	kidney(1)	c.T4559C						PASS	.	T	THR/ILE	309,1075		34,241,417	121.0	92.0	101.0		4621	6.1	1.0	12	dbSNP_116	101	85,3095		3,79,1508	yes	missense	PTPRQ	NM_001145026.1	89	37,320,1925	CC,CT,TT		2.673,22.3266,8.6328	possibly-damaging	1692/2300	81007527	394,4170	692	1590	2282	SO:0001583	missense	374462	exon26			TCCAGATTCACAA	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.5063T>C	12.37:g.81007527T>C	ENSP00000266688:p.Ile1688Thr	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	166	80	0.481928	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	37		136|136	0.06227106227106227|0.06227106227106227	106|106	0.21544715447154472|0.21544715447154472	10|10	0.027624309392265192|0.027624309392265192	0|0	0.0|0.0	20|20	0.026385224274406333|0.026385224274406333	T|T	14.34|14.34	2.505294|2.505294	0.44558|0.44558	0.223266|0.223266	0.02673|0.02673	ENSG00000139304|ENSG00000139304	ENST00000532722|ENST00000266688	.|T	.|0.42131	.|0.98	6.05|6.05	6.05|6.05	0.98169|0.98169	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.23204|0.23204	P|P	0.99812628|0.99812628	.|P	.|0.45672	.|0.864	.|P	.|0.48368	.|0.575	T|T	0.03587|0.03587	-1.1022|-1.1022	3|7	.|0.22706	.|T	.|0.39	.|.	16.5932|16.5932	0.84781|0.84781	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs7963963;rs56704090;rs7963963|rs7963963;rs56704090;rs7963963	.|1734	.|Q9UMZ3	.|PTPRQ_HUMAN	L|T	1389|1688	.|ENSP00000266688:I1688T	.|ENSP00000266688:I1688T	F|I	+|+	1|2	0|0	PTPRQ|PTPRQ	79531658|79531658	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.708000|0.708000	0.40852|0.40852	4.640000|4.640000	0.61368|0.61368	2.320000|2.320000	0.78422|0.78422	0.528000|0.528000	0.53228|0.53228	TTC|ATT	T|0.920;C|0.080	0.080	strong		0.378	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
DSPP	1834	hgsc.bcm.edu	37	4	88536448	88536448	+	Silent	SNP	C	C	T	rs111205175		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88536448C>T	ENST00000282478.7	+	4	2667	c.2634C>T	c.(2632-2634)gaC>gaT	p.D878D	DSPP_ENST00000399271.1_Silent_p.D878D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	878	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgacagcagtgata	0.498																																					p.D878D		Atlas-SNP	.											.	DSPP	174	.	0			c.C2634T						PASS	.						70.0	84.0	79.0					4																	88536448		1633	2930	4563	SO:0001819	synonymous_variant	1834	exon5			CAGTGACAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2634C>T	4.37:g.88536448C>T		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	334	31	0.0928144	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
Unknown	0	hgsc.bcm.edu	37	17	17326604	17326604	+	IGR	SNP	C	C	T	rs370938128|rs7225976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17326604C>T								NT5M (75629 upstream) : Y_RNA (37153 downstream)																							CATGATGGGGCAAATGCCAGA	0.473													T|||	2100	0.419329	0.7912	0.2651	5008	,	,		23244	0.1875		0.3201	False		,,,				2504	0.3671				p.A140V		Atlas-SNP	.											.	.	.	.	0			c.C419T						PASS	.																																			SO:0001628	intergenic_variant	140776	exon3			ATGGGGCAAATGC																													17.37:g.17326604C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_001243312		Missense_Mutation	SNP		37																																																																																				C|0.662;T|0.338	0.338	strong	0	0.473								
OR52J3	119679	hgsc.bcm.edu	37	11	5068661	5068661	+	Silent	SNP	A	A	G	rs2500019|rs386750099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5068661A>G	ENST00000380370.1	+	1	906	c.906A>G	c.(904-906)gaA>gaG	p.E302E		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	302						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)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGATTCGAGAACGAGTGCTCT	0.383													G|||	2444	0.488019	0.5923	0.4971	5008	,	,		21199	0.2619		0.508	False		,,,				2504	0.5532				p.E302E		Atlas-SNP	.											.	OR52J3	77	.	0			c.A906G						PASS	.	G		2432,1970		689,1054,458	58.0	55.0	56.0		906	-0.4	0.0	11	dbSNP_100	56	4226,4370		1065,2096,1137	no	coding-synonymous	OR52J3	NM_001001916.2		1754,3150,1595	GG,GA,AA		49.1624,44.7524,48.7767		302/312	5068661	6658,6340	2201	4298	6499	SO:0001819	synonymous_variant	119679	exon1			TCGAGAACGAGTG	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.906A>G	11.37:g.5068661A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_001001916	Q6IFE4	Silent	SNP	ENST00000380370.1	37	CCDS31370.1																																																																																			A|0.493;G|0.507	0.507	strong		0.383	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
CHRDL2	25884	hgsc.bcm.edu	37	11	74413872	74413872	+	Silent	SNP	A	A	G	rs34528207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:74413872A>G	ENST00000376332.3	-	9	1583	c.1087T>C	c.(1087-1089)Ttg>Ctg	p.L363L	CHRDL2_ENST00000263671.5_Silent_p.L363L|CHRDL2_ENST00000534159.1_5'UTR	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	363					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|ossification (GO:0001503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)|skin(2)	15	Hepatocellular(1;0.098)					ATCTCCACCAAGTCCGAGGCC	0.642											OREG0021223	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1465	0.292532	0.3835	0.1268	5008	,	,		16956	0.3264		0.1332	False		,,,				2504	0.4162				p.L363L		Atlas-SNP	.											.	CHRDL2	47	.	0			c.T1087C						PASS	.	G		1425,2975	683.6+/-404.3	225,975,1000	112.0	109.0	110.0		1087	3.1	1.0	11	dbSNP_126	110	1180,7406	764.1+/-407.6	70,1040,3183	no	coding-synonymous	CHRDL2	NM_015424.3		295,2015,4183	GG,GA,AA		13.7433,32.3864,20.0601		363/452	74413872	2605,10381	2200	4293	6493	SO:0001819	synonymous_variant	25884	exon9			CCACCAAGTCCGA	AL110168	CCDS8234.1, CCDS60893.1	11q13.4	2013-09-20			ENSG00000054938	ENSG00000054938			24168	protein-coding gene	gene with protein product		613127				12853144, 12975309	Standard	NM_015424		Approved	BNF1	uc001ovh.3	Q6WN34	OTTHUMG00000165623	ENST00000376332.3:c.1087T>C	11.37:g.74413872A>G		Somatic	39	0	0	1152	WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_015424	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Silent	SNP	ENST00000376332.3	37																																																																																				A|0.791;G|0.209	0.209	strong		0.642	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1		
LCT	3938	hgsc.bcm.edu	37	2	136587238	136587238	+	Silent	SNP	G	G	C	rs3816088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:136587238G>C	ENST00000264162.2	-	3	739	c.729C>G	c.(727-729)gtC>gtG	p.V243V		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	243	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)	AGAGGAAATCGACCGTGTCCT	0.408													G|||	252	0.0503195	0.1059	0.0202	5008	,	,		17781	0.0516		0.0298	False		,,,				2504	0.0164				p.V243V		Atlas-SNP	.											.	LCT	309	.	0			c.C729G						PASS	.	G		479,3927	224.9+/-240.9	31,417,1755	126.0	126.0	126.0		729	-10.4	0.0	2	dbSNP_107	126	190,8410	83.4+/-145.9	3,184,4113	no	coding-synonymous	LCT	NM_002299.2		34,601,5868	CC,CG,GG		2.2093,10.8715,5.1438		243/1928	136587238	669,12337	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon3			GAAATCGACCGTG	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.729C>G	2.37:g.136587238G>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	25	0.390625	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.942;C|0.058	0.058	strong		0.408	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
FAM65B	9750	hgsc.bcm.edu	37	6	24848331	24848331	+	Silent	SNP	T	T	C	rs35698586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24848331T>C	ENST00000259698.4	-	12	1174	c.999A>G	c.(997-999)gcA>gcG	p.A333A	FAM65B_ENST00000538035.1_Silent_p.A362A|FAM65B_ENST00000378023.4_Silent_p.A333A|FAM65B_ENST00000510784.2_Silent_p.A367A|FAM65B_ENST00000540914.1_Silent_p.A333A	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	333					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						GAAGGGCTGCTGCCTTGTTCC	0.517													C|||	110	0.0219649	0.0779	0.0043	5008	,	,		19139	0.0		0.004	False		,,,				2504	0.0				p.A333A		Atlas-SNP	.											.	FAM65B	134	.	0			c.A999G						PASS	.	C	,	255,3729		6,243,1743	85.0	85.0	85.0		999,999	-6.8	0.0	6	dbSNP_126	85	8,8334		0,8,4163	no	coding-synonymous,coding-synonymous	FAM65B	NM_014722.2,NM_015864.2	,	6,251,5906	CC,CT,TT		0.0959,6.4006,2.1337	,	333/1069,333/592	24848331	263,12063	1992	4171	6163	SO:0001819	synonymous_variant	9750	exon12			GGCTGCTGCCTTG	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"""myogenesis-related and NCAM-associated protein homolog (chicken)"""	611410	"""chromosome 6 open reading frame 32"""	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.999A>G	6.37:g.24848331T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_015864	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Silent	SNP	ENST00000259698.4	37	CCDS47383.1																																																																																			T|0.985;C|0.015	0.015	strong		0.517	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
FAM214A	56204	hgsc.bcm.edu	37	15	52901283	52901283	+	Missense_Mutation	SNP	T	T	C	rs61731670|rs386783993	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52901283T>C	ENST00000261844.7	-	6	1980	c.1828A>G	c.(1828-1830)Act>Gct	p.T610A	FAM214A_ENST00000546305.2_Missense_Mutation_p.T617A	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	610				T -> A (in Ref. 2; BAF85606/BAG57301 and 5; AAI09129). {ECO:0000305}.													ATTGAGGAAGTTGATAAACTA	0.333													T|||	2157	0.430711	0.4402	0.2968	5008	,	,		17056	0.8482		0.167	False		,,,				2504	0.3538				p.T610A		Atlas-SNP	.											.	.	.	.	0			c.A1828G						PASS	.	T	ALA/THR	1334,2336		232,870,733	112.0	119.0	117.0		1828	2.1	0.0	15	dbSNP_129	117	1230,6926		116,998,2964	yes	missense	KIAA1370	NM_019600.2	58	348,1868,3697	CC,CT,TT		15.0809,36.3488,21.681	benign	610/1077	52901283	2564,9262	1835	4078	5913	SO:0001583	missense	56204	exon6			AGGAAGTTGATAA	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.1828A>G	15.37:g.52901283T>C	ENSP00000261844:p.Thr610Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	67	27	0.402985	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	760	0.34798534798534797	156	0.3170731707317073	86	0.23756906077348067	424	0.7412587412587412	94	0.12401055408970976	T	1.003	-0.690316	0.03303	0.363488	0.150809	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T	0.30448	1.53;1.53	5.92	2.07	0.26955	.	0.209202	0.49916	N	0.000136	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.14023	0.01;0.004	T	0.20174	-1.0283	9	0.29301	T	0.29	.	5.2861	0.15702	0.1281:0.1543:0.0:0.7176	rs61731670	617;610	F5H8G0;Q32MH5	.;K1370_HUMAN	A	610;610;609;617	ENSP00000261844:T610A;ENSP00000443598:T617A	ENSP00000261844:T610A	T	-	1	0	KIAA1370	50688575	0.807000	0.29009	0.042000	0.18584	0.040000	0.13550	1.242000	0.32755	0.452000	0.26830	0.533000	0.62120	ACT	T|0.697;C|0.303	0.303	strong		0.333	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	162929	162929	+	Silent	SNP	G	G	C	rs75342794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162929G>C	ENST00000283426.6	+	11	1724	c.1674G>C	c.(1672-1674)tcG>tcC	p.S558S		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	558							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		AGGCTACCTCGGTGGCTGCAG	0.652													G|||	255	0.0509185	0.1838	0.0159	5008	,	,		15694	0.0		0.001	False		,,,				2504	0.0				p.S558S		Atlas-SNP	.											PLEKHG4B_ENST00000283426,NS,carcinoma,+2,1	PLEKHG4B	167	1	0			c.G1674C						PASS	.	G		691,3685		51,589,1548	25.0	27.0	26.0		1674	-1.1	0.0	5	dbSNP_131	26	13,8555		0,13,4271	no	coding-synonymous	PLEKHG4B	NM_052909.3		51,602,5819	CC,CG,GG		0.1517,15.7907,5.4388		558/1272	162929	704,12240	2188	4284	6472	SO:0001819	synonymous_variant	153478	exon11			TACCTCGGTGGCT	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1674G>C	5.37:g.162929G>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	187	99	0.529412	NM_052909		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																			G|0.941;C|0.059	0.059	strong		0.652	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
OR14I1	401994	hgsc.bcm.edu	37	1	248844959	248844959	+	Missense_Mutation	SNP	T	T	C	rs55871516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248844959T>C	ENST00000342623.3	-	1	670	c.647A>G	c.(646-648)tAt>tGt	p.Y216C		NM_001004734.1	NP_001004734.1	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I, member 1	216			Y -> C (in dbSNP:rs55871516).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y216C(1)		NS(1)|breast(4)|large_intestine(2)|lung(24)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	35						GATTTGGAAATAGGAGATCAT	0.483													T|||	665	0.132788	0.1649	0.0865	5008	,	,		20268	0.128		0.1173	False		,,,				2504	0.1431				p.Y216C		Atlas-SNP	.											OR14I1,right_lower_lobe,carcinoma,-1,2	OR14I1	64	2	1	Substitution - Missense(1)	stomach(1)	c.A647G						PASS	.	T	CYS/TYR	674,3732		47,580,1576	78.0	83.0	82.0		647	3.5	0.0	1	dbSNP_129	82	992,7608		58,876,3366	yes	missense	OR14I1	NM_001004734.1	194	105,1456,4942	CC,CT,TT		11.5349,15.2973,12.8095	probably-damaging	216/312	248844959	1666,11340	2203	4300	6503	SO:0001583	missense	401994	exon1			TGGAAATAGGAGA		CCDS31125.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000189181	ENSG00000189181		"""GPCR / Class A : Olfactory receptors"""	19575	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BU, member 1"""	OR5BU1P, OR5BU1			Standard	NM_001004734		Approved		uc001ieu.1	A6ND48	OTTHUMG00000040378	ENST00000342623.3:c.647A>G	1.37:g.248844959T>C	ENSP00000339726:p.Tyr216Cys	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	104	45	0.432692	NM_001004734		Missense_Mutation	SNP	ENST00000342623.3	37	CCDS31125.1	291	0.13324175824175824	89	0.18089430894308944	37	0.10220994475138122	73	0.12762237762237763	92	0.12137203166226913	.	20.4	3.983867	0.74474	0.152973	0.115349	ENSG00000189181	ENST00000342623	T	0.00520	6.85	3.49	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41938	D	0.000794	T	0.00012	0.0000	H	0.99104	4.43	0.31092	P	0.710709	D	0.89917	1.0	D	0.97110	1.0	T	0.01966	-1.1238	9	0.87932	D	0	.	9.9498	0.41631	0.0:0.0:0.0:1.0	rs55871516	216	A6ND48	O14I1_HUMAN	C	216	ENSP00000339726:Y216C	ENSP00000339726:Y216C	Y	-	2	0	OR14I1	246911582	0.989000	0.36119	0.016000	0.15963	0.659000	0.38960	2.521000	0.45563	1.422000	0.47177	0.443000	0.29094	TAT	T|0.871;C|0.129	0.129	strong		0.483	OR14I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097128.1	NM_001004734	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74206658	74206658	+	Silent	SNP	G	G	A	rs758773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	110	0	0		WXS	Illumina HiSeq	Phase_I	128	56	0.4375	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	
ANK1	286	hgsc.bcm.edu	37	8	41548003	41548003	+	Missense_Mutation	SNP	T	T	C	rs10093583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:41548003T>C	ENST00000347528.4	-	32	4056	c.3973A>G	c.(3973-3975)Atg>Gtg	p.M1325V	ANK1_ENST00000352337.4_Missense_Mutation_p.M1325V|ANK1_ENST00000396942.1_Missense_Mutation_p.M1325V|ANK1_ENST00000265709.8_Missense_Mutation_p.M1366V|ANK1_ENST00000289734.7_Missense_Mutation_p.M1325V|ANK1_ENST00000379758.2_Missense_Mutation_p.M1325V|ANK1_ENST00000396945.1_Missense_Mutation_p.M1325V	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1325	UPA domain. {ECO:0000250}.		M -> V (in dbSNP:rs10093583).		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)			TTTACAGGCATGGCCAGACGG	0.572													T|||	202	0.0403355	0.1377	0.0187	5008	,	,		18237	0.0		0.007	False		,,,				2504	0.0				p.M1366V		Atlas-SNP	.											.	ANK1	497	.	0			c.A4096G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET	518,3888	238.0+/-249.6	28,462,1713	56.0	60.0	59.0		3973,4096,3973,3973,3973	5.1	1.0	8	dbSNP_119	59	55,8545	35.3+/-89.8	1,53,4246	yes	missense,missense,missense,missense,missense	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	21,21,21,21,21	29,515,5959	CC,CT,TT		0.6395,11.7567,4.4057	benign,benign,benign,benign,benign	1325/1881,1366/1898,1325/1857,1325/1882,1325/1720	41548003	573,12433	2203	4300	6503	SO:0001583	missense	286	exon33			CAGGCATGGCCAG	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.3973A>G	8.37:g.41548003T>C	ENSP00000339620:p.Met1325Val	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	78|78	0.03571428571428571|0.03571428571428571	67|67	0.13617886178861788|0.13617886178861788	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	T|T	10.60|10.60	1.395238|1.395238	0.25205|0.25205	0.117567|0.117567	0.006395|0.006395	ENSG00000029534|ENSG00000029534	ENST00000520299|ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	.|T;T;T;T;T;T;T	.|0.21191	.|2.02;2.02;2.02;2.02;2.02;2.02;2.02	5.08|5.08	5.08|5.08	0.68730|0.68730	.|.	.|0.184594	.|0.47093	.|D	.|0.000258	T|T	0.00073|0.00073	0.0002|0.0002	N|N	0.01352|0.01352	-0.895|-0.895	0.46631|0.46631	P|P	8.639999999999759E-4|8.639999999999759E-4	.|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	.|0.04013	.|0.001;0.001;0.0;0.0;0.001;0.0	T|T	0.08554|0.08554	-1.0716|-1.0716	4|9	.|0.52906	.|T	.|0.07	.|.	10.3554|10.3554	0.43960|0.43960	0.0:0.0:0.1645:0.8355|0.0:0.0:0.1645:0.8355	rs10093583;rs52831655;rs10093583|rs10093583;rs52831655;rs10093583	.|1366;1325;1325;1325;1325;641	.|P16157-21;P16157-4;P16157;P16157-5;P16157-3;B3KX39	.|.;.;ANK1_HUMAN;.;.;.	R|V	646|1325;1325;1325;1325;1325;1325;1366;1325	.|ENSP00000339620:M1325V;ENSP00000289734:M1325V;ENSP00000369082:M1325V;ENSP00000380149:M1325V;ENSP00000380147:M1325V;ENSP00000309131:M1325V;ENSP00000265709:M1366V	.|ENSP00000265709:M1366V	H|M	-|-	2|1	0|0	ANK1|ANK1	41667160|41667160	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.822000|0.822000	0.46500|0.46500	2.390000|2.390000	0.44416|0.44416	2.123000|2.123000	0.65237|0.65237	0.460000|0.460000	0.39030|0.39030	CAT|ATG	T|0.955;C|0.045	0.045	strong		0.572	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
KLHL6	89857	hgsc.bcm.edu	37	3	183226213	183226213	+	Silent	SNP	A	A	G	rs16857710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183226213A>G	ENST00000341319.3	-	3	578	c.543T>C	c.(541-543)gcT>gcC	p.A181A		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	181	BACK.				B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)			p.A181A(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)			AGTGTGTGTCAGCCAGCCTCA	0.488													G|||	732	0.146166	0.3298	0.0461	5008	,	,		21081	0.1796		0.002	False		,,,				2504	0.0828				p.A181A		Atlas-SNP	.											KLHL6,NS,carcinoma,0,1	KLHL6	100	1	1	Substitution - coding silent(1)	stomach(1)	c.T543C						PASS	.	G		1372,3034	690.3+/-405.2	209,954,1040	73.0	78.0	76.0		543	-8.7	0.3	3	dbSNP_123	76	18,8582	818.4+/-406.9	0,18,4282	no	coding-synonymous	KLHL6	NM_130446.2		209,972,5322	GG,GA,AA		0.2093,31.1394,10.6874		181/622	183226213	1390,11616	2203	4300	6503	SO:0001819	synonymous_variant	89857	exon3			TGTGTCAGCCAGC	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.543T>C	3.37:g.183226213A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	149	88	0.590604	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	37	CCDS3245.2																																																																																			A|0.870;G|0.130	0.130	strong		0.488	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
KIF7	374654	hgsc.bcm.edu	37	15	90196113	90196113	+	Missense_Mutation	SNP	G	G	A	rs141865394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90196113G>A	ENST00000394412.3	-	2	125	c.49C>T	c.(49-51)Cgg>Tgg	p.R17W		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	17	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)			AGGGCAACCCGCACTGGGGCC	0.687													G|||	26	0.00519169	0.0174	0.0029	5008	,	,		15541	0.001		0.0	False		,,,				2504	0.0				p.R17W		Atlas-SNP	.											.	KIF7	130	.	0			c.C49T						PASS	.						12.0	17.0	16.0					15																	90196113		688	1589	2277	SO:0001583	missense	374654	exon2			CAACCCGCACTGG	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.49C>T	15.37:g.90196113G>A	ENSP00000377934:p.Arg17Trp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	13	0.005952380952380952	10	0.02032520325203252	2	0.0055248618784530384	1	0.0017482517482517483	0	0.0	G	12.35	1.912773	0.33721	.	.	ENSG00000166813	ENST00000394412	T	0.74526	-0.85	4.66	2.23	0.28157	Kinesin, motor domain (3);	.	.	.	.	T	0.80597	0.4653	H	0.96048	3.76	0.35264	D	0.779872	D	0.76494	0.999	P	0.59424	0.857	D	0.89286	0.3615	9	0.87932	D	0	.	12.8485	0.57844	0.0:0.0:0.5816:0.4184	.	17	Q2M1P5	KIF7_HUMAN	W	17	ENSP00000377934:R17W	ENSP00000377934:R17W	R	-	1	2	KIF7	87997117	0.008000	0.16893	0.921000	0.36526	0.005000	0.04900	0.750000	0.26334	0.144000	0.18951	-0.262000	0.10625	CGG	G|0.994;A|0.006	0.006	strong		0.687	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525	
OBSCN	84033	hgsc.bcm.edu	37	1	228402508	228402508	+	Silent	SNP	C	C	T	rs2776853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228402508C>T	ENST00000422127.1	+	5	1581	c.1537C>T	c.(1537-1539)Ctg>Ttg	p.L513L	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.L513L|C1orf145_ENST00000295012.5_5'Flank|OBSCN_ENST00000284548.11_Silent_p.L513L|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	513					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)				GAAGCCTCCCCTGCAACCCCC	0.612													C|||	1381	0.275759	0.3086	0.353	5008	,	,		17070	0.1706		0.3618	False		,,,				2504	0.1963				p.L513L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C1537T						PASS	.	C	,	1272,2538		201,870,834	35.0	39.0	38.0		1537,1537	3.6	0.0	1	dbSNP_100	38	3213,5025		632,1949,1538	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	833,2819,2372	TT,TC,CC		39.0022,33.3858,37.2261	,	513/7969,513/6621	228402508	4485,7563	1905	4119	6024	SO:0001819	synonymous_variant	84033	exon5			CCTCCCCTGCAAC	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.1537C>T	1.37:g.228402508C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	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|0.687;T|0.313	0.313	strong		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CPN1	1369	hgsc.bcm.edu	37	10	101835764	101835764	+	Silent	SNP	C	C	G	rs61754515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101835764C>G	ENST00000370418.3	-	2	575	c.324G>C	c.(322-324)cgG>cgC	p.R108R		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	108	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)		GGTTCCTGTTCCGGAACTCCT	0.602													C|||	187	0.0373403	0.1324	0.0159	5008	,	,		18603	0.0		0.001	False		,,,				2504	0.0				p.R108R		Atlas-SNP	.											.	CPN1	62	.	0			c.G324C						PASS	.			560,3846	250.3+/-257.4	33,494,1676	143.0	118.0	126.0		324	-2.5	0.1	10	dbSNP_129	126	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	CPN1	NM_001308.2		33,499,5971	GG,GC,CC		0.0581,12.7099,4.3441		108/459	101835764	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	1369	exon2			CCTGTTCCGGAAC	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.324G>C	10.37:g.101835764C>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	37	CCDS7486.1																																																																																			C|0.959;G|0.041	0.041	strong		0.602	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
LPCAT3	10162	hgsc.bcm.edu	37	12	7091918	7091918	+	Silent	SNP	C	C	T	rs3764031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	170	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	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	
ATP13A4	84239	hgsc.bcm.edu	37	3	193180592	193180592	+	Silent	SNP	G	G	A	rs59451116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:193180592G>A	ENST00000342695.4	-	13	1804	c.1482C>T	c.(1480-1482)gaC>gaT	p.D494D	ATP13A4_ENST00000295548.3_Silent_p.D494D|ATP13A4_ENST00000392443.3_Silent_p.D475D	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	494						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		GGTCCAAGCCGTCCCTTGTTA	0.488													A|||	1477	0.294928	0.2905	0.3141	5008	,	,		17830	0.3046		0.1918	False		,,,				2504	0.3834				p.D494D		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C1482T						PASS	.	A		1191,3215	710.1+/-407.8	142,907,1154	111.0	99.0	103.0		1482	2.0	1.0	3	dbSNP_129	103	1706,6894	737.6+/-407.0	169,1368,2763	no	coding-synonymous	ATP13A4	NM_032279.2		311,2275,3917	AA,AG,GG		19.8372,27.0313,22.2743		494/1197	193180592	2897,10109	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon13			CAAGCCGTCCCTT	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.1482C>T	3.37:g.193180592G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			G|0.762;A|0.238	0.238	strong		0.488	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
USP35	57558	hgsc.bcm.edu	37	11	77911224	77911224	+	Missense_Mutation	SNP	T	T	C	rs115848453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77911224T>C	ENST00000529308.1	+	5	1243	c.982T>C	c.(982-984)Tct>Cct	p.S328P	USP35_ENST00000530267.1_Intron|USP35_ENST00000526425.1_Missense_Mutation_p.S59P|USP35_ENST00000530535.1_Intron|USP35_ENST00000441408.2_5'UTR	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	328					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)			AGCTGCCTTGTCTGTGCTCAA	0.602													T|||	28	0.00559105	0.0212	0.0	5008	,	,		18945	0.0		0.0	False		,,,				2504	0.0				p.S328P		Atlas-SNP	.											.	USP35	179	.	0			c.T982C						PASS	.	T	PRO/SER	46,4006		1,44,1981	105.0	108.0	107.0		982	5.0	1.0	11	dbSNP_132	107	0,8330		0,0,4165	yes	missense	USP35	NM_020798.2	74	1,44,6146	CC,CT,TT		0.0,1.1352,0.3715	probably-damaging	328/1019	77911224	46,12336	2026	4165	6191	SO:0001583	missense	57558	exon5			GCCTTGTCTGTGC	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.982T>C	11.37:g.77911224T>C	ENSP00000431876:p.Ser328Pro	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	182	71	0.39011	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	T	9.269	1.045301	0.19748	0.011352	0.0	ENSG00000118369	ENST00000528910;ENST00000529308;ENST00000526425	T;T;T	0.68624	-0.34;-0.34;0.91	4.97	4.97	0.65823	Armadillo-like helical (1);	0.253449	0.28161	N	0.016373	T	0.40094	0.1103	N	0.13098	0.295	0.80722	D	1	D	0.53885	0.963	P	0.48425	0.577	T	0.50972	-0.8764	10	0.29301	T	0.29	-4.9719	14.8266	0.70117	0.0:0.0:0.0:1.0	.	328	Q9P2H5	UBP35_HUMAN	P	84;328;59	ENSP00000436001:S84P;ENSP00000431876:S328P;ENSP00000434942:S59P	ENSP00000434942:S59P	S	+	1	0	USP35	77588872	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.519000	0.45546	2.092000	0.63282	0.533000	0.62120	TCT	T|0.995;C|0.005	0.005	strong		0.602	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
ATP10A	57194	hgsc.bcm.edu	37	15	25963484	25963484	+	Missense_Mutation	SNP	C	C	T	rs116055743	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25963484C>T	ENST00000356865.6	-	8	1537	c.1426G>A	c.(1426-1428)Ggc>Agc	p.G476S		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	476					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GACACCGAGCCCCCTCTGGGC	0.706													C|||	24	0.00479233	0.0182	0.0	5008	,	,		14866	0.0		0.0	False		,,,				2504	0.0				p.G476S		Atlas-SNP	.											.	ATP10A	270	.	0			c.G1426A						PASS	.	C	SER/GLY	84,4314		0,84,2115	29.0	25.0	26.0		1426	0.9	0.0	15	dbSNP_132	26	0,8594		0,0,4297	yes	missense	ATP10A	NM_024490.3	56	0,84,6412	TT,TC,CC		0.0,1.91,0.6466	benign	476/1500	25963484	84,12908	2199	4297	6496	SO:0001583	missense	57194	exon8			CCGAGCCCCCTCT	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1426G>A	15.37:g.25963484C>T	ENSP00000349325:p.Gly476Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	9.534	1.111487	0.20714	0.0191	0.0	ENSG00000206190	ENST00000356865	T	0.64991	-0.13	5.14	0.881	0.19166	HAD-like domain (1);	0.228496	0.44688	N	0.000436	T	0.29684	0.0741	L	0.46741	1.465	0.19300	N	0.999978	B	0.10296	0.003	B	0.11329	0.006	T	0.24261	-1.0165	10	0.07030	T	0.85	-7.1028	8.7017	0.34329	0.0:0.6623:0.0:0.3377	.	476	O60312	AT10A_HUMAN	S	476	ENSP00000349325:G476S	ENSP00000349325:G476S	G	-	1	0	ATP10A	23514577	0.382000	0.25148	0.000000	0.03702	0.225000	0.24961	2.423000	0.44705	-0.104000	0.12154	0.655000	0.94253	GGC	C|0.994;T|0.006	0.006	strong		0.706	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
MGARP	84709	hgsc.bcm.edu	37	4	140201259	140201259	+	Silent	SNP	G	G	A	rs28536098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:140201259G>A	ENST00000398955.1	-	1	233	c.54C>T	c.(52-54)ccC>ccT	p.P18P		NM_032623.3	NP_116012.2	Q8TDB4	HUMMR_HUMAN	mitochondria-localized glutamic acid-rich protein	18					anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cellular response to gonadotropin-releasing hormone (GO:0097211)|cellular response to hypoxia (GO:0071456)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of mitochondrion organization (GO:0010822)|protein targeting to mitochondrion (GO:0006626)|retrograde axon cargo transport (GO:0008090)	integral component of mitochondrial outer membrane (GO:0031307)|mitochondrion (GO:0005739)											CGGGGTTGGGGGGCGCCCTCA	0.721													G|||	426	0.0850639	0.2988	0.0274	5008	,	,		14723	0.001		0.0	False		,,,				2504	0.0112				p.P18P		Atlas-SNP	.											.	.	.	.	0			c.C54T						PASS	.	G		921,2799		112,697,1051	14.0	17.0	16.0		54	2.0	1.0	4	dbSNP_125	16	18,8074		0,18,4028	no	coding-synonymous	C4orf49	NM_032623.3		112,715,5079	AA,AG,GG		0.2224,24.7581,7.9495		18/241	140201259	939,10873	1860	4046	5906	SO:0001819	synonymous_variant	84709	exon1			GTTGGGGGGCGCC	AF484960	CCDS43269.1	4q31.1	2014-02-19	2014-02-19	2012-04-17	ENSG00000137463	ENSG00000137463			29969	protein-coding gene	gene with protein product	"""ovary-specific acidic protein"", ""corneal endothelium-specific protein 1"", ""hypoxia up-regulated mitochondrial movement regulator"""		"""chromosome 4 open reading frame 49"""	C4orf49			Standard	NM_032623		Approved	OSAP, CESP-1, HUMMR	uc003ihr.1	Q8TDB4	OTTHUMG00000161325	ENST00000398955.1:c.54C>T	4.37:g.140201259G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_032623	Q9BZC3	Silent	SNP	ENST00000398955.1	37	CCDS43269.1																																																																																			G|0.947;A|0.053	0.053	strong		0.721	MGARP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364536.1	NM_032623	
DGKI	9162	hgsc.bcm.edu	37	7	137263067	137263067	+	Silent	SNP	T	T	A	rs61751966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:137263067T>A	ENST00000288490.5	-	16	1647	c.1647A>T	c.(1645-1647)gcA>gcT	p.A549A	DGKI_ENST00000424189.2_Silent_p.A549A|DGKI_ENST00000453654.2_Silent_p.A249A|DGKI_ENST00000446122.1_Silent_p.A549A	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	549					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						TCTCTGGATTTGCTTCTGTGA	0.373													T|||	88	0.0175719	0.0325	0.0058	5008	,	,		19858	0.0		0.0089	False		,,,				2504	0.0327				p.A549A		Atlas-SNP	.											DGKI_ENST00000288490,NS,carcinoma,-2,2	DGKI	335	2	0			c.A1647T						PASS	.	T		99,4305	78.8+/-117.2	0,99,2103	67.0	68.0	68.0		1647	2.7	1.0	7	dbSNP_129	68	57,8541	35.9+/-90.5	1,55,4243	no	coding-synonymous	DGKI	NM_004717.2		1,154,6346	AA,AT,TT		0.6629,2.248,1.1998		549/1066	137263067	156,12846	2202	4299	6501	SO:0001819	synonymous_variant	9162	exon16			TGGATTTGCTTCT	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.1647A>T	7.37:g.137263067T>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	37	CCDS5845.1																																																																																			T|0.987;A|0.013	0.013	strong		0.373	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	
TTN	7273	hgsc.bcm.edu	37	2	179613147	179613147	+	Intron	SNP	G	G	C	rs75785339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179613147G>C	ENST00000591111.1	-	45	10585				TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.H4660Q|TTN_ENST00000589042.1_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000578746.1_RNA			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)			TAGAGATATTGTGTGTGTCAG	0.373													C|||	193	0.0385383	0.1407	0.0101	5008	,	,		18083	0.0		0.0	False		,,,				2504	0.0				p.H4660Q		Atlas-SNP	.											.	TTN	18412	.	0			c.C13980G						PASS	.	C	,,GLN/HIS,,	523,3883	761.1+/-413.0	31,461,1711	88.0	98.0	95.0		,,13980,,	0.5	0.0	2	dbSNP_131	95	8,8588	808.7+/-407.2	0,8,4290	yes	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,24,,	31,469,6001	CC,CG,GG		0.0931,11.8702,4.084	,,,,	,,4660/5605,,	179613147	531,12471	2203	4298	6501	SO:0001627	intron_variant	7273	exon46			GATATTGTGTGTG	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.10360+4703C>G	2.37:g.179613147G>C		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	317	147	0.463722	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		68	0.031135531135531136	63	0.12804878048780488	5	0.013812154696132596	0	0.0	0	0.0	C	6.309	0.425027	0.11987	0.118702	9.31E-4	ENSG00000155657	ENST00000360870	T	0.54479	0.57	5.05	0.501	0.16925	.	.	.	.	.	T	0.00210	0.0006	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14952	-1.0454	8	0.16896	T	0.51	.	0.9872	0.01449	0.2832:0.2095:0.3228:0.1845	.	4660	Q8WZ42-6	.	Q	4660	ENSP00000354117:H4660Q	ENSP00000354117:H4660Q	H	-	3	2	TTN	179321392	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-1.023000	0.03607	0.113000	0.18004	-0.127000	0.14921	CAC	G|0.964;C|0.036	0.036	strong		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
STPG1	90529	hgsc.bcm.edu	37	1	24710405	24710405	+	Missense_Mutation	SNP	A	A	G	rs11538189	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24710405A>G	ENST00000374409.1	-	4	532	c.278T>C	c.(277-279)aTg>aCg	p.M93T	STPG1_ENST00000440416.1_Missense_Mutation_p.M46T|STPG1_ENST00000337248.4_Missense_Mutation_p.M93T|STPG1_ENST00000468303.1_5'UTR|STPG1_ENST00000003583.8_Missense_Mutation_p.M46T	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	93				M -> T (in Ref. 2; AAH35061). {ECO:0000305}.	apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											TGAGGGAAACATGCAAGTTCC	0.413													A|||	545	0.108826	0.2277	0.1052	5008	,	,		23154	0.002		0.1133	False		,,,				2504	0.0562				p.M93T		Atlas-SNP	.											.	.	.	.	0			c.T278C						PASS	.	A	THR/MET,THR/MET,THR/MET,THR/MET	986,3420	370.8+/-319.7	115,756,1332	182.0	174.0	177.0		278,278,2,137	1.9	0.4	1	dbSNP_120	177	1062,7538	224.8+/-261.1	61,940,3299	yes	missense,missense,missense,missense	C1orf201	NM_001199012.1,NM_001199013.1,NM_001199014.1,NM_178122.4	81,81,81,81	176,1696,4631	GG,GA,AA		12.3488,22.3786,15.7466	benign,benign,benign,benign	93/335,93/335,1/243,46/288	24710405	2048,10958	2203	4300	6503	SO:0001583	missense	90529	exon4			GGAAACATGCAAG	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.278T>C	1.37:g.24710405A>G	ENSP00000363530:p.Met93Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001199012	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Missense_Mutation	SNP	ENST00000374409.1	37	CCDS55581.1	227|227	0.10393772893772894|0.10393772893772894	94|94	0.1910569105691057|0.1910569105691057	38|38	0.10497237569060773|0.10497237569060773	0|0	0.0|0.0	95|95	0.12532981530343007|0.12532981530343007	A|A	0.015|0.015	-1.557354|-1.557354	0.00910|0.00910	0.223786|0.223786	0.123488|0.123488	ENSG00000001460|ENSG00000001460	ENST00000435187|ENST00000374409;ENST00000440416;ENST00000003583;ENST00000337248;ENST00000437986	.|.	.|.	.|.	6.03|6.03	1.88|1.88	0.25563|0.25563	.|.	.|0.713850	.|0.13631	.|N	.|0.373758	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00538|0.00538	-1.39|-1.39	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	0.38607|0.38607	-0.9653|-0.9653	4|8	.|0.11794	.|T	.|0.64	-53.1322|-53.1322	5.7789|5.7789	0.18295|0.18295	0.2232:0.1405:0.6363:0.0|0.2232:0.1405:0.6363:0.0	rs12090888;rs52816239;rs12090888|rs12090888;rs52816239;rs12090888	.|93;46	.|Q5TH74;Q5TH74-3	.|CA201_HUMAN;.	R|T	70|93;46;46;93;93	.|.	.|ENSP00000003583:M46T	C|M	-|-	1|2	0|0	C1orf201|C1orf201	24582992|24582992	0.678000|0.678000	0.27586|0.27586	0.354000|0.354000	0.25760|0.25760	0.031000|0.031000	0.12232|0.12232	0.639000|0.639000	0.24690|0.24690	0.446000|0.446000	0.26666|0.26666	-0.904000|-0.904000	0.02843|0.02843	TGT|ATG	G|0.139;A|0.861	0.139	strong		0.413	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122	
EML1	2009	hgsc.bcm.edu	37	14	100331876	100331876	+	Silent	SNP	T	T	C	rs11160553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:100331876T>C	ENST00000262233.6	+	3	415	c.276T>C	c.(274-276)ccT>ccC	p.P92P	EML1_ENST00000327921.9_Silent_p.P61P|EML1_ENST00000556758.1_3'UTR|EML1_ENST00000334192.4_Silent_p.P92P	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	92					brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				AGACCCTGCCTTTAAGAACCA	0.478													T|||	917	0.183107	0.143	0.196	5008	,	,		20476	0.1369		0.3082	False		,,,				2504	0.1472				p.P92P		Atlas-SNP	.											.	EML1	97	.	0			c.T276C						PASS	.	T	,	871,3535	338.1+/-305.1	78,715,1410	97.0	89.0	91.0		276,276	2.9	1.0	14	dbSNP_120	91	2692,5908	428.1+/-355.8	435,1822,2043	no	coding-synonymous,coding-synonymous	EML1	NM_001008707.1,NM_004434.2	,	513,2537,3453	CC,CT,TT		31.3023,19.7685,27.395	,	92/835,92/816	100331876	3563,9443	2203	4300	6503	SO:0001819	synonymous_variant	2009	exon3			CCTGCCTTTAAGA	AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"""WD repeat domain containing"""	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.276T>C	14.37:g.100331876T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Silent	SNP	ENST00000262233.6	37	CCDS32155.1																																																																																			T|0.760;C|0.240	0.240	strong		0.478	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707	
CFAP74	85452	hgsc.bcm.edu	37	1	1888193	1888193	+	IGR	SNP	C	C	A	rs3820011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	125	0	0		WXS	Illumina HiSeq	Phase_I	149	76	0.510067	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								
CYP2F1	1572	hgsc.bcm.edu	37	19	41622189	41622189	+	Silent	SNP	G	G	A	rs305968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41622189G>A	ENST00000331105.2	+	2	168	c.96G>A	c.(94-96)ccG>ccA	p.P32P		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	32					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						AGCTGCCTCCGGGACCCAGAC	0.547													A|||	2074	0.414137	0.5787	0.4957	5008	,	,		20578	0.2798		0.3131	False		,,,				2504	0.3763				p.P32P		Atlas-SNP	.											.	CYP2F1	60	.	0			c.G96A						PASS	.	A		2395,2011	561.6+/-380.8	657,1081,465	184.0	179.0	181.0		96	0.3	0.8	19	dbSNP_79	181	2632,5968	687.3+/-404.2	410,1812,2078	no	coding-synonymous	CYP2F1	NM_000774.3		1067,2893,2543	AA,AG,GG		30.6047,45.6423,38.6514		32/492	41622189	5027,7979	2203	4300	6503	SO:0001819	synonymous_variant	1572	exon2			GCCTCCGGGACCC	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"""Cytochrome P450s"""	2632	protein-coding gene	gene with protein product		124070	"""cytochrome P450, subfamily IIF, polypeptide 1"""	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.96G>A	19.37:g.41622189G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Silent	SNP	ENST00000331105.2	37	CCDS12572.1																																																																																			G|0.601;A|0.399	0.399	strong		0.547	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
CAGE1	285782	hgsc.bcm.edu	37	6	7379031	7379031	+	Missense_Mutation	SNP	G	G	A	rs10223538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7379031G>A	ENST00000512086.1	-	4	708	c.506C>T	c.(505-507)aCt>aTt	p.T169I	CAGE1_ENST00000379918.4_Missense_Mutation_p.T169I|CAGE1_ENST00000502583.1_Missense_Mutation_p.T169I|CAGE1_ENST00000296742.7_Missense_Mutation_p.T33I|CAGE1_ENST00000509324.1_Intron|CAGE1_ENST00000338150.4_Missense_Mutation_p.T169I			Q8TC20	CAGE1_HUMAN	cancer antigen 1	169			T -> I (in dbSNP:rs10223538).							breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					AGAAACACTAGTTTCCATTGG	0.388													G|||	216	0.043131	0.1543	0.0159	5008	,	,		16170	0.0		0.0	False		,,,				2504	0.001				p.T169I		Atlas-SNP	.											.	CAGE1	165	.	0			c.C506T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR	470,3226		30,410,1408	123.0	121.0	122.0		506,506,98	0.7	0.5	6	dbSNP_119	122	5,8187		0,5,4091	yes	missense,missense,missense	CAGE1	NM_001170692.1,NM_001170693.1,NM_205864.2	89,89,89	30,415,5499	AA,AG,GG		0.061,12.7165,3.9956	possibly-damaging,possibly-damaging,possibly-damaging	169/840,169/825,33/642	7379031	475,11413	1848	4096	5944	SO:0001583	missense	285782	exon4			ACACTAGTTTCCA	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"""cancer/testis antigen 95"""	608304	"""cancer/testis antigen 3"""	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.506C>T	6.37:g.7379031G>A	ENSP00000427583:p.Thr169Ile	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Missense_Mutation	SNP	ENST00000512086.1	37		74	0.03388278388278388	69	0.1402439024390244	5	0.013812154696132596	0	0.0	0	0.0	G	13.88	2.367959	0.42003	0.127165	6.1E-4	ENSG00000164304	ENST00000541116;ENST00000379918;ENST00000502583;ENST00000296742;ENST00000512086;ENST00000338150;ENST00000542431;ENST00000512691	T;T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23;1.23	5.23	0.698	0.18087	.	0.571069	0.16966	N	0.192296	T	0.12817	0.0311	L	0.56769	1.78	0.09310	N	1	B	0.20052	0.041	B	0.21917	0.037	T	0.26189	-1.0110	10	0.87932	D	0	-2.6713	2.1016	0.03681	0.1193:0.3601:0.3254:0.1953	rs10223538;rs52806665;rs10223538	169	Q8TC20	CAGE1_HUMAN	I	169;169;169;33;169;169;169;181	ENSP00000369250:T169I;ENSP00000425493:T169I;ENSP00000296742:T33I;ENSP00000427583:T169I;ENSP00000338107:T169I;ENSP00000423789:T181I	ENSP00000296742:T33I	T	-	2	0	CAGE1	7324030	0.274000	0.24191	0.457000	0.27056	0.637000	0.38172	0.554000	0.23407	0.271000	0.22005	0.655000	0.94253	ACT	G|0.944;A|0.056	0.056	strong		0.388	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745	
ZNF443	10224	hgsc.bcm.edu	37	19	12541035	12541035	+	Missense_Mutation	SNP	A	A	G	rs145053669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12541035A>G	ENST00000301547.5	-	4	2148	c.1951T>C	c.(1951-1953)Tgt>Cgt	p.C651R	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	651					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						CATTCCTTACATTCATATGGG	0.388													.|||	24	0.00479233	0.0182	0.0	5008	,	,		20850	0.0		0.0	False		,,,				2504	0.0				p.C651R		Atlas-SNP	.											.	ZNF443	63	.	0			c.T1951C						PASS	.	A	ARG/CYS	85,4321	71.4+/-109.4	0,85,2118	128.0	131.0	130.0		1951	1.0	0.0	19	dbSNP_134	130	5,8595	4.3+/-15.6	0,5,4295	no	missense	ZNF443	NM_005815.4	180	0,90,6413	GG,GA,AA		0.0581,1.9292,0.692	probably-damaging	651/672	12541035	90,12916	2203	4300	6503	SO:0001583	missense	10224	exon4			CCTTACATTCATA	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1951T>C	19.37:g.12541035A>G	ENSP00000301547:p.Cys651Arg	Somatic	395	0	0		WXS	Illumina HiSeq	Phase_I	374	205	0.548128	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	A	10.64	1.406169	0.25378	0.019292	5.81E-4	ENSG00000180855	ENST00000301547;ENST00000411622	D	0.85258	-1.96	1.01	1.01	0.19927	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.85691	0.5755	H	0.95982	3.75	0.26843	N	0.96833	D	0.89917	1.0	D	0.80764	0.994	T	0.78565	-0.2155	9	0.87932	D	0	.	7.541	0.27737	1.0:0.0:0.0:0.0	.	651	Q9Y2A4	ZN443_HUMAN	R	651;623	ENSP00000301547:C651R	ENSP00000301547:C651R	C	-	1	0	ZNF443	12402035	0.269000	0.24143	0.006000	0.13384	0.010000	0.07245	2.194000	0.42668	0.711000	0.32018	0.333000	0.21579	TGT	A|0.993;G|0.007	0.007	strong		0.388	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
KIF2C	11004	hgsc.bcm.edu	37	1	45218895	45218895	+	Silent	SNP	A	A	T	rs3795713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:45218895A>T	ENST00000372224.4	+	6	644	c.531A>T	c.(529-531)cgA>cgT	p.R177R	KIF2C_ENST00000372217.1_Silent_p.R123R|KIF2C_ENST00000493027.1_Intron|KIF2C_ENST00000372222.3_Silent_p.R64R|KIF2C_ENST00000372218.4_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						scavenged	.	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	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	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	
TP53INP1	94241	hgsc.bcm.edu	37	8	95942773	95942773	+	Silent	SNP	G	G	A	rs77630257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:95942773G>A	ENST00000342697.4	-	4	1064	c.657C>T	c.(655-657)caC>caT	p.H219H	NDUFAF6_ENST00000396113.1_Intron|TP53INP1_ENST00000378776.4_Silent_p.H164H|TP53INP1_ENST00000448464.2_3'UTR	NM_033285.3	NP_150601.1	Q96A56	T53I1_HUMAN	tumor protein p53 inducible nuclear protein 1	219					apoptotic process (GO:0006915)|autophagic cell death (GO:0048102)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to hydroperoxide (GO:0071447)|cellular response to methyl methanesulfonate (GO:0072703)|cellular response to UV (GO:0034644)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription, DNA-templated (GO:0045893)|response to heat (GO:0009408)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	antioxidant activity (GO:0016209)			kidney(2)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	9	Breast(36;8.75e-07)					CTTGCCGAGGGTGGCAATCCC	0.473													G|||	42	0.00838658	0.0303	0.0029	5008	,	,		19735	0.0		0.0	False		,,,				2504	0.0				p.H219H		Atlas-SNP	.											.	TP53INP1	22	.	0			c.C657T						PASS	.	G	,	125,4281	92.5+/-131.2	1,123,2079	205.0	211.0	209.0		,657	5.2	1.0	8	dbSNP_132	209	0,8600		0,0,4300	no	utr-3,coding-synonymous	TP53INP1	NM_001135733.1,NM_033285.3	,	1,123,6379	AA,AG,GG		0.0,2.837,0.9611	,	,219/241	95942773	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	94241	exon4			CCGAGGGTGGCAA	AF409115	CCDS6265.1, CCDS47899.1	8q22	2004-03-11				ENSG00000164938			18022	protein-coding gene	gene with protein product		606185				11511362, 12438758	Standard	NM_033285		Approved	DKFZp434M1317, FLJ22139, P53DINP1, SIP, TP53INP1A, TP53INP1B, Teap	uc003yhg.3	Q96A56		ENST00000342697.4:c.657C>T	8.37:g.95942773G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	201	82	0.40796	NM_033285	B2RCE5|Q969R9	Silent	SNP	ENST00000342697.4	37	CCDS6265.1																																																																																			A|0.010;G|0.990	0.010	strong		0.473	TP53INP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379818.1		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552075	32552075	+	Missense_Mutation	SNP	A	A	G	rs1064664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32552075A>G	ENST00000360004.5	-	2	286	c.181T>C	c.(181-183)Tat>Cat	p.Y61H		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	61	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						TCCTGGTTATAGAAGTATCTG	0.602										Multiple Myeloma(14;0.17)			A|||	1550	0.309505	0.3563	0.2536	5008	,	,		8929	0.3105		0.2753	False		,,,				2504	0.32				p.Y61H		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.T181C						PASS	.	A	HIS/TYR	1387,2991		280,827,1082	33.0	32.0	32.0		181	-2.2	0.0	6	dbSNP_86	32	2316,6222		443,1430,2396	no	missense	HLA-DRB1	NM_002124.3	83	723,2257,3478	GG,GA,AA		27.1258,31.6811,28.6699		61/267	32552075	3703,9213	2189	4269	6458	SO:0001583	missense	3123	exon2			GGTTATAGAAGTA	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.181T>C	6.37:g.32552075A>G	ENSP00000353099:p.Tyr61His	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	72	23	0.319444	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	781	0.3576007326007326	226	0.45934959349593496	123	0.3397790055248619	185	0.32342657342657344	247	0.3258575197889182	.	5.967	0.362360	0.11296	0.316811	0.271258	ENSG00000196126	ENST00000360004	T	0.00468	7.22	3.52	-2.17	0.07059	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);	0.345489	0.31257	N	0.007971	T	0.00109	0.0003	.	.	.	0.80722	P	0.0	B	0.17465	0.022	B	0.32465	0.146	T	0.18524	-1.0334	8	0.29301	T	0.29	.	8.5659	0.33538	0.699:0.0:0.301:0.0	rs1064664;rs3205646;rs3208327;rs9269949;rs16822554;rs17879673;rs33909544	61	P01911	2B1F_HUMAN	H	61	ENSP00000353099:Y61H	ENSP00000353099:Y61H	Y	-	1	0	HLA-DRB1	32660053	0.263000	0.24083	0.001000	0.08648	0.002000	0.02628	0.001000	0.13038	-0.511000	0.06514	-1.289000	0.01358	TAT	G|0.352;A|0.648	0.352	strong		0.602	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
RAPGEF6	51735	hgsc.bcm.edu	37	5	130840385	130840385	+	Silent	SNP	A	A	G	rs10063129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:130840385A>G	ENST00000509018.1	-	11	1393	c.1188T>C	c.(1186-1188)atT>atC	p.I396I	RAPGEF6_ENST00000296859.6_Silent_p.I396I|RAPGEF6_ENST00000307984.5_Silent_p.I396I|CTC-432M15.3_ENST00000514667.1_Silent_p.I446I|RAPGEF6_ENST00000510071.1_Silent_p.I396I|RAPGEF6_ENST00000507093.1_Silent_p.I396I|RAPGEF6_ENST00000308008.6_Silent_p.I396I|RAPGEF6_ENST00000512052.1_Silent_p.I111I	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	396					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		GTACCATAACAATTTCTCCCT	0.398													A|||	406	0.0810703	0.2496	0.0418	5008	,	,		18225	0.0		0.0368	False		,,,				2504	0.0102				p.I396I	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.T1188C						PASS	.	A	,,,,,	913,3493	351.8+/-311.4	86,741,1376	197.0	181.0	186.0		1188,1188,1188,1188,1188,1188	3.2	1.0	5	dbSNP_119	186	299,8301	109.0+/-169.6	4,291,4005	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAPGEF6	NM_001164386.1,NM_001164387.1,NM_001164388.1,NM_001164389.1,NM_001164390.1,NM_016340.5	,,,,,	90,1032,5381	GG,GA,AA		3.4767,20.7217,9.3188	,,,,,	396/1610,396/1510,396/1505,396/1392,396/828,396/1602	130840385	1212,11794	2203	4300	6503	SO:0001819	synonymous_variant	51735	exon11			CATAACAATTTCT	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.1188T>C	5.37:g.130840385A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	166	78	0.46988	NM_016340	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Silent	SNP	ENST00000509018.1	37	CCDS34225.1																																																																																			A|0.912;G|0.088	0.088	strong		0.398	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340	
CYP27C1	339761	hgsc.bcm.edu	37	2	127953054	127953054	+	Silent	SNP	A	A	C	rs7568070	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:127953054A>C	ENST00000335247.7	-	5	706	c.576T>G	c.(574-576)acT>acG	p.T192T	CYP27C1_ENST00000409327.1_Silent_p.T192T	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	192						membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.T192T(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		GGAGGTACACAGTCCAAGACA	0.542													C|||	1399	0.279353	0.4644	0.1499	5008	,	,		17596	0.1141		0.2664	False		,,,				2504	0.3047				p.T192T		Atlas-SNP	.											CYP27C1,NS,carcinoma,0,1	CYP27C1	52	1	1	Substitution - coding silent(1)	stomach(1)	c.T576G						PASS	.	C		1929,2477	624.5+/-394.3	419,1091,693	87.0	74.0	79.0		576	-8.9	0.2	2	dbSNP_116	79	2374,6226	701.5+/-405.2	334,1706,2260	no	coding-synonymous	CYP27C1	NM_001001665.3		753,2797,2953	CC,CA,AA		27.6047,43.7812,33.0847		192/373	127953054	4303,8703	2203	4300	6503	SO:0001819	synonymous_variant	339761	exon5			GTACACAGTCCAA	AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684		"""Cytochrome P450s"""	33480	protein-coding gene	gene with protein product							Standard	NM_001001665		Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.576T>G	2.37:g.127953054A>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	159	85	0.534591	NM_001001665	Q6ZNI7	Silent	SNP	ENST00000335247.7	37	CCDS33285.1																																																																																			A|0.696;C|0.304	0.304	strong		0.542	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665	
MUC4	4585	hgsc.bcm.edu	37	3	195509076	195509076	+	Missense_Mutation	SNP	G	G	T	rs35479616		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509076G>T	ENST00000463781.3	-	2	9834	c.9375C>A	c.(9373-9375)gaC>gaA	p.D3125E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3125E	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)		CTGAGGAAGTGTCGGTGACAG	0.582																																					p.D3125E		Atlas-SNP	.											.	MUC4	1505	.	0			c.C9375A						PASS	.						12.0	7.0	9.0					3																	195509076		656	1515	2171	SO:0001583	missense	4585	exon2			GGAAGTGTCGGTG	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.9375C>A	3.37:g.195509076G>T	ENSP00000417498:p.Asp3125Glu	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	282	24	0.0851064	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	7.172	0.587888	0.13812	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29397	1.59;1.57	.	.	.	.	.	.	.	.	T	0.14787	0.0357	N	0.19112	0.55	0.19300	N	0.999979	B	0.19200	0.034	B	0.04013	0.001	T	0.27606	-1.0069	7	.	.	.	.	3.2503	0.06812	0.362:0.0:0.638:0.0	.	2997	E7ESK3	.	E	3125	ENSP00000417498:D3125E;ENSP00000420243:D3125E	.	D	-	3	2	MUC4	196993855	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.931000	0.01556	-0.000000	0.14550	0.000000	0.15137	GAC	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC17	140453	hgsc.bcm.edu	37	7	100678820	100678820	+	Missense_Mutation	SNP	T	T	C	rs386716198|rs4367469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678820T>C	ENST00000306151.4	+	3	4187	c.4123T>C	c.(4123-4125)Tgt>Cgt	p.C1375R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1375	59 X approximate tandem repeats.|Ser-rich.		C -> R (in dbSNP:rs4367469). {ECO:0000269|PubMed:9299468}.		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)					TACTGAAGCCTGTTCATCTCC	0.483																																					p.C1375R		Atlas-SNP	.											.	MUC17	804	.	0			c.T4123C						PASS	.	C	ARG/CYS	1301,3105		206,889,1108	232.0	241.0	238.0		4123	-0.5	0.0	7	dbSNP_111	238	999,7601		57,885,3358	no	missense	MUC17	NM_001040105.1	180	263,1774,4466	CC,CT,TT		11.6163,29.5279,17.6841	benign	1375/4494	100678820	2300,10706	2203	4300	6503	SO:0001583	missense	140453	exon3			GAAGCCTGTTCAT	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.4123T>C	7.37:g.100678820T>C	ENSP00000302716:p.Cys1375Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	350	0.16025641025641027	113	0.22967479674796748	35	0.09668508287292818	125	0.21853146853146854	77	0.10158311345646438	N	0.035	-1.311408	0.01342	0.295279	0.116163	ENSG00000169876	ENST00000306151	T	0.02974	4.09	0.838	-0.487	0.12060	.	.	.	.	.	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	0.43343	-0.9397	8	0.17832	T	0.49	.	2.045	0.03558	0.4021:0.3014:0.0:0.2965	rs4367469;rs10374415	1375	Q685J3	MUC17_HUMAN	R	1375	ENSP00000302716:C1375R	ENSP00000302716:C1375R	C	+	1	0	MUC17	100465540	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.262000	0.08682	-0.774000	0.04590	-4.225000	0.00009	TGT	T|0.834;C|0.166	0.166	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
DES	1674	hgsc.bcm.edu	37	2	220290674	220290674	+	Missense_Mutation	SNP	G	G	A	rs73991549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220290674G>A	ENST00000373960.3	+	9	1461	c.1375G>A	c.(1375-1377)Gtc>Atc	p.V459I	AC053503.6_ENST00000431827.1_RNA	NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	459	Tail.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)	p.V459I(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		TCCCCAGGTCGTCAGTGAGGC	0.607													G|||	49	0.00978435	0.0325	0.0072	5008	,	,		19604	0.0		0.001	False		,,,				2504	0.0				p.V459I		Atlas-SNP	.											DES,brain,glioma,0,2	DES	53	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.G1375A	GRCh37	CM070889	DES	M	rs73991549	PASS	.	G	ILE/VAL	157,4249	107.3+/-145.7	2,153,2048	173.0	151.0	158.0		1375	4.2	1.0	2	dbSNP_130	158	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DES	NM_001927.3	29	2,154,6347	AA,AG,GG		0.0116,3.5633,1.2148	benign	459/471	220290674	158,12848	2203	4300	6503	SO:0001583	missense	1674	exon9			CAGGTCGTCAGTG	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"""Intermediate filaments type III"""	2770	protein-coding gene	gene with protein product	"""intermediate filament protein"""	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.1375G>A	2.37:g.220290674G>A	ENSP00000363071:p.Val459Ile	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Missense_Mutation	SNP	ENST00000373960.3	37	CCDS33383.1	14	0.00641025641025641	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.078	0.771762	0.16051	0.035633	1.16E-4	ENSG00000175084	ENST00000373960	D	0.96913	-4.17	5.17	4.23	0.50019	.	0.000000	0.35207	N	0.003373	T	0.77572	0.4150	L	0.41961	1.31	0.39176	D	0.962688	P	0.36587	0.559	B	0.31547	0.132	D	0.86120	0.1568	10	0.06891	T	0.86	.	13.8879	0.63719	0.0:0.1537:0.8463:0.0	.	459	P17661	DESM_HUMAN	I	459	ENSP00000363071:V459I	ENSP00000363071:V459I	V	+	1	0	DES	219998918	1.000000	0.71417	0.999000	0.59377	0.834000	0.47266	7.003000	0.76310	2.409000	0.81822	0.655000	0.94253	GTC	G|0.989;A|0.011	0.011	strong		0.607	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249605	71249605	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249605C>T	ENST00000398534.3	+	1	535	c.504C>T	c.(502-504)tgC>tgT	p.C168C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	168	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						CCAGCTGCTGCAAGCCCTGCT	0.592																																					p.C168C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.C504T						PASS	.						134.0	144.0	141.0					11																	71249605		2200	4294	6494	SO:0001819	synonymous_variant	57830	exon1			CTGCTGCAAGCCC	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.504C>T	11.37:g.71249605C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	195	32	0.164103	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																			.	.	none		0.592	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
DPCR1	135656	hgsc.bcm.edu	37	6	30919878	30919878	+	Missense_Mutation	SNP	G	G	C	rs11970154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30919878G>C	ENST00000462446.1	+	2	3665	c.3637G>C	c.(3637-3639)Ggg>Cgg	p.G1213R	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_Missense_Mutation_p.G55R			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	337						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						AGAAAACCTGGGGAACACCAC	0.453													G|||	924	0.184505	0.4145	0.1614	5008	,	,		20677	0.0605		0.1491	False		,,,				2504	0.0542				p.G1213R		Atlas-SNP	.											.	DPCR1	99	.	0			c.G3637C						PASS	.	G	ARG/GLY	1532,2874	485.1+/-360.2	283,966,954	143.0	144.0	144.0		3637	-2.9	0.0	6	dbSNP_120	144	1045,7555	221.6+/-259.0	62,921,3317	yes	missense	DPCR1	NM_080870.3	125	345,1887,4271	CC,CG,GG		12.1512,34.7708,19.8139	possibly-damaging	1213/1394	30919878	2577,10429	2203	4300	6503	SO:0001583	missense	135656	exon2			AACCTGGGGAACA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.3637G>C	6.37:g.30919878G>C	ENSP00000417182:p.Gly1213Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	385	0.1762820512820513	190	0.3861788617886179	54	0.14917127071823205	44	0.07692307692307693	97	0.1279683377308707	G	3.993	-0.003997	0.07773	0.347708	0.121512	ENSG00000168631	ENST00000462446;ENST00000450344;ENST00000304311	T;T	0.21191	2.02;2.04	3.26	-2.87	0.05700	.	.	.	.	.	T	0.02807	0.0084	N	0.19112	0.55	0.80722	P	0.0	P	0.34615	0.459	B	0.31751	0.135	T	0.38329	-0.9666	8	0.20046	T	0.44	-0.0399	6.4088	0.21680	0.3898:0.1277:0.4825:0.0	rs11970154;rs52799830;rs61397826;rs11970154	1213	E9PEI6	.	R	1213;337;55	ENSP00000417182:G1213R;ENSP00000305948:G55R	ENSP00000305948:G55R	G	+	1	0	DPCR1	31027857	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.144000	0.10280	-1.457000	0.01919	-1.183000	0.01708	GGG	G|0.816;C|0.184	0.184	strong		0.453	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919081	12919081	+	Missense_Mutation	SNP	C	C	T	rs45443899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919081C>T	ENST00000240189.2	+	2	304	c.217C>T	c.(217-219)Ctt>Ttt	p.L73F		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	73					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)		GATGAAGACGCTTCATCTGGA	0.557													.|||	669	0.133586	0.2821	0.1081	5008	,	,		22898	0.0159		0.1083	False		,,,				2504	0.0982				p.L73F		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.C217T						PASS	.	C	PHE/LEU	1066,3336	386.8+/-326.2	162,742,1297	154.0	164.0	161.0		217	0.8	0.1	1	dbSNP_127	161	937,7655	206.5+/-248.5	79,779,3438	yes	missense	PRAMEF2	NM_023014.1	22	241,1521,4735	TT,TC,CC		10.9055,24.2163,15.4148	probably-damaging	73/475	12919081	2003,10991	2201	4296	6497	SO:0001583	missense	65122	exon2			AAGACGCTTCATC		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.217C>T	1.37:g.12919081C>T	ENSP00000240189:p.Leu73Phe	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	342	177	0.517544	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	261	0.11950549450549451	131	0.266260162601626	41	0.1132596685082873	7	0.012237762237762238	82	0.10817941952506596	C	7.557	0.663873	0.14710	0.242163	0.109055	ENSG00000120952	ENST00000240189	T	0.16597	2.33	0.842	0.842	0.18927	.	0.886493	0.09599	N	0.780473	T	0.00012	0.0000	L	0.39147	1.195	0.80722	P	0.0	D	0.62365	0.991	P	0.59643	0.861	T	0.39901	-0.9591	9	0.49607	T	0.09	.	5.0452	0.14480	0.0:1.0:0.0:0.0	rs45443899	73	O60811	PRAM2_HUMAN	F	73	ENSP00000240189:L73F	ENSP00000240189:L73F	L	+	1	0	PRAMEF2	12841668	0.000000	0.05858	0.055000	0.19348	0.048000	0.14542	0.446000	0.21694	0.759000	0.33084	0.194000	0.17425	CTT	C|0.860;T|0.140	0.140	strong		0.557	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
NCKAP5L	57701	hgsc.bcm.edu	37	12	50189602	50189602	+	Missense_Mutation	SNP	A	A	G	rs3813526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50189602A>G	ENST00000335999.6	-	8	2242	c.2041T>C	c.(2041-2043)Tca>Cca	p.S681P		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	677										central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						TTCTTCTCTGAGCCCAGGGCC	0.677													G|||	1386	0.276757	0.233	0.3847	5008	,	,		12823	0.5466		0.0537	False		,,,				2504	0.2106				p.S681P		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.T2041C						PASS	.	G	PRO/SER	696,2928		77,542,1193	9.0	10.0	10.0		2041	0.7	1.0	12	dbSNP_107	10	348,7692		10,328,3682	yes	missense	NCKAP5L	NM_001037806.3	74	87,870,4875	GG,GA,AA		4.3284,19.2053,8.9506	benign	681/1335	50189602	1044,10620	1812	4020	5832	SO:0001583	missense	57701	exon8			TCTCTGAGCCCAG	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.2041T>C	12.37:g.50189602A>G	ENSP00000337998:p.Ser681Pro	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Missense_Mutation	SNP	ENST00000335999.6	37	CCDS41781.2	607|607	0.27793040293040294|0.27793040293040294	121|121	0.2459349593495935|0.2459349593495935	126|126	0.34806629834254144|0.34806629834254144	321|321	0.5611888111888111|0.5611888111888111	39|39	0.051451187335092345|0.051451187335092345	G|G	3.069|3.069	-0.191536|-0.191536	0.06299|0.06299	0.192053|0.192053	0.043284|0.043284	ENSG00000167566|ENSG00000167566	ENST00000433948|ENST00000335999;ENST00000354423	.|T	.|0.46451	.|0.87	4.06|4.06	0.656|0.656	0.17844|0.17844	.|.	.|0.487974	.|0.17508	.|N	.|0.171724	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	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.44050|0.44050	-0.9353|-0.9353	4|9	.|0.17832	.|T	.|0.49	0.0997|0.0997	0.9826|0.9826	0.01439|0.01439	0.1921:0.1398:0.3704:0.2976|0.1921:0.1398:0.3704:0.2976	rs3813526;rs56785821;rs3813526|rs3813526;rs56785821;rs3813526	.|677;677	.|E2QRB5;Q9HCH0-2	.|.;.	P|P	395|681;677	.|ENSP00000337998:S681P	.|ENSP00000337998:S681P	L|S	-|-	2|1	0|0	NCKAP5L|NCKAP5L	48475869|48475869	0.000000|0.000000	0.05858|0.05858	0.982000|0.982000	0.44146|0.44146	0.954000|0.954000	0.61252|0.61252	-1.403000|-1.403000	0.02497|0.02497	0.062000|0.062000	0.16340|0.16340	-0.215000|-0.215000	0.12644|0.12644	CTC|TCA	A|0.741;G|0.259	0.259	strong		0.677	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497	
COG6	57511	hgsc.bcm.edu	37	13	40229891	40229891	+	Missense_Mutation	SNP	G	G	A	rs3812882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:40229891G>A	ENST00000455146.3	+	1	78	c.28G>A	c.(28-30)Gca>Aca	p.A10T	COG6_ENST00000416691.1_Missense_Mutation_p.A10T	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	10			A -> T (in dbSNP:rs3812882). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.6}.		glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		GGAAGTGGTCGCAGTGTCTGC	0.687													G|||	2426	0.484425	0.5008	0.5879	5008	,	,		13338	0.4573		0.3777	False		,,,				2504	0.5266				p.A10T		Atlas-SNP	.											.	COG6	49	.	0			c.G28A						PASS	.	G	THR/ALA,THR/ALA	2156,2206		575,1006,600	13.0	14.0	14.0		28,28	2.7	0.0	13	dbSNP_107	14	3484,5028		840,1804,1612	yes	missense,missense	COG6	NM_001145079.1,NM_020751.2	58,58	1415,2810,2212	AA,AG,GG		40.9305,49.4269,43.8092	possibly-damaging,possibly-damaging	10/616,10/658	40229891	5640,7234	2181	4256	6437	SO:0001583	missense	57511	exon1			GTGGTCGCAGTGT	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"""Components of oligomeric golgi complex"""	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.28G>A	13.37:g.40229891G>A	ENSP00000397441:p.Ala10Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	84	57	0.678571	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	37	CCDS9370.1	1021	0.4674908424908425	253	0.5142276422764228	211	0.5828729281767956	262	0.458041958041958	295	0.3891820580474934	G	27.1	4.802264	0.90538	0.494269	0.409305	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000422759;ENST00000455146	T;T;T	0.38077	1.16;1.17;1.18	5.52	2.68	0.31781	.	0.801127	0.11428	N	0.565084	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B;B	0.10296	0.003;0.003	B;B	0.04013	0.001;0.001	T	0.43686	-0.9376	9	0.23891	T	0.37	-20.1481	4.4269	0.11507	0.0858:0.1523:0.6047:0.1571	rs3812882;rs58038583;rs3812882	31;10	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	T	10;41;10;10	ENSP00000403733:A10T;ENSP00000412877:A10T;ENSP00000397441:A10T	ENSP00000255468:A41T	A	+	1	0	COG6	39127891	0.000000	0.05858	0.003000	0.11579	0.521000	0.34408	-0.010000	0.12743	0.621000	0.30232	0.561000	0.74099	GCA	G|0.525;A|0.475	0.475	strong		0.687	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3		
ABL1	25	hgsc.bcm.edu	37	9	133760592	133760592	+	Missense_Mutation	SNP	C	C	T	rs2229067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133760592C>T	ENST00000318560.5	+	11	3296	c.2915C>T	c.(2914-2916)tCg>tTg	p.S972L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	972	F-actin-binding.|Pro-rich.		S -> L (in dbSNP:rs2229067). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		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)	GCCAAGCCGTCGGGGACCCCC	0.672			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								C|||	93	0.0185703	0.0431	0.0245	5008	,	,		15811	0.0		0.0189	False		,,,				2504	0.0				p.S991L		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2972T						PASS	.	C	LEU/SER,LEU/SER	190,4214	111.6+/-149.8	4,182,2016	41.0	51.0	48.0		2915,2972	2.4	0.0	9	dbSNP_98	48	172,8420	75.7+/-138.4	0,172,4124	yes	missense,missense	ABL1	NM_005157.4,NM_007313.2	145,145	4,354,6140	TT,TC,CC		2.0019,4.3143,2.7855	benign,benign	972/1131,991/1150	133760592	362,12634	2202	4296	6498	SO:0001583	missense	25	exon11			AGCCGTCGGGGAC	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.2915C>T	9.37:g.133760592C>T	ENSP00000323315:p.Ser972Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	96	60	0.625	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	39	0.017857142857142856	16	0.032520325203252036	9	0.024861878453038673	0	0.0	14	0.018469656992084433	C	9.404	1.078707	0.20227	0.043143	0.020019	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.11495	2.77;2.77	5.27	2.43	0.29744	F-actin binding (1);	1.170500	0.05873	N	0.625078	T	0.01800	0.0057	N	0.22421	0.69	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.12156	0.004;0.007	T	0.35871	-0.9771	10	0.42905	T	0.14	.	7.9383	0.29944	0.0:0.6637:0.0:0.3363	rs2229067;rs2229067	972;1009	P00519;Q59FK4	ABL1_HUMAN;.	L	787;991;972	ENSP00000361423:S991L;ENSP00000323315:S972L	ENSP00000323315:S972L	S	+	2	0	ABL1	132750413	0.000000	0.05858	0.009000	0.14445	0.707000	0.40811	0.591000	0.23969	0.613000	0.30089	-0.258000	0.10820	TCG	C|0.971;T|0.029	0.029	strong		0.672	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
TPO	7173	hgsc.bcm.edu	37	2	1418188	1418188	+	Missense_Mutation	SNP	C	C	T	rs151268825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1418188C>T	ENST00000345913.4	+	2	99	c.8C>T	c.(7-9)gCg>gTg	p.A3V	TPO_ENST00000382201.3_Missense_Mutation_p.A3V|TPO_ENST00000382198.1_Missense_Mutation_p.A3V|TPO_ENST00000329066.4_Missense_Mutation_p.A3V|TPO_ENST00000346956.3_Missense_Mutation_p.A3V|TPO_ENST00000349624.3_Missense_Mutation_p.A3V|TPO_ENST00000382269.3_Missense_Mutation_p.A3V|TPO_ENST00000497517.2_Intron|TPO_ENST00000337415.3_Missense_Mutation_p.A3V|TPO_ENST00000539820.1_Missense_Mutation_p.A3V	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	3					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)	AGAATGAGAGCGCTCGCTGTG	0.522													C|||	16	0.00319489	0.0106	0.0014	5008	,	,		16782	0.0		0.0	False		,,,				2504	0.001				p.A3V		Atlas-SNP	.											TPO,NS,carcinoma,-1,1	TPO	224	1	0			c.C8T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	16,4390	22.3+/-47.3	0,16,2187	71.0	69.0	70.0		8,8,8,8,8,8	-5.3	0.0	2	dbSNP_134	70	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	64,64,64,64,64,64	0,16,6487	TT,TC,CC		0.0,0.3631,0.123	benign,benign,benign,benign,benign,benign	3/934,3/934,3/877,3/877,3/890,3/761	1418188	16,12990	2203	4300	6503	SO:0001583	missense	7173	exon2			TGAGAGCGCTCGC		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.8C>T	2.37:g.1418188C>T	ENSP00000318820:p.Ala3Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.67	1.414818	0.25465	0.003631	0.0	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198	T;T;T;T;T;T;T;T;T;T	0.65732	0.31;-0.17;-0.17;-0.11;0.15;0.31;-0.17;-0.06;0.34;0.15	5.39	-5.3	0.02738	.	1.351910	0.04684	N	0.412836	T	0.41903	0.1179	N	0.13043	0.29	0.09310	N	1	B;B;B;B;B	0.17852	0.003;0.012;0.024;0.014;0.004	B;B;B;B;B	0.10450	0.005;0.003;0.003;0.001;0.002	T	0.32161	-0.9917	10	0.41790	T	0.15	-1.8566	9.1002	0.36664	0.0:0.1854:0.127:0.6876	.	3;3;3;3;3	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	V	3	ENSP00000371704:A3V;ENSP00000337263:A3V;ENSP00000318820:A3V;ENSP00000263886:A3V;ENSP00000332044:A3V;ENSP00000444840:A3V;ENSP00000329869:A3V;ENSP00000371636:A3V;ENSP00000390994:A3V;ENSP00000371633:A3V	ENSP00000329869:A3V	A	+	2	0	TPO	1397195	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.480000	0.00983	-0.936000	0.03723	-0.768000	0.03414	GCG	C|0.999;T|0.001	0.001	strong		0.522	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
OGG1	4968	hgsc.bcm.edu	37	3	9796508	9796508	+	Missense_Mutation	SNP	G	G	A	rs1805373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9796508G>A	ENST00000344629.7	+	4	1029	c.686G>A	c.(685-687)cGa>cAa	p.R229Q	OGG1_ENST00000339511.5_Missense_Mutation_p.R229Q|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Missense_Mutation_p.R229Q|OGG1_ENST00000449570.2_Missense_Mutation_p.R229Q|OGG1_ENST00000349503.5_Missense_Mutation_p.R229Q|OGG1_ENST00000302008.8_Missense_Mutation_p.R229Q|OGG1_ENST00000302003.7_Missense_Mutation_p.R229Q			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	229			R -> Q (in dbSNP:rs1805373). {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)					CAGCAGCTACGAGAGTCCTCA	0.642								Base excision repair (BER), DNA glycosylases					G|||	141	0.028155	0.1029	0.0072	5008	,	,		19186	0.0		0.0	False		,,,				2504	0.0				p.R229Q		Atlas-SNP	.											.	OGG1	57	.	0			c.G686A	GRCh37	CM074394	OGG1	M	rs1805373	PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG,GLN/ARG	384,4022	185.7+/-212.7	11,362,1830	33.0	28.0	30.0		686,686,686,686,686,,686,686	3.1	0.8	3	dbSNP_98	30	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense,missense,missense,intron,missense,missense	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	43,43,43,43,43,,43,43	11,365,6127	AA,AG,GG		0.0349,8.7154,2.9755	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	229/346,229/325,229/411,229/425,229/358,,229/357,229/323	9796508	387,12619	2203	4300	6503	SO:0001583	missense	4968	exon4			AGCTACGAGAGTC	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.686G>A	3.37:g.9796508G>A	ENSP00000342851:p.Arg229Gln	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	146	59	0.40411	NM_016819	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	37	CCDS2581.1	43|43	0.019688644688644688|0.019688644688644688	39|39	0.07926829268292683|0.07926829268292683	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.07|16.07	3.017581|3.017581	0.54576|0.54576	0.087154|0.087154	3.49E-4|3.49E-4	ENSG00000114026|ENSG00000114026	ENST00000441094|ENST00000302003;ENST00000344629;ENST00000302036;ENST00000349503;ENST00000339511;ENST00000449570;ENST00000302008;ENST00000339542	.|T;T;T;T;T;T;T	.|0.56275	.|0.47;0.47;0.47;0.47;0.47;0.47;0.47	5.78|5.78	3.07|3.07	0.35406|0.35406	.|HhH-GPD domain (2);DNA glycosylase (2);	.|0.261230	.|0.45361	.|N	.|0.000369	T|T	0.03520|0.03520	0.0101|0.0101	M|M	0.76938|0.76938	2.355|2.355	0.53005|0.53005	D|D	0.999968|0.999968	.|D;D;P;P;D;P;B;P	.|0.61697	.|0.982;0.99;0.954;0.907;0.977;0.954;0.312;0.933	.|B;B;B;B;B;B;B;B	.|0.43331	.|0.345;0.416;0.299;0.133;0.133;0.299;0.019;0.082	T|T	0.02320|0.02320	-1.1177|-1.1177	5|10	.|0.54805	.|T	.|0.06	-3.3716|-3.3716	11.2674|11.2674	0.49118|0.49118	0.1972:0.0:0.8028:0.0|0.1972:0.0:0.8028:0.0	rs1805373;rs2266693;rs52816862;rs56468739;rs1805373|rs1805373;rs2266693;rs52816862;rs56468739;rs1805373	.|72;229;229;229;229;229;229;229	.|F8WA07;E5KPM6;E5KPM5;E5KPM7;E5KPM9;E5KPN0;O15527;O15527-2	.|.;.;.;.;.;.;OGG1_HUMAN;.	K|Q	127|229;229;229;229;229;229;229;72	.|ENSP00000305584:R229Q;ENSP00000342851:R229Q;ENSP00000306561:R229Q;ENSP00000303132:R229Q;ENSP00000345520:R229Q;ENSP00000403598:R229Q;ENSP00000305527:R229Q	.|ENSP00000305584:R229Q	E|R	+|+	1|2	0|0	OGG1|OGG1	9771508|9771508	0.813000|0.813000	0.29090|0.29090	0.768000|0.768000	0.31515|0.31515	0.370000|0.370000	0.29829|0.29829	2.465000|2.465000	0.45075|0.45075	0.384000|0.384000	0.24942|0.24942	-0.203000|-0.203000	0.12734|0.12734	GAG|CGA	G|0.969;A|0.031	0.031	strong		0.642	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821	
TNIK	23043	hgsc.bcm.edu	37	3	170824990	170824990	+	Silent	SNP	G	G	A	rs904617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:170824990G>A	ENST00000436636.2	-	21	2732	c.2388C>T	c.(2386-2388)taC>taT	p.Y796Y	MIR569_ENST00000385228.1_RNA|TNIK_ENST00000341852.6_Silent_p.Y712Y|TNIK_ENST00000488470.1_Silent_p.Y741Y|TNIK_ENST00000475336.1_Intron|TNIK_ENST00000369326.5_Intron|TNIK_ENST00000538048.1_Intron|TNIK_ENST00000460047.1_Intron|TNIK_ENST00000284483.8_Intron|TNIK_ENST00000357327.5_Silent_p.Y767Y|TNIK_ENST00000470834.1_Intron	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	796	Mediates interaction with NEDD4.				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)			TAGCTTTTTTGTAGCTCTGAA	0.353													A|||	443	0.0884585	0.2859	0.0231	5008	,	,		20309	0.0109		0.001	False		,,,				2504	0.0378				p.Y796Y		Atlas-SNP	.											.	TNIK	313	.	0			c.C2388T						PASS	.	A	,,,,,,,	877,2825		104,669,1078	58.0	54.0	55.0		,2301,,2223,,2136,,2388	4.7	1.0	3	dbSNP_86	55	20,8188		0,20,4084	no	intron,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	TNIK	NM_001161560.1,NM_001161561.1,NM_001161562.1,NM_001161563.1,NM_001161564.1,NM_001161565.1,NM_001161566.1,NM_015028.2	,,,,,,,	104,689,5162	AA,AG,GG		0.2437,23.6899,7.5315	,,,,,,,	,767/1332,,741/1306,,712/1277,,796/1361	170824990	897,11013	1851	4104	5955	SO:0001819	synonymous_variant	23043	exon21			TTTTTTGTAGCTC	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.2388C>T	3.37:g.170824990G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Silent	SNP	ENST00000436636.2	37	CCDS46956.1																																																																																			G|0.926;A|0.074	0.074	strong		0.353	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
SFSWAP	6433	hgsc.bcm.edu	37	12	132237789	132237789	+	Silent	SNP	C	C	T	rs202066133		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132237789C>T	ENST00000261674.4	+	8	1344	c.1203C>T	c.(1201-1203)acC>acT	p.T401T	SFSWAP_ENST00000541286.1_Silent_p.T401T	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	401					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						CTGGCGTGACCGTGTCTAACT	0.637													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16980	0.0		0.0	False		,,,				2504	0.0				p.T401T		Atlas-SNP	.											.	SFSWAP	69	.	0			c.C1203T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	174.0	146.0	156.0		1203	-2.4	0.9	12		156	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SFSWAP	NM_004592.2		0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308		401/952	132237789	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	6433	exon8			CGTGACCGTGTCT	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.1203C>T	12.37:g.132237789C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	170	70	0.411765	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	7.548	0.662175	0.14645	6.81E-4	1.16E-4	ENSG00000061936	ENST00000537164	.	.	.	5.41	-2.37	0.06643	.	.	.	.	.	T	0.51517	0.1679	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45818	-0.9235	4	.	.	.	-14.7257	7.8087	0.29217	0.0:0.2462:0.2063:0.5475	.	.	.	.	L	41	.	.	P	+	2	0	SFSWAP	130803742	0.647000	0.27304	0.908000	0.35775	0.652000	0.38707	-0.321000	0.08018	-0.413000	0.07507	0.561000	0.74099	CCG	C|1.000;T|0.000	0.000	strong		0.637	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
PRUNE	58497	hgsc.bcm.edu	37	1	150999737	150999737	+	Silent	SNP	A	A	G	rs11204762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150999737A>G	ENST00000271620.3	+	6	864	c.708A>G	c.(706-708)aaA>aaG	p.K236K	PRUNE_ENST00000368934.1_Silent_p.K54K|PRUNE_ENST00000368937.1_Silent_p.K54K|PRUNE_ENST00000368935.1_Silent_p.K4K|PRUNE_ENST00000368936.1_Silent_p.K54K|PRUNE_ENST00000271619.8_Silent_p.K77K|PRUNE_ENST00000467771.1_3'UTR	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	104	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	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	
CEMIP	57214	hgsc.bcm.edu	37	15	81217024	81217024	+	Silent	SNP	G	G	A	rs28566789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81217024G>A	ENST00000394685.3	+	18	2684	c.2265G>A	c.(2263-2265)ccG>ccA	p.P755P	KIAA1199_ENST00000356249.5_Silent_p.P755P|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Silent_p.P755P			Q8WUJ3	CEMIP_HUMAN		755					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						ACAAGCGGCCGTTCCTCTCAA	0.532													G|||	139	0.0277556	0.0998	0.0086	5008	,	,		19966	0.0		0.001	False		,,,				2504	0.0				p.P755P		Atlas-SNP	.											.	KIAA1199	118	.	0			c.G2265A						PASS	.	G		341,4065	178.3+/-207.1	17,307,1879	123.0	101.0	108.0		2265	-0.2	1.0	15	dbSNP_125	108	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KIAA1199	NM_018689.1		17,309,6177	AA,AG,GG		0.0233,7.7394,2.6372		755/1362	81217024	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	57214	exon17			GCGGCCGTTCCTC																												ENST00000394685.3:c.2265G>A	15.37:g.81217024G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	196	92	0.469388	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																			G|0.973;A|0.027	0.027	strong		0.532	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
SORL1	6653	hgsc.bcm.edu	37	11	121367626	121367626	+	Silent	SNP	T	T	C	rs12364988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	57	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	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	
CELSR1	9620	hgsc.bcm.edu	37	22	46787694	46787694	+	Missense_Mutation	SNP	A	A	G	rs6008794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46787694A>G	ENST00000262738.3	-	15	5983	c.5984T>C	c.(5983-5985)cTa>cCa	p.L1995P		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1995	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		L -> P (in dbSNP:rs6008794).		anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GTCCTGGGCTAGGAGCTTGTA	0.637													G|||	1377	0.27496	0.7413	0.1398	5008	,	,		16398	0.0129		0.159	False		,,,				2504	0.1299				p.L1995P		Atlas-SNP	.											.	CELSR1	242	.	0			c.T5984C						PASS	.	G	PRO/LEU	2860,1544		955,950,297	26.0	35.0	32.0		5984	3.4	0.7	22	dbSNP_114	32	1210,7390		77,1056,3167	yes	missense	CELSR1	NM_014246.1	98	1032,2006,3464	GG,GA,AA		14.0698,35.059,31.2981	benign	1995/3015	46787694	4070,8934	2202	4300	6502	SO:0001583	missense	9620	exon15			TGGGCTAGGAGCT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5984T>C	22.37:g.46787694A>G	ENSP00000262738:p.Leu1995Pro	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	537	0.24587912087912087	359	0.7296747967479674	53	0.1464088397790055	7	0.012237762237762238	118	0.15567282321899736	G	0.013	-1.617194	0.00828	0.64941	0.140698	ENSG00000075275	ENST00000262738	T	0.68479	-0.33	4.52	3.4	0.38934	.	0.295595	0.27486	N	0.019156	T	0.00012	0.0000	N	0.01454	-0.855	0.24745	P	0.99301956	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.41716	-0.9493	9	0.14656	T	0.56	.	7.2011	0.25881	0.1006:0.0:0.6132:0.2863	rs6008794;rs7290897;rs57574545;rs6008794	316;1995	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	P	1995	ENSP00000262738:L1995P	ENSP00000262738:L1995P	L	-	2	0	CELSR1	45166358	0.995000	0.38212	0.720000	0.30636	0.016000	0.09150	2.771000	0.47670	0.924000	0.37069	-0.355000	0.07637	CTA	A|0.696;G|0.304	0.304	strong		0.637	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
IFI44L	10964	hgsc.bcm.edu	37	1	79095581	79095581	+	Missense_Mutation	SNP	T	T	C	rs987495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:79095581T>C	ENST00000370751.5	+	4	883	c.704T>C	c.(703-705)aTc>aCc	p.I235T	IFI44L_ENST00000476521.1_3'UTR|IFI44L_ENST00000342282.3_5'UTR	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	235			I -> T (in dbSNP:rs987495). {ECO:0000269|Ref.1}.		defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)				endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						GGGTCTGATATCACCAGCATA	0.408													T|||	1074	0.214457	0.1195	0.2709	5008	,	,		15403	0.245		0.2505	False		,,,				2504	0.2342				p.I235T		Atlas-SNP	.											IFI44L,NS,carcinoma,-1,1	IFI44L	93	1	0			c.T704C						PASS	.	T	THR/ILE	638,3768	274.9+/-272.2	44,550,1609	81.0	82.0	81.0		704	-5.6	0.0	1	dbSNP_86	81	2111,6489	364.0+/-333.3	259,1593,2448	yes	missense	IFI44L	NM_006820.2	89	303,2143,4057	CC,CT,TT		24.5465,14.4803,21.1364	benign	235/453	79095581	2749,10257	2203	4300	6503	SO:0001583	missense	10964	exon4			CTGATATCACCAG	AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"""chromosome 1 open reading frame 29"""	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.704T>C	1.37:g.79095581T>C	ENSP00000359787:p.Ile235Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_006820	Q86TE1|Q96B64|Q99984	Missense_Mutation	SNP	ENST00000370751.5	37	CCDS687.2	468	0.21428571428571427	45	0.09146341463414634	84	0.23204419889502761	141	0.2465034965034965	198	0.2612137203166227	T	0.144	-1.098806	0.01843	0.144803	0.245465	ENSG00000137959	ENST00000370751;ENST00000450498	T;T	0.13196	2.82;2.61	2.82	-5.64	0.02466	.	1.995390	0.02289	N	0.070148	T	0.00936	0.0031	N	0.02539	-0.55	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35699	-0.9778	9	0.12430	T	0.62	3.8519	4.0787	0.09916	0.406:0.1735:0.0:0.4204	rs987495;rs3766326;rs52810523;rs58826484;rs987495	235	Q53G44	IF44L_HUMAN	T	235;212	ENSP00000359787:I235T;ENSP00000400784:I212T	ENSP00000359787:I235T	I	+	2	0	IFI44L	78868169	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.687000	0.01927	-2.136000	0.00810	-2.622000	0.00156	ATC	T|0.785;G|0.001	.	strong		0.408	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820	
SORBS1	10580	hgsc.bcm.edu	37	10	97154762	97154762	+	Silent	SNP	G	G	A	rs17110703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:97154762G>A	ENST00000361941.3	-	12	1319	c.1293C>T	c.(1291-1293)tcC>tcT	p.S431S	SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000371227.4_Intron|SORBS1_ENST00000474353.2_Intron|SORBS1_ENST00000354106.3_Silent_p.S422S|SORBS1_ENST00000347291.4_Silent_p.S299S|SORBS1_ENST00000371247.2_Silent_p.S431S|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000277982.5_Silent_p.S431S|SORBS1_ENST00000371246.2_Silent_p.S431S|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000393949.1_Silent_p.S422S|SORBS1_ENST00000607232.1_Intron	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TGGTACCTTCGGAAGTTTGCT	0.393													G|||	188	0.0375399	0.1369	0.0086	5008	,	,		19554	0.0		0.001	False		,,,				2504	0.0				p.S431S		Atlas-SNP	.											.	SORBS1	185	.	0			c.C1293T						PASS	.	G	,,,,,,	505,3901	233.6+/-246.7	26,453,1724	237.0	281.0	266.0		1293,1293,,,,,	4.9	1.0	10	dbSNP_123	266	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	,,,,,,	26,462,6015	AA,AG,GG		0.1047,11.4616,3.952	,,,,,,	431/1293,431/1152,,,,,	97154762	514,12492	2203	4300	6503	SO:0001819	synonymous_variant	10580	exon12			ACCTTCGGAAGTT	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.1293C>T	10.37:g.97154762G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	214	108	0.504673	NM_001034955		Silent	SNP	ENST00000361941.3	37	CCDS31255.1																																																																																			G|0.952;A|0.048	0.048	strong		0.393	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
PIK3C2G	5288	hgsc.bcm.edu	37	12	18715673	18715673	+	Silent	SNP	A	A	G	rs11044184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18715673A>G	ENST00000266497.5	+	25	3542	c.3504A>G	c.(3502-3504)aaA>aaG	p.K1168K	PIK3C2G_ENST00000433979.1_Silent_p.K1168K|PIK3C2G_ENST00000538779.1_Silent_p.K1209K			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1168	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TCCCTGTTAAATTGAATAACT	0.383													A|||	273	0.0545128	0.1989	0.0144	5008	,	,		17230	0.0		0.0	False		,,,				2504	0.0				p.K1168K		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A3504G						PASS	.	A		672,3034		63,546,1244	68.0	64.0	65.0		3504	-0.7	1.0	12	dbSNP_120	65	5,8185		0,5,4090	no	coding-synonymous	PIK3C2G	NM_004570.4		63,551,5334	GG,GA,AA		0.0611,18.1328,5.691		1168/1446	18715673	677,11219	1853	4095	5948	SO:0001819	synonymous_variant	5288	exon26			TGTTAAATTGAAT	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.3504A>G	12.37:g.18715673A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	192	85	0.442708	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																			A|0.941;G|0.059	0.059	strong		0.383	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
DENND3	22898	hgsc.bcm.edu	37	8	142154291	142154291	+	Missense_Mutation	SNP	G	G	A	rs307761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:142154291G>A	ENST00000262585.2	+	5	706	c.428G>A	c.(427-429)aGt>aAt	p.S143N	DENND3_ENST00000519811.1_Missense_Mutation_p.S223N|DENND3_ENST00000424248.1_Missense_Mutation_p.S143N	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	143	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.		S -> N (in dbSNP:rs307761).		cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			GAAGTGGACAGTCATATAAAA	0.388													G|||	1739	0.347244	0.5787	0.2839	5008	,	,		18533	0.4583		0.1123	False		,,,				2504	0.2065				p.S143N		Atlas-SNP	.											.	DENND3	127	.	0			c.G428A						PASS	.	G	ASN/SER	2185,2221	584.7+/-386.1	540,1105,558	101.0	102.0	102.0		428	2.4	0.7	8	dbSNP_79	102	868,7732	196.5+/-241.4	43,782,3475	yes	missense	DENND3	NM_014957.2	46	583,1887,4033	AA,AG,GG		10.093,49.5915,23.4738	benign	143/1199	142154291	3053,9953	2203	4300	6503	SO:0001583	missense	22898	exon5			TGGACAGTCATAT	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"""DENN/MADD domain containing"", ""WD repeat domain containing"""	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.428G>A	8.37:g.142154291G>A	ENSP00000262585:p.Ser143Asn	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	37	CCDS34947.1	679	0.3108974358974359	260	0.5284552845528455	80	0.22099447513812154	260	0.45454545454545453	79	0.10422163588390501	G	0.838	-0.742757	0.03088	0.495915	0.10093	ENSG00000105339	ENST00000262585;ENST00000424248;ENST00000519811;ENST00000523058	T;T;T;T	0.10573	2.86;2.86;2.86;2.86	4.93	2.4	0.29515	DENN (3);	0.606836	0.18863	N	0.129064	T	0.00012	0.0000	N	0.04203	-0.255	0.47037	P	7.059999999999844E-4	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.39035	-0.9633	9	0.07482	T	0.82	-23.2708	12.9249	0.58254	0.9282:0.0:0.0718:0.0	rs307761;rs52830744;rs59579350;rs307761	223;143	E9PF32;A2RUS2	.;DEND3_HUMAN	N	143;143;223;223	ENSP00000262585:S143N;ENSP00000410594:S143N;ENSP00000428714:S223N;ENSP00000430786:S223N	ENSP00000262585:S143N	S	+	2	0	DENND3	142223473	1.000000	0.71417	0.677000	0.29947	0.028000	0.11728	3.858000	0.55979	0.306000	0.22856	-1.421000	0.01109	AGT	G|0.722;A|0.278	0.278	strong		0.388	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957	
CDC5L	988	hgsc.bcm.edu	37	6	44387305	44387305	+	Silent	SNP	T	T	C	rs11571982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44387305T>C	ENST00000371477.3	+	9	1511	c.1212T>C	c.(1210-1212)acT>acC	p.T404T		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	404	Interaction with PPP1R8.				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)			TTGTACAGACTCCAAACACAG	0.398													T|||	58	0.0115815	0.0393	0.0086	5008	,	,		20954	0.0		0.0	False		,,,				2504	0.0				p.T404T		Atlas-SNP	.											.	CDC5L	86	.	0			c.T1212C						PASS	.	T		140,4266	100.3+/-138.9	1,138,2064	154.0	138.0	143.0		1212	0.3	1.0	6	dbSNP_120	143	0,8600		0,0,4300	no	coding-synonymous	CDC5L	NM_001253.2		1,138,6364	CC,CT,TT		0.0,3.1775,1.0764		404/803	44387305	140,12866	2203	4300	6503	SO:0001819	synonymous_variant	988	exon9			ACAGACTCCAAAC	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.1212T>C	6.37:g.44387305T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_001253	Q76N46|Q99974	Silent	SNP	ENST00000371477.3	37	CCDS4912.1																																																																																			T|0.989;C|0.011	0.011	strong		0.398	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1		
KIRREL2	84063	hgsc.bcm.edu	37	19	36349752	36349752	+	Missense_Mutation	SNP	G	G	A	rs404299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000347900.6_Missense_Mutation_p.A120T|KIRREL2_ENST00000262625.7_Missense_Mutation_p.A170T	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	244	0	0		WXS	Illumina HiSeq	Phase_I	204	203	0.995098	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	
CDC14A	8556	hgsc.bcm.edu	37	1	100928421	100928421	+	Silent	SNP	C	C	T	rs74667145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100928421C>T	ENST00000336454.3	+	9	1177	c.822C>T	c.(820-822)atC>atT	p.I274I	RP5-837M10.4_ENST00000432210.1_RNA|CDC14A_ENST00000370124.3_Silent_p.I274I|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000544534.1_Silent_p.I274I|CDC14A_ENST00000542213.1_Silent_p.I216I|CDC14A_ENST00000361544.6_Silent_p.I274I	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	274	B.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		AAGGGGCCATCGCCGTTCACT	0.527													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18751	0.0		0.0	False		,,,				2504	0.0				p.I274I		Atlas-SNP	.											.	CDC14A	65	.	0			c.C822T						PASS	.	C	,,	20,4386	28.1+/-56.4	0,20,2183	60.0	51.0	54.0		822,822,822	-3.7	0.1	1	dbSNP_132	54	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	0,20,6483	TT,TC,CC		0.0,0.4539,0.1538	,,	274/595,274/624,274/384	100928421	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	8556	exon9			GGCCATCGCCGTT	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1718	protein-coding gene	gene with protein product		603504	"""CDC10 (cell division cycle 10, S. cerevisiae, homolog)"", ""CDC14 cell division cycle 14 homolog A (S. cerevisiae)"""			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.822C>T	1.37:g.100928421C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			C|0.999;T|0.001	0.001	strong		0.527	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	
PDE6A	5145	hgsc.bcm.edu	37	5	149324153	149324153	+	Silent	SNP	G	G	A	rs34230349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149324153G>A	ENST00000255266.5	-	1	203	c.84C>T	c.(82-84)taC>taT	p.Y28Y		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	28					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	GCTTGGCCCGGTAGTGGAGGT	0.572													G|||	84	0.0167732	0.0461	0.0058	5008	,	,		18582	0.0099		0.0	False		,,,				2504	0.0092				p.Y28Y		Atlas-SNP	.											.	PDE6A	98	.	0			c.C84T						PASS	.	G		199,4207	124.5+/-161.8	2,195,2006	48.0	43.0	45.0		84	2.0	1.0	5	dbSNP_126	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PDE6A	NM_000440.2		2,196,6305	AA,AG,GG		0.0116,4.5166,1.5378		28/861	149324153	200,12806	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			GGCCCGGTAGTGG		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.84C>T	5.37:g.149324153G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|0.984;A|0.016	0.016	strong		0.572	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
ABCC1	4363	hgsc.bcm.edu	37	16	16230427	16230427	+	Silent	SNP	C	C	T	rs34526519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16230427C>T	ENST00000399410.3	+	29	4393	c.4218C>T	c.(4216-4218)gcC>gcT	p.A1406A	ABCC1_ENST00000346370.5_Silent_p.A1350A|ABCC1_ENST00000349029.5_Silent_p.A1291A|ABCC1_ENST00000345148.5_Silent_p.A1406A|ABCC1_ENST00000399408.2_Silent_p.A1416A|ABCC1_ENST00000351154.5_Silent_p.A1347A	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1406	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	TGGAGCTGGCCCACCTGAAGG	0.562													C|||	28	0.00559105	0.0166	0.0058	5008	,	,		18552	0.0		0.002	False		,,,				2504	0.0				p.A1406A		Atlas-SNP	.											.	ABCC1	156	.	0			c.C4218T						PASS	.	C	,,,,	64,3882		0,64,1909	51.0	52.0	52.0		4218,4041,4050,3873,4218	-12.1	0.2	16	dbSNP_126	52	6,8310		0,6,4152	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	0,70,6061	TT,TC,CC		0.0722,1.6219,0.5709	,,,,	1406/1532,1347/1473,1350/1476,1291/1417,1406/1467	16230427	70,12192	1973	4158	6131	SO:0001819	synonymous_variant	4363	exon29			GCTGGCCCACCTG	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.4218C>T	16.37:g.16230427C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			C|0.994;T|0.006	0.006	strong		0.562	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
SH2D3A	10045	hgsc.bcm.edu	37	19	6760974	6760974	+	Missense_Mutation	SNP	T	T	C	rs7258236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6760974T>C	ENST00000245908.6	-	3	363	c.94A>G	c.(94-96)Aat>Gat	p.N32D	SH2D3A_ENST00000599563.1_5'UTR|SH2D3A_ENST00000437152.3_Intron	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	32	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		N -> D (in dbSNP:rs7258236). {ECO:0000269|PubMed:10187783, ECO:0000269|PubMed:12975309}.		JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						AAGTCGCCATTTTGCTGAAGA	0.592													C|||	1304	0.260383	0.469	0.1571	5008	,	,		16006	0.0565		0.2247	False		,,,				2504	0.2986				p.N32D		Atlas-SNP	.											.	SH2D3A	53	.	0			c.A94G						PASS	.	C	ASP/ASN	1830,2574		382,1066,754	22.0	21.0	21.0		94	3.7	0.9	19	dbSNP_116	21	1858,6738		225,1408,2665	yes	missense	SH2D3A	NM_005490.2	23	607,2474,3419	CC,CT,TT		21.6147,41.5531,28.3692	benign	32/577	6760974	3688,9312	2202	4298	6500	SO:0001583	missense	10045	exon3			CGCCATTTTGCTG	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"""SH2 domain containing"""	16885	protein-coding gene	gene with protein product		604721	"""SH2 domain-containing 3A"""			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.94A>G	19.37:g.6760974T>C	ENSP00000245908:p.Asn32Asp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Missense_Mutation	SNP	ENST00000245908.6	37	CCDS12173.1	482	0.2206959706959707	206	0.4186991869918699	64	0.17679558011049723	37	0.06468531468531469	175	0.23087071240105542	C	2.186	-0.386345	0.04966	0.415531	0.216147	ENSG00000125731	ENST00000245908	T	0.59772	0.24	4.81	3.74	0.42951	SH2 motif (5);	0.000000	0.44097	N	0.000482	T	0.00012	0.0000	N	0.01235	-0.94	0.09310	P	0.999999928166	B	0.02656	0.0	B	0.04013	0.001	T	0.39482	-0.9612	9	0.02654	T	1	-11.7979	7.1734	0.25730	0.0:0.7255:0.0:0.2745	rs7258236;rs60821729;rs7258236	32	Q9BRG2	SH23A_HUMAN	D	32	ENSP00000245908:N32D	ENSP00000245908:N32D	N	-	1	0	SH2D3A	6711974	0.356000	0.24930	0.940000	0.37924	0.840000	0.47671	0.652000	0.24888	1.285000	0.44548	-0.222000	0.12452	AAT	T|0.735;C|0.265	0.265	strong		0.592	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490	
MUC4	4585	hgsc.bcm.edu	37	3	195515102	195515102	+	Missense_Mutation	SNP	G	G	C	rs199995135		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515102G>C	ENST00000463781.3	-	2	3808	c.3349C>G	c.(3349-3351)Cac>Gac	p.H1117D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H1117D	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	556					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.H1117D(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)		GGGGTGGTGTGACCTGTGGAT	0.567																																					p.H1117D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.C3349G						scavenged	.						14.0	8.0	9.0					3																	195515102		671	1542	2213	SO:0001583	missense	4585	exon2			TGGTGTGACCTGT	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.3349C>G	3.37:g.195515102G>C	ENSP00000417498:p.His1117Asp	Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	346	19	0.0549133	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	.	.	.	.	.	.	.	.	.	.	-	0.907	-0.720205	0.03182	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.44;1.44	0.814	-1.63	0.08345	.	.	.	.	.	T	0.14270	0.0345	N	0.19112	0.55	0.09310	N	1	B	0.14805	0.011	B	0.21546	0.035	T	0.28170	-1.0052	8	.	.	.	.	0.2358	0.00186	0.3536:0.2031:0.2397:0.2036	.	1117	E7ESK3	.	D	1117	ENSP00000417498:H1117D;ENSP00000420243:H1117D	.	H	-	1	0	MUC4	196999497	0.000000	0.05858	0.000000	0.03702	0.130000	0.20726	-2.660000	0.00851	-2.057000	0.00897	0.064000	0.15345	CAC	.	.	weak		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PACS2	23241	hgsc.bcm.edu	37	14	105860919	105860919	+	Silent	SNP	C	C	T	rs201014934		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105860919C>T	ENST00000325438.8	+	24	3084	c.2580C>T	c.(2578-2580)gaC>gaT	p.D860D	PACS2_ENST00000458164.2_Silent_p.D875D|PACS2_ENST00000551743.1_Silent_p.D374D|PACS2_ENST00000447393.1_Silent_p.D864D|PACS2_ENST00000551801.1_Silent_p.D61D|PACS2_ENST00000430725.2_Silent_p.D785D|PACS2_ENST00000547217.1_Silent_p.D830D			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	860					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)		AGTGCAGCGACGTCAAGTTCT	0.667													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17322	0.0		0.0	False		,,,				2504	0.0				p.D875D		Atlas-SNP	.											PACS2,NS,carcinoma,+2,1	PACS2	75	1	0			c.C2625T						scavenged	.	C	,	1,4405	2.1+/-5.4	0,1,2202	131.0	97.0	109.0		2592,2580	-2.0	0.9	14		109	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PACS2	NM_001100913.2,NM_015197.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	864/894,860/890	105860919	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23241	exon25			CAGCGACGTCAAG	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.2580C>T	14.37:g.105860919C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	122	2	0.0163934	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Silent	SNP	ENST00000325438.8	37	CCDS32168.1																																																																																			C|1.000;T|0.000	0.000	strong		0.667	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355	
DIRAS1	148252	hgsc.bcm.edu	37	19	2717256	2717256	+	Silent	SNP	C	C	G	rs3745812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	108	0	0		WXS	Illumina HiSeq	Phase_I	119	63	0.529412	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		
HMCN1	83872	hgsc.bcm.edu	37	1	186050417	186050417	+	Missense_Mutation	SNP	A	A	G	rs10798035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186050417A>G	ENST00000271588.4	+	56	8907	c.8678A>G	c.(8677-8679)gAg>gGg	p.E2893G	HMCN1_ENST00000367492.2_Missense_Mutation_p.E2893G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2893	Ig-like C2-type 27.		E -> G (in dbSNP:rs10798035). {ECO:0000269|PubMed:14570714}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GCACTGATAGAGTGTTTATCC	0.463													A|||	2918	0.582668	0.6952	0.6311	5008	,	,		14601	0.5694		0.499	False		,,,				2504	0.4959				p.E2893G		Atlas-SNP	.											HMCN1,NS,carcinoma,0,2	HMCN1	797	2	0			c.A8678G						PASS	.	A	GLY/GLU	2939,1467	678.7+/-403.6	1003,933,267	159.0	152.0	155.0		8678	5.9	1.0	1	dbSNP_120	155	4279,4321	576.2+/-390.4	1079,2121,1100	yes	missense	HMCN1	NM_031935.2	98	2082,3054,1367	GG,GA,AA		49.7558,33.2955,44.5025	possibly-damaging	2893/5636	186050417	7218,5788	2203	4300	6503	SO:0001583	missense	83872	exon56			TGATAGAGTGTTT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8678A>G	1.37:g.186050417A>G	ENSP00000271588:p.Glu2893Gly	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1286	0.5888278388278388	327	0.6646341463414634	228	0.6298342541436464	344	0.6013986013986014	387	0.5105540897097626	A	27.2	4.808057	0.90707	0.667045	0.497558	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.30182	1.54;1.54	5.86	5.86	0.93980	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.188863	0.56097	D	0.000030	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	0.99999577304	D	0.76494	0.999	D	0.83275	0.996	T	0.46638	-0.9177	9	0.48119	T	0.1	.	14.8163	0.70036	1.0:0.0:0.0:0.0	rs10798035;rs52812505;rs56779083;rs10798035	2893	Q96RW7	HMCN1_HUMAN	G	2893	ENSP00000271588:E2893G;ENSP00000356462:E2893G	ENSP00000271588:E2893G	E	+	2	0	HMCN1	184317040	1.000000	0.71417	0.995000	0.50966	0.856000	0.48823	8.904000	0.92590	2.241000	0.73720	0.533000	0.62120	GAG	A|0.425;G|0.575	0.575	strong		0.463	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
SCARB1	949	hgsc.bcm.edu	37	12	125263039	125263039	+	3'UTR	SNP	C	C	T	rs701103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125263039C>T	ENST00000415380.2	-	0	1870				SCARB1_ENST00000376788.1_3'UTR|SCARB1_ENST00000261693.6_3'UTR|SCARB1_ENST00000339570.5_Missense_Mutation_p.G499R			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1						adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	GGGGGCTGTCCGCTGGGAGAG	0.692													C|||	305	0.0609026	0.2224	0.0144	5008	,	,		12888	0.0		0.001	False		,,,				2504	0.0				p.G499R		Atlas-SNP	.											.	SCARB1	40	.	0			c.G1495A						PASS	.	C	ARG/GLY,	644,3422		39,566,1428	7.0	11.0	10.0		1495,	1.5	0.0	12	dbSNP_86	10	16,8256		0,16,4120	yes	missense,utr-3	SCARB1	NM_001082959.1,NM_005505.4	125,	39,582,5548	TT,TC,CC		0.1934,15.8387,5.3493	,	499/507,	125263039	660,11678	2033	4136	6169	SO:0001624	3_prime_UTR_variant	949	exon12			GCTGTCCGCTGGG	Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060			1664	protein-coding gene	gene with protein product		601040	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1"""	CD36L1		7689561	Standard	NM_001082959		Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000415380.2:c.*86G>A	12.37:g.125263039C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_001082959	F8W8N0|Q14016|Q52LZ5|Q6KFX4	Missense_Mutation	SNP	ENST00000415380.2	37		100	0.045787545787545784	92	0.18699186991869918	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	12.90	2.077750	0.36662	0.158387	0.001934	ENSG00000073060	ENST00000339570	T	0.61158	0.13	4.36	1.45	0.22620	.	.	.	.	.	T	0.00073	0.0002	L	0.36672	1.1	0.53688	P	2.4000000000024002E-5	B	0.33135	0.399	B	0.24006	0.05	T	0.03773	-1.1005	8	0.44086	T	0.13	.	4.3702	0.11244	0.0:0.5966:0.1882:0.2152	rs701103;rs747156;rs60594950	499	F8W8N0	.	R	499	ENSP00000343795:G499R	ENSP00000343795:G499R	G	-	1	0	SCARB1	123828992	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.608000	0.05641	-0.010000	0.14271	0.455000	0.32223	GGA	C|0.956;T|0.044	0.044	strong		0.692	SCARB1-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000400165.1	NM_005505	
KRT16	3868	hgsc.bcm.edu	37	17	39768756	39768756	+	Missense_Mutation	SNP	C	C	T	rs367990963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39768756C>T	ENST00000301653.4	-	1	249	c.185G>A	c.(184-186)tGc>tAc	p.C62Y		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	62	Head.				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)				CCCCAGCCCGCAGGCTCCCCC	0.687													c|||	4	0.000798722	0.003	0.0	5008	,	,		14972	0.0		0.0	False		,,,				2504	0.0				p.C62Y		Atlas-SNP	.											.	KRT16	45	.	0			c.G185A						PASS	.	C	TYR/CYS	4,4352		0,4,2174	28.0	35.0	32.0		185	3.3	1.0	17		32	0,8536		0,0,4268	no	missense	KRT16	NM_005557.3	194	0,4,6442	TT,TC,CC		0.0,0.0918,0.031	benign	62/474	39768756	4,12888	2178	4268	6446	SO:0001583	missense	3868	exon1			AGCCCGCAGGCTC	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.185G>A	17.37:g.39768756C>T	ENSP00000301653:p.Cys62Tyr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Missense_Mutation	SNP	ENST00000301653.4	37	CCDS11401.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484513	0.44147	9.18E-4	0.0	ENSG00000186832	ENST00000301653	T	0.75260	-0.92	4.33	3.33	0.38152	.	0.000000	0.53938	D	0.000045	T	0.55924	0.1951	N	0.19112	0.55	0.30188	N	0.799798	B	0.31256	0.316	B	0.28553	0.091	T	0.55717	-0.8097	10	0.35671	T	0.21	.	9.6049	0.39628	0.1605:0.6847:0.1548:0.0	.	62	P08779	K1C16_HUMAN	Y	62	ENSP00000301653:C62Y	ENSP00000301653:C62Y	C	-	2	0	KRT16	37022282	0.046000	0.20272	0.997000	0.53966	0.971000	0.66376	0.141000	0.16076	1.127000	0.42034	0.462000	0.41574	TGC	.	.	weak		0.687	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557	
TNRC6C	57690	hgsc.bcm.edu	37	17	76093866	76093866	+	Intron	SNP	T	T	C	rs2290906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76093866T>C	ENST00000588061.1	+	19	5033				TNRC6C_ENST00000541771.1_Intron|TNRC6C_ENST00000544502.1_Silent_p.S1446S|TNRC6C_ENST00000588847.1_Silent_p.S1446S|TNRC6C_ENST00000301624.4_Intron|TNRC6C_ENST00000335749.4_Silent_p.S1446S			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C						embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|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)|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 gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CGCTGCCTTCTTCGAGTGCCT	0.587													C|||	1470	0.29353	0.4107	0.2666	5008	,	,		19861	0.2976		0.1252	False		,,,				2504	0.3231				p.S1446S		Atlas-SNP	.											.	TNRC6C	173	.	0			c.T4338C						PASS	.	C	,	489,895		86,317,289	43.0	40.0	41.0		4338,	2.6	1.0	17	dbSNP_100	41	468,2714		31,406,1154	no	coding-synonymous,intron	TNRC6C	NM_001142640.1,NM_018996.3	,	117,723,1443	CC,CT,TT		14.7077,35.3324,20.9593	,	1446/1727,	76093866	957,3609	692	1591	2283	SO:0001627	intron_variant	57690	exon18			GCCTTCTTCGAGT	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.4307-558T>C	17.37:g.76093866T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_001142640	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Silent	SNP	ENST00000588061.1	37	CCDS45798.1																																																																																			T|0.737;C|0.263	0.263	strong		0.587	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996	
PARP14	54625	hgsc.bcm.edu	37	3	122419292	122419292	+	Missense_Mutation	SNP	A	A	G	rs7632072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122419292A>G	ENST00000474629.2	+	6	2157	c.1891A>G	c.(1891-1893)Act>Gct	p.T631A		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	631					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CTCCCCAAACACTGTAATCAT	0.348													A|||	278	0.0555112	0.1218	0.0576	5008	,	,		21423	0.001		0.0487	False		,,,				2504	0.0276				p.T631A		Atlas-SNP	.											.	PARP14	242	.	0			c.A1891G						PASS	.	A	ALA/THR	342,3342		18,306,1518	31.0	30.0	31.0		1891	2.1	0.0	3	dbSNP_116	31	361,7841		5,351,3745	yes	missense	PARP14	NM_017554.2	58	23,657,5263	GG,GA,AA		4.4014,9.2834,5.9145	probably-damaging	631/1802	122419292	703,11183	1842	4101	5943	SO:0001583	missense	54625	exon6			CCAAACACTGTAA	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1891A>G	3.37:g.122419292A>G	ENSP00000418194:p.Thr631Ala	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	111	0.050824175824175824	49	0.09959349593495935	22	0.06077348066298342	1	0.0017482517482517483	39	0.051451187335092345	A	13.04	2.119612	0.37436	0.092834	0.044014	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.10099	2.91	6.06	2.12	0.27331	.	0.174182	0.39759	N	0.001269	T	0.00271	0.0008	M	0.66939	2.045	0.09310	N	1	P;B	0.38827	0.649;0.376	B;B	0.33690	0.168;0.055	T	0.30268	-0.9984	10	0.36615	T	0.2	.	3.82	0.08832	0.663:0.1354:0.0717:0.1299	rs7632072;rs52827643;rs7632072	631;631	Q460N5-4;Q460N5	.;PAR14_HUMAN	A	631;550	ENSP00000418194:T631A	ENSP00000381228:T550A	T	+	1	0	PARP14	123901982	0.014000	0.17966	0.001000	0.08648	0.003000	0.03518	1.250000	0.32850	0.497000	0.27926	0.533000	0.62120	ACT	A|0.950;G|0.050	0.050	strong		0.348	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
C9orf50	375759	hgsc.bcm.edu	37	9	132377769	132377769	+	Missense_Mutation	SNP	G	G	A	rs117566704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132377769G>A	ENST00000372478.4	-	4	1075	c.874C>T	c.(874-876)Cgc>Tgc	p.R292C	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	292										central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				TTACCTGAGCGTCTGCGCTCC	0.642													g|||	3	0.000599042	0.0015	0.0	5008	,	,		18538	0.0		0.0	False		,,,				2504	0.001				p.R292C		Atlas-SNP	.											.	C9orf50	25	.	0			c.C874T						PASS	.		CYS/ARG	11,4395	17.9+/-39.9	0,11,2192	53.0	45.0	48.0		874	0.8	0.0	9	dbSNP_132	48	0,8600		0,0,4300	yes	missense	C9orf50	NM_199350.3	180	0,11,6492	AA,AG,GG		0.0,0.2497,0.0846	benign	292/432	132377769	11,12995	2203	4300	6503	SO:0001583	missense	375759	exon4			CTGAGCGTCTGCG	AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.874C>T	9.37:g.132377769G>A	ENSP00000361556:p.Arg292Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_199350	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	37	CCDS35159.1	.	.	.	.	.	.	.	.	.	.	g	6.146	0.395061	0.11638	0.002497	0.0	ENSG00000179058	ENST00000372478	T	0.18657	2.2	3.17	0.799	0.18667	.	1.485060	0.04472	N	0.376207	T	0.11196	0.0273	N	0.05124	-0.11	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30238	-0.9985	10	0.46703	T	0.11	1.6017	5.7707	0.18251	0.5791:0.0:0.4209:0.0	.	292	Q5SZB4	CI050_HUMAN	C	292	ENSP00000361556:R292C	ENSP00000361556:R292C	R	-	1	0	C9orf50	131417590	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.457000	0.21875	-0.097000	0.12307	-1.479000	0.00991	CGC	A|0.001;C|0.002;G|0.998	0.001	strong		0.642	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350	
RP1	6101	hgsc.bcm.edu	37	8	55534093	55534093	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:55534093G>T	ENST00000220676.1	+	2	715	c.567G>T	c.(565-567)gaG>gaT	p.E189D		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	189	Doublecortin 2. {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)			ACCTGACAGAGGTCATGCAGC	0.587																																					p.E189D	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											RP1,right_lower_lobe,carcinoma,+1,1	RP1	429	1	0			c.G567T						scavenged	.						121.0	125.0	124.0					8																	55534093		2203	4300	6503	SO:0001583	missense	6101	exon2			GACAGAGGTCATG	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.567G>T	8.37:g.55534093G>T	ENSP00000220676:p.Glu189Asp	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	247	3	0.0121457	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.590932	0.46214	.	.	ENSG00000104237	ENST00000220676	D	0.93189	-3.18	5.14	-0.985	0.10256	Doublecortin domain (5);	1.196210	0.06179	N	0.679130	D	0.91710	0.7379	L	0.52905	1.665	0.09310	N	1	P	0.47484	0.896	P	0.49192	0.602	T	0.82343	-0.0504	10	0.56958	D	0.05	2.3985	3.2718	0.06884	0.3372:0.1079:0.4457:0.1092	.	189	P56715	RP1_HUMAN	D	189	ENSP00000220676:E189D	ENSP00000220676:E189D	E	+	3	2	RP1	55696646	1.000000	0.71417	0.050000	0.19076	0.304000	0.27724	0.810000	0.27183	-0.032000	0.13758	-0.142000	0.14014	GAG	.	.	none		0.587	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
SSTR3	6753	hgsc.bcm.edu	37	22	37602611	37602611	+	Missense_Mutation	SNP	C	C	G	rs229568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37602611C>G	ENST00000328544.3	-	2	1765	c.1232G>C	c.(1231-1233)aGc>aCc	p.S411T	SSTR3_ENST00000402501.1_Missense_Mutation_p.S411T	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	411			S -> T (in dbSNP:rs229568).		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)	GCGCATCGTGCTGGACTTCTC	0.657													C|||	319	0.0636981	0.2284	0.0202	5008	,	,		16100	0.0		0.003	False		,,,				2504	0.0				p.S411T		Atlas-SNP	.											.	SSTR3	42	.	0			c.G1232C						PASS	.	C	THR/SER	912,3494	340.7+/-306.4	97,718,1388	55.0	59.0	58.0		1232	3.4	0.0	22	dbSNP_79	58	7,8593	5.7+/-21.5	0,7,4293	yes	missense	SSTR3	NM_001051.2	58	97,725,5681	GG,GC,CC		0.0814,20.699,7.066	benign	411/419	37602611	919,12087	2203	4300	6503	SO:0001583	missense	6753	exon2			ATCGTGCTGGACT		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.1232G>C	22.37:g.37602611C>G	ENSP00000330138:p.Ser411Thr	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_001051	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	37	CCDS13944.1	117	0.05357142857142857	107	0.21747967479674796	8	0.022099447513812154	0	0.0	2	0.002638522427440633	C	8.330	0.826175	0.16749	0.20699	8.14E-4	ENSG00000183473	ENST00000328544;ENST00000402501	T;T	0.73047	-0.71;-0.71	5.51	3.4	0.38934	.	1.198980	0.05892	N	0.628461	T	0.00073	0.0002	L	0.43152	1.355	0.42474	P	0.00717000000000001	B	0.27559	0.181	B	0.19148	0.024	T	0.04255	-1.0965	9	0.56958	D	0.05	.	12.2253	0.54457	0.0:0.8595:0.0:0.1405	rs229568;rs16997931;rs229568	411	P32745	SSR3_HUMAN	T	411	ENSP00000330138:S411T;ENSP00000384904:S411T	ENSP00000330138:S411T	S	-	2	0	SSTR3	35932557	0.000000	0.05858	0.027000	0.17364	0.063000	0.16089	0.291000	0.18994	1.328000	0.45358	0.491000	0.48974	AGC	C|0.934;G|0.066	0.066	strong		0.657	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1		
C10orf71	118461	hgsc.bcm.edu	37	10	50531520	50531520	+	Silent	SNP	C	C	A	rs73307889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50531520C>A	ENST00000374144.3	+	3	1218	c.930C>A	c.(928-930)acC>acA	p.T310T	C10orf71_ENST00000323868.4_Silent_p.T310T			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	310										endometrium(1)	1						GGGACACGACCTTGCTAAGAG	0.567													C|||	98	0.0195687	0.0719	0.0043	5008	,	,		19049	0.0		0.0	False		,,,				2504	0.0				p.T310T		Atlas-SNP	.											C10orf71_ENST00000374144,NS,carcinoma,+1,2	C10orf71	179	2	0			c.C930A						scavenged	.	C	,	237,3885		7,223,1831	70.0	79.0	76.0		930,930	-1.9	0.0	10	dbSNP_130	76	3,8405		0,3,4201	no	coding-synonymous,coding-synonymous	C10orf71	NM_001135196.1,NM_199459.3	,	7,226,6032	AA,AC,CC		0.0357,5.7496,1.9154	,	310/1436,310/720	50531520	240,12290	2061	4204	6265	SO:0001819	synonymous_variant	118461	exon3			CACGACCTTGCTA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.930C>A	10.37:g.50531520C>A		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			C|0.984;A|0.016	0.016	strong		0.567	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
ACOT12	134526	hgsc.bcm.edu	37	5	80655766	80655766	+	Missense_Mutation	SNP	T	T	G	rs147339997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80655766T>G	ENST00000307624.3	-	5	480	c.452A>C	c.(451-453)gAa>gCa	p.E151A	ACOT12_ENST00000513751.1_Missense_Mutation_p.E151A	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	151					acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		AAAGGTATCTTCATGTTGTAA	0.333													T|||	11	0.00219649	0.0083	0.0	5008	,	,		17992	0.0		0.0	False		,,,				2504	0.0				p.E151A		Atlas-SNP	.											.	ACOT12	57	.	0			c.A452C						PASS	.	T	ALA/GLU	45,4361	47.5+/-82.1	0,45,2158	127.0	124.0	125.0		452	5.0	0.7	5	dbSNP_134	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ACOT12	NM_130767.2	107	0,46,6457	GG,GT,TT		0.0116,1.0213,0.3537	possibly-damaging	151/556	80655766	46,12960	2203	4300	6503	SO:0001583	missense	134526	exon5			GTATCTTCATGTT	AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"""Acyl CoA thioesterases"", ""StAR-related lipid transfer (START) domain containing"""	24436	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 15"""	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.452A>C	5.37:g.80655766T>G	ENSP00000303246:p.Glu151Ala	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	152	79	0.519737	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	37	CCDS4055.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	0.472	-0.883839	0.02530	0.010213	1.16E-4	ENSG00000172497	ENST00000307624;ENST00000513751	T;T	0.30981	1.51;1.51	5.04	5.04	0.67666	.	0.058734	0.64402	D	0.000004	T	0.14570	0.0352	L	0.35249	1.045	0.47094	D	0.999312	B;B	0.13145	0.0;0.007	B;B	0.12156	0.001;0.007	T	0.06734	-1.0810	10	0.11794	T	0.64	-31.4031	9.2551	0.37579	0.0:0.0858:0.0:0.9142	.	151;151	Q5FWE9;Q8WYK0	.;ACO12_HUMAN	A	151	ENSP00000303246:E151A;ENSP00000421628:E151A	ENSP00000303246:E151A	E	-	2	0	ACOT12	80691522	0.996000	0.38824	0.705000	0.30386	0.094000	0.18550	1.765000	0.38481	2.030000	0.59900	0.533000	0.62120	GAA	T|0.996;G|0.004	0.004	strong		0.333	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767	
SERPINH1	871	hgsc.bcm.edu	37	11	75279846	75279846	+	Silent	SNP	C	C	T	rs649257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:75279846C>T	ENST00000524558.1	+	3	2128	c.693C>T	c.(691-693)acC>acT	p.T231T	SERPINH1_ENST00000358171.3_Silent_p.T231T|SERPINH1_ENST00000530284.1_Silent_p.T231T|SERPINH1_ENST00000533603.1_Silent_p.T231T|SERPINH1_ENST00000525876.1_Silent_p.T14T			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	231					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T231T(1)		endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					GGTCCTATACCGTGGGTGTCA	0.567													C|||	1888	0.376997	0.4766	0.379	5008	,	,		19111	0.2103		0.2972	False		,,,				2504	0.4949				p.T231T		Atlas-SNP	.											SERPINH1,NS,carcinoma,0,1	SERPINH1	33	1	1	Substitution - coding silent(1)	stomach(1)	c.C693T						PASS	.	C	,	1954,2446	553.2+/-378.7	444,1066,690	149.0	113.0	125.0		693,693	-11.4	0.2	11	dbSNP_83	125	2616,5970	422.8+/-354.1	383,1850,2060	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	827,2916,2750	TT,TC,CC		30.4682,44.4091,35.1917	,	231/419,231/419	75279846	4570,8416	2200	4293	6493	SO:0001819	synonymous_variant	871	exon3			CTATACCGTGGGT	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.693C>T	11.37:g.75279846C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																			C|0.660;T|0.340	0.340	strong		0.567	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
OPN3	23596	hgsc.bcm.edu	37	1	241803317	241803317	+	Silent	SNP	C	C	G	rs73139034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241803317C>G	ENST00000366554.2	-	1	346	c.240G>C	c.(238-240)ctG>ctC	p.L80L	OPN3_ENST00000469376.1_5'UTR|OPN3_ENST00000331838.5_Silent_p.L80L	NM_014322.2	NP_055137.2	Q9H1Y3	OPN3_HUMAN	opsin 3	80					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)			TGATGTTGACCAGGAGGAGGT	0.627													C|||	144	0.028754	0.1036	0.0101	5008	,	,		7429	0.0		0.0	False		,,,				2504	0.0				p.L80L		Atlas-SNP	.											.	OPN3	28	.	0			c.G240C						PASS	.	C		408,3996	196.7+/-221.0	16,376,1810	59.0	56.0	57.0		240	3.9	0.8	1	dbSNP_130	57	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous	OPN3	NM_014322.2		16,379,6107	GG,GC,CC		0.0349,9.2643,3.1606		80/403	241803317	411,12593	2202	4300	6502	SO:0001819	synonymous_variant	23596	exon1			GTTGACCAGGAGG	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	ENST00000366554.2:c.240G>C	1.37:g.241803317C>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	94	52	0.553191	NM_014322	Q8IX08|Q9Y344	Silent	SNP	ENST00000366554.2	37	CCDS31072.1																																																																																			C|0.969;G|0.031	0.031	strong		0.627	OPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095713.1	NM_014322	
MSH3	4437	hgsc.bcm.edu	37	5	79966029	79966029	+	Silent	SNP	G	G	A	rs1805355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79966029G>A	ENST00000265081.6	+	4	773	c.693G>A	c.(691-693)ccG>ccA	p.P231P		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	231	Interaction with EXO1.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		TCTATACGCCGCTAGAATTAC	0.378								Mismatch excision repair (MMR)					G|||	916	0.182907	0.1974	0.2651	5008	,	,		16920	0.3383		0.0537	False		,,,				2504	0.0777				p.P231P	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.G693A						PASS	.	G		797,3609	319.3+/-296.1	66,665,1472	133.0	131.0	131.0		693	-6.6	0.0	5	dbSNP_92	131	524,8076	146.6+/-202.2	14,496,3790	no	coding-synonymous	MSH3	NM_002439.3		80,1161,5262	AA,AG,GG		6.093,18.089,10.1569		231/1138	79966029	1321,11685	2203	4300	6503	SO:0001819	synonymous_variant	4437	exon4			TACGCCGCTAGAA	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.693G>A	5.37:g.79966029G>A		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	192	190	0.989583	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	37	CCDS34195.1																																																																																			G|0.817;A|0.183	0.183	strong		0.378	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
MUC4	4585	hgsc.bcm.edu	37	3	195510725	195510725	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195510725G>A	ENST00000463781.3	-	2	8185	c.7726C>T	c.(7726-7728)Cct>Tct	p.P2576S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2576S	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)		ACAGGAAGAGGGGTGGCGTGA	0.592																																					p.P2576S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C7726T						scavenged	.						30.0	25.0	27.0					3																	195510725		683	1583	2266	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	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.7726C>T	3.37:g.195510725G>A	ENSP00000417498:p.Pro2576Ser	Somatic	246	17	0.0691057		WXS	Illumina HiSeq	Phase_I	209	23	0.110048	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	.	.	.	.	.	.	.	.	.	.	-	7.199	0.593028	0.13875	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27104	1.7;1.69	1.19	-0.323	0.12709	.	.	.	.	.	T	0.10809	0.0264	N	0.19112	0.55	0.09310	N	1	P	0.36222	0.544	B	0.25884	0.064	T	0.21930	-1.0231	8	.	.	.	.	4.7061	0.12849	0.0:0.0:0.4363:0.5637	rs4927785	2576	E7ESK3	.	S	2576	ENSP00000417498:P2576S;ENSP00000420243:P2576S	.	P	-	1	0	MUC4	196995120	0.007000	0.16637	0.010000	0.14722	0.093000	0.18481	0.708000	0.25719	0.661000	0.30985	0.264000	0.19307	CCT	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
UBR4	23352	hgsc.bcm.edu	37	1	19422060	19422060	+	Silent	SNP	G	G	A	rs2236378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19422060G>A	ENST00000375254.3	-	93	13632	c.13605C>T	c.(13603-13605)gtC>gtT	p.V4535V	UBR4_ENST00000375226.2_Silent_p.V4511V|UBR4_ENST00000543981.1_Silent_p.V199V|UBR4_ENST00000375224.1_Silent_p.V242V|UBR4_ENST00000375217.2_Silent_p.V4528V|UBR4_ENST00000375267.2_Silent_p.V4535V|UBR4_ENST00000467272.2_5'UTR|UBR4_ENST00000429347.2_Silent_p.V98V	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	4535					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)			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)		TCCCCAGCATGACGTTCAAGG	0.502													G|||	131	0.0261581	0.0174	0.0202	5008	,	,		22565	0.0585		0.0	False		,,,				2504	0.0358				p.V4535V		Atlas-SNP	.											.	UBR4	415	.	0			c.C13605T						PASS	.	G		71,4335	65.3+/-102.7	0,71,2132	175.0	132.0	147.0		13605	5.8	1.0	1	dbSNP_98	147	5,8595	3.7+/-12.6	0,5,4295	yes	coding-synonymous	UBR4	NM_020765.2		0,76,6427	AA,AG,GG		0.0581,1.6114,0.5843		4535/5184	19422060	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon93			CAGCATGACGTTC	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.13605C>T	1.37:g.19422060G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	200	95	0.475	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			G|0.989;A|0.011	0.011	strong		0.502	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
ZNF577	84765	hgsc.bcm.edu	37	19	52375809	52375809	+	Silent	SNP	A	A	G	rs142094475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52375809A>G	ENST00000301399.5	-	7	1799	c.1434T>C	c.(1432-1434)taT>taC	p.Y478Y	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Silent_p.Y419Y|ZNF577_ENST00000451628.2_Silent_p.Y419Y	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	478					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TATCTGTAAGATACAAGATAT	0.353													A|||	8	0.00159744	0.0023	0.0072	5008	,	,		19580	0.0		0.0	False		,,,				2504	0.0				p.Y478Y		Atlas-SNP	.											.	ZNF577	63	.	0			c.T1434C						PASS	.	A	,	19,4385		0,19,2183	40.0	40.0	40.0		1257,1434	1.9	0.0	19	dbSNP_134	40	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ZNF577	NM_001135590.1,NM_032679.2	,	0,19,6483	GG,GA,AA		0.0,0.4314,0.1461	,	419/427,478/486	52375809	19,12985	2202	4300	6502	SO:0001819	synonymous_variant	84765	exon7			TGTAAGATACAAG	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1434T>C	19.37:g.52375809A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			A|0.998;G|0.002	0.002	strong		0.353	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
CCDC184	387856	hgsc.bcm.edu	37	12	48577925	48577925	+	Missense_Mutation	SNP	A	A	G	rs140861476		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48577925A>G	ENST00000316554.3	+	1	560	c.20A>G	c.(19-21)gAg>gGg	p.E7G		NM_001013635.3	NP_001013657.3	Q52MB2	CC184_HUMAN		7						cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)	4						GGTCTGCTGGAGATCATGACC	0.706																																					p.E7G		Atlas-SNP	.											.	C12orf68	11	.	0			c.A20G						PASS	.	A	GLY/GLU	3,4403		0,3,2200	28.0	36.0	33.0		20	4.9	1.0	12	dbSNP_134	33	0,8598		0,0,4299	no	missense	C12orf68	NM_001013635.3	98	0,3,6499	GG,GA,AA		0.0,0.0681,0.0231	benign	7/195	48577925	3,13001	2203	4299	6502	SO:0001583	missense	387856	exon1			TGCTGGAGATCAT																												ENST00000316554.3:c.20A>G	12.37:g.48577925A>G	ENSP00000320849:p.Glu7Gly	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_001013635	Q96MK5|Q96N39	Missense_Mutation	SNP	ENST00000316554.3	37	CCDS31785.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.623833	0.46840	6.81E-4	0.0	ENSG00000177875	ENST00000316554	T	0.57273	0.41	4.9	4.9	0.64082	.	0.000000	0.52532	D	0.000075	T	0.50939	0.1645	N	0.08118	0	0.35002	D	0.756066	D	0.76494	0.999	D	0.78314	0.991	T	0.66304	-0.5957	10	0.87932	D	0	-21.6442	10.8402	0.46710	1.0:0.0:0.0:0.0	.	7	Q52MB2	CL068_HUMAN	G	7	ENSP00000320849:E7G	ENSP00000320849:E7G	E	+	2	0	C12orf68	46864192	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.151000	0.58105	2.049000	0.60858	0.491000	0.48974	GAG	A|1.000;G|0.000	0.000	weak		0.706	C12orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406514.1		
SSPO	23145	hgsc.bcm.edu	37	7	149499284	149499284	+	RNA	SNP	C	C	T	rs56163742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149499284C>T	ENST00000378016.2	+	0	7652							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)			TTTGTGCAGGCCTGCCCAGGT	0.677													C|||	743	0.148363	0.2549	0.0951	5008	,	,		16105	0.0853		0.1074	False		,,,				2504	0.1493				p.A2551V		Atlas-SNP	.											.	.	.	.	0			c.C7652T						PASS	.	C		595,2759		48,499,1130	4.0	6.0	5.0		7656	4.7	1.0	7	dbSNP_129	5	595,6489		28,539,2975	no	coding-notMod3	SSPO	NM_198455.2		76,1038,4105	TT,TC,CC		8.3992,17.74,11.4007			149499284	1190,9248	1677	3542	5219			23145	exon51			TGCAGGCCTGCCC	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.149499284C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.873;T|0.127	0.127	strong		0.677	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
COL9A3	1299	hgsc.bcm.edu	37	20	61463522	61463522	+	Missense_Mutation	SNP	C	C	A	rs751557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61463522C>A	ENST00000343916.3	+	25	1307	c.1304C>A	c.(1303-1305)gCa>gAa	p.A435E		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	435	Triple-helical region 3 (COL3).		A -> E (in dbSNP:rs751557). {ECO:0000269|PubMed:11565064, ECO:0000269|PubMed:8586434}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					GGAGGTGCCGCAGGCCCTAAG	0.602													C|||	1066	0.212859	0.447	0.1729	5008	,	,		20947	0.0496		0.2177	False		,,,				2504	0.0879				p.A435E		Atlas-SNP	.											COL9A3,caecum,carcinoma,0,1	COL9A3	70	1	0			c.C1304A						PASS	.	C	GLU/ALA	1747,2659	513.9+/-368.5	338,1071,794	58.0	61.0	60.0		1304	4.2	0.4	20	dbSNP_86	60	1774,6826	317.9+/-313.4	185,1404,2711	yes	missense	COL9A3	NM_001853.3	107	523,2475,3505	AA,AC,CC		20.6279,39.6505,27.0721	probably-damaging	435/685	61463522	3521,9485	2203	4300	6503	SO:0001583	missense	1299	exon25			GTGCCGCAGGCCC	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.1304C>A	20.37:g.61463522C>A	ENSP00000341640:p.Ala435Glu	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	190	88	0.463158	NM_001853	Q13681|Q9H4G9|Q9UPE2	Missense_Mutation	SNP	ENST00000343916.3	37	CCDS13505.1	464	0.21245421245421245	204	0.4146341463414634	66	0.18232044198895028	32	0.055944055944055944	162	0.21372031662269128	C	10.51	1.371130	0.24771	0.396505	0.206279	ENSG00000092758	ENST00000343916	D	0.93712	-3.27	5.2	4.23	0.50019	.	0.843935	0.10592	N	0.656672	T	0.00012	0.0000	N	0.05078	-0.115	0.80722	P	0.0	B	0.23185	0.081	B	0.25506	0.061	T	0.04664	-1.0935	9	0.07325	T	0.83	.	12.5103	0.56002	0.0:0.868:0.0:0.132	rs751557;rs59729765;rs751557	435	Q14050	CO9A3_HUMAN	E	435	ENSP00000341640:A435E	ENSP00000341640:A435E	A	+	2	0	COL9A3	60933967	0.003000	0.15002	0.425000	0.26659	0.227000	0.25037	0.934000	0.28910	2.584000	0.87258	0.462000	0.41574	GCA	T|0.003;G|0.006	.	strong		0.602	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
CDH23	64072	hgsc.bcm.edu	37	10	73562744	73562744	+	Silent	SNP	G	G	A	rs10823849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73562744G>A	ENST00000224721.6	+	53	7592	c.7587G>A	c.(7585-7587)gcG>gcA	p.A2529A	CDH23_ENST00000475158.1_3'UTR|CDH23_ENST00000398788.3_Silent_p.A284A	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2524	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.A2529A(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ATGAGCCGGCGGGCACCTCGG	0.577													G|||	1645	0.328474	0.2307	0.3444	5008	,	,		20495	0.5298		0.2783	False		,,,				2504	0.2935				p.A2524A		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - coding silent(1)	stomach(1)	c.G7572A						PASS	.	G	,,	904,3136		96,712,1212	69.0	73.0	72.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	852,852,7572	-10.0	0.4	10	dbSNP_120	72	2180,6174		306,1568,2303	no	coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171933.1,NM_001171934.1,NM_022124.5	,,	402,2280,3515	AA,AG,GG		26.0953,22.3762,24.883	,,	284/1115,284/1080,2524/3355	73562744	3084,9310	2020	4177	6197	SO:0001819	synonymous_variant	64072	exon52			GCCGGCGGGCACC	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.7587G>A	10.37:g.73562744G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	140	82	0.585714	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				G|0.681;A|0.319	0.319	strong		0.577	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
FMN2	56776	hgsc.bcm.edu	37	1	240371223	240371223	+	Silent	SNP	C	C	T	rs71297737|rs575452021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:240371223C>T	ENST00000319653.9	+	5	3341	c.3111C>T	c.(3109-3111)ccC>ccT	p.P1037P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1037	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)			CCCCACTTCCCGGAGCGGGCA	0.731													C|||	1089	0.217452	0.2088	0.2046	5008	,	,		4578	0.0883		0.2674	False		,,,				2504	0.32				p.P1037P		Atlas-SNP	.											FMN2,NS,carcinoma,0,3	FMN2	451	3	0			c.C3111T						scavenged	.						3.0	5.0	4.0					1																	240371223		1456	3181	4637	SO:0001819	synonymous_variant	56776	exon5			ACTTCCCGGAGCG	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.3111C>T	1.37:g.240371223C>T		Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	197	34	0.172589	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			.	.	none		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
PRR14L	253143	hgsc.bcm.edu	37	22	32109305	32109305	+	Missense_Mutation	SNP	T	T	C	rs112331962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32109305T>C	ENST00000327423.6	-	4	4709	c.4520A>G	c.(4519-4521)cAt>cGt	p.H1507R	PRR14L_ENST00000434485.1_Missense_Mutation_p.H1507R|PRR14L_ENST00000397493.2_Missense_Mutation_p.H1507R	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1507										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						AAAGGCACCATGTATTTGATC	0.473													T|||	191	0.038139	0.1377	0.013	5008	,	,		19854	0.0		0.0	False		,,,				2504	0.0				p.H1507R		Atlas-SNP	.											.	PRR14L	198	.	0			c.A4520G						PASS	.	T	ARG/HIS	138,1246		3,132,557	169.0	140.0	149.0		4520	-0.7	0.0	22	dbSNP_132	149	3,3179		0,3,1588	yes	missense	PRR14L	NM_173566.2	29	3,135,2145	CC,CT,TT		0.0943,9.9711,3.088	benign	1507/2152	32109305	141,4425	692	1591	2283	SO:0001583	missense	253143	exon4			GCACCATGTATTT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.4520A>G	22.37:g.32109305T>C	ENSP00000331845:p.His1507Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	37	CCDS13900.2	66	0.03021978021978022	63	0.12804878048780488	3	0.008287292817679558	0	0.0	0	0.0	T	3.362	-0.130293	0.06753	0.099711	9.43E-4	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.05786	3.39;3.41;3.4	5.59	-0.745	0.11098	.	0.617385	0.14488	N	0.316502	T	0.00039	0.0001	L	0.44542	1.39	0.09310	N	1	B;B;B	0.12013	0.003;0.003;0.005	B;B;B	0.09377	0.004;0.003;0.004	T	0.44892	-0.9298	9	.	.	.	0.0323	1.9244	0.03314	0.1203:0.3338:0.2122:0.3338	.	1507;1507;1507	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	R	1507	ENSP00000380630:H1507R;ENSP00000331845:H1507R;ENSP00000388314:H1507R	.	H	-	2	0	PRR14L	30439305	0.000000	0.05858	0.024000	0.17045	0.610000	0.37248	-1.136000	0.03222	0.073000	0.16731	-1.151000	0.01829	CAT	T|0.975;C|0.025	0.025	strong		0.473	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
EPS15	2060	hgsc.bcm.edu	37	1	51826921	51826921	+	Missense_Mutation	SNP	T	T	C	rs17567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:51826921T>C	ENST00000371733.3	-	24	2562	c.2466A>G	c.(2464-2466)atA>atG	p.I822M	EPS15_ENST00000396122.4_Missense_Mutation_p.I499M|EPS15_ENST00000371730.2_Missense_Mutation_p.I688M	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	822	15 X 3 AA repeats of D-P-F.|Pro-rich.		I -> M (in dbSNP:rs17567). {ECO:0000269|PubMed:8183552}.		cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						GATCACAAAATATTTCAGGAT	0.408			T	MLL	ALL								C|||	1169	0.233427	0.5673	0.1643	5008	,	,		18708	0.0119		0.2038	False		,,,				2504	0.09				p.I822M		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	.	EPS15	72	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.A2466G						PASS	.	C	MET/ILE,MET/ILE	2266,2140	579.9+/-385.0	583,1100,520	160.0	153.0	155.0		1524,2466	5.8	1.0	1	dbSNP_63	155	1982,6618	723.4+/-406.5	228,1526,2546	yes	missense,missense	EPS15	NM_001159969.1,NM_001981.2	10,10	811,2626,3066	CC,CT,TT		23.0465,48.5701,32.6618	benign,benign	508/583,822/897	51826921	4248,8758	2203	4300	6503	SO:0001583	missense	2060	exon24			ACAAAATATTTCA	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"""EF-hand domain containing"""	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.2466A>G	1.37:g.51826921T>C	ENSP00000360798:p.Ile822Met	Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Missense_Mutation	SNP	ENST00000371733.3	37	CCDS557.1	512	0.23443223443223443	284	0.5772357723577236	57	0.1574585635359116	11	0.019230769230769232	160	0.21108179419525067	C	11.41	1.631297	0.28978	0.514299	0.230465	ENSG00000085832	ENST00000371730;ENST00000371733;ENST00000396122	T;T;T	0.42131	0.98;0.98;0.98	5.85	5.85	0.93711	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.42189	-0.9466	8	0.32370	T	0.25	.	8.8043	0.34927	0.0:0.8244:0.0:0.1756	rs17567;rs12753160;rs17846526;rs17859599;rs52820243;rs58525844;rs17567	688;822;508	B1AUU8;P42566;P42566-2	.;EPS15_HUMAN;.	M	688;822;499	ENSP00000360795:I688M;ENSP00000360798:I822M;ENSP00000379428:I499M	ENSP00000360795:I688M	I	-	3	3	EPS15	51599509	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	0.672000	0.25187	1.492000	0.48499	-0.186000	0.12905	ATA	T|0.702;C|0.298	0.298	strong		0.408	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	
FBXO10	26267	hgsc.bcm.edu	37	9	37537892	37537892	+	Missense_Mutation	SNP	G	G	T	rs7044561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:37537892G>T	ENST00000432825.2	-	3	682	c.634C>A	c.(634-636)Cac>Aac	p.H212N	RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Intron|FBXO10_ENST00000543968.1_5'Flank	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	212			H -> N (found in a patient with lymphoma; dbSNP:rs7044561). {ECO:0000269|PubMed:23431138}.		apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		ACCTGGATGTGCCCGTTCTCA	0.488													G|||	76	0.0151757	0.0575	0.0	5008	,	,		21854	0.0		0.0	False		,,,				2504	0.0				p.H212N		Atlas-SNP	.											.	FBXO10	75	.	0			c.C634A						PASS	.	G	ASN/HIS	171,3729		8,155,1787	85.0	85.0	85.0		634	5.3	1.0	9	dbSNP_116	85	5,8263		0,5,4129	yes	missense	FBXO10	NM_012166.2	68	8,160,5916	TT,TG,GG		0.0605,4.3846,1.4464	benign	212/957	37537892	176,11992	1950	4134	6084	SO:0001583	missense	26267	exon3			GGATGTGCCCGTT	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.634C>A	9.37:g.37537892G>T	ENSP00000403802:p.His212Asn	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	37	CCDS47966.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	G	16.84	3.233921	0.58886	0.043846	6.05E-4	ENSG00000147912	ENST00000432825	T	0.40756	1.02	5.3	5.3	0.74995	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.054328	0.85682	D	0.000000	T	0.06462	0.0166	N	0.14661	0.345	0.80722	D	1	B	0.25105	0.118	B	0.23852	0.049	T	0.05484	-1.0882	10	0.02654	T	1	-29.9635	18.0885	0.89466	0.0:0.0:1.0:0.0	rs7044561;rs52804171;rs7044561	212	Q9UK96	FBX10_HUMAN	N	212	ENSP00000403802:H212N	ENSP00000276960:H212N	H	-	1	0	FBXO10	37527892	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.345000	0.97053	2.631000	0.89168	0.655000	0.94253	CAC	G|0.983;T|0.017	0.017	strong		0.488	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
MBP	4155	hgsc.bcm.edu	37	18	74701936	74701936	+	Silent	SNP	G	G	A	rs76912958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:74701936G>A	ENST00000397869.3	-	2	304	c.258C>T	c.(256-258)ccC>ccT	p.P86P	MBP_ENST00000382582.3_Silent_p.P112P|MBP_ENST00000359645.3_Silent_p.P112P|MBP_ENST00000397875.3_Silent_p.P86P|MBP_ENST00000354542.4_Intron|MBP_ENST00000526111.1_Silent_p.P64P|MBP_ENST00000578193.1_Silent_p.P86P|MBP_ENST00000528160.1_Intron|MBP_ENST00000527041.1_Intron|MBP_ENST00000355994.2_Silent_p.P219P|MBP_ENST00000580402.1_Silent_p.P219P|MBP_ENST00000397866.4_Silent_p.P86P|MBP_ENST00000397865.5_Silent_p.P86P|MBP_ENST00000579129.1_Silent_p.P219P			P13727	PRG2_HUMAN	myelin basic protein	0					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)	Sargramostim(DB00020)	AGTGGACTACGGGGTTTTCAT	0.572													G|||	129	0.0257588	0.0923	0.0101	5008	,	,		17532	0.0		0.0	False		,,,				2504	0.0				p.P219P	NSCLC(17;72 1131 19392)	Atlas-SNP	.											.	MBP	45	.	0			c.C657T						PASS	.	G	,,,,	327,4079	172.3+/-202.3	8,311,1884	179.0	160.0	167.0		336,258,258,657,336	-6.3	1.0	18	dbSNP_131	167	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MBP	NM_001025081.1,NM_001025090.1,NM_001025092.1,NM_001025101.1,NM_002385.2	,,,,	8,315,6180	AA,AG,GG		0.0465,7.4217,2.545	,,,,	112/198,86/172,86/161,219/305,112/187	74701936	331,12675	2203	4300	6503	SO:0001819	synonymous_variant	4155	exon5			GACTACGGGGTTT		CCDS12011.1, CCDS32847.1, CCDS42448.1, CCDS42449.1, CCDS42450.1	18q23	2008-08-01			ENSG00000197971	ENSG00000197971			6925	protein-coding gene	gene with protein product		159430				2425357	Standard	XM_005266699		Approved		uc010xfd.2	P02686	OTTHUMG00000132874	ENST00000397869.3:c.258C>T	18.37:g.74701936G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	148	72	0.486486	NM_001025101	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Silent	SNP	ENST00000397869.3	37																																																																																				G|0.977;A|0.023	0.023	strong		0.572	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1	NM_001025081	
PWWP2B	170394	hgsc.bcm.edu	37	10	134219291	134219291	+	Silent	SNP	C	C	T	rs139452616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134219291C>T	ENST00000305233.5	+	2	1346	c.1287C>T	c.(1285-1287)gaC>gaT	p.D429D	PWWP2B_ENST00000368609.4_Silent_p.D429D	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	429										central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)		ACAGCCTGGACGAGGCCAGAT	0.697													C|||	57	0.0113818	0.0393	0.0058	5008	,	,		15963	0.0		0.001	False		,,,				2504	0.0				p.D429D		Atlas-SNP	.											.	PWWP2B	33	.	0			c.C1287T						PASS	.	C	,	156,4234	103.4+/-141.9	3,150,2042	30.0	29.0	29.0		1287,1287	-7.2	0.1	10	dbSNP_134	29	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous,coding-synonymous	PWWP2B	NM_001098637.1,NM_138499.3	,	3,152,6338	TT,TC,CC		0.0233,3.5535,1.2167	,	429/500,429/591	134219291	158,12828	2195	4298	6493	SO:0001819	synonymous_variant	170394	exon2			CCTGGACGAGGCC	AK128663	CCDS7667.2	10q26.3	2009-06-03	2007-10-22	2007-10-22	ENSG00000171813	ENSG00000171813			25150	protein-coding gene	gene with protein product			"""PWWP domain containing 2"""	PWWP2			Standard	NM_001098637		Approved	bA432J24.1, FLJ46823	uc001lll.4	Q6NUJ5	OTTHUMG00000019286	ENST00000305233.5:c.1287C>T	10.37:g.134219291C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	17	12	0.705882	NM_001098637	A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Silent	SNP	ENST00000305233.5	37	CCDS7667.2																																																																																			C|0.986;T|0.014	0.014	strong		0.697	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499	
LTBP2	4053	hgsc.bcm.edu	37	14	74973926	74973926	+	Missense_Mutation	SNP	C	C	A	rs139481866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74973926C>A	ENST00000261978.4	-	26	4249	c.3863G>T	c.(3862-3864)gGc>gTc	p.G1288V	LTBP2_ENST00000556690.1_Intron	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1288	Cys-rich.|EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		AGGCTGGCAGCCCAGAACACA	0.567													C|||	9	0.00179712	0.0053	0.0029	5008	,	,		19539	0.0		0.0	False		,,,				2504	0.0				p.G1288V		Atlas-SNP	.											.	LTBP2	158	.	0			c.G3863T						PASS	.	C	VAL/GLY	20,4386	28.1+/-56.4	0,20,2183	85.0	80.0	82.0		3863	2.4	0.8	14	dbSNP_134	82	0,8600		0,0,4300	yes	missense	LTBP2	NM_000428.2	109	0,20,6483	AA,AC,CC		0.0,0.4539,0.1538	probably-damaging	1288/1822	74973926	20,12986	2203	4300	6503	SO:0001583	missense	4053	exon26			TGGCAGCCCAGAA		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.3863G>T	14.37:g.74973926C>A	ENSP00000261978:p.Gly1288Val	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	339	178	0.525074	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	37	CCDS9831.1	6	0.0027472527472527475	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	0	0.0	C	14.80	2.643520	0.47258	0.004539	0.0	ENSG00000119681	ENST00000261978	D	0.86694	-2.16	5.22	2.36	0.29203	EGF-like calcium-binding (2);	0.521247	0.16060	N	0.231509	D	0.83147	0.5191	L	0.37630	1.12	0.80722	D	1	D	0.67145	0.996	D	0.66351	0.943	T	0.78610	-0.2137	10	0.30078	T	0.28	.	6.5858	0.22620	0.0:0.6598:0.1289:0.2113	.	1288	Q14767	LTBP2_HUMAN	V	1288	ENSP00000261978:G1288V	ENSP00000261978:G1288V	G	-	2	0	LTBP2	74043679	0.996000	0.38824	0.761000	0.31378	0.370000	0.29829	0.463000	0.21972	0.192000	0.20272	-0.224000	0.12420	GGC	C|0.998;A|0.002	0.002	strong		0.567	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	
CAP2	10486	hgsc.bcm.edu	37	6	17541324	17541324	+	Missense_Mutation	SNP	A	A	G	rs34206659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:17541324A>G	ENST00000229922.2	+	9	1479	c.947A>G	c.(946-948)tAt>tGt	p.Y316C	CAP2_ENST00000465994.1_Missense_Mutation_p.Y252C|CAP2_ENST00000489374.1_Missense_Mutation_p.Y204C|CAP2_ENST00000493172.1_Intron|CAP2_ENST00000378990.2_Missense_Mutation_p.Y290C	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	316			Y -> C (in dbSNP:rs34206659).		activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			CCTAAATCTTATCCTTCTCAA	0.453													A|||	101	0.0201677	0.0446	0.0202	5008	,	,		18252	0.0		0.0278	False		,,,				2504	0.0				p.Y316C		Atlas-SNP	.											.	CAP2	61	.	0			c.A947G						PASS	.	A	CYS/TYR	213,4193	131.0+/-167.6	6,201,1996	148.0	130.0	136.0		947	-5.5	0.0	6	dbSNP_126	136	166,8434	77.2+/-139.8	1,164,4135	yes	missense	CAP2	NM_006366.2	194	7,365,6131	GG,GA,AA		1.9302,4.8343,2.914	benign	316/478	17541324	379,12627	2203	4300	6503	SO:0001583	missense	10486	exon9			AATCTTATCCTTC	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.947A>G	6.37:g.17541324A>G	ENSP00000229922:p.Tyr316Cys	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	173	89	0.514451	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Missense_Mutation	SNP	ENST00000229922.2	37	CCDS4539.1	52	0.023809523809523808	25	0.0508130081300813	9	0.024861878453038673	0	0.0	18	0.023746701846965697	a	6.187	0.402667	0.11696	0.048343	0.019302	ENSG00000112186	ENST00000229922;ENST00000378994;ENST00000489374;ENST00000378990;ENST00000465994	T;T;T;T	0.07908	3.15;3.15;3.15;3.15	5.56	-5.54	0.02544	.	0.914521	0.09670	N	0.771298	T	0.00967	0.0032	N	0.08118	0	0.09310	N	1	B;P;B;B	0.36010	0.064;0.532;0.427;0.427	B;B;B;B	0.30251	0.006;0.06;0.113;0.113	T	0.47983	-0.9074	10	0.38643	T	0.18	0.1298	7.3393	0.26627	0.1983:0.6213:0.0763:0.1041	rs34206659	204;252;290;316	B7Z385;B7Z1C4;E9PDI2;P40123	.;.;.;CAP2_HUMAN	C	316;233;204;290;252	ENSP00000229922:Y316C;ENSP00000417705:Y204C;ENSP00000368275:Y290C;ENSP00000418604:Y252C	ENSP00000229922:Y316C	Y	+	2	0	CAP2	17649303	0.000000	0.05858	0.000000	0.03702	0.100000	0.18952	0.769000	0.26604	-0.443000	0.07180	0.460000	0.39030	TAT	A|0.971;G|0.029	0.029	strong		0.453	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
RECQL	5965	hgsc.bcm.edu	37	12	21623179	21623179	+	Silent	SNP	T	T	C	rs17849408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21623179T>C	ENST00000444129.2	-	15	2367	c.1899A>G	c.(1897-1899)caA>caG	p.Q633Q	PYROXD1_ENST00000240651.9_3'UTR|RECQL_ENST00000421138.2_Silent_p.Q633Q|PYROXD1_ENST00000538582.1_3'UTR	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	633					DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)	membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						TAGAACCAGATTGCTGAAGCA	0.343								Other identified genes with known or suspected DNA repair function					T|||	755	0.150759	0.1483	0.1066	5008	,	,		14793	0.2917		0.0895	False		,,,				2504	0.1033				p.Q633Q		Atlas-SNP	.											.	RECQL	45	.	0			c.A1899G						PASS	.	T	,,	365,4037	173.0+/-202.9	28,309,1864	60.0	62.0	61.0		1899,,1899	-1.3	0.2	12	dbSNP_129	61	604,7978	154.8+/-208.9	25,554,3712	no	coding-synonymous,utr-3,coding-synonymous	RECQL,PYROXD1	NM_002907.3,NM_024854.3,NM_032941.2	,,	53,863,5576	CC,CT,TT		7.038,8.2917,7.463	,,	633/650,,633/650	21623179	969,12015	2201	4291	6492	SO:0001819	synonymous_variant	5965	exon16			ACCAGATTGCTGA	D37984	CCDS31756.1	12p12.1	2014-03-07	2014-03-07	2014-03-07	ENSG00000004700	ENSG00000004700			9948	protein-coding gene	gene with protein product	"""DNA helicase Q1-like"""	600537	"""RecQ protein-like (DNA helicase Q1-like)"""			7527136, 7961977	Standard	NM_002907		Approved	RecQ1, RecQL1	uc001rex.3	P46063	OTTHUMG00000169131	ENST00000444129.2:c.1899A>G	12.37:g.21623179T>C		Somatic	803	0	0		WXS	Illumina HiSeq	Phase_I	784	357	0.455357	NM_032941	A8K6G2	Silent	SNP	ENST00000444129.2	37	CCDS31756.1																																																																																			T|0.893;C|0.107	0.107	strong		0.343	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907	
ITGB6	3694	hgsc.bcm.edu	37	2	160968628	160968628	+	Silent	SNP	A	A	G	rs16844790	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160968628A>G	ENST00000283249.2	-	13	2301	c.2064T>C	c.(2062-2064)aaT>aaC	p.N688N	ITGB6_ENST00000409872.1_Silent_p.N688N|ITGB6_ENST00000428609.2_Silent_p.N646N|ITGB6_ENST00000409967.2_Silent_p.N581N	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	688					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						TTTTCCCCTCATTATCTGTAG	0.403													A|||	1074	0.214457	0.2247	0.4222	5008	,	,		18655	0.1796		0.1551	False		,,,				2504	0.1503				p.N688N		Atlas-SNP	.											.	ITGB6	68	.	0			c.T2064C						PASS	.	A		927,3479	355.4+/-313.0	96,735,1372	220.0	199.0	206.0		2064	-6.7	1.0	2	dbSNP_123	206	1501,7099	283.6+/-296.2	144,1213,2943	no	coding-synonymous	ITGB6	NM_000888.3		240,1948,4315	GG,GA,AA		17.4535,21.0395,18.6683		688/789	160968628	2428,10578	2203	4300	6503	SO:0001819	synonymous_variant	3694	exon13			CCCCTCATTATCT		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.2064T>C	2.37:g.160968628A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	177	89	0.502825	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Silent	SNP	ENST00000283249.2	37	CCDS2212.1																																																																																			A|0.805;G|0.195	0.195	strong		0.403	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888	
KIAA1551	55196	hgsc.bcm.edu	37	12	32134122	32134122	+	Missense_Mutation	SNP	T	T	C	rs75434030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:32134122T>C	ENST00000312561.4	+	4	647	c.233T>C	c.(232-234)aTg>aCg	p.M78T	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	78																	GTTTCTGATATGCATAATGGG	0.373													T|||	33	0.00658946	0.0242	0.0014	5008	,	,		22474	0.0		0.0	False		,,,				2504	0.0				p.M78T		Atlas-SNP	.											.	.	.	.	0			c.T233C						PASS	.	T	THR/MET	109,4297	84.8+/-123.5	1,107,2095	85.0	83.0	83.0		233	-1.3	0.0	12	dbSNP_131	83	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C12orf35	NM_018169.3	81	1,108,6394	CC,CT,TT		0.0116,2.4739,0.8458	possibly-damaging	78/1748	32134122	110,12896	2203	4300	6503	SO:0001583	missense	55196	exon4			CTGATATGCATAA	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.233T>C	12.37:g.32134122T>C	ENSP00000310338:p.Met78Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	168	91	0.541667	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	T	10.56	1.385451	0.25031	0.024739	1.16E-4	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.09073	3.02;3.02	5.39	-1.28	0.09318	.	0.664905	0.14503	N	0.315631	T	0.01976	0.0062	L	0.29908	0.895	0.09310	N	1	B	0.13145	0.007	B	0.15484	0.013	T	0.40720	-0.9548	9	.	.	.	.	1.6516	0.02773	0.1117:0.2639:0.2202:0.4042	.	78	Q9HCM1	CL035_HUMAN	T	78	ENSP00000310338:M78T;ENSP00000370442:M78T	.	M	+	2	0	C12orf35	32025389	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.467000	0.06664	-0.141000	0.11374	0.528000	0.53228	ATG	T|0.995;C|0.005	0.005	strong		0.373	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84607758	84607758	+	Silent	SNP	T	T	A	rs10867826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	375	2	0.00533333		WXS	Illumina HiSeq	Phase_I	490	307	0.626531	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	
PKDREJ	10343	hgsc.bcm.edu	37	22	46657798	46657798	+	Silent	SNP	A	A	G	rs6007748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	77	0	0		WXS	Illumina HiSeq	Phase_I	100	60	0.6	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	
CENPF	1063	hgsc.bcm.edu	37	1	214787130	214787130	+	Silent	SNP	G	G	A	rs2070064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:214787130G>A	ENST00000366955.3	+	2	201	c.33G>A	c.(31-33)ggG>ggA	p.G11G		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0	Interaction with SNAP25 and required for localization to the cytoplasm. {ECO:0000250}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GGAAAGAAGGGCTGCCTACAA	0.413													C|||	1183	0.236222	0.0522	0.3156	5008	,	,		14102	0.121		0.499	False		,,,				2504	0.2771				p.G11G	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,NS,carcinoma,0,1	CENPF	321	1	0			c.G33A						PASS	.	C		525,3881		42,441,1720	75.0	82.0	80.0		33	3.1	1.0	1	dbSNP_96	80	4450,4150		1142,2166,992	no	coding-synonymous	CENPF	NM_016343.3		1184,2607,2712	AA,AG,GG		48.2558,11.9156,38.2516		11/3115	214787130	4975,8031	2203	4300	6503	SO:0001819	synonymous_variant	1063	exon2			AGAAGGGCTGCCT	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.33G>A	1.37:g.214787130G>A		Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	191	89	0.465969	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																			G|0.653;A|0.345	0.345	strong		0.413	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
RFX7	64864	hgsc.bcm.edu	37	15	56387581	56387581	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56387581C>T	ENST00000559447.2	-	9	2325	c.2054G>A	c.(2053-2055)tGg>tAg	p.W685*	RFX7_ENST00000317318.6_Nonsense_Mutation_p.W782*|RFX7_ENST00000422057.1_Nonsense_Mutation_p.W685*|RFX7_ENST00000423270.1_Nonsense_Mutation_p.W782*			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	685					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.W685*(1)|p.W782*(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GATTTGTTGCCATCCATTTGG	0.378																																					p.W782X		Atlas-SNP	.											RFX7_ENST00000423270,NS,lymphoid_neoplasm,0,2	RFX7	170	2	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G2345A						PASS	.						124.0	116.0	118.0					15																	56387581		1850	4096	5946	SO:0001587	stop_gained	64864	exon9			TGTTGCCATCCAT			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.2054G>A	15.37:g.56387581C>T	ENSP00000453281:p.Trp685*	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	95	27	0.284211	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Nonsense_Mutation	SNP	ENST00000559447.2	37		.	.	.	.	.	.	.	.	.	.	C	30	5.054224	0.93793	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	.	.	.	5.44	4.32	0.51571	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-4.9265	14.1694	0.65500	0.0:0.9149:0.0:0.0851	.	.	.	.	X	685;782;782	.	ENSP00000313299:W782X	W	-	2	0	RFX7	54174873	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	5.485000	0.66850	2.531000	0.85337	0.563000	0.77884	TGG	.	.	none		0.378	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
NUP35	129401	hgsc.bcm.edu	37	2	183993085	183993085	+	Silent	SNP	A	A	G	rs61743390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:183993085A>G	ENST00000295119.4	+	2	214	c.111A>G	c.(109-111)ggA>ggG	p.G37G	NUP35_ENST00000409798.1_Silent_p.G20G|NUP35_ENST00000497330.1_3'UTR|NUP35_ENST00000541912.1_5'UTR	NM_138285.3	NP_612142.2	Q8NFH5	NUP53_HUMAN	nucleoporin 35kDa	37					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)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	8						TCTTACCTGGATTTTTAATGG	0.438													A|||	44	0.00878594	0.0333	0.0	5008	,	,		14995	0.0		0.0	False		,,,				2504	0.0				p.G37G		Atlas-SNP	.											.	NUP35	28	.	0			c.A111G						PASS	.	A		148,4258	101.6+/-140.2	0,148,2055	80.0	78.0	79.0		111	2.7	1.0	2	dbSNP_129	79	2,8598		0,2,4298	no	coding-synonymous	NUP35	NM_138285.3		0,150,6353	GG,GA,AA		0.0233,3.3591,1.1533		37/327	183993085	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	129401	exon2			ACCTGGATTTTTA	AF514993	CCDS2290.1, CCDS74614.1	2q32	2008-02-05			ENSG00000163002	ENSG00000163002			29797	protein-coding gene	gene with protein product		608140					Standard	XM_005246284		Approved	MP44	uc002upf.3	Q8NFH5	OTTHUMG00000132621	ENST00000295119.4:c.111A>G	2.37:g.183993085A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_138285	B4DP57|B4DYB4|Q4ZFZ9|Q53S95|Q8TDJ1	Silent	SNP	ENST00000295119.4	37	CCDS2290.1																																																																																			A|0.989;G|0.011	0.011	strong		0.438	NUP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255865.1	NM_138285	
MICA	100507436	hgsc.bcm.edu	37	6	31379794	31379794	+	Silent	SNP	C	C	T	rs1051797|rs386699191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31379794C>T	ENST00000449934.2	+	4	738	c.684C>T	c.(682-684)tcC>tcT	p.S228S	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)				GCAGGGCTTCCAGCTTCTATC	0.587													t|||	1823	0.364018	0.4773	0.4063	5008	,	,		19466	0.2996		0.3141	False		,,,				2504	0.2986				p.S228S		Atlas-SNP	.											.	MICA	21	.	0			c.C684T						PASS	.						21.0	25.0	24.0					6																	31379794		692	1591	2283	SO:0001819	synonymous_variant	100507436	exon4			GGCTTCCAGCTTC	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.684C>T	6.37:g.31379794C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.698;T|0.302	0.302	strong		0.587	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
TICAM2	353376	hgsc.bcm.edu	37	5	114916351	114916351	+	Silent	SNP	T	T	G	rs7705473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:114916351T>G	ENST00000427199.2	-	2	1044	c.603A>C	c.(601-603)ggA>ggC	p.G201G	TICAM2_ENST00000513729.1_5'Flank|TMED7-TICAM2_ENST00000282382.4_Silent_p.G370G|TICAM2_ENST00000408996.4_Silent_p.G370G|TMED7-TICAM2_ENST00000333314.3_3'UTR	NM_021649.6	NP_067681.1	Q86XR7	TCAM2_HUMAN	toll-like receptor adaptor molecule 2	201	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to lipopolysaccharide (GO:0071222)|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 chemokine (C-C motif) ligand 5 production (GO:0071650)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18-mediated signaling pathway (GO:2000494)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|response to interleukin-12 (GO:0070671)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			cervix(1)|kidney(1)|lung(2)|soft_tissue(1)	5		all_cancers(142;0.0223)|all_epithelial(76;0.000869)|Prostate(80;0.0115)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;4.38e-07)|Epithelial(69;1.62e-06)|all cancers(49;6.93e-05)		GTGTAGGAAATCCACGACTTT	0.418													G|||	60	0.0119808	0.0439	0.0014	5008	,	,		18528	0.0		0.001	False		,,,				2504	0.0				p.G370G		Atlas-SNP	.											.	.	.	.	0			c.A1110C						PASS	.	G	,,	169,4235	809.3+/-416.0	2,165,2035	76.0	80.0	79.0		1110,,603	5.9	1.0	5	dbSNP_116	79	0,8600		0,0,4300	no	coding-synonymous,utr-3,coding-synonymous	TICAM2,TMED7-TICAM2	NM_001164468.2,NM_001164469.2,NM_021649.6	,,	2,165,6335	GG,GT,TT		0.0,3.8374,1.2996	,,	370/405,,201/236	114916351	169,12835	2202	4300	6502	SO:0001819	synonymous_variant	100302736	exon4			AGGAAATCCACGA	AY232653	CCDS4119.1	5q22.3	2012-11-21			ENSG00000243414	ENSG00000243414			21354	protein-coding gene	gene with protein product		608321					Standard	NM_021649		Approved	TRAM, TICAM-2, TIRP		Q86XR7	OTTHUMG00000162905	ENST00000427199.2:c.603A>C	5.37:g.114916351T>G		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	172	97	0.563953	NM_001164468	B3Y698|Q6JUT2	Silent	SNP	ENST00000427199.2	37	CCDS4119.1																																																																																			T|0.989;G|0.011	0.011	strong		0.418	TICAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338755.1	NM_021649	
ICAM1	3383	hgsc.bcm.edu	37	19	10385540	10385540	+	Missense_Mutation	SNP	A	A	T	rs5491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10385540A>T	ENST00000264832.3	+	2	492	c.167A>T	c.(166-168)aAg>aTg	p.K56M	ICAM1_ENST00000423829.2_Intron|CTD-2369P2.5_ENST00000592893.1_RNA	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	56	Ig-like C2-type 1.		K -> M (in Kilifi; at homozygosity it is associated with increased susceptibility to cerebral malaria; dbSNP:rs5491). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:9259284, ECO:0000269|Ref.6}.		adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	GACCAGCCCAAGTTGTTGGGC	0.562													a|||	423	0.0844649	0.2504	0.0173	5008	,	,		19414	0.0526		0.007	False		,,,				2504	0.0204				p.K56M		Atlas-SNP	.											.	ICAM1	32	.	0			c.A167T	GRCh37	CM970747	ICAM1	M	rs5491	PASS	.	A	MET/LYS	934,3472	357.6+/-314.0	103,728,1372	99.0	95.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	167	-5.4	0.0	19	dbSNP_52	96	26,8574	16.6+/-54.9	0,26,4274	yes	missense	ICAM1	NM_000201.2	95	103,754,5646	TT,TA,AA		0.3023,21.1984,7.3812	benign	56/533	10385540	960,12046	2203	4300	6503	SO:0001583	missense	3383	exon2			AGCCCAAGTTGTT		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	5344	protein-coding gene	gene with protein product	"""human rhinovirus receptor"""	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.167A>T	19.37:g.10385540A>T	ENSP00000264832:p.Lys56Met	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_000201	B2R6M3|Q5NKV7|Q96B50	Missense_Mutation	SNP	ENST00000264832.3	37	CCDS12231.1	164	0.07509157509157509	114	0.23170731707317074	7	0.019337016574585635	36	0.06293706293706294	7	0.009234828496042216	a	10.23	1.293021	0.23564	0.211984	0.003023	ENSG00000090339	ENST00000264832	T	0.15487	2.42	4.45	-5.4	0.02656	Intercellular adhesion molecule, N-terminal (1);Immunoglobulin-like fold (1);	8.976480	0.00166	N	0.000000	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	5.000000000032756E-6	B	0.22146	0.065	B	0.31442	0.13	T	0.30794	-0.9966	9	0.48119	T	0.1	1.2014	2.5057	0.04645	0.109:0.3535:0.3044:0.2331	rs5491;rs52822152;rs57463344;rs5491	56	P05362	ICAM1_HUMAN	M	56	ENSP00000264832:K56M	ENSP00000264832:K56M	K	+	2	0	ICAM1	10246540	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.205000	0.00559	-1.363000	0.02164	-1.831000	0.00592	AAG	A|0.924;T|0.076	0.076	strong		0.562	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1		
COL6A5	256076	hgsc.bcm.edu	37	3	130150704	130150704	+	Missense_Mutation	SNP	A	A	G	rs61750883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130150704A>G	ENST00000432398.2	+	33	6138	c.5644A>G	c.(5644-5646)Atc>Gtc	p.I1882V	COL6A5_ENST00000265379.6_Missense_Mutation_p.I1882V	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1882	Nonhelical region.|VWFA 8. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						TAGGTCATCCATCATCACGGC	0.473													A|||	60	0.0119808	0.0431	0.0043	5008	,	,		20100	0.0		0.0	False		,,,				2504	0.0				p.I1882V		Atlas-SNP	.											.	COL6A5	205	.	0			c.A5644G						PASS	.	A	VAL/ILE	68,1316		3,62,627	197.0	163.0	173.0		5644	-2.3	0.4	3	dbSNP_129	173	0,3182		0,0,1591	yes	missense	COL6A5	NM_153264.5	29	3,62,2218	GG,GA,AA		0.0,4.9133,1.4893	benign	1882/2527	130150704	68,4498	692	1591	2283	SO:0001583	missense	256076	exon33			TCATCCATCATCA	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.5644A>G	3.37:g.130150704A>G	ENSP00000390895:p.Ile1882Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		14|14	0.00641025641025641|0.00641025641025641	14|14	0.028455284552845527|0.028455284552845527	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	1.127|1.127	-0.653563|-0.653563	0.03480|0.03480	0.049133|0.049133	0.0|0.0	ENSG00000172752|ENSG00000172752	ENST00000512836|ENST00000432398;ENST00000265379	.|T;T	.|0.13196	.|2.61;2.61	5.64|5.64	-2.28|-2.28	0.06826|0.06826	.|.	.|.	.|.	.|.	.|.	T|T	0.02193|0.02193	0.0068|0.0068	L|L	0.52266|0.52266	1.64|1.64	0.09310|0.09310	N|N	1|1	.|P	.|0.40083	.|0.702	.|P	.|0.45449	.|0.481	T|T	0.22730|0.22730	-1.0208|-1.0208	5|9	.|0.16420	.|T	.|0.52	.|.	11.0646|11.0646	0.47968|0.47968	0.5749:0.0:0.4251:0.0|0.5749:0.0:0.4251:0.0	rs61750883|rs61750883	.|1882	.|A8TX70-2	.|.	R|V	133|1882	.|ENSP00000390895:I1882V;ENSP00000265379:I1882V	.|ENSP00000265379:I1882V	H|I	+|+	2|1	0|0	COL6A5|COL6A5	131633394|131633394	0.004000|0.004000	0.15560|0.15560	0.400000|0.400000	0.26346|0.26346	0.036000|0.036000	0.12997|0.12997	0.173000|0.173000	0.16724|0.16724	-0.386000|-0.386000	0.07821|0.07821	-0.379000|-0.379000	0.06801|0.06801	CAT|ATC	A|0.993;G|0.007	0.007	strong		0.473	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
TTC3	7267	hgsc.bcm.edu	37	21	38538319	38538319	+	Missense_Mutation	SNP	A	A	G	rs61998236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38538319A>G	ENST00000399017.2	+	33	6550	c.3803A>G	c.(3802-3804)gAt>gGt	p.D1268G	TTC3_ENST00000355666.1_Missense_Mutation_p.D1268G|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Missense_Mutation_p.D1268G	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1268					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GTTTCTGAGGATGGGCAACCC	0.473													A|||	125	0.0249601	0.0908	0.0058	5008	,	,		18238	0.0		0.001	False		,,,				2504	0.0				p.D1268G	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A3803G						PASS	.	A	GLY/ASP,GLY/ASP	324,4080	159.2+/-191.8	10,304,1888	60.0	67.0	65.0		3803,3803	1.4	0.0	21	dbSNP_129	65	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TTC3	NM_001001894.1,NM_003316.3	94,94	10,306,6186	GG,GA,AA		0.0233,7.3569,2.5069	possibly-damaging,possibly-damaging	1268/2026,1268/2026	38538319	326,12678	2202	4300	6502	SO:0001583	missense	7267	exon33			CTGAGGATGGGCA	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.3803A>G	21.37:g.38538319A>G	ENSP00000381981:p.Asp1268Gly	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	184	88	0.478261	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	58	0.026556776556776556	53	0.10772357723577236	5	0.013812154696132596	0	0.0	0	0.0	A	11.72	1.723822	0.30593	0.073569	2.33E-4	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.13196	2.61;2.61;2.61	3.85	1.38	0.22167	.	0.913911	0.09206	N	0.834038	T	0.00241	0.0007	L	0.51422	1.61	0.09310	N	1	B;B	0.17268	0.021;0.001	B;B	0.15484	0.013;0.002	T	0.38308	-0.9667	9	.	.	.	-2.4084	3.1193	0.06386	0.6771:0.0:0.1149:0.208	rs61998236	326;1268	Q5GIT6;P53804	.;TTC3_HUMAN	G	1268	ENSP00000347889:D1268G;ENSP00000381981:D1268G;ENSP00000346791:D1268G	.	D	+	2	0	TTC3	37460189	0.001000	0.12720	0.000000	0.03702	0.406000	0.30931	0.854000	0.27791	0.292000	0.22492	0.533000	0.62120	GAT	A|0.974;G|0.026	0.026	strong		0.473	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
SLC12A3	6559	hgsc.bcm.edu	37	16	56919216	56919216	+	Missense_Mutation	SNP	A	A	G	rs61746763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:56919216A>G	ENST00000563236.1	+	15	1890	c.1865A>G	c.(1864-1866)aAc>aGc	p.N622S	SLC12A3_ENST00000262502.5_Missense_Mutation_p.N621S|SLC12A3_ENST00000438926.2_Missense_Mutation_p.N622S|SLC12A3_ENST00000566786.1_Missense_Mutation_p.N621S			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	622					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	GGCTCCTACAACCTGGCCCTC	0.597													A|||	84	0.0167732	0.0598	0.0058	5008	,	,		19315	0.0		0.001	False		,,,				2504	0.0				p.N622S		Atlas-SNP	.											.	SLC12A3	99	.	0			c.A1865G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	155,4165		1,153,2006	80.0	62.0	68.0		1865,1862,1865	5.4	1.0	16	dbSNP_129	68	15,8429		0,15,4207	yes	missense,missense,missense	SLC12A3	NM_000339.2,NM_001126107.1,NM_001126108.1	46,46,46	1,168,6213	GG,GA,AA		0.1776,3.588,1.3319	benign,benign,benign	622/1031,621/1030,622/1022	56919216	170,12594	2160	4222	6382	SO:0001583	missense	6559	exon15			CCTACAACCTGGC		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"""Solute carriers"""	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.1865A>G	16.37:g.56919216A>G	ENSP00000456149:p.Asn622Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	NM_001126108	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	37	CCDS58464.1	39	0.017857142857142856	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	12.22	1.872882	0.33069	0.03588	0.001776	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	5.4	5.4	0.78164	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	T	0.06826	0.0174	L	0.37561	1.115	0.80722	D	1	B;P;B	0.36110	0.048;0.537;0.343	B;P;B	0.50049	0.039;0.629;0.343	T	0.11446	-1.0587	9	0.11794	T	0.64	.	15.1083	0.72336	1.0:0.0:0.0:0.0	rs61746763	621;622;622	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	S	621;622	.	ENSP00000262502:N622S	N	+	2	0	SLC12A3	55476717	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.253000	0.78320	2.048000	0.60808	0.533000	0.62120	AAC	A|0.981;G|0.019	0.019	strong		0.597	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		
CSF2RA	1438	hgsc.bcm.edu	37	X	1428421	1428421	+	3'UTR	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1428421G>T	ENST00000381524.3	+	0	1438				CSF2RA_ENST00000355432.3_Missense_Mutation_p.R358L|CSF2RA_ENST00000361536.3_3'UTR|CSF2RA_ENST00000498153.1_3'UTR|CSF2RA_ENST00000381500.1_3'UTR|CSF2RA_ENST00000355805.2_3'UTR|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000432318.2_3'UTR|CSF2RA_ENST00000417535.2_3'UTR|CSF2RA_ENST00000381529.3_3'UTR|CSF2RA_ENST00000501036.2_3'UTR			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)						response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	TCCGCGACACGGGGGAACTGT	0.498																																					p.R358L	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.G1073T						PASS	.	T	,,,,,LEU/ARG,,	1324,3082		206,912,1085	249.0	229.0	236.0		,,,,,1073,,	-0.7	0.0	X	dbSNP_134	236	478,8114		20,438,3838	yes	utr-3,utr-3,utr-3,utr-3,utr-3,missense,utr-3,utr-3	CSF2RA	NM_001161529.1,NM_001161530.1,NM_001161532.1,NM_006140.4,NM_172245.2,NM_172246.2,NM_172247.2,NM_172249.2	,,,,,102,,	226,1350,4923	TT,TG,GG		5.5633,30.0499,13.8637	,,,,,,,	,,,,,358/378,,	1428421	1802,11196	2203	4296	6499	SO:0001624	3_prime_UTR_variant	1438	exon11			CGACACGGGGGAA	M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"""CD molecules"", ""Pseudoautosomal regions / PAR1"""	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.*49G>T	X.37:g.1428421G>T		Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	246	111	0.451219	NM_172246	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Missense_Mutation	SNP	ENST00000381524.3	37	CCDS35191.1	339	0.15521978021978022	162	0.32926829268292684	38	0.10497237569060773	80	0.13986013986013987	59	0.07783641160949868	.	0	-2.586937	0.00128	0.300499	0.055633	ENSG00000198223	ENST00000355432	T	0.45276	0.9	0.69	-0.685	0.11328	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36648	-0.9739	7	0.87932	D	0	.	.	.	.	.	359	P15509-5	.	L	358	ENSP00000347606:R358L	ENSP00000347606:R358L	R	+	2	0	CSF2RA	1388421	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.367000	0.07553	-1.076000	0.03125	-2.336000	0.00247	CGG	T|0.144;G|0.854;A|0.002	0.144	strong		0.498	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2		
BMP1	649	hgsc.bcm.edu	37	8	22059413	22059413	+	Silent	SNP	C	C	G	rs28710878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22059413C>G	ENST00000306385.5	+	16	2875	c.2205C>G	c.(2203-2205)ctC>ctG	p.L735L	BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	735	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)		GCTTCGTCCTCCATGACAACA	0.587													C|||	171	0.0341454	0.1218	0.0144	5008	,	,		20500	0.0		0.0	False		,,,				2504	0.0				p.L735L		Atlas-SNP	.											.	BMP1	131	.	0			c.C2205G						PASS	.	C		457,3949	210.8+/-231.2	22,413,1768	97.0	69.0	78.0		2205	-2.0	0.9	8	dbSNP_125	78	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	BMP1	NM_006129.4		22,415,6066	GG,GC,CC		0.0233,10.3722,3.5291		735/987	22059413	459,12547	2203	4300	6503	SO:0001819	synonymous_variant	649	exon16			CGTCCTCCATGAC		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.2205C>G	8.37:g.22059413C>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_006129	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			C|0.970;G|0.030	0.030	strong		0.587	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
LAMA1	284217	hgsc.bcm.edu	37	18	6966296	6966296	+	Splice_Site	SNP	G	G	A	rs73390557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6966296G>A	ENST00000389658.3	-	49	6993	c.6900C>T	c.(6898-6900)agC>agT	p.S2300S		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2300					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)				CATTCTGGGAGCTGCAAAGCA	0.458													G|||	223	0.0445288	0.1573	0.0187	5008	,	,		17231	0.001		0.001	False		,,,				2504	0.0				p.S2300S		Atlas-SNP	.											.	LAMA1	458	.	0			c.C6900T						PASS	.	G		631,3775	267.7+/-268.0	35,561,1607	40.0	39.0	39.0		6900	0.6	1.0	18	dbSNP_130	39	6,8594	3.7+/-12.6	0,6,4294	yes	coding-synonymous-near-splice	LAMA1	NM_005559.3		35,567,5901	AA,AG,GG		0.0698,14.3214,4.8977		2300/3076	6966296	637,12369	2203	4300	6503	SO:0001630	splice_region_variant	284217	exon49			CTGGGAGCTGCAA	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.6900-1C>T	18.37:g.6966296G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	32	13	0.40625	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.950;A|0.050	0.050	strong		0.458	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	Silent
TRIM22	10346	hgsc.bcm.edu	37	11	5719649	5719649	+	Silent	SNP	T	T	C	rs78484876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5719649T>C	ENST00000379965.3	+	4	901	c.624T>C	c.(622-624)ggT>ggC	p.G208G	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	208					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)		TGGAGGAAGGTGAGGTGAATG	0.512													T|||	135	0.0269569	0.0825	0.0072	5008	,	,		20336	0.0		0.004	False		,,,				2504	0.0174				p.G208G	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.T624C						PASS	.	T	,	248,3932		10,228,1852	70.0	78.0	76.0		612,624	-3.5	0.0	11	dbSNP_132	76	25,8435		0,25,4205	no	coding-synonymous,coding-synonymous	TRIM22	NM_001199573.1,NM_006074.4	,	10,253,6057	CC,CT,TT		0.2955,5.933,2.1598	,	204/495,208/499	5719649	273,12367	2090	4230	6320	SO:0001819	synonymous_variant	10346	exon4			GGAAGGTGAGGTG	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.624T>C	11.37:g.5719649T>C		Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	239	116	0.485356	NM_006074	Q05CQ0|Q15521	Silent	SNP	ENST00000379965.3	37	CCDS41612.1																																																																																			T|0.990;C|0.010	0.010	strong		0.512	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90500189	90500189	+	Missense_Mutation	SNP	C	C	G	rs77127003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:90500189C>G	ENST00000325643.5	+	4	853	c.787C>G	c.(787-789)Ctg>Gtg	p.L263V		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	263	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CGACTCCAGCCTGGCTGGACT	0.617													.|||	253	0.0505192	0.0938	0.0922	5008	,	,		17918	0.001		0.0308	False		,,,				2504	0.0337				p.L263V		Atlas-SNP	.											.	.	.	.	0			c.C787G						PASS	.	C	VAL/LEU	428,3978		22,384,1797	62.0	66.0	64.0		787	-3.3	0.0	9	dbSNP_131	64	305,8295		5,295,4000	no	missense	C9orf79	NM_178828.4	32	27,679,5797	GG,GC,CC		3.5465,9.714,5.6359	benign	263/1446	90500189	733,12273	2203	4300	6503	SO:0001583	missense	286234	exon4			TCCAGCCTGGCTG	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.787C>G	9.37:g.90500189C>G	ENSP00000322640:p.Leu263Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	123	82	0.666667	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	104	0.047619047619047616	47	0.09552845528455285	33	0.09116022099447514	0	0.0	24	0.0316622691292876	.	3.872	-0.027620	0.07589	0.09714	0.035465	ENSG00000177992	ENST00000325643	T	0.05513	3.43	1.98	-3.34	0.04943	.	.	.	.	.	T	0.00178	0.0005	M	0.64404	1.975	0.09310	N	1	B	0.32573	0.376	B	0.28784	0.094	T	0.32107	-0.9919	9	0.51188	T	0.08	.	0.2178	0.00164	0.2083:0.2735:0.2064:0.3118	.	263	Q6ZUB1	CI079_HUMAN	V	263	ENSP00000322640:L263V	ENSP00000322640:L263V	L	+	1	2	C9orf79	89690009	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.046000	0.14035	-0.914000	0.03827	-0.519000	0.04390	CTG	C|0.948;G|0.052	0.052	strong		0.617	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
FBLN2	2199	hgsc.bcm.edu	37	3	13679335	13679335	+	Silent	SNP	C	C	T	rs1061376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:13679335C>T	ENST00000295760.7	+	17	3540	c.3471C>T	c.(3469-3471)gaC>gaT	p.D1157D	FBLN2_ENST00000404922.3_Silent_p.D1204D|FBLN2_ENST00000492059.1_Silent_p.D1204D|FBLN2_ENST00000535798.1_Silent_p.D1183D	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	144	0	0		WXS	Illumina HiSeq	Phase_I	147	81	0.55102	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	
CMYA5	202333	hgsc.bcm.edu	37	5	79024915	79024915	+	Silent	SNP	G	G	C	rs16877111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79024915G>C	ENST00000446378.2	+	2	358	c.327G>C	c.(325-327)cgG>cgC	p.R109R		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	109					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)		TGTGTAGTCGGGAAGGGTCAA	0.433													G|||	692	0.138179	0.4758	0.0447	5008	,	,		14105	0.0		0.0219	False		,,,				2504	0.0102				p.R109R		Atlas-SNP	.											.	CMYA5	643	.	0			c.G327C						PASS	.	G		1475,2247		298,879,684	245.0	243.0	243.0		327	-1.0	0.1	5	dbSNP_123	243	172,8018		2,168,3925	no	coding-synonymous	CMYA5	NM_153610.3		300,1047,4609	CC,CG,GG		2.1001,39.6292,13.8264		109/4070	79024915	1647,10265	1861	4095	5956	SO:0001819	synonymous_variant	202333	exon2			TAGTCGGGAAGGG	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.327G>C	5.37:g.79024915G>C		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			G|0.893;C|0.107	0.107	strong		0.433	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
AMER1	139285	hgsc.bcm.edu	37	X	63412690	63412690	+	Missense_Mutation	SNP	A	A	C	rs34677493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:63412690A>C	ENST00000330258.3	-	2	749	c.477T>G	c.(475-477)ttT>ttG	p.F159L	AMER1_ENST00000374869.3_Missense_Mutation_p.F159L|AMER1_ENST00000403336.1_Missense_Mutation_p.F159L	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	159			F -> L (in dbSNP:rs34677493).		adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									GCATAGAGGGAAACTTCTCAG	0.532													A|||	528	0.139868	0.3722	0.0288	3775	,	,		12073	0.0		0.004	False		,,,				2504	0.0123				p.F159L		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.T477G						PASS	.	A	LEU/PHE	1683,2152		332,780,239,520,332	42.0	43.0	43.0		477	0.9	0.0	X	dbSNP_126	43	42,6686		0,35,7,2393,1865	yes	missense	FAM123B	NM_152424.3	22	332,815,246,2913,2197	CC,CA,C,AA,A		0.6243,43.8853,16.3306	benign	159/1136	63412690	1725,8838	2203	4300	6503	SO:0001583	missense	139285	exon2			AGAGGGAAACTTC	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.477T>G	X.37:g.63412690A>C	ENSP00000329117:p.Phe159Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	193	0.11633514165159735	121	0.32180851063829785	7	0.019886363636363636	0	0.0	1	0.0013227513227513227	A	0.031	-1.334923	0.01287	0.438853	0.006243	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.16457	2.34;2.34;2.34	4.93	0.952	0.19584	.	0.964567	0.08637	N	0.916136	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.48410	-0.9038	9	0.27082	T	0.32	0.9455	0.4629	0.00519	0.2626:0.1486:0.1604:0.4284	rs34677493	159	Q5JTC6	F123B_HUMAN	L	159	ENSP00000364003:F159L;ENSP00000329117:F159L;ENSP00000384722:F159L	ENSP00000329117:F159L	F	-	3	2	FAM123B	63329415	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-0.359000	0.07632	0.182000	0.20032	0.486000	0.48141	TTT	0|0.013;C|0.188	0.188	strong		0.532	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
CLEC16A	23274	hgsc.bcm.edu	37	16	11114174	11114174	+	Silent	SNP	A	A	G	rs61741309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11114174A>G	ENST00000409790.1	+	12	1658	c.1428A>G	c.(1426-1428)caA>caG	p.Q476Q	CLEC16A_ENST00000409552.3_Silent_p.Q458Q	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						AGAGCACGCAATGGAGCAGGT	0.632													A|||	245	0.0489217	0.18	0.0101	5008	,	,		21149	0.0		0.0	False		,,,				2504	0.0				p.Q476Q		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1428G						PASS	.	A		489,3493		31,427,1533	16.0	19.0	18.0		1428	4.4	1.0	16	dbSNP_129	18	4,8358		0,4,4177	no	coding-synonymous	CLEC16A	NM_015226.2		31,431,5710	GG,GA,AA		0.0478,12.2803,3.9938		476/1054	11114174	493,11851	1991	4181	6172	SO:0001819	synonymous_variant	23274	exon11			CACGCAATGGAGC	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.1428A>G	16.37:g.11114174A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			A|0.962;G|0.038	0.038	strong		0.632	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435194	7435194	+	Silent	SNP	G	G	A	rs12498567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:7435194G>A	ENST00000319098.4	-	1	1506	c.1413C>T	c.(1411-1413)ggC>ggT	p.G471G	SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000507866.2_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	471	Saposin B-type 4. {ECO:0000255|PROSITE- ProRule:PRU00415}.				sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						GGGTCCTGGGGCCGTGGCAGG	0.642													G|||	577	0.115216	0.1036	0.1138	5008	,	,		17473	0.1111		0.1839	False		,,,				2504	0.0654				p.G471G		Atlas-SNP	.											PSAPL1_ENST00000319098,NS,carcinoma,-1,2	PSAPL1	51	2	0			c.C1413T						PASS	.	G	,	490,3460		32,426,1517	19.0	22.0	21.0		1413,	-1.3	0.0	4	dbSNP_120	21	1450,6834		121,1208,2813	no	coding-synonymous,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	,	153,1634,4330	AA,AG,GG		17.5036,12.4051,15.8574	,	471/522,	7435194	1940,10294	1975	4142	6117	SO:0001819	synonymous_variant	768239	exon1			CCTGGGGCCGTGG	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.1413C>T	4.37:g.7435194G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_001085382	A0A184|Q8N7T4	Silent	SNP	ENST00000319098.4	37	CCDS47009.1																																																																																			G|0.868;A|0.132	0.132	strong		0.642	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
GEN1	348654	hgsc.bcm.edu	37	2	17961321	17961321	+	Silent	SNP	A	A	G	rs16983864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:17961321A>G	ENST00000381254.2	+	13	1555	c.1341A>G	c.(1339-1341)gcA>gcG	p.A447A	GEN1_ENST00000317402.7_Silent_p.A447A|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	447					DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TGTTTGAAGCAGCATATCCTG	0.308								Homologous recombination					A|||	236	0.0471246	0.1377	0.0072	5008	,	,		18870	0.0308		0.005	False		,,,				2504	0.0133				p.A447A		Atlas-SNP	.											.	GEN1	79	.	0			c.A1341G						PASS	.	A	,	466,3940	216.4+/-235.1	23,420,1760	62.0	64.0	64.0		1341,1341	-0.6	1.0	2	dbSNP_123	64	34,8566	22.8+/-68.1	0,34,4266	no	coding-synonymous,coding-synonymous	GEN1	NM_001130009.1,NM_182625.3	,	23,454,6026	GG,GA,AA		0.3953,10.5765,3.8444	,	447/909,447/909	17961321	500,12506	2203	4300	6503	SO:0001819	synonymous_variant	348654	exon13			TGAAGCAGCATAT	AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"""Holliday junction resolvase"""	612449	"""Gen endonuclease homolog 1 (Drosophila)"""			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.1341A>G	2.37:g.17961321A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_182625	Q17RS9|Q6ZN37	Silent	SNP	ENST00000381254.2	37	CCDS1691.1																																																																																			A|0.963;G|0.037	0.037	strong		0.308	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625	
NUP54	53371	hgsc.bcm.edu	37	4	77069474	77069474	+	Silent	SNP	G	G	A	rs35442986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77069474G>A	ENST00000264883.3	-	1	194	c.54C>T	c.(52-54)acC>acT	p.T18T	NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000514987.1_Silent_p.T18T|NUP54_ENST00000458189.2_5'UTR|NUP54_ENST00000515460.1_5'UTR	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	18	9 X 2 AA repeats of F-G.|Gly-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)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						CGGGGGCCGCGGTGGCTGCAG	0.662													G|||	462	0.0922524	0.2867	0.0288	5008	,	,		15198	0.0556		0.003	False		,,,				2504	0.0041				p.T18T		Atlas-SNP	.											.	NUP54	48	.	0			c.C54T						PASS	.	G		827,3543		93,641,1451	14.0	19.0	18.0		54	3.0	1.0	4	dbSNP_126	18	13,8571		0,13,4279	no	coding-synonymous	NUP54	NM_017426.2		93,654,5730	AA,AG,GG		0.1514,18.9245,6.4845		18/508	77069474	840,12114	2185	4292	6477	SO:0001819	synonymous_variant	53371	exon1			GGCCGCGGTGGCT	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.54C>T	4.37:g.77069474G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	220	115	0.522727	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Silent	SNP	ENST00000264883.3	37	CCDS3576.1																																																																																			G|0.914;A|0.086	0.086	strong		0.662	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
PLK2	10769	hgsc.bcm.edu	37	5	57753149	57753149	+	Silent	SNP	A	A	G	rs17767072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:57753149A>G	ENST00000274289.3	-	7	1167	c.867T>C	c.(865-867)taT>taC	p.Y289Y	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	289	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		TTATGCACCTATAAGTTTCTT	0.423													A|||	590	0.117812	0.1967	0.2017	5008	,	,		18271	0.0		0.1282	False		,,,				2504	0.0624				p.Y289Y		Atlas-SNP	.											.	PLK2	71	.	0			c.T867C						PASS	.	A		789,3617	315.8+/-294.3	89,611,1503	64.0	65.0	65.0		867	0.6	1.0	5	dbSNP_123	65	957,7643	209.0+/-250.3	56,845,3399	no	coding-synonymous	PLK2	NM_006622.2		145,1456,4902	GG,GA,AA		11.1279,17.9074,13.4246		289/686	57753149	1746,11260	2203	4300	6503	SO:0001819	synonymous_variant	10769	exon7			GCACCTATAAGTT		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.867T>C	5.37:g.57753149A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	71	41	0.577465	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	37	CCDS3974.1																																																																																			A|0.871;G|0.129	0.129	strong		0.423	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622	
MGARP	84709	hgsc.bcm.edu	37	4	140187985	140187985	+	Missense_Mutation	SNP	G	G	A	rs544624566|rs6823412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:140187985G>A	ENST00000398955.1	-	4	670	c.491C>T	c.(490-492)gCg>gTg	p.A164V		NM_032623.3	NP_116012.2	Q8TDB4	HUMMR_HUMAN	mitochondria-localized glutamic acid-rich protein	164					anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cellular response to gonadotropin-releasing hormone (GO:0097211)|cellular response to hypoxia (GO:0071456)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of mitochondrion organization (GO:0010822)|protein targeting to mitochondrion (GO:0006626)|retrograde axon cargo transport (GO:0008090)	integral component of mitochondrial outer membrane (GO:0031307)|mitochondrion (GO:0005739)											TTCCCTCGCCGCTGCATCTGT	0.532													G|||	179	0.0357428	0.1278	0.0144	5008	,	,		17899	0.0		0.0	False		,,,				2504	0.0				p.A164V		Atlas-SNP	.											.	.	.	.	0			c.C491T						PASS	.	G	VAL/ALA	512,3560		40,432,1564	193.0	188.0	189.0		491	-3.0	0.0	4	dbSNP_116	189	11,8371		0,11,4180	yes	missense	C4orf49	NM_032623.3	64	40,443,5744	AA,AG,GG		0.1312,12.5737,4.1995	benign	164/241	140187985	523,11931	2036	4191	6227	SO:0001583	missense	84709	exon4			CTCGCCGCTGCAT	AF484960	CCDS43269.1	4q31.1	2014-02-19	2014-02-19	2012-04-17	ENSG00000137463	ENSG00000137463			29969	protein-coding gene	gene with protein product	"""ovary-specific acidic protein"", ""corneal endothelium-specific protein 1"", ""hypoxia up-regulated mitochondrial movement regulator"""		"""chromosome 4 open reading frame 49"""	C4orf49			Standard	NM_032623		Approved	OSAP, CESP-1, HUMMR	uc003ihr.1	Q8TDB4	OTTHUMG00000161325	ENST00000398955.1:c.491C>T	4.37:g.140187985G>A	ENSP00000381928:p.Ala164Val	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	189	98	0.518519	NM_032623	Q9BZC3	Missense_Mutation	SNP	ENST00000398955.1	37	CCDS43269.1	56	0.02564102564102564	50	0.1016260162601626	6	0.016574585635359115	0	0.0	0	0.0	G	12.97	2.097423	0.37048	0.125737	0.001312	ENSG00000137463	ENST00000398955	T	0.57752	0.38	5.23	-3.02	0.05446	.	1.807910	0.02960	N	0.142981	T	0.00384	0.0012	L	0.27053	0.805	0.09310	N	1	B	0.17465	0.022	B	0.12156	0.007	T	0.13737	-1.0498	10	0.72032	D	0.01	-14.4927	1.2453	0.01971	0.1551:0.2366:0.2469:0.3614	rs6823412	164	Q8TDB4	CD049_HUMAN	V	164	ENSP00000381928:A164V	ENSP00000381928:A164V	A	-	2	0	C4orf49	140407435	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.580000	0.05827	-0.266000	0.09339	0.467000	0.42956	GCG	G|0.983;A|0.017	0.017	strong		0.532	MGARP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364536.1	NM_032623	
MUC17	140453	hgsc.bcm.edu	37	7	100679316	100679316	+	Missense_Mutation	SNP	T	T	A	rs199509433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100679316T>A	ENST00000306151.4	+	3	4683	c.4619T>A	c.(4618-4620)gTc>gAc	p.V1540D		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1540	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)					ACTCCTGCTGTCACCAGCACA	0.473																																					p.V1540D		Atlas-SNP	.											MUC17,right_upper_lobe,carcinoma,-1,1	MUC17	804	1	0			c.T4619A						PASS	.	A	ASP/VAL	60,4346	815.8+/-416.2	0,60,2143	253.0	227.0	236.0		4619	-1.8	0.0	7	dbSNP_134	236	19,8581	817.2+/-406.9	0,19,4281	no	missense	MUC17	NM_001040105.1	152	0,79,6424	AA,AT,TT		0.2209,1.3618,0.6074	benign	1540/4494	100679316	79,12927	2203	4300	6503	SO:0001583	missense	140453	exon3			CTGCTGTCACCAG	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.4619T>A	7.37:g.100679316T>A	ENSP00000302716:p.Val1540Asp	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	187	42	0.224599	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	1.210	-0.629938	0.03610	0.013618	0.002209	ENSG00000169876	ENST00000306151	T	0.02498	4.27	0.922	-1.84	0.07809	.	.	.	.	.	T	0.00724	0.0024	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41305	-0.9516	9	0.10902	T	0.67	.	2.1043	0.03687	0.3027:0.0:0.2101:0.4872	.	1540	Q685J3	MUC17_HUMAN	D	1540	ENSP00000302716:V1540D	ENSP00000302716:V1540D	V	+	2	0	MUC17	100466036	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.547000	0.00114	-2.533000	0.00490	-2.239000	0.00288	GTC	T|0.906;A|0.094	0.094	strong		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
LRRIQ3	127255	hgsc.bcm.edu	37	1	74649119	74649119	+	Splice_Site	SNP	C	C	T	rs143858191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:74649119C>T	ENST00000395089.1	-	1	249		c.e1+1		LRRIQ3_ENST00000370911.3_Splice_Site|LRRIQ3_ENST00000370909.2_Splice_Site|LRRIQ3_ENST00000354431.4_Splice_Site			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3											NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						CTATTGCTTACCTGATTTCCA	0.299													C|||	12	0.00239617	0.0091	0.0	5008	,	,		16045	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.249+1G>A						PASS	.	C		32,4368	34.3+/-65.2	2,28,2170	61.0	67.0	65.0			5.3	1.0	1	dbSNP_134	65	0,8588		0,0,4294	yes	splice-5	LRRIQ3	NM_001105659.1		2,28,6464	TT,TC,CC		0.0,0.7273,0.2464			74649119	32,12956	2200	4294	6494	SO:0001630	splice_region_variant	127255	exon3			TGCTTACCTGATT	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.249+1G>A	1.37:g.74649119C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Splice_Site	SNP	ENST00000395089.1	37	CCDS41350.1	5	0.0022893772893772895	4	0.008130081300813009	0	0.0	0	0.0	1	0.0013192612137203166	C	17.79	3.476396	0.63737	0.007273	0.0	ENSG00000162620	ENST00000395089;ENST00000354431;ENST00000370909;ENST00000388972;ENST00000444984;ENST00000370911	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0114	0.89225	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRRIQ3	74421707	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	5.083000	0.64456	2.601000	0.87937	0.655000	0.94253	.	C|0.998;T|0.002	0.002	strong		0.299	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258	Intron
TTLL2	83887	hgsc.bcm.edu	37	6	167755063	167755063	+	Missense_Mutation	SNP	G	G	A	rs34931196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:167755063G>A	ENST00000239587.5	+	3	1763	c.1675G>A	c.(1675-1677)Gtt>Att	p.V559I		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	559			V -> I (in dbSNP:rs34931196).		cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CTTTGTTCTTGTTTTTCCTTT	0.468													G|||	140	0.0279553	0.1036	0.0043	5008	,	,		20361	0.0		0.0	False		,,,				2504	0.0				p.V559I		Atlas-SNP	.											.	TTLL2	82	.	0			c.G1675A						PASS	.	G	ILE/VAL	347,4059	179.7+/-208.2	15,317,1871	92.0	89.0	90.0		1675	1.7	0.9	6	dbSNP_126	90	4,8596	3.7+/-12.6	0,4,4296	yes	missense	TTLL2	NM_031949.4	29	15,321,6167	AA,AG,GG		0.0465,7.8756,2.6988	benign	559/593	167755063	351,12655	2203	4300	6503	SO:0001583	missense	83887	exon3			GTTCTTGTTTTTC	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1675G>A	6.37:g.167755063G>A	ENSP00000239587:p.Val559Ile	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	166	67	0.403614	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	37	CCDS5301.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	G	0.039	-1.293630	0.01375	0.078756	4.65E-4	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.02121	4.44	4.04	1.67	0.24075	.	0.415985	0.21849	N	0.068208	T	0.00300	0.0009	N	0.04203	-0.255	0.21627	N	0.99962	B	0.06786	0.001	B	0.04013	0.001	T	0.41734	-0.9492	10	0.02654	T	1	.	6.3218	0.21223	0.6774:0.0:0.3226:0.0	rs34931196	559	Q9BWV7	TTLL2_HUMAN	I	559;486	ENSP00000239587:V559I	ENSP00000239587:V559I	V	+	1	0	TTLL2	167675053	1.000000	0.71417	0.874000	0.34290	0.452000	0.32318	0.911000	0.28584	0.164000	0.19529	-0.339000	0.08088	GTT	G|0.970;A|0.030	0.030	strong		0.468	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
AHNAK2	113146	hgsc.bcm.edu	37	14	105406238	105406238	+	Missense_Mutation	SNP	A	A	C	rs2819419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105406238A>C	ENST00000333244.5	-	7	15669	c.15550T>G	c.(15550-15552)Tac>Gac	p.Y5184D	AHNAK2_ENST00000557457.1_Missense_Mutation_p.Y182D	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5184			Y -> D (in dbSNP:rs2819419). {ECO:0000269|PubMed:17974005}.			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)		p.Y154D(1)		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)			TCCTGCGAGTACTTGGTCATG	0.557													C|||	2959	0.590855	0.7632	0.5216	5008	,	,		21547	0.4127		0.5467	False		,,,				2504	0.636				p.Y5184D		Atlas-SNP	.											AHNAK2,NS,carcinoma,0,1	AHNAK2	719	1	1	Substitution - Missense(1)	stomach(1)	c.T15550G						PASS	.	C	ASP/TYR	2973,979		1117,739,120	184.0	193.0	190.0		15550	2.0	0.0	14	dbSNP_100	190	4532,3802		1244,2044,879	yes	missense	AHNAK2	NM_138420.2	160	2361,2783,999	CC,CA,AA		45.6204,24.7723,38.9142	benign	5184/5796	105406238	7505,4781	1976	4167	6143	SO:0001583	missense	113146	exon7			GCGAGTACTTGGT	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.15550T>G	14.37:g.105406238A>C	ENSP00000353114:p.Tyr5184Asp	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1209	0.5535714285714286	381	0.774390243902439	202	0.5580110497237569	222	0.3881118881118881	404	0.5329815303430079	C	0.013	-1.626373	0.00813	0.752277	0.543796	ENSG00000185567	ENST00000557457;ENST00000333244	T;T	0.02552	4.25;5.4	3.85	2.0	0.26442	.	0.610414	0.13077	N	0.415632	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	0.04191	-1.0970	9	0.12766	T	0.61	.	3.6893	0.08340	0.1932:0.5963:0.0:0.2104	rs2819419;rs17232090;rs60333253;rs2819419	5184	Q8IVF2	AHNK2_HUMAN	D	182;5184	ENSP00000450998:Y182D;ENSP00000353114:Y5184D	ENSP00000353114:Y5184D	Y	-	1	0	AHNAK2	104477283	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.242000	0.08928	0.225000	0.20959	-0.217000	0.12591	TAC	A|0.417;C|0.583	0.583	strong		0.557	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OR8S1	341568	hgsc.bcm.edu	37	12	48919793	48919793	+	Missense_Mutation	SNP	T	T	C	rs2705143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48919793T>C	ENST00000310194.1	+	1	379	c.379T>C	c.(379-381)Tgc>Cgc	p.C127R	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	127				C -> R (in Ref. 1; BAC05832). {ECO:0000305}.		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						TGCTGCCATCTGCCGCCCACT	0.542													T|||	1277	0.254992	0.3419	0.1585	5008	,	,		20153	0.248		0.168	False		,,,				2504	0.3027				p.C127R		Atlas-SNP	.											.	OR8S1	47	.	0			c.T379C						PASS	.	T	ARG/CYS	1214,3192	422.1+/-339.6	163,888,1152	132.0	120.0	124.0		379	3.9	1.0	12	dbSNP_100	124	1529,7071	288.1+/-298.6	130,1269,2901	no	missense	OR8S1	NM_001005203.2	180	293,2157,4053	CC,CT,TT		17.7791,27.5533,21.0903	possibly-damaging	127/360	48919793	2743,10263	2203	4300	6503	SO:0001583	missense	341568	exon1			GCCATCTGCCGCC		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.379T>C	12.37:g.48919793T>C	ENSP00000310632:p.Cys127Arg	Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	206	206	1	NM_001005203		Missense_Mutation	SNP	ENST00000310194.1	37	CCDS31789.1	486	0.22252747252747251	173	0.3516260162601626	64	0.17679558011049723	127	0.22202797202797203	122	0.16094986807387862	T	13.17	2.156350	0.38021	0.275533	0.177791	ENSG00000197376	ENST00000310194	T	0.06218	3.33	5.03	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	D	0.000415	T	0.00012	0.0000	H	0.94542	3.55	0.19300	P	0.9999782305	B	0.22080	0.064	B	0.27262	0.078	T	0.16217	-1.0410	9	0.66056	D	0.02	-51.5792	8.8554	0.35225	0.0:0.0888:0.0:0.9112	rs2705143	127	Q8NH09	OR8S1_HUMAN	R	127	ENSP00000310632:C127R	ENSP00000310632:C127R	C	+	1	0	OR8S1	47206060	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	1.736000	0.38187	0.939000	0.37446	0.533000	0.62120	TGC	T|0.781;C|0.219	0.219	strong		0.542	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1		
ZNF630	57232	hgsc.bcm.edu	37	X	47918205	47918205	+	Silent	SNP	G	G	A	rs501128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47918205G>A	ENST00000409324.3	-	5	1852	c.1626C>T	c.(1624-1626)ccC>ccT	p.P542P	ZNF630_ENST00000442455.3_Silent_p.P528P|ZNF630_ENST00000276054.4_Silent_p.P418P|ZNF630-AS1_ENST00000436124.1_RNA	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	542					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						TACACTCATAGGGTTTCTCCC	0.448													G|||	2415	0.639735	0.4486	0.5231	3775	,	,		15237	0.6567		0.4115	False		,,,				2504	0.3916				p.P542P		Atlas-SNP	.											.	ZNF630	71	.	0			c.C1626T						PASS	.	G	,	2169,1655		539,767,324,325,238	52.0	48.0	49.0		1626,1584	-2.4	0.0	X	dbSNP_83	49	3605,3110		717,1173,998,538,861	no	coding-synonymous,coding-synonymous	ZNF630	NM_001037735.2,NM_001190255.1	,	1256,1940,1322,863,1099	AA,AG,A,GG,G		46.3142,43.2793,45.213	,	542/658,528/644	47918205	5774,4765	2193	4287	6480	SO:0001819	synonymous_variant	57232	exon5			CTCATAGGGTTTC	AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"""Zinc fingers, C2H2-type"", ""-"""	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.1626C>T	X.37:g.47918205G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	149	44	0.295302	NM_001037735	F8WAG4|Q5H8Z5	Silent	SNP	ENST00000409324.3	37	CCDS35237.2																																																																																			0|0.004;A|0.588	0.588	strong		0.448	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735	
ZP4	57829	hgsc.bcm.edu	37	1	238050136	238050136	+	Silent	SNP	T	T	C	rs520720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:238050136T>C	ENST00000366570.4	-	6	932	c.774A>G	c.(772-774)gaA>gaG	p.E258E	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	258	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			TTGCCACCAGTTCATTTTCAT	0.473													T|||	703	0.140375	0.4955	0.0504	5008	,	,		21047	0.0		0.0119	False		,,,				2504	0.001				p.E258E	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											ZP4,NS,carcinoma,-2,1	ZP4	161	1	0			c.A774G						PASS	.	T		1753,2653	522.2+/-370.7	356,1041,806	192.0	176.0	182.0		774	-0.6	0.5	1	dbSNP_83	182	123,8477	62.4+/-124.4	0,123,4177	no	coding-synonymous	ZP4	NM_021186.3		356,1164,4983	CC,CT,TT		1.4302,39.7867,14.4241		258/541	238050136	1876,11130	2203	4300	6503	SO:0001819	synonymous_variant	57829	exon6			CACCAGTTCATTT	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.774A>G	1.37:g.238050136T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_021186	B2RAE1	Silent	SNP	ENST00000366570.4	37	CCDS1615.1																																																																																			T|0.856;C|0.144	0.144	strong		0.473	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
ZNF41	7592	hgsc.bcm.edu	37	X	47308509	47308509	+	Missense_Mutation	SNP	A	A	C	rs34301930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47308509A>C	ENST00000377065.4	-	5	1299	c.660T>G	c.(658-660)aaT>aaG	p.N220K	ZNF41_ENST00000397050.2_Missense_Mutation_p.N230K|ZNF41_ENST00000313116.7_Missense_Mutation_p.N220K|ZNF41_ENST00000465311.1_5'Flank	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	262					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				AATTGTTACCATTTCCAAAAA	0.368													A|||	113	0.0299338	0.0832	0.0043	3775	,	,		14437	0.0		0.0	False		,,,				2504	0.0				p.N220K		Atlas-SNP	.											.	ZNF41	71	.	0			c.T660G						PASS	.	A	LYS/ASN,LYS/ASN	343,3492		8,285,42,1339,529	150.0	140.0	144.0		660,660	3.2	0.3	X	dbSNP_126	144	3,6725		0,3,0,2425,1872	yes	missense,missense	ZNF41	NM_007130.2,NM_153380.2	94,94	8,288,42,3764,2401	CC,CA,C,AA,A		0.0446,8.9439,3.2756	possibly-damaging,possibly-damaging	220/780,220/780	47308509	346,10217	2203	4300	6503	SO:0001583	missense	7592	exon5			GTTACCATTTCCA	X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"""Zinc fingers, C2H2-type"", ""-"""	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.660T>G	X.37:g.47308509A>C	ENSP00000366265:p.Asn220Lys	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	230	123	0.534783	NM_007130	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	37	CCDS14279.1	36	0.0216998191681736	25	0.05296610169491525	0	0.0	0	0.0	0	0.0	A	4.551	0.102356	0.08731	0.089439	4.46E-4	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050	T;T;T	0.06068	3.35;3.35;3.35	3.2	3.2	0.36748	.	0.000000	0.37715	N	0.001972	T	0.00210	0.0006	N	0.08118	0	0.44254	P	0.0028960000000000097	P;P;B;P;P	0.50156	0.932;0.932;0.257;0.932;0.888	B;B;B;P;B	0.47981	0.424;0.424;0.074;0.563;0.36	T	0.37957	-0.9683	9	0.62326	D	0.03	.	9.1657	0.37050	1.0:0.0:0.0:0.0	rs34301930	220;222;230;254;262	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	K	220;220;230	ENSP00000315173:N220K;ENSP00000366265:N220K;ENSP00000380243:N230K	ENSP00000315173:N220K	N	-	3	2	ZNF41	47193453	0.000000	0.05858	0.255000	0.24374	0.075000	0.17131	0.061000	0.14366	1.514000	0.48869	0.412000	0.27726	AAT	A|0.966;C|0.034	0.034	strong		0.368	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380	
MGAM	8972	hgsc.bcm.edu	37	7	141750613	141750613	+	Missense_Mutation	SNP	T	T	A	rs145430437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141750613T>A	ENST00000549489.2	+	24	2849	c.2754T>A	c.(2752-2754)aaT>aaA	p.N918K	MGAM_ENST00000475668.2_Missense_Mutation_p.N918K	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	918					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)	TGAAACACAATGGTGTCCCAA	0.373													t|||	53	0.0105831	0.0378	0.0043	5008	,	,		20002	0.0		0.0	False		,,,				2504	0.0				p.N918K		Atlas-SNP	.											.	MGAM	767	.	0			c.T2754A						PASS	.	T	LYS/ASN	121,3617		1,119,1749	105.0	95.0	98.0		2754	0.9	0.1	7	dbSNP_134	98	0,8200		0,0,4100	no	missense	MGAM	NM_004668.2	94	1,119,5849	AA,AT,TT		0.0,3.237,1.0136	possibly-damaging	918/1858	141750613	121,11817	1869	4100	5969	SO:0001583	missense	8972	exon24			ACACAATGGTGTC	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.2754T>A	7.37:g.141750613T>A	ENSP00000447378:p.Asn918Lys	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	259	112	0.432432	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	T	16.84	3.233340	0.58886	0.03237	0.0	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.89746	-2.56	5.81	0.868	0.19090	.	0.000000	0.53938	D	0.000059	T	0.57140	0.2033	M	0.86028	2.79	0.09310	N	1	P	0.45768	0.866	B	0.34590	0.186	T	0.69258	-0.5192	10	0.72032	D	0.01	.	9.1608	0.37021	0.0:0.3617:0.0:0.6383	.	918	O43451	MGA_HUMAN	K	918;918;795	ENSP00000447378:N918K	ENSP00000316431:N795K	N	+	3	2	MGAM	141397082	0.061000	0.20836	0.090000	0.20809	0.275000	0.26752	-0.197000	0.09518	-0.065000	0.13021	-0.479000	0.04858	AAT	T|0.988;A|0.012	0.012	strong		0.373	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
SMC1B	27127	hgsc.bcm.edu	37	22	45767455	45767455	+	Silent	SNP	A	A	G	rs136569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45767455A>G	ENST00000357450.4	-	14	2208	c.2209T>C	c.(2209-2211)Tta>Cta	p.L737L	SMC1B_ENST00000404354.3_Silent_p.L737L	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	737					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)		TCACTTTGTAACTGAGATTGT	0.289													G|||	3567	0.71226	0.9546	0.5375	5008	,	,		17860	0.7054		0.506	False		,,,				2504	0.728				p.L737L		Atlas-SNP	.											.	SMC1B	215	.	0			c.T2209C						PASS	.	G		3209,411		1426,357,27	72.0	66.0	68.0		2209	4.6	1.0	22	dbSNP_78	68	3896,4216		933,2030,1093	no	coding-synonymous	SMC1B	NM_148674.3		2359,2387,1120	GG,GA,AA		48.0276,11.3536,39.4391		737/1236	45767455	7105,4627	1810	4056	5866	SO:0001819	synonymous_variant	27127	exon14			TTTGTAACTGAGA	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.2209T>C	22.37:g.45767455A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																			A|0.380;G|0.620	0.620	strong		0.289	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
PLIN4	729359	hgsc.bcm.edu	37	19	4512945	4512945	+	Missense_Mutation	SNP	C	C	T	rs75031432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512945C>T	ENST00000301286.3	-	3	984	c.985G>A	c.(985-987)Ggt>Agt	p.G329S		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	329	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						TTCATGGCACCAGTCACCCCA	0.567													C|||	840	0.167732	0.4539	0.1037	5008	,	,		18994	0.0119		0.0934	False		,,,				2504	0.0634				p.G329S		Atlas-SNP	.											PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	0			c.G985A						scavenged	.						39.0	40.0	39.0					19																	4512945		1862	4105	5967	SO:0001583	missense	729359	exon3			TGGCACCAGTCAC	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.985G>A	19.37:g.4512945C>T	ENSP00000301286:p.Gly329Ser	Somatic	386	3	0.00777202		WXS	Illumina HiSeq	Phase_I	266	10	0.037594	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.776204	0.49786	.	.	ENSG00000167676	ENST00000301286	T	0.13901	2.55	4.53	1.21	0.21127	.	0.420915	0.19796	N	0.105865	T	0.13543	0.0328	L	0.46157	1.445	0.80722	P	0.0	D	0.54397	0.966	P	0.45794	0.493	T	0.19353	-1.0308	9	0.87932	D	0	-15.096	7.3812	0.26856	0.0:0.7112:0.0:0.2888	rs56366613	329	Q96Q06	PLIN4_HUMAN	S	329	ENSP00000301286:G329S	ENSP00000301286:G329S	G	-	1	0	PLIN4	4463945	0.091000	0.21658	0.003000	0.11579	0.001000	0.01503	0.810000	0.27183	0.906000	0.36621	0.407000	0.27541	GGT	C|0.826;T|0.174	0.174	strong		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
OR52E4	390081	hgsc.bcm.edu	37	11	5906205	5906205	+	Missense_Mutation	SNP	G	G	A	rs4757987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	286	0	0		WXS	Illumina HiSeq	Phase_I	316	151	0.477848	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	
CYB5R2	51700	hgsc.bcm.edu	37	11	7687715	7687715	+	Missense_Mutation	SNP	T	T	C	rs12801394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7687715T>C	ENST00000533558.1	-	8	1181	c.625A>G	c.(625-627)Aac>Gac	p.N209D	CYB5R2_ENST00000524790.1_Missense_Mutation_p.N209D|CYB5R2_ENST00000528585.1_Intron|CYB5R2_ENST00000299498.6_Missense_Mutation_p.N209D|CYB5R2_ENST00000299497.9_Missense_Mutation_p.N209D			Q6BCY4	NB5R2_HUMAN	cytochrome b5 reductase 2	209			N -> D (in dbSNP:rs12801394). {ECO:0000269|PubMed:10611283, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		oxidation-reduction process (GO:0055114)|sterol biosynthetic process (GO:0016126)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11				Epithelial(150;5.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TACCACAGGTTGAACTGGTCT	0.512											OREG0020724	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3938	0.786342	0.8525	0.6787	5008	,	,		18935	0.8165		0.7634	False		,,,				2504	0.7658				p.N209D		Atlas-SNP	.											.	CYB5R2	23	.	0			c.A625G						PASS	.	C	ASP/ASN	3751,651	278.4+/-274.2	1587,577,37	171.0	147.0	155.0		625	-0.6	0.0	11	dbSNP_121	155	6621,1971	345.5+/-325.8	2542,1537,217	yes	missense	CYB5R2	NM_016229.3	23	4129,2114,254	CC,CT,TT		22.9399,14.7887,20.1785	benign	209/277	7687715	10372,2622	2201	4296	6497	SO:0001583	missense	51700	exon8			ACAGGTTGAACTG	AF169802	CCDS7780.1	11p15.4	2014-08-12			ENSG00000166394	ENSG00000166394	1.6.2.2		24376	protein-coding gene	gene with protein product		608342				10611283	Standard	XM_005252973		Approved		uc001mfm.3	Q6BCY4	OTTHUMG00000165665	ENST00000533558.1:c.625A>G	11.37:g.7687715T>C	ENSP00000437041:p.Asn209Asp	Somatic	149	0	0	643	WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_016229	Q9BVA3|Q9UF68|Q9UHJ0	Missense_Mutation	SNP	ENST00000533558.1	37	CCDS7780.1	1720	0.7875457875457875	420	0.8536585365853658	254	0.7016574585635359	461	0.8059440559440559	585	0.7717678100263852	C	8.160	0.789250	0.16258	0.852113	0.770601	ENSG00000166394	ENST00000524790;ENST00000299498;ENST00000533558;ENST00000299497	D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13	5.79	-0.576	0.11731	Oxidoreductase FAD/NAD(P)-binding (1);	1.013800	0.07867	N	0.967262	T	0.00012	0.0000	N	0.20986	0.625	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45131	-0.9282	9	0.52906	T	0.07	-0.0752	8.1297	0.31020	0.0:0.2108:0.111:0.6782	rs12801394;rs17856046;rs52811226;rs60257764;rs12801394	209	Q6BCY4	NB5R2_HUMAN	D	209	ENSP00000435916:N209D;ENSP00000299498:N209D;ENSP00000437041:N209D;ENSP00000299497:N209D	ENSP00000299497:N209D	N	-	1	0	CYB5R2	7644291	0.414000	0.25408	0.006000	0.13384	0.116000	0.19942	1.336000	0.33850	-0.687000	0.05162	-3.273000	0.00048	AAC	T|0.205;C|0.795	0.795	strong		0.512	CYB5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385679.1	NM_016229	
LILRB2	10288	hgsc.bcm.edu	37	19	54782327	54782327	+	Missense_Mutation	SNP	G	G	C	rs7247025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782327G>C	ENST00000391749.4	-	7	1316	c.1045C>G	c.(1045-1047)Cgg>Ggg	p.R349G	LILRB2_ENST00000391748.1_Missense_Mutation_p.R349G|LILRB2_ENST00000391746.1_Missense_Mutation_p.R349G|LILRB2_ENST00000434421.1_Missense_Mutation_p.R233G|LILRB2_ENST00000314446.5_Missense_Mutation_p.R349G|LILRB2_ENST00000471216.1_5'Flank	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	349	Ig-like C2-type 4.		R -> G (in dbSNP:rs7247025).		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)		TGGAACTGCCGCCATGACTGA	0.562													.|||	735	0.146765	0.4985	0.0432	5008	,	,		17798	0.0288		0.003	False		,,,				2504	0.0143				p.R349G		Atlas-SNP	.											.	LILRB2	94	.	0			c.C1045G						PASS	.	C	GLY/ARG,GLY/ARG	1651,2755	593.4+/-388.0	347,957,899	97.0	98.0	98.0		1045,1045	-4.8	0.0	19	dbSNP_116	98	68,8532	814.4+/-407.0	0,68,4232	no	missense,missense	LILRB2	NM_001080978.2,NM_005874.3	125,125	347,1025,5131	CC,CG,GG		0.7907,37.4716,13.217	benign,benign	349/598,349/599	54782327	1719,11287	2203	4300	6503	SO:0001583	missense	10288	exon7			ACTGCCGCCATGA	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.1045C>G	19.37:g.54782327G>C	ENSP00000375629:p.Arg349Gly	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	332	329	0.990964	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	201	0.09203296703296704	171	0.3475609756097561	11	0.03038674033149171	18	0.03146853146853147	1	0.0013192612137203166	C	0.100	-1.153328	0.01700	0.374716	0.007907	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.02103	4.45;4.45;4.45;4.45;4.45	2.38	-4.76	0.03229	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	2.622570	0.01630	N	0.023492	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.08055	0.003;0.003;0.003	T	0.48479	-0.9032	9	0.22109	T	0.4	.	6.6779	0.23103	0.0:0.5003:0.311:0.1886	rs7247025;rs59173896;rs7247025	349;366;349	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	G	349;349;349;349;233	ENSP00000375628:R349G;ENSP00000319960:R349G;ENSP00000375629:R349G;ENSP00000375626:R349G;ENSP00000410117:R233G	ENSP00000319960:R349G	R	-	1	2	LILRB2	59474139	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.420000	0.00236	-1.984000	0.00985	-1.871000	0.00553	CGG	A|0.000;C|0.121;G|0.878	0.121	strong		0.562	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
APOBEC3B	9582	hgsc.bcm.edu	37	22	39380131	39380131	+	Silent	SNP	C	C	T	rs113972364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39380131C>T	ENST00000333467.3	+	2	114	c.69C>T	c.(67-69)aaC>aaT	p.N23N	APOBEC3B_ENST00000407298.3_Silent_p.N23N|APOBEC3B_ENST00000402182.3_Silent_p.N23N	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	23					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)					ACTTTGAAAACGAACCCATCC	0.522													C|||	118	0.0235623	0.087	0.0043	5008	,	,		17697	0.0		0.0	False		,,,				2504	0.0				p.N23N		Atlas-SNP	.											.	APOBEC3B	32	.	0			c.C69T						PASS	.	C		276,4118		27,222,1948	73.0	76.0	75.0		69	0.2	0.0	22	dbSNP_132	75	3,8517		0,3,4257	no	coding-synonymous	APOBEC3B	NM_004900.3		27,225,6205	TT,TC,CC		0.0352,6.2813,2.1604		23/383	39380131	279,12635	2197	4260	6457	SO:0001819	synonymous_variant	9582	exon2			TGAAAACGAACCC	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.69C>T	22.37:g.39380131C>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	244	96	0.393443	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			C|0.974;T|0.026	0.026	strong		0.522	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
DNAH3	55567	hgsc.bcm.edu	37	16	21051209	21051209	+	Missense_Mutation	SNP	G	G	C	rs330150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:21051209G>C	ENST00000261383.3	-	33	4694	c.4695C>G	c.(4693-4695)atC>atG	p.I1565M	DNAH3_ENST00000415178.1_Missense_Mutation_p.I1565M	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1565	AAA 1. {ECO:0000250}.		I -> M (in dbSNP:rs330150).		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.I1565M(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		AGTAGAGGGAGATTTCTCCAA	0.478													G|||	670	0.133786	0.2247	0.0749	5008	,	,		22218	0.1409		0.1103	False		,,,				2504	0.0695				p.I1565M		Atlas-SNP	.											DNAH3_ENST00000261383,NS,carcinoma,0,2	DNAH3	1142	2	2	Substitution - Missense(2)	stomach(2)	c.C4695G						PASS	.	G	MET/ILE	875,3527	343.3+/-307.6	90,695,1416	138.0	130.0	133.0		4695	2.3	1.0	16	dbSNP_79	133	868,7732	196.9+/-241.7	42,784,3474	yes	missense	DNAH3	NM_017539.1	10	132,1479,4890	CC,CG,GG		10.093,19.8773,13.4056	probably-damaging	1565/4117	21051209	1743,11259	2201	4300	6501	SO:0001583	missense	55567	exon33			GAGGGAGATTTCT	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.4695C>G	16.37:g.21051209G>C	ENSP00000261383:p.Ile1565Met	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	327	0.14972527472527472	130	0.26422764227642276	31	0.0856353591160221	89	0.1555944055944056	77	0.10158311345646438	G	17.38	3.374222	0.61735	0.198773	0.10093	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.57107	0.42;0.42	5.48	2.27	0.28462	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	H	0.95470	3.675	0.09310	P	0.99999932496	D	0.89917	1.0	D	0.97110	1.0	T	0.06917	-1.0800	9	0.87932	D	0	.	5.0246	0.14378	0.2757:0.0:0.511:0.2132	rs330150;rs52802211;rs330150	1565	Q8TD57	DYH3_HUMAN	M	1565	ENSP00000261383:I1565M;ENSP00000394245:I1565M	ENSP00000261383:I1565M	I	-	3	3	DNAH3	20958710	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.457000	0.21875	0.787000	0.33731	0.650000	0.86243	ATC	G|0.853;C|0.146	0.146	strong		0.478	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ZNF844	284391	hgsc.bcm.edu	37	19	12186761	12186761	+	Missense_Mutation	SNP	A	A	G	rs7259845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12186761A>G	ENST00000439326.3	+	4	1001	c.826A>G	c.(826-828)Act>Gct	p.T276A	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	276			T -> A (in dbSNP:rs7259845).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						AAGAACTCACACTGGAGAGAA	0.408													.|||	1455	0.290535	0.73	0.1455	5008	,	,		20627	0.0853		0.161	False		,,,				2504	0.1442				p.T276A		Atlas-SNP	.											.	ZNF844	69	.	0			c.A826G						PASS	.	A	ALA/THR	887,497		287,313,92	42.0	40.0	40.0		826	1.5	0.0	19	dbSNP_116	40	416,2766		25,366,1200	yes	missense	ZNF844	NM_001136501.1	58	312,679,1292	GG,GA,AA		13.0735,35.9104,28.537	benign	276/667	12186761	1303,3263	692	1591	2283	SO:0001583	missense	284391	exon4			ACTCACACTGGAG	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.826A>G	19.37:g.12186761A>G	ENSP00000392024:p.Thr276Ala	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	46	0.638889	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	573	0.2623626373626374	339	0.6890243902439024	53	0.1464088397790055	53	0.09265734265734266	128	0.16886543535620052	A	14.28	2.487242	0.44249	0.640896	0.130735	ENSG00000223547	ENST00000439326;ENST00000541708;ENST00000535505	T	0.26518	1.73	2.5	1.45	0.22620	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.62266	1.93	0.09310	P	0.999999999404092	B	0.32302	0.363	B	0.30316	0.114	T	0.25779	-1.0122	8	0.59425	D	0.04	.	6.394	0.21603	0.8647:0.0:0.1353:0.0	rs7259845;rs52791364;rs59360268;rs7259845	276	Q08AG5	ZN844_HUMAN	A	276;276;251	ENSP00000392024:T276A	ENSP00000392024:T276A	T	+	1	0	ZNF844	12047761	0.076000	0.21285	0.014000	0.15608	0.565000	0.35776	1.389000	0.34453	0.202000	0.20498	0.172000	0.16884	ACT	A|0.715;G|0.285	0.285	strong		0.408	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
ACVR1C	130399	hgsc.bcm.edu	37	2	158390468	158390468	+	Missense_Mutation	SNP	T	T	C	rs7594480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:158390468T>C	ENST00000243349.8	-	9	1804	c.1444A>G	c.(1444-1446)Ata>Gta	p.I482V	ACVR1C_ENST00000409680.3_Missense_Mutation_p.I432V|ACVR1C_ENST00000348328.5_Missense_Mutation_p.I325V|ACVR1C_ENST00000335450.7_Missense_Mutation_p.I402V	NM_001111032.1|NM_145259.2	NP_001104502.1|NP_660302.2			activin A receptor, type IC											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	42						AGTTGAGATATAGTCTTCTTA	0.403													T|||	761	0.151957	0.4357	0.1455	5008	,	,		16872	0.0		0.0686	False		,,,				2504	0.0153				p.I482V		Atlas-SNP	.											.	ACVR1C	85	.	0			c.A1444G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1658,2748	506.2+/-366.3	310,1038,855	97.0	106.0	103.0		1294,1204,973,1444	5.5	0.8	2	dbSNP_116	103	562,8038	153.0+/-207.5	29,504,3767	yes	missense,missense,missense,missense	ACVR1C	NM_001111031.1,NM_001111032.1,NM_001111033.1,NM_145259.2	29,29,29,29	339,1542,4622	CC,CT,TT		6.5349,37.6305,17.069	benign,benign,benign,benign	432/444,402/414,325/337,482/494	158390468	2220,10786	2203	4300	6503	SO:0001583	missense	130399	exon9			GAGATATAGTCTT	BC022530	CCDS2205.1, CCDS46432.1, CCDS46433.1, CCDS46434.1	2q24.2	2008-02-05			ENSG00000123612	ENSG00000123612			18123	protein-coding gene	gene with protein product		608981					Standard	NM_145259		Approved	ALK7, ACVRLK7	uc002tzk.4	Q8NER5	OTTHUMG00000131964	ENST00000243349.8:c.1444A>G	2.37:g.158390468T>C	ENSP00000243349:p.Ile482Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_145259		Missense_Mutation	SNP	ENST00000243349.8	37	CCDS2205.1	307	0.14056776556776557	209	0.4247967479674797	48	0.13259668508287292	0	0.0	50	0.06596306068601583	T	15.05	2.717460	0.48622	0.376305	0.065349	ENSG00000123612	ENST00000243349;ENST00000409680;ENST00000348328;ENST00000335450	D;D;D;D	0.91686	-2.34;-2.23;-2.89;-2.3	5.51	5.51	0.81932	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	D	0.000064	T	0.00012	0.0000	L	0.49126	1.545	0.22975	P	0.99848377	B;B;B	0.23806	0.038;0.091;0.017	B;B;B	0.28465	0.09;0.066;0.05	T	0.01169	-1.1430	9	0.72032	D	0.01	.	15.2629	0.73637	0.0:0.0:0.0:1.0	rs7594480;rs52813590;rs7594480	325;402;482	Q8NER5-2;Q8NER5-3;Q8NER5	.;.;ACV1C_HUMAN	V	482;432;325;402	ENSP00000243349:I482V;ENSP00000387168:I432V;ENSP00000335139:I325V;ENSP00000335178:I402V	ENSP00000243349:I482V	I	-	1	0	ACVR1C	158098714	0.993000	0.37304	0.832000	0.32986	0.996000	0.88848	2.177000	0.42509	2.080000	0.62538	0.482000	0.46254	ATA	T|0.843;C|0.157	0.157	strong		0.403	ACVR1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254924.2	NM_145259	
PARD3B	117583	hgsc.bcm.edu	37	2	206364737	206364737	+	Silent	SNP	T	T	C	rs10197347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:206364737T>C	ENST00000406610.2	+	21	3369	c.3162T>C	c.(3160-3162)tcT>tcC	p.S1054S	PARD3B_ENST00000358768.2_Silent_p.S992S|PARD3B_ENST00000351153.1_Silent_p.S985S|PARD3B_ENST00000349953.3_Silent_p.S953S|PARD3B_ENST00000488622.1_3'UTR	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	1054					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)		CAAGGCCATCTGAGTATGACC	0.438													T|||	2246	0.448482	0.3601	0.5692	5008	,	,		21928	0.4871		0.4115	False		,,,				2504	0.4806				p.S992S		Atlas-SNP	.											.	PARD3B	314	.	0			c.T2976C						PASS	.	T	,,	1436,2416		266,904,756	216.0	198.0	203.0		2955,2976,2859	2.5	1.0	2	dbSNP_119	203	3152,5096		639,1874,1611	yes	coding-synonymous,coding-synonymous,coding-synonymous	PARD3B	NM_057177.6,NM_152526.5,NM_205863.3	,,	905,2778,2367	CC,CT,TT		38.2153,37.2793,37.9174	,,	985/1137,992/1144,953/1105	206364737	4588,7512	1926	4124	6050	SO:0001819	synonymous_variant	117583	exon20			GCCATCTGAGTAT	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.3162T>C	2.37:g.206364737T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_152526	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	37																																																																																				T|0.587;C|0.413	0.413	strong		0.438	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
EXPH5	23086	hgsc.bcm.edu	37	11	108380740	108380740	+	Missense_Mutation	SNP	G	G	C	rs36005552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108380740G>C	ENST00000265843.4	-	6	5604	c.5494C>G	c.(5494-5496)Cga>Gga	p.R1832G	EXPH5_ENST00000443411.1_Missense_Mutation_p.R1644G|EXPH5_ENST00000428840.1_Missense_Mutation_p.R1756G|EXPH5_ENST00000525344.1_Missense_Mutation_p.R1825G	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1832					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AGGGTCAGTCGACTCAGGGCA	0.443													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		20136	0.0		0.0	False		,,,				2504	0.0				p.R1832G		Atlas-SNP	.											.	EXPH5	193	.	0			c.C5494G						PASS	.	G	GLY/ARG	134,4268	96.2+/-134.9	0,134,2067	63.0	63.0	63.0		5494	0.4	0.0	11	dbSNP_126	63	0,8596		0,0,4298	yes	missense	EXPH5	NM_015065.2	125	0,134,6365	CC,CG,GG		0.0,3.0441,1.0309	benign	1832/1990	108380740	134,12864	2201	4298	6499	SO:0001583	missense	23086	exon6			TCAGTCGACTCAG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.5494C>G	11.37:g.108380740G>C	ENSP00000265843:p.Arg1832Gly	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	89	56	0.629214	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	G	8.864	0.947649	0.18356	0.030441	0.0	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956	T;T;T;T	0.03181	4.24;4.17;4.02;4.24	6.17	0.414	0.16406	.	1.706240	0.03093	N	0.160006	T	0.01092	0.0036	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.18263	0.021	T	0.43294	-0.9400	10	0.41790	T	0.15	7.6536	3.311	0.07016	0.1263:0.1752:0.4527:0.2458	rs36005552	1832	Q8NEV8	EXPH5_HUMAN	G	1832;1756;1644;1825;662	ENSP00000265843:R1832G;ENSP00000391966:R1756G;ENSP00000411390:R1644G;ENSP00000432546:R1825G	ENSP00000265843:R1832G	R	-	1	2	EXPH5	107885950	0.000000	0.05858	0.047000	0.18901	0.426000	0.31534	0.086000	0.14935	0.144000	0.18951	0.655000	0.94253	CGA	G|0.990;C|0.010	0.010	strong		0.443	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
TBC1D31	93594	hgsc.bcm.edu	37	8	124154697	124154697	+	Splice_Site	SNP	G	G	T	rs10101626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124154697G>T	ENST00000287380.1	+	19	2925		c.e19+1		TBC1D31_ENST00000309336.3_Intron|TBC1D31_ENST00000522420.1_Splice_Site|TBC1D31_ENST00000378080.2_Intron|TBC1D31_ENST00000327098.5_Intron|TBC1D31_ENST00000521676.1_Splice_Site|TBC1D31_ENST00000518805.1_Splice_Site	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31							centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										AGCCAAGAAGGTAAAAAATAG	0.323													G|||	1026	0.204872	0.2534	0.1614	5008	,	,		16505	0.1825		0.1948	False		,,,				2504	0.2035				.		Atlas-SNP	.											.	WDR67	97	.	0			c.2835+1G>T						PASS	.						36.0	37.0	37.0					8																	124154697		2202	4299	6501	SO:0001630	splice_region_variant	93594	exon19			AAGAAGGTAAAAA	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.2835+1G>T	8.37:g.124154697G>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_145647	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Splice_Site	SNP	ENST00000287380.1	37	CCDS6338.1	458	0.2097069597069597	130	0.26422764227642276	51	0.1408839779005525	128	0.22377622377622378	149	0.19656992084432717	G	11.00	1.509071	0.27036	.	.	ENSG00000156787	ENST00000287380;ENST00000522420;ENST00000521676;ENST00000518805	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8646	0.88792	0.0:0.0:1.0:0.0	rs10101626;rs17375320;rs57669972;rs10101626	.	.	.	.	-1	.	.	.	+	.	.	WDR67	124223878	1.000000	0.71417	0.997000	0.53966	0.092000	0.18411	6.243000	0.72384	2.529000	0.85273	0.471000	0.43371	.	G|0.784;T|0.216	0.216	strong		0.323	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	Intron
ARSF	416	hgsc.bcm.edu	37	X	3028289	3028289	+	Silent	SNP	C	C	T	rs5983011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:3028289C>T	ENST00000381127.1	+	10	1607	c.1386C>T	c.(1384-1386)gaC>gaT	p.D462D	ARSF_ENST00000537104.1_Silent_p.D462D|ARSF_ENST00000359361.2_Silent_p.D462D	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	462					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		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)				TCCCCAAGGACGACAGTGAGT	0.572													c|||	389	0.103046	0.1732	0.1225	3775	,	,		14967	0.0		0.0666	False		,,,				2504	0.0082				p.D462D		Atlas-SNP	.											.	ARSF	97	.	0			c.C1386T						PASS	.	C	,,	796,3039		69,541,117,1022,454	116.0	87.0	97.0		1386,1386,1386	-1.3	0.0	X	dbSNP_114	97	507,6221		16,335,140,2077,1732	no	coding-synonymous,coding-synonymous,coding-synonymous	ARSF	NM_001201538.1,NM_001201539.1,NM_004042.4	,,	85,876,257,3099,2186	TT,TC,T,CC,C		7.5357,20.7562,12.3355	,,	462/591,462/591,462/591	3028289	1303,9260	2203	4300	6503	SO:0001819	synonymous_variant	416	exon10			CAAGGACGACAGT	X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"""Arylsulfatase family"""	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.1386C>T	X.37:g.3028289C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	168	89	0.529762	NM_004042	Q8TCC5	Silent	SNP	ENST00000381127.1	37	CCDS14123.1																																																																																			C|0.874;0|0.003	.	strong		0.572	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1		
CDC6	990	hgsc.bcm.edu	37	17	38457151	38457151	+	Missense_Mutation	SNP	G	G	A	rs13706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38457151G>A	ENST00000209728.4	+	10	1792	c.1321G>A	c.(1321-1323)Gtt>Att	p.V441I	CTD-2267D19.6_ENST00000602403.1_lincRNA	NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	441			V -> I (in dbSNP:rs13706). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						CATCTCAGAAGTTGATGGTAA	0.428													G|||	1402	0.279952	0.5348	0.183	5008	,	,		21220	0.3482		0.1113	False		,,,				2504	0.1074				p.V441I		Atlas-SNP	.											.	CDC6	53	.	0			c.G1321A	GRCh37	CM065057	CDC6	M	rs13706	PASS	.	G	ILE/VAL	2014,2392	561.4+/-380.7	479,1056,668	217.0	194.0	202.0		1321	3.8	1.0	17	dbSNP_52	202	950,7650	208.7+/-250.1	57,836,3407	yes	missense	CDC6	NM_001254.3	29	536,1892,4075	AA,AG,GG		11.0465,45.7104,22.7895	possibly-damaging	441/561	38457151	2964,10042	2203	4300	6503	SO:0001583	missense	990	exon10			TCAGAAGTTGATG	U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"""CDC6 (cell division cycle 6, S. cerevisiae) homolog"", ""CDC6 cell division cycle 6 homolog (S. cerevisiae)"", ""cell division cycle 6 homolog (S. cerevisiae)"""	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.1321G>A	17.37:g.38457151G>A	ENSP00000209728:p.Val441Ile	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	205	202	0.985366	NM_001254	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	37	CCDS11365.1	608	0.2783882783882784	255	0.5182926829268293	62	0.1712707182320442	215	0.3758741258741259	76	0.10026385224274406	G	19.42	3.823558	0.71143	0.457104	0.110465	ENSG00000094804	ENST00000209728	T	0.52983	0.64	5.96	3.82	0.43975	.	0.185081	0.46442	N	0.000289	T	0.00012	0.0000	L	0.54908	1.71	0.24597	P	0.99379435	P	0.44578	0.838	B	0.44224	0.444	T	0.49670	-0.8915	9	0.17369	T	0.5	-11.9661	10.4299	0.44400	0.204:0.0:0.796:0.0	rs13706;rs1048815;rs2230629;rs3188865;rs17852245;rs57349852;rs13706	441	Q99741	CDC6_HUMAN	I	441	ENSP00000209728:V441I	ENSP00000209728:V441I	V	+	1	0	CDC6	35710677	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	4.003000	0.57061	1.539000	0.49286	0.655000	0.94253	GTT	G|0.734;A|0.266	0.266	strong		0.428	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1		
EFCAB11	90141	hgsc.bcm.edu	37	14	90398907	90398907	+	Silent	SNP	G	G	A	rs8778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:90398907G>A	ENST00000316738.7	-	4	310	c.282C>T	c.(280-282)aaC>aaT	p.N94N	EFCAB11_ENST00000267544.9_Silent_p.N31N|EFCAB11_ENST00000556609.1_Silent_p.N46N|EFCAB11_ENST00000556005.1_Silent_p.N70N|EFCAB11_ENST00000555872.1_Silent_p.N70N|RP11-33N16.3_ENST00000555070.1_RNA|EFCAB11_ENST00000538485.2_Silent_p.N94N|EFCAB11_ENST00000550103.2_5'UTR	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	78	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	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	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713821	32713821	+	Silent	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	593	0	0		WXS	Illumina HiSeq	Phase_I	645	24	0.0372093	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	
CROT	54677	hgsc.bcm.edu	37	7	86986863	86986863	+	Intron	SNP	T	T	C	rs75642989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:86986863T>C	ENST00000331536.3	+	4	300				CROT_ENST00000412227.2_Intron|CROT_ENST00000442291.1_Intron|CROT_ENST00000419147.2_Silent_p.D52D	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase						carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	ttgatccagatgctaagagag	0.483													C|||	89	0.0177716	0.0658	0.0029	5008	,	,		19249	0.0		0.0	False		,,,				2504	0.0				p.D52D		Atlas-SNP	.											.	CROT	81	.	0			c.T156C						PASS	.	C	,	61,1323		2,57,633	146.0	124.0	130.0		156,	0.2	0.0	7	dbSNP_132	130	1,3181		0,1,1590	no	coding-synonymous,intron	CROT	NM_001143935.1,NM_021151.3	,	2,58,2223	CC,CT,TT		0.0314,4.4075,1.3579	,	52/641,	86986863	62,4504	692	1591	2283	SO:0001627	intron_variant	54677	exon4			TCCAGATGCTAAG		CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.116-1659T>C	7.37:g.86986863T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_001143935	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Silent	SNP	ENST00000331536.3	37	CCDS5604.1																																																																																			T|0.986;C|0.014	0.014	strong		0.483	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151	
SFXN2	118980	hgsc.bcm.edu	37	10	104486822	104486822	+	Silent	SNP	C	C	T	rs35094483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:104486822C>T	ENST00000369893.5	+	3	407	c.240C>T	c.(238-240)ccC>ccT	p.P80P	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	80					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		CCTTCCACCCCGACACTGGGG	0.597													C|||	166	0.033147	0.121	0.0086	5008	,	,		18582	0.0		0.0	False		,,,				2504	0.0				p.P80P		Atlas-SNP	.											.	SFXN2	40	.	0			c.C240T						PASS	.	C		444,3962	212.2+/-232.1	13,418,1772	84.0	74.0	77.0		240	-5.3	1.0	10	dbSNP_126	77	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SFXN2	NM_178858.4		13,420,6070	TT,TC,CC		0.0233,10.0772,3.4292		80/323	104486822	446,12560	2203	4300	6503	SO:0001819	synonymous_variant	118980	exon3			CCACCCCGACACT	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.240C>T	10.37:g.104486822C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	191	190	0.994764	NM_178858	Q5JSM6	Silent	SNP	ENST00000369893.5	37	CCDS7539.1																																																																																			C|0.969;T|0.031	0.031	strong		0.597	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359	
FAAH	2166	hgsc.bcm.edu	37	1	46874246	46874246	+	Missense_Mutation	SNP	C	C	T	rs77101686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46874246C>T	ENST00000243167.8	+	8	1151	c.1067C>T	c.(1066-1068)gCg>gTg	p.A356V	FAAH_ENST00000493735.1_3'UTR	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	356					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	CTTGAGGCTGCGGGGCACACG	0.617													C|||	42	0.00838658	0.0076	0.0	5008	,	,		20191	0.0159		0.0	False		,,,				2504	0.0164				p.A356V		Atlas-SNP	.											FAAH,colon,carcinoma,-1,1	FAAH	36	1	0			c.C1067T						scavenged	.	C	VAL/ALA	8,4398	15.5+/-35.6	0,8,2195	152.0	156.0	155.0		1067	5.4	1.0	1	dbSNP_131	155	4,8596	3.7+/-12.6	0,4,4296	yes	missense	FAAH	NM_001441.2	64	0,12,6491	TT,TC,CC		0.0465,0.1816,0.0923	probably-damaging	356/580	46874246	12,12994	2203	4300	6503	SO:0001583	missense	2166	exon8			AGGCTGCGGGGCA	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.1067C>T	1.37:g.46874246C>T	ENSP00000243167:p.Ala356Val	Somatic	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	68	43	0.632353	NM_001441	D3DQ19|Q52M86|Q5TDF8	Missense_Mutation	SNP	ENST00000243167.8	37	CCDS535.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	11	0.019230769230769232	0	0.0	C	31	5.097033	0.94197	0.001816	4.65E-4	ENSG00000117480	ENST00000243167;ENST00000396325	T	0.56776	0.44	5.4	5.4	0.78164	Amidase signature domain (2);	0.000000	0.85682	D	0.000000	T	0.65238	0.2672	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.65573	0.936	T	0.79065	-0.1956	10	0.87932	D	0	0.6812	19.1897	0.93660	0.0:1.0:0.0:0.0	.	356	O00519	FAAH1_HUMAN	V	356;63	ENSP00000243167:A356V	ENSP00000243167:A356V	A	+	2	0	FAAH	46646833	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.585000	0.67497	2.548000	0.85928	0.655000	0.94253	GCG	C|0.998;T|0.002	0.002	strong		0.617	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
DCTN1	1639	hgsc.bcm.edu	37	2	74593482	74593482	+	Silent	SNP	G	G	A	rs140986485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74593482G>A	ENST00000361874.3	-	23	2966	c.2649C>T	c.(2647-2649)agC>agT	p.S883S	DCTN1_ENST00000409240.1_Silent_p.S846S|DCTN1_ENST00000495643.1_5'UTR|DCTN1_ENST00000409567.3_Silent_p.S863S|RP11-287D1.3_ENST00000451608.2_5'Flank|DCTN1_ENST00000409438.1_Silent_p.S749S|DCTN1_ENST00000409868.1_Silent_p.S866S|DCTN1_ENST00000394003.3_Silent_p.S876S|DCTN1_ENST00000407639.2_Silent_p.S749S	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	883					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						CATAGGGGCTGCTGGAGGGGG	0.582													G|||	13	0.00259585	0.0098	0.0	5008	,	,		18862	0.0		0.0	False		,,,				2504	0.0				p.S883S		Atlas-SNP	.											.	DCTN1	110	.	0			c.C2649T						PASS	.	G	,,,,,	26,4380	32.6+/-62.9	0,26,2177	50.0	54.0	53.0		2589,2247,2538,2628,2649,2247	5.4	1.0	2	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	,,,,,	0,26,6477	AA,AG,GG		0.0,0.5901,0.1999	,,,,,	863/1254,749/1140,846/1237,876/1272,883/1279,749/1145	74593482	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	1639	exon23			GGGGCTGCTGGAG		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.2649C>T	2.37:g.74593482G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	37	CCDS1939.1																																																																																			G|0.997;A|0.003	0.003	strong		0.582	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
ZNF597	146434	hgsc.bcm.edu	37	16	3486736	3486736	+	Silent	SNP	G	G	A	rs34461484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3486736G>A	ENST00000301744.4	-	4	1198	c.963C>T	c.(961-963)gaC>gaT	p.D321D		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	321					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(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						AGCGTTCAGAGTCCTCGTCGT	0.488													G|||	102	0.0203674	0.0726	0.0072	5008	,	,		20540	0.0		0.001	False		,,,				2504	0.0				p.D321D		Atlas-SNP	.											.	ZNF597	41	.	0			c.C963T						PASS	.	G		239,4155	141.9+/-177.2	4,231,1962	70.0	66.0	67.0		963	-7.5	0.0	16	dbSNP_126	67	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ZNF597	NM_152457.1		4,236,6257	AA,AG,GG		0.0581,5.4392,1.8778		321/425	3486736	244,12750	2197	4300	6497	SO:0001819	synonymous_variant	146434	exon4			TTCAGAGTCCTCG	AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"""Zinc fingers, C2H2-type"", ""-"""	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.963C>T	16.37:g.3486736G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_152457		Silent	SNP	ENST00000301744.4	37	CCDS10505.1																																																																																			G|0.985;A|0.015	0.015	strong		0.488	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457	
OR2T27	403239	hgsc.bcm.edu	37	1	248813473	248813473	+	Missense_Mutation	SNP	A	A	C	rs78776291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813473A>C	ENST00000344889.3	-	1	712	c.713T>G	c.(712-714)gTg>gGg	p.V238G		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCAGGTGGCCACAGCCTTTCC	0.527													A|||	333	0.0664936	0.2375	0.0245	5008	,	,		19295	0.0		0.002	False		,,,				2504	0.0				p.V238G		Atlas-SNP	.											.	OR2T27	52	.	0			c.T713G						PASS	.	A	GLY/VAL	869,3497		137,595,1451	49.0	32.0	38.0		713	2.3	0.6	1	dbSNP_131	38	8,8502		0,8,4247	no	missense	OR2T27	NM_001001824.1	109	137,603,5698	CC,CA,AA		0.094,19.9038,6.8111	possibly-damaging	238/318	248813473	877,11999	2183	4255	6438	SO:0001583	missense	403239	exon1			GTGGCCACAGCCT		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.713T>G	1.37:g.248813473A>C	ENSP00000342008:p.Val238Gly	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	193	108	0.559586	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	37	CCDS31124.1	119	0.05448717948717949	116	0.23577235772357724	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	.	9.994	1.231495	0.22626	0.199038	9.4E-4	ENSG00000187701	ENST00000344889	T	0.00158	8.65	3.42	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.212577	0.23378	N	0.048838	T	0.00012	0.0000	L	0.33339	1.005	0.34364	P	0.308697	P	0.37038	0.579	B	0.43623	0.425	T	0.27400	-1.0075	9	0.87932	D	0	.	7.831	0.29342	0.8936:0.0:0.1064:0.0	.	238	Q8NH04	O2T27_HUMAN	G	238	ENSP00000342008:V238G	ENSP00000342008:V238G	V	-	2	0	OR2T27	246880096	0.031000	0.19500	0.564000	0.28396	0.057000	0.15508	3.181000	0.50903	0.513000	0.28278	-0.548000	0.04221	GTG	A|0.941;C|0.059	0.059	strong		0.527	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
ZNF839	55778	hgsc.bcm.edu	37	14	102807671	102807671	+	Missense_Mutation	SNP	C	C	T	rs9464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102807671C>T	ENST00000558850.1	+	8	1941	c.1591C>T	c.(1591-1593)Cca>Tca	p.P531S	ZNF839_ENST00000420933.2_3'UTR|ZNF839_ENST00000262236.5_Missense_Mutation_p.P533S|AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000559185.1_Missense_Mutation_p.P531S|ZNF839_ENST00000442396.2_Missense_Mutation_p.P647S	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	531			P -> S (in dbSNP:rs9464).				metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TTTTTCCCCTCCAGTAAATGT	0.537													C|||	368	0.0734824	0.1906	0.0403	5008	,	,		18164	0.001		0.0616	False		,,,				2504	0.0256				p.P647S		Atlas-SNP	.											.	ZNF839	41	.	0			c.C1939T						PASS	.	C	SER/PRO	667,3377		54,559,1409	133.0	132.0	132.0		1939	1.5	0.0	14	dbSNP_52	132	465,7903		15,435,3734	yes	missense	ZNF839	NM_018335.3	74	69,994,5143	TT,TC,CC		5.5569,16.4936,9.1202	benign	647/928	102807671	1132,11280	2022	4184	6206	SO:0001583	missense	55778	exon8			TCCCCTCCAGTAA	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.1591C>T	14.37:g.102807671C>T	ENSP00000453363:p.Pro531Ser	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	257	113	0.439689	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Missense_Mutation	SNP	ENST00000558850.1	37	CCDS58336.1	141	0.06456043956043957	83	0.16869918699186992	17	0.04696132596685083	0	0.0	41	0.05408970976253298	C	8.132	0.783314	0.16189	0.164936	0.055569	ENSG00000022976	ENST00000442396;ENST00000262236;ENST00000398436;ENST00000420933	T;T	0.17370	2.28;2.33	4.56	1.54	0.23209	.	1.160120	0.06378	N	0.714782	T	0.00039	0.0001	N	0.19112	0.55	0.09310	N	1	B;B;B	0.33103	0.397;0.187;0.187	B;B;B	0.28991	0.097;0.058;0.058	T	0.38243	-0.9670	10	0.15499	T	0.54	.	13.5885	0.61946	0.0:0.5279:0.4721:0.0	rs9464;rs3209420;rs52826173;rs59898673;rs9464	647;533;531	A8K0R7-5;A8K0R7-2;A8K0R7	.;.;ZN839_HUMAN	S	647;533;199;65	ENSP00000399863:P647S;ENSP00000262236:P533S	ENSP00000262236:P533S	P	+	1	0	ZNF839	101877424	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.167000	0.16602	0.074000	0.16767	0.514000	0.50259	CCA	T|0.080;G|0.001	0.080	strong		0.537	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
AARS2	57505	hgsc.bcm.edu	37	6	44279824	44279824	+	Silent	SNP	C	C	T	rs75506489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44279824C>T	ENST00000244571.4	-	2	422	c.420G>A	c.(418-420)ggG>ggA	p.G140G	RP11-444E17.6_ENST00000505802.1_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AATATTCACCCCCAAAGGCCC	0.483													C|||	108	0.0215655	0.0809	0.0014	5008	,	,		21967	0.0		0.0	False		,,,				2504	0.0				p.G140G		Atlas-SNP	.											.	AARS2	77	.	0			c.G420A						PASS	.	C		220,4186	132.5+/-169.0	3,214,1986	177.0	170.0	172.0		420	1.7	1.0	6	dbSNP_132	172	1,8599		0,1,4299	no	coding-synonymous	AARS2	NM_020745.2		3,215,6285	TT,TC,CC		0.0116,4.9932,1.6992		140/986	44279824	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	57505	exon2			TTCACCCCCAAAG	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	21022	protein-coding gene	gene with protein product	"""alanine tRNA ligase 2, mitochondrial"""	612035	"""alanyl-tRNA synthetase like"", ""alanyl-tRNA synthetase 2, mitochondrial (putative)"""	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.420G>A	6.37:g.44279824C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	137	53	0.386861	NM_020745		Silent	SNP	ENST00000244571.4	37	CCDS34464.1																																																																																			C|0.980;T|0.020	0.020	strong		0.483	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745	
DDX58	23586	hgsc.bcm.edu	37	9	32492529	32492529	+	Missense_Mutation	SNP	G	G	A	rs55789327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:32492529G>A	ENST00000379883.2	-	4	588	c.431C>T	c.(430-432)tCt>tTt	p.S144F	DDX58_ENST00000545044.1_Intron|DDX58_ENST00000379868.1_Intron|DDX58_ENST00000379882.1_Missense_Mutation_p.S99F|DDX58_ENST00000542096.1_Missense_Mutation_p.S73F	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	144	CARD 2.				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)		CCCCTTAGTAGAGCAAATCTA	0.373													G|||	239	0.0477236	0.1104	0.0072	5008	,	,		21117	0.0407		0.0	False		,,,				2504	0.0481				p.S144F		Atlas-SNP	.											.	DDX58	82	.	0			c.C431T						PASS	.	G	PHE/SER	349,4057	179.4+/-207.9	15,319,1869	120.0	115.0	117.0		431	-2.0	0.0	9	dbSNP_129	117	6,8594	5.0+/-18.6	0,6,4294	yes	missense	DDX58	NM_014314.3	155	15,325,6163	AA,AG,GG		0.0698,7.921,2.7295	benign	144/926	32492529	355,12651	2203	4300	6503	SO:0001583	missense	23586	exon4			TTAGTAGAGCAAA	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.431C>T	9.37:g.32492529G>A	ENSP00000369213:p.Ser144Phe	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	203	108	0.53202	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	82	0.037545787545787544	54	0.10975609756097561	4	0.011049723756906077	24	0.04195804195804196	0	0.0	G	8.541	0.873187	0.17322	0.07921	6.98E-4	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000542096;ENST00000542960	T;T;T	0.35789	1.29;1.29;1.29	5.22	-2.04	0.07343	.	1.364960	0.05002	N	0.469210	T	0.00384	0.0012	N	0.20685	0.6	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.002	B;B;B	0.09377	0.004;0.002;0.002	T	0.21109	-1.0255	10	0.56958	D	0.05	0.2274	1.0358	0.01548	0.407:0.1539:0.2819:0.1572	rs55789327	99;73;144	O95786-2;B3KWW1;O95786	.;.;DDX58_HUMAN	F	99;144;73;144	ENSP00000369212:S99F;ENSP00000369213:S144F;ENSP00000442160:S73F	ENSP00000369212:S99F	S	-	2	0	DDX58	32482529	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.367000	0.07553	-0.191000	0.10448	-0.157000	0.13467	TCT	G|0.972;A|0.028	0.028	strong		0.373	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
HECTD1	25831	hgsc.bcm.edu	37	14	31578762	31578762	+	Silent	SNP	C	C	T	rs17097735	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:31578762C>T	ENST00000399332.1	-	36	6809	c.6321G>A	c.(6319-6321)gaG>gaA	p.E2107E	HECTD1_ENST00000553700.1_Silent_p.E2107E	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2107					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)		TTCTCGTTCGCTCCACAGTGG	0.458													T|||	1463	0.292133	0.5038	0.1585	5008	,	,		17990	0.2897		0.1064	False		,,,				2504	0.2945				p.E2107E		Atlas-SNP	.											.	HECTD1	159	.	0			c.G6321A						PASS	.	T		1657,2387		359,939,724	90.0	90.0	90.0		6321	3.2	1.0	14	dbSNP_123	90	1068,7304		59,950,3177	no	coding-synonymous	HECTD1	NM_015382.2		418,1889,3901	TT,TC,CC		12.7568,40.9743,21.9475		2107/2611	31578762	2725,9691	2022	4186	6208	SO:0001819	synonymous_variant	25831	exon36			CGTTCGCTCCACA	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.6321G>A	14.37:g.31578762C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	155	67	0.432258	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1	535	0.24496336996336995	235	0.47764227642276424	59	0.16298342541436464	167	0.291958041958042	74	0.09762532981530343	T	9.054	0.992889	0.18966	0.409743	0.127568	ENSG00000092148	ENST00000554882	.	.	.	5.56	3.24	0.37175	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48269	-0.9050	3	.	.	.	-14.6745	8.8967	0.35470	0.0:0.3664:0.0:0.6335	rs17097735;rs17097735	.	.	.	N	473	.	.	S	-	2	0	HECTD1	30648513	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.082000	0.30803	0.103000	0.17682	-0.550000	0.04213	AGC	C|0.750;T|0.250	0.250	strong		0.458	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
PLCL2	23228	hgsc.bcm.edu	37	3	17053499	17053499	+	Silent	SNP	A	A	G	rs4602367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:17053499A>G	ENST00000418129.2	+	2	2748	c.2283A>G	c.(2281-2283)ggA>ggG	p.G761G	PLCL2_ENST00000432376.1_Silent_p.G761G|PLCL2_ENST00000396755.2_Silent_p.G761G	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	887	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						GAGGAGGAGGAAAGCCTCATA	0.478													G|||	3116	0.622204	0.674	0.5821	5008	,	,		17772	0.626		0.5338	False		,,,				2504	0.6677				p.G761G		Atlas-SNP	.											.	PLCL2	145	.	0			c.A2283G						PASS	.	G	,	2794,1612	496.5+/-363.6	866,1062,275	96.0	101.0	99.0		2665,2283	3.9	1.0	3	dbSNP_111	99	4537,4063	557.6+/-387.1	1208,2121,971	yes	coding-synonymous,coding-synonymous	PLCL2	NM_001144382.1,NM_015184.5	,	2074,3183,1246	GG,GA,AA		47.2442,36.5865,43.6337	,	887/1128,761/1002	17053499	7331,5675	2203	4300	6503	SO:0001819	synonymous_variant	23228	exon2			AGGAGGAAAGCCT	AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"""phospholipase C, epsilon 2"""	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.2283A>G	3.37:g.17053499A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	137	73	0.532847	NM_015184	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Silent	SNP	ENST00000418129.2	37	CCDS33713.1	1266	0.5796703296703297	330	0.6707317073170732	182	0.5027624309392266	351	0.6136363636363636	403	0.5316622691292876	G	9.466	1.094255	0.20471	0.634135	0.527558	ENSG00000154822	ENST00000419842	.	.	.	5.74	3.92	0.45320	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.43048	-0.9415	3	.	.	.	.	7.7303	0.28783	0.1332:0.2531:0.6137:0.0	rs4602367;rs58093973;rs4602367	.	.	.	G	505	.	.	E	+	2	0	PLCL2	17028503	0.997000	0.39634	1.000000	0.80357	0.967000	0.64934	0.418000	0.21230	0.352000	0.24053	-0.320000	0.08662	GAA	A|0.441;G|0.559	0.559	strong		0.478	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3		
EAF2	55840	hgsc.bcm.edu	37	3	121563355	121563355	+	Silent	SNP	T	T	C	rs9884018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121563355T>C	ENST00000273668.2	+	2	233	c.162T>C	c.(160-162)ggT>ggC	p.G54G	EAF2_ENST00000451944.2_Silent_p.G54G	NM_018456.4	NP_060926.2	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	54	Necessary for interaction with ELL.				apoptotic process (GO:0006915)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	ELL-EAF complex (GO:0032783)|transcription elongation factor complex (GO:0008023)	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)	p.G54G(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)	9				GBM - Glioblastoma multiforme(114;0.0972)		TTGAGGTTGGTGAAGGTGAAC	0.323													T|||	1233	0.246206	0.1339	0.1455	5008	,	,		16668	0.6161		0.1382	False		,,,				2504	0.1994				p.G54G	Esophageal Squamous(194;1942 2097 24663 29345 31866)	Atlas-SNP	.											EAF2,NS,carcinoma,0,1	EAF2	26	1	1	Substitution - coding silent(1)	prostate(1)	c.T162C						PASS	.	T		715,3691	299.3+/-285.7	70,575,1558	125.0	129.0	128.0		162	3.3	1.0	3	dbSNP_119	128	1184,7416	241.5+/-271.8	85,1014,3201	no	coding-synonymous	EAF2	NM_018456.4		155,1589,4759	CC,CT,TT		13.7674,16.2279,14.601		54/261	121563355	1899,11107	2203	4300	6503	SO:0001819	synonymous_variant	55840	exon2			GGTTGGTGAAGGT	AF517829	CCDS3006.1	3q21.1	2007-08-01			ENSG00000145088	ENSG00000145088			23115	protein-coding gene	gene with protein product		607659				12446457, 12907652	Standard	NM_018456		Approved	BM040, TRAITS, U19	uc003een.3	Q96CJ1	OTTHUMG00000159424	ENST00000273668.2:c.162T>C	3.37:g.121563355T>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	209	111	0.5311	NM_018456	Q9NZ82	Silent	SNP	ENST00000273668.2	37	CCDS3006.1																																																																																			T|0.799;C|0.201	0.201	strong		0.323	EAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355247.1	NM_018456	
RFC1	5981	hgsc.bcm.edu	37	4	39306504	39306504	+	Silent	SNP	C	C	G	rs2066792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39306504C>G	ENST00000381897.1	-	15	2176	c.2043G>C	c.(2041-2043)cgG>cgC	p.R681R	RFC1_ENST00000349703.2_Silent_p.R680R	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	681					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						TGCTCTTACTCCGGGTGTCAC	0.433													C|||	397	0.0792732	0.2821	0.0346	5008	,	,		17846	0.0		0.0	False		,,,				2504	0.0				p.R681R	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.G2043C						PASS	.	C	,	1058,3348	387.9+/-326.7	128,802,1273	261.0	268.0	266.0		2043,2040	1.7	1.0	4	dbSNP_94	266	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,coding-synonymous	RFC1	NM_001204747.1,NM_002913.4	,	128,807,5568	GG,GC,CC		0.0581,24.0127,8.1732	,	681/1149,680/1148	39306504	1063,11943	2203	4300	6503	SO:0001819	synonymous_variant	5981	exon15			CTTACTCCGGGTG	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"""ATPases / AAA-type"""	9969	protein-coding gene	gene with protein product		102579	"""replication factor C (activator 1) 1 (145kD)"""			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.2043G>C	4.37:g.39306504C>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	161	77	0.478261	NM_001204747	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	ENST00000381897.1	37	CCDS56329.1																																																																																			C|0.922;G|0.078	0.078	strong		0.433	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913	
ZNF285	26974	hgsc.bcm.edu	37	19	44890841	44890841	+	Silent	SNP	G	G	A	rs59953894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44890841G>A	ENST00000330997.4	-	4	1630	c.1566C>T	c.(1564-1566)agC>agT	p.S522S	ZNF285_ENST00000544719.2_Silent_p.S522S|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000591679.1_Silent_p.S529S	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	522					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						CTGAATTCCGGCTGAAGCCTT	0.418													g|||	228	0.0455272	0.1505	0.0346	5008	,	,		22939	0.001		0.003	False		,,,				2504	0.001				p.S522S		Atlas-SNP	.											.	ZNF285	86	.	0			c.C1566T						PASS	.	G		537,3869	238.7+/-250.0	28,481,1694	92.0	93.0	93.0		1566	0.0	0.1	19	dbSNP_129	93	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous	ZNF285	NM_152354.3		28,497,5978	AA,AG,GG		0.186,12.1879,4.2519		522/591	44890841	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	26974	exon4			ATTCCGGCTGAAG	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.1566C>T	19.37:g.44890841G>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	201	84	0.41791	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Silent	SNP	ENST00000330997.4	37	CCDS12638.1																																																																																			G|0.962;A|0.038	0.038	strong		0.418	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
C9orf78	51759	hgsc.bcm.edu	37	9	132591509	132591509	+	Silent	SNP	A	A	G	rs3818553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132591509A>G	ENST00000372447.3	-	8	806	c.753T>C	c.(751-753)ggT>ggC	p.G251G	C9orf78_ENST00000461762.1_5'UTR	NM_016520.2	NP_057604.1	Q9NZ63	CI078_HUMAN	chromosome 9 open reading frame 78	251						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.G251G(1)		kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)	13		Ovarian(14;0.00556)				TCTCCGTGTCACCTACTCTCA	0.597													G|||	1190	0.23762	0.2194	0.2147	5008	,	,		17171	0.2143		0.2734	False		,,,				2504	0.2658				p.G251G		Atlas-SNP	.											C9orf78,NS,carcinoma,0,1	C9orf78	26	1	1	Substitution - coding silent(1)	stomach(1)	c.T753C						PASS	.	G		995,3411	730.4+/-410.2	109,777,1317	62.0	60.0	61.0		753	-11.9	0.2	9	dbSNP_107	61	2145,6455	714.0+/-406.0	276,1593,2431	no	coding-synonymous	C9orf78	NM_016520.2		385,2370,3748	GG,GA,AA		24.9419,22.5828,24.1427		251/290	132591509	3140,9866	2203	4300	6503	SO:0001819	synonymous_variant	51759	exon8			CGTGTCACCTACT	BC017570	CCDS6931.1	9q34.2	2012-03-16			ENSG00000136819	ENSG00000136819			24932	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 59"""					11042152, 12097419	Standard	NM_016520		Approved	HSPC220, HCA59	uc004byp.3	Q9NZ63	OTTHUMG00000020796	ENST00000372447.3:c.753T>C	9.37:g.132591509A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	122	44	0.360656	NM_016520	B3KPX8|Q8WVU6|Q9NT39	Silent	SNP	ENST00000372447.3	37	CCDS6931.1	516	0.23626373626373626	95	0.19308943089430894	82	0.2265193370165746	127	0.22202797202797203	212	0.2796833773087071	G	9.641	1.139016	0.21205	0.225828	0.249419	ENSG00000136819	ENST00000435276	.	.	.	5.95	-11.9	0.00025	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999997752	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.5548	0.22454	0.2478:0.2074:0.465:0.0798	rs3818553;rs3818553	.	.	.	R	176	.	.	X	-	1	0	C9orf78	131631330	0.000000	0.05858	0.217000	0.23759	0.854000	0.48673	-2.932000	0.00688	-2.722000	0.00388	-1.140000	0.01884	TGA	A|0.766;G|0.234	0.234	strong		0.597	C9orf78-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054625.1	NM_016520	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48517538	48517538	+	Missense_Mutation	SNP	G	G	A	rs62129078|rs369872763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48517538G>A	ENST00000339841.2	+	3	359	c.181G>A	c.(181-183)Ggc>Agc	p.G61S	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	61	Fibronectin type-II 1. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		CGTGTACAACGGCCAGTGGAA	0.488													g|||	750	0.14976	0.1831	0.1225	5008	,	,		16645	0.0724		0.1531	False		,,,				2504	0.2004				p.G61S		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.G181A						PASS	.	G	SER/GLY	794,3612	319.3+/-296.1	74,646,1483	156.0	135.0	142.0		181	1.1	0.0	19	dbSNP_129	142	1284,7316	254.7+/-279.9	87,1110,3103	yes	missense	ELSPBP1	NM_022142.4	56	161,1756,4586	AA,AG,GG		14.9302,18.0209,15.9772	possibly-damaging	61/224	48517538	2078,10928	2203	4300	6503	SO:0001583	missense	64100	exon3			TACAACGGCCAGT	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.181G>A	19.37:g.48517538G>A	ENSP00000340660:p.Gly61Ser	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	315	0.14423076923076922	98	0.1991869918699187	58	0.16022099447513813	47	0.08216783216783216	112	0.14775725593667546	G	11.26	1.587673	0.28268	0.180209	0.149302	ENSG00000169393	ENST00000339841	T	0.52983	0.64	3.27	1.14	0.20703	Fibronectin, type II, collagen-binding (4);Kringle-like fold (2);	0.734607	0.11192	N	0.589780	T	0.00039	0.0001	M	0.71920	2.185	0.80722	P	0.0	P	0.37864	0.61	B	0.39617	0.305	T	0.07849	-1.0751	9	0.18276	T	0.48	.	5.4873	0.16757	0.2546:0.0:0.7454:0.0	rs62129078	61	Q96BH3	ESPB1_HUMAN	S	61	ENSP00000340660:G61S	ENSP00000340660:G61S	G	+	1	0	ELSPBP1	53209350	0.005000	0.15991	0.001000	0.08648	0.009000	0.06853	0.606000	0.24194	0.397000	0.25310	0.544000	0.68410	GGC	G|0.845;A|0.155	0.155	strong		0.488	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
PCDHB14	56122	hgsc.bcm.edu	37	5	140603794	140603794	+	Silent	SNP	C	C	T	rs59600730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140603794C>T	ENST00000239449.4	+	1	717	c.717C>T	c.(715-717)gcC>gcT	p.A239A	PCDHB14_ENST00000515856.2_Silent_p.A86A	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	239	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)			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)			ATGATAATGCCCCTGAGTTTC	0.517													t|||	132	0.0263578	0.0946	0.0086	5008	,	,		16922	0.0		0.001	False		,,,				2504	0.0				p.A239A	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C717T						PASS	.	T		304,4102		8,288,1907	70.0	72.0	71.0		717	-1.6	1.0	5	dbSNP_129	71	3,8597		0,3,4297	no	coding-synonymous	PCDHB14	NM_018934.2		8,291,6204	TT,TC,CC		0.0349,6.8997,2.3604		239/799	140603794	307,12699	2203	4300	6503	SO:0001819	synonymous_variant	56122	exon1			TAATGCCCCTGAG	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.717C>T	5.37:g.140603794C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	74	25	0.337838	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			C|0.977;T|0.023	0.023	strong		0.517	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
MX1	4599	hgsc.bcm.edu	37	21	42821113	42821113	+	Silent	SNP	T	T	C	rs2070229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:42821113T>C	ENST00000398600.2	+	16	2348	c.1323T>C	c.(1321-1323)cgT>cgC	p.R441R	MX1_ENST00000398598.3_Silent_p.R441R|MX1_ENST00000288383.6_Silent_p.R418R|MX1_ENST00000455164.2_Silent_p.R441R	NM_001144925.1	NP_001138397.1	P20591	MX1_HUMAN	MX dynamin-like GTPase 1	441	Middle domain.|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)				ATCAGTATCGTGGTAGAGAGC	0.373													T|||	1691	0.33766	0.5567	0.2608	5008	,	,		16436	0.2381		0.2952	False		,,,				2504	0.2423				p.R441R		Atlas-SNP	.											MX1,NS,carcinoma,+1,1	MX1	58	1	0			c.T1323C						PASS	.	T	,,	2256,2150	591.5+/-387.6	581,1094,528	74.0	84.0	81.0		1323,1323,1323	-4.5	0.9	21	dbSNP_96	81	2582,6018	418.7+/-352.8	376,1830,2094	no	coding-synonymous,coding-synonymous,coding-synonymous	MX1	NM_001144925.1,NM_001178046.1,NM_002462.3	,,	957,2924,2622	CC,CT,TT		30.0233,48.7971,37.1982	,,	441/663,441/663,441/663	42821113	4838,8168	2203	4300	6503	SO:0001819	synonymous_variant	4599	exon16			GTATCGTGGTAGA		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.1323T>C	21.37:g.42821113T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001144925	B2RDA5|B3KU10|C9IYV7|C9J8D6|C9JN19|C9JN88|C9JUL1|C9JZS6|D3DSI8|Q86YP5|Q96CI3	Silent	SNP	ENST00000398600.2	37	CCDS13673.1																																																																																			T|0.624;C|0.376	0.376	strong		0.373	MX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195161.2		
CCDC144A	9720	hgsc.bcm.edu	37	17	16664991	16664991	+	Missense_Mutation	SNP	G	G	A	rs55685346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16664991G>A	ENST00000360524.8	+	13	3701	c.3625G>A	c.(3625-3627)Gag>Aag	p.E1209K	RP11-219A15.1_ENST00000448331.3_Missense_Mutation_p.E1209K|CCDC144A_ENST00000443444.2_Missense_Mutation_p.E1209K|CCDC144A_ENST00000456009.1_Missense_Mutation_p.E975K|CCDC144A_ENST00000399273.1_Missense_Mutation_p.E1209K	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	1209								p.E1209K(1)									AGCAAGGAAGGAGATAGAAGA	0.333													G|||	1235	0.246605	0.3918	0.1628	5008	,	,		22102	0.2103		0.0765	False		,,,				2504	0.3221				p.E1209K		Atlas-SNP	.											CCDC144B,NS,carcinoma,0,1	CCDC144A	53	1	1	Substitution - Missense(1)	prostate(1)	c.G3625A						PASS	.	G	LYS/GLU	1182,2446		164,854,796	45.0	60.0	55.0		3625	2.1	0.0	17	dbSNP_134	55	507,7633		9,489,3572	no	missense	CCDC144A	NM_014695.1	56	173,1343,4368	AA,AG,GG		6.2285,32.5799,14.3525	benign	1209/1428	16664991	1689,10079	1814	4070	5884	SO:0001583	missense	9720	exon13			AGGAAGGAGATAG	BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.3625G>A	17.37:g.16664991G>A	ENSP00000353717:p.Glu1209Lys	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	445	117	0.262921	NM_014695	O60311|Q6ZU57	Missense_Mutation	SNP	ENST00000360524.8	37	CCDS45621.1	384	0.17582417582417584	183	0.3719512195121951	57	0.1574585635359116	98	0.17132867132867133	46	0.06068601583113457	.	2.937	-0.219717	0.06061	0.325799	0.062285	ENSG00000170160	ENST00000399273;ENST00000443444;ENST00000360524;ENST00000456009	T;T;T;T	0.03635	3.86;3.86;3.86;3.94	2.1	2.1	0.27182	.	.	.	.	.	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	P;B	0.43352	0.804;0.018	B;B	0.40066	0.318;0.006	T	0.45775	-0.9238	8	0.15499	T	0.54	.	9.8677	0.41154	0.0:0.0:1.0:0.0	rs3869489;rs4003975;rs4996825;rs3869489	975;1209	A2RUR9-3;A2RUR9	.;C144A_HUMAN	K	1209;1209;1209;975	ENSP00000382215:E1209K;ENSP00000439262:E1209K;ENSP00000353717:E1209K;ENSP00000394201:E975K	ENSP00000353717:E1209K	E	+	1	0	CCDC144A	16605716	0.997000	0.39634	0.003000	0.11579	0.003000	0.03518	2.952000	0.49097	1.160000	0.42584	0.184000	0.17185	GAG	.	.	weak		0.333	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1		
PLOD2	5352	hgsc.bcm.edu	37	3	145794607	145794607	+	Missense_Mutation	SNP	A	A	G	rs115199093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:145794607A>G	ENST00000360060.3	-	14	1753	c.1576T>C	c.(1576-1578)Tat>Cat	p.Y526H	PLOD2_ENST00000282903.5_Missense_Mutation_p.Y547H|PLOD2_ENST00000461497.1_Missense_Mutation_p.Y207H|PLOD2_ENST00000494950.1_Missense_Mutation_p.Y492H|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	526					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|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)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	TCATTGTTATAATGGGAAGTA	0.299													A|||	8	0.00159744	0.0053	0.0014	5008	,	,		15142	0.0		0.0	False		,,,				2504	0.0				p.Y547H		Atlas-SNP	.											.	PLOD2	81	.	0			c.T1639C						PASS	.	A	HIS/TYR,HIS/TYR	26,4380	32.6+/-62.9	0,26,2177	90.0	98.0	96.0		1576,1639	3.7	1.0	3	dbSNP_132	96	1,8573	1.2+/-3.3	0,1,4286	yes	missense,missense	PLOD2	NM_000935.2,NM_182943.2	83,83	0,27,6463	GG,GA,AA		0.0117,0.5901,0.208	benign,benign	526/738,547/759	145794607	27,12953	2203	4287	6490	SO:0001583	missense	5352	exon15			TGTTATAATGGGA	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"""lysyl hydroxlase 2"""	601865	"""procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"""			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.1576T>C	3.37:g.145794607A>G	ENSP00000353170:p.Tyr526His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	156	78	0.5	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	37	CCDS3131.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	17.15	3.315084	0.60524	0.005901	1.17E-4	ENSG00000152952	ENST00000461497;ENST00000282903;ENST00000360060;ENST00000494950	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	5.12	3.72	0.42706	.	0.178784	0.50627	D	0.000101	T	0.80834	0.4699	L	0.51422	1.61	0.45183	D	0.99819	P;P;P;P	0.47545	0.865;0.773;0.738;0.897	P;P;P;P	0.52109	0.628;0.492;0.69;0.497	T	0.79610	-0.1732	10	0.42905	T	0.14	-10.2013	8.8487	0.35186	0.8839:0.0:0.1161:0.0	.	492;526;547;207	E7ETU9;O00469;O00469-2;B3KWS3	.;PLOD2_HUMAN;.;.	H	207;547;526;492	ENSP00000419354:Y207H;ENSP00000282903:Y547H;ENSP00000353170:Y526H;ENSP00000420094:Y492H	ENSP00000282903:Y547H	Y	-	1	0	PLOD2	147277297	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	3.164000	0.50770	0.604000	0.29930	0.529000	0.55759	TAT	A|0.998;G|0.002	0.002	strong		0.299	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417768	105417768	+	Silent	SNP	C	C	A	rs2396458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417768C>A	ENST00000333244.5	-	7	4139	c.4020G>T	c.(4018-4020)gtG>gtT	p.V1340V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1340						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)			CTGGGGCAGACACCCCGAACG	0.612													.|||	80	0.0159744	0.0605	0.0	5008	,	,		13723	0.0		0.0	False		,,,				2504	0.0				p.V1340V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G4020T						PASS	.	C		912,2740		433,46,1347	129.0	120.0	124.0		4020	-8.3	0.0	14	dbSNP_100	124	227,6321		100,27,3147	no	coding-synonymous	AHNAK2	NM_138420.2		533,73,4494	AA,AC,CC		3.4667,24.9726,11.1667		1340/5796	105417768	1139,9061	1826	3274	5100	SO:0001819	synonymous_variant	113146	exon7			GGCAGACACCCCG	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.4020G>T	14.37:g.105417768C>A		Somatic	383	0	0		WXS	Illumina HiSeq	Phase_I	256	255	0.996094	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.809;A|0.191	0.191	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MUC4	4585	hgsc.bcm.edu	37	3	195508385	195508385	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508385C>G	ENST00000463781.3	-	2	10525	c.10066G>C	c.(10066-10068)Ggt>Cgt	p.G3356R	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G3356R	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)		GTGGCGTGACCTGTGGATACT	0.597																																					p.G3356R		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G10066C						PASS	.						39.0	30.0	33.0					3																	195508385		690	1584	2274	SO:0001583	missense	4585	exon2			CGTGACCTGTGGA	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.10066G>C	3.37:g.195508385C>G	ENSP00000417498:p.Gly3356Arg	Somatic	413	0	0		WXS	Illumina HiSeq	Phase_I	352	26	0.0738636	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	5.357	0.251158	0.10130	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.49720	0.77;0.87	1.03	1.03	0.20045	.	.	.	.	.	T	0.22513	0.0543	N	0.19112	0.55	0.09310	N	1	P	0.50156	0.932	B	0.34824	0.19	T	0.10200	-1.0640	8	.	.	.	.	3.5123	0.07713	0.0:0.6981:0.0:0.3019	.	3228	E7ESK3	.	R	3356	ENSP00000417498:G3356R;ENSP00000420243:G3356R	.	G	-	1	0	MUC4	196993164	0.000000	0.05858	0.003000	0.11579	0.018000	0.09664	-1.956000	0.01522	0.494000	0.27859	0.089000	0.15464	GGT	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PALLD	23022	hgsc.bcm.edu	37	4	169433444	169433444	+	Silent	SNP	C	C	T	rs72695199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169433444C>T	ENST00000505667.1	+	2	962	c.789C>T	c.(787-789)agC>agT	p.S263S	PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000333488.4_Silent_p.S140S|PALLD_ENST00000261509.6_Silent_p.S263S			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	115	0	0		WXS	Illumina HiSeq	Phase_I	125	77	0.616	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	
FLG	2312	hgsc.bcm.edu	37	1	152285541	152285541	+	Silent	SNP	T	T	C	rs116417983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152285541T>C	ENST00000368799.1	-	3	1856	c.1821A>G	c.(1819-1821)caA>caG	p.Q607Q	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	607	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)			GCCCCGATGATTGTCCCTGGC	0.567									Ichthyosis				T|||	94	0.01877	0.0688	0.0043	5008	,	,		18467	0.0		0.0	False		,,,				2504	0.0				p.Q607Q		Atlas-SNP	.											.	FLG	900	.	0			c.A1821G						PASS	.	T		186,4220	120.0+/-157.7	5,176,2022	287.0	283.0	284.0		1821	-1.6	0.0	1	dbSNP_132	284	0,8600		0,0,4300	no	coding-synonymous	FLG	NM_002016.1		5,176,6322	CC,CT,TT		0.0,4.2215,1.4301		607/4062	152285541	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGATGATTGTCCC	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.1821A>G	1.37:g.152285541T>C		Somatic	535	0	0		WXS	Illumina HiSeq	Phase_I	542	253	0.46679	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			T|0.986;C|0.014	0.014	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CAPN6	827	hgsc.bcm.edu	37	X	110491865	110491865	+	Silent	SNP	G	G	A	rs17879776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:110491865G>A	ENST00000324068.1	-	10	1583	c.1416C>T	c.(1414-1416)acC>acT	p.T472T	CAPN6_ENST00000541758.1_Silent_p.T217T	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	472	Domain III.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						GCTGGAACATGGTTGGGACAA	0.522													G|||	24	0.00635762	0.0174	0.0014	3775	,	,		13145	0.0		0.0	False		,,,				2504	0.0				p.T472T		Atlas-SNP	.											.	CAPN6	120	.	0			c.C1416T						PASS	.	G		91,3744		1,78,11,1553,560	105.0	87.0	93.0		1416	4.2	1.0	X	dbSNP_124	93	0,6728		0,0,0,2428,1872	no	coding-synonymous	CAPN6	NM_014289.3		1,78,11,3981,2432	AA,AG,A,GG,G		0.0,2.3729,0.8615		472/642	110491865	91,10472	2203	4300	6503	SO:0001819	synonymous_variant	827	exon10			GAACATGGTTGGG	AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.1416C>T	X.37:g.110491865G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	141	50	0.35461	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Silent	SNP	ENST00000324068.1	37	CCDS14555.1																																																																																			G|0.991;A|0.009	0.009	strong		0.522	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1		
EIF4G1	1981	hgsc.bcm.edu	37	3	184039304	184039304	+	Missense_Mutation	SNP	A	A	G	rs16858632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184039304A>G	ENST00000346169.2	+	10	1203	c.932A>G	c.(931-933)tAt>tGt	p.Y311C	EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000342981.4_Missense_Mutation_p.Y311C|EIF4G1_ENST00000435046.2_Missense_Mutation_p.Y115C|EIF4G1_ENST00000319274.6_Missense_Mutation_p.Y311C|EIF4G1_ENST00000392537.2_Missense_Mutation_p.Y224C|EIF4G1_ENST00000411531.1_Missense_Mutation_p.Y271C|EIF4G1_ENST00000427845.1_Missense_Mutation_p.Y224C|EIF4G1_ENST00000350481.5_Missense_Mutation_p.Y147C|EIF4G1_ENST00000352767.3_Missense_Mutation_p.Y318C|EIF4G1_ENST00000414031.1_Missense_Mutation_p.Y271C|EIF4G1_ENST00000434061.2_Missense_Mutation_p.Y115C|EIF4G1_ENST00000382330.3_Missense_Mutation_p.Y318C|EIF4G1_ENST00000441154.1_Missense_Mutation_p.Y147C|EIF4G1_ENST00000424196.1_Missense_Mutation_p.Y318C	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	311			Y -> C (in dbSNP:rs16858632). {ECO:0000269|PubMed:21907011}.		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)			GGGGAGCCATATCGCCTCTCT	0.493													A|||	104	0.0207668	0.0749	0.0072	5008	,	,		19071	0.0		0.0	False		,,,				2504	0.0				p.Y318C		Atlas-SNP	.											.	EIF4G1	151	.	0			c.A953G						PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	263,4143	151.0+/-185.0	8,247,1948	61.0	61.0	61.0		953,953,344,932,932,440,671	3.1	1.0	3	dbSNP_123	61	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense,missense,missense	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	194,194,194,194,194,194,194	8,250,6245	GG,GA,AA		0.0349,5.9691,2.0452	benign,benign,benign,benign,benign,benign,benign	318/1607,318/1607,115/1405,311/1601,311/1600,147/1436,224/1513	184039304	266,12740	2203	4300	6503	SO:0001583	missense	1981	exon11			AGCCATATCGCCT	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.932A>G	3.37:g.184039304A>G	ENSP00000316879:p.Tyr311Cys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	137	64	0.467153	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	37	CCDS3259.1	36	0.016483516483516484	34	0.06910569105691057	2	0.0055248618784530384	0	0.0	0	0.0	A	11.01	1.512111	0.27036	0.059691	3.49E-4	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000444134;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000428387;ENST00000434061;ENST00000427607;ENST00000457456;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.52526	4.06;4.06;3.96;0.66;2.96;2.96;4.06;3.13;3.87;4.06;3.97;4.06;4.06;4.06;4.06;2.54;3.87;0.81;3.87;0.84;1.32;3.87	5.5	3.12	0.35913	.	0.732877	0.13056	N	0.417280	T	0.02418	0.0074	N	0.19112	0.55	0.29831	N	0.830056	B;B;B;B	0.26081	0.0;0.0;0.141;0.001	B;B;B;B	0.22753	0.001;0.001;0.041;0.001	T	0.05468	-1.0883	10	0.54805	T	0.06	-0.6548	6.9547	0.24563	0.755:0.1607:0.0843:0.0	rs16858632;rs16858632	318;311;311;318	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	C	311;271;224;115;311;318;318;252;147;318;224;311;311;318;271;147;147;115;115;115;115;115	ENSP00000316879:Y311C;ENSP00000391935:Y271C;ENSP00000376320:Y224C;ENSP00000407244:Y115C;ENSP00000391412:Y311C;ENSP00000413159:Y318C;ENSP00000371767:Y318C;ENSP00000403269:Y252C;ENSP00000317600:Y147C;ENSP00000338020:Y318C;ENSP00000407682:Y224C;ENSP00000343450:Y311C;ENSP00000323737:Y311C;ENSP00000416255:Y318C;ENSP00000395974:Y271C;ENSP00000398145:Y147C;ENSP00000399858:Y147C;ENSP00000411707:Y115C;ENSP00000411826:Y115C;ENSP00000409545:Y115C;ENSP00000399969:Y115C;ENSP00000404754:Y115C	ENSP00000323737:Y311C	Y	+	2	0	EIF4G1	185521998	0.889000	0.30405	0.999000	0.59377	0.971000	0.66376	1.202000	0.32271	1.106000	0.41623	0.533000	0.62120	TAT	A|0.976;G|0.024	0.024	strong		0.493	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
VCAN	1462	hgsc.bcm.edu	37	5	82835545	82835545	+	Silent	SNP	A	A	G	rs160279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82835545A>G	ENST00000265077.3	+	8	7288	c.6723A>G	c.(6721-6723)agA>agG	p.R2241R	VCAN_ENST00000343200.5_Silent_p.R1254R|VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2241	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AAGGCATGAGACCAACAATTC	0.388													A|||	2356	0.470447	0.5091	0.5288	5008	,	,		21131	0.3919		0.5249	False		,,,				2504	0.4018				p.R2241R		Atlas-SNP	.											VCAN,NS,carcinoma,+2,1	VCAN	498	1	0			c.A6723G						PASS	.	A	,,,	2201,2205	586.2+/-386.4	547,1107,549	67.0	66.0	66.0		,3762,,6723	-5.1	0.0	5	dbSNP_79	66	4263,4337	572.8+/-389.8	1066,2131,1103	no	intron,coding-synonymous,intron,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	1613,3238,1652	GG,GA,AA		49.5698,49.9546,49.7001	,,,	,1254/2410,,2241/3397	82835545	6464,6542	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			CATGAGACCAACA	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.6723A>G	5.37:g.82835545A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			G|0.496;N|0.000	0.496	strong		0.388	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
SIRPB1	10326	hgsc.bcm.edu	37	20	1546805	1546805	+	Missense_Mutation	SNP	G	G	A	rs62623705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1546805G>A	ENST00000381605.4	-	5	1257	c.1193C>T	c.(1192-1194)gCc>gTc	p.A398V	SIRPB1_ENST00000381603.3_Missense_Mutation_p.A181V|SIRPB1_ENST00000262929.5_Missense_Mutation_p.A180V|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	398					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						TTACAGTCAGGCCTTCTGTTT	0.587													.|||	295	0.0589058	0.0537	0.0576	5008	,	,		18458	0.002		0.1352	False		,,,				2504	0.047				p.A398V		Atlas-SNP	.											SIRPB1,caecum,carcinoma,-1,1	SIRPB1	83	1	0			c.C1193T						PASS	.	G	VAL/ALA,VAL/ALA	302,4104		9,284,1910	52.0	43.0	46.0		542,1193	-2.8	0.0	20	dbSNP_129	46	1097,7503		70,957,3273	yes	missense,missense	SIRPB1	NM_001083910.2,NM_006065.3	64,64	79,1241,5183	AA,AG,GG		12.7558,6.8543,10.7566	benign,benign	181/182,398/399	1546805	1399,11607	2203	4300	6503	SO:0001583	missense	10326	exon5			AGTCAGGCCTTCT	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.1193C>T	20.37:g.1546805G>A	ENSP00000371018:p.Ala398Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	159	0.07280219780219781	25	0.0508130081300813	22	0.06077348066298342	2	0.0034965034965034965	110	0.14511873350923482	.	13.59	2.281769	0.40394	0.068543	0.127558	ENSG00000101307	ENST00000381605;ENST00000381603;ENST00000262929	T;T;T	0.02837	4.14;4.5;4.51	3.3	-2.85	0.05734	.	1.026210	0.07809	N	0.957890	T	0.00039	0.0001	L	0.56769	1.78	0.80722	P	0.0	B;B	0.34290	0.01;0.447	B;B	0.30646	0.005;0.118	T	0.40979	-0.9534	9	0.87932	D	0	.	0.2986	0.00269	0.2264:0.1687:0.2622:0.3427	.	398;181	O00241;O00241-2	SIRB1_HUMAN;.	V	398;181;180	ENSP00000371018:A398V;ENSP00000371016:A181V;ENSP00000262929:A180V	ENSP00000262929:A180V	A	-	2	0	SIRPB1	1494805	0.037000	0.19845	0.001000	0.08648	0.283000	0.27025	0.143000	0.16115	-0.434000	0.07275	0.563000	0.77884	GCC	G|0.904;A|0.096	0.096	strong		0.587	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
CLEC4C	170482	hgsc.bcm.edu	37	12	7890040	7890040	+	Missense_Mutation	SNP	G	G	T	rs77889141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7890040G>T	ENST00000542353.1	-	5	856	c.366C>A	c.(364-366)aaC>aaA	p.N122K	CLEC4C_ENST00000540085.1_Missense_Mutation_p.N91K|CLEC4C_ENST00000354629.5_Missense_Mutation_p.N91K|CLEC4C_ENST00000360345.3_Missense_Mutation_p.N122K	NM_130441.2	NP_569708.1	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C	122	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			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)		CTTCCCTGGTGTTGATCACCA	0.408													G|||	88	0.0175719	0.0635	0.0043	5008	,	,		-128	0.0		0.001	False		,,,				2504	0.0				p.N122K		Atlas-SNP	.											.	CLEC4C	44	.	0			c.C366A						PASS	.	G	LYS/ASN,LYS/ASN	235,4171	137.7+/-173.5	10,215,1978	129.0	126.0	127.0		366,273	2.6	0.2	12	dbSNP_131	127	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	CLEC4C	NM_130441.2,NM_203503.1	94,94	10,218,6275	TT,TG,GG		0.0349,5.3336,1.8299	possibly-damaging,possibly-damaging	122/214,91/183	7890040	238,12768	2203	4300	6503	SO:0001583	missense	170482	exon5			CCTGGTGTTGATC	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.366C>A	12.37:g.7890040G>T	ENSP00000440428:p.Asn122Lys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_130441	D3DUU3|Q3T1C3|Q6UXS8|Q8WXX8	Missense_Mutation	SNP	ENST00000542353.1	37	CCDS8583.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	G	10.90	1.482342	0.26598	0.053336	3.49E-4	ENSG00000198178	ENST00000542353;ENST00000354629;ENST00000540085;ENST00000360345;ENST00000537530;ENST00000543765	T;T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27;2.27	2.62	2.62	0.31277	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.03390	0.0098	L	0.46614	1.455	0.09310	N	1	P;P	0.51057	0.557;0.941	B;P	0.51615	0.169;0.675	T	0.04885	-1.0920	9	0.27082	T	0.32	.	8.9424	0.35738	0.0:0.0:1.0:0.0	.	91;122	Q8WTT0-2;Q8WTT0	.;CLC4C_HUMAN	K	122;91;91;122;44;82	ENSP00000440428:N122K;ENSP00000346648:N91K;ENSP00000445338:N91K;ENSP00000353500:N122K;ENSP00000438649:N44K;ENSP00000442457:N82K	ENSP00000346648:N91K	N	-	3	2	CLEC4C	7781307	0.976000	0.34144	0.165000	0.22776	0.054000	0.15201	1.943000	0.40253	1.784000	0.52394	0.603000	0.83216	AAC	G|0.981;T|0.019	0.019	strong		0.408	CLEC4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399750.1	NM_203503	
TDRD5	163589	hgsc.bcm.edu	37	1	179564885	179564885	+	Missense_Mutation	SNP	A	A	G	rs147268063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179564885A>G	ENST00000367614.1	+	4	1122	c.763A>G	c.(763-765)Atg>Gtg	p.M255V	TDRD5_ENST00000444136.1_Missense_Mutation_p.M255V|TDRD5_ENST00000294848.8_Missense_Mutation_p.M255V	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	255					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						AATAATGAGCATGGAAAAGAC	0.383													A|||	16	0.00319489	0.0121	0.0	5008	,	,		17514	0.0		0.0	False		,,,				2504	0.0				p.M255V		Atlas-SNP	.											.	TDRD5	149	.	0			c.A763G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET	39,4367	44.6+/-78.6	0,39,2164	88.0	89.0	89.0		763,763,763,763	-11.4	0.0	1	dbSNP_134	89	0,8600		0,0,4300	yes	missense,missense,missense,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_173533.3	21,21,21,21	0,39,6464	GG,GA,AA		0.0,0.8852,0.2999	benign,benign,benign,benign	255/1036,255/1036,255/982,255/982	179564885	39,12967	2203	4300	6503	SO:0001583	missense	163589	exon4			ATGAGCATGGAAA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.763A>G	1.37:g.179564885A>G	ENSP00000356586:p.Met255Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	3.552	-0.091465	0.07053	0.008852	0.0	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.10960	2.82;2.82;3.01	5.69	-11.4	0.00090	.	1.295340	0.05464	N	0.551832	T	0.02455	0.0075	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29792	-1.0000	10	0.16896	T	0.51	-18.0062	3.1803	0.06582	0.3073:0.3169:0.2888:0.0871	.	255;255	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	V	255	ENSP00000356586:M255V;ENSP00000294848:M255V;ENSP00000406052:M255V	ENSP00000294848:M255V	M	+	1	0	TDRD5	177831508	0.000000	0.05858	0.000000	0.03702	0.648000	0.38561	-0.275000	0.08525	-1.928000	0.01059	0.477000	0.44152	ATG	A|0.997;G|0.003	0.003	strong		0.383	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
PRB1	5542	hgsc.bcm.edu	37	12	11506774	11506774	+	Missense_Mutation	SNP	C	C	T	rs202083397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11506774C>T	ENST00000500254.2	-	3	300	c.263G>A	c.(262-264)cGa>cAa	p.R88Q	PRB1_ENST00000546254.1_Missense_Mutation_p.R88Q|PRB1_ENST00000545626.1_Missense_Mutation_p.R88Q	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1	149	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].					extracellular region (GO:0005576)		p.R88Q(1)		NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			TCGGGGACTTCGGGACTTGTC	0.607																																					p.R88Q		Atlas-SNP	.											PRB1,NS,malignant_melanoma,0,1	PRB1	33	1	1	Substitution - Missense(1)	NS(1)	c.G263A						scavenged	.						166.0	204.0	191.0					12																	11506774		2162	4273	6435	SO:0001583	missense	5542	exon3			GGACTTCGGGACT		CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.263G>A	12.37:g.11506774C>T	ENSP00000420826:p.Arg88Gln	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	445	109	0.244944	NM_199353	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Missense_Mutation	SNP	ENST00000500254.2	37	CCDS8642.1	.	.	.	.	.	.	.	.	.	.	.	2.983	-0.209775	0.06140	.	.	ENSG00000251655	ENST00000545626;ENST00000500254;ENST00000546254	T;T;T	0.03745	3.87;3.82;3.82	1.32	-2.64	0.06114	.	.	.	.	.	T	0.00998	0.0033	N	0.00771	-1.2	0.09310	N	1	B;B;B	0.18968	0.032;0.032;0.032	B;B;B	0.08055	0.002;0.003;0.003	T	0.46076	-0.9217	9	0.07325	T	0.83	.	5.9689	0.19340	0.0:0.3818:0.0:0.6182	.	95;88;88	Q86YA1;G3V1R1;G3V1M9	.;.;.	Q	88	ENSP00000444249:R88Q;ENSP00000420826:R88Q;ENSP00000442127:R88Q	ENSP00000420826:R88Q	R	-	2	0	PRB1	11398041	0.003000	0.15002	0.000000	0.03702	0.004000	0.04260	0.491000	0.22419	-0.775000	0.04584	0.391000	0.25812	CGA	C|0.783;T|0.218	0.218	strong		0.607	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039	
TXNDC11	51061	hgsc.bcm.edu	37	16	11773261	11773261	+	Silent	SNP	G	G	C	rs8191350	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11773261G>C	ENST00000356957.3	-	13	2855	c.2748C>G	c.(2746-2748)acC>acG	p.T916T	TXNDC11_ENST00000283033.5_Silent_p.T889T|TXNDC11_ENST00000570917.1_5'UTR			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	916					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						ACGTGTTCTCGGTAAGGAGGT	0.617													G|||	117	0.0233626	0.087	0.0029	5008	,	,		17720	0.0		0.0	False		,,,				2504	0.0				p.T889T		Atlas-SNP	.											.	TXNDC11	75	.	0			c.C2667G						PASS	.	G		362,4032	181.2+/-209.3	18,326,1853	61.0	60.0	61.0		2667	-11.3	0.0	16	dbSNP_117	61	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	TXNDC11	NM_015914.5		18,330,6149	CC,CG,GG		0.0465,8.2385,2.8167		889/959	11773261	366,12628	2197	4300	6497	SO:0001819	synonymous_variant	51061	exon12			GTTCTCGGTAAGG	BC013727	CCDS32387.1	16p13.13	2008-09-29				ENSG00000153066			28030	protein-coding gene	gene with protein product	"""EF-hand binding protein 1"""					8619474, 9110174	Standard	XM_005255346		Approved	EFP1	uc002dbg.1	Q6PKC3		ENST00000356957.3:c.2748C>G	16.37:g.11773261G>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Silent	SNP	ENST00000356957.3	37																																																																																				G|0.970;C|0.030	0.030	strong		0.617	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914	
DBN1	1627	hgsc.bcm.edu	37	5	176885145	176885145	+	Missense_Mutation	SNP	A	A	C	rs139935466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176885145A>C	ENST00000309007.5	-	12	1909	c.1690T>G	c.(1690-1692)Tca>Gca	p.S564A	DBN1_ENST00000393565.1_Missense_Mutation_p.S610A|DBN1_ENST00000292385.5_Missense_Mutation_p.S566A|DBN1_ENST00000512501.1_Missense_Mutation_p.S296A|DBN1_ENST00000393563.4_Missense_Mutation_p.S296A	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	564					actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	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)			TCAAGGGCTGAGGGCAGAGTT	0.642													A|||	23	0.00459265	0.0151	0.0014	5008	,	,		15225	0.0		0.002	False		,,,				2504	0.0				p.S566A		Atlas-SNP	.											.	DBN1	122	.	0			c.T1696G						PASS	.	A	ALA/SER,ALA/SER	45,4361		1,43,2159	35.0	40.0	39.0		1690,1696	2.1	1.0	5	dbSNP_134	39	0,8592		0,0,4296	yes	missense,missense	DBN1	NM_004395.3,NM_080881.2	99,99	1,43,6455	CC,CA,AA		0.0,1.0213,0.3462	possibly-damaging,possibly-damaging	564/650,566/652	176885145	45,12953	2203	4296	6499	SO:0001583	missense	1627	exon13			GGGCTGAGGGCAG		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.1690T>G	5.37:g.176885145A>C	ENSP00000308532:p.Ser564Ala	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	37	CCDS4420.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	A	3.494	-0.103186	0.06967	0.010213	0.0	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000512501;ENST00000393563	T;T;T;T;T	0.32023	1.48;1.48;1.47;1.47;1.5	4.71	2.09	0.27110	.	1.730350	0.02752	N	0.117546	T	0.09686	0.0238	N	0.08118	0	0.18873	N	0.999983	P;B;B;B	0.35107	0.484;0.401;0.005;0.247	B;B;B;B	0.34038	0.174;0.115;0.004;0.107	T	0.24584	-1.0156	10	0.37606	T	0.19	-8.9664	9.4796	0.38893	0.7209:0.0:0.0:0.2791	.	514;610;564;566	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	A	564;566;610;296;296	ENSP00000308532:S564A;ENSP00000292385:S566A;ENSP00000377195:S610A;ENSP00000423208:S296A;ENSP00000377193:S296A	ENSP00000292385:S566A	S	-	1	0	DBN1	176817751	0.998000	0.40836	0.954000	0.39281	0.247000	0.25773	1.322000	0.33689	0.916000	0.36871	0.379000	0.24179	TCA	A|0.995;C|0.005	0.005	strong		0.642	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881	
DNAH14	127602	hgsc.bcm.edu	37	1	225373101	225373101	+	Missense_Mutation	SNP	G	G	T	rs6679852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225373101G>T	ENST00000445597.2	+	24	4363	c.4363G>T	c.(4363-4365)Gtt>Ttt	p.V1455F	DNAH14_ENST00000439375.2_Missense_Mutation_p.V1860F|DNAH14_ENST00000430092.1_Missense_Mutation_p.V1860F			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1455					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CTTCTTATCAGTTGCAGAAAG	0.328													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		14919	0.0		0.0	False		,,,				2504	0.0				p.V1860F		Atlas-SNP	.											.	DNAH14	300	.	0			c.G5578T						PASS	.	G	PHE/VAL	41,1343		0,41,651	110.0	97.0	101.0		5578	-9.8	0.0	1	dbSNP_116	101	0,3182		0,0,1591	no	missense	DNAH14	NM_001373.1	50	0,41,2242	TT,TG,GG		0.0,2.9624,0.8979	benign	1860/4516	225373101	41,4525	692	1591	2283	SO:0001583	missense	127602	exon36			TTATCAGTTGCAG	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.4363G>T	1.37:g.225373101G>T	ENSP00000409472:p.Val1455Phe	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	6.488	0.458267	0.12342	0.029624	0.0	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375;ENST00000328556	T;T;T;T	0.31247	3.21;1.5;1.5;1.7	4.91	-9.83	0.00482	.	.	.	.	.	T	0.03520	0.0101	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.12477	-1.0546	9	0.17369	T	0.5	.	4.9175	0.13853	0.126:0.2314:0.4721:0.1704	rs6679852;rs52818506;rs6679852	1860	Q0VDD8-4	.	F	1455;1860;1860;954	ENSP00000409472:V1455F;ENSP00000414402:V1860F;ENSP00000392061:V1860F;ENSP00000332424:V954F	ENSP00000332424:V954F	V	+	1	0	DNAH14	223439724	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.758000	0.00787	-2.863000	0.00326	-0.467000	0.05162	GTT	G|0.994;T|0.006	0.006	strong		0.328	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
NMT1	4836	hgsc.bcm.edu	37	17	43181223	43181223	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43181223C>T	ENST00000592782.1	+	11	1442	c.1311C>T	c.(1309-1311)gaC>gaT	p.D437D	NMT1_ENST00000258960.2_Silent_p.D437D			P30419	NMT1_HUMAN	N-myristoyltransferase 1	437					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)				TCATGAGCGACGCCCTTGTCC	0.567																																					p.D437D		Atlas-SNP	.											.	NMT1	31	.	0			c.C1311T						PASS	.						226.0	220.0	222.0					17																	43181223		2203	4300	6503	SO:0001819	synonymous_variant	4836	exon10			GAGCGACGCCCTT		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.1311C>T	17.37:g.43181223C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_021079	A8K7C1|Q9UE09	Silent	SNP	ENST00000592782.1	37	CCDS11494.1																																																																																			.	.	none		0.567	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079	
AHNAK2	113146	hgsc.bcm.edu	37	14	105408827	105408827	+	Missense_Mutation	SNP	A	A	C	rs11850949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105408827A>C	ENST00000333244.5	-	7	13080	c.12961T>G	c.(12961-12963)Ttg>Gtg	p.L4321V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4321						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)			GACACATCCAACGAGGCCTCG	0.587													A|||	2658	0.530751	0.5741	0.5086	5008	,	,		20106	0.378		0.5378	False		,,,				2504	0.638				p.L4321V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T12961G						PASS	.	A	VAL/LEU	2396,1520		731,934,293	181.0	195.0	191.0		12961	-6.6	0.0	14	dbSNP_120	191	4450,3822		1225,2000,911	no	missense	AHNAK2	NM_138420.2	32	1956,2934,1204	CC,CA,AA		46.2041,38.8151,43.83	benign	4321/5796	105408827	6846,5342	1958	4136	6094	SO:0001583	missense	113146	exon7			CATCCAACGAGGC	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.12961T>G	14.37:g.105408827A>C	ENSP00000353114:p.Leu4321Val	Somatic	269	1	0.00371747		WXS	Illumina HiSeq	Phase_I	254	113	0.444882	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1007	0.4610805860805861	261	0.5304878048780488	186	0.5138121546961326	178	0.3111888111888112	382	0.503957783641161	a	4.408	0.075405	0.08485	0.611849	0.537959	ENSG00000185567	ENST00000333244	T	0.01933	4.55	3.31	-6.62	0.01813	.	0.941667	0.08520	N	0.933571	T	0.00012	0.0000	N	0.02275	-0.615	0.58432	P	2.9999999999752447E-6	P	0.34629	0.46	B	0.40375	0.327	T	0.42015	-0.9476	9	0.05525	T	0.97	.	3.6938	0.08357	0.2186:0.4052:0.2895:0.0867	rs11850949	4321	Q8IVF2	AHNK2_HUMAN	V	4321	ENSP00000353114:L4321V	ENSP00000353114:L4321V	L	-	1	2	AHNAK2	104479872	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.122000	0.03267	-3.473000	0.00156	-2.694000	0.00139	TTG	A|0.540;C|0.460	0.460	strong		0.587	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OAS1	4938	hgsc.bcm.edu	37	12	113357442	113357442	+	3'UTR	SNP	G	G	A	rs2660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113357442G>A	ENST00000202917.5	+	0	1550				RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Missense_Mutation_p.G397R|OAS1_ENST00000551241.1_Intron	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa						cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						gatccagagaggacaaagctc	0.502													G|||	3945	0.78774	0.9728	0.7954	5008	,	,		19804	0.745		0.6551	False		,,,				2504	0.7127				p.G397R		Atlas-SNP	.											.	OAS1	128	.	0			c.G1189A						PASS	.	G	ARG/GLY,	4067,339	771.8+/-413.8	1875,317,11	49.0	38.0	42.0		1189,	0.6	0.0	12	dbSNP_36	42	5555,3045	635.3+/-399.0	1811,1933,556	yes	missense,utr-3	OAS1	NM_001032409.1,NM_016816.2	125,	3686,2250,567	AA,AG,GG		35.407,7.6941,26.0188	,	397/415,	113357442	9622,3384	2203	4300	6503	SO:0001624	3_prime_UTR_variant	4938	exon6			CAGAGAGGACAAA	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"""2',5'-oligoadenylate synthetase 1 (40-46 kD)"""	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.*84G>A	12.37:g.113357442G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_001032409	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	37	CCDS41838.1	1710	0.782967032967033	483	0.9817073170731707	280	0.7734806629834254	447	0.7814685314685315	500	0.6596306068601583	G	3.465	-0.109085	0.06924	0.923059	0.64593	ENSG00000089127	ENST00000445409	T	0.09445	2.98	2.51	0.603	0.17541	.	2585.470000	0.00166	N	0.000000	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.22800	0.075	B	0.16722	0.016	T	0.24404	-1.0161	8	0.07175	T	0.84	.	4.7613	0.13110	0.3187:0.0:0.6813:0.0	rs2660;rs3168660;rs17834423;rs56511560;rs56662468;rs2660	397	P00973-3	.	R	397	ENSP00000388001:G397R	ENSP00000388001:G397R	G	+	1	0	OAS1	111841825	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.758000	0.04766	0.170000	0.19704	-0.225000	0.12378	GGA	G|0.225;A|0.775	0.775	strong		0.502	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2		
SIRPB1	10326	hgsc.bcm.edu	37	20	1592120	1592120	+	Intron	SNP	G	G	T	rs1135201		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1592120G>T	ENST00000381605.4	-	1	141				SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Missense_Mutation_p.R106S|SIRPB1_ENST00000568365.1_Missense_Mutation_p.R106S|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000381596.1_5'UTR	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						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						TTACTGATGCGGATGGAAAAG	0.512																																					p.R106S		Atlas-SNP	.											SIRPB1_ENST00000279477,NS,carcinoma,0,1	SIRPB1	83	1	0			c.C316A						scavenged	.						105.0	121.0	117.0					20																	1592120		448	1337	1785	SO:0001627	intron_variant	10326	exon2			TGATGCGGATGGA	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.76+8394C>A	20.37:g.1592120G>T		Somatic	367	1	0.0027248		WXS	Illumina HiSeq	Phase_I	371	17	0.0458221	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	560	0.2564102564102564	150	0.3048780487804878	74	0.20441988950276244	183	0.31993006993006995	153	0.20184696569920843	.	2.402	-0.337253	0.05278	.	.	ENSG00000101307	ENST00000279477;ENST00000381596	T	0.65364	-0.15	2.65	-2.79	0.05841	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.52266	1.64	0.34870	D	0.743495	B	0.31435	0.323	B	0.31869	0.137	T	0.37753	-0.9692	9	0.37606	T	0.19	.	4.2858	0.10855	0.1304:0.0:0.2968:0.5727	rs1135201;rs3197735	106	Q5TFQ8	SIRBL_HUMAN	S	106	ENSP00000279477:R106S	ENSP00000279477:R106S	R	-	1	0	SIRPB1	1540120	0.081000	0.21417	0.142000	0.22268	0.020000	0.10135	0.000000	0.12993	-0.294000	0.08973	-2.062000	0.00397	CGC	G|0.744;T|0.256	0.256	strong		0.512	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
ZNF460	10794	hgsc.bcm.edu	37	19	57802782	57802782	+	Silent	SNP	C	C	T	rs80302225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57802782C>T	ENST00000360338.3	+	3	1195	c.873C>T	c.(871-873)taC>taT	p.Y291Y	ZNF460_ENST00000537645.1_Silent_p.Y250Y	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CCTTTACCTACCGCTCCAATT	0.493													c|||	23	0.00459265	0.0166	0.0014	5008	,	,		22183	0.0		0.0	False		,,,				2504	0.0				p.Y291Y		Atlas-SNP	.											.	ZNF460	59	.	0			c.C873T						PASS	.	C		66,4340	62.9+/-100.1	2,62,2139	88.0	81.0	83.0		873	0.3	0.0	19	dbSNP_132	83	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF460	NM_006635.3		2,63,6438	TT,TC,CC		0.0116,1.498,0.5151		291/563	57802782	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			TACCTACCGCTCC	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.873C>T	19.37:g.57802782C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			C|0.994;T|0.006	0.006	strong		0.493	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
DYNLT3	6990	hgsc.bcm.edu	37	X	37701048	37701048	+	Silent	SNP	G	G	A	rs11771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37701048G>A	ENST00000378578.4	-	3	309	c.183C>T	c.(181-183)gcC>gcT	p.A61A	TM4SF2_ENST00000465127.1_Intron|DYNLT3_ENST00000378581.3_Silent_p.A61A|DYNLT3_ENST00000432389.2_Silent_p.A67A	NM_006520.2	NP_006511.1	P51808	DYLT3_HUMAN	dynein, light chain, Tctex-type 3	61					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)|transport (GO:0006810)	cytoplasmic dynein complex (GO:0005868)|kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	motor activity (GO:0003774)			endometrium(1)|lung(1)|skin(1)	3						TATATTTATAGGCTTTTCCCA	0.363													A|||	1325	0.350993	0.5477	0.1571	3775	,	,		10720	0.1825		0.1183	False		,,,				2504	0.1933				p.A61A		Atlas-SNP	.											.	DYNLT3	9	.	0			c.C183T						PASS	.	A		2474,1359		683,737,371,211,200	129.0	118.0	122.0		183	2.6	1.0	X	dbSNP_52	122	1043,5685		52,652,287,1724,1585	no	coding-synonymous	DYNLT3	NM_006520.2		735,1389,658,1935,1785	AA,AG,A,GG,G		15.5024,35.4553,33.3018		61/117	37701048	3517,7044	2202	4300	6502	SO:0001819	synonymous_variant	6990	exon3			TTTATAGGCTTTT	U02556	CCDS14243.1	Xp21	2013-01-18	2005-11-25	2005-11-25	ENSG00000165169	ENSG00000165169		"""Cytoplasmic dyneins"""	11694	protein-coding gene	gene with protein product		300302	"""t-complex-associated-testis-expressed 1-like"""	TCTE1L		8004092	Standard	NM_006520		Approved	TCTEX1L	uc004dds.3	P51808	OTTHUMG00000033172	ENST00000378578.4:c.183C>T	X.37:g.37701048G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_006520	Q6ICS3	Silent	SNP	ENST00000378578.4	37	CCDS14243.1																																																																																			G|0.663;0|0.004	.	strong		0.363	DYNLT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080876.1	NM_006520	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580941	140580941	+	Missense_Mutation	SNP	G	G	A	rs138686663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140580941G>A	ENST00000354757.3	+	1	1594	c.1594G>A	c.(1594-1596)Ggc>Agc	p.G532S	PCDHB11_ENST00000536699.1_Missense_Mutation_p.G167S	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	532	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.G532S(2)		NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTCCGCGTGGGCGCCACAGA	0.677																																					p.G532S		Atlas-SNP	.											PCDHB11,NS,carcinoma,0,3	PCDHB11	162	3	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G1594A						PASS	.						51.0	67.0	62.0					5																	140580941		2202	4300	6502	SO:0001583	missense	56125	exon1			CGCGTGGGCGCCA	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.1594G>A	5.37:g.140580941G>A	ENSP00000346802:p.Gly532Ser	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	496	79	0.159274	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	g	11.84	1.758724	0.31137	.	.	ENSG00000197479	ENST00000536699;ENST00000354757	T;T	0.01647	4.71;4.71	2.51	-5.02	0.02982	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.01695	0.0054	N	0.11845	0.185	0.09310	N	0.999999	B	0.26081	0.141	B	0.40375	0.327	T	0.50056	-0.8872	9	0.34782	T	0.22	.	8.9541	0.35807	0.3349:0.5322:0.1329:0.0	.	532	Q9Y5F2	PCDBB_HUMAN	S	167;532	ENSP00000440344:G167S;ENSP00000346802:G532S	ENSP00000346802:G532S	G	+	1	0	PCDHB11	140561125	0.000000	0.05858	0.010000	0.14722	0.109000	0.19521	-4.241000	0.00268	-1.731000	0.01360	0.298000	0.19748	GGC	G|0.970;A|0.030	0.030	strong		0.677	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
BIRC6	57448	hgsc.bcm.edu	37	2	32713706	32713706	+	Missense_Mutation	SNP	A	A	T	rs2366894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32713706A>T	ENST00000421745.2	+	42	8154	c.8020A>T	c.(8020-8022)Act>Tct	p.T2674S		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2674				T -> S (in Ref. 2; AAF75772). {ECO:0000305}.	apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.T2674S(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TTCTAGTTCAACTGGAAACAA	0.308													T|||	2809	0.560903	0.708	0.6398	5008	,	,		15225	0.3433		0.6412	False		,,,				2504	0.4479				p.T2674S	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,NS,carcinoma,0,3	BIRC6	838	3	1	Substitution - Missense(1)	stomach(1)	c.A8020T						PASS	.	T	SER/THR	2989,1255		1089,811,222	24.0	23.0	23.0		8020	4.5	1.0	2	dbSNP_100	23	5250,3014		1754,1742,636	yes	missense	BIRC6	NM_016252.3	58	2843,2553,858	TT,TA,AA		36.4714,29.5712,34.1302	benign	2674/4858	32713706	8239,4269	2122	4132	6254	SO:0001583	missense	57448	exon42			AGTTCAACTGGAA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.8020A>T	2.37:g.32713706A>T	ENSP00000393596:p.Thr2674Ser	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	204	204	1	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	1262	0.5778388278388278	330	0.6707317073170732	246	0.6795580110497238	209	0.36538461538461536	477	0.6292875989445911	T	3.123	-0.180114	0.06380	0.704288	0.635286	ENSG00000115760	ENST00000421745	T	0.73047	-0.71	5.67	4.48	0.54585	.	0.216003	0.40469	N	0.001086	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	0.46871	-0.9160	9	0.02654	T	1	.	7.3633	0.26758	0.2499:0.0:0.1305:0.6196	rs2366894;rs52828077;rs2366894	2674	Q9NR09	BIRC6_HUMAN	S	2674	ENSP00000393596:T2674S	ENSP00000393596:T2674S	T	+	1	0	BIRC6	32567210	0.994000	0.37717	1.000000	0.80357	0.992000	0.81027	1.242000	0.32755	0.402000	0.25451	-0.257000	0.10917	ACT	A|0.424;T|0.576	0.576	strong		0.308	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
DNAH17	8632	hgsc.bcm.edu	37	17	76522784	76522784	+	Silent	SNP	G	G	A	rs61744545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76522784G>A	ENST00000585328.1	-	24	3775	c.3651C>T	c.(3649-3651)cgC>cgT	p.R1217R	DNAH17_ENST00000389840.5_Silent_p.R1220R	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1220	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)			ACGGGGCCTCGCGCCTGAACC	0.582													.|||	317	0.0632987	0.0318	0.0576	5008	,	,		14498	0.0129		0.0825	False		,,,				2504	0.1421				p.R1220R		Atlas-SNP	.											DNAH17,NS,carcinoma,-2,1	DNAH17	347	1	0			c.C3660T						PASS	.	G		131,3799		0,131,1834	46.0	50.0	48.0		3660	-8.7	0.0	17	dbSNP_129	48	846,7442		45,756,3343	no	coding-synonymous	DNAH17	NM_173628.3		45,887,5177	AA,AG,GG		10.2075,3.3333,7.9964		1220/4463	76522784	977,11241	1965	4144	6109	SO:0001819	synonymous_variant	8632	exon24			GGCCTCGCGCCTG	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.3651C>T	17.37:g.76522784G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	130	61	0.469231	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.933;A|0.067	0.067	strong		0.582	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
PTPN13	5783	hgsc.bcm.edu	37	4	87653594	87653594	+	Silent	SNP	A	A	G	rs201078979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:87653594A>G	ENST00000411767.2	+	11	1713	c.1650A>G	c.(1648-1650)ccA>ccG	p.P550P	PTPN13_ENST00000511467.1_Silent_p.P550P|PTPN13_ENST00000427191.2_Silent_p.P550P|PTPN13_ENST00000436978.1_Silent_p.P550P|PTPN13_ENST00000316707.6_Silent_p.P550P			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	550					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CAATTGAACCATTTATATCTT	0.289													A|||	8	0.00159744	0.0061	0.0	5008	,	,		17350	0.0		0.0	False		,,,				2504	0.0				p.P550P		Atlas-SNP	.											.	PTPN13	203	.	0			c.A1650G						PASS	.	A	,,,	19,3581		0,19,1781	57.0	53.0	54.0		1650,1650,1650,1650	3.2	1.0	4		54	1,8119		0,1,4059	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	,,,	0,20,5840	GG,GA,AA		0.0123,0.5278,0.1706	,,,	550/2467,550/2486,550/2295,550/2491	87653594	20,11700	1800	4060	5860	SO:0001819	synonymous_variant	5783	exon11			TGAACCATTTATA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.1650A>G	4.37:g.87653594A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			A|0.999;G|0.001	0.001	strong		0.289	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
LRRC14	9684	hgsc.bcm.edu	37	8	145741702	145741702	+	5'Flank	SNP	C	C	G	rs4244612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145741702C>G	ENST00000292524.1	+	0	0				RECQL4_ENST00000428558.2_Missense_Mutation_p.E267D|LRRC14_ENST00000529022.1_5'Flank|CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000532237.1_5'UTR	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-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;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TCTCCCAGGGCTCCTCGTTCC	0.672													C|||	2242	0.447684	0.4198	0.464	5008	,	,		16664	0.4821		0.3827	False		,,,				2504	0.5051				p.E267D		Atlas-SNP	.											.	RECQL4	75	.	0			c.G801C						PASS	.	C	ASP/GLU	1614,2322		356,902,710	20.0	23.0	22.0		801	-3.0	0.0	8	dbSNP_111	22	3184,5124		620,1944,1590	yes	missense	RECQL4	NM_004260.3	45	976,2846,2300	GG,GC,CC		38.3245,41.0061,39.1865	benign	267/1209	145741702	4798,7446	1968	4154	6122	SO:0001631	upstream_gene_variant	9401	exon5			CCAGGGCTCCTCG	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		8.37:g.145741702C>G	Exception_encountered	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_004260	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			C|0.586;G|0.414	0.414	strong		0.672	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
HLA-G	3135	hgsc.bcm.edu	37	6	29795636	29795636	+	Silent	SNP	G	G	A	rs1630223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29795636G>A	ENST00000360323.6	+	1	39	c.15G>A	c.(13-15)gcG>gcA	p.A5A	HLA-G_ENST00000376818.3_Silent_p.A5A|HLA-G_ENST00000428701.1_Silent_p.A5A|HLA-G_ENST00000376815.3_Silent_p.A5A|HLA-G_ENST00000376828.2_Silent_p.A10A			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	5					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						TGGTCATGGCGCCCCGAACCC	0.652													g|||	2726	0.544329	0.5083	0.4654	5008	,	,		14134	0.6032		0.4324	False		,,,				2504	0.7035				p.A5A		Atlas-SNP	.											.	HLA-G	90	.	0			c.G15A						PASS	.	G		1538,1484		392,754,365	42.0	47.0	45.0		15	1.7	0.0	6	dbSNP_89	45	2507,2911		598,1311,800	no	coding-synonymous	HLA-G	NM_002127.5		990,2065,1165	AA,AG,GG		46.2717,49.1066,47.9265		5/339	29795636	4045,4395	1511	2709	4220	SO:0001819	synonymous_variant	3135	exon2			CATGGCGCCCCGA		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.15G>A	6.37:g.29795636G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	201	91	0.452736	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			G|0.509;A|0.491	0.491	strong		0.652	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
OR4D9	390199	hgsc.bcm.edu	37	11	59282838	59282838	+	Silent	SNP	G	G	A	rs75125922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59282838G>A	ENST00000329328.3	+	1	453	c.453G>A	c.(451-453)ggG>ggA	p.G151G		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	151				ASWVGGF -> GFLGGGL (in Ref. 2; AC019093). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						CCTGGGTGGGGGGCTTTGTCC	0.547													G|||	180	0.0359425	0.1331	0.0058	5008	,	,		18390	0.0		0.0	False		,,,				2504	0.0				p.G151G		Atlas-SNP	.											.	OR4D9	47	.	0			c.G453A						PASS	.	G		451,3951	215.8+/-234.7	18,415,1768	81.0	79.0	79.0		453	2.1	1.0	11	dbSNP_131	79	2,8588	1.2+/-3.3	0,2,4293	no	coding-synonymous	OR4D9	NM_001004711.1		18,417,6061	AA,AG,GG		0.0233,10.2453,3.4868		151/315	59282838	453,12539	2201	4295	6496	SO:0001819	synonymous_variant	390199	exon1			GGTGGGGGGCTTT	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"""GPCR / Class A : Olfactory receptors"""	15178	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily D, member 9 pseudogene"""				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.453G>A	11.37:g.59282838G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	144	72	0.5	NM_001004711	Q6IFF3	Silent	SNP	ENST00000329328.3	37	CCDS31564.1																																																																																			G|0.966;A|0.034	0.034	strong		0.547	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711	
HIST1H4C	8364	hgsc.bcm.edu	37	6	26104382	26104382	+	Silent	SNP	C	C	T	rs2229767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26104382C>T	ENST00000377803.2	+	1	279	c.207C>T	c.(205-207)gaC>gaT	p.D69D		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	69					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						TTATTCGAGACGCCGTCACCT	0.542													c|||	175	0.0349441	0.1248	0.013	5008	,	,		17220	0.0		0.001	False		,,,				2504	0.0				p.D69D		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.C207T						PASS	.	T		437,3969		27,383,1793	74.0	66.0	69.0		207	0.8	1.0	6	dbSNP_98	69	29,8571		0,29,4271	no	coding-synonymous	HIST1H4C	NM_003542.3		27,412,6064	TT,TC,CC		0.3372,9.9183,3.583		69/104	26104382	466,12540	2203	4300	6503	SO:0001819	synonymous_variant	8364	exon1			TCGAGACGCCGTC	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.207C>T	6.37:g.26104382C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	171	81	0.473684	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377803.2	37	CCDS4583.1																																																																																			C|0.963;T|0.037	0.037	strong		0.542	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542	
SLC27A5	10998	hgsc.bcm.edu	37	19	59023166	59023166	+	Missense_Mutation	SNP	G	G	A	rs34415062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:59023166G>A	ENST00000263093.2	-	1	266	c.157C>T	c.(157-159)Cgg>Tgg	p.R53W	SLC27A5_ENST00000601355.1_Missense_Mutation_p.R53W	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	53			R -> W (in dbSNP:rs34415062).		bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		AGCCAGGGCCGTGCTAACATG	0.697													g|||	810	0.161741	0.1823	0.1715	5008	,	,		16961	0.0565		0.2187	False		,,,				2504	0.1769				p.R53W		Atlas-SNP	.											.	SLC27A5	58	.	0			c.C157T						PASS	.	A	TRP/ARG	758,3572		76,606,1483	9.0	10.0	10.0		157	-8.6	0.0	19	dbSNP_126	10	1437,7025		126,1185,2920	yes	missense	SLC27A5	NM_012254.2	101	202,1791,4403	AA,AG,GG		16.9818,17.5058,17.1592	benign	53/691	59023166	2195,10597	2165	4231	6396	SO:0001583	missense	10998	exon1			AGGGCCGTGCTAA	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.157C>T	19.37:g.59023166G>A	ENSP00000263093:p.Arg53Trp	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	354	0.1620879120879121	103	0.20934959349593496	64	0.17679558011049723	34	0.05944055944055944	153	0.20184696569920843	g	10.06	1.248102	0.22880	0.175058	0.169818	ENSG00000083807	ENST00000263093	T	0.55760	0.5	4.31	-8.62	0.00881	.	3.204120	0.01052	N	0.004491	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03394	-1.1041	9	0.37606	T	0.19	0.0155	6.2565	0.20877	0.2565:0.0993:0.5413:0.103	rs34415062;rs34415062	53	Q9Y2P5	S27A5_HUMAN	W	53	ENSP00000263093:R53W	ENSP00000263093:R53W	R	-	1	2	SLC27A5	63714978	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.165000	0.01274	-3.044000	0.00262	-0.372000	0.07161	CGG	G|0.817;A|0.183	0.183	strong		0.697	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
OR2W5	441932	hgsc.bcm.edu	37	1	247654993	247654993	+	RNA	SNP	T	T	C	rs10925061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247654993T>C	ENST00000522351.1	+	0	624							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 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)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	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;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			TTGCCATGTCTTGTGAGGAAA	0.562													C|||	1621	0.323682	0.4546	0.2536	5008	,	,		18968	0.2659		0.3231	False		,,,				2504	0.2566				p.S188S		Atlas-SNP	.											.	OR2W5	97	.	0			c.T564C						PASS	.	C		1929,2477	624.9+/-394.4	429,1071,703	141.0	141.0	141.0		564	-0.5	0.5	1	dbSNP_120	141	2608,5992	688.5+/-404.3	394,1820,2086	no	coding-synonymous	OR2W5	NM_001004698.2		823,2891,2789	CC,CT,TT		30.3256,43.7812,34.8839		188/321	247654993	4537,8469	2203	4300	6503			441932	exon1			CATGTCTTGTGAG			1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"""GPCR / Class A : Olfactory receptors"""	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		1.37:g.247654993T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	127	57	0.448819	NM_001004698	B9EH85	Silent	SNP	ENST00000522351.1	37																																																																																				T|0.645;C|0.355	0.355	strong		0.562	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
SSMEM1	136263	hgsc.bcm.edu	37	7	129855837	129855837	+	Missense_Mutation	SNP	C	C	T	rs4728190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:129855837C>T	ENST00000297819.3	+	3	313	c.262C>T	c.(262-264)Cgg>Tgg	p.R88W		NM_145268.3	NP_660311.1	Q8WWF3	SSMM1_HUMAN	serine-rich single-pass membrane protein 1	88			R -> W (in dbSNP:rs4728190).			integral component of membrane (GO:0016021)											TTCCTGTAAGCGGCAAAGCAA	0.408													C|||	936	0.186901	0.357	0.1499	5008	,	,		22584	0.0069		0.2366	False		,,,				2504	0.1176				p.R88W		Atlas-SNP	.											.	.	.	.	0			c.C262T						PASS	.	C	TRP/ARG	1516,2890	482.6+/-359.5	262,992,949	113.0	103.0	106.0		262	-3.0	0.0	7	dbSNP_111	106	2057,6543	357.1+/-330.6	239,1579,2482	yes	missense	C7orf45	NM_145268.3	101	501,2571,3431	TT,TC,CC		23.9186,34.4076,27.4719	benign	88/245	129855837	3573,9433	2203	4300	6503	SO:0001583	missense	0	exon3			TGTAAGCGGCAAA	AK097635	CCDS5816.1	7q32.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000165120	ENSG00000165120			29580	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 45"""	C7orf45		12477932	Standard	NM_145268		Approved	FLJ40316	uc003vpp.3	Q8WWF3	OTTHUMG00000157844	ENST00000297819.3:c.262C>T	7.37:g.129855837C>T	ENSP00000297819:p.Arg88Trp	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	183	84	0.459016	NM_145268		Missense_Mutation	SNP	ENST00000297819.3	37	CCDS5816.1	425	0.1945970695970696	179	0.3638211382113821	61	0.1685082872928177	1	0.0017482517482517483	184	0.24274406332453827	C	4.155	0.027164	0.08054	0.344076	0.239186	ENSG00000165120	ENST00000297819	T	0.49720	0.77	5.84	-2.95	0.05564	.	0.712332	0.13336	N	0.395538	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.38993	-0.9635	9	0.42905	T	0.14	-0.0013	2.0059	0.03477	0.1078:0.357:0.2119:0.3233	rs4728190;rs52821550;rs57504232;rs4728190	88	Q8WWF3	CG045_HUMAN	W	88	ENSP00000297819:R88W	ENSP00000297819:R88W	R	+	1	2	C7orf45	129643073	0.158000	0.22850	0.000000	0.03702	0.001000	0.01503	-0.011000	0.12721	-0.684000	0.05183	-1.287000	0.01368	CGG	C|0.758;T|0.242	0.242	strong		0.408	SSMEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349768.1	NM_145268	
DNAH9	1770	hgsc.bcm.edu	37	17	11540079	11540079	+	Silent	SNP	C	C	T	rs8065057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11540079C>T	ENST00000262442.4	+	9	1832	c.1764C>T	c.(1762-1764)caC>caT	p.H588H	DNAH9_ENST00000454412.2_Silent_p.H588H	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	588	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)		ACAGTCAGCACGTCCAGGAGG	0.438													T|||	54	0.0107827	0.0393	0.0029	5008	,	,		22057	0.0		0.0	False		,,,				2504	0.0				p.H588H		Atlas-SNP	.											.	DNAH9	695	.	0			c.C1764T						PASS	.	T		210,4196	807.3+/-415.9	3,204,1996	145.0	138.0	140.0		1764	-0.4	0.6	17	dbSNP_116	140	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous	DNAH9	NM_001372.3		3,206,6294	TT,TC,CC		0.0233,4.7662,1.63		588/4487	11540079	212,12794	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon9			TCAGCACGTCCAG	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.1764C>T	17.37:g.11540079C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	93	36	0.387097	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.984;T|0.016	0.016	strong		0.438	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
CCAR2	57805	hgsc.bcm.edu	37	8	22472473	22472473	+	Silent	SNP	G	G	A	rs112997942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22472473G>A	ENST00000308511.4	+	11	1413	c.1164G>A	c.(1162-1164)gcG>gcA	p.A388A	CCAR2_ENST00000389279.3_Silent_p.A388A|RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000520861.1_Silent_p.A63A			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	388					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										TCCGCTGTGCGCAGGCCCAGA	0.627													G|||	37	0.00738818	0.0265	0.0029	5008	,	,		20145	0.0		0.0	False		,,,				2504	0.0				p.A388A		Atlas-SNP	.											.	KIAA1967	72	.	0			c.G1164A						PASS	.	G		87,4317	67.0+/-104.6	0,87,2115	46.0	34.0	38.0		1164	-11.1	0.0	8	dbSNP_132	38	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA1967	NM_021174.5		0,88,6414	AA,AG,GG		0.0116,1.9755,0.6767		388/924	22472473	88,12916	2202	4300	6502	SO:0001819	synonymous_variant	57805	exon11			CTGTGCGCAGGCC	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1164G>A	8.37:g.22472473G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Silent	SNP	ENST00000308511.4	37	CCDS34863.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	9.159	1.018179	0.19355	0.019755	1.16E-4	ENSG00000158941	ENST00000520738	.	.	.	5.53	-11.1	0.00147	.	.	.	.	.	T	0.25531	0.0621	.	.	.	0.40931	D	0.984397	.	.	.	.	.	.	T	0.49351	-0.8949	4	.	.	.	-11.8395	5.7525	0.18154	0.4761:0.2759:0.182:0.066	.	.	.	.	H	80	.	.	R	+	2	0	KIAA1967	22528418	0.000000	0.05858	0.010000	0.14722	0.924000	0.55760	-2.064000	0.01387	-2.862000	0.00326	-0.793000	0.03317	CGC	G|0.993;A|0.007	0.007	strong		0.627	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
SLC24A5	283652	hgsc.bcm.edu	37	15	48426484	48426484	+	Missense_Mutation	SNP	A	A	G	rs1426654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:48426484A>G	ENST00000341459.3	+	3	404	c.331A>G	c.(331-333)Aca>Gca	p.T111A	SLC24A5_ENST00000449382.2_Missense_Mutation_p.T51A	NM_205850.2	NP_995322.1	Q71RS6	NCKX5_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 5	111			T -> A (associated with SHEP4; greatly reduced exchange activity; dbSNP:rs1426654). {ECO:0000269|PubMed:16357253, ECO:0000269|PubMed:17999355}.		ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|negative regulation of melanin biosynthetic process (GO:0048022)|response to stimulus (GO:0050896)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|skin(1)|upper_aerodigestive_tract(1)	27		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		TGTTGCAGGCACAACTTTCAT	0.378													G|||	2816	0.5623	0.9259	0.4107	5008	,	,		20353	0.9881		0.003	False		,,,				2504	0.3149				p.T111A		Atlas-SNP	.											.	SLC24A5	64	.	0			c.A331G	GRCh37	CM054862	SLC24A5	M	rs1426654	PASS	.	G	ALA/THR	3388,1008	373.9+/-321.0	1323,742,133	156.0	163.0	161.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	331	5.6	1.0	15	dbSNP_88	161	42,8552	816.9+/-406.9	1,40,4256	yes	missense	SLC24A5	NM_205850.2	58	1324,782,4389	GG,GA,AA		0.4887,22.9299,26.4049	benign	111/501	48426484	3430,9560	2198	4297	6495	SO:0001583	missense	283652	exon3			GCAGGCACAACTT	AF348468	CCDS10128.1	15q21.1	2014-01-28	2013-07-18		ENSG00000188467	ENSG00000188467		"""Solute carriers"""	20611	protein-coding gene	gene with protein product	"""oculocutaneous albinism 6 (autosomal recessive)"""	609802	"""solute carrier family 24, member 5"""			23364476	Standard	XM_005254308		Approved	JSX, OCA6	uc001zwe.3	Q71RS6	OTTHUMG00000131494	ENST00000341459.3:c.331A>G	15.37:g.48426484A>G	ENSP00000341550:p.Thr111Ala	Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	190	190	1	NM_205850	A5X8Z8|A5X8Z9|Q14CT4|Q6DKH3	Missense_Mutation	SNP	ENST00000341459.3	37	CCDS10128.1	1141	0.5224358974358975	454	0.9227642276422764	120	0.3314917127071823	564	0.986013986013986	3	0.00395778364116095	G	9.239	1.037742	0.19669	0.770701	0.004887	ENSG00000188467	ENST00000341459;ENST00000449382	T;T	0.61510	0.1;0.1	5.55	5.55	0.83447	Sodium/calcium exchanger membrane region (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00007	-3.17	0.44908	P	0.0020719999999999628	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44817	-0.9303	9	0.02654	T	1	.	14.8111	0.69996	0.0685:0.0:0.9315:0.0	rs1426654;rs52802038;rs58147390;rs1426654	51;111	A5X8Z9;Q71RS6	.;NCKX5_HUMAN	A	111;51	ENSP00000341550:T111A;ENSP00000389966:T51A	ENSP00000341550:T111A	T	+	1	0	SLC24A5	46213776	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.460000	0.80816	1.604000	0.50143	-0.186000	0.12905	ACA	A|0.618;G|0.382	0.382	strong		0.378	SLC24A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254340.2	NM_205850	
MTPN	136319	hgsc.bcm.edu	37	7	135614740	135614740	+	Silent	SNP	T	T	C	rs17168527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:135614740T>C	ENST00000393085.3	-	4	506	c.291A>G	c.(289-291)aaA>aaG	p.K97K	MTPN_ENST00000435723.1_Silent_p.K31K|AC015987.1_ENST00000419211.1_RNA|LUZP6_ENST00000589735.1_5'Flank	NM_001128619.2|NM_145808.3	NP_001122091.2|NP_665807.1	P58546	MTPN_HUMAN	myotrophin	97					catecholamine metabolic process (GO:0006584)|cell growth (GO:0016049)|cerebellar granule cell differentiation (GO:0021707)|neuron differentiation (GO:0030182)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell growth (GO:0030307)|positive regulation of macromolecule biosynthetic process (GO:0010557)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein metabolic process (GO:0051247)|regulation of barbed-end actin filament capping (GO:2000812)|regulation of striated muscle tissue development (GO:0016202)|regulation of translation (GO:0006417)|skeletal muscle tissue regeneration (GO:0043403)|striated muscle cell differentiation (GO:0051146)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|nucleus (GO:0005634)				endometrium(1)|lung(4)|prostate(1)	6						CATCTGGGCCTTTCACAGTCT	0.502													T|||	300	0.0599042	0.0976	0.0692	5008	,	,		15429	0.006		0.0825	False		,,,				2504	0.0348				p.K97K		Atlas-SNP	.											.	MTPN	10	.	0			c.A291G						PASS	.	T	,	456,3950	209.5+/-230.2	18,420,1765	167.0	134.0	145.0		,291	3.7	1.0	7	dbSNP_123	145	763,7837	173.3+/-223.8	44,675,3581	no	utr-5,coding-synonymous	MTPN,LUZP6	NM_001128619.1,NM_145808.3	,	62,1095,5346	CC,CT,TT		8.8721,10.3495,9.3726	,	,97/119	135614740	1219,11787	2203	4300	6503	SO:0001819	synonymous_variant	136319	exon4			TGGGCCTTTCACA	AC015987	CCDS5842.1	7q33-q35	2013-01-10			ENSG00000105887	ENSG00000105887		"""Ankyrin repeat domain containing"""	15667	protein-coding gene	gene with protein product	"""granule cell differentiation protein"""	606484				11474205	Standard	NM_145808		Approved	MYOTROPHIN, GCDP, V-1		P58546	OTTHUMG00000155627	ENST00000393085.3:c.291A>G	7.37:g.135614740T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_145808		Silent	SNP	ENST00000393085.3	37	CCDS5842.1																																																																																			T|0.921;C|0.079	0.079	strong		0.502	MTPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340921.1	NM_145808	
REPIN1	29803	hgsc.bcm.edu	37	7	150068981	150068981	+	Silent	SNP	G	G	A	rs149624173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150068981G>A	ENST00000425389.2	+	1	729	c.651G>A	c.(649-651)agG>agA	p.R217R	REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000489432.2_Silent_p.R274R|REPIN1_ENST00000540729.1_Silent_p.R217R|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000444957.1_Silent_p.R217R|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000397281.2_Silent_p.R217R	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	217					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)			cccggcccaggggccgccccg	0.716													G|||	21	0.00419329	0.0159	0.0	5008	,	,		9749	0.0		0.0	False		,,,				2504	0.0				p.R274R		Atlas-SNP	.											.	REPIN1	74	.	0			c.G822A						PASS	.	G	,,,	38,3468		0,38,1715	8.0	10.0	9.0		822,651,651,651	1.7	0.9	7	dbSNP_134	9	0,7798		0,0,3899	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	,,,	0,38,5614	AA,AG,GG		0.0,1.0839,0.3362	,,,	274/625,217/568,217/568,217/568	150068981	38,11266	1753	3899	5652	SO:0001819	synonymous_variant	29803	exon3			GCCCAGGGGCCGC	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.651G>A	7.37:g.150068981G>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	7	4	0.571429	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Silent	SNP	ENST00000425389.2	37	CCDS43677.1																																																																																			G|0.994;A|0.006	0.006	strong		0.716	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
SLFN13	146857	hgsc.bcm.edu	37	17	33769211	33769211	+	Missense_Mutation	SNP	C	C	T	rs77814846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33769211C>T	ENST00000285013.6	-	5	1568	c.1293G>A	c.(1291-1293)atG>atA	p.M431I	SLFN13_ENST00000526861.1_Missense_Mutation_p.M431I|SLFN13_ENST00000542635.1_Missense_Mutation_p.M431I|SLFN13_ENST00000533791.1_Missense_Mutation_p.M431I|SLFN13_ENST00000534689.1_Missense_Mutation_p.M113I|SLFN13_ENST00000360502.2_Missense_Mutation_p.M113I	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	431						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		AGAAAGGTCGCATTTGCTTGT	0.488													C|||	74	0.0147764	0.053	0.0058	5008	,	,		18201	0.0		0.0	False		,,,				2504	0.0				p.M431I		Atlas-SNP	.											.	SLFN13	79	.	0			c.G1293A						PASS	.	C	ILE/MET	199,4207	124.9+/-162.1	3,193,2007	91.0	82.0	85.0		1293	-6.2	0.0	17	dbSNP_131	85	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SLFN13	NM_144682.5	10	3,195,6305	TT,TC,CC		0.0233,4.5166,1.5454	benign	431/898	33769211	201,12805	2203	4300	6503	SO:0001583	missense	146857	exon5			AGGTCGCATTTGC	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.1293G>A	17.37:g.33769211C>T	ENSP00000285013:p.Met431Ile	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	c	0.430	-0.903761	0.02453	0.045166	2.33E-4	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689;ENST00000532210	T;T;T;T;T;T	0.16597	4.64;4.06;4.64;4.64;4.06;2.33	3.09	-6.17	0.02091	.	0.757041	0.12071	N	0.502241	T	0.00552	0.0018	N	0.17474	0.49	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.13407	0.009;0.0	T	0.36866	-0.9730	10	0.05525	T	0.97	.	1.256	0.01991	0.1521:0.2533:0.1508:0.4438	.	113;431	Q68D06-2;Q68D06	.;SLN13_HUMAN	I	431;113;431;431;113;100	ENSP00000285013:M431I;ENSP00000353692:M113I;ENSP00000434439:M431I;ENSP00000444016:M431I;ENSP00000435442:M113I;ENSP00000435328:M100I	ENSP00000285013:M431I	M	-	3	0	SLFN13	30793324	0.000000	0.05858	0.001000	0.08648	0.138000	0.21146	-0.875000	0.04205	-1.010000	0.03396	0.205000	0.17691	ATG	C|0.987;T|0.013	0.013	strong		0.488	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
GPR179	440435	hgsc.bcm.edu	37	17	36482372	36482372	+	Silent	SNP	A	A	C	rs58740367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36482372A>C	ENST00000342292.4	-	11	7100	c.7080T>G	c.(7078-7080)acT>acG	p.T2360T	GPR179_ENST00000584976.1_Intron	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	2360					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				AAGGATAGACAGTGGGAGGGG	0.498													A|||	291	0.058107	0.2148	0.0101	5008	,	,		20612	0.0		0.0	False		,,,				2504	0.0				p.T2360T		Atlas-SNP	.											.	GPR179	170	.	0			c.T7080G						PASS	.	A		644,3154		58,528,1313	73.0	67.0	69.0		7080	1.3	0.1	17	dbSNP_129	69	3,8259		0,3,4128	no	coding-synonymous	GPR179	NM_001004334.2		58,531,5441	CC,CA,AA		0.0363,16.9563,5.3648		2360/2368	36482372	647,11413	1899	4131	6030	SO:0001819	synonymous_variant	440435	exon11			ATAGACAGTGGGA		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.7080T>G	17.37:g.36482372A>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			A|0.955;C|0.045	0.045	strong		0.498	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
POLH	5429	hgsc.bcm.edu	37	6	43581586	43581586	+	Silent	SNP	G	G	A	rs3734690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43581586G>A	ENST00000372236.4	+	11	1729	c.1434G>A	c.(1432-1434)acG>acA	p.T478T	POLH_ENST00000372226.1_3'UTR|POLH_ENST00000535400.1_Silent_p.T416T	NM_006502.2	NP_006493.1	O75417	DPOLQ_HUMAN	polymerase (DNA directed), eta	0	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)			breast(4)|endometrium(5)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			AAGCAACCACGTCTCTGGAAT	0.502								DNA polymerases (catalytic subunits)	Xeroderma Pigmentosum				G|||	351	0.0700879	0.1354	0.0303	5008	,	,		18346	0.0298		0.0338	False		,,,				2504	0.089				p.T478T		Atlas-SNP	.											POLH,NS,carcinoma,+1,1	POLH	54	1	0			c.G1434A						PASS	.	G		462,3944	217.1+/-235.6	34,394,1775	52.0	55.0	54.0		1434	-1.4	0.0	6	dbSNP_107	54	262,8338	101.2+/-162.5	3,256,4041	no	coding-synonymous	POLH	NM_006502.2		37,650,5816	AA,AG,GG		3.0465,10.4857,5.5667		478/714	43581586	724,12282	2203	4300	6503	SO:0001819	synonymous_variant	5429	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AACCACGTCTCTG	AB024313	CCDS4902.1	6p21	2014-09-17			ENSG00000170734	ENSG00000170734			9181	protein-coding gene	gene with protein product		603968				10385124, 10398605	Standard	NM_006502		Approved	RAD30A, XP-V	uc003ovq.4	Q9Y253	OTTHUMG00000014743	ENST00000372236.4:c.1434G>A	6.37:g.43581586G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_006502	O95160|Q6VMB5	Silent	SNP	ENST00000372236.4	37	CCDS4902.1																																																																																			G|0.939;A|0.061	0.061	strong		0.502	POLH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040666.1	NM_006502	
REST	5978	hgsc.bcm.edu	37	4	57798189	57798189	+	Silent	SNP	G	G	A	rs2227901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57798189G>A	ENST00000309042.7	+	4	3479	c.3165G>A	c.(3163-3165)gcG>gcA	p.A1055A		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	1055	Interaction with RCOR1.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CAGTCAAAGCGGCTAAGGGAG	0.433													G|||	1270	0.253594	0.2595	0.2161	5008	,	,		20278	0.3661		0.1849	False		,,,				2504	0.227				p.A1055A		Atlas-SNP	.											.	REST	104	.	0			c.G3165A						PASS	.	G	,	1041,3365	384.9+/-325.5	111,819,1273	80.0	77.0	78.0		3165,3165	1.1	0.0	4	dbSNP_98	78	1641,6959	303.6+/-306.5	143,1355,2802	no	coding-synonymous,coding-synonymous	REST	NM_001193508.1,NM_005612.4	,	254,2174,4075	AA,AG,GG		19.0814,23.6269,20.6213	,	1055/1098,1055/1098	57798189	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	5978	exon4			CAAAGCGGCTAAG	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.3165G>A	4.37:g.57798189G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	145	67	0.462069	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Silent	SNP	ENST00000309042.7	37	CCDS3509.1																																																																																			G|0.791;A|0.209	0.209	strong		0.433	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
ARNTL2	56938	hgsc.bcm.edu	37	12	27553566	27553566	+	Missense_Mutation	SNP	A	A	G	rs1037921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27553566A>G	ENST00000266503.5	+	10	1037	c.1019A>G	c.(1018-1020)aAc>aGc	p.N340S	RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000546179.1_Missense_Mutation_p.N303S|ARNTL2_ENST00000261178.5_Missense_Mutation_p.N292S|ARNTL2_ENST00000542388.1_Missense_Mutation_p.N255S|ARNTL2_ENST00000395901.2_Missense_Mutation_p.N303S|ARNTL2_ENST00000311001.5_Missense_Mutation_p.N326S|ARNTL2_ENST00000544915.1_Missense_Mutation_p.N306S			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	340			N -> S (in dbSNP:rs1037921).		circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|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)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					AAGAAAGACAACAGTAATTTT	0.383													A|||	164	0.0327476	0.0242	0.0115	5008	,	,		15831	0.001		0.0537	False		,,,				2504	0.0706				p.N340S		Atlas-SNP	.											.	ARNTL2	54	.	0			c.A1019G						PASS	.	A	SER/ASN	106,4300	82.4+/-120.9	0,106,2097	110.0	112.0	111.0		1019	0.4	0.0	12	dbSNP_86	111	415,8185	130.2+/-188.1	7,401,3892	yes	missense	ARNTL2	NM_020183.3	46	7,507,5989	GG,GA,AA		4.8256,2.4058,4.0058	benign	340/637	27553566	521,12485	2203	4300	6503	SO:0001583	missense	56938	exon10			AAGACAACAGTAA	AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"""Basic helix-loop-helix proteins"""	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.1019A>G	12.37:g.27553566A>G	ENSP00000266503:p.Asn340Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_020183	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Missense_Mutation	SNP	ENST00000266503.5	37	CCDS8712.1	68|68	0.031135531135531136|0.031135531135531136	16|16	0.032520325203252036|0.032520325203252036	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	45|45	0.059366754617414245|0.059366754617414245	A|A	0.021|0.021	-1.431239|-1.431239	0.01117|0.01117	0.024058|0.024058	0.048256|0.048256	ENSG00000029153|ENSG00000029153	ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388|ENST00000457040	T;T;T;T;T;T;T|.	0.05649|.	3.58;3.57;3.41;3.57;3.58;3.58;3.57|.	3.59|3.59	0.4|0.4	0.16331|0.16331	.|.	0.461885|.	0.25280|.	N|.	0.031806|.	T|T	0.00695|0.00695	0.0023|0.0023	N|N	0.00197|0.00197	-1.87|-1.87	0.09310|0.09310	N|N	1|1	B;B;B;B;B;B|.	0.06786|.	0.001;0.0;0.001;0.0;0.0;0.0|.	B;B;B;B;B;B|.	0.06405|.	0.002;0.0;0.002;0.002;0.001;0.0|.	T|T	0.33854|0.33854	-0.9852|-0.9852	10|5	0.07813|.	T|.	0.8|.	.|.	11.1064|11.1064	0.48205|0.48205	0.1307:0.0:0.8693:0.0|0.1307:0.0:0.8693:0.0	rs1037921;rs17414198;rs52796079;rs57238219;rs1037921|rs1037921;rs17414198;rs52796079;rs57238219;rs1037921	303;306;303;292;326;340|.	F5H402;Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1|.	.;.;.;.;.;BMAL2_HUMAN|.	S|A	306;303;303;326;292;340;255|292	ENSP00000442438:N306S;ENSP00000379238:N303S;ENSP00000438545:N303S;ENSP00000312247:N326S;ENSP00000261178:N292S;ENSP00000266503:N340S;ENSP00000445836:N255S|.	ENSP00000261178:N292S|.	N|T	+|+	2|1	0|0	ARNTL2|ARNTL2	27444833|27444833	0.991000|0.991000	0.36638|0.36638	0.001000|0.001000	0.08648|0.08648	0.916000|0.916000	0.54674|0.54674	3.930000|3.930000	0.56522|0.56522	-0.050000|-0.050000	0.13356|0.13356	-0.250000|-0.250000	0.11733|0.11733	AAC|ACA	A|0.963;G|0.037	0.037	strong		0.383	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183	
SPATA16	83893	hgsc.bcm.edu	37	3	172835125	172835125	+	Missense_Mutation	SNP	T	T	C	rs1515442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:172835125T>C	ENST00000351008.3	-	2	580	c.397A>G	c.(397-399)Atg>Gtg	p.M133V		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	133			M -> V (in dbSNP:rs1515442). {ECO:0000269|PubMed:17665087}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			CGAACACCCATTTCATCAATG	0.413													C|||	2146	0.428514	0.7247	0.3055	5008	,	,		22397	0.374		0.2465	False		,,,				2504	0.3589				p.M133V		Atlas-SNP	.											SPATA16,NS,carcinoma,+2,1	SPATA16	111	1	0			c.A397G						PASS	.	C	VAL/MET	2875,1531	484.4+/-360.0	951,973,279	291.0	266.0	274.0		397	5.7	1.0	3	dbSNP_88	274	2381,6219	701.5+/-405.2	336,1709,2255	yes	missense	SPATA16	NM_031955.5	21	1287,2682,2534	CC,CT,TT		27.686,34.7481,40.4121	benign	133/570	172835125	5256,7750	2203	4300	6503	SO:0001583	missense	83893	exon2			CACCCATTTCATC	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.397A>G	3.37:g.172835125T>C	ENSP00000341765:p.Met133Val	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	261	137	0.524904	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	37	CCDS3221.1	866	0.3965201465201465	336	0.6829268292682927	108	0.2983425414364641	233	0.40734265734265734	189	0.24934036939313983	C	4.300	0.054895	0.08291	0.652519	0.27686	ENSG00000144962	ENST00000351008	T	0.13901	2.55	5.67	5.67	0.87782	.	0.221006	0.31335	N	0.007839	T	0.00012	0.0000	N	0.08118	0	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.19031	-1.0318	9	0.37606	T	0.19	-8.0923	9.6819	0.40076	0.0:0.7837:0.1403:0.0761	rs1515442;rs52810826;rs57404795;rs1515442	133	Q9BXB7	SPT16_HUMAN	V	133	ENSP00000341765:M133V	ENSP00000341765:M133V	M	-	1	0	SPATA16	174317819	1.000000	0.71417	0.970000	0.41538	0.167000	0.22549	1.498000	0.35660	1.405000	0.46838	-0.227000	0.12334	ATG	T|0.604;C|0.396	0.396	strong		0.413	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955	
PCSK5	5125	hgsc.bcm.edu	37	9	78938043	78938043	+	Missense_Mutation	SNP	G	G	A	rs2495207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:78938043G>A	ENST00000545128.1	+	31	4635	c.4097G>A	c.(4096-4098)cGc>cAc	p.R1366H		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1366	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						GCAGACTCGCGCCACTGTGTC	0.567													G|||	1605	0.320487	0.4667	0.2349	5008	,	,		14582	0.1369		0.3529	False		,,,				2504	0.3395				p.R1366H		Atlas-SNP	.											.	PCSK5	329	.	0			c.G4097A						PASS	.	G	HIS/ARG	793,959		189,415,272	30.0	28.0	28.0		4097	-1.5	0.0	9	dbSNP_100	28	1346,2636		236,874,881	yes	missense	PCSK5	NM_001190482.1	29	425,1289,1153	AA,AG,GG		33.8021,45.2626,37.3038	possibly-damaging	1366/1861	78938043	2139,3595	876	1991	2867	SO:0001583	missense	5125	exon31			ACTCGCGCCACTG		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.4097G>A	9.37:g.78938043G>A	ENSP00000446280:p.Arg1366His	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	128	86	0.671875	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	685	0.31364468864468864	239	0.48577235772357724	98	0.27071823204419887	76	0.13286713286713286	272	0.35883905013192613	G	12.57	1.976900	0.34848	0.452626	0.338021	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.29397	1.57;1.6	5.65	-1.45	0.08828	.	0.871179	0.10360	N	0.684122	T	0.00012	0.0000	M	0.62016	1.91	0.80722	P	0.0	.	.	.	.	.	.	T	0.47923	-0.9079	7	0.42905	T	0.14	-12.1217	7.6077	0.28112	0.4202:0.1113:0.4685:0.0	rs2495207;rs17721339;rs56436828;rs61557544;rs2495207	.	.	.	H	1366;1096;1066	ENSP00000446280:R1366H;ENSP00000411654:R1066H	ENSP00000365945:R1096H	R	+	2	0	PCSK5	78127863	0.000000	0.05858	0.013000	0.15412	0.082000	0.17680	-0.184000	0.09698	0.077000	0.16863	0.650000	0.86243	CGC	G|0.668;A|0.332	0.332	strong		0.567	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PCDHB15	56121	hgsc.bcm.edu	37	5	140627184	140627184	+	Missense_Mutation	SNP	C	C	G	rs79326925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140627184C>G	ENST00000231173.3	+	1	2038	c.2038C>G	c.(2038-2040)Caa>Gaa	p.Q680E		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	680					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.Q680K(1)		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)			GGCCCCGGCCCAAGCCCAGGC	0.672													C|||	103	0.0205671	0.0734	0.0072	5008	,	,		16390	0.0		0.001	False		,,,				2504	0.0				p.Q680E		Atlas-SNP	.											.	PCDHB15	138	.	1	Substitution - Missense(1)	lung(1)	c.C2038G						PASS	.	C	GLU/GLN	247,4147		5,237,1955	62.0	68.0	66.0		2038	0.1	0.0	5	dbSNP_131	66	0,8572		0,0,4286	no	missense	PCDHB15	NM_018935.2	29	5,237,6241	GG,GC,CC		0.0,5.6213,1.905	benign	680/788	140627184	247,12719	2197	4286	6483	SO:0001583	missense	56121	exon1			CCGGCCCAAGCCC	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.2038C>G	5.37:g.140627184C>G	ENSP00000231173:p.Gln680Glu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	109	63	0.577982	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	C	8.308	0.821498	0.16678	0.056213	0.0	ENSG00000113248	ENST00000231173	T	0.46063	0.88	4.25	0.0585	0.14328	.	.	.	.	.	T	0.01592	0.0051	L	0.31120	0.905	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.09185	-1.0686	9	0.10636	T	0.68	.	15.5586	0.76219	0.0:0.5083:0.4917:0.0	.	680	Q9Y5E8	PCDBF_HUMAN	E	680	ENSP00000231173:Q680E	ENSP00000231173:Q680E	Q	+	1	0	PCDHB15	140607368	0.000000	0.05858	0.000000	0.03702	0.360000	0.29518	-0.150000	0.10189	-0.255000	0.09486	0.549000	0.68633	CAA	C|0.979;G|0.021	0.021	strong		0.672	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
NCLN	56926	hgsc.bcm.edu	37	19	3207398	3207398	+	Silent	SNP	G	G	A	rs76473246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3207398G>A	ENST00000246117.4	+	14	1994	c.1563G>A	c.(1561-1563)ccG>ccA	p.P521P	NCLN_ENST00000590671.1_Silent_p.P447P	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	521					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)		GAGTCAAGCCGGCCGTCTTTG	0.652													A|||	149	0.0297524	0.1059	0.013	5008	,	,		16237	0.0		0.0	False		,,,				2504	0.0				p.P521P		Atlas-SNP	.											.	NCLN	27	.	0			c.G1563A						PASS	.	A		442,3964	778.2+/-414.3	15,412,1776	137.0	132.0	134.0		1563	-8.7	0.7	19	dbSNP_131	134	4,8596	812.7+/-407.1	0,4,4296	no	coding-synonymous	NCLN	NM_020170.3		15,416,6072	AA,AG,GG		0.0465,10.0318,3.4292		521/564	3207398	446,12560	2203	4300	6503	SO:0001819	synonymous_variant	56926	exon14			CAAGCCGGCCGTC	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.1563G>A	19.37:g.3207398G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_020170	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Silent	SNP	ENST00000246117.4	37	CCDS32869.1																																																																																			G|0.967;A|0.033	0.033	strong		0.652	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1	NM_020170	
USP6	9098	hgsc.bcm.edu	37	17	5037241	5037241	+	Silent	SNP	G	G	A	rs117611547		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5037241G>A	ENST00000574788.1	+	15	2674	c.444G>A	c.(442-444)gtG>gtA	p.V148V	USP6_ENST00000304328.5_5'UTR|USP6_ENST00000332776.4_Silent_p.V148V|USP6_ENST00000250066.6_Silent_p.V148V			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	148	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.V148V(3)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						ACCTGGACGTGAGGACGACTC	0.557			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts																																p.V148V		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	USP6_ENST00000250066,NS,carcinoma,0,3	USP6	213	3	3	Substitution - coding silent(3)	ovary(2)|skin(1)	c.G444A						scavenged	.						220.0	174.0	189.0					17																	5037241		2203	4300	6503	SO:0001819	synonymous_variant	9098	exon7			GGACGTGAGGACG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.444G>A	17.37:g.5037241G>A		Somatic	92	3	0.0326087		WXS	Illumina HiSeq	Phase_I	105	4	0.0380952	NM_004505	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	37	CCDS11069.2																																																																																			.	.	weak		0.557	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
SMARCA2	6595	hgsc.bcm.edu	37	9	2039779	2039779	+	Silent	SNP	G	G	A	rs376509101|rs62639301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2039779G>A	ENST00000382203.1	+	4	878	c.669G>A	c.(667-669)caG>caA	p.Q223Q	RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000349721.2_Silent_p.Q223Q|SMARCA2_ENST00000382194.1_Silent_p.Q223Q|SMARCA2_ENST00000491574.1_3'UTR|SMARCA2_ENST00000357248.2_Silent_p.Q223Q			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	223	Poly-Gln.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|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)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		agcagcaacagcagcagcagc	0.642																																					p.Q223Q		Atlas-SNP	.											SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	0			c.G669A						scavenged	.						10.0	13.0	12.0					9																	2039779		2187	4260	6447	SO:0001819	synonymous_variant	6595	exon4			GCAACAGCAGCAG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.669G>A	9.37:g.2039779G>A		Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			G|0.889;A|0.111	0.111	strong		0.642	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
AOC1	26	hgsc.bcm.edu	37	7	150554553	150554553	+	Missense_Mutation	SNP	C	C	T	rs1049742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150554553C>T	ENST00000493429.1	+	4	1579	c.995C>T	c.(994-996)tCc>tTc	p.S332F	AOC1_ENST00000467291.1_Missense_Mutation_p.S332F|AOC1_ENST00000360937.4_Missense_Mutation_p.S332F|AOC1_ENST00000416793.2_Missense_Mutation_p.S332F			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	332			S -> F (in dbSNP:rs1049742). {ECO:0000269|PubMed:8595053, ECO:0000269|Ref.4}.		amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	CGCTCCTCCTCCGGGCTGCAG	0.667													C|||	266	0.053115	0.0877	0.0605	5008	,	,		14622	0.002		0.0785	False		,,,				2504	0.0276				p.S332F		Atlas-SNP	.											.	ABP1	92	.	0			c.C995T						PASS	.	C	PHE/SER	379,4021		22,335,1843	29.0	31.0	30.0		995	5.0	0.1	7	dbSNP_86	30	634,7962		17,600,3681	yes	missense	ABP1	NM_001091.2	155	39,935,5524	TT,TC,CC		7.3755,8.6136,7.7947	probably-damaging	332/752	150554553	1013,11983	2200	4298	6498	SO:0001583	missense	26	exon2			CCTCCTCCGGGCT	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.995C>T	7.37:g.150554553C>T	ENSP00000418614:p.Ser332Phe	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	37	CCDS43679.1	126	0.057692307692307696	43	0.08739837398373984	26	0.0718232044198895	0	0.0	57	0.07519788918205805	C	17.14	3.312468	0.60414	0.086136	0.073755	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000360937;ENST00000416793;ENST00000437714;ENST00000483043	T;T;T;T;T	0.04194	3.68;3.68;3.68;3.68;3.68	4.96	4.96	0.65561	Copper amine oxidase, C-terminal (3);	0.350050	0.28630	N	0.014677	T	0.00906	0.0030	M	0.87547	2.89	0.18873	N	0.999987	P;D	0.62365	0.914;0.991	P;D	0.71414	0.646;0.973	T	0.00022	-1.2336	10	0.72032	D	0.01	-17.8832	16.083	0.81017	0.0:1.0:0.0:0.0	rs1049742;rs3189948;rs1049742	332;332	C9J690;P19801	.;ABP1_HUMAN	F	332;332;332;332;208;332	ENSP00000418614:S332F;ENSP00000418328:S332F;ENSP00000354193:S332F;ENSP00000411613:S332F;ENSP00000417392:S332F	ENSP00000354193:S332F	S	+	2	0	ABP1	150185486	0.006000	0.16342	0.094000	0.20943	0.974000	0.67602	2.255000	0.43222	2.735000	0.93741	0.561000	0.74099	TCC	C|0.946;T|0.054	0.054	strong		0.667	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
FAM86B1	85002	hgsc.bcm.edu	37	8	12044042	12044042	+	Silent	SNP	G	G	A	rs148527538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:12044042G>A	ENST00000448228.2	-	5	508	c.459C>T	c.(457-459)agC>agT	p.S153S	FAM86B1_ENST00000533852.2_Silent_p.S187S|FAM86B1_ENST00000321602.8_Intron|FAM86B1_ENST00000533513.1_3'UTR|FAM86B1_ENST00000534520.1_Intron	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	153								p.S187S(1)		kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		TGTGAGGGTCGCTGAAGATGT	0.612																																					p.S153S		Atlas-SNP	.											FAM86B1,NS,carcinoma,0,1	FAM86B1	7	1	1	Substitution - coding silent(1)	stomach(1)	c.C459T						scavenged	.						32.0	36.0	35.0					8																	12044042		1480	2621	4101	SO:0001819	synonymous_variant	85002	exon5			AGGGTCGCTGAAG	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.459C>T	8.37:g.12044042G>A		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	474	49	0.103376	NM_001083537		Silent	SNP	ENST00000448228.2	37	CCDS59512.1																																																																																			G|0.500;A|0.500	0.500	strong		0.612	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916	
TMEM60	85025	hgsc.bcm.edu	37	7	77423574	77423574	+	Silent	SNP	G	G	A	rs7953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:77423574G>A	ENST00000257663.3	-	2	493	c.117C>T	c.(115-117)ttC>ttT	p.F39F		NM_032936.3	NP_116325.1	Q9H2L4	TMM60_HUMAN	transmembrane protein 60	39						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)	4						AGACTGGAATGAATATGAGGA	0.448													A|||	2838	0.566693	0.8646	0.4424	5008	,	,		20016	0.3165		0.508	False		,,,				2504	0.5706				p.F39F		Atlas-SNP	.											.	TMEM60	24	.	0			c.C117T						PASS	.	A		3494,912	348.2+/-309.8	1386,722,95	76.0	76.0	76.0		117	3.8	1.0	7	dbSNP_52	76	4227,4373	583.0+/-391.5	1081,2065,1154	no	coding-synonymous	TMEM60	NM_032936.3		2467,2787,1249	AA,AG,GG		49.1512,20.699,40.6351		39/134	77423574	7721,5285	2203	4300	6503	SO:0001819	synonymous_variant	85025	exon2			TGGAATGAATATG	AF260336	CCDS5593.1	7q11.23	2005-07-25	2005-07-25	2005-07-25	ENSG00000135211	ENSG00000135211			21754	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 35"""	C7orf35			Standard	NM_032936		Approved	DC32	uc003ugn.3	Q9H2L4	OTTHUMG00000130689	ENST00000257663.3:c.117C>T	7.37:g.77423574G>A		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_032936	A4D1C3|Q86UM0	Silent	SNP	ENST00000257663.3	37	CCDS5593.1																																																																																			G|0.424;A|0.576	0.576	strong		0.448	TMEM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253185.2	NM_032936	
THOP1	7064	hgsc.bcm.edu	37	19	2790508	2790508	+	Missense_Mutation	SNP	C	C	T	rs76198851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2790508C>T	ENST00000307741.6	+	2	309	c.106C>T	c.(106-108)Cgc>Tgc	p.R36C		NM_003249.3	NP_003240.1	P52888	THOP1_HUMAN	thimet oligopeptidase 1	36					intracellular signal transduction (GO:0035556)|peptide metabolic process (GO:0006518)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			NS(1)|central_nervous_system(1)|endometrium(1)|lung(8)|ovary(2)|skin(1)	14				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)		GATAGAGGAGCGCACCAGGGA	0.612													C|||	13	0.00259585	0.0098	0.0	5008	,	,		20345	0.0		0.0	False		,,,				2504	0.0				p.R36C		Atlas-SNP	.											.	THOP1	49	.	0			c.C106T						PASS	.	C	CYS/ARG	28,4378	36.0+/-67.5	0,28,2175	115.0	95.0	102.0		106	3.9	0.0	19	dbSNP_131	102	0,8600		0,0,4300	yes	missense	THOP1	NM_003249.3	180	0,28,6475	TT,TC,CC		0.0,0.6355,0.2153	probably-damaging	36/690	2790508	28,12978	2203	4300	6503	SO:0001583	missense	7064	exon2			GAGGAGCGCACCA		CCDS12095.1	19p13.3	2008-02-05				ENSG00000172009	3.4.24.15		11793	protein-coding gene	gene with protein product		601117				9790774	Standard	NM_003249		Approved		uc002lwj.3	P52888		ENST00000307741.6:c.106C>T	19.37:g.2790508C>T	ENSP00000304467:p.Arg36Cys	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_003249	B3KSE2|Q9UCB3	Missense_Mutation	SNP	ENST00000307741.6	37	CCDS12095.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	16.20	3.056103	0.55325	0.006355	0.0	ENSG00000172009	ENST00000307741	T	0.08193	3.12	4.9	3.86	0.44501	Neurolysin/Thimet oligopeptidase, N-terminal (1);	0.130158	0.52532	D	0.000063	T	0.11879	0.0289	M	0.68952	2.095	0.50039	D	0.999846	D	0.67145	0.996	P	0.53450	0.726	T	0.00494	-1.1706	10	0.66056	D	0.02	-22.5297	8.1975	0.31405	0.1546:0.7598:0.0:0.0856	.	36	P52888	THOP1_HUMAN	C	36	ENSP00000304467:R36C	ENSP00000304467:R36C	R	+	1	0	THOP1	2741508	0.704000	0.27836	0.010000	0.14722	0.544000	0.35116	3.482000	0.53186	1.055000	0.40461	0.561000	0.74099	CGC	C|0.998;T|0.002	0.002	strong		0.612	THOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451587.2		
SLX4	84464	hgsc.bcm.edu	37	16	3656557	3656557	+	Silent	SNP	G	G	A	rs28516461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3656557G>A	ENST00000294008.3	-	3	1318	c.678C>T	c.(676-678)caC>caT	p.H226H		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	226	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CTTCTGAAGCGTGTCTCAAAC	0.542								Direct reversal of damage					G|||	660	0.131789	0.3139	0.0576	5008	,	,		18893	0.0337		0.0179	False		,,,				2504	0.1564				p.H226H		Atlas-SNP	.											.	SLX4	173	.	0			c.C678T						PASS	.	G		1109,3285	399.5+/-331.2	132,845,1220	222.0	221.0	221.0		678	-1.2	0.0	16	dbSNP_125	221	127,8473	64.2+/-126.4	0,127,4173	no	coding-synonymous	SLX4	NM_032444.2		132,972,5393	AA,AG,GG		1.4767,25.239,9.5121		226/1835	3656557	1236,11758	2197	4300	6497	SO:0001819	synonymous_variant	84464	exon3			TGAAGCGTGTCTC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.678C>T	16.37:g.3656557G>A		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	259	121	0.467181	NM_032444	Q69YT8|Q8TF15|Q96JP1	Silent	SNP	ENST00000294008.3	37	CCDS10506.2																																																																																			G|0.891;A|0.109	0.109	strong		0.542	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
ZNF469	84627	hgsc.bcm.edu	37	16	88501999	88501999	+	Silent	SNP	G	G	A	rs116696830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88501999G>A	ENST00000437464.1	+	2	8037	c.8037G>A	c.(8035-8037)gcG>gcA	p.A2679A	ZNF469_ENST00000565624.1_Silent_p.A2707A	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2679					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						AGGGTGCAGCGGAGACTGACC	0.662													G|||	61	0.0121805	0.0416	0.0072	5008	,	,		15538	0.0		0.0	False		,,,				2504	0.001				p.A2679A		Atlas-SNP	.											.	ZNF469	121	.	0			c.G8037A						PASS	.	G		51,1333		1,49,642	26.0	31.0	30.0		8037	-9.1	0.0	16	dbSNP_132	30	0,3180		0,0,1590	yes	coding-synonymous	ZNF469	NM_001127464.1		1,49,2232	AA,AG,GG		0.0,3.685,1.1174		2679/3926	88501999	51,4513	692	1590	2282	SO:0001819	synonymous_variant	84627	exon2			TGCAGCGGAGACT	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.8037G>A	16.37:g.88501999G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			G|0.992;A|0.008	0.008	strong		0.662	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
DIDO1	11083	hgsc.bcm.edu	37	20	61512185	61512185	+	Missense_Mutation	SNP	G	G	C	rs41282984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61512185G>C	ENST00000266070.4	-	16	5448	c.5123C>G	c.(5122-5124)tCt>tGt	p.S1708C	DIDO1_ENST00000395343.1_Missense_Mutation_p.S1708C	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1708			S -> C (in dbSNP:rs41282984).		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)					CCTTCCAGCAGAATGAAGATT	0.652													G|||	277	0.0553115	0.1097	0.0216	5008	,	,		15522	0.0198		0.0596	False		,,,				2504	0.0378				p.S1708C	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C5123G						PASS	.	G	CYS/SER,CYS/SER	505,3901	229.1+/-243.8	20,465,1718	58.0	68.0	64.0		5123,5123	1.8	0.0	20	dbSNP_127	64	678,7922	167.4+/-219.2	33,612,3655	yes	missense,missense	DIDO1	NM_001193369.1,NM_033081.2	112,112	53,1077,5373	CC,CG,GG		7.8837,11.4616,9.0958	possibly-damaging,possibly-damaging	1708/2241,1708/2241	61512185	1183,11823	2203	4300	6503	SO:0001583	missense	11083	exon16			CCAGCAGAATGAA	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.5123C>G	20.37:g.61512185G>C	ENSP00000266070:p.Ser1708Cys	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	120	63	0.525	NM_001193369	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	127	0.05815018315018315	53	0.10772357723577236	12	0.03314917127071823	10	0.017482517482517484	52	0.06860158311345646	G	11.14	1.550129	0.27652	0.114616	0.078837	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.08896	3.04;3.04	5.31	1.8	0.24995	.	0.165815	0.28371	N	0.015596	T	0.00109	0.0003	N	0.19112	0.55	0.58432	P	5.000000000032756E-6	B	0.09022	0.002	B	0.04013	0.001	T	0.31861	-0.9928	9	0.54805	T	0.06	-0.623	4.2819	0.10836	0.4482:0.4274:0.1244:0.0	rs41282984	1708	Q9BTC0	DIDO1_HUMAN	C	1708	ENSP00000266070:S1708C;ENSP00000378752:S1708C	ENSP00000266070:S1708C	S	-	2	0	DIDO1	60982630	0.903000	0.30736	0.001000	0.08648	0.047000	0.14425	2.065000	0.41442	0.071000	0.16664	0.655000	0.94253	TCT	G|0.921;C|0.079	0.079	strong		0.652	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
CBX2	84733	hgsc.bcm.edu	37	17	77757845	77757845	+	Silent	SNP	C	C	T	rs8080971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77757845C>T	ENST00000310942.4	+	5	707	c.603C>T	c.(601-603)ccC>ccT	p.P201P		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	201					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)			GCAAGCTGCCCCCTCCACTCA	0.701													C|||	291	0.058107	0.2005	0.0274	5008	,	,		14296	0.0		0.007	False		,,,				2504	0.0				p.P201P		Atlas-SNP	.											.	CBX2	50	.	0			c.C603T						PASS	.	C		735,3657		66,603,1527	19.0	26.0	23.0		603	-3.6	0.9	17	dbSNP_116	23	27,8559		0,27,4266	no	coding-synonymous	CBX2	NM_005189.2		66,630,5793	TT,TC,CC		0.3145,16.735,5.8715		201/533	77757845	762,12216	2196	4293	6489	SO:0001819	synonymous_variant	84733	exon5			GCTGCCCCCTCCA	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.603C>T	17.37:g.77757845C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	68	49	0.720588	NM_005189	Q0VDA5|Q9BTB1	Silent	SNP	ENST00000310942.4	37	CCDS32757.1																																																																																			C|0.948;T|0.052	0.052	strong		0.701	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
MAPK1	5594	hgsc.bcm.edu	37	22	22162126	22162126	+	Silent	SNP	A	A	G	rs3729910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:22162126A>G	ENST00000215832.6	-	2	317	c.129T>C	c.(127-129)taT>taC	p.Y43Y	MAPK1_ENST00000398822.3_Silent_p.Y43Y|MAPK1_ENST00000544786.1_Silent_p.Y43Y	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	43	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|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)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|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, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	TGACATTATCATAAGCAGAGC	0.383													A|||	153	0.0305511	0.0174	0.0461	5008	,	,		20863	0.0238		0.0537	False		,,,				2504	0.0204				p.Y43Y		Atlas-SNP	.											.	MAPK1	38	.	0			c.T129C						PASS	.	A	,	95,4311	76.8+/-115.0	1,93,2109	96.0	97.0	97.0		129,129	4.5	1.0	22	dbSNP_107	97	522,8078	146.2+/-201.8	18,486,3796	no	coding-synonymous,coding-synonymous	MAPK1	NM_002745.4,NM_138957.2	,	19,579,5905	GG,GA,AA		6.0698,2.1562,4.744	,	43/361,43/361	22162126	617,12389	2203	4300	6503	SO:0001819	synonymous_variant	5594	exon2			ATTATCATAAGCA	M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1			Standard	NM_138957		Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.129T>C	22.37:g.22162126A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	69	37	0.536232	NM_002745	A8CZ64	Silent	SNP	ENST00000215832.6	37	CCDS13795.1																																																																																			A|0.955;G|0.045	0.045	strong		0.383	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075396.2		
ZFPM2	23414	hgsc.bcm.edu	37	8	106814695	106814695	+	Silent	SNP	C	C	G	rs35998713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:106814695C>G	ENST00000407775.2	+	8	2635	c.2385C>G	c.(2383-2385)gtC>gtG	p.V795V	RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000378472.4_Silent_p.V526V|ZFPM2_ENST00000520492.1_Silent_p.V663V|ZFPM2_ENST00000517361.1_Silent_p.V663V|RP11-152P17.2_ENST00000509144.2_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	795					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			CAGGAATTGTCTCTAAACACT	0.453													C|||	332	0.0662939	0.1717	0.0403	5008	,	,		21165	0.0069		0.0268	False		,,,				2504	0.044				p.V795V		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C2385G						PASS	.	C		496,3310		32,432,1439	62.0	59.0	60.0		2385	4.8	1.0	8	dbSNP_126	60	191,8081		1,189,3946	no	coding-synonymous	ZFPM2	NM_012082.3		33,621,5385	GG,GC,CC		2.309,13.0321,5.688		795/1152	106814695	687,11391	1903	4136	6039	SO:0001819	synonymous_variant	23414	exon8			AATTGTCTCTAAA	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.2385C>G	8.37:g.106814695C>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	172	83	0.482558	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Silent	SNP	ENST00000407775.2	37	CCDS47908.1																																																																																			C|0.952;G|0.048	0.048	strong		0.453	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
BHLHE41	79365	hgsc.bcm.edu	37	12	26275297	26275297	+	Missense_Mutation	SNP	G	G	T	rs121912617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26275297G>T	ENST00000242728.4	-	5	1498	c.1151C>A	c.(1150-1152)cCg>cAg	p.P384Q	RP11-283G6.3_ENST00000535914.1_RNA|RP11-283G6.3_ENST00000545819.1_RNA	NM_030762.2	NP_110389.1	Q9C0J9	BHE41_HUMAN	basic helix-loop-helix family, member e41	384	Ala/Gly-rich.		P -> R (associated with short sleep phenotype). {ECO:0000269|PubMed:19679812}.		cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|MRF binding (GO:0043426)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)	5						CAGCGGGAACGGGGCGGCAGC	0.741													G|||	36	0.0071885	0.0227	0.0086	5008	,	,		4052	0.0		0.0	False		,,,				2504	0.0				p.P384Q		Atlas-SNP	.											.	BHLHE41	20	.	0			c.C1151A						PASS	.						2.0	3.0	2.0					12																	26275297		1465	3164	4629	SO:0001583	missense	79365	exon5			GGGAACGGGGCGG	AB044088	CCDS8706.1	12p12.1	2011-12-05	2009-01-12	2009-01-12	ENSG00000123095	ENSG00000123095		"""Basic helix-loop-helix proteins"""	16617	protein-coding gene	gene with protein product	"""differentially expressed in chondrocytes 2"", ""Enhancer-of-split and hairy-related protein 1"""	606200	"""basic helix-loop-helix domain containing, class B, 3"""	BHLHB3		11162494, 18557763	Standard	NM_030762		Approved	DEC2, SHARP-1, SHARP1, bHLHe41	uc001rhb.3	Q9C0J9	OTTHUMG00000169174	ENST00000242728.4:c.1151C>A	12.37:g.26275297G>T	ENSP00000242728:p.Pro384Gln	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_030762	A2I2N8	Missense_Mutation	SNP	ENST00000242728.4	37	CCDS8706.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.622122	0.46840	.	.	ENSG00000123095	ENST00000242728	T	0.79141	-1.24	3.09	3.09	0.35607	.	1.892810	0.04121	U	0.316359	T	0.75280	0.3828	L	0.38838	1.175	0.80722	D	1	D	0.53151	0.958	P	0.44860	0.462	T	0.68443	-0.5407	10	0.87932	D	0	.	11.9445	0.52920	0.0:0.0:1.0:0.0	.	384	Q9C0J9	BHE41_HUMAN	Q	384	ENSP00000242728:P384Q	ENSP00000242728:P384Q	P	-	2	0	BHLHE41	26166564	1.000000	0.71417	0.985000	0.45067	0.044000	0.14063	7.845000	0.86875	1.435000	0.47434	0.471000	0.43371	CCG	.	.	alt		0.741	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762	
OR5L2	26338	hgsc.bcm.edu	37	11	55595114	55595114	+	Silent	SNP	G	G	T	rs34929168|rs386753701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55595114G>T	ENST00000378397.1	+	1	420	c.420G>T	c.(418-420)ctG>ctT	p.L140L		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	140						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)				CTCAGAAGCTGCGTGTGGAGC	0.522										HNSCC(27;0.073)			N|||	449	0.0896565	0.1309	0.0403	5008	,	,		21339	0.0853		0.0924	False		,,,				2504	0.0706				p.L140L		Atlas-SNP	.											.	OR5L2	135	.	0			c.G420T						PASS	.						211.0	182.0	192.0					11																	55595114		2200	4296	6496	SO:0001819	synonymous_variant	26338	exon1			GAAGCTGCGTGTG	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.420G>T	11.37:g.55595114G>T		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	280	126	0.45	NM_001004739	Q6IF66|Q96RB2	Silent	SNP	ENST00000378397.1	37	CCDS31511.1																																																																																			G|0.913;T|0.087	0.087	strong		0.522	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
KMT2C	58508	hgsc.bcm.edu	37	7	151873853	151873853	+	Silent	SNP	C	C	T	rs6464211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151873853C>T	ENST00000262189.6	-	38	8903	c.8685G>A	c.(8683-8685)caG>caA	p.Q2895Q	KMT2C_ENST00000355193.2_Silent_p.Q2895Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2895					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)										GAGTGGATGCCTGAATGACAT	0.398													T|||	1917	0.382788	0.7549	0.2392	5008	,	,		20363	0.3016		0.17	False		,,,				2504	0.2843				p.Q2895Q		Atlas-SNP	.											.	MLL3	1564	.	0			c.G8685A						PASS	.	T		3030,1376	455.9+/-351.1	1049,932,222	94.0	93.0	93.0		8685	-3.6	0.0	7	dbSNP_116	93	1408,7192	753.3+/-407.4	126,1156,3018	no	coding-synonymous	MLL3	NM_170606.2		1175,2088,3240	TT,TC,CC		16.3721,31.2301,34.1227		2895/4912	151873853	4438,8568	2203	4300	6503	SO:0001819	synonymous_variant	58508	exon38			GGATGCCTGAATG	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.8685G>A	7.37:g.151873853C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	173	86	0.49711	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1	754	0.34523809523809523	358	0.7276422764227642	92	0.2541436464088398	170	0.2972027972027972	134	0.17678100263852242	T	0.007	-1.957464	0.00465	0.687699	0.163721	ENSG00000055609	ENST00000360104	.	.	.	5.12	-3.6	0.04570	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46798	P	7.970000000000477E-4	.	.	.	.	.	.	T	0.38436	-0.9661	3	.	.	.	.	0.8674	0.01206	0.1496:0.2894:0.2562:0.3048	rs6464211;rs13236845;rs60172642;rs6464211	.	.	.	S	401	.	.	G	-	1	0	MLL3	151504786	0.092000	0.21681	0.000000	0.03702	0.138000	0.21146	0.169000	0.16641	-1.511000	0.01794	-1.256000	0.01477	GGC	C|0.643;T|0.357	0.357	strong		0.398	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
RGS3	5998	hgsc.bcm.edu	37	9	116346118	116346118	+	Missense_Mutation	SNP	G	G	A	rs41305473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116346118G>A	ENST00000374140.2	+	21	2635	c.2426G>A	c.(2425-2427)cGg>cAg	p.R809Q	RGS3_ENST00000462143.1_Missense_Mutation_p.R130Q|RP11-168K11.2_ENST00000428429.1_RNA|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000374134.3_Missense_Mutation_p.R130Q|RGS3_ENST00000343817.5_Missense_Mutation_p.R528Q|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000350696.5_Missense_Mutation_p.R809Q	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	809	Pro-rich.		R -> Q (in dbSNP:rs41305473).		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						TCCCCCACCCGGGACCTTCCA	0.617													g|||	428	0.0854633	0.18	0.0692	5008	,	,		17267	0.0		0.1034	False		,,,				2504	0.0389				p.R809Q		Atlas-SNP	.											.	RGS3	251	.	0			c.G2426A						PASS	.	G	GLN/ARG,GLN/ARG,,GLN/ARG	803,3603	322.9+/-297.8	85,633,1485	128.0	142.0	137.0		389,1583,,2426	2.6	1.0	9	dbSNP_127	137	900,7700	200.7+/-244.4	40,820,3440	yes	missense,missense,intron,missense	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4	43,43,,43	125,1453,4925	AA,AG,GG		10.4651,18.2251,13.094	benign,benign,,benign	130/520,528/918,,809/1199	116346118	1703,11303	2203	4300	6503	SO:0001583	missense	5998	exon21			CCACCCGGGACCT	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.2426G>A	9.37:g.116346118G>A	ENSP00000363255:p.Arg809Gln	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	62	0.666667	NM_144488	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	190	0.08699633699633699	82	0.16666666666666666	28	0.07734806629834254	0	0.0	80	0.10554089709762533	g	4.500	0.092706	0.08632	0.182251	0.104651	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000343817;ENST00000462143;ENST00000374134	T;T;T;T;T	0.55760	1.0;1.0;0.5;0.51;0.51	4.97	2.57	0.30868	.	0.286735	0.28914	N	0.013727	T	0.00039	0.0001	N	0.01874	-0.695	0.09310	P	0.999999999897227	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	0.14896	-1.0456	9	0.05525	T	0.97	.	2.2403	0.04018	0.5987:0.1609:0.0857:0.1548	rs41305473;rs61754069	148;705;130;528;699;809	B4DWF9;P49796-6;Q6ZV17;P49796-4;B3KWG8;P49796	.;.;.;.;.;RGS3_HUMAN	Q	809;809;528;130;130	ENSP00000363255:R809Q;ENSP00000259406:R809Q;ENSP00000340284:R528Q;ENSP00000420356:R130Q;ENSP00000363249:R130Q	ENSP00000340284:R528Q	R	+	2	0	RGS3	115385939	0.847000	0.29606	0.953000	0.39169	0.214000	0.24535	0.807000	0.27140	0.424000	0.26061	-0.285000	0.09966	CGG	G|0.884;A|0.116	0.116	strong		0.617	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
ZNF554	115196	hgsc.bcm.edu	37	19	2834595	2834595	+	Silent	SNP	C	C	T	rs61744481	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2834595C>T	ENST00000317243.5	+	5	1560	c.1362C>T	c.(1360-1362)caC>caT	p.H454H		NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	454					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCAACCAGCACGAGCGAACTC	0.542													C|||	314	0.0626997	0.1619	0.0159	5008	,	,		20720	0.0		0.0328	False		,,,				2504	0.0573				p.H454H		Atlas-SNP	.											.	ZNF554	47	.	0			c.C1362T						PASS	.	C		727,3675	281.1+/-275.7	65,597,1539	63.0	74.0	70.0		1362	-5.7	0.1	19	dbSNP_129	70	228,8370	91.9+/-153.9	2,224,4073	no	coding-synonymous	ZNF554	NM_001102651.1		67,821,5612	TT,TC,CC		2.6518,16.5152,7.3462		454/539	2834595	955,12045	2201	4299	6500	SO:0001819	synonymous_variant	115196	exon5			CCAGCACGAGCGA	AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"""Zinc fingers, C2H2-type"", ""-"""	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.1362C>T	19.37:g.2834595C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	134	73	0.544776	NM_001102651	Q8NAT3|Q9BWN3	Silent	SNP	ENST00000317243.5	37	CCDS42462.1																																																																																			C|0.961;T|0.039	0.039	strong		0.542	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303	
TNC	3371	hgsc.bcm.edu	37	9	117804544	117804544	+	Silent	SNP	T	T	C	rs1061495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117804544T>C	ENST00000350763.4	-	18	5613	c.5202A>G	c.(5200-5202)acA>acG	p.T1734T	TNC_ENST00000535648.1_Silent_p.T1279T|TNC_ENST00000341037.4_Silent_p.T1552T|TNC_ENST00000423613.2_Silent_p.T1461T|TNC_ENST00000537320.1_Silent_p.T1097T|TNC_ENST00000542877.1_Silent_p.T1371T|TNC_ENST00000340094.3_Silent_p.T1370T|TNC_ENST00000346706.3_Silent_p.T1188T|TNC_ENST00000345230.3_Silent_p.T1097T	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1734	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CCACTTGGGCTGTGGGTGCCC	0.517													t|||	1417	0.282947	0.528	0.2795	5008	,	,		17872	0.1478		0.2575	False		,,,				2504	0.1196				p.T1734T		Atlas-SNP	.											.	TNC	282	.	0			c.A5202G						PASS	.	T		2170,2236	585.4+/-386.2	545,1080,578	102.0	98.0	100.0		5202	-7.2	0.6	9	dbSNP_86	100	2197,6403	374.9+/-337.6	295,1607,2398	no	coding-synonymous	TNC	NM_002160.3		840,2687,2976	CC,CT,TT		25.5465,49.251,33.5768		1734/2202	117804544	4367,8639	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon18			TTGGGCTGTGGGT		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5202A>G	9.37:g.117804544T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	94	25	0.265957	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1	623	0.28525641025641024	262	0.532520325203252	95	0.26243093922651933	68	0.11888111888111888	198	0.2612137203166227	t	0.947	-0.707721	0.03230	0.49251	0.255465	ENSG00000041982	ENST00000544972	.	.	.	6.08	-7.17	0.01511	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.46289	-0.9202	3	.	.	.	.	2.9726	0.05927	0.1397:0.4085:0.1194:0.3325	rs1061495;rs3202589;rs17435046;rs1061495	.	.	.	G	297	.	.	S	-	1	0	TNC	116844365	0.056000	0.20664	0.591000	0.28745	0.159000	0.22180	0.132000	0.15891	-1.139000	0.02881	-2.708000	0.00134	AGC	T|0.688;C|0.312	0.312	strong		0.517	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
APC2	10297	hgsc.bcm.edu	37	19	1469030	1469030	+	Silent	SNP	A	A	G	rs265278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1469030A>G	ENST00000535453.1	+	14	7443	c.5730A>G	c.(5728-5730)aaA>aaG	p.K1910K	APC2_ENST00000238483.4_Silent_p.K1636K|APC2_ENST00000233607.2_Silent_p.K1910K|C19orf25_ENST00000588427.1_Intron			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGTGCCCAAAACGCCGGCGC	0.756													G|||	998	0.199281	0.6036	0.062	5008	,	,		7467	0.0248		0.0497	False		,,,				2504	0.0838				p.K1910K		Atlas-SNP	.											.	APC2	50	.	0			c.A5730G						PASS	.	G		912,2062		65,782,640	2.0	3.0	3.0		5730	4.1	0.0	19	dbSNP_79	3	244,6352		4,236,3058	no	coding-synonymous	APC2	NM_005883.2		69,1018,3698	GG,GA,AA		3.6992,30.6658,12.0794		1910/2304	1469030	1156,8414	1487	3298	4785	SO:0001819	synonymous_variant	10297	exon15			GCCCAAAACGCCG		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"""Armadillo repeat containing"""	24036	protein-coding gene	gene with protein product	"""adenomatous polyposis coli like"""	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.5730A>G	19.37:g.1469030A>G		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	23	17	0.73913	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	37	CCDS12068.1																																																																																			A|0.833;G|0.167	0.167	strong		0.756	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883	
FUK	197258	hgsc.bcm.edu	37	16	70508544	70508544	+	Missense_Mutation	SNP	C	C	T	rs17883716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70508544C>T	ENST00000288078.6	+	17	2334	c.2102C>T	c.(2101-2103)cCg>cTg	p.P701L	FUK_ENST00000571514.1_Missense_Mutation_p.P192L|FUK_ENST00000378912.2_Missense_Mutation_p.P733L	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	701			P -> L (in dbSNP:rs17883716). {ECO:0000269|Ref.3}.			cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				GTGGAACTGCCGGGACCTGGG	0.657													C|||	2	0.000399361	0.0	0.0	5008	,	,		17514	0.0		0.002	False		,,,				2504	0.0				p.P701L		Atlas-SNP	.											.	FUK	72	.	0			c.C2102T						PASS	.	C	LEU/PRO	3,4111		0,3,2054	34.0	43.0	40.0		2102	3.7	0.9	16	dbSNP_124	40	25,8379		0,25,4177	yes	missense	FUK	NM_145059.2	98	0,28,6231	TT,TC,CC		0.2975,0.0729,0.2237	possibly-damaging	701/1085	70508544	28,12490	2057	4202	6259	SO:0001583	missense	197258	exon17			AACTGCCGGGACC		CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"""L-fucose kinase"""	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085	ENST00000288078.6:c.2102C>T	16.37:g.70508544C>T	ENSP00000288078:p.Pro701Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	37	CCDS10891.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.20	3.054738	0.55325	7.29E-4	0.002975	ENSG00000157353	ENST00000288078;ENST00000378912;ENST00000538525	T;T	0.08634	3.12;3.07	5.77	3.72	0.42706	.	0.176184	0.50627	N	0.000110	T	0.09468	0.0233	M	0.66939	2.045	0.80722	D	1	P;P;P	0.52692	0.579;0.955;0.955	B;B;B	0.42087	0.072;0.375;0.267	T	0.27365	-1.0076	10	0.12766	T	0.61	-16.2145	9.0313	0.36260	0.146:0.7799:0.0:0.0741	rs17883716;rs17883716	733;607;701	Q8N0W3-2;B2RDL5;Q8N0W3	.;.;FUK_HUMAN	L	701;733;15	ENSP00000288078:P701L;ENSP00000368192:P733L	ENSP00000288078:P701L	P	+	2	0	FUK	69066045	0.990000	0.36364	0.878000	0.34440	0.674000	0.39518	2.878000	0.48515	1.463000	0.47967	-0.140000	0.14226	CCG	C|0.995;T|0.005	0.005	strong		0.657	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
MECOM	2122	hgsc.bcm.edu	37	3	168833976	168833976	+	Missense_Mutation	SNP	C	C	T	rs149928659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:168833976C>T	ENST00000464456.1	-	7	2320	c.1120G>A	c.(1120-1122)Gag>Aag	p.E374K	MECOM_ENST00000472280.1_Missense_Mutation_p.E375K|MECOM_ENST00000433243.2_Missense_Mutation_p.E375K|MECOM_ENST00000460814.1_Missense_Mutation_p.E374K|MECOM_ENST00000494292.1_Missense_Mutation_p.E562K|MECOM_ENST00000392736.3_Missense_Mutation_p.E374K|MECOM_ENST00000468789.1_Missense_Mutation_p.E374K|MECOM_ENST00000264674.3_Missense_Mutation_p.E439K	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						GAGGACCTCTCGGGCTGGAGC	0.493													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17401	0.0		0.0	False		,,,				2504	0.0				p.E562K		Atlas-SNP	.											.	MECOM	216	.	0			c.G1684A						PASS	.						360.0	301.0	321.0					3																	168833976		2203	4300	6503	SO:0001583	missense	2122	exon8			ACCTCTCGGGCTG	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.1120G>A	3.37:g.168833976C>T	ENSP00000419770:p.Glu374Lys	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	187	90	0.481283	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	37	CCDS54669.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	13.87	2.365132	0.41902	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243	T;T;T;T;T;T;T;T	0.07021	3.29;3.28;3.25;3.38;3.23;3.28;3.24;3.38	6.03	6.03	0.97812	.	0.000000	0.53938	D	0.000059	T	0.11495	0.0280	L	0.54323	1.7	0.51482	D	0.999928	P;P;P;P;P	0.45569	0.826;0.789;0.861;0.789;0.491	B;B;B;B;B	0.35510	0.204;0.128;0.101;0.182;0.06	T	0.01608	-1.1313	10	0.59425	D	0.04	-16.0383	20.5568	0.99304	0.0:1.0:0.0:0.0	.	562;375;562;439;374	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	K	439;374;374;375;562;374;374;375	ENSP00000264674:E439K;ENSP00000376493:E374K;ENSP00000419770:E374K;ENSP00000420048:E375K;ENSP00000417899:E562K;ENSP00000419995:E374K;ENSP00000420466:E374K;ENSP00000394302:E375K	ENSP00000264674:E439K	E	-	1	0	MECOM	170316670	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.830000	0.69324	2.861000	0.98227	0.655000	0.94253	GAG	C|0.999;T|0.001	0.001	strong		0.493	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
RBM44	375316	hgsc.bcm.edu	37	2	238725833	238725833	+	Missense_Mutation	SNP	A	A	G	rs73086770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238725833A>G	ENST00000409864.1	+	3	528	c.274A>G	c.(274-276)Agt>Ggt	p.S92G	RBM44_ENST00000444524.2_Intron|RBM44_ENST00000316997.4_Missense_Mutation_p.S92G			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	91						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		TAACACAGAGAGTACTCAGTT	0.323													A|||	182	0.0363419	0.1286	0.0144	5008	,	,		19482	0.0		0.002	False		,,,				2504	0.0				p.S92G		Atlas-SNP	.											.	RBM44	167	.	0			c.A274G						PASS	.	A	GLY/SER	365,3309		23,319,1495	60.0	60.0	60.0		274	3.2	0.0	2	dbSNP_130	60	19,8129		0,19,4055	yes	missense	RBM44	NM_001080504.2	56	23,338,5550	GG,GA,AA		0.2332,9.9347,3.2482	possibly-damaging	92/1053	238725833	384,11438	1837	4074	5911	SO:0001583	missense	375316	exon3			ACAGAGAGTACTC	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.274A>G	2.37:g.238725833A>G	ENSP00000386727:p.Ser92Gly	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	213	85	0.399061	NM_001080504	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	88	0.040293040293040296	79	0.16056910569105692	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	A	9.408	1.079719	0.20309	0.099347	0.002332	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.33216	1.42;1.42	5.62	3.15	0.36227	.	0.588960	0.17242	N	0.181502	T	0.00073	0.0002	L	0.39898	1.24	0.80722	P	0.0	P	0.49090	0.919	B	0.39339	0.297	T	0.11941	-1.0567	9	0.32370	T	0.25	-3.005	9.875	0.41197	0.6671:0.3329:0.0:0.0	.	91	Q6ZP01	RBM44_HUMAN	G	92	ENSP00000321179:S92G;ENSP00000386727:S92G	ENSP00000321179:S92G	S	+	1	0	RBM44	238390572	0.000000	0.05858	0.000000	0.03702	0.785000	0.44390	0.011000	0.13264	0.374000	0.24650	0.460000	0.39030	AGT	A|0.967;G|0.033	0.033	strong		0.323	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504	
CABP5	56344	hgsc.bcm.edu	37	19	48543923	48543923	+	Silent	SNP	C	C	A	rs12982629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48543923C>A	ENST00000293255.2	-	3	307	c.177G>T	c.(175-177)acG>acT	p.T59T		NM_019855.4	NP_062829.1	Q9NP86	CABP5_HUMAN	calcium binding protein 5	59	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				signal transduction (GO:0007165)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	11		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)		TGTAACCCATCGTCCTCATGA	0.522													c|||	710	0.141773	0.0825	0.2248	5008	,	,		19329	0.0099		0.2724	False		,,,				2504	0.1646				p.T59T		Atlas-SNP	.											.	CABP5	28	.	0			c.G177T						PASS	.	C		548,3858	247.5+/-255.7	31,486,1686	123.0	101.0	108.0		177	-8.8	0.2	19	dbSNP_121	108	2440,6160	404.0+/-348.0	353,1734,2213	no	coding-synonymous	CABP5	NM_019855.4		384,2220,3899	AA,AC,CC		28.3721,12.4376,22.974		59/174	48543923	2988,10018	2203	4300	6503	SO:0001819	synonymous_variant	56344	exon3			ACCCATCGTCCTC	AF169159	CCDS12709.1	19q13.33	2014-08-12			ENSG00000105507	ENSG00000105507		"""EF-hand domain containing"""	13714	protein-coding gene	gene with protein product		607315	"""calcium binding protein 3"""	CABP3		10625670	Standard	NM_019855		Approved	CaBP3	uc002phu.2	Q9NP86	OTTHUMG00000183139	ENST00000293255.2:c.177G>T	19.37:g.48543923C>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_019855	A0AUY4	Silent	SNP	ENST00000293255.2	37	CCDS12709.1																																																																																			C|0.798;A|0.202	0.202	strong		0.522	CABP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465212.1	NM_019855	
SYTL3	94120	hgsc.bcm.edu	37	6	159184507	159184507	+	Silent	SNP	C	C	T	rs2291386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159184507C>T	ENST00000297239.9	+	16	1883	c.1689C>T	c.(1687-1689)aaC>aaT	p.N563N	SYTL3_ENST00000367081.3_Silent_p.N289N|MIR3918_ENST00000581555.1_RNA|SYTL3_ENST00000360448.3_Silent_p.N495N			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	563	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	calcium-dependent phospholipid binding (GO:0005544)			endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		TTGGAATGAACGACCGCTTGC	0.478													C|||	547	0.109225	0.3139	0.0346	5008	,	,		20174	0.0268		0.0427	False		,,,				2504	0.0389				p.N563N		Atlas-SNP	.											.	SYTL3	49	.	0			c.C1689T						PASS	.	C	,,,	1092,3314	395.6+/-329.7	152,788,1263	94.0	92.0	93.0		1485,1689,1689,1485	-5.2	0.8	6	dbSNP_100	93	398,8202	127.0+/-185.4	9,380,3911	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYTL3	NM_001009991.3,NM_001242384.1,NM_001242394.1,NM_001242395.1	,,,	161,1168,5174	TT,TC,CC		4.6279,24.7844,11.4563	,,,	495/543,563/611,563/611,495/543	159184507	1490,11516	2203	4300	6503	SO:0001819	synonymous_variant	94120	exon18			AATGAACGACCGC	AK055750	CCDS34563.1, CCDS56458.1	6q25.3	2008-07-04			ENSG00000164674	ENSG00000164674			15587	protein-coding gene	gene with protein product						11773082	Standard	NM_001242384		Approved	SLP3, exophilin-6	uc003qrp.3	Q4VX76	OTTHUMG00000015916	ENST00000297239.9:c.1689C>T	6.37:g.159184507C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_001242384	Q496J4|Q496J6|Q5U3B9	Silent	SNP	ENST00000297239.9	37	CCDS56458.1																																																																																			C|0.879;T|0.121	0.121	strong		0.478	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042876.1		
USH2A	7399	hgsc.bcm.edu	37	1	216258194	216258194	+	Silent	SNP	G	G	T	rs56110889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:216258194G>T	ENST00000307340.3	-	25	5399	c.5013C>A	c.(5011-5013)ggC>ggA	p.G1671G	RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA|USH2A_ENST00000366943.2_Silent_p.G1671G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1671	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)		CCTTGAGACAGCCCACAAAAC	0.328										HNSCC(13;0.011)			G|||	530	0.105831	0.1906	0.0951	5008	,	,		17135	0.0		0.163	False		,,,				2504	0.0491				p.G1671G		Atlas-SNP	.											.	USH2A	1168	.	0			c.C5013A						PASS	.	G		844,3562	331.2+/-301.9	100,644,1459	83.0	85.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5013	2.9	1.0	1	dbSNP_129	85	1481,7119	280.2+/-294.4	139,1203,2958	no	coding-synonymous	USH2A	NM_206933.2		239,1847,4417	TT,TG,GG		17.2209,19.1557,17.8764		1671/5203	216258194	2325,10681	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon25			GAGACAGCCCACA	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.5013C>A	1.37:g.216258194G>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			G|0.844;T|0.156	0.156	strong		0.328	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
NLRP3	114548	hgsc.bcm.edu	37	1	247587408	247587408	+	Silent	SNP	C	C	T	rs7525979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247587408C>T	ENST00000336119.3	+	3	1409	c.663C>T	c.(661-663)acC>acT	p.T221T	NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000391827.2_Silent_p.T221T|NLRP3_ENST00000366497.2_Silent_p.T221T|NLRP3_ENST00000348069.2_Silent_p.T221T|NLRP3_ENST00000366496.2_Silent_p.T221T|NLRP3_ENST00000391828.3_Silent_p.T221T	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	221	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CTGTGCACACCGTGGTGTTCC	0.562													C|||	584	0.116613	0.2277	0.0879	5008	,	,		19117	0.131		0.0547	False		,,,				2504	0.0358				p.T221T		Atlas-SNP	.											.	NLRP3	286	.	0			c.C663T						PASS	.	C	,,,,	968,3438	364.4+/-316.9	103,762,1338	77.0	71.0	73.0		663,663,663,663,663	-8.5	0.0	1	dbSNP_116	73	531,8069	147.3+/-202.7	14,503,3783	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP3	NM_001079821.2,NM_001127461.2,NM_001127462.2,NM_004895.4,NM_183395.2	,,,,	117,1265,5121	TT,TC,CC		6.1744,21.97,11.5254	,,,,	221/1037,221/980,221/980,221/1037,221/923	247587408	1499,11507	2203	4300	6503	SO:0001819	synonymous_variant	114548	exon3			GCACACCGTGGTG	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.663C>T	1.37:g.247587408C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	231	109	0.471861	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Silent	SNP	ENST00000336119.3	37	CCDS1632.1																																																																																			C|0.877;T|0.123	0.123	strong		0.562	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
TNFSF15	9966	hgsc.bcm.edu	37	9	117568219	117568219	+	Missense_Mutation	SNP	C	C	T	rs150191342	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117568219C>T	ENST00000374045.4	-	1	187	c.74G>A	c.(73-75)aGg>aAg	p.R25K		NM_001204344.1|NM_005118.3	NP_001191273.1|NP_005109.2	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily, member 15	25					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cytokine metabolic process (GO:0042107)|immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(1)	11						GGCCTTGGGCCTGCAGCTGCC	0.627													C|||	20	0.00399361	0.0151	0.0	5008	,	,		17651	0.0		0.0	False		,,,				2504	0.0				p.R25K		Atlas-SNP	.											.	TNFSF15	23	.	0			c.G74A						PASS	.	C	LYS/ARG	54,4352	53.6+/-89.4	1,52,2150	64.0	58.0	60.0		74	3.2	0.5	9	dbSNP_134	60	0,8600		0,0,4300	yes	missense	TNFSF15	NM_005118.3	26	1,52,6450	TT,TC,CC		0.0,1.2256,0.4152	benign	25/252	117568219	54,12952	2203	4300	6503	SO:0001583	missense	9966	exon1			TTGGGCCTGCAGC	AF039390	CCDS6809.1	9q32	2008-07-21			ENSG00000181634	ENSG00000181634		"""Tumor necrosis factor (ligand) superfamily"""	11931	protein-coding gene	gene with protein product	"""vascular endothelial cell growth inhibitor"", ""TNF superfamily ligand TL1A"", ""TNF ligand-related molecule 1"", ""vascular endothelial growth inhibitor-192A"""	604052				9434163	Standard	NM_005118		Approved	TL1, VEGI, TL1A, VEGI192A, MGC129934, MGC129935	uc004bjh.3	O95150	OTTHUMG00000021011	ENST00000374045.4:c.74G>A	9.37:g.117568219C>T	ENSP00000363157:p.Arg25Lys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	108	75	0.694444	NM_005118	Q3SX69|Q5VJK8|Q5VWH1|Q8NFE9	Missense_Mutation	SNP	ENST00000374045.4	37	CCDS6809.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	12.31	1.898972	0.33535	0.012256	0.0	ENSG00000181634	ENST00000374045	T	0.28069	1.63	5.11	3.23	0.37069	.	2.547720	0.01464	N	0.015995	T	0.14700	0.0355	N	0.24115	0.695	0.48696	D	0.999692	B	0.20261	0.043	B	0.19946	0.027	T	0.44862	-0.9300	10	0.02654	T	1	-17.7812	6.6172	0.22782	0.0:0.7011:0.1969:0.102	.	25	O95150	TNF15_HUMAN	K	25	ENSP00000363157:R25K	ENSP00000363157:R25K	R	-	2	0	TNFSF15	116608040	0.122000	0.22280	0.461000	0.27105	0.699000	0.40488	0.565000	0.23578	0.616000	0.30141	0.484000	0.47621	AGG	C|0.996;T|0.004	0.004	strong		0.627	TNFSF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055424.2	NM_005118	
TSHZ3	57616	hgsc.bcm.edu	37	19	31767717	31767717	+	Silent	SNP	G	G	A	rs61744745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:31767717G>A	ENST00000240587.4	-	2	3309	c.2982C>T	c.(2980-2982)caC>caT	p.H994H		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	994					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GTGACTCTAGGTGACTGATGT	0.473													G|||	174	0.0347444	0.1301	0.0029	5008	,	,		20088	0.0		0.0	False		,,,				2504	0.0				p.H994H		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C2982T						PASS	.	G		440,3966	211.8+/-231.9	19,402,1782	120.0	105.0	110.0		2982	2.5	1.0	19	dbSNP_129	110	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	TSHZ3	NM_020856.2		19,406,6078	AA,AG,GG		0.0465,9.9864,3.4138		994/1082	31767717	444,12562	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CTCTAGGTGACTG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2982C>T	19.37:g.31767717G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	167	86	0.51497	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.961;A|0.039	0.039	strong		0.473	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
ARHGEF26	26084	hgsc.bcm.edu	37	3	153840389	153840389	+	Missense_Mutation	SNP	T	T	C	rs13096373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:153840389T>C	ENST00000356448.4	+	2	892	c.608T>C	c.(607-609)tTt>tCt	p.F203S	ARHGEF26-AS1_ENST00000480639.1_RNA|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.F203S|ARHGEF26-AS1_ENST00000491862.1_RNA|ARHGEF26_ENST00000465817.1_Missense_Mutation_p.F203S|ARHGEF26-AS1_ENST00000467912.1_RNA|ARHGEF26-AS1_ENST00000479270.1_RNA	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	203			F -> S (in dbSNP:rs13096373). {ECO:0000269|PubMed:15221005}.		endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						CGGGGGCTCTTTCCTGGGCCC	0.587													C|||	1624	0.324281	0.469	0.3415	5008	,	,		12777	0.4514		0.1103	False		,,,				2504	0.2055				p.F203S	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.T608C						PASS	.	C	SER/PHE	1414,2216		292,830,693	21.0	24.0	23.0		608	3.9	0.0	3	dbSNP_121	23	985,7165		80,825,3170	yes	missense	ARHGEF26	NM_015595.3	155	372,1655,3863	CC,CT,TT		12.0859,38.9532,20.365	benign	203/872	153840389	2399,9381	1815	4075	5890	SO:0001583	missense	26084	exon2			GGCTCTTTCCTGG	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24490	protein-coding gene	gene with protein product	"""Src homology 3 domain-containing guanine nucleotide exchange factor"""					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.608T>C	3.37:g.153840389T>C	ENSP00000348828:p.Phe203Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	37	CCDS46938.1	727	0.33287545787545786	250	0.508130081300813	119	0.3287292817679558	276	0.4825174825174825	82	0.10817941952506596	C	0.010	-1.750579	0.00669	0.389532	0.120859	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.47177	0.85;0.85;2.67	3.91	3.91	0.45181	.	0.341216	0.28515	N	0.015074	T	0.00012	0.0000	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	0.46386	-0.9195	9	0.02654	T	1	-3.7174	5.5786	0.17236	0.0:0.6885:0.2012:0.1103	rs13096373	203;203	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	S	203	ENSP00000348828:F203S;ENSP00000423418:F203S;ENSP00000423295:F203S	ENSP00000348828:F203S	F	+	2	0	ARHGEF26	155323079	0.006000	0.16342	0.015000	0.15790	0.141000	0.21300	0.431000	0.21444	0.867000	0.35654	-0.215000	0.12644	TTT	T|0.706;C|0.294	0.294	strong		0.587	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595	
SERPINA5	5104	hgsc.bcm.edu	37	14	95056407	95056407	+	Missense_Mutation	SNP	G	G	C	rs6114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95056407G>C	ENST00000554866.1	+	3	763	c.649G>C	c.(649-651)Ggc>Cgc	p.G217R	SERPINA5_ENST00000554276.1_Missense_Mutation_p.G217R|RP11-986E7.7_ENST00000553947.1_5'Flank|SERPINA5_ENST00000329597.7_Missense_Mutation_p.G217R|SERPINA5_ENST00000553780.1_Missense_Mutation_p.G217R			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	217			G -> R (in dbSNP:rs6114). {ECO:0000269|PubMed:10391209, ECO:0000269|Ref.6}.		fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CAACCACAAAGGCACCCAAGA	0.453													G|||	129	0.0257588	0.0923	0.0101	5008	,	,		19756	0.0		0.0	False		,,,				2504	0.0				p.G217R		Atlas-SNP	.											.	SERPINA5	69	.	0			c.G649C						PASS	.	G	ARG/GLY	374,4032	190.5+/-216.4	22,330,1851	71.0	65.0	67.0		649	-2.1	0.0	14	dbSNP_52	67	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SERPINA5	NM_000624.4	125	22,331,6150	CC,CG,GG		0.0116,8.4884,2.8833	benign	217/407	95056407	375,12631	2203	4300	6503	SO:0001583	missense	5104	exon4			CACAAAGGCACCC	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.649G>C	14.37:g.95056407G>C	ENSP00000451126:p.Gly217Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	121	50	0.413223	NM_000624	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	37	CCDS9928.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	G	1.396	-0.579550	0.03854	0.084884	1.16E-4	ENSG00000188488	ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000537685;ENST00000438291;ENST00000554276	D;D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	4.63	-2.09	0.07232	Serpin domain (3);	1.511820	0.03611	N	0.234832	T	0.03564	0.0102	N	0.02751	-0.505	0.09310	N	1	B;B	0.18461	0.024;0.028	B;B	0.26864	0.074;0.023	T	0.23226	-1.0194	10	0.33141	T	0.24	.	3.7717	0.08645	0.3912:0.0:0.3351:0.2737	rs6114;rs6114	217;217	G3V5Q9;P05154	.;IPSP_HUMAN	R	217;217;217;217;217;69;141;217	ENSP00000450837:G217R;ENSP00000452469:G217R;ENSP00000451126:G217R;ENSP00000333203:G217R;ENSP00000450745:G217R;ENSP00000451610:G217R	ENSP00000333203:G217R	G	+	1	0	SERPINA5	94126160	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	-1.700000	0.01905	-0.323000	0.08602	-0.378000	0.06908	GGC	G|0.974;C|0.026	0.026	strong		0.453	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
C15orf41	84529	hgsc.bcm.edu	37	15	36946303	36946303	+	Missense_Mutation	SNP	C	C	G	rs3784678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:36946303C>G	ENST00000566621.1	+	4	467	c.217C>G	c.(217-219)Ctg>Gtg	p.L73V	C15orf41_ENST00000567389.1_5'UTR|RP11-16L14.2_ENST00000565366.1_RNA|C15orf41_ENST00000437989.2_Missense_Mutation_p.L73V|C15orf41_ENST00000562877.1_5'UTR|C15orf41_ENST00000338183.4_5'UTR|C15orf41_ENST00000569302.1_Missense_Mutation_p.L73V	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	73			L -> V (in dbSNP:rs3784678).							kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		GTCTAGGTACCTGAATGGAGT	0.448													C|||	2489	0.497005	0.3782	0.3818	5008	,	,		18193	0.6815		0.4423	False		,,,				2504	0.6053				p.L73V		Atlas-SNP	.											.	C15orf41	24	.	0			c.C217G						PASS	.	C	VAL/LEU,	1239,1893		241,757,568	96.0	85.0	89.0		217,	5.5	1.0	15	dbSNP_107	89	3286,3870		758,1770,1050	yes	missense,utr-5	C15orf41	NM_001130010.1,NM_032499.4	32,	999,2527,1618	GG,GC,CC		45.9195,39.5594,43.9833	possibly-damaging,	73/282,	36946303	4525,5763	1566	3578	5144	SO:0001583	missense	84529	exon4			AGGTACCTGAATG	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.217C>G	15.37:g.36946303C>G	ENSP00000455397:p.Leu73Val	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	156	63	0.403846	NM_001130010	B2RD87	Missense_Mutation	SNP	ENST00000566621.1	37	CCDS45215.1	1078	0.4935897435897436	206	0.4186991869918699	137	0.3784530386740331	380	0.6643356643356644	355	0.4683377308707124	C	15.37	2.813509	0.50527	0.395594	0.459195	ENSG00000186073	ENST00000437989	T	0.47177	0.85	5.5	5.5	0.81552	.	.	.	.	.	T	0.00012	0.0000	L	0.46741	1.465	0.09310	P	1.0	P	0.46512	0.879	P	0.46076	0.503	T	0.47289	-0.9129	8	0.40728	T	0.16	-2.9736	12.8542	0.57876	0.0:0.9263:0.0:0.0737	rs3784678;rs17657081;rs60628223;rs3784678	73	Q9Y2V0	CO041_HUMAN	V	73	ENSP00000401362:L73V	ENSP00000401362:L73V	L	+	1	2	C15orf41	34733595	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.645000	0.54389	2.854000	0.98071	0.655000	0.94253	CTG	C|0.492;G|0.508	0.508	strong		0.448	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499	
SYTL2	54843	hgsc.bcm.edu	37	11	85447611	85447611	+	Silent	SNP	T	T	C	rs680498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:85447611T>C	ENST00000528231.1	-	5	793	c.516A>G	c.(514-516)tcA>tcG	p.S172S	SYTL2_ENST00000389960.4_Silent_p.S172S|SYTL2_ENST00000316356.4_Silent_p.S173S|SYTL2_ENST00000527523.1_Silent_p.S124S|SYTL2_ENST00000524452.1_Silent_p.S172S	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	172					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TTTGTTGTGATGAGTGACCTT	0.313													C|||	3275	0.653954	0.823	0.5677	5008	,	,		16958	0.6171		0.6551	False		,,,				2504	0.5235				p.S173S		Atlas-SNP	.											SYTL2_ENST00000316356,bladder,carcinoma,-1,1	SYTL2	231	1	0			c.A519G						PASS	.	C	,,	3463,943	356.9+/-313.7	1363,737,103	128.0	126.0	127.0		516,519,516	2.2	0.3	11	dbSNP_83	127	5655,2941	456.2+/-364.0	1884,1887,527	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3	,,	3247,2624,630	CC,CT,TT		34.2136,21.4026,29.8723	,,	172/935,173/936,172/911	85447611	9118,3884	2203	4298	6501	SO:0001819	synonymous_variant	54843	exon5			TTGTGATGAGTGA	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.516A>G	11.37:g.85447611T>C		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_001162953	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			C|0.687;T|0.313	0.687	strong		0.313	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
ACOT11	26027	hgsc.bcm.edu	37	1	55073630	55073630	+	Silent	SNP	C	C	T	rs78753605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55073630C>T	ENST00000371316.3	+	15	1600	c.1518C>T	c.(1516-1518)atC>atT	p.I506I	ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_Silent_p.I506I	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	506	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				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						CCTATGTCATCGCGCTGAGGT	0.642													C|||	83	0.0165735	0.0605	0.0029	5008	,	,		18552	0.001		0.0	False		,,,				2504	0.0				p.I506I	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-SNP	.											.	ACOT11	105	.	0			c.C1518T						PASS	.	C	,	201,4205	126.6+/-163.6	4,193,2006	93.0	90.0	91.0		1518,1518	-6.9	0.9	1	dbSNP_132	91	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ACOT11	NM_015547.3,NM_147161.3	,	4,194,6305	TT,TC,CC		0.0116,4.562,1.5531	,	506/608,506/595	55073630	202,12804	2203	4300	6503	SO:0001819	synonymous_variant	26027	exon15			TGTCATCGCGCTG	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.1518C>T	1.37:g.55073630C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	157	87	0.55414	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Silent	SNP	ENST00000371316.3	37	CCDS592.1																																																																																			C|0.984;T|0.016	0.016	strong		0.642	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547	
FLG	2312	hgsc.bcm.edu	37	1	152279841	152279841	+	Missense_Mutation	SNP	G	G	C	rs3126074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152279841G>C	ENST00000368799.1	-	3	7556	c.7521C>G	c.(7519-7521)caC>caG	p.H2507Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	368	0	0		WXS	Illumina HiSeq	Phase_I	476	476	1	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	
MICA	100507436	hgsc.bcm.edu	37	6	31380153	31380153	+	Missense_Mutation	SNP	T	T	C	rs199843678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31380153T>C	ENST00000449934.2	+	5	998	c.944T>C	c.(943-945)gTt>gCt	p.V315A	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)				GTTTCTGCTGTTGCTGCTGGC	0.458																																					p.V315A		Atlas-SNP	.											MICA,uveal_tract,malignant_melanoma,0,1	MICA	21	1	0			c.T944C						PASS	.						288.0	263.0	270.0					6																	31380153		692	1591	2283	SO:0001583	missense	100507436	exon5			CTGCTGTTGCTGC	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.944T>C	6.37:g.31380153T>C	ENSP00000413079:p.Val315Ala	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	103	17	0.165049	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	-	2.519	-0.311081	0.05458	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.01203	5.61;5.18	1.55	-2.91	0.05631	.	.	.	.	.	T	0.00178	0.0005	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.27226	-1.0080	9	0.38643	T	0.18	.	6.6027	0.22708	0.0:0.3216:0.0:0.6784	.	177;315	Q5SS58;Q96QC4	.;.	A	177;315;272;315;206	ENSP00000413079:V315A;ENSP00000402410:V206A	ENSP00000365394:V315A	V	+	2	0	MICA	31488132	0.000000	0.05858	0.000000	0.03702	0.111000	0.19643	-3.279000	0.00529	-0.980000	0.03524	-0.576000	0.04144	GTT	T|0.973;C|0.027	0.027	strong		0.458	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
COG8	84342	hgsc.bcm.edu	37	16	69373414	69373414	+	Silent	SNP	T	T	C	rs11542583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69373414T>C	ENST00000306875.4	-	1	156	c.42A>G	c.(40-42)acA>acG	p.T14T	RP11-343C2.7_ENST00000564737.1_Intron|NIP7_ENST00000569637.2_5'Flank|RP11-343C2.9_ENST00000563634.1_Intron|NIP7_ENST00000254941.6_5'Flank|COG8_ENST00000562081.1_Silent_p.T14T|NIP7_ENST00000254940.5_5'UTR	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	14					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						GAGCCGCTGCTGTGGCCGTGG	0.677													C|||	1290	0.257588	0.3192	0.2161	5008	,	,		14793	0.0833		0.2853	False		,,,				2504	0.3548				p.T14T		Atlas-SNP	.											.	COG8	32	.	0			c.A42G						PASS	.	C		1459,2839		233,993,923	15.0	15.0	15.0		42	-1.1	0.0	16	dbSNP_120	15	2691,5805		446,1799,2003	no	coding-synonymous	COG8	NM_032382.4		679,2792,2926	CC,CT,TT		31.6737,33.946,32.4371		14/613	69373414	4150,8644	2149	4248	6397	SO:0001819	synonymous_variant	84342	exon1			CGCTGCTGTGGCC	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"""Components of oligomeric golgi complex"""	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.42A>G	16.37:g.69373414T>C		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_032382	Q0VAK2|Q8WVV6|Q9H6F8	Silent	SNP	ENST00000306875.4	37	CCDS10876.1																																																																																			T|0.711;C|0.289	0.289	strong		0.677	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382	
CSMD1	64478	hgsc.bcm.edu	37	8	3245054	3245054	+	Missense_Mutation	SNP	C	C	T	rs73657835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:3245054C>T	ENST00000520002.1	-	19	3302	c.2747G>A	c.(2746-2748)aGg>aAg	p.R916K	CSMD1_ENST00000602557.1_Missense_Mutation_p.R916K|CSMD1_ENST00000542608.1_Missense_Mutation_p.R915K|CSMD1_ENST00000537824.1_Missense_Mutation_p.R915K|CSMD1_ENST00000539096.1_Missense_Mutation_p.R915K|CSMD1_ENST00000602723.1_Missense_Mutation_p.R916K|CSMD1_ENST00000400186.3_Missense_Mutation_p.R916K			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	916	Sushi 5. {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)		CTGGTGGTTCCTCTCACAGAC	0.597													C|||	175	0.0349441	0.1225	0.0173	5008	,	,		18677	0.0		0.001	False		,,,				2504	0.0				p.R915K		Atlas-SNP	.											CSMD1_ENST00000537824,NS,carcinoma,+1,2	CSMD1	1469	2	0			c.G2744A						PASS	.	C	LYS/ARG	365,3837		16,333,1752	43.0	49.0	47.0		2744	1.2	0.1	8	dbSNP_130	47	0,8430		0,0,4215	yes	missense	CSMD1	NM_033225.5	26	16,333,5967	TT,TC,CC		0.0,8.6863,2.8895	benign	915/3565	3245054	365,12267	2101	4215	6316	SO:0001583	missense	64478	exon18			TGGTTCCTCTCAC			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.2747G>A	8.37:g.3245054C>T	ENSP00000430733:p.Arg916Lys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	C	0.079	-1.186530	0.01620	0.086863	0.0	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0;-0.0	5.11	1.25	0.21368	Complement control module (2);Sushi/SCR/CCP (3);	0.221554	0.38959	N	0.001512	T	0.00178	0.0005	N	0.01277	-0.915	0.09310	N	0.999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.003	T	0.08659	-1.0711	10	0.02654	T	1	.	8.3499	0.32297	0.0:0.6186:0.0:0.3814	.	916;916;916	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	K	916;916;778;915;915;915	ENSP00000383047:R916K;ENSP00000430733:R916K;ENSP00000441462:R915K;ENSP00000446243:R915K;ENSP00000441675:R915K	ENSP00000320445:R778K	R	-	2	0	CSMD1	3232461	0.012000	0.17670	0.095000	0.20976	0.375000	0.29983	0.150000	0.16263	-0.053000	0.13289	-0.157000	0.13467	AGG	C|0.966;T|0.034	0.034	strong		0.597	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
CAPN9	10753	hgsc.bcm.edu	37	1	230914729	230914729	+	Missense_Mutation	SNP	A	A	C	rs1933631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230914729A>C	ENST00000271971.2	+	9	1077	c.964A>C	c.(964-966)Aag>Cag	p.K322Q	CAPN9_ENST00000366666.2_Missense_Mutation_p.K259Q|CAPN9_ENST00000354537.1_Missense_Mutation_p.K296Q|RP11-99J16__A.2_ENST00000412344.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000452640.1_RNA	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	322	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		K -> Q (in dbSNP:rs1933631). {ECO:0000269|Ref.3}.		digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				GATGGCATTTAAGGACTTCAA	0.493													A|||	1659	0.33127	0.3888	0.2075	5008	,	,		17427	0.1875		0.3201	False		,,,				2504	0.501				p.K322Q		Atlas-SNP	.											.	CAPN9	116	.	0			c.A964C						PASS	.	A	GLN/LYS,GLN/LYS	1669,2737	506.6+/-366.4	316,1037,850	65.0	54.0	58.0		964,886	-3.5	0.0	1	dbSNP_92	58	2765,5835	437.6+/-358.7	422,1921,1957	yes	missense,missense	CAPN9	NM_006615.2,NM_016452.1	53,53	738,2958,2807	CC,CA,AA		32.1512,37.8802,34.092	benign,benign	322/691,296/665	230914729	4434,8572	2203	4300	6503	SO:0001583	missense	10753	exon9			GCATTTAAGGACT	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.964A>C	1.37:g.230914729A>C	ENSP00000271971:p.Lys322Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	37	CCDS1586.1	631	0.2889194139194139	196	0.3983739837398374	76	0.20994475138121546	103	0.18006993006993008	256	0.33773087071240104	A	4.329	0.060364	0.08339	0.378802	0.321512	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	T;T;T	0.15603	2.41;2.41;2.41	5.24	-3.49	0.04724	Peptidase C2, calpain, catalytic domain (3);	0.854162	0.10872	N	0.624846	T	0.00012	0.0000	N	0.01686	-0.76	0.80722	P	0.0	B;B;B	0.25105	0.017;0.118;0.017	B;B;B	0.20384	0.005;0.029;0.005	T	0.37267	-0.9713	9	0.02654	T	1	.	2.0781	0.03628	0.2162:0.282:0.3632:0.1385	rs1933631;rs17788932;rs52813786;rs60788299;rs1933631	259;296;322	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	Q	322;296;259	ENSP00000271971:K322Q;ENSP00000346538:K296Q;ENSP00000355626:K259Q	ENSP00000271971:K322Q	K	+	1	0	CAPN9	228981352	0.990000	0.36364	0.001000	0.08648	0.294000	0.27393	1.483000	0.35497	-0.677000	0.05231	-0.490000	0.04691	AAG	A|0.692;C|0.308	0.308	strong		0.493	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
ATG2A	23130	hgsc.bcm.edu	37	11	64677270	64677270	+	Missense_Mutation	SNP	C	C	T	rs61746812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64677270C>T	ENST00000377264.3	-	14	2102	c.1990G>A	c.(1990-1992)Gtg>Atg	p.V664M	ATG2A_ENST00000421419.2_Missense_Mutation_p.V664M	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	664					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						TCAGCCCGCACGGCCTGGCCC	0.701													C|||	91	0.0181709	0.0635	0.0072	5008	,	,		14186	0.0		0.002	False		,,,				2504	0.0				p.V664M		Atlas-SNP	.											ATG2A,NS,carcinoma,0,1	ATG2A	133	1	0			c.G1990A						PASS	.	C	MET/VAL	252,4150		10,232,1959	24.0	28.0	26.0		1990	4.3	1.0	11	dbSNP_129	26	0,8590		0,0,4295	yes	missense	ATG2A	NM_015104.2	21	10,232,6254	TT,TC,CC		0.0,5.7247,1.9397	probably-damaging	664/1939	64677270	252,12740	2201	4295	6496	SO:0001583	missense	23130	exon14			CCCGCACGGCCTG		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.1990G>A	11.37:g.64677270C>T	ENSP00000366475:p.Val664Met	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	26|26	0.011904761904761904|0.011904761904761904	24|24	0.04878048780487805|0.04878048780487805	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	19.46|19.46	3.831305|3.831305	0.71258|0.71258	0.057247|0.057247	0.0|0.0	ENSG00000110046|ENSG00000110046	ENST00000418259|ENST00000421419;ENST00000377264	.|T;T	.|0.11712	.|2.75;2.75	4.28|4.28	4.28|4.28	0.50868|0.50868	.|.	.|0.000000	.|0.64402	.|D	.|0.000002	T|T	0.02970|0.02970	0.0088|0.0088	L|L	0.55481|0.55481	1.735|1.735	0.45541|0.45541	D|D	0.99849|0.99849	.|D	.|0.89917	.|1.0	.|D	.|0.85130	.|0.997	T|T	0.00024|0.00024	-1.2328|-1.2328	5|10	.|0.72032	.|D	.|0.01	.|.	12.4406|12.4406	0.55623|0.55623	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|664	.|Q2TAZ0	.|ATG2A_HUMAN	H|M	465|664	.|ENSP00000410522:V664M;ENSP00000366475:V664M	.|ENSP00000366475:V664M	R|V	-|-	2|1	0|0	ATG2A|ATG2A	64433846|64433846	0.981000|0.981000	0.34729|0.34729	0.998000|0.998000	0.56505|0.56505	0.890000|0.890000	0.51754|0.51754	2.528000|2.528000	0.45624|0.45624	2.386000|2.386000	0.81285|0.81285	0.561000|0.561000	0.74099|0.74099	CGT|GTG	C|0.978;T|0.022	0.022	strong		0.701	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
EMR1	2015	hgsc.bcm.edu	37	19	6897464	6897464	+	Missense_Mutation	SNP	C	C	G	rs330880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6897464C>G	ENST00000312053.4	+	5	457	c.420C>G	c.(418-420)agC>agG	p.S140R	EMR1_ENST00000250572.8_Missense_Mutation_p.S140R|EMR1_ENST00000381407.5_Intron|EMR1_ENST00000450315.3_Splice_Site|EMR1_ENST00000601198.1_3'UTR|AC020895.1_ENST00000580648.1_RNA|EMR1_ENST00000381404.4_Missense_Mutation_p.S88R	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	140	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		S -> R (in dbSNP:rs330880). {ECO:0000269|PubMed:7601460}.		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)					TCACCAGCAGCGTCTGCCCTG	0.488													g|||	2513	0.501797	0.8328	0.4496	5008	,	,		18558	0.4831		0.2734	False		,,,				2504	0.3456				p.S140R		Atlas-SNP	.											.	EMR1	153	.	0			c.C420G						PASS	.	G	ARG/SER	3211,1195	416.3+/-337.5	1181,849,173	96.0	79.0	85.0		420	-3.2	0.0	19	dbSNP_79	85	2630,5970	687.8+/-404.2	410,1810,2080	yes	missense	EMR1	NM_001974.3	110	1591,2659,2253	GG,GC,CC		30.5814,27.1221,44.91	benign	140/887	6897464	5841,7165	2203	4300	6503	SO:0001583	missense	2015	exon5			CAGCAGCGTCTGC	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.420C>G	19.37:g.6897464C>G	ENSP00000311545:p.Ser140Arg	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	244	114	0.467213	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	1030|1030	0.4716117216117216|0.4716117216117216	395|395	0.8028455284552846|0.8028455284552846	147|147	0.40607734806629836|0.40607734806629836	290|290	0.506993006993007|0.506993006993007	198|198	0.2612137203166227|0.2612137203166227	G|G	2.796|2.796	-0.250332|-0.250332	0.05867|0.05867	0.728779|0.728779	0.305814|0.305814	ENSG00000174837|ENSG00000174837	ENST00000450315|ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572	.|D;D;D	.|0.91996	.|-2.95;-2.95;-2.95	4.12|4.12	-3.22|-3.22	0.05125|0.05125	.|EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.52501|0.52501	P|P	4.599999999999049E-5|4.599999999999049E-5	.|B;B;B	.|0.06786	.|0.0;0.0;0.001	.|B;B;B	.|0.12156	.|0.001;0.005;0.007	.|T	.|0.38067	.|-0.9678	.|8	.|0.15499	.|T	.|0.54	.|.	5.443|5.443	0.16519|0.16519	0.3573:0.4541:0.1886:0.0|0.3573:0.4541:0.1886:0.0	rs330880;rs2228537;rs52813683;rs60071314;rs330880|rs330880;rs2228537;rs52813683;rs60071314;rs330880	.|140;88;140	.|Q14246-2;E9PD45;Q14246	.|.;.;EMR1_HUMAN	.|R	-1|140;140;88;140	.|ENSP00000311545:S140R;ENSP00000370811:S88R;ENSP00000250572:S140R	.|ENSP00000250572:S140R	.|S	+|+	.|3	.|2	EMR1|EMR1	6848464|6848464	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.976000|-1.976000	0.01497|0.01497	-0.762000|-0.762000	0.04664|0.04664	-0.215000|-0.215000	0.12644|0.12644	.|AGC	C|0.551;G|0.449	0.449	strong		0.488	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
ZNF844	284391	hgsc.bcm.edu	37	19	12186857	12186857	+	Missense_Mutation	SNP	G	G	C	rs6511763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12186857G>C	ENST00000439326.3	+	4	1097	c.922G>C	c.(922-924)Gct>Cct	p.A308P	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	308			A -> P (in dbSNP:rs6511763).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						TGAGGAGAAGGCTTATGAATG	0.413													.|||	1455	0.290535	0.73	0.1455	5008	,	,		21988	0.0853		0.161	False		,,,				2504	0.1442				p.A308P		Atlas-SNP	.											.	ZNF844	69	.	0			c.G922C						PASS	.	C	PRO/ALA	887,497		287,313,92	67.0	64.0	65.0		922	1.4	0.0	19	dbSNP_116	65	416,2766		25,366,1200	yes	missense	ZNF844	NM_001136501.1	27	312,679,1292	CC,CG,GG		13.0735,35.9104,28.537	benign	308/667	12186857	1303,3263	692	1591	2283	SO:0001583	missense	284391	exon4			GAGAAGGCTTATG	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.922G>C	19.37:g.12186857G>C	ENSP00000392024:p.Ala308Pro	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	572	0.2619047619047619	339	0.6890243902439024	53	0.1464088397790055	53	0.09265734265734266	127	0.16754617414248021	C	1.412	-0.575281	0.03882	0.640896	0.130735	ENSG00000223547	ENST00000439326;ENST00000541708;ENST00000535505	T	0.10192	2.9	2.5	1.42	0.22433	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00047	-2.43	0.26978	P	0.9654259	B	0.02656	0.0	B	0.01281	0.0	T	0.33929	-0.9849	8	0.02654	T	1	.	5.9876	0.19442	0.0:0.6833:0.1951:0.1217	rs6511763;rs52826403;rs60463492;rs6511763	308	Q08AG5	ZN844_HUMAN	P	308;308;283	ENSP00000392024:A308P	ENSP00000392024:A308P	A	+	1	0	ZNF844	12047857	0.000000	0.05858	0.001000	0.08648	0.403000	0.30841	0.066000	0.14489	-0.014000	0.14175	-0.980000	0.02579	GCT	G|0.739;C|0.261	0.261	strong		0.413	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
ITGAX	3687	hgsc.bcm.edu	37	16	31371674	31371674	+	Missense_Mutation	SNP	G	G	A	rs2230428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	182	0	0		WXS	Illumina HiSeq	Phase_I	182	82	0.450549	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	
PDIA6	10130	hgsc.bcm.edu	37	2	10933294	10933294	+	Silent	SNP	C	C	T	rs114716918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10933294C>T	ENST00000272227.3	-	5	528	c.381G>A	c.(379-381)gcG>gcA	p.A127A	PDIA6_ENST00000381611.4_Silent_p.A132A|PDIA6_ENST00000404371.2_Silent_p.A179A|PDIA6_ENST00000404824.2_Silent_p.A175A|PDIA6_ENST00000540494.1_Silent_p.A124A	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	127	Thioredoxin 1. {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)		GAGCACTCAGCGCAGCATCTA	0.562													C|||	65	0.0129792	0.0469	0.0043	5008	,	,		16285	0.0		0.0	False		,,,				2504	0.0				p.A127A	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											PDIA6,NS,carcinoma,-1,1	PDIA6	31	1	0			c.G381A						PASS	.	C		124,4282	91.6+/-130.3	2,120,2081	88.0	78.0	81.0		381	-11.8	0.0	2	dbSNP_132	81	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	PDIA6	NM_005742.2		2,125,6376	TT,TC,CC		0.0581,2.8143,0.9918		127/441	10933294	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	10130	exon5			ACTCAGCGCAGCA	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.381G>A	2.37:g.10933294C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	161	83	0.515528	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	37	CCDS1675.1																																																																																			C|0.990;T|0.010	0.010	strong		0.562	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742	
FER1L6	654463	hgsc.bcm.edu	37	8	124987404	124987404	+	Missense_Mutation	SNP	A	A	G	rs77810887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124987404A>G	ENST00000522917.1	+	8	747	c.541A>G	c.(541-543)Aac>Gac	p.N181D	FER1L6_ENST00000399018.1_Missense_Mutation_p.N181D	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	181						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TCAGTTCTGCAACAAGTGGGC	0.557													G|||	75	0.014976	0.056	0.0014	5008	,	,		19342	0.0		0.0	False		,,,				2504	0.0				p.N181D		Atlas-SNP	.											.	FER1L6	268	.	0			c.A541G						PASS	.	G	ASP/ASN	198,3804		4,190,1807	93.0	91.0	92.0		541	5.5	1.0	8	dbSNP_131	92	0,8352		0,0,4176	yes	missense	FER1L6	NM_001039112.2	23	4,190,5983	GG,GA,AA		0.0,4.9475,1.6027	benign	181/1858	124987404	198,12156	2001	4176	6177	SO:0001583	missense	654463	exon8			TTCTGCAACAAGT	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.541A>G	8.37:g.124987404A>G	ENSP00000428280:p.Asn181Asp	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	288	150	0.520833	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	G	8.521	0.868834	0.17322	0.049475	0.0	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.80480	-1.38;-1.38	5.5	5.5	0.81552	C2 calcium/lipid-binding domain, CaLB (1);FerIin domain (1);	0.220886	0.37012	N	0.002292	T	0.24812	0.0602	N	0.10760	0.04	0.22342	N	0.999181	B	0.02656	0.0	B	0.06405	0.002	T	0.24404	-1.0161	10	0.28530	T	0.3	.	14.8757	0.70493	0.069:0.0:0.931:0.0	.	181	Q2WGJ9	FR1L6_HUMAN	D	181	ENSP00000428280:N181D;ENSP00000381982:N181D	ENSP00000381982:N181D	N	+	1	0	FER1L6	125056585	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.931000	0.40134	1.487000	0.48415	-0.215000	0.12644	AAC	A|0.988;G|0.012	0.012	strong		0.557	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
TACC2	10579	hgsc.bcm.edu	37	10	123970173	123970173	+	Missense_Mutation	SNP	T	T	C	rs7083331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123970173T>C	ENST00000369005.1	+	9	6573	c.6233T>C	c.(6232-6234)aTc>aCc	p.I2078T	TACC2_ENST00000515273.1_Missense_Mutation_p.I2082T|TACC2_ENST00000334433.3_Missense_Mutation_p.I2078T|TACC2_ENST00000368999.1_Missense_Mutation_p.I156T|TACC2_ENST00000453444.2_Missense_Mutation_p.I2082T|TACC2_ENST00000358010.1_Missense_Mutation_p.I224T|TACC2_ENST00000369004.3_Missense_Mutation_p.I156T|TACC2_ENST00000360561.3_Missense_Mutation_p.I156T|TACC2_ENST00000260733.3_Missense_Mutation_p.I156T|TACC2_ENST00000515603.1_Missense_Mutation_p.I2033T|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000513429.1_Missense_Mutation_p.I224T|TACC2_ENST00000369000.1_5'UTR	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2078			I -> T (in dbSNP:rs7083331).		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TCCGTCCCCATCTCTAAGTCT	0.567													T|||	522	0.104233	0.3737	0.0375	5008	,	,		16691	0.0		0.002	False		,,,				2504	0.0				p.I2078T		Atlas-SNP	.											.	TACC2	271	.	0			c.T6233C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE,THR/ILE	1380,3026	456.5+/-351.3	234,912,1057	98.0	95.0	96.0		467,467,671,6233	2.1	0.1	10	dbSNP_116	96	21,8579	14.0+/-48.4	0,21,4279	yes	missense,missense,missense,missense	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	89,89,89,89	234,933,5336	CC,CT,TT		0.2442,31.3209,10.772	benign,benign,benign,benign	156/1027,156/997,224/1095,2078/2949	123970173	1401,11605	2203	4300	6503	SO:0001583	missense	10579	exon9			TCCCCATCTCTAA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.6233T>C	10.37:g.123970173T>C	ENSP00000358001:p.Ile2078Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	188	0.08608058608058608	177	0.3597560975609756	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	T	2.370	-0.344560	0.05208	0.313209	0.002442	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000514539	T;T;T;T;T;T;T;T;T;T;T;T	0.08370	4.02;3.63;4.02;4.04;4.02;3.63;4.02;3.52;3.52;3.52;3.52;3.1	5.5	2.1	0.27182	.	1.500250	0.04801	N	0.433439	T	0.00012	0.0000	N	0.01352	-0.895	0.52099	P	5.8000000000002494E-5	B;B;B;B;B;B;B;B;B	0.13145	0.002;0.007;0.0;0.007;0.007;0.0;0.0;0.001;0.007	B;B;B;B;B;B;B;B;B	0.12156	0.004;0.007;0.001;0.007;0.007;0.002;0.002;0.004;0.007	T	0.47535	-0.9110	9	0.11794	T	0.64	0.8103	7.4447	0.27205	0.0:0.4578:0.0:0.5422	rs7083331;rs52830245;rs7083331	173;2082;156;2033;2082;156;156;224;2078	E9PGB3;E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	T	2078;224;2082;2033;2078;224;2082;2068;156;156;156;156;173	ENSP00000358001:I2078T;ENSP00000425062:I224T;ENSP00000424467:I2082T;ENSP00000427618:I2033T;ENSP00000334280:I2078T;ENSP00000350701:I224T;ENSP00000395048:I2082T;ENSP00000353763:I156T;ENSP00000357995:I156T;ENSP00000422815:I156T;ENSP00000260733:I156T;ENSP00000420967:I173T	ENSP00000260733:I156T	I	+	2	0	TACC2	123960163	0.000000	0.05858	0.128000	0.21923	0.313000	0.28021	0.587000	0.23909	0.130000	0.18549	0.533000	0.62120	ATC	T|0.899;C|0.101	0.101	strong		0.567	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
SLC30A8	169026	hgsc.bcm.edu	37	8	118184784	118184784	+	Missense_Mutation	SNP	G	G	A	rs16889462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:118184784G>A	ENST00000456015.2	+	8	974	c.974G>A	c.(973-975)cGg>cAg	p.R325Q	SLC30A8_ENST00000521243.1_Missense_Mutation_p.R276Q|SLC30A8_ENST00000427715.2_Missense_Mutation_p.R276Q|SLC30A8_ENST00000519688.1_Missense_Mutation_p.R276Q	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	325			R -> Q (in dbSNP:rs16889462).|R -> W (in dbSNP:rs13266634). {ECO:0000269|PubMed:17293876}.		cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			GCAGCCAGCCGGGACAGCCAA	0.493													G|||	245	0.0489217	0.1301	0.0115	5008	,	,		19557	0.0635		0.0	False		,,,				2504	0.001				p.R325Q	Ovarian(162;1202 1922 6011 16223 52092)	Atlas-SNP	.											.	SLC30A8	102	.	0			c.G974A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	449,3957	216.8+/-235.3	24,401,1778	87.0	84.0	85.0		827,827,827,827,974	-2.3	0.9	8	dbSNP_123	85	7,8593	6.4+/-24.3	0,7,4293	yes	missense,missense,missense,missense,missense	SLC30A8	NM_001172811.1,NM_001172813.1,NM_001172814.1,NM_001172815.1,NM_173851.2	43,43,43,43,43	24,408,6071	AA,AG,GG		0.0814,10.1906,3.5061	benign,benign,benign,benign,benign	276/321,276/321,276/321,276/321,325/370	118184784	456,12550	2203	4300	6503	SO:0001583	missense	169026	exon8			CCAGCCGGGACAG		CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"""Solute carriers"""	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.974G>A	8.37:g.118184784G>A	ENSP00000415011:p.Arg325Gln	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	125	72	0.576	NM_173851	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation	SNP	ENST00000456015.2	37	CCDS6322.1	88	0.040293040293040296	56	0.11382113821138211	5	0.013812154696132596	27	0.0472027972027972	0	0.0	G	12.53	1.966104	0.34659	0.101906	8.14E-4	ENSG00000164756	ENST00000521243;ENST00000427715;ENST00000519688;ENST00000456015	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.15	-2.29	0.06805	.	1.130630	0.06487	N	0.733902	T	0.00845	0.0028	N	0.12182	0.205	0.09310	N	0.999998	B	0.11235	0.004	B	0.04013	0.001	T	0.04178	-1.0971	10	0.38643	T	0.18	0.3986	6.4085	0.21678	0.4817:0.1284:0.3899:0.0	rs16889462;rs16889462	325	Q8IWU4	ZNT8_HUMAN	Q	276;276;276;325	ENSP00000428545:R276Q;ENSP00000407505:R276Q;ENSP00000431069:R276Q;ENSP00000415011:R325Q	ENSP00000407505:R276Q	R	+	2	0	SLC30A8	118253965	0.001000	0.12720	0.924000	0.36721	0.515000	0.34225	-0.269000	0.08596	-0.103000	0.12175	-0.157000	0.13467	CGG	A|0.044;G|0.956	0.044	strong		0.493	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851	
CYP4A22	284541	hgsc.bcm.edu	37	1	47603338	47603338	+	Missense_Mutation	SNP	G	G	A	rs112604161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47603338G>A	ENST00000371891.3	+	1	212	c.181G>A	c.(181-183)Ggg>Agg	p.G61R	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000371890.3_Missense_Mutation_p.G61R|CYP4A22_ENST00000294337.3_Missense_Mutation_p.G61R|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	61						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTGGCTCTTCGGGCACATCCA	0.602													G|||	54	0.0107827	0.0378	0.0014	5008	,	,		19903	0.0		0.003	False		,,,				2504	0.0				p.G61R	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.G181A						PASS	.	G	ARG/GLY	153,4253	102.5+/-141.1	4,145,2054	46.0	40.0	42.0		181	2.5	0.0	1	dbSNP_132	42	1,8599	1.2+/-3.3	0,1,4299	no	missense	CYP4A22	NM_001010969.2	125	4,146,6353	AA,AG,GG		0.0116,3.4725,1.1841	probably-damaging	61/520	47603338	154,12852	2203	4300	6503	SO:0001583	missense	284541	exon1			CTCTTCGGGCACA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.181G>A	1.37:g.47603338G>A	ENSP00000360958:p.Gly61Arg	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	171	82	0.479532	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	21	0.009615384615384616	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	g	17.36	3.368930	0.61624	0.034725	1.16E-4	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.78481	-1.08;-1.18;-1.18	2.47	2.47	0.30058	.	0.000000	0.85682	D	0.000000	T	0.75474	0.3854	H	0.96460	3.825	0.53005	D	0.999967	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86371	0.1723	10	0.87932	D	0	.	13.1509	0.59488	0.0:0.0:1.0:0.0	.	61;61	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	R	61	ENSP00000360957:G61R;ENSP00000360958:G61R;ENSP00000294337:G61R	ENSP00000294337:G61R	G	+	1	0	CYP4A22	47375925	1.000000	0.71417	0.009000	0.14445	0.114000	0.19823	4.707000	0.61852	1.071000	0.40834	0.205000	0.17691	GGG	G|0.987;A|0.013	0.013	strong		0.602	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
ELL	8178	hgsc.bcm.edu	37	19	18561473	18561473	+	Silent	SNP	G	G	A	rs34868531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18561473G>A	ENST00000262809.4	-	8	1350	c.1279C>T	c.(1279-1281)Ctg>Ttg	p.L427L	ELL_ENST00000596124.3_Silent_p.L294L	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	427					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)		AGCAGGGGCAGGCCGAGGCGC	0.677			T	MLL	AL								G|||	107	0.0213658	0.0681	0.0144	5008	,	,		12206	0.0		0.007	False		,,,				2504	0.0				p.L427L		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.C1279T						PASS	.	G		212,4120		2,208,1956	19.0	11.0	14.0		1279	-0.1	0.0	19	dbSNP_126	14	45,8491		0,45,4223	no	coding-synonymous	ELL	NM_006532.3		2,253,6179	AA,AG,GG		0.5272,4.8938,1.9972		427/622	18561473	257,12611	2166	4268	6434	SO:0001819	synonymous_variant	8178	exon8			GGGGCAGGCCGAG	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.1279C>T	19.37:g.18561473G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	106	58	0.54717	NM_006532		Silent	SNP	ENST00000262809.4	37	CCDS12380.1																																																																																			G|0.980;A|0.020	0.020	strong		0.677	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532	
CNTNAP1	8506	hgsc.bcm.edu	37	17	40841001	40841001	+	Missense_Mutation	SNP	G	G	C	rs35437096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40841001G>C	ENST00000264638.4	+	10	1781	c.1564G>C	c.(1564-1566)Gtg>Ctg	p.V522L	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	522	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		V -> L (in dbSNP:rs35437096).		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)		CCTGACTCTGGTGGAGGGCCG	0.562													G|||	202	0.0403355	0.143	0.0173	5008	,	,		17992	0.0		0.001	False		,,,				2504	0.0				p.V522L		Atlas-SNP	.											CNTNAP1,uveal_tract,malignant_melanoma,-1,1	CNTNAP1	116	1	0			c.G1564C						scavenged	.	G	LEU/VAL	536,3870	243.1+/-252.9	38,460,1705	138.0	126.0	130.0		1564	3.7	1.0	17	dbSNP_126	130	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CNTNAP1	NM_003632.2	32	38,464,6001	CC,CG,GG		0.0465,12.1652,4.1519	benign	522/1385	40841001	540,12466	2203	4300	6503	SO:0001583	missense	8506	exon10			ACTCTGGTGGAGG	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.1564G>C	17.37:g.40841001G>C	ENSP00000264638:p.Val522Leu	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_003632		Missense_Mutation	SNP	ENST00000264638.4	37	CCDS11436.1	58	0.026556776556776556	48	0.0975609756097561	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	G	13.62	2.290608	0.40494	0.121652	4.65E-4	ENSG00000108797	ENST00000264638	T	0.76186	-1.0	4.73	3.72	0.42706	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.181748	0.37715	N	0.001970	T	0.01695	0.0054	L	0.45352	1.415	0.33613	D	0.60377	B	0.06786	0.001	B	0.06405	0.002	T	0.37478	-0.9704	10	0.39692	T	0.17	.	9.0628	0.36444	0.083:0.2588:0.6582:0.0	rs35437096	522	P78357	CNTP1_HUMAN	L	522	ENSP00000264638:V522L	ENSP00000264638:V522L	V	+	1	0	CNTNAP1	38094527	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	2.118000	0.41949	2.449000	0.82847	0.561000	0.74099	GTG	G|0.961;C|0.039	0.039	strong		0.562	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632	
ABLIM1	3983	hgsc.bcm.edu	37	10	116203801	116203801	+	Silent	SNP	A	A	C	rs74158004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116203801A>C	ENST00000277895.5	-	17	2017	c.1920T>G	c.(1918-1920)tcT>tcG	p.S640S	ABLIM1_ENST00000369253.2_Silent_p.S263S|ABLIM1_ENST00000369266.3_Silent_p.S317S|ABLIM1_ENST00000533213.2_Silent_p.S580S|ABLIM1_ENST00000392952.3_Silent_p.S317S|ABLIM1_ENST00000369252.4_Silent_p.S580S	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	640					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		AGTTGATGGGAGAATCGTAGC	0.512													C|||	165	0.0329473	0.1233	0.0029	5008	,	,		16633	0.0		0.0	False		,,,				2504	0.0				p.S640S		Atlas-SNP	.											.	ABLIM1	131	.	0			c.T1920G						PASS	.	C	,,,	418,3988	788.2+/-414.9	31,356,1816	185.0	183.0	184.0		1740,1824,1920,951	-1.1	1.0	10	dbSNP_130	184	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABLIM1	NM_001003407.1,NM_001003408.1,NM_002313.5,NM_006720.3	,,,	31,358,6114	CC,CA,AA		0.0233,9.4871,3.2293	,,,	580/719,608/747,640/779,317/456	116203801	420,12586	2203	4300	6503	SO:0001819	synonymous_variant	3983	exon17			GATGGGAGAATCG	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1920T>G	10.37:g.116203801A>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Silent	SNP	ENST00000277895.5	37	CCDS7590.1	57	0.0260989010989011	56	0.11382113821138211	1	0.0027624309392265192	0	0.0	0	0.0	C	7.510	0.654490	0.14580	0.094871	2.33E-4	ENSG00000099204	ENST00000392955	.	.	.	5.79	-1.12	0.09808	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.04268	-1.0964	4	.	.	.	.	3.7237	0.08466	0.5347:0.1057:0.0608:0.2988	.	.	.	.	R	514	.	.	L	-	2	0	ABLIM1	116193791	0.990000	0.36364	0.988000	0.46212	0.621000	0.37620	0.259000	0.18405	-0.380000	0.07894	-2.704000	0.00135	CTC	A|0.963;C|0.037	0.037	strong		0.512	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3		
CTC1	80169	hgsc.bcm.edu	37	17	8135446	8135446	+	Silent	SNP	G	G	A	rs3027235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8135446G>A	ENST00000315684.8	-	13	2167	c.2160C>T	c.(2158-2160)acC>acT	p.T720T		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	720					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						CCTCTGGGCCGGTGGGATCTG	0.577													G|||	217	0.0433307	0.087	0.1009	5008	,	,		17092	0.0099		0.0139	False		,,,				2504	0.0082				p.T720T		Atlas-SNP	.											.	CTC1	75	.	0			c.C2160T						PASS	.	G		260,3684		9,242,1721	21.0	22.0	22.0		2160	2.3	0.0	17	dbSNP_102	22	124,8160		3,118,4021	no	coding-synonymous	CTC1	NM_025099.5		12,360,5742	AA,AG,GG		1.4969,6.5923,3.1403		720/1218	8135446	384,11844	1972	4142	6114	SO:0001819	synonymous_variant	80169	exon13			TGGGCCGGTGGGA	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.2160C>T	17.37:g.8135446G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	37	CCDS42259.1																																																																																			G|0.964;A|0.036	0.036	strong		0.577	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
CD109	135228	hgsc.bcm.edu	37	6	74497152	74497152	+	Missense_Mutation	SNP	G	G	A	rs5023688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	97	0	0		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	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	
CNPY4	245812	hgsc.bcm.edu	37	7	99722173	99722173	+	Missense_Mutation	SNP	G	G	A	rs60551236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99722173G>A	ENST00000262932.3	+	5	634	c.502G>A	c.(502-504)Gga>Aga	p.G168R	CNPY4_ENST00000480692.1_3'UTR|RP11-506M12.1_ENST00000494221.1_RNA|MBLAC1_ENST00000398075.2_5'Flank	NM_152755.1	NP_689968.1	Q8N129	CNPY4_HUMAN	canopy FGF signaling regulator 4	168	Glu-rich.		G -> R (in dbSNP:rs60551236).			extracellular region (GO:0005576)				breast(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGACATTGTGGGAGACTGGTA	0.507													G|||	109	0.0217652	0.0794	0.0058	5008	,	,		20245	0.0		0.0	False		,,,				2504	0.0				p.G168R		Atlas-SNP	.											.	CNPY4	18	.	0			c.G502A						PASS	.	G	ARG/GLY	343,4063	179.7+/-208.2	14,315,1874	105.0	105.0	105.0		502	5.9	1.0	7	dbSNP_129	105	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CNPY4	NM_152755.1	125	14,317,6172	AA,AG,GG		0.0233,7.7848,2.6526	possibly-damaging	168/249	99722173	345,12661	2203	4300	6503	SO:0001583	missense	245812	exon5			ATTGTGGGAGACT	AK075537	CCDS34701.1	7q22.1	2013-07-23	2013-07-23		ENSG00000166997	ENSG00000166997			28631	protein-coding gene	gene with protein product	"""protein associated with TLR4"""	610047	"""canopy 4 homolog (zebrafish)"""			12975309	Standard	NM_152755		Approved	MGC40499, PRAT4B	uc003uto.3	Q8N129	OTTHUMG00000154817	ENST00000262932.3:c.502G>A	7.37:g.99722173G>A	ENSP00000262932:p.Gly168Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_152755	Q8WUN9	Missense_Mutation	SNP	ENST00000262932.3	37	CCDS34701.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	G	29.2	4.986631	0.93106	0.077848	2.33E-4	ENSG00000166997	ENST00000262932	T	0.34859	1.34	5.94	5.94	0.96194	.	0.106425	0.64402	D	0.000007	T	0.02304	0.0071	N	0.08118	0	0.43489	D	0.995729	D	0.64830	0.994	D	0.66497	0.944	T	0.04400	-1.0954	10	0.23302	T	0.38	-10.3151	15.8634	0.79043	0.0:0.0:1.0:0.0	rs60551236	168	Q8N129	CNPY4_HUMAN	R	168	ENSP00000262932:G168R	ENSP00000262932:G168R	G	+	1	0	CNPY4	99560109	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	7.907000	0.87430	2.826000	0.97356	0.561000	0.74099	GGA	G|0.979;A|0.021	0.021	strong		0.507	CNPY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337224.4	NM_152755	
NPR1	4881	hgsc.bcm.edu	37	1	153662340	153662340	+	Missense_Mutation	SNP	G	G	A	rs35240348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153662340G>A	ENST00000368680.3	+	19	3288	c.2816G>A	c.(2815-2817)cGg>cAg	p.R939Q		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	939	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.		R -> Q (in dbSNP:rs35240348). {ECO:0000269|PubMed:17344846}.		body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|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)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CGGAACGGGCGGCTACACGCC	0.672													G|||	502	0.10024	0.2224	0.0634	5008	,	,		14790	0.001		0.0726	False		,,,				2504	0.092				p.R939Q	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											.	NPR1	104	.	0			c.G2816A						PASS	.	G	GLN/ARG	837,3561		84,669,1446	32.0	31.0	31.0		2816	-0.3	1.0	1	dbSNP_126	31	660,7934		21,618,3658	yes	missense	NPR1	NM_000906.3	43	105,1287,5104	AA,AG,GG		7.6798,19.0314,11.5225	benign	939/1062	153662340	1497,11495	2199	4297	6496	SO:0001583	missense	4881	exon19			ACGGGCGGCTACA	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.2816G>A	1.37:g.153662340G>A	ENSP00000357669:p.Arg939Gln	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	160	85	0.53125	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	CCDS1051.1	191	0.08745421245421245	111	0.22560975609756098	29	0.08011049723756906	1	0.0017482517482517483	50	0.06596306068601583	G	3.607	-0.080328	0.07141	0.190314	0.076798	ENSG00000169418	ENST00000368680;ENST00000428723;ENST00000368677	D	0.84298	-1.83	2.87	-0.294	0.12831	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.520095	0.17319	N	0.178596	T	0.45696	0.1355	N	0.12831	0.26	0.46499	P	9.280000000000399E-4	B;B	0.12630	0.006;0.001	B;B	0.04013	0.001;0.001	T	0.07462	-1.0771	9	0.34782	T	0.22	.	2.5862	0.04831	0.4105:0.0:0.3539:0.2356	rs35240348;rs61737918	418;939	B7Z4Y7;P16066	.;ANPRA_HUMAN	Q	939;418;120	ENSP00000357669:R939Q	ENSP00000357666:R120Q	R	+	2	0	NPR1	151928964	1.000000	0.71417	0.981000	0.43875	0.463000	0.32649	2.021000	0.41020	-0.063000	0.13065	0.462000	0.41574	CGG	G|0.890;A|0.110	0.110	strong		0.672	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906	
CTAGE5	4253	hgsc.bcm.edu	37	14	39736693	39736693	+	Silent	SNP	G	G	T	rs34909359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:39736693G>T	ENST00000280083.3	+	1	344	c.30G>T	c.(28-30)ccG>ccT	p.P10P	RP11-407N17.5_ENST00000553520.1_RNA|CTAGE5_ENST00000341749.3_Intron|CTAGE5_ENST00000556148.1_5'UTR|CTAGE5_ENST00000396165.4_Intron|RP11-407N17.3_ENST00000603904.1_Intron|RP11-407N17.5_ENST00000605298.1_RNA|RP11-407N17.3_ENST00000553728.1_Intron|CTAGE5_ENST00000557038.1_Intron|CTAGE5_ENST00000348007.3_Silent_p.P10P|CTAGE5_ENST00000396158.2_Silent_p.P10P|CTAGE5_ENST00000341502.5_Silent_p.P10P			O15320	CTGE5_HUMAN	CTAGE family, member 5	10					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)		CCCCTCAACCGTATTTGGGGC	0.662													G|||	100	0.0199681	0.0711	0.0086	5008	,	,		16634	0.0		0.0	False		,,,				2504	0.0				p.P10P		Atlas-SNP	.											.	CTAGE5	75	.	0			c.G30T						PASS	.	G	,,,	285,4121	149.2+/-183.4	6,273,1924	31.0	33.0	32.0		30,,30,	2.4	0.0	14	dbSNP_126	32	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,intron,coding-synonymous,intron	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	,,,	6,275,6222	TT,TG,GG		0.0233,6.4685,2.2067	,,,	10/805,,10/762,	39736693	287,12719	2203	4300	6503	SO:0001819	synonymous_variant	4253	exon1			TCAACCGTATTTG	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.30G>T	14.37:g.39736693G>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Silent	SNP	ENST00000280083.3	37	CCDS9674.1																																																																																			G|0.979;T|0.021	0.021	strong		0.662	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
SENP7	57337	hgsc.bcm.edu	37	3	101177848	101177848	+	Missense_Mutation	SNP	T	T	G	rs6809436|rs386663936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101177848T>G	ENST00000394095.2	-	4	288	c.235A>C	c.(235-237)Aaa>Caa	p.K79Q	SENP7_ENST00000314261.7_Missense_Mutation_p.K79Q|Y_RNA_ENST00000364684.1_RNA|SENP7_ENST00000394094.2_Missense_Mutation_p.K79Q|SENP7_ENST00000358203.3_Missense_Mutation_p.K46Q|SENP7_ENST00000348610.3_Missense_Mutation_p.K46Q|SENP7_ENST00000394091.1_Missense_Mutation_p.K46Q	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	79			K -> Q (in dbSNP:rs6809436).			intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			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						ATATGTTTTTTATTTTTATGG	0.338													T|||	357	0.0712859	0.146	0.0591	5008	,	,		16527	0.0		0.0845	False		,,,				2504	0.0389				p.K79Q		Atlas-SNP	.											.	SENP7	170	.	0			c.A235C						PASS	.	T	GLN/LYS,GLN/LYS	625,3781	269.8+/-269.2	50,525,1628	222.0	215.0	218.0		235,235	2.3	0.1	3	dbSNP_116	218	701,7899	173.2+/-223.7	20,661,3619	yes	missense,missense	SENP7	NM_001077203.1,NM_020654.3	53,53	70,1186,5247	GG,GT,TT		8.1512,14.1852,10.1953	benign,benign	79/986,79/1051	101177848	1326,11680	2203	4300	6503	SO:0001583	missense	57337	exon4			GTTTTTTATTTTT		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.235A>C	3.37:g.101177848T>G	ENSP00000377655:p.Lys79Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	125	68	0.544	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	161	0.07371794871794872	80	0.16260162601626016	21	0.058011049723756904	0	0.0	60	0.079155672823219	T	13.43	2.234760	0.39498	0.141852	0.081512	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.41758	1.97;1.97;0.99;1.84;1.84;1.98	4.78	2.28	0.28536	.	0.250311	0.27495	N	0.019104	T	0.00109	0.0003	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B	0.30281	0.033;0.033;0.275;0.019	B;B;B;B	0.28232	0.022;0.022;0.087;0.01	T	0.08973	-1.0696	9	0.72032	D	0.01	-0.4982	9.0229	0.36211	0.0:0.0:0.3622:0.6378	rs6809436;rs52800936;rs57603507;rs6809436	46;79;46;79	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	Q	79;79;79;46;46;46	ENSP00000377655:K79Q;ENSP00000377654:K79Q;ENSP00000313624:K79Q;ENSP00000377651:K46Q;ENSP00000350936:K46Q;ENSP00000342159:K46Q	ENSP00000313624:K79Q	K	-	1	0	SENP7	102660538	1.000000	0.71417	0.051000	0.19133	0.487000	0.33371	1.220000	0.32491	0.290000	0.22444	0.533000	0.62120	AAA	T|0.902;G|0.098	0.098	strong		0.338	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
RPP21	79897	hgsc.bcm.edu	37	6	30314566	30314566	+	Silent	SNP	T	T	G	rs35287137|rs1060065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30314566T>G	ENST00000442966.2	+	5	457	c.444T>G	c.(442-444)acT>acG	p.T148T	TRIM39-RPP21_ENST00000513556.1_Silent_p.T409T|RPP21_ENST00000428040.2_Silent_p.T171T|RPP21_ENST00000436442.2_3'UTR|RPP21_ENST00000433076.2_Silent_p.T156T			Q9H633	RPP21_HUMAN	ribonuclease P/MRP 21kDa subunit	148					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						AAATGCAGACTCAGGGTTCCA	0.433													T|||	1866	0.372604	0.3018	0.4496	5008	,	,		21469	0.505		0.2435	False		,,,				2504	0.41				p.T497T		Atlas-SNP	.											.	.	.	.	0			c.T1491G						PASS	.	T	,,,	841,2181		114,613,784	161.0	165.0	164.0		1491,468,,444	-0.3	0.0	6	dbSNP_86	164	1311,4107		159,993,1557	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous	RPP21,TRIM39-RPP21	NM_001199119.1,NM_001199120.1,NM_001199121.1,NM_024839.2	,,,	273,1606,2341	GG,GT,TT		24.1971,27.8293,25.4976	,,,	497/504,156/163,,148/155	30314566	2152,6288	1511	2709	4220	SO:0001819	synonymous_variant	202658	exon10			GCAGACTCAGGGT	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.444T>G	6.37:g.30314566T>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	153	76	0.496732	NM_001199119	A2AAZ8|B0S834|B0S835|Q5JPL9|Q5JPM1|Q5STF8|Q5STF9|Q5STG2|Q5SU41|Q5SU42|Q86Y49|Q86Y50|Q86Y51|Q96F16	Silent	SNP	ENST00000442966.2	37	CCDS4679.1																																																																																			.	.	alt		0.433	RPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076451.2	NM_024839	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262047	39262047	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39262047A>G	ENST00000391415.1	+	1	464	c.407A>G	c.(406-408)aAg>aGg	p.K136R		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	136	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						agctgctgcaagccccagtgc	0.652																																					p.K136R		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,6	KRTAP4-9	110	6	0			c.A407G						scavenged	.						5.0	11.0	9.0					17																	39262047		641	1516	2157	SO:0001583	missense	100132386	exon1			GCTGCAAGCCCCA	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.407A>G	17.37:g.39262047A>G	ENSP00000375234:p.Lys136Arg	Somatic	128	3	0.0234375		WXS	Illumina HiSeq	Phase_I	163	16	0.0981595	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	0.037	-1.300357	0.01364	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.18657	2.2	2.79	-1.86	0.07760	.	0.545403	0.13007	N	0.421236	T	0.03053	0.0090	N	0.00107	-2.115	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45086	-0.9285	10	0.07644	T	0.81	.	7.5488	0.27783	0.4766:0.0:0.5234:0.0	.	136	Q9BYQ8	KRA49_HUMAN	R	124;136;127	ENSP00000375234:K136R	ENSP00000334461:K127R	K	+	2	0	KRTAP4-9	36515573	0.025000	0.19082	0.001000	0.08648	0.082000	0.17680	0.008000	0.13197	-0.213000	0.10094	-0.814000	0.03130	AAG	.	.	none		0.652	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
UTP20	27340	hgsc.bcm.edu	37	12	101693534	101693534	+	Missense_Mutation	SNP	C	C	G	rs4764643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101693534C>G	ENST00000261637.4	+	13	1679	c.1505C>G	c.(1504-1506)tCt>tGt	p.S502C		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	502			S -> C (in dbSNP:rs4764643).		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						CATCTTTTATCTATAATTAAG	0.338													C|||	529	0.105631	0.0439	0.1254	5008	,	,		19257	0.0288		0.1849	False		,,,				2504	0.1728				p.S502C		Atlas-SNP	.											.	UTP20	222	.	0			c.C1505G						PASS	.	C	CYS/SER	249,4157	140.8+/-176.2	7,235,1961	63.0	66.0	65.0		1505	5.8	0.0	12	dbSNP_111	65	1627,6971	300.4+/-304.9	169,1289,2841	yes	missense	UTP20	NM_014503.2	112	176,1524,4802	GG,GC,CC		18.923,5.6514,14.4263	probably-damaging	502/2786	101693534	1876,11128	2203	4299	6502	SO:0001583	missense	27340	exon13			TTTTATCTATAAT	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.1505C>G	12.37:g.101693534C>G	ENSP00000261637:p.Ser502Cys	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	239	0.10943223443223443	27	0.054878048780487805	50	0.13812154696132597	17	0.02972027972027972	145	0.19129287598944592	C	13.57	2.277826	0.40294	0.056514	0.18923	ENSG00000120800	ENST00000261637	T	0.67698	-0.28	5.75	5.75	0.90469	Armadillo-type fold (1);	0.055091	0.85682	D	0.000000	T	0.00210	0.0006	L	0.36672	1.1	0.39688	P	0.028996000000000022	D	0.56521	0.976	P	0.49192	0.602	T	0.00885	-1.1527	9	0.51188	T	0.08	-11.3363	18.1211	0.89572	0.0:1.0:0.0:0.0	rs4764643;rs56577815;rs4764643	502	O75691	UTP20_HUMAN	C	502	ENSP00000261637:S502C	ENSP00000261637:S502C	S	+	2	0	UTP20	100217665	0.661000	0.27430	0.019000	0.16419	0.014000	0.08584	2.834000	0.48167	2.716000	0.92895	0.650000	0.86243	TCT	C|0.865;G|0.135	0.135	strong		0.338	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
OR2T8	343172	hgsc.bcm.edu	37	1	248084470	248084470	+	Missense_Mutation	SNP	C	C	T	rs140846339|rs547311711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248084470C>T	ENST00000319968.4	+	1	151	c.151C>T	c.(151-153)Cac>Tac	p.H51Y		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H51D(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)			TCACTGGGACCACCGGCTCCA	0.532													C|||	94	0.01877	0.0666	0.0014	5008	,	,		15432	0.002		0.001	False		,,,				2504	0.002				p.H51Y		Atlas-SNP	.											OR2T8,rectum,carcinoma,0,2	OR2T8	67	2	1	Substitution - Missense(1)	large_intestine(1)	c.C151T						scavenged	.						61.0	60.0	60.0					1																	248084470		2201	4297	6498	SO:0001583	missense	343172	exon1			TGGGACCACCGGC		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.151C>T	1.37:g.248084470C>T	ENSP00000326225:p.His51Tyr	Somatic	718	2	0.00278552		WXS	Illumina HiSeq	Phase_I	1052	191	0.181559	NM_001005522		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	.	.	.	.	.	.	.	.	.	.	c	7.674	0.687584	0.14973	.	.	ENSG00000177462	ENST00000319968	T	0.00428	7.44	3.65	0.32	0.15878	GPCR, rhodopsin-like superfamily (1);	3.036110	0.01499	U	0.017405	T	0.00300	0.0009	L	0.31476	0.935	0.09310	N	1	B	0.09022	0.002	B	0.17098	0.017	T	0.45920	-0.9228	10	0.45353	T	0.12	.	2.7852	0.05372	0.0:0.3992:0.2448:0.3561	.	51	A6NH00	OR2T8_HUMAN	Y	51	ENSP00000326225:H51Y	ENSP00000326225:H51Y	H	+	1	0	OR2T8	246151093	0.118000	0.22208	0.005000	0.12908	0.016000	0.09150	-0.265000	0.08644	0.228000	0.21019	0.603000	0.83216	CAC	.	.	weak		0.532	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
CACNB2	783	hgsc.bcm.edu	37	10	18828635	18828635	+	Missense_Mutation	SNP	T	T	G	rs58225473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:18828635T>G	ENST00000324631.7	+	14	2025	c.1965T>G	c.(1963-1965)gaT>gaG	p.D655E	RP11-499P20.2_ENST00000436485.1_RNA|CACNB2_ENST00000377319.3_Missense_Mutation_p.D562E|CACNB2_ENST00000377331.2_Missense_Mutation_p.D603E|CACNB2_ENST00000377329.4_Missense_Mutation_p.D601E|CACNB2_ENST00000396576.2_Missense_Mutation_p.D600E|CACNB2_ENST00000282343.8_Missense_Mutation_p.D627E|CACNB2_ENST00000377315.4_Missense_Mutation_p.D607E|RP11-499P20.2_ENST00000425669.1_RNA|CACNB2_ENST00000377328.1_Missense_Mutation_p.D405E|CACNB2_ENST00000352115.6_Missense_Mutation_p.D631E	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	655					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GGAACAGGGATGTTTACATCC	0.413													T|||	486	0.0970447	0.0953	0.1138	5008	,	,		16792	0.0		0.1978	False		,,,				2504	0.0838				p.D655E		Atlas-SNP	.											.	CACNB2	220	.	0			c.T1965G						PASS	.	T	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	485,3921		25,435,1743	63.0	61.0	62.0		1800,1767,1821,1881,1809,1803,1851,1965,1893	2.8	1.0	10	dbSNP_129	62	1486,7110		130,1226,2942	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense	CACNB2	NM_000724.3,NM_001167945.1,NM_201570.2,NM_201571.3,NM_201572.3,NM_201590.2,NM_201593.2,NM_201596.2,NM_201597.2	45,45,45,45,45,45,45,45,45	155,1661,4685	GG,GT,TT		17.2871,11.0077,15.1592	benign,benign,benign,benign,benign,benign,benign,benign,benign	600/606,589/595,607/613,627/633,603/609,601/607,617/623,655/661,631/637	18828635	1971,11031	2203	4298	6501	SO:0001583	missense	783	exon14			CAGGGATGTTTAC	U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995		"""Calcium channel subunits"""	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2		9254841, 8494331	Standard	NM_201596		Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.1965T>G	10.37:g.18828635T>G	ENSP00000320025:p.Asp655Glu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	59	36	0.610169	NM_201596	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	Missense_Mutation	SNP	ENST00000324631.7	37	CCDS7125.1	242	0.1108058608058608	50	0.1016260162601626	40	0.11049723756906077	0	0.0	152	0.20052770448548812	T	14.90	2.673763	0.47781	0.110077	0.172871	ENSG00000165995	ENST00000324631;ENST00000352115;ENST00000377328;ENST00000282343;ENST00000377331;ENST00000396576;ENST00000377319;ENST00000377329;ENST00000377315	D;D;D;D;D;D;D;D;D	0.85702	-1.84;-1.87;-2.02;-1.82;-1.88;-1.83;-1.88;-1.83;-1.83	5.17	2.76	0.32466	.	0.047638	0.85682	N	0.000000	T	0.00608	0.0020	L	0.52573	1.65	0.22457	P	0.999087671	B;D;B;D;B;B;D;D;B;B;D;B	0.89917	0.008;1.0;0.001;0.996;0.005;0.011;0.99;0.996;0.013;0.031;0.998;0.014	B;D;B;D;B;B;D;D;B;B;D;B	0.83275	0.015;0.996;0.006;0.99;0.021;0.015;0.98;0.99;0.021;0.026;0.995;0.015	T	0.32771	-0.9894	9	0.59425	D	0.04	-13.1197	12.0567	0.53540	0.0:0.0:0.2731:0.7269	rs58225473	627;405;607;577;601;611;562;603;627;617;631;655	Q5QJA0;A6PVM6;Q5VVH1;Q6TME1;Q08289-3;Q59H42;Q08289-6;A6PVM7;Q08289-4;Q08289-7;Q08289-8;Q08289	.;.;.;.;.;.;.;.;.;.;.;CACB2_HUMAN	E	655;631;405;627;603;600;562;601;607	ENSP00000320025:D655E;ENSP00000344474:D631E;ENSP00000366545:D405E;ENSP00000282343:D627E;ENSP00000366548:D603E;ENSP00000379821:D600E;ENSP00000366536:D562E;ENSP00000366546:D601E;ENSP00000366532:D607E	ENSP00000282343:D627E	D	+	3	2	CACNB2	18868641	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.309000	0.33539	0.407000	0.25591	0.533000	0.62120	GAT	T|0.858;G|0.142	0.142	strong		0.413	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047072.2	NM_000724	
CLU	1191	hgsc.bcm.edu	37	8	27457512	27457512	+	Missense_Mutation	SNP	T	T	G	rs9331936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27457512T>G	ENST00000316403.10	-	7	1354	c.949A>C	c.(949-951)Aac>Cac	p.N317H	CLU_ENST00000405140.3_Missense_Mutation_p.N317H|CLU_ENST00000546343.1_Missense_Mutation_p.N328H|CLU_ENST00000560366.1_Missense_Mutation_p.N369H|CLU_ENST00000523500.1_Missense_Mutation_p.N317H			P10909	CLUS_HUMAN	clusterin	317			N -> H (in dbSNP:rs9331936). {ECO:0000269|Ref.6}.		blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		TGGGAGGGGTTGTTGGTGGAA	0.527													T|||	327	0.0652955	0.2398	0.013	5008	,	,		20819	0.0		0.001	False		,,,				2504	0.0				p.N317H		Atlas-SNP	.											.	CLU	54	.	0			c.A949C						PASS	.	T	HIS/ASN	869,3537	336.3+/-304.3	81,707,1415	57.0	53.0	54.0		949	-1.3	0.0	8	dbSNP_119	54	10,8590	7.1+/-27.0	0,10,4290	yes	missense	CLU	NM_203339.2	68	81,717,5705	GG,GT,TT		0.1163,19.7231,6.7584	probably-damaging	317/450	27457512	879,12127	2203	4300	6503	SO:0001583	missense	1191	exon7			AGGGGTTGTTGGT	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"""complement lysis inhibitor"", ""sulfated glycoprotein 2"", ""testosterone-repressed prostate message 2"", ""apolipoprotein J"""	185430	"""clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"""	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.949A>C	8.37:g.27457512T>G	ENSP00000315130:p.Asn317His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Missense_Mutation	SNP	ENST00000316403.10	37	CCDS47832.1	135|135	0.061813186813186816|0.061813186813186816	131|131	0.266260162601626|0.266260162601626	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	T|T	15.93|15.93	2.978011|2.978011	0.53720|0.53720	0.197231|0.197231	0.001163|0.001163	ENSG00000120885|ENSG00000120885	ENST00000316403;ENST00000546343;ENST00000405140;ENST00000523500;ENST00000380446;ENST00000520012|ENST00000522098	T;T;T|.	0.24350|.	1.86;1.86;1.86|.	5.62|5.62	-1.32|-1.32	0.09201|0.09201	Clusterin, C-terminal (1);|.	0.361968|.	0.34603|.	N|.	0.003825|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.76838|0.76838	2.35|2.35	0.80722|0.80722	P|P	0.0|0.0	D;D;D;D|.	0.76494|.	0.998;0.999;0.999;0.999|.	D;D;D;D|.	0.72338|.	0.972;0.974;0.974;0.977|.	T|T	0.11591|0.11591	-1.0581|-1.0581	9|4	0.62326|.	D|.	0.03|.	-24.2564|-24.2564	5.937|5.937	0.19171|0.19171	0.0:0.4821:0.1723:0.3456|0.0:0.4821:0.1723:0.3456	rs9331936;rs11555230|rs9331936;rs11555230	182;369;328;317|.	E7ETA7;P10909-2;P10909-5;P10909|.	.;.;.;CLUS_HUMAN|.	H|P	369;328;317;317;142;182|179	ENSP00000446413:N328H;ENSP00000385419:N317H;ENSP00000429620:N317H|.	ENSP00000315130:N369H|.	N|Q	-|-	1|2	0|0	CLU|CLU	27513429|27513429	1.000000|1.000000	0.71417|0.71417	0.002000|0.002000	0.10522|0.10522	0.004000|0.004000	0.04260|0.04260	2.424000|2.424000	0.44714|0.44714	-0.154000|-0.154000	0.11118|0.11118	-0.250000|-0.250000	0.11733|0.11733	AAC|CAA	T|0.922;G|0.078	0.078	strong		0.527	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831	
TLR1	7096	hgsc.bcm.edu	37	4	38798935	38798935	+	Silent	SNP	C	C	T	rs5743614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38798935C>T	ENST00000502213.2	-	3	1747	c.1518G>A	c.(1516-1518)tcG>tcA	p.S506S	TLR1_ENST00000308979.2_Silent_p.S506S|TLR1_ENST00000510552.1_5'Flank			Q15399	TLR1_HUMAN	toll-like receptor 1	506					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						AGAAATCAGCCGATGGGTGGG	0.418													c|||	2802	0.559505	0.8404	0.4654	5008	,	,		18263	0.5992		0.2744	False		,,,				2504	0.499				p.S506S	GBM(5;216 373 40795 46382)	Atlas-SNP	.											TLR1,NS,carcinoma,-1,1	TLR1	70	1	0			c.G1518A						PASS	.						75.0	79.0	78.0					4																	38798935		2202	4280	6482	SO:0001819	synonymous_variant	7096	exon4			ATCAGCCGATGGG	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1518G>A	4.37:g.38798935C>T		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	269	217	0.806691	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	37	CCDS33973.1																																																																																			C|0.575;T|0.425	0.425	strong		0.418	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
DCHS2	54798	hgsc.bcm.edu	37	4	155219318	155219318	+	Missense_Mutation	SNP	C	C	G	rs28561984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155219318C>G	ENST00000357232.4	-	18	4782	c.4783G>C	c.(4783-4785)Gag>Cag	p.E1595Q		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1595	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> Q (in dbSNP:rs28561984).		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)		GTAGGCGACTCGGGGGAAAGA	0.428													G|||	406	0.0810703	0.261	0.0418	5008	,	,		19868	0.0109		0.0179	False		,,,				2504	0.0031				p.E1595Q		Atlas-SNP	.											.	DCHS2	594	.	0			c.G4783C						PASS	.						89.0	90.0	89.0					4																	155219318		2203	4300	6503	SO:0001583	missense	54798	exon18			GCGACTCGGGGGA	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.4783G>C	4.37:g.155219318C>G	ENSP00000349768:p.Glu1595Gln	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	206	94	0.456311	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	173	0.07921245421245421	142	0.2886178861788618	11	0.03038674033149171	6	0.01048951048951049	14	0.018469656992084433	G	0.003	-2.426918	0.00186	.	.	ENSG00000197410	ENST00000357232	T	0.61627	0.09	5.66	0.139	0.14798	Cadherin (2);Cadherin-like (1);	0.917277	0.09327	N	0.817476	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	0.25916	-1.0118	9	0.10377	T	0.69	.	3.0954	0.06308	0.1424:0.376:0.2865:0.1951	rs28561984	1595	Q6V1P9	PCD23_HUMAN	Q	1595	ENSP00000349768:E1595Q	ENSP00000349768:E1595Q	E	-	1	0	DCHS2	155438768	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.438000	0.21559	-0.142000	0.11354	-0.127000	0.14921	GAG	C|0.867;G|0.027;T|0.106	0.027	strong		0.428	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
HLA-C	3107	hgsc.bcm.edu	37	6	31237275	31237275	+	Missense_Mutation	SNP	G	G	A	rs41559915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31237275G>A	ENST00000376228.5	-	6	1057	c.1043C>T	c.(1042-1044)gCt>gTt	p.A348V	HLA-C_ENST00000383329.3_Missense_Mutation_p.A354V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	354					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						CTTACACGCAGCCTGAGAGCA	0.557													G|||	167	0.0333466	0.0605	0.013	5008	,	,		18640	0.0069		0.006	False		,,,				2504	0.0665				p.A348V		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,-1,2	HLA-C	92	2	0			c.C1043T						PASS	.	G	VAL/ALA	216,4190		7,202,1994	64.0	68.0	67.0		1043	1.8	0.0	6	dbSNP_127	67	39,8561		0,39,4261	yes	missense	HLA-C	NM_002117.5	64	7,241,6255	AA,AG,GG		0.4535,4.9024,1.9606	benign	348/367	31237275	255,12751	2203	4300	6503	SO:0001583	missense	3107	exon6			CACGCAGCCTGAG	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.1043C>T	6.37:g.31237275G>A	ENSP00000365402:p.Ala348Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	155	81	0.522581	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	33	0.01510989010989011	22	0.044715447154471545	5	0.013812154696132596	1	0.0017482517482517483	5	0.006596306068601583	.	11.21	1.572853	0.28092	0.049024	0.004535	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000539307	T;T	0.04317	3.65;3.65	2.67	1.75	0.24633	MHC class I, alpha chain, C-terminal (1);	.	.	.	.	T	0.13243	0.0321	M	0.93106	3.38	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.997;0.997;0.997	T	0.03898	-1.0994	9	0.72032	D	0.01	.	6.7409	0.23435	0.0:0.0:0.7201:0.2799	rs41559915	348;354;348	A6H578;A2AEA2;P10321	.;.;1C07_HUMAN	V	348;354;385	ENSP00000365402:A348V;ENSP00000372819:A354V	ENSP00000365402:A348V	A	-	2	0	HLA-C	31345254	0.040000	0.19996	0.002000	0.10522	0.176000	0.22953	1.465000	0.35299	0.670000	0.31165	0.298000	0.19748	GCT	G|0.981;A|0.019	0.019	strong		0.557	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
KMT2D	8085	hgsc.bcm.edu	37	12	49437753	49437753	+	Silent	SNP	G	G	A	rs111924728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49437753G>A	ENST00000301067.7	-	22	5216	c.5217C>T	c.(5215-5217)ggC>ggT	p.G1739G		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1739					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)										GCTCCACGGCGCCCTCTGCAG	0.562											OREG0021780	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	104	0.0207668	0.0696	0.0014	5008	,	,		20550	0.0		0.0	False		,,,				2504	0.0112				p.G1739G		Atlas-SNP	.											.	MLL2	1173	.	0			c.C5217T						PASS	.	G		261,4001		8,245,1878	137.0	140.0	139.0		5217	1.6	0.5	12	dbSNP_132	139	3,8483		0,3,4240	no	coding-synonymous	MLL2	NM_003482.3		8,248,6118	AA,AG,GG		0.0354,6.1239,2.0709		1739/5538	49437753	264,12484	2131	4243	6374	SO:0001819	synonymous_variant	8085	exon22			CACGGCGCCCTCT	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.5217C>T	12.37:g.49437753G>A		Somatic	123	0	0	962	WXS	Illumina HiSeq	Phase_I	97	42	0.43299	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			G|0.986;A|0.014	0.014	strong		0.562	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
SLC26A10	65012	hgsc.bcm.edu	37	12	58017665	58017665	+	Nonsense_Mutation	SNP	G	G	A	rs115563091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:58017665G>A	ENST00000320442.4	+	8	1411	c.1100G>A	c.(1099-1101)tGg>tAg	p.W367*	SLC26A10_ENST00000379218.2_Nonsense_Mutation_p.W367*	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	367						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)					GTGCTGCTGTGGCTGGGGCCC	0.562													G|||	6	0.00119808	0.0045	0.0	5008	,	,		18555	0.0		0.0	False		,,,				2504	0.0				p.W367X		Atlas-SNP	.											.	SLC26A10	89	.	0			c.G1100A						PASS	.	G	stop/TRP	21,4385		0,21,2182	98.0	100.0	100.0		1100	3.9	1.0	12	dbSNP_132	100	0,8600		0,0,4300	yes	stop-gained	SLC26A10	NM_133489.2		0,21,6482	AA,AG,GG		0.0,0.4766,0.1615		367/564	58017665	21,12985	2203	4300	6503	SO:0001587	stop_gained	65012	exon8			TGCTGTGGCTGGG		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.1100G>A	12.37:g.58017665G>A	ENSP00000320217:p.Trp367*	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Nonsense_Mutation	SNP	ENST00000320442.4	37	CCDS8949.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	37	6.630732	0.97718	0.004766	0.0	ENSG00000135502	ENST00000320442;ENST00000379218	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	14.2309	0.65892	0.0:0.0:1.0:0.0	.	.	.	.	X	367	.	ENSP00000320217:W367X	W	+	2	0	SLC26A10	56303932	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	4.320000	0.59203	2.471000	0.83476	0.561000	0.74099	TGG	G|0.999;A|0.001	0.001	strong		0.562	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2		
SDHA	6389	hgsc.bcm.edu	37	5	235364	235364	+	Silent	SNP	C	C	T	rs35277230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:235364C>T	ENST00000264932.6	+	9	1285	c.1170C>T	c.(1168-1170)ttC>ttT	p.F390F	SDHA_ENST00000510361.1_Silent_p.F342F|SDHA_ENST00000504309.1_Silent_p.F390F	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	390					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)	CCATGATCTTCGCTGGCGTGG	0.602									Familial Paragangliomas				C|||	569	0.113618	0.4107	0.0317	5008	,	,		17489	0.0		0.004	False		,,,				2504	0.0				p.F390F		Atlas-SNP	.											.	SDHA	80	.	0			c.C1170T						PASS	.	C		1431,2975		235,961,1007	67.0	60.0	63.0		1170	-6.5	0.3	5	dbSNP_126	63	30,8570		0,30,4270	no	coding-synonymous	SDHA	NM_004168.2		235,991,5277	TT,TC,CC		0.3488,32.4784,11.2333		390/665	235364	1461,11545	2203	4300	6503	SO:0001819	synonymous_variant	6389	exon9	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	GATCTTCGCTGGC	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.1170C>T	5.37:g.235364C>T		Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	321	161	0.501558	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			C|0.899;T|0.101	0.101	strong		0.602	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
DLGAP1	9229	hgsc.bcm.edu	37	18	3814148	3814148	+	Silent	SNP	C	C	G	rs3786431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3814148C>G	ENST00000315677.3	-	5	1678	c.1083G>C	c.(1081-1083)acG>acC	p.T361T	DLGAP1_ENST00000534970.1_Silent_p.T73T|DLGAP1_ENST00000539435.1_Silent_p.T59T|DLGAP1_ENST00000581527.1_Silent_p.T361T|DLGAP1_ENST00000584874.1_Silent_p.T361T|DLGAP1_ENST00000515196.2_Silent_p.T361T|DLGAP1_ENST00000400155.1_Silent_p.T67T|DLGAP1_ENST00000478161.1_5'UTR|DLGAP1_ENST00000400147.2_Silent_p.T59T|DLGAP1_ENST00000581699.1_Silent_p.T67T|snoU13_ENST00000459060.1_RNA|DLGAP1_ENST00000400145.2_Silent_p.T59T|DLGAP1_ENST00000400149.3_Silent_p.T69T|DLGAP1_ENST00000400150.3_Silent_p.T67T	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	361					synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				GCTTAGGACTCGTGTCTGAGT	0.502													C|||	668	0.133387	0.3101	0.0576	5008	,	,		15513	0.0605		0.0358	False		,,,				2504	0.1237				p.T361T		Atlas-SNP	.											.	DLGAP1	201	.	0			c.G1083C						PASS	.	C	,,,,,,,	1133,3273	407.8+/-334.4	145,843,1215	157.0	142.0	147.0		177,1083,219,219,201,177,177,1083	-9.3	0.8	18	dbSNP_107	147	270,8330	102.7+/-163.9	2,266,4032	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLGAP1	NM_001003809.2,NM_001242761.1,NM_001242762.1,NM_001242763.1,NM_001242764.1,NM_001242765.1,NM_001242766.1,NM_004746.3	,,,,,,,	147,1109,5247	GG,GC,CC		3.1395,25.7149,10.7873	,,,,,,,	59/676,361/930,73/662,73/700,67/684,59/628,59/686,361/978	3814148	1403,11603	2203	4300	6503	SO:0001819	synonymous_variant	9229	exon5			AGGACTCGTGTCT	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"""discs, large (Drosophila) homolog-associated protein 1"""			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.1083G>C	18.37:g.3814148C>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Silent	SNP	ENST00000315677.3	37	CCDS11836.1																																																																																			C|0.896;G|0.104	0.104	strong		0.502	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4		
KLHL36	79786	hgsc.bcm.edu	37	16	84691256	84691256	+	Silent	SNP	C	C	T	rs12102528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84691256C>T	ENST00000564996.1	+	3	984	c.843C>T	c.(841-843)ccC>ccT	p.P281P	KLHL36_ENST00000258157.5_Silent_p.P281P	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	281					protein ubiquitination (GO:0016567)					endometrium(3)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CGGCCCAGCCCGTCATGCAGA	0.677													C|||	79	0.0157748	0.0567	0.0058	5008	,	,		17332	0.0		0.0	False		,,,				2504	0.0				p.P281P		Atlas-SNP	.											.	KLHL36	51	.	0			c.C843T						PASS	.	C		208,4182		6,196,1993	29.0	28.0	28.0		843	-3.6	1.0	16	dbSNP_120	28	1,8595		0,1,4297	no	coding-synonymous	KLHL36	NM_024731.2		6,197,6290	TT,TC,CC		0.0116,4.738,1.6094		281/617	84691256	209,12777	2195	4298	6493	SO:0001819	synonymous_variant	79786	exon3			CCAGCCCGTCATG	AK022605	CCDS10948.1	16q24.1	2013-02-22	2013-02-22	2008-07-07	ENSG00000135686	ENSG00000135686		"""Kelch-like"", ""BTB/POZ domain containing"""	17844	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 44"", ""kelch-like 36 (Drosophila)"""	C16orf44			Standard	NM_024731		Approved	FLJ12543	uc002fig.3	Q8N4N3	OTTHUMG00000137642	ENST00000564996.1:c.843C>T	16.37:g.84691256C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_024731	Q8N5G6|Q9H9U6	Silent	SNP	ENST00000564996.1	37	CCDS10948.1																																																																																			C|0.984;T|0.016	0.016	strong		0.677	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2		
TMEM8B	51754	hgsc.bcm.edu	37	9	35842480	35842480	+	Silent	SNP	A	A	G	rs7037450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35842480A>G	ENST00000377991.4	+	7	1060	c.45A>G	c.(43-45)gaA>gaG	p.E15E	TMEM8B_ENST00000473947.1_Intron|TMEM8B_ENST00000377996.1_Silent_p.E15E|TMEM8B_ENST00000439587.2_Silent_p.E15E|TMEM8B_ENST00000377988.2_Silent_p.E15E	NM_001042589.2	NP_001036054.1	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B	15					cell-matrix adhesion (GO:0007160)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle (GO:0007346)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	7						TGCCCCCAGAACCGCCATCCC	0.701													G|||	154	0.0307508	0.1089	0.0101	5008	,	,		17224	0.0		0.003	False		,,,				2504	0.0				p.E15E		Atlas-SNP	.											.	TMEM8B	53	.	0			c.A45G						PASS	.	G	,,	474,3932	759.4+/-412.9	36,402,1765	32.0	33.0	32.0		45,45,45	4.8	1.0	9	dbSNP_116	32	21,8577	804.0+/-407.3	0,21,4278	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM8B	NM_001042589.1,NM_001042590.1,NM_016446.3	,,	36,423,6043	GG,GA,AA		0.2442,10.7581,3.8065	,,	15/473,15/473,15/339	35842480	495,12509	2203	4299	6502	SO:0001819	synonymous_variant	51754	exon6			CCCAGAACCGCCA	BC043384	CCDS6595.1, CCDS43800.1	9p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000137103	ENSG00000137103			21427	protein-coding gene	gene with protein product	"""nasopharyngeal carcinoma expressed 6"""		"""chromosome 9 open reading frame 127"""	C9orf127		12918109, 8619474	Standard	NM_016446		Approved	NAG-5, NGX6	uc003zym.4	A6NDV4	OTTHUMG00000019885	ENST00000377991.4:c.45A>G	9.37:g.35842480A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_001042590	B3KQF3|O75539|Q49AB1|Q4KMX5|Q5TCW5|Q9HBY2|Q9P0U7	Silent	SNP	ENST00000377991.4	37	CCDS43800.1																																																																																			A|0.962;G|0.038	0.038	strong		0.701	TMEM8B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052388.2	NM_016446	
CEP85L	387119	hgsc.bcm.edu	37	6	118887215	118887215	+	Missense_Mutation	SNP	T	T	A	rs9489444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118887215T>A	ENST00000368491.3	-	3	1118	c.497A>T	c.(496-498)gAt>gTt	p.D166V	CEP85L_ENST00000472713.1_5'UTR|CEP85L_ENST00000368488.5_Missense_Mutation_p.D169V|CEP85L_ENST00000360290.3_Missense_Mutation_p.D64V|CEP85L_ENST00000392500.3_Missense_Mutation_p.D169V|CEP85L_ENST00000419517.2_Missense_Mutation_p.D166V	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	166			D -> V (in dbSNP:rs9489444).			centrosome (GO:0005813)|cytoplasm (GO:0005737)											GCCACAGTTATCCGGGGCAGT	0.498													T|||	191	0.038139	0.121	0.0144	5008	,	,		20125	0.0099		0.004	False		,,,				2504	0.0072				p.D169V		Atlas-SNP	.											.	CEP85L	26	.	0			c.A506T						PASS	.	T	VAL/ASP,VAL/ASP,VAL/ASP	363,4043	186.0+/-213.0	18,327,1858	134.0	122.0	126.0		497,506,497	2.1	0.0	6	dbSNP_119	126	36,8564	24.6+/-71.5	0,36,4264	yes	missense,missense,missense	C6orf204	NM_001042475.2,NM_001178035.1,NM_206921.2	152,152,152	18,363,6122	AA,AT,TT		0.4186,8.2388,3.0678	benign,benign,benign	166/806,169/809,166/497	118887215	399,12607	2203	4300	6503	SO:0001583	missense	387119	exon4			CAGTTATCCGGGG	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.497A>T	6.37:g.118887215T>A	ENSP00000357477:p.Asp166Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	202	114	0.564356	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	72	0.03296703296703297	60	0.12195121951219512	6	0.016574585635359115	3	0.005244755244755245	3	0.00395778364116095	T	4.848	0.157562	0.09236	0.082388	0.004186	ENSG00000111860	ENST00000368491;ENST00000368488;ENST00000434604;ENST00000392500;ENST00000360290;ENST00000419517	T;T;T;T;T;T	0.25912	2.94;2.93;2.35;2.11;1.77;2.12	5.86	2.12	0.27331	.	0.629920	0.16930	N	0.193714	T	0.04998	0.0134	N	0.24115	0.695	0.47308	P	6.110000000000282E-4	B;B;B;B;B	0.18610	0.029;0.023;0.013;0.005;0.005	B;B;B;B;B	0.15052	0.011;0.012;0.012;0.007;0.004	T	0.32322	-0.9911	9	0.38643	T	0.18	-0.0495	4.4874	0.11797	0.1127:0.0771:0.117:0.6932	rs9489444;rs52812528;rs9489444	64;169;166;169;166	B4DYT2;Q5SZL2-2;G3V0H3;F8W6J2;Q5SZL2	.;.;.;.;CF204_HUMAN	V	166;169;169;169;64;166	ENSP00000357477:D166V;ENSP00000357474:D169V;ENSP00000392131:D169V;ENSP00000376288:D169V;ENSP00000353434:D64V;ENSP00000393317:D166V	ENSP00000353434:D64V	D	-	2	0	C6orf204	118993908	0.760000	0.28428	0.001000	0.08648	0.018000	0.09664	1.002000	0.29796	0.130000	0.18549	0.533000	0.62120	GAT	T|0.964;A|0.036	0.036	strong		0.498	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
ARSH	347527	hgsc.bcm.edu	37	X	2933311	2933311	+	Missense_Mutation	SNP	G	G	A	rs61995728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:2933311G>A	ENST00000381130.2	+	4	641	c.641G>A	c.(640-642)aGt>aAt	p.S214N		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	214					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)				TGGTACTCTAGTTATGGATTT	0.458													G|||	120	0.0317881	0.0862	0.0086	3775	,	,		14863	0.0		0.0	False		,,,				2504	0.0				p.S214N		Atlas-SNP	.											.	ARSH	72	.	0			c.G641A						PASS	.	G	ASN/SER	491,3344		32,349,78,1251,493	170.0	115.0	134.0		641	4.0	0.0	X	dbSNP_129	134	6,6722		0,4,2,2424,1870	yes	missense	ARSH	NM_001011719.1	46	32,353,80,3675,2363	AA,AG,A,GG,G		0.0892,12.8031,4.7051	probably-damaging	214/563	2933311	497,10066	2203	4300	6503	SO:0001583	missense	347527	exon4			ACTCTAGTTATGG	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.641G>A	X.37:g.2933311G>A	ENSP00000370522:p.Ser214Asn	Somatic	314	1	0.00318471		WXS	Illumina HiSeq	Phase_I	310	132	0.425806	NM_001011719		Missense_Mutation	SNP	ENST00000381130.2	37	CCDS35198.1	45	0.027124773960216998	29	0.06223175965665236	2	0.00558659217877095	0	0.0	0	0.0	G	10.51	1.369111	0.24771	0.128031	8.92E-4	ENSG00000205667	ENST00000381130	D	0.93712	-3.27	4.03	4.03	0.46877	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.436377	0.25558	N	0.029844	T	0.23133	0.0559	M	0.76433	2.335	0.80722	P	0.0	D	0.54397	0.966	P	0.61477	0.889	T	0.64829	-0.6315	9	0.26408	T	0.33	.	10.8038	0.46504	0.0:0.0:0.8104:0.1896	rs61995728	214	Q5FYA8	ARSH_HUMAN	N	214	ENSP00000370522:S214N	ENSP00000370522:S214N	S	+	2	0	ARSH	2943311	0.007000	0.16637	0.002000	0.10522	0.065000	0.16274	1.501000	0.35693	1.629000	0.50426	0.556000	0.70494	AGT	G|0.952;A|0.048	0.048	strong		0.458	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
RIC3	79608	hgsc.bcm.edu	37	11	8159843	8159843	+	Missense_Mutation	SNP	G	G	A	rs73411617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:8159843G>A	ENST00000309737.6	-	3	402	c.403C>T	c.(403-405)Cct>Tct	p.P135S	RIC3_ENST00000425599.2_Missense_Mutation_p.P135S|RIC3_ENST00000335425.7_Intron|RIC3_ENST00000343202.4_Missense_Mutation_p.P135S|RIC3_ENST00000539720.1_Missense_Mutation_p.P86S|RIC3_ENST00000530060.1_5'UTR			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	135					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)		GTGTTTCCAGGCATGGCAGTA	0.453													G|||	272	0.0543131	0.0809	0.0202	5008	,	,		15958	0.0417		0.0229	False		,,,				2504	0.0879				p.P135S		Atlas-SNP	.											.	RIC3	42	.	0			c.C403T						PASS	.	G	,SER/PRO,SER/PRO,SER/PRO	227,4175	135.3+/-171.4	6,215,1980	295.0	284.0	288.0		,403,403,403	2.8	1.0	11	dbSNP_130	288	298,8294	110.8+/-171.2	2,294,4000	yes	intron,missense,missense,missense	RIC3	NM_001135109.1,NM_001206671.1,NM_001206672.1,NM_024557.3	,74,74,74	8,509,5980	AA,AG,GG		3.4683,5.1567,4.0403	,benign,benign,benign	,135/370,135/289,135/369	8159843	525,12469	2201	4296	6497	SO:0001583	missense	79608	exon3			TTCCAGGCATGGC		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.403C>T	11.37:g.8159843G>A	ENSP00000308820:p.Pro135Ser	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	123	54	0.439024	NM_001206672	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Missense_Mutation	SNP	ENST00000309737.6	37	CCDS55742.1	84	0.038461538461538464	41	0.08333333333333333	7	0.019337016574585635	24	0.04195804195804196	12	0.0158311345646438	G	9.655	1.142697	0.21205	0.051567	0.034683	ENSG00000166405	ENST00000343202;ENST00000309737;ENST00000543346;ENST00000539720;ENST00000425599;ENST00000531450	T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69	5.78	2.83	0.33086	.	0.507406	0.21009	N	0.081709	T	0.00875	0.0029	L	0.35723	1.085	0.38464	D	0.947287	B;P;B;B	0.46859	0.046;0.885;0.015;0.005	B;B;B;B	0.39805	0.018;0.31;0.02;0.02	T	0.07578	-1.0765	10	0.26408	T	0.33	.	10.4847	0.44715	0.0715:0.4431:0.4854:0.0	.	135;135;135;135	B7Z1U4;B0B1U0;Q7Z5B4;Q7Z5B4-5	.;.;RIC3_HUMAN;.	S	135;135;135;86;135;135	ENSP00000344904:P135S;ENSP00000308820:P135S;ENSP00000443871:P86S;ENSP00000395320:P135S;ENSP00000431658:P135S	ENSP00000308820:P135S	P	-	1	0	RIC3	8116419	0.643000	0.27269	0.960000	0.40013	0.733000	0.41908	0.812000	0.27211	0.330000	0.23485	-0.233000	0.12211	CCT	G|0.958;A|0.042	0.042	strong		0.453	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557	
MORC1	27136	hgsc.bcm.edu	37	3	108780895	108780895	+	Silent	SNP	T	T	A	rs79817474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108780895T>A	ENST00000483760.1	-	11	949	c.906A>T	c.(904-906)atA>atT	p.I302I	MORC1_ENST00000232603.5_Silent_p.I302I					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						CTTCTTTCAATATGGATTCAG	0.343													T|||	38	0.00758786	0.0265	0.0043	5008	,	,		19655	0.0		0.0	False		,,,				2504	0.0				p.I302I		Atlas-SNP	.											.	MORC1	211	.	0			c.A906T						PASS	.	T		125,4281	92.0+/-130.7	2,121,2080	191.0	175.0	181.0		906	-8.9	0.0	3	dbSNP_132	181	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MORC1	NM_014429.3		2,123,6378	AA,AT,TT		0.0233,2.837,0.9765		302/985	108780895	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	27136	exon11			TTTCAATATGGAT	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.906A>T	3.37:g.108780895T>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	121	68	0.561983	NM_014429		Silent	SNP	ENST00000483760.1	37																																																																																				T|0.989;A|0.011	0.011	strong		0.343	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
MT-ND5	4540	hgsc.bcm.edu	37	M	14000	14000	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:14000T>A	ENST00000361567.2	+	1	1664	c.1664T>A	c.(1663-1665)cTa>cAa	p.L555Q	MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	555					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CCTCCTAGACCTAACCTGACT	0.438																																					p.L555Q		Atlas-SNP	.											.	.	.	.	0			c.T1664A						PASS	.																																			SO:0001583	missense	0	exon1			TAGACCTAACCTG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1664T>A	M.37:g.14000T>A	ENSP00000354813:p.Leu555Gln	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.438	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
SLC26A8	116369	hgsc.bcm.edu	37	6	35987425	35987425	+	Silent	SNP	T	T	C	rs61743377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35987425T>C	ENST00000490799.1	-	2	413	c.60A>G	c.(58-60)tcA>tcG	p.S20S	SLC26A8_ENST00000355574.2_Silent_p.S20S|SLC26A8_ENST00000394602.2_Silent_p.S20S	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						CATATGCGAATGAGTTTCGCC	0.448													T|||	74	0.0147764	0.0552	0.0014	5008	,	,		18599	0.0		0.0	False		,,,				2504	0.0				p.S20S		Atlas-SNP	.											.	SLC26A8	95	.	0			c.A60G						PASS	.	T	,,	234,4172	136.9+/-172.8	5,224,1974	182.0	140.0	154.0		60,60,60	-2.6	0.0	6	dbSNP_129	154	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	,,	5,225,6273	CC,CT,TT		0.0116,5.3109,1.8069	,,	20/971,20/971,20/866	35987425	235,12771	2203	4300	6503	SO:0001819	synonymous_variant	116369	exon2			TGCGAATGAGTTT	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.60A>G	6.37:g.35987425T>C		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	205	89	0.434146	NM_052961		Silent	SNP	ENST00000490799.1	37	CCDS4813.1																																																																																			T|0.986;C|0.014	0.014	strong		0.448	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
OR13F1	138805	hgsc.bcm.edu	37	9	107266813	107266813	+	Silent	SNP	C	C	T	rs61754949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107266813C>T	ENST00000334726.2	+	1	359	c.270C>T	c.(268-270)aaC>aaT	p.N90N		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	90						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						CAGGGAGAAACACTATTTCAT	0.517													C|||	55	0.0109824	0.0401	0.0029	5008	,	,		20598	0.0		0.0	False		,,,				2504	0.0				p.N90N		Atlas-SNP	.											.	OR13F1	75	.	0			c.C270T						PASS	.	C		161,4245	108.2+/-146.6	3,155,2045	132.0	117.0	122.0		270	2.2	0.9	9	dbSNP_129	122	0,8600		0,0,4300	no	coding-synonymous	OR13F1	NM_001004485.1		3,155,6345	TT,TC,CC		0.0,3.6541,1.2379		90/320	107266813	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	138805	exon1			GAGAAACACTATT		CCDS35087.1	9q31.1	2013-09-24			ENSG00000186881	ENSG00000186881		"""GPCR / Class A : Olfactory receptors"""	14723	protein-coding gene	gene with protein product							Standard	NM_001004485		Approved		uc011lvm.2	Q8NGS4	OTTHUMG00000020404	ENST00000334726.2:c.270C>T	9.37:g.107266813C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	168	47	0.279762	NM_001004485	Q6IF50	Silent	SNP	ENST00000334726.2	37	CCDS35087.1																																																																																			C|0.987;T|0.013	0.013	strong		0.517	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1		
ZNF844	284391	hgsc.bcm.edu	37	19	12186372	12186372	+	Missense_Mutation	SNP	G	G	A	rs10422576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12186372G>A	ENST00000439326.3	+	4	612	c.437G>A	c.(436-438)cGt>cAt	p.R146H	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	146			R -> H (in dbSNP:rs10422576).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						TGTCAACAACGTAAGAAAGCC	0.423													.|||	104	0.0207668	0.0772	0.0029	5008	,	,		18101	0.0		0.0	False		,,,				2504	0.0				p.R146H		Atlas-SNP	.											.	ZNF844	69	.	0			c.G437A						PASS	.	A	HIS/ARG	76,1308		2,72,618	88.0	76.0	79.0		437	-2.1	0.0	19	dbSNP_119	79	0,3182		0,0,1591	yes	missense	ZNF844	NM_001136501.1	29	2,72,2209	AA,AG,GG		0.0,5.4913,1.6645	probably-damaging	146/667	12186372	76,4490	692	1591	2283	SO:0001583	missense	284391	exon4			AACAACGTAAGAA	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.437G>A	19.37:g.12186372G>A	ENSP00000392024:p.Arg146His	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	A	6.262	0.416387	0.11870	0.054913	0.0	ENSG00000223547	ENST00000439326;ENST00000541708	T	0.27720	1.65	2.12	-2.12	0.07165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00815	0.0027	N	0.02916	-0.46	0.18873	N	0.999986	B	0.02656	0.0	B	0.01281	0.0	T	0.21211	-1.0252	9	0.72032	D	0.01	.	6.0456	0.19758	0.4102:0.0:0.5898:0.0	rs56481038	146	Q08AG5	ZN844_HUMAN	H	146	ENSP00000392024:R146H	ENSP00000392024:R146H	R	+	2	0	ZNF844	12047372	0.809000	0.29036	0.000000	0.03702	0.005000	0.04900	1.933000	0.40153	-0.554000	0.06150	-1.906000	0.00525	CGT	.	.	weak		0.423	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
PSG8	440533	hgsc.bcm.edu	37	19	43269686	43269686	+	Silent	SNP	C	C	T	rs61393109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43269686C>T	ENST00000306511.4	-	1	145	c.48G>A	c.(46-48)aaG>aaA	p.K16K	PSG8_ENST00000406636.3_Silent_p.K16K|PSG8_ENST00000404209.4_Silent_p.K16K|PSG8_ENST00000401467.2_Intron	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	16						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)				GCAGGAGCCCCTTCCAGGTGA	0.577													.|||	54	0.0107827	0.0386	0.0043	5008	,	,		18083	0.0		0.0	False		,,,				2504	0.0				p.K16K		Atlas-SNP	.											.	PSG8	101	.	0			c.G48A						PASS	.	C	,,	106,2916		3,100,1408	111.0	113.0	112.0		48,48,48	-2.0	0.0	19	dbSNP_129	112	1,5417		0,1,2708	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	,,	3,101,4116	TT,TC,CC		0.0185,3.5076,1.2678	,,	16/420,16/298,16/427	43269686	107,8333	1511	2709	4220	SO:0001819	synonymous_variant	440533	exon1			GAGCCCCTTCCAG	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.48G>A	19.37:g.43269686C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_001130168	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Silent	SNP	ENST00000306511.4	37	CCDS33037.1																																																																																			C|0.988;T|0.012	0.012	strong		0.577	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
ZSCAN25	221785	hgsc.bcm.edu	37	7	99217424	99217424	+	Silent	SNP	G	G	A	rs10282706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99217424G>A	ENST00000394152.2	+	4	522	c.195G>A	c.(193-195)gaG>gaA	p.E65E	ZSCAN25_ENST00000334715.3_Silent_p.E65E|ZSCAN25_ENST00000262941.6_Silent_p.E65E|ZSCAN25_ENST00000466948.1_3'UTR	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	65	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AGCTCCAGGAGCTCTGTCGTC	0.612													A|||	1722	0.34385	0.6914	0.1916	5008	,	,		18685	0.2817		0.0596	False		,,,				2504	0.3384				p.E65E		Atlas-SNP	.											.	.	.	.	0			c.G195A						PASS	.	A		2514,1892	542.5+/-376.0	714,1086,403	71.0	79.0	77.0		195	-0.9	1.0	7	dbSNP_119	77	674,7926	788.3+/-407.6	32,610,3658	no	coding-synonymous	ZNF498	NM_145115.2		746,1696,4061	AA,AG,GG		7.8372,42.9414,24.5118		65/545	99217424	3188,9818	2203	4300	6503	SO:0001819	synonymous_variant	221785	exon4			CCAGGAGCTCTGT	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"""-"", ""Zinc fingers, C2H2-type"""	21961	protein-coding gene	gene with protein product			"""zinc finger protein 498"""	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.195G>A	7.37:g.99217424G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Silent	SNP	ENST00000394152.2	37	CCDS5671.2																																																																																			G|0.735;A|0.265	0.265	strong		0.612	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115	
PPP1R3F	89801	hgsc.bcm.edu	37	X	49137916	49137916	+	Missense_Mutation	SNP	T	T	C	rs17148347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49137916T>C	ENST00000055335.6	+	2	1068	c.1052T>C	c.(1051-1053)tTt>tCt	p.F351S	PPP1R3F_ENST00000438316.1_Missense_Mutation_p.F23S|PPP1R3F_ENST00000466508.1_Missense_Mutation_p.F6S|PPP1R3F_ENST00000376188.1_Missense_Mutation_p.F6S|PPP1R3F_ENST00000495799.1_Missense_Mutation_p.F6S	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	351			F -> S (in dbSNP:rs17148347).		regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					GATAACACCTTTGCCATGGGT	0.433													C|||	340	0.0900662	0.2405	0.0231	3775	,	,		15353	0.0		0.0	False		,,,				2504	0.0061				p.F351S		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.T1052C						PASS	.	C	SER/PHE,SER/PHE	985,2850		118,601,148,913,423	102.0	81.0	88.0		17,1052	2.6	0.0	X	dbSNP_123	88	5,6723		0,4,1,2424,1871	yes	missense,missense	PPP1R3F	NM_001184745.1,NM_033215.4	155,155	118,605,149,3337,2294	CC,CT,C,TT,T		0.0743,25.6845,9.3723	benign,benign	6/454,351/800	49137916	990,9573	2203	4300	6503	SO:0001583	missense	89801	exon2			ACACCTTTGCCAT		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14944	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3F"""			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.1052T>C	X.37:g.49137916T>C	ENSP00000055335:p.Phe351Ser	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	37	CCDS35254.1	100	0.06027727546714889	65	0.14705882352941177	7	0.019662921348314606	0	0.0	0	0.0	C	0.009	-1.809591	0.00606	0.256845	7.43E-4	ENSG00000049769	ENST00000466508;ENST00000438316;ENST00000055335;ENST00000495799;ENST00000376188	T;T;T;T;T	0.51574	0.98;1.1;0.7;0.98;0.98	4.46	2.64	0.31445	.	0.552969	0.15282	N	0.270636	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	0.35400	-0.9790	9	0.14656	T	0.56	1.4767	5.832	0.18586	0.0:0.633:0.0:0.367	rs17148347;rs52792101;rs59868791;rs17148347	23;37;351	F5H262;A2VDJ8;Q6ZSY5	.;.;PPR3F_HUMAN	S	6;23;351;6;6	ENSP00000420687:F6S;ENSP00000415548:F23S;ENSP00000055335:F351S;ENSP00000417535:F6S;ENSP00000365359:F6S	ENSP00000055335:F351S	F	+	2	0	PPP1R3F	49024860	0.247000	0.23920	0.042000	0.18584	0.007000	0.05969	0.130000	0.15850	0.099000	0.17552	-0.170000	0.13304	TTT	0|0.016;C|0.097	0.097	strong		0.433	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
CDC42EP2	10435	hgsc.bcm.edu	37	11	65088498	65088498	+	Silent	SNP	T	T	C	rs4149835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65088498T>C	ENST00000544348.1	+	2	735	c.129T>C	c.(127-129)atT>atC	p.I43I	CDC42EP2_ENST00000533419.1_Silent_p.I43I|CDC42EP2_ENST00000279249.2_Silent_p.I43I			O14613	BORG1_HUMAN	CDC42 effector protein (Rho GTPase binding) 2	43	CRIB. {ECO:0000255|PROSITE- ProRule:PRU00057}.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	GTP-Rho binding (GO:0017049)|Rho GTPase activator activity (GO:0005100)			lung(1)	1						CCATTCATATTGGCAGTGGCG	0.612													C|||	393	0.0784744	0.2791	0.0303	5008	,	,		19020	0.0		0.003	False		,,,				2504	0.0				p.I43I		Atlas-SNP	.											.	CDC42EP2	13	.	0			c.T129C						PASS	.	C		1061,3341	705.0+/-407.2	120,821,1260	59.0	59.0	59.0		129	-9.5	0.1	11	dbSNP_110	59	9,8585	804.3+/-407.3	0,9,4288	no	coding-synonymous	CDC42EP2	NM_006779.3		120,830,5548	CC,CT,TT		0.1047,24.1027,8.2333		43/211	65088498	1070,11926	2201	4297	6498	SO:0001819	synonymous_variant	10435	exon2			TCATATTGGCAGT	AF098290	CCDS8099.1	11q13	2008-07-18				ENSG00000149798			16263	protein-coding gene	gene with protein product	"""CRIB-containing BOGR1 protein"""	606132				10490598, 11035016	Standard	NM_006779		Approved	CEP2, BORG1	uc001odl.3	O14613		ENST00000544348.1:c.129T>C	11.37:g.65088498T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_006779	B2RD85|Q9UNS0	Silent	SNP	ENST00000544348.1	37	CCDS8099.1																																																																																			T|0.914;C|0.086	0.086	strong		0.612	CDC42EP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387258.1	NM_006779	
ARHGDIB	397	hgsc.bcm.edu	37	12	15095558	15095558	+	Silent	SNP	C	C	G	rs4703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15095558C>G	ENST00000228945.4	-	6	648	c.504G>C	c.(502-504)gcG>gcC	p.A168A	ARHGDIB_ENST00000541546.1_Silent_p.A168A|ARHGDIB_ENST00000539131.1_5'UTR|ARHGDIB_ENST00000541644.1_Silent_p.A168A	NM_001175.4	NP_001166.3	P52566	GDIR2_HUMAN	Rho GDP dissociation inhibitor (GDI) beta	168					actin cytoskeleton organization (GO:0030036)|cellular component movement (GO:0006928)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of cell adhesion (GO:0007162)|regulation of catalytic activity (GO:0050790)|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)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTPase activator activity (GO:0005096)|Rho GDP-dissociation inhibitor activity (GO:0005094)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	15						ACGTGCCTCGCGCCAGCATGC	0.527													G|||	2413	0.481829	0.4062	0.5418	5008	,	,		18515	0.5714		0.5606	False		,,,				2504	0.3681				p.A168A		Atlas-SNP	.											.	ARHGDIB	33	.	0			c.G504C						PASS	.	G		1872,2534	632.7+/-395.9	399,1074,730	214.0	160.0	178.0		504	0.4	1.0	12	dbSNP_52	178	4558,4042	556.9+/-387.0	1223,2112,965	no	coding-synonymous	ARHGDIB	NM_001175.4		1622,3186,1695	GG,GC,CC		47.0,42.4875,49.4387		168/202	15095558	6430,6576	2203	4300	6503	SO:0001819	synonymous_variant	397	exon6			GCCTCGCGCCAGC	L07916	CCDS8671.1	12p12.3	2014-01-30				ENSG00000111348		"""Endogenous ligands"""	679	protein-coding gene	gene with protein product		602843		RAP1GN1, GDIA2, GDID4		8434008, 8356058	Standard	NM_001175		Approved	Ly-GDI, RhoGDI2	uc001rcq.1	P52566		ENST00000228945.4:c.504G>C	12.37:g.15095558C>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_001175	B5BU79	Silent	SNP	ENST00000228945.4	37	CCDS8671.1	1144	0.5238095238095238	185	0.37601626016260165	198	0.5469613259668509	323	0.5646853146853147	438	0.5778364116094987	G	10.09	1.255670	0.22965	0.424875	0.53	ENSG00000111348	ENST00000536592	.	.	.	4.41	0.426	0.16479	.	0.126644	0.52532	D	0.000079	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.43015	-0.9417	5	0.87932	D	0	-13.7797	2.097	0.03670	0.249:0.1353:0.4772:0.1386	rs4703;rs3180518;rs17850457;rs4703	.	.	.	P	162	.	ENSP00000445185:A162P	A	-	1	0	ARHGDIB	14986825	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	1.293000	0.33353	-0.017000	0.14103	-0.126000	0.14955	GCG	C|0.500;G|0.500	0.500	strong		0.527	ARHGDIB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400871.1	NM_001175	
PLCL2	23228	hgsc.bcm.edu	37	3	17051328	17051328	+	Silent	SNP	T	T	C	rs7653834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:17051328T>C	ENST00000418129.2	+	2	577	c.112T>C	c.(112-114)Tta>Cta	p.L38L	PLCL2_ENST00000432376.1_Silent_p.L38L|PLCL2_ENST00000396755.2_Silent_p.L38L|PLCL2_ENST00000460467.1_3'UTR	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	164	Gly-rich.				B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						TAGGTACTTTTTACTGGATGC	0.408													T|||	2268	0.452875	0.5061	0.2911	5008	,	,		19008	0.5466		0.3211	False		,,,				2504	0.5348				p.L38L		Atlas-SNP	.											.	PLCL2	145	.	0			c.T112C						PASS	.	T	,	2111,2295	574.3+/-383.7	492,1127,584	66.0	64.0	65.0		494,112	3.4	1.0	3	dbSNP_116	65	2763,5837	438.4+/-358.9	459,1845,1996	no	coding-synonymous,coding-synonymous	PLCL2	NM_001144382.1,NM_015184.5	,	951,2972,2580	CC,CT,TT		32.1279,47.9119,37.475	,	164/1128,38/1002	17051328	4874,8132	2203	4300	6503	SO:0001819	synonymous_variant	23228	exon2			TACTTTTTACTGG	AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"""phospholipase C, epsilon 2"""	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.112T>C	3.37:g.17051328T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	156	67	0.429487	NM_015184	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Silent	SNP	ENST00000418129.2	37	CCDS33713.1																																																																																			C|0.402;N|0.000	0.402	strong		0.408	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3		
CEACAM4	1089	hgsc.bcm.edu	37	19	42125710	42125710	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42125710A>G	ENST00000221954.2	-	7	838	c.728T>C	c.(727-729)gTc>gCc	p.V243A		NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	243						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						AACCTAAGAGACCACATCTGC	0.532																																					p.V243A		Atlas-SNP	.											CEACAM4,NS,neuroblastoma,+1,1	CEACAM4	42	1	0			c.T728C						PASS	.						114.0	109.0	111.0					19																	42125710		2203	4300	6503	SO:0001583	missense	1089	exon7			TAAGAGACCACAT	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"""Immunoglobulin superfamily / V-set domain containing"""	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.728T>C	19.37:g.42125710A>G	ENSP00000221954:p.Val243Ala	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_001817	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	37	CCDS33033.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.908731	0.00508	.	.	ENSG00000105352	ENST00000221954	T	0.01139	5.28	2.4	-3.74	0.04385	.	.	.	.	.	T	0.00440	0.0014	N	0.02142	-0.665	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.43956	-0.9359	9	0.06365	T	0.9	.	3.7364	0.08512	0.3171:0.4027:0.2802:0.0	.	243	O75871	CEAM4_HUMAN	A	243	ENSP00000221954:V243A	ENSP00000221954:V243A	V	-	2	0	CEACAM4	46817550	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.439000	0.02414	-0.683000	0.05190	-0.427000	0.05922	GTC	.	.	none		0.532	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817	
CCNL1	57018	hgsc.bcm.edu	37	3	156877707	156877707	+	Silent	SNP	A	A	T	rs9814142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:156877707A>T	ENST00000295926.3	-	1	295	c.177T>A	c.(175-177)atT>atA	p.I59I	CCNL1_ENST00000461804.1_Silent_p.I59I|CCNL1_ENST00000295925.4_Silent_p.I59I	NM_020307.2	NP_064703.1	Q9UK58	CCNL1_HUMAN	cyclin L1	59					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|nucleus (GO:0005634)				NS(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308)			TCTCCTCCGGAATCAGAGAGT	0.632													A|||	329	0.0656949	0.034	0.0879	5008	,	,		14739	0.0903		0.0477	False		,,,				2504	0.0859				p.I59I		Atlas-SNP	.											CCNL1,NS,carcinoma,0,1	CCNL1	53	1	0			c.T177A						scavenged	.	A		157,4249		2,153,2048	33.0	29.0	31.0		177	-9.6	0.0	3	dbSNP_119	31	365,8235		10,345,3945	no	coding-synonymous	CCNL1	NM_020307.2		12,498,5993	TT,TA,AA		4.2442,3.5633,4.0135		59/527	156877707	522,12484	2203	4300	6503	SO:0001819	synonymous_variant	57018	exon1			CTCCGGAATCAGA	AF180920	CCDS3178.1	3q25.31	2008-02-05			ENSG00000163660	ENSG00000163660			20569	protein-coding gene	gene with protein product		613384				11980906	Standard	NM_020307		Approved	ania-6a	uc003fbf.3	Q9UK58	OTTHUMG00000158713	ENST00000295926.3:c.177T>A	3.37:g.156877707A>T		Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	151	80	0.529801	NM_020307	B3KMY3|Q6NVY9|Q6UWS7|Q8NI48|Q96QT0|Q9NZF3	Silent	SNP	ENST00000295926.3	37	CCDS3178.1																																																																																			A|0.954;T|0.046	0.046	strong		0.632	CCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351859.1	NM_020307	
FAH	2184	hgsc.bcm.edu	37	15	80460421	80460421	+	Silent	SNP	C	C	T	rs116272698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80460421C>T	ENST00000407106.1	+	7	638	c.483C>T	c.(481-483)ggC>ggT	p.G161G	FAH_ENST00000539156.1_Silent_p.G91G|RP11-2E17.2_ENST00000568836.1_lincRNA|FAH_ENST00000558627.1_3'UTR|FAH_ENST00000561421.1_Silent_p.G161G|FAH_ENST00000261755.5_Silent_p.G161G			P16930	FAAA_HUMAN	fumarylacetoacetate hydrolase (fumarylacetoacetase)	161					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	fumarylacetoacetase activity (GO:0004334)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GCTACCATGGCCGTGCCTCCT	0.522									Tyrosinemia, type 1				C|||	45	0.00898562	0.0318	0.0043	5008	,	,		19054	0.0		0.0	False		,,,				2504	0.0				p.G161G		Atlas-SNP	.											.	FAH	36	.	0			c.C483T						PASS	.	C		124,4282	91.1+/-129.8	0,124,2079	116.0	93.0	101.0		483	-0.1	1.0	15	dbSNP_132	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAH	NM_000137.2		0,125,6378	TT,TC,CC		0.0116,2.8143,0.9611		161/420	80460421	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	2184	exon6	Familial Cancer Database	Fumarylacetoacetase Deficiency, Hepatorenal Tyrosinemia, Hereditary Tyrosinemia 1, HT1	CCATGGCCGTGCC	M55150	CCDS10314.1	15q25.1	2012-08-30			ENSG00000103876	ENSG00000103876	3.7.1.2		3579	protein-coding gene	gene with protein product		613871				1998338, 2336361	Standard	NM_000137		Approved		uc002bfm.2	P16930	OTTHUMG00000144187	ENST00000407106.1:c.483C>T	15.37:g.80460421C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	220	105	0.477273	NM_000137	B2R9X1|D3DW95|Q53XA7	Silent	SNP	ENST00000407106.1	37	CCDS10314.1																																																																																			C|0.990;T|0.010	0.010	strong		0.522	FAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291392.2		
ACE2	59272	hgsc.bcm.edu	37	X	15582298	15582298	+	Missense_Mutation	SNP	T	T	C	rs41303171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:15582298T>C	ENST00000252519.3	-	17	2260	c.2158A>G	c.(2158-2160)Aac>Gac	p.N720D	ACE2_ENST00000427411.1_Missense_Mutation_p.N720D|ACE2_ENST00000471548.1_5'UTR			Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2	720					angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|angiotensin-mediated drinking behavior (GO:0003051)|cellular protein metabolic process (GO:0044267)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|receptor biosynthetic process (GO:0032800)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell proliferation (GO:0042127)|regulation of cytokine production (GO:0001817)|regulation of inflammatory response (GO:0050727)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|response to virus (GO:0009615)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|endopeptidase activity (GO:0004175)|glycoprotein binding (GO:0001948)|peptide hormone binding (GO:0017046)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	32	Hepatocellular(33;0.183)				Lisinopril(DB00722)|Moexipril(DB00691)	TCTAGGCTGTTGTCATTCAGA	0.448													T|||	17	0.00450331	0.0	0.0029	3775	,	,		14206	0.0		0.0139	False		,,,				2504	0.001				p.N720D		Atlas-SNP	.											.	ACE2	87	.	0			c.A2158G						PASS	.	T	ASP/ASN	9,3826		0,8,1,1624,570	190.0	171.0	177.0		2158	3.7	0.9	X	dbSNP_127	177	176,6552		2,124,48,2302,1824	yes	missense	ACE2	NM_021804.2	23	2,132,49,3926,2394	CC,CT,C,TT,T		2.6159,0.2347,1.7514	benign	720/806	15582298	185,10378	2203	4300	6503	SO:0001583	missense	59272	exon18			GGCTGTTGTCATT	AF291820	CCDS14169.1	Xp22	2013-06-12	2013-06-12		ENSG00000130234	ENSG00000130234	3.4.17.23		13557	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	300335	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 2"""			10969042	Standard	NM_021804		Approved		uc004cxb.2	Q9BYF1	OTTHUMG00000021177	ENST00000252519.3:c.2158A>G	X.37:g.15582298T>C	ENSP00000252519:p.Asn720Asp	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	212	87	0.410377	NM_021804	C7ECU1|Q6UWP0|Q86WT0|Q9NRA7|Q9UFZ6	Missense_Mutation	SNP	ENST00000252519.3	37	CCDS14169.1	14	0.008438818565400843	0	0.0	2	0.0055248618784530384	0	0.0	11	0.01455026455026455	T	9.414	1.081380	0.20309	0.002347	0.026159	ENSG00000130234	ENST00000252519;ENST00000427411	D;D	0.85258	-1.96;-1.96	6.16	3.74	0.42951	.	0.405345	0.30676	N	0.009120	T	0.63558	0.2521	M	0.64567	1.98	0.26304	N	0.977924	B	0.12630	0.006	B	0.17979	0.02	T	0.67473	-0.5662	10	0.52906	T	0.07	-7.3294	9.172	0.37089	0.0:0.1533:0.0:0.8467	rs41303171	720	Q9BYF1	ACE2_HUMAN	D	720	ENSP00000252519:N720D;ENSP00000389326:N720D	ENSP00000252519:N720D	N	-	1	0	ACE2	15492219	0.957000	0.32711	0.894000	0.35097	0.079000	0.17450	0.719000	0.25881	0.922000	0.37019	0.481000	0.45027	AAC	T|0.986;C|0.014	0.014	strong		0.448	ACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055867.1		
OSBP2	23762	hgsc.bcm.edu	37	22	31091139	31091139	+	Silent	SNP	A	A	G	rs13053290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31091139A>G	ENST00000332585.6	+	1	347	c.243A>G	c.(241-243)gaA>gaG	p.E81E	OSBP2_ENST00000382310.3_Silent_p.E81E|OSBP2_ENST00000446658.2_Silent_p.E81E|OSBP2_ENST00000407373.1_Intron|OSBP2_ENST00000403222.3_Intron	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	81					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						CAAGATCGGAACCTGTGTCCG	0.682													g|||	1261	0.251797	0.525	0.2104	5008	,	,		11206	0.004		0.2972	False		,,,				2504	0.1207				p.E81E		Atlas-SNP	.											OSBP2,NS,carcinoma,0,1	OSBP2	52	1	0			c.A243G						PASS	.	T		1980,2314		487,1006,654	30.0	40.0	37.0		243	-0.1	0.0	22	dbSNP_121	37	2443,6075		333,1777,2149	no	coding-synonymous	OSBP2	NM_030758.3		820,2783,2803	GG,GA,AA		28.6804,46.1109,34.5223		81/917	31091139	4423,8389	2147	4259	6406	SO:0001819	synonymous_variant	23762	exon1			ATCGGAACCTGTG		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.243A>G	22.37:g.31091139A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_030758	B0QYG1|B4DK24|B4DKE4|B4DTR3|F5H2A3|O60396|Q0VF99|Q8NA37|Q9BY96|Q9BZF0	Silent	SNP	ENST00000332585.6	37	CCDS43002.1																																																																																			A|0.726;G|0.274	0.274	strong		0.682	OSBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321547.2	NM_030758	
FAAH	2166	hgsc.bcm.edu	37	1	46877885	46877885	+	Missense_Mutation	SNP	C	C	G	rs75429705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46877885C>G	ENST00000243167.8	+	13	1511	c.1427C>G	c.(1426-1428)gCc>gGc	p.A476G		NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	476					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	CCCATGCTGGCCCCTGCTCTG	0.637													G|||	43	0.00858626	0.0076	0.0	5008	,	,		17547	0.0169		0.0	False		,,,				2504	0.0164				p.A476G		Atlas-SNP	.											.	FAAH	36	.	0			c.C1427G						PASS	.	G	GLY/ALA	6,4354		0,6,2174	73.0	72.0	72.0		1427	4.7	1.0	1	dbSNP_131	72	4,8536		0,4,4266	no	missense	FAAH	NM_001441.2	60	0,10,6440	GG,GC,CC		0.0468,0.1376,0.0775	benign	476/580	46877885	10,12890	2180	4270	6450	SO:0001583	missense	2166	exon13			TGCTGGCCCCTGC	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.1427C>G	1.37:g.46877885C>G	ENSP00000243167:p.Ala476Gly	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	196	107	0.545918	NM_001441	D3DQ19|Q52M86|Q5TDF8	Missense_Mutation	SNP	ENST00000243167.8	37	CCDS535.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	11	0.019230769230769232	0	0.0	G	6.661	0.490412	0.12702	0.001376	4.68E-4	ENSG00000117480	ENST00000243167	T	0.64991	-0.13	4.66	4.66	0.58398	Amidase signature domain (2);	0.120287	0.56097	N	0.000022	T	0.22085	0.0532	N	0.04297	-0.235	0.21105	N	0.999789	B	0.02656	0.0	B	0.01281	0.0	T	0.04537	-1.0944	10	0.08599	T	0.76	-24.7092	15.0542	0.71901	0.0:0.1428:0.8572:0.0	.	476	O00519	FAAH1_HUMAN	G	476	ENSP00000243167:A476G	ENSP00000243167:A476G	A	+	2	0	FAAH	46650472	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	6.705000	0.74644	1.203000	0.43233	-0.120000	0.15030	GCC	C|0.997;G|0.003	0.003	strong		0.637	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
CDC20B	166979	hgsc.bcm.edu	37	5	54410099	54410099	+	Missense_Mutation	SNP	G	G	A	rs444527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:54410099G>A	ENST00000381375.2	-	12	1652	c.1507C>T	c.(1507-1509)Cgg>Tgg	p.R503W	CDC20B_ENST00000322374.6_Missense_Mutation_p.R461W|CDC20B_ENST00000296733.1_Missense_Mutation_p.R499W|CDC20B_ENST00000334206.5_3'UTR			Q86Y33	CD20B_HUMAN	cell division cycle 20B	503			R -> W (in dbSNP:rs444527). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.					p.R499W(1)		kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			gaaaacacccgggtctggtct	0.537													G|||	849	0.169529	0.0401	0.147	5008	,	,		17932	0.1865		0.2127	False		,,,				2504	0.2986				p.R503W		Atlas-SNP	.											CDC20B,bladder,carcinoma,+2,2	CDC20B	61	2	1	Substitution - Missense(1)	stomach(1)	c.C1507T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	270,4136	154.4+/-187.8	13,244,1946	96.0	90.0	92.0		1381,1507,1495	1.7	0.3	5	dbSNP_80	92	1642,6958	303.4+/-306.4	161,1320,2819	yes	missense,missense,missense	CDC20B	NM_001145734.2,NM_001170402.1,NM_152623.2	101,101,101	174,1564,4765	AA,AG,GG		19.093,6.128,14.7009	probably-damaging,probably-damaging,probably-damaging	461/478,503/520,499/516	54410099	1912,11094	2203	4300	6503	SO:0001583	missense	166979	exon12			ACACCCGGGTCTG	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.1507C>T	5.37:g.54410099G>A	ENSP00000370781:p.Arg503Trp	Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	210	104	0.495238	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	37	CCDS54852.1	339	0.15521978021978022	23	0.046747967479674794	59	0.16298342541436464	91	0.1590909090909091	166	0.21899736147757257	G	15.65	2.897041	0.52121	0.06128	0.19093	ENSG00000164287	ENST00000296733;ENST00000381375;ENST00000322374	T;T;T	0.60548	0.18;0.18;0.18	3.73	1.7	0.24286	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.521154	0.14995	N	0.286491	T	0.00039	0.0001	L	0.27975	0.815	0.58432	P	4.000000000004E-6	D;D;D	0.65815	0.993;0.995;0.986	P;P;P	0.58520	0.752;0.84;0.636	T	0.04961	-1.0915	9	0.72032	D	0.01	-18.0434	4.2399	0.10643	0.123:0.0:0.6533:0.2237	rs444527;rs17839390;rs59073991;rs444527	461;503;499	Q86Y33-3;Q86Y33;Q86Y33-2	.;CD20B_HUMAN;.	W	499;503;461	ENSP00000296733:R499W;ENSP00000370781:R503W;ENSP00000315720:R461W	ENSP00000296733:R499W	R	-	1	2	CDC20B	54445856	0.057000	0.20700	0.334000	0.25495	0.958000	0.62258	0.257000	0.18369	0.876000	0.35872	0.563000	0.77884	CGG	G|0.861;A|0.139	0.139	strong		0.537	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
BCAN	63827	hgsc.bcm.edu	37	1	156621252	156621252	+	Silent	SNP	G	G	A	rs146863260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156621252G>A	ENST00000329117.5	+	7	1404	c.1068G>A	c.(1066-1068)tcG>tcA	p.S356S	BCAN_ENST00000361588.5_Silent_p.S356S|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	356			S -> L (in dbSNP:rs12065791).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|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 disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCACAGACTCGGCCCAGCCTT	0.562													G|||	19	0.00379393	0.0144	0.0	5008	,	,		18343	0.0		0.0	False		,,,				2504	0.0				p.S356S		Atlas-SNP	.											.	BCAN	174	.	0			c.G1068A						PASS	.	G	,	62,4344	58.7+/-95.3	0,62,2141	47.0	44.0	45.0		1068,1068	1.5	0.9	1	dbSNP_134	45	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	BCAN	NM_021948.4,NM_198427.1	,	0,62,6441	AA,AG,GG		0.0,1.4072,0.4767	,	356/912,356/672	156621252	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	63827	exon7			AGACTCGGCCCAG	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1068G>A	1.37:g.156621252G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Silent	SNP	ENST00000329117.5	37	CCDS1149.1																																																																																			G|0.994;A|0.006	0.006	strong		0.562	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
CYP8B1	1582	hgsc.bcm.edu	37	3	42916596	42916596	+	Missense_Mutation	SNP	T	T	C	rs35764459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:42916596T>C	ENST00000316161.4	-	1	1037	c.713A>G	c.(712-714)aAg>aGg	p.K238R	CYP8B1_ENST00000437102.1_Missense_Mutation_p.K238R|RP11-141M3.5_ENST00000471537.1_RNA|KRBOX1_ENST00000426937.1_Intron	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	238			K -> R (in dbSNP:rs35764459).		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)			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)		GGAGAGCATCTTGTGAAAGAG	0.572													T|||	108	0.0215655	0.0779	0.0072	5008	,	,		18049	0.0		0.0	False		,,,				2504	0.0				p.K238R		Atlas-SNP	.											.	CYP8B1	59	.	0			c.A713G						PASS	.	T	ARG/LYS	305,4099		8,289,1905	25.0	27.0	26.0		713	4.2	0.0	3	dbSNP_126	26	7,8589		0,7,4291	yes	missense	CYP8B1	NM_004391.2	26	8,296,6196	CC,CT,TT		0.0814,6.9255,2.4	benign	238/502	42916596	312,12688	2202	4298	6500	SO:0001583	missense	1582	exon1			AGCATCTTGTGAA	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.713A>G	3.37:g.42916596T>C	ENSP00000318867:p.Lys238Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_004391	B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	37	CCDS2707.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	T	10.40	1.340138	0.24339	0.069255	8.14E-4	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.69685	-0.42;-0.42	5.34	4.18	0.49190	.	0.469912	0.21438	N	0.074528	T	0.05410	0.0143	L	0.38838	1.175	0.09310	N	1	B;B	0.28258	0.205;0.205	B;B	0.29077	0.098;0.098	T	0.05566	-1.0877	10	0.42905	T	0.14	-8.3878	8.1412	0.31084	0.0:0.1655:0.0:0.8345	rs35764459;rs56678767	238;238	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	R	238	ENSP00000404499:K238R;ENSP00000318867:K238R	ENSP00000318867:K238R	K	-	2	0	CYP8B1	42891600	0.004000	0.15560	0.011000	0.14972	0.684000	0.39900	1.063000	0.30567	0.885000	0.36088	0.449000	0.29647	AAG	T|0.977;C|0.023	0.023	strong		0.572	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391	
JAK2	3717	hgsc.bcm.edu	37	9	5050706	5050706	+	Silent	SNP	C	C	T	rs2230722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5050706C>T	ENST00000381652.3	+	6	983	c.489C>T	c.(487-489)caC>caT	p.H163H	JAK2_ENST00000544510.1_Silent_p.H14H|JAK2_ENST00000539801.1_Silent_p.H163H	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	86	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	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		
SERPINH1	871	hgsc.bcm.edu	37	11	75282882	75282882	+	Silent	SNP	G	G	A	rs585821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:75282882G>A	ENST00000524558.1	+	5	2446	c.1011G>A	c.(1009-1011)ttG>ttA	p.L337L	SERPINH1_ENST00000358171.3_Silent_p.L337L|SERPINH1_ENST00000533603.1_Silent_p.L337L|SERPINH1_ENST00000525876.1_Silent_p.L120L			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	337					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					AGGCCGACTTGTCACGCATGT	0.587													G|||	1887	0.376797	0.4758	0.3775	5008	,	,		18407	0.2073		0.2972	False		,,,				2504	0.499				p.L337L		Atlas-SNP	.											.	SERPINH1	33	.	0			c.G1011A						PASS	.	G	,	1940,2460	550.6+/-378.1	437,1066,697	66.0	51.0	56.0		1011,1011	2.3	1.0	11	dbSNP_83	56	2609,5977	420.8+/-353.5	377,1855,2061	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	814,2921,2758	AA,AG,GG		30.3867,44.0909,35.03	,	337/419,337/419	75282882	4549,8437	2200	4293	6493	SO:0001819	synonymous_variant	871	exon5			CGACTTGTCACGC	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.1011G>A	11.37:g.75282882G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																			G|0.662;A|0.338	0.338	strong		0.587	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
LY6G6C	80740	hgsc.bcm.edu	37	6	31687008	31687008	+	Silent	SNP	G	G	A	rs1065356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31687008G>A	ENST00000375819.2	-	3	408	c.243C>T	c.(241-243)cgC>cgT	p.R81R	LY6G6C_ENST00000495859.1_Silent_p.R25R	NM_025261.2	NP_079537.1	O95867	LY66C_HUMAN	lymphocyte antigen 6 complex, locus G6C	81	UPAR/Ly6.					anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(1)|large_intestine(1)|lung(1)|skin(1)	4						GACCCAGCTTGCGGTTGGTTT	0.577													g|||	1610	0.321486	0.5144	0.3012	5008	,	,		19313	0.1935		0.2525	False		,,,				2504	0.2781				p.R81R		Atlas-SNP	.											LY6G6C,NS,adenocarcinoma,-1,1	LY6G6C	9	1	0			c.C243T						PASS	.			2069,2337	572.6+/-383.4	484,1101,618	162.0	146.0	151.0		243	2.4	0.8	6	dbSNP_86	151	1863,6737	331.4+/-319.6	219,1425,2656	no	coding-synonymous	LY6G6C	NM_025261.2		703,2526,3274	AA,AG,GG		21.6628,46.9587,30.2322		81/126	31687008	3932,9074	2203	4300	6503	SO:0001819	synonymous_variant	80740	exon3			CAGCTTGCGGTTG		CCDS4714.1	6p21	2008-08-29	2002-07-29	2002-08-01	ENSG00000204421	ENSG00000204421			13936	protein-coding gene	gene with protein product		610435	"""chromosome 6 open reading frame 24"""	C6orf24		10384126, 12079290	Standard	NM_025261		Approved	G6c, NG24	uc003nwh.3	O95867	OTTHUMG00000031251	ENST00000375819.2:c.243C>T	6.37:g.31687008G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	181	87	0.480663	NM_025261	Q5SRS8|Q8IY94	Silent	SNP	ENST00000375819.2	37	CCDS4714.1																																																																																			G|0.690;A|0.310	0.310	strong		0.577	LY6G6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076530.2		
OGFR	11054	hgsc.bcm.edu	37	20	61444697	61444697	+	Missense_Mutation	SNP	G	G	C	rs6122315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61444697G>C	ENST00000290291.6	+	7	1755	c.1730G>C	c.(1729-1731)aGc>aCc	p.S577T	OGFR_ENST00000370461.1_Missense_Mutation_p.S525T	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	577	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].		S -> T (in dbSNP:rs6122315). {ECO:0000269|PubMed:10677613, ECO:0000269|PubMed:11214971, ECO:0000269|Ref.2}.	S -> I (in Ref. 1; AAF64406). {ECO:0000305}.	opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CCAGCCGAGAGCCCATCGGAG	0.746													G|||	1836	0.366613	0.4523	0.3386	5008	,	,		8711	0.4425		0.2813	False		,,,				2504	0.2802				p.S577T		Atlas-SNP	.											OGFR,colon,carcinoma,0,3	OGFR	63	3	0			c.G1730C						PASS	.						4.0	8.0	7.0					20																	61444697		1542	3467	5009	SO:0001583	missense	11054	exon7			CCGAGAGCCCATC	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1730G>C	20.37:g.61444697G>C	ENSP00000290291:p.Ser577Thr	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	814	0.3727106227106227	201	0.40853658536585363	122	0.3370165745856354	257	0.4493006993006993	234	0.3087071240105541	N	0.731	-0.780004	0.02929	.	.	ENSG00000060491	ENST00000290291;ENST00000357163;ENST00000370469;ENST00000370461	T;T	0.40225	1.04;1.04	1.6	0.0673	0.14365	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.17465	0.022	B	0.08055	0.003	T	0.46062	-0.9218	8	0.08599	T	0.76	.	5.1866	0.15187	0.1685:0.2423:0.5892:0.0	rs6122315;rs11543350;rs61541616	577	Q9NZT2	OGFR_HUMAN	T	577;557;412;525	ENSP00000290291:S577T;ENSP00000359491:S525T	ENSP00000290291:S577T	S	+	2	0	OGFR	60915142	0.000000	0.05858	0.002000	0.10522	0.012000	0.07955	-0.633000	0.05483	-0.232000	0.09811	0.089000	0.15464	AGC	G|0.636;C|0.364	0.364	strong		0.746	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
FKBP8	23770	hgsc.bcm.edu	37	19	18652521	18652521	+	Missense_Mutation	SNP	G	G	A	rs11574806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18652521G>A	ENST00000596558.2	-	2	369	c.260C>T	c.(259-261)gCc>gTc	p.A87V	FKBP8_ENST00000608443.1_Missense_Mutation_p.A87V|FKBP8_ENST00000597960.3_Missense_Mutation_p.A87V|FKBP8_ENST00000453489.2_Missense_Mutation_p.A116V|FKBP8_ENST00000610101.1_Missense_Mutation_p.A87V|FKBP8_ENST00000222308.4_Missense_Mutation_p.A87V			Q14318	FKBP8_HUMAN	FK506 binding protein 8, 38kDa	87	Glu-rich.		A -> V (in dbSNP:rs11574806).		apoptotic process (GO:0006915)|camera-type eye development (GO:0043010)|cell fate specification (GO:0001708)|chaperone-mediated protein folding (GO:0061077)|dorsal/ventral neural tube patterning (GO:0021904)|intracellular signal transduction (GO:0035556)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|positive regulation of BMP signaling pathway (GO:0030513)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of gene expression (GO:0010468)|smoothened signaling pathway (GO:0007224)|viral process (GO:0016032)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	FK506 binding (GO:0005528)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						TGGGGCCGGGGCTGGGGCGGG	0.687													G|||	492	0.0982428	0.3495	0.0317	5008	,	,		15475	0.0		0.008	False		,,,				2504	0.0				p.A87V		Atlas-SNP	.											.	FKBP8	69	.	0			c.C260T						PASS	.	G	VAL/ALA	1254,3140		180,894,1123	21.0	27.0	25.0		260	-0.5	0.0	19	dbSNP_120	25	63,8527		1,61,4233	yes	missense	FKBP8	NM_012181.3	64	181,955,5356	AA,AG,GG		0.7334,28.5389,10.1433	possibly-damaging	87/414	18652521	1317,11667	2197	4295	6492	SO:0001583	missense	23770	exon2			GCCGGGGCTGGGG	L37033	CCDS32961.1	19p12	2013-01-10	2002-08-29		ENSG00000105701	ENSG00000105701		"""Tetratricopeptide (TTC) repeat domain containing"""	3724	protein-coding gene	gene with protein product	"""FK506-binding protein 8 (38kD)"""	604840	"""FK506-binding protein 8 (38kD)"""			7543869	Standard	NM_012181		Approved	FKBP38, FKBPr38	uc002njj.1	Q14318		ENST00000596558.2:c.260C>T	19.37:g.18652521G>A	ENSP00000472302:p.Ala87Val	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	197	103	0.522843	NM_012181	C8C9T5|Q53GU3|Q7Z349|Q86YK6	Missense_Mutation	SNP	ENST00000596558.2	37		177	0.08104395604395605	158	0.32113821138211385	11	0.03038674033149171	0	0.0	8	0.010554089709762533	G	8.232	0.804782	0.16467	0.285389	0.007334	ENSG00000105701	ENST00000222308;ENST00000544835;ENST00000453489	T;T;T	0.37752	1.18;1.71;1.42	3.54	-0.469	0.12142	.	0.537430	0.17884	N	0.158757	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.16166	0.016;0.005;0.008	B;B;B	0.12156	0.007;0.001;0.002	T	0.45440	-0.9261	9	0.28530	T	0.3	-7.3641	8.5767	0.33603	0.0:0.0:0.3907:0.6093	rs11574806;rs11574806	116;87;87	B7Z6M0;Q14318;Q14318-2	.;FKBP8_HUMAN;.	V	87;87;116	ENSP00000222308:A87V;ENSP00000441267:A87V;ENSP00000388891:A116V	ENSP00000222308:A87V	A	-	2	0	FKBP8	18513521	0.879000	0.30193	0.030000	0.17652	0.242000	0.25591	2.151000	0.42263	0.263000	0.21812	0.491000	0.48974	GCC	G|0.907;A|0.093	0.093	strong		0.687	FKBP8-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000466374.3	NM_012181	
WDR35	57539	hgsc.bcm.edu	37	2	20135283	20135283	+	Silent	SNP	T	T	C	rs6741091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20135283T>C	ENST00000345530.3	-	22	2644	c.2529A>G	c.(2527-2529)gaA>gaG	p.E843E	WDR35_ENST00000416055.2_Silent_p.E408E|WDR35_ENST00000281405.4_Silent_p.E832E	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	85	0	0		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	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	
SYCP1	6847	hgsc.bcm.edu	37	1	115537343	115537343	+	Silent	SNP	T	T	C	rs17033011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:115537343T>C	ENST00000369522.3	+	31	2968	c.2728T>C	c.(2728-2730)Ttg>Ctg	p.L910L	SYCP1_ENST00000369518.1_Silent_p.L910L|SYCP1_ENST00000477590.1_3'UTR	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	910					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGAAGAGACATTGAAAACACT	0.274													T|||	185	0.0369409	0.1354	0.0086	5008	,	,		12816	0.0		0.0	False		,,,				2504	0.0				p.L910L		Atlas-SNP	.											.	SYCP1	149	.	0			c.T2728C						PASS	.			470,3920	196.0+/-220.5	22,426,1747	32.0	35.0	34.0		2728	-1.8	0.0	1	dbSNP_123	34	6,8570	4.3+/-15.6	0,6,4282	no	coding-synonymous	SYCP1	NM_003176.2		22,432,6029	CC,CT,TT		0.07,10.7062,3.6711		910/977	115537343	476,12490	2195	4288	6483	SO:0001819	synonymous_variant	6847	exon31			GAGACATTGAAAA	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"""cancer/testis antigen 8"""	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2728T>C	1.37:g.115537343T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_003176	O14963|Q5VXJ6	Silent	SNP	ENST00000369522.3	37	CCDS879.1																																																																																			T|0.954;C|0.046	0.046	strong		0.274	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176	
FAM110A	83541	hgsc.bcm.edu	37	20	825579	825579	+	Silent	SNP	G	G	A	rs8124809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:825579G>A	ENST00000304189.2	+	3	513	c.132G>A	c.(130-132)gaG>gaA	p.E44E	FAM110A_ENST00000541082.1_Silent_p.E44E|FAM110A_ENST00000381939.1_Silent_p.E44E|FAM110A_ENST00000246100.3_Silent_p.E44E|FAM110A_ENST00000381941.3_Silent_p.E44E			Q9BQ89	F110A_HUMAN	family with sequence similarity 110, member A	44						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|lung(2)	3						GCGCTGTGGAGCGCCTGGAGG	0.687													G|||	73	0.0145767	0.053	0.0043	5008	,	,		11046	0.0		0.0	False		,,,				2504	0.0				p.E44E		Atlas-SNP	.											.	FAM110A	18	.	0			c.G132A						PASS	.	G	,,	204,4158		1,202,1978	12.0	12.0	12.0		132,132,132	4.0	1.0	20	dbSNP_116	12	3,8543		0,3,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM110A	NM_001042353.1,NM_031424.4,NM_207121.3	,,	1,205,6248	AA,AG,GG		0.0351,4.6768,1.6037	,,	44/296,44/296,44/296	825579	207,12701	2181	4273	6454	SO:0001819	synonymous_variant	83541	exon2			TGTGGAGCGCCTG	BC012800	CCDS13008.1	20p13	2007-06-21	2007-03-21	2007-03-21	ENSG00000125898	ENSG00000125898			16188	protein-coding gene	gene with protein product		611393	"""chromosome 20 open reading frame 55"""	C20orf55		17499476	Standard	NM_001042353		Approved	bA371L19.3	uc002wef.1	Q9BQ89	OTTHUMG00000031649	ENST00000304189.2:c.132G>A	20.37:g.825579G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	157	86	0.547771	NM_207121	D3DVW2|Q5R1M7	Silent	SNP	ENST00000304189.2	37	CCDS13008.1																																																																																			A|0.020;C|0.000;G|0.979	0.020	strong		0.687	FAM110A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077489.1	NM_031424	
ZNF250	58500	hgsc.bcm.edu	37	8	146115367	146115367	+	Silent	SNP	A	A	G	rs2735906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:146115367A>G	ENST00000292579.7	-	3	251	c.135T>C	c.(133-135)ggT>ggC	p.G45G	ZNF250_ENST00000342660.6_Silent_p.G40G|ZNF250_ENST00000417550.2_Silent_p.G40G|ZNF250_ENST00000543949.1_Silent_p.G45G	NM_001109689.3|NM_021061.4	NP_001103159.1|NP_066405.1	P15622	ZN250_HUMAN	zinc finger protein 250	45	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(4)|kidney(2)|lung(8)|skin(1)	15	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)		TTCTGTAGAGACCCCTCTGAG	0.552													G|||	4562	0.910942	0.9735	0.8746	5008	,	,		18636	1.0		0.7614	False		,,,				2504	0.9141				p.G45G	NSCLC(16;520 556 24096 40084 43446)	Atlas-SNP	.											.	ZNF250	37	.	0			c.T135C						PASS	.	G	,	4134,272	152.9+/-186.6	1944,246,13	65.0	54.0	58.0		120,135	1.7	1.0	8	dbSNP_100	58	6469,2131	364.7+/-333.6	2424,1621,255	no	coding-synonymous,coding-synonymous	ZNF250	NM_001109689.3,NM_021061.4	,	4368,1867,268	GG,GA,AA		24.7791,6.1734,18.4761	,	40/556,45/561	146115367	10603,2403	2203	4300	6503	SO:0001819	synonymous_variant	58500	exon3			GTAGAGACCCCTC	AK095705	CCDS34972.1, CCDS55282.1	8q24.3	2013-01-08	2004-11-08			ENSG00000196150		"""Zinc fingers, C2H2-type"", ""-"""	13044	protein-coding gene	gene with protein product			"""zinc finger protein 647"""	ZNF647		12477932	Standard	NM_021061		Approved	MGC9718, ZFP647	uc003zer.4	P15622		ENST00000292579.7:c.135T>C	8.37:g.146115367A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	168	78	0.464286	NM_021061	D3DWP1|Q59HE9|Q8N942|Q96AH9	Silent	SNP	ENST00000292579.7	37	CCDS34972.1																																																																																			A|0.155;G|0.845	0.845	strong		0.552	ZNF250-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382968.1	NM_021061	
DRC1	92749	hgsc.bcm.edu	37	2	26678040	26678040	+	Missense_Mutation	SNP	G	G	T	rs3172008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26678040G>T	ENST00000288710.2	+	16	2179	c.2105G>T	c.(2104-2106)aGt>aTt	p.S702I		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	702			S -> I (in dbSNP:rs3172008).		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)											CTGGAAAACAGTTCTCTGGAG	0.582													G|||	700	0.139776	0.3548	0.0793	5008	,	,		18349	0.0823		0.0467	False		,,,				2504	0.047				p.S702I		Atlas-SNP	.											CCDC164,NS,carcinoma,+1,2	CCDC164	84	2	0			c.G2105T						PASS	.	G	ILE/SER	1299,3107	437.2+/-344.9	199,901,1103	86.0	99.0	94.0		2105	-4.4	0.0	2	dbSNP_105	94	393,8207	125.5+/-184.1	1,391,3908	yes	missense	CCDC164	NM_145038.2	142	200,1292,5011	TT,TG,GG		4.5698,29.4825,13.0094	benign	702/741	26678040	1692,11314	2203	4300	6503	SO:0001583	missense	92749	exon16			AAAACAGTTCTCT	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.2105G>T	2.37:g.26678040G>T	ENSP00000288710:p.Ser702Ile	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	128	52	0.40625	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	37	CCDS1723.1	256	0.11721611721611722	165	0.3353658536585366	26	0.0718232044198895	35	0.06118881118881119	30	0.0395778364116095	G	11.67	1.706520	0.30232	0.294825	0.045698	ENSG00000157856	ENST00000288710	T	0.46819	0.86	5.38	-4.36	0.03645	.	2.656320	0.00907	N	0.002436	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.26002	0.139	B	0.24006	0.05	T	0.24799	-1.0150	9	0.49607	T	0.09	8.668	8.1501	0.31134	0.3804:0.0:0.5015:0.1181	rs3172008;rs17421703;rs58541120;rs3172008	702	Q96MC2	CC164_HUMAN	I	702	ENSP00000288710:S702I	ENSP00000288710:S702I	S	+	2	0	CCDC164	26531544	0.000000	0.05858	0.000000	0.03702	0.154000	0.21943	-1.540000	0.02200	-1.149000	0.02843	-0.345000	0.07892	AGT	G|0.870;N|0.001	.	strong		0.582	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038	
ABCC12	94160	hgsc.bcm.edu	37	16	48174766	48174766	+	Silent	SNP	A	A	G	rs16945872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48174766A>G	ENST00000311303.3	-	4	834	c.489T>C	c.(487-489)atT>atC	p.I163I	ABCC12_ENST00000448542.1_Silent_p.I163I|ABCC12_ENST00000416054.1_Silent_p.I163I	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	163	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)				TGCACAGTCCAATGCCAACCC	0.537													a|||	189	0.0377396	0.1399	0.0058	5008	,	,		19380	0.0		0.0	False		,,,				2504	0.0				p.I163I		Atlas-SNP	.											.	ABCC12	190	.	0			c.T489C						PASS	.	A		477,3925	225.9+/-241.6	24,429,1748	98.0	96.0	97.0		489	-2.6	0.0	16	dbSNP_123	97	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	ABCC12	NM_033226.2		24,436,6041	GG,GA,AA		0.0814,10.836,3.7225		163/1360	48174766	484,12518	2201	4300	6501	SO:0001819	synonymous_variant	94160	exon4			CAGTCCAATGCCA	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.489T>C	16.37:g.48174766A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	37	CCDS10730.1																																																																																			A|0.955;G|0.045	0.045	strong		0.537	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274343	39274343	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39274343A>G	ENST00000391413.2	-	1	263	c.225T>C	c.(223-225)tgT>tgC	p.C75C		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	75	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCTGGGGCGACAGCAGCTGG	0.657																																					p.C75C		Atlas-SNP	.											KRTAP4-11,NS,malignant_melanoma,0,2	KRTAP4-11	94	2	0			c.T225C						scavenged	.																																			SO:0001819	synonymous_variant	653240	exon1			GGGGCGACAGCAG	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.225T>C	17.37:g.39274343A>G		Somatic	175	4	0.0228571		WXS	Illumina HiSeq	Phase_I	150	14	0.0933333	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.	.	none		0.657	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
KRT32	3882	hgsc.bcm.edu	37	17	39619186	39619186	+	Missense_Mutation	SNP	G	G	C	rs2604956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39619186G>C	ENST00000225899.3	-	6	1216	c.1113C>G	c.(1111-1113)gaC>gaG	p.D371E		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	371	Coil 2.|Rod.			D -> E (in Ref. 1; CAA62284 and 4; CAA57179). {ECO:0000305}.	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)				GCCGCTCCAGGTCAGCCCGGA	0.647													G|||	232	0.0463259	0.0408	0.0375	5008	,	,		17222	0.0476		0.0765	False		,,,				2504	0.0276				p.D371E		Atlas-SNP	.											KRT32,brain,glioma,0,2	KRT32	57	2	0			c.C1113G						PASS	.	G	GLU/ASP	180,4226	116.7+/-154.6	5,170,2028	79.0	77.0	78.0		1113	4.0	1.0	17	dbSNP_100	78	811,7789	188.4+/-235.4	37,737,3526	no	missense	KRT32	NM_002278.3	45	42,907,5554	CC,CG,GG		9.4302,4.0853,7.6196	possibly-damaging	371/449	39619186	991,12015	2203	4300	6503	SO:0001583	missense	3882	exon6			CTCCAGGTCAGCC	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.1113C>G	17.37:g.39619186G>C	ENSP00000225899:p.Asp371Glu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	154	73	0.474026	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	131	0.059981684981684984	21	0.042682926829268296	15	0.04143646408839779	30	0.05244755244755245	65	0.08575197889182058	G	16.62	3.173510	0.57584	0.040853	0.094302	ENSG00000108759	ENST00000225899	D	0.87412	-2.25	4.98	4.01	0.46588	Filament (1);	0.000000	0.40144	N	0.001178	T	0.29716	0.0742	L	0.43152	1.355	0.34582	P	0.28545200000000004	D	0.89917	1.0	D	0.97110	1.0	T	0.71852	-0.4467	9	0.26408	T	0.33	.	6.6185	0.22790	0.1617:0.1481:0.6903:0.0	rs2604956	371	Q14532	K1H2_HUMAN	E	371	ENSP00000225899:D371E	ENSP00000225899:D371E	D	-	3	2	KRT32	36872712	0.995000	0.38212	0.998000	0.56505	0.690000	0.40134	0.290000	0.18975	1.216000	0.43427	0.491000	0.48974	GAC	G|0.927;C|0.073	0.073	strong		0.647	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
TBCD	6904	hgsc.bcm.edu	37	17	80828203	80828203	+	Silent	SNP	C	C	T	rs36018199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80828203C>T	ENST00000355528.4	+	14	1552	c.1422C>T	c.(1420-1422)ttC>ttT	p.F474F	TBCD_ENST00000397466.2_Silent_p.F88F|TBCD_ENST00000539345.2_Silent_p.F474F	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	474					'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)			GCTGGGCCTTCGCGCGTGCCT	0.647													C|||	53	0.0105831	0.0023	0.0101	5008	,	,		19389	0.0		0.0368	False		,,,				2504	0.0061				p.F474F		Atlas-SNP	.											.	TBCD	94	.	0			c.C1422T						PASS	.	C		39,4273		1,37,2118	37.0	43.0	41.0		1422	-6.2	0.6	17	dbSNP_126	41	406,8106		11,384,3861	no	coding-synonymous	TBCD	NM_005993.4		12,421,5979	TT,TC,CC		4.7697,0.9045,3.4701		474/1193	80828203	445,12379	2156	4256	6412	SO:0001819	synonymous_variant	6904	exon14			GGCCTTCGCGCGT	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.1422C>T	17.37:g.80828203C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Silent	SNP	ENST00000355528.4	37	CCDS45818.1																																																																																			C|0.977;T|0.023	0.023	strong		0.647	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
ACOX3	8310	hgsc.bcm.edu	37	4	8394094	8394094	+	Silent	SNP	G	G	A	rs28627156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:8394094G>A	ENST00000356406.5	-	11	1343	c.1266C>T	c.(1264-1266)tgC>tgT	p.C422C	ACOX3_ENST00000503233.1_Silent_p.C422C|ACOX3_ENST00000413009.2_Silent_p.C422C|RNA5SP152_ENST00000365184.1_RNA	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	422					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						ACGCCTCCCGGCATTCCTGAA	0.602													G|||	614	0.122604	0.326	0.0533	5008	,	,		18339	0.003		0.0805	False		,,,				2504	0.0634				p.C422C		Atlas-SNP	.											.	ACOX3	70	.	0			c.C1266T						PASS	.	G	,	1237,3169	427.2+/-341.4	173,891,1139	154.0	158.0	157.0		1266,1266	3.2	1.0	4	dbSNP_125	157	615,7985	161.1+/-214.1	28,559,3713	no	coding-synonymous,coding-synonymous	ACOX3	NM_001101667.1,NM_003501.2	,	201,1450,4852	AA,AG,GG		7.1512,28.0754,14.2396	,	422/625,422/701	8394094	1852,11154	2203	4300	6503	SO:0001819	synonymous_variant	8310	exon11			CTCCCGGCATTCC	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"""acyl-Coenzyme A oxidase 3, pristanoyl"""			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.1266C>T	4.37:g.8394094G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_001101667	Q96AJ8	Silent	SNP	ENST00000356406.5	37	CCDS3401.1																																																																																			G|0.872;A|0.128	0.128	strong		0.602	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4		
PSG6	5675	hgsc.bcm.edu	37	19	43420451	43420451	+	Missense_Mutation	SNP	G	G	C	rs386809477|rs3198831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43420451G>C	ENST00000292125.2	-	2	297	c.253C>G	c.(253-255)Cac>Gac	p.H85D	PSG6_ENST00000601833.1_Missense_Mutation_p.H14D|PSG6_ENST00000187910.2_Missense_Mutation_p.H85D|PSG6_ENST00000402603.4_Missense_Mutation_p.H85D	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	85	Ig-like V-type.		H -> D (in dbSNP:rs3198831). {ECO:0000269|PubMed:2271648, ECO:0000269|PubMed:2346748}.		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				ATTTGACCGTGTACTACATAT	0.443													.|||	2271	0.453474	0.5991	0.4265	5008	,	,		21337	0.4325		0.2525	False		,,,				2504	0.5041				p.H85D		Atlas-SNP	.											.	PSG6	89	.	0			c.C253G						PASS	.	C	ASP/HIS,ASP/HIS	2533,1869		767,999,435	312.0	293.0	300.0		253,253	-4.2	0.0	19	dbSNP_105	300	2232,6366		347,1538,2414	yes	missense,missense	PSG6	NM_001031850.2,NM_002782.3	81,81	1114,2537,2849	CC,CG,GG		25.9595,42.458,36.6538	,	85/425,85/436	43420451	4765,8235	2201	4299	6500	SO:0001583	missense	5675	exon2			GACCGTGTACTAC		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.253C>G	19.37:g.43420451G>C	ENSP00000292125:p.His85Asp	Somatic	303	1	0.00330033		WXS	Illumina HiSeq	Phase_I	287	286	0.996516	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	37	CCDS12613.1	850	0.3891941391941392	293	0.5955284552845529	130	0.35911602209944754	231	0.40384615384615385	196	0.25857519788918204	N	0.005	-2.167004	0.00318	0.57542	0.259595	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.63744	-0.06;-0.06;-0.06	2.24	-4.23	0.03789	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00033	-2.575	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	0.34153	-0.9840	8	0.02654	T	1	.	5.3567	0.16065	0.2634:0.2385:0.4981:0.0	rs3198831;rs52810447;rs3198831	85;85;85	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	D	85	ENSP00000187910:H85D;ENSP00000385736:H85D;ENSP00000292125:H85D	ENSP00000187910:H85D	H	-	1	0	PSG6	48112291	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.739000	0.01840	-1.078000	0.03117	-1.041000	0.02371	CAC	G|0.625;C|0.375	0.375	strong		0.443	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37451768	37451768	+	Missense_Mutation	SNP	T	T	G	rs41276130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:37451768T>G	ENST00000602533.1	+	17	1925	c.1826T>G	c.(1825-1827)tTg>tGg	p.L609W	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.L609W|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.L609W			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	665					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						GAACAAACATTGAGAGCAGGT	0.328													.|||	209	0.0417332	0.0272	0.049	5008	,	,		15937	0.0		0.0885	False		,,,				2504	0.0511				p.L609W		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.T1826G						PASS	.	T	TRP/LEU	141,3483		1,139,1672	99.0	88.0	91.0		1826	-0.2	0.0	10	dbSNP_127	91	759,7371		29,701,3335	no	missense	ANKRD30A	NM_052997.2	61	30,840,5007	GG,GT,TT		9.3358,3.8907,7.657	possibly-damaging	609/1342	37451768	900,10854	1812	4065	5877	SO:0001583	missense	91074	exon17			AAACATTGAGAGC	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.1826T>G	10.37:g.37451768T>G	ENSP00000473551:p.Leu609Trp	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	221	105	0.475113	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		139	0.06364468864468864	27	0.054878048780487805	23	0.06353591160220995	0	0.0	89	0.11741424802110818	.	9.596	1.127302	0.20959	0.038907	0.093358	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.09911	2.94;2.93	0.882	-0.146	0.13432	.	.	.	.	.	T	0.00144	0.0004	L	0.36672	1.1	0.09310	N	1	D	0.58620	0.983	P	0.47075	0.536	T	0.31024	-0.9958	9	0.56958	D	0.05	.	3.2093	0.06677	0.0:0.6711:0.0:0.3289	rs41276130	665	Q9BXX3	AN30A_HUMAN	W	609	ENSP00000354432:L609W;ENSP00000363792:L609W	ENSP00000354432:L609W	L	+	2	0	ANKRD30A	37491774	0.000000	0.05858	0.034000	0.17996	0.190000	0.23558	-1.984000	0.01487	-0.041000	0.13558	0.076000	0.15429	TTG	T|0.930;G|0.070	0.070	strong		0.328	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
CCDC18	343099	hgsc.bcm.edu	37	1	93720153	93720153	+	Missense_Mutation	SNP	G	G	T	rs61729705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:93720153G>T	ENST00000343253.7	+	24	3823	c.3321G>T	c.(3319-3321)agG>agT	p.R1107S	CCDC18_ENST00000338949.4_3'UTR|CCDC18_ENST00000334652.5_3'UTR|CCDC18_ENST00000401026.3_Missense_Mutation_p.R1108S|CCDC18_ENST00000557479.1_Missense_Mutation_p.R1226S			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	1107										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		CACAACAAAGGATGAAAGAAA	0.323													G|||	487	0.0972444	0.3366	0.0288	5008	,	,		19033	0.0159		0.002	False		,,,				2504	0.0041				p.R1108S		Atlas-SNP	.											.	CCDC18	93	.	0			c.G3324T						PASS	.	G	SER/ARG	1093,2575		157,779,898	125.0	131.0	129.0		3324	0.4	1.0	1	dbSNP_129	129	13,8157		1,11,4073	yes	missense	CCDC18	NM_206886.3	110	158,790,4971	TT,TG,GG		0.1591,29.7983,9.3428	benign	1108/1300	93720153	1106,10732	1834	4085	5919	SO:0001583	missense	343099	exon24			ACAAAGGATGAAA			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.3321G>T	1.37:g.93720153G>T	ENSP00000343377:p.Arg1107Ser	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	200	90	0.45	NM_206886	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		175|175	0.08012820512820513|0.08012820512820513	150|150	0.3048780487804878|0.3048780487804878	12|12	0.03314917127071823|0.03314917127071823	11|11	0.019230769230769232|0.019230769230769232	2|2	0.002638522427440633|0.002638522427440633	G|G	5.074|5.074	0.199375|0.199375	0.09652|0.09652	0.297983|0.297983	0.001591|0.001591	ENSG00000122483|ENSG00000122483	ENST00000370276|ENST00000343253;ENST00000401026;ENST00000557479	.|.	.|.	.|.	5.02|5.02	0.449|0.449	0.16619|0.16619	.|.	.|0.782786	.|0.12361	.|N	.|0.475673	T|T	0.06462|0.06462	0.0166|0.0166	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	P|P	0.99999902352|0.99999902352	.|P;B	.|0.35575	.|0.51;0.006	.|B;B	.|0.36666	.|0.23;0.005	T|T	0.30149|0.30149	-0.9988|-0.9988	4|8	.|0.21540	.|T	.|0.41	.|.	5.0771|5.0771	0.14638|0.14638	0.5374:0.1787:0.2838:0.0|0.5374:0.1787:0.2838:0.0	rs61729705|rs61729705	.|26;1226	.|Q5T9S4;G3V388	.|.;.	V|S	1161|1107;1108;1226	.|.	.|ENSP00000343377:R1107S	G|R	+|+	2|3	0|2	CCDC18|CCDC18	93492741|93492741	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.453000|0.453000	0.32348|0.32348	0.703000|0.703000	0.25646|0.25646	0.243000|0.243000	0.21327|0.21327	-0.143000|-0.143000	0.13931|0.13931	GGA|AGG	A|0.000;G|0.947;T|0.053	0.053	strong		0.323	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
CSNK2B	1460	hgsc.bcm.edu	37	6	31635710	31635710	+	Silent	SNP	T	T	C	rs14365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31635710T>C	ENST00000375882.2	+	3	294	c.138T>C	c.(136-138)taT>taC	p.Y46Y	GPANK1_ENST00000375893.2_5'Flank|CSNK2B-LY6G5B-1181_ENST00000375880.2_Silent_p.Y46Y|CSNK2B_ENST00000375866.2_Silent_p.Y46Y|LY6G5B_ENST00000409525.1_5'Flank|GPANK1_ENST00000375900.4_5'Flank|GPANK1_ENST00000375906.1_5'Flank|GPANK1_ENST00000375896.4_5'Flank|CSNK2B_ENST00000375885.4_Silent_p.Y65Y|LY6G5B_ENST00000375864.4_5'Flank|CSNK2B_ENST00000375865.2_Silent_p.Y46Y|GPANK1_ENST00000375895.2_5'Flank	NM_001282385.1|NM_001320.5	NP_001269314.1|NP_001311.3	P67870	CSK2B_HUMAN	casein kinase 2, beta polypeptide	46					adiponectin-activated signaling pathway (GO:0033211)|axon guidance (GO:0007411)|cellular protein complex assembly (GO:0043623)|endothelial tube morphogenesis (GO:0061154)|mitotic cell cycle (GO:0000278)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell proliferation (GO:0008285)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|protein phosphorylation (GO:0006468)|regulation of DNA binding (GO:0051101)|regulation of protein kinase activity (GO:0045859)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein kinase CK2 complex (GO:0005956)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein kinase regulator activity (GO:0019887)|receptor binding (GO:0005102)|transcription factor binding (GO:0008134)			central_nervous_system(5)|endometrium(1)|large_intestine(2)|liver(1)|urinary_tract(1)	10						TCCCTCACTATCGACAAGCTC	0.468													T|||	1520	0.303514	0.4312	0.3501	5008	,	,		20497	0.2976		0.2237	False		,,,				2504	0.1861				p.Y46Y		Atlas-SNP	.											.	CSNK2B	15	.	0			c.T138C						PASS	.	T		1747,2659	521.1+/-370.4	342,1063,798	136.0	124.0	128.0		138	4.6	1.0	6	dbSNP_52	128	1656,6944	304.6+/-307.0	153,1350,2797	yes	coding-synonymous	CSNK2B	NM_001320.5		495,2413,3595	CC,CT,TT		19.2558,39.6505,26.1648		46/216	31635710	3403,9603	2203	4300	6503	SO:0001819	synonymous_variant	1460	exon3			TCACTATCGACAA	M30448	CCDS4712.1	6p21.33	2013-01-17			ENSG00000204435	ENSG00000204435	2.7.11.1		2460	protein-coding gene	gene with protein product		115441				2276748, 9503014	Standard	NM_001320		Approved		uc003nvr.1	P67870	OTTHUMG00000177888	ENST00000375882.2:c.138T>C	6.37:g.31635710T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	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	
YTHDC2	64848	hgsc.bcm.edu	37	5	112888882	112888882	+	Missense_Mutation	SNP	A	A	T	rs72805422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	29	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	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	
VWA5B1	127731	hgsc.bcm.edu	37	1	20640969	20640969	+	Silent	SNP	G	G	A	rs114916291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:20640969G>A	ENST00000375079.2	+	4	643	c.447G>A	c.(445-447)tcG>tcA	p.S149S	RP4-745E8.2_ENST00000444923.1_RNA|VWA5B1_ENST00000375083.4_Silent_p.S149S|VWA5B1_ENST00000289815.8_Silent_p.S149S|VWA5B1_ENST00000289825.4_5'UTR	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	149	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.					extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						GCACCTCCTCGGAGCTCCCAA	0.617													G|||	76	0.0151757	0.0499	0.0072	5008	,	,		17445	0.0		0.005	False		,,,				2504	0.0				p.S149S		Atlas-SNP	.											.	VWA5B1	44	.	0			c.G447A						PASS	.	G		66,1318		3,60,629	46.0	45.0	46.0		447	-11.2	0.5	1	dbSNP_132	46	37,3145		0,37,1554	no	coding-synonymous	VWA5B1	NM_001039500.2		3,97,2183	AA,AG,GG		1.1628,4.7688,2.2558		149/1216	20640969	103,4463	692	1591	2283	SO:0001819	synonymous_variant	127731	exon4			CTCCTCGGAGCTC	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.447G>A	1.37:g.20640969G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	68	0.591304	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Silent	SNP	ENST00000375079.2	37																																																																																				G|0.988;A|0.012	0.012	strong		0.617	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
MAPK10	5602	hgsc.bcm.edu	37	4	86950354	86950354	+	Silent	SNP	A	A	G	rs148438622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:86950354A>G	ENST00000359221.3	-	13	1774	c.1248T>C	c.(1246-1248)ccT>ccC	p.P416P	MAPK10_ENST00000395157.3_Silent_p.P271P|MAPK10_ENST00000395160.3_Silent_p.P271P|MAPK10_ENST00000395161.2_Silent_p.P416P|MAPK10_ENST00000395169.3_Silent_p.P378P|MAPK10_ENST00000361569.2_Silent_p.P416P|MAPK10_ENST00000395166.1_Silent_p.P378P|MAPK10_ENST00000449047.2_Silent_p.P271P			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	416					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)			breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		GAGTACCTGAAGGAGAAGGCT	0.353																																					p.P416P		Atlas-SNP	.											MAPK10_ENST00000449047,colon,carcinoma,-2,2	MAPK10	106	2	0			c.T1248C						PASS	.	A	,,,	5,4401	11.4+/-27.6	0,5,2198	215.0	200.0	205.0		1248,1134,813,1248	6.0	1.0	4	dbSNP_134	205	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPK10	NM_002753.3,NM_138980.2,NM_138981.2,NM_138982.2	,,,	0,5,6498	GG,GA,AA		0.0,0.1135,0.0384	,,,	416/423,378/427,271/278,416/465	86950354	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5602	exon13			ACCTGAAGGAGAA	U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.1248T>C	4.37:g.86950354A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_002753	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Silent	SNP	ENST00000359221.3	37	CCDS34026.1	.	.	.	.	.	.	.	.	.	.	A	10.37	1.331983	0.24167	0.001135	0.0	ENSG00000109339	ENST00000515400	.	.	.	5.96	5.96	0.96718	.	.	.	.	.	T	0.63850	0.2546	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62955	-0.6744	4	.	.	.	-10.1507	11.1954	0.48709	0.9281:0.0:0.0718:0.0	.	.	.	.	L	329	.	.	F	-	1	0	MAPK10	87169378	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.314000	0.51943	2.278000	0.76064	0.533000	0.62120	TTC	A|1.000;G|0.000	0.000	strong		0.353	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2		
NOTCH3	4854	hgsc.bcm.edu	37	19	15291576	15291576	+	Missense_Mutation	SNP	C	C	G	rs35769976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15291576C>G	ENST00000263388.2	-	19	3133	c.3058G>C	c.(3058-3060)Gcc>Ccc	p.A1020P		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1020	EGF-like 26. {ECO:0000255|PROSITE- ProRule:PRU00076}.		A -> P (in dbSNP:rs35769976).		forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			AGGCAATAGGCCCCAGTCTGG	0.632													C|||	552	0.110224	0.3669	0.0375	5008	,	,		17984	0.001		0.0129	False		,,,				2504	0.0276				p.A1020P		Atlas-SNP	.											.	NOTCH3	340	.	0			c.G3058C	GRCh37	CM085589	NOTCH3	M	rs35769976	PASS	.	C	PRO/ALA	1294,3106		226,842,1132	39.0	35.0	37.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3058	1.4	0.0	19	dbSNP_126	37	122,8478		0,122,4178	yes	missense	NOTCH3	NM_000435.2	27	226,964,5310	GG,GC,CC		1.4186,29.4091,10.8923	benign	1020/2322	15291576	1416,11584	2200	4300	6500	SO:0001583	missense	4854	exon19			AATAGGCCCCAGT	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.3058G>C	19.37:g.15291576C>G	ENSP00000263388:p.Ala1020Pro	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	183	0.08379120879120878	149	0.30284552845528456	22	0.06077348066298342	0	0.0	12	0.0158311345646438	C	9.463	1.093538	0.20471	0.294091	0.014186	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.91792	-2.91	5.13	1.44	0.22558	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.32190	N	0.006458	T	0.00012	0.0000	N	0.26130	0.795	0.43965	P	0.003354999999999997	B;B	0.21309	0.054;0.027	B;B	0.28638	0.092;0.075	T	0.04128	-1.0975	9	0.37606	T	0.19	.	7.3526	0.26700	0.0:0.6162:0.1375:0.2462	rs35769976;rs60155197	971;1020	Q59FL3;Q9UM47	.;NOTC3_HUMAN	P	1020;970	ENSP00000263388:A1020P	ENSP00000263388:A1020P	A	-	1	0	NOTCH3	15152576	0.000000	0.05858	0.018000	0.16275	0.401000	0.30781	-1.039000	0.03550	0.569000	0.29329	0.563000	0.77884	GCC	C|0.886;G|0.114	0.114	strong		0.632	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
ACVR1B	91	hgsc.bcm.edu	37	12	52370181	52370181	+	Silent	SNP	G	G	A	rs115556161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52370181G>A	ENST00000257963.4	+	3	479	c.402G>A	c.(400-402)ccG>ccA	p.P134P	ACVR1B_ENST00000415850.2_Silent_p.P134P|ACVR1B_ENST00000541224.1_Silent_p.P134P|ACVR1B_ENST00000426655.2_Silent_p.P134P|ACVR1B_ENST00000542485.1_Silent_p.P82P	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	134					activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	TCGCCGGCCCGGTGTTCCTCC	0.542													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		19147	0.0		0.0	False		,,,				2504	0.0				p.P134P		Atlas-SNP	.											.	ACVR1B	167	.	0			c.G402A						PASS	.	G	,,	52,4354	52.9+/-88.7	0,52,2151	162.0	157.0	159.0		402,246,402	-10.8	0.7	12	dbSNP_132	159	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ACVR1B	NM_004302.4,NM_020327.3,NM_020328.3	,,	0,53,6450	AA,AG,GG		0.0116,1.1802,0.4075	,,	134/506,82/454,134/547	52370181	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	91	exon3			CGGCCCGGTGTTC		CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.402G>A	12.37:g.52370181G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	167	85	0.508982	NM_020328	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Silent	SNP	ENST00000257963.4	37	CCDS8816.1																																																																																			G|0.994;A|0.006	0.006	strong		0.542	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328	
OR2T8	343172	hgsc.bcm.edu	37	1	248085124	248085124	+	Missense_Mutation	SNP	G	G	A	rs4590708	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248085124G>A	ENST00000319968.4	+	1	805	c.805G>A	c.(805-807)Gac>Aac	p.D269N		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	269						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)|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)			CACTAACCACGACAAGGTTGT	0.488													G|||	1755	0.350439	0.2769	0.2709	5008	,	,		12953	0.5387		0.1998	False		,,,				2504	0.4673				p.D269N		Atlas-SNP	.											.	OR2T8	67	.	0			c.G805A						PASS	.	G	ASN/ASP	1112,3294	383.0+/-324.7	143,826,1234	111.0	102.0	105.0		805	3.6	0.0	1	dbSNP_111	105	1898,6698	333.8+/-320.7	204,1490,2604	no	missense	OR2T8	NM_001005522.1	23	347,2316,3838	AA,AG,GG		22.08,25.2383,23.1503	benign	269/313	248085124	3010,9992	2203	4298	6501	SO:0001583	missense	343172	exon1			AACCACGACAAGG		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.805G>A	1.37:g.248085124G>A	ENSP00000326225:p.Asp269Asn	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	587	240	0.408859	NM_001005522		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	684	0.3131868131868132	130	0.26422764227642276	95	0.26243093922651933	308	0.5384615384615384	151	0.19920844327176782	G	12.38	1.919763	0.33908	0.252383	0.2208	ENSG00000177462	ENST00000319968	T	0.00216	8.53	3.56	3.56	0.40772	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34133	U	0.004239	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	P	0.40970	0.734	B	0.43301	0.415	T	0.00000	-1.3415	9	0.66056	D	0.02	.	8.9138	0.35570	0.1066:0.0:0.8934:0.0	rs4590708	269	A6NH00	OR2T8_HUMAN	N	269	ENSP00000326225:D269N	ENSP00000326225:D269N	D	+	1	0	OR2T8	246151747	0.000000	0.05858	0.005000	0.12908	0.012000	0.07955	0.194000	0.17135	1.816000	0.52996	0.404000	0.27445	GAC	G|0.755;A|0.245	0.245	strong		0.488	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
FAM35A	54537	hgsc.bcm.edu	37	10	88912541	88912541	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:88912541T>G	ENST00000298784.1	+	3	1544	c.1430T>G	c.(1429-1431)aTt>aGt	p.I477S	FAM35A_ENST00000298786.4_Missense_Mutation_p.I477S|RN7SL733P_ENST00000582253.1_RNA	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	477								p.I477S(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						GTTACAGTAATTGATCAATCA	0.378																																					p.I477S	Ovarian(175;703 2004 25460 32514 43441)	Atlas-SNP	.											FAM35A,NS,carcinoma,0,1	FAM35A	48	1	1	Substitution - Missense(1)	prostate(1)	c.T1430G						scavenged	.						41.0	42.0	42.0					10																	88912541		2197	4279	6476	SO:0001583	missense	54537	exon3			CAGTAATTGATCA	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.1430T>G	10.37:g.88912541T>G	ENSP00000298784:p.Ile477Ser	Somatic	353	0	0		WXS	Illumina HiSeq	Phase_I	343	12	0.0349854	NM_019054	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	4.685|4.685	0.127308|0.127308	0.08981|0.08981	.|.	.|.	ENSG00000122376|ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313|ENST00000342900	T;T;T|.	0.64260|.	-0.09;-0.09;-0.09|.	3.92|3.92	-1.26|-1.26	0.09376|0.09376	.|.	1.097140|.	0.07191|.	N|.	0.855695|.	T|T	0.34861|0.34861	0.0912|0.0912	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|.	0.32829|.	0.386|.	B|.	0.31101|.	0.124|.	T|T	0.36163|0.36163	-0.9759|-0.9759	9|4	0.37606|.	T|.	0.19|.	-0.8006|-0.8006	10.715|10.715	0.46006|0.46006	0.0:0.4414:0.0:0.5586|0.0:0.4414:0.0:0.5586	.|.	477|.	Q86V20|.	FA35A_HUMAN|.	S|K	477|131	ENSP00000298786:I477S;ENSP00000298784:I477S;ENSP00000351064:I477S|.	ENSP00000298784:I477S|.	I|N	+|+	2|3	0|2	FAM35A|FAM35A	88902521|88902521	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.938000|0.938000	0.57974|0.57974	-0.111000|-0.111000	0.10807|0.10807	-0.121000|-0.121000	0.11787|0.11787	0.438000|0.438000	0.28831|0.28831	ATT|AAT	.	.	none		0.378	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054	
RAB4A	5867	hgsc.bcm.edu	37	1	229431613	229431613	+	Silent	SNP	T	T	C	rs114366150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229431613T>C	ENST00000366690.4	+	4	454	c.246T>C	c.(244-246)taT>taC	p.Y82Y	RAB4A_ENST00000473894.1_3'UTR	NM_004578.2	NP_004569.2	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family	82					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein transporter activity (GO:0008565)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)				CGAGAAGTTATTACCGAGGCG	0.522													T|||	9	0.00179712	0.0053	0.0029	5008	,	,		18011	0.0		0.0	False		,,,				2504	0.0				p.Y82Y	Esophageal Squamous(11;250 603 9619 16563)	Atlas-SNP	.											.	RAB4A	29	.	0			c.T246C						PASS	.	T		34,4372	39.2+/-71.8	0,34,2169	76.0	78.0	77.0		246	-5.4	0.8	1	dbSNP_132	77	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RAB4A	NM_004578.2		0,35,6468	CC,CT,TT		0.0116,0.7717,0.2691		82/219	229431613	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	5867	exon4			AAGTTATTACCGA	BC004309	CCDS31050.1, CCDS73046.1	1q42-q43	2014-04-03		2002-02-28	ENSG00000168118	ENSG00000168118		"""RAB, member RAS oncogene"""	9781	protein-coding gene	gene with protein product		179511		RAB4			Standard	NM_004578		Approved	HRES-1/RAB4	uc001hth.4	P20338	OTTHUMG00000037627	ENST00000366690.4:c.246T>C	1.37:g.229431613T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_004578	Q5T7P7|Q9BQ44	Silent	SNP	ENST00000366690.4	37	CCDS31050.1																																																																																			T|0.998;C|0.002	0.002	strong		0.522	RAB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091727.3	NM_004578	
CCDC102B	79839	hgsc.bcm.edu	37	18	66678192	66678192	+	Missense_Mutation	SNP	G	G	C	rs9963788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:66678192G>C	ENST00000360242.5	+	7	1402	c.1285G>C	c.(1285-1287)Gcc>Ccc	p.A429P	CCDC102B_ENST00000584156.1_Missense_Mutation_p.A429P|CCDC102B_ENST00000319445.6_Missense_Mutation_p.A429P	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	429			A -> P (in dbSNP:rs9963788).							breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				CCTTCAACATGCCTACTATAA	0.323													G|||	354	0.0706869	0.2572	0.0202	5008	,	,		17747	0.0		0.0	False		,,,				2504	0.0				p.A429P		Atlas-SNP	.											.	CCDC102B	92	.	0			c.G1285C						PASS	.	G	PRO/ALA,PRO/ALA	913,3493	333.9+/-303.2	116,681,1406	68.0	66.0	67.0		1285,1285	4.5	0.1	18	dbSNP_119	67	9,8591	4.3+/-15.6	0,9,4291	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	27,27	116,690,5697	CC,CG,GG		0.1047,20.7217,7.089	probably-damaging,probably-damaging	429/514,429/514	66678192	922,12084	2203	4300	6503	SO:0001583	missense	79839	exon9			CAACATGCCTACT	AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 14"", ""aminoacylase 1-like"""	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.1285G>C	18.37:g.66678192G>C	ENSP00000353377:p.Ala429Pro	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	127	0.05815018315018315	122	0.24796747967479674	5	0.013812154696132596	0	0.0	0	0.0	G	12.64	1.997195	0.35226	0.207217	0.001047	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.12879	2.64;2.64	5.4	4.53	0.55603	.	0.266261	0.26851	N	0.022162	T	0.00012	0.0000	L	0.46157	1.445	0.09310	P	1.0	D	0.89917	1.0	D	0.66979	0.948	T	0.21759	-1.0236	9	0.59425	D	0.04	-2.2619	9.8768	0.41209	0.0944:0.0:0.9056:0.0	rs9963788;rs52813873;rs59666069;rs9963788	429	Q68D86	C102B_HUMAN	P	429	ENSP00000316237:A429P;ENSP00000353377:A429P	ENSP00000316237:A429P	A	+	1	0	CCDC102B	64829172	0.997000	0.39634	0.131000	0.22000	0.981000	0.71138	3.552000	0.53705	1.276000	0.44395	0.650000	0.86243	GCC	G|0.928;C|0.072	0.072	strong		0.323	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
FRZB	2487	hgsc.bcm.edu	37	2	183703336	183703336	+	Missense_Mutation	SNP	G	G	A	rs288326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:183703336G>A	ENST00000295113.4	-	4	1207	c.598C>T	c.(598-600)Cgg>Tgg	p.R200W		NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein	200	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.		R -> W (in dbSNP:rs288326). {ECO:0000269|PubMed:15210948}.		brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			ACTTTAGCCCGAATGACTGGG	0.383													G|||	220	0.0439297	0.0091	0.0865	5008	,	,		20003	0.0		0.1243	False		,,,				2504	0.0235				p.R200W		Atlas-SNP	.											.	FRZB	42	.	0			c.C598T						PASS	.	G	TRP/ARG	149,4257	103.4+/-141.9	3,143,2057	85.0	83.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	598	3.2	1.0	2	dbSNP_79	84	1007,7593	215.0+/-254.5	80,847,3373	yes	missense	FRZB	NM_001463.3	101	83,990,5430	AA,AG,GG		11.7093,3.3818,8.8882	probably-damaging	200/326	183703336	1156,11850	2203	4300	6503	SO:0001583	missense	2487	exon4			TAGCCCGAATGAC	U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"""Secreted frizzled-related proteins"""	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.598C>T	2.37:g.183703336G>A	ENSP00000295113:p.Arg200Trp	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	144	79	0.548611	NM_001463	O00181|Q99686	Missense_Mutation	SNP	ENST00000295113.4	37	CCDS2286.1	120	0.054945054945054944	2	0.0040650406504065045	36	0.09944751381215469	0	0.0	82	0.10817941952506596	G	18.43	3.621849	0.66787	0.033818	0.117093	ENSG00000162998	ENST00000295113	T	0.24151	1.87	5.05	3.18	0.36537	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.000000	0.85682	D	0.000000	T	0.00695	0.0023	L	0.50333	1.59	0.09310	P	0.999999791505	D	0.89917	1.0	D	0.85130	0.997	T	0.05989	-1.0852	9	0.87932	D	0	.	12.7575	0.57343	0.0:0.0:0.5724:0.4275	rs288326;rs52830699;rs288326	200	Q92765	SFRP3_HUMAN	W	200	ENSP00000295113:R200W	ENSP00000295113:R200W	R	-	1	2	FRZB	183411581	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	2.246000	0.43142	0.483000	0.27608	0.557000	0.71058	CGG	G|0.945;A|0.055	0.055	strong		0.383	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463	
ITGA2B	3674	hgsc.bcm.edu	37	17	42457087	42457087	+	Silent	SNP	C	C	T	rs79289329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42457087C>T	ENST00000262407.5	-	18	1879	c.1848G>A	c.(1846-1848)gtG>gtA	p.V616V	ITGA2B_ENST00000353281.4_Silent_p.V616V	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	616					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	CTCCATGCAGCACGACAGCAG	0.607													C|||	26	0.00519169	0.0174	0.0043	5008	,	,		19396	0.0		0.0	False		,,,				2504	0.0				p.V616V		Atlas-SNP	.											.	ITGA2B	88	.	0			c.G1848A						PASS	.	C		70,4336	61.7+/-98.7	0,70,2133	109.0	106.0	107.0		1848	1.2	0.9	17	dbSNP_132	107	0,8600		0,0,4300	no	coding-synonymous	ITGA2B	NM_000419.3		0,70,6433	TT,TC,CC		0.0,1.5887,0.5382		616/1040	42457087	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	3674	exon18			ATGCAGCACGACA		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.1848G>A	17.37:g.42457087C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	37	CCDS32665.1																																																																																			C|0.994;T|0.006	0.006	strong		0.607	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		
OR6Q1	219952	hgsc.bcm.edu	37	11	57799371	57799371	+	Missense_Mutation	SNP	G	G	C	rs1374570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57799371G>C	ENST00000302622.3	+	1	970	c.947G>C	c.(946-948)gGa>gCa	p.G316A	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	316			G -> A (in dbSNP:rs1374570).			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)				TTTTGGAAGGGACAGTGAGGA	0.448													G|||	2094	0.418131	0.4871	0.5418	5008	,	,		21163	0.244		0.5417	False		,,,				2504	0.2894				p.G316A		Atlas-SNP	.											OR6Q1,NS,carcinoma,-1,1	OR6Q1	58	1	0			c.G947C						PASS	.	G	ALA/GLY	2168,2114		585,998,558	39.0	41.0	40.0		947	2.4	0.0	11	dbSNP_88	40	4542,3790		1282,1978,906	yes	missense	OR6Q1	NM_001005186.2	60	1867,2976,1464	CC,CG,GG		45.4873,49.3695,46.8051	benign	316/318	57799371	6710,5904	2141	4166	6307	SO:0001583	missense	219952	exon1			GGAAGGGACAGTG	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.947G>C	11.37:g.57799371G>C	ENSP00000307734:p.Gly316Ala	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Missense_Mutation	SNP	ENST00000302622.3	37	CCDS31541.1	1028	0.4706959706959707	247	0.5020325203252033	210	0.580110497237569	159	0.27797202797202797	412	0.5435356200527705	G	10.01	1.234500	0.22626	0.506305	0.545127	ENSG00000172381	ENST00000302622	T	0.02103	4.45	4.29	2.38	0.29361	.	0.640127	0.12873	N	0.432114	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.24258	0.1	B	0.21708	0.036	T	0.09378	-1.0677	9	0.56958	D	0.05	.	11.799	0.52116	0.0:0.3418:0.6582:0.0	rs1374570;rs52838041;rs1374570	316	Q8NGQ2	OR6Q1_HUMAN	A	316	ENSP00000307734:G316A	ENSP00000307734:G316A	G	+	2	0	OR6Q1	57555947	0.000000	0.05858	0.001000	0.08648	0.164000	0.22412	0.146000	0.16180	0.443000	0.26582	-0.122000	0.15005	GGA	G|0.500;C|0.500	0.500	strong		0.448	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
SLC1A7	6512	hgsc.bcm.edu	37	1	53558366	53558366	+	Silent	SNP	T	T	C	rs12129653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53558366T>C	ENST00000371494.4	-	7	1018	c.891A>G	c.(889-891)tcA>tcG	p.S297S	SLC1A7_ENST00000488036.1_5'Flank	NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7	297					dicarboxylic acid transport (GO:0006835)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Colorectal(1306;0.234)		CCACGGTGACTGAGTAGAAGC	0.577													C|||	729	0.145567	0.0779	0.2839	5008	,	,		17255	0.247		0.0487	False		,,,				2504	0.1339				p.S297S	NSCLC(128;80 1811 21245 38490 51715)	Atlas-SNP	.											.	SLC1A7	65	.	0			c.A891G						PASS	.	C		365,4041	793.1+/-415.2	12,341,1850	96.0	102.0	100.0		891	-10.2	0.0	1	dbSNP_120	100	423,8177	800.3+/-407.4	12,399,3889	no	coding-synonymous	SLC1A7	NM_006671.4		24,740,5739	CC,CT,TT		4.9186,8.2842,6.0587		297/561	53558366	788,12218	2203	4300	6503	SO:0001819	synonymous_variant	6512	exon7			GGTGACTGAGTAG	U76362	CCDS574.1, CCDS72796.1, CCDS72797.1, CCDS72798.1	1p32.3	2013-05-22			ENSG00000162383	ENSG00000162383		"""Solute carriers"""	10945	protein-coding gene	gene with protein product		604471				9108121	Standard	NM_001287597		Approved	EAAT5	uc001cuy.3	O00341	OTTHUMG00000008937	ENST00000371494.4:c.891A>G	1.37:g.53558366T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	152	65	0.427632	NM_006671	Q5VVZ0|Q969Z8|Q9BW45	Silent	SNP	ENST00000371494.4	37	CCDS574.1																																																																																			T|0.913;C|0.087	0.087	strong		0.577	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1	NM_006671	
WDR72	256764	hgsc.bcm.edu	37	15	53908062	53908062	+	Missense_Mutation	SNP	T	T	C	rs60404950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:53908062T>C	ENST00000396328.1	-	15	2580	c.2341A>G	c.(2341-2343)Aag>Gag	p.K781E	WDR72_ENST00000557913.1_Missense_Mutation_p.K778E|WDR72_ENST00000559418.1_Missense_Mutation_p.K791E|WDR72_ENST00000360509.5_Missense_Mutation_p.K781E	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	781			K -> E (in dbSNP:rs60404950).							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)		CTTGATGGCTTAGGCTGCATT	0.383													T|||	666	0.132987	0.4289	0.0591	5008	,	,		19694	0.0		0.0408	False		,,,				2504	0.0174				p.K781E		Atlas-SNP	.											.	WDR72	177	.	0			c.A2341G						PASS	.	T	GLU/LYS	1524,2864	480.1+/-358.7	279,966,949	191.0	183.0	186.0		2341	3.3	0.1	15	dbSNP_129	186	333,8253	115.7+/-175.5	5,323,3965	yes	missense	WDR72	NM_182758.2	56	284,1289,4914	CC,CT,TT		3.8784,34.7311,14.3132	benign	781/1103	53908062	1857,11117	2194	4293	6487	SO:0001583	missense	256764	exon15			ATGGCTTAGGCTG	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.2341A>G	15.37:g.53908062T>C	ENSP00000379619:p.Lys781Glu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	251	0.11492673992673992	200	0.4065040650406504	21	0.058011049723756904	0	0.0	30	0.0395778364116095	T	7.837	0.721074	0.15372	0.347311	0.038784	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.40225	1.04;1.04	5.69	3.34	0.38264	.	0.532914	0.20459	N	0.091925	T	0.00012	0.0000	N	0.17082	0.46	0.58432	P	5.000000000032756E-6	B	0.10296	0.003	B	0.08055	0.003	T	0.44236	-0.9341	9	0.40728	T	0.16	.	5.2646	0.15591	0.0:0.1549:0.316:0.5291	rs60404950	781	Q3MJ13	WDR72_HUMAN	E	781	ENSP00000379619:K781E;ENSP00000353699:K781E	ENSP00000353699:K781E	K	-	1	0	WDR72	51695354	0.540000	0.26410	0.050000	0.19076	0.499000	0.33736	1.038000	0.30254	0.419000	0.25927	-0.376000	0.06991	AAG	T|0.871;C|0.129	0.129	strong		0.383	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
QRICH2	84074	hgsc.bcm.edu	37	17	74289500	74289500	+	Silent	SNP	G	G	A	rs3803737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74289500G>A	ENST00000262765.5	-	4	989	c.810C>T	c.(808-810)gtC>gtT	p.V270V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	270										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						GCTCATCCACGACAAATGGTA	0.517													G|||	2351	0.469449	0.7073	0.3098	5008	,	,		26072	0.5724		0.2753	False		,,,				2504	0.3548				p.V270V		Atlas-SNP	.											.	QRICH2	143	.	0			c.C810T						PASS	.	G		2925,1481	679.3+/-403.7	976,973,254	138.0	115.0	122.0		810	0.2	0.0	17	dbSNP_107	122	2483,6117	406.9+/-349.0	347,1789,2164	no	coding-synonymous	QRICH2	NM_032134.1		1323,2762,2418	AA,AG,GG		28.8721,33.6133,41.5808		270/1664	74289500	5408,7598	2203	4300	6503	SO:0001819	synonymous_variant	84074	exon4			ATCCACGACAAAT	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.810C>T	17.37:g.74289500G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																			G|0.557;A|0.443	0.443	strong		0.517	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
AFF4	27125	hgsc.bcm.edu	37	5	132232148	132232148	+	Missense_Mutation	SNP	C	C	G	rs138811630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132232148C>G	ENST00000265343.5	-	11	2553	c.2174G>C	c.(2173-2175)aGa>aCa	p.R725T	AFF4_ENST00000378595.3_Missense_Mutation_p.R725T	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	725					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCCTGGTATTCTAGTCAAAAG	0.453													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18395	0.0		0.0	False		,,,				2504	0.0				p.R725T	Ovarian(126;889 1733 2942 10745 11605)	Atlas-SNP	.											.	AFF4	120	.	0			c.G2174C						PASS	.	C	THR/ARG	8,4398	12.9+/-30.5	0,8,2195	125.0	125.0	125.0		2174	4.9	1.0	5	dbSNP_134	125	0,8600		0,0,4300	yes	missense	AFF4	NM_014423.3	71	0,8,6495	GG,GC,CC		0.0,0.1816,0.0615	probably-damaging	725/1164	132232148	8,12998	2203	4300	6503	SO:0001583	missense	27125	exon11			GGTATTCTAGTCA	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"""ALL1 fused gene from 5q31"""	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.2174G>C	5.37:g.132232148C>G	ENSP00000265343:p.Arg725Thr	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	196	89	0.454082	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	37	CCDS4164.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	21.2	4.115328	0.77323	0.001816	0.0	ENSG00000072364	ENST00000265343;ENST00000378595	T;T	0.78481	-1.18;-1.18	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.89385	0.6700	M	0.85777	2.775	0.58432	D	0.999998	D;D	0.67145	0.996;0.991	D;D	0.77557	0.99;0.987	D	0.91090	0.4906	10	0.72032	D	0.01	-16.5422	18.443	0.90673	0.0:1.0:0.0:0.0	.	725;725	Q9UHB7-2;Q9UHB7	.;AFF4_HUMAN	T	725	ENSP00000265343:R725T;ENSP00000367858:R725T	ENSP00000265343:R725T	R	-	2	0	AFF4	132260047	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.593000	0.82686	2.417000	0.82017	0.563000	0.77884	AGA	C|0.999;G|0.001	0.001	strong		0.453	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423	
LMLN	89782	hgsc.bcm.edu	37	3	197701913	197701913	+	Splice_Site	SNP	G	G	T	rs7373165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:197701913G>T	ENST00000330198.4	+	3	340	c.318G>T	c.(316-318)gaG>gaT	p.E106D	LMLN_ENST00000332636.5_Splice_Site_p.E54D|LMLN_ENST00000482695.1_Splice_Site_p.E54D|LMLN_ENST00000420910.2_Splice_Site_p.E106D	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	106			E -> D (in dbSNP:rs7373165).		cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		TTATTTTCAGGTTGCTCCCTG	0.338													G|||	1049	0.209465	0.5197	0.1023	5008	,	,		18661	0.0109		0.1173	False		,,,				2504	0.1656				p.E106D		Atlas-SNP	.											.	LMLN	53	.	0			c.G318T						PASS	.	G	ASP/GLU,ASP/GLU	1969,2437	531.5+/-373.2	443,1083,677	64.0	78.0	74.0		318,318	3.6	1.0	3	dbSNP_116	74	940,7660	204.0+/-246.8	37,866,3397	yes	missense-near-splice,missense-near-splice	LMLN	NM_001136049.2,NM_033029.3	45,45	480,1949,4074	TT,TG,GG		10.9302,44.6891,22.3666	benign,benign	106/693,106/656	197701913	2909,10097	2203	4300	6503	SO:0001630	splice_region_variant	89782	exon3			TTTCAGGTTGCTC	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.318-1G>T	3.37:g.197701913G>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_001136049	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	37	CCDS3332.1	374	0.17124542124542125	243	0.49390243902439024	37	0.10220994475138122	7	0.012237762237762238	87	0.11477572559366754	G	11.75	1.731285	0.30684	0.446891	0.109302	ENSG00000185621	ENST00000482695;ENST00000330198;ENST00000419117;ENST00000420910;ENST00000332636	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	4.44	3.56	0.40772	.	0.259681	0.31233	N	0.008017	T	0.00012	0.0000	N	0.14661	0.345	0.41280	P	0.013098999999999972	B;B;B;B	0.09022	0.001;0.002;0.002;0.0	B;B;B;B	0.15052	0.012;0.005;0.006;0.003	T	0.47699	-0.9097	8	.	.	.	.	8.1783	0.31296	0.1096:0.0:0.8904:0.0	rs7373165;rs52803239;rs58900520;rs7373165	106;54;106;54	Q96KR4;F8WCE5;F8WB28;Q96KR4-2	LMLN_HUMAN;.;.;.	D	54;106;34;106;54	ENSP00000418324:E54D;ENSP00000328829:E106D;ENSP00000390872:E34D;ENSP00000410926:E106D;ENSP00000328611:E54D	.	E	+	3	2	LMLN	199186310	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.868000	0.27982	1.084000	0.41184	0.558000	0.71614	GAG	G|0.784;T|0.216	0.216	strong		0.338	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029	Missense_Mutation
ZNF518B	85460	hgsc.bcm.edu	37	4	10447679	10447679	+	Missense_Mutation	SNP	C	C	T	rs10007352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:10447679C>T	ENST00000326756.3	-	3	712	c.274G>A	c.(274-276)Ggt>Agt	p.G92S		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	92			G -> S (in dbSNP:rs10007352).		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.G92S(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						GGAGCTGCACCGAGGCTGCAC	0.418													C|||	721	0.14397	0.3177	0.0346	5008	,	,		20671	0.1597		0.003	False		,,,				2504	0.1155				p.G92S		Atlas-SNP	.											ZNF518B,NS,carcinoma,0,1	ZNF518B	116	1	1	Substitution - Missense(1)	stomach(1)	c.G274A						PASS	.	C	SER/GLY	1121,3285	402.4+/-332.3	154,813,1236	120.0	119.0	120.0		274	3.0	0.0	4	dbSNP_119	120	28,8572	20.4+/-63.3	0,28,4272	yes	missense	ZNF518B	NM_053042.2	56	154,841,5508	TT,TC,CC		0.3256,25.4426,8.8344	possibly-damaging	92/1075	10447679	1149,11857	2203	4300	6503	SO:0001583	missense	85460	exon3			CTGCACCGAGGCT	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.274G>A	4.37:g.10447679C>T	ENSP00000317614:p.Gly92Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	260	0.11904761904761904	157	0.31910569105691056	14	0.03867403314917127	86	0.15034965034965034	3	0.00395778364116095	C	7.662	0.685199	0.14973	0.254426	0.003256	ENSG00000178163	ENST00000326756	T	0.01430	4.9	5.76	2.97	0.34412	.	0.764126	0.11463	N	0.561517	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.28801	0.223	B	0.16289	0.015	T	0.28554	-1.0040	9	0.02654	T	1	-3.7661	5.6028	0.17363	0.0:0.3823:0.4186:0.1991	rs10007352	92	Q9C0D4	Z518B_HUMAN	S	92	ENSP00000317614:G92S	ENSP00000317614:G92S	G	-	1	0	ZNF518B	10056777	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.775000	0.26689	0.787000	0.33731	0.650000	0.86243	GGT	C|0.906;T|0.094	0.094	strong		0.418	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036505	33036505	+	Silent	SNP	G	G	C	rs1042434	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33036505G>C	ENST00000419277.1	-	5	834	c.705C>G	c.(703-705)gtC>gtG	p.V235V	HLA-DPA1_ENST00000463066.1_5'Flank|HLA-DPA1_ENST00000428995.1_Silent_p.V235V	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	235					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CGATGATGCCGACTAGGCCCA	0.582													C|||	2381	0.475439	0.7095	0.2997	5008	,	,		18440	0.6796		0.1889	False		,,,				2504	0.3681				p.V235V		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C705G						PASS	.	C	,,	1707,1313		479,749,282	104.0	126.0	118.0		705,705,705	2.5	0.6	6	dbSNP_86	118	968,4450		74,820,1815	yes	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	553,1569,2097	CC,CG,GG		17.8664,43.4768,31.7018	,,	235/261,235/261,235/261	33036505	2675,5763	1510	2709	4219	SO:0001819	synonymous_variant	3113	exon4			GATGCCGACTAGG	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.705C>G	6.37:g.33036505G>C		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	154	153	0.993506	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1	946	0.43315018315018317	350	0.7113821138211383	96	0.26519337016574585	371	0.6486013986013986	129	0.17018469656992086	C	0.676	-0.800149	0.02841	0.565232	0.178664	ENSG00000231389	ENST00000437811	.	.	.	3.4	2.51	0.30379	.	.	.	.	.	T	0.24624	0.0597	.	.	.	0.09310	P	0.999999832037	.	.	.	.	.	.	T	0.08351	-1.0726	3	.	.	.	.	7.1427	0.25564	0.1821:0.4624:0.3555:0.0	rs1042434;rs3181901;rs17850578	.	.	.	G	103	.	.	R	-	1	2	HLA-DPA1	33144483	0.085000	0.21516	0.599000	0.28851	0.111000	0.19643	0.007000	0.13174	0.212000	0.20703	-0.847000	0.03039	CGG	G|0.663;C|0.337	0.337	strong		0.582	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
GPR179	440435	hgsc.bcm.edu	37	17	36493598	36493598	+	Silent	SNP	A	A	G	rs9894059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36493598A>G	ENST00000342292.4	-	3	929	c.909T>C	c.(907-909)gtT>gtC	p.V303V		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	303					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TCTCCAGGGGAACACACTATG	0.562													G|||	1295	0.258586	0.5968	0.1326	5008	,	,		18903	0.119		0.1481	False		,,,				2504	0.1483				p.V303V		Atlas-SNP	.											.	GPR179	170	.	0			c.T909C						PASS	.	G		1898,2078		474,950,564	46.0	55.0	52.0		909	0.6	1.0	17	dbSNP_119	52	925,7381		58,809,3286	no	coding-synonymous	GPR179	NM_001004334.2		532,1759,3850	GG,GA,AA		11.1365,47.7364,22.9849		303/2368	36493598	2823,9459	1988	4153	6141	SO:0001819	synonymous_variant	440435	exon3			CAGGGGAACACAC		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.909T>C	17.37:g.36493598A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			A|0.762;G|0.238	0.238	strong		0.562	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
CCDC116	164592	hgsc.bcm.edu	37	22	21991224	21991224	+	Silent	SNP	C	C	T	rs45533832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21991224C>T	ENST00000292779.3	+	5	1868	c.1707C>T	c.(1705-1707)acC>acT	p.T569T		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)					CTGCCTGCACCGGCATGGGTT	0.577													C|||	124	0.0247604	0.0893	0.0086	5008	,	,		20745	0.0		0.0	False		,,,				2504	0.0				p.T569T		Atlas-SNP	.											.	CCDC116	56	.	0			c.C1707T						PASS	.	C		279,4127	155.5+/-188.7	7,265,1931	77.0	78.0	78.0		1707	-7.8	0.0	22	dbSNP_127	78	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CCDC116	NM_152612.2		7,269,6227	TT,TC,CC		0.0465,6.3323,2.1759		569/614	21991224	283,12723	2203	4300	6503	SO:0001819	synonymous_variant	164592	exon5			CTGCACCGGCATG	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.1707C>T	22.37:g.21991224C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_152612	Q8N9Y9	Silent	SNP	ENST00000292779.3	37	CCDS13791.1																																																																																			C|0.974;T|0.026	0.026	strong		0.577	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
MSH2	4436	hgsc.bcm.edu	37	2	47637246	47637246	+	Missense_Mutation	SNP	A	A	G	rs17217772|rs63751227|rs63750924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47637246A>G	ENST00000233146.2	+	3	603	c.380A>G	c.(379-381)aAt>aGt	p.N127S	MSH2_ENST00000543555.1_Missense_Mutation_p.N61S|MSH2_ENST00000406134.1_Missense_Mutation_p.N127S	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	127			N -> S (in HNPCC1; shows significantly decreased repair efficiency when associated with variant Pro-328; presumed to enhance cancer risk considerably when associated with Pro-328; this concomitant defect with another variant could explain its recurrent occurrence in CRC patients; dbSNP:rs17217772). {ECO:0000269|PubMed:12655564, ECO:0000269|Ref.9}.		ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCTCCTGGCAATctctctcag	0.333			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	124	0.0247604	0.087	0.0115	5008	,	,		17721	0.0		0.001	False		,,,				2504	0.0				p.N127S		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.A380G	GRCh37	CD982801|CM011415|CM081337	MSH2	D|M	rs17217772	PASS	.	A	SER/ASN	339,4067	176.2+/-205.4	17,305,1881	178.0	180.0	180.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	380	4.6	1.0	2	dbSNP_123	180	4,8596	3.7+/-12.6	0,4,4296	no	missense	MSH2	NM_000251.1	46	17,309,6177	GG,GA,AA		0.0465,7.6941,2.6372	possibly-damaging	127/935	47637246	343,12663	2203	4300	6503	SO:0001583	missense	4436	exon3	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	CTGGCAATCTCTC	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.380A>G	2.37:g.47637246A>G	ENSP00000233146:p.Asn127Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_000251	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	37	CCDS1834.1	41|41	0.018772893772893772|0.018772893772893772	36|36	0.07317073170731707|0.07317073170731707	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	A|A	15.07|15.07	2.724903|2.724903	0.48833|0.48833	0.076941|0.076941	4.65E-4|4.65E-4	ENSG00000095002|ENSG00000095002	ENST00000413880|ENST00000233146;ENST00000454849;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000448533;ENST00000394792	.|D;D;D;D	.|0.89485	.|-2.52;-2.52;-2.52;-2.52	5.73|5.73	4.59|4.59	0.56863|0.56863	.|DNA mismatch repair protein MutS-like, N-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.62551|0.62551	0.2437|0.2437	M|M	0.93150|0.93150	3.385|3.385	0.80722|0.80722	D|D	1|1	.|P;P	.|0.51057	.|0.941;0.912	.|P;P	.|0.60068	.|0.812;0.868	T|T	0.77913|0.77913	-0.2410|-0.2410	6|10	0.18276|0.87932	T|D	0.48|0	-16.5115|-16.5115	11.6216|11.6216	0.51121|0.51121	0.9307:0.0:0.0693:0.0|0.9307:0.0:0.0693:0.0	rs17217772;rs60111901|rs17217772;rs60111901	.|127;127	.|E9PHA6;P43246	.|.;MSH2_HUMAN	V|S	13|127;61;61;127;127;127;127;127;127	.|ENSP00000233146:N127S;ENSP00000411482:N61S;ENSP00000442697:N61S;ENSP00000384199:N127S	ENSP00000402969:I13V|ENSP00000233146:N127S	I|N	+|+	1|2	0|0	MSH2|MSH2	47490750|47490750	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.064000|0.064000	0.16182|0.16182	9.227000|9.227000	0.95236|0.95236	1.008000|1.008000	0.39264|0.39264	-0.322000|-0.322000	0.08575|0.08575	ATC|AAT	A|0.965;G|0.035	0.035	strong		0.333	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
LRRC71	149499	hgsc.bcm.edu	37	1	156902678	156902678	+	Missense_Mutation	SNP	G	G	A	rs11264585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156902678G>A	ENST00000337428.7	+	15	1751	c.1597G>A	c.(1597-1599)Gcc>Acc	p.A533T	LRRC71_ENST00000490146.1_3'UTR|ARHGEF11_ENST00000487682.1_5'Flank	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	533			A -> T (in dbSNP:rs11264585).							endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						TCCTGCGTACGCCATAATCCA	0.498													G|||	121	0.0241613	0.0862	0.0101	5008	,	,		18240	0.0		0.0	False		,,,				2504	0.0				p.A533T		Atlas-SNP	.											.	LRRC71	33	.	0			c.G1597A						PASS	.	G	THR/ALA	265,3689		9,247,1721	48.0	46.0	47.0		1597	-11.0	0.0	1	dbSNP_120	47	3,8317		0,3,4157	yes	missense	LRRC71	NM_144702.2	58	9,250,5878	AA,AG,GG		0.0361,6.7021,2.1835	benign	533/560	156902678	268,12006	1977	4160	6137	SO:0001583	missense	149499	exon15			GCGTACGCCATAA	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.1597G>A	1.37:g.156902678G>A	ENSP00000336661:p.Ala533Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	37	CCDS44249.1	34	0.015567765567765568	28	0.056910569105691054	6	0.016574585635359115	0	0.0	0	0.0	G	1.828	-0.470466	0.04445	0.067021	3.61E-4	ENSG00000160838	ENST00000337428	T	0.18810	2.19	5.48	-11.0	0.00169	.	1.768440	0.02711	N	0.112830	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22417	-1.0217	10	0.12766	T	0.61	-0.0908	4.8021	0.13301	0.2877:0.1877:0.4323:0.0923	rs11264585;rs52828876;rs11264585	533	Q8N4P6	LRC71_HUMAN	T	533	ENSP00000336661:A533T	ENSP00000336661:A533T	A	+	1	0	LRRC71	155169302	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.651000	0.05372	-2.183000	0.00763	-1.149000	0.01842	GCC	G|0.981;A|0.019	0.019	strong		0.498	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702	
DNHD1	144132	hgsc.bcm.edu	37	11	6550004	6550004	+	Missense_Mutation	SNP	A	A	G	rs2344828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6550004A>G	ENST00000527990.2	+	9	2090	c.2090A>G	c.(2089-2091)cAg>cGg	p.Q697R	DNHD1_ENST00000254579.6_Missense_Mutation_p.Q697R			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	697					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)		AATATACAACAGGTGCTGCTG	0.537													A|||	3656	0.730032	0.6944	0.6585	5008	,	,		20172	0.874		0.6302	False		,,,				2504	0.7832				p.Q697R		Atlas-SNP	.											DNHD1,colon,carcinoma,0,1	DNHD1	198	1	0			c.A2090G						PASS	.	A	ARG/GLN	955,429		327,301,64	54.0	45.0	48.0		2090	4.5	0.0	11	dbSNP_100	48	2141,1041		726,689,176	yes	missense	DNHD1	NM_144666.2	43	1053,990,240	GG,GA,AA		32.7153,30.9971,32.1945	possibly-damaging	697/4754	6550004	3096,1470	692	1591	2283	SO:0001583	missense	144132	exon11			TACAACAGGTGCT	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.2090A>G	11.37:g.6550004A>G	ENSP00000436180:p.Gln697Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	1562	0.7152014652014652	353	0.717479674796748	236	0.6519337016574586	487	0.8513986013986014	486	0.6411609498680739	A	5.599	0.295334	0.10622	0.690029	0.672847	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.27104	1.69;1.69	5.6	4.48	0.54585	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.20052	0.041	B	0.21917	0.037	T	0.12708	-1.0537	8	0.24483	T	0.36	.	8.4785	0.33027	0.9121:0.0:0.0879:0.0	rs2344828;rs52806435;rs58180413;rs2344828	697	Q96M86	DNHD1_HUMAN	R	697	ENSP00000254579:Q697R;ENSP00000436180:Q697R	ENSP00000254579:Q697R	Q	+	2	0	DNHD1	6506580	0.741000	0.28217	0.007000	0.13788	0.001000	0.01503	1.937000	0.40193	0.951000	0.37770	-0.280000	0.10049	CAG	A|0.275;G|0.725	0.725	strong		0.537	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
MERTK	10461	hgsc.bcm.edu	37	2	112740561	112740561	+	Silent	SNP	A	A	G	rs115203717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:112740561A>G	ENST00000295408.4	+	8	1544	c.1287A>G	c.(1285-1287)gcA>gcG	p.A429A	MERTK_ENST00000421804.2_Silent_p.A429A|MERTK_ENST00000409780.1_Silent_p.A253A			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	429	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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						GGCAGAGTGCAGGGATTTCCG	0.448													A|||	28	0.00559105	0.0197	0.0029	5008	,	,		19646	0.0		0.0	False		,,,				2504	0.0				p.A429A		Atlas-SNP	.											.	MERTK	112	.	0			c.A1287G						PASS	.	A		48,4358	50.9+/-86.3	1,46,2156	111.0	106.0	108.0		1287	-9.6	0.0	2	dbSNP_132	108	0,8600		0,0,4300	no	coding-synonymous	MERTK	NM_006343.2		1,46,6456	GG,GA,AA		0.0,1.0894,0.3691		429/1000	112740561	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	10461	exon8			GAGTGCAGGGATT	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.1287A>G	2.37:g.112740561A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	123	54	0.439024	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	37	CCDS2094.1																																																																																			A|0.995;G|0.005	0.005	strong		0.448	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
TTN	7273	hgsc.bcm.edu	37	2	179554305	179554305	+	Missense_Mutation	SNP	C	C	T	rs2244492	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179554305C>T	ENST00000591111.1	-	121	31137	c.30913G>A	c.(30913-30915)Gga>Aga	p.G10305R	TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G10622R|TTN_ENST00000342992.6_Missense_Mutation_p.G9378R|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.			G -> R (in Ref. 3; CAD12456). {ECO:0000305}.	adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCACAACTCCCTTCTGTACT	0.358													T|||	2070	0.413339	0.6067	0.3501	5008	,	,		19129	0.1677		0.3827	False		,,,				2504	0.4816				p.G10622R		Atlas-SNP	.											.	TTN	18412	.	0			c.G31864A						PASS	.	T	,,,ARG/GLY	2207,1503		654,899,302	229.0	224.0	225.0		,,,28132	5.3	1.0	2	dbSNP_100	225	2955,5243		514,1927,1658	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,125	1168,2826,1960	TT,TC,CC		36.0454,40.5121,43.349	,,,benign	,,,9378/33424	179554305	5162,6746	1855	4099	5954	SO:0001583	missense	7273	exon123			CAACTCCCTTCTG	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.30913G>A	2.37:g.179554305C>T	ENSP00000465570:p.Gly10305Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	178	178	1	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		812	0.3717948717948718	292	0.5934959349593496	139	0.3839779005524862	84	0.14685314685314685	297	0.391820580474934	T	10.60	1.396903	0.25205	0.594879	0.360454	ENSG00000155657	ENST00000342992;ENST00000414766	T;T	0.63913	-0.07;-0.07	5.34	5.34	0.76211	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.9999999999991834	.	.	.	.	.	.	T	0.41980	-0.9478	6	0.87932	D	0	.	10.226	0.43225	0.0:0.0756:0.0:0.9244	rs2244492;rs17355152;rs2244492	.	.	.	R	9378;500	ENSP00000343764:G9378R;ENSP00000401501:G500R	ENSP00000343764:G9378R	G	-	1	0	TTN	179262550	0.313000	0.24554	0.960000	0.40013	0.986000	0.74619	3.252000	0.51461	0.971000	0.38288	-0.254000	0.11334	GGA	C|0.624;T|0.376	0.376	strong		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
EEF1A2	1917	hgsc.bcm.edu	37	20	62126185	62126185	+	Silent	SNP	A	A	G	rs310617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62126185A>G	ENST00000298049.7	-	3	664	c.594T>C	c.(592-594)ggT>ggC	p.G198G	EEF1A2_ENST00000217182.3_Silent_p.G198G			Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha 2	198	tr-type G.				positive regulation of apoptotic process (GO:0043065)|response to inorganic substance (GO:0010035)	eukaryotic translation elongation factor 1 complex (GO:0005853)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(14)|stomach(1)	20	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			GCATGTTGTCACCGTGCCAGC	0.672													G|||	2963	0.591653	0.59	0.5029	5008	,	,		14466	0.6181		0.5934	False		,,,				2504	0.6278				p.G198G		Atlas-SNP	.											EEF1A2,NS,carcinoma,0,3	EEF1A2	60	3	0			c.T594C						PASS	.	G		2603,1785	624.9+/-394.4	770,1063,361	37.0	31.0	33.0		594	-7.8	0.1	20	dbSNP_79	33	4849,3747	606.6+/-395.1	1394,2061,843	no	coding-synonymous	EEF1A2	NM_001958.2		2164,3124,1204	GG,GA,AA		43.59,40.6791,42.6063		198/464	62126185	7452,5532	2194	4298	6492	SO:0001819	synonymous_variant	1917	exon4			GTTGTCACCGTGC	AF163763	CCDS13522.1	20q13.3	2010-06-03			ENSG00000101210	ENSG00000101210			3192	protein-coding gene	gene with protein product		602959	"""statin-like"", ""statin"""	STNL, STN		8354261, 8812466	Standard	NM_001958		Approved	EEF1AL, HS1	uc002yfe.2	Q05639	OTTHUMG00000033076	ENST00000298049.7:c.594T>C	20.37:g.62126185A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	51	50	0.980392	NM_001958	B5BUF3|E1P5J1|P54266|Q0VGC7	Silent	SNP	ENST00000298049.7	37	CCDS13522.1																																																																																			A|0.419;G|0.581	0.581	strong		0.672	EEF1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080495.1	NM_001958	
ZNF708	7562	hgsc.bcm.edu	37	19	21477431	21477431	+	Missense_Mutation	SNP	T	T	C	rs1781873	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21477431T>C	ENST00000356929.3	-	4	534	c.337A>G	c.(337-339)Aaa>Gaa	p.K113E		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	49					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						TCCACACTTTTACAGCCTTTC	0.393													T|||	3110	0.621006	0.7436	0.562	5008	,	,		17016	0.629		0.5089	False		,,,				2504	0.6043				p.K113E		Atlas-SNP	.											.	ZNF708	66	.	0			c.A337G						PASS	.	T	GLU/LYS	3110,1296		1100,910,193	152.0	138.0	143.0		337	-0.6	0.0	19	dbSNP_89	143	4486,4114		1227,2032,1041	yes	missense	ZNF708	NM_021269.2	56	2327,2942,1234	CC,CT,TT		47.8372,29.4144,41.5962	benign	113/564	21477431	7596,5410	2203	4300	6503	SO:0001583	missense	7562	exon4			CACTTTTACAGCC	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"""Zinc fingers, C2H2-type"", ""-"""	12945	protein-coding gene	gene with protein product			"""zinc finger protein 15-like 1 (KOX 8)"", ""zinc finger protein 708"", ""zinc finger protein 708 (KOX8)"""	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.337A>G	19.37:g.21477431T>C	ENSP00000349401:p.Lys113Glu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	91	52	0.571429	NM_021269	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	1334	0.6108058608058609	367	0.7459349593495935	208	0.574585635359116	380	0.6643356643356644	379	0.5	.	0.884	-0.727862	0.03158	0.705856	0.521628	ENSG00000182141	ENST00000356929	T	0.06218	3.33	1.07	-0.564	0.11774	.	.	.	.	.	T	0.00012	0.0000	N	0.11341	0.13	0.80722	P	0.0	B	0.11235	0.004	B	0.12837	0.008	T	0.08249	-1.0731	8	0.17369	T	0.5	.	3.2122	0.06686	0.0:0.3246:0.0:0.6753	rs1781873;rs52805708;rs59165625;rs1781873	113	P17019	ZN708_HUMAN	E	113	ENSP00000349401:K113E	ENSP00000349401:K113E	K	-	1	0	ZNF708	21269271	0.000000	0.05858	0.023000	0.16930	0.022000	0.10575	-0.330000	0.07925	-0.428000	0.07339	-0.436000	0.05848	AAA	T|0.407;C|0.593	0.593	strong		0.393	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269	
PSG11	5680	hgsc.bcm.edu	37	19	43529027	43529027	+	Silent	SNP	A	A	G	rs1058958|rs34787457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	201	0	0		WXS	Illumina HiSeq	Phase_I	175	75	0.428571	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	
CXXC5	51523	hgsc.bcm.edu	37	5	139060486	139060486	+	Silent	SNP	G	G	A	rs356445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:139060486G>A	ENST00000302517.3	+	2	1092	c.378G>A	c.(376-378)gcG>gcA	p.A126A	CXXC5_ENST00000511048.1_Silent_p.A126A	NM_016463.7	NP_057547.5	Q7LFL8	CXXC5_HUMAN	CXXC finger protein 5	126					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCCATGGCGGTGGACAAAA	0.652													G|||	957	0.191094	0.5015	0.0634	5008	,	,		16819	0.0585		0.0517	False		,,,				2504	0.1421				p.A126A		Atlas-SNP	.											CXXC5,NS,carcinoma,0,1	CXXC5	27	1	0			c.G378A						PASS	.						68.0	83.0	78.0					5																	139060486		2111	4242	6353	SO:0001819	synonymous_variant	51523	exon2			CATGGCGGTGGAC	AK024338	CCDS43370.1	5q31.3	2014-02-18	2011-12-01						26943	protein-coding gene	gene with protein product	"""retinoid-inducible nuclear factor"", ""WT1-induced Inhibitor of Dishevelled"""	612752				11042152, 19001364, 19182210, 20220130	Standard	NM_016463		Approved	HSPC195, RINF, WID	uc010jfg.1	Q7LFL8		ENST00000302517.3:c.378G>A	5.37:g.139060486G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	26	9	0.346154	NM_016463	B3KND0|C8CBA8|Q8TB79|Q9NV51|Q9P0S8	Silent	SNP	ENST00000302517.3	37	CCDS43370.1																																																																																			G|0.837;A|0.163	0.163	strong		0.652	CXXC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372744.1	NM_016463	
COL6A6	131873	hgsc.bcm.edu	37	3	130289687	130289687	+	Silent	SNP	C	C	T	rs59562634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130289687C>T	ENST00000358511.6	+	6	2458	c.2427C>T	c.(2425-2427)gaC>gaT	p.D809D	COL6A6_ENST00000453409.2_Silent_p.D809D	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	809	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						AAGTTTTAGACGTTGTGTTTG	0.388													T|||	352	0.0702875	0.2526	0.0245	5008	,	,		20800	0.0		0.001	False		,,,				2504	0.0				p.D809D		Atlas-SNP	.											.	COL6A6	497	.	0			c.C2427T						PASS	.	T		838,2942		86,666,1138	85.0	88.0	87.0		2427	-7.7	0.0	3	dbSNP_129	87	16,8238		0,16,4111	no	coding-synonymous	COL6A6	NM_001102608.1		86,682,5249	TT,TC,CC		0.1938,22.1693,7.0966		809/2264	130289687	854,11180	1890	4127	6017	SO:0001819	synonymous_variant	131873	exon6			TTTAGACGTTGTG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.2427C>T	3.37:g.130289687C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																			C|0.945;T|0.055	0.055	strong		0.388	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
ECSIT	51295	hgsc.bcm.edu	37	19	11618846	11618846	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11618846G>C	ENST00000270517.7	-	5	891	c.756C>G	c.(754-756)gaC>gaG	p.D252E	ECSIT_ENST00000591104.1_Missense_Mutation_p.D252E|CTC-398G3.6_ENST00000585656.1_5'Flank|ECSIT_ENST00000592312.1_Missense_Mutation_p.D136E|ECSIT_ENST00000588998.1_Missense_Mutation_p.D38E|ECSIT_ENST00000417981.2_Missense_Mutation_p.D38E|ZNF653_ENST00000293771.5_5'Flank|ECSIT_ENST00000591352.1_5'UTR|ECSIT_ENST00000252440.7_Missense_Mutation_p.D252E|ZNF653_ENST00000593191.1_5'Flank	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	252					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						CACCTGTTGAGTCTTTGGGCA	0.552																																					p.D252E		Atlas-SNP	.											.	ECSIT	32	.	0			c.C756G						PASS	.						104.0	112.0	109.0					19																	11618846		2203	4300	6503	SO:0001583	missense	51295	exon5			TGTTGAGTCTTTG	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.756C>G	19.37:g.11618846G>C	ENSP00000270517:p.Asp252Glu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_001142464	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	37	CCDS12262.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.360534	0.24598	.	.	ENSG00000130159	ENST00000270517;ENST00000417981;ENST00000252440	T;T;T	0.77098	-1.07;1.56;-1.07	3.81	0.321	0.15883	.	0.520943	0.20641	N	0.088408	T	0.68952	0.3057	M	0.65975	2.015	0.09310	N	1	B;B;B	0.15930	0.015;0.008;0.003	B;B;B	0.19946	0.027;0.009;0.015	T	0.54397	-0.8300	10	0.26408	T	0.33	-23.9198	5.4189	0.16390	0.117:0.4096:0.4734:0.0	.	38;252;252	E9PAN9;Q9BQ95-2;Q9BQ95	.;.;ECSIT_HUMAN	E	252;38;252	ENSP00000270517:D252E;ENSP00000412712:D38E;ENSP00000252440:D252E	ENSP00000252440:D252E	D	-	3	2	ECSIT	11479846	0.109000	0.22037	0.016000	0.15963	0.074000	0.17049	0.357000	0.20199	0.312000	0.23038	0.561000	0.74099	GAC	.	.	none		0.552	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581	
ATP11A	23250	hgsc.bcm.edu	37	13	113508839	113508839	+	Silent	SNP	G	G	C	rs9549573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113508839G>C	ENST00000487903.1	+	19	2326	c.2238G>C	c.(2236-2238)ctG>ctC	p.L746L	ATP11A_ENST00000375645.3_Silent_p.L746L|ATP11A_ENST00000283558.8_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	50	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	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	
ZNF835	90485	hgsc.bcm.edu	37	19	57175484	57175484	+	Silent	SNP	A	A	G	rs7250003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	76	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	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	
OR2W1	26692	hgsc.bcm.edu	37	6	29012116	29012116	+	Silent	SNP	G	G	A	rs7341218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29012116G>A	ENST00000377175.1	-	1	901	c.837C>T	c.(835-837)acC>acT	p.T279T		NM_030903.3	NP_112165.1	Q9Y3N9	OR2W1_HUMAN	olfactory receptor, family 2, subfamily W, member 1	279						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(6)|lung(12)|ovary(2)|skin(1)	23						GAGTGATGACGGTGTAAAAGA	0.433													G|||	1444	0.288339	0.354	0.2839	5008	,	,		18806	0.3929		0.1889	False		,,,				2504	0.1973				p.T279T		Atlas-SNP	.											.	OR2W1	36	.	0			c.C837T						PASS	.	G	,	961,2061		143,675,693	108.0	84.0	93.0		,837	-1.5	1.0	6	dbSNP_116	93	907,4511		78,751,1880	no	utr-5,coding-synonymous	OR2W1,LOC100129636	NM_001195202.1,NM_030903.3	,	221,1426,2573	AA,AG,GG		16.7405,31.8001,22.1327	,	,279/321	29012116	1868,6572	1511	2709	4220	SO:0001819	synonymous_variant	26692	exon1			GATGACGGTGTAA	AL035402	CCDS4656.1	6p22.1	2012-08-09			ENSG00000204704	ENSG00000204704		"""GPCR / Class A : Olfactory receptors"""	8281	protein-coding gene	gene with protein product							Standard	NM_030903		Approved	hs6M1-15	uc003nlw.2	Q9Y3N9	OTTHUMG00000031048	ENST00000377175.1:c.837C>T	6.37:g.29012116G>A		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	216	91	0.421296	NM_030903	B0S7Y5|Q5JNZ1|Q6IEU0|Q96R17|Q9GZL0|Q9GZL1	Silent	SNP	ENST00000377175.1	37	CCDS4656.1																																																																																			G|0.748;A|0.252	0.252	strong		0.433	OR2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076053.2		
ARHGAP31	57514	hgsc.bcm.edu	37	3	119133183	119133183	+	Missense_Mutation	SNP	G	G	A	rs3732413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119133183G>A	ENST00000264245.4	+	12	2939	c.2407G>A	c.(2407-2409)Ggc>Agc	p.G803S		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	803			G -> S (in dbSNP:rs3732413). {ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:15489334}.		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						TTCAAAGGGCGGCCCGGAAAG	0.562													A|||	4235	0.845647	0.9266	0.755	5008	,	,		18508	0.8482		0.7853	False		,,,				2504	0.8599				p.G803S	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.G2407A						PASS	.	A	SER/GLY	3463,305		1588,287,9	56.0	57.0	56.0		2407	-10.1	0.0	3	dbSNP_107	56	6498,1712		2565,1368,172	yes	missense	ARHGAP31	NM_020754.2	56	4153,1655,181	AA,AG,GG		20.8526,8.0945,16.8392	benign	803/1445	119133183	9961,2017	1884	4105	5989	SO:0001583	missense	57514	exon12			AAGGGCGGCCCGG		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"""Rho GTPase activating proteins"""	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.2407G>A	3.37:g.119133183G>A	ENSP00000264245:p.Gly803Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_020754	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	37	CCDS43135.1	1815	0.8310439560439561	459	0.9329268292682927	273	0.7541436464088398	497	0.8688811188811189	586	0.7730870712401056	A	9.638	1.138205	0.21123	0.919055	0.791474	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.05139	3.49	5.3	-10.1	0.00402	.	0.997463	0.08124	N	0.994327	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	0.35895	-0.9770	9	0.02654	T	1	.	8.7904	0.34848	0.5801:0.0:0.1905:0.2294	rs3732413;rs17203090;rs52792832;rs57843911;rs3732413	803	Q2M1Z3	RHG31_HUMAN	S	803	ENSP00000264245:G803S	ENSP00000264245:G803S	G	+	1	0	ARHGAP31	120615873	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.179000	0.01259	-3.054000	0.00259	-0.977000	0.02584	GGC	G|0.160;A|0.840	0.840	strong		0.562	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2		
KNG1	3827	hgsc.bcm.edu	37	3	186459646	186459646	+	Silent	SNP	G	G	A	rs5030085	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186459646G>A	ENST00000265023.4	+	10	1673	c.1461G>A	c.(1459-1461)ggG>ggA	p.G487G	RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000609726.1_RNA|RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000596329.1_RNA|KNG1_ENST00000287611.2_Intron	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	487	His-rich.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		AACACCAAGGGGGCCATGTCC	0.448													G|||	166	0.033147	0.0613	0.0375	5008	,	,		24917	0.0129		0.0258	False		,,,				2504	0.0204				p.G487G		Atlas-SNP	.											.	KNG1	129	.	0			c.G1461A						PASS	.	G	,,	242,3822		2,238,1792	61.0	58.0	59.0		,1461,	-3.8	0.0	3	dbSNP_113	59	231,8101		5,221,3940	no	intron,coding-synonymous,intron	KNG1	NM_000893.3,NM_001102416.2,NM_001166451.1	,,	7,459,5732	AA,AG,GG		2.7724,5.9547,3.8157	,,	,487/645,	186459646	473,11923	2032	4166	6198	SO:0001819	synonymous_variant	3827	exon10			CCAAGGGGGCCAT		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"""Endogenous ligands"""	6383	protein-coding gene	gene with protein product	"""alpha-2-thiol proteinase inhibitor"", ""bradykinin"""	612358	"""kininogen"""	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.1461G>A	3.37:g.186459646G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_001102416	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Silent	SNP	ENST00000265023.4	37	CCDS43183.1																																																																																			G|0.965;A|0.035	0.035	strong		0.448	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416	
CLCN6	1185	hgsc.bcm.edu	37	1	11906068	11906068	+	IGR	SNP	A	A	G	rs5065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11906068A>G	ENST00000346436.6	+	0	5583				NPPA-AS1_ENST00000400892.2_RNA|NPPA-AS1_ENST00000446542.1_RNA|NPPA_ENST00000376476.1_Nonstop_Mutation_p.*102R|NPPA_ENST00000376480.3_Nonstop_Mutation_p.*152R	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6						cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	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;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TGTTATCTTCAGTACTGCAAA	0.517													G|||	897	0.179113	0.4183	0.1138	5008	,	,		18871	0.0129		0.1233	False		,,,				2504	0.1309				p.X152R		Atlas-SNP	.											.	NPPA	14	.	0			c.T454C	GRCh37	CM040788	NPPA	M	rs5065	PASS	.	G	ARG/stop	1800,2606	641.4+/-397.5	380,1040,783	151.0	136.0	141.0		454	0.9	1.0	1	dbSNP_52	141	1335,7265	756.5+/-407.5	97,1141,3062	yes	stop-lost	NPPA	NM_006172.3		477,2181,3845	GG,GA,AA		15.5233,40.8534,24.1043		152/152	11906068	3135,9871	2203	4300	6503	SO:0001628	intergenic_variant	4878	exon3			ATCTTCAGTACTG	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299		1.37:g.11906068A>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_006172	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	CCDS138.1	304	0.1391941391941392	174	0.35365853658536583	41	0.1132596685082873	4	0.006993006993006993	85	0.11213720316622691	G	5.706	0.314728	0.10789	0.408534	0.155233	ENSG00000175206	ENST00000376480;ENST00000376476	.	.	.	5.47	0.954	0.19595	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.1248	0.03735	0.2569:0.1343:0.4715:0.1373	rs5065;rs198363;rs1130764;rs3189984;rs17413194;rs17856153;rs57081035;rs5065	.	.	.	R	152;102	.	.	X	-	1	0	NPPA	11828655	0.997000	0.39634	0.976000	0.42696	0.154000	0.21943	0.306000	0.19279	0.041000	0.15688	-0.128000	0.14901	TGA	A|0.796;G|0.204	0.204	strong		0.517	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
TECPR2	9895	hgsc.bcm.edu	37	14	102909991	102909991	+	Silent	SNP	C	C	T	rs17100923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102909991C>T	ENST00000359520.7	+	12	2986	c.2760C>T	c.(2758-2760)agC>agT	p.S920S	TECPR2_ENST00000558678.1_Silent_p.S920S	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	920					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						CAGGTCTGAGCGTGGATCGCC	0.532													C|||	431	0.0860623	0.2383	0.0403	5008	,	,		15922	0.001		0.0616	False		,,,				2504	0.0256				p.S920S		Atlas-SNP	.											.	TECPR2	114	.	0			c.C2760T						PASS	.	C	,	930,3476	351.1+/-311.1	87,756,1360	79.0	58.0	65.0		2760,2760	-10.0	0.1	14	dbSNP_123	65	505,8095	143.1+/-199.2	17,471,3812	no	coding-synonymous,coding-synonymous	TECPR2	NM_001172631.1,NM_014844.3	,	104,1227,5172	TT,TC,CC		5.8721,21.1076,11.0334	,	920/1268,920/1412	102909991	1435,11571	2203	4300	6503	SO:0001819	synonymous_variant	9895	exon12			TCTGAGCGTGGAT	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.2760C>T	14.37:g.102909991C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Silent	SNP	ENST00000359520.7	37	CCDS32162.1																																																																																			C|0.899;T|0.101	0.101	strong		0.532	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844	
IL1R1	3554	hgsc.bcm.edu	37	2	102781466	102781466	+	Silent	SNP	A	A	G	rs144946641	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102781466A>G	ENST00000410023.1	+	4	612	c.294A>G	c.(292-294)gtA>gtG	p.V98V	IL1R1_ENST00000233946.3_Silent_p.V98V|IL1R1_ENST00000409329.1_Silent_p.V98V|IL1R1_ENST00000409929.1_Silent_p.V98V|IL1R1_ENST00000424272.1_Silent_p.V98V|IL1R1_ENST00000409589.1_Silent_p.V98V|IL1R1_ENST00000409288.1_Silent_p.V98V			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	98	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)	p.V98V(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	ATTGCGTGGTAAGGTAAGAGA	0.358													A|||	16	0.00319489	0.0121	0.0	5008	,	,		18836	0.0		0.0	False		,,,				2504	0.0				p.V98V		Atlas-SNP	.											IL1R1,NS,carcinoma,0,1	IL1R1	52	1	1	Substitution - coding silent(1)	lung(1)	c.A294G						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	99.0	90.0	93.0		294	-5.0	0.3	2	dbSNP_134	93	0,8600		0,0,4300	no	coding-synonymous	IL1R1	NM_000877.2		0,24,6479	GG,GA,AA		0.0,0.5447,0.1845		98/570	102781466	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	3554	exon3			CGTGGTAAGGTAA	M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.294A>G	2.37:g.102781466A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_000877	Q587I7	Silent	SNP	ENST00000410023.1	37	CCDS2055.1																																																																																			A|0.998;G|0.002	0.002	strong		0.358	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1		
DNAH9	1770	hgsc.bcm.edu	37	17	11592928	11592928	+	Silent	SNP	C	C	T	rs35922062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11592928C>T	ENST00000262442.4	+	20	3857	c.3789C>T	c.(3787-3789)atC>atT	p.I1263I	DNAH9_ENST00000454412.2_Silent_p.I1263I	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1263	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)		CCAGGCACATCGAGATCCAGC	0.493													c|||	58	0.0115815	0.0424	0.0029	5008	,	,		19643	0.0		0.0	False		,,,				2504	0.0				p.I1263I		Atlas-SNP	.											.	DNAH9	695	.	0			c.C3789T						PASS	.	T		164,4242	111.6+/-149.8	6,152,2045	115.0	106.0	109.0		3789	-11.2	0.0	17	dbSNP_126	109	1,8599		0,1,4299	no	coding-synonymous	DNAH9	NM_001372.3		6,153,6344	TT,TC,CC		0.0116,3.7222,1.2686		1263/4487	11592928	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon20			GCACATCGAGATC	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.3789C>T	17.37:g.11592928C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.988;T|0.012	0.012	strong		0.493	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
CFAP46	54777	hgsc.bcm.edu	37	10	134659626	134659626	+	Missense_Mutation	SNP	A	A	G	rs10870341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134659626A>G	ENST00000368586.5	-	44	6473	c.6373T>C	c.(6373-6375)Tgc>Cgc	p.C2125R	TTC40_ENST00000263170.5_Missense_Mutation_p.C286R	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTGTCTTGGCACCGGAGCTGG	0.672													G|||	845	0.16873	0.2867	0.1167	5008	,	,		14135	0.0744		0.1352	False		,,,				2504	0.1779				p.C2125R		Atlas-SNP	.											.	TTC40	100	.	0			c.T6373C						PASS	.	G	ARG/CYS	1111,3287	684.6+/-404.4	154,803,1242	36.0	37.0	36.0		1309	-1.5	0.0	10	dbSNP_120	36	1057,7543	747.6+/-407.3	67,923,3310	yes	missense	C10orf92	NM_001200049.1	180	221,1726,4552	GG,GA,AA		12.2907,25.2615,16.6795	benign	437/1028	134659626	2168,10830	2199	4300	6499	SO:0001583	missense	54777	exon44			CTTGGCACCGGAG																												ENST00000368586.5:c.6373T>C	10.37:g.134659626A>G	ENSP00000357575:p.Cys2125Arg	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	145	67	0.462069	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	310	0.14194139194139194	125	0.2540650406504065	51	0.1408839779005525	39	0.06818181818181818	95	0.12532981530343007	G	0.001	-2.939895	0.00052	0.252615	0.122907	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.11063	3.04;2.81	4.38	-1.49	0.08718	.	1.969230	0.02798	N	0.122830	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	0.43228	-0.9404	9	0.11485	T	0.65	.	6.2058	0.20602	0.307:0.2289:0.4641:0.0	rs10870341;rs61193559;rs10870341	286	Q8IYW2	CJ092_HUMAN	R	2125;286	ENSP00000357575:C2125R;ENSP00000263170:C286R	ENSP00000263170:C286R	C	-	1	0	C10orf93	134509616	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.032000	0.13732	-0.729000	0.04875	-3.198000	0.00054	TGC	A|0.840;G|0.160	0.160	strong		0.672	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
ZNF831	128611	hgsc.bcm.edu	37	20	57766397	57766397	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:57766397C>T	ENST00000371030.2	+	1	323	c.323C>T	c.(322-324)cCg>cTg	p.P108L		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	108	Pro-rich.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GTGGGGAAGCCGGCGGCCCCT	0.701																																					p.P108L		Atlas-SNP	.											.	ZNF831	287	.	0			c.C323T						PASS	.						9.0	12.0	11.0					20																	57766397		2020	4160	6180	SO:0001583	missense	128611	exon1			GGAAGCCGGCGGC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.323C>T	20.37:g.57766397C>T	ENSP00000360069:p.Pro108Leu	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.079440	0.36662	.	.	ENSG00000124203	ENST00000371030	T	0.05649	3.41	5.2	3.14	0.36123	.	.	.	.	.	T	0.03739	0.0106	N	0.19112	0.55	0.09310	N	1	P	0.42908	0.793	B	0.31547	0.132	T	0.39722	-0.9600	9	0.66056	D	0.02	-0.6362	7.8433	0.29410	0.2296:0.6849:0.0:0.0855	.	108	Q5JPB2	ZN831_HUMAN	L	108	ENSP00000360069:P108L	ENSP00000360069:P108L	P	+	2	0	ZNF831	57199792	0.703000	0.27826	0.694000	0.30210	0.923000	0.55619	1.411000	0.34702	1.194000	0.43101	0.561000	0.74099	CCG	.	.	none		0.701	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604721	140604721	+	Silent	SNP	C	C	A	rs2910003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604721C>A	ENST00000239449.4	+	1	1644	c.1644C>A	c.(1642-1644)cgC>cgA	p.R548R	PCDHB14_ENST00000515856.2_Silent_p.R395R	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	548	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)|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)			CGCTGGTGCGCGTGCTGGTGC	0.711													c|||	1818	0.363019	0.6543	0.3329	5008	,	,		16379	0.1359		0.3211	False		,,,				2504	0.2679				p.R548R	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											PCDHB14,NS,carcinoma,+2,1	PCDHB14	132	1	0			c.C1644A						PASS	.						35.0	39.0	37.0					5																	140604721		2202	4297	6499	SO:0001819	synonymous_variant	56122	exon1			GGTGCGCGTGCTG	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.1644C>A	5.37:g.140604721C>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			C|0.642;A|0.358	0.358	strong		0.711	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
RGS3	5998	hgsc.bcm.edu	37	9	116356389	116356389	+	Intron	SNP	C	C	T	rs57845277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116356389C>T	ENST00000374140.2	+	23	3289				RGS3_ENST00000462143.1_Intron|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000374134.3_Intron|RGS3_ENST00000343817.5_Intron|RGS3_ENST00000462403.1_Missense_Mutation_p.R64W|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000350696.5_Intron	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						GTCCCAGCCCCGGCTTGTGCC	0.637													C|||	54	0.0107827	0.0393	0.0029	5008	,	,		15146	0.0		0.0	False		,,,				2504	0.0				p.R64W		Atlas-SNP	.											.	RGS3	251	.	0			c.C190T						PASS	.	C	,,,,TRP/ARG	146,4260		5,136,2062	66.0	74.0	71.0		,,,,190	-5.5	0.0	9	dbSNP_129	71	1,8599		0,1,4299	no	intron,intron,intron,intron,missense	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4,NM_144489.2	,,,,101	5,137,6361	TT,TC,CC		0.0116,3.3137,1.1302	,,,,	,,,,64/312	116356389	147,12859	2203	4300	6503	SO:0001627	intron_variant	5998	exon1			CAGCCCCGGCTTG	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.3081-321C>T	9.37:g.116356389C>T		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	259	94	0.362934	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	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	1.749	-0.489752	0.04352	0.033137	1.16E-4	ENSG00000138835	ENST00000462403	T	0.62232	0.04	4.25	-5.51	0.02568	.	.	.	.	.	T	0.12390	0.0301	N	0.08118	0	0.20074	N	0.999939	B	0.02656	0.0	B	0.01281	0.0	T	0.09707	-1.0662	9	0.87932	D	0	.	0.1774	0.00120	0.2449:0.2726:0.1703:0.3122	rs57845277	64	Q5VZ06	.	W	64	ENSP00000436168:R64W	ENSP00000436168:R64W	R	+	1	2	RGS3	115396210	0.000000	0.05858	0.010000	0.14722	0.220000	0.24768	-2.218000	0.01219	-1.939000	0.01044	-1.946000	0.00489	CGG	C|0.988;T|0.012	0.012	strong		0.637	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
ZNF682	91120	hgsc.bcm.edu	37	19	20117685	20117685	+	Missense_Mutation	SNP	G	G	A	rs2075090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:20117685G>A	ENST00000397165.2	-	4	786	c.626C>T	c.(625-627)aCc>aTc	p.T209I	ZNF682_ENST00000358523.5_Missense_Mutation_p.T177I|ZNF682_ENST00000397162.1_Missense_Mutation_p.T177I|ZNF682_ENST00000596019.1_Intron|ZNF682_ENST00000597972.1_Missense_Mutation_p.T215I|ZNF682_ENST00000595736.1_Missense_Mutation_p.T133I	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	209			T -> I (in dbSNP:rs2075090). {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)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						CCACTTAAAGGTTTTGCCACA	0.378													g|||	621	0.124002	0.1316	0.17	5008	,	,		19963	0.1954		0.0378	False		,,,				2504	0.0961				p.T209I		Atlas-SNP	.											.	ZNF682	51	.	0			c.C626T						PASS	.	G	ILE/THR,ILE/THR	456,3668		29,398,1635	50.0	52.0	52.0		530,626	-0.6	0.0	19	dbSNP_96	52	283,8185		5,273,3956	yes	missense,missense	ZNF682	NM_001077349.1,NM_033196.2	89,89	34,671,5591	AA,AG,GG		3.342,11.0572,5.8688	possibly-damaging,possibly-damaging	177/467,209/499	20117685	739,11853	2062	4234	6296	SO:0001583	missense	91120	exon4			TTAAAGGTTTTGC	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.626C>T	19.37:g.20117685G>A	ENSP00000380351:p.Thr209Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	37	CCDS42533.1	252	0.11538461538461539	72	0.14634146341463414	50	0.13812154696132597	105	0.18356643356643357	25	0.032981530343007916	G	6.697	0.497203	0.12762	0.110572	0.03342	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000358523	T;T;T	0.36157	1.27;1.27;1.27	1.08	-0.578	0.11724	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	M	0.64080	1.96	0.58432	P	5.999999999950489E-6	B	0.23249	0.082	B	0.25987	0.065	T	0.12785	-1.0534	8	0.72032	D	0.01	.	5.2114	0.15318	0.244:0.0:0.756:0.0	rs2075090;rs60679185;rs2075090	209	O95780	ZN682_HUMAN	I	209;177;177	ENSP00000380351:T209I;ENSP00000380348:T177I;ENSP00000351324:T177I	ENSP00000351324:T177I	T	-	2	0	ZNF682	19978685	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.410000	0.07151	-0.354000	0.08212	-0.350000	0.07774	ACC	G|0.895;A|0.105	0.105	strong		0.378	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196	
SSPO	23145	hgsc.bcm.edu	37	7	149474393	149474393	+	RNA	SNP	A	A	G	rs709061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149474393A>G	ENST00000378016.2	+	0	437							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)			CCCTGGGGACAAAGCTGGTGG	0.657													G|||	1470	0.29353	0.7352	0.1427	5008	,	,		15625	0.1131		0.17	False		,,,				2504	0.1166				p.Q146R		Atlas-SNP	.											.	.	.	.	0			c.A437G						PASS	.	G	ARG/GLN	2144,1706		593,958,374	8.0	11.0	10.0		437	-0.2	0.5	7	dbSNP_86	10	1170,6872		105,960,2956	yes	missense	SSPO	NM_198455.2	43	698,1918,3330	GG,GA,AA		14.5486,44.3117,27.8675	benign	146/5148	149474393	3314,8578	1925	4021	5946			23145	exon4			GGGGACAAAGCTG	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.149474393A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				A|0.738;G|0.262	0.262	strong		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
OR8H2	390151	hgsc.bcm.edu	37	11	55872620	55872620	+	Silent	SNP	G	G	C	rs61745328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55872620G>C	ENST00000313503.1	+	1	102	c.102G>C	c.(100-102)ctG>ctC	p.L34L		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	34						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L34L(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					TATTTCTCCTGATATACCTAA	0.428										HNSCC(53;0.14)			g|||	37	0.00738818	0.0242	0.0058	5008	,	,		19540	0.0		0.001	False		,,,				2504	0.0				p.L34L		Atlas-SNP	.											OR8H2,colon,carcinoma,0,1	OR8H2	117	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G102C						scavenged	.						257.0	246.0	250.0					11																	55872620		2201	4296	6497	SO:0001819	synonymous_variant	390151	exon1			TCTCCTGATATAC	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.102G>C	11.37:g.55872620G>C		Somatic	253	2	0.00790514		WXS	Illumina HiSeq	Phase_I	245	90	0.367347	NM_001005200	Q6IFC1	Silent	SNP	ENST00000313503.1	37	CCDS31518.1																																																																																			G|0.993;C|0.007	0.007	strong		0.428	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
CCDC132	55610	hgsc.bcm.edu	37	7	92926102	92926102	+	Missense_Mutation	SNP	A	A	G	rs374290264		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:92926102A>G	ENST00000305866.5	+	15	1344	c.1216A>G	c.(1216-1218)Ata>Gta	p.I406V	CCDC132_ENST00000317751.6_Missense_Mutation_p.I137V|CCDC132_ENST00000535481.1_Missense_Mutation_p.I126V|CCDC132_ENST00000544910.1_Missense_Mutation_p.I376V|CCDC132_ENST00000541136.1_Missense_Mutation_p.I217V	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	406						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			TGATTTGTCTATATTCAAATA	0.294																																					p.I406V		Atlas-SNP	.											.	CCDC132	136	.	0			c.A1216G						PASS	.	A	VAL/ILE	2,3616		0,2,1807	89.0	86.0	87.0		1216	4.8	1.0	7		87	0,8124		0,0,4062	no	missense	CCDC132	NM_017667.2	29	0,2,5869	GG,GA,AA		0.0,0.0553,0.017	benign	406/965	92926102	2,11740	1809	4062	5871	SO:0001583	missense	55610	exon15			TTGTCTATATTCA	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1216A>G	7.37:g.92926102A>G	ENSP00000307666:p.Ile406Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	9.350	1.065336	0.20067	5.53E-4	0.0	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751	T	0.41065	1.01	4.82	4.82	0.62117	.	0.178206	0.47455	D	0.000238	T	0.22205	0.0535	N	0.03608	-0.345	0.27582	N	0.949545	B;B;B	0.12630	0.001;0.006;0.0	B;B;B	0.10450	0.001;0.005;0.0	T	0.10800	-1.0614	10	0.30078	T	0.28	-3.5357	14.7032	0.69168	1.0:0.0:0.0:0.0	.	126;376;406	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	V	406;376;217;126;137	ENSP00000325582:I137V	ENSP00000307666:I406V	I	+	1	0	CCDC132	92764038	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.164000	0.77533	1.951000	0.56629	0.455000	0.32223	ATA	.	.	weak		0.294	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
SYNGR2	9144	hgsc.bcm.edu	37	17	76167047	76167047	+	Silent	SNP	C	C	T	rs1062668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76167047C>T	ENST00000225777.3	+	2	308	c.249C>T	c.(247-249)gcC>gcT	p.A83A	SYNGR2_ENST00000585591.1_Silent_p.A83A|SYNGR2_ENST00000589711.1_Intron|SYNGR2_ENST00000588282.1_Silent_p.A83A|SYNGR2_ENST00000590201.1_Silent_p.A27A|SYNGR2_ENST00000592456.1_3'UTR			O43760	SNG2_HUMAN	synaptogyrin 2	83	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				protein targeting (GO:0006605)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)				endometrium(2)|large_intestine(1)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	7			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.0994)			TGGCCTCGGCCTTCTTCTTGG	0.582													C|||	383	0.0764776	0.0386	0.1153	5008	,	,		19484	0.002		0.1203	False		,,,				2504	0.1319				p.A83A		Atlas-SNP	.											SYNGR2,NS,carcinoma,+2,1	SYNGR2	17	1	0			c.C249T						scavenged	.	C		252,4154	146.5+/-181.1	7,238,1958	121.0	98.0	106.0		249	3.9	1.0	17	dbSNP_86	106	1254,7346	250.7+/-277.5	87,1080,3133	no	coding-synonymous	SYNGR2	NM_004710.3		94,1318,5091	TT,TC,CC		14.5814,5.7195,11.5793		83/225	76167047	1506,11500	2203	4300	6503	SO:0001819	synonymous_variant	9144	exon2			CTCGGCCTTCTTC	AJ002308	CCDS11753.1	17q25.3	2014-09-11			ENSG00000108639	ENSG00000108639			11499	protein-coding gene	gene with protein product	"""cellugyrin"""	603926				9760194	Standard	NM_004710		Approved		uc002juu.1	O43760	OTTHUMG00000177457	ENST00000225777.3:c.249C>T	17.37:g.76167047C>T		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_004710	O43762|Q3KQZ2|Q658S7	Silent	SNP	ENST00000225777.3	37	CCDS11753.1																																																																																			C|0.889;T|0.111	0.111	strong		0.582	SYNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437009.2		
COMMD10	51397	hgsc.bcm.edu	37	5	115428381	115428381	+	Missense_Mutation	SNP	T	T	G	rs1129495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:115428381T>G	ENST00000274458.4	+	4	445	c.383T>G	c.(382-384)aTt>aGt	p.I128S	COMMD10_ENST00000515539.1_Missense_Mutation_p.I114S	NM_016144.2	NP_057228.1	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10	128			I -> S (in dbSNP:rs1129495).							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)		CGGCAGAGAATTCTGGCTCCC	0.333													T|||	714	0.142572	0.2753	0.0706	5008	,	,		18223	0.1736		0.0696	False		,,,				2504	0.0573				p.I128S		Atlas-SNP	.											.	COMMD10	18	.	0			c.T383G						PASS	.	T	SER/ILE	969,3435	364.9+/-317.2	112,745,1345	81.0	78.0	79.0		383	2.1	0.9	5	dbSNP_86	79	527,8073	148.9+/-204.1	17,493,3790	yes	missense	COMMD10	NM_016144.2	142	129,1238,5135	GG,GT,TT		6.1279,22.0027,11.5042	benign	128/203	115428381	1496,11508	2202	4300	6502	SO:0001583	missense	51397	exon4			AGAGAATTCTGGC	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.383T>G	5.37:g.115428381T>G	ENSP00000274458:p.Ile128Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	53	0.654321	NM_016144	D3DT07|Q9P077	Missense_Mutation	SNP	ENST00000274458.4	37	CCDS34215.1	307	0.14056776556776557	140	0.2845528455284553	22	0.06077348066298342	92	0.16083916083916083	53	0.06992084432717678	T	0.011	-1.699478	0.00725	0.220027	0.061279	ENSG00000145781	ENST00000274458;ENST00000515539;ENST00000506589	T;T;T	0.06528	3.29;3.29;3.29	5.87	2.12	0.27331	.	0.196983	0.51477	D	0.000094	T	0.00012	0.0000	L	0.35414	1.06	0.33450	P	0.41641799999999995	B	0.22800	0.075	B	0.18263	0.021	T	0.47433	-0.9118	9	0.07175	T	0.84	-24.9333	6.6026	0.22708	0.0:0.1389:0.1305:0.7306	rs62652038	128	Q9Y6G5	COMDA_HUMAN	S	128;114;84	ENSP00000274458:I128S;ENSP00000427319:I114S;ENSP00000424611:I84S	ENSP00000274458:I128S	I	+	2	0	COMMD10	115456280	1.000000	0.71417	0.946000	0.38457	0.160000	0.22226	4.865000	0.62998	0.191000	0.20236	-0.250000	0.11733	ATT	T|0.876;G|0.124	0.124	strong		0.333	COMMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371033.1	NM_016144	
NDNF	79625	hgsc.bcm.edu	37	4	121958691	121958691	+	Silent	SNP	T	T	C	rs3733559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	95	39	0.410526	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	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12908107	12908107	+	Silent	SNP	G	G	A	rs12566484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12908107G>A	ENST00000317869.6	-	2	261	c.36C>T	c.(34-36)caC>caT	p.H12H		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	12						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						AGTTCATGGAGTGAGGATCCA	0.463																																					p.H12H		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	0			c.C36T						PASS	.	G		390,4016	162.2+/-194.2	0,390,1813	188.0	174.0	179.0		36	0.1	0.0	1	dbSNP_131	179	44,8556	17.3+/-56.4	0,44,4256	no	coding-synonymous	HNRNPCL1	NM_001013631.1		0,434,6069	AA,AG,GG		0.5116,8.8516,3.3369		12/294	12908107	434,12572	2203	4300	6503	SO:0001819	synonymous_variant	343069	exon2			CATGGAGTGAGGA	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"""RNA binding motif (RRM) containing"""	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.36C>T	1.37:g.12908107G>A		Somatic	951	1	0.00105152		WXS	Illumina HiSeq	Phase_I	772	138	0.178756	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	37	CCDS30591.1																																																																																			G|0.955;A|0.045	0.045	strong		0.463	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
FUT6	2528	hgsc.bcm.edu	37	19	5832209	5832209	+	Missense_Mutation	SNP	G	G	A	rs778805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5832209G>A	ENST00000318336.4	-	3	1564	c.370C>T	c.(370-372)Ccg>Tcg	p.P124S	FUT6_ENST00000592563.1_Missense_Mutation_p.P124S|FUT6_ENST00000524754.1_Missense_Mutation_p.P124S|FUT6_ENST00000286955.5_Missense_Mutation_p.P124S|FUT6_ENST00000527106.1_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	PASS	.	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	185	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	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	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52115645	52115645	+	Missense_Mutation	SNP	G	G	C	rs3829655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52115645G>C	ENST00000534261.2	-	10	1894	c.1495C>G	c.(1495-1497)Ccc>Gcc	p.P499A	SIGLEC5_ENST00000570106.2_Missense_Mutation_p.P499A|SIGLEC5_ENST00000222107.4_Missense_Mutation_p.P499A|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.P499A|SIGLEC5_ENST00000429354.3_Missense_Mutation_p.P499A			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	499			P -> A (in dbSNP:rs3829655). {ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		TGATCTCCGGGGCTGTCTGGC	0.498													G|||	2180	0.435304	0.3275	0.4683	5008	,	,		19086	0.5794		0.4225	False		,,,				2504	0.4223				p.P499A		Atlas-SNP	.											.	SIGLEC5	67	.	0			c.C1495G						PASS	.	G	ALA/PRO	1423,2983	460.7+/-352.7	244,935,1024	72.0	75.0	74.0		1495	-1.3	0.0	19	dbSNP_107	74	3753,4847	527.6+/-381.2	800,2153,1347	yes	missense	SIGLEC5	NM_003830.2	27	1044,3088,2371	CC,CG,GG		43.6395,32.2969,39.797	benign	499/552	52115645	5176,7830	2203	4300	6503	SO:0001583	missense	8778	exon9			CTCCGGGGCTGTC	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1495C>G	19.37:g.52115645G>C	ENSP00000473238:p.Pro499Ala	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	NM_003830		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	970	0.4441391941391941	151	0.30691056910569103	166	0.4585635359116022	319	0.5576923076923077	334	0.44063324538258575	G	8.436	0.849683	0.17034	0.322969	0.436395	ENSG00000105501	ENST00000222107;ENST00000429354	T;T	0.59364	0.27;0.27	3.52	-1.27	0.09347	.	.	.	.	.	T	0.00012	0.0000	M	0.64567	1.98	0.80722	P	0.0	P	0.52463	0.953	B	0.42462	0.388	T	0.40270	-0.9572	8	0.52906	T	0.07	.	1.8675	0.03201	0.1081:0.1749:0.3589:0.3581	rs3829655;rs17852717;rs3829655	499	O15389	SIGL5_HUMAN	A	499	ENSP00000222107:P499A;ENSP00000415200:P499A	ENSP00000222107:P499A	P	-	1	0	SIGLEC5	56807457	0.005000	0.15991	0.005000	0.12908	0.005000	0.04900	0.278000	0.18753	-0.109000	0.12044	-0.152000	0.13540	CCC	G|0.577;C|0.423	0.423	strong		0.498	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
MGAT1	4245	hgsc.bcm.edu	37	5	180218831	180218831	+	Silent	SNP	G	G	A	rs2070924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180218831G>A	ENST00000446023.2	-	3	1891	c.1141C>T	c.(1141-1143)Ctg>Ttg	p.L381L	MGAT1_ENST00000393340.3_Silent_p.L381L|MGAT1_ENST00000427865.2_Silent_p.L381L|MGAT1_ENST00000307826.4_Silent_p.L381L|MGAT1_ENST00000333055.3_Silent_p.L381L	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	381					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|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)			ACCTCCCCCAGCTCCTTCCGG	0.612													G|||	585	0.116813	0.0976	0.0418	5008	,	,		18311	0.2143		0.0537	False		,,,				2504	0.1605				p.L381L		Atlas-SNP	.											.	MGAT1	48	.	0			c.C1141T						PASS	.	G	,,,,	352,4054	183.6+/-211.2	15,322,1866	73.0	64.0	67.0		1141,1141,1141,1141,1141	4.0	1.0	5	dbSNP_96	67	307,8293	111.0+/-171.3	8,291,4001	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	,,,,	23,613,5867	AA,AG,GG		3.5698,7.9891,5.0669	,,,,	381/446,381/446,381/446,381/446,381/446	180218831	659,12347	2203	4300	6503	SO:0001819	synonymous_variant	4245	exon3			CCCCCAGCTCCTT	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.1141C>T	5.37:g.180218831G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Silent	SNP	ENST00000446023.2	37	CCDS4458.1																																																																																			G|0.925;A|0.075	0.075	strong		0.612	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
CCDC130	81576	hgsc.bcm.edu	37	19	13873793	13873793	+	Missense_Mutation	SNP	C	C	A	rs138278370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13873793C>A	ENST00000586600.1	+	11	1605	c.1102C>A	c.(1102-1104)Cag>Aag	p.Q368K	MRI1_ENST00000319545.8_5'Flank|MRI1_ENST00000040663.6_5'Flank|CCDC130_ENST00000221554.8_Missense_Mutation_p.Q368K			P13994	CC130_HUMAN	coiled-coil domain containing 130	368					response to virus (GO:0009615)					endometrium(2)|kidney(1)|large_intestine(3)|ovary(1)|skin(2)|urinary_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)			AGGCTCCTCCCAGGAGGCAGC	0.667													C|||	22	0.00439297	0.0159	0.0014	5008	,	,		13510	0.0		0.0	False		,,,				2504	0.0				p.Q368K		Atlas-SNP	.											.	CCDC130	25	.	0			c.C1102A						PASS	.	C	LYS/GLN	82,4310		0,82,2114	14.0	17.0	16.0		1102	4.5	0.0	19	dbSNP_134	16	1,8579		0,1,4289	yes	missense	CCDC130	NM_030818.2	53	0,83,6403	AA,AC,CC		0.0117,1.867,0.6398	benign	368/397	13873793	83,12889	2196	4290	6486	SO:0001583	missense	81576	exon10			TCCTCCCAGGAGG	AF250306	CCDS12296.1	19p13.13	2008-02-05				ENSG00000104957			28118	protein-coding gene	gene with protein product						3203696	Standard	NM_030818		Approved	MGC10471	uc002mxc.1	P13994		ENST00000586600.1:c.1102C>A	19.37:g.13873793C>A	ENSP00000465776:p.Gln368Lys	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	40	13	0.325	NM_030818	Q9BQ72	Missense_Mutation	SNP	ENST00000586600.1	37	CCDS12296.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	11.27	1.590016	0.28357	0.01867	1.17E-4	ENSG00000104957	ENST00000221554	T	0.27557	1.66	4.49	4.49	0.54785	.	0.852666	0.09747	N	0.761109	T	0.13970	0.0338	L	0.57536	1.79	0.24401	N	0.994709	B;B	0.27625	0.183;0.183	B;B	0.25506	0.061;0.061	T	0.37407	-0.9707	10	0.06494	T	0.89	-10.5446	8.8286	0.35069	0.0:0.8959:0.0:0.1041	.	368;368	B3KUZ1;P13994	.;CC130_HUMAN	K	368	ENSP00000221554:Q368K	ENSP00000221554:Q368K	Q	+	1	0	CCDC130	13734793	0.003000	0.15002	0.033000	0.17914	0.220000	0.24768	0.327000	0.19663	2.230000	0.72887	0.491000	0.48974	CAG	C|0.994;A|0.006	0.006	strong		0.667	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818	
SLC24A1	9187	hgsc.bcm.edu	37	15	65918277	65918277	+	Missense_Mutation	SNP	C	C	T	rs35398714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65918277C>T	ENST00000261892.6	+	2	2146	c.1859C>T	c.(1858-1860)gCc>gTc	p.A620V	SLC24A1_ENST00000399033.4_Missense_Mutation_p.A620V|SLC24A1_ENST00000546330.1_Missense_Mutation_p.A620V|SLC24A1_ENST00000339868.6_Missense_Mutation_p.A620V|SLC24A1_ENST00000544319.2_Missense_Mutation_p.A620V|SLC24A1_ENST00000537259.1_Missense_Mutation_p.A620V	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	620					calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						AGGCCAGTGGCCAAGGTCATG	0.537													C|||	20	0.00399361	0.0151	0.0	5008	,	,		23355	0.0		0.0	False		,,,				2504	0.0				p.A620V		Atlas-SNP	.											.	SLC24A1	58	.	0			c.C1859T						PASS	.	C	VAL/ALA	40,4044		0,40,2002	101.0	98.0	99.0		1859	4.0	0.8	15	dbSNP_126	99	0,8416		0,0,4208	yes	missense	SLC24A1	NM_004727.2	64	0,40,6210	TT,TC,CC		0.0,0.9794,0.32	benign	620/1100	65918277	40,12460	2042	4208	6250	SO:0001583	missense	9187	exon2			CAGTGGCCAAGGT	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"""Solute carriers"""	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.1859C>T	15.37:g.65918277C>T	ENSP00000261892:p.Ala620Val	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_004727	O43485|O75184|Q17RM9	Missense_Mutation	SNP	ENST00000261892.6	37	CCDS45284.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	13.30	2.196553	0.38806	0.009794	0.0	ENSG00000074621	ENST00000537259;ENST00000261892;ENST00000339868;ENST00000544319;ENST00000399033;ENST00000546330	T;T;T;T;T;T	0.65916	0.08;-0.16;-0.15;0.12;-0.18;-0.15	6.06	3.97	0.46021	.	0.354666	0.29737	N	0.011329	T	0.33235	0.0856	L	0.35793	1.09	0.25586	N	0.986742	B;B;B;B;B	0.28026	0.084;0.051;0.051;0.198;0.125	B;B;B;B;B	0.33846	0.046;0.02;0.02;0.171;0.119	T	0.28396	-1.0045	10	0.30078	T	0.28	.	6.3771	0.21513	0.0:0.6781:0.1434:0.1785	rs35398714	620;620;620;620;620	O60721-2;Q17RM9;O60721;F5H127;B4E1W0	.;.;NCKX1_HUMAN;.;.	V	620	ENSP00000439693:A620V;ENSP00000261892:A620V;ENSP00000341837:A620V;ENSP00000445163:A620V;ENSP00000381991:A620V;ENSP00000439190:A620V	ENSP00000261892:A620V	A	+	2	0	SLC24A1	63705331	1.000000	0.71417	0.763000	0.31416	0.072000	0.16883	2.208000	0.42797	0.705000	0.31890	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.537	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727	
GMPPA	29926	hgsc.bcm.edu	37	2	220371035	220371035	+	Silent	SNP	C	C	G	rs1046474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220371035C>G	ENST00000358215.3	+	12	1422	c.1053C>G	c.(1051-1053)gcC>gcG	p.A351A	AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373908.1_Silent_p.A351A|GMPPA_ENST00000373917.3_Silent_p.A404A|GMPPA_ENST00000313597.5_Silent_p.A351A|GMPPA_ENST00000341142.3_Silent_p.A351A	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	351					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		GACGCTGGGCCCGCGTGGAGG	0.622													C|||	263	0.052516	0.0129	0.0908	5008	,	,		18788	0.001		0.161	False		,,,				2504	0.0204				p.A351A		Atlas-SNP	.											.	GMPPA	50	.	0			c.C1053G						PASS	.	C	,	171,4235	115.4+/-153.4	7,157,2039	73.0	73.0	73.0		1053,1053	0.6	0.9	2	dbSNP_86	73	1430,7170	274.6+/-291.3	112,1206,2982	no	coding-synonymous,coding-synonymous	GMPPA	NM_013335.3,NM_205847.2	,	119,1363,5021	GG,GC,CC		16.6279,3.8811,12.3097	,	351/421,351/421	220371035	1601,11405	2203	4300	6503	SO:0001819	synonymous_variant	29926	exon12			CTGGGCCCGCGTG	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.1053C>G	2.37:g.220371035C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Silent	SNP	ENST00000358215.3	37	CCDS2441.1																																																																																			C|0.888;G|0.112	0.112	strong		0.622	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335	
CCDC127	133957	hgsc.bcm.edu	37	5	205574	205574	+	Silent	SNP	G	G	A	rs73730755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:205574G>A	ENST00000296824.3	-	3	753	c.621C>T	c.(619-621)gcC>gcT	p.A207A		NM_145265.2	NP_660308.1	Q96BQ5	CC127_HUMAN	coiled-coil domain containing 127	207										breast(1)|endometrium(4)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12			all cancers(22;0.0236)|Lung(60;0.113)			CGGTGAGACCGGCTGCCATCT	0.532													G|||	569	0.113618	0.4092	0.0317	5008	,	,		18402	0.0		0.004	False		,,,				2504	0.002				p.A207A		Atlas-SNP	.											CCDC127,NS,carcinoma,-2,2	CCDC127	27	2	0			c.C621T						PASS	.	G		1427,2979	464.9+/-354.0	232,963,1008	85.0	80.0	82.0		621	-1.5	0.1	5	dbSNP_130	82	30,8570	19.2+/-60.6	0,30,4270	no	coding-synonymous	CCDC127	NM_145265.2		232,993,5278	AA,AG,GG		0.3488,32.3877,11.2025		207/261	205574	1457,11549	2203	4300	6503	SO:0001819	synonymous_variant	133957	exon3			GAGACCGGCTGCC	AK098567	CCDS3852.1	5p15.33	2008-02-05			ENSG00000164366	ENSG00000164366			30520	protein-coding gene	gene with protein product						12477932	Standard	NM_145265		Approved	FLJ25701	uc003jam.1	Q96BQ5	OTTHUMG00000161586	ENST00000296824.3:c.621C>T	5.37:g.205574G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_145265		Silent	SNP	ENST00000296824.3	37	CCDS3852.1																																																																																			G|0.900;A|0.100	0.100	strong		0.532	CCDC127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365459.2	NM_145265	
MC5R	4161	hgsc.bcm.edu	37	18	13826139	13826139	+	Silent	SNP	C	C	T	rs45613135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13826139C>T	ENST00000324750.3	+	1	597	c.375C>T	c.(373-375)tcC>tcT	p.S125S	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	125					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|melanocortin receptor activity (GO:0004977)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|upper_aerodigestive_tract(1)	41						TCTGCATTTCCGTGGTGGCAT	0.522													C|||	5	0.000998403	0.0	0.0	5008	,	,		25904	0.0		0.003	False		,,,				2504	0.002				p.S125S		Atlas-SNP	.											.	MC5R	83	.	0			c.C375T						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	139.0	117.0	125.0		375	-6.4	0.9	18	dbSNP_127	125	95,8505	52.7+/-113.3	0,95,4205	no	coding-synonymous	MC5R	NM_005913.2		0,105,6398	TT,TC,CC		1.1047,0.227,0.8073		125/326	13826139	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	4161	exon1			CATTTCCGTGGTG	AY268429	CCDS11868.1	18p11.2	2012-08-10			ENSG00000176136	ENSG00000176136		"""GPCR / Class A : Melanocortin receptors"""	6933	protein-coding gene	gene with protein product		600042				8396929	Standard	NM_005913		Approved		uc010xaf.2	P33032	OTTHUMG00000131720	ENST00000324750.3:c.375C>T	18.37:g.13826139C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	219	97	0.442922	NM_005913	B0YJ34|Q502V1	Silent	SNP	ENST00000324750.3	37	CCDS11868.1																																																																																			C|0.994;T|0.006	0.006	strong		0.522	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913	
RDH8	50700	hgsc.bcm.edu	37	19	10132358	10132358	+	Missense_Mutation	SNP	G	G	A	rs142753796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10132358G>A	ENST00000171214.1	+	6	1118	c.869G>A	c.(868-870)cGc>cAc	p.R290H	RDH8_ENST00000591589.1_Missense_Mutation_p.R310H	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	290					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)	CGCTGTCCACGCCTCCTCAAC	0.607													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17925	0.0		0.0	False		,,,				2504	0.0				p.R310H		Atlas-SNP	.											.	RDH8	51	.	0			c.G929A						PASS	.	G	HIS/ARG	7,4399	12.9+/-30.5	0,7,2196	113.0	108.0	110.0		869	0.6	1.0	19	dbSNP_134	110	0,8600		0,0,4300	yes	missense	RDH8	NM_015725.2	29	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	benign	290/312	10132358	7,12999	2203	4300	6503	SO:0001583	missense	50700	exon6			GTCCACGCCTCCT	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.869G>A	19.37:g.10132358G>A	ENSP00000171214:p.Arg290His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	95	54	0.568421	NM_015725	Q9H838	Missense_Mutation	SNP	ENST00000171214.1	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.22	1.874004	0.33069	0.001589	0.0	ENSG00000080511	ENST00000171214	D	0.82803	-1.65	4.23	0.581	0.17407	.	0.728843	0.13435	N	0.388095	T	0.67059	0.2853	N	0.21142	0.635	0.22142	N	0.999337	B	0.11235	0.004	B	0.06405	0.002	T	0.53322	-0.8455	10	0.33940	T	0.23	.	5.0034	0.14275	0.2203:0.3107:0.469:0.0	.	290	Q9NYR8	RDH8_HUMAN	H	290	ENSP00000171214:R290H	ENSP00000171214:R290H	R	+	2	0	RDH8	9993358	0.044000	0.20184	0.991000	0.47740	0.717000	0.41224	1.418000	0.34782	0.730000	0.32425	0.297000	0.19635	CGC	G|0.999;A|0.001	0.001	strong		0.607	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
MAG	4099	hgsc.bcm.edu	37	19	35790503	35790503	+	Silent	SNP	G	G	A	rs3746248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35790503G>A	ENST00000392213.3	+	5	621	c.462G>A	c.(460-462)gaG>gaA	p.E154E	MAG_ENST00000597035.1_3'UTR|MAG_ENST00000361922.4_Silent_p.E154E|MAG_ENST00000537831.2_Silent_p.E129E	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	154	Ig-like C2-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CAGGCACGGAGGTGGAGGTCA	0.687													g|||	2010	0.401358	0.7617	0.2435	5008	,	,		7953	0.3512		0.2068	False		,,,				2504	0.2781				p.E154E		Atlas-SNP	.											.	MAG	172	.	0			c.G462A						PASS	.		,,	2934,1472	647.8+/-398.6	993,948,262	29.0	31.0	30.0		387,462,462	1.9	1.0	19	dbSNP_107	30	1841,6759	313.9+/-311.6	193,1455,2652	no	coding-synonymous,coding-synonymous,coding-synonymous	MAG	NM_001199216.1,NM_002361.3,NM_080600.2	,,	1186,2403,2914	AA,AG,GG		21.407,33.409,36.7138	,,	129/602,154/627,154/583	35790503	4775,8231	2203	4300	6503	SO:0001819	synonymous_variant	4099	exon5			CACGGAGGTGGAG	M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6783	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 4A"""	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.462G>A	19.37:g.35790503G>A		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	234	105	0.448718	NM_080600	B7Z2E5|F5GYC0|Q567S4	Silent	SNP	ENST00000392213.3	37	CCDS12455.1																																																																																			G|0.616;A|0.384	0.384	strong		0.687	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600	
ATP13A2	23400	hgsc.bcm.edu	37	1	17314702	17314702	+	Silent	SNP	C	C	T	rs3738815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17314702C>T	ENST00000326735.8	-	25	2823	c.2790G>A	c.(2788-2790)tcG>tcA	p.S930S	ATP13A2_ENST00000341676.5_Silent_p.S886S|ATP13A2_ENST00000452699.1_Silent_p.S925S|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2	930					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGACGCTGAACGAAGTGTCAA	0.607													C|||	1457	0.290935	0.1369	0.3429	5008	,	,		21211	0.5774		0.2058	False		,,,				2504	0.2546				p.S930S		Atlas-SNP	.											ATP13A2,NS,carcinoma,-1,1	ATP13A2	85	1	0			c.G2790A						scavenged	.	C	,,	659,3747	280.5+/-275.4	56,547,1600	142.0	127.0	132.0		2775,2658,2790	-11.0	0.0	1	dbSNP_107	132	1657,6943	305.7+/-307.6	145,1367,2788	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	201,1914,4388	TT,TC,CC		19.2674,14.9569,17.8072	,,	925/1176,886/1159,930/1181	17314702	2316,10690	2203	4300	6503	SO:0001819	synonymous_variant	23400	exon25			GCTGAACGAAGTG	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2790G>A	1.37:g.17314702C>T		Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	150	74	0.493333	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			C|0.770;T|0.230	0.230	strong		0.607	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
ASPG	374569	hgsc.bcm.edu	37	14	104559919	104559919	+	Missense_Mutation	SNP	T	T	C	rs1770984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:104559919T>C	ENST00000551177.1	+	3	375	c.283T>C	c.(283-285)Tgc>Cgc	p.C95R	ASPG_ENST00000455920.2_Missense_Mutation_p.C95R|ASPG_ENST00000546892.2_Missense_Mutation_p.C95R	NM_001080464.2	NP_001073933.2	Q86U10	LPP60_HUMAN	asparaginase	95	Asparaginase.|Asparaginase/glutaminase. {ECO:0000255|PROSITE-ProRule:PRU01068}.		C -> R (in dbSNP:rs1770984).		asparagine metabolic process (GO:0006528)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)		1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|asparaginase activity (GO:0004067)|lysophospholipase activity (GO:0004622)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	11						TGAGTGGGTTTGCCTTGCCCA	0.642													C|||	2067	0.41274	0.6823	0.3314	5008	,	,		11380	0.3869		0.1809	False		,,,				2504	0.3712				p.C95R		Atlas-SNP	.											.	ASPG	34	.	0			c.T283C						PASS	.	C	ARG/CYS	2289,1867		605,1079,394	77.0	89.0	85.0		283	2.5	0.7	14	dbSNP_89	85	1424,6954		120,1184,2885	yes	missense	ASPG	NM_001080464.2	180	725,2263,3279	CC,CT,TT		16.9969,44.923,29.6234	benign	95/574	104559919	3713,8821	2078	4189	6267	SO:0001583	missense	374569	exon3			TGGGTTTGCCTTG		CCDS45170.1, CCDS45170.2	14q32.33	2014-03-14	2014-03-14	2008-11-06	ENSG00000166183	ENSG00000166183	3.1.1.5, 3.5.1.1	"""Ankyrin repeat domain containing"""	20123	protein-coding gene	gene with protein product	"""60-kDa-lysophospholipase"""		"""chromosome 14 open reading frame 76"", ""asparaginase homolog (S. cerevisiae)"""	C14orf76			Standard	NM_001080464		Approved		uc001yoq.2	Q86U10		ENST00000551177.1:c.283T>C	14.37:g.104559919T>C	ENSP00000450040:p.Cys95Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_001080464	B9EGQ2|Q8IV80	Missense_Mutation	SNP	ENST00000551177.1	37	CCDS45170.2	870|870	0.3983516483516483|0.3983516483516483	368|368	0.7479674796747967|0.7479674796747967	131|131	0.36187845303867405|0.36187845303867405	230|230	0.4020979020979021|0.4020979020979021	141|141	0.18601583113456466|0.18601583113456466	C|C	0.005|0.005	-2.183746|-2.183746	0.00305|0.00305	0.55077|0.55077	0.169969|0.169969	ENSG00000166183|ENSG00000166183	ENST00000551177;ENST00000299234;ENST00000546892;ENST00000455920|ENST00000551170	T;T;T|.	0.18338|.	2.22;2.22;2.22|.	3.57|3.57	2.46|2.46	0.29980|0.29980	.|.	0.458541|.	0.22121|.	N|.	0.064331|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00462|0.00462	-1.47|-1.47	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0|.	T|T	0.28586|0.28586	-1.0039|-1.0039	9|4	0.02654|.	T|.	1|.	-7.6268|-7.6268	4.4634|4.4634	0.11676|0.11676	0.4411:0.4302:0.0:0.1287|0.4411:0.4302:0.0:0.1287	rs1770984;rs2758759;rs60259119;rs1770984|rs1770984;rs2758759;rs60259119;rs1770984	95;95;95;123|.	G3V1Y8;Q86U10;Q86U10-3;E5RFC2|.	.;LPP60_HUMAN;.;.|.	R|S	95;123;95;95|31	ENSP00000450040:C95R;ENSP00000448911:C95R;ENSP00000389003:C95R|.	ENSP00000299234:C123R|.	C|L	+|+	1|2	0|0	ASPG|ASPG	103629672|103629672	0.000000|0.000000	0.05858|0.05858	0.735000|0.735000	0.30896|0.30896	0.359000|0.359000	0.29487|0.29487	0.723000|0.723000	0.25939|0.25939	0.637000|0.637000	0.30526|0.30526	-0.320000|-0.320000	0.08662|0.08662	TGC|TTG	T|0.635;C|0.365	0.365	strong		0.642	ASPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407005.1	NM_001080464	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25258655	25258655	+	Missense_Mutation	SNP	A	A	G	rs61742723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:25258655A>G	ENST00000328086.7	-	5	1665	c.862T>C	c.(862-864)Tgg>Cgg	p.W288R		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	288	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		CCTAGAGTCCATGGCTCCTTT	0.423													A|||	532	0.10623	0.2481	0.1124	5008	,	,		22162	0.0159		0.0626	False		,,,				2504	0.0481				p.W288R		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.T862C						PASS	.	A	ARG/TRP	938,3456	356.9+/-313.7	106,726,1365	133.0	124.0	127.0		862	5.0	0.2	16	dbSNP_129	127	519,8081	146.8+/-202.3	18,483,3799	yes	missense	ZKSCAN2	NM_001012981.4	101	124,1209,5164	GG,GA,AA		6.0349,21.3473,11.2129	probably-damaging	288/968	25258655	1457,11537	2197	4300	6497	SO:0001583	missense	342357	exon5			GAGTCCATGGCTC	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	25677	protein-coding gene	gene with protein product			"""zinc finger protein 694"""	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.862T>C	16.37:g.25258655A>G	ENSP00000331626:p.Trp288Arg	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	220	0.10073260073260074	128	0.2601626016260163	34	0.09392265193370165	11	0.019230769230769232	47	0.06200527704485488	A	16.45	3.125886	0.56721	0.213473	0.060349	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.12984	2.63	6.06	4.97	0.65823	Krueppel-associated box (2);	0.306645	0.29246	N	0.012715	T	0.00012	0.0000	M	0.79123	2.44	0.31262	P	0.692825	B;P;B	0.43701	0.014;0.815;0.024	B;P;B	0.47430	0.02;0.547;0.02	T	0.21109	-1.0255	9	0.59425	D	0.04	-7.9632	10.3613	0.43996	0.9232:0.0:0.0768:0.0	.	84;288;288	B4DYF0;Q63HK3-2;Q63HK3	.;.;ZKSC2_HUMAN	R	288	ENSP00000331626:W288R	ENSP00000331626:W288R	W	-	1	0	ZKSCAN2	25166156	0.996000	0.38824	0.198000	0.23420	0.737000	0.42083	2.967000	0.49216	1.119000	0.41883	0.533000	0.62120	TGG	A|0.891;G|0.109	0.109	strong		0.423	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
FRMD1	79981	hgsc.bcm.edu	37	6	168457966	168457966	+	Silent	SNP	G	G	A	rs3734899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:168457966G>A	ENST00000283309.6	-	11	1525	c.1461C>T	c.(1459-1461)gaC>gaT	p.D487D	FRMD1_ENST00000440994.2_Silent_p.D419D|FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000537786.1_Silent_p.D258D	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	487						cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		GCTGCATGTCGTCCAGGCCAT	0.672													G|||	1981	0.395567	0.1074	0.353	5008	,	,		17417	0.4871		0.493	False		,,,				2504	0.6207				p.D487D	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.C1461T						PASS	.	G	,	746,3660	296.1+/-284.1	69,608,1526	37.0	34.0	35.0		1257,1461	-5.5	0.0	6	dbSNP_107	35	3924,4676	536.6+/-383.0	877,2170,1253	no	coding-synonymous,coding-synonymous	FRMD1	NM_001122841.1,NM_024919.3	,	946,2778,2779	AA,AG,GG		45.6279,16.9315,35.9065	,	419/482,487/550	168457966	4670,8336	2203	4300	6503	SO:0001819	synonymous_variant	79981	exon11			CATGTCGTCCAGG		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.1461C>T	6.37:g.168457966G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	150	79	0.526667	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Silent	SNP	ENST00000283309.6	37	CCDS5306.1																																																																																			G|0.633;A|0.367	0.367	strong		0.672	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919	
BRSK1	84446	hgsc.bcm.edu	37	19	55823421	55823421	+	Silent	SNP	G	G	C	rs113284733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55823421G>C	ENST00000309383.1	+	19	2599	c.2322G>C	c.(2320-2322)ggG>ggC	p.G774G	BRSK1_ENST00000590333.1_Silent_p.G790G|BRSK1_ENST00000326848.7_Silent_p.G469G|CTD-2105E13.14_ENST00000596786.1_RNA	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	774					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)		CCACCAACGGGACCCCTCTGC	0.706													G|||	16	0.00319489	0.0113	0.0014	5008	,	,		6575	0.0		0.0	False		,,,				2504	0.0				p.G774G		Atlas-SNP	.											.	BRSK1	192	.	0			c.G2322C						PASS	.	G		13,3847		0,13,1917	6.0	7.0	7.0		2322	2.6	1.0	19	dbSNP_132	7	0,7676		0,0,3838	no	coding-synonymous	BRSK1	NM_032430.1		0,13,5755	CC,CG,GG		0.0,0.3368,0.1127		774/779	55823421	13,11523	1930	3838	5768	SO:0001819	synonymous_variant	84446	exon19			CAACGGGACCCCT	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.2322G>C	19.37:g.55823421G>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			G|0.998;C|0.002	0.002	strong		0.706	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
ACTBL2	345651	hgsc.bcm.edu	37	5	56778213	56778213	+	Missense_Mutation	SNP	C	C	T	rs73757391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:56778213C>T	ENST00000423391.1	-	1	423	c.322G>A	c.(322-324)Gag>Aag	p.E108K	CTD-2023N9.1_ENST00000506106.1_RNA|AC025470.1_ENST00000584598.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	108						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(3)|pancreas(1)|prostate(2)	28		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		AGGGGTGCCTCGGTGAGGAGG	0.527													C|||	126	0.0251597	0.0946	0.0014	5008	,	,		23302	0.0		0.0	False		,,,				2504	0.0				p.E108K		Atlas-SNP	.											.	ACTBL2	65	.	0			c.G322A						PASS	.	C	LYS/GLU	340,4066	179.0+/-207.6	20,300,1883	105.0	89.0	95.0		322	4.0	0.9	5	dbSNP_130	95	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ACTBL2	NM_001017992.2	56	20,302,6181	TT,TC,CC		0.0233,7.7167,2.6296	possibly-damaging	108/377	56778213	342,12664	2203	4300	6503	SO:0001583	missense	345651	exon1			GTGCCTCGGTGAG		CCDS34163.1	5q11.2	2014-08-08			ENSG00000169067	ENSG00000169067			17780	protein-coding gene	gene with protein product		614835					Standard	NM_001017992		Approved	DKFZp686D0972	uc003jrm.3	Q562R1	OTTHUMG00000162330	ENST00000423391.1:c.322G>A	5.37:g.56778213C>T	ENSP00000416706:p.Glu108Lys	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	187	99	0.529412	NM_001017992	B2RPJ1|Q562R2|Q562S9|Q562X8	Missense_Mutation	SNP	ENST00000423391.1	37	CCDS34163.1	45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	C	13.74	2.327453	0.41197	0.077167	2.33E-4	ENSG00000169067	ENST00000423391	D	0.96940	-4.18	4.91	4.04	0.47022	Actin/actin-like conserved site (1);	0.000000	0.64402	D	0.000005	D	0.82774	0.5110	H	0.98295	4.195	0.48762	D	0.999703	D	0.89917	1.0	D	0.78314	0.991	T	0.76862	-0.2802	10	0.87932	D	0	.	11.3815	0.49761	0.0:0.9109:0.0:0.0891	.	108	Q562R1	ACTBL_HUMAN	K	108	ENSP00000416706:E108K	ENSP00000416706:E108K	E	-	1	0	ACTBL2	56813970	1.000000	0.71417	0.920000	0.36463	0.468000	0.32798	5.904000	0.69886	1.279000	0.44446	0.655000	0.94253	GAG	C|0.973;T|0.027	0.027	strong		0.527	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1	NM_001017992	
KLK6	5653	hgsc.bcm.edu	37	19	51465096	51465096	+	Silent	SNP	C	C	G	rs1701950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51465096C>G	ENST00000376851.3	-	5	925	c.486G>C	c.(484-486)ctG>ctC	p.L162L	KLK6_ENST00000456750.2_Silent_p.L55L|KLK6_ENST00000310157.2_Silent_p.L162L|CTB-147C22.8_ENST00000601506.1_RNA|KLK6_ENST00000376853.4_Intron|KLK6_ENST00000391808.1_Silent_p.L55L|KLK6_ENST00000594641.1_Silent_p.L162L	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	162	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		CACGGGACACCAGGTGGATGT	0.577													C|||	408	0.0814696	0.1853	0.049	5008	,	,		19122	0.0		0.1024	False		,,,				2504	0.0266				p.L162L		Atlas-SNP	.											.	KLK6	35	.	0			c.G486C						PASS	.		,,	739,3667		59,621,1523	156.0	120.0	132.0		486,165,486	2.0	1.0	19	dbSNP_89	132	883,7717		45,793,3462	no	coding-synonymous,coding-synonymous,coding-synonymous	KLK6	NM_001012964.1,NM_001012965.1,NM_002774.3	,,	104,1414,4985	GG,GC,CC		10.2674,16.7726,12.4712	,,	162/245,55/138,162/245	51465096	1622,11384	2203	4300	6503	SO:0001819	synonymous_variant	5653	exon5			GGACACCAGGTGG	U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6367	protein-coding gene	gene with protein product		602652	"""protease, serine, 18"", ""kallikrein 6 (neurosin, zyme)"""	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.486G>C	19.37:g.51465096C>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_001012964	A6NJA1|A8MW09|Q6H301	Silent	SNP	ENST00000376851.3	37	CCDS12811.1																																																																																			C|0.883;G|0.117	0.117	strong		0.577	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774	
RNF207	388591	hgsc.bcm.edu	37	1	6269340	6269340	+	Silent	SNP	A	A	G	rs4908865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6269340A>G	ENST00000377939.4	+	6	691	c.564A>G	c.(562-564)gcA>gcG	p.A188A	RNF207_ENST00000377948.2_5'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	188						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		AGAGCCGGGCACACTGCGTGG	0.746													G|||	721	0.14397	0.3011	0.0793	5008	,	,		10697	0.0813		0.0755	False		,,,				2504	0.1125				p.A188A		Atlas-SNP	.											.	RNF207	45	.	0			c.A564G						PASS	.	G		718,2718		65,588,1065	6.0	6.0	6.0		564	-4.8	0.6	1	dbSNP_111	6	391,7075		10,371,3352	no	coding-synonymous	RNF207	NM_207396.2		75,959,4417	GG,GA,AA		5.2371,20.8964,10.1724		188/635	6269340	1109,9793	1718	3733	5451	SO:0001819	synonymous_variant	388591	exon6			CCGGGCACACTGC	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.564A>G	1.37:g.6269340A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	37	10	0.27027	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Silent	SNP	ENST00000377939.4	37	CCDS59.2																																																																																			A|0.848;G|0.152	0.152	strong		0.746	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
OR10G9	219870	hgsc.bcm.edu	37	11	123894317	123894317	+	Missense_Mutation	SNP	G	G	T	rs77206991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123894317G>T	ENST00000375024.1	+	1	598	c.598G>T	c.(598-600)Gtg>Ttg	p.V200L		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V200L(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)		GGTCATCTTTGTGGACATTGG	0.547													T|||	436	0.0870607	0.1059	0.1556	5008	,	,		21948	0.1438		0.007	False		,,,				2504	0.0368				p.V200L		Atlas-SNP	.											OR10G9,NS,carcinoma,0,1	OR10G9	80	1	1	Substitution - Missense(1)	stomach(1)	c.G598T						PASS	.	T	LEU/VAL	399,4003	200.8+/-224.0	19,361,1821	259.0	228.0	238.0		598	2.6	0.7	11	dbSNP_131	238	30,8568	20.4+/-63.3	0,30,4269	yes	missense	OR10G9	NM_001001953.1	32	19,391,6090	TT,TG,GG		0.3489,9.0641,3.3	benign	200/312	123894317	429,12571	2201	4299	6500	SO:0001583	missense	219870	exon1			ATCTTTGTGGACA	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.598G>T	11.37:g.123894317G>T	ENSP00000364164:p.Val200Leu	Somatic	488	2	0.00409836		WXS	Illumina HiSeq	Phase_I	518	288	0.555985	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	213	0.09752747252747253	59	0.11991869918699187	66	0.18232044198895028	82	0.14335664335664336	6	0.0079155672823219	g	8.076	0.771331	0.16051	0.090641	0.003489	ENSG00000236981	ENST00000375024	T	0.00193	8.58	3.48	2.57	0.30868	GPCR, rhodopsin-like superfamily (1);	0.166261	0.28072	N	0.016712	T	0.00012	0.0000	L	0.38838	1.175	0.47905	P	4.6000000000001595E-4	B	0.06786	0.001	B	0.12837	0.008	T	0.37641	-0.9697	9	0.66056	D	0.02	.	11.3769	0.49733	0.0:0.0:0.8166:0.1834	.	200	Q8NGN4	O10G9_HUMAN	L	200	ENSP00000364164:V200L	ENSP00000364164:V200L	V	+	1	0	OR10G9	123399527	0.000000	0.05858	0.662000	0.29724	0.190000	0.23558	-1.075000	0.03423	0.807000	0.34208	-0.121000	0.15023	GTG	G|0.950;T|0.050	0.050	strong		0.547	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
CFAP57	149465	hgsc.bcm.edu	37	1	43649393	43649393	+	Silent	SNP	T	T	C	rs663336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43649393T>C	ENST00000372492.4	+	4	930	c.606T>C	c.(604-606)gcT>gcC	p.A202A	WDR65_ENST00000528956.1_Silent_p.A202A	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		202										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				ACTATCTAGCTCACACCTGGG	0.493													C|||	1322	0.263978	0.3949	0.2637	5008	,	,		18592	0.3185		0.0666	False		,,,				2504	0.2342				p.A202A		Atlas-SNP	.											.	WDR65	76	.	0			c.T606C						PASS	.	C	,,	1611,2795	663.1+/-401.2	290,1031,882	110.0	107.0	108.0		606,606,606	0.5	1.0	1	dbSNP_83	108	662,7938	789.2+/-407.6	32,598,3670	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	322,1629,4552	CC,CT,TT		7.6977,36.5638,17.4765	,,	202/699,202/699,202/699	43649393	2273,10733	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon4			TCTAGCTCACACC																												ENST00000372492.4:c.606T>C	1.37:g.43649393T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	162	72	0.444444	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				T|0.801;C|0.199	0.199	strong		0.493	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
CXorf36	79742	hgsc.bcm.edu	37	X	45059838	45059838	+	Splice_Site	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:45059838C>A	ENST00000398000.2	-	1	308		c.e1+1		RP11-342D14.1_ENST00000438181.1_RNA|CXorf36_ENST00000377934.4_Splice_Site|RP11-342D14.1_ENST00000450527.1_RNA	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36							extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						GATATTCTGACCTTATTTCTT	0.368																																					.		Atlas-SNP	.											.	CXorf36	53	.	0			c.233+1G>T						PASS	.						45.0	43.0	43.0					X																	45059838		2203	4299	6502	SO:0001630	splice_region_variant	79742	exon2			TTCTGACCTTATT	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.233+1G>T	X.37:g.45059838C>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Splice_Site	SNP	ENST00000398000.2	37	CCDS48096.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.340498	0.60963	.	.	ENSG00000147113	ENST00000398000;ENST00000377934	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7275	0.77774	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CXorf36	44944782	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.738000	0.68613	2.074000	0.62210	0.415000	0.27848	.	.	.	none		0.368	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689	Intron
WDR49	151790	hgsc.bcm.edu	37	3	167217964	167217964	+	Missense_Mutation	SNP	A	A	G	rs13060964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:167217964A>G	ENST00000308378.3	-	14	2257	c.1952T>C	c.(1951-1953)cTg>cCg	p.L651P	WDR49_ENST00000479765.1_Intron|WDR49_ENST00000453925.2_Missense_Mutation_p.L616P|WDR49_ENST00000476376.1_Missense_Mutation_p.L476P	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	77	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	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	
SPIRE2	84501	hgsc.bcm.edu	37	16	89927102	89927102	+	Missense_Mutation	SNP	G	G	A	rs28478911		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89927102G>A	ENST00000378247.3	+	10	1517	c.1474G>A	c.(1474-1476)Gcg>Acg	p.A492T	SPIRE2_ENST00000393062.2_Missense_Mutation_p.A492T	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	492					actin cytoskeleton organization (GO:0030036)|cleavage furrow formation (GO:0036089)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|intracellular transport (GO:0046907)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		TACCTGTCCCGCGAGTGTCTC	0.642											OREG0024056	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0008	0.0	5008	,	,		14998	0.0		0.0	False		,,,				2504	0.0				p.A492T		Atlas-SNP	.											SPIRE2,colon,carcinoma,-1,1	SPIRE2	63	1	0			c.G1474A						PASS	.	G	THR/ALA	3,4371		0,3,2184	29.0	28.0	28.0		1474	1.9	0.0	16	dbSNP_125	28	0,8572		0,0,4286	no	missense	SPIRE2	NM_032451.1	58	0,3,6470	AA,AG,GG		0.0,0.0686,0.0232	benign	492/715	89927102	3,12943	2187	4286	6473	SO:0001583	missense	84501	exon10			TGTCCCGCGAGTG	AL834408	CCDS32516.1	16q24	2013-08-27	2013-08-27			ENSG00000204991			30623	protein-coding gene	gene with protein product		609217	"""spire homolog 2 (Drosophila)"", ""spire family actin nucleation factor 2"""			11347906	Standard	NM_032451		Approved	spir-2, KIAA1832	uc002foz.1	Q8WWL2		ENST00000378247.3:c.1474G>A	16.37:g.89927102G>A	ENSP00000367494:p.Ala492Thr	Somatic	67	0	0	1271	WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_032451	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Missense_Mutation	SNP	ENST00000378247.3	37	CCDS32516.1	.	.	.	.	.	.	.	.	.	.	G	6.872	0.530358	0.13127	6.86E-4	0.0	ENSG00000204991	ENST00000378247;ENST00000393062	T;T	0.43688	0.95;0.94	5.08	1.87	0.25490	.	0.915637	0.09208	N	0.833668	T	0.25382	0.0617	N	0.22421	0.69	0.09310	N	0.999999	B;B;B;B	0.15719	0.001;0.014;0.008;0.001	B;B;B;B	0.10450	0.001;0.005;0.002;0.001	T	0.27571	-1.0070	10	0.15066	T	0.55	-9.4382	6.2595	0.20891	0.1685:0.1545:0.6769:0.0	rs28478911	359;492;444;492	Q8WWL2-4;Q8WWL2-2;Q8WWL2-3;Q8WWL2	.;.;.;SPIR2_HUMAN	T	492	ENSP00000367494:A492T;ENSP00000376782:A492T	ENSP00000367494:A492T	A	+	1	0	SPIRE2	88454603	0.002000	0.14202	0.001000	0.08648	0.000000	0.00434	1.200000	0.32247	0.668000	0.31126	-0.794000	0.03295	GCG	G|1.000;|0.000	.	weak		0.642	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462	
C2CD3	26005	hgsc.bcm.edu	37	11	73759251	73759251	+	Splice_Site	SNP	T	T	C	rs1632242|rs200356969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73759251T>C	ENST00000334126.7	-	28	5720	c.5494A>G	c.(5494-5496)Aga>Gga	p.R1832G	C2CD3_ENST00000313663.7_Splice_Site_p.R1832G			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1832			R -> G (in dbSNP:rs1632242).		brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TTCACTCACCTCCCAGGAGAG	0.438													T|||	243	0.0485224	0.1778	0.0115	5008	,	,		19079	0.0		0.0	False		,,,				2504	0.0				p.R1832G		Atlas-SNP	.											.	C2CD3	288	.	0			c.A5494G						PASS	.						56.0	52.0	53.0					11																	73759251		2200	4293	6493	SO:0001630	splice_region_variant	26005	exon28			CTCACCTCCCAGG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.5495+1A>G	11.37:g.73759251T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		76|76	0.0347985347985348|0.0347985347985348	71|71	0.1443089430894309|0.1443089430894309	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	T|T	11.88|11.88	1.770709|1.770709	0.31320|0.31320	.|.	.|.	ENSG00000168014|ENSG00000168014	ENST00000538361|ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	.|T;T;T	.|0.15952	.|2.73;2.77;2.38	4.75|4.75	4.75|4.75	0.60458|0.60458	.|.	.|0.440230	.|0.27172	.|N	.|0.020590	T|T	0.00144|0.00144	0.0004|0.0004	M|M	0.72894|0.72894	2.215|2.215	0.34135|0.34135	P|P	0.334317|0.334317	.|P	.|0.35272	.|0.493	.|B	.|0.33620	.|0.167	T|T	0.09292|0.09292	-1.0681|-1.0681	4|9	.|0.44086	.|T	.|0.13	-5.0634|-5.0634	10.8098|10.8098	0.46540|0.46540	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs1632242;rs52837313;rs1632242|rs1632242;rs52837313;rs1632242	.|1832	.|Q4AC94-1	.|.	G|G	65|1832;1832;1813;640	.|ENSP00000334379:R1832G;ENSP00000323339:R1832G;ENSP00000388750:R640G	.|ENSP00000323339:R1832G	E|R	-|-	2|1	0|2	C2CD3|C2CD3	73436899|73436899	0.997000|0.997000	0.39634|0.39634	0.981000|0.981000	0.43875|0.43875	0.172000|0.172000	0.22775|0.22775	2.829000|2.829000	0.48128|0.48128	2.114000|2.114000	0.64651|0.64651	0.533000|0.533000	0.62120|0.62120	GAG|AGA	T|0.962;C|0.038	0.038	strong		0.438	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	Missense_Mutation
PCDHGA9	56107	hgsc.bcm.edu	37	5	140784427	140784427	+	Silent	SNP	T	T	C	rs3749769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140784427T>C	ENST00000573521.1	+	1	1908	c.1908T>C	c.(1906-1908)gaT>gaC	p.D636D	PCDHGA8_ENST00000398604.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	636	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAGATAGAGATGCGCTCAAAC	0.612													.|||	644	0.128594	0.177	0.1527	5008	,	,		20005	0.1181		0.0586	False		,,,				2504	0.1288				p.D636D		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.T1908C						PASS	.	T	,,,,,,,,,,,,,,	784,3586		74,636,1475	40.0	47.0	45.0		,,,,,,,,1908,,,,,,1908	-10.6	0.0	5	dbSNP_107	45	644,7946		26,592,3677	no	intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032089.1	,,,,,,,,,,,,,,	100,1228,5152	CC,CT,TT		7.4971,17.9405,11.0185	,,,,,,,,,,,,,,	,,,,,,,,636/933,,,,,,636/829	140784427	1428,11532	2185	4295	6480	SO:0001819	synonymous_variant	56107	exon1			TAGAGATGCGCTC	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.1908T>C	5.37:g.140784427T>C		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	238	110	0.462185	NM_032089	A2RU65|Q9Y5C9	Silent	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			T|0.875;C|0.125	0.125	strong		0.612	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33541216	33541216	+	Missense_Mutation	SNP	G	G	C	rs111814125		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.																																			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	303	0	0		WXS	Illumina HiSeq	Phase_I	388	62	0.159794	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	
OR52E6	390078	hgsc.bcm.edu	37	11	5862653	5862653	+	Missense_Mutation	SNP	T	T	C	rs4357719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5862653T>C	ENST00000329322.5	-	1	474	c.475A>G	c.(475-477)Att>Gtt	p.I159V	OR52E6_ENST00000379946.2_Missense_Mutation_p.I163V|TRIM5_ENST00000380027.1_Intron	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	136	0	0		WXS	Illumina HiSeq	Phase_I	174	87	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	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	
KIRREL3	84623	hgsc.bcm.edu	37	11	126294661	126294661	+	Silent	SNP	G	G	A	rs34844660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:126294661G>A	ENST00000525144.2	-	17	2400	c.2151C>T	c.(2149-2151)agC>agT	p.S717S	KIRREL3_ENST00000416561.2_Silent_p.S184S|KIRREL3_ENST00000529097.2_Silent_p.S705S	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	717	Ser-rich.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AGCTGCTGTCGCTGAGGGAGC	0.627													G|||	69	0.013778	0.0514	0.0014	5008	,	,		19048	0.0		0.0	False		,,,				2504	0.0				p.S717S		Atlas-SNP	.											.	KIRREL3	183	.	0			c.C2151T						PASS	.	G		148,4198		0,148,2025	74.0	82.0	79.0		2151	4.0	1.0	11	dbSNP_126	79	0,8562		0,0,4281	no	coding-synonymous	KIRREL3	NM_032531.3		0,148,6306	AA,AG,GG		0.0,3.4054,1.1466		717/779	126294661	148,12760	2173	4281	6454	SO:0001819	synonymous_variant	84623	exon17			GCTGTCGCTGAGG	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.2151C>T	11.37:g.126294661G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	54	0.495413	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Silent	SNP	ENST00000525144.2	37	CCDS53723.1																																																																																			G|0.992;A|0.008	0.008	strong		0.627	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531	
DNAH17	8632	hgsc.bcm.edu	37	17	76570924	76570924	+	Silent	SNP	G	G	A	rs61745225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76570924G>A	ENST00000585328.1	-	2	340	c.216C>T	c.(214-216)ctC>ctT	p.L72L	DNAH17_ENST00000389840.5_Silent_p.L72L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	72	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)			CTTTGGACTTGAGGGACTGGG	0.557													G|||	358	0.0714856	0.2496	0.0375	5008	,	,		17437	0.0		0.002	False		,,,				2504	0.0				p.L72L		Atlas-SNP	.											.	DNAH17	347	.	0			c.C216T						PASS	.	G		781,3257		77,627,1315	118.0	126.0	123.0		216	4.1	1.0	17	dbSNP_129	123	15,8343		0,15,4164	no	coding-synonymous	DNAH17	NM_173628.3		77,642,5479	AA,AG,GG		0.1795,19.3413,6.4214		72/4463	76570924	796,11600	2019	4179	6198	SO:0001819	synonymous_variant	8632	exon2			GGACTTGAGGGAC	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.216C>T	17.37:g.76570924G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	205	85	0.414634	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.948;A|0.052	0.052	strong		0.557	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
YY1AP1	55249	hgsc.bcm.edu	37	1	155658085	155658085	+	Intron	SNP	T	T	C	rs2666826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155658085T>C	ENST00000295566.4	-	2	71				YY1AP1_ENST00000404643.1_Intron|DAP3_ENST00000421487.2_5'Flank|YY1AP1_ENST00000368330.2_Intron|DAP3_ENST00000368336.5_5'Flank|YY1AP1_ENST00000311573.5_5'UTR|YY1AP1_ENST00000361831.5_Intron|DAP3_ENST00000343043.3_5'Flank|DAP3_ENST00000471642.2_Intron|YY1AP1_ENST00000368339.5_Silent_p.E57E|YY1AP1_ENST00000476093.1_Intron|DAP3_ENST00000465375.1_5'Flank|YY1AP1_ENST00000359205.5_Intron|DAP3_ENST00000535183.1_5'Flank|YY1AP1_ENST00000407221.1_Intron|YY1AP1_ENST00000355499.4_Intron|YY1AP1_ENST00000438245.2_5'UTR|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000405763.3_Silent_p.E57E|YY1AP1_ENST00000368340.5_Silent_p.E57E|YY1AP1_ENST00000347088.5_Intron|MSTO1_ENST00000452804.2_Intron	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1						regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					CTGGGATCGTTTCCCCTCGCA	0.637													.|||	2662	0.53155	0.8041	0.3631	5008	,	,		15905	0.6855		0.2972	False		,,,				2504	0.365				p.E57E		Atlas-SNP	.											YY1AP1_ENST00000368339,NS,carcinoma,0,1	YY1AP1	104	1	0			c.A171G						PASS	.																																			SO:0001627	intron_variant	55249	exon1			GATCGTTTCCCCT	BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.48-93A>G	1.37:g.155658085T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001198904	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Silent	SNP	ENST00000295566.4	37	CCDS1115.1																																																																																			T|0.472;C|0.528	0.528	strong		0.637	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118	
BSN	8927	hgsc.bcm.edu	37	3	49690496	49690496	+	Silent	SNP	C	C	T	rs11709525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49690496C>T	ENST00000296452.4	+	5	3621	c.3507C>T	c.(3505-3507)tcC>tcT	p.S1169S		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1169					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		AGACACCCTCCGGCAGCTCCA	0.602													C|||	1039	0.207468	0.2632	0.1657	5008	,	,		19657	0.0565		0.3241	False		,,,				2504	0.1973				p.S1169S		Atlas-SNP	.											BSN,NS,carcinoma,0,1	BSN	272	1	0			c.C3507T						PASS	.	C		1179,3227	381.6+/-324.1	150,879,1174	33.0	35.0	35.0		3507	-9.8	0.0	3	dbSNP_120	35	2556,6044	384.5+/-341.1	405,1746,2149	no	coding-synonymous	BSN	NM_003458.3		555,2625,3323	TT,TC,CC		29.7209,26.759,28.7175		1169/3927	49690496	3735,9271	2203	4300	6503	SO:0001819	synonymous_variant	8927	exon5			ACCCTCCGGCAGC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3507C>T	3.37:g.49690496C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			C|0.731;G|0.000;T|0.269	0.269	strong		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
OR9K2	441639	hgsc.bcm.edu	37	12	55524172	55524172	+	Missense_Mutation	SNP	G	G	A	rs7306491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55524172G>A	ENST00000305377.5	+	1	708	c.620G>A	c.(619-621)cGc>cAc	p.R207H		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	207			R -> H (in dbSNP:rs7306491).			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						TGTGATTCTCGCCCACTTCAG	0.358													G|||	1521	0.303714	0.4062	0.2435	5008	,	,		21809	0.1141		0.334	False		,,,				2504	0.3722				p.R207H		Atlas-SNP	.											.	OR9K2	63	.	0			c.G620A						PASS	.	G	HIS/ARG	1696,2710	512.4+/-368.1	304,1088,811	133.0	124.0	127.0		620	4.1	0.1	12	dbSNP_116	127	2777,5823	440.7+/-359.6	456,1865,1979	yes	missense	OR9K2	NM_001005243.1	29	760,2953,2790	AA,AG,GG		32.2907,38.493,34.3918	benign	207/336	55524172	4473,8533	2203	4300	6503	SO:0001583	missense	441639	exon1			ATTCTCGCCCACT	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.620G>A	12.37:g.55524172G>A	ENSP00000307598:p.Arg207His	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	156	85	0.544872	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	37	CCDS31814.1	622	0.2847985347985348	198	0.4024390243902439	102	0.281767955801105	73	0.12762237762237763	249	0.32849604221635886	G	7.087	0.571398	0.13623	0.38493	0.322907	ENSG00000170605	ENST00000305377	T	0.00123	8.7	4.98	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.140643	0.34133	N	0.004231	T	0.00012	0.0000	N	0.02345	-0.59	0.58432	P	4.000000000004E-6	B	0.14805	0.011	B	0.18263	0.021	T	0.03566	-1.1024	9	0.66056	D	0.02	-9.1617	8.3649	0.32380	0.0866:0.2652:0.6482:0.0	rs7306491;rs52802498;rs59789791;rs7306491	207	Q8NGE7	OR9K2_HUMAN	H	207	ENSP00000307598:R207H	ENSP00000307598:R207H	R	+	2	0	OR9K2	53810439	0.000000	0.05858	0.085000	0.20634	0.302000	0.27658	-0.020000	0.12525	1.466000	0.48025	0.650000	0.86243	CGC	G|0.681;A|0.319	0.319	strong		0.358	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
NFASC	23114	hgsc.bcm.edu	37	1	204939763	204939763	+	Silent	SNP	C	C	T	rs6690894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204939763C>T	ENST00000401399.1	+	10	1222	c.1023C>T	c.(1021-1023)gaC>gaT	p.D341D	NFASC_ENST00000339876.6_Silent_p.D341D|NFASC_ENST00000367172.4_Silent_p.D341D|NFASC_ENST00000367169.4_Silent_p.D341D|NFASC_ENST00000360049.4_Silent_p.D352D|NFASC_ENST00000338515.6_Silent_p.D341D|NFASC_ENST00000338586.6_Silent_p.D341D|NFASC_ENST00000404076.1_Silent_p.D335D|NFASC_ENST00000404907.1_Silent_p.D352D|NFASC_ENST00000539706.1_Silent_p.D352D|NFASC_ENST00000367171.4_Silent_p.D341D|NFASC_ENST00000513543.1_Silent_p.D352D|NFASC_ENST00000403080.1_Silent_p.D341D|NFASC_ENST00000367170.4_Silent_p.D341D			O94856	NFASC_HUMAN	neurofascin	341	Ig-like C2-type 4.				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)			ACTGGCTGGACGAACCCAAGA	0.552													C|||	104	0.0207668	0.0764	0.0029	5008	,	,		18345	0.0		0.0	False		,,,				2504	0.001				p.D352D		Atlas-SNP	.											.	NFASC	396	.	0			c.C1056T						PASS	.	C	,,,,,	288,4118	158.9+/-191.5	13,262,1928	87.0	76.0	80.0		1023,1023,1056,1056,1005,1056	-8.8	0.4	1	dbSNP_116	80	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFASC	NM_001005388.2,NM_001005389.1,NM_001160331.1,NM_001160332.1,NM_001160333.1,NM_015090.3	,,,,,	13,263,6227	TT,TC,CC		0.0116,6.5365,2.2221	,,,,,	341/1241,341/620,352/1190,352/1175,335/614,352/1170	204939763	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	23114	exon11			GCTGGACGAACCC	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.1023C>T	1.37:g.204939763C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	131	60	0.458015	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	C	8.636	0.894786	0.17613	0.065365	1.16E-4	ENSG00000163531	ENST00000367173	.	.	.	5.64	-8.77	0.00827	.	.	.	.	.	T	0.12475	0.0303	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68655	-0.5351	4	.	.	.	.	17.7033	0.88301	0.0:0.1936:0.0:0.8064	rs6690894;rs6690894	.	.	.	M	311	.	.	T	+	2	0	NFASC	203206386	0.189000	0.23263	0.369000	0.25952	0.985000	0.73830	-0.441000	0.06879	-2.495000	0.00514	-0.797000	0.03246	ACG	C|0.974;T|0.026	0.026	strong		0.552	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
ZNF212	7988	hgsc.bcm.edu	37	7	148947564	148947564	+	Silent	SNP	C	C	T	rs138413836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:148947564C>T	ENST00000335870.2	+	2	467	c.339C>T	c.(337-339)aaC>aaT	p.N113N		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	113					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)			GGCTGGAGAACGTGGAGAACC	0.617													C|||	13	0.00259585	0.0091	0.0014	5008	,	,		15049	0.0		0.0	False		,,,				2504	0.0				p.N113N		Atlas-SNP	.											.	ZNF212	28	.	0			c.C339T						PASS	.	C		33,4373	37.6+/-69.7	0,33,2170	68.0	83.0	78.0		339	3.2	1.0	7	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous	ZNF212	NM_012256.3		0,33,6470	TT,TC,CC		0.0,0.749,0.2537		113/496	148947564	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	7988	exon2			GGAGAACGTGGAG	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.339C>T	7.37:g.148947564C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	104	59	0.567308	NM_012256	B2RCF4|Q13396|Q8N664	Silent	SNP	ENST00000335870.2	37	CCDS5896.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.867	1.197790	0.22037	0.00749	0.0	ENSG00000170260	ENST00000481584	.	.	.	5.95	3.17	0.36434	.	.	.	.	.	T	0.49115	0.1538	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44922	-0.9296	4	.	.	.	-30.1409	7.8161	0.29260	0.0:0.7392:0.0:0.2608	.	.	.	.	C	11	.	.	R	+	1	0	ZNF212	148578497	0.992000	0.36948	1.000000	0.80357	0.983000	0.72400	1.139000	0.31504	0.412000	0.25729	-0.222000	0.12452	CGT	C|0.999;T|0.001	0.001	strong		0.617	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037522	33037522	+	Missense_Mutation	SNP	T	T	C	rs1042178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33037522T>C	ENST00000419277.1	-	3	371	c.242A>G	c.(241-243)cAa>cGa	p.Q81R	HLA-DPA1_ENST00000463066.1_5'UTR|HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.Q81R	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	81	Alpha-1.		Q -> R (in allele DPA1*01:08, allele DPA1*02:01, allele DPA1*02:02, allele DPA1*02:03, allele DPA1*02:04 and allele DPA1*04:01; dbSNP:rs1042178).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						GGAAAAGGCTTGGCCAAACTC	0.478													.|||	2196	0.438498	0.5809	0.281	5008	,	,		19699	0.6796		0.1869	False		,,,				2504	0.3681				p.Q81R		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.A242G						PASS	.	C	ARG/GLN,ARG/GLN,ARG/GLN	1412,1610		328,756,427	85.0	96.0	92.0		242,242,242	-4.5	0.0	6	dbSNP_86	92	953,4465		72,809,1828	no	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	43,43,43	400,1565,2255	CC,CT,TT		17.5895,46.724,28.0213	benign,benign,benign	81/261,81/261,81/261	33037522	2365,6075	1511	2709	4220	SO:0001583	missense	3113	exon2			AAGGCTTGGCCAA	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.242A>G	6.37:g.33037522T>C	ENSP00000393566:p.Gln81Arg	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	127	124	0.976378	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	862	0.3946886446886447	276	0.5609756097560976	87	0.24033149171270718	371	0.6486013986013986	128	0.16886543535620052	C	0.008	-1.876631	0.00537	0.46724	0.175895	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.00717	5.79;5.79;5.79	3.0	-4.48	0.03515	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	0.767258	0.11484	N	0.559428	T	0.00144	0.0004	N	0.04705	-0.18	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24190	-1.0167	9	0.05525	T	0.97	.	13.2798	0.60208	0.0:0.1377:0.0:0.8623	rs1042178;rs2308915;rs3173302;rs16868557;rs16868559;rs45614833;rs52792876;rs60098014;rs1042178	81	P20036	DPA1_HUMAN	R	81	ENSP00000393566:Q81R;ENSP00000402872:Q81R;ENSP00000390929:Q81R	ENSP00000393566:Q81R	Q	-	2	0	HLA-DPA1	33145500	0.000000	0.05858	0.000000	0.03702	0.683000	0.39861	-3.957000	0.00325	-1.675000	0.01459	-1.124000	0.02001	CAA	T|0.688;C|0.310	0.310	strong		0.478	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
RBM12	10137	hgsc.bcm.edu	37	20	34241530	34241530	+	Missense_Mutation	SNP	T	T	C	rs17092928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34241530T>C	ENST00000374114.3	-	3	1978	c.1715A>G	c.(1714-1716)aAt>aGt	p.N572S	CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000352393.4_Intron|RBM12_ENST00000359646.1_Missense_Mutation_p.N572S|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317677.5_5'UTR|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397443.1_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.N572S|CPNE1_ENST00000317619.3_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	572			N -> S (in dbSNP:rs17092928).			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)			ATGTACAGCATTTTCATCCAC	0.408													T|||	124	0.0247604	0.09	0.0072	5008	,	,		22183	0.0		0.0	False		,,,				2504	0.0				p.N572S		Atlas-SNP	.											.	RBM12	93	.	0			c.A1715G						PASS	.	T	SER/ASN,SER/ASN,,,SER/ASN,SER/ASN,,,,	267,4139	150.7+/-184.7	3,261,1939	194.0	187.0	189.0		1715,1715,,,1715,1715,,,,	3.7	1.0	20	dbSNP_123	189	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,intron,utr-5,missense,missense,intron,intron,intron,intron	CPNE1,RBM12	NM_001198838.1,NM_001198840.1,NM_001198863.1,NM_003915.5,NM_006047.5,NM_152838.3,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	46,46,,,46,46,,,,	3,265,6235	CC,CT,TT		0.0465,6.0599,2.0837	benign,benign,,,benign,benign,,,,	572/933,572/933,,,572/933,572/933,,,,	34241530	271,12735	2203	4300	6503	SO:0001583	missense	10137	exon2			ACAGCATTTTCAT	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.1715A>G	20.37:g.34241530T>C	ENSP00000363228:p.Asn572Ser	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	148	78	0.527027	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	37	CCDS13261.1	48	0.02197802197802198	43	0.08739837398373984	5	0.013812154696132596	0	0.0	0	0.0	T	8.105	0.777613	0.16120	0.060599	4.65E-4	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	T;T;T	0.15487	2.42;2.42;2.42	4.83	3.69	0.42338	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.200400	0.42682	N	0.000670	T	0.00496	0.0016	L	0.38175	1.15	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17289	-1.0374	10	0.37606	T	0.19	-5.5476	10.7607	0.46264	0.0:0.0756:0.0:0.9244	rs17092928;rs52836153;rs17092928	572	Q9NTZ6	RBM12_HUMAN	S	572;572;572;371	ENSP00000363228:N572S;ENSP00000352668:N572S;ENSP00000363217:N572S	ENSP00000339879:N371S	N	-	2	0	RBM12	33704944	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.686000	0.61700	0.827000	0.34685	0.460000	0.39030	AAT	T|0.978;C|0.022	0.022	strong		0.408	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047	
ZNF217	7764	hgsc.bcm.edu	37	20	52192308	52192308	+	Missense_Mutation	SNP	A	A	C	rs61758384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52192308A>C	ENST00000371471.2	-	4	3420	c.2995T>G	c.(2995-2997)Tgt>Ggt	p.C999G	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.C999G			O75362	ZN217_HUMAN	zinc finger protein 217	999					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)			GCAGGCACACAAGTGTAAAGT	0.527													A|||	51	0.0101837	0.0356	0.0058	5008	,	,		21128	0.0		0.0	False		,,,				2504	0.0				p.C999G		Atlas-SNP	.											ZNF217,NS,carcinoma,+1,1	ZNF217	227	1	0			c.T2995G						PASS	.	A	GLY/CYS	187,4219	116.3+/-154.2	1,185,2017	61.0	58.0	59.0		2995	4.8	0.0	20	dbSNP_129	59	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZNF217	NM_006526.2	159	1,187,6315	CC,CA,AA		0.0233,4.2442,1.4532	possibly-damaging	999/1049	52192308	189,12817	2203	4300	6503	SO:0001583	missense	7764	exon3			GCACACAAGTGTA	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.2995T>G	20.37:g.52192308A>C	ENSP00000360526:p.Cys999Gly	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	A	16.16	3.044296	0.55110	0.042442	2.33E-4	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000437222;ENST00000395971	T;T	0.11821	2.74;2.74	4.79	4.79	0.61399	.	0.463445	0.23003	N	0.053056	T	0.07773	0.0195	L	0.59436	1.845	0.19945	N	0.999949	D	0.71674	0.998	P	0.60682	0.878	T	0.01081	-1.1458	10	0.72032	D	0.01	-8.6365	12.5619	0.56286	1.0:0.0:0.0:0.0	rs61758384	999	O75362	ZN217_HUMAN	G	999;999;87;159	ENSP00000360526:C999G;ENSP00000304308:C999G	ENSP00000304308:C999G	C	-	1	0	ZNF217	51625715	0.948000	0.32251	0.008000	0.14137	0.003000	0.03518	5.216000	0.65246	1.791000	0.52520	0.528000	0.53228	TGT	A|0.985;C|0.015	0.015	strong		0.527	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
PLXNC1	10154	hgsc.bcm.edu	37	12	94658920	94658920	+	Silent	SNP	C	C	T	rs2230759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:94658920C>T	ENST00000258526.4	+	21	3765	c.3516C>T	c.(3514-3516)ccC>ccT	p.P1172P	PLXNC1_ENST00000545312.1_5'UTR|PLXNC1_ENST00000547057.1_Silent_p.P219P	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1172					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						ACAAGGGTCCCGTGGATGTAA	0.443													C|||	204	0.0407348	0.1225	0.0231	5008	,	,		18168	0.0		0.0199	False		,,,				2504	0.0061				p.P1172P		Atlas-SNP	.											.	PLXNC1	135	.	0			c.C3516T						PASS	.	C		485,3921	225.9+/-241.6	38,409,1756	193.0	205.0	201.0		3516	-9.1	0.1	12	dbSNP_98	201	125,8475	64.9+/-127.2	4,117,4179	no	coding-synonymous	PLXNC1	NM_005761.2		42,526,5935	TT,TC,CC		1.4535,11.0077,4.6901		1172/1569	94658920	610,12396	2203	4300	6503	SO:0001819	synonymous_variant	10154	exon21			GGGTCCCGTGGAT	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.3516C>T	12.37:g.94658920C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	171	74	0.432749	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			C|0.959;T|0.041	0.041	strong		0.443	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
ATP2A3	489	hgsc.bcm.edu	37	17	3840928	3840928	+	Silent	SNP	A	A	G	rs3179783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3840928A>G	ENST00000352011.3	-	15	2157	c.2103T>C	c.(2101-2103)acT>acC	p.T701T	ATP2A3_ENST00000397041.3_Silent_p.T701T|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000309890.7_Silent_p.T701T|ATP2A3_ENST00000397035.3_Silent_p.T701T|ATP2A3_ENST00000397043.3_Silent_p.T701T|ATP2A3_ENST00000359983.3_Silent_p.T701T			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	701					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		CTCCATCGCCAGTCTGTGGGC	0.612													A|||	1039	0.207468	0.3578	0.17	5008	,	,		20549	0.0655		0.1918	False		,,,				2504	0.1933				p.T701T	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T2103C						PASS	.	A	,,,,,,	1436,2970	455.5+/-351.0	245,946,1012	42.0	38.0	40.0		2103,2103,2103,2103,2103,2103,2103	-1.1	1.0	17	dbSNP_105	40	1710,6890	307.6+/-308.5	157,1396,2747	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	402,2342,3759	GG,GA,AA		19.8837,32.5919,24.1888	,,,,,,	701/1000,701/1053,701/1045,701/1044,701/1030,701/999,701/1030	3840928	3146,9860	2203	4300	6503	SO:0001819	synonymous_variant	489	exon15			ATCGCCAGTCTGT		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.2103T>C	17.37:g.3840928A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			A|0.782;G|0.218	0.218	strong		0.612	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
LRRTM3	347731	hgsc.bcm.edu	37	10	68687179	68687179	+	Silent	SNP	C	C	T	rs35733981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:68687179C>T	ENST00000361320.4	+	2	1083	c.505C>T	c.(505-507)Ctg>Ttg	p.L169L	CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.2_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	169					positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						GTCTAACTCCCTGAGAACCAT	0.488													C|||	185	0.0369409	0.1233	0.0072	5008	,	,		17671	0.001		0.004	False		,,,				2504	0.0123				p.L169L		Atlas-SNP	.											.	LRRTM3	241	.	0			c.C505T						PASS	.	C	,,	426,3980	204.5+/-226.7	23,380,1800	85.0	91.0	89.0		,,505	4.5	1.0	10	dbSNP_126	89	77,8523	44.5+/-102.8	0,77,4223	no	intron,intron,coding-synonymous	CTNNA3,LRRTM3	NM_001127384.1,NM_013266.2,NM_178011.3	,,	23,457,6023	TT,TC,CC		0.8953,9.6686,3.8674	,,	,,169/582	68687179	503,12503	2203	4300	6503	SO:0001819	synonymous_variant	347731	exon2			AACTCCCTGAGAA	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.505C>T	10.37:g.68687179C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Silent	SNP	ENST00000361320.4	37	CCDS7270.1																																																																																			C|0.964;T|0.036	0.036	strong		0.488	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011	
JMY	133746	hgsc.bcm.edu	37	5	78573790	78573790	+	Missense_Mutation	SNP	A	A	T	rs13182512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	72	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	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	
LRRC71	149499	hgsc.bcm.edu	37	1	156902281	156902281	+	Missense_Mutation	SNP	T	T	G	rs822431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156902281T>G	ENST00000337428.7	+	14	1661	c.1507T>G	c.(1507-1509)Tcc>Gcc	p.S503A	LRRC71_ENST00000490146.1_3'UTR|ARHGEF11_ENST00000487682.1_5'Flank	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	503			S -> A (in dbSNP:rs822431).					p.S503A(1)		endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						GATGCAGTTCTCCAAGGCCAA	0.597													T|||	1417	0.282947	0.447	0.2997	5008	,	,		17869	0.2917		0.175	False		,,,				2504	0.1513				p.S503A		Atlas-SNP	.											LRRC71,NS,carcinoma,0,1	LRRC71	33	1	1	Substitution - Missense(1)	stomach(1)	c.T1507G						PASS	.	T	ALA/SER	1753,2541		395,963,789	65.0	75.0	72.0		1507	0.6	1.0	1	dbSNP_86	72	1468,7064		128,1212,2926	yes	missense	LRRC71	NM_144702.2	99	523,2175,3715	GG,GT,TT		17.2058,40.8244,25.1131	benign	503/560	156902281	3221,9605	2147	4266	6413	SO:0001583	missense	149499	exon14			CAGTTCTCCAAGG	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.1507T>G	1.37:g.156902281T>G	ENSP00000336661:p.Ser503Ala	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	185	79	0.427027	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	37	CCDS44249.1	631	0.2889194139194139	204	0.4146341463414634	113	0.31215469613259667	188	0.32867132867132864	126	0.1662269129287599	T	9.430	1.085354	0.20390	0.408244	0.172058	ENSG00000160838	ENST00000337428	T	0.20598	2.06	4.59	0.602	0.17535	.	0.698180	0.12516	N	0.462092	T	0.03305	0.0096	L	0.29908	0.895	0.42428	P	0.007337999999999956	B;B	0.09022	0.0;0.002	B;B	0.09377	0.001;0.004	T	0.41645	-0.9497	9	0.23891	T	0.37	-17.0122	0.4647	0.00522	0.1848:0.2001:0.1681:0.4469	rs822431;rs60893033;rs822431	503;289	Q8N4P6;Q8N4P6-2	LRC71_HUMAN;.	A	503	ENSP00000336661:S503A	ENSP00000336661:S503A	S	+	1	0	LRRC71	155168905	0.114000	0.22134	0.998000	0.56505	0.956000	0.61745	-0.154000	0.10130	0.265000	0.21872	0.460000	0.39030	TCC	T|0.706;G|0.294	0.294	strong		0.597	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702	
ZNF667	63934	hgsc.bcm.edu	37	19	56952615	56952615	+	Silent	SNP	A	A	G	rs61740673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56952615A>G	ENST00000504904.3	-	7	2468	c.1749T>C	c.(1747-1749)taT>taC	p.Y583Y	ZNF667_ENST00000342634.3_Silent_p.Y711Y|ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000292069.6_Silent_p.Y583Y			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	583					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		TACTACATTCATAGGGTTTCT	0.398													A|||	158	0.0315495	0.0961	0.0159	5008	,	,		20645	0.0		0.0159	False		,,,				2504	0.0041				p.Y583Y		Atlas-SNP	.											ZNF667,NS,NS,-2,1	ZNF667	95	1	0			c.T1749C						PASS	.	A		393,4013	197.7+/-221.8	16,361,1826	120.0	115.0	117.0		1749	-0.7	0.4	19	dbSNP_129	117	96,8504	53.1+/-113.8	0,96,4204	no	coding-synonymous	ZNF667	NM_022103.3		16,457,6030	GG,GA,AA		1.1163,8.9197,3.7598		583/611	56952615	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	63934	exon5			ACATTCATAGGGT		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1749T>C	19.37:g.56952615A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Silent	SNP	ENST00000504904.3	37	CCDS12944.1																																																																																			A|0.965;G|0.035	0.035	strong		0.398	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
PITRM1	10531	hgsc.bcm.edu	37	10	3187831	3187831	+	Missense_Mutation	SNP	C	C	T	rs34837384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3187831C>T	ENST00000224949.4	-	21	2448	c.2414G>A	c.(2413-2415)cGg>cAg	p.R805Q	PITRM1-AS1_ENST00000441377.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380994.1_Missense_Mutation_p.R363Q|PITRM1_ENST00000451104.2_Missense_Mutation_p.R707Q|PITRM1_ENST00000464395.1_5'UTR|PITRM1_ENST00000380989.2_Missense_Mutation_p.R806Q			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	805			R -> Q (in dbSNP:rs34837384).		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						CTTTTTACTCCGACCGATGCT	0.547													C|||	45	0.00898562	0.0325	0.0029	5008	,	,		17900	0.0		0.0	False		,,,				2504	0.0				p.R806Q		Atlas-SNP	.											.	PITRM1	109	.	0			c.G2417A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	145,3603		5,135,1734	51.0	52.0	52.0		2417,2120,2414	3.4	0.0	10	dbSNP_126	52	1,7975		0,1,3987	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	43,43,43	5,136,5721	TT,TC,CC		0.0125,3.8687,1.2453	benign,benign,benign	806/1039,707/940,805/1038	3187831	146,11578	1874	3988	5862	SO:0001583	missense	10531	exon21			TTACTCCGACCGA	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.2414G>A	10.37:g.3187831C>T	ENSP00000224949:p.Arg805Gln	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	c	13.97	2.394997	0.42512	0.038687	1.25E-4	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104;ENST00000424714	T;T;T;T;T	0.54866	1.57;1.57;1.57;1.57;0.55	5.29	3.43	0.39272	Peptidase M16, C-terminal (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.301189	0.35495	N	0.003174	T	0.14570	0.0352	L	0.46947	1.48	0.09310	N	1	B;B;B;B;B	0.24043	0.017;0.045;0.056;0.056;0.096	B;B;B;B;B	0.26969	0.005;0.046;0.075;0.075;0.075	T	0.08126	-1.0737	10	0.17369	T	0.5	-8.921	12.181	0.54211	0.0:0.8592:0.0:0.1408	rs34837384	798;707;806;805;798	E9PDX6;E7ES23;C9JSL2;Q5JRX3;B4DH07	.;.;.;PREP_HUMAN;.	Q	805;798;806;363;707;24	ENSP00000224949:R805Q;ENSP00000370377:R806Q;ENSP00000370382:R363Q;ENSP00000401201:R707Q;ENSP00000402072:R24Q	ENSP00000224949:R805Q	R	-	2	0	PITRM1	3177831	0.021000	0.18746	0.004000	0.12327	0.004000	0.04260	1.792000	0.38754	0.725000	0.32318	0.462000	0.41574	CGG	C|0.992;T|0.008	0.008	strong		0.547	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
SIGLEC5	8778	hgsc.bcm.edu	37	19	52130488	52130488	+	Silent	SNP	G	G	A	rs17740650	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52130488G>A	ENST00000534261.2	-	8	1695	c.1296C>T	c.(1294-1296)ctC>ctT	p.L432L	SIGLEC5_ENST00000570106.2_Silent_p.L432L|SIGLEC5_ENST00000222107.4_Silent_p.L432L|SIGLEC5_ENST00000599649.1_Silent_p.L432L|SIGLEC5_ENST00000429354.3_Silent_p.L432L			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	432					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		CTCCTGTCCCGAGGTTCGATC	0.557													G|||	1226	0.244808	0.1392	0.1599	5008	,	,		19796	0.6329		0.1133	False		,,,				2504	0.183				p.L432L		Atlas-SNP	.											.	SIGLEC5	67	.	0			c.C1296T						PASS	.	G		652,3754	279.3+/-274.7	43,566,1594	97.0	84.0	88.0		1296	-0.2	0.0	19	dbSNP_123	88	939,7661	205.9+/-248.2	53,833,3414	no	coding-synonymous	SIGLEC5	NM_003830.2		96,1399,5008	AA,AG,GG		10.9186,14.798,12.2328		432/552	52130488	1591,11415	2203	4300	6503	SO:0001819	synonymous_variant	8778	exon7			TGTCCCGAGGTTC	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1296C>T	19.37:g.52130488G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_003830		Silent	SNP	ENST00000534261.2	37	CCDS33088.1																																																																																			G|0.811;A|0.188	0.188	strong		0.557	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249530	71249530	+	Silent	SNP	T	T	C	rs532438179|rs369043826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249530T>C	ENST00000398534.3	+	1	460	c.429T>C	c.(427-429)tgT>tgC	p.C143C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	143	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						AGCCCTGCTGTTCCCAGTCCA	0.612																																					p.C143C		Atlas-SNP	.											KRTAP5-8,NS,carcinoma,+1,1	KRTAP5-8	28	1	0			c.T429C						scavenged	.						146.0	159.0	155.0					11																	71249530		2200	4294	6494	SO:0001819	synonymous_variant	57830	exon1			CTGCTGTTCCCAG	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.429T>C	11.37:g.71249530T>C		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	229	16	0.069869	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																			.	.	none		0.612	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
FAM134B	54463	hgsc.bcm.edu	37	5	16475209	16475209	+	Missense_Mutation	SNP	G	G	C	rs34432513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16475209G>C	ENST00000306320.9	-	9	1221	c.1135C>G	c.(1135-1137)Cag>Gag	p.Q379E	FAM134B_ENST00000399793.2_Missense_Mutation_p.Q238E	NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	379			Q -> E (in dbSNP:rs34432513).		sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						CTGTCCAACTGTTCCTTCTTT	0.453													G|||	57	0.0113818	0.0393	0.0058	5008	,	,		20685	0.0		0.001	False		,,,				2504	0.0				p.Q379E		Atlas-SNP	.											.	FAM134B	72	.	0			c.C1135G						PASS	.	G	GLU/GLN,GLU/GLN	137,3809		4,129,1840	165.0	161.0	162.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1135,712	3.9	0.0	5	dbSNP_126	162	2,8320		0,2,4159	yes	missense,missense	FAM134B	NM_001034850.1,NM_019000.3	29,29	4,131,5999	CC,CG,GG		0.024,3.4719,1.133	benign,benign	379/498,238/357	16475209	139,12129	1973	4161	6134	SO:0001583	missense	54463	exon9			CCAACTGTTCCTT	BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153			25964	protein-coding gene	gene with protein product		613114				19838196, 24327336	Standard	NM_001034850		Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.1135C>G	5.37:g.16475209G>C	ENSP00000304642:p.Gln379Glu	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	206	104	0.504854	NM_001034850	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	Missense_Mutation	SNP	ENST00000306320.9	37	CCDS43304.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	0.004	-2.276501	0.00254	0.034719	2.4E-4	ENSG00000154153	ENST00000399793;ENST00000306320	T;T	0.43688	0.96;0.94	5.7	3.86	0.44501	.	0.782790	0.11830	N	0.525295	T	0.01976	0.0062	N	0.25647	0.755	0.09310	N	1	B;B	0.23442	0.085;0.034	B;B	0.19666	0.026;0.022	T	0.10823	-1.0613	10	0.02654	T	1	-0.8582	10.5977	0.45347	0.0:0.1293:0.6027:0.2681	rs34432513	379;238	Q9H6L5;Q9H6L5-2	F134B_HUMAN;.	E	238;379	ENSP00000382691:Q238E;ENSP00000304642:Q379E	ENSP00000304642:Q379E	Q	-	1	0	FAM134B	16528209	0.617000	0.27043	0.001000	0.08648	0.391000	0.30476	4.123000	0.57917	0.704000	0.31869	0.655000	0.94253	CAG	G|0.984;C|0.016	0.016	strong		0.453	FAM134B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366090.1	NM_001034850	
SELPLG	6404	hgsc.bcm.edu	37	12	109017674	109017674	+	Missense_Mutation	SNP	A	A	G	rs63748999|rs372173288|rs201851784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109017674A>G	ENST00000550948.1	-	2	634	c.410T>C	c.(409-411)gTg>gCg	p.V137A	SELPLG_ENST00000228463.6_Missense_Mutation_p.V153A|SELPLG_ENST00000388962.3_Intron			Q14242	SELPL_HUMAN	selectin P ligand	137	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						CTCCGTGGGCACTGGTTGAGT	0.612													G|||	1010	0.201677	0.1097	0.1412	5008	,	,		19840	0.3413		0.171	False		,,,				2504	0.2566				p.V153A		Atlas-SNP	.											SELPLG_ENST00000550948,NS,carcinoma,0,7	SELPLG	138	7	0			c.T458C						scavenged	.						159.0	124.0	136.0					12																	109017674		2199	4273	6472	SO:0001583	missense	6404	exon2			GTGGGCACTGGTT		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.410T>C	12.37:g.109017674A>G	ENSP00000447752:p.Val137Ala	Somatic	295	5	0.0169492		WXS	Illumina HiSeq	Phase_I	230	62	0.269565	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	G	0.025	-1.376284	0.01214	.	.	ENSG00000110876	ENST00000550948;ENST00000228463	T;T	0.12984	2.63;2.63	3.42	-5.49	0.02584	.	.	.	.	.	T	0.03390	0.0098	N	0.04880	-0.145	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.39251	-0.9623	9	0.02654	T	1	0.1678	0.7612	0.01007	0.3376:0.1925:0.2876:0.1824	.	153;137	B7Z5C7;Q14242	.;SELPL_HUMAN	A	137;153	ENSP00000447752:V137A;ENSP00000228463:V153A	ENSP00000228463:V153A	V	-	2	0	SELPLG	107541803	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.356000	0.02609	-1.321000	0.02281	-1.471000	0.01009	GTG	A|0.896;G|0.104	0.104	strong		0.612	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
PSPH	5723	hgsc.bcm.edu	37	7	56088811	56088811	+	Missense_Mutation	SNP	T	T	C	rs78599516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:56088811T>C	ENST00000395471.3	-	4	900	c.95A>G	c.(94-96)gAt>gGt	p.D32G	PSPH_ENST00000275605.3_Missense_Mutation_p.D32G|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	32			D -> N (in PSPHD; dbSNP:rs28933976). {ECO:0000269|PubMed:14673469}.		cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GGCTAGCTCATCGATTCCTTC	0.448																																					p.D32G		Atlas-SNP	.											.	PSPH	23	.	0			c.A95G						PASS	.	T	GLY/ASP	1124,3282		0,1124,1079	142.0	108.0	120.0		95	4.4	1.0	7	dbSNP_132	120	256,8344		0,256,4044	yes	missense	PSPH	NM_004577.3	94	0,1380,5123	CC,CT,TT		2.9767,25.5107,10.6105	possibly-damaging	32/226	56088811	1380,11626	2203	4300	6503	SO:0001583	missense	5723	exon4			AGCTCATCGATTC	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.95A>G	7.37:g.56088811T>C	ENSP00000378854:p.Asp32Gly	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	271	85	0.313653	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	708	0.3241758241758242	240	0.4878048780487805	97	0.26795580110497236	227	0.3968531468531469	144	0.18997361477572558	T	14.84	2.655594	0.47467	0.255107	0.029767	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626;ENST00000419984;ENST00000421312	D;D;D;D;D	0.89617	-2.54;-2.54;-2.54;-1.91;-1.91	5.6	4.44	0.53790	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);Phosphoserine phosphatase, domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.96269	3.795	0.80722	D	1	P;P	0.49185	0.92;0.846	D;D	0.65773	0.938;0.938	T	0.00000	-1.3334	10	0.87932	D	0	-27.8562	13.1471	0.59467	0.0:0.069:0.0:0.931	.	32;32	Q53EY1;P78330	.;SERB_HUMAN	G	32	ENSP00000275605:D32G;ENSP00000378854:D32G;ENSP00000398653:D32G;ENSP00000399660:D32G;ENSP00000390952:D32G	ENSP00000275605:D32G	D	-	2	0	PSPH	56056305	1.000000	0.71417	0.988000	0.46212	0.010000	0.07245	6.109000	0.71528	0.409000	0.25649	-1.431000	0.01090	GAT	T|0.746;C|0.254	0.254	strong		0.448	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
CNTN4	152330	hgsc.bcm.edu	37	3	2787338	2787338	+	Silent	SNP	G	G	A	rs116041691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:2787338G>A	ENST00000397461.1	+	5	699	c.315G>A	c.(313-315)tcG>tcA	p.S105S	CNTN4_ENST00000427331.1_Silent_p.S105S|CNTN4_ENST00000418658.1_Silent_p.S105S	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	105	Ig-like C2-type 1.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		CGACAAACTCGTTTGGAACAA	0.408													G|||	28	0.00559105	0.0212	0.0	5008	,	,		17052	0.0		0.0	False		,,,				2504	0.0				p.S105S		Atlas-SNP	.											CNTN4_ENST00000418658,NS,carcinoma,0,1	CNTN4	335	1	0			c.G315A						PASS	.	G	,	64,3818		1,62,1878	146.0	137.0	140.0		315,315	-7.4	0.7	3	dbSNP_132	140	1,8275		0,1,4137	no	coding-synonymous,coding-synonymous	CNTN4	NM_001206955.1,NM_175607.2	,	1,63,6015	AA,AG,GG		0.0121,1.6486,0.5346	,	105/1027,105/1027	2787338	65,12093	1941	4138	6079	SO:0001819	synonymous_variant	152330	exon6			AAACTCGTTTGGA	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.315G>A	3.37:g.2787338G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	78	48	0.615385	NM_175607	B2RAX3|Q8IX14|Q8TC35	Silent	SNP	ENST00000397461.1	37	CCDS43041.1																																																																																			G|0.996;A|0.004	0.004	strong		0.408	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
FBLN2	2199	hgsc.bcm.edu	37	3	13612936	13612936	+	Missense_Mutation	SNP	A	A	G	rs3732666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:13612936A>G	ENST00000295760.7	+	2	1150	c.1081A>G	c.(1081-1083)Agc>Ggc	p.S361G	FBLN2_ENST00000404922.3_Missense_Mutation_p.S361G|FBLN2_ENST00000492059.1_Missense_Mutation_p.S361G|FBLN2_ENST00000535798.1_Missense_Mutation_p.S387G	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	361	N.|Subdomain NB (Cys-free).		S -> G (in dbSNP:rs3732666).		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)			GCATGCACCGAGCCTGGGCAA	0.662													G|||	2341	0.467452	0.7587	0.2824	5008	,	,		16187	0.5496		0.1869	False		,,,				2504	0.409				p.S361G		Atlas-SNP	.											.	FBLN2	137	.	0			c.A1081G						PASS	.	G	GLY/SER,GLY/SER,GLY/SER	2822,1480		954,914,283	35.0	47.0	43.0		1081,1081,1081	1.9	0.0	3	dbSNP_107	43	1671,6801		179,1313,2744	no	missense,missense,missense	FBLN2	NM_001004019.1,NM_001165035.1,NM_001998.2	56,56,56	1133,2227,3027	GG,GA,AA		19.7238,34.4026,35.173	benign,benign,benign	361/1232,361/1232,361/1185	13612936	4493,8281	2151	4236	6387	SO:0001583	missense	2199	exon2			GCACCGAGCCTGG	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.1081A>G	3.37:g.13612936A>G	ENSP00000295760:p.Ser361Gly	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_001998	B7Z9C5|Q8IUI0|Q8IUI1	Missense_Mutation	SNP	ENST00000295760.7	37	CCDS46762.1	913	0.41804029304029305	342	0.6951219512195121	98	0.27071823204419887	340	0.5944055944055944	133	0.17546174142480211	G	5.775	0.327445	0.10956	0.655974	0.197238	ENSG00000163520	ENST00000535798;ENST00000404922;ENST00000295760;ENST00000492059	T;T;T;T	0.79554	-1.28;-1.23;-1.19;-1.23	4.82	1.9	0.25705	.	2.938210	0.00827	N	0.001632	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	0.42949	-0.9421	9	0.20519	T	0.43	.	4.8974	0.13757	0.2617:0.1534:0.5849:0.0	rs3732666;rs3732666	361;361;387	P98095;P98095-2;F5H1F3	FBLN2_HUMAN;.;.	G	387;361;361;361	ENSP00000445705:S387G;ENSP00000384169:S361G;ENSP00000295760:S361G;ENSP00000420042:S361G	ENSP00000295760:S361G	S	+	1	0	FBLN2	13587937	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.151000	0.10175	-0.056000	0.13221	-0.124000	0.14976	AGC	A|0.603;G|0.397	0.397	strong		0.662	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019	
B4GALNT4	338707	hgsc.bcm.edu	37	11	372700	372700	+	Silent	SNP	G	G	C	rs35475866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:372700G>C	ENST00000329962.6	+	3	294	c.294G>C	c.(292-294)ggG>ggC	p.G98G		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	98					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)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		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)		TTCCTGGGGGGGCTGGGAGGC	0.647													.|||	1656	0.330671	0.3253	0.2997	5008	,	,		10061	0.3839		0.2952	False		,,,				2504	0.3415				p.G98G		Atlas-SNP	.											B4GALNT4,rectum,carcinoma,0,1	B4GALNT4	83	1	0			c.G294C						PASS	.	G		1430,2946		245,940,1003	18.0	21.0	20.0		294	-1.3	0.0	11	dbSNP_126	20	2375,6187		331,1713,2237	no	coding-synonymous	B4GALNT4	NM_178537.4		576,2653,3240	CC,CG,GG		27.7388,32.6782,29.4095		98/1040	372700	3805,9133	2188	4281	6469	SO:0001819	synonymous_variant	338707	exon3			TGGGGGGGCTGGG	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.294G>C	11.37:g.372700G>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_178537	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																			G|0.714;C|0.286	0.286	strong		0.647	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
NUP133	55746	hgsc.bcm.edu	37	1	229636561	229636561	+	Missense_Mutation	SNP	C	C	T	rs75411588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229636561C>T	ENST00000261396.3	-	4	546	c.455G>A	c.(454-456)aGt>aAt	p.S152N	NUP133_ENST00000537506.1_Missense_Mutation_p.S136N|NUP133_ENST00000366678.3_Missense_Mutation_p.S152N	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	152					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 organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|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)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TAAGTCGGCACTCCAGTGGAA	0.388													C|||	163	0.0325479	0.1135	0.0115	5008	,	,		19355	0.0		0.003	False		,,,				2504	0.002				p.S152N		Atlas-SNP	.											.	NUP133	111	.	0			c.G455A						PASS	.	C	ASN/SER	400,4006	198.4+/-222.2	12,376,1815	59.0	58.0	58.0		455	2.0	0.7	1	dbSNP_131	58	7,8593	6.4+/-24.3	0,7,4293	yes	missense	NUP133	NM_018230.2	46	12,383,6108	TT,TC,CC		0.0814,9.0785,3.1293	benign	152/1157	229636561	407,12599	2203	4300	6503	SO:0001583	missense	55746	exon4			TCGGCACTCCAGT		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.455G>A	1.37:g.229636561C>T	ENSP00000261396:p.Ser152Asn	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	46	0.021062271062271064	42	0.08536585365853659	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	9.530	1.110704	0.20714	0.090785	8.14E-4	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506;ENST00000366678	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	5.93	1.98	0.26296	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.372720	0.33813	N	0.004533	T	0.00524	0.0017	L	0.32530	0.975	0.47214	D	0.999358	B	0.09022	0.002	B	0.08055	0.003	T	0.21042	-1.0257	10	0.16420	T	0.52	-7.1368	6.2296	0.20728	0.0:0.558:0.1243:0.3178	.	152	Q8WUM0	NU133_HUMAN	N	152;152;152;136;152	ENSP00000261396:S152N;ENSP00000355640:S152N;ENSP00000443496:S136N;ENSP00000355639:S152N	ENSP00000261396:S152N	S	-	2	0	NUP133	227703184	0.996000	0.38824	0.673000	0.29887	0.384000	0.30261	0.731000	0.26058	0.845000	0.35118	0.557000	0.71058	AGT	C|0.972;T|0.028	0.028	strong		0.388	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
SYCE1	93426	hgsc.bcm.edu	37	10	135370633	135370633	+	Silent	SNP	C	C	T	rs8181356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135370633C>T	ENST00000343131.5	-	7	506	c.402G>A	c.(400-402)aaG>aaA	p.K134K	SYCE1_ENST00000432597.2_Silent_p.K98K|SPRN_ENST00000541506.1_Intron|SYCE1_ENST00000368517.3_Silent_p.K98K	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	134					synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.K134K(1)|p.K98K(1)		breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		AAATTCTCTCCTTGCACTCCT	0.552													C|||	775	0.154752	0.0454	0.1715	5008	,	,		21865	0.2698		0.1093	False		,,,				2504	0.2188				p.K134K		Atlas-SNP	.											SYCE1_ENST00000343131,NS,carcinoma,0,2	SYCE1	81	2	2	Substitution - coding silent(2)	stomach(2)	c.G402A						PASS	.	C	,,	260,4146	142.7+/-177.9	6,248,1949	274.0	260.0	264.0		402,402,294	0.3	1.0	10	dbSNP_117	264	815,7785	186.2+/-233.7	45,725,3530	no	coding-synonymous,coding-synonymous,coding-synonymous	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	,,	51,973,5479	TT,TC,CC		9.4767,5.901,8.2654	,,	134/319,134/352,98/283	135370633	1075,11931	2203	4300	6503	SO:0001819	synonymous_variant	93426	exon7			TCTCTCCTTGCAC	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.402G>A	10.37:g.135370633C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	182	97	0.532967	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Silent	SNP	ENST00000343131.5	37	CCDS44501.1																																																																																			C|0.889;T|0.111	0.111	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
DCP1B	196513	hgsc.bcm.edu	37	12	2102455	2102455	+	Silent	SNP	A	A	C	rs150415068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:2102455A>C	ENST00000280665.6	-	3	373	c.294T>G	c.(292-294)ccT>ccG	p.P98P	DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000397173.4_5'UTR	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	98					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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			AGAGAAGGAAAGGGTCCTGGA	0.403													A|||	4	0.000798722	0.0	0.0014	5008	,	,		19112	0.0		0.003	False		,,,				2504	0.0				p.P98P		Atlas-SNP	.											DCP1B,rectum,carcinoma,0,6	DCP1B	63	6	0			c.T294G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	148.0	156.0	153.0		294	0.6	1.0	12	dbSNP_134	153	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous	DCP1B	NM_152640.3		0,21,6482	CC,CA,AA		0.2209,0.0454,0.1615		98/618	2102455	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	196513	exon3			AAGGAAAGGGTCC	AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"""DCP1 decapping enzyme homolog B (S. cerevisiae)"""			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.294T>G	12.37:g.2102455A>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	185	85	0.459459	NM_152640	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Silent	SNP	ENST00000280665.6	37	CCDS31727.1																																																																																			A|0.998;C|0.002	0.002	strong		0.403	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640	
CEP350	9857	hgsc.bcm.edu	37	1	180013235	180013235	+	Missense_Mutation	SNP	T	T	G	rs12124336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:180013235T>G	ENST00000367607.3	+	21	4967	c.4549T>G	c.(4549-4551)Tca>Gca	p.S1517A		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1517	Ser-rich.		S -> A (in dbSNP:rs12124336).		microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						GACCCTTGACTCAAAGCATCA	0.333													T|||	306	0.0611022	0.1271	0.0432	5008	,	,		17468	0.002		0.0368	False		,,,				2504	0.0706				p.S1517A		Atlas-SNP	.											.	CEP350	418	.	0			c.T4549G						PASS	.	T	ALA/SER	540,3858		36,468,1695	53.0	48.0	50.0		4549	4.6	1.0	1	dbSNP_120	50	312,8272		7,298,3987	yes	missense	CEP350	NM_014810.4	99	43,766,5682	GG,GT,TT		3.6347,12.2783,6.5629	possibly-damaging	1517/3118	180013235	852,12130	2199	4292	6491	SO:0001583	missense	9857	exon21			CTTGACTCAAAGC	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.4549T>G	1.37:g.180013235T>G	ENSP00000356579:p.Ser1517Ala	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	108|108	0.04945054945054945|0.04945054945054945	68|68	0.13821138211382114|0.13821138211382114	15|15	0.04143646408839779|0.04143646408839779	2|2	0.0034965034965034965|0.0034965034965034965	23|23	0.030343007915567283|0.030343007915567283	T|T	18.03|18.03	3.533272|3.533272	0.64972|0.64972	0.122783|0.122783	0.036347|0.036347	ENSG00000135837|ENSG00000135837	ENST00000418229|ENST00000367607	.|T	.|0.58940	.|0.3	5.69|5.69	4.55|4.55	0.56014|0.56014	.|.	.|0.211967	.|0.23608	.|N	.|0.046377	T|T	0.00724|0.00724	0.0024|0.0024	L|L	0.27053|0.27053	0.805|0.805	0.30332|0.30332	N|N	0.786512|0.786512	.|D;P	.|0.58268	.|0.982;0.905	.|D;B	.|0.67548	.|0.952;0.35	T|T	0.01776|0.01776	-1.1276|-1.1276	5|9	.|.	.|.	.|.	.|.	10.5443|10.5443	0.45052|0.45052	0.1443:0.0:0.0:0.8557|0.1443:0.0:0.0:0.8557	rs12124336;rs12124336|rs12124336;rs12124336	.|1517;1517	.|E7EU22;Q5VT06	.|.;CE350_HUMAN	R|A	125|1517	.|ENSP00000356579:S1517A	.|.	L|S	+|+	2|1	0|0	CEP350|CEP350	178279858|178279858	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.733000|0.733000	0.41908|0.41908	2.668000|2.668000	0.46816|0.46816	0.964000|0.964000	0.38108|0.38108	0.454000|0.454000	0.30748|0.30748	CTC|TCA	T|0.934;G|0.066	0.066	strong		0.333	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
PLEKHA7	144100	hgsc.bcm.edu	37	11	16837788	16837788	+	Silent	SNP	G	G	A	rs217750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	67	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	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	
DIDO1	11083	hgsc.bcm.edu	37	20	61538601	61538601	+	Silent	SNP	C	C	T	rs34820000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61538601C>T	ENST00000266070.4	-	5	1597	c.1272G>A	c.(1270-1272)gcG>gcA	p.A424A	DIDO1_ENST00000354665.4_Silent_p.A424A|DIDO1_ENST00000370366.1_Silent_p.A424A|DIDO1_ENST00000370371.4_Silent_p.A424A|DIDO1_ENST00000370368.1_Silent_p.A424A|DIDO1_ENST00000395340.1_Silent_p.A424A|DIDO1_ENST00000395335.2_Silent_p.A424A|DIDO1_ENST00000395343.1_Silent_p.A424A|DIDO1_ENST00000266071.5_Silent_p.A424A	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	424					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)					ACTTCATTGTCGCTGCGGCGT	0.522													C|||	330	0.0658946	0.1218	0.0447	5008	,	,		18192	0.0238		0.0497	False		,,,				2504	0.0654				p.A424A	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1_ENST00000370371,NS,carcinoma,-1,2	DIDO1	321	2	0			c.G1272A						PASS	.	C	,,,,,	535,3871	243.1+/-252.9	31,473,1699	225.0	216.0	219.0		1272,1272,1272,1272,1272,1272	-7.2	0.1	20	dbSNP_126	219	485,8115	140.6+/-197.1	13,459,3828	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_001193370.1,NM_022105.4,NM_033081.2,NM_080796.3,NM_080797.3	,,,,,	44,932,5527	TT,TC,CC		5.6395,12.1425,7.8425	,,,,,	424/2241,424/1190,424/563,424/2241,424/563,424/1190	61538601	1020,11986	2203	4300	6503	SO:0001819	synonymous_variant	11083	exon5			CATTGTCGCTGCG	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.1272G>A	20.37:g.61538601C>T		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	262	121	0.461832	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			C|0.924;T|0.076	0.076	strong		0.522	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
APOH	350	hgsc.bcm.edu	37	17	64216797	64216797	+	Missense_Mutation	SNP	G	G	T	rs114459902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:64216797G>T	ENST00000205948.6	-	5	516	c.479C>A	c.(478-480)gCt>gAt	p.A160D		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	160	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			ATTGTTTCCAGCTGATGGCTT	0.408													G|||	29	0.00579073	0.0212	0.0014	5008	,	,		19051	0.0		0.0	False		,,,				2504	0.0				p.A160D	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.C479A						PASS	.	G	ASP/ALA	83,4323	70.3+/-108.2	0,83,2120	127.0	123.0	124.0		479	0.9	0.0	17	dbSNP_133	124	0,8600		0,0,4300	yes	missense	APOH	NM_000042.2	126	0,83,6420	TT,TG,GG		0.0,1.8838,0.6382	benign	160/346	64216797	83,12923	2203	4300	6503	SO:0001583	missense	350	exon5			TTTCCAGCTGATG		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.479C>A	17.37:g.64216797G>T	ENSP00000205948:p.Ala160Asp	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	147	57	0.387755	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	g	4.559	0.103783	0.08731	0.018838	0.0	ENSG00000091583	ENST00000205948	T	0.30448	1.53	5.2	0.92	0.19397	Complement control module (2);Sushi/SCR/CCP (3);	0.940200	0.09067	N	0.853424	T	0.11665	0.0284	L	0.53729	1.69	0.09310	N	0.999999	B	0.29378	0.243	B	0.22601	0.04	T	0.25398	-1.0133	10	0.15066	T	0.55	.	4.9343	0.13932	0.3059:0.0:0.5587:0.1354	.	160	P02749	APOH_HUMAN	D	160	ENSP00000205948:A160D	ENSP00000205948:A160D	A	-	2	0	APOH	61647259	0.000000	0.05858	0.013000	0.15412	0.335000	0.28730	-0.346000	0.07760	0.036000	0.15547	-0.271000	0.10264	GCT	G|0.993;T|0.007	0.007	strong		0.408	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
OR10T2	128360	hgsc.bcm.edu	37	1	158369210	158369210	+	Missense_Mutation	SNP	A	A	G	rs6660222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158369210A>G	ENST00000334438.1	-	1	46	c.47T>C	c.(46-48)gTg>gCg	p.V16A		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	16			V -> A (in dbSNP:rs6660222).			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)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					GGAGAAACCCACCAGGATGAA	0.448													A|||	103	0.0205671	0.0772	0.0	5008	,	,		18704	0.0		0.0	False		,,,				2504	0.001				p.V16A		Atlas-SNP	.											.	OR10T2	76	.	0			c.T47C						PASS	.	A	ALA/VAL	237,4169	128.2+/-165.1	5,227,1971	35.0	39.0	37.0		47	4.7	0.9	1	dbSNP_116	37	0,8600		0,0,4300	yes	missense	OR10T2	NM_001004475.1	64	5,227,6271	GG,GA,AA		0.0,5.379,1.8222	benign	16/315	158369210	237,12769	2203	4300	6503	SO:0001583	missense	128360	exon1			AAACCCACCAGGA	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.47T>C	1.37:g.158369210A>G	ENSP00000334115:p.Val16Ala	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	38	0.0173992673992674	38	0.07723577235772358	0	0.0	0	0.0	0	0.0	A	10.40	1.341006	0.24339	0.05379	0.0	ENSG00000186306	ENST00000334438	T	0.01406	4.93	4.65	4.65	0.58169	.	0.000000	0.34411	U	0.003988	T	0.00637	0.0021	L	0.41710	1.295	0.20764	N	0.99986	B	0.34161	0.439	B	0.36666	0.23	T	0.48658	-0.9016	10	0.87932	D	0	.	4.0026	0.09587	0.7202:0.0:0.0962:0.1837	rs6660222;rs52824469;rs56643236;rs6660222	16	Q8NGX3	O10T2_HUMAN	A	16	ENSP00000334115:V16A	ENSP00000334115:V16A	V	-	2	0	OR10T2	156635834	0.176000	0.23096	0.922000	0.36590	0.528000	0.34623	1.079000	0.30766	1.939000	0.56221	0.482000	0.46254	GTG	A|0.976;G|0.024	0.024	strong		0.448	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
LRRFIP2	9209	hgsc.bcm.edu	37	3	37144480	37144480	+	Missense_Mutation	SNP	G	G	A	rs143314448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37144480G>A	ENST00000336686.4	-	15	888	c.808C>T	c.(808-810)Cgc>Tgc	p.R270C	LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.R270C|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000396428.2_Intron|LRRFIP2_ENST00000354379.4_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	270	DVL3-binding.|Ser-rich.				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						CGATTGGAGCGACTGAAATAA	0.403													G|||	5	0.000998403	0.0038	0.0	5008	,	,		15844	0.0		0.0	False		,,,				2504	0.0				p.R270C		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.C808T						PASS	.	G	,CYS/ARG,	12,4386		0,12,2187	79.0	61.0	67.0		,808,	6.2	1.0	3	dbSNP_134	67	0,8592		0,0,4296	yes	intron,missense,intron	LRRFIP2	NM_001134369.1,NM_006309.2,NM_017724.2	,180,	0,12,6483	AA,AG,GG		0.0,0.2729,0.0924	,probably-damaging,	,270/722,	37144480	12,12978	2199	4296	6495	SO:0001583	missense	9209	exon16			TGGAGCGACTGAA	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.808C>T	3.37:g.37144480G>A	ENSP00000338727:p.Arg270Cys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	33	5.265897	0.95399	0.002729	0.0	ENSG00000093167	ENST00000421307;ENST00000336686	T;T	0.56275	0.47;0.47	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.63628	0.2527	N	0.22421	0.69	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64859	-0.6308	10	0.66056	D	0.02	-8.9955	20.4549	0.99139	0.0:0.0:1.0:0.0	.	270	Q9Y608	LRRF2_HUMAN	C	270	ENSP00000392217:R270C;ENSP00000338727:R270C	ENSP00000338727:R270C	R	-	1	0	LRRFIP2	37119484	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	6.226000	0.72277	2.937000	0.99478	0.650000	0.86243	CGC	G|0.999;A|0.001	0.001	strong		0.403	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	
XCR1	2829	hgsc.bcm.edu	37	3	46063329	46063329	+	Silent	SNP	T	T	C	rs2230322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46063329T>C	ENST00000309285.3	-	2	467	c.111A>G	c.(109-111)ctA>ctG	p.L37L	XCR1_ENST00000542109.1_Silent_p.L37L	NM_001024644.1	NP_001019815.1	P46094	XCR1_HUMAN	chemokine (C motif) receptor 1	37					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol (GO:0051209)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CCAGGCAGTATAGGACAGTGG	0.557													C|||	1166	0.232827	0.4425	0.0908	5008	,	,		17479	0.0466		0.1243	False		,,,				2504	0.3538				p.L37L		Atlas-SNP	.											.	XCR1	51	.	0			c.A111G						PASS	.	C	,	1744,2662	648.0+/-398.6	342,1060,801	113.0	107.0	109.0		111,111	-2.5	0.8	3	dbSNP_98	109	971,7629	774.7+/-407.7	46,879,3375	no	coding-synonymous,coding-synonymous	XCR1	NM_001024644.1,NM_005283.2	,	388,1939,4176	CC,CT,TT		11.2907,39.5824,20.875	,	37/334,37/334	46063329	2715,10291	2203	4300	6503	SO:0001819	synonymous_variant	2829	exon2			GCAGTATAGGACA		CCDS2736.1	3p21.3-p21.1	2012-11-19	2006-01-13	2002-08-23	ENSG00000173578	ENSG00000173578		"""GPCR / Class A : Chemokine receptors : X-C motif"""	1625	protein-coding gene	gene with protein product		600552	"""chemokine (C motif) XC receptor 1"""	GPR5, CCXCR1		7832990, 10400311	Standard	NM_005283		Approved		uc003cpf.3	P46094	OTTHUMG00000133449	ENST00000309285.3:c.111A>G	3.37:g.46063329T>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	166	90	0.542169	NM_001024644		Silent	SNP	ENST00000309285.3	37	CCDS2736.1																																																																																			T|0.794;C|0.206	0.206	strong		0.557	XCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257322.2		
NOD1	10392	hgsc.bcm.edu	37	7	30491081	30491081	+	Missense_Mutation	SNP	G	G	A	rs151170709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30491081G>A	ENST00000222823.4	-	6	2477	c.1952C>T	c.(1951-1953)aCg>aTg	p.T651M		NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	651					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|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)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|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 cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|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 tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|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)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						CCAGATGAACGTGGGCATGGC	0.622													G|||	4	0.000798722	0.003	0.0	5008	,	,		18686	0.0		0.0	False		,,,				2504	0.0				p.T651M		Atlas-SNP	.											.	NOD1	79	.	0			c.C1952T						PASS	.	G	MET/THR	18,4388	26.2+/-53.5	0,18,2185	44.0	45.0	45.0		1952	5.6	1.0	7	dbSNP_134	45	0,8600		0,0,4300	yes	missense	NOD1	NM_006092.2	81	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	probably-damaging	651/954	30491081	18,12988	2203	4300	6503	SO:0001583	missense	10392	exon6			ATGAACGTGGGCA	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.1952C>T	7.37:g.30491081G>A	ENSP00000222823:p.Thr651Met	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_006092	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	37	CCDS5427.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	17.46	3.395795	0.62177	0.004085	0.0	ENSG00000106100	ENST00000222823	T	0.71103	-0.54	5.61	5.61	0.85477	.	0.192032	0.52532	D	0.000072	T	0.70046	0.3179	M	0.63428	1.95	0.80722	D	1	D	0.71674	0.998	P	0.54706	0.759	T	0.74636	-0.3599	10	0.49607	T	0.09	.	12.283	0.54776	0.0:0.0:0.7325:0.2675	.	651	Q9Y239	NOD1_HUMAN	M	651	ENSP00000222823:T651M	ENSP00000222823:T651M	T	-	2	0	NOD1	30457606	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.689000	0.68234	2.652000	0.90054	0.655000	0.94253	ACG	G|0.998;A|0.002	0.002	strong		0.622	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
IFIH1	64135	hgsc.bcm.edu	37	2	163128824	163128824	+	Missense_Mutation	SNP	T	T	C	rs3747517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:163128824T>C	ENST00000263642.2	-	13	2923	c.2528A>G	c.(2527-2529)cAt>cGt	p.H843R		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	843	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		H -> R (in dbSNP:rs3747517). {ECO:0000269|PubMed:14645903, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						AACTGTCTCATGTTCGATAAC	0.413													C|||	2954	0.589856	0.5764	0.7666	5008	,	,		19956	0.3135		0.7505	False		,,,				2504	0.6022				p.H843R		Atlas-SNP	.											IFIH1,face,carcinoma,-1,1	IFIH1	102	1	0			c.A2528G	GRCh37	CM065280	IFIH1	M	rs3747517	PASS	.	C	ARG/HIS	2751,1655	506.4+/-366.4	869,1013,321	106.0	92.0	97.0		2528	5.8	1.0	2	dbSNP_107	97	6244,2356	393.3+/-344.3	2269,1706,325	yes	missense	IFIH1	NM_022168.2	29	3138,2719,646	CC,CT,TT		27.3953,37.5624,30.8396	benign	843/1026	163128824	8995,4011	2203	4300	6503	SO:0001583	missense	64135	exon13			GTCTCATGTTCGA	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.2528A>G	2.37:g.163128824T>C	ENSP00000263642:p.His843Arg	Somatic	301	1	0.00332226		WXS	Illumina HiSeq	Phase_I	212	212	1	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	1329	0.6085164835164835	295	0.5995934959349594	274	0.7569060773480663	197	0.34440559440559443	563	0.7427440633245382	C	7.862	0.726267	0.15439	0.624376	0.726047	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.03717	3.83	5.76	5.76	0.90799	Helicase, C-terminal (1);	0.045520	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00008	-3.105	0.45718	P	0.0013760000000000439	B	0.02656	0.0	B	0.01281	0.0	T	0.38478	-0.9659	9	0.02654	T	1	-7.9174	15.0983	0.72253	0.0:0.9321:0.0:0.0679	rs3747517;rs34318023;rs56698395;rs3747517	843	Q9BYX4	IFIH1_HUMAN	R	843	ENSP00000263642:H843R	ENSP00000263642:H843R	H	-	2	0	IFIH1	162837070	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.684000	0.61686	1.449000	0.47699	-0.128000	0.14901	CAT	T|0.368;C|0.632	0.632	strong		0.413	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168	
CCL14	6358	hgsc.bcm.edu	37	17	34313612	34313612	+	Missense_Mutation	SNP	G	G	A	rs75238886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34313612G>A	ENST00000394509.4	-	1	182	c.74C>T	c.(73-75)tCc>tTc	p.S25F	CCL14_ENST00000536149.1_Missense_Mutation_p.S25F|CCL14_ENST00000480944.2_5'UTR|CTB-186H2.3_ENST00000593057.1_Intron|CTB-186H2.3_ENST00000591669.1_Missense_Mutation_p.E20K|CCL14_ENST00000586216.1_Missense_Mutation_p.S25F|CCL15-CCL14_ENST00000481427.2_3'UTR|CCL14_ENST00000435911.2_Missense_Mutation_p.S25F			Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14	25					cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)	extracellular space (GO:0005615)				large_intestine(1)|lung(6)	7		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTCACGTGAGGAGGATTCAGT	0.562													G|||	128	0.0255591	0.0197	0.0144	5008	,	,		16475	0.0466		0.0368	False		,,,				2504	0.0082				p.S25F		Atlas-SNP	.											.	CCL14	22	.	0			c.C74T						PASS	.	G	PHE/SER,PHE/SER	103,4303	81.9+/-120.4	1,101,2101	203.0	145.0	164.0		74,74	1.5	0.0	17	dbSNP_132	164	253,8347	99.9+/-161.4	0,253,4047	yes	missense,missense	CCL14	NM_032962.4,NM_032963.3	155,155	1,354,6148	AA,AG,GG		2.9419,2.3377,2.7372	probably-damaging,probably-damaging	25/110,25/94	34313612	356,12650	2203	4300	6503	SO:0001583	missense	6358	exon1			CGTGAGGAGGATT	Z49270	CCDS32624.1, CCDS45652.1	17q11.2	2014-04-10	2002-08-22	2002-08-23	ENSG00000213494	ENSG00000276409		"""Chemokine ligands"", ""Endogenous ligands"""	10612	protein-coding gene	gene with protein product		601392	"""small inducible cytokine subfamily A (Cys-Cys), member 14"""	SCYA14		8661057	Standard	NM_032963		Approved	HCC-1, HCC-3, NCC-2, SCYL2, CKb1, MCIF	uc010wcq.1	Q16627	OTTHUMG00000188403	ENST00000394509.4:c.74C>T	17.37:g.34313612G>A	ENSP00000378017:p.Ser25Phe	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	131	71	0.541985	NM_032962	E1P649|E1P650|Q13954	Missense_Mutation	SNP	ENST00000394509.4	37	CCDS32624.1	65	0.02976190476190476	10	0.02032520325203252	6	0.016574585635359115	19	0.033216783216783216	30	0.0395778364116095	G	13.77	2.335048	0.41398	0.023377	0.029419	ENSG00000213494	ENST00000394509;ENST00000536149;ENST00000435911	T;T;T	0.03831	4.14;3.79;3.79	4.74	1.52	0.23074	Chemokine interleukin-8-like domain (1);	0.920382	0.09005	U	0.862372	T	0.02119	0.0066	.	.	.	0.09310	N	1	D;D	0.57571	0.965;0.98	P;P	0.55303	0.598;0.773	T	0.34750	-0.9816	9	0.42905	T	0.14	.	7.2842	0.26328	0.0:0.1675:0.4863:0.3462	.	25;25	Q16627;Q16627-2	CCL14_HUMAN;.	F	25	ENSP00000378017:S25F;ENSP00000441771:S25F;ENSP00000409197:S25F	ENSP00000378017:S25F	S	-	2	0	CCL14	31337725	0.012000	0.17670	0.000000	0.03702	0.004000	0.04260	1.387000	0.34430	0.180000	0.19960	-0.302000	0.09304	TCC	G|0.973;A|0.027	0.027	strong		0.562	CCL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272892.2	NM_032962	
WDR11	55717	hgsc.bcm.edu	37	10	122649482	122649482	+	Silent	SNP	A	A	G	rs2289337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:122649482A>G	ENST00000263461.6	+	18	2550	c.2304A>G	c.(2302-2304)gcA>gcG	p.A768A	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.A768A(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						AATTAATAGCAATGTACAATG	0.398													A|||	987	0.197085	0.2579	0.1628	5008	,	,		15097	0.0962		0.2207	False		,,,				2504	0.2188				p.A768A		Atlas-SNP	.											WDR11,NS,carcinoma,0,1	WDR11	95	1	1	Substitution - coding silent(1)	stomach(1)	c.A2304G						PASS	.	A		1230,3176	420.2+/-338.9	180,870,1153	113.0	107.0	109.0		2304	-2.9	1.0	10	dbSNP_100	109	1909,6691	338.5+/-322.8	216,1477,2607	yes	coding-synonymous	WDR11	NM_018117.11		396,2347,3760	GG,GA,AA		22.1977,27.9165,24.135		768/1225	122649482	3139,9867	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon18			AATAGCAATGTAC	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.2304A>G	10.37:g.122649482A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			T|0.005;G|0.229	0.229	strong		0.398	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
SLC44A2	57153	hgsc.bcm.edu	37	19	10713212	10713212	+	Silent	SNP	G	G	A	rs115559926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10713212G>A	ENST00000407327.4	+	1	27	c.6G>A	c.(4-6)gaG>gaA	p.E2E		NM_001145056.1	NP_001138528.1	Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	2					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	CGGCCATGGAGGACGAGCGGA	0.771													G|||	86	0.0171725	0.0643	0.0014	5008	,	,		6430	0.0		0.0	False		,,,				2504	0.0				p.E2E		Atlas-SNP	.											.	SLC44A2	56	.	0			c.G6A						PASS	.						7.0	12.0	11.0					19																	10713212		643	1532	2175	SO:0001819	synonymous_variant	57153	exon1			CATGGAGGACGAG	AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"""Solute carriers"""	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000407327.4:c.6G>A	19.37:g.10713212G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	21	13	0.619048	NM_001145056	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Silent	SNP	ENST00000407327.4	37	CCDS54216.1																																																																																			G|0.986;A|0.014	0.014	strong		0.771	SLC44A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452044.1		
NCOR2	9612	hgsc.bcm.edu	37	12	124856660	124856660	+	Silent	SNP	T	T	A	rs3741513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124856660T>A	ENST00000405201.1	-	20	2715	c.2715A>T	c.(2713-2715)acA>acT	p.T905T	NCOR2_ENST00000397355.1_Silent_p.T888T|NCOR2_ENST00000429285.2_Silent_p.T887T|NCOR2_ENST00000404621.1_Silent_p.T887T|NCOR2_ENST00000356219.3_Silent_p.T905T|NCOR2_ENST00000404121.2_Silent_p.T458T			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	905					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)		AGCTCTTGGCTGTGGTGGCCC	0.711													T|||	1929	0.385184	0.2549	0.5893	5008	,	,		11859	0.1677		0.5805	False		,,,				2504	0.4397				p.T905T		Atlas-SNP	.											.	NCOR2	475	.	0			c.A2715T						PASS	.	T	,,	1515,2681		291,933,874	27.0	37.0	34.0		2661,2661,2715	-5.4	0.0	12	dbSNP_107	34	5130,3294		1586,1958,668	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	1877,2891,1542	AA,AT,TT		39.1026,36.1058,47.3455	,,	887/2459,887/2505,905/2515	124856660	6645,5975	2098	4212	6310	SO:0001819	synonymous_variant	9612	exon22			CTTGGCTGTGGTG	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.2715A>T	12.37:g.124856660T>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			T|0.535;A|0.465	0.465	strong		0.711	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
OR2A25	392138	hgsc.bcm.edu	37	7	143771536	143771536	+	Missense_Mutation	SNP	G	G	A	rs6951485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	192	0	0		WXS	Illumina HiSeq	Phase_I	276	273	0.98913	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		
RARS2	57038	hgsc.bcm.edu	37	6	88279282	88279282	+	Silent	SNP	T	T	C	rs7748563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88279282T>C	ENST00000369536.5	-	2	108	c.63A>G	c.(61-63)ccA>ccG	p.P21P		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	21					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)		TCAAGTTTTCTGGTGGAAGAT	0.313													T|||	68	0.0135783	0.0477	0.0058	5008	,	,		18264	0.0		0.001	False		,,,				2504	0.0				p.P21P		Atlas-SNP	.											.	RARS2	61	.	0			c.A63G						PASS	.	T		160,4246	107.8+/-146.2	5,150,2048	110.0	113.0	112.0		63	2.8	1.0	6	dbSNP_116	112	0,8600		0,0,4300	no	coding-synonymous	RARS2	NM_020320.3		5,150,6348	CC,CT,TT		0.0,3.6314,1.2302		21/579	88279282	160,12846	2203	4300	6503	SO:0001819	synonymous_variant	57038	exon2			GTTTTCTGGTGGA	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.63A>G	6.37:g.88279282T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	157	71	0.452229	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Silent	SNP	ENST00000369536.5	37	CCDS5011.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	T	14.17	2.456129	0.43634	0.036314	0.0	ENSG00000146282	ENST00000369523	.	.	.	5.2	2.75	0.32379	.	.	.	.	.	T	0.41026	0.1141	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33137	-0.9880	5	0.39692	T	0.17	.	5.3844	0.16211	0.0:0.0915:0.177:0.7315	rs7748563;rs7748563	.	.	.	G	9	.	ENSP00000358536:R9G	R	-	1	2	RARS2	88336001	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	0.869000	0.27996	0.374000	0.24650	0.528000	0.53228	AGA	T|0.987;C|0.013	0.013	strong		0.313	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
RDH12	145226	hgsc.bcm.edu	37	14	68193731	68193731	+	Missense_Mutation	SNP	G	G	A	rs17852293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:68193731G>A	ENST00000551171.1	+	7	806	c.482G>A	c.(481-483)cGg>cAg	p.R161Q	RDH12_ENST00000539142.1_Missense_Mutation_p.R161Q|RDH12_ENST00000267502.3_Missense_Mutation_p.R161Q	NM_152443.2	NP_689656.2	Q96NR8	RDH12_HUMAN	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)	161			R -> Q (in dbSNP:rs17852293). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16269441, ECO:0000269|PubMed:21602930}.		photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	intracellular (GO:0005622)|photoreceptor inner segment membrane (GO:0060342)	retinol dehydrogenase activity (GO:0004745)			large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(4)	12				all cancers(60;0.000704)|OV - Ovarian serous cystadenocarcinoma(108;0.00161)|BRCA - Breast invasive adenocarcinoma(234;0.00953)	Vitamin A(DB00162)	CTCCTGGAGCGGCTAAAGGTG	0.587													G|||	527	0.105232	0.0885	0.1513	5008	,	,		20733	0.1101		0.1143	False		,,,				2504	0.0808				p.R161Q		Atlas-SNP	.											RDH12,brain,glioma,0,1	RDH12	43	1	0			c.G482A						PASS	.	G	GLN/ARG	421,3985	206.8+/-228.3	17,387,1799	70.0	63.0	65.0		482	0.7	1.0	14	dbSNP_123	65	1135,7465	233.6+/-266.8	76,983,3241	yes	missense	RDH12	NM_152443.2	43	93,1370,5040	AA,AG,GG		13.1977,9.5552,11.9637	benign	161/317	68193731	1556,11450	2203	4300	6503	SO:0001583	missense	145226	exon7			TGGAGCGGCTAAA	AK054835	CCDS9787.1	14q24.1	2013-02-14	2006-05-09		ENSG00000139988	ENSG00000139988	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19977	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 2"""	608830	"""retinol dehydrogenase 12 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_152443		Approved	FLJ30273, SDR7C2, LCA13, RP53	uc001xjz.4	Q96NR8		ENST00000551171.1:c.482G>A	14.37:g.68193731G>A	ENSP00000449079:p.Arg161Gln	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_152443	B2RDA2|Q8TAW6	Missense_Mutation	SNP	ENST00000551171.1	37	CCDS9787.1	241	0.11034798534798534	41	0.08333333333333333	47	0.1298342541436464	64	0.11188811188811189	89	0.11741424802110818	G	10.09	1.253769	0.22965	0.095552	0.131977	ENSG00000139988	ENST00000551171;ENST00000267502;ENST00000539142	D;D;D	0.89415	-2.51;-2.51;-2.51	5.66	0.738	0.18319	NAD(P)-binding domain (1);	0.197807	0.44483	N	0.000444	T	0.02342	0.0072	N	0.17901	0.54	0.34473	P	0.297021	B	0.26602	0.154	B	0.21917	0.037	T	0.29119	-1.0022	9	0.25751	T	0.34	.	5.8805	0.18852	0.2948:0.0:0.5847:0.1205	rs17852293	161	Q96NR8	RDH12_HUMAN	Q	161	ENSP00000449079:R161Q;ENSP00000267502:R161Q;ENSP00000438715:R161Q	ENSP00000267502:R161Q	R	+	2	0	RDH12	67263484	1.000000	0.71417	0.984000	0.44739	0.305000	0.27757	2.495000	0.45337	-0.123000	0.11745	-0.895000	0.02911	CGG	G|0.882;A|0.118	0.118	strong		0.587	RDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406918.1		
RAB40AL	282808	hgsc.bcm.edu	37	X	102192301	102192301	+	Silent	SNP	C	C	T	rs34191945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192301C>T	ENST00000218249.5	+	1	102	c.55C>T	c.(55-57)Ctg>Ttg	p.L19L	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	19					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						CAAGTTCCTGCTGGTGGGCGA	0.672													.|||	863	0.228609	0.3154	0.0648	3775	,	,		10089	0.1171		0.005	False		,,,				2504	0.2843				p.L19L		Atlas-SNP	.											.	RAB40AL	33	.	0			c.C55T						PASS	.	T		1374,2461		201,760,212,671,359	45.0	56.0	52.0		55	0.0	0.8	X	dbSNP_126	52	36,6692		0,28,8,2400,1864	no	coding-synonymous	RAB40AL	NM_001031834.1		201,788,220,3071,2223	TT,TC,T,CC,C		0.5351,35.8279,13.3485		19/279	102192301	1410,9153	2203	4300	6503	SO:0001819	synonymous_variant	282808	exon1			TTCCTGCTGGTGG	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"""Ras like GTPase"""	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.55C>T	X.37:g.102192301C>T		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	253	252	0.996047	NM_001031834	Q495H3	Silent	SNP	ENST00000218249.5	37	CCDS35353.1																																																																																			C|0.858;T|0.142	0.142	strong		0.672	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592193	1592193	+	Intron	SNP	C	C	T	rs371465078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1592193C>T	ENST00000381605.4	-	1	141				SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Silent_p.Q81Q|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000568365.1_Silent_p.Q81Q	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						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						GGCCTTCTTTCTGATTGTAGA	0.522													t|||	2823	0.563698	0.68	0.3876	5008	,	,		6072	0.631		0.3748	False		,,,				2504	0.6564				p.Q81Q		Atlas-SNP	.											SIRPB1_ENST00000279477,NS,malignant_melanoma,0,1	SIRPB1	83	1	0			c.G243A						PASS	.						94.0	111.0	106.0					20																	1592193		447	1317	1764	SO:0001627	intron_variant	10326	exon2			TTCTTTCTGATTG	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.76+8321G>A	20.37:g.1592193C>T		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	328	33	0.10061	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			.	.	weak		0.522	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
ALG1L	200810	hgsc.bcm.edu	37	3	125649403	125649403	+	Silent	SNP	C	C	A	rs7615952	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125649403C>A	ENST00000340333.3	-	5	508	c.345G>T	c.(343-345)ctG>ctT	p.L115L	FAM86JP_ENST00000485843.1_RNA	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like	115							transferase activity, transferring glycosyl groups (GO:0016757)			large_intestine(2)|lung(2)	4						TGGCTACCTGCAGAGCTGCCA	0.577													.|||	1172	0.234026	0.4841	0.1527	5008	,	,		17875	0.1071		0.172	False		,,,				2504	0.1483				p.L135L		Atlas-SNP	.											.	ALG1L	12	.	0			c.G405T						PASS	.	C	,	1082,1666		199,684,491	60.0	56.0	57.0		345,405	0.0	0.8	3	dbSNP_116	57	729,3933		73,583,1675	no	coding-synonymous,coding-synonymous	ALG1L	NM_001015050.2,NM_001195223.1	,	272,1267,2166	AA,AC,CC		15.6371,39.3741,24.4399	,	115/188,135/208	125649403	1811,5599	1374	2331	3705	SO:0001819	synonymous_variant	200810	exon6			TACCTGCAGAGCT	BC073816	CCDS33840.1, CCDS74998.1	3q21.2	2013-02-22	2013-02-22		ENSG00000189366	ENSG00000189366		"""Glycosyltransferase group 1 domain containing"""	33721	protein-coding gene	gene with protein product	"""asparagine-linked glycosylation 1-like 1"""		"""asparagine-linked glycosylation 1-like"""				Standard	NM_001015050		Approved	ALG1L1	uc003eig.2	Q6GMV1	OTTHUMG00000159588	ENST00000340333.3:c.345G>T	3.37:g.125649403C>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_001195223	D3DNA5	Silent	SNP	ENST00000340333.3	37	CCDS33840.1																																																																																			.	.	weak		0.577	ALG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356347.1	NM_001015050	
SPATA7	55812	hgsc.bcm.edu	37	14	88852166	88852166	+	Missense_Mutation	SNP	G	G	A	rs4904448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:88852166G>A	ENST00000393545.4	+	1	293	c.4G>A	c.(4-6)Gat>Aat	p.D2N	SPATA7_ENST00000356583.5_Missense_Mutation_p.D2N|SPATA7_ENST00000554102.1_3'UTR|SPATA7_ENST00000045347.7_Missense_Mutation_p.D2N|SPATA7_ENST00000556553.1_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						scavenged	.	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	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	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		
ALG3	10195	hgsc.bcm.edu	37	3	183963000	183963000	+	Silent	SNP	A	A	G	rs2233464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183963000A>G	ENST00000397676.3	-	4	621	c.591T>C	c.(589-591)ggT>ggC	p.G197G	EIF2B5_ENST00000444495.1_Intron|ALG3_ENST00000445626.2_Silent_p.G149G|ALG3_ENST00000455059.1_Silent_p.G157G|ALG3_ENST00000418734.2_Silent_p.G141G|ALG3_ENST00000463495.1_5'Flank	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase	197					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)			kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AAAAGCAGCAACCCCAGCCCC	0.542													G|||	247	0.0493211	0.1808	0.0115	5008	,	,		20053	0.0		0.0	False		,,,				2504	0.0				p.G197G		Atlas-SNP	.											.	ALG3	48	.	0			c.T591C						PASS	.	G	,	483,3459		24,435,1512	36.0	42.0	40.0		447,591	2.0	1.0	3	dbSNP_98	40	4,8306		0,4,4151	no	coding-synonymous,coding-synonymous	ALG3	NM_001006941.2,NM_005787.5	,	24,439,5663	GG,GA,AA		0.0481,12.2527,3.9749	,	149/391,197/439	183963000	487,11765	1971	4155	6126	SO:0001819	synonymous_variant	10195	exon4			GCAGCAACCCCAG	BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	23056	protein-coding gene	gene with protein product	"""carbohydrate deficient glycoprotein syndrome type IV"", ""dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase"", ""dol-P-Man dependent alpha-1,3- mannosyltransferase"""	608750	"""asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"""			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823	ENST00000397676.3:c.591T>C	3.37:g.183963000A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	136	67	0.492647	NM_005787	A8JZZ6|Q9BT71	Silent	SNP	ENST00000397676.3	37	CCDS46968.1																																																																																			A|0.962;G|0.038	0.038	strong		0.542	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787	
NR1H3	10062	hgsc.bcm.edu	37	11	47282024	47282024	+	Silent	SNP	C	C	T	rs2279238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:47282024C>T	ENST00000467728.1	+	3	1535	c.297C>T	c.(295-297)agC>agT	p.S99S	NR1H3_ENST00000405853.3_Silent_p.S99S|NR1H3_ENST00000529540.1_3'UTR|NR1H3_ENST00000441012.2_Silent_p.S99S|NR1H3_ENST00000481889.2_Silent_p.S54S|NR1H3_ENST00000527949.1_Silent_p.S8S|NR1H3_ENST00000407404.1_Silent_p.S99S|NR1H3_ENST00000405576.1_Silent_p.S54S|NR1H3_ENST00000395397.3_Silent_p.S54S			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	99					apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|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 hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						AGCTATGCAGCGTGTGTGGGG	0.582													C|||	1772	0.353834	0.4228	0.2622	5008	,	,		19004	0.6726		0.1521	False		,,,				2504	0.2045				p.S105S		Atlas-SNP	.											.	NR1H3	52	.	0			c.C315T	GRCh37	CM066153	NR1H3	M	rs2279238	PASS	.	C	,,	1612,2790	498.1+/-364.0	290,1032,879	73.0	68.0	70.0		297,162,297	-6.7	0.9	11	dbSNP_100	70	1281,7315	253.3+/-279.0	94,1093,3111	no	coding-synonymous,coding-synonymous,coding-synonymous	NR1H3	NM_001130101.1,NM_001130102.1,NM_005693.2	,,	384,2125,3990	TT,TC,CC		14.9023,36.6197,22.2573	,,	99/388,54/403,99/448	47282024	2893,10105	2201	4298	6499	SO:0001819	synonymous_variant	10062	exon4			ATGCAGCGTGTGT	U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434		"""Nuclear hormone receptors"""	7966	protein-coding gene	gene with protein product	"""liver X receptor-alpha"""	602423				8621574, 7744246	Standard	NM_005693		Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.297C>T	11.37:g.47282024C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_001251934	A8K3J9|D3DQR1|Q8IW13|Q96H87	Silent	SNP	ENST00000467728.1	37	CCDS7929.1																																																																																			C|0.733;T|0.267	0.267	strong		0.582	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319214.3		
NFATC4	4776	hgsc.bcm.edu	37	14	24839165	24839165	+	Silent	SNP	C	C	T	rs2228233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24839165C>T	ENST00000250373.4	+	2	702	c.561C>T	c.(559-561)gaC>gaT	p.D187D	NFATC4_ENST00000557451.1_Silent_p.D117D|NFATC4_ENST00000554966.1_Silent_p.D200D|NFATC4_ENST00000554661.1_Silent_p.D117D|NFATC4_ENST00000556279.1_Silent_p.D219D|NFATC4_ENST00000555590.1_Silent_p.D200D|NFATC4_ENST00000440487.2_3'UTR|NFATC4_ENST00000554050.1_Silent_p.D187D|NFATC4_ENST00000554344.1_Silent_p.D117D|NFATC4_ENST00000422617.3_Silent_p.D175D|NFATC4_ENST00000554591.1_Silent_p.D250D|NFATC4_ENST00000553469.1_Silent_p.D219D|NFATC4_ENST00000555453.1_Silent_p.D175D|NFATC4_ENST00000424781.2_Silent_p.D200D|NFATC4_ENST00000413692.2_Silent_p.D250D|NFATC4_ENST00000556169.1_Silent_p.D175D|NFATC4_ENST00000555167.1_5'Flank|NFATC4_ENST00000556759.1_5'Flank|NFATC4_ENST00000554473.1_5'Flank|NFATC4_ENST00000539237.2_Silent_p.D219D|NFATC4_ENST00000553708.1_Silent_p.D187D|NFATC4_ENST00000553879.1_Silent_p.D117D	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	187	Pro-rich.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		ATGCCTCTGACGAGGCAGCCC	0.677													C|||	2004	0.40016	0.3986	0.4323	5008	,	,		13805	0.4692		0.2644	False		,,,				2504	0.4479				p.D250D		Atlas-SNP	.											.	NFATC4	115	.	0			c.C750T						PASS	.	C	,,,,	1539,2789		287,965,912	23.0	25.0	24.0		750,561,351,750,561	-7.2	0.2	14	dbSNP_98	24	2264,6272		323,1618,2327	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFATC4	NM_001136022.1,NM_001198965.1,NM_001198966.1,NM_001198967.1,NM_004554.4	,,,,	610,2583,3239	TT,TC,CC		26.523,35.5591,29.5631	,,,,	250/965,187/795,117/833,250/858,187/903	24839165	3803,9061	2164	4268	6432	SO:0001819	synonymous_variant	4776	exon3			CTCTGACGAGGCA	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"""Nuclear factor of activated T-cells"""	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.561C>T	14.37:g.24839165C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Silent	SNP	ENST00000250373.4	37	CCDS9629.1																																																																																			C|0.667;T|0.333	0.333	strong		0.677	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554	
CTNND2	1501	hgsc.bcm.edu	37	5	10973727	10973727	+	Silent	SNP	G	G	A	rs1566622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:10973727G>A	ENST00000304623.8	-	22	3705	c.3516C>T	c.(3514-3516)ttC>ttT	p.F1172F	CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000503622.1_Silent_p.F835F|CTNND2_ENST00000458100.2_Silent_p.F739F|CTNND2_ENST00000511377.1_Silent_p.F1081F|CTNND2_ENST00000359640.2_Silent_p.F1114F	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	1172					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.F1172F(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						CCTGGTCCTCGAAGAAGGACT	0.547													G|||	616	0.123003	0.1573	0.0836	5008	,	,		18194	0.2093		0.0746	False		,,,				2504	0.0654				p.F1172F		Atlas-SNP	.											CTNND2,colon,carcinoma,-2,3	CTNND2	289	3	1	Substitution - coding silent(1)	skin(1)	c.C3516T						PASS	.	G		611,3795	266.2+/-267.1	41,529,1633	142.0	120.0	128.0		3516	-0.9	1.0	5	dbSNP_88	128	748,7852	180.3+/-229.3	41,666,3593	no	coding-synonymous	CTNND2	NM_001332.2		82,1195,5226	AA,AG,GG		8.6977,13.8675,10.449		1172/1226	10973727	1359,11647	2203	4300	6503	SO:0001819	synonymous_variant	1501	exon22			GTCCTCGAAGAAG	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"""Armadillo repeat containing"""	2516	protein-coding gene	gene with protein product	"""neural plakophilin-related arm-repeat protein"""	604275	"""catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"""			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.3516C>T	5.37:g.10973727G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	178	89	0.5	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Silent	SNP	ENST00000304623.8	37	CCDS3881.1																																																																																			G|0.882;A|0.118	0.118	strong		0.547	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332	
CD163	9332	hgsc.bcm.edu	37	12	7636027	7636027	+	Silent	SNP	A	A	G	rs78817356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7636027A>G	ENST00000359156.4	-	12	3226	c.3024T>C	c.(3022-3024)tgT>tgC	p.C1008C	CD163_ENST00000396620.3_Silent_p.C1041C|CD163_ENST00000541972.1_Silent_p.C996C|CD163_ENST00000539632.1_5'UTR|CD163_ENST00000432237.2_Silent_p.C1008C	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	1008	SRCR 9. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	GTCTGGCAGGACAATCCCACA	0.507													A|||	144	0.028754	0.1014	0.013	5008	,	,		-128	0.0		0.001	False		,,,				2504	0.0				p.C1008C		Atlas-SNP	.											.	CD163	221	.	0			c.T3024C						PASS	.	A	,	305,4101	164.4+/-196.0	6,293,1904	131.0	112.0	118.0		3024,3024	0.5	1.0	12	dbSNP_131	118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CD163	NM_004244.5,NM_203416.3	,	6,294,6203	GG,GA,AA		0.0116,6.9224,2.3528	,	1008/1157,1008/1122	7636027	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	9332	exon12			GGCAGGACAATCC	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"""CD molecules"""	1631	protein-coding gene	gene with protein product		605545	"""CD163 antigen"""			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.3024T>C	12.37:g.7636027A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	37	CCDS8578.1	42	0.019230769230769232	35	0.07113821138211382	7	0.019337016574585635	0	0.0	0	0.0	A	10.17	1.275594	0.23307	0.069224	1.16E-4	ENSG00000177575	ENST00000537626	.	.	.	5.4	0.458	0.16670	.	.	.	.	.	T	0.08313	0.0207	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.04103	-1.0977	4	.	.	.	.	8.3663	0.32389	0.6729:0.0:0.3271:0.0	.	.	.	.	A	21	.	.	V	-	2	0	CD163	7527294	0.000000	0.05858	0.998000	0.56505	0.984000	0.73092	-0.124000	0.10595	0.121000	0.18284	-0.388000	0.06559	GTC	A|0.978;G|0.022	0.022	strong		0.507	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416	
ADAMTSL5	339366	hgsc.bcm.edu	37	19	1506799	1506799	+	Silent	SNP	C	C	T	rs79538691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1506799C>T	ENST00000413997.2	-	10	1010	c.1011G>A	c.(1009-1011)gtG>gtA	p.V337V	ADAMTSL5_ENST00000395467.2_Silent_p.V96V|CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000590562.1_5'UTR|ADAMTSL5_ENST00000330475.4_Silent_p.V327V			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	337						extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTGAGGCTCCACCCCCCGGG	0.711													C|||	101	0.0201677	0.0756	0.0014	5008	,	,		10308	0.0		0.0	False		,,,				2504	0.0				p.V327V		Atlas-SNP	.											.	ADAMTSL5	24	.	0			c.G981A						PASS	.	C		192,3668		2,188,1740	7.0	10.0	9.0		981	1.9	0.8	19	dbSNP_131	9	1,7767		0,1,3883	no	coding-synonymous	ADAMTSL5	NM_213604.2		2,189,5623	TT,TC,CC		0.0129,4.9741,1.6598		327/472	1506799	193,11435	1930	3884	5814	SO:0001819	synonymous_variant	339366	exon10			AGGCTCCACCCCC	BC040620	CCDS12071.1	19p13.3	2008-02-05	2006-02-07	2006-02-07		ENSG00000185761			27912	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain containing 6"""	THSD6			Standard	NM_213604		Approved		uc002ltd.2	Q6ZMM2		ENST00000413997.2:c.1011G>A	19.37:g.1506799C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_213604	B4DXK7|Q8IW95	Silent	SNP	ENST00000413997.2	37																																																																																				C|0.982;T|0.018	0.018	strong		0.711	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding		XM_294919	
FOXA3	3171	hgsc.bcm.edu	37	19	46375779	46375779	+	Silent	SNP	C	C	T	rs16980091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	81	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	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		
IFITM3	10410	hgsc.bcm.edu	37	11	320649	320649	+	Silent	SNP	G	G	A	rs11553885	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:320649G>A	ENST00000399808.4	-	1	401	c.165C>T	c.(163-165)ccC>ccT	p.P55P	RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Silent_p.P34P|IFITM3_ENST00000526811.1_Silent_p.P34P|RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.14_ENST00000602809.1_lincRNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	55					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.P55P(5)		central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-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;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		CGACATGGTCGGGCACGGAGG	0.637																																					p.P55P		Atlas-SNP	.											IFITM3,caecum,carcinoma,0,23	IFITM3	132	23	5	Substitution - coding silent(5)	endometrium(4)|central_nervous_system(1)	c.C165T						scavenged	.						93.0	98.0	96.0					11																	320649		2062	4173	6235	SO:0001819	synonymous_variant	10410	exon1			ATGGTCGGGCACG	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"""interferon induced transmembrane protein 3 (1-8U)"""			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.165C>T	11.37:g.320649G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	17	0.137097	NM_021034	Q53Y76|Q96HK8|Q96J15	Silent	SNP	ENST00000399808.4	37	CCDS41585.1																																																																																			G|0.946;A|0.054	0.054	strong		0.637	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034	
CLEC2D	29121	hgsc.bcm.edu	37	12	9833628	9833628	+	Splice_Site	SNP	C	C	T	rs3764021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9833628C>T	ENST00000290855.6	+	2	193	c.171C>T	c.(169-171)agC>agT	p.S57S	CLEC2D_ENST00000487752.1_3'UTR|CLEC2D_ENST00000543300.1_Splice_Site_p.S57S|CLEC2D_ENST00000261340.7_Splice_Site_p.S57S|CLEC2D_ENST00000545918.1_Intron|CLEC2D_ENST00000261339.6_Intron	NM_013269.5	NP_037401.1	Q9UHP7	CLC2D_HUMAN	C-type lectin domain family 2, member D	57					cell surface receptor signaling pathway (GO:0007166)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|stomach(1)	9						CTGCTTTAAGCGGTAAGTGAA	0.299													C|||	2327	0.464657	0.5635	0.4092	5008	,	,		-128	0.371		0.4692	False		,,,				2504	0.4622				p.S57S		Atlas-SNP	.											CLEC2D_ENST00000290855,colon,carcinoma,0,4	CLEC2D	54	4	0			c.C171T						PASS	.	C	,,,,	2403,2001	614.1+/-392.3	643,1117,442	120.0	117.0	118.0	http://www.ncbi.nlm.nih.gov/pubmed?term	171,,171,,171	-2.4	0.0	12	dbSNP_107	118	4075,4521	558.0+/-387.2	980,2115,1203	yes	coding-synonymous-near-splice,intron,coding-synonymous-near-splice,intron,coding-synonymous-near-splice	CLEC2D	NM_001004419.3,NM_001197317.1,NM_001197318.1,NM_001197319.1,NM_013269.4	,,,,	1623,3232,1645	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	47.4058,45.436,49.8308	,,,,	57/195,,57/133,,57/192	9833628	6478,6522	2202	4298	6500	SO:0001630	splice_region_variant	29121	exon2			TTTAAGCGGTAAG	AF133299	CCDS8602.1, CCDS31741.1, CCDS55800.1, CCDS55801.1, CCDS55802.1	12p13.31	2011-05-24	2005-09-29		ENSG00000069493	ENSG00000069493		"""C-type lectin domain containing"""	14351	protein-coding gene	gene with protein product	"""C-type lectin related f"", ""lectin-like transcript 1"""	605659	"""C-type lectin superfamily 2, member D"""				Standard	NM_013269		Approved	LLT1, CLAX, OCIL	uc001qwf.3	Q9UHP7	OTTHUMG00000168369	ENST00000290855.6:c.172+1C>T	12.37:g.9833628C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_001004419	D6CI39|D6CI40|D6CI41|Q6YID5|Q8WUP7|Q9HD37|Q9HD38	Silent	SNP	ENST00000290855.6	37	CCDS8602.1																																																																																			C|0.519;T|0.481	0.481	strong		0.299	CLEC2D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000335424.2	NM_013269	Silent
PPP2R2C	5522	hgsc.bcm.edu	37	4	6325086	6325086	+	Silent	SNP	G	G	A	rs3796403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6325086G>A	ENST00000382599.4	-	9	1503	c.1287C>T	c.(1285-1287)atC>atT	p.I429I	PPP2R2C_ENST00000506140.1_Silent_p.I422I|PPP2R2C_ENST00000515571.1_Silent_p.I412I|PPP2R2C_ENST00000335585.5_Silent_p.I429I|PPP2R2C_ENST00000507294.1_Silent_p.I422I			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	429					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						TGGTGGCGGCGATGGCAATGA	0.577													G|||	3274	0.653754	0.4266	0.6614	5008	,	,		18326	0.9385		0.5795	False		,,,				2504	0.7382				p.I429I		Atlas-SNP	.											.	PPP2R2C	63	.	0			c.C1287T						PASS	.	G	,,,	2013,2393	560.8+/-380.6	460,1093,650	197.0	144.0	162.0		1266,1266,1236,1287	-0.2	0.7	4	dbSNP_107	162	5064,3536	631.1+/-398.4	1488,2088,724	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP2R2C	NM_001206994.1,NM_001206995.1,NM_001206996.1,NM_181876.2	,,,	1948,3181,1374	AA,AG,GG		41.1163,45.6877,45.5867	,,,	422/441,422/441,412/431,429/448	6325086	7077,5929	2203	4300	6503	SO:0001819	synonymous_variant	5522	exon9			GGCGGCGATGGCA	AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9306	protein-coding gene	gene with protein product	"""PP2A subunit B isoform gamma"""	605997	"""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform"""			10574460, 10945473	Standard	NM_020416		Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.1287C>T	4.37:g.6325086G>A		Somatic	365	0	0		WXS	Illumina HiSeq	Phase_I	389	388	0.997429	NM_181876	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Silent	SNP	ENST00000382599.4	37																																																																																				G|0.407;A|0.593	0.593	strong		0.577	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876	
ENAM	10117	hgsc.bcm.edu	37	4	71509086	71509086	+	Missense_Mutation	SNP	T	T	C	rs7671281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71509086T>C	ENST00000396073.3	+	9	2224	c.1943T>C	c.(1942-1944)aTa>aCa	p.I648T	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	648			I -> T (in dbSNP:rs7671281). {ECO:0000269|PubMed:18245370}.		amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CAGAAGGAGATAGTCCCTTAT	0.453													C|||	910	0.181709	0.5348	0.111	5008	,	,		18323	0.0228		0.0487	False		,,,				2504	0.0552				p.I648T		Atlas-SNP	.											.	ENAM	140	.	0			c.T1943C						PASS	.	C	THR/ILE	1951,2455	620.5+/-393.6	430,1091,682	111.0	116.0	114.0		1943	0.5	0.0	4	dbSNP_116	114	377,8223	802.2+/-407.3	4,369,3927	yes	missense	ENAM	NM_031889.2	89	434,1460,4609	CC,CT,TT		4.3837,44.2805,17.8994	benign	648/1143	71509086	2328,10678	2203	4300	6503	SO:0001583	missense	10117	exon9			AGGAGATAGTCCC	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1943T>C	4.37:g.71509086T>C	ENSP00000379383:p.Ile648Thr	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	123	53	0.430894	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	341	0.15613553113553114	258	0.524390243902439	40	0.11049723756906077	5	0.008741258741258742	38	0.05013192612137203	C	0.011	-1.711190	0.00712	0.442805	0.043837	ENSG00000132464	ENST00000396073	T	0.25414	1.8	5.65	0.53	0.17102	.	0.377541	0.23112	N	0.051783	T	0.00012	0.0000	N	0.00049	-2.415	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43261	-0.9402	9	0.02654	T	1	-2.606	1.0929	0.01667	0.1455:0.3194:0.2828:0.2523	rs7671281;rs52818760;rs7671281	648	Q9NRM1	ENAM_HUMAN	T	648	ENSP00000379383:I648T	ENSP00000379383:I648T	I	+	2	0	ENAM	71727950	0.000000	0.05858	0.020000	0.16555	0.939000	0.58152	-0.766000	0.04725	0.342000	0.23796	-0.119000	0.15052	ATA	T|0.819;C|0.181	0.181	strong		0.453	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889	
TNFRSF8	943	hgsc.bcm.edu	37	1	12186058	12186058	+	Missense_Mutation	SNP	A	A	G	rs2230625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12186058A>G	ENST00000263932.2	+	11	1426	c.1204A>G	c.(1204-1206)Agc>Ggc	p.S402G	TNFRSF8_ENST00000479933.2_3'UTR|TNFRSF8_ENST00000413146.2_5'UTR|TNFRSF8_ENST00000417814.2_Missense_Mutation_p.S291G	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	402			S -> G (in dbSNP:rs2230625). {ECO:0000269|Ref.5}.		cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-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;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	GGTCGGCTCCAGCGCCTTCCT	0.612													A|||	454	0.090655	0.177	0.036	5008	,	,		16773	0.129		0.0209	False		,,,				2504	0.045				p.S402G		Atlas-SNP	.											TNFRSF8,NS,carcinoma,-2,1	TNFRSF8	70	1	0			c.A1204G						PASS	.	A	GLY/SER,	745,3661	306.9+/-289.7	60,625,1518	194.0	168.0	177.0		1204,	-7.8	0.0	1	dbSNP_98	177	166,8434	76.6+/-139.3	1,164,4135	yes	missense,utr-5	TNFRSF8	NM_001243.3,NM_152942.2	56,	61,789,5653	GG,GA,AA		1.9302,16.9088,7.0045	benign,	402/596,	12186058	911,12095	2203	4300	6503	SO:0001583	missense	943	exon11			GGCTCCAGCGCCT	M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.1204A>G	1.37:g.12186058A>G	ENSP00000263932:p.Ser402Gly	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	331	167	0.504532	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Missense_Mutation	SNP	ENST00000263932.2	37	CCDS144.1	171	0.0782967032967033	83	0.16869918699186992	12	0.03314917127071823	63	0.11013986013986014	13	0.017150395778364115	A	4.408	0.075392	0.08485	0.169088	0.019302	ENSG00000120949	ENST00000263932;ENST00000417814	T;T	0.07908	3.15;3.15	3.87	-7.75	0.01236	.	6.146930	0.00166	N	0.000012	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.34304	-0.9834	9	0.14252	T	0.57	-0.1276	8.9345	0.35691	0.2079:0.0:0.6671:0.125	rs2230625;rs2297728;rs11569913;rs57411254;rs11569913	291;402	D3YTD8;P28908	.;TNR8_HUMAN	G	402;291	ENSP00000263932:S402G;ENSP00000390650:S291G	ENSP00000263932:S402G	S	+	1	0	TNFRSF8	12108645	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-2.703000	0.00822	-1.694000	0.01425	0.533000	0.62120	AGC	A|0.922;G|0.078	0.078	strong		0.612	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1		
C1QL2	165257	hgsc.bcm.edu	37	2	119915750	119915750	+	Silent	SNP	G	G	T	rs113019193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:119915750G>T	ENST00000272520.3	-	1	715	c.96C>A	c.(94-96)atC>atA	p.I32I		NM_182528.3	NP_872334.2	Q7Z5L3	C1QL2_HUMAN	complement component 1, q subcomponent-like 2	32					protein oligomerization (GO:0051259)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)				NS(1)|endometrium(1)|large_intestine(3)|pancreas(1)|prostate(1)	7						AAGGGTCGCAGATCATGCGGC	0.721										HNSCC(49;0.14)			G|||	87	0.0173722	0.0628	0.0043	5008	,	,		7998	0.0		0.001	False		,,,				2504	0.0				p.I32I		Atlas-SNP	.											.	C1QL2	25	.	0			c.C96A						PASS	.	G		134,3240		1,132,1554	6.0	7.0	7.0		96	3.3	1.0	2	dbSNP_132	7	8,7550		0,8,3771	no	coding-synonymous	C1QL2	NM_182528.3		1,140,5325	TT,TG,GG		0.1058,3.9715,1.2989		32/288	119915750	142,10790	1687	3779	5466	SO:0001819	synonymous_variant	165257	exon1			GTCGCAGATCATG	AF525315	CCDS42737.1	2q14.2	2009-05-20			ENSG00000144119	ENSG00000144119			24181	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 10"""	614330				18783346	Standard	NM_182528		Approved	CTRP10, C1QTNF10	uc002tlo.2	Q7Z5L3	OTTHUMG00000153271	ENST00000272520.3:c.96C>A	2.37:g.119915750G>T		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	7	4	0.571429	NM_182528		Silent	SNP	ENST00000272520.3	37	CCDS42737.1																																																																																			G|0.981;T|0.019	0.019	strong		0.721	C1QL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330527.2	NM_182528	
ISYNA1	51477	hgsc.bcm.edu	37	19	18547209	18547209	+	Silent	SNP	G	G	A	rs61743954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18547209G>A	ENST00000338128.8	-	6	907	c.690C>T	c.(688-690)aaC>aaT	p.N230N	ISYNA1_ENST00000317018.6_Silent_p.N28N|ISYNA1_ENST00000457269.4_Silent_p.N176N|ISYNA1_ENST00000578963.1_Silent_p.N102N|ISYNA1_ENST00000545187.1_Silent_p.N80N	NM_001170938.1|NM_016368.4	NP_001164409.1|NP_057452.1	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	230					inositol biosynthetic process (GO:0006021)|inositol phosphate metabolic process (GO:0043647)|phospholipid biosynthetic process (GO:0008654)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-3-phosphate synthase activity (GO:0004512)			breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	12						AGCGCTCCGTGTTCGCCGTCC	0.632																																					p.N230N		Atlas-SNP	.											.	ISYNA1	31	.	0			c.C690T						PASS	.	G	,,	205,4201	129.8+/-166.5	5,195,2003	104.0	93.0	97.0		528,240,690	1.6	0.5	19	dbSNP_129	97	54,8546	34.8+/-89.0	0,54,4246	no	coding-synonymous,coding-synonymous,coding-synonymous	ISYNA1	NM_001170938.1,NM_001170939.1,NM_016368.4	,,	5,249,6249	AA,AG,GG		0.6279,4.6527,1.9914	,,	176/505,80/409,230/559	18547209	259,12747	2203	4300	6503	SO:0001819	synonymous_variant	51477	exon6			CTCCGTGTTCGCC		CCDS12379.1, CCDS54234.1, CCDS62603.1	19p13.11	2014-09-04			ENSG00000105655	ENSG00000105655	5.5.1.4		29821	protein-coding gene	gene with protein product	"""myo-inositol 1-phosphate synthase"""	611670				15024000, 12941308	Standard	NM_016368		Approved	Ino1, INOS, IPS	uc002njd.2	Q9NPH2	OTTHUMG00000179027	ENST00000338128.8:c.690C>T	19.37:g.18547209G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_016368	B3KRT1|G5E9U0|Q6NXT5|Q7Z525|Q9BT65|Q9H2Y2|Q9NSU0|Q9NVW7	Silent	SNP	ENST00000338128.8	37	CCDS12379.1																																																																																			G|0.982;A|0.018	0.018	strong		0.632	ISYNA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444469.2	NM_016368	
MYH4	4622	hgsc.bcm.edu	37	17	10354747	10354747	+	Missense_Mutation	SNP	C	C	T	rs200121484		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10354747C>T	ENST00000255381.2	-	28	3871	c.3761G>A	c.(3760-3762)cGc>cAc	p.R1254H	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1254					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)	p.R1254H(1)		NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						CTCTAGGGTGCGGCACATTTT	0.418													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11762	0.0		0.0	False		,,,				2504	0.0				p.R1254H		Atlas-SNP	.											MYH4,caecum,carcinoma,0,1	MYH4	349	1	1	Substitution - Missense(1)	large_intestine(1)	c.G3761A						PASS	.	C	HIS/ARG	5,4401	9.9+/-24.2	0,5,2198	159.0	139.0	146.0		3761	3.6	1.0	17		146	0,8600		0,0,4300	yes	missense	MYH4	NM_017533.2	29	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	probably-damaging	1254/1940	10354747	5,13001	2203	4300	6503	SO:0001583	missense	4622	exon28			AGGGTGCGGCACA		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.3761G>A	17.37:g.10354747C>T	ENSP00000255381:p.Arg1254His	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	202	99	0.490099	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.511257	0.64522	0.001135	0.0	ENSG00000141048	ENST00000255381	T	0.78924	-1.22	5.62	3.64	0.41730	Myosin tail (1);	0.000000	0.37219	U	0.002181	T	0.76300	0.3968	M	0.65975	2.015	0.44359	D	0.997257	B	0.18863	0.031	B	0.26770	0.073	T	0.73688	-0.3904	10	0.59425	D	0.04	.	12.8771	0.57996	0.0:0.8666:0.0:0.1334	.	1254	Q9Y623	MYH4_HUMAN	H	1254	ENSP00000255381:R1254H	ENSP00000255381:R1254H	R	-	2	0	MYH4	10295472	0.952000	0.32445	0.963000	0.40424	0.878000	0.50629	2.224000	0.42945	0.845000	0.35118	0.655000	0.94253	CGC	.	.	weak		0.418	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
RUNDC3A	10900	hgsc.bcm.edu	37	17	42392622	42392622	+	Silent	SNP	T	T	C	rs708386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42392622T>C	ENST00000426726.3	+	7	1003	c.729T>C	c.(727-729)gaT>gaC	p.D243D	RUNDC3A_ENST00000225441.7_Silent_p.D243D|AC003102.3_ENST00000588097.1_RNA|RUNDC3A_ENST00000590941.1_Silent_p.D238D	NM_001144825.1	NP_001138297.1	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A	243	Interaction with RAP2A. {ECO:0000250}.				positive regulation of cGMP biosynthetic process (GO:0030828)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanylate cyclase activator activity (GO:0030250)|small GTPase regulator activity (GO:0005083)			large_intestine(1)|lung(1)|ovary(2)	4		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		TCGTCACCGATGAGGACAGCT	0.682													C|||	3162	0.63139	0.711	0.5634	5008	,	,		10721	0.9097		0.3877	False		,,,				2504	0.5358				p.D243D	Pancreas(82;1061 1416 11136 20771 23901)	Atlas-SNP	.											.	RUNDC3A	30	.	0			c.T729C						PASS	.	C	,,	2366,1526		763,840,343	8.0	13.0	11.0		729,714,729	1.1	1.0	17	dbSNP_86	11	2711,5087		530,1651,1718	no	coding-synonymous,coding-synonymous,coding-synonymous	RUNDC3A	NM_001144825.1,NM_001144826.1,NM_006695.4	,,	1293,2491,2061	CC,CT,TT		34.7653,39.2086,43.4303	,,	243/447,238/401,243/406	42392622	5077,6613	1946	3899	5845	SO:0001819	synonymous_variant	10900	exon7			CACCGATGAGGAC	AF055026	CCDS45698.1, CCDS45699.1, CCDS59294.1	17q21.31	2008-02-05			ENSG00000108309	ENSG00000108309			16984	protein-coding gene	gene with protein product		605448				9523700	Standard	NM_006695		Approved	RPIP8, RAP2IP	uc002igl.4	Q59EK9	OTTHUMG00000169259	ENST00000426726.3:c.729T>C	17.37:g.42392622T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_001144825	B2R974|O15483|O60651|Q7Z3S2|Q9UF50	Silent	SNP	ENST00000426726.3	37	CCDS45698.1																																																																																			T|0.367;C|0.633	0.633	strong		0.682	RUNDC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403173.2	NM_006695	
POU5F1B	5462	hgsc.bcm.edu	37	8	128428721	128428721	+	Silent	SNP	C	C	T	rs192151034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:128428721C>T	ENST00000465342.2	+	2	1767	c.610C>T	c.(610-612)Ctg>Ttg	p.L204L	POU5F1B_ENST00000391675.1_Silent_p.L204L|CASC8_ENST00000501396.1_RNA|CASC8_ENST00000523825.1_RNA|CASC8_ENST00000502082.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	204	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|prostate(1)|urinary_tract(1)	3						GCGGCCCTTGCTGCAGAAGTG	0.502													c|||	78	0.0155751	0.053	0.0115	5008	,	,		19515	0.0		0.0	False		,,,				2504	0.0				p.L204L		Atlas-SNP	.											.	POU5F1B	32	.	0			c.C610T						PASS	.	C		73,1311		2,69,621	17.0	21.0	20.0		610	1.1	0.8	8		20	0,3180		0,0,1590	no	coding-synonymous	POU5F1B	NM_001159542.1		2,69,2211	TT,TC,CC		0.0,5.2746,1.5995		204/360	128428721	73,4491	692	1590	2282	SO:0001819	synonymous_variant	5462	exon1			CCCTTGCTGCAGA	AF268615	CCDS55274.1	8q24.21	2011-06-20	2009-04-15	2009-04-15	ENSG00000212993	ENSG00000212993		"""Homeoboxes / POU class"""	9223	protein-coding gene	gene with protein product		615739	"""POU domain class 5, transcription factor 1 pseudogene 1"", ""POU class 5 homeobox 1 pseudogene 1"""	OTF3P1, POU5F1P1		1408763	Standard	NM_001159542		Approved	OTF3C	uc003ysf.3	Q06416	OTTHUMG00000157807	ENST00000465342.2:c.610C>T	8.37:g.128428721C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	159	86	0.540881	NM_001159542	D5K9S4|D5K9S9|D5K9T0|D5K9T1|D5K9T3|D5K9U3|D5K9U6|D5K9V4|D5K9V6|D5K9W0|D5K9W2|D5K9W7|D5K9X2|D5K9X3|D5K9X5|D5K9X8|D5K9X9|E9LRB1|E9LRB2|E9LRH5|E9LRH6|E9LRH7|E9LRK4|E9LRK5|E9LRK7|E9LRK8|E9LRM7|E9LRM9|E9LRN2|E9LRN4|E9LRN5|E9LRP8|E9LRQ0|E9LRQ2|E9LRQ3|E9LRQ4|E9LRQ5|E9LRS3|Q2VIK6|Q9BZV7|Q9BZV9	Silent	SNP	ENST00000465342.2	37	CCDS55274.1																																																																																			C|0.985;T|0.015	0.015	strong		0.502	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542	
C6orf211	79624	hgsc.bcm.edu	37	6	151789868	151789868	+	Missense_Mutation	SNP	G	G	A	rs35972078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:151789868G>A	ENST00000367294.3	+	5	1208	c.949G>A	c.(949-951)Gct>Act	p.A317T	C6orf211_ENST00000545879.1_Missense_Mutation_p.A198T	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	317			A -> T (in dbSNP:rs35972078).							breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		CAAGTGTGGGGCTGACTGGGA	0.378													G|||	396	0.0790735	0.0658	0.0778	5008	,	,		18970	0.0159		0.1183	False		,,,				2504	0.1227				p.A317T		Atlas-SNP	.											C6orf211,NS,carcinoma,0,1	C6orf211	30	1	0			c.G949A						PASS	.	G	THR/ALA	320,4086	172.7+/-202.6	5,310,1888	85.0	87.0	86.0		949	3.0	0.7	6	dbSNP_126	86	1076,7524	225.5+/-261.6	63,950,3287	yes	missense	C6orf211	NM_024573.1	58	68,1260,5175	AA,AG,GG		12.5116,7.2628,10.7335	benign	317/442	151789868	1396,11610	2203	4300	6503	SO:0001583	missense	79624	exon5			TGTGGGGCTGACT	AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.949G>A	6.37:g.151789868G>A	ENSP00000356263:p.Ala317Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	111	44	0.396396	NM_024573	Q96FC6|Q9UFY5	Missense_Mutation	SNP	ENST00000367294.3	37	CCDS5233.1	168	0.07692307692307693	30	0.06097560975609756	33	0.09116022099447514	10	0.017482517482517484	95	0.12532981530343007	G	5.785	0.329209	0.10956	0.072628	0.125116	ENSG00000146476	ENST00000367294;ENST00000545879	T;T	0.07216	3.21;3.21	6.16	3.03	0.35002	Domain of unknown function DUF89 (2);	1.279400	0.05047	N	0.477484	T	0.01558	0.0050	N	0.13168	0.305	0.58432	P	6.999999999979245E-6	B	0.06786	0.001	B	0.09377	0.004	T	0.42832	-0.9428	9	0.18276	T	0.48	.	7.1424	0.25564	0.2135:0.1503:0.6361:0.0	rs35972078	317	Q9H993	CF211_HUMAN	T	317;198	ENSP00000356263:A317T;ENSP00000444121:A198T	ENSP00000356263:A317T	A	+	1	0	C6orf211	151831561	0.942000	0.31987	0.736000	0.30914	0.262000	0.26303	1.691000	0.37721	0.908000	0.36671	0.650000	0.86243	GCT	G|0.904;A|0.096	0.096	strong		0.378	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573	
BCL10	8915	hgsc.bcm.edu	37	1	85733374	85733374	+	Missense_Mutation	SNP	C	C	T	rs3768235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:85733374C>T	ENST00000370580.1	-	3	1375	c.638G>A	c.(637-639)gGa>gAa	p.G213E		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	213			G -> E (in MALT lymphoma and mesothelioma; dbSNP:rs3768235). {ECO:0000269|PubMed:10319863, ECO:0000269|PubMed:10380921}.		adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.G213E(1)		haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		TGCACAAGTTCCTTCTTCTTC	0.418			T	IGH@	MALT								C|||	361	0.0720847	0.0023	0.0447	5008	,	,		14270	0.1538		0.0527	False		,,,				2504	0.1217				p.G213E	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	BCL10,NS,carcinoma,0,2	BCL10	39	2	1	Substitution - Missense(1)	stomach(1)	c.G638A						PASS	.	C	GLU/GLY	58,4348	55.5+/-91.7	0,58,2145	74.0	78.0	77.0		638	-0.9	0.6	1	dbSNP_107	77	487,8113	139.4+/-196.0	19,449,3832	yes	missense	BCL10	NM_003921.4	98	19,507,5977	TT,TC,CC		5.6628,1.3164,4.1904	benign	213/234	85733374	545,12461	2203	4300	6503	SO:0001583	missense	8915	exon3			CAAGTTCCTTCTT	AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"""CARD-like apoptotic protein"", ""CARD-containing apoptotic signaling protein"", ""CARD containing molecule enhancing NF-kB"", ""caspase-recruiting domain-containing protein"", ""CARD-containing proapoptotic protein"""	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.638G>A	1.37:g.85733374C>T	ENSP00000359612:p.Gly213Glu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	95	37	0.389474	NM_003921	Q5VUF1	Missense_Mutation	SNP	ENST00000370580.1	37	CCDS704.1	160	0.07326007326007326	3	0.006097560975609756	21	0.058011049723756904	99	0.17307692307692307	37	0.048812664907651716	C	14.86	2.661528	0.47572	0.013164	0.056628	ENSG00000142867	ENST00000370580;ENST00000271015	.	.	.	5.52	-0.914	0.10497	.	1.081190	0.06839	N	0.795318	T	0.03959	0.0111	N	0.03608	-0.345	0.51482	P	7.500000000004725E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.36866	-0.9730	8	0.12766	T	0.61	-6.0907	5.2652	0.15595	0.1443:0.3063:0.0:0.5494	rs3768235;rs3768235	213	O95999	BCL10_HUMAN	E	213	.	ENSP00000271015:G213E	G	-	2	0	BCL10	85505962	0.622000	0.27085	0.615000	0.29064	0.961000	0.63080	0.254000	0.18314	-0.113000	0.11958	0.467000	0.42956	GGA	C|0.942;T|0.058	0.058	strong		0.418	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921	
SLC12A8	84561	hgsc.bcm.edu	37	3	124826408	124826408	+	Missense_Mutation	SNP	T	T	C	rs6773138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124826408T>C	ENST00000393469.4	-	9	1671	c.1622A>G	c.(1621-1623)aAg>aGg	p.K541R	SLC12A8_ENST00000469902.1_Missense_Mutation_p.K541R|SLC12A8_ENST00000423114.2_Missense_Mutation_p.K570R|SLC12A8_ENST00000314584.7_Missense_Mutation_p.K294R|SLC12A8_ENST00000465475.1_5'UTR|SLC12A8_ENST00000430155.2_Missense_Mutation_p.K342R	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	541			K -> R (in dbSNP:rs6773138).		potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						CCCTTCGCTCTTGGAAGTCTG	0.557													C|||	649	0.129593	0.2912	0.0548	5008	,	,		19346	0.0635		0.0278	False		,,,				2504	0.137				p.K541R		Atlas-SNP	.											.	SLC12A8	81	.	0			c.A1622G						PASS	.	C	ARG/LYS,ARG/LYS	1016,3172		125,766,1203	97.0	105.0	102.0		1622,1622	0.3	0.0	3	dbSNP_116	102	278,8192		3,272,3960	yes	missense,missense	SLC12A8	NM_001195483.1,NM_024628.5	26,26	128,1038,5163	CC,CT,TT		3.2822,24.2598,10.2228	benign,benign	541/715,541/715	124826408	1294,11364	2094	4235	6329	SO:0001583	missense	84561	exon10			TCGCTCTTGGAAG		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.1622A>G	3.37:g.124826408T>C	ENSP00000377112:p.Lys541Arg	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	207	207	1	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Missense_Mutation	SNP	ENST00000393469.4	37	CCDS43143.1	207	0.09478021978021978	139	0.28252032520325204	16	0.04419889502762431	35	0.06118881118881119	17	0.022427440633245383	C	3.631	-0.075615	0.07184	0.242598	0.032822	ENSG00000221955	ENST00000430155;ENST00000393469;ENST00000423114;ENST00000469902;ENST00000314584	D;D;D;D;T	0.88201	-1.84;-2.34;-2.35;-2.34;-1.44	5.27	0.269	0.15631	.	.	.	.	.	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	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	0.08827	-1.0703	8	0.10902	T	0.67	.	5.3238	0.15895	0.0948:0.5567:0.0932:0.2553	rs6773138;rs52837397;rs56737175;rs6773138	294;570;541;342	A0AV02-4;A0AV02-2;A0AV02;A0AV02-3	.;.;S12A8_HUMAN;.	R	342;541;570;541;294	ENSP00000415713:K342R;ENSP00000377112:K541R;ENSP00000404243:K570R;ENSP00000418783:K541R;ENSP00000323632:K294R	ENSP00000323632:K294R	K	-	2	0	SLC12A8	126309098	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.682000	0.05185	-0.078000	0.12730	-1.736000	0.00690	AAG	T|0.903;C|0.097	0.097	strong		0.557	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628	
ABCA4	24	hgsc.bcm.edu	37	1	94461717	94461717	+	Missense_Mutation	SNP	C	C	A	rs6666652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:94461717C>A	ENST00000370225.3	-	49	6850	c.6764G>T	c.(6763-6765)aGt>aTt	p.S2255I	ABCA4_ENST00000536513.1_Missense_Mutation_p.S525I|ABCA4_ENST00000535881.1_Missense_Mutation_p.S374I	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	2255			S -> I (in dbSNP:rs6666652). {ECO:0000269|PubMed:11379881, ECO:0000269|PubMed:11384574, ECO:0000269|PubMed:11385708}.		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)		GAGGTCATGACTTTCAGTCTG	0.507													A|||	886	0.176917	0.5197	0.0836	5008	,	,		21183	0.0308		0.0457	False		,,,				2504	0.0654				p.S2255I		Atlas-SNP	.											.	ABCA4	275	.	0			c.G6764T	GRCh37	CM023000	ABCA4	M	rs6666652	PASS	.	A	ILE/SER	2105,2301	603.0+/-390.0	505,1095,603	81.0	79.0	80.0		6764	-2.0	0.0	1	dbSNP_116	80	400,8200	801.7+/-407.4	11,378,3911	yes	missense	ABCA4	NM_000350.2	142	516,1473,4514	AA,AC,CC		4.6512,47.7758,19.2603	benign	2255/2274	94461717	2505,10501	2203	4300	6503	SO:0001583	missense	24	exon49			TCATGACTTTCAG	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.6764G>T	1.37:g.94461717C>A	ENSP00000359245:p.Ser2255Ile	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	333	0.15247252747252749	257	0.5223577235772358	31	0.0856353591160221	16	0.027972027972027972	29	0.03825857519788918	A	6.016	0.371274	0.11409	0.477758	0.046512	ENSG00000198691	ENST00000546054;ENST00000370225;ENST00000536513;ENST00000535881	D;D;D	0.90788	-2.73;-2.26;-2.36	5.76	-1.96	0.07525	.	0.662303	0.15823	N	0.242891	T	0.58935	0.2157	N	0.12746	0.255	0.27272	P	0.9583392	B	0.02656	0.0	B	0.01281	0.0	T	0.39742	-0.9599	9	0.45353	T	0.12	.	1.7058	0.02881	0.4404:0.0882:0.2356:0.2358	rs6666652;rs17357750;rs52834333;rs60521300;rs6666652	2255	P78363	ABCA4_HUMAN	I	1047;2255;525;374	ENSP00000359245:S2255I;ENSP00000439707:S525I;ENSP00000443203:S374I	ENSP00000359245:S2255I	S	-	2	0	ABCA4	94234305	0.874000	0.30092	0.048000	0.18961	0.075000	0.17131	0.684000	0.25364	-0.457000	0.07033	-0.525000	0.04345	AGT	C|0.816;A|0.184	0.184	strong		0.507	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
RP1L1	94137	hgsc.bcm.edu	37	8	10480377	10480377	+	Missense_Mutation	SNP	G	G	C	rs6601495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10480377G>C	ENST00000382483.3	-	2	558	c.335C>G	c.(334-336)aCc>aGc	p.T112S	RP1L1_ENST00000329335.3_5'UTR	NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	112	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.		T -> S (in dbSNP:rs6601495).		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)		TCCACTGGGGGTCTTGGGGGG	0.657													g|||	1058	0.211262	0.7731	0.0418	5008	,	,		14667	0.001		0.006	False		,,,				2504	0.0				p.T112S		Atlas-SNP	.											.	RP1L1	453	.	0			c.C335G						PASS	.		SER/THR	2202,1650		628,946,352	15.0	17.0	16.0		335	3.9	0.5	8	dbSNP_116	16	34,8210		0,34,4088	yes	missense	RP1L1	NM_178857.5	58	628,980,4440	CC,CG,GG		0.4124,42.8349,18.4854	probably-damaging	112/2401	10480377	2236,9860	1926	4122	6048	SO:0001583	missense	94137	exon2			CTGGGGGTCTTGG	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.335C>G	8.37:g.10480377G>C	ENSP00000371923:p.Thr112Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	376	0.17216117216117216	360	0.7317073170731707	14	0.03867403314917127	0	0.0	2	0.002638522427440633	g	10.27	1.302651	0.23736	0.571651	0.004124	ENSG00000183638	ENST00000382483	D	0.86497	-2.13	4.74	3.86	0.44501	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.37353	P	0.08909199999999995	P	0.34546	0.456	B	0.31614	0.133	T	0.48670	-0.9015	8	0.66056	D	0.02	-8.4292	12.1318	0.53946	0.0831:0.0:0.9169:0.0	rs6601495;rs59306823;rs6601495	112	A6NKC6	.	S	112	ENSP00000371923:T112S	ENSP00000371923:T112S	T	-	2	0	RP1L1	10517787	1.000000	0.71417	0.476000	0.27291	0.223000	0.24884	5.164000	0.64954	1.236000	0.43740	0.550000	0.68814	ACC	G|0.841;C|0.159	0.159	strong		0.657	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
TMEM200A	114801	hgsc.bcm.edu	37	6	130761804	130761804	+	Silent	SNP	C	C	T	rs12200105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:130761804C>T	ENST00000296978.3	+	3	1108	c.237C>T	c.(235-237)gcC>gcT	p.A79A	TMEM200A_ENST00000545622.1_Silent_p.A79A|TMEM200A_ENST00000392429.1_Silent_p.A79A	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	79						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TTGCTATGGCCGTTCTTGGAT	0.418													C|||	1312	0.261981	0.5408	0.2248	5008	,	,		19198	0.1339		0.172	False		,,,				2504	0.136				p.A79A		Atlas-SNP	.											.	TMEM200A	108	.	0			c.C237T						PASS	.	C		2008,2398	562.1+/-380.9	465,1078,660	99.0	100.0	100.0		237	-9.9	0.9	6	dbSNP_120	100	1382,7218	268.3+/-287.8	119,1144,3037	no	coding-synonymous	TMEM200A	NM_052913.2		584,2222,3697	TT,TC,CC		16.0698,45.5742,26.0649		79/492	130761804	3390,9616	2203	4300	6503	SO:0001819	synonymous_variant	114801	exon3			TATGGCCGTTCTT	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"""KIAA1913"""	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.237C>T	6.37:g.130761804C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_001258277	Q96PX5	Silent	SNP	ENST00000296978.3	37	CCDS5140.1																																																																																			C|0.743;T|0.257	0.257	strong		0.418	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913	
AGGF1	55109	hgsc.bcm.edu	37	5	76332530	76332530	+	Silent	SNP	T	T	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:76332530T>G	ENST00000312916.7	+	4	1048	c.666T>G	c.(664-666)ggT>ggG	p.G222G		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	222					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		ACAGCACTGGTTTCTATTATG	0.423																																					p.G222G		Atlas-SNP	.											AGGF1,NS,carcinoma,+2,1	AGGF1	71	1	0			c.T666G						scavenged	.						48.0	49.0	49.0					5																	76332530		2203	4300	6503	SO:0001819	synonymous_variant	55109	exon4			CACTGGTTTCTAT	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"""G patch domain containing"""	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.666T>G	5.37:g.76332530T>G		Somatic	170	3	0.0176471		WXS	Illumina HiSeq	Phase_I	192	7	0.0364583	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Silent	SNP	ENST00000312916.7	37	CCDS4035.1																																																																																			.	.	none		0.423	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
PRAM1	84106	hgsc.bcm.edu	37	19	8564288	8564288	+	Missense_Mutation	SNP	C	C	T	rs58466313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8564288C>T	ENST00000423345.4	-	2	924	c.404G>A	c.(403-405)gGg>gAg	p.G135E	PRAM1_ENST00000255612.3_Missense_Mutation_p.G135E			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	183	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						CGGAGTGGCCCCCAGCTGTGG	0.657													T|||	813	0.16234	0.5802	0.0519	5008	,	,		12320	0.0		0.004	False		,,,				2504	0.0061				p.G135E		Atlas-SNP	.											.	PRAM1	53	.	0			c.G404A						PASS	.	T	GLU/GLY	1453,2153		274,905,624	35.0	39.0	38.0		404	3.3	0.0	19	dbSNP_129	38	54,7706		2,50,3828	yes	missense	PRAM1	NM_032152.4	98	276,955,4452	TT,TC,CC		0.6959,40.294,13.2588	benign	135/671	8564288	1507,9859	1803	3880	5683	SO:0001583	missense	84106	exon2			GTGGCCCCCAGCT	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.404G>A	19.37:g.8564288C>T	ENSP00000408342:p.Gly135Glu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	286	0.13095238095238096	266	0.540650406504065	18	0.049723756906077346	0	0.0	2	0.002638522427440633	T	0.056	-1.237003	0.01493	0.40294	0.006959	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.11385	2.78;2.78	4.32	3.31	0.37934	.	0.543293	0.15485	N	0.259864	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	0.44159	-0.9346	9	0.02654	T	1	.	2.7649	0.05317	0.1891:0.2063:0.0:0.6046	rs58466313	135;183	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	E	135	ENSP00000255612:G135E;ENSP00000408342:G135E	ENSP00000255612:G135E	G	-	2	0	PRAM1	8470288	0.008000	0.16893	0.008000	0.14137	0.015000	0.08874	1.805000	0.38883	0.811000	0.34303	-0.340000	0.08031	GGG	C|0.891;T|0.109	0.109	strong		0.657	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152	
FREM2	341640	hgsc.bcm.edu	37	13	39424253	39424253	+	Missense_Mutation	SNP	C	C	G	rs35252750|rs9548506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39424253C>G	ENST00000280481.7	+	9	6674	c.6458C>G	c.(6457-6459)aCt>aGt	p.T2153S	FREM2_ENST00000482551.1_3'UTR	NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2153	Calx-beta 4.		T -> S (in dbSNP:rs9548506). {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)		ATCCATAGGACTGGGGATGTC	0.458													G|||	460	0.091853	0.0802	0.2478	5008	,	,		19704	0.001		0.0885	False		,,,				2504	0.0941				p.T2153S		Atlas-SNP	.											.	FREM2	385	.	0			c.C6458G						PASS	.	G	SER/THR	8,4398		3,2,2198	122.0	110.0	114.0		6458	3.1	0.8	13	dbSNP_119	114	22,8578		4,14,4282	yes	missense	FREM2	NM_207361.4	58	7,16,6480	GG,GC,CC		0.2558,0.1816,0.2307	benign	2153/3170	39424253	30,12976	2203	4300	6503	SO:0001583	missense	341640	exon9			ATAGGACTGGGGA	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.6458C>G	13.37:g.39424253C>G	ENSP00000280481:p.Thr2153Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	125	0.05723443223443223	27	0.054878048780487805	62	0.1712707182320442	1	0.0017482517482517483	35	0.04617414248021108	G	0.174	-1.069032	0.01918	0.001816	0.002558	ENSG00000150893	ENST00000280481	T	0.29917	1.55	5.79	3.13	0.36017	Na-Ca exchanger/integrin-beta4 (2);	0.091594	0.85682	N	0.000000	T	0.00039	0.0001	N	0.00991	-1.07	0.54753	P	1.7000000000044757E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36480	-0.9746	9	0.02654	T	1	.	8.9843	0.35983	0.1235:0.2282:0.6482:0.0	rs9548506;rs9548506	2153;2153	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	S	2153	ENSP00000280481:T2153S	ENSP00000280481:T2153S	T	+	2	0	FREM2	38322253	1.000000	0.71417	0.751000	0.31187	0.013000	0.08279	3.496000	0.53288	0.100000	0.17581	-0.120000	0.15030	ACT	C|0.913;G|0.087	0.087	strong		0.458	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
MUC4	4585	hgsc.bcm.edu	37	3	195512181	195512181	+	Silent	SNP	G	G	A	rs202182738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512181G>A	ENST00000463781.3	-	2	6729	c.6270C>T	c.(6268-6270)tcC>tcT	p.S2090S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S2090S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		CGTGACCTGTGGATATTGAGG	0.552																																					p.S2090S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C6270T						PASS	.						25.0	26.0	26.0					3																	195512181		690	1581	2271	SO:0001819	synonymous_variant	4585	exon2			ACCTGTGGATATT	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.6270C>T	3.37:g.195512181G>A		Somatic	581	1	0.00172117		WXS	Illumina HiSeq	Phase_I	274	63	0.229927	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|0.965;A|0.034	0.034	strong		0.552	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC17	140453	hgsc.bcm.edu	37	7	100680336	100680336	+	Missense_Mutation	SNP	C	C	T	rs74687161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100680336C>T	ENST00000306151.4	+	3	5703	c.5639C>T	c.(5638-5640)gCc>gTc	p.A1880V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1880	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)					ACAACAGTGGCCAGTTCTGAA	0.498													-|||	251	0.0501198	0.1823	0.0144	5008	,	,		24216	0.0		0.0	False		,,,				2504	0.0				p.A1880V		Atlas-SNP	.											.	MUC17	804	.	0			c.C5639T						PASS	.	C	VAL/ALA	665,3741		90,485,1628	240.0	251.0	247.0		5639	-0.3	0.0	7	dbSNP_131	247	6,8594		0,6,4294	no	missense	MUC17	NM_001040105.1	64	90,491,5922	TT,TC,CC		0.0698,15.0931,5.1592	benign	1880/4494	100680336	671,12335	2203	4300	6503	SO:0001583	missense	140453	exon3			CAGTGGCCAGTTC	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.5639C>T	7.37:g.100680336C>T	ENSP00000302716:p.Ala1880Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	79	0.036172161172161175	77	0.1565040650406504	2	0.0055248618784530384	0	0.0	0	0.0	c	3.374	-0.127886	0.06753	0.150931	6.98E-4	ENSG00000169876	ENST00000306151	T	0.02656	4.21	0.824	-0.353	0.12594	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.16802	0.019	B	0.08055	0.003	T	0.45977	-0.9224	8	0.18276	T	0.48	.	5.508	0.16864	0.0:0.7655:0.0:0.2345	.	1880	Q685J3	MUC17_HUMAN	V	1880	ENSP00000302716:A1880V	ENSP00000302716:A1880V	A	+	2	0	MUC17	100467056	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.179000	0.16840	-0.086000	0.12550	0.134000	0.15878	GCC	C|0.958;T|0.042	0.042	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SIDT1	54847	hgsc.bcm.edu	37	3	113323785	113323785	+	Missense_Mutation	SNP	G	G	T	rs61732220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113323785G>T	ENST00000264852.4	+	14	2092	c.1366G>T	c.(1366-1368)Gcg>Tcg	p.A456S	SIDT1_ENST00000463226.1_3'UTR|SIDT1_ENST00000393830.3_Missense_Mutation_p.A456S	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						TGTGTTTTACGCGCTGCCCGT	0.468													G|||	91	0.0181709	0.0666	0.0043	5008	,	,		15956	0.0		0.0	False		,,,				2504	0.0				p.A456S		Atlas-SNP	.											.	SIDT1	99	.	0			c.G1366T						PASS	.	G	SER/ALA	281,4125	155.2+/-188.4	10,261,1932	129.0	119.0	122.0		1366	5.9	1.0	3	dbSNP_129	122	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SIDT1	NM_017699.2	99	10,263,6230	TT,TG,GG		0.0233,6.3777,2.1759	benign	456/828	113323785	283,12723	2203	4300	6503	SO:0001583	missense	54847	exon14			TTTTACGCGCTGC	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.1366G>T	3.37:g.113323785G>T	ENSP00000264852:p.Ala456Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_017699	Q17RR4	Missense_Mutation	SNP	ENST00000264852.4	37	CCDS2974.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	G	15.33	2.801458	0.50315	0.063777	2.33E-4	ENSG00000072858	ENST00000264852;ENST00000393830	T;T	0.21361	2.01;2.01	5.88	5.88	0.94601	.	0.090977	0.47852	D	0.000207	T	0.02193	0.0068	L	0.51914	1.62	0.80722	D	1	B;B	0.29766	0.215;0.256	B;B	0.37047	0.154;0.24	T	0.01460	-1.1349	10	0.26408	T	0.33	-3.7185	20.2441	0.98394	0.0:0.0:1.0:0.0	rs61732220	456;456	Q9NXL6-2;Q9NXL6	.;SIDT1_HUMAN	S	456	ENSP00000264852:A456S;ENSP00000377416:A456S	ENSP00000264852:A456S	A	+	1	0	SIDT1	114806475	1.000000	0.71417	1.000000	0.80357	0.066000	0.16364	9.697000	0.98697	2.774000	0.95407	0.655000	0.94253	GCG	G|0.981;T|0.019	0.019	strong		0.468	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
ADAMTS17	170691	hgsc.bcm.edu	37	15	100821467	100821467	+	Silent	SNP	G	G	A	rs7496640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	28	0	0		WXS	Illumina HiSeq	Phase_I	37	25	0.675676	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	
MUC2	4583	hgsc.bcm.edu	37	11	1085941	1085941	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1085941G>A	ENST00000441003.2	+	22	2808	c.2781G>A	c.(2779-2781)acG>acA	p.T927T	MUC2_ENST00000359061.5_Silent_p.T927T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	927	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)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T927T(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)	GGCAGAGGACGGAGCTGAAGT	0.652																																					p.T927T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	2	Substitution - coding silent(2)	lung(2)	c.G2781A						scavenged	.						49.0	56.0	54.0					11																	1085941		2122	4215	6337	SO:0001819	synonymous_variant	4583	exon22			GAGGACGGAGCTG	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.2781G>A	11.37:g.1085941G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	66	2	0.030303	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
LMBR1L	55716	hgsc.bcm.edu	37	12	49498635	49498635	+	Silent	SNP	G	G	T	rs141166526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49498635G>T	ENST00000267102.8	-	4	567	c.225C>A	c.(223-225)gcC>gcA	p.A75A	LMBR1L_ENST00000395141.4_Silent_p.A70A|LMBR1L_ENST00000553204.1_5'UTR|LMBR1L_ENST00000547382.1_Silent_p.A75A	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	75	LCN1-binding.				endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CAGCACCCAGGGCAATTGCCA	0.587													G|||	22	0.00439297	0.0166	0.0	5008	,	,		22882	0.0		0.0	False		,,,				2504	0.0				p.A75A		Atlas-SNP	.											LMBR1L_ENST00000267102,colon,carcinoma,-1,2	LMBR1L	61	2	0			c.C225A						PASS	.	G		50,4356	48.9+/-83.8	0,50,2153	108.0	78.0	88.0		225	5.2	1.0	12	dbSNP_134	88	0,8600		0,0,4300	no	coding-synonymous	LMBR1L	NM_018113.2		0,50,6453	TT,TG,GG		0.0,1.1348,0.3844		75/490	49498635	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	55716	exon4			ACCCAGGGCAATT	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"""limb region 1 homolog (mouse)-like"""			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.225C>A	12.37:g.49498635G>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Silent	SNP	ENST00000267102.8	37	CCDS8780.2																																																																																			G|0.996;T|0.004	0.004	strong		0.587	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113	
PKP3	11187	hgsc.bcm.edu	37	11	403764	403764	+	Silent	SNP	C	C	T	rs113114984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:403764C>T	ENST00000331563.2	+	10	2146	c.2070C>T	c.(2068-2070)gaC>gaT	p.D690D		NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	690					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)		GGAACAAGGACGAGATGTGTG	0.602													c|||	181	0.0361422	0.0477	0.0259	5008	,	,		19612	0.0605		0.0258	False		,,,				2504	0.0133				p.D690D		Atlas-SNP	.											.	PKP3	36	.	0			c.C2070T						PASS	.			191,4193	118.8+/-156.5	2,187,2003	94.0	85.0	88.0		2070	-3.7	1.0	11	dbSNP_132	88	158,8412	75.1+/-137.7	3,152,4130	no	coding-synonymous	PKP3	NM_007183.2		5,339,6133	TT,TC,CC		1.8436,4.3568,2.6941		690/798	403764	349,12605	2192	4285	6477	SO:0001819	synonymous_variant	11187	exon10			CAAGGACGAGATG	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.2070C>T	11.37:g.403764C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_007183	F8J390|Q53EX8	Silent	SNP	ENST00000331563.2	37	CCDS7695.1																																																																																			C|0.969;T|0.031	0.031	strong		0.602	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183	
OR4C16	219428	hgsc.bcm.edu	37	11	55340057	55340057	+	Missense_Mutation	SNP	G	G	A	rs144962866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55340057G>A	ENST00000314634.3	+	1	454	c.454G>A	c.(454-456)Gtg>Atg	p.V152M		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	152						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				GGGATCCTGTGTGCATTCTTT	0.488													g|||	34	0.00678914	0.025	0.0014	5008	,	,		19716	0.0		0.0	False		,,,				2504	0.0				p.V152M		Atlas-SNP	.											.	OR4C16	104	.	0			c.G454A						PASS	.	G	MET/VAL	101,4301	79.9+/-118.3	2,97,2102	149.0	137.0	141.0		454	-2.6	0.3	11	dbSNP_134	141	0,8592		0,0,4296	yes	missense	OR4C16	NM_001004701.2	21	2,97,6398	AA,AG,GG		0.0,2.2944,0.7773	benign	152/311	55340057	101,12893	2201	4296	6497	SO:0001583	missense	219428	exon1			TCCTGTGTGCATT	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.454G>A	11.37:g.55340057G>A	ENSP00000324913:p.Val152Met	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	159	85	0.534591	NM_001004701	Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	G	9.386	1.074257	0.20227	0.022944	0.0	ENSG00000181935	ENST00000314634	T	0.39997	1.05	4.83	-2.58	0.06228	GPCR, rhodopsin-like superfamily (1);	0.267871	0.27139	N	0.020760	T	0.16428	0.0395	L	0.39566	1.225	0.09310	N	1	B	0.18461	0.028	B	0.32211	0.142	T	0.25363	-1.0134	10	0.62326	D	0.03	.	5.5455	0.17061	0.4732:0.1409:0.3859:0.0	.	152	Q8NGL9	OR4CG_HUMAN	M	152	ENSP00000324913:V152M	ENSP00000324913:V152M	V	+	1	0	OR4C16	55096633	0.000000	0.05858	0.326000	0.25389	0.412000	0.31113	-3.095000	0.00607	-0.293000	0.08986	-0.272000	0.10252	GTG	G|0.994;A|0.006	0.006	strong		0.488	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
RANBP1	5902	hgsc.bcm.edu	37	22	20112868	20112868	+	Silent	SNP	C	C	T	rs111311060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:20112868C>T	ENST00000331821.3	+	4	450	c.348C>T	c.(346-348)agC>agT	p.S116S	RANBP1_ENST00000402752.1_Silent_p.S116S|SNORA77_ENST00000578179.1_RNA|RANBP1_ENST00000430524.1_Silent_p.S26S	NM_002882.2	NP_002873.1	P43487	RANG_HUMAN	RAN binding protein 1	116	RanBD1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				intracellular transport (GO:0046907)|positive regulation of mitotic centrosome separation (GO:0046604)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|spindle organization (GO:0007051)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|Ran GTPase binding (GO:0008536)			breast(1)|large_intestine(1)|lung(1)|ovary(1)	4	Colorectal(54;0.0993)					ACGCAGGTAGCGACCGTGCCT	0.607													C|||	15	0.00299521	0.0113	0.0	5008	,	,		18036	0.0		0.0	False		,,,				2504	0.0				p.S116S		Atlas-SNP	.											.	RANBP1	19	.	0			c.C348T						PASS	.	C		33,4373	38.4+/-70.7	0,33,2170	62.0	57.0	59.0		348	-10.0	0.4	22	dbSNP_132	59	0,8600		0,0,4300	no	coding-synonymous	RANBP1	NM_002882.2		0,33,6470	TT,TC,CC		0.0,0.749,0.2537		116/202	20112868	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	5902	exon4			AGGTAGCGACCGT	D38076	CCDS13775.1, CCDS63408.1, CCDS74823.1	22q11.21	2008-06-16			ENSG00000099901	ENSG00000099901			9847	protein-coding gene	gene with protein product		601180				7616957, 10330396	Standard	NM_001278639		Approved	HTF9A	uc002zro.1	P43487	OTTHUMG00000150490	ENST00000331821.3:c.348C>T	22.37:g.20112868C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	180	91	0.505556	NM_002882	Q53EY3	Silent	SNP	ENST00000331821.3	37	CCDS13775.1																																																																																			C|0.997;T|0.003	0.003	strong		0.607	RANBP1-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343733.1	NM_002882	
PCNXL3	399909	hgsc.bcm.edu	37	11	65403666	65403666	+	Silent	SNP	C	C	T	rs61732727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65403666C>T	ENST00000355703.3	+	33	6020	c.5481C>T	c.(5479-5481)gcC>gcT	p.A1827A	SIPA1_ENST00000534313.1_5'Flank|MIR4690_ENST00000578459.1_RNA	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1827	Gly-rich.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						GCTGTGGCGCCGGCTGCAATA	0.632													C|||	160	0.0319489	0.1112	0.0173	5008	,	,		17328	0.0		0.001	False		,,,				2504	0.0				p.A1827A		Atlas-SNP	.											.	PCNXL3	140	.	0			c.C5481T						PASS	.	C		352,3732		7,338,1697	27.0	32.0	30.0		5481	-7.7	0.9	11	dbSNP_129	30	4,8360		0,4,4178	no	coding-synonymous	PCNXL3	NM_032223.2		7,342,5875	TT,TC,CC		0.0478,8.619,2.8599		1827/2035	65403666	356,12092	2042	4182	6224	SO:0001819	synonymous_variant	399909	exon33			TGGCGCCGGCTGC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.5481C>T	11.37:g.65403666C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	151	78	0.516556	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	37	CCDS44650.1																																																																																			C|0.974;T|0.026	0.026	strong		0.632	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
PCED1B	91523	hgsc.bcm.edu	37	12	47629179	47629179	+	Silent	SNP	G	G	T	rs79990001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:47629179G>T	ENST00000546455.1	+	4	1064	c.333G>T	c.(331-333)tcG>tcT	p.S111S	PCED1B_ENST00000432328.1_Silent_p.S111S|RP11-493L12.3_ENST00000547748.1_RNA			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	111							hydrolase activity (GO:0016787)										AGCTGCAGTCGGGCGAGCACG	0.572													G|||	122	0.024361	0.0877	0.0072	5008	,	,		17862	0.0		0.001	False		,,,				2504	0.0				p.S111S		Atlas-SNP	.											FAM113B,rectum,carcinoma,+1,1	.	.	1	0			c.G333T						PASS	.	G		310,4096	167.3+/-198.3	8,294,1901	104.0	116.0	112.0		333	-8.4	0.0	12	dbSNP_132	112	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAM113B	NM_138371.1		8,295,6200	TT,TG,GG		0.0116,7.0359,2.3912		111/433	47629179	311,12695	2203	4300	6503	SO:0001819	synonymous_variant	91523	exon2			GCAGTCGGGCGAG	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.333G>T	12.37:g.47629179G>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_138371	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																			G|0.974;T|0.026	0.026	strong		0.572	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
GAS8	2622	hgsc.bcm.edu	37	16	90095582	90095582	+	Intron	SNP	T	T	C	rs62640380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:90095582T>C	ENST00000268699.4	+	2	212				C16orf3_ENST00000408886.2_Missense_Mutation_p.S57G|GAS8_ENST00000536122.1_Intron|GAS8_ENST00000540721.1_Intron	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		acggggcagcttacggggcag	0.662																																					p.S57G		Atlas-SNP	.											C16orf3,rectum,carcinoma,0,1	C16orf3	14	1	0			c.A169G						PASS	.						20.0	20.0	20.0					16																	90095582		2195	4300	6495	SO:0001627	intron_variant	750	exon1			GGCAGCTTACGGG	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1452T>C	16.37:g.90095582T>C		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	242	30	0.123967	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	t	1.231	-0.623993	0.03636	.	.	ENSG00000221819	ENST00000408886	T	0.48836	0.8	.	.	.	.	.	.	.	.	T	0.23330	0.0564	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.33266	-0.9875	3	.	.	.	.	.	.	.	.	65	O95177	CP003_HUMAN	G	57	ENSP00000386218:S57G	.	S	-	1	0	C16orf3	88623083	0.042000	0.20092	0.034000	0.17996	0.035000	0.12851	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	AGC	T|0.833;C|0.167	0.167	strong		0.662	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
XDH	7498	hgsc.bcm.edu	37	2	31611143	31611143	+	Missense_Mutation	SNP	C	C	T	rs45523133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31611143C>T	ENST00000379416.3	-	7	562	c.514G>A	c.(514-516)Gga>Aga	p.G172R	XDH_ENST00000491727.1_5'UTR	NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	172			G -> R (in dbSNP:rs45523133). {ECO:0000269|PubMed:8135849, 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)	TTCCCATCTCCTCCACAGCAT	0.433													C|||	202	0.0403355	0.0151	0.0245	5008	,	,		21582	0.0575		0.0348	False		,,,				2504	0.0736				p.G172R	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.G514A	GRCh37	CM086585	XDH	M	rs45523133	PASS	.	C	ARG/GLY	74,4332	66.4+/-103.9	1,72,2130	145.0	129.0	134.0		514	5.4	1.0	2	dbSNP_127	134	224,8376	93.3+/-155.3	2,220,4078	yes	missense	XDH	NM_000379.3	125	3,292,6208	TT,TC,CC		2.6047,1.6795,2.2913	benign	172/1334	31611143	298,12708	2203	4300	6503	SO:0001583	missense	7498	exon7			CATCTCCTCCACA	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.514G>A	2.37:g.31611143C>T	ENSP00000368727:p.Gly172Arg	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	154	79	0.512987	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	37	CCDS1775.1	87	0.03983516483516483	4	0.008130081300813009	12	0.03314917127071823	46	0.08041958041958042	25	0.032981530343007916	C	13.67	2.305294	0.40795	0.016795	0.026047	ENSG00000158125	ENST00000379416	T	0.54071	0.59	5.4	5.4	0.78164	[2Fe-2S]-binding (2);Xanthine dehydrogenase, small subunit (1);	0.051706	0.85682	D	0.000000	T	0.06600	0.0169	M	0.91972	3.26	0.58432	D	0.999997	B	0.17268	0.021	B	0.21917	0.037	T	0.35574	-0.9783	10	0.16420	T	0.52	.	10.5522	0.45095	0.0:0.9115:0.0:0.0885	rs45523133	172	P47989	XDH_HUMAN	R	172	ENSP00000368727:G172R	ENSP00000368727:G172R	G	-	1	0	XDH	31464647	0.638000	0.27225	0.998000	0.56505	0.073000	0.16967	1.791000	0.38744	2.700000	0.92200	0.563000	0.77884	GGA	C|0.972;T|0.028	0.028	strong		0.433	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
STARD7	56910	hgsc.bcm.edu	37	2	96859034	96859034	+	Silent	SNP	A	A	G	rs997547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	247	0	0		WXS	Illumina HiSeq	Phase_I	224	98	0.4375	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		
MRPL15	29088	hgsc.bcm.edu	37	8	55047893	55047893	+	Missense_Mutation	SNP	G	G	A	rs200980911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:55047893G>A	ENST00000260102.4	+	1	124	c.50G>A	c.(49-51)cGg>cAg	p.R17Q		NM_014175.3	NP_054894.1	Q9P015	RM15_HUMAN	mitochondrial ribosomal protein L15	17					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)|skin(3)	10		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)			GACCTACTCCGGGGCCTGCCG	0.677													g|||	8	0.00159744	0.0045	0.0029	5008	,	,		12630	0.0		0.0	False		,,,				2504	0.0				p.R17Q		Atlas-SNP	.											.	MRPL15	26	.	0			c.G50A						PASS	.	G	GLN/ARG	20,4078		0,20,2029	11.0	13.0	12.0		50	5.1	0.5	8		12	0,8010		0,0,4005	yes	missense	MRPL15	NM_014175.3	43	0,20,6034	AA,AG,GG		0.0,0.488,0.1652	benign	17/297	55047893	20,12088	2049	4005	6054	SO:0001583	missense	29088	exon1			TACTCCGGGGCCT	AB051619	CCDS6158.1	8q11.2-q13	2012-09-13			ENSG00000137547	ENSG00000137547		"""Mitochondrial ribosomal proteins / large subunits"""	14054	protein-coding gene	gene with protein product		611828				11543634	Standard	NM_014175		Approved	RPML7, MRP-L7, HSPC145, L15mt, MRP-L15	uc003xsa.2	Q9P015	OTTHUMG00000164315	ENST00000260102.4:c.50G>A	8.37:g.55047893G>A	ENSP00000260102:p.Arg17Gln	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	222	106	0.477477	NM_014175	Q96Q54|Q9H0Y1	Missense_Mutation	SNP	ENST00000260102.4	37	CCDS6158.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	19.81	3.897077	0.72639	0.00488	0.0	ENSG00000137547	ENST00000260102;ENST00000519831	.	.	.	5.07	5.07	0.68467	.	0.111607	0.64402	D	0.000010	T	0.68714	0.3031	L	0.52759	1.655	0.45648	D	0.998575	D	0.69078	0.997	D	0.70227	0.968	T	0.73827	-0.3860	9	0.54805	T	0.06	-19.3451	18.8755	0.92332	0.0:0.0:1.0:0.0	.	17	Q9P015	RM15_HUMAN	Q	17	.	ENSP00000260102:R17Q	R	+	2	0	MRPL15	55210446	0.990000	0.36364	0.459000	0.27081	0.769000	0.43574	5.342000	0.65970	2.533000	0.85409	0.650000	0.86243	CGG	G|0.997;A|0.003	0.003	strong		0.677	MRPL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378254.1	NM_014175	
PWP2	5822	hgsc.bcm.edu	37	21	45538685	45538685	+	Missense_Mutation	SNP	C	C	T	rs150440839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45538685C>T	ENST00000291576.7	+	9	1149	c.1022C>T	c.(1021-1023)tCg>tTg	p.S341L		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	341					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)		ATCAATAGCTCGGGGGACTGG	0.607													C|||	13	0.00259585	0.0098	0.0	5008	,	,		16887	0.0		0.0	False		,,,				2504	0.0				p.S341L		Atlas-SNP	.											.	PWP2	64	.	0			c.C1022T						PASS	.	C	LEU/SER	38,4368	43.1+/-76.7	0,38,2165	127.0	99.0	108.0		1022	5.1	0.9	21	dbSNP_134	108	0,8600		0,0,4300	yes	missense	PWP2	NM_005049.2	145	0,38,6465	TT,TC,CC		0.0,0.8625,0.2922	benign	341/920	45538685	38,12968	2203	4300	6503	SO:0001583	missense	5822	exon9			ATAGCTCGGGGGA		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.1022C>T	21.37:g.45538685C>T	ENSP00000291576:p.Ser341Leu	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	NM_005049	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	37	CCDS33579.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	19.96	3.924314	0.73213	0.008625	0.0	ENSG00000241945	ENST00000291576	T	0.44881	0.91	5.05	5.05	0.67936	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (2);WD40-repeat-containing domain (1);	0.462069	0.24755	N	0.035863	T	0.22205	0.0535	L	0.59436	1.845	0.41576	D	0.988714	P	0.39352	0.669	B	0.27887	0.084	T	0.32214	-0.9915	10	0.49607	T	0.09	-12.9707	16.9482	0.86236	0.0:1.0:0.0:0.0	.	341	Q15269	PWP2_HUMAN	L	341	ENSP00000291576:S341L	ENSP00000291576:S341L	S	+	2	0	PWP2	44363113	1.000000	0.71417	0.933000	0.37362	0.909000	0.53808	5.017000	0.64047	2.501000	0.84356	0.555000	0.69702	TCG	C|0.996;T|0.004	0.004	strong		0.607	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049	
ABCB5	340273	hgsc.bcm.edu	37	7	20725366	20725366	+	Silent	SNP	T	T	G	rs115722120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20725366T>G	ENST00000404938.2	+	16	2569	c.1917T>G	c.(1915-1917)acT>acG	p.T639T	ABCB5_ENST00000258738.6_Silent_p.T194T	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	639					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						CATATTCTACTGAAAGAAAGA	0.368													T|||	18	0.00359425	0.0129	0.0	5008	,	,		16557	0.0		0.001	False		,,,				2504	0.0				p.T639T		Atlas-SNP	.											.	ABCB5	357	.	0			c.T1917G						PASS	.	T	,	61,4345	58.1+/-94.6	0,61,2142	94.0	85.0	88.0		1917,582	1.8	0.0	7	dbSNP_132	88	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ABCB5	NM_001163941.1,NM_178559.5	,	0,61,6442	GG,GT,TT		0.0,1.3845,0.469	,	639/1258,194/813	20725366	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	340273	exon16			TTCTACTGAAAGA	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.1917T>G	7.37:g.20725366T>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	185	85	0.459459	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent	SNP	ENST00000404938.2	37	CCDS55090.1																																																																																			T|0.995;G|0.005	0.005	strong		0.368	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
ENOSF1	55556	hgsc.bcm.edu	37	18	712568	712568	+	Missense_Mutation	SNP	G	G	A	rs3786349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:712568G>A	ENST00000251101.7	-	1	108	c.20C>T	c.(19-21)tCc>tTc	p.S7F	ENOSF1_ENST00000580982.1_Missense_Mutation_p.S7F|ENOSF1_ENST00000383578.3_5'UTR|ENOSF1_ENST00000539164.1_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	17	0	0		WXS	Illumina HiSeq	Phase_I	21	16	0.761905	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	
RAPGEF3	10411	hgsc.bcm.edu	37	12	48151822	48151822	+	Missense_Mutation	SNP	C	C	G	rs11168230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48151822C>G	ENST00000449771.2	-	2	134	c.46G>C	c.(46-48)Gct>Cct	p.A16P	RAPGEF3_ENST00000395358.3_Missense_Mutation_p.A16P|RAPGEF3_ENST00000171000.4_5'UTR|RAPGEF3_ENST00000405493.2_5'UTR|RAPGEF3_ENST00000549151.1_5'UTR|RAPGEF3_ENST00000549347.1_5'UTR|RAPGEF3_ENST00000548919.1_5'UTR|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.A16P|SLC48A1_ENST00000547002.1_5'Flank			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	16			A -> P (in dbSNP:rs11168230). {ECO:0000269|PubMed:15489334}.		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)		TCCTCCACAGCCAGGCCCACC	0.657													C|||	1487	0.296925	0.2988	0.2709	5008	,	,		16982	0.2004		0.335	False		,,,				2504	0.3732				p.A16P		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.G46C						PASS	.	C	PRO/ALA,,	1187,3177		185,817,1180	13.0	14.0	14.0		46,,	2.0	0.9	12	dbSNP_120	14	2586,5970		408,1770,2100	no	missense,utr-5,utr-5	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	27,,	593,2587,3280	GG,GC,CC		30.2244,27.1998,29.2028	possibly-damaging,,	16/924,,	48151822	3773,9147	2182	4278	6460	SO:0001583	missense	10411	exon2			CCACAGCCAGGCC	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.46G>C	12.37:g.48151822C>G	ENSP00000395708:p.Ala16Pro	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	611	0.27976190476190477	138	0.2804878048780488	103	0.2845303867403315	122	0.21328671328671328	248	0.32717678100263853	C	16.11	3.029273	0.54790	0.271998	0.302244	ENSG00000079337	ENST00000449771;ENST00000389212;ENST00000397089;ENST00000395358	T;T;T	0.62498	0.02;0.02;0.02	5.12	1.99	0.26369	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.22240	P	0.999267639	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.0;0.004;0.001	T	0.26430	-1.0103	8	0.30078	T	0.28	.	4.294	0.10892	0.0:0.5898:0.1857:0.2245	rs11168230;rs11168230	28;16;16	B7Z5J6;O95398-2;O95398	.;.;RPGF3_HUMAN	P	16;16;28;16	ENSP00000395708:A16P;ENSP00000373864:A16P;ENSP00000378764:A16P	ENSP00000373864:A16P	A	-	1	0	RAPGEF3	46438089	0.037000	0.19845	0.918000	0.36340	0.989000	0.77384	0.843000	0.27640	0.540000	0.28808	0.591000	0.81541	GCT	C|0.721;G|0.279	0.279	strong		0.657	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
FREM1	158326	hgsc.bcm.edu	37	9	14863863	14863863	+	Silent	SNP	A	A	G	rs61740262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14863863A>G	ENST00000380880.3	-	3	1056	c.273T>C	c.(271-273)taT>taC	p.Y91Y	FREM1_ENST00000380881.4_Silent_p.Y91Y|FREM1_ENST00000422223.2_Silent_p.Y91Y			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	91					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)		CATTGTGAACATACTTGACTT	0.393													A|||	159	0.0317492	0.112	0.013	5008	,	,		22501	0.0		0.001	False		,,,				2504	0.001				p.Y91Y		Atlas-SNP	.											.	FREM1	261	.	0			c.T273C						PASS	.	A		313,3603		19,275,1664	115.0	113.0	113.0		273	2.9	0.8	9	dbSNP_129	113	12,8276		0,12,4132	yes	coding-synonymous	FREM1	NM_144966.5		19,287,5796	GG,GA,AA		0.1448,7.9928,2.6631		91/2180	14863863	325,11879	1958	4144	6102	SO:0001819	synonymous_variant	158326	exon4			GTGAACATACTTG	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.273T>C	9.37:g.14863863A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	121	65	0.53719	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			A|0.975;G|0.025	0.025	strong		0.393	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
CD80	941	hgsc.bcm.edu	37	3	119256187	119256187	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119256187C>T	ENST00000264246.3	-	4	859	c.497G>A	c.(496-498)gGa>gAa	p.G166E	CD80_ENST00000383668.3_Intron|CD80_ENST00000383669.3_Missense_Mutation_p.G166E|CD80_ENST00000478182.1_Missense_Mutation_p.G166E	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	166	Ig-like C2-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)	TGGAAAACCTCCAGAGGTTGA	0.388																																					p.G166E	Melanoma(132;135 1764 1806 5833 14593)	Atlas-SNP	.											CD80,NS,malignant_melanoma,-1,1	CD80	35	1	0			c.G497A						scavenged	.						84.0	79.0	81.0					3																	119256187		2203	4300	6503	SO:0001583	missense	941	exon4			AAACCTCCAGAGG		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.497G>A	3.37:g.119256187C>T	ENSP00000264246:p.Gly166Glu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	139	3	0.0215827	NM_005191	Q5DTA9|Q5DTB0	Missense_Mutation	SNP	ENST00000264246.3	37	CCDS2989.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.577737	0.65878	.	.	ENSG00000121594	ENST00000264246;ENST00000478182;ENST00000383669	T;T;T	0.22336	1.96;1.96;1.96	5.23	3.3	0.37823	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.270380	0.26792	N	0.022467	T	0.43590	0.1254	M	0.83692	2.655	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.36114	-0.9761	10	0.52906	T	0.07	-18.2596	6.4559	0.21930	0.0:0.7817:0.0:0.2183	.	166;166	Q5DTB0;P33681	.;CD80_HUMAN	E	166	ENSP00000264246:G166E;ENSP00000418364:G166E;ENSP00000373165:G166E	ENSP00000264246:G166E	G	-	2	0	CD80	120738877	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.978000	0.40598	1.447000	0.47661	-0.142000	0.14014	GGA	.	.	none		0.388	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191	
NOTCH4	4855	hgsc.bcm.edu	37	6	32190484	32190484	+	Silent	SNP	G	G	A	rs8192569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32190484G>A	ENST00000375023.3	-	3	393	c.255C>T	c.(253-255)ccC>ccT	p.P85P		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	85	EGF-like 2. {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						CTAGGGGAGCGGGAAGCAGGG	0.627													G|||	1077	0.215056	0.3306	0.1412	5008	,	,		18266	0.2371		0.1024	False		,,,				2504	0.2045				p.P85P		Atlas-SNP	.											.	NOTCH4	201	.	0			c.C255T						PASS	.	G		1251,3155	428.7+/-342.0	182,887,1134	61.0	65.0	64.0		255	-0.0	0.1	6	dbSNP_117	64	771,7829	183.0+/-231.3	49,673,3578	no	coding-synonymous	NOTCH4	NM_004557.3		231,1560,4712	AA,AG,GG		8.9651,28.3931,15.5467		85/2004	32190484	2022,10984	2203	4300	6503	SO:0001819	synonymous_variant	4855	exon3			GGGAGCGGGAAGC		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.255C>T	6.37:g.32190484G>A		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			G|0.838;A|0.162	0.162	strong		0.627	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
EIF3M	10480	hgsc.bcm.edu	37	11	32610617	32610617	+	Missense_Mutation	SNP	G	G	T	rs140562244	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:32610617G>T	ENST00000531120.1	+	4	437	c.374G>T	c.(373-375)tGc>tTc	p.C125F	EIF3M_ENST00000524896.1_Intron	NM_006360.4	NP_006351.2			eukaryotic translation initiation factor 3, subunit M											breast(3)|endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16	Breast(20;0.109)					ACAGTGTATTGCAGCCTTATT	0.408																																					p.C125F		Atlas-SNP	.											.	EIF3M	37	.	0			c.G374T						PASS	.	G	PHE/CYS	14,4390	14.3+/-33.2	0,14,2188	115.0	102.0	106.0		374	5.8	1.0	11	dbSNP_134	106	0,8598		0,0,4299	yes	missense	EIF3M	NM_006360.3	205	0,14,6487	TT,TG,GG		0.0,0.3179,0.1077	benign	125/375	32610617	14,12988	2202	4299	6501	SO:0001583	missense	10480	exon4			TGTATTGCAGCCT	AK131064	CCDS7880.1	11p13	2012-12-13	2007-07-27	2007-07-27	ENSG00000149100	ENSG00000149100			24460	protein-coding gene	gene with protein product	"""transport and golgi organization 7 homolog (Drosophila)"""	609641	"""PCI domain containing 1 (herpesvirus entry mediator)"""	PCID1		15919898, 15919899	Standard	NM_006360		Approved	hfl-B5, FLJ29030, GA17, eIF3m, TANGO7	uc001mtu.4	Q7L2H7	OTTHUMG00000166258	ENST00000531120.1:c.374G>T	11.37:g.32610617G>T	ENSP00000436049:p.Cys125Phe	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	154	21	0.136364	NM_006360		Missense_Mutation	SNP	ENST00000531120.1	37	CCDS7880.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	14.72	2.618767	0.46736	0.003179	0.0	ENSG00000149100	ENST00000531120;ENST00000323213;ENST00000533439	T;T	0.36878	1.23;1.23	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.45498	0.1345	L	0.59436	1.845	0.80722	D	1	D	0.61080	0.989	P	0.62014	0.897	T	0.27536	-1.0071	10	0.12766	T	0.61	-25.8093	20.0797	0.97768	0.0:0.0:1.0:0.0	.	125	Q7L2H7	EIF3M_HUMAN	F	125;62;62	ENSP00000436049:C125F;ENSP00000319910:C62F	ENSP00000319910:C62F	C	+	2	0	EIF3M	32567193	1.000000	0.71417	1.000000	0.80357	0.365000	0.29674	9.476000	0.97823	2.752000	0.94435	0.467000	0.42956	TGC	G|0.998;T|0.002	0.002	strong		0.408	EIF3M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388762.2	NM_006360	
FRMD8	83786	hgsc.bcm.edu	37	11	65164357	65164357	+	Silent	SNP	C	C	T	rs12417665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65164357C>T	ENST00000317568.5	+	7	832	c.669C>T	c.(667-669)gcC>gcT	p.A223A	FRMD8_ENST00000355991.5_Silent_p.A167A|FRMD8_ENST00000416776.2_Silent_p.A189A	NM_031904.3	NP_114110.1	Q9BZ67	FRMD8_HUMAN	FERM domain containing 8	223	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|urinary_tract(1)	17						GGGCCAGGGCCGGGCCGGGCG	0.721													C|||	715	0.142772	0.121	0.3401	5008	,	,		14498	0.0615		0.161	False		,,,				2504	0.0971				p.A223A		Atlas-SNP	.											.	FRMD8	28	.	0			c.C669T						PASS	.	C		568,3814		45,478,1668	13.0	14.0	14.0		669	-8.4	0.2	11	dbSNP_120	14	1289,7269		102,1085,3092	no	coding-synonymous	FRMD8	NM_031904.3		147,1563,4760	TT,TC,CC		15.0619,12.9621,14.3509		223/465	65164357	1857,11083	2191	4279	6470	SO:0001819	synonymous_variant	83786	exon7			CAGGGCCGGGCCG	AK074850	CCDS8102.1, CCDS73320.1	11q13.1	2007-08-14			ENSG00000126391	ENSG00000126391			25462	protein-coding gene	gene with protein product						12477932	Standard	NM_031904		Approved	FLJ90369, FKSG44	uc001odu.4	Q9BZ67	OTTHUMG00000166275	ENST00000317568.5:c.669C>T	11.37:g.65164357C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	12	9	0.75	NM_031904	B4E2P1|Q86V56|Q8NCB5	Silent	SNP	ENST00000317568.5	37	CCDS8102.1																																																																																			C|0.850;T|0.150	0.150	strong		0.721	FRMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388833.1	NM_031904	
MMEL1	79258	hgsc.bcm.edu	37	1	2526746	2526746	+	Missense_Mutation	SNP	A	A	G	rs3748816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	207	0	0		WXS	Illumina HiSeq	Phase_I	260	108	0.415385	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	
NRK	203447	hgsc.bcm.edu	37	X	105152282	105152282	+	Missense_Mutation	SNP	G	G	A	rs209373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:105152282G>A	ENST00000243300.9	+	12	1375	c.1072G>A	c.(1072-1074)Gtg>Atg	p.V358M	NRK_ENST00000428173.2_Missense_Mutation_p.V359M	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	358			V -> M (in dbSNP:rs209373). {ECO:0000269|PubMed:17344846}.		activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						ACAGTACACCGTGAGAAGATT	0.353										HNSCC(51;0.14)			A|||	1404	0.371921	0.5567	0.1441	3775	,	,		14623	0.1796		0.168	False		,,,				2504	0.2229				p.V358M		Atlas-SNP	.											.	NRK	321	.	0			c.G1072A						PASS	.	A	MET/VAL	1890,1045		518,533,321,171,170	45.0	39.0	41.0		1072	1.8	0.0	X	dbSNP_79	41	1294,4681		129,677,359,1402,1200	yes	missense	NRK	NM_198465.2	21	647,1210,680,1573,1370	AA,AG,A,GG,G		21.6569,35.6048,35.7351	benign	358/1583	105152282	3184,5726	1713	3767	5480	SO:0001583	missense	203447	exon12			TACACCGTGAGAA	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.1072G>A	X.37:g.105152282G>A	ENSP00000434830:p.Val358Met	Somatic	449	0	0		WXS	Illumina HiSeq	Phase_I	444	444	1	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		522	0.31464737793851716	192	0.6	38	0.11377245508982035	54	0.10344827586206896	82	0.11781609195402298	A	0.017	-1.498128	0.01001	0.643952	0.216569	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.76839	1.81;-1.05	4.2	1.83	0.25207	Protein kinase-like domain (1);	1.004370	0.08017	N	0.991435	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45673	-0.9245	9	0.30854	T	0.27	.	5.7859	0.18333	0.6408:0.0:0.3592:0.0	rs209373;rs615456;rs52833891;rs60442877;rs209373	26;358	Q7Z2Y5-2;Q7Z2Y5	.;NRK_HUMAN	M	358;359	ENSP00000434830:V358M;ENSP00000438378:V359M	ENSP00000434830:V358M	V	+	1	0	NRK	105038938	0.025000	0.19082	0.042000	0.18584	0.980000	0.70556	1.472000	0.35376	-0.013000	0.14199	-0.314000	0.08810	GTG	0|0.030;A|0.341	0.341	strong		0.353	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465	
FES	2242	hgsc.bcm.edu	37	15	91436965	91436965	+	Silent	SNP	C	C	T	rs2227989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91436965C>T	ENST00000328850.3	+	17	2269	c.2127C>T	c.(2125-2127)gcC>gcT	p.A709A	FES_ENST00000394300.3_Silent_p.A651A|FES_ENST00000444422.2_Silent_p.A639A|FES_ENST00000414248.2_Silent_p.A581A|FES_ENST00000394302.1_Silent_p.A568A|FES_ENST00000450438.2_Silent_p.A581A	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	709	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)			lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GAGAGGAAGCCGATGGGGTCT	0.597													T|||	396	0.0790735	0.2829	0.0274	5008	,	,		19349	0.0		0.003	False		,,,				2504	0.0				p.A709A		Atlas-SNP	.											.	FES	102	.	0			c.C2127T						PASS	.	T	,,,	1132,3264	713.0+/-408.2	156,820,1222	69.0	77.0	74.0		1953,1917,1743,2127	-10.7	0.1	15	dbSNP_98	74	15,8581	816.6+/-406.9	0,15,4283	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FES	NM_001143783.1,NM_001143784.1,NM_001143785.1,NM_002005.3	,,,	156,835,5505	TT,TC,CC		0.1745,25.7507,8.8285	,,,	651/765,639/753,581/695,709/823	91436965	1147,11845	2198	4298	6496	SO:0001819	synonymous_variant	2242	exon17			GGAAGCCGATGGG	X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"""SH2 domain containing"""	3657	protein-coding gene	gene with protein product	"""Oncogene FES, feline sarcoma virus"", ""c-fes/fps protein"""	190030	"""feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog"", ""feline sarcoma oncogene"""			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.2127C>T	15.37:g.91436965C>T		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_002005	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Silent	SNP	ENST00000328850.3	37	CCDS10365.1																																																																																			C|0.910;T|0.090	0.090	strong		0.597	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005	
F5	2153	hgsc.bcm.edu	37	1	169511734	169511734	+	Missense_Mutation	SNP	T	T	C	rs4525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	249	0	0		WXS	Illumina HiSeq	Phase_I	322	158	0.490683	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	
MUC4	4585	hgsc.bcm.edu	37	3	195509605	195509605	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509605T>C	ENST00000463781.3	-	2	9305	c.8846A>G	c.(8845-8847)gAc>gGc	p.D2949G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D2949G	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)		TGAGGAAGTGTCGGTGACAGG	0.587																																					p.D2949G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.A8846G						scavenged	.						10.0	8.0	9.0					3																	195509605		648	1502	2150	SO:0001583	missense	4585	exon2			GAAGTGTCGGTGA	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.8846A>G	3.37:g.195509605T>C	ENSP00000417498:p.Asp2949Gly	Somatic	292	2	0.00684932		WXS	Illumina HiSeq	Phase_I	204	29	0.142157	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	6.649	0.488291	0.12641	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.45;1.44	.	.	.	.	.	.	.	.	T	0.16938	0.0407	N	0.19112	0.55	0.09310	N	1	P	0.50617	0.937	B	0.42319	0.383	T	0.13683	-1.0500	7	.	.	.	.	5.3345	0.15949	0.0:1.0E-4:0.0:0.9999	.	2821	E7ESK3	.	G	2949	ENSP00000417498:D2949G;ENSP00000420243:D2949G	.	D	-	2	0	MUC4	196994384	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.288000	0.08377	0.000000	0.14550	0.000000	0.15137	GAC	T|0.625;C|0.375	0.375	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FLG	2312	hgsc.bcm.edu	37	1	152280788	152280788	+	Missense_Mutation	SNP	T	T	G	rs66954353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152280788T>G	ENST00000368799.1	-	3	6609	c.6574A>C	c.(6574-6576)Aaa>Caa	p.K2192Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	417	0	0		WXS	Illumina HiSeq	Phase_I	774	367	0.47416	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	
COL21A1	81578	hgsc.bcm.edu	37	6	55925698	55925698	+	Missense_Mutation	SNP	A	A	C	rs545860371		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:55925698A>C	ENST00000244728.5	-	26	2740	c.2343T>G	c.(2341-2343)gaT>gaG	p.D781E	COL21A1_ENST00000535941.1_Missense_Mutation_p.D781E|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000370808.2_Missense_Mutation_p.D181E|COL21A1_ENST00000370819.1_Missense_Mutation_p.D778E	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	781	Collagen-like 5.				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)			CGGGCTTCCCATCCAAACCTG	0.473													A|||	1	0.000199681	0.0	0.0	5008	,	,		15984	0.001		0.0	False		,,,				2504	0.0				p.D781E		Atlas-SNP	.											.	COL21A1	201	.	0			c.T2343G						PASS	.						44.0	43.0	43.0					6																	55925698		1837	4081	5918	SO:0001583	missense	81578	exon26			CTTCCCATCCAAA	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.2343T>G	6.37:g.55925698A>C	ENSP00000244728:p.Asp781Glu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	92	23	0.25	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.513616	0.27123	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;D	0.93133	-3.17;-3.17;-3.17;-3.16	4.9	3.74	0.42951	.	0.191909	0.35739	N	0.003010	T	0.80336	0.4604	N	0.25201	0.72	0.32304	N	0.56468	D;D;P;D	0.57571	0.975;0.98;0.789;0.98	P;P;B;P	0.52454	0.573;0.699;0.444;0.699	T	0.75255	-0.3382	10	0.07644	T	0.81	.	4.3365	0.11089	0.6951:0.0:0.1586:0.1463	.	181;781;781;138	Q96P44-2;B7ZLK3;Q96P44;B3KU30	.;.;COLA1_HUMAN;.	E	781;778;781;778;181	ENSP00000244728:D781E;ENSP00000359855:D778E;ENSP00000444384:D781E;ENSP00000359844:D181E	ENSP00000244728:D781E	D	-	3	2	COL21A1	56033657	1.000000	0.71417	0.996000	0.52242	0.986000	0.74619	1.167000	0.31847	0.830000	0.34757	0.533000	0.62120	GAT	.	.	none		0.473	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
ANGPTL1	9068	hgsc.bcm.edu	37	1	178834231	178834231	+	Silent	SNP	T	T	C	rs6689778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:178834231T>C	ENST00000234816.2	-	3	1128	c.681A>G	c.(679-681)caA>caG	p.Q227Q	ANGPTL1_ENST00000367629.1_Silent_p.Q227Q|RALGPS2_ENST00000367634.2_Intron|RALGPS2_ENST00000367635.3_Intron	NM_004673.3	NP_004664.1	O95841	ANGL1_HUMAN	angiopoietin-like 1	227					transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(2)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	14						GAGTATACTGTTGGCTGTTAG	0.498													A|||	283	0.0565096	0.2035	0.0202	5008	,	,		18124	0.0		0.0	False		,,,				2504	0.0				p.Q227Q		Atlas-SNP	.											.	ANGPTL1	41	.	0			c.A681G						PASS	.	A	,	822,3584		80,662,1461	118.0	108.0	111.0		681,	-8.9	0.1	1	dbSNP_116	111	4,8596		0,4,4296	no	coding-synonymous,intron	ANGPTL1,RALGPS2	NM_004673.3,NM_152663.3	,	80,666,5757	CC,CT,TT		0.0465,18.6564,6.3509	,	227/492,	178834231	826,12180	2203	4300	6503	SO:0001819	synonymous_variant	9068	exon3			ATACTGTTGGCTG	AF107253	CCDS1327.1	1q25.2	2013-02-06			ENSG00000116194	ENSG00000116194		"""Fibrinogen C domain containing"""	489	protein-coding gene	gene with protein product	"""angioarrestin"""	603874		ANGPT3		10025962, 9286704	Standard	NM_004673		Approved	ANG3, AngY, ARP1	uc001gma.3	O95841	OTTHUMG00000035075	ENST00000234816.2:c.681A>G	1.37:g.178834231T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	128	48	0.375	NM_004673	Q5T5Z5	Silent	SNP	ENST00000234816.2	37	CCDS1327.1																																																																																			T|0.939;C|0.061	0.061	strong		0.498	ANGPTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084924.1	NM_004673	
OR2L3	391192	hgsc.bcm.edu	37	1	248224216	248224216	+	Missense_Mutation	SNP	C	C	T	rs6658227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248224216C>T	ENST00000359959.3	+	1	233	c.233C>T	c.(232-234)cCt>cTt	p.P78L	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	78			P -> L (in dbSNP:rs6658227).			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(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	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;0.0278)			ACCATTGTTCCTAAGATGGCA	0.443													c|||	941	0.187899	0.298	0.098	5008	,	,		22692	0.254		0.1441	False		,,,				2504	0.0798				p.P78L		Atlas-SNP	.											.	OR2L3	97	.	0			c.C233T						PASS	.	C	LEU/PRO,	1206,3200		158,890,1155	298.0	275.0	283.0		233,	2.0	0.9	1	dbSNP_116	283	1187,7413		90,1007,3203	no	missense,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	98,	248,1897,4358	TT,TC,CC		13.8023,27.3718,18.3992	probably-damaging,	78/313,	248224216	2393,10613	2203	4300	6503	SO:0001583	missense	391192	exon1			TTGTTCCTAAGAT	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"""GPCR / Class A : Olfactory receptors"""	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.233C>T	1.37:g.248224216C>T	ENSP00000353044:p.Pro78Leu	Somatic	392	0	0		WXS	Illumina HiSeq	Phase_I	409	193	0.471883	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	465	0.2129120879120879	148	0.3008130081300813	37	0.10220994475138122	172	0.3006993006993007	108	0.1424802110817942	.	14.47	2.544357	0.45280	0.273718	0.138023	ENSG00000198128	ENST00000359959	T	0.01854	4.6	2.05	2.05	0.26809	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31697	U	0.007204	T	0.00012	0.0000	M	0.93854	3.465	0.09310	P	0.99999426361	D	0.54964	0.969	P	0.61070	0.883	T	0.31943	-0.9925	9	0.87932	D	0	.	11.9647	0.53027	0.0:1.0:0.0:0.0	rs6658227;rs59129511;rs6658227	78	Q8NG85	OR2L3_HUMAN	L	78	ENSP00000353044:P78L	ENSP00000353044:P78L	P	+	2	0	OR2L3	246290839	0.991000	0.36638	0.866000	0.34008	0.388000	0.30384	2.852000	0.48310	1.124000	0.41980	0.462000	0.41574	CCT	C|0.801;T|0.199	0.199	strong		0.443	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
DENND2A	27147	hgsc.bcm.edu	37	7	140225578	140225578	+	Silent	SNP	G	G	A	rs61737086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140225578G>A	ENST00000275884.6	-	15	2937	c.2520C>T	c.(2518-2520)gaC>gaT	p.D840D	DENND2A_ENST00000496613.1_Silent_p.D840D|DENND2A_ENST00000537639.1_Silent_p.D840D			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	840	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				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)					TGTTGACGAGGTCAACCACAA	0.537													G|||	248	0.0495208	0.171	0.0101	5008	,	,		18548	0.0		0.0	False		,,,				2504	0.0153				p.D840D		Atlas-SNP	.											.	DENND2A	132	.	0			c.C2520T						PASS	.	G		507,3455		30,447,1504	49.0	53.0	52.0		2520	2.6	1.0	7	dbSNP_129	52	4,8336		0,4,4166	no	coding-synonymous	DENND2A	NM_015689.3		30,451,5670	AA,AG,GG		0.048,12.7966,4.1538		840/1010	140225578	511,11791	1981	4170	6151	SO:0001819	synonymous_variant	27147	exon14			GACGAGGTCAACC	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.2520C>T	7.37:g.140225578G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1																																																																																			G|0.968;A|0.032	0.032	strong		0.537	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
SNX30	401548	hgsc.bcm.edu	37	9	115580008	115580008	+	Silent	SNP	G	G	C	rs10117709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:115580008G>C	ENST00000374232.3	+	3	536	c.372G>C	c.(370-372)ctG>ctC	p.L124L		NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	124	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						AGTTTGACCTGCCAGAATATT	0.433													G|||	3829	0.764577	0.6384	0.7939	5008	,	,		18242	0.7877		0.7932	False		,,,				2504	0.8609				p.L124L		Atlas-SNP	.											.	SNX30	32	.	0			c.G372C						PASS	.	G		2506,1166		844,818,174	119.0	106.0	110.0		372	3.7	1.0	9	dbSNP_119	110	6573,1613		2651,1271,171	no	coding-synonymous	SNX30	NM_001012994.1		3495,2089,345	CC,CG,GG		19.7044,31.7538,23.4357		124/438	115580008	9079,2779	1836	4093	5929	SO:0001819	synonymous_variant	401548	exon3			TGACCTGCCAGAA	AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158		"""Sorting nexins"""	23685	protein-coding gene	gene with protein product							Standard	NM_001012994		Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.372G>C	9.37:g.115580008G>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	229	228	0.995633	NM_001012994		Silent	SNP	ENST00000374232.3	37	CCDS43865.1																																																																																			G|0.217;C|0.783	0.783	strong		0.433	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053700.1		
OR51Q1	390061	hgsc.bcm.edu	37	11	5443887	5443887	+	Missense_Mutation	SNP	T	T	C	rs10838093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5443887T>C	ENST00000300778.4	+	1	547	c.457T>C	c.(457-459)Tgc>Cgc	p.C153R	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	153			C -> R (in dbSNP:rs10838093).	CCV -> RCI (in Ref. 3; BAC05778). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATCATTTGCTGCTGTGTTCT	0.512													C|||	2272	0.453674	0.2799	0.3991	5008	,	,		21029	0.7024		0.3986	False		,,,				2504	0.5276				p.C153R		Atlas-SNP	.											OR51Q1,colon,carcinoma,-1,1	OR51Q1	79	1	0			c.T457C						PASS	.	C	ARG/CYS	1316,3086	694.4+/-405.8	202,912,1087	261.0	224.0	236.0		457	3.1	1.0	11	dbSNP_120	236	3370,5224	641.7+/-399.7	675,2020,1602	yes	missense	OR51Q1	NM_001004757.2	180	877,2932,2689	CC,CT,TT		39.2134,29.8955,36.0572	benign	153/318	5443887	4686,8310	2201	4297	6498	SO:0001583	missense	390061	exon1			ATTTGCTGCTGTG	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.457T>C	11.37:g.5443887T>C	ENSP00000300778:p.Cys153Arg	Somatic	298	1	0.0033557		WXS	Illumina HiSeq	Phase_I	226	225	0.995575	NM_001004757	B2RNN1	Missense_Mutation	SNP	ENST00000300778.4	37	CCDS31381.1	966	0.4423076923076923	139	0.28252032520325204	148	0.4088397790055249	395	0.6905594405594405	284	0.37467018469656993	C	0.004	-2.346301	0.00219	0.298955	0.392134	ENSG00000167360	ENST00000300778	T	0.36520	1.25	5.0	3.09	0.35607	GPCR, rhodopsin-like superfamily (1);	0.102173	0.44097	N	0.000496	T	0.00012	0.0000	N	0.00008	-3.13	0.52099	P	5.900000000003125E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.44390	-0.9331	9	0.02654	T	1	.	6.8803	0.24168	0.1413:0.7052:0.0:0.1535	rs10838093;rs52801150;rs57444579;rs10838093	153	Q8NH59	O51Q1_HUMAN	R	153	ENSP00000300778:C153R	ENSP00000300778:C153R	C	+	1	0	OR51Q1	5400463	0.000000	0.05858	0.991000	0.47740	0.181000	0.23173	-1.070000	0.03440	0.308000	0.22923	-1.239000	0.01543	TGC	C|0.398;N|0.001	0.398	strong		0.512	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
APOBEC4	403314	hgsc.bcm.edu	37	1	183617693	183617693	+	Missense_Mutation	SNP	G	G	A	rs16861394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:183617693G>A	ENST00000308641.4	-	2	495	c.224C>T	c.(223-225)tCt>tTt	p.S75F	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)	75			S -> F (in dbSNP:rs16861394).		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						CAGGCTACCAGAAGAAGTTTT	0.398													G|||	473	0.0944489	0.18	0.036	5008	,	,		20453	0.1091		0.0318	False		,,,				2504	0.0695				p.S75F		Atlas-SNP	.											.	APOBEC4	45	.	0			c.C224T						PASS	.	G	,PHE/SER	668,3738	280.8+/-275.6	46,576,1581	129.0	136.0	133.0		,224	5.3	1.0	1	dbSNP_123	133	242,8358	96.3+/-158.1	1,240,4059	yes	intron,missense	RGL1,APOBEC4	NM_015149.3,NM_203454.2	,155	47,816,5640	AA,AG,GG		2.814,15.1611,6.9968	,possibly-damaging	,75/368	183617693	910,12096	2203	4300	6503	SO:0001583	missense	403314	exon2			CTACCAGAAGAAG	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.224C>T	1.37:g.183617693G>A	ENSP00000310622:p.Ser75Phe	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	222	108	0.486486	NM_203454	Q8N7F6	Missense_Mutation	SNP	ENST00000308641.4	37	CCDS1358.1	155	0.07097069597069597	73	0.1483739837398374	16	0.04419889502762431	43	0.07517482517482517	23	0.030343007915567283	G	18.18	3.566986	0.65651	0.151611	0.02814	ENSG00000173627	ENST00000308641	T	0.65916	-0.18	5.28	5.28	0.74379	APOBEC-like, N-terminal (1);	0.114900	0.37437	N	0.002087	T	0.00845	0.0028	L	0.32530	0.975	0.24382	P	0.99478436	D	0.76494	0.999	D	0.67382	0.951	T	0.14783	-1.0460	9	0.72032	D	0.01	-4.8324	18.5089	0.90909	0.0:0.0:1.0:0.0	rs16861394;rs52805225;rs57960453;rs16861394	75	Q8WW27	ABEC4_HUMAN	F	75	ENSP00000310622:S75F	ENSP00000310622:S75F	S	-	2	0	APOBEC4	181884316	1.000000	0.71417	0.964000	0.40570	0.953000	0.61014	2.860000	0.48372	2.466000	0.83321	0.655000	0.94253	TCT	G|0.928;A|0.072	0.072	strong		0.398	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454	
SSPO	23145	hgsc.bcm.edu	37	7	149523277	149523277	+	RNA	SNP	A	A	G	rs1004200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149523277A>G	ENST00000378016.2	+	0	14363							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)			ATGGAGCGACATCGGACTTGT	0.652													A|||	2248	0.448882	0.7027	0.3732	5008	,	,		19271	0.4286		0.3052	False		,,,				2504	0.3282				p.H4787R		Atlas-SNP	.											.	.	.	.	0			c.A14360G						PASS	.	A	ARG/HIS	2525,1401		843,839,281	37.0	46.0	43.0		14379	1.6	0.0	7	dbSNP_86	43	2714,5562		449,1816,1873	no	missense	SSPO	NM_198455.2	29	1292,2655,2154	GG,GA,AA		32.7936,35.6852,42.9356	benign	4787/5148	149523277	5239,6963	1963	4138	6101			23145	exon101			AGCGACATCGGAC	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.149523277A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				A|0.586;G|0.414	0.414	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CPEB2	132864	hgsc.bcm.edu	37	4	15005604	15005604	+	5'UTR	SNP	G	G	A	rs112476821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:15005604G>A	ENST00000507071.1	+	0	83				CPEB2_ENST00000541112.1_Missense_Mutation_p.S436N|RP11-665G4.1_ENST00000502344.1_RNA|RP11-665G4.1_ENST00000513384.1_RNA|CPEB2_ENST00000538197.1_Missense_Mutation_p.S436N|CPEB2_ENST00000259997.5_5'UTR|CPEB2_ENST00000382401.3_5'UTR|CPEB2_ENST00000442003.2_Missense_Mutation_p.S436N|CPEB2_ENST00000345451.3_5'UTR|CPEB2_ENST00000382395.3_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	10	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	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	
ZNF679	168417	hgsc.bcm.edu	37	7	63727210	63727210	+	Missense_Mutation	SNP	G	G	A	rs142919190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:63727210G>A	ENST00000421025.1	+	5	1468	c.1199G>A	c.(1198-1200)aGt>aAt	p.S400N	ZNF679_ENST00000255746.4_Missense_Mutation_p.S400N	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	400					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						AATCATAAGAGTATGCATACT	0.338													.|||	38	0.00758786	0.0287	0.0	5008	,	,		18314	0.0		0.0	False		,,,				2504	0.0				p.S400N		Atlas-SNP	.											ZNF679,NS,carcinoma,0,1	ZNF679	80	1	0			c.G1199A						PASS	.	G	ASN/SER	29,1355		0,29,663	26.0	25.0	25.0		1199	0.8	0.5	7	dbSNP_134	25	0,3182		0,0,1591	no	missense	ZNF679	NM_153363.2	46	0,29,2254	AA,AG,GG		0.0,2.0954,0.6351	benign	400/412	63727210	29,4537	692	1591	2283	SO:0001583	missense	168417	exon5			ATAAGAGTATGCA	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"""Zinc fingers, C2H2-type"", ""-"""	28650	protein-coding gene	gene with protein product	"""hypothetical protein MGC42415"""					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.1199G>A	7.37:g.63727210G>A	ENSP00000416809:p.Ser400Asn	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	34	20	0.588235	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	11.97	1.796444	0.31777	0.020954	0.0	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.01139	5.28;5.28	0.819	0.819	0.18785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00496	0.0016	N	0.11818	0.18	0.21020	N	0.999808	B	0.25007	0.116	B	0.28011	0.085	T	0.49560	-0.8927	9	0.62326	D	0.03	.	6.9957	0.24780	0.0:0.0:1.0:0.0	.	400	Q8IYX0	ZN679_HUMAN	N	400	ENSP00000416809:S400N;ENSP00000255746:S400N	ENSP00000255746:S400N	S	+	2	0	ZNF679	63364645	0.000000	0.05858	0.476000	0.27291	0.477000	0.33069	-0.030000	0.12308	0.191000	0.20236	0.194000	0.17425	AGT	G|0.997;A|0.003	0.003	strong		0.338	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363	
CDYL	9425	hgsc.bcm.edu	37	6	4892381	4892381	+	Silent	SNP	C	C	T	rs734783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4892381C>T	ENST00000328908.5	+	4	752	c.621C>T	c.(619-621)acC>acT	p.T207T	CDYL_ENST00000343762.5_Silent_p.T21T|CDYL_ENST00000397588.3_Silent_p.T153T|CDYL_ENST00000449732.2_Silent_p.T21T|CDYL_ENST00000472453.1_Intron			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	207	Interaction with EZH2.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		AGAGCAGGACCGCAGTGGACG	0.587													C|||	250	0.0499201	0.18	0.0159	5008	,	,		19239	0.0		0.001	False		,,,				2504	0.0				p.T153T		Atlas-SNP	.											.	CDYL	74	.	0			c.C459T						PASS	.	C	,,	664,3742	284.3+/-277.5	59,546,1598	66.0	67.0	67.0		63,63,459	3.8	0.8	6	dbSNP_86	67	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous,coding-synonymous,coding-synonymous	CDYL	NM_001143970.1,NM_001143971.1,NM_004824.3	,,	59,566,5878	TT,TC,CC		0.2326,15.0704,5.2591	,,	21/413,21/413,153/545	4892381	684,12322	2203	4300	6503	SO:0001819	synonymous_variant	9425	exon2			CAGGACCGCAGTG	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.621C>T	6.37:g.4892381C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Silent	SNP	ENST00000328908.5	37																																																																																				C|0.956;T|0.044	0.044	strong		0.587	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824	
OR10C1	442194	hgsc.bcm.edu	37	6	29408090	29408090	+	Missense_Mutation	SNP	A	A	G	rs17177632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29408090A>G	ENST00000444197.2	+	1	1008	c.298A>G	c.(298-300)Atg>Gtg	p.M100V	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	100			M -> V (in dbSNP:rs17177632).			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)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TGCTCTCCAGATGTTCTTCTT	0.592													A|||	316	0.063099	0.152	0.0562	5008	,	,		20074	0.0456		0.0159	False		,,,				2504	0.0143				p.M100V		Atlas-SNP	.											.	OR10C1	58	.	0			c.A298G						PASS	.	A	VAL/MET	340,2678		23,294,1192	98.0	97.0	97.0		298	1.9	0.8	6	dbSNP_123	97	93,5325		2,89,2618	yes	missense	OR10C1	NM_013941.3	21	25,383,3810	GG,GA,AA		1.7165,11.2657,5.1328	possibly-damaging	100/313	29408090	433,8003	1509	2709	4218	SO:0001583	missense	442194	exon1			CTCCAGATGTTCT		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.298A>G	6.37:g.29408090A>G	ENSP00000419119:p.Met100Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	157	74	0.471338	NM_013941	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	37	CCDS34364.1	132	0.06043956043956044	85	0.17276422764227642	17	0.04696132596685083	24	0.04195804195804196	6	0.0079155672823219	A	12.71	2.018954	0.35606	0.112657	0.017165	ENSG00000206474	ENST00000444197	T	0.02015	4.5	3.11	1.91	0.25777	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47455	D	0.000226	T	0.01976	0.0062	L	0.35288	1.05	0.41272	P	0.013148999999999966	D	0.57257	0.979	D	0.74348	0.983	T	0.47235	-0.9133	9	0.72032	D	0.01	.	3.9297	0.09279	0.6003:0.1852:0.2145:0.0	rs17177632	100	Q96KK4	O10C1_HUMAN	V	100	ENSP00000419119:M100V	ENSP00000419119:M100V	M	+	1	0	OR10C1	29516069	0.000000	0.05858	0.849000	0.33467	0.718000	0.41266	-0.815000	0.04481	0.399000	0.25367	0.165000	0.16767	ATG	A|0.945;G|0.055	0.055	strong		0.592	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2		
OR7A10	390892	hgsc.bcm.edu	37	19	14952017	14952017	+	Missense_Mutation	SNP	T	T	A	rs11880955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14952017T>A	ENST00000248058.1	-	1	672	c.673A>T	c.(673-675)Ata>Tta	p.I225L		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	225			I -> L (in dbSNP:rs11880955).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					ATTGCACGTATGGAGGAAACT	0.463													.|||	725	0.144768	0.2179	0.1297	5008	,	,		22434	0.0903		0.1551	False		,,,				2504	0.1022				p.I225L		Atlas-SNP	.											.	OR7A10	33	.	0			c.A673T						PASS	.	T	LEU/ILE	1043,3363	382.5+/-324.5	129,785,1289	75.0	67.0	70.0		673	2.8	0.8	19	dbSNP_120	70	1462,7138	278.3+/-293.3	141,1180,2979	no	missense	OR7A10	NM_001005190.1	5	270,1965,4268	AA,AT,TT		17.0,23.6723,19.2603	benign	225/310	14952017	2505,10501	2203	4300	6503	SO:0001583	missense	390892	exon1			CACGTATGGAGGA		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.673A>T	19.37:g.14952017T>A	ENSP00000248058:p.Ile225Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	301	0.13782051282051283	106	0.21544715447154472	52	0.143646408839779	27	0.0472027972027972	116	0.15303430079155672	t	9.153	1.016847	0.19355	0.236723	0.17	ENSG00000127515	ENST00000248058	T	0.00227	8.5	2.75	2.75	0.32379	GPCR, rhodopsin-like superfamily (1);	0.174607	0.25645	U	0.029254	T	0.00012	0.0000	M	0.84683	2.71	0.80722	P	0.0	B	0.33612	0.419	B	0.42738	0.396	T	0.11743	-1.0575	9	0.46703	T	0.11	.	9.0825	0.36561	0.0:0.0:0.0:1.0	rs11880955;rs41345444;rs11880955	225	O76100	OR7AA_HUMAN	L	225	ENSP00000248058:I225L	ENSP00000248058:I225L	I	-	1	0	OR7A10	14813017	0.000000	0.05858	0.843000	0.33291	0.558000	0.35554	-0.384000	0.07389	1.301000	0.44836	0.113000	0.15668	ATA	T|0.831;A|0.169	0.169	strong		0.463	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
MTTP	4547	hgsc.bcm.edu	37	4	100504575	100504575	+	Missense_Mutation	SNP	G	G	C	rs2306986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100504575G>C	ENST00000265517.5	+	3	497	c.294G>C	c.(292-294)gaG>gaC	p.E98D	MTTP_ENST00000511045.1_Missense_Mutation_p.E125D|MTTP_ENST00000422897.2_Missense_Mutation_p.E98D|MTTP_ENST00000457717.1_Missense_Mutation_p.E98D			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	98	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		E -> D (in dbSNP:rs2306986).		cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	AGAGAGGAGAGAAGAGCATCT	0.383													G|||	592	0.118211	0.205	0.072	5008	,	,		16968	0.2143		0.0159	False		,,,				2504	0.0399				p.E98D		Atlas-SNP	.											.	MTTP	127	.	0			c.G294C						PASS	.	G	ASP/GLU	818,3586	319.3+/-296.1	78,662,1462	112.0	121.0	118.0		294	2.7	1.0	4	dbSNP_100	118	351,8249	117.6+/-177.1	5,341,3954	yes	missense	MTTP	NM_000253.2	45	83,1003,5416	CC,CG,GG		4.0814,18.574,8.9895	benign	98/895	100504575	1169,11835	2202	4300	6502	SO:0001583	missense	4547	exon4			AGGAGAGAAGAGC		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.294G>C	4.37:g.100504575G>C	ENSP00000265517:p.Glu98Asp	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	306	142	0.464052	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	276	0.12637362637362637	98	0.1991869918699187	21	0.058011049723756904	142	0.24825174825174826	15	0.01978891820580475	G	11.36	1.614497	0.28712	0.18574	0.040814	ENSG00000138823	ENST00000506883;ENST00000511045;ENST00000457717;ENST00000265517;ENST00000422897;ENST00000538053	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	5.71	2.66	0.31614	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.311546	0.39687	N	0.001285	T	0.00012	0.0000	N	0.08118	0	0.46167	P	0.0010970000000000146	B;P;P	0.40302	0.202;0.712;0.712	B;B;B	0.39617	0.183;0.159;0.305	T	0.24764	-1.0151	8	.	.	.	-2.4524	4.55	0.12107	0.303:0.0:0.5391:0.1579	rs2306986;rs52838208;rs2306986	125;98;98	E9PBP6;P55157;Q6P5T3	.;MTP_HUMAN;.	D	108;125;98;98;98;98	ENSP00000426755:E108D;ENSP00000427679:E125D;ENSP00000400821:E98D;ENSP00000265517:E98D;ENSP00000407350:E98D	.	E	+	3	2	MTTP	100723598	0.683000	0.27633	1.000000	0.80357	0.921000	0.55340	0.170000	0.16663	0.771000	0.33359	-0.140000	0.14226	GAG	G|0.897;C|0.103	0.103	strong		0.383	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
PCCA	5095	hgsc.bcm.edu	37	13	100992428	100992428	+	Missense_Mutation	SNP	A	A	T	rs112237881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:100992428A>T	ENST00000376285.1	+	18	1596	c.1558A>T	c.(1558-1560)Agt>Tgt	p.S520C	PCCA_ENST00000376279.3_Missense_Mutation_p.S520C|PCCA_ENST00000376286.4_Missense_Mutation_p.S494C	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	520					biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	GCTAACCAAGAGTGAGAAGAA	0.348													A|||	14	0.00279553	0.0098	0.0014	5008	,	,		20036	0.0		0.0	False		,,,				2504	0.0				p.S520C		Atlas-SNP	.											.	PCCA	59	.	0			c.A1558T						PASS	.	A	CYS/SER,CYS/SER,CYS/SER	18,4388	25.3+/-52.1	0,18,2185	145.0	133.0	137.0		1558,1480,1558	4.1	0.0	13	dbSNP_132	137	0,8600		0,0,4300	yes	missense,missense,missense	PCCA	NM_000282.3,NM_001127692.2,NM_001178004.1	112,112,112	0,18,6485	TT,TA,AA		0.0,0.4085,0.1384	benign,benign,benign	520/729,494/703,520/682	100992428	18,12988	2203	4300	6503	SO:0001583	missense	5095	exon18			ACCAAGAGTGAGA	X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"""propionyl Coenzyme A carboxylase, alpha polypeptide"""			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.1558A>T	13.37:g.100992428A>T	ENSP00000365462:p.Ser520Cys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_001178004	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	37	CCDS9496.2	6|6	0.0027472527472527475|0.0027472527472527475	5|5	0.01016260162601626|0.01016260162601626	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	A|A	11.63|11.63	1.697151|1.697151	0.30142|0.30142	0.004085|0.004085	0.0|0.0	ENSG00000175198|ENSG00000175198	ENST00000443601|ENST00000376286;ENST00000376279;ENST00000376285;ENST00000424527;ENST00000376254;ENST00000536640	.|D;D;D;D	.|0.97186	.|-4.27;-4.25;-4.28;-1.72	5.3|5.3	4.08|4.08	0.47627|0.47627	.|.	.|1.227710	.|0.05174	.|N	.|0.499995	D|D	0.94165|0.94165	0.8128|0.8128	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.29886	.|0.26;0.221;0.26	.|B;B;B	.|0.41440	.|0.246;0.357;0.246	D|D	0.88437|0.88437	0.3039|0.3039	5|10	.|0.66056	.|D	.|0.02	.|.	11.3631|11.3631	0.49655|0.49655	0.693:0.307:0.0:0.0|0.693:0.307:0.0:0.0	.|.	.|520;494;520	.|C9JPQ8;P05165-2;P05165	.|.;.;PCCA_HUMAN	S|C	111|494;520;520;54;111;16	.|ENSP00000365463:S494C;ENSP00000365456:S520C;ENSP00000365462:S520C;ENSP00000396050:S54C	.|ENSP00000365430:S111C	R|S	+|+	3|1	2|0	PCCA|PCCA	99790429|99790429	0.447000|0.447000	0.25673|0.25673	0.022000|0.022000	0.16811|0.16811	0.327000|0.327000	0.28475|0.28475	1.075000|1.075000	0.30716|0.30716	0.923000|0.923000	0.37045|0.37045	0.528000|0.528000	0.53228|0.53228	AGA|AGT	A|0.997;T|0.003	0.003	strong		0.348	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2		
KIAA1468	57614	hgsc.bcm.edu	37	18	59941254	59941254	+	Silent	SNP	A	A	C	rs17069686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:59941254A>C	ENST00000398130.2	+	21	3034	c.2802A>C	c.(2800-2802)gtA>gtC	p.V934V	KIAA1468_ENST00000256858.6_Silent_p.V968V	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	934										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)				TAGAAGATGTAATGACGCTGC	0.363													A|||	301	0.0601038	0.084	0.0504	5008	,	,		15040	0.005		0.0686	False		,,,				2504	0.0828				p.V934V		Atlas-SNP	.											.	KIAA1468	93	.	0			c.A2802C						PASS	.	A		347,4059	178.7+/-207.4	10,327,1866	142.0	136.0	138.0		2802	3.8	1.0	18	dbSNP_123	138	599,8001	157.0+/-210.8	25,549,3726	no	coding-synonymous	KIAA1468	NM_020854.3		35,876,5592	CC,CA,AA		6.9651,7.8756,7.2736		934/1217	59941254	946,12060	2203	4300	6503	SO:0001819	synonymous_variant	57614	exon21			AGATGTAATGACG	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.2802A>C	18.37:g.59941254A>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	131	42	0.320611	NM_020854		Silent	SNP	ENST00000398130.2	37	CCDS11979.2																																																																																			A|0.938;C|0.062	0.062	strong		0.363	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854	
FKBP14	55033	hgsc.bcm.edu	37	7	30054492	30054492	+	Silent	SNP	C	C	T	rs142474407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30054492C>T	ENST00000222803.5	-	4	670	c.495G>A	c.(493-495)aaG>aaA	p.K165K	AC007285.6_ENST00000422239.1_RNA|AC007285.6_ENST00000419103.1_RNA	NM_017946.3	NP_060416.1	Q9NWM8	FKB14_HUMAN	FK506 binding protein 14, 22 kDa	165	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|large_intestine(2)|lung(2)	5						CAAACTCCTTCTTTAAATATG	0.348													C|||	10	0.00199681	0.0076	0.0	5008	,	,		14950	0.0		0.0	False		,,,				2504	0.0				p.K165K		Atlas-SNP	.											.	FKBP14	18	.	0			c.G495A						PASS	.	C		39,4367	38.4+/-70.7	1,37,2165	85.0	80.0	82.0		495	5.0	1.0	7	dbSNP_134	82	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FKBP14	NM_017946.2		1,38,6464	TT,TC,CC		0.0116,0.8852,0.3076		165/212	30054492	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	55033	exon4			CTCCTTCTTTAAA	AK000738	CCDS5423.1	7p15	2014-09-17	2002-08-29		ENSG00000106080	ENSG00000106080		"""EF-hand domain containing"""	18625	protein-coding gene	gene with protein product		614505	"""FK506 binding protein 14 (22 kDa)"""			12036304	Standard	NM_017946		Approved	FLJ20731, FKBP22	uc003tal.2	Q9NWM8	OTTHUMG00000023442	ENST00000222803.5:c.495G>A	7.37:g.30054492C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	66	42	0.636364	NM_017946		Silent	SNP	ENST00000222803.5	37	CCDS5423.1																																																																																			C|0.997;T|0.003	0.003	strong		0.348	FKBP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214229.1	NM_017946	
EXO5	64789	hgsc.bcm.edu	37	1	40980731	40980731	+	Missense_Mutation	SNP	G	G	T	rs11208299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:40980731G>T	ENST00000372703.1	+	2	1589	c.515G>T	c.(514-516)gGg>gTg	p.G172V	RP11-656D10.6_ENST00000437060.1_RNA|EXO5_ENST00000296380.4_Missense_Mutation_p.G172V|RP11-656D10.5_ENST00000453437.1_RNA|EXO5_ENST00000358527.2_Missense_Mutation_p.G172V			Q9H790	EXO5_HUMAN	exonuclease 5	172			G -> V (polymorphism that does not affect exonuclease activity; dbSNP:rs11208299). {ECO:0000269|PubMed:15489334}.		DNA catabolic process, exonucleolytic (GO:0000738)|interstrand cross-link repair (GO:0036297)	cytosol (GO:0005829)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)										TTTGGGGAAGGGGAGGGTGTA	0.502													T|||	2715	0.542133	0.6997	0.536	5008	,	,		20246	0.5		0.3757	False		,,,				2504	0.5481				p.G172V		Atlas-SNP	.											.	.	.	.	0			c.G515T						PASS	.	T	VAL/GLY	2811,1595	493.4+/-362.7	897,1017,289	82.0	88.0	86.0		515	4.0	1.0	1	dbSNP_120	86	3196,5404	651.2+/-400.8	582,2032,1686	yes	missense	DEM1	NM_022774.1	109	1479,3049,1975	TT,TG,GG		37.1628,36.2006,46.1864	benign	172/374	40980731	6007,6999	2203	4300	6503	SO:0001583	missense	64789	exon3			GGGAAGGGGAGGG	AK024797	CCDS453.1	1p34.2	2012-11-02	2012-10-30	2012-10-30	ENSG00000164002	ENSG00000164002			26115	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 176"", ""defects in morphology 1 homolog (S. cerevisiae)"""	C1orf176, DEM1		23095756	Standard	NM_022774		Approved	FLJ21144	uc001cfp.3	Q9H790	OTTHUMG00000007305	ENST00000372703.1:c.515G>T	1.37:g.40980731G>T	ENSP00000361788:p.Gly172Val	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_022774	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Missense_Mutation	SNP	ENST00000372703.1	37	CCDS453.1	1122	0.5137362637362637	357	0.725609756097561	185	0.511049723756906	295	0.5157342657342657	285	0.3759894459102902	T	0.127	-1.118333	0.01785	0.637994	0.371628	ENSG00000164002	ENST00000358527;ENST00000372703;ENST00000420209;ENST00000296380;ENST00000418186;ENST00000443729;ENST00000419161	T;T;T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83;1.83;1.83	5.09	3.96	0.45880	.	0.692054	0.12336	N	0.477953	T	0.00012	0.0000	N	0.00025	-2.675	0.38200	P	0.059826999999999964	B	0.02656	0.0	B	0.01281	0.0	T	0.41431	-0.9509	9	0.02654	T	1	-5.5314	5.3966	0.16273	0.0:0.0896:0.1772:0.7333	rs11208299;rs17845666;rs17858602;rs52798759;rs60314009;rs11208299	172	Q9H790	EXO5_HUMAN	V	172	ENSP00000351328:G172V;ENSP00000361788:G172V;ENSP00000398437:G172V;ENSP00000296380:G172V;ENSP00000391240:G172V;ENSP00000409715:G172V;ENSP00000392115:G172V	ENSP00000296380:G172V	G	+	2	0	DEM1	40753318	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.213000	0.42844	0.504000	0.28082	-0.264000	0.10439	GGG	G|0.508;T|0.492	0.492	strong		0.502	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774	
C4orf51	646603	hgsc.bcm.edu	37	4	146653620	146653620	+	Missense_Mutation	SNP	G	G	A	rs10008599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:146653620G>A	ENST00000438731.1	+	6	517	c.517G>A	c.(517-519)Gat>Aat	p.D173N	C4orf51_ENST00000508981.1_3'UTR	NM_001080531.1	NP_001074000.1	C9J302	CD051_HUMAN	chromosome 4 open reading frame 51	173										haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)	6						TGGACGGTGCGATTCTGAAAG	0.473													G|||	386	0.0770767	0.1362	0.0778	5008	,	,		13978	0.001		0.1183	False		,,,				2504	0.0327				p.D173N		Atlas-SNP	.											.	C4orf51	18	.	0			c.G517A						PASS	.	G	ASN/ASP	473,3461		36,401,1530	58.0	61.0	60.0		517	-0.4	0.0	4	dbSNP_119	60	1010,7298		64,882,3208	yes	missense	C4orf51	NM_001080531.1	23	100,1283,4738	AA,AG,GG		12.157,12.0234,12.114	possibly-damaging	173/203	146653620	1483,10759	1967	4154	6121	SO:0001583	missense	646603	exon6			CGGTGCGATTCTG		CCDS47140.1	4q31.21	2009-09-09			ENSG00000237136	ENSG00000237136			37264	protein-coding gene	gene with protein product							Standard	NM_001080531		Approved		uc003ikk.3	C9J302	OTTHUMG00000161367	ENST00000438731.1:c.517G>A	4.37:g.146653620G>A	ENSP00000391404:p.Asp173Asn	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_001080531		Missense_Mutation	SNP	ENST00000438731.1	37	CCDS47140.1	188	0.08608058608058608	63	0.12804878048780488	32	0.08839779005524862	1	0.0017482517482517483	92	0.12137203166226913	G	16.17	3.046140	0.55110	0.120234	0.12157	ENSG00000237136	ENST00000438731	.	.	.	3.77	-0.356	0.12583	.	.	.	.	.	T	0.00241	0.0007	N	0.24115	0.695	0.80722	P	0.0	B	0.21688	0.059	B	0.12837	0.008	T	0.13176	-1.0519	7	0.87932	D	0	.	2.3842	0.04362	0.1325:0.1847:0.4956:0.1872	rs10008599	173	C9J302	CD051_HUMAN	N	173	.	ENSP00000391404:D173N	D	+	1	0	C4orf51	146873070	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.031000	0.12287	-0.097000	0.12307	0.555000	0.69702	GAT	G|0.908;A|0.092	0.092	strong		0.473	C4orf51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080531	
MUC17	140453	hgsc.bcm.edu	37	7	100684593	100684593	+	Missense_Mutation	SNP	G	G	A	rs35988443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100684593G>A	ENST00000306151.4	+	3	9960	c.9896G>A	c.(9895-9897)aGc>aAc	p.S3299N		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3299	59 X approximate tandem repeats.|Ser-rich.		S -> N (in dbSNP:rs35988443).		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)					TCTGAAACGAGCACCCTTTCA	0.512													G|||	563	0.11242	0.1634	0.0807	5008	,	,		26032	0.0665		0.1173	False		,,,				2504	0.1084				p.S3299N		Atlas-SNP	.											.	MUC17	804	.	0			c.G9896A						PASS	.	G	ASN/SER	640,3766	275.4+/-272.5	43,554,1606	307.0	314.0	312.0		9896	-1.5	0.0	7	dbSNP_126	312	987,7613	213.6+/-253.5	57,873,3370	no	missense	MUC17	NM_001040105.1	46	100,1427,4976	AA,AG,GG		11.4767,14.5256,12.5096	possibly-damaging	3299/4494	100684593	1627,11379	2203	4300	6503	SO:0001583	missense	140453	exon3			AAACGAGCACCCT	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.9896G>A	7.37:g.100684593G>A	ENSP00000302716:p.Ser3299Asn	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	132	64	0.484848	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	213	0.09752747252747253	65	0.13211382113821138	32	0.08839779005524862	29	0.050699300699300696	87	0.11477572559366754	g	0.265	-0.996778	0.02145	0.145256	0.114767	ENSG00000169876	ENST00000306151	T	0.02121	4.44	0.754	-1.51	0.08664	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.13594	0.008	B	0.15870	0.014	T	0.46275	-0.9203	8	0.24483	T	0.36	.	3.8023	0.08763	0.2104:0.2466:0.543:0.0	rs35988443;rs58884530	3299	Q685J3	MUC17_HUMAN	N	3299	ENSP00000302716:S3299N	ENSP00000302716:S3299N	S	+	2	0	MUC17	100471313	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.085000	0.11250	-1.089000	0.03073	0.134000	0.15878	AGC	G|0.888;A|0.112	0.112	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
RSL24D1	51187	hgsc.bcm.edu	37	15	55489065	55489065	+	Silent	SNP	G	G	A	rs9300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55489065G>A	ENST00000260443.4	-	1	200	c.24C>T	c.(22-24)ttC>ttT	p.F8F	RSL24D1_ENST00000565854.1_5'Flank	NM_016304.2	NP_057388.1	Q9UHA3	RLP24_HUMAN	ribosomal L24 domain containing 1	8					ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)		p.F8F(1)		central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)	7						GCCCCGAACAGAAATAACACT	0.537											OREG0023135	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1354	0.270367	0.5492	0.1326	5008	,	,		19967	0.1379		0.1918	False		,,,				2504	0.2086				p.F8F		Atlas-SNP	.											RSL24D1,NS,carcinoma,0,1	RSL24D1	11	1	1	Substitution - coding silent(1)	stomach(1)	c.C24T						PASS	.	G		2125,2261	578.1+/-384.6	507,1111,575	116.0	90.0	99.0		24	3.5	1.0	15	dbSNP_52	99	1627,6957	301.4+/-305.4	146,1335,2811	no	coding-synonymous	RSL24D1	NM_016304.2		653,2446,3386	AA,AG,GG		18.9539,48.4496,28.9283		8/164	55489065	3752,9218	2193	4292	6485	SO:0001819	synonymous_variant	51187	exon1			CGAACAGAAATAA	AF201949	CCDS10152.1	15q21	2009-02-27	2009-02-27	2009-02-27	ENSG00000137876	ENSG00000137876			18479	protein-coding gene	gene with protein product		613262	"""chromosome 15 open reading frame 15"""	C15orf15		12808088, 11707418	Standard	NM_016304		Approved	HRP-L30-iso, L30, RPL24L, RPL24	uc002acn.3	Q9UHA3	OTTHUMG00000131957	ENST00000260443.4:c.24C>T	15.37:g.55489065G>A		Somatic	76	0	0	1008	WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_016304	B2RD72|Q561V8|Q8N6S8|Q96B04|Q96C76|Q96HJ1	Silent	SNP	ENST00000260443.4	37	CCDS10152.1																																																																																			G|0.721;A|0.279	0.279	strong		0.537	RSL24D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254916.1	NM_016304	
FZD10	11211	hgsc.bcm.edu	37	12	130647709	130647709	+	Silent	SNP	G	G	C	rs10848026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:130647709G>C	ENST00000229030.4	+	1	706	c.222G>C	c.(220-222)ctG>ctC	p.L74L	FZD10-AS1_ENST00000505807.2_RNA|FZD10_ENST00000539839.1_Missense_Mutation_p.G42R			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	74	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		TCGCGCCGCTGGTGGAGTACG	0.647													G|||	1603	0.320088	0.3313	0.1988	5008	,	,		12082	0.4722		0.1819	False		,,,				2504	0.3763				p.L74L		Atlas-SNP	.											.	FZD10	95	.	0			c.G222C						PASS	.	G		1308,3098		220,868,1115	40.0	39.0	39.0		222	0.0	1.0	12	dbSNP_120	39	1675,6917		159,1357,2780	no	coding-synonymous	FZD10	NM_007197.3		379,2225,3895	CC,CG,GG		19.4949,29.6868,22.9497		74/582	130647709	2983,10015	2203	4296	6499	SO:0001819	synonymous_variant	11211	exon1			GCCGCTGGTGGAG	AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"""GPCR / Class F : Frizzled receptors"", ""CD molecules"""	4039	protein-coding gene	gene with protein product		606147	"""frizzled (Drosophila) homolog 10"", ""frizzled homolog 10 (Drosophila)"", ""frizzled 10, seven transmembrane spanning receptor"", ""frizzled family receptor 10"""			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.222G>C	12.37:g.130647709G>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	134	58	0.432836	NM_007197		Silent	SNP	ENST00000229030.4	37	CCDS9267.1	632	0.2893772893772894	162	0.32926829268292684	73	0.20165745856353592	264	0.46153846153846156	133	0.17546174142480211	G	9.459	1.092508	0.20471	0.296868	0.194949	ENSG00000111432	ENST00000539839	.	.	.	4.4	0.0303	0.14166	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46020	-0.9221	4	0.87932	D	0	.	9.7557	0.40502	0.0775:0.4099:0.5125:0.0	rs10848026;rs10848026	.	.	.	R	42	.	ENSP00000438460:G42R	G	+	1	0	FZD10	129213662	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	1.702000	0.37836	-0.345000	0.08325	-0.305000	0.09177	GGT	G|0.760;C|0.240	0.240	strong		0.647	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ZNF765	91661	hgsc.bcm.edu	37	19	53911041	53911041	+	Missense_Mutation	SNP	A	A	G	rs116731689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53911041A>G	ENST00000396408.3	+	4	350	c.233A>G	c.(232-234)gAa>gGa	p.E78G	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	78	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(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		CAAAGACATGAAAGTCATCAC	0.378													.|||	152	0.0303514	0.1112	0.0029	5008	,	,		19693	0.0		0.003	False		,,,				2504	0.0				p.E78G		Atlas-SNP	.											.	ZNF765	61	.	0			c.A233G						PASS	.	A	GLY/GLU	374,4018	175.9+/-205.1	16,342,1838	73.0	74.0	74.0		233	1.2	0.0	19	dbSNP_132	74	6,8586	3.0+/-9.4	0,6,4290	yes	missense	ZNF765	NM_001040185.1	98	16,348,6128	GG,GA,AA		0.0698,8.5155,2.9267	benign	78/524	53911041	380,12604	2196	4296	6492	SO:0001583	missense	91661	exon4			GACATGAAAGTCA	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.233A>G	19.37:g.53911041A>G	ENSP00000379689:p.Glu78Gly	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	264	129	0.488636	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Missense_Mutation	SNP	ENST00000396408.3	37	CCDS46171.1	47	0.02152014652014652	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	A	13.11	2.139154	0.37728	0.085155	6.98E-4	ENSG00000196417	ENST00000396408;ENST00000505866	T;T	0.08896	3.04;4.0	1.21	1.21	0.21127	Krueppel-associated box (1);	.	.	.	.	T	0.00241	0.0007	N	0.17082	0.46	0.09310	N	1	B	0.34241	0.444	B	0.38880	0.284	T	0.47471	-0.9115	8	.	.	.	.	4.4592	0.11657	1.0:0.0:0.0:0.0	.	78	Q7L2R6	ZN765_HUMAN	G	78;25	ENSP00000379689:E78G;ENSP00000421579:E25G	.	E	+	2	0	ZNF765	58602853	0.000000	0.05858	0.013000	0.15412	0.045000	0.14185	0.406000	0.21032	0.523000	0.28482	0.147000	0.16070	GAA	A|0.975;G|0.025	0.025	strong		0.378	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372	
PABPC1	26986	hgsc.bcm.edu	37	8	101721756	101721756	+	Silent	SNP	A	A	C	rs57799615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721756A>C	ENST00000318607.5	-	8	2304	c.1176T>G	c.(1174-1176)gtT>gtG	p.V392V	PABPC1_ENST00000519004.1_Silent_p.V347V|PABPC1_ENST00000522387.1_Silent_p.V360V|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	392					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			CAGGGTTGGGAACAGCTCGTA	0.498																																					p.V392V		Atlas-SNP	.											.	PABPC1	76	.	0			c.T1176G						PASS	.						155.0	135.0	142.0					8																	101721756		2203	4300	6503	SO:0001819	synonymous_variant	26986	exon8			GTTGGGAACAGCT	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.1176T>G	8.37:g.101721756A>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	391	132	0.337596	NM_002568	Q15097|Q93004	Silent	SNP	ENST00000318607.5	37	CCDS6289.1	251|251	0.11492673992673992|0.11492673992673992	138|138	0.2804878048780488|0.2804878048780488	18|18	0.049723756906077346|0.049723756906077346	33|33	0.057692307692307696|0.057692307692307696	62|62	0.08179419525065963|0.08179419525065963	C|C	10.08|10.08	1.251048|1.251048	0.22880|0.22880	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000517403;ENST00000519100|ENST00000519596	.|.	.|.	.|.	5.19|5.19	4.3|4.3	0.51218|0.51218	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.03619|0.03619	-1.1019|-1.1019	4|4	.|.	.|.	.|.	.|.	5.5819|5.5819	0.17254|0.17254	0.1355:0.5308:0.2616:0.0721|0.1355:0.5308:0.2616:0.0721	rs57799615;rs61745491|rs57799615;rs61745491	.|.	.|.	.|.	C|A	45;261|225	.|.	.|.	F|S	-|-	2|1	0|0	PABPC1|PABPC1	101790932|101790932	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	0.926000|0.926000	0.28804|0.28804	0.692000|0.692000	0.31613|0.31613	-0.121000|-0.121000	0.15023|0.15023	TTC|TCC	A|0.887;C|0.113	0.113	strong		0.498	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
UNC45A	55898	hgsc.bcm.edu	37	15	91485730	91485730	+	Missense_Mutation	SNP	C	C	G	rs115978927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91485730C>G	ENST00000418476.2	+	7	791	c.751C>G	c.(751-753)Cag>Gag	p.Q251E	UNC45A_ENST00000553671.2_Intron|UNC45A_ENST00000394275.2_Missense_Mutation_p.Q236E	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	251					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CGTGGAAAGCCAGGCTGTGTC	0.557													C|||	48	0.00958466	0.0325	0.0072	5008	,	,		19205	0.0		0.0	False		,,,				2504	0.0				p.Q251E		Atlas-SNP	.											.	UNC45A	57	.	0			c.C751G						PASS	.	C	GLU/GLN,GLU/GLN	99,4297	79.3+/-117.8	1,97,2100	118.0	109.0	112.0		706,751	4.6	1.0	15	dbSNP_132	112	1,8595	1.2+/-3.3	0,1,4297	yes	missense,missense	UNC45A	NM_001039675.1,NM_018671.3	29,29	1,98,6397	GG,GC,CC		0.0116,2.252,0.7697	benign,benign	236/930,251/945	91485730	100,12892	2198	4298	6496	SO:0001583	missense	55898	exon7			GAAAGCCAGGCTG		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"""smooth muscle cell associated protein-1"""	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.751C>G	15.37:g.91485730C>G	ENSP00000407487:p.Gln251Glu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	37	CCDS10367.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	3.104	-0.184173	0.06340	0.02252	1.16E-4	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.44482	0.92;0.92	5.5	4.56	0.56223	Armadillo-like helical (1);Armadillo-type fold (1);	0.329961	0.31051	N	0.008356	T	0.06872	0.0175	N	0.01109	-1.01	0.28195	N	0.927606	B;B;B;B	0.12630	0.004;0.006;0.0;0.0	B;B;B;B	0.08055	0.002;0.003;0.001;0.001	T	0.12708	-1.0537	10	0.02654	T	1	-19.8406	13.9263	0.63964	0.0:0.6338:0.3662:0.0	.	251;243;251;236	B4DZL0;B4DLE6;Q9H3U1;A8K6F7	.;.;UN45A_HUMAN;.	E	236;251	ENSP00000377816:Q236E;ENSP00000407487:Q251E	ENSP00000377816:Q236E	Q	+	1	0	UNC45A	89286734	0.984000	0.35163	1.000000	0.80357	0.929000	0.56500	3.726000	0.54977	1.405000	0.46838	0.558000	0.71614	CAG	C|0.991;G|0.009	0.009	strong		0.557	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
MAB21L3	126868	hgsc.bcm.edu	37	1	116670774	116670774	+	Silent	SNP	A	A	G	rs10754431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:116670774A>G	ENST00000369500.3	+	6	934	c.669A>G	c.(667-669)ggA>ggG	p.G223G	MAB21L3_ENST00000464946.1_3'UTR	NM_152367.2	NP_689580.2	Q8N8X9	MB213_HUMAN	mab-21-like 3 (C. elegans)	223										breast(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|urinary_tract(1)	19						AGTCGTTTGGATTTAACTTGT	0.468													G|||	2091	0.417532	0.9009	0.2983	5008	,	,		21590	0.2748		0.2227	False		,,,				2504	0.1963				p.G223G		Atlas-SNP	.											.	MAB21L3	33	.	0			c.A669G						PASS	.	G		3409,997	370.8+/-319.7	1330,749,124	108.0	116.0	113.0		669	0.2	0.4	1	dbSNP_120	113	1850,6750	730.1+/-406.7	190,1470,2640	no	coding-synonymous	MAB21L3	NM_152367.2		1520,2219,2764	GG,GA,AA		21.5116,22.6282,40.4352		223/363	116670774	5259,7747	2203	4300	6503	SO:0001819	synonymous_variant	126868	exon6			GTTTGGATTTAAC	AK096035	CCDS886.1	1p13.1	2011-02-23	2011-02-23	2011-02-23	ENSG00000173212	ENSG00000173212			26787	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 161"""	C1orf161		14702039	Standard	NM_152367		Approved	FLJ38716	uc001egc.1	Q8N8X9	OTTHUMG00000012110	ENST00000369500.3:c.669A>G	1.37:g.116670774A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_152367	Q5TDL7	Silent	SNP	ENST00000369500.3	37	CCDS886.1																																																																																			A|0.608;G|0.392	0.392	strong		0.468	MAB21L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033486.1	NM_152367	
CCAR2	57805	hgsc.bcm.edu	37	8	22473281	22473281	+	Silent	SNP	C	C	G	rs6558166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22473281C>G	ENST00000308511.4	+	13	1713	c.1464C>G	c.(1462-1464)acC>acG	p.T488T	CCAR2_ENST00000389279.3_Silent_p.T488T|RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000520861.1_Silent_p.T163T			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	488					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										CAGAGGCCACCACACAGCAGG	0.582													C|||	683	0.136382	0.3843	0.0533	5008	,	,		17798	0.0218		0.0338	False		,,,				2504	0.0838				p.T488T		Atlas-SNP	.											.	KIAA1967	72	.	0			c.C1464G						PASS	.	C		1403,3003	461.1+/-352.8	225,953,1025	102.0	109.0	106.0		1464	-7.3	0.0	8	dbSNP_116	106	281,8319	104.6+/-165.6	5,271,4024	no	coding-synonymous	KIAA1967	NM_021174.5		230,1224,5049	GG,GC,CC		3.2674,31.8429,12.9479		488/924	22473281	1684,11322	2203	4300	6503	SO:0001819	synonymous_variant	57805	exon13			GGCCACCACACAG	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1464C>G	8.37:g.22473281C>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Silent	SNP	ENST00000308511.4	37	CCDS34863.1	243	0.11126373626373626	187	0.3800813008130081	19	0.052486187845303865	8	0.013986013986013986	29	0.03825857519788918	C	1.026	-0.683484	0.03353	0.318429	0.032674	ENSG00000158941	ENST00000520738	.	.	.	6.07	-7.32	0.01436	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.29027	-1.0025	3	.	.	.	-2.2864	8.8665	0.35289	0.0:0.1723:0.2147:0.613	rs6558166;rs60027725;rs6558166	.	.	.	R	180	.	.	P	+	2	0	KIAA1967	22529226	0.000000	0.05858	0.000000	0.03702	0.146000	0.21551	-2.745000	0.00796	-1.379000	0.02118	0.655000	0.94253	CCA	C|0.882;G|0.118	0.118	strong		0.582	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
OR8D1	283159	hgsc.bcm.edu	37	11	124179902	124179902	+	Missense_Mutation	SNP	G	G	A	rs57552127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124179902G>A	ENST00000357821.2	-	1	831	c.761C>T	c.(760-762)tCc>tTc	p.S254F		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	254						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(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		GAAGGTAATGGACCCAAAGAA	0.517													G|||	558	0.111422	0.3313	0.0793	5008	,	,		17923	0.0357		0.002	False		,,,				2504	0.0276				p.S254F		Atlas-SNP	.											OR8D1,NS,carcinoma,+1,1	OR8D1	53	1	0			c.C761T						PASS	.	G	PHE/SER	1305,3097	441.2+/-346.3	182,941,1078	97.0	89.0	91.0		761	3.2	0.1	11	dbSNP_129	91	11,8587	7.1+/-27.0	0,11,4288	yes	missense	OR8D1	NM_001002917.1	155	182,952,5366	AA,AG,GG		0.1279,29.6456,10.1231	probably-damaging	254/309	124179902	1316,11684	2201	4299	6500	SO:0001583	missense	283159	exon1			GTAATGGACCCAA	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"""GPCR / Class A : Olfactory receptors"""	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.761C>T	11.37:g.124179902G>A	ENSP00000350474:p.Ser254Phe	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	122	43	0.352459	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Missense_Mutation	SNP	ENST00000357821.2	37	CCDS31706.1	218	0.09981684981684982	171	0.3475609756097561	24	0.06629834254143646	21	0.03671328671328671	2	0.002638522427440633	g	9.039	0.989200	0.18966	0.296456	0.001279	ENSG00000196341	ENST00000357821	T	0.00179	8.61	4.08	3.17	0.36434	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35970	U	0.002868	T	0.00012	0.0000	M	0.75085	2.285	0.80722	P	0.0	D	0.89917	1.0	D	0.83275	0.996	T	0.54549	-0.8277	9	0.87932	D	0	.	11.4812	0.50326	0.0896:0.0:0.9104:0.0	rs57552127	254	Q8WZ84	OR8D1_HUMAN	F	254	ENSP00000350474:S254F	ENSP00000350474:S254F	S	-	2	0	OR8D1	123685112	0.003000	0.15002	0.109000	0.21407	0.002000	0.02628	1.325000	0.33724	0.949000	0.37715	-0.363000	0.07495	TCC	G|0.906;A|0.094	0.094	strong		0.517	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917	
SLC6A3	6531	hgsc.bcm.edu	37	5	1409226	1409226	+	Silent	SNP	G	G	C	rs8179035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:1409226G>C	ENST00000270349.9	-	11	1540	c.1413C>G	c.(1411-1413)gtC>gtG	p.V471V	SLC6A3_ENST00000453492.2_Silent_p.V471V	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	471			V -> I (in dbSNP:rs75916702). {ECO:0000269|PubMed:21179162}.		adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GGAGCGTGAAGACGTAGATGC	0.572													G|||	21	0.00419329	0.0129	0.0029	5008	,	,		17164	0.0		0.002	False		,,,				2504	0.0				p.V471V		Atlas-SNP	.											SLC6A3,NS,carcinoma,-1,1	SLC6A3	102	1	0			c.C1413G						PASS	.	G		59,4343	55.5+/-91.7	0,59,2142	56.0	49.0	51.0		1413	0.7	1.0	5	dbSNP_125	51	1,8589		0,1,4294	no	coding-synonymous	SLC6A3	NM_001044.4		0,60,6436	CC,CG,GG		0.0116,1.3403,0.4618		471/621	1409226	60,12932	2201	4295	6496	SO:0001819	synonymous_variant	6531	exon11			CGTGAAGACGTAG		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"""Solute carriers"""	11049	protein-coding gene	gene with protein product	"""dopamine transporter"""	126455	"""solute carrier family 6 (neurotransmitter transporter, dopamine), member 3"", ""dopamine transporter 1"""	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1413C>G	5.37:g.1409226G>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_001044	A2RUN4|Q14996	Silent	SNP	ENST00000270349.9	37	CCDS3863.1																																																																																			G|0.995;C|0.005	0.005	strong		0.572	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044	
TBPL2	387332	hgsc.bcm.edu	37	14	55903716	55903716	+	Missense_Mutation	SNP	C	C	A	rs45612333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55903716C>A	ENST00000247219.5	-	2	241	c.171G>T	c.(169-171)agG>agT	p.R57S		NM_199047.2	NP_950248.1			TATA box binding protein like 2											endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8						ACAGGGGAGACCTGGGTGGGG	0.453													C|||	237	0.0473243	0.034	0.0677	5008	,	,		20723	0.005		0.0795	False		,,,				2504	0.0613				p.R57S		Atlas-SNP	.											.	TBPL2	27	.	0			c.G171T						PASS	.	C	SER/ARG	151,4231	94.4+/-133.1	2,147,2042	81.0	86.0	84.0		171	0.4	0.0	14	dbSNP_127	84	762,7824	176.2+/-226.1	37,688,3568	yes	missense	TBPL2	NM_199047.2	110	39,835,5610	AA,AC,CC		8.8749,3.4459,7.0404	benign	57/376	55903716	913,12055	2191	4293	6484	SO:0001583	missense	387332	exon2			GGGAGACCTGGGT	AY457923	CCDS9724.1	14q22.2	2004-06-03			ENSG00000182521	ENSG00000182521			19841	protein-coding gene	gene with protein product		608964				14634207	Standard	NM_199047		Approved	TRF3, TBP2	uc001xby.3	Q6SJ96	OTTHUMG00000140313	ENST00000247219.5:c.171G>T	14.37:g.55903716C>A	ENSP00000247219:p.Arg57Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_199047		Missense_Mutation	SNP	ENST00000247219.5	37	CCDS9724.1	108	0.04945054945054945	21	0.042682926829268296	30	0.08287292817679558	1	0.0017482517482517483	56	0.07387862796833773	C	0.650	-0.809813	0.02798	0.034459	0.088749	ENSG00000182521	ENST00000247219	T	0.41758	0.99	4.99	0.384	0.16244	.	1.845360	0.02244	N	0.066064	T	0.00936	0.0031	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.04386	-1.0955	10	0.07325	T	0.83	11.7785	0.6339	0.00799	0.2488:0.372:0.1409:0.2383	rs45612333	57	Q6SJ96	TBPL2_HUMAN	S	57	ENSP00000247219:R57S	ENSP00000247219:R57S	R	-	3	2	TBPL2	54973469	0.002000	0.14202	0.037000	0.18230	0.480000	0.33159	-0.072000	0.11486	0.507000	0.28148	0.563000	0.77884	AGG	C|0.933;A|0.067	0.067	strong		0.453	TBPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276916.1	NM_199047	
MAP3K9	4293	hgsc.bcm.edu	37	14	71199452	71199452	+	Silent	SNP	G	G	A	rs3829955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:71199452G>A	ENST00000554752.2	-	11	2633	c.2634C>T	c.(2632-2634)aaC>aaT	p.N878N	MAP3K9_ENST00000555993.2_Silent_p.N892N|MAP3K9_ENST00000554146.1_Silent_p.N606N|MAP3K9_ENST00000553414.1_Silent_p.N611N|MAP3K9_ENST00000381250.4_Silent_p.N855N	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	878	Pro-rich.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		TGACCAGGGGGTTGTGGGTAC	0.597													G|||	1261	0.251797	0.2163	0.2983	5008	,	,		18132	0.3363		0.2217	False		,,,				2504	0.2106				p.N892N	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.C2676T						PASS	.	G		1009,3397	376.1+/-321.9	109,791,1303	99.0	105.0	103.0		2676	1.5	1.0	14	dbSNP_107	103	1810,6790	326.2+/-317.3	193,1424,2683	no	coding-synonymous	MAP3K9	NM_033141.2		302,2215,3986	AA,AG,GG		21.0465,22.9006,21.6746		892/1119	71199452	2819,10187	2203	4300	6503	SO:0001819	synonymous_variant	4293	exon12			CAGGGGGTTGTGG	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.2634C>T	14.37:g.71199452G>A		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	329	181	0.550152	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Silent	SNP	ENST00000554752.2	37																																																																																				G|0.774;A|0.226	0.226	strong		0.597	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2		
POLRMT	5442	hgsc.bcm.edu	37	19	622304	622304	+	Missense_Mutation	SNP	G	G	A	rs41545023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:622304G>A	ENST00000588649.2	-	9	1780	c.1696C>T	c.(1696-1698)Ccc>Tcc	p.P566S	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	566					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)		AGGGGCCAGGGCTGCTCCCGC	0.706													G|||	32	0.00638978	0.0212	0.0058	5008	,	,		13734	0.0		0.0	False		,,,				2504	0.0				p.P566S		Atlas-SNP	.											.	POLRMT	91	.	0			c.C1696T						PASS	.	G	SER/PRO	59,4143		0,59,2042	5.0	6.0	6.0		1696	3.0	1.0	19	dbSNP_127	6	0,8252		0,0,4126	no	missense	POLRMT	NM_005035.3	74	0,59,6168	AA,AG,GG		0.0,1.4041,0.4737	benign	566/1231	622304	59,12395	2101	4126	6227	SO:0001583	missense	5442	exon9			GCCAGGGCTGCTC		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.1696C>T	19.37:g.622304G>A	ENSP00000465759:p.Pro566Ser	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	7.555	0.663560	0.14710	0.014041	0.0	ENSG00000099821	ENST00000215591	T	0.41065	1.01	4.15	3.02	0.34903	.	0.759629	0.13016	N	0.420516	T	0.26231	0.0640	M	0.64170	1.965	0.26553	N	0.973879	B	0.22683	0.073	B	0.20184	0.028	T	0.12553	-1.0543	10	0.30078	T	0.28	-50.68	2.8775	0.05636	0.1015:0.271:0.4629:0.1646	rs41545023	566	O00411	RPOM_HUMAN	S	566	ENSP00000215591:P566S	ENSP00000215591:P566S	P	-	1	0	POLRMT	573304	0.788000	0.28762	1.000000	0.80357	0.557000	0.35523	1.680000	0.37607	2.309000	0.77851	0.561000	0.74099	CCC	.	.	weak		0.706	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
FSCB	84075	hgsc.bcm.edu	37	14	44975606	44975606	+	Missense_Mutation	SNP	G	G	T	rs3809429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:44975606G>T	ENST00000340446.4	-	1	876	c.585C>A	c.(583-585)caC>caA	p.H195Q	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000556228.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	195			H -> Q (in dbSNP:rs3809429). {ECO:0000269|PubMed:15489334}.			sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)	p.H195Q(1)		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)		GAAATTCAGGGTGTTCACTAG	0.403													G|||	1360	0.271565	0.2859	0.3055	5008	,	,		19485	0.3968		0.1193	False		,,,				2504	0.2556				p.H195Q		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	1	Substitution - Missense(1)	stomach(1)	c.C585A						PASS	.	G	GLN/HIS	1185,3221	414.8+/-337.0	157,871,1175	134.0	140.0	138.0		585	-2.3	0.3	14	dbSNP_107	138	947,7653	206.5+/-248.5	50,847,3403	yes	missense	FSCB	NM_032135.3	24	207,1718,4578	TT,TG,GG		11.0116,26.8951,16.3924	probably-damaging	195/826	44975606	2132,10874	2203	4300	6503	SO:0001583	missense	84075	exon1			TTCAGGGTGTTCA	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.585C>A	14.37:g.44975606G>T	ENSP00000344579:p.His195Gln	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	542	0.24816849816849818	138	0.2804878048780488	97	0.26795580110497236	223	0.38986013986013984	84	0.11081794195250659	G	9.402	1.078233	0.20227	0.268951	0.110116	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.24350	1.86	4.2	-2.28	0.06826	.	.	.	.	.	T	0.00012	0.0000	L	0.53249	1.67	0.58432	P	1.0000000000287557E-6	P	0.37573	0.6	B	0.38500	0.275	T	0.43798	-0.9369	8	0.19590	T	0.45	-3.8899	4.8286	0.13428	0.5279:0.1605:0.3116:0.0	rs3809429;rs17846266;rs17859288;rs52805697;rs61689159;rs3809429	195	Q5H9T9	FSCB_HUMAN	Q	195	ENSP00000344579:H195Q	ENSP00000344579:H195Q	H	-	3	2	FSCB	44045356	0.026000	0.19158	0.284000	0.24805	0.229000	0.25112	-0.134000	0.10436	-0.303000	0.08856	-2.303000	0.00259	CAC	G|0.789;T|0.211	0.211	strong		0.403	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
OBSCN	84033	hgsc.bcm.edu	37	1	228559994	228559994	+	Missense_Mutation	SNP	C	C	T	rs500049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228559994C>T	ENST00000422127.1	+	94	21559	c.21515C>T	c.(21514-21516)gCg>gTg	p.A7172V	OBSCN_ENST00000570156.2_Missense_Mutation_p.A8129V|OBSCN_ENST00000366707.4_Missense_Mutation_p.A4806V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7172			A -> V (in dbSNP:rs500049). {ECO:0000269|PubMed:10997877}.		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)				CAGGAACAGGCGACCATGCGC	0.672													C|||	2950	0.589058	0.708	0.389	5008	,	,		17715	0.5625		0.504	False		,,,				2504	0.6851				p.A8129V		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,2	OBSCN	2142	2	0			c.C24386T						PASS	.	C	VAL/ALA	2727,1409		914,899,255	13.0	15.0	14.0		21515	3.7	0.6	1	dbSNP_83	14	4210,4154		1110,1990,1082	yes	missense	OBSCN	NM_001098623.1	64	2024,2889,1337	TT,TC,CC		49.6652,34.0667,44.504	possibly-damaging	7172/7969	228559994	6937,5563	2068	4182	6250	SO:0001583	missense	84033	exon105			AACAGGCGACCAT	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.21515C>T	1.37:g.228559994C>T	ENSP00000409493:p.Ala7172Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	206	101	0.490291	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	1222	0.5595238095238095	364	0.7398373983739838	155	0.4281767955801105	324	0.5664335664335665	379	0.5	C	13.96	2.391908	0.42410	0.659333	0.503348	ENSG00000154358	ENST00000422127;ENST00000366707	T;T	0.63913	-0.02;-0.07	4.63	3.71	0.42584	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.26078	P	0.9811296	B	0.11235	0.004	B	0.08055	0.003	T	0.41875	-0.9484	8	0.02654	T	1	.	11.6121	0.51066	0.0:0.9061:0.0:0.0939	rs500049;rs827831;rs1697612;rs500049	7172	Q5VST9	OBSCN_HUMAN	V	7172;4806	ENSP00000409493:A7172V;ENSP00000355668:A4806V	ENSP00000355668:A4806V	A	+	2	0	OBSCN	226626617	0.008000	0.16893	0.588000	0.28705	0.035000	0.12851	2.164000	0.42387	0.587000	0.29643	-1.164000	0.01763	GCG	C|0.427;T|0.573	0.573	strong		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412005	105412005	+	Silent	SNP	A	A	G	rs28564728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105412005A>G	ENST00000333244.5	-	7	9902	c.9783T>C	c.(9781-9783)gaT>gaC	p.D3261D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3261						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)			GGGCCGTCACATCCATCTTCG	0.612													.|||	1867	0.372804	0.3744	0.3775	5008	,	,		15923	0.1687		0.494	False		,,,				2504	0.453				p.D3261D		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T9783C						PASS	.	T		534,3168		41,452,1358	98.0	73.0	81.0		9783	-1.4	0.0	14	dbSNP_125	81	2628,5254		702,1224,2015	no	coding-synonymous	AHNAK2	NM_138420.2		743,1676,3373	GG,GA,AA		33.3418,14.4246,27.2963		3261/5796	105412005	3162,8422	1851	3941	5792	SO:0001819	synonymous_variant	113146	exon7			CGTCACATCCATC	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.9783T>C	14.37:g.105412005A>G		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	314	60	0.191083	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.449;G|0.551	0.551	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
FREM1	158326	hgsc.bcm.edu	37	9	14857744	14857744	+	Missense_Mutation	SNP	A	A	C	rs145369669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14857744A>C	ENST00000380880.3	-	5	1418	c.635T>G	c.(634-636)cTg>cGg	p.L212R	FREM1_ENST00000380881.4_Missense_Mutation_p.L212R|FREM1_ENST00000422223.2_Missense_Mutation_p.L212R			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	212					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)		TTTTGCTCTCAGTTCTAGAAT	0.428													A|||	18	0.00359425	0.0136	0.0	5008	,	,		19720	0.0		0.0	False		,,,				2504	0.0				p.L212R		Atlas-SNP	.											.	FREM1	261	.	0			c.T635G						PASS	.	A	ARG/LEU	53,3683		0,53,1815	71.0	70.0	70.0		635	4.9	1.0	9	dbSNP_134	70	0,8198		0,0,4099	yes	missense	FREM1	NM_144966.5	102	0,53,5914	CC,CA,AA		0.0,1.4186,0.4441	benign	212/2180	14857744	53,11881	1868	4099	5967	SO:0001583	missense	158326	exon6			GCTCTCAGTTCTA	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.635T>G	9.37:g.14857744A>C	ENSP00000370262:p.Leu212Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	a	6.809	0.518344	0.13005	0.014186	0.0	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.11385	2.78;2.78;2.78	6.03	4.86	0.63082	.	0.387478	0.27668	N	0.018341	T	0.04634	0.0126	N	0.22421	0.69	0.09310	N	0.999998	P	0.51791	0.948	B	0.39876	0.312	T	0.36237	-0.9756	10	0.25751	T	0.34	-4.1637	10.3897	0.44162	0.7497:0.0:0.0:0.2503	.	212	Q5H8C1	FREM1_HUMAN	R	212	ENSP00000370263:L212R;ENSP00000412940:L212R;ENSP00000370262:L212R	ENSP00000370257:L212R	L	-	2	0	FREM1	14847744	0.590000	0.26815	0.952000	0.39060	0.064000	0.16182	4.254000	0.58798	2.314000	0.78098	0.456000	0.33151	CTG	A|0.997;C|0.003	0.003	strong		0.428	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
KCNJ6	3763	hgsc.bcm.edu	37	21	39087396	39087396	+	Missense_Mutation	SNP	C	C	T	rs202012431		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:39087396C>T	ENST00000609713.1	-	3	653	c.64G>A	c.(64-66)Gaa>Aaa	p.E22K	KCNJ6-IT1_ENST00000435001.1_RNA|KCNJ6_ENST00000288309.6_Missense_Mutation_p.E22K	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	22					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	ACTGGGCTTTCGACGTCCTGA	0.522													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18256	0.0		0.0	False		,,,				2504	0.0				p.E22K	Pancreas(48;379 1118 2936 19024 28214)	Atlas-SNP	.											KCNJ6,NS,carcinoma,0,1	KCNJ6	58	1	0			c.G64A						scavenged	.						91.0	83.0	86.0					21																	39087396		2005	4172	6177	SO:0001583	missense	3763	exon3			GGCTTTCGACGTC	U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.64G>A	21.37:g.39087396C>T	ENSP00000477437:p.Glu22Lys	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	164	3	0.0182927	NM_002240	Q3MJ74|Q53WW6	Missense_Mutation	SNP	ENST00000609713.1	37	CCDS42927.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	18.14	3.557156	0.65425	.	.	ENSG00000157542	ENST00000400482;ENST00000288309	D;D	0.89196	-2.48;-2.48	5.8	5.8	0.92144	.	0.485962	0.24542	N	0.037633	D	0.83751	0.5322	L	0.31926	0.97	0.80722	D	1	B	0.30511	0.282	B	0.14578	0.011	T	0.81899	-0.0721	10	0.56958	D	0.05	.	18.2511	0.90004	0.0:1.0:0.0:0.0	.	22	P48051	IRK6_HUMAN	K	22	ENSP00000383330:E22K;ENSP00000288309:E22K	ENSP00000288309:E22K	E	-	1	0	KCNJ6	38009266	1.000000	0.71417	0.966000	0.40874	0.848000	0.48234	7.175000	0.77632	2.744000	0.94065	0.655000	0.94253	GAA	C|1.000;T|0.000	0.000	strong		0.522	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194828.2	NM_002240	
ARSD	414	hgsc.bcm.edu	37	X	2825403	2825403	+	Missense_Mutation	SNP	A	A	G	rs2228431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:2825403A>G	ENST00000381154.1	-	10	1766	c.1691T>C	c.(1690-1692)aTg>aCg	p.M564T	ARSD-AS1_ENST00000414053.1_RNA	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	564			M -> T (in dbSNP:rs2228431).		cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GATGTTGCTCATGGAAAACTG	0.627													N|||	823	0.218013	0.1876	0.0937	3775	,	,		12785	0.3313		0.0348	False		,,,				2504	0.1442				p.M564T		Atlas-SNP	.											.	ARSD	47	.	0			c.T1691C						PASS	.	G	THR/MET	956,2879		116,583,141,933,430	36.0	34.0	34.0		1691	-5.8	0.0	X	dbSNP_98	34	320,6408		13,202,92,2213,1780	yes	missense	ARSD	NM_001669.3	81	129,785,233,3146,2210	GG,GA,G,AA,A		4.7562,24.9283,12.0799	benign	564/594	2825403	1276,9287	2203	4300	6503	SO:0001583	missense	414	exon10			TTGCTCATGGAAA	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.1691T>C	X.37:g.2825403A>G	ENSP00000370546:p.Met564Thr	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	291	139	0.477663	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	381	0.22965641952983726	82	0.19523809523809524	26	0.07738095238095238	128	0.29767441860465116	19	0.025675675675675677	g	2.506	-0.314007	0.05422	0.249283	0.047562	ENSG00000006756	ENST00000381154	D	0.89343	-2.5	2.9	-5.8	0.02347	Alkaline-phosphatase-like, core domain (1);	1.400680	0.04841	N	0.440493	T	0.00012	0.0000	N	0.05124	-0.11	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07849	-1.0751	9	0.21014	T	0.42	.	5.4477	0.16546	0.6198:0.0:0.2561:0.1242	rs2228431;rs17331021;rs56831853;rs2228431	564	P51689	ARSD_HUMAN	T	564	ENSP00000370546:M564T	ENSP00000370546:M564T	M	-	2	0	ARSD	2835403	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.031000	0.13710	-2.691000	0.00403	-1.918000	0.00516	ATG	0|0.003;G|0.184	0.184	strong		0.627	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
MUC4	4585	hgsc.bcm.edu	37	3	195508188	195508188	+	Missense_Mutation	SNP	G	G	C	rs372617756		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508188G>C	ENST00000463781.3	-	2	10722	c.10263C>G	c.(10261-10263)caC>caG	p.H3421Q	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3421Q	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)		GAGGGGTGGCGTGACCTGTGG	0.582																																					p.H3421Q		Atlas-SNP	.											MUC4_ENST00000463781,NS,haematopoietic_neoplasm,0,3	MUC4	1505	3	0			c.C10263G						scavenged	.						27.0	21.0	23.0					3																	195508188		689	1578	2267	SO:0001583	missense	4585	exon2			GGTGGCGTGACCT	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.10263C>G	3.37:g.195508188G>C	ENSP00000417498:p.His3421Gln	Somatic	263	9	0.0342205		WXS	Illumina HiSeq	Phase_I	262	35	0.133588	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	0.582	-0.836831	0.02692	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28069	1.64;1.63	0.894	-1.79	0.07932	.	.	.	.	.	T	0.14356	0.0347	N	0.19112	0.55	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.24083	-1.0170	8	.	.	.	.	2.7208	0.05200	0.5694:0.0:0.2083:0.2223	.	3293	E7ESK3	.	Q	3421	ENSP00000417498:H3421Q;ENSP00000420243:H3421Q	.	H	-	3	2	MUC4	196992967	0.000000	0.05858	0.005000	0.12908	0.009000	0.06853	0.471000	0.22100	-1.769000	0.01297	-1.783000	0.00646	CAC	.	.	alt		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAM109B	150368	hgsc.bcm.edu	37	22	42473586	42473586	+	Missense_Mutation	SNP	C	C	T	rs61736039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42473586C>T	ENST00000321753.3	+	3	476	c.289C>T	c.(289-291)Cgc>Tgc	p.R97C	snoU13_ENST00000458891.1_RNA|SMDT1_ENST00000331479.3_5'Flank	NM_001002034.2	NP_001002034.2	Q6ICB4	SESQ2_HUMAN	family with sequence similarity 109, member B	97	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						CCCTGGAGTGCGCCCACACCT	0.662													C|||	111	0.0221645	0.0794	0.0058	5008	,	,		16709	0.0		0.002	False		,,,				2504	0.0				p.R97C		Atlas-SNP	.											.	FAM109B	22	.	0			c.C289T						PASS	.	C	CYS/ARG	356,4050	184.0+/-211.4	14,328,1861	69.0	73.0	72.0		289	4.0	0.8	22	dbSNP_129	72	2,8598	2.2+/-6.3	0,2,4298	yes	missense	FAM109B	NM_001002034.2	180	14,330,6159	TT,TC,CC		0.0233,8.0799,2.7526	probably-damaging	97/260	42473586	358,12648	2203	4300	6503	SO:0001583	missense	150368	exon3			GGAGTGCGCCCAC	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.289C>T	22.37:g.42473586C>T	ENSP00000312753:p.Arg97Cys	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	129	60	0.465116	NM_001002034	Q3SXQ3|Q8N6L9	Missense_Mutation	SNP	ENST00000321753.3	37	CCDS33655.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	C	14.36	2.512399	0.44660	0.080799	2.33E-4	ENSG00000177096	ENST00000321753;ENST00000419475	T;T	0.76839	-1.05;-1.05	5.01	3.95	0.45737	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.211920	0.38492	N	0.001667	T	0.33206	0.0855	M	0.83012	2.62	0.51012	D	0.999905	D	0.76494	0.999	P	0.61201	0.885	T	0.69738	-0.5064	10	0.66056	D	0.02	-12.5019	13.5179	0.61551	0.2769:0.7231:0.0:0.0	rs61736039	97	Q6ICB4	SESQ2_HUMAN	C	97	ENSP00000312753:R97C;ENSP00000396170:R97C	ENSP00000312753:R97C	R	+	1	0	FAM109B	40803532	1.000000	0.71417	0.758000	0.31321	0.031000	0.12232	3.245000	0.51407	2.299000	0.77371	0.655000	0.94253	CGC	C|0.975;T|0.025	0.025	strong		0.662	FAM109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322084.1	NM_001002034	
WDFY4	57705	hgsc.bcm.edu	37	10	50165258	50165258	+	Missense_Mutation	SNP	G	G	A	rs61733228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50165258G>A	ENST00000325239.5	+	51	8089	c.8062G>A	c.(8062-8064)Gtc>Atc	p.V2688I	WDFY4_ENST00000413659.2_3'UTR|WDFY4_ENST00000465910.1_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	2688	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					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						CATGAGTGACGTCAGGGAGCT	0.577													g|||	35	0.00698882	0.0257	0.0	5008	,	,		21298	0.001		0.0	False		,,,				2504	0.0				p.V2688I		Atlas-SNP	.											.	WDFY4	205	.	0			c.G8062A						PASS	.		ILE/VAL	34,1350		0,34,658	86.0	93.0	91.0		8062	5.6	1.0	10	dbSNP_129	91	0,3182		0,0,1591	yes	missense	WDFY4	NM_020945.1	29	0,34,2249	AA,AG,GG		0.0,2.4566,0.7446	probably-damaging	2688/3185	50165258	34,4532	692	1591	2283	SO:0001583	missense	57705	exon52			AGTGACGTCAGGG	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.8062G>A	10.37:g.50165258G>A	ENSP00000320563:p.Val2688Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	24|24	0.01098901098901099|0.01098901098901099	22|22	0.044715447154471545|0.044715447154471545	0|0	0.0|0.0	2|2	0.0034965034965034965|0.0034965034965034965	0|0	0.0|0.0	g|g	34|34	5.379064|5.379064	0.95945|0.95945	0.024566|0.024566	0.0|0.0	ENSG00000128815|ENSG00000128815	ENST00000312002|ENST00000426033;ENST00000325239;ENST00000544136	.|T	.|0.81330	.|-1.48	5.57|5.57	5.57|5.57	0.84162|0.84162	.|BEACH domain (4);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.73869|0.73869	0.3642|0.3642	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.994;1.0	.|D;D	.|0.81914	.|0.975;0.995	T|T	0.82857|0.82857	-0.0250|-0.0250	5|9	.|.	.|.	.|.	.|.	18.5788|18.5788	0.91164|0.91164	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs61733228|rs61733228	.|151;2688	.|B4DWY9;Q6ZS81	.|.;WDFY4_HUMAN	H|I	1778|2688;2688;151	.|ENSP00000320563:V2688I	.|.	R|V	+|+	2|1	0|0	WDFY4|WDFY4	49835264|49835264	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.993000|0.993000	0.82548|0.82548	7.927000|7.927000	0.87577|0.87577	2.628000|2.628000	0.89032|0.89032	0.645000|0.645000	0.84053|0.84053	CGT|GTC	G|0.988;A|0.012	0.012	strong		0.577	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
C10orf90	118611	hgsc.bcm.edu	37	10	128192985	128192985	+	Missense_Mutation	SNP	C	C	T	rs11245007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:128192985C>T	ENST00000284694.7	-	3	904	c.784G>A	c.(784-786)Gat>Aat	p.D262N	C10orf90_ENST00000356858.3_Missense_Mutation_p.D215N|C10orf90_ENST00000454341.1_Missense_Mutation_p.D262N|C10orf90_ENST00000544758.1_Missense_Mutation_p.D359N|C10orf90_ENST00000392694.1_Missense_Mutation_p.D215N|C10orf90_ENST00000368674.1_5'UTR	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	262			D -> N (in dbSNP:rs11245007). {ECO:0000269|PubMed:15489334}.		mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TAGATTGAATCTGGACACTGC	0.522											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2507	0.500599	0.6876	0.4121	5008	,	,		17270	0.5099		0.3082	False		,,,				2504	0.499				p.D262N		Atlas-SNP	.											.	C10orf90	121	.	0			c.G784A						PASS	.	T	ASN/ASP	2620,1786	525.9+/-371.7	780,1060,363	107.0	114.0	112.0		784	1.6	0.0	10	dbSNP_120	112	2596,6004	688.7+/-404.3	388,1820,2092	yes	missense	C10orf90	NM_001004298.2	23	1168,2880,2455	TT,TC,CC		30.186,40.5356,40.1046	benign	262/700	128192985	5216,7790	2203	4300	6503	SO:0001583	missense	118611	exon3			TTGAATCTGGACA	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"""fragile-site associated tumor suppressor"""					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.784G>A	10.37:g.128192985C>T	ENSP00000284694:p.Asp262Asn	Somatic	105	0	0	1563	WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	37	CCDS31310.1	973	0.44551282051282054	330	0.6707317073170732	140	0.3867403314917127	273	0.4772727272727273	230	0.3034300791556728	T	2.249	-0.371988	0.05034	0.594644	0.30186	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.14516	2.82;2.83;2.74;2.81;2.5	5.38	1.59	0.23543	.	0.558322	0.17356	N	0.177212	T	0.00012	0.0000	N	0.00268	-1.735	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	0.34650	-0.9820	9	0.02654	T	1	-6.3276	5.2208	0.15368	0.0:0.1499:0.286:0.5641	rs11245007;rs52797966;rs56501299;rs60291468;rs11245007	359;359;215;262;262	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	N	215;262;262;359;262;215;215	ENSP00000284694:D262N;ENSP00000398786:D262N;ENSP00000444369:D359N;ENSP00000405995:D262N;ENSP00000376459:D215N	ENSP00000284694:D262N	D	-	1	0	C10orf90	128182975	0.005000	0.15991	0.000000	0.03702	0.011000	0.07611	1.599000	0.36751	-0.113000	0.11958	-1.062000	0.02293	GAT	C|0.557;T|0.443	0.443	strong		0.522	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
BPIFC	254240	hgsc.bcm.edu	37	22	32831830	32831830	+	Missense_Mutation	SNP	G	G	A	rs73884913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32831830G>A	ENST00000397452.1	-	9	895	c.785C>T	c.(784-786)cCc>cTc	p.P262L	BPIFC_ENST00000432451.2_Missense_Mutation_p.P76L|BPIFC_ENST00000534972.1_5'UTR|BPIFC_ENST00000300399.3_Missense_Mutation_p.P262L			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	262						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										TGGTGAGAAGGGGGGGTCGGT	0.458													G|||	180	0.0359425	0.1301	0.0101	5008	,	,		17689	0.0		0.001	False		,,,				2504	0.0				p.P262L		Atlas-SNP	.											.	.	.	.	0			c.C785T						PASS	.	G	LEU/PRO	464,3942	221.0+/-238.3	20,424,1759	75.0	84.0	81.0		785	2.4	0.0	22	dbSNP_130	81	2,8598	2.2+/-6.3	0,2,4298	yes	missense	BPIFC	NM_174932.2	98	20,426,6057	AA,AG,GG		0.0233,10.5311,3.583	probably-damaging	262/508	32831830	466,12540	2203	4300	6503	SO:0001583	missense	254240	exon8			GAGAAGGGGGGGT	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.785C>T	22.37:g.32831830G>A	ENSP00000380594:p.Pro262Leu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_174932	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	37	CCDS13906.1	67	0.030677655677655676	64	0.13008130081300814	3	0.008287292817679558	0	0.0	0	0.0	G	6.586	0.476412	0.12521	0.105311	2.33E-4	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000432451	T;T;T	0.08282	3.11;3.11;3.11	5.65	2.37	0.29283	.	0.056016	0.64402	N	0.000001	T	0.00144	0.0004	M	0.87180	2.865	0.21184	N	0.999763	B;B	0.22909	0.023;0.077	B;B	0.25884	0.046;0.064	T	0.16158	-1.0412	10	0.52906	T	0.07	-13.1446	7.7921	0.29127	0.0752:0.0:0.6379:0.2869	.	76;262	A2RRF1;Q8NFQ6	.;BPIFC_HUMAN	L	262;262;76	ENSP00000380594:P262L;ENSP00000300399:P262L;ENSP00000408920:P76L	ENSP00000300399:P262L	P	-	2	0	BPIFC	31161830	0.987000	0.35691	0.041000	0.18516	0.022000	0.10575	2.319000	0.43788	0.311000	0.23014	-0.803000	0.03203	CCC	G|0.967;A|0.033	0.033	strong		0.458	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
USP33	23032	hgsc.bcm.edu	37	1	78184325	78184325	+	Splice_Site	SNP	A	A	G	rs12142671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:78184325A>G	ENST00000370793.1	-	17	2132	c.1786T>C	c.(1786-1788)Ttg>Ctg	p.L596L	USP33_ENST00000370792.3_Splice_Site_p.L588L|USP33_ENST00000357428.1_Splice_Site_p.L596L|USP33_ENST00000370794.3_Splice_Site_p.L565L	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	596	USP.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						CCATTTCTCAACCTAAGGGGA	0.303													A|||	1781	0.355631	0.4433	0.1988	5008	,	,		18363	0.2698		0.2744	False		,,,				2504	0.5204				p.L596L	Melanoma(152;72 1870 11110 26780 42647)	Atlas-SNP	.											.	USP33	87	.	0			c.T1786C						PASS	.	A	,,	1765,2635	488.8+/-361.3	373,1019,808	40.0	45.0	43.0		1786,1693,1762	2.5	1.0	1	dbSNP_120	43	2128,6452	353.5+/-329.1	289,1550,2451	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	USP33	NM_015017.3,NM_201624.1,NM_201626.1	,,	662,2569,3259	GG,GA,AA		24.8019,40.1136,29.9923	,,	596/943,565/912,588/829	78184325	3893,9087	2200	4290	6490	SO:0001630	splice_region_variant	23032	exon17			TTCTCAACCTAAG	AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"""Ubiquitin-specific peptidases"""	20059	protein-coding gene	gene with protein product		615146	"""ubiquitin specific protease 33"""			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.1785-1T>C	1.37:g.78184325A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	180	179	0.994444	NM_015017	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Silent	SNP	ENST00000370793.1	37	CCDS678.1																																																																																			A|0.689;G|0.311	0.311	strong		0.303	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017	Silent
CELSR1	9620	hgsc.bcm.edu	37	22	46760481	46760481	+	Missense_Mutation	SNP	C	C	G	rs9615351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	81	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	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	
FLT4	2324	hgsc.bcm.edu	37	5	180058720	180058720	+	Silent	SNP	G	G	A	rs150736691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180058720G>A	ENST00000261937.6	-	2	195	c.117C>T	c.(115-117)caC>caT	p.H39H	FLT4_ENST00000393347.3_Silent_p.H39H|FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Silent_p.H39H	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	39	Ig-like C2-type 1.				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)	TGTCGATGACGTGTGACTCCT	0.637																																					p.H39H	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C117T						PASS	.	G	,	20,4384	27.2+/-55.0	0,20,2182	114.0	95.0	101.0		117,117	1.4	0.0	5	dbSNP_134	101	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FLT4	NM_002020.4,NM_182925.4	,	0,20,6482	AA,AG,GG		0.0,0.4541,0.1538	,	39/1299,39/1364	180058720	20,12984	2202	4300	6502	SO:0001819	synonymous_variant	2324	exon2			GATGACGTGTGAC	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.117C>T	5.37:g.180058720G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	51	30	0.588235	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																			G|0.999;A|0.001	0.001	strong		0.637	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
REXO1	57455	hgsc.bcm.edu	37	19	1819125	1819125	+	Missense_Mutation	SNP	T	T	C	rs2396359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1819125T>C	ENST00000170168.4	-	8	2750	c.2656A>G	c.(2656-2658)Agt>Ggt	p.S886G	CTB-31O20.4_ENST00000593201.1_RNA|MIR1909_ENST00000411312.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	886			S -> G (in dbSNP:rs2396359). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|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)		CTGCGGCCACTGGTTTCTGGA	0.672													.|||	1907	0.380791	0.5802	0.4207	5008	,	,		12655	0.3819		0.2097	False		,,,				2504	0.2577				p.S886G		Atlas-SNP	.											REXO1,NS,carcinoma,0,1	REXO1	55	1	0			c.A2656G						PASS	.	T	GLY/SER	2323,2079		630,1063,508	25.0	29.0	28.0		2656	1.9	0.4	19	dbSNP_100	28	1844,6748		200,1444,2652	yes	missense	REXO1	NM_020695.3	56	830,2507,3160	CC,CT,TT		21.4618,47.2285,32.0686	benign	886/1222	1819125	4167,8827	2201	4296	6497	SO:0001583	missense	57455	exon8			GGCCACTGGTTTC	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.2656A>G	19.37:g.1819125T>C	ENSP00000170168:p.Ser886Gly	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_020695	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	37	CCDS32866.1	800	0.3663003663003663	287	0.5833333333333334	135	0.3729281767955801	224	0.3916083916083916	154	0.20316622691292877	T	9.016	0.983646	0.18889	0.527715	0.214618	ENSG00000079313	ENST00000170168;ENST00000543452	T	0.13778	2.56	3.98	1.86	0.25419	.	0.272384	0.33075	U	0.005318	T	0.00012	0.0000	N	0.17082	0.46	0.37150	P	0.09788699999999995	B;B	0.22276	0.005;0.067	B;B	0.16722	0.004;0.016	T	0.35001	-0.9806	9	0.36615	T	0.2	-8.8227	6.6073	0.22731	0.0:0.1987:0.0:0.8013	rs2396359;rs11537979;rs17853032;rs2396359	195;886	B4DWY3;Q8N1G1	.;REXO1_HUMAN	G	886;158	ENSP00000170168:S886G	ENSP00000170168:S886G	S	-	1	0	REXO1	1770125	0.620000	0.27068	0.435000	0.26784	0.448000	0.32197	0.966000	0.29331	0.214000	0.20742	0.459000	0.35465	AGT	T|0.668;C|0.332	0.332	strong		0.672	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
SCAF1	58506	hgsc.bcm.edu	37	19	50156762	50156762	+	Missense_Mutation	SNP	A	A	T	rs201628577		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50156762A>T	ENST00000360565.3	+	7	3240	c.3116A>T	c.(3115-3117)gAg>gTg	p.E1039V		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1039	Glu-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		gaggaggaggagCAGCAGCCT	0.692																																					p.E1039V		Atlas-SNP	.											.	SCAF1	78	.	0			c.A3116T						PASS	.	A	VAL/GLU	4,4388		0,4,2192	9.0	12.0	11.0		3116	4.7	1.0	19		11	0,8566		0,0,4283	no	missense	SCAF1	NM_021228.2	121	0,4,6475	TT,TA,AA		0.0,0.0911,0.0309	possibly-damaging	1039/1313	50156762	4,12954	2196	4283	6479	SO:0001583	missense	58506	exon7			AGGAGGAGCAGCA	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.3116A>T	19.37:g.50156762A>T	ENSP00000353769:p.Glu1039Val	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	37	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	10.60	1.395512	0.25205	9.11E-4	0.0	ENSG00000126461	ENST00000360565	T	0.33865	1.39	5.74	4.67	0.58626	.	.	.	.	.	T	0.25344	0.0616	N	0.19112	0.55	0.24915	N	0.992013	P	0.41131	0.739	B	0.41332	0.354	T	0.05784	-1.0864	8	.	.	.	-21.1177	9.6199	0.39714	0.8441:0.0:0.0:0.1559	.	1039	Q9H7N4	SFR19_HUMAN	V	1039	ENSP00000353769:E1039V	.	E	+	2	0	SCAF1	54848574	1.000000	0.71417	1.000000	0.80357	0.216000	0.24613	1.552000	0.36244	2.189000	0.69895	0.533000	0.62120	GAG	.	.	weak		0.692	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
PTCD3	55037	hgsc.bcm.edu	37	2	86358214	86358214	+	Missense_Mutation	SNP	G	G	C	rs146203968		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86358214G>C	ENST00000254630.7	+	16	1317	c.1251G>C	c.(1249-1251)caG>caC	p.Q417H		NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	417					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						AGTTTTTTCAGTCAGCCATGA	0.318													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16645	0.0		0.0	False		,,,				2504	0.0				p.Q417H		Atlas-SNP	.											.	PTCD3	51	.	0			c.G1251C						PASS	.	G	HIS/GLN	1,4405	2.1+/-5.4	0,1,2202	78.0	78.0	78.0		1251	1.9	1.0	2	dbSNP_134	78	0,8592		0,0,4296	no	missense	PTCD3	NM_017952.5	24	0,1,6498	CC,CG,GG		0.0,0.0227,0.0077	benign	417/690	86358214	1,12997	2203	4296	6499	SO:0001583	missense	55037	exon16			TTTTCAGTCAGCC		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.1251G>C	2.37:g.86358214G>C	ENSP00000254630:p.Gln417His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	142	65	0.457746	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Missense_Mutation	SNP	ENST00000254630.7	37	CCDS33235.1	.	.	.	.	.	.	.	.	.	.	G	9.979	1.227623	0.22542	2.27E-4	0.0	ENSG00000132300	ENST00000254630	T	0.31769	1.48	6.16	1.9	0.25705	.	0.469117	0.24400	N	0.038860	T	0.22704	0.0548	L	0.44542	1.39	0.58432	D	0.999994	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.06481	-1.0824	10	0.56958	D	0.05	-1.4753	5.8329	0.18590	0.2275:0.0:0.6349:0.1376	.	8;417	Q96EY7-2;Q96EY7	.;PTCD3_HUMAN	H	417	ENSP00000254630:Q417H	ENSP00000254630:Q417H	Q	+	3	2	PTCD3	86211725	0.976000	0.34144	0.999000	0.59377	0.903000	0.53119	0.568000	0.23623	0.488000	0.27723	-0.158000	0.13435	CAG	G|1.000;C|0.000	0.000	weak		0.318	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952	
DUOX2	50506	hgsc.bcm.edu	37	15	45398438	45398438	+	Missense_Mutation	SNP	T	T	C	rs57659670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45398438T>C	ENST00000603300.1	-	17	2235	c.2033A>G	c.(2032-2034)cAt>cGt	p.H678R	DUOX2_ENST00000389039.6_Missense_Mutation_p.H678R	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	678			H -> R (in dbSNP:rs57659670).		adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CACAGTGAGATGCCTGTTCAG	0.602													C|||	826	0.164936	0.4198	0.1744	5008	,	,		19240	0.0476		0.0676	False		,,,				2504	0.0348				p.H678R		Atlas-SNP	.											.	DUOX2	137	.	0			c.A2033G	GRCh37	CM085365	DUOX2	M	rs57659670	PASS	.	C	ARG/HIS	1705,2691	649.9+/-399.0	346,1013,839	103.0	73.0	83.0		2033	-0.4	0.0	15	dbSNP_129	83	647,7949	789.5+/-407.6	31,585,3682	yes	missense	DUOX2	NM_014080.4	29	377,1598,4521	CC,CT,TT		7.5268,38.7853,18.1034	benign	678/1549	45398438	2352,10640	2198	4298	6496	SO:0001583	missense	50506	exon17			GTGAGATGCCTGT	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.2033A>G	15.37:g.45398438T>C	ENSP00000475084:p.His678Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	328	0.15018315018315018	199	0.40447154471544716	46	0.1270718232044199	32	0.055944055944055944	51	0.06728232189973615	C	0.070	-1.204245	0.01568	0.387853	0.075268	ENSG00000140279	ENST00000389039	.	.	.	5.31	-0.369	0.12534	.	0.592094	0.17582	N	0.169066	T	0.00012	0.0000	N	0.01109	-1.01	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44314	-0.9336	8	0.02654	T	1	0.0456	10.8392	0.46704	0.0:0.596:0.0:0.404	rs57659670	678;240	Q9NRD8;Q59GU9	DUOX2_HUMAN;.	R	678	.	ENSP00000373691:H678R	H	-	2	0	DUOX2	43185730	0.000000	0.05858	0.007000	0.13788	0.688000	0.40055	-0.073000	0.11468	-0.230000	0.09840	-0.213000	0.12676	CAT	T|0.831;C|0.169	0.169	strong		0.602	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
SPATA20	64847	hgsc.bcm.edu	37	17	48628092	48628092	+	Silent	SNP	A	A	G	rs1132414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48628092A>G	ENST00000356488.4	+	10	1232	c.1149A>G	c.(1147-1149)gaA>gaG	p.E383E	SPATA20_ENST00000006658.6_Silent_p.E399E|SPATA20_ENST00000393244.3_Silent_p.E339E|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	383					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			ATAGCGCAGAAGATGCAGACT	0.672											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1497	0.298922	0.68	0.2349	5008	,	,		16897	0.0427		0.2535	False		,,,				2504	0.1401				p.E399E		Atlas-SNP	.											.	SPATA20	59	.	0			c.A1197G						PASS	.	G		2682,1724	489.2+/-361.4	834,1014,355	47.0	59.0	55.0		1197	4.7	1.0	17	dbSNP_86	55	2185,6409	687.2+/-404.2	267,1651,2379	no	coding-synonymous	SPATA20	NM_022827.2		1101,2665,2734	GG,GA,AA		25.4247,39.1285,37.4385		399/803	48628092	4867,8133	2203	4297	6500	SO:0001819	synonymous_variant	64847	exon11			CGCAGAAGATGCA		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1149A>G	17.37:g.48628092A>G		Somatic	77	0	0	119	WXS	Illumina HiSeq	Phase_I	80	80	1	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Silent	SNP	ENST00000356488.4	37	CCDS58563.1																																																																																			A|0.652;G|0.348	0.348	strong		0.672	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
BZRAP1	9256	hgsc.bcm.edu	37	17	56388356	56388356	+	Silent	SNP	C	C	T	rs61745692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56388356C>T	ENST00000343736.4	-	19	3463	c.3300G>A	c.(3298-3300)gcG>gcA	p.A1100A	BZRAP1_ENST00000268893.6_Silent_p.A1040A|BZRAP1_ENST00000355701.3_Silent_p.A1100A			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1100	Pro-rich.					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)					AAGCAAGGGGCGCTCTGGCCT	0.692													C|||	151	0.0301518	0.1097	0.0086	5008	,	,		16644	0.0		0.0	False		,,,				2504	0.0				p.A1100A		Atlas-SNP	.											BZRAP1_ENST00000355701,caecum,carcinoma,0,2	BZRAP1	287	2	0			c.G3300A						PASS	.	C	,	391,4007		15,361,1823	17.0	22.0	20.0		3300,3120	-3.6	0.3	17	dbSNP_129	20	3,8591		0,3,4294	no	coding-synonymous,coding-synonymous	BZRAP1	NM_004758.2,NM_024418.1	,	15,364,6117	TT,TC,CC		0.0349,8.8904,3.0326	,	1100/1858,1040/1798	56388356	394,12598	2199	4297	6496	SO:0001819	synonymous_variant	9256	exon19			AAGGGGCGCTCTG	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.3300G>A	17.37:g.56388356C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	161	86	0.534162	NM_004758	O75111|Q8N5W3	Silent	SNP	ENST00000343736.4	37	CCDS11605.1																																																																																			C|0.968;T|0.032	0.032	strong		0.692	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
GINS1	9837	hgsc.bcm.edu	37	20	25398790	25398790	+	Missense_Mutation	SNP	G	G	A	rs6076347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:25398790G>A	ENST00000262460.4	+	4	383	c.289G>A	c.(289-291)Gtc>Atc	p.V97I	GINS1_ENST00000484893.1_3'UTR|GINS1_ENST00000429262.2_Missense_Mutation_p.V97I	NM_021067.3	NP_066545.3	Q14691	PSF1_HUMAN	GINS complex subunit 1 (Psf1 homolog)	97			V -> I (in dbSNP:rs6076347). {ECO:0000269|PubMed:15489334}.		DNA strand elongation involved in DNA replication (GO:0006271)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	7						ATATGGTAGCGTCTTGCCAAA	0.423													G|||	1157	0.23103	0.0908	0.4035	5008	,	,		20574	0.0069		0.4592	False		,,,				2504	0.2945				p.V97I		Atlas-SNP	.											GINS1,caecum,carcinoma,0,1	GINS1	25	1	0			c.G289A						PASS	.	G	ILE/VAL	691,3715	291.0+/-281.2	53,585,1565	233.0	197.0	209.0		289	0.3	0.9	20	dbSNP_114	209	4039,4561	557.4+/-387.0	922,2195,1183	yes	missense	GINS1	NM_021067.3	29	975,2780,2748	AA,AG,GG		46.9651,15.6832,36.3678	benign	97/197	25398790	4730,8276	2203	4300	6503	SO:0001583	missense	9837	exon4			GGTAGCGTCTTGC	BC012542	CCDS33451.1	20p11.21	2006-05-04			ENSG00000101003	ENSG00000101003			28980	protein-coding gene	gene with protein product		610608				8724849, 8786132	Standard	NM_021067		Approved	KIAA0186, PSF1	uc002wuv.1	Q14691	OTTHUMG00000032124	ENST00000262460.4:c.289G>A	20.37:g.25398790G>A	ENSP00000262460:p.Val97Ile	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	175	95	0.542857	NM_021067	Q9NQE2|Q9NQI7	Missense_Mutation	SNP	ENST00000262460.4	37	CCDS33451.1	542	0.24816849816849818	46	0.09349593495934959	151	0.4171270718232044	3	0.005244755244755245	342	0.45118733509234826	G	1.713	-0.498511	0.04291	0.156832	0.469651	ENSG00000101003	ENST00000262460;ENST00000429262	T;T	0.46451	0.87;0.87	5.52	0.267	0.15622	.	0.246537	0.39687	N	0.001294	T	0.00012	0.0000	N	0.11341	0.13	0.27456	P	0.9533019	B	0.09022	0.002	B	0.06405	0.002	T	0.48163	-0.9059	9	0.13108	T	0.6	-3.2614	11.4953	0.50404	0.2885:0.0:0.7115:0.0	rs6076347;rs17850933;rs52823022;rs56483564;rs57237708;rs6076347	97	Q14691	PSF1_HUMAN	I	97	ENSP00000262460:V97I;ENSP00000408669:V97I	ENSP00000262460:V97I	V	+	1	0	GINS1	25346790	1.000000	0.71417	0.851000	0.33527	0.437000	0.31866	3.032000	0.49736	0.043000	0.15746	-1.305000	0.01319	GTC	G|0.689;A|0.311	0.311	strong		0.423	GINS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078433.1	NM_021067	
MGAT5B	146664	hgsc.bcm.edu	37	17	74921072	74921072	+	Silent	SNP	G	G	C	rs3889145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	100	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	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	
SRGAP3	9901	hgsc.bcm.edu	37	3	9034605	9034605	+	Missense_Mutation	SNP	C	C	G	rs150617309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9034605C>G	ENST00000383836.3	-	20	2970	c.2543G>C	c.(2542-2544)gGg>gCg	p.G848A	SRGAP3_ENST00000360413.3_Missense_Mutation_p.G824A	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	848					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		CATCACCCCCCCAAAGCCGTA	0.557			T	RAF1	pilocytic astrocytoma																																p.G848A		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.G2543C						PASS	.						83.0	79.0	81.0					3																	9034605		2203	4300	6503	SO:0001583	missense	9901	exon20			ACCCCCCCAAAGC	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"""Rho GTPase activating proteins"""	19744	protein-coding gene	gene with protein product		606525	"""SLIT-ROBO Rho GTPase activating protein 2"""	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.2543G>C	3.37:g.9034605C>G	ENSP00000373347:p.Gly848Ala	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	37	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	C	5.202	0.222874	0.09863	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.22134	1.97;2.37	5.17	5.17	0.71159	.	0.270733	0.35708	N	0.003023	T	0.12860	0.0312	N	0.22421	0.69	0.47621	D	0.999477	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.002	T	0.04551	-1.0943	10	0.02654	T	1	.	13.9514	0.64118	0.0:0.8479:0.1521:0.0	.	824;848	O43295-2;O43295	.;SRGP2_HUMAN	A	848;824	ENSP00000373347:G848A;ENSP00000353587:G824A	ENSP00000353587:G824A	G	-	2	0	SRGAP3	9009605	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.779000	0.55379	2.410000	0.81850	0.591000	0.81541	GGG	C|1.000;G|0.000	0.000	alt		0.557	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3		
ZNF781	163115	hgsc.bcm.edu	37	19	38160255	38160255	+	Silent	SNP	A	A	C	rs73932934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38160255A>C	ENST00000590008.1	-	5	1647	c.795T>G	c.(793-795)ctT>ctG	p.L265L	ZFP30_ENST00000586732.1_Intron|ZNF781_ENST00000593040.1_5'Flank|ZNF781_ENST00000358582.4_Silent_p.L265L			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						CAATTGTTAAAAGCTCTACCA	0.383													A|||	189	0.0377396	0.1354	0.0144	5008	,	,		20442	0.0		0.0	False		,,,				2504	0.0				p.L265L		Atlas-SNP	.											.	ZNF781	66	.	0			c.T795G						PASS	.	A		401,4005	196.7+/-221.0	20,361,1822	87.0	91.0	90.0		795	1.4	0.0	19	dbSNP_130	90	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ZNF781	NM_152605.3		20,364,6119	CC,CA,AA		0.0349,9.1012,3.1063		265/328	38160255	404,12602	2203	4300	6503	SO:0001819	synonymous_variant	163115	exon4			TGTTAAAAGCTCT	AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"""Zinc fingers, C2H2-type"""	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.795T>G	19.37:g.38160255A>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_152605	Q2VPJ8	Silent	SNP	ENST00000590008.1	37	CCDS12507.1																																																																																			A|0.967;C|0.033	0.033	strong		0.383	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605	
CNTNAP2	26047	hgsc.bcm.edu	37	7	146829390	146829390	+	Silent	SNP	C	C	T	rs78543192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:146829390C>T	ENST00000361727.3	+	8	1653	c.1137C>T	c.(1135-1137)aaC>aaT	p.N379N		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	379					adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TCTTTTTCAACGCTACAAGTT	0.458										HNSCC(39;0.1)			T|||	30	0.00599042	0.0219	0.0014	5008	,	,		20040	0.0		0.0	False		,,,				2504	0.0				p.N379N		Atlas-SNP	.											CNTNAP2,colon,carcinoma,0,2	CNTNAP2	392	2	0			c.C1137T						PASS	.	T		66,4340	820.5+/-416.4	0,66,2137	126.0	121.0	122.0		1137	3.3	1.0	7	dbSNP_132	122	0,8600		0,0,4300	no	coding-synonymous	CNTNAP2	NM_014141.5		0,66,6437	TT,TC,CC		0.0,1.498,0.5075		379/1332	146829390	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	26047	exon8			TTTCAACGCTACA	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1137C>T	7.37:g.146829390C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	37	CCDS5889.1																																																																																			C|0.995;T|0.005	0.005	strong		0.458	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1		
CLCA4	22802	hgsc.bcm.edu	37	1	87043733	87043733	+	Silent	SNP	C	C	T	rs2231601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87043733C>T	ENST00000370563.3	+	12	2142	c.2100C>T	c.(2098-2100)taC>taT	p.Y700Y	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	700					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		GAGCCGCGTACATACCAGGCT	0.403													C|||	204	0.0407348	0.149	0.0101	5008	,	,		17663	0.0		0.0	False		,,,				2504	0.0				p.Y700Y		Atlas-SNP	.											.	CLCA4	131	.	0			c.C2100T						PASS	.	C		472,3276		21,430,1423	42.0	41.0	41.0		2100	-7.0	0.0	1	dbSNP_98	41	0,8218		0,0,4109	no	coding-synonymous	CLCA4	NM_012128.3		21,430,5532	TT,TC,CC		0.0,12.5934,3.9445		700/920	87043733	472,11494	1874	4109	5983	SO:0001819	synonymous_variant	22802	exon12			CGCGTACATACCA	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2100C>T	1.37:g.87043733C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Silent	SNP	ENST00000370563.3	37	CCDS41355.1																																																																																			C|0.976;T|0.024	0.024	strong		0.403	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
PAQR6	79957	hgsc.bcm.edu	37	1	156213921	156213921	+	Silent	SNP	C	C	T	rs7513351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156213921C>T	ENST00000292291.5	-	8	1192	c.1034G>A	c.(1033-1035)tGa>tAa	p.*345*	PAQR6_ENST00000356983.2_Missense_Mutation_p.E263K|PAQR6_ENST00000540423.1_Silent_p.*342*|PAQR6_ENST00000368270.1_Silent_p.*321*|PAQR6_ENST00000492619.1_5'UTR|PAQR6_ENST00000335852.1_Missense_Mutation_p.E263K	NM_001272104.1|NM_001272105.1|NM_198406.2	NP_001259033.1|NP_001259034.1|NP_940798.1	Q6TCH4	PAQR6_HUMAN	progestin and adipoQ receptor family member VI	0						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			lung(4)|ovary(1)	5	Hepatocellular(266;0.158)					GATGGGGCCTCACTGTTGTTT	0.637													C|||	1098	0.219249	0.1604	0.3026	5008	,	,		19101	0.256		0.1481	False		,,,				2504	0.2751				p.E263K	GBM(16;219 398 12385 32425 38531)	Atlas-SNP	.											.	PAQR6	23	.	0			c.G787A						PASS	.	C	LYS/GLU,	698,3708	293.6+/-282.7	63,572,1568	67.0	70.0	69.0		787,1034	-3.6	0.3	1	dbSNP_116	69	1413,7187	273.1+/-290.5	114,1185,3001	yes	missense,coding-synonymous	PAQR6	NM_024897.2,NM_198406.1	56,	177,1757,4569	TT,TC,CC		16.4302,15.842,16.231	,	263/352,345/345	156213921	2111,10895	2203	4300	6503	SO:0001819	synonymous_variant	79957	exon7			GGGCCTCACTGTT	AF455045	CCDS1135.1, CCDS1136.1, CCDS60301.1, CCDS72945.1, CCDS72946.1	1q23	2008-02-05			ENSG00000160781	ENSG00000160781			30132	protein-coding gene	gene with protein product		614579				12477932	Standard	NM_024897		Approved	FLJ22672	uc010phh.2	Q6TCH4	OTTHUMG00000017490	ENST00000292291.5:c.1034G>A	1.37:g.156213921C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_024897	B7Z9R9|D3DVB4|D3DVB6|Q5TCK9|Q6PDU0|Q7Z4Q7|Q7Z4Q9|Q8N121|Q8N3M2|Q9H621	Missense_Mutation	SNP	ENST00000292291.5	37	CCDS1136.1	436	0.19963369963369965	76	0.15447154471544716	116	0.32044198895027626	138	0.24125874125874125	106	0.13984168865435356	C	17.16	3.319012	0.60524	0.15842	0.164302	ENSG00000160781	ENST00000360733;ENST00000335852;ENST00000356983	T;T;T	0.38240	1.15;1.15;1.15	5.24	-3.56	0.04626	.	.	.	.	.	T	0.08492	0.0211	.	.	.	0.49130	P	2.4299999999999322E-4	B;B;B	0.26602	0.154;0.154;0.006	B;B;B	0.23716	0.048;0.048;0.016	T	0.35943	-0.9768	7	0.87932	D	0	.	2.5753	0.04805	0.1144:0.4297:0.1128:0.3431	rs7513351;rs58089457;rs7513351	195;123;263	B4DJ42;Q7Z4Q8;Q6TCH4-2	.;.;.	K	263	ENSP00000353961:E263K;ENSP00000338330:E263K;ENSP00000349474:E263K	ENSP00000338330:E263K	E	-	1	0	PAQR6	154480545	0.958000	0.32768	0.268000	0.24571	0.091000	0.18340	0.235000	0.17948	-0.222000	0.09958	0.462000	0.41574	GAG	C|0.818;T|0.182	0.182	strong		0.637	PAQR6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046297.2	NM_024897	
SDF2	6388	hgsc.bcm.edu	37	17	26982341	26982341	+	Silent	SNP	A	A	G	rs35579310	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26982341A>G	ENST00000247020.4	-	2	610	c.312T>C	c.(310-312)caT>caC	p.H104H	SDF2_ENST00000592250.1_5'UTR	NM_006923.3	NP_008854.2	Q99470	SDF2_HUMAN	stromal cell-derived factor 2	104	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				protein glycosylation (GO:0006486)|protein O-linked mannosylation (GO:0035269)	extracellular space (GO:0005615)|membrane (GO:0016020)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Lung NSC(42;0.00431)					AGTGGTGACTATGGAGGTTTC	0.537													A|||	47	0.00938498	0.0325	0.0058	5008	,	,		21075	0.0		0.0	False		,,,				2504	0.0				p.H104H		Atlas-SNP	.											.	SDF2	17	.	0			c.T312C						PASS	.	A		123,4283	91.6+/-130.3	1,121,2081	156.0	134.0	141.0		312	-0.8	1.0	17	dbSNP_126	141	0,8600		0,0,4300	no	coding-synonymous	SDF2	NM_006923.2		1,121,6381	GG,GA,AA		0.0,2.7916,0.9457		104/212	26982341	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	6388	exon2			GTGACTATGGAGG	BC001406	CCDS11238.1	17q11.2	2004-02-16			ENSG00000132581	ENSG00000132581			10675	protein-coding gene	gene with protein product		602934				8918255	Standard	NR_045585		Approved		uc002hbw.3	Q99470	OTTHUMG00000132681	ENST00000247020.4:c.312T>C	17.37:g.26982341A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	137	58	0.423358	NM_006923	Q9BQ79	Silent	SNP	ENST00000247020.4	37	CCDS11238.1																																																																																			A|0.991;G|0.009	0.009	strong		0.537	SDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255965.2	NM_006923	
FGFR3	2261	hgsc.bcm.edu	37	4	1803251	1803251	+	Silent	SNP	T	T	C	rs2305181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1803251T>C	ENST00000260795.2	+	4	705	c.603T>C	c.(601-603)atT>atC	p.I201I	FGFR3_ENST00000340107.4_Silent_p.I201I|FGFR3_ENST00000352904.1_Silent_p.I201I|FGFR3_ENST00000412135.2_Silent_p.I201I|FGFR3_ENST00000481110.2_Silent_p.I201I|FGFR3_ENST00000440486.2_Silent_p.I201I			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	201	Ig-like C2-type 2.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	AGCACCGCATTGGAGGCATCA	0.721		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome				N|||	527	0.105232	0.3359	0.0461	5008	,	,		10686	0.0298		0.0119	False		,,,				2504	0.0092				p.I201I		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	.	FGFR3	3320	.	0			c.T603C						PASS	.	C	,,	1007,3249		98,811,1219	7.0	7.0	7.0		603,603,603	-6.3	0.9	4	dbSNP_100	7	68,8282		1,66,4108	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	99,877,5327	CC,CT,TT		0.8144,23.6607,8.5277	,,	201/807,201/809,201/695	1803251	1075,11531	2128	4175	6303	SO:0001819	synonymous_variant	2261	exon5	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	CCGCATTGGAGGC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.603T>C	4.37:g.1803251T>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			T|0.879;C|0.121	0.121	strong		0.721	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
UCP2	7351	hgsc.bcm.edu	37	11	73689104	73689104	+	Missense_Mutation	SNP	G	G	A	rs660339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73689104G>A	ENST00000310473.3	-	4	1006	c.164C>T	c.(163-165)gCc>gTc	p.A55V	UCP2_ENST00000542615.1_5'Flank|UCP2_ENST00000536983.1_Missense_Mutation_p.A55V	NM_003355.2	NP_003346.2	P55851	UCP2_HUMAN	uncoupling protein 2 (mitochondrial, proton carrier)	55			A -> V (in dbSNP:rs660339). {ECO:0000269|PubMed:9133562, ECO:0000269|Ref.4, ECO:0000269|Ref.7, ECO:0000269|Ref.8}.		aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to amino acid starvation (GO:0034198)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|female pregnancy (GO:0007565)|liver regeneration (GO:0097421)|mitochondrial transport (GO:0006839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|positive regulation of cell death (GO:0010942)|proton transport (GO:0015992)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				large_intestine(1)|lung(3)|prostate(1)	5	Breast(11;0.000112)					CTGGGCGCTGGCTGTAGCGCG	0.617													g|||	2084	0.416134	0.447	0.4409	5008	,	,		18773	0.4177		0.4046	False		,,,				2504	0.3671				p.A55V	Colon(191;388 2040 43557 45622 48925)	Atlas-SNP	.											.	UCP2	24	.	0			c.C164T	GRCh37	CM994639	UCP2	M	rs660339	PASS	.	G	VAL/ALA	1923,2477	547.2+/-377.2	391,1141,668	38.0	42.0	41.0		164	5.1	1.0	11	dbSNP_83	41	3503,5083	510.0+/-377.4	717,2069,1507	yes	missense	UCP2	NM_003355.2	64	1108,3210,2175	AA,AG,GG		40.799,43.7045,41.7835	benign	55/310	73689104	5426,7560	2200	4293	6493	SO:0001583	missense	7351	exon4			GCGCTGGCTGTAG	U76367	CCDS8228.1	11q13	2014-02-12						"""Solute carriers"""	12518	protein-coding gene	gene with protein product		601693	"""body mass index QTL 4"", ""body mass index quantitative trait 4"""	BMIQ4		9196039, 11381268	Standard	NM_003355		Approved	SLC25A8	uc001oup.1	P55851		ENST00000310473.3:c.164C>T	11.37:g.73689104G>A	ENSP00000312029:p.Ala55Val	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	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	
HPGD	3248	hgsc.bcm.edu	37	4	175414444	175414444	+	Missense_Mutation	SNP	T	T	G	rs200207595		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:175414444T>G	ENST00000296522.6	-	6	966	c.520A>C	c.(520-522)Agt>Cgt	p.S174R	HPGD_ENST00000542498.1_Intron|HPGD_ENST00000422112.2_Missense_Mutation_p.S106R|HPGD_ENST00000510901.1_Missense_Mutation_p.S53R|HPGD_ENST00000541923.1_Missense_Mutation_p.S53R|HPGD_ENST00000296521.7_Intron	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)	174					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)			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)		CTCACACCACTGTTCATAAGA	0.363																																					p.S174R		Atlas-SNP	.											.	HPGD	19	.	0			c.A520C						PASS	.	T	ARG/SER,	4,4402	8.1+/-20.4	0,4,2199	96.0	91.0	93.0		520,	5.6	1.0	4		93	0,8598		0,0,4299	yes	missense,intron	HPGD	NM_000860.4,NM_001145816.1	110,	0,4,6498	GG,GT,TT		0.0,0.0908,0.0308	possibly-damaging,	174/267,	175414444	4,13000	2203	4299	6502	SO:0001583	missense	3248	exon6			CACCACTGTTCAT		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.520A>C	4.37:g.175414444T>G	ENSP00000296522:p.Ser174Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	121	53	0.438017	NM_000860	B4DTA4|B4DU74|B4DV57|D3DP43|E7EV11|O00749|Q06F08|Q12998	Missense_Mutation	SNP	ENST00000296522.6	37	CCDS3821.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.146678	0.57151	9.08E-4	0.0	ENSG00000164120	ENST00000296522;ENST00000510901;ENST00000422112;ENST00000541923;ENST00000506910;ENST00000514584	D;D;T;D;D;D	0.82433	-1.61;-1.61;-1.29;-1.61;-1.61;-1.61	5.58	5.58	0.84498	NAD(P)-binding domain (1);	0.099373	0.64402	D	0.000001	T	0.79816	0.4511	L	0.31371	0.925	0.80722	D	1	P;D;D	0.71674	0.925;0.98;0.998	B;P;P	0.60682	0.446;0.595;0.878	T	0.76613	-0.2895	10	0.02654	T	1	.	9.2337	0.37453	0.2704:0.0:0.0:0.7296	.	106;174;53	E7EV11;P15428;B4DU74	.;PGDH_HUMAN;.	R	174;53;106;53;53;53	ENSP00000296522:S174R;ENSP00000422418:S53R;ENSP00000398720:S106R;ENSP00000438017:S53R;ENSP00000423066:S53R;ENSP00000423110:S53R	ENSP00000296522:S174R	S	-	1	0	HPGD	175651019	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.963000	0.56773	2.119000	0.64992	0.533000	0.62120	AGT	.	.	weak		0.363	HPGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362228.3		
HRC	3270	hgsc.bcm.edu	37	19	49657751	49657751	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657751A>G	ENST00000252825.4	-	1	930	c.744T>C	c.(742-744)gaT>gaC	p.D248D	HRC_ENST00000595625.1_Silent_p.D248D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	248	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Asp-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)	p.D248D(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		catcatcatcatcgtcatctt	0.507																																					p.D248D	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											HRC,caecum,carcinoma,0,1	HRC	85	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T744C						PASS	.						132.0	95.0	107.0					19																	49657751		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			ATCATCATCGTCA		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.744T>C	19.37:g.49657751A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	135	7	0.0518519	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			.	.	none		0.507	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
ADO	84890	hgsc.bcm.edu	37	10	64564892	64564892	+	Missense_Mutation	SNP	G	G	T	rs2236295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:64564892G>T	ENST00000373783.1	+	1	377	c.73G>T	c.(73-75)Ggg>Tgg	p.G25W	RP11-436D10.3_ENST00000425290.1_RNA	NM_032804.5	NP_116193.2	Q96SZ5	AEDO_HUMAN	2-aminoethanethiol (cysteamine) dioxygenase	25			G -> W (in dbSNP:rs2236295). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)	cysteamine dioxygenase activity (GO:0047800)|metal ion binding (GO:0046872)			lung(2)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					CCGGGGCAGCGGGGGCGGCCG	0.706													G|||	1060	0.211661	0.028	0.2305	5008	,	,		10717	0.1677		0.3678	False		,,,				2504	0.3313				p.G25W		Atlas-SNP	.											.	ADO	10	.	0			c.G73T						PASS	.	G	TRP/GLY	356,3958		29,298,1830	9.0	10.0	9.0		73	2.0	1.0	10	dbSNP_98	9	3015,5439		561,1893,1773	yes	missense	ADO	NM_032804.5	184	590,2191,3603	TT,TG,GG		35.6636,8.2522,26.4019	possibly-damaging	25/271	64564892	3371,9397	2157	4227	6384	SO:0001583	missense	84890	exon1			GGCAGCGGGGGCG	BC028589	CCDS7266.2	10q21.3	2007-08-28	2007-08-28	2007-08-28	ENSG00000181915	ENSG00000181915	1.13.11.19		23506	protein-coding gene	gene with protein product	"""cysteamine dioxygenase"""	611392	"""chromosome 10 open reading frame 22"""	C10orf22		17581819	Standard	NM_032804		Approved	FLJ14547	uc001jmg.3	Q96SZ5	OTTHUMG00000018306	ENST00000373783.1:c.73G>T	10.37:g.64564892G>T	ENSP00000362888:p.Gly25Trp	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	13	9	0.692308	NM_032804	B1AL29	Missense_Mutation	SNP	ENST00000373783.1	37	CCDS7266.2	480	0.21978021978021978	20	0.04065040650406504	94	0.2596685082872928	90	0.15734265734265734	276	0.3641160949868074	g	17.48	3.401343	0.62288	0.082522	0.356636	ENSG00000181915	ENST00000373783	T	0.23348	1.91	3.86	1.95	0.26073	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.39150	P	0.037799999999999945	D	0.57899	0.981	P	0.48627	0.584	T	0.46665	-0.9175	8	0.37606	T	0.19	.	5.5759	0.17222	0.1642:0.1938:0.642:0.0	rs2236295	25	Q96SZ5	AEDO_HUMAN	W	25	ENSP00000362888:G25W	ENSP00000362888:G25W	G	+	1	0	ADO	64234898	0.998000	0.40836	0.994000	0.49952	0.783000	0.44284	2.261000	0.43276	0.948000	0.37687	0.651000	0.88453	GGG	G|0.779;T|0.221	0.221	strong		0.706	ADO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048243.2	NM_032804	
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24383061	24383061	+	IGR	SNP	C	C	T	rs11796308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24383061C>T								AC004552.1 (16038 upstream) : PDK3 (100276 downstream)																							CACAGGGTTCCGCACTAGGTT	0.627													C|||	1092	0.289272	0.4735	0.1628	3775	,	,		12939	0.0794		0.0686	False		,,,				2504	0.2086				p.S728S		Atlas-SNP	.											.	.	.	.	0			c.C2184T						PASS	.	C		1369,1258		312,492,253,255,256	37.0	37.0	37.0		2184	-6.4	0.0	X	dbSNP_120	37	578,4920		24,346,184,1546,1482	no	coding-synonymous	FAM48B1	NM_001136234.1		336,838,437,1801,1738	TT,TC,T,CC,C		10.5129,47.8873,23.9631		728/888	24383061	1947,6178	1568	3582	5150	SO:0001628	intergenic_variant	100130302	exon1			GGGTTCCGCACTA																													X.37:g.24383061C>T		Somatic	446	2	0.00448431		WXS	Illumina HiSeq	Phase_I	498	249	0.5	NM_001136234		Silent	SNP		37																																																																																				C|0.719;0|0.006	.	strong	0	0.627								
RAI1	10743	hgsc.bcm.edu	37	17	17696526	17696526	+	Silent	SNP	G	G	A	rs61999281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17696526G>A	ENST00000353383.1	+	3	733	c.264G>A	c.(262-264)caG>caA	p.Q88Q	RAI1_ENST00000261641.6_Silent_p.Q88Q	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	88					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		TGCCCACACAGCAAGGCCTGC	0.687													G|||	105	0.0209665	0.0749	0.0086	5008	,	,		12762	0.0		0.0	False		,,,				2504	0.0				p.Q88Q		Atlas-SNP	.											.	RAI1	121	.	0			c.G264A						PASS	.	G		283,4099		11,261,1919	12.0	14.0	14.0		264	1.9	0.7	17	dbSNP_129	14	1,8583		0,1,4291	no	coding-synonymous	RAI1	NM_030665.3		11,262,6210	AA,AG,GG		0.0116,6.4582,2.1903		88/1907	17696526	284,12682	2191	4292	6483	SO:0001819	synonymous_variant	10743	exon3			CACACAGCAAGGC	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.264G>A	17.37:g.17696526G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			G|0.980;A|0.020	0.020	strong		0.687	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
ATG2A	23130	hgsc.bcm.edu	37	11	64681360	64681360	+	Missense_Mutation	SNP	C	C	T	rs12293826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64681360C>T	ENST00000377264.3	-	4	635	c.523G>A	c.(523-525)Gtc>Atc	p.V175I	ATG2A_ENST00000421419.2_Missense_Mutation_p.V175I	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	175			V -> I (in dbSNP:rs12293826).		autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						ACCCTCACGACAGTGTCCAGG	0.602													C|||	258	0.0515176	0.18	0.0245	5008	,	,		19362	0.0		0.003	False		,,,				2504	0.0				p.V175I		Atlas-SNP	.											.	ATG2A	133	.	0			c.G523A						PASS	.	C	ILE/VAL	739,3663	301.5+/-286.9	74,591,1536	112.0	96.0	101.0		523	2.6	0.9	11	dbSNP_120	101	3,8591	2.2+/-6.3	0,3,4294	yes	missense	ATG2A	NM_015104.2	29	74,594,5830	TT,TC,CC		0.0349,16.7878,5.7094	benign	175/1939	64681360	742,12254	2201	4297	6498	SO:0001583	missense	23130	exon4			TCACGACAGTGTC		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.523G>A	11.37:g.64681360C>T	ENSP00000366475:p.Val175Ile	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	85	0.03891941391941392	76	0.15447154471544716	9	0.024861878453038673	0	0.0	0	0.0	c	13.28	2.190900	0.38707	0.167878	3.49E-4	ENSG00000110046	ENST00000421419;ENST00000377264;ENST00000227459	T;T	0.56275	0.47;0.47	3.89	2.61	0.31194	.	0.073749	0.52532	D	0.000064	T	0.00073	0.0002	N	0.11364	0.135	0.34629	P	0.280571	B	0.02656	0.0	B	0.04013	0.001	T	0.05131	-1.0904	9	0.34782	T	0.22	.	4.4866	0.11792	0.0:0.6331:0.0:0.3669	rs12293826;rs52838292;rs12293826	175	Q2TAZ0	ATG2A_HUMAN	I	175	ENSP00000410522:V175I;ENSP00000366475:V175I	ENSP00000227459:V175I	V	-	1	0	ATG2A	64437936	0.840000	0.29493	0.858000	0.33744	0.791000	0.44710	1.131000	0.31406	0.964000	0.38108	0.457000	0.33378	GTC	C|0.940;T|0.060	0.060	strong		0.602	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
FHL2	2274	hgsc.bcm.edu	37	2	105977761	105977761	+	Silent	SNP	G	G	A	rs11124029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:105977761G>A	ENST00000409807.1	-	6	1153	c.819C>T	c.(817-819)ccC>ccT	p.P273P	FHL2_ENST00000409177.1_Silent_p.P389P|FHL2_ENST00000393353.3_Silent_p.P273P|FHL2_ENST00000344213.4_Silent_p.P383P|FHL2_ENST00000393352.3_Silent_p.P273P|FHL2_ENST00000358129.4_Silent_p.P273P|FHL2_ENST00000322142.8_Silent_p.P273P|FHL2_ENST00000408995.1_Silent_p.P273P|AC012360.6_ENST00000457290.2_RNA|FHL2_ENST00000336660.5_3'UTR			Q14192	FHL2_HUMAN	four and a half LIM domains 2	273	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|atrial cardiac muscle cell development (GO:0055014)|cellular lipid metabolic process (GO:0044255)|heart trabecula formation (GO:0060347)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|M band (GO:0031430)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Z disc (GO:0030018)	androgen receptor binding (GO:0050681)|identical protein binding (GO:0042802)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9						TCCCACAGTCGGGGCACAGGA	0.498													g|||	558	0.111422	0.0809	0.1614	5008	,	,		20874	0.0258		0.1988	False		,,,				2504	0.1155				p.P273P		Atlas-SNP	.											.	FHL2	18	.	0			c.C819T						PASS	.	A	,,,	453,3953	217.1+/-235.6	24,405,1774	117.0	110.0	113.0		819,819,819,819	-11.0	0.5	2	dbSNP_120	113	1685,6915	308.6+/-309.0	154,1377,2769	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FHL2	NM_001039492.2,NM_001450.3,NM_201555.1,NM_201557.3	,,,	178,1782,4543	AA,AG,GG		19.593,10.2814,16.4386	,,,	273/280,273/280,273/280,273/280	105977761	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	2274	exon7			ACAGTCGGGGCAC		CCDS2070.1	2q12.2	2014-09-17			ENSG00000115641	ENSG00000115641			3703	protein-coding gene	gene with protein product		602633				8753811	Standard	NM_201557		Approved	SLIM3, DRAL	uc002tcy.3	Q14192	OTTHUMG00000153120	ENST00000409807.1:c.819C>T	2.37:g.105977761G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001039492	Q13229|Q13644|Q2I5I4|Q5TM15|Q9P294	Silent	SNP	ENST00000409807.1	37	CCDS2070.1																																																																																			G|0.852;A|0.148	0.148	strong		0.498	FHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329654.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29912085	29912085	+	Missense_Mutation	SNP	C	C	T	rs148794540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29912085C>T	ENST00000396634.1	+	6	1147	c.806C>T	c.(805-807)gCg>gTg	p.A269V	HLA-A_ENST00000376809.5_Missense_Mutation_p.A269V|HLA-A_ENST00000376802.2_Missense_Mutation_p.A269V|HLA-A_ENST00000376806.5_Missense_Mutation_p.A269V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	269	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						CAGAAGTGGGCGGCTGTGGTG	0.627									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.A269V		Atlas-SNP	.											.	HLA-A	89	.	0			c.C806T						PASS	.						30.0	30.0	30.0					6																	29912085		1510	2703	4213	SO:0001583	missense	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGTGGGCGGCTGT	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.806C>T	6.37:g.29912085C>T	ENSP00000379873:p.Ala269Val	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	377	68	0.180371	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	111	0.050824175824175824	52	0.10569105691056911	28	0.07734806629834254	5	0.008741258741258742	26	0.03430079155672823	.	10.60	1.394867	0.25205	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000536480;ENST00000376809;ENST00000376802	T;T;T;T	0.02737	4.18;4.18;4.18;4.18	3.69	3.69	0.42338	Immunoglobulin-like (4);Immunoglobulin C1-set (8);Immunoglobulin-like fold (4);	0.171004	0.27023	N	0.021307	T	0.04634	0.0126	L	0.48174	1.505	0.27755	N	0.944011	D;B;D;B;D;B;B	0.89917	0.998;0.118;1.0;0.029;1.0;0.029;0.029	D;B;D;B;D;B;B	0.83275	0.951;0.02;0.996;0.02;0.996;0.02;0.02	T	0.13899	-1.0492	10	0.59425	D	0.04	.	11.1517	0.48462	0.0:1.0:0.0:0.0	rs41562917	148;269;269;269;269;269;269	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	V	269;269;57;269;269	ENSP00000379873:A269V;ENSP00000366002:A269V;ENSP00000366005:A269V;ENSP00000365998:A269V	ENSP00000365998:A269V	A	+	2	0	HLA-A	30020064	0.015000	0.18098	0.947000	0.38551	0.843000	0.47879	-0.097000	0.11042	2.070000	0.61991	0.485000	0.47835	GCG	C|0.973;T|0.027	0.027	strong		0.627	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ESPNL	339768	hgsc.bcm.edu	37	2	239025645	239025645	+	Silent	SNP	C	C	T	rs11897736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239025645C>T	ENST00000343063.3	+	5	1220	c.957C>T	c.(955-957)tgC>tgT	p.C319C	ESPNL_ENST00000409169.1_Intron	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	319										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)		ACCGGGACTGCGCCCAGTACC	0.692													T|||	985	0.196685	0.2874	0.1412	5008	,	,		16520	0.2302		0.1322	False		,,,				2504	0.1452				p.C319C		Atlas-SNP	.											.	ESPNL	63	.	0			c.C957T						PASS	.	T		1121,3279	696.8+/-406.1	172,777,1251	51.0	41.0	44.0		957	-5.5	0.8	2	dbSNP_120	44	1413,7179	743.9+/-407.2	128,1157,3011	no	coding-synonymous	ESPNL	NM_194312.2		300,1934,4262	TT,TC,CC		16.4455,25.4773,19.5043		319/1006	239025645	2534,10458	2200	4296	6496	SO:0001819	synonymous_variant	339768	exon5			GGACTGCGCCCAG	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.957C>T	2.37:g.239025645C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	108	59	0.546296	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			C|0.808;T|0.192	0.192	strong		0.692	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
DLK2	65989	hgsc.bcm.edu	37	6	43418691	43418691	+	Silent	SNP	G	G	A	rs1214748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43418691G>A	ENST00000357338.3	-	6	1438	c.738C>T	c.(736-738)acC>acT	p.T246T	DLK2_ENST00000372488.3_Silent_p.T246T|DLK2_ENST00000372485.1_Silent_p.T240T|DLK2_ENST00000414245.1_Silent_p.T240T	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	246	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	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)			CAAGCTCACAGGTCTTGCCAC	0.657													A|||	1397	0.278954	0.5424	0.2147	5008	,	,		17896	0.0804		0.2863	False		,,,				2504	0.1656				p.T246T		Atlas-SNP	.											.	DLK2	22	.	0			c.C738T						PASS	.	A	,	2210,2196	571.7+/-383.1	559,1092,552	57.0	62.0	60.0		738,738	-2.5	1.0	6	dbSNP_87	60	2673,5927	671.5+/-402.8	426,1821,2053	no	coding-synonymous,coding-synonymous	DLK2	NM_023932.2,NM_206539.1	,	985,2913,2605	AA,AG,GG		31.0814,49.8411,37.5442	,	246/384,246/384	43418691	4883,8123	2203	4300	6503	SO:0001819	synonymous_variant	65989	exon6			CTCACAGGTCTTG	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"""EGF-like-domain, multiple 9"""	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.738C>T	6.37:g.43418691G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Silent	SNP	ENST00000357338.3	37	CCDS4897.1	577	0.2641941391941392	247	0.5020325203252033	81	0.22375690607734808	41	0.07167832167832168	208	0.27440633245382584	A	7.951	0.744851	0.15710	0.501589	0.310814	ENSG00000171462	ENST00000430324	.	.	.	4.94	-2.45	0.06481	.	.	.	.	.	T	0.11793	0.0287	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.27434	-1.0074	3	.	.	.	.	4.7667	0.13135	0.2858:0.1157:0.4846:0.1138	rs1214748;rs1674840;rs58292939;rs1214748	.	.	.	L	152	.	.	P	-	2	0	DLK2	43526669	0.115000	0.22152	0.995000	0.50966	0.918000	0.54935	-0.388000	0.07352	-0.280000	0.09154	-0.521000	0.04368	CCT	A|0.330;C|0.006	0.330	strong		0.657	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932	
PREP	5550	hgsc.bcm.edu	37	6	105821449	105821449	+	Silent	SNP	A	A	G	rs9486069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:105821449A>G	ENST00000369110.3	-	5	582	c.390T>C	c.(388-390)taT>taC	p.Y130Y		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	130					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	CGCTGAACGCATAACCTATGG	0.463													G|||	1743	0.348043	0.8215	0.1988	5008	,	,		22397	0.002		0.2932	False		,,,				2504	0.227				p.Y130Y		Atlas-SNP	.											.	PREP	65	.	0			c.T390C						PASS	.	G		3241,1165	407.8+/-334.4	1209,823,171	71.0	65.0	67.0		390	3.5	1.0	6	dbSNP_119	67	2406,6194	699.6+/-405.1	341,1724,2235	no	coding-synonymous	PREP	NM_002726.4		1550,2547,2406	GG,GA,AA		27.9767,26.4412,43.4184		130/711	105821449	5647,7359	2203	4300	6503	SO:0001819	synonymous_variant	5550	exon5			GAACGCATAACCT		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.390T>C	6.37:g.105821449A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_002726	Q8N6D4	Silent	SNP	ENST00000369110.3	37	CCDS5053.1																																																																																			A|0.586;G|0.414	0.414	strong		0.463	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
ERBB3	2065	hgsc.bcm.edu	37	12	56494998	56494998	+	Missense_Mutation	SNP	A	A	T	rs773123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56494998A>T	ENST00000267101.3	+	27	3795	c.3355A>T	c.(3355-3357)Agc>Tgc	p.S1119C	ERBB3_ENST00000415288.2_Missense_Mutation_p.S1060C|ERBB3_ENST00000553131.1_Missense_Mutation_p.S360C|RP11-603J24.9_ENST00000548861.1_5'Flank|ERBB3_ENST00000450146.2_Missense_Mutation_p.S476C|ERBB3_ENST00000549832.1_Missense_Mutation_p.S239C	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	1119			S -> C (in dbSNP:rs773123). {ECO:0000269|PubMed:17344846}.		cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			TAGGAGCCGGAGCAGGAGCCG	0.617													A|||	333	0.0664936	0.0787	0.0663	5008	,	,		13463	0.002		0.1123	False		,,,				2504	0.0695				p.S1119C		Atlas-SNP	.											.	ERBB3	350	.	0			c.A3355T						PASS	.	A	CYS/SER	384,4022	193.6+/-218.7	15,354,1834	56.0	53.0	54.0		3355	5.9	1.0	12	dbSNP_86	54	916,7684	202.8+/-246.0	53,810,3437	yes	missense	ERBB3	NM_001982.3	112	68,1164,5271	TT,TA,AA		10.6512,8.7154,9.9954	probably-damaging	1119/1343	56494998	1300,11706	2203	4300	6503	SO:0001583	missense	2065	exon27			AGCCGGAGCAGGA	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"""lethal congenital contracture syndrome 2"""	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.3355A>T	12.37:g.56494998A>T	ENSP00000267101:p.Ser1119Cys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	37	CCDS31833.1	136	0.06227106227106227	24	0.04878048780487805	27	0.07458563535911603	1	0.0017482517482517483	84	0.11081794195250659	A	21.3	4.126790	0.77549	0.087154	0.106512	ENSG00000065361	ENST00000267101;ENST00000450146;ENST00000415288;ENST00000550070;ENST00000553131;ENST00000549832	T;T;T;T;T	0.79940	-1.18;-1.1;-1.17;-1.32;-1.06	5.87	5.87	0.94306	.	0.132088	0.53938	D	0.000051	T	0.07279	0.0184	N	0.08118	0	0.20403	P	0.9999099903	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.996	T	0.65759	-0.6090	9	0.52906	T	0.07	.	14.0962	0.65023	1.0:0.0:0.0:0.0	rs773123;rs58303863;rs773123	1060;239;1119	P21860-4;B3KWG5;P21860	.;.;ERBB3_HUMAN	C	1119;476;1060;242;360;239	ENSP00000267101:S1119C;ENSP00000399178:S476C;ENSP00000408340:S1060C;ENSP00000449129:S360C;ENSP00000448729:S239C	ENSP00000267101:S1119C	S	+	1	0	ERBB3	54781265	1.000000	0.71417	0.981000	0.43875	0.990000	0.78478	6.234000	0.72326	2.371000	0.80710	0.533000	0.62120	AGC	A|0.908;T|0.092	0.092	strong		0.617	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		
FKBPL	63943	hgsc.bcm.edu	37	6	32097089	32097089	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32097089C>T	ENST00000375156.3	-	2	739	c.469G>A	c.(469-471)Ggg>Agg	p.G157R	ATF6B_ENST00000375201.4_5'Flank|ATF6B_ENST00000375203.3_5'Flank|ATF6B_ENST00000468502.1_5'Flank	NM_022110.3	NP_071393.2	Q9UIM3	FKBPL_HUMAN	FK506 binding protein like	157					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)|response to radiation (GO:0009314)	endoplasmic reticulum membrane (GO:0005789)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)										ATGAGCTCCCCCCAAGTTTCC	0.592																																					p.G157R		Atlas-SNP	.											.	FKBPL	25	.	0			c.G469A						PASS	.						188.0	201.0	196.0					6																	32097089		2203	4300	6503	SO:0001583	missense	63943	exon2			GCTCCCCCCAAGT	AF139374	CCDS4738.1	6p21.3	2013-12-13	2001-11-28		ENSG00000204315	ENSG00000204315		"""Tetratricopeptide (TTC) repeat domain containing"""	13949	protein-coding gene	gene with protein product	"""WAF-1/CIP1 stabilizing protein 39"""		"""FK506-binding protein like"""			9056895	Standard	NM_022110		Approved	DIR1, NG7, WISp39	uc003nzr.3	Q9UIM3	OTTHUMG00000031129	ENST00000375156.3:c.469G>A	6.37:g.32097089C>T	ENSP00000364298:p.Gly157Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_022110	A8K5V3|B0UYX8|Q9H5G3	Missense_Mutation	SNP	ENST00000375156.3	37	CCDS4738.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.686625	0.68157	.	.	ENSG00000204315	ENST00000375156	T	0.80994	-1.44	5.23	3.46	0.39613	.	0.000000	0.42548	D	0.000691	T	0.47820	0.1466	N	0.24115	0.695	0.38007	D	0.934418	B	0.32829	0.386	B	0.29353	0.101	T	0.42172	-0.9467	10	0.23891	T	0.37	-13.8519	9.3205	0.37962	0.0:0.8274:0.0:0.1726	.	157	Q9UIM3	FKBPL_HUMAN	R	157	ENSP00000364298:G157R	ENSP00000364298:G157R	G	-	1	0	FKBPL	32205067	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.754000	0.47532	0.793000	0.33875	0.462000	0.41574	GGG	.	.	none		0.592	FKBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076221.2		
ADIPOR2	79602	hgsc.bcm.edu	37	12	1893170	1893170	+	Silent	SNP	C	C	T	rs9805042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:1893170C>T	ENST00000357103.4	+	7	1214	c.963C>T	c.(961-963)taC>taT	p.Y321Y		NM_024551.2	NP_078827.2	Q86V24	ADR2_HUMAN	adiponectin receptor 2	321					adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|female pregnancy (GO:0007565)|heart development (GO:0007507)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of cell growth (GO:0030308)|positive regulation of glucose import (GO:0046326)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|receptor activity (GO:0004872)	p.Y321Y(1)		endometrium(1)|large_intestine(3)|lung(7)|stomach(1)	12	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			CCAGCCTCTACATCACAGGAG	0.547													C|||	1189	0.23742	0.5416	0.111	5008	,	,		18023	0.1111		0.1302	False		,,,				2504	0.1564				p.Y321Y		Atlas-SNP	.											ADIPOR2,NS,carcinoma,0,1	ADIPOR2	30	1	1	Substitution - coding silent(1)	stomach(1)	c.C963T						PASS	.	C		2031,2375	565.5+/-381.7	484,1063,656	90.0	84.0	86.0		963	-5.4	0.2	12	dbSNP_119	86	1097,7503	228.6+/-263.6	61,975,3264	no	coding-synonymous	ADIPOR2	NM_024551.2		545,2038,3920	TT,TC,CC		12.7558,46.0962,24.0504		321/387	1893170	3128,9878	2203	4300	6503	SO:0001819	synonymous_variant	79602	exon7			CCTCTACATCACA	AY424280	CCDS8511.1	12p13	2012-08-22			ENSG00000006831	ENSG00000006831		"""GPCR / Unclassified : Adiponectin receptors"""	24041	protein-coding gene	gene with protein product		607946				12802337	Standard	NM_024551		Approved	PAQR2, ACDCR2	uc001qjm.3	Q86V24	OTTHUMG00000130139	ENST00000357103.4:c.963C>T	12.37:g.1893170C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	159	155	0.974843	NM_024551	Q53YY5|Q9H737	Silent	SNP	ENST00000357103.4	37	CCDS8511.1																																																																																			C|0.770;T|0.230	0.230	strong		0.547	ADIPOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252447.2	NM_024551	
SLC7A13	157724	hgsc.bcm.edu	37	8	87241847	87241847	+	Silent	SNP	G	G	A	rs7814198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	46	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	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	
TXNDC8	255220	hgsc.bcm.edu	37	9	113091523	113091523	+	Missense_Mutation	SNP	T	T	G	rs7041938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113091523T>G	ENST00000374511.3	-	3	226	c.178A>C	c.(178-180)Aac>Cac	p.N60H	TXNDC8_ENST00000374510.4_Missense_Mutation_p.N60H|TXNDC8_ENST00000374507.4_Intron|TXNDC8_ENST00000423740.2_Intron			Q6A555	TXND8_HUMAN	thioredoxin domain containing 8 (spermatozoa)	60	Thioredoxin.		N -> H (in dbSNP:rs7041938).		acrosome assembly (GO:0001675)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|sperm flagellum (GO:0036126)				endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4						GGAGAATTGTTCACATCCACA	0.289													T|||	491	0.0980431	0.0446	0.1643	5008	,	,		18731	0.0774		0.1173	False		,,,				2504	0.1247				p.N60H		Atlas-SNP	.											.	TXNDC8	30	.	0			c.A178C						PASS	.	T	HIS/ASN	284,4120	157.4+/-190.3	9,266,1927	103.0	103.0	103.0		178	0.1	0.2	9	dbSNP_116	103	1068,7524	221.7+/-259.0	70,928,3298	yes	missense	TXNDC8	NM_001003936.2	68	79,1194,5225	GG,GT,TT		12.4302,6.4487,10.4032	possibly-damaging	60/116	113091523	1352,11644	2202	4296	6498	SO:0001583	missense	255220	exon3			AATTGTTCACATC	BC035743	CCDS35104.1, CCDS69639.1, CCDS75872.1	9q31.3	2007-08-16	2007-08-16	2007-08-16	ENSG00000204193	ENSG00000204193			31454	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 3"""						Standard	XM_005251879		Approved	bA427L11.2, TRX6, SPTRX-3	uc004bes.3	Q6A555	OTTHUMG00000020481	ENST00000374511.3:c.178A>C	9.37:g.113091523T>G	ENSP00000363635:p.Asn60His	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	21	13	0.619048	NM_001003936	A1L4I2|A6NDK7|Q5T934	Missense_Mutation	SNP	ENST00000374511.3	37		214	0.09798534798534798	26	0.052845528455284556	48	0.13259668508287292	46	0.08041958041958042	94	0.12401055408970976	T	10.25	1.297687	0.23650	0.064487	0.124302	ENSG00000204193	ENST00000374511;ENST00000374510	T;T	0.22539	1.95;1.95	4.07	0.139	0.14798	.	0.502303	0.18424	N	0.141656	T	0.00178	0.0005	N	0.20986	0.625	0.80722	P	0.0	D	0.60575	0.988	P	0.52066	0.689	T	0.13980	-1.0489	9	0.87932	D	0	-0.0906	6.2333	0.20747	0.0:0.5362:0.0:0.4638	rs7041938;rs17806208;rs52792001;rs56845930;rs7041938	60	Q6A555-2	.	H	60	ENSP00000363635:N60H;ENSP00000363634:N60H	ENSP00000363634:N60H	N	-	1	0	TXNDC8	112131344	0.978000	0.34361	0.163000	0.22734	0.431000	0.31685	0.376000	0.20535	0.018000	0.15052	-0.468000	0.05107	AAC	T|0.904;G|0.096	0.096	strong		0.289	TXNDC8-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001003936	
CDC25B	994	hgsc.bcm.edu	37	20	3782702	3782702	+	Silent	SNP	G	G	A	rs2228465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3782702G>A	ENST00000245960.5	+	10	1750	c.1053G>A	c.(1051-1053)agG>agA	p.R351R	CDC25B_ENST00000467519.1_3'UTR|CDC25B_ENST00000344256.6_Silent_p.R287R|CDC25B_ENST00000439880.2_Silent_p.R337R|CDC25B_ENST00000340833.4_Silent_p.R310R|CDC25B_ENST00000379598.5_Silent_p.R260R	NM_004358.3|NM_021872.2|NM_021873.2	NP_004349.1|NP_068658.1|NP_068659.1	P30305	MPIP2_HUMAN	cell division cycle 25B	351					female meiosis I (GO:0007144)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|oocyte maturation (GO:0001556)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein kinase activity (GO:0045860)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(1)	18						ATAAGCGGAGGCGGAGCGTGA	0.657													G|||	167	0.0333466	0.0477	0.0303	5008	,	,		16765	0.0198		0.0318	False		,,,				2504	0.0317				p.R351R		Atlas-SNP	.											.	CDC25B	76	.	0			c.G1053A						PASS	.	G	,,	189,4205		9,171,2017	29.0	25.0	27.0		1011,930,1053	2.5	1.0	20	dbSNP_98	27	291,8277		8,275,4001	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC25B	NM_004358.3,NM_021872.2,NM_021873.2	,,	17,446,6018	AA,AG,GG		3.3964,4.3013,3.7031	,,	337/567,310/540,351/581	3782702	480,12482	2197	4284	6481	SO:0001819	synonymous_variant	994	exon10			GCGGAGGCGGAGC		CCDS13065.1, CCDS13066.1, CCDS13067.1, CCDS74700.1, CCDS74701.1	20p13	2013-01-17	2013-01-17		ENSG00000101224	ENSG00000101224		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"""	1726	protein-coding gene	gene with protein product		116949	"""cell division cycle 25B"", ""cell division cycle 25 homolog B (S. cerevisiae)"", ""cell division cycle 25 homolog B (S. pombe)"""			1836978	Standard	NM_021873		Approved		uc002wjn.3	P30305	OTTHUMG00000031764	ENST00000245960.5:c.1053G>A	20.37:g.3782702G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_021873	D3DVY1|D3DVY2|D3DVY3|D3DVY4|O43551|Q13971|Q5JX77|Q6RSS1|Q9BRA6	Silent	SNP	ENST00000245960.5	37	CCDS13067.1																																																																																			G|0.956;A|0.044	0.044	strong		0.657	CDC25B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077779.2	NM_021874	
NLRP8	126205	hgsc.bcm.edu	37	19	56477710	56477710	+	Missense_Mutation	SNP	T	T	C	rs306496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56477710T>C	ENST00000291971.3	+	5	2416	c.2345T>C	c.(2344-2346)gTg>gCg	p.V782A	NLRP8_ENST00000590542.1_Missense_Mutation_p.V782A	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	782			V -> A (in dbSNP:rs306496).		neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CTATGCAGGGTGCTGAGATCC	0.537													C|||	3298	0.658546	0.7746	0.6326	5008	,	,		17458	0.6885		0.5239	False		,,,				2504	0.6278				p.V782A		Atlas-SNP	.											.	NLRP8	225	.	0			c.T2345C						PASS	.	C	ALA/VAL	3302,1104	399.2+/-331.1	1248,806,149	120.0	114.0	116.0		2345	1.8	0.0	19	dbSNP_79	116	4412,4188	569.8+/-389.3	1142,2128,1030	yes	missense	NLRP8	NM_176811.2	64	2390,2934,1179	CC,CT,TT		48.6977,25.0567,40.6889	benign	782/1049	56477710	7714,5292	2203	4300	6503	SO:0001583	missense	126205	exon5			GCAGGGTGCTGAG	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2345T>C	19.37:g.56477710T>C	ENSP00000291971:p.Val782Ala	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	1391	0.6369047619047619	377	0.766260162601626	226	0.6243093922651933	392	0.6853146853146853	396	0.5224274406332454	C	0.009	-1.838815	0.00573	0.749433	0.513023	ENSG00000179709	ENST00000291971	T	0.50001	0.76	1.82	1.82	0.25136	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41161	-0.9524	8	0.02654	T	1	.	4.4907	0.11812	0.0:0.8003:0.0:0.1997	rs306496;rs52822657;rs59914054;rs306496	782;782	Q86W28-2;Q86W28	.;NALP8_HUMAN	A	782	ENSP00000291971:V782A	ENSP00000291971:V782A	V	+	2	0	NLRP8	61169522	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.242000	0.18087	0.325000	0.23359	-0.226000	0.12346	GTG	T|0.382;C|0.618	0.618	strong		0.537	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
KIAA1244	57221	hgsc.bcm.edu	37	6	138584685	138584685	+	Missense_Mutation	SNP	T	T	G	rs7764091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138584685T>G	ENST00000251691.4	+	12	2231	c.2065T>G	c.(2065-2067)Tct>Gct	p.S689A		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		TCGGCTCCTGTCTCTCTCCAA	0.527													G|||	1487	0.296925	0.5749	0.2233	5008	,	,		19009	0.371		0.0895	False		,,,				2504	0.1104				p.S689A		Atlas-SNP	.											.	KIAA1244	236	.	0			c.T2065G						PASS	.	G	ALA/SER	2151,2245		544,1063,591	46.0	51.0	50.0		2065	5.2	1.0	6	dbSNP_116	50	739,7859		35,669,3595	yes	missense	KIAA1244	NM_020340.4	99	579,1732,4186	GG,GT,TT		8.595,48.9308,22.241	benign	689/2178	138584685	2890,10104	2198	4299	6497	SO:0001583	missense	57221	exon12			CTCCTGTCTCTCT	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.2065T>G	6.37:g.138584685T>G	ENSP00000251691:p.Ser689Ala	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	629	0.288003663003663	270	0.5487804878048781	71	0.19613259668508287	221	0.38636363636363635	67	0.08839050131926121	G	0.018	-1.468445	0.01053	0.489308	0.08595	ENSG00000112379	ENST00000251691	T	0.40476	1.03	5.17	5.17	0.71159	SEC7-like (1);	253.487000	0.00166	N	0.000000	T	0.06735	0.0172	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30031	-0.9992	9	0.02654	T	1	-32.0037	9.0639	0.36451	0.0735:0.0:0.7781:0.1483	rs7764091;rs52831040;rs58555015;rs7764091	689	Q5TH69	BIG3_HUMAN	A	689	ENSP00000251691:S689A	ENSP00000251691:S689A	S	+	1	0	KIAA1244	138626378	1.000000	0.71417	0.991000	0.47740	0.075000	0.17131	2.458000	0.45014	1.326000	0.45319	-0.121000	0.15023	TCT	T|0.728;G|0.272	0.272	strong		0.527	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
LIPC	3990	hgsc.bcm.edu	37	15	58833993	58833993	+	Missense_Mutation	SNP	G	G	A	rs6078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:58833993G>A	ENST00000356113.6	+	5	898	c.283G>A	c.(283-285)Gtg>Atg	p.V95M	LIPC_ENST00000299022.5_Missense_Mutation_p.V95M|LIPC_ENST00000414170.3_Missense_Mutation_p.V95M|LIPC_ENST00000433326.2_Intron			P11150	LIPC_HUMAN	lipase, hepatic	95			V -> M (in dbSNP:rs6078). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:12966036}.		cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		GGTGGACGGCGTGCTAGAAAA	0.612													A|||	622	0.124201	0.0787	0.0562	5008	,	,		16230	0.3284		0.0348	False		,,,				2504	0.1155				p.V95M		Atlas-SNP	.											.	LIPC	56	.	0			c.G283A	GRCh37	CM004612	LIPC	M	rs6078	PASS	.	A	MET/VAL	327,4057	786.6+/-414.8	10,307,1875	37.0	46.0	43.0		283	-9.2	0.0	15	dbSNP_52	43	239,8345	802.7+/-407.3	4,231,4057	yes	missense	LIPC	NM_000236.2	21	14,538,5932	AA,AG,GG		2.7842,7.4589,4.3646	benign	95/500	58833993	566,12402	2192	4292	6484	SO:0001583	missense	3990	exon3			GACGGCGTGCTAG		CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.283G>A	15.37:g.58833993G>A	ENSP00000348425:p.Val95Met	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_000236	A2RUB4|A8K9B6|O43571|P78529|Q99465	Missense_Mutation	SNP	ENST00000356113.6	37	CCDS10166.1	248	0.11355311355311355	42	0.08536585365853659	17	0.04696132596685083	169	0.29545454545454547	20	0.026385224274406333	A	0.001	-3.862964	0.00003	0.074589	0.027842	ENSG00000166035	ENST00000356113;ENST00000414170;ENST00000299022	D;D;D	0.90844	-2.74;-2.74;-2.74	4.6	-9.2	0.00682	Lipase, N-terminal (1);	1.503030	0.03930	N	0.285141	T	0.00012	0.0000	N	0.00605	-1.335	0.80722	P	0.0	B	0.25272	0.122	B	0.14023	0.01	T	0.40776	-0.9545	9	0.02654	T	1	.	3.3549	0.07165	0.4972:0.0701:0.1608:0.272	rs6078;rs17301836;rs6078	95	P11150	LIPC_HUMAN	M	95	ENSP00000348425:V95M;ENSP00000395569:V95M;ENSP00000299022:V95M	ENSP00000299022:V95M	V	+	1	0	LIPC	56621285	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.112000	0.03299	-7.950000	0.00000	-4.297000	0.00007	GTG	G|0.926;A|0.074	0.074	strong		0.612	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1		
MUC4	4585	hgsc.bcm.edu	37	3	195511236	195511236	+	Missense_Mutation	SNP	G	G	T	rs534701413		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511236G>T	ENST00000463781.3	-	2	7674	c.7215C>A	c.(7213-7215)gaC>gaA	p.D2405E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D2405E	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)		CTGAGGAAGTGTCGGTGACAG	0.587																																					p.D2405E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,3	MUC4	1505	3	0			c.C7215A						PASS	.						35.0	37.0	37.0					3																	195511236		689	1589	2278	SO:0001583	missense	4585	exon2			GGAAGTGTCGGTG	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.7215C>A	3.37:g.195511236G>T	ENSP00000417498:p.Asp2405Glu	Somatic	637	0	0		WXS	Illumina HiSeq	Phase_I	235	19	0.0808511	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	8.514	0.867217	0.17250	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.58;1.56	.	.	.	.	.	.	.	.	T	0.31199	0.0789	N	0.19112	0.55	0.09310	N	1	P	0.37781	0.608	P	0.55508	0.777	T	0.36163	-0.9759	7	.	.	.	.	6.6894	0.23163	2.0E-4:0.0:0.9998:0.0	.	2405	E7ESK3	.	E	2405	ENSP00000417498:D2405E;ENSP00000420243:D2405E	.	D	-	3	2	MUC4	196995631	0.000000	0.05858	0.004000	0.12327	0.079000	0.17450	-3.039000	0.00633	0.482000	0.27582	0.000000	0.15137	GAC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TLE6	79816	hgsc.bcm.edu	37	19	2994921	2994921	+	Silent	SNP	G	G	A	rs34551565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2994921G>A	ENST00000246112.4	+	17	1839	c.1638G>A	c.(1636-1638)acG>acA	p.T546T	TLE6_ENST00000452088.1_Silent_p.T423T	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	546					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)		CTCCAGTCACGTGCTGTGACG	0.622													G|||	1456	0.290735	0.3495	0.3329	5008	,	,		11993	0.3343		0.2266	False		,,,				2504	0.2025				p.T546T		Atlas-SNP	.											.	TLE6	68	.	0			c.G1638A						PASS	.	G	,	1371,3035	427.6+/-341.6	234,903,1066	75.0	48.0	57.0		1638,1269	0.4	0.1	19	dbSNP_126	57	1860,6740	302.9+/-306.2	200,1460,2640	no	coding-synonymous,coding-synonymous	TLE6	NM_001143986.1,NM_024760.2	,	434,2363,3706	AA,AG,GG		21.6279,31.1167,24.8424	,	546/573,423/450	2994921	3231,9775	2203	4300	6503	SO:0001819	synonymous_variant	79816	exon17			AGTCACGTGCTGT	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.1638G>A	19.37:g.2994921G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001143986	J3KMZ1	Silent	SNP	ENST00000246112.4	37	CCDS45910.1																																																																																			G|0.736;A|0.264	0.264	strong		0.622	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760	
ZFP82	284406	hgsc.bcm.edu	37	19	36884651	36884651	+	Silent	SNP	C	C	A	rs114627398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36884651C>A	ENST00000392161.3	-	5	833	c.591G>T	c.(589-591)ccG>ccT	p.P197P	ZFP82_ENST00000392171.1_Silent_p.P197P	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	197					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TACATTCATACGGTTTTTCAC	0.408													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		22380	0.0		0.0	False		,,,				2504	0.0				p.P197P		Atlas-SNP	.											.	ZFP82	71	.	0			c.G591T						PASS	.	G		150,4256		4,142,2057	88.0	78.0	81.0		591	-4.1	1.0	19	dbSNP_132	81	2,8598		0,2,4298	no	coding-synonymous	ZFP82	NM_133466.2		4,144,6355	AA,AC,CC		0.0233,3.4044,1.1687		197/533	36884651	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	284406	exon5			TTCATACGGTTTT	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"""Zinc fingers, C2H2-type"", ""-"""	28682	protein-coding gene	gene with protein product			"""zinc finger protein 545"", ""zinc finger protein 82 homolog (mouse)"", ""zinc finger protein 82"""	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.591G>T	19.37:g.36884651C>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	176	90	0.511364	NM_133466	Q8NC63|Q8TF53	Silent	SNP	ENST00000392161.3	37	CCDS12493.1																																																																																			C|0.989;A|0.011	0.011	strong		0.408	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466	
LILRA1	11024	hgsc.bcm.edu	37	19	55105923	55105923	+	Silent	SNP	C	C	A	rs10416264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55105923C>A	ENST00000251372.3	+	3	234	c.52C>A	c.(52-54)Cgg>Agg	p.R18R	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000418536.2_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Silent_p.R18R	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	18					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		TCTGGGCCCCCGGACCCACGT	0.662													a|||	812	0.162141	0.4032	0.0994	5008	,	,		16324	0.0079		0.0924	False		,,,				2504	0.1115				p.R18R		Atlas-SNP	.											LILRA1,colon,carcinoma,-1,1	LILRA1	105	1	0			c.C52A						PASS	.	A		1505,2901	639.2+/-397.1	265,975,963	62.0	75.0	71.0		52	-0.3	0.0	19	dbSNP_119	71	791,7809	773.1+/-407.7	40,711,3549	no	coding-synonymous	LILRA1	NM_006863.1		305,1686,4512	AA,AC,CC		9.1977,34.158,17.6534		18/490	55105923	2296,10710	2203	4300	6503	SO:0001819	synonymous_variant	11024	exon3			GGCCCCCGGACCC	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.52C>A	19.37:g.55105923C>A		Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	256	124	0.484375	NM_006863	O75018|Q3MJA6	Silent	SNP	ENST00000251372.3	37	CCDS12901.1																																																																																			C|0.834;A|0.166	0.166	strong		0.662	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
TAB2	23118	hgsc.bcm.edu	37	6	149699333	149699333	+	Silent	SNP	A	A	G	rs13215304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:149699333A>G	ENST00000367456.1	+	4	859	c.282A>G	c.(280-282)ggA>ggG	p.G94G	TAB2_ENST00000286332.5_Silent_p.G94G|TAB2_ENST00000392282.1_Silent_p.G94G|TAB2_ENST00000536230.1_Silent_p.G62G|TAB2_ENST00000538427.1_Silent_p.G94G			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	94					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						GAAGAGAAGGAAGTAGGATGA	0.428													A|||	55	0.0109824	0.0	0.0288	5008	,	,		20789	0.001		0.0328	False		,,,				2504	0.001				p.G94G		Atlas-SNP	.											TAB2,NS,carcinoma,+2,1	TAB2	55	1	0			c.A282G						scavenged	.	A		32,4374	36.0+/-67.5	0,32,2171	132.0	115.0	120.0		282	3.3	1.0	6	dbSNP_121	120	268,8332	103.1+/-164.3	4,260,4036	no	coding-synonymous	TAB2	NM_015093.4		4,292,6207	GG,GA,AA		3.1163,0.7263,2.3066		94/694	149699333	300,12706	2203	4300	6503	SO:0001819	synonymous_variant	23118	exon5			AGAAGGAAGTAGG	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.282A>G	6.37:g.149699333A>G		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_015093	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Silent	SNP	ENST00000367456.1	37	CCDS5214.1																																																																																			A|0.977;G|0.023	0.023	strong		0.428	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3		
PGM2	55276	hgsc.bcm.edu	37	4	37836302	37836302	+	Silent	SNP	T	T	C	rs3752683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:37836302T>C	ENST00000381967.4	+	3	412	c.312T>C	c.(310-312)agT>agC	p.S104S	PGM2_ENST00000544359.1_5'UTR|PGM2_ENST00000537241.1_Intron	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	104					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						TCGTGATCAGTTTTGACGCCC	0.338													C|||	1722	0.34385	0.6755	0.2781	5008	,	,		14222	0.2748		0.2167	False		,,,				2504	0.1442				p.S104S		Atlas-SNP	.											.	PGM2	45	.	0			c.T312C						PASS	.	C		2711,1695	651.8+/-399.3	835,1041,327	91.0	102.0	99.0		312	2.3	1.0	4	dbSNP_107	99	1856,6744	331.4+/-319.6	196,1464,2640	no	coding-synonymous	PGM2	NM_018290.3		1031,2505,2967	CC,CT,TT		21.5814,38.4703,35.1146		104/613	37836302	4567,8439	2203	4300	6503	SO:0001819	synonymous_variant	55276	exon3			GATCAGTTTTGAC	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"""phosphopentomutase"""	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.312T>C	4.37:g.37836302T>C		Somatic	327	2	0.00611621		WXS	Illumina HiSeq	Phase_I	275	275	1	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Silent	SNP	ENST00000381967.4	37	CCDS3443.1																																																																																			T|0.651;C|0.349	0.349	strong		0.338	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290	
ECT2	1894	hgsc.bcm.edu	37	3	172480580	172480580	+	Missense_Mutation	SNP	A	A	G	rs138074177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:172480580A>G	ENST00000392692.3	+	10	1165	c.989A>G	c.(988-990)tAt>tGt	p.Y330C	ECT2_ENST00000417960.1_Missense_Mutation_p.Y298C|ECT2_ENST00000540509.1_Missense_Mutation_p.Y330C|ECT2_ENST00000441497.2_Missense_Mutation_p.Y299C|ECT2_ENST00000427830.1_Missense_Mutation_p.Y299C|ECT2_ENST00000232458.5_Missense_Mutation_p.Y299C	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2	330	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				activation of protein kinase activity (GO:0032147)|activation of Rac GTPase activity (GO:0032863)|activation of Rho GTPase activity (GO:0032862)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular response to calcium ion (GO:0071277)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of Rho GTPase activity (GO:0032321)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|centralspindlin complex (GO:0097149)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			AAGAAACTTTATGTTGTCAAG	0.313													A|||	2	0.000399361	0.0008	0.0	5008	,	,		17827	0.0		0.001	False		,,,				2504	0.0				p.Y330C		Atlas-SNP	.											.	ECT2	79	.	0			c.A989G						PASS	.	A	CYS/TYR	3,4403	6.2+/-15.9	0,3,2200	89.0	90.0	90.0		896	4.7	1.0	3	dbSNP_134	90	2,8596	2.2+/-6.3	0,2,4297	yes	missense	ECT2	NM_018098.4	194	0,5,6497	GG,GA,AA		0.0233,0.0681,0.0384	probably-damaging	299/884	172480580	5,12999	2203	4299	6502	SO:0001583	missense	1894	exon10			AACTTTATGTTGT	AA206473	CCDS3220.1, CCDS58860.1	3q26.1-q26.2	2014-03-11	2014-03-11		ENSG00000114346	ENSG00000114346		"""Rho guanine nucleotide exchange factors"""	3155	protein-coding gene	gene with protein product		600586	"""epithelial cell transforming sequence 2 oncogene"""			8464478, 10579713	Standard	NM_018098		Approved	ARHGEF31	uc003fil.2	Q9H8V3	OTTHUMG00000156762	ENST00000392692.3:c.989A>G	3.37:g.172480580A>G	ENSP00000376457:p.Tyr330Cys	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	144	74	0.513889	NM_001258315	Q0MT80|Q2M269|Q6U836|Q9NSV8|Q9NVW9	Missense_Mutation	SNP	ENST00000392692.3	37	CCDS58860.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	A|A	16.30|16.30	3.083153|3.083153	0.55861|0.55861	6.81E-4|6.81E-4	2.33E-4|2.33E-4	ENSG00000114346|ENSG00000114346	ENST00000444250|ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000441497;ENST00000540509	.|T;T;T;T;T;T	.|0.79141	.|-1.24;-1.24;-1.24;-1.24;-1.24;-1.24	5.84|5.84	4.65|4.65	0.58169|0.58169	.|.	.|0.105654	.|0.64402	.|D	.|0.000003	D|D	0.85106|0.85106	0.5621|0.5621	M|M	0.73598|0.73598	2.24|2.24	0.53688|0.53688	D|D	0.999974|0.999974	.|P;D;P;P	.|0.58620	.|0.783;0.983;0.941;0.929	.|B;P;P;P	.|0.61003	.|0.325;0.882;0.753;0.525	D|D	0.85632|0.85632	0.1271|0.1271	5|10	.|0.62326	.|D	.|0.03	-13.9317|-13.9317	11.9979|11.9979	0.53214|0.53214	0.8666:0.0:0.0:0.1334|0.8666:0.0:0.0:0.1334	.|.	.|330;330;299;298	.|Q9H8V3;Q9H8V3-3;G5E9L8;Q9H8V3-2	.|ECT2_HUMAN;.;.;.	V|C	2|299;330;299;298;299;330	.|ENSP00000232458:Y299C;ENSP00000376457:Y330C;ENSP00000401910:Y299C;ENSP00000415876:Y298C;ENSP00000412259:Y299C;ENSP00000443160:Y330C	.|ENSP00000232458:Y299C	M|Y	+|+	1|2	0|0	ECT2|ECT2	173963274|173963274	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.323000|4.323000	0.59221|0.59221	0.990000|0.990000	0.38787|0.38787	0.482000|0.482000	0.46254|0.46254	ATG|TAT	A|0.999;G|0.001	0.001	strong		0.313	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	NM_018098	
DOCK4	9732	hgsc.bcm.edu	37	7	111400275	111400275	+	Missense_Mutation	SNP	T	T	C	rs374962931		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:111400275T>C	ENST00000437633.1	-	39	4353	c.4097A>G	c.(4096-4098)aAc>aGc	p.N1366S	DOCK4_ENST00000494651.2_Missense_Mutation_p.N249S|DOCK4_ENST00000428084.1_Missense_Mutation_p.N1375S	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1366	DHR-2.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				ATCGGGCTGGTTGGCGTGCTG	0.552																																					p.N1366S		Atlas-SNP	.											.	DOCK4	365	.	0			c.A4097G						PASS	.	T	SER/ASN	2,4310		0,2,2154	184.0	186.0	185.0		4097	4.6	1.0	7		185	0,8506		0,0,4253	no	missense	DOCK4	NM_014705.3	46	0,2,6407	CC,CT,TT		0.0,0.0464,0.0156	benign	1366/1967	111400275	2,12816	2156	4253	6409	SO:0001583	missense	9732	exon39			GGCTGGTTGGCGT		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.4097A>G	7.37:g.111400275T>C	ENSP00000404179:p.Asn1366Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	139	63	0.453237	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.83|11.83	1.755933|1.755933	0.31137|0.31137	4.64E-4|4.64E-4	0.0|0.0	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288|ENST00000423057;ENST00000445943	T;T;T|.	0.05996|.	4.12;3.36;4.12|.	4.62|4.62	4.62|4.62	0.57501|0.57501	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53965|0.53965	0.1829|0.1829	L|L	0.29908|0.29908	0.895|0.895	0.49798|0.49798	D|D	0.999821|0.999821	B;B;B;B;B|.	0.28998|.	0.112;0.178;0.22;0.23;0.178|.	B;B;B;B;B|.	0.30716|.	0.023;0.051;0.119;0.119;0.084|.	T|T	0.50931|0.50931	-0.8769|-0.8769	10|5	0.02654|.	T|.	1|.	.|.	14.4645|14.4645	0.67475|0.67475	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	273;249;1411;1366;1375|.	B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2|.	.;.;.;DOCK4_HUMAN;.|.	S|A	1354;1375;249;1366;1363|827;1399	ENSP00000410746:N1375S;ENSP00000440944:N249S;ENSP00000404179:N1366S|.	ENSP00000345432:N1363S|.	N|T	-|-	2|1	0|0	DOCK4|DOCK4	111187511|111187511	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.086000|6.086000	0.71352|0.71352	2.066000|2.066000	0.61787|0.61787	0.482000|0.482000	0.46254|0.46254	AAC|ACC	.	.	weak		0.552	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
RABEP1	9135	hgsc.bcm.edu	37	17	5284719	5284719	+	Silent	SNP	T	T	C	rs1065482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5284719T>C	ENST00000546142.2	+	17	2593	c.2406T>C	c.(2404-2406)aaT>aaC	p.N802N	NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000537505.1_Silent_p.N759N|RABEP1_ENST00000408982.2_Silent_p.N769N|RABEP1_ENST00000341923.6_Silent_p.N769N|RABEP1_ENST00000262477.6_Silent_p.N802N			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	802					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						AAGAGAAGAATAAAGCTCAGA	0.393													C|||	2765	0.552117	0.3964	0.4251	5008	,	,		21936	0.8254		0.4394	False		,,,				2504	0.6871				p.N802N		Atlas-SNP	.											.	RABEP1	59	.	0			c.T2406C						PASS	.	C	,	1531,2177		327,877,650	86.0	85.0	85.0		2307,2406	1.4	1.0	17	dbSNP_86	85	3199,4993		619,1961,1516	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	946,2838,2166	CC,CT,TT		39.0503,41.2891,39.7479	,	769/830,802/863	5284719	4730,7170	1854	4096	5950	SO:0001819	synonymous_variant	9135	exon17			GAAGAATAAAGCT	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2406T>C	17.37:g.5284719T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			T|0.500;C|0.500	0.500	strong		0.393	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
MKI67	4288	hgsc.bcm.edu	37	10	129906468	129906468	+	Silent	SNP	C	C	T	rs4750936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129906468C>T	ENST00000368654.3	-	13	4011	c.3636G>A	c.(3634-3636)caG>caA	p.Q1212Q	MKI67_ENST00000368653.3_Silent_p.Q852Q	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1212	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)				CCTTAGGAGTCTGTAGCTGTC	0.493													T|||	1164	0.232428	0.3419	0.2277	5008	,	,		19866	0.2609		0.1571	False		,,,				2504	0.136				p.Q1212Q		Atlas-SNP	.											.	MKI67	363	.	0			c.G3636A						PASS	.	T	,	1357,3049	692.1+/-405.5	206,945,1052	138.0	135.0	136.0		2556,3636	-2.9	0.0	10	dbSNP_111	136	1491,7109	749.1+/-407.4	137,1217,2946	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	343,2162,3998	TT,TC,CC		17.3372,30.7989,21.8976	,	852/2897,1212/3257	129906468	2848,10158	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			AGGAGTCTGTAGC	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.3636G>A	10.37:g.129906468C>T		Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	325	158	0.486154	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			C|0.782;T|0.218	0.218	strong		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
MYO18B	84700	hgsc.bcm.edu	37	22	26423124	26423124	+	Missense_Mutation	SNP	G	G	C	rs6004901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26423124G>C	ENST00000407587.2	+	43	7356	c.7187G>C	c.(7186-7188)gGc>gCc	p.G2396A	MYO18B_ENST00000536101.1_Missense_Mutation_p.G2395A|MYO18B_ENST00000335473.7_Missense_Mutation_p.G2395A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2395						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GACGATGCGGGCTGTCCAGAC	0.592													G|||	488	0.0974441	0.2663	0.0476	5008	,	,		15885	0.004		0.0348	False		,,,				2504	0.0654				p.G2395A		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7184C						PASS	.	G	ALA/GLY	855,3101		95,665,1218	66.0	72.0	70.0		7184	-1.6	0.0	22	dbSNP_114	70	253,8029		6,241,3894	yes	missense	MYO18B	NM_032608.5	60	101,906,5112	CC,CG,GG		3.0548,21.6127,9.0538	benign	2395/2568	26423124	1108,11130	1978	4141	6119	SO:0001583	missense	84700	exon43			ATGCGGGCTGTCC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7187G>C	22.37:g.26423124G>C	ENSP00000386096:p.Gly2396Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		166|166	0.076007326007326|0.076007326007326	119|119	0.241869918699187|0.241869918699187	22|22	0.06077348066298342|0.06077348066298342	4|4	0.006993006993006993|0.006993006993006993	21|21	0.027704485488126648|0.027704485488126648	G|G	0.007|0.007	-1.985354|-1.985354	0.00443|0.00443	0.216127|0.216127	0.030548|0.030548	ENSG00000133454|ENSG00000133454	ENST00000543971|ENST00000536101;ENST00000335473;ENST00000407587	.|D;D;D	.|0.86956	.|-2.17;-2.17;-2.19	5.12|5.12	-1.6|-1.6	0.08426|0.08426	.|.	.|0.491877	.|0.18417	.|N	.|0.141867	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.45581|0.45581	1.43|1.43	0.80722|0.80722	P|P	0.0|0.0	.|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;0.001;0.001;0.003;0.003	T|T	0.02877|0.02877	-1.1099|-1.1099	4|9	.|0.19147	.|T	.|0.46	.|.	1.509|1.509	0.02492|0.02492	0.1649:0.2383:0.3545:0.2424|0.1649:0.2383:0.3545:0.2424	rs6004901;rs52824215;rs6004901|rs6004901;rs52824215;rs6004901	.|1908;2397;2395;2396;2395	.|Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.|.;.;MY18B_HUMAN;.;.	P|A	345|2395;2395;2396	.|ENSP00000441229:G2395A;ENSP00000334563:G2395A;ENSP00000386096:G2396A	.|ENSP00000334563:G2395A	A|G	+|+	1|2	0|0	MYO18B|MYO18B	24753124|24753124	0.003000|0.003000	0.15002|0.15002	0.011000|0.011000	0.14972|0.14972	0.130000|0.130000	0.20726|0.20726	0.135000|0.135000	0.15952|0.15952	0.154000|0.154000	0.19237|0.19237	-0.264000|-0.264000	0.10439|0.10439	GCT|GGC	G|0.912;C|0.088	0.088	strong		0.592	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
KRT3	3850	hgsc.bcm.edu	37	12	53189696	53189696	+	Missense_Mutation	SNP	C	C	G	rs28721426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53189696C>G	ENST00000417996.2	-	1	205	c.131G>C	c.(130-132)gGc>gCc	p.G44A	KRT3_ENST00000309505.3_Missense_Mutation_p.G44A	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	44	Gly-rich.|Head.		G -> A (in dbSNP:rs28721426).		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						GCTCCGGAAGCCATAGGCCCC	0.682													C|||	693	0.138379	0.2943	0.1167	5008	,	,		14277	0.002		0.163	False		,,,				2504	0.0583				p.G44A		Atlas-SNP	.											.	KRT3	65	.	0			c.G131C						PASS	.	C	ALA/GLY	1173,3233	401.5+/-332.0	155,863,1185	43.0	58.0	53.0		131	4.9	0.4	12	dbSNP_125	53	1542,7056	283.6+/-296.2	171,1200,2928	yes	missense	KRT3	NM_057088.2	60	326,2063,4113	GG,GC,CC		17.9344,26.6228,20.8782	probably-damaging	44/629	53189696	2715,10289	2203	4299	6502	SO:0001583	missense	3850	exon1			CGGAAGCCATAGG		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.131G>C	12.37:g.53189696C>G	ENSP00000413479:p.Gly44Ala	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	108	57	0.527778	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	37	CCDS44895.1	317	0.14514652014652016	147	0.29878048780487804	45	0.12430939226519337	0	0.0	125	0.16490765171503957	c	8.538	0.872561	0.17322	0.266228	0.179344	ENSG00000186442	ENST00000417996;ENST00000309505	D;D	0.93763	-3.28;-3.28	4.94	4.94	0.65067	.	0.000000	0.47852	D	0.000218	T	0.00039	0.0001	L	0.28504	0.86	0.31019	P	0.718341	D	0.71674	0.998	P	0.61533	0.89	T	0.00000	-1.3191	9	0.35671	T	0.21	.	16.0488	0.80740	0.0:1.0:0.0:0.0	rs28721426;rs59935660	44	P12035	K2C3_HUMAN	A	44	ENSP00000413479:G44A;ENSP00000312206:G44A	ENSP00000312206:G44A	G	-	2	0	KRT3	51475963	0.699000	0.27786	0.381000	0.26106	0.020000	0.10135	4.308000	0.59129	2.460000	0.83146	0.555000	0.69702	GGC	C|0.847;G|0.153	0.153	strong		0.682	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
HLA-E	3133	hgsc.bcm.edu	37	6	30458933	30458933	+	Silent	SNP	G	G	C	rs11548296	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30458933G>C	ENST00000376630.4	+	4	695	c.630G>C	c.(628-630)gtG>gtC	p.V210V		NM_005516.5	NP_005507.3	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	210	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protection from natural killer cell mediated cytotoxicity (GO:0042270)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)|ovary(3)|skin(1)|urinary_tract(1)	18						AGACACACGTGACTCACCACC	0.582													G|||	138	0.0275559	0.0847	0.0159	5008	,	,		19155	0.001		0.0099	False		,,,				2504	0.0041				p.V210V		Atlas-SNP	.											.	HLA-E	35	.	0			c.G630C						PASS	.	G		194,2828		6,182,1323	126.0	146.0	139.0		630	0.6	0.7	6	dbSNP_120	139	58,5360		0,58,2651	no	coding-synonymous	HLA-E	NM_005516.5		6,240,3974	CC,CG,GG		1.0705,6.4196,2.9858		210/359	30458933	252,8188	1511	2709	4220	SO:0001819	synonymous_variant	3133	exon4			ACACGTGACTCAC	M20022	CCDS34379.1	6p21.3	2013-01-11			ENSG00000204592	ENSG00000204592		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4962	protein-coding gene	gene with protein product		143010				3131426	Standard	NM_005516		Approved		uc003nqg.3	P13747	OTTHUMG00000031155	ENST00000376630.4:c.630G>C	6.37:g.30458933G>C		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	236	122	0.516949	NM_005516	Q30169|Q9BT83|Q9GIY7|Q9GIY8	Silent	SNP	ENST00000376630.4	37	CCDS34379.1																																																																																			G|0.977;C|0.023	0.023	strong		0.582	HLA-E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076282.2	NM_005516	
CNGA2	1260	hgsc.bcm.edu	37	X	150912502	150912502	+	Silent	SNP	G	G	A	rs113295831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:150912502G>A	ENST00000329903.4	+	6	1560	c.1527G>A	c.(1525-1527)caG>caA	p.Q509Q		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	509					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)					GTGTGACTCAGTATGCTCTGC	0.512													G|||	10	0.00264901	0.0015	0.0014	3775	,	,		16976	0.0		0.007	False		,,,				2504	0.0				p.Q509Q		Atlas-SNP	.											.	CNGA2	136	.	0			c.G1527A						PASS	.	G		5,3830		0,4,1,1628,570	170.0	139.0	150.0		1527	1.6	1.0	X	dbSNP_132	150	48,6680		0,34,14,2394,1858	no	coding-synonymous	CNGA2	NM_005140.1		0,38,15,4022,2428	AA,AG,A,GG,G		0.7134,0.1304,0.5018		509/665	150912502	53,10510	2203	4300	6503	SO:0001819	synonymous_variant	1260	exon7			GACTCAGTATGCT	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.1527G>A	X.37:g.150912502G>A		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	239	140	0.585774	NM_005140	A0AVD0	Silent	SNP	ENST00000329903.4	37	CCDS14701.1																																																																																			G|0.996;A|0.004	0.004	strong		0.512	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140	
SH3TC1	54436	hgsc.bcm.edu	37	4	8228948	8228948	+	Silent	SNP	T	T	C	rs55642964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:8228948T>C	ENST00000245105.3	+	12	1594	c.1527T>C	c.(1525-1527)ccT>ccC	p.P509P	SH3TC1_ENST00000514274.1_3'UTR|SH3TC1_ENST00000539824.1_Silent_p.P433P	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	509										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						TGAACGCCCCTGGGTACAAGG	0.657													C|||	1150	0.229633	0.0749	0.2723	5008	,	,		16902	0.3274		0.3211	False		,,,				2504	0.2137				p.P509P	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.T1527C						PASS	.	C		506,3880		26,454,1713	17.0	14.0	15.0		1527	-9.3	0.0	4	dbSNP_129	15	2668,5920		452,1764,2078	no	coding-synonymous	SH3TC1	NM_018986.3		478,2218,3791	CC,CT,TT		31.0666,11.5367,24.4643		509/1337	8228948	3174,9800	2193	4294	6487	SO:0001819	synonymous_variant	54436	exon12			CGCCCCTGGGTAC	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.1527T>C	4.37:g.8228948T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	37	CCDS3399.1																																																																																			T|0.759;C|0.241	0.241	strong		0.657	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
GPR101	83550	hgsc.bcm.edu	37	X	136112707	136112707	+	Missense_Mutation	SNP	A	A	G	rs5931046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:136112707A>G	ENST00000298110.1	-	1	1126	c.1127T>C	c.(1126-1128)cTc>cCc	p.L376P		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	376			L -> P (in dbSNP:rs5931046).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					ACTGGGTGGGAGGCTCTCCGG	0.507													A|||	809	0.214305	0.1952	0.0879	3775	,	,		16325	0.1022		0.1302	False		,,,				2504	0.2618				p.L376P		Atlas-SNP	.											.	GPR101	96	.	0			c.T1127C						PASS	.	A	PRO/LEU	820,3015		90,506,134,1036,437	208.0	168.0	182.0		1127	2.8	0.3	X	dbSNP_114	182	993,5735		44,606,299,1778,1573	yes	missense	GPR101	NM_054021.1	98	134,1112,433,2814,2010	GG,GA,G,AA,A		14.7592,21.382,17.1637	benign	376/509	136112707	1813,8750	2203	4300	6503	SO:0001583	missense	83550	exon1			GGTGGGAGGCTCT	AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"""GPCR / Class A : Orphans"""	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.1127T>C	X.37:g.136112707A>G	ENSP00000298110:p.Leu376Pro	Somatic	469	1	0.0021322		WXS	Illumina HiSeq	Phase_I	480	170	0.354167	NM_054021	Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	37	CCDS14662.1	263	0.15852923447860157	69	0.1597222222222222	22	0.0658682634730539	29	0.053703703703703705	57	0.08073654390934844	A	11.49	1.655079	0.29425	0.21382	0.147592	ENSG00000165370	ENST00000298110	T	0.65732	-0.17	5.37	2.76	0.32466	GPCR, rhodopsin-like superfamily (1);	0.939181	0.08641	N	0.915523	T	0.00073	0.0002	N	0.22421	0.69	0.58432	P	5.999999999950489E-6	P	0.42123	0.771	P	0.52514	0.701	T	0.06127	-1.0844	9	0.34782	T	0.22	-2.6823	8.445	0.32836	0.6002:0.3998:0.0:0.0	rs5931046;rs6635366;rs58517641;rs5931046	376	Q96P66	GP101_HUMAN	P	376	ENSP00000298110:L376P	ENSP00000298110:L376P	L	-	2	0	GPR101	135940373	0.023000	0.18921	0.257000	0.24404	0.938000	0.57974	0.345000	0.19979	0.768000	0.33290	0.430000	0.28490	CTC	A|0.808;0|0.012	.	strong		0.507	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1		
TNS1	7145	hgsc.bcm.edu	37	2	218674614	218674614	+	Silent	SNP	C	C	T	rs13417442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218674614C>T	ENST00000171887.4	-	30	5345	c.4893G>A	c.(4891-4893)acG>acA	p.T1631T	TNS1_ENST00000419504.1_Silent_p.T1617T|TNS1_ENST00000430930.1_Silent_p.T1610T	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1631					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)		TGGCAGCTGGCGTGGGGTCTG	0.562																																					p.T1631T		Atlas-SNP	.											.	TNS1	251	.	0			c.G4893A						PASS	.			188,4218	120.8+/-158.4	8,172,2023	93.0	84.0	87.0		4893	-5.2	0.9	2	dbSNP_121	87	628,7972	162.5+/-215.2	27,574,3699	yes	coding-synonymous	TNS1	NM_022648.4		35,746,5722	TT,TC,CC		7.3023,4.2669,6.274		1631/1736	218674614	816,12190	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon30			AGCTGGCGTGGGG	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.4893G>A	2.37:g.218674614C>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	230	136	0.591304	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			C|0.934;T|0.066	0.066	strong		0.562	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
PABPC3	5042	hgsc.bcm.edu	37	13	25671755	25671755	+	Silent	SNP	G	G	A	rs116223079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25671755G>A	ENST00000281589.3	+	1	1456	c.1419G>A	c.(1417-1419)acG>acA	p.T473T		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	473					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		TCATGTCAACGCAGCGTGTTG	0.537																																					p.T473T		Atlas-SNP	.											PABPC3,bladder,carcinoma,+1,1	PABPC3	129	1	0			c.G1419A						scavenged	.						96.0	87.0	90.0					13																	25671755		2203	4300	6503	SO:0001819	synonymous_variant	5042	exon1			GTCAACGCAGCGT	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1419G>A	13.37:g.25671755G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	116	5	0.0431034	NM_030979	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	37	CCDS9311.1																																																																																			G|0.911;A|0.089	0.089	strong		0.537	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
TNS1	7145	hgsc.bcm.edu	37	2	218683257	218683257	+	Silent	SNP	A	A	G	rs2571442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218683257A>G	ENST00000171887.4	-	24	3938	c.3486T>C	c.(3484-3486)gcT>gcC	p.A1162A	TNS1_ENST00000419504.1_Silent_p.A1149A|TNS1_ENST00000430930.1_Silent_p.A1141A	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1162					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)		ACTGAGCTCGAGCCTGGCTTT	0.612													G|||	2016	0.402556	0.4977	0.4294	5008	,	,		18855	0.246		0.4066	False		,,,				2504	0.4121				p.A1162A		Atlas-SNP	.											.	TNS1	251	.	0			c.T3486C						PASS	.	G		2023,2383	612.3+/-391.9	468,1087,648	55.0	59.0	57.0		3486	0.2	0.9	2	dbSNP_100	57	3561,5039	627.6+/-398.0	749,2063,1488	no	coding-synonymous	TNS1	NM_022648.4		1217,3150,2136	GG,GA,AA		41.407,45.9147,42.934		1162/1736	218683257	5584,7422	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon24			AGCTCGAGCCTGG	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.3486T>C	2.37:g.218683257A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	180	178	0.988889	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			T|0.000;G|0.418;A|0.582	0.418	strong		0.612	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
PLIN4	729359	hgsc.bcm.edu	37	19	4508905	4508905	+	Missense_Mutation	SNP	C	C	T	rs77763884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4508905C>T	ENST00000301286.3	-	4	3534	c.3535G>A	c.(3535-3537)Gtt>Att	p.V1179I		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1179						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						CCTAAACGAACGAAGTAGCTC	0.652													C|||	176	0.0351438	0.0794	0.0144	5008	,	,		15863	0.0		0.0129	False		,,,				2504	0.0491				p.V1179I		Atlas-SNP	.											PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	0			c.G3535A						PASS	.	C	ILE/VAL	281,3785		9,263,1761	40.0	50.0	46.0		3535	1.8	0.0	19	dbSNP_131	46	125,8221		1,123,4049	yes	missense	PLIN4	NM_001080400.1	29	10,386,5810	TT,TC,CC		1.4977,6.911,3.271	possibly-damaging	1179/1358	4508905	406,12006	2033	4173	6206	SO:0001583	missense	729359	exon4			AACGAACGAAGTA	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.3535G>A	19.37:g.4508905C>T	ENSP00000301286:p.Val1179Ile	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	50	0.022893772893772892	38	0.07723577235772358	4	0.011049723756906077	0	0.0	8	0.010554089709762533	C	10.25	1.298940	0.23650	0.06911	0.014977	ENSG00000167676	ENST00000301286	T	0.22539	1.95	5.11	1.78	0.24846	.	0.365586	0.19456	N	0.113801	T	0.00845	0.0028	L	0.49778	1.585	0.09310	N	1	P	0.47409	0.895	B	0.42692	0.395	T	0.10405	-1.0631	10	0.22706	T	0.39	-16.8474	7.0052	0.24831	0.0:0.7005:0.0:0.2995	.	1179	Q96Q06	PLIN4_HUMAN	I	1179	ENSP00000301286:V1179I	ENSP00000301286:V1179I	V	-	1	0	PLIN4	4459905	0.919000	0.31177	0.002000	0.10522	0.005000	0.04900	1.756000	0.38390	0.165000	0.19558	-0.300000	0.09419	GTT	C|0.979;T|0.021	0.021	strong		0.652	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
TAS2R20	259295	hgsc.bcm.edu	37	12	11150054	11150054	+	Missense_Mutation	SNP	C	C	T	rs79420812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11150054C>T	ENST00000538986.1	-	1	420	c.421G>A	c.(421-423)Gtt>Att	p.V141I	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	141				VCH -> ICQ (in Ref. 3; AAU21140). {ECO:0000305}.	sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V141I(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						AGGTGACAAACCAAAAAGAAC	0.388													C|||	916	0.182907	0.0371	0.1225	5008	,	,		20886	0.3185		0.2227	False		,,,				2504	0.2423				p.V141I		Atlas-SNP	.											TAS2R20,NS,carcinoma,0,1	TAS2R20	17	1	1	Substitution - Missense(1)	ovary(1)	c.G421A						PASS	.	C	ILE/VAL	239,4167	139.6+/-175.2	7,225,1971	128.0	114.0	118.0		421	-5.9	0.0	12	dbSNP_131	118	1704,6896	311.7+/-310.5	167,1370,2763	yes	missense	TAS2R20	NM_176889.2	29	174,1595,4734	TT,TC,CC		19.814,5.4244,14.9393	benign	141/310	11150054	1943,11063	2203	4300	6503	SO:0001583	missense	259295	exon1			GACAAACCAAAAA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.421G>A	12.37:g.11150054C>T	ENSP00000441624:p.Val141Ile	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	402	0.18406593406593408	19	0.03861788617886179	50	0.13812154696132597	171	0.29895104895104896	162	0.21372031662269128	C	2.515	-0.312165	0.05422	0.054244	0.19814	ENSG00000255837	ENST00000538986	T	0.36340	1.26	2.93	-5.87	0.02297	.	0.867467	0.09448	U	0.800842	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.12156	0.007	T	0.39078	-0.9631	9	0.25751	T	0.34	.	1.3021	0.02081	0.4189:0.2764:0.1245:0.1802	.	141	P59543	T2R20_HUMAN	I	141	ENSP00000441624:V141I	ENSP00000441624:V141I	V	-	1	0	TAS2R20	11041321	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.252000	0.00539	-1.958000	0.01019	-0.964000	0.02622	GTT	C|0.838;T|0.162	0.162	strong		0.388	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
LAMTOR1	55004	hgsc.bcm.edu	37	11	71817250	71817250	+	5'Flank	SNP	G	G	A	rs181092713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71817250G>A	ENST00000278671.5	-	0	0				snoU13_ENST00000459046.1_RNA|LAMTOR1_ENST00000538404.1_5'Flank|LRTOMT_ENST00000435085.1_Missense_Mutation_p.V118I|LAMTOR1_ENST00000535107.1_5'Flank|LRTOMT_ENST00000307198.7_Missense_Mutation_p.V118I|LRTOMT_ENST00000419228.1_Missense_Mutation_p.V78I|LRTOMT_ENST00000439209.1_Intron|LAMTOR1_ENST00000545249.1_5'Flank	NM_017907.2	NP_060377.1	Q6IAA8	LTOR1_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 1						cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|cholesterol homeostasis (GO:0042632)|endosome localization (GO:0032439)|endosome organization (GO:0007032)|lysosome localization (GO:0032418)|lysosome organization (GO:0007040)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of TOR signaling (GO:0032008)|regulation of cholesterol efflux (GO:0010874)|regulation of cholesterol esterification (GO:0010872)|regulation of cholesterol import (GO:0060620)|regulation of receptor recycling (GO:0001919)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|Ragulator complex (GO:0071986)				cervix(1)	1						CATGGGGCCTGTCAAAGGTCA	0.562													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18621	0.0		0.0	False		,,,				2504	0.0				p.V118I		Atlas-SNP	.											.	LRTOMT	20	.	0			c.G352A						PASS	.	G	ILE/VAL	21,1363		0,21,671	35.0	38.0	37.0		352	1.4	1.0	11		37	0,3182		0,0,1591	no	missense	LRTOMT	NM_001145308.2	29	0,21,2262	AA,AG,GG		0.0,1.5173,0.4599	benign	118/292	71817250	21,4545	692	1591	2283	SO:0001631	upstream_gene_variant	220074	exon7			GGGCCTGTCAAAG	AK000632	CCDS8209.1	11q13.4	2011-05-18	2011-02-15	2011-02-15	ENSG00000149357	ENSG00000149357			26068	protein-coding gene	gene with protein product	"""p27kip1 releasing factor from RhoA"", ""protein associated with DRMs and endosomes"""	613510	"""chromosome 11 open reading frame 59"""	C11orf59		12358155	Standard	NM_017907		Approved	FLJ20625, p18, p27RF-Rho, Pdro, Ragulator1	uc001ort.3	Q6IAA8	OTTHUMG00000167869		11.37:g.71817250G>A	Exception_encountered	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	15	6	0.4	NM_001145309	Q8WZ09|Q9NWT0	Missense_Mutation	SNP	ENST00000278671.5	37	CCDS8209.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	13.30	2.195071	0.38806	0.015173	0.0	ENSG00000184154	ENST00000419228;ENST00000435085;ENST00000307198	T;T;T	0.21734	1.99;1.99;1.99	4.59	1.43	0.22495	.	.	.	.	.	T	0.05364	0.0142	N	0.21240	0.645	0.21445	N	0.99969	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.26573	-1.0099	9	0.38643	T	0.18	-3.0892	2.2276	0.03988	0.1802:0.2893:0.404:0.1265	.	118;78	Q8WZ04;Q8WZ04-2	TOMT_HUMAN;.	I	78;118;118	ENSP00000392233:V78I;ENSP00000409789:V118I;ENSP00000305742:V118I	ENSP00000305742:V78I	V	+	1	0	LRTOMT	71494898	0.617000	0.27043	0.999000	0.59377	0.980000	0.70556	1.049000	0.30392	0.642000	0.30620	0.462000	0.41574	GTC	G|0.998;A|0.002	0.002	strong		0.562	LAMTOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396733.1	NM_017907	
SERPINF1	5176	hgsc.bcm.edu	37	17	1680002	1680002	+	Silent	SNP	T	T	C	rs6828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1680002T>C	ENST00000254722.4	+	7	1126	c.963T>C	c.(961-963)taT>taC	p.Y321Y		NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	321					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						AGCTGAGTTATGAAGGCGAAG	0.552													C|||	3890	0.776757	0.9198	0.7565	5008	,	,		20324	0.7758		0.7386	False		,,,				2504	0.638				p.Y321Y		Atlas-SNP	.											.	SERPINF1	31	.	0			c.T963C						PASS	.	C		3928,478	225.2+/-241.2	1746,436,21	111.0	101.0	104.0		963	-8.6	0.1	17	dbSNP_52	104	6088,2512	411.9+/-350.6	2162,1764,374	no	coding-synonymous	SERPINF1	NM_002615.5		3908,2200,395	CC,CT,TT		29.2093,10.8488,22.9894		321/419	1680002	10016,2990	2203	4300	6503	SO:0001819	synonymous_variant	5176	exon7			GAGTTATGAAGGC	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.963T>C	17.37:g.1680002T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	138	58	0.42029	NM_002615	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Silent	SNP	ENST00000254722.4	37	CCDS11012.1																																																																																			C|0.782;G|0.000;N|0.000;T|0.218	0.782	strong		0.552	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615	
DNAH9	1770	hgsc.bcm.edu	37	17	11687721	11687721	+	Silent	SNP	G	G	A	rs16945337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11687721G>A	ENST00000262442.4	+	41	7994	c.7926G>A	c.(7924-7926)gcG>gcA	p.A2642A	DNAH9_ENST00000454412.2_Silent_p.A2642A	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2642	AAA 3. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		ACTTCCCGGCGTCCCTGCAGA	0.542													G|||	239	0.0477236	0.0877	0.0058	5008	,	,		17425	0.002		0.0348	False		,,,				2504	0.0838				p.A2642A		Atlas-SNP	.											DNAH9,NS,carcinoma,+1,1	DNAH9	695	1	0			c.G7926A						PASS	.	G		358,4048	185.0+/-212.2	14,330,1859	177.0	169.0	172.0		7926	-2.6	0.0	17	dbSNP_123	172	195,8405	86.1+/-148.5	0,195,4105	no	coding-synonymous	DNAH9	NM_001372.3		14,525,5964	AA,AG,GG		2.2674,8.1253,4.2519		2642/4487	11687721	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon41			CCCGGCGTCCCTG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.7926G>A	17.37:g.11687721G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	192	91	0.473958	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.956;A|0.044	0.044	strong		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
MUC4	4585	hgsc.bcm.edu	37	3	195515113	195515113	+	Missense_Mutation	SNP	A	A	G	rs71321849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515113A>G	ENST00000463781.3	-	2	3797	c.3338T>C	c.(3337-3339)gTa>gCa	p.V1113A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V1113A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	544					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	0.567													.|||	247	0.0493211	0.1679	0.0202	5008	,	,		17898	0.001		0.005	False		,,,				2504	0.0051				p.V1113A		Atlas-SNP	.											.	MUC4	1505	.	0			c.T3338C						PASS	.						12.0	7.0	9.0					3																	195515113		666	1536	2202	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.3338T>C	3.37:g.195515113A>G	ENSP00000417498:p.Val1113Ala	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	335	34	0.101493	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	.	.	.	.	.	.	.	.	.	.	-	2.657	-0.280535	0.05642	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.46;1.46	0.814	-1.63	0.08345	.	.	.	.	.	T	0.16041	0.0386	N	0.19112	0.55	0.09310	N	1	B	0.15473	0.013	B	0.21546	0.035	T	0.32322	-0.9911	8	.	.	.	.	5.3188	0.15870	0.6312:0.0:0.3688:0.0	.	1113	E7ESK3	.	A	1113	ENSP00000417498:V1113A;ENSP00000420243:V1113A	.	V	-	2	0	MUC4	196999508	0.000000	0.05858	0.000000	0.03702	0.285000	0.27093	-0.337000	0.07852	-0.728000	0.04882	0.055000	0.15244	GTA	A|0.500;G|0.500	0.500	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PDE11A	50940	hgsc.bcm.edu	37	2	178682603	178682603	+	Silent	SNP	T	T	C	rs6720891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:178682603T>C	ENST00000286063.6	-	8	1943	c.1626A>G	c.(1624-1626)gcA>gcG	p.A542A	PDE11A_ENST00000449286.2_Silent_p.A184A|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000389683.3_Silent_p.A98A|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	83	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	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		
MYT1	4661	hgsc.bcm.edu	37	20	62871232	62871232	+	Silent	SNP	C	C	T	rs3003149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62871232C>T	ENST00000328439.1	+	22	3577	c.3213C>T	c.(3211-3213)ctC>ctT	p.L1071L	MYT1_ENST00000536311.1_Silent_p.L1098L	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					TCCAAAGTCTCGCCAATATCC	0.602													C|||	823	0.164337	0.3434	0.1095	5008	,	,		18477	0.005		0.1302	False		,,,				2504	0.1605				p.L1071L	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.C3213T						PASS	.	C		1334,3072	447.1+/-348.2	202,930,1071	108.0	111.0	110.0		3213	-11.4	0.7	20	dbSNP_101	110	972,7628	211.8+/-252.3	67,838,3395	no	coding-synonymous	MYT1	NM_004535.2		269,1768,4466	TT,TC,CC		11.3023,30.2769,17.7303		1071/1122	62871232	2306,10700	2203	4300	6503	SO:0001819	synonymous_variant	4661	exon22			AAGTCTCGCCAAT	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"""Zinc fingers, C2HC-type containing"""	7622	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 2"""	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.3213C>T	20.37:g.62871232C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000328439.1	37	CCDS13558.1																																																																																			C|0.826;T|0.174	0.174	strong		0.602	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238671940	238671940	+	Silent	SNP	C	C	T	rs15232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238671940C>T	ENST00000392000.4	+	11	1701	c.1584C>T	c.(1582-1584)aaC>aaT	p.N528N	LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000289175.6_Silent_p.N472N|LRRFIP1_ENST00000244815.5_Silent_p.N504N	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	528	DNA-binding.				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)		CTGAGGGCAACTGTCAGGAAG	0.473													T|||	741	0.147963	0.3238	0.0893	5008	,	,		19463	0.1369		0.0348	False		,,,				2504	0.0798				p.N528N		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.C1584T						PASS	.	T	,,,,	1336,3070	694.0+/-405.8	222,892,1089	81.0	86.0	84.0		,,1584,1416,1512	-2.2	0.0	2	dbSNP_52	84	249,8351	808.3+/-407.2	4,241,4055	no	intron,intron,coding-synonymous,coding-synonymous,coding-synonymous	LRRFIP1	NM_001137550.1,NM_001137551.1,NM_001137552.1,NM_001137553.1,NM_004735.3	,,,,	226,1133,5144	TT,TC,CC		2.8953,30.3223,12.1867	,,,,	,,528/809,472/753,504/785	238671940	1585,11421	2203	4300	6503	SO:0001819	synonymous_variant	9208	exon11			GGGCAACTGTCAG	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.1584C>T	2.37:g.238671940C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	114	64	0.561404	NM_001137552	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Silent	SNP	ENST00000392000.4	37	CCDS46552.1																																																																																			C|0.855;T|0.145	0.145	strong		0.473	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
PDK2	5164	hgsc.bcm.edu	37	17	48174794	48174794	+	Silent	SNP	C	C	T	rs11546968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48174794C>T	ENST00000503176.1	+	2	287	c.126C>T	c.(124-126)agC>agT	p.S42S	PDK2_ENST00000007708.3_5'UTR|PDK2_ENST00000511026.1_3'UTR	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	42					cellular metabolic process (GO:0044237)|cellular response to nutrient (GO:0031670)|cellular response to reactive oxygen species (GO:0034614)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of gluconeogenesis (GO:0006111)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						CAGGATCCAGCAATGCCTGTG	0.552									Autosomal Dominant Polycystic Kidney Disease				C|||	15	0.00299521	0.0113	0.0	5008	,	,		20973	0.0		0.0	False		,,,				2504	0.0				p.S42S		Atlas-SNP	.											.	PDK2	41	.	0			c.C126T						PASS	.	C	,,,	53,4353	52.9+/-88.7	0,53,2150	80.0	64.0	69.0		,,126,126	3.2	1.0	17	dbSNP_120	69	5,8595	4.3+/-15.6	0,5,4295	no	utr-5,utr-5,coding-synonymous,coding-synonymous	PDK2	NM_001199898.1,NM_001199899.1,NM_001199900.1,NM_002611.4	,,,	0,58,6445	TT,TC,CC		0.0581,1.2029,0.4459	,,,	,,42/200,42/408	48174794	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	5164	exon2	Familial Cancer Database	ADPKD	ATCCAGCAATGCC	L42451	CCDS11559.1, CCDS56039.1	17q21.33	2012-07-18	2005-11-16		ENSG00000005882	ENSG00000005882			8810	protein-coding gene	gene with protein product		602525	"""pyruvate dehydrogenase kinase, isoenzyme 2"""			7499431	Standard	NM_001199898		Approved	PDHK2	uc002iqc.3	Q15119	OTTHUMG00000161948	ENST00000503176.1:c.126C>T	17.37:g.48174794C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_002611	A8K3A7|B3KNW0|Q6P515|Q9BS05	Silent	SNP	ENST00000503176.1	37	CCDS11559.1																																																																																			C|0.997;T|0.003	0.003	strong		0.552	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2	NM_002611	
MED12	9968	hgsc.bcm.edu	37	X	70339715	70339715	+	Silent	SNP	A	A	G	rs201566660		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70339715A>G	ENST00000374080.3	+	3	416	c.384A>G	c.(382-384)caA>caG	p.Q128Q	MED12_ENST00000374102.1_Silent_p.Q128Q|MED12_ENST00000333646.6_Silent_p.Q128Q			Q93074	MED12_HUMAN	mediator complex subunit 12	128					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					CACTCACGCAACTAGCCAAAA	0.502			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome						.|||	9	0.00238411	0.0061	0.0014	3775	,	,		15678	0.0		0.0	False		,,,				2504	0.0				p.Q128Q		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.A384G						PASS	.	A		31,3377		0,27,4,1392,566	33.0	32.0	33.0		384	-3.8	1.0	X		33	0,6498		0,0,0,2353,1792	no	coding-synonymous	MED12	NM_005120.2		0,27,4,3745,2358	GG,GA,G,AA,A		0.0,0.9096,0.3129		128/2178	70339715	31,9875	1989	4145	6134	SO:0001819	synonymous_variant	9968	exon3			CACGCAACTAGCC	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.384A>G	X.37:g.70339715A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	152	68	0.447368	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1	2	0.0012055455093429777	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	.	6.865	0.528992	0.13127	0.009096	0.0	ENSG00000184634	ENST00000429213	.	.	.	5.73	-3.76	0.04359	.	.	.	.	.	T	0.33585	0.0868	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35226	-0.9797	4	.	.	.	-1.517	4.2759	0.10809	0.1879:0.4151:0.308:0.089	.	.	.	.	S	113	.	.	N	+	2	0	MED12	70256440	1.000000	0.71417	0.980000	0.43619	0.912000	0.54170	0.874000	0.28065	-0.477000	0.06832	-1.276000	0.01395	AAC	A|0.999;G|0.001	0.001	strong		0.502	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
MIS18BP1	55320	hgsc.bcm.edu	37	14	45693152	45693152	+	Missense_Mutation	SNP	A	A	G	rs190280845		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45693152A>G	ENST00000310806.4	-	11	3096	c.2638T>C	c.(2638-2640)Tgg>Cgg	p.W880R		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	880	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				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)			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						TTCTCATTCCATTCCTTATCC	0.368													A|||	1	0.000199681	0.0	0.0014	5008	,	,		19353	0.0		0.0	False		,,,				2504	0.0				p.W880R		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.T2638C						PASS	.	A	ARG/TRP	0,4406		0,0,2203	79.0	76.0	77.0		2638	5.7	1.0	14		77	2,8598	2.2+/-6.3	0,2,4298	no	missense	MIS18BP1	NM_018353.4	101	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	probably-damaging	880/1133	45693152	2,13004	2203	4300	6503	SO:0001583	missense	55320	exon11			CATTCCATTCCTT	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.2638T>C	14.37:g.45693152A>G	ENSP00000309790:p.Trp880Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	18.20	3.570745	0.65765	0.0	2.33E-4	ENSG00000129534	ENST00000310806	T	0.79845	-1.31	5.72	5.72	0.89469	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	D	0.89308	0.6678	M	0.79475	2.455	0.54753	D	0.999986	D	0.89917	1.0	D	0.87578	0.998	D	0.90273	0.4309	10	0.66056	D	0.02	-5.0352	14.245	0.65983	1.0:0.0:0.0:0.0	.	880	Q6P0N0	M18BP_HUMAN	R	880	ENSP00000309790:W880R	ENSP00000309790:W880R	W	-	1	0	MIS18BP1	44762902	1.000000	0.71417	0.999000	0.59377	0.850000	0.48378	3.594000	0.54008	2.311000	0.77944	0.533000	0.62120	TGG	A|1.000;G|0.000	0.000	strong		0.368	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2		
PRKAR1B	5575	hgsc.bcm.edu	37	7	720274	720274	+	Silent	SNP	A	A	G	rs200458521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:720274A>G	ENST00000406797.1	-	3	441	c.267T>C	c.(265-267)ccT>ccC	p.P89P	PRKAR1B_ENST00000360274.4_Silent_p.P89P|PRKAR1B_ENST00000544935.1_Silent_p.P89P|PRKAR1B_ENST00000403562.1_Silent_p.P89P|PRKAR1B_ENST00000537384.1_Silent_p.P89P	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	89	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CCTTCACCACAGGGTTCGGGG	0.632													a|||	9	0.00179712	0.0061	0.0014	5008	,	,		15949	0.0		0.0	False		,,,				2504	0.0				p.P89P		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.T267C						PASS	.	A	,,,,,	22,4384	24.3+/-50.5	0,22,2181	51.0	51.0	51.0		267,267,267,267,267,267	-9.8	0.1	7		51	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKAR1B	NM_001164758.1,NM_001164759.1,NM_001164760.1,NM_001164761.1,NM_001164762.1,NM_002735.2	,,,,,	0,22,6481	GG,GA,AA		0.0,0.4993,0.1692	,,,,,	89/382,89/382,89/382,89/382,89/382,89/382	720274	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	5575	exon3			CACCACAGGGTTC	M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	2.7.11.1		9390	protein-coding gene	gene with protein product		176911				1358799, 3479018	Standard	NM_002735		Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.267T>C	7.37:g.720274A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_001164760	Q8N422	Silent	SNP	ENST00000406797.1	37	CCDS34579.1																																																																																			A|0.998;G|0.002	0.002	strong		0.632	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1		
CNOT1	23019	hgsc.bcm.edu	37	16	58587737	58587737	+	Silent	SNP	C	C	T	rs11866002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58587737C>T	ENST00000317147.5	-	22	3251	c.2919G>A	c.(2917-2919)caG>caA	p.Q973Q	CNOT1_ENST00000569240.1_Silent_p.Q968Q|CNOT1_ENST00000569732.1_Intron|CNOT1_ENST00000441024.2_Silent_p.Q973Q|CNOT1_ENST00000245138.4_5'Flank	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	973	Interaction with ZFP36.				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)		AAGCCAAATGCTGACAATACT	0.368													C|||	2430	0.485224	0.6687	0.2983	5008	,	,		18562	0.5704		0.3211	False		,,,				2504	0.4509				p.Q973Q		Atlas-SNP	.											.	CNOT1	359	.	0			c.G2919A						PASS	.	C	,	2658,1738	646.7+/-398.4	835,988,375	128.0	128.0	128.0		2919,2919	2.9	1.0	16	dbSNP_120	128	2515,6085	411.5+/-350.5	380,1755,2165	no	coding-synonymous,coding-synonymous	CNOT1	NM_016284.3,NM_206999.1	,	1215,2743,2540	TT,TC,CC		29.2442,39.5359,39.8046	,	973/2377,973/1552	58587737	5173,7823	2198	4300	6498	SO:0001819	synonymous_variant	23019	exon22			CAAATGCTGACAA	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.2919G>A	16.37:g.58587737C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	37	CCDS10799.1																																																																																			C|0.556;T|0.444	0.444	strong		0.368	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
ABCA10	10349	hgsc.bcm.edu	37	17	67212046	67212046	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:67212046T>C	ENST00000269081.4	-	9	1677	c.768A>G	c.(766-768)ggA>ggG	p.G256G	ABCA10_ENST00000416101.2_Silent_p.G256G|ABCA10_ENST00000432313.2_Silent_p.G256G	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	256					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)					ACACAGTGAATCCCAGACATC	0.418																																					p.G256G		Atlas-SNP	.											ABCA10,NS,carcinoma,0,1	ABCA10	209	1	0			c.A768G						scavenged	.						74.0	74.0	74.0					17																	67212046		2203	4300	6503	SO:0001819	synonymous_variant	10349	exon9			AGTGAATCCCAGA	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.768A>G	17.37:g.67212046T>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	202	4	0.019802	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Silent	SNP	ENST00000269081.4	37	CCDS11684.1																																																																																			.	.	none		0.418	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282	
OR13F1	138805	hgsc.bcm.edu	37	9	107267352	107267352	+	Missense_Mutation	SNP	T	T	C	rs7847413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107267352T>C	ENST00000334726.2	+	1	898	c.809T>C	c.(808-810)aTa>aCa	p.I270T		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	270			I -> T (in dbSNP:rs7847413).			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(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						TCACAGGAAATAGACAAATTT	0.468													T|||	1178	0.235224	0.3457	0.1427	5008	,	,		17624	0.3284		0.1054	False		,,,				2504	0.1892				p.I270T		Atlas-SNP	.											.	OR13F1	75	.	0			c.T809C						PASS	.	T	THR/ILE	1394,3012	458.2+/-351.9	217,960,1026	86.0	84.0	84.0		809	1.9	0.9	9	dbSNP_116	84	852,7748	194.2+/-239.7	52,748,3500	yes	missense	OR13F1	NM_001004485.1	89	269,1708,4526	CC,CT,TT		9.907,31.6387,17.269	benign	270/320	107267352	2246,10760	2203	4300	6503	SO:0001583	missense	138805	exon1			AGGAAATAGACAA		CCDS35087.1	9q31.1	2013-09-24			ENSG00000186881	ENSG00000186881		"""GPCR / Class A : Olfactory receptors"""	14723	protein-coding gene	gene with protein product							Standard	NM_001004485		Approved		uc011lvm.2	Q8NGS4	OTTHUMG00000020404	ENST00000334726.2:c.809T>C	9.37:g.107267352T>C	ENSP00000334452:p.Ile270Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	118	44	0.372881	NM_001004485	Q6IF50	Missense_Mutation	SNP	ENST00000334726.2	37	CCDS35087.1	471	0.21565934065934067	160	0.3252032520325203	43	0.11878453038674033	188	0.32867132867132864	80	0.10554089709762533	T	6.365	0.435499	0.12045	0.316387	0.09907	ENSG00000186881	ENST00000334726	T	0.00115	8.71	4.3	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	0.265123	0.27613	N	0.018596	T	0.00012	0.0000	N	0.11000	0.08	0.46631	P	8.629999999999471E-4	B	0.16166	0.016	B	0.18871	0.023	T	0.00102	-1.2062	9	0.22706	T	0.39	.	7.4916	0.27464	0.0:0.1872:0.0:0.8128	rs7847413;rs52823428;rs7847413	270	Q8NGS4	O13F1_HUMAN	T	270	ENSP00000334452:I270T	ENSP00000334452:I270T	I	+	2	0	OR13F1	106307173	0.000000	0.05858	0.942000	0.38095	0.995000	0.86356	0.026000	0.13599	0.419000	0.25927	0.533000	0.62120	ATA	T|0.794;C|0.206	0.206	strong		0.468	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1		
SERPINB12	89777	hgsc.bcm.edu	37	18	61234144	61234144	+	Missense_Mutation	SNP	G	G	A	rs56812375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61234144G>A	ENST00000269491.1	+	7	1118	c.1118G>A	c.(1117-1119)cGa>cAa	p.R373Q	SERPINB12_ENST00000382768.1_Missense_Mutation_p.R393Q	NM_080474.1	NP_536722.1	Q96P63	SPB12_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 12	373					hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of protein catabolic process (GO:0042177)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(5)|lung(19)|skin(1)	26						AGGTCACTACGATCTTGGGTG	0.453													G|||	172	0.034345	0.1256	0.0086	5008	,	,		21067	0.0		0.0	False		,,,				2504	0.0				p.R373Q		Atlas-SNP	.											SERPINB12,colon,carcinoma,0,1	SERPINB12	55	1	0			c.G1118A						PASS	.	G	GLN/ARG	455,3951	218.1+/-236.3	27,401,1775	78.0	77.0	77.0		1118	3.3	0.0	18	dbSNP_129	77	1,8599		0,1,4299	yes	missense	SERPINB12	NM_080474.1	43	27,402,6074	AA,AG,GG		0.0116,10.3268,3.5061	benign	373/406	61234144	456,12550	2203	4300	6503	SO:0001583	missense	89777	exon7			CACTACGATCTTG	AF411191	CCDS11984.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166634	ENSG00000166634		"""Serine (or cysteine) peptidase inhibitors"""	14220	protein-coding gene	gene with protein product		615662	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 12"""			24172014	Standard	NM_080474		Approved	YUKOPIN	uc010xen.2	Q96P63	OTTHUMG00000132789	ENST00000269491.1:c.1118G>A	18.37:g.61234144G>A	ENSP00000269491:p.Arg373Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_080474	Q3SYB4	Missense_Mutation	SNP	ENST00000269491.1	37	CCDS11984.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	G	6.154	0.396700	0.11638	0.103268	1.16E-4	ENSG00000166634	ENST00000269491;ENST00000382768	D;D	0.84146	-1.81;-1.81	6.01	3.29	0.37713	Serpin domain (3);	2.339550	0.01636	N	0.023778	T	0.08179	0.0204	N	0.16656	0.425	0.09310	N	1	B;B	0.26363	0.147;0.004	B;B	0.29524	0.103;0.001	T	0.49303	-0.8954	10	0.12766	T	0.61	.	7.6332	0.28251	0.0:0.6835:0.1241:0.1924	rs56812375;rs61741590	393;373	Q3SYB4;Q96P63	.;SPB12_HUMAN	Q	373;393	ENSP00000269491:R373Q;ENSP00000372218:R393Q	ENSP00000269491:R373Q	R	+	2	0	SERPINB12	59385124	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.232000	0.09055	0.892000	0.36259	-0.133000	0.14855	CGA	G|0.972;A|0.028	0.028	strong		0.453	SERPINB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256197.1	NM_080474	
CR1	1378	hgsc.bcm.edu	37	1	207737312	207737312	+	Silent	SNP	T	T	C	rs56232421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207737312T>C	ENST00000367049.4	+	22	3690	c.3690T>C	c.(3688-3690)taT>taC	p.Y1230Y	RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367051.1_Silent_p.Y780Y|CR1_ENST00000367052.1_Intron|CR1_ENST00000367053.1_Silent_p.Y780Y|CR1_ENST00000400960.2_Silent_p.Y780Y	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	780	Sushi 19. {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)	p.Y1230Y(1)|p.Y780Y(1)|p.Y785Y(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						AGCCCGGCTATGACCTCAGAG	0.577													-|||	995	0.198682	0.4675	0.0749	5008	,	,		10279	0.1508		0.0308	False		,,,				2504	0.1452				p.Y1230Y		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,0,2	CR1	354	2	3	Substitution - coding silent(3)	prostate(3)	c.T3690C						scavenged	.						60.0	128.0	112.0					1																	207737312		1285	4057	5342	SO:0001819	synonymous_variant	1378	exon22			CGGCTATGACCTC	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.3690T>C	1.37:g.207737312T>C		Somatic	1018	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	37	CCDS44308.1																																																																																			C|1.000;|0.000	1.000	weak		0.577	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
OR1J1	347168	hgsc.bcm.edu	37	9	125239449	125239449	+	Missense_Mutation	SNP	G	G	A	rs192344372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125239449G>A	ENST00000259357.2	-	1	786	c.757C>T	c.(757-759)Cgg>Tgg	p.R253W	RP11-542K23.9_ENST00000412262.2_RNA	NM_001004451.1	NP_001004451.1	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J, 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)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	16						ATAATTGTCCGATAATAGATA	0.453													C|||	3	0.000599042	0.0023	0.0	5008	,	,		23406	0.0		0.0	False		,,,				2504	0.0				p.R253W		Atlas-SNP	.											OR1J1,colon,carcinoma,0,1	OR1J1	46	1	0			c.C757T						PASS	.						135.0	129.0	131.0					9																	125239449		2203	4300	6503	SO:0001583	missense	347168	exon1			TTGTCCGATAATA	AL353767	CCDS35120.1	9q33.2	2013-09-20			ENSG00000136834	ENSG00000136834		"""GPCR / Class A : Olfactory receptors"""	8208	protein-coding gene	gene with protein product							Standard	NM_001004451		Approved	hg32	uc011lyu.2	Q8NGS3	OTTHUMG00000020603	ENST00000259357.2:c.757C>T	9.37:g.125239449G>A	ENSP00000259357:p.Arg253Trp	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	137	92	0.671533	NM_001004451	A3KFL8|Q6IF10|Q96R88	Missense_Mutation	SNP	ENST00000259357.2	37	CCDS35120.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	18.97	3.734988	0.69189	.	.	ENSG00000136834	ENST00000259357	T	0.37058	1.22	4.93	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000015	T	0.23965	0.0580	N	0.24115	0.695	0.35696	D	0.81525	P	0.36874	0.572	B	0.26614	0.071	T	0.35176	-0.9799	10	0.87932	D	0	.	14.8875	0.70582	0.0:0.8554:0.1446:0.0	.	253	Q8NGS3	OR1J1_HUMAN	W	253	ENSP00000259357:R253W	ENSP00000259357:R253W	R	-	1	2	OR1J1	124279270	0.076000	0.21285	1.000000	0.80357	0.049000	0.14656	1.108000	0.31123	1.482000	0.48325	-0.181000	0.13052	CGG	G|0.999;A|0.001	0.001	strong		0.453	OR1J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053931.1		
COL20A1	57642	hgsc.bcm.edu	37	20	61944193	61944193	+	Silent	SNP	T	T	C	rs4809530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61944193T>C	ENST00000358894.6	+	16	2083	c.1983T>C	c.(1981-1983)gaT>gaC	p.D661D	COL20A1_ENST00000435874.1_Silent_p.D668D|COL20A1_ENST00000326996.6_Silent_p.D661D|COL20A1_ENST00000422202.1_Silent_p.D668D	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	661	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					TGCCAGGGGATGCAGTCCAGC	0.662													C|||	323	0.0644968	0.0847	0.036	5008	,	,		15857	0.0139		0.0527	False		,,,				2504	0.1217				p.D661D		Atlas-SNP	.											.	COL20A1	137	.	0			c.T1983C						PASS	.	C		264,3616		10,244,1686	18.0	25.0	22.0		1983	-8.3	0.0	20	dbSNP_111	22	460,7782		15,430,3676	no	coding-synonymous	COL20A1	NM_020882.2		25,674,5362	CC,CT,TT		5.5812,6.8041,5.9726		661/1285	61944193	724,11398	1940	4121	6061	SO:0001819	synonymous_variant	57642	exon16			AGGGGATGCAGTC	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.1983T>C	20.37:g.61944193T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	152	75	0.493421	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Silent	SNP	ENST00000358894.6	37	CCDS46628.1																																																																																			T|0.956;C|0.044	0.044	strong		0.662	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
DDX58	23586	hgsc.bcm.edu	37	9	32487521	32487521	+	Silent	SNP	T	T	C	rs2274863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:32487521T>C	ENST00000379883.2	-	9	1480	c.1323A>G	c.(1321-1323)acA>acG	p.T441T	DDX58_ENST00000545044.1_Silent_p.T238T|DDX58_ENST00000379868.1_Silent_p.T238T|DDX58_ENST00000379882.1_Silent_p.T396T|DDX58_ENST00000542096.1_Silent_p.T370T	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	441	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)		TGTGTTTGACTGTTGCTATCA	0.443													T|||	433	0.0864617	0.1505	0.0288	5008	,	,		19802	0.1617		0.0	False		,,,				2504	0.0521				p.T441T		Atlas-SNP	.											.	DDX58	82	.	0			c.A1323G						PASS	.	T		498,3908	230.1+/-244.4	34,430,1739	135.0	123.0	127.0		1323	1.0	1.0	9	dbSNP_100	127	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous	DDX58	NM_014314.3		34,446,6023	CC,CT,TT		0.186,11.3028,3.952		441/926	32487521	514,12492	2203	4300	6503	SO:0001819	synonymous_variant	23586	exon9			TTTGACTGTTGCT	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.1323A>G	9.37:g.32487521T>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	210	85	0.404762	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Silent	SNP	ENST00000379883.2	37	CCDS6526.1																																																																																			T|0.921;C|0.079	0.079	strong		0.443	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51918360	51918360	+	Missense_Mutation	SNP	A	A	G	rs61741672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51918360A>G	ENST00000339313.5	-	8	1449	c.1333T>C	c.(1333-1335)Tcc>Ccc	p.S445P	SIGLEC10_ENST00000432469.2_Intron|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.S445P|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.S387P|SIGLEC10_ENST00000353836.5_Intron|SIGLEC10_ENST00000436984.2_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000441969.3_Intron|SIGLEC10_ENST00000525998.1_Intron			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	445					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)		AGCTTCGGGGAGTCTGAGGGG	0.687													g|||	1213	0.242212	0.382	0.1974	5008	,	,		16798	0.2113		0.1471	False		,,,				2504	0.2147				p.S445P		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.T1333C						PASS	.	G	PRO/SER,,,,,,PRO/SER	1434,2972		248,938,1017	21.0	24.0	23.0		1159,,,,,,1333	-0.1	0.1	19	dbSNP_129	23	1173,7425		88,997,3214	no	missense,intron,intron,intron,intron,intron,missense	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	74,,,,,,74	336,1935,4231	GG,GA,AA		13.6427,32.5465,20.0477	benign,,,,,,benign	387/640,,,,,,445/698	51918360	2607,10397	2203	4299	6502	SO:0001583	missense	89790	exon8			TCGGGGAGTCTGA	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.1333T>C	19.37:g.51918360A>G	ENSP00000345243:p.Ser445Pro	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	NM_033130	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	455	0.20833333333333334	176	0.35772357723577236	66	0.18232044198895028	105	0.18356643356643357	108	0.1424802110817942	.	0.005	-2.126313	0.00342	0.325465	0.136427	ENSG00000142512	ENST00000356298;ENST00000439889;ENST00000339313	T;T;T	0.07114	3.22;3.22;3.22	4.83	-0.0502	0.13831	Immunoglobulin-like fold (1);	0.681929	0.13484	N	0.384443	T	0.00012	0.0000	N	0.00101	-2.135	0.48632	P	3.1800000000004047E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41378	-0.9512	9	0.02654	T	1	.	6.3375	0.21304	0.1762:0.4455:0.3783:0.0	.	387;445	Q96LC7-3;Q96LC7	.;SIG10_HUMAN	P	445;387;445	ENSP00000348646:S445P;ENSP00000389132:S387P;ENSP00000345243:S445P	ENSP00000345243:S445P	S	-	1	0	SIGLEC10	56610172	0.996000	0.38824	0.149000	0.22428	0.064000	0.16182	0.332000	0.19751	-0.430000	0.07318	-1.147000	0.01851	TCC	A|0.792;G|0.208	0.208	strong		0.687	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
GRK4	2868	hgsc.bcm.edu	37	4	3039150	3039150	+	Missense_Mutation	SNP	T	T	C	rs1801058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:3039150T>C	ENST00000398052.4	+	14	1800	c.1457T>C	c.(1456-1458)gTg>gCg	p.V486A	GRK4_ENST00000398051.4_Missense_Mutation_p.V454A|GRK4_ENST00000509545.1_3'UTR|GRK4_ENST00000504933.1_Missense_Mutation_p.V486A|GRK4_ENST00000345167.6_Missense_Mutation_p.V454A	NM_182982.2	NP_892027.2	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4	486	AGC-kinase C-terminal.		V -> A (in dbSNP:rs1801058). {ECO:0000269|PubMed:1338872, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8135832, ECO:0000269|PubMed:8626439, ECO:0000269|PubMed:9092566}.		G-protein coupled receptor internalization (GO:0002031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			lung(1)|upper_aerodigestive_tract(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CAGTTCTCGGTGGTGAAAGGG	0.532											OREG0016045	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	3472	0.693291	0.91	0.6427	5008	,	,		19188	0.5337		0.5696	False		,,,				2504	0.728				p.V486A		Atlas-SNP	.											.	GRK4	72	.	0			c.T1457C	GRCh37	CM066866	GRK4	M	rs1801058	PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	3727,679	763.0+/-413.2	1583,561,59	224.0	216.0	219.0		1361,1457,1457	-6.2	0.0	4	dbSNP_89	219	5057,3543	630.5+/-398.4	1460,2137,703	yes	missense,missense,missense	GRK4	NM_001004056.1,NM_001004057.1,NM_182982.2	64,64,64	3043,2698,762	CC,CT,TT		41.1977,15.4108,32.4619	benign,benign,benign	454/547,486/533,486/579	3039150	8784,4222	2203	4300	6503	SO:0001583	missense	2868	exon14			TCTCGGTGGTGAA		CCDS33946.1, CCDS33947.1, CCDS47002.1, CCDS68656.1	4p16.3	2008-02-05	2004-02-04	2004-02-06	ENSG00000125388	ENSG00000125388			4543	protein-coding gene	gene with protein product		137026	"""G protein-coupled receptor kinase 2-like (Drosophila)"""	GPRK2L		1338872	Standard	NM_182982		Approved	GPRK4	uc003ggn.1	P32298	OTTHUMG00000159914	ENST00000398052.4:c.1457T>C	4.37:g.3039150T>C	ENSP00000381129:p.Val486Ala	Somatic	220	0	0	608	WXS	Illumina HiSeq	Phase_I	225	224	0.995556	NM_182982	O00641|O00642|Q13293|Q13294|Q13295|Q14453|Q14725|Q15313|Q15314|Q15315|Q15316|Q17RH6|Q53EQ8	Missense_Mutation	SNP	ENST00000398052.4	37	CCDS33946.1	1394	0.6382783882783882	452	0.9186991869918699	231	0.638121546961326	282	0.493006993006993	429	0.5659630606860159	T	10.83	1.459936	0.26248	0.845892	0.588023	ENSG00000125388	ENST00000398051;ENST00000398052;ENST00000345167;ENST00000504933	T;T;T;T	0.24350	1.86;1.86;1.86;1.86	4.73	-6.21	0.02065	AGC-kinase, C-terminal (2);	0.207018	0.40728	N	0.001032	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.08055	0.002;0.001;0.003;0.001	T	0.39961	-0.9588	9	0.51188	T	0.08	-0.1758	13.1461	0.59463	0.0:0.3815:0.0:0.6185	rs1801058;rs52812762;rs56574318;rs56725050;rs1801058	454;454;486;486	P32298-3;P32298-2;P32298-4;P32298	.;.;.;GRK4_HUMAN	A	454;486;454;486	ENSP00000381128:V454A;ENSP00000381129:V486A;ENSP00000264764:V454A;ENSP00000427445:V486A	ENSP00000264764:V454A	V	+	2	0	GRK4	3008948	0.007000	0.16637	0.000000	0.03702	0.000000	0.00434	1.985000	0.40668	-2.045000	0.00910	-1.430000	0.01095	GTG	T|0.327;C|0.673	0.673	strong		0.532	GRK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358176.2	NM_005307	
PM20D1	148811	hgsc.bcm.edu	37	1	205814485	205814485	+	Missense_Mutation	SNP	G	G	A	rs1104899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:205814485G>A	ENST00000367136.4	-	3	501	c.457C>T	c.(457-459)Cgg>Tgg	p.R153W	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	153			R -> W (in dbSNP:rs1104899). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			AGTGTGCCCCGACCATAGATG	0.562													G|||	1251	0.2498	0.1868	0.2536	5008	,	,		19480	0.255		0.2515	False		,,,				2504	0.3252				p.R153W		Atlas-SNP	.											.	PM20D1	56	.	0			c.C457T						PASS	.	G	TRP/ARG	895,3511	346.2+/-308.9	80,735,1388	103.0	98.0	100.0		457	4.0	0.9	1	dbSNP_86	100	2145,6455	368.8+/-335.2	247,1651,2402	yes	missense	PM20D1	NM_152491.4	101	327,2386,3790	AA,AG,GG		24.9419,20.3132,23.3738	probably-damaging	153/503	205814485	3040,9966	2203	4300	6503	SO:0001583	missense	148811	exon3			TGCCCCGACCATA		CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.457C>T	1.37:g.205814485G>A	ENSP00000356104:p.Arg153Trp	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	505	0.23122710622710624	104	0.21138211382113822	77	0.212707182320442	134	0.23426573426573427	190	0.25065963060686014	G	12.74	2.027395	0.35797	0.203132	0.249419	ENSG00000162877	ENST00000367136	T	0.61980	0.06	5.85	3.96	0.45880	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.93106	3.38	0.19300	P	0.9999726049	D	0.67145	0.996	D	0.69142	0.962	T	0.22382	-1.0218	9	0.72032	D	0.01	.	5.2168	0.15346	0.07:0.1252:0.5523:0.2525	rs1104899;rs4451603;rs17855849;rs52830326;rs60653286;rs1104899	153	Q6GTS8	P20D1_HUMAN	W	153	ENSP00000356104:R153W	ENSP00000356104:R153W	R	-	1	2	PM20D1	204081108	0.998000	0.40836	0.946000	0.38457	0.005000	0.04900	2.648000	0.46647	0.793000	0.33875	-0.254000	0.11334	CGG	G|0.759;A|0.241	0.241	strong		0.562	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
OTOGL	283310	hgsc.bcm.edu	37	12	80761411	80761411	+	Missense_Mutation	SNP	G	G	T	rs11114416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:80761411G>T	ENST00000547103.1	+	53	6345	c.6339G>T	c.(6337-6339)ttG>ttT	p.L2113F	OTOGL_ENST00000546620.1_Missense_Mutation_p.L144F|OTOGL_ENST00000458043.2_Missense_Mutation_p.L2125F			Q3ZCN5	OTOGL_HUMAN	otogelin-like	2113					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TAAAGTATTTGGAAGAAGACT	0.323													G|||	851	0.169928	0.1846	0.2075	5008	,	,		14825	0.0417		0.1819	False		,,,				2504	0.2434				p.L2125F		Atlas-SNP	.											C12orf64,NS,carcinoma,-1,1	OTOGL	235	1	0			c.G6375T						scavenged	.	G	PHE/LEU	807,3593		72,663,1465	68.0	65.0	66.0		6375	2.7	1.0	12	dbSNP_120	66	1648,6936		165,1318,2809	yes	missense	OTOGL	NM_173591.3	22	237,1981,4274	TT,TG,GG		19.1985,18.3409,18.9079	benign	2125/2345	80761411	2455,10529	2200	4292	6492	SO:0001583	missense	283310	exon53			GTATTTGGAAGAA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.6339G>T	12.37:g.80761411G>T	ENSP00000447211:p.Leu2113Phe	Somatic	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	102	42	0.411765	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		323|323	0.1478937728937729|0.1478937728937729	86|86	0.17479674796747968|0.17479674796747968	75|75	0.20718232044198895|0.20718232044198895	26|26	0.045454545454545456|0.045454545454545456	136|136	0.17941952506596306|0.17941952506596306	G|G	7.587|7.587	0.670053|0.670053	0.14776|0.14776	0.183409|0.183409	0.191985|0.191985	ENSG00000165899|ENSG00000165899	ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182|ENST00000298820	T;T;T;T|.	0.45276|.	2.32;2.32;2.23;0.9|.	5.53|5.53	2.66|2.66	0.31614|0.31614	.|.	0.498844|.	0.17868|.	N|.	0.159272|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.41027|0.41027	1.25|1.25	0.38267|0.38267	P|P	0.057950999999999975|0.057950999999999975	B|.	0.13594|.	0.008|.	B|.	0.16722|.	0.016|.	T|T	0.08889|0.08889	-1.0700|-1.0700	9|4	0.10636|.	T|.	0.68|.	.|.	9.0285|9.0285	0.36245|0.36245	0.1297:0.0:0.7494:0.1209|0.1297:0.0:0.7494:0.1209	rs11114416;rs52818722;rs11114416|rs11114416;rs52818722;rs11114416	490|.	Q3ZCN5|.	OTOGL_HUMAN|.	F|L	2113;2125;144;142|533	ENSP00000447211:L2113F;ENSP00000400895:L2125F;ENSP00000449094:L144F;ENSP00000449641:L142F|.	ENSP00000400895:L2125F|.	L|W	+|+	3|2	2|0	OTOGL|OTOGL	79285542|79285542	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.341000|0.341000	0.28922|0.28922	1.200000|1.200000	0.32247|0.32247	0.354000|0.354000	0.24105|0.24105	-0.198000|-0.198000	0.12761|0.12761	TTG|TGG	G|0.827;T|0.173	0.173	strong		0.323	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
ZNF835	90485	hgsc.bcm.edu	37	19	57175121	57175121	+	Silent	SNP	G	G	A	rs115625349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	136	0	0		WXS	Illumina HiSeq	Phase_I	137	61	0.445255	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	
FAM13A	10144	hgsc.bcm.edu	37	4	89668859	89668859	+	Missense_Mutation	SNP	C	C	T	rs7657817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:89668859C>T	ENST00000264344.5	-	18	2512	c.2305G>A	c.(2305-2307)Gtt>Att	p.V769I	FAM13A_ENST00000511976.1_Missense_Mutation_p.V355I|FAM13A_ENST00000508369.1_Missense_Mutation_p.V443I|FAM13A_ENST00000503556.1_Missense_Mutation_p.V429I|FAM13A_ENST00000395002.2_Missense_Mutation_p.V443I|FAM13A_ENST00000513837.1_Missense_Mutation_p.V415I	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	769			V -> I (in dbSNP:rs7657817). {ECO:0000269|PubMed:15489334}.		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(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						GTGGCTTCAACACTGGGCTTT	0.498													C|||	1405	0.280551	0.4705	0.232	5008	,	,		17339	0.246		0.1769	False		,,,				2504	0.2004				p.V769I		Atlas-SNP	.											.	FAM13A	181	.	0			c.G2305A						PASS	.	C	ILE/VAL,ILE/VAL	1878,2528	542.2+/-376.0	402,1074,727	158.0	178.0	171.0		1327,2305	2.6	0.0	4	dbSNP_116	171	1473,7127	280.8+/-294.7	131,1211,2958	yes	missense,missense	FAM13A	NM_001015045.1,NM_014883.2	29,29	533,2285,3685	TT,TC,CC		17.1279,42.6237,25.765	benign,benign	443/698,769/1024	89668859	3351,9655	2203	4300	6503	SO:0001583	missense	10144	exon18			CTTCAACACTGGG	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"""Rho GTPase activating proteins"""	19367	protein-coding gene	gene with protein product		613299	"""family with sequence similarity 13, member A1"""	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.2305G>A	4.37:g.89668859C>T	ENSP00000264344:p.Val769Ile	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	213	98	0.460094	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	37	CCDS34029.1	563	0.25778388278388276	212	0.43089430894308944	76	0.20994475138121546	142	0.24825174825174826	133	0.17546174142480211	C	6.635	0.485567	0.12641	0.426237	0.171279	ENSG00000138640	ENST00000395002;ENST00000264344;ENST00000503556;ENST00000511976;ENST00000508369;ENST00000513837	T;T;T;T;T;T	0.47528	0.84;2.12;1.43;1.46;1.43;1.43	5.26	2.56	0.30785	.	0.382752	0.26594	N	0.023510	T	0.00012	0.0000	N	0.25647	0.755	0.23430	P	0.9976995	B;B;B;B;B;B	0.31077	0.052;0.11;0.307;0.084;0.041;0.052	B;B;B;B;B;B	0.24155	0.05;0.028;0.051;0.037;0.037;0.037	T	0.47649	-0.9101	9	0.35671	T	0.21	.	6.4235	0.21756	0.0:0.6571:0.132:0.2109	rs7657817;rs52825255;rs58300926;rs7657817	415;355;769;443;429;443	O94988-6;E9PGM7;O94988;O94988-3;O94988-5;O94988-1	.;.;FA13A_HUMAN;.;.;.	I	443;769;429;355;443;415	ENSP00000378450:V443I;ENSP00000264344:V769I;ENSP00000427189:V429I;ENSP00000421914:V355I;ENSP00000421562:V443I;ENSP00000423252:V415I	ENSP00000264344:V769I	V	-	1	0	FAM13A	89887882	0.977000	0.34250	0.009000	0.14445	0.003000	0.03518	2.603000	0.46266	0.790000	0.33803	-0.878000	0.02970	GTT	C|0.745;T|0.255	0.255	strong		0.498	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
ZBED5	58486	hgsc.bcm.edu	37	11	10876100	10876100	+	Silent	SNP	C	C	T	rs2232921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:10876100C>T	ENST00000432999.2	-	3	891	c.393G>A	c.(391-393)caG>caA	p.Q131Q	ZBED5_ENST00000525350.1_Intron|ZBED5_ENST00000413761.2_Silent_p.Q131Q	NM_001143667.1|NM_021211.3	NP_001137139.1|NP_067034.2	Q49AG3	ZBED5_HUMAN	zinc finger, BED-type containing 5	131							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)	4						ataatacacactgagcatgag	0.303													C|||	416	0.0830671	0.2927	0.0346	5008	,	,		19978	0.0		0.005	False		,,,				2504	0.0				p.Q131Q		Atlas-SNP	.											.	ZBED5	50	.	0			c.G393A						PASS	.	C	,	363,1021		52,259,381	102.0	81.0	87.0		393,393	1.4	1.0	11	dbSNP_98	87	9,3171		0,9,1581	no	coding-synonymous,coding-synonymous	ZBED5	NM_001143667.1,NM_021211.3	,	52,268,1962	TT,TC,CC		0.283,26.2283,8.1507	,	131/694,131/694	10876100	372,4192	692	1590	2282	SO:0001819	synonymous_variant	58486	exon3			TACACACTGAGCA	AF205601		11p15.3	2013-05-03			ENSG00000236287	ENSG00000236287		"""Zinc fingers, BED-type"""	30803	protein-coding gene	gene with protein product		615251				10607616, 23533661	Standard	NM_021211		Approved	Buster1	uc009ygh.3	Q49AG3	OTTHUMG00000150341	ENST00000432999.2:c.393G>A	11.37:g.10876100C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	79	46	0.582278	NM_021211	B2RCC1|Q05D82|Q86WW3|Q9NT24|Q9UBJ4	Silent	SNP	ENST00000432999.2	37																																																																																				C|0.891;T|0.109	0.109	strong		0.303	ZBED5-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000317691.1	NM_021211	
F8	2157	hgsc.bcm.edu	37	X	154158285	154158285	+	Missense_Mutation	SNP	G	G	C	rs1800291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:154158285G>C	ENST00000360256.4	-	14	3980	c.3780C>G	c.(3778-3780)gaC>gaG	p.D1260E		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1260	B.		D -> E (in dbSNP:rs1800291). {ECO:0000269|PubMed:12195713, ECO:0000269|PubMed:8644728, ECO:0000269|Ref.6}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CATATGCCCCGTCATATGAAC	0.373													C|||	968	0.256424	0.5408	0.1282	3775	,	,		13663	0.0327		0.1004	False		,,,				2504	0.0307				p.D1260E		Atlas-SNP	.											.	F8	646	.	0			c.C3780G	GRCh37	CM960556	F8	M	rs1800291	PASS	.	C	GLU/ASP	2492,1343		702,712,376,218,195	93.0	80.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3780	0.8	0.0	X	dbSNP_89	84	1168,5559		77,709,305,1642,1566	yes	missense	F8	NM_000132.3	45	779,1421,681,1860,1761	CC,CG,C,GG,G		17.3629,35.0196,34.6525	benign	1260/2352	154158285	3660,6902	2203	4299	6502	SO:0001583	missense	2157	exon14			TGCCCCGTCATAT	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"""Factor VIIIF8B"", ""hemophilia A"""	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3780C>G	X.37:g.154158285G>C	ENSP00000353393:p.Asp1260Glu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	34	0.357895	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	408	0.24593128390596744	167	0.5030120481927711	34	0.10303030303030303	21	0.03804347826086957	57	0.0800561797752809	c	0.001	-2.940936	0.00052	0.649804	0.173629	ENSG00000185010	ENST00000360256	D	0.98777	-5.13	5.0	0.78	0.18556	.	0.229900	0.30311	N	0.009907	T	0.00012	0.0000	N	0.00104	-2.125	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48525	-0.9028	9	0.02654	T	1	-0.5074	4.356	0.11178	0.0:0.3526:0.1713:0.476	rs1800291;rs12857528;rs52807479;rs1800291	1260	P00451	FA8_HUMAN	E	1260	ENSP00000353393:D1260E	ENSP00000353393:D1260E	D	-	3	2	F8	153811479	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.490000	0.06482	-0.282000	0.09128	-0.260000	0.10688	GAC	G|0.649;0|0.032	.	strong		0.373	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
PGPEP1L	145814	hgsc.bcm.edu	37	15	99512877	99512877	+	Missense_Mutation	SNP	C	C	T	rs78254881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:99512877C>T	ENST00000378919.6	-	4	353	c.148G>A	c.(148-150)Gtc>Atc	p.V50I	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_5'UTR	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	50							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						ACATGCACGACGAGCTGTGTG	0.602													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		16700	0.0		0.0	False		,,,				2504	0.0				p.V50I		Atlas-SNP	.											.	PGPEP1L	26	.	0			c.G148A						PASS	.	C	ILE/VAL,	145,4113		4,137,1988	77.0	82.0	80.0		148,	0.1	0.1	15	dbSNP_131	80	5,8489		0,5,4242	yes	missense,utr-5	PGPEP1L	NM_001102612.2,NM_001167902.1	29,	4,142,6230	TT,TC,CC		0.0589,3.4054,1.1763	benign,	50/197,	99512877	150,12602	2129	4247	6376	SO:0001583	missense	145814	exon4			GCACGACGAGCTG		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.148G>A	15.37:g.99512877C>T	ENSP00000368199:p.Val50Ile	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	25	0.011446886446886446	20	0.04065040650406504	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	4.380	0.070062	0.08436	0.034054	5.89E-4	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.54279	0.58	4.36	0.0993	0.14502	.	.	.	.	.	T	0.11024	0.0269	L	0.41573	1.285	0.09310	N	1	B	0.22346	0.068	B	0.18561	0.022	T	0.12502	-1.0545	9	0.40728	T	0.16	-23.075	3.4626	0.07539	0.1898:0.3126:0.0:0.4976	.	50	A6NFU8	PGPIL_HUMAN	I	50;43	ENSP00000368199:V50I	ENSP00000368199:V50I	V	-	1	0	PGPEP1L	97330400	0.000000	0.05858	0.065000	0.19835	0.005000	0.04900	0.029000	0.13666	0.141000	0.18875	-0.827000	0.03088	GTC	C|0.986;T|0.014	0.014	strong		0.602	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
PCNT	5116	hgsc.bcm.edu	37	21	47754471	47754471	+	Missense_Mutation	SNP	G	G	A	rs58106867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47754471G>A	ENST00000359568.5	+	3	535	c.428G>A	c.(427-429)cGt>cAt	p.R143H	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	143					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)					CCAGAACAGCGTGGGATGTTC	0.542																																					p.R143H		Atlas-SNP	.											PCNT,caecum,adenoma,0,1	PCNT	283	1	0			c.G428A						scavenged	.						183.0	119.0	141.0					21																	47754471		2203	4300	6503	SO:0001583	missense	5116	exon3			AACAGCGTGGGAT	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.428G>A	21.37:g.47754471G>A	ENSP00000352572:p.Arg143His	Somatic	283	2	0.00706714		WXS	Illumina HiSeq	Phase_I	323	11	0.0340557	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	g	6.506	0.461555	0.12342	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01430	4.9	0.428	-0.857	0.10693	.	.	.	.	.	T	0.00815	0.0027	N	0.20986	0.625	0.21473	N	0.999673	D;D	0.59357	0.985;0.975	B;B	0.32724	0.151;0.072	T	0.50923	-0.8770	8	0.40728	T	0.16	.	.	.	.	rs58106867	25;143	O95613-2;O95613	.;PCNT_HUMAN	H	143	ENSP00000352572:R143H	ENSP00000338675:R143H	R	+	2	0	PCNT	46578899	0.031000	0.19500	0.029000	0.17559	0.020000	0.10135	-2.283000	0.01155	-0.638000	0.05509	0.205000	0.17691	CGT	G|0.991;A|0.010	0.010	strong		0.542	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
GPHN	10243	hgsc.bcm.edu	37	14	67147887	67147887	+	Missense_Mutation	SNP	G	G	T	rs117256383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:67147887G>T	ENST00000315266.5	+	2	1248	c.127G>T	c.(127-129)Gta>Tta	p.V43L	GPHN_ENST00000459628.1_Missense_Mutation_p.V43L|GPHN_ENST00000305960.9_Missense_Mutation_p.V43L|GPHN_ENST00000543237.1_Missense_Mutation_p.V43L|GPHN_ENST00000478722.1_Missense_Mutation_p.V43L	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	43	MPT Mo-transferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)	p.V43L(1)		large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		CAAAGATCTCGTACAAGATCC	0.303			T	MLL	AL								G|||	15	0.00299521	0.0	0.0029	5008	,	,		14816	0.0		0.0119	False		,,,				2504	0.001				p.V43L		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	GPHN_ENST00000478722,NS,carcinoma,0,2	GPHN	79	2	1	Substitution - Missense(1)	endometrium(1)	c.G127T						PASS	.	G	LEU/VAL,LEU/VAL	11,4395	16.8+/-37.8	0,11,2192	91.0	93.0	92.0		127,127	5.1	1.0	14	dbSNP_132	92	122,8478	62.8+/-124.8	0,122,4178	yes	missense,missense	GPHN	NM_001024218.1,NM_020806.4	32,32	0,133,6370	TT,TG,GG		1.4186,0.2497,1.0226	possibly-damaging,possibly-damaging	43/737,43/770	67147887	133,12873	2203	4300	6503	SO:0001583	missense	10243	exon2			GATCTCGTACAAG	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.127G>T	14.37:g.67147887G>T	ENSP00000312771:p.Val43Leu	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_001024218	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	37	CCDS32103.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	13.26	2.183452	0.38609	0.002497	0.014186	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000459628;ENST00000543237;ENST00000305960	T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56	5.11	5.11	0.69529	Molybdenum cofactor synthesis (1);Molybdopterin binding (4);	0.063980	0.64402	D	0.000008	T	0.39091	0.1065	N	0.02120	-0.675	0.47994	D	0.999564	B;B;B;B;B	0.26147	0.005;0.143;0.006;0.023;0.002	B;B;B;B;B	0.26693	0.006;0.072;0.011;0.019;0.006	T	0.48570	-0.9024	10	0.41790	T	0.15	-5.8887	16.0118	0.80409	0.0:0.0:1.0:0.0	.	43;43;43;43;43	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2;G3V582	.;.;GEPH_HUMAN;.;.	L	43	ENSP00000312771:V43L;ENSP00000417901:V43L;ENSP00000452220:V43L;ENSP00000438404:V43L;ENSP00000303019:V43L	ENSP00000303019:V43L	V	+	1	0	GPHN	66217640	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	6.850000	0.75420	2.374000	0.81015	0.579000	0.79373	GTA	G|0.993;T|0.007	0.007	strong		0.303	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806	
MUC5B	727897	hgsc.bcm.edu	37	11	1262312	1262312	+	Missense_Mutation	SNP	G	G	A	rs10835639	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1262312G>A	ENST00000529681.1	+	31	4260	c.4202G>A	c.(4201-4203)cGc>cAc	p.R1401H	MUC5B_ENST00000447027.1_Missense_Mutation_p.R1404H|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1401	7 X Cys-rich subdomain repeats.		R -> H (in dbSNP:rs10835639).		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)		GACTGTGACCGCATGCGGGGG	0.667													g|||	681	0.135982	0.1067	0.1282	5008	,	,		16163	0.3105		0.003	False		,,,				2504	0.138				p.R1401H		Atlas-SNP	.											.	MUC5B	473	.	0			c.G4202A						PASS	.		HIS/ARG	334,3912		17,300,1806	25.0	32.0	30.0		4202	-8.8	0.0	11	dbSNP_120	30	10,8450		0,10,4220	yes	missense	MUC5B	NM_002458.2	29	17,310,6026	AA,AG,GG		0.1182,7.8662,2.7074	benign	1401/5763	1262312	344,12362	2123	4230	6353	SO:0001583	missense	727897	exon31			GTGACCGCATGCG	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.4202G>A	11.37:g.1262312G>A	ENSP00000436812:p.Arg1401His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	89	52	0.58427	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	256	0.11721611721611722	49	0.09959349593495935	37	0.10220994475138122	168	0.2937062937062937	2	0.002638522427440633	g	5.080	0.200476	0.09652	0.078662	0.001182	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17213	2.29;2.29	4.39	-8.78	0.00824	.	.	.	.	.	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B;B	0.20052	0.041;0.023	B;B	0.12837	0.008;0.005	T	0.24190	-1.0167	8	0.87932	D	0	.	3.2169	0.06702	0.3283:0.414:0.1804:0.0773	rs10835639	2094;1404	A7Y9J9;E9PBJ0	.;.	H	1401;1404;1402;1471	ENSP00000436812:R1401H;ENSP00000415793:R1404H	ENSP00000343037:R1402H	R	+	2	0	MUC5B	1218888	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-10.746000	0.00005	-4.160000	0.00068	-2.213000	0.00299	CGC	G|0.894;A|0.106	0.106	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
CSF3R	1441	hgsc.bcm.edu	37	1	36933493	36933493	+	Silent	SNP	G	G	A	rs3917998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36933493G>A	ENST00000373106.1	-	14	2341	c.1794C>T	c.(1792-1794)atC>atT	p.I598I	CSF3R_ENST00000331941.5_Silent_p.I598I|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000373103.1_Silent_p.I598I|CSF3R_ENST00000440588.2_Silent_p.I598I|CSF3R_ENST00000338937.5_Silent_p.I598I|CSF3R_ENST00000373104.1_Silent_p.I598I|CSF3R_ENST00000418048.2_Silent_p.I598I|CSF3R_ENST00000361632.4_Silent_p.I598I	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	598	Fibronectin type-III 5. {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)	CCATGAGGTGGATGTGATACA	0.632													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		18146	0.0		0.0	False		,,,				2504	0.0				p.I598I		Atlas-SNP	.											.	CSF3R	157	.	0			c.C1794T						PASS	.	G	,,	110,4296	85.3+/-124.0	1,108,2094	62.0	72.0	68.0		1794,1794,1794	0.9	0.8	1	dbSNP_108	68	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSF3R	NM_000760.3,NM_156039.3,NM_172313.2	,,	1,113,6389	AA,AG,GG		0.0581,2.4966,0.8842	,,	598/837,598/864,598/784	36933493	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	1441	exon14			GAGGTGGATGTGA	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.1794C>T	1.37:g.36933493G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	142	69	0.485915	NM_156039		Silent	SNP	ENST00000373106.1	37	CCDS413.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	1.164	-0.642824	0.03531	0.024966	5.81E-4	ENSG00000119535	ENST00000464465	.	.	.	5.33	0.847	0.18961	.	.	.	.	.	T	0.37625	0.1010	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31166	-0.9953	4	.	.	.	-20.3197	6.8146	0.23822	0.0808:0.1894:0.6261:0.1037	rs3917998;rs3917998	.	.	.	F	150	.	.	S	-	2	0	CSF3R	36706080	0.985000	0.35326	0.819000	0.32651	0.078000	0.17371	0.083000	0.14871	0.245000	0.21373	-0.797000	0.03246	TCC	G|0.991;A|0.009	0.009	strong		0.632	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039	
LMAN1L	79748	hgsc.bcm.edu	37	15	75116009	75116009	+	Missense_Mutation	SNP	C	C	T	rs114366521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75116009C>T	ENST00000309664.5	+	12	1448	c.1309C>T	c.(1309-1311)Ctt>Ttt	p.L437F	LMAN1L_ENST00000379709.3_Missense_Mutation_p.L425F|CPLX3_ENST00000395018.4_5'Flank|RP11-414J4.2_ENST00000564823.1_RNA	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	437						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GCAGGAGGAGCTTCGGGGCCC	0.622													C|||	107	0.0213658	0.0802	0.0014	5008	,	,		18201	0.0		0.0	False		,,,				2504	0.0				p.L437F		Atlas-SNP	.											.	LMAN1L	43	.	0			c.C1309T						PASS	.	C	PHE/LEU	273,4121	151.4+/-185.3	7,259,1931	48.0	49.0	49.0		1309	2.4	0.1	15	dbSNP_132	49	2,8588	2.2+/-6.3	0,2,4293	yes	missense	LMAN1L	NM_021819.2	22	7,261,6224	TT,TC,CC		0.0233,6.213,2.118	probably-damaging	437/527	75116009	275,12709	2197	4295	6492	SO:0001583	missense	79748	exon12			GAGGAGCTTCGGG	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.1309C>T	15.37:g.75116009C>T	ENSP00000310431:p.Leu437Phe	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_021819	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	37	CCDS10270.1	40	0.018315018315018316	40	0.08130081300813008	0	0.0	0	0.0	0	0.0	C	9.345	1.064140	0.20067	0.06213	2.33E-4	ENSG00000140506	ENST00000309664;ENST00000379709	T;T	0.44482	0.98;0.92	4.29	2.38	0.29361	.	0.262772	0.25414	N	0.030848	T	0.02727	0.0082	N	0.22421	0.69	0.20821	N	0.999843	D;D	0.61080	0.989;0.982	P;P	0.59487	0.858;0.726	T	0.00995	-1.1487	10	0.72032	D	0.01	.	7.9218	0.29850	0.1831:0.6403:0.1766:0.0	.	425;437	Q9HAT1-3;Q9HAT1	.;LMA1L_HUMAN	F	437;425	ENSP00000310431:L437F;ENSP00000369031:L425F	ENSP00000310431:L437F	L	+	1	0	LMAN1L	72903062	0.225000	0.23685	0.138000	0.22173	0.009000	0.06853	1.393000	0.34497	0.530000	0.28619	-0.226000	0.12346	CTT	C|0.981;T|0.019	0.019	strong		0.622	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		
C10orf71	118461	hgsc.bcm.edu	37	10	50531931	50531931	+	Silent	SNP	G	G	A	rs75053680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50531931G>A	ENST00000374144.3	+	3	1629	c.1341G>A	c.(1339-1341)ctG>ctA	p.L447L	C10orf71_ENST00000323868.4_Silent_p.L447L			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	447										endometrium(1)	1						GTAAGCTCCTGACCCCCATCA	0.522													G|||	21	0.00419329	0.0008	0.0058	5008	,	,		17546	0.0		0.0139	False		,,,				2504	0.002				p.L447L		Atlas-SNP	.											C10orf71_ENST00000374144,NS,carcinoma,+2,2	C10orf71	179	2	0			c.G1341A						PASS	.	G	,	16,4066		0,16,2025	71.0	75.0	74.0		1341,1341	2.6	1.0	10	dbSNP_132	74	164,8262		3,158,4052	no	coding-synonymous,coding-synonymous	C10orf71	NM_001135196.1,NM_199459.3	,	3,174,6077	AA,AG,GG		1.9464,0.392,1.4391	,	447/1436,447/720	50531931	180,12328	2041	4213	6254	SO:0001819	synonymous_variant	118461	exon3			GCTCCTGACCCCC	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.1341G>A	10.37:g.50531931G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			G|0.996;A|0.004	0.004	strong		0.522	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
TAS2R16	50833	hgsc.bcm.edu	37	7	122634843	122634843	+	Silent	SNP	C	C	T	rs1204014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:122634843C>T	ENST00000249284.2	-	1	911	c.846G>A	c.(844-846)acG>acA	p.T282T		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	282					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	bitter taste receptor activity (GO:0033038)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TCCTTTTCAACGTAGGGCTGC	0.423													T|||	501	0.10004	0.323	0.0432	5008	,	,		21099	0.0		0.0378	False		,,,				2504	0.0061				p.T282T		Atlas-SNP	.											TAS2R16,right_lower_lobe,carcinoma,-1,2	TAS2R16	57	2	0			c.G846A						PASS	.	T		1246,3160	700.8+/-406.7	171,904,1128	110.0	113.0	112.0		846	0.5	0.0	7	dbSNP_87	112	367,8233	800.7+/-407.4	11,345,3944	no	coding-synonymous	TAS2R16	NM_016945.2		182,1249,5072	TT,TC,CC		4.2674,28.2796,12.402		282/292	122634843	1613,11393	2203	4300	6503	SO:0001819	synonymous_variant	50833	exon1			TTTCAACGTAGGG	AF227139	CCDS5785.1	7q31.1-q31.3	2012-08-22			ENSG00000128519	ENSG00000128519		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14921	protein-coding gene	gene with protein product		604867				10761934	Standard	NM_016945		Approved	T2R16	uc003vkl.1	Q9NYV7	OTTHUMG00000157090	ENST00000249284.2:c.846G>A	7.37:g.122634843C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	112	46	0.410714	NM_016945	A4D0X2|Q502V3|Q549U8|Q645W1	Silent	SNP	ENST00000249284.2	37	CCDS5785.1																																																																																			C|0.884;T|0.116	0.116	strong		0.423	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945	
RREB1	6239	hgsc.bcm.edu	37	6	7229619	7229619	+	Silent	SNP	G	G	A	rs12192672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7229619G>A	ENST00000349384.6	+	10	1601	c.1287G>A	c.(1285-1287)gcG>gcA	p.A429A	RREB1_ENST00000379933.3_Silent_p.A429A|RREB1_ENST00000379938.2_Silent_p.A429A|RREB1_ENST00000334984.6_Silent_p.A429A	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	429					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)				TTCTCCCCGCGACCAAGGACA	0.582													G|||	1019	0.203474	0.3351	0.1715	5008	,	,		18982	0.0417		0.3082	False		,,,				2504	0.1074				p.A429A		Atlas-SNP	.											.	RREB1	242	.	0			c.G1287A						PASS	.	G	,,,	1391,3015	457.3+/-351.6	220,951,1032	60.0	55.0	57.0		1287,1287,1287,1287	-9.4	0.2	6	dbSNP_120	57	2390,6210	397.7+/-345.9	338,1714,2248	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	,,,	558,2665,3280	AA,AG,GG		27.7907,31.5706,29.0712	,,,	429/1688,429/1743,429/1477,429/1688	7229619	3781,9225	2203	4300	6503	SO:0001819	synonymous_variant	6239	exon10			CCCCGCGACCAAG	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.1287G>A	6.37:g.7229619G>A		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	CCDS34336.1																																																																																			G|0.736;A|0.264	0.264	strong		0.582	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
ASMTL	8623	hgsc.bcm.edu	37	X	1537953	1537953	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1537953C>T	ENST00000381317.3	-	10	1332	c.1300G>A	c.(1300-1302)Ggc>Agc	p.G434S	ASMTL_ENST00000416733.2_Missense_Mutation_p.G358S|ASMTL_ENST00000534940.1_Missense_Mutation_p.G376S|ASMTL_ENST00000381333.4_Missense_Mutation_p.G418S	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	156	0	0		WXS	Illumina HiSeq	Phase_I	178	103	0.578652	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	
CBFA2T3	863	hgsc.bcm.edu	37	16	88968048	88968048	+	Silent	SNP	T	T	C	rs76033980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88968048T>C	ENST00000268679.4	-	2	564	c.168A>G	c.(166-168)aaA>aaG	p.K56K	CBFA2T3_ENST00000448839.1_Intron|CBFA2T3_ENST00000360302.2_5'UTR|CBFA2T3_ENST00000436887.2_Silent_p.K56K|CBFA2T3_ENST00000327483.5_5'UTR	NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 3	56	Mediates interaction with PDE7A (in isoform 2).|Mediates localization to the nucleus. {ECO:0000250}.|Pro-rich.|Required for nucleolar targeting (in isoform 1).				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)		AGGCCTTAGCTTTCCTGTCCA	0.672			T	RUNX1	AML								C|||	252	0.0503195	0.0991	0.0461	5008	,	,		14614	0.0218		0.0239	False		,,,				2504	0.044				p.K56K		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.A168G						PASS	.	C	,	416,3978	765.9+/-413.4	23,370,1804	33.0	37.0	36.0		168,	3.0	0.4	16	dbSNP_131	36	231,8369	798.7+/-407.4	3,225,4072	no	coding-synonymous,utr-5	CBFA2T3	NM_005187.5,NM_175931.2	,	26,595,5876	CC,CT,TT		2.686,9.4675,4.9792	,	56/654,	88968048	647,12347	2197	4300	6497	SO:0001819	synonymous_variant	863	exon2			CTTAGCTTTCCTG	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.168A>G	16.37:g.88968048T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_005187	D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6	Silent	SNP	ENST00000268679.4	37	CCDS10972.1																																																																																			T|0.958;C|0.042	0.042	strong		0.672	CBFA2T3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269545.2	NM_005187	
GAS8	2622	hgsc.bcm.edu	37	16	90095484	90095484	+	Intron	SNP	C	C	T	rs3785184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:90095484C>T	ENST00000268699.4	+	2	212				GAS8_ENST00000536122.1_Intron|GAS8_ENST00000540721.1_Intron|C16orf3_ENST00000408886.2_Silent_p.T89T	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		AGCTGCTGCCCGTCTCCCTGT	0.597													C|||	1176	0.234824	0.0946	0.2968	5008	,	,		16761	0.62		0.1213	False		,,,				2504	0.1002				p.T89T		Atlas-SNP	.											C16orf3,rectum,carcinoma,-2,2	C16orf3	14	2	0			c.G267A						PASS	.	C	,	352,3822		14,324,1749	85.0	47.0	60.0		267,	-0.4	0.0	16	dbSNP_107	60	648,7580		23,602,3489	no	coding-synonymous,intron	C16orf3,GAS8	NM_001214.3,NM_001481.2	,	37,926,5238	TT,TC,CC		7.8755,8.4332,8.0632	,	89/118,	90095484	1000,11402	2087	4114	6201	SO:0001627	intron_variant	750	exon1			GCTGCCCGTCTCC	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1354C>T	16.37:g.90095484C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	150	42	0.28	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Silent	SNP	ENST00000268699.4	37	CCDS10992.1																																																																																			C|0.821;T|0.179	0.179	strong		0.597	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
ITGA2	3673	hgsc.bcm.edu	37	5	52369002	52369002	+	Silent	SNP	G	G	A	rs3212327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	138	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	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	
ABCC2	1244	hgsc.bcm.edu	37	10	101604107	101604107	+	Missense_Mutation	SNP	C	C	T	rs17216317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101604107C>T	ENST00000370449.4	+	28	3985	c.3872C>T	c.(3871-3873)cCg>cTg	p.P1291L		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1291			P -> L (altered transporter activity; dbSNP:rs17216317). {ECO:0000269|PubMed:22290738}.		cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	AAGAGGCCTCCGCCAGATTGG	0.532													C|||	55	0.0109824	0.0363	0.0086	5008	,	,		20061	0.0		0.001	False		,,,				2504	0.0				p.P1291L		Atlas-SNP	.											.	ABCC2	160	.	0			c.C3872T						PASS	.		LEU/PRO	145,4261	101.2+/-139.8	3,139,2061	95.0	89.0	91.0		3872	5.8	1.0	10	dbSNP_126	91	3,8597	2.2+/-6.3	0,3,4297	yes	missense	ABCC2	NM_000392.3	98	3,142,6358	TT,TC,CC		0.0349,3.291,1.1379	probably-damaging	1291/1546	101604107	148,12858	2203	4300	6503	SO:0001583	missense	1244	exon28			GGCCTCCGCCAGA	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.3872C>T	10.37:g.101604107C>T	ENSP00000359478:p.Pro1291Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	18.14	3.557532	0.65425	0.03291	3.49E-4	ENSG00000023839	ENST00000370449	D	0.89681	-2.55	5.79	5.79	0.91817	.	0.099134	0.64402	D	0.000001	D	0.84556	0.5498	M	0.65320	2	0.80722	D	1	D	0.69078	0.997	D	0.64687	0.928	D	0.87880	0.2677	10	0.87932	D	0	-8.0E-4	15.6234	0.76829	0.1379:0.8621:0.0:0.0	rs17216317;rs52825311;rs61667815	1291	Q92887	MRP2_HUMAN	L	1291	ENSP00000359478:P1291L	ENSP00000359478:P1291L	P	+	2	0	ABCC2	101594097	1.000000	0.71417	0.968000	0.41197	0.881000	0.50899	5.706000	0.68362	2.733000	0.93635	0.655000	0.94253	CCG	C|0.988;T|0.012	0.012	strong		0.532	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
TMBIM6	7009	hgsc.bcm.edu	37	12	50152193	50152193	+	Silent	SNP	G	G	A	rs4563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50152193G>A	ENST00000267115.5	+	6	448	c.363G>A	c.(361-363)acG>acA	p.T121T	TMBIM6_ENST00000547798.1_Silent_p.T84T|TMBIM6_ENST00000549385.1_Silent_p.T121T|TMBIM6_ENST00000395006.4_Silent_p.T121T|TMBIM6_ENST00000423828.1_Silent_p.T179T|TMBIM6_ENST00000552699.1_Silent_p.T179T	NM_003217.2	NP_003208.2	P55061	BI1_HUMAN	transmembrane BAX inhibitor motif containing 6	121					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)				lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	6						TCATGGGCACGGCAATGATCT	0.463													A|||	1093	0.218251	0.5635	0.1138	5008	,	,		21428	0.0823		0.1004	False		,,,				2504	0.0869				p.T179T		Atlas-SNP	.											.	TMBIM6	26	.	0			c.G537A						PASS	.	A	,	2093,2313	603.2+/-390.1	505,1083,615	202.0	157.0	172.0		537,363	-0.8	1.0	12	dbSNP_52	172	832,7768	781.8+/-407.6	45,742,3513	no	coding-synonymous,coding-synonymous	TMBIM6	NM_001098576.1,NM_003217.2	,	550,1825,4128	AA,AG,GG		9.6744,47.5034,22.4896	,	179/296,121/238	50152193	2925,10081	2203	4300	6503	SO:0001819	synonymous_variant	7009	exon6			GGGCACGGCAATG	X75861	CCDS31797.1, CCDS44875.1	12q13.12	2013-10-08	2008-09-17	2008-09-17	ENSG00000139644	ENSG00000139644			11723	protein-coding gene	gene with protein product	"""BAX inhibitor 1"""	600748	"""testis enhanced gene transcript"""	TEGT		8530040, 9660918	Standard	NM_001098576		Approved	BI-1, BAXI1	uc001ruy.2	P55061	OTTHUMG00000169652	ENST00000267115.5:c.363G>A	12.37:g.50152193G>A		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	198	198	1	NM_001098576	B2R5M4|F8W034|O14938|Q643A7|Q96J50	Silent	SNP	ENST00000267115.5	37	CCDS31797.1																																																																																			G|0.790;A|0.210	0.210	strong		0.463	TMBIM6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405289.1	NM_003217	
VPS8	23355	hgsc.bcm.edu	37	3	184766301	184766301	+	Missense_Mutation	SNP	T	T	C	rs3821750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184766301T>C	ENST00000437079.3	+	47	4262	c.4091T>C	c.(4090-4092)aTc>aCc	p.I1364T	VPS8_ENST00000446204.2_Missense_Mutation_p.I1272T|VPS8_ENST00000287546.4_Missense_Mutation_p.I1364T|VPS8_ENST00000436792.2_Missense_Mutation_p.I1362T	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	77	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	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	
APRT	353	hgsc.bcm.edu	37	16	88874545	88874545	+	IGR	SNP	G	G	T	rs3218720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88874545G>T	ENST00000378364.3	-	0	947				CDT1_ENST00000301019.4_Silent_p.L500L	NM_000485.2	NP_000476.1	P07741	APT_HUMAN	adenine phosphoribosyltransferase						adenine salvage (GO:0006168)|AMP salvage (GO:0044209)|cellular response to insulin stimulus (GO:0032869)|grooming behavior (GO:0007625)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	adenine binding (GO:0002055)|adenine phosphoribosyltransferase activity (GO:0003999)|AMP binding (GO:0016208)			cervix(1)|endometrium(1)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)	AGCACCTGCTGCTCCTCTCCG	0.662													G|||	217	0.0433307	0.1581	0.0115	5008	,	,		18032	0.0		0.0	False		,,,				2504	0.0				p.L500L		Atlas-SNP	.											.	CDT1	30	.	0			c.G1500T						PASS	.	G		651,3741		50,551,1595	42.0	31.0	35.0		1500	2.8	0.1	16	dbSNP_106	35	6,8592		0,6,4293	no	coding-synonymous	CDT1	NM_030928.3		50,557,5888	TT,TG,GG		0.0698,14.8224,5.0577		500/547	88874545	657,12333	2196	4299	6495	SO:0001628	intergenic_variant	81620	exon10			CCTGCTGCTCCTC		CCDS32511.1, CCDS45546.1	16q24	2012-10-02				ENSG00000198931	2.4.2.7		626	protein-coding gene	gene with protein product		102600					Standard	NM_000485		Approved		uc002flv.3	P07741			16.37:g.88874545G>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	121	118	0.975207	NM_030928	G5E9J2|Q3KP55|Q68DF9	Silent	SNP	ENST00000378364.3	37	CCDS32511.1																																																																																			G|0.953;T|0.047	0.047	strong		0.662	APRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430000.2	NM_000485	
DMXL2	23312	hgsc.bcm.edu	37	15	51868289	51868289	+	Silent	SNP	T	T	C	rs34998785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51868289T>C	ENST00000251076.5	-	2	464	c.177A>G	c.(175-177)caA>caG	p.Q59Q	DMXL2_ENST00000560421.1_5'UTR|DMXL2_ENST00000449909.3_Silent_p.Q59Q|DMXL2_ENST00000543779.2_Silent_p.Q59Q	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	59						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)		CACAGCTGACTTGGATGTTTC	0.343													T|||	125	0.0249601	0.0885	0.0101	5008	,	,		16960	0.0		0.001	False		,,,				2504	0.0				p.Q59Q		Atlas-SNP	.											.	DMXL2	262	.	0			c.A177G						PASS	.	T	,,	399,3991	196.7+/-221.0	26,347,1822	150.0	139.0	143.0		177,177,177	5.3	1.0	15	dbSNP_126	143	10,8576	7.7+/-29.5	0,10,4283	no	coding-synonymous,coding-synonymous,coding-synonymous	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	,,	26,357,6105	CC,CT,TT		0.1165,9.0888,3.152	,,	59/3038,59/2401,59/3037	51868289	409,12567	2195	4293	6488	SO:0001819	synonymous_variant	23312	exon2			GCTGACTTGGATG	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.177A>G	15.37:g.51868289T>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			T|0.966;C|0.034	0.034	strong		0.343	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
TMC3	342125	hgsc.bcm.edu	37	15	81641872	81641872	+	Missense_Mutation	SNP	G	G	T	rs61740148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81641872G>T	ENST00000359440.5	-	11	1255	c.1120C>A	c.(1120-1122)Cca>Aca	p.P374T	RP11-761I4.3_ENST00000559781.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.P375T|RP11-761I4.3_ENST00000560851.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						AAGGCTGATGGTGCTATCATG	0.577													G|||	58	0.0115815	0.0408	0.0058	5008	,	,		16696	0.0		0.0	False		,,,				2504	0.0				p.P374T		Atlas-SNP	.											.	TMC3	112	.	0			c.C1120A						PASS	.	G	THR/PRO	172,4164		3,166,1999	107.0	111.0	110.0		1120	5.0	0.6	15	dbSNP_129	110	1,8523		0,1,4261	yes	missense	TMC3	NM_001080532.1	38	3,167,6260	TT,TG,GG		0.0117,3.9668,1.3453	probably-damaging	374/1101	81641872	173,12687	2168	4262	6430	SO:0001583	missense	342125	exon11			CTGATGGTGCTAT	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.1120C>A	15.37:g.81641872G>T	ENSP00000352413:p.Pro374Thr	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	211	99	0.469194	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	G	16.89	3.247828	0.59103	0.039668	1.17E-4	ENSG00000188869	ENST00000359440	D	0.91237	-2.81	5.02	5.02	0.67125	.	0.129405	0.53938	D	0.000052	D	0.87466	0.6184	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89179	0.3542	10	0.87932	D	0	-13.1745	18.3718	0.90409	0.0:0.0:1.0:0.0	.	374;374	Q7Z5M5-2;Q7Z5M5	.;TMC3_HUMAN	T	374	ENSP00000352413:P374T	ENSP00000352413:P374T	P	-	1	0	TMC3	79428927	1.000000	0.71417	0.619000	0.29118	0.082000	0.17680	9.398000	0.97281	2.322000	0.78497	0.655000	0.94253	CCA	G|0.990;T|0.010	0.010	strong		0.577	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841	
TRAPPC8	22878	hgsc.bcm.edu	37	18	29487567	29487567	+	Silent	SNP	C	C	A	rs34176695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:29487567C>A	ENST00000283351.4	-	9	1580	c.1245G>T	c.(1243-1245)ccG>ccT	p.P415P	TRAPPC8_ENST00000582513.1_Silent_p.P415P|TRAPPC8_ENST00000582539.1_Silent_p.P361P	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	415					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GTGCTTCCGGCGGATACCTGT	0.333													C|||	265	0.0529153	0.0877	0.0447	5008	,	,		15573	0.0109		0.0636	False		,,,				2504	0.044				p.P415P		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.G1245T						PASS	.	C		369,4037	182.9+/-210.6	13,343,1847	51.0	52.0	52.0		1245	-2.4	0.9	18	dbSNP_126	52	576,8024	152.5+/-207.1	19,538,3743	no	coding-synonymous	TRAPPC8	NM_014939.3		32,881,5590	AA,AC,CC		6.6977,8.3749,7.2659		415/1436	29487567	945,12061	2203	4300	6503	SO:0001819	synonymous_variant	22878	exon9			TTCCGGCGGATAC	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"""Trafficking protein particle complex"""	29169	protein-coding gene	gene with protein product	"""general sporulation gene 1 homolog (S. cerevisiae)"""	614136	"""KIAA1012"""	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.1245G>T	18.37:g.29487567C>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_014939	A0JP15|B3KME5|Q9H0L2	Silent	SNP	ENST00000283351.4	37	CCDS11901.1																																																																																			C|0.935;A|0.065	0.065	strong		0.333	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939	
RELN	5649	hgsc.bcm.edu	37	7	103251218	103251218	+	Missense_Mutation	SNP	T	T	C	rs3025962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103251218T>C	ENST00000428762.1	-	22	3091	c.2932A>G	c.(2932-2934)Aca>Gca	p.T978A	RELN_ENST00000343529.5_Missense_Mutation_p.T978A|RELN_ENST00000424685.2_Missense_Mutation_p.T978A	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	978			T -> A (in dbSNP:rs3025962).		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)		CTTGCTGATGTAAATTCCTGA	0.413													T|||	92	0.0183706	0.0651	0.0086	5008	,	,		18923	0.0		0.0	False		,,,				2504	0.0				p.T978A	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A2932G						PASS	.	T	ALA/THR,ALA/THR	211,4195	131.0+/-167.6	4,203,1996	146.0	123.0	131.0		2932,2932	6.1	1.0	7	dbSNP_102	131	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	58,58	4,206,6293	CC,CT,TT		0.0349,4.7889,1.6454	probably-damaging,probably-damaging	978/3461,978/3459	103251218	214,12792	2203	4300	6503	SO:0001583	missense	5649	exon22			CTGATGTAAATTC		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.2932A>G	7.37:g.103251218T>C	ENSP00000392423:p.Thr978Ala	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	T	23.6	4.434312	0.83776	0.047889	3.49E-4	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.24908	1.83;2.09;1.83	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.06325	0.0163	M	0.61703	1.905	0.58432	D	0.999994	D;D	0.76494	0.999;0.982	D;D	0.83275	0.996;0.952	T	0.01235	-1.1410	10	0.62326	D	0.03	.	15.2149	0.73258	0.0:0.0:0.0:1.0	rs3025962;rs52799777;rs3025962	978;978	P78509-2;P78509	.;RELN_HUMAN	A	978	ENSP00000392423:T978A;ENSP00000345694:T978A;ENSP00000388446:T978A	ENSP00000345694:T978A	T	-	1	0	RELN	103038454	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.358000	0.79466	2.333000	0.79357	0.533000	0.62120	ACA	T|0.978;C|0.022	0.022	strong		0.413	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
TMEM200C	645369	hgsc.bcm.edu	37	18	5891637	5891637	+	Silent	SNP	C	C	A	rs28656885	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:5891637C>A	ENST00000581347.2	-	3	1071	c.426G>T	c.(424-426)ccG>ccT	p.P142P	RP11-945C19.4_ENST00000580845.1_RNA|TMEM200C_ENST00000383490.2_Silent_p.P142P|RP11-945C19.4_ENST00000577694.1_RNA|RP11-945C19.4_ENST00000582939.1_RNA			A6NKL6	T200C_HUMAN	transmembrane protein 200C	142						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)	12						AGGAGGAGGACGGGGAGGCGG	0.652													A|||	1704	0.340256	0.4319	0.3444	5008	,	,		13431	0.2986		0.3598	False		,,,				2504	0.2362				p.P142P		Atlas-SNP	.											.	TMEM200C	30	.	0			c.G426T						PASS	.	A		1809,2421		391,1027,697	58.0	71.0	67.0		426	-8.4	0.0	18	dbSNP_125	67	3219,5213		630,1959,1627	no	coding-synonymous	TMEM200C	NM_001080209.1		1021,2986,2324	AA,AC,CC		38.176,42.766,39.7094		142/622	5891637	5028,7634	2115	4216	6331	SO:0001819	synonymous_variant	645369	exon1			GGAGGACGGGGAG		CCDS45825.1	18p11.31	2009-09-08			ENSG00000206432	ENSG00000206432			37208	protein-coding gene	gene with protein product						15722956	Standard	NM_001080209		Approved	TTMA	uc002kmx.1	A6NKL6		ENST00000581347.2:c.426G>T	18.37:g.5891637C>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_001080209		Silent	SNP	ENST00000581347.2	37	CCDS45825.1																																																																																			C|0.642;A|0.358	0.358	strong		0.652	TMEM200C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441917.4	NM_001080209	
HMMR	3161	hgsc.bcm.edu	37	5	162902516	162902516	+	Missense_Mutation	SNP	T	T	C	rs299290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162902516T>C	ENST00000358715.3	+	11	1139	c.1103T>C	c.(1102-1104)gTt>gCt	p.V368A	HMMR_ENST00000432118.2_Missense_Mutation_p.V282A|HMMR_ENST00000393915.4_Missense_Mutation_p.V369A|HMMR_ENST00000353866.3_Missense_Mutation_p.V353A			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	114	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	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	
PBOV1	59351	hgsc.bcm.edu	37	6	138539372	138539372	+	Missense_Mutation	SNP	C	C	T	rs73774688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138539372C>T	ENST00000527246.2	-	1	255	c.161G>A	c.(160-162)cGa>cAa	p.R54Q	KIAA1244_ENST00000251691.4_Intron	NM_021635.2	NP_067648.1	Q9GZY1	PBOV1_HUMAN	prostate and breast cancer overexpressed 1	54						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)	1	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00055)|GBM - Glioblastoma multiforme(68;0.000674)		TTCTTTTTTTCGAAATACCTt	0.398													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		20845	0.0		0.0	False		,,,				2504	0.0				p.R54Q		Atlas-SNP	.											PBOV1_ENST00000527246,NS,carcinoma,-1,2	PBOV1	12	2	0			c.G161A						PASS	.	C	GLN/ARG,	107,4299	69.2+/-107.0	0,107,2096	124.0	121.0	122.0		161,	0.7	0.0	6	dbSNP_130	122	0,8600		0,0,4300	yes	missense,intron	KIAA1244,PBOV1	NM_021635.2,NM_020340.4	43,	0,107,6396	TT,TC,CC		0.0,2.4285,0.8227	probably-damaging,	54/136,	138539372	107,12899	2203	4300	6503	SO:0001583	missense	59351	exon1			TTTTTTCGAAATA	AF189269	CCDS5190.1	6q23.3	2012-02-09			ENSG00000254440	ENSG00000254440			21079	protein-coding gene	gene with protein product		605669				12553037, 11156405	Standard	NM_021635		Approved	UC28, UROC28	uc003qhv.3	Q9GZY1	OTTHUMG00000167040	ENST00000527246.2:c.161G>A	6.37:g.138539372C>T	ENSP00000432353:p.Arg54Gln	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	160	75	0.46875	NM_021635		Missense_Mutation	SNP	ENST00000527246.2	37	CCDS5190.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	6.594	0.478015	0.12521	0.024285	0.0	ENSG00000254440	ENST00000527246	T	0.43294	0.95	2.62	0.733	0.18289	.	.	.	.	.	T	0.05868	0.0153	N	0.08118	0	0.09310	N	1	D	0.56035	0.974	B	0.32342	0.144	T	0.16394	-1.0404	9	0.87932	D	0	.	5.1595	0.15054	0.0:0.6937:0.0:0.3063	.	54	Q9GZY1	PBOV1_HUMAN	Q	54	ENSP00000432353:R54Q	ENSP00000432353:R54Q	R	-	2	0	PBOV1	138581065	0.004000	0.15560	0.005000	0.12908	0.122000	0.20287	0.148000	0.16224	0.034000	0.15491	-0.880000	0.02959	CGA	C|0.991;T|0.009	0.009	strong		0.398	PBOV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392617.1	NM_021635	
CAST	831	hgsc.bcm.edu	37	5	96082128	96082128	+	Splice_Site	SNP	C	C	T	rs78054235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:96082128C>T	ENST00000341926.3	+	15	1196	c.1034C>T	c.(1033-1035)aCg>aTg	p.T345M	CAST_ENST00000508608.1_Splice_Site_p.T391M|CAST_ENST00000511049.1_Splice_Site_p.T331M|CAST_ENST00000359176.4_Splice_Site_p.T409M|CAST_ENST00000325674.7_Splice_Site_p.T393M|CAST_ENST00000508830.1_Splice_Site_p.T428M|CAST_ENST00000509903.1_Splice_Site_p.T310M|CAST_ENST00000395813.1_Splice_Site_p.T428M|CAST_ENST00000510756.1_Splice_Site_p.T406M|CAST_ENST00000504465.1_Splice_Site_p.T273M|CAST_ENST00000508579.1_Splice_Site_p.T60M|CAST_ENST00000309190.5_Splice_Site_p.T323M|CAST_ENST00000338252.3_Splice_Site_p.T332M|CAST_ENST00000395812.2_Splice_Site_p.T387M|CAST_ENST00000348386.3_3'UTR|CAST_ENST00000515663.1_Splice_Site_p.T68M|CAST_ENST00000511782.1_Splice_Site_p.T331M			P20810	ICAL_HUMAN	calpastatin	345					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		AAACCAGCCACGGTAAATTTT	0.418													c|||	63	0.0125799	0.0454	0.0014	5008	,	,		20246	0.0		0.0	False		,,,				2504	0.002				p.T387M		Atlas-SNP	.											.	CAST	58	.	0			c.C1160T						PASS	.	T	MET/THR,MET/THR,MET/THR	135,4271	98.0+/-136.7	2,131,2070	121.0	125.0	124.0		1160,995,968	1.3	1.0	5	dbSNP_131	124	2,8598	2.2+/-6.3	0,2,4298	yes	missense-near-splice,missense-near-splice,missense-near-splice	CAST	NM_001042440.2,NM_001190442.1,NM_173060.3	81,81,81	2,133,6368	TT,TC,CC		0.0233,3.064,1.0534	benign,benign,benign	387/751,332/696,323/687	96082128	137,12869	2203	4300	6503	SO:0001630	splice_region_variant	831	exon15			CAGCCACGGTAAA	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.1035+1C>T	5.37:g.96082128C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	225	112	0.497778	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Missense_Mutation	SNP	ENST00000341926.3	37		21|21	0.009615384615384616|0.009615384615384616	20|20	0.04065040650406504|0.04065040650406504	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	c|c	8.238|8.238	0.806130|0.806130	0.16467|0.16467	0.03064|0.03064	2.33E-4|2.33E-4	ENSG00000153113|ENSG00000153113	ENST00000437034|ENST00000338252;ENST00000508830;ENST00000511097;ENST00000395813;ENST00000359176;ENST00000325674;ENST00000395812;ENST00000510756;ENST00000508608;ENST00000341926;ENST00000511049;ENST00000309190;ENST00000510156;ENST00000504465;ENST00000509903;ENST00000511782;ENST00000508579;ENST00000503828;ENST00000515663	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.22743	.|2.24;2.24;1.94;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24	6.17|6.17	1.3|1.3	0.21679|0.21679	.|.	.|0.548082	.|0.21244	.|N	.|0.077779	T|T	0.05731|0.05731	0.0150|0.0150	L|L	0.36672|0.36672	1.1|1.1	0.24426|0.24426	N|N	0.994593|0.994593	.|P;P;B;D;B;D;B;B;B;B;B;P;B;P;B;B;B	.|0.59767	.|0.867;0.79;0.366;0.962;0.43;0.986;0.132;0.055;0.178;0.284;0.055;0.84;0.245;0.741;0.451;0.378;0.178	.|B;B;B;B;B;P;B;B;B;B;B;B;B;B;B;B;B	.|0.57057	.|0.345;0.199;0.108;0.417;0.21;0.812;0.131;0.021;0.057;0.1;0.061;0.234;0.058;0.287;0.066;0.058;0.197	T|T	0.03043|0.03043	-1.1079|-1.1079	5|10	.|0.46703	.|T	.|0.11	-0.1946|-0.1946	5.1484|5.1484	0.14996|0.14996	0.1336:0.5121:0.0:0.3543|0.1336:0.5121:0.0:0.3543	.|.	.|273;193;391;68;96;68;331;310;323;304;345;393;387;409;406;428;332	.|E9PDE4;B7Z8S8;B7Z468;E7EQA0;Q86YM9;E7EPY6;E7EVY3;E9PCH5;G5E946;P20810-4;P20810;P20810-5;G5E9D3;P20810-7;E7ESM9;P20810-6;P20810-2	.|.;.;.;.;.;.;.;.;.;.;ICAL_HUMAN;.;.;.;.;.;.	W|M	97|332;428;393;428;409;393;387;406;391;345;331;323;345;273;310;331;60;60;68	.|ENSP00000343421:T332M;ENSP00000425721:T428M;ENSP00000422951:T393M;ENSP00000379158:T428M;ENSP00000352098:T409M;ENSP00000320319:T393M;ENSP00000379157:T387M;ENSP00000422176:T406M;ENSP00000422677:T391M;ENSP00000339914:T345M;ENSP00000421130:T331M;ENSP00000312523:T323M;ENSP00000422325:T345M;ENSP00000425670:T273M;ENSP00000426946:T310M;ENSP00000423638:T331M;ENSP00000425787:T60M;ENSP00000422807:T60M;ENSP00000422929:T68M	.|ENSP00000312523:T323M	R|T	+|+	1|2	2|0	CAST|CAST	96107884|96107884	0.001000|0.001000	0.12720|0.12720	0.998000|0.998000	0.56505|0.56505	0.117000|0.117000	0.20001|0.20001	-0.754000|-0.754000	0.04787|0.04787	0.168000|0.168000	0.19655|0.19655	-0.733000|-0.733000	0.03571|0.03571	CGG|ACG	C|0.988;T|0.012	0.012	strong		0.418	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062	Missense_Mutation
SIRPA	140885	hgsc.bcm.edu	37	20	1902292	1902292	+	Missense_Mutation	SNP	G	G	A	rs200513155		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1902292G>A	ENST00000358771.4	+	3	840	c.688G>A	c.(688-690)Gtg>Atg	p.V230M	SIRPA_ENST00000356025.3_Missense_Mutation_p.V230M|SIRPA_ENST00000400068.3_Missense_Mutation_p.V230M	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	230	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.V230M(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CATCTGCGAGGTGGCCCACGT	0.612																																					p.V230M	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA_ENST00000400068,NS,carcinoma,0,5	SIRPA	83	5	1	Substitution - Missense(1)	lung(1)	c.G688A						scavenged	.						66.0	57.0	60.0					20																	1902292		2203	4296	6499	SO:0001583	missense	140885	exon4			TGCGAGGTGGCCC	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.688G>A	20.37:g.1902292G>A	ENSP00000351621:p.Val230Met	Somatic	547	0	0		WXS	Illumina HiSeq	Phase_I	572	15	0.0262238	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	23	0.010531135531135532	4	0.008130081300813009	2	0.0055248618784530384	6	0.01048951048951049	11	0.014511873350923483	G	19.90	3.912586	0.72983	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.13538	2.58;2.58;2.58	4.86	4.86	0.63082	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.115071	0.38720	N	0.001599	T	0.38081	0.1027	H	0.95294	3.65	0.45634	D	0.99856	D;D;D	0.69078	0.993;0.984;0.997	D;P;P	0.62955	0.909;0.562;0.878	T	0.57556	-0.7791	10	0.66056	D	0.02	.	13.7542	0.62926	0.0:0.0:1.0:0.0	.	210;230;230	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	M	230	ENSP00000382941:V230M;ENSP00000348307:V230M;ENSP00000351621:V230M	ENSP00000348307:V230M	V	+	1	0	SIRPA	1850292	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	1.834000	0.39171	2.718000	0.92993	0.650000	0.86243	GTG	G|0.989;A|0.011	0.011	strong		0.612	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
C16orf82	162083	hgsc.bcm.edu	37	16	27078462	27078462	+	lincRNA	SNP	T	T	C	rs114324679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27078462T>C	ENST00000505035.1	+	0	435				RP11-673P17.2_ENST00000565783.1_RNA			Q7Z2V1	TNT_HUMAN	chromosome 16 open reading frame 82																		CATGCAGGAGTGGCTCAGGAG	0.607													C|||	96	0.0191693	0.0711	0.0014	5008	,	,		17070	0.0		0.001	False		,,,				2504	0.0				p.V49A		Atlas-SNP	.											.	.	.	.	0			c.T146C						PASS	.	C	ALA/VAL	219,4001		6,207,1897	21.0	26.0	24.0		146	-3.7	0.0	16	dbSNP_132	24	6,8484		0,6,4239	yes	missense	C16orf82	NM_001145545.1	64	6,213,6136	CC,CT,TT		0.0707,5.1896,1.7703	benign	49/155	27078462	225,12485	2110	4245	6355			162083	exon1			CAGGAGTGGCTCA	BC031257		16p12.1	2013-01-24			ENSG00000234186	ENSG00000234186			30755	other	unknown						12477932	Standard	NM_001145545		Approved	TNT	uc010vcm.2	Q7Z2V1	OTTHUMG00000161986		16.37:g.27078462T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_001145545	B9EGC2|Q8NEF0	Missense_Mutation	SNP	ENST00000505035.1	37																																																																																				T|0.984;C|0.016	0.016	strong		0.607	C16orf82-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000366634.1	NM_001145545	
PTPRF	5792	hgsc.bcm.edu	37	1	44083519	44083519	+	Silent	SNP	G	G	A	rs641351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44083519G>A	ENST00000359947.4	+	25	4648	c.4308G>A	c.(4306-4308)agG>agA	p.R1436R	PTPRF_ENST00000422171.2_Silent_p.R795R|PTPRF_ENST00000372414.3_Silent_p.R1436R|PTPRF_ENST00000372413.3_Silent_p.R1427R|PTPRF_ENST00000438120.1_Silent_p.R1427R|PTPRF_ENST00000496447.1_3'UTR	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1436	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)				ATTTCTGGAGGATGGTGTGGG	0.617													A|||	3692	0.73722	0.9455	0.5764	5008	,	,		19953	0.7649		0.7157	False		,,,				2504	0.5634				p.R1436R		Atlas-SNP	.											.	PTPRF	172	.	0			c.G4308A						PASS	.	A	,	4040,366	186.7+/-213.5	1857,326,20	54.0	53.0	53.0		4308,4281	2.3	1.0	1	dbSNP_83	53	6431,2169	370.0+/-335.7	2440,1551,309	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	4297,1877,329	AA,AG,GG		25.2209,8.3069,19.491	,	1436/1908,1427/1899	44083519	10471,2535	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon25			CTGGAGGATGGTG	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.4308G>A	1.37:g.44083519G>A		Somatic	333	0	0		WXS	Illumina HiSeq	Phase_I	259	258	0.996139	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	1671|1671	0.7651098901098901|0.7651098901098901	459|459	0.9329268292682927|0.9329268292682927	238|238	0.6574585635359116|0.6574585635359116	425|425	0.743006993006993|0.743006993006993	549|549	0.7242744063324539|0.7242744063324539	A|A	10.11|10.11	1.260861|1.260861	0.23051|0.23051	0.916931|0.916931	0.747791|0.747791	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	5.58|5.58	2.32|2.32	0.28847|0.28847	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.16571|0.16571	-1.0398|-1.0398	3|3	.|.	.|.	.|.	.|.	9.1101|9.1101	0.36723|0.36723	0.1843:0.2027:0.613:0.0|0.1843:0.2027:0.613:0.0	rs641351;rs1065774;rs17380724;rs57918403|rs641351;rs1065774;rs17380724;rs57918403	.|.	.|.	.|.	N|E	820;861|1082	.|.	.|.	D|G	+|+	1|2	0|0	PTPRF|PTPRF	43856106|43856106	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.907000|0.907000	0.53573|0.53573	1.439000|1.439000	0.35013|0.35013	0.384000|0.384000	0.24942|0.24942	-0.834000|-0.834000	0.03071|0.03071	GAT|GGA	A|0.793;G|0.207;T|0.000	0.793	strong		0.617	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
FNDC7	163479	hgsc.bcm.edu	37	1	109273351	109273351	+	Missense_Mutation	SNP	C	C	A	rs76462144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109273351C>A	ENST00000370017.3	+	9	1957	c.1680C>A	c.(1678-1680)aaC>aaA	p.N560K	FNDC7_ENST00000271311.2_Missense_Mutation_p.N561K	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	560	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				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)		CAGTAATCAACGTGAGCTGGA	0.453													C|||	140	0.0279553	0.1006	0.0086	5008	,	,		19811	0.0		0.001	False		,,,				2504	0.0				p.N560K		Atlas-SNP	.											FNDC7_ENST00000370017,NS,carcinoma,0,2	FNDC7	113	2	0			c.C1680A						PASS	.	C	LYS/ASN	382,4024	193.3+/-218.5	18,346,1839	151.0	133.0	139.0		1680	-0.3	1.0	1	dbSNP_131	139	4,8596	3.7+/-12.6	0,4,4296	yes	missense	FNDC7	NM_001144937.1	94	18,350,6135	AA,AC,CC		0.0465,8.67,2.9679	probably-damaging	560/734	109273351	386,12620	2203	4300	6503	SO:0001583	missense	163479	exon9			AATCAACGTGAGC		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.1680C>A	1.37:g.109273351C>A	ENSP00000359034:p.Asn560Lys	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	153	77	0.503268	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	37	CCDS44185.1	67|67	0.030677655677655676|0.030677655677655676	63|63	0.12804878048780488|0.12804878048780488	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	C|C	19.57|19.57	3.852633|3.852633	0.71719|0.71719	0.0867|0.0867	4.65E-4|4.65E-4	ENSG00000143107|ENSG00000143107	ENST00000370017;ENST00000271311|ENST00000445274	D;D|.	0.99220|.	-5.58;-5.58|.	6.05|6.05	-0.336|-0.336	0.12658|0.12658	Fibronectin, type III (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58337|0.58337	0.2115|0.2115	M|M	0.72894|0.72894	2.215|2.215	0.48135|0.48135	D|D	0.999597|0.999597	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.998|.	T|T	0.62300|0.62300	-0.6883|-0.6883	10|5	0.05833|.	T|.	0.94|.	-25.7874|-25.7874	12.6633|12.6633	0.56826|0.56826	0.0:0.563:0.0:0.437|0.0:0.563:0.0:0.437	.|.	561;560|.	Q5VTL7;E9PAZ5|.	FNDC7_HUMAN;.|.	K|S	560;561|336	ENSP00000359034:N560K;ENSP00000271311:N561K|.	ENSP00000271311:N561K|.	N|R	+|+	3|1	2|0	FNDC7|FNDC7	109074874|109074874	0.002000|0.002000	0.14202|0.14202	0.998000|0.998000	0.56505|0.56505	0.989000|0.989000	0.77384|0.77384	-1.351000|-1.351000	0.02622|0.02622	0.023000|0.023000	0.15187|0.15187	0.655000|0.655000	0.94253|0.94253	AAC|CGT	A|0.027;C|0.973;T|0.000	0.027	strong		0.453	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
MUC16	94025	hgsc.bcm.edu	37	19	9061559	9061559	+	Silent	SNP	C	C	G	rs1423052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	421	0	0		WXS	Illumina HiSeq	Phase_I	430	234	0.544186	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	
FAM131C	348487	hgsc.bcm.edu	37	1	16385178	16385178	+	Silent	SNP	G	G	A	rs80297394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16385178G>A	ENST00000375662.4	-	7	780	c.597C>T	c.(595-597)ccC>ccT	p.P199P	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	199								p.P199P(2)		large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		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;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGGCCGCTGGGAAGGCTGT	0.647																																					p.P199P		Atlas-SNP	.											FAM131C,NS,carcinoma,0,2	FAM131C	21	2	2	Substitution - coding silent(2)	prostate(1)|lung(1)	c.C597T						scavenged	.						22.0	21.0	22.0					1																	16385178		2007	4137	6144	SO:0001819	synonymous_variant	348487	exon7			GCCGCTGGGAAGG		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.597C>T	1.37:g.16385178G>A		Somatic	492	2	0.00406504		WXS	Illumina HiSeq	Phase_I	739	176	0.23816	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			G|0.931;A|0.069	0.069	strong		0.647	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
FLG2	388698	hgsc.bcm.edu	37	1	152324397	152324397	+	Silent	SNP	G	G	A	rs79983774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152324397G>A	ENST00000388718.5	-	3	5937	c.5865C>T	c.(5863-5865)caC>caT	p.H1955H	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1955					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTACTCACTGTGGCCAGATC	0.532													g|||	341	0.0680911	0.2421	0.0231	5008	,	,		27530	0.0		0.005	False		,,,				2504	0.0				p.H1955H		Atlas-SNP	.											.	FLG2	431	.	0			c.C5865T						PASS	.	G		841,3565	331.8+/-302.1	70,701,1432	329.0	310.0	316.0		5865	-2.1	0.0	1	dbSNP_131	316	25,8575	17.9+/-57.8	0,25,4275	no	coding-synonymous	FLG2	NM_001014342.2		70,726,5707	AA,AG,GG		0.2907,19.0876,6.6585		1955/2392	152324397	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			CTCACTGTGGCCA	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.5865C>T	1.37:g.152324397G>A		Somatic	383	0	0		WXS	Illumina HiSeq	Phase_I	426	211	0.495305	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			G|0.940;A|0.060	0.060	strong		0.532	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084435	31084435	+	Intron	SNP	G	G	A	rs1062470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	37	18	0.486486	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	
NBPF3	84224	hgsc.bcm.edu	37	1	21795287	21795287	+	Silent	SNP	G	G	A	rs10157037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21795287G>A	ENST00000318249.5	+	3	590	c.240G>A	c.(238-240)tcG>tcA	p.S80S	NBPF3_ENST00000342104.5_Silent_p.S80S|NBPF3_ENST00000318220.6_Silent_p.S24S|NBPF3_ENST00000454000.2_Intron	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	80						cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ACAAGAAATCGCGCCCCCAGC	0.502											OREG0013205	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	267	0.0533147	0.1467	0.0951	5008	,	,		17981	0.001		0.002	False		,,,				2504	0.0041				p.K80K		Atlas-SNP	.											.	NBPF3	55	.	0			c.A240A						PASS	.	G		498,3908		32,434,1737	85.0	99.0	94.0		240	-2.3	0.0	1	dbSNP_119	94	57,8543		1,55,4244	no	coding-synonymous	NBPF3	NM_032264.2		33,489,5981	AA,AG,GG		0.6628,11.3028,4.2673		80/634	21795287	555,12451	2203	4300	6503	SO:0001819	synonymous_variant	84224	exon3			GAAATCGCGCCCC	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.240G>A	1.37:g.21795287G>A		Somatic	195	0	0	751	WXS	Illumina HiSeq	Phase_I	191	95	0.497382	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Silent	SNP	ENST00000318249.5	37	CCDS216.1																																																																																			G|0.953;A|0.047	0.047	strong		0.502	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
TF	7018	hgsc.bcm.edu	37	3	133473445	133473445	+	Silent	SNP	C	C	T	rs41298987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133473445C>T	ENST00000402696.3	+	4	917	c.432C>T	c.(430-432)tcC>tcT	p.S144S	TF_ENST00000264998.3_Silent_p.S17S|TF_ENST00000475382.1_3'UTR|TFP1_ENST00000460564.1_RNA	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	144	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)	TAGGCAGGTCCGCTGGGTGGA	0.522													C|||	64	0.0127796	0.0446	0.0043	5008	,	,		20464	0.002		0.0	False		,,,				2504	0.0				p.S144S		Atlas-SNP	.											TF,rectum,carcinoma,0,1	TF	116	1	0			c.C432T						PASS	.	C		151,4255	103.8+/-142.4	1,149,2053	182.0	178.0	179.0		432	-10.5	0.1	3	dbSNP_127	179	0,8600		0,0,4300	no	coding-synonymous	TF	NM_001063.3		1,149,6353	TT,TC,CC		0.0,3.4271,1.161		144/699	133473445	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon4			CAGGTCCGCTGGG		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.432C>T	3.37:g.133473445C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	164	89	0.542683	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			C|0.988;T|0.012	0.012	strong		0.522	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
GRIA3	2892	hgsc.bcm.edu	37	X	122537277	122537277	+	Silent	SNP	T	T	C	rs502434	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:122537277T>C	ENST00000371251.1	+	9	1252	c.1200T>C	c.(1198-1200)aaT>aaC	p.N400N	GRIA3_ENST00000541091.1_Silent_p.N384N|GRIA3_ENST00000264357.5_Silent_p.N400N|GRIA3_ENST00000371256.5_Silent_p.N400N|GRIA3_ENST00000542149.1_Silent_p.N400N			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	400					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	GCTACTGGAATGAGTATGAAA	0.423													T|||	1997	0.529007	0.3003	0.4308	3775	,	,		13991	0.5208		0.4682	False		,,,				2504	0.3119				p.N400N		Atlas-SNP	.											.	GRIA3	386	.	0			c.T1200C						PASS	.	T	,	1647,2188		290,803,264,539,307	210.0	194.0	199.0		1200,1200	2.2	1.0	X	dbSNP_83	199	4115,2613		895,1165,1160,368,712	no	coding-synonymous,coding-synonymous	GRIA3	NM_000828.4,NM_007325.4	,	1185,1968,1424,907,1019	CC,CT,C,TT,T		38.8377,42.9465,45.4511	,	400/895,400/895	122537277	5762,4801	2203	4300	6503	SO:0001819	synonymous_variant	2892	exon9			CTGGAATGAGTAT	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4573	protein-coding gene	gene with protein product		305915	"""glutamate receptor, ionotrophic, AMPA 3"""	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.1200T>C	X.37:g.122537277T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	134	76	0.567164	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Silent	SNP	ENST00000371251.1	37	CCDS14604.1																																																																																			T|0.440;0|0.004	.	strong		0.423	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828	
TNFAIP6	7130	hgsc.bcm.edu	37	2	152226570	152226570	+	Missense_Mutation	SNP	A	A	G	rs1046668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152226570A>G	ENST00000243347.3	+	4	506	c.431A>G	c.(430-432)cAa>cGa	p.Q144R	MIR4773-1_ENST00000585225.1_RNA|RN7SL124P_ENST00000498656.2_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	55	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	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	
C2orf54	79919	hgsc.bcm.edu	37	2	241835379	241835379	+	Silent	SNP	G	G	A	rs12105122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	18	0	0		WXS	Illumina HiSeq	Phase_I	37	25	0.675676	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	
CEACAM8	1088	hgsc.bcm.edu	37	19	43093718	43093718	+	Silent	SNP	C	C	T	rs10413332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43093718C>T	ENST00000244336.5	-	3	695	c.594G>A	c.(592-594)agG>agA	p.R198R	CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000594624.2_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	198	Ig-like C2-type 1.				immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				GAGTGAGGGTCCTGTTGCCAT	0.522													C|||	355	0.0708866	0.2542	0.0231	5008	,	,		18633	0.0		0.003	False		,,,				2504	0.0				p.R198R		Atlas-SNP	.											.	CEACAM8	44	.	0			c.G594A						PASS	.	C		874,3532	341.2+/-306.6	92,690,1421	271.0	241.0	251.0		594	1.3	0.6	19	dbSNP_119	251	18,8582	10.5+/-38.8	0,18,4282	no	coding-synonymous	CEACAM8	NM_001816.3		92,708,5703	TT,TC,CC		0.2093,19.8366,6.8584		198/350	43093718	892,12114	2203	4300	6503	SO:0001819	synonymous_variant	1088	exon3			GAGGGTCCTGTTG	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.594G>A	19.37:g.43093718C>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	291	123	0.42268	NM_001816	O60399|Q16574	Silent	SNP	ENST00000244336.5	37	CCDS12610.1																																																																																			C|0.938;T|0.062	0.062	strong		0.522	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249125	71249125	+	Silent	SNP	A	A	G	rs537752041|rs113379698|rs55848980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249125A>G	ENST00000398534.3	+	1	55	c.24A>G	c.(22-24)ggA>ggG	p.G8G		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	8						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						GCTGCTCTGGAGGCTGTGGCT	0.652																																					p.G8G		Atlas-SNP	.											KRTAP5-8,rectum,carcinoma,0,2	KRTAP5-8	28	2	0			c.A24G						scavenged	.						47.0	66.0	60.0					11																	71249125		2189	4280	6469	SO:0001819	synonymous_variant	57830	exon1			CTCTGGAGGCTGT	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.24A>G	11.37:g.71249125A>G		Somatic	327	1	0.0030581		WXS	Illumina HiSeq	Phase_I	234	55	0.235043	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																			A|0.500;G|0.500	0.500	weak		0.652	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
COX10	1352	hgsc.bcm.edu	37	17	14005439	14005439	+	Silent	SNP	G	G	A	rs2159132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:14005439G>A	ENST00000261643.3	+	4	581	c.504G>A	c.(502-504)ctG>ctA	p.L168L	COX10_ENST00000537334.1_5'UTR|COX10_ENST00000536205.1_Intron	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	168					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)		TCGCAGCTCTGGTTGTAAGTA	0.493													A|||	2463	0.491813	0.5053	0.4813	5008	,	,		15872	0.3462		0.5855	False		,,,				2504	0.5348				p.L168L		Atlas-SNP	.											.	COX10	36	.	0			c.G504A						PASS	.	A		2250,2156	583.9+/-385.9	553,1144,506	158.0	133.0	142.0		504	-10.5	0.0	17	dbSNP_96	142	4975,3625	523.5+/-380.3	1422,2131,747	yes	coding-synonymous	COX10	NM_001303.3		1975,3275,1253	AA,AG,GG		42.1512,48.9333,44.4487		168/444	14005439	7225,5781	2203	4300	6503	SO:0001819	synonymous_variant	1352	exon4			AGCTCTGGTTGTA	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.504G>A	17.37:g.14005439G>A		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Silent	SNP	ENST00000261643.3	37	CCDS11166.1																																																																																			G|0.468;A|0.532	0.532	strong		0.493	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303	
HMHA1	23526	hgsc.bcm.edu	37	19	1085690	1085690	+	Silent	SNP	G	G	A	rs149960692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1085690G>A	ENST00000313093.2	+	23	3327	c.3096G>A	c.(3094-3096)tcG>tcA	p.S1032S	HMHA1_ENST00000591169.1_3'UTR|POLR2E_ENST00000585838.1_5'Flank|HMHA1_ENST00000586866.1_Silent_p.S1036S|HMHA1_ENST00000590214.1_Silent_p.S1059S|HMHA1_ENST00000536472.1_Silent_p.S900S|HMHA1_ENST00000543365.1_Silent_p.S915S|HMHA1_ENST00000590577.1_Silent_p.S667S|HMHA1_ENST00000539243.2_Silent_p.S1048S	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	1032					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)		ATTCGGACTCGGACCTAGAGG	0.617													g|||	36	0.0071885	0.0272	0.0	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.S1048S		Atlas-SNP	.											.	HMHA1	78	.	0			c.G3144A						PASS	.	G		87,4271		1,85,2093	10.0	13.0	12.0		3096	-6.4	1.0	19	dbSNP_134	12	1,8533		0,1,4266	no	coding-synonymous	HMHA1	NM_012292.2		1,86,6359	AA,AG,GG		0.0117,1.9963,0.6826		1032/1137	1085690	88,12804	2179	4267	6446	SO:0001819	synonymous_variant	23526	exon23			GGACTCGGACCTA	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.3096G>A	19.37:g.1085690G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	119	63	0.529412	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			G|0.993;A|0.007	0.007	strong		0.617	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
ITGAL	3683	hgsc.bcm.edu	37	16	30495496	30495496	+	Silent	SNP	C	C	T	rs7191097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30495496C>T	ENST00000356798.6	+	9	1098	c.918C>T	c.(916-918)ccC>ccT	p.P306P	RP11-297C4.2_ENST00000569459.1_RNA|ITGAL_ENST00000358164.5_Silent_p.P223P|ITGAL_ENST00000433423.2_Intron|RNU7-61P_ENST00000515897.1_RNA|RP11-297C4.3_ENST00000562525.1_RNA	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	306	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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)			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)	CATCAAAACCCGCGAGCGAGT	0.468													C|||	423	0.0844649	0.3086	0.0159	5008	,	,		18600	0.0		0.004	False		,,,				2504	0.0				p.P306P	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.C918T						PASS	.	C	,	1274,3120	434.7+/-344.0	192,890,1115	110.0	112.0	111.0		669,918	-3.8	0.0	16	dbSNP_116	111	27,8573	17.9+/-57.8	1,25,4274	no	coding-synonymous,coding-synonymous	ITGAL	NM_001114380.1,NM_002209.2	,	193,915,5389	TT,TC,CC		0.314,28.9941,10.0123	,	223/1087,306/1171	30495496	1301,11693	2197	4300	6497	SO:0001819	synonymous_variant	3683	exon9			AAAACCCGCGAGC		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.918C>T	16.37:g.30495496C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																			C|0.900;T|0.100	0.100	strong		0.468	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2		
ZNF799	90576	hgsc.bcm.edu	37	19	12502161	12502161	+	Missense_Mutation	SNP	A	A	T	rs541416821		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12502161A>T	ENST00000430385.3	-	4	1251	c.1051T>A	c.(1051-1053)Tca>Aca	p.S351T	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Missense_Mutation_p.S319T	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S351T(1)|p.S138T(1)		breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						CTTTTCAGTGAACTAGGACAA	0.413																																					p.S351T		Atlas-SNP	.											ZNF799_ENST00000430385,NS,carcinoma,0,2	ZNF799	111	2	2	Substitution - Missense(2)	kidney(2)	c.T1051A						scavenged	.						161.0	157.0	158.0					19																	12502161		2203	4300	6503	SO:0001583	missense	90576	exon4			TCAGTGAACTAGG	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"""Zinc fingers, C2H2-type"", ""-"""	28071	protein-coding gene	gene with protein product			"""zinc finger protein 842"""	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1051T>A	19.37:g.12502161A>T	ENSP00000411084:p.Ser351Thr	Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	117	5	0.042735	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	37	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.574140	0.28092	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.07567	3.18;3.18	1.31	1.31	0.21738	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09949	0.0244	N	0.16478	0.41	0.09310	N	1	D	0.60575	0.988	P	0.60173	0.87	T	0.34378	-0.9831	9	0.30078	T	0.28	.	6.6913	0.23174	1.0:0.0:0.0:0.0	.	351	Q96GE5	ZN799_HUMAN	T	319;351	ENSP00000415278:S319T;ENSP00000411084:S351T	ENSP00000415278:S319T	S	-	1	0	ZNF799	12363161	0.000000	0.05858	0.005000	0.12908	0.140000	0.21249	0.679000	0.25291	0.846000	0.35142	0.352000	0.21897	TCA	.	.	none		0.413	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821	
OBSCN	84033	hgsc.bcm.edu	37	1	228504591	228504591	+	Missense_Mutation	SNP	C	C	A	rs61825301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228504591C>A	ENST00000422127.1	+	51	13511	c.13467C>A	c.(13465-13467)caC>caA	p.H4489Q	OBSCN_ENST00000284548.11_Missense_Mutation_p.H4489Q|OBSCN_ENST00000570156.2_Missense_Mutation_p.H5446Q|OBSCN_ENST00000366709.4_Missense_Mutation_p.H1608Q|OBSCN_ENST00000366707.4_Missense_Mutation_p.H2123Q	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4489	Ig-like 46.			H -> Q (in Ref. 1; CAC44768). {ECO:0000305}.	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)				GCAGTCACCACGCCCTACTGC	0.716													c|||	728	0.145367	0.121	0.2349	5008	,	,		14096	0.1518		0.159	False		,,,				2504	0.0941				p.H5446Q		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C16338A						PASS	.		GLN/HIS,GLN/HIS	675,3615		55,565,1525	9.0	14.0	12.0		13467,13467	0.2	0.1	1	dbSNP_129	12	1406,7004		118,1170,2917	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	24,24	173,1735,4442	AA,AC,CC		16.7182,15.7343,16.3858	probably-damaging,probably-damaging	4489/7969,4489/6621	228504591	2081,10619	2145	4205	6350	SO:0001583	missense	84033	exon62			TCACCACGCCCTA	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.13467C>A	1.37:g.228504591C>A	ENSP00000409493:p.His4489Gln	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	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	346	0.15842490842490842	50	0.1016260162601626	86	0.23756906077348067	87	0.1520979020979021	123	0.16226912928759896	c	12.44	1.937450	0.34189	0.157343	0.167182	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.76968	-1.06;-1.06;0.09;0.6	5.41	0.187	0.15109	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.149471	0.46758	D	0.000266	T	0.00073	0.0002	L	0.59967	1.855	0.49130	P	2.4400000000002198E-4	D;D	0.76494	0.998;0.999	P;D	0.64042	0.835;0.921	T	0.16158	-1.0412	9	0.29301	T	0.29	.	9.7878	0.40686	0.0:0.5739:0.0:0.4261	rs61825301	4489;4489	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	Q	4489;4489;2123;1608	ENSP00000284548:H4489Q;ENSP00000409493:H4489Q;ENSP00000355668:H2123Q;ENSP00000355670:H1608Q	ENSP00000284548:H4489Q	H	+	3	2	OBSCN	226571214	0.000000	0.05858	0.074000	0.20217	0.153000	0.21895	-0.722000	0.04958	-0.223000	0.09943	0.550000	0.68814	CAC	C|0.841;A|0.159	0.159	strong		0.716	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OR5H1	26341	hgsc.bcm.edu	37	3	97852229	97852229	+	Missense_Mutation	SNP	T	T	A	rs9849637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	272	0	0		WXS	Illumina HiSeq	Phase_I	289	288	0.99654	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	
OR5B3	441608	hgsc.bcm.edu	37	11	58169996	58169996	+	Missense_Mutation	SNP	T	T	C	rs12279895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58169996T>C	ENST00000309403.2	-	1	886	c.887A>G	c.(886-888)aAg>aGg	p.K296R		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	296			K -> R (in dbSNP:rs12279895).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K296R(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GAATGCACTCTTCACTTCCTT	0.428													T|||	1453	0.290136	0.3533	0.2695	5008	,	,		20749	0.1448		0.3628	False		,,,				2504	0.2945				p.K296R		Atlas-SNP	.											OR5B3,NS,carcinoma,0,1	OR5B3	65	1	1	Substitution - Missense(1)	stomach(1)	c.A887G						PASS	.	T	ARG/LYS	1442,2960	468.1+/-355.0	229,984,988	159.0	132.0	142.0		887	3.9	0.9	11	dbSNP_120	142	3093,5497	473.7+/-368.7	549,1995,1751	yes	missense	OR5B3	NM_001005469.1	26	778,2979,2739	CC,CT,TT		36.007,32.7578,34.9061	possibly-damaging	296/315	58169996	4535,8457	2201	4295	6496	SO:0001583	missense	441608	exon1			GCACTCTTCACTT	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.887A>G	11.37:g.58169996T>C	ENSP00000308270:p.Lys296Arg	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	231	113	0.489177	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	655	0.2999084249084249	195	0.39634146341463417	89	0.24585635359116023	95	0.1660839160839161	276	0.3641160949868074	t	7.380	0.628589	0.14257	0.327578	0.36007	ENSG00000172769	ENST00000309403	T	0.23552	1.9	3.92	3.92	0.45320	.	0.314716	0.22940	N	0.053786	T	0.00012	0.0000	L	0.42744	1.35	0.80722	P	0.0	B	0.31752	0.338	B	0.33620	0.167	T	0.46190	-0.9209	9	0.72032	D	0.01	-24.2061	7.7587	0.28940	0.187:0.0:0.0:0.813	rs12279895;rs52812066;rs60634758;rs12279895	296	Q8NH48	OR5B3_HUMAN	R	296	ENSP00000308270:K296R	ENSP00000308270:K296R	K	-	2	0	OR5B3	57926572	0.022000	0.18835	0.891000	0.34965	0.096000	0.18686	0.918000	0.28678	1.768000	0.52137	0.533000	0.62120	AAG	T|0.672;C|0.328	0.328	strong		0.428	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
ZNF492	57615	hgsc.bcm.edu	37	19	22847917	22847917	+	Silent	SNP	T	T	C	rs201040917		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22847917T>C	ENST00000456783.2	+	4	1690	c.1446T>C	c.(1444-1446)tgT>tgC	p.C482C	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	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)			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)				GTGAAGAATGTGGCAAAGCCT	0.373																																					p.C482C		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,+1,1	ZNF492	129	1	0			c.T1446C						scavenged	.	T		172,3876		2,168,1854	27.0	39.0	36.0		1446	1.1	0.5	19	dbSNP_134	36	4,8488		0,4,4242	no	coding-synonymous	ZNF492	NM_020855.2		2,172,6096	CC,CT,TT		0.0471,4.249,1.4035		482/532	22847917	176,12364	2024	4246	6270	SO:0001819	synonymous_variant	57615	exon4			AGAATGTGGCAAA	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.1446T>C	19.37:g.22847917T>C		Somatic	310	1	0.00322581		WXS	Illumina HiSeq	Phase_I	26	23	0.884615	NM_020855	Q08EI7|Q08EI8	Silent	SNP	ENST00000456783.2	37	CCDS46032.1																																																																																			T|0.500;C|0.500	0.500	weak		0.373	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
WNT3A	89780	hgsc.bcm.edu	37	1	228238443	228238443	+	Missense_Mutation	SNP	G	G	A	rs61743220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228238443G>A	ENST00000284523.1	+	3	478	c.400G>A	c.(400-402)Gcc>Acc	p.A134T	WNT3A_ENST00000366753.2_Missense_Mutation_p.A134T	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	134					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|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)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	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)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				AGGCACGGCCGCCATCTGTGG	0.627													G|||	31	0.0061901	0.0234	0.0	5008	,	,		17447	0.0		0.0	False		,,,				2504	0.0				p.A134T		Atlas-SNP	.											.	WNT3A	40	.	0			c.G400A						PASS	.	G	THR/ALA	115,4291	86.3+/-125.0	1,113,2089	80.0	72.0	75.0		400	-2.0	0.0	1	dbSNP_129	75	0,8600		0,0,4300	yes	missense	WNT3A	NM_033131.3	58	1,113,6389	AA,AG,GG		0.0,2.6101,0.8842	benign	134/353	228238443	115,12891	2203	4300	6503	SO:0001583	missense	89780	exon3			ACGGCCGCCATCT	AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.400G>A	1.37:g.228238443G>A	ENSP00000284523:p.Ala134Thr	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	167	79	0.473054	NM_033131	Q3SY79|Q3SY80|Q969P2	Missense_Mutation	SNP	ENST00000284523.1	37	CCDS1564.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	0.524	-0.860772	0.02610	0.026101	0.0	ENSG00000154342	ENST00000284523;ENST00000366753	T;T	0.75367	-0.93;-0.93	4.78	-1.98	0.07480	.	0.443415	0.23894	N	0.043517	T	0.15782	0.0380	N	0.00771	-1.2	0.24533	N	0.994101	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.25984	-1.0116	10	0.10377	T	0.69	.	12.1436	0.54012	0.6823:0.0:0.3177:0.0	rs61743220	134;134	P56704;Q3SY79	WNT3A_HUMAN;.	T	134	ENSP00000284523:A134T;ENSP00000355715:A134T	ENSP00000284523:A134T	A	+	1	0	WNT3A	226305066	0.916000	0.31088	0.005000	0.12908	0.134000	0.20937	1.632000	0.37102	-0.810000	0.04375	-1.094000	0.02160	GCC	G|0.992;A|0.008	0.008	strong		0.627	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131	
LCN15	389812	hgsc.bcm.edu	37	9	139657874	139657874	+	Missense_Mutation	SNP	G	G	C	rs11145871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139657874G>C	ENST00000316144.5	-	4	377	c.353C>G	c.(352-354)tCc>tGc	p.S118C	LCN15_ENST00000482511.1_5'UTR	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15	118					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						GACGGCGAAGGAGCTGTAGTC	0.642													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		8323	0.0		0.0	False		,,,				2504	0.0				p.S118C		Atlas-SNP	.											.	LCN15	11	.	0			c.C353G						PASS	.	G	CYS/SER	55,4351	54.2+/-90.2	1,53,2149	83.0	75.0	77.0		353	3.8	0.3	9	dbSNP_120	77	0,8600		0,0,4300	yes	missense	LCN15	NM_203347.1	112	1,53,6449	CC,CG,GG		0.0,1.2483,0.4229	probably-damaging	118/185	139657874	55,12951	2203	4300	6503	SO:0001583	missense	389812	exon4			GCGAAGGAGCTGT		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"""Lipocalins"""	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943	ENST00000316144.5:c.353C>G	9.37:g.139657874G>C	ENSP00000313833:p.Ser118Cys	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	37	21	0.567568	NM_203347		Missense_Mutation	SNP	ENST00000316144.5	37	CCDS7006.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	14.93	2.681579	0.47991	0.012483	0.0	ENSG00000177984	ENST00000316144	T	0.08720	3.06	3.76	3.76	0.43208	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.023620	0.07803	N	0.956885	T	0.17577	0.0422	M	0.71581	2.175	0.09310	N	1	D	0.69078	0.997	P	0.58077	0.832	T	0.08700	-1.0709	10	0.62326	D	0.03	.	11.2408	0.48968	0.0:0.0:1.0:0.0	rs11145871	118	Q6UWW0	LCN15_HUMAN	C	118	ENSP00000313833:S118C	ENSP00000313833:S118C	S	-	2	0	LCN15	138777695	0.919000	0.31177	0.273000	0.24645	0.776000	0.43924	2.771000	0.47670	2.104000	0.64026	0.561000	0.74099	TCC	G|0.994;C|0.006	0.006	strong		0.642	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347	
SCN1A	6323	hgsc.bcm.edu	37	2	166900425	166900425	+	Silent	SNP	C	C	T	rs145035963		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166900425C>T	ENST00000303395.4	-	11	1796	c.1797G>A	c.(1795-1797)gaG>gaA	p.E599E	AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000423058.2_Silent_p.E599E|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000409050.1_Silent_p.E599E|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Silent_p.E599E			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	599					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCTCGTTATCCTCAAAGGTGC	0.527													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20315	0.0		0.0	False		,,,				2504	0.0				p.E599E		Atlas-SNP	.											.	SCN1A	641	.	0			c.G1797A						PASS	.	C	,,,	4,4402	8.1+/-20.4	0,4,2199	168.0	148.0	155.0		1797,1797,1797,1797	3.3	1.0	2	dbSNP_134	155	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	,,,	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	,,,	599/2010,599/1982,599/2010,599/1999	166900425	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	6323	exon11			GTTATCCTCAAAG	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1797G>A	2.37:g.166900425C>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	195	111	0.569231	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																			C|1.000;T|0.000	0.000	strong		0.527	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
NEIL2	252969	hgsc.bcm.edu	37	8	11640853	11640853	+	Silent	SNP	C	C	T	rs112549959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11640853C>T	ENST00000284503.6	+	4	1232	c.633C>T	c.(631-633)ggC>ggT	p.G211G	NEIL2_ENST00000436750.3_Silent_p.G211G|NEIL2_ENST00000455213.2_Silent_p.G211G|NEIL2_ENST00000403422.3_Silent_p.G150G|NEIL2_ENST00000528323.1_Silent_p.G95G	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	211					base-excision repair (GO:0006284)|nucleotide-excision repair (GO:0006289)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		AAGCTCTAGGCCAGGCTCAGC	0.517								Base excision repair (BER), DNA glycosylases					C|||	22	0.00439297	0.0159	0.0014	5008	,	,		23388	0.0		0.0	False		,,,				2504	0.0				p.G211G		Atlas-SNP	.											.	NEIL2	14	.	0			c.C633T						PASS	.	C	,,,	45,4361	48.2+/-83.0	0,45,2158	119.0	104.0	109.0		633,450,285,633	-3.7	0.1	8	dbSNP_132	109	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEIL2	NM_001135746.1,NM_001135747.1,NM_001135748.1,NM_145043.2	,,,	0,45,6458	TT,TC,CC		0.0,1.0213,0.346	,,,	211/333,150/272,95/217,211/333	11640853	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	252969	exon4			TCTAGGCCAGGCT	AK056206	CCDS5984.1, CCDS47802.1, CCDS47803.1	8p23.1	2010-04-27	2010-04-27		ENSG00000154328	ENSG00000154328			18956	protein-coding gene	gene with protein product		608933	"""nei like 2 (E. coli)"""			12097317, 17686777	Standard	NM_145043		Approved	NEH2, FLJ31644, MGC2832, MGC4505	uc003wue.2	Q969S2	OTTHUMG00000090753	ENST00000284503.6:c.633C>T	8.37:g.11640853C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	207	97	0.468599	NM_001135746	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Silent	SNP	ENST00000284503.6	37	CCDS5984.1																																																																																			C|0.996;T|0.004	0.004	strong		0.517	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043	
SKA1	220134	hgsc.bcm.edu	37	18	47908556	47908556	+	Missense_Mutation	SNP	G	G	A	rs6507992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47908556G>A	ENST00000285116.3	+	4	482	c.271G>A	c.(271-273)Gtt>Att	p.V91I	SKA1_ENST00000488454.1_5'UTR|SKA1_ENST00000417656.2_Missense_Mutation_p.V91I|SKA1_ENST00000398452.2_Missense_Mutation_p.V91I	NM_001039535.2|NM_145060.3	NP_001034624.1|NP_659497.1	Q96BD8	SKA1_HUMAN	spindle and kinetochore associated complex subunit 1	91			V -> I (in dbSNP:rs6507992). {ECO:0000269|PubMed:14702039}.		cell division (GO:0051301)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|spindle microtubule (GO:0005876)	microtubule binding (GO:0008017)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(1)|prostate(1)	13						TAAAGAAAACGTTCCTTCCCA	0.348													A|||	4027	0.804113	0.9251	0.7954	5008	,	,		18656	0.88		0.5994	False		,,,				2504	0.7791				p.V91I		Atlas-SNP	.											.	SKA1	21	.	0			c.G271A						PASS	.	A	ILE/VAL,ILE/VAL	3874,532	241.2+/-251.7	1713,448,42	84.0	87.0	86.0		271,271	2.0	1.0	18	dbSNP_116	86	5215,3385	501.5+/-375.5	1582,2051,667	yes	missense,missense	SKA1	NM_001039535.2,NM_145060.3	29,29	3295,2499,709	AA,AG,GG		39.3605,12.0744,30.1169	benign,benign	91/256,91/256	47908556	9089,3917	2203	4300	6503	SO:0001583	missense	220134	exon4			GAAAACGTTCCTT	BC015706	CCDS11946.1	18q21.1	2013-01-17	2009-08-19	2009-08-19	ENSG00000154839	ENSG00000154839			28109	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 24"""	C18orf24		17093495	Standard	NM_145060		Approved	MGC10200	uc002leu.3	Q96BD8	OTTHUMG00000132685	ENST00000285116.3:c.271G>A	18.37:g.47908556G>A	ENSP00000285116:p.Val91Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_001039535	B2R9Y6|B4E0P4	Missense_Mutation	SNP	ENST00000285116.3	37	CCDS11946.1	1664	0.7619047619047619	444	0.9024390243902439	268	0.7403314917127072	501	0.8758741258741258	451	0.5949868073878628	A	0.085	-1.176961	0.01646	0.879256	0.606395	ENSG00000154839	ENST00000285116;ENST00000417656;ENST00000398452	T;T;T	0.44881	0.91;0.91;0.91	5.66	1.95	0.26073	.	0.337447	0.33092	N	0.005289	T	0.00012	0.0000	N	0.02721	-0.515	0.09310	P	0.9999999999992604	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.41088	-0.9528	9	0.02654	T	1	-1.2451	8.559	0.33498	0.6853:0.0:0.3147:0.0	rs6507992;rs17661226;rs52818481;rs60344562;rs6507992	91;91	Q96BD8-2;Q96BD8	.;SKA1_HUMAN	I	91	ENSP00000285116:V91I;ENSP00000397222:V91I;ENSP00000381470:V91I	ENSP00000285116:V91I	V	+	1	0	SKA1	46162554	0.999000	0.42202	0.994000	0.49952	0.238000	0.25445	1.084000	0.30828	0.085000	0.17107	-0.361000	0.07541	GTT	G|0.256;A|0.744	0.744	strong		0.348	SKA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255982.2	NM_145060	
MUC17	140453	hgsc.bcm.edu	37	7	100677523	100677523	+	Missense_Mutation	SNP	A	A	C	rs10238201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677523A>C	ENST00000306151.4	+	3	2890	c.2826A>C	c.(2824-2826)agA>agC	p.R942S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	942	59 X approximate tandem repeats.|Ser-rich.		R -> S (in dbSNP:rs10238201).		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)					CTGAGGCTAGAACACTTTCAG	0.512													C|||	886	0.176917	0.2572	0.0879	5008	,	,		34163	0.1617		0.1103	False		,,,				2504	0.2157				p.R942S		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.A2826C						scavenged	.	C	SER/ARG	227,4179	779.7+/-414.4	0,227,1976	347.0	310.0	323.0		2826	-1.7	0.0	7	dbSNP_119	323	271,8329	790.0+/-407.6	0,271,4029	no	missense	MUC17	NM_001040105.1	110	0,498,6005	CC,CA,AA		3.1512,5.1521,3.829	benign	942/4494	100677523	498,12508	2203	4300	6503	SO:0001583	missense	140453	exon3			GGCTAGAACACTT	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.2826A>C	7.37:g.100677523A>C	ENSP00000302716:p.Arg942Ser	Somatic	133	3	0.0225564		WXS	Illumina HiSeq	Phase_I	222	87	0.391892	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	216	0.0989010989010989	72	0.14634146341463414	28	0.07734806629834254	52	0.09090909090909091	64	0.08443271767810026	C	1.927	-0.446949	0.04572	0.051521	0.031512	ENSG00000169876	ENST00000306151	T	0.02787	4.16	0.838	-1.68	0.08212	.	.	.	.	.	T	0.00012	0.0000	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34453	-0.9828	9	0.02654	T	1	.	3.2808	0.06915	0.3868:0.4201:0.0:0.1932	rs10238201	942	Q685J3	MUC17_HUMAN	S	942	ENSP00000302716:R942S	ENSP00000302716:R942S	R	+	3	2	MUC17	100464243	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-2.481000	0.00982	-2.432000	0.00556	-1.396000	0.01147	AGA	A|0.908;C|0.092	0.092	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ASAH1	427	hgsc.bcm.edu	37	8	17942204	17942204	+	5'Flank	SNP	C	C	T	rs13263632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17942204C>T	ENST00000262097.6	-	0	0				ASAH1_ENST00000417108.2_5'Flank|ASAH1_ENST00000381733.4_Missense_Mutation_p.S36N|CTD-2547L16.1_ENST00000499554.2_RNA|ASAH1_ENST00000520781.1_5'Flank|ASAH1_ENST00000314146.10_Missense_Mutation_p.S36N|CTD-2547L16.1_ENST00000517747.1_RNA|ASAH1_ENST00000520051.1_5'UTR|CTD-2547L16.1_ENST00000517798.1_RNA|CTD-2547L16.1_ENST00000505114.2_RNA|CTD-2547L16.1_ENST00000521775.1_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	63	0	0	721	WXS	Illumina HiSeq	Phase_I	56	26	0.464286	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	
ERP27	121506	hgsc.bcm.edu	37	12	15070187	15070187	+	Missense_Mutation	SNP	T	T	C	rs79989395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15070187T>C	ENST00000266397.2	-	5	1074	c.501A>G	c.(499-501)atA>atG	p.I167M	ERP27_ENST00000540097.1_Missense_Mutation_p.I66M|ERP27_ENST00000544881.1_5'UTR	NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	167						endoplasmic reticulum (GO:0005783)				breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						CCTTGTTCATTATCAGGAGGA	0.448													T|||	84	0.0167732	0.0	0.0	5008	,	,		21252	0.0446		0.0119	False		,,,				2504	0.0276				p.I167M		Atlas-SNP	.											.	ERP27	37	.	0			c.A501G						PASS	.	T	MET/ILE	2,4404	4.2+/-10.8	0,2,2201	215.0	187.0	196.0		501	-6.1	0.3	12	dbSNP_131	196	5,8595	4.3+/-15.6	0,5,4295	yes	missense	ERP27	NM_152321.2	10	0,7,6496	CC,CT,TT		0.0581,0.0454,0.0538	benign	167/274	15070187	7,12999	2203	4300	6503	SO:0001583	missense	121506	exon5			GTTCATTATCAGG	AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055		"""Protein disulfide isomerases"""	26495	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 8"""	610642	"""chromosome 12 open reading frame 46"", ""endoplasmic reticulum protein 27 kDa"""	C12orf46		12975309, 16940051	Standard	XM_005253303		Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000266397.2:c.501A>G	12.37:g.15070187T>C	ENSP00000266397:p.Ile167Met	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	224	120	0.535714	NM_152321		Missense_Mutation	SNP	ENST00000266397.2	37	CCDS8670.1	33	0.01510989010989011	0	0.0	0	0.0	21	0.03671328671328671	12	0.0158311345646438	T	9.988	1.229927	0.22542	4.54E-4	5.81E-4	ENSG00000139055	ENST00000266397;ENST00000540097	T;T	0.33654	1.4;1.4	5.36	-6.13	0.02118	Thioredoxin-like fold (1);	0.598338	0.18680	N	0.134197	T	0.02418	0.0074	N	0.08118	0	0.09310	N	1	B	0.19445	0.036	B	0.16289	0.015	T	0.05209	-1.0899	10	0.51188	T	0.08	-5.0132	1.6157	0.02703	0.2276:0.2012:0.1121:0.4592	.	167	Q96DN0	ERP27_HUMAN	M	167;66	ENSP00000266397:I167M;ENSP00000440573:I66M	ENSP00000266397:I167M	I	-	3	3	ERP27	14961454	0.046000	0.20272	0.291000	0.24904	0.964000	0.63967	-1.746000	0.01829	-0.977000	0.03537	-0.462000	0.05337	ATA	T|0.995;C|0.005	0.005	strong		0.448	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321	
TSPYL5	85453	hgsc.bcm.edu	37	8	98289922	98289922	+	Missense_Mutation	SNP	C	C	T	rs200123082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:98289922C>T	ENST00000322128.3	-	1	254	c.151G>A	c.(151-153)Gca>Aca	p.A51T		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	51					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					TGCACCTGTGCCGCCTGGGTG	0.746													C|||	37	0.00738818	0.0257	0.0043	5008	,	,		10609	0.0		0.0	False		,,,				2504	0.0				p.A51T		Atlas-SNP	.											.	TSPYL5	48	.	0			c.G151A						PASS	.	C	THR/ALA	59,4045		1,57,1994	5.0	7.0	6.0		151	1.2	0.0	8		6	2,8036		0,2,4017	yes	missense	TSPYL5	NM_033512.2	58	1,59,6011	TT,TC,CC		0.0249,1.4376,0.5024	possibly-damaging	51/418	98289922	61,12081	2052	4019	6071	SO:0001583	missense	85453	exon1			CCTGTGCCGCCTG	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.151G>A	8.37:g.98289922C>T	ENSP00000322802:p.Ala51Thr	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_033512	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	37	CCDS34927.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	C	2.842	-0.240359	0.05944	0.014376	2.49E-4	ENSG00000180543	ENST00000322128	T	0.23754	1.89	4.03	1.24	0.21308	.	0.260319	0.20293	N	0.095194	T	0.04998	0.0134	N	0.20986	0.625	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.32719	-0.9896	10	0.02654	T	1	-1.04	3.5525	0.07851	0.1976:0.5914:0.0:0.211	.	51	Q86VY4	TSYL5_HUMAN	T	51	ENSP00000322802:A51T	ENSP00000322802:A51T	A	-	1	0	TSPYL5	98359098	0.996000	0.38824	0.014000	0.15608	0.014000	0.08584	2.417000	0.44653	0.261000	0.21753	-0.258000	0.10820	GCA	C|0.994;T|0.006	0.006	strong		0.746	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512	
APOC2	344	hgsc.bcm.edu	37	19	45452429	45452429	+	Missense_Mutation	SNP	A	A	C	rs5126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45452429A>C	ENST00000590360.1	+	4	351	c.229A>C	c.(229-231)Aaa>Caa	p.K77Q	APOC2_ENST00000591597.1_Missense_Mutation_p.K63Q|APOC2_ENST00000252490.4_Missense_Mutation_p.K77Q|APOC4-APOC2_ENST00000589057.1_Missense_Mutation_p.K154Q|APOC2_ENST00000592257.1_3'UTR|APOC4_ENST00000419266.2_3'UTR|APOC2_ENST00000585786.1_3'UTR			P02655	APOC2_HUMAN	apolipoprotein C-II	77	Lipoprotein lipase cofactor.		K -> Q (in Africa; dbSNP:rs5126). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:3944271}.		cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(1)|liver(1)|lung(3)	6	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)		CTTGTACAGCAAAAGCACAGC	0.567													A|||	39	0.00778754	0.0287	0.0014	5008	,	,		15843	0.0		0.0	False		,,,				2504	0.0				p.K77Q		Atlas-SNP	.											.	APOC2	9	.	0			c.A229C						PASS	.	A	GLN/LYS	85,4321	47.5+/-82.1	1,83,2119	79.0	66.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	229	2.0	0.4	19	dbSNP_52	71	0,8600		0,0,4300	yes	missense	APOC2	NM_000483.4	53	1,83,6419	CC,CA,AA		0.0,1.9292,0.6535	probably-damaging	77/102	45452429	85,12921	2203	4300	6503	SO:0001583	missense	344	exon4			TACAGCAAAAGCA	X00568	CCDS12650.1	19q13.2	2013-01-24			ENSG00000234906	ENSG00000234906		"""Apolipoproteins"""	609	protein-coding gene	gene with protein product		608083					Standard	NM_000483		Approved			P02655	OTTHUMG00000180847	ENST00000590360.1:c.229A>C	19.37:g.45452429A>C	ENSP00000466775:p.Lys77Gln	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_000483	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Missense_Mutation	SNP	ENST00000590360.1	37	CCDS12650.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	A	15.05	2.717211	0.48622	0.019292	0.0	ENSG00000234906	ENST00000252490	D	0.86164	-2.08	4.25	1.97	0.26223	ApoC-II domain (1);	0.331465	0.21058	U	0.080867	T	0.66616	0.2807	M	0.77820	2.39	0.19300	N	0.999973	P	0.39216	0.664	B	0.36504	0.226	T	0.68573	-0.5373	10	0.48119	T	0.1	-0.0013	4.4429	0.11582	0.621:0.2662:0.1128:0.0	rs5126;rs52806093;rs5126	77	P02655	APOC2_HUMAN	Q	77	ENSP00000252490:K77Q	ENSP00000252490:K77Q	K	+	1	0	APOC2	50144269	0.077000	0.21312	0.448000	0.26945	0.770000	0.43624	0.076000	0.14712	0.113000	0.18004	0.323000	0.21402	AAA	A|0.991;C|0.009	0.009	strong		0.567	APOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453261.1	NM_000483	
OR52I1	390037	hgsc.bcm.edu	37	11	4615869	4615869	+	Missense_Mutation	SNP	C	C	G	rs78745657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4615869C>G	ENST00000530443.2	+	1	601	c.601C>G	c.(601-603)Ctc>Gtc	p.L201V	OR52I1_ENST00000450052.2_Missense_Mutation_p.L225V	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	201						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)		GCCCAGCAGTCTCTACAGTCT	0.493													C|||	75	0.014976	0.0227	0.0	5008	,	,		22142	0.0367		0.001	False		,,,				2504	0.0072				p.L201V		Atlas-SNP	.											.	OR52I1	29	.	0			c.C601G						PASS	.	C	VAL/LEU	75,4327	65.8+/-103.3	1,73,2127	168.0	161.0	163.0		601	5.0	1.0	11	dbSNP_131	163	2,8588	2.2+/-6.3	0,2,4293	no	missense	OR52I1	NM_001005169.1	32	1,75,6420	GG,GC,CC		0.0233,1.7038,0.5927	probably-damaging	201/325	4615869	77,12915	2201	4295	6496	SO:0001583	missense	390037	exon1			AGCAGTCTCTACA	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.601C>G	11.37:g.4615869C>G	ENSP00000436453:p.Leu201Val	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	279	144	0.516129	NM_001005169	Q6IF91	Missense_Mutation	SNP	ENST00000530443.2	37	CCDS59223.1	38	0.0173992673992674	15	0.03048780487804878	0	0.0	21	0.03671328671328671	2	0.002638522427440633	C	13.11	2.140228	0.37825	0.017038	2.33E-4	ENSG00000232268	ENST00000450052;ENST00000530443	T;T	0.37915	1.17;1.17	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40302	N	0.001137	T	0.20820	0.0501	L	0.45581	1.43	0.31746	N	0.635184	D	0.89917	1.0	D	0.91635	0.999	T	0.17198	-1.0377	9	0.30854	T	0.27	-16.639	16.0681	0.80903	0.0:1.0:0.0:0.0	.	201	Q8NGK6	O52I1_HUMAN	V	225;201	ENSP00000409094:L225V;ENSP00000436453:L201V	ENSP00000409094:L225V	L	+	1	0	OR52I1	4572445	0.000000	0.05858	1.000000	0.80357	0.841000	0.47740	-1.429000	0.02437	2.741000	0.93983	0.555000	0.69702	CTC	C|0.983;G|0.017	0.017	strong		0.493	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169	
ZNF415	55786	hgsc.bcm.edu	37	19	53612055	53612055	+	Missense_Mutation	SNP	T	T	C	rs10410030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53612055T>C	ENST00000500065.4	-	4	1576	c.1243A>G	c.(1243-1245)Aat>Gat	p.N415D	ZNF415_ENST00000455735.2_Missense_Mutation_p.N463D|ZNF415_ENST00000601493.1_Missense_Mutation_p.N185D|ZNF415_ENST00000421033.1_Missense_Mutation_p.N427D|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.N463D|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000440291.1_Missense_Mutation_p.N402D|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000243643.4_Missense_Mutation_p.N415D	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	463					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		CCACATTCATTGCATTTGTAA	0.408													T|||	609	0.121605	0.2292	0.1412	5008	,	,		24059	0.002		0.1322	False		,,,				2504	0.0746				p.N415D		Atlas-SNP	.											.	ZNF415	68	.	0			c.A1243G						PASS	.	T	ASP/ASN,ASP/ASN,ASP/ASN	870,3536	339.1+/-305.6	93,684,1426	87.0	86.0	86.0		1243,1243,1243	-2.3	0.0	19	dbSNP_119	86	1352,7248	264.5+/-285.6	116,1120,3064	yes	missense,missense,missense	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	23,23,23	209,1804,4490	CC,CT,TT		15.7209,19.7458,17.0844	benign,benign,benign	415/556,415/556,415/556	53612055	2222,10784	2203	4300	6503	SO:0001583	missense	55786	exon4			ATTCATTGCATTT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.1243A>G	19.37:g.53612055T>C	ENSP00000439435:p.Asn415Asp	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	37	CCDS54313.1	249	0.11401098901098901	90	0.18292682926829268	59	0.16298342541436464	1	0.0017482517482517483	99	0.13060686015831136	T	12.29	1.892683	0.33442	0.197458	0.157209	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.07327	3.2;3.2;3.2;3.2;3.2;3.2	2.77	-2.29	0.06805	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00521	-1.4	0.80722	P	0.0	B;B;B;B;B;B	0.22414	0.002;0.043;0.005;0.002;0.005;0.069	B;B;B;B;B;B	0.29440	0.003;0.102;0.01;0.003;0.005;0.062	T	0.46176	-0.9210	8	0.37606	T	0.19	.	4.8591	0.13573	0.1501:0.4097:0.0:0.4402	rs10410030;rs17846658;rs17859755;rs52797631;rs10410030	415;463;463;415;402;427	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	D	415;415;463;427;463;402	ENSP00000243643:N415D;ENSP00000439435:N415D;ENSP00000396492:N463D;ENSP00000395055:N427D;ENSP00000388787:N463D;ENSP00000414601:N402D	ENSP00000243643:N415D	N	-	1	0	ZNF415	58303867	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-4.986000	0.00163	-0.870000	0.04047	-0.425000	0.05940	AAT	T|0.842;C|0.158	0.158	strong		0.408	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355	
SPATA2	9825	hgsc.bcm.edu	37	20	48522263	48522263	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48522263C>T	ENST00000422556.1	-	3	1805	c.1456G>A	c.(1456-1458)Gct>Act	p.A486T	SPATA2_ENST00000289431.5_Missense_Mutation_p.A486T|SPATA2_ENST00000543716.1_Missense_Mutation_p.A349T	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	486					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	20	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			TAATGGTAAGCGCTGAGGCAG	0.562																																					p.A486T		Atlas-SNP	.											.	SPATA2	36	.	0			c.G1456A						PASS	.						167.0	154.0	159.0					20																	48522263		2203	4300	6503	SO:0001583	missense	9825	exon3			GGTAAGCGCTGAG	AB018300	CCDS13422.1	20q13.13	2014-06-13			ENSG00000158480	ENSG00000158480			14681	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 145"""	607662					Standard	NM_001135773		Approved	KIAA0757, PD1, tamo, PPP1R145	uc002xuw.3	Q9UM82	OTTHUMG00000032704	ENST00000422556.1:c.1456G>A	20.37:g.48522263C>T	ENSP00000416799:p.Ala486Thr	Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	371	188	0.506739	NM_006038	E1P626|O94857	Missense_Mutation	SNP	ENST00000422556.1	37	CCDS13422.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.721788	0.48728	.	.	ENSG00000158480	ENST00000289431;ENST00000422556;ENST00000543716	T;T;T	0.48201	0.83;0.83;0.82	5.08	0.988	0.19796	.	0.293281	0.28198	N	0.016236	T	0.40570	0.1122	L	0.59436	1.845	0.36765	D	0.883515	B	0.18968	0.032	B	0.14023	0.01	T	0.36601	-0.9741	10	0.42905	T	0.14	-10.862	10.0211	0.42044	0.0:0.7242:0.0:0.2758	.	486	Q9UM82	SPAT2_HUMAN	T	486;486;349	ENSP00000289431:A486T;ENSP00000416799:A486T;ENSP00000438855:A349T	ENSP00000289431:A486T	A	-	1	0	SPATA2	47955670	1.000000	0.71417	0.974000	0.42286	0.448000	0.32197	2.904000	0.48719	0.057000	0.16193	0.455000	0.32223	GCT	.	.	none		0.562	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038	
URB2	9816	hgsc.bcm.edu	37	1	229770827	229770827	+	Missense_Mutation	SNP	C	C	T	rs115641620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229770827C>T	ENST00000258243.2	+	4	603	c.467C>T	c.(466-468)tCg>tTg	p.S156L		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	156						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						CTTTGCTGGTCGGCCTGCAGG	0.587													C|||	43	0.00858626	0.0318	0.0014	5008	,	,		21011	0.0		0.0	False		,,,				2504	0.0				p.S156L		Atlas-SNP	.											.	URB2	152	.	0			c.C467T						PASS	.	C	LEU/SER	113,4293	87.8+/-126.4	1,111,2091	62.0	53.0	56.0		467	-7.6	0.0	1	dbSNP_132	56	1,8599		0,1,4299	no	missense	URB2	NM_014777.2	145	1,112,6390	TT,TC,CC		0.0116,2.5647,0.8765	benign	156/1525	229770827	114,12892	2203	4300	6503	SO:0001583	missense	9816	exon4			GCTGGTCGGCCTG	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.467C>T	1.37:g.229770827C>T	ENSP00000258243:p.Ser156Leu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	0.017	-1.506370	0.00992	0.025647	1.16E-4	ENSG00000135763	ENST00000258243	T	0.09911	2.93	5.68	-7.55	0.01327	.	0.884065	0.09779	N	0.756927	T	0.01558	0.0050	N	0.04994	-0.135	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40251	-0.9573	9	.	.	.	-0.0083	19.9267	0.97106	0.0:0.1135:0.0:0.8865	.	156	Q14146	URB2_HUMAN	L	156	ENSP00000258243:S156L	.	S	+	2	0	URB2	227837450	0.045000	0.20229	0.000000	0.03702	0.006000	0.05464	0.359000	0.20233	-1.352000	0.02194	-1.684000	0.00734	TCG	C|0.992;T|0.008	0.008	strong		0.587	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
GABPA	2551	hgsc.bcm.edu	37	21	27107251	27107251	+	5'UTR	SNP	C	C	G	rs71649640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:27107251C>G	ENST00000354828.3	+	0	371				ATP5J_ENST00000400087.3_Intron|GABPA_ENST00000400075.3_5'Flank|ATP5J_ENST00000457143.2_Splice_Site_p.G6R|ATP5J_ENST00000400099.1_Intron|ATP5J_ENST00000400093.3_Intron|ATP5J_ENST00000400094.1_5'Flank|ATP5J_ENST00000400090.3_Intron|ATP5J_ENST00000284971.3_5'UTR	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa						cell differentiation (GO:0030154)|in utero embryonic development (GO:0001701)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	24						CACGCCTACCCGCCATCGCAA	0.662													C|||	60	0.0119808	0.0446	0.0014	5008	,	,		16320	0.0		0.0	False		,,,				2504	0.0				p.G6R		Atlas-SNP	.											.	ATP5J	13	.	0			c.G16C						PASS	.	C	,,ARG/GLY,,	126,3852		2,122,1865	15.0	22.0	20.0		,,16,,	3.9	1.0	21	dbSNP_130	20	1,8301		0,1,4150	yes	intron,intron,missense-near-splice,utr-5,intron	ATP5J	NM_001003696.1,NM_001003697.1,NM_001003701.1,NM_001003703.1,NM_001685.4	,,125,,	2,123,6015	GG,GC,CC		0.012,3.1674,1.0342	,,,,	,,6/117,,	27107251	127,12153	1989	4151	6140	SO:0001623	5_prime_UTR_variant	522	exon1			CCTACCCGCCATC		CCDS13575.1	21q21-q22.1	2008-07-31	2002-08-29		ENSG00000154727	ENSG00000154727			4071	protein-coding gene	gene with protein product	"""human nuclear respiratory factor-2 subunit alpha"", ""nuclear respiratory factor 2 alpha subunit"""	600609	"""GA-binding protein transcription factor, alpha subunit (60kD)"""			8441384	Standard	NM_002040		Approved	E4TF1A, NFT2, NRF2, E4TF1-60, NRF2A	uc002yly.4	Q06546	OTTHUMG00000078443	ENST00000354828.3:c.-157C>G	21.37:g.27107251C>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_001003701	Q12939	Missense_Mutation	SNP	ENST00000354828.3	37	CCDS13575.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	C	21.0	4.088791	0.76756	0.031674	1.2E-4	ENSG00000154723	ENST00000457143	.	.	.	4.83	3.92	0.45320	.	.	.	.	.	T	0.29817	0.0745	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46062	-0.9218	5	0.37606	T	0.19	.	11.0432	0.47844	0.0:0.8121:0.1879:0.0	.	.	.	.	R	6	.	ENSP00000389649:G6R	G	-	1	0	ATP5J	26029122	0.918000	0.31147	0.990000	0.47175	0.998000	0.95712	1.903000	0.39858	1.359000	0.45940	0.655000	0.94253	GGA	C|0.990;G|0.010	0.010	strong		0.662	GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171365.1	NM_002040	
GAB2	9846	hgsc.bcm.edu	37	11	77936166	77936166	+	Silent	SNP	A	A	G	rs1385600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	70	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	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	
ZNF804B	219578	hgsc.bcm.edu	37	7	88963401	88963401	+	Missense_Mutation	SNP	C	C	T	rs141118086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88963401C>T	ENST00000333190.4	+	4	1714	c.1105C>T	c.(1105-1107)Cca>Tca	p.P369S		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	369							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TTCCTTCAGCCCACCAAACAT	0.393										HNSCC(36;0.09)			C|||	81	0.0161741	0.0575	0.0058	5008	,	,		18756	0.0		0.001	False		,,,				2504	0.0				p.P369S		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C1105T						PASS	.	C	SER/PRO	239,4165	136.1+/-172.1	7,225,1970	43.0	48.0	46.0		1105	3.1	0.8	7	dbSNP_134	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF804B	NM_181646.2	74	7,226,6269	TT,TC,CC		0.0116,5.4269,1.8456	probably-damaging	369/1350	88963401	240,12764	2202	4300	6502	SO:0001583	missense	219578	exon4			TTCAGCCCACCAA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1105C>T	7.37:g.88963401C>T	ENSP00000329638:p.Pro369Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	26	0.011904761904761904	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	11.61	1.688835	0.29962	0.054269	1.16E-4	ENSG00000182348	ENST00000333190	T	0.05199	3.48	4.86	3.07	0.35406	.	0.639011	0.14589	N	0.310354	T	0.01092	0.0036	M	0.67953	2.075	0.09310	N	1	B	0.34372	0.451	B	0.23150	0.044	T	0.17623	-1.0363	10	0.41790	T	0.15	-1.6547	11.2317	0.48916	0.0:0.8527:0.0:0.1473	.	369	A4D1E1	Z804B_HUMAN	S	369	ENSP00000329638:P369S	ENSP00000329638:P369S	P	+	1	0	ZNF804B	88801337	0.052000	0.20516	0.793000	0.32043	0.997000	0.91878	1.203000	0.32284	0.670000	0.31165	0.655000	0.94253	CCA	C|0.986;T|0.014	0.014	strong		0.393	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
XYLT1	64131	hgsc.bcm.edu	37	16	17353090	17353090	+	Missense_Mutation	SNP	G	G	C	rs113276942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:17353090G>C	ENST00000261381.6	-	3	752	c.668C>G	c.(667-669)gCc>gGc	p.A223G		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	223					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GTTGGCTGCGGCTCTGTCCCC	0.592													G|||	265	0.0529153	0.1914	0.0173	5008	,	,		17039	0.0		0.0	False		,,,				2504	0.0				p.A223G		Atlas-SNP	.											XYLT1,NS,carcinoma,+1,1	XYLT1	147	1	0			c.C668G						PASS	.	G	GLY/ALA	697,3697	288.1+/-279.7	67,563,1567	106.0	117.0	113.0		668	4.5	0.0	16	dbSNP_132	113	19,8581	11.2+/-40.8	0,19,4281	yes	missense	XYLT1	NM_022166.3	60	67,582,5848	CC,CG,GG		0.2209,15.8625,5.5102	benign	223/960	17353090	716,12278	2197	4300	6497	SO:0001583	missense	64131	exon3			GCTGCGGCTCTGT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.668C>G	16.37:g.17353090G>C	ENSP00000261381:p.Ala223Gly	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	197	110	0.558376	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	89	0.04075091575091575	81	0.16463414634146342	8	0.022099447513812154	0	0.0	0	0.0	G	9.870	1.198774	0.22121	0.158625	0.002209	ENSG00000103489	ENST00000261381	T	0.04809	3.55	5.43	4.47	0.54385	.	0.429861	0.27500	N	0.019098	T	0.00039	0.0001	L	0.44542	1.39	0.09310	N	1	B	0.32245	0.361	B	0.19148	0.024	T	0.49021	-0.8982	10	0.31617	T	0.26	-19.7884	11.4244	0.50001	0.1501:0.0:0.8499:0.0	.	223	Q86Y38	XYLT1_HUMAN	G	223	ENSP00000261381:A223G	ENSP00000261381:A223G	A	-	2	0	XYLT1	17260591	0.015000	0.18098	0.011000	0.14972	0.446000	0.32137	1.886000	0.39688	1.296000	0.44742	0.655000	0.94253	GCC	G|0.950;C|0.050	0.050	strong		0.592	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
HPS5	11234	hgsc.bcm.edu	37	11	18330522	18330522	+	Silent	SNP	A	A	G	rs146455658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18330522A>G	ENST00000349215.3	-	6	859	c.582T>C	c.(580-582)ctT>ctC	p.L194L	HPS5_ENST00000438420.2_Silent_p.L80L|HPS5_ENST00000531848.1_Silent_p.L80L|HPS5_ENST00000396253.3_Silent_p.L80L	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	194					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						AGGATCGAGTAAGTGAAGATA	0.388									Hermansky-Pudlak syndrome				A|||	2	0.000399361	0.0008	0.0014	5008	,	,		16667	0.0		0.0	False		,,,				2504	0.0				p.L194L		Atlas-SNP	.											.	HPS5	70	.	0			c.T582C						PASS	.	A	,,	15,4383	22.3+/-47.3	0,15,2184	136.0	118.0	124.0		240,582,240	0.2	1.0	11	dbSNP_134	124	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	HPS5	NM_007216.3,NM_181507.1,NM_181508.1	,,	0,15,6477	GG,GA,AA		0.0,0.3411,0.1155	,,	80/1016,194/1130,80/1016	18330522	15,12969	2199	4293	6492	SO:0001819	synonymous_variant	11234	exon6	Familial Cancer Database	HPS, HPS1-8	TCGAGTAAGTGAA	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.582T>C	11.37:g.18330522A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Silent	SNP	ENST00000349215.3	37	CCDS7836.1																																																																																			A|0.999;G|0.001	0.001	strong		0.388	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
PTPN5	84867	hgsc.bcm.edu	37	11	18751041	18751041	+	Silent	SNP	C	C	T	rs1550870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000396170.1_Silent_p.V489V|PTPN5_ENST00000396168.1_Silent_p.V497V|PTPN5_ENST00000396167.2_Silent_p.V489V|PTPN5_ENST00000477854.1_Silent_p.V325V|PTPN5_ENST00000396171.4_Silent_p.V521V|PTPN5_ENST00000396166.3_Silent_p.V127V	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	35	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	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	
STAP2	55620	hgsc.bcm.edu	37	19	4333711	4333711	+	Missense_Mutation	SNP	C	C	T	rs7247504	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4333711C>T	ENST00000594605.1	-	3	400	c.277G>A	c.(277-279)Gat>Aat	p.D93N	STAP2_ENST00000600324.1_Missense_Mutation_p.D93N	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	93	PH.		D -> N (in dbSNP:rs7247504). {ECO:0000269|PubMed:10980601, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		ATCTCCTGATCCCGGAGAATC	0.552													N|||	3283	0.655551	0.7814	0.5965	5008	,	,		17191	0.7044		0.5507	False		,,,				2504	0.5849				p.D93N		Atlas-SNP	.											.	STAP2	38	.	0			c.G277A						PASS	.		ASN/ASP,ASN/ASP	3256,1150	406.2+/-333.8	1221,814,168	70.0	66.0	67.0		277,277	-1.8	0.1	19	dbSNP_116	67	4666,3934	547.7+/-385.2	1279,2108,913	yes	missense,missense	STAP2	NM_001013841.1,NM_017720.2	23,23	2500,2922,1081	TT,TC,CC		45.7442,26.1008,39.0897	benign,benign	93/404,93/450	4333711	7922,5084	2203	4300	6503	SO:0001583	missense	55620	exon3			CCTGATCCCGGAG	AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078			30430	protein-coding gene	gene with protein product		607881				10980601, 11441184	Standard	XM_005259592		Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000594605.1:c.277G>A	19.37:g.4333711C>T	ENSP00000471052:p.Asp93Asn	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	69	26	0.376812	NM_001013841	A6NKK3|Q9NXI2	Missense_Mutation	SNP	ENST00000594605.1	37	CCDS45926.1	1402	0.641941391941392	383	0.7784552845528455	211	0.5828729281767956	406	0.7097902097902098	402	0.5303430079155673	T	0.006	-2.022811	0.00414	0.738992	0.542558	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	5.02	-1.78	0.07957	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.631198	0.16064	N	0.231325	T	0.00012	0.0000	N	0.01789	-0.72	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.28332	-1.0047	8	0.87932	D	0	-2.1795	7.2493	0.26140	0.0:0.479:0.1394:0.3816	rs7247504;rs17855353;rs7247504	93;93	Q9UGK3-2;Q9UGK3	.;STAP2_HUMAN	N	93	.	ENSP00000317912:D93N	D	-	1	0	STAP2	4284711	0.018000	0.18449	0.077000	0.20336	0.041000	0.13682	-0.077000	0.11394	-0.599000	0.05798	-1.302000	0.01329	GAT	C|0.373;T|0.627	0.627	strong		0.552	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841	
LILRB3	11025	hgsc.bcm.edu	37	19	54721049	54721049	+	Silent	SNP	A	A	G	rs60566950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54721049A>G	ENST00000391750.1	-	14	1945	c.1809T>C	c.(1807-1809)ctT>ctC	p.L603L	LILRB3_ENST00000424807.1_Silent_p.L603L|LILRA6_ENST00000419410.2_Silent_p.L604L|LILRA6_ENST00000270464.5_Silent_p.L604L|LILRB3_ENST00000346401.6_Silent_p.L615L|LILRB3_ENST00000245620.9_Silent_p.L604L|LILRB3_ENST00000469273.1_5'UTR|LILRB3_ENST00000407860.2_Silent_p.L620L|LILRA6_ENST00000440558.2_Silent_p.L603L|LILRA6_ENST00000391735.3_3'UTR			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	603					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCTTCCGTCTAAGGGTCAAGC	0.632													.|||	155	0.0309505	0.0998	0.0086	5008	,	,		17459	0.0		0.0	False		,,,				2504	0.0174				p.L604L		Atlas-SNP	.											LILRB3,NS,carcinoma,0,1	LILRB3	67	1	0			c.T1812C						scavenged	.	A	,	147,4257		24,99,2079	104.0	105.0	104.0		1812,1809	0.8	0.0	19	dbSNP_129	104	5,8595		0,5,4295	no	coding-synonymous,coding-synonymous	LILRB3	NM_001081450.1,NM_006864.2	,	24,104,6374	GG,GA,AA		0.0581,3.3379,1.1689	,	604/633,603/632	54721049	152,12852	2202	4300	6502	SO:0001819	synonymous_variant	11025	exon13			CCGTCTAAGGGTC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1809T>C	19.37:g.54721049A>G		Somatic	423	5	0.0118203		WXS	Illumina HiSeq	Phase_I	479	244	0.509395	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			A|0.980;G|0.020	0.020	strong		0.632	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
PNO1	56902	hgsc.bcm.edu	37	2	68385240	68385240	+	Silent	SNP	C	C	G	rs61735657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:68385240C>G	ENST00000263657.2	+	1	265	c.174C>G	c.(172-174)ccC>ccG	p.P58P	WDR92_ENST00000295121.6_5'Flank|WDR92_ENST00000409164.1_5'Flank|WDR92_ENST00000406245.2_5'Flank|RP11-474G23.1_ENST00000406334.3_Silent_p.T150T|WDR92_ENST00000492039.2_5'Flank	NM_020143.2	NP_064528.1	Q9NRX1	PNO1_HUMAN	partner of NOB1 homolog (S. cerevisiae)	58						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						CGAAGAGGCCCGTCTTCCCAC	0.672													C|||	109	0.0217652	0.0779	0.0	5008	,	,		15102	0.0		0.001	False		,,,				2504	0.0051				p.P58P	NSCLC(83;642 1410 13044 32832 40058)	Atlas-SNP	.											.	PNO1	17	.	0			c.C174G						PASS	.	C		289,4109		7,275,1917	13.0	19.0	17.0		174	-4.9	0.9	2	dbSNP_129	17	17,8575		0,17,4279	no	coding-synonymous	PNO1	NM_020143.2		7,292,6196	GG,GC,CC		0.1979,6.5712,2.3557		58/253	68385240	306,12684	2199	4296	6495	SO:0001819	synonymous_variant	56902	exon1			GAGGCCCGTCTTC	AF164799	CCDS1885.1	2p14	2010-07-06			ENSG00000115946	ENSG00000115946			32790	protein-coding gene	gene with protein product	"""RNA binding protein"""		"""KH-type RNA binding protein 1"", ""KH-type RNA-binding protein 1"""	KHRBP1		15497447	Standard	NM_020143		Approved	RRP20	uc002seh.3	Q9NRX1	OTTHUMG00000129563	ENST00000263657.2:c.174C>G	2.37:g.68385240C>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_020143	A8K6Q0|Q53G13|Q8WVB8	Silent	SNP	ENST00000263657.2	37	CCDS1885.1																																																																																			C|0.979;G|0.021	0.021	strong		0.672	PNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251756.1	NM_020143	
SMARCAL1	50485	hgsc.bcm.edu	37	2	217285104	217285104	+	Missense_Mutation	SNP	C	C	G	rs2066522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:217285104C>G	ENST00000357276.4	+	5	1275	c.945C>G	c.(943-945)agC>agG	p.S315R	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.S315R	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	315			S -> R (in dbSNP:rs2066522).		cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		CCTCCACCAGCAGTGAGGGAC	0.572									Schimke Immuno-Osseous Dysplasia				C|||	170	0.0339457	0.0809	0.0331	5008	,	,		17373	0.0		0.0338	False		,,,				2504	0.0061				p.S315R		Atlas-SNP	.											SMARCAL1,right_upper_lobe,carcinoma,+1,1	SMARCAL1	93	1	0			c.C945G						scavenged	.	C	ARG/SER,ARG/SER	353,4053	181.9+/-209.8	17,319,1867	90.0	73.0	79.0		945,945	-0.2	0.0	2	dbSNP_98	79	249,8351	99.3+/-160.8	2,245,4053	yes	missense,missense	SMARCAL1	NM_001127207.1,NM_014140.3	110,110	19,564,5920	GG,GC,CC		2.8953,8.0118,4.6286	possibly-damaging,possibly-damaging	315/955,315/955	217285104	602,12404	2203	4300	6503	SO:0001583	missense	50485	exon5	Familial Cancer Database	SIOD	CACCAGCAGTGAG	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"""HepA-related protein"", ""ATP-driven annealing helicase"""	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.945C>G	2.37:g.217285104C>G	ENSP00000349823:p.Ser315Arg	Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	160	76	0.475	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	37	CCDS2403.1	65	0.02976190476190476	36	0.07317073170731707	9	0.024861878453038673	0	0.0	20	0.026385224274406333	C	19.69	3.875544	0.72180	0.080118	0.028953	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000427645;ENST00000392128;ENST00000412913	D;D;T;D;T	0.85955	-2.04;-2.04;1.51;-2.05;0.68	3.96	-0.186	0.13272	.	1.145540	0.06356	N	0.710693	T	0.14614	0.0353	L	0.36672	1.1	0.09310	N	1	P	0.43287	0.802	B	0.31614	0.133	T	0.38436	-0.9661	10	0.38643	T	0.18	.	7.9086	0.29776	0.0:0.6035:0.0:0.3965	rs2066522;rs2266768;rs52816735;rs2066522	315	Q9NZC9	SMAL1_HUMAN	R	315;315;214;179;35	ENSP00000349823:S315R;ENSP00000350940:S315R;ENSP00000392997:S214R;ENSP00000375974:S179R;ENSP00000390248:S35R	ENSP00000349823:S315R	S	+	3	2	SMARCAL1	216993349	0.000000	0.05858	0.001000	0.08648	0.897000	0.52465	0.450000	0.21762	0.000000	0.14550	0.561000	0.74099	AGC	C|0.957;G|0.043	0.043	strong		0.572	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2		
CRIPAK	285464	hgsc.bcm.edu	37	4	1388817	1388817	+	Missense_Mutation	SNP	C	C	G	rs200606324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1388817C>G	ENST00000324803.4	+	1	3478	c.518C>G	c.(517-519)cCa>cGa	p.P173R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	173					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)			CACACGTGCCCATGTGGAGTG	0.677													N|||	940	0.1877	0.3328	0.1398	5008	,	,		18475	0.0992		0.0378	False		,,,				2504	0.271				p.P173R		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,7	CRIPAK	185	7	0			c.C518G						PASS	.						192.0	130.0	151.0					4																	1388817		2194	4201	6395	SO:0001583	missense	285464	exon1			CGTGCCCATGTGG	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.518C>G	4.37:g.1388817C>G	ENSP00000323978:p.Pro173Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	156	21	0.134615	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	c	1.909	-0.451230	0.04572	.	.	ENSG00000179979	ENST00000324803	T	0.19250	2.16	1.25	0.276	0.15663	Post-SET domain (1);	.	.	.	.	T	0.08358	0.0208	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40079	-0.9582	9	0.17369	T	0.5	.	4.4738	0.11726	0.0:0.5796:0.2425:0.1779	.	173	Q8N1N5	CRPAK_HUMAN	R	173	ENSP00000323978:P173R	ENSP00000323978:P173R	P	+	2	0	CRIPAK	1378817	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.368000	0.07543	-0.338000	0.08413	-1.976000	0.00459	CCA	CATGT|0.500;GACGC|0.500	.	alt		0.677	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201835	32201835	+	RNA	SNP	A	A	C	rs9982675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:32201835A>C	ENST00000452750.1	-	0	243							Q8IUC3	KRA71_HUMAN	keratin associated protein 7-1 (gene/pseudogene)							intermediate filament (GO:0005882)											CAGGTTGTTGATGTTGCTACC	0.562													A|||	2463	0.491813	0.4266	0.6354	5008	,	,		18212	0.4454		0.4781	False		,,,				2504	0.5399				p.I61S		Atlas-SNP	.											.	.	.	.	0			c.T182G						PASS	.						72.0	73.0	72.0					21																	32201835		692	1591	2283			337878	exon2			TTGTTGATGTTGC	AJ457063	CCDS74780.1	21q22.1	2014-04-10	2010-03-12		ENSG00000184586	ENSG00000274749		"""Keratin associated proteins"""	18934	protein-coding gene	gene with protein product			"""keratin associated protein 7-1"""			12359730	Standard	NM_181606		Approved	KAP7.1	uc011adj.2	Q8IUC3	OTTHUMG00000188305		21.37:g.32201835A>C		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	225	104	0.462222	NM_181606	Q3LI56	Missense_Mutation	SNP	ENST00000452750.1	37																																																																																				A|0.504;C|0.496	0.496	strong		0.562	KRTAP7-1-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000128248.3	NM_181606	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	143359	143359	+	Missense_Mutation	SNP	G	G	A	rs114876243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:143359G>A	ENST00000283426.6	+	2	657	c.607G>A	c.(607-609)Gtc>Atc	p.V203I	Y_RNA_ENST00000362670.1_RNA	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	203							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GTCCGGGGTCGTCACCCTCCC	0.637													G|||	85	0.0169728	0.0643	0.0	5008	,	,		19147	0.0		0.0	False		,,,				2504	0.0				p.V203I		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.G607A						PASS	.	G	ILE/VAL	217,4189		9,199,1995	34.0	39.0	37.0		607	-3.8	0.0	5	dbSNP_132	37	3,8589		0,3,4293	yes	missense	PLEKHG4B	NM_052909.3	29	9,202,6288	AA,AG,GG		0.0349,4.9251,1.6926	benign	203/1272	143359	220,12778	2203	4296	6499	SO:0001583	missense	153478	exon2			GGGGTCGTCACCC	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.607G>A	5.37:g.143359G>A	ENSP00000283426:p.Val203Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	.	0.015	-1.543641	0.00934	0.049251	3.49E-4	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.18174	2.23;2.23	2.87	-3.76	0.04359	.	.	.	.	.	T	0.00754	0.0025	N	0.04090	-0.28	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.38308	-0.9667	9	0.05620	T	0.96	.	7.5065	0.27547	0.5943:0.0:0.4057:0.0	.	203	Q96PX9	PKH4B_HUMAN	I	203;117	ENSP00000283426:V203I;ENSP00000422493:V117I	ENSP00000283426:V203I	V	+	1	0	PLEKHG4B	196359	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	-0.481000	0.06552	-0.665000	0.05317	-0.752000	0.03492	GTC	G|0.985;A|0.015	0.015	strong		0.637	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
MROH6	642475	hgsc.bcm.edu	37	8	144654249	144654249	+	Missense_Mutation	SNP	G	G	A	rs386731217|rs10866911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144654249G>A	ENST00000398882.3	-	2	657	c.401C>T	c.(400-402)aCc>aTc	p.T134I	MROH6_ENST00000533679.1_5'Flank|NAPRT1_ENST00000460623.1_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	134			T -> I (in dbSNP:rs10866911).														TGAGGACAGGGTGAGCACTGT	0.652													G|||	1604	0.320288	0.1135	0.4135	5008	,	,		14836	0.3562		0.5229	False		,,,				2504	0.2883				p.T134I		Atlas-SNP	.											.	.	.	.	0			c.C401T						PASS	.	G	ILE/THR	690,3340		63,564,1388	23.0	27.0	26.0		401	-1.4	0.8	8	dbSNP_120	26	4386,3968		1196,1994,987	yes	missense	C8orf73	NM_001100878.1	89	1259,2558,2375	AA,AG,GG		47.4982,17.1216,40.9884	probably-damaging	134/720	144654249	5076,7308	2015	4177	6192	SO:0001583	missense	642475	exon2			GACAGGGTGAGCA	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"""maestro heat-like repeat containing"""	27814	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 73"""	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.401C>T	8.37:g.144654249G>A	ENSP00000381857:p.Thr134Ile	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	159	79	0.496855	NM_001100878	A8MWB1	Missense_Mutation	SNP	ENST00000398882.3	37	CCDS47928.1	822	0.37637362637362637	62	0.12601626016260162	176	0.4861878453038674	184	0.32167832167832167	400	0.5277044854881267	G	15.51	2.853888	0.51270	0.171216	0.525018	ENSG00000204839	ENST00000398882;ENST00000529971	T;T	0.24350	4.19;1.86	4.3	-1.38	0.09027	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.26688	P	0.9714051	B;B	0.19583	0.037;0.004	B;B	0.17433	0.018;0.003	T	0.47005	-0.9150	8	0.15952	T	0.53	-21.3409	6.1376	0.20241	0.2014:0.4988:0.2998:0.0	rs10866911;rs58968135	134;134	E9PPP7;A6NGR9	.;CH073_HUMAN	I	134	ENSP00000381857:T134I;ENSP00000436959:T134I	ENSP00000381857:T134I	T	-	2	0	C8orf73	144725392	0.990000	0.36364	0.806000	0.32338	0.652000	0.38707	1.349000	0.33998	-0.139000	0.11414	-0.519000	0.04390	ACC	G|0.611;A|0.389	0.389	strong		0.652	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878	
EP400	57634	hgsc.bcm.edu	37	12	132508389	132508389	+	Silent	SNP	A	A	G	rs7133119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132508389A>G	ENST00000333577.4	+	25	4975	c.4866A>G	c.(4864-4866)ccA>ccG	p.P1622P	EP400_ENST00000389562.2_Silent_p.P1585P|EP400_ENST00000389561.2_Silent_p.P1586P|EP400_ENST00000330386.6_Silent_p.P1505P|EP400_ENST00000332482.4_Silent_p.P1549P			Q96L91	EP400_HUMAN	E1A binding protein p400	1622					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.P1585P(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		TGGCTCAGCCAGAGACGCCGG	0.582													G|||	1646	0.328674	0.7973	0.1729	5008	,	,		15201	0.1458		0.1282	False		,,,				2504	0.2004				p.P1586P		Atlas-SNP	.											EP400,NS,carcinoma,0,1	EP400	370	1	1	Substitution - coding silent(1)	stomach(1)	c.A4758G						PASS	.	G		3023,1383	454.4+/-350.6	1055,913,235	48.0	49.0	49.0		4758	-10.4	0.6	12	dbSNP_116	49	982,7618	773.8+/-407.7	59,864,3377	no	coding-synonymous	EP400	NM_015409.4		1114,1777,3612	GG,GA,AA		11.4186,31.389,30.7935		1586/3124	132508389	4005,9001	2203	4300	6503	SO:0001819	synonymous_variant	57634	exon24			TCAGCCAGAGACG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.4866A>G	12.37:g.132508389A>G		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	230	228	0.991304	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				A|0.700;G|0.300	0.300	strong		0.582	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
USP6	9098	hgsc.bcm.edu	37	17	5042837	5042837	+	Missense_Mutation	SNP	C	C	T	rs61745111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5042837C>T	ENST00000574788.1	+	22	3596	c.1366C>T	c.(1366-1368)Cgg>Tgg	p.R456W	USP6_ENST00000304328.5_Missense_Mutation_p.R139W|USP6_ENST00000332776.4_Missense_Mutation_p.R456W|USP6_ENST00000250066.6_Missense_Mutation_p.R456W			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	456					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.R456W(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GTCAATGCCCCGGCTCCCAAC	0.612			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								C|||	509	0.101637	0.1982	0.0375	5008	,	,		18531	0.0784		0.1153	False		,,,				2504	0.0266				p.R456W		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	USP6,NS,carcinoma,0,1	USP6	213	1	1	Substitution - Missense(1)	lung(1)	c.C1366T						scavenged	.	C	TRP/ARG	710,3696	291.3+/-281.4	62,586,1555	51.0	59.0	56.0		1366	-0.5	0.0	17	dbSNP_129	56	951,7649	208.3+/-249.8	52,847,3401	yes	missense	USP6	NM_004505.2	101	114,1433,4956	TT,TC,CC		11.0581,16.1144,12.771	benign	456/1407	5042837	1661,11345	2203	4300	6503	SO:0001583	missense	9098	exon14			ATGCCCCGGCTCC	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.1366C>T	17.37:g.5042837C>T	ENSP00000460380:p.Arg456Trp	Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	250	0.11446886446886446	97	0.19715447154471544	16	0.04419889502762431	52	0.09090909090909091	85	0.11213720316622691	C	1.018	-0.685710	0.03328	0.161144	0.110581	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.25749	2.19;2.68;1.78	0.266	-0.532	0.11890	.	0.290613	0.37012	N	0.002286	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38373	-0.9664	8	0.87932	D	0	.	.	.	.	rs61745111	139;456	P35125-2;P35125	.;UBP6_HUMAN	W	456;456;139	ENSP00000328010:R456W;ENSP00000250066:R456W;ENSP00000305473:R139W	ENSP00000250066:R456W	R	+	1	2	USP6	4983561	0.025000	0.19082	0.000000	0.03702	0.000000	0.00434	-1.254000	0.02874	-2.211000	0.00737	-2.287000	0.00268	CGG	C|0.881;T|0.119	0.119	strong		0.612	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
TNFRSF21	27242	hgsc.bcm.edu	37	6	47251772	47251772	+	Missense_Mutation	SNP	C	C	T	rs148459670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:47251772C>T	ENST00000296861.2	-	3	1538	c.1145G>A	c.(1144-1146)cGg>cAg	p.R382Q		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	382					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			GGGATCCTGCCGGGGCCCCTT	0.527													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17459	0.0		0.0	False		,,,				2504	0.0				p.R382Q		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.G1145A						PASS	.	C	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	91.0	99.0	96.0		1145	6.2	1.0	6	dbSNP_134	96	0,8600		0,0,4300	yes	missense	TNFRSF21	NM_014452.3	43	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging	382/656	47251772	3,13003	2203	4300	6503	SO:0001583	missense	27242	exon3			TCCTGCCGGGGCC	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	13469	protein-coding gene	gene with protein product	"""death receptor 6"""	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1145G>A	6.37:g.47251772C>T	ENSP00000296861:p.Arg382Gln	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	269	137	0.509294	NM_014452	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	37	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892611	0.91889	6.81E-4	0.0	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.66099	-0.19	6.17	6.17	0.99709	.	0.162308	0.56097	D	0.000032	T	0.65450	0.2692	L	0.59436	1.845	0.47374	D	0.999408	D	0.71674	0.998	P	0.56788	0.806	T	0.68689	-0.5342	10	0.87932	D	0	.	13.9957	0.64397	0.0:0.9315:0.0:0.0685	.	382	O75509	TNR21_HUMAN	Q	382;71	ENSP00000296861:R382Q	ENSP00000296861:R382Q	R	-	2	0	TNFRSF21	47359731	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.682000	0.54656	2.941000	0.99782	0.655000	0.94253	CGG	C|1.000;T|0.000	0.000	strong		0.527	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452	
ABRA	137735	hgsc.bcm.edu	37	8	107782335	107782335	+	Silent	SNP	G	G	A	rs11996457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:107782335G>A	ENST00000311955.3	-	1	138	c.84C>T	c.(82-84)agC>agT	p.S28S		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)			CTCGGGCCAAGCTGATGACCA	0.647													G|||	1405	0.280551	0.5378	0.1686	5008	,	,		17334	0.1944		0.2247	False		,,,				2504	0.1585				p.S28S		Atlas-SNP	.											ABRA,NS,adenoma,0,1	ABRA	57	1	0			c.C84T						PASS	.	G		2079,2327	567.8+/-382.2	499,1081,623	61.0	65.0	64.0		84	0.7	0.5	8	dbSNP_120	64	1815,6785	324.5+/-316.5	182,1451,2667	no	coding-synonymous	ABRA	NM_139166.4		681,2532,3290	AA,AG,GG		21.1047,47.1857,29.94		28/382	107782335	3894,9112	2203	4300	6503	SO:0001819	synonymous_variant	137735	exon1			GGCCAAGCTGATG	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.84C>T	8.37:g.107782335G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_139166		Silent	SNP	ENST00000311955.3	37	CCDS6305.1																																																																																			G|0.710;A|0.290	0.290	strong		0.647	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166	
DUOX1	53905	hgsc.bcm.edu	37	15	45444572	45444572	+	Silent	SNP	T	T	C	rs114272662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45444572T>C	ENST00000321429.4	+	26	3689	c.3282T>C	c.(3280-3282)tcT>tcC	p.S1094S	DUOX1_ENST00000389037.3_Silent_p.S1094S|DUOX1_ENST00000561166.1_Silent_p.S740S|CTD-2651B20.1_ENST00000558039.1_lincRNA	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1094	Ferric oxidoreductase.|Interaction with TXNDC11. {ECO:0000250}.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CCAGCATCTCTTTCATGTTCT	0.602													T|||	137	0.0273562	0.0976	0.0086	5008	,	,		20873	0.0		0.002	False		,,,				2504	0.0				p.S1094S		Atlas-SNP	.											.	DUOX1	125	.	0			c.T3282C						PASS	.	T	,	415,3981	202.1+/-225.0	17,381,1800	212.0	155.0	174.0		3282,3282	2.2	1.0	15	dbSNP_132	174	7,8589	5.0+/-18.6	0,7,4291	no	coding-synonymous,coding-synonymous	DUOX1	NM_017434.3,NM_175940.1	,	17,388,6091	CC,CT,TT		0.0814,9.4404,3.2482	,	1094/1552,1094/1552	45444572	422,12570	2198	4298	6496	SO:0001819	synonymous_variant	53905	exon26			CATCTCTTTCATG	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.3282T>C	15.37:g.45444572T>C		Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	219	116	0.52968	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																			T|0.968;C|0.032	0.032	strong		0.602	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
GLB1L2	89944	hgsc.bcm.edu	37	11	134226278	134226278	+	Silent	SNP	C	C	T	rs3802928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134226278C>T	ENST00000535456.2	+	6	830	c.642C>T	c.(640-642)taC>taT	p.Y214Y	GLB1L2_ENST00000389881.3_Silent_p.Y214Y|GLB1L2_ENST00000339772.7_Silent_p.Y214Y|GLB1L2_ENST00000529077.1_3'UTR	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	214					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)	p.Y214Y(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		ACATGCCCTACGTCAAGAAGG	0.458													C|||	634	0.126597	0.2027	0.0677	5008	,	,		17955	0.1944		0.0596	False		,,,				2504	0.0644				p.Y214Y		Atlas-SNP	.											GLB1L2,NS,carcinoma,0,1	GLB1L2	79	1	1	Substitution - coding silent(1)	stomach(1)	c.C642T						scavenged	.	C		833,3569	330.7+/-301.6	85,663,1453	128.0	135.0	132.0		642	-1.6	0.0	11	dbSNP_107	132	415,8179	130.2+/-188.1	15,385,3897	no	coding-synonymous	GLB1L2	NM_138342.3		100,1048,5350	TT,TC,CC		4.829,18.9232,9.603		214/637	134226278	1248,11748	2201	4297	6498	SO:0001819	synonymous_variant	89944	exon6			GCCCTACGTCAAG		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.642C>T	11.37:g.134226278C>T		Somatic	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Silent	SNP	ENST00000535456.2	37	CCDS31724.1	264	0.12087912087912088	89	0.18089430894308944	20	0.055248618784530384	115	0.20104895104895104	40	0.052770448548812667	C	0.027	-1.362446	0.01235	0.189232	0.04829	ENSG00000149328	ENST00000525089;ENST00000533324	.	.	.	5.76	-1.59	0.08453	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.22779	P	0.9987403	.	.	.	.	.	.	T	0.17289	-1.0374	3	.	.	.	-11.4588	11.0134	0.47675	0.0:0.4036:0.0:0.5964	rs3802928;rs57061991;rs3802928	.	.	.	C	153;42	.	.	R	+	1	0	GLB1L2	133731488	0.000000	0.05858	0.009000	0.14445	0.018000	0.09664	-1.437000	0.02419	-0.616000	0.05671	-0.137000	0.14449	CGT	C|0.888;T|0.112	0.112	strong		0.458	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	
GSE1	23199	hgsc.bcm.edu	37	16	85690900	85690900	+	Missense_Mutation	SNP	G	G	A	rs35446008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:85690900G>A	ENST00000253458.7	+	8	1506	c.1330G>A	c.(1330-1332)Ggc>Agc	p.G444S	GSE1_ENST00000405402.2_Missense_Mutation_p.G340S|GSE1_ENST00000393243.1_Missense_Mutation_p.G371S|RN7SL381P_ENST00000577658.1_RNA	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	444				G -> S (in Ref. 1; BAA11499). {ECO:0000305}.													GAAGGATGCCGGCCTGCAGGC	0.642													G|||	67	0.0133786	0.0484	0.0043	5008	,	,		16388	0.0		0.0	False		,,,				2504	0.0				p.G444S		Atlas-SNP	.											.	.	.	.	0			c.G1330A						PASS	.	G	SER/GLY,SER/GLY	180,4216	110.4+/-148.6	4,172,2022	51.0	51.0	51.0		1018,1330	4.0	0.9	16	dbSNP_126	51	1,8597	1.2+/-3.3	0,1,4298	yes	missense,missense	KIAA0182	NM_001134473.1,NM_014615.2	56,56	4,173,6320	AA,AG,GG		0.0116,4.0946,1.393	benign,benign	340/1114,444/1218	85690900	181,12813	2198	4299	6497	SO:0001583	missense	23199	exon8			GATGCCGGCCTGC	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"""genetic suppressor element 1"""		"""KIAA0182"", ""Gse1 coiled-coil protein homolog (mouse)"""	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.1330G>A	16.37:g.85690900G>A	ENSP00000253458:p.Gly444Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Missense_Mutation	SNP	ENST00000253458.7	37	CCDS10952.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	8.046	0.765024	0.15914	0.040946	1.16E-4	ENSG00000131149	ENST00000405402;ENST00000253458;ENST00000393243	T;T;T	0.30981	1.51;1.51;1.51	5.07	4.04	0.47022	.	0.488693	0.24152	N	0.041074	T	0.02083	0.0065	N	0.01705	-0.755	0.22457	N	0.999083	B;B	0.32203	0.325;0.36	B;B	0.21151	0.033;0.027	T	0.14227	-1.0480	10	0.18276	T	0.48	-34.1225	12.2615	0.54652	0.0:0.0:0.702:0.298	rs35446008	371;444	Q14687-3;Q14687	.;GSE1_HUMAN	S	340;444;371	ENSP00000384839:G340S;ENSP00000253458:G444S;ENSP00000376934:G371S	ENSP00000253458:G444S	G	+	1	0	KIAA0182	84248401	0.732000	0.28121	0.941000	0.38009	0.471000	0.32888	1.422000	0.34826	2.367000	0.80283	0.561000	0.74099	GGC	G|0.985;A|0.015	0.015	strong		0.642	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615	
ZNF141	7700	hgsc.bcm.edu	37	4	367290	367290	+	Missense_Mutation	SNP	A	A	G	rs61733102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:367290A>G	ENST00000240499.7	+	4	1213	c.1064A>G	c.(1063-1065)aAt>aGt	p.N355S	ZNF141_ENST00000512994.1_Intron|ZNF141_ENST00000505939.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	355					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|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)			breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						TCAAAACTGAATGAACATAAG	0.408													a|||	13	0.00259585	0.0098	0.0	5008	,	,		20026	0.0		0.0	False		,,,				2504	0.0				p.N355S		Atlas-SNP	.											.	ZNF141	48	.	0			c.A1064G						PASS	.	A	SER/ASN	33,4373	36.8+/-68.6	0,33,2170	37.0	40.0	39.0		1064	-2.5	0.0	4	dbSNP_129	39	0,8596		0,0,4298	no	missense	ZNF141	NM_003441.2	46	0,33,6468	GG,GA,AA		0.0,0.749,0.2538	benign	355/475	367290	33,12969	2203	4298	6501	SO:0001583	missense	7700	exon4			AACTGAATGAACA	L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"""Zinc fingers, C2H2-type"", ""-"""	12926	protein-coding gene	gene with protein product		194648	"""zinc finger protein 141 (clone pHZ-44)"""	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.1064A>G	4.37:g.367290A>G	ENSP00000240499:p.Asn355Ser	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_003441	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	37	CCDS33931.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	10.25	1.299693	0.23650	0.00749	0.0	ENSG00000131127	ENST00000240499	T	0.03272	3.99	1.24	-2.48	0.06423	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01558	0.0050	N	0.25992	0.78	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.46762	-0.9168	8	.	.	.	.	2.176	0.03862	0.556:0.0:0.1963:0.2477	rs61733102	355	Q15928	ZN141_HUMAN	S	355	ENSP00000240499:N355S	.	N	+	2	0	ZNF141	357290	0.000000	0.05858	0.001000	0.08648	0.756000	0.42949	-0.780000	0.04654	-1.529000	0.01754	-0.856000	0.03024	AAT	A|0.998;G|0.002	0.002	strong		0.408	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441	
CD200R1L	344807	hgsc.bcm.edu	37	3	112545875	112545875	+	Missense_Mutation	SNP	G	G	A	rs61740125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112545875G>A	ENST00000398214.1	-	4	869	c.644C>T	c.(643-645)aCt>aTt	p.T215I	CD200R1L_ENST00000488794.1_Missense_Mutation_p.T194I|CD200R1L_ENST00000448932.1_Missense_Mutation_p.T194I	NM_001008784.2	NP_001008784.2	Q6Q8B3	MO2R2_HUMAN	CD200 receptor 1-like	215	Ig-like C2-type.					integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(2)	19						CTTGTTGCCAGTCAAATGGGA	0.453													G|||	201	0.0401358	0.0968	0.0115	5008	,	,		19144	0.002		0.001	False		,,,				2504	0.0634				p.T215I		Atlas-SNP	.											.	CD200R1L	47	.	0			c.C644T						PASS	.	G	ILE/THR,ILE/THR	351,4045	164.4+/-196.0	7,337,1854	66.0	70.0	68.0		644,581	3.5	0.3	3	dbSNP_129	68	6,8592	5.0+/-18.6	0,6,4293	yes	missense,missense	CD200R1L	NM_001008784.2,NM_001199215.1	89,89	7,343,6147	AA,AG,GG		0.0698,7.9845,2.7474	probably-damaging,probably-damaging	215/272,194/251	112545875	357,12637	2198	4299	6497	SO:0001583	missense	344807	exon4			TTGCCAGTCAAAT	AY284976	CCDS43131.1, CCDS56267.1	3q13.2	2014-05-15	2008-10-08		ENSG00000206531	ENSG00000206531		"""Immunoglobulin superfamily / C2-set domain containing"""	24665	protein-coding gene	gene with protein product	"""CD200 receptor 2"""						Standard	NM_001008784		Approved	CD200RLa, CD200R2	uc003dzi.1	Q6Q8B3	OTTHUMG00000159283	ENST00000398214.1:c.644C>T	3.37:g.112545875G>A	ENSP00000381272:p.Thr215Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_001008784	Q6WHB7	Missense_Mutation	SNP	ENST00000398214.1	37	CCDS43131.1	71	0.03250915750915751	65	0.13211382113821138	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	G	16.52	3.146835	0.57151	0.079845	6.98E-4	ENSG00000206531	ENST00000398214;ENST00000488794;ENST00000448932	T;T;T	0.76578	-1.03;-1.03;-1.03	4.35	3.45	0.39498	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.276049	0.31279	N	0.007923	T	0.07324	0.0185	M	0.87547	2.89	0.34063	P	0.342499	D	0.76494	0.999	D	0.72982	0.979	T	0.63220	-0.6686	9	0.72032	D	0.01	.	10.1628	0.42862	0.0:0.2033:0.7967:0.0	.	215	Q6Q8B3	MO2R2_HUMAN	I	215;194;194	ENSP00000381272:T215I;ENSP00000418413:T194I;ENSP00000415132:T194I	ENSP00000381272:T215I	T	-	2	0	CD200R1L	114028565	0.138000	0.22547	0.331000	0.25455	0.900000	0.52787	2.570000	0.45981	1.126000	0.42016	0.655000	0.94253	ACT	G|0.979;A|0.021	0.021	strong		0.453	CD200R1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354365.1	NM_001008784	
ITGA11	22801	hgsc.bcm.edu	37	15	68603345	68603345	+	Missense_Mutation	SNP	C	C	T	rs146663204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68603345C>T	ENST00000315757.7	-	26	3247	c.3161G>A	c.(3160-3162)cGt>cAt	p.R1054H	ITGA11_ENST00000423218.2_Missense_Mutation_p.R1055H	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	1054					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)			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						CTGTGGAGCACGACGCAAGTC	0.607													C|||	22	0.00439297	0.0166	0.0	5008	,	,		17947	0.0		0.0	False		,,,				2504	0.0				p.R1054H		Atlas-SNP	.											.	ITGA11	110	.	0			c.G3161A						PASS	.	C	HIS/ARG	64,4062		1,62,2000	37.0	38.0	38.0		3161	-0.7	0.0	15	dbSNP_134	38	0,8378		0,0,4189	yes	missense	ITGA11	NM_001004439.1	29	1,62,6189	TT,TC,CC		0.0,1.5511,0.5118	benign	1054/1189	68603345	64,12440	2063	4189	6252	SO:0001583	missense	22801	exon26			GGAGCACGACGCA	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.3161G>A	15.37:g.68603345C>T	ENSP00000327290:p.Arg1054His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	88	33	0.375	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	0.254	-1.004438	0.02112	0.015511	0.0	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.51325	0.71;0.8	4.72	-0.744	0.11101	.	0.394401	0.31051	N	0.008356	T	0.11024	0.0269	N	0.05383	-0.06	0.09310	N	0.99999	B;B	0.11235	0.0;0.004	B;B	0.08055	0.002;0.003	T	0.13522	-1.0506	10	0.23891	T	0.37	.	8.4623	0.32936	0.0:0.5066:0.0:0.4934	.	1054;1054	A8K8T0;Q9UKX5	.;ITA11_HUMAN	H	1054;1055;689	ENSP00000327290:R1054H;ENSP00000403392:R1055H	ENSP00000327290:R1054H	R	-	2	0	ITGA11	66390399	0.024000	0.19004	0.024000	0.17045	0.267000	0.26476	0.065000	0.14466	0.021000	0.15133	0.655000	0.94253	CGT	C|0.997;T|0.003	0.003	strong		0.607	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
TARBP1	6894	hgsc.bcm.edu	37	1	234529540	234529540	+	Silent	SNP	G	G	A	rs1134756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:234529540G>A	ENST00000040877.1	-	27	4286	c.4287C>T	c.(4285-4287)gaC>gaT	p.D1429D	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1429					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)			TCTTCTGAACGTCGGTCCACT	0.423													G|||	1147	0.229034	0.5401	0.1844	5008	,	,		17146	0.0853		0.0875	False		,,,				2504	0.1339				p.D1429D		Atlas-SNP	.											.	TARBP1	111	.	0			c.C4287T						PASS	.	G		2023,2383	563.2+/-381.1	474,1075,654	89.0	93.0	92.0		4287	-2.1	0.1	1	dbSNP_86	92	713,7887	173.9+/-224.3	33,647,3620	no	coding-synonymous	TARBP1	NM_005646.3		507,1722,4274	AA,AG,GG		8.2907,45.9147,21.0364		1429/1622	234529540	2736,10270	2203	4300	6503	SO:0001819	synonymous_variant	6894	exon27			CTGAACGTCGGTC		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.4287C>T	1.37:g.234529540G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	142	64	0.450704	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			G|0.798;A|0.202	0.202	strong		0.423	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
OR11H12	440153	hgsc.bcm.edu	37	14	19377859	19377859	+	Missense_Mutation	SNP	T	T	C	rs61969156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	556	1	0.00179856		WXS	Illumina HiSeq	Phase_I	500	39	0.078	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	
OR7A17	26333	hgsc.bcm.edu	37	19	14991643	14991643	+	Silent	SNP	G	G	A	rs10401818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	186	0	0		WXS	Illumina HiSeq	Phase_I	162	162	1	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	
PYROXD2	84795	hgsc.bcm.edu	37	10	100144782	100144782	+	Missense_Mutation	SNP	C	C	T	rs2296441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:100144782C>T	ENST00000370575.4	-	15	1645	c.1597G>A	c.(1597-1599)Gcc>Acc	p.A533T	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	533			A -> T (in dbSNP:rs2296441). {ECO:0000269|PubMed:14702039}.				oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						ACGGGGCGGGCGAAGTAGAGC	0.607													C|||	2026	0.404553	0.3691	0.4121	5008	,	,		18541	0.4425		0.2634	False		,,,				2504	0.5532				p.A533T		Atlas-SNP	.											.	PYROXD2	43	.	0			c.G1597A						PASS	.	C	THR/ALA	1642,2764	502.2+/-365.2	309,1024,870	82.0	78.0	79.0		1597	5.2	1.0	10	dbSNP_100	79	2610,5990	422.3+/-354.0	421,1768,2111	yes	missense	PYROXD2	NM_032709.2	58	730,2792,2981	TT,TC,CC		30.3488,37.2674,32.6926	benign	533/582	100144782	4252,8754	2203	4300	6503	SO:0001583	missense	84795	exon15			GGCGGGCGAAGTA	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.1597G>A	10.37:g.100144782C>T	ENSP00000359607:p.Ala533Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_032709	D3DR61|Q5TAA9|Q9BRQ1	Missense_Mutation	SNP	ENST00000370575.4	37	CCDS7474.1	788	0.3608058608058608	179	0.3638211382113821	144	0.39779005524861877	266	0.46503496503496505	199	0.262532981530343	C	10.91	1.483060	0.26598	0.372674	0.303488	ENSG00000119943	ENST00000370575	T	0.48522	0.81	5.16	5.16	0.70880	.	0.102848	0.64402	D	0.000003	T	0.00012	0.0000	L	0.28054	0.825	0.19945	P	0.9999441106	B	0.25048	0.117	B	0.14023	0.01	T	0.43734	-0.9373	9	0.15066	T	0.55	-20.8698	8.1427	0.31093	0.1586:0.7598:0.0:0.0816	rs2296441;rs57309996;rs2296441	533	Q8N2H3	PYRD2_HUMAN	T	533	ENSP00000359607:A533T	ENSP00000359607:A533T	A	-	1	0	PYROXD2	100134772	0.477000	0.25909	0.991000	0.47740	0.968000	0.65278	0.920000	0.28705	2.394000	0.81467	0.557000	0.71058	GCC	C|0.662;T|0.338	0.338	strong		0.607	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709	
GOLT1A	127845	hgsc.bcm.edu	37	1	204172060	204172060	+	Silent	SNP	G	G	C	rs6689599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204172060G>C	ENST00000308302.3	-	2	266	c.81C>G	c.(79-81)ctC>ctG	p.L27L	GOLT1A_ENST00000475517.1_5'Flank	NM_198447.1	NP_940849.1			golgi transport 1A											kidney(1)|lung(2)|urinary_tract(1)	4	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.244)			CAAAGTACAGGAGTGTTCCAA	0.552													G|||	464	0.0926518	0.2413	0.0836	5008	,	,		19032	0.006		0.0517	False		,,,				2504	0.0297				p.L27L		Atlas-SNP	.											.	GOLT1A	15	.	0			c.C81G						PASS	.	G		985,3421	369.1+/-318.9	126,733,1344	122.0	108.0	113.0		81	2.8	1.0	1	dbSNP_116	113	473,8127	140.0+/-196.6	8,457,3835	no	coding-synonymous	GOLT1A	NM_198447.1		134,1190,5179	CC,CG,GG		5.5,22.3559,11.2102		27/133	204172060	1458,11548	2203	4300	6503	SO:0001819	synonymous_variant	127845	exon2			GTACAGGAGTGTT	BC058832	CCDS1443.1	1q32.1	2010-06-24	2010-06-24		ENSG00000174567	ENSG00000174567			24766	protein-coding gene	gene with protein product			"""golgi transport 1 homolog A (S. cerevisiae)"""			12477932	Standard	NM_198447		Approved	FLJ42654, CGI-141, YMR292W, GOT1, MGC62027	uc001has.1	Q6ZVE7	OTTHUMG00000036056	ENST00000308302.3:c.81C>G	1.37:g.204172060G>C		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	208	98	0.471154	NM_198447		Silent	SNP	ENST00000308302.3	37	CCDS1443.1																																																																																			G|0.897;C|0.103	0.103	strong		0.552	GOLT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087887.1	NM_198447	
PIH1D1	55011	hgsc.bcm.edu	37	19	49950356	49950356	+	Splice_Site	SNP	C	C	G	rs397831687|rs12443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49950356C>G	ENST00000262265.5	-	7	847	c.612G>C	c.(610-612)ggG>ggC	p.G204G	PIH1D1_ENST00000602226.1_5'Flank|PIH1D1_ENST00000596049.1_Splice_Site_p.G204G	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	204					box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		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;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		GCTTTTCAGGCCTGAGGAGGA	0.607													G|||	3395	0.677915	0.8964	0.6412	5008	,	,		19297	0.4067		0.7545	False		,,,				2504	0.6094				p.G204G		Atlas-SNP	.											PIH1D1,NS,carcinoma,0,1	PIH1D1	23	1	0			c.G612C						PASS	.	G		3797,609	263.4+/-265.5	1638,521,44	82.0	84.0	83.0		612	3.5	1.0	19	dbSNP_52	83	6595,2005	348.7+/-327.1	2519,1557,224	yes	coding-synonymous-near-splice	PIH1D1	NM_017916.2		4157,2078,268	GG,GC,CC		23.314,13.8221,20.0984		204/291	49950356	10392,2614	2203	4300	6503	SO:0001630	splice_region_variant	55011	exon7			TTCAGGCCTGAGG	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.612-1G>C	19.37:g.49950356C>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_017916	B4DGN7|B4E2X7|Q9BVL0	Silent	SNP	ENST00000262265.5	37	CCDS12765.1																																																																																			C|0.246;G|0.754	0.754	strong		0.607	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916	Silent
MORC1	27136	hgsc.bcm.edu	37	3	108690221	108690221	+	Missense_Mutation	SNP	G	G	A	rs2593943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108690221G>A	ENST00000483760.1	-	24	2486	c.2443C>T	c.(2443-2445)Cat>Tat	p.H815Y	MORC1_ENST00000232603.5_Missense_Mutation_p.H836Y					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						GGTAGCTGATGCTCAGGAAAA	0.408													A|||	1688	0.337061	0.4342	0.2824	5008	,	,		18970	0.1071		0.4314	False		,,,				2504	0.3845				p.H836Y		Atlas-SNP	.											.	MORC1	211	.	0			c.C2506T						PASS	.	A	TYR/HIS	1987,2419	617.3+/-392.9	445,1097,661	116.0	119.0	118.0		2506	2.2	1.0	3	dbSNP_100	118	3625,4975	624.8+/-397.6	773,2079,1448	yes	missense	MORC1	NM_014429.3	83	1218,3176,2109	AA,AG,GG		42.1512,45.0976,43.1493	benign	836/985	108690221	5612,7394	2203	4300	6503	SO:0001583	missense	27136	exon25			GCTGATGCTCAGG	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.2443C>T	3.37:g.108690221G>A	ENSP00000417282:p.His815Tyr	Somatic	313	1	0.00319489		WXS	Illumina HiSeq	Phase_I	303	155	0.511551	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	37		722	0.3305860805860806	221	0.4491869918699187	122	0.3370165745856354	43	0.07517482517482517	336	0.44327176781002636	A	0.482	-0.879434	0.02550	0.450976	0.421512	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.04862	3.54;3.54	4.69	2.2	0.27929	.	0.815127	0.10356	N	0.684562	T	0.00012	0.0000	N	0.01352	-0.895	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45396	-0.9264	9	0.02654	T	1	-1.0664	4.1247	0.10121	0.6363:0.1762:0.1875:0.0	rs2593943;rs17593430;rs52816473;rs59891599;rs2593943	815;836	E7ERX1;Q86VD1	.;MORC1_HUMAN	Y	836;815	ENSP00000232603:H836Y;ENSP00000417282:H815Y	ENSP00000232603:H836Y	H	-	1	0	MORC1	110172911	0.744000	0.28250	0.973000	0.42090	0.912000	0.54170	1.068000	0.30629	0.055000	0.16094	-0.260000	0.10688	CAT	G|0.607;A|0.392	0.392	strong		0.408	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
EPHA10	284656	hgsc.bcm.edu	37	1	38197214	38197214	+	Missense_Mutation	SNP	G	G	A	rs141193695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38197214G>A	ENST00000373048.4	-	7	1531	c.1532C>T	c.(1531-1533)gCg>gTg	p.A511V	EPHA10_ENST00000540011.1_Missense_Mutation_p.A6V|EPHA10_ENST00000427468.2_Missense_Mutation_p.A511V|EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000330210.7_Missense_Mutation_p.A6V	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	511	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GACTGTGGGCGCCCCTGTCTT	0.587													G|||	4	0.000798722	0.003	0.0	5008	,	,		15942	0.0		0.0	False		,,,				2504	0.0				p.A511V		Atlas-SNP	.											EPHA10,colon,carcinoma,+1,1	EPHA10	120	1	0			c.C1532T						PASS	.	G	VAL/ALA	16,3888		0,16,1936	106.0	106.0	106.0		1532	2.9	0.3	1	dbSNP_134	106	1,8293		0,1,4146	yes	missense	EPHA10	NM_001099439.1	64	0,17,6082	AA,AG,GG		0.0121,0.4098,0.1394	possibly-damaging	511/1009	38197214	17,12181	1952	4147	6099	SO:0001583	missense	284656	exon7			GTGGGCGCCCCTG	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.1532C>T	1.37:g.38197214G>A	ENSP00000362139:p.Ala511Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	47	0.02152014652014652	14	0.028455284552845527	4	0.011049723756906077	9	0.015734265734265736	20	0.026385224274406333	G	11.32	1.603665	0.28534	0.004098	1.21E-4	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000540011;ENST00000373048	T;T;T;T	0.76448	-1.02;0.36;-1.02;0.36	4.77	2.89	0.33648	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.526148	0.16039	N	0.232481	T	0.42268	0.1195	L	0.47016	1.485	0.09310	N	1	B	0.19331	0.035	B	0.10450	0.005	T	0.41305	-0.9516	9	.	.	.	.	5.1724	0.15118	0.172:0.0:0.6615:0.1665	.	511	Q5JZY3	EPHAA_HUMAN	V	6;511;6;511	ENSP00000330379:A6V;ENSP00000397746:A511V;ENSP00000441822:A6V;ENSP00000362139:A511V	.	A	-	2	0	EPHA10	37969801	0.972000	0.33761	0.319000	0.25293	0.345000	0.29048	3.224000	0.51238	0.605000	0.29947	0.563000	0.77884	GCG	G|0.979;A|0.021	0.021	strong		0.587	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
PARVB	29780	hgsc.bcm.edu	37	22	44489868	44489868	+	Missense_Mutation	SNP	T	T	C	rs1983609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44489868T>C	ENST00000338758.7	+	2	236	c.173T>C	c.(172-174)gTg>gCg	p.V58A	PARVB_ENST00000404989.1_Missense_Mutation_p.V21A|PARVB_ENST00000406477.3_Missense_Mutation_p.V91A|PARVB_ENST00000477795.1_3'UTR	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	58			V -> A (in dbSNP:rs1983609). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18691976, ECO:0000269|Ref.1}.		actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				CCCGCCCTGGTGGATGTTCAC	0.547													C|||	4368	0.872204	0.9773	0.8818	5008	,	,		17134	0.9593		0.7386	False		,,,				2504	0.771				p.V91A		Atlas-SNP	.											.	PARVB	44	.	0			c.T272C						PASS	.	C	ALA/VAL,ALA/VAL	4179,227	136.5+/-172.5	1983,213,7	93.0	94.0	94.0		272,173	-4.1	0.0	22	dbSNP_92	94	6540,2060	358.0+/-331.0	2486,1568,246	yes	missense,missense	PARVB	NM_001003828.2,NM_013327.4	64,64	4469,1781,253	CC,CT,TT		23.9535,5.1521,17.5842	benign,benign	91/398,58/365	44489868	10719,2287	2203	4300	6503	SO:0001583	missense	29780	exon3			CCCTGGTGGATGT	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.173T>C	22.37:g.44489868T>C	ENSP00000342492:p.Val58Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	37	CCDS14056.1	1900	0.86996336996337	477	0.9695121951219512	314	0.8674033149171271	553	0.9667832167832168	556	0.7335092348284961	C	0.075	-1.193909	0.01594	0.948479	0.760465	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000402876;ENST00000444029;ENST00000404989	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	4.91	-4.14	0.03892	Calponin homology domain (1);	0.810877	0.11826	N	0.525663	T	0.00012	0.0000	N	0.10685	0.025	0.80722	P	0.0	B;B;B;B	0.10296	0.0;0.0;0.0;0.003	B;B;B;B	0.10450	0.0;0.001;0.001;0.005	T	0.17653	-1.0362	9	0.10111	T	0.7	-9.3018	8.9807	0.35964	0.0:0.4397:0.1084:0.4519	rs1983609;rs5764516;rs17857311;rs52834884;rs61460848;rs1983609	58;21;58;91	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	A	91;58;58;56;21	ENSP00000384515:V91A;ENSP00000342492:V58A;ENSP00000385331:V58A;ENSP00000393758:V56A;ENSP00000384353:V21A	ENSP00000342492:V58A	V	+	2	0	PARVB	42821201	0.004000	0.15560	0.001000	0.08648	0.001000	0.01503	0.009000	0.13219	-1.601000	0.01601	-1.073000	0.02249	GTG	T|0.150;C|0.850	0.850	strong		0.547	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828	
MCM9	254394	hgsc.bcm.edu	37	6	119245024	119245024	+	Silent	SNP	C	C	T	rs12197931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:119245024C>T	ENST00000316316.6	-	3	859	c.573G>A	c.(571-573)tcG>tcA	p.S191S	MCM9_ENST00000316068.3_Silent_p.S191S	NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	191					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)		TGGTTGGAGACGAAGACAAGC	0.418													C|||	491	0.0980431	0.0968	0.049	5008	,	,		20322	0.2014		0.0378	False		,,,				2504	0.09				p.S191S		Atlas-SNP	.											MCM9_ENST00000316316,rectum,carcinoma,-1,2	MCM9	73	2	0			c.G573A						PASS	.	C	,	350,4056	181.2+/-209.3	15,320,1868	84.0	81.0	82.0		573,573	-1.9	1.0	6	dbSNP_120	82	376,8224	122.9+/-181.8	6,364,3930	no	coding-synonymous,coding-synonymous	MCM9	NM_017696.2,NM_153255.4	,	21,684,5798	TT,TC,CC		4.3721,7.9437,5.582	,	191/1144,191/392	119245024	726,12280	2203	4300	6503	SO:0001819	synonymous_variant	254394	exon2			TGGAGACGAAGAC	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.573G>A	6.37:g.119245024C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	143	72	0.503497	NM_017696	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Silent	SNP	ENST00000316316.6	37	CCDS56447.1																																																																																			C|0.923;T|0.077	0.077	strong		0.418	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	
LAMA2	3908	hgsc.bcm.edu	37	6	129762112	129762112	+	Silent	SNP	G	G	A	rs2297738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:129762112G>A	ENST00000421865.2	+	43	6286	c.6237G>A	c.(6235-6237)acG>acA	p.T2079T		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2079	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TCGCCAAAACGAATGCTGTGG	0.418													G|||	914	0.182508	0.1536	0.2334	5008	,	,		21579	0.2202		0.1551	False		,,,				2504	0.1748				p.T2079T		Atlas-SNP	.											.	LAMA2	481	.	0			c.G6237A						PASS	.	G	,	555,3851	250.0+/-257.2	29,497,1677	94.0	83.0	87.0		6237,6237	3.4	1.0	6	dbSNP_100	87	1253,7347	249.9+/-277.0	95,1063,3142	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	124,1560,4819	AA,AG,GG		14.5698,12.5965,13.9013	,	2079/3123,2079/3119	129762112	1808,11198	2203	4300	6503	SO:0001819	synonymous_variant	3908	exon43			CAAAACGAATGCT	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.6237G>A	6.37:g.129762112G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			G|0.845;A|0.155	0.155	strong		0.418	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
COL18A1	80781	hgsc.bcm.edu	37	21	46900062	46900062	+	Missense_Mutation	SNP	G	G	A	rs61738822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46900062G>A	ENST00000359759.4	+	10	2656	c.2635G>A	c.(2635-2637)Gac>Aac	p.D879N	COL18A1_ENST00000400337.2_Missense_Mutation_p.D464N|COL18A1_ENST00000355480.5_Missense_Mutation_p.D644N			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	879	Nonhelical region 3 (NC3).				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)		CTTCAGACACGACAAGCTGGT	0.642													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		14900	0.0		0.0	False		,,,				2504	0.0				p.D644N		Atlas-SNP	.											.	COL18A1	129	.	0			c.G1930A						PASS	.	G	ASN/ASP,ASN/ASP	53,3705		0,53,1826	17.0	22.0	21.0		1930,1390	3.2	0.9	21	dbSNP_129	21	0,8226		0,0,4113	yes	missense,missense	COL18A1	NM_030582.3,NM_130445.2	23,23	0,53,5939	AA,AG,GG		0.0,1.4103,0.4423	possibly-damaging,possibly-damaging	644/1520,464/1340	46900062	53,11931	1879	4113	5992	SO:0001583	missense	80781	exon10			AGACACGACAAGC		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.2635G>A	21.37:g.46900062G>A	ENSP00000352798:p.Asp879Asn	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	17.19	3.325962	0.60743	0.014103	0.0	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.90788	-2.72;-2.73;-2.64	3.19	3.19	0.36642	.	0.545209	0.16627	N	0.206240	D	0.88385	0.6422	L	0.56769	1.78	0.40960	D	0.984616	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.992;0.997;0.997	D	0.89130	0.3509	10	0.59425	D	0.04	.	10.0536	0.42230	0.0:0.0:1.0:0.0	rs61738822	879;644;464	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	N	464;464;644;879;879	ENSP00000383191:D464N;ENSP00000347665:D644N;ENSP00000352798:D879N	ENSP00000347665:D644N	D	+	1	0	COL18A1	45724490	1.000000	0.71417	0.858000	0.33744	0.334000	0.28698	5.592000	0.67543	1.812000	0.52913	0.561000	0.74099	GAC	G|0.996;A|0.004	0.004	strong		0.642	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
PRAMEF2	65122	hgsc.bcm.edu	37	1	12918903	12918903	+	Silent	SNP	G	G	A	rs17038644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12918903G>A	ENST00000240189.2	+	2	126	c.39G>A	c.(37-39)gcG>gcA	p.A13A		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	13					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)		TGGAGCTGGCGGGGCAGAGCC	0.562													.|||	197	0.0393371	0.0908	0.0144	5008	,	,		19026	0.0298		0.0189	False		,,,				2504	0.0184				p.A13A		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G39A						PASS	.	A		276,4126	143.8+/-178.8	19,238,1944	88.0	99.0	95.0		39	-1.7	0.0	1	dbSNP_123	95	7,8587		0,7,4290	no	coding-synonymous	PRAMEF2	NM_023014.1		19,245,6234	AA,AG,GG		0.0815,6.2699,2.1776		13/475	12918903	283,12713	2201	4297	6498	SO:0001819	synonymous_variant	65122	exon2			GCTGGCGGGGCAG		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.39G>A	1.37:g.12918903G>A		Somatic	358	1	0.0027933		WXS	Illumina HiSeq	Phase_I	452	227	0.502212	NM_023014		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			G|0.978;A|0.022	0.022	strong		0.562	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46021546	46021546	+	Missense_Mutation	SNP	C	C	G	rs116074123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46021546C>G	ENST00000380102.2	+	1	1050	c.1025C>G	c.(1024-1026)gCc>gGc	p.A342G	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	342	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						TCCTGCCAGGCCAGCTGCTGC	0.711													-|||	183	0.0365415	0.1331	0.0101	5008	,	,		15282	0.0		0.0	False		,,,				2504	0.0				p.A337G		Atlas-SNP	.											.	KRTAP10-7	41	.	0			c.C1010G						PASS	.	C	,GLY/ALA	439,3945		20,399,1773	32.0	38.0	36.0		,1025	3.7	1.0	21	dbSNP_132	36	4,8554		0,4,4275	no	intron,missense	TSPEAR,KRTAP10-7	NM_144991.2,NM_198689.2	,60	20,403,6048	GG,GC,CC		0.0467,10.0137,3.423	,benign	,342/376	46021546	443,12499	2192	4279	6471	SO:0001583	missense	386675	exon2			GCCAGGCCAGCTG	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.1025C>G	21.37:g.46021546C>G	ENSP00000369445:p.Ala342Gly	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	114	83	0.72807	NM_198689	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	37		50	0.022893772893772892	45	0.09146341463414634	5	0.013812154696132596	0	0.0	0	0.0	c	11.47	1.647906	0.29336	0.100137	4.67E-4	ENSG00000205441	ENST00000380102	T	0.00675	5.88	3.73	3.73	0.42828	.	.	.	.	.	T	0.00039	0.0001	N	0.24115	0.695	0.19575	N	0.999963	B	0.17038	0.02	B	0.14023	0.01	T	0.52586	-0.8556	9	0.72032	D	0.01	.	7.4909	0.27460	0.0:0.8767:0.0:0.1233	.	337	P60409-2	.	G	342	ENSP00000369445:A342G	ENSP00000369445:A342G	A	+	2	0	KRTAP10-7	44845974	0.490000	0.26012	1.000000	0.80357	0.413000	0.31143	1.890000	0.39728	1.805000	0.52779	0.467000	0.42956	GCC	C|0.974;G|0.026	0.026	strong		0.711	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
FHAD1	114827	hgsc.bcm.edu	37	1	15708540	15708540	+	Missense_Mutation	SNP	A	A	G	rs1010294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:15708540A>G	ENST00000375998.4	+	29	3973	c.3973A>G	c.(3973-3975)Att>Gtt	p.I1325V	FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000417793.1_Missense_Mutation_p.I1289V|FHAD1_ENST00000314740.8_Missense_Mutation_p.I578V|FHAD1_ENST00000358897.4_Missense_Mutation_p.I1325V|FHAD1_ENST00000375999.3_Missense_Mutation_p.I1325V			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1325										skin(1)|stomach(1)	2						CAAAGTGTCCATTGAGATGTA	0.532													G|||	2114	0.422125	0.77	0.3055	5008	,	,		22117	0.2589		0.2624	False		,,,				2504	0.3671				p.I1325V		Atlas-SNP	.											.	FHAD1	78	.	0			c.A3973G						PASS	.	G	VAL/ILE	961,423		341,279,72	65.0	67.0	66.0		3973	-4.3	0.0	1	dbSNP_86	66	836,2346		102,632,857	yes	missense	FHAD1	NM_052929.1	29	443,911,929	GG,GA,AA		26.2728,30.5636,39.3561	benign	1325/1413	15708540	1797,2769	692	1591	2283	SO:0001583	missense	114827	exon30			GTGTCCATTGAGA	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.3973A>G	1.37:g.15708540A>G	ENSP00000365166:p.Ile1325Val	Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	312	162	0.519231	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		834	0.38186813186813184	369	0.75	125	0.3453038674033149	141	0.2465034965034965	199	0.262532981530343	G	0.006	-2.038631	0.00402	0.694364	0.262728	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998;ENST00000529606;ENST00000314740;ENST00000314668	T;T;T;T;T;T;T	0.39406	1.17;1.17;1.08;1.17;1.08;1.09;1.14	5.95	-4.31	0.03698	.	.	.	.	.	T	0.00012	0.0000	N	0.00116	-2.08	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38908	-0.9639	8	0.15952	T	0.53	-6.224	7.5924	0.28029	0.5737:0.2316:0.1946:0.0	rs1010294;rs3765368;rs52824203;rs61149895;rs1010294	578;1325	B7WPP2;B1AJZ9	.;FHAD1_HUMAN	V	1325;1289;1325;1325;596;578;560	ENSP00000351770:I1325V;ENSP00000407615:I1289V;ENSP00000365167:I1325V;ENSP00000365166:I1325V;ENSP00000434909:I596V;ENSP00000322979:I578V;ENSP00000318812:I560V	ENSP00000318812:I560V	I	+	1	0	FHAD1	15581127	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-1.470000	0.02346	-0.699000	0.05077	-0.716000	0.03619	ATT	T|0.004;G|0.400	0.400	strong		0.532	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
CD101	9398	hgsc.bcm.edu	37	1	117576631	117576631	+	Missense_Mutation	SNP	C	C	T	rs34248572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117576631C>T	ENST00000256652.4	+	9	3032	c.2974C>T	c.(2974-2976)Cgg>Tgg	p.R992W	CD101_ENST00000369470.1_Missense_Mutation_p.R992W|RP11-27K13.3_ENST00000421254.1_RNA|RP11-27K13.3_ENST00000445523.1_RNA|CD101_ENST00000467588.1_3'UTR	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	992			R -> W (in dbSNP:rs34248572).		cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TTCCAACACACGGAAAGAAAA	0.517													C|||	117	0.0233626	0.0817	0.0115	5008	,	,		19361	0.001		0.0	False		,,,				2504	0.0				p.R992W		Atlas-SNP	.											CD101,NS,carcinoma,-1,1	CD101	95	1	0			c.C2974T						PASS	.	C	TRP/ARG	286,4120	157.0+/-190.0	13,260,1930	123.0	112.0	116.0		2974	-0.3	0.0	1	dbSNP_126	116	5,8595	3.0+/-9.4	0,5,4295	yes	missense	CD101	NM_004258.3	101	13,265,6225	TT,TC,CC		0.0581,6.4911,2.2374	probably-damaging	992/1022	117576631	291,12715	2203	4300	6503	SO:0001583	missense	9398	exon9			AACACACGGAAAG	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.2974C>T	1.37:g.117576631C>T	ENSP00000256652:p.Arg992Trp	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	48	0.02197802197802198	45	0.09146341463414634	3	0.008287292817679558	0	0.0	0	0.0	C	14.76	2.631571	0.46944	0.064911	5.81E-4	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.03772	3.81;3.81	5.83	-0.273	0.12915	.	1.475580	0.04746	N	0.423700	T	0.01523	0.0049	N	0.14661	0.345	0.09310	N	1	D	0.63880	0.993	B	0.44315	0.446	T	0.49234	-0.8961	10	0.72032	D	0.01	-0.5271	9.27	0.37666	0.5351:0.3393:0.1256:0.0	rs34248572	992	Q93033	IGSF2_HUMAN	W	992	ENSP00000256652:R992W;ENSP00000358482:R992W	ENSP00000256652:R992W	R	+	1	2	CD101	117378154	0.000000	0.05858	0.000000	0.03702	0.250000	0.25880	-0.056000	0.11787	0.306000	0.22856	0.563000	0.77884	CGG	C|0.972;T|0.028	0.028	strong		0.517	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
AP3B2	8120	hgsc.bcm.edu	37	15	83334245	83334245	+	Silent	SNP	C	C	T	rs9806343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83334245C>T	ENST00000261722.3	-	16	2142	c.1935G>A	c.(1933-1935)ccG>ccA	p.P645P	AP3B2_ENST00000535359.1_Silent_p.P645P|AP3B2_ENST00000535348.1_Silent_p.P613P|RP11-752G15.3_ENST00000560650.1_RNA	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	645					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			GGGCTTCCTCCGGCCAGTCTG	0.592													C|||	276	0.0551118	0.1241	0.0793	5008	,	,		16999	0.0		0.0258	False		,,,				2504	0.0317				p.P645P		Atlas-SNP	.											.	AP3B2	103	.	0			c.G1935A						PASS	.	C		458,3890		25,408,1741	81.0	93.0	89.0		1935	-6.7	1.0	15	dbSNP_119	89	240,8330		3,234,4048	no	coding-synonymous	AP3B2	NM_004644.3		28,642,5789	TT,TC,CC		2.8005,10.5336,5.4033		645/1083	83334245	698,12220	2174	4285	6459	SO:0001819	synonymous_variant	8120	exon16			TTCCTCCGGCCAG	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.1935G>A	15.37:g.83334245C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	37	CCDS45331.1																																																																																			C|0.956;T|0.044	0.044	strong		0.592	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1		
POLE	5426	hgsc.bcm.edu	37	12	133212582	133212582	+	Silent	SNP	G	G	A	rs5744990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	63	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	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	
TCF3	6929	hgsc.bcm.edu	37	19	1622116	1622116	+	Silent	SNP	G	G	A	rs2240590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1622116G>A	ENST00000262965.5	-	10	1103	c.759C>T	c.(757-759)agC>agT	p.S253S	TCF3_ENST00000395423.3_Silent_p.S202S|TCF3_ENST00000588136.1_Silent_p.S253S|TCF3_ENST00000344749.5_Silent_p.S253S|TCF3_ENST00000453954.2_Silent_p.S169S	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		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)		CCACCGGGCCGCTACCGGGCG	0.741			T	"""PBX1, HLF, TFPT"""	pre B-ALL								g|||	1698	0.339058	0.593	0.2925	5008	,	,		10107	0.244		0.1163	False		,,,				2504	0.3558				p.S253S		Atlas-SNP	.		Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	.	TCF3	72	.	0			c.C759T						PASS	.	G	,	1908,2318		433,1042,638	6.0	7.0	7.0		759,759	2.7	0.2	19	dbSNP_98	7	1001,7343		85,831,3256	no	coding-synonymous,coding-synonymous	TCF3	NM_001136139.2,NM_003200.3	,	518,1873,3894	AA,AG,GG		11.9966,45.1491,23.1424	,	253/652,253/655	1622116	2909,9661	2113	4172	6285	SO:0001819	synonymous_variant	6929	exon10			CGGGCCGCTACCG	M65214	CCDS12074.1, CCDS45899.1	19p13.3	2014-02-13	2013-02-26		ENSG00000071564	ENSG00000071564		"""Basic helix-loop-helix proteins"""	11633	protein-coding gene	gene with protein product	"""transcription factor E2-alpha"", ""immunoglobulin transcription factor 1"", ""kappa-E2-binding factor"", ""E2A immunoglobulin enhancer-binding factor E12/E47"", ""VDR interacting repressor"""	147141				2308859, 1967983	Standard	NM_003200		Approved	E2A, ITF1, MGC129647, MGC129648, bHLHb21, VDIR, E47	uc002ltt.4	P15923	OTTHUMG00000180031	ENST00000262965.5:c.759C>T	19.37:g.1622116G>A		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	20	14	0.7	NM_003200	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000262965.5	37	CCDS12074.1																																																																																			G|0.722;A|0.278	0.278	strong		0.741	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1	NM_003200	
FASLG	356	hgsc.bcm.edu	37	1	172628488	172628488	+	Silent	SNP	G	G	A	rs61756244	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:172628488G>A	ENST00000367721.2	+	1	331	c.147G>A	c.(145-147)ccG>ccA	p.P49P	FASLG_ENST00000340030.3_Silent_p.P49P	NM_000639.1	NP_000630.1	P48023	TNFL6_HUMAN	Fas ligand (TNF superfamily, member 6)	49	Poly-Pro.|Pro-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cellular chloride ion homeostasis (GO:0030644)|endosomal lumen acidification (GO:0048388)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|immune response (GO:0006955)|inflammatory cell apoptotic process (GO:0006925)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of angiogenesis (GO:0016525)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|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 neuron apoptotic process (GO:0043525)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to growth factor (GO:0070848)|response to lipopolysaccharide (GO:0032496)|retinal cell programmed cell death (GO:0046666)|signal transduction (GO:0007165)|T cell apoptotic process (GO:0070231)|transcription, DNA-templated (GO:0006351)	caveola (GO:0005901)|cytoplasmic membrane-bounded vesicle (GO:0016023)|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)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|skin(1)	19						caccaccaccgccaccgccac	0.662													G|||	242	0.0483227	0.1717	0.0216	5008	,	,		10744	0.0		0.0	False		,,,				2504	0.0				p.P49P	Ovarian(28;486 876 30334 44033)	Atlas-SNP	.											.	FASLG	44	.	0			c.G147A						PASS	.	G		714,3692	267.4+/-267.8	68,578,1557	56.0	57.0	57.0		147	-8.6	0.0	1	dbSNP_129	57	7,8593	3.7+/-12.6	0,7,4293	no	coding-synonymous	FASLG	NM_000639.1		68,585,5850	AA,AG,GG		0.0814,16.2052,5.5436		49/282	172628488	721,12285	2203	4300	6503	SO:0001819	synonymous_variant	356	exon1			ACCACCGCCACCG	U11821	CCDS1304.1	1q23	2014-09-17	2005-01-07	2005-01-07	ENSG00000117560	ENSG00000117560		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"", ""Endogenous ligands"""	11936	protein-coding gene	gene with protein product		134638	"""tumor necrosis factor (ligand) superfamily, member 6"""	APT1LG1, TNFSF6		7826947, 9022072	Standard	NM_000639		Approved	FasL, CD178	uc001gis.3	P48023	OTTHUMG00000034841	ENST00000367721.2:c.147G>A	1.37:g.172628488G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	136	60	0.441176	NM_000639	Q9BZP9	Silent	SNP	ENST00000367721.2	37	CCDS1304.1																																																																																			G|0.944;A|0.056	0.056	strong		0.662	FASLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084276.1		
TPRN	286262	hgsc.bcm.edu	37	9	140086940	140086940	+	Silent	SNP	C	C	T	rs115446132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140086940C>T	ENST00000409012.4	-	2	2015	c.1929G>A	c.(1927-1929)gtG>gtA	p.V643V	TPRN_ENST00000541945.1_5'Flank|TPRN_ENST00000321773.2_Silent_p.V582V	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	643					sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						TCTCGGGTCTCACGCTGCTCA	0.642													C|||	20	0.00399361	0.0129	0.0043	5008	,	,		17266	0.0		0.0	False		,,,				2504	0.0				p.V643V		Atlas-SNP	.											.	TPRN	28	.	0			c.G1929A						PASS	.	C		48,4356	46.7+/-81.2	0,48,2154	33.0	26.0	28.0		1929	3.0	0.0	9	dbSNP_132	28	0,8596		0,0,4298	no	coding-synonymous	TPRN	NM_001128228.2		0,48,6452	TT,TC,CC		0.0,1.0899,0.3692		643/712	140086940	48,12952	2202	4298	6500	SO:0001819	synonymous_variant	286262	exon2			GGGTCTCACGCTG	AK074735	CCDS56594.1	9q34.3	2011-01-06	2010-03-24	2010-03-24	ENSG00000176058	ENSG00000176058			26894	protein-coding gene	gene with protein product		613354	"""chromosome 9 open reading frame 75"", ""deafness, autosomal recessive 79"""	C9orf75, DFNB79		20170898, 20170899	Standard	NM_001128228		Approved	FLJ90254	uc004clu.3	Q4KMQ1	OTTHUMG00000020984	ENST00000409012.4:c.1929G>A	9.37:g.140086940C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	71	41	0.577465	NM_001128228	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Silent	SNP	ENST00000409012.4	37	CCDS56594.1																																																																																			C|0.996;T|0.004	0.004	strong		0.642	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691	
NRP2	8828	hgsc.bcm.edu	37	2	206610502	206610502	+	Silent	SNP	T	T	G	rs849563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:206610502T>G	ENST00000357785.5	+	10	1705	c.1674T>G	c.(1672-1674)ccT>ccG	p.P558P	NRP2_ENST00000540841.1_Silent_p.P558P|NRP2_ENST00000540178.1_Silent_p.P558P|NRP2_ENST00000357118.4_Silent_p.P558P|NRP2_ENST00000412873.2_Silent_p.P558P|NRP2_ENST00000360409.3_Silent_p.P558P|NRP2_ENST00000272849.3_Silent_p.P558P			Q99435	NELL2_HUMAN	neuropilin 2	0	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						ATGACACCCCTGACATCCGAA	0.607													T|||	1282	0.25599	0.205	0.2176	5008	,	,		18439	0.4593		0.1223	False		,,,				2504	0.2802				p.P558P		Atlas-SNP	.											.	NRP2	179	.	0			c.T1674G	GRCh37	CM073248	NRP2	M	rs849563	PASS	.	T	,,,,	832,3574	329.3+/-301.0	75,682,1446	110.0	89.0	96.0		1674,1674,1674,1674,1674	-11.7	0.1	2	dbSNP_86	96	1216,7384	245.4+/-274.3	82,1052,3166	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRP2	NM_003872.2,NM_018534.3,NM_201266.1,NM_201267.1,NM_201279.1	,,,,	157,1734,4612	GG,GT,TT		14.1395,18.8833,15.7466	,,,,	558/927,558/907,558/932,558/902,558/910	206610502	2048,10958	2203	4300	6503	SO:0001819	synonymous_variant	8828	exon10			CACCCCTGACATC	AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.1674T>G	2.37:g.206610502T>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_201279	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000357785.5	37	CCDS46496.1																																																																																			T|0.802;G|0.198	0.198	strong		0.607	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1		
HSH2D	84941	hgsc.bcm.edu	37	19	16263946	16263946	+	Silent	SNP	C	C	T	rs1870354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16263946C>T	ENST00000253680.6	+	6	840	c.309C>T	c.(307-309)gaC>gaT	p.D103D	HSH2D_ENST00000593154.2_Silent_p.D103D|HSH2D_ENST00000588246.1_Silent_p.D103D|HSH2D_ENST00000397372.4_Splice_Site			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	103	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(2)	4						CCTCGCTGGACGCCCTGGTCA	0.617													C|||	96	0.0191693	0.0696	0.0043	5008	,	,		17099	0.0		0.001	False		,,,				2504	0.0				p.D103D		Atlas-SNP	.											.	HSH2D	16	.	0			c.C309T						PASS	.	C		236,3872		5,226,1823	26.0	30.0	29.0		309	-3.9	0.2	19	dbSNP_92	29	3,8351		0,3,4174	no	coding-synonymous	HSH2D	NM_032855.2		5,229,5997	TT,TC,CC		0.0359,5.7449,1.9178		103/353	16263946	239,12223	2054	4177	6231	SO:0001819	synonymous_variant	84941	exon6			GCTGGACGCCCTG	AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684		"""SH2 domain containing"""	24920	protein-coding gene	gene with protein product		608349				11700021	Standard	NM_032855		Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000253680.6:c.309C>T	19.37:g.16263946C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_032855	B5ME72|Q6ZNG7	Silent	SNP	ENST00000253680.6	37		30	0.013736263736263736	27	0.054878048780487805	3	0.008287292817679558	0	0.0	0	0.0	C	0.017	-1.489323	0.01018	0.057449	3.59E-4	ENSG00000196684	ENST00000397372	.	.	.	4.63	-3.9	0.04181	.	.	.	.	.	.	.	.	.	.	.	0.22253	N	0.999254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8363	0.13466	0.0:0.3118:0.3055:0.3827	rs1870354;rs1870354	.	.	.	.	-1	.	.	.	+	.	.	HSH2D	16124946	0.000000	0.05858	0.227000	0.23927	0.006000	0.05464	-2.127000	0.01315	-0.294000	0.08973	-0.949000	0.02662	.	C|0.986;T|0.014	0.014	strong		0.617	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855	
PRR16	51334	hgsc.bcm.edu	37	5	120021817	120021817	+	Missense_Mutation	SNP	C	C	A	rs386691752|rs17853861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:120021817C>A	ENST00000407149.2	+	2	537	c.328C>A	c.(328-330)Ccg>Acg	p.P110T	PRR16_ENST00000505123.1_Missense_Mutation_p.P40T|PRR16_ENST00000446965.1_Missense_Mutation_p.P40T|PRR16_ENST00000379551.2_Missense_Mutation_p.P87T			Q569H4	LARGN_HUMAN	proline rich 16	110	Pro-rich.		P -> T (in dbSNP:rs17853861). {ECO:0000269|PubMed:15489334}.		positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)			p.P87T(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CCCAGCACACCCGTCTGCTAT	0.532													C|||	460	0.091853	0.0711	0.085	5008	,	,		18390	0.0536		0.162	False		,,,				2504	0.092				p.P87T		Atlas-SNP	.											PRR16,NS,neuroblastoma,-1,2	PRR16	71	2	1	Substitution - Missense(1)	stomach(1)	c.C259A						PASS	.	C	THR/PRO	352,4054	182.9+/-210.6	14,324,1865	145.0	128.0	134.0		259	5.6	0.7	5	dbSNP_123	134	1363,7237	265.6+/-286.2	111,1141,3048	yes	missense	PRR16	NM_016644.1	38	125,1465,4913	AA,AC,CC		15.8488,7.9891,13.1862	probably-damaging	87/282	120021817	1715,11291	2203	4300	6503	SO:0001583	missense	51334	exon3			GCACACCCGTCTG	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.328C>A	5.37:g.120021817C>A	ENSP00000385118:p.Pro110Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Missense_Mutation	SNP	ENST00000407149.2	37		215	0.09844322344322344	27	0.054878048780487805	32	0.08839779005524862	36	0.06293706293706294	120	0.158311345646438	C	18.99	3.740256	0.69304	0.079891	0.158488	ENSG00000184838	ENST00000407149;ENST00000379551;ENST00000509923;ENST00000505123;ENST00000446965	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.00496	0.0016	L	0.59436	1.845	0.09310	P	0.999999964264	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00118	-1.2033	8	.	.	.	-9.6375	18.3984	0.90507	0.0:1.0:0.0:0.0	rs17853861	110;87	Q569H4;Q569H4-3	PRR16_HUMAN;.	T	110;87;40;40;40	ENSP00000385118:P110T;ENSP00000368869:P87T;ENSP00000421256:P40T;ENSP00000423446:P40T;ENSP00000405491:P40T	.	P	+	1	0	PRR16	120049716	0.997000	0.39634	0.726000	0.30738	0.904000	0.53231	3.306000	0.51881	2.640000	0.89533	0.549000	0.68633	CCG	C|0.881;A|0.119	0.119	strong		0.532	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644	
OBSCN	84033	hgsc.bcm.edu	37	1	228412227	228412227	+	Silent	SNP	T	T	C	rs386640006|rs1771480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228412227T>C	ENST00000422127.1	+	9	2765	c.2721T>C	c.(2719-2721)agT>agC	p.S907S	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.S999S|OBSCN_ENST00000284548.11_Silent_p.S907S|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	907	Ig-like 9.				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)				CAGGAGCCAGTGCCACACTGA	0.612													T|||	2066	0.41254	0.5885	0.402	5008	,	,		17552	0.3849		0.3668	False		,,,				2504	0.2577				p.S999S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T2997C						PASS	.						41.0	43.0	42.0					1																	228412227		2110	4222	6332	SO:0001819	synonymous_variant	84033	exon10			AGCCAGTGCCACA	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.2721T>C	1.37:g.228412227T>C		Somatic	285	1	0.00350877		WXS	Illumina HiSeq	Phase_I	235	230	0.978723	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																																																																																			T|0.612;C|0.388	0.388	strong		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SLC22A1	6580	hgsc.bcm.edu	37	6	160557643	160557643	+	Missense_Mutation	SNP	C	C	T	rs2282143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160557643C>T	ENST00000366963.4	+	6	1169	c.1022C>T	c.(1021-1023)cCg>cTg	p.P341L	SLC22A1_ENST00000324965.4_Missense_Mutation_p.P341L|SLC22A1_ENST00000457470.2_Missense_Mutation_p.P341L	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	341			P -> L (reduction of the MPP uptake. Reduction of the MPP uptake; when associated with V-408. Partly reduction of TEA uptake. Largely localized in the plasma membrane; dbSNP:rs2282143). {ECO:0000269|PubMed:12719534, ECO:0000269|PubMed:14697261, 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)	TTCCGCACGCCGCGCCTGAGG	0.597													C|||	332	0.0662939	0.0764	0.0187	5008	,	,		19321	0.126		0.0089	False		,,,				2504	0.0838				p.P341L		Atlas-SNP	.											SLC22A1,NS,carcinoma,-1,1	SLC22A1	69	1	0			c.C1022T	GRCh37	CM041849	SLC22A1	M	rs2282143	scavenged	.	C	LEU/PRO,LEU/PRO	305,4101	165.4+/-196.9	9,287,1907	158.0	127.0	137.0		1022,1022	4.6	0.0	6	dbSNP_100	137	119,8481	63.1+/-125.2	1,117,4182	yes	missense,missense	SLC22A1	NM_003057.2,NM_153187.1	98,98	10,404,6089	TT,TC,CC		1.3837,6.9224,3.26	probably-damaging,probably-damaging	341/555,341/507	160557643	424,12582	2203	4300	6503	SO:0001583	missense	6580	exon6			GCACGCCGCGCCT	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.1022C>T	6.37:g.160557643C>T	ENSP00000355930:p.Pro341Leu	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	Missense_Mutation	SNP	ENST00000366963.4	37	CCDS5274.1	126	0.057692307692307696	36	0.07317073170731707	8	0.022099447513812154	77	0.1346153846153846	5	0.006596306068601583	C	16.21	3.059342	0.55325	0.069224	0.013837	ENSG00000175003	ENST00000366963;ENST00000324965;ENST00000457470	T;T;T	0.62364	0.03;0.03;0.03	4.56	4.56	0.56223	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.067775	0.64402	D	0.000011	D	0.83755	0.5323	H	0.96861	3.895	0.58432	D	0.999995	D;D	0.76494	0.999;0.998	D;D	0.71184	0.952;0.972	D	0.89931	0.4066	10	0.72032	D	0.01	.	17.3506	0.87322	0.0:1.0:0.0:0.0	rs2282143;rs56860747;rs2282143	341;341	O15245-2;O15245	.;S22A1_HUMAN	L	341	ENSP00000355930:P341L;ENSP00000318103:P341L;ENSP00000409557:P341L	ENSP00000318103:P341L	P	+	2	0	SLC22A1	160477633	0.925000	0.31364	0.000000	0.03702	0.001000	0.01503	4.239000	0.58694	2.085000	0.62840	0.561000	0.74099	CCG	C|0.949;T|0.051	0.051	strong		0.597	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		
AHNAK2	113146	hgsc.bcm.edu	37	14	105407031	105407031	+	Silent	SNP	A	A	G	rs11623422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105407031A>G	ENST00000333244.5	-	7	14876	c.14757T>C	c.(14755-14757)tcT>tcC	p.S4919S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4919						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)			CTGGGCCCTGAGACACACAGG	0.602													G|||	2779	0.554912	0.6437	0.5115	5008	,	,		17679	0.4107		0.5338	False		,,,				2504	0.636				p.S4919S		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	0			c.T14757C						PASS	.	G		2588,1264		876,836,214	43.0	44.0	44.0		14757	-4.6	0.0	14	dbSNP_120	44	4478,3790		1234,2010,890	no	coding-synonymous	AHNAK2	NM_138420.2		2110,2846,1104	GG,GA,AA		45.8394,32.8141,41.6997		4919/5796	105407031	7066,5054	1926	4134	6060	SO:0001819	synonymous_variant	113146	exon7			GCCCTGAGACACA	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.14757T>C	14.37:g.105407031A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.459;G|0.541	0.541	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
VPS13D	55187	hgsc.bcm.edu	37	1	12339619	12339619	+	Missense_Mutation	SNP	A	A	T	rs4845898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12339619A>T	ENST00000358136.3	+	20	4644	c.4514A>T	c.(4513-4515)gAa>gTa	p.E1505V	VPS13D_ENST00000356315.4_Missense_Mutation_p.E1505V	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		ATAGAGAGAGAATCTGAATTG	0.378													A|||	807	0.161142	0.0151	0.2118	5008	,	,		16353	0.1964		0.2356	False		,,,				2504	0.2096				p.E1505V		Atlas-SNP	.											.	VPS13D	316	.	0			c.A4514T						PASS	.	A	VAL/GLU,VAL/GLU	190,4216	121.3+/-158.8	6,178,2019	103.0	104.0	104.0		4514,4514	6.0	1.0	1	dbSNP_111	104	1970,6630	346.9+/-326.4	213,1544,2543	yes	missense,missense	VPS13D	NM_015378.2,NM_018156.2	121,121	219,1722,4562	TT,TA,AA		22.907,4.3123,16.6077	benign,benign	1505/4389,1505/4364	12339619	2160,10846	2203	4300	6503	SO:0001583	missense	55187	exon20			AGAGAGAATCTGA	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.4514A>T	1.37:g.12339619A>T	ENSP00000350854:p.Glu1505Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	172	85	0.494186	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	374|374	0.17124542124542125|0.17124542124542125	13|13	0.026422764227642278|0.026422764227642278	75|75	0.20718232044198895|0.20718232044198895	114|114	0.1993006993006993|0.1993006993006993	172|172	0.22691292875989447|0.22691292875989447	A|A	17.77|17.77	3.471713|3.471713	0.63737|0.63737	0.043123|0.043123	0.22907|0.22907	ENSG00000048707|ENSG00000048707	ENST00000356315;ENST00000358136|ENST00000011700	T;T|.	0.54279|.	0.58;0.59|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.213969|.	0.47852|.	D|.	0.000216|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	P|P	1.0|1.0	P;B|.	0.49559|.	0.925;0.09|.	P;B|.	0.45712|.	0.491;0.046|.	T|T	0.04140|0.04140	-1.0974|-1.0974	9|4	0.38643|.	T|.	0.18|.	.|.	16.542|16.542	0.84395|0.84395	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs4845898;rs17350565;rs4845898|rs4845898;rs17350565;rs4845898	1505;1505|.	Q5THJ4-2;Q5THJ4|.	.;VP13D_HUMAN|.	V|Y	1505|328	ENSP00000348666:E1505V;ENSP00000350854:E1505V|.	ENSP00000348666:E1505V|.	E|N	+|+	2|1	0|0	VPS13D|VPS13D	12262206|12262206	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.771000|4.771000	0.62318|0.62318	2.304000|2.304000	0.77564|0.77564	0.528000|0.528000	0.53228|0.53228	GAA|AAT	A|0.831;T|0.169	0.169	strong		0.378	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
GNAO1	2775	hgsc.bcm.edu	37	16	56368689	56368689	+	Silent	SNP	C	C	T	rs1065375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:56368689C>T	ENST00000262493.6	+	5	1359	c.513C>T	c.(511-513)acC>acT	p.T171T	GNAO1_ENST00000262494.7_Silent_p.T171T	NM_020988.2	NP_066268.1	P09471	GNAO_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O	171				T -> L (in Ref. 2; AAA52584). {ECO:0000305}.	adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|dopamine receptor signaling pathway (GO:0007212)|forebrain development (GO:0030900)|locomotory behavior (GO:0007626)|muscle contraction (GO:0006936)|negative regulation of calcium ion transport (GO:0051926)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|regulation of heart contraction (GO:0008016)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to morphine (GO:0043278)	heterotrimeric G-protein complex (GO:0005834)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	corticotropin-releasing hormone receptor 1 binding (GO:0051430)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|mu-type opioid receptor binding (GO:0031852)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)	17		all_neural(199;0.159)				ACCAGCCCACCGAGCAGGACA	0.577													C|||	2491	0.497404	0.4153	0.5432	5008	,	,		18474	0.7589		0.4026	False		,,,				2504	0.4039				p.T171T		Atlas-SNP	.											.	GNAO1	95	.	0			c.C513T						PASS	.	C	,	1787,2609	527.9+/-372.3	371,1045,782	85.0	65.0	72.0		513,513	-4.3	1.0	16	dbSNP_86	72	3381,5219	500.3+/-375.2	672,2037,1591	no	coding-synonymous,coding-synonymous	GNAO1	NM_020988.2,NM_138736.2	,	1043,3082,2373	TT,TC,CC		39.314,40.6506,39.7661	,	171/355,171/355	56368689	5168,7828	2198	4300	6498	SO:0001819	synonymous_variant	2775	exon5			GCCCACCGAGCAG		CCDS10756.1, CCDS10757.1	16q13	2008-08-01			ENSG00000087258	ENSG00000087258			4389	protein-coding gene	gene with protein product		139311				1899283, 11395521	Standard	NM_020988		Approved	G-ALPHA-o	uc002eit.4	P09471	OTTHUMG00000133241	ENST00000262493.6:c.513C>T	16.37:g.56368689C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_138736	P29777|Q8TD72|Q9UMV4	Silent	SNP	ENST00000262493.6	37	CCDS10756.1																																																																																			C|0.556;T|0.444	0.444	strong		0.577	GNAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256981.2	NM_020988	
NOL8	55035	hgsc.bcm.edu	37	9	95078413	95078413	+	Missense_Mutation	SNP	T	T	C	rs41305617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95078413T>C	ENST00000535387.1	-	6	493	c.494A>G	c.(493-495)aAa>aGa	p.K165R	NOL8_ENST00000545558.1_Missense_Mutation_p.K165R|NOL8_ENST00000358855.4_Missense_Mutation_p.K97R|NOL8_ENST00000542053.1_Missense_Mutation_p.K97R|NOL8_ENST00000442668.2_Missense_Mutation_p.K165R					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						GGGATCATATTTGATGATGTT	0.363													T|||	47	0.00938498	0.0023	0.0144	5008	,	,		20765	0.0		0.0338	False		,,,				2504	0.0				p.K165R		Atlas-SNP	.											.	NOL8	118	.	0			c.A494G						PASS	.	T	ARG/LYS	16,3702		0,16,1843	96.0	85.0	89.0		494	5.1	1.0	9	dbSNP_127	89	231,7979		3,225,3877	yes	missense	NOL8	NM_017948.5	26	3,241,5720	CC,CT,TT		2.8136,0.4303,2.0708	probably-damaging	165/1168	95078413	247,11681	1859	4105	5964	SO:0001583	missense	55035	exon7			TCATATTTGATGA	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.494A>G	9.37:g.95078413T>C	ENSP00000441300:p.Lys165Arg	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	242	91	0.376033	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	33	0.01510989010989011	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	24	0.0316622691292876	T	21.3	4.129430	0.77549	0.004303	0.028136	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670;ENST00000433029;ENST00000421075;ENST00000411621;ENST00000535807	T;T;T;T;T;T;T;T	0.54479	2.12;2.06;2.12;2.32;2.06;1.84;0.57;0.66	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.40815	0.1132	L	0.39147	1.195	0.47659	D	0.999482	D	0.89917	1.0	D	0.87578	0.998	T	0.60949	-0.7161	10	0.87932	D	0	-23.0153	15.1284	0.72500	0.0:0.0:0.0:1.0	rs41305617	165	Q76FK4	NOL8_HUMAN	R	165;167;97;165;165;97;165;165;165;97;97	ENSP00000401177:K165R;ENSP00000351723:K97R;ENSP00000441140:K165R;ENSP00000441300:K165R;ENSP00000440709:K97R;ENSP00000414112:K165R;ENSP00000412471:K165R;ENSP00000390143:K165R	ENSP00000351723:K97R	K	-	2	0	NOL8	94118234	1.000000	0.71417	1.000000	0.80357	0.536000	0.34869	7.001000	0.76297	2.021000	0.59480	0.528000	0.53228	AAA	T|0.986;C|0.014	0.014	strong		0.363	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
GPR98	84059	hgsc.bcm.edu	37	5	90136732	90136732	+	Missense_Mutation	SNP	C	C	G	rs61748627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:90136732C>G	ENST00000405460.2	+	78	17045	c.16949C>G	c.(16948-16950)aCc>aGc	p.T5650S	GPR98_ENST00000425867.2_Missense_Mutation_p.T1311S	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5650					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)		GTGCTCCATACCATCAGCATG	0.408													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		19148	0.0		0.0	False		,,,				2504	0.0				p.T5650S		Atlas-SNP	.											.	GPR98	605	.	0			c.C16949G						PASS	.	C	SER/THR	47,3955		1,45,1955	75.0	75.0	75.0		16949	-6.1	0.0	5	dbSNP_129	75	1,8377		0,1,4188	yes	missense	GPR98	NM_032119.3	58	1,46,6143	GG,GC,CC		0.0119,1.1744,0.3877	benign	5650/6307	90136732	48,12332	2001	4189	6190	SO:0001583	missense	84059	exon78			TCCATACCATCAG	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.16949C>G	5.37:g.90136732C>G	ENSP00000384582:p.Thr5650Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	C	1.382	-0.583061	0.03827	0.011744	1.19E-4	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.28069	1.63;1.63	6.16	-6.11	0.02131	.	0.807701	0.12567	N	0.457630	T	0.01454	0.0047	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.33111	-0.9881	9	.	.	.	.	9.7985	0.40751	0.4619:0.4027:0.1354:0.0	rs61748627	1311;5650;1311	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	S	5650;5650;1311	ENSP00000384582:T5650S;ENSP00000392618:T1311S	.	T	+	2	0	GPR98	90172488	0.001000	0.12720	0.001000	0.08648	0.233000	0.25261	-0.112000	0.10791	-0.739000	0.04809	-0.885000	0.02943	ACC	C|0.988;G|0.012	0.012	strong		0.408	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
DHX33	56919	hgsc.bcm.edu	37	17	5356913	5356913	+	Silent	SNP	C	C	T	rs16954697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5356913C>T	ENST00000225296.3	-	8	1583	c.1383G>A	c.(1381-1383)tcG>tcA	p.S461S	DHX33_ENST00000433302.3_Silent_p.S237S	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	461					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						GAGATGGCTTCGACATGAAGT	0.443													G|||	1042	0.208067	0.2413	0.0994	5008	,	,		19550	0.2331		0.162	False		,,,				2504	0.2618				p.S461S		Atlas-SNP	.											.	DHX33	41	.	0			c.G1383A						PASS	.	G	,	1075,3331		136,803,1264	134.0	120.0	124.0		864,1383	0.3	1.0	17	dbSNP_123	124	1120,7480		76,968,3256	no	coding-synonymous,coding-synonymous	DHX33	NM_001199699.1,NM_020162.3	,	212,1771,4520	TT,TC,CC		13.0233,24.3985,16.8768	,	288/535,461/708	5356913	2195,10811	2203	4300	6503	SO:0001819	synonymous_variant	56919	exon8			TGGCTTCGACATG	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.1383G>A	17.37:g.5356913C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	104	42	0.403846	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Silent	SNP	ENST00000225296.3	37	CCDS11072.1																																																																																			C|0.819;N|0.001	.	strong		0.443	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
OGFR	11054	hgsc.bcm.edu	37	20	61444900	61444900	+	Missense_Mutation	SNP	A	A	C	rs61735508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61444900A>C	ENST00000290291.6	+	7	1958	c.1933A>C	c.(1933-1935)Agc>Cgc	p.S645R	OGFR_ENST00000370461.1_Missense_Mutation_p.S593R	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	645	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].				opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CCCAGGCCCCAGCCCGGCAGG	0.692													a|||	178	0.0355431	0.1233	0.0086	5008	,	,		13505	0.0		0.004	False		,,,				2504	0.0051				p.S645R		Atlas-SNP	.											.	OGFR	63	.	0			c.A1933C						PASS	.	A	ARG/SER	255,4123		7,241,1941	24.0	29.0	28.0		1933	-0.6	0.0	20	dbSNP_129	28	10,8570		0,10,4280	no	missense	OGFR	NM_007346.2	110	7,251,6221	CC,CA,AA		0.1166,5.8246,2.0451	possibly-damaging	645/678	61444900	265,12693	2189	4290	6479	SO:0001583	missense	11054	exon7			GGCCCCAGCCCGG	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1933A>C	20.37:g.61444900A>C	ENSP00000290291:p.Ser645Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	60	0.027472527472527472	53	0.10772357723577236	4	0.011049723756906077	1	0.0017482517482517483	2	0.002638522427440633	A	6.697	0.497303	0.12762	0.058246	0.001166	ENSG00000060491	ENST00000290291;ENST00000357163;ENST00000370469;ENST00000370461	T;T	0.13089	2.62;2.62	0.584	-0.628	0.11537	.	.	.	.	.	T	0.00109	0.0003	N	0.03608	-0.345	0.09310	N	1	P;P;P	0.52842	0.956;0.956;0.956	P;P;P	0.45829	0.494;0.494;0.494	T	0.18493	-1.0335	9	0.22109	T	0.4	.	1.7819	0.03033	0.4838:0.0:0.2359:0.2802	rs61735508	645;628;645	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	R	645;625;480;593	ENSP00000290291:S645R;ENSP00000359491:S593R	ENSP00000290291:S645R	S	+	1	0	OGFR	60915345	0.004000	0.15560	0.002000	0.10522	0.050000	0.14768	-0.440000	0.06888	-0.224000	0.09928	0.076000	0.15429	AGC	A|0.975;C|0.025	0.025	strong		0.692	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
TTN	7273	hgsc.bcm.edu	37	2	179395560	179395560	+	Missense_Mutation	SNP	G	G	A	rs16866380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179395560G>A	ENST00000591111.1	-	308	101083	c.100859C>T	c.(100858-100860)cCg>cTg	p.P33620L	TTN_ENST00000342175.6_Missense_Mutation_p.P26388L|TTN-AS1_ENST00000591867.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P26321L|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P26196L|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P35261L|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P32693L|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000588244.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33620			P -> L. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACGGCTTTCGGGTGAGAAGG	0.498													G|||	397	0.0792732	0.0885	0.0403	5008	,	,		17438	0.1716		0.0318	False		,,,				2504	0.0481				p.P35261L		Atlas-SNP	.											.	TTN	18412	.	0			c.C105782T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	260,3546		9,242,1652	126.0	126.0	126.0		79163,78962,98078,78587	5.0	0.9	2	dbSNP_123	126	171,8049		4,163,3943	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	98,98,98,98	13,405,5595	AA,AG,GG		2.0803,6.8313,3.5839	benign,benign,benign,benign	26388/27119,26321/27052,32693/33424,26196/26927	179395560	431,11595	1903	4110	6013	SO:0001583	missense	7273	exon358			GCTTTCGGGTGAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.100859C>T	2.37:g.179395560G>A	ENSP00000465570:p.Pro33620Leu	Somatic	351	1	0.002849		WXS	Illumina HiSeq	Phase_I	349	171	0.489971	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		178	0.0815018315018315	41	0.08333333333333333	15	0.04143646408839779	100	0.17482517482517482	22	0.029023746701846966	G	14.57	2.573687	0.45902	0.068313	0.020803	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.69175	-0.38;-0.12;-0.14;-0.13	4.99	4.99	0.66335	Ribonuclease H-like (1);	.	.	.	.	T	0.00241	0.0007	L	0.32530	0.975	0.20764	P	0.999855559	B;B;B;B	0.32731	0.382;0.382;0.382;0.382	B;B;B;B	0.17098	0.017;0.017;0.017;0.017	T	0.17776	-1.0358	8	0.87932	D	0	.	18.2867	0.90117	0.0:0.0:1.0:0.0	rs16866380;rs52806480;rs16866380	26196;26321;26388;33620	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	32693;26196;26388;26321;26193	ENSP00000343764:P32693L;ENSP00000434586:P26196L;ENSP00000340554:P26388L;ENSP00000352154:P26321L	ENSP00000340554:P26388L	P	-	2	0	TTN	179103806	0.891000	0.30450	0.934000	0.37439	0.694000	0.40290	5.487000	0.66863	2.321000	0.78463	0.455000	0.32223	CCG	G|0.921;A|0.079	0.079	strong		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ASB18	401036	hgsc.bcm.edu	37	2	237103623	237103623	+	Silent	SNP	A	A	G	rs10166966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:237103623A>G	ENST00000409749.3	-	6	1292	c.1293T>C	c.(1291-1293)gcT>gcC	p.A431A	ASB18_ENST00000330842.6_Silent_p.A402A|AC079135.1_ENST00000483218.1_RNA|AC079135.1_ENST00000415226.1_RNA	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	431	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				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)		GTCTGCGAAGAGCACAGCGGC	0.552													G|||	564	0.11262	0.1891	0.0735	5008	,	,		21199	0.002		0.1352	False		,,,				2504	0.1278				p.A431A		Atlas-SNP	.											.	ASB18	34	.	0			c.T1293C						PASS	.	G		757,3513		66,625,1444	69.0	83.0	78.0		1293	3.8	0.4	2	dbSNP_119	78	965,7525		60,845,3340	no	coding-synonymous	ASB18	NM_212556.2		126,1470,4784	GG,GA,AA		11.3663,17.7283,13.4953		431/467	237103623	1722,11038	2135	4245	6380	SO:0001819	synonymous_variant	401036	exon6			GCGAAGAGCACAG	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.1293T>C	2.37:g.237103623A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_212556	B6ZDL7	Silent	SNP	ENST00000409749.3	37	CCDS46548.1																																																																																			A|0.899;G|0.101	0.101	strong		0.552	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556	
PGBD1	84547	hgsc.bcm.edu	37	6	28269663	28269663	+	Missense_Mutation	SNP	A	A	G	rs1997660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28269663A>G	ENST00000405948.2	+	7	2452	c.2032A>G	c.(2032-2034)Ata>Gta	p.I678V	PGBD1_ENST00000259883.3_Missense_Mutation_p.I678V	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	678			I -> V (in dbSNP:rs1997660).			membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						TGATTTCCGAATAGAAGAAAA	0.403													G|||	2963	0.591653	0.9501	0.4597	5008	,	,		21228	0.6012		0.3091	False		,,,				2504	0.4816				p.I678V		Atlas-SNP	.											.	PGBD1	106	.	0			c.A2032G						PASS	.	G	VAL/ILE,VAL/ILE	3672,734	301.8+/-287.1	1540,592,71	127.0	130.0	129.0		2032,2032	3.6	0.7	6	dbSNP_92	129	2750,5850	680.9+/-403.7	452,1846,2002	yes	missense,missense	PGBD1	NM_001184743.1,NM_032507.3	29,29	1992,2438,2073	GG,GA,AA		31.9767,16.6591,49.3772	benign,benign	678/810,678/810	28269663	6422,6584	2203	4300	6503	SO:0001583	missense	84547	exon7			TTCCGAATAGAAG	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.2032A>G	6.37:g.28269663A>G	ENSP00000385213:p.Ile678Val	Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	1199	0.548992673992674	461	0.9369918699186992	169	0.46685082872928174	346	0.6048951048951049	223	0.2941952506596306	G	0.005	-2.168088	0.00315	0.833409	0.319767	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.16743	2.32;2.32	4.48	3.61	0.41365	.	0.600559	0.12776	N	0.440090	T	0.01124	0.0037	N	0.01109	-1.01	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48502	-0.9030	9	0.02654	T	1	-9.75	7.387	0.26888	0.1999:0.0:0.8001:0.0	rs1997660;rs41538181;rs52791434;rs60280230;rs1997660	678	Q96JS3	PGBD1_HUMAN	V	678	ENSP00000385213:I678V;ENSP00000259883:I678V	ENSP00000259883:I678V	I	+	1	0	PGBD1	28377642	0.082000	0.21442	0.675000	0.29917	0.339000	0.28857	1.091000	0.30915	0.640000	0.30582	-0.186000	0.12905	ATA	A|0.464;G|0.536	0.536	strong		0.403	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
TTN	7273	hgsc.bcm.edu	37	2	179577870	179577870	+	Silent	SNP	T	T	C	rs61232800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179577870T>C	ENST00000591111.1	-	91	26264	c.26040A>G	c.(26038-26040)acA>acG	p.T8680T	TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Silent_p.T8997T|TTN_ENST00000342992.6_Silent_p.T7753T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12837	Ig-like 69.				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)			TAGCTATACATGTGTAGTCAC	0.388													T|||	122	0.024361	0.0893	0.0058	5008	,	,		22217	0.0		0.0	False		,,,				2504	0.0				p.T8997T		Atlas-SNP	.											.	TTN	18412	.	0			c.A26991G						PASS	.	T	,,,	265,3699		10,245,1727	90.0	90.0	90.0		,23259,,	-11.7	0.5	2	dbSNP_129	90	13,8331		0,13,4159	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	10,258,5886	CC,CT,TT		0.1558,6.6852,2.2587	,,,	,7753/33424,,	179577870	278,12030	1982	4172	6154	SO:0001819	synonymous_variant	7273	exon93			TATACATGTGTAG	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.26040A>G	2.37:g.179577870T>C		Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	288	134	0.465278	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|0.981;C|0.019	0.019	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
NOS1	4842	hgsc.bcm.edu	37	12	117691490	117691490	+	Silent	SNP	G	G	A	rs9658446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117691490G>A	ENST00000338101.4	-	17	2707	c.2703C>T	c.(2701-2703)ccC>ccT	p.P901P	NOS1_ENST00000317775.6_Silent_p.P867P|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CTCTGAGGTCGGGCCCATCGC	0.562													G|||	163	0.0325479	0.0983	0.0202	5008	,	,		18019	0.0		0.002	False		,,,				2504	0.0174				p.P901P	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											NOS1,NS,carcinoma,0,1	NOS1	240	1	0			c.C2703T						PASS	.	G	,,,	340,3958		15,310,1824	90.0	97.0	95.0		2601,1593,1593,2703	-7.8	0.8	12	dbSNP_119	95	26,8488		0,26,4231	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	15,336,6055	AA,AG,GG		0.3054,7.9107,2.8567	,,,	867/1435,531/1099,531/1099,901/1469	117691490	366,12446	2149	4257	6406	SO:0001819	synonymous_variant	4842	exon18			GAGGTCGGGCCCA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2703C>T	12.37:g.117691490G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	149	51	0.342282	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.985;A|0.015	0.015	strong		0.562	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
PI16	221476	hgsc.bcm.edu	37	6	36931364	36931364	+	Missense_Mutation	SNP	C	C	G	rs16889318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36931364C>G	ENST00000373674.3	+	5	1574	c.1246C>G	c.(1246-1248)Ctg>Gtg	p.L416V	PI16_ENST00000491324.1_Intron	NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	416			L -> V (in dbSNP:rs16889318).		negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TGGGCGTGCCCTGGCTCTGCA	0.607													C|||	522	0.104233	0.2504	0.0807	5008	,	,		22911	0.0278		0.004	False		,,,				2504	0.1053				p.L416V		Atlas-SNP	.											.	PI16	50	.	0			c.C1246G						PASS	.	C	VAL/LEU,VAL/LEU	881,3525	337.8+/-305.0	88,705,1410	57.0	58.0	57.0		1246,1246	4.1	1.0	6	dbSNP_123	57	28,8572	20.4+/-63.3	0,28,4272	yes	missense,missense	PI16	NM_001199159.1,NM_153370.2	32,32	88,733,5682	GG,GC,CC		0.3256,19.9955,6.9891	probably-damaging,probably-damaging	416/464,416/464	36931364	909,12097	2203	4300	6503	SO:0001583	missense	221476	exon6			CGTGCCCTGGCTC		CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"""microseminoprotein, beta-binding protein"""		"""protease inhibitor 16"""				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.1246C>G	6.37:g.36931364C>G	ENSP00000362778:p.Leu416Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	37	CCDS34440.1	165	0.07554945054945054	116	0.23577235772357724	29	0.08011049723756906	17	0.02972027972027972	3	0.00395778364116095	C	17.47	3.396570	0.62177	0.199955	0.003256	ENSG00000164530	ENST00000373674;ENST00000539035	T	0.19806	2.12	4.94	4.08	0.47627	.	0.000000	0.37178	N	0.002204	T	0.19046	0.0457	L	0.32530	0.975	0.09310	P	1.0	D	0.71674	0.998	D	0.63877	0.919	T	0.03630	-1.1018	9	0.56958	D	0.05	.	11.1122	0.48239	0.0:0.9104:0.0:0.0896	rs16889318;rs16889318	416	Q6UXB8	PI16_HUMAN	V	416;268	ENSP00000362778:L416V	ENSP00000362778:L416V	L	+	1	2	PI16	37039342	0.987000	0.35691	0.999000	0.59377	0.773000	0.43773	0.639000	0.24690	1.325000	0.45301	-0.258000	0.10820	CTG	C|0.929;G|0.071	0.071	strong		0.607	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370	
PENK	5179	hgsc.bcm.edu	37	8	57358432	57358432	+	Silent	SNP	G	G	A	rs3808633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:57358432G>A	ENST00000314922.3	-	1	157	c.81C>T	c.(79-81)agC>agT	p.S27S	PENK_ENST00000518770.1_Silent_p.S27S|PENK_ENST00000451791.2_Silent_p.S27S|PENK_ENST00000523274.1_5'Flank|PENK_ENST00000523051.1_Silent_p.S27S|RP11-17A4.2_ENST00000518662.1_RNA	NM_006211.3	NP_006202.1	P01210	PENK_HUMAN	proenkephalin	27					aggressive behavior (GO:0002118)|behavioral fear response (GO:0001662)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|startle response (GO:0001964)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	21		all_lung(136;0.229)	Epithelial(17;0.000873)|all cancers(17;0.0069)			CGCAATCCTGGCTGCATTCGG	0.657													G|||	668	0.133387	0.2587	0.0821	5008	,	,		15225	0.2063		0.0099	False		,,,				2504	0.0521				p.S27S		Atlas-SNP	.											.	PENK	59	.	0			c.C81T						PASS	.	G	,	1075,3331	366.6+/-317.9	144,787,1272	46.0	46.0	46.0		81,81	4.3	1.0	8	dbSNP_107	46	51,8547	31.7+/-84.0	0,51,4248	no	coding-synonymous,coding-synonymous	PENK	NM_001135690.1,NM_006211.3	,	144,838,5520	AA,AG,GG		0.5932,24.3985,8.6589	,	27/268,27/268	57358432	1126,11878	2203	4299	6502	SO:0001819	synonymous_variant	5179	exon3			ATCCTGGCTGCAT		CCDS6168.1	8q23-q24	2013-02-26				ENSG00000181195		"""Endogenous ligands"""	8831	protein-coding gene	gene with protein product	"""preproenkephalin"""	131330				6281660	Standard	NM_006211		Approved		uc003xsz.2	P01210		ENST00000314922.3:c.81C>T	8.37:g.57358432G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	185	93	0.502703	NM_001135690	B2RC23|Q6FHC6|Q6FHE6	Silent	SNP	ENST00000314922.3	37	CCDS6168.1																																																																																			G|0.909;A|0.091	0.091	strong		0.657	PENK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378645.1		
TRAPPC9	83696	hgsc.bcm.edu	37	8	140999002	140999002	+	Silent	SNP	G	G	A	rs28710457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:140999002G>A	ENST00000438773.2	-	19	2875	c.2742C>T	c.(2740-2742)acC>acT	p.T914T	TRAPPC9_ENST00000389328.4_Silent_p.T1012T|TRAPPC9_ENST00000389327.3_Silent_p.T905T	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	914					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						GCTCATGCTCGGTGGAGTTGA	0.567													G|||	54	0.0107827	0.0378	0.0014	5008	,	,		19691	0.003		0.0	False		,,,				2504	0.0				p.T1012T		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C3036T						PASS	.	G	,	125,3835		1,123,1856	29.0	26.0	27.0		2742,3036	-9.6	0.5	8	dbSNP_125	27	1,7655		0,1,3827	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	1,124,5683	AA,AG,GG		0.0131,3.1566,1.0847	,	914/1149,1012/1247	140999002	126,11490	1980	3828	5808	SO:0001819	synonymous_variant	83696	exon19			ATGCTCGGTGGAG	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.2742C>T	8.37:g.140999002G>A		Somatic	49	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	21	0.009615384615384616	17	0.034552845528455285	1	0.0027624309392265192	3	0.005244755244755245	0	0.0	G	6.618	0.482489	0.12581	0.031566	1.31E-4	ENSG00000167632	ENST00000520857	.	.	.	5.62	-9.63	0.00544	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.9498	0.14008	0.0885:0.1092:0.2516:0.5507	rs28710457	.	.	.	X	758	.	.	R	-	1	2	TRAPPC9	141068184	0.262000	0.24073	0.460000	0.27093	0.679000	0.39708	-0.500000	0.06405	-2.040000	0.00916	-2.131000	0.00343	CGA	G|0.986;A|0.014	0.014	strong		0.567	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
PCDHB16	57717	hgsc.bcm.edu	37	5	140562756	140562756	+	Missense_Mutation	SNP	C	C	G	rs28398442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140562756C>G	ENST00000361016.2	+	1	1777	c.622C>G	c.(622-624)Cta>Gta	p.L208V		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	208	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(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGAGCCTCAACTAAGATTAAC	0.502													C|||	58	0.0115815	0.0431	0.0014	5008	,	,		17472	0.0		0.0	False		,,,				2504	0.0				p.L208V		Atlas-SNP	.											.	PCDHB16	159	.	0			c.C622G						PASS	.	C	VAL/LEU	154,4252	107.3+/-145.7	3,148,2052	65.0	66.0	65.0		622	-8.7	0.0	5	dbSNP_125	65	0,8600		0,0,4300	yes	missense	PCDHB16	NM_020957.1	32	3,148,6352	GG,GC,CC		0.0,3.4952,1.1841	benign	208/777	140562756	154,12852	2203	4300	6503	SO:0001583	missense	57717	exon1			CCTCAACTAAGAT	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.622C>G	5.37:g.140562756C>G	ENSP00000354293:p.Leu208Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	C	2.179	-0.387934	0.04932	0.034952	0.0	ENSG00000196963	ENST00000361016	T	0.49139	0.79	4.69	-8.68	0.00859	Cadherin (4);Cadherin-like (1);	0.962534	0.08410	N	0.950091	T	0.07098	0.0180	L	0.38531	1.155	0.09310	N	1	B	0.21452	0.056	B	0.27170	0.077	T	0.27606	-1.0069	10	0.41790	T	0.15	.	1.2389	0.01958	0.2632:0.3205:0.2274:0.189	rs28398442	208	Q9NRJ7	PCDBG_HUMAN	V	208	ENSP00000354293:L208V	ENSP00000354293:L208V	L	+	1	2	PCDHB16	140542940	0.000000	0.05858	0.001000	0.08648	0.191000	0.23601	-4.894000	0.00173	-1.135000	0.02895	-0.176000	0.13171	CTA	C|0.991;G|0.009	0.009	strong		0.502	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
NEDD4	4734	hgsc.bcm.edu	37	15	56208535	56208535	+	Silent	SNP	G	G	A	rs12440230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56208535G>A	ENST00000508342.1	-	1	794	c.495C>T	c.(493-495)aaC>aaT	p.N165N	NEDD4_ENST00000506154.1_Silent_p.N165N|NEDD4_ENST00000338963.2_Silent_p.N165N|NEDD4_ENST00000435532.3_Intron	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	165	Ser-rich.				adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		AATCACTACCGTTGCTGCTGT	0.418													G|||	990	0.197684	0.1536	0.1455	5008	,	,		22825	0.3591		0.1531	False		,,,				2504	0.1738				p.N165N		Atlas-SNP	.											.	NEDD4	167	.	0			c.C495T						PASS	.	G	,	668,3718	282.8+/-276.7	51,566,1576	143.0	128.0	133.0		,495	-2.1	0.5	15	dbSNP_120	133	1064,7520	223.8+/-260.4	51,962,3279	no	intron,coding-synonymous	NEDD4	NM_006154.2,NM_198400.2	,	102,1528,4855	AA,AG,GG		12.3952,15.2303,13.3539	,	,165/1248	56208535	1732,11238	2193	4292	6485	SO:0001819	synonymous_variant	4734	exon1			ACTACCGTTGCTG	D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"""receptor-potentiating factor 1"""	602278	"""neural precursor cell expressed, developmentally down-regulated 4"""			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.495C>T	15.37:g.56208535G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	225	101	0.448889	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Silent	SNP	ENST00000508342.1	37																																																																																				G|0.846;A|0.154	0.154	strong		0.418	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400	
SIAE	54414	hgsc.bcm.edu	37	11	124506967	124506967	+	Silent	SNP	C	C	T	rs7941327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124506967C>T	ENST00000263593.3	-	10	1624	c.1452G>A	c.(1450-1452)acG>acA	p.T484T	SIAE_ENST00000545756.1_Silent_p.T449T|RNA5SP352_ENST00000363408.1_RNA			Q9HAT2	SIAE_HUMAN	sialic acid acetylesterase	484					carbohydrate metabolic process (GO:0005975)|regulation of immune system process (GO:0002682)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	sialate O-acetylesterase activity (GO:0001681)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	15	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;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)		CACAAGGCCACGTGGTCCAAG	0.557													T|||	771	0.153954	0.4395	0.0476	5008	,	,		18247	0.1022		0.0199	False		,,,				2504	0.0348				p.T484T		Atlas-SNP	.											.	SIAE	37	.	0			c.G1452A						PASS	.	T	,	1643,2759	659.2+/-400.5	312,1019,870	142.0	129.0	133.0		1347,1452	-9.4	0.0	11	dbSNP_116	133	186,8412	810.9+/-407.1	1,184,4114	no	coding-synonymous,coding-synonymous	SIAE	NM_001199922.1,NM_170601.4	,	313,1203,4984	TT,TC,CC		2.1633,37.3239,14.0692	,	449/489,484/524	124506967	1829,11171	2201	4299	6500	SO:0001819	synonymous_variant	54414	exon10			AGGCCACGTGGTC	AF300796	CCDS8449.1, CCDS55795.1	11q24	2005-12-15	2005-12-15	2005-12-15		ENSG00000110013			18187	protein-coding gene	gene with protein product	"""sialic acid-specific acetylesterase II"""	610079	"""Ysg2 homolog (mouse)"""	YSG2		10464298	Standard	NM_001199922		Approved	CSE-C, MGC87009, LSE	uc001qan.3	Q9HAT2		ENST00000263593.3:c.1452G>A	11.37:g.124506967C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	175	97	0.554286	NM_170601	B3KPB0|Q8IUT9|Q9HAU7|Q9NT71	Silent	SNP	ENST00000263593.3	37	CCDS8449.1																																																																																			C|0.852;T|0.148	0.148	strong		0.557	SIAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387070.1	NM_170601	
KBTBD13	390594	hgsc.bcm.edu	37	15	65369395	65369395	+	Missense_Mutation	SNP	C	C	T	rs2919358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65369395C>T	ENST00000432196.2	+	1	242	c.242C>T	c.(241-243)gCc>gTc	p.A81V	RASL12_ENST00000434605.2_5'Flank	NM_001101362.2	NP_001094832.1	C9JR72	KBTBD_HUMAN	kelch repeat and BTB (POZ) domain containing 13	81					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(1)|prostate(1)|skin(1)	3						CTGCTGCAGGCCGTGGAGTGC	0.736													C|||	2613	0.521765	0.6036	0.5447	5008	,	,		9840	0.7312		0.3887	False		,,,				2504	0.316				p.A81V		Atlas-SNP	.											.	KBTBD13	9	.	0			c.C242T						PASS	.	C	VAL/ALA	1463,1441		405,653,394	2.0	3.0	2.0		242	4.6	1.0	15	dbSNP_101	2	2172,4110		500,1172,1469	no	missense	KBTBD13	NM_001101362.2	64	905,1825,1863	TT,TC,CC		34.575,49.6212,39.5711	possibly-damaging	81/459	65369395	3635,5551	1452	3141	4593	SO:0001583	missense	390594	exon1			TGCAGGCCGTGGA		CCDS45281.1	15q22.31	2014-09-17			ENSG00000234438	ENSG00000234438		"""BTB/POZ domain containing"""	37227	protein-coding gene	gene with protein product	"""nemaline myopathy type 6"""	613727				21109227, 22542517	Standard	NM_001101362		Approved	hCG_1645727, NEM6	uc010uis.2	C9JR72		ENST00000432196.2:c.242C>T	15.37:g.65369395C>T	ENSP00000388723:p.Ala81Val	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_001101362		Missense_Mutation	SNP	ENST00000432196.2	37	CCDS45281.1	1197	0.5480769230769231	302	0.6138211382113821	191	0.5276243093922652	410	0.7167832167832168	294	0.38786279683377306	C	20.9	4.061996	0.76187	0.503788	0.34575	ENSG00000234438	ENST00000432196	T	0.67865	-0.29	4.6	4.6	0.57074	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	.	.	.	.	T	0.00012	0.0000	N	0.21324	0.655	0.22629	P	0.99891774	P	0.47034	0.889	P	0.50896	0.653	T	0.37753	-0.9692	8	0.26408	T	0.33	.	17.2241	0.86964	0.0:1.0:0.0:0.0	rs2919358	81	C9JR72	KBTBD_HUMAN	V	81	ENSP00000388723:A81V	ENSP00000388723:A81V	A	+	2	0	KBTBD13	63156448	1.000000	0.71417	0.996000	0.52242	0.931000	0.56810	7.251000	0.78297	2.390000	0.81377	0.650000	0.86243	GCC	C|0.451;T|0.549	0.549	strong		0.736	KBTBD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418468.2	NM_001101362	
ECM1	1893	hgsc.bcm.edu	37	1	150482639	150482639	+	Silent	SNP	C	C	T	rs74352693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150482639C>T	ENST00000369047.4	+	5	491	c.366C>T	c.(364-366)caC>caT	p.H122H	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Silent_p.H149H|ECM1_ENST00000346569.6_Silent_p.H122H	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	122					angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CTCTCCAGCACCCCAATGAAC	0.587													C|||	81	0.0161741	0.0575	0.0072	5008	,	,		18178	0.0		0.0	False		,,,				2504	0.0				p.H149H	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											.	ECM1	96	.	0			c.C447T						PASS	.	C	,,	203,4203	126.1+/-163.2	7,189,2007	138.0	139.0	139.0		447,366,366	-1.3	0.0	1	dbSNP_132	139	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	ECM1	NM_001202858.1,NM_004425.3,NM_022664.2	,,	7,192,6304	TT,TC,CC		0.0349,4.6074,1.5839	,,	149/568,122/541,122/416	150482639	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	1893	exon5			CCAGCACCCCAAT	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.366C>T	1.37:g.150482639C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Silent	SNP	ENST00000369047.4	37	CCDS953.1																																																																																			C|0.982;T|0.018	0.018	strong		0.587	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
FREM2	341640	hgsc.bcm.edu	37	13	39422624	39422624	+	Missense_Mutation	SNP	C	C	T	rs9548505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39422624C>T	ENST00000280481.7	+	8	6412	c.6196C>T	c.(6196-6198)Cgt>Tgt	p.R2066C	FREM2_ENST00000482551.1_3'UTR	NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2066	Calx-beta 3.		R -> C (in dbSNP:rs9548505). {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)		GGGCATCAGCCGTAATTTAGA	0.378													C|||	549	0.109625	0.1445	0.2522	5008	,	,		15477	0.001		0.0895	False		,,,				2504	0.0941				p.R2066C		Atlas-SNP	.											.	FREM2	385	.	0			c.C6196T						PASS	.	C	CYS/ARG	624,3782	272.5+/-270.8	46,532,1625	146.0	142.0	144.0		6196	5.7	0.8	13	dbSNP_119	144	938,7662	208.0+/-249.6	67,804,3429	yes	missense	FREM2	NM_207361.4	180	113,1336,5054	TT,TC,CC		10.907,14.1625,12.0098	probably-damaging	2066/3170	39422624	1562,11444	2203	4300	6503	SO:0001583	missense	341640	exon8			ATCAGCCGTAATT	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.6196C>T	13.37:g.39422624C>T	ENSP00000280481:p.Arg2066Cys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	128	72	0.5625	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	190	0.08699633699633699	61	0.12398373983739837	73	0.20165745856353592	1	0.0017482517482517483	55	0.07255936675461741	C	25.2	4.614809	0.87359	0.141625	0.10907	ENSG00000150893	ENST00000280481	T	0.27557	1.66	5.66	5.66	0.87406	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	M	0.86028	2.79	0.09310	P	0.9999999980019	D;D	0.76494	0.999;0.999	P;D	0.64595	0.906;0.927	T	0.00114	-1.2041	9	0.72032	D	0.01	.	19.7538	0.96281	0.0:1.0:0.0:0.0	rs9548505;rs52831056;rs59917479;rs9548505	2066;2066	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	C	2066	ENSP00000280481:R2066C	ENSP00000280481:R2066C	R	+	1	0	FREM2	38320624	1.000000	0.71417	0.774000	0.31636	0.993000	0.82548	4.804000	0.62554	2.690000	0.91761	0.655000	0.94253	CGT	C|0.894;G|0.000;T|0.106	0.106	strong		0.378	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
GPR98	84059	hgsc.bcm.edu	37	5	90085654	90085654	+	Missense_Mutation	SNP	T	T	C	rs62000408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:90085654T>C	ENST00000405460.2	+	69	14125	c.14029T>C	c.(14029-14031)Ttt>Ctt	p.F4677L	GPR98_ENST00000425867.2_Missense_Mutation_p.F338L	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4677	Calx-beta 32. {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)		CAAGGGCACCTTTGGAGAGAT	0.418													T|||	195	0.0389377	0.1392	0.0144	5008	,	,		15895	0.0		0.001	False		,,,				2504	0.0				p.F4677L		Atlas-SNP	.											.	GPR98	605	.	0			c.T14029C						PASS	.	T	LEU/PHE	398,3186		26,346,1420	49.0	45.0	46.0		14029	-0.6	0.0	5	dbSNP_129	46	2,8114		0,2,4056	yes	missense	GPR98	NM_032119.3	22	26,348,5476	CC,CT,TT		0.0246,11.1049,3.4188	benign	4677/6307	90085654	400,11300	1792	4058	5850	SO:0001583	missense	84059	exon69			GGCACCTTTGGAG	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.14029T>C	5.37:g.90085654T>C	ENSP00000384582:p.Phe4677Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	107	42	0.392523	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	89	0.04075091575091575	82	0.16666666666666666	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	T	1.261	-0.615801	0.03663	0.111049	2.46E-4	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.26518	1.73;1.73	5.39	-0.57	0.11753	.	0.692346	0.15354	N	0.266772	T	0.00039	0.0001	N	0.04090	-0.28	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	0.36016	-0.9765	9	0.24483	T	0.36	.	0.8813	0.01235	0.2085:0.1382:0.2213:0.4319	rs62000408	338;4677;338	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	L	4677;4677;338	ENSP00000384582:F4677L;ENSP00000392618:F338L	ENSP00000296619:F4677L	F	+	1	0	GPR98	90121410	0.290000	0.24343	0.000000	0.03702	0.745000	0.42441	0.717000	0.25851	0.061000	0.16311	0.477000	0.44152	TTT	T|0.959;C|0.041	0.041	strong		0.418	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
RGPD4	285190	hgsc.bcm.edu	37	2	108479432	108479432	+	Missense_Mutation	SNP	G	G	A	rs200501106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:108479432G>A	ENST00000408999.3	+	17	2490	c.2413G>A	c.(2413-2415)Gca>Aca	p.A805T	RGPD4_ENST00000354986.4_Missense_Mutation_p.A805T	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	805					protein targeting to Golgi (GO:0000042)			p.A805T(1)		breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						ACCTCGATGGGCAGAAGATCA	0.313													N|||	2732	0.545527	0.4887	0.487	5008	,	,		16500	0.3502		0.6998	False		,,,				2504	0.7065				p.A805T		Atlas-SNP	.											RGPD4,NS,other,0,1	RGPD4	112	1	1	Substitution - Missense(1)	pancreas(1)	c.G2413A						scavenged	.						18.0	18.0	18.0					2																	108479432		691	1577	2268	SO:0001583	missense	285190	exon17			CGATGGGCAGAAG	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.2413G>A	2.37:g.108479432G>A	ENSP00000386810:p.Ala805Thr	Somatic	985	2	0.00203046		WXS	Illumina HiSeq	Phase_I	881	644	0.730987	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	CCDS46381.1	967	0.44276556776556775	211	0.42886178861788615	165	0.4558011049723757	177	0.3094405594405594	414	0.5461741424802111	-	11.50	1.655837	0.29425	.	.	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.19105	2.17;2.17	2.3	2.3	0.28687	.	.	.	.	.	T	0.00012	0.0000	M	0.64997	1.995	0.30751	P	0.745072	P	0.48911	0.917	P	0.48704	0.587	T	0.33624	-0.9861	8	0.11794	T	0.64	-13.8517	11.5619	0.50782	0.0:0.0:1.0:0.0	.	805	Q7Z3J3	RGPD4_HUMAN	T	805;805;563	ENSP00000347081:A805T;ENSP00000386810:A805T	ENSP00000347081:A805T	A	+	1	0	RGPD4	107845864	1.000000	0.71417	1.000000	0.80357	0.567000	0.35839	6.517000	0.73759	1.299000	0.44798	0.152000	0.16155	GCA	G|0.250;A|0.750	0.750	weak		0.313	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
PODXL2	50512	hgsc.bcm.edu	37	3	127387388	127387388	+	Silent	SNP	C	C	T	rs34716022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127387388C>T	ENST00000342480.6	+	5	1350	c.1311C>T	c.(1309-1311)agC>agT	p.S437S		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	437					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						TCTCTCTGAGCAAGCCCAGCG	0.682													C|||	315	0.0628994	0.2239	0.0231	5008	,	,		17746	0.0		0.003	False		,,,				2504	0.0				p.S437S		Atlas-SNP	.											.	PODXL2	53	.	0			c.C1311T						PASS	.	C		750,3654		52,646,1504	22.0	19.0	20.0		1311	4.3	1.0	3	dbSNP_126	20	8,8586		0,8,4289	no	coding-synonymous	PODXL2	NM_015720.2		52,654,5793	TT,TC,CC		0.0931,17.03,5.8317		437/606	127387388	758,12240	2202	4297	6499	SO:0001819	synonymous_variant	50512	exon5			TCTGAGCAAGCCC	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.1311C>T	3.37:g.127387388C>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	253	133	0.525692	NM_015720	Q6UVY4|Q8WUV6	Silent	SNP	ENST00000342480.6	37	CCDS3044.1																																																																																			C|0.938;T|0.062	0.062	strong		0.682	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720	
LRRC42	115353	hgsc.bcm.edu	37	1	54432019	54432019	+	Silent	SNP	G	G	A	rs2294514	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54432019G>A	ENST00000371370.3	+	8	1499	c.978G>A	c.(976-978)gaG>gaA	p.E326E	LRRC42_ENST00000319223.4_Silent_p.E326E|LRRC42_ENST00000477905.1_3'UTR	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	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	155	155	1	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	
HELQ	113510	hgsc.bcm.edu	37	4	84374692	84374692	+	Missense_Mutation	SNP	A	A	G	rs17006837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84374692A>G	ENST00000295488.3	-	2	866	c.704T>C	c.(703-705)cTg>cCg	p.L235P	MRPS18C_ENST00000295491.4_5'Flank|HELQ_ENST00000510985.1_Missense_Mutation_p.L235P|MRPS18C_ENST00000507349.1_5'Flank|MRPS18C_ENST00000507019.1_5'Flank|HELQ_ENST00000440639.2_5'Flank	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	235			L -> P (in dbSNP:rs17006837).		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						ATTATGGGGCAGTTCCTCATT	0.378								Other identified genes with known or suspected DNA repair function					a|||	675	0.134784	0.4894	0.0331	5008	,	,		20460	0.0		0.004	False		,,,				2504	0.001				p.L235P		Atlas-SNP	.											.	HELQ	95	.	0			c.T704C						PASS	.	G	PRO/LEU	1835,2571	527.1+/-372.1	367,1101,735	132.0	138.0	136.0		704	-1.4	0.0	4	dbSNP_123	136	27,8573	16.0+/-53.3	0,27,4273	yes	missense	HELQ	NM_133636.2	98	367,1128,5008	GG,GA,AA		0.314,41.6478,14.3165	benign	235/1102	84374692	1862,11144	2203	4300	6503	SO:0001583	missense	113510	exon2			TGGGGCAGTTCCT	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.704T>C	4.37:g.84374692A>G	ENSP00000295488:p.Leu235Pro	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	202	0.0924908424908425	187	0.3800813008130081	12	0.03314917127071823	0	0.0	3	0.00395778364116095	a	9.849	1.193106	0.21954	0.416478	0.00314	ENSG00000163312	ENST00000295488;ENST00000510985	T;T	0.69926	0.03;-0.44	5.43	-1.43	0.08884	.	0.989793	0.08215	N	0.980008	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P;B;D;B	0.57571	0.8;0.06;0.98;0.006	B;B;P;B	0.56700	0.278;0.018;0.804;0.003	T	0.20840	-1.0263	9	0.32370	T	0.25	-34.7802	6.3635	0.21441	0.6213:0.1187:0.2599:0.0	rs17006837;rs61470575;rs17006837	235;235;198;235	E3W980;E3W982;Q8TDG4-2;Q8TDG4	.;.;.;HELQ_HUMAN	P	235	ENSP00000295488:L235P;ENSP00000424539:L235P	ENSP00000295488:L235P	L	-	2	0	HELQ	84593716	0.000000	0.05858	0.006000	0.13384	0.002000	0.02628	0.386000	0.20702	-0.126000	0.11682	-1.060000	0.02296	CTG	A|0.864;G|0.136	0.136	strong		0.378	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
TM7SF2	7108	hgsc.bcm.edu	37	11	64882441	64882441	+	Silent	SNP	G	G	A	rs33981236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64882441G>A	ENST00000279263.7	+	7	942	c.780G>A	c.(778-780)gcG>gcA	p.A260A	TM7SF2_ENST00000531029.1_3'UTR|AP003068.12_ENST00000527789.1_RNA|TM7SF2_ENST00000345348.5_Silent_p.A260A|TM7SF2_ENST00000540748.1_Silent_p.A144A	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	260					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						TCATGCTGGCGTTTGGGGACA	0.617													G|||	152	0.0303514	0.0681	0.0187	5008	,	,		20654	0.0317		0.003	False		,,,				2504	0.0143				p.A260A		Atlas-SNP	.											TM7SF2,NS,carcinoma,+1,1	TM7SF2	30	1	0			c.G780A						PASS	.	G		201,4019		2,197,1911	171.0	181.0	178.0		780	-2.3	1.0	11	dbSNP_126	178	14,8428		0,14,4207	no	coding-synonymous	TM7SF2	NM_003273.2		2,211,6118	AA,AG,GG		0.1658,4.763,1.698		260/419	64882441	215,12447	2110	4221	6331	SO:0001819	synonymous_variant	7108	exon7			GCTGGCGTTTGGG	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.780G>A	11.37:g.64882441G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	174	93	0.534483	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Silent	SNP	ENST00000279263.7	37	CCDS41669.1	62	0.028388278388278388	33	0.06707317073170732	7	0.019337016574585635	19	0.033216783216783216	3	0.00395778364116095	G	6.877	0.531230	0.13127	0.04763	0.001658	ENSG00000149809	ENST00000528802	.	.	.	5.23	-2.3	0.06785	.	.	.	.	.	T	0.03520	0.0101	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21655	-1.0239	4	.	.	.	-10.0796	0.2725	0.00233	0.2909:0.1876:0.2797:0.2419	rs33981236	.	.	.	H	88	.	.	R	+	2	0	TM7SF2	64639017	0.000000	0.05858	0.991000	0.47740	0.658000	0.38924	-1.832000	0.01696	-0.207000	0.10187	-1.332000	0.01269	CGT	G|0.981;A|0.019	0.019	strong		0.617	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273	
DEFB135	613209	hgsc.bcm.edu	37	8	11842019	11842019	+	Missense_Mutation	SNP	G	G	A	rs73663074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11842019G>A	ENST00000382208.2	+	2	154	c.154G>A	c.(154-156)Gaa>Aaa	p.E52K		NM_001033017.2	NP_001028189.2	Q30KP9	DB135_HUMAN	defensin, beta 135	52					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|prostate(1)	4						TCTAAAAAACGAACAATATCG	0.388													G|||	220	0.0439297	0.1422	0.013	5008	,	,		20406	0.0		0.0	False		,,,				2504	0.0235				p.E52K		Atlas-SNP	.											.	DEFB135	7	.	0			c.G154A						PASS	.	G	LYS/GLU	467,3281		28,411,1435	112.0	110.0	111.0		154	3.3	0.1	8	dbSNP_130	111	10,8190		0,10,4090	yes	missense	DEFB135	NM_001033017.2	56	28,421,5525	AA,AG,GG		0.122,12.46,3.9923	possibly-damaging	52/78	11842019	477,11471	1874	4100	5974	SO:0001583	missense	613209	exon2			AAAAACGAACAAT	DQ012025	CCDS43710.1	8p23.1	2009-05-27			ENSG00000205883	ENSG00000205883		"""Defensins, beta"""	32400	protein-coding gene	gene with protein product						16033865	Standard	NM_001033017		Approved		uc003wuw.1	Q30KP9	OTTHUMG00000158719	ENST00000382208.2:c.154G>A	8.37:g.11842019G>A	ENSP00000371643:p.Glu52Lys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	103	57	0.553398	NM_001033017	Q4QY37	Missense_Mutation	SNP	ENST00000382208.2	37	CCDS43710.1	89	0.04075091575091575	86	0.17479674796747968	3	0.008287292817679558	0	0.0	0	0.0	G	17.23	3.337441	0.60963	0.1246	0.00122	ENSG00000205883	ENST00000382208	T	0.73575	-0.76	3.34	3.34	0.38264	.	0.000000	0.33005	N	0.005386	T	0.01029	0.0034	.	.	.	0.80722	P	0.0	D	0.89917	1.0	D	0.87578	0.998	T	0.47328	-0.9126	8	0.87932	D	0	-25.449	10.4608	0.44578	0.0:0.0:1.0:0.0	.	52	Q30KP9	DB135_HUMAN	K	52	ENSP00000371643:E52K	ENSP00000371643:E52K	E	+	1	0	DEFB135	11879428	0.515000	0.26210	0.053000	0.19242	0.001000	0.01503	2.965000	0.49200	2.157000	0.67596	0.561000	0.74099	GAA	G|0.959;A|0.041	0.041	strong		0.388	DEFB135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351888.1	NM_001033017	
MUC16	94025	hgsc.bcm.edu	37	19	9065510	9065510	+	Silent	SNP	G	G	A	rs1867692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	63	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	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	
MAG	4099	hgsc.bcm.edu	37	19	35793589	35793589	+	Silent	SNP	C	C	T	rs1126770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35793589C>T	ENST00000392213.3	+	7	1368	c.1209C>T	c.(1207-1209)acC>acT	p.T403T	MAG_ENST00000361922.4_Silent_p.T403T|MAG_ENST00000537831.2_Silent_p.T378T	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	403	Ig-like C2-type 3.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			AGAGGGCCACCGCCTTCAACC	0.622													C|||	1183	0.236222	0.174	0.3271	5008	,	,		16814	0.1677		0.3191	False		,,,				2504	0.2413				p.T403T		Atlas-SNP	.											.	MAG	172	.	0			c.C1209T						PASS	.	C	,,	882,3524	342.3+/-307.1	78,726,1399	92.0	75.0	81.0		1134,1209,1209	-10.5	0.3	19	dbSNP_86	81	2794,5806	443.1+/-360.3	458,1878,1964	no	coding-synonymous,coding-synonymous,coding-synonymous	MAG	NM_001199216.1,NM_002361.3,NM_080600.2	,,	536,2604,3363	TT,TC,CC		32.4884,20.0182,28.2639	,,	378/602,403/627,403/583	35793589	3676,9330	2203	4300	6503	SO:0001819	synonymous_variant	4099	exon7			GGCCACCGCCTTC	M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6783	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 4A"""	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.1209C>T	19.37:g.35793589C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_080600	B7Z2E5|F5GYC0|Q567S4	Silent	SNP	ENST00000392213.3	37	CCDS12455.1																																																																																			C|0.728;T|0.272	0.272	strong		0.622	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600	
TRPV6	55503	hgsc.bcm.edu	37	7	142573613	142573613	+	Silent	SNP	C	C	T	rs79832568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142573613C>T	ENST00000359396.3	-	7	1052	c.807G>A	c.(805-807)acG>acA	p.T269T	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	269					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					GTGGTCCATACGTCCACTGGG	0.532													C|||	117	0.0233626	0.0779	0.0144	5008	,	,		10275	0.0		0.004	False		,,,				2504	0.0				p.T269T		Atlas-SNP	.											.	TRPV6	108	.	0			c.G807A						PASS	.	C		327,4079	172.7+/-202.6	19,289,1895	214.0	162.0	180.0		807	-9.9	0.0	7	dbSNP_131	180	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	TRPV6	NM_018646.2		19,303,6181	TT,TC,CC		0.1628,7.4217,2.6219		269/726	142573613	341,12665	2203	4300	6503	SO:0001819	synonymous_variant	55503	exon7			TCCATACGTCCAC	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.807G>A	7.37:g.142573613C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	170	83	0.488235	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	37	CCDS5874.1																																																																																			C|0.976;T|0.024	0.024	strong		0.532	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	
TCF25	22980	hgsc.bcm.edu	37	16	89940232	89940232	+	Missense_Mutation	SNP	A	A	C	rs13338056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89940232A>C	ENST00000263346.8	+	1	213	c.157A>C	c.(157-159)Aag>Cag	p.K53Q		NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	53					heart development (GO:0007507)|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)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		GGGCGCAGGGAAGGAGGGCGT	0.706													a|||	400	0.0798722	0.1989	0.0245	5008	,	,		6693	0.0		0.004	False		,,,				2504	0.1186				p.K53Q		Atlas-SNP	.											.	TCF25	61	.	0			c.A157C						PASS	.		GLN/LYS	530,3812		26,478,1667	12.0	16.0	15.0		157	3.8	1.0	16	dbSNP_121	15	18,8514		0,18,4248	yes	missense	TCF25	NM_014972.2	53	26,496,5915	CC,CA,AA		0.211,12.2064,4.2566	benign	53/677	89940232	548,12326	2171	4266	6437	SO:0001583	missense	22980	exon1			GCAGGGAAGGAGG	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.157A>C	16.37:g.89940232A>C	ENSP00000263346:p.Lys53Gln	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	27	0.341772	NM_014972	Q2MK75|Q9UPV3	Missense_Mutation	SNP	ENST00000263346.8	37	CCDS10987.1	99	0.04532967032967033	90	0.18292682926829268	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	a	18.59	3.657226	0.67586	0.122064	0.00211	ENSG00000141002	ENST00000263346;ENST00000310554	.	.	.	4.92	3.79	0.43588	.	0.415026	0.24599	N	0.037154	T	0.00073	0.0002	N	0.22421	0.69	0.19300	P	0.999975321	P;B	0.52061	0.95;0.201	P;B	0.48227	0.571;0.036	T	0.06499	-1.0823	8	0.62326	D	0.03	.	4.3462	0.11134	0.6523:0.1755:0.1722:0.0	rs13338056;rs13338056	53;53	B4DVF2;Q9BQ70	.;TCF25_HUMAN	Q	53	.	ENSP00000263346:K53Q	K	+	1	0	TCF25	88467733	0.996000	0.38824	0.977000	0.42913	0.425000	0.31504	0.538000	0.23160	2.078000	0.62432	0.375000	0.23000	AAG	A|0.803;C|0.197	0.197	strong		0.706	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972	
IFI44	10561	hgsc.bcm.edu	37	1	79115905	79115905	+	Missense_Mutation	SNP	T	T	C	rs2070123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	122	0	0		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	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	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238672290	238672290	+	Missense_Mutation	SNP	C	C	T	rs3739040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238672290C>T	ENST00000392000.4	+	11	2051	c.1934C>T	c.(1933-1935)cCg>cTg	p.P645L	LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000289175.6_Missense_Mutation_p.P589L|LRRFIP1_ENST00000244815.5_Missense_Mutation_p.P621L	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	645			P -> L (in dbSNP:rs3739040).		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)		GTTGATTGTCCGGAGAATCCT	0.413													C|||	536	0.107029	0.3192	0.0231	5008	,	,		20476	0.0794		0.005	False		,,,				2504	0.0133				p.P645L		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.C1934T						PASS	.	C	,,LEU/PRO,LEU/PRO,LEU/PRO	1295,3111	436.1+/-344.5	211,873,1119	66.0	67.0	66.0		,,1934,1766,1862	3.5	0.3	2	dbSNP_107	66	35,8565	23.4+/-69.3	0,35,4265	yes	intron,intron,missense,missense,missense	LRRFIP1	NM_001137550.1,NM_001137551.1,NM_001137552.1,NM_001137553.1,NM_004735.3	,,98,98,98	211,908,5384	TT,TC,CC		0.407,29.3917,10.226	,,benign,benign,benign	,,645/809,589/753,621/785	238672290	1330,11676	2203	4300	6503	SO:0001583	missense	9208	exon11			ATTGTCCGGAGAA	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.1934C>T	2.37:g.238672290C>T	ENSP00000375857:p.Pro645Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	NM_001137552	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	37	CCDS46552.1	246	0.11263736263736264	176	0.35772357723577236	15	0.04143646408839779	53	0.09265734265734266	2	0.002638522427440633	C	10.28	1.307765	0.23821	0.293917	0.00407	ENSG00000124831	ENST00000289175;ENST00000244815;ENST00000392000	T;T;T	0.10668	2.85;2.86;2.86	5.27	3.47	0.39725	.	1.421980	0.04652	N	0.407349	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	P;P;P	0.38788	0.647;0.515;0.647	B;B;B	0.28553	0.091;0.042;0.091	T	0.48514	-0.9029	9	0.30854	T	0.27	-5.1128	7.524	0.27645	0.1339:0.7181:0.0:0.1479	rs3739040;rs52790517;rs60372489;rs3739040	589;645;621	Q32MZ4-3;Q32MZ4;Q32MZ4-2	.;LRRF1_HUMAN;.	L	589;621;645	ENSP00000289175:P589L;ENSP00000244815:P621L;ENSP00000375857:P645L	ENSP00000244815:P621L	P	+	2	0	LRRFIP1	238337029	0.000000	0.05858	0.255000	0.24374	0.077000	0.17291	-0.672000	0.05244	0.614000	0.30107	0.609000	0.83330	CCG	C|0.882;T|0.118	0.118	strong		0.413	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
CD200R1	131450	hgsc.bcm.edu	37	3	112648127	112648127	+	Missense_Mutation	SNP	T	T	G	rs199845196|rs4596117|rs71625219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112648127T>G	ENST00000471858.1	-	3	593	c.361A>C	c.(361-363)Acc>Ccc	p.T121P	CD200R1_ENST00000308611.3_Missense_Mutation_p.T144P|CD200R1_ENST00000440122.2_Missense_Mutation_p.T144P|CD200R1_ENST00000490004.1_Missense_Mutation_p.T121P|CD200R1_ENST00000295863.4_Missense_Mutation_p.T99P	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	121	Ig-like V-type.		P -> T (in allele 2; dbSNP:rs4596117). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15274657, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.7}.		regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						ATGGCCACGGTACGAATCTGA	0.448													G|||	3262	0.651358	0.7216	0.6066	5008	,	,		19394	0.7024		0.5328	False		,,,				2504	0.6575				p.T144P		Atlas-SNP	.											CD200R1_ENST00000440122,colon,carcinoma,+2,2	CD200R1	91	2	0			c.A430C						PASS	.	G	PRO/THR,PRO/THR,PRO/THR,PRO/THR	1708,2698		760,188,1255	172.0	167.0	169.0		430,430,361,361	4.6	0.1	3	dbSNP_111	169	1948,6652		819,310,3171	no	missense,missense,missense,missense	CD200R1	NM_138806.3,NM_138939.2,NM_138940.2,NM_170780.2	38,38,38,38	1579,498,4426	GG,GT,TT		22.6512,38.7653,28.1101	benign,benign,benign,benign	144/349,144/189,121/166,121/326	112648127	3656,9350	2203	4300	6503	SO:0001583	missense	131450	exon4			CCACGGTACGAAT	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.361A>C	3.37:g.112648127T>G	ENSP00000418928:p.Thr121Pro	Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	316	316	1	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	37	CCDS2970.1	1375	0.6295787545787546	342	0.6951219512195121	222	0.6132596685082873	398	0.6958041958041958	413	0.5448548812664907	G	0.680	-0.798743	0.02841	0.387653	0.226512	ENSG00000163606	ENST00000471858;ENST00000308611;ENST00000295863;ENST00000440122;ENST00000490004	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.47	4.59	0.56863	.	0.578559	0.17694	N	0.165145	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.43814	-0.9368	6	0.02654	T	1	.	3.9397	0.09321	0.0905:0.2038:0.559:0.1467	rs4596117;rs57150132	.	.	.	P	121;144;99;144;121	ENSP00000418928:T121P;ENSP00000311035:T144P;ENSP00000295863:T99P;ENSP00000405733:T144P;ENSP00000418801:T121P	ENSP00000295863:T99P	T	-	1	0	CD200R1	114130817	0.264000	0.24093	0.053000	0.19242	0.023000	0.10783	0.769000	0.26604	0.670000	0.31165	-0.224000	0.12420	ACC	T|0.404;G|0.596	0.596	strong		0.448	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
PARP14	54625	hgsc.bcm.edu	37	3	122419993	122419993	+	Silent	SNP	C	C	T	rs16833421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122419993C>T	ENST00000474629.2	+	6	2858	c.2592C>T	c.(2590-2592)gcC>gcT	p.A864A		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	864	Macro 1. {ECO:0000255|PROSITE- ProRule:PRU00490}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CGGGCAATGCCACCATCTCCA	0.612													C|||	169	0.033746	0.1188	0.0173	5008	,	,		19518	0.0		0.0	False		,,,				2504	0.0				p.A864A		Atlas-SNP	.											.	PARP14	242	.	0			c.C2592T						PASS	.	C		326,3758		15,296,1731	33.0	35.0	34.0		2592	-0.9	0.0	3	dbSNP_123	34	3,8335		0,3,4166	yes	coding-synonymous	PARP14	NM_017554.2		15,299,5897	TT,TC,CC		0.036,7.9824,2.6485		864/1802	122419993	329,12093	2042	4169	6211	SO:0001819	synonymous_variant	54625	exon6			CAATGCCACCATC	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.2592C>T	3.37:g.122419993C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1																																																																																			C|0.965;T|0.035	0.035	strong		0.612	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
MYLK	4638	hgsc.bcm.edu	37	3	123452859	123452859	+	Silent	SNP	C	C	T	rs115018449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:123452859C>T	ENST00000475616.1	-	7	983	c.984G>A	c.(982-984)tcG>tcA	p.S328S	MYLK_ENST00000360304.3_Silent_p.S328S|MYLK_ENST00000360772.3_Silent_p.S328S|MYLK_ENST00000346322.5_Silent_p.S328S|MYLK_ENST00000359169.1_Silent_p.S328S			Q15746	MYLK_HUMAN	myosin light chain kinase	328					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)		CCGTTCTGGGCGAGTCCTTGC	0.647													C|||	12	0.00239617	0.0091	0.0	5008	,	,		14936	0.0		0.0	False		,,,				2504	0.0				p.S328S		Atlas-SNP	.											MYLK,caecum,carcinoma,0,1	MYLK	224	1	0			c.G984A						PASS	.	C	,,,	42,4364	43.1+/-76.7	0,42,2161	47.0	51.0	49.0		984,984,984,984	-10.9	0.0	3	dbSNP_132	49	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	,,,	0,42,6461	TT,TC,CC		0.0,0.9532,0.3229	,,,	328/1915,328/1846,328/1864,328/1795	123452859	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	4638	exon10			TCTGGGCGAGTCC	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.984G>A	3.37:g.123452859C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	149	65	0.436242	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																																																																																			C|0.998;T|0.002	0.002	strong		0.647	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
BPIFA2	140683	hgsc.bcm.edu	37	20	31761885	31761885	+	Splice_Site	SNP	G	G	T	rs61734343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31761885G>T	ENST00000253362.2	+	4	449	c.303G>T	c.(301-303)ggG>ggT	p.G101G	BPIFA2_ENST00000354932.5_Splice_Site_p.G101G			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	101						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										TTTCACACAGGTTGAAAATCA	0.537													G|||	23	0.00459265	0.0174	0.0	5008	,	,		19612	0.0		0.0	False		,,,				2504	0.0				p.G101G		Atlas-SNP	.											.	.	.	.	0			c.G303T						PASS	.	G		72,4334	64.1+/-101.4	0,72,2131	164.0	110.0	128.0		303	0.6	0.6	20	dbSNP_129	128	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous-near-splice	BPIFA2	NM_080574.2		0,75,6428	TT,TG,GG		0.0349,1.6341,0.5767		101/250	31761885	75,12931	2203	4300	6503	SO:0001630	splice_region_variant	140683	exon4			ACACAGGTTGAAA	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.303-1G>T	20.37:g.31761885G>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	138	58	0.42029	NM_080574	Q9BQQ0	Silent	SNP	ENST00000253362.2	37	CCDS13214.1																																																																																			A|0.003;G|0.992;T|0.005	0.005	strong		0.537	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	Silent
MCHR1	2847	hgsc.bcm.edu	37	22	41077548	41077548	+	Silent	SNP	C	C	T	rs137903389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:41077548C>T	ENST00000249016.4	+	2	1581	c.885C>T	c.(883-885)gcC>gcT	p.A295A	MCHR1_ENST00000381433.2_Silent_p.A169A|MCHR1_ENST00000498400.1_3'UTR	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	295					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|melanin-concentrating hormone receptor activity (GO:0030273)|neuropeptide receptor activity (GO:0008188)	p.A295A(1)		endometrium(5)|large_intestine(7)|lung(6)|pancreas(1)|urinary_tract(1)	20						TCATCACAGCCGCATACGTGA	0.622													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		21982	0.0		0.0	False		,,,				2504	0.0				p.A295A		Atlas-SNP	.											MCHR1,NS,carcinoma,0,1	MCHR1	45	1	1	Substitution - coding silent(1)	pancreas(1)	c.C885T						PASS	.	C		45,4361	46.7+/-81.2	1,43,2159	118.0	81.0	94.0		885	-10.5	0.0	22	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MCHR1	NM_005297.3		1,44,6458	TT,TC,CC		0.0116,1.0213,0.3537		295/423	41077548	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	2847	exon2			CACAGCCGCATAC		CCDS14004.1	22q13.3	2014-06-05	2006-02-15	2006-02-15	ENSG00000128285	ENSG00000128285		"""GPCR / Class A : MCH receptors"""	4479	protein-coding gene	gene with protein product		601751	"""G protein-coupled receptor 24"""	GPR24			Standard	XM_005261581		Approved	SLC1, MCH1R	uc003ayz.3	Q99705	OTTHUMG00000150256	ENST00000249016.4:c.885C>T	22.37:g.41077548C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_005297	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Silent	SNP	ENST00000249016.4	37	CCDS14004.1																																																																																			C|0.997;T|0.003	0.003	strong		0.622	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297	
CILP2	148113	hgsc.bcm.edu	37	19	19655670	19655670	+	Silent	SNP	C	C	T	rs11669558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19655670C>T	ENST00000291495.5	+	8	2401	c.2316C>T	c.(2314-2316)tcC>tcT	p.S772S	CILP2_ENST00000586018.1_Silent_p.S778S	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	772						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCGGCTTCTCCGCCAACCCCC	0.701													c|||	586	0.117013	0.177	0.1167	5008	,	,		12706	0.0		0.166	False		,,,				2504	0.1063				p.S772S		Atlas-SNP	.											.	CILP2	84	.	0			c.C2316T						PASS	.	T		623,3431		40,543,1444	9.0	11.0	10.0		2316	-9.3	0.7	19	dbSNP_120	10	1261,7031		94,1073,2979	no	coding-synonymous	CILP2	NM_153221.2		134,1616,4423	TT,TC,CC		15.2074,15.3675,15.26		772/1157	19655670	1884,10462	2027	4146	6173	SO:0001819	synonymous_variant	148113	exon8			CTTCTCCGCCAAC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.2316C>T	19.37:g.19655670C>T		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	12	7	0.583333	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			C|0.874;T|0.126	0.126	strong		0.701	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
FREM2	341640	hgsc.bcm.edu	37	13	39424254	39424254	+	Silent	SNP	T	T	C	rs35252750|rs9548507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39424254T>C	ENST00000280481.7	+	9	6675	c.6459T>C	c.(6457-6459)acT>acC	p.T2153T	FREM2_ENST00000482551.1_3'UTR	NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2153	Calx-beta 4.		T -> S (in dbSNP:rs9548506). {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)		TCCATAGGACTGGGGATGTCC	0.453													C|||	460	0.091853	0.0802	0.2478	5008	,	,		19720	0.001		0.0885	False		,,,				2504	0.0941				p.T2153T		Atlas-SNP	.											.	FREM2	385	.	0			c.T6459C						PASS	.	C		4,4402		2,0,2201	122.0	110.0	114.0		6459	-2.7	0.7	13	dbSNP_119	114	22,8578		5,12,4283	no	coding-synonymous	FREM2	NM_207361.4		7,12,6484	CC,CT,TT		0.2558,0.0908,0.1999		2153/3170	39424254	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon9			TAGGACTGGGGAT	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.6459T>C	13.37:g.39424254T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			T|0.912;C|0.088	0.088	strong		0.453	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
SGCD	6444	hgsc.bcm.edu	37	5	155771579	155771579	+	Silent	SNP	T	T	C	rs1801193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:155771579T>C	ENST00000435422.3	+	2	568	c.81T>C	c.(79-81)taT>taC	p.Y27Y	SGCD_ENST00000337851.4_Silent_p.Y28Y|SGCD_ENST00000517913.1_Silent_p.Y28Y|SGCD_ENST00000447401.1_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	303	1	0.00330033		WXS	Illumina HiSeq	Phase_I	327	136	0.415902	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		
PFKP	5214	hgsc.bcm.edu	37	10	3177944	3177944	+	Silent	SNP	C	C	T	rs61731934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3177944C>T	ENST00000381125.4	+	21	2215	c.2139C>T	c.(2137-2139)acC>acT	p.T713T	PFKP_ENST00000381075.2_Silent_p.T705T|PFKP_ENST00000381072.1_Silent_p.T131T|PITRM1_ENST00000464395.1_5'Flank	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	713	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)		AATTTACCACCGATGATTCCA	0.413													C|||	53	0.0105831	0.0356	0.0043	5008	,	,		18020	0.0		0.001	False		,,,				2504	0.002				p.T713T		Atlas-SNP	.											PFKP_ENST00000381075,NS,carcinoma,+2,2	PFKP	182	2	0			c.C2139T						PASS	.	C	,	224,4182	130.6+/-167.2	9,206,1988	62.0	63.0	63.0		2115,2139	-7.3	0.0	10	dbSNP_129	63	5,8595	5.0+/-18.6	0,5,4295	yes	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	9,211,6283	TT,TC,CC		0.0581,5.084,1.7607	,	705/777,713/785	3177944	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon21			TACCACCGATGAT	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.2139C>T	10.37:g.3177944C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	c	2.293	-0.362014	0.05103	0.05084	5.81E-4	ENSG00000067057	ENST00000433193	.	.	.	5.21	-7.26	0.01466	.	.	.	.	.	T	0.19846	0.0477	.	.	.	0.48288	D	0.999629	.	.	.	.	.	.	T	0.59413	-0.7459	4	.	.	.	.	13.2504	0.60048	0.0:0.5807:0.1633:0.256	rs61731934	.	.	.	L	66	.	.	P	+	2	0	PFKP	3167944	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.635000	0.00108	-1.087000	0.03081	-1.012000	0.02466	CCG	C|0.983;T|0.017	0.017	strong		0.413	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
LILRA1	11024	hgsc.bcm.edu	37	19	55107343	55107343	+	Missense_Mutation	SNP	T	T	C	rs10425981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55107343T>C	ENST00000251372.3	+	6	1083	c.901T>C	c.(901-903)Tac>Cac	p.Y301H	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000418536.2_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	301	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CTCCGGTGCATACAACCTCTC	0.682																																					p.Y301H		Atlas-SNP	.											.	LILRA1	105	.	0			c.T901C						PASS	.	C	HIS/TYR	1769,2627		391,987,820	36.0	53.0	47.0		901	0.7	0.1	19	dbSNP_119	47	564,8034		40,484,3775	no	missense	LILRA1	NM_006863.1	83	431,1471,4595	CC,CT,TT		6.5597,40.2411,17.9544	benign	301/490	55107343	2333,10661	2198	4299	6497	SO:0001583	missense	11024	exon6			GGTGCATACAACC	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.901T>C	19.37:g.55107343T>C	ENSP00000251372:p.Tyr301His	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	174	161	0.925287	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	472	0.21611721611721613	192	0.3902439024390244	81	0.22375690607734808	147	0.256993006993007	52	0.06860158311345646	C	0.006	-2.081843	0.00371	0.402411	0.065597	ENSG00000104974	ENST00000251372	T	0.00730	5.77	1.73	0.667	0.17907	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.926202	0.08862	N	0.882865	T	0.00012	0.0000	N	0.01438	-0.865	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.13407	0.009	T	0.30534	-0.9975	9	0.02654	T	1	.	4.1781	0.10362	0.0:0.6043:0.0:0.3957	rs10425981	301	O75019	LIRA1_HUMAN	H	301	ENSP00000251372:Y301H	ENSP00000251372:Y301H	Y	+	1	0	LILRA1	59799155	0.000000	0.05858	0.075000	0.20258	0.011000	0.07611	-0.152000	0.10159	-0.049000	0.13379	-1.033000	0.02402	TAC	T|0.832;C|0.168	0.168	strong		0.682	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
SPATA31C1	441452	hgsc.bcm.edu	37	9	90537856	90537856	+	RNA	SNP	A	A	G	rs512437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:90537856A>G	ENST00000602681.1	+	0	1927							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GCCTCCTTCAATAAGCCACTT	0.443													.|||	1468	0.293131	0.1611	0.3271	5008	,	,		15140	0.1438		0.492	False		,,,				2504	0.3967				p.I1012V		Atlas-SNP	.											.	.	.	.	0			c.A3034G						PASS	.						20.0	32.0	28.0					9																	90537856		677	1431	2108			441452	exon4			CCTTCAATAAGCC	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"""family with sequence similarity 75, member C1"""	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		9.37:g.90537856A>G		Somatic	840	0	0		WXS	Illumina HiSeq	Phase_I	509	501	0.984283	NM_001145124		Missense_Mutation	SNP	ENST00000602681.1	37																																																																																				A|0.767;G|0.233	0.233	strong		0.443	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124	
TATDN2	9797	hgsc.bcm.edu	37	3	10312534	10312534	+	Silent	SNP	G	G	A	rs56261813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:10312534G>A	ENST00000287652.4	+	4	2719	c.1668G>A	c.(1666-1668)ctG>ctA	p.L556L	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Silent_p.L556L	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	556					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						AAGAGGATCTGGTCTGGGGGG	0.517													G|||	164	0.0327476	0.1157	0.0159	5008	,	,		19427	0.0		0.0	False		,,,				2504	0.0				p.L556L		Atlas-SNP	.											.	TATDN2	59	.	0			c.G1668A						PASS	.	G		451,3955	209.2+/-230.0	23,405,1775	110.0	114.0	112.0		1668	2.1	1.0	3	dbSNP_129	112	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	TATDN2	NM_014760.3		23,408,6072	AA,AG,GG		0.0349,10.236,3.4907		556/762	10312534	454,12552	2203	4300	6503	SO:0001819	synonymous_variant	9797	exon4			GGATCTGGTCTGG	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.1668G>A	3.37:g.10312534G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_014760	Q3MIL9|Q5BKU0	Silent	SNP	ENST00000287652.4	37	CCDS33698.1																																																																																			G|0.960;A|0.040	0.040	strong		0.517	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
VNN1	8876	hgsc.bcm.edu	37	6	133035098	133035098	+	Missense_Mutation	SNP	G	G	A	rs2294757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133035098G>A	ENST00000367928.4	-	1	90	c.77C>T	c.(76-78)aCt>aTt	p.T26I		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	26	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		T -> I (in dbSNP:rs2294757). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9790769, ECO:0000269|Ref.2, 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)		AACAGCTGCAGTGAAAGTGTC	0.473													A|||	2873	0.573682	0.8971	0.5735	5008	,	,		20031	0.3819		0.3708	False		,,,				2504	0.5429				p.T26I		Atlas-SNP	.											.	VNN1	69	.	0			c.C77T						PASS	.	A	ILE/THR	3639,767	310.2+/-291.5	1520,599,84	99.0	86.0	90.0		77	-3.6	0.0	6	dbSNP_100	90	3131,5469	657.0+/-401.4	593,1945,1762	yes	missense	VNN1	NM_004666.2	89	2113,2544,1846	AA,AG,GG		36.407,17.4081,47.9471	benign	26/514	133035098	6770,6236	2203	4300	6503	SO:0001583	missense	8876	exon1			GCTGCAGTGAAAG	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.77C>T	6.37:g.133035098G>A	ENSP00000356905:p.Thr26Ile	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	1146	0.5247252747252747	425	0.8638211382113821	207	0.5718232044198895	229	0.40034965034965037	285	0.3759894459102902	A	0.032	-1.330392	0.01298	0.825919	0.36407	ENSG00000112299	ENST00000367928	D	0.85773	-2.03	5.38	-3.64	0.04515	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (2);	0.319072	0.30244	N	0.010067	T	0.27663	0.0680	N	0.01405	-0.89	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18967	-1.0320	9	0.02654	T	1	-26.8441	8.625	0.33883	0.5771:0.0:0.3332:0.0897	rs2294757;rs17604841;rs52808755;rs58995129;rs2294757	26	O95497	VNN1_HUMAN	I	26	ENSP00000356905:T26I	ENSP00000356905:T26I	T	-	2	0	VNN1	133076791	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	0.164000	0.16542	-1.290000	0.02372	-2.692000	0.00139	ACT	G|0.474;A|0.525	0.525	strong		0.473	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
ABCA8	10351	hgsc.bcm.edu	37	17	66928468	66928468	+	Missense_Mutation	SNP	G	G	C	rs62638729|rs386798698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66928468G>C	ENST00000269080.2	-	6	895	c.758C>G	c.(757-759)gCc>gGc	p.A253G	ABCA8_ENST00000586539.1_Missense_Mutation_p.A253G|ABCA8_ENST00000430352.2_Missense_Mutation_p.A253G	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	253					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)					TGTCATCAAGGCCTTCATCCT	0.388													C|||	380	0.0758786	0.2716	0.0231	5008	,	,		20420	0.0		0.005	False		,,,				2504	0.0				p.A253G		Atlas-SNP	.											.	ABCA8	213	.	0			c.C758G						PASS	.						89.0	81.0	84.0					17																	66928468		2203	4300	6503	SO:0001583	missense	10351	exon6			ATCAAGGCCTTCA	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.758C>G	17.37:g.66928468G>C	ENSP00000269080:p.Ala253Gly	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	132	0.06043956043956044	120	0.24390243902439024	10	0.027624309392265192	0	0.0	2	0.002638522427440633	C	5.598	0.295055	0.10622	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000428549	D;D	0.87571	-2.27;-2.27	4.85	-0.973	0.10297	.	0.589518	0.15272	N	0.271169	T	0.00039	0.0001	N	0.00483	-1.445	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.18398	-1.0338	10	0.52906	T	0.07	.	6.2111	0.20630	0.1354:0.2547:0.5285:0.0813	rs62638729	192;253;253;253;253	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	G	253;253;192;253	ENSP00000269080:A253G;ENSP00000402814:A253G	ENSP00000269080:A253G	A	-	2	0	ABCA8	64440063	0.000000	0.05858	0.000000	0.03702	0.505000	0.33919	-0.762000	0.04745	-0.174000	0.10743	-0.224000	0.12420	GCC	G|0.945;C|0.055	0.055	strong		0.388	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
SMYD1	150572	hgsc.bcm.edu	37	2	88396123	88396123	+	Silent	SNP	C	C	G	rs2970912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:88396123C>G	ENST00000419482.2	+	6	793	c.708C>G	c.(706-708)ctC>ctG	p.L236L	SMYD1_ENST00000444564.2_Silent_p.L223L|SMYD1_ENST00000438570.1_Intron	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	236	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						GAATTGAGCTCCGGGCCCTAG	0.507													C|||	1572	0.313898	0.4244	0.2579	5008	,	,		20727	0.1627		0.3559	False		,,,				2504	0.317				p.L236L		Atlas-SNP	.											.	SMYD1	95	.	0			c.C708G						PASS	.	C		1785,2621	526.0+/-371.8	357,1071,775	97.0	96.0	96.0		708	1.3	1.0	2	dbSNP_101	96	3134,5466	473.7+/-368.7	570,1994,1736	no	coding-synonymous	SMYD1	NM_198274.3		927,3065,2511	GG,GC,CC		36.4419,40.5129,37.821		236/491	88396123	4919,8087	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon6			TGAGCTCCGGGCC	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.708C>G	2.37:g.88396123C>G		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	156	154	0.987179	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			C|0.650;G|0.350	0.350	strong		0.507	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
CIB1	10519	hgsc.bcm.edu	37	15	90771787	90771787	+	IGR	SNP	G	G	A	rs16944065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90771787G>A	ENST00000328649.6	-	0	1247				SEMA4B_ENST00000411539.2_Missense_Mutation_p.S809N|SEMA4B_ENST00000332496.6_Missense_Mutation_p.S809N|SEMA4B_ENST00000379122.3_Intron	NM_006384.3	NP_006375.2	Q99828	CIB1_HUMAN	calcium and integrin binding 1 (calmyrin)						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to growth factor stimulus (GO:0071363)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to tumor necrosis factor (GO:0071356)|cytoplasmic microtubule organization (GO:0031122)|double-strand break repair (GO:0006302)|endomitotic cell cycle (GO:0007113)|extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|platelet formation (GO:0030220)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|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-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of male germ cell proliferation (GO:2000256)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell division (GO:0051302)|regulation of cell proliferation (GO:0042127)|response to ischemia (GO:0002931)|spermatid development (GO:0007286)|thrombopoietin-mediated signaling pathway (GO:0038163)	cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|protein anchor (GO:0043495)|Ras GTPase binding (GO:0017016)			lung(1)|prostate(1)	2	Melanoma(11;0.00551)|Lung NSC(78;0.0141)|all_lung(78;0.0303)		BRCA - Breast invasive adenocarcinoma(143;0.00269)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			AGGCCACTCAGCATCCAAGAC	0.652													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		16568	0.0		0.0	False		,,,				2504	0.0				p.S809N		Atlas-SNP	.											.	SEMA4B	51	.	0			c.G2426A						PASS	.	G	ASN/SER,ASN/SER	156,3862		0,156,1853	29.0	34.0	32.0		2426,2426	4.8	1.0	15	dbSNP_123	32	3,8309		0,3,4153	yes	missense,missense	SEMA4B	NM_020210.3,NM_198925.2	46,46	0,159,6006	AA,AG,GG		0.0361,3.8825,1.2895	benign,benign	809/838,809/838	90771787	159,12171	2009	4156	6165	SO:0001628	intergenic_variant	10509	exon15			CACTCAGCATCCA	U82226	CCDS10360.1, CCDS73781.1	15q25.3-q26	2013-01-10			ENSG00000185043	ENSG00000185043		"""EF-hand domain containing"""	16920	protein-coding gene	gene with protein product		602293				9030514, 10826701	Standard	NM_006384		Approved	SIP2-28, CALMYRIN, CIB, KIP	uc031qtq.1	Q99828	OTTHUMG00000149808		15.37:g.90771787G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_020210	B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971	Missense_Mutation	SNP	ENST00000328649.6	37	CCDS10360.1	45	0.020604395604395604	23	0.046747967479674794	4	0.011049723756906077	6	0.01048951048951049	12	0.0158311345646438	G	12.52	1.963517	0.34659	0.038825	3.61E-4	ENSG00000185033	ENST00000332496;ENST00000411539	T;T	0.21543	2.0;2.0	4.75	4.75	0.60458	.	0.102022	0.64402	D	0.000003	T	0.01558	0.0050	N	0.11560	0.145	0.80722	D	1	B;B	0.26120	0.142;0.072	B;B	0.23018	0.043;0.031	T	0.20140	-1.0284	10	0.34782	T	0.22	.	10.5938	0.45325	0.0988:0.0:0.9012:0.0	rs16944065;rs16944065	809;804	Q2NL81;Q9NPR2	.;SEM4B_HUMAN	N	809	ENSP00000332204:S809N;ENSP00000394720:S809N	ENSP00000332204:S809N	S	+	2	0	SEMA4B	88572791	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.820000	0.55693	2.624000	0.88883	0.561000	0.74099	AGC	G|0.979;A|0.021	0.021	strong		0.652	CIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313419.1		
CD80	941	hgsc.bcm.edu	37	3	119263607	119263607	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119263607T>C	ENST00000264246.3	-	3	570	c.208A>G	c.(208-210)Aag>Gag	p.K70E	CD80_ENST00000383668.3_Missense_Mutation_p.K70E|CD80_ENST00000383669.3_Missense_Mutation_p.K70E|CD80_ENST00000478182.1_Missense_Mutation_p.K70E	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	70	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)	ACCATTTTCTTCTCCTTTTGC	0.458																																					p.K70E	Melanoma(132;135 1764 1806 5833 14593)	Atlas-SNP	.											CD80,rectum,carcinoma,+2,1	CD80	35	1	0			c.A208G						scavenged	.						179.0	154.0	163.0					3																	119263607		2203	4300	6503	SO:0001583	missense	941	exon3			TTTTCTTCTCCTT		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.208A>G	3.37:g.119263607T>C	ENSP00000264246:p.Lys70Glu	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	308	5	0.0162338	NM_005191	Q5DTA9|Q5DTB0	Missense_Mutation	SNP	ENST00000264246.3	37	CCDS2989.1	.	.	.	.	.	.	.	.	.	.	T	8.282	0.815768	0.16607	.	.	ENSG00000121594	ENST00000264246;ENST00000478182;ENST00000383669;ENST00000383668	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.13	-10.3	0.00346	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.319310	0.00824	N	0.001601	T	0.28200	0.0696	L	0.31926	0.97	0.09310	N	1	B;B;B;B	0.24043	0.035;0.05;0.096;0.096	B;B;B;B	0.26969	0.034;0.041;0.075;0.075	T	0.04855	-1.0922	10	0.19147	T	0.46	0.0323	10.4548	0.44544	0.0:0.4302:0.3977:0.172	.	70;70;70;70	Q5DTA9;Q5DTB0;A0N0P2;P33681	.;.;.;CD80_HUMAN	E	70	ENSP00000264246:K70E;ENSP00000418364:K70E;ENSP00000373165:K70E;ENSP00000373164:K70E	ENSP00000264246:K70E	K	-	1	0	CD80	120746297	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.101000	0.01344	-2.110000	0.00837	-0.321000	0.08615	AAG	.	.	none		0.458	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191	
C19orf54	284325	hgsc.bcm.edu	37	19	41248532	41248532	+	Silent	SNP	G	G	A	rs36071297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41248532G>A	ENST00000378313.2	-	6	981	c.862C>T	c.(862-864)Ctg>Ttg	p.L288L	C19orf54_ENST00000598485.2_Intron|C19orf54_ENST00000339153.3_Silent_p.L116L|C19orf54_ENST00000594163.1_5'Flank|C19orf54_ENST00000598729.1_Silent_p.L116L|C19orf54_ENST00000470681.1_3'UTR	NM_198476.3	NP_940878.3	Q5BKX5	CS054_HUMAN	chromosome 19 open reading frame 54	288										breast(1)|lung(1)|urinary_tract(2)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TGCTTGGACAGCAGGTAGACA	0.657													G|||	137	0.0273562	0.0998	0.0072	5008	,	,		19677	0.0		0.0	False		,,,				2504	0.0				p.L288L		Atlas-SNP	.											.	C19orf54	13	.	0			c.C862T						PASS	.	G		321,4085	170.1+/-200.6	11,299,1893	43.0	38.0	39.0		862	5.5	1.0	19	dbSNP_126	39	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	C19orf54	NM_198476.3		11,302,6190	AA,AG,GG		0.0349,7.2855,2.4912		288/352	41248532	324,12682	2203	4300	6503	SO:0001819	synonymous_variant	284325	exon6			TGGACAGCAGGTA	AK123126	CCDS12564.2	19q13.2	2012-10-26			ENSG00000188493	ENSG00000188493			24758	protein-coding gene	gene with protein product							Standard	NM_198476		Approved	FLJ41131	uc002oou.1	Q5BKX5	OTTHUMG00000150174	ENST00000378313.2:c.862C>T	19.37:g.41248532G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	145	78	0.537931	NM_198476	A8MSZ5|B4DNU7	Silent	SNP	ENST00000378313.2	37	CCDS12564.2																																																																																			G|0.905;A|0.095	0.095	strong		0.657	C19orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316701.1	NM_198476	
CYP2B6	1555	hgsc.bcm.edu	37	19	41497274	41497274	+	Missense_Mutation	SNP	C	C	T	rs8192709|rs71337213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41497274C>T	ENST00000324071.4	+	1	71	c.64C>T	c.(64-66)Cgc>Tgc	p.R22C		NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	22			R -> C (in allele CYP2B6*2 and allele CYP2B6*10; dbSNP:rs8192709). {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)	p.R22C(1)		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)	CCTGGTTCAGCGCCACCCTAA	0.592													C|||	238	0.047524	0.0416	0.0432	5008	,	,		16955	0.0466		0.0626	False		,,,				2504	0.044				p.R22C		Atlas-SNP	.											CYP2B6,NS,carcinoma,0,1	CYP2B6	79	1	1	Substitution - Missense(1)	prostate(1)	c.C64T						PASS	.	C	CYS/ARG	167,4239	110.4+/-148.6	4,159,2040	173.0	171.0	172.0		64	-3.9	0.0	19	dbSNP_117	172	461,8139	138.3+/-195.1	8,445,3847	no	missense	CYP2B6	NM_000767.4	180	12,604,5887	TT,TC,CC		5.3605,3.7903,4.8285	possibly-damaging	22/492	41497274	628,12378	2203	4300	6503	SO:0001583	missense	1555	exon1			GTTCAGCGCCACC	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.64C>T	19.37:g.41497274C>T	ENSP00000324648:p.Arg22Cys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_000767	B4DWP3|Q2V565|Q9UK46	Missense_Mutation	SNP	ENST00000324071.4	37	CCDS12570.1	116	0.05311355311355311	30	0.06097560975609756	17	0.04696132596685083	21	0.03671328671328671	48	0.0633245382585752	C	12.39	1.924590	0.34002	0.037903	0.053605	ENSG00000197408	ENST00000324071	T	0.72051	-0.62	3.1	-3.9	0.04181	.	2.434140	0.01832	U	0.034741	T	0.07728	0.0194	N	0.08118	0	0.09310	N	1	D	0.57899	0.981	B	0.38106	0.265	T	0.39820	-0.9595	10	0.87932	D	0	.	5.104	0.14773	0.2444:0.3357:0.4199:0.0	rs8192709;rs8192709	22	P20813	CP2B6_HUMAN	C	22	ENSP00000324648:R22C	ENSP00000324648:R22C	R	+	1	0	CYP2B6	46189114	0.005000	0.15991	0.000000	0.03702	0.006000	0.05464	-0.000000	0.12993	-0.500000	0.06614	-0.735000	0.03563	CGC	C|0.950;T|0.050	0.050	strong		0.592	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	
HRNR	388697	hgsc.bcm.edu	37	1	152193049	152193049	+	Silent	SNP	C	C	T	rs114845154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152193049C>T	ENST00000368801.2	-	3	1131	c.1056G>A	c.(1054-1056)gaG>gaA	p.E352E	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	352					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)			CTGAGCCAGACTCATGTTGCC	0.557													C|||	95	0.0189696	0.0696	0.0043	5008	,	,		22156	0.0		0.0	False		,,,				2504	0.0				p.E352E		Atlas-SNP	.											HRNR,NS,carcinoma,-2,1	HRNR	403	1	0			c.G1056A						PASS	.	C		188,4218	120.8+/-158.4	2,184,2017	118.0	121.0	120.0		1056	-8.3	0.0	1	dbSNP_132	120	0,8600		0,0,4300	no	coding-synonymous	HRNR	NM_001009931.1		2,184,6317	TT,TC,CC		0.0,4.2669,1.4455		352/2851	152193049	188,12818	2203	4300	6503	SO:0001819	synonymous_variant	388697	exon3			GCCAGACTCATGT	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.1056G>A	1.37:g.152193049C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	123	54	0.439024	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			C|0.985;T|0.015	0.015	strong		0.557	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
OR2T4	127074	hgsc.bcm.edu	37	1	248525060	248525060	+	Missense_Mutation	SNP	T	T	A	rs28491677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248525060T>A	ENST00000366475.1	+	1	178	c.178T>A	c.(178-180)Tgt>Agt	p.C60S		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGCACTACTTTGTGTGGTCAT	0.488													t|||	1477	0.294928	0.2421	0.2709	5008	,	,		20455	0.4276		0.1809	False		,,,				2504	0.364				p.C60S		Atlas-SNP	.											OR2T4,NS,carcinoma,-1,1	OR2T4	126	1	0			c.T178A						scavenged	.						176.0	175.0	175.0					1																	248525060		2203	4300	6503	SO:0001583	missense	127074	exon1			CTACTTTGTGTGG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.178T>A	1.37:g.248525060T>A	ENSP00000355431:p.Cys60Ser	Somatic	807	3	0.00371747		WXS	Illumina HiSeq	Phase_I	715	290	0.405594	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	500	0.22893772893772893	101	0.20528455284552846	72	0.19889502762430938	210	0.36713286713286714	117	0.15435356200527706	t	9.676	1.147970	0.21288	.	.	ENSG00000196944	ENST00000366475	T	0.02944	4.1	3.48	2.33	0.28932	.	0.441217	0.19340	N	0.116665	T	0.00012	0.0000	N	0.00746	-1.225	0.80722	P	0.0	B	0.09022	0.002	B	0.11329	0.006	T	0.41574	-0.9501	9	0.59425	D	0.04	.	8.6683	0.34134	0.1713:0.0:0.0:0.8287	rs28491677;rs58960769	60	Q8NH00	OR2T4_HUMAN	S	60	ENSP00000355431:C60S	ENSP00000355431:C60S	C	+	1	0	OR2T4	246591683	0.044000	0.20184	0.001000	0.08648	0.025000	0.11179	2.832000	0.48152	0.248000	0.21435	-0.510000	0.04470	TGT	T|0.787;A|0.213	0.213	strong		0.488	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
LRFN3	79414	hgsc.bcm.edu	37	19	36435564	36435564	+	Silent	SNP	G	G	A	rs2293756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	3	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	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	
MUC2	4583	hgsc.bcm.edu	37	11	1075850	1075850	+	Silent	SNP	G	G	A	rs11825969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1075850G>A	ENST00000441003.2	+	2	303	c.276G>A	c.(274-276)gaG>gaA	p.E92E	MUC2_ENST00000359061.5_Silent_p.E92E	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	92	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCGGGGTGGAGTCCATCCTGC	0.647													G|||	582	0.116214	0.2179	0.0821	5008	,	,		16206	0.001		0.2078	False		,,,				2504	0.0276				p.E92E		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.G276A						PASS	.	G		840,3090		104,632,1229	23.0	26.0	25.0		276	-0.8	0.0	11	dbSNP_120	25	1728,6528		193,1342,2593	no	coding-synonymous	MUC2	NM_002457.2		297,1974,3822	AA,AG,GG		20.9302,21.374,21.0734		92/2813	1075850	2568,9618	1965	4128	6093	SO:0001819	synonymous_variant	4583	exon2			GGTGGAGTCCATC	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.276G>A	11.37:g.1075850G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				G|0.844;A|0.156	0.156	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CEP89	84902	hgsc.bcm.edu	37	19	33406328	33406328	+	Missense_Mutation	SNP	G	G	A	rs113919201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33406328G>A	ENST00000305768.5	-	14	1568	c.1480C>T	c.(1480-1482)Cgt>Tgt	p.R494C		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	494					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CATTTGGCACGTAAAATCTCC	0.423													G|||	36	0.0071885	0.025	0.0043	5008	,	,		15861	0.0		0.0	False		,,,				2504	0.0				p.R494C		Atlas-SNP	.											CEP89,NS,carcinoma,+1,1	CEP89	82	1	0			c.C1480T						PASS	.	G	CYS/ARG	99,4307	79.9+/-118.3	3,93,2107	123.0	109.0	114.0		1480	3.5	0.0	19	dbSNP_132	114	0,8600		0,0,4300	yes	missense	CEP89	NM_032816.3	180	3,93,6407	AA,AG,GG		0.0,2.2469,0.7612	benign	494/784	33406328	99,12907	2203	4300	6503	SO:0001583	missense	84902	exon14			TGGCACGTAAAAT	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.1480C>T	19.37:g.33406328G>A	ENSP00000306105:p.Arg494Cys	Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	244	128	0.52459	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	15	0.006868131868131868	12	0.024390243902439025	3	0.008287292817679558	0	0.0	0	0.0	G	6.345	0.431801	0.12045	0.022469	0.0	ENSG00000121289	ENST00000305768	D	0.88201	-2.35	5.6	3.45	0.39498	.	1.178400	0.05586	N	0.573762	T	0.80385	0.4613	L	0.60455	1.87	0.24756	N	0.992952	B;B	0.14438	0.004;0.01	B;B	0.09377	0.004;0.002	T	0.71318	-0.4629	10	0.52906	T	0.07	1.9766	11.2548	0.49048	0.0701:0.1277:0.8023:0.0	.	247;494	Q96ST8-2;Q96ST8	.;CEP89_HUMAN	C	494	ENSP00000306105:R494C	ENSP00000306105:R494C	R	-	1	0	CEP89	38098168	0.414000	0.25408	0.000000	0.03702	0.009000	0.06853	1.725000	0.38074	0.708000	0.31955	0.591000	0.81541	CGT	G|0.991;A|0.009	0.009	strong		0.423	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
IRS4	8471	hgsc.bcm.edu	37	X	107978342	107978342	+	Silent	SNP	T	T	A	rs375938401|rs80131334|rs1800993	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:107978342T>A	ENST00000372129.2	-	1	1309	c.1233A>T	c.(1231-1233)cgA>cgT	p.R411R	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	411					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GCAGTCTTCCTCGCCTGGAGT	0.642													T|||	171	0.045298	0.0401	0.0562	3775	,	,		13003	0.002		0.0398	False		,,,				2504	0.0378				p.R411R		Atlas-SNP	.											.	IRS4	253	.	0			c.A1233T						PASS	.	T		11,3824		0,0,11,1632,560	49.0	43.0	45.0		1233	0.9	0.1	X	dbSNP_131	45	29,6699		1,1,26,2426,1846	no	coding-synonymous	IRS4	NM_003604.2		1,1,37,4058,2406	AA,AT,A,TT,T		0.431,0.2868,0.3787		411/1258	107978342	40,10523	2203	4300	6503	SO:0001819	synonymous_variant	8471	exon1			TCTTCCTCGCCTG	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1233A>T	X.37:g.107978342T>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	111	66	0.594595	NM_003604		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																			T|0.950;A|0.050	0.050	strong		0.642	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
GPC3	2719	hgsc.bcm.edu	37	X	132730541	132730541	+	Silent	SNP	A	A	G	rs2314298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:132730541A>G	ENST00000370818.3	-	7	1945	c.1500T>C	c.(1498-1500)gaT>gaC	p.D500D	GPC3_ENST00000543339.1_Silent_p.D446D|GPC3_ENST00000394299.2_Silent_p.D523D	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	500					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|body morphogenesis (GO:0010171)|bone mineralization (GO:0030282)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cell proliferation involved in metanephros development (GO:0072203)|chondroitin sulfate metabolic process (GO:0030204)|coronary vasculature development (GO:0060976)|embryonic hindlimb morphogenesis (GO:0035116)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lung development (GO:0030324)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesonephric duct morphogenesis (GO:0072180)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of growth (GO:0045926)|negative regulation of smoothened signaling pathway (GO:0045879)|osteoclast differentiation (GO:0030316)|phototransduction, visible light (GO:0007603)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endocytosis (GO:0045807)|positive regulation of glucose import (GO:0046326)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	peptidyl-dipeptidase inhibitor activity (GO:0060422)			breast(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|prostate(1)|skin(2)	36	Acute lymphoblastic leukemia(192;0.000127)					CATCTTCATCATCACCGCAGT	0.448			"""T, D, Mis, N, F, S"""			Wilms tumour			Simpson-Golabi-Behmel syndrome				a|||	247	0.0654305	0.1823	0.0086	3775	,	,		13843	0.0		0.0	False		,,,				2504	0.0				p.D523D		Atlas-SNP	.	yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	.	GPC3	88	.	0			c.T1569C						PASS	.	A	,,,	844,2991		83,548,130,1001,441	240.0	203.0	216.0		1569,1452,1338,1500	-8.8	0.0	X	dbSNP_100	216	9,6719		0,6,3,2422,1869	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPC3	NM_001164617.1,NM_001164618.1,NM_001164619.1,NM_004484.3	,,,	83,554,133,3423,2310	GG,GA,G,AA,A		0.1338,22.0078,8.0754	,,,	523/604,484/565,446/527,500/581	132730541	853,9710	2203	4300	6503	SO:0001819	synonymous_variant	2719	exon8	Familial Cancer Database	SGBS	TTCATCATCACCG	L47125	CCDS14638.1, CCDS55496.1	Xq26	2014-09-17			ENSG00000147257	ENSG00000147257		"""Proteoglycans / Cell Surface : Glypicans"""	4451	protein-coding gene	gene with protein product	"""glypican proteoglycan 3"""	300037		SDYS		8589713, 9787072	Standard	NM_004484		Approved	OCI-5, SGBS, SGBS1, SGB, DGSX	uc010nrn.2	P51654	OTTHUMG00000022448	ENST00000370818.3:c.1500T>C	X.37:g.132730541A>G		Somatic	421	0	0		WXS	Illumina HiSeq	Phase_I	461	297	0.644252	NM_001164617	C9JLE3|G3V1R0|Q2L880|Q2L882	Silent	SNP	ENST00000370818.3	37	CCDS14638.1	88	0.05304400241109102	57	0.1313364055299539	1	0.002777777777777778	0	0.0	0	0.0	a	2.240	-0.373954	0.05034	0.220078	0.001338	ENSG00000147257	ENST00000406757	.	.	.	4.73	-8.77	0.00827	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.21290	P	0.99973057	.	.	.	.	.	.	T	0.40997	-0.9533	3	.	.	.	.	17.6231	0.88087	0.3063:0.0:0.6937:0.0	rs2314298;rs60128560;rs2314298	.	.	.	T	230	.	.	M	-	2	0	GPC3	132558207	0.013000	0.17824	0.034000	0.17996	0.609000	0.37215	-1.591000	0.02100	-2.800000	0.00352	-3.172000	0.00057	ATG	A|0.905;G|0.095	0.095	strong		0.448	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484	
R3HDML	140902	hgsc.bcm.edu	37	20	42965863	42965863	+	Silent	SNP	C	C	T	rs3746570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42965863C>T	ENST00000217043.2	+	1	238	c.66C>T	c.(64-66)aaC>aaT	p.N22N		NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	22						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)			AGGCAGTGAACGCCTTGATAA	0.662													C|||	798	0.159345	0.1369	0.2392	5008	,	,		16802	0.0913		0.1551	False		,,,				2504	0.2076				p.N22N		Atlas-SNP	.											.	R3HDML	33	.	0			c.C66T						PASS	.	C		673,3733	274.3+/-271.8	56,561,1586	43.0	42.0	42.0		66	-8.9	0.0	20	dbSNP_107	42	1302,7296	246.7+/-275.0	96,1110,3093	no	coding-synonymous	R3HDML	NM_178491.2		152,1671,4679	TT,TC,CC		15.1431,15.2746,15.1876		22/254	42965863	1975,11029	2203	4299	6502	SO:0001819	synonymous_variant	140902	exon1			AGTGAACGCCTTG	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.66C>T	20.37:g.42965863C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_178491		Silent	SNP	ENST00000217043.2	37	CCDS13329.1																																																																																			C|0.845;T|0.155	0.155	strong		0.662	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491	
ITIH2	3698	hgsc.bcm.edu	37	10	7759595	7759595	+	Silent	SNP	C	C	T	rs7072478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:7759595C>T	ENST00000358415.4	+	6	640	c.474C>T	c.(472-474)agC>agT	p.S158S	ITIH2_ENST00000379587.4_Silent_p.S147S|ITIH2_ENST00000480387.1_3'UTR	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	158	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				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)	p.S158S(1)		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						TTAGGAGCAGCGCTCTTGATA	0.488													C|||	1037	0.207069	0.2201	0.2781	5008	,	,		21172	0.2202		0.172	False		,,,				2504	0.1616				p.S158S		Atlas-SNP	.											ITIH2,NS,carcinoma,0,1	ITIH2	144	1	1	Substitution - coding silent(1)	stomach(1)	c.C474T						PASS	.	C		994,3412	370.3+/-319.5	113,768,1322	163.0	174.0	171.0		474	-8.4	0.0	10	dbSNP_116	171	1200,7400	243.3+/-273.0	84,1032,3184	no	coding-synonymous	ITIH2	NM_002216.2		197,1800,4506	TT,TC,CC		13.9535,22.5601,16.8691		158/947	7759595	2194,10812	2203	4300	6503	SO:0001819	synonymous_variant	3698	exon6			GAGCAGCGCTCTT	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.474C>T	10.37:g.7759595C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																			C|0.819;T|0.181	0.181	strong		0.488	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
OR2A14	135941	hgsc.bcm.edu	37	7	143826697	143826697	+	Missense_Mutation	SNP	C	C	G	rs2961161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	352	1	0.00284091		WXS	Illumina HiSeq	Phase_I	336	335	0.997024	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		
CIZ1	25792	hgsc.bcm.edu	37	9	130941451	130941451	+	Silent	SNP	C	C	T	rs45536439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130941451C>T	ENST00000393608.1	-	8	1237	c.1035G>A	c.(1033-1035)gcG>gcA	p.A345A	CIZ1_ENST00000357558.5_Silent_p.A345A|CIZ1_ENST00000325721.8_Silent_p.A316A|CIZ1_ENST00000277465.4_Silent_p.A345A|CIZ1_ENST00000372954.1_Silent_p.A321A|CIZ1_ENST00000372938.5_Silent_p.A345A|CIZ1_ENST00000372948.3_Silent_p.A345A|CIZ1_ENST00000541172.1_Silent_p.A244A|CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000538431.1_Silent_p.A345A	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	345	Gln-rich.				maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						TCTGTGTTTGCGCCTGCTTCT	0.617													C|||	174	0.0347444	0.1225	0.0159	5008	,	,		20540	0.0		0.001	False		,,,				2504	0.0				p.A375A		Atlas-SNP	.											.	CIZ1	75	.	0			c.G1125A						PASS	.	C	,,,,	553,3853	248.7+/-256.4	38,477,1688	63.0	64.0	64.0		1035,1035,1020,963,1035	-5.6	0.9	9	dbSNP_127	64	13,8587	7.7+/-29.5	0,13,4287	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	,,,,	38,490,5975	TT,TC,CC		0.1512,12.5511,4.3518	,,,,	345/843,345/899,340/838,321/819,345/899	130941451	566,12440	2203	4300	6503	SO:0001819	synonymous_variant	25792	exon8			TGTTTGCGCCTGC	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.1035G>A	9.37:g.130941451C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	70	0.59322	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	37	CCDS6894.1																																																																																			C|0.961;T|0.039	0.039	strong		0.617	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127	
TG	7038	hgsc.bcm.edu	37	8	133881996	133881996	+	Missense_Mutation	SNP	G	G	A	rs116340633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133881996G>A	ENST00000220616.4	+	3	239	c.199G>A	c.(199-201)Ggc>Agc	p.G67S	TG_ENST00000377869.1_Missense_Mutation_p.G67S	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	67	Thyroglobulin type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CCAGAACGACGGCCGCTCCTG	0.642													G|||	26	0.00519169	0.0106	0.0	5008	,	,		15975	0.0		0.0119	False		,,,				2504	0.0				p.G67S		Atlas-SNP	.											.	TG	416	.	0			c.G199A						PASS	.	G	SER/GLY	51,4355	52.3+/-87.9	0,51,2152	59.0	55.0	57.0		199	4.5	0.1	8	dbSNP_132	57	82,8518	47.2+/-106.3	0,82,4218	yes	missense	TG	NM_003235.4	56	0,133,6370	AA,AG,GG		0.9535,1.1575,1.0226	probably-damaging	67/2769	133881996	133,12873	2203	4300	6503	SO:0001583	missense	7038	exon3			AACGACGGCCGCT	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.199G>A	8.37:g.133881996G>A	ENSP00000220616:p.Gly67Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	75	48	0.64	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	16	0.007326007326007326	4	0.008130081300813009	0	0.0	0	0.0	12	0.0158311345646438	G	27.6	4.849775	0.91277	0.011575	0.009535	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.62232	0.04;0.04	5.44	4.51	0.55191	Thyroglobulin type-1 (6);	0.205829	0.34314	N	0.004066	T	0.52092	0.1713	L	0.39245	1.2	0.32812	D	0.501558	D	0.76494	0.999	P	0.62435	0.902	T	0.69243	-0.5196	10	0.46703	T	0.11	.	13.1275	0.59364	0.0:0.1603:0.8397:0.0	.	67	P01266	THYG_HUMAN	S	67	ENSP00000367100:G67S;ENSP00000220616:G67S	ENSP00000220616:G67S	G	+	1	0	TG	133951178	0.998000	0.40836	0.098000	0.21074	0.191000	0.23601	2.801000	0.47908	2.550000	0.86006	0.462000	0.41574	GGC	G|0.992;A|0.008	0.008	strong		0.642	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
MUC17	140453	hgsc.bcm.edu	37	7	100678740	100678740	+	Missense_Mutation	SNP	T	T	C	rs4269454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678740T>C	ENST00000306151.4	+	3	4107	c.4043T>C	c.(4042-4044)cTg>cCg	p.L1348P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1348	59 X approximate tandem repeats.|Ser-rich.		L -> P (in dbSNP:rs4269454). {ECO:0000269|PubMed:9299468}.		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)					AACACCACACTGGTGGCCAGT	0.463													N|||	1193	0.238219	0.351	0.1023	5008	,	,		25539	0.252		0.1213	False		,,,				2504	0.2883				p.L1348P		Atlas-SNP	.											.	MUC17	804	.	0			c.T4043C						PASS	.	C	PRO/LEU	1348,3058	693.0+/-405.6	209,930,1064	228.0	227.0	227.0		4043	-1.7	0.0	7	dbSNP_111	227	999,7601	773.3+/-407.7	57,885,3358	no	missense	MUC17	NM_001040105.1	98	266,1815,4422	CC,CT,TT		11.6163,30.5946,18.0455	benign	1348/4494	100678740	2347,10659	2203	4300	6503	SO:0001583	missense	140453	exon3			CCACACTGGTGGC	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.4043T>C	7.37:g.100678740T>C	ENSP00000302716:p.Leu1348Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	144	70	0.486111	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	430	0.19688644688644688	159	0.3231707317073171	42	0.11602209944751381	140	0.24475524475524477	89	0.11741424802110818	c	0.013	-1.645144	0.00792	0.305946	0.116163	ENSG00000169876	ENST00000306151	T	0.03212	4.01	0.861	-1.72	0.08107	.	.	.	.	.	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	0.44050	-0.9353	8	0.27785	T	0.31	.	3.1089	0.06351	0.1991:0.2846:0.0:0.5164	rs4269454;rs10374373;rs52835910;rs4269454	1348	Q685J3	MUC17_HUMAN	P	1348	ENSP00000302716:L1348P	ENSP00000302716:L1348P	L	+	2	0	MUC17	100465460	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.110000	0.01334	-3.604000	0.00133	-3.178000	0.00056	CTG	T|0.821;C|0.179	0.179	strong		0.463	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CDC42BPB	9578	hgsc.bcm.edu	37	14	103406169	103406169	+	Silent	SNP	C	C	T	rs60475222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103406169C>T	ENST00000361246.2	-	33	4995	c.4707G>A	c.(4705-4707)agG>agA	p.R1569R	RP11-365N19.2_ENST00000560931.1_RNA	NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		GCTCCTACCGCCTCTGCTGCA	0.597													C|||	35	0.00698882	0.0257	0.0014	5008	,	,		19254	0.0		0.0	False		,,,				2504	0.0				p.R1569R		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.G4707A						PASS	.	C		110,4296	86.8+/-125.4	2,106,2095	147.0	158.0	155.0		4707	3.4	1.0	14	dbSNP_129	155	0,8600		0,0,4300	no	coding-synonymous	CDC42BPB	NM_006035.3		2,106,6395	TT,TC,CC		0.0,2.4966,0.8458		1569/1712	103406169	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	9578	exon33			CTACCGCCTCTGC	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.4707G>A	14.37:g.103406169C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	216	96	0.444444	NM_006035		Silent	SNP	ENST00000361246.2	37	CCDS9978.1																																																																																			C|0.992;T|0.008	0.008	strong		0.597	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035	
CTF1	1489	hgsc.bcm.edu	37	16	30910830	30910830	+	Silent	SNP	C	C	T	rs8059269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30910830C>T	ENST00000279804.2	+	2	157	c.120C>T	c.(118-120)taC>taT	p.Y40Y	CTF1_ENST00000395019.3_Silent_p.Y39Y	NM_001142544.1|NM_001330.3	NP_001136016.1|NP_001321.1	Q16619	CTF1_HUMAN	cardiotrophin 1	40					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|leukemia inhibitory factor signaling pathway (GO:0048861)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|neuron development (GO:0048666)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	leukemia inhibitory factor receptor binding (GO:0005146)			large_intestine(1)|urinary_tract(1)	2			Colorectal(24;0.198)			TCACCAAATACGCTGAGCAGC	0.592													C|||	143	0.0285543	0.1051	0.0058	5008	,	,		11807	0.0		0.0	False		,,,				2504	0.0				p.Y40Y		Atlas-SNP	.											.	CTF1	3	.	0			c.C120T						PASS	.	C	,	349,4045	180.5+/-208.7	14,321,1862	67.0	61.0	63.0		117,120	-0.7	1.0	16	dbSNP_116	63	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous,coding-synonymous	CTF1	NM_001142544.1,NM_001330.3	,	14,325,6158	TT,TC,CC		0.0465,7.9426,2.7166	,	39/201,40/202	30910830	353,12641	2197	4300	6497	SO:0001819	synonymous_variant	1489	exon2			CAAATACGCTGAG	U43030	CCDS10694.1, CCDS45464.1	16p11.2	2014-09-17			ENSG00000150281	ENSG00000150281			2499	protein-coding gene	gene with protein product		600435				8833032	Standard	NM_001330		Approved	CT-1, CT1	uc002dzw.3	Q16619	OTTHUMG00000132413	ENST00000279804.2:c.120C>T	16.37:g.30910830C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	188	83	0.441489	NM_001330	A8MVX4|Q5U5Y7	Silent	SNP	ENST00000279804.2	37	CCDS10694.1																																																																																			C|0.965;T|0.035	0.035	strong		0.592	CTF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255550.1	NM_001330	
MT-ND4	4538	hgsc.bcm.edu	37	M	10873	10873	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10873T>C	ENST00000361381.2	+	1	114	c.114T>C	c.(112-114)ccT>ccC	p.P38P	MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TS2_ENST00000387449.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	38					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						AGCATCATCCCCCTACTATTT	0.403																																					p.P38P		Atlas-SNP	.											.	.	.	.	0			c.T114C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CATCCCTCTACTA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.114T>C	M.37:g.10873T>C		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	6	6	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.403	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
ZNF596	169270	hgsc.bcm.edu	37	8	195254	195254	+	Missense_Mutation	SNP	C	C	A	rs2074718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:195254C>A	ENST00000398612.1	+	6	790	c.407C>A	c.(406-408)aCg>aAg	p.T136K	ZNF596_ENST00000308811.4_Missense_Mutation_p.T136K|ZNF596_ENST00000320552.2_Missense_Mutation_p.T66K	NM_001042415.1|NM_001042416.1	NP_001035880.1|NP_001035881.1	Q8TC21	ZN596_HUMAN	zinc finger protein 596	136			T -> K (in dbSNP:rs2074718).		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)|endometrium(2)|large_intestine(6)|lung(5)	14		all_cancers(2;4.81e-29)|all_epithelial(2;5.03e-19)|Lung NSC(2;8.68e-08)|all_lung(2;1.52e-07)|Ovarian(12;0.00965)|Colorectal(14;0.0367)|all_neural(12;0.0837)|Myeloproliferative disorder(644;0.116)|all_hematologic(2;0.138)|Acute lymphoblastic leukemia(644;0.242)		Epithelial(5;3.77e-18)|all cancers(2;5.2e-17)|OV - Ovarian serous cystadenocarcinoma(5;5.37e-09)|BRCA - Breast invasive adenocarcinoma(11;1.7e-06)|Colorectal(2;6.51e-05)|READ - Rectum adenocarcinoma(2;0.0276)|COAD - Colon adenocarcinoma(149;0.0702)		TACATGAGAACGAAACACTTT	0.343													.|||	901	0.179912	0.3411	0.0519	5008	,	,		21221	0.2063		0.0805	False		,,,				2504	0.1278				p.T136K		Atlas-SNP	.											.	ZNF596	34	.	0			c.C407A						PASS	.	A	LYS/THR,LYS/THR,LYS/THR	1444,2962		252,940,1011	80.0	81.0	81.0		407,407,407	2.5	0.3	8	dbSNP_96	81	655,7945		16,623,3661	yes	missense,missense,missense	ZNF596	NM_001042415.1,NM_001042416.1,NM_173539.2	78,78,78	268,1563,4672	AA,AC,CC		7.6163,32.7735,16.1387	benign,benign,benign	136/505,136/505,136/505	195254	2099,10907	2203	4300	6503	SO:0001583	missense	169270	exon6			TGAGAACGAAACA	BC026190	CCDS5951.2	8p23.3	2013-01-08			ENSG00000172748	ENSG00000172748		"""Zinc fingers, C2H2-type"", ""-"""	27268	protein-coding gene	gene with protein product						12477932	Standard	NM_001287256		Approved		uc003wot.3	Q8TC21	OTTHUMG00000086931	ENST00000398612.1:c.407C>A	8.37:g.195254C>A	ENSP00000381613:p.Thr136Lys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	150	84	0.56	NM_173539	B2R8P4|O95015|Q8N9X0	Missense_Mutation	SNP	ENST00000398612.1	37	CCDS5951.2	382	0.1749084249084249	167	0.3394308943089431	21	0.058011049723756904	129	0.22552447552447552	65	0.08575197889182058	.	2.992	-0.207879	0.06180	0.327735	0.076163	ENSG00000172748	ENST00000521145;ENST00000308811;ENST00000320552;ENST00000398612	T;T;T;T	0.60040	2.5;0.22;3.52;0.22	2.49	2.49	0.30216	.	.	.	.	.	T	0.00012	0.0000	N	0.00462	-1.47	0.54753	P	1.6000000000016E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.32188	-0.9916	8	0.52906	T	0.07	.	7.1816	0.25776	0.7719:0.2281:0.0:0.0	rs2074718;rs52814433;rs2074718	136	Q8TC21	ZN596_HUMAN	K	136;136;66;136	ENSP00000429671:T136K;ENSP00000310033:T136K;ENSP00000318719:T66K;ENSP00000381613:T136K	ENSP00000310033:T136K	T	+	2	0	ZNF596	185254	0.413000	0.25400	0.269000	0.24586	0.009000	0.06853	2.238000	0.43070	0.388000	0.25054	-0.335000	0.08231	ACG	C|0.837;A|0.163	0.163	strong		0.343	ZNF596-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195858.4	NM_173539	
CLCA4	22802	hgsc.bcm.edu	37	1	87045696	87045696	+	Missense_Mutation	SNP	G	G	C	rs2231604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87045696G>C	ENST00000370563.3	+	14	2470	c.2428G>C	c.(2428-2430)Gta>Cta	p.V810L	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	810			V -> L (in dbSNP:rs2231604). {ECO:0000269|PubMed:15489334}.		chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		TGCTCTTCAAGTAAATACTAC	0.333													G|||	275	0.0549121	0.1944	0.0115	5008	,	,		18080	0.005		0.0	False		,,,				2504	0.0051				p.V810L		Atlas-SNP	.											.	CLCA4	131	.	0			c.G2428C						PASS	.	G	LEU/VAL	642,3036		52,538,1249	57.0	51.0	53.0		2428	4.9	0.9	1	dbSNP_98	53	2,8174		0,2,4086	yes	missense	CLCA4	NM_012128.3	32	52,540,5335	CC,CG,GG		0.0245,17.4551,5.4328	probably-damaging	810/920	87045696	644,11210	1839	4088	5927	SO:0001583	missense	22802	exon14			CTTCAAGTAAATA	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2428G>C	1.37:g.87045696G>C	ENSP00000359594:p.Val810Leu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	149	59	0.395973	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Missense_Mutation	SNP	ENST00000370563.3	37	CCDS41355.1	109	0.04990842490842491	102	0.2073170731707317	5	0.013812154696132596	2	0.0034965034965034965	0	0.0	G	14.30	2.494809	0.44352	0.174551	2.45E-4	ENSG00000016602	ENST00000370563	T	0.03717	3.83	5.82	4.91	0.64330	.	0.000000	0.64402	D	0.000001	T	0.04048	0.0113	M	0.80847	2.515	0.09310	P	1.0	P;P	0.47350	0.894;0.894	P;P	0.45071	0.468;0.468	T	0.25398	-1.0133	9	0.44086	T	0.13	-20.4313	10.9104	0.47106	0.071:0.1305:0.7984:0.0	rs2231604;rs52796222;rs2231604	362;810	Q9NXP1;Q14CN2	.;CLCA4_HUMAN	L	810	ENSP00000359594:V810L	ENSP00000359594:V810L	V	+	1	0	CLCA4	86818284	0.999000	0.42202	0.888000	0.34837	0.308000	0.27856	2.265000	0.43311	1.477000	0.48234	-0.237000	0.12165	GTA	G|0.950;C|0.050	0.050	strong		0.333	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
MUC4	4585	hgsc.bcm.edu	37	3	195505813	195505813	+	Missense_Mutation	SNP	T	T	C	rs562396488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195505813T>C	ENST00000463781.3	-	2	13097	c.12638A>G	c.(12637-12639)gAc>gGc	p.D4213G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D4213G	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.D4213G(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)		TGAGGAAGTGTCGGTGACAGG	0.592													.|||	73	0.0145767	0.0151	0.0144	5008	,	,		14193	0.0159		0.0189	False		,,,				2504	0.0082				p.D4213G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,5	MUC4	1505	5	2	Substitution - Missense(2)	endometrium(2)	c.A12638G						scavenged	.						26.0	23.0	24.0					3																	195505813		690	1577	2267	SO:0001583	missense	4585	exon2			GAAGTGTCGGTGA	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.12638A>G	3.37:g.195505813T>C	ENSP00000417498:p.Asp4213Gly	Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	252	22	0.0873016	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	0.010	-1.784645	0.00628	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.44;1.46	.	.	.	.	.	.	.	.	T	0.12689	0.0308	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.24190	-1.0167	7	.	.	.	.	3.8908	0.09117	0.0:0.332:0.0:0.668	.	4085	E7ESK3	.	G	4213	ENSP00000417498:D4213G;ENSP00000420243:D4213G	.	D	-	2	0	MUC4	196990592	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-1.874000	0.01133	-1.876000	0.00548	GAC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NLRP13	126204	hgsc.bcm.edu	37	19	56413532	56413532	+	Silent	SNP	G	G	A	rs7258847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56413532G>A	ENST00000342929.3	-	9	2657	c.2658C>T	c.(2656-2658)caC>caT	p.H886H	NLRP13_ENST00000588751.1_Silent_p.H886H	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	886							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)		CATCTGACAAGTGCTTGCAAG	0.582													G|||	744	0.148562	0.0287	0.1787	5008	,	,		15155	0.0456		0.2803	False		,,,				2504	0.2597				p.H886H		Atlas-SNP	.											.	NLRP13	220	.	0			c.C2658T						PASS	.	G		289,4117	161.1+/-193.3	8,273,1922	91.0	69.0	77.0		2658	1.5	0.0	19	dbSNP_116	77	2291,6309	386.3+/-341.8	337,1617,2346	no	coding-synonymous	NLRP13	NM_176810.2		345,1890,4268	AA,AG,GG		26.6395,6.5592,19.837		886/1044	56413532	2580,10426	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon9			TGACAAGTGCTTG	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.2658C>T	19.37:g.56413532G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			G|0.824;A|0.176	0.176	strong		0.582	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
MYO18B	84700	hgsc.bcm.edu	37	22	26422980	26422980	+	Missense_Mutation	SNP	A	A	G	rs2236005	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26422980A>G	ENST00000407587.2	+	43	7212	c.7043A>G	c.(7042-7044)cAa>cGa	p.Q2348R	MYO18B_ENST00000536101.1_Missense_Mutation_p.Q2347R|MYO18B_ENST00000335473.7_Missense_Mutation_p.Q2347R			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2347						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TCGAAAACCCAATTCAGTTCC	0.567													G|||	2135	0.426318	0.9107	0.2522	5008	,	,		18809	0.244		0.174	False		,,,				2504	0.3425				p.Q2347R		Atlas-SNP	.											MYO18B,NS,carcinoma,-1,1	MYO18B	322	1	0			c.A7040G						PASS	.	G	ARG/GLN	2970,896		1156,658,119	72.0	80.0	78.0		7040	3.8	0.0	22	dbSNP_98	78	1273,6995		103,1067,2964	yes	missense	MYO18B	NM_032608.5	43	1259,1725,3083	GG,GA,AA		15.3967,23.1764,34.9679	benign	2347/2568	26422980	4243,7891	1933	4134	6067	SO:0001583	missense	84700	exon43			AAACCCAATTCAG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7043A>G	22.37:g.26422980A>G	ENSP00000386096:p.Gln2348Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		761|761	0.3484432234432234|0.3484432234432234	424|424	0.8617886178861789|0.8617886178861789	84|84	0.23204419889502761|0.23204419889502761	135|135	0.23601398601398602|0.23601398601398602	118|118	0.15567282321899736|0.15567282321899736	G|G	0.003|0.003	-2.419485|-2.419485	0.00188|0.00188	0.768236|0.768236	0.153967|0.153967	ENSG00000133454|ENSG00000133454	ENST00000543971|ENST00000536101;ENST00000335473;ENST00000407587	.|D;D;D	.|0.84589	.|-1.86;-1.86;-1.87	4.89|4.89	3.78|3.78	0.43462|0.43462	.|.	.|0.274240	.|0.23176	.|N	.|0.051064	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;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B	.|0.01281	.|0.0;0.0;0.0;0.0;0.0	T|T	0.42699|0.42699	-0.9436|-0.9436	4|9	.|0.02654	.|T	.|1	.|.	4.7014|4.7014	0.12828|0.12828	0.2629:0.0:0.5664:0.1706|0.2629:0.0:0.5664:0.1706	rs2236005;rs56868966;rs2236005|rs2236005;rs56868966;rs2236005	.|1860;2349;2347;2348;2347	.|Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.|.;.;MY18B_HUMAN;.;.	D|R	297|2347;2347;2348	.|ENSP00000441229:Q2347R;ENSP00000334563:Q2347R;ENSP00000386096:Q2348R	.|ENSP00000334563:Q2347R	N|Q	+|+	1|2	0|0	MYO18B|MYO18B	24752980|24752980	0.121000|0.121000	0.22262|0.22262	0.005000|0.005000	0.12908|0.12908	0.094000|0.094000	0.18550|0.18550	2.406000|2.406000	0.44557|0.44557	1.056000|1.056000	0.40484|0.40484	-0.355000|-0.355000	0.07637|0.07637	AAT|CAA	A|0.618;G|0.382	0.382	strong		0.567	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
PSG6	5675	hgsc.bcm.edu	37	19	43414875	43414875	+	Missense_Mutation	SNP	A	A	C	rs59587483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43414875A>C	ENST00000292125.2	-	3	607	c.563T>G	c.(562-564)aTg>aGg	p.M188R	PSG6_ENST00000187910.2_Missense_Mutation_p.M188R|PSG6_ENST00000402603.4_Missense_Mutation_p.M188R	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	188	Ig-like C2-type 1.		M -> R (in dbSNP:rs59587483).		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				CCTGTGAGTCATAGGGAGGTT	0.488																																					p.M188R		Atlas-SNP	.											.	PSG6	89	.	0			c.T563G						PASS	.	G	ARG/MET,ARG/MET	490,3912		33,424,1744	229.0	231.0	230.0		563,563	-3.3	0.0	19	dbSNP_129	230	4,8596		0,4,4296	yes	missense,missense	PSG6	NM_001031850.2,NM_002782.3	91,91	33,428,6040	CC,CA,AA		0.0465,11.1313,3.7994	,	188/425,188/436	43414875	494,12508	2201	4300	6501	SO:0001583	missense	5675	exon3			TGAGTCATAGGGA		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.563T>G	19.37:g.43414875A>C	ENSP00000292125:p.Met188Arg	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	294	133	0.452381	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	37	CCDS12613.1	74	0.03388278388278388	67	0.13617886178861788	5	0.013812154696132596	2	0.0034965034965034965	0	0.0	N	0.033	-1.323644	0.01309	0.111313	4.65E-4	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.00705	5.81;5.81;5.81	1.64	-3.28	0.05033	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.30973	0.018;0.074;0.302	B;B;B	0.28709	0.048;0.056;0.093	T	0.42361	-0.9456	8	0.51188	T	0.08	.	2.1928	0.03904	0.4901:0.193:0.0:0.3168	rs59587483	188;188;188	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	R	188	ENSP00000187910:M188R;ENSP00000385736:M188R;ENSP00000292125:M188R	ENSP00000187910:M188R	M	-	2	0	PSG6	48106715	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.991000	0.00318	-0.913000	0.03832	-1.229000	0.01577	ATG	A|0.960;C|0.040	0.040	strong		0.488	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
RPP40	10799	hgsc.bcm.edu	37	6	4999011	4999011	+	Silent	SNP	A	A	G	rs12214401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4999011A>G	ENST00000380051.2	-	5	542	c.498T>C	c.(496-498)tcT>tcC	p.S166S	RPP40_ENST00000464646.1_Silent_p.S106S|RPP40_ENST00000319533.5_Silent_p.S143S	NM_006638.2	NP_006629.2	O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	166					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			NS(1)|breast(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	14	Ovarian(93;0.11)	all_hematologic(90;0.0895)				TGAAAGACCAAGATATTCTTT	0.269													A|||	268	0.0535144	0.118	0.0216	5008	,	,		15522	0.0		0.0318	False		,,,				2504	0.0665				p.S166S		Atlas-SNP	.											.	RPP40	36	.	0			c.T498C						PASS	.	A		435,3929		24,387,1771	30.0	32.0	31.0		498	3.3	1.0	6	dbSNP_120	31	298,8268		5,288,3990	no	coding-synonymous	RPP40	NM_006638.2		29,675,5761	GG,GA,AA		3.4789,9.9679,5.669		166/364	4999011	733,12197	2182	4283	6465	SO:0001819	synonymous_variant	10799	exon5			AGACCAAGATATT	U94317	CCDS34333.1, CCDS69040.1, CCDS75391.1	6p25.1	2012-05-21	2007-06-26	2004-03-19	ENSG00000124787	ENSG00000124787			20992	protein-coding gene	gene with protein product		606117	"""ribonuclease P1"", ""ribonuclease P 40kDa subunit"""	RNASEP1		9630247	Standard	NM_006638		Approved	bA428J1.3	uc003mwl.3	O75818	OTTHUMG00000014168	ENST00000380051.2:c.498T>C	6.37:g.4999011A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_006638	Q5VX97|Q8WVK8	Silent	SNP	ENST00000380051.2	37	CCDS34333.1																																																																																			A|0.944;G|0.056	0.056	strong		0.269	RPP40-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039733.2	NM_006638	
SH2D4A	63898	hgsc.bcm.edu	37	8	19221784	19221784	+	Missense_Mutation	SNP	A	A	G	rs35319139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:19221784A>G	ENST00000265807.3	+	7	1319	c.908A>G	c.(907-909)aAa>aGa	p.K303R	SH2D4A_ENST00000518040.1_Missense_Mutation_p.K258R|SH2D4A_ENST00000519207.1_Missense_Mutation_p.K303R	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	303					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)		TATCCTCAAAAACCTCTTAGG	0.473													A|||	113	0.0225639	0.0825	0.0043	5008	,	,		16415	0.0		0.001	False		,,,				2504	0.0				p.K303R		Atlas-SNP	.											.	SH2D4A	49	.	0			c.A908G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	338,4068	177.6+/-206.5	7,324,1872	52.0	50.0	51.0		908,773,908	2.1	0.0	8	dbSNP_126	51	0,8600		0,0,4300	yes	missense,missense,missense	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	26,26,26	7,324,6172	GG,GA,AA		0.0,7.6714,2.5988	benign,benign,benign	303/455,258/410,303/455	19221784	338,12668	2203	4300	6503	SO:0001583	missense	63898	exon7			CTCAAAAACCTCT	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.908A>G	8.37:g.19221784A>G	ENSP00000265807:p.Lys303Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	36	0.016483516483516484	34	0.06910569105691057	2	0.0055248618784530384	0	0.0	0	0.0	A	6.884	0.532610	0.13127	0.076714	0.0	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207	T;T;T	0.12672	2.66;2.66;2.66	5.75	2.12	0.27331	.	0.818608	0.11013	N	0.609227	T	0.00300	0.0009	N	0.04203	-0.255	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.45440	-0.9261	10	0.11794	T	0.64	.	4.2604	0.10739	0.6516:0.1741:0.1743:0.0	rs35319139	258;303	B4DDR1;Q9H788	.;SH24A_HUMAN	R	303;258;303	ENSP00000265807:K303R;ENSP00000429482:K258R;ENSP00000428684:K303R	ENSP00000265807:K303R	K	+	2	0	SH2D4A	19266064	0.000000	0.05858	0.000000	0.03702	0.779000	0.44077	0.275000	0.18698	0.443000	0.26582	0.460000	0.39030	AAA	A|0.973;G|0.027	0.027	strong		0.473	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
C2orf16	84226	hgsc.bcm.edu	37	2	27801493	27801493	+	Missense_Mutation	SNP	T	T	C	rs1919127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27801493T>C	ENST00000408964.2	+	1	2105	c.2054T>C	c.(2053-2055)gTg>gCg	p.V685A		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	685			V -> A (in dbSNP:rs1919127).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CTTCAGGCTGTGAAATCTACA	0.403													T|||	1539	0.307308	0.1732	0.5231	5008	,	,		21205	0.5079		0.2644	False		,,,				2504	0.1728				p.V685A		Atlas-SNP	.											.	C2orf16	357	.	0			c.T2054C						PASS	.	T	ALA/VAL	687,3047		60,567,1240	82.0	78.0	79.0		2054	1.8	0.0	2	dbSNP_92	79	2218,6008		299,1620,2194	yes	missense	C2orf16	NM_032266.3	64	359,2187,3434	CC,CT,TT		26.9633,18.3985,24.2893	possibly-damaging	685/1985	27801493	2905,9055	1867	4113	5980	SO:0001583	missense	84226	exon1			AGGCTGTGAAATC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.2054T>C	2.37:g.27801493T>C	ENSP00000386190:p.Val685Ala	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	150	75	0.5	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	772	0.3534798534798535	72	0.14634146341463414	171	0.4723756906077348	322	0.5629370629370629	207	0.27308707124010556	T	12.13	1.845535	0.32606	0.183985	0.269633	ENSG00000221843	ENST00000408964	T	0.07021	3.23	4.27	1.81	0.25067	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.33318	0.408	B	0.28553	0.091	T	0.27706	-1.0066	8	0.30078	T	0.28	.	3.4217	0.07396	0.2069:0.1085:0.0:0.6846	rs1919127;rs17006144;rs57887820;rs1919127	685	Q68DN1	CB016_HUMAN	A	685	ENSP00000386190:V685A	ENSP00000386190:V685A	V	+	2	0	C2orf16	27654997	0.001000	0.12720	0.003000	0.11579	0.752000	0.42762	0.405000	0.21015	0.391000	0.25143	0.459000	0.35465	GTG	T|0.680;C|0.320	0.320	strong		0.403	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
SLC47A2	146802	hgsc.bcm.edu	37	17	19607432	19607432	+	Silent	SNP	C	C	T	rs34169093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19607432C>T	ENST00000325411.5	-	11	1127	c.1077G>A	c.(1075-1077)gcG>gcA	p.A359A	SLC47A2_ENST00000350657.5_Silent_p.A337A|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	359					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	GCACAGTATCCGCAGCCCCCA	0.617													C|||	311	0.0621006	0.1831	0.0187	5008	,	,		18054	0.0		0.0268	False		,,,				2504	0.0297				p.A359A		Atlas-SNP	.											.	SLC47A2	61	.	0			c.G1077A						PASS	.	C	,	663,3743	278.7+/-274.4	51,561,1591	50.0	49.0	50.0		969,1077	-0.3	0.0	17	dbSNP_126	50	237,8363	94.7+/-156.6	2,233,4065	no	coding-synonymous,coding-synonymous	SLC47A2	NM_001099646.1,NM_152908.3	,	53,794,5656	TT,TC,CC		2.7558,15.0477,6.9199	,	323/567,359/603	19607432	900,12106	2203	4300	6503	SO:0001819	synonymous_variant	146802	exon11			AGTATCCGCAGCC	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.1077G>A	17.37:g.19607432C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Silent	SNP	ENST00000325411.5	37	CCDS11211.1																																																																																			C|0.935;T|0.065	0.065	strong		0.617	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
COL4A1	1282	hgsc.bcm.edu	37	13	110804809	110804809	+	Silent	SNP	G	G	A	rs650724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:110804809G>A	ENST00000375820.4	-	51	4921	c.4800C>T	c.(4798-4800)tcC>tcT	p.S1600S		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1600	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			AGGAGCCGGGGGACGCCAGGG	0.597													G|||	634	0.126597	0.2292	0.2277	5008	,	,		18525	0.0089		0.1074	False		,,,				2504	0.0573				p.S1600S		Atlas-SNP	.											.	COL4A1	372	.	0			c.C4800T						PASS	.	G		893,3513	338.6+/-305.4	91,711,1401	46.0	40.0	42.0		4800	-0.8	0.3	13	dbSNP_83	42	849,7751	189.7+/-236.4	35,779,3486	no	coding-synonymous	COL4A1	NM_001845.4		126,1490,4887	AA,AG,GG		9.8721,20.2678,13.3938		1600/1670	110804809	1742,11264	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon51			GCCGGGGGACGCC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.4800C>T	13.37:g.110804809G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			G|0.870;A|0.130	0.130	strong		0.597	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
ENAM	10117	hgsc.bcm.edu	37	4	71508869	71508869	+	Missense_Mutation	SNP	T	T	C	rs2609428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71508869T>C	ENST00000396073.3	+	9	2007	c.1726T>C	c.(1726-1728)Ttt>Ctt	p.F576L	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	576			F -> L (in dbSNP:rs2609428).		amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CTCTCCACCTTTTAAGGAAGA	0.443													T|||	197	0.0393371	0.1346	0.0144	5008	,	,		20189	0.0		0.0089	False		,,,				2504	0.0				p.F576L		Atlas-SNP	.											.	ENAM	140	.	0			c.T1726C						PASS	.	T	LEU/PHE	528,3878	231.7+/-245.5	27,474,1702	161.0	168.0	166.0		1726	3.5	0.9	4	dbSNP_100	166	29,8571	18.5+/-59.3	0,29,4271	yes	missense	ENAM	NM_031889.2	22	27,503,5973	CC,CT,TT		0.3372,11.9837,4.2826	benign	576/1143	71508869	557,12449	2203	4300	6503	SO:0001583	missense	10117	exon9			CCACCTTTTAAGG	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1726T>C	4.37:g.71508869T>C	ENSP00000379383:p.Phe576Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	137	62	0.452555	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	80	0.03663003663003663	72	0.14634146341463414	5	0.013812154696132596	0	0.0	3	0.00395778364116095	T	12.85	2.062285	0.36373	0.119837	0.003372	ENSG00000132464	ENST00000396073	T	0.40756	1.02	5.83	3.45	0.39498	.	0.216214	0.33438	N	0.004920	T	0.00109	0.0003	N	0.20574	0.59	0.41757	P	0.010307999999999984	B	0.23735	0.09	B	0.26969	0.075	T	0.14008	-1.0488	9	0.05620	T	0.96	-5.2885	6.2822	0.21013	0.0:0.1986:0.0:0.8014	rs2609428;rs2609428	576	Q9NRM1	ENAM_HUMAN	L	576	ENSP00000379383:F576L	ENSP00000379383:F576L	F	+	1	0	ENAM	71727733	0.757000	0.28394	0.948000	0.38648	0.909000	0.53808	0.881000	0.28173	1.034000	0.39945	0.533000	0.62120	TTT	T|0.952;C|0.048	0.048	strong		0.443	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889	
RHOT2	89941	hgsc.bcm.edu	37	16	722548	722548	+	Silent	SNP	A	A	G	rs1128550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	77	33	0.428571	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	
OAS2	4939	hgsc.bcm.edu	37	12	113425154	113425154	+	Intron	SNP	C	C	G	rs1293767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113425154C>G	ENST00000342315.4	+	2	662				RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000449768.2_Missense_Mutation_p.S163R|OAS2_ENST00000392583.2_Intron	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa						cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GCCAAAGAAGCGGGTGCCAGA	0.493													G|||	4274	0.853435	0.9894	0.804	5008	,	,		19034	0.9137		0.675	False		,,,				2504	0.8262				p.S163R	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.C489G						PASS	.	G	ARG/SER,,	4087,253		1924,239,7	29.0	34.0	32.0		489,,	0.0	0.0	12	dbSNP_87	32	5853,2715		2016,1821,447	yes	missense,intron,intron	OAS2	NM_001032731.1,NM_002535.2,NM_016817.2	110,,	3940,2060,454	GG,GC,CC		31.6877,5.8295,22.9935	,,	163/173,,	113425154	9940,2968	2170	4284	6454	SO:0001627	intron_variant	4939	exon2			AAGAAGCGGGTGC	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.448+41C>G	12.37:g.113425154C>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001032731	A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	37	CCDS31906.1	1810	0.8287545787545788	485	0.9857723577235772	285	0.787292817679558	519	0.9073426573426573	521	0.6873350923482849	G	0.013	-1.613994	0.00835	0.941705	0.683123	ENSG00000111335	ENST00000449768	T	0.11169	2.8	2.91	0.0253	0.14145	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.12344	-1.0551	6	.	.	.	.	3.3519	0.07155	0.3816:0.2063:0.4121:0.0	rs1293767;rs17835904;rs58147375	163	Q6PJ33	.	R	163	ENSP00000411763:S163R	.	S	+	3	2	OAS2	111909537	0.007000	0.16637	0.000000	0.03702	0.001000	0.01503	0.257000	0.18369	-0.255000	0.09486	-0.729000	0.03580	AGC	C|0.212;G|0.788	0.788	strong		0.493	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1		
KIF4A	24137	hgsc.bcm.edu	37	X	69561780	69561780	+	Splice_Site	SNP	T	T	G	rs1199457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:69561780T>G	ENST00000374403.3	+	11	1347	c.1265T>G	c.(1264-1266)tTg>tGg	p.L422W	KIF4A_ENST00000374388.3_Splice_Site_p.L422W	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	422			L -> W (in dbSNP:rs1199457). {ECO:0000269|PubMed:10978527, ECO:0000269|PubMed:15489334}.		anterograde axon cargo transport (GO:0008089)|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)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						AGGATCATTTTGGTAAGCCCC	0.403													T|||	451	0.11947	0.2799	0.0375	3775	,	,		12134	0.0		0.0398	False		,,,				2504	0.0153				p.L422W		Atlas-SNP	.											.	KIF4A	118	.	0			c.T1265G						PASS	.	T	TRP/LEU	1333,2502		212,708,201,712,370	95.0	95.0	95.0		1265	4.8	1.0	X	dbSNP_87	95	323,6405		3,227,90,2198,1782	yes	missense-near-splice	KIF4A	NM_012310.4	61	215,935,291,2910,2152	GG,GT,G,TT,T		4.8008,34.7588,15.6774	possibly-damaging	422/1233	69561780	1656,8907	2203	4300	6503	SO:0001630	splice_region_variant	24137	exon11			TCATTTTGGTAAG	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"""Kinesins"""	13339	protein-coding gene	gene with protein product	"""chromokinesin"""	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1266+1T>G	X.37:g.69561780T>G		Somatic	344	0	0		WXS	Illumina HiSeq	Phase_I	331	175	0.528701	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Missense_Mutation	SNP	ENST00000374403.3	37	CCDS14401.1	160	0.09644364074743822	73	0.17464114832535885	13	0.03672316384180791	0	0.0	20	0.0273224043715847	T	18.31	3.595877	0.66332	0.347588	0.048008	ENSG00000090889	ENST00000374388;ENST00000374403	T;T	0.52983	0.64;0.64	4.77	4.77	0.60923	.	0.151044	0.31167	N	0.008127	T	0.00012	0.0000	L	0.27053	0.805	0.20307	P	0.9999110836	D;D	0.67145	0.995;0.996	P;D	0.63703	0.844;0.917	T	0.31861	-0.9928	9	0.72032	D	0.01	.	12.2319	0.54492	0.0:0.0:0.0:1.0	rs1199457;rs52827837;rs1199457	422;422	O95239;O95239-2	KIF4A_HUMAN;.	W	422	ENSP00000363509:L422W;ENSP00000363524:L422W	ENSP00000363509:L422W	L	+	2	0	KIF4A	69478505	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	3.976000	0.56867	1.765000	0.52091	0.345000	0.21793	TTG	T|0.841;0|0.015	.	strong		0.403	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	Missense_Mutation
GPR179	440435	hgsc.bcm.edu	37	17	36485753	36485753	+	Silent	SNP	G	G	C	rs35803744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36485753G>C	ENST00000342292.4	-	11	3719	c.3699C>G	c.(3697-3699)ctC>ctG	p.L1233L	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1233					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CAGCGCTGCCGAGGGACTGGA	0.572													C|||	1523	0.304113	0.8026	0.1628	5008	,	,		17462	0.125		0.1561	False		,,,				2504	0.0675				p.L1233L		Atlas-SNP	.											.	GPR179	170	.	0			c.C3699G						PASS	.	C		2595,1261		896,803,229	82.0	91.0	88.0		3699	-0.3	0.1	17	dbSNP_126	88	1026,7264		67,892,3186	no	coding-synonymous	GPR179	NM_001004334.2		963,1695,3415	CC,CG,GG		12.3764,32.7023,29.8123		1233/2368	36485753	3621,8525	1928	4145	6073	SO:0001819	synonymous_variant	440435	exon11			GCTGCCGAGGGAC		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.3699C>G	17.37:g.36485753G>C		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	160	159	0.99375	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			G|0.772;C|0.228	0.228	strong		0.572	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
SRRT	51593	hgsc.bcm.edu	37	7	100486110	100486110	+	Silent	SNP	C	C	T	rs11171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100486110C>T	ENST00000347433.4	+	20	2729	c.2571C>T	c.(2569-2571)gaC>gaT	p.D857D	SRRT_ENST00000432932.1_Silent_p.D852D|SRRT_ENST00000457580.2_Silent_p.D853D|SRRT_ENST00000388793.4_Silent_p.D856D			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	857					cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						TTCGTGGAGACCCAAGGGCCA	0.557													C|||	425	0.0848642	0.2126	0.0663	5008	,	,		18638	0.002		0.0537	False		,,,				2504	0.0429				p.D857D		Atlas-SNP	.											.	SRRT	108	.	0			c.C2571T						PASS	.	C	,,,	778,3628	314.1+/-293.5	67,644,1492	111.0	102.0	105.0		2568,2559,2556,2571	5.1	1.0	7	dbSNP_52	105	416,8184	129.2+/-187.3	14,388,3898	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SRRT	NM_001128852.1,NM_001128853.1,NM_001128854.1,NM_015908.5	,,,	81,1032,5390	TT,TC,CC		4.8372,17.6577,9.1804	,,,	856/876,853/873,852/872,857/877	100486110	1194,11812	2203	4300	6503	SO:0001819	synonymous_variant	51593	exon20			TGGAGACCCAAGG		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"""arsenite resistance protein"""	614469	"""serrate RNA effector molecule homolog (Arabidopsis)"""			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2571C>T	7.37:g.100486110C>T		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	244	125	0.512295	NM_015908	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Silent	SNP	ENST00000347433.4	37	CCDS34709.1	187	0.08562271062271062	112	0.22764227642276422	29	0.08011049723756906	1	0.0017482517482517483	45	0.059366754617414245	C	14.74	2.625608	0.46840	0.176577	0.048372	ENSG00000087087	ENST00000342198;ENST00000445337	.	.	.	5.09	5.09	0.68999	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.00408	-1.1758	4	0.87932	D	0	.	16.0149	0.80430	0.0:1.0:0.0:0.0	rs11171;rs1053804;rs1132992;rs3167782;rs3194359;rs11541869;rs17162539;rs17884480;rs57867297;rs11171	.	.	.	I	221;92	.	ENSP00000344670:T221I	T	+	2	0	SRRT	100324046	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	0.654000	0.24918	2.363000	0.80096	0.478000	0.44815	ACC	C|0.905;T|0.095	0.095	strong		0.557	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908	
NSD1	64324	hgsc.bcm.edu	37	5	176636882	176636882	+	Silent	SNP	C	C	T	rs1363405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176636882C>T	ENST00000439151.2	+	5	1527	c.1482C>T	c.(1480-1482)tgC>tgT	p.C494C	NSD1_ENST00000347982.4_Silent_p.C225C|NSD1_ENST00000361032.4_Silent_p.C391C|NSD1_ENST00000354179.4_Silent_p.C225C	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	494					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)		AAAAGCCTTGCGCTAAATCTC	0.418			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			T|||	2344	0.468051	0.7693	0.3343	5008	,	,		17503	0.5298		0.1988	False		,,,				2504	0.3691				p.C494C		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.C1482T						PASS	.	T	,	2971,1435	464.3+/-353.8	1012,947,244	76.0	77.0	77.0		1482,675	4.3	1.0	5	dbSNP_88	77	1635,6965	741.5+/-407.2	157,1321,2822	no	coding-synonymous,coding-synonymous	NSD1	NM_022455.4,NM_172349.2	,	1169,2268,3066	TT,TC,CC		19.0116,32.5692,35.4144	,	494/2697,225/2428	176636882	4606,8400	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	GCCTTGCGCTAAA	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.1482C>T	5.37:g.176636882C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	98	96	0.979592	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																			C|0.607;T|0.393	0.393	strong		0.418	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
MAML3	55534	hgsc.bcm.edu	37	4	140811114	140811114	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:140811114C>T	ENST00000509479.2	-	2	2332	c.1476G>A	c.(1474-1476)caG>caA	p.Q492Q	MAML3_ENST00000398940.1_Silent_p.Q31Q|MAML3_ENST00000327122.5_Silent_p.Q336Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgtt	0.542																																					p.Q492Q		Atlas-SNP	.											MAML3_ENST00000509479,colon,carcinoma,0,4	MAML3	192	4	0			c.G1476A						scavenged	.						15.0	19.0	18.0					4																	140811114		2185	4284	6469	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1476G>A	4.37:g.140811114C>T		Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	98	6	0.0612245	NM_018717		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																			.	.	none		0.542	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
HOMEZ	57594	hgsc.bcm.edu	37	14	23744826	23744826	+	Missense_Mutation	SNP	T	T	A	rs35076736|rs76331664|rs67447855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23744826T>A	ENST00000357460.5	-	2	1775	c.1611A>T	c.(1609-1611)gaA>gaT	p.E537D	HOMEZ_ENST00000561013.1_Missense_Mutation_p.E539D|HOMEZ_ENST00000431326.2_Missense_Mutation_p.E539D	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	537	Poly-Asp.				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)		catcatcatcttcctcctcct	0.483																																					p.E537D		Atlas-SNP	.											.	HOMEZ	80	.	0			c.A1611T						PASS	.						39.0	39.0	39.0					14																	23744826		2192	4262	6454	SO:0001583	missense	57594	exon2			ATCATCTTCCTCC	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.1611A>T	14.37:g.23744826T>A	ENSP00000350049:p.Glu537Asp	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	135	15	0.111111	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Missense_Mutation	SNP	ENST00000357460.5	37	CCDS45085.1	.	.	.	.	.	.	.	.	.	.	T	0.034	-1.315721	0.01331	.	.	ENSG00000215271	ENST00000357460;ENST00000431326	T;T	0.63744	-0.06;-0.06	.	.	.	Armadillo-like helical (1);	.	.	.	.	T	0.45478	0.1344	N	0.08118	0	0.09310	N	1	B;B	0.32829	0.386;0.267	B;B	0.42462	0.388;0.217	T	0.47812	-0.9088	7	0.87932	D	0	.	.	.	.	.	539;537	F8WCA3;Q8IX15	.;HOMEZ_HUMAN	D	537;539	ENSP00000350049:E537D;ENSP00000406579:E539D	ENSP00000350049:E537D	E	-	3	2	HOMEZ	22814666	0.017000	0.18338	0.112000	0.21494	0.037000	0.13140	-2.594000	0.00896	0.319000	0.23209	0.314000	0.21332	GAA	.	.	weak		0.483	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
OR10G4	390264	hgsc.bcm.edu	37	11	123887164	123887164	+	Missense_Mutation	SNP	A	A	C	rs4936881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123887164A>C	ENST00000320891.4	+	1	883	c.883A>C	c.(883-885)Aag>Cag	p.K295Q		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	295			K -> Q (in dbSNP:rs4936881).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K295Q(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CAAGGAGGTGAAGAAAGCTGT	0.413													a|||	2142	0.427716	0.469	0.5029	5008	,	,		20676	0.3591		0.4404	False		,,,				2504	0.3763				p.K295Q		Atlas-SNP	.											OR10G4,NS,carcinoma,-2,2	OR10G4	77	2	1	Substitution - Missense(1)	stomach(1)	c.A883C						PASS	.	A	GLN/LYS	2107,2295	574.0+/-383.7	510,1087,604	78.0	73.0	75.0		883	3.4	0.9	11	dbSNP_111	75	3918,4678	545.6+/-384.8	872,2174,1252	yes	missense	OR10G4	NM_001004462.1	53	1382,3261,1856	CC,CA,AA		45.5793,47.8646,46.3533	benign	295/312	123887164	6025,6973	2201	4298	6499	SO:0001583	missense	390264	exon1			GAGGTGAAGAAAG	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.883A>C	11.37:g.123887164A>C	ENSP00000325076:p.Lys295Gln	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	157	154	0.980892	NM_001004462	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	977	0.44734432234432236	223	0.4532520325203252	192	0.5303867403314917	231	0.40384615384615385	331	0.4366754617414248	a	13.05	2.121331	0.37436	0.478646	0.455793	ENSG00000254737	ENST00000320891	T	0.39406	1.08	3.38	3.38	0.38709	.	0.162599	0.28772	N	0.014191	T	0.00012	0.0000	L	0.42632	1.34	0.41583	P	0.011248000000000036	B	0.30021	0.265	B	0.31337	0.128	T	0.48317	-0.9046	9	0.72032	D	0.01	.	11.9412	0.52903	1.0:0.0:0.0:0.0	rs4936881;rs4936881	295	Q8NGN3	O10G4_HUMAN	Q	295	ENSP00000325076:K295Q	ENSP00000325076:K295Q	K	+	1	0	OR10G4	123392374	0.772000	0.28567	0.943000	0.38184	0.941000	0.58515	3.532000	0.53553	1.547000	0.49401	0.473000	0.43528	AAG	A|0.539;C|0.461	0.461	strong		0.413	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
PROSER2	254427	hgsc.bcm.edu	37	10	11912381	11912381	+	Silent	SNP	G	G	A	rs191542752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:11912381G>A	ENST00000277570.5	+	4	1438	c.1284G>A	c.(1282-1284)ctG>ctA	p.L428L	PROSER2_ENST00000379200.1_Silent_p.L232L|PROSER2-AS1_ENST00000445498.1_RNA|PROSER2-AS1_ENST00000453242.1_RNA	NM_153256.3	NP_694988.3	Q86WR7	PRSR2_HUMAN	proline and serine rich 2	428																	TGCGGAAGCTGGGGCTGCTCA	0.726													G|||	45	0.00898562	0.031	0.0058	5008	,	,		11702	0.0		0.0	False		,,,				2504	0.0				p.L428L		Atlas-SNP	.											.	.	.	.	0			c.G1284A						PASS	.	G		34,2126		0,34,1046	1.0	1.0	1.0		1284	-10.4	0.7	10		1	1,4447		0,1,2223	no	coding-synonymous	C10orf47	NM_153256.3		0,35,3269	AA,AG,GG		0.0225,1.5741,0.5297		428/436	11912381	35,6573	1080	2224	3304	SO:0001819	synonymous_variant	254427	exon4			GAAGCTGGGGCTG	BC017269	CCDS7085.1	10p14	2014-02-19	2014-02-19	2012-12-05	ENSG00000148426	ENSG00000148426			23728	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 47"", ""proline and serine-rich protein 2"""	C10orf47		12477932	Standard	NM_153256		Approved	MGC35403	uc001ikx.3	Q86WR7	OTTHUMG00000017673	ENST00000277570.5:c.1284G>A	10.37:g.11912381G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_153256	D3DRR8|Q5W0J9|Q5W0K0|Q5W0K1|Q5W0K2|Q6PJC8|Q8N317	Silent	SNP	ENST00000277570.5	37	CCDS7085.1																																																																																			G|0.993;A|0.007	0.007	strong		0.726	PROSER2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090189.2	NM_153256	
SLC12A6	9990	hgsc.bcm.edu	37	15	34551082	34551082	+	Silent	SNP	G	G	A	rs7164902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34551082G>A	ENST00000354181.3	-	5	967	c.475C>T	c.(475-477)Ctg>Ttg	p.L159L	SLC12A6_ENST00000451844.2_Silent_p.L20L|SLC12A6_ENST00000558589.1_Silent_p.L150L|SLC12A6_ENST00000397707.2_Silent_p.L144L|SLC12A6_ENST00000558667.1_Silent_p.L159L|SLC12A6_ENST00000560164.1_Silent_p.L20L|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000458406.2_Silent_p.L100L|SLC12A6_ENST00000560611.1_Silent_p.L159L|SLC12A6_ENST00000290209.5_Silent_p.L108L|SLC12A6_ENST00000397702.2_Silent_p.L100L			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	159					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	CCTTGAGTCAGATTAGTGTAA	0.448													G|||	1386	0.276757	0.1982	0.2161	5008	,	,		18454	0.3542		0.2406	False		,,,				2504	0.3834				p.L159L		Atlas-SNP	.											.	SLC12A6	205	.	0			c.C475T						PASS	.	G	,,,,,	951,3451	361.4+/-315.7	105,741,1355	231.0	217.0	222.0		298,298,448,430,322,475	2.8	1.0	15	dbSNP_116	222	2092,6504	361.6+/-332.4	259,1574,2465	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC12A6	NM_001042494.1,NM_001042495.1,NM_001042496.1,NM_001042497.1,NM_005135.2,NM_133647.1	,,,,,	364,2315,3820	AA,AG,GG		24.3369,21.6038,23.4113	,,,,,	100/1092,100/1092,150/1142,144/1136,108/1100,159/1151	34551082	3043,9955	2201	4298	6499	SO:0001819	synonymous_variant	9990	exon4			GAGTCAGATTAGT	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.475C>T	15.37:g.34551082G>A		Somatic	400	0	0		WXS	Illumina HiSeq	Phase_I	334	333	0.997006	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Silent	SNP	ENST00000354181.3	37	CCDS58352.1																																																																																			G|0.751;A|0.249	0.249	strong		0.448	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
SAG	6295	hgsc.bcm.edu	37	2	234235820	234235820	+	Silent	SNP	C	C	T	rs2304773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234235820C>T	ENST00000409110.1	+	7	719	c.489C>T	c.(487-489)gcC>gcT	p.A163A	SAG_ENST00000449594.2_Silent_p.A29A	NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	163					cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		GCACCGATGCCGAAGAGGACA	0.567													C|||	532	0.10623	0.2171	0.0793	5008	,	,		19748	0.0377		0.1004	False		,,,				2504	0.0521				p.A163A		Atlas-SNP	.											.	SAG	77	.	0			c.C489T						PASS	.	C		745,3379		70,605,1387	128.0	129.0	129.0		489	-7.9	0.0	2	dbSNP_100	129	874,7518		42,790,3364	no	coding-synonymous	SAG	NM_000541.4		112,1395,4751	TT,TC,CC		10.4147,18.065,12.9354		163/406	234235820	1619,10897	2062	4196	6258	SO:0001819	synonymous_variant	6295	exon7			CGATGCCGAAGAG		CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.489C>T	2.37:g.234235820C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_000541	A0FDN6|Q53SV3|Q99858	Silent	SNP	ENST00000409110.1	37	CCDS46545.1																																																																																			C|0.893;T|0.107	0.107	strong		0.567	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1	NM_000541	
AQP7	364	hgsc.bcm.edu	37	9	33385134	33385134	+	3'UTR	SNP	C	C	T	rs61073250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:33385134C>T	ENST00000537089.1	-	0	1298				AQP7_ENST00000377425.4_3'UTR			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)		TTGGGCAATACGGTTATCCCG	0.562													c|||	234	0.0467252	0.1732	0.0072	5008	,	,		18995	0.0		0.0	False		,,,				2504	0.0				p.V300I		Atlas-SNP	.											.	AQP7	58	.	0			c.G898A						PASS	.	C	ILE/VAL	519,3887	236.1+/-248.4	25,469,1709	142.0	140.0	141.0		898	0.9	0.0	9	dbSNP_129	141	8,8592	6.4+/-24.3	0,8,4292	no	missense	AQP7	NM_001170.1	29	25,477,6001	TT,TC,CC		0.093,11.7794,4.052	benign	300/343	33385134	527,12479	2203	4300	6503	SO:0001624	3_prime_UTR_variant	364	exon8			GCAATACGGTTAT	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.*482G>A	9.37:g.33385134C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	150	87	0.58	NM_001170	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		76	0.0347985347985348	73	0.1483739837398374	3	0.008287292817679558	0	0.0	0	0.0	c	10.83	1.461549	0.26248	0.117794	9.3E-4	ENSG00000165269	ENST00000379507;ENST00000297988	D;D	0.86164	-2.07;-2.08	3.75	0.85	0.18980	.	.	.	.	.	T	0.01124	0.0037	L	0.32530	0.975	0.09310	N	1	B	0.26602	0.154	B	0.17098	0.017	T	0.04128	-1.0975	9	0.39692	T	0.17	0.5079	3.07	0.06227	0.2121:0.5537:0.0:0.2342	rs61073250	300	O14520	AQP7_HUMAN	I	299;300	ENSP00000368821:V299I;ENSP00000297988:V300I	ENSP00000297988:V300I	V	-	1	0	AQP7	33375134	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.123000	0.10611	-0.001000	0.14495	-0.354000	0.07668	GTA	C|0.964;T|0.036	0.036	strong		0.562	AQP7-202	KNOWN	basic	protein_coding	protein_coding		NM_001170	
BCAR3	8412	hgsc.bcm.edu	37	1	94049576	94049576	+	Splice_Site	SNP	A	A	G	rs78645541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:94049576A>G	ENST00000370244.1	-	8	1320	c.1032T>C	c.(1030-1032)atT>atC	p.I344I	BCAR3_ENST00000466632.1_5'UTR|BCAR3_ENST00000370247.3_Splice_Site_p.I253I|BCAR3_ENST00000370243.1_Splice_Site_p.I344I|BCAR3_ENST00000260502.6_Splice_Site_p.I344I|BCAR3_ENST00000539242.1_Splice_Site_p.I20I	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	344					lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		GAAACATACCAATCGGCAGGT	0.522													A|||	34	0.00678914	0.025	0.0014	5008	,	,		18298	0.0		0.0	False		,,,				2504	0.0				p.I344I		Atlas-SNP	.											.	BCAR3	62	.	0			c.T1032C						PASS	.	A		122,4284	91.6+/-130.3	1,120,2082	95.0	93.0	93.0		1032	0.0	0.9	1	dbSNP_131	93	0,8600		0,0,4300	yes	coding-synonymous-near-splice	BCAR3	NM_003567.2		1,120,6382	GG,GA,AA		0.0,2.769,0.938		344/826	94049576	122,12884	2203	4300	6503	SO:0001630	splice_region_variant	8412	exon6			CATACCAATCGGC	U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"""SH2 domain containing"""	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.1033+1T>C	1.37:g.94049576A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	146	81	0.554795	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Silent	SNP	ENST00000370244.1	37	CCDS745.1																																																																																			A|0.992;G|0.008	0.008	strong		0.522	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1		Silent
EXPH5	23086	hgsc.bcm.edu	37	11	108384207	108384207	+	Missense_Mutation	SNP	C	C	T	rs2846412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108384207C>T	ENST00000265843.4	-	6	2137	c.2027G>A	c.(2026-2028)aGc>aAc	p.S676N	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000443411.1_Missense_Mutation_p.S488N|EXPH5_ENST00000428840.1_Missense_Mutation_p.S600N|EXPH5_ENST00000525344.1_Missense_Mutation_p.S669N	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	676			S -> N (in dbSNP:rs2846412). {ECO:0000269|PubMed:12062444, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TGAATTGCTGCTGGTCACAGT	0.413													T|||	3211	0.641174	0.6982	0.5533	5008	,	,		20113	0.8542		0.4384	False		,,,				2504	0.6155				p.S676N		Atlas-SNP	.											.	EXPH5	193	.	0			c.G2027A						PASS	.	T	ASN/SER	2893,1509	479.2+/-358.4	976,941,284	119.0	114.0	116.0		2027	1.1	0.0	11	dbSNP_100	116	3627,4969	624.4+/-397.6	786,2055,1457	yes	missense	EXPH5	NM_015065.2	46	1762,2996,1741	TT,TC,CC		42.194,34.2799,49.8384	benign	676/1990	108384207	6520,6478	2201	4298	6499	SO:0001583	missense	23086	exon6			TTGCTGCTGGTCA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.2027G>A	11.37:g.108384207C>T	ENSP00000265843:p.Ser676Asn	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	1351	0.6185897435897436	333	0.676829268292683	176	0.4861878453038674	506	0.8846153846153846	336	0.44327176781002636	T	0.006	-2.111572	0.00353	0.657201	0.42194	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.03831	4.38;4.3;4.15;4.38;4.23;3.79	6.03	1.14	0.20703	.	0.625758	0.16479	N	0.212613	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	0.22661	-1.0210	9	0.02654	T	1	-0.745	9.5688	0.39416	0.0:0.3732:0.0:0.6268	rs2846412;rs3824986;rs52806719;rs59043239;rs2846412	676	Q8NEV8	EXPH5_HUMAN	N	676;600;488;669;520;600;488	ENSP00000265843:S676N;ENSP00000391966:S600N;ENSP00000411390:S488N;ENSP00000432546:S669N;ENSP00000432683:S600N;ENSP00000446434:S488N	ENSP00000265843:S676N	S	-	2	0	EXPH5	107889417	0.006000	0.16342	0.000000	0.03702	0.004000	0.04260	0.673000	0.25203	-0.041000	0.13558	-1.396000	0.01147	AGC	C|0.440;T|0.560	0.560	strong		0.413	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
FMO2	2327	hgsc.bcm.edu	37	1	171162583	171162583	+	Missense_Mutation	SNP	T	T	C	rs2020860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171162583T>C	ENST00000209929.7	+	3	400	c.242T>C	c.(241-243)tTc>tCc	p.F81S	FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Missense_Mutation_p.F81S			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	81					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TTTCCAAACTTCCTGCATAAT	0.353													T|||	516	0.103035	0.298	0.0476	5008	,	,		16096	0.002		0.0447	False		,,,				2504	0.0429				p.F81S		Atlas-SNP	.											FMO2,colon,carcinoma,+1,1	FMO2	66	1	0			c.T242C						PASS	.	T	SER/PHE	1075,3331	373.0+/-320.6	151,773,1279	75.0	76.0	75.0		242	5.4	1.0	1	dbSNP_98	75	409,8191	123.1+/-182.0	13,383,3904	yes	missense	FMO2	NM_001460.2	155	164,1156,5183	CC,CT,TT		4.7558,24.3985,11.4101	probably-damaging	81/472	171162583	1484,11522	2203	4300	6503	SO:0001583	missense	2327	exon3			CAAACTTCCTGCA	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.242T>C	1.37:g.171162583T>C	ENSP00000209929:p.Phe81Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	205	0.09386446886446886	156	0.3170731707317073	18	0.049723756906077346	0	0.0	31	0.040897097625329816	T	22.7	4.324261	0.81580	0.243985	0.047558	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.60920	0.15;0.15	5.44	5.44	0.79542	.	0.172296	0.53938	D	0.000041	T	0.81754	0.4889	H	0.97265	3.97	0.23834	P	0.99671674	D	0.76494	0.999	D	0.78314	0.991	D	0.88765	0.3260	9	0.87932	D	0	-14.2724	15.165	0.72818	0.0:0.0:0.0:1.0	rs2020860;rs2266704;rs56518508;rs57046818;rs2020860	81	Q99518	FMO2_HUMAN	S	81	ENSP00000209929:F81S;ENSP00000405905:F81S	ENSP00000209929:F81S	F	+	2	0	FMO2	169429207	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.960000	0.49161	2.062000	0.61559	0.533000	0.62120	TTC	T|0.895;C|0.105	0.105	strong		0.353	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
XPR1	9213	hgsc.bcm.edu	37	1	180804033	180804033	+	Silent	SNP	C	C	T	rs61742073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:180804033C>T	ENST00000367590.4	+	10	1356	c.1158C>T	c.(1156-1158)ttC>ttT	p.F386F	XPR1_ENST00000367589.3_Silent_p.F386F	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	386					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						CAGCCCCCTTCCATAAGGTAG	0.403													C|||	258	0.0515176	0.1808	0.0259	5008	,	,		19539	0.0		0.001	False		,,,				2504	0.0				p.F386F		Atlas-SNP	.											.	XPR1	76	.	0			c.C1158T						PASS	.	C	,	636,3770	267.1+/-267.6	45,546,1612	64.0	65.0	64.0		1158,1158	4.3	1.0	1	dbSNP_129	64	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	XPR1	NM_001135669.1,NM_004736.3	,	45,550,5908	TT,TC,CC		0.0465,14.4349,4.9208	,	386/632,386/697	180804033	640,12366	2203	4300	6503	SO:0001819	synonymous_variant	9213	exon10			CCCCTTCCATAAG	AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.1158C>T	1.37:g.180804033C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	37	CCDS1340.1																																																																																			C|0.949;T|0.051	0.051	strong		0.403	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736	
GPR75-ASB3	100302652	hgsc.bcm.edu	37	2	53955850	53955850	+	Splice_Site	SNP	C	C	T	rs17521008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:53955850C>T	ENST00000263634.3	-	5	737	c.603G>A	c.(601-603)tcG>tcA	p.S201S	GPR75-ASB3_ENST00000352846.3_Splice_Site_p.S239S|GPR75-ASB3_ENST00000482829.1_5'UTR|GPR75-ASB3_ENST00000406687.1_Splice_Site_p.S128S|GPR75-ASB3_ENST00000394717.2_Splice_Site_p.S128S|ASB3_ENST00000498475.2_5'UTR|ASB3_ENST00000406625.2_Splice_Site_p.S236S	NM_016115.4	NP_057199.1			GPR75-ASB3 readthrough									p.S201S(1)									TAATCTTACCCGATGAAATAA	0.368													C|||	860	0.171725	0.1074	0.2046	5008	,	,		18067	0.1637		0.1799	False		,,,				2504	0.2352				p.S239S		Atlas-SNP	.											ASB3,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.G717A						PASS	.	C	,,,	518,3888	236.8+/-248.8	36,446,1721	85.0	84.0	84.0		717,384,603,384	-11.4	0.0	2	dbSNP_123	84	1641,6959	302.0+/-305.7	161,1319,2820	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ASB3,GPR75-ASB3	NM_001164165.1,NM_001201965.1,NM_016115.4,NM_145863.2	,,,	197,1765,4541	TT,TC,CC		19.0814,11.7567,16.6	,,,	239/557,128/446,201/519,128/446	53955850	2159,10847	2203	4300	6503	SO:0001630	splice_region_variant	100302652	exon5			CTTACCCGATGAA		CCDS54361.1	2p16	2013-01-23			ENSG00000115239	ENSG00000115239			40043	other	readthrough							Standard	NM_001164165		Approved				OTTHUMG00000129279	ENST00000263634.3:c.604+1G>A	2.37:g.53955850C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_001164165		Silent	SNP	ENST00000263634.3	37	CCDS1846.1	348	0.15934065934065933	65	0.13211382113821138	74	0.20441988950276244	85	0.1486013986013986	124	0.16358839050131926	C	0.049	-1.254936	0.01457	0.117567	0.190814	ENSG00000115239	ENST00000406053	.	.	.	5.72	-11.4	0.00090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.03306	-1.1050	3	.	.	.	.	2.567	0.04785	0.2366:0.0914:0.2099:0.4621	rs17521008	.	.	.	R	194	.	.	G	-	1	0	ASB3	53809354	0.000000	0.05858	0.003000	0.11579	0.836000	0.47400	-4.365000	0.00245	-4.807000	0.00031	-2.943000	0.00086	GGG	C|0.834;T|0.166	0.166	strong		0.368	GPR75-ASB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251402.3		Silent
RBP1	5947	hgsc.bcm.edu	37	3	139257727	139257727	+	Missense_Mutation	SNP	T	T	C	rs34674353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:139257727T>C	ENST00000483943.2	-	2	334	c.334A>G	c.(334-336)Atg>Gtg	p.M112V	RP11-319G6.1_ENST00000515247.1_RNA|RBP1_ENST00000232219.2_Missense_Mutation_p.M112V|RBP1_ENST00000492918.1_Missense_Mutation_p.M112V|RP11-319G6.1_ENST00000381790.3_RNA	NM_001130993.1	NP_001124465.1	P09455	RET1_HUMAN	retinol binding protein 1, cellular	50					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	5					Acitretin(DB00459)|Vitamin A(DB00162)	CGGATGATCATATGGTCACCG	0.532													T|||	48	0.00958466	0.034	0.0043	5008	,	,		19972	0.0		0.0	False		,,,				2504	0.0				p.M112V		Atlas-SNP	.											.	RBP1	39	.	0			c.A334G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	98,4308	79.3+/-117.8	0,98,2105	242.0	194.0	210.0		334,334,334	5.3	1.0	3	dbSNP_126	210	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	RBP1	NM_002899.3,NM_001130993.1,NM_001130992.1	21,21,21	0,100,6403	CC,CT,TT		0.0233,2.2242,0.7689	benign,benign,benign	112/198,112/154,112/158	139257727	100,12906	2203	4300	6503	SO:0001583	missense	5947	exon2			TGATCATATGGTC		CCDS3110.2, CCDS46925.1, CCDS46926.1	3q21-q23	2013-03-01	2001-11-28		ENSG00000114115	ENSG00000114115		"""Fatty acid binding protein family"""	9919	protein-coding gene	gene with protein product		180260	"""retinol-binding protein 1, cellular"""			1654334, 9858824	Standard	NM_002899		Approved	CRABP-I, CRBP1, CRBP, RBPC, CRBPI	uc003eti.2	P09455	OTTHUMG00000155751	ENST00000483943.2:c.334A>G	3.37:g.139257727T>C	ENSP00000424813:p.Met112Val	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	274	141	0.514599	NM_002899	A8K2Q0|B7Z7A0|E7EWV0|F2Z2F2|Q6FGX8	Missense_Mutation	SNP	ENST00000483943.2	37	CCDS46925.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	T	14.91	2.676656	0.47886	0.022242	2.33E-4	ENSG00000114115	ENST00000232219;ENST00000483943;ENST00000492918	T;T;T	0.21031	2.03;2.03;2.03	5.28	5.28	0.74379	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.057277	0.64402	D	0.000002	T	0.12050	0.0293	L	0.33485	1.01	0.45979	D	0.998796	P;P;B	0.37548	0.599;0.543;0.04	P;B;B	0.45167	0.472;0.243;0.072	T	0.02484	-1.1152	10	0.28530	T	0.3	.	14.3982	0.67025	0.0:0.0:0.0:1.0	rs34674353	112;112;50	F2Z2F2;E7EWV0;P09455	.;.;RET1_HUMAN	V	112	ENSP00000232219:M112V;ENSP00000424813:M112V;ENSP00000429166:M112V	ENSP00000232219:M112V	M	-	1	0	RBP1	140740417	1.000000	0.71417	0.999000	0.59377	0.834000	0.47266	4.774000	0.62339	1.988000	0.58038	0.455000	0.32223	ATG	T|0.992;C|0.008	0.008	strong		0.532	RBP1-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341497.2	NM_002899	
ADCY3	109	hgsc.bcm.edu	37	2	25064193	25064193	+	Silent	SNP	G	G	A	rs2241759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:25064193G>A	ENST00000260600.5	-	5	1982	c.1131C>T	c.(1129-1131)ccC>ccT	p.P377P	ADCY3_ENST00000405392.1_5'UTR	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	377					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					CCCGGTAGTCGGGCAAGCCGC	0.632													A|||	2557	0.510583	0.3555	0.4438	5008	,	,		17167	0.7421		0.4791	False		,,,				2504	0.5613				p.P377P		Atlas-SNP	.											.	ADCY3	114	.	0			c.C1131T						PASS	.	A		1609,2793		304,1001,896	36.0	36.0	36.0		1131	-7.6	0.9	2	dbSNP_98	36	4197,4399		1066,2065,1167	yes	coding-synonymous	ADCY3	NM_004036.3		1370,3066,2063	AA,AG,GG		48.825,36.5516,44.6684		377/1145	25064193	5806,7192	2201	4298	6499	SO:0001819	synonymous_variant	109	exon5			GTAGTCGGGCAAG	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.1131C>T	2.37:g.25064193G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_004036	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	37	CCDS1715.1																																																																																			G|0.520;A|0.480	0.480	strong		0.632	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
PIKFYVE	200576	hgsc.bcm.edu	37	2	209215571	209215571	+	Silent	SNP	T	T	C	rs13020468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:209215571T>C	ENST00000264380.4	+	37	5669	c.5511T>C	c.(5509-5511)atT>atC	p.I1837I		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1837	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				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						GTGAAGTGATTCTGGACAGCA	0.458													T|||	140	0.0279553	0.0643	0.0144	5008	,	,		16709	0.0		0.0308	False		,,,				2504	0.0143				p.I1837I		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.T5511C						PASS	.	T		229,4177	136.5+/-172.5	5,219,1979	139.0	133.0	135.0		5511	0.0	1.0	2	dbSNP_121	135	252,8348	99.9+/-161.4	2,248,4050	no	coding-synonymous	PIKFYVE	NM_015040.3		7,467,6029	CC,CT,TT		2.9302,5.1975,3.6983		1837/2099	209215571	481,12525	2203	4300	6503	SO:0001819	synonymous_variant	200576	exon37			AGTGATTCTGGAC	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.5511T>C	2.37:g.209215571T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	37	CCDS2382.1																																																																																			T|0.967;C|0.033	0.033	strong		0.458	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
MTERF4	130916	hgsc.bcm.edu	37	2	242036769	242036769	+	Silent	SNP	G	G	A	rs10171090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242036769G>A	ENST00000391980.2	-	3	652	c.594C>T	c.(592-594)gtC>gtT	p.V198V	MTERFD2_ENST00000406593.1_Silent_p.V10V|MTERFD2_ENST00000407095.3_Silent_p.V198V|MTERFD2_ENST00000464344.2_Intron|MTERFD2_ENST00000495694.1_Intron	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		198					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		TGAGAAGCCTGACAGTGTCGT	0.473													G|||	111	0.0221645	0.0772	0.013	5008	,	,		21463	0.0		0.0	False		,,,				2504	0.0				p.V198V		Atlas-SNP	.											.	MTERFD2	33	.	0			c.C594T						PASS	.	G		262,4144	148.8+/-183.1	9,244,1950	101.0	87.0	92.0		594	-1.5	0.0	2	dbSNP_119	92	0,8600		0,0,4300	no	coding-synonymous	MTERFD2	NM_182501.3		9,244,6250	AA,AG,GG		0.0,5.9464,2.0145		198/382	242036769	262,12744	2203	4300	6503	SO:0001819	synonymous_variant	130916	exon3			AAGCCTGACAGTG																												ENST00000391980.2:c.594C>T	2.37:g.242036769G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	118	52	0.440678	NM_182501	A8K6K0|Q9P0E0	Silent	SNP	ENST00000391980.2	37	CCDS2544.1																																																																																			G|0.978;A|0.022	0.022	strong		0.473	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4		
SNAI1	6615	hgsc.bcm.edu	37	20	48600631	48600631	+	Missense_Mutation	SNP	T	T	C	rs4647958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48600631T>C	ENST00000244050.2	+	2	414	c.353T>C	c.(352-354)gTc>gCc	p.V118A		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	118	Ser-rich.		V -> A (in dbSNP:rs4647958). {ECO:0000269|PubMed:11245431}.		cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|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 regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			TCTACTTCAGTCTCTTCCTTG	0.632													C|||	1466	0.292732	0.7171	0.232	5008	,	,		16710	0.0913		0.1262	False		,,,				2504	0.1411				p.V118A		Atlas-SNP	.											.	SNAI1	28	.	0			c.T353C						PASS	.	C	ALA/VAL	2737,1669	504.2+/-365.8	873,991,339	54.0	63.0	60.0		353	1.6	0.3	20	dbSNP_111	60	1057,7543	765.5+/-407.6	65,927,3308	yes	missense	SNAI1	NM_005985.3	64	938,1918,3647	CC,CT,TT		12.2907,37.8802,29.1712	benign	118/265	48600631	3794,9212	2203	4300	6503	SO:0001583	missense	6615	exon2			CTTCAGTCTCTTC	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	11128	protein-coding gene	gene with protein product		604238	"""snail 1 (drosophila homolog), zinc finger protein"", ""snail homolog 1 (Drosophila)"""			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.353T>C	20.37:g.48600631T>C	ENSP00000244050:p.Val118Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_005985	B2R842|Q9P113|Q9UBP7|Q9UHH7	Missense_Mutation	SNP	ENST00000244050.2	37	CCDS13423.1	577	0.2641941391941392	346	0.7032520325203252	86	0.23756906077348067	54	0.0944055944055944	91	0.12005277044854881	C	4.606	0.112656	0.08831	0.621198	0.122907	ENSG00000124216	ENST00000244050	T	0.19532	2.14	4.62	1.56	0.23342	.	0.487743	0.23079	N	0.052178	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32640	-0.9899	9	0.07644	T	0.81	-10.9503	8.8673	0.35294	0.0:0.6126:0.0:0.3874	rs4647958;rs52828116;rs58528306;rs4647958	118	O95863	SNAI1_HUMAN	A	118	ENSP00000244050:V118A	ENSP00000244050:V118A	V	+	2	0	SNAI1	48034038	0.000000	0.05858	0.256000	0.24389	0.937000	0.57800	-0.026000	0.12392	0.158000	0.19367	-0.226000	0.12346	GTC	T|0.722;C|0.278	0.278	strong		0.632	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1		
GBA	2629	hgsc.bcm.edu	37	1	155210498	155210498	+	Missense_Mutation	SNP	T	T	C	rs150466109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155210498T>C	ENST00000327247.5	-	3	270	c.38A>G	c.(37-39)aAg>aGg	p.K13R	GBA_ENST00000428024.3_Intron|GBA_ENST00000427500.3_Missense_Mutation_p.K13R|GBA_ENST00000536770.1_Missense_Mutation_p.K13R|GBA_ENST00000368373.3_Missense_Mutation_p.K13R|GBA_ENST00000493842.1_5'UTR	NM_001005741.2|NM_001005742.2	NP_001005741.1|NP_001005742.1	P04062	GLCM_HUMAN	glucosidase, beta, acid	13					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glucosylceramide catabolic process (GO:0006680)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of MAP kinase activity (GO:0043407)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of water loss via skin (GO:0033561)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to pH (GO:0009268)|response to testosterone (GO:0033574)|response to thyroid hormone (GO:0097066)|skin morphogenesis (GO:0043589)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)|termination of signal transduction (GO:0023021)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)	glucosylceramidase activity (GO:0004348)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	26	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)		Velaglucerase alfa(DB06720)	ACTCAAAGGCTTGGGACATTC	0.557									Gaucher disease type I				t|||	118	0.0235623	0.084	0.0072	5008	,	,		19504	0.002		0.0	False		,,,				2504	0.0				p.K13R		Atlas-SNP	.											.	GBA	46	.	0			c.A38G	GRCh37	CM065215	GBA	M	rs150466109	PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,,ARG/LYS	312,4094	166.9+/-198.0	11,290,1902	154.0	142.0	146.0		38,38,38,,38	-0.4	0.0	1	dbSNP_134	146	3,8597	2.2+/-6.3	0,3,4297	no	missense,missense,missense,intron,missense	GBA	NM_000157.3,NM_001005741.2,NM_001005742.2,NM_001171811.1,NM_001171812.1	26,26,26,,26	11,293,6199	CC,CT,TT		0.0349,7.0813,2.422	benign,benign,benign,,benign	13/537,13/537,13/537,,13/488	155210498	315,12691	2203	4300	6503	SO:0001583	missense	2629	exon3	Familial Cancer Database	glucocerebrosidase insufficiency	AAAGGCTTGGGAC	M19285	CCDS1102.1, CCDS53373.1, CCDS53374.1	1q22	2010-01-19	2010-01-19		ENSG00000177628	ENSG00000177628	3.2.1.21		4177	protein-coding gene	gene with protein product		606463	"""glucosylceramidase"", ""glucosidase, beta; acid (includes glucosylceramidase)"""	GLUC		3359914	Standard	NM_001005742		Approved	GBA1	uc001fjl.3	P04062	OTTHUMG00000035841	ENST00000327247.5:c.38A>G	1.37:g.155210498T>C	ENSP00000314508:p.Lys13Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_001005742	A8K796|B7Z5G2|B7Z6S1|J3KQG4|J3KQK9|Q16545|Q4VX22|Q6I9R6|Q9UMJ8	Missense_Mutation	SNP	ENST00000327247.5	37	CCDS1102.1	44	0.020146520146520148	43	0.08739837398373984	1	0.0027624309392265192	0	0.0	0	0.0	T	5.065	0.197635	0.09652	0.070813	3.49E-4	ENSG00000177628	ENST00000427500;ENST00000368373;ENST00000327247;ENST00000536770;ENST00000402928	D;D;D;D	0.99474	-5.59;-5.62;-5.62;-5.97	3.32	-0.397	0.12423	.	1.116300	0.07210	U	0.859048	D	0.90789	0.7108	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	D	0.91133	0.4939	10	0.24483	T	0.36	.	2.0673	0.03605	0.2405:0.2836:0.0:0.4759	.	13;13;13	B7Z5G2;F5H241;P04062	.;.;GLCM_HUMAN	R	13	ENSP00000402577:K13R;ENSP00000357357:K13R;ENSP00000314508:K13R;ENSP00000445560:K13R	ENSP00000314508:K13R	K	-	2	0	GBA	153477122	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.370000	0.07523	0.052000	0.16007	0.482000	0.46254	AAG	T|0.979;C|0.021	0.021	strong		0.557	GBA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087204.1	NM_000157	
TNNC2	7125	hgsc.bcm.edu	37	20	44452697	44452697	+	Silent	SNP	C	C	A	rs4629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44452697C>A	ENST00000372555.3	-	5	476	c.384G>T	c.(382-384)acG>acT	p.T128T	TNNC2_ENST00000372557.1_Silent_p.T113T	NM_003279.2	NP_003270.1	P02585	TNNC2_HUMAN	troponin C type 2 (fast)	128	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				muscle filament sliding (GO:0030049)|regulation of muscle contraction (GO:0006937)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(115;0.0122)			Felodipine(DB01023)	TCTCCTCGTCCGTCACGTGCT	0.612													C|||	2027	0.404752	0.1815	0.5476	5008	,	,		17060	0.5308		0.5378	False		,,,				2504	0.3384				p.T128T		Atlas-SNP	.											.	TNNC2	12	.	0			c.G384T						PASS	.	C		1148,3258	406.4+/-333.9	155,838,1210	162.0	141.0	148.0		384	-5.9	0.9	20	dbSNP_52	148	4562,4038	596.6+/-393.6	1206,2150,944	no	coding-synonymous	TNNC2	NM_003279.2		1361,2988,2154	AA,AC,CC		46.9535,26.0554,43.9028		128/161	44452697	5710,7296	2203	4300	6503	SO:0001819	synonymous_variant	7125	exon5			CTCGTCCGTCACG		CCDS13375.1	20q12-q13.11	2013-01-10	2005-09-12		ENSG00000101470	ENSG00000101470		"""EF-hand domain containing"""	11944	protein-coding gene	gene with protein product		191039	"""troponin C2, fast"""			2373703	Standard	NM_003279		Approved		uc002xpr.3	P02585	OTTHUMG00000032623	ENST00000372555.3:c.384G>T	20.37:g.44452697C>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	115	62	0.53913	NM_003279	Q6FH92	Silent	SNP	ENST00000372555.3	37	CCDS13375.1																																																																																			C|0.569;A|0.431	0.431	strong		0.612	TNNC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079524.3	NM_003279	
NCF1	653361	hgsc.bcm.edu	37	7	74193672	74193672	+	Missense_Mutation	SNP	C	C	T	rs146125534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:74193672C>T	ENST00000289473.4	+	4	369	c.299C>T	c.(298-300)aCg>aTg	p.T100M	NCF1_ENST00000443956.3_3'UTR	NM_000265.4	NP_000256.4	P14598	NCF1_HUMAN	neutrophil cytosolic factor 1	100	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)|cell proliferation (GO:0008283)|cellular defense response (GO:0006968)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|leukotriene metabolic process (GO:0006691)|negative regulation of smooth muscle contraction (GO:0045986)|neutrophil mediated killing of fungus (GO:0070947)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|protein targeting to membrane (GO:0006612)|respiratory burst (GO:0045730)|respiratory burst involved in defense response (GO:0002679)|response to yeast (GO:0001878)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagolysosome (GO:0032010)|rough endoplasmic reticulum (GO:0005791)	electron carrier activity (GO:0009055)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10					Dextromethorphan(DB00514)	TACTGCGGCACGCTCATGAGC	0.627																																					p.T100M		Atlas-SNP	.											NCF1,NS,carcinoma,0,1	NCF1	26	1	0			c.C299T						scavenged	.	C	MET/THR	9,4363		0,9,2177	30.0	17.0	21.0		299	2.4	0.2	7	dbSNP_134	21	30,8460		0,30,4215	no	missense	NCF1	NM_000265.4	81	0,39,6392	TT,TC,CC		0.3534,0.2059,0.3032	probably-damaging	100/391	74193672	39,12823	2186	4245	6431	SO:0001583	missense	653361	exon4			GCGGCACGCTCAT	M25665	CCDS34657.1	7q11.23	2014-09-17	2008-07-31		ENSG00000158517	ENSG00000158517			7660	protein-coding gene	gene with protein product	"""NADPH oxidase organizer 2"", ""chronic granulomatous disease, autosomal 1"""	608512	"""neutrophil cytosolic factor 1 (47kD, chronic granulomatous disease, autosomal 1)"""				Standard	NM_000265		Approved	p47phox, NOXO2, NCF1A, SH3PXD1A	uc022aft.1	P14598	OTTHUMG00000149965	ENST00000289473.4:c.299C>T	7.37:g.74193672C>T	ENSP00000289473:p.Thr100Met	Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	367	61	0.166213	NM_000265	A6NEH2|A8K7S9|O43842|Q2PP07|Q53FR5|Q9BU90|Q9BXI7|Q9BXI8|Q9UDV9|Q9UMU2	Missense_Mutation	SNP	ENST00000289473.4	37	CCDS34657.1	.	.	.	.	.	.	.	.	.	.	c	7.503	0.653151	0.14580	0.002059	0.003534	ENSG00000158517	ENST00000289473;ENST00000433458;ENST00000471594;ENST00000442021	T;T;T	0.39406	1.08;1.08;1.08	3.38	2.44	0.29823	Phox homologous domain (5);	1.232380	0.05605	N	0.577140	T	0.44953	0.1318	L	0.47716	1.5	0.24195	N	0.995534	P;D	0.67145	0.933;0.996	B;P	0.46320	0.097;0.512	T	0.42548	-0.9445	10	0.66056	D	0.02	-0.3076	11.343	0.49543	0.0:0.8052:0.1948:0.0	.	100;100	P14598-2;P14598	.;NCF1_HUMAN	M	100;100;74;107	ENSP00000289473:T100M;ENSP00000392870:T100M;ENSP00000401935:T107M	ENSP00000289473:T100M	T	+	2	0	NCF1	73831608	0.006000	0.16342	0.168000	0.22838	0.186000	0.23388	2.266000	0.43320	0.507000	0.28148	0.442000	0.29010	ACG	C|0.999;T|0.001	0.001	strong		0.627	NCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314560.1	NM_000265	
LILRB5	10990	hgsc.bcm.edu	37	19	54755922	54755922	+	Missense_Mutation	SNP	C	C	T	rs34889610|rs12977062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54755922C>T	ENST00000316219.5	-	12	1728	c.1621G>A	c.(1621-1623)Gct>Act	p.A541T	LILRB5_ENST00000345866.6_Missense_Mutation_p.A442T|LILRB5_ENST00000449561.2_Missense_Mutation_p.A542T|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000450632.1_Missense_Mutation_p.A533T	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	541					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CTCACCCGAGCATCCATCTCC	0.627													.|||	896	0.178914	0.1112	0.1484	5008	,	,		14643	0.0992		0.2525	False		,,,				2504	0.2986				p.A542T		Atlas-SNP	.											.	LILRB5	176	.	0			c.G1624A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	478,3928		27,424,1752	111.0	110.0	110.0		1624,1324,1621	-2.3	0.0	19	dbSNP_121	110	1746,6854		240,1266,2794	no	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	58,58,58	267,1690,4546	TT,TC,CC		20.3023,10.8488,17.0998	benign,benign,benign	542/592,442/492,541/591	54755922	2224,10782	2203	4300	6503	SO:0001583	missense	10990	exon12			CCCGAGCATCCAT	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1621G>A	19.37:g.54755922C>T	ENSP00000320390:p.Ala541Thr	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	211	106	0.50237	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	275	0.1259157509157509	59	0.11991869918699187	60	0.16574585635359115	23	0.04020979020979021	133	0.17546174142480211	C	0.189	-1.054678	0.01965	0.108488	0.203023	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00466	7.33;7.23;7.33;7.33	1.7	-2.32	0.06745	.	.	.	.	.	T	0.00012	0.0000	N	0.00413	-1.525	0.80722	P	0.0	B;B;B;B	0.15473	0.001;0.013;0.0;0.0	B;B;B;B	0.15052	0.001;0.012;0.002;0.001	T	0.23332	-1.0191	8	0.02654	T	1	.	3.7856	0.08698	0.0:0.3933:0.2823:0.3244	rs12977062;rs12977062	533;442;542;541	C9JMK7;O75023-2;O75023-3;O75023	.;.;.;LIRB5_HUMAN	T	541;533;542;442	ENSP00000320390:A541T;ENSP00000414225:A533T;ENSP00000406478:A542T;ENSP00000263430:A442T	ENSP00000320390:A541T	A	-	1	0	LILRB5	59447734	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	-0.640000	0.05440	-0.658000	0.05366	-0.606000	0.04082	GCT	TG|1.000;|0.000	.	alt		0.627	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
LILRA3	11026	hgsc.bcm.edu	37	19	54802105	54802105	+	Silent	SNP	C	C	T	rs1975046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54802105C>T	ENST00000251390.3	-	6	1174	c.1083G>A	c.(1081-1083)ggG>ggA	p.G361G	LILRA3_ENST00000391744.3_Silent_p.G297G|LILRA3_ENST00000391745.1_Silent_p.G378G	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	361	Ig-like C2-type 4.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AATCAGCTGCCCCCTCCTTGG	0.597													.|||	1149	0.229433	0.6483	0.0821	5008	,	,		11141	0.1131		0.007	False		,,,				2504	0.1166				p.G361G		Atlas-SNP	.											.	LILRA3	65	.	0			c.G1083A						PASS	.	C	,	2591,1797		861,869,464	104.0	92.0	96.0		891,1083	-1.1	0.0	19	dbSNP_92	96	74,8246		17,40,4103	no	coding-synonymous,coding-synonymous	LILRA3	NM_001172654.1,NM_006865.3	,	878,909,4567	TT,TC,CC		0.8894,40.9526,20.971	,	297/376,361/440	54802105	2665,10043	2194	4160	6354	SO:0001819	synonymous_variant	11026	exon6			AGCTGCCCCCTCC	U91926		19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.1083G>A	19.37:g.54802105C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Silent	SNP	ENST00000251390.3	37	CCDS12887.1																																																																																			C|0.794;T|0.206	0.206	strong		0.597	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
GSDMC	56169	hgsc.bcm.edu	37	8	130760850	130760850	+	Missense_Mutation	SNP	A	A	G	rs4144738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:130760850A>G	ENST00000276708.4	-	14	2305	c.1424T>C	c.(1423-1425)aTg>aCg	p.M475T		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	475			M -> T (in dbSNP:rs4144738). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)		p.M475T(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						ATCCAGCTCCATCCTAAGGCC	0.587													A|||	3542	0.707268	0.9402	0.6427	5008	,	,		20453	0.744		0.4702	False		,,,				2504	0.6442				p.M475T		Atlas-SNP	.											GSDMC,NS,carcinoma,0,1	GSDMC	71	1	1	Substitution - Missense(1)	stomach(1)	c.T1424C						PASS	.	A	THR/MET	3853,553	776.1+/-414.1	1694,465,44	107.0	98.0	101.0		1424	4.7	0.0	8	dbSNP_110	101	3920,4680	547.3+/-385.1	909,2102,1289	yes	missense	GSDMC	NM_031415.2	81	2603,2567,1333	GG,GA,AA		45.5814,12.5511,40.2353	possibly-damaging	475/509	130760850	7773,5233	2203	4300	6503	SO:0001583	missense	56169	exon14			AGCTCCATCCTAA	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"""melanoma-derived leucine zipper, extra-nuclear factor"""	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.1424T>C	8.37:g.130760850A>G	ENSP00000276708:p.Met475Thr	Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	176	176	1	NM_031415	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	37	CCDS6360.1	1444	0.6611721611721612	456	0.926829268292683	226	0.6243093922651933	411	0.7185314685314685	351	0.4630606860158311	A	15.34	2.805191	0.50315	0.874489	0.455814	ENSG00000147697	ENST00000276708	T	0.24350	1.86	4.72	4.72	0.59763	.	0.534882	0.19047	N	0.124142	T	0.00012	0.0000	M	0.63843	1.955	0.80722	P	0.0	D	0.69078	0.997	D	0.65233	0.933	T	0.02081	-1.1217	9	0.87932	D	0	.	10.5105	0.44860	1.0:0.0:0.0:0.0	rs4144738;rs17855854;rs52804384;rs61422280;rs4144738	475	Q9BYG8	GSDMC_HUMAN	T	475	ENSP00000276708:M475T	ENSP00000276708:M475T	M	-	2	0	GSDMC	130830032	0.005000	0.15991	0.005000	0.12908	0.172000	0.22775	2.231000	0.43009	1.997000	0.58415	0.477000	0.44152	ATG	A|0.363;G|0.637	0.637	strong		0.587	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1		
SPNS2	124976	hgsc.bcm.edu	37	17	4436354	4436354	+	Silent	SNP	C	C	T	rs61746307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4436354C>T	ENST00000329078.3	+	7	1228	c.1018C>T	c.(1018-1020)Ctg>Ttg	p.L340L		NM_001124758.1	NP_001118230.1	Q8IVW8	SPNS2_HUMAN	spinster homolog 2 (Drosophila)	340					B cell homeostasis (GO:0001782)|bone development (GO:0060348)|lymph node development (GO:0048535)|lymphocyte migration (GO:0072676)|regulation of eye pigmentation (GO:0048073)|regulation of humoral immune response (GO:0002920)|sphingolipid metabolic process (GO:0006665)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell homeostasis (GO:0043029)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	sphingolipid transporter activity (GO:0046624)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6						CCCGCTCTACCTGCACCGCGC	0.701													C|||	77	0.0153754	0.0522	0.0101	5008	,	,		17617	0.0		0.001	False		,,,				2504	0.0				p.L340L		Atlas-SNP	.											.	SPNS2	24	.	0			c.C1018T						PASS	.	C		138,2998		5,128,1435	30.0	32.0	31.0		1018	2.7	1.0	17	dbSNP_129	31	2,7162		0,2,3580	no	coding-synonymous	SPNS2	NM_001124758.1		5,130,5015	TT,TC,CC		0.0279,4.4005,1.3592		340/550	4436354	140,10160	1568	3582	5150	SO:0001819	synonymous_variant	124976	exon7			CTCTACCTGCACC	BC041772	CCDS42237.1	17p13.2	2008-12-15				ENSG00000183018			26992	protein-coding gene	gene with protein product		612584				12815463	Standard	NM_001124758		Approved		uc002fxx.2	Q8IVW8		ENST00000329078.3:c.1018C>T	17.37:g.4436354C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	139	68	0.489209	NM_001124758	B9A1T3	Silent	SNP	ENST00000329078.3	37	CCDS42237.1																																																																																			C|0.989;T|0.011	0.011	strong		0.701	SPNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438802.1		
WDR90	197335	hgsc.bcm.edu	37	16	716273	716273	+	Missense_Mutation	SNP	T	T	C	rs11866949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:716273T>C	ENST00000293879.4	+	37	4663	c.4663T>C	c.(4663-4665)Tgc>Cgc	p.C1555R	WDR90_ENST00000315764.4_Missense_Mutation_p.C154R|WDR90_ENST00000549091.1_Missense_Mutation_p.C1557R|WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000547944.1_Missense_Mutation_p.C154R|RHOT2_ENST00000315082.4_5'Flank			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1555			C -> R (in dbSNP:rs11866949).							endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GAGCCACCCCTGCACAGGGAC	0.622													C|||	1806	0.360623	0.7927	0.2133	5008	,	,		18164	0.3224		0.1163	False		,,,				2504	0.1718				p.C1555R		Atlas-SNP	.											.	WDR90	107	.	0			c.T4663C						PASS	.	C	ARG/CYS	2575,1497		813,949,274	43.0	52.0	49.0		4663	-3.8	0.0	16	dbSNP_120	49	1045,7297		58,929,3184	yes	missense	WDR90	NM_145294.4	180	871,1878,3458	CC,CT,TT		12.527,36.7633,29.1606	benign	1555/1749	716273	3620,8794	2036	4171	6207	SO:0001583	missense	197335	exon37			CACCCCTGCACAG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.4663T>C	16.37:g.716273T>C	ENSP00000293879:p.Cys1555Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	696	0.31868131868131866	373	0.758130081300813	63	0.17403314917127072	184	0.32167832167832167	76	0.10026385224274406	C	2.766	-0.256870	0.05829	0.632367	0.12527	ENSG00000161996	ENST00000549091;ENST00000293879;ENST00000547944;ENST00000315764	T;T;T;T	0.61980	3.57;1.81;0.06;1.84	4.48	-3.8	0.04307	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.579510	0.03030	N	0.151901	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.31943	-0.9925	9	0.12430	T	0.62	.	6.6725	0.23076	0.1253:0.3526:0.0:0.5221	rs11866949;rs61157244;rs11866949	154;154;154;1555	Q96KV7-10;Q96KV7-7;G3V201;Q96KV7	.;.;.;WDR90_HUMAN	R	1557;1555;154;154	ENSP00000448122:C1557R;ENSP00000293879:C1555R;ENSP00000449576:C154R;ENSP00000322808:C154R	ENSP00000293879:C1555R	C	+	1	0	WDR90	656274	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-1.058000	0.03482	-0.600000	0.05790	-1.381000	0.01174	TGC	T|0.694;C|0.306	0.306	strong		0.622	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
WDR87	83889	hgsc.bcm.edu	37	19	38380501	38380501	+	Silent	SNP	G	G	A	rs143655348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38380501G>A	ENST00000303868.5	-	6	3917	c.3693C>T	c.(3691-3693)ggC>ggT	p.G1231G	WDR87_ENST00000447313.2_Silent_p.G1270G	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	1231										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						TTGACCTGCGGCCAGATATTC	0.468													G|||	23	0.00459265	0.0166	0.0014	5008	,	,		18970	0.0		0.0	False		,,,				2504	0.0				p.G1231G		Atlas-SNP	.											.	WDR87	191	.	0			c.C3693T						PASS	.	G		26,1358		1,24,667	130.0	101.0	110.0		3693	-3.6	0.0	19	dbSNP_134	110	0,3182		0,0,1591	no	coding-synonymous	WDR87	NM_031951.3		1,24,2258	AA,AG,GG		0.0,1.8786,0.5694		1231/2874	38380501	26,4540	692	1591	2283	SO:0001819	synonymous_variant	83889	exon6			CCTGCGGCCAGAT	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.3693C>T	19.37:g.38380501G>A		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	195	95	0.487179	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			G|0.994;A|0.006	0.006	strong		0.468	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
TG	7038	hgsc.bcm.edu	37	8	133953676	133953676	+	Missense_Mutation	SNP	A	A	G	rs61744679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133953676A>G	ENST00000220616.4	+	26	5162	c.5122A>G	c.(5122-5124)Att>Gtt	p.I1708V	TG_ENST00000377869.1_Missense_Mutation_p.I1651V|TG_ENST00000542445.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1708					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)		GTACAACCCCATTGTGTTCTC	0.502													A|||	140	0.0279553	0.1014	0.0086	5008	,	,		22921	0.0		0.0	False		,,,				2504	0.0				p.I1708V		Atlas-SNP	.											.	TG	416	.	0			c.A5122G						PASS	.	A	VAL/ILE	382,4024	193.0+/-218.2	19,344,1840	170.0	143.0	153.0		5122	-0.3	0.0	8	dbSNP_129	153	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TG	NM_003235.4	29	19,347,6137	GG,GA,AA		0.0349,8.67,2.9602	benign	1708/2769	133953676	385,12621	2203	4300	6503	SO:0001583	missense	7038	exon26			AACCCCATTGTGT	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.5122A>G	8.37:g.133953676A>G	ENSP00000220616:p.Ile1708Val	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	286	144	0.503497	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	A	0	-2.653927	0.00109	0.0867	3.49E-4	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;T	0.60548	0.18;0.18	5.81	-0.269	0.12930	.	1.039030	0.07593	N	0.922337	T	0.00210	0.0006	N	0.00268	-1.735	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12604	-1.0541	10	0.02654	T	1	.	4.2539	0.10708	0.2662:0.0:0.4355:0.2983	rs61744679	1708	P01266	THYG_HUMAN	V	1651;514;1708	ENSP00000367100:I1651V;ENSP00000220616:I1708V	ENSP00000220616:I1708V	I	+	1	0	TG	134022858	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	0.340000	0.19892	0.055000	0.16094	-1.652000	0.00757	ATT	A|0.964;G|0.036	0.036	strong		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
MXD3	83463	hgsc.bcm.edu	37	5	176734855	176734855	+	Silent	SNP	G	G	C	rs4568379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176734855G>C	ENST00000439742.2	-	5	910	c.432C>G	c.(430-432)gcC>gcG	p.A144A	MXD3_ENST00000427908.2_Silent_p.A144A|MXD3_ENST00000423571.2_Silent_p.A144A|MXD3_ENST00000513063.1_Silent_p.A144A	NM_031300.3	NP_112590.1	Q9BW11	MAD3_HUMAN	MAX dimerization protein 3	144					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)			GCTCCCGCTCGGCCGCCCCTG	0.697													G|||	1039	0.207468	0.3555	0.1686	5008	,	,		11663	0.0258		0.2276	False		,,,				2504	0.2014				p.A144A		Atlas-SNP	.											.	MXD3	13	.	0			c.C432G						PASS	.	G	,	1112,2786		174,764,1011	8.0	10.0	10.0		432,432	-8.5	0.0	5	dbSNP_111	10	1622,6156		180,1262,2447	no	coding-synonymous,coding-synonymous	MXD3	NM_001142935.1,NM_031300.3	,	354,2026,3458	CC,CG,GG		20.8537,28.5274,23.4156	,	144/194,144/207	176734855	2734,8942	1949	3889	5838	SO:0001819	synonymous_variant	83463	exon5			CCGCTCGGCCGCC	BC000745	CCDS4416.1, CCDS47347.1	5q35.3	2013-03-20			ENSG00000213347	ENSG00000213347		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	14008	protein-coding gene	gene with protein product		609450					Standard	NM_031300		Approved	MAD3, bHLHc13	uc003mgb.2	Q9BW11	OTTHUMG00000130854	ENST00000439742.2:c.432C>G	5.37:g.176734855G>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	26	25	0.961538	NM_001142935	B4E0J1|Q53HK1|Q7Z4Y0|Q8NDJ7|Q96ME3	Silent	SNP	ENST00000439742.2	37	CCDS4416.1																																																																																			G|0.800;C|0.200	0.200	strong		0.697	MXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253427.1		
KIR3DL1	3811	hgsc.bcm.edu	37	19	55341575	55341575	+	Missense_Mutation	SNP	G	G	C	rs1130513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55341575G>C	ENST00000391728.4	+	9	1213	c.1180G>C	c.(1180-1182)Gag>Cag	p.E394Q	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.E377Q|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.E299Q|KIR2DS4_ENST00000339924.8_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.E394Q|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.E377Q	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	394			E -> Q (in dbSNP:rs1130513).		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)		ACAAGACCCTGAGGAGGTGAC	0.522													c|||	884	0.176518	0.1815	0.1758	5008	,	,		15583	0.1111		0.2942	False		,,,				2504	0.1166				p.E394Q		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.G1180C						PASS	.	C	GLN/GLU	897,3447		194,509,1469	237.0	218.0	225.0		1180	0.7	0.0	19	dbSNP_86	225	2044,6284		538,968,2658	no	missense	KIR3DL1	NM_013289.2	29	732,1477,4127	CC,CG,GG		24.5437,20.6492,23.2086		394/445	55341575	2941,9731	2172	4164	6336	SO:0001583	missense	3811	exon9			GACCCTGAGGAGG	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.1180G>C	19.37:g.55341575G>C	ENSP00000375608:p.Glu394Gln	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	113	45	0.39823	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	376	0.17216117216117216	65	0.13211382113821138	58	0.16022099447513813	54	0.0944055944055944	199	0.262532981530343	-	0.003	-2.458893	0.00173	0.206492	0.245437	ENSG00000167633	ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T	0.00475	7.26;7.37;7.26;7.37;7.17	0.719	0.719	0.18208	.	.	.	.	.	T	0.00012	0.0000	N	0.00085	-2.2	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	0.26155	-1.0111	7	0.02654	T	1	.	.	.	.	rs1130513;rs3189435;rs16986003	377;299;394	Q15702;Q14946;P43629	.;.;KI3L1_HUMAN	Q	394;377;372;394;377;299	ENSP00000443350:E394Q;ENSP00000442355:E377Q;ENSP00000375608:E394Q;ENSP00000326868:E377Q;ENSP00000350901:E299Q	ENSP00000326868:E377Q	E	+	1	0	KIR3DL1	60033387	0.139000	0.22563	0.002000	0.10522	0.006000	0.05464	0.000000	0.12993	-0.105000	0.12132	-1.123000	0.02005	GAG	G|0.828;C|0.172	0.172	strong		0.522	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
PCDHB6	56130	hgsc.bcm.edu	37	5	140530852	140530852	+	Silent	SNP	G	G	C	rs246708	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140530852G>C	ENST00000231136.1	+	1	1014	c.1014G>C	c.(1012-1014)gtG>gtC	p.V338V	PCDHB6_ENST00000543635.1_Silent_p.V202V	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	338	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCTGGACGTGAATGACAATG	0.468													G|||	1122	0.224042	0.4909	0.2406	5008	,	,		18488	0.0407		0.169	False		,,,				2504	0.0971				p.V338V		Atlas-SNP	.											PCDHB6,NS,carcinoma,+2,1	PCDHB6	161	1	0			c.G1014C						PASS	.	G		1871,2535	542.4+/-376.0	393,1085,725	102.0	98.0	99.0		1014	0.0	0.9	5	dbSNP_79	99	1580,7020	295.5+/-302.4	152,1276,2872	no	coding-synonymous	PCDHB6	NM_018939.2		545,2361,3597	CC,CG,GG		18.3721,42.4648,26.5339		338/795	140530852	3451,9555	2203	4300	6503	SO:0001819	synonymous_variant	56130	exon1			GGACGTGAATGAC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1014G>C	5.37:g.140530852G>C		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	223	105	0.470852	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	37	CCDS4248.1																																																																																			G|0.747;C|0.253	0.253	strong		0.468	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
MICA	100507436	hgsc.bcm.edu	37	6	31379823	31379823	+	Missense_Mutation	SNP	C	C	G	rs1051799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31379823C>G	ENST00000449934.2	+	4	767	c.713C>G	c.(712-714)aCc>aGc	p.T238S	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)				ATCATACTGACCTGGCGTCAG	0.602													c|||	1823	0.364018	0.4773	0.4063	5008	,	,		18600	0.2996		0.3141	False		,,,				2504	0.2986				p.T238S		Atlas-SNP	.											.	MICA	21	.	0			c.C713G						PASS	.						17.0	19.0	18.0					6																	31379823		692	1588	2280	SO:0001583	missense	100507436	exon4			TACTGACCTGGCG	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.713C>G	6.37:g.31379823C>G	ENSP00000413079:p.Thr238Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	727	0.33287545787545786	205	0.4166666666666667	155	0.4281767955801105	147	0.256993006993007	220	0.29023746701846964	c	8.349	0.830533	0.16749	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.02812	4.15;4.15	2.52	-0.436	0.12275	.	1.351150	0.05555	U	0.568191	T	0.00724	0.0024	.	.	.	0.80722	P	0.0	B;B	0.23735	0.09;0.007	B;B	0.27076	0.076;0.033	T	0.48725	-0.9010	8	0.42905	T	0.14	.	2.5921	0.04845	0.2201:0.3535:0.0:0.4264	rs1051799;rs3192175;rs17200337;rs17845522;rs17858412;rs17881640;rs1051799	100;238	Q5SS58;Q96QC4	.;.	S	100;238;195;238;129	ENSP00000413079:T238S;ENSP00000402410:T129S	ENSP00000365394:T238S	T	+	2	0	MICA	31487802	0.026000	0.19158	0.013000	0.15412	0.012000	0.07955	-0.351000	0.07711	0.021000	0.15133	0.444000	0.29173	ACC	C|0.703;G|0.297	0.297	strong		0.602	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
RPL8	6132	hgsc.bcm.edu	37	8	146015749	146015749	+	Silent	SNP	C	C	T	rs1060859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:146015749C>T	ENST00000262584.3	-	5	838	c.606G>A	c.(604-606)gtG>gtA	p.V202V	RPL8_ENST00000527914.1_Silent_p.V93V|RPL8_ENST00000394920.2_Silent_p.V202V|RPL8_ENST00000529163.1_5'UTR|RPL8_ENST00000528957.1_Silent_p.V202V	NM_000973.3	NP_000964.1	P62917	RL8_HUMAN	ribosomal protein L8	202					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)|focal adhesion (GO:0005925)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			kidney(12)|lung(7)|prostate(1)	20	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.191)		CATTCATGGCCACACCCCGTA	0.542													C|||	418	0.0834665	0.3011	0.0245	5008	,	,		17625	0.0		0.002	False		,,,				2504	0.001				p.V202V		Atlas-SNP	.											.	RPL8	29	.	0			c.G606A						PASS	.	C	,	1141,3265	404.9+/-333.3	155,831,1217	124.0	99.0	108.0		606,606	3.3	1.0	8	dbSNP_86	108	11,8589	7.1+/-27.0	0,11,4289	no	coding-synonymous,coding-synonymous	RPL8	NM_000973.3,NM_033301.1	,	155,842,5506	TT,TC,CC		0.1279,25.8965,8.8575	,	202/258,202/258	146015749	1152,11854	2203	4300	6503	SO:0001819	synonymous_variant	6132	exon5			CATGGCCACACCC	Z28407	CCDS6433.1	8q24.3	2011-04-06			ENSG00000161016	ENSG00000161016		"""L ribosomal proteins"""	10368	protein-coding gene	gene with protein product		604177				7506540, 9582194	Standard	NM_033301		Approved	L8	uc003zec.3	P62917	OTTHUMG00000165249	ENST00000262584.3:c.606G>A	8.37:g.146015749C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	138	72	0.521739	NM_033301	A8K094|D3DWN2|P25120|Q567Q7|Q969V7|Q9BWQ9	Silent	SNP	ENST00000262584.3	37	CCDS6433.1																																																																																			C|0.908;T|0.092	0.092	strong		0.542	RPL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382948.1	NM_000973	
TMEM44	93109	hgsc.bcm.edu	37	3	194325103	194325103	+	Silent	SNP	G	G	A	rs745169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:194325103G>A	ENST00000392432.2	-	10	1435	c.1230C>T	c.(1228-1230)ccC>ccT	p.P410P	TMEM44_ENST00000381975.3_Missense_Mutation_p.P362L|TMEM44_ENST00000347147.4_Silent_p.P363P|TMEM44_ENST00000273580.7_Silent_p.P363P|TMEM44_ENST00000473092.1_Silent_p.P363P	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	410						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|urinary_tract(1)	8	all_cancers(143;1.41e-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;9.06e-06)		GGTACGACGGGGGGTCCTGCA	0.657													G|||	314	0.0626997	0.2277	0.0101	5008	,	,		15940	0.002		0.001	False		,,,				2504	0.0031				p.P362L		Atlas-SNP	.											.	TMEM44	42	.	0			c.C1085T						PASS	.	G	,,LEU/PRO,	772,3568		78,616,1476	29.0	26.0	27.0		1089,1230,1085,1089	-5.4	0.4	3	dbSNP_86	27	9,8525		0,9,4258	yes	coding-synonymous,coding-synonymous,missense,coding-synonymous	TMEM44	NM_001011655.2,NM_001166305.1,NM_001166306.1,NM_138399.4	,,98,	78,625,5734	AA,AG,GG		0.1055,17.788,6.0665	,,,	363/429,410/476,362/397,363/439	194325103	781,12093	2170	4267	6437	SO:0001819	synonymous_variant	93109	exon9			CGACGGGGGGTCC	AL833026	CCDS3308.1, CCDS33921.1, CCDS3308.2, CCDS54698.1, CCDS54699.1	3q29	2005-08-16			ENSG00000145014	ENSG00000145014			25120	protein-coding gene	gene with protein product							Standard	NM_138399		Approved	DKFZp686O18124	uc010hzn.3	Q2T9K0	OTTHUMG00000156023	ENST00000392432.2:c.1230C>T	3.37:g.194325103G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_001166306	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	106	0.048534798534798536	102	0.2073170731707317	4	0.011049723756906077	0	0.0	0	0.0	G	11.04	1.523178	0.27211	0.17788	0.001055	ENSG00000145014	ENST00000381975;ENST00000429560	T	0.35789	1.29	5.23	-5.43	0.02632	.	0.095734	0.42964	D	0.000626	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999837588	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.002	T	0.09552	-1.0669	8	0.66056	D	0.02	-23.756	7.3059	0.26447	0.3646:0.466:0.1694:0.0	rs745169;rs745169	94;362	Q6PL43;Q2T9K0-4	.;.	L	362;94	ENSP00000371402:P362L	ENSP00000371402:P362L	P	-	2	0	TMEM44	195806392	0.819000	0.29175	0.431000	0.26735	0.097000	0.18754	-0.564000	0.05936	-1.360000	0.02172	0.447000	0.29281	CCC	G|0.930;A|0.070	0.070	strong		0.657	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399	
CCBL2	56267	hgsc.bcm.edu	37	1	89453966	89453966	+	Missense_Mutation	SNP	G	G	A	rs74100109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89453966G>A	ENST00000260508.4	-	2	405	c.68C>T	c.(67-69)tCt>tTt	p.S23F	CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000370485.2_Missense_Mutation_p.S23F|RBMXL1_ENST00000413769.1_5'UTR|RBMXL1_ENST00000321792.5_Intron|CCBL2_ENST00000446900.2_5'UTR|RBMXL1_ENST00000399794.2_5'UTR	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	23					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	mitochondrion (GO:0005739)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|kynurenine-glyoxylate transaminase activity (GO:0047315)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|ovary(2)|skin(2)|soft_tissue(1)	18		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)		GATTTTGGAAGAAGAAATTGT	0.348													G|||	45	0.00898562	0.0318	0.0043	5008	,	,		17385	0.0		0.0	False		,,,				2504	0.0				p.S23F		Atlas-SNP	.											.	CCBL2	138	.	0			c.C68T						PASS	.	G	PHE/SER,,,	148,4258	96.2+/-134.9	4,140,2059	58.0	64.0	62.0		68,,,	4.6	1.0	1	dbSNP_130	62	0,8600		0,0,4300	yes	missense,intron,utr-5,intron	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	155,,,	4,140,6359	AA,AG,GG		0.0,3.3591,1.1379	benign,,,	23/455,,,	89453966	148,12858	2203	4300	6503	SO:0001583	missense	56267	exon2			TTGGAAGAAGAAA	AF091090	CCDS30766.1, CCDS30767.1	1p22.2	2009-06-23			ENSG00000137944	ENSG00000137944			33238	protein-coding gene	gene with protein product		610656				16376499	Standard	NM_001008662		Approved	RBM1, RP11-82K18.3, KAT3	uc001dmp.2	Q6YP21	OTTHUMG00000010617	ENST00000260508.4:c.68C>T	1.37:g.89453966G>A	ENSP00000260508:p.Ser23Phe	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	328	159	0.484756	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Missense_Mutation	SNP	ENST00000260508.4	37	CCDS30766.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	G	9.181	1.023703	0.19433	0.033591	0.0	ENSG00000137944	ENST00000260508;ENST00000370485;ENST00000370486	T;T	0.72725	-0.68;-0.52	5.5	4.58	0.56647	.	0.894418	0.09587	N	0.782010	T	0.43233	0.1238	N	0.22421	0.69	0.80722	D	1	B	0.25169	0.119	B	0.24269	0.052	T	0.42447	-0.9451	10	0.52906	T	0.07	-4.0555	9.248	0.37539	0.0959:0.0:0.9041:0.0	.	23	Q6YP21	KAT3_HUMAN	F	23	ENSP00000260508:S23F;ENSP00000359517:S23F	ENSP00000260508:S23F	S	-	2	0	CCBL2	89226554	0.999000	0.42202	0.970000	0.41538	0.267000	0.26476	3.285000	0.51716	2.588000	0.87417	0.650000	0.86243	TCT	G|0.988;A|0.012	0.012	strong		0.348	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661	
FUT1	2523	hgsc.bcm.edu	37	19	49253717	49253717	+	Silent	SNP	G	G	T	rs838138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49253717G>T	ENST00000310160.3	-	4	1796	c.822C>A	c.(820-822)acC>acA	p.T274T	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	274					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		CGCCCTGGGAGGTGTCGATGT	0.577													G|||	267	0.0533147	0.1884	0.0259	5008	,	,		20123	0.0		0.0	False		,,,				2504	0.0				p.T274T		Atlas-SNP	.											.	FUT1	44	.	0			c.C822A						PASS	.	G		653,3753	279.0+/-274.6	52,549,1602	166.0	127.0	140.0		822	1.1	0.3	19	dbSNP_86	140	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	FUT1	NM_000148.3		52,551,5900	TT,TG,GG		0.0233,14.8207,5.0361		274/366	49253717	655,12351	2203	4300	6503	SO:0001819	synonymous_variant	2523	exon4			CTGGGAGGTGTCG		CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"""Blood group antigens"", ""Fucosyltransferases"""	4012	protein-coding gene	gene with protein product		211100	"""fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)"", ""fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"""	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.822C>A	19.37:g.49253717G>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_000148	O14505|O14506|O14507	Silent	SNP	ENST00000310160.3	37	CCDS12733.1																																																																																			G|0.955;T|0.045	0.045	strong		0.577	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148	
C1orf27	54953	hgsc.bcm.edu	37	1	186355168	186355168	+	Missense_Mutation	SNP	A	A	G	rs115570554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186355168A>G	ENST00000287859.6	+	4	408	c.283A>G	c.(283-285)Att>Gtt	p.I95V	C1orf27_ENST00000367470.3_Missense_Mutation_p.I95V|C1orf27_ENST00000419367.3_Intron|C1orf27_ENST00000432021.3_Missense_Mutation_p.I95V	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	95						integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						AGTATTTATTATTACTACTTT	0.289													A|||	21	0.00419329	0.0151	0.0014	5008	,	,		15027	0.0		0.0	False		,,,				2504	0.0				p.I95V		Atlas-SNP	.											.	C1orf27	41	.	0			c.A283G						PASS	.	A	VAL/ILE,,VAL/ILE	36,3532		0,36,1748	54.0	51.0	52.0		283,,283	2.5	1.0	1	dbSNP_132	52	0,8118		0,0,4059	yes	missense,intron,missense	C1orf27	NM_001164245.1,NM_001164246.1,NM_017847.5	29,,29	0,36,5807	GG,GA,AA		0.0,1.009,0.3081	benign,,benign	95/432,,95/455	186355168	36,11650	1784	4059	5843	SO:0001583	missense	54953	exon4			TTTATTATTACTA	BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"""transactivated by recombinant transforming growth factor beta"""	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.283A>G	1.37:g.186355168A>G	ENSP00000287859:p.Ile95Val	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_001164245	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Missense_Mutation	SNP	ENST00000287859.6	37	CCDS53448.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	A	1.145	-0.648372	0.03506	0.01009	0.0	ENSG00000157181	ENST00000367470;ENST00000432021;ENST00000287859	T;T;T	0.38401	1.14;1.14;1.14	4.97	2.47	0.30058	.	0.271361	0.41500	N	0.000862	T	0.12860	0.0312	L	0.29908	0.895	0.33076	D	0.535996	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.22382	-1.0218	10	0.05833	T	0.94	-21.9948	4.69	0.12776	0.6635:0.1637:0.1728:0.0	.	95;95	Q5SWX8-2;Q5SWX8	.;ODR4_HUMAN	V	95	ENSP00000356440:I95V;ENSP00000402029:I95V;ENSP00000287859:I95V	ENSP00000287859:I95V	I	+	1	0	C1orf27	184621791	0.727000	0.28069	0.998000	0.56505	0.985000	0.73830	0.258000	0.18387	0.851000	0.35264	-0.263000	0.10527	ATT	A|0.997;G|0.003	0.003	strong		0.289	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847	
PDE9A	5152	hgsc.bcm.edu	37	21	44192574	44192574	+	Missense_Mutation	SNP	C	C	T	rs147305658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44192574C>T	ENST00000291539.6	+	19	1772	c.1712C>T	c.(1711-1713)aCg>aTg	p.T571M	PDE9A_ENST00000335440.6_Missense_Mutation_p.T469M|PDE9A_ENST00000335512.4_Missense_Mutation_p.T511M|PDE9A_ENST00000539837.1_Missense_Mutation_p.T443M|PDE9A_ENST00000398229.3_Missense_Mutation_p.T437M|PDE9A_ENST00000328862.6_Missense_Mutation_p.T545M|PDE9A_ENST00000398225.3_Missense_Mutation_p.T530M|PDE9A_ENST00000398224.3_Missense_Mutation_p.T444M|PDE9A_ENST00000398236.3_Missense_Mutation_p.T485M|PDE9A_ENST00000398234.3_Missense_Mutation_p.T470M|PDE9A_ENST00000398227.3_Missense_Mutation_p.T411M|PDE9A_ENST00000380328.2_Missense_Mutation_p.T518M|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000349112.3_Missense_Mutation_p.T443M|PDE9A_ENST00000398232.3_Missense_Mutation_p.T504M	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	571					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	GACAGCTTGACGTCTGGGGCC	0.527													C|||	3	0.000599042	0.0023	0.0	5008	,	,		18440	0.0		0.0	False		,,,				2504	0.0				p.T571M		Atlas-SNP	.											.	PDE9A	69	.	0			c.C1712T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	23,4381	29.9+/-59.1	0,23,2179	68.0	55.0	59.0		1532,1331,1328,1553,1409,1091,1091,1454,1232,1061,1310,1406,1091,1061,1511,1589,1634,1091,1091,1712	1.4	0.0	21	dbSNP_134	59	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81	0,23,6479	TT,TC,CC		0.0,0.5223,0.1769	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	511/534,444/467,443/466,518/541,470/493,364/387,364/387,485/508,411/434,354/377,437/460,469/492,364/387,354/377,504/527,530/553,545/568,364/387,364/387,571/594	44192574	23,12981	2202	4300	6502	SO:0001583	missense	5152	exon19			GCTTGACGTCTGG	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.1712C>T	21.37:g.44192574C>T	ENSP00000291539:p.Thr571Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	62	38	0.612903	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	8.057	0.767372	0.15983	0.005223	0.0	ENSG00000160191	ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000328862;ENST00000335440;ENST00000398225;ENST00000398229;ENST00000398227;ENST00000349112;ENST00000398224	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.69926	-0.4;-0.39;-0.42;-0.41;-0.44;-0.4;-0.4;-0.43;-0.41;-0.42;-0.4;-0.4;-0.39;-0.4	3.3	1.42	0.22433	.	2.420000	0.01711	N	0.027724	T	0.45756	0.1358	L	0.32530	0.975	0.09310	N	1	P;B;B;P;P;P;B;B;B;B;B;P;B;B;B	0.45044	0.588;0.069;0.145;0.759;0.849;0.759;0.145;0.069;0.145;0.145;0.301;0.849;0.301;0.145;0.308	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.36244	0.216;0.028;0.04;0.176;0.176;0.115;0.093;0.013;0.079;0.049;0.124;0.176;0.22;0.102;0.048	T	0.48055	-0.9068	10	0.48119	T	0.1	.	6.1538	0.20326	0.0:0.7003:0.1902:0.1095	.	504;485;470;545;530;463;511;354;411;437;443;469;518;444;571	O76083-13;O76083-8;O76083-6;O76083-15;O76083-14;O76083-16;O76083-2;O76083-10;O76083-9;O76083-11;O76083-4;O76083-12;O76083-5;O76083-3;O76083	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PDE9A_HUMAN	M	511;443;571;518;504;470;485;545;469;530;437;411;443;444	ENSP00000335242:T511M;ENSP00000441899:T443M;ENSP00000291539:T571M;ENSP00000369685:T518M;ENSP00000381287:T504M;ENSP00000381289:T470M;ENSP00000381291:T485M;ENSP00000328699:T545M;ENSP00000335365:T469M;ENSP00000381281:T530M;ENSP00000381285:T437M;ENSP00000381283:T411M;ENSP00000344730:T443M;ENSP00000381280:T444M	ENSP00000291539:T571M	T	+	2	0	PDE9A	43065643	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.028000	0.13644	0.392000	0.25172	-0.234000	0.12200	ACG	C|0.999;T|0.001	0.001	strong		0.527	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
OR6C76	390326	hgsc.bcm.edu	37	12	55820358	55820358	+	Silent	SNP	G	G	A	rs12322458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55820358G>A	ENST00000328314.3	+	1	321	c.321G>A	c.(319-321)acG>acA	p.T107T		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	107						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)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TTGGCTCAACGGAGTTTTTCC	0.408													g|||	97	0.019369	0.0673	0.0115	5008	,	,		15616	0.0		0.0	False		,,,				2504	0.0				p.T107T		Atlas-SNP	.											.	OR6C76	98	.	0			c.G321A						PASS	.			262,4144	140.0+/-175.5	7,248,1948	116.0	128.0	124.0		321	-1.2	0.7	12	dbSNP_120	124	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous	OR6C76	NM_001005183.1		7,251,6243	AA,AG,GG		0.0349,5.9464,2.0381		107/313	55820358	265,12737	2203	4298	6501	SO:0001819	synonymous_variant	390326	exon1			CTCAACGGAGTTT		CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"""GPCR / Class A : Olfactory receptors"""	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.321G>A	12.37:g.55820358G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_001005183		Silent	SNP	ENST00000328314.3	37	CCDS31823.1																																																																																			G|0.978;A|0.022	0.022	strong		0.408	OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
ADAM12	8038	hgsc.bcm.edu	37	10	127753478	127753478	+	Silent	SNP	G	G	A	rs1278279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:127753478G>A	ENST00000368679.4	-	14	1824	c.1515C>T	c.(1513-1515)aaC>aaT	p.N505N	ADAM12_ENST00000467145.1_5'UTR|ADAM12_ENST00000368676.4_Silent_p.N505N	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	103	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	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		
FAM188B	84182	hgsc.bcm.edu	37	7	30831144	30831144	+	Silent	SNP	C	C	T	rs16875355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30831144C>T	ENST00000265299.6	+	5	1104	c.1027C>T	c.(1027-1029)Ctg>Ttg	p.L343L	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	343										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCAGGAGAGGCTGGAAAGAGC	0.577													C|||	769	0.153554	0.323	0.0591	5008	,	,		19581	0.2054		0.0209	False		,,,				2504	0.0746				p.L343L		Atlas-SNP	.											.	FAM188B	62	.	0			c.C1027T						PASS	.	C		1052,3036		128,796,1120	40.0	50.0	47.0		1027	4.6	1.0	7	dbSNP_123	47	211,8197		4,203,3997	no	coding-synonymous	FAM188B	NM_032222.2		132,999,5117	TT,TC,CC		2.5095,25.7339,10.1072		343/758	30831144	1263,11233	2044	4204	6248	SO:0001819	synonymous_variant	84182	exon5			GAGAGGCTGGAAA	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.1027C>T	7.37:g.30831144C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_032222	Q71AZ7|Q9H6D2	Silent	SNP	ENST00000265299.6	37	CCDS43565.1																																																																																			C|0.861;T|0.139	0.139	strong		0.577	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
IRGQ	126298	hgsc.bcm.edu	37	19	44098963	44098963	+	Silent	SNP	C	C	G	rs304725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44098963C>G	ENST00000602269.1	-	1	713	c.528G>C	c.(526-528)cgG>cgC	p.R176R	ZNF576_ENST00000336564.4_5'Flank|L34079.2_ENST00000594374.1_5'Flank|IRGQ_ENST00000601520.1_5'Flank|ZNF576_ENST00000391965.2_5'Flank|ZNF576_ENST00000533118.1_5'Flank|SRRM5_ENST00000526798.1_5'Flank|SRRM5_ENST00000607544.1_5'Flank|IRGQ_ENST00000422989.1_Silent_p.R176R|ZNF576_ENST00000525771.1_5'Flank|ZNF576_ENST00000529930.1_5'Flank|ZNF576_ENST00000528387.1_5'Flank			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	176										endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				GCACTCACCTCCGCAGCGCTT	0.657													C|||	2470	0.493211	0.4017	0.5274	5008	,	,		12894	0.4911		0.5427	False		,,,				2504	0.544				p.R176R		Atlas-SNP	.											.	IRGQ	40	.	0			c.G528C						PASS	.	C		1940,2460		440,1060,700	19.0	22.0	21.0		528	4.8	1.0	19	dbSNP_79	21	4601,3987		1242,2117,935	no	coding-synonymous	IRGQ	NM_001007561.2		1682,3177,1635	GG,GC,CC		46.4252,44.0909,49.6381		176/624	44098963	6541,6447	2200	4294	6494	SO:0001819	synonymous_variant	126298	exon2			TCACCTCCGCAGC	AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"""immunity-related GTPase family, Q1"""	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.528G>C	19.37:g.44098963C>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	52	17	0.326923	NM_001007561	B2RNP3	Silent	SNP	ENST00000602269.1	37	CCDS33040.1																																																																																			C|0.497;G|0.503	0.503	strong		0.657	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48597114	48597114	+	Silent	SNP	C	C	T	rs28498091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48597114C>T	ENST00000323776.5	+	7	1173	c.1011C>T	c.(1009-1011)caC>caT	p.H337H	MYCBPAP_ENST00000468821.1_3'UTR|MYCBPAP_ENST00000436259.2_Silent_p.H300H	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			CCATCACTCACATCAGGAAGC	0.577													C|||	832	0.166134	0.3631	0.0937	5008	,	,		21016	0.0496		0.1421	False		,,,				2504	0.0961				p.H337H		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.C1011T						PASS	.	C		1566,2840	487.6+/-361.0	285,996,922	74.0	62.0	66.0		1011	2.3	0.0	17	dbSNP_125	66	1235,7365	245.8+/-274.5	90,1055,3155	no	coding-synonymous	MYCBPAP	NM_032133.4		375,2051,4077	TT,TC,CC		14.3605,35.5424,21.5362		337/985	48597114	2801,10205	2203	4300	6503	SO:0001819	synonymous_variant	84073	exon7			CACTCACATCAGG	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.1011C>T	17.37:g.48597114C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	80	45	0.5625	NM_032133		Silent	SNP	ENST00000323776.5	37	CCDS32680.2																																																																																			C|0.802;T|0.198	0.198	strong		0.577	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
MRPS11	64963	hgsc.bcm.edu	37	15	89015930	89015930	+	Silent	SNP	T	T	C	rs9920196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89015930T>C	ENST00000325844.4	+	3	520	c.255T>C	c.(253-255)atT>atC	p.I85I	MRPS11_ENST00000353598.6_Intron|MRPS11_ENST00000557974.1_Intron	NM_022839.3	NP_073750.2	P82912	RT11_HUMAN	mitochondrial ribosomal protein S11	85					DNA damage response, detection of DNA damage (GO:0042769)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(3)	3	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			AGATCCCAATTGCACACATTA	0.458													C|||	389	0.0776757	0.2663	0.0187	5008	,	,		19889	0.006		0.001	False		,,,				2504	0.0174				p.I85I		Atlas-SNP	.											.	MRPS11	14	.	0			c.T255C						PASS	.	C	,	1023,3379	726.8+/-409.8	129,765,1307	59.0	58.0	58.0		255,	-5.0	0.8	15	dbSNP_119	58	8,8590	818.9+/-406.8	0,8,4291	no	coding-synonymous,intron	MRPS11	NM_022839.3,NM_176805.2	,	129,773,5598	CC,CT,TT		0.093,23.2394,7.9308	,	85/195,	89015930	1031,11969	2201	4299	6500	SO:0001819	synonymous_variant	64963	exon3			CCCAATTGCACAC	AB051349	CCDS10342.1, CCDS10343.1	15q25	2012-09-13			ENSG00000181991	ENSG00000181991		"""Mitochondrial ribosomal proteins / small subunits"""	14050	protein-coding gene	gene with protein product	"""cervical cancer proto-oncogene 2"""	611977				11402041	Standard	NM_022839		Approved	FLJ23406, HCC-2, FLJ22512	uc002bml.3	P82912	OTTHUMG00000148678	ENST00000325844.4:c.255T>C	15.37:g.89015930T>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	201	100	0.497512	NM_022839	B2RD52|Q969D7|Q96GI3|Q9BYC3	Silent	SNP	ENST00000325844.4	37	CCDS10342.1																																																																																			T|0.922;C|0.078	0.078	strong		0.458	MRPS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309067.2	NM_022839	
DNHD1	144132	hgsc.bcm.edu	37	11	6549995	6549995	+	Missense_Mutation	SNP	A	A	G	rs7480644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6549995A>G	ENST00000527990.2	+	9	2081	c.2081A>G	c.(2080-2082)aAt>aGt	p.N694S	DNHD1_ENST00000254579.6_Missense_Mutation_p.N694S			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	694					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)		CAGGCACTGAATATACAACAG	0.537													A|||	3633	0.725439	0.6831	0.6571	5008	,	,		20488	0.87		0.6302	False		,,,				2504	0.7802				p.N694S		Atlas-SNP	.											DNHD1,colon,carcinoma,0,1	DNHD1	198	1	0			c.A2081G						PASS	.	A	SER/ASN	937,447		321,295,76	55.0	47.0	49.0		2081	-0.9	0.0	11	dbSNP_116	49	2141,1041		726,689,176	yes	missense	DNHD1	NM_144666.2	46	1047,984,252	GG,GA,AA		32.7153,32.2977,32.5887	benign	694/4754	6549995	3078,1488	692	1591	2283	SO:0001583	missense	144132	exon11			CACTGAATATACA	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.2081A>G	11.37:g.6549995A>G	ENSP00000436180:p.Asn694Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	1547	0.7083333333333334	342	0.6951219512195121	235	0.649171270718232	484	0.8461538461538461	486	0.6411609498680739	A	2.474	-0.321286	0.05386	0.677023	0.672847	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.26223	1.75;1.75	5.6	-0.949	0.10376	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.14012	0.009	B	0.10450	0.005	T	0.27739	-1.0065	8	0.09338	T	0.73	.	1.8355	0.03139	0.4088:0.3113:0.1243:0.1556	rs7480644;rs58671974;rs7480644	694	Q96M86	DNHD1_HUMAN	S	694	ENSP00000254579:N694S;ENSP00000436180:N694S	ENSP00000254579:N694S	N	+	2	0	DNHD1	6506571	0.001000	0.12720	0.006000	0.13384	0.022000	0.10575	-0.181000	0.09740	-0.478000	0.06823	-1.017000	0.02453	AAT	A|0.284;G|0.716	0.716	strong		0.537	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919240	51919240	+	Silent	SNP	C	C	T	rs79484306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51919240C>T	ENST00000339313.5	-	5	1052	c.936G>A	c.(934-936)ggG>ggA	p.G312G	SIGLEC10_ENST00000356298.5_Silent_p.G312G|SIGLEC10_ENST00000525998.1_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000439889.2_Silent_p.G254G|SIGLEC10_ENST00000353836.5_Silent_p.G312G|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000432469.2_Silent_p.G229G|SIGLEC10_ENST00000436984.2_Silent_p.G264G|SIGLEC10_ENST00000441969.3_Silent_p.G254G|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000442846.3_Intron			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	312	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CAGCCTTCACCCCGGGCAGCT	0.672																																					p.G312G		Atlas-SNP	.											SIGLEC12_ENST00000439889,NS,carcinoma,-2,2	SIGLEC10	112	2	0			c.G936A						PASS	.						37.0	42.0	40.0					19																	51919240		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			CTTCACCCCGGGC	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.936G>A	19.37:g.51919240C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	223	50	0.224215	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			C|0.910;T|0.090	0.090	strong		0.672	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
ANK1	286	hgsc.bcm.edu	37	8	41522407	41522407	+	Intron	SNP	G	G	C	rs112350393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:41522407G>C	ENST00000347528.4	-	40	5478				RP11-930P14.1_ENST00000585088.1_RNA|RP11-930P14.1_ENST00000520418.1_RNA|ANK1_ENST00000352337.4_Intron|ANK1_ENST00000396942.1_Intron|ANK1_ENST00000522543.1_Missense_Mutation_p.D45E|RP11-930P14.1_ENST00000522388.1_RNA|ANK1_ENST00000314214.8_Missense_Mutation_p.D45E|ANK1_ENST00000265709.8_Intron|ANK1_ENST00000289734.7_Intron|ANK1_ENST00000522231.1_Missense_Mutation_p.D45E|ANK1_ENST00000457297.1_Missense_Mutation_p.D45E|ANK1_ENST00000379758.2_Intron|ANK1_ENST00000396945.1_Intron	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic						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)			CCAGCTCCTTGTCCAGCTCCT	0.612													G|||	147	0.029353	0.1104	0.0014	5008	,	,		18468	0.0		0.0	False		,,,				2504	0.0				p.D45E		Atlas-SNP	.											.	ANK1	497	.	0			c.C135G						PASS	.	G	,GLU/ASP,,,,,GLU/ASP,GLU/ASP	405,4001	200.8+/-224.0	31,343,1829	80.0	58.0	65.0		,135,,,,,135,135	4.6	1.0	8	dbSNP_132	65	4,8596	3.0+/-9.4	0,4,4296	yes	intron,missense,intron,intron,intron,intron,missense,missense	ANK1	NM_000037.3,NM_001142445.1,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2,NM_020478.4,NM_020480.4	,45,,,,,45,45	31,347,6125	CC,CG,GG		0.0465,9.192,3.1447	,,,,,,,	,45/157,,,,,45/156,45/110	41522407	409,12597	2203	4300	6503	SO:0001627	intron_variant	286	exon1			CTCCTTGTCCAGC	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.5395-1147C>G	8.37:g.41522407G>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_020478	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	36	0.016483516483516484	36	0.07317073170731707	0	0.0	0	0.0	0	0.0	G	24.8	4.569350	0.86439	0.09192	4.65E-4	ENSG00000029534	ENST00000457297;ENST00000522231;ENST00000522543;ENST00000314214;ENST00000348036;ENST00000335651	D;D;D	0.87334	-1.81;-2.24;-2.19	5.51	4.63	0.57726	.	.	.	.	.	T	0.41534	0.1163	M	0.67953	2.075	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.83275	0.996;0.994;0.996;0.996	T	0.72087	-0.4396	9	0.72032	D	0.01	.	12.8445	0.57821	0.078:0.0:0.9219:0.0	.	45;45;45;45	Q6PK32;A0PJN8;Q53ER1;E5RFL7	.;.;.;.	E	45	ENSP00000428750:D45E;ENSP00000430368:D45E;ENSP00000319123:D45E	ENSP00000319123:D45E	D	-	3	2	ANK1	41641564	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	4.545000	0.60698	2.585000	0.87301	0.563000	0.77884	GAC	G|0.969;C|0.031	0.031	strong		0.612	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
DDC	1644	hgsc.bcm.edu	37	7	50607694	50607694	+	Silent	SNP	G	G	A	rs11575302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:50607694G>A	ENST00000444124.2	-	3	434	c.234C>T	c.(232-234)gcC>gcT	p.A78A	DDC_ENST00000431062.1_Silent_p.A78A|AC018705.5_ENST00000454521.1_RNA|DDC_ENST00000357936.5_Silent_p.A78A|DDC_ENST00000426377.1_Intron|DDC_ENST00000380984.4_Silent_p.A78A|DDC_ENST00000489162.1_5'UTR	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	78	2 X approximate tandem repeats.				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)	TGGGGAAGTAGGCGAAGAAGT	0.642													G|||	224	0.0447284	0.1415	0.0144	5008	,	,		20045	0.001		0.0169	False		,,,				2504	0.0092				p.A78A		Atlas-SNP	.											.	DDC	100	.	0			c.C234T						PASS	.	G	,,,,,,	616,3788	259.5+/-263.1	36,544,1622	108.0	87.0	94.0		234,234,,234,,234,234	3.7	1.0	7	dbSNP_120	94	125,8475	63.1+/-125.2	0,125,4175	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous,coding-synonymous	DDC	NM_000790.3,NM_001082971.1,NM_001242886.1,NM_001242887.1,NM_001242888.1,NM_001242889.1,NM_001242890.1	,,,,,,	36,669,5797	AA,AG,GG		1.4535,13.9873,5.6982	,,,,,,	78/481,78/481,,78/433,,78/388,78/339	50607694	741,12263	2202	4300	6502	SO:0001819	synonymous_variant	1644	exon3			GAAGTAGGCGAAG		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.234C>T	7.37:g.50607694G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	177	70	0.39548	NM_001082971	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Silent	SNP	ENST00000444124.2	37	CCDS5511.1	76	0.0347985347985348	57	0.11585365853658537	7	0.019337016574585635	0	0.0	12	0.0158311345646438	G	16.15	3.042691	0.55003	0.139873	0.014535	ENSG00000132437	ENST00000430300	.	.	.	5.5	3.66	0.41972	.	.	.	.	.	T	0.00784	0.0026	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00103	-1.2060	4	.	.	.	-21.0922	11.6003	0.50999	0.1488:0.0:0.8512:0.0	rs11575302;rs11575302	.	.	.	L	44	.	.	P	-	2	0	DDC	50575188	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.849000	0.27723	1.284000	0.44531	0.655000	0.94253	CCT	G|0.948;A|0.052	0.052	strong		0.642	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1		
THAP11	57215	hgsc.bcm.edu	37	16	67876805	67876805	+	Silent	SNP	A	A	G	rs28434205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67876805A>G	ENST00000303596.1	+	1	593	c.348A>G	c.(346-348)caA>caG	p.Q116Q	CENPT_ENST00000562787.1_Intron	NM_020457.2	NP_065190.2	Q96EK4	THA11_HUMAN	THAP domain containing 11	116	Gln-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.Q116Q(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	8		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		aacagcagcaacagcagcagc	0.682																																					p.Q116Q		Atlas-SNP	.											THAP11,bladder,carcinoma,0,3	THAP11	27	3	1	Substitution - coding silent(1)	lung(1)	c.A348G						PASS	.	G	,	14,3828		0,14,1907	21.0	26.0	24.0		348,	-3.2	0.7	16	dbSNP_125	24	20,7612		0,20,3796	no	coding-synonymous,intron	THAP11,CENPT	NM_020457.2,NM_025082.3	,	0,34,5703	GG,GA,AA		0.2621,0.3644,0.2963	,	116/315,	67876805	34,11440	1921	3816	5737	SO:0001819	synonymous_variant	57215	exon1			GCAGCAACAGCAG	AB015338	CCDS10847.1	16q22.1	2013-01-25			ENSG00000168286	ENSG00000168286		"""THAP (C2CH-type zinc finger) domain containing"""	23194	protein-coding gene	gene with protein product		609119				12575992, 8325628	Standard	NM_020457		Approved	HRIHFB2206, CTG-B45d, CTG-B43a	uc002euo.3	Q96EK4	OTTHUMG00000137546	ENST00000303596.1:c.348A>G	16.37:g.67876805A>G		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	19	7	0.368421	NM_020457	A4UCT5|A8K002|O94795	Silent	SNP	ENST00000303596.1	37	CCDS10847.1																																																																																			A|0.991;G|0.009	0.009	strong		0.682	THAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268879.1	NM_020457	
CDRT4	284040	hgsc.bcm.edu	37	17	15341183	15341183	+	Missense_Mutation	SNP	A	A	C	rs2954759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15341183A>C	ENST00000312177.6	-	4	643	c.363T>G	c.(361-363)caT>caG	p.H121Q	CDRT4_ENST00000519354.1_5'UTR|TVP23C-CDRT4_ENST00000522212.2_3'UTR	NM_001204477.1	NP_001191406.1	Q8N9R6	CDRT4_HUMAN	CMT1A duplicated region transcript 4	121			H -> Q (in dbSNP:rs2954759).							endometrium(3)|skin(1)	4				UCEC - Uterine corpus endometrioid carcinoma (92;0.0874)		TGGAATCCGCATGTAAGTGTG	0.488													A|||	1603	0.320088	0.3646	0.2305	5008	,	,		19529	0.4583		0.0984	False		,,,				2504	0.409				p.H122Q		Atlas-SNP	.											.	CDRT4	11	.	0			c.T366G						PASS	.	A	GLN/HIS,	1487,2919	476.8+/-357.7	251,985,967	153.0	136.0	142.0		366,	-9.4	0.0	17	dbSNP_101	142	863,7737	195.8+/-240.9	43,777,3480	yes	missense,utr-3	CDRT4,FAM18B2-CDRT4	NM_001204477.1,NM_001204478.1	24,	294,1762,4447	CC,CA,AA		10.0349,33.7494,18.0686	possibly-damaging,	122/153,	15341183	2350,10656	2203	4300	6503	SO:0001583	missense	284040	exon4			ATCCGCATGTAAG	BC029542	CCDS73995.1	17p12	2011-09-28			ENSG00000239704	ENSG00000239704			14383	protein-coding gene	gene with protein product						11381029	Standard	NM_001204477		Approved	FLJ36674	uc002gop.2	Q8N9R6	OTTHUMG00000059070	ENST00000312177.6:c.363T>G	17.37:g.15341183A>C	ENSP00000310031:p.His121Gln	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	190	189	0.994737	NM_001204477	A8MSL9|Q8IZ19	Missense_Mutation	SNP	ENST00000312177.6	37		599	0.2742673992673993	190	0.3861788617886179	81	0.22375690607734808	254	0.44405594405594406	74	0.09762532981530343	A	8.850	0.944256	0.18356	0.337494	0.100349	ENSG00000239704	ENST00000520956;ENST00000312177	T	0.30448	1.53	4.67	-9.35	0.00633	.	0.925264	0.09032	N	0.858570	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.43310	-0.9399	9	0.27785	T	0.31	-3.8928	1.3169	0.02109	0.3108:0.2808:0.2765:0.1319	rs2954759;rs2954759	121	Q8N9R6	CDRT4_HUMAN	Q	122;121	ENSP00000310031:H121Q	ENSP00000310031:H121Q	H	-	3	2	CDRT4	15281908	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.801000	0.01743	-1.745000	0.01337	-1.283000	0.01379	CAT	A|0.767;C|0.233	0.233	strong		0.488	CDRT4-001	KNOWN	non_canonical_conserved|non_canonical_other|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000130383.7	NM_173622	
SF3A1	10291	hgsc.bcm.edu	37	22	30733111	30733111	+	Silent	SNP	C	C	A	rs2229807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30733111C>A	ENST00000215793.8	-	13	2164	c.2010G>T	c.(2008-2010)gtG>gtT	p.V670V	SF3A1_ENST00000439242.1_Silent_p.V605V	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	670					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						GTGGGGGATGCACAGGGGGCA	0.572													A|||	769	0.153554	0.1331	0.1556	5008	,	,		17096	0.1448		0.2535	False		,,,				2504	0.0859				p.V670V		Atlas-SNP	.											.	SF3A1	61	.	0			c.G2010T						PASS	.	A	,	667,3739	763.8+/-413.2	56,555,1592	55.0	55.0	55.0		1815,2010	-2.6	0.9	22	dbSNP_98	55	2193,6407	711.1+/-405.8	284,1625,2391	no	coding-synonymous,coding-synonymous	SF3A1	NM_001005409.1,NM_005877.4	,	340,2180,3983	AA,AC,CC		25.5,15.1384,21.9899	,	605/729,670/794	30733111	2860,10146	2203	4300	6503	SO:0001819	synonymous_variant	10291	exon13			GGGATGCACAGGG	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"""splicing factor 3a, subunit 1, 120kD"""			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.2010G>T	22.37:g.30733111C>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	134	77	0.574627	NM_005877	E9PAW1	Silent	SNP	ENST00000215793.8	37	CCDS13875.1																																																																																			C|0.795;A|0.205	0.205	strong		0.572	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877	
SSPO	23145	hgsc.bcm.edu	37	7	149509691	149509691	+	RNA	SNP	G	G	A	rs73727635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149509691G>A	ENST00000378016.2	+	0	9965							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)			TATAGCCCCTGTGGCCCTCCG	0.632													G|||	305	0.0609026	0.205	0.0216	5008	,	,		17503	0.004		0.003	False		,,,				2504	0.0123				p.C3322Y		Atlas-SNP	.											.	.	.	.	0			c.G9965A						PASS	.	G		732,3432		57,618,1407	73.0	81.0	79.0		9975	4.5	1.0	7	dbSNP_130	79	37,8389		0,37,4176	no	coding-notMod3	SSPO	NM_198455.2		57,655,5583	AA,AG,GG		0.4391,17.5793,6.108			149509691	769,11821	2082	4213	6295			23145	exon70			GCCCCTGTGGCCC	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.149509691G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.960;A|0.040	0.040	strong		0.632	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
SH3RF2	153769	hgsc.bcm.edu	37	5	145428665	145428665	+	Silent	SNP	C	C	A	rs35937996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:145428665C>A	ENST00000511217.1	+	6	1231	c.1179C>A	c.(1177-1179)gcC>gcA	p.A393A	SH3RF2_ENST00000359120.4_Silent_p.A393A			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	393	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)			CCTACTCAGCCCATGGACCCG	0.627											OREG0016895	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	103	0.0205671	0.0673	0.0072	5008	,	,		17530	0.0		0.0	False		,,,				2504	0.0092				p.A393A		Atlas-SNP	.											.	SH3RF2	58	.	0			c.C1179A						PASS	.	C		232,4174	136.5+/-172.5	2,228,1973	72.0	59.0	63.0		1179	4.3	1.0	5	dbSNP_126	63	0,8600		0,0,4300	no	coding-synonymous	SH3RF2	NM_152550.3		2,228,6273	AA,AC,CC		0.0,5.2655,1.7838		393/730	145428665	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	153769	exon7			CTCAGCCCATGGA	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.1179C>A	5.37:g.145428665C>A		Somatic	74	0	0	1694	WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_152550	A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Silent	SNP	ENST00000511217.1	37	CCDS4280.1																																																																																			C|0.982;A|0.018	0.018	strong		0.627	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550	
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156084	39156084	+	Missense_Mutation	SNP	T	T	C	rs386797022|rs9897046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39156084T>C	ENST00000391587.1	-	1	54	c.22A>G	c.(22-24)Agc>Ggc	p.S8G		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	8	3 X 5 AA repeats of C-C-X(3).		S -> G (in dbSNP:rs9897046).			keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				ACACTGCAGCTGCGAGAGGCA	0.557													.|||	1497	0.298922	0.6112	0.2061	5008	,	,		18132	0.2312		0.1223	False		,,,				2504	0.1943				p.S8G		Atlas-SNP	.											.	KRTAP3-2	11	.	0			c.A22G						PASS	.	C	GLY/SER	1814,2592		562,690,951	65.0	76.0	72.0		22	-0.5	0.1	17	dbSNP_119	72	766,7826		42,682,3572	no	missense	KRTAP3-2	NM_031959.2	56	604,1372,4523	CC,CT,TT		8.9153,41.1711,19.8492	benign	8/99	39156084	2580,10418	2203	4296	6499	SO:0001583	missense	83897	exon1			TGCAGCTGCGAGA	AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"""Keratin associated proteins"""	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.22A>G	17.37:g.39156084T>C	ENSP00000375429:p.Ser8Gly	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	178	61	0.342697	NM_031959		Missense_Mutation	SNP	ENST00000391587.1	37	CCDS32644.1	575	0.2632783882783883	275	0.5589430894308943	68	0.1878453038674033	143	0.25	89	0.11741424802110818	C	0.013	-1.614825	0.00835	0.411711	0.089153	ENSG00000212900	ENST00000391587	T	0.24350	1.86	5.76	-0.514	0.11958	.	0.289408	0.30356	N	0.009810	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46303	-0.9201	8	0.30078	T	0.28	.	9.5685	0.39414	0.2876:0.5656:0.0:0.1468	rs9897046	8	Q9BYR7	KRA32_HUMAN	G	8	ENSP00000375429:S8G	ENSP00000375429:S8G	S	-	1	0	KRTAP3-2	36409610	0.300000	0.24435	0.100000	0.21137	0.009000	0.06853	-0.147000	0.10234	-0.762000	0.04664	-4.665000	0.00003	AGC	C|0.266;N|0.000	0.266	strong		0.557	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257685.1		
FMN2	56776	hgsc.bcm.edu	37	1	240371409	240371409	+	Silent	SNP	G	G	T	rs373533409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:240371409G>T	ENST00000319653.9	+	5	3527	c.3297G>T	c.(3295-3297)ccG>ccT	p.P1099P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1099	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)			TACCCCCTCCGCCCCCTCTAC	0.731																																					p.P1099P		Atlas-SNP	.											FMN2,NS,neuroblastoma,0,1	FMN2	451	1	0			c.G3297T						scavenged	.						6.0	8.0	8.0					1																	240371409		2016	4072	6088	SO:0001819	synonymous_variant	56776	exon5			CCCTCCGCCCCCT	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.3297G>T	1.37:g.240371409G>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	149	7	0.0469799	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			.	.	none		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
TLE6	79816	hgsc.bcm.edu	37	19	2994903	2994903	+	Silent	SNP	T	T	C	rs34831575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2994903T>C	ENST00000246112.4	+	17	1821	c.1620T>C	c.(1618-1620)ccT>ccC	p.P540P	TLE6_ENST00000452088.1_Silent_p.P417P	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	540					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)		TCCAGGTGCCTGAGATGTCTC	0.597													t|||	1588	0.317093	0.4077	0.3919	5008	,	,		11958	0.3353		0.2356	False		,,,				2504	0.2065				p.P540P		Atlas-SNP	.											.	TLE6	68	.	0			c.T1620C						PASS	.	C	,	1572,2832		304,964,934	63.0	42.0	49.0		1620,1251	-3.0	0.0	19	dbSNP_126	49	1893,6705		207,1479,2613	no	coding-synonymous,coding-synonymous	TLE6	NM_001143986.1,NM_024760.2	,	511,2443,3547	CC,CT,TT		22.0167,35.6948,26.6497	,	540/573,417/450	2994903	3465,9537	2202	4299	6501	SO:0001819	synonymous_variant	79816	exon17			GGTGCCTGAGATG	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.1620T>C	19.37:g.2994903T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001143986	J3KMZ1	Silent	SNP	ENST00000246112.4	37	CCDS45910.1	704	0.32234432234432236	186	0.3780487804878049	125	0.3453038674033149	206	0.36013986013986016	187	0.24670184696569922	t	4.589	0.109429	0.08780	0.356948	0.220167	ENSG00000104953	ENST00000441927	.	.	.	3.37	-3.05	0.05396	.	.	.	.	.	.	.	.	.	.	.	0.23496	P	0.99755694	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.3614	5.1751	0.15131	0.0:0.3401:0.1554:0.5044	rs34831575	.	.	.	R	417	.	.	X	+	1	0	TLE6	2945903	.	.	0.008000	0.14137	0.003000	0.03518	.	.	-0.787000	0.04510	-0.946000	0.02672	TGA	T|0.715;C|0.285	0.285	strong		0.597	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760	
FERMT3	83706	hgsc.bcm.edu	37	11	63988045	63988045	+	Silent	SNP	G	G	A	rs3802932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:63988045G>A	ENST00000279227.5	+	12	1556	c.1461G>A	c.(1459-1461)ccG>ccA	p.P487P	FERMT3_ENST00000345728.5_Silent_p.P483P	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	487	FERM.				integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						GTGGGGGCCCGGGCAACCACC	0.682													G|||	828	0.165335	0.1172	0.147	5008	,	,		15893	0.4762		0.0726	False		,,,				2504	0.0184				p.P487P		Atlas-SNP	.											URP2,NS,carcinoma,0,2	FERMT3	51	2	0			c.G1461A						scavenged	.	G	,	431,3951		29,373,1789	11.0	13.0	12.0		1449,1461	-8.6	0.0	11	dbSNP_107	12	480,8084		24,432,3826	no	coding-synonymous,coding-synonymous	FERMT3	NM_031471.5,NM_178443.2	,	53,805,5615	AA,AG,GG		5.6049,9.8357,7.0369	,	483/664,487/668	63988045	911,12035	2191	4282	6473	SO:0001819	synonymous_variant	83706	exon12			GGGCCCGGGCAAC	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	23151	protein-coding gene	gene with protein product	"""kindlin-3"""	607901	"""fermitin family homolog 3 (Drosophila)"""				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.1461G>A	11.37:g.63988045G>A		Somatic	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	80	46	0.575	NM_178443	Q8IUA1|Q8N207|Q9BT48	Silent	SNP	ENST00000279227.5	37	CCDS8060.1	432	0.1978021978021978	65	0.13211382113821138	45	0.12430939226519337	271	0.4737762237762238	51	0.06728232189973615	G	0.006	-2.020701	0.00418	0.098357	0.056049	ENSG00000149781	ENST00000545896	T	0.56611	0.45	4.31	-8.61	0.00885	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25357	P	0.9888111	.	.	.	.	.	.	T	0.11767	-1.0574	5	0.38643	T	0.18	-6.5345	0.571	0.00695	0.3445:0.2066:0.2388:0.21	rs3802932	.	.	.	Q	46	ENSP00000440209:R46Q	ENSP00000440209:R46Q	R	+	2	0	FERMT3	63744621	0.000000	0.05858	0.024000	0.17045	0.006000	0.05464	-1.539000	0.02202	-3.948000	0.00088	-2.961000	0.00082	CGG	G|0.808;A|0.192	0.192	strong		0.682	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471	
EIF1AD	84285	hgsc.bcm.edu	37	11	65767578	65767578	+	Missense_Mutation	SNP	G	G	A	rs35497370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65767578G>A	ENST00000312234.2	-	3	476	c.142C>T	c.(142-144)Cgc>Tgc	p.R48C	EIF1AD_ENST00000526451.1_Missense_Mutation_p.R48C|EIF1AD_ENST00000525767.1_5'UTR|EIF1AD_ENST00000533544.1_Missense_Mutation_p.R48C|EIF1AD_ENST00000527249.1_Missense_Mutation_p.R48C|BANF1_ENST00000445560.2_5'Flank|BANF1_ENST00000527348.1_5'Flank|BANF1_ENST00000533166.1_5'Flank|BANF1_ENST00000312175.2_5'Flank|EIF1AD_ENST00000529964.1_Missense_Mutation_p.R48C	NM_001242481.1|NM_001242482.1|NM_001242483.1|NM_032325.3	NP_001229410.1|NP_001229411.1|NP_001229412.1|NP_115701.2	Q8N9N8	EIF1A_HUMAN	eukaryotic translation initiation factor 1A domain containing	48	S1-like. {ECO:0000255|PROSITE- ProRule:PRU00181}.					intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	translation initiation factor activity (GO:0003743)			lung(5)	5						ACCAGGAAGCGCTGCCCTTGG	0.517													G|||	16	0.00319489	0.0113	0.0014	5008	,	,		21003	0.0		0.0	False		,,,				2504	0.0				p.R48C		Atlas-SNP	.											EIF1AD,colon,carcinoma,+1,1	EIF1AD	10	1	0			c.C142T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	29,4373	36.0+/-67.5	0,29,2172	128.0	115.0	119.0		142,142,142,142,142,142,142	5.3	1.0	11	dbSNP_126	119	0,8592		0,0,4296	yes	missense,missense,missense,missense,missense,missense,missense	EIF1AD	NM_001242481.1,NM_001242482.1,NM_001242483.1,NM_001242484.1,NM_001242485.1,NM_001242486.1,NM_032325.3	180,180,180,180,180,180,180	0,29,6468	AA,AG,GG		0.0,0.6588,0.2232	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	48/166,48/166,48/166,48/166,48/166,48/166,48/166	65767578	29,12965	2201	4296	6497	SO:0001583	missense	84285	exon3			GGAAGCGCTGCCC	AK094129	CCDS8124.1	11q13.1	2009-05-27				ENSG00000175376			28147	protein-coding gene	gene with protein product						12477932	Standard	NM_001242482		Approved	MGC11102, haponin	uc001ogn.2	Q8N9N8		ENST00000312234.2:c.142C>T	11.37:g.65767578G>A	ENSP00000309175:p.Arg48Cys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_001242483	B2R4N5|Q9BSC1	Missense_Mutation	SNP	ENST00000312234.2	37	CCDS8124.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	26.8	4.770117	0.90108	0.006588	0.0	ENSG00000175376	ENST00000526451;ENST00000312234;ENST00000529964;ENST00000533544;ENST00000527249;ENST00000530462;ENST00000532707;ENST00000527051	T;T;T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87	5.31	5.31	0.75309	Nucleic acid-binding, OB-fold-like (1);RNA-binding domain, S1, IF1 type (2);Nucleic acid-binding, OB-fold (1);	0.170574	0.50627	D	0.000112	T	0.51381	0.1671	M	0.62723	1.935	0.80722	D	1	D	0.60575	0.988	P	0.61477	0.889	T	0.58532	-0.7620	10	0.59425	D	0.04	.	16.4684	0.84092	0.0:0.0:1.0:0.0	rs35497370	48	Q8N9N8	EIF1A_HUMAN	C	48	ENSP00000436644:R48C;ENSP00000309175:R48C;ENSP00000435942:R48C;ENSP00000434056:R48C;ENSP00000435439:R48C;ENSP00000435891:R48C;ENSP00000433320:R48C;ENSP00000432135:R48C	ENSP00000309175:R48C	R	-	1	0	EIF1AD	65524154	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.963000	0.49184	2.488000	0.83962	0.561000	0.74099	CGC	G|0.997;A|0.003	0.003	strong		0.517	EIF1AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391072.1	NM_032325	
VWDE	221806	hgsc.bcm.edu	37	7	12400783	12400783	+	Missense_Mutation	SNP	C	C	T	rs35171886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12400783C>T	ENST00000275358.3	-	15	3337	c.3149G>A	c.(3148-3150)tGt>tAt	p.C1050Y		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1050						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						CTTTATAGTACATGAGTCATT	0.303													C|||	541	0.108027	0.0416	0.0764	5008	,	,		16911	0.1935		0.1044	False		,,,				2504	0.136				p.C1050Y		Atlas-SNP	.											.	VWDE	123	.	0			c.G3149A						PASS	.	C	TYR/CYS	66,1318		1,64,627	54.0	46.0	48.0		3149	4.3	0.4	7	dbSNP_126	48	346,2806		21,304,1251	yes	missense	VWDE	NM_001135924.1	194	22,368,1878	TT,TC,CC		10.9772,4.7688,9.0829	probably-damaging	1050/1591	12400783	412,4124	692	1576	2268	SO:0001583	missense	221806	exon15			ATAGTACATGAGT		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.3149G>A	7.37:g.12400783C>T	ENSP00000275358:p.Cys1050Tyr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	268	0.1227106227106227	20	0.04065040650406504	28	0.07734806629834254	133	0.23251748251748253	87	0.11477572559366754	C	13.96	2.394208	0.42410	0.047688	0.109772	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.89552	-2.53	4.27	4.27	0.50696	.	0.094876	0.85682	D	0.000000	T	0.00468	0.0015	M	0.76574	2.34	0.25395	P	0.9884941	D	0.89917	1.0	D	0.73380	0.98	T	0.00000	-1.2894	9	0.87932	D	0	.	16.2252	0.82286	0.0:1.0:0.0:0.0	rs35171886	1050	Q8N2E2	VWDE_HUMAN	Y	1050;504	ENSP00000275358:C1050Y	ENSP00000275358:C1050Y	C	-	2	0	VWDE	12367308	1.000000	0.71417	0.450000	0.26969	0.109000	0.19521	6.263000	0.72521	2.372000	0.80975	0.655000	0.94253	TGT	C|0.884;T|0.116	0.116	strong		0.303	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
ATAD3B	83858	hgsc.bcm.edu	37	1	1431105	1431105	+	Missense_Mutation	SNP	A	A	G	rs199599542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1431105A>G	ENST00000308647.7	+	16	1971	c.1855A>G	c.(1855-1857)Atg>Gtg	p.M619V		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	619						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)		ATGCTCCTGGATGGGGACTGG	0.667																																					p.M619V		Atlas-SNP	.											.	ATAD3B	68	.	0			c.A1855G						PASS	.						40.0	41.0	40.0					1																	1431105		2201	4300	6501	SO:0001583	missense	83858	exon16			TCCTGGATGGGGA	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.1855A>G	1.37:g.1431105A>G	ENSP00000311766:p.Met619Val	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	171	14	0.0818713	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	g	0.001	-3.345532	0.00016	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.92965	-3.14	1.17	-2.33	0.06724	.	20.081800	0.03609	N	0.234515	T	0.81912	0.4923	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	0.63795	-0.6556	10	0.59425	D	0.04	.	3.1198	0.06387	0.4569:0.0:0.3217:0.2214	.	573;619	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	V	453;619	ENSP00000311766:M619V	ENSP00000311766:M619V	M	+	1	0	ATAD3B	1420968	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.647000	0.01997	-3.583000	0.00137	-2.537000	0.00180	ATG	A|0.994;G|0.006	0.006	strong		0.667	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
KCNV2	169522	hgsc.bcm.edu	37	9	2717922	2717922	+	Silent	SNP	C	C	G	rs10967705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2717922C>G	ENST00000382082.3	+	1	421	c.183C>G	c.(181-183)ggC>ggG	p.G61G		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	61					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)		ACGAAGACGGCGAGGAGGAGG	0.657													G|||	3307	0.660343	0.6346	0.7435	5008	,	,		18238	0.7728		0.5746	False		,,,				2504	0.6084				p.G61G		Atlas-SNP	.											.	KCNV2	72	.	0			c.C183G						PASS	.	G		2797,1609	496.5+/-363.6	880,1037,286	152.0	115.0	128.0		183	-10.7	0.0	9	dbSNP_120	128	4850,3750	529.9+/-381.7	1382,2086,832	no	coding-synonymous	KCNV2	NM_133497.3		2262,3123,1118	GG,GC,CC		43.6047,36.5184,41.2041		61/546	2717922	7647,5359	2203	4300	6503	SO:0001819	synonymous_variant	169522	exon1			AGACGGCGAGGAG	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.183C>G	9.37:g.2717922C>G		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	177	177	1	NM_133497	Q5T6X0	Silent	SNP	ENST00000382082.3	37	CCDS6447.1																																																																																			C|0.389;G|0.611	0.611	strong		0.657	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
KNG1	3827	hgsc.bcm.edu	37	3	186459775	186459775	+	Silent	SNP	C	C	T	rs5030086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186459775C>T	ENST00000265023.4	+	10	1802	c.1590C>T	c.(1588-1590)gaC>gaT	p.D530D	RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000609726.1_RNA|RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000596329.1_RNA|KNG1_ENST00000287611.2_Intron	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	530					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		CTTCTGAAGACAGTACTACAC	0.443													T|||	166	0.033147	0.0613	0.0375	5008	,	,		24246	0.0129		0.0258	False		,,,				2504	0.0204				p.D530D		Atlas-SNP	.											.	KNG1	129	.	0			c.C1590T						PASS	.	T	,,	230,3702		4,222,1740	77.0	73.0	74.0		,1590,	-6.8	0.0	3	dbSNP_113	74	230,8070		5,220,3925	no	intron,coding-synonymous,intron	KNG1	NM_000893.3,NM_001102416.2,NM_001166451.1	,,	9,442,5665	TT,TC,CC		2.7711,5.8494,3.7606	,,	,530/645,	186459775	460,11772	1966	4150	6116	SO:0001819	synonymous_variant	3827	exon10			TGAAGACAGTACT		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"""Endogenous ligands"""	6383	protein-coding gene	gene with protein product	"""alpha-2-thiol proteinase inhibitor"", ""bradykinin"""	612358	"""kininogen"""	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.1590C>T	3.37:g.186459775C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_001102416	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Silent	SNP	ENST00000265023.4	37	CCDS43183.1																																																																																			C|0.965;T|0.035	0.035	strong		0.443	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416	
PEG3	5178	hgsc.bcm.edu	37	19	57327420	57327420	+	Missense_Mutation	SNP	C	C	A	rs35947541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57327420C>A	ENST00000326441.9	-	10	2753	c.2390G>T	c.(2389-2391)aGt>aTt	p.S797I	ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.S797I|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000599935.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.S671I|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.S673I	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	797					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TTTTGGTTTACTGGGCCCTGC	0.448													C|||	47	0.00938498	0.0325	0.0058	5008	,	,		20278	0.0		0.0	False		,,,				2504	0.0				p.S797I		Atlas-SNP	.											.	PEG3	414	.	0			c.G2390T						PASS	.	C	ILE/SER,ILE/SER,ILE/SER,ILE/SER,,,ILE/SER,	90,4316	75.2+/-113.4	2,86,2115	170.0	164.0	166.0		2390,2012,2390,2018,,,2390,	-8.0	0.0	19	dbSNP_126	166	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense,missense,intron,intron,missense,intron	PEG3,ZIM2	NM_001146184.1,NM_001146185.1,NM_001146186.1,NM_001146187.1,NM_001146326.1,NM_001146327.1,NM_006210.2,NM_015363.4	142,142,142,142,,,142,	2,93,6408	AA,AC,CC		0.0814,2.0427,0.7458	benign,benign,benign,benign,,,benign,	797/1589,671/1463,797/1589,673/1465,,,797/1589,	57327420	97,12909	2203	4300	6503	SO:0001583	missense	5178	exon9			GGTTTACTGGGCC	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.2390G>T	19.37:g.57327420C>A	ENSP00000326581:p.Ser797Ile	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	269	132	0.490706	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	C	7.904	0.734982	0.15574	0.020427	8.14E-4	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02763	4.17;4.17	3.98	-7.96	0.01144	.	1.068300	0.07224	N	0.861338	T	0.00967	0.0032	L	0.35723	1.085	.	.	.	B;B;B	0.10296	0.001;0.003;0.003	B;B;B	0.10450	0.002;0.005;0.005	T	0.46105	-0.9215	9	0.51188	T	0.08	0.2926	0.5139	0.00600	0.2901:0.135:0.2875:0.2874	rs35947541	673;797;732	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	I	797	ENSP00000326581:S797I;ENSP00000403051:S797I	ENSP00000326581:S797I	S	-	2	0	ZIM2	62019232	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.085000	0.00611	-2.096000	0.00852	-1.105000	0.02106	AGT	C|0.993;A|0.007	0.007	strong		0.448	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
ATP8A1	10396	hgsc.bcm.edu	37	4	42629038	42629038	+	Silent	SNP	C	C	T	rs16854624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:42629038C>T	ENST00000381668.5	-	2	369	c.138G>A	c.(136-138)ctG>ctA	p.L46L	ATP8A1_ENST00000510289.1_Silent_p.L46L|ATP8A1_ENST00000264449.10_Silent_p.L46L	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	46					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	AGAATTTTGTCAGCTGGGGCT	0.438													C|||	414	0.0826677	0.1543	0.0418	5008	,	,		18233	0.0377		0.0795	False		,,,				2504	0.0644				p.L46L		Atlas-SNP	.											.	ATP8A1	206	.	0			c.G138A						PASS	.	C	,	691,3715	287.2+/-279.2	55,581,1567	112.0	103.0	106.0		138,138	3.0	1.0	4	dbSNP_123	106	653,7947	166.4+/-218.3	32,589,3679	no	coding-synonymous,coding-synonymous	ATP8A1	NM_001105529.1,NM_006095.2	,	87,1170,5246	TT,TC,CC		7.593,15.6832,10.3337	,	46/1150,46/1165	42629038	1344,11662	2203	4300	6503	SO:0001819	synonymous_variant	10396	exon2			TTTTGTCAGCTGG	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"""ATPases / P-type"""	13531	protein-coding gene	gene with protein product		609542	"""ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"""			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.138G>A	4.37:g.42629038C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	147	57	0.387755	NM_001105529	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Silent	SNP	ENST00000381668.5	37	CCDS3466.1																																																																																			C|0.910;T|0.090	0.090	strong		0.438	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095	
TET1	80312	hgsc.bcm.edu	37	10	70332672	70332672	+	Missense_Mutation	SNP	T	T	A	rs12773594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70332672T>A	ENST00000373644.4	+	2	786	c.577T>A	c.(577-579)Tcc>Acc	p.S193T		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	193			S -> T (in dbSNP:rs12773594).		chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TCAGTTTTGGTCCCAAAGAGT	0.478													T|||	860	0.171725	0.0983	0.1513	5008	,	,		20171	0.1726		0.1849	False		,,,				2504	0.271				p.S193T		Atlas-SNP	.											.	TET1	255	.	0			c.T577A						PASS	.	T	THR/SER	494,3912	227.2+/-242.5	28,438,1737	61.0	61.0	61.0		577	2.5	0.7	10	dbSNP_121	61	1291,7309	252.3+/-278.5	105,1081,3114	yes	missense	TET1	NM_030625.2	58	133,1519,4851	AA,AT,TT		15.0116,11.212,13.7244	benign	193/2137	70332672	1785,11221	2203	4300	6503	SO:0001583	missense	80312	exon2			TTTTGGTCCCAAA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.577T>A	10.37:g.70332672T>A	ENSP00000362748:p.Ser193Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	344	0.1575091575091575	29	0.05894308943089431	64	0.17679558011049723	111	0.19405594405594406	140	0.18469656992084432	T	11.91	1.780553	0.31502	0.11212	0.150116	ENSG00000138336	ENST00000373644	T	0.07688	3.17	5.0	2.55	0.30701	.	1.544370	0.04021	N	0.299769	T	0.00012	0.0000	N	0.24115	0.695	0.53005	P	3.6000000000036E-5	P	0.43477	0.808	B	0.29785	0.107	T	0.46062	-0.9218	9	0.27785	T	0.31	.	6.9496	0.24538	0.0:0.1915:0.0:0.8085	rs12773594;rs52825337;rs12773594	193	Q8NFU7	TET1_HUMAN	T	193	ENSP00000362748:S193T	ENSP00000362748:S193T	S	+	1	0	TET1	70002678	0.006000	0.16342	0.655000	0.29622	0.917000	0.54804	-0.025000	0.12413	0.301000	0.22738	0.460000	0.39030	TCC	T|0.854;A|0.146	0.146	strong		0.478	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
OR4K15	81127	hgsc.bcm.edu	37	14	20443751	20443751	+	Missense_Mutation	SNP	T	T	G	rs139828094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20443751T>G	ENST00000305051.5	+	1	149	c.74T>G	c.(73-75)aTg>aGg	p.M25R		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CCAAAATCGATGAATGAGACA	0.383													T|||	23	0.00459265	0.0174	0.0	5008	,	,		20008	0.0		0.0	False		,,,				2504	0.0				p.M25R		Atlas-SNP	.											.	OR4K15	82	.	0			c.T74G						PASS	.	T	ARG/MET	56,4350		0,56,2147	103.0	104.0	103.0		74	2.0	1.0	14	dbSNP_134	103	2,8596		0,2,4297	yes	missense	OR4K15	NM_001005486.1	91	0,58,6444	GG,GT,TT		0.0233,1.271,0.446	probably-damaging	25/349	20443751	58,12946	2203	4299	6502	SO:0001583	missense	81127	exon1			AATCGATGAATGA		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.74T>G	14.37:g.20443751T>G	ENSP00000304077:p.Met25Arg	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	193	102	0.528497	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	.	12.07	1.827026	0.32329	0.01271	2.33E-4	ENSG00000169488	ENST00000305051	T	0.01414	4.92	3.26	1.98	0.26296	.	0.000000	0.53938	D	0.000058	T	0.02970	0.0088	M	0.90595	3.13	0.22754	N	0.998776	D	0.63880	0.993	D	0.67382	0.951	T	0.12941	-1.0528	10	0.72032	D	0.01	.	2.5999	0.04864	0.2303:0.1328:0.0:0.6369	.	25	Q8NH41	OR4KF_HUMAN	R	25	ENSP00000304077:M25R	ENSP00000304077:M25R	M	+	2	0	OR4K15	19513591	0.762000	0.28451	0.970000	0.41538	0.716000	0.41182	1.136000	0.31467	1.335000	0.45486	0.383000	0.25322	ATG	T|0.994;G|0.006	0.006	strong		0.383	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
C17orf78	284099	hgsc.bcm.edu	37	17	35743010	35743010	+	Missense_Mutation	SNP	C	C	G	rs1714987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	145	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	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	
MMP14	4323	hgsc.bcm.edu	37	14	23312923	23312923	+	Silent	SNP	T	T	C	rs2236307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23312923T>C	ENST00000311852.6	+	6	1116	c.855T>C	c.(853-855)ggT>ggC	p.G285G	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	285					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)	CCCCAGGGGGTGAGTCAGGGT	0.572													T|||	1360	0.271565	0.3313	0.1671	5008	,	,		16355	0.3562		0.2018	False		,,,				2504	0.2495				p.G285G		Atlas-SNP	.											.	MMP14	40	.	0			c.T855C						PASS	.	T		1343,3063	447.5+/-348.4	189,965,1049	100.0	111.0	108.0		855	0.8	0.8	14	dbSNP_98	108	1816,6784	326.7+/-317.5	197,1422,2681	no	coding-synonymous	MMP14	NM_004995.2		386,2387,3730	CC,CT,TT		21.1163,30.4812,24.2888		285/583	23312923	3159,9847	2203	4300	6503	SO:0001819	synonymous_variant	4323	exon6			AGGGGGTGAGTCA		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.855T>C	14.37:g.23312923T>C		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	NM_004995	A8K5L0|Q6GSF3|Q92678	Silent	SNP	ENST00000311852.6	37	CCDS9577.1																																																																																			A|0.000;C|0.247;G|0.000;T|0.753	0.247	strong		0.572	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	
AKNAD1	254268	hgsc.bcm.edu	37	1	109395230	109395230	+	Silent	SNP	A	A	G	rs142279898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109395230A>G	ENST00000370001.3	-	2	325	c.57T>C	c.(55-57)taT>taC	p.Y19Y	AKNAD1_ENST00000369995.3_Silent_p.Y19Y|AKNAD1_ENST00000369994.1_Silent_p.Y19Y|AKNAD1_ENST00000357393.4_Intron	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	19						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						GGTCCCCATCATAAGGCAAAT	0.438													A|||	15	0.00299521	0.0113	0.0	5008	,	,		19172	0.0		0.0	False		,,,				2504	0.0				p.Y19Y		Atlas-SNP	.											.	AKNAD1	83	.	0			c.T57C						PASS	.	A		29,4377	33.5+/-64.1	0,29,2174	72.0	72.0	72.0		57	-0.7	1.0	1	dbSNP_134	72	0,8598		0,0,4299	no	coding-synonymous	AKNAD1	NM_152763.3		0,29,6473	GG,GA,AA		0.0,0.6582,0.223		19/837	109395230	29,12975	2203	4299	6502	SO:0001819	synonymous_variant	254268	exon2			CCCATCATAAGGC	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.57T>C	1.37:g.109395230A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Silent	SNP	ENST00000370001.3	37	CCDS791.2																																																																																			A|0.998;G|0.002	0.002	strong		0.438	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
GLIS3	169792	hgsc.bcm.edu	37	9	4118262	4118262	+	Missense_Mutation	SNP	C	C	A	rs75462592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:4118262C>A	ENST00000324333.10	-	3	944	c.751G>T	c.(751-753)Ggc>Tgc	p.G251C	GLIS3_ENST00000381971.3_Missense_Mutation_p.G406C	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	251					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|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 core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TTGACCAGGCCTGGCTGCAGG	0.721													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		10239	0.0		0.0	False		,,,				2504	0.0				p.G406C		Atlas-SNP	.											.	GLIS3	152	.	0			c.G1216T						PASS	.	C	CYS/GLY,CYS/GLY	67,3403		1,65,1669	5.0	6.0	5.0		1216,751	5.5	0.4	9	dbSNP_131	5	2,6878		0,2,3438	yes	missense,missense	GLIS3	NM_001042413.1,NM_152629.3	159,159	1,67,5107	AA,AC,CC		0.0291,1.9308,0.6667	possibly-damaging,possibly-damaging	406/931,251/776	4118262	69,10281	1735	3440	5175	SO:0001583	missense	169792	exon4			CCAGGCCTGGCTG	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.751G>T	9.37:g.4118262C>A	ENSP00000325494:p.Gly251Cys	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	24	18	0.75	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	C	12.40	1.925708	0.34002	0.019308	2.91E-4	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.10960	2.84;2.82	5.49	5.49	0.81192	.	0.299519	0.22308	U	0.061772	T	0.04770	0.0129	N	0.22421	0.69	0.09310	N	0.999999	D;D	0.57257	0.979;0.964	P;B	0.50378	0.639;0.436	T	0.05115	-1.0905	10	0.38643	T	0.18	.	19.359	0.94428	0.0:1.0:0.0:0.0	.	406;251	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	C	251;406	ENSP00000325494:G251C;ENSP00000371398:G406C	ENSP00000325494:G251C	G	-	1	0	GLIS3	4108262	0.000000	0.05858	0.385000	0.26158	0.649000	0.38597	1.002000	0.29796	2.555000	0.86185	0.655000	0.94253	GGC	C|0.993;A|0.007	0.007	strong		0.721	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629	
LRRC6	23639	hgsc.bcm.edu	37	8	133637659	133637659	+	Missense_Mutation	SNP	G	G	A	rs2293979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	201	0	0		WXS	Illumina HiSeq	Phase_I	210	210	1	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	
CNGB1	1258	hgsc.bcm.edu	37	16	57935442	57935442	+	Missense_Mutation	SNP	G	G	A	rs112002818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57935442G>A	ENST00000251102.8	-	28	2942	c.2882C>T	c.(2881-2883)gCa>gTa	p.A961V	CNGB1_ENST00000564448.1_Missense_Mutation_p.A955V	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	961			A -> S (in dbSNP:rs16942445).		cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						CTGAAAGAGTGCGACTTTGCT	0.537													G|||	200	0.0399361	0.0015	0.0187	5008	,	,		22717	0.0079		0.0726	False		,,,				2504	0.1063				p.A961V	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.C2882T						PASS	.	G	VAL/ALA	41,4089		0,41,2024	111.0	115.0	113.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2882	4.9	1.0	16	dbSNP_132	113	504,7910		22,460,3725	yes	missense	CNGB1	NM_001297.4	64	22,501,5749	AA,AG,GG		5.99,0.9927,4.3447	benign	961/1252	57935442	545,11999	2065	4207	6272	SO:0001583	missense	1258	exon28			AAGAGTGCGACTT	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2882C>T	16.37:g.57935442G>A	ENSP00000251102:p.Ala961Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	37	CCDS42169.1	74	0.03388278388278388	1	0.0020325203252032522	9	0.024861878453038673	5	0.008741258741258742	59	0.07783641160949868	G	13.26	2.183705	0.38609	0.009927	0.0599	ENSG00000070729	ENST00000251102	D	0.96651	-4.08	4.87	4.87	0.63330	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.070612	0.56097	D	0.000026	T	0.58793	0.2147	L	0.53249	1.67	0.80722	D	1	B;B	0.31383	0.321;0.308	B;B	0.34590	0.086;0.186	T	0.76383	-0.2979	10	0.34782	T	0.22	.	10.6253	0.45504	0.0877:0.0:0.9123:0.0	.	333;961	Q14028-2;Q14028	.;CNGB1_HUMAN	V	961	ENSP00000251102:A961V	ENSP00000251102:A961V	A	-	2	0	CNGB1	56492943	1.000000	0.71417	0.993000	0.49108	0.064000	0.16182	4.769000	0.62300	2.245000	0.73994	0.561000	0.74099	GCA	G|0.958;A|0.042	0.042	strong		0.537	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
MAP2K2	5605	hgsc.bcm.edu	37	19	4110552	4110552	+	Silent	SNP	C	C	G	rs10424722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4110552C>G	ENST00000262948.5	-	3	658	c.405G>C	c.(403-405)ggG>ggC	p.G135G	MAP2K2_ENST00000394867.4_Silent_p.G38G|MAP2K2_ENST00000599345.1_5'UTR	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	135	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|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)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|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)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|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 cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)						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)	Bosutinib(DB06616)|Trametinib(DB08911)	TGTAGAAGGCCCCGTAGAAGC	0.602													C|||	239	0.0477236	0.1755	0.0101	5008	,	,		16819	0.0		0.0	False		,,,				2504	0.0				p.G135G		Atlas-SNP	.											.	MAP2K2	72	.	0			c.G405C						PASS	.	C		628,3778	272.8+/-271.0	51,526,1626	87.0	74.0	79.0		405	-3.6	1.0	19	dbSNP_119	79	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	MAP2K2	NM_030662.3		51,531,5921	GG,GC,CC		0.0581,14.2533,4.867		135/401	4110552	633,12373	2203	4300	6503	SO:0001819	synonymous_variant	5605	exon3			GAAGGCCCCGTAG	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.405G>C	19.37:g.4110552C>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	38	0.678571	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			C|0.956;G|0.044	0.044	strong		0.602	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2		
MAL2	114569	hgsc.bcm.edu	37	8	120233968	120233968	+	Missense_Mutation	SNP	G	G	A	rs2303398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120233968G>A	ENST00000276681.6	+	3	376	c.274G>A	c.(274-276)Gct>Act	p.A92T	MAL2_ENST00000521748.1_3'UTR|RP11-4K16.2_ENST00000522828.1_lincRNA	NM_052886.2	NP_443118.1	Q969L2	MAL2_HUMAN	mal, T-cell differentiation protein 2 (gene/pseudogene)	92	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.		A -> T (in dbSNP:rs2303398).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)						all_cancers(13;1.91e-26)|Lung NSC(37;8.61e-08)|Ovarian(258;0.018)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000967)			TGGCATGGTGGCTCAAATTGA	0.433													A|||	563	0.11242	0.3238	0.0331	5008	,	,		19676	0.0308		0.0	False		,,,				2504	0.0828				p.A92T		Atlas-SNP	.											.	.	.	.	0			c.G274A						PASS	.	A	THR/ALA	1171,2763		182,807,978	128.0	127.0	127.0		275	5.2	1.0	8	dbSNP_100	127	21,8295		0,21,4137	yes	missense	MAL2	NM_052886.2	58	182,828,5115	AA,AG,GG		0.2525,29.7661,9.7306	benign	92/177	120233968	1192,11058	1967	4158	6125	SO:0001583	missense	114569	exon3			ATGGTGGCTCAAA	AL117612	CCDS75780.1	8q23	2011-01-26	2011-01-26			ENSG00000147676			13634	protein-coding gene	gene with protein product	"""MAL proteolipid protein 2"""	609684				11549320	Standard	NM_052886		Approved		uc003yop.3	Q969L2		ENST00000276681.6:c.274G>A	8.37:g.120233968G>A	ENSP00000475434:p.Ala92Thr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	135	88	0.651852	NM_052886	B2R520|Q6ZMD9	Missense_Mutation	SNP	ENST00000276681.6	37																																																																																				G|0.895;A|0.105	0.105	strong		0.433	MAL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052886	
ITGB5	3693	hgsc.bcm.edu	37	3	124515308	124515308	+	Silent	SNP	A	A	G	rs1803825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	50	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	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	
BBS2	583	hgsc.bcm.edu	37	16	56545175	56545175	+	Missense_Mutation	SNP	T	T	C	rs11373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:56545175T>C	ENST00000245157.5	-	3	787	c.367A>G	c.(367-369)Att>Gtt	p.I123V	BBS2_ENST00000568104.1_Missense_Mutation_p.I123V|BBS2_ENST00000561951.1_5'UTR	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	123			I -> V (polymorphism in linkage disequilibrium with G-75 in a Bedouin kindred; dbSNP:rs11373). {ECO:0000269|PubMed:11285252, ECO:0000269|PubMed:15666242, ECO:0000269|PubMed:15770229}.		adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						CCCAGCACAATTGCATTTGCC	0.413									Bardet-Biedl syndrome				T|||	1320	0.263578	0.2458	0.2767	5008	,	,		18413	0.4127		0.1789	False		,,,				2504	0.2117				p.I123V		Atlas-SNP	.											.	BBS2	67	.	0			c.A367G						PASS	.	T	VAL/ILE	994,3402	372.5+/-320.4	102,790,1306	116.0	98.0	104.0		367	0.5	1.0	16	dbSNP_52	104	1546,7054	290.9+/-300.1	138,1270,2892	yes	missense	BBS2	NM_031885.3	29	240,2060,4198	CC,CT,TT		17.9767,22.6115,19.5445	benign	123/722	56545175	2540,10456	2198	4300	6498	SO:0001583	missense	583	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GCACAATTGCATT	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.367A>G	16.37:g.56545175T>C	ENSP00000245157:p.Ile123Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_031885	Q96CM0|Q96SN9	Missense_Mutation	SNP	ENST00000245157.5	37	CCDS32451.1	578	0.26465201465201466	110	0.22357723577235772	93	0.2569060773480663	236	0.4125874125874126	139	0.18337730870712401	T	5.499	0.277020	0.10403	0.226115	0.179767	ENSG00000125124	ENST00000245157	D	0.82167	-1.58	5.9	0.542	0.17174	WD40 repeat-like-containing domain (1);	0.376395	0.31976	N	0.006774	T	0.00012	0.0000	N	0.16307	0.4	0.34697	P	0.273659	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.25117	-1.0141	9	0.14656	T	0.56	-3.2293	5.865	0.18771	0.0:0.3239:0.1315:0.5446	rs11373;rs1129878;rs3177663;rs3188184;rs11555777;rs17295965;rs17354402;rs17845410;rs17858274;rs52799276;rs57383601;rs11373	123;123	A8K0N9;Q9BXC9	.;BBS2_HUMAN	V	123	ENSP00000245157:I123V	ENSP00000245157:I123V	I	-	1	0	BBS2	55102676	0.997000	0.39634	0.994000	0.49952	0.608000	0.37181	0.402000	0.20965	-0.180000	0.10637	-0.276000	0.10085	ATT	T|0.778;C|0.222	0.222	strong		0.413	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885	
TET2	54790	hgsc.bcm.edu	37	4	106158216	106158216	+	Silent	SNP	G	G	A	rs3796927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:106158216G>A	ENST00000540549.1	+	3	3977	c.3117G>A	c.(3115-3117)tcG>tcA	p.S1039S	TET2_ENST00000394764.1_Silent_p.S1039S|TET2_ENST00000413648.2_Silent_p.S1039S|TET2_ENST00000305737.2_Silent_p.S1039S|TET2_ENST00000380013.4_Silent_p.S1039S|TET2_ENST00000513237.1_Silent_p.S1060S|TET2_ENST00000545826.1_Silent_p.S1039S			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1039					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.K1038fs*14(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ACGCCAAGTCGTTATTTGACC	0.438			"""Mis N, F"""		MDS								G|||	454	0.090655	0.2791	0.0173	5008	,	,		22756	0.0615		0.0089	False		,,,				2504	0.002				p.S1039S		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.G3117A						PASS	.	G	,	1176,3230	413.9+/-336.6	172,832,1199	84.0	77.0	79.0		3117,3117	-9.7	0.0	4	dbSNP_107	79	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous,coding-synonymous	TET2	NM_001127208.2,NM_017628.4	,	172,849,5482	AA,AG,GG		0.1977,26.6909,9.1727	,	1039/2003,1039/1166	106158216	1193,11813	2203	4300	6503	SO:0001819	synonymous_variant	54790	exon3			CAAGTCGTTATTT	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.3117G>A	4.37:g.106158216G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	159	69	0.433962	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	37	CCDS47120.1																																																																																			G|0.895;A|0.105	0.105	strong		0.438	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
INCENP	3619	hgsc.bcm.edu	37	11	61906216	61906216	+	Missense_Mutation	SNP	G	G	A	rs61751226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61906216G>A	ENST00000394818.3	+	6	1349	c.1147G>A	c.(1147-1149)Gag>Aag	p.E383K	INCENP_ENST00000278849.4_Missense_Mutation_p.E383K	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	383					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						CGAGGAGGCTGAGCCTGTGGC	0.642													G|||	58	0.0115815	0.0159	0.0	5008	,	,		17187	0.0		0.0	False		,,,				2504	0.0378				p.E383K		Atlas-SNP	.											.	INCENP	122	.	0			c.G1147A						PASS	.	G	LYS/GLU,LYS/GLU	83,4321	72.0+/-110.0	2,79,2121	47.0	53.0	51.0		1147,1147	1.9	0.0	11	dbSNP_129	51	1,8597		0,1,4298	yes	missense,missense	INCENP	NM_020238.2,NM_001040694.1	56,56	2,80,6419	AA,AG,GG		0.0116,1.8847,0.6461	benign,benign	383/915,383/919	61906216	84,12918	2202	4299	6501	SO:0001583	missense	3619	exon6			GAGGCTGAGCCTG	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.1147G>A	11.37:g.61906216G>A	ENSP00000378295:p.Glu383Lys	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	9.415	1.081416	0.20309	0.018847	1.16E-4	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.16743	2.37;2.32	4.98	1.93	0.25924	.	0.347185	0.24786	N	0.035604	T	0.05731	0.0150	M	0.68952	2.095	0.09310	N	1	P;B;B	0.43788	0.817;0.208;0.132	B;B;B	0.36666	0.23;0.038;0.017	T	0.12682	-1.0538	10	0.08381	T	0.77	.	4.7767	0.13182	0.1895:0.1777:0.6328:0.0	rs61751226	383;383;383	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	K	383	ENSP00000378295:E383K;ENSP00000278849:E383K	ENSP00000278849:E383K	E	+	1	0	INCENP	61662792	0.351000	0.24887	0.039000	0.18376	0.000000	0.00434	2.664000	0.46783	0.816000	0.34421	-0.768000	0.03414	GAG	G|0.995;A|0.005	0.005	strong		0.642	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
IRGC	56269	hgsc.bcm.edu	37	19	44223125	44223125	+	Silent	SNP	C	C	T	rs346049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44223125C>T	ENST00000244314.5	+	2	614	c.415C>T	c.(415-417)Ctg>Ttg	p.L139L		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	139	IRG-type G.					membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				CTTCTTCCTGCTGGTCTCCCC	0.637													C|||	882	0.176118	0.4697	0.1081	5008	,	,		12871	0.001		0.1262	False		,,,				2504	0.0593				p.L139L	Colon(189;350 2037 11447 13433 38914)	Atlas-SNP	.											.	IRGC	67	.	0			c.C415T						PASS	.	C		1863,2515		415,1033,741	14.0	13.0	14.0		415	0.8	0.4	19	dbSNP_79	14	983,7575		68,847,3364	no	coding-synonymous	IRGC	NM_019612.3		483,1880,4105	TT,TC,CC		11.4863,42.5537,22.0006		139/464	44223125	2846,10090	2189	4279	6468	SO:0001819	synonymous_variant	56269	exon2			TTCCTGCTGGTCT	BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"""immunity-related GTPase family, cinema 1"""	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.415C>T	19.37:g.44223125C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_019612	Q05BR8	Silent	SNP	ENST00000244314.5	37	CCDS12629.1																																																																																			C|0.805;T|0.195	0.195	strong		0.637	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612	
C2orf16	84226	hgsc.bcm.edu	37	2	27804114	27804114	+	Missense_Mutation	SNP	C	C	T	rs13392197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27804114C>T	ENST00000408964.2	+	1	4726	c.4675C>T	c.(4675-4677)Cat>Tat	p.H1559Y	ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1559	Arg-rich.		H -> Y (in dbSNP:rs13392197).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GAGAACCCGTCATAACCCCTC	0.537													C|||	59	0.0117812	0.0408	0.0043	5008	,	,		18030	0.0		0.002	False		,,,				2504	0.0				p.H1559Y		Atlas-SNP	.											.	C2orf16	357	.	0			c.C4675T						PASS	.	C	TYR/HIS	130,3650		3,124,1763	118.0	118.0	118.0		4675	-5.8	0.0	2	dbSNP_121	118	3,8217		0,3,4107	yes	missense	C2orf16	NM_032266.3	83	3,127,5870	TT,TC,CC		0.0365,3.4392,1.1083	benign	1559/1985	27804114	133,11867	1890	4110	6000	SO:0001583	missense	84226	exon1			ACCCGTCATAACC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4675C>T	2.37:g.27804114C>T	ENSP00000386190:p.His1559Tyr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	24	0.01098901098901099	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	5.555	0.287230	0.10513	0.034392	3.65E-4	ENSG00000221843	ENST00000408964	T	0.04809	3.55	4.05	-5.76	0.02376	.	.	.	.	.	T	0.00552	0.0018	N	0.25647	0.755	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47699	-0.9097	9	0.08381	T	0.77	.	2.2504	0.04042	0.1341:0.3469:0.1054:0.4136	rs13392197;rs52835437;rs13392197	1559	Q68DN1	CB016_HUMAN	Y	1559	ENSP00000386190:H1559Y	ENSP00000386190:H1559Y	H	+	1	0	C2orf16	27657618	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.314000	0.01125	-1.329000	0.02258	-0.379000	0.06801	CAT	C|0.983;T|0.017	0.017	strong		0.537	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
TPPP	11076	hgsc.bcm.edu	37	5	665280	665280	+	Silent	SNP	T	T	C	rs1697963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:665280T>C	ENST00000360578.5	-	4	718	c.597A>G	c.(595-597)tcA>tcG	p.S199S	AC026740.1_ENST00000594226.1_5'Flank|CEP72_ENST00000514507.1_Intron	NM_007030.2	NP_008961.1	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	199					microtubule bundle formation (GO:0001578)|microtubule polymerization (GO:0046785)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein polymerization (GO:0032273)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		ACACATAGCCTGACTCGTCCA	0.657													t|||	3613	0.721446	0.9266	0.6988	5008	,	,		18015	0.6915		0.6064	False		,,,				2504	0.6094				p.S199S		Atlas-SNP	.											TPPP,caecum,carcinoma,0,1	TPPP	24	1	0			c.A597G						PASS	.	C		3915,491	780.6+/-414.4	1734,447,22	88.0	78.0	82.0		597	-10.2	0.1	5	dbSNP_89	82	5212,3388	640.3+/-399.6	1582,2048,670	no	coding-synonymous	TPPP	NM_007030.2		3316,2495,692	CC,CT,TT		39.3953,11.1439,29.8247		199/220	665280	9127,3879	2203	4300	6503	SO:0001819	synonymous_variant	11076	exon4			ATAGCCTGACTCG	AB017016	CCDS3856.1	5p15.33	2008-02-05			ENSG00000171368	ENSG00000171368			24164	protein-coding gene	gene with protein product	"""brain specific protein p25 alpha"""	608773				10083737, 12093283, 15590652, 17105200	Standard	NM_007030		Approved	p25alpha, TPPP1, p25, TPPP/p25	uc003jbh.4	O94811	OTTHUMG00000131011	ENST00000360578.5:c.597A>G	5.37:g.665280T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_007030		Silent	SNP	ENST00000360578.5	37	CCDS3856.1																																																																																			T|0.288;C|0.712	0.712	strong		0.657	TPPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253645.3	NM_007030	
C15orf54	400360	hgsc.bcm.edu	37	15	39544809	39544809	+	Missense_Mutation	SNP	G	G	C	rs115130297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39544809G>C	ENST00000318578.3	+	2	841	c.473G>C	c.(472-474)aGg>aCg	p.R158T	C15orf54_ENST00000561223.1_Missense_Mutation_p.R158T|RP11-624L4.1_ENST00000558209.1_RNA|RP11-624L4.1_ENST00000560484.1_RNA|RP11-624L4.1_ENST00000561058.1_RNA	NM_207445.2	NP_997328.1	Q8N8G6	CO054_HUMAN	chromosome 15 open reading frame 54	158										NS(1)|haematopoietic_and_lymphoid_tissue(2)|lung(2)	5		all_cancers(109;5.39e-14)|all_epithelial(112;3.14e-12)|Lung NSC(122;9.74e-10)|all_lung(180;2.23e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;1.19e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0706)		AGGGGAGAGAGGGGACATTTT	0.448													G|||	16	0.00319489	0.0121	0.0	5008	,	,		21387	0.0		0.0	False		,,,				2504	0.0				p.R158T		Atlas-SNP	.											.	C15orf54	18	.	0			c.G473C						PASS	.	G	THR/ARG	28,4372	34.3+/-65.2	0,28,2172	98.0	84.0	88.0		473	0.3	0.0	15	dbSNP_132	88	0,8594		0,0,4297	yes	missense	C15orf54	NM_207445.2	71	0,28,6469	CC,CG,GG		0.0,0.6364,0.2155	benign	158/184	39544809	28,12966	2200	4297	6497	SO:0001583	missense	400360	exon2			GAGAGAGGGGACA		CCDS10049.1	15q14	2014-09-10			ENSG00000175746	ENSG00000175746			33797	protein-coding gene	gene with protein product							Standard	NM_207445		Approved	FLJ39531	uc001zkg.2	Q8N8G6	OTTHUMG00000129843	ENST00000318578.3:c.473G>C	15.37:g.39544809G>C	ENSP00000323686:p.Arg158Thr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	165	88	0.533333	NM_207445	B7ZVZ9	Missense_Mutation	SNP	ENST00000318578.3	37	CCDS10049.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	4.682	0.126814	0.08931	0.006364	0.0	ENSG00000175746	ENST00000318578	T	0.39406	1.08	3.57	0.297	0.15762	.	.	.	.	.	T	0.09247	0.0228	N	0.08118	0	0.09310	N	1	B	0.25312	0.123	B	0.16289	0.015	T	0.15235	-1.0444	9	0.87932	D	0	.	2.1381	0.03768	0.1165:0.1939:0.4906:0.199	.	158	Q8N8G6	CO054_HUMAN	T	158	ENSP00000323686:R158T	ENSP00000323686:R158T	R	+	2	0	C15orf54	37332101	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.520000	0.06252	-0.036000	0.13669	0.609000	0.83330	AGG	G|0.997;C|0.003	0.003	strong		0.448	C15orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252083.1	NM_207445	
PLSCR5	389158	hgsc.bcm.edu	37	3	146311832	146311832	+	Missense_Mutation	SNP	G	G	T	rs12107687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:146311832G>T	ENST00000443512.1	-	4	1331	c.328C>A	c.(328-330)Cgt>Agt	p.R110S	PLSCR5_ENST00000492200.1_Missense_Mutation_p.R110S|PLSCR5_ENST00000482567.1_Missense_Mutation_p.R98S	NM_001085420.1	NP_001078889.1	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	110			R -> S (in dbSNP:rs12107687).							endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						CAGAAAGTACGATTGAAGCAG	0.433													G|||	76	0.0151757	0.0545	0.0058	5008	,	,		14788	0.0		0.0	False		,,,				2504	0.0				p.R110S		Atlas-SNP	.											.	PLSCR5	35	.	0			c.C328A						PASS	.	G	SER/ARG	192,3650		3,186,1732	141.0	139.0	139.0		328	5.7	1.0	3	dbSNP_120	139	2,8270		0,2,4134	yes	missense	PLSCR5	NM_001085420.1	110	3,188,5866	TT,TG,GG		0.0242,4.9974,1.6015	probably-damaging	110/272	146311832	194,11920	1921	4136	6057	SO:0001583	missense	389158	exon4			AAGTACGATTGAA	AY436642	CCDS46931.1	3q24	2004-06-28			ENSG00000231213	ENSG00000231213			19952	protein-coding gene	gene with protein product							Standard	NM_001085420		Approved		uc010hvc.3	A0PG75	OTTHUMG00000159437	ENST00000443512.1:c.328C>A	3.37:g.146311832G>T	ENSP00000390111:p.Arg110Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_001085420	B2RXK5	Missense_Mutation	SNP	ENST00000443512.1	37	CCDS46931.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	G	19.70	3.876593	0.72180	0.049974	2.42E-4	ENSG00000231213	ENST00000492200;ENST00000482567;ENST00000443512	T;T;T	0.56103	0.48;0.48;0.48	5.69	5.69	0.88448	Tubby, C-terminal (1);	.	.	.	.	T	0.44456	0.1294	H	0.94222	3.51	0.39506	D	0.968276	D;D	0.89917	0.984;1.0	P;D	0.83275	0.871;0.996	T	0.76570	-0.2911	9	0.87932	D	0	-22.5708	14.6371	0.68696	0.0:0.0:0.8546:0.1454	rs12107687;rs52836343;rs12107687	98;110	B2RXK5;A0PG75	.;PLS5_HUMAN	S	110;98;110	ENSP00000417184:R110S;ENSP00000418626:R98S;ENSP00000390111:R110S	ENSP00000390111:R110S	R	-	1	0	PLSCR5	147794522	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.190000	0.58365	2.679000	0.91253	0.650000	0.86243	CGT	G|0.987;T|0.013	0.013	strong		0.433	PLSCR5-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355365.1	XM_371670	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103152919	103152919	+	Silent	SNP	G	G	A	rs12574626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	47	0	0		WXS	Illumina HiSeq	Phase_I	28	20	0.714286	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	
CD300LD	100131439	hgsc.bcm.edu	37	17	72584764	72584764	+	Missense_Mutation	SNP	C	C	T	rs783239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72584764C>T	ENST00000375352.1	-	2	345	c.265G>A	c.(265-267)Gtg>Atg	p.V89M	C17orf77_ENST00000392620.1_Intron|C17orf77_ENST00000328023.2_5'Flank	NM_001115152.1	NP_001108624.1	Q6UXZ3	CLM4_HUMAN	CD300 molecule-like family member d	89	Ig-like V-type.		V -> M (in dbSNP:rs783239).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V89M(1)		large_intestine(1)|lung(2)|prostate(1)|stomach(1)	5						ACGGTGAACACGTGGTTTTTC	0.423													T|||	1715	0.342452	0.6604	0.2161	5008	,	,		24754	0.249		0.1829	False		,,,				2504	0.2628				p.V89M		Atlas-SNP	.											CD300LD,NS,carcinoma,0,1	CD300LD	16	1	1	Substitution - Missense(1)	stomach(1)	c.G265A						PASS	.	T	MET/VAL,	1777,1359		504,769,295	370.0	303.0	324.0		265,	-0.5	0.0	17	dbSNP_86	324	1529,5635		168,1193,2221	yes	missense,intron	C17orf77,CD300LD	NM_001115152.1,NM_152460.2	21,	672,1962,2516	TT,TC,CC		21.3428,43.3355,32.0971	benign,	89/195,	72584764	3306,6994	1568	3582	5150	SO:0001583	missense	100131439	exon2			TGAACACGTGGTT		CCDS42379.1	17q25.1	2014-05-15			ENSG00000204345	ENSG00000204345		"""Immunoglobulin superfamily / V-set domain containing"""	16848	protein-coding gene	gene with protein product						22291008	Standard	NM_001115152		Approved	CMRF35A4, CD300D	uc002jkz.2	Q6UXZ3	OTTHUMG00000067614	ENST00000375352.1:c.265G>A	17.37:g.72584764C>T	ENSP00000364501:p.Val89Met	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	227	111	0.488987	NM_001115152		Missense_Mutation	SNP	ENST00000375352.1	37	CCDS42379.1	695	0.3182234432234432	332	0.6747967479674797	87	0.24033149171270718	133	0.23251748251748253	143	0.18865435356200527	T	9.306	1.054409	0.19907	0.566645	0.213428	ENSG00000204345	ENST00000375352	T	0.65364	-0.15	4.67	-0.509	0.11977	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.005160	0.03034	N	0.152512	T	0.00012	0.0000	L	0.58810	1.83	0.80722	P	0.0	B	0.23316	0.083	B	0.23419	0.046	T	0.47983	-0.9074	9	0.37606	T	0.19	.	4.8858	0.13703	0.142:0.326:0.0:0.532	rs783239;rs58833921;rs783239	89	Q6UXZ3	CLM4_HUMAN	M	89	ENSP00000364501:V89M	ENSP00000364501:V89M	V	-	1	0	CD300LD	70096359	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.650000	0.05378	-0.727000	0.04888	-0.361000	0.07541	GTG	C|0.680;T|0.320	0.320	strong		0.423	CD300LD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145099.1	NM_001115152	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377012	168377012	+	lincRNA	SNP	G	G	T	rs78475769		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:168377012G>T	ENST00000538528.1	-	0	607																											CAGTGTGTGGGGAGGAGAAGA	0.637																																					p.S107S		Atlas-SNP	.											.	.	.	.	0			c.C321A						PASS	.						13.0	11.0	12.0					6																	168377012		691	1589	2280			0	exon1			GTGTGGGGAGGAG																													6.37:g.168377012G>T		Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	401	25	0.0623441	NM_001129895		Silent	SNP	ENST00000538528.1	37																																																																																				T|1.000;|0.000	1.000	weak		0.637	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
KDM3B	51780	hgsc.bcm.edu	37	5	137754695	137754695	+	Silent	SNP	T	T	C	rs7726234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:137754695T>C	ENST00000314358.5	+	14	3689	c.3489T>C	c.(3487-3489)ggT>ggC	p.G1163G	KDM3B_ENST00000542866.1_Silent_p.G195G|KDM3B_ENST00000394866.1_Silent_p.G819G|KDM3B_ENST00000508386.1_3'UTR	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1163					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						CCTTCTCTGGTGGAGGAGGAC	0.493													C|||	3396	0.678115	0.5681	0.6715	5008	,	,		19126	0.8532		0.5924	False		,,,				2504	0.7393				p.G1163G		Atlas-SNP	.											KDM3B,NS,carcinoma,0,1	KDM3B	177	1	0			c.T3489C						PASS	.	C		2574,1832	533.0+/-373.6	737,1100,366	97.0	99.0	98.0		3489	-11.3	0.0	5	dbSNP_116	98	5021,3579	519.1+/-379.4	1473,2075,752	no	coding-synonymous	KDM3B	NM_016604.3		2210,3175,1118	CC,CT,TT		41.6163,41.5797,41.6039		1163/1762	137754695	7595,5411	2203	4300	6503	SO:0001819	synonymous_variant	51780	exon14			CTCTGGTGGAGGA	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.3489T>C	5.37:g.137754695T>C		Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	219	97	0.442922	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	37	CCDS34242.1																																																																																			T|0.382;C|0.618	0.618	strong		0.493	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
PGS1	9489	hgsc.bcm.edu	37	17	76422599	76422599	+	IGR	SNP	C	C	T	rs35973257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76422599C>T	ENST00000262764.6	+	0	2201				DNAH17_ENST00000389840.5_Missense_Mutation_p.R4308Q|DNAH17_ENST00000585328.1_Missense_Mutation_p.R4280Q|DNAH17_ENST00000586052.1_5'UTR|AC061992.1_ENST00000600087.1_Missense_Mutation_p.P64L	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)			GGGGTAGGCCCGGGCCACCCA	0.597													C|||	61	0.0121805	0.003	0.0259	5008	,	,		20290	0.0		0.0338	False		,,,				2504	0.0051				p.R4285Q	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	DNAH17	347	.	0			c.G12854A						PASS	.	C	GLN/ARG	25,4381	31.7+/-61.6	0,25,2178	56.0	60.0	59.0		12854	5.0	1.0	17	dbSNP_126	59	285,8315	105.8+/-166.7	4,277,4019	yes	missense	DNAH17	NM_173628.3	43	4,302,6197	TT,TC,CC		3.314,0.5674,2.3835	possibly-damaging	4285/4463	76422599	310,12696	2203	4300	6503	SO:0001628	intergenic_variant	8632	exon79			TAGGCCCGGGCCA		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.76422599C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	124	49	0.395161	NM_173628	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Missense_Mutation	SNP	ENST00000262764.6	37	CCDS42391.1	51	0.023351648351648352	6	0.012195121951219513	12	0.03314917127071823	1	0.0017482517482517483	32	0.04221635883905013	C	17.54	3.416107	0.62511	0.005674	0.03314	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.09350	2.99	5.03	5.03	0.67393	.	0.275476	0.25997	N	0.026969	T	0.02970	0.0088	M	0.73372	2.23	0.33890	D	0.63722	P	0.45827	0.867	B	0.42959	0.403	T	0.08680	-1.0710	10	0.36615	T	0.2	.	7.4763	0.27378	0.1681:0.7425:0.0:0.0893	rs35973257	4280	E7EUM8	.	Q	4280;4308	ENSP00000374490:R4308Q	ENSP00000300671:R4280Q	R	-	2	0	DNAH17	73934194	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.411000	0.34702	2.608000	0.88229	0.655000	0.94253	CGG	C|0.976;T|0.024	0.024	strong		0.597	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	
IVL	3713	hgsc.bcm.edu	37	1	152883036	152883036	+	Missense_Mutation	SNP	C	C	T	rs4459054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152883036C>T	ENST00000368764.3	+	2	827	c.763C>T	c.(763-765)Ctc>Ttc	p.L255F	IVL_ENST00000392667.2_Missense_Mutation_p.L109F			P07476	INVO_HUMAN	involucrin	255	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gcagctggagctctctgagca	0.657													C|||	107	0.0213658	0.0779	0.0058	5008	,	,		19088	0.0		0.0	False		,,,				2504	0.0				p.L255F		Atlas-SNP	.											IVL,NS,carcinoma,-2,1	IVL	100	1	0			c.C763T						PASS	.		PHE/LEU	213,3727		5,203,1762	10.0	10.0	10.0		763	-0.7	0.0	1	dbSNP_111	10	3,7787		0,3,3892	no	missense	IVL	NM_005547.2	22	5,206,5654	TT,TC,CC		0.0385,5.4061,1.8414	benign	255/586	152883036	216,11514	1970	3895	5865	SO:0001583	missense	3713	exon2			CTGGAGCTCTCTG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.763C>T	1.37:g.152883036C>T	ENSP00000357753:p.Leu255Phe	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	208	88	0.423077	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	0.147	-1.096036	0.01843	0.054061	3.85E-4	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.11821	2.96;2.74	0.329	-0.658	0.11428	.	.	.	.	.	T	0.01835	0.0058	L	0.29908	0.895	0.09310	N	1	B	0.32245	0.361	B	0.28305	0.088	T	0.47328	-0.9126	9	0.11794	T	0.64	.	4.7855	0.13223	0.3488:0.6511:0.0:1.0E-4	rs4459054;rs7413034	255	P07476	INVO_HUMAN	F	255;109	ENSP00000357753:L255F;ENSP00000376435:L109F	ENSP00000357753:L255F	L	+	1	0	IVL	151149660	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.401000	0.07232	-0.793000	0.04475	0.123000	0.15791	CTC	C|0.986;T|0.014	0.014	strong		0.657	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
RBM20	282996	hgsc.bcm.edu	37	10	112540884	112540884	+	Missense_Mutation	SNP	C	C	A	rs7908490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:112540884C>A	ENST00000369519.3	+	2	575	c.517C>A	c.(517-519)Ccc>Acc	p.P173T		NM_001134363.1	NP_001127835.1	Q5T481	RBM20_HUMAN	RNA binding motif protein 20	173			P -> T (in dbSNP:rs7908490).		heart development (GO:0007507)|mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(4)|kidney(3)|large_intestine(1)|ovary(1)|skin(2)	12						TGCCTTTTCACCCCCCAGCCA	0.597													C|||	135	0.0269569	0.0976	0.0086	5008	,	,		19513	0.0		0.0	False		,,,				2504	0.0				p.P173T		Atlas-SNP	.											.	RBM20	50	.	0			c.C517A						PASS	.	C	THR/PRO	98,1286		2,94,596	34.0	33.0	33.0		517	1.5	0.1	10	dbSNP_116	33	0,3182		0,0,1591	yes	missense	RBM20	NM_001134363.1	38	2,94,2187	AA,AC,CC		0.0,7.0809,2.1463	probably-damaging	173/1228	112540884	98,4468	692	1591	2283	SO:0001583	missense	282996	exon2			TTTTCACCCCCCA	BX648563	CCDS44477.1	10q25.3	2014-09-17			ENSG00000203867	ENSG00000203867		"""RNA binding motif (RRM) containing"""	27424	protein-coding gene	gene with protein product		613171					Standard	NM_001134363		Approved		uc001kzf.2	Q5T481	OTTHUMG00000019043	ENST00000369519.3:c.517C>A	10.37:g.112540884C>A	ENSP00000358532:p.Pro173Thr	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	129	54	0.418605	NM_001134363	A6NIP5|B5A868|Q5JVI1	Missense_Mutation	SNP	ENST00000369519.3	37	CCDS44477.1	43	0.019688644688644688	39	0.07926829268292683	4	0.011049723756906077	0	0.0	0	0.0	C	11.77	1.736804	0.30774	0.070809	0.0	ENSG00000203867	ENST00000369519;ENST00000539821	D	0.89617	-2.54	5.51	1.54	0.23209	.	.	.	.	.	T	0.13543	0.0328	N	0.14661	0.345	0.09310	N	1	B	0.30824	0.296	B	0.19946	0.027	T	0.43458	-0.9390	9	0.34782	T	0.22	.	0.4254	0.00463	0.2389:0.2976:0.228:0.2354	rs7908490;rs7908490	173	Q5T481	RBM20_HUMAN	T	173	ENSP00000358532:P173T	ENSP00000358532:P173T	P	+	1	0	RBM20	112530874	0.009000	0.17119	0.087000	0.20705	0.988000	0.76386	0.078000	0.14761	0.279000	0.22186	0.591000	0.81541	CCC	C|0.970;A|0.030	0.030	strong		0.597	RBM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050339.2	NM_001134363	
ROS1	6098	hgsc.bcm.edu	37	6	117681560	117681560	+	Silent	SNP	G	G	T	rs140639104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117681560G>T	ENST00000368508.3	-	22	3588	c.3390C>A	c.(3388-3390)gcC>gcA	p.A1130A	ROS1_ENST00000368507.3_Silent_p.A1125A|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1130	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		TAGATGTAAAGGCCCTAACCT	0.368			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								G|||	12	0.00239617	0.0083	0.0014	5008	,	,		17507	0.0		0.0	False		,,,				2504	0.0				p.A1130A		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.C3390A						PASS	.	G		37,4369	41.6+/-74.8	0,37,2166	81.0	76.0	78.0		3390	1.1	1.0	6	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous	ROS1	NM_002944.2		0,37,6466	TT,TG,GG		0.0,0.8398,0.2845		1130/2348	117681560	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	6098	exon22			TGTAAAGGCCCTA	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.3390C>A	6.37:g.117681560G>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	73	24	0.328767	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																			G|0.998;T|0.002	0.002	strong		0.368	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
LRIT2	340745	hgsc.bcm.edu	37	10	85981756	85981756	+	Missense_Mutation	SNP	G	G	T	rs74145770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85981756G>T	ENST00000372113.4	-	3	1578	c.1573C>A	c.(1573-1575)Cca>Aca	p.P525T	LRIT2_ENST00000538192.1_Missense_Mutation_p.P535T	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	525						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						CAGACAGCTGGATGTTCTCTA	0.592													G|||	227	0.0453275	0.1672	0.0086	5008	,	,		19768	0.0		0.0	False		,,,				2504	0.0				p.P525T		Atlas-SNP	.											.	LRIT2	81	.	0			c.C1573A						PASS	.	G	THR/PRO	600,3806	252.1+/-258.6	50,500,1653	117.0	105.0	109.0		1573	-5.7	0.0	10	dbSNP_130	109	18,8582	12.6+/-44.7	0,18,4282	yes	missense	LRIT2	NM_001017924.2	38	50,518,5935	TT,TG,GG		0.2093,13.6178,4.7517	benign	525/551	85981756	618,12388	2203	4300	6503	SO:0001583	missense	340745	exon3			CAGCTGGATGTTC		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.1573C>A	10.37:g.85981756G>T	ENSP00000361185:p.Pro525Thr	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	208	119	0.572115	NM_001017924	B7ZME6	Missense_Mutation	SNP	ENST00000372113.4	37	CCDS31234.1	91	0.041666666666666664	87	0.17682926829268292	4	0.011049723756906077	0	0.0	0	0.0	G	0.610	-0.825514	0.02734	0.136178	0.002093	ENSG00000204033	ENST00000372113;ENST00000538192	T;T	0.16597	2.33;2.33	4.57	-5.65	0.02459	.	1.918670	0.02557	N	0.096284	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.12013	0.005;0.001	B;B	0.06405	0.002;0.001	T	0.31336	-0.9947	9	0.13108	T	0.6	.	3.6424	0.08172	0.1993:0.4518:0.2433:0.1056	.	535;525	B7ZME6;A6NDA9	.;LRIT2_HUMAN	T	525;535	ENSP00000361185:P525T;ENSP00000438264:P535T	ENSP00000361185:P525T	P	-	1	0	LRIT2	85971736	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.226000	0.09139	-1.353000	0.02191	0.655000	0.94253	CCA	G|0.957;T|0.043	0.043	strong		0.592	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
NLRC4	58484	hgsc.bcm.edu	37	2	32463353	32463353	+	Missense_Mutation	SNP	A	A	G	rs202095832		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32463353A>G	ENST00000404025.2	-	7	2857	c.2369T>C	c.(2368-2370)cTg>cCg	p.L790P	NLRC4_ENST00000360906.5_Missense_Mutation_p.L790P|NLRC4_ENST00000402280.1_Missense_Mutation_p.L790P|NLRC4_ENST00000342905.6_Missense_Mutation_p.L125P			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	790					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					CATCTTCTTCAGGTTTTTCAG	0.368													A|||	1	0.000199681	0.0008	0.0	5008	,	,		19319	0.0		0.0	False		,,,				2504	0.0				p.L790P		Atlas-SNP	.											.	NLRC4	165	.	0			c.T2369C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	3,4403	6.2+/-15.9	0,3,2200	101.0	101.0	101.0		2369,2369,2369	4.6	0.9	2		101	0,8600		0,0,4300	no	missense,missense,missense	NLRC4	NM_001199138.1,NM_001199139.1,NM_021209.4	98,98,98	0,3,6500	GG,GA,AA		0.0,0.0681,0.0231	probably-damaging,probably-damaging,probably-damaging	790/1025,790/1025,790/1025	32463353	3,13003	2203	4300	6503	SO:0001583	missense	58484	exon6			TTCTTCAGGTTTT	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"""Nucleotide-binding domain and leucine rich repeat containing"""	16412	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4"", ""NOD-like receptor C4"""	606831	"""caspase recruitment domain family, member 12"""	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.2369T>C	2.37:g.32463353A>G	ENSP00000385090:p.Leu790Pro	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	.	.	.	.	.	.	.	.	.	.	A	12.13	1.846213	0.32606	6.81E-4	0.0	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000342905;ENST00000404025	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	4.63	4.63	0.57726	.	0.000000	0.31949	N	0.006818	T	0.64527	0.2606	M	0.63843	1.955	0.34053	D	0.656327	D;D	0.71674	0.998;0.994	D;P	0.65874	0.939;0.879	T	0.71251	-0.4648	9	0.34782	T	0.22	-3.8349	10.6228	0.45489	1.0:0.0:0.0:0.0	.	125;790	Q9NPP4-2;Q9NPP4	.;NLRC4_HUMAN	P	790;790;125;790	ENSP00000354159:L790P;ENSP00000385428:L790P;ENSP00000339666:L125P;ENSP00000385090:L790P	ENSP00000339666:L125P	L	-	2	0	NLRC4	32316857	0.984000	0.35163	0.947000	0.38551	0.111000	0.19643	1.992000	0.40737	2.088000	0.63022	0.533000	0.62120	CTG	.	.	weak		0.368	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209	
MUC16	94025	hgsc.bcm.edu	37	19	9068990	9068990	+	Missense_Mutation	SNP	G	G	T	rs35092547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9068990G>T	ENST00000397910.4	-	3	18659	c.18456C>A	c.(18454-18456)caC>caA	p.H6152Q		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6154	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CGATGGTCTTGTGTGTAGATA	0.507													g|||	49	0.00978435	0.0008	0.0216	5008	,	,		17653	0.001		0.0268	False		,,,				2504	0.0051				p.H6152Q		Atlas-SNP	.											.	MUC16	4315	.	0			c.C18456A						PASS	.	G	GLN/HIS	17,4221		0,17,2102	66.0	70.0	69.0		18456	-2.7	0.0	19	dbSNP_126	69	249,8207		5,239,3984	yes	missense	MUC16	NM_024690.2	24	5,256,6086	TT,TG,GG		2.9447,0.4011,2.0955	benign	6152/14508	9068990	266,12428	2119	4228	6347	SO:0001583	missense	94025	exon3			GGTCTTGTGTGTA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.18456C>A	19.37:g.9068990G>T	ENSP00000381008:p.His6152Gln	Somatic	428	1	0.00233645		WXS	Illumina HiSeq	Phase_I	499	277	0.55511	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	28	0.01282051282051282	0	0.0	6	0.016574585635359115	1	0.0017482517482517483	21	0.027704485488126648	g	2.171	-0.389912	0.04932	0.004011	0.029447	ENSG00000181143	ENST00000397910	T	0.02525	4.26	1.35	-2.71	0.05986	.	.	.	.	.	T	0.00468	0.0015	N	0.08118	0	.	.	.	B	0.31174	0.311	B	0.20577	0.03	T	0.44452	-0.9327	8	0.87932	D	0	.	2.4961	0.04621	0.3275:0.0:0.4389:0.2335	rs35092547;rs61737587	6152	B5ME49	.	Q	6152	ENSP00000381008:H6152Q	ENSP00000381008:H6152Q	H	-	3	2	MUC16	8929990	0.000000	0.05858	0.000000	0.03702	0.173000	0.22820	-2.276000	0.01161	-1.154000	0.02825	0.163000	0.16589	CAC	G|0.981;T|0.019	0.019	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
RAB3IL1	5866	hgsc.bcm.edu	37	11	61672265	61672265	+	Silent	SNP	T	T	C	rs174474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61672265T>C	ENST00000394836.2	-	6	904	c.747A>G	c.(745-747)cgA>cgG	p.R249R	RAB3IL1_ENST00000301773.5_Silent_p.R223R	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	249					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						CCACGTCCTCTCGGTACACCC	0.667													C|||	1571	0.313698	0.27	0.2003	5008	,	,		15287	0.3353		0.2336	False		,,,				2504	0.5133				p.R249R		Atlas-SNP	.											RAB3IL1,NS,carcinoma,-2,1	RAB3IL1	39	1	0			c.A747G						PASS	.	C		1226,3178	670.8+/-402.4	167,892,1143	29.0	29.0	29.0		747	-2.0	1.0	11	dbSNP_79	29	1940,6658	699.3+/-405.1	222,1496,2581	no	coding-synonymous	RAB3IL1	NM_013401.2		389,2388,3724	CC,CT,TT		22.5634,27.8383,24.3501		249/383	61672265	3166,9836	2202	4299	6501	SO:0001819	synonymous_variant	5866	exon6			GTCCTCTCGGTAC	AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.747A>G	11.37:g.61672265T>C		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	298	120	0.402685	NM_013401	Q86V32|Q9P1Q8	Silent	SNP	ENST00000394836.2	37	CCDS8014.1																																																																																			T|0.759;C|0.241	0.241	strong		0.667	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401	
EXPH5	23086	hgsc.bcm.edu	37	11	108383560	108383560	+	Missense_Mutation	SNP	T	T	A	rs10890850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108383560T>A	ENST00000265843.4	-	6	2784	c.2674A>T	c.(2674-2676)Aat>Tat	p.N892Y	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000443411.1_Missense_Mutation_p.N704Y|EXPH5_ENST00000428840.1_Missense_Mutation_p.N816Y|EXPH5_ENST00000525344.1_Missense_Mutation_p.N885Y	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	892			N -> Y (in dbSNP:rs10890850).		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AGGGAAGAATTCTTTGATGGT	0.438													T|||	270	0.0539137	0.1316	0.0115	5008	,	,		19382	0.0119		0.002	False		,,,				2504	0.0757				p.N892Y		Atlas-SNP	.											.	EXPH5	193	.	0			c.A2674T						PASS	.	T	TYR/ASN	493,3909	229.8+/-244.2	29,435,1737	182.0	167.0	172.0		2674	-2.0	0.0	11	dbSNP_120	172	9,8587	7.1+/-27.0	0,9,4289	yes	missense	EXPH5	NM_015065.2	143	29,444,6026	AA,AT,TT		0.1047,11.1995,3.8621	benign	892/1990	108383560	502,12496	2201	4298	6499	SO:0001583	missense	23086	exon6			AAGAATTCTTTGA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.2674A>T	11.37:g.108383560T>A	ENSP00000265843:p.Asn892Tyr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	130	86	0.661538	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	59	0.027014652014652016	46	0.09349593495934959	5	0.013812154696132596	7	0.012237762237762238	1	0.0013192612137203166	T	14.92	2.680490	0.47886	0.111995	0.001047	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04603	4.17;4.1;3.95;4.17;4.02;3.59	5.74	-1.97	0.07503	.	0.712890	0.13437	N	0.387972	T	0.00109	0.0003	L	0.44542	1.39	0.09310	N	1	P	0.49090	0.919	B	0.43445	0.42	T	0.40813	-0.9543	10	0.72032	D	0.01	-0.8859	6.5046	0.22188	0.0:0.4682:0.1578:0.3739	rs10890850;rs10890850	892	Q8NEV8	EXPH5_HUMAN	Y	892;816;704;885;816;704	ENSP00000265843:N892Y;ENSP00000391966:N816Y;ENSP00000411390:N704Y;ENSP00000432546:N885Y;ENSP00000432683:N816Y;ENSP00000446434:N704Y	ENSP00000265843:N892Y	N	-	1	0	EXPH5	107888770	0.000000	0.05858	0.002000	0.10522	0.230000	0.25150	-0.173000	0.09854	-0.270000	0.09285	0.460000	0.39030	AAT	T|0.967;A|0.033	0.033	strong		0.438	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
F5	2153	hgsc.bcm.edu	37	1	169512093	169512093	+	Silent	SNP	A	A	G	rs6017	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	149	0	0		WXS	Illumina HiSeq	Phase_I	141	68	0.482269	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	
HMCN1	83872	hgsc.bcm.edu	37	1	185958737	185958737	+	Missense_Mutation	SNP	A	A	G	rs7539719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:185958737A>G	ENST00000271588.4	+	21	3395	c.3166A>G	c.(3166-3168)Aca>Gca	p.T1056A	HMCN1_ENST00000367492.2_Missense_Mutation_p.T1056A|HMCN1_ENST00000485744.1_3'UTR	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1056	Ig-like C2-type 7.		T -> A (in dbSNP:rs7539719).		response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGCCACCAATACAGCCGGCTA	0.488													G|||	923	0.184305	0.5961	0.0692	5008	,	,		14054	0.006		0.0268	False		,,,				2504	0.0552				p.T1056A		Atlas-SNP	.											.	HMCN1	797	.	0			c.A3166G						PASS	.	G	ALA/THR	2115,2291	601.2+/-389.7	521,1073,609	101.0	95.0	97.0		3166	4.5	0.0	1	dbSNP_116	97	184,8416	811.2+/-407.1	1,182,4117	yes	missense	HMCN1	NM_031935.2	58	522,1255,4726	GG,GA,AA		2.1395,48.0027,17.6765	benign	1056/5636	185958737	2299,10707	2203	4300	6503	SO:0001583	missense	83872	exon21			ACCAATACAGCCG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.3166A>G	1.37:g.185958737A>G	ENSP00000271588:p.Thr1056Ala	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	168	82	0.488095	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	337	0.1543040293040293	292	0.5934959349593496	26	0.0718232044198895	3	0.005244755244755245	16	0.021108179419525065	G	0.034	-1.316804	0.01331	0.480027	0.021395	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.66099	-0.19;-0.19	5.45	4.53	0.55603	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.050912	0.85682	N	0.000000	T	0.00012	0.0000	N	0.03294	-0.36	0.48236	P	3.8199999999999346E-4	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.44847	-0.9301	9	0.02654	T	1	.	8.5679	0.33552	0.138:0.1258:0.7363:0.0	rs7539719;rs52799885;rs7539719	440;1056	Q96RW7-3;Q96RW7	.;HMCN1_HUMAN	A	1056	ENSP00000271588:T1056A;ENSP00000356462:T1056A	ENSP00000271588:T1056A	T	+	1	0	HMCN1	184225360	1.000000	0.71417	0.012000	0.15200	0.005000	0.04900	3.494000	0.53273	0.689000	0.31550	-0.119000	0.15052	ACA	A|0.821;G|0.179	0.179	strong		0.488	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
MUC4	4585	hgsc.bcm.edu	37	3	195511397	195511397	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511397G>A	ENST00000463781.3	-	2	7513	c.7054C>T	c.(7054-7056)Cct>Tct	p.P2352S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2352S	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)		ACATGAAGAGGGGTGGCGTGA	0.587																																					p.P2352S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,3	MUC4	1505	3	0			c.C7054T						scavenged	.						16.0	14.0	14.0					3																	195511397		675	1561	2236	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	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.7054C>T	3.37:g.195511397G>A	ENSP00000417498:p.Pro2352Ser	Somatic	377	1	0.00265252		WXS	Illumina HiSeq	Phase_I	142	9	0.0633803	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	5.636	0.301959	0.10678	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.56;1.56	.	.	.	.	.	.	.	.	T	0.12050	0.0293	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.31475	-0.9942	7	.	.	.	.	4.3952	0.11360	0.3325:0.0:0.6675:0.0	rs6799339	2352	E7ESK3	.	S	2352	ENSP00000417498:P2352S;ENSP00000420243:P2352S	.	P	-	1	0	MUC4	196995792	0.025000	0.19082	0.006000	0.13384	0.066000	0.16364	0.045000	0.14013	-0.417000	0.07461	0.064000	0.15345	CCT	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ABCA6	23460	hgsc.bcm.edu	37	17	67109493	67109493	+	Silent	SNP	A	A	G	rs2058128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:67109493A>G	ENST00000284425.2	-	15	2085	c.1911T>C	c.(1909-1911)ctT>ctC	p.L637L		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	637	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					GTTCATCTAAAAGCAAAATCT	0.363													G|||	631	0.125998	0.4531	0.0447	5008	,	,		20176	0.0		0.001	False		,,,				2504	0.0				p.L637L		Atlas-SNP	.											.	ABCA6	210	.	0			c.T1911C						PASS	.	G		1650,2756	653.9+/-399.7	293,1064,846	57.0	56.0	57.0		1911	-4.0	0.7	17	dbSNP_94	57	11,8587	817.7+/-406.9	0,11,4288	no	coding-synonymous	ABCA6	NM_080284.2		293,1075,5134	GG,GA,AA		0.1279,37.4489,12.773		637/1618	67109493	1661,11343	2203	4299	6502	SO:0001819	synonymous_variant	23460	exon15			ATCTAAAAGCAAA	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"""ATP binding cassette transporters / subfamily A"""	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.1911T>C	17.37:g.67109493A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	37	CCDS11683.1																																																																																			A|0.876;G|0.124	0.124	strong		0.363	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284	
ODF1	4956	hgsc.bcm.edu	37	8	103573086	103573086	+	Missense_Mutation	SNP	T	T	C	rs11995900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103573086T>C	ENST00000285402.3	+	2	883	c.727T>C	c.(727-729)Ttt>Ctt	p.F243L	ODF1_ENST00000518835.1_Missense_Mutation_p.F36L	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	243			F -> L (in dbSNP:rs11995900).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			TGGAAGCCGATTTTCCTGTAG	0.537													T|||	386	0.0770767	0.2587	0.0303	5008	,	,		19863	0.0129		0.0099	False		,,,				2504	0.0				p.F243L		Atlas-SNP	.											.	ODF1	55	.	0			c.T727C						PASS	.	T	LEU/PHE	1038,3368	365.1+/-317.3	121,796,1286	93.0	100.0	97.0		727	4.0	1.0	8	dbSNP_120	97	37,8563	22.8+/-68.1	0,37,4263	yes	missense	ODF1	NM_024410.3	22	121,833,5549	CC,CT,TT		0.4302,23.5588,8.2654	benign	243/251	103573086	1075,11931	2203	4300	6503	SO:0001583	missense	4956	exon2			AGCCGATTTTCCT	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"""Heat shock proteins / HSPB"""	8113	protein-coding gene	gene with protein product	"""cancer/testis antigen 133"""	182878	"""outer dense fibre of sperm tails 1"""			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.727T>C	8.37:g.103573086T>C	ENSP00000285402:p.Phe243Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	NM_024410	Q3SX72	Missense_Mutation	SNP	ENST00000285402.3	37	CCDS6293.1	170	0.07783882783882784	146	0.2967479674796748	11	0.03038674033149171	9	0.015734265734265736	4	0.005277044854881266	T	15.81	2.942523	0.53079	0.235588	0.004302	ENSG00000155087	ENST00000285402;ENST00000518835	T;T	0.29655	1.56;1.73	5.18	3.95	0.45737	.	0.114042	0.40302	N	0.001133	T	0.00012	0.0000	N	0.22421	0.69	0.32344	P	0.559367	B	0.11235	0.004	B	0.12156	0.007	T	0.24083	-1.0170	9	0.87932	D	0	-31.0421	8.7103	0.34380	0.1694:0.0:0.0:0.8306	rs11995900;rs52827661;rs59122996;rs11995900	243	Q14990	ODFP1_HUMAN	L	243;36	ENSP00000285402:F243L;ENSP00000430023:F36L	ENSP00000285402:F243L	F	+	1	0	ODF1	103642262	0.945000	0.32115	1.000000	0.80357	0.997000	0.91878	2.400000	0.44504	2.106000	0.64143	0.528000	0.53228	TTT	T|0.911;C|0.089	0.089	strong		0.537	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1		
PON2	5445	hgsc.bcm.edu	37	7	95039394	95039394	+	Missense_Mutation	SNP	C	C	G	rs17876152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:95039394C>G	ENST00000222572.3	-	6	760	c.514G>C	c.(514-516)Gtt>Ctt	p.V172L	PON2_ENST00000536183.1_Missense_Mutation_p.V193L|PON2_ENST00000483292.1_5'UTR|PON2_ENST00000433091.2_Missense_Mutation_p.V160L			Q15165	PON2_HUMAN	paraoxonase 2	172			V -> L (in dbSNP:rs17876152). {ECO:0000269|Ref.5}.		aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			GCCGGTCCAACAGCTGTGATG	0.358													C|||	54	0.0107827	0.0378	0.0014	5008	,	,		15286	0.0		0.002	False		,,,				2504	0.001				p.V172L	GBM(42;803 823 13649 23368 31463)	Atlas-SNP	.											.	PON2	32	.	0			c.G514C						PASS	.	C	LEU/VAL,LEU/VAL	149,4257	104.3+/-142.8	2,145,2056	82.0	78.0	79.0		514,478	5.0	1.0	7	dbSNP_124	79	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	PON2	NM_000305.2,NM_001018161.1	32,32	2,147,6354	GG,GC,CC		0.0233,3.3818,1.161	benign,benign	172/355,160/343	95039394	151,12855	2203	4300	6503	SO:0001583	missense	5445	exon6			GTCCAACAGCTGT	M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"""Paraoxonases"""	9205	protein-coding gene	gene with protein product	"""paraoxonase nirs"", ""arylesterase 2"""	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.514G>C	7.37:g.95039394C>G	ENSP00000222572:p.Val172Leu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	37	CCDS5640.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	C	9.490	1.100457	0.20552	0.033818	2.33E-4	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.40756	2.27;1.02;2.27	4.97	4.97	0.65823	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.11067	0.0270	L	0.58302	1.8	0.51767	D	0.999939	B;B	0.12013	0.005;0.005	B;B	0.18263	0.021;0.021	T	0.03240	-1.1057	10	0.20519	T	0.43	-18.3381	10.5089	0.44849	0.0:0.7892:0.1357:0.0752	rs17876152;rs58276578	172;172	A4D1H7;Q15165	.;PON2_HUMAN	L	193;170;160;172	ENSP00000440282:V193L;ENSP00000404622:V160L;ENSP00000222572:V172L	ENSP00000222572:V172L	V	-	1	0	PON2	94877330	0.359000	0.24955	1.000000	0.80357	0.502000	0.33828	0.451000	0.21779	2.754000	0.94517	0.650000	0.86243	GTT	C|0.983;G|0.017	0.017	strong		0.358	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305	
BRDT	676	hgsc.bcm.edu	37	1	92442695	92442695	+	Missense_Mutation	SNP	A	A	C	rs1156281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:92442695A>C	ENST00000362005.3	+	7	1132	c.714A>C	c.(712-714)aaA>aaC	p.K238N	BRDT_ENST00000394530.3_Missense_Mutation_p.K192N|BRDT_ENST00000484781.1_3'UTR|BRDT_ENST00000402388.1_Missense_Mutation_p.K238N|BRDT_ENST00000370389.2_Missense_Mutation_p.K165N|BRDT_ENST00000399546.2_Missense_Mutation_p.K238N	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	238			K -> N (in dbSNP:rs1156281). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		TCACAGAAAAATCAGTGGCAC	0.368													A|||	947	0.189097	0.1513	0.134	5008	,	,		19037	0.3859		0.0755	False		,,,				2504	0.1933				p.K242N		Atlas-SNP	.											.	BRDT	133	.	0			c.A726C						PASS	.	A	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	562,3844	244.3+/-253.7	39,484,1680	58.0	56.0	57.0		714,726,576,576,495,714,714	3.2	0.2	1	dbSNP_87	57	497,8103	142.2+/-198.4	18,461,3821	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	94,94,94,94,94,94,94	57,945,5501	CC,CA,AA		5.7791,12.7553,8.1424	benign,benign,benign,benign,benign,benign,benign	238/948,242/952,192/902,192/902,165/875,238/948,238/948	92442695	1059,11947	2203	4300	6503	SO:0001583	missense	676	exon6			AGAAAAATCAGTG	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.714A>C	1.37:g.92442695A>C	ENSP00000354568:p.Lys238Asn	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	129	59	0.457364	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	405	0.18543956043956045	63	0.12804878048780488	41	0.1132596685082873	241	0.42132867132867136	60	0.079155672823219	A	13.80	2.344740	0.41498	0.127553	0.057791	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000394530;ENST00000426141;ENST00000402388	T;T;T;T;T;T	0.11063	3.1;3.1;3.1;3.14;2.81;3.1	5.58	3.21	0.36854	.	1.092130	0.06940	N	0.812580	T	0.06962	0.0177	L	0.34521	1.04	0.42066	P	0.008811000000000013	D;D;P;D	0.53312	0.959;0.959;0.944;0.959	P;P;P;P	0.52343	0.503;0.503;0.696;0.503	T	0.25882	-1.0119	9	0.72032	D	0.01	-3.2232	7.8455	0.29422	0.7881:0.1391:0.0727:0.0	rs1156281;rs52816607;rs58411058;rs1156281	192;192;242;238	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	N	238;165;238;238;192;238;238	ENSP00000354568:K238N;ENSP00000359416:K165N;ENSP00000387822:K238N;ENSP00000378038:K192N;ENSP00000404969:K238N;ENSP00000384051:K238N	ENSP00000354568:K238N	K	+	3	2	BRDT	92215283	0.991000	0.36638	0.150000	0.22450	0.181000	0.23173	2.784000	0.47774	0.467000	0.27218	0.533000	0.62120	AAA	A|0.865;C|0.135	0.135	strong		0.368	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
TTN	7273	hgsc.bcm.edu	37	2	179393111	179393111	+	Missense_Mutation	SNP	A	A	G	rs16866378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179393111A>G	ENST00000591111.1	-	311	102568	c.102344T>C	c.(102343-102345)gTa>gCa	p.V34115A	TTN_ENST00000342175.6_Missense_Mutation_p.V26883A|TTN-AS1_ENST00000591867.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V26816A|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V26691A|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V35756A|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V33188A|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000587576.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000588244.1_RNA			Q8WZ42	TITIN_HUMAN	titin	34115	Ig-like 151.|Ser-rich.		V -> A. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGGGAGTATACATTTCTGGA	0.398													A|||	461	0.0920527	0.1354	0.0403	5008	,	,		19459	0.1736		0.0318	False		,,,				2504	0.0481				p.V35756A		Atlas-SNP	.											.	TTN	18412	.	0			c.T107267C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	443,3287		29,385,1451	113.0	102.0	105.0		80648,80447,99563,80072	1.2	0.0	2	dbSNP_123	105	170,8040		4,162,3939	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	64,64,64,64	33,547,5390	GG,GA,AA		2.0706,11.8767,5.134	benign,benign,benign,benign	26883/27119,26816/27052,33188/33424,26691/26927	179393111	613,11327	1865	4105	5970	SO:0001583	missense	7273	exon361			GAGTATACATTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.102344T>C	2.37:g.179393111A>G	ENSP00000465570:p.Val34115Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		205	0.09386446886446886	68	0.13821138211382114	15	0.04143646408839779	100	0.17482517482517482	22	0.029023746701846966	A	7.782	0.709636	0.15239	0.118767	0.020706	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	5.25	1.24	0.21308	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00210	0.0006	L	0.45744	1.44	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.001	B;B;B;B;B	0.09377	0.001;0.001;0.003;0.004;0.002	T	0.12941	-1.0528	8	0.87932	D	0	.	9.8416	0.41002	0.6746:0.0:0.3254:0.0	rs16866378;rs52835227;rs16866378	26691;26816;26883;34115;33188	D3DPF9;E7EQE6;E7ET18;Q8WZ42;A6NKB1	.;.;.;TITIN_HUMAN;.	A	33188;26691;26883;26816;26688	ENSP00000343764:V33188A;ENSP00000434586:V26691A;ENSP00000340554:V26883A;ENSP00000352154:V26816A	ENSP00000340554:V26883A	V	-	2	0	TTN	179101357	0.258000	0.24033	0.021000	0.16686	0.083000	0.17756	4.288000	0.59007	0.410000	0.25675	0.454000	0.30748	GTA	A|0.906;G|0.094	0.094	strong		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TAF1	6872	hgsc.bcm.edu	37	X	70595132	70595132	+	Silent	SNP	T	T	C	rs5981106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70595132T>C	ENST00000373790.4	+	4	579	c.528T>C	c.(526-528)acT>acC	p.T176T	TAF1_ENST00000276072.3_Silent_p.T176T|TAF1_ENST00000423759.1_Silent_p.T176T|TAF1_ENST00000449580.1_Silent_p.T176T	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	176	Protein kinase 1.				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)				ATTCTATTACTGGTGGTAAGT	0.438													C|||	293	0.0776159	0.2012	0.0274	3775	,	,		12232	0.0		0.005	False		,,,				2504	0.0031				p.T176T		Atlas-SNP	.											.	TAF1	439	.	0			c.T528C						PASS	.	C	,	921,2914		89,609,134,934,437	96.0	82.0	87.0		528,528	-6.1	0.0	X	dbSNP_114	87	38,6690		0,28,10,2400,1862	no	coding-synonymous,coding-synonymous	TAF1	NM_004606.3,NM_138923.2	,	89,637,144,3334,2299	CC,CT,C,TT,T		0.5648,24.0156,9.0789	,	176/1894,176/1873	70595132	959,9604	2203	4300	6503	SO:0001819	synonymous_variant	6872	exon4			TATTACTGGTGGT		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.528T>C	X.37:g.70595132T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	158	67	0.424051	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	37	CCDS35325.1																																																																																			T|0.891;C|0.109	0.109	strong		0.438	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
KIAA0319L	79932	hgsc.bcm.edu	37	1	35900615	35900615	+	Silent	SNP	A	A	G	rs3814302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35900615A>G	ENST00000325722.3	-	21	3264	c.3030T>C	c.(3028-3030)gaT>gaC	p.D1010D	KIAA0319L_ENST00000373266.4_Silent_p.D447D	NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	1010						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)				AGATGGCATCATCGCTGTCCA	0.547													G|||	2272	0.453674	0.7239	0.3674	5008	,	,		22270	0.7679		0.0497	False		,,,				2504	0.2413				p.D1010D		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.T3030C						PASS	.	G		2634,1772	524.6+/-371.4	807,1020,376	100.0	88.0	92.0		3030	-9.4	0.3	1	dbSNP_107	92	285,8315	806.6+/-407.2	7,271,4022	no	coding-synonymous	KIAA0319L	NM_024874.4		814,1291,4398	GG,GA,AA		3.314,40.2179,22.4435		1010/1050	35900615	2919,10087	2203	4300	6503	SO:0001819	synonymous_variant	79932	exon21			GGCATCATCGCTG	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.3030T>C	1.37:g.35900615A>G		Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	240	119	0.495833	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Silent	SNP	ENST00000325722.3	37	CCDS390.1																																																																																			A|0.669;G|0.331	0.331	strong		0.547	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390162	208390162	+	Missense_Mutation	SNP	T	T	C	rs4844658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:208390162T>C	ENST00000367033.3	-	2	1863	c.1106A>G	c.(1105-1107)gAg>gGg	p.E369G		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	369	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		E -> G (in dbSNP:rs4844658). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9455484}.		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)		CTGCAGGCGCTCCTTGATCTG	0.602													T|||	594	0.11861	0.0121	0.2032	5008	,	,		21845	0.1429		0.2087	False		,,,				2504	0.0849				p.E369G		Atlas-SNP	.											.	PLXNA2	178	.	0			c.A1106G						PASS	.	T	GLY/GLU	148,4258	101.6+/-140.2	3,142,2058	68.0	66.0	66.0		1106	5.8	1.0	1	dbSNP_111	66	1646,6954	303.3+/-306.4	168,1310,2822	yes	missense	PLXNA2	NM_025179.3	98	171,1452,4880	CC,CT,TT		19.1395,3.3591,13.7936	benign	369/1895	208390162	1794,11212	2203	4300	6503	SO:0001583	missense	5362	exon2			AGGCGCTCCTTGA	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.1106A>G	1.37:g.208390162T>C	ENSP00000356000:p.Glu369Gly	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	306	0.1401098901098901	11	0.022357723577235773	64	0.17679558011049723	72	0.1258741258741259	159	0.20976253298153033	T	19.24	3.789846	0.70337	0.033591	0.191395	ENSG00000076356	ENST00000367033	T	0.12039	2.72	5.84	5.84	0.93424	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.123712	0.53938	D	0.000054	T	0.00039	0.0001	M	0.83603	2.65	0.19300	P	0.9999736942	D;P	0.57257	0.979;0.66	P;B	0.57846	0.828;0.215	T	0.07888	-1.0749	9	0.87932	D	0	.	11.3143	0.49383	0.1358:0.0:0.0:0.8642	rs4844658;rs17458917;rs4844658	423;369	O75051-2;O75051	.;PLXA2_HUMAN	G	369	ENSP00000356000:E369G	ENSP00000356000:E369G	E	-	2	0	PLXNA2	206456785	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.876000	0.69667	2.232000	0.73038	0.533000	0.62120	GAG	T|0.865;C|0.135	0.135	strong		0.602	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
GALR1	2587	hgsc.bcm.edu	37	18	74962810	74962810	+	Silent	SNP	G	G	T	rs5375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:74962810G>T	ENST00000299727.3	+	1	306	c.306G>T	c.(304-306)gtG>gtT	p.V102V		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	102					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)		CCACCTGGGTGCTGGGCGCCT	0.612													G|||	321	0.0640974	0.146	0.0231	5008	,	,		16293	0.0466		0.0288	False		,,,				2504	0.0368				p.V102V		Atlas-SNP	.											GALR1,NS,carcinoma,0,1	GALR1	53	1	0			c.G306T						PASS	.	G		517,3889	236.5+/-248.6	27,463,1713	129.0	114.0	119.0		306	3.4	1.0	18	dbSNP_52	119	264,8336	101.9+/-163.1	3,258,4039	no	coding-synonymous	GALR1	NM_001480.3		30,721,5752	TT,TG,GG		3.0698,11.734,6.0049		102/350	74962810	781,12225	2203	4300	6503	SO:0001819	synonymous_variant	2587	exon1			CTGGGTGCTGGGC	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.306G>T	18.37:g.74962810G>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	166	93	0.560241	NM_001480	Q4VBL7	Silent	SNP	ENST00000299727.3	37	CCDS12012.1																																																																																			G|0.936;T|0.064	0.064	strong		0.612	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1		
ISLR2	57611	hgsc.bcm.edu	37	15	74425505	74425505	+	Missense_Mutation	SNP	C	C	T	rs3889598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:74425505C>T	ENST00000361742.3	+	4	1179	c.410C>T	c.(409-411)tCt>tTt	p.S137F	ISLR2_ENST00000445793.1_Missense_Mutation_p.S137F|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000565540.1_Missense_Mutation_p.S137F|ISLR2_ENST00000419208.1_Missense_Mutation_p.S137F|ISLR2_ENST00000453268.2_Missense_Mutation_p.S137F|ISLR2_ENST00000565159.1_Missense_Mutation_p.S137F|ISLR2_ENST00000435464.1_Missense_Mutation_p.S137F	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	137			S -> F (in dbSNP:rs3889598).		positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						CGCCTGGGCTCTCTGCCCCGG	0.632													C|||	176	0.0351438	0.0484	0.0274	5008	,	,		20350	0.0427		0.0179	False		,,,				2504	0.0327				p.S137F		Atlas-SNP	.											ISLR2,rectum,carcinoma,0,2	ISLR2	78	2	0			c.C410T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER,PHE/SER	182,4214	115.0+/-153.0	1,180,2017	57.0	60.0	59.0		410,410,410,410	4.5	1.0	15	dbSNP_108	59	123,8471	62.4+/-124.4	0,123,4174	yes	missense,missense,missense,missense	ISLR2	NM_001130136.1,NM_001130137.1,NM_001130138.1,NM_020851.2	155,155,155,155	1,303,6191	TT,TC,CC		1.4312,4.1401,2.348	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	137/746,137/746,137/746,137/746	74425505	305,12685	2198	4297	6495	SO:0001583	missense	57611	exon4			TGGGCTCTCTGCC		CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.410C>T	15.37:g.74425505C>T	ENSP00000355402:p.Ser137Phe	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_001130138	A8K352|Q9P263	Missense_Mutation	SNP	ENST00000361742.3	37	CCDS10259.1	76	0.0347985347985348	35	0.07113821138211382	9	0.024861878453038673	20	0.03496503496503497	12	0.0158311345646438	C	8.408	0.843473	0.16963	0.041401	0.014312	ENSG00000167178	ENST00000445793;ENST00000361742;ENST00000435464;ENST00000453268;ENST00000395121;ENST00000419208	T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34	4.46	4.46	0.54185	.	0.318283	0.29417	U	0.012202	T	0.04272	0.0118	L	0.42632	1.34	0.38781	D	0.95476	B	0.29232	0.238	B	0.27380	0.079	T	0.07693	-1.0759	10	0.37606	T	0.19	.	8.8313	0.35085	0.2745:0.5872:0.1383:0.0	rs3889598;rs4556747;rs3889598	137	Q6UXK2	ISLR2_HUMAN	F	137	ENSP00000403244:S137F;ENSP00000355402:S137F;ENSP00000411443:S137F;ENSP00000411834:S137F;ENSP00000408872:S137F	ENSP00000355402:S137F	S	+	2	0	ISLR2	72212558	0.002000	0.14202	0.979000	0.43373	0.867000	0.49689	0.610000	0.24253	2.042000	0.60477	0.407000	0.27541	TCT	C|0.973;T|0.027	0.027	strong		0.632	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851	
MGAM	8972	hgsc.bcm.edu	37	7	141752213	141752213	+	Silent	SNP	C	C	A	rs386718585|rs2961085	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	66	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	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		
SELPLG	6404	hgsc.bcm.edu	37	12	109017673	109017673	+	Silent	SNP	C	C	T	rs63748999|rs558357966|rs372173288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109017673C>T	ENST00000550948.1	-	2	635	c.411G>A	c.(409-411)gtG>gtA	p.V137V	SELPLG_ENST00000228463.6_Silent_p.V153V|SELPLG_ENST00000388962.3_Intron			Q14242	SELPL_HUMAN	selectin P ligand	137	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						CCTCCGTGGGCACTGGTTGAG	0.617													c|||	441	0.0880591	0.0272	0.0504	5008	,	,		19600	0.2034		0.0795	False		,,,				2504	0.0869				p.V153V		Atlas-SNP	.											SELPLG_ENST00000550948,NS,carcinoma,-1,7	SELPLG	138	7	0			c.G459A						scavenged	.						159.0	124.0	136.0					12																	109017673		2199	4274	6473	SO:0001819	synonymous_variant	6404	exon2			CGTGGGCACTGGT		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.411G>A	12.37:g.109017673C>T		Somatic	294	4	0.0136054		WXS	Illumina HiSeq	Phase_I	232	55	0.237069	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Silent	SNP	ENST00000550948.1	37	CCDS31895.2																																																																																			.	.	none		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
THSD7B	80731	hgsc.bcm.edu	37	2	138030234	138030234	+	Splice_Site	SNP	C	C	T	rs12622896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:138030234C>T	ENST00000409968.1	+	11	2574		c.e11+2		THSD7B_ENST00000272643.3_Splice_Site|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000413152.2_Splice_Site			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B							integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		TGTATATCGGCAAGTAGTTAC	0.378													T|||	245	0.0489217	0.0809	0.0231	5008	,	,		17286	0.0595		0.0159	False		,,,				2504	0.047				.		Atlas-SNP	.											.	THSD7B	506	.	0			c.2303+2C>T						PASS	.	T		198,3588		5,188,1700	149.0	145.0	146.0			5.9	1.0	2	dbSNP_120	146	72,8164		1,70,4047	yes	splice-5	THSD7B	NM_001080427.1		6,258,5747	TT,TC,CC		0.8742,5.2298,2.2459			138030234	270,11752	1893	4118	6011	SO:0001630	splice_region_variant	80731	exon10			TATCGGCAAGTAG			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.2396+2C>T	2.37:g.138030234C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_001080427		Splice_Site	SNP	ENST00000409968.1	37		79	0.036172161172161175	27	0.054878048780487805	8	0.022099447513812154	31	0.05419580419580419	13	0.017150395778364115	T	13.25	2.179761	0.38511	0.052298	0.008742	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2029	0.48751	0.0:0.0726:0.0:0.9274	rs12622896;rs52826023;rs12622896	.	.	.	.	-1	.	.	.	+	.	.	THSD7B	137746704	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	4.425000	0.59875	1.049000	0.40321	-0.254000	0.11334	.	C|0.961;T|0.039	0.039	strong		0.378	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9	Intron
MFRP	83552	hgsc.bcm.edu	37	11	119216867	119216867	+	Missense_Mutation	SNP	G	G	C	rs139436396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119216867G>C	ENST00000530681.1	-	3	304	c.160C>G	c.(160-162)Cgg>Ggg	p.R54G	MFRP_ENST00000555262.1_Missense_Mutation_p.R54G|MFRP_ENST00000449574.2_Missense_Mutation_p.R54G|C1QTNF5_ENST00000445041.2_5'UTR|MFRP_ENST00000529147.1_5'UTR|MFRP_ENST00000360167.4_Missense_Mutation_p.R54G	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	54			R -> G (in dbSNP:rs139436396). {ECO:0000269|PubMed:16352475}.		embryo development (GO:0009790)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|urinary_tract(1)	18		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		CGAGGACGCCGACCTGCGGGT	0.642													G|||	55	0.0109824	0.0371	0.0086	5008	,	,		17805	0.0		0.0	False		,,,				2504	0.0				p.R54G		Atlas-SNP	.											.	MFRP	63	.	0			c.C160G						PASS	.	G	,GLY/ARG	111,4267		2,107,2080	19.0	18.0	18.0		,160	4.3	0.8	11	dbSNP_134	18	1,8565		0,1,4282	yes	utr-5,missense	MFRP,C1QTNF5	NM_015645.3,NM_031433.2	,125	2,108,6362	CC,CG,GG		0.0117,2.5354,0.8653	,benign	,54/580	119216867	112,12832	2189	4283	6472	SO:0001583	missense	83552	exon3			GACGCCGACCTGC	AB055505	CCDS8421.1	11q23.3	2014-01-28			ENSG00000235718	ENSG00000235718			18121	protein-coding gene	gene with protein product	"""membrane-type frizzled-related protein"", ""complement C1q tumor necrosis factor-related protein 5 precursor variant 1"""	606227				11263980	Standard	NM_031433		Approved	FLJ30570, rd6, NNO2, C1QTNF5	uc001pwj.2	Q9BY79		ENST00000530681.1:c.160C>G	11.37:g.119216867G>C	ENSP00000456533:p.Arg54Gly	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_031433	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Missense_Mutation	SNP	ENST00000530681.1	37	CCDS8421.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	G	17.80	3.477400	0.63849	0.025354	1.17E-4	ENSG00000235718	ENST00000555262;ENST00000449574;ENST00000360167	T;T;T	0.67698	-0.28;-0.28;1.88	5.24	4.27	0.50696	.	0.647065	0.15397	N	0.264485	T	0.29126	0.0724	L	0.27053	0.805	0.24539	N	0.994075	P;B	0.39157	0.662;0.319	B;B	0.37833	0.259;0.097	T	0.26643	-1.0097	10	0.30078	T	0.28	-13.8891	13.6734	0.62438	0.0:0.1544:0.8456:0.0	.	54;54	B4DHN8;Q9BY79	.;MFRP_HUMAN	G	54	ENSP00000450509:R54G;ENSP00000391664:R54G;ENSP00000353291:R54G	ENSP00000353291:R54G	R	-	1	2	MFRP	118722077	0.010000	0.17322	0.842000	0.33263	0.537000	0.34900	0.833000	0.27504	2.601000	0.87937	0.655000	0.94253	CGG	G|0.990;C|0.010	0.010	strong		0.642	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433	
OR1L3	26735	hgsc.bcm.edu	37	9	125437725	125437725	+	Missense_Mutation	SNP	T	T	C	rs16912096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125437725T>C	ENST00000304820.2	+	1	411	c.317T>C	c.(316-318)gTt>gCt	p.V106A		NM_001005234.1	NP_001005234.1	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L, member 3	106			V -> A (in dbSNP:rs16912096).			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(2)|lung(6)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	16						TTCTTCCTGGTTTTTGGAAAC	0.423													T|||	397	0.0792732	0.2224	0.0231	5008	,	,		22639	0.0734		0.001	False		,,,				2504	0.0123				p.V106A		Atlas-SNP	.											OR1L3,NS,carcinoma,+1,1	OR1L3	51	1	0			c.T317C						PASS	.	T	ALA/VAL	812,3594	326.4+/-299.6	77,658,1468	151.0	154.0	153.0		317	-0.3	0.2	9	dbSNP_123	153	12,8588	7.1+/-27.0	0,12,4288	yes	missense	OR1L3	NM_001005234.1	64	77,670,5756	CC,CT,TT		0.1395,18.4294,6.3355	benign	106/325	125437725	824,12182	2203	4300	6503	SO:0001583	missense	26735	exon1			TCCTGGTTTTTGG		CCDS35128.1	9q33.2	2013-09-20			ENSG00000171481	ENSG00000171481		"""GPCR / Class A : Olfactory receptors"""	8215	protein-coding gene	gene with protein product							Standard	NM_001005234		Approved	OR9-D	uc011lzb.2	Q8NH93	OTTHUMG00000020619	ENST00000304820.2:c.317T>C	9.37:g.125437725T>C	ENSP00000302863:p.Val106Ala	Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_001005234	B2RNF4|Q6IFN1	Missense_Mutation	SNP	ENST00000304820.2	37	CCDS35128.1	148	0.06776556776556776	92	0.18699186991869918	7	0.019337016574585635	48	0.08391608391608392	1	0.0013192612137203166	T	0.284	-0.984222	0.02180	0.184294	0.001395	ENSG00000171481	ENST00000304820	T	0.00333	8.07	4.54	-0.329	0.12686	GPCR, rhodopsin-like superfamily (1);	0.474644	0.15407	U	0.263970	T	0.00012	0.0000	N	0.00855	-1.145	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.00107	-1.2052	9	0.13853	T	0.58	-4.8218	8.9232	0.35623	0.0:0.4499:0.0:0.5501	rs16912096;rs16912096	106	Q8NH93	OR1L3_HUMAN	A	106	ENSP00000302863:V106A	ENSP00000302863:V106A	V	+	2	0	OR1L3	124477546	0.000000	0.05858	0.231000	0.23993	0.948000	0.59901	-0.588000	0.05774	0.065000	0.16485	-0.308000	0.09152	GTT	T|0.931;C|0.069	0.069	strong		0.423	OR1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053950.1		
MCM5	4174	hgsc.bcm.edu	37	22	35815880	35815880	+	Silent	SNP	G	G	A	rs133427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:35815880G>A	ENST00000216122.4	+	14	1861	c.1707G>A	c.(1705-1707)aaG>aaA	p.K569K	MCM5_ENST00000382011.5_Silent_p.K526K	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	569					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						CCTGCAGGAAGTGTGGCCCCC	0.632													G|||	661	0.131989	0.2428	0.0692	5008	,	,		18288	0.0476		0.0825	False		,,,				2504	0.1646				p.K569K		Atlas-SNP	.											.	MCM5	54	.	0			c.G1707A						PASS	.	G		852,3554	311.1+/-291.9	82,688,1433	44.0	47.0	46.0		1707	1.0	0.9	22	dbSNP_78	46	654,7946	157.3+/-211.0	25,604,3671	no	coding-synonymous	MCM5	NM_006739.3		107,1292,5104	AA,AG,GG		7.6047,19.3373,11.5793		569/735	35815880	1506,11500	2203	4300	6503	SO:0001819	synonymous_variant	4174	exon14			CAGGAAGTGTGGC		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"""minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)"", ""MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"""	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.1707G>A	22.37:g.35815880G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	164	79	0.481707	NM_006739	O60785|Q14578|Q9BTJ4|Q9BWL8	Silent	SNP	ENST00000216122.4	37	CCDS13915.1																																																																																			G|0.878;A|0.122	0.122	strong		0.632	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3		
RASA2	5922	hgsc.bcm.edu	37	3	141248572	141248572	+	Missense_Mutation	SNP	A	A	C	rs144759014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141248572A>C	ENST00000452898.1	+	4	413	c.378A>C	c.(376-378)gaA>gaC	p.E126D	RASA2_ENST00000286364.3_Missense_Mutation_p.E126D	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	126					intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						TCAAAAAAGAAGACTTGTGTA	0.318													A|||	3	0.000599042	0.0023	0.0	5008	,	,		15787	0.0		0.0	False		,,,				2504	0.0				p.E126D		Atlas-SNP	.											RASA2_ENST00000286364,temporal_lobe,glioma,+2,2	RASA2	169	2	0			c.A378C						PASS	.	A	ASP/GLU	7,4399	12.9+/-30.5	0,7,2196	72.0	74.0	74.0		378	4.7	1.0	3	dbSNP_134	74	0,8598		0,0,4299	yes	missense	RASA2	NM_006506.2	45	0,7,6495	CC,CA,AA		0.0,0.1589,0.0538	possibly-damaging	126/850	141248572	7,12997	2203	4299	6502	SO:0001583	missense	5922	exon4			AAAAGAAGACTTG	AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"""Pleckstrin homology (PH) domain containing"""	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.378A>C	3.37:g.141248572A>C	ENSP00000391677:p.Glu126Asp	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Missense_Mutation	SNP	ENST00000452898.1	37		.	.	.	.	.	.	.	.	.	.	A	16.18	3.051372	0.55218	0.001589	0.0	ENSG00000155903	ENST00000286364;ENST00000452898	T;T	0.70869	-0.52;-0.52	5.84	4.68	0.58851	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.055137	0.64402	D	0.000001	T	0.70064	0.3181	M	0.80183	2.485	0.46356	D	0.999007	B;B;B	0.23490	0.051;0.086;0.051	B;B;B	0.31686	0.063;0.134;0.063	T	0.63060	-0.6721	10	0.21014	T	0.42	.	8.3803	0.32468	0.8469:0.0:0.1531:0.0	.	126;126;126	A8K7K1;G3V0F9;Q15283	.;.;RASA2_HUMAN	D	126	ENSP00000286364:E126D;ENSP00000391677:E126D	ENSP00000286364:E126D	E	+	3	2	RASA2	142731262	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.541000	0.36126	1.030000	0.39839	0.533000	0.62120	GAA	A|1.000;C|0.000	0.000	strong		0.318	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506	
MT-CO1	4512	hgsc.bcm.edu	37	M	6071	6071	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:6071T>C	ENST00000361624.2	+	1	168	c.168T>C	c.(166-168)gtT>gtC	p.V56V	MT-TI_ENST00000387365.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-ATP8_ENST00000361851.1_5'Flank|MT-TL1_ENST00000386347.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TC_ENST00000387405.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TY_ENST00000387409.1_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	56					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						ATCTACAACGTTATCGTCACA	0.498																																					p.V56V		Atlas-SNP	.											.	.	.	.	0			c.T168C						PASS	.																																			SO:0001819	synonymous_variant	5742	exon1			CAACGTTATCGTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.168T>C	M.37:g.6071T>C		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	ENST00000361624	Q34770	Silent	SNP	ENST00000361624.2	37																																																																																				.	.	none		0.498	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028	
KRT3	3850	hgsc.bcm.edu	37	12	53189427	53189427	+	Missense_Mutation	SNP	C	C	G	rs148531142		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53189427C>G	ENST00000417996.2	-	1	474	c.400G>C	c.(400-402)Gct>Cct	p.A134P	KRT3_ENST00000309505.3_Missense_Mutation_p.A134P	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	134	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						aagccaccagcccctccaaag	0.632																																					p.A134P		Atlas-SNP	.											.	KRT3	65	.	0			c.G400C						PASS	.						141.0	187.0	172.0					12																	53189427		2178	4256	6434	SO:0001583	missense	3850	exon1			CACCAGCCCCTCC		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.400G>C	12.37:g.53189427C>G	ENSP00000413479:p.Ala134Pro	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	170	36	0.211765	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	37	CCDS44895.1	.	.	.	.	.	.	.	.	.	.	c	6.997	0.554067	0.13374	.	.	ENSG00000186442	ENST00000417996;ENST00000309505	D;D	0.85171	-1.95;-1.95	3.45	0.361	0.16107	.	0.198436	0.24869	N	0.034957	T	0.76428	0.3986	L	0.46157	1.445	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.61446	-0.7061	10	0.33940	T	0.23	.	7.7249	0.28755	0.1722:0.493:0.3348:0.0	.	134	P12035	K2C3_HUMAN	P	134	ENSP00000413479:A134P;ENSP00000312206:A134P	ENSP00000312206:A134P	A	-	1	0	KRT3	51475694	0.000000	0.05858	0.001000	0.08648	0.428000	0.31595	-0.074000	0.11450	-0.174000	0.10743	0.603000	0.83216	GCT	.	.	none		0.632	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
BZRAP1	9256	hgsc.bcm.edu	37	17	56386118	56386118	+	Silent	SNP	A	A	G	rs2680689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56386118A>G	ENST00000343736.4	-	22	4678	c.4515T>C	c.(4513-4515)gaT>gaC	p.D1505D	BZRAP1_ENST00000268893.6_Silent_p.D1445D|BZRAP1_ENST00000355701.3_Silent_p.D1505D			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						PASS	.	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	82	0	0		WXS	Illumina HiSeq	Phase_I	88	48	0.545455	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	
KCNT1	57582	hgsc.bcm.edu	37	9	138651648	138651648	+	Silent	SNP	A	A	G	rs61739517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138651648A>G	ENST00000263604.3	+	11	921	c.921A>G	c.(919-921)ccA>ccG	p.P307P	KCNT1_ENST00000491806.2_Silent_p.P293P|KCNT1_ENST00000371757.2_Silent_p.P326P|KCNT1_ENST00000488444.2_Silent_p.P307P|KCNT1_ENST00000490355.2_Silent_p.P307P|KCNT1_ENST00000486577.2_Silent_p.P287P|KCNT1_ENST00000298480.5_Silent_p.P326P|KCNT1_ENST00000487664.1_Silent_p.P281P			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	307					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		AGATCTGGCCATCGCAGCTGC	0.642													A|||	142	0.0283546	0.1051	0.0043	5008	,	,		20814	0.0		0.0	False		,,,				2504	0.0				p.P326P		Atlas-SNP	.											.	KCNT1	139	.	0			c.A978G						PASS	.	A		385,4021	194.0+/-219.0	20,345,1838	137.0	98.0	111.0		978	-9.7	0.7	9	dbSNP_129	111	4,8596	1.2+/-3.3	0,4,4296	no	coding-synonymous	KCNT1	NM_020822.2		20,349,6134	GG,GA,AA		0.0465,8.7381,2.9909		326/1236	138651648	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	57582	exon11			CTGGCCATCGCAG	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.921A>G	9.37:g.138651648A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	116	39	0.336207	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Silent	SNP	ENST00000263604.3	37																																																																																				A|0.967;G|0.033	0.033	strong		0.642	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822	
UBR1	197131	hgsc.bcm.edu	37	15	43237572	43237572	+	Silent	SNP	T	T	C	rs16957277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43237572T>C	ENST00000290650.4	-	47	5283	c.5205A>G	c.(5203-5205)caA>caG	p.Q1735Q	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1735					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GATTAGTCTCTTGGCTCCTAG	0.453													T|||	452	0.0902556	0.1702	0.0403	5008	,	,		18833	0.0526		0.0497	False		,,,				2504	0.0982				p.Q1735Q		Atlas-SNP	.											.	UBR1	124	.	0			c.A5205G						PASS	.	T		536,3870	241.5+/-251.9	31,474,1698	139.0	125.0	130.0		5205	1.2	1.0	15	dbSNP_123	130	299,8299	109.8+/-170.3	6,287,4006	no	coding-synonymous	UBR1	NM_174916.2		37,761,5704	CC,CT,TT		3.4776,12.1652,6.4211		1735/1750	43237572	835,12169	2203	4299	6502	SO:0001819	synonymous_variant	197131	exon47			AGTCTCTTGGCTC		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.5205A>G	15.37:g.43237572T>C		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	173	96	0.554913	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Silent	SNP	ENST00000290650.4	37	CCDS10091.1																																																																																			T|0.928;C|0.072	0.072	strong		0.453	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
QRICH2	84074	hgsc.bcm.edu	37	17	74288410	74288410	+	Missense_Mutation	SNP	C	C	T	rs80109605		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74288410C>T	ENST00000262765.5	-	4	2079	c.1900G>A	c.(1900-1902)Ggt>Agt	p.G634S		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	634	Gln-rich.							p.I630_G639delIVQRGLVQPG(3)		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						tgcaccaaaccacgctgaact	0.527																																					p.G634S		Atlas-SNP	.											.	QRICH2	143	.	3	Deletion - In frame(3)	stomach(3)	c.G1900A						PASS	.						68.0	85.0	79.0					17																	74288410		2201	4298	6499	SO:0001583	missense	84074	exon4			CCAAACCACGCTG	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.1900G>A	17.37:g.74288410C>T	ENSP00000262765:p.Gly634Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	152	22	0.144737	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.323061	0.24080	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.23950	1.88	5.11	1.94	0.25998	.	.	.	.	.	T	0.38878	0.1057	M	0.84082	2.675	0.80722	P	0.0	P;P	0.51537	0.946;0.897	P;P	0.50314	0.637;0.485	T	0.56007	-0.8050	8	0.44086	T	0.13	-8.3819	9.1736	0.37098	0.0:0.7577:0.0:0.2423	.	634;634	B5MD94;Q9H0J4	.;QRIC2_HUMAN	S	634	ENSP00000262765:G634S	ENSP00000262765:G634S	G	-	1	0	QRICH2	71800005	0.000000	0.05858	0.019000	0.16419	0.008000	0.06430	0.238000	0.18004	1.089000	0.41292	0.555000	0.69702	GGT	.	.	weak		0.527	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
SCN7A	6332	hgsc.bcm.edu	37	2	167262835	167262835	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:167262835C>T	ENST00000409855.1	-	25	4430	c.4304G>A	c.(4303-4305)gGt>gAt	p.G1435D		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1435					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)	CCCATCCCAACCAGCAAATAT	0.378																																					p.G1435D		Atlas-SNP	.											SCN7A_ENST00000409855,NS,carcinoma,-1,2	SCN7A	410	2	0			c.G4304A						scavenged	.						169.0	162.0	164.0					2																	167262835		1880	4139	6019	SO:0001583	missense	6332	exon25			TCCCAACCAGCAA	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.4304G>A	2.37:g.167262835C>T	ENSP00000386796:p.Gly1435Asp	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	298	5	0.0167785	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.101208	0.76983	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.99886	-7.52	5.14	4.26	0.50523	Ion transport (1);	0.000000	0.64402	D	0.000009	D	0.99816	0.9919	M	0.65975	2.015	0.51482	D	0.999928	D	0.89917	1.0	D	0.97110	1.0	D	0.96529	0.9391	10	0.87932	D	0	.	11.7194	0.51672	0.0:0.9142:0.0:0.0858	.	1435	Q01118	SCN7A_HUMAN	D	1435	ENSP00000386796:G1435D	ENSP00000259060:G1435D	G	-	2	0	SCN7A	166971081	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	7.548000	0.82154	1.540000	0.49301	0.591000	0.81541	GGT	.	.	none		0.378	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
DDX20	11218	hgsc.bcm.edu	37	1	112308972	112308972	+	Silent	SNP	G	G	A	rs197413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:112308972G>A	ENST00000369702.4	+	11	2546	c.1926G>A	c.(1924-1926)gtG>gtA	p.V642V	DDX20_ENST00000475700.1_Silent_p.V250V	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	642					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAGTCCCTGTGTTGGCAAGTA	0.443													A|||	2403	0.479832	0.7428	0.5115	5008	,	,		19455	0.3403		0.4185	False		,,,				2504	0.3088				p.V642V		Atlas-SNP	.											.	DDX20	50	.	0			c.G1926A						PASS	.	A		2992,1414	455.7+/-351.1	1018,956,229	47.0	48.0	48.0		1926	-2.6	0.0	1	dbSNP_79	48	3349,5251	639.0+/-399.4	671,2007,1622	no	coding-synonymous	DDX20	NM_007204.4		1689,2963,1851	AA,AG,GG		38.9419,32.0926,48.7544		642/825	112308972	6341,6665	2203	4300	6503	SO:0001819	synonymous_variant	11218	exon11			CCCTGTGTTGGCA	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.1926G>A	1.37:g.112308972G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Silent	SNP	ENST00000369702.4	37	CCDS842.1																																																																																			G|0.512;A|0.488	0.488	strong		0.443	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
HSDL1	83693	hgsc.bcm.edu	37	16	84158248	84158248	+	Missense_Mutation	SNP	G	G	C	rs4378600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84158248G>C	ENST00000219439.4	-	6	1156	c.980C>G	c.(979-981)tCc>tGc	p.S327C	HSDL1_ENST00000565275.1_5'Flank|HSDL1_ENST00000434463.3_Missense_Mutation_p.S272C	NM_001146051.1|NM_031463.4	NP_001139523.1|NP_113651.4	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1	327			S -> C (in dbSNP:rs4378600). {ECO:0000269|PubMed:14702039}.			mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7						GGCTGTGCAGGATAAGGCTTC	0.428													G|||	1238	0.247204	0.236	0.1729	5008	,	,		21727	0.2331		0.3161	False		,,,				2504	0.2587				p.S327C		Atlas-SNP	.											.	HSDL1	23	.	0			c.C980G						PASS	.	G	CYS/SER,CYS/SER	1021,3379	378.0+/-322.7	118,785,1297	112.0	98.0	103.0		815,980	5.6	1.0	16	dbSNP_111	103	2505,6095	410.7+/-350.2	346,1813,2141	yes	missense,missense	HSDL1	NM_001146051.1,NM_031463.4	112,112	464,2598,3438	CC,CG,GG		29.1279,23.2045,27.1231	benign,benign	272/276,327/331	84158248	3526,9474	2200	4300	6500	SO:0001583	missense	83693	exon6			GTGCAGGATAAGG	AF237684	CCDS10942.1, CCDS54046.1	16q24	2011-09-20			ENSG00000103160	ENSG00000103160		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	16475	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 12C, member 3"""					12153137, 19027726	Standard	NM_031463		Approved	SDR12C3	uc002fhk.2	Q3SXM5	OTTHUMG00000137635	ENST00000219439.4:c.980C>G	16.37:g.84158248G>C	ENSP00000219439:p.Ser327Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	124	54	0.435484	NM_031463	B4DSL2|D3DUL4|Q3SXM4|Q8NC98|Q9BY22	Missense_Mutation	SNP	ENST00000219439.4	37	CCDS10942.1	546	0.25	115	0.23373983739837398	71	0.19613259668508287	123	0.21503496503496503	237	0.31266490765171506	G	13.14	2.147509	0.37923	0.232045	0.291279	ENSG00000103160	ENST00000434463;ENST00000219439	T;D	0.83673	-1.12;-1.75	5.6	5.6	0.85130	.	0.580099	0.17534	N	0.170776	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	P;P	0.50710	0.726;0.938	B;B	0.40101	0.319;0.319	T	0.03619	-1.1019	9	0.56958	D	0.05	-30.9015	12.4939	0.55916	0.077:0.0:0.923:0.0	rs4378600;rs17652812;rs52833604;rs4378600	272;327	B4DSL2;Q3SXM5	.;HSDL1_HUMAN	C	272;327	ENSP00000407437:S272C;ENSP00000219439:S327C	ENSP00000219439:S327C	S	-	2	0	HSDL1	82715749	0.982000	0.34865	0.993000	0.49108	0.401000	0.30781	4.775000	0.62346	2.808000	0.96608	0.650000	0.86243	TCC	G|0.737;C|0.263	0.263	strong		0.428	HSDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269076.3	NM_031463	
GAS8	2622	hgsc.bcm.edu	37	16	90097748	90097748	+	Silent	SNP	C	C	T	rs2302513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:90097748C>T	ENST00000268699.4	+	3	254	c.132C>T	c.(130-132)cgC>cgT	p.R44R	GAS8_ENST00000536122.1_Silent_p.R19R|GAS8_ENST00000540721.1_3'UTR|C16orf3_ENST00000408886.2_5'Flank	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	44	Regulates microtubule-binding. {ECO:0000250}.				cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		AGCTGGACCGCGAGCGGGAGG	0.642													c|||	1244	0.248403	0.1233	0.2954	5008	,	,		16413	0.627		0.1213	False		,,,				2504	0.1247				p.R44R		Atlas-SNP	.											GAS8,NS,carcinoma,+1,1	GAS8	29	1	0			c.C132T						PASS	.	T		549,3847	242.8+/-252.7	39,471,1688	80.0	73.0	75.0		132	-11.8	0.1	16	dbSNP_100	75	802,7798	187.9+/-235.0	46,710,3544	no	coding-synonymous	GAS8	NM_001481.2		85,1181,5232	TT,TC,CC		9.3256,12.4886,10.3955		44/479	90097748	1351,11645	2198	4300	6498	SO:0001819	synonymous_variant	2622	exon3			GGACCGCGAGCGG	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.132C>T	16.37:g.90097748C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	37	21	0.567568	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Silent	SNP	ENST00000268699.4	37	CCDS10992.1																																																																																			T|0.179;G|0.000;C|0.821	0.179	strong		0.642	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
TMEM259	91304	hgsc.bcm.edu	37	19	1014398	1014398	+	Silent	SNP	A	A	G	rs7146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	177	0	0		WXS	Illumina HiSeq	Phase_I	172	87	0.505814	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	
BAZ2A	11176	hgsc.bcm.edu	37	12	56994170	56994170	+	Silent	SNP	C	C	T	rs1527140	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56994170C>T	ENST00000551812.1	-	24	4906	c.4713G>A	c.(4711-4713)gaG>gaA	p.E1571E	BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000549884.1_Silent_p.E1569E|BAZ2A_ENST00000179765.5_Silent_p.E1539E|BAZ2A_ENST00000379441.3_Silent_p.E1541E	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1571					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						GTGCCAGTCCCTCCCTGCCCC	0.607													T|||	660	0.131789	0.4357	0.0403	5008	,	,		17929	0.0		0.0129	False		,,,				2504	0.044				p.E1571E		Atlas-SNP	.											.	BAZ2A	263	.	0			c.G4713A						PASS	.	T		1302,2840		216,870,985	53.0	59.0	57.0		4713	1.7	1.0	12	dbSNP_88	57	137,8255		2,133,4061	no	coding-synonymous	BAZ2A	NM_013449.3		218,1003,5046	TT,TC,CC		1.6325,31.4341,11.4808		1571/1906	56994170	1439,11095	2071	4196	6267	SO:0001819	synonymous_variant	11176	exon24			CAGTCCCTCCCTG	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.4713G>A	12.37:g.56994170C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Silent	SNP	ENST00000551812.1	37	CCDS44924.1																																																																																			C|0.900;T|0.100	0.100	strong		0.607	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	
ACACB	32	hgsc.bcm.edu	37	12	109637234	109637234	+	Silent	SNP	G	G	T	rs73398054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109637234G>T	ENST00000338432.7	+	18	2774	c.2655G>T	c.(2653-2655)acG>acT	p.T885T	ACACB_ENST00000377854.5_Silent_p.T885T|ACACB_ENST00000377848.3_Silent_p.T885T			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	885					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)	GCAATAAGACGTGTGTGTTTG	0.552													G|||	34	0.00678914	0.0234	0.0043	5008	,	,		18076	0.0		0.0	False		,,,				2504	0.0				p.T885T		Atlas-SNP	.											.	ACACB	330	.	0			c.G2655T						PASS	.						146.0	131.0	136.0					12																	109637234		2203	4300	6503	SO:0001819	synonymous_variant	32	exon17			TAAGACGTGTGTG	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.2655G>T	12.37:g.109637234G>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			A|0.006;G|0.992;T|0.002	0.002	strong		0.552	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
FAM71E2	284418	hgsc.bcm.edu	37	19	55870478	55870478	+	Silent	SNP	C	C	T	rs79366553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	83	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	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	
UTP23	84294	hgsc.bcm.edu	37	8	117783975	117783975	+	Missense_Mutation	SNP	C	C	T	rs16888728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:117783975C>T	ENST00000309822.2	+	3	745	c.644C>T	c.(643-645)cCg>cTg	p.P215L	UTP23_ENST00000357148.3_Intron|UTP23_ENST00000517820.1_Intron|UTP23_ENST00000520733.1_Intron	NM_032334.2	NP_115710.2	Q9BRU9	UTP23_HUMAN	UTP23, small subunit (SSU) processome component, homolog (yeast)	215			P -> L (in dbSNP:rs16888728).		rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	12						AAAAAGGCACCGGACACACAA	0.373													C|||	956	0.190895	0.4614	0.0821	5008	,	,		16387	0.0129		0.1133	False		,,,				2504	0.1656				p.P215L		Atlas-SNP	.											UTP23,NS,carcinoma,0,1	UTP23	38	1	0			c.C644T						PASS	.	C	LEU/PRO	1571,2829		276,1019,905	41.0	45.0	43.0		644	-0.5	0.1	8	dbSNP_123	43	843,7751		46,751,3500	yes	missense	UTP23	NM_032334.2	98	322,1770,4405	TT,TC,CC		9.8092,35.7045,18.5778	benign	215/250	117783975	2414,10580	2200	4297	6497	SO:0001583	missense	84294	exon3			AGGCACCGGACAC		CCDS6320.1	8q24.11	2008-06-12	2008-06-12	2008-06-12		ENSG00000147679			28224	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 53"""	C8orf53		16769905	Standard	NM_032334		Approved	MGC14595	uc003yoc.3	Q9BRU9		ENST00000309822.2:c.644C>T	8.37:g.117783975C>T	ENSP00000308332:p.Pro215Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_032334	B2RE25|Q96NJ8	Missense_Mutation	SNP	ENST00000309822.2	37	CCDS6320.1	335	0.1533882783882784	206	0.4186991869918699	36	0.09944751381215469	9	0.015734265734265736	84	0.11081794195250659	C	8.050	0.765744	0.15983	0.357045	0.098092	ENSG00000147679	ENST00000309822	T	0.24151	1.87	5.96	-0.543	0.11851	.	0.696157	0.14855	N	0.294442	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.47787	-0.9090	9	0.28530	T	0.3	0.0651	7.2669	0.26234	0.5083:0.3659:0.1257:0.0	rs16888728;rs52795925;rs16888728	215	Q9BRU9	UTP23_HUMAN	L	215	ENSP00000308332:P215L	ENSP00000308332:P215L	P	+	2	0	UTP23	117853156	0.998000	0.40836	0.098000	0.21074	0.567000	0.35839	1.576000	0.36504	-0.081000	0.12662	-0.262000	0.10625	CCG	C|0.812;N|0.001;T|0.186	0.186	strong		0.373	UTP23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381173.1	NM_032334	
DNAH8	1769	hgsc.bcm.edu	37	6	38841101	38841101	+	Silent	SNP	G	G	A	rs9380795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:38841101G>A	ENST00000359357.3	+	50	7172	c.6918G>A	c.(6916-6918)aaG>aaA	p.K2306K	DNAH8_ENST00000441566.1_Silent_p.K2270K|DNAH8_ENST00000449981.2_Silent_p.K2523K			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2306	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|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						CATATATGAAGCTAAATCTCA	0.358													A|||	2671	0.533347	0.3601	0.6138	5008	,	,		20435	0.8333		0.3767	False		,,,				2504	0.5624				p.K2523K		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G7569A						PASS	.	A		1583,2823	667.0+/-401.8	296,991,916	105.0	94.0	98.0		7569	1.9	1.0	6	dbSNP_119	98	3682,4918	622.1+/-397.3	790,2102,1408	no	coding-synonymous	DNAH8	NM_001206927.1		1086,3093,2324	AA,AG,GG		42.814,35.9283,40.4813		2523/4708	38841101	5265,7741	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon52			TATGAAGCTAAAT	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.6918G>A	6.37:g.38841101G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				G|0.558;A|0.442	0.442	strong		0.358	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
MOAP1	64112	hgsc.bcm.edu	37	14	93652734	93652734	+	5'Flank	SNP	C	C	T	rs61744704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:93652734C>T	ENST00000556883.1	-	0	0				RP11-371E8.4_ENST00000557048.1_Intron|MOAP1_ENST00000298894.4_5'Flank|TMEM251_ENST00000283534.4_Silent_p.A38A|TMEM251_ENST00000415050.2_Silent_p.A76A|RP11-371E8.4_ENST00000557574.1_Silent_p.A38A			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1						apoptotic signaling pathway (GO:0097190)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	13		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		ACAGGCTGGCCTTGGAACACA	0.478													C|||	20	0.00399361	0.0151	0.0	5008	,	,		18903	0.0		0.0	False		,,,				2504	0.0				p.A76A		Atlas-SNP	.											.	.	.	.	0			c.C228T						PASS	.	C	,	42,3868		0,42,1913	165.0	163.0	164.0		228,114	-0.2	1.0	14	dbSNP_129	164	0,8292		0,0,4146	no	coding-synonymous,coding-synonymous	C14orf109	NM_001098621.1,NM_015676.1	,	0,42,6059	TT,TC,CC		0.0,1.0742,0.3442	,	76/170,38/132	93652734	42,12160	1955	4146	6101	SO:0001631	upstream_gene_variant	26175	exon2			GCTGGCCTTGGAA	BC015044	CCDS9908.1	14q32.12	2012-02-09			ENSG00000165943	ENSG00000165943		"""Paraneoplastic Ma antigens"""	16658	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 4"""	609485				11060313	Standard	NM_022151		Approved	MAP-1, PNMA4	uc001ybj.3	Q96BY2	OTTHUMG00000169184		14.37:g.93652734C>T	Exception_encountered	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	263	133	0.505703	NM_001098621	B2RDF6|Q9H833|Q9HAS1	Silent	SNP	ENST00000556883.1	37	CCDS9908.1																																																																																			C|0.997;T|0.003	0.003	strong		0.478	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1		
F2RL2	2151	hgsc.bcm.edu	37	5	75913784	75913784	+	Missense_Mutation	SNP	T	T	C	rs2069683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:75913784T>C	ENST00000296641.4	-	2	951	c.748A>G	c.(748-750)Aac>Gac	p.N250D	IQGAP2_ENST00000379730.3_Intron|F2RL2_ENST00000504899.1_Missense_Mutation_p.N228D|IQGAP2_ENST00000396234.3_Intron|IQGAP2_ENST00000274364.6_Intron|IQGAP2_ENST00000502745.1_Intron	NM_004101.3	NP_004092.1	O00254	PAR3_HUMAN	coagulation factor II (thrombin) receptor-like 2	250			N -> D (in dbSNP:rs2069683). {ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|metabolic process (GO:0008152)|platelet activation (GO:0030168)|response to wounding (GO:0009611)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|thrombin receptor activity (GO:0015057)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3)	32		all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)		TCGCAAGTGTTGTGAACATCA	0.413													T|||	229	0.0457268	0.0832	0.0317	5008	,	,		21688	0.0813		0.0129	False		,,,				2504	0.002				p.N250D		Atlas-SNP	.											.	F2RL2	57	.	0			c.A748G						PASS	.	T	ASP/ASN,	328,4078	175.1+/-204.6	4,320,1879	76.0	74.0	74.0		748,	2.7	0.1	5	dbSNP_96	74	63,8537	37.8+/-93.5	1,61,4238	yes	missense,intron	F2RL2,IQGAP2	NM_004101.2,NM_006633.2	23,	5,381,6117	CC,CT,TT		0.7326,7.4444,3.0063	benign,	250/375,	75913784	391,12615	2203	4300	6503	SO:0001583	missense	2151	exon2			AAGTGTTGTGAAC	U92971	CCDS4031.1, CCDS58959.1	5q13	2012-08-08			ENSG00000164220	ENSG00000164220		"""GPCR / Class A : Protease activated receptors"""	3539	protein-coding gene	gene with protein product	"""proteinase-activated receptor-3"""	601919				9087410, 9722561	Standard	NM_004101		Approved	PAR3	uc003kem.4	O00254	OTTHUMG00000102119	ENST00000296641.4:c.748A>G	5.37:g.75913784T>C	ENSP00000296641:p.Asn250Asp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_004101	B2R754|B4DQ13|Q52M68|Q7Z3W3	Missense_Mutation	SNP	ENST00000296641.4	37	CCDS4031.1	125	0.05723443223443223	50	0.1016260162601626	7	0.019337016574585635	58	0.10139860139860139	10	0.013192612137203167	T	0.012	-1.648326	0.00785	0.074444	0.007326	ENSG00000164220	ENST00000296641;ENST00000504899	T;T	0.36878	1.23;1.23	5.09	2.7	0.31948	GPCR, rhodopsin-like superfamily (1);	0.483463	0.24748	N	0.035936	T	0.00412	0.0013	N	0.11673	0.155	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.25572	-1.0128	9	0.06236	T	0.91	-7.4832	9.4239	0.38567	0.0:0.2243:0.0:0.7757	rs2069683;rs17748489;rs52831711;rs58834474;rs2069683	250	O00254	PAR3_HUMAN	D	250;228	ENSP00000296641:N250D;ENSP00000426703:N228D	ENSP00000296641:N250D	N	-	1	0	F2RL2	75949540	0.996000	0.38824	0.078000	0.20375	0.415000	0.31203	2.448000	0.44926	0.003000	0.14656	-1.450000	0.01041	AAC	T|0.957;C|0.043	0.043	strong		0.413	F2RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219958.3		
ERP27	121506	hgsc.bcm.edu	37	12	15070169	15070169	+	Silent	SNP	T	T	A	rs35203261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15070169T>A	ENST00000266397.2	-	5	1092	c.519A>T	c.(517-519)ccA>ccT	p.P173P	ERP27_ENST00000540097.1_Silent_p.P72P|ERP27_ENST00000544881.1_5'UTR	NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	173						endoplasmic reticulum (GO:0005783)				breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						CTTCATACTCTGGGGAGGCCT	0.458													T|||	123	0.0245607	0.09	0.0043	5008	,	,		20881	0.0		0.0	False		,,,				2504	0.001				p.P173P		Atlas-SNP	.											.	ERP27	37	.	0			c.A519T						PASS	.	T		319,4087	170.5+/-200.9	8,303,1892	216.0	184.0	195.0		519	0.8	1.0	12	dbSNP_126	195	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ERP27	NM_152321.2		8,307,6188	AA,AT,TT		0.0465,7.2401,2.4835		173/274	15070169	323,12683	2203	4300	6503	SO:0001819	synonymous_variant	121506	exon5			ATACTCTGGGGAG	AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055		"""Protein disulfide isomerases"""	26495	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 8"""	610642	"""chromosome 12 open reading frame 46"", ""endoplasmic reticulum protein 27 kDa"""	C12orf46		12975309, 16940051	Standard	XM_005253303		Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000266397.2:c.519A>T	12.37:g.15070169T>A		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	229	102	0.445415	NM_152321		Silent	SNP	ENST00000266397.2	37	CCDS8670.1																																																																																			T|0.980;A|0.020	0.020	strong		0.458	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321	
C15orf39	56905	hgsc.bcm.edu	37	15	75499995	75499995	+	Missense_Mutation	SNP	T	T	G	rs28509789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75499995T>G	ENST00000360639.2	+	2	1926	c.1606T>G	c.(1606-1608)Tca>Gca	p.S536A	C15orf39_ENST00000567617.1_Missense_Mutation_p.S536A|C15orf39_ENST00000394987.4_Missense_Mutation_p.S536A			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	536			S -> A (in dbSNP:rs28509789). {ECO:0000269|PubMed:15498874}.			cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						TGAGCCTGACTCAGCCCCAGC	0.617													T|||	1965	0.392372	0.4697	0.4078	5008	,	,		18530	0.3264		0.2773	False		,,,				2504	0.4632				p.S536A		Atlas-SNP	.											C15orf39,bladder,carcinoma,-1,1	C15orf39	64	1	0			c.T1606G						PASS	.	T	ALA/SER	1955,2437		448,1059,689	25.0	26.0	26.0		1606	-3.5	0.0	15	dbSNP_125	26	2337,6247		327,1683,2282	yes	missense	C15orf39	NM_015492.4	99	775,2742,2971	GG,GT,TT		27.2251,44.5128,33.0764	benign	536/1048	75499995	4292,8684	2196	4292	6488	SO:0001583	missense	56905	exon2			CCTGACTCAGCCC	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 38~Name Same As HGNC:28782"""				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.1606T>G	15.37:g.75499995T>G	ENSP00000353854:p.Ser536Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	37	CCDS10276.1	749	0.34294871794871795	224	0.45528455284552843	141	0.38950276243093923	189	0.3304195804195804	195	0.25725593667546176	T	3.832	-0.035507	0.07497	0.445128	0.272251	ENSG00000167173	ENST00000360639;ENST00000394987	T;T	0.80393	-1.37;-1.37	4.84	-3.54	0.04653	.	1.653880	0.03470	N	0.213444	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.31888	-0.9927	9	0.08381	T	0.77	.	0.2702	0.00230	0.2813:0.1842:0.2851:0.2495	rs28509789	536	Q6ZRI6	CO039_HUMAN	A	536	ENSP00000353854:S536A;ENSP00000378438:S536A	ENSP00000353854:S536A	S	+	1	0	C15orf39	73287048	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.873000	0.04214	-0.640000	0.05495	0.460000	0.39030	TCA	T|0.662;G|0.338	0.338	strong		0.617	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492	
CEACAM8	1088	hgsc.bcm.edu	37	19	43093793	43093793	+	Silent	SNP	G	G	A	rs10418988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43093793G>A	ENST00000244336.5	-	3	620	c.519C>T	c.(517-519)aaC>aaT	p.N173N	CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000594624.2_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	173	Ig-like C2-type 1.				immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				GGTAGGTTGTGTTCTGAGTCT	0.567													G|||	102	0.0203674	0.0719	0.0072	5008	,	,		17179	0.0		0.002	False		,,,				2504	0.0				p.N173N		Atlas-SNP	.											.	CEACAM8	44	.	0			c.C519T						PASS	.	G		240,4166	141.5+/-176.9	6,228,1969	220.0	192.0	201.0		519	1.4	0.5	19	dbSNP_119	201	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	CEACAM8	NM_001816.3		6,239,6258	AA,AG,GG		0.1279,5.4471,1.9299		173/350	43093793	251,12755	2203	4300	6503	SO:0001819	synonymous_variant	1088	exon3			GGTTGTGTTCTGA	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.519C>T	19.37:g.43093793G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	231	104	0.450216	NM_001816	O60399|Q16574	Silent	SNP	ENST00000244336.5	37	CCDS12610.1																																																																																			G|0.977;A|0.023	0.023	strong		0.567	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
AP4E1	23431	hgsc.bcm.edu	37	15	51294832	51294832	+	Silent	SNP	G	G	A	rs3825798	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51294832G>A	ENST00000261842.5	+	21	3493	c.3387G>A	c.(3385-3387)caG>caA	p.Q1129Q	AP4E1_ENST00000561397.1_3'UTR|AP4E1_ENST00000560508.1_Silent_p.Q1054Q	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	1129					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		TACTGTATCAGTGTCAAAAGG	0.408													G|||	1022	0.204073	0.0673	0.1974	5008	,	,		19045	0.4653		0.2197	False		,,,				2504	0.1084				p.Q1129Q		Atlas-SNP	.											AP4E1,NS,carcinoma,0,1	AP4E1	78	1	0			c.G3387A						PASS	.	G		472,3920	223.0+/-239.6	35,402,1759	205.0	162.0	176.0		3387	3.6	1.0	15	dbSNP_107	176	1989,6597	349.5+/-327.4	218,1553,2522	no	coding-synonymous	AP4E1	NM_007347.3		253,1955,4281	AA,AG,GG		23.1656,10.7468,18.9629		1129/1138	51294832	2461,10517	2196	4293	6489	SO:0001819	synonymous_variant	23431	exon21			GTATCAGTGTCAA	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.3387G>A	15.37:g.51294832G>A		Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	226	115	0.50885	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Silent	SNP	ENST00000261842.5	37	CCDS32240.1																																																																																			G|0.794;A|0.206	0.206	strong		0.408	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
FKTN	2218	hgsc.bcm.edu	37	9	108366499	108366499	+	Missense_Mutation	SNP	G	G	A	rs34006675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:108366499G>A	ENST00000223528.2	+	5	497	c.373G>A	c.(373-375)Ggc>Agc	p.G125S	FKTN_ENST00000357998.5_Missense_Mutation_p.G125S|FKTN_ENST00000602661.1_Missense_Mutation_p.G125S|FKTN_ENST00000448551.2_Missense_Mutation_p.G125S|FKTN_ENST00000540160.1_Missense_Mutation_p.G125S	NM_006731.2	NP_006722.2	O75072	FKTN_HUMAN	fukutin	125			G -> S (in a patient diagnosed with Walker-Warburg syndrome; dbSNP:rs34006675). {ECO:0000269|PubMed:18177472}.		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						GTTCTAGGAAGGCTGGTTTCG	0.373													G|||	186	0.0371406	0.1263	0.013	5008	,	,		19669	0.0		0.008	False		,,,				2504	0.002				p.G125S		Atlas-SNP	.											.	FKTN	47	.	0			c.G373A	GRCh37	CM080364	FKTN	M	rs34006675	PASS	.	G	SER/GLY,SER/GLY,SER/GLY	382,4024	194.0+/-219.0	22,338,1843	84.0	86.0	86.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	373,373,373	1.7	1.0	9	dbSNP_126	86	98,8502	54.0+/-114.7	1,96,4203	yes	missense,missense,missense	FKTN	NM_001079802.1,NM_001198963.1,NM_006731.2	56,56,56	23,434,6046	AA,AG,GG		1.1395,8.67,3.6906	benign,benign,benign	125/462,125/431,125/462	108366499	480,12526	2203	4300	6503	SO:0001583	missense	2218	exon5			TAGGAAGGCTGGT		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.373G>A	9.37:g.108366499G>A	ENSP00000223528:p.Gly125Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_006731	B4DUX9|J3KP13|Q3MIJ1|Q96TE1|Q9P295	Missense_Mutation	SNP	ENST00000223528.2	37	CCDS6766.1	77	0.035256410256410256	65	0.13211382113821138	7	0.019337016574585635	0	0.0	5	0.006596306068601583	G	17.19	3.325170	0.60634	0.0867	0.011395	ENSG00000106692	ENST00000223528;ENST00000448551;ENST00000540160;ENST00000357998;ENST00000374705	D;D;T;D;T	0.89939	-2.26;-2.59;-1.42;-2.59;-1.45	5.07	1.71	0.24356	.	0.628558	0.17157	N	0.184851	T	0.05181	0.0138	L	0.41236	1.265	0.32344	N	0.559308	P;B;B	0.51351	0.944;0.085;0.047	P;B;B	0.48270	0.572;0.023;0.023	T	0.52830	-0.8523	10	0.19147	T	0.46	-9.476	9.4051	0.38457	0.334:0.0:0.666:0.0	rs34006675	125;125;125	B4E2W4;B4DUX9;O75072	.;.;FKTN_HUMAN	S	125;125;125;125;102	ENSP00000223528:G125S;ENSP00000399140:G125S;ENSP00000439423:G125S;ENSP00000350687:G125S;ENSP00000363837:G102S	ENSP00000223528:G125S	G	+	1	0	FKTN	107406320	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	2.142000	0.42177	0.526000	0.28541	0.563000	0.77884	GGC	G|0.968;A|0.032	0.032	strong		0.373	FKTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053505.1	NM_006731	
NWD2	57495	hgsc.bcm.edu	37	4	37435524	37435524	+	Silent	SNP	C	C	T	rs17604216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:37435524C>T	ENST00000309447.5	+	5	1436	c.588C>T	c.(586-588)aaC>aaT	p.N196N		NM_001144990.1	NP_001138462.1	Q9ULI1	NWD2_HUMAN		196										breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(2)|skin(2)	16						ATGCTGAAAACGAGAAGACAT	0.338													C|||	506	0.101038	0.2201	0.1095	5008	,	,		18055	0.1032		0.0179	False		,,,				2504	0.0174				p.N196N		Atlas-SNP	.											.	KIAA1239	79	.	0			c.C588T						PASS	.	C		287,1097		35,217,440	96.0	87.0	89.0		588	-1.9	1.0	4	dbSNP_123	89	74,3108		0,74,1517	no	coding-synonymous	KIAA1239	NM_001144990.1		35,291,1957	TT,TC,CC		2.3256,20.737,7.9063		196/1743	37435524	361,4205	692	1591	2283	SO:0001819	synonymous_variant	57495	exon5			TGAAAACGAGAAG																												ENST00000309447.5:c.588C>T	4.37:g.37435524C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	212	112	0.528302	NM_001144990	A8MRU1	Silent	SNP	ENST00000309447.5	37	CCDS47040.1																																																																																			C|0.902;T|0.098	0.098	strong		0.338	KIAA1239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347551.2		
FANCM	57697	hgsc.bcm.edu	37	14	45644589	45644589	+	Missense_Mutation	SNP	G	G	T	rs1367580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45644589G>T	ENST00000267430.5	+	14	2717	c.2632G>T	c.(2632-2634)Gta>Tta	p.V878L	FANCM_ENST00000542564.2_Missense_Mutation_p.V852L	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	878			V -> L (in dbSNP:rs1367580). {ECO:0000269|PubMed:10997877}.		DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TATAGATTCTGTAGATAATGA	0.279								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				T|||	1163	0.232228	0.4478	0.1729	5008	,	,		17096	0.128		0.1282	False		,,,				2504	0.1973				p.V878L		Atlas-SNP	.											.	FANCM	225	.	0			c.G2632T						PASS	.	T	LEU/VAL	1460,2928		243,974,977	45.0	52.0	50.0		2632	4.1	0.0	14	dbSNP_88	50	1020,7556		62,896,3330	yes	missense	FANCM	NM_020937.2	32	305,1870,4307	TT,TG,GG		11.8937,33.2726,19.1299	benign	878/2049	45644589	2480,10484	2194	4288	6482	SO:0001583	missense	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GATTCTGTAGATA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.2632G>T	14.37:g.45644589G>T	ENSP00000267430:p.Val878Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	36	22	0.611111	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	469	0.21474358974358973	228	0.4634146341463415	57	0.1574585635359116	75	0.13111888111888112	109	0.1437994722955145	T	0	-2.589270	0.00128	0.332726	0.118937	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.16324	2.94;2.93;2.35	5.24	4.08	0.47627	.	1.095180	0.06954	N	0.815069	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	0.48536	-0.9027	9	0.02654	T	1	.	6.7797	0.23638	0.0:0.0815:0.1533:0.7651	rs1367580;rs3759676;rs52832869;rs61645397;rs1367580	852;878	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	L	878;852;394	ENSP00000267430:V878L;ENSP00000442493:V852L;ENSP00000452033:V394L	ENSP00000267430:V878L	V	+	1	0	FANCM	44714339	0.653000	0.27358	0.003000	0.11579	0.027000	0.11550	0.856000	0.27818	0.383000	0.24910	-0.335000	0.08231	GTA	G|0.796;T|0.204	0.204	strong		0.279	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
EML2	24139	hgsc.bcm.edu	37	19	46142624	46142624	+	Missense_Mutation	SNP	A	A	C	rs201822741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46142624A>C	ENST00000245925.3	-	1	61	c.11T>G	c.(10-12)tTt>tGt	p.F4C	EML2_ENST00000589876.1_Missense_Mutation_p.F4C|AC006132.1_ENST00000593161.1_5'Flank|MIR330_ENST00000362196.1_RNA|EML2_ENST00000587152.1_Intron|EML2_ENST00000536630.1_Intron	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	4					negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CCCAGCTCCAAAGCTACTCAT	0.726													A|||	48	0.00958466	0.0325	0.0072	5008	,	,		12182	0.0		0.0	False		,,,				2504	0.0				p.F4C		Atlas-SNP	.											.	EML2	64	.	0			c.T11G						PASS	.		,,CYS/PHE	90,4006		0,90,1958	15.0	17.0	16.0		,,11	4.6	1.0	19	dbSNP_134	16	1,8033		0,1,4016	yes	intron,intron,missense	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	,,205	0,91,5974	CC,CA,AA		0.0124,2.1973,0.7502	,,	,,4/650	46142624	91,12039	2048	4017	6065	SO:0001583	missense	24139	exon1			GCTCCAAAGCTAC	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.11T>G	19.37:g.46142624A>C	ENSP00000245925:p.Phe4Cys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_012155	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	13	0.005952380952380952	8	0.016260162601626018	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	A	14.61	2.585437	0.46110	0.021973	1.24E-4	ENSG00000125746	ENST00000245925	T	0.26067	1.76	4.58	4.58	0.56647	.	1.865290	0.03249	U	0.181627	T	0.26666	0.0652	L	0.29908	0.895	0.80722	D	1	D;B	0.76494	0.999;0.118	D;B	0.74674	0.984;0.053	T	0.03034	-1.1080	10	0.59425	D	0.04	44.314	10.2951	0.43618	1.0:0.0:0.0:0.0	.	4;4	B7Z918;O95834	.;EMAL2_HUMAN	C	4	ENSP00000245925:F4C	ENSP00000245925:F4C	F	-	2	0	EML2	50834464	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.633000	0.54295	1.932000	0.55993	0.454000	0.30748	TTT	A|0.994;C|0.006	0.006	strong		0.726	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
MRPS10	55173	hgsc.bcm.edu	37	6	42185564	42185564	+	Silent	SNP	A	A	C	rs9471809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42185564A>C	ENST00000053468.3	-	1	39	c.24T>G	c.(22-24)ggT>ggG	p.G8G		NM_018141.3	NP_060611.2	P82664	RT10_HUMAN	mitochondrial ribosomal protein S10	8						mitochondrion (GO:0005739)|ribosome (GO:0005840)				endometrium(1)|lung(1)	2	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00528)			GGCACACAGCACCGAACGCTG	0.607													C|||	1485	0.296526	0.6906	0.2579	5008	,	,		14949	0.1141		0.2038	False		,,,				2504	0.0746				p.G8G		Atlas-SNP	.											.	MRPS10	9	.	0			c.T24G						PASS	.	C		2567,1839		765,1037,401	24.0	28.0	27.0		24	-10.5	0.0	6	dbSNP_119	27	1825,6775		202,1421,2677	no	coding-synonymous	MRPS10	NM_018141.3		967,2458,3078	CC,CA,AA		21.2209,41.7385,33.769		8/202	42185564	4392,8614	2203	4300	6503	SO:0001819	synonymous_variant	55173	exon1			CACAGCACCGAAC		CCDS4866.1	6p21.1	2012-09-13			ENSG00000048544	ENSG00000048544		"""Mitochondrial ribosomal proteins / small subunits"""	14502	protein-coding gene	gene with protein product		611976				11279123	Standard	NM_018141		Approved	FLJ10567	uc003osa.4	P82664	OTTHUMG00000014694	ENST00000053468.3:c.24T>G	6.37:g.42185564A>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_018141	B2RE89|Q9H3E5|Q9NVR3	Silent	SNP	ENST00000053468.3	37	CCDS4866.1																																																																																			A|0.679;C|0.321	0.321	strong		0.607	MRPS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040547.1		
LNP1	348801	hgsc.bcm.edu	37	3	100174722	100174722	+	Silent	SNP	G	G	A	rs1132022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	366	1	0.00273224		WXS	Illumina HiSeq	Phase_I	431	222	0.515081	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		
ZNF778	197320	hgsc.bcm.edu	37	16	89294595	89294595	+	Silent	SNP	C	C	T	rs74466939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89294595C>T	ENST00000433976.2	+	6	2147	c.1815C>T	c.(1813-1815)atC>atT	p.I605I	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Silent_p.I563I	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	605					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)		CACACCTTATCGTGCACATAA	0.473													C|||	813	0.16234	0.1248	0.2651	5008	,	,		22985	0.1746		0.0815	False		,,,				2504	0.2106				p.I633I		Atlas-SNP	.											.	ZNF778	67	.	0			c.C1899T						PASS	.	C	,	557,3831	227.8+/-242.9	39,479,1676	92.0	96.0	95.0		1899,1815	-1.7	0.0	16	dbSNP_131	95	860,7738	190.1+/-236.7	45,770,3484	no	coding-synonymous,coding-synonymous	ZNF778	NM_001201407.1,NM_182531.3	,	84,1249,5160	TT,TC,CC		10.0023,12.6937,10.9118	,	633/758,605/730	89294595	1417,11569	2194	4299	6493	SO:0001819	synonymous_variant	197320	exon7			CCTTATCGTGCAC	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.1815C>T	16.37:g.89294595C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	89	33	0.370787	NM_001201407	Q08AG0	Silent	SNP	ENST00000433976.2	37	CCDS45550.1																																																																																			C|0.863;T|0.137	0.137	strong		0.473	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531	
RESP18	389075	hgsc.bcm.edu	37	2	220197321	220197321	+	Missense_Mutation	SNP	C	C	T	rs2385405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220197321C>T	ENST00000333527.5	-	2	156	c.157G>A	c.(157-159)Gag>Aag	p.E53K	RESP18_ENST00000392083.1_5'UTR	NM_001007089.3	NP_001007090.3	Q5W5W9	RES18_HUMAN	regulated endocrine-specific protein 18	11					in utero embryonic development (GO:0001701)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|rough endoplasmic reticulum lumen (GO:0048237)|secretory granule (GO:0030141)				endometrium(1)|prostate(1)	2						TGGAGCCCCTCGGAGCTCCCA	0.692													C|||	2321	0.463458	0.91	0.3285	5008	,	,		13722	0.1845		0.2763	False		,,,				2504	0.4356				p.E53K		Atlas-SNP	.											.	RESP18	13	.	0			c.G157A						PASS	.	C	LYS/GLU	1095,289		445,205,42	13.0	20.0	18.0		157	-3.8	0.0	2	dbSNP_100	18	867,2297		126,615,841	yes	missense	RESP18	NM_001007089.3	56	571,820,883	TT,TC,CC		27.402,20.8815,43.1398	benign	53/229	220197321	1962,2586	692	1582	2274	SO:0001583	missense	389075	exon2			GCCCCTCGGAGCT	AF437883	CCDS33382.2	2q35	2012-12-07	2012-12-07		ENSG00000182698	ENSG00000182698			33762	protein-coding gene	gene with protein product		612721	"""regulated endocrine-specific protein 18 homolog (rat)"""			17951542, 7988462	Standard	NM_001007089		Approved		uc002vlc.4	Q5W5W9	OTTHUMG00000150223	ENST00000333527.5:c.157G>A	2.37:g.220197321C>T	ENSP00000330269:p.Glu53Lys	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_001007089	A8MQ49|Q38I23|Q5W5X0	Missense_Mutation	SNP	ENST00000333527.5	37	CCDS33382.2	874	0.4001831501831502	436	0.8861788617886179	147	0.40607734806629836	101	0.17657342657342656	190	0.25065963060686014	C	4.800	0.148690	0.09134	0.791185	0.27402	ENSG00000182698	ENST00000333527	.	.	.	4.22	-3.82	0.04281	.	0.925255	0.08882	N	0.879916	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	0.35025	-0.9805	8	0.15499	T	0.54	.	0.239	0.00190	0.2494:0.2112:0.2723:0.2672	rs2385405;rs2385405	53	Q5W5W9-2	.	K	53	.	ENSP00000330269:E53K	E	-	1	0	RESP18	219905565	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.038000	0.13862	-0.596000	0.05821	-2.788000	0.00116	GAG	C|0.555;T|0.445	0.445	strong		0.692	RESP18-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316885.1	NM_001007089	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72518009	72518009	+	Missense_Mutation	SNP	A	A	G	rs4747096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72518009A>G	ENST00000373207.1	+	21	3146	c.3146A>G	c.(3145-3147)gAa>gGa	p.E1049G	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.E1052G	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1049			E -> G (in dbSNP:rs4747096).		collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CCACAATCTGAACCCCTACAT	0.537													G|||	1092	0.218051	0.1694	0.2305	5008	,	,		21129	0.37		0.1849	False		,,,				2504	0.1524				p.E1052G		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.A3155G						PASS	.	G	GLY/GLU,GLY/GLU	830,3576	746.6+/-411.8	76,678,1449	118.0	103.0	108.0		3146,3155	3.0	0.0	10	dbSNP_111	108	1387,7213	753.3+/-407.4	114,1159,3027	yes	missense,missense	ADAMTS14	NM_080722.3,NM_139155.2	98,98	190,1837,4476	GG,GA,AA		16.1279,18.8379,17.046	benign,benign	1049/1224,1052/1227	72518009	2217,10789	2203	4300	6503	SO:0001583	missense	140766	exon21			AATCTGAACCCCT	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.3146A>G	10.37:g.72518009A>G	ENSP00000362303:p.Glu1049Gly	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	512	0.23443223443223443	85	0.17276422764227642	71	0.19613259668508287	213	0.3723776223776224	143	0.18865435356200527	G	3.106	-0.183744	0.06340	0.188379	0.161279	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.61742	0.08;0.11	3.88	2.98	0.34508	.	0.684465	0.13976	N	0.349826	T	0.00012	0.0000	N	0.01219	-0.95	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41822	-0.9487	9	0.20519	T	0.43	.	4.9891	0.14205	0.1808:0.0:0.6537:0.1655	rs4747096;rs52814326;rs59944244;rs4747096	1049;1052	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	G	1052;1049	ENSP00000362304:E1052G;ENSP00000362303:E1049G	ENSP00000362303:E1049G	E	+	2	0	ADAMTS14	72188015	0.609000	0.26975	0.001000	0.08648	0.084000	0.17831	1.663000	0.37429	0.334000	0.23590	-0.974000	0.02594	GAA	A|0.804;G|0.196;N|0.001	0.196	strong		0.537	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
CLSPN	63967	hgsc.bcm.edu	37	1	36225948	36225948	+	Missense_Mutation	SNP	T	T	C	rs7537203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	153	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	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	
B3GNT4	79369	hgsc.bcm.edu	37	12	122689181	122689181	+	Missense_Mutation	SNP	C	C	G	rs7136356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122689181C>G	ENST00000324189.4	+	2	372	c.16C>G	c.(16-18)Cct>Gct	p.P6A	B3GNT4_ENST00000546192.1_Intron|B3GNT4_ENST00000545141.1_Intron|B3GNT4_ENST00000535274.1_5'UTR	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	6			P -> A (in dbSNP:rs7136356). {ECO:0000269|PubMed:15489334}.		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)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		TCCTCCCCAGCCTTCCGCAGC	0.662													C|||	2278	0.454872	0.5023	0.2752	5008	,	,		11614	0.6706		0.2684	False		,,,				2504	0.4877				p.P6A		Atlas-SNP	.											.	B3GNT4	35	.	0			c.C16G						PASS	.	C	ALA/PRO	2024,2380	553.3+/-378.7	455,1114,633	43.0	43.0	43.0		16	0.3	0.0	12	dbSNP_116	43	2591,6009	406.7+/-348.9	387,1817,2096	yes	missense	B3GNT4	NM_030765.2	27	842,2931,2729	GG,GC,CC		30.1279,45.9582,35.4891	benign	6/379	122689181	4615,8389	2202	4300	6502	SO:0001583	missense	79369	exon2			CCCCAGCCTTCCG	AB049586	CCDS9227.1	12q24	2013-02-19						"""Beta 3-glycosyltransferases"""	15683	protein-coding gene	gene with protein product		605864				11042166	Standard	NM_030765		Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000324189.4:c.16C>G	12.37:g.122689181C>G	ENSP00000319636:p.Pro6Ala	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Missense_Mutation	SNP	ENST00000324189.4	37	CCDS9227.1	982	0.44963369963369965	235	0.47764227642276424	110	0.30386740331491713	412	0.7202797202797203	225	0.29683377308707126	C	5.415	0.261747	0.10239	0.459582	0.301279	ENSG00000176383	ENST00000324189	T	0.30981	1.51	1.27	0.349	0.16032	.	4.240170	0.01356	N	0.012079	T	0.00012	0.0000	N	0.14661	0.345	0.50813	P	1.0799999999999699E-4	B	0.09022	0.002	B	0.04013	0.001	T	0.44574	-0.9319	9	0.33141	T	0.24	.	3.4869	0.07624	0.0:0.729:0.0:0.271	rs7136356;rs17855557;rs60259781	6	Q9C0J1	B3GN4_HUMAN	A	6	ENSP00000319636:P6A	ENSP00000319636:P6A	P	+	1	0	B3GNT4	121255134	0.000000	0.05858	0.001000	0.08648	0.444000	0.32077	-0.098000	0.11024	0.106000	0.17784	0.313000	0.20887	CCT	C|0.628;G|0.372	0.372	strong		0.662	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765	
DSE	29940	hgsc.bcm.edu	37	6	116720466	116720466	+	Missense_Mutation	SNP	G	G	T	rs76186865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116720466G>T	ENST00000331677.3	+	3	497	c.53G>T	c.(52-54)tGc>tTc	p.C18F	DSE_ENST00000540275.1_3'UTR|DSE_ENST00000537543.1_Missense_Mutation_p.C37F|DSE_ENST00000359564.2_Missense_Mutation_p.C18F|DSE_ENST00000452085.3_Missense_Mutation_p.C18F			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	18					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)		TATTTGCTTTGCTTTGTGTCA	0.498													G|||	175	0.0349441	0.1263	0.0058	5008	,	,		17864	0.0		0.004	False		,,,				2504	0.0				p.C18F		Atlas-SNP	.											.	DSE	98	.	0			c.G53T						PASS	.	G	PHE/CYS,PHE/CYS	409,3997	201.1+/-224.2	28,353,1822	78.0	72.0	74.0		53,53	4.8	0.1	6	dbSNP_131	74	23,8577	16.0+/-53.3	1,21,4278	yes	missense,missense	DSE	NM_001080976.1,NM_013352.2	205,205	29,374,6100	TT,TG,GG		0.2674,9.2828,3.3215	benign,benign	18/959,18/959	116720466	432,12574	2203	4300	6503	SO:0001583	missense	29940	exon2			TGCTTTGCTTTGT	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.53G>T	6.37:g.116720466G>T	ENSP00000332151:p.Cys18Phe	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	70	0.03205128205128205	67	0.13617886178861788	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	7.264	0.605736	0.14002	0.092828	0.002674	ENSG00000111817	ENST00000430252;ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96	5.65	4.76	0.60689	.	0.151973	0.64402	D	0.000006	T	0.10766	0.0263	L	0.36672	1.1	0.44373	D	0.997279	B;B	0.18968	0.032;0.013	B;B	0.18561	0.022;0.009	T	0.02424	-1.1161	10	0.62326	D	0.03	-6.9295	15.1889	0.73028	0.0684:0.0:0.9316:0.0	.	37;18	B7Z765;Q9UL01	.;DSE_HUMAN	F	18;18;37;18;18	ENSP00000397597:C18F;ENSP00000404049:C18F;ENSP00000441152:C37F;ENSP00000332151:C18F;ENSP00000352567:C18F	ENSP00000332151:C18F	C	+	2	0	DSE	116827159	1.000000	0.71417	0.104000	0.21259	0.051000	0.14879	5.884000	0.69729	2.941000	0.99782	0.655000	0.94253	TGC	G|0.970;T|0.030	0.030	strong		0.498	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
CNGA4	1262	hgsc.bcm.edu	37	11	6262945	6262945	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6262945T>C	ENST00000379936.2	+	5	1317	c.1202T>C	c.(1201-1203)aTc>aCc	p.I401T	CNGA4_ENST00000533426.1_Missense_Mutation_p.I170T	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	401					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 cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GATGATGGTATCACACAGTAT	0.502																																					p.I401T		Atlas-SNP	.											CNGA4,arm,malignant_melanoma,-1,1	CNGA4	96	1	0			c.T1202C						scavenged	.						262.0	223.0	236.0					11																	6262945		2201	4296	6497	SO:0001583	missense	1262	exon5			ATGGTATCACACA	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2152	protein-coding gene	gene with protein product		609472	"""cyclic nucleotide gated channel beta 2"""	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.1202T>C	11.37:g.6262945T>C	ENSP00000369268:p.Ile401Thr	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	176	2	0.0113636	NM_001037329		Missense_Mutation	SNP	ENST00000379936.2	37	CCDS31408.1	.	.	.	.	.	.	.	.	.	.	T	15.21	2.764941	0.49574	.	.	ENSG00000132259	ENST00000533426;ENST00000379936	D;D	0.96522	-4.04;-4.04	5.0	5.0	0.66597	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.264148	0.36303	N	0.002667	D	0.89164	0.6637	N	0.04320	-0.23	0.42043	D	0.991081	B;B;B	0.15141	0.012;0.001;0.006	B;B;B	0.20577	0.03;0.012;0.009	D	0.85541	0.1215	10	0.14656	T	0.56	.	13.6811	0.62487	0.0:0.0:0.0:1.0	.	170;401;361	B4DYQ8;Q8IV77;Q8IV77-2	.;CNGA4_HUMAN;.	T	170;401	ENSP00000433399:I170T;ENSP00000369268:I401T	ENSP00000369268:I401T	I	+	2	0	CNGA4	6219521	0.065000	0.20965	0.919000	0.36401	0.967000	0.64934	2.558000	0.45879	2.092000	0.63282	0.533000	0.62120	ATC	.	.	none		0.502	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329	
CDC27	996	hgsc.bcm.edu	37	17	45234301	45234301	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45234301C>A	ENST00000066544.3	-	7	913	c.820G>T	c.(820-822)Gct>Tct	p.A274S	CDC27_ENST00000446365.2_Missense_Mutation_p.A213S|CDC27_ENST00000527547.1_Missense_Mutation_p.A274S|CDC27_ENST00000531206.1_Missense_Mutation_p.A274S|CDC27_ENST00000528748.1_5'Flank	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	274					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.A274S(3)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						GGACTAAGAGCTGCTGGTCCT	0.363																																					p.A274S		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,+1,10	CDC27	337	10	3	Substitution - Missense(3)	prostate(3)	c.G820T						scavenged	.						62.0	65.0	64.0					17																	45234301		2201	4292	6493	SO:0001583	missense	996	exon7			TAAGAGCTGCTGG	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.820G>T	17.37:g.45234301C>A	ENSP00000066544:p.Ala274Ser	Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	46	2	0.0434783	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	C	13.06	2.125822	0.37533	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68181	-0.31;-0.3;-0.05;-0.31;0.78	5.64	4.68	0.58851	.	0.058237	0.64402	D	0.000002	T	0.46171	0.1379	N	0.11560	0.145	0.50039	D	0.999845	B;B;B;B	0.23442	0.085;0.079;0.073;0.003	B;B;B;B	0.22880	0.013;0.028;0.042;0.004	T	0.36212	-0.9757	10	0.25106	T	0.35	-20.3108	12.4418	0.55629	0.0:0.9186:0.0:0.0814	.	213;274;274;274	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	S	274;274;213;274;274	ENSP00000066544:A274S;ENSP00000434614:A274S;ENSP00000392802:A213S;ENSP00000437339:A274S;ENSP00000432105:A274S	ENSP00000066544:A274S	A	-	1	0	CDC27	42589300	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.048000	0.41278	1.400000	0.46741	0.460000	0.39030	GCT	.	.	none		0.363	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
FAM179B	23116	hgsc.bcm.edu	37	14	45431636	45431636	+	Silent	SNP	C	C	T	rs141982460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45431636C>T	ENST00000361577.3	+	1	226	c.12C>T	c.(10-12)gcC>gcT	p.A4A	FAM179B_ENST00000382233.2_Silent_p.A4A|FAM179B_ENST00000361462.2_Silent_p.A4A|KLHL28_ENST00000355081.2_5'Flank|KLHL28_ENST00000396128.4_5'Flank|KLHL28_ENST00000553817.1_5'Flank	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	4										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TGGCGGCTGCCCCCTCCGCGC	0.617													C|||	4	0.000798722	0.003	0.0	5008	,	,		16675	0.0		0.0	False		,,,				2504	0.0				p.A4A		Atlas-SNP	.											.	FAM179B	115	.	0			c.C12T						PASS	.	C		24,4370		0,24,2173	21.0	24.0	23.0		12	0.9	0.3	14	dbSNP_134	23	0,8568		0,0,4284	no	coding-synonymous	FAM179B	NM_015091.2		0,24,6457	TT,TC,CC		0.0,0.5462,0.1852		4/1721	45431636	24,12938	2197	4284	6481	SO:0001819	synonymous_variant	23116	exon1			GGCTGCCCCCTCC	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.12C>T	14.37:g.45431636C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_015091	Q68D66|Q6PG27	Silent	SNP	ENST00000361577.3	37	CCDS9681.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18473933	18473933	+	Missense_Mutation	SNP	T	T	G	rs201637656		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18473933T>G	ENST00000266497.5	+	6	1213	c.1175T>G	c.(1174-1176)cTt>cGt	p.L392R	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.L392R|RERGL_ENST00000541632.1_5'Flank|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.L392R|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.L392R			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	392					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				CTGAATCAACTTCTAGAATTT	0.303																																					p.L392R		Atlas-SNP	.											PIK3C2G_ENST00000433979,NS,carcinoma,+1,2	PIK3C2G	315	2	0			c.T1175G						PASS	.	T	ARG/LEU	3,3597		0,3,1797	50.0	49.0	49.0		1175	4.6	1.0	12		49	0,8118		0,0,4059	yes	missense	PIK3C2G	NM_004570.4	102	0,3,5856	GG,GT,TT		0.0,0.0833,0.0256	probably-damaging	392/1446	18473933	3,11715	1800	4059	5859	SO:0001583	missense	5288	exon7			ATCAACTTCTAGA	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1175T>G	12.37:g.18473933T>G	ENSP00000266497:p.Leu392Arg	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	256	121	0.472656	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	T	16.78	3.216850	0.58452	8.33E-4	0.0	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.65916	1.12;-0.18;-0.18;-0.08	4.57	4.57	0.56435	.	0.000000	0.52532	D	0.000071	T	0.72787	0.3504	M	0.63843	1.955	0.42403	D	0.992574	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.71184	0.957;0.972;0.938	T	0.72516	-0.4269	10	0.40728	T	0.16	-22.2094	10.628	0.45519	0.0:0.0:0.0:1.0	.	391;392;392	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	R	392	ENSP00000443850:L392R;ENSP00000404845:L392R;ENSP00000266497:L392R;ENSP00000445381:L392R	ENSP00000266497:L392R	L	+	2	0	PIK3C2G	18365200	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.773000	0.55333	2.281000	0.76405	0.528000	0.53228	CTT	.	.	weak		0.303	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
PSG11	5680	hgsc.bcm.edu	37	19	43519270	43519270	+	Missense_Mutation	SNP	A	A	G	rs111493043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43519270A>G	ENST00000401740.1	-	4	1065	c.962T>C	c.(961-963)aTt>aCt	p.I321T	PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000403486.1_Missense_Mutation_p.I199T|PSG11_ENST00000320078.7_Missense_Mutation_p.I321T|PSG11_ENST00000306322.7_Missense_Mutation_p.I199T			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	414	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.I321T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				CCACTTACCAATGACTCTGAT	0.463													.|||	184	0.0367412	0.0287	0.0029	5008	,	,		21410	0.0883		0.0	False		,,,				2504	0.0562				p.I321T		Atlas-SNP	.											PSG11,NS,carcinoma,0,1	PSG11	57	1	1	Substitution - Missense(1)	stomach(1)	c.T962C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE	140,4258	99.8+/-138.5	10,120,2069	138.0	132.0	134.0		596,962,596	-2.0	0.0	19	dbSNP_132	134	16,8580	11.2+/-40.8	0,16,4282	yes	missense,missense,missense	PSG11	NM_001113410.1,NM_002785.2,NM_203287.1	89,89,89	10,136,6351	GG,GA,AA		0.1861,3.1833,1.2006	,,	199/214,321/336,199/214	43519270	156,12838	2199	4298	6497	SO:0001583	missense	5680	exon4			TTACCAATGACTC	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.962T>C	19.37:g.43519270A>G	ENSP00000384995:p.Ile321Thr	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	236	112	0.474576	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	68	0.031135531135531136	18	0.036585365853658534	0	0.0	50	0.08741258741258741	0	0.0	a	0.012	-1.679652	0.00751	0.031833	0.001861	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	0.976	-1.95	0.07548	Immunoglobulin-like fold (1);	.	.	.	.	T	0.01558	0.0050	N	0.02539	-0.55	0.09310	N	1	B;B	0.13594	0.004;0.008	B;B	0.15484	0.012;0.013	T	0.02020	-1.1228	9	0.29301	T	0.29	.	2.7499	0.05277	0.2605:0.0:0.4834:0.2561	.	199;321	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	T	321;199;199;321	ENSP00000319140:I321T;ENSP00000385427:I199T;ENSP00000304913:I199T;ENSP00000384995:I321T	ENSP00000304913:I199T	I	-	2	0	PSG11	48211110	0.002000	0.14202	0.003000	0.11579	0.005000	0.04900	-1.447000	0.02396	-1.624000	0.01556	-1.386000	0.01163	ATT	A|0.982;G|0.018	0.018	strong		0.463	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
KIAA1456	57604	hgsc.bcm.edu	37	8	12879016	12879016	+	Silent	SNP	T	T	A	rs75377133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:12879016T>A	ENST00000524591.2	+	5	1317	c.828T>A	c.(826-828)gtT>gtA	p.V276V	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	276							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						ACACAGAAGTTTGGGCCAGTA	0.418													T|||	107	0.0213658	0.0794	0.0014	5008	,	,		19745	0.0		0.001	False		,,,				2504	0.0				p.V276V		Atlas-SNP	.											.	KIAA1456	20	.	0			c.T828A						PASS	.	T	,	301,3443		12,277,1583	81.0	78.0	79.0		450,828	-9.9	0.0	8	dbSNP_132	79	3,8199		0,3,4098	no	coding-synonymous,coding-synonymous	KIAA1456	NM_001099677.1,NM_020844.2	,	12,280,5681	AA,AT,TT		0.0366,8.0395,2.5448	,	150/329,276/455	12879016	304,11642	1872	4101	5973	SO:0001819	synonymous_variant	57604	exon5			AGAAGTTTGGGCC	BC035082	CCDS47808.1	8p22	2013-10-04	2011-02-23	2011-02-23	ENSG00000250305	ENSG00000250305			26725	protein-coding gene	gene with protein product		615666	"""chromosome 8 open reading frame 79"""	C8orf79		23381944	Standard	NM_020844		Approved	FLJ36980	uc010lsq.3	Q8N9K7	OTTHUMG00000165477	ENST00000524591.2:c.828T>A	8.37:g.12879016T>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_020844	Q96AW6	Silent	SNP	ENST00000524591.2	37	CCDS47808.1																																																																																			T|0.989;A|0.011	0.011	strong		0.418	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677	
PLIN4	729359	hgsc.bcm.edu	37	19	4511791	4511791	+	Silent	SNP	A	A	C	rs62115193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4511791A>C	ENST00000301286.3	-	3	2138	c.2139T>G	c.(2137-2139)acT>acG	p.T713T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	713	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						CCTTGGTACCAGTTAGGACAG	0.592													a|||	1546	0.308706	0.3782	0.3487	5008	,	,		39118	0.256		0.3052	False		,,,				2504	0.2444				p.T713T		Atlas-SNP	.											.	PLIN4	191	.	0			c.T2139G						PASS	.						241.0	254.0	249.0					19																	4511791		2116	4227	6343	SO:0001819	synonymous_variant	729359	exon3			GGTACCAGTTAGG	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.2139T>G	19.37:g.4511791A>C		Somatic	443	0	0		WXS	Illumina HiSeq	Phase_I	505	84	0.166337	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			A|0.500;C|0.500	0.500	strong		0.592	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
SNAPC4	6621	hgsc.bcm.edu	37	9	139292751	139292751	+	Splice_Site	SNP	C	C	T	rs7031489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139292751C>T	ENST00000298532.2	-	1	498	c.130G>A	c.(130-132)Gat>Aat	p.D44N		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		AGGGGCTTACCTGCTTCAGAA	0.557													C|||	36	0.0071885	0.0257	0.0029	5008	,	,		15053	0.0		0.0	False		,,,				2504	0.0				p.D44N		Atlas-SNP	.											.	SNAPC4	82	.	0			c.G130A						PASS	.	C	ASN/ASP	86,4320	73.1+/-111.1	0,86,2117	105.0	108.0	107.0		130	4.2	0.8	9	dbSNP_116	107	12,8588	9.1+/-34.3	0,12,4288	yes	missense-near-splice	SNAPC4	NM_003086.2	23	0,98,6405	TT,TC,CC		0.1395,1.9519,0.7535	benign	44/1470	139292751	98,12908	2203	4300	6503	SO:0001630	splice_region_variant	6621	exon1			GCTTACCTGCTTC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.130+1G>A	9.37:g.139292751C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	91	30	0.32967	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	c	12.43	1.935886	0.34189	0.019519	0.001395	ENSG00000165684	ENST00000298532	T	0.28895	1.59	4.18	4.18	0.49190	.	0.853272	0.10561	N	0.660279	T	0.15609	0.0376	L	0.46157	1.445	0.26436	N	0.975854	B	0.32245	0.361	B	0.29440	0.102	T	0.05835	-1.0861	9	.	.	.	-10.7631	14.4014	0.67050	0.0:1.0:0.0:0.0	rs7031489;rs7031489	44	Q5SXM2	SNPC4_HUMAN	N	44	ENSP00000298532:D44N	.	D	-	1	0	SNAPC4	138412572	0.988000	0.35896	0.779000	0.31741	0.410000	0.31052	3.351000	0.52232	2.327000	0.79052	0.651000	0.88453	GAT	C|0.991;T|0.009	0.009	strong		0.557	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	Missense_Mutation
TEKT5	146279	hgsc.bcm.edu	37	16	10775855	10775855	+	Silent	SNP	G	G	A	rs71389065|rs12918646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:10775855G>A	ENST00000283025.2	-	4	929	c.858C>T	c.(856-858)gaC>gaT	p.D286D		NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	286						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						CTTACGTGCCGTCAATTTTCT	0.542													G|||	1476	0.294728	0.143	0.4006	5008	,	,		21540	0.5446		0.159	False		,,,				2504	0.3067				p.D286D		Atlas-SNP	.											TEKT5,pharynx,carcinoma,-2,1	TEKT5	66	1	0			c.C858T						PASS	.	G		720,3674	298.7+/-285.4	72,576,1549	252.0	191.0	212.0		858	-4.4	0.3	16	dbSNP_121	212	1634,6966	298.2+/-303.8	162,1310,2828	no	coding-synonymous	TEKT5	NM_144674.1		234,1886,4377	AA,AG,GG		19.0,16.386,18.1161		286/486	10775855	2354,10640	2197	4300	6497	SO:0001819	synonymous_variant	146279	exon4			CGTGCCGTCAATT		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.858C>T	16.37:g.10775855G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	168	80	0.47619	NM_144674	A1L3Z3	Silent	SNP	ENST00000283025.2	37	CCDS10542.1																																																																																			ATG|0.500;GTC|0.500	.	alt		0.542	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
OR7D2	162998	hgsc.bcm.edu	37	19	9296664	9296664	+	Silent	SNP	T	T	C	rs56246934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9296664T>C	ENST00000344248.2	+	1	386	c.207T>C	c.(205-207)gtT>gtC	p.V69V		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	69					regulation of transcription, DNA-templated (GO:0006355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						TGTCCTGGGTTGACATCTGTT	0.537													T|||	1136	0.226837	0.0787	0.2003	5008	,	,		19645	0.2768		0.3012	False		,,,				2504	0.318				p.V69V		Atlas-SNP	.											.	OR7D2	55	.	0			c.T207C						PASS	.	T		491,3915	228.5+/-243.3	18,455,1730	126.0	117.0	120.0		207	-4.4	0.0	19	dbSNP_129	120	2569,6031	417.1+/-352.3	359,1851,2090	no	coding-synonymous	OR7D2	NM_175883.2		377,2306,3820	CC,CT,TT		29.8721,11.1439,23.5276		69/313	9296664	3060,9946	2203	4300	6503	SO:0001819	synonymous_variant	162998	exon1			CTGGGTTGACATC	AK095468	CCDS32900.1	19p13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.207T>C	19.37:g.9296664T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_175883	Q6IFJ7|Q8N133	Silent	SNP	ENST00000344248.2	37	CCDS32900.1																																																																																			T|0.761;C|0.239	0.239	strong		0.537	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1		
NKX2-5	1482	hgsc.bcm.edu	37	5	172662024	172662024	+	Silent	SNP	T	T	C	rs2277923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:172662024T>C	ENST00000329198.4	-	1	336	c.63A>G	c.(61-63)gaA>gaG	p.E21E	NKX2-5_ENST00000424406.2_Silent_p.E21E|NKX2-5_ENST00000521848.1_Silent_p.E21E	NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	21			E -> Q (in TOF and ASD7). {ECO:0000269|PubMed:11714651, ECO:0000269|PubMed:14607454, ECO:0000269|PubMed:15810002}.		adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|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 via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GCTGCTGCTGTTCCAGGTTTA	0.677													C|||	2683	0.535743	0.7254	0.5058	5008	,	,		12062	0.6339		0.2823	False		,,,				2504	0.4601				p.E21E	Esophageal Squamous(72;810 1219 2387 13420 44943)	Atlas-SNP	.											.	NKX2-5	42	.	0			c.A63G						PASS	.	C	,,	2801,1545		920,961,292	22.0	27.0	25.0		63,63,63	2.9	1.0	5	dbSNP_100	25	2392,6110		379,1634,2238	no	coding-synonymous,coding-synonymous,coding-synonymous	NKX2-5	NM_001166175.1,NM_001166176.1,NM_004387.3	,,	1299,2595,2530	CC,CT,TT		28.1346,35.5499,40.4187	,,	21/113,21/152,21/325	172662024	5193,7655	2173	4251	6424	SO:0001819	synonymous_variant	1482	exon1			CTGCTGTTCCAGG	AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"""Homeoboxes / ANTP class : NKL subclass"""	2488	protein-coding gene	gene with protein product	"""tinman paralog (Drosophila)"""	600584	"""cardiac-specific homeo box"", ""NK2 transcription factor related, locus 5 (Drosophila)"""	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.63A>G	5.37:g.172662024T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	164	73	0.445122	NM_004387	A8K3K0|B4DNB6|E9PBU6	Silent	SNP	ENST00000329198.4	37	CCDS4387.1																																																																																			T|0.555;C|0.445	0.445	strong		0.677	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2		
GSDMA	284110	hgsc.bcm.edu	37	17	38122117	38122117	+	Silent	SNP	G	G	A	rs16965465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38122117G>A	ENST00000301659.4	+	2	295	c.177G>A	c.(175-177)acG>acA	p.T59T		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	59					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CCGACTACACGCTGCTGGATG	0.637													A|||	351	0.0700879	0.2315	0.036	5008	,	,		17304	0.0		0.0149	False		,,,				2504	0.0051				p.T59T		Atlas-SNP	.											GSDMA,NS,carcinoma,+1,1	GSDMA	26	1	0			c.G177A						PASS	.	A		683,3313		60,563,1375	21.0	24.0	23.0		177	1.0	1.0	17	dbSNP_123	23	53,8223		1,51,4086	no	coding-synonymous	GSDMA	NM_178171.4		61,614,5461	AA,AG,GG		0.6404,17.0921,5.9974		59/446	38122117	736,11536	1998	4138	6136	SO:0001819	synonymous_variant	284110	exon2			CTACACGCTGCTG	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.177G>A	17.37:g.38122117G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	42	16	0.380952	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Silent	SNP	ENST00000301659.4	37	CCDS45669.1																																																																																			G|0.930;A|0.070	0.070	strong		0.637	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
COL15A1	1306	hgsc.bcm.edu	37	9	101822220	101822220	+	Silent	SNP	C	C	T	rs4480177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101822220C>T	ENST00000375001.3	+	36	3810	c.3387C>T	c.(3385-3387)ccC>ccT	p.P1129P		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	1129	Triple-helical region 9 (COL9).				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)				CAGGGCTTCCCGGATCCAGAA	0.463													C|||	1930	0.385383	0.4024	0.3473	5008	,	,		15742	0.5268		0.2038	False		,,,				2504	0.4305				p.P1129P		Atlas-SNP	.											.	COL15A1	211	.	0			c.C3387T						PASS	.	C		1684,2722	512.4+/-368.1	327,1030,846	138.0	135.0	136.0		3387	-11.1	0.1	9	dbSNP_111	136	1741,6859	317.0+/-313.0	183,1375,2742	no	coding-synonymous	COL15A1	NM_001855.3		510,2405,3588	TT,TC,CC		20.2442,38.2206,26.334		1129/1389	101822220	3425,9581	2203	4300	6503	SO:0001819	synonymous_variant	1306	exon36			GCTTCCCGGATCC	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.3387C>T	9.37:g.101822220C>T		Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	218	139	0.637615	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																			C|0.706;T|0.294	0.294	strong		0.463	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
SLC7A4	6545	hgsc.bcm.edu	37	22	21385843	21385843	+	Silent	SNP	G	G	A	rs2072549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21385843G>A	ENST00000382932.2	-	2	326	c.259C>T	c.(259-261)Cta>Tta	p.L87L	AC002472.11_ENST00000450652.1_RNA|MIR649_ENST00000384843.1_RNA|SLC7A4_ENST00000403586.1_Silent_p.L87L	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	87					basic amino acid transport (GO:0015802)|cellular amino acid metabolic process (GO:0006520)|transport (GO:0006810)	integral component of membrane (GO:0016021)	basic amino acid transmembrane transporter activity (GO:0015174)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GCATAGCATAGGGCTGCCAGC	0.637													G|||	1045	0.208666	0.1566	0.2853	5008	,	,		17782	0.3294		0.2097	False		,,,				2504	0.0992				p.L87L		Atlas-SNP	.											.	SLC7A4	50	.	0			c.C259T						PASS	.	G		759,3647	304.6+/-288.6	63,633,1507	66.0	49.0	55.0		259	5.4	0.6	22	dbSNP_96	55	1693,6907	305.3+/-307.4	174,1345,2781	no	coding-synonymous	SLC7A4	NM_004173.2		237,1978,4288	AA,AG,GG		19.686,17.2265,18.8528		87/636	21385843	2452,10554	2203	4300	6503	SO:0001819	synonymous_variant	6545	exon2			AGCATAGGGCTGC	AJ000730	CCDS33608.1	22q11.21	2013-07-19	2013-07-19		ENSG00000099960	ENSG00000099960		"""Solute carriers"""	11062	protein-coding gene	gene with protein product		603752	"""solute carrier family 7 (cationic amino acid transporter, y+ system), member 4"", ""solute carrier family 7 (orphan transporter), member 4"""			9598310, 11665818	Standard	NM_004173		Approved	HCAT3, CAT-4, VH	uc002zud.3	O43246	OTTHUMG00000150896	ENST00000382932.2:c.259C>T	22.37:g.21385843G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Silent	SNP	ENST00000382932.2	37	CCDS33608.1																																																																																			G|0.789;A|0.211	0.211	strong		0.637	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173	
XPR1	9213	hgsc.bcm.edu	37	1	180849394	180849394	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:180849394A>G	ENST00000367590.4	+	14	2189	c.1991A>G	c.(1990-1992)aAc>aGc	p.N664S	XPR1_ENST00000367589.3_Missense_Mutation_p.N599S	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	664					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						TGGAAGTACAACCAGAGCATA	0.512																																					p.N664S		Atlas-SNP	.											.	XPR1	76	.	0			c.A1991G						PASS	.						155.0	146.0	149.0					1																	180849394		2203	4300	6503	SO:0001583	missense	9213	exon14			AGTACAACCAGAG	AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.1991A>G	1.37:g.180849394A>G	ENSP00000356562:p.Asn664Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	ENST00000367590.4	37	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	A	8.539	0.872854	0.17322	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T	0.40476	1.03	5.56	1.18	0.20946	.	0.390605	0.32002	N	0.006729	T	0.10852	0.0265	N	0.00823	-1.155	0.20821	N	0.999847	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.35649	-0.9780	10	0.06891	T	0.86	-0.9318	7.5346	0.27702	0.4444:0.0:0.5556:0.0	.	599;664	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	S	664;599	ENSP00000356562:N664S	ENSP00000356561:N599S	N	+	2	0	XPR1	179116017	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	1.285000	0.33261	0.243000	0.21327	-0.462000	0.05337	AAC	.	.	none		0.512	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736	
LYST	1130	hgsc.bcm.edu	37	1	235972867	235972867	+	Silent	SNP	T	T	C	rs1063128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235972867T>C	ENST00000389794.3	-	5	1425	c.1251A>G	c.(1249-1251)caA>caG	p.Q417Q	LYST_ENST00000389793.2_Silent_p.Q417Q|LYST_ENST00000536965.1_Silent_p.Q417Q			Q99698	LYST_HUMAN	lysosomal trafficking regulator	417					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)			AAGCTGCACTTTGAAGACAAC	0.378													T|||	1519	0.303315	0.4887	0.2997	5008	,	,		19059	0.0655		0.4254	False		,,,				2504	0.1748				p.Q417Q		Atlas-SNP	.											.	LYST	370	.	0			c.A1251G						PASS	.	T		2242,2164	582.9+/-385.7	572,1098,533	82.0	86.0	85.0		1251	-1.2	1.0	1	dbSNP_86	85	3435,5165	503.9+/-376.0	678,2079,1543	no	coding-synonymous	LYST	NM_000081.2		1250,3177,2076	CC,CT,TT		39.9419,49.1148,43.6491		417/3802	235972867	5677,7329	2203	4300	6503	SO:0001819	synonymous_variant	1130	exon5			TGCACTTTGAAGA	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.1251A>G	1.37:g.235972867T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			T|0.619;C|0.381	0.381	strong		0.378	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
OR1L1	26737	hgsc.bcm.edu	37	9	125424507	125424507	+	Silent	SNP	A	A	C	rs70156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	148	0	0		WXS	Illumina HiSeq	Phase_I	196	125	0.637755	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			
CEACAM20	125931	hgsc.bcm.edu	37	19	45033485	45033485	+	RNA	SNP	A	A	G	rs62116895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45033485A>G	ENST00000454753.1	-	0	326							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)				ACTCACCTGAAAGCAGGATTC	0.587													g|||	1067	0.213059	0.4569	0.1657	5008	,	,		16546	0.1587		0.0954	False		,,,				2504	0.0941				p.L16L		Atlas-SNP	.											.	CEACAM20	31	.	0			c.T48C						PASS	.		,,,	1683,2519		343,997,761	53.0	59.0	57.0		48,48,48,48	1.2	0.8	19	dbSNP_129	57	730,7710		38,654,3528	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	,,,	381,1651,4289	GG,GA,AA		8.6493,40.0524,19.0872	,,,	16/597,16/492,16/504,16/585	45033485	2413,10229	2101	4220	6321			125931	exon1			ACCTGAAAGCAGG	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.45033485A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_001102600		Silent	SNP	ENST00000454753.1	37																																																																																				A|0.815;G|0.185	0.185	strong		0.587	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
EIF4ENIF1	56478	hgsc.bcm.edu	37	22	31838085	31838085	+	Silent	SNP	G	G	A	rs5997988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31838085G>A	ENST00000397525.1	-	17	2449	c.2226C>T	c.(2224-2226)agC>agT	p.S742S	EIF4ENIF1_ENST00000441289.1_5'Flank|EIF4ENIF1_ENST00000330125.5_Silent_p.S742S|EIF4ENIF1_ENST00000397523.1_Silent_p.S718S|EIF4ENIF1_ENST00000382180.2_Silent_p.S397S|EIF4ENIF1_ENST00000344710.5_Silent_p.S568S	NM_001164501.1	NP_001157973.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	742						cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TGGGTACAGAGCTGGATGACA	0.478													G|||	1621	0.323682	0.4039	0.3026	5008	,	,		18314	0.0377		0.4583	False		,,,				2504	0.3865				p.S742S		Atlas-SNP	.											.	EIF4ENIF1	80	.	0			c.C2226T						PASS	.	G	,,	1863,2543	539.4+/-375.3	388,1087,728	104.0	109.0	107.0		2226,1704,2226	-0.7	0.3	22	dbSNP_114	107	3953,4647	550.0+/-385.6	907,2139,1254	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF4ENIF1	NM_001164501.1,NM_001164502.1,NM_019843.3	,,	1295,3226,1982	AA,AG,GG		45.9651,42.2833,44.7178	,,	742/986,568/812,742/986	31838085	5816,7190	2203	4300	6503	SO:0001819	synonymous_variant	56478	exon17			TACAGAGCTGGAT	AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708			16687	protein-coding gene	gene with protein product		607445				10856257	Standard	NM_019843		Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000397525.1:c.2226C>T	22.37:g.31838085G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	159	82	0.515723	NM_019843	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	Silent	SNP	ENST00000397525.1	37	CCDS13898.1																																																																																			G|0.611;A|0.389	0.389	strong		0.478	EIF4ENIF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127926.1	NM_019843	
EHD4	30844	hgsc.bcm.edu	37	15	42192885	42192885	+	Silent	SNP	G	G	A	rs113393602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42192885G>A	ENST00000220325.4	-	6	1667	c.1584C>T	c.(1582-1584)ctC>ctT	p.L528L	RP11-23P13.6_ENST00000564432.2_RNA	NM_139265.3	NP_644670.1	Q9H223	EHD4_HUMAN	EH-domain containing 4	528	EH. {ECO:0000255|PROSITE- ProRule:PRU00077}.				cellular response to growth factor stimulus (GO:0071363)|endocytic recycling (GO:0032456)|pinocytosis (GO:0006907)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein homooligomerization (GO:0051260)|regulation of endocytosis (GO:0030100)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|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)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(7)|ovary(2)|stomach(1)|urinary_tract(1)	20		all_cancers(109;2.54e-12)|all_epithelial(112;6.59e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		OV - Ovarian serous cystadenocarcinoma(18;1.6e-19)|GBM - Glioblastoma multiforme(94;3.77e-06)|COAD - Colon adenocarcinoma(120;0.0474)|Colorectal(105;0.0538)		AGGGGGGCACGAGGTGGGGGG	0.677													G|||	205	0.0409345	0.0234	0.0634	5008	,	,		14759	0.0129		0.0517	False		,,,				2504	0.0665				p.L528L		Atlas-SNP	.											.	EHD4	46	.	0			c.C1584T						PASS	.	G		133,4269		2,129,2070	22.0	22.0	22.0		1584	-8.8	0.8	15	dbSNP_132	22	494,8100		17,460,3820	no	coding-synonymous	EHD4	NM_139265.3		19,589,5890	AA,AG,GG		5.7482,3.0214,4.8246		528/542	42192885	627,12369	2201	4297	6498	SO:0001819	synonymous_variant	30844	exon6			GGGCACGAGGTGG	AF181265	CCDS10081.1	15q11.1	2013-01-10			ENSG00000103966	ENSG00000103966		"""EF-hand domain containing"""	3245	protein-coding gene	gene with protein product		605892		PAST4		10673336, 11533061	Standard	NM_139265		Approved		uc001zot.3	Q9H223	OTTHUMG00000130370	ENST00000220325.4:c.1584C>T	15.37:g.42192885G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	27	16	0.592593	NM_139265	Q9HAR1|Q9NZN2	Silent	SNP	ENST00000220325.4	37	CCDS10081.1																																																																																			A|0.047;C|0.000;G|0.953	0.047	strong		0.677	EHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252737.2	NM_139265	
SPTA1	6708	hgsc.bcm.edu	37	1	158587368	158587368	+	Missense_Mutation	SNP	T	T	C	rs111980420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158587368T>C	ENST00000368147.4	-	47	6739	c.6559A>G	c.(6559-6561)Aaa>Gaa	p.K2187E		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2187					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)					CCTGTTTCTTTGAGCAATGAT	0.343													T|||	50	0.00998403	0.0363	0.0029	5008	,	,		21215	0.0		0.0	False		,,,				2504	0.0				p.K2187E		Atlas-SNP	.											.	SPTA1	720	.	0			c.A6559G						PASS	.	T	GLU/LYS	109,3607		1,107,1750	110.0	101.0	104.0		6559	4.0	1.0	1	dbSNP_132	104	1,8199		0,1,4099	yes	missense	SPTA1	NM_003126.2	56	1,108,5849	CC,CT,TT		0.0122,2.9333,0.9231	benign	2187/2420	158587368	110,11806	1858	4100	5958	SO:0001583	missense	6708	exon47			TTTCTTTGAGCAA	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.6559A>G	1.37:g.158587368T>C	ENSP00000357129:p.Lys2187Glu	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	190	112	0.589474	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	T	5.051	0.195152	0.09599	0.029333	1.22E-4	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.53423	0.62;0.62	5.15	4.01	0.46588	.	0.000000	0.33792	N	0.004556	T	0.07728	0.0194	N	0.12182	0.205	0.34813	D	0.737938	B	0.10296	0.003	B	0.09377	0.004	T	0.27262	-1.0079	10	0.02654	T	1	.	5.5016	0.16831	0.0:0.0873:0.1765:0.7361	.	2187	P02549	SPTA1_HUMAN	E	2187;2184	ENSP00000357130:K2187E;ENSP00000357129:K2184E	ENSP00000357129:K2184E	K	-	1	0	SPTA1	156853992	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.835000	0.48175	1.068000	0.40764	0.533000	0.62120	AAA	T|0.994;C|0.006	0.006	strong		0.343	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390155	208390155	+	Silent	SNP	C	C	T	rs4844657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	92	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	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	
GCLC	2729	hgsc.bcm.edu	37	6	53365102	53365102	+	Silent	SNP	C	C	T	rs17881359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:53365102C>T	ENST00000229416.6	-	14	2007	c.1524G>A	c.(1522-1524)acG>acA	p.T508T	RP1-27K12.4_ENST00000508884.1_RNA	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	508					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	CAGCGAGCTCCGTGCTGTTCT	0.567													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		18765	0.0		0.0	False		,,,				2504	0.0				p.T508T		Atlas-SNP	.											.	GCLC	58	.	0			c.G1524A						PASS	.	C	,	76,4330	67.0+/-104.6	0,76,2127	148.0	129.0	136.0		1410,1524	-10.5	0.0	6	dbSNP_124	136	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GCLC	NM_001197115.1,NM_001498.3	,	0,76,6427	TT,TC,CC		0.0,1.7249,0.5843	,	470/600,508/638	53365102	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	2729	exon14			GAGCTCCGTGCTG	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.1524G>A	6.37:g.53365102C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	176	82	0.465909	NM_001498	Q14399	Silent	SNP	ENST00000229416.6	37	CCDS4952.1																																																																																			C|0.994;T|0.006	0.006	strong		0.567	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2		
SPHKAP	80309	hgsc.bcm.edu	37	2	228882588	228882588	+	Silent	SNP	T	T	C	rs73994847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228882588T>C	ENST00000392056.3	-	7	3028	c.2982A>G	c.(2980-2982)aaA>aaG	p.K994K	SPHKAP_ENST00000344657.5_Silent_p.K994K	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	994						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GAGGCTTGTGTTTCCTCACAG	0.537													T|||	177	0.0353435	0.1301	0.0072	5008	,	,		20344	0.0		0.0	False		,,,				2504	0.0				p.K994K		Atlas-SNP	.											.	SPHKAP	750	.	0			c.A2982G						PASS	.	T	,	552,3854	246.8+/-255.3	32,488,1683	83.0	74.0	77.0		2982,2982	-4.0	1.0	2	dbSNP_130	77	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	SPHKAP	NM_001142644.1,NM_030623.3	,	32,493,5978	CC,CT,TT		0.0581,12.5284,4.2826	,	994/1701,994/1672	228882588	557,12449	2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			CTTGTGTTTCCTC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.2982A>G	2.37:g.228882588T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	37	CCDS46537.1																																																																																			T|0.953;C|0.047	0.047	strong		0.537	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
TENM4	26011	hgsc.bcm.edu	37	11	78387356	78387356	+	Silent	SNP	C	C	T	rs59660398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:78387356C>T	ENST00000278550.7	-	30	5799	c.5337G>A	c.(5335-5337)gcG>gcA	p.A1779A		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1779					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CAGTCTGCAGCGCCACCTCCA	0.632													C|||	301	0.0601038	0.2224	0.0101	5008	,	,		15294	0.0		0.0	False		,,,				2504	0.0				p.A1779A		Atlas-SNP	.											.	.	.	.	0			c.G5337A						PASS	.	C		802,3514		60,682,1416	30.0	37.0	35.0		5337	-9.4	0.2	11	dbSNP_129	35	15,8485		0,15,4235	no	coding-synonymous	ODZ4	NM_001098816.2		60,697,5651	TT,TC,CC		0.1765,18.582,6.3748		1779/2770	78387356	817,11999	2158	4250	6408	SO:0001819	synonymous_variant	26011	exon30			CTGCAGCGCCACC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5337G>A	11.37:g.78387356C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			C|0.963;T|0.037	0.037	strong		0.632	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
OSER1	51526	hgsc.bcm.edu	37	20	42826379	42826379	+	Splice_Site	SNP	C	C	T	rs11274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42826379C>T	ENST00000372970.2	-	6	372	c.192G>A	c.(190-192)ggG>ggA	p.G64G	OSER1_ENST00000255174.2_Splice_Site_p.G64G			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	64					cellular response to hydrogen peroxide (GO:0070301)												TCCTTGTAGACCTAAAGAGGA	0.408													C|||	1916	0.382588	0.6346	0.1571	5008	,	,		22340	0.4782		0.1561	False		,,,				2504	0.3364				p.G64G		Atlas-SNP	.											.	C20orf111	28	.	0			c.G192A						PASS	.	C		2370,2036	589.2+/-387.1	648,1074,481	36.0	36.0	36.0		192	2.0	1.0	20	dbSNP_52	36	1276,7324	243.8+/-273.2	90,1096,3114	yes	coding-synonymous-near-splice	C20orf111	NM_016470.7		738,2170,3595	TT,TC,CC		14.8372,46.2097,28.0332		64/293	42826379	3646,9360	2203	4300	6503	SO:0001630	splice_region_variant	51526	exon4			TGTAGACCTAAAG	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"""peroxide-inducible transcript 1"", ""oxidative stress-responsive 1"""		"""chromosome 20 open reading frame 111"""	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.192-1G>A	20.37:g.42826379C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Silent	SNP	ENST00000372970.2	37	CCDS13327.1																																																																																			C|0.685;N|0.000	.	strong		0.408	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470	Silent
PTPN1	5770	hgsc.bcm.edu	37	20	49191191	49191191	+	Splice_Site	SNP	A	A	G	rs35414863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:49191191A>G	ENST00000371621.3	+	5	666	c.492A>G	c.(490-492)acA>acG	p.T164T	RP4-530I15.9_ENST00000431019.1_RNA|PTPN1_ENST00000541713.1_Splice_Site_p.T91T	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	164	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	aAAACCTTACAGTGAGTATAG	0.398													A|||	113	0.0225639	0.0772	0.0144	5008	,	,		21947	0.0		0.001	False		,,,				2504	0.0				p.T164T		Atlas-SNP	.											.	PTPN1	36	.	0			c.A492G						PASS	.	A		344,4062	179.7+/-208.2	11,322,1870	117.0	116.0	117.0		492	-10.3	0.0	20	dbSNP_126	117	19,8581	13.3+/-46.6	0,19,4281	yes	coding-synonymous-near-splice	PTPN1	NM_002827.2		11,341,6151	GG,GA,AA		0.2209,7.8075,2.791		164/436	49191191	363,12643	2203	4300	6503	SO:0001630	splice_region_variant	5770	exon5			CCTTACAGTGAGT		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.492+1A>G	20.37:g.49191191A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	37	CCDS13430.1																																																																																			A|0.976;G|0.024	0.024	strong		0.398	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2		Silent
RNASEH1	246243	hgsc.bcm.edu	37	2	3597974	3597974	+	Silent	SNP	T	T	C	rs10186193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:3597974T>C	ENST00000315212.3	-	4	853	c.498A>G	c.(496-498)ccA>ccG	p.P166P	RP13-512J5.1_ENST00000438485.1_5'Flank	NM_002936.3	NP_002927.2	O60930	RNH1_HUMAN	ribonuclease H1	166	RNase H. {ECO:0000255|PROSITE- ProRule:PRU00408}.				mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	13	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0713)|Epithelial(75;0.167)|all cancers(51;0.22)		AAGGATGGCCTGGCCCCCAGT	0.498													C|||	1881	0.375599	0.6233	0.2305	5008	,	,		17040	0.2371		0.3479	False		,,,				2504	0.3149				p.P166P		Atlas-SNP	.											.	RNASEH1	27	.	0			c.A498G						PASS	.	C		2631,1775	521.1+/-370.4	820,991,392	110.0	124.0	119.0		498	-10.9	0.1	2	dbSNP_119	119	3150,5450	652.1+/-400.9	596,1958,1746	yes	coding-synonymous	RNASEH1	NM_002936.3		1416,2949,2138	CC,CT,TT		36.6279,40.286,44.4487		166/287	3597974	5781,7225	2203	4300	6503	SO:0001819	synonymous_variant	246243	exon4			ATGGCCTGGCCCC	AF039652	CCDS1647.1	2p25	2008-03-11			ENSG00000171865	ENSG00000171865	3.1.26.-		18466	protein-coding gene	gene with protein product	"""RNase H1"""	604123				12036296, 17964265	Standard	XR_244873		Approved		uc002qxt.3	O60930	OTTHUMG00000090279	ENST00000315212.3:c.498A>G	2.37:g.3597974T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_002936	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Silent	SNP	ENST00000315212.3	37	CCDS1647.1																																																																																			T|0.579;C|0.421	0.421	strong		0.498	RNASEH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206605.2		
ODAM	54959	hgsc.bcm.edu	37	4	71062426	71062426	+	Silent	SNP	C	C	T	rs17704351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	182	0	0		WXS	Illumina HiSeq	Phase_I	218	105	0.481651	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	
SLX4	84464	hgsc.bcm.edu	37	16	3650987	3650987	+	Missense_Mutation	SNP	T	T	C	rs113490934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3650987T>C	ENST00000294008.3	-	5	1796	c.1156A>G	c.(1156-1158)Atg>Gtg	p.M386V		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	386	Interaction with SLX4IP, ERCC4 and MSH2.		M -> V (in dbSNP:rs113490934). {ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TACCTGAACATGGGTGGGCTG	0.517								Direct reversal of damage					C|||	273	0.0545128	0.0507	0.0706	5008	,	,		19560	0.0506		0.0646	False		,,,				2504	0.0419				p.M386V		Atlas-SNP	.											.	SLX4	173	.	0			c.A1156G						PASS	.	C	VAL/MET	271,4123	783.8+/-414.6	7,257,1933	39.0	40.0	40.0		1156	2.4	0.0	16	dbSNP_132	40	575,8025	774.0+/-407.7	15,545,3740	yes	missense	SLX4	NM_032444.2	21	22,802,5673	CC,CT,TT		6.686,6.1675,6.5107	benign	386/1835	3650987	846,12148	2197	4300	6497	SO:0001583	missense	84464	exon5			TGAACATGGGTGG	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.1156A>G	16.37:g.3650987T>C	ENSP00000294008:p.Met386Val	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	146	44	0.30137	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	121	0.0554029304029304	25	0.0508130081300813	24	0.06629834254143646	24	0.04195804195804196	48	0.0633245382585752	C	3.500	-0.102080	0.06967	0.061675	0.06686	ENSG00000188827	ENST00000294008	T	0.18810	2.19	5.46	2.41	0.29592	.	2.158740	0.01671	N	0.025592	T	0.00496	0.0016	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36383	-0.9750	10	0.02654	T	1	.	5.0684	0.14594	0.145:0.6271:0.0:0.2279	.	386	Q8IY92	SLX4_HUMAN	V	386	ENSP00000294008:M386V	ENSP00000294008:M386V	M	-	1	0	SLX4	3590988	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.435000	0.21510	0.084000	0.17077	-0.128000	0.14901	ATG	T|0.945;C|0.055	0.055	strong		0.517	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
NLGN4X	57502	hgsc.bcm.edu	37	X	5821468	5821468	+	Silent	SNP	C	C	G	rs61741754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:5821468C>G	ENST00000381095.3	-	5	1878	c.1251G>C	c.(1249-1251)cgG>cgC	p.R417R	NLGN4X_ENST00000381093.2_Silent_p.R437R|NLGN4X_ENST00000275857.6_Silent_p.R417R|NLGN4X_ENST00000381092.1_Silent_p.R417R|NLGN4X_ENST00000538097.1_Silent_p.R417R	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	417					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						TGATAGTCTCCCGCAAAGTGT	0.542													c|||	232	0.061457	0.1604	0.0259	3775	,	,		12595	0.0		0.002	False		,,,				2504	0.0				p.R417R		Atlas-SNP	.											.	NLGN4X	191	.	0			c.G1251C						PASS	.	G	,	580,2948		38,395,109,1058,437	6.0	7.0	7.0		1251,1251	-1.2	0.0	X	dbSNP_134	7	4,6426		0,4,0,2331,1760	no	coding-synonymous,coding-synonymous	NLGN4X	NM_020742.2,NM_181332.1	,	38,399,109,3389,2197	GG,GC,G,CC,C		0.0622,16.4399,5.8646	,	417/817,417/817	5821468	584,9374	2037	4095	6132	SO:0001819	synonymous_variant	57502	exon5			AGTCTCCCGCAAA	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"""neuroligin 4"""	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1251G>C	X.37:g.5821468C>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	229	125	0.545852	NM_181332	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	37	CCDS14126.1																																																																																			C|0.870;G|0.130	0.130	strong		0.542	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742	
CDC42BPG	55561	hgsc.bcm.edu	37	11	64594212	64594212	+	Missense_Mutation	SNP	T	T	G	rs61744174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64594212T>G	ENST00000342711.5	-	35	4443	c.4444A>C	c.(4444-4446)Agc>Cgc	p.S1482R		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						TCGGAGAAGCTGTGGGGCCGC	0.697													T|||	89	0.0177716	0.062	0.0072	5008	,	,		13371	0.0		0.002	False		,,,				2504	0.0				p.S1482R		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.A4444C						PASS	.	T	ARG/SER	188,4154		6,176,1989	10.0	14.0	12.0		4444	4.9	1.0	11	dbSNP_129	12	0,8458		0,0,4229	no	missense	CDC42BPG	NM_017525.2	110	6,176,6218	GG,GT,TT		0.0,4.3298,1.4688	probably-damaging	1482/1552	64594212	188,12612	2171	4229	6400	SO:0001583	missense	55561	exon35			AGAAGCTGTGGGG	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.4444A>C	11.37:g.64594212T>G	ENSP00000345133:p.Ser1482Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	40	13	0.325	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	37	CCDS31601.1	29	0.013278388278388278	25	0.0508130081300813	4	0.011049723756906077	0	0.0	0	0.0	t	17.89	3.500160	0.64298	0.043298	0.0	ENSG00000171219	ENST00000342711	T	0.69435	-0.4	4.92	4.92	0.64577	.	0.000000	0.50627	D	0.000114	T	0.25827	0.0629	M	0.71581	2.175	0.26185	N	0.979679	P	0.40476	0.718	B	0.41860	0.368	T	0.45264	-0.9273	10	0.27785	T	0.31	.	11.2564	0.49056	0.0:0.0:0.0:1.0	.	1482	Q6DT37	MRCKG_HUMAN	R	1482	ENSP00000345133:S1482R	ENSP00000345133:S1482R	S	-	1	0	CDC42BPG	64350788	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.830000	0.39131	1.985000	0.57927	0.478000	0.44815	AGC	T|0.987;G|0.013	0.013	strong		0.697	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	
GABBR2	9568	hgsc.bcm.edu	37	9	101304193	101304193	+	Missense_Mutation	SNP	C	C	T	rs369347155		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101304193C>T	ENST00000259455.2	-	3	1051	c.592G>A	c.(592-594)Gtg>Atg	p.V198M	GABBR2_ENST00000477471.1_5'UTR	NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	198					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)	p.V198L(1)	NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	AGCGTGCCCACGCGCTTCCAC	0.522																																					p.V198M		Atlas-SNP	.											GABBR2,NS,carcinoma,0,1	GABBR2	126	1	1	Substitution - Missense(1)	lung(1)	c.G592A						scavenged	.	C	MET/VAL	0,4406		0,0,2203	156.0	112.0	127.0		592	5.1	1.0	9		127	1,8599	1.2+/-3.3	0,1,4299	no	missense	GABBR2	NM_005458.7	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	198/942	101304193	1,13005	2203	4300	6503	SO:0001583	missense	9568	exon3			TGCCCACGCGCTT	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.592G>A	9.37:g.101304193C>T	ENSP00000259455:p.Val198Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	3	0.0238095	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	C	33	5.198200	0.94997	0.0	1.16E-4	ENSG00000136928	ENST00000259455	D	0.88277	-2.36	5.09	5.09	0.68999	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.94466	0.8219	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95024	0.8163	10	0.87932	D	0	-12.6839	16.3412	0.83082	0.0:1.0:0.0:0.0	.	198	O75899	GABR2_HUMAN	M	198	ENSP00000259455:V198M	ENSP00000259455:V198M	V	-	1	0	GABBR2	100344014	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.661000	0.83786	2.538000	0.85594	0.655000	0.94253	GTG	.	.	weak		0.522	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
TRIM17	51127	hgsc.bcm.edu	37	1	228601506	228601506	+	Missense_Mutation	SNP	C	C	T	rs116188608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228601506C>T	ENST00000366697.2	-	2	1473	c.517G>A	c.(517-519)Gag>Aag	p.E173K	TRIM17_ENST00000295033.3_Missense_Mutation_p.E173K|TRIM17_ENST00000456946.2_Missense_Mutation_p.E173K|TRIM17_ENST00000366698.2_Missense_Mutation_p.E173K			Q9Y577	TRI17_HUMAN	tripartite motif containing 17	173					protein autoubiquitination (GO:0051865)	intracellular (GO:0005622)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	10		Prostate(94;0.0724)				ACCTGCCACTCGGCTAAGCTC	0.607													C|||	54	0.0107827	0.0378	0.0043	5008	,	,		16452	0.0		0.001	False		,,,				2504	0.0				p.E173K		Atlas-SNP	.											.	TRIM17	66	.	0			c.G517A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	193,4213	121.3+/-158.8	1,191,2011	120.0	90.0	100.0		517,517,517	1.6	0.1	1	dbSNP_132	100	0,8600		0,0,4300	yes	missense,missense,missense	TRIM17	NM_001024940.2,NM_001134855.1,NM_016102.3	56,56,56	1,191,6311	TT,TC,CC		0.0,4.3804,1.4839	benign,benign,benign	173/478,173/344,173/478	228601506	193,12813	2203	4300	6503	SO:0001583	missense	51127	exon3			GCCACTCGGCTAA	AF156271	CCDS1571.1, CCDS44327.1	1q42	2013-01-09	2011-01-25	2001-11-30	ENSG00000162931	ENSG00000162931		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	13430	protein-coding gene	gene with protein product	"""ring finger protein 16"", ""RING finger protein terf"", ""testis RING finger protein"""	606123	"""tripartite motif-containing 17"""	RNF16		9792805, 10894938	Standard	NM_016102		Approved	terf, RBCC	uc001hsv.3	Q9Y577	OTTHUMG00000039974	ENST00000366697.2:c.517G>A	1.37:g.228601506C>T	ENSP00000355658:p.Glu173Lys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	109	44	0.40367	NM_001024940	B4DVJ2|Q5VST8	Missense_Mutation	SNP	ENST00000366697.2	37	CCDS1571.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	0.010	-1.780416	0.00634	0.043804	0.0	ENSG00000162931	ENST00000366697;ENST00000366698;ENST00000295033;ENST00000456946;ENST00000479800;ENST00000355586	T;T;T;T;T;T	0.18810	3.58;3.58;3.58;3.58;3.58;2.19	3.5	1.56	0.23342	.	0.000000	0.38663	N	0.001611	T	0.03520	0.0101	M	0.66939	2.045	0.09310	N	1	B;B	0.20550	0.046;0.004	B;B	0.17433	0.018;0.002	T	0.30149	-0.9988	10	0.08599	T	0.76	.	4.9406	0.13963	0.0:0.6631:0.2166:0.1203	.	173;173	Q9Y577-2;Q9Y577	.;TRI17_HUMAN	K	173;173;173;173;146;173	ENSP00000355658:E173K;ENSP00000355659:E173K;ENSP00000295033:E173K;ENSP00000403312:E173K;ENSP00000430468:E146K;ENSP00000347794:E173K	ENSP00000295033:E173K	E	-	1	0	TRIM17	226668129	0.008000	0.16893	0.143000	0.22291	0.036000	0.12997	0.247000	0.18179	0.452000	0.26830	-0.254000	0.11334	GAG	C|0.986;T|0.014	0.014	strong		0.607	TRIM17-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096439.2	NM_016102	
ASCL1	429	hgsc.bcm.edu	37	12	103352649	103352649	+	Silent	SNP	C	C	G	rs731682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:103352649C>G	ENST00000266744.3	+	1	1186	c.627C>G	c.(625-627)gtC>gtG	p.V209V		NM_004316.3	NP_004307.2	P50553	ASCL1_HUMAN	achaete-scute family bHLH transcription factor 1	209					adrenal chromaffin cell differentiation (GO:0061104)|carotid body glomus cell differentiation (GO:0061103)|cell maturation (GO:0048469)|cellular response to magnetism (GO:0071259)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|lung epithelial cell differentiation (GO:0060487)|lung neuroendocrine cell differentiation (GO:0061100)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroblast fate determination (GO:0007400)|neuroblast proliferation (GO:0007405)|neurogenesis (GO:0022008)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron fate commitment (GO:0003359)|Notch signaling pathway (GO:0007219)|olfactory pit development (GO:0060166)|oligodendrocyte development (GO:0014003)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial cell differentiation (GO:0030856)|regulation of gene expression (GO:0010468)|regulation of mitotic cell cycle (GO:0007346)|regulation of timing of subpallium neuron differentiation (GO:0060165)|response to epidermal growth factor (GO:0070849)|response to folic acid (GO:0051593)|response to lithium ion (GO:0010226)|response to retinoic acid (GO:0032526)|spinal cord association neuron differentiation (GO:0021527)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|stomach neuroendocrine cell differentiation (GO:0061102)|subpallium neuron fate commitment (GO:0060163)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)|vestibular nucleus development (GO:0021750)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)			NS(3)|large_intestine(1)|lung(1)	5						GCTCGCCGGTCTCATCCTACT	0.647													C|||	357	0.0712859	0.205	0.0317	5008	,	,		15749	0.0		0.0457	False		,,,				2504	0.0184				p.V209V		Atlas-SNP	.											.	ASCL1	16	.	0			c.C627G						PASS	.	C		887,3515		96,695,1410	28.0	31.0	30.0		627	1.9	1.0	12	dbSNP_86	30	463,8125		15,433,3846	no	coding-synonymous	ASCL1	NM_004316.3		111,1128,5256	GG,GC,CC		5.3912,20.1499,10.3926		209/237	103352649	1350,11640	2201	4294	6495	SO:0001819	synonymous_variant	429	exon1			GCCGGTCTCATCC	L08424	CCDS31886.1	12q22-q23	2013-10-17	2013-10-17			ENSG00000139352		"""Basic helix-loop-helix proteins"""	738	protein-coding gene	gene with protein product		100790	"""achaete-scute complex (Drosophila) homolog-like 1"", ""achaete-scute complex-like 1 (Drosophila)"", ""achaete-scute complex homolog 1 (Drosophila)"""			8390674	Standard	NM_004316		Approved	ASH1, HASH1, bHLHa46	uc001tjr.4	P50553		ENST00000266744.3:c.627C>G	12.37:g.103352649C>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	172	73	0.424419	NM_004316	A8K3C4|Q9BQ30	Silent	SNP	ENST00000266744.3	37	CCDS31886.1																																																																																			C|0.917;G|0.083	0.083	strong		0.647	ASCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406707.1		
CCDC110	256309	hgsc.bcm.edu	37	4	186379735	186379735	+	Missense_Mutation	SNP	T	T	C	rs6827370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:186379735T>C	ENST00000307588.3	-	6	2081	c.2006A>G	c.(2005-2007)cAa>cGa	p.Q669R	CCDC110_ENST00000510617.1_Missense_Mutation_p.Q669R|CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000393540.3_Missense_Mutation_p.Q632R	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	669			Q -> R (in dbSNP:rs6827370).			nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		GGCAGTAGATTGGTAGGTTTG	0.323													T|||	1068	0.213259	0.2965	0.1599	5008	,	,		17673	0.2698		0.1223	False		,,,				2504	0.1738				p.Q669R		Atlas-SNP	.											.	CCDC110	78	.	0			c.A2006G						PASS	.	T	ARG/GLN,ARG/GLN	1265,3137	397.0+/-330.2	179,907,1115	74.0	80.0	78.0		1895,2006	3.0	0.2	4	dbSNP_116	78	938,7654	202.5+/-245.8	53,832,3411	yes	missense,missense	CCDC110	NM_001145411.1,NM_152775.3	43,43	232,1739,4526	CC,CT,TT		10.9171,28.7369,16.954	benign,benign	632/797,669/834	186379735	2203,10791	2201	4296	6497	SO:0001583	missense	256309	exon6			GTAGATTGGTAGG	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.2006A>G	4.37:g.186379735T>C	ENSP00000306776:p.Gln669Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_152775	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	37	CCDS3843.1	419	0.19184981684981686	152	0.3089430894308943	45	0.12430939226519337	125	0.21853146853146854	97	0.1279683377308707	T	6.827	0.521826	0.13005	0.287369	0.109171	ENSG00000168491	ENST00000393540;ENST00000307588;ENST00000510617	T;T;T	0.32515	1.45;1.45;1.45	5.54	3.02	0.34903	.	0.512841	0.17867	N	0.159308	T	0.00012	0.0000	L	0.35723	1.085	0.80722	P	0.0	B;B;B	0.18166	0.026;0.026;0.026	B;B;B	0.17433	0.018;0.018;0.018	T	0.42378	-0.9455	9	0.14656	T	0.56	-0.2388	8.2339	0.31614	0.0:0.2298:0.0:0.7702	rs6827370;rs52809614;rs58133308;rs6827370	669;632;669	B4DZA2;Q8TBZ0-2;Q8TBZ0	.;.;CC110_HUMAN	R	632;669;669	ENSP00000377172:Q632R;ENSP00000306776:Q669R;ENSP00000427246:Q669R	ENSP00000306776:Q669R	Q	-	2	0	CCDC110	186616729	0.623000	0.27094	0.209000	0.23619	0.953000	0.61014	1.465000	0.35299	0.438000	0.26450	0.528000	0.53228	CAA	T|0.816;C|0.184	0.184	strong		0.323	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
WDR87	83889	hgsc.bcm.edu	37	19	38382328	38382328	+	Silent	SNP	C	C	T	rs953370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38382328C>T	ENST00000303868.5	-	5	3365	c.3141G>A	c.(3139-3141)ccG>ccA	p.P1047P	WDR87_ENST00000447313.2_Silent_p.P1086P	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	1047										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						AAGAAAAAGCCGGCTTTTCAT	0.458													C|||	3236	0.646166	0.795	0.5331	5008	,	,		18527	0.8214		0.4036	False		,,,				2504	0.5941				p.P1047P		Atlas-SNP	.											.	WDR87	191	.	0			c.G3141A						PASS	.	C		1012,372		371,270,51	122.0	109.0	113.0		3141	1.1	0.1	19	dbSNP_86	113	1247,1935		254,739,598	no	coding-synonymous	WDR87	NM_031951.3		625,1009,649	TT,TC,CC		39.1892,26.8786,49.4744		1047/2874	38382328	2259,2307	692	1591	2283	SO:0001819	synonymous_variant	83889	exon5			AAAAGCCGGCTTT	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.3141G>A	19.37:g.38382328C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	119	47	0.394958	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			C|0.366;T|0.634	0.634	strong		0.458	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786737	75786737	+	Missense_Mutation	SNP	A	A	T	rs78297221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75786737A>T	ENST00000478296.1	-	4	2163	c.1887T>A	c.(1885-1887)aaT>aaA	p.N629K	ZNF717_ENST00000400845.3_Missense_Mutation_p.N672K|ZNF717_ENST00000422325.1_Missense_Mutation_p.N679K|ZNF717_ENST00000477374.1_Intron|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	669					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						GTTTTTCCACATTCATTACAT	0.383																																					p.N679K		Atlas-SNP	.											ZNF717,colon,carcinoma,0,1	ZNF717	160	1	0			c.T2037A						PASS	.						13.0	13.0	13.0					3																	75786737		625	1547	2172	SO:0001583	missense	100131827	exon5			TTCCACATTCATT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1887T>A	3.37:g.75786737A>T	ENSP00000419377:p.Asn629Lys	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		1056	0.4835164835164835	176	0.35772357723577236	183	0.505524861878453	279	0.48776223776223776	418	0.5514511873350924	.	12.68	2.009160	0.35415	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.06142	3.34;3.5;3.5	1.57	1.57	0.23409	.	.	.	.	.	T	0.00012	0.0000	L	0.35341	1.055	0.35632	P	0.18974500000000005	P	0.35272	0.493	B	0.21360	0.034	T	0.30534	-0.9975	8	0.40728	T	0.16	.	7.274	0.26273	1.0:0.0:0.0:0.0	.	679	C9JSV9	.	K	629;679;672	ENSP00000419377:N629K;ENSP00000409514:N679K;ENSP00000383643:N672K	ENSP00000383643:N672K	N	-	3	2	ZNF717	75869427	1.000000	0.71417	0.018000	0.16275	0.015000	0.08874	6.119000	0.71590	1.007000	0.39238	0.445000	0.29226	AAT	A|0.517;T|0.483	0.483	strong		0.383	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
DNMBP	23268	hgsc.bcm.edu	37	10	101716112	101716112	+	Missense_Mutation	SNP	G	G	C	rs35924554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101716112G>C	ENST00000324109.4	-	4	1210	c.1119C>G	c.(1117-1119)aaC>aaG	p.N373K	DNMBP-AS1_ENST00000434409.1_RNA|DNMBP_ENST00000342239.3_Missense_Mutation_p.N373K	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	373			N -> K (in dbSNP:rs35924554).		intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		CCTGATAAGAGTTTCTGTCTG	0.557													G|||	248	0.0495208	0.0893	0.062	5008	,	,		18015	0.0288		0.0398	False		,,,				2504	0.0184				p.N373K		Atlas-SNP	.											.	DNMBP	173	.	0			c.C1119G						PASS	.		LYS/ASN	338,4068	176.6+/-205.7	9,320,1874	93.0	94.0	93.0		1119	-1.3	0.0	10	dbSNP_126	93	344,8256	117.4+/-177.0	5,334,3961	yes	missense	DNMBP	NM_015221.2	94	14,654,5835	CC,CG,GG		4.0,7.6714,5.2437	benign	373/1578	101716112	682,12324	2203	4300	6503	SO:0001583	missense	23268	exon4			ATAAGAGTTTCTG	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.1119C>G	10.37:g.101716112G>C	ENSP00000315659:p.Asn373Lys	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	116	0.05311355311355311	49	0.09959349593495935	21	0.058011049723756904	20	0.03496503496503497	26	0.03430079155672823	G	3.528	-0.096237	0.07010	0.076714	0.04	ENSG00000107554	ENST00000342239;ENST00000324109	T;T	0.11169	2.85;2.8	5.53	-1.33	0.09172	.	1.860880	0.02542	N	0.094741	T	0.00178	0.0005	N	0.19112	0.55	0.80722	P	0.0	B	0.20887	0.049	B	0.16722	0.016	T	0.27806	-1.0063	9	0.06494	T	0.89	2.8121	5.6267	0.17487	0.3019:0.2417:0.4563:0.0	rs35924554;rs61751506	373	Q6XZF7	DNMBP_HUMAN	K	373	ENSP00000344914:N373K;ENSP00000315659:N373K	ENSP00000315659:N373K	N	-	3	2	DNMBP	101706102	0.005000	0.15991	0.000000	0.03702	0.106000	0.19336	0.245000	0.18142	0.069000	0.16605	0.561000	0.74099	AAC	G|0.947;C|0.053	0.053	strong		0.557	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
TRPM8	79054	hgsc.bcm.edu	37	2	234863788	234863788	+	Missense_Mutation	SNP	G	G	A	rs7593557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234863788G>A	ENST00000324695.4	+	11	1296	c.1256G>A	c.(1255-1257)aGt>aAt	p.S419N	TRPM8_ENST00000433712.2_Missense_Mutation_p.S107N|AC005538.5_ENST00000455991.1_RNA	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	419			S -> N (in dbSNP:rs7593557).		calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.S419N(1)		breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	TTCAGCACCAGTGAGCAAGAC	0.488													A|||	1725	0.344449	0.6362	0.1571	5008	,	,		21237	0.4444		0.0527	False		,,,				2504	0.2802				p.S419N		Atlas-SNP	.											TRPM8,NS,carcinoma,0,1	TRPM8	146	1	1	Substitution - Missense(1)	stomach(1)	c.G1256A						PASS	.	A	ASN/SER	2336,2070	569.8+/-382.7	617,1102,484	89.0	86.0	87.0		1256	6.0	0.9	2	dbSNP_116	87	499,8101	797.0+/-407.5	14,471,3815	yes	missense	TRPM8	NM_024080.4	46	631,1573,4299	AA,AG,GG		5.8023,46.9814,21.7976	benign	419/1105	234863788	2835,10171	2203	4300	6503	SO:0001583	missense	79054	exon11			GCACCAGTGAGCA	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.1256G>A	2.37:g.234863788G>A	ENSP00000323926:p.Ser419Asn	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	145	83	0.572414	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	658	0.30128205128205127	298	0.6056910569105691	71	0.19613259668508287	247	0.4318181818181818	42	0.055408970976253295	A	13.05	2.121907	0.37436	0.530186	0.058023	ENSG00000144481	ENST00000324695;ENST00000433712	T;T	0.35789	1.29;1.29	5.99	5.99	0.97316	.	0.207539	0.42682	N	0.000679	T	0.00012	0.0000	N	0.15975	0.35	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37934	-0.9684	9	0.08599	T	0.76	-25.8811	11.2408	0.48968	0.9284:0.0:0.0716:0.0	rs7593557;rs52800345;rs59539312;rs7593557	107;419	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	N	419;107	ENSP00000323926:S419N;ENSP00000404423:S107N	ENSP00000323926:S419N	S	+	2	0	TRPM8	234528527	0.999000	0.42202	0.908000	0.35775	0.586000	0.36452	3.631000	0.54280	1.092000	0.41356	-0.254000	0.11334	AGT	G|0.732;A|0.268	0.268	strong		0.488	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
SH3BP2	6452	hgsc.bcm.edu	37	4	2826912	2826912	+	Silent	SNP	C	C	G	rs16843413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2826912C>G	ENST00000356331.5	+	5	678	c.417C>G	c.(415-417)ccC>ccG	p.P139P	SH3BP2_ENST00000452765.2_Silent_p.P139P|SH3BP2_ENST00000515183.1_3'UTR|SH3BP2_ENST00000442312.2_Silent_p.P167P|SH3BP2_ENST00000435136.2_Silent_p.P139P|SH3BP2_ENST00000503393.2_Silent_p.P196P|SH3BP2_ENST00000511747.1_Silent_p.P139P	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	139					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)		AAGACCTGCCCTTGGACACCA	0.697									Cherubism				c|||	735	0.146765	0.292	0.1499	5008	,	,		17726	0.0645		0.0616	False		,,,				2504	0.1207				p.P196P		Atlas-SNP	.											.	SH3BP2	43	.	0			c.C588G						PASS	.	C	,,,	1025,3359		137,751,1304	44.0	41.0	42.0		417,501,588,417	-3.1	0.1	4	dbSNP_123	42	516,8064		23,470,3797	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH3BP2	NM_001122681.1,NM_001145855.1,NM_001145856.1,NM_003023.4	,,,	160,1221,5101	GG,GC,CC		6.014,23.3805,11.8868	,,,	139/562,167/590,196/619,139/562	2826912	1541,11423	2192	4290	6482	SO:0001819	synonymous_variant	6452	exon5	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	CCTGCCCTTGGAC	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.417C>G	4.37:g.2826912C>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	148	62	0.418919	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Silent	SNP	ENST00000356331.5	37	CCDS33944.1																																																																																			C|0.875;G|0.125	0.125	strong		0.697	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023	
RIPK3	11035	hgsc.bcm.edu	37	14	24805463	24805463	+	Missense_Mutation	SNP	G	G	T	rs3212254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24805463G>T	ENST00000216274.5	-	10	1693	c.1475C>A	c.(1474-1476)cCa>cAa	p.P492Q	RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000396747.3_5'Flank|ADCY4_ENST00000310677.4_5'Flank|RP11-934B9.3_ENST00000555591.1_Intron|ADCY4_ENST00000418030.2_5'Flank|ADCY4_ENST00000554068.2_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	80	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	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	
BRD7	29117	hgsc.bcm.edu	37	16	50368671	50368671	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50368671C>G	ENST00000394688.3	-	7	997	c.838G>C	c.(838-840)Gga>Cga	p.G280R	BRD7_ENST00000394689.2_Missense_Mutation_p.G280R			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	280					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				TCGGCATCTCCAGAGTCCTCT	0.473																																					p.G280R		Atlas-SNP	.											.	BRD7	61	.	0			c.G838C						PASS	.						138.0	142.0	141.0					16																	50368671		2198	4300	6498	SO:0001583	missense	29117	exon7			CATCTCCAGAGTC	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"""bromodomain-containing 7"""			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.838G>C	16.37:g.50368671C>G	ENSP00000378180:p.Gly280Arg	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	194	58	0.298969	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	37	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	C	8.023	0.760146	0.15846	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.30981	1.51;1.51	5.47	3.42	0.39159	.	0.486780	0.23583	N	0.046637	T	0.18173	0.0436	L	0.29908	0.895	0.09310	N	1	B;P	0.35923	0.393;0.528	B;B	0.37943	0.133;0.261	T	0.10636	-1.0621	10	0.14252	T	0.57	-13.1079	5.4568	0.16594	0.1802:0.6543:0.0:0.1655	.	280;280	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	R	280	ENSP00000378180:G280R;ENSP00000378181:G280R	ENSP00000378180:G280R	G	-	1	0	BRD7	48926172	0.849000	0.29639	0.418000	0.26571	0.791000	0.44710	1.471000	0.35365	2.733000	0.93635	0.650000	0.86243	GGA	.	.	none		0.473	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263	
LRP1	4035	hgsc.bcm.edu	37	12	57578696	57578696	+	Silent	SNP	C	C	T	rs140921686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57578696C>T	ENST00000243077.3	+	39	6727	c.6261C>T	c.(6259-6261)cgC>cgT	p.R2087R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2087					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)	GTGAGAACCGCGAGGTGGTTC	0.542													C|||	18	0.00359425	0.0023	0.0	5008	,	,		21048	0.0149		0.0	False		,,,				2504	0.0				p.R2087R		Atlas-SNP	.											.	LRP1	428	.	0			c.C6261T						PASS	.	C		6,4400	11.4+/-27.6	0,6,2197	189.0	162.0	171.0		6261	-10.3	0.7	12	dbSNP_134	171	0,8600		0,0,4300	no	coding-synonymous	LRP1	NM_002332.2		0,6,6497	TT,TC,CC		0.0,0.1362,0.0461		2087/4545	57578696	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon39			GAACCGCGAGGTG	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.6261C>T	12.37:g.57578696C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	144	79	0.548611	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.999;T|0.001	0.001	strong		0.542	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
GLB1L2	89944	hgsc.bcm.edu	37	11	134244123	134244123	+	Silent	SNP	C	C	G	rs3741097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000339772.7_Silent_p.T560T|GLB1L2_ENST00000529077.1_3'UTR	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	172	0	0		WXS	Illumina HiSeq	Phase_I	173	84	0.485549	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	
DEPDC5	9681	hgsc.bcm.edu	37	22	32194581	32194581	+	Silent	SNP	A	A	G	rs16989495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32194581A>G	ENST00000382112.3	+	13	955	c.885A>G	c.(883-885)caA>caG	p.Q295Q	DEPDC5_ENST00000536766.1_Silent_p.Q267Q|DEPDC5_ENST00000382105.2_Silent_p.Q295Q|DEPDC5_ENST00000535622.1_Silent_p.Q295Q|DEPDC5_ENST00000400242.3_Silent_p.Q295Q|DEPDC5_ENST00000266091.3_Silent_p.Q295Q|DEPDC5_ENST00000400249.2_Silent_p.Q295Q|DEPDC5_ENST00000382111.2_Silent_p.Q295Q|DEPDC5_ENST00000400248.2_Silent_p.Q295Q|DEPDC5_ENST00000400246.1_Silent_p.Q295Q	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	295					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GCTTTCCTCAAGGAGATAATT	0.413													a|||	192	0.0383387	0.0242	0.0187	5008	,	,		4706	0.0218		0.0408	False		,,,				2504	0.0859				p.Q295Q		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A885G						PASS	.	A	,,,,	74,3622		0,74,1774	88.0	76.0	79.0		885,885,885,885,885	0.1	1.0	22	dbSNP_123	79	239,7987		3,233,3877	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DEPDC5	NM_001007188.2,NM_001136029.2,NM_001242896.1,NM_001242897.1,NM_014662.3	,,,,	3,307,5651	GG,GA,AA		2.9054,2.0022,2.6254	,,,,	295/560,295/1595,295/1604,295/1504,295/1573	32194581	313,11609	1848	4113	5961	SO:0001819	synonymous_variant	9681	exon14			TCCTCAAGGAGAT	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.885A>G	22.37:g.32194581A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_001242897	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Silent	SNP	ENST00000382112.3	37	CCDS46692.1																																																																																			A|0.965;G|0.035	0.035	strong		0.413	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
MUC4	4585	hgsc.bcm.edu	37	3	195515434	195515434	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515434G>A	ENST00000463781.3	-	2	3476	c.3017C>T	c.(3016-3018)gCc>gTc	p.A1006V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1006V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	430	Repeat.|Ser-rich.				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)		AAGAGGGGTGGCGTGACCTGT	0.582																																					p.A1006V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,4	MUC4	1505	4	0			c.C3017T						scavenged	.																																			SO:0001583	missense	4585	exon2			GGGGTGGCGTGAC	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.3017C>T	3.37:g.195515434G>A	ENSP00000417498:p.Ala1006Val	Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	580	21	0.0362069	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	9.241	1.038324	0.19669	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36520	1.26;1.25	1.24	1.24	0.21308	.	.	.	.	.	T	0.16642	0.0400	N	0.08118	0	0.09310	N	1	B	0.21381	0.055	B	0.12156	0.007	T	0.23476	-1.0187	8	.	.	.	.	8.5353	0.33360	0.0:0.0:1.0:0.0	.	1006	E7ESK3	.	V	1006	ENSP00000417498:A1006V;ENSP00000420243:A1006V	.	A	-	2	0	MUC4	196999829	.	.	0.002000	0.10522	0.173000	0.22820	.	.	1.018000	0.39521	0.064000	0.15345	GCC	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ARHGEF1	9138	hgsc.bcm.edu	37	19	42392310	42392310	+	Silent	SNP	C	C	T	rs2288509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42392310C>T	ENST00000354532.3	+	3	220	c.72C>T	c.(70-72)atC>atT	p.I24I	ARHGEF1_ENST00000378152.4_Silent_p.I39I|ARHGEF1_ENST00000337665.4_Silent_p.I39I|ARHGEF1_ENST00000347545.4_Silent_p.I24I|ARHGEF1_ENST00000599846.1_Silent_p.I24I|ARHGEF1_ENST00000596957.1_Intron	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1	24					cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I39I(1)		breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		TCAGCATCATCGGGGCTGAGG	0.637													c|||	1338	0.267173	0.6762	0.0663	5008	,	,		16808	0.2054		0.0139	False		,,,				2504	0.181				p.I39I		Atlas-SNP	.											ARHGEF1,colon,carcinoma,0,2	ARHGEF1	95	2	1	Substitution - coding silent(1)	stomach(1)	c.C117T						scavenged	.		,,	2464,1942	623.1+/-394.1	706,1052,445	131.0	146.0	141.0		72,72,117	-7.6	0.3	19	dbSNP_100	141	68,8532	39.8+/-96.3	0,68,4232	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF1	NM_004706.3,NM_198977.1,NM_199002.1	,,	706,1120,4677	TT,TC,CC		0.7907,44.0763,19.4679	,,	24/913,24/880,39/928	42392310	2532,10474	2203	4300	6503	SO:0001819	synonymous_variant	9138	exon3			CATCATCGGGGCT	U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"""Rho guanine nucleotide exchange factors"""	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.72C>T	19.37:g.42392310C>T		Somatic	60	1	0.0166667		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_199002	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Silent	SNP	ENST00000354532.3	37	CCDS12591.1																																																																																			C|0.782;T|0.218	0.218	strong		0.637	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002	
PLA2R1	22925	hgsc.bcm.edu	37	2	160901403	160901403	+	Silent	SNP	C	C	T	rs35005192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160901403C>T	ENST00000283243.7	-	2	581	c.375G>A	c.(373-375)ccG>ccA	p.P125P	PLA2R1_ENST00000392771.1_Silent_p.P125P	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	125	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						AGTACTGCAGCGGGCCTGTGA	0.502													C|||	27	0.00539137	0.0204	0.0	5008	,	,		17735	0.0		0.0	False		,,,				2504	0.0				p.P125P		Atlas-SNP	.											.	PLA2R1	153	.	0			c.G375A						PASS	.	C	,,	59,4347	56.8+/-93.2	0,59,2144	82.0	82.0	82.0		375,375,375	-12.1	0.0	2	dbSNP_126	82	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	,,	0,59,6444	TT,TC,CC		0.0,1.3391,0.4536	,,	125/1325,125/1462,125/1464	160901403	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	22925	exon2			CTGCAGCGGGCCT	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.375G>A	2.37:g.160901403C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	137	58	0.423358	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	37	CCDS33309.1																																																																																			C|0.994;T|0.006	0.006	strong		0.502	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
UTP18	51096	hgsc.bcm.edu	37	17	49350802	49350802	+	Silent	SNP	A	A	C	rs2318789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:49350802A>C	ENST00000225298.7	+	5	759	c.702A>C	c.(700-702)ggA>ggC	p.G234G		NM_016001.2	NP_057085.2	Q9Y5J1	UTP18_HUMAN	UTP18 small subunit (SSU) processome component homolog (yeast)	234					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			TTCCAAGAGGAATCTTGAAGG	0.398													A|||	2134	0.426118	0.1248	0.4424	5008	,	,		13944	0.6071		0.4791	False		,,,				2504	0.5808				p.G234G		Atlas-SNP	.											.	UTP18	28	.	0			c.A702C						PASS	.	A		655,3107		56,543,1282	131.0	123.0	125.0		702	0.6	1.0	17	dbSNP_100	125	3821,4393		903,2015,1189	no	coding-synonymous	UTP18	NM_016001.2		959,2558,2471	CC,CA,AA		46.5181,17.411,37.3747		234/557	49350802	4476,7500	1881	4107	5988	SO:0001819	synonymous_variant	51096	exon5			AAGAGGAATCTTG	AF151806	CCDS42362.1	17q21.33	2013-05-21	2011-12-09	2006-05-16	ENSG00000011260	ENSG00000011260		"""WD repeat domain containing"""	24274	protein-coding gene	gene with protein product		612816	"""WD repeat domain 50"""	WDR50		10810093, 8619474, 15590835	Standard	NM_016001		Approved	CGI-48	uc002its.3	Q9Y5J1	OTTHUMG00000162370	ENST00000225298.7:c.702A>C	17.37:g.49350802A>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_016001	Q9H4N6	Silent	SNP	ENST00000225298.7	37	CCDS42362.1																																																																																			A|0.569;C|0.431	0.431	strong		0.398	UTP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368654.1	NM_016001	
DCST1	149095	hgsc.bcm.edu	37	1	155006999	155006999	+	Silent	SNP	C	C	T	rs6680600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155006999C>T	ENST00000295542.1	+	3	246	c.150C>T	c.(148-150)ctC>ctT	p.L50L	DCST1_ENST00000368419.2_Silent_p.L50L|DCST1_ENST00000423025.2_Silent_p.L50L|DCST2_ENST00000368424.3_5'Flank|DCST2_ENST00000295536.5_5'Flank|DCST1_ENST00000392480.1_Silent_p.L50L	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	50						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			TCACTGCTCTCCTGCTGGGGG	0.652													C|||	2833	0.565695	0.4266	0.5922	5008	,	,		16607	0.8819		0.3579	False		,,,				2504	0.6227				p.L50L		Atlas-SNP	.											.	DCST1	69	.	0			c.C150T						PASS	.	C	,	1897,2509	533.7+/-373.8	383,1131,689	64.0	76.0	72.0		150,150	4.3	1.0	1	dbSNP_116	72	2962,5638	451.6+/-362.7	512,1938,1850	no	coding-synonymous,coding-synonymous	DCST1	NM_001143687.2,NM_152494.3	,	895,3069,2539	TT,TC,CC		34.4419,43.0549,37.3597	,	50/682,50/707	155006999	4859,8147	2203	4300	6503	SO:0001819	synonymous_variant	149095	exon3			TGCTCTCCTGCTG	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.150C>T	1.37:g.155006999C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Silent	SNP	ENST00000295542.1	37	CCDS1083.1																																																																																			C|0.550;T|0.450	0.450	strong		0.652	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494	
TRIM16	10626	hgsc.bcm.edu	37	17	15554561	15554561	+	Missense_Mutation	SNP	C	C	A	rs2074890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15554561C>A	ENST00000578237.1	-	6	1218	c.363G>T	c.(361-363)gaG>gaT	p.E121D	RP11-385D13.1_ENST00000455584.2_Missense_Mutation_p.E121D|RP11-640I15.1_ENST00000584540.1_RNA|TRIM16_ENST00000416464.2_Intron|TRIM16_ENST00000581224.1_Intron|TRIM16_ENST00000336708.7_Missense_Mutation_p.E121D			O95361	TRI16_HUMAN	tripartite motif containing 16	121			E -> D (in dbSNP:rs2074890).		histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)	p.E121D(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		CCTTCACTGGCTCGGTCAGCA	0.562													C|||	770	0.153754	0.323	0.0418	5008	,	,		22362	0.1508		0.0378	False		,,,				2504	0.1268				p.E121D		Atlas-SNP	.											TRIM16,NS,carcinoma,0,1	TRIM16	45	1	1	Substitution - Missense(1)	stomach(1)	c.G363T						PASS	.	C	ASP/GLU	1100,3306	397.2+/-330.3	141,818,1244	161.0	143.0	149.0		363	3.4	1.0	17	dbSNP_96	149	405,8195	127.5+/-185.8	13,379,3908	yes	missense	TRIM16	NM_006470.3	45	154,1197,5152	AA,AC,CC		4.7093,24.966,11.5716		121/565	15554561	1505,11501	2203	4300	6503	SO:0001583	missense	10626	exon4			CACTGGCTCGGTC	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"""Tripartite motif containing / Tripartite motif containing"""	17241	protein-coding gene	gene with protein product	"""estrogen-responsive B box protein"""	609505	"""tripartite motif-containing 16"""			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.363G>T	17.37:g.15554561C>A	ENSP00000463188:p.Glu121Asp	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	191	80	0.418848	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Missense_Mutation	SNP	ENST00000578237.1	37	CCDS11171.1	280|280	0.1282051282051282|0.1282051282051282	145|145	0.29471544715447157|0.29471544715447157	18|18	0.049723756906077346|0.049723756906077346	84|84	0.14685314685314685|0.14685314685314685	33|33	0.04353562005277045|0.04353562005277045	c|c	12.57|12.57	1.977817|1.977817	0.34942|0.34942	0.24966|0.24966	0.047093|0.047093	ENSG00000221926|ENSG00000251537	ENST00000336708|ENST00000455584	T|T	0.43688|0.48201	0.94|0.82	5.47|5.47	3.44|3.44	0.39384|0.39384	Zinc finger, B-box (1);|.	0.461817|.	0.23021|.	N|.	0.052847|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.35414|0.35414	1.06|1.06	0.38089|0.38089	P|P	0.06308800000000003|0.06308800000000003	B;P|.	0.49090|.	0.018;0.919|.	B;P|.	0.44447|.	0.009;0.45|.	T|T	0.31833|0.31833	-0.9929|-0.9929	9|5	0.02654|.	T|.	1|.	.|.	6.6454|6.6454	0.22933|0.22933	0.0:0.7009:0.1508:0.1483|0.0:0.7009:0.1508:0.1483	rs2074890;rs59821626;rs2074890|rs2074890;rs59821626;rs2074890	121;135|.	O95361;Q59EB2|.	TRI16_HUMAN;.|.	D|I	121|136	ENSP00000338989:E121D|ENSP00000402644:S136I	ENSP00000338989:E121D|.	E|S	-|-	3|2	2|0	TRIM16|RP11-385D13.1	15495286|15495286	0.999000|0.999000	0.42202|0.42202	0.974000|0.974000	0.42286|0.42286	0.810000|0.810000	0.45777|0.45777	0.495000|0.495000	0.22483|0.22483	0.650000|0.650000	0.30769|0.30769	0.563000|0.563000	0.77884|0.77884	GAG|AGC	C|0.869;A|0.131	0.131	strong		0.562	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	
TRIM31	11074	hgsc.bcm.edu	37	6	30080274	30080274	+	Silent	SNP	G	G	A	rs2517598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30080274G>A	ENST00000376734.3	-	2	434	c.309C>T	c.(307-309)caC>caT	p.H103H	TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000540829.1_Silent_p.H103H|TRIM31_ENST00000485864.1_5'Flank	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	103					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						CGCAGAAATAGTGGAACATCT	0.493													A|||	606	0.121006	0.093	0.1297	5008	,	,		21287	0.0873		0.1252	False		,,,				2504	0.183				p.H103H		Atlas-SNP	.											.	TRIM31	40	.	0			c.C309T						PASS	.	A		306,2716		16,274,1221	138.0	122.0	127.0		309	-3.8	0.0	6	dbSNP_100	127	785,4633		51,683,1975	no	coding-synonymous	TRIM31	NM_007028.3		67,957,3196	AA,AG,GG		14.4887,10.1257,12.9265		103/426	30080274	1091,7349	1511	2709	4220	SO:0001819	synonymous_variant	11074	exon2			GAAATAGTGGAAC	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.309C>T	6.37:g.30080274G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	135	59	0.437037	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			G|0.878;A|0.122	0.122	strong		0.493	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
DNM1L	10059	hgsc.bcm.edu	37	12	32860302	32860302	+	Splice_Site	SNP	G	G	A	rs2272238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:32860302G>A	ENST00000549701.1	+	3	326	c.252G>A	c.(250-252)ggG>ggA	p.G84G	DNM1L_ENST00000548671.1_3'UTR|DNM1L_ENST00000553257.1_Splice_Site_p.G97G|DNM1L_ENST00000266481.6_Splice_Site_p.G84G|Y_RNA_ENST00000364693.1_RNA|DNM1L_ENST00000381000.4_Splice_Site_p.G97G|DNM1L_ENST00000547312.1_Splice_Site_p.G84G|DNM1L_ENST00000358214.5_Splice_Site_p.G97G|DNM1L_ENST00000452533.2_Splice_Site_p.G84G|DNM1L_ENST00000414834.2_Splice_Site_p.G29E			O00429	DNM1L_HUMAN	dynamin 1-like	84	Dynamin-type G.|GTPase domain.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					TTTTTCCAGGGGTGGAAGCAG	0.284													G|||	721	0.14397	0.2103	0.1037	5008	,	,		14724	0.0833		0.164	False		,,,				2504	0.1247				p.G84G		Atlas-SNP	.											.	DNM1L	52	.	0			c.G252A						PASS	.	G	,,	861,3543	329.6+/-301.1	79,703,1420	89.0	92.0	91.0		252,252,252	-3.5	1.0	12	dbSNP_100	91	1251,7323	248.6+/-276.2	102,1047,3138	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	DNM1L	NM_005690.3,NM_012062.3,NM_012063.2	,,	181,1750,4558	AA,AG,GG		14.5906,19.5504,16.2737	,,	84/700,84/737,84/711	32860302	2112,10866	2202	4287	6489	SO:0001630	splice_region_variant	10059	exon3			TCCAGGGGTGGAA	AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.251-1G>A	12.37:g.32860302G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	167	167	1	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Silent	SNP	ENST00000549701.1	37	CCDS8729.1	306	0.1401098901098901	108	0.21951219512195122	37	0.10220994475138122	41	0.07167832167832168	120	0.158311345646438	G	15.65	2.895173	0.52121	0.195504	0.145906	ENSG00000087470	ENST00000414834	D	0.95447	-3.71	4.81	-3.54	0.04653	.	0.295993	0.19558	U	0.111387	T	0.00328	0.0010	.	.	.	0.44432	P	0.0026439999999999797	B	0.02656	0.0	B	0.01281	0.0	T	0.50617	-0.8807	8	0.87932	D	0	.	2.0606	0.03591	0.2703:0.219:0.3991:0.1115	rs2272238;rs2272238	29	B4DGC9	.	E	29	ENSP00000404160:G29E	ENSP00000404160:G29E	G	+	2	0	DNM1L	32751569	0.125000	0.22332	0.993000	0.49108	0.998000	0.95712	-0.519000	0.06260	-0.090000	0.12462	0.650000	0.86243	GGG	G|0.839;A|0.161	0.161	strong		0.284	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062	Silent
MYO3B	140469	hgsc.bcm.edu	37	2	171256771	171256771	+	Missense_Mutation	SNP	C	C	T	rs148136770|rs552913139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:171256771C>T	ENST00000408978.4	+	17	2008	c.1865C>T	c.(1864-1866)tCt>tTt	p.S622F	MYO3B_ENST00000409044.3_Missense_Mutation_p.S622F|MYO3B_ENST00000334231.6_Missense_Mutation_p.S631F|MYO3B_ENST00000602629.1_3'UTR	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	622	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						GCTATTTCCTCTCAACATCAG	0.408																																					p.S622F		Atlas-SNP	.											.	MYO3B	320	.	0			c.C1865T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER	5,3711		0,5,1853	199.0	181.0	187.0		1865,1865,1865	6.0	1.0	2	dbSNP_134	187	0,8214		0,0,4107	yes	missense,missense,missense	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	155,155,155	0,5,5960	TT,TC,CC		0.0,0.1346,0.0419	possibly-damaging,possibly-damaging,possibly-damaging	622/1315,622/1276,622/1342	171256771	5,11925	1858	4107	5965	SO:0001583	missense	140469	exon17			TTTCCTCTCAACA		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1865C>T	2.37:g.171256771C>T	ENSP00000386213:p.Ser622Phe	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	C	32	5.164240	0.94727	0.001346	0.0	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.79454	-1.27;-1.27;-1.25;-1.27	6.03	6.03	0.97812	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.89047	0.6604	M	0.86268	2.805	0.80722	D	1	D;P;P	0.58268	0.982;0.539;0.885	P;B;P	0.61132	0.884;0.281;0.688	D	0.89522	0.3779	10	0.87932	D	0	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	622;622;622	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	F	622;622;621;631;631	ENSP00000386497:S622F;ENSP00000386213:S622F;ENSP00000446237:S631F;ENSP00000335100:S631F	ENSP00000314213:S621F	S	+	2	0	MYO3B	170965017	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.818000	0.86416	2.861000	0.98227	0.655000	0.94253	TCT	C|0.999;T|0.001	0.001	strong		0.408	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
ZNF404	342908	hgsc.bcm.edu	37	19	44377991	44377991	+	Silent	SNP	G	G	A	rs78841585		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44377991G>A	ENST00000587539.1	-	3	374	c.375C>T	c.(373-375)aaC>aaT	p.N125N	ZNF404_ENST00000324394.6_Silent_p.N123N	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				TCTCTCTTGTGTTATTTCTCT	0.348																																					p.N122N		Atlas-SNP	.											.	ZNF404	46	.	0			c.C366T						PASS	.	G		821,2851		107,607,1122	119.0	135.0	130.0		375	-0.5	0.0	19	dbSNP_132	130	11,8193		0,11,4091	no	coding-synonymous	ZNF404	NM_001033719.2		107,618,5213	AA,AG,GG		0.1341,22.3584,7.0057		125/553	44377991	832,11044	1836	4102	5938	SO:0001819	synonymous_variant	342908	exon2			TCTTGTGTTATTT	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.375C>T	19.37:g.44377991G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	120	33	0.275	NM_001033719	A4FU30|K7ELF2	Silent	SNP	ENST00000587539.1	37	CCDS59394.1																																																																																			G|0.939;A|0.061	0.061	strong		0.348	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719	
C1orf64	149563	hgsc.bcm.edu	37	1	16330816	16330816	+	Silent	SNP	C	C	T	rs1763617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16330816C>T	ENST00000329454.2	+	1	86	c.18C>T	c.(16-18)gaC>gaT	p.D6D	RP11-5P18.5_ENST00000437156.1_RNA	NM_178840.2	NP_849162.1	Q8NEQ6	CA064_HUMAN	chromosome 1 open reading frame 64	6										breast(2)|endometrium(1)|lung(3)	6		Colorectal(325;0.000435)|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;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;2.08e-05)|BRCA - Breast invasive adenocarcinoma(304;9.19e-05)|Kidney(64;0.000165)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0114)|READ - Rectum adenocarcinoma(331;0.0649)		CGTCAGAAGACCCCAGGGACT	0.642													C|||	977	0.195088	0.1369	0.2089	5008	,	,		15718	0.2917		0.1581	False		,,,				2504	0.2025				p.D6D		Atlas-SNP	.											.	C1orf64	16	.	0			c.C18T						PASS	.	C		662,3732		51,560,1586	39.0	37.0	37.0		18	2.0	0.0	1	dbSNP_89	37	1253,7331		89,1075,3128	no	coding-synonymous	C1orf64	NM_178840.2		140,1635,4714	TT,TC,CC		14.5969,15.066,14.7557		6/170	16330816	1915,11063	2197	4292	6489	SO:0001819	synonymous_variant	149563	exon1			AGAAGACCCCAGG	AK127425	CCDS166.1	1p36.13	2013-10-11			ENSG00000183888	ENSG00000183888			28339	protein-coding gene	gene with protein product	"""ER-related factor"""					22341523	Standard	NM_178840		Approved	MGC24047, ERRF	uc001axn.3	Q8NEQ6	OTTHUMG00000009523	ENST00000329454.2:c.18C>T	1.37:g.16330816C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	233	116	0.497854	NM_178840	B3KXI9	Silent	SNP	ENST00000329454.2	37	CCDS166.1																																																																																			C|0.835;T|0.165	0.165	strong		0.642	C1orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026317.1	NM_178840	
SLC52A3	113278	hgsc.bcm.edu	37	20	744510	744510	+	Silent	SNP	G	G	A	rs3746806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:744510G>A	ENST00000217254.7	-	3	946	c.705C>T	c.(703-705)ctC>ctT	p.L235L	SLC52A3_ENST00000381944.3_Silent_p.L235L|SLC52A3_ENST00000473664.1_Intron	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	235					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)										AGAACGCCACGAGGCAGCAGG	0.622																																					p.L235L		Atlas-SNP	.											C20orf54,colon,carcinoma,-2,1	.	.	1	0			c.C705T						PASS	.	G		140,4266	98.9+/-137.6	3,134,2066	80.0	72.0	75.0		705	0.5	0.0	20	dbSNP_107	75	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	C20orf54	NM_033409.3		3,137,6363	AA,AG,GG		0.0349,3.1775,1.0995		235/470	744510	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon3			CGCCACGAGGCAG	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.705C>T	20.37:g.744510G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			A|0.009;C|0.000;G|0.991	0.009	strong		0.622	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
AMOT	154796	hgsc.bcm.edu	37	X	112022687	112022687	+	Missense_Mutation	SNP	T	T	C	rs147791527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:112022687T>C	ENST00000524145.1	-	11	2769	c.2695A>G	c.(2695-2697)Act>Gct	p.T899A	AMOT_ENST00000371962.1_Missense_Mutation_p.T667A|AMOT_ENST00000304758.1_Missense_Mutation_p.T490A|AMOT_ENST00000371959.3_Missense_Mutation_p.T899A|MIR4329_ENST00000582643.1_RNA			Q4VCS5	AMOT_HUMAN	angiomotin	899					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						gtggcagcagtggcagtgatg	0.607													T|||	32	0.00847682	0.0242	0.0	3775	,	,		10806	0.0		0.0	False		,,,				2504	0.0				p.T899A		Atlas-SNP	.											.	AMOT	204	.	0			c.A2695G						PASS	.	T	ALA/THR,ALA/THR	65,3719		0,54,11,1560,545	47.0	27.0	34.0		1468,2695	-1.9	0.0	X	dbSNP_134	34	0,6636		0,0,0,2405,1826	yes	missense,missense	AMOT	NM_133265.2,NM_001113490.1	58,58	0,54,11,3965,2371	CC,CT,C,TT,T		0.0,1.7178,0.6238	benign,benign	490/676,899/1085	112022687	65,10355	2170	4231	6401	SO:0001583	missense	154796	exon10			CAGCAGTGGCAGT	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.2695A>G	X.37:g.112022687T>C	ENSP00000429013:p.Thr899Ala	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	116	82	0.706897	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	14	0.008438818565400843	10	0.02066115702479339	0	0.0	0	0.0	0	0.0	T	7.595	0.671638	0.14776	0.017178	0.0	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145;ENST00000432214	T;T;T;T	0.39592	1.07;2.17;2.41;2.17	5.08	-1.92	0.07618	.	0.574197	0.15760	N	0.245998	T	0.10637	0.0260	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16897	-1.0387	10	0.08599	T	0.76	0.0865	1.9616	0.03387	0.1442:0.3726:0.1459:0.3373	.	899	Q4VCS5	AMOT_HUMAN	A	490;899;667;899;139	ENSP00000305557:T490A;ENSP00000361027:T899A;ENSP00000361030:T667A;ENSP00000429013:T899A	ENSP00000305557:T490A	T	-	1	0	AMOT	111909343	0.990000	0.36364	0.019000	0.16419	0.904000	0.53231	1.464000	0.35288	-0.085000	0.12573	0.430000	0.28490	ACT	T|0.990;C|0.010	0.010	strong		0.607	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265	
PDZRN4	29951	hgsc.bcm.edu	37	12	41900463	41900463	+	Missense_Mutation	SNP	G	G	A	rs35577124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:41900463G>A	ENST00000402685.2	+	4	1057	c.1049G>A	c.(1048-1050)cGt>cAt	p.R350H	PDZRN4_ENST00000298919.7_Missense_Mutation_p.R90H|PDZRN4_ENST00000539469.2_Missense_Mutation_p.R92H	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	350							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				GCCAAGCTTCGTCCACCTACC	0.493													G|||	586	0.117013	0.2269	0.1383	5008	,	,		20154	0.1736		0.001	False		,,,				2504	0.0143				p.R350H		Atlas-SNP	.											PDZRN4_ENST00000402685,NS,malignant_melanoma,+1,2	PDZRN4	346	2	0			c.G1049A						scavenged	.	G	HIS/ARG,HIS/ARG	846,3560	333.6+/-303.0	87,672,1444	163.0	136.0	145.0		1049,275	2.2	0.2	12	dbSNP_126	145	12,8588	7.1+/-27.0	0,12,4288	yes	missense,missense	PDZRN4	NM_001164595.1,NM_013377.3	29,29	87,684,5732	AA,AG,GG		0.1395,19.2011,6.597	possibly-damaging,possibly-damaging	350/1037,92/779	41900463	858,12148	2203	4300	6503	SO:0001583	missense	29951	exon4			AGCTTCGTCCACC	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1049G>A	12.37:g.41900463G>A	ENSP00000384197:p.Arg350His	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	151	62	0.410596	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	37	CCDS53777.1	240	0.10989010989010989	111	0.22560975609756098	46	0.1270718232044199	83	0.1451048951048951	0	0.0	G	13.23	2.176068	0.38413	0.192011	0.001395	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.73363	-0.74;3.74;3.74	5.08	2.18	0.27775	.	1.544220	0.05000	N	0.468870	T	0.00178	0.0005	M	0.73598	2.24	0.22954	P	0.99851589	D;P;P	0.89917	1.0;0.945;0.872	D;B;B	0.79784	0.993;0.301;0.396	T	0.06661	-1.0814	9	0.66056	D	0.02	-25.004	10.4928	0.44760	0.2219:0.0:0.7781:0.0	rs35577124	350;90;92	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	H	350;92;90	ENSP00000384197:R350H;ENSP00000439990:R92H;ENSP00000298919:R90H	ENSP00000298919:R90H	R	+	2	0	PDZRN4	40186730	0.997000	0.39634	0.156000	0.22583	0.421000	0.31385	4.856000	0.62932	0.360000	0.24265	-0.986000	0.02555	CGT	G|0.921;A|0.079	0.079	strong		0.493	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
CCDC37	348807	hgsc.bcm.edu	37	3	126142189	126142189	+	Silent	SNP	C	C	A	rs78360289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126142189C>A	ENST00000352312.1	+	12	1203	c.1104C>A	c.(1102-1104)ccC>ccA	p.P368P	CCDC37_ENST00000505024.1_Silent_p.P369P|CCDC37_ENST00000393425.1_Silent_p.P369P	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	368										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		CCATCCCCCCCACGCAGGAGG	0.662																																					p.P368P		Atlas-SNP	.											.	CCDC37	69	.	0			c.C1104A						PASS	.						41.0	36.0	38.0					3																	126142189		2203	4300	6503	SO:0001819	synonymous_variant	348807	exon12			CCCCCCCACGCAG	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1104C>A	3.37:g.126142189C>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	148	79	0.533784	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																			C|0.992;T|0.008	.	alt		0.662	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
CALML3	810	hgsc.bcm.edu	37	10	5567366	5567366	+	Silent	SNP	G	G	A	rs1142825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5567366G>A	ENST00000315238.1	+	1	443	c.318G>A	c.(316-318)ctG>ctA	p.L106L	CALML3-AS1_ENST00000543008.1_RNA|RP11-116G8.5_ENST00000442008.2_RNA|CALML3-AS1_ENST00000545372.1_RNA|CALML3-AS1_ENST00000542093.1_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	54	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	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	
CALHM1	255022	hgsc.bcm.edu	37	10	105215071	105215071	+	Missense_Mutation	SNP	C	C	T	rs114015468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105215071C>T	ENST00000329905.5	-	2	1125	c.989G>A	c.(988-990)gGt>gAt	p.G330D	CALHM2_ENST00000260743.5_5'Flank|CALHM2_ENST00000369788.3_5'Flank|RP11-225H22.4_ENST00000411906.1_RNA|CALHM2_ENST00000393235.1_5'Flank	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	330					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						CCGGGGCCCACCCCCAGCCCA	0.662													C|||	63	0.0125799	0.0477	0.0	5008	,	,		17190	0.0		0.0	False		,,,				2504	0.0				p.G330D		Atlas-SNP	.											.	CALHM1	33	.	0			c.G989A						PASS	.	C	ASP/GLY	151,4255	95.7+/-134.4	1,149,2053	30.0	27.0	28.0		989	1.8	0.0	10	dbSNP_132	28	1,8599	2.2+/-6.3	0,1,4299	yes	missense	CALHM1	NM_001001412.3	94	1,150,6352	TT,TC,CC		0.0116,3.4271,1.1687	benign	330/347	105215071	152,12854	2203	4300	6503	SO:0001583	missense	255022	exon2			GGCCCACCCCCAG	BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"""family with sequence similarity 26, member C"""	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.989G>A	10.37:g.105215071C>T	ENSP00000329926:p.Gly330Asp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	123	75	0.609756	NM_001001412	Q5W091	Missense_Mutation	SNP	ENST00000329905.5	37	CCDS7550.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	0.028	-1.354143	0.01256	0.034271	1.16E-4	ENSG00000185933	ENST00000329905	T	0.17054	2.3	4.8	1.83	0.25207	.	1.229190	0.05379	N	0.536826	T	0.01661	0.0053	N	0.08118	0	0.09310	N	1	B	0.22414	0.069	B	0.18561	0.022	T	0.36625	-0.9740	10	0.13108	T	0.6	-4.9354	5.3984	0.16283	0.0:0.5539:0.146:0.3001	.	330	Q8IU99	CAHM1_HUMAN	D	330	ENSP00000329926:G330D	ENSP00000329926:G330D	G	-	2	0	CALHM1	105205061	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.057000	0.11768	0.169000	0.19679	-0.379000	0.06801	GGT	C|0.988;T|0.012	0.012	strong		0.662	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412	
MC1R	4157	hgsc.bcm.edu	37	16	89985984	89985984	+	Silent	SNP	G	G	A	rs3212364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89985984G>A	ENST00000555147.1	+	1	1698	c.318G>A	c.(316-318)ctG>ctA	p.L106L	RP11-566K11.4_ENST00000554623.1_RNA|RP11-566K11.7_ENST00000570217.1_RNA|TUBB3_ENST00000556922.1_Silent_p.L106L|MC1R_ENST00000555427.1_Silent_p.L106L|TUBB3_ENST00000554444.1_5'Flank	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	106					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)		CCGGTGCACTGGTGGCCCGGG	0.647									Melanoma, Familial Clustering of				G|||	56	0.0111821	0.0401	0.0043	5008	,	,		18870	0.0		0.0	False		,,,				2504	0.0				p.L106L		Atlas-SNP	.											.	MC1R	20	.	0			c.G318A						PASS	.	G		179,4203		4,171,2016	42.0	51.0	48.0		318	4.8	0.2	16	dbSNP_106	48	2,8582		0,2,4290	no	coding-synonymous	MC1R	NM_002386.3		4,173,6306	AA,AG,GG		0.0233,4.0849,1.396		106/318	89985984	181,12785	2191	4292	6483	SO:0001819	synonymous_variant	4157	exon1	Familial Cancer Database		TGCACTGGTGGCC		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.318G>A	16.37:g.89985984G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Silent	SNP	ENST00000555147.1	37	CCDS56011.1																																																																																			G|0.991;A|0.009	0.009	strong		0.647	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71360282	71360282	+	Missense_Mutation	SNP	G	G	A	rs13010513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71360282G>A	ENST00000244230.2	+	2	696	c.344G>A	c.(343-345)cGt>cAt	p.R115H	MPHOSPH10_ENST00000498451.2_Missense_Mutation_p.R115H|MCEE_ENST00000244217.5_5'Flank|MPHOSPH10_ENST00000468427.1_3'UTR	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	115			R -> H (in dbSNP:rs13010513).		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						GAACAGGAACGTGAAGAGGAT	0.403													G|||	957	0.191094	0.1891	0.1729	5008	,	,		19641	0.2282		0.1342	False		,,,				2504	0.227				p.R115H		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.G344A						PASS	.	G	HIS/ARG	862,3544	335.2+/-303.8	83,696,1424	71.0	69.0	70.0		344	2.8	0.0	2	dbSNP_121	70	1450,7150	276.9+/-292.6	121,1208,2971	yes	missense	MPHOSPH10	NM_005791.2	29	204,1904,4395	AA,AG,GG		16.8605,19.5642,17.7764	benign	115/682	71360282	2312,10694	2203	4300	6503	SO:0001583	missense	10199	exon2			AGGAACGTGAAGA	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.344G>A	2.37:g.71360282G>A	ENSP00000244230:p.Arg115His	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	167	79	0.473054	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	365	0.1671245421245421	95	0.19308943089430894	61	0.1685082872928177	103	0.18006993006993008	106	0.13984168865435356	G	5.476	0.272902	0.10349	0.195642	0.168605	ENSG00000124383	ENST00000244230	T	0.10288	2.89	4.61	2.81	0.32909	.	0.722586	0.14295	N	0.328668	T	0.00012	0.0000	N	0.14661	0.345	0.29172	P	0.877071	P;P	0.40250	0.709;0.455	B;B	0.28638	0.092;0.083	T	0.47302	-0.9128	9	0.45353	T	0.12	.	5.0267	0.14389	0.1887:0.1724:0.6389:0.0	rs13010513;rs52815322;rs13010513	115;115	B3KPV5;O00566	.;MPP10_HUMAN	H	115	ENSP00000244230:R115H	ENSP00000244230:R115H	R	+	2	0	MPHOSPH10	71213790	0.137000	0.22531	0.003000	0.11579	0.632000	0.37999	0.394000	0.20834	0.696000	0.31696	-0.228000	0.12330	CGT	G|0.825;A|0.175	0.175	strong		0.403	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
C1orf158	93190	hgsc.bcm.edu	37	1	12819401	12819401	+	Silent	SNP	G	G	A	rs115263357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12819401G>A	ENST00000288048.5	+	3	600	c.384G>A	c.(382-384)aaG>aaA	p.K128K	C1orf158_ENST00000376210.3_Silent_p.K90K	NM_152290.2	NP_689503.2	Q8N1D5	CA158_HUMAN	chromosome 1 open reading frame 158	128										central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|ovary(1)|skin(2)|urinary_tract(3)	10	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;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCAGAGAAGTCTGACTTTC	0.522													G|||	33	0.00658946	0.0227	0.0043	5008	,	,		20187	0.0		0.0	False		,,,				2504	0.0				p.K128K		Atlas-SNP	.											.	C1orf158	28	.	0			c.G384A						PASS	.	G		78,4328		0,78,2125	86.0	88.0	87.0		384	1.4	0.3	1	dbSNP_132	87	0,8600		0,0,4300	no	coding-synonymous	C1orf158	NM_152290.2		0,78,6425	AA,AG,GG		0.0,1.7703,0.5997		128/195	12819401	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	93190	exon3			AGAGAAGTCTGAC	BX647383	CCDS147.1	1p36.21	2008-02-05			ENSG00000157330	ENSG00000157330			28567	protein-coding gene	gene with protein product						12477932	Standard	NM_152290		Approved	MGC35194	uc001auh.3	Q8N1D5	OTTHUMG00000001888	ENST00000288048.5:c.384G>A	1.37:g.12819401G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_152290	Q5VUY4	Silent	SNP	ENST00000288048.5	37	CCDS147.1																																																																																			G|0.993;A|0.007	0.007	strong		0.522	C1orf158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005325.1	NM_152290	
DCTN1	1639	hgsc.bcm.edu	37	2	74596321	74596321	+	Silent	SNP	T	T	C	rs13429423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74596321T>C	ENST00000361874.3	-	15	1922	c.1605A>G	c.(1603-1605)acA>acG	p.T535T	DCTN1_ENST00000409240.1_Silent_p.T498T|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409567.3_Silent_p.T515T|DCTN1_ENST00000409438.1_Silent_p.T401T|DCTN1_ENST00000409868.1_Silent_p.T518T|DCTN1_ENST00000394003.3_Silent_p.T528T|DCTN1_ENST00000407639.2_Silent_p.T401T	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	535					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						CCTGCTGGTTTGTCAGTTCCC	0.532													T|||	222	0.0443291	0.1611	0.013	5008	,	,		20259	0.0		0.0	False		,,,				2504	0.0				p.T535T		Atlas-SNP	.											.	DCTN1	110	.	0			c.A1605G						PASS	.	T	,,,,,	590,3816	259.5+/-263.1	37,516,1650	137.0	126.0	130.0		1545,1203,1494,1584,1605,1203	-3.8	1.0	2	dbSNP_121	130	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	,,,,,	37,522,5944	CC,CT,TT		0.0698,13.3908,4.5825	,,,,,	515/1254,401/1140,498/1237,528/1272,535/1279,401/1145	74596321	596,12410	2203	4300	6503	SO:0001819	synonymous_variant	1639	exon15			CTGGTTTGTCAGT		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.1605A>G	2.37:g.74596321T>C		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	305	151	0.495082	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	37	CCDS1939.1																																																																																			T|0.956;C|0.044	0.044	strong		0.532	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
MMAA	166785	hgsc.bcm.edu	37	4	146576418	146576418	+	Missense_Mutation	SNP	G	G	C	rs2270655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:146576418G>C	ENST00000281317.5	+	7	2299	c.1089G>C	c.(1087-1089)caG>caC	p.Q363H	MMAA_ENST00000541599.1_Missense_Mutation_p.Q82H	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	363			Q -> H (in dbSNP:rs2270655). {ECO:0000269|PubMed:15523652}.		cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GGAAGCAACAGAAAGTTTGGA	0.478													G|||	405	0.0808706	0.0477	0.0605	5008	,	,		15287	0.0942		0.0447	False		,,,				2504	0.1636				p.Q363H		Atlas-SNP	.											.	MMAA	46	.	0			c.G1089C	GRCh37	CD043682	MMAA	D	rs2270655	PASS	.	G	HIS/GLN	202,4204	128.2+/-165.1	9,184,2010	106.0	107.0	107.0		1089	4.8	1.0	4	dbSNP_100	107	461,8139	137.8+/-194.7	8,445,3847	yes	missense	MMAA	NM_172250.2	24	17,629,5857	CC,CG,GG		5.3605,4.5847,5.0976	benign	363/419	146576418	663,12343	2203	4300	6503	SO:0001583	missense	166785	exon7			GCAACAGAAAGTT	AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"""methylmalonic aciduria (cobalamin deficiency) type A"""			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.1089G>C	4.37:g.146576418G>C	ENSP00000281317:p.Gln363His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	NM_172250	B3KX40|Q495G7	Missense_Mutation	SNP	ENST00000281317.5	37	CCDS3766.1	132	0.06043956043956044	22	0.044715447154471545	21	0.058011049723756904	55	0.09615384615384616	34	0.044854881266490766	G	13.49	2.252058	0.39797	0.045847	0.053605	ENSG00000151611	ENST00000281317;ENST00000537246;ENST00000541599	D;D	0.91351	-2.83;-2.83	5.69	4.84	0.62591	.	0.152974	0.64402	N	0.000013	T	0.15912	0.0383	L	0.35793	1.09	0.22050	P	0.999397658	B	0.06786	0.001	B	0.09377	0.004	T	0.65664	-0.6113	9	0.38643	T	0.18	-3.2926	9.8119	0.40828	0.0732:0.1462:0.7807:0.0	rs2270655;rs52810156;rs2270655	363	Q8IVH4	MMAA_HUMAN	H	363;363;82	ENSP00000281317:Q363H;ENSP00000442284:Q82H	ENSP00000281317:Q363H	Q	+	3	2	MMAA	146795868	1.000000	0.71417	0.999000	0.59377	0.810000	0.45777	3.159000	0.50731	1.380000	0.46344	0.561000	0.74099	CAG	G|0.944;C|0.056	0.056	strong		0.478	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2		
ZNF566	84924	hgsc.bcm.edu	37	19	36940675	36940675	+	Missense_Mutation	SNP	T	T	C	rs35217571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36940675T>C	ENST00000434377.2	-	5	542	c.461A>G	c.(460-462)cAc>cGc	p.H154R	ZNF566_ENST00000454319.1_Missense_Mutation_p.H155R|ZNF566_ENST00000493391.1_Missense_Mutation_p.H50R|ZNF566_ENST00000424129.2_Missense_Mutation_p.H154R|ZNF566_ENST00000392170.2_Missense_Mutation_p.H155R	NM_032838.4	NP_116227.1	Q969W8	ZN566_HUMAN	zinc finger protein 566	154					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24	Esophageal squamous(110;0.162)					GGATGGATGGTGACTCAAAGT	0.393													T|||	78	0.0155751	0.0575	0.0029	5008	,	,		19069	0.0		0.0	False		,,,				2504	0.0				p.H155R		Atlas-SNP	.											.	ZNF566	40	.	0			c.A464G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	208,4198	129.0+/-165.8	6,196,2001	146.0	145.0	145.0		464,461,461,461	2.8	0.6	19	dbSNP_126	145	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense,missense	ZNF566	NM_001145343.1,NM_001145344.1,NM_001145345.1,NM_032838.4	29,29,29,29	6,203,6294	CC,CT,TT		0.0814,4.7208,1.6531	benign,benign,benign,benign	155/420,154/419,154/419,154/419	36940675	215,12791	2203	4300	6503	SO:0001583	missense	84924	exon5			GGATGGTGACTCA	AK074497	CCDS12494.1, CCDS46061.1, CCDS74346.1	19q13.12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	25919	protein-coding gene	gene with protein product						12477932	Standard	NM_001145343		Approved	FLJ14779, MGC12515	uc010xtf.2	Q969W8		ENST00000434377.2:c.461A>G	19.37:g.36940675T>C	ENSP00000415520:p.His154Arg	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	159	89	0.559748	NM_001145343	B7ZL95|Q2M3J1	Missense_Mutation	SNP	ENST00000434377.2	37	CCDS12494.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	T	0.347	-0.946931	0.02304	0.047208	8.14E-4	ENSG00000186017	ENST00000454319;ENST00000434377;ENST00000392170;ENST00000424129;ENST00000452939;ENST00000427002	T;T;T;T;T;T	0.04862	3.66;3.65;3.66;3.65;3.54;6.16	3.77	2.76	0.32466	.	0.718904	0.12064	N	0.502915	T	0.00637	0.0021	L	0.28054	0.825	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46582	-0.9181	10	0.20046	T	0.44	.	3.8345	0.08888	0.0:0.1142:0.2214:0.6644	rs35217571	155;154	B7ZL95;Q969W8	.;ZN566_HUMAN	R	155;154;155;154;154;155	ENSP00000394207:H155R;ENSP00000415520:H154R;ENSP00000376010:H155R;ENSP00000401259:H154R;ENSP00000411526:H154R;ENSP00000400651:H155R	ENSP00000376010:H155R	H	-	2	0	ZNF566	41632515	0.045000	0.20229	0.589000	0.28718	0.313000	0.28021	0.622000	0.24433	0.836000	0.34901	0.454000	0.30748	CAC	T|0.986;C|0.014	0.014	strong		0.393	ZNF566-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000341054.1	NM_032838	
PCNX	22990	hgsc.bcm.edu	37	14	71514668	71514668	+	Missense_Mutation	SNP	G	G	C	rs78161372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:71514668G>C	ENST00000304743.2	+	22	4751	c.4305G>C	c.(4303-4305)ttG>ttC	p.L1435F	PCNX_ENST00000238570.5_Missense_Mutation_p.L1435F|PCNX_ENST00000439984.3_Missense_Mutation_p.L1324F	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1435						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)		CCATGCTGTTGGATCTCTTCT	0.358													G|||	26	0.00519169	0.0174	0.0043	5008	,	,		15956	0.0		0.0	False		,,,				2504	0.0				p.L1435F		Atlas-SNP	.											.	PCNX	198	.	0			c.G4305C						PASS	.	G	PHE/LEU	62,4342	59.3+/-96.0	0,62,2140	129.0	120.0	123.0		4305	3.2	1.0	14	dbSNP_132	123	0,8598		0,0,4299	yes	missense	PCNX	NM_014982.2	22	0,62,6439	CC,CG,GG		0.0,1.4078,0.4768	possibly-damaging	1435/2342	71514668	62,12940	2202	4299	6501	SO:0001583	missense	22990	exon22			GCTGTTGGATCTC	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.4305G>C	14.37:g.71514668G>C	ENSP00000304192:p.Leu1435Phe	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	226	102	0.451327	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	7|7	0.003205128205128205|0.003205128205128205	6|6	0.012195121951219513|0.012195121951219513	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	14.02|14.02	2.412251|2.412251	0.42817|0.42817	0.014078|0.014078	0.0|0.0	ENSG00000100731|ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984|ENST00000554691	T;T;T|.	0.12147|.	3.14;3.11;2.71|.	5.41|5.41	3.19|3.19	0.36642|0.36642	.|.	0.212294|.	0.41001|.	D|.	0.000979|.	T|T	0.40619|0.40619	0.1124|0.1124	L|L	0.53249|0.53249	1.67|1.67	0.47819|0.47819	D|D	0.999528|0.999528	P;P;P|.	0.50272|.	0.879;0.609;0.933|.	P;B;B|.	0.47573|.	0.55;0.235;0.441|.	T|T	0.45041|0.45041	-0.9288|-0.9288	10|5	0.02654|.	T|.	1|.	.|.	2.1506|2.1506	0.03798|0.03798	0.3175:0.0:0.433:0.2494|0.3175:0.0:0.433:0.2494	.|.	1435;1324;1435|.	Q96RV3-3;B2RTR6;Q96RV3|.	.;.;PCX1_HUMAN|.	F|S	1435;1435;1324|494	ENSP00000304192:L1435F;ENSP00000238570:L1435F;ENSP00000396617:L1324F|.	ENSP00000238570:L1435F|.	L|W	+|+	3|2	2|0	PCNX|PCNX	70584421|70584421	0.927000|0.927000	0.31430|0.31430	0.978000|0.978000	0.43139|0.43139	0.996000|0.996000	0.88848|0.88848	0.071000|0.071000	0.14594|0.14594	1.412000|1.412000	0.46977|0.46977	0.655000|0.655000	0.94253|0.94253	TTG|TGG	G|0.995;C|0.005	0.005	strong		0.358	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
OR2T3	343173	hgsc.bcm.edu	37	1	248636934	248636934	+	Missense_Mutation	SNP	G	G	T	rs148766825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248636934G>T	ENST00000359594.2	+	1	308	c.283G>T	c.(283-285)Gat>Tat	p.D95Y		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	95						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACTGGAGATGATACCATTTC	0.552													.|||	287	0.0573083	0.2065	0.0173	5008	,	,		20624	0.0		0.001	False		,,,				2504	0.001				p.D95Y		Atlas-SNP	.											.	OR2T3	79	.	0			c.G283T						PASS	.	T	TYR/ASP	740,3640	744.5+/-411.6	104,532,1554	59.0	51.0	54.0		283	-3.5	0.0	1	dbSNP_134	54	11,8581	817.4+/-406.9	0,11,4285	no	missense	OR2T3	NM_001005495.1	160	104,543,5839	TT,TG,GG		0.128,16.895,5.7894	benign	95/319	248636934	751,12221	2190	4296	6486	SO:0001583	missense	343173	exon1			GGAGATGATACCA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.283G>T	1.37:g.248636934G>T	ENSP00000352604:p.Asp95Tyr	Somatic	635	2	0.00314961		WXS	Illumina HiSeq	Phase_I	441	278	0.630385	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	101	0.04624542124542125	96	0.1951219512195122	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	t	5.919	0.353667	0.11182	0.16895	0.00128	ENSG00000196539	ENST00000359594	T	0.36340	1.26	2.65	-3.45	0.04781	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22034	-1.0228	9	0.72032	D	0.01	.	1.1933	0.01869	0.4366:0.2119:0.224:0.1274	.	95	Q8NH03	OR2T3_HUMAN	Y	95	ENSP00000352604:D95Y	ENSP00000352604:D95Y	D	+	1	0	OR2T3	246703557	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.501000	0.22578	-2.758000	0.00371	-3.175000	0.00056	GAT	G|1.000;|0.000	.	weak		0.552	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
GGT1	2678	hgsc.bcm.edu	37	22	25010746	25010746	+	Silent	SNP	T	T	C	rs4049881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25010746T>C	ENST00000400382.1	+	6	923	c.168T>C	c.(166-168)gaT>gaC	p.D56D	GGT1_ENST00000400380.1_Silent_p.D56D|GGT1_ENST00000400383.1_Silent_p.D56D|GGT1_ENST00000406383.2_Silent_p.D56D|GGT1_ENST00000248923.4_Silent_p.D56D			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	56					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	ATGGCAGGGATGCACTGCGGG	0.622													t|||	343	0.0684904	0.2209	0.0231	5008	,	,		14046	0.003		0.002	False		,,,				2504	0.0307				p.D56D		Atlas-SNP	.											.	GGT1	68	.	0			c.T168C						PASS	.	C	,,,	589,3461		50,489,1486	41.0	46.0	45.0		168,168,168,168	-7.5	0.0	22	dbSNP_108	45	5,8363		0,5,4179	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GGT1	NM_001032364.2,NM_001032365.2,NM_005265.2,NM_013430.2	,,,	50,494,5665	CC,CT,TT		0.0598,14.5432,4.7834	,,,	56/570,56/570,56/570,56/570	25010746	594,11824	2025	4184	6209	SO:0001819	synonymous_variant	2678	exon6			CAGGGATGCACTG	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.168T>C	22.37:g.25010746T>C		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	269	127	0.472119	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Silent	SNP	ENST00000400382.1	37	CCDS42992.1																																																																																			T|0.970;C|0.030	0.030	strong		0.622	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
NCL	4691	hgsc.bcm.edu	37	2	232326417	232326417	+	Silent	SNP	C	C	T	rs1131171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:232326417C>T	ENST00000322723.4	-	3	687	c.447G>A	c.(445-447)gaG>gaA	p.E149E	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	149	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		tgtcatcatcctcctcttcat	0.522													.|||	2088	0.416933	0.4818	0.3141	5008	,	,		26008	0.5992		0.2018	False		,,,				2504	0.4356				p.E149E		Atlas-SNP	.											.	NCL	80	.	0			c.G447A						PASS	.	C		1981,2425	557.3+/-379.7	441,1099,663	469.0	282.0	345.0		447	-3.4	0.2	2	dbSNP_86	345	1570,7030	293.4+/-301.3	143,1284,2873	no	coding-synonymous	NCL	NM_005381.2		584,2383,3536	TT,TC,CC		18.2558,44.9614,27.3028		149/711	232326417	3551,9455	2203	4300	6503	SO:0001819	synonymous_variant	4691	exon3			ATCATCCTCCTCT		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.447G>A	2.37:g.232326417C>T		Somatic	419	0	0		WXS	Illumina HiSeq	Phase_I	444	196	0.441441	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	37	CCDS33397.1																																																																																			C|0.662;T|0.338	0.338	strong		0.522	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381	
AGRN	375790	hgsc.bcm.edu	37	1	978804	978804	+	Missense_Mutation	SNP	C	C	T	rs144164397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:978804C>T	ENST00000379370.2	+	8	1620	c.1570C>T	c.(1570-1572)Cgg>Tgg	p.R524W		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	524	Kazal-like 5. {ECO:0000255|PROSITE- ProRule:PRU00798}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		TACCCTCGGGCGGGAGATCCA	0.687													C|||	6	0.00119808	0.003	0.0029	5008	,	,		13574	0.0		0.0	False		,,,				2504	0.0				p.R524W		Atlas-SNP	.											.	AGRN	110	.	0			c.C1570T						PASS	.	C	TRP/ARG	12,4360		0,12,2174	32.0	33.0	32.0		1570	3.8	0.6	1	dbSNP_134	32	0,8582		0,0,4291	yes	missense	AGRN	NM_198576.3	101	0,12,6465	TT,TC,CC		0.0,0.2745,0.0926	probably-damaging	524/2046	978804	12,12942	2186	4291	6477	SO:0001583	missense	375790	exon8			CTCGGGCGGGAGA	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.1570C>T	1.37:g.978804C>T	ENSP00000368678:p.Arg524Trp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	15.96	2.987733	0.53934	0.002745	0.0	ENSG00000188157	ENST00000379370	T	0.04454	3.62	4.76	3.76	0.43208	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.533856	0.15977	N	0.235503	T	0.20941	0.0504	M	0.82433	2.59	0.37536	D	0.918126	D	0.89917	1.0	D	0.77557	0.99	T	0.02275	-1.1184	10	0.87932	D	0	-11.7757	9.9656	0.41723	0.4775:0.5225:0.0:0.0	.	524	O00468	AGRIN_HUMAN	W	524	ENSP00000368678:R524W	ENSP00000368678:R524W	R	+	1	2	AGRN	968667	0.998000	0.40836	0.597000	0.28824	0.014000	0.08584	3.246000	0.51414	2.195000	0.70347	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.687	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
SEC14L3	266629	hgsc.bcm.edu	37	22	30860831	30860831	+	Missense_Mutation	SNP	G	G	A	rs115090125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30860831G>A	ENST00000215812.4	-	8	730	c.640C>T	c.(640-642)Cgc>Tgc	p.R214C	SEC14L3_ENST00000539629.1_Missense_Mutation_p.R155C|SEC14L3_ENST00000540910.1_Missense_Mutation_p.R137C|SEC14L3_ENST00000402286.1_Missense_Mutation_p.R137C|SEC14L3_ENST00000403066.1_Missense_Mutation_p.R155C|SEC14L3_ENST00000415957.2_Missense_Mutation_p.R155C|SEC14L3_ENST00000401751.1_Missense_Mutation_p.R155C	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	214	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		R -> H (in dbSNP:rs2269961).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	ATTTTCCTGCGAGTGTCCTCA	0.443													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		23216	0.0		0.0	False		,,,				2504	0.0				p.R214C	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.C640T						PASS	.	G	CYS/ARG	34,4372	40.0+/-72.8	0,34,2169	179.0	154.0	162.0		640	4.4	1.0	22	dbSNP_132	162	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SEC14L3	NM_174975.4	180	0,35,6468	AA,AG,GG		0.0116,0.7717,0.2691	probably-damaging	214/401	30860831	35,12971	2203	4300	6503	SO:0001583	missense	266629	exon8			TCCTGCGAGTGTC	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.640C>T	22.37:g.30860831G>A	ENSP00000215812:p.Arg214Cys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	148	75	0.506757	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	20.1	3.931583	0.73442	0.007717	1.16E-4	ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	T;T;T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27	5.5	4.43	0.53597	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.000000	0.85682	D	0.000000	D	0.86615	0.5975	M	0.91510	3.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71414	0.973;0.973	D	0.90030	0.4134	10	0.87932	D	0	-11.635	14.7515	0.69530	0.0:0.0:0.8547:0.1453	.	137;214	E9PE57;Q9UDX4	.;S14L3_HUMAN	C	155;155;214;137;155;155;137	ENSP00000385941:R155C;ENSP00000401864:R155C;ENSP00000215812:R214C;ENSP00000385004:R137C;ENSP00000383896:R155C;ENSP00000444691:R155C;ENSP00000439752:R137C	ENSP00000215812:R214C	R	-	1	0	SEC14L3	29190831	1.000000	0.71417	0.996000	0.52242	0.707000	0.40811	4.312000	0.59154	2.593000	0.87608	0.655000	0.94253	CGC	G|0.997;A|0.003	0.003	strong		0.443	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
PYGM	5837	hgsc.bcm.edu	37	11	64520569	64520569	+	Silent	SNP	G	G	A	rs11231865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64520569G>A	ENST00000164139.3	-	12	1892	c.1494C>T	c.(1492-1494)ccC>ccT	p.P498P	PYGM_ENST00000462303.1_5'Flank|PYGM_ENST00000377432.3_Silent_p.P410P	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	498					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTGCCAGCCCGGGGTTACACA	0.572													G|||	177	0.0353435	0.1293	0.0058	5008	,	,		18308	0.0		0.002	False		,,,				2504	0.0				p.P498P		Atlas-SNP	.											.	PYGM	77	.	0			c.C1494T						PASS	.	G	,	539,3863	245.3+/-254.3	24,491,1686	202.0	231.0	221.0		1230,1494	-11.6	0.1	11	dbSNP_120	221	1,8593		0,1,4296	no	coding-synonymous,coding-synonymous	PYGM	NM_001164716.1,NM_005609.2	,	24,492,5982	AA,AG,GG		0.0116,12.2444,4.1551	,	410/755,498/843	64520569	540,12456	2201	4297	6498	SO:0001819	synonymous_variant	5837	exon12			CAGCCCGGGGTTA		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"""Glycogen phosphorylases"""	9726	protein-coding gene	gene with protein product	"""McArdle syndrome"", ""glycogen storage disease type V"", ""glycogen phosphorylase, muscle form"""	608455	"""phosphorylase, glycogen; muscle"""				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.1494C>T	11.37:g.64520569G>A		Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	221	121	0.547511	NM_005609	A0AVK1|A6NDY6	Silent	SNP	ENST00000164139.3	37	CCDS8079.1																																																																																			G|0.963;A|0.037	0.037	strong		0.572	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609	
GRIN3A	116443	hgsc.bcm.edu	37	9	104432462	104432462	+	Silent	SNP	A	A	G	rs200841145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:104432462A>G	ENST00000361820.3	-	3	2832	c.2232T>C	c.(2230-2232)ttT>ttC	p.F744F		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	744					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)	GGTTCATTAGAAACCTTCCAG	0.433													A|||	3	0.000599042	0.0015	0.0014	5008	,	,		19652	0.0		0.0	False		,,,				2504	0.0				p.F744F		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T2232C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	90.0	86.0	87.0		2232	5.4	1.0	9		87	0,8600		0,0,4300	no	coding-synonymous	GRIN3A	NM_133445.2		0,3,6500	GG,GA,AA		0.0,0.0681,0.0231		744/1116	104432462	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon3			CATTAGAAACCTT		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.2232T>C	9.37:g.104432462A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	79	48	0.607595	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			A|1.000;G|0.000	0.000	strong		0.433	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
MICALCL	84953	hgsc.bcm.edu	37	11	12315186	12315186	+	Missense_Mutation	SNP	G	G	A	rs10741578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	107	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	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	
ICAM3	3385	hgsc.bcm.edu	37	19	10444603	10444603	+	Missense_Mutation	SNP	C	C	G	rs2230399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10444603C>G	ENST00000160262.5	-	7	1782	c.1574G>C	c.(1573-1575)aGc>aCc	p.S525T	RAVER1_ENST00000293677.6_5'Flank|ICAM3_ENST00000589261.1_Missense_Mutation_p.S448T	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	525			S -> T (in dbSNP:rs2230399).		extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			CAGATAGGTGCTCTCCTCCCT	0.582													C|||	494	0.0986422	0.2383	0.0346	5008	,	,		14915	0.003		0.0755	False		,,,				2504	0.0777				p.S525T		Atlas-SNP	.											ICAM3,NS,adenoma,0,1	ICAM3	29	1	0			c.G1574C						PASS	.	C	THR/SER	880,3526	344.1+/-307.9	82,716,1405	194.0	163.0	174.0		1574	1.0	0.0	19	dbSNP_98	174	726,7874	177.2+/-226.9	26,674,3600	yes	missense	ICAM3	NM_002162.3	58	108,1390,5005	GG,GC,CC		8.4419,19.9728,12.3481	possibly-damaging	525/548	10444603	1606,11400	2203	4300	6503	SO:0001583	missense	3385	exon7			TAGGTGCTCTCCT		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.1574G>C	19.37:g.10444603C>G	ENSP00000160262:p.Ser525Thr	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	233	233	1	NM_002162	Q6PD68	Missense_Mutation	SNP	ENST00000160262.5	37	CCDS12235.1	195	0.08928571428571429	124	0.25203252032520324	15	0.04143646408839779	1	0.0017482517482517483	55	0.07255936675461741	C	11.53	1.667187	0.29604	0.199728	0.084419	ENSG00000076662	ENST00000160262	T	0.02606	4.23	4.39	0.959	0.19624	.	1.288390	0.05251	N	0.513919	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	P	0.39480	0.675	B	0.28553	0.091	T	0.48833	-0.9000	9	0.34782	T	0.22	-4.6196	4.6192	0.12442	0.0:0.6156:0.1808:0.2037	rs2230399;rs2230399	525	P32942	ICAM3_HUMAN	T	525	ENSP00000160262:S525T	ENSP00000160262:S525T	S	-	2	0	ICAM3	10305603	0.001000	0.12720	0.001000	0.08648	0.009000	0.06853	-0.193000	0.09573	0.197000	0.20387	-0.291000	0.09656	AGC	C|0.889;G|0.111	0.111	strong		0.582	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		
CXorf65	158830	hgsc.bcm.edu	37	X	70325881	70325881	+	Silent	SNP	G	G	A	rs138762266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70325881G>A	ENST00000374251.5	-	3	267	c.219C>T	c.(217-219)taC>taT	p.Y73Y		NM_001025265.2	NP_001020436.1	A6NEN9	CX065_HUMAN	chromosome X open reading frame 65	73										breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)	10						TACAAACGTAGTAGGTGCTTC	0.443													G|||	10	0.00264901	0.0068	0.0014	3775	,	,		16348	0.0		0.0	False		,,,				2504	0.0				p.Y73Y		Atlas-SNP	.											.	CXorf65	23	.	0			c.C219T						PASS	.	G		41,3794		0,37,4,1595,567	169.0	128.0	142.0		219	3.1	0.9	X	dbSNP_134	142	0,6728		0,0,0,2428,1872	no	coding-synonymous	CXorf65	NM_001025265.2		0,37,4,4023,2439	AA,AG,A,GG,G		0.0,1.0691,0.3881		73/184	70325881	41,10522	2203	4300	6503	SO:0001819	synonymous_variant	158830	exon3			AACGTAGTAGGTG	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.219C>T	X.37:g.70325881G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	174	77	0.442529	NM_001025265		Silent	SNP	ENST00000374251.5	37	CCDS35324.1																																																																																			G|0.996;A|0.004	0.004	strong		0.443	CXorf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057089.2	NM_001025265	
CYB5B	80777	hgsc.bcm.edu	37	16	69458746	69458746	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69458746C>T	ENST00000512062.1	+	1	319	c.148C>T	c.(148-150)Cgc>Tgc	p.R50C	CYB5B_ENST00000561792.1_Missense_Mutation_p.R50C|CYB5B_ENST00000515314.1_Missense_Mutation_p.R50C|CYB5B_ENST00000307892.8_Missense_Mutation_p.R54C			O43169	CYB5B_HUMAN	cytochrome b5 type B (outer mitochondrial membrane)	50	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	heme binding (GO:0020037)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|lung(2)	8		Ovarian(137;0.101)				CGATGTCACCCGCTTCCTCAA	0.592																																					p.R54C		Atlas-SNP	.											.	CYB5B	12	.	0			c.C160T						PASS	.						52.0	53.0	53.0					16																	69458746		2066	4196	6262	SO:0001583	missense	80777	exon1			GTCACCCGCTTCC		CCDS10880.2	16q22.1	2006-02-02			ENSG00000103018	ENSG00000103018			24374	protein-coding gene	gene with protein product		611964				11867265, 14733950	Standard	NM_030579		Approved	CYB5-M	uc002exg.1	O43169	OTTHUMG00000133020	ENST00000512062.1:c.148C>T	16.37:g.69458746C>T	ENSP00000423679:p.Arg50Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	89	4	0.0449438	NM_030579	A8K6B1|Q96CC3|Q9BT35	Missense_Mutation	SNP	ENST00000512062.1	37		.	.	.	.	.	.	.	.	.	.	C	16.35	3.099759	0.56183	.	.	ENSG00000103018	ENST00000512062;ENST00000307892;ENST00000515314	T;T;T	0.77229	-1.08;-1.08;-1.08	5.88	2.86	0.33363	Cytochrome b5 (5);	0.620650	0.18955	N	0.126564	T	0.62344	0.2420	N	0.26092	0.79	0.58432	D	0.999999	B;B;B	0.30584	0.286;0.047;0.004	B;B;B	0.28638	0.092;0.012;0.005	T	0.57843	-0.7741	10	0.87932	D	0	-12.3637	6.394	0.21603	0.1369:0.6613:0.1316:0.0702	.	50;50;50	D6RFH4;O43169;Q5HYD9	.;CYB5B_HUMAN;.	C	50;54;50	ENSP00000423679:R50C;ENSP00000308430:R54C;ENSP00000421492:R50C	ENSP00000308430:R54C	R	+	1	0	CYB5B	68016247	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.771000	0.38542	0.382000	0.24878	0.655000	0.94253	CGC	.	.	none		0.592	CYB5B-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256606.2	NM_030579	
EXOC6B	23233	hgsc.bcm.edu	37	2	72707874	72707874	+	Silent	SNP	A	A	G	rs653220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:72707874A>G	ENST00000272427.6	-	17	1801	c.1671T>C	c.(1669-1671)gtT>gtC	p.V557V	EXOC6B_ENST00000410104.1_Silent_p.V557V	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	557					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)				breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						TAATAATCTGAACAAGCTAGA	0.363													G|||	1741	0.347644	0.9546	0.2118	5008	,	,		20736	0.0069		0.2346	False		,,,				2504	0.091				p.V557V		Atlas-SNP	.											.	EXOC6B	93	.	0			c.T1671C						PASS	.	G		2983,751		1207,569,91	54.0	54.0	54.0		1671	-0.5	1.0	2	dbSNP_83	54	1882,6312		214,1454,2429	yes	coding-synonymous	EXOC6B	NM_015189.1		1421,2023,2520	GG,GA,AA		22.968,20.1125,40.7864		557/812	72707874	4865,7063	1867	4097	5964	SO:0001819	synonymous_variant	23233	exon17			AATCTGAACAAGC	AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036			17085	protein-coding gene	gene with protein product		607880	"""SEC15-like 2 (S. cerevisiae)"", ""SEC15 homolog B (S. cerevisiae)"""	SEC15L2, SEC15B		10231032, 11406615	Standard	NM_015189		Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.1671T>C	2.37:g.72707874A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_015189	B8ZZY3	Silent	SNP	ENST00000272427.6	37	CCDS46333.1																																																																																			A|0.639;G|0.361	0.361	strong		0.363	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327558.1	XM_039570	
SHROOM2	357	hgsc.bcm.edu	37	X	9863929	9863929	+	Missense_Mutation	SNP	G	G	A	rs146519576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:9863929G>A	ENST00000380913.3	+	4	2071	c.1981G>A	c.(1981-1983)Ggc>Agc	p.G661S		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	661					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)				GGATGGCACCGGCCGCTGGAG	0.652													G|||	6	0.0015894	0.0038	0.0014	3775	,	,		11713	0.0		0.0	False		,,,				2504	0.0				p.G661S		Atlas-SNP	.											.	SHROOM2	139	.	0			c.G1981A						PASS	.	G	SER/GLY	8,3745		0,6,2,1598,543	10.0	10.0	10.0		1981	1.2	0.0	X	dbSNP_134	10	4,6600		0,4,0,2400,1796	yes	missense	SHROOM2	NM_001649.2	56	0,10,2,3998,2339	AA,AG,A,GG,G		0.0606,0.2132,0.1159	benign	661/1617	9863929	12,10345	2149	4200	6349	SO:0001583	missense	357	exon4			GGCACCGGCCGCT	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.1981G>A	X.37:g.9863929G>A	ENSP00000370299:p.Gly661Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_001649	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	37	CCDS14135.1	.	.	.	.	.	.	.	.	.	.	G	4.289	0.052893	0.08291	0.002132	6.06E-4	ENSG00000146950	ENST00000380913	T	0.39406	1.08	4.92	1.21	0.21127	Apx/shroom, ASD1 (1);	1.413420	0.04081	N	0.309622	T	0.28830	0.0715	L	0.44542	1.39	0.20196	N	0.999928	P	0.40398	0.716	B	0.25405	0.06	T	0.18335	-1.0340	10	0.11485	T	0.65	-1.4736	9.2772	0.37707	0.3048:0.0:0.6952:0.0	.	661	Q13796	SHRM2_HUMAN	S	661	ENSP00000370299:G661S	ENSP00000370299:G661S	G	+	1	0	SHROOM2	9823929	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.067000	0.14510	-0.181000	0.10619	-1.129000	0.01985	GGC	G|0.998;A|0.002	0.002	strong		0.652	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
MGAM	8972	hgsc.bcm.edu	37	7	141754629	141754629	+	Missense_Mutation	SNP	G	G	C	rs145885349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141754629G>C	ENST00000549489.2	+	27	3330	c.3235G>C	c.(3235-3237)Gag>Cag	p.E1079Q	MGAM_ENST00000475668.2_Missense_Mutation_p.E1079Q	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1079	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)	CAGCACCCCTGAGGGTCAACT	0.448													g|||	21	0.00419329	0.0151	0.0014	5008	,	,		18921	0.0		0.0	False		,,,				2504	0.0				p.E1079Q		Atlas-SNP	.											MGAM_ENST00000549489,caecum,carcinoma,-2,3	MGAM	767	3	0			c.G3235C						PASS	.	G	GLN/GLU	46,3784		0,46,1869	135.0	129.0	131.0		3235	2.3	0.0	7	dbSNP_134	131	0,8230		0,0,4115	no	missense	MGAM	NM_004668.2	29	0,46,5984	CC,CG,GG		0.0,1.201,0.3814	possibly-damaging	1079/1858	141754629	46,12014	1915	4115	6030	SO:0001583	missense	8972	exon27			ACCCCTGAGGGTC	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.3235G>C	7.37:g.141754629G>C	ENSP00000447378:p.Glu1079Gln	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	191	94	0.492147	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	6	0.0027472527472527475	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	0	0.0	G	11.01	1.514051	0.27123	0.01201	0.0	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	T	0.30714	1.52	4.24	2.31	0.28768	Glycoside hydrolase-type carbohydrate-binding (1);	0.422018	0.17369	N	0.176760	T	0.28001	0.0690	M	0.76838	2.35	0.09310	N	1	B	0.15719	0.014	B	0.11329	0.006	T	0.28235	-1.0050	10	0.54805	T	0.06	.	12.7162	0.57117	0.0:0.3182:0.6818:0.0	.	1079	O43451	MGA_HUMAN	Q	1079;1079;956	ENSP00000447378:E1079Q	ENSP00000316431:E956Q	E	+	1	0	MGAM	141401098	0.000000	0.05858	0.001000	0.08648	0.119000	0.20118	0.690000	0.25451	0.207000	0.20607	-0.515000	0.04445	GAG	G|0.997;C|0.003	0.003	strong		0.448	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
MOGS	7841	hgsc.bcm.edu	37	2	74690378	74690378	+	Missense_Mutation	SNP	C	C	T	rs1063588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74690378C>T	ENST00000233616.4	-	3	877	c.715G>A	c.(715-717)Gac>Aac	p.D239N	MOGS_ENST00000462443.1_5'UTR|MOGS_ENST00000535045.1_3'UTR|MOGS_ENST00000452063.2_Missense_Mutation_p.D133N|MOGS_ENST00000409065.1_Intron	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	239			D -> N (in dbSNP:rs1063588). {ECO:0000269|PubMed:7635146}.		cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						AAGCGGAAGTCACCAAGTTCA	0.527													C|||	2598	0.51877	0.8086	0.3127	5008	,	,		20904	0.8214		0.1581	False		,,,				2504	0.3323				p.D239N		Atlas-SNP	.											.	MOGS	58	.	0			c.G715A						PASS	.	C	ASN/ASP,ASN/ASP	2661,1287		899,863,212	116.0	119.0	118.0		397,715	4.8	1.0	2	dbSNP_86	118	1138,7210		82,974,3118	yes	missense,missense	MOGS	NM_001146158.1,NM_006302.2	23,23	981,1837,3330	TT,TC,CC		13.632,32.5988,30.8962	benign,benign	133/732,239/838	74690378	3799,8497	1974	4174	6148	SO:0001583	missense	7841	exon3			GGAAGTCACCAAG	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"""glucosidase I"", ""processing A-glucosidase I"""	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.715G>A	2.37:g.74690378C>T	ENSP00000233616:p.Asp239Asn	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	248	248	1	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	37	CCDS42700.1	1064	0.48717948717948717	387	0.7865853658536586	94	0.2596685082872928	469	0.8199300699300699	114	0.1503957783641161	C	12.59	1.983034	0.34942	0.674012	0.13632	ENSG00000115275	ENST00000233616;ENST00000452063;ENST00000448666;ENST00000414701	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	4.85	4.85	0.62838	.	0.243944	0.41194	D	0.000925	T	0.00012	0.0000	N	0.17800	0.525	0.09310	P	1.0	P	0.36616	0.561	B	0.36666	0.23	T	0.07558	-1.0766	9	0.21014	T	0.42	-20.9003	13.3472	0.60580	0.0:1.0:0.0:0.0	rs1063588;rs3204621;rs58978224;rs1063588	239	Q13724	MOGS_HUMAN	N	239;133;133;120	ENSP00000233616:D239N;ENSP00000388201:D133N;ENSP00000410992:D133N;ENSP00000396298:D120N	ENSP00000233616:D239N	D	-	1	0	MOGS	74543886	0.998000	0.40836	1.000000	0.80357	0.950000	0.60333	0.994000	0.29693	2.504000	0.84457	0.655000	0.94253	GAC	C|0.531;T|0.469	0.469	strong		0.527	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302	
SARAF	51669	hgsc.bcm.edu	37	8	29927182	29927182	+	Missense_Mutation	SNP	G	G	A	rs34416759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:29927182G>A	ENST00000256255.6	-	3	933	c.676C>T	c.(676-678)Cca>Tca	p.P226S	TMEM66_ENST00000545648.1_Missense_Mutation_p.P54S|TMEM66_ENST00000536273.1_Missense_Mutation_p.P54S	NM_016127.4	NP_057211.4	Q96BY9	SARAF_HUMAN		226					calcium ion transport (GO:0006816)|regulation of store-operated calcium entry (GO:2001256)	integral component of endoplasmic reticulum membrane (GO:0030176)				endometrium(2)|large_intestine(1)|lung(11)	14				KIRC - Kidney renal clear cell carcinoma(542;0.0993)|Kidney(114;0.119)		TTAAAGCCTGGGGGAGGAGGT	0.507													G|||	44	0.00878594	0.031	0.0043	5008	,	,		18064	0.0		0.0	False		,,,				2504	0.0				p.P226S		Atlas-SNP	.											.	TMEM66	23	.	0			c.C676T						PASS	.	G	SER/PRO	135,4271	95.3+/-134.0	4,127,2072	119.0	102.0	108.0		676	-0.4	0.0	8	dbSNP_126	108	0,8600		0,0,4300	yes	missense	TMEM66	NM_016127.4	74	4,127,6372	AA,AG,GG		0.0,3.064,1.038	benign	226/340	29927182	135,12871	2203	4300	6503	SO:0001583	missense	51669	exon3			AGCCTGGGGGAGG																												ENST00000256255.6:c.676C>T	8.37:g.29927182G>A	ENSP00000256255:p.Pro226Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	159	64	0.402516	NM_016127	B3KQQ4|B7Z9J1|D3DSU7|H9MHJ8|H9MHJ9|Q53HE8|Q9UNZ3|Q9Y683	Missense_Mutation	SNP	ENST00000256255.6	37	CCDS6074.1	16|16	0.007326007326007326|0.007326007326007326	15|15	0.03048780487804878|0.03048780487804878	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.64|13.64	2.296786|2.296786	0.40594|0.40594	0.03064|0.03064	0.0|0.0	ENSG00000133872|ENSG00000133872	ENST00000518296|ENST00000256255;ENST00000545648;ENST00000541035;ENST00000536273;ENST00000523127;ENST00000522794	T|T;T;T;T;T	0.58940|0.57752	0.3|0.38;0.38;0.38;0.38;0.38	5.82|5.82	-0.4|-0.4	0.12411|0.12411	.|.	0.360290|0.360290	0.32244|0.32244	N|N	0.006371|0.006371	T|T	0.21427|0.21427	0.0516|0.0516	L|L	0.61036|0.61036	1.89|1.89	0.41958|0.41958	D|D	0.990696|0.990696	.|B;B	.|0.25390	.|0.125;0.125	.|B;B	.|0.27170	.|0.077;0.077	T|T	0.09751|0.09751	-1.0660|-1.0660	8|10	0.72032|0.48119	D|T	0.01|0.1	-4.2187|-4.2187	7.801|7.801	0.29174|0.29174	0.0663:0.457:0.3642:0.1125|0.0663:0.457:0.3642:0.1125	rs34416759|rs34416759	.|226;226	.|B3KQQ4;Q96BY9	.|.;TMM66_HUMAN	L|S	95|226;54;190;54;124;190	ENSP00000427769:P95L|ENSP00000256255:P226S;ENSP00000441351:P54S;ENSP00000441723:P54S;ENSP00000428323:P124S;ENSP00000429630:P190S	ENSP00000427769:P95L|ENSP00000256255:P226S	P|P	-|-	2|1	0|0	TMEM66|TMEM66	30046724|30046724	0.985000|0.985000	0.35326|0.35326	0.020000|0.020000	0.16555|0.16555	0.991000|0.991000	0.79684|0.79684	1.791000|1.791000	0.38744|0.38744	-0.381000|-0.381000	0.07882|0.07882	-0.182000|-0.182000	0.12963|0.12963	CCC|CCA	G|0.990;A|0.010	0.010	strong		0.507	TMEM66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257254.4		
CD5L	922	hgsc.bcm.edu	37	1	157805650	157805650	+	Missense_Mutation	SNP	A	A	T	rs11537583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157805650A>T	ENST00000368174.4	-	3	447	c.351T>A	c.(349-351)gaT>gaA	p.D117E	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	117	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.		D -> E (in dbSNP:rs11537583).		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)			CAGCATCTTCATCATGTGAAC	0.493													A|||	602	0.120208	0.1619	0.2147	5008	,	,		20779	0.1736		0.007	False		,,,				2504	0.0583				p.D117E		Atlas-SNP	.											.	CD5L	112	.	0			c.T351A						PASS	.	A	GLU/ASP	605,3801	264.7+/-266.2	44,517,1642	145.0	145.0	145.0		351	-9.4	0.0	1	dbSNP_120	145	64,8536	38.3+/-94.2	0,64,4236	yes	missense	CD5L	NM_005894.2	45	44,581,5878	TT,TA,AA		0.7442,13.7313,5.1438	benign	117/348	157805650	669,12337	2203	4300	6503	SO:0001583	missense	922	exon3			ATCTTCATCATGT	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.351T>A	1.37:g.157805650A>T	ENSP00000357156:p.Asp117Glu	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	166	91	0.548193	NM_005894	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	37	CCDS1171.1	254	0.1163003663003663	91	0.18495934959349594	47	0.1298342541436464	111	0.19405594405594406	5	0.006596306068601583	A	0.034	-1.316803	0.01331	0.137313	0.007442	ENSG00000073754	ENST00000368174	T	0.32988	1.43	4.68	-9.36	0.00629	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	2.958050	0.01125	N	0.005879	T	0.02455	0.0075	N	0.25144	0.715	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.34675	-0.9819	9	0.02654	T	1	.	1.0475	0.01572	0.355:0.1891:0.2995:0.1564	rs11537583;rs16839277;rs52820854;rs11537583	117	O43866	CD5L_HUMAN	E	117	ENSP00000357156:D117E	ENSP00000357156:D117E	D	-	3	2	CD5L	156072274	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.389000	0.00488	-4.209000	0.00065	-0.624000	0.04008	GAT	A|0.920;T|0.080	0.080	strong		0.493	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037626	33037626	+	Silent	SNP	C	C	G	rs1042174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33037626C>G	ENST00000419277.1	-	3	267	c.138G>C	c.(136-138)acG>acC	p.T46T	HLA-DPA1_ENST00000428995.1_Silent_p.T46T|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	46	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						TTGGTCTATGCGTCTGTACAA	0.433													.|||	2309	0.461062	0.7171	0.2882	5008	,	,		20289	0.6518		0.1491	False		,,,				2504	0.362				p.T46T		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G138C						PASS	.	G	,,	1588,1432		465,658,387	56.0	80.0	71.0		138,138,138	-6.2	0.0	6	dbSNP_86	71	710,4706		49,612,2047	yes	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	514,1270,2434	GG,GC,CC		13.1093,47.4172,27.2404	,,	46/261,46/261,46/261	33037626	2298,6138	1510	2708	4218	SO:0001819	synonymous_variant	3113	exon2			TCTATGCGTCTGT	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.138G>C	6.37:g.33037626C>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1																																																																																			C|0.687;G|0.313	0.313	strong		0.433	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
MST1L	11223	hgsc.bcm.edu	37	1	17085589	17085589	+	RNA	SNP	A	A	C	rs3863807|rs371449598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17085589A>C	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										TCAGCGGACCAGCGCTGGCAC	0.701																																					p.W378G		Atlas-SNP	.											.	.	.	.	0			c.T1132G						PASS	.																																					11223	exon9			CGGACCAGCGCTG	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.17085589A>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	196	18	0.0918367	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	13.02	2.113315	0.37339	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	0.000000	0.39615	N	0.001307	T	0.64405	0.2595	.	.	.	.	.	.	D	0.89917	1.0	D	0.91635	0.999	T	0.67317	-0.5701	6	0.87932	D	0	.	4.4758	0.11739	0.9992:0.0:8.0E-4:0.0	rs3863807;rs9701101	378	Q2TV78-2	.	G	368;378;378	.	ENSP00000439273:W378G	W	-	1	0	MST1P9	16958176	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	5.617000	0.67716	-0.000000	0.14550	0.000000	0.15137	TGG	A|0.994;C|0.006	0.006	strong		0.701	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
MAP3K19	80122	hgsc.bcm.edu	37	2	135744416	135744416	+	Missense_Mutation	SNP	C	C	G	rs1112542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:135744416C>G	ENST00000375845.3	-	7	2056	c.2026G>C	c.(2026-2028)Gag>Cag	p.E676Q	MAP3K19_ENST00000392915.1_Missense_Mutation_p.E693Q|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.E563Q	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	676			E -> Q (in dbSNP:rs1112542).				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										CTTTCAGTCTCTCGCACATGA	0.403													C|||	627	0.1252	0.1316	0.0403	5008	,	,		21345	0.3819		0.004	False		,,,				2504	0.0368				p.E676Q		Atlas-SNP	.											.	.	.	.	0			c.G2026C						PASS	.	C	,GLN/GLU	608,3798	266.2+/-267.1	40,528,1635	169.0	158.0	162.0		,2026	4.7	1.0	2	dbSNP_86	162	47,8553	31.7+/-84.0	0,47,4253	yes	intron,missense	YSK4	NM_001018046.1,NM_025052.3	,29	40,575,5888	GG,GC,CC		0.5465,13.7994,5.0361	,possibly-damaging	,676/1329	135744416	655,12351	2203	4300	6503	SO:0001583	missense	80122	exon7			CAGTCTCTCGCAC	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.2026G>C	2.37:g.135744416C>G	ENSP00000365005:p.Glu676Gln	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	298	0.13644688644688643	65	0.13211382113821138	10	0.027624309392265192	220	0.38461538461538464	3	0.00395778364116095	C	10.03	1.237971	0.22711	0.137994	0.005465	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915;ENST00000437365	T;T;T;T	0.74632	-0.8;-0.76;1.52;-0.86	5.67	4.74	0.60224	.	0.122354	0.36815	N	0.002389	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	1.0	P;D;P	0.76494	0.679;0.999;0.813	B;D;B	0.65323	0.373;0.934;0.206	T	0.10683	-1.0619	9	0.87932	D	0	.	14.4797	0.67573	0.0:0.8537:0.1463:0.0	rs1112542;rs1112542	563;693;676	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	Q	676;563;693;66	ENSP00000365005:E676Q;ENSP00000351140:E563Q;ENSP00000376647:E693Q;ENSP00000392827:E66Q	ENSP00000351140:E563Q	E	-	1	0	YSK4	135460886	1.000000	0.71417	0.968000	0.41197	0.018000	0.09664	3.362000	0.52314	2.667000	0.90743	0.561000	0.74099	GAG	C|0.915;G|0.085	0.085	strong		0.403	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
CLCN7	1186	hgsc.bcm.edu	37	16	1509123	1509123	+	Silent	SNP	G	G	A	rs12923538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1509123G>A	ENST00000382745.4	-	7	1265	c.660C>T	c.(658-660)caC>caT	p.H220H	CLCN7_ENST00000448525.1_Silent_p.H196H|CLCN7_ENST00000262318.8_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	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	256	140	0.546875	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	
ZCCHC6	79670	hgsc.bcm.edu	37	9	88959938	88959938	+	Silent	SNP	C	C	T	rs791323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:88959938C>T	ENST00000375963.3	-	5	1123	c.951G>A	c.(949-951)ctG>ctA	p.L317L	ZCCHC6_ENST00000375961.2_Silent_p.L317L|ZCCHC6_ENST00000375947.1_Silent_p.L150L|ZCCHC6_ENST00000375960.2_Silent_p.L317L|ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000375948.1_5'Flank	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	188	0	0		WXS	Illumina HiSeq	Phase_I	187	62	0.331551	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	
ACTG2	72	hgsc.bcm.edu	37	2	74140616	74140616	+	Silent	SNP	C	C	T	rs34286914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74140616C>T	ENST00000409624.1	+	7	1099	c.456C>T	c.(454-456)atC>atT	p.I152I	ACTG2_ENST00000409731.3_Silent_p.I109I|ACTG2_ENST00000345517.3_Silent_p.I152I			P63267	ACTH_HUMAN	actin, gamma 2, smooth muscle, enteric	152					muscle contraction (GO:0006936)	blood microparticle (GO:0072562)|cell periphery (GO:0071944)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			large_intestine(3)|lung(14)|skin(1)	18						CCACAGGCATCGTCCTGGATT	0.507													C|||	124	0.0247604	0.0908	0.0043	5008	,	,		20140	0.0		0.001	False		,,,				2504	0.0				p.I152I		Atlas-SNP	.											.	ACTG2	37	.	0			c.C456T						PASS	.	C	,	388,4018	193.6+/-218.7	20,348,1835	106.0	98.0	101.0		327,456	-9.2	0.3	2	dbSNP_126	101	2,8598		0,2,4298	no	coding-synonymous,coding-synonymous	ACTG2	NM_001199893.1,NM_001615.3	,	20,350,6133	TT,TC,CC		0.0233,8.8062,2.9986	,	109/334,152/377	74140616	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	72	exon6			AGGCATCGTCCTG		CCDS1930.1, CCDS56124.1	2p13.1	2008-05-20			ENSG00000163017	ENSG00000163017			145	protein-coding gene	gene with protein product		102545		ACTL3, ACTA3		1710027, 1673027	Standard	NM_001199893		Approved	ACTSG	uc002sjw.3	P63267	OTTHUMG00000129813	ENST00000409624.1:c.456C>T	2.37:g.74140616C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_001615	B2R7E7|B4E315|D6W5H8|E9PG30|P12718|Q504R1|Q6FI22	Silent	SNP	ENST00000409624.1	37	CCDS1930.1																																																																																			C|0.976;T|0.024	0.024	strong		0.507	ACTG2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328086.1	NM_001615	
AGFG2	3268	hgsc.bcm.edu	37	7	100151719	100151719	+	Missense_Mutation	SNP	G	G	A	rs61742738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100151719G>A	ENST00000300176.4	+	5	711	c.589G>A	c.(589-591)Gtc>Atc	p.V197I	AGFG2_ENST00000262935.4_Intron|AGFG2_ENST00000474713.1_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	197					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTCCAAGCCCGTCAGTCAGTC	0.597													G|||	203	0.0405351	0.143	0.0144	5008	,	,		19840	0.001		0.003	False		,,,				2504	0.0				p.V197I		Atlas-SNP	.											.	AGFG2	44	.	0			c.G589A						PASS	.	G	ILE/VAL	588,3818	259.2+/-262.9	40,508,1655	69.0	62.0	64.0		589	3.3	1.0	7	dbSNP_129	64	15,8585	10.5+/-38.8	0,15,4285	yes	missense	AGFG2	NM_006076.4	29	40,523,5940	AA,AG,GG		0.1744,13.3454,4.6363	benign	197/482	100151719	603,12403	2203	4300	6503	SO:0001583	missense	3268	exon5			AAGCCCGTCAGTC	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"""ADP-ribosylation factor GTPase activating proteins"""	5177	protein-coding gene	gene with protein product		604019	"""HIV-1 Rev binding protein-like"""	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.589G>A	7.37:g.100151719G>A	ENSP00000300176:p.Val197Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	37	CCDS5697.1	76	0.0347985347985348	69	0.1402439024390244	5	0.013812154696132596	0	0.0	2	0.002638522427440633	G	6.520	0.464149	0.12402	0.133454	0.001744	ENSG00000106351	ENST00000300176	T	0.22945	1.93	5.1	3.31	0.37934	.	0.980801	0.08316	N	0.964634	T	0.00144	0.0004	N	0.25485	0.75	0.09310	P	0.9999999999537761	B	0.14438	0.01	B	0.06405	0.002	T	0.22695	-1.0209	9	0.23891	T	0.37	-29.7338	8.266	0.31815	0.1791:0.0:0.8209:0.0	rs61742738	197	O95081	AGFG2_HUMAN	I	197	ENSP00000300176:V197I	ENSP00000300176:V197I	V	+	1	0	AGFG2	99989655	0.823000	0.29233	0.979000	0.43373	0.187000	0.23431	1.897000	0.39799	0.877000	0.35895	-0.125000	0.14975	GTC	G|0.959;A|0.041	0.041	strong		0.597	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076	
PTX4	390667	hgsc.bcm.edu	37	16	1536140	1536140	+	Missense_Mutation	SNP	C	C	T	rs386787711|rs79505704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536140C>T	ENST00000447419.2	-	3	1262	c.1237G>A	c.(1237-1239)Gga>Aga	p.G413R	PTX4_ENST00000440447.2_3'UTR|PTX4_ENST00000293922.1_Missense_Mutation_p.G408R			Q96A99	PTX4_HUMAN	pentraxin 4, long	413	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						CTGTCGAATCCGCCCCCCACG	0.662													C|||	87	0.0173722	0.0643	0.0029	5008	,	,		16723	0.0		0.0	False		,,,				2504	0.0				p.G408R		Atlas-SNP	.											.	PTX4	46	.	0			c.G1222A						PASS	.						57.0	55.0	55.0					16																	1536140		2199	4300	6499	SO:0001583	missense	390667	exon3			CGAATCCGCCCCC		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.1237G>A	16.37:g.1536140C>T	ENSP00000445277:p.Gly413Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	C	13.11	2.138909	0.37728	.	.	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.65364	-0.15;-0.15	5.45	3.39	0.38822	.	0.128923	0.51477	D	0.000092	T	0.09202	0.0227	M	0.63428	1.95	0.09310	N	0.999999	D	0.56287	0.975	P	0.55011	0.766	T	0.10382	-1.0632	10	0.18710	T	0.47	.	8.671	0.34149	0.0:0.7615:0.1535:0.085	.	408	Q96A99-2	.	R	413;408	ENSP00000445277:G413R;ENSP00000293922:G408R	ENSP00000293922:G408R	G	-	1	0	PTX4	1476141	0.000000	0.05858	0.048000	0.18961	0.000000	0.00434	0.922000	0.28734	1.318000	0.45170	-0.251000	0.11542	GGA	C|0.987;T|0.013	0.013	strong		0.662	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
IFNAR1	3454	hgsc.bcm.edu	37	21	34721782	34721782	+	Missense_Mutation	SNP	C	C	T	rs17875834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:34721782C>T	ENST00000270139.3	+	8	1228	c.1076C>T	c.(1075-1077)aCg>aTg	p.T359M	IFNAR1_ENST00000442357.2_Missense_Mutation_p.T359M|IFNAR1_ENST00000416947.2_Missense_Mutation_p.T290M	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	359	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> M (in dbSNP:rs17875834). {ECO:0000269|Ref.5}.		cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""""""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)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	TCTGGAAACACGCCTGTGATC	0.338													C|||	315	0.0628994	0.2307	0.0101	5008	,	,		17009	0.002		0.001	False		,,,				2504	0.0				p.T359M	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											IFNAR1,caecum,carcinoma,0,1	IFNAR1	44	1	0			c.C1076T						PASS	.	C	MET/THR	677,3729	286.0+/-278.5	47,583,1573	56.0	55.0	55.0		1076	-1.0	0.0	21	dbSNP_124	55	4,8594	3.0+/-9.4	0,4,4295	yes	missense	IFNAR1	NM_000629.2	81	47,587,5868	TT,TC,CC		0.0465,15.3654,5.2369	benign	359/558	34721782	681,12323	2203	4299	6502	SO:0001583	missense	3454	exon8			GAAACACGCCTGT		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"""Interferons"""	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.1076C>T	21.37:g.34721782C>T	ENSP00000270139:p.Thr359Met	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Missense_Mutation	SNP	ENST00000270139.3	37	CCDS13624.1	130	0.05952380952380952	126	0.25609756097560976	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	8.320	0.823991	0.16678	0.153654	4.65E-4	ENSG00000142166	ENST00000416947;ENST00000270139;ENST00000442357	T;T;T	0.40756	1.02;1.02;1.55	4.43	-1.01	0.10169	Fibronectin, type III (2);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	1.665550	0.02913	N	0.136918	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.22146	0.065	B	0.11329	0.006	T	0.20538	-1.0272	9	0.45353	T	0.12	.	0.7942	0.01063	0.4848:0.1669:0.1883:0.16	rs17875834;rs17875834	359	P17181	INAR1_HUMAN	M	290;359;359	ENSP00000395606:T290M;ENSP00000270139:T359M;ENSP00000407406:T359M	ENSP00000270139:T359M	T	+	2	0	IFNAR1	33643652	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.564000	0.05936	-0.375000	0.07955	-0.272000	0.10252	ACG	C|0.930;T|0.070	0.070	strong		0.338	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		
SSPO	23145	hgsc.bcm.edu	37	7	149488909	149488909	+	RNA	SNP	C	C	T	rs893600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149488909C>T	ENST00000378016.2	+	0	5250							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)			TCACAGTGGACGGTGAATGGA	0.657													C|||	131	0.0261581	0.0946	0.0086	5008	,	,		18103	0.0		0.0	False		,,,				2504	0.0				p.D1750D		Atlas-SNP	.											.	.	.	.	0			c.C5250T						PASS	.	C		247,3859		6,235,1812	14.0	18.0	16.0		5254	-5.8	0.4	7	dbSNP_86	16	6,8318		0,6,4156	yes	coding-notMod3	SSPO	NM_198455.2		6,241,5968	TT,TC,CC		0.0721,6.0156,2.0354			149488909	253,12177	2053	4162	6215			23145	exon35			AGTGGACGGTGAA	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.149488909C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	159	77	0.484277	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.979;T|0.021	0.021	strong		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
POLG2	11232	hgsc.bcm.edu	37	17	62492582	62492582	+	Missense_Mutation	SNP	C	C	T	rs1427463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62492582C>T	ENST00000539111.2	-	1	572	c.505G>A	c.(505-507)Gca>Aca	p.A169T		NM_007215.3	NP_009146.2	Q9UHN1	DPOG2_HUMAN	polymerase (DNA directed), gamma 2, accessory subunit	169			A -> T (in dbSNP:rs1427463). {ECO:0000269|PubMed:10666468, ECO:0000269|PubMed:15489334}.		DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)	extracellular vesicular exosome (GO:0070062)|mitochondrial chromosome (GO:0000262)|mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(4)|skin(2)|stomach(1)|urinary_tract(1)	15	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			TCAAGAAATGCTACTAGCTGT	0.463													C|||	1450	0.289537	0.8033	0.2161	5008	,	,		21332	0.0278		0.1163	False		,,,				2504	0.0951				p.A169T	Colon(3;18 21 435 17652 48887)	Atlas-SNP	.											.	POLG2	29	.	0			c.G505A						PASS	.	C	THR/ALA	3023,1383	689.6+/-405.1	1059,905,239	122.0	130.0	128.0		505	1.6	1.0	17	dbSNP_88	128	827,7773	190.8+/-237.2	39,749,3512	yes	missense	POLG2	NM_007215.3	58	1098,1654,3751	TT,TC,CC		9.6163,31.389,29.6017	benign	169/486	62492582	3850,9156	2203	4300	6503	SO:0001583	missense	11232	exon1			GAAATGCTACTAG	U94703	CCDS32706.1	17q23.3	2012-05-18			ENSG00000256525	ENSG00000256525		"""DNA polymerases"""	9180	protein-coding gene	gene with protein product		604983				9153213	Standard	NM_007215		Approved	MTPOLB, HP55	uc002jei.3	Q9UHN1		ENST00000539111.2:c.505G>A	17.37:g.62492582C>T	ENSP00000442563:p.Ala169Thr	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	156	78	0.5	NM_007215	O00419|Q0IJ81|Q96GW2|Q9UK35|Q9UK94	Missense_Mutation	SNP	ENST00000539111.2	37	CCDS32706.1	546	0.25	364	0.7398373983739838	71	0.19613259668508287	21	0.03671328671328671	90	0.11873350923482849	C	10.75	1.439392	0.25900	0.68611	0.096163	ENSG00000256525	ENST00000539111	T	0.76968	-1.06	5.15	1.58	0.23477	.	0.328747	0.32868	N	0.005554	T	0.00012	0.0000	L	0.32530	0.975	0.31367	P	0.6806829999999999	B;B	0.12630	0.006;0.006	B;B	0.04013	0.001;0.001	T	0.43861	-0.9365	9	0.02654	T	1	-6.3804	10.0895	0.42439	0.0:0.7458:0.0:0.2542	rs1427463;rs3744408;rs1427463	169;169	E5KS15;Q9UHN1	.;DPOG2_HUMAN	T	169	ENSP00000442563:A169T	ENSP00000442563:A169T	A	-	1	0	POLG2	59923044	0.000000	0.05858	1.000000	0.80357	0.986000	0.74619	-0.630000	0.05502	0.591000	0.29711	0.555000	0.69702	GCA	C|0.726;T|0.274	0.274	strong		0.463	POLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443820.1	NM_007215	
WWC3	55841	hgsc.bcm.edu	37	X	10085227	10085227	+	Silent	SNP	T	T	C	rs7058143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	106	0	0		WXS	Illumina HiSeq	Phase_I	123	51	0.414634	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	
ZNF449	203523	hgsc.bcm.edu	37	X	134483151	134483151	+	Silent	SNP	C	C	T	rs2286479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:134483151C>T	ENST00000339249.4	+	3	611	c.471C>T	c.(469-471)gcC>gcT	p.A157A		NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	157					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(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					CCCAGGAGGCCCCAGTAGCAG	0.577													C|||	580	0.153642	0.2814	0.0994	3775	,	,		13215	0.1161		0.007	False		,,,				2504	0.0153				p.A157A		Atlas-SNP	.											.	ZNF449	68	.	0			c.C471T						PASS	.	C		1170,2665		160,669,181,803,390	170.0	141.0	150.0		471	2.7	0.0	X	dbSNP_100	150	76,6652		0,63,13,2365,1859	no	coding-synonymous	ZNF449	NM_152695.5		160,732,194,3168,2249	TT,TC,T,CC,C		1.1296,30.5085,11.7959		157/519	134483151	1246,9317	2203	4300	6503	SO:0001819	synonymous_variant	203523	exon3			GGAGGCCCCAGTA	AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"""-"", ""Zinc fingers, C2H2-type"""	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.471C>T	X.37:g.134483151C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	109	62	0.568807	NM_152695	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Silent	SNP	ENST00000339249.4	37	CCDS14649.1																																																																																			0|0.003;T|0.143	0.143	strong		0.577	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695	
EFCAB5	374786	hgsc.bcm.edu	37	17	28381141	28381141	+	Silent	SNP	C	C	G	rs4074170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:28381141C>G	ENST00000394835.3	+	10	2361	c.2169C>G	c.(2167-2169)acC>acG	p.T723T	EFCAB5_ENST00000394832.2_Silent_p.T723T|EFCAB5_ENST00000536908.2_Silent_p.T667T|EFCAB5_ENST00000541045.1_Silent_p.T380T|EFCAB5_ENST00000378738.3_Silent_p.T723T|EFCAB5_ENST00000320856.5_Silent_p.T723T	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	723							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						AAGTTCCAACCTTAAGCAGAA	0.388													G|||	2859	0.570887	0.9327	0.4669	5008	,	,		20652	0.2917		0.5656	False		,,,				2504	0.4489				p.T723T		Atlas-SNP	.											.	EFCAB5	122	.	0			c.C2169G						PASS	.	G	,	3203,509		1383,437,36	21.0	20.0	21.0		2001,2169	3.0	0.0	17	dbSNP_108	21	4436,3744		1218,2000,872	no	coding-synonymous,coding-synonymous	EFCAB5	NM_001145053.1,NM_198529.3	,	2601,2437,908	GG,GC,CC		45.7702,13.7123,35.7635	,	667/857,723/1504	28381141	7639,4253	1856	4090	5946	SO:0001819	synonymous_variant	374786	exon10			TCCAACCTTAAGC	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.2169C>G	17.37:g.28381141C>G		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	207	98	0.47343	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	37	CCDS11254.2																																																																																			C|0.514;G|0.486	0.486	strong		0.388	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
CTNNBL1	56259	hgsc.bcm.edu	37	20	36396429	36396429	+	Missense_Mutation	SNP	C	C	G	rs186475150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36396429C>G	ENST00000361383.6	+	7	850	c.733C>G	c.(733-735)Ctg>Gtg	p.L245V	CTNNBL1_ENST00000405275.2_Missense_Mutation_p.L218V|CTNNBL1_ENST00000473857.1_3'UTR|CTNNBL1_ENST00000373473.1_Missense_Mutation_p.L58V	NM_030877.3	NP_110517.2	Q8WYA6	CTBL1_HUMAN	catenin, beta like 1	245					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|positive regulation of apoptotic process (GO:0043065)|RNA splicing (GO:0008380)|somatic diversification of immunoglobulins (GO:0016445)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(6)|lung(6)|ovary(3)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				TCTACAGTGGCTGTTGAAGAG	0.517													C|||	15	0.00299521	0.0113	0.0	5008	,	,		18099	0.0		0.0	False		,,,				2504	0.0				p.L245V	Ovarian(184;582 2038 3273 4106 42608)	Atlas-SNP	.											.	CTNNBL1	78	.	0			c.C733G						PASS	.						108.0	108.0	108.0					20																	36396429		2203	4300	6503	SO:0001583	missense	56259	exon7			CAGTGGCTGTTGA	AL023804	CCDS13298.1	20q11.23-q12	2011-06-03	2002-05-27	2002-05-31	ENSG00000132792	ENSG00000132792			15879	protein-coding gene	gene with protein product	"""nuclear associated protein"""	611537	"""chromosome 20 open reading frame 33"""	C20orf33		12659813, 21385873	Standard	NM_030877		Approved	FLJ21108, P14L, P14, NAP, NYD-SP19	uc021wdj.1	Q8WYA6	OTTHUMG00000032428	ENST00000361383.6:c.733C>G	20.37:g.36396429C>G	ENSP00000355050:p.Leu245Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	199	107	0.537688	NM_030877	B4DE16|Q0VAL9|Q0VAM0|Q53HI8|Q5JWZ2|Q5JWZ3|Q5JWZ7|Q5JWZ8|Q8N454|Q8NCL2|Q8TBD6|Q96KD2|Q9H7A5|Q9NQF9|Q9NTX0|Q9Y3M7	Missense_Mutation	SNP	ENST00000361383.6	37	CCDS13298.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	18.66	3.670848	0.67814	.	.	ENSG00000132792	ENST00000361383;ENST00000405275;ENST00000373473	T;T;T	0.69806	-0.28;-0.28;-0.43	5.8	2.36	0.29203	Armadillo-like helical (1);Armadillo-type fold (1);	0.071705	0.64402	N	0.000019	T	0.58991	0.2161	M	0.76727	2.345	0.80722	D	1	D;D	0.57571	0.98;0.964	P;P	0.53401	0.725;0.629	T	0.70389	-0.4885	10	0.52906	T	0.07	-14.1169	11.9885	0.53161	0.0:0.7773:0.0:0.2227	.	245;58	Q8WYA6;Q8WYA6-2	CTBL1_HUMAN;.	V	245;218;58	ENSP00000355050:L245V;ENSP00000384355:L218V;ENSP00000362572:L58V	ENSP00000355050:L245V	L	+	1	2	CTNNBL1	35829843	1.000000	0.71417	0.988000	0.46212	0.998000	0.95712	0.916000	0.28651	0.797000	0.33971	0.655000	0.94253	CTG	C|0.995;G|0.005	0.005	strong		0.517	CTNNBL1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079125.1	NM_030877	
OR5F1	338674	hgsc.bcm.edu	37	11	55761528	55761528	+	Missense_Mutation	SNP	T	T	C	rs35607186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55761528T>C	ENST00000278409.1	-	1	573	c.574A>G	c.(574-576)Aca>Gca	p.T192A		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	192			T -> A (in dbSNP:rs35607186).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					TTCAGGATTGTGTCAGAACAA	0.453													T|||	457	0.091254	0.1293	0.0403	5008	,	,		19955	0.0913		0.0944	False		,,,				2504	0.0726				p.T192A		Atlas-SNP	.											OR5F1,NS,carcinoma,+1,1	OR5F1	116	1	0			c.A574G						scavenged	.	T	ALA/THR	514,3888	235.5+/-248.0	35,444,1722	90.0	84.0	86.0		574	3.0	0.6	11	dbSNP_126	86	725,7867	176.3+/-226.2	31,663,3602	yes	missense	OR5F1	NM_003697.1	58	66,1107,5324	CC,CT,TT		8.4381,11.6765,9.5352	benign	192/315	55761528	1239,11755	2201	4296	6497	SO:0001583	missense	338674	exon1			GGATTGTGTCAGA	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"""GPCR / Class A : Olfactory receptors"""	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.574A>G	11.37:g.55761528T>C	ENSP00000278409:p.Thr192Ala	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	141	69	0.489362	NM_003697	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	37	CCDS31515.1	203	0.09294871794871795	74	0.15040650406504066	18	0.049723756906077346	45	0.07867132867132867	66	0.0870712401055409	T	14.83	2.653859	0.47362	0.116765	0.084381	ENSG00000149133	ENST00000278409	T	0.00235	8.48	3.03	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.81341	2.54	0.33552	P	0.40374	P	0.34997	0.479	B	0.40066	0.318	T	0.05616	-1.0874	8	0.66056	D	0.02	.	6.9603	0.24593	0.2046:0.0:0.0:0.7954	rs35607186	192	O95221	OR5F1_HUMAN	A	192	ENSP00000278409:T192A	ENSP00000278409:T192A	T	-	1	0	OR5F1	55518104	0.001000	0.12720	0.605000	0.28930	0.483000	0.33249	0.499000	0.22546	1.167000	0.42706	0.247000	0.18012	ACA	T|0.905;C|0.095	0.095	strong		0.453	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697	
GJB4	127534	hgsc.bcm.edu	37	1	35227306	35227306	+	Missense_Mutation	SNP	C	C	A	rs78499418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35227306C>A	ENST00000339480.1	+	2	821	c.451C>A	c.(451-453)Cgc>Agc	p.R151S	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	151					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)				TATCTTCCACCGCCTCTACAA	0.597													C|||	224	0.0447284	0.0991	0.0807	5008	,	,		20226	0.0317		0.0	False		,,,				2504	0.0051				p.R151S		Atlas-SNP	.											.	GJB4	51	.	0			c.C451A						PASS	.	C	SER/ARG	388,4018	195.7+/-220.2	16,356,1831	61.0	51.0	54.0		451	2.8	1.0	1	dbSNP_131	54	7,8593	5.0+/-18.6	0,7,4293	yes	missense	GJB4	NM_153212.2	110	16,363,6124	AA,AC,CC		0.0814,8.8062,3.0371	benign	151/267	35227306	395,12611	2203	4300	6503	SO:0001583	missense	127534	exon2			TTCCACCGCCTCT		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.451C>A	1.37:g.35227306C>A	ENSP00000345868:p.Arg151Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_153212	B3KQ82	Missense_Mutation	SNP	ENST00000339480.1	37	CCDS383.1	110	0.05036630036630037	58	0.11788617886178862	31	0.0856353591160221	21	0.03671328671328671	0	0.0	C	14.68	2.606763	0.46527	0.088062	8.14E-4	ENSG00000189433	ENST00000339480	D	0.95272	-3.66	5.73	2.76	0.32466	Gap junction protein, cysteine-rich domain (1);	0.176980	0.50627	D	0.000107	T	0.12050	0.0293	L	0.45352	1.415	0.53688	P	2.5000000000052758E-5	B	0.20780	0.048	B	0.20577	0.03	T	0.61865	-0.6975	9	0.32370	T	0.25	.	2.7568	0.05295	0.1289:0.5283:0.1251:0.2177	.	151	Q9NTQ9	CXB4_HUMAN	S	151	ENSP00000345868:R151S	ENSP00000345868:R151S	R	+	1	0	GJB4	34999893	0.000000	0.05858	0.951000	0.38953	0.977000	0.68977	-0.582000	0.05814	0.319000	0.23209	0.655000	0.94253	CGC	C|0.966;A|0.034	0.034	strong		0.597	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
ALKBH4	54784	hgsc.bcm.edu	37	7	102098035	102098035	+	Missense_Mutation	SNP	G	G	A	rs150409598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:102098035G>A	ENST00000292566.3	-	3	754	c.715C>T	c.(715-717)Cgc>Tgc	p.R239C		NM_017621.3	NP_060091.1	Q9NXW9	ALKB4_HUMAN	alkB, alkylation repair homolog 4 (E. coli)	239					actomyosin structure organization (GO:0031032)|cleavage furrow ingression (GO:0036090)|protein demethylation (GO:0006482)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	contractile ring (GO:0070938)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)	actin binding (GO:0003779)|demethylase activity (GO:0032451)|metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			kidney(1)|lung(5)|skin(2)	8						AGCAGGGAGCGGGCGGGTAAG	0.701													G|||	22	0.00439297	0.0144	0.0029	5008	,	,		15602	0.0		0.0	False		,,,				2504	0.001				p.R239C		Atlas-SNP	.											.	ALKBH4	21	.	0			c.C715T						PASS	.	G	CYS/ARG	17,4385		0,17,2184	20.0	19.0	19.0		715	3.0	1.0	7	dbSNP_134	19	0,8590		0,0,4295	no	missense	ALKBH4	NM_017621.3	180	0,17,6479	AA,AG,GG		0.0,0.3862,0.1308	probably-damaging	239/303	102098035	17,12975	2201	4295	6496	SO:0001583	missense	54784	exon3			GGGAGCGGGCGGG	BC017096	CCDS5723.1	7q22.1	2006-02-09			ENSG00000160993	ENSG00000160993		"""Alkylation repair homologs"""	21900	protein-coding gene	gene with protein product		613302					Standard	NM_017621		Approved	FLJ20013	uc003uzl.3	Q9NXW9	OTTHUMG00000157720	ENST00000292566.3:c.715C>T	7.37:g.102098035G>A	ENSP00000292566:p.Arg239Cys	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	28	0.583333	NM_017621	Q53H92|Q9H6A4	Missense_Mutation	SNP	ENST00000292566.3	37	CCDS5723.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	15.57	2.873700	0.51695	0.003862	0.0	ENSG00000160993	ENST00000292566	T	0.15718	2.4	5.08	3.05	0.35203	Oxoglutarate/iron-dependent oxygenase (1);	0.100392	0.64402	N	0.000011	T	0.11153	0.0272	M	0.89658	3.05	0.80722	D	1	P	0.49447	0.924	P	0.45577	0.486	T	0.02805	-1.1108	10	0.59425	D	0.04	-5.0926	7.4982	0.27503	0.0954:0.0:0.6433:0.2613	.	239	Q9NXW9	ALKB4_HUMAN	C	239	ENSP00000292566:R239C	ENSP00000292566:R239C	R	-	1	0	ALKBH4	101885040	0.994000	0.37717	0.991000	0.47740	0.438000	0.31896	1.036000	0.30228	1.137000	0.42214	0.561000	0.74099	CGC	G|0.996;A|0.004	0.004	strong		0.701	ALKBH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349503.1	NM_017621	
FBXO34	55030	hgsc.bcm.edu	37	14	55818162	55818162	+	Missense_Mutation	SNP	C	C	T	rs74050979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55818162C>T	ENST00000313833.4	+	2	1299	c.1054C>T	c.(1054-1056)Cct>Tct	p.P352S	FBXO34_ENST00000440021.1_Missense_Mutation_p.P352S	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	352										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						GGATTGTGGCCCTTCAAGAGC	0.532													C|||	74	0.0147764	0.053	0.0058	5008	,	,		18923	0.0		0.0	False		,,,				2504	0.0				p.P352S		Atlas-SNP	.											.	FBXO34	61	.	0			c.C1054T						PASS	.	C	SER/PRO,SER/PRO	248,4158	143.8+/-178.8	7,234,1962	118.0	112.0	114.0		1054,1054	1.2	0.0	14	dbSNP_130	114	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	74,74	7,237,6259	TT,TC,CC		0.0349,5.6287,1.9299	benign,benign	352/712,352/712	55818162	251,12755	2203	4300	6503	SO:0001583	missense	55030	exon2			TGTGGCCCTTCAA	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1054C>T	14.37:g.55818162C>T	ENSP00000313159:p.Pro352Ser	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	207	90	0.434783	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	C	2.024	-0.423983	0.04734	0.056287	3.49E-4	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.17528	2.27;2.27	5.29	1.21	0.21127	.	0.444948	0.20885	N	0.083928	T	0.01695	0.0054	M	0.66939	2.045	0.09310	N	1	B	0.10296	0.003	B	0.15484	0.013	T	0.14090	-1.0485	10	0.36615	T	0.2	-19.68	8.4711	0.32986	0.0:0.6402:0.0:0.3598	.	352	Q9NWN3	FBX34_HUMAN	S	352	ENSP00000313159:P352S;ENSP00000394117:P352S	ENSP00000313159:P352S	P	+	1	0	FBXO34	54887915	0.000000	0.05858	0.001000	0.08648	0.034000	0.12701	0.391000	0.20784	0.388000	0.25054	0.650000	0.86243	CCT	C|0.979;T|0.021	0.021	strong		0.532	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
TDP1	55775	hgsc.bcm.edu	37	14	90429749	90429749	+	Silent	SNP	A	A	G	rs3825663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:90429749A>G	ENST00000335725.4	+	3	541	c.291A>G	c.(289-291)caA>caG	p.Q97Q	TDP1_ENST00000393454.2_Silent_p.Q97Q|TDP1_ENST00000555565.1_Intron|TDP1_ENST00000357382.3_5'UTR|TDP1_ENST00000393452.3_Silent_p.Q97Q|TDP1_ENST00000555880.1_Silent_p.Q97Q	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	97					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		ATGAGCTGCAACCAGAAATGC	0.488								Repair of DNA-protein crosslinks					G|||	1355	0.270567	0.8207	0.1254	5008	,	,		20488	0.0357		0.0398	False		,,,				2504	0.1094				p.Q97Q		Atlas-SNP	.											.	TDP1	47	.	0			c.A291G						PASS	.	G	,	3033,1373	452.8+/-350.1	1075,883,245	72.0	85.0	81.0		291,291	-10.5	0.0	14	dbSNP_107	81	395,8205	801.7+/-407.4	9,377,3914	yes	coding-synonymous,coding-synonymous	TDP1	NM_001008744.1,NM_018319.3	,	1084,1260,4159	GG,GA,AA		4.593,31.1621,26.3571	,	97/609,97/609	90429749	3428,9578	2203	4300	6503	SO:0001819	synonymous_variant	55775	exon3			GCTGCAACCAGAA	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.291A>G	14.37:g.90429749A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Silent	SNP	ENST00000335725.4	37	CCDS9888.1																																																																																			A|0.735;G|0.265	0.265	strong		0.488	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319	
CDAN1	146059	hgsc.bcm.edu	37	15	43017426	43017426	+	Silent	SNP	T	T	G	rs16957091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43017426T>G	ENST00000356231.3	-	27	3497	c.3474A>C	c.(3472-3474)ctA>ctC	p.L1158L		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	1158					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)		CCAGCTCCCGTAGCAAGAATA	0.577													G|||	2311	0.461462	0.9554	0.1916	5008	,	,		19027	0.254		0.2346	False		,,,				2504	0.4325				p.L1158L		Atlas-SNP	.											.	CDAN1	70	.	0			c.A3474C						PASS	.	G		3640,766	312.5+/-292.6	1518,604,81	69.0	64.0	66.0		3474	3.0	1.0	15	dbSNP_123	66	1955,6643	724.7+/-406.5	240,1475,2584	no	coding-synonymous	CDAN1	NM_138477.2		1758,2079,2665	GG,GT,TT		22.7378,17.3854,43.0252		1158/1228	43017426	5595,7409	2203	4299	6502	SO:0001819	synonymous_variant	146059	exon27			CTCCCGTAGCAAG	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.3474A>C	15.37:g.43017426T>G		Somatic	217	2	0.00921659		WXS	Illumina HiSeq	Phase_I	170	170	1	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Silent	SNP	ENST00000356231.3	37	CCDS32209.1																																																																																			T|0.565;G|0.435	0.435	strong		0.577	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
INPPL1	3636	hgsc.bcm.edu	37	11	71945332	71945332	+	Silent	SNP	A	A	G	rs61736312	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71945332A>G	ENST00000298229.2	+	20	2424	c.2220A>G	c.(2218-2220)tcA>tcG	p.S740S	INPPL1_ENST00000541756.1_Silent_p.S498S|INPPL1_ENST00000538751.1_Silent_p.S498S	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	740					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CAGGGCTCTCAAAGACTTCAG	0.532													G|||	790	0.157748	0.3018	0.1196	5008	,	,		19677	0.1508		0.0746	False		,,,				2504	0.0828				p.S740S		Atlas-SNP	.											.	INPPL1	120	.	0			c.A2220G						PASS	.	G		1168,3232		153,862,1185	74.0	63.0	67.0		2220	-11.0	0.3	11	dbSNP_129	67	523,8063		13,497,3783	no	coding-synonymous	INPPL1	NM_001567.3		166,1359,4968	GG,GA,AA		6.0913,26.5455,13.0217		740/1259	71945332	1691,11295	2200	4293	6493	SO:0001819	synonymous_variant	3636	exon20			GCTCTCAAAGACT	Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"""Sterile alpha motif (SAM) domain containing"", ""SH2 domain containing"""	6080	protein-coding gene	gene with protein product	"""51C protein"""	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.2220A>G	11.37:g.71945332A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	149	61	0.409396	NM_001567	B2RTX5|Q13577|Q13578	Silent	SNP	ENST00000298229.2	37	CCDS8213.1																																																																																			A|0.867;G|0.133	0.133	strong		0.532	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567	
IGF2R	3482	hgsc.bcm.edu	37	6	160517481	160517481	+	Silent	SNP	C	C	T	rs1803989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160517481C>T	ENST00000356956.1	+	45	6814	c.6666C>T	c.(6664-6666)ctC>ctT	p.L2222L	RP11-288H12.3_ENST00000569097.1_RNA|IGF2R_ENST00000475584.1_3'UTR	NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2222					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)	ACGGCGATCTCGATGTCGTGT	0.498													C|||	1149	0.229433	0.2564	0.2017	5008	,	,		22131	0.4216		0.0547	False		,,,				2504	0.1943				p.L2222L		Atlas-SNP	.											.	IGF2R	251	.	0			c.C6666T						PASS	.	C		1012,3394	376.3+/-322.0	133,746,1324	287.0	203.0	232.0		6666	-7.7	0.3	6	dbSNP_89	232	493,8107	143.3+/-199.3	15,463,3822	no	coding-synonymous	IGF2R	NM_000876.2		148,1209,5146	TT,TC,CC		5.7326,22.9687,11.5716		2222/2492	160517481	1505,11501	2203	4300	6503	SO:0001819	synonymous_variant	3482	exon45			CGATCTCGATGTC	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.6666C>T	6.37:g.160517481C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	171	75	0.438596	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			C|0.839;T|0.161	0.161	strong		0.498	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
CYP4F12	66002	hgsc.bcm.edu	37	19	15794463	15794463	+	Missense_Mutation	SNP	G	G	C	rs57578760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794463G>C	ENST00000550308.1	+	7	1188	c.808G>C	c.(808-810)Gtc>Ctc	p.V270L	CYP4F12_ENST00000324632.10_Missense_Mutation_p.V270L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	270					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CACAGACGCTGTCATCCGGGA	0.537													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20833	0.0		0.001	False		,,,				2504	0.0				p.V270L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.G808C						PASS	.	G	LEU/VAL	254,4142		0,254,1944	93.0	93.0	93.0		808	-1.0	0.1	19	dbSNP_129	93	2,8594		0,2,4296	no	missense	CYP4F12	NM_023944.3	32	0,256,6240	CC,CG,GG		0.0233,5.778,1.9704	possibly-damaging	270/525	15794463	256,12736	2198	4298	6496	SO:0001583	missense	66002	exon7			GACGCTGTCATCC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.808G>C	19.37:g.15794463G>C	ENSP00000448998:p.Val270Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	154	44	0.285714	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	.	11.57	1.677010	0.29783	0.05778	2.33E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.67698	-0.28;-0.28	2.47	-0.985	0.10256	.	0.093718	0.42172	U	0.000741	T	0.25680	0.0625	M	0.76002	2.32	0.31890	N	0.617322	P	0.51147	0.942	P	0.58577	0.841	T	0.62029	-0.6940	10	0.87932	D	0	.	6.6191	0.22792	0.3804:0.0:0.6196:0.0	rs57578760	270	Q9HCS2	CP4FC_HUMAN	L	270	ENSP00000448998:V270L;ENSP00000321821:V270L	ENSP00000321821:V270L	V	+	1	0	CYP4F12	15655463	0.981000	0.34729	0.078000	0.20375	0.184000	0.23303	1.826000	0.39092	-0.124000	0.11724	0.491000	0.48974	GTC	G|0.973;C|0.027	0.027	strong		0.537	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417731	105417731	+	Missense_Mutation	SNP	G	G	C	rs199870471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417731G>C	ENST00000333244.5	-	7	4176	c.4057C>G	c.(4057-4059)Ctg>Gtg	p.L1353V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1353						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)			GGTGCAGACAGGTCCACGGAG	0.597													.|||	284	0.0567093	0.0113	0.1311	5008	,	,		13717	0.0129		0.1153	False		,,,				2504	0.0501				p.L1353V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4057G						PASS	.						125.0	106.0	114.0					14																	105417731		1812	2876	4688	SO:0001583	missense	113146	exon7			CAGACAGGTCCAC	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.4057C>G	14.37:g.105417731G>C	ENSP00000353114:p.Leu1353Val	Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	261	108	0.413793	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	0.008	-1.901985	0.00517	.	.	ENSG00000185567	ENST00000333244	T	0.01933	4.55	4.27	0.17	0.15021	.	.	.	.	.	T	0.00784	0.0026	N	0.01529	-0.815	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46721	-0.9171	9	0.02654	T	1	-1.5949	5.7398	0.18087	0.0:0.3359:0.4011:0.263	.	1353	Q8IVF2	AHNK2_HUMAN	V	1353	ENSP00000353114:L1353V	ENSP00000353114:L1353V	L	-	1	2	AHNAK2	104488776	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.272000	0.01165	-0.259000	0.09432	-1.901000	0.00528	CTG	.	.	weak		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OAS3	4940	hgsc.bcm.edu	37	12	113376452	113376452	+	Silent	SNP	C	C	T	rs1859329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113376452C>T	ENST00000228928.7	+	1	296	c.117C>T	c.(115-117)gcC>gcT	p.A39A	OAS3_ENST00000548514.1_Silent_p.A39A|OAS3_ENST00000546638.1_3'UTR|OAS3_ENST00000551007.1_Silent_p.A39A|RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	39	OAS domain 1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						TGGCCGCTGCCCTGAGGGAGC	0.701													C|||	3937	0.786142	0.9887	0.7738	5008	,	,		12918	0.748		0.6352	False		,,,				2504	0.7157				p.A39A		Atlas-SNP	.											.	OAS3	63	.	0			c.C117T						PASS	.	C		3337,247		1556,225,11	7.0	8.0	8.0		117	0.8	0.0	12	dbSNP_92	8	5199,2777		1738,1723,527	no	coding-synonymous	OAS3	NM_006187.2		3294,1948,538	TT,TC,CC		34.817,6.8917,26.1592		39/1088	113376452	8536,3024	1792	3988	5780	SO:0001819	synonymous_variant	4940	exon1			CGCTGCCCTGAGG	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.117C>T	12.37:g.113376452C>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	21	20	0.952381	NM_006187	Q2HJ14|Q9H3P5	Silent	SNP	ENST00000228928.7	37	CCDS44981.1																																																																																			T|0.775;C|0.225	0.775	strong		0.701	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
PSG2	5670	hgsc.bcm.edu	37	19	43579642	43579642	+	Silent	SNP	A	A	G	rs1803670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43579642A>G	ENST00000406487.1	-	3	671	c.573T>C	c.(571-573)caT>caC	p.H191H		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	191	Ig-like C2-type 1.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				GCTGAAACCTATGAGTCATAG	0.493													A|||	1309	0.261382	0.5477	0.1729	5008	,	,		19639	0.0655		0.165	False		,,,				2504	0.2382				p.H191H		Atlas-SNP	.											.	PSG2	84	.	0			c.T573C						PASS	.	A		2058,2346		511,1036,655	253.0	259.0	257.0		573	0.2	0.0	19	dbSNP_131	257	1666,6930		169,1328,2801	no	coding-synonymous	PSG2	NM_031246.3		680,2364,3456	GG,GA,AA		19.3811,46.7302,28.6462		191/336	43579642	3724,9276	2202	4298	6500	SO:0001819	synonymous_variant	5670	exon3			AAACCTATGAGTC		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.573T>C	19.37:g.43579642A>G		Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	286	136	0.475524	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			A|0.738;G|0.262	0.262	strong		0.493	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209179939	209179939	+	Missense_Mutation	SNP	A	A	G	rs16840913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:209179939A>G	ENST00000264380.4	+	15	2007	c.1849A>G	c.(1849-1851)Atg>Gtg	p.M617V		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	617			M -> V (in dbSNP:rs16840913).		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						TAACCACATGATGGCACTACT	0.408													A|||	141	0.028155	0.0651	0.0144	5008	,	,		19992	0.0		0.0308	False		,,,				2504	0.0143				p.M617V		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.A1849G						PASS	.	A	VAL/MET	229,4177	136.5+/-172.5	5,219,1979	102.0	84.0	90.0		1849	4.5	1.0	2	dbSNP_123	90	245,8355	97.7+/-159.3	2,241,4057	yes	missense	PIKFYVE	NM_015040.3	21	7,460,6036	GG,GA,AA		2.8488,5.1975,3.6445	possibly-damaging	617/2099	209179939	474,12532	2203	4300	6503	SO:0001583	missense	200576	exon15			CACATGATGGCAC	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.1849A>G	2.37:g.209179939A>G	ENSP00000264380:p.Met617Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	50	0.022893772893772892	27	0.054878048780487805	4	0.011049723756906077	0	0.0	19	0.025065963060686015	A	16.98	3.270494	0.59540	0.051975	0.028488	ENSG00000115020	ENST00000264380;ENST00000392200;ENST00000452564	T;T	0.77750	-1.12;-1.12	5.64	4.49	0.54785	.	0.000000	0.85682	D	0.000000	T	0.42337	0.1198	N	0.25647	0.755	0.80722	D	1	P;P	0.50156	0.932;0.726	D;P	0.67103	0.949;0.762	T	0.62676	-0.6804	10	0.25751	T	0.34	-20.3305	11.7245	0.51702	0.931:0.0:0.069:0.0	rs16840913;rs52824421;rs16840913	617;561	Q9Y2I7;E9PDH4	FYV1_HUMAN;.	V	617;193;561	ENSP00000264380:M617V;ENSP00000405736:M561V	ENSP00000264380:M617V	M	+	1	0	PIKFYVE	208888184	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	1.083000	0.41159	0.528000	0.53228	ATG	A|0.965;G|0.035	0.035	strong		0.408	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
FBXO34	55030	hgsc.bcm.edu	37	14	55818706	55818706	+	Missense_Mutation	SNP	T	T	C	rs3742569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55818706T>C	ENST00000313833.4	+	2	1843	c.1598T>C	c.(1597-1599)cTg>cCg	p.L533P	FBXO34_ENST00000440021.1_Missense_Mutation_p.L533P	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	533			L -> P (in dbSNP:rs3742569). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.					p.L533P(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						CCATTTGTACTGCCAGCCTCT	0.502													t|||	1992	0.397764	0.4713	0.3314	5008	,	,		19439	0.3185		0.4245	False		,,,				2504	0.3998				p.L533P		Atlas-SNP	.											FBXO34,NS,carcinoma,0,1	FBXO34	61	1	1	Substitution - Missense(1)	stomach(1)	c.T1598C						PASS	.	C	PRO/LEU,PRO/LEU	1984,2422	617.4+/-393.0	424,1136,643	130.0	126.0	127.0		1598,1598	-1.4	0.0	14	dbSNP_107	127	3629,4971	625.6+/-397.7	784,2061,1455	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	98,98	1208,3197,2098	CC,CT,TT		42.1977,45.0295,43.157	benign,benign	533/712,533/712	55818706	5613,7393	2203	4300	6503	SO:0001583	missense	55030	exon2			TTGTACTGCCAGC	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1598T>C	14.37:g.55818706T>C	ENSP00000313159:p.Leu533Pro	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	217	107	0.493088	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	857	0.3923992673992674	224	0.45528455284552843	119	0.3287292817679558	191	0.3339160839160839	323	0.4261213720316623	C	0.442	-0.898108	0.02472	0.450295	0.421977	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.20069	2.1;2.1	5.49	-1.35	0.09114	.	0.711289	0.12725	N	0.444330	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45512	-0.9256	9	0.42905	T	0.14	-15.7575	11.6878	0.51497	0.0:0.3231:0.0:0.6769	rs3742569;rs17674206;rs52807065;rs61280222;rs3742569	533	Q9NWN3	FBX34_HUMAN	P	533	ENSP00000313159:L533P;ENSP00000394117:L533P	ENSP00000313159:L533P	L	+	2	0	FBXO34	54888459	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.774000	0.04684	-0.553000	0.06158	-0.716000	0.03619	CTG	T|0.582;C|0.418	0.418	strong		0.502	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
SLC22A16	85413	hgsc.bcm.edu	37	6	110777962	110777962	+	Silent	SNP	A	A	G	rs6907567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:110777962A>G	ENST00000368919.3	-	2	378	c.312T>C	c.(310-312)aaT>aaC	p.N104N	SLC22A16_ENST00000461487.1_5'UTR|SLC22A16_ENST00000439654.1_Silent_p.N104N|SLC22A16_ENST00000330550.4_Silent_p.N70N|SLC22A16_ENST00000456137.2_Silent_p.N104N	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	104					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)	TCTCCCTCTTATTCCTGCTAC	0.473													G|||	1573	0.314097	0.3888	0.2406	5008	,	,		19928	0.4107		0.2207	False		,,,				2504	0.2618				p.N104N		Atlas-SNP	.											.	SLC22A16	81	.	0			c.T312C						PASS	.	G		1600,2806	663.6+/-401.2	281,1038,884	241.0	238.0	239.0		312	0.3	0.0	6	dbSNP_116	239	1917,6683	726.4+/-406.6	180,1557,2563	no	coding-synonymous	SLC22A16	NM_033125.2		461,2595,3447	GG,GA,AA		22.2907,36.3141,27.0414		104/578	110777962	3517,9489	2203	4300	6503	SO:0001819	synonymous_variant	85413	exon2			CCTCTTATTCCTG		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.312T>C	6.37:g.110777962A>G		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	317	144	0.454259	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Silent	SNP	ENST00000368919.3	37	CCDS5084.1																																																																																			A|0.716;G|0.284	0.284	strong		0.473	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
LOXL2	4017	hgsc.bcm.edu	37	8	23174481	23174481	+	Silent	SNP	G	G	A	rs7357444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:23174481G>A	ENST00000389131.3	-	9	1986	c.1617C>T	c.(1615-1617)gcC>gcT	p.A539A		NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	539	SRCR 4. {ECO:0000255|PROSITE- ProRule:PRU00196}.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		AGGCAACTCCGGCCCCGTACT	0.657													G|||	366	0.0730831	0.1286	0.1412	5008	,	,		16494	0.0595		0.0129	False		,,,				2504	0.0256				p.A539A		Atlas-SNP	.											.	LOXL2	97	.	0			c.C1617T						PASS	.	G		558,3846	250.0+/-257.2	42,474,1686	51.0	46.0	48.0		1617	-6.8	0.8	8	dbSNP_116	48	43,8557	27.9+/-77.7	0,43,4257	no	coding-synonymous	LOXL2	NM_002318.2		42,517,5943	AA,AG,GG		0.5,12.6703,4.6217		539/775	23174481	601,12403	2202	4300	6502	SO:0001819	synonymous_variant	4017	exon9			AACTCCGGCCCCG	U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.1617C>T	8.37:g.23174481G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_002318	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Silent	SNP	ENST00000389131.3	37	CCDS34864.1																																																																																			G|0.949;A|0.051	0.051	strong		0.657	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1		
VPS9D1	9605	hgsc.bcm.edu	37	16	89778919	89778919	+	Silent	SNP	T	T	C	rs139626173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89778919T>C	ENST00000389386.3	-	6	679	c.555A>G	c.(553-555)ctA>ctG	p.L185L	VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000565452.1_5'Flank|VPS9D1_ENST00000561976.1_Silent_p.L115L	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	185					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										TCTGCCGCTGTAGAGAGAGGG	0.662													t|||	80	0.0159744	0.0575	0.0058	5008	,	,		12775	0.0		0.0	False		,,,				2504	0.0				p.L185L		Atlas-SNP	.											.	.	.	.	0			c.A555G						PASS	.			191,3575		3,185,1695	49.0	56.0	54.0		555	0.6	1.0	16	dbSNP_134	54	4,8210		0,4,4103	no	coding-synonymous	C16orf7	NM_004913.2		3,189,5798	CC,CT,TT		0.0487,5.0717,1.6277		185/632	89778919	195,11785	1883	4107	5990	SO:0001819	synonymous_variant	9605	exon6			CCGCTGTAGAGAG	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.555A>G	16.37:g.89778919T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	38	27	0.710526	NM_004913		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																			T|0.989;C|0.011	0.011	strong		0.662	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913	
TYW1	55253	hgsc.bcm.edu	37	7	66660247	66660247	+	Silent	SNP	T	T	C	rs55673383		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:66660247T>C	ENST00000359626.5	+	15	2064	c.1900T>C	c.(1900-1902)Ttg>Ctg	p.L634L		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	634					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)	p.L634L(1)		breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				TGTCCACGAGTTGGTGGATCT	0.478																																					p.L634L		Atlas-SNP	.											TYW1,NS,carcinoma,0,1	TYW1	71	1	1	Substitution - coding silent(1)	stomach(1)	c.T1900C						scavenged	.						147.0	152.0	150.0					7																	66660247		2203	4299	6502	SO:0001819	synonymous_variant	55253	exon15			CACGAGTTGGTGG	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1900T>C	7.37:g.66660247T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	138	37	0.268116	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	37	CCDS5538.1																																																																																			T|0.500;C|0.500	0.500	weak		0.478	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
CPB2	1361	hgsc.bcm.edu	37	13	46638826	46638826	+	Silent	SNP	G	G	A	rs2277440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:46638826G>A	ENST00000181383.4	-	8	769	c.753C>T	c.(751-753)atC>atT	p.I251I	CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606243.1_RNA|CPB2_ENST00000439329.3_Silent_p.I214I|CPB2-AS1_ENST00000606991.1_RNA|CPB2-AS1_ENST00000606351.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	251					blood coagulation (GO:0007596)|cellular response to glucose stimulus (GO:0071333)|fibrinolysis (GO:0042730)|liver regeneration (GO:0097421)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of plasminogen activation (GO:0010757)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to heat (GO:0009408)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.I251I(1)		NS(1)|cervix(1)|large_intestine(3)|liver(1)|lung(9)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		GGTCTGTTCCGATGCAATGAT	0.423													G|||	718	0.143371	0.1112	0.1556	5008	,	,		20854	0.2917		0.0626	False		,,,				2504	0.1084				p.I251I		Atlas-SNP	.											CPB2,NS,carcinoma,0,1	CPB2	60	1	1	Substitution - coding silent(1)	stomach(1)	c.C753T						PASS	.	G	,	546,3860	247.2+/-255.5	39,468,1696	188.0	156.0	167.0		753,642	-11.3	0.0	13	dbSNP_100	167	544,8056	149.2+/-204.3	10,524,3766	no	coding-synonymous,coding-synonymous	CPB2	NM_001872.3,NM_016413.3	,	49,992,5462	AA,AG,GG		6.3256,12.3922,8.3807	,	251/424,214/361	46638826	1090,11916	2203	4300	6503	SO:0001819	synonymous_variant	1361	exon8			TGTTCCGATGCAA	M75106	CCDS9401.1, CCDS73568.1	13q14.11	2012-02-10	2007-02-21		ENSG00000080618	ENSG00000080618			2300	protein-coding gene	gene with protein product	"""thrombin-activatable fibrinolysis inhibitor"", ""carboxypeptidase U"", ""plasma carboxypeptidase B"", ""carboxypeptidase R"""	603101	"""carboxypeptidase B2 (plasma, carboxypeptidase U)"""			1939207, 1427879	Standard	NM_001278541		Approved	CPU, PCPB, TAFI	uc001vaw.3	Q96IY4	OTTHUMG00000016867	ENST00000181383.4:c.753C>T	13.37:g.46638826G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_001872	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Silent	SNP	ENST00000181383.4	37	CCDS9401.1																																																																																			G|0.890;A|0.110	0.110	strong		0.423	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872	
ITPR2	3709	hgsc.bcm.edu	37	12	26816779	26816779	+	Splice_Site	SNP	C	C	T	rs77639758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26816779C>T	ENST00000381340.3	-	15	1968	c.1552G>A	c.(1552-1554)Gta>Ata	p.V518I		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	518					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)	ATTCCAAATACCTATCAGGAA	0.338													C|||	19	0.00379393	0.0136	0.0014	5008	,	,		15680	0.0		0.0	False		,,,				2504	0.0				p.V518I		Atlas-SNP	.											.	ITPR2	270	.	0			c.G1552A						PASS	.	C	ILE/VAL	30,3602		0,30,1786	151.0	148.0	149.0		1552	4.5	1.0	12	dbSNP_131	149	0,8144		0,0,4072	yes	missense-near-splice	ITPR2	NM_002223.2	29	0,30,5858	TT,TC,CC		0.0,0.826,0.2548	benign	518/2702	26816779	30,11746	1816	4072	5888	SO:0001630	splice_region_variant	3709	exon15			CAAATACCTATCA	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.1552-1G>A	12.37:g.26816779C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	4.645	0.119815	0.08881	0.00826	0.0	ENSG00000123104	ENST00000381340	D	0.96885	-4.16	4.5	4.5	0.54988	Intracellular calcium-release channel (1);	0.053381	0.64402	D	0.000001	T	0.78317	0.4264	N	0.01242	-0.935	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.77744	-0.2473	10	0.02654	T	1	.	5.5858	0.17274	0.0:0.7597:0.0:0.2403	.	518	Q14571	ITPR2_HUMAN	I	518	ENSP00000370744:V518I	ENSP00000370744:V518I	V	-	1	0	ITPR2	26708046	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	4.869000	0.63028	2.489000	0.83994	0.655000	0.94253	GTA	C|0.998;T|0.002	0.002	strong		0.338	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	Missense_Mutation
MICALCL	84953	hgsc.bcm.edu	37	11	12315915	12315915	+	Missense_Mutation	SNP	A	A	G	rs1493954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	24	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	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	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240577	39240577	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39240577A>G	ENST00000391417.4	+	1	119	c.119A>G	c.(118-120)tAc>tGc	p.Y40C		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	40	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						ACCACCTGCTACCGCCCCAGC	0.657																																					p.Y40C		Atlas-SNP	.											.	KRTAP4-7	49	.	0			c.A119G						PASS	.						13.0	22.0	19.0					17																	39240577		692	1590	2282	SO:0001583	missense	100132476	exon1			CCTGCTACCGCCC	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.119A>G	17.37:g.39240577A>G	ENSP00000375236:p.Tyr40Cys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	135	16	0.118519	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-2.883871	0.00061	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00666	5.91	3.63	1.53	0.23141	.	0.603408	0.12340	N	0.477557	T	0.00412	0.0013	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44390	-0.9331	9	0.02654	T	1	.	5.5941	0.17317	0.2179:0.1587:0.6234:0.0	.	40	Q9BYR0	KRA47_HUMAN	C	40	ENSP00000375236:Y40C	ENSP00000375236:Y40C	Y	+	2	0	KRTAP4-9;KRTAP4-7	36494103	0.873000	0.30073	0.022000	0.16811	0.001000	0.01503	1.032000	0.30178	-0.124000	0.11724	-2.594000	0.00164	TAC	.	.	none		0.657	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
COL5A1	1289	hgsc.bcm.edu	37	9	137707834	137707834	+	Splice_Site	SNP	G	G	A	rs3827848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:137707834G>A	ENST00000371817.3	+	52	4536	c.4122G>A	c.(4120-4122)acG>acA	p.T1374T		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1374	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.T1374T(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCGGGCAGACGGTGAGTCCAC	0.552													G|||	650	0.129792	0.1014	0.0994	5008	,	,		20008	0.1696		0.1392	False		,,,				2504	0.1391				p.T1374T		Atlas-SNP	.											COL5A1,NS,carcinoma,0,2	COL5A1	323	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.G4122A						PASS	.	G		486,3920	228.1+/-243.1	34,418,1751	143.0	131.0	135.0		4122	3.2	1.0	9	dbSNP_107	135	1358,7242	264.8+/-285.7	114,1130,3056	yes	coding-synonymous-near-splice	COL5A1	NM_000093.3		148,1548,4807	AA,AG,GG		15.7907,11.0304,14.1781		1374/1839	137707834	1844,11162	2203	4300	6503	SO:0001630	splice_region_variant	1289	exon52			GCAGACGGTGAGT	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4122+1G>A	9.37:g.137707834G>A		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	237	76	0.320675	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			G|0.865;A|0.135	0.135	strong		0.552	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Silent
CHAT	1103	hgsc.bcm.edu	37	10	50824117	50824117	+	Intron	SNP	G	G	A	rs1880676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50824117G>A	ENST00000337653.2	+	2	439				CHAT_ENST00000395559.2_Intron|CHAT_ENST00000460699.1_Intron|CHAT_ENST00000395562.2_Missense_Mutation_p.D7N|CHAT_ENST00000351556.3_Intron|CHAT_ENST00000455728.2_Intron|CHAT_ENST00000339797.1_Intron	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase						adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	GGAATGCAGAGATGAAGCACT	0.502													G|||	809	0.161542	0.0061	0.1686	5008	,	,		23013	0.1716		0.2316	False		,,,				2504	0.2843				p.D7N		Atlas-SNP	.											CHAT_ENST00000395562,NS,meningioma,0,1	CHAT	162	1	0			c.G19A						PASS	.	G	,ASN/ASP,,,,,	157,2979		6,145,1417	205.0	171.0	181.0		,19,,,,,	3.2	0.0	10	dbSNP_92	181	1775,5389		221,1333,2028	yes	intron,missense,utr-5,intron,intron,intron,intron	CHAT	NM_001142929.1,NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3,NM_020985.3,NM_020986.3	,23,,,,,	227,1478,3445	AA,AG,GG		24.7767,5.0064,18.7573	,,,,,,	,7/667,,,,,	50824117	1932,8368	1568	3582	5150	SO:0001627	intron_variant	1103	exon2			TGCAGAGATGAAG	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.287-431G>A	10.37:g.50824117G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	138	67	0.485507	NM_001142933	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	334	0.15293040293040294	5	0.01016260162601626	77	0.212707182320442	89	0.1555944055944056	163	0.21503957783641162	G	13.30	2.197365	0.38806	0.050064	0.247767	ENSG00000070748	ENST00000395562	D	0.85088	-1.94	3.16	3.16	0.36331	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.36813	P	0.11398900000000001	.	.	.	.	.	.	T	0.00984	-1.1491	5	0.87932	D	0	.	10.0691	0.42322	0.0:0.0:1.0:0.0	rs1880676;rs56499801;rs59491670;rs1880676	.	.	.	N	7	ENSP00000378929:D7N	ENSP00000378929:D7N	D	+	1	0	CHAT	50494123	0.004000	0.15560	0.013000	0.15412	0.005000	0.04900	1.413000	0.34725	2.090000	0.63153	0.655000	0.94253	GAT	G|0.836;A|0.164	0.164	strong		0.502	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
C8orf74	203076	hgsc.bcm.edu	37	8	10557760	10557760	+	Missense_Mutation	SNP	A	A	G	rs57041981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10557760A>G	ENST00000304519.5	+	4	693	c.664A>G	c.(664-666)Atc>Gtc	p.I222V	RP1L1_ENST00000329335.3_Intron	NM_001040032.1	NP_001035121	Q6P047	CH074_HUMAN	chromosome 8 open reading frame 74	222			I -> V (in dbSNP:rs57041981).							central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13				COAD - Colon adenocarcinoma(149;0.0811)		GGAGAGCCTCATCTGCCAGGC	0.592													G|||	1241	0.247804	0.7247	0.111	5008	,	,		14931	0.123		0.0099	False		,,,				2504	0.0736				p.I222V		Atlas-SNP	.											.	C8orf74	28	.	0			c.A664G						PASS	.	G	VAL/ILE	2298,1754		663,972,391	64.0	71.0	69.0		664	-1.6	0.0	8	dbSNP_129	69	56,8294		0,56,4119	yes	missense	C8orf74	NM_001040032.1	29	663,1028,4510	GG,GA,AA		0.6707,43.2873,18.9808	benign	222/295	10557760	2354,10048	2026	4175	6201	SO:0001583	missense	203076	exon4			AGCCTCATCTGCC	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.664A>G	8.37:g.10557760A>G	ENSP00000307129:p.Ile222Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_001040032	A2RUD6	Missense_Mutation	SNP	ENST00000304519.5	37	CCDS47800.1	476	0.21794871794871795	358	0.7276422764227642	28	0.07734806629834254	86	0.15034965034965034	4	0.005277044854881266	G	0.021	-1.419368	0.01136	0.567127	0.006707	ENSG00000171060	ENST00000304519	T	0.28255	1.62	5.01	-1.59	0.08453	.	0.452401	0.20972	N	0.082365	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	0.39418	-0.9615	9	0.05620	T	0.96	.	10.9154	0.47133	0.4434:0.0:0.5566:0.0	rs57041981;rs61748919	222	Q6P047	CH074_HUMAN	V	222	ENSP00000307129:I222V	ENSP00000307129:I222V	I	+	1	0	C8orf74	10595170	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.083000	0.11286	-0.786000	0.04516	-1.163000	0.01768	ATC	A|0.822;G|0.178	0.178	strong		0.592	C8orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375675.1	NM_001040032	
MUC4	4585	hgsc.bcm.edu	37	3	195512079	195512079	+	Silent	SNP	C	C	A	rs200031229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512079C>A	ENST00000463781.3	-	2	6831	c.6372G>T	c.(6370-6372)ggG>ggT	p.G2124G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.G2124G	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)		GGGTGGTGTCCCCTGTGGATA	0.567																																					p.G2124G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.G6372T						PASS	.						76.0	67.0	70.0					3																	195512079		691	1590	2281	SO:0001819	synonymous_variant	4585	exon2			GGTGTCCCCTGTG	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.6372G>T	3.37:g.195512079C>A		Somatic	632	3	0.00474684		WXS	Illumina HiSeq	Phase_I	354	195	0.550847	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																																																																																			C|0.922;A|0.078	0.078	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HRCT1	646962	hgsc.bcm.edu	37	9	35906601	35906601	+	Missense_Mutation	SNP	C	C	A	rs565823201|rs112212538		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35906601C>A	ENST00000354323.2	+	1	413	c.317C>A	c.(316-318)cCc>cAc	p.P106H	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	106	His-rich.					integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						caccaccacccccaccgccac	0.677																																					p.P106H		Atlas-SNP	.											.	HRCT1	14	.	0			c.C317A						PASS	.						6.0	6.0	6.0					9																	35906601		1795	3578	5373	SO:0001583	missense	646962	exon1			ACCACCCCCACCG		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.317C>A	9.37:g.35906601C>A	ENSP00000346283:p.Pro106His	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	36	22	0.611111	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	337	0.1543040293040293	82	0.16666666666666666	47	0.1298342541436464	45	0.07867132867132867	163	0.21503957783641162	C	1.568	-0.535019	0.04082	.	.	ENSG00000196196	ENST00000354323	.	.	.	0.571	-1.14	0.09741	.	2.262810	0.02394	N	0.080002	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	P	0.36944	0.574	B	0.32465	0.146	T	0.09751	-1.0660	7	0.87932	D	0	-19.8215	.	.	.	.	106	Q6UXD1	HRCT1_HUMAN	H	106	.	ENSP00000346283:P106H	P	+	2	0	HRCT1	35896601	0.000000	0.05858	0.011000	0.14972	0.341000	0.28922	-0.113000	0.10774	-1.188000	0.02705	-0.718000	0.03613	CCC	C|0.846;A|0.154	0.154	strong		0.677	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
ULK4	54986	hgsc.bcm.edu	37	3	41952852	41952852	+	Missense_Mutation	SNP	T	T	C	rs35263917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:41952852T>C	ENST00000301831.4	-	11	1504	c.1042A>G	c.(1042-1044)Agt>Ggt	p.S348G	ULK4_ENST00000420927.1_Missense_Mutation_p.S348G	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	348			S -> G (in dbSNP:rs35263917). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TCAAGAGTACTCTTAGGCCGA	0.343													T|||	421	0.0840655	0.0635	0.0908	5008	,	,		20625	0.002		0.166	False		,,,				2504	0.1074				p.S348G		Atlas-SNP	.											ULK4_ENST00000301831,colon,carcinoma,+1,2	ULK4	150	2	0			c.A1042G						PASS	.	T	GLY/SER	283,3385		9,265,1560	94.0	88.0	90.0		1042	5.2	0.9	3	dbSNP_126	90	1227,6941		90,1047,2947	yes	missense	ULK4	NM_017886.2	56	99,1312,4507	CC,CT,TT		15.022,7.7154,12.7577	possibly-damaging	348/1276	41952852	1510,10326	1834	4084	5918	SO:0001583	missense	54986	exon11			GAGTACTCTTAGG	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1042A>G	3.37:g.41952852T>C	ENSP00000301831:p.Ser348Gly	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	203	100	0.492611	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	198	0.09065934065934066	31	0.06300813008130081	32	0.08839779005524862	2	0.0034965034965034965	133	0.17546174142480211	T	21.5	4.164150	0.78339	0.077154	0.15022	ENSG00000168038	ENST00000301831;ENST00000420927	T;T	0.69040	0.42;-0.37	5.22	5.22	0.72569	.	0.707959	0.15193	N	0.275422	T	0.00300	0.0009	M	0.71581	2.175	0.09310	P	1.0	P	0.48911	0.917	B	0.43950	0.437	T	0.20907	-1.0261	9	0.62326	D	0.03	.	14.1258	0.65219	0.0:0.0:0.0:1.0	rs35263917;rs61740620	348	Q96C45	ULK4_HUMAN	G	348	ENSP00000301831:S348G;ENSP00000412187:S348G	ENSP00000301831:S348G	S	-	1	0	ULK4	41927856	1.000000	0.71417	0.918000	0.36340	0.766000	0.43426	5.411000	0.66386	1.979000	0.57680	0.529000	0.55759	AGT	T|0.887;C|0.113	0.113	strong		0.343	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
SERPINH1	871	hgsc.bcm.edu	37	11	75277757	75277757	+	Silent	SNP	C	C	G	rs650241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:75277757C>G	ENST00000524558.1	+	2	1798	c.363C>G	c.(361-363)tcC>tcG	p.S121S	SERPINH1_ENST00000358171.3_Silent_p.S121S|SERPINH1_ENST00000530284.1_Silent_p.S121S|SERPINH1_ENST00000533603.1_Silent_p.S121S|SERPINH1_ENST00000525876.1_5'Flank			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	121					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					TCAGCAACTCCACGGCGCGCA	0.672													C|||	1868	0.373003	0.4614	0.3804	5008	,	,		16855	0.2103		0.2972	False		,,,				2504	0.4939				p.S121S		Atlas-SNP	.											SERPINH1,NS,carcinoma,0,1	SERPINH1	33	1	0			c.C363G						PASS	.	C	,	1898,2502		424,1050,726	20.0	18.0	18.0		363,363	4.1	0.9	11	dbSNP_83	18	2587,5991		381,1825,2083	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	805,2875,2809	GG,GC,CC		30.1585,43.1364,34.5585	,	121/419,121/419	75277757	4485,8493	2200	4289	6489	SO:0001819	synonymous_variant	871	exon2			CAACTCCACGGCG	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.363C>G	11.37:g.75277757C>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																			C|0.668;G|0.332	0.332	strong		0.672	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
YY1AP1	55249	hgsc.bcm.edu	37	1	155629982	155629982	+	Missense_Mutation	SNP	C	C	T	rs145852062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155629982C>T	ENST00000295566.4	-	11	1880	c.1857G>A	c.(1855-1857)atG>atA	p.M619I	YY1AP1_ENST00000404643.1_Missense_Mutation_p.M553I|YY1AP1_ENST00000368330.2_Missense_Mutation_p.M573I|YY1AP1_ENST00000311573.5_Missense_Mutation_p.M542I|YY1AP1_ENST00000361831.5_Missense_Mutation_p.M562I|YY1AP1_ENST00000368339.5_Missense_Mutation_p.M711I|YY1AP1_ENST00000359205.5_Missense_Mutation_p.M562I|YY1AP1_ENST00000535662.1_Missense_Mutation_p.M419I|YY1AP1_ENST00000407221.1_Missense_Mutation_p.M542I|YY1AP1_ENST00000355499.4_Missense_Mutation_p.M573I|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000368340.5_Missense_Mutation_p.M691I|YY1AP1_ENST00000347088.5_Missense_Mutation_p.M573I|MSTO1_ENST00000452804.2_Intron	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	619					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					CAGGCTGGATCATGTTACAGC	0.537													C|||	100	0.0199681	0.0719	0.0072	5008	,	,		19458	0.0		0.0	False		,,,				2504	0.0				p.M711I		Atlas-SNP	.											.	YY1AP1	104	.	0			c.G2133A						PASS	.	C	,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	286,4120	156.6+/-189.7	10,266,1927	87.0	80.0	83.0		,1521,1719,1857,1686,1659,2073,2133,1719,1719,1686,1686	2.5	1.0	1	dbSNP_134	83	2,8592	1.2+/-3.3	0,2,4295	no	utr-3,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	YY1AP1	NM_001198906.1,NM_139121.2,NM_139119.2,NM_139118.2,NM_018253.3,NM_001198905.1,NM_001198904.1,NM_001198903.1,NM_001198902.1,NM_001198901.1,NM_001198900.1,NM_001198899.1	,10,10,10,10,10,10,10,10,10,10,10	10,268,6222	TT,TC,CC		0.0233,6.4911,2.2154	,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	,507/685,573/751,619/797,562/740,553/731,691/869,711/889,573/751,573/751,562/740,562/740	155629982	288,12712	2203	4297	6500	SO:0001583	missense	55249	exon10			CTGGATCATGTTA	BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.1857G>A	1.37:g.155629982C>T	ENSP00000295566:p.Met619Ile	Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	320	162	0.50625	NM_001198903	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	37	CCDS1115.1	34	0.015567765567765568	31	0.06300813008130081	3	0.008287292817679558	0	0.0	0	0.0	c	13.31	2.198345	0.38806	0.064911	2.33E-4	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000535662	T;T;T;T;T;T;T;T;T;T;T;T	0.23552	1.96;1.96;1.97;1.96;1.96;1.92;1.95;1.96;1.97;1.98;1.9;1.97	2.53	2.53	0.30540	.	0.744128	0.12619	N	0.453204	T	0.13457	0.0326	L	0.47716	1.5	0.80722	D	1	B;B;B;B;B	0.21905	0.009;0.013;0.031;0.062;0.053	B;B;B;B;B	0.34652	0.015;0.02;0.187;0.068;0.013	T	0.08207	-1.0733	10	0.16896	T	0.51	.	13.0809	0.59114	0.0:1.0:0.0:0.0	.	711;553;619;573;691	B4DMP2;Q9H869-4;Q9H869;Q9H869-2;Q5VYZ1	.;.;YYAP1_HUMAN;.;.	I	562;573;542;573;562;691;619;573;542;553;711;419	ENSP00000352134:M562I;ENSP00000347686:M573I;ENSP00000311138:M542I;ENSP00000316079:M573I;ENSP00000355298:M562I;ENSP00000357324:M691I;ENSP00000295566:M619I;ENSP00000357314:M573I;ENSP00000385791:M542I;ENSP00000385390:M553I;ENSP00000357323:M711I;ENSP00000437926:M419I	ENSP00000295566:M619I	M	-	3	0	YY1AP1	153896606	1.000000	0.71417	0.995000	0.50966	0.972000	0.66771	2.589000	0.46145	1.419000	0.47118	0.306000	0.20318	ATG	C|0.981;T|0.019	0.019	strong		0.537	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118	
KMT2C	58508	hgsc.bcm.edu	37	7	151927070	151927070	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151927070C>T	ENST00000262189.6	-	18	3132	c.2914G>A	c.(2914-2916)Gga>Aga	p.G972R	KMT2C_ENST00000355193.2_Missense_Mutation_p.G972R	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	972					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)										AGTAATCTTCCTTCTGCTCCT	0.353																																					p.G972R		Atlas-SNP	.											MLL3_ENST00000355193,bladder,carcinoma,+1,4	MLL3	1564	4	0			c.G2914A						scavenged	.						63.0	52.0	56.0					7																	151927070		2199	4278	6477	SO:0001583	missense	58508	exon18			ATCTTCCTTCTGC	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.2914G>A	7.37:g.151927070C>T	ENSP00000262189:p.Gly972Arg	Somatic	1867	4	0.00214247		WXS	Illumina HiSeq	Phase_I	1500	179	0.119333	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.99|18.99	3.739123|3.739123	0.69304|0.69304	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193|ENST00000418673	D;D|.	0.88664|.	-2.41;-2.41|.	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|.	0.40469|.	U|.	0.001093|.	T|T	0.74794|0.74794	0.3763|0.3763	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.75252|0.75252	-0.3383|-0.3383	10|5	0.87932|.	D|.	0|.	.|.	17.9348|17.9348	0.89009|0.89009	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	972;33|.	Q8NEZ4;Q8NEZ4-2|.	MLL3_HUMAN;.|.	R|K	972|127	ENSP00000262189:G972R;ENSP00000347325:G972R|.	ENSP00000262189:G972R|.	G|R	-|-	1|2	0|0	MLL3|MLL3	151558003|151558003	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.770000|7.770000	0.85390|0.85390	2.303000|2.303000	0.77524|0.77524	0.460000|0.460000	0.39030|0.39030	GGA|AGG	.	.	none		0.353	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
CAMSAP2	23271	hgsc.bcm.edu	37	1	200776641	200776641	+	Silent	SNP	C	C	T	rs7552353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200776641C>T	ENST00000236925.4	+	3	586	c.537C>T	c.(535-537)gaC>gaT	p.D179D	CAMSAP2_ENST00000358823.2_Silent_p.D179D|CAMSAP2_ENST00000413307.2_Silent_p.D179D			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	179					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										ATATTGAGGACGCTGTCATGT	0.368													C|||	1259	0.251398	0.2216	0.2738	5008	,	,		14960	0.3552		0.0994	False		,,,				2504	0.3252				p.D179D		Atlas-SNP	.											.	.	.	.	0			c.C537T						PASS	.	C		904,3502	350.3+/-310.7	99,706,1398	118.0	111.0	114.0		537	-0.2	1.0	1	dbSNP_116	114	698,7902	172.6+/-223.3	27,644,3629	no	coding-synonymous	CAMSAP2	NM_203459.1		126,1350,5027	TT,TC,CC		8.1163,20.5175,12.3174		179/1479	200776641	1602,11404	2203	4300	6503	SO:0001819	synonymous_variant	23271	exon3			TGAGGACGCTGTC	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"""calmodulin regulated spectrin-associated protein 1-like 1"""	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.537C>T	1.37:g.200776641C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Silent	SNP	ENST00000236925.4	37																																																																																				C|0.838;T|0.162	0.162	strong		0.368	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459	
LILRA6	79168	hgsc.bcm.edu	37	19	54744771	54744771	+	Silent	SNP	A	A	G	rs142457810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54744771A>G	ENST00000396365.2	-	5	930	c.891T>C	c.(889-891)taT>taC	p.Y297Y	LILRA6_ENST00000419410.2_Silent_p.Y297Y|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000245621.5_Silent_p.Y297Y|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Silent_p.Y297Y|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	297	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGTGTGCACCATAGCACCTGT	0.687																																					p.Y297Y		Atlas-SNP	.											.	LILRA6	75	.	0			c.T891C						PASS	.						57.0	71.0	67.0					19																	54744771		2203	4300	6503	SO:0001819	synonymous_variant	79168	exon5			TGCACCATAGCAC	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.891T>C	19.37:g.54744771A>G		Somatic	380	1	0.00263158		WXS	Illumina HiSeq	Phase_I	471	124	0.26327	NM_024318		Silent	SNP	ENST00000396365.2	37	CCDS42610.1																																																																																			A|0.570;G|0.430	0.430	strong		0.687	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
ANXA11	311	hgsc.bcm.edu	37	10	81926702	81926702	+	Missense_Mutation	SNP	G	G	A	rs1049550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:81926702G>A	ENST00000438331.1	-	8	1170	c.688C>T	c.(688-690)Cgc>Tgc	p.R230C	ANXA11_ENST00000535999.1_Missense_Mutation_p.R230C|ANXA11_ENST00000422982.3_Missense_Mutation_p.R230C|ANXA11_ENST00000360615.4_Missense_Mutation_p.R230C|ANXA11_ENST00000265447.4_Missense_Mutation_p.R230C|ANXA11_ENST00000372231.3_Missense_Mutation_p.R230C|ANXA11_ENST00000537102.1_Missense_Mutation_p.R197C	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	230			R -> C (in dbSNP:rs1049550).		cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			TTGTTGGAGCGACTCCCCAGG	0.637													.|||	1964	0.392173	0.1551	0.4654	5008	,	,		14900	0.6429		0.4503	False		,,,				2504	0.3425				p.R230C		Atlas-SNP	.											.	ANXA11	32	.	0			c.C688T	GRCh37	CM064971	ANXA11	M	rs1049550	PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	891,3515		93,705,1405	58.0	49.0	52.0	http://omim.org/entry/612388	688,688,688	4.3	1.0	10	dbSNP_86	52	3521,5079		740,2041,1519	yes	missense,missense,missense	ANXA11	NM_001157.2,NM_145868.1,NM_145869.1	180,180,180	833,2746,2924	AA,AG,GG		40.9419,20.2224,33.9228	probably-damaging,probably-damaging,probably-damaging	230/506,230/506,230/506	81926702	4412,8594	2203	4300	6503	SO:0001583	missense	311	exon7			TGGAGCGACTCCC	L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"""Annexins"""	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.688C>T	10.37:g.81926702G>A	ENSP00000398610:p.Arg230Cys	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_145868	B4DVE7	Missense_Mutation	SNP	ENST00000438331.1	37	CCDS7364.1	927	0.42445054945054944	72	0.14634146341463414	152	0.4198895027624309	370	0.6468531468531469	333	0.4393139841688654	.	24.1	4.488911	0.84962	0.202224	0.409419	ENSG00000122359	ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000424188;ENST00000537102	T;T;T;T;T;T;T	0.12879	2.64;2.64;2.64;2.64;2.64;2.64;2.64	5.26	4.35	0.52113	Annexin repeat, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.96833	3.89	0.09310	P	0.9999999781241	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.996	T	0.45026	-0.9289	9	0.72032	D	0.01	.	9.1797	0.37134	0.0:0.16:0.6742:0.1658	rs1049550;rs1802933;rs2070070;rs2228426;rs3189725;rs17676239;rs52830790;rs1049550	330;230;230	B7Z6L0;Q5T0G8;P50995	.;.;ANX11_HUMAN	C	230;230;230;230;230;230;230;137;197	ENSP00000361305:R230C;ENSP00000404412:R230C;ENSP00000398610:R230C;ENSP00000353827:R230C;ENSP00000265447:R230C;ENSP00000441748:R230C;ENSP00000441400:R197C	ENSP00000265447:R230C	R	-	1	0	ANXA11	81916682	1.000000	0.71417	0.974000	0.42286	0.984000	0.73092	7.474000	0.81024	1.360000	0.45960	0.561000	0.74099	CGC	G|0.630;T|0.004	.	strong		0.637	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869	
MRS2	57380	hgsc.bcm.edu	37	6	24418749	24418749	+	Silent	SNP	G	G	A	rs141564147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24418749G>A	ENST00000378386.3	+	9	1143	c.1050G>A	c.(1048-1050)tcG>tcA	p.S350S	MRS2_ENST00000543597.1_Silent_p.S59S|MRS2_ENST00000443868.2_Silent_p.S353S|MRS2_ENST00000378353.1_Silent_p.S350S|MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000535061.1_Silent_p.S300S|MRS2_ENST00000274747.7_3'UTR	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	350						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						TCTCTCTTTCGCTCTTTGGAC	0.443													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		15837	0.0		0.0	False		,,,				2504	0.0				p.S350S		Atlas-SNP	.											.	MRS2	31	.	0			c.G1050A						PASS	.	G		50,4356	50.9+/-86.3	1,48,2154	171.0	167.0	168.0		1050	-10.8	0.0	6	dbSNP_134	168	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	MRS2	NM_020662.2		1,51,6451	AA,AG,GG		0.0349,1.1348,0.4075		350/444	24418749	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	57380	exon9			TCTTTCGCTCTTT	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.1050G>A	6.37:g.24418749G>A		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	261	118	0.452107	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	37	CCDS4552.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	G	9.599	1.128145	0.20959	0.011348	3.49E-4	ENSG00000124532	ENST00000446191	.	.	.	5.41	-10.8	0.00216	.	.	.	.	.	T	0.13670	0.0331	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43393	-0.9394	4	.	.	.	-16.4762	0.5483	0.00658	0.2381:0.1624:0.2797:0.3198	.	.	.	.	H	169	.	.	R	+	2	0	MRS2	24526728	0.008000	0.16893	0.026000	0.17262	0.987000	0.75469	-1.057000	0.03486	-2.703000	0.00397	-0.163000	0.13421	CGC	G|0.996;A|0.004	0.004	strong		0.443	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1		
GOPC	57120	hgsc.bcm.edu	37	6	117896421	117896421	+	Missense_Mutation	SNP	C	C	T	rs374207248		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117896421C>T	ENST00000368498.2	-	4	644	c.569G>A	c.(568-570)cGt>cAt	p.R190H	GOPC_ENST00000535237.1_Missense_Mutation_p.R190H|GOPC_ENST00000052569.6_Missense_Mutation_p.R182H|GOPC_ENST00000467125.1_5'Flank	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	190					apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)		GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		TATATGTCTACGAAGGGCTTC	0.408			O	ROS1	glioblastoma																																p.R190H		Atlas-SNP	.		Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	GOPC,rectum,carcinoma,-1,1	GOPC	29	1	0			c.G569A						scavenged	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	142.0	124.0	130.0		545,569	5.7	1.0	6		130	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GOPC	NM_001017408.2,NM_020399.3	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	182/455,190/463	117896421	1,13005	2203	4300	6503	SO:0001583	missense	57120	exon4			TGTCTACGAAGGG	AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.569G>A	6.37:g.117896421C>T	ENSP00000357484:p.Arg190His	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	241	3	0.0124481	NM_020399	A6NM30|Q59FS4|Q969U8	Missense_Mutation	SNP	ENST00000368498.2	37	CCDS5117.1	.	.	.	.	.	.	.	.	.	.	C	31	5.062458	0.93898	0.0	1.16E-4	ENSG00000047932	ENST00000052569;ENST00000368498;ENST00000535237	D;T;T	0.84442	-1.85;2.08;0.79	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.86276	0.5894	L	0.60455	1.87	0.80722	D	1	D;D	0.67145	0.996;0.993	P;P	0.52672	0.706;0.512	D	0.85784	0.1363	10	0.48119	T	0.1	-20.0627	19.7117	0.96099	0.0:1.0:0.0:0.0	.	182;190	Q9HD26-2;Q9HD26	.;GOPC_HUMAN	H	182;190;190	ENSP00000052569:R182H;ENSP00000357484:R190H;ENSP00000445690:R190H	ENSP00000052569:R182H	R	-	2	0	GOPC	118003114	1.000000	0.71417	0.996000	0.52242	0.924000	0.55760	7.818000	0.86416	2.660000	0.90430	0.591000	0.81541	CGT	.	.	weak		0.408	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399	
CRAMP1L	57585	hgsc.bcm.edu	37	16	1682281	1682281	+	Silent	SNP	A	A	G	rs3169425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1682281A>G	ENST00000397412.3	+	4	708	c.609A>G	c.(607-609)gcA>gcG	p.A203A	CRAMP1L_ENST00000436138.3_Silent_p.A200A|LA16c-431H6.6_ENST00000454337.1_Missense_Mutation_p.K8E|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	89	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	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		
CTAGE4	100128553	hgsc.bcm.edu	37	7	143882697	143882697	+	Missense_Mutation	SNP	A	A	G	rs145692929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143882697A>G	ENST00000486333.1	+	1	2139	c.2101A>G	c.(2101-2103)Atc>Gtc	p.I701V		NM_198495.2	NP_940897.2	Q8IX94	CTGE4_HUMAN	CTAGE family, member 4	701	Pro-rich.			IS -> VR (in Ref. 1; BAF84925). {ECO:0000305}.		integral component of membrane (GO:0016021)				endometrium(1)|ovary(2)	3						TCTTGCTCCAATCAGCGGTCC	0.507																																					p.I701V		Atlas-SNP	.											CTAGE4,right_upper_lobe,carcinoma,-2,1	CTAGE4	10	1	0			c.A2101G						scavenged	.						5.0	8.0	7.0					7																	143882697		623	1434	2057	SO:0001583	missense	100128553	exon1			GCTCCAATCAGCG	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.2101A>G	7.37:g.143882697A>G	ENSP00000419539:p.Ile701Val	Somatic	439	4	0.00911162		WXS	Illumina HiSeq	Phase_I	754	416	0.551724	NM_198495	A8K871|O95046	Missense_Mutation	SNP	ENST00000486333.1	37	CCDS55176.1	.	.	.	.	.	.	.	.	.	.	.	1.245	-0.620260	0.03636	.	.	ENSG00000225932	ENST00000486333	T	0.05513	3.43	.	.	.	.	.	.	.	.	T	0.03011	0.0089	N	0.17248	0.465	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.46857	-0.9161	7	0.02654	T	1	.	.	.	.	.	701	Q8IX94	CTGE4_HUMAN	V	701	ENSP00000419539:I701V	ENSP00000419539:I701V	I	+	1	0	CTAGE4	143513630	0.921000	0.31238	0.013000	0.15412	0.013000	0.08279	0.158000	0.16422	0.149000	0.19098	0.147000	0.16070	ATC	A|0.500;G|0.500	0.500	strong		0.507	CTAGE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349970.1	NM_198495	
SRCAP	10847	hgsc.bcm.edu	37	16	30748715	30748715	+	Missense_Mutation	SNP	G	G	A	rs144295177		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30748715G>A	ENST00000262518.4	+	34	7739	c.7354G>A	c.(7354-7356)Gct>Act	p.A2452T	SRCAP_ENST00000395059.2_Missense_Mutation_p.A2390T|SRCAP_ENST00000344771.4_Missense_Mutation_p.A2294T	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2452	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			ttcagctccggctgcaattcc	0.587																																					p.A2452T		Atlas-SNP	.											.	SRCAP	298	.	0			c.G7354A						PASS	.	G	THR/ALA	3,4389	6.2+/-15.9	0,3,2193	124.0	89.0	101.0		7354	1.9	0.2	16	dbSNP_134	101	0,8596		0,0,4298	yes	missense	SRCAP	NM_006662.2	58	0,3,6491	AA,AG,GG		0.0,0.0683,0.0231	benign	2452/3231	30748715	3,12985	2196	4298	6494	SO:0001583	missense	10847	exon34			GCTCCGGCTGCAA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.7354G>A	16.37:g.30748715G>A	ENSP00000262518:p.Ala2452Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	8.548	0.874873	0.17395	6.83E-4	0.0	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91521	-2.85;-2.85;-2.86	3.9	1.89	0.25635	.	.	.	.	.	T	0.77164	0.4090	N	0.08118	0	0.19575	N	0.999965	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.61441	-0.7062	9	0.17369	T	0.5	2.0848	6.8859	0.24199	0.1034:0.1777:0.7189:0.0	.	2390;2452	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	T	2452;2390;2294	ENSP00000262518:A2452T;ENSP00000378499:A2390T;ENSP00000343042:A2294T	ENSP00000262518:A2452T	A	+	1	0	SRCAP	30656216	0.830000	0.29337	0.206000	0.23566	0.629000	0.37895	1.913000	0.39956	0.317000	0.23160	0.306000	0.20318	GCT	G|1.000;A|0.000	0.000	weak		0.587	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
H6PD	9563	hgsc.bcm.edu	37	1	9322194	9322194	+	Silent	SNP	C	C	T	rs145706807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9322194C>T	ENST00000377403.2	+	4	1124	c.822C>T	c.(820-822)ctC>ctT	p.L274L	H6PD_ENST00000602477.1_Silent_p.L285L	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	274	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)		TCCTCACCCTCGTGGCCATGG	0.637													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19119	0.0		0.0	False		,,,				2504	0.0				p.L274L		Atlas-SNP	.											.	H6PD	71	.	0			c.C822T						PASS	.	C		7,4399	14.3+/-33.2	0,7,2196	68.0	63.0	65.0		822	-10.5	0.2	1	dbSNP_134	65	0,8600		0,0,4300	no	coding-synonymous	H6PD	NM_004285.3		0,7,6496	TT,TC,CC		0.0,0.1589,0.0538		274/792	9322194	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	9563	exon4			CACCCTCGTGGCC	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.822C>T	1.37:g.9322194C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	213	126	0.591549	NM_004285	Q4TT33|Q66I35|Q68DT3	Silent	SNP	ENST00000377403.2	37	CCDS101.1																																																																																			C|0.999;T|0.001	0.001	strong		0.637	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
METTL3	56339	hgsc.bcm.edu	37	14	21967916	21967916	+	Silent	SNP	A	A	G	rs1139130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	172	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	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	
RAB3D	9545	hgsc.bcm.edu	37	19	11436221	11436221	+	Silent	SNP	A	A	G	rs12981706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11436221A>G	ENST00000222120.3	-	5	773	c.513T>C	c.(511-513)aaT>aaC	p.N171N	RAB3D_ENST00000589655.1_Silent_p.N171N|CTC-510F12.4_ENST00000586356.1_RNA|CTC-510F12.6_ENST00000586051.1_RNA|TSPAN16_ENST00000316737.1_Intron	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	171					exocytosis (GO:0006887)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)|zymogen granule (GO:0042588)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|ovary(2)	14						CCTGCTTCACATTGATGTTCT	0.557													A|||	286	0.0571086	0.1762	0.0187	5008	,	,		14659	0.0		0.0318	False		,,,				2504	0.0082				p.N171N		Atlas-SNP	.											.	RAB3D	24	.	0			c.T513C						PASS	.	A	,	617,3789	268.6+/-268.5	43,531,1629	146.0	132.0	136.0		513,	-6.2	1.0	19	dbSNP_121	136	293,8307	108.0+/-168.7	3,287,4010	no	coding-synonymous,intron	RAB3D,TSPAN16	NM_004283.3,NM_012466.2	,	46,818,5639	GG,GA,AA		3.407,14.0036,6.9968	,	171/220,	11436221	910,12096	2203	4300	6503	SO:0001819	synonymous_variant	9545	exon5			CTTCACATTGATG	AF081353	CCDS12257.1	19p13.2	2012-10-02			ENSG00000105514	ENSG00000105514		"""RAB, member RAS oncogene"""	9779	protein-coding gene	gene with protein product	"""Rab3D upregulated with myeloid differentiation"", ""glioblastoma overexpressed"""	604350		GOV		10023084, 10072586	Standard	NM_004283		Approved	RAB16, D2-2, RAD3D	uc002mqx.3	O95716	OTTHUMG00000180835	ENST00000222120.3:c.513T>C	19.37:g.11436221A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	48	16	0.333333	NM_004283		Silent	SNP	ENST00000222120.3	37	CCDS12257.1																																																																																			A|0.939;G|0.061;T|0.000	0.061	strong		0.557	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1	NM_004283	
CXCR5	643	hgsc.bcm.edu	37	11	118764382	118764382	+	Silent	SNP	G	G	T	rs2230319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118764382G>T	ENST00000292174.4	+	2	305	c.129G>T	c.(127-129)ggG>ggT	p.G43G		NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	43					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)		CCACAGAGGGGCCCCTCATGG	0.597													G|||	275	0.0549121	0.202	0.0101	5008	,	,		17609	0.0		0.001	False		,,,				2504	0.0				p.G43G		Atlas-SNP	.											.	CXCR5	34	.	0			c.G129T						PASS	.	G	,	589,3811	259.8+/-263.3	34,521,1645	87.0	83.0	85.0		129,	-1.9	0.9	11	dbSNP_98	85	8,8582	5.7+/-21.5	0,8,4287	no	coding-synonymous,utr-5	CXCR5	NM_001716.4,NM_032966.2	,	34,529,5932	TT,TG,GG		0.0931,13.3864,4.5958	,	43/373,	118764382	597,12393	2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			AGAGGGGCCCCTC	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.129G>T	11.37:g.118764382G>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	114	67	0.587719	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			G|0.952;T|0.048	0.048	strong		0.597	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716	
NOLC1	9221	hgsc.bcm.edu	37	10	103920255	103920255	+	Silent	SNP	T	T	A	rs145855726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:103920255T>A	ENST00000605788.1	+	10	1381	c.1146T>A	c.(1144-1146)ggT>ggA	p.G382G	NOLC1_ENST00000405356.1_Silent_p.G392G|NOLC1_ENST00000488254.2_Silent_p.G383G|NOLC1_ENST00000603742.1_Silent_p.G101G	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	382	11 X 12 AA approximate repeats of an acidic serine cluster.|Interacts with RPA194.				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)		AGCCAGCTGGTACCACCAAGA	0.542													T|||	7	0.00139776	0.0053	0.0	5008	,	,		20457	0.0		0.0	False		,,,				2504	0.0				p.G382G		Atlas-SNP	.											.	NOLC1	61	.	0			c.T1146A						PASS	.	T		31,4375	36.0+/-67.5	0,31,2172	63.0	67.0	66.0		1146	-1.0	0.0	10	dbSNP_134	66	0,8600		0,0,4300	yes	coding-synonymous	NOLC1	NM_004741.3		0,31,6472	AA,AT,TT		0.0,0.7036,0.2384		382/700	103920255	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	9221	exon10			AGCTGGTACCACC	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.1146T>A	10.37:g.103920255T>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_004741	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																			T|0.997;A|0.003	0.003	strong		0.542	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
MEGF10	84466	hgsc.bcm.edu	37	5	126769146	126769146	+	Silent	SNP	T	T	C	rs11950427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:126769146T>C	ENST00000274473.6	+	15	2052	c.1785T>C	c.(1783-1785)ccT>ccC	p.P595P	MEGF10_ENST00000503335.2_Silent_p.P595P	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	595	EGF-like 11. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				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)		CATGCTCCCCTGATGATGGCA	0.557													C|||	959	0.191494	0.3283	0.0965	5008	,	,		20867	0.0992		0.1431	False		,,,				2504	0.2188				p.P595P		Atlas-SNP	.											MEGF10,colon,carcinoma,+2,1	MEGF10	152	1	0			c.T1785C						PASS	.	C		1285,3121	699.6+/-406.5	204,877,1122	122.0	116.0	118.0		1785	-12.3	0.0	5	dbSNP_120	118	1271,7329	759.9+/-407.6	84,1103,3113	no	coding-synonymous	MEGF10	NM_032446.2		288,1980,4235	CC,CT,TT		14.7791,29.1648,19.6525		595/1141	126769146	2556,10450	2203	4300	6503	SO:0001819	synonymous_variant	84466	exon15			CTCCCCTGATGAT	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.1785T>C	5.37:g.126769146T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	178	76	0.426966	NM_032446	Q68DE5|Q8WUL3	Silent	SNP	ENST00000274473.6	37	CCDS4142.1																																																																																			T|0.815;C|0.185	0.185	strong		0.557	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	
OR2H1	26716	hgsc.bcm.edu	37	6	29429732	29429732	+	Silent	SNP	T	T	C	rs61732184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29429732T>C	ENST00000377136.1	+	4	651	c.186T>C	c.(184-186)tcT>tcC	p.S62S	OR2H1_ENST00000442615.1_Silent_p.S62S|OR2H1_ENST00000377132.1_Silent_p.S62S|OR2H1_ENST00000377133.1_Silent_p.S62S|OR2H1_ENST00000396792.2_Silent_p.S62S|OR2H1_ENST00000473369.1_Intron			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						TTTTCCTCTCTGACCTCTCCT	0.527													T|||	174	0.0347444	0.1044	0.013	5008	,	,		20433	0.0119		0.0119	False		,,,				2504	0.0031				p.S62S		Atlas-SNP	.											.	OR2H1	38	.	0			c.T186C						PASS	.	T		301,2721		17,267,1227	138.0	135.0	136.0		186	-0.0	1.0	6	dbSNP_129	136	33,5385		0,33,2676	no	coding-synonymous	OR2H1	NM_030883.3		17,300,3903	CC,CT,TT		0.6091,9.9603,3.9573		62/317	29429732	334,8106	1511	2709	4220	SO:0001819	synonymous_variant	26716	exon3			CCTCTCTGACCTC	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.186T>C	6.37:g.29429732T>C		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	303	139	0.458746	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Silent	SNP	ENST00000377136.1	37	CCDS4660.1																																																																																			T|0.964;C|0.036	0.036	strong		0.527	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
NDOR1	27158	hgsc.bcm.edu	37	9	140108468	140108468	+	Silent	SNP	C	C	T	rs114934623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140108468C>T	ENST00000344894.5	+	5	543	c.460C>T	c.(460-462)Ctg>Ttg	p.L154L	NDOR1_ENST00000427047.2_Intron|NDOR1_ENST00000458322.2_Silent_p.L154L|NDOR1_ENST00000371521.4_Silent_p.L154L	NM_001144028.1|NM_014434.2	NP_001137500.1|NP_055249.1			NADPH dependent diflavin oxidoreductase 1											breast(1)|endometrium(5)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		GGACAGGGTTCTGGGGCTGTA	0.711													C|||	26	0.00519169	0.0182	0.0029	5008	,	,		14886	0.0		0.0	False		,,,				2504	0.0				p.L154L		Atlas-SNP	.											.	NDOR1	71	.	0			c.C460T						PASS	.	C	,,,	43,4245		0,43,2101	18.0	22.0	21.0		460,,460,460	2.3	0.6	9	dbSNP_132	21	0,8378		0,0,4189	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	NDOR1	NM_001144026.1,NM_001144027.1,NM_001144028.1,NM_014434.2	,,,	0,43,6290	TT,TC,CC		0.0,1.0028,0.3395	,,,	154/607,,154/591,154/598	140108468	43,12623	2144	4189	6333	SO:0001819	synonymous_variant	27158	exon5			AGGGTTCTGGGGC	BC015735	CCDS7036.1, CCDS48061.1, CCDS48062.1, CCDS48063.1	9q34.3	2008-02-05			ENSG00000188566	ENSG00000188566			29838	protein-coding gene	gene with protein product	"""NADPH dependent FMN and FAD containing oxidoreductase"""	606073				10625700, 12631275	Standard	XM_005266066		Approved	NR1, bA350O14.9	uc004clx.3	Q9UHB4	OTTHUMG00000020986	ENST00000344894.5:c.460C>T	9.37:g.140108468C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	69	15	0.217391	NM_001144026		Silent	SNP	ENST00000344894.5	37	CCDS7036.1																																																																																			C|0.994;T|0.006	0.006	strong		0.711	NDOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254704.1	NM_014434	
HOXC10	3226	hgsc.bcm.edu	37	12	54379610	54379610	+	Silent	SNP	G	G	C	rs145093077		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:54379610G>C	ENST00000303460.4	+	1	641	c.567G>C	c.(565-567)tcG>tcC	p.S189S	HOXC-AS3_ENST00000513165.1_RNA|RP11-834C11.12_ENST00000513209.1_5'Flank|HOXC-AS3_ENST00000567780.1_RNA|HOXC-AS3_ENST00000509870.1_RNA|HOXC-AS3_ENST00000514702.1_RNA	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	189					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|neuromuscular process (GO:0050905)|positive regulation of cell proliferation (GO:0008284)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(3)|lung(14)|pancreas(1)	20						ATCTGGAATCGCCTCAGCTGG	0.647																																					p.S189S		Atlas-SNP	.											.	HOXC10	42	.	0			c.G567C						PASS	.						32.0	36.0	35.0					12																	54379610		2203	4299	6502	SO:0001819	synonymous_variant	3226	exon1			GGAATCGCCTCAG		CCDS8868.1	12q13.13	2011-06-20	2005-12-22		ENSG00000180818	ENSG00000180818		"""Homeoboxes / ANTP class : HOXL subclass"""	5122	protein-coding gene	gene with protein product		605560	"""homeo box C10"""	HOX3I		1358459	Standard	NM_017409		Approved		uc001sen.3	Q9NYD6	OTTHUMG00000160031	ENST00000303460.4:c.567G>C	12.37:g.54379610G>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_017409	O15219|O15220|Q9BVD5	Silent	SNP	ENST00000303460.4	37	CCDS8868.1																																																																																			G|1.000;A|0.000	.	alt		0.647	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2		
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036435	33036435	+	Missense_Mutation	SNP	T	T	G	rs1126769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33036435T>G	ENST00000419277.1	-	5	904	c.775A>C	c.(775-777)Acc>Ccc	p.T259P	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.T259P|HLA-DPA1_ENST00000463066.1_5'Flank	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	259			T -> P (in allele DPA1*02:01, allele DPA1*02:02 and allele DPA1*04:01; dbSNP:rs1126769).		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						TTTCACAGGGTCCCCTGGGCC	0.527													G|||	2190	0.4373	0.5794	0.2839	5008	,	,		17401	0.6746		0.1859	False		,,,				2504	0.3681				p.T259P		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.A775C						PASS	.	G	PRO/THR,PRO/THR,PRO/THR	1231,1783		320,591,596	64.0	92.0	82.0		775,775,775	2.9	0.9	6	dbSNP_86	82	830,4584		70,690,1947	yes	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	38,38,38	390,1281,2543	GG,GT,TT		15.3306,40.8427,24.4542	benign,benign,benign	259/261,259/261,259/261	33036435	2061,6367	1507	2707	4214	SO:0001583	missense	3113	exon4			ACAGGGTCCCCTG	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.775A>C	6.37:g.33036435T>G	ENSP00000393566:p.Thr259Pro	Somatic	444	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.010|0.010	-1.787475|-1.787475	0.00628|0.00628	0.408427|0.408427	0.153306|0.153306	ENSG00000231389|ENSG00000231389	ENST00000437811|ENST00000419277;ENST00000428995	.|T;T	.|0.01560	.|4.77;4.77	3.8|3.8	2.93|2.93	0.34026|0.34026	.|.	.|0.593771	.|0.12507	.|N	.|0.462837	T|T	0.00144|0.00144	0.0004|0.0004	N|N	0.00124|0.00124	-2.055|-2.055	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.29397|0.29397	-1.0013|-1.0013	4|9	.|0.02654	.|T	.|1	.|.	4.9947|4.9947	0.14233|0.14233	0.1136:0.0:0.6795:0.2069|0.1136:0.0:0.6795:0.2069	rs1126769;rs2308935;rs3182009;rs17411807|rs1126769;rs2308935;rs3182009;rs17411807	.|259	.|P20036	.|DPA1_HUMAN	A|P	126|259	.|ENSP00000393566:T259P;ENSP00000402872:T259P	.|ENSP00000393566:T259P	D|T	-|-	2|1	0|0	HLA-DPA1|HLA-DPA1	33144413|33144413	0.004000|0.004000	0.15560|0.15560	0.929000|0.929000	0.37066|0.37066	0.174000|0.174000	0.22865|0.22865	0.215000|0.215000	0.17562|0.17562	0.229000|0.229000	0.21039|0.21039	-0.764000|-0.764000	0.03450|0.03450	GAC|ACC	T|0.815;G|0.185	0.185	strong		0.527	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
DAOA	267012	hgsc.bcm.edu	37	13	106119446	106119446	+	Missense_Mutation	SNP	G	G	A	rs2391191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:106119446G>A	ENST00000375936.3	+	2	135	c.89G>A	c.(88-90)aGg>aAg	p.R30K	DAOA_ENST00000329625.5_5'UTR|DAOA-AS1_ENST00000448407.1_RNA	NM_001161812.1|NM_172370.3	NP_001155284.1|NP_758958.3	P59103	DAOA_HUMAN	D-amino acid oxidase activator	30			R -> K (in dbSNP:rs2391191). {ECO:0000269|PubMed:12364586}.		negative regulation of D-amino-acid oxidase activity (GO:1900758)|positive regulation of catalytic activity (GO:0043085)	Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	13	Lung NSC(43;0.01)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					GGTTTTCAAAGGAGCATTCTT	0.299													G|||	1812	0.361821	0.0673	0.4049	5008	,	,		15285	0.626		0.3877	False		,,,				2504	0.4305				p.R30K		Atlas-SNP	.											.	DAOA	26	.	0			c.G89A	GRCh37	CM045704	DAOA	M	rs2391191	PASS	.	G	,,LYS/ARG	411,3175		32,347,1414	85.0	82.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,89	-0.3	0.0	13	dbSNP_100	83	3026,5090		573,1880,1605	yes	utr-5,utr-5,missense	DAOA	NM_001161812.1,NM_001161814.1,NM_172370.3	,,26	605,2227,3019	AA,AG,GG		37.2844,11.4612,29.371	,,	,,30/154	106119446	3437,8265	1793	4058	5851	SO:0001583	missense	267012	exon2			TTCAAAGGAGCAT	AY138547	CCDS41905.1, CCDS53880.1, CCDS59242.1	13q33.2	2011-08-01			ENSG00000182346	ENSG00000182346			21191	protein-coding gene	gene with protein product	"""G72 transcript"""	607408				12364586, 15057823	Standard	NM_001161814		Approved	G72	uc010tjg.2	P59103	OTTHUMG00000041333	ENST00000375936.3:c.89G>A	13.37:g.106119446G>A	ENSP00000365103:p.Arg30Lys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_172370	A6NKG7|Q0VAE6|Q5VX59|Q86Y17|Q8IWM4	Missense_Mutation	SNP	ENST00000375936.3	37	CCDS41905.1	844	0.38644688644688646	29	0.05894308943089431	143	0.39502762430939226	374	0.6538461538461539	298	0.39313984168865435	G	12.27	1.888219	0.33348	0.114612	0.372844	ENSG00000182346	ENST00000375936	T	0.29142	1.58	3.17	-0.301	0.12800	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.33103	0.397	B	0.28638	0.092	T	0.42865	-0.9426	8	0.09338	T	0.73	.	0.7383	0.00969	0.1871:0.2174:0.3739:0.2216	rs2391191;rs52812974;rs59455029;rs2391191	30	P59103	DAOA_HUMAN	K	30	ENSP00000365103:R30K	ENSP00000365103:R30K	R	+	2	0	DAOA	104917447	0.000000	0.05858	0.000000	0.03702	0.249000	0.25844	0.160000	0.16462	-0.095000	0.12351	0.557000	0.71058	AGG	G|0.570;A|0.430	0.430	strong		0.299	DAOA-005	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099040.2	NM_172370	
CST1	1469	hgsc.bcm.edu	37	20	23731412	23731412	+	Missense_Mutation	SNP	G	G	A	rs2070856	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23731412G>A	ENST00000304749.2	-	1	162	c.92C>T	c.(91-93)cCg>cTg	p.P31L	CST1_ENST00000398402.1_Missense_Mutation_p.P31L	NM_001898.2	NP_001889.2	P01037	CYTN_HUMAN	cystatin SN	31			P -> L (in dbSNP:rs2070856).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			kidney(1)|large_intestine(1)|lung(8)|ovary(1)|stomach(1)|urinary_tract(1)	13	Lung NSC(19;0.0676)|all_lung(19;0.148)					GATGCCACCCGGGATTATCCT	0.567													.|||	891	0.177915	0.2315	0.0937	5008	,	,		14900	0.0764		0.1113	False		,,,				2504	0.3384				p.P31L		Atlas-SNP	.											.	CST1	37	.	0			c.C92T						PASS	.	G	LEU/PRO	908,3498	352.1+/-311.5	88,732,1383	117.0	101.0	107.0		92	-2.9	0.0	20	dbSNP_96	107	1157,7443	237.9+/-269.6	75,1007,3218	yes	missense	CST1	NM_001898.2	98	163,1739,4601	AA,AG,GG		13.4535,20.6083,15.8773	benign	31/142	23731412	2065,10941	2203	4300	6503	SO:0001583	missense	1469	exon1			CCACCCGGGATTA	M19169	CCDS13160.1	20p11.2	2008-04-15			ENSG00000170373	ENSG00000170373			2473	protein-coding gene	gene with protein product		123855					Standard	NM_001898		Approved		uc002wtp.3	P01037	OTTHUMG00000032085	ENST00000304749.2:c.92C>T	20.37:g.23731412G>A	ENSP00000305731:p.Pro31Leu	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	187	81	0.433155	NM_001898	Q96LE6|Q9UCQ6	Missense_Mutation	SNP	ENST00000304749.2	37	CCDS13160.1	285	0.1304945054945055	117	0.23780487804878048	41	0.1132596685082873	44	0.07692307692307693	83	0.10949868073878628	G	2.600	-0.293234	0.05568	0.206083	0.134535	ENSG00000170373	ENST00000304749;ENST00000398402	T;T	0.12672	2.66;2.66	1.45	-2.91	0.05631	Proteinase inhibitor I25, cystatin (1);	0.902916	0.09313	N	0.819400	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.42716	-0.9435	9	0.06236	T	0.91	.	5.9667	0.19328	0.6797:0.0:0.3203:0.0	rs2070856;rs2234831;rs58967935;rs2070856	31	P01037	CYTN_HUMAN	L	31	ENSP00000305731:P31L;ENSP00000381439:P31L	ENSP00000305731:P31L	P	-	2	0	CST1	23679412	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.296000	0.19083	-1.070000	0.03149	-1.207000	0.01640	CCG	G|0.847;A|0.153	0.153	strong		0.567	CST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078351.2	NM_001898	
C5orf30	90355	hgsc.bcm.edu	37	5	102612166	102612166	+	Silent	SNP	T	T	C	rs17155192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:102612166T>C	ENST00000319933.2	+	3	854	c.546T>C	c.(544-546)gaT>gaC	p.D182D	C5orf30_ENST00000510890.1_Silent_p.D182D|C5orf30_ENST00000515669.1_Silent_p.D182D	NM_033211.2	NP_149988.1	Q96GV9	CE030_HUMAN	chromosome 5 open reading frame 30	182					cilium morphogenesis (GO:0060271)|protein transport (GO:0015031)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9		all_cancers(142;2.22e-05)|all_epithelial(76;9.54e-08)|Prostate(80;0.0174)|Colorectal(57;0.0551)|Ovarian(225;0.11)|Lung NSC(167;0.136)|all_lung(232;0.18)		Epithelial(69;2.84e-14)|COAD - Colon adenocarcinoma(37;0.00762)		AGCCAGCTGATACAGAAGTGC	0.458													C|||	335	0.066893	0.2383	0.0159	5008	,	,		18507	0.0		0.008	False		,,,				2504	0.001				p.D182D		Atlas-SNP	.											.	C5orf30	18	.	0			c.T546C						PASS	.	C		942,3460	692.5+/-405.5	100,742,1359	50.0	53.0	52.0		546	4.4	1.0	5	dbSNP_123	52	96,8504	808.2+/-407.2	1,94,4205	no	coding-synonymous	C5orf30	NM_033211.2		101,836,5564	CC,CT,TT		1.1163,21.3994,7.9834		182/207	102612166	1038,11964	2201	4300	6501	SO:0001819	synonymous_variant	90355	exon3			AGCTGATACAGAA		CCDS4095.1	5q21.1	2012-02-23			ENSG00000181751	ENSG00000181751			25052	protein-coding gene	gene with protein product						22085962	Standard	NM_033211		Approved	FLJ25291	uc003kog.1	Q96GV9	OTTHUMG00000128738	ENST00000319933.2:c.546T>C	5.37:g.102612166T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_033211		Silent	SNP	ENST00000319933.2	37	CCDS4095.1																																																																																			T|0.926;C|0.074	0.074	strong		0.458	C5orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250649.1	NM_033211	
OR2T4	127074	hgsc.bcm.edu	37	1	248525650	248525650	+	Silent	SNP	C	C	T	rs28602650	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248525650C>T	ENST00000366475.1	+	1	768	c.768C>T	c.(766-768)acC>acT	p.T256T		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	256						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCTCCTCACCATCCACGGGA	0.512													t|||	1473	0.294129	0.2398	0.2709	5008	,	,		21451	0.4276		0.1799	False		,,,				2504	0.364				p.T256T		Atlas-SNP	.											.	OR2T4	126	.	0			c.C768T						PASS	.	T		1061,3345	723.4+/-409.4	140,781,1282	130.0	127.0	128.0		768	-0.3	0.2	1	dbSNP_125	128	1394,7206	753.1+/-407.4	112,1170,3018	no	coding-synonymous	OR2T4	NM_001004696.1		252,1951,4300	TT,TC,CC		16.2093,24.0808,18.8759		256/349	248525650	2455,10551	2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			CCTCACCATCCAC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.768C>T	1.37:g.248525650C>T		Somatic	893	2	0.00223964		WXS	Illumina HiSeq	Phase_I	925	450	0.486486	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			C|0.791;T|0.209	0.209	strong		0.512	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48598823	48598823	+	Missense_Mutation	SNP	A	A	G	rs156631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48598823A>G	ENST00000599921.1	-	7	964	c.607T>C	c.(607-609)Tct>Cct	p.S203P	PLA2G4C_ENST00000354276.3_Missense_Mutation_p.S203P|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.S213P|PLA2G4C_ENST00000413144.2_Missense_Mutation_p.S203P			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	203	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		S -> P (in dbSNP:rs156631). {ECO:0000269|PubMed:10085124, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		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)		CCCAGTGCAGAGAAGCCAGCG	0.527													G|||	3151	0.629193	0.7784	0.5014	5008	,	,		19060	0.8681		0.3797	False		,,,				2504	0.5286				p.S213P		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.T637C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER	3143,1263	432.6+/-343.3	1133,877,193	117.0	134.0	128.0		637,607,607	2.2	0.8	19	dbSNP_79	128	3215,5385	652.3+/-400.9	591,2033,1676	yes	missense,missense,missense	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	74,74,74	1724,2910,1869	GG,GA,AA		37.3837,28.6655,48.8851	benign,benign,benign	213/552,203/528,203/542	48598823	6358,6648	2203	4300	6503	SO:0001583	missense	8605	exon7			GTGCAGAGAAGCC	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.607T>C	19.37:g.48598823A>G	ENSP00000469473:p.Ser203Pro	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	103	57	0.553398	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	1350	0.6181318681318682	380	0.7723577235772358	184	0.5082872928176796	503	0.8793706293706294	283	0.3733509234828496	G	0.020	-1.436880	0.01098	0.713345	0.373837	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.04119	3.7;3.7	3.31	2.22	0.28083	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.167772	0.39985	N	0.001211	T	0.00012	0.0000	N	0.00327	-1.64	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.11767	-1.0574	9	0.13470	T	0.59	-6.9264	6.3932	0.21599	0.2736:0.0:0.7264:0.0	rs156631;rs3745739;rs17358791;rs56790404;rs156631	203	Q9UP65	PA24C_HUMAN	P	203	ENSP00000346228:S203P;ENSP00000400036:S203P	ENSP00000346228:S203P	S	-	1	0	PLA2G4C	53290635	0.974000	0.33945	0.765000	0.31456	0.483000	0.33249	0.859000	0.27858	0.506000	0.28125	-0.971000	0.02607	TCT	T|0.003;G|0.559	0.559	strong		0.527	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
CD14	929	hgsc.bcm.edu	37	5	140011468	140011468	+	Silent	SNP	C	C	G	rs4914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140011468C>G	ENST00000302014.6	-	2	1730	c.1101G>C	c.(1099-1101)ctG>ctC	p.L367L	CD14_ENST00000401743.2_Silent_p.L367L	NM_000591.3	NP_000582.1	P08571	CD14_HUMAN	CD14 molecule	367					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|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)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|phagocytosis (GO:0006909)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of endocytosis (GO:0045807)|positive regulation of tumor necrosis factor production (GO:0032760)|response to ethanol (GO:0045471)|response to heat (GO:0009408)|response to magnesium ion (GO:0032026)|response to tumor necrosis factor (GO:0034612)|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 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)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|opsonin receptor activity (GO:0001847)|peptidoglycan receptor activity (GO:0016019)			endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCCTTGGAGCAGCACCAGGG	0.612													C|||	319	0.0636981	0.0651	0.072	5008	,	,		17850	0.0238		0.1093	False		,,,				2504	0.0501				p.L367L		Atlas-SNP	.											.	CD14	20	.	0			c.G1101C						PASS	.	C	,,,	342,4064	170.5+/-200.9	16,310,1877	56.0	62.0	60.0		1101,1101,1101,1101	4.5	1.0	5	dbSNP_52	60	993,7607	209.1+/-250.4	58,877,3365	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD14	NM_000591.3,NM_001040021.2,NM_001174104.1,NM_001174105.1	,,,	74,1187,5242	GG,GC,CC		11.5465,7.7621,10.2645	,,,	367/376,367/376,367/376,367/376	140011468	1335,11671	2203	4300	6503	SO:0001819	synonymous_variant	929	exon3			TTGGAGCAGCACC		CCDS4232.1	5q31.3	2012-09-20	2006-03-28		ENSG00000170458	ENSG00000170458		"""CD molecules"""	1628	protein-coding gene	gene with protein product		158120	"""CD14 antigen"""			2472171, 2462937	Standard	NM_000591		Approved		uc003lgi.2	P08571	OTTHUMG00000129507	ENST00000302014.6:c.1101G>C	5.37:g.140011468C>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	185	99	0.535135	NM_001174105	Q53XT5|Q96FR6|Q96L99|Q9UNS3	Silent	SNP	ENST00000302014.6	37	CCDS4232.1																																																																																			C|0.905;G|0.095	0.095	strong		0.612	CD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251681.2	NM_000591	
EPHA3	2042	hgsc.bcm.edu	37	3	89498428	89498428	+	Silent	SNP	G	G	A	rs1398197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:89498428G>A	ENST00000336596.2	+	14	2625	c.2400G>A	c.(2398-2400)aaG>aaA	p.K800K	EPHA3_ENST00000494014.1_Silent_p.K800K	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	800	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CCTACCGCAAGTTCACGTCAG	0.443										TSP Lung(6;0.00050)			G|||	564	0.11262	0.2625	0.0879	5008	,	,		16928	0.0516		0.0457	False		,,,				2504	0.0593				p.K800K		Atlas-SNP	.											.	EPHA3	501	.	0			c.G2400A						PASS	.	G		999,3407	373.2+/-320.7	121,757,1325	231.0	216.0	221.0		2400	-2.4	1.0	3	dbSNP_88	221	502,8098	143.9+/-199.8	14,474,3812	no	coding-synonymous	EPHA3	NM_005233.5		135,1231,5137	AA,AG,GG		5.8372,22.6736,11.5408		800/984	89498428	1501,11505	2203	4300	6503	SO:0001819	synonymous_variant	2042	exon14			CCGCAAGTTCACG	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2400G>A	3.37:g.89498428G>A		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	227	116	0.511013	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	37	CCDS2922.1																																																																																			G|0.889;A|0.111	0.111	strong		0.443	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
ABCB5	340273	hgsc.bcm.edu	37	7	20766752	20766752	+	Missense_Mutation	SNP	G	G	T	rs35885925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20766752G>T	ENST00000404938.2	+	22	3367	c.2715G>T	c.(2713-2715)caG>caT	p.Q905H	ABCB5_ENST00000258738.6_Missense_Mutation_p.Q460H	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	905	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.		Q -> H (in dbSNP:rs35885925).		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						AGATGCTTCAGACTCAACACA	0.358													G|||	104	0.0207668	0.0756	0.0058	5008	,	,		18547	0.0		0.0	False		,,,				2504	0.0				p.Q905H		Atlas-SNP	.											.	ABCB5	357	.	0			c.G2715T						PASS	.	G	HIS/GLN,HIS/GLN	270,4136	154.0+/-187.5	9,252,1942	99.0	105.0	103.0		2715,1380	1.6	0.7	7	dbSNP_126	103	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ABCB5	NM_001163941.1,NM_178559.5	24,24	9,254,6240	TT,TG,GG		0.0233,6.128,2.0913	possibly-damaging,possibly-damaging	905/1258,460/813	20766752	272,12734	2203	4300	6503	SO:0001583	missense	340273	exon22			GCTTCAGACTCAA	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.2715G>T	7.37:g.20766752G>T	ENSP00000384881:p.Gln905His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	G	5.753	0.323381	0.10900	0.06128	2.33E-4	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.90197	-2.63;-2.63	4.43	1.61	0.23674	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.332317	0.24615	N	0.037015	T	0.39545	0.1082	L	0.55990	1.75	0.23260	N	0.998027	B;B;B	0.18310	0.027;0.01;0.003	B;B;B	0.21546	0.035;0.025;0.021	T	0.62900	-0.6756	10	0.46703	T	0.11	.	6.0759	0.19915	0.1851:0.1728:0.6421:0.0	rs35885925;rs57355100	905;83;460	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	H	905;460	ENSP00000384881:Q905H;ENSP00000258738:Q460H	ENSP00000258738:Q460H	Q	+	3	2	ABCB5	20733277	0.952000	0.32445	0.664000	0.29753	0.655000	0.38815	1.962000	0.40442	0.362000	0.24319	0.655000	0.94253	CAG	G|0.979;T|0.021	0.021	strong		0.358	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
GTSE1	51512	hgsc.bcm.edu	37	22	46709881	46709881	+	Missense_Mutation	SNP	G	G	A	rs6008622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	53	0	0	941	WXS	Illumina HiSeq	Phase_I	64	34	0.53125	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	
SUN1	23353	hgsc.bcm.edu	37	7	878583	878583	+	Missense_Mutation	SNP	G	G	T	rs114826023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:878583G>T	ENST00000405266.1	+	2	250	c.226G>T	c.(226-228)Ggc>Tgc	p.G76C	SUN1_ENST00000457378.2_Missense_Mutation_p.G97C|SUN1_ENST00000425407.2_Missense_Mutation_p.G26C|SUN1_ENST00000401592.1_Missense_Mutation_p.G76C|SUN1_ENST00000456758.2_Missense_Mutation_p.G134C|SUN1_ENST00000403868.1_Missense_Mutation_p.G76C|SUN1_ENST00000389574.3_Missense_Mutation_p.G26C|SUN1_ENST00000452783.2_Missense_Mutation_p.G76C|SUN1_ENST00000469755.1_3'UTR			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	76	LMNA-binding.				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						TGCCGACAGCGGCACCAGCAG	0.602													G|||	15	0.00299521	0.0113	0.0	5008	,	,		18035	0.0		0.0	False		,,,				2504	0.0				p.G97C		Atlas-SNP	.											.	SUN1	157	.	0			c.G289T						PASS	.	G	CYS/GLY,CYS/GLY,CYS/GLY,CYS/GLY,CYS/GLY	16,4036		0,16,2010	34.0	33.0	34.0		226,226,289,226,76	-2.4	0.0	7	dbSNP_132	34	0,8402		0,0,4201	yes	missense,missense,missense,missense,missense	SUN1	NM_001130965.2,NM_001171944.1,NM_001171945.1,NM_001171946.1,NM_025154.5	159,159,159,159,159	0,16,6211	TT,TG,GG		0.0,0.3949,0.1285	benign,benign,benign,benign,benign	76/786,76/683,97/279,76/258,26/703	878583	16,12438	2026	4201	6227	SO:0001583	missense	23353	exon4			GACAGCGGCACCA	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.226G>T	7.37:g.878583G>T	ENSP00000384116:p.Gly76Cys	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37		10	0.004578754578754579	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.524	0.869408	0.17322	0.003949	0.0	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000452783;ENST00000435699;ENST00000440380;ENST00000439679;ENST00000424128;ENST00000457598;ENST00000421580;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407;ENST00000450881	T;T;T;T;T;T;T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88	4.42	-2.43	0.06522	.	2.242240	0.01866	N	0.036910	T	0.06600	0.0169	N	0.00677	-1.265	0.09310	N	1	B;B;B;B;B	0.11235	0.0;0.001;0.001;0.004;0.0	B;B;B;B;B	0.12156	0.004;0.003;0.0;0.007;0.002	T	0.10474	-1.0628	10	0.46703	T	0.11	-1.7076	1.8943	0.03254	0.3095:0.0848:0.3628:0.2429	.	76;76;97;26;76	E9PDU4;E9PF23;F8WD13;O94901-5;O94901-3	.;.;.;.;.	C	134;26;97;76;76;76;76;76;76;76;76;76;76;76;26;51	ENSP00000388743:G134C;ENSP00000374225:G26C;ENSP00000395952:G97C;ENSP00000413439:G76C;ENSP00000388430:G76C;ENSP00000413188:G76C;ENSP00000404965:G76C;ENSP00000394381:G76C;ENSP00000384116:G76C;ENSP00000384015:G76C;ENSP00000383947:G76C;ENSP00000392309:G26C;ENSP00000392595:G51C	ENSP00000297445:G76C	G	+	1	0	SUN1	845109	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.218000	0.09240	-0.617000	0.05664	-0.266000	0.10368	GGC	G|0.997;T|0.003	0.003	strong		0.602	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
ESYT1	23344	hgsc.bcm.edu	37	12	56531154	56531154	+	Silent	SNP	T	T	C	rs2271192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56531154T>C	ENST00000394048.5	+	17	2199	c.1935T>C	c.(1933-1935)acT>acC	p.T645T	ESYT1_ENST00000267113.4_Silent_p.T655T|ESYT1_ENST00000541590.1_Silent_p.T655T	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	645	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						AGTTTGGGACTGAGGTGAGTC	0.552													C|||	926	0.184904	0.4879	0.1081	5008	,	,		19063	0.0208		0.1153	False		,,,				2504	0.0706				p.T655T		Atlas-SNP	.											.	ESYT1	84	.	0			c.T1965C						PASS	.	C	,	1841,2565	635.5+/-396.4	396,1049,758	99.0	100.0	99.0		1965,1935	-8.7	0.4	12	dbSNP_100	99	940,7660	776.6+/-407.7	57,826,3417	no	coding-synonymous,coding-synonymous	ESYT1	NM_001184796.1,NM_015292.2	,	453,1875,4175	CC,CT,TT		10.9302,41.7839,21.3824	,	655/1115,645/1105	56531154	2781,10225	2203	4300	6503	SO:0001819	synonymous_variant	23344	exon17			TGGGACTGAGGTG	AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"""Synaptotagmins"""	29534	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member A"""	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.1935T>C	12.37:g.56531154T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	135	134	0.992593	NM_001184796	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Silent	SNP	ENST00000394048.5	37	CCDS8904.1																																																																																			T|0.802;C|0.198	0.198	strong		0.552	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292	
CPNE4	131034	hgsc.bcm.edu	37	3	131268824	131268824	+	Silent	SNP	T	T	C	rs11915192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:131268824T>C	ENST00000512055.1	-	18	3395	c.1269A>G	c.(1267-1269)tcA>tcG	p.S423S	CPNE4_ENST00000511604.1_Silent_p.S423S|CPNE4_ENST00000429747.1_Silent_p.S423S|CPNE4_ENST00000512332.1_Silent_p.S441S|CPNE4_ENST00000502818.1_Silent_p.S441S			Q96A23	CPNE4_HUMAN	copine IV	423	VWFA.					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						CCTCTGACGCTGACTTGGCAA	0.517													T|||	878	0.175319	0.2443	0.1268	5008	,	,		20206	0.1141		0.1352	False		,,,				2504	0.2209				p.S423S		Atlas-SNP	.											.	CPNE4	112	.	0			c.A1269G						PASS	.	T		952,3454	360.9+/-315.4	98,756,1349	157.0	135.0	142.0		1269	1.2	1.0	3	dbSNP_120	142	1191,7409	242.9+/-272.7	67,1057,3176	no	coding-synonymous	CPNE4	NM_130808.1		165,1813,4525	CC,CT,TT		13.8488,21.6069,16.477		423/558	131268824	2143,10863	2203	4300	6503	SO:0001819	synonymous_variant	131034	exon14			TGACGCTGACTTG	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.1269A>G	3.37:g.131268824T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_130808	D3DNC5|Q8TEX1	Silent	SNP	ENST00000512055.1	37	CCDS3072.1																																																																																			T|0.840;C|0.160	0.160	strong		0.517	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808	
FOXA2	3170	hgsc.bcm.edu	37	20	22563134	22563134	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:22563134A>G	ENST00000377115.4	-	3	909	c.728T>C	c.(727-729)tTc>tCc	p.F243S	FOXA2_ENST00000419308.2_Missense_Mutation_p.F249S	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	243					adult locomotory behavior (GO:0008344)|cell development (GO:0048468)|cell differentiation in hindbrain (GO:0021533)|cell fate specification (GO:0001708)|chromatin modification (GO:0016568)|connective tissue development (GO:0061448)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral neural tube patterning (GO:0021904)|ectoderm formation (GO:0001705)|endocrine pancreas development (GO:0031018)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|in utero embryonic development (GO:0001701)|lung epithelial cell differentiation (GO:0060487)|negative regulation of detection of glucose (GO:2000971)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter by glucose (GO:0000433)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|regulation of blood coagulation (GO:0030193)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in detection of glucose (GO:2000976)|response to interleukin-6 (GO:0070741)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|urinary_tract(1)	22	Lung NSC(19;0.188)					GCCGTTCTCGAACATGTTGCC	0.662																																					p.F249S		Atlas-SNP	.											.	FOXA2	48	.	0			c.T746C						PASS	.						19.0	22.0	21.0					20																	22563134		2203	4300	6503	SO:0001583	missense	3170	exon2			TTCTCGAACATGT	AF147787	CCDS13147.1, CCDS46585.1	20p11	2008-04-10		2002-09-20	ENSG00000125798	ENSG00000125798		"""Forkhead boxes"""	5022	protein-coding gene	gene with protein product		600288	"""hepatocyte nuclear factor 3, beta"""	HNF3B		9119385, 11875061	Standard	NM_153675		Approved		uc002wsm.3	Q9Y261	OTTHUMG00000032041	ENST00000377115.4:c.728T>C	20.37:g.22563134A>G	ENSP00000366319:p.Phe243Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	110	38	0.345455	NM_021784	Q8WUW4|Q96DF7	Missense_Mutation	SNP	ENST00000377115.4	37	CCDS13147.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.784481	0.70222	.	.	ENSG00000125798	ENST00000377115;ENST00000419308;ENST00000319993;ENST00000444877	D;D;D	0.96073	-3.9;-3.9;-3.9	4.98	3.87	0.44632	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.64402	U	0.000006	D	0.97629	0.9223	M	0.88512	2.96	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	D	0.97315	0.9940	10	0.87932	D	0	.	10.4372	0.44443	0.9206:0.0:0.0794:0.0	.	243;249	Q9Y261;B0ZTD4	FOXA2_HUMAN;.	S	243;243;249;129	ENSP00000366319:F243S;ENSP00000400341:F243S;ENSP00000315955:F249S	ENSP00000315955:F249S	F	-	2	0	FOXA2	22511134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.437000	0.80417	0.723000	0.32274	0.468000	0.43344	TTC	.	.	none		0.662	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1		
GUCY2D	3000	hgsc.bcm.edu	37	17	7915912	7915912	+	Missense_Mutation	SNP	C	C	T	rs34598902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7915912C>T	ENST00000254854.4	+	10	2251	c.2101C>T	c.(2101-2103)Ccc>Tcc	p.P701S		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	701	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> S (polymorphism that at homozygosity may be associated with Leber congenital amaurosis in some populations; dbSNP:rs34598902). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:17724218, ECO:0000269|PubMed:21602930}.		intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				ACCGGAGCCTCCCAGAGCGGA	0.592													C|||	417	0.0832668	0.0378	0.0576	5008	,	,		15329	0.2173		0.0169	False		,,,				2504	0.093				p.P701S		Atlas-SNP	.											.	GUCY2D	82	.	0			c.C2101T	GRCh37	CM994059	GUCY2D	M	rs34598902	PASS	.	C	SER/PRO	171,4235	109.5+/-147.8	0,171,2032	60.0	60.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2101	4.4	0.4	17	dbSNP_126	60	165,8435	75.4+/-138.0	1,163,4136	yes	missense	GUCY2D	NM_000180.3	74	1,334,6168	TT,TC,CC		1.9186,3.8811,2.5834	benign	701/1104	7915912	336,12670	2203	4300	6503	SO:0001583	missense	3000	exon10			GAGCCTCCCAGAG	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"""cone rod dystrophy 6"""	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.2101C>T	17.37:g.7915912C>T	ENSP00000254854:p.Pro701Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	38	24	0.631579	NM_000180	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	37	CCDS11127.1	180	0.08241758241758242	16	0.032520325203252036	19	0.052486187845303865	129	0.22552447552447552	16	0.021108179419525065	C	13.81	2.347301	0.41599	0.038811	0.019186	ENSG00000132518	ENST00000254854	D	0.81499	-1.5	5.34	4.37	0.52481	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.49305	D	0.000152	T	0.00073	0.0002	N	0.21545	0.675	0.80722	P	0.0	P	0.42871	0.792	B	0.42692	0.395	T	0.05099	-1.0906	9	0.19590	T	0.45	.	9.328	0.38005	0.0:0.774:0.1461:0.0799	rs34598902	701	Q02846	GUC2D_HUMAN	S	701	ENSP00000254854:P701S	ENSP00000254854:P701S	P	+	1	0	GUCY2D	7856637	0.010000	0.17322	0.373000	0.26003	0.239000	0.25481	2.216000	0.42871	1.494000	0.48533	-0.142000	0.14014	CCC	C|0.956;T|0.044	0.044	strong		0.592	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
HIGD2A	192286	hgsc.bcm.edu	37	5	175815874	175815874	+	Silent	SNP	T	T	C	rs1060588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:175815874T>C	ENST00000274787.2	+	1	127	c.54T>C	c.(52-54)ccT>ccC	p.P18P	NOP16_ENST00000509257.1_5'Flank|NOP16_ENST00000510123.1_5'Flank|NOP16_ENST00000389158.5_5'UTR|NOP16_ENST00000507413.1_5'Flank	NM_138820.2	NP_620175.1	Q9BW72	HIG2A_HUMAN	HIG1 hypoxia inducible domain family, member 2A	18					negative regulation of apoptotic process (GO:0043066)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)				large_intestine(1)	1	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.0965)		CATCGAAGCCTCCAGTCATTG	0.582													T|||	398	0.0794728	0.1846	0.0648	5008	,	,		16148	0.0		0.0905	False		,,,				2504	0.0184				p.P18P		Atlas-SNP	.											.	HIGD2A	7	.	0			c.T54C						PASS	.	T		704,3702	270.7+/-269.8	46,612,1545	81.0	89.0	86.0		54	2.5	0.9	5	dbSNP_86	86	826,7774	179.5+/-228.6	41,744,3515	no	coding-synonymous	HIGD2A	NM_138820.2		87,1356,5060	CC,CT,TT		9.6047,15.9782,11.7638		18/107	175815874	1530,11476	2203	4300	6503	SO:0001819	synonymous_variant	192286	exon1			GAAGCCTCCAGTC	BC007502	CCDS4401.1	5q35.2	2009-03-17	2009-03-17		ENSG00000146066	ENSG00000146066			28311	protein-coding gene	gene with protein product			"""HIG1 domain family, member 2A"""			12477932	Standard	NM_138820		Approved	MGC2198	uc003meg.3	Q9BW72	OTTHUMG00000130657	ENST00000274787.2:c.54T>C	5.37:g.175815874T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_138820		Silent	SNP	ENST00000274787.2	37	CCDS4401.1																																																																																			T|0.893;C|0.107	0.107	strong		0.582	HIGD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253147.1	NM_138820	
TRPV2	51393	hgsc.bcm.edu	37	17	16325968	16325968	+	Silent	SNP	A	A	G	rs8121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16325968A>G	ENST00000338560.7	+	4	789	c.390A>G	c.(388-390)ggA>ggG	p.G130G	TRPV2_ENST00000577397.1_5'UTR	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	130	Required for interaction with SLC50A1. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.G130G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TTAAGGACGGAGTCAATGCCT	0.572													G|||	1960	0.391374	0.6475	0.3818	5008	,	,		18556	0.2321		0.3877	False		,,,				2504	0.2198				p.G130G		Atlas-SNP	.											TRPV2,right_upper_lobe,carcinoma,+1,2	TRPV2	74	2	1	Substitution - coding silent(1)	stomach(1)	c.A390G						PASS	.	G		2586,1820	532.3+/-373.4	765,1056,382	82.0	67.0	72.0		390	-5.9	0.0	17	dbSNP_52	72	3364,5236	641.2+/-399.7	648,2068,1584	no	coding-synonymous	TRPV2	NM_016113.4		1413,3124,1966	GG,GA,AA		39.1163,41.3073,45.7481		130/765	16325968	5950,7056	2203	4300	6503	SO:0001819	synonymous_variant	51393	exon4			GGACGGAGTCAAT	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.390A>G	17.37:g.16325968A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	118	67	0.567797	NM_016113	A6NML2|A8K0Z0|Q9Y670	Silent	SNP	ENST00000338560.7	37	CCDS32576.1	889	0.40705128205128205	301	0.6117886178861789	153	0.42265193370165743	148	0.25874125874125875	287	0.3786279683377309	G	0.717	-0.784796	0.02907	0.586927	0.391163	ENSG00000187688	ENST00000455666	.	.	.	5.24	-5.94	0.02247	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999865	.	.	.	.	.	.	T	0.46569	-0.9182	3	.	.	.	-7.0661	0.4381	0.00482	0.2267:0.1978:0.2647:0.3108	rs8121;rs1129232;rs3186904;rs60740001;rs8121	.	.	.	G	88	.	.	S	+	1	0	TRPV2	16266693	0.000000	0.05858	0.029000	0.17559	0.089000	0.18198	-1.548000	0.02184	-1.326000	0.02266	-0.812000	0.03155	AGT	A|0.561;G|0.439	0.439	strong		0.572	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
SCUBE1	80274	hgsc.bcm.edu	37	22	43614316	43614316	+	Silent	SNP	C	C	G	rs9620123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:43614316C>G	ENST00000360835.4	-	15	1962	c.1836G>C	c.(1834-1836)gcG>gcC	p.A612A		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	612					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)				GCCCCTCCAGCGCCTTGGCTG	0.632													G|||	1907	0.380791	0.559	0.17	5008	,	,		19957	0.5268		0.1879	False		,,,				2504	0.3374				p.A612A		Atlas-SNP	.											.	SCUBE1	105	.	0			c.G1836C						PASS	.	G		2170,2236	587.7+/-386.8	527,1116,560	92.0	91.0	91.0		1836	-2.0	0.1	22	dbSNP_119	91	1277,7323	756.1+/-407.5	96,1085,3119	no	coding-synonymous	SCUBE1	NM_173050.3		623,2201,3679	GG,GC,CC		14.8488,49.251,26.5032		612/989	43614316	3447,9559	2203	4300	6503	SO:0001819	synonymous_variant	80274	exon15			CTCCAGCGCCTTG		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.1836G>C	22.37:g.43614316C>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_173050	Q5R336	Silent	SNP	ENST00000360835.4	37	CCDS14048.1																																																																																			C|0.719;G|0.281	0.281	strong		0.632	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
QRICH2	84074	hgsc.bcm.edu	37	17	74289242	74289242	+	Silent	SNP	T	T	C	rs3803736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74289242T>C	ENST00000262765.5	-	4	1247	c.1068A>G	c.(1066-1068)caA>caG	p.Q356Q		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	356										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						CCAGGCCATGTTGATCGACGA	0.493													T|||	431	0.0860623	0.2042	0.0303	5008	,	,		26753	0.0605		0.0308	False		,,,				2504	0.0491				p.Q356Q		Atlas-SNP	.											.	QRICH2	143	.	0			c.A1068G						PASS	.	T		819,3587	328.5+/-300.6	71,677,1455	174.0	139.0	151.0		1068	-7.8	0.0	17	dbSNP_107	151	219,8381	90.9+/-153.0	5,209,4086	no	coding-synonymous	QRICH2	NM_032134.1		76,886,5541	CC,CT,TT		2.5465,18.5883,7.9809		356/1664	74289242	1038,11968	2203	4300	6503	SO:0001819	synonymous_variant	84074	exon4			GCCATGTTGATCG	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.1068A>G	17.37:g.74289242T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																			T|0.916;C|0.084	0.084	strong		0.493	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
FAM160A1	729830	hgsc.bcm.edu	37	4	152571711	152571711	+	Missense_Mutation	SNP	C	C	T	rs77993711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:152571711C>T	ENST00000505231.1	+	9	2677	c.2518C>T	c.(2518-2520)Cat>Tat	p.H840Y	FAM160A1_ENST00000435205.1_Missense_Mutation_p.H840Y			Q05DH4	F16A1_HUMAN	family with sequence similarity 160, member A1	840										endometrium(2)|kidney(1)	3						TGCCAGTCGCCATCCCGTGAG	0.478													C|||	18	0.00359425	0.0136	0.0	5008	,	,		18392	0.0		0.0	False		,,,				2504	0.0				p.H840Y		Atlas-SNP	.											.	FAM160A1	60	.	0			c.C2518T						PASS	.	C	TYR/HIS	14,1370		0,14,678	40.0	46.0	44.0		2518	4.7	0.0	4	dbSNP_132	44	0,3182		0,0,1591	no	missense	FAM160A1	NM_001109977.1	83	0,14,2269	TT,TC,CC		0.0,1.0116,0.3066	benign	840/1041	152571711	14,4552	692	1591	2283	SO:0001583	missense	729830	exon11			AGTCGCCATCCCG		CCDS47146.1	4q31.3	2012-11-30			ENSG00000164142	ENSG00000164142			34237	protein-coding gene	gene with protein product							Standard	NM_001109977		Approved	FLJ43373	uc003imj.2	Q05DH4	OTTHUMG00000161675	ENST00000505231.1:c.2518C>T	4.37:g.152571711C>T	ENSP00000421580:p.His840Tyr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_001109977	Q6ZUS2	Missense_Mutation	SNP	ENST00000505231.1	37	CCDS47146.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	0.040	-1.290594	0.01387	0.010116	0.0	ENSG00000164142	ENST00000435205;ENST00000505231	T;T	0.11930	2.73;2.73	4.68	4.68	0.58851	.	1.923240	0.02458	N	0.086292	T	0.08358	0.0208	L	0.44542	1.39	0.09310	N	1	B	0.24483	0.104	B	0.17433	0.018	T	0.13683	-1.0500	10	0.59425	D	0.04	.	9.8454	0.41024	0.0:0.779:0.1417:0.0794	.	840	Q05DH4	F16A1_HUMAN	Y	840	ENSP00000413196:H840Y;ENSP00000421580:H840Y	ENSP00000413196:H840Y	H	+	1	0	FAM160A1	152791161	0.006000	0.16342	0.004000	0.12327	0.035000	0.12851	2.082000	0.41605	2.320000	0.78422	0.655000	0.94253	CAT	C|0.995;T|0.005	0.005	strong		0.478	FAM160A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365691.1	NM_001109977	
HUNK	30811	hgsc.bcm.edu	37	21	33371442	33371442	+	Missense_Mutation	SNP	T	T	C	rs150499320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33371442T>C	ENST00000270112.2	+	11	2450	c.2090T>C	c.(2089-2091)cTa>cCa	p.L697P		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	697					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						CTGCAGCCCCTAGCCCCTGTG	0.582													T|||	5	0.000998403	0.0038	0.0	5008	,	,		17188	0.0		0.0	False		,,,				2504	0.0				p.L697P		Atlas-SNP	.											.	HUNK	74	.	0			c.T2090C						PASS	.	T	PRO/LEU	9,4397	14.3+/-33.2	0,9,2194	63.0	71.0	69.0		2090	-2.9	0.0	21	dbSNP_134	69	0,8600		0,0,4300	yes	missense	HUNK	NM_014586.1	98	0,9,6494	CC,CT,TT		0.0,0.2043,0.0692	benign	697/715	33371442	9,12997	2203	4300	6503	SO:0001583	missense	30811	exon11			AGCCCCTAGCCCC	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"""hormonally upregulated Neu-associated kinase"""			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.2090T>C	21.37:g.33371442T>C	ENSP00000270112:p.Leu697Pro	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	128	55	0.429688	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	37	CCDS13610.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	3.433	-0.115606	0.06881	0.002043	0.0	ENSG00000142149	ENST00000270112	T	0.70164	-0.46	4.42	-2.92	0.05615	.	1.836150	0.03075	N	0.157723	T	0.39306	0.1073	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40553	-0.9557	10	0.51188	T	0.08	-1.0E-4	10.8545	0.46792	0.0:0.2362:0.0:0.7638	.	697	P57058	HUNK_HUMAN	P	697	ENSP00000270112:L697P	ENSP00000270112:L697P	L	+	2	0	HUNK	32293313	0.002000	0.14202	0.011000	0.14972	0.070000	0.16714	-0.019000	0.12546	-0.588000	0.05882	-0.462000	0.05337	CTA	T|0.999;C|0.001	0.001	strong		0.582	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586	
MUC17	140453	hgsc.bcm.edu	37	7	100682831	100682831	+	Missense_Mutation	SNP	C	C	G	rs34223735		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100682831C>G	ENST00000306151.4	+	3	8198	c.8134C>G	c.(8134-8136)Ctt>Gtt	p.L2712V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2712	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)					GGCTAGCACCCTTTCAACAAC	0.493																																					p.L2712V		Atlas-SNP	.											.	MUC17	804	.	0			c.C8134G						PASS	.						257.0	264.0	262.0					7																	100682831		2203	4300	6503	SO:0001583	missense	140453	exon3			AGCACCCTTTCAA	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.8134C>G	7.37:g.100682831C>G	ENSP00000302716:p.Leu2712Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	146	9	0.0616438	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.446165	0.01089	.	.	ENSG00000169876	ENST00000306151	T	0.04049	3.72	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.02494	0.0076	N	0.17082	0.46	0.09310	N	1	B	0.17667	0.023	B	0.09377	0.004	T	0.48875	-0.8996	9	0.14656	T	0.56	.	3.6497	0.08198	2.0E-4:0.5059:0.4937:2.0E-4	rs34223735	2712	Q685J3	MUC17_HUMAN	V	2712	ENSP00000302716:L2712V	ENSP00000302716:L2712V	L	+	1	0	MUC17	100469551	0.018000	0.18449	0.005000	0.12908	0.081000	0.17604	-0.783000	0.04638	0.132000	0.18615	0.134000	0.15878	CTT	.	.	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
GAL3ST1	9514	hgsc.bcm.edu	37	22	30953295	30953295	+	Missense_Mutation	SNP	C	C	T	rs2267161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30953295C>T	ENST00000402321.1	-	2	402	c.85G>A	c.(85-87)Gtg>Atg	p.V29M	GAL3ST1_ENST00000338911.5_Missense_Mutation_p.V29M|GAL3ST1_ENST00000443111.2_Missense_Mutation_p.V29M|GAL3ST1_ENST00000402369.1_Missense_Mutation_p.V29M|GAL3ST1_ENST00000406361.1_Missense_Mutation_p.V29M|GAL3ST1_ENST00000406955.1_Missense_Mutation_p.V29M|GAL3ST1_ENST00000401975.1_Missense_Mutation_p.V29M			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	29			V -> M (in dbSNP:rs2267161). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.		galactosylceramide biosynthetic process (GO:0006682)|glycosphingolipid metabolic process (GO:0006687)|myelination (GO:0042552)|protein N-linked glycosylation (GO:0006487)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21						TAGGAGTACACCAGCAGCAGG	0.652													C|||	1552	0.309904	0.3646	0.2536	5008	,	,		17788	0.3502		0.326	False		,,,				2504	0.2178				p.V29M		Atlas-SNP	.											.	GAL3ST1	44	.	0			c.G85A						PASS	.	C	MET/VAL	1647,2759	502.0+/-365.1	326,995,882	89.0	91.0	91.0		85	1.1	0.9	22	dbSNP_100	91	2732,5868	436.8+/-358.4	420,1892,1988	yes	missense	GAL3ST1	NM_004861.1	21	746,2887,2870	TT,TC,CC		31.7674,37.3808,33.6691	benign	29/424	30953295	4379,8627	2203	4300	6503	SO:0001583	missense	9514	exon3			AGTACACCAGCAG	D88667	CCDS13879.1	22q12.2	2007-04-02			ENSG00000128242	ENSG00000128242		"""Sulfotransferases, membrane-bound"""	24240	protein-coding gene	gene with protein product	"""cerebroside (3' phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase"""	602300				9847074, 9030544	Standard	NM_004861		Approved	CST	uc003aii.1	Q99999	OTTHUMG00000151200	ENST00000402321.1:c.85G>A	22.37:g.30953295C>T	ENSP00000385735:p.Val29Met	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	347	172	0.495677	NM_004861	Q96C63	Missense_Mutation	SNP	ENST00000402321.1	37	CCDS13879.1	691	0.3163919413919414	167	0.3394308943089431	90	0.24861878453038674	197	0.34440559440559443	237	0.31266490765171506	C	13.74	2.327313	0.41197	0.373808	0.317674	ENSG00000128242	ENST00000406955;ENST00000402321;ENST00000402369;ENST00000401975;ENST00000338911;ENST00000406361;ENST00000443111;ENST00000441967;ENST00000431313;ENST00000452827;ENST00000437282;ENST00000416358;ENST00000427899;ENST00000423299;ENST00000443136;ENST00000423371;ENST00000428682;ENST00000453479;ENST00000426220;ENST00000447224;ENST00000411821;ENST00000445645;ENST00000448604	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.18960	2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18	5.58	1.09	0.20402	.	0.269973	0.36268	N	0.002686	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.9999999999999958	B	0.25904	0.137	B	0.29716	0.106	T	0.49495	-0.8934	9	0.33141	T	0.24	-10.4855	7.6791	0.28502	0.2039:0.1191:0.677:0.0	rs2267161;rs17845430;rs17856591;rs17858302;rs61593263;rs2267161	29	Q99999	G3ST1_HUMAN	M	29	ENSP00000385825:V29M;ENSP00000385735:V29M;ENSP00000384122:V29M;ENSP00000384388:V29M;ENSP00000343234:V29M;ENSP00000385207:V29M;ENSP00000402587:V29M;ENSP00000390545:V29M;ENSP00000395080:V29M;ENSP00000405017:V29M;ENSP00000401426:V29M;ENSP00000391485:V29M;ENSP00000397092:V29M;ENSP00000391996:V29M;ENSP00000405381:V29M;ENSP00000401074:V29M;ENSP00000389876:V29M;ENSP00000398380:V29M;ENSP00000414542:V29M;ENSP00000412995:V29M;ENSP00000394912:V29M;ENSP00000399649:V29M;ENSP00000390068:V29M	ENSP00000343234:V29M	V	-	1	0	GAL3ST1	29283295	1.000000	0.71417	0.931000	0.37212	0.726000	0.41606	1.007000	0.29860	0.316000	0.23135	-0.147000	0.13772	GTG	C|0.671;T|0.329	0.329	strong		0.652	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321745.1	NM_004861	
OR2AE1	81392	hgsc.bcm.edu	37	7	99473801	99473801	+	Missense_Mutation	SNP	A	A	G	rs73403577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99473801A>G	ENST00000316368.2	-	1	879	c.856T>C	c.(856-858)Tct>Cct	p.S286P		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	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(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					TAAATCAGAGAATTCAATGTG	0.453													G|||	372	0.0742812	0.2557	0.0288	5008	,	,		20421	0.001		0.002	False		,,,				2504	0.0112				p.S286P		Atlas-SNP	.											OR2AE1,rectum,carcinoma,+1,1	OR2AE1	32	1	0			c.T856C						PASS	.	G	PRO/SER	952,3454	734.8+/-410.6	103,746,1354	112.0	116.0	115.0		856	2.7	0.2	7	dbSNP_130	115	22,8578	818.3+/-406.9	0,22,4278	yes	missense	OR2AE1	NM_001005276.1	74	103,768,5632	GG,GA,AA		0.2558,21.6069,7.4889	benign	286/324	99473801	974,12032	2203	4300	6503	SO:0001583	missense	81392	exon1			TCAGAGAATTCAA	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"""GPCR / Class A : Olfactory receptors"""	15087	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily AE, member 2"""	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.856T>C	7.37:g.99473801A>G	ENSP00000313936:p.Ser286Pro	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	150	74	0.493333	NM_001005276	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	140	0.0641025641025641	127	0.258130081300813	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	G	0.005	-2.228017	0.00280	0.216069	0.002558	ENSG00000244623	ENST00000316368	T	0.14516	2.5	3.56	2.68	0.31781	GPCR, rhodopsin-like superfamily (1);	0.201466	0.24843	N	0.035141	T	0.00012	0.0000	N	0.00081	-2.22	0.51012	P	9.099999999995223E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43475	-0.9389	9	0.02654	T	1	.	7.3678	0.26783	0.0999:0.1697:0.7304:0.0	.	286	Q8NHA4	O2AE1_HUMAN	P	286	ENSP00000313936:S286P	ENSP00000313936:S286P	S	-	1	0	OR2AE1	99311737	1.000000	0.71417	0.200000	0.23457	0.127000	0.20565	2.295000	0.43576	0.508000	0.28173	-3.352000	0.00042	TCT	A|0.933;G|0.067	0.067	strong		0.453	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1		
FOXD4	2298	hgsc.bcm.edu	37	9	117637	117637	+	Silent	SNP	G	G	A	rs138098441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117637G>A	ENST00000382500.2	-	1	780	c.483C>T	c.(481-483)tgC>tgT	p.C161C		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	161					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)		TCTTGACGAAGCAGTCGTTCA	0.637													.|||	119	0.023762	0.0847	0.0101	5008	,	,		14103	0.0		0.0	False		,,,				2504	0.0				p.C161C		Atlas-SNP	.											.	FOXD4	75	.	0			c.C483T						PASS	.	G		293,4087		3,287,1900	104.0	143.0	130.0		483	2.2	1.0	9	dbSNP_134	130	1,8567		0,1,4283	no	coding-synonymous	FOXD4	NM_207305.3		3,288,6183	AA,AG,GG		0.0117,6.6895,2.2706		161/440	117637	294,12654	2190	4284	6474	SO:0001819	synonymous_variant	2298	exon1			GACGAAGCAGTCG	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.483C>T	9.37:g.117637G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	228	115	0.504386	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Silent	SNP	ENST00000382500.2	37	CCDS34975.1																																																																																			G|0.974;A|0.026	0.026	strong		0.637	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
LMNTD1	160492	hgsc.bcm.edu	37	12	25671871	25671871	+	Silent	SNP	A	A	G	rs34028410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25671871A>G	ENST00000282881.6	-	7	1133	c.984T>C	c.(982-984)ccT>ccC	p.P328P	IFLTD1_ENST00000458174.2_Silent_p.P349P|IFLTD1_ENST00000445693.1_Silent_p.P265P|IFLTD1_ENST00000413632.2_Silent_p.P309P|IFLTD1_ENST00000539744.1_Silent_p.P231P	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		328					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GGCTGCGATTAGGGAAAACGG	0.448													G|||	88	0.0175719	0.0628	0.0072	5008	,	,		20109	0.0		0.0	False		,,,				2504	0.0				p.P349P		Atlas-SNP	.											.	IFLTD1	121	.	0			c.T1047C						PASS	.	G	,,,	251,4155	803.2+/-415.7	5,241,1957	101.0	101.0	101.0		795,1047,927,984	-2.9	0.0	12	dbSNP_126	101	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	,,,	5,242,6256	GG,GA,AA		0.0116,5.6968,1.9376	,,,	265/326,349/410,309/370,328/389	25671871	252,12754	2203	4300	6503	SO:0001819	synonymous_variant	160492	exon8			GCGATTAGGGAAA																												ENST00000282881.6:c.984T>C	12.37:g.25671871A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	151	79	0.523179	NM_001145728	B4DL27|B4DY70|Q8IY38	Silent	SNP	ENST00000282881.6	37	CCDS8704.1	20	0.009157509157509158	17	0.034552845528455285	3	0.008287292817679558	0	0.0	0	0.0	G	1.210	-0.629928	0.03610	0.056968	1.16E-4	ENSG00000152936	ENST00000543629	.	.	.	4.95	-2.93	0.05598	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999994	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.2418	0.8046	0.01082	0.3824:0.1182:0.2583:0.241	rs34028410	.	.	.	Q	103	.	.	X	-	1	0	IFLTD1	25563138	0.330000	0.24705	0.000000	0.03702	0.293000	0.27360	0.047000	0.14056	-0.848000	0.04163	-0.930000	0.02707	TAA	A|0.980;G|0.020	0.020	strong		0.448	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
KRT84	3890	hgsc.bcm.edu	37	12	52777578	52777578	+	Missense_Mutation	SNP	C	C	T	rs386763043|rs1613931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52777578C>T	ENST00000257951.3	-	2	617	c.551G>A	c.(550-552)cGg>cAg	p.R184Q	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	184	Coil 1A.|Rod.		R -> Q (in dbSNP:rs1613931).		hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)	p.R184L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CTCTAGGAACCGAACCTAAAT	0.493													C|||	1664	0.332268	0.6172	0.3199	5008	,	,		22846	0.1954		0.2068	False		,,,				2504	0.226				p.R184Q		Atlas-SNP	.											KRT84,colon,carcinoma,0,1	KRT84	61	1	1	Substitution - Missense(1)	large_intestine(1)	c.G551A						PASS	.	C	GLN/ARG	2138,2268		715,708,780	57.0	58.0	57.0		551	5.3	1.0	12	dbSNP_89	57	1299,7301		180,939,3181	yes	missense	KRT84	NM_033045.3	43	895,1647,3961	TT,TC,CC		15.1047,48.5247,26.4263	probably-damaging	184/601	52777578	3437,9569	2203	4300	6503	SO:0001583	missense	3890	exon2			AGGAACCGAACCT	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.551G>A	12.37:g.52777578C>T	ENSP00000257951:p.Arg184Gln	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	664	0.304029304029304	288	0.5853658536585366	100	0.27624309392265195	117	0.20454545454545456	159	0.20976253298153033	C	36	5.730439	0.96856	0.485247	0.151047	ENSG00000161849	ENST00000257951	D	0.92099	-2.97	5.32	5.32	0.75619	Filament (1);	0.000000	0.45867	D	0.000325	T	0.00012	0.0000	M	0.87180	2.865	0.21355	P	0.999713097	D	0.89917	1.0	D	0.91635	0.999	T	0.21415	-1.0246	9	0.72032	D	0.01	.	19.5787	0.95455	0.0:1.0:0.0:0.0	rs1613931;rs61083896	184	Q9NSB2	KRT84_HUMAN	Q	184	ENSP00000257951:R184Q	ENSP00000257951:R184Q	R	-	2	0	KRT84	51063845	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	5.903000	0.69877	2.941000	0.99782	0.655000	0.94253	CGG	C|0.686;T|0.314	0.314	strong		0.493	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
DNAH3	55567	hgsc.bcm.edu	37	16	20996868	20996868	+	Missense_Mutation	SNP	A	A	T	rs34179606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20996868A>T	ENST00000261383.3	-	48	7195	c.7196T>A	c.(7195-7197)aTc>aAc	p.I2399N	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2399	AAA 4. {ECO:0000250}.		I -> N (in dbSNP:rs34179606).		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)		GGCCTTGCTGATGTTGTTGAA	0.488													A|||	67	0.0133786	0.0507	0.0	5008	,	,		20170	0.0		0.0	False		,,,				2504	0.0				p.I2399N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T7196A						PASS	.	A	ASN/ILE	139,4263	98.9+/-137.6	2,135,2064	142.0	122.0	129.0		7196	4.8	1.0	16	dbSNP_126	129	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DNAH3	NM_017539.1	149	2,138,6361	TT,TA,AA		0.0349,3.1577,1.0921	benign	2399/4117	20996868	142,12860	2201	4300	6501	SO:0001583	missense	55567	exon48			TTGCTGATGTTGT	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.7196T>A	16.37:g.20996868A>T	ENSP00000261383:p.Ile2399Asn	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	A	12.96	2.093349	0.36952	0.031577	3.49E-4	ENSG00000158486	ENST00000261383	T	0.22945	1.93	4.79	4.79	0.61399	.	0.272346	0.29438	N	0.012143	T	0.06645	0.0170	L	0.48174	1.505	0.80722	D	1	P	0.39480	0.675	B	0.42343	0.384	T	0.00920	-1.1514	10	0.39692	T	0.17	.	10.7686	0.46308	0.9222:0.0:0.0778:0.0	rs34179606	2399	Q8TD57	DYH3_HUMAN	N	2399	ENSP00000261383:I2399N	ENSP00000261383:I2399N	I	-	2	0	DNAH3	20904369	0.994000	0.37717	0.975000	0.42487	0.937000	0.57800	2.961000	0.49168	1.930000	0.55929	0.533000	0.62120	ATC	A|0.989;T|0.011	0.011	strong		0.488	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
TTC21B	79809	hgsc.bcm.edu	37	2	166781188	166781188	+	Splice_Site	SNP	G	G	A	rs16851307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166781188G>A	ENST00000243344.7	-	12	1524	c.1387C>T	c.(1387-1389)Cct>Tct	p.P463S		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	463			P -> S (in dbSNP:rs16851307).		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						GGACTTGCAGGCTAAACAAAA	0.353													G|||	55	0.0109824	0.0386	0.0058	5008	,	,		13522	0.0		0.0	False		,,,				2504	0.0				p.P463S		Atlas-SNP	.											.	TTC21B	130	.	0			c.C1387T						PASS	.	G	SER/PRO	192,4214	119.2+/-156.9	6,180,2017	46.0	46.0	46.0		1387	5.8	1.0	2	dbSNP_123	46	0,8600		0,0,4300	yes	missense-near-splice	TTC21B	NM_024753.3	74	6,180,6317	AA,AG,GG		0.0,4.3577,1.4762	benign	463/1317	166781188	192,12814	2203	4300	6503	SO:0001630	splice_region_variant	79809	exon12			TTGCAGGCTAAAC	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.1387-1C>T	2.37:g.166781188G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	115	44	0.382609	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	37	CCDS33315.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	G	19.77	3.889969	0.72524	0.043577	0.0	ENSG00000123607	ENST00000243344	T	0.63417	-0.04	5.76	5.76	0.90799	.	0.049003	0.85682	D	0.000000	T	0.26195	0.0639	M	0.74389	2.26	0.80722	D	1	P	0.39748	0.686	B	0.38156	0.266	T	0.53927	-0.8369	10	0.36615	T	0.2	-18.9007	19.9766	0.97312	0.0:0.0:1.0:0.0	rs16851307;rs52837751;rs58123452;rs16851307	463	Q7Z4L5	TT21B_HUMAN	S	463	ENSP00000243344:P463S	ENSP00000243344:P463S	P	-	1	0	TTC21B	166489434	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	6.194000	0.72082	2.728000	0.93425	0.561000	0.74099	CCT	G|0.983;A|0.017	0.017	strong		0.353	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	Missense_Mutation
SMC1B	27127	hgsc.bcm.edu	37	22	45782903	45782903	+	Silent	SNP	T	T	C	rs6007010	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45782903T>C	ENST00000357450.4	-	11	1754	c.1755A>G	c.(1753-1755)ctA>ctG	p.L585L	SMC1B_ENST00000404354.3_Silent_p.L585L	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	585	Flexible hinge.				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)		TAAGCTCCCTTAGTCTTTCAT	0.323													T|||	2837	0.566494	0.9054	0.3977	5008	,	,		21535	0.5268		0.3728	False		,,,				2504	0.4683				p.L585L		Atlas-SNP	.											SMC1B_ENST00000357450,NS,carcinoma,-1,4	SMC1B	215	4	0			c.A1755G						PASS	.	T		3069,633		1281,507,63	148.0	139.0	142.0		1755	-6.2	0.2	22	dbSNP_114	142	2935,5279		530,1875,1702	no	coding-synonymous	SMC1B	NM_148674.3		1811,2382,1765	CC,CT,TT		35.7317,17.0989,49.614		585/1236	45782903	6004,5912	1851	4107	5958	SO:0001819	synonymous_variant	27127	exon11			CTCCCTTAGTCTT	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.1755A>G	22.37:g.45782903T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	111	64	0.576577	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																			T|0.518;C|0.482	0.482	strong		0.323	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
LYSMD1	388695	hgsc.bcm.edu	37	1	151138250	151138250	+	5'UTR	SNP	G	G	T	rs113805704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151138250G>T	ENST00000368908.5	-	0	145				SCNM1_ENST00000368905.4_5'Flank|LYSMD1_ENST00000440902.2_Missense_Mutation_p.S3R	NM_212551.4	NP_997716.1	Q96S90	LYSM1_HUMAN	LysM, putative peptidoglycan-binding, domain containing 1											endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7	Lung SC(34;0.00471)|Ovarian(49;0.0147)|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)			TCAAAGGTCCGCTCCGCATAA	0.537													G|||	38	0.00758786	0.0287	0.0	5008	,	,		18656	0.0		0.0	False		,,,				2504	0.0				p.S3R		Atlas-SNP	.											.	LYSMD1	23	.	0			c.C9A						PASS	.	G	ARG/SER,,	33,1351		1,31,660	142.0	137.0	138.0		9,,	-8.1	0.0	1	dbSNP_132	138	1,3181		0,1,1590	yes	missense,intron,utr-5	LYSMD1,TNFAIP8L2-SCNM1	NM_001136543.1,NM_001204848.1,NM_212551.4	110,,	1,32,2250	TT,TG,GG		0.0314,2.3844,0.7446	,,	3/180,,	151138250	34,4532	692	1591	2283	SO:0001623	5_prime_UTR_variant	388695	exon1			AGGTCCGCTCCGC	BX647911	CCDS986.1, CCDS44218.1	1q21.2	2008-02-05			ENSG00000163155	ENSG00000163155			32070	protein-coding gene	gene with protein product						12477932	Standard	NM_212551		Approved	SB145, MGC35223, RP11-68I18.5	uc001ewy.3	Q96S90	OTTHUMG00000012260	ENST00000368908.5:c.-516C>A	1.37:g.151138250G>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001136543	B4DQA1|Q69YX9	Missense_Mutation	SNP	ENST00000368908.5	37	CCDS986.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	16.76	3.211662	0.58452	0.023844	3.14E-4	ENSG00000163155	ENST00000440902	T	0.32988	1.43	4.06	-8.13	0.01073	.	.	.	.	.	T	0.05090	0.0136	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.27606	-1.0069	8	0.87932	D	0	.	0.7224	0.00943	0.307:0.2957:0.1987:0.1986	.	3	Q96S90-2	.	R	3	ENSP00000404059:S3R	ENSP00000404059:S3R	S	-	3	2	LYSMD1	149404874	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.795000	0.01752	-2.291000	0.00666	0.603000	0.83216	AGC	G|0.994;T|0.006	0.006	strong		0.537	LYSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034070.3	NM_212551	
OR6K2	81448	hgsc.bcm.edu	37	1	158669980	158669980	+	Missense_Mutation	SNP	G	G	A	rs111363268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158669980G>A	ENST00000359610.2	-	1	506	c.463C>T	c.(463-465)Ccc>Tcc	p.P155S		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					TCAGGAAGGGGTGTGATAAAG	0.488													G|||	119	0.023762	0.0847	0.0086	5008	,	,		23707	0.0		0.001	False		,,,				2504	0.0				p.P155S		Atlas-SNP	.											OR6K2,right_upper_lobe,carcinoma,+2,1	OR6K2	104	1	0			c.C463T						PASS	.	G	SER/PRO	340,4066	178.7+/-207.4	12,316,1875	123.0	107.0	113.0		463	3.9	0.1	1	dbSNP_132	113	2,8598	1.2+/-3.3	0,2,4298	yes	missense	OR6K2	NM_001005279.1	74	12,318,6173	AA,AG,GG		0.0233,7.7167,2.6296	possibly-damaging	155/325	158669980	342,12664	2203	4300	6503	SO:0001583	missense	81448	exon1			GAAGGGGTGTGAT	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"""GPCR / Class A : Olfactory receptors"""	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.463C>T	1.37:g.158669980G>A	ENSP00000352626:p.Pro155Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	37	CCDS30902.1	37	0.01694139194139194	36	0.07317073170731707	1	0.0027624309392265192	0	0.0	0	0.0	G	10.46	1.356369	0.24598	0.077167	2.33E-4	ENSG00000196171	ENST00000359610	T	0.29142	1.58	4.84	3.92	0.45320	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37955	N	0.001874	T	0.06050	0.0157	N	0.00879	-1.12	0.09310	N	1	D	0.56035	0.974	P	0.60236	0.871	T	0.03807	-1.1002	10	0.18710	T	0.47	-12.7456	3.6905	0.08344	0.0886:0.1687:0.5679:0.1749	.	155	Q8NGY2	OR6K2_HUMAN	S	155	ENSP00000352626:P155S	ENSP00000352626:P155S	P	-	1	0	OR6K2	156936604	0.000000	0.05858	0.145000	0.22337	0.977000	0.68977	-0.103000	0.10940	1.232000	0.43678	0.650000	0.86243	CCC	G|0.977;A|0.023	0.023	strong		0.488	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279	
LMO1	4004	hgsc.bcm.edu	37	11	8246181	8246181	+	Silent	SNP	A	A	G	rs1042359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:8246181A>G	ENST00000335790.3	-	4	948	c.453T>C	c.(451-453)ttT>ttC	p.F151F	LMO1_ENST00000534484.1_Silent_p.F140F|LMO1_ENST00000428101.2_Silent_p.F150F	NM_002315.2	NP_002306.1	P25800	RBTN1_HUMAN	LIM domain only 1 (rhombotin 1)	151					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|skin(1)	5				Epithelial(150;1.59e-07)|BRCA - Breast invasive adenocarcinoma(625;0.203)		CTTGGGATTCAAAGGTGCCAT	0.552			"""T, A"""	TRD@	"""T-ALL, neuroblastoma"""	neuroblastoma							A|||	898	0.179313	0.3759	0.1225	5008	,	,		16806	0.0585		0.1431	False		,,,				2504	0.1155				p.F151F		Atlas-SNP	.	yes	Dom	yes		11	11p15	4004	LIM domain only 1 (rhombotin 1) (RBTN1)		L	.	LMO1	14	.	0			c.T453C						PASS	.	A		1221,2657		189,843,907	67.0	68.0	68.0		453	3.2	1.0	11	dbSNP_86	68	1344,6948		105,1134,2907	no	coding-synonymous	LMO1	NM_002315.1		294,1977,3814	GG,GA,AA		16.2084,31.4853,21.0764		151/157	8246181	2565,9605	1939	4146	6085	SO:0001819	synonymous_variant	4004	exon4			GGATTCAAAGGTG	M26682	CCDS44534.1, CCDS58118.1	11p15	2014-09-17			ENSG00000166407	ENSG00000166407			6641	protein-coding gene	gene with protein product		186921		RBTN1		2034676, 1703797	Standard	NM_002315		Approved	TTG1, RHOM1	uc001mgh.2	P25800	OTTHUMG00000165833	ENST00000335790.3:c.453T>C	11.37:g.8246181A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	123	68	0.552846	NM_002315	E9PSF5|Q4VBC5|Q8IXR0	Silent	SNP	ENST00000335790.3	37	CCDS44534.1																																																																																			G|0.176;N|0.002	0.176	strong		0.552	LMO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386503.2	NM_002315	
PLCD4	84812	hgsc.bcm.edu	37	2	219492924	219492924	+	Silent	SNP	T	T	C	rs612874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219492924T>C	ENST00000450993.2	+	7	1284	c.945T>C	c.(943-945)tgT>tgC	p.C315C	PLCD4_ENST00000417849.1_Silent_p.C315C|PLCD4_ENST00000432688.1_Silent_p.C315C	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	315	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		ACCAGCTTTGTGGCCAGAGCA	0.532													T|||	2549	0.508986	0.0711	0.5879	5008	,	,		20994	0.7827		0.5934	False		,,,				2504	0.6759				p.C315C		Atlas-SNP	.											.	PLCD4	51	.	0			c.T945C						PASS	.	T		635,3433		57,521,1456	152.0	146.0	148.0		945	0.8	1.0	2	dbSNP_83	148	4788,3576		1396,1996,790	no	coding-synonymous	PLCD4	NM_032726.3		1453,2517,2246	CC,CT,TT		42.7547,15.6096,43.6213		315/763	219492924	5423,7009	2034	4182	6216	SO:0001819	synonymous_variant	84812	exon7			GCTTTGTGGCCAG	AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"""EF-hand domain containing"""	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.945T>C	2.37:g.219492924T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	133	77	0.578947	NM_032726	Q53FS8	Silent	SNP	ENST00000450993.2	37	CCDS46516.1																																																																																			T|0.503;C|0.497	0.497	strong		0.532	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1		
GIGYF2	26058	hgsc.bcm.edu	37	2	233708806	233708806	+	Silent	SNP	A	A	G	rs3816334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233708806A>G	ENST00000409547.1	+	26	3251	c.2940A>G	c.(2938-2940)caA>caG	p.Q980Q	GIGYF2_ENST00000409480.1_Silent_p.Q1002Q|GIGYF2_ENST00000373563.4_Silent_p.Q980Q|GIGYF2_ENST00000452341.2_Missense_Mutation_p.T823A|GIGYF2_ENST00000409196.3_Silent_p.Q974Q|GIGYF2_ENST00000373566.3_Silent_p.Q1002Q|GIGYF2_ENST00000409451.3_Silent_p.Q1001Q	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	980	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		agcagcagcaacagcaacagc	0.483													G|||	3207	0.640375	0.7595	0.6945	5008	,	,		16531	0.6458		0.7137	False		,,,				2504	0.3599				p.Q1001Q		Atlas-SNP	.											GIGYF2_ENST00000409451,colon,carcinoma,0,2	GIGYF2	288	2	0			c.A3003G						PASS	.	G	,,,	3241,1165	396.7+/-330.2	1195,851,157	43.0	44.0	44.0		2940,3003,2922,2940	2.3	1.0	2	dbSNP_107	44	5577,3021	445.9+/-361.1	1813,1951,535	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GIGYF2	NM_001103146.1,NM_001103147.1,NM_001103148.1,NM_015575.3	,,,	3008,2802,692	GG,GA,AA		35.1361,26.4412,32.1901	,,,	980/1300,1001/1321,974/1294,980/1300	233708806	8818,4186	2203	4299	6502	SO:0001819	synonymous_variant	26058	exon26			GCAGCAACAGCAA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2940A>G	2.37:g.233708806A>G		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	235	234	0.995745	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Silent	SNP	ENST00000409547.1	37	CCDS33401.1	1557	0.7129120879120879	366	0.7439024390243902	257	0.7099447513812155	391	0.6835664335664335	543	0.716358839050132	G	0.410	-0.913782	0.02415	0.735588	0.648639	ENSG00000204120	ENST00000452341	T	0.79033	-1.23	5.17	2.29	0.28610	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47441	P	5.749999999999922E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.38415	-0.9662	7	0.87932	D	0	-11.8084	5.7189	0.17976	0.2827:0.0:0.5921:0.1252	rs3816334;rs17846516;rs17859588;rs60210793;rs3816334	823	E9PC50	.	A	823	ENSP00000411505:T823A	ENSP00000411505:T823A	T	+	1	0	GIGYF2	233417050	1.000000	0.71417	0.969000	0.41365	0.650000	0.38633	0.963000	0.29293	0.185000	0.20105	-0.215000	0.12644	ACA	A|0.313;G|0.687	0.687	strong		0.483	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
AKAP1	8165	hgsc.bcm.edu	37	17	55183726	55183726	+	Missense_Mutation	SNP	G	G	A	rs61731968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:55183726G>A	ENST00000337714.3	+	2	1134	c.901G>A	c.(901-903)Gag>Aag	p.E301K	AKAP1_ENST00000314126.3_Missense_Mutation_p.E301K|AKAP1_ENST00000572557.1_Missense_Mutation_p.E301K|AKAP1_ENST00000539273.1_Missense_Mutation_p.E301K|AKAP1_ENST00000571629.1_Missense_Mutation_p.E301K	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	301					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					TAGAGGTGTCGAGGGAGAACT	0.547													G|||	345	0.0688898	0.2496	0.0159	5008	,	,		18330	0.002		0.002	False		,,,				2504	0.0				p.E301K		Atlas-SNP	.											.	AKAP1	73	.	0			c.G901A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	946,3460	357.1+/-313.8	103,740,1360	79.0	86.0	84.0		901,901,901	1.9	0.0	17	dbSNP_129	84	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense	AKAP1	NM_001242902.1,NM_001242903.1,NM_003488.3	56,56,56	103,745,5655	AA,AG,GG		0.0581,21.4707,7.312	benign,benign,benign	301/904,301/904,301/904	55183726	951,12055	2203	4300	6503	SO:0001583	missense	8165	exon3			GGTGTCGAGGGAG	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Tudor domain containing"""	367	protein-coding gene	gene with protein product	"""protein kinase anchoring protein 1"", ""dual specificity A-kinase-anchoring protein 1"", ""protein phosphatase 1, regulatory subunit 43"", ""tudor domain containing 17"""	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.901G>A	17.37:g.55183726G>A	ENSP00000337736:p.Glu301Lys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	114	49	0.429825	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	37	CCDS11594.1	132	0.06043956043956044	127	0.258130081300813	3	0.008287292817679558	2	0.0034965034965034965	0	0.0	G	10.31	1.315692	0.23908	0.214707	5.81E-4	ENSG00000121057	ENST00000337714;ENST00000314126;ENST00000427138;ENST00000539273	T;T;T	0.17213	2.56;2.29;2.56	5.15	1.85	0.25348	.	1.753900	0.02141	N	0.057175	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.31599	0.33	B	0.18561	0.022	T	0.38329	-0.9666	9	0.21014	T	0.42	2.3366	2.2365	0.04010	0.3265:0.0:0.4319:0.2416	rs61731968	301	Q92667	AKAP1_HUMAN	K	301;301;343;301	ENSP00000337736:E301K;ENSP00000314075:E301K;ENSP00000443139:E301K	ENSP00000314075:E301K	E	+	1	0	AKAP1	52538725	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-0.248000	0.08854	0.193000	0.20303	0.561000	0.74099	GAG	G|0.927;A|0.073	0.073	strong		0.547	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1		
MAN2B2	23324	hgsc.bcm.edu	37	4	6611560	6611560	+	Missense_Mutation	SNP	G	G	A	rs61733399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6611560G>A	ENST00000285599.3	+	13	2078	c.2042G>A	c.(2041-2043)cGc>cAc	p.R681H	MAN2B2_ENST00000504248.1_Missense_Mutation_p.R630H|MAN2B2_ENST00000504960.1_3'UTR	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	681					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						TATGCAATCCGCTCCCGGCTC	0.572													G|||	86	0.0171725	0.0613	0.0072	5008	,	,		18387	0.0		0.0	False		,,,				2504	0.0				p.R681H		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G2042A						PASS	.		HIS/ARG	207,4199	128.6+/-165.4	4,199,2000	76.0	78.0	78.0		2042	0.2	0.0	4	dbSNP_129	78	3,8597	3.0+/-9.4	0,3,4297	yes	missense	MAN2B2	NM_015274.1	29	4,202,6297	AA,AG,GG		0.0349,4.6981,1.6146	benign	681/1010	6611560	210,12796	2203	4300	6503	SO:0001583	missense	23324	exon13			CAATCCGCTCCCG	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.2042G>A	4.37:g.6611560G>A	ENSP00000285599:p.Arg681His	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	30|30	0.013736263736263736|0.013736263736263736	25|25	0.0508130081300813|0.0508130081300813	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	g|g	0.366|0.366	-0.936607|-0.936607	0.02340|0.02340	0.046981|0.046981	3.49E-4|3.49E-4	ENSG00000013288|ENSG00000013288	ENST00000505907|ENST00000285599;ENST00000504248	.|T;T	.|0.78364	.|-1.17;-1.17	4.28|4.28	0.172|0.172	0.15031|0.15031	.|Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	.|0.616553	.|0.17323	.|N	.|0.178421	T|T	0.10465|0.10465	0.0256|0.0256	N|N	0.01705|0.01705	-0.755|-0.755	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.09022	.|0.002;0.001;0.002	.|B;B;B	.|0.08055	.|0.003;0.003;0.003	T|T	0.11348|0.11348	-1.0591|-1.0591	5|10	.|0.14656	.|T	.|0.56	-9.5755|-9.5755	4.7133|4.7133	0.12882|0.12882	0.4981:0.0:0.0855:0.4164|0.4981:0.0:0.0855:0.4164	rs61733399|rs61733399	.|630;681;681	.|E9PCD7;Q9Y2E5;Q9Y2E5-2	.|.;MA2B2_HUMAN;.	T|H	680|681;630	.|ENSP00000285599:R681H;ENSP00000423129:R630H	.|ENSP00000285599:R681H	A|R	+|+	1|2	0|0	MAN2B2|MAN2B2	6662461|6662461	0.000000|0.000000	0.05858|0.05858	0.015000|0.015000	0.15790|0.15790	0.083000|0.083000	0.17756|0.17756	0.078000|0.078000	0.14761|0.14761	-0.229000|-0.229000	0.09854|0.09854	-0.482000|-0.482000	0.04802|0.04802	GCT|CGC	G|0.981;A|0.019	0.019	strong		0.572	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
PTP4A1	7803	hgsc.bcm.edu	37	6	64289996	64289996	+	Silent	SNP	C	C	T	rs1681943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:64289996C>T	ENST00000370651.3	+	6	1592	c.439C>T	c.(439-441)Ctg>Ttg	p.L147L	PTP4A1_ENST00000370650.2_Silent_p.L122L	NM_003463.3	NP_003454.1	Q93096	TP4A1_HUMAN	protein tyrosine phosphatase type IVA, member 1	147	Tyrosine-protein phosphatase.				cell cycle (GO:0007049)|multicellular organismal development (GO:0007275)|positive regulation of cell migration (GO:0030335)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			large_intestine(3)|lung(4)|skin(1)	8	all_cancers(3;0.071)|all_epithelial(2;0.0146)|Lung NSC(77;0.175)		Epithelial(2;0.0365)|LUSC - Lung squamous cell carcinoma(74;0.0644)|all cancers(2;0.112)|Lung(124;0.13)			CAAGCAACTTCTGTATTTGGA	0.393													c|||	111	0.0221645	0.0825	0.0029	5008	,	,		16877	0.0		0.0	False		,,,				2504	0.0				p.L147L	Pancreas(91;1019 1502 28028 38110 51645)	Atlas-SNP	.											.	PTP4A1	13	.	0			c.C439T						PASS	.	C		303,4103	162.2+/-194.2	14,275,1914	101.0	101.0	101.0		439	-0.7	1.0	6	dbSNP_89	101	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	PTP4A1	NM_003463.3		14,278,6211	TT,TC,CC		0.0349,6.877,2.3528		147/174	64289996	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	7803	exon6			CAACTTCTGTATT	U48296	CCDS4965.1	6q12	2011-06-09			ENSG00000112245	ENSG00000112245		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"""	9634	protein-coding gene	gene with protein product		601585				9642300	Standard	NM_003463		Approved	PTPCAAX1, PRL-1	uc003pel.3	Q93096	OTTHUMG00000014949	ENST00000370651.3:c.439C>T	6.37:g.64289996C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_003463	B2R6C8|O00648|Q49A54	Silent	SNP	ENST00000370651.3	37	CCDS4965.1																																																																																			C|0.980;T|0.020	0.020	strong		0.393	PTP4A1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041083.2		
KRTAP19-8	728299	hgsc.bcm.edu	37	21	32410619	32410619	+	Silent	SNP	A	A	G	rs2833198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:32410619A>G	ENST00000382822.2	-	1	176	c.144T>C	c.(142-144)tgT>tgC	p.C48C		NM_001099219.1	NP_001092689.1	Q3LI54	KR198_HUMAN	keratin associated protein 19-8	48						intermediate filament (GO:0005882)				endometrium(2)|upper_aerodigestive_tract(1)	3						ATGGTCGGCAACAGCTGAATC	0.502													G|||	1187	0.237021	0.5144	0.3256	5008	,	,		16311	0.1339		0.0318	False		,,,				2504	0.1166				p.C48C		Atlas-SNP	.											.	KRTAP19-8	9	.	0			c.T144C						PASS	.	G		1889,2517	613.5+/-392.2	422,1045,736	92.0	113.0	106.0		144	-4.2	0.0	21	dbSNP_100	106	346,8254	799.6+/-407.4	6,334,3960	no	coding-synonymous	KRTAP19-8	NM_001099219.1		428,1379,4696	GG,GA,AA		4.0233,42.8734,17.1844		48/64	32410619	2235,10771	2203	4300	6503	SO:0001819	synonymous_variant	728299	exon1			TCGGCAACAGCTG	AB096964	CCDS42917.1	21q22.11	2007-11-23			ENSG00000206102	ENSG00000206102		"""Keratin associated proteins"""	33898	protein-coding gene	gene with protein product							Standard	NM_001099219		Approved		uc010glt.3	Q3LI54	OTTHUMG00000057787	ENST00000382822.2:c.144T>C	21.37:g.32410619A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_001099219		Silent	SNP	ENST00000382822.2	37	CCDS42917.1																																																																																			A|0.811;G|0.188	0.188	strong		0.502	KRTAP19-8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000128239.3	NM_001099219	
ARL4D	379	hgsc.bcm.edu	37	17	41477670	41477670	+	Silent	SNP	G	G	A	rs61749921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41477670G>A	ENST00000320033.4	+	2	777	c.570G>A	c.(568-570)agG>agA	p.R190R		NM_001661.3	NP_001652.2	P49703	ARL4D_HUMAN	ADP-ribosylation factor-like 4D	190					GTP catabolic process (GO:0006184)|protein secretion (GO:0009306)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.155)		TCCTCAAGAGGAAGAAGGCAG	0.622													G|||	83	0.0165735	0.0613	0.0029	5008	,	,		16722	0.0		0.0	False		,,,				2504	0.0				p.R190R		Atlas-SNP	.											.	ARL4D	16	.	0			c.G570A						PASS	.	G		190,4178		2,186,1996	19.0	19.0	19.0		570	-0.6	1.0	17	dbSNP_129	19	1,8523		0,1,4261	no	coding-synonymous	ARL4D	NM_001661.3		2,187,6257	AA,AG,GG		0.0117,4.3498,1.4815		190/202	41477670	191,12701	2184	4262	6446	SO:0001819	synonymous_variant	379	exon2			CAAGAGGAAGAAG	AB060692	CCDS11463.1	17q21.31	2014-05-09	2005-11-03	2005-11-03	ENSG00000175906	ENSG00000175906		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	656	protein-coding gene	gene with protein product		600732	"""ADP-ribosylation factor 4-like"""	ARF4L		7590735	Standard	NM_001661		Approved		uc002idt.3	P49703		ENST00000320033.4:c.570G>A	17.37:g.41477670G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_001661	B2RC59|D3DX43	Silent	SNP	ENST00000320033.4	37	CCDS11463.1																																																																																			G|0.979;A|0.021	0.021	strong		0.622	ARL4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453481.2	NM_001661	
PASK	23178	hgsc.bcm.edu	37	2	242066830	242066830	+	Silent	SNP	G	G	A	rs2240544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242066830G>A	ENST00000405260.1	-	10	2198	c.1500C>T	c.(1498-1500)caC>caT	p.H500H	PASK_ENST00000234040.4_Silent_p.H500H|PASK_ENST00000539818.1_Silent_p.H284H|PASK_ENST00000544142.1_Silent_p.H314H|PASK_ENST00000403638.3_Silent_p.H500H|PASK_ENST00000358649.4_Silent_p.H500H	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	500					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		CCTGTTCACCGTGCACTGGCA	0.552													G|||	413	0.0824681	0.0968	0.0951	5008	,	,		17808	0.123		0.0606	False		,,,				2504	0.0348				p.H500H		Atlas-SNP	.											.	PASK	230	.	0			c.C1500T						PASS	.	G		470,3936	223.9+/-240.3	27,416,1760	85.0	87.0	86.0		1500	-9.7	0.0	2	dbSNP_98	86	568,8032	154.2+/-208.4	18,532,3750	no	coding-synonymous	PASK	NM_015148.2		45,948,5510	AA,AG,GG		6.6047,10.6673,7.9809		500/1324	242066830	1038,11968	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon10			TTCACCGTGCACT	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.1500C>T	2.37:g.242066830G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			G|0.910;A|0.090	0.090	strong		0.552	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
CEP192	55125	hgsc.bcm.edu	37	18	13068191	13068191	+	Silent	SNP	C	C	A	rs143595675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13068191C>A	ENST00000325971.8	+	21	4518	c.2925C>A	c.(2923-2925)ggC>ggA	p.G975G	CEP192_ENST00000506447.1_Silent_p.G1571G|CEP192_ENST00000430049.2_Silent_p.G1096G			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	975					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GGCTAGCAGGCCCTTCTGTGG	0.498													C|||	24	0.00479233	0.0174	0.0014	5008	,	,		16806	0.0		0.0	False		,,,				2504	0.0				p.G1571G		Atlas-SNP	.											.	CEP192	340	.	0			c.C4713A						PASS	.	C		51,4355	52.3+/-87.9	0,51,2152	72.0	74.0	73.0		4713	-5.3	0.0	18	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CEP192	NM_032142.3		0,52,6451	AA,AC,CC		0.0116,1.1575,0.3998		1571/2538	13068191	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	55125	exon23			AGCAGGCCCTTCT	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.2925C>A	18.37:g.13068191C>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	37																																																																																				C|0.996;A|0.004	0.004	strong		0.498	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
PEMT	10400	hgsc.bcm.edu	37	17	17425631	17425631	+	Missense_Mutation	SNP	C	C	T	rs897453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17425631C>T	ENST00000395783.1	-	3	351	c.172G>A	c.(172-174)Gtc>Atc	p.V58I	PEMT_ENST00000395782.1_Missense_Mutation_p.V58I|PEMT_ENST00000435340.2_Missense_Mutation_p.V73I|PEMT_ENST00000395781.2_Missense_Mutation_p.V95I|PEMT_ENST00000255389.5_Missense_Mutation_p.V95I	NM_007169.2	NP_009100.2	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase	58			V -> I (in dbSNP:rs897453). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.|V -> L (in dbSNP:rs897453).		cell proliferation (GO:0008283)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	phosphatidyl-N-dimethylethanolamine N-methyltransferase activity (GO:0080101)|phosphatidyl-N-methylethanolamine N-methyltransferase activity (GO:0000773)|phosphatidylethanolamine N-methyltransferase activity (GO:0004608)			endometrium(1)|kidney(1)|large_intestine(2)|prostate(3)	7				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)		AGGATGGTGACGCTTAGAGAG	0.602													C|||	996	0.198882	0.0635	0.2767	5008	,	,		18536	0.0952		0.4513	False		,,,				2504	0.1738				p.V95I		Atlas-SNP	.											.	PEMT	12	.	0			c.G283A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	574,3832	253.4+/-259.3	51,472,1680	127.0	92.0	104.0		172,283,172	-5.1	0.0	17	dbSNP_86	104	3877,4723	542.3+/-384.2	852,2173,1275	yes	missense,missense,missense	PEMT	NM_007169.2,NM_148172.1,NM_148173.1	29,29,29	903,2645,2955	TT,TC,CC		45.0814,13.0277,34.2227	benign,benign,benign	58/200,95/237,58/200	17425631	4451,8555	2203	4300	6503	SO:0001583	missense	10400	exon3			TGGTGACGCTTAG	AF176806	CCDS11186.1, CCDS11187.1, CCDS58520.1	17p11.2	2008-02-05			ENSG00000133027	ENSG00000133027	2.1.1.17		8830	protein-coding gene	gene with protein product		602391				9989271, 17881348	Standard	NM_148173		Approved	PEMPT, PEMT2	uc002grl.4	Q9UBM1	OTTHUMG00000059290	ENST00000395783.1:c.172G>A	17.37:g.17425631C>T	ENSP00000379129:p.Val58Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_001267552	A8MZ66|B4DY41|D3DXC3|Q6IAQ5|Q86VL3|Q9BW86|Q9UHY6|Q9Y6V9	Missense_Mutation	SNP	ENST00000395783.1	37	CCDS11187.1	539	0.2467948717948718	30	0.06097560975609756	115	0.31767955801104975	51	0.08916083916083917	343	0.4525065963060686	C	1.927	-0.446896	0.04572	0.130277	0.450814	ENSG00000133027	ENST00000255389;ENST00000395783;ENST00000395782;ENST00000435340;ENST00000395781;ENST00000421096	T;T;T;T;T	0.25579	2.43;2.42;2.42;1.79;1.8	4.87	-5.06	0.02946	.	1.493750	0.04051	N	0.304729	T	0.00012	0.0000	N	0.11284	0.12	0.80722	P	0.0	B;B;B	0.10296	0.002;0.003;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.45381	-0.9265	9	0.13853	T	0.58	-40.4928	4.3382	0.11097	0.2841:0.1905:0.0:0.5254	rs897453;rs1044987;rs3184799;rs3744119;rs17796661;rs17849340;rs56524175;rs897453	95;95;58	A8MZ66;Q9UBM1-2;Q9UBM1	.;.;PEMT_HUMAN	I	95;58;58;73;95;95	ENSP00000255389:V95I;ENSP00000379129:V58I;ENSP00000379128:V58I;ENSP00000391288:V73I;ENSP00000379127:V95I	ENSP00000255389:V95I	V	-	1	0	PEMT	17366356	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	-0.039000	0.12124	-0.796000	0.04456	-0.254000	0.11334	GTC	T|0.286;G|0.001;C|0.713;N|0.000	0.286	strong		0.602	PEMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131657.1	NM_007169	
CRYL1	51084	hgsc.bcm.edu	37	13	21086599	21086599	+	Silent	SNP	G	G	A	rs7139733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:21086599G>A	ENST00000298248.7	-	2	194	c.132C>T	c.(130-132)aaC>aaT	p.N44N	CRYL1_ENST00000382812.1_Silent_p.N22N	NM_015974.2	NP_057058.2	Q9Y2S2	CRYL1_HUMAN	crystallin, lambda 1	44					fatty acid metabolic process (GO:0006631)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|L-gulonate 3-dehydrogenase activity (GO:0050104)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)			NS(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)		TTTCCAGGGCGTTCCTTATCT	0.527													G|||	557	0.111222	0.1483	0.1052	5008	,	,		17005	0.0198		0.1799	False		,,,				2504	0.089				p.N44N		Atlas-SNP	.											.	CRYL1	28	.	0			c.C132T						PASS	.	G		591,3201		44,503,1349	73.0	71.0	71.0		132	-10.7	0.0	13	dbSNP_116	71	1199,7047		97,1005,3021	no	coding-synonymous	CRYL1	NM_015974.2		141,1508,4370	AA,AG,GG		14.5404,15.5854,14.8696		44/320	21086599	1790,10248	1896	4123	6019	SO:0001819	synonymous_variant	51084	exon2			CAGGGCGTTCCTT	AF077049	CCDS41871.1	13q11	2008-07-18			ENSG00000165475	ENSG00000165475			18246	protein-coding gene	gene with protein product	"""crystallin, lamda 1"", ""L-gulonate 3-dehydrogenase"", ""lambda-crystallin homolog"""	609877				12527201	Standard	NM_015974		Approved	GDH, lambda-CRY, MGC149525, MGC149526	uc001une.3	Q9Y2S2	OTTHUMG00000016516	ENST00000298248.7:c.132C>T	13.37:g.21086599G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_015974	A0PJ43|B3KN92|Q0VDI1|Q7Z4Z9|Q9P0G7	Silent	SNP	ENST00000298248.7	37	CCDS41871.1																																																																																			G|0.896;A|0.104	0.104	strong		0.527	CRYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044071.1	NM_015974	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994763	45994763	+	Silent	SNP	C	C	T	rs115169164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45994763C>T	ENST00000400374.3	+	1	1158	c.1128C>T	c.(1126-1128)ccC>ccT	p.P376P	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_5'Flank	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	376	36 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						GCTGCGTGCCCGTCCCTTCCT	0.711													.|||	103	0.0205671	0.0696	0.0144	5008	,	,		17408	0.0		0.0	False		,,,				2504	0.001				p.P376P		Atlas-SNP	.											.	KRTAP10-4	44	.	0			c.C1128T						PASS	.	C	,	273,4133	143.8+/-178.8	3,267,1933	59.0	72.0	68.0		,1128	2.3	0.1	21	dbSNP_132	68	1,8589		0,1,4294	no	intron,coding-synonymous	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,	3,268,6227	TT,TC,CC		0.0116,6.1961,2.1083	,	,376/402	45994763	274,12722	2203	4295	6498	SO:0001819	synonymous_variant	386672	exon1			CGTGCCCGTCCCT	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.1128C>T	21.37:g.45994763C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_198687	Q08AS0	Silent	SNP	ENST00000400374.3	37	CCDS42957.1																																																																																			C|0.980;T|0.020	0.020	strong		0.711	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
COL4A1	1282	hgsc.bcm.edu	37	13	110850842	110850842	+	Silent	SNP	A	A	G	rs995224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:110850842A>G	ENST00000375820.4	-	21	1378	c.1257T>C	c.(1255-1257)ccT>ccC	p.P419P	COL4A1_ENST00000543140.1_Silent_p.P419P	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	419	Triple-helical region.				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)			CAGGGGGCCCAGGGGAACCAG	0.592													a|||	1034	0.20647	0.2073	0.3732	5008	,	,		16322	0.0546		0.2664	False		,,,				2504	0.182				p.P419P		Atlas-SNP	.											.	COL4A1	372	.	0			c.T1257C						PASS	.			950,3456	326.9+/-299.8	107,736,1360	45.0	53.0	50.0		1257	-6.4	0.0	13	dbSNP_86	50	2334,6266	360.6+/-332.0	332,1670,2298	no	coding-synonymous	COL4A1	NM_001845.4		439,2406,3658	GG,GA,AA		27.1395,21.5615,25.2499		419/1670	110850842	3284,9722	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon21			GGGCCCAGGGGAA	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.1257T>C	13.37:g.110850842A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	108	32	0.296296	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			T|0.000;G|0.240;C|0.000;A|0.760	0.240	strong		0.592	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
MT-ND5	4540	hgsc.bcm.edu	37	M	13506	13506	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:13506C>T	ENST00000361567.2	+	1	1170	c.1170C>T	c.(1168-1170)taC>taT	p.Y390Y	MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	390					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ACAGGTTTCTACTCCAAAGAC	0.468																																					p.Y390Y		Atlas-SNP	.											.	.	.	.	0			c.C1170T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TTTCTACTCCAAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1170C>T	M.37:g.13506C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.468	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
STK38L	23012	hgsc.bcm.edu	37	12	27450671	27450671	+	Silent	SNP	G	G	T	rs56140810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27450671G>T	ENST00000389032.3	+	2	187	c.18G>T	c.(16-18)ggG>ggT	p.G6G	STK38L_ENST00000539577.1_Intron	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					TGACGGCAGGGACTACAACAA	0.373													G|||	124	0.0247604	0.0862	0.013	5008	,	,		18491	0.0		0.001	False		,,,				2504	0.0				p.G6G		Atlas-SNP	.											.	STK38L	44	.	0			c.G18T						PASS	.	G		384,4022	185.0+/-212.2	18,348,1837	90.0	90.0	90.0		18	5.2	1.0	12	dbSNP_129	90	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	STK38L	NM_015000.3		18,352,6133	TT,TG,GG		0.0465,8.7154,2.9832		6/465	27450671	388,12618	2203	4300	6503	SO:0001819	synonymous_variant	23012	exon2			GGCAGGGACTACA	AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"""nuclear Dbf2-related 2"""	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.18G>T	12.37:g.27450671G>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_015000		Silent	SNP	ENST00000389032.3	37	CCDS31761.1																																																																																			G|0.972;T|0.028	0.028	strong		0.373	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000	
CSGALNACT1	55790	hgsc.bcm.edu	37	8	19316086	19316086	+	Silent	SNP	G	G	A	rs12155539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:19316086G>A	ENST00000454498.2	-	5	1715	c.702C>T	c.(700-702)caC>caT	p.H234H	CSGALNACT1_ENST00000332246.6_Silent_p.H234H|CSGALNACT1_ENST00000518542.1_5'UTR|CSGALNACT1_ENST00000522854.1_Silent_p.H234H|CSGALNACT1_ENST00000311540.4_Silent_p.H234H|CSGALNACT1_ENST00000544602.1_Silent_p.H234H	NM_001130518.1	NP_001123990.1	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 1	234					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|endochondral ossification (GO:0001958)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|heparin biosynthetic process (GO:0030210)|nervous system development (GO:0007399)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|UDP-glucuronate metabolic process (GO:0046398)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|intracellular (GO:0005622)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|glucuronosyltransferase activity (GO:0015020)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)|peptidoglycan glycosyltransferase activity (GO:0008955)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				Colorectal(111;0.182)		GTTTGAATTCGTGTTTGTGGT	0.423													G|||	2298	0.458866	0.1997	0.5576	5008	,	,		18551	0.8581		0.3519	False		,,,				2504	0.4376				p.H234H		Atlas-SNP	.											CSGALNACT1,colon,carcinoma,0,1	CSGALNACT1	72	1	0			c.C702T						PASS	.	G	,	977,3429	365.9+/-317.6	95,787,1321	301.0	276.0	284.0		702,702	-6.8	0.5	8	dbSNP_120	284	3104,5496	475.7+/-369.2	532,2040,1728	no	coding-synonymous,coding-synonymous	CSGALNACT1	NM_001130518.1,NM_018371.4	,	627,2827,3049	AA,AG,GG		36.093,22.1743,31.3778	,	234/533,234/533	19316086	4081,8925	2203	4300	6503	SO:0001819	synonymous_variant	55790	exon5			GAATTCGTGTTTG	AK002126	CCDS6010.1	8p21.3	2013-02-19				ENSG00000147408		"""Beta 4-glycosyltransferases"""	24290	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase"""					17145758, 12446672	Standard	NM_018371		Approved	CSGalNAcT-1, FLJ11264, ChGn	uc011kyo.2	Q8TDX6		ENST00000454498.2:c.702C>T	8.37:g.19316086G>A		Somatic	332	1	0.00301205		WXS	Illumina HiSeq	Phase_I	351	149	0.424501	NM_018371	B2RBE4|Q6P9G6|Q8IUF9|Q9NSQ7|Q9NUM9	Silent	SNP	ENST00000454498.2	37	CCDS6010.1																																																																																			G|0.616;A|0.384	0.384	strong		0.423	CSGALNACT1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375204.1	NM_018371	
TMEM187	8269	hgsc.bcm.edu	37	X	153247745	153247745	+	Missense_Mutation	SNP	A	A	G	rs7350355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153247745A>G	ENST00000369982.4	+	2	979	c.232A>G	c.(232-234)Atg>Gtg	p.M78V	MIR3202-1_ENST00000580198.1_RNA	NM_003492.2	NP_003483.1	Q14656	TM187_HUMAN	transmembrane protein 187	78			M -> V (in dbSNP:rs7350355).			integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|large_intestine(1)|lung(1)|prostate(2)	5	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGGCGGCGCGATGGGGCTGGG	0.692													G|||	2039	0.540132	0.4644	0.3991	3775	,	,		12161	0.5546		0.1461	False		,,,				2504	0.4519				p.M78V		Atlas-SNP	.											.	TMEM187	21	.	0			c.A232G						PASS	.	G	VAL/MET	2148,1682		503,806,336,322,232	33.0	29.0	30.0		232	2.7	0.0	X	dbSNP_116	30	1229,5494		76,721,356,1630,1513	yes	missense	TMEM187	NM_003492.2	21	579,1527,692,1952,1745	GG,GA,G,AA,A		18.2805,43.9164,32.0004	benign	78/262	153247745	3377,7176	2199	4296	6495	SO:0001583	missense	8269	exon2			GGCGCGATGGGGC	X92475	CCDS14739.1	Xq28	2007-03-14	2007-03-14	2007-03-14	ENSG00000177854	ENSG00000177854			13705	protein-coding gene	gene with protein product		300059	"""chromosome X open reading frame 12"""	CXorf12		8661027	Standard	NM_003492		Approved	ITBA1, DXS9878E	uc004fjq.2	Q14656	OTTHUMG00000024220	ENST00000369982.4:c.232A>G	X.37:g.153247745A>G	ENSP00000358999:p.Met78Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	138	49	0.355072	NM_003492	B2RC47|Q6IAV7	Missense_Mutation	SNP	ENST00000369982.4	37	CCDS14739.1	761	0.458710066305003	156	0.4126984126984127	91	0.30743243243243246	208	0.5683060109289617	80	0.11594202898550725	G	6.827	0.521765	0.13005	0.560836	0.182805	ENSG00000177854	ENST00000369982	T	0.20881	2.04	3.6	2.71	0.32032	.	3.362720	0.01821	N	0.034052	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	0.45948	-0.9226	9	0.12430	T	0.62	.	4.6881	0.12767	0.2141:0.1773:0.6086:0.0	rs7350355;rs57609307;rs7350355	78	Q14656	TM187_HUMAN	V	78	ENSP00000358999:M78V	ENSP00000358999:M78V	M	+	1	0	TMEM187	152900939	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.132000	0.15891	0.012000	0.14892	-0.396000	0.06452	ATG	A|0.587;0|0.003	.	strong		0.692	TMEM187-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061093.1	NM_003492	
SLX4	84464	hgsc.bcm.edu	37	16	3647692	3647692	+	Missense_Mutation	SNP	A	A	C	rs74319927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3647692A>C	ENST00000294008.3	-	7	2011	c.1371T>G	c.(1369-1371)aaT>aaG	p.N457K		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	457	Interaction with SLX4IP, ERCC4 and MSH2.		N -> K (in dbSNP:rs74319927). {ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TGCGACTTTTATTCTCTAGAG	0.552								Direct reversal of damage					C|||	275	0.0549121	0.0507	0.0706	5008	,	,		16428	0.0506		0.0656	False		,,,				2504	0.0429				p.N457K		Atlas-SNP	.											.	SLX4	173	.	0			c.T1371G						PASS	.	C	LYS/ASN	264,4124		8,248,1938	42.0	51.0	48.0		1371	5.2	1.0	16	dbSNP_131	48	581,8017		16,549,3734	yes	missense	SLX4	NM_032444.2	94	24,797,5672	CC,CA,AA		6.7574,6.0164,6.507	benign	457/1835	3647692	845,12141	2194	4299	6493	SO:0001583	missense	84464	exon7			ACTTTTATTCTCT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.1371T>G	16.37:g.3647692A>C	ENSP00000294008:p.Asn457Lys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	124	0.056776556776556776	26	0.052845528455284556	24	0.06629834254143646	24	0.04195804195804196	50	0.06596306068601583	C	5.789	0.329828	0.10956	0.060164	0.067574	ENSG00000188827	ENST00000294008	T	0.16324	2.35	5.19	5.19	0.71726	.	0.000000	0.64402	N	0.000011	T	0.00300	0.0009	N	0.00399	-1.545	0.20489	N	0.999898	B	0.02656	0.0	B	0.01281	0.0	T	0.39292	-0.9621	10	0.02654	T	1	.	8.0402	0.30517	0.1615:0.7518:0.0:0.0867	.	457	Q8IY92	SLX4_HUMAN	K	457	ENSP00000294008:N457K	ENSP00000294008:N457K	N	-	3	2	SLX4	3587693	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	0.674000	0.25218	1.195000	0.43115	-0.121000	0.15023	AAT	A|0.941;C|0.059	0.059	strong		0.552	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350782	50350782	+	Silent	SNP	C	C	T	rs113799046		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:50350782C>T	ENST00000289292.7	-	6	3643	c.3360G>A	c.(3358-3360)caG>caA	p.Q1120Q	SHROOM4_ENST00000460112.3_Silent_p.Q1004Q|SHROOM4_ENST00000376020.2_Silent_p.Q1120Q			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1120	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)					gctgcttctgctgctgGGCTG	0.587																																					p.Q1120Q		Atlas-SNP	.											.	SHROOM4	171	.	0			c.G3360A						PASS	.						23.0	21.0	22.0					X																	50350782		2201	4297	6498	SO:0001819	synonymous_variant	57477	exon6			CTTCTGCTGCTGG	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.3360G>A	X.37:g.50350782C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	97	7	0.0721649	NM_020717	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	37	CCDS35277.1																																																																																			C|0.500;T|0.500	0.500	weak		0.587	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
NOP14	8602	hgsc.bcm.edu	37	4	2955361	2955361	+	Missense_Mutation	SNP	T	T	G	rs111987238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2955361T>G	ENST00000314262.6	-	5	672	c.624A>C	c.(622-624)caA>caC	p.Q208H	NOP14-AS1_ENST00000515194.1_RNA|NOP14_ENST00000398071.4_Missense_Mutation_p.Q208H|NOP14-AS1_ENST00000503709.1_RNA|NOP14_ENST00000502735.1_Missense_Mutation_p.Q208H|NOP14_ENST00000416614.2_Missense_Mutation_p.Q208H	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	208					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)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						CTCGTTGAGCTTGTCTCTCCC	0.498													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		19504	0.0		0.0	False		,,,				2504	0.0				p.Q208H		Atlas-SNP	.											.	NOP14	69	.	0			c.A624C						PASS	.	T	HIS/GLN	58,4348	56.8+/-93.2	0,58,2145	229.0	213.0	219.0		624	-1.6	0.2	4	dbSNP_132	219	0,8600		0,0,4300	yes	missense	NOP14	NM_003703.1	24	0,58,6445	GG,GT,TT		0.0,1.3164,0.4459	probably-damaging	208/858	2955361	58,12948	2203	4300	6503	SO:0001583	missense	8602	exon5			TTGAGCTTGTCTC	AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"""NOP14 homolog (S. cerevisiae)"""	611526	"""chromosome 4 open reading frame 9"", ""nucleolar protein 14"", ""nucleolar protein 14 homolog (yeast)"", ""NOP14 nucleolar protein homolog (yeast)"""	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.624A>C	4.37:g.2955361T>G	ENSP00000315674:p.Gln208His	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Missense_Mutation	SNP	ENST00000314262.6	37	CCDS33945.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	T	12.38	1.921617	0.33908	0.013164	0.0	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	4.64	-1.62	0.08372	.	0.000000	0.85682	D	0.000000	T	0.54935	0.1889	M	0.91818	3.245	0.48762	D	0.999708	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.69953	-0.5005	10	0.87932	D	0	-37.2025	11.6825	0.51466	0.0:0.4263:0.0:0.5737	.	208;208	E9PFK5;P78316	.;NOP14_HUMAN	H	208;208;208;208;107	ENSP00000405068:Q208H;ENSP00000315674:Q208H;ENSP00000427415:Q208H;ENSP00000381146:Q208H	ENSP00000315674:Q208H	Q	-	3	2	NOP14	2925159	0.987000	0.35691	0.169000	0.22859	0.121000	0.20230	0.274000	0.18680	-0.361000	0.08125	-0.415000	0.06103	CAA	T|0.995;G|0.005	0.005	strong		0.498	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703	
SOWAHB	345079	hgsc.bcm.edu	37	4	77817362	77817362	+	Silent	SNP	T	T	C	rs2703131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77817362T>C	ENST00000334306.2	-	1	1640	c.1641A>G	c.(1639-1641)ttA>ttG	p.L547L		NM_001029870.1	NP_001025041.1	A6NEL2	SWAHB_HUMAN	sosondowah ankyrin repeat domain family member B	547																	GTTTTAGTGATAAACCTGCAT	0.617													T|||	975	0.194688	0.2216	0.1844	5008	,	,		18462	0.0873		0.2366	False		,,,				2504	0.2331				p.L547L		Atlas-SNP	.											.	.	.	.	0			c.A1641G						PASS	.	T		889,3517	343.6+/-307.7	97,695,1411	45.0	47.0	46.0		1641	2.3	0.0	4	dbSNP_100	46	1850,6750	329.6+/-318.8	188,1474,2638	no	coding-synonymous	ANKRD56	NM_001029870.1		285,2169,4049	CC,CT,TT		21.5116,20.177,21.0595		547/794	77817362	2739,10267	2203	4300	6503	SO:0001819	synonymous_variant	345079	exon1			TAGTGATAAACCT		CCDS34017.1	4q21.1	2013-01-10	2012-01-12	2012-01-12	ENSG00000186212	ENSG00000186212		"""Ankyrin repeat domain containing"""	32958	protein-coding gene	gene with protein product			"""ankyrin repeat domain 56"""	ANKRD56		22234889	Standard	NM_001029870		Approved		uc003hki.3	A6NEL2	OTTHUMG00000160876	ENST00000334306.2:c.1641A>G	4.37:g.77817362T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_001029870	B2RP29	Silent	SNP	ENST00000334306.2	37	CCDS34017.1																																																																																			T|0.804;C|0.196	0.196	strong		0.617	SOWAHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362762.1	NM_001029870	
SLC52A3	113278	hgsc.bcm.edu	37	20	744570	744570	+	Silent	SNP	G	G	A	rs6054605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:744570G>A	ENST00000217254.7	-	3	886	c.645C>T	c.(643-645)ccC>ccT	p.P215P	SLC52A3_ENST00000381944.3_Silent_p.P215P|SLC52A3_ENST00000473664.1_Intron	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	215					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)										AGAAGTGGGCGGGAAGGTAGC	0.607													G|||	692	0.138179	0.0522	0.072	5008	,	,		18546	0.4534		0.0497	False		,,,				2504	0.0675				p.P215P		Atlas-SNP	.											.	.	.	.	0			c.C645T						PASS	.	G		199,4207	121.3+/-158.8	4,191,2008	57.0	49.0	52.0		645	-9.9	0.0	20	dbSNP_114	52	437,8163	131.5+/-189.3	7,423,3870	no	coding-synonymous	C20orf54	NM_033409.3		11,614,5878	AA,AG,GG		5.0814,4.5166,4.8901		215/470	744570	636,12370	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon3			GTGGGCGGGAAGG	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.645C>T	20.37:g.744570G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			G|0.908;A|0.092	0.092	strong		0.607	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
SIRPA	140885	hgsc.bcm.edu	37	20	1895965	1895965	+	Missense_Mutation	SNP	C	C	A	rs17855614|rs373583167|rs386811662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1895965C>A	ENST00000358771.4	+	2	452	c.300C>A	c.(298-300)aaC>aaA	p.N100K	SIRPA_ENST00000356025.3_Missense_Mutation_p.N100K|SIRPA_ENST00000400068.3_Missense_Mutation_p.N100K	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	100	Ig-like V-type.		N -> E (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CAAAGAGAAACAACATGGACT	0.517													C|||	480	0.0958466	0.0386	0.1095	5008	,	,		14804	0.1835		0.0537	False		,,,				2504	0.1166				p.N100K	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,brain,glioma,0,4	SIRPA	83	4	0			c.C300A						scavenged	.																																			SO:0001583	missense	140885	exon3			GAGAAACAACATG	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.300C>A	20.37:g.1895965C>A	ENSP00000351621:p.Asn100Lys	Somatic	564	0	0		WXS	Illumina HiSeq	Phase_I	362	26	0.0718232	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.533326	0.27387	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02158	4.42;4.42;4.42	5.11	0.771	0.18504	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.743450	0.02696	N	0.111247	T	0.04634	0.0126	M	0.65975	2.015	0.09310	N	1	B;B;B	0.33299	0.003;0.407;0.039	B;B;B	0.31812	0.056;0.136;0.082	T	0.44345	-0.9334	10	0.72032	D	0.01	.	8.1767	0.31285	0.0:0.4423:0.4696:0.0881	rs17855614	80;100;100	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	K	100	ENSP00000382941:N100K;ENSP00000348307:N100K;ENSP00000351621:N100K	ENSP00000348307:N100K	N	+	3	2	SIRPA	1843965	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-0.328000	0.07945	0.028000	0.15324	-0.315000	0.08773	AAC	.	.	weak		0.517	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
ABCB1	5243	hgsc.bcm.edu	37	7	87179256	87179256	+	Missense_Mutation	SNP	G	G	A	rs142600685		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:87179256G>A	ENST00000265724.3	-	14	1882	c.1465C>T	c.(1465-1467)Cgc>Tgc	p.R489C	ABCB1_ENST00000543898.1_Missense_Mutation_p.R425C	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	489	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CGGCCATAGCGAATGTTTTCA	0.428													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20930	0.0		0.0	False		,,,				2504	0.0				p.R489C		Atlas-SNP	.											ABCB1,NS,carcinoma,0,2	ABCB1	263	2	0			c.C1465T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	236.0	218.0	224.0		1465	5.3	1.0	7	dbSNP_134	224	0,8600		0,0,4300	yes	missense	ABCB1	NM_000927.4	180	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	probably-damaging	489/1281	87179256	6,13000	2203	4300	6503	SO:0001583	missense	5243	exon14			CATAGCGAATGTT	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"""CD molecules"", ""ATP binding cassette transporters / subfamily B"""	40	protein-coding gene	gene with protein product	"""multidrug resistance protein 1"""	171050	"""colchicin sensitivity"""	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.1465C>T	7.37:g.87179256G>A	ENSP00000265724:p.Arg489Cys	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858540	0.71834	0.001362	0.0	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.90955	-2.76;-2.76	6.16	5.29	0.74685	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.048148	0.85682	D	0.000000	D	0.93074	0.7795	M	0.64260	1.97	0.80722	D	1	B;P	0.49862	0.256;0.929	B;P	0.56216	0.116;0.794	D	0.93216	0.6604	10	0.54805	T	0.06	-11.5298	15.7393	0.77876	0.0651:0.0:0.9349:0.0	.	425;489	B5AK60;P08183	.;MDR1_HUMAN	C	270;489;425	ENSP00000265724:R489C;ENSP00000444095:R425C	ENSP00000265724:R489C	R	-	1	0	ABCB1	87017192	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.779000	0.47734	1.622000	0.50330	0.650000	0.86243	CGC	G|0.999;A|0.001	0.001	strong		0.428	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
TATDN2	9797	hgsc.bcm.edu	37	3	10311949	10311949	+	Silent	SNP	T	T	C	rs145595744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:10311949T>C	ENST00000287652.4	+	4	2134	c.1083T>C	c.(1081-1083)tcT>tcC	p.S361S	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Silent_p.S361S	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	361					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						CGGAGCCTTCTTCCTTCACCA	0.522													T|||	18	0.00359425	0.0136	0.0	5008	,	,		20081	0.0		0.0	False		,,,				2504	0.0				p.S361S		Atlas-SNP	.											.	TATDN2	59	.	0			c.T1083C						PASS	.	T		28,4378	34.3+/-65.2	1,26,2176	168.0	162.0	164.0		1083	-5.2	0.0	3	dbSNP_134	164	0,8600		0,0,4300	no	coding-synonymous	TATDN2	NM_014760.3		1,26,6476	CC,CT,TT		0.0,0.6355,0.2153		361/762	10311949	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	9797	exon4			GCCTTCTTCCTTC	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.1083T>C	3.37:g.10311949T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	131	80	0.610687	NM_014760	Q3MIL9|Q5BKU0	Silent	SNP	ENST00000287652.4	37	CCDS33698.1																																																																																			T|0.997;C|0.003	0.003	strong		0.522	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
MAN1C1	57134	hgsc.bcm.edu	37	1	26080052	26080052	+	Silent	SNP	C	C	T	rs12073358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26080052C>T	ENST00000374332.4	+	5	1242	c.912C>T	c.(910-912)ggC>ggT	p.G304G	MAN1C1_ENST00000263979.3_Silent_p.G124G|MAN1C1_ENST00000374329.1_Silent_p.G75G|MAN1C1_ENST00000473891.1_3'UTR	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	304					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		TCCCAAAGGGCGTGGTGAGCT	0.582													C|||	303	0.0605032	0.2179	0.0187	5008	,	,		18717	0.0		0.001	False		,,,				2504	0.001				p.G304G		Atlas-SNP	.											MAN1C1,NS,carcinoma,0,1	MAN1C1	48	1	0			c.C912T						PASS	.	C		659,3747	278.7+/-274.4	52,555,1596	46.0	44.0	45.0		912	-4.3	0.2	1	dbSNP_120	45	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	MAN1C1	NM_020379.2		52,566,5885	TT,TC,CC		0.1279,14.9569,5.1515		304/631	26080052	670,12336	2203	4300	6503	SO:0001819	synonymous_variant	57134	exon5			AAAGGGCGTGGTG	AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.912C>T	1.37:g.26080052C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	NM_020379	A6NNE2|B2RNP2|Q9Y545	Silent	SNP	ENST00000374332.4	37	CCDS265.1																																																																																			C|0.953;T|0.047	0.047	strong		0.582	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379	
NUDT18	79873	hgsc.bcm.edu	37	8	21965113	21965113	+	Missense_Mutation	SNP	T	T	C	rs3739435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	83	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	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	
RNF122	79845	hgsc.bcm.edu	37	8	33416189	33416189	+	Silent	SNP	G	G	A	rs3735950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	70	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	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	
DNAH17	8632	hgsc.bcm.edu	37	17	76464916	76464916	+	Missense_Mutation	SNP	G	G	A	rs635874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76464916G>A	ENST00000585328.1	-	55	8670	c.8546C>T	c.(8545-8547)tCg>tTg	p.S2849L	DNAH17_ENST00000389840.5_Missense_Mutation_p.S2840L|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2840	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(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)			CAGGAACACCGAGGGAACGTT	0.542													G|||	588	0.117412	0.2723	0.0893	5008	,	,		19385	0.0605		0.0696	False		,,,				2504	0.0358				p.S2854L		Atlas-SNP	.											.	DNAH17	347	.	0			c.C8561T						PASS	.	G	LEU/SER	1019,3167		129,761,1203	80.0	85.0	83.0		8561	5.0	1.0	17	dbSNP_83	83	497,7909		14,469,3720	yes	missense	DNAH17	NM_173628.3	145	143,1230,4923	AA,AG,GG		5.9124,24.343,12.0394		2854/4463	76464916	1516,11076	2093	4203	6296	SO:0001583	missense	8632	exon55			AACACCGAGGGAA	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.8546C>T	17.37:g.76464916G>A	ENSP00000465516:p.Ser2849Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		271	0.12408424908424909	156	0.3170731707317073	28	0.07734806629834254	35	0.06118881118881119	52	0.06860158311345646	G	15.44	2.834471	0.50951	0.24343	0.059124	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.47869	0.83	4.99	4.99	0.66335	.	.	.	.	.	T	0.00012	0.0000	N	0.11364	0.135	0.29297	P	0.868968	.	.	.	.	.	.	T	0.39742	-0.9599	6	0.32370	T	0.25	.	15.4091	0.74902	0.0:0.1392:0.8608:0.0	rs635874;rs52813249;rs59866694;rs635874	.	.	.	L	2849;2840	ENSP00000374490:S2840L	ENSP00000300671:S2849L	S	-	2	0	DNAH17	73976511	1.000000	0.71417	0.971000	0.41717	0.739000	0.42172	6.493000	0.73658	2.327000	0.79052	0.650000	0.86243	TCG	G|0.874;A|0.126	0.126	strong		0.542	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
DNMT1	1786	hgsc.bcm.edu	37	19	10267077	10267077	+	Silent	SNP	T	T	C	rs2228611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10267077T>C	ENST00000340748.4	-	17	1576	c.1341A>G	c.(1339-1341)ccA>ccG	p.P447P	DNMT1_ENST00000540357.1_Silent_p.P447P|DNMT1_ENST00000359526.4_Silent_p.P463P			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	447	DNA replication foci-targeting sequence. {ECO:0000250}.|Homodimerization.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CTTCAAGAGATGGGTCATCAT	0.478													C|||	2674	0.533946	0.5204	0.4539	5008	,	,		15091	0.6488		0.4612	False		,,,				2504	0.5654				p.P463P		Atlas-SNP	.											.	DNMT1	148	.	0			c.A1389G						PASS	.	C	,	2180,2226	591.9+/-387.7	554,1072,577	125.0	113.0	117.0		1389,1341	-11.3	0.0	19	dbSNP_98	117	4208,4392	584.4+/-391.7	1025,2158,1117	no	coding-synonymous,coding-synonymous	DNMT1	NM_001130823.1,NM_001379.2	,	1579,3230,1694	CC,CT,TT		48.9302,49.478,49.1158	,	463/1633,447/1617	10267077	6388,6618	2203	4300	6503	SO:0001819	synonymous_variant	1786	exon18			AAGAGATGGGTCA	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.1341A>G	19.37:g.10267077T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Silent	SNP	ENST00000340748.4	37	CCDS12228.1																																																																																			T|0.475;C|0.525	0.525	strong		0.478	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
FGFR2	2263	hgsc.bcm.edu	37	10	123310871	123310871	+	Missense_Mutation	SNP	A	A	G	rs755793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123310871A>G	ENST00000358487.5	-	5	829	c.557T>C	c.(556-558)aTg>aCg	p.M186T	FGFR2_ENST00000457416.2_Missense_Mutation_p.M186T|FGFR2_ENST00000357555.5_Missense_Mutation_p.M97T|FGFR2_ENST00000360144.3_Missense_Mutation_p.M97T|FGFR2_ENST00000359354.2_Missense_Mutation_p.M186T|FGFR2_ENST00000356226.4_Missense_Mutation_p.M71T|FGFR2_ENST00000369061.4_Missense_Mutation_p.M186T|FGFR2_ENST00000346997.2_Missense_Mutation_p.M186T|FGFR2_ENST00000369059.1_Missense_Mutation_p.M71T|FGFR2_ENST00000369056.1_Missense_Mutation_p.M186T|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000369060.4_Missense_Mutation_p.M186T|FGFR2_ENST00000351936.6_Missense_Mutation_p.M186T	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	186	Ig-like C2-type 2.		M -> T (in dbSNP:rs755793). {ECO:0000269|PubMed:11781872, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.15}.		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|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 homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	CATGGTTGGCATTGGGTTCCC	0.517		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				G|||	629	0.125599	0.3638	0.1066	5008	,	,		15709	0.0645		0.007	False		,,,				2504	0.002				p.M186T		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.T557C	GRCh37	CM071761	FGFR2	M	rs755793	PASS	.	G	THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET	1295,3111	698.3+/-406.3	194,907,1102	115.0	107.0	109.0		557,557,557,290,212,557,212,290,557	3.9	0.8	10	dbSNP_86	109	15,8585	818.8+/-406.8	0,15,4285	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense	FGFR2	NM_000141.4,NM_001144913.1,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_001144919.1,NM_022970.3	81,81,81,81,81,81,81,81,81	194,922,5387	GG,GA,AA		0.1744,29.3917,10.0723	benign,benign,benign,benign,benign,benign,benign,benign,benign	186/822,186/770,186/710,97/708,71/707,186/706,71/705,97/681,186/823	123310871	1310,11696	2203	4300	6503	SO:0001583	missense	2263	exon5	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	GTTGGCATTGGGT	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.557T>C	10.37:g.123310871A>G	ENSP00000351276:p.Met186Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	93	37	0.397849	NM_022970	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	263	0.12042124542124542	176	0.35772357723577236	42	0.11602209944751381	40	0.06993006993006994	5	0.006596306068601583	G	0.006	-2.076963	0.00375	0.293917	0.001744	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553;ENST00000359354	T;T;T;T;T;T;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;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	4.89	3.86	0.44501	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.389842	0.28279	N	0.015928	T	0.00012	0.0000	N	0.00855	-1.145	0.80722	P	0.0	B;B;B;B;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;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B;B;B	0.09377	0.0;0.001;0.0;0.002;0.0;0.0;0.003;0.0;0.004;0.0;0.0;0.002	T	0.29941	-0.9995	9	0.02654	T	1	.	9.2544	0.37575	0.2804:0.0:0.7196:0.0	rs755793;rs52828989;rs60409063;rs755793	205;205;71;186;205;186;97;71;186;205;97;186	D3DRD9;D3DRD4;B5A963;B5A960;D3DRD5;P21802-18;P21802-21;P21802-20;P21802;D3DRE0;P21802-22;P21802-17	.;.;.;.;.;.;.;.;FGFR2_HUMAN;.;.;.	T	97;186;186;186;71;186;71;186;186;186;97;186;186;97;186	ENSP00000350166:M97T;ENSP00000358057:M186T;ENSP00000351276:M186T;ENSP00000348559:M71T;ENSP00000358056:M186T;ENSP00000358055:M71T;ENSP00000263451:M186T;ENSP00000410294:M186T;ENSP00000309878:M186T;ENSP00000353262:M97T;ENSP00000358052:M186T;ENSP00000358054:M186T;ENSP00000337665:M97T;ENSP00000352309:M186T	ENSP00000337665:M97T	M	-	2	0	FGFR2	123300861	0.028000	0.19301	0.838000	0.33150	0.277000	0.26821	1.098000	0.31000	1.065000	0.40693	-0.166000	0.13349	ATG	A|0.878;G|0.122	0.122	strong		0.517	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
ZNF658	26149	hgsc.bcm.edu	37	9	40784132	40784132	+	Silent	SNP	A	A	G	rs142151197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:40784132A>G	ENST00000602553.1	-	4	507	c.213T>C	c.(211-213)gaT>gaC	p.D71D	ZNF658_ENST00000377626.3_Silent_p.D71D|ZNF658_ENST00000441795.1_Silent_p.D69D			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	71	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TCAGGAATTCATCTTCTAAAG	0.433													A|||	68	0.0135783	0.0514	0.0	5008	,	,		13262	0.0		0.0	False		,,,				2504	0.0				p.D71D		Atlas-SNP	.											.	ZNF658	100	.	0			c.T213C						PASS	.	A		146,4260	97.1+/-135.8	1,144,2058	32.0	36.0	34.0		213	-3.4	0.0	9	dbSNP_134	34	2,8592	2.2+/-6.3	0,2,4295	no	coding-synonymous	ZNF658	NM_033160.5		1,146,6353	GG,GA,AA		0.0233,3.3137,1.1385		71/1060	40784132	148,12852	2203	4297	6500	SO:0001819	synonymous_variant	26149	exon4			GAATTCATCTTCT	AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"""Zinc fingers, C2H2-type"", ""-"""	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.213T>C	9.37:g.40784132A>G		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	264	93	0.352273	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Silent	SNP	ENST00000602553.1	37	CCDS35023.1																																																																																			.	.	weak		0.433	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160	
OR6C76	390326	hgsc.bcm.edu	37	12	55820927	55820927	+	Missense_Mutation	SNP	C	C	T	rs73327795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55820927C>T	ENST00000328314.3	+	1	890	c.890C>T	c.(889-891)gCa>gTa	p.A297V		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	297						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)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GTGAAACAAGCATTTAAGGAT	0.353													c|||	104	0.0207668	0.0719	0.013	5008	,	,		14924	0.0		0.0	False		,,,				2504	0.0				p.A297V		Atlas-SNP	.											.	OR6C76	98	.	0			c.C890T						PASS	.		VAL/ALA	273,4133		6,261,1936	35.0	37.0	37.0		890	3.4	0.4	12	dbSNP_130	37	2,8590		0,2,4294	yes	missense	OR6C76	NM_001005183.1	64	6,263,6230	TT,TC,CC		0.0233,6.1961,2.1157	benign	297/313	55820927	275,12723	2203	4296	6499	SO:0001583	missense	390326	exon1			AACAAGCATTTAA		CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"""GPCR / Class A : Olfactory receptors"""	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.890C>T	12.37:g.55820927C>T	ENSP00000328402:p.Ala297Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_001005183		Missense_Mutation	SNP	ENST00000328314.3	37	CCDS31823.1	41	0.018772893772893772	38	0.07723577235772358	3	0.008287292817679558	0	0.0	0	0.0	c	11.52	1.664546	0.29604	0.061961	2.33E-4	ENSG00000185821	ENST00000328314	T	0.44881	0.91	4.25	3.36	0.38483	.	0.000000	0.46442	U	0.000298	T	0.03095	0.0091	M	0.74647	2.275	0.09310	N	1	B	0.33940	0.433	B	0.35899	0.213	T	0.04811	-1.0925	10	0.59425	D	0.04	.	10.1138	0.42579	0.0:0.8992:0.0:0.1008	.	297	A6NM76	O6C76_HUMAN	V	297	ENSP00000328402:A297V	ENSP00000328402:A297V	A	+	2	0	OR6C76	54107194	0.109000	0.22037	0.419000	0.26584	0.684000	0.39900	2.983000	0.49345	1.154000	0.42482	-0.205000	0.12727	GCA	C|0.983;T|0.017	0.017	strong		0.353	OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
DHX37	57647	hgsc.bcm.edu	37	12	125441347	125441347	+	Silent	SNP	T	T	C	rs12300199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125441347T>C	ENST00000308736.2	-	18	2441	c.2343A>G	c.(2341-2343)gcA>gcG	p.A781A	DHX37_ENST00000544745.1_Silent_p.A568A	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	781							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		CGTAGCGGGGTGCCACGGGGA	0.637													T|||	302	0.0603035	0.1044	0.0331	5008	,	,		19415	0.0536		0.0308	False		,,,				2504	0.0573				p.A781A		Atlas-SNP	.											.	DHX37	114	.	0			c.A2343G						PASS	.	T		391,4015	196.7+/-221.0	14,363,1826	96.0	92.0	94.0		2343	-10.5	0.7	12	dbSNP_120	94	330,8270	114.4+/-174.4	12,306,3982	no	coding-synonymous	DHX37	NM_032656.3		26,669,5808	CC,CT,TT		3.8372,8.8743,5.5436		781/1158	125441347	721,12285	2203	4300	6503	SO:0001819	synonymous_variant	57647	exon18			GCGGGGTGCCACG	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.2343A>G	12.37:g.125441347T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	109	43	0.394495	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1																																																																																			T|0.943;C|0.057	0.057	strong		0.637	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
PIWIL4	143689	hgsc.bcm.edu	37	11	94335037	94335037	+	Missense_Mutation	SNP	C	C	A	rs35885673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94335037C>A	ENST00000299001.6	+	12	1668	c.1457C>A	c.(1456-1458)aCc>aAc	p.T486N	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	486					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TCTTTGAATACCTGGTTGATT	0.403													C|||	155	0.0309505	0.1036	0.013	5008	,	,		19752	0.0		0.003	False		,,,				2504	0.0061				p.T486N		Atlas-SNP	.											.	PIWIL4	70	.	0			c.C1457A						PASS	.	C	ASN/THR	344,4058	182.2+/-210.1	17,310,1874	161.0	156.0	158.0		1457	0.3	0.0	11	dbSNP_126	158	30,8566	21.0+/-64.5	0,30,4268	yes	missense	PIWIL4	NM_152431.2	65	17,340,6142	AA,AC,CC		0.349,7.8146,2.8774	benign	486/853	94335037	374,12624	2201	4298	6499	SO:0001583	missense	143689	exon12			TGAATACCTGGTT	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1457C>A	11.37:g.94335037C>A	ENSP00000299001:p.Thr486Asn	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	144	66	0.458333	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	49	0.022435897435897436	43	0.08739837398373984	6	0.016574585635359115	0	0.0	0	0.0	C	0.008	-1.862658	0.00552	0.078146	0.00349	ENSG00000134627	ENST00000299001	T	0.03441	3.93	5.05	0.257	0.15574	Ribonuclease H-like (1);	0.749315	0.12149	N	0.495051	T	0.00039	0.0001	N	0.00661	-1.28	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49771	-0.8904	10	0.02654	T	1	-5.5732	5.8364	0.18609	0.5293:0.3107:0.16:0.0	rs35885673	486	Q7Z3Z4	PIWL4_HUMAN	N	486	ENSP00000299001:T486N	ENSP00000299001:T486N	T	+	2	0	PIWIL4	93974685	0.997000	0.39634	0.017000	0.16124	0.169000	0.22640	1.860000	0.39428	-0.099000	0.12263	0.655000	0.94253	ACC	C|0.975;A|0.025	0.025	strong		0.403	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
MUC4	4585	hgsc.bcm.edu	37	3	195509559	195509559	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509559G>A	ENST00000463781.3	-	2	9351	c.8892C>T	c.(8890-8892)acC>acT	p.T2964T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2964T	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.T2964T(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)		AGGAAGTGTCGGTGACAGGAA	0.582																																					p.T2964T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	1	Substitution - coding silent(1)	endometrium(1)	c.C8892T						PASS	.						9.0	8.0	8.0					3																	195509559		627	1488	2115	SO:0001819	synonymous_variant	4585	exon2			AGTGTCGGTGACA	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.8892C>T	3.37:g.195509559G>A		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	187	24	0.128342	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																																																																																			.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KIF20B	9585	hgsc.bcm.edu	37	10	91532574	91532574	+	Missense_Mutation	SNP	A	A	G	rs150021584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:91532574A>G	ENST00000371728.3	+	32	5436	c.5371A>G	c.(5371-5373)Ata>Gta	p.I1791V	KIF20B_ENST00000416354.1_Missense_Mutation_p.I1821V|KIF20B_ENST00000260753.4_Missense_Mutation_p.I1751V|KIF20B_ENST00000478929.1_3'UTR	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1791	Interaction with PIN1.				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						TCCTATTGATATATCAGGCCA	0.323													A|||	3	0.000599042	0.0023	0.0	5008	,	,		15182	0.0		0.0	False		,,,				2504	0.0				p.I1751V		Atlas-SNP	.											.	KIF20B	191	.	0			c.A5251G						PASS	.	A	VAL/ILE	17,4389	22.3+/-47.3	0,17,2186	137.0	137.0	137.0		5251	4.8	1.0	10	dbSNP_134	137	0,8600		0,0,4300	yes	missense	KIF20B	NM_016195.2	29	0,17,6486	GG,GA,AA		0.0,0.3858,0.1307	benign	1751/1781	91532574	17,12989	2203	4300	6503	SO:0001583	missense	9585	exon32			ATTGATATATCAG	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.5371A>G	10.37:g.91532574A>G	ENSP00000360793:p.Ile1791Val	Somatic	407	1	0.002457		WXS	Illumina HiSeq	Phase_I	389	182	0.467866	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		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	19.08	3.757963	0.69648	0.003858	0.0	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000371728	T;T;T	0.54479	0.57;0.57;0.57	5.91	4.76	0.60689	.	0.125603	0.35235	N	0.003352	T	0.49983	0.1589	M	0.66939	2.045	0.80722	D	1	P;P	0.43287	0.702;0.802	B;B	0.40677	0.182;0.337	T	0.52961	-0.8505	10	0.66056	D	0.02	-7.6635	8.0076	0.30334	0.7238:0.1411:0.0:0.1351	.	1791;1751	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	V	1751;1821;1791	ENSP00000260753:I1751V;ENSP00000411545:I1821V;ENSP00000360793:I1791V	ENSP00000260753:I1751V	I	+	1	0	KIF20B	91522554	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	2.459000	0.45023	1.027000	0.39758	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	strong		0.323	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
KLHDC4	54758	hgsc.bcm.edu	37	16	87743072	87743072	+	Missense_Mutation	SNP	C	C	T	rs61735154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:87743072C>T	ENST00000270583.5	-	10	1304	c.1246G>A	c.(1246-1248)Gaa>Aaa	p.E416K	KLHDC4_ENST00000566349.1_5'UTR|KLHDC4_ENST00000347925.5_Missense_Mutation_p.E385K|KLHDC4_ENST00000353170.5_Missense_Mutation_p.E359K	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	416										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		AGGCTGTCTTCGTCCTCAGAC	0.677													C|||	101	0.0201677	0.0726	0.0072	5008	,	,		12720	0.0		0.0	False		,,,				2504	0.0				p.E416K		Atlas-SNP	.											.	KLHDC4	45	.	0			c.G1246A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	239,4155	133.7+/-170.0	4,231,1962	37.0	39.0	38.0		1075,1153,1246	5.3	0.2	16	dbSNP_129	38	0,8598		0,0,4299	no	missense,missense,missense	KLHDC4	NM_001184854.1,NM_001184856.1,NM_017566.3	56,56,56	4,231,6261	TT,TC,CC		0.0,5.4392,1.8396	benign,benign,benign	359/464,385/490,416/521	87743072	239,12753	2197	4299	6496	SO:0001583	missense	54758	exon10			TGTCTTCGTCCTC	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.1246G>A	16.37:g.87743072C>T	ENSP00000270583:p.Glu416Lys	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_017566	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Missense_Mutation	SNP	ENST00000270583.5	37	CCDS10963.1	41	0.018772893772893772	36	0.07317073170731707	5	0.013812154696132596	0	0.0	0	0.0	C	14.89	2.668986	0.47677	0.054392	0.0	ENSG00000104731	ENST00000270583;ENST00000347925;ENST00000353170	T;T;T	0.08807	3.83;3.05;3.59	5.27	5.27	0.74061	.	0.518149	0.21288	N	0.077021	T	0.00936	0.0031	M	0.69823	2.125	0.80722	D	1	B;D;D	0.57571	0.145;0.98;0.967	B;P;B	0.45449	0.04;0.481;0.229	T	0.27088	-1.0084	10	0.06757	T	0.87	-0.0563	17.8669	0.88797	0.0:1.0:0.0:0.0	.	359;385;416	Q8TBB5-2;Q8TBB5-3;Q8TBB5	.;.;KLDC4_HUMAN	K	416;385;359	ENSP00000270583:E416K;ENSP00000325717:E385K;ENSP00000262530:E359K	ENSP00000270583:E416K	E	-	1	0	KLHDC4	86300573	1.000000	0.71417	0.217000	0.23759	0.110000	0.19582	5.604000	0.67626	2.467000	0.83353	0.313000	0.20887	GAA	C|0.978;T|0.022	0.022	strong		0.677	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566	
ZNF404	342908	hgsc.bcm.edu	37	19	44378063	44378063	+	Silent	SNP	T	T	C	rs79324499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44378063T>C	ENST00000587539.1	-	3	302	c.303A>G	c.(301-303)agA>agG	p.R101R	ZNF404_ENST00000324394.6_Silent_p.R99R	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	101					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)				CCACTTTAGGTCTCTGTTGTC	0.348													T|||	394	0.0786741	0.2753	0.0418	5008	,	,		18012	0.0		0.001	False		,,,				2504	0.0				p.R98R		Atlas-SNP	.											.	ZNF404	46	.	0			c.A294G						PASS	.	T		842,2840		107,628,1106	136.0	144.0	142.0		303	2.0	0.0	19	dbSNP_132	142	12,8152		0,12,4070	no	coding-synonymous	ZNF404	NM_001033719.2		107,640,5176	CC,CT,TT		0.147,22.868,7.2092		101/553	44378063	854,10992	1841	4082	5923	SO:0001819	synonymous_variant	342908	exon2			TTTAGGTCTCTGT	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.303A>G	19.37:g.44378063T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	118	52	0.440678	NM_001033719	A4FU30|K7ELF2	Silent	SNP	ENST00000587539.1	37	CCDS59394.1																																																																																			T|0.939;C|0.061	0.061	strong		0.348	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719	
OR52L1	338751	hgsc.bcm.edu	37	11	6007743	6007743	+	Missense_Mutation	SNP	A	A	G	rs4436525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6007743A>G	ENST00000332249.4	-	1	472	c.418T>C	c.(418-420)Tgc>Cgc	p.C140R		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	140			C -> R (in dbSNP:rs4436525). {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)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCTACATAGCAATCCAGAGCC	0.527													.|||	4011	0.800919	0.7428	0.853	5008	,	,		22693	0.8681		0.7863	False		,,,				2504	0.7883				p.C140R	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											.	OR52L1	100	.	0			c.T418C						PASS	.	G	ARG/CYS	3038,1074		1115,808,133	43.0	44.0	44.0		418	2.5	1.0	11	dbSNP_111	44	6419,1983		2474,1471,256	no	missense	OR52L1	NM_001005173.2	180	3589,2279,389	GG,GA,AA		23.6015,26.1187,24.4286	benign	140/330	6007743	9457,3057	2056	4201	6257	SO:0001583	missense	338751	exon1			CATAGCAATCCAG	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"""GPCR / Class A : Olfactory receptors"""	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.418T>C	11.37:g.6007743A>G	ENSP00000330338:p.Cys140Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	104	39	0.375	NM_001005173	B2RPA6|Q6IFK9	Missense_Mutation	SNP	ENST00000332249.4	37	CCDS44529.1	1691	0.7742673992673993	346	0.7032520325203252	296	0.8176795580110497	496	0.8671328671328671	553	0.7295514511873351	G	0.011	-1.724626	0.00694	0.738813	0.763985	ENSG00000183313	ENST00000332249	T	0.04809	3.55	3.5	2.46	0.29980	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41500	N	0.000875	T	0.00012	0.0000	.	.	.	0.31669	P	0.6446270000000001	B	0.02656	0.0	B	0.01281	0.0	T	0.31752	-0.9932	8	0.02654	T	1	.	6.3452	0.21345	0.1058:0.0:0.7146:0.1796	rs4436525;rs41442444;rs58231611;rs4436525	140	Q8NGH7	O52L1_HUMAN	R	140	ENSP00000330338:C140R	ENSP00000330338:C140R	C	-	1	0	OR52L1	5964319	0.998000	0.40836	0.996000	0.52242	0.516000	0.34256	1.845000	0.39279	0.588000	0.29660	-0.642000	0.03964	TGC	A|0.286;G|0.714	0.714	strong		0.527	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173	
KCNJ11	3767	hgsc.bcm.edu	37	11	17408630	17408630	+	Missense_Mutation	SNP	C	C	T	rs5215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:17408630C>T	ENST00000339994.4	-	1	1576	c.1009G>A	c.(1009-1011)Gtc>Atc	p.V337I	KCNJ11_ENST00000526747.1_5'Flank|KCNJ11_ENST00000528731.1_Missense_Mutation_p.V250I	NM_000525.3	NP_000516.3	Q14654	KCJ11_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 11	337			I -> V (linked to K-23; dbSNP:rs5215). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:15807877, ECO:0000269|PubMed:16429405, ECO:0000269|PubMed:16554811, ECO:0000269|PubMed:8897013, ECO:0000269|PubMed:9032109}.		cellular response to glucose stimulus (GO:0071333)|cellular response to nicotine (GO:0071316)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|negative regulation of insulin secretion (GO:0046676)|neurological system process (GO:0050877)|positive regulation of cation channel activity (GO:2001259)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ischemia (GO:0002931)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	ATP-sensitive potassium channel complex (GO:0008282)|axolemma (GO:0030673)|cell body fiber (GO:0070852)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|ion channel binding (GO:0044325)|potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(3)|skin(2)	16				READ - Rectum adenocarcinoma(2;0.0276)|Colorectal(2;0.0633)	Diazoxide(DB01119)|Glimepiride(DB00222)|Glyburide(DB01016)|Ibutilide(DB00308)|Levosimendan(DB00922)|Thiamylal(DB01154)|Verapamil(DB00661)|Yohimbine(DB01392)	GGCACTTTGACGGTGTTGCCA	0.617											OREG0020810	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	3659	0.730631	0.9546	0.7032	5008	,	,		20339	0.6617		0.6471	False		,,,				2504	0.6043				p.V337I		Atlas-SNP	.											.	KCNJ11	39	.	0			c.G1009A						PASS	.	T	ILE/VAL,ILE/VAL	4018,382	190.2+/-216.2	1833,352,15	165.0	145.0	152.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1009,748	-6.0	0.8	11	dbSNP_52	152	5488,3098	473.5+/-368.6	1740,2008,545	yes	missense,missense	KCNJ11	NM_000525.3,NM_001166290.1	29,29	3573,2360,560	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	36.082,8.6818,26.7981	benign,benign	337/391,250/304	17408630	9506,3480	2200	4293	6493	SO:0001583	missense	3767	exon1			CTTTGACGGTGTT	D50582	CCDS31436.1, CCDS53606.1	11p15.1	2011-07-05						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6257	protein-coding gene	gene with protein product		600937				7502040, 16382105	Standard	NM_001166290		Approved	Kir6.2, BIR	uc001mna.3	Q14654		ENST00000339994.4:c.1009G>A	11.37:g.17408630C>T	ENSP00000345708:p.Val337Ile	Somatic	207	0	0	717	WXS	Illumina HiSeq	Phase_I	229	227	0.991266	NM_000525	B4DWI4|E9PNK0|Q2M1H7|Q58EX3|Q8IW96	Missense_Mutation	SNP	ENST00000339994.4	37	CCDS31436.1	1573	0.7202380952380952	465	0.9451219512195121	250	0.6906077348066298	355	0.6206293706293706	503	0.6635883905013192	T	11.98	1.800702	0.31869	0.913182	0.63918	ENSG00000187486	ENST00000339994;ENST00000528731	D;D	0.94138	-3.36;-3.36	5.43	-5.99	0.02213	.	0.498835	0.19829	N	0.105135	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.11235	0.004	B	0.13407	0.009	T	0.54754	-0.8246	8	0.48119	T	0.1	.	21.9712	0.99964	0.0:0.8139:0.0:0.1861	rs5215;rs56731467;rs5215	337	B2RC52	.	I	337;250	ENSP00000345708:V337I;ENSP00000434755:V250I	ENSP00000345708:V337I	V	-	1	0	KCNJ11	17365206	0.007000	0.16637	0.778000	0.31720	0.975000	0.68041	-0.140000	0.10342	-1.420000	0.02009	-0.361000	0.07541	GTC	C|0.272;T|0.728	0.728	strong		0.617	KCNJ11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387037.1	NM_000525	
USH1C	10083	hgsc.bcm.edu	37	11	17531057	17531057	+	Intron	SNP	C	C	A	rs139996942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:17531057C>A	ENST00000318024.4	-	16	1393				USH1C_ENST00000005226.7_Missense_Mutation_p.R620L|USH1C_ENST00000527020.1_Intron|USH1C_ENST00000527720.1_Intron|USH1C_ENST00000529563.1_Intron	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)						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						GGGCAGTGGGCGGGTGGGAGT	0.637													C|||	55	0.0109824	0.0401	0.0029	5008	,	,		9520	0.0		0.0	False		,,,				2504	0.0				p.R620L		Atlas-SNP	.											USH1C,NS,carcinoma,-1,2	USH1C	157	2	0			c.G1859T	GRCh37	CM024263	ush1cpst	M	rs139996942	scavenged	.	C	,LEU/ARG	139,4261	97.6+/-136.3	3,133,2064	46.0	46.0	46.0		,1859	5.9	1.0	11	dbSNP_134	46	1,8585	1.2+/-3.3	0,1,4292	yes	intron,missense	USH1C	NM_005709.3,NM_153676.3	,102	3,134,6356	AA,AC,CC		0.0116,3.1591,1.0781	,benign	,620/900	17531057	140,12846	2200	4293	6493	SO:0001627	intron_variant	10083	exon18			AGTGGGCGGGTGG	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.1285-7530G>T	11.37:g.17531057C>A		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	37	CCDS31438.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	C	15.92	2.975208	0.53720	0.031591	1.16E-4	ENSG00000006611	ENST00000005226	T	0.37411	1.2	5.93	5.93	0.95920	.	0.378995	0.24557	N	0.037515	T	0.10165	0.0249	.	.	.	0.27896	N	0.93916	D	0.54207	0.965	B	0.44224	0.444	T	0.22277	-1.0221	9	0.66056	D	0.02	.	11.2233	0.48869	0.0:0.9172:0.0:0.0828	.	620	Q7RTU8	.	L	620	ENSP00000005226:R620L	ENSP00000005226:R620L	R	-	2	0	USH1C	17487633	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.046000	0.30354	2.814000	0.96858	0.591000	0.81541	CGC	C|0.988;A|0.012	0.012	strong		0.637	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709	
TACC1	6867	hgsc.bcm.edu	37	8	38684853	38684853	+	Silent	SNP	T	T	C	rs2037204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:38684853T>C	ENST00000317827.4	+	5	1999	c.1620T>C	c.(1618-1620)ccT>ccC	p.P540P	TACC1_ENST00000518415.1_Intron|TACC1_ENST00000348567.4_Silent_p.P102P|TACC1_ENST00000520973.1_Intron|TACC1_ENST00000379931.3_Silent_p.P552P|TACC1_ENST00000520615.1_Silent_p.P345P|TACC1_ENST00000330691.6_Silent_p.P114P|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000443286.2_Intron|TACC1_ENST00000520611.1_5'UTR|TACC1_ENST00000276520.8_Silent_p.P130P|TACC1_ENST00000519416.1_Silent_p.P344P|TACC1_ENST00000520340.1_Intron	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	540					cell cycle (GO:0007049)|cell division (GO:0051301)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				breast(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(3)	17		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			CCAATGTTCCTGTGTCTACCA	0.443													C|||	1657	0.330871	0.4002	0.2839	5008	,	,		23795	0.2698		0.3897	False		,,,				2504	0.273				p.P540P		Atlas-SNP	.											.	TACC1	98	.	0			c.T1620C						PASS	.	C	,,	1678,2728	656.0+/-400.0	315,1048,840	209.0	159.0	176.0		390,1035,1620	-10.9	0.0	8	dbSNP_94	176	3602,4998	626.7+/-397.9	773,2056,1471	no	coding-synonymous,coding-synonymous,coding-synonymous	TACC1	NM_001122824.1,NM_001146216.2,NM_006283.2	,,	1088,3104,2311	CC,CT,TT		41.8837,38.0844,40.5966	,,	130/396,345/611,540/806	38684853	5280,7726	2203	4300	6503	SO:0001819	synonymous_variant	6867	exon5			TGTTCCTGTGTCT	AF049910	CCDS6109.1, CCDS47845.1, CCDS55224.1	8p11	2012-12-20			ENSG00000147526	ENSG00000147526			11522	protein-coding gene	gene with protein product		605301					Standard	NM_006283		Approved		uc010lwp.3	O75410	OTTHUMG00000164018	ENST00000317827.4:c.1620T>C	8.37:g.38684853T>C		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	299	117	0.391304	NM_006283	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Silent	SNP	ENST00000317827.4	37	CCDS6109.1	763	0.34935897435897434	203	0.41260162601626016	106	0.292817679558011	154	0.2692307692307692	300	0.39577836411609496	C	5.060	0.196794	0.09599	0.380844	0.418837	ENSG00000147526	ENST00000518809	.	.	.	5.46	-10.9	0.00192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20563	P	0.999885482	.	.	.	.	.	.	T	0.50285	-0.8846	3	.	.	.	-6.3423	21.8296	0.99961	0.0:0.2203:0.0:0.7797	rs2037204;rs3739250;rs58345429;rs2037204	.	.	.	P	190	.	.	L	+	2	0	TACC1	38804010	0.000000	0.05858	0.030000	0.17652	0.696000	0.40369	-4.510000	0.00223	-3.618000	0.00131	-2.575000	0.00170	CTG	T|0.626;C|0.374	0.374	strong		0.443	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376768.1	NM_006283	
GPR78	27201	hgsc.bcm.edu	37	4	8589023	8589023	+	Missense_Mutation	SNP	G	G	A	rs9685931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:8589023G>A	ENST00000382487.4	+	3	1442	c.1025G>A	c.(1024-1026)cGc>cAc	p.R342H	GPR78_ENST00000509216.1_3'UTR	NM_080819.4	NP_543009.2	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	342			R -> H (in dbSNP:rs9685931).		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(4)|kidney(4)|large_intestine(1)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	26						AGAACCCCGCGCCCAGCGTCC	0.637													G|||	585	0.116813	0.2035	0.0548	5008	,	,		16899	0.0427		0.1143	False		,,,				2504	0.1227				p.R342H		Atlas-SNP	.											GPR78,NS,carcinoma,0,3	GPR78	58	3	0			c.G1025A						PASS	.	G	HIS/ARG	863,3539		83,697,1421	42.0	47.0	45.0		1025	-4.0	0.0	4	dbSNP_119	45	941,7645		51,839,3403	yes	missense	GPR78	NM_080819.2	29	134,1536,4824	AA,AG,GG		10.9597,19.6047,13.8897	benign	342/364	8589023	1804,11184	2201	4293	6494	SO:0001583	missense	27201	exon3			CCCCGCGCCCAGC	AF411107	CCDS3403.1	4p16.1	2012-08-21			ENSG00000155269	ENSG00000155269		"""GPCR / Class A : Orphans"""	4528	protein-coding gene	gene with protein product		606921				11574155	Standard	NM_080819		Approved		uc003glk.4	Q96P69	OTTHUMG00000128483	ENST00000382487.4:c.1025G>A	4.37:g.8589023G>A	ENSP00000371927:p.Arg342His	Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	235	125	0.531915	NM_080819	Q8NGV3	Missense_Mutation	SNP	ENST00000382487.4	37	CCDS3403.1	249	0.11401098901098901	112	0.22764227642276422	24	0.06629834254143646	25	0.043706293706293704	88	0.11609498680738786	G	0.040	-1.286694	0.01387	0.196047	0.109597	ENSG00000155269	ENST00000382487	T	0.61742	0.08	2.02	-4.03	0.04021	.	.	.	.	.	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	0.06734	-1.0810	8	0.25106	T	0.35	.	3.3539	0.07162	0.1861:0.1529:0.509:0.152	rs9685931;rs17857471;rs52825020;rs9685931	342	Q96P69	GPR78_HUMAN	H	342	ENSP00000371927:R342H	ENSP00000371927:R342H	R	+	2	0	GPR78	8639923	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-2.614000	0.00443	-2.912000	0.00091	CGC	G|0.871;A|0.129	0.129	strong		0.637	GPR78-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359201.1		
SNX31	169166	hgsc.bcm.edu	37	8	101648164	101648164	+	Missense_Mutation	SNP	C	C	G	rs2187016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101648164C>G	ENST00000311812.2	-	3	367	c.217G>C	c.(217-219)Gat>Cat	p.D73H		NM_152628.3	NP_689841.3	Q8N9S9	SNX31_HUMAN	sorting nexin 31	73	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.		D -> H (in dbSNP:rs2187016). {ECO:0000269|PubMed:14702039}.		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)			CTCCTCTCATCAGCCATAGCT	0.418													C|||	1659	0.33127	0.5234	0.2795	5008	,	,		18466	0.2579		0.165	False		,,,				2504	0.3548				p.D73H		Atlas-SNP	.											.	SNX31	66	.	0			c.G217C						PASS	.	C	HIS/ASP	2006,2400	561.8+/-380.8	458,1090,655	104.0	97.0	99.0		217	2.0	1.0	8	dbSNP_96	99	1862,6738	332.8+/-320.3	210,1442,2648	yes	missense	SNX31	NM_152628.3	81	668,2532,3303	GG,GC,CC		21.6512,45.5288,29.7401	possibly-damaging	73/441	101648164	3868,9138	2203	4300	6503	SO:0001583	missense	169166	exon3			TCTCATCAGCCAT		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.217G>C	8.37:g.101648164C>G	ENSP00000312368:p.Asp73His	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	111	43	0.387387	NM_152628	C9J6L9|Q8N0U9	Missense_Mutation	SNP	ENST00000311812.2	37	CCDS6288.1	591	0.2706043956043956	238	0.483739837398374	101	0.27900552486187846	123	0.21503496503496503	129	0.17018469656992086	C	15.29	2.788555	0.49997	0.455288	0.216512	ENSG00000174226	ENST00000311812;ENST00000520352;ENST00000520661;ENST00000520743	T;T;T;T	0.35789	1.53;1.53;1.53;1.29	5.72	1.95	0.26073	Phox homologous domain (5);	0.559257	0.18809	N	0.130569	T	0.00012	0.0000	L	0.43923	1.385	0.09310	P	0.9999999999941089	P	0.43542	0.81	P	0.53006	0.715	T	0.48514	-0.9029	9	0.66056	D	0.02	-0.032	8.8661	0.35286	0.0:0.6339:0.0:0.3661	rs2187016;rs52823880;rs58315921;rs2187016	73	Q8N9S9	SNX31_HUMAN	H	73;7;74;99	ENSP00000312368:D73H;ENSP00000428210:D7H;ENSP00000428855:D74H;ENSP00000428262:D99H	ENSP00000312368:D73H	D	-	1	0	SNX31	101717340	0.659000	0.27411	0.977000	0.42913	0.892000	0.51952	0.190000	0.17057	0.079000	0.16929	-0.266000	0.10368	GAT	C|0.720;G|0.280	0.280	strong		0.418	SNX31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379910.1	NM_152628	
AVL9	23080	hgsc.bcm.edu	37	7	32612837	32612837	+	Silent	SNP	T	T	C	rs138053039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:32612837T>C	ENST00000318709.4	+	12	1598	c.1377T>C	c.(1375-1377)caT>caC	p.H459H	AVL9_ENST00000409301.1_Silent_p.H459H|AVL9_ENST00000404479.1_Intron	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	459					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCCAGATCCATGATCCAGAAC	0.502													T|||	76	0.0151757	0.0537	0.0072	5008	,	,		16693	0.0		0.0	False		,,,				2504	0.0				p.H459H		Atlas-SNP	.											.	AVL9	66	.	0			c.T1377C						PASS	.	T		167,4239	109.5+/-147.8	1,165,2037	86.0	67.0	74.0		1377	-3.5	1.0	7	dbSNP_134	74	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	AVL9	NM_015060.1		1,168,6334	CC,CT,TT		0.0349,3.7903,1.3071		459/649	32612837	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	23080	exon12			GATCCATGATCCA	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1377T>C	7.37:g.32612837T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_015060	Q92573	Silent	SNP	ENST00000318709.4	37	CCDS34613.1																																																																																			T|0.988;C|0.012	0.012	strong		0.502	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
SIGLEC8	27181	hgsc.bcm.edu	37	19	51957556	51957556	+	Missense_Mutation	SNP	T	T	C	rs3829659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51957556T>C	ENST00000321424.3	-	6	1228	c.1162A>G	c.(1162-1164)Agg>Ggg	p.R388G	SIGLEC8_ENST00000430817.1_Missense_Mutation_p.R279G|SIGLEC8_ENST00000597352.1_5'Flank|SIGLEC8_ENST00000340550.5_Missense_Mutation_p.R295G	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	388			R -> G (in dbSNP:rs3829659).		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.R388G(1)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GATTTCTTCCTGCAGGACCTC	0.592													t|||	1637	0.326877	0.5461	0.255	5008	,	,		17901	0.2321		0.2714	False		,,,				2504	0.2362				p.R388G		Atlas-SNP	.											SIGLEC8,NS,carcinoma,0,1	SIGLEC8	130	1	1	Substitution - Missense(1)	stomach(1)	c.A1162G						PASS	.	C	GLY/ARG	2365,2041		638,1089,476	96.0	90.0	92.0		1162	-0.1	0.0	19	dbSNP_107	92	2089,6511		251,1587,2462	no	missense	SIGLEC8	NM_014442.2	125	889,2676,2938	CC,CT,TT		24.2907,46.3232,34.2457	probably-damaging	388/500	51957556	4454,8552	2203	4300	6503	SO:0001583	missense	27181	exon6			TCTTCCTGCAGGA	AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.1162A>G	19.37:g.51957556T>C	ENSP00000321077:p.Arg388Gly	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	210	101	0.480952	NM_014442	Q7Z728	Missense_Mutation	SNP	ENST00000321424.3	37	CCDS33086.1	725	0.33195970695970695	262	0.532520325203252	107	0.2955801104972376	135	0.23601398601398602	221	0.29155672823219	.	11.33	1.607566	0.28623	0.536768	0.242907	ENSG00000105366	ENST00000430817;ENST00000321424;ENST00000340550	T;T;T	0.73681	0.62;-0.77;0.19	2.09	-0.0729	0.13737	.	.	.	.	.	T	0.00012	0.0000	M	0.86502	2.82	0.80722	P	0.0	D;P;P	0.89917	1.0;0.909;0.915	D;B;B	0.69142	0.962;0.382;0.236	T	0.38067	-0.9678	8	0.62326	D	0.03	.	4.3104	0.10967	0.0:0.361:0.0:0.639	rs3829659;rs3829659	279;295;388	C9JT30;Q9NYZ4-2;Q9NYZ4	.;.;SIGL8_HUMAN	G	279;388;295	ENSP00000389142:R279G;ENSP00000321077:R388G;ENSP00000339448:R295G	ENSP00000321077:R388G	R	-	1	2	SIGLEC8	56649368	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.711000	0.05019	-0.079000	0.12707	-0.475000	0.04921	AGG	T|0.647;C|0.353	0.353	strong		0.592	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442	
ENDOV	284131	hgsc.bcm.edu	37	17	78395734	78395734	+	Missense_Mutation	SNP	G	G	A	rs34933300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78395734G>A	ENST00000518137.1	+	3	363	c.335G>A	c.(334-336)cGg>cAg	p.R112Q	ENDOV_ENST00000520284.1_Intron|MIR4730_ENST00000584535.1_RNA|ENDOV_ENST00000522751.1_Intron|ENDOV_ENST00000517795.1_Intron|ENDOV_ENST00000518644.1_Missense_Mutation_p.R29Q|ENDOV_ENST00000518907.1_Intron|ENDOV_ENST00000520367.1_Intron|ENDOV_ENST00000517295.2_Missense_Mutation_p.R29Q|ENDOV_ENST00000323854.5_Intron|ENDOV_ENST00000518901.1_Intron	NM_173627.3	NP_775898.2	Q8N8Q3	ENDOV_HUMAN	endonuclease V	112			R -> Q (in dbSNP:rs34933300). {ECO:0000269|Ref.2}.		DNA repair (GO:0006281)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|magnesium ion binding (GO:0000287)|single-stranded RNA binding (GO:0003727)|structure-specific DNA binding (GO:0043566)			endometrium(1)|lung(1)|pancreas(1)|prostate(1)	4						CAGCAGCTGCGGGAGAAGGAG	0.652								Direct reversal of damage					G|||	620	0.123802	0.0499	0.1729	5008	,	,		17428	0.004		0.2684	False		,,,				2504	0.1636				p.R112Q		Atlas-SNP	.											.	ENDOV	26	.	0			c.G335A						PASS	.	G	,,GLN/ARG	352,3896		14,324,1786	32.0	37.0	35.0		,,335	-3.7	0.0	17	dbSNP_126	35	2156,6316		302,1552,2382	yes	intron,intron,missense	ENDOV	NM_001164637.1,NM_001164638.1,NM_173627.3	,,43	316,1876,4168	AA,AG,GG		25.4485,8.2863,19.717	,,benign	,,112/283	78395734	2508,10212	2124	4236	6360	SO:0001583	missense	284131	exon3			AGCTGCGGGAGAA		CCDS54172.1, CCDS54173.1, CCDS54174.1	17q25.3	2011-05-05			ENSG00000173818	ENSG00000173818			26640	protein-coding gene	gene with protein product						12853604	Standard	NM_001164638		Approved	FLJ35220	uc021ueo.1	Q8N8Q3	OTTHUMG00000164638	ENST00000518137.1:c.335G>A	17.37:g.78395734G>A	ENSP00000429190:p.Arg112Gln	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	47	14	0.297872	NM_173627	I3L3S4|Q6P2G2|Q86X99|Q8NAK0	Missense_Mutation	SNP	ENST00000518137.1	37	CCDS54172.1	307	0.14056776556776557	33	0.06707317073170732	69	0.19060773480662985	0	0.0	205	0.2704485488126649	G	7.998	0.754864	0.15846	0.082863	0.254485	ENSG00000173818	ENST00000518137;ENST00000523228;ENST00000517295	T;T	0.17691	2.26;2.26	4.63	-3.72	0.04411	.	0.635443	0.15397	N	0.264527	T	0.00012	0.0000	N	0.10782	0.045	0.53688	P	2.6999999999999247E-5	B	0.24483	0.104	B	0.19391	0.025	T	0.37314	-0.9711	9	0.06099	T	0.92	-6.2061	11.1273	0.48325	0.4437:0.0:0.5563:0.0	rs34933300	112	Q8N8Q3	ENDOV_HUMAN	Q	112;29;87	ENSP00000429190:R112Q;ENSP00000429603:R29Q	ENSP00000428283:R87Q	R	+	2	0	ENDOV	76010329	0.726000	0.28059	0.005000	0.12908	0.020000	0.10135	-0.103000	0.10940	-1.173000	0.02758	-0.469000	0.05056	CGG	G|0.855;A|0.145	0.145	strong		0.652	ENDOV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379487.1	NM_173627	
HRNR	388697	hgsc.bcm.edu	37	1	152191116	152191116	+	Missense_Mutation	SNP	C	C	T	rs138107632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152191116C>T	ENST00000368801.2	-	3	3064	c.2989G>A	c.(2989-2991)Ggc>Agc	p.G997S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	997					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)			CCATGTTGGCCGTGGCCCAAA	0.582													C|||	96	0.0191693	0.0696	0.0043	5008	,	,		24162	0.001		0.0	False		,,,				2504	0.0				p.G997S		Atlas-SNP	.											.	HRNR	403	.	0			c.G2989A						PASS	.	C	SER/GLY	190,4216	121.3+/-158.8	4,182,2017	136.0	140.0	139.0		2989	-1.5	0.0	1	dbSNP_134	139	0,8594		0,0,4297	no	missense	HRNR	NM_001009931.1	56	4,182,6314	TT,TC,CC		0.0,4.3123,1.4615	probably-damaging	997/2851	152191116	190,12810	2203	4297	6500	SO:0001583	missense	388697	exon3			GTTGGCCGTGGCC	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.2989G>A	1.37:g.152191116C>T	ENSP00000357791:p.Gly997Ser	Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	266	124	0.466165	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	26	0.011904761904761904	22	0.044715447154471545	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	C	9.275	1.046626	0.19748	0.043123	0.0	ENSG00000197915	ENST00000368801	T	0.01705	4.68	3.65	-1.49	0.08718	.	.	.	.	.	T	0.00271	0.0008	N	0.04297	-0.235	0.09310	N	1	D	0.57899	0.981	B	0.37943	0.261	T	0.37934	-0.9684	9	0.12430	T	0.62	.	7.1807	0.25770	0.0:0.4928:0.0:0.5072	.	997	Q86YZ3	HORN_HUMAN	S	997	ENSP00000357791:G997S	ENSP00000357791:G997S	G	-	1	0	HRNR	150457740	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.954000	0.03873	-0.422000	0.07405	0.556000	0.70494	GGC	C|0.985;T|0.015	0.015	strong		0.582	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
RGS3	5998	hgsc.bcm.edu	37	9	116346236	116346236	+	Silent	SNP	G	G	A	rs41301525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116346236G>A	ENST00000374140.2	+	21	2753	c.2544G>A	c.(2542-2544)gcG>gcA	p.A848A	RGS3_ENST00000462143.1_Silent_p.A169A|RP11-168K11.2_ENST00000428429.1_RNA|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000374134.3_Silent_p.A169A|RGS3_ENST00000343817.5_Silent_p.A567A|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000350696.5_Silent_p.A848A	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	848					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						ACCCACCTGCGGCCCCCAGGC	0.642													G|||	421	0.0840655	0.18	0.0663	5008	,	,		17005	0.0		0.0974	False		,,,				2504	0.0399				p.A848A		Atlas-SNP	.											.	RGS3	251	.	0			c.G2544A						PASS	.	G	,,,	797,3609	319.1+/-295.9	83,631,1489	48.0	54.0	52.0		507,1701,,2544	0.2	0.1	9	dbSNP_127	52	862,7738	194.8+/-240.1	39,784,3477	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4	,,,	122,1415,4966	AA,AG,GG		10.0233,18.089,12.7557	,,,	169/520,567/918,,848/1199	116346236	1659,11347	2203	4300	6503	SO:0001819	synonymous_variant	5998	exon21			ACCTGCGGCCCCC	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.2544G>A	9.37:g.116346236G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	105	68	0.647619	NM_144488	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|0.886;A|0.114	0.114	strong		0.642	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
USP40	55230	hgsc.bcm.edu	37	2	234386134	234386134	+	Silent	SNP	A	A	G	rs2971863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234386134A>G	ENST00000427112.2	-	31	3647	c.3612T>C	c.(3610-3612)caT>caC	p.H1204H	USP40_ENST00000450966.1_Silent_p.H1216H|USP40_ENST00000251722.6_Silent_p.H1204H			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1204					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		TGCTCTGCTCATGGAGGGCTT	0.582													G|||	1283	0.25619	0.5053	0.1542	5008	,	,		18552	0.1438		0.2455	False		,,,				2504	0.1186				p.H1216H		Atlas-SNP	.											.	USP40	174	.	0			c.T3648C						PASS	.	G		1725,2407		364,997,705	53.0	59.0	57.0		3648	-5.2	0.0	2	dbSNP_101	57	1772,6656		190,1392,2632	no	coding-synonymous	USP40	NM_018218.2		554,2389,3337	GG,GA,AA		21.0252,41.7473,27.8424		1216/1248	234386134	3497,9063	2066	4214	6280	SO:0001819	synonymous_variant	55230	exon31			CTGCTCATGGAGG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3612T>C	2.37:g.234386134A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	91	29	0.318681	NM_018218	Q6NX38|Q70EL0	Silent	SNP	ENST00000427112.2	37	CCDS46547.1																																																																																			A|0.746;G|0.254	0.254	strong		0.582	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
UACA	55075	hgsc.bcm.edu	37	15	70959576	70959576	+	Silent	SNP	C	C	T	rs61746327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70959576C>T	ENST00000322954.6	-	16	3632	c.3447G>A	c.(3445-3447)gtG>gtA	p.V1149V	UACA_ENST00000379983.2_Silent_p.V1136V|UACA_ENST00000560441.1_Silent_p.V1134V|UACA_ENST00000539319.1_Silent_p.V1040V	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1149					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						GCAGTTTGGTCACTGTCTGCT	0.393													C|||	49	0.00978435	0.0356	0.0029	5008	,	,		20629	0.0		0.0	False		,,,				2504	0.0				p.V1149V		Atlas-SNP	.											.	UACA	235	.	0			c.G3447A						PASS	.	C	,	148,4250	100.7+/-139.4	1,146,2052	179.0	178.0	179.0		3408,3447	4.7	0.8	15	dbSNP_129	179	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	1,146,6349	TT,TC,CC		0.0,3.3652,1.1392	,	1136/1404,1149/1417	70959576	148,12844	2199	4297	6496	SO:0001819	synonymous_variant	55075	exon16			TTTGGTCACTGTC	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.3447G>A	15.37:g.70959576C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	161	68	0.42236	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			C|0.989;T|0.011	0.011	strong		0.393	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
GPRIN3	285513	hgsc.bcm.edu	37	4	90169925	90169925	+	Missense_Mutation	SNP	A	A	G	rs7653897	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:90169925A>G	ENST00000609438.1	-	2	1855	c.1337T>C	c.(1336-1338)gTg>gCg	p.V446A	GPRIN3_ENST00000333209.4_Missense_Mutation_p.V446A	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	446			V -> A (in dbSNP:rs7653897). {ECO:0000269|PubMed:14702039}.							breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CTCTTCCCTCACTGGAGTCAT	0.468													G|||	3120	0.623003	0.7625	0.3545	5008	,	,		20323	0.5526		0.5686	False		,,,				2504	0.7536				p.V446A		Atlas-SNP	.											.	GPRIN3	90	.	0			c.T1337C						PASS	.	G	ALA/VAL	3194,1212	423.2+/-340.0	1155,884,164	90.0	91.0	90.0		1337	-10.8	0.0	4	dbSNP_116	90	4653,3947	549.1+/-385.5	1230,2193,877	yes	missense	GPRIN3	NM_198281.2	64	2385,3077,1041	GG,GA,AA		45.8953,27.5079,39.6663	benign	446/777	90169925	7847,5159	2203	4300	6503	SO:0001583	missense	285513	exon2			TCCCTCACTGGAG	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.1337T>C	4.37:g.90169925A>G	ENSP00000476603:p.Val446Ala	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	151	64	0.423841	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	1239	0.5673076923076923	360	0.7317073170731707	134	0.3701657458563536	331	0.5786713286713286	414	0.5461741424802111	G	0.011	-1.709431	0.00712	0.724921	0.541047	ENSG00000185477	ENST00000333209	T	0.08458	3.09	5.38	-10.8	0.00216	.	2.155060	0.02835	N	0.127258	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	0.32561	-0.9902	9	0.02654	T	1	10.8119	2.4337	0.04477	0.379:0.2827:0.0727:0.2657	rs7653897;rs17774444;rs7653897	446	Q6ZVF9	GRIN3_HUMAN	A	446	ENSP00000328672:V446A	ENSP00000328672:V446A	V	-	2	0	GPRIN3	90388948	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.239000	0.01198	-5.479000	0.00014	-3.542000	0.00031	GTG	A|0.398;G|0.602	0.602	strong		0.468	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
LRIT1	26103	hgsc.bcm.edu	37	10	85993923	85993923	+	Silent	SNP	C	C	T	rs149121025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85993923C>T	ENST00000372105.3	-	3	822	c.801G>A	c.(799-801)ttG>ttA	p.L267L		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	267	Ig-like C2-type.					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						CTGTGCCACCCAAAAGGGACC	0.622													C|||	11	0.00219649	0.0083	0.0	5008	,	,		19368	0.0		0.0	False		,,,				2504	0.0				p.L267L		Atlas-SNP	.											LRIT1,NS,haematopoietic_neoplasm,0,1	LRIT1	73	1	0			c.G801A						PASS	.	C		27,4379	34.3+/-65.2	0,27,2176	73.0	72.0	72.0		801	5.9	1.0	10	dbSNP_134	72	0,8600		0,0,4300	no	coding-synonymous	LRIT1	NM_015613.2		0,27,6476	TT,TC,CC		0.0,0.6128,0.2076		267/624	85993923	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	26103	exon3			GCCACCCAAAAGG	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.801G>A	10.37:g.85993923C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_015613	Q0QD41|Q9Y4N7	Silent	SNP	ENST00000372105.3	37	CCDS7373.1																																																																																			C|0.998;T|0.002	0.002	strong		0.622	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
RNF17	56163	hgsc.bcm.edu	37	13	25356053	25356053	+	Silent	SNP	T	T	C	rs9707144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25356053T>C	ENST00000255324.5	+	6	634	c.582T>C	c.(580-582)ttT>ttC	p.F194F	RNF17_ENST00000255325.6_Silent_p.F194F|RNF17_ENST00000255326.4_3'UTR|RNF17_ENST00000381921.1_Silent_p.F194F	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	194					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)		AGAAACAGTTTGACCAACTTT	0.333													T|||	2193	0.437899	0.4871	0.4712	5008	,	,		16212	0.4315		0.3748	False		,,,				2504	0.4192				p.F194F		Atlas-SNP	.											.	RNF17	259	.	0			c.T582C						PASS	.	T	,	2091,2315	572.8+/-383.4	493,1105,605	143.0	157.0	152.0		582,582	1.7	1.0	13	dbSNP_119	152	3483,5117	510.5+/-377.5	679,2125,1496	no	coding-synonymous,coding-synonymous	RNF17	NM_001184993.1,NM_031277.2	,	1172,3230,2101	CC,CT,TT		40.5,47.458,42.8571	,	194/1620,194/1624	25356053	5574,7432	2203	4300	6503	SO:0001819	synonymous_variant	56163	exon6			ACAGTTTGACCAA	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.582T>C	13.37:g.25356053T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	37	CCDS9308.2																																																																																			T|0.556;C|0.444	0.444	strong		0.333	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12920067	12920067	+	Silent	SNP	C	C	G	rs17038709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12920067C>G	ENST00000240189.2	+	3	894	c.807C>G	c.(805-807)ctC>ctG	p.L269L		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	269					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)		TGGAACACCTCCAGTTGCTTA	0.463													.|||	548	0.109425	0.1263	0.0994	5008	,	,		21768	0.131		0.1083	False		,,,				2504	0.0726				p.L269L		Atlas-SNP	.											PRAMEF2,NS,carcinoma,+2,1	PRAMEF2	85	1	0			c.C807G						PASS	.	C		618,3788	260.7+/-263.8	63,492,1648	91.0	91.0	91.0		807	0.8	0.0	1	dbSNP_123	91	978,7610	209.0+/-250.3	81,816,3397	no	coding-synonymous	PRAMEF2	NM_023014.1		144,1308,5045	GG,GC,CC		11.388,14.0263,12.2826		269/475	12920067	1596,11398	2203	4294	6497	SO:0001819	synonymous_variant	65122	exon3			ACACCTCCAGTTG		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.807C>G	1.37:g.12920067C>G		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	244	123	0.504098	NM_023014		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			C|0.887;G|0.113	0.113	strong		0.463	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
PSG11	5680	hgsc.bcm.edu	37	19	43529026	43529026	+	Missense_Mutation	SNP	C	C	T	rs2471952|rs34787457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	198	0	0		WXS	Illumina HiSeq	Phase_I	176	78	0.443182	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	
AMZ1	155185	hgsc.bcm.edu	37	7	2752487	2752487	+	Missense_Mutation	SNP	G	G	A	rs7776970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	152	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	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	
GDNF	2668	hgsc.bcm.edu	37	5	37835752	37835752	+	Intron	SNP	A	A	C	rs529935219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37835752A>C	ENST00000326524.2	-	2	174				GDNF_ENST00000381826.4_Silent_p.S3S|GDNF_ENST00000427982.1_Silent_p.S3S|GDNF_ENST00000515058.1_Intron|GDNF_ENST00000344622.4_5'Flank	NM_000514.3	NP_000505.1	P39905	GDNF_HUMAN	glial cell derived neurotrophic factor						adult locomotory behavior (GO:0008344)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|enteric nervous system development (GO:0048484)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|metanephros development (GO:0001656)|mRNA stabilization (GO:0048255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|organ induction (GO:0001759)|peristalsis (GO:0030432)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|postganglionic parasympathetic nervous system development (GO:0021784)|postsynaptic membrane organization (GO:0001941)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of morphogenesis of a branching structure (GO:0060688)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|ureteric bud formation (GO:0060676)	extracellular region (GO:0005576)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(8)|skin(2)	15	all_lung(31;0.00118)					TGTTAGGCAAAGACTGCATTT	0.418													A|||	11	0.00219649	0.0083	0.0	5008	,	,		19977	0.0		0.0	False		,,,				2504	0.0				p.S3S		Atlas-SNP	.											.	GDNF	56	.	0			c.T9G						PASS	.																																			SO:0001627	intron_variant	2668	exon1			AGGCAAAGACTGC		CCDS3922.1, CCDS3923.1, CCDS54845.1, CCDS54846.1, CCDS75237.1	5p13.1-p12	2014-01-30			ENSG00000168621	ENSG00000168621		"""Endogenous ligands"""	4232	protein-coding gene	gene with protein product	"""astrocyte-derived trophic factor"", ""glial cell line derived neurotrophic factor"", ""glial derived neurotrophic factor"""	600837				8493557	Standard	NM_199231		Approved	ATF1, ATF2, HFB1-GDNF	uc011cpg.2	P39905	OTTHUMG00000090809	ENST00000326524.2:c.26-828T>G	5.37:g.37835752A>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	128	50	0.390625	NM_001190468	B7WPK7|O95448|O95449|O95986|Q6FH33|Q96L44|Q9UD32|Q9UD33|Q9UMV2|Q9UP67|Q9UP97	Silent	SNP	ENST00000326524.2	37	CCDS3922.1																																																																																			.	.	none		0.418	GDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207606.1	NM_000514	
MAP2K1	5604	hgsc.bcm.edu	37	15	66779597	66779597	+	Silent	SNP	A	A	T	rs146869577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:66779597A>T	ENST00000307102.5	+	8	1458	c.927A>T	c.(925-927)gcA>gcT	p.A309A	CTD-3185P2.1_ENST00000565387.1_RNA|CTD-3185P2.2_ENST00000602360.1_RNA|MAP2K1_ENST00000566326.1_Silent_p.A133A	NM_002755.3	NP_002746.1	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	309	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi inheritance (GO:0048313)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte differentiation (GO:0030216)|labyrinthine layer development (GO:0060711)|MAPK cascade (GO:0000165)|melanosome transport (GO:0032402)|mitotic nuclear division (GO:0007067)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell proliferation (GO:0008285)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|neurotrophin TRK receptor signaling pathway (GO:0048011)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|regulation of vascular smooth muscle contraction (GO:0003056)|response to axon injury (GO:0048678)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|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)|vesicle transport along microtubule (GO:0047496)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine phosphatase activity (GO:0004728)			endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(8)|urinary_tract(1)	20					Bosutinib(DB06616)|Trametinib(DB08911)	CTCCCATGGCAATTTTTGAGT	0.393													A|||	25	0.00499201	0.0182	0.0014	5008	,	,		20753	0.0		0.0	False		,,,				2504	0.0				p.A309A		Atlas-SNP	.											.	MAP2K1	115	.	0			c.A927T						PASS	.	A		61,4341	58.1+/-94.6	0,61,2140	141.0	130.0	134.0		927	-5.7	1.0	15	dbSNP_134	134	0,8598		0,0,4299	no	coding-synonymous	MAP2K1	NM_002755.3		0,61,6439	TT,TA,AA		0.0,1.3857,0.4692		309/394	66779597	61,12939	2201	4299	6500	SO:0001819	synonymous_variant	5604	exon8			CATGGCAATTTTT	L11284	CCDS10216.1	15q22.1-q22.33	2014-09-17			ENSG00000169032	ENSG00000169032	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6840	protein-coding gene	gene with protein product		176872		PRKMK1		9465908, 8388392	Standard	NM_002755		Approved	MEK1, MAPKK1	uc010bhq.3	Q02750	OTTHUMG00000133196	ENST00000307102.5:c.927A>T	15.37:g.66779597A>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_002755		Silent	SNP	ENST00000307102.5	37	CCDS10216.1																																																																																			A|0.995;T|0.005	0.005	strong		0.393	MAP2K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256906.4		
RIPK4	54101	hgsc.bcm.edu	37	21	43161766	43161766	+	Silent	SNP	C	C	T	rs61740546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43161766C>T	ENST00000352483.2	-	9	1795	c.1731G>A	c.(1729-1731)tcG>tcA	p.S577S	AP001615.9_ENST00000423276.1_RNA|RIPK4_ENST00000544709.1_Silent_p.S466S|RIPK4_ENST00000542057.1_Silent_p.S466S|RIPK4_ENST00000332512.3_Silent_p.S529S			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	577					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CCTCGTTGACCGAGGCGTTCT	0.637													C|||	87	0.0173722	0.0658	0.0	5008	,	,		20784	0.0		0.0	False		,,,				2504	0.0				p.S529S		Atlas-SNP	.											.	RIPK4	151	.	0			c.G1587A						PASS	.	C		245,4161	140.4+/-175.9	7,231,1965	77.0	63.0	67.0		1587	-5.3	0.0	21	dbSNP_129	67	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	RIPK4	NM_020639.2		7,233,6263	TT,TC,CC		0.0233,5.5606,1.8991		529/785	43161766	247,12759	2203	4300	6503	SO:0001819	synonymous_variant	54101	exon8			GTTGACCGAGGCG	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.1731G>A	21.37:g.43161766C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_020639	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				C|0.980;G|0.000	.	strong		0.637	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
DHDH	27294	hgsc.bcm.edu	37	19	49442735	49442735	+	Silent	SNP	C	C	T	rs2270940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49442735C>T	ENST00000221403.2	+	4	436	c.396C>T	c.(394-396)tcC>tcT	p.S132S	DHDH_ENST00000523250.1_Intron|DHDH_ENST00000522614.1_Silent_p.S132S	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	132					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		TTCCTGCCTCCGAGGCTCTGA	0.567													C|||	418	0.0834665	0.2269	0.0259	5008	,	,		17562	0.0268		0.0278	False		,,,				2504	0.046				p.S132S		Atlas-SNP	.											.	DHDH	35	.	0			c.C396T						PASS	.	C		856,3550	335.2+/-303.8	90,676,1437	88.0	91.0	90.0		396	-10.2	0.0	19	dbSNP_100	90	193,8407	84.2+/-146.7	3,187,4110	no	coding-synonymous	DHDH	NM_014475.3		93,863,5547	TT,TC,CC		2.2442,19.4281,8.0655		132/335	49442735	1049,11957	2203	4300	6503	SO:0001819	synonymous_variant	27294	exon4			TGCCTCCGAGGCT	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.396C>T	19.37:g.49442735C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_014475		Silent	SNP	ENST00000221403.2	37	CCDS12741.1																																																																																			C|0.924;T|0.076	0.076	strong		0.567	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
TAC3	6866	hgsc.bcm.edu	37	12	57406234	57406234	+	Missense_Mutation	SNP	A	A	G	rs73334764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57406234A>G	ENST00000458521.2	-	6	454	c.295T>C	c.(295-297)Tct>Cct	p.S99P	TAC3_ENST00000415231.1_Missense_Mutation_p.S99P|TAC3_ENST00000441881.1_Missense_Mutation_p.S81P	NM_013251.3	NP_037383.1	Q9UHF0	TKNK_HUMAN	tachykinin 3	99					female pregnancy (GO:0007565)|neuropeptide signaling pathway (GO:0007218)|tachykinin receptor signaling pathway (GO:0007217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						TCCGTAGGAGAGTCTAGGGTA	0.488													A|||	125	0.0249601	0.0893	0.0101	5008	,	,		16633	0.0		0.0	False		,,,				2504	0.0				p.S99P		Atlas-SNP	.											.	TAC3	11	.	0			c.T295C						PASS	.	A	PRO/SER,PRO/SER	347,4059	180.8+/-209.0	17,313,1873	73.0	66.0	68.0		241,295	-0.9	0.0	12	dbSNP_130	68	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense	TAC3	NM_001178054.1,NM_013251.3	74,74	17,315,6171	GG,GA,AA		0.0233,7.8756,2.6834	possibly-damaging,possibly-damaging	81/104,99/122	57406234	349,12657	2203	4300	6503	SO:0001583	missense	6866	exon6			TAGGAGAGTCTAG	AF186112	CCDS8928.1, CCDS53803.1	12q13-q21	2013-02-26	2008-07-31		ENSG00000166863	ENSG00000166863		"""Endogenous ligands"""	11521	protein-coding gene	gene with protein product	"""preprotachykinin-B"""	162330	"""neuromedin K"", ""neurokinin beta"""	NKNB		3479225, 10866201	Standard	NM_013251		Approved	ZNEUROK1, NKB	uc001smp.3	Q9UHF0	OTTHUMG00000156958	ENST00000458521.2:c.295T>C	12.37:g.57406234A>G	ENSP00000404056:p.Ser99Pro	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_013251	Q6IAG2|Q71BC6|Q71BC9	Missense_Mutation	SNP	ENST00000458521.2	37	CCDS8928.1	40	0.018315018315018316	36	0.07317073170731707	4	0.011049723756906077	0	0.0	0	0.0	A	10.20	1.285372	0.23478	0.078756	2.33E-4	ENSG00000166863	ENST00000458521;ENST00000441881;ENST00000415231	D;T;D	0.83250	-1.7;-1.07;-1.7	5.0	-0.857	0.10693	.	.	.	.	.	T	0.09512	0.0234	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.15263	-1.0443	9	0.40728	T	0.16	.	6.259	0.20889	0.1768:0.0:0.4637:0.3595	.	99;81	Q9UHF0;Q9UHF0-3	TKNK_HUMAN;.	P	99;81;99	ENSP00000404056:S99P;ENSP00000408208:S81P;ENSP00000402995:S99P	ENSP00000300108:S99P	S	-	1	0	TAC3	55692501	0.002000	0.14202	0.003000	0.11579	0.008000	0.06430	-0.120000	0.10660	0.002000	0.14630	-0.490000	0.04691	TCT	A|0.971;G|0.029	0.029	strong		0.488	TAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346793.1	NM_001006667	
ARL14	80117	hgsc.bcm.edu	37	3	160395483	160395483	+	Missense_Mutation	SNP	C	C	A	rs35633732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:160395483C>A	ENST00000320767.2	+	1	536	c.349C>A	c.(349-351)Cct>Act	p.P117T		NM_025047.2	NP_079323.1	Q8N4G2	ARL14_HUMAN	ADP-ribosylation factor-like 14	117			P -> T (in dbSNP:rs35633732).		small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	GTP binding (GO:0005525)			lung(6)	6			Lung(72;7.02e-05)|LUSC - Lung squamous cell carcinoma(72;7.23e-05)			TAAAAATGTGCCTGTTGTTCT	0.443													C|||	224	0.0447284	0.1641	0.0086	5008	,	,		21657	0.0		0.001	False		,,,				2504	0.0				p.P117T		Atlas-SNP	.											.	ARL14	16	.	0			c.C349A						PASS	.	C	THR/PRO	635,3771	273.1+/-271.2	46,543,1614	75.0	69.0	71.0		349	5.9	0.8	3	dbSNP_126	71	7,8593	5.0+/-18.6	0,7,4293	yes	missense	ARL14	NM_025047.2	38	46,550,5907	AA,AC,CC		0.0814,14.4122,4.9362	probably-damaging	117/193	160395483	642,12364	2203	4300	6503	SO:0001583	missense	80117	exon1			AATGTGCCTGTTG	AK026248	CCDS3192.1	3q25.33	2014-05-09	2005-11-03	2005-11-03	ENSG00000179674	ENSG00000179674		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	22974	protein-coding gene	gene with protein product		614439	"""ADP-ribosylation factor 7"""	ARF7		15367757	Standard	NM_025047		Approved	FLJ22595	uc003fdq.3	Q8N4G2	OTTHUMG00000159031	ENST00000320767.2:c.349C>A	3.37:g.160395483C>A	ENSP00000323847:p.Pro117Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_025047	Q9H655	Missense_Mutation	SNP	ENST00000320767.2	37	CCDS3192.1	122	0.055860805860805864	100	0.2032520325203252	5	0.013812154696132596	4	0.006993006993006993	13	0.017150395778364115	C	16.30	3.085550	0.55861	0.144122	8.14E-4	ENSG00000179674	ENST00000320767	T	0.74315	-0.83	5.95	5.95	0.96441	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.00496	0.0016	M	0.75150	2.29	0.09310	P	0.99999024684	D	0.89917	1.0	D	0.97110	1.0	T	0.02539	-1.1144	9	0.54805	T	0.06	-21.0946	19.3683	0.94473	0.0:1.0:0.0:0.0	rs35633732;rs35633732	117	Q8N4G2	ARL14_HUMAN	T	117	ENSP00000323847:P117T	ENSP00000323847:P117T	P	+	1	0	ARL14	161878177	0.994000	0.37717	0.842000	0.33263	0.656000	0.38851	3.803000	0.55560	2.822000	0.97130	0.563000	0.77884	CCT	C|0.942;A|0.058	0.058	strong		0.443	ARL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352958.1	NM_025047	
SLC40A1	30061	hgsc.bcm.edu	37	2	190437572	190437572	+	Splice_Site	SNP	G	G	A	rs11568344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:190437572G>A	ENST00000261024.2	-	4	813	c.387C>T	c.(385-387)ctC>ctT	p.L129L	SLC40A1_ENST00000418714.1_5'Flank	NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	129					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			GAGAACTTACGAGAACCCATC	0.383													G|||	164	0.0327476	0.118	0.0115	5008	,	,		19151	0.0		0.0	False		,,,				2504	0.0				p.L129L		Atlas-SNP	.											.	SLC40A1	51	.	0			c.C387T						PASS	.	G		492,3914	228.5+/-243.3	22,448,1733	77.0	73.0	74.0		387	0.8	1.0	2	dbSNP_121	74	4,8596	2.2+/-6.3	0,4,4296	yes	coding-synonymous-near-splice	SLC40A1	NM_014585.5		22,452,6029	AA,AG,GG		0.0465,11.1666,3.8136		129/572	190437572	496,12510	2203	4300	6503	SO:0001630	splice_region_variant	30061	exon4			ACTTACGAGAACC	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"""Solute carriers"""	10909	protein-coding gene	gene with protein product	"""ferroportin 1"""	604653	"""solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"""	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.387+1C>T	2.37:g.190437572G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	196	98	0.5	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Silent	SNP	ENST00000261024.2	37	CCDS2299.1																																																																																			G|0.960;A|0.040	0.040	strong		0.383	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2		Silent
TLL2	7093	hgsc.bcm.edu	37	10	98240156	98240156	+	Missense_Mutation	SNP	T	T	A	rs61738802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98240156T>A	ENST00000357947.3	-	2	461	c.236A>T	c.(235-237)aAa>aTa	p.K79I	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	79					cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		GTCTCTGGCTTTGTCAATGTG	0.502													T|||	19	0.00379393	0.0144	0.0	5008	,	,		22069	0.0		0.0	False		,,,				2504	0.0				p.K79I		Atlas-SNP	.											.	TLL2	122	.	0			c.A236T						PASS	.	T	ILE/LYS	66,4340	61.7+/-98.7	1,64,2138	285.0	234.0	251.0		236	3.4	0.4	10	dbSNP_129	251	1,8599		0,1,4299	yes	missense	TLL2	NM_012465.3	102	1,65,6437	AA,AT,TT		0.0116,1.498,0.5151	benign	79/1016	98240156	67,12939	2203	4300	6503	SO:0001583	missense	7093	exon2			CTGGCTTTGTCAA	AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.236A>T	10.37:g.98240156T>A	ENSP00000350630:p.Lys79Ile	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	256	118	0.460938	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	16.21	3.058034	0.55325	0.01498	1.16E-4	ENSG00000095587	ENST00000357947	T	0.16457	2.34	5.74	3.37	0.38596	.	0.384078	0.18126	U	0.150896	T	0.07863	0.0197	L	0.38175	1.15	0.24846	N	0.992434	B	0.34103	0.437	B	0.29716	0.106	T	0.22695	-1.0209	10	0.72032	D	0.01	.	4.0306	0.09708	0.0:0.1654:0.1858:0.6489	rs61738802	79	Q9Y6L7	TLL2_HUMAN	I	79	ENSP00000350630:K79I	ENSP00000350630:K79I	K	-	2	0	TLL2	98230146	0.920000	0.31207	0.364000	0.25888	0.337000	0.28794	1.236000	0.32683	0.959000	0.37980	0.459000	0.35465	AAA	T|0.986;A|0.014	0.014	strong		0.502	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1		
NDUFS4	4724	hgsc.bcm.edu	37	5	52856572	52856572	+	Missense_Mutation	SNP	T	T	A	rs145347909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:52856572T>A	ENST00000296684.5	+	1	108	c.80T>A	c.(79-81)gTt>gAt	p.V27D		NM_002495.2	NP_002486.1	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase)	27					brain development (GO:0007420)|cAMP-mediated signaling (GO:0019933)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|positive regulation of fibroblast proliferation (GO:0048146)|reactive oxygen species metabolic process (GO:0072593)|regulation of protein phosphorylation (GO:0001932)|respiratory electron transport chain (GO:0022904)|response to cAMP (GO:0051591)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(3)	10		Lung NSC(810;8.27e-05)|Breast(144;0.0848)				GCCCTTTCCGTTTCCAGGGTT	0.547													T|||	6	0.00119808	0.0038	0.0014	5008	,	,		15687	0.0		0.0	False		,,,				2504	0.0				p.V27D		Atlas-SNP	.											.	NDUFS4	17	.	0			c.T80A						PASS	.	T	ASP/VAL	9,4397	15.5+/-35.6	0,9,2194	108.0	97.0	101.0		80	-0.2	0.1	5	dbSNP_134	101	0,8600		0,0,4300	yes	missense	NDUFS4	NM_002495.2	152	0,9,6494	AA,AT,TT		0.0,0.2043,0.0692	possibly-damaging	27/176	52856572	9,12997	2203	4300	6503	SO:0001583	missense	4724	exon1			TTTCCGTTTCCAG	AF020351	CCDS3960.1	5q11.1	2011-07-04	2002-08-29		ENSG00000164258	ENSG00000164258		"""Mitochondrial respiratory chain complex / Complex I"""	7711	protein-coding gene	gene with protein product	"""complex I 18kDa subunit"""	602694	"""NADH dehydrogenase (ubiquinone) Fe-S protein 4 (18kD) (NADH-coenzyme Q reductase)"""			9463323, 9763677	Standard	NM_002495		Approved	AQDQ, CI-18	uc003jpe.2	O43181	OTTHUMG00000096987	ENST00000296684.5:c.80T>A	5.37:g.52856572T>A	ENSP00000296684:p.Val27Asp	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_002495	Q9BS69	Missense_Mutation	SNP	ENST00000296684.5	37	CCDS3960.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	12.86	2.065131	0.36470	0.002043	0.0	ENSG00000164258	ENST00000296684;ENST00000506765	T	0.69040	-0.37	4.72	-0.216	0.13153	.	1.026790	0.07670	N	0.935325	T	0.49236	0.1545	L	0.54323	1.7	0.19775	N	0.999952	B	0.29085	0.232	B	0.26517	0.07	T	0.38373	-0.9664	10	0.30854	T	0.27	-17.1517	7.242	0.26102	0.0:0.3826:0.0:0.6174	.	27	O43181	NDUS4_HUMAN	D	27;23	ENSP00000296684:V27D	ENSP00000296684:V27D	V	+	2	0	NDUFS4	52892329	0.912000	0.30974	0.063000	0.19743	0.310000	0.27922	0.131000	0.15870	-0.025000	0.13918	0.533000	0.62120	GTT	T|0.999;A|0.001	0.001	strong		0.547	NDUFS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214062.2	NM_002495	
MUC4	4585	hgsc.bcm.edu	37	3	195505811	195505811	+	Missense_Mutation	SNP	T	T	C	rs201373238		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195505811T>C	ENST00000463781.3	-	2	13099	c.12640A>G	c.(12640-12642)Act>Gct	p.T4214A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T4214A	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)		GCTGAGGAAGTGTCGGTGACA	0.592																																					p.T4214A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	0			c.A12640G						scavenged	.						29.0	25.0	26.0					3																	195505811		691	1580	2271	SO:0001583	missense	4585	exon2			AGGAAGTGTCGGT	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.12640A>G	3.37:g.195505811T>C	ENSP00000417498:p.Thr4214Ala	Somatic	237	4	0.0168776		WXS	Illumina HiSeq	Phase_I	248	30	0.120968	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	3.021	-0.201775	0.06219	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.5;1.47	0.285	-0.57	0.11753	.	.	.	.	.	T	0.11110	0.0271	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.01281	0.0	T	0.26780	-1.0093	7	.	.	.	.	.	.	.	.	4086	E7ESK3	.	A	4214	ENSP00000417498:T4214A;ENSP00000420243:T4214A	.	T	-	1	0	MUC4	196990590	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-1.688000	0.01435	-1.741000	0.00685	ACT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SIDT2	51092	hgsc.bcm.edu	37	11	117062989	117062989	+	Missense_Mutation	SNP	C	C	T	rs12285035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117062989C>T	ENST00000324225.4	+	20	2423	c.1892C>T	c.(1891-1893)aCg>aTg	p.T631M	SIDT2_ENST00000431081.2_Missense_Mutation_p.T628M|SIDT2_ENST00000532062.1_5'Flank	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	631			T -> M (in dbSNP:rs12285035).		cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	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;0.000219)|all cancers(92;0.00144)		AAAGGGAACACGGCGTTCTGG	0.617													C|||	83	0.0165735	0.0575	0.0086	5008	,	,		18145	0.0		0.001	False		,,,				2504	0.0				p.T631M		Atlas-SNP	.											.	SIDT2	82	.	0			c.C1892T						PASS	.	C	MET/THR	214,4188	129.8+/-166.5	6,202,1993	114.0	97.0	103.0		1892	3.4	0.9	11	dbSNP_120	103	2,8590	2.2+/-6.3	0,2,4294	yes	missense	SIDT2	NM_001040455.1	81	6,204,6287	TT,TC,CC		0.0233,4.8614,1.6623	benign	631/833	117062989	216,12778	2201	4296	6497	SO:0001583	missense	51092	exon20			GGAACACGGCGTT	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.1892C>T	11.37:g.117062989C>T	ENSP00000314023:p.Thr631Met	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_001040455	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	37	CCDS31682.1	34	0.015567765567765568	29	0.05894308943089431	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.873	1.199548	0.22121	0.048614	2.33E-4	ENSG00000149577	ENST00000324225;ENST00000278951;ENST00000431081	T;T;T	0.21932	1.98;1.98;1.98	5.47	3.36	0.38483	.	0.304899	0.37761	N	0.001945	T	0.00784	0.0026	N	0.02247	-0.625	0.35238	D	0.777525	B;B;B;B	0.16166	0.013;0.005;0.006;0.016	B;B;B;B	0.15484	0.007;0.003;0.008;0.013	T	0.22661	-1.0210	10	0.32370	T	0.25	-5.8591	8.774	0.34751	0.0:0.6961:0.0:0.3039	rs12285035;rs52809888;rs12285035	652;628;631;652	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	M	631;652;628	ENSP00000314023:T631M;ENSP00000278951:T652M;ENSP00000399635:T628M	ENSP00000278951:T652M	T	+	2	0	SIDT2	116568199	0.066000	0.20996	0.886000	0.34754	0.994000	0.84299	0.421000	0.21280	1.308000	0.44962	0.655000	0.94253	ACG	C|0.978;T|0.022	0.022	strong		0.617	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996	
IQCG	84223	hgsc.bcm.edu	37	3	197665599	197665599	+	Missense_Mutation	SNP	G	G	T	rs9880989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:197665599G>T	ENST00000265239.6	-	5	759	c.335C>A	c.(334-336)gCc>gAc	p.A112D	IQCG_ENST00000480302.1_5'UTR|IQCG_ENST00000453254.1_Missense_Mutation_p.A112D|IQCG_ENST00000455191.1_Missense_Mutation_p.A112D	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	112			A -> D (in dbSNP:rs9880989). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		GATTGTTGAGGCCATTGGAAG	0.363													G|||	1411	0.281749	0.5197	0.1715	5008	,	,		19781	0.2302		0.166	False		,,,				2504	0.2106				p.A112D		Atlas-SNP	.											.	IQCG	44	.	0			c.C335A						PASS	.	G	ASP/ALA,ASP/ALA	1969,2437	556.0+/-379.4	417,1135,651	234.0	252.0	246.0		335,335	-6.9	0.0	3	dbSNP_119	246	1428,7172	275.3+/-291.7	117,1194,2989	yes	missense,missense	IQCG	NM_001134435.1,NM_032263.3	126,126	534,2329,3640	TT,TG,GG		16.6047,44.6891,26.1187	benign,benign	112/444,112/444	197665599	3397,9609	2203	4300	6503	SO:0001583	missense	84223	exon5			GTTGAGGCCATTG	AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 9"""	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.335C>A	3.37:g.197665599G>T	ENSP00000265239:p.Ala112Asp	Somatic	279	1	0.00358423		WXS	Illumina HiSeq	Phase_I	257	257	1	NM_032263	Q9BST2|Q9HAG8	Missense_Mutation	SNP	ENST00000265239.6	37	CCDS3331.1	554	0.25366300366300365	255	0.5182926829268293	51	0.1408839779005525	121	0.21153846153846154	127	0.16754617414248021	G	7.330	0.618799	0.14129	0.446891	0.166047	ENSG00000114473	ENST00000265239;ENST00000455191;ENST00000453254;ENST00000416896	T;T;T;T	0.44083	0.93;0.93;1.0;0.95	5.14	-6.87	0.01671	.	3.994100	0.00465	N	0.000112	T	0.00012	0.0000	L	0.45581	1.43	0.80722	P	0.0	B;P	0.36959	0.302;0.575	B;B	0.29353	0.101;0.093	T	0.39375	-0.9617	9	0.12103	T	0.63	2.991	5.5736	0.17210	0.1712:0.133:0.5647:0.1311	rs9880989;rs52808997;rs60834300;rs9880989	112;112	C9JKX8;Q9H095	.;IQCG_HUMAN	D	112;112;112;93	ENSP00000265239:A112D;ENSP00000407736:A112D;ENSP00000389897:A112D;ENSP00000406411:A93D	ENSP00000265239:A112D	A	-	2	0	IQCG	199149996	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-1.100000	0.03339	-0.975000	0.03546	0.558000	0.71614	GCC	G|0.736;T|0.264	0.264	strong		0.363	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263	
VWDE	221806	hgsc.bcm.edu	37	7	12409209	12409209	+	Missense_Mutation	SNP	G	G	A	rs77088407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12409209G>A	ENST00000275358.3	-	12	2911	c.2723C>T	c.(2722-2724)tCc>tTc	p.S908F		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	908						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						AAAGCTTGGGGAACACGCACA	0.398													G|||	93	0.0185703	0.0688	0.0029	5008	,	,		19786	0.0		0.0	False		,,,				2504	0.0				p.S908F		Atlas-SNP	.											.	VWDE	123	.	0			c.C2723T						PASS	.	G	PHE/SER	59,1325		1,57,634	93.0	76.0	81.0		2723	-1.6	0.0	7	dbSNP_132	81	1,3181		0,1,1590	yes	missense	VWDE	NM_001135924.1	155	1,58,2224	AA,AG,GG		0.0314,4.263,1.3141	benign	908/1591	12409209	60,4506	692	1591	2283	SO:0001583	missense	221806	exon12			CTTGGGGAACACG		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.2723C>T	7.37:g.12409209G>A	ENSP00000275358:p.Ser908Phe	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	161	81	0.503106	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	0	-2.705590	0.00096	0.04263	3.14E-4	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.81579	-1.51	4.83	-1.63	0.08345	.	0.700766	0.14662	N	0.305885	T	0.10680	0.0261	N	0.04508	-0.205	0.21984	N	0.999433	B	0.02656	0.0	B	0.04013	0.001	T	0.14643	-1.0465	10	0.06236	T	0.91	.	9.7136	0.40260	0.6228:0.0:0.3772:0.0	.	908	Q8N2E2	VWDE_HUMAN	F	908;362	ENSP00000275358:S908F	ENSP00000275358:S908F	S	-	2	0	VWDE	12375734	1.000000	0.71417	0.015000	0.15790	0.012000	0.07955	1.322000	0.33689	-0.444000	0.07170	-1.099000	0.02127	TCC	G|0.985;A|0.015	0.015	strong		0.398	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
CLEC4A	50856	hgsc.bcm.edu	37	12	8290881	8290881	+	Nonstop_Mutation	SNP	T	T	C	rs74810750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:8290881T>C	ENST00000229332.5	+	6	959	c.712T>C	c.(712-714)Tga>Cga	p.*238R	CLEC4A_ENST00000352620.3_Nonstop_Mutation_p.*205R|CLEC4A_ENST00000360500.3_Nonstop_Mutation_p.*199R|CLEC4A_ENST00000345999.3_Nonstop_Mutation_p.*166R	NM_016184.3|NM_194447.2|NM_194450.2	NP_057268.1|NP_919429.2|NP_919432.1	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A	0					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|large_intestine(2)|lung(4)|prostate(1)	11				Kidney(36;0.0915)		GATCCACTTATGAACTGAACA	0.393													t|||	32	0.00638978	0.0227	0.0029	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.X238R		Atlas-SNP	.											.	CLEC4A	28	.	0			c.T712C						PASS	.	T	ARG/stop,ARG/stop,ARG/stop,ARG/stop	70,4336	64.1+/-101.4	1,68,2134	229.0	204.0	212.0		712,595,496,613	1.6	0.9	12	dbSNP_132	212	2,8598	2.2+/-6.3	0,2,4298	yes	stop-lost,stop-lost,stop-lost,stop-lost	CLEC4A	NM_016184.3,NM_194447.2,NM_194448.2,NM_194450.2	,,,	1,70,6432	CC,CT,TT		0.0233,1.5887,0.5536	,,,	238/238,199/199,166/166,205/205	8290881	72,12934	2203	4300	6503	SO:0001578	stop_lost	50856	exon6			CACTTATGAACTG	AJ133532	CCDS8590.1, CCDS8591.1, CCDS8592.1, CCDS41745.1	12p13	2005-02-09	2005-02-09	2005-02-09	ENSG00000111729	ENSG00000111729		"""C-type lectin domain containing"""	13257	protein-coding gene	gene with protein product		605306	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6"""	CLECSF6		10438934	Standard	NM_016184		Approved	DCIR, DDB27	uc001qtz.1	Q9UMR7	OTTHUMG00000168571	ENST00000229332.5:c.712T>C	12.37:g.8290881T>C	ENSP00000229332:p.*238Argext*6	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	162	72	0.444444	NM_016184	Q17R69|Q8WXW9|Q9H2Z9|Q9NS33|Q9UI34	Missense_Mutation	SNP	ENST00000229332.5	37	CCDS8590.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	T	7.275	0.607941	0.14002	0.015887	2.33E-4	ENSG00000111729	ENST00000229332;ENST00000345999;ENST00000352620;ENST00000360500	.	.	.	4.12	1.65	0.23941	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3429	0.32254	0.0:0.0:0.3962:0.6038	.	.	.	.	R	238;166;205;199	.	.	X	+	1	0	CLEC4A	8182148	0.320000	0.24616	0.897000	0.35233	0.152000	0.21847	0.699000	0.25586	0.346000	0.23899	0.477000	0.44152	TGA	T|0.994;C|0.006	0.006	strong		0.393	CLEC4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400257.1	NM_194450	
MCRS1	10445	hgsc.bcm.edu	37	12	49952668	49952668	+	Silent	SNP	G	G	A	rs2303305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49952668G>A	ENST00000550165.1	-	15	1526	c.1260C>T	c.(1258-1260)ctC>ctT	p.L420L	MCRS1_ENST00000546244.1_Silent_p.L229L|MCRS1_ENST00000547182.1_5'UTR|MCRS1_ENST00000357123.4_Silent_p.L433L|MCRS1_ENST00000343810.4_Silent_p.L420L			Q96EZ8	MCRS1_HUMAN	microspherule protein 1	420					cellular protein modification process (GO:0006464)|chromatin organization (GO:0006325)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|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)|Ino80 complex (GO:0031011)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)	23						TGGAGCCACAGAGCACCGGCC	0.567													G|||	544	0.108626	0.1891	0.0836	5008	,	,		20234	0.0823		0.0875	False		,,,				2504	0.0665				p.L433L		Atlas-SNP	.											.	MCRS1	40	.	0			c.C1299T						PASS	.	G	,	748,3658	305.8+/-289.2	61,626,1516	61.0	58.0	59.0		1299,1260	-2.7	1.0	12	dbSNP_100	59	720,7880	174.8+/-225.0	30,660,3610	no	coding-synonymous,coding-synonymous	MCRS1	NM_001012300.1,NM_006337.3	,	91,1286,5126	AA,AG,GG		8.3721,16.9768,11.2871	,	433/476,420/463	49952668	1468,11538	2203	4300	6503	SO:0001819	synonymous_variant	10445	exon13			GCCACAGAGCACC	BC011794	CCDS8787.1, CCDS31795.1, CCDS61118.1	12q13.12	2011-07-06				ENSG00000187778		"""INO80 complex subunits"""	6960	protein-coding gene	gene with protein product	"""INO80 complex subunit Q"""	609504				9765390, 9654073	Standard	NM_006337		Approved	ICP22BP, MSP58, P78, MCRS2, INO80Q	uc001rui.1	Q96EZ8		ENST00000550165.1:c.1260C>T	12.37:g.49952668G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_001012300	O14742|O75497|Q6VN53|Q7Z372	Silent	SNP	ENST00000550165.1	37	CCDS8787.1																																																																																			G|0.892;A|0.108	0.108	strong		0.567	MCRS1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405102.1	NM_006337	
CMYA5	202333	hgsc.bcm.edu	37	5	79029288	79029288	+	Missense_Mutation	SNP	C	C	A	rs1428223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79029288C>A	ENST00000446378.2	+	2	4731	c.4700C>A	c.(4699-4701)gCa>gAa	p.A1567E		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1567			A -> E (in dbSNP:rs1428223).		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)		p.A1567E(1)		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)		GAGGAAACAGCAAGTTCATCT	0.413													C|||	1383	0.276158	0.5915	0.085	5008	,	,		22494	0.3621		0.0815	False		,,,				2504	0.0971				p.A1567E		Atlas-SNP	.											CMYA5,NS,carcinoma,0,1	CMYA5	643	1	1	Substitution - Missense(1)	stomach(1)	c.C4700A						PASS	.	C	GLU/ALA	1891,1921		479,933,494	114.0	117.0	116.0		4700	0.7	0.0	5	dbSNP_88	116	713,7539		39,635,3452	yes	missense	CMYA5	NM_153610.3	107	518,1568,3946	AA,AC,CC		8.6403,49.6065,21.5849	benign	1567/4070	79029288	2604,9460	1906	4126	6032	SO:0001583	missense	202333	exon2			AAACAGCAAGTTC	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.4700C>A	5.37:g.79029288C>A	ENSP00000394770:p.Ala1567Glu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	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	626	0.2866300366300366	304	0.6178861788617886	31	0.0856353591160221	232	0.40559440559440557	59	0.07783641160949868	C	12.67	2.006665	0.35415	0.496065	0.086403	ENSG00000164309	ENST00000446378	T	0.04015	3.73	5.93	0.655	0.17839	.	0.773350	0.11773	N	0.530922	T	0.00012	0.0000	N	0.25890	0.77	0.80722	P	0.0	B	0.15473	0.013	B	0.14023	0.01	T	0.21348	-1.0248	9	0.13470	T	0.59	.	3.6245	0.08108	0.4691:0.319:0.1289:0.0831	rs1428223;rs16877137;rs59656657	1567	Q8N3K9	CMYA5_HUMAN	E	1567	ENSP00000394770:A1567E	ENSP00000394770:A1567E	A	+	2	0	CMYA5	79065044	0.000000	0.05858	0.023000	0.16930	0.085000	0.17905	-0.731000	0.04909	0.381000	0.24851	0.655000	0.94253	GCA	C|0.752;A|0.248	0.248	strong		0.413	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
CACNA1A	773	hgsc.bcm.edu	37	19	13323261	13323261	+	Silent	SNP	C	C	T	rs7249722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13323261C>T	ENST00000360228.5	-	42	6125	c.6126G>A	c.(6124-6126)acG>acA	p.T2042T	CACNA1A_ENST00000573710.2_Silent_p.T2043T	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	2043					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TCCATGTGCCCGTCTTCTGGA	0.647													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		15991	0.0		0.0	False		,,,				2504	0.0				p.T2043T		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G6129A						PASS	.	C	,,,,	100,3864		1,98,1883	30.0	34.0	33.0		6144,6129,6126,6135,6144	-8.6	0.8	19	dbSNP_116	33	1,8295		0,1,4147	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	1,99,6030	TT,TC,CC		0.0121,2.5227,0.8238	,,,,	2048/2267,2043/2262,2042/2507,2045/2264,2048/2513	13323261	101,12159	1982	4148	6130	SO:0001819	synonymous_variant	773	exon42			TGTGCCCGTCTTC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.6126G>A	19.37:g.13323261C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			C|0.996;T|0.004	0.004	strong		0.647	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
CROCC	9696	hgsc.bcm.edu	37	1	17265560	17265560	+	Missense_Mutation	SNP	C	C	T	rs9435793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17265560C>T	ENST00000375541.5	+	12	1600	c.1531C>T	c.(1531-1533)Ccc>Tcc	p.P511S	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)		CCGCCGAGGCCCCTCCCCGGC	0.731																																					p.P511S		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	0			c.C1531T						scavenged	.						6.0	6.0	6.0					1																	17265560		2007	3902	5909	SO:0001583	missense	9696	exon12			CGAGGCCCCTCCC	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.1531C>T	1.37:g.17265560C>T	ENSP00000364691:p.Pro511Ser	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	12	3	0.25	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	781	0.3576007326007326	171	0.3475609756097561	123	0.3397790055248619	240	0.4195804195804196	247	0.3258575197889182	C	11.08	1.532985	0.27387	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.09255	3.0	5.39	4.42	0.53409	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.28995	N	0.887822	B;B;P	0.38504	0.007;0.001;0.634	B;B;B	0.41813	0.013;0.002;0.367	T	0.40213	-0.9575	9	0.07644	T	0.81	.	8.3381	0.32228	0.0:0.7587:0.1582:0.0831	rs9435793;rs58724462	374;374;511	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	S	511;392	ENSP00000364691:P511S	ENSP00000364691:P511S	P	+	1	0	CROCC	17138147	0.959000	0.32827	1.000000	0.80357	0.963000	0.63663	1.779000	0.38624	2.702000	0.92279	0.561000	0.74099	CCC	C|0.643;T|0.357	0.357	strong		0.731	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
APOBEC3C	27350	hgsc.bcm.edu	37	22	39413957	39413957	+	Missense_Mutation	SNP	G	G	A	rs141108460		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39413957G>A	ENST00000361441.4	+	3	641	c.361G>A	c.(361-363)Gcc>Acc	p.A121T	APOBEC3D_ENST00000381568.4_Intron	NM_014508.2	NP_055323.2	Q9NRW3	ABC3C_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3C	121					cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6	Melanoma(58;0.04)					CATCTTCACCGCCCGCCTCTA	0.587																																					p.A121T		Atlas-SNP	.											.	APOBEC3C	21	.	0			c.G361A						PASS	.	G	THR/ALA	1,4405		0,1,2202	113.0	118.0	117.0		361	-2.5	0.0	22	dbSNP_134	117	0,8600		0,0,4300	no	missense	APOBEC3C	NM_014508.2	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	121/191	39413957	1,13005	2203	4300	6503	SO:0001583	missense	27350	exon3			TTCACCGCCCGCC	AF165520	CCDS13983.1	22q13.1-q13.2	2014-01-28			ENSG00000244509	ENSG00000244509		"""Apolipoprotein B mRNA editing enzymes"""	17353	protein-coding gene	gene with protein product		607750				11863358	Standard	NM_014508		Approved	APOBEC1L, PBI, bK150C2.3, ARDC2, ARDC4, ARP5	uc003awr.3	Q9NRW3	OTTHUMG00000151087	ENST00000361441.4:c.361G>A	22.37:g.39413957G>A	ENSP00000355340:p.Ala121Thr	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	276	114	0.413043	NM_014508	B2R884|Q5JZ92|Q7Z2N7|Q96F12	Missense_Mutation	SNP	ENST00000361441.4	37	CCDS13983.1	.	.	.	.	.	.	.	.	.	.	.	15.12	2.740041	0.49045	2.27E-4	0.0	ENSG00000244509	ENST00000361441	T	0.67523	-0.27	2.01	-2.48	0.06423	APOBEC-like, N-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.79936	0.4532	M	0.89095	3.005	0.38181	D	0.939611	D	0.89917	1.0	D	0.72982	0.979	T	0.79897	-0.1609	9	0.87932	D	0	.	8.5433	0.33406	0.0:0.0:0.4067:0.5932	.	121	Q9NRW3	ABC3C_HUMAN	T	121	ENSP00000355340:A121T	ENSP00000355340:A121T	A	+	1	0	APOBEC3C	37743903	0.644000	0.27277	0.035000	0.18076	0.027000	0.11550	0.674000	0.25218	-0.470000	0.06901	0.479000	0.44913	GCC	G|1.000;A|0.000	0.000	weak		0.587	APOBEC3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321241.2	NM_014508	
SIGLEC9	27180	hgsc.bcm.edu	37	19	51628395	51628395	+	Missense_Mutation	SNP	C	C	T	rs144549146		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51628395C>T	ENST00000250360.3	+	1	231	c.164C>T	c.(163-165)cCa>cTa	p.P55L	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.P55L	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	55	Ig-like V-type.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		TACCCTGGCCCAGTAGTTCAT	0.602													.|||	1	0.000199681	0.0008	0.0	5008	,	,		16792	0.0		0.0	False		,,,				2504	0.0				p.P55L		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.C164T						PASS	.	C	LEU/PRO,LEU/PRO	3,4403		0,3,2200	120.0	87.0	98.0		164,164	0.7	0.0	19	dbSNP_134	98	0,8600		0,0,4300	no	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	98,98	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	possibly-damaging,possibly-damaging	55/480,55/464	51628395	3,13003	2203	4300	6503	SO:0001583	missense	27180	exon1			CTGGCCCAGTAGT	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.164C>T	19.37:g.51628395C>T	ENSP00000250360:p.Pro55Leu	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	227	108	0.475771	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	11.96	1.794120	0.31777	6.81E-4	0.0	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.54071	0.59;0.59	2.88	0.675	0.17952	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	5.876730	0.00810	N	0.001498	T	0.62344	0.2420	M	0.80183	2.485	0.09310	N	1	P	0.41947	0.766	P	0.46208	0.507	T	0.41466	-0.9507	10	0.62326	D	0.03	.	4.9958	0.14237	0.0:0.6975:0.0:0.3025	.	55	Q9Y336	SIGL9_HUMAN	L	55	ENSP00000413861:P55L;ENSP00000250360:P55L	ENSP00000250360:P55L	P	+	2	0	SIGLEC9	56320207	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.035000	0.12205	0.010000	0.14839	0.397000	0.26171	CCA	C|1.000;T|0.000	0.000	strong		0.602	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441	
ALOX15B	247	hgsc.bcm.edu	37	17	7950952	7950952	+	Silent	SNP	C	C	A	rs9898751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7950952C>A	ENST00000380183.4	+	12	1789	c.1650C>A	c.(1648-1650)tcC>tcA	p.S550S	ALOX15B_ENST00000573359.1_Silent_p.S476S|ALOX15B_ENST00000572022.1_Silent_p.S538S|ALOX15B_ENST00000380173.2_Silent_p.S521S	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	550	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)	p.S550S(2)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						TCACCTGCTCCGCCAAGCATG	0.627													A|||	2241	0.447484	0.5855	0.5043	5008	,	,		18084	0.3423		0.4105	False		,,,				2504	0.3671				p.S550S		Atlas-SNP	.											ALOX15B,NS,carcinoma,0,2	ALOX15B	66	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(1)|stomach(1)	c.C1650A						scavenged	.	A	,,	2378,2028	556.3+/-379.5	642,1094,467	47.0	41.0	43.0		1563,1428,1650	-1.7	0.9	17	dbSNP_119	43	3429,5171	627.2+/-397.9	699,2031,1570	no	coding-synonymous,coding-synonymous,coding-synonymous	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	,,	1341,3125,2037	AA,AC,CC		39.8721,46.0281,44.6486	,,	521/648,476/603,550/677	7950952	5807,7199	2203	4300	6503	SO:0001819	synonymous_variant	247	exon12			CTGCTCCGCCAAG	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1650C>A	17.37:g.7950952C>A		Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Silent	SNP	ENST00000380183.4	37	CCDS11128.1																																																																																			C|0.565;A|0.435	0.435	strong		0.627	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
ZNF714	148206	hgsc.bcm.edu	37	19	21300142	21300142	+	Silent	SNP	A	A	C	rs112722125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21300142A>C	ENST00000596143.1	+	5	997	c.672A>C	c.(670-672)ggA>ggC	p.G224G	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000596053.1_Intron	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	224					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						TTCATACTGGAGAGAAACCCT	0.403													.|||	272	0.0543131	0.0643	0.0403	5008	,	,		19819	0.001		0.1133	False		,,,				2504	0.045				p.G224G		Atlas-SNP	.											.	ZNF714	121	.	0			c.A672C						PASS	.	A		263,4107		12,239,1934	46.0	48.0	47.0		672	-0.9	0.1	19	dbSNP_132	47	701,7891		25,651,3620	no	coding-synonymous	ZNF714	NM_182515.3		37,890,5554	CC,CA,AA		8.1588,6.0183,7.4371		224/555	21300142	964,11998	2185	4296	6481	SO:0001819	synonymous_variant	148206	exon5			TACTGGAGAGAAA	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.672A>C	19.37:g.21300142A>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_182515	Q49AI1|Q86W65|Q8ND40	Silent	SNP	ENST00000596143.1	37	CCDS54239.1																																																																																			A|0.933;C|0.067	0.067	strong		0.403	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
IQUB	154865	hgsc.bcm.edu	37	7	123097468	123097468	+	Silent	SNP	T	T	C	rs10234745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:123097468T>C	ENST00000466202.1	-	12	2736	c.2160A>G	c.(2158-2160)gcA>gcG	p.A720A	RNU6-296P_ENST00000384608.1_RNA|IQUB_ENST00000324698.6_Silent_p.A720A|RP11-332K15.1_ENST00000419832.1_RNA	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	720					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)		p.A720A(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						GATGAGCAGCTGCTTCATCTT	0.403													C|||	1688	0.337061	0.3926	0.2781	5008	,	,		16262	0.3909		0.2972	False		,,,				2504	0.2894				p.A720A		Atlas-SNP	.											IQUB,colon,carcinoma,0,2	IQUB	117	2	1	Substitution - coding silent(1)	stomach(1)	c.A2160G						PASS	.	C		1779,2627	642.8+/-397.7	372,1035,796	98.0	102.0	100.0		2160	-11.7	0.0	7	dbSNP_119	100	2376,6224	700.4+/-405.1	324,1728,2248	no	coding-synonymous	IQUB	NM_178827.4		696,2763,3044	CC,CT,TT		27.6279,40.3768,31.9468		720/792	123097468	4155,8851	2203	4300	6503	SO:0001819	synonymous_variant	154865	exon12			AGCAGCTGCTTCA	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.2160A>G	7.37:g.123097468T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Silent	SNP	ENST00000466202.1	37	CCDS5787.1																																																																																			T|0.682;C|0.318	0.318	strong		0.403	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
PIGR	5284	hgsc.bcm.edu	37	1	207106444	207106444	+	Silent	SNP	A	A	G	rs172361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207106444A>G	ENST00000356495.4	-	7	1956	c.1773T>C	c.(1771-1773)ttT>ttC	p.F591F	PIGR_ENST00000487208.1_5'Flank	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	591					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)	p.F591F(1)		central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CAATCTCCCGAAAACCAGAGT	0.552													A|||	1304	0.260383	0.7398	0.1916	5008	,	,		20444	0.121		0.0258	False		,,,				2504	0.046				p.F591F		Atlas-SNP	.											PIGR,NS,carcinoma,0,1	PIGR	98	1	1	Substitution - coding silent(1)	stomach(1)	c.T1773C						scavenged	.	A		2791,1615	662.4+/-401.0	915,961,327	84.0	84.0	84.0		1773	0.4	0.0	1	dbSNP_79	84	251,8349	98.1+/-159.7	7,237,4056	no	coding-synonymous	PIGR	NM_002644.3		922,1198,4383	GG,GA,AA		2.9186,36.6546,23.3892		591/765	207106444	3042,9964	2203	4300	6503	SO:0001819	synonymous_variant	5284	exon7			CTCCCGAAAACCA		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"""Immunoglobulin superfamily / V-set domain containing"""	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1773T>C	1.37:g.207106444A>G		Somatic	86	2	0.0232558		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_002644	Q68D81|Q8IZY7	Silent	SNP	ENST00000356495.4	37	CCDS1474.1																																																																																			A|0.773;G|0.227	0.227	strong		0.552	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644	
HAUS6	54801	hgsc.bcm.edu	37	9	19058425	19058425	+	Silent	SNP	G	G	A	rs11515236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	240	0	0		WXS	Illumina HiSeq	Phase_I	125	123	0.984	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	
PIEZO1	9780	hgsc.bcm.edu	37	16	88781040	88781040	+	IGR	SNP	A	A	G	rs8059048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88781040A>G	ENST00000301015.9	-	0	8072				CTU2_ENST00000378384.3_Missense_Mutation_p.Q329R|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000453996.2_Missense_Mutation_p.Q416R|CTU2_ENST00000312060.5_Missense_Mutation_p.Q416R|CTU2_ENST00000567949.1_Missense_Mutation_p.Q487R	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						CGTCTCTCCCAGATGCAGTCA	0.697													A|||	1612	0.321885	0.1793	0.3746	5008	,	,		14539	0.6647		0.1958	False		,,,				2504	0.2536				p.Q416R		Atlas-SNP	.											CTU2_ENST00000453996,NS,carcinoma,0,4	CTU2	66	4	0			c.A1247G						PASS	.	A	ARG/GLN,ARG/GLN	890,3492	338.6+/-305.4	104,682,1405	45.0	46.0	45.0		1247,1247	1.9	0.1	16	dbSNP_116	45	1636,6956	299.7+/-304.6	171,1294,2831	yes	missense,missense	CTU2	NM_001012759.1,NM_001012762.1	43,43	275,1976,4236	GG,GA,AA		19.041,20.3104,19.4697	benign,benign	416/516,416/486	88781040	2526,10448	2191	4296	6487	SO:0001628	intergenic_variant	348180	exon12			TCTCCCAGATGCA	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.88781040A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	166	76	0.457831	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	734	0.3360805860805861	84	0.17073170731707318	126	0.34806629834254144	375	0.6555944055944056	149	0.19656992084432717	A	10.10	1.258563	0.23051	0.203104	0.19041	ENSG00000174177	ENST00000378384;ENST00000312060;ENST00000453996	T;T;T	0.52754	0.65;0.65;0.65	4.32	1.86	0.25419	.	0.070349	0.64402	D	0.000019	T	0.00012	0.0000	L	0.52573	1.65	0.58432	P	4.000000000004E-6	B;B;B	0.15473	0.013;0.01;0.012	B;B;B	0.18263	0.013;0.021;0.009	T	0.35475	-0.9787	9	0.39692	T	0.17	.	4.6795	0.12727	0.4951:0.1719:0.0:0.333	rs8059048;rs60525594;rs8059048	329;416;416	Q2VPK5-3;Q2VPK5-5;Q2VPK5	.;.;CTU2_HUMAN	R	329;416;416	ENSP00000367635:Q329R;ENSP00000308617:Q416R;ENSP00000388320:Q416R	ENSP00000308617:Q416R	Q	+	2	0	CTU2	87308541	0.004000	0.15560	0.077000	0.20336	0.048000	0.14542	-0.277000	0.08502	0.108000	0.17862	0.379000	0.24179	CAG	A|0.751;G|0.249	0.249	strong		0.697	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
MUC5B	727897	hgsc.bcm.edu	37	11	1250488	1250488	+	Silent	SNP	C	C	T	rs2075859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1250488C>T	ENST00000529681.1	+	9	1123	c.1065C>T	c.(1063-1065)tgC>tgT	p.C355C	MUC5B_ENST00000447027.1_Silent_p.C355C|MUC5B_ENST00000531082.1_3'UTR	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	355	TIL 1.				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)		CGCAGCTCTGCGAGGACCACT	0.682													c|||	1967	0.392772	0.2814	0.4366	5008	,	,		14317	0.6052		0.34	False		,,,				2504	0.3476				p.C355C		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C1065T						PASS	.	C		1063,3051		143,777,1137	22.0	28.0	26.0		1065	-0.9	0.8	11	dbSNP_96	26	2915,5479		531,1853,1813	no	coding-synonymous	MUC5B	NM_002458.2		674,2630,2950	TT,TC,CC		34.7272,25.8386,31.8036		355/5763	1250488	3978,8530	2057	4197	6254	SO:0001819	synonymous_variant	727897	exon9			GCTCTGCGAGGAC	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.1065C>T	11.37:g.1250488C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	136	74	0.544118	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.604;T|0.396	0.396	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SEC24D	9871	hgsc.bcm.edu	37	4	119659518	119659518	+	Silent	SNP	G	G	A	rs1128403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:119659518G>A	ENST00000280551.6	-	19	2632	c.2394C>T	c.(2392-2394)ctC>ctT	p.L798L	SEC24D_ENST00000429811.2_Silent_p.L354L|SEC24D_ENST00000505134.1_5'UTR|SEC24D_ENST00000419654.2_Silent_p.L354L|SEC24D_ENST00000511481.1_Silent_p.L429L|SEC24D_ENST00000379735.5_Silent_p.L799L			O94855	SC24D_HUMAN	SEC24 family member D	798					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)|in utero embryonic development (GO:0001701)|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)	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)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						AAGGCTGGTGGAGAACTGCTT	0.403													G|||	197	0.0393371	0.1309	0.0202	5008	,	,		19037	0.0		0.008	False		,,,				2504	0.002				p.L798L		Atlas-SNP	.											.	SEC24D	96	.	0			c.C2394T						PASS	.	G		499,3907	234.6+/-247.4	25,449,1729	100.0	89.0	93.0		2394	-10.1	0.1	4	dbSNP_86	93	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	SEC24D	NM_014822.2		25,477,6001	AA,AG,GG		0.3256,11.3255,4.052		798/1033	119659518	527,12479	2203	4300	6503	SO:0001819	synonymous_variant	9871	exon19			CTGGTGGAGAACT	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.2394C>T	4.37:g.119659518G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	178	75	0.421348	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	37	CCDS3710.1																																																																																			G|0.956;A|0.044	0.044	strong		0.403	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		
LILRB1	10859	hgsc.bcm.edu	37	19	55148031	55148031	+	Silent	SNP	T	T	C	rs41308746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55148031T>C	ENST00000396331.1	+	15	2091	c.1734T>C	c.(1732-1734)ccT>ccC	p.P578P	LILRB1_ENST00000396317.1_Silent_p.P562P|LILRB1_ENST00000396321.2_Silent_p.P578P|LILRB1_ENST00000396327.3_Silent_p.P579P|AC009892.10_ENST00000456337.1_Intron|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000418536.2_Silent_p.P562P|LILRB1_ENST00000448689.1_3'UTR|LILRB1_ENST00000396315.1_Silent_p.P580P|LILRB1_ENST00000396332.4_Silent_p.P579P|LILRB1_ENST00000324602.7_Silent_p.P580P|LILRB1_ENST00000434867.2_Silent_p.P578P|LILRB1_ENST00000427581.2_Silent_p.P629P	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	578					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CCTCTCCTCCTTCCCCACTGT	0.582										HNSCC(37;0.09)			t|||	554	0.110623	0.1785	0.0893	5008	,	,		16680	0.0139		0.1491	False		,,,				2504	0.0941				p.P580P		Atlas-SNP	.											LILRB1,NS,carcinoma,+2,1	LILRB1	140	1	0			c.T1740C						scavenged	.						111.0	95.0	100.0					19																	55148031		2200	4295	6495	SO:0001819	synonymous_variant	10859	exon14			TCCTCCTTCCCCA	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1734T>C	19.37:g.55148031T>C		Somatic	335	6	0.0179104		WXS	Illumina HiSeq	Phase_I	409	6	0.0146699	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																			.	.	weak		0.582	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
PABPC1	26986	hgsc.bcm.edu	37	8	101730064	101730064	+	Missense_Mutation	SNP	G	G	A	rs72681442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101730064G>A	ENST00000318607.5	-	3	1568	c.440C>T	c.(439-441)aCg>aTg	p.T147M	PABPC1_ENST00000519004.1_Missense_Mutation_p.T102M|PABPC1_ENST00000522387.1_Missense_Mutation_p.T115M|PABPC1_ENST00000519596.1_5'Flank	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	147	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TGCTTCCTGCGTCTCAAAGTG	0.338																																					p.T147M		Atlas-SNP	.											PABPC1,NS,carcinoma,0,1	PABPC1	76	1	0			c.C440T						scavenged	.						91.0	86.0	88.0					8																	101730064		2203	4300	6503	SO:0001583	missense	26986	exon3			TCCTGCGTCTCAA	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.440C>T	8.37:g.101730064G>A	ENSP00000313007:p.Thr147Met	Somatic	448	0	0		WXS	Illumina HiSeq	Phase_I	427	22	0.0515222	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.6|21.6	4.172071|4.172071	0.78452|0.78452	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519100|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387;ENST00000518196	.|D;D;T;T	.|0.88201	.|-2.35;-2.35;2.22;2.22	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.64402	.|D	.|0.000003	D|D	0.93543|0.93543	0.7939|0.7939	M|M	0.72576|0.72576	2.205|2.205	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.71674	.|0.997;0.997;0.998	.|P;P;P	.|0.61328	.|0.874;0.712;0.887	D|D	0.93826|0.93826	0.7123|0.7123	5|10	.|0.72032	.|D	.|0.01	.|.	19.4675|19.4675	0.94948|0.94948	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|115;147;147	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	C|M	19|147;147;102;115;102	.|ENSP00000313007:T147M;ENSP00000429594:T102M;ENSP00000429395:T115M;ENSP00000430159:T102M	.|ENSP00000313007:T147M	R|T	-|-	1|2	0|0	PABPC1|PABPC1	101799240|101799240	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.981000|0.981000	0.71138|0.71138	9.831000|9.831000	0.99420|0.99420	2.683000|2.683000	0.91414|0.91414	0.650000|0.650000	0.86243|0.86243	CGC|ACG	G|0.823;A|0.177	0.177	strong		0.338	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
ERICH6	131831	hgsc.bcm.edu	37	3	150391789	150391789	+	Missense_Mutation	SNP	C	C	T	rs11919896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150391789C>T	ENST00000295910.6	-	11	1349	c.1297G>A	c.(1297-1299)Ggg>Agg	p.G433R	FAM194A_ENST00000491361.1_Missense_Mutation_p.G287R	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						AACTTGCTCCCATGTTTGTAG	0.338													C|||	120	0.0239617	0.084	0.0101	5008	,	,		20313	0.0		0.002	False		,,,				2504	0.0				p.G433R		Atlas-SNP	.											.	FAM194A	91	.	0			c.G1297A						PASS	.	C	ARG/GLY	318,4088	171.2+/-201.5	8,302,1893	153.0	148.0	149.0		1297	4.9	0.5	3	dbSNP_120	149	2,8598	1.2+/-3.3	0,2,4298	yes	missense	FAM194A	NM_152394.3	125	8,304,6191	TT,TC,CC		0.0233,7.2174,2.4604	probably-damaging	433/664	150391789	320,12686	2203	4300	6503	SO:0001583	missense	131831	exon11			TGCTCCCATGTTT																												ENST00000295910.6:c.1297G>A	3.37:g.150391789C>T	ENSP00000295910:p.Gly433Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	48	0.02197802197802198	42	0.08536585365853659	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	19.68	3.873229	0.72180	0.072174	2.33E-4	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.14893	2.47;2.47	4.94	4.94	0.65067	.	0.238409	0.29307	N	0.012528	T	0.01905	0.0060	M	0.68593	2.085	0.39844	D	0.973152	D	0.89917	1.0	D	0.97110	1.0	T	0.00144	-1.1994	10	0.54805	T	0.06	-12.8489	17.0788	0.86593	0.0:1.0:0.0:0.0	rs11919896;rs52830969;rs11919896	433	Q7L0X2	F194A_HUMAN	R	433;287;391	ENSP00000295910:G433R;ENSP00000419366:G287R	ENSP00000295910:G433R	G	-	1	0	FAM194A	151874479	0.965000	0.33210	0.523000	0.27875	0.854000	0.48673	3.537000	0.53590	2.540000	0.85666	0.655000	0.94253	GGG	C|0.970;T|0.030	0.030	strong		0.338	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
TAS2R16	50833	hgsc.bcm.edu	37	7	122635386	122635386	+	Silent	SNP	C	C	G	rs2692396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:122635386C>G	ENST00000249284.2	-	1	368	c.303G>C	c.(301-303)gtG>gtC	p.V101V		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	101					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	bitter taste receptor activity (GO:0033038)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TGCAGTAGAACACGGTAAGCA	0.378													G|||	442	0.0882588	0.3222	0.0216	5008	,	,		20954	0.0		0.0	False		,,,				2504	0.001				p.V101V		Atlas-SNP	.											.	TAS2R16	57	.	0			c.G303C						PASS	.	G		1015,3391		167,681,1355	76.0	76.0	76.0		303	-2.8	0.0	7	dbSNP_100	76	6,8594		0,6,4294	no	coding-synonymous	TAS2R16	NM_016945.2		167,687,5649	GG,GC,CC		0.0698,23.0368,7.8502		101/292	122635386	1021,11985	2203	4300	6503	SO:0001819	synonymous_variant	50833	exon1			GTAGAACACGGTA	AF227139	CCDS5785.1	7q31.1-q31.3	2012-08-22			ENSG00000128519	ENSG00000128519		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14921	protein-coding gene	gene with protein product		604867				10761934	Standard	NM_016945		Approved	T2R16	uc003vkl.1	Q9NYV7	OTTHUMG00000157090	ENST00000249284.2:c.303G>C	7.37:g.122635386C>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	126	53	0.420635	NM_016945	A4D0X2|Q502V3|Q549U8|Q645W1	Silent	SNP	ENST00000249284.2	37	CCDS5785.1																																																																																			C|0.916;G|0.084	0.084	strong		0.378	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945	
MCEE	84693	hgsc.bcm.edu	37	2	71351641	71351641	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71351641T>C	ENST00000244217.5	-	2	90	c.73A>G	c.(73-75)Aca>Gca	p.T25A	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	25					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)			kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						GCTCTTACTGTTGGAATGGGA	0.418																																					p.T25A		Atlas-SNP	.											.	MCEE	19	.	0			c.A73G						PASS	.						87.0	95.0	92.0					2																	71351641		2203	4300	6503	SO:0001583	missense	84693	exon2			TTACTGTTGGAAT	AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"""glyoxalase domain containing 2"""	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.73A>G	2.37:g.71351641T>C	ENSP00000244217:p.Thr25Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_032601	Q53TP1|Q8WW63	Missense_Mutation	SNP	ENST00000244217.5	37	CCDS1915.1	.	.	.	.	.	.	.	.	.	.	T	11.40	1.627801	0.28978	.	.	ENSG00000124370	ENST00000244217	T	0.62941	-0.01	5.33	-5.38	0.02673	.	0.745129	0.13573	N	0.377891	T	0.42494	0.1205	L	0.35723	1.085	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26849	-1.0091	10	0.20519	T	0.43	-5.2959	9.1858	0.37170	0.1202:0.5708:0.0:0.3089	.	25	Q96PE7	MCEE_HUMAN	A	25	ENSP00000244217:T25A	ENSP00000244217:T25A	T	-	1	0	MCEE	71205149	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.466000	0.06672	-0.914000	0.03827	0.528000	0.53228	ACA	.	.	none		0.418	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601	
SLC25A46	91137	hgsc.bcm.edu	37	5	110097208	110097208	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:110097208A>G	ENST00000355943.3	+	8	1109	c.983A>G	c.(982-984)gAc>gGc	p.D328G	SLC25A46_ENST00000509432.1_Missense_Mutation_p.D115G|SLC25A46_ENST00000513807.1_Missense_Mutation_p.D166G|SLC25A46_ENST00000509442.2_Missense_Mutation_p.D237G|SLC25A46_ENST00000513706.1_3'UTR|SLC25A46_ENST00000447245.2_Missense_Mutation_p.D247G|SLC25A46_ENST00000504098.1_Missense_Mutation_p.D182G	NM_138773.1	NP_620128.1	Q96AG3	S2546_HUMAN	solute carrier family 25, member 46	328					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)		CTTTGTTCTGACGTTATACTT	0.428																																					p.D328G		Atlas-SNP	.											SLC25A46,NS,carcinoma,-1,1	SLC25A46	33	1	0			c.A983G						scavenged	.						290.0	279.0	283.0					5																	110097208		2202	4300	6502	SO:0001583	missense	91137	exon8			GTTCTGACGTTAT	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.983A>G	5.37:g.110097208A>G	ENSP00000348211:p.Asp328Gly	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	107	3	0.0280374	NM_138773	A8K2F2|B3KRE6|B4DTA3|D3DSZ6|D6R9W7|Q04197	Missense_Mutation	SNP	ENST00000355943.3	37	CCDS4100.1	.	.	.	.	.	.	.	.	.	.	A	19.81	3.896300	0.72639	.	.	ENSG00000164209	ENST00000513807;ENST00000509442;ENST00000355943;ENST00000514046;ENST00000447245;ENST00000504098;ENST00000509432	T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	5.51	4.31	0.51392	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.82038	0.4950	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82678	-0.0338	10	0.72032	D	0.01	-14.5613	12.4675	0.55768	0.86:0.14:0.0:0.0	.	237;328	B4DY98;Q96AG3	.;S2546_HUMAN	G	166;237;328;182;247;182;115	ENSP00000421134:D166G;ENSP00000424136:D237G;ENSP00000348211:D328G;ENSP00000399717:D247G;ENSP00000425708:D182G;ENSP00000426604:D115G	ENSP00000348211:D328G	D	+	2	0	SLC25A46	110125107	1.000000	0.71417	0.989000	0.46669	0.995000	0.86356	8.417000	0.90247	0.873000	0.35799	0.528000	0.53228	GAC	.	.	none		0.428	SLC25A46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250721.5	NM_138773	
DYX1C1	161582	hgsc.bcm.edu	37	15	55790053	55790053	+	Missense_Mutation	SNP	T	T	C	rs61733359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55790053T>C	ENST00000321149.3	-	3	495	c.128A>G	c.(127-129)aAc>aGc	p.N43S	DYX1C1_ENST00000380679.1_Missense_Mutation_p.N43S|DYX1C1_ENST00000448430.2_Missense_Mutation_p.N43S|DYX1C1_ENST00000457155.2_Missense_Mutation_p.N43S|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000348518.3_Missense_Mutation_p.N43S	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	43	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.|Mediates interaction with ESR1 and STUB1.				cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		TGGAGGAAAGTTGACCTATGC	0.363													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		17266	0.0		0.0	False		,,,				2504	0.0				p.N43S		Atlas-SNP	.											.	DYX1C1	54	.	0			c.A128G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	59,4327	55.5+/-91.7	0,59,2134	81.0	81.0	81.0		128,128,128	3.6	1.0	15	dbSNP_129	81	1,8583		0,1,4291	yes	missense,missense,missense	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	46,46,46	0,60,6425	CC,CT,TT		0.0116,1.3452,0.4626	benign,benign,benign	43/377,43/382,43/421	55790053	60,12910	2193	4292	6485	SO:0001583	missense	161582	exon3			GGAAAGTTGACCT		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.128A>G	15.37:g.55790053T>C	ENSP00000323275:p.Asn43Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_001033560	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	T	15.43	2.830177	0.50845	0.013452	1.16E-4	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	4.72	3.56	0.40772	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	0.272597	0.33610	U	0.004729	T	0.10723	0.0262	N	0.17872	0.535	0.30138	N	0.804168	B;B;B	0.32526	0.057;0.119;0.374	B;B;B	0.34138	0.082;0.078;0.176	T	0.16958	-1.0385	10	0.02654	T	1	.	7.8669	0.29543	0.0:0.1574:0.0:0.8426	.	43;43;43	Q8WXU2-3;Q8WXU2;Q8WXU2-2	.;DYXC1_HUMAN;.	S	43	ENSP00000403412:N43S;ENSP00000370054:N43S;ENSP00000402640:N43S;ENSP00000323275:N43S;ENSP00000299561:N43S	ENSP00000323275:N43S	N	-	2	0	DYX1C1	53577345	1.000000	0.71417	0.980000	0.43619	0.984000	0.73092	1.407000	0.34657	1.984000	0.57885	0.459000	0.35465	AAC	T|0.995;C|0.005	0.005	strong		0.363	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
FLG	2312	hgsc.bcm.edu	37	1	152281172	152281172	+	Missense_Mutation	SNP	T	T	G	rs74129455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281172T>G	ENST00000368799.1	-	3	6225	c.6190A>C	c.(6190-6192)Aaa>Caa	p.K2064Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2064	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)			GGCCCAGCTTTTCCCTGTGCT	0.562									Ichthyosis																												p.K2064Q		Atlas-SNP	.											FLG,lower_third,carcinoma,+2,1	FLG	900	1	0			c.A6190C						PASS	.	G	GLN/LYS	1356,3050		0,1356,847	396.0	319.0	345.0		6190	-5.2	0.0	1	dbSNP_130	345	13,8587		0,13,4287	yes	missense	FLG	NM_002016.1	53	0,1369,5134	GG,GT,TT		0.1512,30.7762,10.5259	benign	2064/4062	152281172	1369,11637	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CAGCTTTTCCCTG	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.6190A>C	1.37:g.152281172T>G	ENSP00000357789:p.Lys2064Gln	Somatic	396	0	0		WXS	Illumina HiSeq	Phase_I	740	360	0.486486	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	4.971	0.180348	0.09443	0.307762	0.001512	ENSG00000143631	ENST00000368799	T	0.00864	5.6	2.61	-5.22	0.02806	.	.	.	.	.	T	0.00039	0.0001	N	0.00053	-2.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34428	-0.9829	9	0.02654	T	1	.	8.5592	0.33501	0.0:0.112:0.1925:0.6954	.	2064	P20930	FILA_HUMAN	Q	2064	ENSP00000357789:K2064Q	ENSP00000357789:K2064Q	K	-	1	0	FLG	150547796	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.771000	0.00370	-2.303000	0.00656	-0.332000	0.08345	AAA	T|0.500;G|0.500	0.500	strong		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
C4BPB	725	hgsc.bcm.edu	37	1	207269919	207269919	+	Silent	SNP	C	C	T	rs8942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207269919C>T	ENST00000243611.5	+	4	756	c.462C>T	c.(460-462)aaC>aaT	p.N154N	C4BPB_ENST00000367076.3_Silent_p.N153N|C4BPB_ENST00000391923.1_Silent_p.N154N|C4BPB_ENST00000367078.3_Silent_p.N154N	NM_000716.3	NP_000707.1	P20851	C4BPB_HUMAN	complement component 4 binding protein, beta	154	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)				breast(2)|lung(1)|ovary(1)	4						AAGGAAATAACTTCACCTTAG	0.468													T|||	1952	0.389776	0.885	0.2867	5008	,	,		20355	0.1617		0.1769	False		,,,				2504	0.2474				p.N154N		Atlas-SNP	.											.	C4BPB	19	.	0			c.C462T						PASS	.	T	,,,,	3366,1040	381.8+/-324.2	1304,758,141	101.0	101.0	101.0		462,459,462,459,462	-2.0	0.0	1	dbSNP_52	101	1614,6986	742.6+/-407.2	155,1304,2841	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C4BPB	NM_000716.3,NM_001017364.1,NM_001017365.1,NM_001017366.1,NM_001017367.1	,,,,	1459,2062,2982	TT,TC,CC		18.7674,23.6042,38.29	,,,,	154/253,153/252,154/253,153/252,154/253	207269919	4980,8026	2203	4300	6503	SO:0001819	synonymous_variant	725	exon5			AAATAACTTCACC	L11245	CCDS1476.1, CCDS31005.1	1q32	2008-07-18	2001-11-28		ENSG00000123843	ENSG00000123843			1328	protein-coding gene	gene with protein product	"""complement component 4 binding protein, beta chain"", ""C4b binding protein, beta chain"""	120831	"""complement component 4-binding protein, beta"""	C4BP		2300577, 8325877	Standard	XM_005273255		Approved		uc001hfj.3	P20851	OTTHUMG00000036035	ENST00000243611.5:c.462C>T	1.37:g.207269919C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_001017365	A5JYP8|D3DT81|Q5VVR0|Q9BS25	Silent	SNP	ENST00000243611.5	37	CCDS1476.1																																																																																			C|0.623;T|0.377	0.377	strong		0.468	C4BPB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087847.2	NM_000716	
MUC5B	727897	hgsc.bcm.edu	37	11	1267325	1267325	+	Missense_Mutation	SNP	T	T	C	rs55813014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1267325T>C	ENST00000529681.1	+	31	9273	c.9215T>C	c.(9214-9216)tTc>tCc	p.F3072S	MUC5B_ENST00000447027.1_Missense_Mutation_p.F3075S|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3072	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.		F -> S (in dbSNP:rs3021161). {ECO:0000269|PubMed:9013550}.	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)		ATCCCCTCCTTCACCCTTGGG	0.607													N|||	2407	0.480631	0.348	0.5576	5008	,	,		18233	0.6558		0.4573	False		,,,				2504	0.4489				p.F3072S		Atlas-SNP	.											.	MUC5B	473	.	0			c.T9215C						PASS	.	C	SER/PHE	847,3291		220,407,1442	154.0	163.0	160.0		9215	-0.5	0.0	11	dbSNP_129	160	2932,5428		897,1138,2145	no	missense	MUC5B	NM_002458.2	155	1117,1545,3587	CC,CT,TT		35.0718,20.4688,30.2368	benign	3072/5763	1267325	3779,8719	2069	4180	6249	SO:0001583	missense	727897	exon31			CCTCCTTCACCCT	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.9215T>C	11.37:g.1267325T>C	ENSP00000436812:p.Phe3072Ser	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	248	113	0.455645	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	896	0.41025641025641024	119	0.241869918699187	156	0.430939226519337	337	0.5891608391608392	284	0.37467018469656993	C	3.245	-0.154468	0.06544	0.204688	0.350718	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.18016	2.24;2.42	1.82	-0.504	0.11997	.	.	.	.	.	T	0.00012	0.0000	N	0.02802	-0.49	0.80722	P	0.0	B;B	0.15141	0.012;0.0	B;B	0.04013	0.001;0.0	T	0.37079	-0.9721	8	0.87932	D	0	.	6.2501	0.20842	0.0:0.5527:0.0:0.4473	rs55813014;rs61296301	3655;3075	A7Y9J9;E9PBJ0	.;.	S	3072;3075;3044;3032	ENSP00000436812:F3072S;ENSP00000415793:F3075S	ENSP00000343037:F3044S	F	+	2	0	MUC5B	1223901	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	0.258000	0.18387	-0.825000	0.04290	-1.762000	0.00668	TTC	T|0.574;C|0.426	0.426	strong		0.607	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
TTC21A	199223	hgsc.bcm.edu	37	3	39166887	39166887	+	Missense_Mutation	SNP	C	C	T	rs74824603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39166887C>T	ENST00000431162.2	+	11	1414	c.1280C>T	c.(1279-1281)gCg>gTg	p.A427V	TTC21A_ENST00000301819.6_Missense_Mutation_p.A427V|TTC21A_ENST00000440121.1_Missense_Mutation_p.A378V			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	427										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)		GAGACCACAGCGCTCCTGAAG	0.552											OREG0015487	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	12	0.00239617	0.0083	0.0014	5008	,	,		22490	0.0		0.0	False		,,,				2504	0.0				p.A427V		Atlas-SNP	.											.	TTC21A	96	.	0			c.C1280T						PASS	.						74.0	74.0	74.0					3																	39166887		2029	4198	6227	SO:0001583	missense	199223	exon11			CCACAGCGCTCCT	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.1280C>T	3.37:g.39166887C>T	ENSP00000398211:p.Ala427Val	Somatic	129	0	0	883	WXS	Illumina HiSeq	Phase_I	130	61	0.469231	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	C	5.561	0.288299	0.10513	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.36157	1.27;1.27;1.27	5.73	0.827	0.18835	.	0.834776	0.10720	N	0.641804	T	0.21022	0.0506	L	0.34521	1.04	0.09310	N	1	B;B;B	0.21309	0.031;0.054;0.032	B;B;B	0.12156	0.007;0.004;0.005	T	0.24657	-1.0154	10	0.27785	T	0.31	-0.2644	1.2509	0.01982	0.2566:0.4043:0.1248:0.2143	.	378;427;427	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	V	427;409;427;378	ENSP00000301819:A427V;ENSP00000398211:A427V;ENSP00000410882:A378V	ENSP00000301819:A427V	A	+	2	0	TTC21A	39141891	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	0.215000	0.17562	0.074000	0.16767	0.609000	0.83330	GCG	A|0.004;C|0.994;T|0.001	0.001	strong		0.552	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
PDE11A	50940	hgsc.bcm.edu	37	2	178592452	178592452	+	Silent	SNP	C	C	A	rs77341035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:178592452C>A	ENST00000286063.6	-	12	2294	c.1977G>T	c.(1975-1977)cgG>cgT	p.R659R	PDE11A_ENST00000449286.2_Silent_p.R301R|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000389683.3_Silent_p.R215R|PDE11A_ENST00000409504.1_Silent_p.R301R|PDE11A_ENST00000358450.4_Silent_p.R409R	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	659	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)	ATAGAACCATCCGATAGTTTT	0.468									Primary Pigmented Nodular Adrenocortical Disease, Familial				C|||	54	0.0107827	0.0393	0.0029	5008	,	,		22848	0.0		0.0	False		,,,				2504	0.0				p.R659R		Atlas-SNP	.											.	PDE11A	283	.	0			c.G1977T						PASS	.	C	,,,	96,4310	77.8+/-116.1	0,96,2107	185.0	153.0	164.0		645,1227,903,1977	-7.6	0.9	2	dbSNP_131	164	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE11A	NM_001077196.1,NM_001077197.1,NM_001077358.1,NM_016953.3	,,,	0,97,6406	AA,AC,CC		0.0116,2.1788,0.7458	,,,	215/490,409/684,301/576,659/934	178592452	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	50940	exon12	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AACCATCCGATAG	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.1977G>T	2.37:g.178592452C>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Silent	SNP	ENST00000286063.6	37	CCDS33334.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	C	11.02	1.515710	0.27123	0.021788	1.16E-4	ENSG00000128655	ENST00000433879	.	.	.	5.67	-7.56	0.01322	.	.	.	.	.	T	0.10252	0.0251	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39014	-0.9634	4	.	.	.	.	2.2102	0.03945	0.1021:0.2177:0.3161:0.3641	.	.	.	.	V	267	.	.	G	-	2	0	PDE11A	178300698	0.947000	0.32204	0.922000	0.36590	0.991000	0.79684	-0.087000	0.11215	-0.991000	0.03476	-0.290000	0.09829	GGA	C|0.989;A|0.011	0.011	strong		0.468	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
KLK7	5650	hgsc.bcm.edu	37	19	51480840	51480840	+	Silent	SNP	C	C	G	rs1654528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51480840C>G	ENST00000391807.1	-	6	815	c.714G>C	c.(712-714)gtG>gtC	p.V238V	CTB-147C22.9_ENST00000594512.1_RNA|KLK7_ENST00000597707.1_Silent_p.V166V|KLK7_ENST00000595820.1_Silent_p.V238V|KLK7_ENST00000336317.4_Silent_p.V125V	NM_139277.2	NP_644806.1	P49862	KLK7_HUMAN	kallikrein-related peptidase 7	238	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(2)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895)		TGAACTTGCACACTTGAGTGT	0.507													G|||	580	0.115815	0.3313	0.0648	5008	,	,		19553	0.0		0.0487	False		,,,				2504	0.0491				p.V238V		Atlas-SNP	.											.	KLK7	40	.	0			c.G714C						PASS	.		,,	1126,3280	717.1+/-408.7	133,860,1210	200.0	172.0	181.0		498,714,714	0.8	1.0	19	dbSNP_89	181	504,8096	796.9+/-407.5	15,474,3811	yes	coding-synonymous,coding-synonymous,coding-synonymous	KLK7	NM_001207053.1,NM_005046.3,NM_139277.2	,,	148,1334,5021	GG,GC,CC		5.8605,25.5561,12.5327	,,	166/182,238/254,238/254	51480840	1630,11376	2203	4300	6503	SO:0001819	synonymous_variant	5650	exon6			CTTGCACACTTGA	L33404	CCDS12812.1, CCDS59414.1	19q13.33	2011-09-07	2006-10-27			ENSG00000169035		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6368	protein-coding gene	gene with protein product		604438	"""kallikrein 7 (chymotryptic, stratum corneum)"""	PRSS6		8034709, 16800724, 16800723	Standard	NM_005046		Approved	SCCE	uc021uyj.1	P49862		ENST00000391807.1:c.714G>C	19.37:g.51480840C>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_139277	A8K0U5|Q8N5N9|Q8NFV7	Silent	SNP	ENST00000391807.1	37	CCDS12812.1																																																																																			C|0.884;G|0.116	0.116	strong		0.507	KLK7-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464344.1	NM_005046	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232575051	232575051	+	Silent	SNP	G	G	A	rs189356281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232575051G>A	ENST00000366630.1	-	14	4192	c.3834C>T	c.(3832-3834)ctC>ctT	p.L1278L	SIPA1L2_ENST00000308942.4_Silent_p.L352L|SIPA1L2_ENST00000262861.4_Silent_p.L1278L			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1278					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)				GCACAGGGCCGAGGATGGTGG	0.667													G|||	21	0.00419329	0.0144	0.0	5008	,	,		18627	0.0		0.002	False		,,,				2504	0.0				p.L1278L		Atlas-SNP	.											SIPA1L2,colon,carcinoma,-2,1	SIPA1L2	218	1	0			c.C3834T						scavenged	.	G		77,3971		0,77,1947	37.0	41.0	40.0		3834	-10.3	0.0	1		40	3,8363		0,3,4180	no	coding-synonymous	SIPA1L2	NM_020808.3		0,80,6127	AA,AG,GG		0.0359,1.9022,0.6444		1278/1723	232575051	80,12334	2024	4183	6207	SO:0001819	synonymous_variant	57568	exon13			AGGGCCGAGGATG	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.3834C>T	1.37:g.232575051G>A		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	123	61	0.495935	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																			G|0.996;A|0.004	0.004	strong		0.667	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
PCDHA9	9752	hgsc.bcm.edu	37	5	140229581	140229581	+	Missense_Mutation	SNP	G	G	C	rs59056023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140229581G>C	ENST00000532602.1	+	1	2534	c.1501G>C	c.(1501-1503)Gag>Cag	p.E501Q	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.E501Q|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	501	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> Q (in dbSNP:rs59056023).		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(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGGTTGGGCGAGCGCTCGCT	0.672													.|||	319	0.0636981	0.2307	0.0187	5008	,	,		14972	0.0		0.001	False		,,,				2504	0.0				p.E501Q	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G1501C						PASS	.	G	GLN/GLU,,,,,,,,,,,GLN/GLU	877,3515	327.2+/-299.9	127,623,1446	59.0	65.0	63.0		1501,,,,,,,,,,,1501	3.6	1.0	5	dbSNP_129	63	7,8531	4.3+/-15.6	1,5,4263	no	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_014005.3,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_031857.1	29,,,,,,,,,,,29	128,628,5709	CC,CG,GG		0.082,19.9681,6.8368	,,,,,,,,,,,	501/843,,,,,,,,,,,501/951	140229581	884,12046	2196	4269	6465	SO:0001583	missense	9752	exon1			TTGGGCGAGCGCT	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1501G>C	5.37:g.140229581G>C	ENSP00000436042:p.Glu501Gln	Somatic	300	1	0.00333333		WXS	Illumina HiSeq	Phase_I	346	173	0.5	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	129	0.059065934065934064	109	0.22154471544715448	11	0.03038674033149171	1	0.0017482517482517483	8	0.010554089709762533	G	14.45	2.539010	0.45176	0.199681	8.2E-4	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.53640	0.69;0.61	3.56	3.56	0.40772	Cadherin (4);Cadherin-like (1);	0.000000	0.31760	U	0.007116	T	0.00039	0.0001	N	0.25245	0.725	0.49687	P	1.8499999999999073E-4	P;P	0.48834	0.916;0.904	P;P	0.61722	0.893;0.631	T	0.06162	-1.0842	9	0.87932	D	0	.	8.4611	0.32927	0.0:0.1643:0.6673:0.1684	rs59056023	501;501	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	Q	501	ENSP00000436042:E501Q;ENSP00000367362:E501Q	ENSP00000367362:E501Q	E	+	1	0	PCDHA9	140209765	0.000000	0.05858	1.000000	0.80357	0.295000	0.27426	-0.372000	0.07504	1.973000	0.57446	0.306000	0.20318	GAG	G|0.939;C|0.061	0.061	strong		0.672	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
TENM2	57451	hgsc.bcm.edu	37	5	167674472	167674472	+	Silent	SNP	G	G	A	rs17070023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:167674472G>A	ENST00000518659.1	+	27	6567	c.6528G>A	c.(6526-6528)acG>acA	p.T2176T	TENM2_ENST00000545108.1_Silent_p.T2175T|TENM2_ENST00000403607.2_Silent_p.T2000T|TENM2_ENST00000519204.1_Silent_p.T2055T|TENM2_ENST00000520394.1_Silent_p.T1937T	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2176					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										ACTGGATGACGGTGCAATATG	0.547													G|||	532	0.10623	0.1815	0.0634	5008	,	,		21125	0.004		0.0825	False		,,,				2504	0.1646				p.T2167T		Atlas-SNP	.											ODZ2_ENST00000519204,NS,carcinoma,+1,6	.	.	6	0			c.G6501A						PASS	.	G		616,3524		45,526,1499	108.0	103.0	105.0		6501	-11.0	0.2	5	dbSNP_123	105	764,7646		32,700,3473	no	coding-synonymous	ODZ2	NM_001122679.1		77,1226,4972	AA,AG,GG		9.0844,14.8792,10.996		2167/2766	167674472	1380,11170	2070	4205	6275	SO:0001819	synonymous_variant	57451	exon27			GATGACGGTGCAA	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.6528G>A	5.37:g.167674472G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	125	70	0.56	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				G|0.910;A|0.090	0.090	strong		0.547	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
TSGA10	80705	hgsc.bcm.edu	37	2	99722135	99722135	+	Missense_Mutation	SNP	C	C	T	rs146207401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99722135C>T	ENST00000393483.3	-	8	1080	c.236G>A	c.(235-237)cGa>cAa	p.R79Q	TSGA10_ENST00000355053.4_Missense_Mutation_p.R79Q|TSGA10_ENST00000542655.1_Missense_Mutation_p.R79Q|TSGA10_ENST00000539964.1_Missense_Mutation_p.R79Q|TSGA10_ENST00000478090.1_5'UTR|TSGA10_ENST00000410001.1_Missense_Mutation_p.R79Q	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	79					cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						CATTTCTCGTCGAAGTCGGGT	0.368																																					p.R79Q		Atlas-SNP	.											.	TSGA10	81	.	0			c.G236A						PASS	.	C	GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	203.0	195.0	198.0		236,236	5.0	1.0	2	dbSNP_134	198	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TSGA10	NM_025244.2,NM_182911.3	43,43	0,4,6499	TT,TC,CC		0.0233,0.0454,0.0308	probably-damaging,probably-damaging	79/699,79/699	99722135	4,13002	2203	4300	6503	SO:0001583	missense	80705	exon7			TCTCGTCGAAGTC	AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"""cancer/testis antigen 79"""	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.236G>A	2.37:g.99722135C>T	ENSP00000377123:p.Arg79Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_182911	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.031503	0.93575	4.54E-4	2.33E-4	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482;ENST00000542655	T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56	4.99	4.99	0.66335	.	0.158903	0.29853	N	0.011034	T	0.64746	0.2626	L	0.59436	1.845	0.34409	D	0.696207	D;D	0.71674	0.998;0.998	P;P	0.59889	0.865;0.865	T	0.69423	-0.5149	10	0.28530	T	0.3	-6.6381	17.049	0.86513	0.0:1.0:0.0:0.0	.	79;79	B7Z925;Q9BZW7	.;TSG10_HUMAN	Q	79	ENSP00000377123:R79Q;ENSP00000386956:R79Q;ENSP00000347161:R79Q;ENSP00000444419:R79Q;ENSP00000386508:R79Q;ENSP00000377122:R79Q;ENSP00000445623:R79Q	ENSP00000347161:R79Q	R	-	2	0	TSGA10	99088567	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	4.326000	0.59241	2.601000	0.87937	0.650000	0.86243	CGA	C|0.999;T|0.001	0.001	strong		0.368	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12854428	12854428	+	Missense_Mutation	SNP	C	C	T	rs1769774		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12854428C>T	ENST00000332296.7	+	3	755	c.652C>T	c.(652-654)Cca>Tca	p.P218S	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	218			P -> S (in dbSNP:rs1769774).		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)		CATGTCCTGGCCACGTCTGAT	0.393																																					p.P218S		Atlas-SNP	.											.	PRAMEF1	78	.	0			c.C652T						PASS	.	G	SER/PRO	959,3447		7,945,1251	298.0	273.0	282.0		652	-0.5	0.0	1	dbSNP_89	282	2715,5885		261,2193,1846	no	missense	PRAMEF1	NM_023013.2	74	268,3138,3097	TT,TC,CC		31.5698,21.7658,28.2485	benign	218/475	12854428	3674,9332	2203	4300	6503	SO:0001583	missense	65121	exon3			TCCTGGCCACGTC	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.652C>T	1.37:g.12854428C>T	ENSP00000332134:p.Pro218Ser	Somatic	618	1	0.00161812		WXS	Illumina HiSeq	Phase_I	666	251	0.376877	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	626	0.2866300366300366	87	0.17682926829268292	101	0.27900552486187846	215	0.3758741258741259	223	0.2941952506596306	.	0.007	-2.005143	0.00426	0.217658	0.315698	ENSG00000116721	ENST00000332296	T	0.14640	2.49	1.61	-0.486	0.12064	.	2.279790	0.02045	N	0.049591	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.15719	0.014	B	0.20384	0.029	T	0.47328	-0.9126	9	0.20046	T	0.44	.	2.601	0.04867	0.0:0.4561:0.3162:0.2277	rs1769774	218	O95521	PRAM1_HUMAN	S	218	ENSP00000332134:P218S	ENSP00000332134:P218S	P	+	1	0	PRAMEF1	12777015	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.115000	0.10741	-0.146000	0.11274	-0.445000	0.05633	CCA	C|0.713;T|0.287	0.287	strong		0.393	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
HEPHL1	341208	hgsc.bcm.edu	37	11	93844722	93844722	+	Silent	SNP	C	C	T	rs76467816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:93844722C>T	ENST00000315765.9	+	19	3236	c.3228C>T	c.(3226-3228)tcC>tcT	p.S1076S		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	1076	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TTCCTTACTCCACCACATCTC	0.428													C|||	147	0.029353	0.1067	0.0086	5008	,	,		20649	0.0		0.0	False		,,,				2504	0.0				p.S1076S		Atlas-SNP	.											.	HEPHL1	144	.	0			c.C3228T						PASS	.	C		310,3668		15,280,1694	48.0	47.0	48.0		3228	-4.0	0.9	11	dbSNP_131	48	1,8347		0,1,4173	no	coding-synonymous	HEPHL1	NM_001098672.1		15,281,5867	TT,TC,CC		0.012,7.7929,2.5231		1076/1160	93844722	311,12015	1989	4174	6163	SO:0001819	synonymous_variant	341208	exon19			TTACTCCACCACA	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.3228C>T	11.37:g.93844722C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	194	193	0.994845	NM_001098672	Q3C1W7	Silent	SNP	ENST00000315765.9	37	CCDS44710.1																																																																																			C|0.979;T|0.021	0.021	strong		0.428	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
SMPD2	6610	hgsc.bcm.edu	37	6	109764535	109764535	+	Missense_Mutation	SNP	G	G	T	rs1476387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:109764535G>T	ENST00000258052.3	+	9	1154	c.795G>T	c.(793-795)agG>agT	p.R265S	PPIL6_ENST00000521072.2_5'Flank|PPIL6_ENST00000440797.2_5'Flank|PPIL6_ENST00000424445.2_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	176	0	0		WXS	Illumina HiSeq	Phase_I	188	188	1	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		
LEFTY1	10637	hgsc.bcm.edu	37	1	226074635	226074635	+	Missense_Mutation	SNP	C	C	T	rs61739581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226074635C>T	ENST00000272134.5	-	4	972	c.893G>A	c.(892-894)cGg>cAg	p.R298Q	RP4-559A3.7_ENST00000432920.2_3'UTR|LEFTY1_ENST00000492457.1_5'Flank	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	298					cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					CGGGGGCTGCCGGCAGGTGCC	0.642													c|||	331	0.0660942	0.236	0.0245	5008	,	,		16397	0.0		0.002	False		,,,				2504	0.0				p.R298Q		Atlas-SNP	.											.	LEFTY1	30	.	0			c.G893A						PASS	.	C	GLN/ARG	866,3536		78,710,1413	16.0	20.0	19.0		893	-8.0	0.7	1	dbSNP_129	19	12,8578		0,12,4283	no	missense	LEFTY1	NM_020997.3	43	78,722,5696	TT,TC,CC		0.1397,19.6729,6.758	benign	298/367	226074635	878,12114	2201	4295	6496	SO:0001583	missense	10637	exon4			GGCTGCCGGCAGG	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"""left-right determination, factor B"""	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.893G>A	1.37:g.226074635C>T	ENSP00000272134:p.Arg298Gln	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	285	134	0.470175	NM_020997	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	124	0.056776556776556776	114	0.23170731707317074	10	0.027624309392265192	0	0.0	0	0.0	c	6.256	0.415350	0.11870	0.196729	0.001397	ENSG00000243709	ENST00000272134	D	0.83506	-1.73	4.0	-7.99	0.01131	Transforming growth factor-beta, C-terminal (3);	0.426594	0.27613	N	0.018587	T	0.00039	0.0001	N	0.11131	0.1	0.53688	P	2.6999999999999247E-5	B	0.02656	0.0	B	0.06405	0.002	T	0.23261	-1.0193	9	0.12430	T	0.62	.	3.7673	0.08627	0.2397:0.4502:0.0985:0.2116	.	298	O75610	LFTY1_HUMAN	Q	298	ENSP00000272134:R298Q	ENSP00000272134:R298Q	R	-	2	0	LEFTY1	224141258	0.810000	0.29049	0.721000	0.30653	0.735000	0.41995	-0.153000	0.10144	-2.307000	0.00653	-0.993000	0.02533	CGG	C|0.939;T|0.061	0.061	strong		0.642	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997	
TG	7038	hgsc.bcm.edu	37	8	133906136	133906136	+	Missense_Mutation	SNP	G	G	C	rs16893332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133906136G>C	ENST00000220616.4	+	11	3003	c.2963G>C	c.(2962-2964)cGt>cCt	p.R988P	TG_ENST00000377869.1_Missense_Mutation_p.R988P	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	988	Thyroglobulin type-1 8. {ECO:0000255|PROSITE-ProRule:PRU00500}.		R -> P (in dbSNP:rs16893332).		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)		CAGTTTCTGCGTGGGAGTGAT	0.577													g|||	277	0.0553115	0.1036	0.013	5008	,	,		18344	0.1052		0.0119	False		,,,				2504	0.0133				p.R988P		Atlas-SNP	.											.	TG	416	.	0			c.G2963C						PASS	.		PRO/ARG	400,4006	196.0+/-220.5	28,344,1831	67.0	63.0	64.0		2963	-0.2	0.1	8	dbSNP_123	64	16,8584	11.2+/-40.8	0,16,4284	no	missense	TG	NM_003235.4	103	28,360,6115	CC,CG,GG		0.186,9.0785,3.1985	benign	988/2769	133906136	416,12590	2203	4300	6503	SO:0001583	missense	7038	exon11			TTCTGCGTGGGAG	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.2963G>C	8.37:g.133906136G>C	ENSP00000220616:p.Arg988Pro	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	173	82	0.473988	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	117	0.05357142857142857	54	0.10975609756097561	5	0.013812154696132596	46	0.08041958041958042	12	0.0158311345646438	g	11.38	1.621796	0.28889	0.090785	0.00186	ENSG00000042832	ENST00000377869;ENST00000220616	T;T	0.60548	0.18;0.18	5.14	-0.246	0.13022	Thyroglobulin type-1 (1);	1.557920	0.03552	N	0.225609	T	0.00845	0.0028	L	0.36672	1.1	0.80722	P	0.0	P	0.43578	0.811	B	0.33846	0.171	T	0.08994	-1.0695	9	0.42905	T	0.14	.	1.1324	0.01748	0.3158:0.2552:0.2984:0.1306	rs16893332;rs56509792;rs16893332	988	P01266	THYG_HUMAN	P	988	ENSP00000367100:R988P;ENSP00000220616:R988P	ENSP00000220616:R988P	R	+	2	0	TG	133975318	0.000000	0.05858	0.059000	0.19551	0.028000	0.11728	-0.061000	0.11693	0.194000	0.20326	0.380000	0.24917	CGT	A|0.002;C|0.049;G|0.950	0.049	strong		0.577	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
DSPP	1834	hgsc.bcm.edu	37	4	88534065	88534065	+	Missense_Mutation	SNP	G	G	A	rs3750025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88534065G>A	ENST00000282478.7	+	3	760	c.727G>A	c.(727-729)Gat>Aat	p.D243N	DSPP_ENST00000399271.1_Missense_Mutation_p.D243N|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	243			D -> N (in dbSNP:rs3750025).		biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		GGATAATTCCGATGGGAGTCC	0.458													G|||	526	0.105032	0.0197	0.062	5008	,	,		22061	0.3651		0.0209	False		,,,				2504	0.0695				p.D243N		Atlas-SNP	.											.	DSPP	174	.	0			c.G727A						PASS	.	G	ASN/ASP	93,4005		0,93,1956	104.0	115.0	111.0		727	3.7	0.8	4	dbSNP_107	111	174,8206		1,172,4017	yes	missense	DSPP	NM_014208.3	23	1,265,5973	AA,AG,GG		2.0764,2.2694,2.1398	probably-damaging	243/1302	88534065	267,12211	2049	4190	6239	SO:0001583	missense	1834	exon4			AATTCCGATGGGA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.727G>A	4.37:g.88534065G>A	ENSP00000282478:p.Asp243Asn	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	157	79	0.503185	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	251	0.11492673992673992	18	0.036585365853658534	29	0.08011049723756906	191	0.3339160839160839	13	0.017150395778364115	G	8.391	0.839843	0.16891	0.022694	0.020764	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.92545	-3.06;-3.06	4.59	3.74	0.42951	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	0.37891	P	0.069295	D	0.64830	0.994	P	0.56278	0.795	T	0.00000	-1.4240	8	0.59425	D	0.04	-1.7006	12.3912	0.55360	0.0:0.1711:0.8289:0.0	rs3750025;rs16996089;rs52794219;rs61697660;rs3750025	243	Q9NZW4	DSPP_HUMAN	N	243	ENSP00000382213:D243N;ENSP00000282478:D243N	ENSP00000282478:D243N	D	+	1	0	DSPP	88753089	0.999000	0.42202	0.751000	0.31187	0.310000	0.27922	2.779000	0.47734	1.146000	0.42352	-0.310000	0.09108	GAT	G|0.906;A|0.094	0.094	strong		0.458	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
RBPJL	11317	hgsc.bcm.edu	37	20	43945377	43945377	+	Missense_Mutation	SNP	C	C	A	rs35220957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43945377C>A	ENST00000343694.3	+	12	1404	c.1332C>A	c.(1330-1332)agC>agA	p.S444R	RBPJL_ENST00000372743.1_Missense_Mutation_p.S443R|RBPJL_ENST00000372741.3_Silent_p.R448R|RBPJL_ENST00000464504.1_3'UTR	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	444	IPT/TIG.				positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	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 (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				CCTTCTGCAGCGACTGGCGCT	0.701													C|||	73	0.0145767	0.0454	0.0072	5008	,	,		12791	0.0		0.004	False		,,,				2504	0.0041				p.S444R		Atlas-SNP	.											.	RBPJL	67	.	0			c.C1332A						PASS	.	C	ARG/SER	179,4221		1,177,2022	17.0	23.0	21.0		1332	-2.0	0.7	20	dbSNP_126	21	17,8571		0,17,4277	yes	missense	RBPJL	NM_014276.2	110	1,194,6299	AA,AC,CC		0.198,4.0682,1.5091	possibly-damaging	444/518	43945377	196,12792	2200	4294	6494	SO:0001583	missense	11317	exon12			CTGCAGCGACTGG	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.1332C>A	20.37:g.43945377C>A	ENSP00000341243:p.Ser444Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	39	25	0.641026	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	29	0.013278388278388278	22	0.044715447154471545	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	16.39	3.108689	0.56291	0.040682	0.00198	ENSG00000124232	ENST00000372743;ENST00000343694	T;T	0.17054	2.3;2.3	5.48	-2.02	0.07388	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.121014	0.56097	D	0.000034	T	0.02727	0.0082	L	0.42245	1.32	0.37489	D	0.916303	D	0.57257	0.979	P	0.48189	0.57	T	0.35101	-0.9802	10	0.19147	T	0.46	-19.8204	5.1298	0.14903	0.2229:0.4288:0.0:0.3483	rs35220957;rs59797878	444	Q9UBG7	RBPJL_HUMAN	R	443;444	ENSP00000361828:S443R;ENSP00000341243:S444R	ENSP00000341243:S444R	S	+	3	2	RBPJL	43378791	0.191000	0.23288	0.652000	0.29579	0.983000	0.72400	-0.568000	0.05909	-0.198000	0.10333	0.549000	0.68633	AGC	C|0.988;A|0.012	0.012	strong		0.701	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
ZNF213	7760	hgsc.bcm.edu	37	16	3190767	3190767	+	Missense_Mutation	SNP	G	G	A	rs143851164		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3190767G>A	ENST00000396878.3	+	6	1274	c.799G>A	c.(799-801)Gac>Aac	p.D267N	ZNF213_ENST00000574902.1_Missense_Mutation_p.D267N|ZNF213_ENST00000416391.2_Missense_Mutation_p.D109N|ZNF213_ENST00000576416.1_Missense_Mutation_p.D267N	NM_001134655.1|NM_004220.2	NP_001128127.1|NP_004211.1	O14771	ZN213_HUMAN	zinc finger protein 213	267	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	16						GACAGGCAGCGACGTGACTGT	0.692																																					p.D267N		Atlas-SNP	.											.	ZNF213	36	.	0			c.G799A						PASS	.	G	ASN/ASP,ASN/ASP	1,4387		0,1,2193	34.0	38.0	37.0		799,799	-0.4	0.0	16	dbSNP_134	37	0,8598		0,0,4299	no	missense,missense	ZNF213	NM_001134655.1,NM_004220.2	23,23	0,1,6492	AA,AG,GG		0.0,0.0228,0.0077	benign,benign	267/460,267/460	3190767	1,12985	2194	4299	6493	SO:0001583	missense	7760	exon6			GGCAGCGACGTGA	AF017433	CCDS10495.1	16p13.3	2014-05-13	2007-02-20	2007-02-20	ENSG00000085644	ENSG00000085644		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13005	protein-coding gene	gene with protein product		608387				9653642, 10023065	Standard	NM_004220		Approved	CR53, ZKSCAN21, ZSCAN53	uc010uws.2	O14771	OTTHUMG00000177519	ENST00000396878.3:c.799G>A	16.37:g.3190767G>A	ENSP00000380087:p.Asp267Asn	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	33	20	0.606061	NM_004220	A8K1B9|B4DMG6|Q96IS1	Missense_Mutation	SNP	ENST00000396878.3	37	CCDS10495.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.409959	0.25465	2.28E-4	0.0	ENSG00000085644	ENST00000396878;ENST00000416391	T;T	0.05319	3.46;3.46	4.23	-0.444	0.12245	Krueppel-associated box (1);	1.158390	0.06689	N	0.769413	T	0.03348	0.0097	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.10450	0.005	T	0.44907	-0.9297	10	0.52906	T	0.07	.	3.1334	0.06431	0.099:0.3134:0.4223:0.1652	.	267	O14771	ZN213_HUMAN	N	267;109	ENSP00000380087:D267N;ENSP00000403892:D109N	ENSP00000380087:D267N	D	+	1	0	ZNF213	3130768	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-0.566000	0.05922	-0.371000	0.08004	-1.048000	0.02349	GAC	G|1.000;A|0.000	0.000	weak		0.692	ZNF213-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437334.1	NM_004220	
C5orf55	116349	hgsc.bcm.edu	37	5	442675	442675	+	Missense_Mutation	SNP	C	C	T	rs139173233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:442675C>T	ENST00000408966.2	-	1	583	c.263G>A	c.(262-264)gGc>gAc	p.G88D	EXOC3_ENST00000512944.1_5'Flank	NM_138464.2	NP_612473.1	Q8N2X6	CE055_HUMAN	chromosome 5 open reading frame 55	88						extracellular region (GO:0005576)				large_intestine(1)|lung(2)	3						CATCCGGTGGCCACCCATCCC	0.642													C|||	210	0.0419329	0.059	0.0764	5008	,	,		16381	0.0198		0.0219	False		,,,				2504	0.0378				p.G88D		Atlas-SNP	.											.	C5orf55	11	.	0			c.G263A						PASS	.	C	ASP/GLY	173,3641		6,161,1740	75.0	82.0	80.0		263	0.9	0.0	5	dbSNP_134	80	188,8056		1,186,3935	yes	missense	C5orf55	NM_138464.2	94	7,347,5675	TT,TC,CC		2.2804,4.5359,2.9939	probably-damaging	88/120	442675	361,11697	1907	4122	6029	SO:0001583	missense	116349	exon1			CGGTGGCCACCCA	BC014011	CCDS43298.1	5p15.33	2012-02-24			ENSG00000221990	ENSG00000221990			25175	protein-coding gene	gene with protein product						12477932	Standard	NM_138464		Approved		uc010ita.3	Q8N2X6	OTTHUMG00000162235	ENST00000408966.2:c.263G>A	5.37:g.442675C>T	ENSP00000386139:p.Gly88Asp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	47	29	0.617021	NM_138464	Q96CR9	Missense_Mutation	SNP	ENST00000408966.2	37	CCDS43298.1	82	0.037545787545787544	28	0.056910569105691054	26	0.0718232044198895	13	0.022727272727272728	15	0.01978891820580475	C	7.570	0.666493	0.14710	0.045359	0.022804	ENSG00000221990	ENST00000408966	T	0.46819	0.86	0.849	0.849	0.18972	.	.	.	.	.	T	0.02193	0.0068	N	0.08118	0	0.09310	N	1	D	0.55172	0.97	P	0.46275	0.51	T	0.02966	-1.1088	9	0.87932	D	0	.	4.9993	0.14257	0.0:1.0:0.0:0.0	.	88	Q8N2X6	CE055_HUMAN	D	88	ENSP00000386139:G88D	ENSP00000386139:G88D	G	-	2	0	C5orf55	495675	0.001000	0.12720	0.001000	0.08648	0.053000	0.15095	0.039000	0.13884	0.745000	0.32763	0.205000	0.17691	GGC	C|0.966;T|0.034	0.034	strong		0.642	C5orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368033.1	NM_138464	
BCL9L	283149	hgsc.bcm.edu	37	11	118773204	118773204	+	Silent	SNP	G	G	A	rs7119065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118773204G>A	ENST00000334801.3	-	6	2212	c.1248C>T	c.(1246-1248)gaC>gaT	p.D416D	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	416	Necessary for interaction with CTNNB1. {ECO:0000250}.|Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GTCGCTCAATGTCTCGCAGCG	0.682													G|||	294	0.0587061	0.2156	0.0101	5008	,	,		12409	0.0		0.002	False		,,,				2504	0.0				p.D416D		Atlas-SNP	.											BCL9L_ENST00000392849,right_upper_lobe,carcinoma,-1,2	BCL9L	254	2	0			c.C1248T						PASS	.	G		615,3783		41,533,1625	27.0	30.0	29.0		1248	3.6	1.0	11	dbSNP_116	29	11,8575		0,11,4282	no	coding-synonymous	BCL9L	NM_182557.2		41,544,5907	AA,AG,GG		0.1281,13.9836,4.8213		416/1500	118773204	626,12358	2199	4293	6492	SO:0001819	synonymous_variant	283149	exon6			CTCAATGTCTCGC	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.1248C>T	11.37:g.118773204G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	30	19	0.633333	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																			G|0.949;A|0.051	0.051	strong		0.682	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
GZF1	64412	hgsc.bcm.edu	37	20	23350790	23350790	+	Silent	SNP	C	C	T	rs10485644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	184	0	0		WXS	Illumina HiSeq	Phase_I	201	100	0.497512	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	
LRP2	4036	hgsc.bcm.edu	37	2	170097707	170097707	+	Missense_Mutation	SNP	T	T	G	rs17848149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170097707T>G	ENST00000263816.3	-	25	4121	c.3836A>C	c.(3835-3837)gAc>gCc	p.D1279A	LRP2_ENST00000443831.1_Missense_Mutation_p.D1142A	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1279	LDL-receptor class A 14. {ECO:0000255|PROSITE-ProRule:PRU00124}.		D -> A (in dbSNP:rs17848149).		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)"""	GTTTCCGTTGTCACAGTGGAA	0.517													T|||	212	0.0423323	0.0764	0.0086	5008	,	,		22653	0.0208		0.0288	False		,,,				2504	0.0562				p.D1279A		Atlas-SNP	.											.	LRP2	751	.	0			c.A3836C						PASS	.	T	ALA/ASP	363,4043	186.7+/-213.5	8,347,1848	167.0	136.0	147.0		3836	0.7	0.8	2	dbSNP_123	147	156,8444	75.1+/-137.7	2,152,4146	yes	missense	LRP2	NM_004525.2	126	10,499,5994	GG,GT,TT		1.814,8.2388,3.9905	possibly-damaging	1279/4656	170097707	519,12487	2203	4300	6503	SO:0001583	missense	4036	exon25			CCGTTGTCACAGT		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.3836A>C	2.37:g.170097707T>G	ENSP00000263816:p.Asp1279Ala	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	160	63	0.39375	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	73	0.033424908424908424	34	0.06910569105691057	4	0.011049723756906077	13	0.022727272727272728	22	0.029023746701846966	T	7.435	0.639498	0.14386	0.082388	0.01814	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.95069	-3.6;-3.6	5.85	0.7	0.18099	.	0.140595	0.64402	N	0.000007	T	0.27731	0.0682	N	0.04805	-0.155	0.48341	D	0.999631	B;B	0.25105	0.039;0.118	B;B	0.33690	0.168;0.133	T	0.54050	-0.8351	10	0.09084	T	0.74	.	6.4511	0.21903	0.0:0.1926:0.1207:0.6868	rs17848149;rs17848149	1142;1279	E9PC35;P98164	.;LRP2_HUMAN	A	1279;1142	ENSP00000263816:D1279A;ENSP00000409813:D1142A	ENSP00000263816:D1279A	D	-	2	0	LRP2	169805953	1.000000	0.71417	0.768000	0.31515	0.035000	0.12851	2.866000	0.48420	-0.099000	0.12263	-0.256000	0.11100	GAC	T|0.963;G|0.037	0.037	strong		0.517	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
SSPO	23145	hgsc.bcm.edu	37	7	149481205	149481205	+	RNA	SNP	T	T	C	rs73727609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149481205T>C	ENST00000378016.2	+	0	2687							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)			AGTGCCACCATGAAGGAGTGC	0.652													T|||	76	0.0151757	0.056	0.0029	5008	,	,		17147	0.0		0.0	False		,,,				2504	0.0				p.M896T		Atlas-SNP	.											.	.	.	.	0			c.T2687C						PASS	.	T		157,3863		1,155,1854	14.0	18.0	17.0		2689	1.3	0.0	7	dbSNP_130	17	2,8280		0,2,4139	yes	coding-notMod3	SSPO	NM_198455.2		1,157,5993	CC,CT,TT		0.0241,3.9055,1.2925			149481205	159,12143	2010	4141	6151			23145	exon18			CCACCATGAAGGA	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.149481205T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.986;C|0.014	0.014	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
USP11	8237	hgsc.bcm.edu	37	X	47107038	47107038	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47107038C>T	ENST00000218348.3	+	20	2694	c.2694C>T	c.(2692-2694)agC>agT	p.S898S	USP11_ENST00000377107.2_Silent_p.S855S	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	898	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						ACAAGGACAGCGGCCAGTGGC	0.512																																					p.S898S		Atlas-SNP	.											.	USP11	93	.	0			c.C2694T						PASS	.						156.0	114.0	129.0					X																	47107038		2203	4300	6503	SO:0001819	synonymous_variant	8237	exon20			GGACAGCGGCCAG	U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"""Ubiquitin-specific peptidases"""	12609	protein-coding gene	gene with protein product		300050	"""ubiquitin specific protease 11"""			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.2694C>T	X.37:g.47107038C>T		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	240	111	0.4625	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Silent	SNP	ENST00000218348.3	37	CCDS14277.1																																																																																			.	.	none		0.512	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651	
KRT8	3856	hgsc.bcm.edu	37	12	53298699	53298699	+	Missense_Mutation	SNP	G	G	A	rs201807576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53298699G>A	ENST00000552551.1	-	2	499	c.67C>T	c.(67-69)Cgc>Tgc	p.R23C	KRT8_ENST00000546897.1_Missense_Mutation_p.R23C|KRT8_ENST00000293308.6_Missense_Mutation_p.R23C|KRT8_ENST00000552150.1_Missense_Mutation_p.R51C			P05787	K2C8_HUMAN	keratin 8	23	Head.|Ser-rich.				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)	GTGTAGGAGCGGCTGCTGAAG	0.667																																					p.R51C		Atlas-SNP	.											KRT8,colon,carcinoma,0,2	KRT8	41	2	0			c.C151T						scavenged	.						11.0	13.0	13.0					12																	53298699		1953	3904	5857	SO:0001583	missense	3856	exon2			AGGAGCGGCTGCT	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.67C>T	12.37:g.53298699G>A	ENSP00000447566:p.Arg23Cys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	122	6	0.0491803	NM_001256282	A8K4H3|B0AZN5|F8VXB4|Q14099|Q14716|Q14717|Q53GJ0|Q6DHW5|Q6GMY0|Q6P4C7|Q96J60	Missense_Mutation	SNP	ENST00000552551.1	37	CCDS8841.1	.	.	.	.	.	.	.	.	.	.	-	13.69	2.312705	0.40895	.	.	ENSG00000170421	ENST00000552551;ENST00000293308;ENST00000547916;ENST00000546897;ENST00000552150;ENST00000546826;ENST00000548998;ENST00000547413;ENST00000546542	D;D;D;D;D;D;D;T	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-0.98	4.71	4.71	0.59529	.	0.431059	0.26883	N	0.022003	T	0.75824	0.3902	L	0.33293	1	0.41950	D	0.99065	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.15484	0.013;0.005;0.002	T	0.69450	-0.5142	10	0.27082	T	0.32	.	9.653	0.39908	0.0974:0.0:0.9026:0.0	.	51;23;23	F8VXB4;F8VU64;P05787	.;.;K2C8_HUMAN	C	23;23;23;23;51;23;63;23;101	ENSP00000447566:R23C;ENSP00000293308:R23C;ENSP00000447402:R23C;ENSP00000449404:R51C;ENSP00000447881:R23C;ENSP00000447040:R63C;ENSP00000448681:R23C;ENSP00000450228:R101C	ENSP00000293308:R23C	R	-	1	0	KRT8	51584966	0.070000	0.21116	1.000000	0.80357	0.819000	0.46315	0.097000	0.15168	2.582000	0.87167	0.531000	0.56144	CGC	G|0.944;A|0.055	0.055	strong		0.667	KRT8-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406385.1	NM_002273	
ARL5C	390790	hgsc.bcm.edu	37	17	37316988	37316988	+	Missense_Mutation	SNP	T	T	C	rs16522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37316988T>C	ENST00000269586.7	-	5	346	c.347A>G	c.(346-348)cAg>cGg	p.Q116R	ARL5C_ENST00000444555.1_Missense_Mutation_p.Q116R	NM_001143968.1	NP_001137440.1	A6NH57	ARL5C_HUMAN	ADP-ribosylation factor-like 5C	116					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)										TGAAGCATCCTGTAGAGCCTG	0.557													C|||	698	0.139377	0.0439	0.1124	5008	,	,		21098	0.2609		0.168	False		,,,				2504	0.1329				p.Q116R		Atlas-SNP	.											.	ARL5C	3	.	0			c.A347G						PASS	.	C	ARG/GLN	103,1281		1,101,590	47.0	44.0	45.0		347	-1.9	0.0	17	dbSNP_54	45	459,2723		25,409,1157	yes	missense	ARL5C	NM_001143968.1	43	26,510,1747	CC,CT,TT		14.4249,7.4422,12.3084	benign	116/180	37316988	562,4004	692	1591	2283	SO:0001583	missense	390790	exon5			GCATCCTGTAGAG		CCDS45664.1	17q12	2014-05-09	2005-11-08	2005-11-08	ENSG00000141748	ENSG00000141748		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	31111	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 12"""	ARL12			Standard	NM_001143968		Approved		uc010wea.2	A6NH57		ENST00000269586.7:c.347A>G	17.37:g.37316988T>C	ENSP00000269586:p.Gln116Arg	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_001143968		Missense_Mutation	SNP	ENST00000269586.7	37	CCDS45664.1	340	0.15567765567765568	28	0.056910569105691054	48	0.13259668508287292	137	0.2395104895104895	127	0.16754617414248021	C	0.038	-1.296182	0.01364	0.074422	0.144249	ENSG00000141748	ENST00000444555;ENST00000269586	T;T	0.61980	0.06;0.06	3.81	-1.94	0.07571	Small GTP-binding protein domain (1);	0.515982	0.18278	N	0.146105	T	0.00012	0.0000	N	0.04018	-0.295	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.07868	-1.0750	9	0.02654	T	1	-0.2891	5.5222	0.16939	0.1521:0.2667:0.0:0.5812	rs16522;rs60715918;rs16522	116	A6NH57	ARL5C_HUMAN	R	116	ENSP00000387615:Q116R;ENSP00000269586:Q116R	ENSP00000269586:Q116R	Q	-	2	0	ARL5C	34570514	0.003000	0.15002	0.000000	0.03702	0.036000	0.12997	-0.024000	0.12435	-0.826000	0.04284	-0.119000	0.15052	CAG	A|0.012;C|0.144	0.144	strong		0.557	ARL5C-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444566.1	NM_001143968	
GPR112	139378	hgsc.bcm.edu	37	X	135430044	135430044	+	Silent	SNP	T	T	C	rs877761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:135430044T>C	ENST00000394143.1	+	6	4470	c.4179T>C	c.(4177-4179)acT>acC	p.T1393T	GPR112_ENST00000370652.1_Silent_p.T1393T|GPR112_ENST00000412101.1_Silent_p.T1188T|GPR112_ENST00000287534.4_Silent_p.T1330T|GPR112_ENST00000394141.1_Silent_p.T1188T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1393					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CTCCCAGGACTGTGGAAATGA	0.448													c|||	2014	0.53351	0.5983	0.3847	3775	,	,		16408	0.255		0.3817	False		,,,				2504	0.3221				p.T1393T		Atlas-SNP	.											.	GPR112	459	.	0			c.T4179C						PASS	.			2878,957		910,628,430,94,141	170.0	160.0	163.0		4179	-1.4	0.0	X	dbSNP_86	163	3231,3497		571,1175,914,682,958	no	coding-synonymous	GPR112	NM_153834.3		1481,1803,1344,776,1099	CC,CT,C,TT,T		48.0232,24.9544,42.1661		1393/3081	135430044	6109,4454	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			CAGGACTGTGGAA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4179T>C	X.37:g.135430044T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	178	108	0.606742	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			T|0.432;0|0.003	.	strong		0.448	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
DSEL	92126	hgsc.bcm.edu	37	18	65180706	65180706	+	Silent	SNP	T	T	C	rs9959648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:65180706T>C	ENST00000310045.7	-	2	2643	c.1170A>G	c.(1168-1170)caA>caG	p.Q390Q	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	380					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				TACTCCACCTTTGGGCAGTTG	0.443													T|||	189	0.0377396	0.1362	0.013	5008	,	,		18891	0.0		0.0	False		,,,				2504	0.0				p.Q390Q		Atlas-SNP	.											.	DSEL	196	.	0			c.A1170G						PASS	.	T		566,3840	252.7+/-259.0	39,488,1676	117.0	104.0	108.0		1170	0.4	1.0	18	dbSNP_119	108	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	DSEL	NM_032160.2		39,491,5973	CC,CT,TT		0.0349,12.8461,4.3749		390/1223	65180706	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	92126	exon2			CCACCTTTGGGCA	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.1170A>G	18.37:g.65180706T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_032160	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	37	CCDS11995.1																																																																																			T|0.949;C|0.051	0.051	strong		0.443	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
FASTKD1	79675	hgsc.bcm.edu	37	2	170413700	170413700	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170413700T>C	ENST00000453153.2	-	6	1425	c.1079A>G	c.(1078-1080)aAa>aGa	p.K360R	FASTKD1_ENST00000453929.2_Missense_Mutation_p.K360R	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	360					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						AAGATACCTTTTAATCAGACA	0.378																																					p.K360R		Atlas-SNP	.											.	FASTKD1	86	.	0			c.A1079G						PASS	.						140.0	133.0	135.0					2																	170413700		2203	4300	6503	SO:0001583	missense	79675	exon6			TACCTTTTAATCA	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.1079A>G	2.37:g.170413700T>C	ENSP00000400513:p.Lys360Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	37	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.486556	0.44249	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.18810	2.19;2.19	5.02	5.02	0.67125	.	0.200255	0.52532	D	0.000064	T	0.25901	0.0631	M	0.74881	2.28	0.33094	D	0.538328	P;B	0.48350	0.909;0.053	B;B	0.43623	0.425;0.039	T	0.42396	-0.9454	10	0.25751	T	0.34	.	10.0946	0.42466	0.0:0.0:0.1684:0.8316	.	360;360	Q53R41-2;Q53R41	.;FAKD1_HUMAN	R	360	ENSP00000400513:K360R;ENSP00000403229:K360R	ENSP00000400513:K360R	K	-	2	0	FASTKD1	170121946	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	3.291000	0.51764	2.006000	0.58801	0.533000	0.62120	AAA	.	.	none		0.378	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
OR52B6	340980	hgsc.bcm.edu	37	11	5602275	5602275	+	Missense_Mutation	SNP	A	A	G	rs1077126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5602275A>G	ENST00000345043.2	+	1	169	c.169A>G	c.(169-171)Act>Gct	p.T57A	HBG2_ENST00000380259.2_Intron|AC015691.13_ENST00000394793.2_RNA	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	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	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	237	237	1	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	
PCF11	51585	hgsc.bcm.edu	37	11	82875359	82875359	+	Silent	SNP	G	G	A	rs7130527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:82875359G>A	ENST00000298281.4	+	4	1070	c.618G>A	c.(616-618)caG>caA	p.Q206Q		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	206					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|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 factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TAATAAGGCAGCAGTTACTGG	0.428													A|||	519	0.103634	0.1641	0.0663	5008	,	,		15411	0.0496		0.0805	False		,,,				2504	0.1278				p.Q206Q		Atlas-SNP	.											.	PCF11	220	.	0			c.G618A						PASS	.	A		547,3157		44,459,1349	58.0	52.0	54.0		618	-2.9	1.0	11	dbSNP_116	54	702,7482		27,648,3417	no	coding-synonymous	PCF11	NM_015885.3		71,1107,4766	AA,AG,GG		8.5777,14.7678,10.5064		206/1556	82875359	1249,10639	1852	4092	5944	SO:0001819	synonymous_variant	51585	exon4			AAGGCAGCAGTTA	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.618G>A	11.37:g.82875359G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	37	CCDS44689.1																																																																																			G|0.905;A|0.095	0.095	strong		0.428	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
ITGA2	3673	hgsc.bcm.edu	37	5	52369086	52369086	+	Silent	SNP	G	G	A	rs3213805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	215	0	0		WXS	Illumina HiSeq	Phase_I	202	94	0.465347	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	
PIEZO1	9780	hgsc.bcm.edu	37	16	88779739	88779739	+	IGR	SNP	A	A	G	rs11549837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88779739A>G	ENST00000301015.9	-	0	8072				CTU2_ENST00000378384.3_Missense_Mutation_p.M166V|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000453996.2_Missense_Mutation_p.M253V|CTU2_ENST00000312060.5_Missense_Mutation_p.M253V|CTU2_ENST00000567949.1_Missense_Mutation_p.M324V	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						GATCCTCCACATGGCCCGAGC	0.652													A|||	2267	0.452676	0.4372	0.4308	5008	,	,		12324	0.6637		0.3439	False		,,,				2504	0.3834				p.M253V		Atlas-SNP	.											.	CTU2	66	.	0			c.A757G						PASS	.	A	VAL/MET,VAL/MET	1823,2551	528.6+/-372.4	375,1073,739	55.0	56.0	55.0		757,757	1.5	1.0	16	dbSNP_120	55	2924,5664	454.5+/-363.5	500,1924,1870	yes	missense,missense	CTU2	NM_001012759.1,NM_001012762.1	21,21	875,2997,2609	GG,GA,AA		34.0475,41.6781,36.6224	benign,benign	253/516,253/486	88779739	4747,8215	2187	4294	6481	SO:0001628	intergenic_variant	348180	exon8			CTCCACATGGCCC	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.88779739A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	988	0.4523809523809524	189	0.38414634146341464	145	0.4005524861878453	375	0.6555944055944056	279	0.36807387862796836	A	0.119	-1.128461	0.01756	0.416781	0.340475	ENSG00000174177	ENST00000378384;ENST00000312060;ENST00000453996	T;T;T	0.14766	2.48;2.48;2.48	5.04	1.54	0.23209	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.534670	0.19256	N	0.118787	T	0.00012	0.0000	N	0.00101	-2.135	0.46927	P	7.420000000000204E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.27157	-1.0082	9	0.09843	T	0.71	.	4.674	0.12703	0.2557:0.0:0.5924:0.1518	rs11549837;rs59473378	166;253;253	Q2VPK5-3;Q2VPK5-5;Q2VPK5	.;.;CTU2_HUMAN	V	166;253;253	ENSP00000367635:M166V;ENSP00000308617:M253V;ENSP00000388320:M253V	ENSP00000308617:M253V	M	+	1	0	CTU2	87307240	0.000000	0.05858	0.986000	0.45419	0.760000	0.43138	0.845000	0.27668	0.492000	0.27815	-0.177000	0.13119	ATG	A|0.607;G|0.393	0.393	strong		0.652	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
VWF	7450	hgsc.bcm.edu	37	12	6103072	6103072	+	Missense_Mutation	SNP	C	C	T	rs2229446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6103072C>T	ENST00000261405.5	-	37	6808	c.6554G>A	c.(6553-6555)cGg>cAg	p.R2185Q		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2185			R -> Q (in dbSNP:rs2229446).		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CCCGTTGGTCCGACAGAGGTG	0.552													C|||	342	0.0682907	0.2428	0.0245	5008	,	,		17441	0.0		0.002	False		,,,				2504	0.002				p.R2185Q		Atlas-SNP	.											VWF,rectum,carcinoma,-1,1	VWF	338	1	0			c.G6554A	GRCh37	CM070322	VWF	M	rs76342212	PASS	.	C	GLN/ARG	877,3529	337.0+/-304.7	89,699,1415	71.0	60.0	63.0		6554	5.3	1.0	12	dbSNP_131	63	13,8587	8.4+/-32.0	0,13,4287	yes	missense	VWF	NM_000552.3	43	89,712,5702	TT,TC,CC		0.1512,19.9047,6.843	probably-damaging	2185/2814	6103072	890,12116	2203	4300	6503	SO:0001583	missense	7450	exon37			TTGGTCCGACAGA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.6554G>A	12.37:g.6103072C>T	ENSP00000261405:p.Arg2185Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	110	0.05036630036630037	102	0.2073170731707317	8	0.022099447513812154	0	0.0	0	0.0	C	22.3	4.275153	0.80580	0.199047	0.001512	ENSG00000110799	ENST00000261405	T	0.75367	-0.93	5.3	5.3	0.74995	Uncharacterised domain, cysteine-rich (2);	0.000000	0.40385	N	0.001115	T	0.00241	0.0007	L	0.43646	1.37	0.09310	P	1.0	D	0.89917	1.0	D	0.87578	0.998	T	0.01405	-1.1363	9	0.51188	T	0.08	.	17.9818	0.89144	0.0:1.0:0.0:0.0	rs2229446;rs11537643;rs52798162;rs11537643	2185	P04275	VWF_HUMAN	Q	2185	ENSP00000261405:R2185Q	ENSP00000261405:R2185Q	R	-	2	0	VWF	5973333	0.998000	0.40836	0.994000	0.49952	0.987000	0.75469	3.949000	0.56668	2.482000	0.83794	0.655000	0.94253	CGG	C|0.939;T|0.061	0.061	strong		0.552	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
TNFAIP3	7128	hgsc.bcm.edu	37	6	138196066	138196066	+	Missense_Mutation	SNP	T	T	G	rs2230926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138196066T>G	ENST00000237289.4	+	3	446	c.380T>G	c.(379-381)tTc>tGc	p.F127C		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	127	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.		F -> C (in dbSNP:rs2230926). {ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|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 interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.L126fs*87(1)|p.W113_F140del(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		AAGGCGCTGTTCAGCACGCTC	0.498			"""D, N, F"""		"""marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"""								T|||	699	0.139577	0.4092	0.0778	5008	,	,		19066	0.0506		0.0239	False		,,,				2504	0.0297				p.F127C	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		Rec	yes		6	6q23	7128	"""tumor necrosis factor, alpha-induced protein 3"""		L	TNFAIP3,eye,lymphoid_neoplasm,0,1	TNFAIP3	340	1	27	Whole gene deletion(25)|Deletion - In frame(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(27)	c.T380G	GRCh37	CM083789	TNFAIP3	M	rs2230926	PASS	.	T	CYS/PHE	1570,2836	491.8+/-362.2	290,990,923	120.0	109.0	112.0	http://omim.org/entry/612378|http://www.ncbi.nlm.nih.gov/pubmed?term	380	-0.1	0.9	6	dbSNP_98	112	276,8324	103.6+/-164.7	10,256,4034	yes	missense	TNFAIP3	NM_006290.2	205	300,1246,4957	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	3.2093,35.6332,14.1934	benign	127/791	138196066	1846,11160	2203	4300	6503	SO:0001583	missense	7128	exon3			CGCTGTTCAGCAC	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"""OTU domain containing"""	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.380T>G	6.37:g.138196066T>G	ENSP00000237289:p.Phe127Cys	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	180	94	0.522222	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	37	CCDS5187.1	270	0.12362637362637363	185	0.37601626016260165	27	0.07458563535911603	41	0.07167832167832168	17	0.022427440633245383	T	12.83	2.055887	0.36277	0.356332	0.032093	ENSG00000118503	ENST00000420009;ENST00000237289;ENST00000535574;ENST00000535332;ENST00000539356;ENST00000544646;ENST00000536070	T;T	0.30714	1.52;1.52	5.97	-0.0566	0.13805	Ovarian tumour, otubain (2);	0.318945	0.38897	N	0.001540	T	0.06554	0.0168	L	0.31926	0.97	0.29434	P	0.85964	B	0.13594	0.008	B	0.17722	0.019	T	0.23154	-1.0196	9	0.32370	T	0.25	-4.7828	3.4675	0.07555	0.2368:0.0676:0.1098:0.5858	rs2230926;rs5029942;rs52802446;rs61407535;rs2230926	127	P21580	TNAP3_HUMAN	C	127	ENSP00000401562:F127C;ENSP00000237289:F127C	ENSP00000237289:F127C	F	+	2	0	TNFAIP3	138237759	1.000000	0.71417	0.922000	0.36590	0.934000	0.57294	1.341000	0.33907	0.125000	0.18397	0.533000	0.62120	TTC	T|0.857;G|0.143	0.143	strong		0.498	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1		
CCDC168	643677	hgsc.bcm.edu	37	13	103383417	103383417	+	Missense_Mutation	SNP	T	T	C	rs9554897	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103383417T>C	ENST00000322527.2	-	1	5742	c.5743A>G	c.(5743-5745)Aaa>Gaa	p.K1915E		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1915			K -> E (in dbSNP:rs9554897). {ECO:0000269|PubMed:14702039}.														CCTTTTTCTTTTACTGAGTGG	0.388													T|||	1690	0.33746	0.3608	0.3545	5008	,	,		21052	0.1587		0.3877	False		,,,				2504	0.4264				p.K6544E		Atlas-SNP	.											.	.	.	.	0			c.A19630G						PASS	.	T	GLU/LYS	493,891		94,305,293	133.0	115.0	120.0		19630	-6.2	0.0	13	dbSNP_119	120	1269,1913		256,757,578	yes	missense	CCDC168	NM_001146197.1	56	350,1062,871	CC,CT,TT		39.8806,35.6214,38.5896	benign	6544/7082	103383417	1762,2804	692	1591	2283	SO:0001583	missense	643677	exon4			TTTCTTTTACTGA		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.5743A>G	13.37:g.103383417T>C	ENSP00000320232:p.Lys1915Glu	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	237	130	0.548523	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		699	0.32005494505494503	170	0.34552845528455284	141	0.38950276243093923	99	0.17307692307692307	289	0.3812664907651715	T	0.724	-0.782461	0.02907	0.356214	0.398806	ENSG00000175820	ENST00000322527	T	0.03242	4.0	5.53	-6.17	0.02091	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.15473	0.013	B	0.16722	0.016	T	0.43909	-0.9362	8	0.06365	T	0.9	.	9.4401	0.38664	0.0:0.271:0.1014:0.6276	rs9554897;rs17592424;rs52805221;rs58718993;rs9554897	1915	Q8NDH2	CC168_HUMAN	E	1915	ENSP00000320232:K1915E	ENSP00000320232:K1915E	K	-	1	0	CCDC168	102181418	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.003000	0.03682	-1.216000	0.02607	-0.250000	0.11733	AAA	C|0.312;N|0.000	0.312	strong		0.388	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
PCDH12	51294	hgsc.bcm.edu	37	5	141336858	141336858	+	Missense_Mutation	SNP	C	C	T	rs140883612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141336858C>T	ENST00000231484.3	-	1	1769	c.559G>A	c.(559-561)Ggc>Agc	p.G187S	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	187	Cadherin 2. {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)			TCATCAGGGCCCACAATGACA	0.507													C|||	42	0.00838658	0.0303	0.0029	5008	,	,		19922	0.0		0.0	False		,,,				2504	0.0				p.G187S		Atlas-SNP	.											.	PCDH12	133	.	0			c.G559A						PASS	.	C	SER/GLY	104,4302	81.4+/-119.9	0,104,2099	102.0	111.0	108.0		559	5.0	1.0	5	dbSNP_134	108	0,8600		0,0,4300	yes	missense	PCDH12	NM_016580.2	56	0,104,6399	TT,TC,CC		0.0,2.3604,0.7996	probably-damaging	187/1185	141336858	104,12902	2203	4300	6503	SO:0001583	missense	51294	exon1			CAGGGCCCACAAT	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.559G>A	5.37:g.141336858C>T	ENSP00000231484:p.Gly187Ser	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	225	106	0.471111	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	10.27	1.304137	0.23736	0.023604	0.0	ENSG00000113555	ENST00000231484	T	0.19669	2.13	4.98	4.98	0.66077	Cadherin (4);Cadherin-like (1);	0.127172	0.52532	D	0.000076	T	0.10294	0.0252	L	0.39898	1.24	0.35472	D	0.797432	D	0.62365	0.991	P	0.60541	0.876	T	0.06058	-1.0848	10	0.13108	T	0.6	.	9.2129	0.37328	0.0:0.9043:0.0:0.0957	.	187	Q9NPG4	PCD12_HUMAN	S	187	ENSP00000231484:G187S	ENSP00000231484:G187S	G	-	1	0	PCDH12	141317042	0.001000	0.12720	1.000000	0.80357	0.554000	0.35429	0.429000	0.21412	2.605000	0.88082	0.655000	0.94253	GGC	C|0.991;T|0.009	0.009	strong		0.507	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
OBSCN	84033	hgsc.bcm.edu	37	1	228486404	228486404	+	Intron	SNP	C	C	T	rs56021350	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228486404C>T	ENST00000422127.1	+	43	11703				OBSCN_ENST00000359599.6_3'UTR|OBSCN_ENST00000284548.11_Intron|OBSCN_ENST00000570156.2_Missense_Mutation_p.T4399M|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000366707.4_Missense_Mutation_p.T1089M	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)				ACCTCGGCCACGCTCACTGTC	0.547													C|||	831	0.165935	0.1982	0.2378	5008	,	,		21966	0.1518		0.1581	False		,,,				2504	0.0941				p.T4399M		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	0			c.C13196T						PASS	.	C	,	402,1350		37,328,511	99.0	84.0	89.0		,	-4.7	0.0	1	dbSNP_129	89	712,3270		62,588,1341	no	intron,intron	OBSCN	NM_001098623.1,NM_052843.2	,	99,916,1852	TT,TC,CC		17.8805,22.9452,19.428	,	,	228486404	1114,4620	876	1991	2867	SO:0001627	intron_variant	84033	exon49			CGGCCACGCTCAC	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.11659+3660C>T	1.37:g.228486404C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	33	12	0.363636	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	380	0.17399267399267399	86	0.17479674796747968	85	0.23480662983425415	87	0.1520979020979021	122	0.16094986807387862	C	8.711	0.911956	0.17907	0.229452	0.178805	ENSG00000154358	ENST00000366707	T	0.68903	-0.36	4.68	-4.67	0.03319	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.24119	-1.0169	5	0.33940	T	0.23	.	12.6558	0.56786	0.0:0.3898:0.0:0.6102	rs56021350;rs61825284	.	.	.	M	1089	ENSP00000355668:T1089M	ENSP00000355668:T1089M	T	+	2	0	OBSCN	226553027	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.459000	0.01000	-1.387000	0.02095	-0.254000	0.11334	ACG	C|0.825;T|0.175	0.175	strong		0.547	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MDH2	4191	hgsc.bcm.edu	37	7	75677504	75677504	+	Missense_Mutation	SNP	C	C	T	rs6720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75677504C>T	ENST00000315758.5	+	1	120	c.26C>T	c.(25-27)gCc>gTc	p.A9V	STYXL1_ENST00000248600.1_5'Flank|STYXL1_ENST00000360591.3_5'Flank|STYXL1_ENST00000451157.1_5'Flank|STYXL1_ENST00000431581.1_5'Flank|STYXL1_ENST00000460184.2_5'Flank|STYXL1_ENST00000359697.3_5'Flank|MDH2_ENST00000490105.1_3'UTR|MDH2_ENST00000461263.2_Missense_Mutation_p.A9V|MDH2_ENST00000443006.1_5'UTR|MDH2_ENST00000432020.2_Missense_Mutation_p.A9V|STYXL1_ENST00000340062.5_5'Flank	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	9			A -> V (in dbSNP:rs17849553). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|internal protein amino acid acetylation (GO:0006475)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	L-malate dehydrogenase activity (GO:0030060)|malate dehydrogenase (NADP+) activity (GO:0046554)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(2)	14						GCCCGGCCTGCCAGCGCTGCT	0.741													c|||	2615	0.522165	0.7073	0.4164	5008	,	,		14327	0.6071		0.327	False		,,,				2504	0.4601				p.A9V		Atlas-SNP	.											MDH2,NS,carcinoma,0,1	MDH2	35	1	0			c.C26T						PASS	.	C	VAL/ALA	2410,1644		759,892,376	9.0	7.0	8.0		26	0.6	0.0	7	dbSNP_123	8	2255,5607		413,1429,2089	no	missense	MDH2	NM_005918.2	64	1172,2321,2465	TT,TC,CC		28.6823,40.5525,39.149	benign	9/339	75677504	4665,7251	2027	3931	5958	SO:0001583	missense	4191	exon1			GGCCTGCCAGCGC		CCDS5581.1, CCDS64691.1, CCDS75622.1	7q11.23	2013-09-20			ENSG00000146701	ENSG00000146701	1.1.1.37		6971	protein-coding gene	gene with protein product		154100					Standard	NM_005918		Approved		uc003ueo.3	P40926	OTTHUMG00000023827	ENST00000315758.5:c.26C>T	7.37:g.75677504C>T	ENSP00000327070:p.Ala9Val	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	24	16	0.666667	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Missense_Mutation	SNP	ENST00000315758.5	37	CCDS5581.1	1104	0.5054945054945055	353	0.717479674796748	147	0.40607734806629836	356	0.6223776223776224	248	0.32717678100263853	C	15.67	2.903178	0.52333	0.594475	0.286823	ENSG00000146701	ENST00000315758;ENST00000432020	T;T	0.41758	0.99;0.99	5.57	0.558	0.17266	.	0.307415	0.35262	N	0.003322	T	0.00012	0.0000	L	0.33624	1.015	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34054	-0.9844	9	0.25751	T	0.34	-8.1463	9.0275	0.36239	0.0:0.6206:0.0:0.3794	rs6720	9;9	E9PDB2;P40926	.;MDHM_HUMAN	V	9	ENSP00000327070:A9V;ENSP00000408649:A9V	ENSP00000327070:A9V	A	+	2	0	MDH2	75515440	0.001000	0.12720	0.004000	0.12327	0.754000	0.42855	0.356000	0.20181	0.047000	0.15862	0.650000	0.86243	GCC	C|0.494;T|0.506	0.506	strong		0.741	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1		
DNHD1	144132	hgsc.bcm.edu	37	11	6524072	6524072	+	Missense_Mutation	SNP	A	A	C	rs11605196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6524072A>C	ENST00000527990.2	+	2	836	c.836A>C	c.(835-837)cAg>cCg	p.Q279P	DNHD1_ENST00000254579.6_Missense_Mutation_p.Q279P|DNHD1_ENST00000354685.3_Missense_Mutation_p.Q279P			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	279			Q -> P (in dbSNP:rs11605196).		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)		CTGGATAGCCAGGTGATGACT	0.502													A|||	499	0.0996406	0.0408	0.147	5008	,	,		20522	0.0169		0.1789	False		,,,				2504	0.1493				p.Q279P		Atlas-SNP	.											.	DNHD1	198	.	0			c.A836C						PASS	.	A	PRO/GLN,PRO/GLN	277,4125	155.2+/-188.4	10,257,1934	122.0	102.0	109.0		836,836	4.5	0.0	11	dbSNP_120	109	1636,6956	302.2+/-305.8	165,1306,2825	yes	missense,missense	DNHD1	NM_144666.2,NM_173589.3	76,76	175,1563,4759	CC,CA,AA		19.041,6.2926,14.7222	benign,benign	279/4754,279/598	6524072	1913,11081	2201	4296	6497	SO:0001583	missense	144132	exon3			ATAGCCAGGTGAT	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.836A>C	11.37:g.6524072A>C	ENSP00000436180:p.Gln279Pro	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	99	38	0.383838	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	224	0.10256410256410256	26	0.052845528455284556	46	0.1270718232044199	11	0.019230769230769232	141	0.18601583113456466	A	11.40	1.627054	0.28978	0.062926	0.19041	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.27890	1.64;2.65;1.64	5.64	4.52	0.55395	.	0.540708	0.18166	N	0.149607	T	0.00039	0.0001	L	0.40543	1.245	0.80722	P	0.0	P;B	0.44578	0.838;0.004	B;B	0.41813	0.367;0.004	T	0.18178	-1.0345	9	0.28530	T	0.3	.	8.2343	0.31616	0.9095:0.0:0.0905:0.0	rs11605196;rs52824639;rs11605196	279;279	Q96M86;Q96M86-4	DNHD1_HUMAN;.	P	279	ENSP00000254579:Q279P;ENSP00000346716:Q279P;ENSP00000436180:Q279P	ENSP00000254579:Q279P	Q	+	2	0	DNHD1	6480648	0.000000	0.05858	0.019000	0.16419	0.032000	0.12392	0.115000	0.15540	0.971000	0.38288	0.460000	0.39030	CAG	A|0.862;C|0.138	0.138	strong		0.502	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
CBLC	23624	hgsc.bcm.edu	37	19	45285734	45285734	+	Silent	SNP	G	G	A	rs10416628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45285734G>A	ENST00000270279.3	+	4	828	c.765G>A	c.(763-765)agG>agA	p.R255R	CBLC_ENST00000341505.4_Silent_p.R255R	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	255	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|SH2-like.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				AGGCCTGCAGGGACAAGCCAG	0.612			M		AML								G|||	144	0.028754	0.1021	0.013	5008	,	,		17150	0.0		0.0	False		,,,				2504	0.0				p.R255R		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.G765A						PASS	.	G	,	407,3999		15,377,1811	62.0	57.0	59.0		765,765	-2.1	1.0	19	dbSNP_119	59	4,8596		0,4,4296	no	coding-synonymous,coding-synonymous	CBLC	NM_001130852.1,NM_012116.3	,	15,381,6107	AA,AG,GG		0.0465,9.2374,3.1601	,	255/429,255/475	45285734	411,12595	2203	4300	6503	SO:0001819	synonymous_variant	23624	exon4			CTGCAGGGACAAG	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.765G>A	19.37:g.45285734G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Silent	SNP	ENST00000270279.3	37	CCDS12643.1																																																																																			G|0.958;A|0.042	0.042	strong		0.612	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
COL27A1	85301	hgsc.bcm.edu	37	9	116930100	116930100	+	Missense_Mutation	SNP	G	G	A	rs2567707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116930100G>A	ENST00000356083.3	+	3	656	c.265G>A	c.(265-267)Gtc>Atc	p.V89I		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	89	Laminin G-like.		V -> I (in dbSNP:rs2567707).		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						CACGGGCACCGTCATTCCTGC	0.662													G|||	678	0.135383	0.1634	0.1427	5008	,	,		16185	0.001		0.2704	False		,,,				2504	0.092				p.V89I		Atlas-SNP	.											.	COL27A1	200	.	0			c.G265A						PASS	.	G	ILE/VAL	732,3674	296.4+/-284.2	61,610,1532	56.0	62.0	60.0		265	0.9	0.0	9	dbSNP_100	60	2199,6401	364.2+/-333.4	272,1655,2373	yes	missense	COL27A1	NM_032888.2	29	333,2265,3905	AA,AG,GG		25.5698,16.6137,22.5358	benign	89/1861	116930100	2931,10075	2203	4300	6503	SO:0001583	missense	85301	exon3			GGCACCGTCATTC	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.265G>A	9.37:g.116930100G>A	ENSP00000348385:p.Val89Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	52	0.675325	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	332	0.152014652014652	82	0.16666666666666666	61	0.1685082872928177	1	0.0017482517482517483	188	0.24802110817941952	G	1.272	-0.612896	0.03690	0.166137	0.255698	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	T;T	0.02140	4.43;4.43	5.32	0.882	0.19172	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.20610	0.595	0.80722	P	0.0	B	0.22211	0.066	B	0.11329	0.006	T	0.44143	-0.9347	8	0.20046	T	0.44	.	8.2128	0.31494	0.4585:0.0:0.5415:0.0	rs2567707;rs17801084;rs52825865;rs57459248;rs2567707	89	Q8IZC6	CORA1_HUMAN	I	89;89;36;36	ENSP00000348385:V89I;ENSP00000391328:V36I	ENSP00000348385:V89I	V	+	1	0	COL27A1	115969921	0.001000	0.12720	0.011000	0.14972	0.085000	0.17905	-0.062000	0.11674	0.249000	0.21456	-0.439000	0.05793	GTC	G|0.811;A|0.189	0.189	strong		0.662	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
DNAH10	196385	hgsc.bcm.edu	37	12	124387586	124387586	+	Silent	SNP	A	A	G	rs61587964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124387586A>G	ENST00000409039.3	+	56	9412	c.9387A>G	c.(9385-9387)gcA>gcG	p.A3129A		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3129	Stalk. {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)		CGACCCTGGCAGAGGTCATGC	0.562													G|||	1793	0.358027	0.6135	0.2968	5008	,	,		20262	0.2788		0.2515	False		,,,				2504	0.2474				p.A3129A		Atlas-SNP	.											.	DNAH10	888	.	0			c.A9387G						PASS	.	G		2197,2005		544,1109,448	51.0	62.0	59.0		9387	-4.4	0.3	12	dbSNP_129	59	1880,6568		222,1436,2566	no	coding-synonymous	DNAH10	NM_207437.3		766,2545,3014	GG,GA,AA		22.2538,47.7154,32.2292		3129/4472	124387586	4077,8573	2101	4224	6325	SO:0001819	synonymous_variant	196385	exon56			CCTGGCAGAGGTC	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.9387A>G	12.37:g.124387586A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			A|0.680;G|0.320	0.320	strong		0.562	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
BRD7	29117	hgsc.bcm.edu	37	16	50368626	50368626	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50368626T>C	ENST00000394688.3	-	7	1042	c.883A>G	c.(883-885)Aaa>Gaa	p.K295E	BRD7_ENST00000394689.2_Missense_Mutation_p.K295E			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	295					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				TTTTACTTTTTATTTTCTTTG	0.488																																					p.K295E		Atlas-SNP	.											.	BRD7	61	.	0			c.A883G						PASS	.						95.0	110.0	105.0					16																	50368626		2192	4296	6488	SO:0001583	missense	29117	exon7			ACTTTTTATTTTC	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"""bromodomain-containing 7"""			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.883A>G	16.37:g.50368626T>C	ENSP00000378180:p.Lys295Glu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	84	8	0.0952381	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	37	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.058696	0.36277	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.52754	0.65;0.65	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.49321	0.1550	M	0.67953	2.075	0.47374	D	0.999409	B;B	0.27910	0.193;0.161	B;B	0.31442	0.13;0.079	T	0.45891	-0.9230	10	0.34782	T	0.22	.	14.6369	0.68696	0.0:0.0:0.0:1.0	.	295;295	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	E	295	ENSP00000378180:K295E;ENSP00000378181:K295E	ENSP00000378180:K295E	K	-	1	0	BRD7	48926127	1.000000	0.71417	0.995000	0.50966	0.266000	0.26442	4.022000	0.57203	2.254000	0.74563	0.528000	0.53228	AAA	.	.	none		0.488	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253931	39253931	+	Missense_Mutation	SNP	G	G	A	rs150613353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39253931G>A	ENST00000333822.4	-	1	462	c.406C>T	c.(406-408)Cgc>Tgc	p.R136C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	136	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						caagaggggcggcagcagctg	0.662													G|||	232	0.0463259	0.1664	0.0159	5008	,	,		14984	0.0		0.001	False		,,,				2504	0.0				p.R136C		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C406T						PASS	.						6.0	8.0	8.0					17																	39253931		682	1556	2238	SO:0001583	missense	728224	exon1			AGGGGCGGCAGCA	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.406C>T	17.37:g.39253931G>A	ENSP00000328444:p.Arg136Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	123	54	0.439024	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	75	0.034340659340659344	69	0.1402439024390244	6	0.016574585635359115	0	0.0	0	0.0	.	12.52	1.962330	0.34659	.	.	ENSG00000204880	ENST00000333822	T	0.01484	4.84	3.73	3.73	0.42828	.	1.159130	0.06715	U	0.773946	T	0.00039	0.0001	M	0.75447	2.3	0.32957	P	0.47942799999999997	B	0.29936	0.262	B	0.19666	0.026	T	0.33701	-0.9858	9	0.66056	D	0.02	.	7.5536	0.27812	0.1225:0.0:0.8775:0.0	.	136	Q9BYQ9	KRA48_HUMAN	C	136	ENSP00000328444:R136C	ENSP00000328444:R136C	R	-	1	0	KRTAP4-8	36507457	0.000000	0.05858	0.820000	0.32676	0.259000	0.26198	-1.031000	0.03578	1.794000	0.52575	0.449000	0.29647	CGC	G|0.966;A|0.034	0.034	strong		0.662	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
ERN2	10595	hgsc.bcm.edu	37	16	23721865	23721865	+	Missense_Mutation	SNP	C	C	T	rs9932495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23721865C>T	ENST00000457008.2	-	3	243	c.205G>A	c.(205-207)Gtc>Atc	p.V69I	CTD-2385L22.1_ENST00000563611.1_RNA|ERN2_ENST00000256797.4_Missense_Mutation_p.V117I					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		CCTTCGATGACGGGATCTGCA	0.507													C|||	104	0.0207668	0.0756	0.0014	5008	,	,		21483	0.0		0.001	False		,,,				2504	0.002				p.V117I		Atlas-SNP	.											.	ERN2	131	.	0			c.G349A						PASS	.	C	ILE/VAL	242,4152	141.1+/-176.5	7,228,1962	206.0	200.0	202.0		349	-3.1	0.4	16	dbSNP_119	202	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ERN2	NM_033266.3	29	7,229,6261	TT,TC,CC		0.0116,5.5075,1.8701	benign	117/975	23721865	243,12751	2197	4300	6497	SO:0001583	missense	10595	exon3			CGATGACGGGATC	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"""ER to nucleus signalling 2"""			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.205G>A	16.37:g.23721865C>T	ENSP00000413812:p.Val69Ile	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_033266		Missense_Mutation	SNP	ENST00000457008.2	37		31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	5.726	0.318420	0.10845	0.055075	1.16E-4	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.21361	2.01;2.01	4.91	-3.07	0.05363	.	0.439897	0.27147	N	0.020713	T	0.00724	0.0024	N	0.05574	-0.02	0.25356	N	0.988828	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.28073	-1.0055	10	0.19147	T	0.46	.	6.6045	0.22718	0.0:0.4318:0.2707:0.2975	rs9932495;rs52791098;rs9932495	69;69	E7ETG2;A5YM65	.;.	I	117;69	ENSP00000256797:V117I;ENSP00000413812:V69I	ENSP00000256797:V117I	V	-	1	0	ERN2	23629366	0.991000	0.36638	0.383000	0.26132	0.543000	0.35085	0.246000	0.18160	-0.855000	0.04125	-0.379000	0.06801	GTC	C|0.981;T|0.019	0.019	strong		0.507	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1		
MYO16	23026	hgsc.bcm.edu	37	13	109496813	109496813	+	Missense_Mutation	SNP	T	T	C	rs16973313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:109496813T>C	ENST00000357550.2	+	9	1195	c.1154T>C	c.(1153-1155)aTg>aCg	p.M385T	MYO16_ENST00000251041.5_Missense_Mutation_p.M385T|MYO16_ENST00000356711.2_Missense_Mutation_p.M385T	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)			GAAAACCCCATGATGAGCGGT	0.408													C|||	475	0.0948482	0.1392	0.0648	5008	,	,		16606	0.0734		0.1282	False		,,,				2504	0.044				p.M407T		Atlas-SNP	.											.	MYO16	285	.	0			c.T1220C						PASS	.	C	THR/MET,THR/MET	610,3796	769.6+/-413.7	42,526,1635	116.0	110.0	112.0		1220,1154	0.4	0.0	13	dbSNP_123	112	1147,7453	766.4+/-407.6	73,1001,3226	yes	missense,missense	MYO16	NM_001198950.1,NM_015011.1	81,81	115,1527,4861	CC,CT,TT		13.3372,13.8448,13.5091	benign,benign	407/1881,385/1859	109496813	1757,11249	2203	4300	6503	SO:0001583	missense	23026	exon10			ACCCCATGATGAG		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.1154T>C	13.37:g.109496813T>C	ENSP00000350160:p.Met385Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	237	0.10851648351648352	76	0.15447154471544716	19	0.052486187845303865	49	0.08566433566433566	93	0.12269129287598944	C	0.009	-1.816107	0.00595	0.138448	0.133372	ENSG00000041515	ENST00000356711;ENST00000397258;ENST00000357550;ENST00000251041;ENST00000375857	D;D;D	0.95001	-3.58;-3.58;-3.58	5.31	0.421	0.16451	.	1.080970	0.07352	N	0.882520	T	0.02156	0.0067	N	0.03177	-0.4	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47724	-0.9095	8	.	.	.	.	7.6801	0.28509	0.0:0.5358:0.1082:0.3561	rs16973313;rs56423595;rs16973313	385;385	Q9Y6X6-2;Q9Y6X6	.;MYO16_HUMAN	T	385;385;385;385;173	ENSP00000349145:M385T;ENSP00000350160:M385T;ENSP00000251041:M385T	.	M	+	2	0	MYO16	108294814	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.271000	0.08572	-0.159000	0.11021	-0.722000	0.03604	ATG	T|0.882;C|0.118	0.118	strong		0.408	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
GPATCH1	55094	hgsc.bcm.edu	37	19	33587298	33587298	+	Silent	SNP	C	C	T	rs114017497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33587298C>T	ENST00000170564.2	+	7	1112	c.798C>T	c.(796-798)ggC>ggT	p.G266G		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	266					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)					AGAGAGCTGGCGATCTTGGAG	0.413													C|||	37	0.00738818	0.0257	0.0043	5008	,	,		16637	0.0		0.0	False		,,,				2504	0.0				p.G266G	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.C798T						PASS	.	C		114,4292	87.3+/-125.9	4,106,2093	75.0	78.0	77.0		798	2.0	0.0	19	dbSNP_132	77	0,8600		0,0,4300	no	coding-synonymous	GPATCH1	NM_018025.2		4,106,6393	TT,TC,CC		0.0,2.5874,0.8765		266/932	33587298	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon7			AGCTGGCGATCTT	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.798C>T	19.37:g.33587298C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			C|0.991;T|0.009	0.009	strong		0.413	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
LAMP1	3916	hgsc.bcm.edu	37	13	113973832	113973832	+	Missense_Mutation	SNP	C	C	T	rs9577229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113973832C>T	ENST00000332556.4	+	5	805	c.611C>T	c.(610-612)gCg>gTg	p.A204V	LAMP1_ENST00000397181.3_Missense_Mutation_p.A151V	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	204	Hinge.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)	p.A204V(1)		NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			GCGCCCCCTGCGCCACCCAGC	0.637													C|||	399	0.0796725	0.1641	0.0533	5008	,	,		17650	0.1399		0.001	False		,,,				2504	0.0031				p.A204V		Atlas-SNP	.											LAMP1,NS,carcinoma,0,1	LAMP1	41	1	1	Substitution - Missense(1)	stomach(1)	c.C611T						PASS	.	C	VAL/ALA	623,3433		48,527,1453	45.0	57.0	53.0		611	0.2	0.0	13	dbSNP_119	53	7,8377		0,7,4185	yes	missense	LAMP1	NM_005561.3	64	48,534,5638	TT,TC,CC		0.0835,15.36,5.0643	benign	204/418	113973832	630,11810	2028	4192	6220	SO:0001583	missense	3916	exon5			CCCCTGCGCCACC	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"""CD molecules"""	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.611C>T	13.37:g.113973832C>T	ENSP00000333298:p.Ala204Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Missense_Mutation	SNP	ENST00000332556.4	37	CCDS41909.1	181	0.08287545787545787	87	0.17682926829268292	17	0.04696132596685083	77	0.1346153846153846	0	0.0	C	11.66	1.705958	0.30232	0.1536	8.35E-4	ENSG00000185896	ENST00000332556;ENST00000397181	T;T	0.35048	1.33;1.33	5.34	0.159	0.14968	.	1.126930	0.06515	N	0.738742	T	0.00039	0.0001	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.16396	0.007;0.017	B;B	0.13407	0.005;0.009	T	0.24584	-1.0156	9	0.17832	T	0.49	-0.0066	2.9161	0.05752	0.1393:0.5386:0.105:0.2171	rs9577229	151;204	B4DWL3;P11279	.;LAMP1_HUMAN	V	204;151	ENSP00000333298:A204V;ENSP00000415354:A151V	ENSP00000333298:A204V	A	+	2	0	LAMP1	113021833	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.108000	0.15396	-0.282000	0.09128	-1.080000	0.02220	GCG	C|0.947;T|0.053	0.053	strong		0.637	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2		
DLC1	10395	hgsc.bcm.edu	37	8	12950315	12950315	+	Silent	SNP	G	G	T	rs568182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:12950315G>T	ENST00000276297.4	-	13	3955	c.3546C>A	c.(3544-3546)cgC>cgA	p.R1182R	DLC1_ENST00000358919.2_Silent_p.R745R|DLC1_ENST00000512044.2_Silent_p.R779R|DLC1_ENST00000520226.1_Silent_p.R671R|DLC1_ENST00000510318.1_5'UTR	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	1182	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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						TGGCCTGCAGGCGCTGGTCCT	0.542													G|||	566	0.113019	0.2481	0.0562	5008	,	,		19641	0.0268		0.0557	False		,,,				2504	0.1186				p.R1182R		Atlas-SNP	.											DLC1,NS,carcinoma,-1,2	DLC1	411	2	0			c.C3546A						PASS	.	G	,,	1000,3406	371.0+/-319.8	103,794,1306	46.0	40.0	42.0		2013,2235,3546	0.1	1.0	8	dbSNP_83	42	466,8134	137.0+/-194.0	8,450,3842	no	coding-synonymous,coding-synonymous,coding-synonymous	DLC1	NM_001164271.1,NM_006094.4,NM_182643.2	,,	111,1244,5148	TT,TG,GG		5.4186,22.6963,11.2717	,,	671/1018,745/1092,1182/1529	12950315	1466,11540	2203	4300	6503	SO:0001819	synonymous_variant	10395	exon13			CTGCAGGCGCTGG	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.3546C>A	8.37:g.12950315G>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																			G|0.887;T|0.113	0.113	strong		0.542	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
DOPEY1	23033	hgsc.bcm.edu	37	6	83850049	83850049	+	Missense_Mutation	SNP	A	A	T	rs9444039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:83850049A>T	ENST00000349129.2	+	23	5602	c.5342A>T	c.(5341-5343)cAa>cTa	p.Q1781L	DOPEY1_ENST00000237163.5_Missense_Mutation_p.Q1762L|DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Missense_Mutation_p.Q1772L	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	1781			Q -> L (in dbSNP:rs9444039).		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)		ATACTGCATCAAGCTGATTCT	0.408													A|||	272	0.0543131	0.0998	0.0216	5008	,	,		18015	0.0804		0.002	False		,,,				2504	0.0429				p.Q1781L		Atlas-SNP	.											.	DOPEY1	190	.	0			c.A5342T						PASS	.	A	LEU/GLN,LEU/GLN	319,4087	170.1+/-200.6	7,305,1891	167.0	154.0	159.0		5315,5342	5.5	1.0	6	dbSNP_119	159	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	DOPEY1	NM_001199942.1,NM_015018.3	113,113	7,310,6186	TT,TA,AA		0.0581,7.2401,2.4912	benign,benign	1772/2477,1781/2466	83850049	324,12682	2203	4300	6503	SO:0001583	missense	23033	exon23			TGCATCAAGCTGA	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.5342A>T	6.37:g.83850049A>T	ENSP00000195654:p.Gln1781Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	98	0.04487179487179487	42	0.08536585365853659	8	0.022099447513812154	47	0.08216783216783216	1	0.0013192612137203166	A	9.349	1.065010	0.20067	0.072401	5.81E-4	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.26067	1.8;1.76	5.47	5.47	0.80525	.	0.053593	0.85682	D	0.000000	T	0.05777	0.0151	N	0.19112	0.55	0.80722	D	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.14980	-1.0453	10	0.07325	T	0.83	.	11.6173	0.51096	0.8592:0.0:0.0:0.1408	rs9444039;rs52792741;rs9444039	1672;1772;1781	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	L	1781;1762;1762	ENSP00000195654:Q1781L;ENSP00000237163:Q1762L	ENSP00000237163:Q1762L	Q	+	2	0	DOPEY1	83906768	1.000000	0.71417	1.000000	0.80357	0.098000	0.18820	3.673000	0.54591	2.201000	0.70794	0.477000	0.44152	CAA	A|0.968;T|0.032	0.032	strong		0.408	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
RYR3	6263	hgsc.bcm.edu	37	15	34111969	34111969	+	Silent	SNP	C	C	T	rs58745096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34111969C>T	ENST00000389232.4	+	77	10789	c.10719C>T	c.(10717-10719)gaC>gaT	p.D3573D	RYR3_ENST00000415757.3_Silent_p.D3568D	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3573					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)		AATTGGAAGACGACCCTTTGT	0.338													C|||	91	0.0181709	0.0666	0.0029	5008	,	,		14784	0.0		0.001	False		,,,				2504	0.0				p.D3573D		Atlas-SNP	.											RYR3,NS,carcinoma,0,1	RYR3	760	1	0			c.C10719T						PASS	.	C		163,3477		5,153,1662	318.0	297.0	303.0		10719	-6.1	0.9	15	dbSNP_129	303	2,8170		0,2,4084	no	coding-synonymous	RYR3	NM_001036.3		5,155,5746	TT,TC,CC		0.0245,4.478,1.3969		3573/4871	34111969	165,11647	1820	4086	5906	SO:0001819	synonymous_variant	6263	exon77			GGAAGACGACCCT		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.10719C>T	15.37:g.34111969C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	174	87	0.5	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			C|0.984;T|0.016	0.016	strong		0.338	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914013	31914013	+	Missense_Mutation	SNP	G	G	A	rs115563631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31914013G>A	ENST00000334046.5	-	1	170	c.140C>T	c.(139-141)tCa>tTa	p.S47L		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	47						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						TTCACGGCATGATGGGCGGCA	0.507													g|||	55	0.0109824	0.0401	0.0029	5008	,	,		15048	0.0		0.0	False		,,,				2504	0.0				p.S47L		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.C140T						PASS	.	G	LEU/SER	161,4245	109.1+/-147.4	2,157,2044	110.0	120.0	117.0		140	2.1	0.0	21	dbSNP_132	117	3,8597	3.7+/-12.6	0,3,4297	yes	missense	KRTAP19-6	NM_181612.2	145	2,160,6341	AA,AG,GG		0.0349,3.6541,1.261	possibly-damaging	47/59	31914013	164,12842	2203	4300	6503	SO:0001583	missense	337973	exon1			CGGCATGATGGGC	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"""Keratin associated proteins"""	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.140C>T	21.37:g.31914013G>A	ENSP00000375107:p.Ser47Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_181612	Q3LI71	Missense_Mutation	SNP	ENST00000334046.5	37	CCDS13598.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	g	7.582	0.668877	0.14776	0.036541	3.49E-4	ENSG00000186925	ENST00000334046;ENST00000437381	T	0.10005	2.92	3.96	2.1	0.27182	.	2.101130	0.03499	N	0.217738	T	0.02380	0.0073	.	.	.	0.09310	N	1	P	0.36616	0.561	B	0.36504	0.226	T	0.30179	-0.9987	9	0.87932	D	0	.	6.6627	0.23022	0.2276:0.0:0.7724:0.0	.	47	Q3LI70	KR196_HUMAN	L	47	ENSP00000375107:S47L	ENSP00000375107:S47L	S	-	2	0	KRTAP19-6	30835884	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.310000	0.08135	0.272000	0.22027	0.597000	0.82753	TCA	G|0.985;A|0.015	0.015	strong		0.507	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4		
DOCK7	85440	hgsc.bcm.edu	37	1	63119442	63119442	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:63119442C>T	ENST00000340370.5	-	4	360	c.343G>A	c.(343-345)Gac>Aac	p.D115N	DOCK7_ENST00000404627.2_Missense_Mutation_p.D115N|DOCK7_ENST00000251157.5_Missense_Mutation_p.D115N	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	115					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						CTTATACAGTCTCTAACATGT	0.303																																					p.D115N		Atlas-SNP	.											.	DOCK7	184	.	0			c.G343A						PASS	.						61.0	62.0	62.0					1																	63119442		2203	4297	6500	SO:0001583	missense	85440	exon4			TACAGTCTCTAAC		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.343G>A	1.37:g.63119442C>T	ENSP00000340742:p.Asp115Asn	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	149	45	0.302013	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	34	5.339631	0.95783	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.49720	0.77;0.77;0.77	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.64193	0.2576	M	0.78049	2.395	0.80722	D	1	D;D;P;P;D	0.65815	0.992;0.995;0.923;0.923;0.993	D;D;P;P;D	0.66979	0.925;0.948;0.772;0.772;0.913	T	0.64330	-0.6433	10	0.48119	T	0.1	.	18.898	0.92432	0.0:1.0:0.0:0.0	.	115;115;115;115;115	Q96NI0;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3	.;.;.;.;.	N	115	ENSP00000251157:D115N;ENSP00000340742:D115N;ENSP00000384446:D115N	ENSP00000251157:D115N	D	-	1	0	DOCK7	62892030	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.651000	0.83577	2.699000	0.92147	0.655000	0.94253	GAC	.	.	none		0.303	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
HSPA9	3313	hgsc.bcm.edu	37	5	137902339	137902339	+	Silent	SNP	T	T	C	rs1042665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:137902339T>C	ENST00000297185.3	-	9	1073	c.948A>G	c.(946-948)aaA>aaG	p.K316K	HSPA9_ENST00000501917.2_5'UTR	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	316					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGAGTTCACATTTAGCCTTTT	0.408													T|||	2103	0.419928	0.3464	0.2464	5008	,	,		18698	0.7629		0.2485	False		,,,				2504	0.4652				p.K316K		Atlas-SNP	.											.	HSPA9	49	.	0			c.A948G						PASS	.	T		1401,3005	460.3+/-352.6	225,951,1027	156.0	143.0	147.0		948	-1.3	0.8	5	dbSNP_86	147	1896,6704	337.2+/-322.2	191,1514,2595	no	coding-synonymous	HSPA9	NM_004134.6		416,2465,3622	CC,CT,TT		22.0465,31.7975,25.3498		316/680	137902339	3297,9709	2203	4300	6503	SO:0001819	synonymous_variant	3313	exon9			TTCACATTTAGCC	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"""Heat shock proteins / HSP70"""	5244	protein-coding gene	gene with protein product		600548	"""heat shock 70kDa protein 9B (mortalin-2)"""	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.948A>G	5.37:g.137902339T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Silent	SNP	ENST00000297185.3	37	CCDS4208.1																																																																																			T|0.686;C|0.314	0.314	strong		0.408	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134	
LILRB2	10288	hgsc.bcm.edu	37	19	54782731	54782731	+	Silent	SNP	G	G	A	rs10404685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782731G>A	ENST00000391749.4	-	6	1162	c.891C>T	c.(889-891)taC>taT	p.Y297Y	LILRB2_ENST00000391748.1_Silent_p.Y297Y|LILRB2_ENST00000391746.1_Silent_p.Y297Y|LILRB2_ENST00000434421.1_Silent_p.Y181Y|LILRB2_ENST00000314446.5_Silent_p.Y297Y|LILRB2_ENST00000471216.1_5'Flank	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	297	Ig-like C2-type 3.				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)		TGTGTGCACCGTAGCATCTGT	0.672													.|||	464	0.0926518	0.2905	0.0375	5008	,	,		13500	0.0298		0.0129	False		,,,				2504	0.0112				p.Y297Y		Atlas-SNP	.											.	LILRB2	94	.	0			c.C891T						PASS	.	G	,	1006,3400	364.1+/-316.8	119,768,1316	36.0	34.0	35.0		891,891	-5.7	0.0	19	dbSNP_119	35	168,8412	69.0+/-131.5	2,164,4124	no	coding-synonymous,coding-synonymous	LILRB2	NM_001080978.2,NM_005874.3	,	121,932,5440	AA,AG,GG		1.958,22.8325,9.0405	,	297/598,297/599	54782731	1174,11812	2203	4290	6493	SO:0001819	synonymous_variant	10288	exon6			TGCACCGTAGCAT	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.891C>T	19.37:g.54782731G>A		Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	239	153	0.640167	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Silent	SNP	ENST00000391749.4	37	CCDS12886.1																																																																																			G|0.904;A|0.096	0.096	strong		0.672	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
EFHC1	114327	hgsc.bcm.edu	37	6	52343899	52343899	+	Missense_Mutation	SNP	T	T	C	rs1266787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:52343899T>C	ENST00000371068.5	+	8	1446	c.1343T>C	c.(1342-1344)aTg>aCg	p.M448T	EFHC1_ENST00000433625.2_Missense_Mutation_p.M357T|EFHC1_ENST00000538167.1_Missense_Mutation_p.M429T	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	448	DM10 3. {ECO:0000255|PROSITE- ProRule:PRU00665}.		M -> T (in dbSNP:rs1266787). {ECO:0000269|PubMed:17159113}.			axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					GCTACCGACATGATCAGTATC	0.433													T|||	362	0.0722843	0.2194	0.0317	5008	,	,		20846	0.0		0.0408	False		,,,				2504	0.0092				p.M448T		Atlas-SNP	.											.	EFHC1	68	.	0			c.T1343C						PASS	.	T	THR/MET,THR/MET	864,3542	338.6+/-305.4	90,684,1429	138.0	128.0	132.0		1286,1343	3.6	1.0	6	dbSNP_87	132	256,8344	100.6+/-161.9	6,244,4050	yes	missense,missense	EFHC1	NM_001172420.1,NM_018100.3	81,81	96,928,5479	CC,CT,TT		2.9767,19.6096,8.6114	benign,benign	429/622,448/641	52343899	1120,11886	2203	4300	6503	SO:0001583	missense	114327	exon8			CCGACATGATCAG	AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"""EF-hand domain containing"""	16406	protein-coding gene	gene with protein product	"""myoclonin-1"""	608815	"""epilepsy, juvenile myoclonic 1"""	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.1343T>C	6.37:g.52343899T>C	ENSP00000360107:p.Met448Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Missense_Mutation	SNP	ENST00000371068.5	37	CCDS4942.1	143	0.06547619047619048	102	0.2073170731707317	10	0.027624309392265192	0	0.0	31	0.040897097625329816	T	9.035	0.988215	0.18966	0.196096	0.029767	ENSG00000096093	ENST00000371068;ENST00000433625;ENST00000538167	T;T;T	0.20598	2.06;2.06;2.06	5.89	3.56	0.40772	Uncharacterised domain DM10 (2);	0.239792	0.56097	N	0.000036	T	0.02193	0.0068	N	0.04090	-0.28	0.26521	P	0.9744209	B;B;B	0.22003	0.063;0.003;0.001	B;B;B	0.21360	0.034;0.015;0.004	T	0.41752	-0.9491	9	0.02654	T	1	-5.8112	9.4922	0.38967	0.0:0.2001:0.0:0.7999	rs1266787;rs1266787	429;357;448	F5GZD8;B7Z2S4;Q5JVL4	.;.;EFHC1_HUMAN	T	448;357;429	ENSP00000360107:M448T;ENSP00000416492:M357T;ENSP00000444521:M429T	ENSP00000360107:M448T	M	+	2	0	EFHC1	52451858	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.699000	0.47077	1.066000	0.40716	0.477000	0.44152	ATG	A|0.004;C|0.085	0.085	strong		0.433	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100	
PHYHIPL	84457	hgsc.bcm.edu	37	10	61005244	61005244	+	Missense_Mutation	SNP	G	G	C	rs2452505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:61005244G>C	ENST00000373880.4	+	5	1288	c.1024G>C	c.(1024-1026)Gtg>Ctg	p.V342L	PHYHIPL_ENST00000373878.3_Missense_Mutation_p.V316L	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	342			V -> L (in dbSNP:rs2452505). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.5}.			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						GGATCTTTCTGTGGGCACCGT	0.443													C|||	3704	0.739617	0.4781	0.8703	5008	,	,		18638	0.8829		0.8688	False		,,,				2504	0.7198				p.V342L		Atlas-SNP	.											.	PHYHIPL	44	.	0			c.G1024C						PASS	.	C	LEU/VAL,LEU/VAL	2376,2030	564.4+/-381.4	661,1054,488	74.0	70.0	71.0		946,1024	5.6	1.0	10	dbSNP_100	71	7239,1361	265.6+/-286.2	3059,1121,120	yes	missense,missense	PHYHIPL	NM_001143774.1,NM_032439.3	32,32	3720,2175,608	CC,CG,GG		15.8256,46.0735,26.0726	benign,benign	316/351,342/377	61005244	9615,3391	2203	4300	6503	SO:0001583	missense	84457	exon5			CTTTCTGTGGGCA	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.1024G>C	10.37:g.61005244G>C	ENSP00000362987:p.Val342Leu	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	129	76	0.589147	NM_032439	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Missense_Mutation	SNP	ENST00000373880.4	37	CCDS7254.1	1687	0.7724358974358975	222	0.45121951219512196	310	0.856353591160221	499	0.8723776223776224	656	0.8654353562005277	C	1.226	-0.625495	0.03610	0.539265	0.841744	ENSG00000165443	ENST00000373880;ENST00000373878	T;T	0.35236	1.32;1.32	5.56	5.56	0.83823	.	0.124557	0.35970	N	0.002863	T	0.00012	0.0000	N	0.00347	-1.61	0.09310	P	0.9999999999956716	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37820	-0.9689	9	0.02654	T	1	-27.1979	10.0761	0.42362	0.0:0.7902:0.1386:0.0712	rs2452505;rs17845284;rs17858117;rs52790960;rs2452505	316;342	Q96FC7-2;Q96FC7	.;PHIPL_HUMAN	L	342;316	ENSP00000362987:V342L;ENSP00000362985:V316L	ENSP00000362985:V316L	V	+	1	0	PHYHIPL	60675250	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	1.542000	0.36137	1.359000	0.45940	-0.120000	0.15030	GTG	G|0.259;C|0.741	0.741	strong		0.443	PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439	
TRRAP	8295	hgsc.bcm.edu	37	7	98558922	98558922	+	Silent	SNP	G	G	A	rs34983214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:98558922G>A	ENST00000359863.4	+	45	6716	c.6507G>A	c.(6505-6507)acG>acA	p.T2169T	TRRAP_ENST00000446306.3_Silent_p.T2150T|TRRAP_ENST00000355540.3_Silent_p.T2151T	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2169	Interaction with TP53.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			ATATCTGCACGGGCCTAGAAG	0.507													G|||	32	0.00638978	0.0219	0.0029	5008	,	,		14881	0.0		0.001	False		,,,				2504	0.0				p.T2169T		Atlas-SNP	.											.	TRRAP	863	.	0			c.G6507A						PASS	.	G		78,4328	68.1+/-105.8	0,78,2125	162.0	161.0	162.0		6453	-10.9	0.0	7	dbSNP_126	162	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRRAP	NM_003496.3		0,80,6423	AA,AG,GG		0.0233,1.7703,0.6151		2151/3831	98558922	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	8295	exon45			CTGCACGGGCCTA	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.6507G>A	7.37:g.98558922G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	18	0.008241758241758242	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	7.407	0.633881	0.14322	0.017703	2.33E-4	ENSG00000196367	ENST00000456197	.	.	.	5.47	-10.9	0.00192	.	.	.	.	.	T	0.12860	0.0312	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37842	-0.9688	4	.	.	.	.	1.7278	0.02925	0.4473:0.1858:0.2241:0.1428	rs34983214	.	.	.	Q	1891	.	.	R	+	2	0	TRRAP	98396858	0.000000	0.05858	0.019000	0.16419	0.892000	0.51952	-2.537000	0.00939	-2.796000	0.00354	-0.136000	0.14681	CGG	G|0.993;A|0.007	0.007	strong		0.507	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
GFRA4	64096	hgsc.bcm.edu	37	20	3640568	3640568	+	Silent	SNP	C	C	T	rs74740423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3640568C>T	ENST00000319242.3	-	5	887	c.888G>A	c.(886-888)ccG>ccA	p.P296P	GFRA4_ENST00000290417.2_Silent_p.P266P			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	296					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			large_intestine(1)|lung(2)	3						AGAGCAGGGCCGGGAGAGCCA	0.647													C|||	147	0.029353	0.1051	0.0115	5008	,	,		18655	0.0		0.0	False		,,,				2504	0.0				p.P296P		Atlas-SNP	.											.	GFRA4	10	.	0			c.G888A						PASS	.	C	,	405,3999		13,379,1810	29.0	30.0	29.0		798,888	2.8	0.3	20	dbSNP_131	29	3,8589		0,3,4293	no	coding-synonymous,coding-synonymous	GFRA4	NM_022139.3,NM_145762.2	,	13,382,6103	TT,TC,CC		0.0349,9.1962,3.1394	,	266/270,296/300	3640568	408,12588	2202	4296	6498	SO:0001819	synonymous_variant	64096	exon5			CAGGGCCGGGAGA	AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"""persephin receptor"""					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.888G>A	20.37:g.3640568C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	41	23	0.560976	NM_145762	Q5JT74|Q9H191|Q9H192	Silent	SNP	ENST00000319242.3	37	CCDS13056.1																																																																																			C|0.968;T|0.032	0.032	strong		0.647	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762	
PEX11G	92960	hgsc.bcm.edu	37	19	7547074	7547074	+	Missense_Mutation	SNP	A	A	C	rs2303146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7547074A>C	ENST00000221480.1	-	3	281	c.273T>G	c.(271-273)tgT>tgG	p.C91W	PEX11G_ENST00000599519.1_5'UTR|PEX11G_ENST00000593942.1_Missense_Mutation_p.C21W	NM_001270539.1|NM_080662.3	NP_001257468.1|NP_542393.1	Q96HA9	PX11C_HUMAN	peroxisomal biogenesis factor 11 gamma	91			C -> W (in dbSNP:rs2303146).		peroxisome fission (GO:0016559)|regulation of peroxisome size (GO:0044375)	integral component of peroxisomal membrane (GO:0005779)|intrinsic component of peroxisomal membrane (GO:0031231)|peroxisome (GO:0005777)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(1)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	7						GGACGGAGACACAGCGGACAA	0.632													C|||	2291	0.457468	0.7201	0.3055	5008	,	,		18080	0.4435		0.326	False		,,,				2504	0.3599				p.C91W		Atlas-SNP	.											.	PEX11G	16	.	0			c.T273G						PASS	.	C	TRP/CYS	2773,1611		888,997,307	35.0	31.0	33.0		273	-3.5	0.0	19	dbSNP_100	33	2669,5909		450,1769,2070	yes	missense	PEX11G	NM_080662.2	215	1338,2766,2377	CC,CA,AA		31.1145,36.7473,41.9843	benign	91/242	7547074	5442,7520	2192	4289	6481	SO:0001583	missense	92960	exon3			GGAGACACAGCGG	BC008780	CCDS12178.1	19p13.2	2008-02-05				ENSG00000104883			20208	protein-coding gene	gene with protein product		607583				12417726	Standard	NM_080662		Approved		uc002mgk.2	Q96HA9		ENST00000221480.1:c.273T>G	19.37:g.7547074A>C	ENSP00000221480:p.Cys91Trp	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_001270539	Q8NDM0	Missense_Mutation	SNP	ENST00000221480.1	37	CCDS12178.1	922	0.42216117216117216	336	0.6829268292682927	101	0.27900552486187846	243	0.42482517482517484	242	0.31926121372031663	C	0.007	-1.998520	0.00435	0.632527	0.311145	ENSG00000104883	ENST00000221480	T	0.40476	1.03	4.76	-3.55	0.04639	.	0.407958	0.31438	N	0.007641	T	0.00012	0.0000	N	0.03891	-0.335	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.39231	-0.9624	9	0.26408	T	0.33	0.2335	9.6386	0.39824	0.5017:0.2648:0.2335:0.0	rs2303146;rs61461499;rs2303146	91	Q96HA9	PX11C_HUMAN	W	91	ENSP00000221480:C91W	ENSP00000221480:C91W	C	-	3	2	PEX11G	7453074	0.004000	0.15560	0.000000	0.03702	0.023000	0.10783	-0.078000	0.11375	-1.121000	0.02949	-0.217000	0.12591	TGT	A|0.557;C|0.443	0.443	strong		0.632	PEX11G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458965.1	NM_080662	
PSPH	5723	hgsc.bcm.edu	37	7	56087423	56087423	+	Missense_Mutation	SNP	G	G	A	rs79451216		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:56087423G>A	ENST00000395471.3	-	5	950	c.145C>T	c.(145-147)Cgg>Tgg	p.R49W	PSPH_ENST00000275605.3_Missense_Mutation_p.R49W|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	49					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)	p.R49W(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			ATGGCTCGCCGTGTCCTAGGA	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		13539	0.0		0.001	False		,,,				2504	0.0				p.R49W		Atlas-SNP	.											PSPH,NS,lymphoid_neoplasm,0,1	PSPH	23	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C145T						scavenged	.						48.0	34.0	39.0					7																	56087423		2203	4300	6503	SO:0001583	missense	5723	exon5			CTCGCCGTGTCCT	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.145C>T	7.37:g.56087423G>A	ENSP00000378854:p.Arg49Trp	Somatic	43	1	0.0232558		WXS	Illumina HiSeq	Phase_I	46	6	0.130435	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.112152	0.37242	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626	D;D;D	0.82526	-1.62;-1.62;-1.62	4.5	3.6	0.41247	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);Phosphoserine phosphatase, domain 2 (1);	0.186825	0.48767	D	0.000180	D	0.82346	0.5017	M	0.77486	2.375	0.80722	D	1	B;B	0.25235	0.106;0.121	B;B	0.21546	0.034;0.035	T	0.81686	-0.0820	10	0.87932	D	0	-7.1074	12.8694	0.57957	0.0:0.0:0.8358:0.1642	.	49;49	Q53EY1;P78330	.;SERB_HUMAN	W	49	ENSP00000275605:R49W;ENSP00000378854:R49W;ENSP00000398653:R49W	ENSP00000275605:R49W	R	-	1	2	PSPH	56054917	0.999000	0.42202	0.920000	0.36463	0.415000	0.31203	3.353000	0.52247	1.076000	0.40961	0.591000	0.81541	CGG	G|0.913;A|0.086	0.086	strong		0.602	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
ACOT1	641371	hgsc.bcm.edu	37	14	74009937	74009937	+	Missense_Mutation	SNP	A	A	G	rs377598014		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74009937A>G	ENST00000311148.4	+	3	1152	c.844A>G	c.(844-846)Atc>Gtc	p.I282V	HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000553558.1_Intron|ACOT1_ENST00000557556.1_Missense_Mutation_p.I256V|HEATR4_ENST00000334988.2_Intron	NM_001037161.1	NP_001032238.1	Q86TX2	ACOT1_HUMAN	acyl-CoA thioesterase 1	282					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		CAGAAATCGCATCAAGGTGAC	0.552																																					p.I282V		Atlas-SNP	.											.	ACOT1	12	.	0			c.A844G						PASS	.	A	VAL/ILE,,	1,4395		0,1,2197	84.0	65.0	72.0		844,,	-4.8	0.0	14		72	0,8584		0,0,4292	no	missense,intron,intron	HEATR4,ACOT1	NM_001037161.1,NM_001220484.1,NM_203309.2	29,,	0,1,6489	GG,GA,AA		0.0,0.0227,0.0077	,,	282/422,,	74009937	1,12979	2198	4292	6490	SO:0001583	missense	641371	exon3			AATCGCATCAAGG	DQ082754	CCDS32117.1	14q24.3	2013-09-20			ENSG00000184227	ENSG00000184227		"""Acyl CoA thioesterases"""	33128	protein-coding gene	gene with protein product		614313				16103133, 16940157	Standard	NM_001037161		Approved	ACH2, CTE-1, LACH2		Q86TX2	OTTHUMG00000171607	ENST00000311148.4:c.844A>G	14.37:g.74009937A>G	ENSP00000311224:p.Ile282Val	Somatic	659	0	0		WXS	Illumina HiSeq	Phase_I	906	319	0.352097	NM_001037161	A1L173|Q3I5F9	Missense_Mutation	SNP	ENST00000311148.4	37	CCDS32117.1	.	.	.	.	.	.	.	.	.	.	-	7.679	0.688575	0.14973	2.27E-4	0.0	ENSG00000184227	ENST00000311148;ENST00000557556	T;T	0.28895	1.59;1.59	4.06	-4.76	0.03229	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.642575	0.16665	N	0.204604	T	0.14830	0.0358	N	0.25789	0.76	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35375	-0.9791	10	0.11794	T	0.64	-8.1147	9.7986	0.40751	0.127:0.2638:0.6092:0.0	.	282	Q86TX2	ACOT1_HUMAN	V	282;256	ENSP00000311224:I282V;ENSP00000451764:I256V	ENSP00000311224:I282V	I	+	1	0	ACOT1	73079690	0.000000	0.05858	0.014000	0.15608	0.043000	0.13939	-2.813000	0.00753	-0.728000	0.04882	0.324000	0.21423	ATC	.	.	weak		0.552	ACOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414432.1	NM_001037161	
BTNL2	56244	hgsc.bcm.edu	37	6	32370859	32370859	+	Missense_Mutation	SNP	C	C	T	rs9461742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32370859C>T	ENST00000374993.1	-	3	561	c.562G>A	c.(562-564)Gtg>Atg	p.V188M	BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000374995.3_Splice_Site_p.V148I|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000454136.3_Missense_Mutation_p.V188M|BTNL2_ENST00000429232.2_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	188	Ig-like V-type 2.		V -> M (in dbSNP:rs9461742).			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						TGCTCAGACACGGCCAGCAGC	0.587													C|||	29	0.00579073	0.0182	0.0058	5008	,	,		19224	0.0		0.0	False		,,,				2504	0.001				p.V188M		Atlas-SNP	.											.	BTNL2	50	.	0			c.G562A						PASS	.	C	MET/VAL	39,2983		0,39,1472	85.0	79.0	81.0		562	-8.9	0.0	6	dbSNP_119	81	4,5412		0,4,2704	no	missense	BTNL2	NM_019602.1	21	0,43,4176	TT,TC,CC		0.0739,1.2905,0.5096	probably-damaging	188/456	32370859	43,8395	1511	2708	4219	SO:0001583	missense	56244	exon3			CAGACACGGCCAG	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.562G>A	6.37:g.32370859C>T	ENSP00000364132:p.Val188Met	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	194	92	0.474227	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		14|14	0.00641025641025641|0.00641025641025641	12|12	0.024390243902439025|0.024390243902439025	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	8.531|8.531	0.871030|0.871030	0.17322|0.17322	0.012905|0.012905	7.39E-4|7.39E-4	ENSG00000204290|ENSG00000204290	ENST00000374995|ENST00000468270;ENST00000374993	T|T	0.02177|0.75704	4.41|-0.96	4.44|4.44	-8.89|-8.89	0.00785|0.00785	.|CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.023030|2.023030	0.02292|0.02292	N|N	0.070382|0.070382	T|T	0.43787|0.43787	0.1263|0.1263	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	1|1	.|P	.|0.50156	.|0.932	.|P	.|0.45232	.|0.474	T|T	0.61926|0.61926	-0.6962|-0.6962	8|10	0.27785|0.35671	T|T	0.31|0.21	.|.	3.5087|3.5087	0.07700|0.07700	0.2462:0.1048:0.4451:0.2038|0.2462:0.1048:0.4451:0.2038	rs9461742;rs9461742|rs9461742;rs9461742	.|188	.|Q9UIR0	.|BTNL2_HUMAN	I|M	148|188	ENSP00000364134:V148I|ENSP00000364132:V188M	ENSP00000364134:V148I|ENSP00000364132:V188M	V|V	-|-	1|1	0|0	BTNL2|BTNL2	32478837|32478837	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.015000|0.015000	0.08874|0.08874	-8.769000|-8.769000	0.00017|0.00017	-2.865000|-2.865000	0.00325|0.00325	-0.172000|-0.172000	0.13284|0.13284	GTT|GTG	C|0.992;T|0.008	0.008	strong		0.587	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
C3	718	hgsc.bcm.edu	37	19	6711070	6711070	+	Missense_Mutation	SNP	C	C	G	rs11569422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6711070C>G	ENST00000245907.6	-	12	1499	c.1407G>C	c.(1405-1407)gaG>gaC	p.E469D		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	469			E -> D (in dbSNP:rs11569422).		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CGTTGAGGGTCTCCCCGGGTC	0.602													C|||	81	0.0161741	0.059	0.0029	5008	,	,		16993	0.0		0.001	False		,,,				2504	0.0				p.E469D		Atlas-SNP	.											.	C3	192	.	0			c.G1407C						PASS	.	C	ASP/GLU	180,4226	116.7+/-154.6	1,178,2024	244.0	215.0	225.0		1407	-10.1	0.0	19	dbSNP_120	225	3,8597	3.0+/-9.4	0,3,4297	yes	missense	C3	NM_000064.2	45	1,181,6321	GG,GC,CC		0.0349,4.0853,1.407	benign	469/1664	6711070	183,12823	2203	4300	6503	SO:0001583	missense	718	exon12			GAGGGTCTCCCCG	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1407G>C	19.37:g.6711070C>G	ENSP00000245907:p.Glu469Asp	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	184	90	0.48913	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	28	0.01282051282051282	27	0.054878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	C	0.018	-1.468540	0.01053	0.040853	3.49E-4	ENSG00000125730	ENST00000245907	T	0.63417	-0.04	5.03	-10.1	0.00402	Alpha-2-macroglobulin, N-terminal 2 (1);	0.352724	0.35013	N	0.003502	T	0.03739	0.0106	N	0.04655	-0.195	0.09310	N	1	B	0.02656	0.0	B	0.13407	0.009	T	0.41448	-0.9508	10	0.02654	T	1	.	9.8878	0.41272	0.0906:0.1208:0.6374:0.1513	rs11569422	469	P01024	CO3_HUMAN	D	469	ENSP00000245907:E469D	ENSP00000245907:E469D	E	-	3	2	C3	6662070	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-1.288000	0.02783	-0.902000	0.03886	-1.288000	0.01363	GAG	C|0.980;G|0.020	0.020	strong		0.602	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
MPZL2	10205	hgsc.bcm.edu	37	11	118133334	118133334	+	Silent	SNP	T	T	C	rs17122002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118133334T>C	ENST00000278937.2	-	3	383	c.255A>G	c.(253-255)caA>caG	p.Q85Q	MPZL2_ENST00000438295.2_Silent_p.Q85Q|MPZL2_ENST00000525647.1_5'Flank	NM_005797.3	NP_005788.1	O60487	MPZL2_HUMAN	myelin protein zero-like 2	85	Ig-like V-type.				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)		CACTCATGGGTTGGAAGGGAT	0.537													T|||	205	0.0409345	0.1467	0.013	5008	,	,		20403	0.0		0.002	False		,,,				2504	0.0				p.Q85Q		Atlas-SNP	.											.	MPZL2	20	.	0			c.A255G						PASS	.	T	,	655,3745	280.8+/-275.6	62,531,1607	62.0	57.0	59.0		255,255	-6.6	0.0	11	dbSNP_123	59	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous,coding-synonymous	MPZL2	NM_005797.3,NM_144765.2	,	62,536,5898	CC,CT,TT		0.0582,14.8864,5.08	,	85/216,85/216	118133334	660,12332	2200	4296	6496	SO:0001819	synonymous_variant	10205	exon3			CATGGGTTGGAAG	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.255A>G	11.37:g.118133334T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	120	70	0.583333	NM_005797	A8K2R1	Silent	SNP	ENST00000278937.2	37	CCDS8393.1																																																																																			T|0.954;C|0.046	0.046	strong		0.537	MPZL2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392113.1	NM_005797	
SHMT2	6472	hgsc.bcm.edu	37	12	57627074	57627074	+	Silent	SNP	G	G	T	rs2229717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57627074G>T	ENST00000328923.3	+	8	1421	c.969G>T	c.(967-969)ctG>ctT	p.L323L	SHMT2_ENST00000553474.1_Silent_p.L302L|SHMT2_ENST00000449049.3_Silent_p.L302L|SHMT2_ENST00000414700.3_Silent_p.L302L|SHMT2_ENST00000557487.1_Silent_p.L313L|SHMT2_ENST00000393827.4_Silent_p.L227L	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	164	0	0		WXS	Illumina HiSeq	Phase_I	157	89	0.566879	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	
PLCE1	51196	hgsc.bcm.edu	37	10	96012108	96012108	+	Silent	SNP	C	C	T	rs61732522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:96012108C>T	ENST00000371380.3	+	8	3367	c.3132C>T	c.(3130-3132)caC>caT	p.H1044H	PLCE1_ENST00000371375.1_Silent_p.H736H|PLCE1_ENST00000260766.3_Silent_p.H1044H|PLCE1_ENST00000371385.3_Silent_p.H736H			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1044					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)				CTTTGGCTCACGCTGTGGAGT	0.483													C|||	151	0.0301518	0.0908	0.0173	5008	,	,		19190	0.0		0.0109	False		,,,				2504	0.0082				p.H1044H		Atlas-SNP	.											.	PLCE1	543	.	0			c.C3132T						PASS	.	C	,	257,3883		6,245,1819	118.0	120.0	119.0		2208,3132	-12.0	0.4	10	dbSNP_129	119	29,8393		0,29,4182	no	coding-synonymous,coding-synonymous	PLCE1	NM_001165979.1,NM_016341.3	,	6,274,6001	TT,TC,CC		0.3443,6.2077,2.2767	,	736/1995,1044/2303	96012108	286,12276	2070	4211	6281	SO:0001819	synonymous_variant	51196	exon9			GGCTCACGCTGTG		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.3132C>T	10.37:g.96012108C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	202	75	0.371287	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	37	CCDS41552.1																																																																																			C|0.983;T|0.017	0.017	strong		0.483	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
WAS	7454	hgsc.bcm.edu	37	X	48546837	48546837	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48546837G>A	ENST00000376701.4	+	9	1001	c.926G>A	c.(925-927)cGc>cAc	p.R309H		NM_000377.2	NP_000368.1	P42768	WASP_HUMAN	Wiskott-Aldrich syndrome	309					actin filament polymerization (GO:0030041)|actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|blood coagulation (GO:0007596)|defense response (GO:0006952)|endosomal transport (GO:0016197)|epidermis development (GO:0008544)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|regulation of catalytic activity (GO:0050790)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|phospholipase binding (GO:0043274)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(315;1.27e-10)				GAGATGAGGCGCCAGGGTGAG	0.562			"""Mis, N, F, S"""			lymphoma																															p.R309H		Atlas-SNP	.		X-linked recessive		Wiskott-Aldrich syndrome	X	Xp11.23-p11.22	7454	Wiskott-Aldrich syndrome		L	.	WAS	51	.	0			c.G926A						PASS	.						41.0	35.0	37.0					X																	48546837		2203	4300	6503	SO:0001583	missense	7454	exon9			TGAGGCGCCAGGG	AF115548	CCDS14303.1	Xp11.4-p11.21	2014-09-17	2012-07-12		ENSG00000015285	ENSG00000015285			12731	protein-coding gene	gene with protein product	"""eczema-thrombocytopenia"""	300392	"""thrombocytopenia 1 (X-linked)"", ""Wiskott-Aldrich syndrome (eczema-thrombocytopenia)"""	IMD2, THC		7795648	Standard	NM_000377		Approved	WASP	uc004dkm.4	P42768	OTTHUMG00000034483	ENST00000376701.4:c.926G>A	X.37:g.48546837G>A	ENSP00000365891:p.Arg309His	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	255	68	0.266667	NM_000377	Q9BU11|Q9UNJ9	Missense_Mutation	SNP	ENST00000376701.4	37	CCDS14303.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110307	0.77210	.	.	ENSG00000015285	ENST00000376701	D	0.95918	-3.85	4.71	4.71	0.59529	Wiscott-Aldrich syndrome, C-terminal (1);	0.055809	0.64402	D	0.000002	D	0.96679	0.8916	L	0.57536	1.79	0.43947	D	0.99661	D	0.89917	1.0	D	0.69142	0.962	D	0.97151	0.9831	10	0.72032	D	0.01	-11.737	14.3592	0.66757	0.0:0.0:1.0:0.0	.	309	P42768	WASP_HUMAN	H	309	ENSP00000365891:R309H	ENSP00000365891:R309H	R	+	2	0	WAS	48431781	1.000000	0.71417	0.997000	0.53966	0.961000	0.63080	4.816000	0.62642	2.055000	0.61198	0.431000	0.28591	CGC	.	.	none		0.562	WAS-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083379.1	NM_000377	
DMBX1	127343	hgsc.bcm.edu	37	1	46978076	46978076	+	Silent	SNP	C	C	A	rs11211298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46978076C>A	ENST00000360032.3	+	4	1058	c.1044C>A	c.(1042-1044)acC>acA	p.T348T	DMBX1_ENST00000371956.4_Silent_p.T353T	NM_172225.1	NP_757379.1			diencephalon/mesencephalon homeobox 1											endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)					CATCAGCTACCCTGAACAGTA	0.642													C|||	284	0.0567093	0.1293	0.0447	5008	,	,		19133	0.0407		0.0179	False		,,,				2504	0.0235				p.T353T		Atlas-SNP	.											.	DMBX1	50	.	0			c.C1059A						PASS	.	C	,	561,3845	241.5+/-251.9	40,481,1682	56.0	60.0	59.0		1059,1044	3.3	1.0	1	dbSNP_120	59	185,8415	82.6+/-145.2	0,185,4115	no	coding-synonymous,coding-synonymous	DMBX1	NM_147192.2,NM_172225.1	,	40,666,5797	AA,AC,CC		2.1512,12.7326,5.7358	,	353/383,348/378	46978076	746,12260	2203	4300	6503	SO:0001819	synonymous_variant	127343	exon4			AGCTACCCTGAAC	AB037699	CCDS536.1	1p34.1	2011-06-20	2004-03-29	2004-03-30	ENSG00000197587	ENSG00000197587		"""Homeoboxes / PRD class"""	19026	protein-coding gene	gene with protein product		607410	"""orthodenticle homolog 3 (Drosophila)"""	OTX3			Standard	NM_147192		Approved	PAXB	uc001cpx.3	Q8NFW5	OTTHUMG00000007982	ENST00000360032.3:c.1044C>A	1.37:g.46978076C>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_147192		Silent	SNP	ENST00000360032.3	37	CCDS536.1																																																																																			C|0.938;A|0.062	0.062	strong		0.642	DMBX1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021895.1		
SRMS	6725	hgsc.bcm.edu	37	20	62173925	62173925	+	Silent	SNP	T	T	G	rs404613|rs386816161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	145	0	0		WXS	Illumina HiSeq	Phase_I	143	141	0.986014	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	
LRWD1	222229	hgsc.bcm.edu	37	7	102112980	102112980	+	Silent	SNP	G	G	A	rs3800987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:102112980G>A	ENST00000292616.5	+	13	1766	c.1614G>A	c.(1612-1614)acG>acA	p.T538T	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	538					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						GCCAGTCCACGGTGGCAGTGG	0.716													G|||	2312	0.461661	0.3139	0.5519	5008	,	,		15340	0.372		0.662	False		,,,				2504	0.4836				p.T538T		Atlas-SNP	.											LRWD1,NS,carcinoma,0,1	LRWD1	41	1	0			c.G1614A						PASS	.	G		1560,2790		317,926,932	11.0	9.0	10.0		1614	-10.2	0.0	7	dbSNP_107	10	5482,3026		1822,1838,594	no	coding-synonymous	LRWD1	NM_152892.1		2139,2764,1526	AA,AG,GG		35.5665,35.8621,45.2325		538/648	102112980	7042,5816	2175	4254	6429	SO:0001819	synonymous_variant	222229	exon13			GTCCACGGTGGCA	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.1614G>A	7.37:g.102112980G>A		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	19	8	0.421053	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1	1113	0.5096153846153846	173	0.3516260162601626	215	0.5939226519337016	227	0.3968531468531469	498	0.6569920844327177	G	0.094	-1.162080	0.01673	0.358621	0.644335	ENSG00000161036	ENST00000488689;ENST00000468175	.	.	.	5.1	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.51767	P	6.799999999995698E-5	.	.	.	.	.	.	T	0.16719	-1.0393	3	.	.	.	-0.1259	4.6709	0.12689	0.5376:0.2198:0.0955:0.1471	rs3800987;rs10316934;rs13244777;rs17845221;rs17858035;rs17858491	.	.	.	Q	149;124	.	.	R	+	2	0	LRWD1	101899985	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-7.784000	0.00030	-3.315000	0.00189	-1.058000	0.02302	CGG	G|0.476;A|0.524	0.524	strong		0.716	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
CYP27A1	1593	hgsc.bcm.edu	37	2	219674482	219674482	+	Silent	SNP	G	G	A	rs692003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219674482G>A	ENST00000258415.4	+	2	865	c.438G>A	c.(436-438)ccG>ccA	p.P146P		NM_000784.3	NP_000775.1	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A, polypeptide 1	146					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	cholestanetriol 26-monooxygenase activity (GO:0047749)|cholesterol 26-hydroxylase activity (GO:0031073)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(3)|urinary_tract(1)	26		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Chenodeoxycholic acid(DB06777)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Pegvisomant(DB00082)	CCTATGGGCCGTTCACCACGT	0.622													G|||	366	0.0730831	0.2632	0.0259	5008	,	,		16942	0.0		0.0	False		,,,				2504	0.0				p.P146P		Atlas-SNP	.											.	CYP27A1	52	.	0			c.G438A						PASS	.	G		877,3529	341.2+/-306.6	84,709,1410	90.0	78.0	82.0		438	2.9	0.9	2	dbSNP_83	82	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	CYP27A1	NM_000784.3		84,717,5702	AA,AG,GG		0.093,19.9047,6.8046		146/532	219674482	885,12121	2203	4300	6503	SO:0001819	synonymous_variant	1593	exon2			TGGGCCGTTCACC	BC017044	CCDS2423.1	2q35	2013-09-19	2003-01-14		ENSG00000135929	ENSG00000135929		"""Cytochrome P450s"""	2605	protein-coding gene	gene with protein product	"""cerebrotendinous xanthomatosis"""	606530	"""cytochrome P450, subfamily XXVIIA (steroid 27-hydroxylase, cerebrotendinous xanthomatosis), polypeptide 1"""	CYP27		2019602	Standard	NM_000784		Approved	CTX, CP27	uc002viz.4	Q02318	OTTHUMG00000048238	ENST00000258415.4:c.438G>A	2.37:g.219674482G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_000784	A8K303|Q6LDB4|Q86YQ6	Silent	SNP	ENST00000258415.4	37	CCDS2423.1																																																																																			G|0.935;A|0.065	0.065	strong		0.622	CYP27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109734.4		
MYH6	4624	hgsc.bcm.edu	37	14	23874523	23874523	+	Silent	SNP	C	C	T	rs2277474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	173	0	0		WXS	Illumina HiSeq	Phase_I	177	93	0.525424	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		
HSD3B1	3283	hgsc.bcm.edu	37	1	120057163	120057163	+	Silent	SNP	G	G	A	rs33913717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120057163G>A	ENST00000369413.3	+	4	1162	c.1017G>A	c.(1015-1017)gcG>gcA	p.A339A	HSD3B1_ENST00000235547.6_Silent_p.A341A|HSD3B1_ENST00000528909.1_Silent_p.A339A			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	339					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	GAGATCTGGCGTATAAGCCAC	0.517													g|||	37	0.00738818	0.0272	0.0014	5008	,	,		21238	0.0		0.0	False		,,,				2504	0.0				p.A339A		Atlas-SNP	.											HSD3B1,caecum,carcinoma,+1,1	HSD3B1	53	1	0			c.G1017A						PASS	.	A		118,4288	89.2+/-127.9	7,104,2092	83.0	73.0	76.0		1017	-6.5	0.0	1	dbSNP_126	76	0,8600		0,0,4300	yes	coding-synonymous	HSD3B1	NM_000862.2		7,104,6392	AA,AG,GG		0.0,2.6782,0.9073		339/374	120057163	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	3283	exon4			TCTGGCGTATAAG	S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5217	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 1"""	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.1017G>A	1.37:g.120057163G>A		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	250	127	0.508	NM_000862	A8K691|Q14545|Q8IV65	Silent	SNP	ENST00000369413.3	37	CCDS903.1																																																																																			G|0.990;A|0.010	0.010	strong		0.517	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862	
C6orf52	347744	hgsc.bcm.edu	37	6	10687746	10687746	+	Missense_Mutation	SNP	G	G	T	rs7749306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10687746G>T	ENST00000426700.2	-	1	37	c.38C>A	c.(37-39)gCt>gAt	p.A13D	C6orf52_ENST00000503680.1_Intron|C6orf52_ENST00000259983.3_Missense_Mutation_p.A13D|C6orf52_ENST00000379586.1_Intron|C6orf52_ENST00000460742.2_Intron|C6orf52_ENST00000467832.2_5'UTR			Q5T4I8	CF052_HUMAN	chromosome 6 open reading frame 52	13			A -> D (in dbSNP:rs7749306).							endometrium(1)|prostate(1)	2						ATTTTGTTGAGCTATGCCAAA	0.388													G|||	1215	0.242612	0.7829	0.0605	5008	,	,		18302	0.0397		0.0239	False		,,,				2504	0.0757				p.A13D		Atlas-SNP	.											.	C6orf52	9	.	0			c.C38A						PASS	.	G	ASP/ALA	897,487		304,289,99	118.0	111.0	113.0		38	2.2	0.0	6	dbSNP_116	113	68,3114		2,64,1525	yes	missense	C6orf52	NM_001145020.1	126	306,353,1624	TT,TG,GG		2.137,35.1879,21.1345	probably-damaging	13/153	10687746	965,3601	692	1591	2283	SO:0001583	missense	347744	exon2			TGTTGAGCTATGC	BC016820	CCDS47371.1	6p24.2	2009-09-22	2007-06-07	2007-06-07	ENSG00000137434	ENSG00000137434			20881	protein-coding gene	gene with protein product						12477932	Standard	NM_001145020		Approved		uc011dij.2	Q5T4I8	OTTHUMG00000014240	ENST00000426700.2:c.38C>A	6.37:g.10687746G>T	ENSP00000410749:p.Ala13Asp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_001145020	Q5T4I7|Q96AS6	Missense_Mutation	SNP	ENST00000426700.2	37	CCDS47371.1	412	0.18864468864468864	355	0.7215447154471545	19	0.052486187845303865	19	0.033216783216783216	19	0.025065963060686015	G	14.42	2.529881	0.45073	0.648121	0.02137	ENSG00000137434	ENST00000259983;ENST00000426700	T;T	0.50001	0.76;0.76	5.02	2.19	0.27852	.	.	.	.	.	T	0.27731	0.0682	L	0.44542	1.39	0.80722	P	0.0	P	0.48016	0.904	P	0.48227	0.571	T	0.09997	-1.0649	8	0.87932	D	0	.	5.6412	0.17565	0.1876:0.167:0.6455:0.0	rs7749306;rs52792406;rs60049344;rs7749306	13	Q5T4I8	CF052_HUMAN	D	13	ENSP00000259983:A13D;ENSP00000410749:A13D	ENSP00000259983:A13D	A	-	2	0	C6orf52	10795732	0.258000	0.24033	0.001000	0.08648	0.044000	0.14063	1.563000	0.36364	0.626000	0.30322	-0.175000	0.13238	GCT	A|0.000;G|0.781;T|0.219	0.219	strong		0.388	C6orf52-002	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039825.2	NM_001145020	
CD1E	913	hgsc.bcm.edu	37	1	158325819	158325819	+	Silent	SNP	G	G	A	rs61734678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158325819G>A	ENST00000368167.3	+	4	1067	c.828G>A	c.(826-828)gcG>gcA	p.A276A	CD1E_ENST00000368157.1_Intron|CD1E_ENST00000368163.3_Intron|CD1E_ENST00000368161.3_Intron|CD1E_ENST00000452291.2_Silent_p.A87A|CD1E_ENST00000368166.3_Silent_p.A87A|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000444681.2_Silent_p.A177A|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368164.3_Intron|CD1E_ENST00000368156.1_Silent_p.A186A|CD1E_ENST00000368165.3_Silent_p.A186A|CD1E_ENST00000434258.1_Silent_p.A274A|CD1E_ENST00000368160.3_Silent_p.A276A	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	276	Ig-like.				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)					TGGATGTGGCGGCTGGGGAGG	0.607													G|||	70	0.0139776	0.0507	0.0043	5008	,	,		15775	0.0		0.0	False		,,,				2504	0.0				p.A276A		Atlas-SNP	.											CD1E,colon,carcinoma,+1,2	CD1E	129	2	0			c.G828A						PASS	.	G	,,,,,,,,,,,,	153,4253	104.3+/-142.8	6,141,2056	85.0	86.0	86.0		828,,,261,,558,,,261,,531,558,828	-8.6	0.0	1	dbSNP_129	86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,intron,coding-synonymous,intron,coding-synonymous,intron,intron,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	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	,,,,,,,,,,,,	6,142,6355	AA,AG,GG		0.0116,3.4725,1.1841	,,,,,,,,,,,,	276/377,,,87/188,,186/299,,,87/200,,177/290,186/287,276/389	158325819	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	913	exon4			TGTGGCGGCTGGG	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.828G>A	1.37:g.158325819G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	249	114	0.457831	NM_030893	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	Silent	SNP	ENST00000368167.3	37	CCDS41417.1																																																																																			G|0.988;A|0.012	0.012	strong		0.607	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893	
OBSCN	84033	hgsc.bcm.edu	37	1	228547691	228547691	+	Intron	SNP	C	C	T	rs367920745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228547691C>T	ENST00000422127.1	+	80	18705				OBSCN_ENST00000284548.11_Silent_p.P6366P|OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366709.4_Silent_p.P3485P|OBSCN_ENST00000366707.4_Intron	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)				GTGCGACCCCCGGAGGGGACC	0.647													C|||	36	0.0071885	0.0272	0.0	5008	,	,		17215	0.0		0.0	False		,,,				2504	0.0				p.P6366P		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C19098T						PASS	.	C	,	82,3694		1,80,1807	17.0	20.0	19.0		,19098	-8.8	0.0	1		19	0,8218		0,0,4109	no	intron,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1,80,5916	TT,TC,CC		0.0,2.1716,0.6837	,	,6366/6621	228547691	82,11912	1888	4109	5997	SO:0001627	intron_variant	84033	exon81			GACCCCCGGAGGG	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.18662-2586C>T	1.37:g.228547691C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	164	83	0.506098	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																																																																																			.	.	none		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ABCA8	10351	hgsc.bcm.edu	37	17	66928460	66928460	+	Missense_Mutation	SNP	T	T	C	rs16973446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66928460T>C	ENST00000269080.2	-	6	903	c.766A>G	c.(766-768)Aca>Gca	p.T256A	ABCA8_ENST00000586539.1_Missense_Mutation_p.T256A|ABCA8_ENST00000430352.2_Missense_Mutation_p.T256A	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	256			T -> A (in dbSNP:rs16973446).		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)					CCCATCATTGTCATCAAGGCC	0.393													T|||	383	0.0764776	0.2738	0.0231	5008	,	,		20528	0.0		0.005	False		,,,				2504	0.0				p.T256A		Atlas-SNP	.											.	ABCA8	213	.	0			c.A766G						PASS	.	T	ALA/THR	1058,3348	384.9+/-325.5	129,800,1274	86.0	79.0	81.0		766	2.6	0.5	17	dbSNP_123	81	17,8583	12.6+/-44.7	0,17,4283	yes	missense	ABCA8	NM_007168.2	58	129,817,5557	CC,CT,TT		0.1977,24.0127,8.2654	benign	256/1582	66928460	1075,11931	2203	4300	6503	SO:0001583	missense	10351	exon6			TCATTGTCATCAA	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.766A>G	17.37:g.66928460T>C	ENSP00000269080:p.Thr256Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	140	0.0641025641025641	128	0.2601626016260163	10	0.027624309392265192	0	0.0	2	0.002638522427440633	T	9.995	1.231776	0.22626	0.240127	0.001977	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000428549	D;D	0.82344	-1.6;-1.6	4.85	2.63	0.31362	.	1.596760	0.03628	N	0.237455	T	0.00039	0.0001	N	0.26130	0.795	0.47407	P	5.819999999999714E-4	B;B;B;B;B	0.22146	0.065;0.02;0.036;0.003;0.02	B;B;B;B;B	0.21360	0.03;0.02;0.021;0.012;0.034	T	0.04041	-1.0982	9	0.42905	T	0.14	.	6.2716	0.20956	0.0:0.1989:0.0:0.8011	rs16973446;rs16973446	195;256;256;256;256	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	A	256;256;195;256	ENSP00000269080:T256A;ENSP00000402814:T256A	ENSP00000269080:T256A	T	-	1	0	ABCA8	64440055	0.856000	0.29760	0.510000	0.27712	0.553000	0.35397	1.060000	0.30530	0.444000	0.26612	-0.385000	0.06624	ACA	T|0.915;C|0.085	0.085	strong		0.393	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
PLA2G4F	255189	hgsc.bcm.edu	37	15	42438380	42438380	+	Silent	SNP	G	G	A	rs80108792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42438380G>A	ENST00000382396.4	-	14	1565	c.1479C>T	c.(1477-1479)taC>taT	p.Y493Y	PLA2G4F_ENST00000397272.3_Silent_p.Y495Y			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	493	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)		TGTAAATGGGGTAAGGGTTCT	0.582													G|||	69	0.013778	0.0507	0.0014	5008	,	,		20601	0.0		0.001	False		,,,				2504	0.0				p.Y493Y		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.C1479T						PASS	.	G		155,4251	105.6+/-144.1	4,147,2052	100.0	89.0	92.0		1479	-2.0	1.0	15	dbSNP_132	92	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PLA2G4F	NM_213600.3		4,148,6350	AA,AG,GG		0.0116,3.5179,1.1996		493/850	42438380	156,12848	2203	4299	6502	SO:0001819	synonymous_variant	255189	exon14			AATGGGGTAAGGG		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.1479C>T	15.37:g.42438380G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_213600	Q6ZMC8	Silent	SNP	ENST00000382396.4	37	CCDS32204.1																																																																																			G|0.988;A|0.012	0.012	strong		0.582	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
ISLR2	57611	hgsc.bcm.edu	37	15	74425410	74425410	+	Silent	SNP	T	T	C	rs3743207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:74425410T>C	ENST00000361742.3	+	4	1084	c.315T>C	c.(313-315)gaT>gaC	p.D105D	ISLR2_ENST00000445793.1_Silent_p.D105D|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000565540.1_Silent_p.D105D|ISLR2_ENST00000419208.1_Silent_p.D105D|ISLR2_ENST00000453268.2_Silent_p.D105D|ISLR2_ENST00000565159.1_Silent_p.D105D|ISLR2_ENST00000435464.1_Silent_p.D105D	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	105					positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						AGAACCTCGATCTGAGCCACA	0.617													C|||	508	0.101438	0.2897	0.0418	5008	,	,		18438	0.0427		0.0209	False		,,,				2504	0.0327				p.D105D		Atlas-SNP	.											.	ISLR2	78	.	0			c.T315C						PASS	.	C	,,,	1118,3278	709.8+/-407.8	140,838,1220	77.0	71.0	73.0		315,315,315,315	2.8	1.0	15	dbSNP_107	73	133,8461	807.3+/-407.2	0,133,4164	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ISLR2	NM_001130136.1,NM_001130137.1,NM_001130138.1,NM_020851.2	,,,	140,971,5384	CC,CT,TT		1.5476,25.4322,9.6305	,,,	105/746,105/746,105/746,105/746	74425410	1251,11739	2198	4297	6495	SO:0001819	synonymous_variant	57611	exon4			CCTCGATCTGAGC		CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.315T>C	15.37:g.74425410T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_001130138	A8K352|Q9P263	Silent	SNP	ENST00000361742.3	37	CCDS10259.1																																																																																			T|0.898;C|0.102	0.102	strong		0.617	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851	
CLRN2	645104	hgsc.bcm.edu	37	4	17517141	17517141	+	Splice_Site	SNP	G	G	A	rs201838208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:17517141G>A	ENST00000511148.2	+	1	354	c.252G>A	c.(250-252)acG>acA	p.T84T		NM_001079827.2	NP_001073296.1	A0PK11	CLRN2_HUMAN	clarin 2	84						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|upper_aerodigestive_tract(1)	15						CCCAATTCACGAGTGAGTATA	0.483													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18289	0.0		0.0	False		,,,				2504	0.0				p.T84T		Atlas-SNP	.											.	CLRN2	40	.	0			c.G252A						PASS	.	G		5,3809		0,5,1902	46.0	45.0	45.0		252	-10.8	0.1	4		45	0,8216		0,0,4108	yes	coding-synonymous-near-splice	CLRN2	NM_001079827.2		0,5,6010	AA,AG,GG		0.0,0.1311,0.0416		84/233	17517141	5,12025	1907	4108	6015	SO:0001630	splice_region_variant	645104	exon1			ATTCACGAGTGAG		CCDS47032.1	4p15.32	2008-01-17			ENSG00000249581	ENSG00000249581			33939	protein-coding gene	gene with protein product						12080385	Standard	NM_001079827		Approved		uc003gpg.1	A0PK11	OTTHUMG00000160273	ENST00000511148.2:c.253+1G>A	4.37:g.17517141G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	148	80	0.540541	NM_001079827		Silent	SNP	ENST00000511148.2	37	CCDS47032.1																																																																																			.	.	weak		0.483	CLRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359990.2	NM_001079827	Silent
CMYA5	202333	hgsc.bcm.edu	37	5	79029749	79029749	+	Missense_Mutation	SNP	A	A	G	rs1428225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79029749A>G	ENST00000446378.2	+	2	5192	c.5161A>G	c.(5161-5163)Atc>Gtc	p.I1721V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1721			I -> V (in dbSNP:rs1428225).		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)		p.I1721V(1)		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)		TCCCAAGATCATCAGCCTAGA	0.418													G|||	1389	0.277356	0.5961	0.085	5008	,	,		18104	0.3621		0.0815	False		,,,				2504	0.0971				p.I1721V		Atlas-SNP	.											CMYA5,NS,carcinoma,0,1	CMYA5	643	1	1	Substitution - Missense(1)	stomach(1)	c.A5161G						scavenged	.	G	VAL/ILE	1877,1849		487,903,473	50.0	52.0	52.0		5161	2.8	0.0	5	dbSNP_88	52	707,7475		39,629,3423	yes	missense	CMYA5	NM_153610.3	29	526,1532,3896	GG,GA,AA		8.6409,49.6243,21.6997	benign	1721/4070	79029749	2584,9324	1863	4091	5954	SO:0001583	missense	202333	exon2			AAGATCATCAGCC	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.5161A>G	5.37:g.79029749A>G	ENSP00000394770:p.Ile1721Val	Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	64	64	1	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	627	0.28708791208791207	305	0.6199186991869918	31	0.0856353591160221	232	0.40559440559440557	59	0.07783641160949868	G	0.001	-3.170670	0.00027	0.503757	0.086409	ENSG00000164309	ENST00000446378	T	0.37752	1.18	3.64	2.77	0.32553	.	.	.	.	.	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	0.47086	-0.9144	8	0.02654	T	1	.	4.7036	0.12839	0.1166:0.0:0.6708:0.2126	rs1428225;rs16877145;rs57809833	1721	Q8N3K9	CMYA5_HUMAN	V	1721	ENSP00000394770:I1721V	ENSP00000394770:I1721V	I	+	1	0	CMYA5	79065505	0.005000	0.15991	0.009000	0.14445	0.001000	0.01503	0.467000	0.22035	0.110000	0.17919	-0.913000	0.02753	ATC	A|0.752;G|0.248	0.248	strong		0.418	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
SLX4	84464	hgsc.bcm.edu	37	16	3645607	3645607	+	Splice_Site	SNP	A	A	G	rs77985244	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3645607A>G	ENST00000294008.3	-	9	2652	c.2012T>C	c.(2011-2013)tTg>tCg	p.L671S		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	671			L -> S (in dbSNP:rs77985244). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						AGTTCTTACCAAGGTGCGGCC	0.667								Direct reversal of damage					G|||	311	0.0621006	0.0779	0.0735	5008	,	,		17478	0.0506		0.0646	False		,,,				2504	0.0419				p.L671S		Atlas-SNP	.											.	SLX4	173	.	0			c.T2012C						PASS	.	G	SER/LEU	402,3992	781.3+/-414.5	20,362,1815	40.0	44.0	42.0		2012	0.9	0.1	16	dbSNP_131	42	582,8018	789.1+/-407.6	15,552,3733	yes	missense-near-splice	SLX4	NM_032444.2	145	35,914,5548	GG,GA,AA		6.7674,9.1488,7.5727	benign	671/1835	3645607	984,12010	2197	4300	6497	SO:0001630	splice_region_variant	84464	exon9			CTTACCAAGGTGC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2013+1T>C	16.37:g.3645607A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	140	0.0641025641025641	44	0.08943089430894309	24	0.06629834254143646	24	0.04195804195804196	48	0.0633245382585752	G	1.261	-0.615866	0.03663	0.091488	0.067674	ENSG00000188827	ENST00000294008	T	0.00995	5.46	5.07	0.88	0.19161	.	0.839455	0.10270	N	0.694860	T	0.00012	0.0000	N	0.00162	-1.95	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39057	-0.9632	10	0.15066	T	0.55	.	7.4261	0.27100	0.4675:0.0:0.5325:0.0	.	671	Q8IY92	SLX4_HUMAN	S	671	ENSP00000294008:L671S	ENSP00000294008:L671S	L	-	2	0	SLX4	3585608	0.263000	0.24083	0.107000	0.21349	0.065000	0.16274	0.569000	0.23638	0.028000	0.15324	-0.215000	0.12644	TTG	A|0.932;G|0.068	0.068	strong		0.667	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	Missense_Mutation
MDC1	9656	hgsc.bcm.edu	37	6	30673013	30673013	+	Missense_Mutation	SNP	A	A	G	rs61733213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30673013A>G	ENST00000376406.3	-	10	4594	c.3947T>C	c.(3946-3948)aTg>aCg	p.M1316T	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Missense_Mutation_p.M1052T	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1316	Interaction with the PRKDC complex.|Pro-rich.			Missing (in Ref. 2; CAH18685). {ECO:0000305}.	DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						GACAGAGGACATATTTGTCCT	0.597								Other conserved DNA damage response genes					a|||	234	0.0467252	0.1278	0.0432	5008	,	,		19113	0.0208		0.0129	False		,,,				2504	0.001				p.M1316T		Atlas-SNP	.											.	MDC1	218	.	0			c.T3947C						PASS	.	C	THR/MET	480,3926	224.9+/-240.9	34,412,1757	141.0	152.0	148.0		3947	-1.8	0.0	6	dbSNP_129	148	95,8505	52.3+/-112.8	1,93,4206	no	missense	MDC1	NM_014641.2	81	35,505,5963	GG,GA,AA		1.1047,10.8942,4.421	benign	1316/2090	30673013	575,12431	2203	4300	6503	SO:0001583	missense	9656	exon10			GAGGACATATTTG	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.3947T>C	6.37:g.30673013A>G	ENSP00000365588:p.Met1316Thr	Somatic	322	1	0.00310559		WXS	Illumina HiSeq	Phase_I	363	186	0.512397	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	100	0.045787545787545784	59	0.11991869918699187	16	0.04419889502762431	17	0.02972027972027972	8	0.010554089709762533	a	2.633	-0.285988	0.05605	0.108942	0.011047	ENSG00000137337	ENST00000376406;ENST00000376405	T;T	0.05139	3.49;3.49	3.32	-1.81	0.07882	.	0.445015	0.16677	N	0.204131	T	0.00637	0.0021	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12837	0.008;0.004	T	0.42103	-0.9471	10	0.12103	T	0.63	.	3.1868	0.06603	0.299:0.311:0.0:0.3899	.	1052;1316	Q14676-2;Q14676	.;MDC1_HUMAN	T	1316;1052	ENSP00000365588:M1316T;ENSP00000365587:M1052T	ENSP00000365587:M1052T	M	-	2	0	MDC1	30780992	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.173000	0.03108	-0.789000	0.04498	-3.196000	0.00055	ATG	A|0.958;G|0.042	0.042	strong		0.597	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
CHD5	26038	hgsc.bcm.edu	37	1	6209363	6209363	+	Silent	SNP	T	T	C	rs12565328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6209363T>C	ENST00000262450.3	-	8	1203	c.1104A>G	c.(1102-1104)gtA>gtG	p.V368V	CHD5_ENST00000378021.1_5'UTR	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)		GGTCCAGGCATACGAGATGGT	0.652													C|||	2623	0.523762	0.7216	0.2147	5008	,	,		17436	0.6538		0.3082	False		,,,				2504	0.5634				p.V368V		Atlas-SNP	.											.	CHD5	267	.	0			c.A1104G						PASS	.	C		2866,1540	481.9+/-359.3	938,990,275	66.0	54.0	58.0		1104	-0.9	1.0	1	dbSNP_120	58	2466,6134	693.8+/-404.7	362,1742,2196	no	coding-synonymous	CHD5	NM_015557.2		1300,2732,2471	CC,CT,TT		28.6744,34.9523,40.9965		368/1955	6209363	5332,7674	2203	4300	6503	SO:0001819	synonymous_variant	26038	exon8			CAGGCATACGAGA	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.1104A>G	1.37:g.6209363T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			T|0.543;C|0.457	0.457	strong		0.652	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
PLIN4	729359	hgsc.bcm.edu	37	19	4512939	4512939	+	Missense_Mutation	SNP	T	T	C	rs201080851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512939T>C	ENST00000301286.3	-	3	990	c.991A>G	c.(991-993)Atg>Gtg	p.M331V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	331	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						GCCACATTCATGGCACCAGTC	0.567													C|||	571	0.114018	0.3555	0.0418	5008	,	,		19316	0.0139		0.0129	False		,,,				2504	0.046				p.M331V		Atlas-SNP	.											.	PLIN4	191	.	0			c.A991G						PASS	.						41.0	48.0	46.0					19																	4512939		1878	4128	6006	SO:0001583	missense	729359	exon3			CATTCATGGCACC	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.991A>G	19.37:g.4512939T>C	ENSP00000301286:p.Met331Val	Somatic	381	0	0		WXS	Illumina HiSeq	Phase_I	260	78	0.3	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	C	0.032	-1.330526	0.01298	.	.	ENSG00000167676	ENST00000301286	T	0.04317	3.65	4.59	-7.01	0.01594	.	1.024380	0.07776	N	0.952612	T	0.02571	0.0078	N	0.16478	0.41	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48222	-0.9054	10	0.11794	T	0.64	-2.0373	9.6981	0.40169	0.0:0.4781:0.1:0.422	.	331	Q96Q06	PLIN4_HUMAN	V	331	ENSP00000301286:M331V	ENSP00000301286:M331V	M	-	1	0	PLIN4	4463939	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.790000	0.00098	-2.169000	0.00777	-0.355000	0.07637	ATG	T|0.984;C|0.016	0.016	strong		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
KRTAP1-5	83895	hgsc.bcm.edu	37	17	39183304	39183304	+	Missense_Mutation	SNP	C	C	T	rs62623375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39183304C>T	ENST00000361883.5	-	1	150	c.104G>A	c.(103-105)tGc>tAc	p.C35Y		NM_031957.1	NP_114163.1	Q9BYS1	KRA15_HUMAN	keratin associated protein 1-5	35	15 X 5 AA repeats of C-C-[QEPVRC]- [TPIVLE]-[SRHVP].					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(2)|kidney(1)|lung(9)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	17		Breast(137;0.00043)	STAD - Stomach adenocarcinoma(17;0.000371)			GCGTGGCTGGCAGCAGCTGGT	0.607													c|||	536	0.107029	0.1891	0.1167	5008	,	,		18047	0.1627		0.0169	False		,,,				2504	0.0245				p.C35Y		Atlas-SNP	.											.	KRTAP1-5	33	.	0			c.G104A						PASS	.	C	TYR/CYS	555,3407		36,483,1462	37.0	44.0	42.0		104	2.2	1.0	17	dbSNP_129	42	124,8218		6,112,4053	yes	missense	KRTAP1-5	NM_031957.1	194	42,595,5515	TT,TC,CC		1.4865,14.0081,5.5185	benign	35/175	39183304	679,11625	1981	4171	6152	SO:0001583	missense	83895	exon1			GGCTGGCAGCAGC	AJ406928	CCDS42321.1	17q21.2	2013-06-25			ENSG00000221852	ENSG00000221852		"""Keratin associated proteins"""	16777	protein-coding gene	gene with protein product		608822				11279113	Standard	NM_031957		Approved	KAP1.5	uc002hvu.3	Q9BYS1	OTTHUMG00000133587	ENST00000361883.5:c.104G>A	17.37:g.39183304C>T	ENSP00000355302:p.Cys35Tyr	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	182	74	0.406593	NM_031957	A6NJW6|A6NLZ6|B6ZDR1|Q52LP6	Missense_Mutation	SNP	ENST00000361883.5	37	CCDS42321.1	256	0.11721611721611722	108	0.21951219512195122	31	0.0856353591160221	100	0.17482517482517482	17	0.022427440633245383	C	10.66	1.411519	0.25465	0.140081	0.014865	ENSG00000221852	ENST00000361883;ENST00000543389	T	0.50001	0.76	2.17	2.17	0.27698	.	.	.	.	.	T	0.00039	0.0001	M	0.89163	3.01	0.35879	P	0.17119600000000001	B	0.21606	0.058	B	0.19391	0.025	T	0.16305	-1.0407	8	0.87932	D	0	.	10.0021	0.41935	0.0:1.0:0.0:0.0	rs62623375	35	Q9BYS1	KRA15_HUMAN	Y	35	ENSP00000355302:C35Y	ENSP00000355302:C35Y	C	-	2	0	KRTAP1-5	36436830	1.000000	0.71417	0.997000	0.53966	0.917000	0.54804	1.035000	0.30216	1.246000	0.43901	0.511000	0.50034	TGC	C|0.882;T|0.118	0.118	strong		0.607	KRTAP1-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257691.1		
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73932560	73932560	+	Silent	SNP	A	A	G	rs17851629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73932560A>G	ENST00000265755.3	+	5	906	c.513A>G	c.(511-513)gaA>gaG	p.E171E	GTF2IRD1_ENST00000424337.2_Silent_p.E171E|GTF2IRD1_ENST00000476977.1_Silent_p.E171E|GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000455841.2_Silent_p.E203E	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	171					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GGCTGCCCGAAGGCCTGGCCT	0.662													G|||	1186	0.236821	0.4682	0.196	5008	,	,		14985	0.0952		0.16	False		,,,				2504	0.1779				p.E203E		Atlas-SNP	.											.	GTF2IRD1	91	.	0			c.A609G						PASS	.	G	,,	1791,2611		358,1075,768	24.0	24.0	24.0		609,513,513	1.6	1.0	7	dbSNP_123	24	1707,6893		165,1377,2758	no	coding-synonymous,coding-synonymous,coding-synonymous	GTF2IRD1	NM_001199207.1,NM_005685.3,NM_016328.2	,,	523,2452,3526	GG,GA,AA		19.8488,40.6861,26.9036	,,	203/977,171/945,171/960	73932560	3498,9504	2201	4300	6501	SO:0001819	synonymous_variant	9569	exon5			GCCCGAAGGCCTG	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.513A>G	7.37:g.73932560A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001199207	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Silent	SNP	ENST00000265755.3	37	CCDS5571.1																																																																																			A|0.744;G|0.256	0.256	strong		0.662	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328	
MUC17	140453	hgsc.bcm.edu	37	7	100675376	100675376	+	Missense_Mutation	SNP	A	A	C	rs10229731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100675376A>C	ENST00000306151.4	+	3	743	c.679A>C	c.(679-681)Aag>Cag	p.K227Q		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	227	59 X approximate tandem repeats.|Ser-rich.		K -> Q (in dbSNP:rs10229731).		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)					CAGCACCATGAAGGTGGCCAG	0.478													C|||	1179	0.235423	0.3396	0.1009	5008	,	,		23835	0.254		0.1213	False		,,,				2504	0.2883				p.K227Q		Atlas-SNP	.											.	MUC17	804	.	0			c.A679C						PASS	.	C	GLN/LYS	1330,3076	695.0+/-405.9	209,912,1082	174.0	177.0	176.0		679	-0.6	0.0	7	dbSNP_119	176	998,7602	773.4+/-407.7	56,886,3358	yes	missense	MUC17	NM_001040105.1	53	265,1798,4440	CC,CA,AA		11.6047,30.1861,17.8994	benign	227/4494	100675376	2328,10678	2203	4300	6503	SO:0001583	missense	140453	exon3			ACCATGAAGGTGG	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.679A>C	7.37:g.100675376A>C	ENSP00000302716:p.Lys227Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	411	0.18818681318681318	142	0.2886178861788618	41	0.1132596685082873	139	0.243006993006993	89	0.11741424802110818	C	0.851	-0.738688	0.03111	0.301861	0.116047	ENSG00000169876	ENST00000306151	T	0.02656	4.21	0.533	-0.628	0.11537	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15719	0.014	B	0.01281	0.0	T	0.42155	-0.9468	7	0.13470	T	0.59	.	.	.	.	rs10229731;rs52834675;rs59400468;rs10229731	227	Q685J3	MUC17_HUMAN	Q	227	ENSP00000302716:K227Q	ENSP00000302716:K227Q	K	+	1	0	MUC17	100462096	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-4.063000	0.00302	-1.118000	0.02961	-1.116000	0.02052	AAG	A|0.825;C|0.175	0.175	strong		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TRIM64C	646754	hgsc.bcm.edu	37	11	49080616	49080616	+	Missense_Mutation	SNP	T	T	C	rs60452246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:49080616T>C	ENST00000530230.1	-	1	48	c.49A>G	c.(49-51)Att>Gtt	p.I17V		NM_001206631.1	NP_001193560.1	A6NLI5	TR64C_HUMAN	tripartite motif containing 64C	17						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						TTCACGCAAATGCAGCAAATG	0.428													T|||	1652	0.329872	0.087	0.5115	5008	,	,		17546	0.3651		0.498	False		,,,				2504	0.32				p.I17V		Atlas-SNP	.											.	TRIM64C	18	.	0			c.A49G						PASS	.																																			SO:0001583	missense	646754	exon1			CGCAAATGCAGCA		CCDS73287.1	11p11.12	2014-04-02	2011-01-25		ENSG00000214891	ENSG00000214891		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	37148	protein-coding gene	gene with protein product			"""tripartite motif-containing 64C"""				Standard	NM_001206631		Approved		uc021qiy.1	A6NLI5	OTTHUMG00000166752	ENST00000530230.1:c.49A>G	11.37:g.49080616T>C	ENSP00000431987:p.Ile17Val	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	244	113	0.463115	NM_001206631		Missense_Mutation	SNP	ENST00000530230.1	37		854	0.391025641025641	46	0.09349593495934959	188	0.5193370165745856	238	0.4160839160839161	382	0.503957783641161	T	6.400	0.441899	0.12164	.	.	ENSG00000214891	ENST00000530230	T	0.25414	1.8	1.55	0.361	0.16107	.	.	.	.	.	T	0.00012	0.0000	L	0.39514	1.22	0.80722	P	0.0	.	.	.	.	.	.	T	0.45205	-0.9277	6	0.42905	T	0.14	.	3.4227	0.07400	0.0:0.2331:0.0:0.7669	rs60452246;rs61886908	.	.	.	V	17	ENSP00000431987:I17V	ENSP00000431987:I17V	I	-	1	0	TRIM64C	49037192	0.827000	0.29292	0.003000	0.11579	0.054000	0.15201	0.855000	0.27805	0.100000	0.17581	0.155000	0.16302	ATT	T|0.586;C|0.414	0.414	strong		0.428	TRIM64C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391366.1		
PTPN23	25930	hgsc.bcm.edu	37	3	47454398	47454398	+	Missense_Mutation	SNP	C	C	T	rs140165828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47454398C>T	ENST00000265562.4	+	25	4711	c.4634C>T	c.(4633-4635)cCg>cTg	p.P1545L	PTPN23_ENST00000431726.1_Missense_Mutation_p.P1419L	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1545	Pro-rich.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TCTTCCTCCCCGCCCCCCCTT	0.701													C|||	9	0.00179712	0.0068	0.0	5008	,	,		11435	0.0		0.0	False		,,,				2504	0.0				p.P1545L		Atlas-SNP	.											PTPN23,NS,carcinoma,-1,1	PTPN23	85	1	0			c.C4634T						PASS	.	C	LEU/PRO	19,4375		0,19,2178	21.0	24.0	23.0		4634	3.9	0.8	3	dbSNP_134	23	0,8586		0,0,4293	yes	missense	PTPN23	NM_015466.2	98	0,19,6471	TT,TC,CC		0.0,0.4324,0.1464	probably-damaging	1545/1637	47454398	19,12961	2197	4293	6490	SO:0001583	missense	25930	exon25			CCTCCCCGCCCCC	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.4634C>T	3.37:g.47454398C>T	ENSP00000265562:p.Pro1545Leu	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	247	116	0.469636	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	13.75	2.328844	0.41197	0.004324	0.0	ENSG00000076201	ENST00000265562	T	0.02916	4.11	3.9	3.9	0.45041	.	0.171581	0.36932	N	0.002332	T	0.02929	0.0087	L	0.27053	0.805	0.50171	D	0.999851	D	0.64830	0.994	P	0.51453	0.67	T	0.50825	-0.8782	10	0.72032	D	0.01	-10.0851	11.2398	0.48962	0.0:0.8134:0.1866:0.0	.	1545	Q9H3S7	PTN23_HUMAN	L	1545	ENSP00000265562:P1545L	ENSP00000265562:P1545L	P	+	2	0	PTPN23	47429402	0.499000	0.26083	0.835000	0.33067	0.668000	0.39293	2.241000	0.43097	2.146000	0.66826	0.563000	0.77884	CCG	C|0.998;T|0.002	0.002	strong		0.701	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
CHST12	55501	hgsc.bcm.edu	37	7	2472662	2472662	+	Missense_Mutation	SNP	G	G	C	rs11537796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2472662G>C	ENST00000258711.6	+	2	523	c.388G>C	c.(388-390)Ggc>Cgc	p.G130R		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	130					carbohydrate biosynthetic process (GO:0016051)|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)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		CGTGCTGCGGGGCTTCTGCGC	0.701													G|||	141	0.028155	0.0968	0.0159	5008	,	,		14367	0.0		0.002	False		,,,				2504	0.0				p.G130R		Atlas-SNP	.											.	CHST12	39	.	0			c.G388C						PASS	.	G	ARG/GLY	361,4045		25,311,1867	35.0	37.0	37.0		388	4.2	0.3	7	dbSNP_120	37	2,8598		0,2,4298	yes	missense	CHST12	NM_018641.4	125	25,313,6165	CC,CG,GG		0.0233,8.1934,2.791	benign	130/415	2472662	363,12643	2203	4300	6503	SO:0001583	missense	55501	exon2			CTGCGGGGCTTCT	AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.388G>C	7.37:g.2472662G>C	ENSP00000258711:p.Gly130Arg	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	21	10	0.47619	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	55	0.025183150183150184	48	0.0975609756097561	5	0.013812154696132596	0	0.0	2	0.002638522427440633	G	2.483	-0.319175	0.05386	0.081934	2.33E-4	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.60548	0.18;1.03	5.09	4.18	0.49190	.	0.697828	0.14301	N	0.328271	T	0.01387	0.0045	N	0.22421	0.69	0.25416	N	0.988316	B	0.19583	0.037	B	0.18871	0.023	T	0.00978	-1.1493	10	0.17832	T	0.49	-6.2778	13.8779	0.63665	0.0:0.2917:0.7083:0.0	rs11537796	130	Q9NRB3	CHSTC_HUMAN	R	130	ENSP00000258711:G130R;ENSP00000411207:G130R	ENSP00000258711:G130R	G	+	1	0	CHST12	2439188	0.021000	0.18746	0.287000	0.24848	0.689000	0.40095	1.514000	0.35834	1.095000	0.41419	0.561000	0.74099	GGC	G|0.970;C|0.030	0.030	strong		0.701	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32714168	32714168	+	Silent	SNP	A	A	G	rs9276437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32714168A>G	ENST00000374940.3	+	4	867	c.765A>G	c.(763-765)ttA>ttG	p.L255L		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	255					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)"""	AAGGGCTCTTATGAATCCCAT	0.517													.|||	786	0.156949	0.3033	0.219	5008	,	,		21502	0.0655		0.1153	False		,,,				2504	0.0521				p.L255L		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.A765G						PASS	.	G		751,2271		79,593,839	119.0	121.0	120.0		765	1.1	0.1	6	dbSNP_118	120	527,4891		14,499,2196	no	coding-synonymous	HLA-DQA2	NM_020056.4		93,1092,3035	GG,GA,AA		9.7268,24.8511,15.1422		255/256	32714168	1278,7162	1511	2709	4220	SO:0001819	synonymous_variant	3118	exon4			GCTCTTATGAATC		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.765A>G	6.37:g.32714168A>G		Somatic	385	2	0.00519481		WXS	Illumina HiSeq	Phase_I	454	250	0.550661	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	37	CCDS4753.1																																																																																			A|0.848;G|0.152	0.152	strong		0.517	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
XCL1	6375	hgsc.bcm.edu	37	1	168549321	168549321	+	Missense_Mutation	SNP	G	G	C	rs56148248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:168549321G>C	ENST00000367818.3	+	2	247	c.82G>C	c.(82-84)Gat>Cat	p.D28H		NM_002995.2	NP_002986.1	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1	28					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)					TGAAGTCTCAGATAAGAGGAC	0.433													G|||	160	0.0319489	0.115	0.0029	5008	,	,		19069	0.001		0.005	False		,,,				2504	0.0				p.D28H		Atlas-SNP	.											.	XCL1	16	.	0			c.G82C						PASS	.	G	HIS/ASP	274,4132		34,206,1963	129.0	132.0	131.0		82	0.2	0.0	1	dbSNP_129	131	4,8596		0,4,4296	no	missense	XCL1	NM_002995.2	81	34,210,6259	CC,CG,GG		0.0465,6.2188,2.1375	benign	28/115	168549321	278,12728	2203	4300	6503	SO:0001583	missense	6375	exon2			GTCTCAGATAAGA	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.82G>C	1.37:g.168549321G>C	ENSP00000356792:p.Asp28His	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	161	68	0.42236	NM_002995	Q52MA8	Missense_Mutation	SNP	ENST00000367818.3	37	CCDS1274.1	44	0.020146520146520148	37	0.07520325203252033	2	0.0055248618784530384	1	0.0017482517482517483	4	0.005277044854881266	G	11.98	1.801914	0.31869	0.062188	4.65E-4	ENSG00000143184	ENST00000367818	T	0.03982	3.74	4.36	0.171	0.15026	Chemokine interleukin-8-like domain (2);	1.336140	0.04578	N	0.394548	T	0.02193	0.0068	L	0.29908	0.895	0.25228	N	0.98985	P	0.44309	0.832	P	0.49085	0.6	T	0.37009	-0.9724	9	0.62326	D	0.03	-0.0463	3.0265	0.06092	0.0977:0.3375:0.3913:0.1734	rs56148248	28	P47992	XCL1_HUMAN	H	28	ENSP00000356792:D28H	ENSP00000356792:D28H	D	+	1	0	XCL1	166815945	0.001000	0.12720	0.006000	0.13384	0.548000	0.35241	0.157000	0.16402	0.172000	0.19760	0.655000	0.94253	GAT	G|0.982;C|0.018	0.018	strong		0.433	XCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083612.1	NM_002995	
PTPRB	5787	hgsc.bcm.edu	37	12	70928616	70928616	+	Silent	SNP	G	G	A	rs3752703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:70928616G>A	ENST00000261266.5	-	28	5576	c.5547C>T	c.(5545-5547)tgC>tgT	p.C1849C	PTPRB_ENST00000550857.1_Silent_p.C1759C|PTPRB_ENST00000538708.1_Silent_p.C1759C|RP11-588H23.3_ENST00000549460.1_RNA|RP11-588H23.3_ENST00000548687.1_RNA|RP11-588H23.3_ENST00000551438.1_RNA|RP11-588H23.3_ENST00000547656.1_RNA|PTPRB_ENST00000334414.6_Silent_p.C2067C|PTPRB_ENST00000451516.2_Silent_p.C1759C|RP11-588H23.3_ENST00000546836.1_RNA|PTPRB_ENST00000550358.1_Silent_p.C1979C	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1849	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)			AACATACACCGCATATCTTAA	0.527													G|||	1961	0.391573	0.4539	0.3357	5008	,	,		19377	0.5278		0.3062	False		,,,				2504	0.2945				p.C2067C		Atlas-SNP	.											PTPRB_ENST00000334414,colon,carcinoma,0,3	PTPRB	676	3	0			c.C6201T						PASS	.	G	,,,	1625,2281		339,947,667	64.0	63.0	63.0		6201,5277,5277,5547	5.5	1.0	12	dbSNP_107	63	2611,5703		423,1765,1969	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	,,,	762,2712,2636	AA,AG,GG		31.4049,41.6027,34.6645	,,,	2067/2216,1759/1908,1759/1908,1849/1998	70928616	4236,7984	1953	4157	6110	SO:0001819	synonymous_variant	5787	exon30			TACACCGCATATC	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.5547C>T	12.37:g.70928616G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	75	28	0.373333	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	37	CCDS44944.1																																																																																			G|0.613;A|0.387	0.387	strong		0.527	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
MYO5A	4644	hgsc.bcm.edu	37	15	52676392	52676392	+	Missense_Mutation	SNP	A	A	G	rs16964944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52676392A>G	ENST00000399231.3	-	15	2123	c.1880T>C	c.(1879-1881)aTg>aCg	p.M627T	MYO5A_ENST00000399233.2_Missense_Mutation_p.M627T|MYO5A_ENST00000358212.6_Missense_Mutation_p.M627T|MYO5A_ENST00000553916.1_Missense_Mutation_p.M627T|MYO5A_ENST00000356338.6_Missense_Mutation_p.M627T	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	627	Myosin motor.		M -> T (in dbSNP:rs16964944).		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)		CTCTTTGGCCATTTGGCCTGG	0.562													A|||	391	0.0780751	0.2057	0.0159	5008	,	,		18377	0.0198		0.003	False		,,,				2504	0.0869				p.M627T		Atlas-SNP	.											.	MYO5A	145	.	0			c.T1880C						PASS	.	A	THR/MET,THR/MET	657,3433		60,537,1448	127.0	141.0	137.0		1880,1880	-2.2	0.0	15	dbSNP_123	137	34,8330		0,34,4148	yes	missense,missense	MYO5A	NM_000259.3,NM_001142495.1	81,81	60,571,5596	GG,GA,AA		0.4065,16.0636,5.5484	benign,benign	627/1856,627/1829	52676392	691,11763	2045	4182	6227	SO:0001583	missense	4644	exon15			TTGGCCATTTGGC		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.1880T>C	15.37:g.52676392A>G	ENSP00000382177:p.Met627Thr	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	293	119	0.406143	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	130	0.05952380952380952	104	0.21138211382113822	9	0.024861878453038673	15	0.026223776223776224	2	0.002638522427440633	A	0.432	-0.902807	0.02453	0.160636	0.004065	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	D;D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.09;-2.09	5.38	-2.17	0.07059	Myosin head, motor domain (2);	0.949777	0.08906	N	0.876581	T	0.00073	0.0002	N	0.00408	-1.53	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04165	-1.0972	9	0.07990	T	0.79	.	10.3897	0.44162	0.4911:0.0:0.5089:0.0	rs16964944;rs52813869;rs16964944	627;627	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	T	627;161;627;627;627;257;627	ENSP00000382177:M627T;ENSP00000382179:M627T;ENSP00000348693:M627T;ENSP00000350945:M627T;ENSP00000451109:M627T	ENSP00000348693:M627T	M	-	2	0	MYO5A	50463684	0.000000	0.05858	0.001000	0.08648	0.497000	0.33675	0.705000	0.25675	-0.492000	0.06687	-0.248000	0.11899	ATG	A|0.942;G|0.058	0.058	strong		0.562	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
PLXNA3	55558	hgsc.bcm.edu	37	X	153689893	153689893	+	Missense_Mutation	SNP	G	G	A	rs35285799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153689893G>A	ENST00000369682.3	+	3	1224	c.1049G>A	c.(1048-1050)cGg>cAg	p.R350Q		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	350	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	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)					GCCCACATCCGGCGCCGCATC	0.622													G|||	65	0.0172185	0.0023	0.0202	3775	,	,		14250	0.0		0.0447	False		,,,				2504	0.0031				p.R350Q		Atlas-SNP	.											.	PLXNA3	156	.	0			c.G1049A						PASS	.	G	GLN/ARG	34,3799		0,33,1,1599,568	137.0	138.0	138.0		1049	4.2	1.0	X	dbSNP_126	138	379,6345		13,245,108,2169,1762	yes	missense	PLXNA3	NM_017514.3	43	13,278,109,3768,2330	AA,AG,A,GG,G		5.6365,0.887,3.9121	probably-damaging	350/1872	153689893	413,10144	2201	4297	6498	SO:0001583	missense	55558	exon3			ACATCCGGCGCCG	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.1049G>A	X.37:g.153689893G>A	ENSP00000358696:p.Arg350Gln	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	29	0.674419	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	40	0.024110910186859555	2	0.0040650406504065045	5	0.014044943820224719	0	0.0	26	0.034759358288770054	G	16.30	3.085515	0.55861	0.00887	0.056365	ENSG00000130827	ENST00000369682	T	0.10477	2.87	5.08	4.22	0.49857	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.124247	0.53938	D	0.000051	T	0.00695	0.0023	N	0.16903	0.455	0.25046	P	0.99116214	B	0.29037	0.231	B	0.29598	0.104	T	0.16719	-1.0393	9	0.48119	T	0.1	.	8.1297	0.31020	0.1897:0.0:0.8103:0.0	rs35285799	350	P51805	PLXA3_HUMAN	Q	350	ENSP00000358696:R350Q	ENSP00000358696:R350Q	R	+	2	0	PLXNA3	153343087	1.000000	0.71417	0.998000	0.56505	0.848000	0.48234	3.197000	0.51028	1.121000	0.41925	0.600000	0.82982	CGG	G|0.967;A|0.033	0.033	strong		0.622	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
EPHB1	2047	hgsc.bcm.edu	37	3	134851605	134851605	+	Silent	SNP	C	C	T	rs56401137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:134851605C>T	ENST00000398015.3	+	5	1381	c.1011C>T	c.(1009-1011)tcC>tcT	p.S337S	EPHB1_ENST00000493838.1_5'UTR|EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	337	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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						ATGAGACGTCCATCATTCTGG	0.557													C|||	219	0.04373	0.1558	0.0159	5008	,	,		19823	0.0		0.002	False		,,,				2504	0.0				p.S337S		Atlas-SNP	.											.	EPHB1	519	.	0			c.C1011T						PASS	.	C		511,3605		36,439,1583	54.0	57.0	56.0		1011	1.8	1.0	3	dbSNP_129	56	10,8396		0,10,4193	no	coding-synonymous	EPHB1	NM_004441.4		36,449,5776	TT,TC,CC		0.119,12.415,4.1607		337/985	134851605	521,12001	2058	4203	6261	SO:0001819	synonymous_variant	2047	exon5			GACGTCCATCATT	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.1011C>T	3.37:g.134851605C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	205	95	0.463415	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Silent	SNP	ENST00000398015.3	37	CCDS46921.1																																																																																			C|0.967;T|0.033	0.033	strong		0.557	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
DIP2A	23181	hgsc.bcm.edu	37	21	47985655	47985655	+	Silent	SNP	C	C	T	rs2248636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	106	0	0		WXS	Illumina HiSeq	Phase_I	137	74	0.540146	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	
DLG2	1740	hgsc.bcm.edu	37	11	83182726	83182726	+	Silent	SNP	G	G	T	rs34857356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:83182726G>T	ENST00000532653.1	-	19	2322	c.2020C>A	c.(2020-2022)Cgg>Agg	p.R674R	DLG2_ENST00000524982.1_Silent_p.R688R|DLG2_ENST00000404783.3_Silent_p.R170R|DLG2_ENST00000330014.6_Silent_p.R613R|DLG2_ENST00000376104.2_Silent_p.R797R|DLG2_ENST00000543673.1_Silent_p.R797R|DLG2_ENST00000376106.3_Silent_p.R156R|DLG2_ENST00000531015.1_Silent_p.R659R|DLG2_ENST00000537455.1_Silent_p.R442R|DLG2_ENST00000398309.2_Silent_p.R692R|DLG2_ENST00000418306.2_Silent_p.R571R|DLG2_ENST00000426717.2_Silent_p.R156R|DLG2_ENST00000280241.8_Silent_p.R731R			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	389					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				TCATTGATCCGATCCTTCATG	0.433													G|||	105	0.0209665	0.0688	0.013	5008	,	,		17636	0.0		0.005	False		,,,				2504	0.0				p.R797R		Atlas-SNP	.											DLG2_ENST00000418306,colon,carcinoma,+2,9	DLG2	448	9	0			c.C2389A						PASS	.	G	,,,,	221,3475		11,199,1638	67.0	65.0	65.0		2389,1711,466,2191,2074	4.2	1.0	11	dbSNP_126	65	11,8175		0,11,4082	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLG2	NM_001142699.1,NM_001142700.1,NM_001142702.1,NM_001206769.1,NM_001364.3	,,,,	11,210,5720	TT,TG,GG		0.1344,5.9794,1.9525	,,,,	797/976,571/750,156/335,731/910,692/871	83182726	232,11650	1848	4093	5941	SO:0001819	synonymous_variant	1740	exon24			TGATCCGATCCTT	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	2901	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 58"""	603583	"""discs, large homolog 2, chapsyn-110 (Drosophila)"""			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.2020C>A	11.37:g.83182726G>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000532653.1	37																																																																																				G|0.984;T|0.016	0.016	strong		0.433	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364	
HMCN1	83872	hgsc.bcm.edu	37	1	186031041	186031041	+	Silent	SNP	C	C	T	rs7522627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186031041C>T	ENST00000271588.4	+	47	7600	c.7371C>T	c.(7369-7371)tgC>tgT	p.C2457C	HMCN1_ENST00000367492.2_Silent_p.C2457C	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2457	Ig-like C2-type 22.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AATATACTTGCGTTGTAAGGA	0.378													T|||	3277	0.654353	0.8495	0.647	5008	,	,		16476	0.5903		0.5348	False		,,,				2504	0.5849				p.C2457C		Atlas-SNP	.											.	HMCN1	797	.	0			c.C7371T						PASS	.	T		3571,835	333.6+/-303.0	1454,663,86	124.0	136.0	132.0		7371	1.9	0.9	1	dbSNP_116	132	4602,3998	553.3+/-386.3	1252,2098,950	no	coding-synonymous	HMCN1	NM_031935.2		2706,2761,1036	TT,TC,CC		46.4884,18.9514,37.1598		2457/5636	186031041	8173,4833	2203	4300	6503	SO:0001819	synonymous_variant	83872	exon47			TACTTGCGTTGTA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7371C>T	1.37:g.186031041C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	108	0.981818	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			C|0.372;T|0.628	0.628	strong		0.378	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
FRMD6	122786	hgsc.bcm.edu	37	14	52186966	52186966	+	Silent	SNP	G	G	A	rs2277495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:52186966G>A	ENST00000344768.5	+	11	1414	c.1218G>A	c.(1216-1218)acG>acA	p.T406T	FRMD6_ENST00000356218.4_Silent_p.T398T|FRMD6_ENST00000395718.2_Silent_p.T398T|FRMD6_ENST00000554167.1_Silent_p.T329T|FRMD6_ENST00000553556.1_Silent_p.T48T			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	406					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)					CCCGGGACACGGGGCCAGAAG	0.617													G|||	1149	0.229433	0.1021	0.2795	5008	,	,		17792	0.2649		0.3211	False		,,,				2504	0.2352				p.T406T		Atlas-SNP	.											.	FRMD6	100	.	0			c.G1218A						PASS	.	G	,	550,3856	248.1+/-256.1	45,460,1698	64.0	61.0	62.0		1194,1194	-12.0	0.0	14	dbSNP_100	62	2673,5927	428.0+/-355.8	395,1883,2022	no	coding-synonymous,coding-synonymous	FRMD6	NM_001042481.1,NM_152330.3	,	440,2343,3720	AA,AG,GG		31.0814,12.483,24.7809	,	398/615,398/615	52186966	3223,9783	2203	4300	6503	SO:0001819	synonymous_variant	122786	exon11			GGACACGGGGCCA	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.1218G>A	14.37:g.52186966G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_001267046	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Silent	SNP	ENST00000344768.5	37	CCDS58318.1																																																																																			G|0.751;C|0.000;A|0.249	0.249	strong		0.617	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330	
C22orf24	25775	hgsc.bcm.edu	37	22	32334021	32334021	+	Missense_Mutation	SNP	T	T	A	rs1984388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32334021T>A	ENST00000248984.3	-	2	198	c.32A>T	c.(31-33)cAt>cTt	p.H11L	C22orf24_ENST00000486651.1_5'UTR|C22orf24_ENST00000543051.1_Missense_Mutation_p.H78L	NM_015372.1	NP_056187.1	Q9Y442	CV024_HUMAN	chromosome 22 open reading frame 24	11			H -> L (in dbSNP:rs1984388).			integral component of membrane (GO:0016021)		p.H11L(1)		central_nervous_system(1)|urinary_tract(1)	2						TGTCTTTTGATGCAGCCCTGT	0.448													A|||	1240	0.247604	0.3865	0.1902	5008	,	,		20694	0.1984		0.1193	False		,,,				2504	0.2832				p.H11L		Atlas-SNP	.											C22orf24_ENST00000248984,NS,carcinoma,0,1	C22orf24	21	1	1	Substitution - Missense(1)	stomach(1)	c.A32T						PASS	.	A	LEU/HIS	1419,2585		260,899,843	230.0	237.0	235.0		32	1.6	0.0	22	dbSNP_92	235	860,7482		43,774,3354	yes	missense	C22orf24	NM_015372.1	99	303,1673,4197	AA,AT,TT		10.3093,35.4396,18.4594	benign	11/161	32334021	2279,10067	2002	4171	6173	SO:0001583	missense	25775	exon2			TTTTGATGCAGCC		CCDS46693.1	22q12.1-q12.3	2004-05-05			ENSG00000128254	ENSG00000128254			23051	protein-coding gene	gene with protein product							Standard	XM_005261497		Approved	HSN44A4A	uc003aly.3	Q9Y442	OTTHUMG00000030834	ENST00000248984.3:c.32A>T	22.37:g.32334021T>A	ENSP00000248984:p.His11Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	104	101	0.971154	NM_015372	B2RCT4|Q5K3R1	Missense_Mutation	SNP	ENST00000248984.3	37	CCDS46693.1	465	0.2129120879120879	206	0.4186991869918699	65	0.17955801104972377	99	0.17307692307692307	95	0.12532981530343007	A	6.644	0.487380	0.12641	0.354396	0.103093	ENSG00000128254	ENST00000248984;ENST00000543051	T;T	0.40225	1.04;1.04	3.8	1.65	0.23941	.	1.655130	0.04181	N	0.326546	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	0.42616	-0.9441	9	0.87932	D	0	.	2.7578	0.05298	0.5954:0.0:0.2151:0.1895	rs1984388;rs3827333;rs1984388	11	Q9Y442	CV024_HUMAN	L	11;78	ENSP00000248984:H11L;ENSP00000437643:H78L	ENSP00000248984:H11L	H	-	2	0	C22orf24	30664021	0.200000	0.23398	0.004000	0.12327	0.064000	0.16182	0.076000	0.14712	0.008000	0.14787	-0.257000	0.10917	CAT	T|0.774;A|0.226	0.226	strong		0.448	C22orf24-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075722.2	NM_015372	
DPEP3	64180	hgsc.bcm.edu	37	16	68011867	68011867	+	Missense_Mutation	SNP	C	C	T	rs16957670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:68011867C>T	ENST00000268793.4	-	5	1178	c.805G>A	c.(805-807)Gtc>Atc	p.V269I	DPEP3_ENST00000574342.1_5'Flank	NM_001129758.1|NM_022357.3	NP_001123230.1|NP_071752.3	Q9H4B8	DPEP3_HUMAN	dipeptidase 3	244					male meiosis (GO:0007140)	anchored component of membrane (GO:0031225)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			breast(4)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0117)|Epithelial(162;0.0481)|all cancers(182;0.236)		AATCCGCTGACGTTGGTGTAC	0.537													C|||	277	0.0553115	0.1664	0.0144	5008	,	,		22471	0.001		0.007	False		,,,				2504	0.0399				p.V269I		Atlas-SNP	.											.	DPEP3	48	.	0			c.G805A						PASS	.	C	ILE/VAL,ILE/VAL	673,3723	282.5+/-276.6	58,557,1583	225.0	149.0	175.0		805,805	-3.0	0.5	16	dbSNP_123	175	31,8569	19.2+/-60.6	0,31,4269	yes	missense,missense	DPEP3	NM_022357.3,NM_001129758.1	29,29	58,588,5852	TT,TC,CC		0.3605,15.3094,5.4171	benign,benign	269/514,269/513	68011867	704,12292	2198	4300	6498	SO:0001583	missense	64180	exon5			CGCTGACGTTGGT	AJ291679	CCDS10856.1	16q22.1	2011-07-22			ENSG00000141096	ENSG00000141096	3.4.13.19		23029	protein-coding gene	gene with protein product		609926					Standard	NM_022357		Approved		uc002evc.4	Q9H4B8	OTTHUMG00000137544	ENST00000268793.4:c.805G>A	16.37:g.68011867C>T	ENSP00000268793:p.Val269Ile	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	149	79	0.530201	NM_001129758	B3KQ48|Q6PEZ5|Q6UXE4	Missense_Mutation	SNP	ENST00000268793.4	37	CCDS10856.1	88	0.040293040293040296	81	0.16463414634146342	5	0.013812154696132596	0	0.0	2	0.002638522427440633	C	0.922	-0.715585	0.03206	0.153094	0.003605	ENSG00000141096	ENST00000268793	T	0.22134	1.97	4.1	-3.04	0.05412	.	0.836197	0.11124	N	0.597112	T	0.00039	0.0001	N	0.16743	0.435	0.80722	P	0.0	B	0.16166	0.016	B	0.18561	0.022	T	0.44050	-0.9353	9	0.15952	T	0.53	.	9.4449	0.38690	0.0:0.3184:0.0:0.6816	rs16957670;rs16957670	244	Q9H4B8	DPEP3_HUMAN	I	269	ENSP00000268793:V269I	ENSP00000268793:V269I	V	-	1	0	DPEP3	66569368	0.014000	0.17966	0.468000	0.27192	0.140000	0.21249	-1.014000	0.03641	-0.515000	0.06479	-0.300000	0.09419	GTC	C|0.936;T|0.064	0.064	strong		0.537	DPEP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268875.3	NM_022357	
FAM174A	345757	hgsc.bcm.edu	37	5	99897880	99897880	+	Missense_Mutation	SNP	A	A	G	rs76060686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:99897880A>G	ENST00000312637.4	+	2	783	c.557A>G	c.(556-558)aAt>aGt	p.N186S	FAM174A_ENST00000505792.1_3'UTR	NM_198507.1	NP_940909.1	Q8TBP5	F174A_HUMAN	family with sequence similarity 174, member A	186						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TTTGATGCCAATCATCCTCGA	0.368													A|||	19	0.00379393	0.0144	0.0	5008	,	,		14171	0.0		0.0	False		,,,				2504	0.0				p.N186S		Atlas-SNP	.											.	FAM174A	13	.	0			c.A557G						PASS	.	A	SER/ASN	98,4308	78.3+/-116.7	1,96,2106	143.0	131.0	135.0		557	2.8	1.0	5	dbSNP_131	135	0,8600		0,0,4300	yes	missense	FAM174A	NM_198507.1	46	1,96,6406	GG,GA,AA		0.0,2.2242,0.7535	benign	186/191	99897880	98,12908	2203	4300	6503	SO:0001583	missense	345757	exon2			ATGCCAATCATCC	AY359108	CCDS4090.1	5q21.1	2008-06-19	2008-06-19	2008-06-19	ENSG00000174132	ENSG00000174132			24943	protein-coding gene	gene with protein product			"""transmembrane protein 157"""	TMEM157		12975309	Standard	NM_198507		Approved	UNQ1912	uc003knj.1	Q8TBP5	OTTHUMG00000128726	ENST00000312637.4:c.557A>G	5.37:g.99897880A>G	ENSP00000307954:p.Asn186Ser	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	242	117	0.483471	NM_198507	A8K0H4	Missense_Mutation	SNP	ENST00000312637.4	37	CCDS4090.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	A	12.69	2.014664	0.35511	0.022242	0.0	ENSG00000174132	ENST00000312637	T	0.50548	0.74	5.21	2.81	0.32909	.	0.211018	0.31145	N	0.008177	T	0.14700	0.0355	L	0.35644	1.08	0.35327	D	0.785245	B	0.31989	0.35	B	0.35655	0.207	T	0.20974	-1.0259	9	.	.	.	-11.1789	8.0143	0.30372	0.8295:0.0:0.1705:0.0	.	186	Q8TBP5	F174A_HUMAN	S	186	ENSP00000307954:N186S	.	N	+	2	0	FAM174A	99925779	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.898000	0.39809	0.319000	0.23209	0.383000	0.25322	AAT	A|0.992;G|0.008	0.008	strong		0.368	FAM174A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250631.2	NM_198507	
PDE9A	5152	hgsc.bcm.edu	37	21	44189166	44189166	+	Silent	SNP	T	T	C	rs1045382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44189166T>C	ENST00000291539.6	+	17	1551	c.1491T>C	c.(1489-1491)ccT>ccC	p.P497P	PDE9A_ENST00000335440.6_Silent_p.P395P|PDE9A_ENST00000335512.4_Silent_p.P437P|PDE9A_ENST00000539837.1_Silent_p.P369P|PDE9A_ENST00000398229.3_Silent_p.P363P|PDE9A_ENST00000328862.6_Silent_p.P471P|PDE9A_ENST00000398225.3_Silent_p.P456P|PDE9A_ENST00000398224.3_Silent_p.P370P|PDE9A_ENST00000398236.3_Silent_p.P411P|PDE9A_ENST00000398234.3_Silent_p.P396P|PDE9A_ENST00000398227.3_Silent_p.P337P|PDE9A_ENST00000380328.2_Silent_p.P444P|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000349112.3_Silent_p.P369P|PDE9A_ENST00000398232.3_Silent_p.P430P	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	497	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	AAGGCCTTCCTGTGGCACCGT	0.512													C|||	2569	0.512979	0.6853	0.4352	5008	,	,		24371	0.4236		0.3718	False		,,,				2504	0.5726				p.P497P		Atlas-SNP	.											.	PDE9A	69	.	0			c.T1491C						PASS	.	C	,,,,,,,,,,,,,,,,,,,	2761,1645	502.9+/-365.4	856,1049,298	171.0	147.0	155.0		1311,1110,1107,1332,1188,870,870,1233,1011,840,1089,1185,870,840,1290,1368,1413,870,870,1491	-9.5	0.1	21	dbSNP_86	155	3112,5488	658.8+/-401.6	587,1938,1775	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	,,,,,,,,,,,,,,,,,,,	1443,2987,2073	CC,CT,TT		36.186,37.3355,45.1561	,,,,,,,,,,,,,,,,,,,	437/534,370/467,369/466,444/541,396/493,290/387,290/387,411/508,337/434,280/377,363/460,395/492,290/387,280/377,430/527,456/553,471/568,290/387,290/387,497/594	44189166	5873,7133	2203	4300	6503	SO:0001819	synonymous_variant	5152	exon17			CCTTCCTGTGGCA	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.1491T>C	21.37:g.44189166T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Silent	SNP	ENST00000291539.6	37	CCDS13690.1																																																																																			T|0.555;C|0.445	0.445	strong		0.512	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
PREX1	57580	hgsc.bcm.edu	37	20	47274733	47274733	+	Missense_Mutation	SNP	T	T	C	rs62621889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47274733T>C	ENST00000371941.3	-	17	1937	c.1915A>G	c.(1915-1917)Atc>Gtc	p.I639V	PREX1_ENST00000396220.1_Missense_Mutation_p.I639V	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	639	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			TTCTCCTCGATGTCAAAGCCA	0.672											OREG0026010	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	51	0.0101837	0.0378	0.0014	5008	,	,		19323	0.0		0.0	False		,,,				2504	0.0				p.I639V		Atlas-SNP	.											.	PREX1	441	.	0			c.A1915G						PASS	.	T	VAL/ILE	146,4260	102.5+/-141.1	1,144,2058	285.0	256.0	266.0		1915	3.9	1.0	20	dbSNP_129	266	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PREX1	NM_020820.3	29	1,145,6357	CC,CT,TT		0.0116,3.3137,1.1302	benign	639/1660	47274733	147,12859	2203	4300	6503	SO:0001583	missense	57580	exon17			CCTCGATGTCAAA	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.1915A>G	20.37:g.47274733T>C	ENSP00000361009:p.Ile639Val	Somatic	155	0	0	945	WXS	Illumina HiSeq	Phase_I	161	68	0.42236	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	12.08	1.832013	0.32421	0.033137	1.16E-4	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.18016	2.24;2.24	4.98	3.86	0.44501	Winged helix-turn-helix transcription repressor DNA-binding (1);PDZ/DHR/GLGF (3);	0.406056	0.19926	U	0.102980	T	0.02494	0.0076	N	0.08118	0	0.34912	D	0.747534	B	0.02656	0.0	B	0.04013	0.001	T	0.12656	-1.0539	10	0.56958	D	0.05	.	6.8339	0.23925	0.0:0.0776:0.2974:0.625	rs62621889	639	Q8TCU6	PREX1_HUMAN	V	639	ENSP00000361009:I639V;ENSP00000379522:I639V	ENSP00000361009:I639V	I	-	1	0	PREX1	46708140	1.000000	0.71417	0.981000	0.43875	0.935000	0.57460	3.185000	0.50934	0.714000	0.32081	0.533000	0.62120	ATC	T|0.989;C|0.011	0.011	strong		0.672	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
LAMA4	3910	hgsc.bcm.edu	37	6	112512905	112512905	+	Silent	SNP	G	G	A	rs2072021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:112512905G>A	ENST00000230538.7	-	6	1048	c.651C>T	c.(649-651)acC>acT	p.T217T	LAMA4_ENST00000389463.4_Silent_p.T217T|LAMA4_ENST00000424408.2_Silent_p.T217T|LAMA4_ENST00000524032.1_5'Flank|LAMA4_ENST00000522006.1_Silent_p.T217T	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	217	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)		ACTTGAATCCGGTGGTGTTGC	0.483													G|||	1587	0.316893	0.6067	0.1816	5008	,	,		18568	0.2619		0.1352	False		,,,				2504	0.2648				p.T217T		Atlas-SNP	.											.	LAMA4	227	.	0			c.C651T						PASS	.	G	,,	2301,2105	602.8+/-390.0	627,1047,529	99.0	84.0	89.0		651,651,651	-11.4	0.0	6	dbSNP_96	89	1048,7552	222.7+/-259.7	55,938,3307	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	,,	682,1985,3836	AA,AG,GG		12.186,47.7758,25.7497	,,	217/1824,217/1817,217/1817	112512905	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	3910	exon6			GAATCCGGTGGTG		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.651C>T	6.37:g.112512905G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1	601|601	0.2751831501831502|0.2751831501831502	271|271	0.5508130081300813|0.5508130081300813	67|67	0.1850828729281768|0.1850828729281768	164|164	0.2867132867132867|0.2867132867132867	99|99	0.13060686015831136|0.13060686015831136	G|G	6.451|6.451	0.451378|0.451378	0.12223|0.12223	0.522242|0.522242	0.12186|0.12186	ENSG00000112769|ENSG00000112769	ENST00000368640|ENST00000521732	.|.	.|.	.|.	5.7|5.7	-11.4|-11.4	0.00090|0.00090	.|.	.|.	.|.	.|.	.|.	T|T	0.02494|0.02494	0.0076|0.0076	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999993|0.9999999999999993	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.09465|0.09465	-1.0673|-1.0673	3|3	.|.	.|.	.|.	.|.	1.8339|1.8339	0.03135|0.03135	0.468:0.1904:0.075:0.2666|0.468:0.1904:0.075:0.2666	rs2072021;rs59269192;rs2072021|rs2072021;rs59269192;rs2072021	.|.	.|.	.|.	L|W	21|37	.|.	.|.	P|R	-|-	2|1	0|2	LAMA4|LAMA4	112619598|112619598	0.000000|0.000000	0.05858|0.05858	0.023000|0.023000	0.16930|0.16930	0.811000|0.811000	0.45836|0.45836	-4.439000|-4.439000	0.00234|0.00234	-4.513000|-4.513000	0.00045|0.00045	-0.982000|-0.982000	0.02568|0.02568	CCG|CGG	G|0.735;A|0.265	0.265	strong		0.483	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
PEX11G	92960	hgsc.bcm.edu	37	19	7542118	7542118	+	Silent	SNP	G	G	A	rs7256275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7542118G>A	ENST00000221480.1	-	5	704	c.696C>T	c.(694-696)gcC>gcT	p.A232A	PEX11G_ENST00000599519.1_5'UTR|PEX11G_ENST00000593942.1_Silent_p.A162A	NM_001270539.1|NM_080662.3	NP_001257468.1|NP_542393.1	Q96HA9	PX11C_HUMAN	peroxisomal biogenesis factor 11 gamma	232					peroxisome fission (GO:0016559)|regulation of peroxisome size (GO:0044375)	integral component of peroxisomal membrane (GO:0005779)|intrinsic component of peroxisomal membrane (GO:0031231)|peroxisome (GO:0005777)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(1)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	7						CCTGGCCGCCGGCCCGGGCCG	0.711													G|||	708	0.141374	0.2254	0.1383	5008	,	,		13753	0.1389		0.0706	False		,,,				2504	0.1053				p.A232A		Atlas-SNP	.											.	PEX11G	16	.	0			c.C696T						PASS	.	G		835,3479		79,677,1401	7.0	11.0	10.0		696	-7.8	0.0	19	dbSNP_116	10	555,7895		21,513,3691	no	coding-synonymous	PEX11G	NM_080662.2		100,1190,5092	AA,AG,GG		6.568,19.3556,10.89		232/242	7542118	1390,11374	2157	4225	6382	SO:0001819	synonymous_variant	92960	exon5			GCCGCCGGCCCGG	BC008780	CCDS12178.1	19p13.2	2008-02-05				ENSG00000104883			20208	protein-coding gene	gene with protein product		607583				12417726	Standard	NM_080662		Approved		uc002mgk.2	Q96HA9		ENST00000221480.1:c.696C>T	19.37:g.7542118G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_080662	Q8NDM0	Silent	SNP	ENST00000221480.1	37	CCDS12178.1																																																																																			G|0.870;A|0.130	0.130	strong		0.711	PEX11G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458965.1	NM_080662	
HOXD8	3234	hgsc.bcm.edu	37	2	176995146	176995146	+	Missense_Mutation	SNP	G	G	A	rs192755857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:176995146G>A	ENST00000313173.4	+	1	679	c.52G>A	c.(52-54)Gcg>Acg	p.A18T	HOXD-AS2_ENST00000440016.2_RNA|HOXD8_ENST00000548663.1_Missense_Mutation_p.A18T|HOXD8_ENST00000429017.1_Intron|HOXD8_ENST00000544999.1_Missense_Mutation_p.A18T|HOXD8_ENST00000450510.2_Missense_Mutation_p.A18T	NM_001199746.1|NM_019558.3	NP_001186675.1|NP_062458.1	P13378	HXD8_HUMAN	homeobox D8	18	Poly-Ala.				anterior/posterior axis specification, embryo (GO:0008595)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(5)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		ggcggcggctgcggcggcggc	0.726													G|||	92	0.0183706	0.0681	0.0029	5008	,	,		5924	0.0		0.0	False		,,,				2504	0.0				p.A18T		Atlas-SNP	.											.	HOXD8	24	.	0			c.G52A						PASS	.						1.0	1.0	1.0					2																	176995146		405	891	1296	SO:0001583	missense	3234	exon1			GCGGCTGCGGCGG		CCDS2268.1, CCDS56148.1, CCDS56149.1	2q31.1	2011-06-20	2005-12-22		ENSG00000175879	ENSG00000175879		"""Homeoboxes / ANTP class : HOXL subclass"""	5139	protein-coding gene	gene with protein product		142985	"""homeo box D8"""	HOX4, HOX4E		1973146, 1358459	Standard	NM_001199747		Approved		uc002uko.3	P13378	OTTHUMG00000132513	ENST00000313173.4:c.52G>A	2.37:g.176995146G>A	ENSP00000315949:p.Ala18Thr	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	9	7	0.777778	NM_001199746	F8WBG7|Q5BL00|Q8IXZ1	Missense_Mutation	SNP	ENST00000313173.4	37	CCDS2268.1	76	0.0347985347985348	32	0.06504065040650407	8	0.022099447513812154	29	0.050699300699300696	7	0.009234828496042216	G	15.69	2.907048	0.52333	.	.	ENSG00000175879	ENST00000313173;ENST00000544999;ENST00000548663;ENST00000450510	D;D;D;D	0.93763	-3.28;-3.25;-3.0;-3.25	2.06	1.06	0.20224	.	.	.	.	.	T	0.30230	0.0758	N	0.08118	0	0.22968	N	0.998491	B;B	0.26081	0.124;0.141	B;B	0.17722	0.014;0.019	T	0.54036	-0.8353	9	0.14656	T	0.56	.	5.7146	0.17952	0.0:0.0:0.6812:0.3188	.	18;18	Q8IXZ1;P13378	.;HXD8_HUMAN	T	18	ENSP00000315949:A18T;ENSP00000437431:A18T;ENSP00000448196:A18T;ENSP00000409026:A18T	ENSP00000315949:A18T	A	+	1	0	HOXD8	176703392	0.986000	0.35501	0.504000	0.27639	0.610000	0.37248	0.000000	0.12993	-0.051000	0.13334	0.186000	0.17326	GCG	G|0.966;A|0.034	0.034	strong		0.726	HOXD8-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255694.1		
TECPR1	25851	hgsc.bcm.edu	37	7	97852399	97852399	+	Missense_Mutation	SNP	G	G	A	rs11762014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	83	0	0		WXS	Illumina HiSeq	Phase_I	123	71	0.577236	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	
RGS9	8787	hgsc.bcm.edu	37	17	63221136	63221136	+	Missense_Mutation	SNP	C	C	T	rs116395890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:63221136C>T	ENST00000262406.9	+	18	1491	c.1424C>T	c.(1423-1425)gCt>gTt	p.A475V	RGS9_ENST00000443584.3_Missense_Mutation_p.A472V|RGS9_ENST00000449996.3_Missense_Mutation_p.A472V	NM_003835.3	NP_003826.2	O75916	RGS9_HUMAN	regulator of G-protein signaling 9	475					dopamine receptor signaling pathway (GO:0007212)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to estrogen (GO:0043627)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(8)|liver(2)|lung(12)|ovary(2)|prostate(3)|skin(3)	41						CAGCACATGGCTCCCAGCCCC	0.642													C|||	27	0.00539137	0.0197	0.0014	5008	,	,		17870	0.0		0.0	False		,,,				2504	0.0				p.A475V		Atlas-SNP	.											.	RGS9	82	.	0			c.C1424T						PASS	.	C	VAL/ALA,VAL/ALA	66,4064		0,66,1999	96.0	112.0	107.0		1415,1424	3.6	0.0	17	dbSNP_132	107	0,8416		0,0,4208	yes	missense,missense	RGS9	NM_001081955.2,NM_003835.3	64,64	0,66,6207	TT,TC,CC		0.0,1.5981,0.5261	possibly-damaging,possibly-damaging	472/672,475/675	63221136	66,12480	2065	4208	6273	SO:0001583	missense	8787	exon18			ACATGGCTCCCAG	AF071476	CCDS42373.1, CCDS45764.1	17q24	2008-07-18	2007-08-14			ENSG00000108370		"""Regulators of G-protein signaling"""	10004	protein-coding gene	gene with protein product	"""regulator of G protein signalling 9"", ""regulator of G protein signalling 9L"", ""regulator of G-protein signaling 9L"""	604067	"""regulator of G-protein signalling 9"""			9765512	Standard	NM_003835		Approved	PERRS, RGS9L, MGC26458, MGC111763	uc002jfe.3	O75916		ENST00000262406.9:c.1424C>T	17.37:g.63221136C>T	ENSP00000262406:p.Ala475Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_003835	A8K3C0|O75573|Q696R2|Q8TD64|Q8TD65|Q9HC32|Q9HC33	Missense_Mutation	SNP	ENST00000262406.9	37	CCDS42373.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	14.11	2.437293	0.43224	0.015981	0.0	ENSG00000108370	ENST00000262406;ENST00000449996	T;T	0.33216	1.42;1.42	4.56	3.58	0.41010	.	0.420099	0.26742	N	0.022729	T	0.09379	0.0231	N	0.19112	0.55	0.09310	N	1	B;B;B	0.31548	0.099;0.22;0.328	B;B;B	0.24394	0.025;0.024;0.053	T	0.17623	-1.0363	10	0.62326	D	0.03	.	12.4444	0.55643	0.0:0.915:0.0:0.085	.	475;475;472	A8K1G1;O75916;O75916-5	.;RGS9_HUMAN;.	V	475;472	ENSP00000262406:A475V;ENSP00000396329:A472V	ENSP00000262406:A475V	A	+	2	0	RGS9	60651598	0.176000	0.23096	0.018000	0.16275	0.782000	0.44232	2.127000	0.42035	2.450000	0.82876	0.561000	0.74099	GCT	C|0.994;T|0.006	0.006	strong		0.642	RGS9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445885.1	NM_003835	
PDCD1LG2	80380	hgsc.bcm.edu	37	9	5557708	5557708	+	Missense_Mutation	SNP	T	T	C	rs7854413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5557708T>C	ENST00000397747.3	+	5	970	c.722T>C	c.(721-723)aTa>aCa	p.I241T	PDCD1LG2_ENST00000397745.2_Missense_Mutation_p.I151T	NM_025239.3	NP_079515.2	Q9BQ51	PD1L2_HUMAN	programmed cell death 1 ligand 2	241			I -> T (in dbSNP:rs7854413).		immune response (GO:0006955)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(2)|lung(4)|prostate(2)	8	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000767)|Lung(218;0.112)		GCCACAGTGATAGCCCTAAGA	0.448													T|||	1402	0.279952	0.6422	0.1326	5008	,	,		22607	0.1151		0.1034	False		,,,				2504	0.2464				p.I241T		Atlas-SNP	.											.	PDCD1LG2	16	.	0			c.T722C						PASS	.	T	THR/ILE	2425,1981	617.9+/-393.1	669,1087,447	195.0	181.0	185.0		722	2.4	0.0	9	dbSNP_116	185	825,7775	190.0+/-236.6	32,761,3507	yes	missense	PDCD1LG2	NM_025239.3	89	701,1848,3954	CC,CT,TT		9.593,44.9614,24.9885	possibly-damaging	241/274	5557708	3250,9756	2203	4300	6503	SO:0001583	missense	80380	exon5			CAGTGATAGCCCT	AF344424	CCDS6465.1	9p24.2	2014-01-30			ENSG00000197646	ENSG00000197646		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	18731	protein-coding gene	gene with protein product	"""B7 dendritic cell molecule"""	605723				11224527	Standard	NM_025239		Approved	PD-L2, Btdc, PDL2, bA574F11.2, CD273, B7-DC	uc003zjg.4	Q9BQ51	OTTHUMG00000019504	ENST00000397747.3:c.722T>C	9.37:g.5557708T>C	ENSP00000380855:p.Ile241Thr	Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	293	293	1	NM_025239	Q14CN8|Q5T7Z6|Q6JXL8|Q6JXL9	Missense_Mutation	SNP	ENST00000397747.3	37	CCDS6465.1	496	0.2271062271062271	304	0.6178861788617886	49	0.13535911602209943	68	0.11888111888111888	75	0.09894459102902374	T	9.427	1.084533	0.20309	0.550386	0.09593	ENSG00000197646	ENST00000397745;ENST00000397747	T;T	0.14640	2.49;5.07	4.68	2.37	0.29283	.	0.328448	0.26112	N	0.026269	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P;B;B	0.43750	0.816;0.301;0.123	B;B;B	0.37239	0.244;0.184;0.02	T	0.25882	-1.0119	9	0.72032	D	0.01	10.8254	5.7861	0.18334	0.0:0.2107:0.0:0.7893	rs7854413;rs52819168;rs58013146;rs7854413	241;151;241	A4GW21;Q9BQ51-2;Q9BQ51	.;.;PD1L2_HUMAN	T	151;241	ENSP00000380853:I151T;ENSP00000380855:I241T	ENSP00000380853:I151T	I	+	2	0	PDCD1LG2	5547708	0.002000	0.14202	0.003000	0.11579	0.003000	0.03518	0.297000	0.19101	0.337000	0.23665	-0.250000	0.11733	ATA	T|0.745;C|0.255	0.255	strong		0.448	PDCD1LG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051634.1	NM_025239	
OPN1LW	5956	hgsc.bcm.edu	37	X	153421912	153421912	+	Silent	SNP	T	T	C	rs1065439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153421912T>C	ENST00000369951.4	+	5	948	c.888T>C	c.(886-888)ggT>ggC	p.G296G		NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	296					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)					CCAACCCTGGTTACGCCTTCC	0.537													C|||	566	0.149934	0.3245	0.0548	3775	,	,		14896	0.0159		0.0606	False		,,,				2504	0.0225				p.G296G		Atlas-SNP	.											.	OPN1LW	87	.	0			c.T888C						PASS	.	C		1383,2445		200,780,203,652,361	392.0	348.0	363.0		888	4.6	1.0	X	dbSNP_86	363	609,6091		23,378,185,2027,1659	no	coding-synonymous	OPN1LW	NM_020061.4		223,1158,388,2679,2020	CC,CT,C,TT,T		9.0896,36.1285,18.921		296/365	153421912	1992,8536	2196	4272	6468	SO:0001819	synonymous_variant	5956	exon5			CCCTGGTTACGCC	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.888T>C	X.37:g.153421912T>C		Somatic	763	2	0.00262123		WXS	Illumina HiSeq	Phase_I	1069	577	0.539757	NM_020061		Silent	SNP	ENST00000369951.4	37	CCDS14742.1																																																																																			0|0.004;C|0.185	0.185	strong		0.537	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061	
TRIM66	9866	hgsc.bcm.edu	37	11	8662516	8662516	+	Missense_Mutation	SNP	T	T	C	rs11042023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:8662516T>C	ENST00000299550.6	-	9	1165	c.971A>G	c.(970-972)cAc>cGc	p.H324R	TRIM66_ENST00000402157.2_Missense_Mutation_p.H322R	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	324						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						TGGGGAGCAGTGGGAGCAGCA	0.622													T|||	2630	0.52516	0.5166	0.5836	5008	,	,		16172	0.4028		0.6302	False		,,,				2504	0.5133				p.H324R		Atlas-SNP	.											TRIM66,rectum,carcinoma,0,1	TRIM66	45	1	0			c.A971G						PASS	.	T	ARG/HIS	739,645		199,341,152	44.0	45.0	45.0		971	5.1	1.0	11	dbSNP_120	45	2089,1093		686,717,188	yes	missense	TRIM66	NM_014818.1	29	885,1058,340	CC,CT,TT		34.3495,46.604,38.064	probably-damaging	324/1217	8662516	2828,1738	692	1591	2283	SO:0001583	missense	9866	exon9			GAGCAGTGGGAGC	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.971A>G	11.37:g.8662516T>C	ENSP00000299550:p.His324Arg	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	148	147	0.993243	NM_014818	Q9BQQ4	Missense_Mutation	SNP	ENST00000299550.6	37		1176	0.5384615384615384	258	0.524390243902439	200	0.5524861878453039	239	0.4178321678321678	479	0.6319261213720316	T	19.19	3.779607	0.70107	0.53396	0.656505	ENSG00000166436	ENST00000299550;ENST00000402157	T;T	0.18174	2.23;2.23	5.1	5.1	0.69264	.	0.000000	0.50627	D	0.000104	T	0.00012	0.0000	M	0.69823	2.125	0.32774	P	0.503443	D	0.76494	0.999	D	0.80764	0.994	T	0.35425	-0.9789	9	0.30078	T	0.28	-15.8813	14.8856	0.70567	0.0:0.0:0.0:1.0	rs11042023;rs52817908;rs58678299;rs11042023	324	O15016	TRI66_HUMAN	R	324;322	ENSP00000299550:H324R;ENSP00000384876:H322R	ENSP00000299550:H324R	H	-	2	0	TRIM66	8619092	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	5.486000	0.66856	1.922000	0.55676	0.397000	0.26171	CAC	T|0.470;C|0.530	0.530	strong		0.622	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
LBH	81606	hgsc.bcm.edu	37	2	30457288	30457288	+	Missense_Mutation	SNP	C	C	T	rs144194149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:30457288C>T	ENST00000395323.3	+	2	252	c.44C>T	c.(43-45)tCg>tTg	p.S15L	LBH_ENST00000467242.1_3'UTR|LBH_ENST00000401506.1_Missense_Mutation_p.S21L|LBH_ENST00000404397.1_Missense_Mutation_p.S15L|LBH_ENST00000407930.2_5'UTR|LBH_ENST00000406087.1_Missense_Mutation_p.S15L	NM_030915.3	NP_112177.2	Q53QV2	LBH_HUMAN	limb bud and heart development	15					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(172;0.155)					TATCTGAGATCGGCCAAGATG	0.537													C|||	12	0.00239617	0.0076	0.0029	5008	,	,		20573	0.0		0.0	False		,,,				2504	0.0				p.S15L		Atlas-SNP	.											.	LBH	14	.	0			c.C44T						PASS	.	C	LEU/SER	58,4348	56.8+/-93.2	1,56,2146	138.0	116.0	124.0		44	4.5	1.0	2	dbSNP_134	124	0,8600		0,0,4300	yes	missense	LBH	NM_030915.3	145	1,56,6446	TT,TC,CC		0.0,1.3164,0.4459	possibly-damaging	15/106	30457288	58,12948	2203	4300	6503	SO:0001583	missense	81606	exon2			TGAGATCGGCCAA	AF110224	CCDS33173.1	2p23.1	2012-12-07	2012-12-07		ENSG00000213626	ENSG00000213626			29532	protein-coding gene	gene with protein product		611763	"""limb bud and heart development homolog (mouse)"""			11230166, 11336496	Standard	NM_030915		Approved		uc002rne.2	Q53QV2	OTTHUMG00000152051	ENST00000395323.3:c.44C>T	2.37:g.30457288C>T	ENSP00000378733:p.Ser15Leu	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	186	98	0.526882	NM_030915	B2RBC2|Q9H0Q1	Missense_Mutation	SNP	ENST00000395323.3	37	CCDS33173.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	21.8	4.205678	0.79127	0.013164	0.0	ENSG00000213626	ENST00000395323;ENST00000406087;ENST00000404397;ENST00000401506	.	.	.	4.47	4.47	0.54385	.	0.250189	0.33895	N	0.004451	T	0.51126	0.1656	L	0.56769	1.78	0.80722	D	1	D	0.62365	0.991	P	0.47134	0.539	T	0.60915	-0.7168	9	0.46703	T	0.11	-7.442	14.6316	0.68660	0.0:1.0:0.0:0.0	.	15	Q53QV2	LBH_HUMAN	L	15;15;15;21	.	ENSP00000378733:S15L	S	+	2	0	LBH	30310792	0.992000	0.36948	0.990000	0.47175	0.952000	0.60782	3.080000	0.50112	2.028000	0.59812	0.455000	0.32223	TCG	C|0.996;T|0.004	0.004	strong		0.537	LBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325091.1	NM_030915	
LPHN3	23284	hgsc.bcm.edu	37	4	62800728	62800728	+	Silent	SNP	T	T	C	rs734644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:62800728T>C	ENST00000514591.1	+	13	2408	c.2079T>C	c.(2077-2079)aaT>aaC	p.N693N	LPHN3_ENST00000506720.1_Silent_p.N761N|LPHN3_ENST00000507625.1_Silent_p.N761N|LPHN3_ENST00000514157.1_Silent_p.N693N|LPHN3_ENST00000512091.2_Silent_p.N693N|LPHN3_ENST00000509896.1_Silent_p.N761N|LPHN3_ENST00000506700.1_Silent_p.N693N|LPHN3_ENST00000508078.1_3'UTR|LPHN3_ENST00000504896.1_Silent_p.N693N|LPHN3_ENST00000506746.1_Silent_p.N761N|LPHN3_ENST00000508946.1_Silent_p.N693N|LPHN3_ENST00000507164.1_Silent_p.N761N|LPHN3_ENST00000508693.1_Silent_p.N761N|LPHN3_ENST00000545650.1_Silent_p.N693N|LPHN3_ENST00000514996.1_Silent_p.N693N|LPHN3_ENST00000511324.1_Silent_p.N761N			Q9HAR2	LPHN3_HUMAN	latrophilin 3	680					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						TCAGGGAGAATACAGACAATA	0.428													C|||	3405	0.679912	0.7988	0.6153	5008	,	,		19917	0.5933		0.7276	False		,,,				2504	0.6053				p.N693N		Atlas-SNP	.											.	LPHN3	800	.	0			c.T2079C						PASS	.	C		3133,799		1248,637,81	94.0	93.0	93.0		2079	4.7	1.0	4	dbSNP_86	93	6240,2080		2330,1580,250	no	coding-synonymous	LPHN3	NM_015236.4		3578,2217,331	CC,CT,TT		25.0,20.3204,23.4982		693/1470	62800728	9373,2879	1966	4160	6126	SO:0001819	synonymous_variant	23284	exon11			GGAGAATACAGAC	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.2079T>C	4.37:g.62800728T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_015236	E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	37	CCDS54768.1	1500	0.6868131868131868	401	0.8150406504065041	227	0.6270718232044199	325	0.5681818181818182	547	0.7216358839050132	C	4.530	0.098427	0.08681	0.796796	0.75	ENSG00000150471	ENST00000502815	.	.	.	5.54	4.69	0.59074	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999954	.	.	.	.	.	.	T	0.17961	-1.0352	3	.	.	.	.	9.924	0.41481	0.0:0.7807:0.0:0.2193	rs734644;rs17226328;rs61382511;rs734644	.	.	.	H	151	.	.	Y	+	1	0	LPHN3	62483323	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	1.626000	0.37039	0.895000	0.36342	-0.128000	0.14901	TAC	T|0.303;C|0.697	0.697	strong		0.428	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1		
OBSCN	84033	hgsc.bcm.edu	37	1	228560700	228560700	+	Silent	SNP	T	T	C	rs512253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228560700T>C	ENST00000422127.1	+	94	22265	c.22221T>C	c.(22219-22221)gaT>gaC	p.D7407D	OBSCN_ENST00000570156.2_Silent_p.D8364D|OBSCN_ENST00000366707.4_Silent_p.D5041D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7407					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)				TGCCGCTGGATGAGCCTGCAG	0.677													C|||	3796	0.757987	0.9365	0.6398	5008	,	,		15865	0.752		0.5636	False		,,,				2504	0.8067				p.D8364D		Atlas-SNP	.											OBSCN_ENST00000570156,rectum,carcinoma,0,5	OBSCN	2142	5	0			c.T25092C						PASS	.	C		3642,576		1602,438,69	16.0	22.0	20.0		22221	-7.7	0.1	1	dbSNP_83	20	4624,3806		1316,1992,907	no	coding-synonymous	OBSCN	NM_001098623.1		2918,2430,976	CC,CT,TT		45.1483,13.6558,34.6458		7407/7969	228560700	8266,4382	2109	4215	6324	SO:0001819	synonymous_variant	84033	exon105			GCTGGATGAGCCT	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.22221T>C	1.37:g.228560700T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	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	6.371	0.436557	0.12104	0.863442	0.548517	ENSG00000154358	ENST00000441106	.	.	.	5.31	-7.65	0.01281	.	.	.	.	.	.	.	.	.	.	.	0.26408	P	0.9763186	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.4422	0.16515	0.1714:0.5044:0.1553:0.1689	rs512253;rs3795815	.	.	.	R	2024	.	.	X	+	1	0	OBSCN	226627323	0.942000	0.31987	0.072000	0.20136	0.009000	0.06853	-0.247000	0.08866	-1.794000	0.01256	-3.149000	0.00058	TGA	T|0.442;C|0.558	0.558	strong		0.677	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
FSCB	84075	hgsc.bcm.edu	37	14	44975052	44975052	+	Missense_Mutation	SNP	A	A	G	rs3825630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:44975052A>G	ENST00000340446.4	-	1	1430	c.1139T>C	c.(1138-1140)cTt>cCt	p.L380P	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	380	Pro-rich.		L -> P (in dbSNP:rs3825630). {ECO:0000269|PubMed:15489334}.			sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)	p.L380P(1)		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)		TTCACCAAGAAGCTCTACTGA	0.522													A|||	1358	0.271166	0.2859	0.3055	5008	,	,		18322	0.3968		0.1193	False		,,,				2504	0.2536				p.L380P		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	1	Substitution - Missense(1)	stomach(1)	c.T1139C						scavenged	.	A	PRO/LEU	1168,3238	363.6+/-316.6	160,848,1195	88.0	101.0	97.0		1139	-0.2	0.0	14	dbSNP_107	97	938,7662	196.9+/-241.7	50,838,3412	yes	missense	FSCB	NM_032135.3	98	210,1686,4607	GG,GA,AA		10.907,26.5093,16.1925	probably-damaging	380/826	44975052	2106,10900	2203	4300	6503	SO:0001583	missense	84075	exon1			CCAAGAAGCTCTA	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.1139T>C	14.37:g.44975052A>G	ENSP00000344579:p.Leu380Pro	Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	148	65	0.439189	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	542	0.24816849816849818	138	0.2804878048780488	97	0.26795580110497236	223	0.38986013986013984	84	0.11081794195250659	a	4.879	0.163307	0.09287	0.265093	0.10907	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.17528	2.27	3.87	-0.16	0.13375	.	.	.	.	.	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.11235	0.004	B	0.08055	0.003	T	0.48502	-0.9030	8	0.30078	T	0.28	.	6.2119	0.20633	0.5846:0.0:0.4154:0.0	rs3825630;rs17855636;rs58475266;rs3825630	380	Q5H9T9	FSCB_HUMAN	P	380	ENSP00000344579:L380P	ENSP00000344579:L380P	L	-	2	0	FSCB	44044802	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.903000	0.04084	-0.139000	0.11414	-0.479000	0.04858	CTT	A|0.796;G|0.204	0.204	strong		0.522	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
OR10T2	128360	hgsc.bcm.edu	37	1	158368541	158368541	+	Missense_Mutation	SNP	A	A	G	rs34465440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158368541A>G	ENST00000334438.1	-	1	715	c.716T>C	c.(715-717)gTc>gCc	p.V239A		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	239						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)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					GGCACAGGTGACAAAGGCCTT	0.483													G|||	1829	0.365216	0.4191	0.3055	5008	,	,		19987	0.2262		0.3131	False		,,,				2504	0.5317				p.V239A		Atlas-SNP	.											OR10T2,colon,carcinoma,-1,1	OR10T2	76	1	0			c.T716C						PASS	.	G	ALA/VAL	1731,2675	649.8+/-398.9	336,1059,808	104.0	97.0	100.0		716	4.6	1.0	1	dbSNP_126	100	2674,5926	684.9+/-404.0	402,1870,2028	yes	missense	OR10T2	NM_001004475.1	64	738,2929,2836	GG,GA,AA		31.093,39.2873,33.869	benign	239/315	158368541	4405,8601	2203	4300	6503	SO:0001583	missense	128360	exon1			CAGGTGACAAAGG	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.716T>C	1.37:g.158368541A>G	ENSP00000334115:p.Val239Ala	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	702	0.32142857142857145	212	0.43089430894308944	98	0.27071823204419887	147	0.256993006993007	245	0.3232189973614776	G	3.269	-0.149557	0.06585	0.392873	0.31093	ENSG00000186306	ENST00000334438	T	0.00058	8.79	4.57	4.57	0.56435	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41823	N	0.000819	T	0.00039	0.0001	N	0.01522	-0.82	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.00065	-1.2148	9	0.30078	T	0.28	.	11.8768	0.52552	0.0869:0.0:0.9131:0.0	rs34465440	239	Q8NGX3	O10T2_HUMAN	A	239	ENSP00000334115:V239A	ENSP00000334115:V239A	V	-	2	0	OR10T2	156635165	0.472000	0.25870	1.000000	0.80357	0.441000	0.31987	2.686000	0.46968	1.151000	0.42436	-0.119000	0.15052	GTC	A|0.662;G|0.338	0.338	strong		0.483	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
IRS2	8660	hgsc.bcm.edu	37	13	110435231	110435231	+	Missense_Mutation	SNP	C	C	T	rs1805097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:110435231C>T	ENST00000375856.3	-	1	3684	c.3170G>A	c.(3169-3171)gGc>gAc	p.G1057D		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	1057			G -> D (in dbSNP:rs1805097). {ECO:0000269|PubMed:12687350}.		brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			TGAGGCGGCGCCCGGGCCCTG	0.746													.|||	1419	0.283347	0.0938	0.4107	5008	,	,		7276	0.3929		0.3161	False		,,,				2504	0.3027				p.G1057D	Melanoma(100;613 2409 40847)	Atlas-SNP	.											.	IRS2	44	.	0			c.G3170A	GRCh37	CM003938	IRS2	M	rs1805097	PASS	.	C	ASP/GLY	464,3506		33,398,1554	5.0	5.0	5.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3170	2.1	0.0	13	dbSNP_89	5	2312,5652		359,1594,2029	yes	missense	IRS2	NM_003749.2	94	392,1992,3583	TT,TC,CC		29.0306,11.6877,23.2613	benign	1057/1339	110435231	2776,9158	1985	3982	5967	SO:0001583	missense	8660	exon1			GCGGCGCCCGGGC	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"""Pleckstrin homology (PH) domain containing"""	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.3170G>A	13.37:g.110435231C>T	ENSP00000365016:p.Gly1057Asp	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	17	14	0.823529	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	37	CCDS9510.1	651	0.2980769230769231	55	0.11178861788617886	134	0.3701657458563536	225	0.39335664335664333	237	0.31266490765171506	C	5.984	0.365448	0.11352	0.116877	0.290306	ENSG00000185950	ENST00000375856	T	0.48522	0.81	4.13	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.23650	0.089	B	0.19946	0.027	T	0.39761	-0.9598	8	0.35671	T	0.21	-3.4542	7.8389	0.29387	0.1819:0.6484:0.1697:0.0	rs1805097;rs17847224	1057	Q9Y4H2	IRS2_HUMAN	D	1057	ENSP00000365016:G1057D	ENSP00000365016:G1057D	G	-	2	0	IRS2	109233232	0.002000	0.14202	0.002000	0.10522	0.006000	0.05464	1.021000	0.30040	0.922000	0.37019	0.644000	0.83932	GGC	C|0.663;T|0.337	0.337	strong		0.746	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749	
ATAD3B	83858	hgsc.bcm.edu	37	1	1425700	1425700	+	Silent	SNP	T	T	C	rs819980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1425700T>C	ENST00000308647.7	+	14	1517	c.1401T>C	c.(1399-1401)atT>atC	p.I467I		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	467						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)		ACAGCCGCATTGACGTGATGG	0.577													N|||	2433	0.485823	0.8487	0.3357	5008	,	,		16643	0.623		0.0994	False		,,,				2504	0.3579				p.I467I		Atlas-SNP	.											ATAD3B,NS,carcinoma,0,2	ATAD3B	68	2	0			c.T1401C						PASS	.	C		3224,1180		1194,836,172	80.0	72.0	75.0		1401	-2.2	0.1	1	dbSNP_86	75	714,7884		45,624,3630	no	coding-synonymous	ATAD3B	NM_031921.4		1239,1460,3802	CC,CT,TT		8.3043,26.7938,30.2876		467/649	1425700	3938,9064	2202	4299	6501	SO:0001819	synonymous_variant	83858	exon14			CCGCATTGACGTG	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.1401T>C	1.37:g.1425700T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	170	75	0.441176	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Silent	SNP	ENST00000308647.7	37	CCDS30.1																																																																																			T|0.629;C|0.371	0.371	strong		0.577	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
ATAD3A	55210	hgsc.bcm.edu	37	1	1458944	1458944	+	Silent	SNP	C	C	T	rs112145664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1458944C>T	ENST00000378755.5	+	9	1198	c.1104C>T	c.(1102-1104)ctC>ctT	p.L368L	ATAD3A_ENST00000536055.1_Silent_p.L241L|ATAD3A_ENST00000378756.3_Silent_p.L320L	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	368					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)			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)		GTGTTGTGCTCAGTGTAAGTC	0.711													N|||	109	0.0217652	0.0756	0.0115	5008	,	,		12972	0.001		0.0	False		,,,				2504	0.0				p.L368L		Atlas-SNP	.											.	ATAD3A	35	.	0			c.C1104T						PASS	.	G	,,	346,4060	177.3+/-206.3	11,324,1868	57.0	56.0	56.0		960,723,1104	2.9	0.9	1	dbSNP_132	56	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ATAD3A	NM_001170535.1,NM_001170536.1,NM_018188.3	,,	11,326,6166	TT,TC,CC		0.0233,7.8529,2.6757	,,	320/587,241/508,368/635	1458944	348,12658	2203	4300	6503	SO:0001819	synonymous_variant	55210	exon9			TGTGCTCAGTGTA	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.1104C>T	1.37:g.1458944C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	186	106	0.569892	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Silent	SNP	ENST00000378755.5	37	CCDS31.1	43	0.019688644688644688	37	0.07520325203252033	6	0.016574585635359115	0	0.0	0	0.0	c	0.686	-0.796159	0.02862	0.078529	2.33E-4	ENSG00000197785	ENST00000339113	.	.	.	4.8	2.93	0.34026	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.355	0.66730	0.0:0.5744:0.4256:0.0	.	.	.	.	X	306	.	.	Q	+	1	0	ATAD3A	1448807	1.000000	0.71417	0.865000	0.33974	0.004000	0.04260	0.553000	0.23391	0.465000	0.27167	-1.655000	0.00754	CAG	C|0.974;T|0.026	0.026	strong		0.711	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188	
NANS	54187	hgsc.bcm.edu	37	9	100819192	100819192	+	Silent	SNP	C	C	T	rs3739670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100819192C>T	ENST00000210444.5	+	1	172	c.102C>T	c.(100-102)gaC>gaT	p.D34D		NM_018946.3	NP_061819.2	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid synthase	34					lipopolysaccharide biosynthetic process (GO:0009103)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	N-acetylneuraminate synthase activity (GO:0050462)|N-acylneuraminate cytidylyltransferase activity (GO:0008781)|N-acylneuraminate-9-phosphate synthase activity (GO:0047444)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	11		Acute lymphoblastic leukemia(62;0.0559)				GCGACCTGGACGTAGCCAAGC	0.726													C|||	1962	0.391773	0.6778	0.2622	5008	,	,		9444	0.124		0.2068	False		,,,				2504	0.5634				p.D34D		Atlas-SNP	.											.	NANS	24	.	0			c.C102T						PASS	.	C		2708,1694		832,1044,325	26.0	27.0	27.0		102	-1.5	1.0	9	dbSNP_107	27	1697,6901		162,1373,2764	no	coding-synonymous	NANS	NM_018946.3		994,2417,3089	TT,TC,CC		19.7371,38.4825,33.8846		34/360	100819192	4405,8595	2201	4299	6500	SO:0001819	synonymous_variant	54187	exon1			CCTGGACGTAGCC	AF161387	CCDS6733.1	9p24.1-p23	2008-07-31	2008-07-31		ENSG00000095380	ENSG00000095380			19237	protein-coding gene	gene with protein product	"""sialic acid synthase"""	605202				10749855	Standard	NM_018946		Approved	SAS	uc004ayc.3	Q9NR45	OTTHUMG00000020341	ENST00000210444.5:c.102C>T	9.37:g.100819192C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	91	56	0.615385	NM_018946	B2RE98|Q8WUV9|Q9BWS6|Q9NVD4	Silent	SNP	ENST00000210444.5	37	CCDS6733.1																																																																																			C|0.679;T|0.321	0.321	strong		0.726	NANS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053359.1	NM_018946	
TRMT12	55039	hgsc.bcm.edu	37	8	125463250	125463250	+	Missense_Mutation	SNP	T	T	C	rs3812475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:125463250T>C	ENST00000328599.3	+	1	203	c.82T>C	c.(82-84)Tgg>Cgg	p.W28R	TRMT12_ENST00000521443.1_3'UTR	NM_017956.3	NP_060426.2	Q53H54	TYW2_HUMAN	tRNA methyltransferase 12 homolog (S. cerevisiae)	28			W -> R (in dbSNP:rs3812475). {ECO:0000269|PubMed:15489334}.		tRNA processing (GO:0008033)		transferase activity (GO:0016740)			breast(2)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GACTGAGCCTTGGTTTACCCA	0.517													C|||	2860	0.571086	0.7814	0.4798	5008	,	,		18795	0.4415		0.495	False		,,,				2504	0.5634				p.W28R		Atlas-SNP	.											.	TRMT12	28	.	0			c.T82C						PASS	.	C	ARG/TRP	3061,1345	447.5+/-348.4	1073,915,215	123.0	128.0	126.0		82	5.2	0.9	8	dbSNP_107	126	4059,4541	595.1+/-393.4	942,2175,1183	yes	missense	TRMT12	NM_017956.3	101	2015,3090,1398	CC,CT,TT		47.1977,30.5266,45.256	benign	28/449	125463250	7120,5886	2203	4300	6503	SO:0001583	missense	55039	exon1			GAGCCTTGGTTTA	AF313041	CCDS6349.1	8q24.13	2011-05-09	2006-11-16		ENSG00000183665	ENSG00000183665			26091	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 2"""	611244	"""tRNA methyltranferase 12 homolog (S. cerevisiae)"""			16005430, 17150819	Standard	NM_017956		Approved	FLJ20772, Trm12, TYW2	uc003yra.4	Q53H54	OTTHUMG00000165022	ENST00000328599.3:c.82T>C	8.37:g.125463250T>C	ENSP00000329858:p.Trp28Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_017956	Q6PKB9|Q96F21|Q9NWK6	Missense_Mutation	SNP	ENST00000328599.3	37	CCDS6349.1	1205	0.5517399267399268	394	0.8008130081300813	189	0.5220994475138122	242	0.4230769230769231	380	0.5013192612137203	C	0.456	-0.891521	0.02491	0.694734	0.471977	ENSG00000183665	ENST00000328599	T	0.38560	1.13	5.15	5.15	0.70609	.	0.426796	0.26563	N	0.023680	T	0.00012	0.0000	N	0.00128	-2.045	0.58432	P	9.99999999995449E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39099	-0.9630	9	0.02654	T	1	-11.5588	10.5383	0.45018	0.0:0.9086:0.0:0.0914	rs3812475;rs17856366;rs52807988;rs59731176;rs3812475	28	Q53H54	TYW2_HUMAN	R	28	ENSP00000329858:W28R	ENSP00000329858:W28R	W	+	1	0	TRMT12	125532431	0.468000	0.25839	0.923000	0.36655	0.456000	0.32438	0.518000	0.22847	1.515000	0.48885	-0.215000	0.12644	TGG	T|0.442;C|0.558	0.558	strong		0.517	TRMT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381465.1	NM_017956	
F11	2160	hgsc.bcm.edu	37	4	187209702	187209702	+	Silent	SNP	G	G	T	rs5971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187209702G>T	ENST00000403665.2	+	15	2164	c.1812G>T	c.(1810-1812)cgG>cgT	p.R604R	F11_ENST00000264692.4_Silent_p.R552R|F11-AS1_ENST00000505103.1_RNA	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	604	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)	p.R604R(1)		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)	AAAGGGAGCGGCCAGGTGTTT	0.567													G|||	448	0.0894569	0.1445	0.0677	5008	,	,		19283	0.0843		0.0537	False		,,,				2504	0.0726				p.R604R		Atlas-SNP	.											F11,NS,carcinoma,0,1	F11	65	1	1	Substitution - coding silent(1)	stomach(1)	c.G1812T						PASS	.	G		544,3862	245.6+/-254.5	39,466,1698	148.0	142.0	144.0		1812	-2.5	0.1	4	dbSNP_52	144	398,8202	127.3+/-185.7	14,370,3916	no	coding-synonymous	F11	NM_000128.3		53,836,5614	TT,TG,GG		4.6279,12.3468,7.2428		604/626	187209702	942,12064	2203	4300	6503	SO:0001819	synonymous_variant	2160	exon15			GGAGCGGCCAGGT	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.1812G>T	4.37:g.187209702G>T		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	283	148	0.522968	NM_000128	D3DP64|Q4W5C2|Q9Y495	Silent	SNP	ENST00000403665.2	37	CCDS3847.1	191	0.08745421245421245	73	0.1483739837398374	24	0.06629834254143646	51	0.08916083916083917	43	0.05672823218997362	G	11.86	1.765587	0.31228	0.123468	0.046279	ENSG00000088926	ENST00000264691	.	.	.	5.05	-2.53	0.06326	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.09310	P	0.999999655879	.	.	.	.	.	.	T	0.21177	-1.0253	3	.	.	.	.	3.3473	0.07140	0.3787:0.0991:0.4209:0.1012	rs5971;rs60887226;rs5971	.	.	.	V	138	.	.	G	+	2	0	F11	187446696	0.000000	0.05858	0.086000	0.20670	0.980000	0.70556	-1.510000	0.02262	-0.335000	0.08451	0.549000	0.68633	GGC	G|0.914;T|0.086	0.086	strong		0.567	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4		
SF3A3	10946	hgsc.bcm.edu	37	1	38433762	38433762	+	Silent	SNP	G	G	A	rs59294668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38433762G>A	ENST00000373019.4	-	15	2281	c.1326C>T	c.(1324-1326)aaC>aaT	p.N442N	SF3A3_ENST00000448721.2_Silent_p.N389N	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	442					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				AGTGAGCAGTGTTTGGGATGC	0.448													G|||	79	0.0157748	0.0545	0.0101	5008	,	,		22415	0.0		0.0	False		,,,				2504	0.0				p.N442N		Atlas-SNP	.											.	SF3A3	37	.	0			c.C1326T						PASS	.	G		199,4207	123.3+/-160.7	7,185,2011	184.0	174.0	177.0		1326	-0.1	1.0	1	dbSNP_129	177	0,8600		0,0,4300	no	coding-synonymous	SF3A3	NM_006802.2		7,185,6311	AA,AG,GG		0.0,4.5166,1.5301		442/502	38433762	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	10946	exon15			AGCAGTGTTTGGG	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"""splicing factor 3a, subunit 3, 60kD"""			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.1326C>T	1.37:g.38433762G>A		Somatic	478	2	0.0041841		WXS	Illumina HiSeq	Phase_I	500	294	0.588	NM_006802	D3DPT5|Q15460|Q5VT87	Silent	SNP	ENST00000373019.4	37	CCDS428.1																																																																																			G|0.983;A|0.017	0.017	strong		0.448	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802	
ATP1A2	477	hgsc.bcm.edu	37	1	160104950	160104950	+	Silent	SNP	C	C	T	rs61734529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160104950C>T	ENST00000361216.3	+	15	2069	c.1980C>T	c.(1978-1980)tgC>tgT	p.C660C	ATP1A2_ENST00000392233.3_Silent_p.C660C	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	660					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CCAAGGCATGCGTGGTGCACG	0.612													C|||	104	0.0207668	0.0779	0.0014	5008	,	,		22206	0.0		0.0	False		,,,				2504	0.0				p.C660C		Atlas-SNP	.											.	ATP1A2	167	.	0			c.C1980T						PASS	.	C		301,4105	164.0+/-195.7	10,281,1912	99.0	72.0	81.0		1980	-6.2	0.4	1	dbSNP_129	81	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ATP1A2	NM_000702.3		10,283,6210	TT,TC,CC		0.0233,6.8316,2.3297		660/1021	160104950	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	477	exon15			GGCATGCGTGGTG	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.1980C>T	1.37:g.160104950C>T		Somatic	356	0	0		WXS	Illumina HiSeq	Phase_I	414	216	0.521739	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	37	CCDS1196.1	34	0.015567765567765568	34	0.06910569105691057	0	0.0	0	0.0	0	0.0	C	9.163	1.019313	0.19355	0.068316	2.33E-4	ENSG00000018625	ENST00000447527	.	.	.	4.44	-6.19	0.02078	.	.	.	.	.	T	0.47173	0.1431	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60662	-0.7219	4	.	.	.	.	13.6226	0.62146	0.0:0.609:0.0:0.391	rs61734529	.	.	.	V	371	.	.	A	+	2	0	ATP1A2	158371574	0.002000	0.14202	0.400000	0.26346	0.942000	0.58702	-1.400000	0.02504	-1.346000	0.02211	0.511000	0.50034	GCG	C|0.978;T|0.022	0.022	strong		0.612	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	
MYH11	4629	hgsc.bcm.edu	37	16	15850204	15850204	+	Silent	SNP	A	A	G	rs2272554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:15850204A>G	ENST00000300036.5	-	14	1852	c.1743T>C	c.(1741-1743)gcT>gcC	p.A581A	MYH11_ENST00000452625.2_Silent_p.A588A|MYH11_ENST00000396324.3_Silent_p.A588A|MYH11_ENST00000576790.2_Silent_p.A581A	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	581	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GTACCTTCCCAGCATAATGGA	0.597			T	CBFB	AML						OREG0023636	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2745	0.548123	0.7481	0.3905	5008	,	,		18888	0.6647		0.4245	False		,,,				2504	0.3967				p.A588A		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.T1764C						PASS	.	G	,,,	2995,1399	459.2+/-352.2	1023,949,225	88.0	72.0	77.0		1764,1764,1743,1743	-10.8	0.1	16	dbSNP_100	77	3489,5111	632.5+/-398.6	727,2035,1538	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	,,,	1750,2984,1763	GG,GA,AA		40.5698,31.8389,49.9	,,,	588/1946,588/1980,581/1973,581/1939	15850204	6484,6510	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon15			CTTCCCAGCATAA	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.1743T>C	16.37:g.15850204A>G		Somatic	132	0	0	705	WXS	Illumina HiSeq	Phase_I	150	148	0.986667	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			A|0.465;G|0.535	0.535	strong		0.597	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
DCANP1	140947	hgsc.bcm.edu	37	5	134782396	134782396	+	Missense_Mutation	SNP	T	T	A	rs67187482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134782396T>A	ENST00000503143.2	-	1	642	c.403A>T	c.(403-405)Agt>Tgt	p.S135C	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		135						nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGTCTGAAACTACAAACCAGA	0.547													T|||	430	0.0858626	0.2867	0.0418	5008	,	,		19738	0.0		0.0179	False		,,,				2504	0.0041				p.S135C		Atlas-SNP	.											.	C5orf20	16	.	0			c.A403T						PASS	.	T	CYS/SER	1116,3290	402.4+/-332.3	149,818,1236	132.0	143.0	139.0		403	-1.8	0.0	5	dbSNP_130	139	119,8481	61.7+/-123.6	1,117,4182	yes	missense	C5orf20	NM_130848.2	112	150,935,5418	AA,AT,TT		1.3837,25.3291,9.4956	benign	135/245	134782396	1235,11771	2203	4300	6503	SO:0001583	missense	140947	exon1			TGAAACTACAAAC																												ENST00000503143.2:c.403A>T	5.37:g.134782396T>A	ENSP00000421871:p.Ser135Cys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	163	0.07463369963369963	132	0.2682926829268293	14	0.03867403314917127	0	0.0	17	0.022427440633245383	T	4.521	0.096694	0.08681	0.253291	0.013837	ENSG00000251380	ENST00000503143	T	0.39056	1.1	2.85	-1.79	0.07932	.	.	.	.	.	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	0.32508	-0.9904	8	0.87932	D	0	.	4.0496	0.09790	0.3788:0.41:0.0:0.2112	.	135	Q8TF63	DCNP1_HUMAN	C	135	ENSP00000421871:S135C	ENSP00000421871:S135C	S	-	1	0	C5orf20	134810295	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.310000	0.19356	-0.278000	0.09180	-0.892000	0.02923	AGT	T|0.905;A|0.095	0.095	strong		0.547	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
EPPK1	83481	hgsc.bcm.edu	37	8	144946271	144946271	+	Missense_Mutation	SNP	C	C	T	rs58368323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144946271C>T	ENST00000525985.1	-	2	1222	c.1151G>A	c.(1150-1152)gGg>gAg	p.G384E				P58107	EPIPL_HUMAN	epiplakin 1	384						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)			GTCCACTAGCCCCTTCTTCAT	0.672													C|||	224	0.0447284	0.1604	0.013	5008	,	,		15903	0.0		0.003	False		,,,				2504	0.0				p.G384E		Atlas-SNP	.											.	EPPK1	199	.	0			c.G1151A						PASS	.	C	GLU/GLY	400,3414		19,362,1526	6.0	7.0	7.0		1151	-1.4	0.7	8	dbSNP_129	7	6,8126		0,6,4060	yes	missense	EPPK1	NM_031308.1	98	19,368,5586	TT,TC,CC		0.0738,10.4877,3.3986	benign	384/2420	144946271	406,11540	1907	4066	5973	SO:0001583	missense	83481	exon1			ACTAGCCCCTTCT	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.1151G>A	8.37:g.144946271C>T	ENSP00000436337:p.Gly384Glu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		83	0.038003663003663	70	0.14227642276422764	4	0.011049723756906077	2	0.0034965034965034965	7	0.009234828496042216	C	9.565	1.119374	0.20877	0.104877	7.38E-4	ENSG00000227184	ENST00000525985	T	0.72835	-0.69	4.96	-1.43	0.08884	.	.	.	.	.	T	0.00524	0.0017	N	0.25789	0.76	0.09310	N	0.999997	B	0.12013	0.005	B	0.09377	0.004	T	0.00870	-1.1533	9	0.16896	T	0.51	.	10.042	0.42164	0.0:0.6982:0.0:0.3018	rs58368323	384	E9PPU0	.	E	384	ENSP00000436337:G384E	ENSP00000436337:G384E	G	-	2	0	EPPK1	145018259	0.000000	0.05858	0.663000	0.29738	0.564000	0.35744	-0.181000	0.09740	-0.542000	0.06249	-0.409000	0.06214	GGG	C|0.961;T|0.039	0.039	strong		0.672	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
PLXNA4	91584	hgsc.bcm.edu	37	7	132192295	132192295	+	Silent	SNP	G	G	A	rs156961|rs200081174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:132192295G>A	ENST00000359827.3	-	2	2120	c.1158C>T	c.(1156-1158)ctC>ctT	p.L386L	PLXNA4_ENST00000423507.2_Silent_p.L386L|PLXNA4_ENST00000378539.5_Silent_p.L386L|PLXNA4_ENST00000321063.4_Silent_p.L386L			Q9HCM2	PLXA4_HUMAN	plexin A4	386	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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						CCTTCACCTTGAGCCAGGCCA	0.612													G|||	1969	0.393171	0.5159	0.3588	5008	,	,		20224	0.2708		0.3917	False		,,,				2504	0.3793				p.L386L		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C1158T						PASS	.	G	,,	2111,2295	547.2+/-377.2	509,1093,601	56.0	45.0	49.0		1158,1158,1158	3.2	1.0	7	dbSNP_79	49	3347,5253	468.8+/-367.4	641,2065,1594	no	coding-synonymous,coding-synonymous,coding-synonymous	PLXNA4	NM_001105543.1,NM_020911.1,NM_181775.3	,,	1150,3158,2195	AA,AG,GG		38.9186,47.9119,41.9652	,,	386/493,386/1895,386/523	132192295	5458,7548	2203	4300	6503	SO:0001819	synonymous_variant	91584	exon2			CACCTTGAGCCAG	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.1158C>T	7.37:g.132192295G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			G|0.594;A|0.406	0.406	strong		0.612	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
KMT2C	58508	hgsc.bcm.edu	37	7	151949068	151949068	+	Missense_Mutation	SNP	C	C	G	rs3735156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151949068C>G	ENST00000262189.6	-	11	1795	c.1577G>C	c.(1576-1578)cGt>cCt	p.R526P	KMT2C_ENST00000355193.2_Missense_Mutation_p.R526P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	526			R -> P (in dbSNP:rs3735156). {ECO:0000269|PubMed:11891048}.		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)										TGGCTGTAAACGATCCATCTC	0.383													G|||	906	0.180911	0.4977	0.1095	5008	,	,		18528	0.0704		0.0109	False		,,,				2504	0.092				p.R526P		Atlas-SNP	.											.	MLL3	1564	.	0			c.G1577C						PASS	.	G	PRO/ARG	1996,2410	616.3+/-392.7	458,1080,665	106.0	96.0	100.0		1577	5.8	0.0	7	dbSNP_107	100	139,8461	813.0+/-407.0	1,137,4162	yes	missense	MLL3	NM_170606.2	103	459,1217,4827	GG,GC,CC		1.6163,45.3019,16.4155	benign	526/4912	151949068	2135,10871	2203	4300	6503	SO:0001583	missense	58508	exon11			TGTAAACGATCCA	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.1577G>C	7.37:g.151949068C>G	ENSP00000262189:p.Arg526Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	102	32	0.313726	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	331	0.15155677655677655	241	0.4898373983739837	37	0.10220994475138122	45	0.07867132867132867	8	0.010554089709762533	G	8.646	0.897097	0.17686	0.453019	0.016163	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.82893	-1.66;-1.66	5.75	5.75	0.90469	.	0.321390	0.22057	N	0.065238	T	0.00012	0.0000	N	0.00197	-1.87	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.30357	-0.9981	9	0.02654	T	1	.	11.4246	0.50003	0.0:0.2354:0.6285:0.1361	rs3735156;rs10376667;rs61450622;rs3735156	526	Q8NEZ4	MLL3_HUMAN	P	526	ENSP00000262189:R526P;ENSP00000347325:R526P	ENSP00000262189:R526P	R	-	2	0	MLL3	151580001	0.893000	0.30496	0.007000	0.13788	0.948000	0.59901	1.962000	0.40442	1.454000	0.47793	-0.120000	0.15030	CGT	C|0.828;G|0.172	0.172	strong		0.383	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
PLD2	5338	hgsc.bcm.edu	37	17	4712395	4712395	+	Splice_Site	SNP	A	A	T	rs1132446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4712395A>T	ENST00000263088.6	+	5	515	c.384A>T	c.(382-384)cgA>cgT	p.R128R	RP11-81A22.5_ENST00000571067.1_lincRNA|PLD2_ENST00000572940.1_Splice_Site_p.R128R	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	128	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)	CTTTCCACAGATTTGCCGTTG	0.577													A|||	1582	0.315895	0.4009	0.2392	5008	,	,		18371	0.3641		0.2922	False		,,,				2504	0.2301				p.R128R		Atlas-SNP	.											.	PLD2	138	.	0			c.A384T						PASS	.	A		1617,2789	498.8+/-364.2	279,1059,865	105.0	113.0	110.0		384	-2.0	1.0	17	dbSNP_86	110	2393,6207	397.6+/-345.8	351,1691,2258	yes	coding-synonymous-near-splice	PLD2	NM_002663.4		630,2750,3123	TT,TA,AA		27.8256,36.7,30.8319		128/934	4712395	4010,8996	2203	4300	6503	SO:0001630	splice_region_variant	5338	exon5			CCACAGATTTGCC	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.384-1A>T	17.37:g.4712395A>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Silent	SNP	ENST00000263088.6	37	CCDS11057.1																																																																																			A|0.682;T|0.318	0.318	strong		0.577	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	Silent
CC2D1A	54862	hgsc.bcm.edu	37	19	14023191	14023191	+	Silent	SNP	G	G	A	rs7250180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14023191G>A	ENST00000318003.7	+	3	493	c.252G>A	c.(250-252)ccG>ccA	p.P84P	CC2D1A_ENST00000589606.1_Silent_p.P84P	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	84					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			TGAGAGACCCGGATGAGGATG	0.632													G|||	480	0.0958466	0.3427	0.0216	5008	,	,		19053	0.0		0.002	False		,,,				2504	0.0102				p.P84P		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G252A						PASS	.	G		1189,3129		165,859,1135	61.0	73.0	69.0		252	-3.8	0.3	19	dbSNP_116	69	29,8473		0,29,4222	no	coding-synonymous	CC2D1A	NM_017721.4		165,888,5357	AA,AG,GG		0.3411,27.5359,9.5008		84/952	14023191	1218,11602	2159	4251	6410	SO:0001819	synonymous_variant	54862	exon3			AGACCCGGATGAG	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.252G>A	19.37:g.14023191G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Silent	SNP	ENST00000318003.7	37	CCDS42512.1																																																																																			G|0.919;A|0.081	0.081	strong		0.632	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
RASSF7	8045	hgsc.bcm.edu	37	11	562421	562421	+	Missense_Mutation	SNP	G	G	A	rs2242182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:562421G>A	ENST00000397583.3	+	3	900	c.467G>A	c.(466-468)cGg>cAg	p.R156Q	RASSF7_ENST00000454668.2_Missense_Mutation_p.R156Q|C11orf35_ENST00000329451.3_5'Flank|RASSF7_ENST00000524468.1_3'UTR|RP11-496I9.1_ENST00000527620.1_RNA|RASSF7_ENST00000397582.3_Missense_Mutation_p.R156Q|RP11-496I9.1_ENST00000527113.1_RNA|RASSF7_ENST00000344375.4_Missense_Mutation_p.R156Q|RASSF7_ENST00000431809.1_Missense_Mutation_p.R156Q	NM_003475.3	NP_003466.1	Q02833	RASF7_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	156			R -> Q (in dbSNP:rs2242182).		apoptotic process (GO:0006915)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(3)	8		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ACAGACCTGCGGGGCCTGGAG	0.701													G|||	409	0.0816693	0.003	0.1398	5008	,	,		16128	0.1696		0.0517	False		,,,				2504	0.0869				p.R156Q	Pancreas(184;1170 3913 7268)	Atlas-SNP	.											.	RASSF7	22	.	0			c.G467A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	33,4161		0,33,2064	12.0	11.0	12.0		467,467,467	1.1	1.0	11	dbSNP_98	12	314,8032		7,300,3866	yes	missense,missense,missense	RASSF7	NM_001143993.1,NM_001143994.1,NM_003475.3	43,43,43	7,333,5930	AA,AG,GG		3.7623,0.7868,2.7671	benign,benign,benign	156/338,156/321,156/374	562421	347,12193	2097	4173	6270	SO:0001583	missense	8045	exon3			ACCTGCGGGGCCT	M91083	CCDS7702.1, CCDS44505.1, CCDS44506.1	11p15.5	2008-02-22	2008-02-22	2005-09-14	ENSG00000099849	ENSG00000099849			1166	protein-coding gene	gene with protein product		143023	"""chromosome 11 open reading frame 13"""	C11orf13		1339391	Standard	NM_001143993		Approved	HRC1, HRAS1	uc001lqc.3	Q02833	OTTHUMG00000132004	ENST00000397583.3:c.467G>A	11.37:g.562421G>A	ENSP00000380713:p.Arg156Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	130	55	0.423077	NM_001143994	G5E9N9|Q3KP41|Q3KP42	Missense_Mutation	SNP	ENST00000397583.3	37	CCDS7702.1	170	0.07783882783882784	2	0.0040650406504065045	35	0.09668508287292818	92	0.16083916083916083	41	0.05408970976253298	G	0.055	-1.239467	0.01493	0.007868	0.037623	ENSG00000099849	ENST00000431809;ENST00000397582;ENST00000344375;ENST00000397583;ENST00000454668	T;T;T;T;T	0.28666	1.61;1.61;1.6;1.6;1.62	3.52	1.13	0.20643	.	0.374590	0.26650	N	0.023219	T	0.00039	0.0001	N	0.00347	-1.61	0.80722	P	0.0	B;B;B	0.10296	0.0;0.003;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.36040	-0.9764	9	0.02654	T	1	0.0495	5.3402	0.15979	0.3872:0.0:0.6128:0.0	rs2242182	156;156;156	G5E9N9;Q02833;Q02833-2	.;RASF7_HUMAN;.	Q	156	ENSP00000403068:R156Q;ENSP00000380712:R156Q;ENSP00000344226:R156Q;ENSP00000380713:R156Q;ENSP00000405606:R156Q	ENSP00000344226:R156Q	R	+	2	0	RASSF7	552421	0.012000	0.17670	0.963000	0.40424	0.208000	0.24298	0.289000	0.18957	0.463000	0.27118	-0.379000	0.06801	CGG	G|0.923;A|0.077	0.077	strong		0.701	RASSF7-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254972.2	NM_003475	
STT3A	3703	hgsc.bcm.edu	37	11	125484044	125484044	+	Silent	SNP	A	A	G	rs12276729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:125484044A>G	ENST00000529196.1	+	15	1823	c.1617A>G	c.(1615-1617)acA>acG	p.T539T	STT3A_ENST00000392708.4_Silent_p.T539T|STT3A_ENST00000531491.1_Silent_p.T447T			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	539					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		CAAACCGAACAATTTTAGTGG	0.403													A|||	228	0.0455272	0.1399	0.0144	5008	,	,		21257	0.0288		0.002	False		,,,				2504	0.002				p.T539T		Atlas-SNP	.											.	STT3A	52	.	0			c.A1617G						PASS	.	A		517,3885	238.4+/-249.8	25,467,1709	212.0	196.0	201.0		1617	-8.6	0.9	11	dbSNP_120	201	5,8593	3.7+/-12.6	0,5,4294	no	coding-synonymous	STT3A	NM_152713.3		25,472,6003	GG,GA,AA		0.0582,11.7447,4.0154		539/706	125484044	522,12478	2201	4299	6500	SO:0001819	synonymous_variant	3703	exon14			CCGAACAATTTTA	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"""dolichyl-diphosphooligosaccharide protein glycotransferase"""	601134	"""integral membrane protein 1"", ""STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)"", ""STT3A, cataylic subunit of the oligosaccharyltransferase complex"""	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.1617A>G	11.37:g.125484044A>G		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	211	82	0.388626	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	37	CCDS8458.1																																																																																			A|0.956;G|0.044	0.044	strong		0.403	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
MROH7	374977	hgsc.bcm.edu	37	1	55119466	55119466	+	Silent	SNP	C	C	T	rs2304315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55119466C>T	ENST00000421030.2	+	3	1152	c.867C>T	c.(865-867)agC>agT	p.S289S	MROH7_ENST00000545244.1_Intron|MROH7_ENST00000409996.1_Intron|MROH7-TTC4_ENST00000414150.2_Silent_p.S289S|MROH7_ENST00000395690.2_Silent_p.S289S|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000454855.2_Intron|MROH7_ENST00000339553.5_Silent_p.S289S	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	289	Ser-rich.					extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CTGATTTGAGCGTGACCATCA	0.522													C|||	335	0.066893	0.1354	0.0447	5008	,	,		20161	0.1032		0.0109	False		,,,				2504	0.0102				p.S289S		Atlas-SNP	.											HEATR8_ENST00000421030,caecum,carcinoma,0,2	.	.	2	0			c.C867T						PASS	.	C		429,3743		14,401,1671	83.0	82.0	83.0		867	-2.6	0.0	1	dbSNP_100	83	27,8411		0,27,4192	no	coding-synonymous	HEATR8	NM_001039464.2		14,428,5863	TT,TC,CC		0.32,10.2828,3.6162		289/1324	55119466	456,12154	2086	4219	6305	SO:0001819	synonymous_variant	374977	exon3			TTTGAGCGTGACC	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.867C>T	1.37:g.55119466C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	37	CCDS41342.2																																																																																			C|0.935;T|0.065	0.065	strong		0.522	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
ENDOU	8909	hgsc.bcm.edu	37	12	48110150	48110150	+	Silent	SNP	G	G	A	rs61734364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48110150G>A	ENST00000422538.3	-	6	806	c.684C>T	c.(682-684)gaC>gaT	p.D228D	RP1-197B17.3_ENST00000547799.1_lincRNA|ENDOU_ENST00000545824.2_Silent_p.D165D|ENDOU_ENST00000229003.3_Silent_p.D187D|ENDOU_ENST00000542202.1_De_novo_Start_OutOfFrame	NM_001172439.1	NP_001165910.1	P21128	ENDOU_HUMAN	endonuclease, polyU-specific	228					female pregnancy (GO:0007565)|immune response (GO:0006955)|proteolysis (GO:0006508)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endoribonuclease activity (GO:0004521)|growth factor activity (GO:0008083)|manganese ion binding (GO:0030145)|polysaccharide binding (GO:0030247)|RNA binding (GO:0003723)|scavenger receptor activity (GO:0005044)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(3)|pancreas(1)|stomach(1)	14						TGAGGAAGGCGTCCTGCTCGG	0.592											OREG0021752	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	109	0.0217652	0.0756	0.0101	5008	,	,		17569	0.001		0.001	False		,,,				2504	0.0				p.D228D		Atlas-SNP	.											.	ENDOU	39	.	0			c.C684T						PASS	.	G	,,	344,4062	180.5+/-208.7	12,320,1871	136.0	124.0	128.0		684,495,561	-9.6	0.0	12	dbSNP_129	128	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	ENDOU	NM_001172439.1,NM_001172440.1,NM_006025.3	,,	12,323,6168	AA,AG,GG		0.0349,7.8075,2.668	,,	228/411,165/348,187/370	48110150	347,12659	2203	4300	6503	SO:0001819	synonymous_variant	8909	exon6			GAAGGCGTCCTGC	M32402	CCDS8754.1, CCDS53784.1, CCDS53785.1	12q13.1	2011-08-31			ENSG00000111405	ENSG00000111405		"""Serine peptidases / Serine peptidases"""	14369	protein-coding gene	gene with protein product		606720				2350438, 1710108, 15755742, 18936097	Standard	NM_006025		Approved	PP11, P11, PRSS26	uc001rpu.2	P21128	OTTHUMG00000169670	ENST00000422538.3:c.684C>T	12.37:g.48110150G>A		Somatic	193	0	0	952	WXS	Illumina HiSeq	Phase_I	204	93	0.455882	NM_001172439	B2RBJ3|B3KQS7|B7Z6E1|Q2NKJ4	Silent	SNP	ENST00000422538.3	37	CCDS53785.1																																																																																			A|0.024;G|0.975;T|0.000	0.024	strong		0.592	ENDOU-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405352.1	NM_006025.2	
OR1D2	4991	hgsc.bcm.edu	37	17	2995994	2995994	+	Silent	SNP	T	T	C	rs769424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2995994T>C	ENST00000331459.1	-	1	296	c.297A>G	c.(295-297)acA>acG	p.T99T		NM_002548.2	NP_002539.2	P34982	OR1D2_HUMAN	olfactory receptor, family 1, subfamily D, member 2	99					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|protein import into nucleus, translocation (GO:0000060)|sensory perception of smell (GO:0007608)|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)			kidney(2)|large_intestine(2)|lung(10)|ovary(1)	15						AGTAGAGCTGTGTCAGACACC	0.537													.|||	1297	0.258986	0.618	0.2435	5008	,	,		22867	0.0317		0.1233	False		,,,				2504	0.1585				p.T99T		Atlas-SNP	.											.	OR1D2	39	.	0			c.A297G						PASS	.	C		2297,2109		604,1089,510	173.0	178.0	176.0		297	-6.0	0.9	17	dbSNP_86	176	1166,7434		73,1020,3207	no	coding-synonymous	OR1D2	NM_002548.2		677,2109,3717	CC,CT,TT		13.5581,47.8665,26.6262		99/313	2995994	3463,9543	2203	4300	6503	SO:0001819	synonymous_variant	4991	exon1			GAGCTGTGTCAGA	U04678	CCDS11019.1	17p13.3	2012-08-09			ENSG00000184166	ENSG00000184166		"""GPCR / Class A : Olfactory receptors"""	8183	protein-coding gene	gene with protein product		164342		OLFR1		1370859, 1840504	Standard	NM_002548		Approved	OR17-4	uc010vrb.2	P34982	OTTHUMG00000090619	ENST00000331459.1:c.297A>G	17.37:g.2995994T>C		Somatic	490	1	0.00204082		WXS	Illumina HiSeq	Phase_I	532	263	0.494361	NM_002548	Q6IFL8|Q96RA4|Q9UM78	Silent	SNP	ENST00000331459.1	37	CCDS11019.1																																																																																			T|0.754;C|0.246	0.246	strong		0.537	OR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207207.1	NM_002548	
VPS13C	54832	hgsc.bcm.edu	37	15	62212781	62212781	+	Silent	SNP	T	T	C	rs17238189	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:62212781T>C	ENST00000261517.5	-	56	7201	c.7128A>G	c.(7126-7128)caA>caG	p.Q2376Q	VPS13C_ENST00000395898.3_Silent_p.Q2333Q|VPS13C_ENST00000249837.3_Silent_p.Q2333Q|VPS13C_ENST00000395896.4_Silent_p.Q2376Q	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						GAATTGCCATTTGTGGCTCAG	0.303													T|||	603	0.120407	0.093	0.2046	5008	,	,		16094	0.2054		0.0249	False		,,,				2504	0.1084				p.Q2376Q		Atlas-SNP	.											.	VPS13C	506	.	0			c.A7128G						PASS	.	T	,,,	431,3975	199.8+/-223.2	25,381,1797	63.0	67.0	65.0		7128,6999,6999,7128	2.2	1.0	15	dbSNP_123	65	189,8397	81.2+/-143.8	3,183,4107	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	,,,	28,564,5904	CC,CT,TT		2.2013,9.7821,4.7722	,,,	2376/3629,2333/3711,2333/3586,2376/3754	62212781	620,12372	2203	4293	6496	SO:0001819	synonymous_variant	54832	exon56			TGCCATTTGTGGC	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.7128A>G	15.37:g.62212781T>C		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	237	112	0.472574	NM_020821		Silent	SNP	ENST00000261517.5	37	CCDS32257.1																																																																																			T|0.930;C|0.070	0.070	strong		0.303	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
ANGPT4	51378	hgsc.bcm.edu	37	20	861853	861853	+	Silent	SNP	G	G	A	rs6086328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:861853G>A	ENST00000381922.3	-	5	1014	c.912C>T	c.(910-912)gtC>gtT	p.V304V	ANGPT4_ENST00000546022.1_Silent_p.V304V	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	304	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						GGATGGTGTAGACACCACTGG	0.572													G|||	335	0.066893	0.2405	0.0216	5008	,	,		18573	0.0		0.002	False		,,,				2504	0.0				p.V304V	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											.	ANGPT4	77	.	0			c.C912T						PASS	.	G		986,3420	370.0+/-319.4	106,774,1323	74.0	62.0	66.0		912	4.9	1.0	20	dbSNP_114	66	14,8586	9.1+/-34.3	0,14,4286	no	coding-synonymous	ANGPT4	NM_015985.2		106,788,5609	AA,AG,GG		0.1628,22.3786,7.6888		304/504	861853	1000,12006	2203	4300	6503	SO:0001819	synonymous_variant	51378	exon5			GGTGTAGACACCA	AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"""Fibrinogen C domain containing"""	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.912C>T	20.37:g.861853G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																			A|0.066;G|0.934	0.066	strong		0.572	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985	
PABPC1	26986	hgsc.bcm.edu	37	8	101719121	101719121	+	Missense_Mutation	SNP	G	G	A	rs79986761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101719121G>A	ENST00000318607.5	-	10	2569	c.1441C>T	c.(1441-1443)Cgt>Tgt	p.R481C	PABPC1_ENST00000519004.1_Missense_Mutation_p.R436C|PABPC1_ENST00000522387.1_Missense_Mutation_p.R449C|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_Intron	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	481					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TCACCAACACGCTGTGTTGAC	0.403																																					p.R481C		Atlas-SNP	.											.	PABPC1	76	.	0			c.C1441T						PASS	.						66.0	64.0	65.0					8																	101719121		2203	4300	6503	SO:0001583	missense	26986	exon10			CAACACGCTGTGT	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.1441C>T	8.37:g.101719121G>A	ENSP00000313007:p.Arg481Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	87	16	0.183908	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.492858	0.64074	.	.	ENSG00000070756	ENST00000318607;ENST00000519004;ENST00000522387;ENST00000522658	T;T;T;T	0.51071	1.56;1.49;2.54;0.72	5.63	5.63	0.86233	.	0.000000	0.64402	D	0.000003	T	0.55016	0.1894	M	0.76727	2.345	0.80722	D	1	P;P;B	0.45986	0.787;0.87;0.001	B;B;B	0.41860	0.205;0.368;0.001	T	0.61922	-0.6963	10	0.62326	D	0.03	.	20.0338	0.97549	0.0:0.0:1.0:0.0	.	449;481;481	E7ERJ7;B3KT93;P11940	.;.;PABP1_HUMAN	C	481;436;449;28	ENSP00000313007:R481C;ENSP00000429594:R436C;ENSP00000429395:R449C;ENSP00000428840:R28C	ENSP00000313007:R481C	R	-	1	0	PABPC1	101788297	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.991000	0.93514	2.816000	0.96949	0.650000	0.86243	CGT	G|0.871;A|0.129	0.129	strong		0.403	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
PARVG	64098	hgsc.bcm.edu	37	22	44594584	44594584	+	Silent	SNP	C	C	G	rs139152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44594584C>G	ENST00000444313.3	+	12	1279	c.795C>G	c.(793-795)ccC>ccG	p.P265P	PARVG_ENST00000422871.1_Silent_p.P265P|PARVG_ENST00000415224.1_Silent_p.P265P	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	265	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|cell-matrix adhesion (GO:0007160)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)	17		Ovarian(80;0.024)|all_neural(38;0.0299)				ACCTCACTCCCAACTCTCCTG	0.418													C|||	1022	0.204073	0.0545	0.2046	5008	,	,		15052	0.1954		0.3966	False		,,,				2504	0.2168				p.P265P		Atlas-SNP	.											.	PARVG	41	.	0			c.C795G						PASS	.	C	,,	455,3951	217.8+/-236.0	28,399,1776	189.0	177.0	181.0		795,795,795	3.9	1.0	22	dbSNP_78	181	3382,5218	500.6+/-375.3	639,2104,1557	no	coding-synonymous,coding-synonymous,coding-synonymous	PARVG	NM_001137605.1,NM_001137606.1,NM_022141.5	,,	667,2503,3333	GG,GC,CC		39.3256,10.3268,29.5018	,,	265/332,265/332,265/332	44594584	3837,9169	2203	4300	6503	SO:0001819	synonymous_variant	64098	exon12			CACTCCCAACTCT	AF237772	CCDS14057.1	22q13.31	2013-01-24			ENSG00000138964	ENSG00000138964		"""Parvins"""	14654	protein-coding gene	gene with protein product		608122				11171322	Standard	NM_022141		Approved		uc003bep.4	Q9HBI0	OTTHUMG00000150473	ENST00000444313.3:c.795C>G	22.37:g.44594584C>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	188	86	0.457447	NM_001137606	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Silent	SNP	ENST00000444313.3	37	CCDS14057.1																																																																																			C|0.712;G|0.288	0.288	strong		0.418	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141	
PECR	55825	hgsc.bcm.edu	37	2	216923679	216923679	+	Missense_Mutation	SNP	C	C	T	rs1429148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	150	0	0		WXS	Illumina HiSeq	Phase_I	152	64	0.421053	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	
RGMA	56963	hgsc.bcm.edu	37	15	93588309	93588309	+	Silent	SNP	C	C	G	rs62021480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:93588309C>G	ENST00000329082.7	-	4	1543	c.1272G>C	c.(1270-1272)gcG>gcC	p.A424A	RGMA_ENST00000542321.2_Silent_p.A408A|RGMA_ENST00000557420.1_3'UTR|RGMA_ENST00000538818.1_Silent_p.A315A|RGMA_ENST00000425933.2_Silent_p.A408A|RGMA_ENST00000557301.1_Silent_p.A432A|RGMA_ENST00000543599.1_Silent_p.A408A|RGMA_ENST00000556658.1_Silent_p.A315A	NM_020211.2	NP_064596	Q96B86	RGMA_HUMAN	repulsive guidance molecule family member a	424					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|neural tube closure (GO:0001843)|regulation of BMP signaling pathway (GO:0030510)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	9	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)			GCCCCGCAGCCGCCCTGCCTG	0.657													C|||	385	0.076877	0.1936	0.0259	5008	,	,		14593	0.0089		0.0666	False		,,,				2504	0.0358				p.A432A		Atlas-SNP	.											RGMA_ENST00000557301,NS,carcinoma,0,4	RGMA	49	4	0			c.G1296C						scavenged	.	C	,,,,,	582,3284		41,500,1392	19.0	21.0	20.0		1296,1224,1224,1224,1224,1272	-9.7	0.0	15	dbSNP_129	20	411,7851		5,401,3725	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RGMA	NM_001166283.1,NM_001166286.1,NM_001166287.1,NM_001166288.1,NM_001166289.1,NM_020211.2	,,,,,	46,901,5117	GG,GC,CC		4.9746,15.0543,8.1877	,,,,,	432/459,408/435,408/435,408/435,408/435,424/451	93588309	993,11135	1933	4131	6064	SO:0001819	synonymous_variant	56963	exon4			CGCAGCCGCCCTG	AL390083	CCDS45357.1, CCDS53973.1, CCDS53974.1	15q26.1	2013-11-06	2013-11-06			ENSG00000182175			30308	protein-coding gene	gene with protein product		607362	"""RGM domain family, member A"""			15975920	Standard	NM_020211		Approved	RGM, RGMa	uc010urc.2	Q96B86		ENST00000329082.7:c.1272G>C	15.37:g.93588309C>G		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_001166283	B2RTW1|B7Z5S8|F5GXQ7|F5GZU6|G3V518|Q0JV97|Q8NC80|Q9H0E6|Q9NPM3	Silent	SNP	ENST00000329082.7	37	CCDS45357.1																																																																																			C|0.928;G|0.072	0.072	strong		0.657	RGMA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415091.1	NM_020211	
ACOT11	26027	hgsc.bcm.edu	37	1	55060362	55060362	+	Missense_Mutation	SNP	G	G	A	rs1702003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55060362G>A	ENST00000371316.3	+	6	687	c.605G>A	c.(604-606)gGc>gAc	p.G202D	ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_Missense_Mutation_p.G202D	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	202			G -> D (in dbSNP:rs1702003). {ECO:0000269|Ref.4}.		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						GCCATTCAGGGCGGTGAGCAG	0.667													A|||	1279	0.255391	0.5371	0.1239	5008	,	,		18319	0.1825		0.0417	False		,,,				2504	0.2628				p.G202D	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-SNP	.											ACOT11_ENST00000371316,colon,carcinoma,+1,2	ACOT11	105	2	0			c.G605A						PASS	.	A	ASP/GLY,ASP/GLY	1976,2430	604.7+/-390.4	466,1044,693	46.0	44.0	45.0		605,605	3.7	0.9	1	dbSNP_89	45	255,8345	795.5+/-407.5	4,247,4049	yes	missense,missense	ACOT11	NM_015547.3,NM_147161.3	94,94	470,1291,4742	AA,AG,GG		2.9651,44.8479,17.1536	benign,benign	202/608,202/595	55060362	2231,10775	2203	4300	6503	SO:0001583	missense	26027	exon6			TTCAGGGCGGTGA	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.605G>A	1.37:g.55060362G>A	ENSP00000360366:p.Gly202Asp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Missense_Mutation	SNP	ENST00000371316.3	37	CCDS592.1	407	0.18635531135531136	235	0.47764227642276424	41	0.1132596685082873	103	0.18006993006993008	28	0.036939313984168866	A	1.445	-0.566615	0.03910	0.448479	0.029651	ENSG00000162390	ENST00000343744;ENST00000371316	T;T	0.09445	3.01;2.98	4.84	3.7	0.42460	.	0.607478	0.17188	N	0.183612	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42632	-0.9440	9	0.06494	T	0.89	-16.4542	6.0048	0.19541	0.6647:0.1772:0.1581:0.0	rs1702003;rs56926025;rs1702003	202;202	Q8WXI4;Q8WXI4-2	ACO11_HUMAN;.	D	202	ENSP00000340260:G202D;ENSP00000360366:G202D	ENSP00000340260:G202D	G	+	2	0	ACOT11	54832950	0.936000	0.31750	0.917000	0.36280	0.843000	0.47879	1.962000	0.40442	0.297000	0.22615	-0.490000	0.04691	GGC	G|0.813;A|0.187	0.187	strong		0.667	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547	
MUC4	4585	hgsc.bcm.edu	37	3	195505828	195505828	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195505828G>T	ENST00000463781.3	-	2	13082	c.12623C>A	c.(12622-12624)cCt>cAt	p.P4208H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4208H	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)		GACAGGAAGAGGGGTGGCGTG	0.592																																					p.P4208H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	0			c.C12623A						PASS	.						17.0	16.0	16.0					3																	195505828		688	1570	2258	SO:0001583	missense	4585	exon2			GGAAGAGGGGTGG	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.12623C>A	3.37:g.195505828G>T	ENSP00000417498:p.Pro4208His	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	292	24	0.0821918	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	4.993	0.184423	0.09495	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36340	1.46;1.26	.	.	.	.	.	.	.	.	T	0.33235	0.0856	N	0.19112	0.55	0.23101	N	0.998295	D	0.56521	0.976	P	0.62298	0.9	T	0.14392	-1.0474	7	.	.	.	.	3.6132	0.08067	2.0E-4:0.4969:0.5026:2.0E-4	.	4080	E7ESK3	.	H	4208	ENSP00000417498:P4208H;ENSP00000420243:P4208H	.	P	-	2	0	MUC4	196990607	.	.	0.019000	0.16419	0.029000	0.11900	.	.	0.088000	0.17205	0.089000	0.15464	CCT	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DIS3	22894	hgsc.bcm.edu	37	13	73349359	73349359	+	Missense_Mutation	SNP	G	G	C	rs7332388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	287	1	0.00348432		WXS	Illumina HiSeq	Phase_I	243	241	0.99177	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	
COTL1	23406	hgsc.bcm.edu	37	16	84651452	84651452	+	Silent	SNP	G	G	C	rs144159131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84651452G>C	ENST00000262428.4	-	1	231	c.69C>G	c.(67-69)gcC>gcG	p.A23A	COTL1_ENST00000564057.1_5'UTR	NM_021149.2	NP_066972.1	Q14019	COTL1_HUMAN	coactosin-like F-actin binding protein 1	23	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				defense response to fungus (GO:0050832)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)			endometrium(1)|large_intestine(1)|liver(1)|lung(2)|skin(1)	6						ACCAGATGACGGCCGAGCCGT	0.706													g|||	3	0.000599042	0.0015	0.0	5008	,	,		7761	0.0		0.0	False		,,,				2504	0.001				p.A23A		Atlas-SNP	.											.	COTL1	17	.	0			c.C69G						PASS	.			4,4354		0,4,2175	19.0	15.0	16.0		69	-5.9	1.0	16	dbSNP_134	16	0,8534		0,0,4267	no	coding-synonymous	COTL1	NM_021149.2		0,4,6442	CC,CG,GG		0.0,0.0918,0.031		23/143	84651452	4,12888	2179	4267	6446	SO:0001819	synonymous_variant	23406	exon1			GATGACGGCCGAG	L54057	CCDS10947.1	16q24.1	2014-03-05	2014-03-05	2002-08-01	ENSG00000103187	ENSG00000103187			18304	protein-coding gene	gene with protein product		606748	"""coactosin-like 1 (Dictyostelium)"""			10051563, 9326934, 16924104	Standard	NM_021149		Approved	CLP	uc002fid.3	Q14019	OTTHUMG00000137634	ENST00000262428.4:c.69C>G	16.37:g.84651452G>C		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_021149	B2RDU3|D3DUL9|Q86XM5	Silent	SNP	ENST00000262428.4	37	CCDS10947.1																																																																																			G|0.999;C|0.001	0.001	strong		0.706	COTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269075.1	NM_021149	
BCL6B	255877	hgsc.bcm.edu	37	17	6930927	6930927	+	Missense_Mutation	SNP	G	G	A	rs201522060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:6930927G>A	ENST00000293805.5	+	9	1521	c.1429G>A	c.(1429-1431)Ggg>Agg	p.G477R		NM_181844.3	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B	477					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			skin(1)	1						CCACATTCTCGGGGGGCCCTA	0.627													G|||	7	0.00139776	0.0045	0.0014	5008	,	,		17141	0.0		0.0	False		,,,				2504	0.0				p.G477R		Atlas-SNP	.											.	BCL6B	85	.	0			c.G1429A						PASS	.	G	ARG/GLY	15,3949		0,15,1967	49.0	54.0	53.0		1429	5.5	1.0	17		53	1,8327		0,1,4163	yes	missense	BCL6B	NM_181844.3	125	0,16,6130	AA,AG,GG		0.012,0.3784,0.1302	probably-damaging	477/480	6930927	16,12276	1982	4164	6146	SO:0001583	missense	255877	exon9			ATTCTCGGGGGGC	AI672318	CCDS42248.1	17p13.1	2014-06-10	2010-04-14		ENSG00000161940	ENSG00000161940		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	1002	protein-coding gene	gene with protein product		608992	"""zinc finger protein 62"", ""B-cell CLL/lymphoma 6, member B (zinc finger protein)"""	ZNF62		9632807	Standard	NM_181844		Approved	ZBTB28, BAZF	uc010clt.1	Q8N143	OTTHUMG00000177882	ENST00000293805.5:c.1429G>A	17.37:g.6930927G>A	ENSP00000293805:p.Gly477Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_181844	Q6PCB4	Missense_Mutation	SNP	ENST00000293805.5	37	CCDS42248.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.560429	0.45590	0.003784	1.2E-4	ENSG00000161940	ENST00000293805	T	0.07114	3.22	5.47	5.47	0.80525	.	0.340325	0.32161	N	0.006486	T	0.08133	0.0203	L	0.29908	0.895	0.38463	D	0.94726	B	0.22541	0.071	B	0.14578	0.011	T	0.15636	-1.0430	10	0.51188	T	0.08	.	14.8178	0.70048	0.0:0.0:1.0:0.0	.	477	Q8N143	BCL6B_HUMAN	R	477	ENSP00000293805:G477R	ENSP00000293805:G477R	G	+	1	0	BCL6B	6871651	0.978000	0.34361	0.999000	0.59377	0.849000	0.48306	4.025000	0.57225	2.584000	0.87258	0.462000	0.41574	GGG	.	.	weak		0.627	BCL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439455.2	NM_181844	
PACS2	23241	hgsc.bcm.edu	37	14	105843179	105843179	+	Silent	SNP	C	C	G	rs4074004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105843179C>G	ENST00000325438.8	+	9	1380	c.876C>G	c.(874-876)acC>acG	p.T292T	PACS2_ENST00000458164.2_Silent_p.T292T|PACS2_ENST00000447393.1_Silent_p.T292T|PACS2_ENST00000430725.2_Silent_p.T217T|PACS2_ENST00000547217.1_Silent_p.T262T			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	292					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)		TGTATGACACCCTGGACATGG	0.677													G|||	666	0.132987	0.4682	0.0259	5008	,	,		17184	0.0179		0.0	False		,,,				2504	0.0112				p.T292T		Atlas-SNP	.											.	PACS2	75	.	0			c.C876G						PASS	.	G	,	1757,2647	642.0+/-397.6	367,1023,812	82.0	72.0	76.0		876,876	-9.2	0.7	14	dbSNP_108	76	13,8587	817.4+/-406.9	0,13,4287	no	coding-synonymous,coding-synonymous	PACS2	NM_001100913.2,NM_015197.3	,	367,1036,5099	GG,GC,CC		0.1512,39.8955,13.6112	,	292/894,292/890	105843179	1770,11234	2202	4300	6502	SO:0001819	synonymous_variant	23241	exon9			TGACACCCTGGAC	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.876C>G	14.37:g.105843179C>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Silent	SNP	ENST00000325438.8	37	CCDS32168.1																																																																																			C|0.880;G|0.120	0.120	strong		0.677	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355	
C9orf172	389813	hgsc.bcm.edu	37	9	139740900	139740900	+	Silent	SNP	C	C	T	rs147735504	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139740900C>T	ENST00000436881.1	+	1	2034	c.2034C>T	c.(2032-2034)aaC>aaT	p.N678N	PHPT1_ENST00000545326.1_5'Flank|PHPT1_ENST00000247665.10_5'Flank|PHPT1_ENST00000371661.1_5'Flank	NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	678										endometrium(2)|large_intestine(1)|lung(6)	9						CCATGTTCAACGCCTGCCTCT	0.682													c|||	31	0.0061901	0.0227	0.0014	5008	,	,		10471	0.0		0.0	False		,,,				2504	0.0				p.N678N		Atlas-SNP	.											.	C9orf172	23	.	0			c.C2034T						PASS	.	C		90,4048		0,90,1979	23.0	28.0	27.0		2034	3.2	1.0	9	dbSNP_134	27	1,8323		0,1,4161	no	coding-synonymous	C9orf172	NM_001080482.2		0,91,6140	TT,TC,CC		0.012,2.175,0.7302		678/977	139740900	91,12371	2069	4162	6231	SO:0001819	synonymous_variant	389813	exon1			GTTCAACGCCTGC		CCDS48059.1	9q34.3	2012-04-03			ENSG00000232434	ENSG00000232434			37284	protein-coding gene	gene with protein product							Standard	NM_001080482		Approved		uc011meh.2	C9J069		ENST00000436881.1:c.2034C>T	9.37:g.139740900C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_001080482		Silent	SNP	ENST00000436881.1	37	CCDS48059.1																																																																																			C|0.994;T|0.006	0.006	strong		0.682	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482	
WDSUB1	151525	hgsc.bcm.edu	37	2	160104988	160104988	+	Missense_Mutation	SNP	T	T	C	rs74475652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160104988T>C	ENST00000409990.3	-	10	1424	c.1168A>G	c.(1168-1170)Att>Gtt	p.I390V	WDSUB1_ENST00000359774.4_Missense_Mutation_p.I390V|WDSUB1_ENST00000392796.3_Missense_Mutation_p.I390V|WDSUB1_ENST00000358147.4_Missense_Mutation_p.I298V|WDSUB1_ENST00000409124.1_Intron	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	390	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.						ubiquitin-protein transferase activity (GO:0004842)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|stomach(3)	16						AGCTCTTCAATTTTCCTCAGC	0.388													T|||	219	0.04373	0.1604	0.0086	5008	,	,		19089	0.0		0.001	False		,,,				2504	0.0				p.I390V		Atlas-SNP	.											.	WDSUB1	39	.	0			c.A1168G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	583,3823	258.3+/-262.4	45,493,1665	100.0	101.0	101.0		1168,1168,1168	3.5	1.0	2	dbSNP_131	101	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	WDSUB1	NM_001128212.1,NM_001128213.1,NM_152528.2	29,29,29	45,495,5963	CC,CT,TT		0.0233,13.232,4.4979	benign,benign,benign	390/477,390/477,390/477	160104988	585,12421	2203	4300	6503	SO:0001583	missense	151525	exon10			CTTCAATTTTCCT	AK093494	CCDS2208.1	2q24.2	2013-01-28	2006-02-17	2005-03-25	ENSG00000196151	ENSG00000196151		"""WD repeat domain containing"", ""Sterile alpha motif (SAM) domain containing"", ""U-box domain containing"""	26697	protein-coding gene	gene with protein product			"""WD repeat and SAM domain containing 1"", ""WD repeat, SAM and U-box domain containing 1"""	WDSAM1		12477932	Standard	NM_152528		Approved	UBOX6, FLJ36175	uc002ual.4	Q8N9V3	OTTHUMG00000132028	ENST00000409990.3:c.1168A>G	2.37:g.160104988T>C	ENSP00000387078:p.Ile390Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_152528	Q53TI9|Q8N6N8	Missense_Mutation	SNP	ENST00000409990.3	37	CCDS2208.1	64	0.029304029304029304	62	0.12601626016260162	2	0.0055248618784530384	0	0.0	0	0.0	T	11.96	1.793785	0.31685	0.13232	2.33E-4	ENSG00000196151	ENST00000359774;ENST00000358147;ENST00000392796;ENST00000409990	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.97	3.55	0.40652	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.114020	0.64402	N	0.000011	T	0.00552	0.0018	M	0.64997	1.995	0.09310	P	1.0	B;B	0.24258	0.009;0.1	B;B	0.28465	0.007;0.09	T	0.08785	-1.0705	9	0.38643	T	0.18	.	10.5342	0.44994	0.0:0.132:0.0:0.868	.	298;390	Q8N9V3-2;Q8N9V3	.;WSDU1_HUMAN	V	390;298;390;390	ENSP00000352820:I390V;ENSP00000350866:I298V;ENSP00000376545:I390V;ENSP00000387078:I390V	ENSP00000350866:I298V	I	-	1	0	WDSUB1	159813234	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	3.080000	0.50112	0.486000	0.27676	0.528000	0.53228	ATT	T|0.958;C|0.042	0.042	strong		0.388	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549589	32549589	+	Missense_Mutation	SNP	A	A	C	rs2308760		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32549589A>C	ENST00000360004.5	-	3	502	c.397T>G	c.(397-399)Tca>Gca	p.S133A		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	133	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						TGGGTCTTTGAAGGATATACA	0.512										Multiple Myeloma(14;0.17)																											p.S133A		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.T397G						PASS	.						55.0	69.0	64.0					6																	32549589		1511	2709	4220	SO:0001583	missense	3123	exon3			TCTTTGAAGGATA	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.397T>G	6.37:g.32549589A>C	ENSP00000353099:p.Ser133Ala	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	172	46	0.267442	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.838831	0.00068	.	.	ENSG00000196126	ENST00000360004	T	0.02890	4.12	3.87	-6.35	0.01975	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.987485	0.08278	N	0.970401	T	0.00328	0.0010	N	0.11892	0.195	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47861	-0.9084	10	0.02654	T	1	.	4.1985	0.10455	0.356:0.3291:0.0:0.3149	rs17433947	133	P01911	2B1F_HUMAN	A	133	ENSP00000353099:S133A	ENSP00000353099:S133A	S	-	1	0	HLA-DRB1	32657567	0.000000	0.05858	0.080000	0.20451	0.022000	0.10575	-2.577000	0.00909	-1.679000	0.01452	-2.825000	0.00108	TCA	.	.	weak		0.512	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
BMP3	651	hgsc.bcm.edu	37	4	81952658	81952658	+	Missense_Mutation	SNP	C	C	G	rs61729824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:81952658C>G	ENST00000282701.2	+	1	540	c.220C>G	c.(220-222)Cgg>Ggg	p.R74G		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	74					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						CCAGGCGGCCCGGACACCGGG	0.687													c|||	28	0.00559105	0.0197	0.0029	5008	,	,		13952	0.0		0.0	False		,,,				2504	0.0				p.R74G		Atlas-SNP	.											.	BMP3	59	.	0			c.C220G						PASS	.						18.0	21.0	20.0					4																	81952658		2199	4298	6497	SO:0001583	missense	651	exon1			GCGGCCCGGACAC	M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"""Bone morphogenetic proteins"""	1070	protein-coding gene	gene with protein product	"""osteogenin"""	112263	"""bone morphogenetic protein 3 (osteogenic)"""				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.220C>G	4.37:g.81952658C>G	ENSP00000282701:p.Arg74Gly	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	c	7.074	0.568893	0.13560	.	.	ENSG00000152785	ENST00000282701	T	0.64803	-0.12	3.44	2.6	0.31112	Transforming growth factor-beta, N-terminal (1);	1.192490	0.06406	N	0.719754	T	0.41880	0.1178	N	0.08118	0	0.09310	N	1	B	0.25007	0.116	B	0.28849	0.095	T	0.35649	-0.9780	10	0.22109	T	0.4	.	7.0017	0.24813	0.0:0.875:0.0:0.125	.	74	P12645	BMP3_HUMAN	G	74	ENSP00000282701:R74G	ENSP00000282701:R74G	R	+	1	2	BMP3	82171682	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.383000	0.07398	1.034000	0.39945	-0.215000	0.12644	CGG	C|0.988;T|0.012	.	alt		0.687	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1		
TMEM127	55654	hgsc.bcm.edu	37	2	96919642	96919642	+	Silent	SNP	C	C	T	rs3852673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:96919642C>T	ENST00000258439.3	-	4	877	c.621G>A	c.(619-621)gcG>gcA	p.A207A	TMEM127_ENST00000432959.1_Silent_p.A207A|TMEM127_ENST00000435268.1_Silent_p.A123A	NM_001193304.2|NM_017849.3	NP_001180233.1|NP_060319.1	O75204	TM127_HUMAN	transmembrane protein 127	207					negative regulation of cell proliferation (GO:0008285)|negative regulation of TOR signaling (GO:0032007)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A207A(1)		endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	5						GCAGCTCCAGCGCCTGCTCCT	0.607													C|||	698	0.139377	0.0469	0.1398	5008	,	,		18524	0.0873		0.1779	False		,,,				2504	0.2781				p.A207A		Atlas-SNP	.											TMEM127,NS,carcinoma,-1,2	TMEM127	13	2	1	Substitution - coding silent(1)	stomach(1)	c.G621A						PASS	.	C	,	304,4102	163.6+/-195.4	12,280,1911	72.0	69.0	70.0		621,621	-11.6	0.4	2	dbSNP_108	70	1500,7100	285.0+/-296.9	136,1228,2936	no	coding-synonymous,coding-synonymous	TMEM127	NM_001193304.2,NM_017849.3	,	148,1508,4847	TT,TC,CC		17.4419,6.8997,13.8705	,	207/239,207/239	96919642	1804,11202	2203	4300	6503	SO:0001819	synonymous_variant	55654	exon4			CTCCAGCGCCTGC	AK000514	CCDS2018.1	2q11.2	2014-09-17			ENSG00000135956	ENSG00000135956			26038	protein-coding gene	gene with protein product		613403				10493829	Standard	NM_017849		Approved	FLJ20507, FLJ22257	uc002svr.3	O75204	OTTHUMG00000130454	ENST00000258439.3:c.621G>A	2.37:g.96919642C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	166	86	0.518072	NM_001193304	D3DXH0	Silent	SNP	ENST00000258439.3	37	CCDS2018.1																																																																																			C|0.874;T|0.126	0.126	strong		0.607	TMEM127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252845.3	NM_017849	
SCAF11	9169	hgsc.bcm.edu	37	12	46321417	46321417	+	Silent	SNP	G	G	A	rs11574971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:46321417G>A	ENST00000369367.3	-	11	2300	c.2067C>T	c.(2065-2067)acC>acT	p.T689T	SCAF11_ENST00000549162.1_Silent_p.T497T|SCAF11_ENST00000465950.1_Silent_p.T374T|SCAF11_ENST00000419565.2_Silent_p.T689T|SCAF11_ENST00000550629.1_5'Flank	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	689					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						TAGGATGTTCGGTCAGCGATT	0.318													G|||	549	0.109625	0.3775	0.0259	5008	,	,		13728	0.004		0.002	False		,,,				2504	0.0266				p.T689T		Atlas-SNP	.											.	SCAF11	145	.	0			c.C2067T						PASS	.	G		1384,3022	457.5+/-351.6	235,914,1054	160.0	162.0	161.0		2067	1.9	0.0	12	dbSNP_120	161	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	SCAF11	NM_004719.2		235,928,5340	AA,AG,GG		0.1628,31.4117,10.7489		689/1464	46321417	1398,11608	2203	4300	6503	SO:0001819	synonymous_variant	9169	exon11			ATGTTCGGTCAGC	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.2067C>T	12.37:g.46321417G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_004719	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	37	CCDS8748.2																																																																																			G|0.894;A|0.106	0.106	strong		0.318	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	
ALDH18A1	5832	hgsc.bcm.edu	37	10	97371146	97371146	+	Silent	SNP	G	G	A	rs1804934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:97371146G>A	ENST00000371224.2	-	16	2114	c.1977C>T	c.(1975-1977)tcC>tcT	p.S659S	ALDH18A1_ENST00000371221.3_Silent_p.S657S	NM_002860.3	NP_002851.2	P54886	P5CS_HUMAN	aldehyde dehydrogenase 18 family, member A1	659	Gamma-glutamyl phosphate reductase.				cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|glutamate metabolic process (GO:0006536)|L-proline biosynthetic process (GO:0055129)|ornithine biosynthetic process (GO:0006592)|proline biosynthetic process (GO:0006561)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glutamate 5-kinase activity (GO:0004349)|glutamate-5-semialdehyde dehydrogenase activity (GO:0004350)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(9)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)		ACTTCACTTCGGAGGGGCTGA	0.468													G|||	125	0.0249601	0.0325	0.0274	5008	,	,		22175	0.0139		0.0318	False		,,,				2504	0.0174				p.S659S		Atlas-SNP	.											.	ALDH18A1	63	.	0			c.C1977T						PASS	.	G	,	180,4226	115.9+/-153.8	3,174,2026	216.0	217.0	217.0		1971,1977	-11.2	0.2	10	dbSNP_89	217	215,8385	90.9+/-153.0	4,207,4089	no	coding-synonymous,coding-synonymous	ALDH18A1	NM_001017423.1,NM_002860.3	,	7,381,6115	AA,AG,GG		2.5,4.0853,3.0371	,	657/794,659/796	97371146	395,12611	2203	4300	6503	SO:0001819	synonymous_variant	5832	exon16			CACTTCGGAGGGG	X94453	CCDS7443.1, CCDS31257.1	10q24.3-q24.6	2004-08-12	2004-08-12	2004-08-12	ENSG00000059573	ENSG00000059573		"""Aldehyde dehydrogenases"""	9722	protein-coding gene	gene with protein product		138250	"""pyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase)"""	GSAS, PYCS		8921385	Standard	XM_006717933		Approved	P5CS	uc001kkz.3	P54886	OTTHUMG00000018815	ENST00000371224.2:c.1977C>T	10.37:g.97371146G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	216	98	0.453704	NM_002860	B2R5Q4|B7Z350|B7Z5X8|B7ZLP1|D3DR44|O95952|Q3KQU2|Q5T566|Q5T567|Q9UM72	Silent	SNP	ENST00000371224.2	37	CCDS7443.1																																																																																			G|0.971;A|0.029	0.029	strong		0.468	ALDH18A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049552.1	NM_002860	
PLXNB2	23654	hgsc.bcm.edu	37	22	50720430	50720430	+	Silent	SNP	G	G	C	rs56110807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50720430G>C	ENST00000449103.1	-	20	3338	c.3198C>G	c.(3196-3198)gcC>gcG	p.A1066A	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Silent_p.A1066A			O15031	PLXB2_HUMAN	plexin B2	1066	IPT/TIG 3.				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)		TGAGGTTGTAGGCCTCTGGCT	0.612													G|||	436	0.0870607	0.3169	0.0245	5008	,	,		17944	0.0		0.0	False		,,,				2504	0.0				p.A1066A		Atlas-SNP	.											.	PLXNB2	172	.	0			c.C3198G						PASS	.	G		954,3276		106,742,1267	54.0	61.0	59.0		3198	2.5	1.0	22	dbSNP_129	59	2,8428		0,2,4213	no	coding-synonymous	PLXNB2	NM_012401.3		106,744,5480	CC,CG,GG		0.0237,22.5532,7.5513		1066/1839	50720430	956,11704	2115	4215	6330	SO:0001819	synonymous_variant	23654	exon20			GTTGTAGGCCTCT		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.3198C>G	22.37:g.50720430G>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	23	0.560976	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1	154	0.07051282051282051	144	0.2926829268292683	10	0.027624309392265192	0	0.0	0	0.0	G	6.393	0.440700	0.12104	0.225532	2.37E-4	ENSG00000196576	ENST00000427829	.	.	.	4.63	2.46	0.29980	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.20538	-1.0272	3	.	.	.	.	10.4218	0.44354	0.1674:0.0:0.8326:0.0	rs56110807	.	.	.	R	84	.	.	P	-	2	0	PLXNB2	49062557	1.000000	0.71417	1.000000	0.80357	0.432000	0.31715	2.715000	0.47210	1.146000	0.42352	0.313000	0.20887	CCT	G|0.953;C|0.047	0.047	strong		0.612	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
TNFSF12	8742	hgsc.bcm.edu	37	17	7460514	7460514	+	Silent	SNP	G	G	A	rs143039184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7460514G>A	ENST00000293825.6	+	7	860	c.597G>A	c.(595-597)gcG>gcA	p.A199A	TNFSF13_ENST00000349228.4_5'Flank|TNFSF12_ENST00000462811.1_3'UTR|TNFSF13_ENST00000396545.4_5'Flank|TNFSF13_ENST00000396542.1_5'Flank|TNFSF12_ENST00000557233.1_Intron|TNFSF13_ENST00000380535.4_5'Flank|TNFSF13_ENST00000483039.1_5'Flank|TNFSF13_ENST00000338784.4_5'Flank|TNFSF12-TNFSF13_ENST00000293826.4_Intron	NM_003809.2	NP_003800.1	O43508	TNF12_HUMAN	tumor necrosis factor (ligand) superfamily, member 12	199					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|endothelial cell migration (GO:0043542)|immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|prostate(2)	11		Prostate(122;0.157)				CAGCCACTGCGGCGAGTTCCC	0.667													G|||	7	0.00139776	0.003	0.0043	5008	,	,		13746	0.0		0.0	False		,,,				2504	0.0				p.A199A		Atlas-SNP	.											.	TNFSF12	20	.	0			c.G597A						PASS	.	G	,	14,4392	21.2+/-45.6	0,14,2189	83.0	65.0	71.0		597,	-7.7	0.0	17	dbSNP_134	71	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,intron	TNFSF12,TNFSF12-TNFSF13	NM_003809.2,NM_172089.3	,	0,18,6485	AA,AG,GG		0.0465,0.3177,0.1384	,	199/250,	7460514	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	8742	exon7			CACTGCGGCGAGT	AF030099	CCDS11109.1	17p13.1	2008-02-01			ENSG00000239697	ENSG00000239697		"""Tumor necrosis factor (ligand) superfamily"""	11927	protein-coding gene	gene with protein product		602695				9405449, 9560343	Standard	NM_003809		Approved	TWEAK, DR3LG, APO3L		O43508	OTTHUMG00000108148	ENST00000293825.6:c.597G>A	17.37:g.7460514G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_003809	Q8IZK7|Q8WUZ7	Silent	SNP	ENST00000293825.6	37	CCDS11109.1																																																																																			G|0.999;A|0.001	0.001	strong		0.667	TNFSF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226951.2	NM_003809	
TG	7038	hgsc.bcm.edu	37	8	133899438	133899438	+	Silent	SNP	C	C	T	rs61742713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133899438C>T	ENST00000220616.4	+	9	1861	c.1821C>T	c.(1819-1821)acC>acT	p.T607T	TG_ENST00000377869.1_Silent_p.T607T	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	607	Thyroglobulin type-1 5. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GCTCCCAGACCTGTGAGCAGA	0.473													C|||	108	0.0215655	0.0802	0.0029	5008	,	,		21407	0.0		0.0	False		,,,				2504	0.0				p.T607T		Atlas-SNP	.											.	TG	416	.	0			c.C1821T						PASS	.	C		290,4116	160.0+/-192.4	12,266,1925	148.0	132.0	137.0		1821	5.0	0.7	8	dbSNP_129	137	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TG	NM_003235.4		12,268,6223	TT,TC,CC		0.0233,6.5819,2.2451		607/2769	133899438	292,12714	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon9			CCAGACCTGTGAG	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.1821C>T	8.37:g.133899438C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	149	77	0.516779	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																			C|0.974;T|0.026	0.026	strong		0.473	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
KLHL4	56062	hgsc.bcm.edu	37	X	86877348	86877348	+	Silent	SNP	G	G	T	rs2273050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:86877348G>T	ENST00000373119.4	+	5	1207	c.1062G>T	c.(1060-1062)ggG>ggT	p.G354G	KLHL4_ENST00000373114.4_Silent_p.G354G	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	354						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						AGTGGGTGGGGCATGATGTGC	0.433													G|||	717	0.189934	0.1513	0.0504	3775	,	,		12144	0.1448		0.1879	False		,,,				2504	0.1503				p.G354G		Atlas-SNP	.											.	KLHL4	263	.	0			c.G1062T						PASS	.	G	,	714,3121		53,505,103,1074,468	159.0	131.0	140.0		1062,1062	-6.9	0.3	X	dbSNP_100	140	1319,5409		93,760,373,1575,1499	no	coding-synonymous,coding-synonymous	KLHL4	NM_019117.4,NM_057162.2	,	146,1265,476,2649,1967	TT,TG,T,GG,G		19.6046,18.618,19.2464	,	354/719,354/721	86877348	2033,8530	2203	4300	6503	SO:0001819	synonymous_variant	56062	exon5			GGTGGGGCATGAT	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"""Kelch-like"", ""BTB/POZ domain containing"""	6355	protein-coding gene	gene with protein product		300348	"""kelch (Drosophila)-like 4"", ""kelch-like 4 (Drosophila)"""			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1062G>T	X.37:g.86877348G>T		Somatic	373	1	0.00268097		WXS	Illumina HiSeq	Phase_I	348	162	0.465517	NM_019117	B2RTW2|Q9Y3J5	Silent	SNP	ENST00000373119.4	37	CCDS14457.1																																																																																			G|0.807;T|0.193	0.193	strong		0.433	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1		
PITRM1	10531	hgsc.bcm.edu	37	10	3180298	3180298	+	Silent	SNP	C	C	T	rs10175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3180298C>T	ENST00000224949.4	-	27	3073	c.3039G>A	c.(3037-3039)aaG>aaA	p.K1013K	PITRM1_ENST00000380994.1_Silent_p.K571K|PITRM1_ENST00000451104.2_Silent_p.K915K|PITRM1_ENST00000464395.1_5'UTR|PITRM1_ENST00000380989.2_Silent_p.K1014K			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	1013					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						CGTGTGTGCTCTTCCCAGTGC	0.607													C|||	1180	0.235623	0.2027	0.3473	5008	,	,		17500	0.1617		0.3121	False		,,,				2504	0.1984				p.K1014K		Atlas-SNP	.											.	PITRM1	109	.	0			c.G3042A						PASS	.	C	,,	989,3275		113,763,1256	46.0	51.0	49.0		3042,2745,3039	1.8	0.2	10	dbSNP_52	49	2305,6179		314,1677,2251	no	coding-synonymous,coding-synonymous,coding-synonymous	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	,,	427,2440,3507	TT,TC,CC		27.1688,23.1942,25.8393	,,	1014/1039,915/940,1013/1038	3180298	3294,9454	2132	4242	6374	SO:0001819	synonymous_variant	10531	exon27			TGTGCTCTTCCCA	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.3039G>A	10.37:g.3180298C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	111	46	0.414414	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent	SNP	ENST00000224949.4	37	CCDS59208.1																																																																																			C|0.756;T|0.244	0.244	strong		0.607	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
SEL1L3	23231	hgsc.bcm.edu	37	4	25806279	25806279	+	Missense_Mutation	SNP	T	T	C	rs16877591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:25806279T>C	ENST00000399878.3	-	10	1782	c.1660A>G	c.(1660-1662)Att>Gtt	p.I554V	SEL1L3_ENST00000502949.1_Missense_Mutation_p.I401V|SEL1L3_ENST00000264868.5_Missense_Mutation_p.I519V	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	554			I -> V (in dbSNP:rs16877591).			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						ATAGAGCTAATTTGGTGAAGA	0.423													T|||	315	0.0628994	0.2307	0.013	5008	,	,		19704	0.001		0.0	False		,,,				2504	0.0				p.I554V		Atlas-SNP	.											.	SEL1L3	62	.	0			c.A1660G						PASS	.	T	VAL/ILE	657,3117		65,527,1295	105.0	101.0	102.0		1660	4.8	1.0	4	dbSNP_123	102	5,8259		0,5,4127	yes	missense	SEL1L3	NM_015187.3	29	65,532,5422	CC,CT,TT		0.0605,17.4086,5.4993	benign	554/1133	25806279	662,11376	1887	4132	6019	SO:0001583	missense	23231	exon10			AGCTAATTTGGTG	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.1660A>G	4.37:g.25806279T>C	ENSP00000382767:p.Ile554Val	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	237	120	0.506329	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	103	0.04716117216117216	98	0.1991869918699187	5	0.013812154696132596	0	0.0	0	0.0	T	2.128	-0.399879	0.04865	0.174086	6.05E-4	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.15139	2.64;2.67;2.45	6.02	4.84	0.62591	Tetratricopeptide-like helical (1);	0.609972	0.19314	N	0.117326	T	0.00012	0.0000	L	0.46157	1.445	0.35888	P	0.17056099999999996	B	0.09022	0.002	B	0.04013	0.001	T	0.35251	-0.9796	9	0.22706	T	0.39	-16.5487	1.9195	0.03304	0.1312:0.1514:0.1366:0.5808	rs16877591;rs56773321;rs16877591	554	Q68CR1	SE1L3_HUMAN	V	554;519;401	ENSP00000382767:I554V;ENSP00000264868:I519V;ENSP00000425438:I401V	ENSP00000264868:I519V	I	-	1	0	SEL1L3	25415377	0.939000	0.31865	1.000000	0.80357	0.338000	0.28826	0.314000	0.19432	1.093000	0.41377	0.533000	0.62120	ATT	T|0.933;C|0.067	0.067	strong		0.423	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
C5orf42	65250	hgsc.bcm.edu	37	5	37158363	37158363	+	Missense_Mutation	SNP	G	G	A	rs16903518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37158363G>A	ENST00000508244.1	-	38	7868	c.7775C>T	c.(7774-7776)cCt>cTt	p.P2592L	C5orf42_ENST00000274258.7_Missense_Mutation_p.P1472L|C5orf42_ENST00000425232.2_Missense_Mutation_p.P2592L			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2592			P -> L (in dbSNP:rs16903518).			integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GGGTGACCAAGGTTTCTCTGA	0.368													G|||	122	0.024361	0.09	0.0043	5008	,	,		17612	0.0		0.0	False		,,,				2504	0.0				p.P2592L		Atlas-SNP	.											.	C5orf42	422	.	0			c.C7775T						PASS	.	G	LEU/PRO	340,4066	177.3+/-206.3	13,314,1876	129.0	125.0	127.0		7775	3.0	0.0	5	dbSNP_123	127	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C5orf42	NM_023073.3	98	13,316,6174	AA,AG,GG		0.0233,7.7167,2.6296	benign	2592/3198	37158363	342,12664	2203	4300	6503	SO:0001583	missense	65250	exon39			GACCAAGGTTTCT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.7775C>T	5.37:g.37158363G>A	ENSP00000421690:p.Pro2592Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	183	92	0.502732	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	45	0.020604395604395604	43	0.08739837398373984	2	0.0055248618784530384	0	0.0	0	0.0	G	7.667	0.686250	0.14973	0.077167	2.33E-4	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.70631	-0.5;-0.5;1.32;1.35	4.88	3.02	0.34903	.	0.626374	0.14293	N	0.328786	T	0.05410	0.0143	L	0.46157	1.445	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.12156	0.004;0.007	T	0.19257	-1.0311	10	0.62326	D	0.03	.	8.7051	0.34349	0.2574:0.0:0.7426:0.0	rs16903518;rs52830390;rs16903518	2592;1472	E9PH94;Q9H799	.;CE042_HUMAN	L	2592;2592;1472;1640;1472	ENSP00000421690:P2592L;ENSP00000389014:P2592L;ENSP00000274258:P1472L;ENSP00000424223:P1640L	ENSP00000274258:P1472L	P	-	2	0	C5orf42	37194120	0.609000	0.26975	0.007000	0.13788	0.048000	0.14542	1.796000	0.38794	0.704000	0.31869	0.563000	0.77884	CCT	G|0.970;A|0.030	0.030	strong		0.368	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
CELSR1	9620	hgsc.bcm.edu	37	22	46860088	46860088	+	Silent	SNP	G	G	C	rs3747251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46860088G>C	ENST00000262738.3	-	2	3698	c.3699C>G	c.(3697-3699)gcC>gcG	p.A1233A	CELSR1_ENST00000395964.1_Silent_p.A1233A	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1233					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)		TGGACAGCACGGCGGCCACCC	0.612													C|||	974	0.194489	0.4894	0.0692	5008	,	,		17384	0.1944		0.0308	False		,,,				2504	0.0532				p.A1233A		Atlas-SNP	.											CELSR1,NS,carcinoma,0,1	CELSR1	242	1	0			c.C3699G						PASS	.	C		1802,2604	637.5+/-396.8	365,1072,766	74.0	66.0	69.0		3699	-4.8	0.9	22	dbSNP_107	69	207,8393	808.2+/-407.2	4,199,4097	no	coding-synonymous	CELSR1	NM_014246.1		369,1271,4863	CC,CG,GG		2.407,40.8988,15.4467		1233/3015	46860088	2009,10997	2203	4300	6503	SO:0001819	synonymous_variant	9620	exon2			CAGCACGGCGGCC	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.3699C>G	22.37:g.46860088G>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1	367	0.16804029304029305	212	0.43089430894308944	18	0.049723756906077346	119	0.20804195804195805	18	0.023746701846965697	C	8.876	0.950443	0.18431	0.408988	0.02407	ENSG00000075275	ENST00000454637	.	.	.	4.75	-4.79	0.03200	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999997367	.	.	.	.	.	.	T	0.43540	-0.9385	3	.	.	.	.	6.1532	0.20322	0.3008:0.1794:0.4523:0.0675	rs3747251;rs3747251	.	.	.	R	608	.	.	P	-	2	0	CELSR1	45238752	0.000000	0.05858	0.897000	0.35233	0.965000	0.64279	-4.855000	0.00177	-0.979000	0.03529	-0.120000	0.15030	CCG	G|0.840;C|0.160	0.160	strong		0.612	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
UCP3	7352	hgsc.bcm.edu	37	11	73717247	73717247	+	Missense_Mutation	SNP	C	C	T	rs2229707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73717247C>T	ENST00000314032.4	-	3	856	c.304G>A	c.(304-306)Gtc>Atc	p.V102I	UCP3_ENST00000348534.4_Missense_Mutation_p.V102I|UCP3_ENST00000426995.2_Missense_Mutation_p.V102I	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	102			V -> I (in obesity; dbSNP:rs2229707). {ECO:0000269|PubMed:9769326}.		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)					ACCTGCTTGACGGAGTCATAG	0.627													C|||	216	0.043131	0.1513	0.013	5008	,	,		19077	0.0		0.005	False		,,,				2504	0.002				p.V102I		Atlas-SNP	.											.	UCP3	31	.	0			c.G304A	GRCh37	CM981987	UCP3	M	rs2229707	PASS	.	C	ILE/VAL,ILE/VAL	524,3876	236.8+/-248.8	36,452,1712	44.0	43.0	44.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	304,304	5.8	1.0	11	dbSNP_98	44	12,8574	9.1+/-34.3	0,12,4281	yes	missense,missense	UCP3	NM_003356.3,NM_022803.2	29,29	36,464,5993	TT,TC,CC		0.1398,11.9091,4.1275	benign,benign	102/313,102/276	73717247	536,12450	2200	4293	6493	SO:0001583	missense	7352	exon3			GCTTGACGGAGTC	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.304G>A	11.37:g.73717247C>T	ENSP00000323740:p.Val102Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	NM_003356	O60475|Q96HL3	Missense_Mutation	SNP	ENST00000314032.4	37	CCDS8229.1	81	0.03708791208791209	75	0.1524390243902439	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	15.72	2.915545	0.52546	0.119091	0.001398	ENSG00000175564	ENST00000314032;ENST00000348534;ENST00000426995	T;T;T	0.78816	-1.21;-1.21;-1.21	5.76	5.76	0.90799	Mitochondrial carrier domain (2);	0.054467	0.64402	D	0.000001	T	0.00967	0.0032	L	0.39020	1.185	0.22933	P	0.99854677	B	0.20459	0.045	B	0.23275	0.045	T	0.24764	-1.0151	9	0.59425	D	0.04	-25.6915	19.5566	0.95351	0.0:1.0:0.0:0.0	rs2229707;rs2734830;rs2229707	102	P55916	UCP3_HUMAN	I	102	ENSP00000323740:V102I;ENSP00000343615:V102I;ENSP00000392143:V102I	ENSP00000323740:V102I	V	-	1	0	UCP3	73394895	1.000000	0.71417	0.990000	0.47175	0.261000	0.26267	5.621000	0.67743	2.724000	0.93272	0.561000	0.74099	GTC	C|0.964;T|0.036	0.036	strong		0.627	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356	
YTHDC2	64848	hgsc.bcm.edu	37	5	112868693	112868693	+	Silent	SNP	C	C	A	rs6594732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	100	0	0		WXS	Illumina HiSeq	Phase_I	94	37	0.393617	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	
BMP10	27302	hgsc.bcm.edu	37	2	69093288	69093288	+	Missense_Mutation	SNP	G	G	T	rs2231345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69093288G>T	ENST00000295379.1	-	2	908	c.750C>A	c.(748-750)aaC>aaA	p.N250K		NM_014482.1	NP_055297.1	O95393	BMP10_HUMAN	bone morphogenetic protein 10	250			N -> K (in dbSNP:rs2231345).		activin receptor signaling pathway (GO:0032924)|adult heart development (GO:0007512)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heart trabecula formation (GO:0060347)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction (GO:0055117)|sarcomere organization (GO:0045214)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Z disc (GO:0030018)	hormone activity (GO:0005179)|receptor serine/threonine kinase binding (GO:0033612)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(15)|ovary(2)	27						TGAGCAAAGGGTTATGCTTAT	0.488													G|||	78	0.0155751	0.0537	0.0101	5008	,	,		22010	0.0		0.0	False		,,,				2504	0.0				p.N250K		Atlas-SNP	.											.	BMP10	70	.	0			c.C750A						PASS	.	G	LYS/ASN	212,4194	129.4+/-166.1	8,196,1999	106.0	94.0	98.0		750	-0.1	0.6	2	dbSNP_98	98	0,8600		0,0,4300	yes	missense	BMP10	NM_014482.1	94	8,196,6299	TT,TG,GG		0.0,4.8116,1.63	benign	250/425	69093288	212,12794	2203	4300	6503	SO:0001583	missense	27302	exon2			CAAAGGGTTATGC	AF101441	CCDS1890.1	2p13.2	2014-09-17			ENSG00000163217	ENSG00000163217		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	20869	protein-coding gene	gene with protein product		608748				10072785	Standard	NM_014482		Approved		uc002sez.1	O95393	OTTHUMG00000129573	ENST00000295379.1:c.750C>A	2.37:g.69093288G>T	ENSP00000295379:p.Asn250Lys	Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	349	168	0.481375	NM_014482	Q53R17|Q6NTE0	Missense_Mutation	SNP	ENST00000295379.1	37	CCDS1890.1	34	0.015567765567765568	29	0.05894308943089431	5	0.013812154696132596	0	0.0	0	0.0	G	0.876	-0.730477	0.03135	0.048116	0.0	ENSG00000163217	ENST00000295379	T	0.63417	-0.04	5.44	-0.119	0.13543	Transforming growth factor-beta, N-terminal (1);	0.340366	0.33457	N	0.004893	T	0.02193	0.0068	N	0.01705	-0.755	0.26995	N	0.965051	B	0.09022	0.002	B	0.06405	0.002	T	0.07501	-1.0769	10	0.05620	T	0.96	.	0.5561	0.00671	0.2685:0.2748:0.2527:0.204	rs2231345;rs52835894;rs2231345	250	O95393	BMP10_HUMAN	K	250	ENSP00000295379:N250K	ENSP00000295379:N250K	N	-	3	2	BMP10	68946792	0.130000	0.22417	0.596000	0.28811	0.989000	0.77384	-0.205000	0.09411	-0.164000	0.10927	0.655000	0.94253	AAC	G|0.979;T|0.021	0.021	strong		0.488	BMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251768.1	NM_014482	
ZNF460	10794	hgsc.bcm.edu	37	19	57802806	57802806	+	Silent	SNP	C	C	T	rs2041109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57802806C>T	ENST00000360338.3	+	3	1219	c.897C>T	c.(895-897)aaC>aaT	p.N299N	ZNF460_ENST00000537645.1_Silent_p.N258N	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	299					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TCTTGCATAACAAGAGCCACA	0.468													c|||	923	0.184305	0.0908	0.3084	5008	,	,		22596	0.1657		0.2515	False		,,,				2504	0.1728				p.N299N		Atlas-SNP	.											.	ZNF460	59	.	0			c.C897T						PASS	.	C		494,3912	229.4+/-244.0	27,440,1736	95.0	85.0	89.0		897	-0.9	0.0	19	dbSNP_94	89	2199,6401	375.0+/-337.6	295,1609,2396	no	coding-synonymous	ZNF460	NM_006635.3		322,2049,4132	TT,TC,CC		25.5698,11.212,20.7058		299/563	57802806	2693,10313	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			GCATAACAAGAGC	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.897C>T	19.37:g.57802806C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			C|0.799;T|0.201	0.201	strong		0.468	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
ABHD12B	145447	hgsc.bcm.edu	37	14	51370852	51370852	+	Missense_Mutation	SNP	C	C	G	rs34800262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:51370852C>G	ENST00000337334.2	+	12	1018	c.1003C>G	c.(1003-1005)Cct>Gct	p.P335A	PYGL_ENST00000532462.1_Intron|ABHD12B_ENST00000353130.1_Missense_Mutation_p.P258A|ABHD12B_ENST00000395752.1_Missense_Mutation_p.P228A	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	335							hydrolase activity (GO:0016787)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					GGTTATCTTTCCTCCTGGCTT	0.443													C|||	596	0.11901	0.0983	0.0865	5008	,	,		21457	0.0913		0.0915	False		,,,				2504	0.227				p.P335A		Atlas-SNP	.											ABHD12B_ENST00000337334,right_upper_lobe,carcinoma,-1,2	ABHD12B	53	2	0			c.C1003G						PASS	.	C	ALA/PRO,ALA/PRO	452,3954	216.8+/-235.3	22,408,1773	213.0	211.0	212.0		1003,772	4.9	1.0	14	dbSNP_126	212	717,7883	175.0+/-225.2	37,643,3620	yes	missense,missense	ABHD12B	NM_001206673.1,NM_181814.1	27,27	59,1051,5393	GG,GC,CC		8.3372,10.2587,8.9882	benign,benign	335/363,258/286	51370852	1169,11837	2203	4300	6503	SO:0001583	missense	145447	exon12			ATCTTTCCTCCTG	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.1003C>G	14.37:g.51370852C>G	ENSP00000336693:p.Pro335Ala	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	235	127	0.540426	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Missense_Mutation	SNP	ENST00000337334.2	37	CCDS55916.1	187	0.08562271062271062	49	0.09959349593495935	18	0.049723756906077346	47	0.08216783216783216	73	0.09630606860158311	C	12.29	1.894362	0.33442	0.102587	0.083372	ENSG00000131969	ENST00000353130;ENST00000337334;ENST00000395752	T;T;T	0.53206	2.25;0.63;2.27	4.94	4.94	0.65067	.	0.426050	0.28589	N	0.014814	T	0.00967	0.0032	L	0.28115	0.83	0.41275	D	0.986877	B;B	0.29085	0.137;0.232	B;B	0.30401	0.115;0.07	T	0.01824	-1.1266	10	0.09843	T	0.71	-19.3759	15.7423	0.77910	0.0:1.0:0.0:0.0	rs34800262	335;258	Q7Z5M8;Q7Z5M8-2	AB12B_HUMAN;.	A	258;335;228	ENSP00000343951:P258A;ENSP00000336693:P335A;ENSP00000379101:P228A	ENSP00000336693:P335A	P	+	1	0	ABHD12B	50440602	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	4.256000	0.58810	2.675000	0.91044	0.655000	0.94253	CCT	C|0.912;G|0.088	0.088	strong		0.443	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1		
GPR97	222487	hgsc.bcm.edu	37	16	57717889	57717889	+	Silent	SNP	C	C	T	rs73554921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57717889C>T	ENST00000333493.4	+	9	1088	c.927C>T	c.(925-927)caC>caT	p.H309H	GPR97_ENST00000327655.6_Silent_p.H99H|GPR97_ENST00000450388.3_Silent_p.H189H|RP11-405F3.4_ENST00000563062.1_RNA	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	309					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CAAAGATCCACGTGGCCCTGG	0.622													.|||	194	0.038738	0.1407	0.0086	5008	,	,		17225	0.0		0.002	False		,,,				2504	0.0				p.H309H		Atlas-SNP	.											.	GPR97	74	.	0			c.C927T						PASS	.	C		535,3861	242.1+/-252.3	34,467,1697	79.0	81.0	80.0		927	-7.7	0.2	16	dbSNP_130	80	29,8571	19.8+/-62.0	0,29,4271	no	coding-synonymous	GPR97	NM_170776.4		34,496,5968	TT,TC,CC		0.3372,12.1702,4.3398		309/550	57717889	564,12432	2198	4300	6498	SO:0001819	synonymous_variant	222487	exon9			GATCCACGTGGCC	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.927C>T	16.37:g.57717889C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	177	85	0.480226	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Silent	SNP	ENST00000333493.4	37	CCDS10786.1																																																																																			C|0.954;T|0.046	0.046	strong		0.622	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
C2orf61	285051	hgsc.bcm.edu	37	2	47380145	47380145	+	Missense_Mutation	SNP	T	T	C	rs17036300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47380145T>C	ENST00000445927.2	-	2	218	c.92A>G	c.(91-93)cAa>cGa	p.Q31R	RP11-761B3.1_ENST00000422269.1_Missense_Mutation_p.Q38R|C2orf61_ENST00000294947.2_Missense_Mutation_p.Q31R	NM_001163561.1	NP_001157033.1	Q8N801	CB061_HUMAN	chromosome 2 open reading frame 61	31			Q -> R (in dbSNP:rs17036300).					p.0?(2)		endometrium(1)|kidney(1)|lung(2)	4		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GGAAGTCTTTTGGGCTGGTTT	0.313													C|||	818	0.163339	0.2799	0.1556	5008	,	,		17237	0.0327		0.0706	False		,,,				2504	0.2413				p.Q31R		Atlas-SNP	.											.	C2orf61	31	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.A92G						PASS	.	C	ARG/GLN,ARG/GLN	1092,3314	718.8+/-408.9	136,820,1247	94.0	96.0	96.0		92,92	-1.1	0.0	2	dbSNP_123	96	687,7903	786.4+/-407.6	21,645,3629	yes	missense,missense	C2orf61	NM_001163561.1,NM_173649.2	43,43	157,1465,4876	CC,CT,TT		7.9977,24.7844,13.6888	benign,benign	31/249,31/178	47380145	1779,11217	2203	4295	6498	SO:0001583	missense	285051	exon2			GTCTTTTGGGCTG	AK097491	CCDS1831.1, CCDS54356.1	2p21	2008-02-05			ENSG00000239605	ENSG00000239605			26850	protein-coding gene	gene with protein product							Standard	NM_173649		Approved	FLJ40172	uc010yog.2	Q8N801	OTTHUMG00000128851	ENST00000445927.2:c.92A>G	2.37:g.47380145T>C	ENSP00000408527:p.Gln31Arg	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_173649	H7C2Z2	Missense_Mutation	SNP	ENST00000445927.2	37	CCDS54356.1	260	0.11904761904761904	135	0.27439024390243905	58	0.16022099447513813	10	0.017482517482517484	57	0.07519788918205805	C	4.974	0.180928	0.09443	0.247844	0.079977	ENSG00000239605	ENST00000445927;ENST00000294947	T;T	0.31247	1.5;1.5	6.06	-1.12	0.09808	.	1.322300	0.05307	N	0.524043	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	0.31081	-0.9956	9	0.05833	T	0.94	-4.6419	5.9633	0.19310	0.1458:0.2593:0.0:0.5949	rs17036300;rs52797992;rs57024040;rs17036300	31	Q8N801	CB061_HUMAN	R	31	ENSP00000408527:Q31R;ENSP00000294947:Q31R	ENSP00000294947:Q31R	Q	-	2	0	C2orf61	47233649	0.002000	0.14202	0.008000	0.14137	0.193000	0.23685	-0.171000	0.09883	-0.067000	0.12976	-0.119000	0.15052	CAA	T|0.866;C|0.134	0.134	strong		0.313	C2orf61-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173649	
PKD1	5310	hgsc.bcm.edu	37	16	2156153	2156153	+	Missense_Mutation	SNP	C	C	G	rs28369051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2156153C>G	ENST00000262304.4	-	19	7850	c.7642G>C	c.(7642-7644)Gag>Cag	p.E2548Q	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Missense_Mutation_p.E2548Q	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2548	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		E -> Q (in dbSNP:rs28369051). {ECO:0000269|PubMed:10577909}.		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						AGGCCCACCTCGAAGTGTGGC	0.701													c|||	192	0.0383387	0.1392	0.0115	5008	,	,		16164	0.0		0.0	False		,,,				2504	0.0				p.E2548Q		Atlas-SNP	.											.	PKD1	184	.	0			c.G7642C						PASS	.		GLN/GLU,GLN/GLU	303,3739		5,293,1723	5.0	8.0	7.0		7642,7642	-4.0	0.0	16	dbSNP_125	7	2,8128		0,2,4063	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	29,29	5,295,5786	GG,GC,CC		0.0246,7.4963,2.5058	benign,benign	2548/4303,2548/4304	2156153	305,11867	2021	4065	6086	SO:0001583	missense	5310	exon19			CCACCTCGAAGTG	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.7642G>C	16.37:g.2156153C>G	ENSP00000262304:p.Glu2548Gln	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	296	138	0.466216	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	79	0.036172161172161175	74	0.15040650406504066	5	0.013812154696132596	0	0.0	0	0.0	c	2.890	-0.229927	0.06022	0.074963	2.46E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101;ENST00000382481	T;T	0.68624	-0.34;-0.34	5.14	-4.01	0.04045	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);Polycystin cation channel (1);	1.060040	0.07309	N	0.875540	T	0.00178	0.0005	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.21688	0.059;0.053	B;B	0.20384	0.012;0.029	T	0.04090	-1.0978	9	0.13108	T	0.6	.	6.7917	0.23703	0.0891:0.3434:0.4431:0.1245	rs28369051	2548;2548	P98161-3;P98161	.;PKD1_HUMAN	Q	2548;2548;1899;827	ENSP00000262304:E2548Q;ENSP00000399501:E2548Q	ENSP00000262304:E2548Q	E	-	1	0	PKD1	2096154	0.000000	0.05858	0.001000	0.08648	0.967000	0.64934	-2.425000	0.01028	-0.502000	0.06596	0.544000	0.68410	GAG	C|0.972;G|0.028	0.028	strong		0.701	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
DIS3L	115752	hgsc.bcm.edu	37	15	66625470	66625470	+	Silent	SNP	G	G	A	rs3759785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:66625470G>A	ENST00000319212.4	+	17	3035	c.2985G>A	c.(2983-2985)gaG>gaA	p.E995E	RP11-352G18.2_ENST00000565993.1_RNA|DIS3L_ENST00000319194.5_Silent_p.E912E	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	995					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						TGAAGAGTGAGTTAGTGAAAG	0.368													G|||	150	0.0299521	0.0038	0.0749	5008	,	,		18740	0.0625		0.0258	False		,,,				2504	0.0041				p.E995E		Atlas-SNP	.											.	DIS3L	175	.	0			c.G2985A						PASS	.	G	,	30,4372	34.3+/-65.2	1,28,2172	93.0	93.0	93.0		2985,2736	-11.6	0.0	15	dbSNP_107	93	169,8429	77.8+/-140.4	4,161,4134	no	coding-synonymous,coding-synonymous	DIS3L	NM_001143688.1,NM_133375.3	,	5,189,6306	AA,AG,GG		1.9656,0.6815,1.5308	,	995/1055,912/972	66625470	199,12801	2201	4299	6500	SO:0001819	synonymous_variant	115752	exon17			GAGTGAGTTAGTG		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.2985G>A	15.37:g.66625470G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Silent	SNP	ENST00000319212.4	37	CCDS45286.1																																																																																			G|0.973;A|0.027	0.027	strong		0.368	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
URB1	9875	hgsc.bcm.edu	37	21	33711077	33711077	+	Silent	SNP	C	C	T	rs58130645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33711077C>T	ENST00000382751.3	-	26	4564	c.4449G>A	c.(4447-4449)tcG>tcA	p.S1483S		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	1483						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						GCAGAAACAGCGAGTGCTGCA	0.592													C|||	91	0.0181709	0.0651	0.0058	5008	,	,		15666	0.0		0.001	False		,,,				2504	0.0				p.S1483S		Atlas-SNP	.											.	URB1	176	.	0			c.G4449A						PASS	.						56.0	57.0	56.0					21																	33711077		692	1591	2283	SO:0001819	synonymous_variant	9875	exon26			AAACAGCGAGTGC	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.4449G>A	21.37:g.33711077C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																			C|0.986;T|0.014	0.014	strong		0.592	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
LAMA1	284217	hgsc.bcm.edu	37	18	7040197	7040197	+	Missense_Mutation	SNP	T	T	C	rs62619829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:7040197T>C	ENST00000389658.3	-	10	1393	c.1300A>G	c.(1300-1302)Aca>Gca	p.T434A		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	434	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTTTCTCCTGTATAACCTTCC	0.507													T|||	77	0.0153754	0.0552	0.0058	5008	,	,		19191	0.0		0.0	False		,,,				2504	0.0				p.T434A		Atlas-SNP	.											.	LAMA1	458	.	0			c.A1300G						PASS	.	T	ALA/THR	190,4216	118.8+/-156.5	2,186,2015	150.0	136.0	141.0		1300	1.4	0.9	18	dbSNP_129	141	5,8595	4.3+/-15.6	0,5,4295	yes	missense	LAMA1	NM_005559.3	58	2,191,6310	CC,CT,TT		0.0581,4.3123,1.4993	benign	434/3076	7040197	195,12811	2203	4300	6503	SO:0001583	missense	284217	exon10			CTCCTGTATAACC	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.1300A>G	18.37:g.7040197T>C	ENSP00000374309:p.Thr434Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	T	2.627	-0.287315	0.05605	0.043123	5.81E-4	ENSG00000101680	ENST00000389658	T	0.60797	0.16	5.32	1.35	0.21983	EGF-like, laminin (4);	0.395100	0.27622	N	0.018551	T	0.08133	0.0203	N	0.12831	0.26	0.25331	N	0.989032	B	0.02656	0.0	B	0.08055	0.003	T	0.10042	-1.0647	10	0.06891	T	0.86	.	8.4468	0.32847	0.0:0.5006:0.0:0.4994	rs62619829	434	P25391	LAMA1_HUMAN	A	434	ENSP00000374309:T434A	ENSP00000374309:T434A	T	-	1	0	LAMA1	7030197	0.000000	0.05858	0.947000	0.38551	0.982000	0.71751	-0.882000	0.04174	0.407000	0.25591	-0.146000	0.13790	ACA	T|0.986;C|0.014	0.014	strong		0.507	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
TTN	7273	hgsc.bcm.edu	37	2	179416556	179416556	+	Silent	SNP	A	A	C	rs11897366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179416556A>C	ENST00000591111.1	-	285	86372	c.86148T>G	c.(86146-86148)acT>acG	p.T28716T	TTN_ENST00000342175.6_Silent_p.T21484T|TTN_ENST00000359218.5_Silent_p.T21417T|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Silent_p.T21292T|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Silent_p.T30357T|TTN_ENST00000342992.6_Silent_p.T27789T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28716	Fibronectin type-III 109. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATGGAATCCAGTAACTTCTG	0.418													A|||	763	0.152356	0.2738	0.183	5008	,	,		22144	0.0258		0.0527	False		,,,				2504	0.1994				p.T30357T		Atlas-SNP	.											.	TTN	18412	.	0			c.T91071G						PASS	.	A	,,,	980,2812		132,716,1048	162.0	165.0	164.0		63876,83367,64251,64452	-0.1	1.0	2	dbSNP_120	164	270,7962		9,252,3855	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	141,968,4903	CC,CA,AA		3.2799,25.8439,10.3959	,,,	21292/26927,27789/33424,21417/27052,21484/27119	179416556	1250,10774	1896	4116	6012	SO:0001819	synonymous_variant	7273	exon335			GAATCCAGTAACT	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.86148T>G	2.37:g.179416556A>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	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|0.880;C|0.120	0.120	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MICA	100507436	hgsc.bcm.edu	37	6	31382882	31382882	+	3'UTR	SNP	C	C	A	rs9266825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31382882C>A	ENST00000449934.2	+	0	1176				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)				CTGATGTCAGCTCTTGGGTCC	0.572													t|||	1717	0.342851	0.4372	0.3516	5008	,	,		14470	0.2996		0.2992	False		,,,				2504	0.2986				p.A373D		Atlas-SNP	.											.	MICA	21	.	0			c.C1118A						PASS	.	C		524,860		108,308,276	173.0	157.0	162.0			-1.5	0.0	6	dbSNP_118	162	821,2361		97,627,867	yes	utr-3	MICA	NM_001177519.1		205,935,1143	AA,AC,CC		25.8014,37.8613,29.4569			31382882	1345,3221	692	1591	2283	SO:0001624	3_prime_UTR_variant	100507436	exon7			TGTCAGCTCTTGG	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.*123C>A	6.37:g.31382882C>A		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_000247		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.666;A|0.334	0.334	strong		0.572	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
IWS1	55677	hgsc.bcm.edu	37	2	128261099	128261099	+	Missense_Mutation	SNP	C	C	T	rs34785867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128261099C>T	ENST00000295321.4	-	4	1532	c.1273G>A	c.(1273-1275)Gta>Ata	p.V425I	AC010976.2_ENST00000599001.1_RNA|IWS1_ENST00000486662.1_5'Flank|IWS1_ENST00000455721.2_Missense_Mutation_p.V432I	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	425	Glu-rich.		V -> I (in dbSNP:rs34785867).		mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		TTGTCTGATACAGCATCACTG	0.383													C|||	98	0.0195687	0.0711	0.0058	5008	,	,		15170	0.0		0.0	False		,,,				2504	0.0				p.V425I		Atlas-SNP	.											.	IWS1	61	.	0			c.G1273A						PASS	.	C	ILE/VAL	309,4097	167.3+/-198.3	10,289,1904	128.0	111.0	117.0		1273	-6.2	0.0	2	dbSNP_126	117	2,8598	1.2+/-3.3	0,2,4298	yes	missense	IWS1	NM_017969.2	29	10,291,6202	TT,TC,CC		0.0233,7.0132,2.3912	benign	425/820	128261099	311,12695	2203	4300	6503	SO:0001583	missense	55677	exon4			CTGATACAGCATC	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.1273G>A	2.37:g.128261099C>T	ENSP00000295321:p.Val425Ile	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	185	184	0.994595	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	37	CCDS2146.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	C	10.39	1.337907	0.24253	0.070132	2.33E-4	ENSG00000163166	ENST00000295321;ENST00000433551;ENST00000455721	T;T	0.31247	2.33;1.5	5.67	-6.15	0.02105	.	1.260290	0.05632	N	0.581936	T	0.01124	0.0037	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24440	-1.0160	10	0.37606	T	0.19	0.5854	9.4352	0.38635	0.1086:0.6567:0.1211:0.1136	rs34785867	425	Q96ST2	IWS1_HUMAN	I	425;378;432	ENSP00000295321:V425I;ENSP00000399245:V432I	ENSP00000295321:V425I	V	-	1	0	IWS1	127977569	0.000000	0.05858	0.003000	0.11579	0.981000	0.71138	-0.215000	0.09279	-1.101000	0.03027	-0.793000	0.03317	GTA	C|0.977;T|0.023	0.023	strong		0.383	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969	
G6PC2	57818	hgsc.bcm.edu	37	2	169764546	169764546	+	Missense_Mutation	SNP	C	C	G	rs2232328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	61	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	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	
PCDHA1	56147	hgsc.bcm.edu	37	5	140167175	140167175	+	Missense_Mutation	SNP	T	T	C	rs61743801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140167175T>C	ENST00000504120.2	+	1	1300	c.1300T>C	c.(1300-1302)Tcg>Ccg	p.S434P	PCDHA1_ENST00000394633.3_Missense_Mutation_p.S434P|PCDHA1_ENST00000378133.3_Missense_Mutation_p.S434P	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	434	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCTCGCCTTCGCTGTGGGC	0.627													.|||	72	0.014377	0.0537	0.0014	5008	,	,		17483	0.0		0.0	False		,,,				2504	0.0				p.S434P		Atlas-SNP	.											.	PCDHA1	387	.	0			c.T1300C						PASS	.	T	PRO/SER,PRO/SER,PRO/SER	236,4170	135.3+/-171.4	10,216,1977	82.0	88.0	86.0		1300,1300,1300	-3.1	0.7	5	dbSNP_129	86	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense,missense	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	74,74,74	10,217,6275	CC,CT,TT		0.0116,5.3563,1.8225	,,	434/951,434/808,434/687	140167175	237,12767	2203	4299	6502	SO:0001583	missense	56147	exon1			TCGCCTTCGCTGT	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1300T>C	5.37:g.140167175T>C	ENSP00000420840:p.Ser434Pro	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	166	81	0.487952	NM_031411	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	t	4.310	0.056796	0.08339	0.053563	1.16E-4	ENSG00000204970	ENST00000504120;ENST00000394633;ENST00000378133	T;T;T	0.44881	0.91;0.91;0.91	3.89	-3.14	0.05250	Cadherin (5);Cadherin-like (1);	0.679068	0.12024	N	0.506656	T	0.02047	0.0064	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.17852	0.024;0.002;0.023	B;B;B	0.32022	0.139;0.002;0.03	T	0.30563	-0.9974	10	0.13853	T	0.58	.	2.4978	0.04626	0.1149:0.2142:0.4488:0.2221	rs61743801	434;434;434	Q9Y5I3;Q9Y5I3-2;Q9Y5I3-3	PCDA1_HUMAN;.;.	P	434	ENSP00000420840:S434P;ENSP00000378129:S434P;ENSP00000367373:S434P	ENSP00000367373:S434P	S	+	1	0	PCDHA1	140147359	0.000000	0.05858	0.741000	0.31004	0.719000	0.41307	-0.511000	0.06321	-0.192000	0.10432	0.369000	0.22263	TCG	T|0.983;C|0.017	0.017	strong		0.627	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
PTX4	390667	hgsc.bcm.edu	37	16	1536138	1536138	+	Silent	SNP	T	T	C	rs386787711|rs114122805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536138T>C	ENST00000447419.2	-	3	1264	c.1239A>G	c.(1237-1239)ggA>ggG	p.G413G	PTX4_ENST00000440447.2_3'UTR|PTX4_ENST00000293922.1_Silent_p.G408G			Q96A99	PTX4_HUMAN	pentraxin 4, long	413	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						AGCTGTCGAATCCGCCCCCCA	0.662													T|||	87	0.0173722	0.0643	0.0029	5008	,	,		16736	0.0		0.0	False		,,,				2504	0.0				p.G408G		Atlas-SNP	.											.	PTX4	46	.	0			c.A1224G						PASS	.						59.0	56.0	57.0					16																	1536138		2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GTCGAATCCGCCC		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.1239A>G	16.37:g.1536138T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				T|0.980;C|0.020	0.020	strong		0.662	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
C2orf54	79919	hgsc.bcm.edu	37	2	241830969	241830969	+	Silent	SNP	G	G	A	rs10171067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241830969G>A	ENST00000388934.4	-	2	884	c.726C>T	c.(724-726)agC>agT	p.S242S	C2orf54_ENST00000307486.8_Silent_p.S93S|C2orf54_ENST00000402775.2_Silent_p.S74S	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	242										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		AGAGCTGGGCGCTGGCCGGCA	0.692													G|||	2640	0.527157	0.7799	0.3473	5008	,	,		17745	0.4415		0.5179	False		,,,				2504	0.411				p.S242S		Atlas-SNP	.											.	C2orf54	14	.	0			c.C726T						PASS	.	G	,	2960,1022		1120,720,151	46.0	54.0	51.0		726,222	-2.7	0.0	2	dbSNP_119	51	4114,4174		1043,2028,1073	no	coding-synonymous,coding-synonymous	C2orf54	NM_001085437.1,NM_024861.2	,	2163,2748,1224	AA,AG,GG		49.638,25.6655,42.3472	,	242/448,74/280	241830969	7074,5196	1991	4144	6135	SO:0001819	synonymous_variant	79919	exon2			CTGGGCGCTGGCC	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.726C>T	2.37:g.241830969G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	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	
SWT1	54823	hgsc.bcm.edu	37	1	185143721	185143721	+	Missense_Mutation	SNP	A	A	G	rs10489579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:185143721A>G	ENST00000367500.4	+	5	607	c.442A>G	c.(442-444)Att>Gtt	p.I148V	SWT1_ENST00000367501.3_Missense_Mutation_p.I148V	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	148			I -> V (in dbSNP:rs10489579). {ECO:0000269|PubMed:15489334}.							breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						TGACCATGGAATTAAAAGCCT	0.368													A|||	2177	0.434704	0.6982	0.3487	5008	,	,		19153	0.2718		0.3439	False		,,,				2504	0.4008				p.I148V		Atlas-SNP	.											.	SWT1	88	.	0			c.A442G						PASS	.	A	VAL/ILE,VAL/ILE	2802,1604	659.4+/-400.6	907,988,308	53.0	53.0	53.0		442,442	0.9	0.0	1	dbSNP_119	53	3071,5529	467.9+/-367.2	556,1959,1785	yes	missense,missense	SWT1	NM_001105518.1,NM_017673.6	29,29	1463,2947,2093	GG,GA,AA		35.7093,36.4049,45.1561	benign,benign	148/901,148/901	185143721	5873,7133	2203	4300	6503	SO:0001583	missense	54823	exon5			CATGGAATTAAAA	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.442A>G	1.37:g.185143721A>G	ENSP00000356470:p.Ile148Val	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	914	0.4184981684981685	350	0.7113821138211383	119	0.3287292817679558	187	0.3269230769230769	258	0.3403693931398417	A	0.583	-0.836082	0.02713	0.635951	0.357093	ENSG00000116668	ENST00000367501;ENST00000367500;ENST00000450350	T;T;T	0.37915	1.17;1.17;1.17	5.35	0.918	0.19386	.	1.040850	0.07571	N	0.918619	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.45687	-0.9244	9	0.11794	T	0.64	.	1.757	0.02984	0.2943:0.2806:0.308:0.1171	rs10489579;rs17845931;rs17858910;rs58368482;rs10489579	148	Q5T5J6	SWT1_HUMAN	V	148	ENSP00000356471:I148V;ENSP00000356470:I148V;ENSP00000401413:I148V	ENSP00000356470:I148V	I	+	1	0	SWT1	183410344	0.955000	0.32602	0.002000	0.10522	0.559000	0.35586	0.566000	0.23593	-0.149000	0.11215	0.455000	0.32223	ATT	G|0.396;N|0.000	0.396	strong		0.368	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
KCNN1	3780	hgsc.bcm.edu	37	19	18084775	18084775	+	Silent	SNP	G	G	A	rs75754669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18084775G>A	ENST00000222249.9	+	3	397	c.78G>A	c.(76-78)ccG>ccA	p.P26P	RNA5SP468_ENST00000516782.1_RNA	NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	26					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	GAGACCCTCCGGACCCTGAGG	0.736													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		10833	0.0		0.0	False		,,,				2504	0.0				p.P26P		Atlas-SNP	.											.	KCNN1	74	.	0			c.G78A						PASS	.	G		61,3441		0,61,1690	6.0	9.0	8.0		78	-0.2	0.2	19	dbSNP_131	8	2,7602		0,2,3800	no	coding-synonymous	KCNN1	NM_002248.3		0,63,5490	AA,AG,GG		0.0263,1.7419,0.5673		26/544	18084775	63,11043	1751	3802	5553	SO:0001819	synonymous_variant	3780	exon3			CCCTCCGGACCCT	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.78G>A	19.37:g.18084775G>A		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				G|0.990;A|0.010	0.010	strong		0.736	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
FCGR2B	2213	hgsc.bcm.edu	37	1	161645058	161645058	+	Missense_Mutation	SNP	T	T	G	rs148534844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161645058T>G	ENST00000358671.5	+	6	853	c.772T>G	c.(772-774)Tac>Gac	p.Y258D	FCGR2B_ENST00000236937.9_Intron|FCGR2B_ENST00000367960.5_Missense_Mutation_p.Y251D|FCGR2B_ENST00000403078.3_Intron|FCGR2B_ENST00000367961.4_Missense_Mutation_p.Y251D|FCGR2B_ENST00000367962.4_Missense_Mutation_p.Y258D|RP11-25K21.1_ENST00000453111.1_RNA	NM_001002275.2|NM_004001.4	NP_001002275.1|NP_003992.3	P31994	FCG2B_HUMAN	Fc fragment of IgG, low affinity IIb, receptor (CD32)	258			Y -> D (in dbSNP:rs148534844). {ECO:0000269|PubMed:8466861}.		immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)						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)|Antithymocyte globulin(DB00098)|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)	TCTCCCAGGATACCCTGAGTG	0.612			T	?	ALL																																p.Y258D		Atlas-SNP	.		Dom	yes		1	1q23	2213	"""Fc fragment of IgG, low affinity IIb, receptor for (CD32)"""		L	.	FCGR2B	33	.	0			c.T772G						PASS	.	T	,,ASP/TYR,ASP/TYR,ASP/TYR	54,4350		0,54,2148	31.0	29.0	29.0		,,769,751,772	-1.8	0.6	1	dbSNP_134	29	1,8599		0,1,4299	no	intron,intron,missense,missense,missense	FCGR2B	NM_001002273.2,NM_001002274.2,NM_001002275.2,NM_001190828.1,NM_004001.4	,,160,160,160	0,55,6447	GG,GT,TT		0.0116,1.2262,0.4229	,,benign,benign,benign	,,257/310,251/304,258/311	161645058	55,12949	2202	4300	6502	SO:0001583	missense	2213	exon6			CCAGGATACCCTG	BC031992	CCDS30924.1, CCDS30925.1, CCDS53414.1	1q23	2013-01-11	2005-02-02		ENSG00000072694	ENSG00000072694		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3618	protein-coding gene	gene with protein product		604590	"""Fc fragment of IgG, low affinity IIb, receptor for (CD32)"""	FCG2, FCGR2		2139735	Standard	NM_004001		Approved	CD32, CD32B	uc001gaz.2	P31994	OTTHUMG00000034470	ENST00000358671.5:c.772T>G	1.37:g.161645058T>G	ENSP00000351497:p.Tyr258Asp	Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	331	141	0.425982	NM_004001	A6H8N3|O95649|Q53X85|Q5VXA9|Q8NIA1	Missense_Mutation	SNP	ENST00000358671.5	37	CCDS30924.1	23	0.010531135531135532	19	0.03861788617886179	4	0.011049723756906077	0	0.0	0	0.0	A	9.704	1.155245	0.21454	0.012262	1.16E-4	ENSG00000072694	ENST00000367962;ENST00000367960;ENST00000367961;ENST00000358671	T;T;T;T	0.27557	4.78;1.66;1.66;4.78	5.06	-1.78	0.07957	.	1.572250	0.03874	N	0.276032	T	0.04318	0.0119	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.002	T	0.27806	-1.0063	10	0.31617	T	0.26	.	3.8406	0.08912	0.4674:0.0:0.1509:0.3817	.	251;258	P31994-3;P31994	.;FCG2B_HUMAN	D	258;251;251;258	ENSP00000356939:Y258D;ENSP00000356937:Y251D;ENSP00000356938:Y251D;ENSP00000351497:Y258D	ENSP00000351497:Y258D	Y	+	1	0	FCGR2B	159911682	0.585000	0.26774	0.642000	0.29436	0.834000	0.47266	0.095000	0.15127	-0.667000	0.05303	-0.384000	0.06662	TAC	T|0.992;G|0.008	0.008	strong		0.612	FCGR2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083337.4	NM_004001	
PLCXD3	345557	hgsc.bcm.edu	37	5	41382536	41382536	+	Silent	SNP	C	C	T	rs16871312	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:41382536C>T	ENST00000377801.3	-	2	278	c.204G>A	c.(202-204)gtG>gtA	p.V68V	PLCXD3_ENST00000328457.3_Silent_p.V68V			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	68	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GCTTTTTGGCCACAGTTCCAA	0.448													C|||	356	0.0710863	0.2632	0.0115	5008	,	,		17078	0.0		0.0	False		,,,				2504	0.0				p.V68V		Atlas-SNP	.											.	PLCXD3	86	.	0			c.G204A						PASS	.	C		1023,3383	371.2+/-319.9	129,765,1309	59.0	65.0	63.0		204	-0.2	1.0	5	dbSNP_123	63	8,8592	4.3+/-15.6	0,8,4292	no	coding-synonymous	PLCXD3	NM_001005473.2		129,773,5601	TT,TC,CC		0.093,23.2183,7.9271		68/322	41382536	1031,11975	2203	4300	6503	SO:0001819	synonymous_variant	345557	exon2			TTTGGCCACAGTT		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.204G>A	5.37:g.41382536C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001005473	A6NL04	Silent	SNP	ENST00000377801.3	37	CCDS34150.1																																																																																			C|0.907;T|0.093	0.093	strong		0.448	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875	
TTN	7273	hgsc.bcm.edu	37	2	179474668	179474668	+	Missense_Mutation	SNP	G	G	A	rs16866412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179474668G>A	ENST00000591111.1	-	222	46783	c.46559C>T	c.(46558-46560)gCg>gTg	p.A15520V	TTN_ENST00000342175.6_Missense_Mutation_p.A8288V|TTN_ENST00000359218.5_Missense_Mutation_p.A8221V|TTN_ENST00000460472.2_Missense_Mutation_p.A8096V|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A17161V|TTN_ENST00000342992.6_Missense_Mutation_p.A14593V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15520	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.		A -> V. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATTGCCTCCGCTGTAGGATT	0.413													G|||	364	0.0726837	0.087	0.0216	5008	,	,		21482	0.1558		0.0209	False		,,,				2504	0.0573				p.A17161V		Atlas-SNP	.											.	TTN	18412	.	0			c.C51482T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	254,3504		8,238,1633	158.0	148.0	151.0		24287,43778,24662,24863	5.7	1.0	2	dbSNP_123	151	108,8118		1,106,4006	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	64,64,64,64	9,344,5639	AA,AG,GG		1.3129,6.7589,3.0207	probably-damaging,probably-damaging,probably-damaging,probably-damaging	8096/26927,14593/33424,8221/27052,8288/27119	179474668	362,11622	1879	4113	5992	SO:0001583	missense	7273	exon272			GCCTCCGCTGTAG	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.46559C>T	2.37:g.179474668G>A	ENSP00000465570:p.Ala15520Val	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	177	79	0.446328	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		159	0.07280219780219781	45	0.09146341463414634	12	0.03314917127071823	89	0.1555944055944056	13	0.017150395778364115	G	16.58	3.162036	0.57368	0.067589	0.013129	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	5.7	5.7	0.88788	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00496	0.0016	L	0.46567	1.45	0.21627	P	0.999615188	D;D;D;D	0.61080	0.98;0.989;0.989;0.98	P;P;P;P	0.54401	0.535;0.751;0.751;0.611	T	0.00837	-1.1546	8	0.87932	D	0	.	19.8424	0.96695	0.0:0.0:1.0:0.0	rs16866412;rs52807556;rs16866412	8096;8221;8288;15520	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	14593;8096;8288;8221;8096	ENSP00000343764:A14593V;ENSP00000434586:A8096V;ENSP00000340554:A8288V;ENSP00000352154:A8221V	ENSP00000340554:A8288V	A	-	2	0	TTN	179182913	1.000000	0.71417	0.975000	0.42487	0.843000	0.47879	9.807000	0.99171	2.673000	0.90976	0.655000	0.94253	GCG	G|0.932;A|0.068	0.068	strong		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RALGPS2	55103	hgsc.bcm.edu	37	1	178745947	178745947	+	Silent	SNP	T	T	G	rs6665037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:178745947T>G	ENST00000367635.3	+	2	386	c.48T>G	c.(46-48)acT>acG	p.T16T	RALGPS2_ENST00000367634.2_Silent_p.T16T	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	16					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TTGCAGCTACTGCTTCTGAGG	0.408													T|||	483	0.0964457	0.1415	0.0648	5008	,	,		13985	0.1012		0.0765	False		,,,				2504	0.0736				p.T16T		Atlas-SNP	.											.	RALGPS2	69	.	0			c.T48G						PASS	.	T		538,3868	245.0+/-254.1	35,468,1700	119.0	103.0	109.0		48	-1.6	1.0	1	dbSNP_116	109	655,7945	165.8+/-217.9	19,617,3664	no	coding-synonymous	RALGPS2	NM_152663.3		54,1085,5364	GG,GT,TT		7.6163,12.2106,9.1727		16/584	178745947	1193,11813	2203	4300	6503	SO:0001819	synonymous_variant	55103	exon2			AGCTACTGCTTCT	AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"""Pleckstrin homology (PH) domain containing"""	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.48T>G	1.37:g.178745947T>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	119	65	0.546219	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Silent	SNP	ENST00000367635.3	37	CCDS1325.1																																																																																			T|0.908;G|0.092	0.092	strong		0.408	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663	
FNDC1	84624	hgsc.bcm.edu	37	6	159647584	159647584	+	Silent	SNP	G	G	A	rs12110595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159647584G>A	ENST00000297267.9	+	9	1352	c.1152G>A	c.(1150-1152)gcG>gcA	p.A384A	FNDC1_ENST00000340366.6_Silent_p.A384A|FNDC1_ENST00000480856.1_3'UTR	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	384	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CTTGGGATGCGCTACCAGAGA	0.473													G|||	264	0.0527157	0.1876	0.0216	5008	,	,		20701	0.001		0.0	False		,,,				2504	0.0				p.A384A		Atlas-SNP	.											.	FNDC1	250	.	0			c.G1152A						PASS	.	G		716,3112		66,584,1264	97.0	94.0	95.0		1152	-10.6	0.0	6	dbSNP_120	95	8,8254		0,8,4123	no	coding-synonymous	FNDC1	NM_032532.2		66,592,5387	AA,AG,GG		0.0968,18.7043,5.9884		384/1895	159647584	724,11366	1914	4131	6045	SO:0001819	synonymous_variant	84624	exon9			GGATGCGCTACCA	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.1152G>A	6.37:g.159647584G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	50	17	0.34	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	111	0.050824175824175824	103	0.20934959349593496	8	0.022099447513812154	0	0.0	0	0.0	G	7.656	0.683920	0.14907	0.187043	9.68E-4	ENSG00000164694	ENST00000329629	T	0.03181	4.02	5.29	-10.6	0.00265	.	0.279587	0.34777	N	0.003696	T	0.00845	0.0028	.	.	.	0.09310	P	0.999999999722547	.	.	.	.	.	.	T	0.17899	-1.0354	6	0.40728	T	0.16	-5.1754	3.7308	0.08492	0.176:0.081:0.3814:0.3616	rs12110595;rs57583348;rs12110595	.	.	.	T	343	ENSP00000333297:A343T	ENSP00000333297:A343T	A	+	1	0	FNDC1	159567572	0.002000	0.14202	0.028000	0.17463	0.773000	0.43773	-1.392000	0.02523	-2.325000	0.00638	-1.283000	0.01379	GCT	G|0.929;A|0.071	0.071	strong		0.473	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
CCDC102B	79839	hgsc.bcm.edu	37	18	66542006	66542006	+	Missense_Mutation	SNP	G	G	T	rs745894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:66542006G>T	ENST00000360242.5	+	5	1154	c.1037G>T	c.(1036-1038)tGt>tTt	p.C346F	CCDC102B_ENST00000358653.5_Missense_Mutation_p.C346F|CCDC102B_ENST00000584156.1_Missense_Mutation_p.C346F|CCDC102B_ENST00000319445.6_Missense_Mutation_p.C346F|CCDC102B_ENST00000577772.1_3'UTR	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	346			C -> F (in dbSNP:rs745894).							breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				AGAGTGATTTGTGAGTTAAGA	0.343													G|||	980	0.195687	0.2882	0.183	5008	,	,		19580	0.1349		0.1382	False		,,,				2504	0.2014				p.C346F		Atlas-SNP	.											.	CCDC102B	92	.	0			c.G1037T						PASS	.	G	PHE/CYS,PHE/CYS	1245,3161	410.6+/-335.4	181,883,1139	94.0	84.0	87.0		1037,1037	-8.9	0.0	18	dbSNP_86	87	1411,7189	260.1+/-283.0	120,1171,3009	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	205,205	301,2054,4148	TT,TG,GG		16.407,28.2569,20.4213	benign,benign	346/514,346/514	66542006	2656,10350	2203	4300	6503	SO:0001583	missense	79839	exon7			TGATTTGTGAGTT	AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 14"", ""aminoacylase 1-like"""	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.1037G>T	18.37:g.66542006G>T	ENSP00000353377:p.Cys346Phe	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	42	16	0.380952	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	388	0.17765567765567766	134	0.27235772357723576	65	0.17955801104972377	72	0.1258741258741259	117	0.15435356200527706	g	0.046	-1.267362	0.01433	0.282569	0.16407	ENSG00000150636	ENST00000319445;ENST00000358653;ENST00000360242	T;T;T	0.18016	2.74;2.24;2.74	4.44	-8.87	0.00792	.	1.308000	0.05188	N	0.502572	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.003	T	0.36744	-0.9735	9	0.51188	T	0.08	1.5173	3.5613	0.07884	0.17:0.2251:0.493:0.112	rs745894;rs52804194;rs60683492;rs745894	346;346	Q68D86-3;Q68D86	.;C102B_HUMAN	F	346	ENSP00000316237:C346F;ENSP00000351479:C346F;ENSP00000353377:C346F	ENSP00000316237:C346F	C	+	2	0	CCDC102B	64692986	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-4.379000	0.00243	-1.839000	0.01186	-0.218000	0.12543	TGT	G|0.804;T|0.196	0.196	strong		0.343	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
EME1	146956	hgsc.bcm.edu	37	17	48453219	48453219	+	Missense_Mutation	SNP	G	G	A	rs114836030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48453219G>A	ENST00000338165.4	+	2	732	c.650G>A	c.(649-651)aGa>aAa	p.R217K	MRPL27_ENST00000507088.1_5'Flank|MRPL27_ENST00000503633.1_5'Flank|EME1_ENST00000393271.2_Missense_Mutation_p.R217K|MRPL27_ENST00000442592.3_5'Flank|MRPL27_ENST00000225969.4_5'Flank|EME1_ENST00000511648.2_Missense_Mutation_p.R217K	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	217					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			CGGCAGCAGAGACAAGCAAGG	0.507								Direct reversal of damage;Homologous recombination					G|||	34	0.00678914	0.0227	0.0058	5008	,	,		22256	0.0		0.0	False		,,,				2504	0.0				p.R217K		Atlas-SNP	.											.	EME1	39	.	0			c.G650A						PASS	.	G	LYS/ARG,LYS/ARG	79,4327	68.7+/-106.4	1,77,2125	82.0	83.0	83.0		650,650	0.3	0.0	17	dbSNP_132	83	0,8600		0,0,4300	yes	missense,missense	EME1	NM_001166131.1,NM_152463.2	26,26	1,77,6425	AA,AG,GG		0.0,1.793,0.6074	benign,benign	217/584,217/571	48453219	79,12927	2203	4300	6503	SO:0001583	missense	146956	exon2			AGCAGAGACAAGC	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.650G>A	17.37:g.48453219G>A	ENSP00000339897:p.Arg217Lys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_152463	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	37	CCDS11565.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	G	0.100	-1.152905	0.01700	0.01793	0.0	ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511648	T;T;T	0.10860	2.83;2.87;2.87	5.11	0.34	0.15985	.	1.089720	0.07057	N	0.833034	T	0.03095	0.0091	L	0.34521	1.04	0.09310	N	1	B;B	0.20052	0.041;0.011	B;B	0.14578	0.011;0.003	T	0.42464	-0.9450	10	0.07644	T	0.81	0.1474	5.5521	0.17095	0.4065:0.1533:0.4403:0.0	.	217;217	Q96AY2-2;Q96AY2	.;EME1_HUMAN	K	217	ENSP00000339897:R217K;ENSP00000376952:R217K;ENSP00000421700:R217K	ENSP00000339897:R217K	R	+	2	0	EME1	45808218	0.000000	0.05858	0.000000	0.03702	0.142000	0.21351	0.423000	0.21313	0.189000	0.20188	-0.145000	0.13849	AGA	G|0.994;A|0.006	0.006	strong		0.507	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
HERC2	8924	hgsc.bcm.edu	37	15	28424100	28424100	+	Silent	SNP	C	C	T	rs9806328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:28424100C>T	ENST00000261609.7	-	59	9204	c.9096G>A	c.(9094-9096)acG>acA	p.T3032T		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)		GGATGGGCACCGTCCCGCTGG	0.612													C|||	716	0.142971	0.5166	0.0375	5008	,	,		11324	0.004		0.001	False		,,,				2504	0.002				p.T3032T		Atlas-SNP	.											.	HERC2	501	.	0			c.G9096A						PASS	.	C		1921,2485	549.9+/-377.9	410,1101,692	82.0	84.0	83.0		9096	-11.2	0.1	15	dbSNP_119	83	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	HERC2	NM_004667.4		410,1108,4985	TT,TC,CC		0.0814,43.5996,14.8239		3032/4835	28424100	1928,11078	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon59			GGGCACCGTCCCG	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.9096G>A	15.37:g.28424100C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			C|0.864;T|0.136	0.136	strong		0.612	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316841	39316841	+	Missense_Mutation	SNP	A	A	T	rs444509|rs535200131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39316841A>T	ENST00000390661.3	-	1	142	c.103T>A	c.(103-105)Tgc>Agc	p.C35S		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	35	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		C -> S (in dbSNP:rs444509).			keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GGGCGGCAGCAGGTGGTCCTG	0.647													A|||	522	0.104233	0.3782	0.0288	5008	,	,		19513	0.0		0.002	False		,,,				2504	0.0				p.C35S		Atlas-SNP	.											.	KRTAP4-4	21	.	0			c.T103A						PASS	.	A	SER/CYS	1206,3164		166,874,1145	38.0	53.0	48.0		103	4.5	1.0	17	dbSNP_80	48	3,8589		0,3,4293	no	missense	KRTAP4-4	NM_032524.1	112	166,877,5438	TT,TA,AA		0.0349,27.5973,9.3273	possibly-damaging	35/167	39316841	1209,11753	2185	4296	6481	SO:0001583	missense	84616	exon1			GGCAGCAGGTGGT	AJ406936	CCDS11383.1	17q21.2	2013-06-25			ENSG00000171396	ENSG00000171396		"""Keratin associated proteins"""	16928	protein-coding gene	gene with protein product			"""keratin associated protein 4-13"""	KRTAP4-13		11279113	Standard	NM_032524		Approved	KAP4.4, KAP4.13	uc002hwc.3	Q9BYR3	OTTHUMG00000133428	ENST00000390661.3:c.103T>A	17.37:g.39316841A>T	ENSP00000375076:p.Cys35Ser	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_032524	Q9BYU7	Missense_Mutation	SNP	ENST00000390661.3	37	CCDS11383.1	187	0.08562271062271062	176	0.35772357723577236	11	0.03038674033149171	0	0.0	0	0.0	.	14.47	2.545823	0.45280	0.275973	3.49E-4	ENSG00000171396	ENST00000390661	T	0.04406	3.63	4.52	4.52	0.55395	.	0.000000	0.44688	U	0.000438	T	0.00012	0.0000	M	0.93150	3.385	0.34592	P	0.28444	P	0.38551	0.636	P	0.47827	0.558	T	0.34179	-0.9839	9	0.44086	T	0.13	.	11.8038	0.52143	1.0:0.0:0.0:0.0	rs444509;rs61402488	35	Q9BYR3	KRA44_HUMAN	S	35	ENSP00000375076:C35S	ENSP00000375076:C35S	C	-	1	0	KRTAP4-4	36570367	1.000000	0.71417	0.961000	0.40146	0.964000	0.63967	2.062000	0.41413	1.660000	0.50760	0.443000	0.29094	TGC	A|0.912;T|0.088	0.088	strong		0.647	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1		
FAM183A	440585	hgsc.bcm.edu	37	1	43621973	43621973	+	Missense_Mutation	SNP	C	C	T	rs59274667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43621973C>T	ENST00000335282.4	+	4	394	c.394C>T	c.(394-396)Cac>Tac	p.H132Y	FAM183A_ENST00000410048.1_Missense_Mutation_p.H104Y|FAM183A_ENST00000409337.1_3'UTR	NM_001101376.2	NP_001094846.2	A6NL82	F183A_HUMAN	family with sequence similarity 183, member A	132										kidney(1)|large_intestine(1)|lung(2)|ovary(3)	7						AGGAGATGATCACCACAAGTA	0.473													C|||	26	0.00519169	0.0197	0.0	5008	,	,		22333	0.0		0.0	False		,,,				2504	0.0				p.H132Y		Atlas-SNP	.											.	FAM183A	28	.	0			c.C394T						PASS	.	C	TYR/HIS	67,3987		1,65,1961	126.0	127.0	127.0		394	-0.6	0.0	1	dbSNP_129	127	0,8370		0,0,4185	yes	missense	FAM183A	NM_001101376.2	83	1,65,6146	TT,TC,CC		0.0,1.6527,0.5393	benign	132/135	43621973	67,12357	2027	4185	6212	SO:0001583	missense	440585	exon4			GATGATCACCACA	AI192630, AI375550, AL139138	CCDS44126.1	1p34.2	2008-08-11			ENSG00000186973	ENSG00000186973			34347	protein-coding gene	gene with protein product						11181995	Standard	NM_001101376		Approved	LOC440585, hCG23177	uc009vwo.3	A6NL82	OTTHUMG00000007286	ENST00000335282.4:c.394C>T	1.37:g.43621973C>T	ENSP00000334415:p.His132Tyr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_001101376	B7ZBL8	Missense_Mutation	SNP	ENST00000335282.4	37	CCDS44126.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	10.05	1.243842	0.22796	0.016527	0.0	ENSG00000186973	ENST00000409706;ENST00000410048;ENST00000409337;ENST00000410025;ENST00000335282	.	.	.	4.08	-0.601	0.11638	.	1.498380	0.03915	N	0.282630	T	0.10637	0.0260	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18272	-1.0342	9	0.49607	T	0.09	.	3.0707	0.06230	0.2209:0.3721:0.0:0.4069	rs59274667;rs61738384	132	A6NL82	F183A_HUMAN	Y	132;104;42;80;132	.	ENSP00000334415:H132Y	H	+	1	0	FAM183A	43394560	0.000000	0.05858	0.000000	0.03702	0.129000	0.20672	-0.229000	0.09098	-0.092000	0.12417	-0.768000	0.03414	CAC	C|0.996;T|0.004	0.004	strong		0.473	FAM183A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019024.3	NM_001101376	
FBN3	84467	hgsc.bcm.edu	37	19	8196643	8196643	+	Silent	SNP	G	G	A	rs61744943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8196643G>A	ENST00000600128.1	-	15	2199	c.1785C>T	c.(1783-1785)cgC>cgT	p.R595R	FBN3_ENST00000601739.1_Silent_p.R595R|FBN3_ENST00000270509.2_Silent_p.R595R			Q75N90	FBN3_HUMAN	fibrillin 3	595	EGF-like 7; 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						GGCACTGGCAGCGGAAGGAGC	0.677													G|||	734	0.146565	0.3684	0.1326	5008	,	,		15157	0.001		0.0944	False		,,,				2504	0.0603				p.R595R		Atlas-SNP	.											.	FBN3	300	.	0			c.C1785T						PASS	.	G		1420,2986		240,940,1023	22.0	22.0	22.0		1785	1.9	0.8	19	dbSNP_129	22	940,7656		58,824,3416	no	coding-synonymous	FBN3	NM_032447.3		298,1764,4439	AA,AG,GG		10.9353,32.2288,18.1511		595/2810	8196643	2360,10642	2203	4298	6501	SO:0001819	synonymous_variant	84467	exon14			CTGGCAGCGGAAG		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.1785C>T	19.37:g.8196643G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	177	81	0.457627	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.823;A|0.177	0.177	strong		0.677	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
CCDC129	223075	hgsc.bcm.edu	37	7	31691582	31691582	+	Missense_Mutation	SNP	G	G	A	rs80081783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:31691582G>A	ENST00000407970.3	+	13	2779	c.2741G>A	c.(2740-2742)cGt>cAt	p.R914H	CCDC129_ENST00000451887.2_Missense_Mutation_p.R940H|CCDC129_ENST00000409210.1_Missense_Mutation_p.R822H|CCDC129_ENST00000319386.3_Missense_Mutation_p.R766H	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	914										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						CAAACGTTACGTGAGGCCCTG	0.478													G|||	30	0.00599042	0.0227	0.0	5008	,	,		17400	0.0		0.0	False		,,,				2504	0.0				p.R940H		Atlas-SNP	.											LOC223075,right_lower_lobe,carcinoma,-1,2	CCDC129	127	2	0			c.G2819A						PASS	.	G	HIS/ARG	56,4350	55.5+/-91.7	0,56,2147	69.0	60.0	63.0		2741	5.2	0.0	7	dbSNP_133	63	0,8600		0,0,4300	yes	missense	CCDC129	NM_194300.2	29	0,56,6447	AA,AG,GG		0.0,1.271,0.4306	probably-damaging	914/1045	31691582	56,12950	2203	4300	6503	SO:0001583	missense	223075	exon13			CGTTACGTGAGGC	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.2741G>A	7.37:g.31691582G>A	ENSP00000384416:p.Arg914His	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	153	77	0.503268	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	26.1	4.700031	0.88924	0.01271	0.0	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	5.21	5.21	0.72293	.	0.000000	0.50627	D	0.000101	T	0.55862	0.1947	M	0.71581	2.175	0.09310	N	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79784	0.966;0.993;0.993;0.984	T	0.59910	-0.7365	10	0.87932	D	0	-17.7013	14.263	0.66097	0.0:0.0:1.0:0.0	.	940;924;914;766	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	H	766;914;940;924;822	ENSP00000313062:R766H;ENSP00000384416:R914H;ENSP00000395835:R940H;ENSP00000387214:R822H	ENSP00000313062:R766H	R	+	2	0	CCDC129	31658107	0.944000	0.32072	0.031000	0.17742	0.664000	0.39144	2.657000	0.46724	2.437000	0.82529	0.561000	0.74099	CGT	G|0.995;A|0.005	0.005	strong		0.478	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
RIN1	9610	hgsc.bcm.edu	37	11	66102088	66102088	+	Silent	SNP	G	G	A	rs3814740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:66102088G>A	ENST00000311320.4	-	6	1308	c.1182C>T	c.(1180-1182)ccC>ccT	p.P394P	RIN1_ENST00000524804.1_5'Flank|RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000424433.2_Silent_p.P289P|RIN1_ENST00000530056.1_Silent_p.P289P	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	394	Ras and 14-3-3 protein binding region.			AGPE -> DGQR (in Ref. 1, 2 and 3). {ECO:0000305}.	associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						CCTGGGGCTCGGGCCCAGCCC	0.721													G|||	740	0.147764	0.3026	0.0836	5008	,	,		11802	0.1399		0.0885	False		,,,				2504	0.0532				p.P394P		Atlas-SNP	.											.	RIN1	64	.	0			c.C1182T						PASS	.	G		1109,3245		154,801,1222	10.0	11.0	11.0		1182	-8.5	0.0	11	dbSNP_107	11	652,7874		43,566,3654	no	coding-synonymous	RIN1	NM_004292.2		197,1367,4876	AA,AG,GG		7.6472,25.4708,13.6724		394/784	66102088	1761,11119	2177	4263	6440	SO:0001819	synonymous_variant	9610	exon6			GGGCTCGGGCCCA	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.1182C>T	11.37:g.66102088G>A		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_004292	O15010|Q00427|Q96CC8	Silent	SNP	ENST00000311320.4	37	CCDS31614.1																																																																																			G|0.847;A|0.153	0.153	strong		0.721	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292	
ERI2	112479	hgsc.bcm.edu	37	16	20809240	20809240	+	Missense_Mutation	SNP	G	G	T	rs61746707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20809240G>T	ENST00000357967.4	-	9	1924	c.1882C>A	c.(1882-1884)Caa>Aaa	p.Q628K	ERI2_ENST00000389345.5_Missense_Mutation_p.Q363K|ERI2_ENST00000563117.1_Missense_Mutation_p.Q535K|ERI2_ENST00000564349.1_Missense_Mutation_p.Q535K|ERI2_ENST00000300005.3_Intron|ERI2_ENST00000569729.1_3'UTR	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	628							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						CTGTTTTCTTGGTATTTCCCG	0.413													G|||	74	0.0147764	0.0545	0.0014	5008	,	,		17542	0.0		0.001	False		,,,				2504	0.0				p.Q628K		Atlas-SNP	.											.	ERI2	50	.	0			c.C1882A						PASS	.	G	LYS/GLN,	53,1331		1,51,640	115.0	94.0	100.0		1882,	3.4	1.0	16	dbSNP_129	100	0,3182		0,0,1591	no	missense,intron	ERI2	NM_001142725.1,NM_080663.2	53,	1,51,2231	TT,TG,GG		0.0,3.8295,1.1608	benign,	628/692,	20809240	53,4513	692	1591	2283	SO:0001583	missense	112479	exon9			TTTCTTGGTATTT	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.1882C>A	16.37:g.20809240G>T	ENSP00000350651:p.Gln628Lys	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	248	114	0.459677	NM_001142725	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Missense_Mutation	SNP	ENST00000357967.4	37	CCDS45436.1	28	0.01282051282051282	28	0.056910569105691054	0	0.0	0	0.0	0	0.0	G	9.624	1.134740	0.21123	0.038295	0.0	ENSG00000196678	ENST00000357967;ENST00000389345	T;T	0.18338	2.26;2.22	5.57	3.44	0.39384	Zinc finger, GRF-type (1);	0.400221	0.26349	N	0.024900	T	0.01029	0.0034	N	0.25245	0.725	0.23204	N	0.99813	B	0.17465	0.022	B	0.15052	0.012	T	0.21586	-1.0241	10	0.33940	T	0.23	-3.6176	8.303	0.32025	0.0:0.2738:0.4857:0.2405	.	628	A8K979	ERI2_HUMAN	K	628;363	ENSP00000350651:Q628K;ENSP00000373996:Q363K	ENSP00000350651:Q628K	Q	-	1	0	ERI2	20716741	0.998000	0.40836	1.000000	0.80357	0.562000	0.35680	2.069000	0.41481	1.450000	0.47717	0.591000	0.81541	CAA	G|0.987;T|0.013	0.013	strong		0.413	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663	
CEP55	55165	hgsc.bcm.edu	37	10	95262890	95262890	+	Silent	SNP	T	T	A	rs61865305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:95262890T>A	ENST00000371485.3	+	3	508	c.204T>A	c.(202-204)gcT>gcA	p.A68A		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	68					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)				TCCTTGAGGCTGAGAAGGAGA	0.383													T|||	128	0.0255591	0.0008	0.0303	5008	,	,		21051	0.0		0.0895	False		,,,				2504	0.0164				p.A68A		Atlas-SNP	.											.	CEP55	35	.	0			c.T204A						PASS	.	T	,	79,4327	69.8+/-107.6	1,77,2125	78.0	74.0	75.0		204,204	2.9	1.0	10	dbSNP_129	75	672,7928	168.8+/-220.3	19,634,3647	no	coding-synonymous,coding-synonymous	CEP55	NM_001127182.1,NM_018131.4	,	20,711,5772	AA,AT,TT		7.814,1.793,5.7743	,	68/465,68/465	95262890	751,12255	2203	4300	6503	SO:0001819	synonymous_variant	55165	exon3			TGAGGCTGAGAAG	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.204T>A	10.37:g.95262890T>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	56	19	0.339286	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Silent	SNP	ENST00000371485.3	37	CCDS7428.1																																																																																			T|0.944;A|0.056	0.056	strong		0.383	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131	
CTBP2	1488	hgsc.bcm.edu	37	10	126715436	126715436	+	Intron	SNP	C	C	T	rs3781411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:126715436C>T	ENST00000337195.5	-	3	458				CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000309035.6_Missense_Mutation_p.R298Q	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		CCCCTCCGCCCGCAGAAAGGC	0.632													C|||	611	0.122005	0.1089	0.2896	5008	,	,		17635	0.0456		0.1352	False		,,,				2504	0.0859				p.R298Q		Atlas-SNP	.											.	CTBP2	100	.	0			c.G893A						PASS	.	C	,,GLN/ARG	449,3957	210.5+/-231.0	18,413,1772	43.0	45.0	44.0		,,893	4.0	1.0	10	dbSNP_107	44	1127,7473	229.1+/-263.9	66,995,3239	yes	intron,intron,missense	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,43	84,1408,5011	TT,TC,CC		13.1047,10.1906,12.1175	,,probably-damaging	,,298/986	126715436	1576,11430	2203	4300	6503	SO:0001627	intron_variant	1488	exon1			TCCGCCCGCAGAA	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12129G>A	10.37:g.126715436C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	202	106	0.524752	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	37	CCDS7643.1	260	0.11904761904761904	48	0.0975609756097561	86	0.23756906077348067	30	0.05244755244755245	96	0.1266490765171504	C	22.1	4.249659	0.80024	0.101906	0.131047	ENSG00000175029	ENST00000309035	D	0.87571	-2.27	4.88	3.96	0.45880	.	0.086330	0.44483	D	0.000446	T	0.00241	0.0007	.	.	.	0.09310	P	1.0	D	0.76494	0.999	P	0.60345	0.873	T	0.00005	-1.2543	8	0.87932	D	0	.	14.1729	0.65522	0.0:0.923:0.0:0.077	rs3781411;rs3781411	298	P56545-2	.	Q	298	ENSP00000311825:R298Q	ENSP00000311825:R298Q	R	-	2	0	CTBP2	126705426	1.000000	0.71417	0.988000	0.46212	0.723000	0.41478	3.859000	0.55987	2.423000	0.82170	0.655000	0.94253	CGG	C|0.882;T|0.118	0.118	strong		0.632	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
OR5L2	26338	hgsc.bcm.edu	37	11	55595018	55595018	+	Silent	SNP	A	A	G	rs61745634|rs34954823|rs386753700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55595018A>G	ENST00000378397.1	+	1	324	c.324A>G	c.(322-324)ggA>ggG	p.G108G		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	108						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G108G(1)		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)				GCACATGTGGAGTCACTGAGG	0.488										HNSCC(27;0.073)			N|||	342	0.0682907	0.0938	0.036	5008	,	,		22005	0.0704		0.0736	False		,,,				2504	0.0491				p.G108G		Atlas-SNP	.											OR5L2,NS,carcinoma,0,2	OR5L2	135	2	1	Substitution - coding silent(1)	stomach(1)	c.A324G						PASS	.						183.0	172.0	176.0					11																	55595018		2197	4293	6490	SO:0001819	synonymous_variant	26338	exon1			ATGTGGAGTCACT	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.324A>G	11.37:g.55595018A>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	135	49	0.362963	NM_001004739	Q6IF66|Q96RB2	Silent	SNP	ENST00000378397.1	37	CCDS31511.1																																																																																			A|0.993;G|0.007	0.007	strong		0.488	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
FRMPD4	9758	hgsc.bcm.edu	37	X	12725701	12725701	+	Silent	SNP	C	C	G	rs6641078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:12725701C>G	ENST00000380682.1	+	13	1907	c.1401C>G	c.(1399-1401)gtC>gtG	p.V467V		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	467	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TTAGCCACGTCAACAGGATCG	0.517													C|||	918	0.243179	0.0106	0.2046	3775	,	,		13918	0.5308		0.0785	False		,,,				2504	0.1513				p.V467V		Atlas-SNP	.											.	FRMPD4	214	.	0			c.C1401G						PASS	.	C		140,3695		0,118,22,1514,549	139.0	116.0	124.0		1401	1.6	1.0	X	dbSNP_116	124	804,5924		38,508,220,1882,1652	no	coding-synonymous	FRMPD4	NM_014728.3		38,626,242,3396,2201	GG,GC,G,CC,C		11.9501,3.6506,8.9369		467/1323	12725701	944,9619	2203	4300	6503	SO:0001819	synonymous_variant	9758	exon13			CCACGTCAACAGG	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.1401C>G	X.37:g.12725701C>G		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	210	98	0.466667	NM_014728	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	37	CCDS35201.1																																																																																			C|0.852;G|0.148	0.148	strong		0.517	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712	
C7orf65	401335	hgsc.bcm.edu	37	7	47698737	47698737	+	Missense_Mutation	SNP	A	A	C	rs114109572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47698737A>C	ENST00000408988.2	+	3	402	c.367A>C	c.(367-369)Act>Cct	p.T123P		NM_001123065.1	NP_001116537.1	Q6ZTY9	CG065_HUMAN	chromosome 7 open reading frame 65	123										endometrium(1)|lung(2)	3						AAATGGTTTCACTGACCCCTG	0.537													A|||	8	0.00159744	0.0061	0.0	5008	,	,		19526	0.0		0.0	False		,,,				2504	0.0				p.T123P		Atlas-SNP	.											.	C7orf65	18	.	0			c.A367C						PASS	.	A	PRO/THR	16,3120		0,16,1552	126.0	114.0	118.0		367	0.6	0.0	7	dbSNP_132	118	0,7164		0,0,3582	yes	missense	C7orf65	NM_001123065.1	38	0,16,5134	CC,CA,AA		0.0,0.5102,0.1553	probably-damaging	123/152	47698737	16,10284	1568	3582	5150	SO:0001583	missense	401335	exon3			GGTTTCACTGACC		CCDS43580.1	7p12.3	2009-02-11			ENSG00000221845	ENSG00000221845			34432	protein-coding gene	gene with protein product							Standard	NM_001123065		Approved	FLJ44108	uc010kyp.1	Q6ZTY9	OTTHUMG00000155550	ENST00000408988.2:c.367A>C	7.37:g.47698737A>C	ENSP00000386198:p.Thr123Pro	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_001123065	A4D2F8	Missense_Mutation	SNP	ENST00000408988.2	37	CCDS43580.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	6.306	0.424633	0.11928	0.005102	0.0	ENSG00000221845	ENST00000408988	.	.	.	0.559	0.559	0.17272	.	.	.	.	.	T	0.26011	0.0634	N	0.08118	0	0.09310	N	1	D	0.69078	0.997	D	0.68483	0.958	T	0.16928	-1.0386	7	0.87932	D	0	.	.	.	.	.	123	Q6ZTY9	CG065_HUMAN	P	123	.	ENSP00000386198:T123P	T	+	1	0	C7orf65	47665262	0.000000	0.05858	0.008000	0.14137	0.008000	0.06430	0.017000	0.13399	0.469000	0.27268	0.459000	0.35465	ACT	A|0.999;C|0.001	0.001	strong		0.537	C7orf65-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340616.1	NM_001123065	
XRCC4	7518	hgsc.bcm.edu	37	5	82648977	82648977	+	Silent	SNP	T	T	G	rs1056503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82648977T>G	ENST00000511817.1	+	8	1007	c.927T>G	c.(925-927)tcT>tcG	p.S309S	XRCC4_ENST00000282268.3_Silent_p.S307S|XRCC4_ENST00000396027.4_Silent_p.S307S|XRCC4_ENST00000338635.6_Silent_p.S309S			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	309					cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		CTGAGACGTCTAAAAAGGAGC	0.338								Non-homologous end-joining					G|||	1881	0.375599	0.4758	0.3329	5008	,	,		17355	0.7063		0.1402	False		,,,				2504	0.1718				p.S309S		Atlas-SNP	.											.	XRCC4	37	.	0			c.T927G						PASS	.	G	,,	1942,2464	617.9+/-393.1	424,1094,685	113.0	123.0	120.0		921,927,921	1.1	0.0	5	dbSNP_86	120	1055,7543	768.5+/-407.6	63,929,3307	no	coding-synonymous,coding-synonymous,coding-synonymous	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	,,	487,2023,3992	GG,GT,TT		12.2703,44.0763,23.0468	,,	307/335,309/337,307/335	82648977	2997,10007	2203	4299	6502	SO:0001819	synonymous_variant	7518	exon8			GACGTCTAAAAAG	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.927T>G	5.37:g.82648977T>G		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	240	113	0.470833	NM_022406	A8K3X4|Q9BS72|Q9UP94	Silent	SNP	ENST00000511817.1	37	CCDS4059.1																																																																																			T|0.685;G|0.315	0.315	strong		0.338	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	
FAM78B	149297	hgsc.bcm.edu	37	1	166039898	166039898	+	Silent	SNP	C	C	G	rs41269662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	67	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	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	
APOF	319	hgsc.bcm.edu	37	12	56755300	56755300	+	Silent	SNP	A	A	C	rs11575217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56755300A>C	ENST00000398189.3	-	2	767	c.690T>G	c.(688-690)gcT>gcG	p.A230A	APOF_ENST00000541105.1_Silent_p.A212A|STAT2_ENST00000418572.2_5'Flank|STAT2_ENST00000557235.1_5'Flank|STAT2_ENST00000314128.4_5'Flank	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	230					cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|high-density lipoprotein particle (GO:0034364)|low-density lipoprotein particle (GO:0034362)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)|receptor binding (GO:0005102)			breast(1)|lung(3)|prostate(1)|stomach(1)	6						CTGACATCCCAGCCATGGTCA	0.517													A|||	212	0.0423323	0.1528	0.0144	5008	,	,		20580	0.0		0.0	False		,,,				2504	0.0				p.A230A		Atlas-SNP	.											.	APOF	13	.	0			c.T690G						PASS	.	A		449,3449		26,397,1526	68.0	70.0	69.0		690	-11.0	0.0	12	dbSNP_120	69	0,8286		0,0,4143	no	coding-synonymous	APOF	NM_001638.2		26,397,5669	CC,CA,AA		0.0,11.5187,3.6852		230/327	56755300	449,11735	1949	4143	6092	SO:0001819	synonymous_variant	319	exon2			CATCCCAGCCATG	L27050	CCDS44923.1	12q13	2013-01-24				ENSG00000175336		"""Apolipoproteins"""	615	protein-coding gene	gene with protein product		107760				8093033	Standard	NM_001638		Approved		uc001sle.1	Q13790		ENST00000398189.3:c.690T>G	12.37:g.56755300A>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	126	53	0.420635	NM_001638	Q8TC13	Silent	SNP	ENST00000398189.3	37	CCDS44923.1																																																																																			A|0.945;C|0.055	0.055	strong		0.517	APOF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410076.1		
LAIR2	3904	hgsc.bcm.edu	37	19	55019371	55019371	+	Missense_Mutation	SNP	C	C	G	rs61737870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55019371C>G	ENST00000301202.2	+	3	458	c.336C>G	c.(334-336)caC>caG	p.H112Q	LAIR2_ENST00000351841.2_Missense_Mutation_p.H112Q	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	112	Ig-like C2-type.					extracellular region (GO:0005576)				central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		GGTCTGAGCACAGTGACTTCC	0.562													C|||	486	0.0970447	0.2405	0.0749	5008	,	,		17558	0.0079		0.0547	False		,,,				2504	0.0542				p.H112Q		Atlas-SNP	.											.	LAIR2	30	.	0			c.C336G						PASS	.	C	GLN/HIS,GLN/HIS	966,3440	365.4+/-317.4	113,740,1350	96.0	97.0	97.0		336,336	-1.5	0.0	19	dbSNP_129	97	405,8195	128.0+/-186.3	15,375,3910	yes	missense,missense	LAIR2	NM_002288.4,NM_021270.3	24,24	128,1115,5260	GG,GC,CC		4.7093,21.9246,10.5413	benign,benign	112/153,112/136	55019371	1371,11635	2203	4300	6503	SO:0001583	missense	3904	exon3			TGAGCACAGTGAC	AF013250	CCDS12897.1, CCDS12898.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167618	ENSG00000167618		"""Leukocyte-associated Ig like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6478	protein-coding gene	gene with protein product		602993	"""leukocyte-associated Ig-like receptor 2"""			9285412	Standard	XM_005277264		Approved	CD306	uc002qgc.3	Q6ISS4	OTTHUMG00000065697	ENST00000301202.2:c.336C>G	19.37:g.55019371C>G	ENSP00000301202:p.His112Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	NM_002288	Q6PEZ4	Missense_Mutation	SNP	ENST00000301202.2	37	CCDS12897.1	188	0.08608058608058608	110	0.22357723577235772	37	0.10220994475138122	3	0.005244755244755245	38	0.05013192612137203	C	6.372	0.436742	0.12104	0.219246	0.047093	ENSG00000167618	ENST00000301202;ENST00000351841	T;T	0.10477	2.87;2.87	3.77	-1.47	0.08772	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.651870	0.03450	N	0.210525	T	0.00012	0.0000	L	0.31752	0.955	0.58432	P	1.0000000000287557E-6	B;B	0.12013	0.002;0.005	B;B	0.12156	0.007;0.007	T	0.43734	-0.9373	8	.	.	.	.	2.9927	0.05988	0.349:0.4225:0.0:0.2286	rs61737870	112;112	Q6ISS4-2;Q6ISS4	.;LAIR2_HUMAN	Q	112	ENSP00000301202:H112Q;ENSP00000301203:H112Q	.	H	+	3	2	LAIR2	59711183	0.045000	0.20229	0.005000	0.12908	0.029000	0.11900	0.010000	0.13242	-0.256000	0.09473	0.313000	0.20887	CAC	C|0.897;G|0.103	0.103	strong		0.562	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1		
CD6	923	hgsc.bcm.edu	37	11	60776209	60776209	+	Missense_Mutation	SNP	C	C	T	rs11230563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000452451.2_Missense_Mutation_p.R225W|CD6_ENST00000346437.4_Missense_Mutation_p.R225W|CD6_ENST00000352009.5_Missense_Mutation_p.R225W|CD6_ENST00000545105.1_Intron	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	89	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	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	
CSMD3	114788	hgsc.bcm.edu	37	8	114111156	114111156	+	Missense_Mutation	SNP	C	C	T	rs73701331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:114111156C>T	ENST00000297405.5	-	5	990	c.746G>A	c.(745-747)aGt>aAt	p.S249N	CSMD3_ENST00000519485.1_5'UTR|CSMD3_ENST00000343508.3_Missense_Mutation_p.S209N|CSMD3_ENST00000352409.3_Missense_Mutation_p.S249N|CSMD3_ENST00000455883.2_Missense_Mutation_p.S249N	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	249	CUB 2. {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						TATGATGCCACTGGATCCTCT	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			C|||	47	0.00938498	0.034	0.0	5008	,	,		16287	0.002		0.0	False		,,,				2504	0.0				p.S249N		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G746A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER	106,4300	82.9+/-121.4	2,102,2099	124.0	107.0	112.0		746,746,626	5.3	1.0	8	dbSNP_130	112	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	46,46,46	2,103,6398	TT,TC,CC		0.0116,2.4058,0.8227	possibly-damaging,possibly-damaging,possibly-damaging	249/3539,249/3708,209/3668	114111156	107,12899	2203	4300	6503	SO:0001583	missense	114788	exon5			ATGCCACTGGATC	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.746G>A	8.37:g.114111156C>T	ENSP00000297405:p.Ser249Asn	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_052900	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	15	0.006868131868131868	14	0.028455284552845527	0	0.0	1	0.0017482517482517483	0	0.0	C	17.36	3.370151	0.61624	0.024058	1.16E-4	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.32	5.32	0.75619	CUB (5);	0.058984	0.64402	D	0.000003	T	0.09686	0.0238	L	0.27944	0.81	0.30352	N	0.784714	P;P;D;P	0.65815	0.763;0.844;0.995;0.753	B;B;D;P	0.75020	0.288;0.445;0.985;0.671	T	0.05920	-1.0856	10	0.02654	T	1	.	19.3517	0.94389	0.0:1.0:0.0:0.0	.	249;249;249;209	Q7Z407-3;Q7Z407-4;Q7Z407;Q7Z407-2	.;.;CSMD3_HUMAN;.	N	209;249;249;249	ENSP00000345799:S209N;ENSP00000297405:S249N;ENSP00000412263:S249N;ENSP00000343124:S249N	ENSP00000297405:S249N	S	-	2	0	CSMD3	114180332	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.889000	0.63171	2.660000	0.90430	0.591000	0.81541	AGT	C|0.990;T|0.010	0.010	strong		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
CASC1	55259	hgsc.bcm.edu	37	12	25267613	25267613	+	Missense_Mutation	SNP	T	T	C	rs34164267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25267613T>C	ENST00000320267.9	-	12	1651	c.1570A>G	c.(1570-1572)Act>Gct	p.T524A	CASC1_ENST00000545133.1_Missense_Mutation_p.T465A|CASC1_ENST00000354189.5_Missense_Mutation_p.T588A|CASC1_ENST00000395990.2_Missense_Mutation_p.T484A|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000537577.1_Missense_Mutation_p.T412A|CASC1_ENST00000395987.3_Missense_Mutation_p.T530A	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	524										breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			TGAATCTCAGTAAATACTGTA	0.338													T|||	156	0.0311502	0.1006	0.0259	5008	,	,		18744	0.0		0.004	False		,,,				2504	0.001				p.T588A		Atlas-SNP	.											.	CASC1	146	.	0			c.A1762G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	351,4055	182.2+/-210.1	14,323,1866	71.0	66.0	67.0		1762,1570,1393,1450,1588	1.7	0.2	12	dbSNP_126	67	42,8558	27.9+/-77.7	1,40,4259	yes	missense,missense,missense,missense,missense	CASC1	NM_001082972.1,NM_001082973.1,NM_001204101.1,NM_001204102.1,NM_018272.3	58,58,58,58,58	15,363,6125	CC,CT,TT		0.4884,7.9664,3.0217	benign,benign,benign,benign,benign	588/691,524/717,465/658,484/677,530/723	25267613	393,12613	2203	4300	6503	SO:0001583	missense	55259	exon13			TCTCAGTAAATAC	AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 54"""					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.1570A>G	12.37:g.25267613T>C	ENSP00000313141:p.Thr524Ala	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_001082972	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Missense_Mutation	SNP	ENST00000320267.9	37	CCDS41762.1	57|57	0.0260989010989011|0.0260989010989011	44|44	0.08943089430894309|0.08943089430894309	12|12	0.03314917127071823|0.03314917127071823	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	T|T	5.664|5.664	0.307097|0.307097	0.10733|0.10733	0.079664|0.079664	0.004884|0.004884	ENSG00000118307|ENSG00000118307	ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395990;ENST00000537577;ENST00000545133;ENST00000389246|ENST00000556006	T;T;T;T;T|.	0.41400|.	1.0;1.65;1.65;1.05;1.05|.	5.62|5.62	1.68|1.68	0.24146|0.24146	.|.	0.413227|.	0.28683|.	N|.	0.014485|.	T|T	0.00754|0.00754	0.0025|0.0025	N|N	0.16478|0.16478	0.41|0.41	0.19575|0.19575	N|N	0.999966|0.999966	B;B;B;B;B|.	0.25441|.	0.005;0.005;0.126;0.003;0.005|.	B;B;B;B;B|.	0.22386|.	0.014;0.013;0.039;0.003;0.022|.	T|T	0.16129|0.16129	-1.0413|-1.0413	10|5	0.22109|.	T|.	0.4|.	-3.2308|-3.2308	8.0803|8.0803	0.30741|0.30741	0.0:0.409:0.0:0.5909|0.0:0.409:0.0:0.5909	rs34164267|rs34164267	412;465;588;524;530|.	F5H555;F5H6T6;Q6TDU7-3;Q6TDU7;F8W8F9|.	.;.;.;CASC1_HUMAN;.|.	A|C	588;530;524;484;412;465;334|360	ENSP00000346126:T588A;ENSP00000379310:T530A;ENSP00000313141:T524A;ENSP00000379313:T484A;ENSP00000437373:T465A|.	ENSP00000313141:T524A|.	T|Y	-|-	1|2	0|0	CASC1|CASC1	25158880|25158880	0.999000|0.999000	0.42202|0.42202	0.170000|0.170000	0.22879|0.22879	0.887000|0.887000	0.51463|0.51463	0.870000|0.870000	0.28010|0.28010	0.092000|0.092000	0.17331|0.17331	0.533000|0.533000	0.62120|0.62120	ACT|TAC	T|0.970;C|0.030	0.030	strong		0.338	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272	
PHC2	1912	hgsc.bcm.edu	37	1	33820520	33820520	+	Silent	SNP	G	G	A	rs79627057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:33820520G>A	ENST00000257118.5	-	7	1364	c.1311C>T	c.(1309-1311)ccC>ccT	p.P437P	PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000431992.1_Silent_p.P408P|PHC2_ENST00000373422.3_Silent_p.P42P|RP11-415J8.5_ENST00000432703.1_RNA|PHC2_ENST00000419414.2_Silent_p.P437P	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	437					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GCACGCCCTCGGGATGTCCAT	0.607													G|||	94	0.01877	0.0651	0.0115	5008	,	,		18903	0.0		0.0	False		,,,				2504	0.0				p.P437P		Atlas-SNP	.											.	PHC2	78	.	0			c.C1311T						PASS	.	G		237,4169	140.4+/-175.9	12,213,1978	72.0	69.0	70.0		1311	-8.6	0.4	1	dbSNP_131	70	0,8600		0,0,4300	no	coding-synonymous	PHC2	NM_198040.2		12,213,6278	AA,AG,GG		0.0,5.379,1.8222		437/859	33820520	237,12769	2203	4300	6503	SO:0001819	synonymous_variant	1912	exon7			GCCCTCGGGATGT	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.1311C>T	1.37:g.33820520G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Silent	SNP	ENST00000257118.5	37	CCDS378.1																																																																																			G|0.981;A|0.019	0.019	strong		0.607	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040	
FCRL2	79368	hgsc.bcm.edu	37	1	157736673	157736673	+	Silent	SNP	C	C	T	rs34445670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157736673C>T	ENST00000361516.3	-	7	1299	c.1251G>A	c.(1249-1251)ctG>ctA	p.L417L	FCRL2_ENST00000368181.4_Silent_p.L133L|FCRL2_ENST00000392274.3_Silent_p.L417L|FCRL2_ENST00000469986.1_Silent_p.L164L	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	417					cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGGCATACAACAGCAAAGCAA	0.418													C|||	92	0.0183706	0.0643	0.0086	5008	,	,		19517	0.0		0.001	False		,,,				2504	0.0				p.L417L		Atlas-SNP	.											.	FCRL2	104	.	0			c.G1251A						PASS	.	C		271,4135	152.5+/-186.2	9,253,1941	135.0	126.0	129.0		1251	-0.2	0.0	1	dbSNP_126	129	0,8600		0,0,4300	no	coding-synonymous	FCRL2	NM_030764.3		9,253,6241	TT,TC,CC		0.0,6.1507,2.0837		417/509	157736673	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	79368	exon7			ATACAACAGCAAA	AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14875	protein-coding gene	gene with protein product		606509	"""SH2 domain-containing phosphatase anchor protein 1"""	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.1251G>A	1.37:g.157736673C>T		Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	336	150	0.446429	NM_030764	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Silent	SNP	ENST00000361516.3	37	CCDS1168.1																																																																																			C|0.983;T|0.017	0.017	strong		0.418	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764	
METTL11B	149281	hgsc.bcm.edu	37	1	170136808	170136808	+	Silent	SNP	G	G	T	rs61745740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:170136808G>T	ENST00000439373.2	+	4	869	c.762G>T	c.(760-762)ctG>ctT	p.L254L		NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	254						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						AGAGTGGGCTGGTGGTGCTGG	0.577													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18267	0.0		0.0	False		,,,				2504	0.0				p.L254L		Atlas-SNP	.											.	METTL11B	18	.	0			c.G762T						PASS	.	G		16,1368		0,16,676	53.0	54.0	54.0		762	5.2	1.0	1	dbSNP_129	54	0,3182		0,0,1591	no	coding-synonymous	METTL11B	NM_001136107.1		0,16,2267	TT,TG,GG		0.0,1.1561,0.3504		254/284	170136808	16,4550	692	1591	2283	SO:0001819	synonymous_variant	149281	exon4			TGGGCTGGTGGTG	AL445203, CAH72139	CCDS44275.1	1q24.2	2012-11-05	2008-06-11	2008-06-11	ENSG00000203740	ENSG00000203740			31932	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 184"""	C1orf184			Standard	NM_001136107		Approved	HOMT1B	uc009wvv.1	Q5VVY1	OTTHUMG00000035959	ENST00000439373.2:c.762G>T	1.37:g.170136808G>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_001136107	B2RXI0	Silent	SNP	ENST00000439373.2	37	CCDS44275.1																																																																																			G|0.999;T|0.001	0.001	strong		0.577	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
OR4D9	390199	hgsc.bcm.edu	37	11	59282685	59282685	+	Silent	SNP	A	A	G	rs76175424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59282685A>G	ENST00000329328.3	+	1	300	c.300A>G	c.(298-300)caA>caG	p.Q100Q		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	100						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(14)|prostate(5)|upper_aerodigestive_tract(1)	26						GTGTCACTCAAATGTTCTTCT	0.463													G|||	180	0.0359425	0.1331	0.0058	5008	,	,		19738	0.0		0.0	False		,,,				2504	0.0				p.Q100Q		Atlas-SNP	.											.	OR4D9	47	.	0			c.A300G						PASS	.	G		451,3951	784.6+/-414.7	18,415,1768	98.0	95.0	96.0		300	0.5	0.1	11	dbSNP_131	96	2,8588	818.8+/-406.8	0,2,4293	no	coding-synonymous	OR4D9	NM_001004711.1		18,417,6061	GG,GA,AA		0.0233,10.2453,3.4868		100/315	59282685	453,12539	2201	4295	6496	SO:0001819	synonymous_variant	390199	exon1			CACTCAAATGTTC	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"""GPCR / Class A : Olfactory receptors"""	15178	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily D, member 9 pseudogene"""				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.300A>G	11.37:g.59282685A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	169	87	0.514793	NM_001004711	Q6IFF3	Silent	SNP	ENST00000329328.3	37	CCDS31564.1																																																																																			A|0.966;G|0.034	0.034	strong		0.463	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711	
CATSPER3	347732	hgsc.bcm.edu	37	5	134343799	134343799	+	Silent	SNP	A	A	G	rs177252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134343799A>G	ENST00000282611.6	+	4	731	c.645A>G	c.(643-645)gcA>gcG	p.A215A		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	215					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACCTGGCTGCAGCTTTTTTCA	0.542													G|||	2549	0.508986	0.6415	0.4078	5008	,	,		15572	0.5615		0.3191	False		,,,				2504	0.5429				p.A215A		Atlas-SNP	.											.	CATSPER3	38	.	0			c.A645G						PASS	.	G		2542,1864	536.5+/-374.5	734,1074,395	117.0	105.0	109.0		645	-0.7	0.0	5	dbSNP_79	109	2576,6024	689.8+/-404.4	382,1812,2106	no	coding-synonymous	CATSPER3	NM_178019.2		1116,2886,2501	GG,GA,AA		29.9535,42.3059,39.3511		215/399	134343799	5118,7888	2203	4300	6503	SO:0001819	synonymous_variant	347732	exon4			GGCTGCAGCTTTT	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.645A>G	5.37:g.134343799A>G		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	257	113	0.439689	NM_178019	Q86XS6	Silent	SNP	ENST00000282611.6	37	CCDS4181.1																																																																																			A|0.562;G|0.438	0.438	strong		0.542	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
PPFIBP2	8495	hgsc.bcm.edu	37	11	7673015	7673015	+	Silent	SNP	G	G	A	rs5864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7673015G>A	ENST00000299492.4	+	23	2764	c.2376G>A	c.(2374-2376)gaG>gaA	p.E792E	PPFIBP2_ENST00000533792.1_Silent_p.E634E|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000528883.1_Silent_p.E680E|PPFIBP2_ENST00000530181.1_Silent_p.E649E	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	792					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CTGAACAGGAGAAGCGAGAGA	0.582													A|||	3308	0.660543	0.7466	0.6138	5008	,	,		19890	0.6012		0.6392	False		,,,				2504	0.6605				p.E792E		Atlas-SNP	.											PPFIBP2,NS,carcinoma,+2,1	PPFIBP2	87	1	0			c.G2376A						PASS	.	A		3235,1167	410.6+/-335.4	1170,895,136	133.0	127.0	129.0		2376	2.2	1.0	11	dbSNP_52	129	5730,2862	449.3+/-362.1	1925,1880,491	no	coding-synonymous	PPFIBP2	NM_003621.2		3095,2775,627	AA,AG,GG		33.3101,26.5107,31.0066		792/877	7673015	8965,4029	2201	4296	6497	SO:0001819	synonymous_variant	8495	exon23			ACAGGAGAAGCGA	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.2376G>A	11.37:g.7673015G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	64	20	0.3125	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Silent	SNP	ENST00000299492.4	37	CCDS31419.1	1444	0.6611721611721612	368	0.7479674796747967	227	0.6270718232044199	359	0.6276223776223776	490	0.6464379947229552	A	8.368	0.834661	0.16820	0.734893	0.666899	ENSG00000166387	ENST00000534552	.	.	.	5.77	2.16	0.27623	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.33163	-0.9879	5	0.37606	T	0.19	-23.889	8.9551	0.35812	0.6941:0.0:0.3059:0.0	rs5864;rs1128011;rs17187285;rs17348501;rs17851927;rs57460904;rs5864	.	.	.	K	24	.	ENSP00000436489:E24K	E	+	1	0	PPFIBP2	7629591	1.000000	0.71417	0.998000	0.56505	0.876000	0.50452	2.058000	0.41374	-0.044000	0.13491	-0.254000	0.11334	GAA	G|0.325;A|0.675	0.675	strong		0.582	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
AKAP12	9590	hgsc.bcm.edu	37	6	151674270	151674270	+	Missense_Mutation	SNP	G	G	A	rs34713284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:151674270G>A	ENST00000253332.1	+	3	4933	c.4744G>A	c.(4744-4746)Gtg>Atg	p.V1582M	AKAP12_ENST00000359755.5_Missense_Mutation_p.V1477M|AKAP12_ENST00000354675.6_Missense_Mutation_p.V1484M|AKAP12_ENST00000402676.2_Missense_Mutation_p.V1582M			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1582				V -> M (in Ref. 4; CAH18338 and 7; AAA35931). {ECO:0000305}.	G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		ACAAGCTCACGTGATAAAAGC	0.483													G|||	395	0.0788738	0.0537	0.0764	5008	,	,		22475	0.0099		0.0895	False		,,,				2504	0.1748				p.V1582M	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.G4744A						PASS	.	G	MET/VAL,MET/VAL	225,4181	136.5+/-172.5	1,223,1979	86.0	86.0	86.0		4744,4450	-5.1	0.0	6	dbSNP_126	86	773,7827	183.7+/-231.9	31,711,3558	yes	missense,missense	AKAP12	NM_005100.3,NM_144497.2	21,21	32,934,5537	AA,AG,GG		8.9884,5.1067,7.6734	benign,benign	1582/1783,1484/1685	151674270	998,12008	2203	4300	6503	SO:0001583	missense	9590	exon4			GCTCACGTGATAA	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.4744G>A	6.37:g.151674270G>A	ENSP00000253332:p.Val1582Met	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	133	0.060897435897435896	30	0.06097560975609756	28	0.07734806629834254	8	0.013986013986013986	67	0.08839050131926121	G	8.712	0.912287	0.17907	0.051067	0.089884	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.08634	3.07;3.07;3.09;3.09	5.01	-5.13	0.02884	.	3.546040	0.01076	N	0.004913	T	0.01287	0.0042	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.17465	0.021;0.021;0.022	B;B;B	0.12156	0.007;0.007;0.003	T	0.44620	-0.9316	9	0.46703	T	0.11	.	2.9664	0.05909	0.1834:0.217:0.4193:0.1803	rs34713284;rs61748677	1477;1484;1582	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	M	1582;1582;1484;1477	ENSP00000384537:V1582M;ENSP00000253332:V1582M;ENSP00000346702:V1484M;ENSP00000352794:V1477M	ENSP00000253332:V1582M	V	+	1	0	AKAP12	151715963	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.048000	0.03517	-0.603000	0.05767	-2.616000	0.00158	GTG	G|0.924;A|0.076	0.076	strong		0.483	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
RECQL5	9400	hgsc.bcm.edu	37	17	73625286	73625286	+	Silent	SNP	G	G	A	rs820190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73625286G>A	ENST00000317905.5	-	16	2376	c.2217C>T	c.(2215-2217)agC>agT	p.S739S	RECQL5_ENST00000443199.2_5'UTR|RECQL5_ENST00000423245.2_Silent_p.S712S	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	739					chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)			breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			TGGCAAGGGAGCTGCCCCCAG	0.647								Other identified genes with known or suspected DNA repair function					G|||	1144	0.228435	0.2247	0.2118	5008	,	,		16511	0.1577		0.3439	False		,,,				2504	0.1994				p.S739S		Atlas-SNP	.											.	RECQL5	77	.	0			c.C2217T						PASS	.	G		843,3013		99,645,1184	31.0	34.0	33.0		2217	-7.5	0.0	17	dbSNP_86	33	2670,5558		429,1812,1873	no	coding-synonymous	RECQL5	NM_004259.6		528,2457,3057	AA,AG,GG		32.4502,21.862,29.0715		739/992	73625286	3513,8571	1928	4114	6042	SO:0001819	synonymous_variant	9400	exon16			AAGGGAGCTGCCC	AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"""RecQ protein 5"""	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.2217C>T	17.37:g.73625286G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Silent	SNP	ENST00000317905.5	37	CCDS42380.1																																																																																			G|0.746;A|0.254	0.254	strong		0.647	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
TMEM132B	114795	hgsc.bcm.edu	37	12	125834095	125834095	+	Silent	SNP	C	C	A	rs1491893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125834095C>A	ENST00000299308.3	+	2	158	c.150C>A	c.(148-150)tcC>tcA	p.S50S	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	50						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)		CAGAGGAGTCCTTTTTCCTTA	0.532													C|||	1374	0.274361	0.1838	0.3458	5008	,	,		17454	0.2728		0.3012	False		,,,				2504	0.32				p.S50S		Atlas-SNP	.											.	TMEM132B	207	.	0			c.C150A						PASS	.	C		793,3097		79,635,1231	132.0	133.0	132.0		150	2.0	0.4	12	dbSNP_88	132	2441,5849		364,1713,2068	no	coding-synonymous	TMEM132B	NM_052907.2		443,2348,3299	AA,AC,CC		29.4451,20.3856,26.5517		50/1079	125834095	3234,8946	1945	4145	6090	SO:0001819	synonymous_variant	114795	exon2			GGAGTCCTTTTTC	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.150C>A	12.37:g.125834095C>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	196	95	0.484694	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																			C|0.737;A|0.262	0.262	strong		0.532	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
TTC29	83894	hgsc.bcm.edu	37	4	147788709	147788709	+	Missense_Mutation	SNP	C	C	T	rs10013280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:147788709C>T	ENST00000325106.4	-	8	1052	c.826G>A	c.(826-828)Gcc>Acc	p.A276T	TTC29_ENST00000513335.1_Missense_Mutation_p.A302T|TTC29_ENST00000398886.4_Missense_Mutation_p.A302T	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	276			A -> T (in dbSNP:rs10013280). {ECO:0000269|Ref.1, ECO:0000269|Ref.2}.					p.A276T(1)		breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					TAGTAAGAGGCTTCCGCTTCC	0.323													C|||	2045	0.408347	0.4478	0.3963	5008	,	,		14931	0.4067		0.3022	False		,,,				2504	0.4744				p.A276T		Atlas-SNP	.											TTC29,NS,carcinoma,0,1	TTC29	63	1	1	Substitution - Missense(1)	prostate(1)	c.G826A						scavenged	.	C	THR/ALA	1461,2169		277,907,631	61.0	59.0	60.0		826	5.4	1.0	4	dbSNP_119	60	2499,5653		385,1729,1962	yes	missense	TTC29	NM_031956.2	58	662,2636,2593	TT,TC,CC		30.6551,40.2479,33.6106	possibly-damaging	276/476	147788709	3960,7822	1815	4076	5891	SO:0001583	missense	83894	exon8			AAGAGGCTTCCGC	AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"""Tetratricopeptide (TTC) repeat domain containing"""	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.826G>A	4.37:g.147788709C>T	ENSP00000316740:p.Ala276Thr	Somatic	252	2	0.00793651		WXS	Illumina HiSeq	Phase_I	274	142	0.518248	NM_031956	A4GU95|Q9BXB6	Missense_Mutation	SNP	ENST00000325106.4	37	CCDS47141.1	756	0.34615384615384615	187	0.3800813008130081	127	0.35082872928176795	221	0.38636363636363635	221	0.29155672823219	C	18.13	3.554978	0.65425	0.402479	0.306551	ENSG00000137473	ENST00000513335;ENST00000398886;ENST00000325106;ENST00000398883;ENST00000504425	T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17	5.45	5.45	0.79879	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.75777	2.31	0.21675	P	0.999592008	D;D;D	0.89917	0.999;1.0;0.999	P;D;P	0.80764	0.863;0.994;0.863	T	0.00717	-1.1596	9	0.49607	T	0.09	-12.7436	19.6493	0.95794	0.0:1.0:0.0:0.0	rs10013280;rs17852200;rs52832245;rs59208732;rs10013280	276;302;276	E7EQ14;G5E9Z5;Q8NA56	.;.;TTC29_HUMAN	T	302;302;276;276;276	ENSP00000423505:A302T;ENSP00000381861:A302T;ENSP00000316740:A276T;ENSP00000425778:A276T	ENSP00000316740:A276T	A	-	1	0	TTC29	148008159	1.000000	0.71417	0.989000	0.46669	0.066000	0.16364	3.914000	0.56401	2.711000	0.92665	0.591000	0.81541	GCC	C|0.648;T|0.352	0.352	strong		0.323	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956	
CHPF	79586	hgsc.bcm.edu	37	2	220404726	220404726	+	Silent	SNP	G	G	A	rs1043832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220404726G>A	ENST00000243776.6	-	4	1955	c.1707C>T	c.(1705-1707)caC>caT	p.H569H	CHPF_ENST00000535926.1_Silent_p.H407H	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	569	Ala-rich.				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)|mitochondrion (GO:0005739)	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(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		GCTCTGCCACGTGGGCCTTGA	0.662													G|||	1534	0.30631	0.1891	0.4841	5008	,	,		17582	0.2738		0.4523	False		,,,				2504	0.2219				p.H569H		Atlas-SNP	.											.	CHPF	56	.	0			c.C1707T						PASS	.	G	,	1094,3308		126,842,1233	27.0	32.0	30.0		1221,1707	-4.6	0.9	2	dbSNP_86	30	3973,4621		940,2093,1264	yes	coding-synonymous,coding-synonymous	CHPF	NM_001195731.1,NM_024536.5	,	1066,2935,2497	AA,AG,GG		46.2299,24.8523,38.9889	,	407/614,569/776	220404726	5067,7929	2201	4297	6498	SO:0001819	synonymous_variant	79586	exon4			TGCCACGTGGGCC	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24291	protein-coding gene	gene with protein product	"""chondroitin sulfate synthase 2"""	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1707C>T	2.37:g.220404726G>A		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Silent	SNP	ENST00000243776.6	37	CCDS2443.1																																																																																			G|0.620;C|0.000;A|0.380	0.380	strong		0.662	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536	
ARID2	196528	hgsc.bcm.edu	37	12	46245077	46245077	+	Silent	SNP	G	G	A	rs7296694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:46245077G>A	ENST00000334344.6	+	15	3343	c.3171G>A	c.(3169-3171)tcG>tcA	p.S1057S	ARID2_ENST00000444670.1_Silent_p.S667S|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000422737.1_Silent_p.S908S|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1057	Gln-rich.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|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)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CTGGTGAGTCGAGTCTGATTA	0.493			"""N, S, F"""		hepatocellular carcinoma								G|||	501	0.10004	0.3442	0.0202	5008	,	,		22635	0.004		0.001	False		,,,				2504	0.0276				p.S1057S		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.G3171A						PASS	.	G		1229,3177	426.4+/-341.1	182,865,1156	148.0	131.0	137.0		3171	-11.8	0.0	12	dbSNP_116	137	9,8591	6.4+/-24.3	0,9,4291	yes	coding-synonymous	ARID2	NM_152641.2		182,874,5447	AA,AG,GG		0.1047,27.8938,9.5187		1057/1836	46245077	1238,11768	2203	4300	6503	SO:0001819	synonymous_variant	196528	exon15			TGAGTCGAGTCTG		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.3171G>A	12.37:g.46245077G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Silent	SNP	ENST00000334344.6	37	CCDS31783.1																																																																																			G|0.905;A|0.095	0.095	strong		0.493	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	
PTOV1	53635	hgsc.bcm.edu	37	19	50358133	50358133	+	Silent	SNP	T	T	G	rs75478119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50358133T>G	ENST00000601675.1	+	4	542	c.438T>G	c.(436-438)ccT>ccG	p.P146P	PTOV1_ENST00000221557.9_Silent_p.P114P|MIR4749_ENST00000578197.1_RNA|PTOV1_ENST00000391842.1_Silent_p.P146P|PTOV1_ENST00000600603.1_Silent_p.P114P|PTOV1_ENST00000599732.1_Silent_p.P146P|PTOV1_ENST00000601638.1_Silent_p.P114P|AC018766.6_ENST00000601211.1_RNA|PTOV1_ENST00000598325.1_3'UTR|AC018766.5_ENST00000593654.1_RNA			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(5)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)	16		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		AGCTGATCCCTCAGCAGCTGC	0.657													G|||	1800	0.359425	0.4123	0.2392	5008	,	,		10608	0.2877		0.3171	False		,,,				2504	0.4908				p.P146P		Atlas-SNP	.											PTOV1,NS,carcinoma,+1,1	PTOV1	41	1	0			c.T438G						PASS	.	G		1777,2629	611.4+/-391.8	361,1055,787	32.0	33.0	33.0		438	-2.8	1.0	19	dbSNP_131	33	2922,5676	653.3+/-401.0	499,1924,1876	no	coding-synonymous	PTOV1	NM_017432.3		860,2979,2663	GG,GT,TT		33.9846,40.3314,36.135		146/417	50358133	4699,8305	2203	4299	6502	SO:0001819	synonymous_variant	53635	exon4			GATCCCTCAGCAG	AF238381	CCDS12782.1	19q13.33	2014-08-28	2008-09-12		ENSG00000104960	ENSG00000104960			9632	protein-coding gene	gene with protein product		610195				12598323, 15713644	Standard	XM_005258998		Approved		uc002pqf.1	Q86YD1	OTTHUMG00000183162	ENST00000601675.1:c.438T>G	19.37:g.50358133T>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Silent	SNP	ENST00000601675.1	37	CCDS12782.1																																																																																			T|0.654;G|0.346	0.346	strong		0.657	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432	
WDR90	197335	hgsc.bcm.edu	37	16	715990	715990	+	Missense_Mutation	SNP	G	G	A	rs7190775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:715990G>A	ENST00000293879.4	+	36	4475	c.4475G>A	c.(4474-4476)cGc>cAc	p.R1492H	WDR90_ENST00000315764.4_Missense_Mutation_p.R91H|WDR90_ENST00000549091.1_Missense_Mutation_p.R1494H|WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000547944.1_Missense_Mutation_p.R91H|RHOT2_ENST00000315082.4_5'Flank			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	31	0	0		WXS	Illumina HiSeq	Phase_I	48	32	0.666667	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	
SPTA1	6708	hgsc.bcm.edu	37	1	158626382	158626382	+	Missense_Mutation	SNP	G	G	A	rs34706737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158626382G>A	ENST00000368147.4	-	20	3050	c.2870C>T	c.(2869-2871)gCt>gTt	p.A957V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	957			A -> V (in dbSNP:rs34706737).		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)					ATTCCGCAGAGCTTTCATACT	0.398													G|||	173	0.0345447	0.1248	0.0101	5008	,	,		16513	0.0		0.001	False		,,,				2504	0.0				p.A957V		Atlas-SNP	.											.	SPTA1	720	.	0			c.C2870T						PASS	.	G	VAL/ALA	340,3368		17,306,1531	170.0	174.0	173.0		2870	2.5	0.0	1	dbSNP_126	173	11,8171		0,11,4080	yes	missense	SPTA1	NM_003126.2	64	17,317,5611	AA,AG,GG		0.1344,9.1694,2.9521	possibly-damaging	957/2420	158626382	351,11539	1854	4091	5945	SO:0001583	missense	6708	exon20			CGCAGAGCTTTCA	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.2870C>T	1.37:g.158626382G>A	ENSP00000357129:p.Ala957Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	73	0.033424908424908424	69	0.1402439024390244	4	0.011049723756906077	0	0.0	0	0.0	G	16.62	3.174122	0.57692	0.091694	0.001344	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.52295	0.67;0.67	5.5	2.53	0.30540	.	0.000000	0.32120	N	0.006555	T	0.42154	0.1190	M	0.66297	2.02	0.40998	D	0.9849	P	0.46952	0.887	P	0.53722	0.733	T	0.31943	-0.9925	10	0.39692	T	0.17	.	9.6117	0.39668	0.0:0.1322:0.4583:0.4095	rs34706737	957	P02549	SPTA1_HUMAN	V	957	ENSP00000357130:A957V;ENSP00000357129:A957V	ENSP00000357129:A957V	A	-	2	0	SPTA1	156893006	0.999000	0.42202	0.038000	0.18304	0.494000	0.33585	2.748000	0.47483	0.395000	0.25257	0.655000	0.94253	GCT	G|0.976;A|0.024	0.024	strong		0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
KLHL24	54800	hgsc.bcm.edu	37	3	183368891	183368891	+	Silent	SNP	C	C	T	rs2293031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183368891C>T	ENST00000454652.2	+	4	1133	c.747C>T	c.(745-747)caC>caT	p.H249H	KLHL24_ENST00000242810.6_Silent_p.H249H|KLHL24_ENST00000476808.1_Silent_p.H249H	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24	249	BACK.					cell projection (GO:0042995)|cytoplasm (GO:0005737)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			CACTGTTACACGAGCTCCTGA	0.443													T|||	1769	0.353235	0.5151	0.2867	5008	,	,		20428	0.4355		0.2714	False		,,,				2504	0.181				p.H249H		Atlas-SNP	.											.	KLHL24	56	.	0			c.C747T						PASS	.	T		2139,2267	597.0+/-388.8	533,1073,597	132.0	122.0	125.0		747	-3.9	0.6	3	dbSNP_100	125	2403,6197	699.6+/-405.1	348,1707,2245	no	coding-synonymous	KLHL24	NM_017644.3		881,2780,2842	TT,TC,CC		27.9419,48.5474,34.9223		249/601	183368891	4542,8464	2203	4300	6503	SO:0001819	synonymous_variant	54800	exon3			GTTACACGAGCTC		CCDS3246.1	3q27.1	2013-02-22	2013-02-22		ENSG00000114796	ENSG00000114796		"""Kelch-like"", ""BTB/POZ domain containing"""	25947	protein-coding gene	gene with protein product		611295	"""kelch-like 24 (Drosophila)"""				Standard	XM_005247552		Approved	DRE1, FLJ20059	uc003flv.3	Q6TFL4	OTTHUMG00000156911	ENST00000454652.2:c.747C>T	3.37:g.183368891C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	157	88	0.56051	NM_017644	A5PLN8|Q9H620|Q9NXT9	Silent	SNP	ENST00000454652.2	37	CCDS3246.1																																																																																			C|0.626;T|0.374	0.374	strong		0.443	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	NM_017644	
PKP1	5317	hgsc.bcm.edu	37	1	201282334	201282334	+	Missense_Mutation	SNP	G	G	A	rs34626929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201282334G>A	ENST00000352845.3	+	3	347	c.347G>A	c.(346-348)cGc>cAc	p.R116H	PKP1_ENST00000263946.3_Missense_Mutation_p.R116H|PKP1_ENST00000367324.3_Missense_Mutation_p.R116H			Q13835	PKP1_HUMAN	plakophilin 1	116			R -> H (in dbSNP:rs34626929).		apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						GACAACAGGCGCTTCAGCTCC	0.582													G|||	125	0.0249601	0.093	0.0014	5008	,	,		15377	0.0		0.001	False		,,,				2504	0.0				p.R116H		Atlas-SNP	.											.	PKP1	127	.	0			c.G347A						PASS	.	G	HIS/ARG,HIS/ARG	335,4069		12,311,1879	12.0	14.0	13.0		347,347	4.2	1.0	1	dbSNP_126	13	5,8591		0,5,4293	yes	missense,missense	PKP1	NM_000299.3,NM_001005337.2	29,29	12,316,6172	AA,AG,GG		0.0582,7.6067,2.6154	probably-damaging,probably-damaging	116/748,116/727	201282334	340,12660	2202	4298	6500	SO:0001583	missense	5317	exon3			ACAGGCGCTTCAG	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"""Armadillo repeat containing"""	9023	protein-coding gene	gene with protein product	"""ectodermal dysplasia/skin fragility syndrome"""	601975	"""plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"""			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.347G>A	1.37:g.201282334G>A	ENSP00000295597:p.Arg116His	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	226	126	0.557522	NM_001005337	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	37	CCDS30966.1	39	0.017857142857142856	39	0.07926829268292683	0	0.0	0	0.0	0	0.0	G	19.95	3.921490	0.73213	0.076067	5.82E-4	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.77750	-1.12;-1.05;-1.05	4.25	4.25	0.50352	.	0.085098	0.50627	D	0.000107	T	0.22085	0.0532	L	0.29908	0.895	0.50467	D	0.999874	D;D	0.89917	0.999;1.0	P;D	0.68621	0.904;0.959	T	0.62553	-0.6830	10	0.46703	T	0.11	-3.6844	15.3441	0.74320	0.0:0.0:1.0:0.0	rs34626929	116;116	Q13835-2;Q13835	.;PKP1_HUMAN	H	116	ENSP00000356293:R116H;ENSP00000263946:R116H;ENSP00000295597:R116H	ENSP00000263946:R116H	R	+	2	0	PKP1	199548957	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.051000	0.71072	2.373000	0.80994	0.491000	0.48974	CGC	G|0.974;A|0.026	0.026	strong		0.582	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
MUC5B	727897	hgsc.bcm.edu	37	11	1264823	1264823	+	Missense_Mutation	SNP	T	T	C	rs200832980|rs4963031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1264823T>C	ENST00000529681.1	+	31	6771	c.6713T>C	c.(6712-6714)cTa>cCa	p.L2238P	MUC5B_ENST00000447027.1_Missense_Mutation_p.L2241P|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2238	7 X Cys-rich subdomain repeats.|Thr-rich.		L -> P (in dbSNP:rs4963031). {ECO:0000269|PubMed:9013550}.		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)		TCCCACACCCTAGCAGCAACC	0.642													c|||	3991	0.796925	0.7526	0.817	5008	,	,		14042	0.9722		0.6889	False		,,,				2504	0.773				p.L2238P		Atlas-SNP	.											MUC5B,brain,glioma,0,2	MUC5B	473	2	0			c.T6713C						PASS	.	C	PRO/LEU	2768,1496		1195,378,559	84.0	122.0	109.0		6713	-0.5	0.0	11	dbSNP_111	109	4759,3685		1955,849,1418	no	missense	MUC5B	NM_002458.2	98	3150,1227,1977	CC,CT,TT		43.6405,35.0844,40.7696	possibly-damaging	2238/5763	1264823	7527,5181	2132	4222	6354	SO:0001583	missense	727897	exon31			ACACCCTAGCAGC	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.6713T>C	11.37:g.1264823T>C	ENSP00000436812:p.Leu2238Pro	Somatic	518	1	0.0019305		WXS	Illumina HiSeq	Phase_I	490	489	0.997959	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	1481	0.6781135531135531	288	0.5853658536585366	249	0.6878453038674033	504	0.8811188811188811	440	0.5804749340369393	c	1.936	-0.444712	0.04604	0.649156	0.563595	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.24350	1.86;2.05	1.87	-0.497	0.12023	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15350	-1.0440	8	0.87932	D	0	.	2.2153	0.03958	0.1675:0.3503:0.3535:0.1287	rs4963031;rs58599618;rs4963031	2876;2241	A7Y9J9;E9PBJ0	.;.	P	2238;2241;2239;2253	ENSP00000436812:L2238P;ENSP00000415793:L2241P	ENSP00000343037:L2239P	L	+	2	0	MUC5B	1221399	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.462000	0.00997	-0.462000	0.06984	-0.684000	0.03749	CTA	T|0.297;C|0.703	0.703	strong		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ZNF780A	284323	hgsc.bcm.edu	37	19	40581677	40581677	+	Silent	SNP	G	G	A	rs337795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40581677G>A	ENST00000595687.2	-	6	881	c.672C>T	c.(670-672)aaC>aaT	p.N224N	ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000340963.5_Silent_p.N224N|ZNF780A_ENST00000594395.1_Silent_p.N225N|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000455521.1_Silent_p.N225N|ZNF780A_ENST00000450241.2_Silent_p.N190N	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	224					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(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TTCCACATTCGTTACATTCAA	0.398													G|||	385	0.076877	0.2761	0.0274	5008	,	,		22376	0.0		0.001	False		,,,				2504	0.0				p.N225N		Atlas-SNP	.											.	ZNF780A	156	.	0			c.C675T						PASS	.	G	,,,	1084,3322	393.5+/-328.9	143,798,1262	92.0	92.0	92.0		672,675,672,	-3.5	0.8	19	dbSNP_79	92	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	143,809,5551	AA,AG,GG		0.1279,24.6028,8.4192	,,,	224/642,225/643,224/642,	40581677	1095,11911	2203	4300	6503	SO:0001819	synonymous_variant	284323	exon6			ACATTCGTTACAT	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"""Zinc fingers, C2H2-type"", ""-"""	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.672C>T	19.37:g.40581677G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001142577	E9PB48|Q6ZN87	Silent	SNP	ENST00000595687.2	37	CCDS33026.2																																																																																			G|0.928;A|0.072	0.072	strong		0.398	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880	
PARP14	54625	hgsc.bcm.edu	37	3	122437536	122437536	+	Missense_Mutation	SNP	C	C	T	rs61732767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122437536C>T	ENST00000474629.2	+	14	4804	c.4538C>T	c.(4537-4539)gCg>gTg	p.A1513V	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1513					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		GAAATTGAGGCGATGATCAAG	0.388													C|||	54	0.0107827	0.0363	0.0086	5008	,	,		21623	0.0		0.0	False		,,,				2504	0.0				p.A1513V		Atlas-SNP	.											.	PARP14	242	.	0			c.C4538T						PASS	.	C	VAL/ALA	89,3737		3,83,1827	209.0	205.0	206.0		4538	-3.8	0.0	3	dbSNP_129	206	1,8273		0,1,4136	yes	missense	PARP14	NM_017554.2	64	3,84,5963	TT,TC,CC		0.0121,2.3262,0.7438	benign	1513/1802	122437536	90,12010	1913	4137	6050	SO:0001583	missense	54625	exon14			TTGAGGCGATGAT	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4538C>T	3.37:g.122437536C>T	ENSP00000418194:p.Ala1513Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	138	51	0.369565	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	20	0.009157509157509158	16	0.032520325203252036	4	0.011049723756906077	0	0.0	0	0.0	C	12.90	2.075995	0.36662	0.023262	1.21E-4	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000310290;ENST00000398157	T	0.31510	1.49	5.05	-3.77	0.04346	.	1.394450	0.04317	N	0.350052	T	0.04815	0.0130	L	0.29908	0.895	0.09310	N	1	B;P	0.37330	0.166;0.59	B;B	0.26094	0.035;0.066	T	0.11324	-1.0592	10	0.30078	T	0.28	.	1.8967	0.03259	0.3644:0.238:0.2884:0.1093	rs61732767	1513;1513	Q460N5-4;Q460N5	.;PAR14_HUMAN	V	1513;1432;116;509	ENSP00000418194:A1513V	ENSP00000310633:A116V	A	+	2	0	PARP14	123920226	0.000000	0.05858	0.005000	0.12908	0.945000	0.59286	0.740000	0.26188	-0.515000	0.06479	-0.271000	0.10264	GCG	C|0.990;T|0.010	0.010	strong		0.388	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
RBPJL	11317	hgsc.bcm.edu	37	20	43938284	43938284	+	Missense_Mutation	SNP	G	G	A	rs35032855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43938284G>A	ENST00000343694.3	+	3	281	c.209G>A	c.(208-210)cGg>cAg	p.R70Q	RBPJL_ENST00000372743.1_Missense_Mutation_p.R70Q|RBPJL_ENST00000372741.3_Missense_Mutation_p.R70Q|MATN4_ENST00000342716.4_5'Flank|MATN4_ENST00000360607.6_5'Flank|MATN4_ENST00000353917.5_5'Flank|MATN4_ENST00000537548.1_5'Flank|MATN4_ENST00000372751.4_5'Flank	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	70					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	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 (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				CAGACTGTGCGGATCCTGCAT	0.607													G|||	57	0.0113818	0.034	0.0058	5008	,	,		19804	0.0		0.004	False		,,,				2504	0.0041				p.R70Q		Atlas-SNP	.											.	RBPJL	67	.	0			c.G209A						PASS	.	G	GLN/ARG	165,4241	109.5+/-147.8	3,159,2041	114.0	93.0	100.0		209	5.5	1.0	20	dbSNP_126	100	17,8583	12.6+/-44.7	0,17,4283	yes	missense	RBPJL	NM_014276.2	43	3,176,6324	AA,AG,GG		0.1977,3.7449,1.3994	benign	70/518	43938284	182,12824	2203	4300	6503	SO:0001583	missense	11317	exon3			CTGTGCGGATCCT	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.209G>A	20.37:g.43938284G>A	ENSP00000341243:p.Arg70Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	23	0.010531135531135532	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	20.6	4.012876	0.75161	0.037449	0.001977	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	D;D;D	0.82711	-1.64;-1.64;-1.64	5.53	5.53	0.82687	LAG1, DNA binding (2);p53-like transcription factor, DNA-binding (1);	0.860937	0.10327	N	0.688044	T	0.41213	0.1149	N	0.22421	0.69	0.20307	N	0.999911	P;P	0.46621	0.881;0.708	B;B	0.35073	0.195;0.189	T	0.57573	-0.7788	10	0.66056	D	0.02	-7.9496	12.2068	0.54356	0.0:0.0:0.7307:0.2693	rs35032855	70;70	Q5QPV1;Q9UBG7	.;RBPJL_HUMAN	Q	70	ENSP00000361828:R70Q;ENSP00000361826:R70Q;ENSP00000341243:R70Q	ENSP00000341243:R70Q	R	+	2	0	RBPJL	43371698	0.992000	0.36948	0.998000	0.56505	0.917000	0.54804	1.776000	0.38594	2.622000	0.88805	0.456000	0.33151	CGG	G|0.988;A|0.012	0.012	strong		0.607	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
EPPK1	83481	hgsc.bcm.edu	37	8	144942097	144942097	+	Silent	SNP	G	G	A	rs73375119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144942097G>A	ENST00000525985.1	-	2	5396	c.5325C>T	c.(5323-5325)caC>caT	p.H1775H				P58107	EPIPL_HUMAN	epiplakin 1	1775						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)			ATTGCAACACGTGTCTCGTGG	0.522													G|||	67	0.0133786	0.0477	0.0043	5008	,	,		20496	0.0		0.001	False		,,,				2504	0.0				p.H1775H		Atlas-SNP	.											EPPK1,NS,NS,-1,1	EPPK1	199	1	0			c.C5325T						PASS	.	G		178,3790		4,170,1810	125.0	120.0	122.0		5325	-10.2	0.0	8	dbSNP_130	122	1,8341		0,1,4170	no	coding-synonymous	EPPK1	NM_031308.1		4,171,5980	AA,AG,GG		0.012,4.4859,1.4541		1775/2420	144942097	179,12131	1984	4171	6155	SO:0001819	synonymous_variant	83481	exon1			CAACACGTGTCTC	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.5325C>T	8.37:g.144942097G>A		Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	260	132	0.507692	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.984;A|0.016	0.016	strong		0.522	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
CASC5	57082	hgsc.bcm.edu	37	15	40916272	40916272	+	Silent	SNP	G	G	A	rs34758606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40916272G>A	ENST00000346991.5	+	11	4278	c.3888G>A	c.(3886-3888)gcG>gcA	p.A1296A	CASC5_ENST00000399668.2_Silent_p.A1270A			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1296					acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TGGAAAAAGCGCAAGTTGAAA	0.363													G|||	68	0.0135783	0.0484	0.0058	5008	,	,		20456	0.0		0.0	False		,,,				2504	0.0				p.A1296A		Atlas-SNP	.											.	CASC5	269	.	0			c.G3888A						PASS	.	G	,	134,3578		6,122,1728	87.0	81.0	83.0		3810,3888	-4.3	0.0	15	dbSNP_126	83	1,8199		0,1,4099	no	coding-synonymous,coding-synonymous	CASC5	NM_144508.3,NM_170589.3	,	6,123,5827	AA,AG,GG		0.0122,3.6099,1.1333	,	1270/2317,1296/2343	40916272	135,11777	1856	4100	5956	SO:0001819	synonymous_variant	57082	exon11			AAAAGCGCAAGTT	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.3888G>A	15.37:g.40916272G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Silent	SNP	ENST00000346991.5	37	CCDS42023.1																																																																																			G|0.991;A|0.009	0.009	strong		0.363	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
SERPINA5	5104	hgsc.bcm.edu	37	14	95053849	95053849	+	Silent	SNP	T	T	C	rs6113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95053849T>C	ENST00000554866.1	+	2	264	c.150T>C	c.(148-150)ttT>ttC	p.F50F	SERPINA5_ENST00000554276.1_Silent_p.F50F|SERPINA5_ENST00000329597.7_Silent_p.F50F|SERPINA5_ENST00000553780.1_Silent_p.F50F			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	50					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)	ACTTTACCTTTGACCTCTACA	0.627													C|||	1378	0.27516	0.6157	0.1182	5008	,	,		18499	0.2798		0.0905	False		,,,				2504	0.1115				p.F50F		Atlas-SNP	.											.	SERPINA5	69	.	0			c.T150C						PASS	.	C		2249,2157	580.2+/-385.1	575,1099,529	47.0	44.0	45.0		150	-8.1	0.0	14	dbSNP_52	45	817,7783	780.7+/-407.7	41,735,3524	no	coding-synonymous	SERPINA5	NM_000624.4		616,1834,4053	CC,CT,TT		9.5,48.956,23.5737		50/407	95053849	3066,9940	2203	4300	6503	SO:0001819	synonymous_variant	5104	exon3			TACCTTTGACCTC	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.150T>C	14.37:g.95053849T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	NM_000624	Q07616|Q9UG30	Silent	SNP	ENST00000554866.1	37	CCDS9928.1																																																																																			C|0.249;N|0.000	0.249	strong		0.627	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
CELA3A	10136	hgsc.bcm.edu	37	1	22328207	22328207	+	Missense_Mutation	SNP	G	G	A	rs11541414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:22328207G>A	ENST00000290122.3	+	1	59	c.40G>A	c.(40-42)Gtt>Att	p.V14I	RN7SL768P_ENST00000584415.1_RNA|CELA3A_ENST00000374663.1_Missense_Mutation_p.V14I	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	14					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						CCTTGTGGCCGTTGGTAAGAC	0.537													G|||	284	0.0567093	0.1755	0.0187	5008	,	,		18400	0.0258		0.0109	False		,,,				2504	0.002				p.V14I		Atlas-SNP	.											.	CELA3A	35	.	0			c.G40A						PASS	.	G	ILE/VAL	543,3853	244.7+/-253.9	48,447,1703	198.0	197.0	197.0		40	1.4	1.0	1	dbSNP_120	197	97,8503	54.8+/-115.7	2,93,4205	no	missense	CELA3A	NM_005747.4	29	50,540,5908	AA,AG,GG		1.1279,12.3521,4.9246		14/271	22328207	640,12356	2198	4300	6498	SO:0001583	missense	10136	exon1			GTGGCCGTTGGTA	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.40G>A	1.37:g.22328207G>A	ENSP00000290122:p.Val14Ile	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	264	135	0.511364	NM_005747	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	37	CCDS220.1	121	0.0554029304029304	91	0.18495934959349594	5	0.013812154696132596	21	0.03671328671328671	4	0.005277044854881266	G	4.477	0.088340	0.08583	0.123521	0.011279	ENSG00000142789	ENST00000290122;ENST00000374663	D;D	0.92911	-2.37;-3.13	3.38	1.44	0.22558	.	.	.	.	.	T	0.00552	0.0018	N	0.13098	0.295	0.58432	P	6.999999999979245E-6	B	0.16802	0.019	B	0.04013	0.001	T	0.21211	-1.0252	8	0.22706	T	0.39	-4.0293	4.8356	0.13464	0.0:0.6486:0.224:0.1274	rs11541414;rs12129372	14	P09093	CEL3A_HUMAN	I	14	ENSP00000290122:V14I;ENSP00000363795:V14I	ENSP00000290122:V14I	V	+	1	0	CELA3A	22200794	0.882000	0.30256	0.999000	0.59377	0.226000	0.24999	-0.001000	0.12947	0.265000	0.21872	-1.210000	0.01631	GTT	G|0.950;A|0.050	0.050	strong		0.537	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747	
F5	2153	hgsc.bcm.edu	37	1	169512120	169512120	+	Silent	SNP	G	G	A	rs6016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	161	0	0		WXS	Illumina HiSeq	Phase_I	157	75	0.477707	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	
C19orf35	374872	hgsc.bcm.edu	37	19	2278755	2278755	+	Missense_Mutation	SNP	C	C	T	rs73518414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	43	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	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	
NOTCH1	4851	hgsc.bcm.edu	37	9	139390958	139390958	+	Silent	SNP	T	T	C	rs11574911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139390958T>C	ENST00000277541.6	-	34	7308	c.7233A>G	c.(7231-7233)ccA>ccG	p.P2411P		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2411	Poly-Pro.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P2412P(1)|p.P2412del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GTGGTGGTGGTGGCGGCTGCA	0.642			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			T|||	160	0.0319489	0.1112	0.0144	5008	,	,		14401	0.0		0.003	False		,,,				2504	0.0				p.P2411P		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1,NS,lymphoid_neoplasm,0,1	NOTCH1	1980	1	2	Substitution - coding silent(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.A7233G						PASS	.	T		313,3979		8,297,1841	22.0	30.0	27.0		7233	-1.5	0.0	9	dbSNP_120	27	17,8511		0,17,4247	no	coding-synonymous	NOTCH1	NM_017617.3		8,314,6088	CC,CT,TT		0.1993,7.2926,2.5741		2411/2556	139390958	330,12490	2146	4264	6410	SO:0001819	synonymous_variant	4851	exon34			TGGTGGTGGCGGC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.7233A>G	9.37:g.139390958T>C		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	31	11	0.354839	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			T|0.968;C|0.032	0.032	strong		0.642	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
DSC2	1824	hgsc.bcm.edu	37	18	28681903	28681903	+	Missense_Mutation	SNP	T	T	C	rs868333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28681903T>C	ENST00000280904.6	-	1	475	c.32A>G	c.(31-33)aAc>aGc	p.N11S	RP11-408H20.2_ENST00000581836.1_RNA|DSC2_ENST00000251081.6_Missense_Mutation_p.N11S	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	11			N -> S (in dbSNP:rs868333). {ECO:0000269|PubMed:20031617}.		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)			GAGGGCTCCGTTCCAGGAGCC	0.751													C|||	428	0.0854633	0.3116	0.0216	5008	,	,		8187	0.001		0.0	False		,,,				2504	0.0				p.N11S		Atlas-SNP	.											.	DSC2	168	.	0			c.A32G						PASS	.						1.0	2.0	2.0					18																	28681903		1051	2094	3145	SO:0001583	missense	1824	exon1			GCTCCGTTCCAGG	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.32A>G	18.37:g.28681903T>C	ENSP00000280904:p.Asn11Ser	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	10	5	0.5	NM_024422		Missense_Mutation	SNP	ENST00000280904.6	37	CCDS11892.1	169	0.07738095238095238	156	0.3170731707317073	7	0.019337016574585635	5	0.008741258741258742	1	0.0013192612137203166	C	7.222	0.597497	0.13875	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000399347	T;T	0.57107	0.45;0.42	4.55	3.59	0.41128	.	.	.	.	.	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	0.38001	-0.9681	8	0.02654	T	1	.	4.9282	0.13903	0.2229:0.6676:0.0:0.1095	rs868333	11;11	Q02487;Q02487-2	DSC2_HUMAN;.	S	11	ENSP00000251081:N11S;ENSP00000280904:N11S	ENSP00000251081:N11S	N	-	2	0	DSC2	26935901	0.000000	0.05858	0.506000	0.27664	0.417000	0.31264	0.324000	0.19610	1.139000	0.42245	-0.186000	0.12905	AAC	T|0.923;C|0.077	0.077	strong		0.751	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949	
MUC4	4585	hgsc.bcm.edu	37	3	195509322	195509322	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509322G>A	ENST00000463781.3	-	2	9588	c.9129C>T	c.(9127-9129)gtC>gtT	p.V3043V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V3043V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	984					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.V3043V(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)		AAGTGTCGGTGACAGGAAGCG	0.612																																					p.V3043V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	kidney(1)	c.C9129T						PASS	.																																			SO:0001819	synonymous_variant	4585	exon2			GTCGGTGACAGGA	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.9129C>T	3.37:g.195509322G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	177	11	0.0621469	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																																																																																			.	.	none		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DSPP	1834	hgsc.bcm.edu	37	4	88537249	88537249	+	Silent	SNP	T	T	C	rs371359066		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88537249T>C	ENST00000282478.7	+	4	3468	c.3435T>C	c.(3433-3435)agT>agC	p.S1145S	DSPP_ENST00000399271.1_Silent_p.S1145S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1145	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagtgacagcagtg	0.567																																					p.S1145S		Atlas-SNP	.											DSPP,NS,carcinoma,0,5	DSPP	174	5	0			c.T3435C						scavenged	.						41.0	55.0	50.0					4																	88537249		1542	2816	4358	SO:0001819	synonymous_variant	1834	exon5			CAGCAGTGACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3435T>C	4.37:g.88537249T>C		Somatic	227	11	0.0484582		WXS	Illumina HiSeq	Phase_I	258	41	0.158915	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
MUC4	4585	hgsc.bcm.edu	37	3	195511396	195511396	+	Missense_Mutation	SNP	G	G	A	rs201453005	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511396G>A	ENST00000463781.3	-	2	7514	c.7055C>T	c.(7054-7056)cCt>cTt	p.P2352L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2352L	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.P2352H(2)|p.P2352L(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)		GACATGAAGAGGGGTGGCGTG	0.582																																					p.P2352L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	kidney(2)|endometrium(1)	c.C7055T						PASS	.						16.0	14.0	14.0					3																	195511396		674	1562	2236	SO:0001583	missense	4585	exon2			TGAAGAGGGGTGG	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.7055C>T	3.37:g.195511396G>A	ENSP00000417498:p.Pro2352Leu	Somatic	381	1	0.00262467		WXS	Illumina HiSeq	Phase_I	140	63	0.45	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	5.268	0.234939	0.09969	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.5;1.51	.	.	.	.	.	.	.	.	T	0.12220	0.0297	N	0.08118	0	0.09310	N	0.999998	B	0.10296	0.003	B	0.06405	0.002	T	0.30357	-0.9981	7	.	.	.	.	2.9304	0.05797	0.3911:0.0:0.6089:0.0	.	2352	E7ESK3	.	L	2352	ENSP00000417498:P2352L;ENSP00000420243:P2352L	.	P	-	2	0	MUC4	196995791	0.028000	0.19301	0.005000	0.12908	0.064000	0.16182	1.205000	0.32308	0.488000	0.27723	0.064000	0.15345	CCT	G|0.991;A|0.008	0.008	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KRT6B	3854	hgsc.bcm.edu	37	12	52844265	52844265	+	Missense_Mutation	SNP	T	T	C	rs652423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52844265T>C	ENST00000252252.3	-	2	727	c.680A>G	c.(679-681)aAc>aGc	p.N227S		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	227	Coil 1B.|Rod.		N -> S (in dbSNP:rs652423). {ECO:0000269|PubMed:2410904, ECO:0000269|PubMed:7543104}.		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)		CCCCACGATGTTGTCCAGCTG	0.577																																					p.N227S		Atlas-SNP	.											.	KRT6B	90	.	0			c.A680G						PASS	.	T	SER/ASN	1455,2951		207,1041,955	196.0	184.0	188.0		680	-1.9	0.0	12	dbSNP_83	188	2618,5982		109,2400,1791	no	missense	KRT6B	NM_005555.3	46	316,3441,2746	CC,CT,TT		30.4419,33.0232,31.3163	benign	227/565	52844265	4073,8933	2203	4300	6503	SO:0001583	missense	3854	exon2			ACGATGTTGTCCA	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.680A>G	12.37:g.52844265T>C	ENSP00000252252:p.Asn227Ser	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	383	181	0.472585	NM_005555	P48669	Missense_Mutation	SNP	ENST00000252252.3	37	CCDS8828.1	772	0.3534798534798535	193	0.39227642276422764	108	0.2983425414364641	241	0.42132867132867136	230	0.3034300791556728	T	0.014	-1.578709	0.00879	0.330232	0.304419	ENSG00000185479	ENST00000252252;ENST00000544607	D	0.90620	-2.7	2.77	-1.87	0.07737	Filament (1);	0.650670	0.15055	N	0.283073	T	0.00012	0.0000	N	0.00996	-1.065	0.80722	P	0.0	B	0.18013	0.025	B	0.20577	0.03	T	0.09378	-1.0677	9	0.02654	T	1	.	5.5903	0.17297	0.121:0.4745:0.3226:0.0818	rs652423;rs1707773;rs2942779;rs7311892;rs11531212;rs58544103;rs652423	227	P04259	K2C6B_HUMAN	S	227	ENSP00000252252:N227S	ENSP00000252252:N227S	N	-	2	0	KRT6B	51130532	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.048000	0.03517	-0.421000	0.07416	-0.817000	0.03123	AAC	T|0.604;C|0.396	0.396	strong		0.577	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
TMPRSS4	56649	hgsc.bcm.edu	37	11	117978578	117978578	+	Missense_Mutation	SNP	G	G	A	rs1894176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117978578G>A	ENST00000437212.3	+	6	744	c.530G>A	c.(529-531)cGg>cAg	p.R177Q	TMPRSS4_ENST00000522824.1_Missense_Mutation_p.R172Q|TMPRSS4_ENST00000534111.1_Missense_Mutation_p.R175Q|TMPRSS4_ENST00000523251.1_Missense_Mutation_p.R137Q|TMPRSS4_ENST00000522307.1_Missense_Mutation_p.R30Q			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	177	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.		R -> Q (in dbSNP:rs1894176).		proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		CTTCGCATGCGGAACTCAAGT	0.547													G|||	204	0.0407348	0.1415	0.0216	5008	,	,		19296	0.0		0.002	False		,,,				2504	0.0				p.R177Q		Atlas-SNP	.											TMPRSS4,NS,carcinoma,-1,1	TMPRSS4	46	1	0			c.G530A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	452,3948	216.1+/-234.9	26,400,1774	67.0	60.0	62.0		515,524,410,530	-7.9	0.0	11	dbSNP_92	62	13,8579	9.1+/-34.3	0,13,4283	yes	missense,missense,missense,missense	TMPRSS4	NM_001083947.1,NM_001173551.1,NM_001173552.1,NM_019894.3	43,43,43,43	26,413,6057	AA,AG,GG		0.1513,10.2727,3.5791	benign,benign,benign,benign	172/433,175/436,137/398,177/438	117978578	465,12527	2200	4296	6496	SO:0001583	missense	56649	exon6			GCATGCGGAACTC	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"""Serine peptidases / Transmembrane"""	11878	protein-coding gene	gene with protein product	"""transmembrane serine protease 3"", ""membrane-type serine protease 2"", ""type II membrane serine protease"""	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.530G>A	11.37:g.117978578G>A	ENSP00000416037:p.Arg177Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	35	0.686275	NM_019894	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	37	CCDS31684.1	84	0.038461538461538464	78	0.15853658536585366	6	0.016574585635359115	0	0.0	0	0.0	G	2.686	-0.274296	0.05679	0.102727	0.001513	ENSG00000137648	ENST00000534111;ENST00000522307;ENST00000523251;ENST00000437212;ENST00000522824;ENST00000522151	T;D;T;T;T;T	0.88201	0.21;-2.35;0.21;0.21;0.21;0.21	5.31	-7.95	0.01148	Speract/scavenger receptor-related (2);	1.636540	0.03489	N	0.216335	T	0.00384	0.0012	N	0.00642	-1.3	0.80722	P	0.0	B;B;B;B;B	0.15719	0.014;0.014;0.008;0.005;0.005	B;B;B;B;B	0.04013	0.001;0.001;0.0;0.001;0.001	T	0.33752	-0.9856	9	0.13108	T	0.6	.	4.6674	0.12673	0.2857:0.1209:0.4751:0.1183	rs1894176;rs1894176	152;137;30;177;175	B7Z900;E7ERX8;E7ESG9;Q9NRS4;Q9NRS4-3	.;.;.;TMPS4_HUMAN;.	Q	175;30;137;177;172;124	ENSP00000435184:R175Q;ENSP00000428814:R30Q;ENSP00000429209:R137Q;ENSP00000416037:R177Q;ENSP00000430547:R172Q;ENSP00000428407:R124Q	ENSP00000416037:R177Q	R	+	2	0	TMPRSS4	117483788	0.000000	0.05858	0.033000	0.17914	0.003000	0.03518	-1.134000	0.03228	-1.008000	0.03404	-1.105000	0.02106	CGG	G|0.955;A|0.045	0.045	strong		0.547	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894	
C1orf53	388722	hgsc.bcm.edu	37	1	197872001	197872001	+	Silent	SNP	G	G	A	rs73083807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:197872001G>A	ENST00000367393.3	+	1	225	c.222G>A	c.(220-222)gcG>gcA	p.A74A		NM_001024594.2	NP_001019765.1	Q5VUE5	CA053_HUMAN	chromosome 1 open reading frame 53	74										endometrium(1)|lung(1)	2						AGTTAACCGCGGCGGAGCGAC	0.756													G|||	123	0.0245607	0.0877	0.0101	5008	,	,		10681	0.0		0.0	False		,,,				2504	0.0				p.A74A		Atlas-SNP	.											.	C1orf53	18	.	0			c.G222A						PASS	.	G		263,3423		4,255,1584	7.0	8.0	8.0		222	0.1	0.0	1	dbSNP_130	8	3,8019		0,3,4008	no	coding-synonymous	C1orf53	NM_001024594.2		4,258,5592	AA,AG,GG		0.0374,7.1351,2.272		74/146	197872001	266,11442	1843	4011	5854	SO:0001819	synonymous_variant	388722	exon1			AACCGCGGCGGAG	BC038214	CCDS44290.1	1q31.3	2011-01-26			ENSG00000203724	ENSG00000203724			30003	protein-coding gene	gene with protein product						15897902	Standard	NM_001024594		Approved		uc001guh.3	Q5VUE5	OTTHUMG00000035659	ENST00000367393.3:c.222G>A	1.37:g.197872001G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_001024594	A1L4N2|Q5VUE4	Silent	SNP	ENST00000367393.3	37	CCDS44290.1																																																																																			G|0.972;A|0.028	0.028	strong		0.756	C1orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086555.1	NM_001024594	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34803947	34803947	+	Silent	SNP	C	C	T	rs4259246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:34803947C>T	ENST00000192788.5	+	8	1026	c.855C>T	c.(853-855)gcC>gcT	p.A285A	UHRF1BP1_ENST00000452449.2_Silent_p.A285A	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	285							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						CTCCACCAGCCCCCAGTGCCC	0.537													T|||	2311	0.461462	0.7723	0.3069	5008	,	,		19389	0.4633		0.335	False		,,,				2504	0.2791				p.A285A		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C855T						PASS	.	T		2664,1394		881,902,246	133.0	151.0	145.0		855	2.2	1.0	6	dbSNP_111	145	2867,5545		491,1885,1830	no	coding-synonymous	UHRF1BP1	NM_017754.3		1372,2787,2076	TT,TC,CC		34.0823,34.3519,44.3545		285/1441	34803947	5531,6939	2029	4206	6235	SO:0001819	synonymous_variant	54887	exon8			ACCAGCCCCCAGT	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.855C>T	6.37:g.34803947C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	NM_017754	Q9NXE0	Silent	SNP	ENST00000192788.5	37	CCDS43455.1																																																																																			C|0.564;T|0.436	0.436	strong		0.537	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
FOXP4	116113	hgsc.bcm.edu	37	6	41533579	41533579	+	Silent	SNP	C	C	A	rs2104506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41533579C>A	ENST00000307972.4	+	1	93	c.81C>A	c.(79-81)gcC>gcA	p.A27A	FOXP4_ENST00000373063.3_Silent_p.A27A|FOXP4_ENST00000373060.1_Silent_p.A27A|FOXP4_ENST00000373057.3_Silent_p.A27A|FOXP4_ENST00000409208.1_Silent_p.A27A			Q8IVH2	FOXP4_HUMAN	forkhead box P4	27					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					CTGGGCAAGCCGATGGCAGCA	0.627													C|||	1939	0.387181	0.5106	0.4049	5008	,	,		20199	0.3393		0.3022	False		,,,				2504	0.3446				p.A27A		Atlas-SNP	.											FOXP4_ENST00000373060,NS,carcinoma,0,2	FOXP4	83	2	0			c.C81A						scavenged	.	C	,,	2010,2390		461,1088,651	85.0	87.0	86.0		81,81,81	-7.3	0.1	6	dbSNP_96	86	2306,6278		327,1652,2313	no	coding-synonymous,coding-synonymous,coding-synonymous	FOXP4	NM_001012426.1,NM_001012427.1,NM_138457.2	,,	788,2740,2964	AA,AC,CC		26.8639,45.6818,33.2409	,,	27/681,27/679,27/668	41533579	4316,8668	2200	4292	6492	SO:0001819	synonymous_variant	116113	exon2			GCAAGCCGATGGC	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.81C>A	6.37:g.41533579C>A		Somatic	185	2	0.0108108		WXS	Illumina HiSeq	Phase_I	208	115	0.552885	NM_001012427	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Silent	SNP	ENST00000307972.4	37	CCDS34447.1																																																																																			C|0.647;A|0.353	0.353	strong		0.627	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457	
AHR	196	hgsc.bcm.edu	37	7	17379157	17379157	+	Missense_Mutation	SNP	G	G	A	rs4986826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:17379157G>A	ENST00000242057.4	+	10	2351	c.1708G>A	c.(1708-1710)Gtt>Att	p.V570I		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	570			V -> I (in dbSNP:rs4986826). {ECO:0000269|PubMed:10739168, ECO:0000269|PubMed:11689007}.		apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|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)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	TTCTGGTGAGGTTGACTTCAG	0.363													G|||	113	0.0225639	0.0756	0.0144	5008	,	,		21431	0.0		0.002	False		,,,				2504	0.001				p.V570I		Atlas-SNP	.											.	AHR	89	.	0			c.G1708A						PASS	.	G	ILE/VAL	285,4121	151.8+/-185.6	14,257,1932	67.0	71.0	69.0		1708	3.4	0.4	7	dbSNP_111	69	17,8583	11.9+/-42.8	0,17,4283	yes	missense	AHR	NM_001621.4	29	14,274,6215	AA,AG,GG		0.1977,6.4685,2.322	benign	570/849	17379157	302,12704	2203	4300	6503	SO:0001583	missense	196	exon10			GGTGAGGTTGACT	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"""Basic helix-loop-helix proteins"""	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.1708G>A	7.37:g.17379157G>A	ENSP00000242057:p.Val570Ile	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	43	27	0.627907	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	37	CCDS5366.1	49	0.022435897435897436	41	0.08333333333333333	8	0.022099447513812154	0	0.0	0	0.0	G	9.679	1.148672	0.21288	0.064685	0.001977	ENSG00000106546	ENST00000242057	T	0.24723	1.84	6.16	3.44	0.39384	.	0.396190	0.28322	N	0.015763	T	0.01489	0.0048	M	0.63428	1.95	0.18873	N	0.999986	B	0.31009	0.303	B	0.33799	0.17	T	0.02132	-1.1208	10	0.38643	T	0.18	.	12.061	0.53562	0.15:0.0:0.85:0.0	rs4986826;rs52830926;rs58070269;rs4986826	570	P35869	AHR_HUMAN	I	570	ENSP00000242057:V570I	ENSP00000242057:V570I	V	+	1	0	AHR	17345682	0.908000	0.30866	0.408000	0.26446	0.911000	0.54048	1.786000	0.38694	0.498000	0.27948	0.650000	0.86243	GTT	G|0.974;A|0.026	0.026	strong		0.363	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621	
OBSCN	84033	hgsc.bcm.edu	37	1	228404864	228404864	+	Missense_Mutation	SNP	G	G	A	rs141921462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228404864G>A	ENST00000422127.1	+	8	2572	c.2528G>A	c.(2527-2529)cGc>cAc	p.R843H	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.R843H|OBSCN_ENST00000284548.11_Missense_Mutation_p.R843H|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	843	Ig-like 8.				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)				TCCGGTGAGCGCTTCTTGCAG	0.662													G|||	36	0.0071885	0.0272	0.0	5008	,	,		16092	0.0		0.0	False		,,,				2504	0.0				p.R843H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G2528A						PASS	.	G	HIS/ARG,HIS/ARG	124,4184		1,122,2031	64.0	72.0	69.0		2528,2528	-2.1	0.0	1	dbSNP_134	69	1,8503		0,1,4251	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	29,29	1,123,6282	AA,AG,GG		0.0118,2.8784,0.9756	probably-damaging,probably-damaging	843/7969,843/6621	228404864	125,12687	2154	4252	6406	SO:0001583	missense	84033	exon8			GTGAGCGCTTCTT	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.2528G>A	1.37:g.228404864G>A	ENSP00000409493:p.Arg843His	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	91	57	0.626374	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	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	.	8.071	0.770330	0.15983	0.028784	1.18E-4	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.52057	0.68;0.68	4.79	-2.11	0.07187	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.987508	0.08243	N	0.975792	T	0.20659	0.0497	L	0.58101	1.795	0.09310	N	0.999998	B;D	0.64830	0.008;0.994	B;P	0.48454	0.003;0.578	T	0.31110	-0.9955	10	0.14656	T	0.56	.	7.3341	0.26599	0.6513:0.0:0.2172:0.1315	.	843;843	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	H	843	ENSP00000284548:R843H;ENSP00000409493:R843H	ENSP00000284548:R843H	R	+	2	0	OBSCN	226471487	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.113000	0.03296	-0.663000	0.05331	-0.768000	0.03414	CGC	G|0.996;A|0.004	0.004	strong		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ACSM2A	123876	hgsc.bcm.edu	37	16	20476974	20476974	+	Missense_Mutation	SNP	C	C	T	rs13332099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20476974C>T	ENST00000573854.1	+	3	427	c.313C>T	c.(313-315)Cgt>Tgt	p.R105C	ACSM2A_ENST00000417235.2_Missense_Mutation_p.R26C|ACSM2A_ENST00000536134.1_5'UTR|ACSM2A_ENST00000396104.2_Missense_Mutation_p.R105C|ACSM2A_ENST00000575558.1_3'UTR|ACSM2A_ENST00000424070.1_Missense_Mutation_p.R105C|ACSM2A_ENST00000219054.6_Missense_Mutation_p.R105C|ACSM2A_ENST00000575690.1_Missense_Mutation_p.R105C	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	105					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)	p.R105G(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						TGGCCTGCAGCGTGGGGATCG	0.577													C|||	31	0.0061901	0.0212	0.0029	5008	,	,		20999	0.0		0.0	False		,,,				2504	0.001				p.R105C		Atlas-SNP	.											ACSM2A,NS,carcinoma,-2,1	ACSM2A	120	1	1	Substitution - Missense(1)	lung(1)	c.C313T						PASS	.	C	CYS/ARG	79,4327	68.1+/-105.8	1,77,2125	121.0	101.0	108.0		313	2.8	1.0	16	dbSNP_121	108	0,8600		0,0,4300	no	missense	ACSM2A	NM_001010845.2	180	1,77,6425	TT,TC,CC		0.0,1.793,0.6074	benign	105/578	20476974	79,12927	2203	4300	6503	SO:0001583	missense	123876	exon4			CTGCAGCGTGGGG	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"""Acyl-CoA synthetase family"""	32017	protein-coding gene	gene with protein product		614358	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.313C>T	16.37:g.20476974C>T	ENSP00000459451:p.Arg105Cys	Somatic	502	0	0		WXS	Illumina HiSeq	Phase_I	521	179	0.34357	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	C	11.81	1.750666	0.31046	0.01793	0.0	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000424070;ENST00000396104	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	3.76	2.79	0.32731	AMP-dependent synthetase/ligase (1);	0.189594	0.27262	N	0.020171	T	0.19967	0.0480	M	0.84326	2.69	0.30993	N	0.721168	P;P	0.37636	0.485;0.603	B;B	0.28916	0.096;0.096	T	0.46569	-0.9182	10	0.56958	D	0.05	-6.0087	6.554	0.22450	0.1772:0.7202:0.0:0.1026	rs13332099	26;105	B7Z8R0;Q08AH3	.;ACS2A_HUMAN	C	26;105;105;105	ENSP00000392169:R26C;ENSP00000219054:R105C;ENSP00000394904:R105C;ENSP00000379411:R105C	ENSP00000219054:R105C	R	+	1	0	ACSM2A	20384475	0.515000	0.26210	0.989000	0.46669	0.734000	0.41952	1.158000	0.31737	0.694000	0.31654	0.298000	0.19748	CGT	C|0.993;T|0.007	0.007	strong		0.577	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845	
DKK3	27122	hgsc.bcm.edu	37	11	12023868	12023868	+	Silent	SNP	A	A	G	rs79628149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:12023868A>G	ENST00000396505.2	-	3	568	c.330T>C	c.(328-330)caT>caC	p.H110H	DKK3_ENST00000525493.1_Silent_p.H110H|DKK3_ENST00000527132.1_Intron|DKK3_ENST00000326932.4_Silent_p.H110H|DKK3_ENST00000450094.2_Silent_p.H110H	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	110					adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		CTCGGTGCACATGGATGGTAT	0.433													A|||	45	0.00898562	0.028	0.0101	5008	,	,		18698	0.0		0.001	False		,,,				2504	0.0				p.H110H		Atlas-SNP	.											.	DKK3	35	.	0			c.T330C						PASS	.	A	,,	109,4293	86.3+/-125.0	0,109,2092	308.0	260.0	276.0		330,330,330	-11.1	0.1	11	dbSNP_132	276	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	DKK3	NM_001018057.1,NM_013253.4,NM_015881.5	,,	0,109,6386	GG,GA,AA		0.0,2.4761,0.8391	,,	110/351,110/351,110/351	12023868	109,12881	2201	4294	6495	SO:0001819	synonymous_variant	27122	exon2			GTGCACATGGATG	AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"""regulated in glioma"""	605416	"""dickkopf (Xenopus laevis) homolog 3"", ""dickkopf 3 homolog (Xenopus laevis)"""			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.330T>C	11.37:g.12023868A>G		Somatic	362	1	0.00276243		WXS	Illumina HiSeq	Phase_I	361	164	0.454294	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Silent	SNP	ENST00000396505.2	37	CCDS7808.1																																																																																			A|0.991;G|0.009	0.009	strong		0.433	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253	
LYPD1	116372	hgsc.bcm.edu	37	2	133403647	133403647	+	Missense_Mutation	SNP	T	T	C	rs139508764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:133403647T>C	ENST00000397463.2	-	3	669	c.397A>G	c.(397-399)Aaa>Gaa	p.K133E	LYPD1_ENST00000345008.6_Missense_Mutation_p.K81E|GPR39_ENST00000329321.3_3'UTR|GPR39_ENST00000470071.1_3'UTR	NM_144586.5	NP_653187.3	Q8N2G4	LYPD1_HUMAN	LY6/PLAUR domain containing 1	133				K -> R (in Ref. 2; BAC85518). {ECO:0000305}.		anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				lung(2)	2						AGGGCTAATTTGAGGAACAGG	0.612													T|||	16	0.00319489	0.0113	0.0014	5008	,	,		16585	0.0		0.0	False		,,,				2504	0.0				p.K133E		Atlas-SNP	.											.	LYPD1	11	.	0			c.A397G						PASS	.	T	GLU/LYS,,GLU/LYS	34,3886		1,32,1927	66.0	73.0	71.0		241,,397	-1.4	0.0	2	dbSNP_134	71	0,8316		0,0,4158	yes	missense,utr-3,missense	GPR39,LYPD1	NM_001077427.2,NM_001508.2,NM_144586.5	56,,56	1,32,6085	CC,CT,TT		0.0,0.8673,0.2779	benign,,benign	81/90,,133/142	133403647	34,12202	1960	4158	6118	SO:0001583	missense	116372	exon3			CTAATTTGAGGAA	AK075487	CCDS42759.1, CCDS46416.1	2q21.2	2008-02-05		2005-08-30	ENSG00000150551	ENSG00000150551			28431	protein-coding gene	gene with protein product		610450		LYPDC1		12477932	Standard	NM_144586		Approved	MGC29643	uc002ttn.3	Q8N2G4	OTTHUMG00000153609	ENST00000397463.2:c.397A>G	2.37:g.133403647T>C	ENSP00000380605:p.Lys133Glu	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	158	85	0.537975	NM_144586	H7BXW6|Q6ZP52|Q6ZWI4|Q96AC2	Missense_Mutation	SNP	ENST00000397463.2	37	CCDS42759.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	8.848	0.943963	0.18281	0.008673	0.0	ENSG00000150551	ENST00000409034;ENST00000397463;ENST00000345008	D;D	0.82526	-1.62;-1.62	5.55	-1.42	0.08913	.	1.164150	0.06065	N	0.658974	T	0.58680	0.2139	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.50833	-0.8781	10	0.42905	T	0.14	-15.7811	8.1786	0.31296	0.0:0.1191:0.444:0.4369	.	133;149	Q8N2G4;Q8N2G4-3	LYPD1_HUMAN;.	E	156;133;81	ENSP00000380605:K133E;ENSP00000340563:K81E	ENSP00000340563:K81E	K	-	1	0	LYPD1	133120117	0.001000	0.12720	0.021000	0.16686	0.724000	0.41520	-0.106000	0.10890	-0.206000	0.10203	0.529000	0.55759	AAA	T|0.998;C|0.002	0.002	strong		0.612	LYPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331821.1	NM_144586	
VLDLR	7436	hgsc.bcm.edu	37	9	2643175	2643175	+	Missense_Mutation	SNP	G	G	C	rs34080096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2643175G>C	ENST00000382100.3	+	5	820	c.464G>C	c.(463-465)aGt>aCt	p.S155T	VLDLR_ENST00000382099.2_Missense_Mutation_p.S155T|RP11-125B21.2_ENST00000599229.1_RNA	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	155	LDL-receptor class A 4. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		ATAACATGTAGTCCCGACGAG	0.473													G|||	15	0.00299521	0.0106	0.0014	5008	,	,		20805	0.0		0.0	False		,,,				2504	0.0				p.S155T		Atlas-SNP	.											.	VLDLR	68	.	0			c.G464C						PASS	.	G	THR/SER,THR/SER	36,4370	40.8+/-73.8	0,36,2167	116.0	122.0	120.0		464,464	4.6	0.0	9	dbSNP_126	120	0,8600		0,0,4300	yes	missense,missense	VLDLR	NM_001018056.1,NM_003383.3	58,58	0,36,6467	CC,CG,GG		0.0,0.8171,0.2768	benign,benign	155/846,155/874	2643175	36,12970	2203	4300	6503	SO:0001583	missense	7436	exon5			CATGTAGTCCCGA		CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"""Low density lipoprotein receptors"""	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.464G>C	9.37:g.2643175G>C	ENSP00000371532:p.Ser155Thr	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	38	22	0.578947	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	Missense_Mutation	SNP	ENST00000382100.3	37	CCDS6446.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	13.70	2.315185	0.40996	0.008171	0.0	ENSG00000147852	ENST00000382100;ENST00000382096;ENST00000382099	D;D;D	0.95588	-3.75;-3.75;-3.75	5.5	4.61	0.57282	.	0.091415	0.48286	D	0.000195	D	0.86789	0.6017	L	0.28776	0.89	0.80722	D	1	B;B;B	0.14805	0.003;0.004;0.011	B;B;B	0.29353	0.013;0.022;0.101	D	0.85668	0.1293	10	0.33940	T	0.23	.	14.3118	0.66422	0.0706:0.0:0.9294:0.0	rs34080096	155;155;155	P98155-2;Q5VVF5;P98155	.;.;VLDLR_HUMAN	T	155;114;155	ENSP00000371532:S155T;ENSP00000371528:S114T;ENSP00000371531:S155T	ENSP00000371528:S114T	S	+	2	0	VLDLR	2633175	1.000000	0.71417	0.028000	0.17463	0.199000	0.23934	5.517000	0.67061	1.558000	0.49541	0.655000	0.94253	AGT	G|0.996;C|0.004	0.004	strong		0.473	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383	
WDR36	134430	hgsc.bcm.edu	37	5	110432841	110432841	+	Silent	SNP	T	T	C	rs17132775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:110432841T>C	ENST00000513710.2	+	3	427	c.423T>C	c.(421-423)taT>taC	p.Y141Y	WDR36_ENST00000505303.1_Silent_p.Y85Y|WDR36_ENST00000506538.2_Silent_p.Y141Y			Q8NI36	WDR36_HUMAN	WD repeat domain 36	141					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)		TTGCTGCTTATGGAAATGTTT	0.388													T|||	212	0.0423323	0.1558	0.0072	5008	,	,		15681	0.0		0.001	False		,,,				2504	0.0				p.Y141Y		Atlas-SNP	.											.	WDR36	111	.	0			c.T423C						PASS	.	T		647,3757	277.5+/-273.7	44,559,1599	179.0	171.0	174.0		423	2.0	1.0	5	dbSNP_123	174	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	WDR36	NM_139281.2		44,567,5891	CC,CT,TT		0.093,14.6912,5.0369		141/952	110432841	655,12349	2202	4300	6502	SO:0001819	synonymous_variant	134430	exon3			TGCTTATGGAAAT	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.423T>C	5.37:g.110432841T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Silent	SNP	ENST00000513710.2	37	CCDS4102.1																																																																																			T|0.951;C|0.049	0.049	strong		0.388	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281	
AHNAK2	113146	hgsc.bcm.edu	37	14	105420927	105420927	+	Silent	SNP	A	A	G	rs879210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105420927A>G	ENST00000333244.5	-	7	980	c.861T>C	c.(859-861)ccT>ccC	p.P287P	AHNAK2_ENST00000557457.1_5'Flank	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	287						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)			GTGCGTCCCTAGGTTCGTAGG	0.622													G|||	1576	0.314696	0.3359	0.2968	5008	,	,		16825	0.0754		0.4652	False		,,,				2504	0.3906				p.P287P		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	0			c.T861C						PASS	.	G		1488,2710		285,918,896	36.0	39.0	38.0		861	-6.7	0.0	14	dbSNP_86	38	3879,4545		915,2049,1248	no	coding-synonymous	AHNAK2	NM_138420.2		1200,2967,2144	GG,GA,AA		46.047,35.4455,42.521		287/5796	105420927	5367,7255	2099	4212	6311	SO:0001819	synonymous_variant	113146	exon7			GTCCCTAGGTTCG	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.861T>C	14.37:g.105420927A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.677;G|0.323	0.323	strong		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
GUCA1A	2978	hgsc.bcm.edu	37	6	42141360	42141360	+	Silent	SNP	C	C	T	rs116114043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42141360C>T	ENST00000394237.1	+	3	985	c.9C>T	c.(7-9)aaC>aaT	p.N3N	GUCA1A_ENST00000053469.4_Silent_p.N3N|GUCA1A_ENST00000372958.1_Silent_p.N3N|GUCA1A_ENST00000541991.1_Silent_p.N3N			P43080	GUC1A_HUMAN	guanylate cyclase activator 1A (retina)	3					phototransduction, visible light (GO:0007603)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;5.54e-05)|Epithelial(12;0.000167)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CAATGGGCAACGTGATGGAGG	0.607													C|||	20	0.00399361	0.0151	0.0	5008	,	,		20437	0.0		0.0	False		,,,				2504	0.0				p.N3N		Atlas-SNP	.											.	GUCA1A	18	.	0			c.C9T						PASS	.	C		59,4347	56.8+/-93.2	0,59,2144	117.0	97.0	104.0		9	2.2	1.0	6	dbSNP_132	104	0,8600		0,0,4300	no	coding-synonymous	GUCA1A	NM_000409.3		0,59,6444	TT,TC,CC		0.0,1.3391,0.4536		3/202	42141360	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	2978	exon3			GGGCAACGTGATG		CCDS4864.1	6p21.1	2013-06-06			ENSG00000048545	ENSG00000048545		"""EF-hand domain containing"""	4678	protein-coding gene	gene with protein product	"""cone dystrophy 3"""	600364	"""chromosome 6 open reading frame 131"""	GUCA, GUCA1, C6orf131		9425234	Standard	NM_000409		Approved	GCAP, GCAP1, COD3, dJ139D8.6, CORD14	uc003orx.3	P43080	OTTHUMG00000014696	ENST00000394237.1:c.9C>T	6.37:g.42141360C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_000409	B3KWT4|Q7Z6T1|Q9NU14	Silent	SNP	ENST00000394237.1	37	CCDS4864.1																																																																																			C|0.995;T|0.005	0.005	strong		0.607	GUCA1A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316582.1		
TEX15	56154	hgsc.bcm.edu	37	8	30702525	30702525	+	Missense_Mutation	SNP	A	A	C	rs323344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:30702525A>C	ENST00000256246.2	-	1	4083	c.4009T>G	c.(4009-4011)Tta>Gta	p.L1337V		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1337			L -> V (in dbSNP:rs323344). {ECO:0000269|PubMed:11279525}.		fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		GCGGCTGATAACTGAGGAATA	0.383													A|||	1635	0.326478	0.8449	0.1571	5008	,	,		20923	0.0704		0.1272	False		,,,				2504	0.2147				p.L1337V		Atlas-SNP	.											.	TEX15	350	.	0			c.T4009G						PASS	.	A	VAL/LEU	3181,1225	696.4+/-406.1	1153,875,175	115.0	130.0	125.0		4009	3.6	0.0	8	dbSNP_79	125	1010,7588	214.8+/-254.3	66,878,3355	yes	missense	TEX15	NM_031271.3	32	1219,1753,3530	CC,CA,AA		11.7469,27.803,32.2285	possibly-damaging	1337/2790	30702525	4191,8813	2203	4299	6502	SO:0001583	missense	56154	exon1			CTGATAACTGAGG	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.4009T>G	8.37:g.30702525A>C	ENSP00000256246:p.Leu1337Val	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	604	0.2765567765567766	411	0.8353658536585366	61	0.1685082872928177	39	0.06818181818181818	93	0.12269129287598944	A	9.942	1.217641	0.22373	0.72197	0.117469	ENSG00000133863	ENST00000256246	T	0.23552	1.9	6.07	3.57	0.40892	.	0.794140	0.11065	N	0.603508	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P	0.37122	0.583	B	0.34652	0.187	T	0.12863	-1.0531	9	0.87932	D	0	.	6.4494	0.21896	0.7626:0.1567:0.0807:0.0	rs323344;rs52799274;rs59808187;rs323344	1337	Q9BXT5	TEX15_HUMAN	V	1337	ENSP00000256246:L1337V	ENSP00000256246:L1337V	L	-	1	2	TEX15	30822067	0.008000	0.16893	0.000000	0.03702	0.019000	0.09904	0.681000	0.25320	0.465000	0.27167	0.533000	0.62120	TTA	A|0.701;C|0.299	0.299	strong		0.383	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
CAP2	10486	hgsc.bcm.edu	37	6	17426846	17426846	+	Silent	SNP	T	T	C	rs59744718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:17426846T>C	ENST00000229922.2	+	3	679	c.147T>C	c.(145-147)ttT>ttC	p.F49F	CAP2_ENST00000489374.1_Silent_p.F49F|CAP2_ENST00000493172.1_Silent_p.F49F|CAP2_ENST00000378990.2_Silent_p.F49F|CAP2_ENST00000465994.1_Silent_p.F49F	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	49					activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			TGGAAGCCTTTGACAAGCTGA	0.537													T|||	173	0.0345447	0.0915	0.0173	5008	,	,		18857	0.0308		0.003	False		,,,				2504	0.0061				p.F49F		Atlas-SNP	.											.	CAP2	61	.	0			c.T147C						PASS	.	T		352,4054	181.9+/-209.8	13,326,1864	113.0	102.0	105.0		147	1.8	1.0	6	dbSNP_129	105	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	CAP2	NM_006366.2		13,340,6150	CC,CT,TT		0.1628,7.9891,2.8141		49/478	17426846	366,12640	2203	4300	6503	SO:0001819	synonymous_variant	10486	exon3			AGCCTTTGACAAG	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.147T>C	6.37:g.17426846T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	37	CCDS4539.1																																																																																			T|0.967;C|0.033	0.033	strong		0.537	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
FBXO42	54455	hgsc.bcm.edu	37	1	16577908	16577908	+	Missense_Mutation	SNP	G	G	C	rs12069239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	183	0	0		WXS	Illumina HiSeq	Phase_I	185	185	1	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		
WFDC3	140686	hgsc.bcm.edu	37	20	44417593	44417593	+	Missense_Mutation	SNP	C	C	A	rs73122754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44417593C>A	ENST00000243938.4	-	3	271	c.188G>T	c.(187-189)cGg>cTg	p.R63L	WFDC3_ENST00000372630.2_Intron|DNTTIP1_ENST00000372622.3_5'Flank|WFDC3_ENST00000481847.1_Intron|WFDC3_ENST00000372632.2_Missense_Mutation_p.R63L	NM_080614.1	NP_542181.1	Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3	63	WAP 1. {ECO:0000255|PROSITE- ProRule:PRU00722}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				TCGGCAGATCCGACCACAGCC	0.532													C|||	141	0.028155	0.0212	0.0389	5008	,	,		17601	0.0		0.0497	False		,,,				2504	0.0368				p.R63L		Atlas-SNP	.											.	WFDC3	18	.	0			c.G188T						PASS	.	C	LEU/ARG	109,4297	84.4+/-122.9	0,109,2094	216.0	197.0	204.0		188	-2.9	0.0	20	dbSNP_131	204	511,8089	145.4+/-201.1	20,471,3809	yes	missense	WFDC3	NM_080614.1	102	20,580,5903	AA,AC,CC		5.9419,2.4739,4.767	benign	63/232	44417593	620,12386	2203	4300	6503	SO:0001583	missense	140686	exon3			CAGATCCGACCAC	AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116		"""WAP four-disulfide core domain containing"""	15957	protein-coding gene	gene with protein product						12206714, 10680116	Standard	NM_080614		Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000243938.4:c.188G>T	20.37:g.44417593C>A	ENSP00000243938:p.Arg63Leu	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_080614	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	Missense_Mutation	SNP	ENST00000243938.4	37	CCDS33478.1	58|58	0.026556776556776556|0.026556776556776556	12|12	0.024390243902439025|0.024390243902439025	12|12	0.03314917127071823|0.03314917127071823	0|0	0.0|0.0	34|34	0.044854881266490766|0.044854881266490766	C|C	0.961|0.961	-0.703300|-0.703300	0.03255|0.03255	0.024739|0.024739	0.059419|0.059419	ENSG00000124116|ENSG00000124116	ENST00000337205|ENST00000243938;ENST00000372632	.|T;T	.|0.73047	.|-0.71;-0.71	4.29|4.29	-2.87|-2.87	0.05700|0.05700	.|Whey acidic protein, 4-disulphide core (5);	.|0.965279	.|0.08394	.|N	.|0.952462	.|T	.|0.12902	.|0.0313	L|L	0.39085|0.39085	1.19|1.19	0.09310|0.09310	N|N	1|1	.|B	.|0.27882	.|0.192	.|B	.|0.26416	.|0.069	.|T	.|0.17561	.|-1.0365	.|10	.|0.41790	.|T	.|0.15	0.0047|0.0047	9.1823|9.1823	0.37149|0.37149	0.0:0.4443:0.0:0.5557|0.0:0.4443:0.0:0.5557	.|.	.|63	.|Q8IUB2	.|WFDC3_HUMAN	X|L	57|63	.|ENSP00000243938:R63L;ENSP00000361715:R63L	.|ENSP00000243938:R63L	G|R	-|-	1|2	0|0	WFDC3|WFDC3	43851000|43851000	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.354000|0.354000	0.29330|0.29330	-1.533000|-1.533000	0.02215|0.02215	-0.658000|-0.658000	0.05366|0.05366	-0.150000|-0.150000	0.13652|0.13652	GGA|CGG	C|0.952;A|0.048	0.048	strong		0.532	WFDC3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316858.1		
SLC35B2	347734	hgsc.bcm.edu	37	6	44223292	44223292	+	Silent	SNP	C	C	T	rs35112470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44223292C>T	ENST00000393812.3	-	4	593	c.450G>A	c.(448-450)acG>acA	p.T150T	SLC35B2_ENST00000538577.1_Silent_p.T57T|SLC35B2_ENST00000495706.1_5'UTR|SLC35B2_ENST00000537814.1_Silent_p.T17T|SLC35B2_ENST00000393810.1_3'UTR|MIR4647_ENST00000583964.1_RNA	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	150					3'-phospho-5'-adenylyl sulfate transmembrane transport (GO:1902559)|3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|3'-phosphoadenosine 5'-phosphosulfate transport (GO:0046963)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity (GO:0046964)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	15	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			ACTGCGAGTCCGTAAAGCGCT	0.587													C|||	114	0.0227636	0.0855	0.0014	5008	,	,		18748	0.0		0.0	False		,,,				2504	0.0				p.T150T		Atlas-SNP	.											.	SLC35B2	40	.	0			c.G450A						PASS	.	C		296,4110	162.2+/-194.2	7,282,1914	94.0	93.0	93.0		450	-11.6	0.5	6	dbSNP_126	93	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	SLC35B2	NM_178148.2		7,289,6207	TT,TC,CC		0.0814,6.7181,2.3297		150/433	44223292	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	347734	exon4			CGAGTCCGTAAAG	AK075456	CCDS34462.1, CCDS69127.1, CCDS75462.1, CCDS75463.1	6p12.1-p11.21	2013-07-17	2013-07-17		ENSG00000157593	ENSG00000157593		"""Solute carriers"""	16872	protein-coding gene	gene with protein product		610788	"""solute carrier family 35, member B2"""				Standard	NM_001286517		Approved	UGTrel4	uc003oxd.3	Q8TB61	OTTHUMG00000014760	ENST00000393812.3:c.450G>A	6.37:g.44223292C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	126	72	0.571429	NM_178148	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Silent	SNP	ENST00000393812.3	37	CCDS34462.1																																																																																			C|0.977;T|0.023	0.023	strong		0.587	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2		
MOB3A	126308	hgsc.bcm.edu	37	19	2078488	2078488	+	Silent	SNP	T	T	C	rs2074894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2078488T>C	ENST00000357066.3	-	3	451	c.72A>G	c.(70-72)ccA>ccG	p.P24P	MOB3A_ENST00000592280.1_Silent_p.P24P|MOB3A_ENST00000592143.1_Intron	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	24						intracellular (GO:0005622)	metal ion binding (GO:0046872)										GCTGGGTGCCTGGCTCAAACT	0.627													C|||	1973	0.39397	0.6528	0.2507	5008	,	,		16431	0.1835		0.329	False		,,,				2504	0.4294				p.P24P		Atlas-SNP	.											MOBKL2A,rectum,carcinoma,0,1	.	.	1	0			c.A72G						PASS	.	C		2793,1613	497.7+/-363.9	887,1019,297	55.0	57.0	56.0		72	-8.5	0.0	19	dbSNP_96	56	2932,5668	665.8+/-402.3	506,1920,1874	no	coding-synonymous	MOB3A	NM_130807.2		1393,2939,2171	CC,CT,TT		34.093,36.6092,44.0181		24/218	2078488	5725,7281	2203	4300	6503	SO:0001819	synonymous_variant	126308	exon3			GGTGCCTGGCTCA	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.72A>G	19.37:g.2078488T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			T|0.597;C|0.403	0.403	strong		0.627	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
LRP2	4036	hgsc.bcm.edu	37	2	170088351	170088351	+	Splice_Site	SNP	G	G	A	rs2302694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170088351G>A	ENST00000263816.3	-	31	5385	c.5100C>T	c.(5098-5100)tcC>tcT	p.S1700S		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1700	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)"""	ATGGATTCACGGCTGCATGAG	0.488													G|||	920	0.183706	0.4228	0.1931	5008	,	,		19030	0.0526		0.1093	False		,,,				2504	0.0654				p.S1700S		Atlas-SNP	.											.	LRP2	751	.	0			c.C5100T						PASS	.	G		1684,2722	509.1+/-367.1	321,1042,840	49.0	54.0	52.0		5100	-1.4	0.0	2	dbSNP_100	52	969,7631	209.8+/-250.9	68,833,3399	yes	coding-synonymous-near-splice	LRP2	NM_004525.2		389,1875,4239	AA,AG,GG		11.2674,38.2206,20.3983		1700/4656	170088351	2653,10353	2203	4300	6503	SO:0001630	splice_region_variant	4036	exon31			ATTCACGGCTGCA		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.5099-1C>T	2.37:g.170088351G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	179	111	0.620112	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			G|0.806;A|0.194	0.194	strong		0.488	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	Silent
SNED1	25992	hgsc.bcm.edu	37	2	241979550	241979550	+	Silent	SNP	T	T	C	rs7571117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241979550T>C	ENST00000310397.8	+	7	1104	c.1104T>C	c.(1102-1104)aaT>aaC	p.N368N	SNED1_ENST00000405547.3_Silent_p.N368N|SNED1_ENST00000401884.1_Silent_p.N368N|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000342631.6_Silent_p.N368N	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	368	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Follistatin-like 1.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		AGGTGGAGAATGGCTCTGCGG	0.612													C|||	2241	0.447484	0.6059	0.3473	5008	,	,		19799	0.3214		0.4602	False		,,,				2504	0.4213				p.N368N		Atlas-SNP	.											.	SNED1	76	.	0			c.T1104C						PASS	.	C		2626,1640		827,972,334	32.0	39.0	37.0		1104	-4.8	0.0	2	dbSNP_116	37	4146,4356		1043,2060,1148	no	coding-synonymous	SNED1	NM_001080437.1		1870,3032,1482	CC,CT,TT		48.765,38.4435,46.9612		368/1414	241979550	6772,5996	2133	4251	6384	SO:0001819	synonymous_variant	25992	exon7			GGAGAATGGCTCT	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.1104T>C	2.37:g.241979550T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1	954|954	0.4368131868131868|0.4368131868131868	291|291	0.5914634146341463|0.5914634146341463	130|130	0.35911602209944754|0.35911602209944754	189|189	0.3304195804195804|0.3304195804195804	344|344	0.45382585751978893|0.45382585751978893	C|C	0.088|0.088	-1.172244|-1.172244	0.01646|0.01646	0.615565|0.615565	0.48765|0.48765	ENSG00000162804|ENSG00000162804	ENST00000431690|ENST00000401644	.|.	.|.	.|.	4.73|4.73	-4.77|-4.77	0.03219|0.03219	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43686|0.43686	-0.9376|-0.9376	3|3	.|.	.|.	.|.	.|.	2.7388|2.7388	0.05247|0.05247	0.1001:0.2577:0.1972:0.445|0.1001:0.2577:0.1972:0.445	rs7571117;rs61028234;rs7571117|rs7571117;rs61028234;rs7571117	.|.	.|.	.|.	T|R	26|65	.|.	.|.	M|W	+|+	2|1	0|0	SNED1|SNED1	241628223|241628223	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-1.799000|-1.799000	0.01746|0.01746	-1.361000|-1.361000	0.02169|0.02169	-0.972000|-0.972000	0.02603|0.02603	ATG|TGG	T|0.554;C|0.446	0.446	strong		0.612	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
SYCP2	10388	hgsc.bcm.edu	37	20	58476774	58476774	+	Silent	SNP	G	G	A	rs6027186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58476774G>A	ENST00000357552.3	-	16	1350	c.1125C>T	c.(1123-1125)gaC>gaT	p.D375D	SYCP2_ENST00000371001.2_Silent_p.D375D			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	375					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			CTAGTGATGCGTCAAAATACA	0.274													A|||	498	0.0994409	0.2814	0.0432	5008	,	,		16573	0.0159		0.0368	False		,,,				2504	0.044				p.D375D		Atlas-SNP	.											SYCP2,caecum,carcinoma,0,1	SYCP2	204	1	0			c.C1125T						PASS	.	A		1031,3367	716.1+/-408.6	123,785,1291	72.0	71.0	71.0		1125	4.5	0.8	20	dbSNP_114	71	314,8262	797.4+/-407.4	3,308,3977	no	coding-synonymous	SYCP2	NM_014258.2		126,1093,5268	AA,AG,GG		3.6614,23.4425,10.3669		375/1531	58476774	1345,11629	2199	4288	6487	SO:0001819	synonymous_variant	10388	exon15			TGATGCGTCAAAA	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1125C>T	20.37:g.58476774G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Silent	SNP	ENST00000357552.3	37	CCDS13482.1																																																																																			G|0.900;A|0.100	0.100	strong		0.274	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	
LRRC3B	116135	hgsc.bcm.edu	37	3	26751526	26751526	+	Silent	SNP	C	C	T	rs141944883		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:26751526C>T	ENST00000396641.2	+	2	955	c.363C>T	c.(361-363)tcC>tcT	p.S121S	AC114877.3_ENST00000446601.1_lincRNA|LRRC3B_ENST00000417744.1_Silent_p.S121S|LRRC3B_ENST00000456208.2_Silent_p.S121S	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	121						integral component of membrane (GO:0016021)		p.S121S(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						TGGACTTGTCCGACAATCGGA	0.473																																					p.S121S		Atlas-SNP	.											LRRC3B,NS,NS,0,1	LRRC3B	51	1	1	Substitution - coding silent(1)	pancreas(1)	c.C363T						scavenged	.	C		0,4406		0,0,2203	62.0	58.0	60.0		363	-1.9	1.0	3	dbSNP_134	60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LRRC3B	NM_052953.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		121/260	26751526	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	116135	exon2			CTTGTCCGACAAT	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.363C>T	3.37:g.26751526C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	137	3	0.0218978	NM_052953	Q5M8T0	Silent	SNP	ENST00000396641.2	37	CCDS2644.1																																																																																			C|1.000;T|0.000	0.000	weak		0.473	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953	
OVGP1	5016	hgsc.bcm.edu	37	1	111957311	111957311	+	Missense_Mutation	SNP	G	G	C	rs10067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111957311G>C	ENST00000369732.3	-	11	1867	c.1812C>G	c.(1810-1812)caC>caG	p.H604Q		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	604			H -> Q (in dbSNP:rs10067).		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.H604Q(1)		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)		CCATCCTGGGGTGAGTGCCCA	0.522													G|||	1477	0.294928	0.4539	0.1628	5008	,	,		18670	0.3919		0.1103	False		,,,				2504	0.2638				p.H604Q		Atlas-SNP	.											OVGP1_ENST00000369728,NS,carcinoma,-1,3	OVGP1	177	3	1	Substitution - Missense(1)	stomach(1)	c.C1812G	GRCh37	CM066158	OVGP1	M	rs10067	PASS	.	G	GLN/HIS	1700,2706	512.9+/-368.2	328,1044,831	79.0	78.0	78.0		1812	0.2	0.0	1	dbSNP_52	78	709,7891	174.6+/-224.8	31,647,3622	yes	missense	OVGP1	NM_002557.3	24	359,1691,4453	CC,CG,GG		8.2442,38.5837,18.5222	benign	604/679	111957311	2409,10597	2203	4300	6503	SO:0001583	missense	5016	exon11			CCTGGGGTGAGTG	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.1812C>G	1.37:g.111957311G>C	ENSP00000358747:p.His604Gln	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	181	78	0.430939	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	568	0.2600732600732601	186	0.3780487804878049	59	0.16298342541436464	240	0.4195804195804196	83	0.10949868073878628	G	6.288	0.421200	0.11928	0.385837	0.082442	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.04119	3.7	3.3	0.215	0.15253	.	32.642700	0.00166	N	0.000000	T	0.01061	0.0035	N	0.14661	0.345	0.80722	P	0.0	B;B	0.12013	0.005;0.005	B;B	0.10450	0.005;0.005	T	0.46582	-0.9181	9	0.66056	D	0.02	2.2789	4.0053	0.09598	0.1197:0.0:0.4665:0.4138	rs10067;rs3767611;rs17027624;rs52822661;rs10067	604;668	Q12889;Q59HH5	OVGP1_HUMAN;.	Q	604;668;412	ENSP00000358747:H604Q	ENSP00000358743:H668Q	H	-	3	2	OVGP1	111758834	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.609000	0.05635	0.059000	0.16252	0.585000	0.79938	CAC	G|0.785;C|0.214	0.214	strong		0.522	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
HYDIN	54768	hgsc.bcm.edu	37	16	70934974	70934974	+	Missense_Mutation	SNP	T	T	C	rs12102425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70934974T>C	ENST00000393567.2	-	53	9131	c.8981A>G	c.(8980-8982)gAg>gGg	p.E2994G		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2994			E -> G (in dbSNP:rs12102425).		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)				CAGGCCGTACTCAGCCTCAGG	0.567																																					p.E2994G		Atlas-SNP	.											.	HYDIN	788	.	0			c.A8981G						PASS	.	T	GLY/GLU	584,3442		0,584,1429	140.0	136.0	138.0		8978	4.4	0.2	16	dbSNP_120	138	146,8200		0,146,4027	yes	missense	HYDIN	NM_032821.2	98	0,730,5456	CC,CT,TT		1.7493,14.5057,5.9004	probably-damaging	2993/5121	70934974	730,11642	2013	4173	6186	SO:0001583	missense	54768	exon53			CCGTACTCAGCCT	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.8981A>G	16.37:g.70934974T>C	ENSP00000377197:p.Glu2994Gly	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	181	46	0.254144	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	183	0.08379120879120878	101	0.20528455284552846	39	0.10773480662983426	28	0.04895104895104895	15	0.01978891820580475	T	14.42	2.529006	0.44969	0.145057	0.017493	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01119	5.31	4.39	4.39	0.52855	.	0.000000	0.32970	U	0.005437	T	0.00012	0.0000	M	0.76002	2.32	0.80722	D	1	D	0.53885	0.963	P	0.50109	0.631	T	0.71570	-0.4553	10	0.34782	T	0.22	.	13.5437	0.61690	0.0:0.0:0.0:1.0	rs12102425;rs12102425	2993	F8WD23	.	G	2994;2993	ENSP00000377197:E2994G	ENSP00000313052:E2993G	E	-	2	0	HYDIN	69492475	1.000000	0.71417	0.158000	0.22627	0.119000	0.20118	4.680000	0.61656	1.747000	0.51819	0.164000	0.16699	GAG	.	.	weak		0.567	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
TEKT4	150483	hgsc.bcm.edu	37	2	95542476	95542476	+	Missense_Mutation	SNP	C	C	T	rs1052809		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:95542476C>T	ENST00000295201.4	+	6	1407	c.1270C>T	c.(1270-1272)Cgc>Tgc	p.R424C	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	424					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						CCATCGTACTCGCTACCCCAC	0.592													C|||	1	0.000199681	0.0	0.0	5008	,	,		19845	0.0		0.0	False		,,,				2504	0.001				p.R424C		Atlas-SNP	.											TEKT4,NS,carcinoma,0,1	TEKT4	72	1	0			c.C1270T						scavenged	.						77.0	53.0	61.0					2																	95542476		2203	4300	6503	SO:0001583	missense	150483	exon6			CGTACTCGCTACC	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.1270C>T	2.37:g.95542476C>T	ENSP00000295201:p.Arg424Cys	Somatic	59	2	0.0338983		WXS	Illumina HiSeq	Phase_I	59	9	0.152542	NM_144705		Missense_Mutation	SNP	ENST00000295201.4	37	CCDS2005.1	.	.	.	.	.	.	.	.	.	.	.	12.76	2.033512	0.35893	.	.	ENSG00000163060	ENST00000295201	T	0.02916	4.11	2.43	2.43	0.29744	.	0.261531	0.37623	N	0.002019	T	0.03651	0.0104	L	0.60455	1.87	0.80722	D	1	P	0.36874	0.572	B	0.32583	0.148	T	0.50792	-0.8786	10	0.44086	T	0.13	-7.0137	10.5484	0.45072	0.0:1.0:0.0:0.0	rs1052809;rs3193279	424	Q8WW24	TEKT4_HUMAN	C	424	ENSP00000295201:R424C	ENSP00000295201:R424C	R	+	1	0	TEKT4	94906203	0.031000	0.19500	0.725000	0.30721	0.755000	0.42902	0.890000	0.28295	1.049000	0.40321	0.281000	0.19383	CGC	C|0.667;T|0.333	0.333	strong		0.592	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
ZNF782	158431	hgsc.bcm.edu	37	9	99581811	99581811	+	Missense_Mutation	SNP	C	C	T	rs4645656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99581811C>T	ENST00000481138.1	-	6	1155	c.494G>A	c.(493-495)cGt>cAt	p.R165H	ZNF782_ENST00000535338.1_Missense_Mutation_p.R33H|ZNF782_ENST00000466833.1_5'UTR	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	165			R -> H (in dbSNP:rs4645656).		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.R165H(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				ACAAACATTACGCTCATGAGC	0.433													T|||	1364	0.272364	0.6271	0.0735	5008	,	,		17730	0.3185		0.0318	False		,,,				2504	0.1339				p.R165H		Atlas-SNP	.											ZNF782,rectum,carcinoma,-1,2	ZNF782	64	2	1	Substitution - Missense(1)	stomach(1)	c.G494A						scavenged	.	T	HIS/ARG	2402,2004	559.9+/-380.3	661,1080,462	83.0	85.0	84.0		494	-4.0	0.0	9	dbSNP_111	84	176,8424	811.3+/-407.1	1,174,4125	yes	missense	ZNF782	NM_001001662.1	29	662,1254,4587	TT,TC,CC		2.0465,45.4834,19.8216	benign	165/700	99581811	2578,10428	2203	4300	6503	SO:0001583	missense	158431	exon6			ACATTACGCTCAT	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.494G>A	9.37:g.99581811C>T	ENSP00000419397:p.Arg165His	Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	107	67	0.626168	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	548	0.2509157509157509	303	0.6158536585365854	27	0.07458563535911603	192	0.3356643356643357	26	0.03430079155672823	T	5.842	0.339619	0.11069	0.545166	0.020465	ENSG00000196597	ENST00000481138;ENST00000535338;ENST00000478850	T;T;T	0.05996	3.53;3.36;5.86	3.38	-4.0	0.04057	.	.	.	.	.	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	0.34254	-0.9836	8	0.17369	T	0.5	.	3.2255	0.06730	0.1753:0.4618:0.0921:0.2708	rs4645656;rs52822922;rs4645656	165	Q6ZMW2	ZN782_HUMAN	H	165;33;165	ENSP00000419397:R165H;ENSP00000440624:R33H;ENSP00000417577:R165H	ENSP00000417577:R165H	R	-	2	0	ZNF782	98621632	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	-0.145000	0.10265	-1.320000	0.02283	-0.987000	0.02553	CGT	C|0.769;T|0.231	0.231	strong		0.433	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
SMYD4	114826	hgsc.bcm.edu	37	17	1686410	1686410	+	Missense_Mutation	SNP	T	T	C	rs9902398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1686410T>C	ENST00000305513.7	-	10	2347	c.2180A>G	c.(2179-2181)tAc>tGc	p.Y727C		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	727			Y -> C (in dbSNP:rs9902398). {ECO:0000269|PubMed:11572484, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.				metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						CTCCACCACGTAGAGACTCCT	0.498													C|||	3890	0.776757	0.9198	0.7565	5008	,	,		16446	0.7758		0.7386	False		,,,				2504	0.638				p.Y727C		Atlas-SNP	.											.	SMYD4	50	.	0			c.A2180G						PASS	.	C	CYS/TYR	3925,481	226.2+/-241.8	1743,439,21	68.0	75.0	73.0		2180	-11.7	0.0	17	dbSNP_119	73	6085,2515	411.6+/-350.5	2159,1767,374	yes	missense	SMYD4	NM_052928.2	194	3902,2206,395	CC,CT,TT		29.2442,10.9169,23.0355	benign	727/805	1686410	10010,2996	2203	4300	6503	SO:0001583	missense	114826	exon10			ACCACGTAGAGAC	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.2180A>G	17.37:g.1686410T>C	ENSP00000304360:p.Tyr727Cys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	1735	0.7944139194139194	455	0.9247967479674797	256	0.7071823204419889	447	0.7814685314685315	577	0.7612137203166227	C	5.222	0.226433	0.09916	0.890831	0.707558	ENSG00000186532	ENST00000305513	T	0.62941	-0.01	5.84	-11.7	0.00046	Tetratricopeptide-like helical (1);	1.753970	0.02292	N	0.070408	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.19583	0.037	B	0.09377	0.004	T	0.47611	-0.9104	9	0.41790	T	0.15	10.414	12.5806	0.56388	0.0647:0.1443:0.069:0.722	rs9902398;rs17857050;rs57727381;rs9902398	727	Q8IYR2	SMYD4_HUMAN	C	727	ENSP00000304360:Y727C	ENSP00000304360:Y727C	Y	-	2	0	SMYD4	1633160	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-3.368000	0.00495	-2.928000	0.00302	-1.212000	0.01626	TAC	T|0.220;C|0.780	0.780	strong		0.498	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
ULBP1	80329	hgsc.bcm.edu	37	6	150285209	150285209	+	Silent	SNP	G	G	C	rs61742437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:150285209G>C	ENST00000229708.3	+	1	67	c.24G>C	c.(22-24)gcG>gcC	p.A8A		NM_025218.2	NP_079494.1	Q9BZM6	N2DL1_HUMAN	UL16 binding protein 1	8					antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			large_intestine(3)|lung(5)|pancreas(1)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.14e-11)		CCAGCCCCGCGTTCCTTCTGT	0.642													G|||	875	0.17472	0.4569	0.1124	5008	,	,		14283	0.0109		0.1064	False		,,,				2504	0.0767				p.A8A		Atlas-SNP	.											.	ULBP1	25	.	0			c.G24C						PASS	.	G		1724,2682	502.2+/-365.2	354,1016,833	43.0	48.0	46.0		24	0.7	0.0	6	dbSNP_129	46	808,7792	184.3+/-232.3	37,734,3529	no	coding-synonymous	ULBP1	NM_025218.2		391,1750,4362	CC,CG,GG		9.3953,39.1285,19.4679		8/245	150285209	2532,10474	2203	4300	6503	SO:0001819	synonymous_variant	80329	exon1			CCCCGCGTTCCTT	AF304377	CCDS5223.1	6q25	2003-04-29			ENSG00000111981	ENSG00000111981			14893	protein-coding gene	gene with protein product		605697				11239445, 11827464	Standard	XM_005267151		Approved	RAET1I	uc003qnp.3	Q9BZM6	OTTHUMG00000015810	ENST00000229708.3:c.24G>C	6.37:g.150285209G>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	151	74	0.490066	NM_025218	Q5VY81|Q8IZW3|Q8IZX6	Silent	SNP	ENST00000229708.3	37	CCDS5223.1																																																																																			G|0.819;C|0.181	0.181	strong		0.642	ULBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042677.2		
KLK4	9622	hgsc.bcm.edu	37	19	51412668	51412668	+	Missense_Mutation	SNP	A	A	C	rs1654551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51412668A>C	ENST00000324041.1	-	2	63	c.64T>G	c.(64-66)Tcg>Gcg	p.S22A	KLK4_ENST00000431178.2_5'Flank|KLK4_ENST00000597441.1_5'Flank	NM_004917.3	NP_004908.3	Q9Y5K2	KLK4_HUMAN	kallikrein-related peptidase 4	22			S -> A (in dbSNP:rs1654551). {ECO:0000269|PubMed:15235027}.		amelogenesis (GO:0097186)|extracellular matrix disassembly (GO:0022617)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(8)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00624)|GBM - Glioblastoma multiforme(134;0.00878)		GAGACGAGCGATCCTGAGGGC	0.637													A|||	644	0.128594	0.2678	0.0605	5008	,	,		11795	0.0873		0.0736	False		,,,				2504	0.0879				p.S22A		Atlas-SNP	.											KLK4,colon,carcinoma,+2,2	KLK4	46	2	0			c.T64G						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	107	0	0		WXS	Illumina HiSeq	Phase_I	131	52	0.396947	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	
OR52E6	390078	hgsc.bcm.edu	37	11	5862937	5862937	+	Missense_Mutation	SNP	C	C	A	rs4495918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5862937C>A	ENST00000329322.5	-	1	190	c.191G>T	c.(190-192)tGc>tTc	p.C64F	OR52E6_ENST00000379946.2_Missense_Mutation_p.C68F|TRIM5_ENST00000380027.1_Intron	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	64			C -> F (in dbSNP:rs4495918).			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)		CATGGCCAGGCAGTAGTACAT	0.448													A|||	1924	0.384185	0.379	0.3184	5008	,	,		22509	0.4593		0.3728	False		,,,				2504	0.3722				p.C64F		Atlas-SNP	.											.	OR52E6	70	.	0			c.G191T						PASS	.	A	PHE/CYS	1620,2782	658.7+/-400.4	294,1032,875	125.0	123.0	124.0		191	3.6	0.5	11	dbSNP_111	124	3008,5584	663.9+/-402.1	533,1942,1821	no	missense	OR52E6	NM_001005167.1	205	827,2974,2696	AA,AC,CC		35.0093,36.8015,35.6164	benign	64/314	5862937	4628,8366	2201	4296	6497	SO:0001583	missense	390078	exon1			GCCAGGCAGTAGT	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.191G>T	11.37:g.5862937C>A	ENSP00000328878:p.Cys64Phe	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	155	79	0.509677	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	0.003	-2.527363	0.00147	0.368015	0.350093	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.00784	5.7;5.7	3.64	3.64	0.41730	GPCR, rhodopsin-like superfamily (1);	0.105180	0.42548	N	0.000695	T	0.00012	0.0000	N	0.00001	-3.875	0.52501	P	4.899999999996574E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.33803	-0.9854	9	0.02654	T	1	.	9.1143	0.36748	0.8144:0.1856:0.0:0.0	rs4495918;rs52836131;rs4495918	64	Q96RD3	O52E6_HUMAN	F	64;68	ENSP00000328878:C64F;ENSP00000369279:C68F	ENSP00000328878:C64F	C	-	2	0	OR52E6	5819513	0.540000	0.26410	0.519000	0.27824	0.036000	0.12997	4.740000	0.62087	0.475000	0.27415	-0.381000	0.06696	TGC	C|0.611;A|0.389	0.389	strong		0.448	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
AKNA	80709	hgsc.bcm.edu	37	9	117104368	117104368	+	Silent	SNP	G	G	A	rs73548990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117104368G>A	ENST00000307564.4	-	20	3956	c.3795C>T	c.(3793-3795)ccC>ccT	p.P1265P	AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374075.5_Silent_p.P1184P|AKNA_ENST00000374079.4_Silent_p.P210P|AKNA_ENST00000374088.3_Silent_p.P1265P|AKNA_ENST00000223791.3_Silent_p.P725P	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1265					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GGGTATCAGCGGGAGGCGGTC	0.567													G|||	130	0.0259585	0.093	0.0072	5008	,	,		18549	0.0		0.002	False		,,,				2504	0.0				p.P1265P		Atlas-SNP	.											.	AKNA	119	.	0			c.C3795T						PASS	.	G		303,4103	164.0+/-195.7	7,289,1907	52.0	51.0	51.0		3795	1.6	0.0	9	dbSNP_130	51	1,8599		0,1,4299	no	coding-synonymous	AKNA	NM_030767.4		7,290,6206	AA,AG,GG		0.0116,6.877,2.3374		1265/1440	117104368	304,12702	2203	4300	6503	SO:0001819	synonymous_variant	80709	exon20			ATCAGCGGGAGGC	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3795C>T	9.37:g.117104368G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	50	34	0.68	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1	56	0.02564102564102564	51	0.10365853658536585	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	4.086	0.013849	0.07959	0.06877	1.16E-4	ENSG00000106948	ENST00000320310	.	.	.	4.95	1.61	0.23674	.	0.482521	0.19304	N	0.117578	T	0.01189	0.0039	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.03130	-1.1069	6	0.87932	D	0	-5.6524	5.4261	0.16427	0.1935:0.0:0.6201:0.1863	.	.	.	.	L	276	.	ENSP00000314538:P276L	P	-	2	0	AKNA	116144189	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.483000	0.02318	0.275000	0.22094	-0.244000	0.11960	CCG	G|0.978;A|0.022	0.022	strong		0.567	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
RPUSD1	113000	hgsc.bcm.edu	37	16	836111	836111	+	Missense_Mutation	SNP	G	G	T	rs112366818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:836111G>T	ENST00000561734.1	-	5	1021	c.778C>A	c.(778-780)Cct>Act	p.P260T	MSLNL_ENST00000442466.1_5'Flank|CHTF18_ENST00000262315.9_5'Flank|CHTF18_ENST00000455171.2_5'Flank|RPUSD1_ENST00000567114.1_Missense_Mutation_p.P131T|CHTF18_ENST00000317063.6_5'Flank|RPUSD1_ENST00000565809.1_3'UTR|RPUSD1_ENST00000007264.2_Missense_Mutation_p.P260T			Q9UJJ7	RUSD1_HUMAN	RNA pseudouridylate synthase domain containing 1	260	Pro-rich.				pseudouridine synthesis (GO:0001522)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			endometrium(3)|lung(2)|skin(2)	7		Hepatocellular(780;0.00335)				TCGGGGTCAGGGTCGGGGGTG	0.721													G|||	227	0.0453275	0.1641	0.0115	5008	,	,		13109	0.0		0.002	False		,,,				2504	0.0				p.P260T		Atlas-SNP	.											.	RPUSD1	19	.	0			c.C778A						PASS	.	G	THR/PRO	471,3899		25,421,1739	18.0	24.0	22.0		778	4.2	1.0	16	dbSNP_132	22	3,8555		0,3,4276	yes	missense	RPUSD1	NM_058192.2	38	25,424,6015	TT,TG,GG		0.0351,10.778,3.6665	possibly-damaging	260/313	836111	474,12454	2185	4279	6464	SO:0001583	missense	113000	exon6			GGTCAGGGTCGGG	AE006465	CCDS10426.1	16p13.3	2013-02-11	2005-01-31	2005-01-31	ENSG00000007376	ENSG00000007376		"""RNA pseudouridylate synthase domain containing"""	14173	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 40"""	C16orf40			Standard	NM_058192		Approved	RLUCL, MGC19600	uc002ckb.3	Q9UJJ7	OTTHUMG00000047840	ENST00000561734.1:c.778C>A	16.37:g.836111G>T	ENSP00000455026:p.Pro260Thr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_058192	D3DU66	Missense_Mutation	SNP	ENST00000561734.1	37	CCDS10426.1	79	0.036172161172161175	75	0.1524390243902439	4	0.011049723756906077	0	0.0	0	0.0	G	10.09	1.256160	0.22965	0.10778	3.51E-4	ENSG00000007376	ENST00000007264	T	0.16743	2.32	4.21	4.21	0.49690	.	0.832292	0.11055	N	0.604570	T	0.00109	0.0003	L	0.44542	1.39	0.20703	N	0.999863	P	0.52316	0.952	P	0.45998	0.5	T	0.08554	-1.0716	10	0.72032	D	0.01	-9.908	12.1354	0.53968	0.0:0.0:1.0:0.0	.	260	Q9UJJ7	RUSD1_HUMAN	T	260	ENSP00000007264:P260T	ENSP00000007264:P260T	P	-	1	0	RPUSD1	776112	0.991000	0.36638	0.987000	0.45799	0.161000	0.22273	2.137000	0.42130	1.920000	0.55613	0.456000	0.33151	CCT	G|0.962;T|0.038	0.038	strong		0.721	RPUSD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420620.1	NM_058192	
MIER2	54531	hgsc.bcm.edu	37	19	307282	307282	+	Missense_Mutation	SNP	T	T	C	rs35042658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:307282T>C	ENST00000264819.4	-	13	1463	c.1453A>G	c.(1453-1455)Agc>Ggc	p.S485G	CTD-3113P16.5_ENST00000591533.1_RNA	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	485			S -> G (in dbSNP:rs35042658).		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)		TCCACATGGCTGGAGATGAGG	0.647													T|||	249	0.0497204	0.1808	0.013	5008	,	,		15517	0.0		0.001	False		,,,				2504	0.0				p.S485G		Atlas-SNP	.											.	MIER2	51	.	0			c.A1453G						PASS	.	T	GLY/SER	552,3848		29,494,1677	28.0	25.0	26.0		1453	3.0	0.2	19	dbSNP_126	26	9,8589		0,9,4290	yes	missense	MIER2	NM_017550.1	56	29,503,5967	CC,CT,TT		0.1047,12.5455,4.316	benign	485/546	307282	561,12437	2200	4299	6499	SO:0001583	missense	54531	exon13			CATGGCTGGAGAT	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.1453A>G	19.37:g.307282T>C	ENSP00000264819:p.Ser485Gly	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	161	85	0.52795	NM_017550	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	37	CCDS32855.1	112	0.05128205128205128	108	0.21951219512195122	4	0.011049723756906077	0	0.0	0	0.0	T	5.043	0.193576	0.09599	0.125455	0.001047	ENSG00000105556	ENST00000264819	T	0.15834	2.39	4.02	3.0	0.34707	.	0.118436	0.38058	N	0.001834	T	0.00012	0.0000	N	0.25485	0.75	0.42449	P	0.007252000000000036	B	0.06786	0.001	B	0.04013	0.001	T	0.37934	-0.9684	9	0.33940	T	0.23	-8.985	5.2116	0.15320	0.0:0.2476:0.0:0.7524	rs35042658	485	Q8N344	MIER2_HUMAN	G	485	ENSP00000264819:S485G	ENSP00000264819:S485G	S	-	1	0	MIER2	258282	1.000000	0.71417	0.220000	0.23810	0.106000	0.19336	1.279000	0.33191	0.701000	0.31803	0.533000	0.62120	AGC	T|0.946;C|0.054	0.054	strong		0.647	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843	
PKD1	5310	hgsc.bcm.edu	37	16	2166538	2166538	+	Missense_Mutation	SNP	G	G	A	rs149022148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2166538G>A	ENST00000262304.4	-	8	1922	c.1714C>T	c.(1714-1716)Ccc>Tcc	p.P572S	PKD1_ENST00000423118.1_Missense_Mutation_p.P572S|RP11-304L19.2_ENST00000562027.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	572			P -> S (in dbSNP:rs149022148). {ECO:0000269|PubMed:11967008}.		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						ACCTCCACGGGCTCGTGCGGG	0.682													g|||	204	0.0407348	0.1467	0.0144	5008	,	,		12972	0.0		0.0	False		,,,				2504	0.0				p.P572S		Atlas-SNP	.											PKD1,caecum,carcinoma,0,1	PKD1	184	1	0			c.C1714T						PASS	.	G	SER/PRO,SER/PRO	422,3878		16,390,1744	7.0	8.0	7.0		1714,1714	1.8	0.0	16	dbSNP_134	7	4,8436		0,4,4216	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	74,74	16,394,5960	AA,AG,GG		0.0474,9.814,3.3438	benign,benign	572/4303,572/4304	2166538	426,12314	2150	4220	6370	SO:0001583	missense	5310	exon8			CCACGGGCTCGTG	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.1714C>T	16.37:g.2166538G>A	ENSP00000262304:p.Pro572Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	86	0.039377289377289376	81	0.16463414634146342	5	0.013812154696132596	0	0.0	0	0.0	G	8.927	0.962500	0.18583	0.09814	4.74E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.34472	1.36;1.36	4.27	1.83	0.25207	Polycystin cation channel (1);	0.410377	0.23245	N	0.050320	T	0.00109	0.0003	L	0.60455	1.87	0.80722	P	0.0	B;B	0.33171	0.4;0.179	B;B	0.30855	0.121;0.057	T	0.10941	-1.0608	9	0.11182	T	0.66	.	7.8856	0.29648	0.0:0.2683:0.5323:0.1994	.	572;572	P98161-3;P98161	.;PKD1_HUMAN	S	572;572;505	ENSP00000262304:P572S;ENSP00000399501:P572S	ENSP00000262304:P572S	P	-	1	0	PKD1	2106539	0.000000	0.05858	0.004000	0.12327	0.034000	0.12701	0.309000	0.19332	0.907000	0.36646	0.555000	0.69702	CCC	G|0.961;A|0.039	0.039	strong		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
PEAR1	375033	hgsc.bcm.edu	37	1	156882996	156882996	+	Silent	SNP	G	G	C	rs822441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	131	0	0		WXS	Illumina HiSeq	Phase_I	138	135	0.978261	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	
LRRC36	55282	hgsc.bcm.edu	37	16	67397580	67397580	+	Missense_Mutation	SNP	G	G	C	rs9922085	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67397580G>C	ENST00000329956.6	+	6	684	c.665G>C	c.(664-666)cGt>cCt	p.R222P	LRRC36_ENST00000435835.3_Missense_Mutation_p.R101P|LRRC36_ENST00000541146.1_5'UTR|LRRC36_ENST00000563189.1_Missense_Mutation_p.R101P|LRRC36_ENST00000290940.7_5'UTR	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36	222			R -> P (in dbSNP:rs9922085).							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)		AATGGTACACGTGATCAGAAA	0.413													C|||	1032	0.20607	0.6415	0.085	5008	,	,		20907	0.003		0.0408	False		,,,				2504	0.0828				p.R222P		Atlas-SNP	.											.	LRRC36	68	.	0			c.G665C						PASS	.	C	PRO/ARG,PRO/ARG	2214,2182	586.8+/-386.5	564,1086,548	130.0	118.0	122.0		302,665	3.8	0.6	16	dbSNP_119	122	368,8232	803.0+/-407.3	9,350,3941	yes	missense,missense	LRRC36	NM_001161575.1,NM_018296.5	103,103	573,1436,4489	CC,CG,GG		4.2791,49.636,19.8677	benign,benign	101/634,222/755	67397580	2582,10414	2198	4300	6498	SO:0001583	missense	55282	exon6			GTACACGTGATCA	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.665G>C	16.37:g.67397580G>C	ENSP00000329943:p.Arg222Pro	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	110	40	0.363636	NM_018296	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Missense_Mutation	SNP	ENST00000329956.6	37	CCDS32467.1	381	0.17445054945054944	314	0.6382113821138211	34	0.09392265193370165	2	0.0034965034965034965	31	0.040897097625329816	C	1.368	-0.586790	0.03827	0.50364	0.042791	ENSG00000159708	ENST00000329956;ENST00000435835	T;T	0.28666	3.3;1.6	5.72	3.78	0.43462	.	0.559885	0.16371	N	0.217329	T	0.00012	0.0000	N	0.00368	-1.59	0.45791	P	0.0013260000000000494	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.40270	-0.9572	9	0.08599	T	0.76	0.0108	5.464	0.16632	0.0:0.662:0.1656:0.1724	rs9922085;rs59066753;rs9922085	101;101;222	B7Z7B3;Q1X8D7-2;Q1X8D7	.;.;LRC36_HUMAN	P	222;101	ENSP00000329943:R222P;ENSP00000411122:R101P	ENSP00000329943:R222P	R	+	2	0	LRRC36	65955081	0.613000	0.27009	0.564000	0.28396	0.516000	0.34256	0.861000	0.27885	0.780000	0.33566	-0.215000	0.12644	CGT	G|0.813;C|0.187	0.187	strong		0.413	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296	
AKAP9	10142	hgsc.bcm.edu	37	7	91622249	91622249	+	Missense_Mutation	SNP	C	C	A	rs138567837		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:91622249C>A	ENST00000359028.2	+	6	717	c.492C>A	c.(490-492)gaC>gaA	p.D164E	AKAP9_ENST00000358100.2_Missense_Mutation_p.D164E|AKAP9_ENST00000394564.1_Missense_Mutation_p.D152E|AKAP9_ENST00000356239.3_Missense_Mutation_p.D152E			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	164					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAGCACAAGACAGTCCGACTC	0.388			T	BRAF	papillary thyroid								C|||	1	0.000199681	0.0008	0.0	5008	,	,		16096	0.0		0.0	False		,,,				2504	0.0				p.D152E		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C456A						PASS	.	C	GLU/ASP,GLU/ASP	4,4402	8.1+/-20.4	0,4,2199	107.0	105.0	106.0		456,456	1.5	1.0	7	dbSNP_134	106	0,8600		0,0,4300	yes	missense,missense	AKAP9	NM_005751.4,NM_147185.2	45,45	0,4,6499	AA,AC,CC		0.0,0.0908,0.0308	benign,benign	152/3908,152/3900	91622249	4,13002	2203	4300	6503	SO:0001583	missense	10142	exon5			ACAAGACAGTCCG	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.492C>A	7.37:g.91622249C>A	ENSP00000351922:p.Asp164Glu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.491	1.100713	0.20552	9.08E-4	0.0	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565;ENST00000394564;ENST00000438114	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.37	1.53	0.23141	.	0.681654	0.12148	N	0.495208	T	0.16981	0.0408	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.19817	0.013;0.01;0.039;0.005	B;B;B;B	0.15870	0.008;0.006;0.014;0.008	T	0.24584	-1.0156	10	0.30854	T	0.27	.	8.8667	0.35291	0.0:0.6341:0.0:0.3659	.	152;152;164;152	Q99996-2;Q99996-3;A4D1E4;Q6PJH3	.;.;.;.	E	152;164;164;164;164;152;103	ENSP00000348573:D152E;ENSP00000351922:D164E;ENSP00000350813:D164E;ENSP00000378065:D152E;ENSP00000391704:D103E	ENSP00000348573:D152E	D	+	3	2	AKAP9	91460185	0.943000	0.32029	0.981000	0.43875	0.717000	0.41224	0.068000	0.14531	0.061000	0.16311	-0.150000	0.13652	GAC	C|1.000;A|0.000	0.000	strong		0.388	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
BIN2	51411	hgsc.bcm.edu	37	12	51696500	51696500	+	Silent	SNP	G	G	A	rs7975715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:51696500G>A	ENST00000267012.4	-	4	343	c.282C>T	c.(280-282)gaC>gaT	p.D94D	BIN2_ENST00000544402.1_Silent_p.D68D|BIN2_ENST00000452142.2_Silent_p.D94D|BIN2_ENST00000604560.1_Silent_p.D67D	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	94	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell chemotaxis (GO:0060326)|membrane tubulation (GO:0097320)|phagocytosis, engulfment (GO:0006911)|podosome assembly (GO:0071800)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|podosome (GO:0002102)	phospholipid binding (GO:0005543)			NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						CCTCATGACCGTCCCACTCGC	0.463													G|||	709	0.141573	0.1982	0.1037	5008	,	,		19444	0.2282		0.0984	False		,,,				2504	0.047				p.D94D		Atlas-SNP	.											.	BIN2	58	.	0			c.C282T						PASS	.	G		747,3659	305.5+/-289.0	56,635,1512	237.0	214.0	222.0		282	-10.4	0.1	12	dbSNP_116	222	924,7676	205.5+/-247.9	58,808,3434	no	coding-synonymous	BIN2	NM_016293.2		114,1443,4946	AA,AG,GG		10.7442,16.9542,12.8479		94/566	51696500	1671,11335	2203	4300	6503	SO:0001819	synonymous_variant	51411	exon4			ATGACCGTCCCAC	AF146531	CCDS8811.1	12q13.13	2012-01-23			ENSG00000110934	ENSG00000110934			1053	protein-coding gene	gene with protein product		605936				10903846	Standard	XM_005268957		Approved	BRAP-1	uc001ryg.3	Q9UBW5		ENST00000267012.4:c.282C>T	12.37:g.51696500G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_016293	Q86VV0|Q9NWK4|Q9UKN4	Silent	SNP	ENST00000267012.4	37	CCDS8811.1																																																																																			G|0.868;A|0.132	0.132	strong		0.463	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1		
DOK6	220164	hgsc.bcm.edu	37	18	67365668	67365668	+	Silent	SNP	A	A	G	rs4426448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:67365668A>G	ENST00000382713.5	+	5	628	c.438A>G	c.(436-438)acA>acG	p.T146T	DOK6_ENST00000584435.1_3'UTR	NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	146	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.									central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	20		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				TTATGCCTACACCAAACCTGG	0.408													G|||	2429	0.485024	0.4213	0.3501	5008	,	,		20482	0.7331		0.4692	False		,,,				2504	0.4274				p.T146T		Atlas-SNP	.											.	DOK6	56	.	0			c.A438G						PASS	.	G		1966,2440	620.0+/-393.5	426,1114,663	124.0	109.0	114.0		438	-5.9	0.7	18	dbSNP_111	114	4006,4594	598.3+/-393.9	916,2174,1210	no	coding-synonymous	DOK6	NM_152721.5		1342,3288,1873	GG,GA,AA		46.5814,44.621,45.9173		146/332	67365668	5972,7034	2203	4300	6503	SO:0001819	synonymous_variant	220164	exon5			GCCTACACCAAAC	AK057795	CCDS32841.1	18q22.2	2013-01-10	2005-01-18	2005-01-18		ENSG00000206052		"""Pleckstrin homology (PH) domain containing"""	28301	protein-coding gene	gene with protein product		611402	"""docking protein 5-like"""	DOK5L		15286081	Standard	NM_152721		Approved	MGC20785, HsT3226	uc002lkl.3	Q6PKX4		ENST00000382713.5:c.438A>G	18.37:g.67365668A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_152721	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Silent	SNP	ENST00000382713.5	37	CCDS32841.1																																																																																			A|0.522;G|0.478	0.478	strong		0.408	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721	
OR1N2	138882	hgsc.bcm.edu	37	9	125316033	125316033	+	Silent	SNP	T	T	C	rs1341042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125316033T>C	ENST00000373688.2	+	1	643	c.585T>C	c.(583-585)taT>taC	p.Y195Y		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						CTCATTTCTATTGTGATCCTA	0.537													C|||	2799	0.558906	0.5961	0.5908	5008	,	,		18406	0.6637		0.4791	False		,,,				2504	0.4601				p.Y195Y		Atlas-SNP	.											.	OR1N2	51	.	0			c.T585C						PASS	.	C		2530,1876	541.1+/-375.7	715,1100,388	168.0	154.0	159.0		585	2.5	1.0	9	dbSNP_88	159	4211,4389	583.4+/-391.5	1011,2189,1100	no	coding-synonymous	OR1N2	NM_001004457.1		1726,3289,1488	CC,CT,TT		48.9651,42.5783,48.1701		195/331	125316033	6741,6265	2203	4300	6503	SO:0001819	synonymous_variant	138882	exon1			TTTCTATTGTGAT		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.585T>C	9.37:g.125316033T>C		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	236	80	0.338983	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Silent	SNP	ENST00000373688.2	37	CCDS35123.1																																																																																			T|0.470;C|0.530	0.530	strong		0.537	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
LIPH	200879	hgsc.bcm.edu	37	3	185229464	185229464	+	Silent	SNP	T	T	C	rs61730237	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:185229464T>C	ENST00000296252.4	-	9	1257	c.1116A>G	c.(1114-1116)aaA>aaG	p.K372K	LIPH_ENST00000424591.2_Silent_p.K338K	NM_139248.2	NP_640341.1	Q8WWY8	LIPH_HUMAN	lipase, member H	372					lipid catabolic process (GO:0016042)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(2)	20	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			CTTGGTGATATTTCTGAAATG	0.393													T|||	1719	0.343251	0.3517	0.3876	5008	,	,		19222	0.2907		0.4493	False		,,,				2504	0.2454				p.K372K		Atlas-SNP	.											.	LIPH	56	.	0			c.A1116G						PASS	.	T		1549,2857	488.5+/-361.2	288,973,942	101.0	98.0	99.0		1116	1.4	1.0	3	dbSNP_129	99	3861,4739	541.5+/-384.0	877,2107,1316	yes	coding-synonymous	LIPH	NM_139248.2		1165,3080,2258	CC,CT,TT		44.8953,35.1566,41.5962		372/452	185229464	5410,7596	2203	4300	6503	SO:0001819	synonymous_variant	200879	exon9			GTGATATTTCTGA	AY093498	CCDS3272.1	3q27	2012-07-31			ENSG00000163898	ENSG00000163898			18483	protein-coding gene	gene with protein product		607365				12213196, 12063250	Standard	XM_006713529		Approved	mPA-PLA1, PLA1B, mPA-PLA1alpha, LPDLR	uc003fpm.3	Q8WWY8	OTTHUMG00000156657	ENST00000296252.4:c.1116A>G	3.37:g.185229464T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_139248	A2IBA7|Q8TEC7	Silent	SNP	ENST00000296252.4	37	CCDS3272.1																																																																																			T|0.597;C|0.403	0.403	strong		0.393	LIPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345153.1		
MKI67	4288	hgsc.bcm.edu	37	10	129907544	129907544	+	Missense_Mutation	SNP	G	G	C	rs2240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129907544G>C	ENST00000368654.3	-	13	2935	c.2560C>G	c.(2560-2562)Ctg>Gtg	p.L854V	MKI67_ENST00000484853.1_5'Flank|MKI67_ENST00000368653.3_Missense_Mutation_p.L494V	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	854			L -> V (in dbSNP:rs2240).		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)				TTTGTCTCCAGAGAAGTCATT	0.428													C|||	1166	0.232827	0.3427	0.2291	5008	,	,		18353	0.2609		0.1571	False		,,,				2504	0.136				p.L854V		Atlas-SNP	.											.	MKI67	363	.	0			c.C2560G						PASS	.	C	VAL/LEU,VAL/LEU	1363,3043	691.3+/-405.4	207,949,1047	215.0	207.0	210.0		1480,2560	-2.7	0.0	10	dbSNP_36	210	1493,7107	749.0+/-407.4	137,1219,2944	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	32,32	344,2168,3991	CC,CG,GG		17.3605,30.9351,21.9591	benign,benign	494/2897,854/3257	129907544	2856,10150	2203	4300	6503	SO:0001583	missense	4288	exon13			TCTCCAGAGAAGT	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.2560C>G	10.37:g.129907544G>C	ENSP00000357643:p.Leu854Val	Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	375	156	0.416	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	488	0.22344322344322345	147	0.29878048780487804	68	0.1878453038674033	150	0.26223776223776224	123	0.16226912928759896	C	0.010	-1.790947	0.00623	0.309351	0.173605	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01369	5.02;4.97	3.48	-2.73	0.05950	.	1.865620	0.03587	N	0.231244	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	0.45440	-0.9261	9	0.27785	T	0.31	.	1.125	0.01732	0.1886:0.2259:0.3634:0.2221	rs2240;rs52809582;rs2240	853;494;854	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	V	854;494;853	ENSP00000357643:L854V;ENSP00000357642:L494V	ENSP00000357642:L494V	L	-	1	2	MKI67	129797534	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.747000	0.01827	-1.216000	0.02607	-0.215000	0.12644	CTG	G|0.776;C|0.224	0.224	strong		0.428	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
MUC17	140453	hgsc.bcm.edu	37	7	100678032	100678032	+	Missense_Mutation	SNP	T	T	C	rs147173571		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678032T>C	ENST00000306151.4	+	3	3399	c.3335T>C	c.(3334-3336)cTg>cCg	p.L1112P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1112	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)					AGCACCAGGCTGGTGGTCAGT	0.512																																					p.L1112P		Atlas-SNP	.											.	MUC17	804	.	0			c.T3335C						PASS	.						494.0	394.0	428.0					7																	100678032		2203	4300	6503	SO:0001583	missense	140453	exon3			CCAGGCTGGTGGT	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.3335T>C	7.37:g.100678032T>C	ENSP00000302716:p.Leu1112Pro	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	352	33	0.09375	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.149	-1.093913	0.01858	.	.	ENSG00000169876	ENST00000306151	T	0.03212	4.01	0.693	-0.391	0.12446	.	.	.	.	.	T	0.01320	0.0043	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48055	-0.9068	8	0.25751	T	0.34	.	.	.	.	.	1112	Q685J3	MUC17_HUMAN	P	1112	ENSP00000302716:L1112P	ENSP00000302716:L1112P	L	+	2	0	MUC17	100464752	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-6.070000	0.00082	-0.165000	0.10908	-1.364000	0.01208	CTG	.	.	weak		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FRMD4B	23150	hgsc.bcm.edu	37	3	69299233	69299233	+	Missense_Mutation	SNP	C	C	G	rs4361282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:69299233C>G	ENST00000398540.3	-	6	602	c.519G>C	c.(517-519)gaG>gaC	p.E173D	FRMD4B_ENST00000542259.1_Missense_Mutation_p.E119D	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	173	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TGGTTTCGCTCTCTACTTCGA	0.433													G|||	1237	0.247005	0.3457	0.2133	5008	,	,		18600	0.2649		0.2237	False		,,,				2504	0.1431				p.E173D		Atlas-SNP	.											.	FRMD4B	90	.	0			c.G519C						PASS	.	G	ASP/GLU	1174,2712		165,844,934	279.0	271.0	273.0		519	4.3	1.0	3	dbSNP_111	273	1816,6458		195,1426,2516	yes	missense	FRMD4B	NM_015123.1	45	360,2270,3450	GG,GC,CC		21.9483,30.211,24.5888	benign	173/1035	69299233	2990,9170	1943	4137	6080	SO:0001583	missense	23150	exon6			TTCGCTCTCTACT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.519G>C	3.37:g.69299233C>G	ENSP00000381549:p.Glu173Asp	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	577	0.2641941391941392	176	0.35772357723577236	73	0.20165745856353592	143	0.25	185	0.24406332453825857	G	1.525	-0.545949	0.04024	0.30211	0.219483	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000493880;ENST00000473029;ENST00000460709	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	5.33	4.33	0.51752	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.106811	0.64402	N	0.000007	T	0.00012	0.0000	N	0.11560	0.145	0.51233	P	8.60000000000305E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10474	-1.0628	9	0.02654	T	1	-15.1785	7.5424	0.27746	0.0:0.1412:0.5798:0.279	rs4361282;rs52807668;rs4361282	17;173	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	D	173;119;64;119;119	ENSP00000381549:E173D;ENSP00000437658:E119D;ENSP00000418962:E64D;ENSP00000418373:E119D;ENSP00000418023:E119D	ENSP00000381549:E173D	E	-	3	2	FRMD4B	69381923	1.000000	0.71417	0.999000	0.59377	0.706000	0.40770	1.131000	0.31406	1.400000	0.46741	-0.187000	0.12897	GAG	C|0.742;G|0.258	0.258	strong		0.433	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1		
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815681	23815681	+	Silent	SNP	G	G	A	rs17574213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:23815681G>A	ENST00000264867.2	-	8	1544	c.1425C>T	c.(1423-1425)gaC>gaT	p.D475D	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	475	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				CTGCTTCGTCGTCAAAAACAG	0.468													G|||	117	0.0233626	0.0174	0.0403	5008	,	,		19749	0.0		0.0497	False		,,,				2504	0.0164				p.D475D	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.C1425T						PASS	.	G		138,4268	98.9+/-137.6	3,132,2068	116.0	104.0	108.0		1425	0.9	1.0	4	dbSNP_123	108	580,8020	155.4+/-209.4	21,538,3741	no	coding-synonymous	PPARGC1A	NM_013261.3		24,670,5809	AA,AG,GG		6.7442,3.1321,5.5205		475/799	23815681	718,12288	2203	4300	6503	SO:0001819	synonymous_variant	10891	exon8			TTCGTCGTCAAAA	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.1425C>T	4.37:g.23815681G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	114	41	0.359649	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Silent	SNP	ENST00000264867.2	37	CCDS3429.1																																																																																			G|0.955;A|0.045	0.045	strong		0.468	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
MAATS1	89876	hgsc.bcm.edu	37	3	119421963	119421963	+	Silent	SNP	C	C	T	rs7612861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119421963C>T	ENST00000273390.5	+	1	95	c.18C>T	c.(16-18)acC>acT	p.T6T	MAATS1_ENST00000463700.1_Silent_p.T6T	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	6						mitochondrion (GO:0005739)											ACGCAGTAACCATCGAGGAGC	0.642													C|||	917	0.183107	0.1672	0.2392	5008	,	,		12639	0.1825		0.1461	False		,,,				2504	0.2035				p.T6T		Atlas-SNP	.											C3orf15,NS,carcinoma,0,1	.	.	1	0			c.C18T						PASS	.	C		780,3598		63,654,1472	27.0	31.0	30.0		18	-0.2	0.3	3	dbSNP_116	30	1036,7524		52,932,3296	no	coding-synonymous	C3orf15	NM_033364.3		115,1586,4768	TT,TC,CC		12.1028,17.8164,14.0362		6/768	119421963	1816,11122	2189	4280	6469	SO:0001819	synonymous_variant	89876	exon1			AGTAACCATCGAG	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.18C>T	3.37:g.119421963C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Silent	SNP	ENST00000273390.5	37	CCDS2994.1																																																																																			C|0.824;T|0.176	0.176	strong		0.642	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
SULF2	55959	hgsc.bcm.edu	37	20	46292910	46292910	+	Missense_Mutation	SNP	C	C	T	rs10048853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:46292910C>T	ENST00000359930.4	-	15	2872	c.2021G>A	c.(2020-2022)cGc>cAc	p.R674H	SULF2_ENST00000467815.1_Missense_Mutation_p.R674H|SULF2_ENST00000361612.4_Missense_Mutation_p.R674H|SULF2_ENST00000484875.1_Missense_Mutation_p.R674H	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	674			R -> H (in dbSNP:rs10048853).		bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						GTGCTTGAGGCGGCCTTTGTG	0.607											OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	90	0.0179712	0.0582	0.0159	5008	,	,		17857	0.0		0.002	False		,,,				2504	0.0				p.R674H		Atlas-SNP	.											.	SULF2	131	.	0			c.G2021A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	189,4217	116.7+/-154.6	4,181,2018	55.0	47.0	50.0		2021,2021,2021	3.1	1.0	20	dbSNP_119	50	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense	SULF2	NM_001161841.1,NM_018837.3,NM_198596.2	29,29,29	4,184,6315	TT,TC,CC		0.0349,4.2896,1.4762	benign,benign,benign	674/871,674/871,674/868	46292910	192,12814	2203	4300	6503	SO:0001583	missense	55959	exon15			TTGAGGCGGCCTT	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.2021G>A	20.37:g.46292910C>T	ENSP00000353007:p.Arg674His	Somatic	92	0	0	938	WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	25|25	0.011446886446886446|0.011446886446886446	16|16	0.032520325203252036|0.032520325203252036	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	13.33|13.33	2.203972|2.203972	0.38905|0.38905	0.042896|0.042896	3.49E-4|3.49E-4	ENSG00000196562|ENSG00000196562	ENST00000495544|ENST00000359930;ENST00000484875;ENST00000361612;ENST00000371978;ENST00000467815	.|T;T;T;T	.|0.22134	.|1.97;1.97;1.97;1.97	5.08|5.08	3.1|3.1	0.35709|0.35709	.|Alkaline-phosphatase-like, core domain (1);	.|0.302855	.|0.32769	.|N	.|0.005668	T|T	0.01523|0.01523	0.0049|0.0049	N|N	0.04959|0.04959	-0.14|-0.14	0.29204|0.29204	N|N	0.875005|0.875005	.|B;B	.|0.09022	.|0.002;0.001	.|B;B	.|0.06405	.|0.002;0.001	T|T	0.29518|0.29518	-1.0009|-1.0009	5|10	.|0.13108	.|T	.|0.6	-22.8637|-22.8637	4.1427|4.1427	0.10201|0.10201	0.0:0.5786:0.1901:0.2313|0.0:0.5786:0.1901:0.2313	rs10048853;rs10048853|rs10048853;rs10048853	.|674;674	.|Q8IWU5-2;Q8IWU5	.|.;SULF2_HUMAN	T|H	29|674;674;674;93;674	.|ENSP00000353007:R674H;ENSP00000418290:R674H;ENSP00000354662:R674H;ENSP00000418442:R674H	.|ENSP00000353007:R674H	A|R	-|-	1|2	0|0	SULF2|SULF2	45726317|45726317	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.796000|0.796000	0.44982|0.44982	1.968000|1.968000	0.40500|0.40500	0.689000|0.689000	0.31550|0.31550	-0.254000|-0.254000	0.11334|0.11334	GCC|CGC	C|0.983;T|0.017	0.017	strong		0.607	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
ECE2	9718	hgsc.bcm.edu	37	3	183967500	183967500	+	Silent	SNP	A	A	C	rs2233461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183967500A>C	ENST00000402825.3	+	1	18	c.18A>C	c.(16-18)gcA>gcC	p.A6A	ALG3_ENST00000397676.3_5'Flank|ECE2_ENST00000324557.4_Silent_p.A6A|ALG3_ENST00000418734.2_5'Flank|ALG3_ENST00000445626.2_5'Flank|EIF2B5_ENST00000444495.1_Intron|ALG3_ENST00000455059.1_5'Flank	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	6	Methyltransferase-like region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTCCAGGGGCAGGTAGGGCGC	0.672											OREG0015944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	246	0.0491214	0.1793	0.013	5008	,	,		15078	0.0		0.0	False		,,,				2504	0.0				p.A6A		Atlas-SNP	.											.	ECE2	303	.	0			c.A18C						PASS	.	C	,	533,3863		28,477,1693	18.0	21.0	20.0		18,18	-10.9	0.0	3	dbSNP_98	20	4,8584		0,4,4290	no	coding-synonymous,coding-synonymous	ECE2	NM_014693.3,NM_032331.3	,	28,481,5983	CC,CA,AA		0.0466,12.1247,4.1359	,	6/884,6/256	183967500	537,12447	2198	4294	6492	SO:0001819	synonymous_variant	9718	exon1			AGGGGCAGGTAGG	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.18A>C	3.37:g.183967500A>C		Somatic	51	0	0	1988	WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Silent	SNP	ENST00000402825.3	37	CCDS3256.2																																																																																			A|0.943;C|0.057	0.057	strong		0.672	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
COL9A3	1299	hgsc.bcm.edu	37	20	61448933	61448933	+	Silent	SNP	C	C	A	rs544133282|rs2273078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61448933C>A	ENST00000343916.3	+	2	96	c.93C>A	c.(91-93)ccC>ccA	p.P31P		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	31	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					TGGGACTccccggcccccccg	0.731													A|||	804	0.160543	0.211	0.1484	5008	,	,		9815	0.251		0.0775	False		,,,				2504	0.093				p.P31P		Atlas-SNP	.											.	COL9A3	70	.	0			c.C93A						PASS	.	A		550,3092		33,484,1304	5.0	7.0	6.0		93	0.2	0.1	20	dbSNP_100	6	409,6799		10,389,3205	no	coding-synonymous	COL9A3	NM_001853.3		43,873,4509	AA,AC,CC		5.6743,15.1016,8.8387		31/685	61448933	959,9891	1821	3604	5425	SO:0001819	synonymous_variant	1299	exon2			ACTCCCCGGCCCC	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.93C>A	20.37:g.61448933C>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_001853	Q13681|Q9H4G9|Q9UPE2	Silent	SNP	ENST00000343916.3	37	CCDS13505.1																																																																																			C|0.816;A|0.184	0.184	strong		0.731	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
PBLD	64081	hgsc.bcm.edu	37	10	70044031	70044031	+	Missense_Mutation	SNP	T	T	C	rs4142048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	103	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	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	
OR10Q1	219960	hgsc.bcm.edu	37	11	57996084	57996084	+	Silent	SNP	G	G	A	rs61902844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57996084G>A	ENST00000316770.2	-	1	306	c.264C>T	c.(262-264)aaC>aaT	p.N88N		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				CCCCCAAAATGTTGGAAAGCA	0.542													g|||	1276	0.254792	0.1369	0.2882	5008	,	,		20320	0.1438		0.4404	False		,,,				2504	0.3139				p.N88N		Atlas-SNP	.											OR10Q1,NS,carcinoma,-2,1	OR10Q1	79	1	0			c.C264T						PASS	.	G		730,3672	300.7+/-286.5	72,586,1543	75.0	69.0	71.0		264	1.7	0.8	11	dbSNP_129	71	3741,4849	533.1+/-382.3	798,2145,1352	no	coding-synonymous	OR10Q1	NM_001004471.2		870,2731,2895	AA,AG,GG		43.5506,16.5834,34.4135		88/320	57996084	4471,8521	2201	4295	6496	SO:0001819	synonymous_variant	219960	exon1			CAAAATGTTGGAA	AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475		"""GPCR / Class A : Olfactory receptors"""	15134	protein-coding gene	gene with protein product							Standard	NM_001004471		Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.264C>T	11.37:g.57996084G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_001004471	Q6IFG4	Silent	SNP	ENST00000316770.2	37	CCDS31547.1																																																																																			G|0.667;A|0.333	0.333	strong		0.542	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471	
FAM135A	57579	hgsc.bcm.edu	37	6	71236216	71236216	+	Silent	SNP	C	C	T	rs7740873	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71236216C>T	ENST00000418814.2	+	15	4043	c.3429C>T	c.(3427-3429)aaC>aaT	p.N1143N	FAM135A_ENST00000457062.2_Silent_p.N930N|FAM135A_ENST00000361499.3_Silent_p.N947N|FAM135A_ENST00000370479.3_Silent_p.N930N|FAM135A_ENST00000505769.1_Silent_p.N723N|FAM135A_ENST00000505868.1_Silent_p.N1143N	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	202	0	0		WXS	Illumina HiSeq	Phase_I	170	85	0.5	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	
CLEC16A	23274	hgsc.bcm.edu	37	16	11133681	11133681	+	Silent	SNP	C	C	T	rs61740118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11133681C>T	ENST00000409790.1	+	14	1838	c.1608C>T	c.(1606-1608)aaC>aaT	p.N536N	CLEC16A_ENST00000465491.1_3'UTR|CLEC16A_ENST00000409552.3_Silent_p.N518N	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						CCACCTACAACCACCCGCTAG	0.552													C|||	64	0.0127796	0.0477	0.0014	5008	,	,		18259	0.0		0.0	False		,,,				2504	0.0				p.N536N		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1608T						PASS	.	C		139,3971		5,129,1921	57.0	61.0	59.0		1608	4.3	1.0	16	dbSNP_129	59	0,8386		0,0,4193	no	coding-synonymous	CLEC16A	NM_015226.2		5,129,6114	TT,TC,CC		0.0,3.382,1.1124		536/1054	11133681	139,12357	2055	4193	6248	SO:0001819	synonymous_variant	23274	exon13			CTACAACCACCCG	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.1608C>T	16.37:g.11133681C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			C|0.989;T|0.011	0.011	strong		0.552	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
KIAA1468	57614	hgsc.bcm.edu	37	18	59895550	59895550	+	Silent	SNP	C	C	T	rs151143967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:59895550C>T	ENST00000398130.2	+	8	1399	c.1167C>T	c.(1165-1167)ttC>ttT	p.F389F	KIAA1468_ENST00000256858.6_Silent_p.F389F	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	389										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)				AAATGGACTTCCTCAAAAATG	0.398													C|||	97	0.019369	0.0219	0.0202	5008	,	,		18532	0.003		0.0258	False		,,,				2504	0.0256				p.F389F		Atlas-SNP	.											.	KIAA1468	93	.	0			c.C1167T						PASS	.	C		115,4291	86.3+/-125.0	1,113,2089	108.0	108.0	108.0		1167	3.9	1.0	18	dbSNP_134	108	227,8373	91.4+/-153.5	1,225,4074	no	coding-synonymous	KIAA1468	NM_020854.3		2,338,6163	TT,TC,CC		2.6395,2.6101,2.6296		389/1217	59895550	342,12664	2203	4300	6503	SO:0001819	synonymous_variant	57614	exon8			GGACTTCCTCAAA	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.1167C>T	18.37:g.59895550C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_020854		Silent	SNP	ENST00000398130.2	37	CCDS11979.2																																																																																			C|0.978;T|0.022	0.022	strong		0.398	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854	
LRRC43	254050	hgsc.bcm.edu	37	12	122674807	122674807	+	Missense_Mutation	SNP	T	T	C	rs77473460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122674807T>C	ENST00000339777.4	+	5	821	c.793T>C	c.(793-795)Tac>Cac	p.Y265H	LRRC43_ENST00000425921.1_Missense_Mutation_p.Y80H	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	265	LRRCT.									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)		CTTGGTGCCCTACTACCGCGG	0.637													T|||	195	0.0389377	0.1415	0.0101	5008	,	,		20541	0.0		0.001	False		,,,				2504	0.0				p.Y265H		Atlas-SNP	.											.	LRRC43	105	.	0			c.T793C						PASS	.	T	HIS/TYR,HIS/TYR	502,3826		30,442,1692	84.0	95.0	92.0		793,238	-1.6	0.9	12	dbSNP_131	92	4,8530		0,4,4263	yes	missense,missense	LRRC43	NM_001098519.1,NM_152759.4	83,83	30,446,5955	CC,CT,TT		0.0469,11.5989,3.9341	possibly-damaging,possibly-damaging	265/657,80/472	122674807	506,12356	2164	4267	6431	SO:0001583	missense	254050	exon5			GTGCCCTACTACC	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.793T>C	12.37:g.122674807T>C	ENSP00000344233:p.Tyr265His	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	176	82	0.465909	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	37	CCDS45001.1	78	0.03571428571428571	75	0.1524390243902439	3	0.008287292817679558	0	0.0	0	0.0	T	9.271	1.045795	0.19748	0.115989	4.69E-4	ENSG00000158113	ENST00000537729;ENST00000339777;ENST00000289014;ENST00000425921	T;T;T	0.23348	1.91;1.91;1.91	5.22	-1.59	0.08453	.	0.926504	0.09255	N	0.827363	T	0.00073	0.0002	N	0.13043	0.29	0.09310	N	1	B	0.18461	0.028	B	0.11329	0.006	T	0.37911	-0.9685	10	0.15499	T	0.54	-14.8888	1.3937	0.02256	0.1943:0.3528:0.2254:0.2275	.	265	Q8N309	LRC43_HUMAN	H	80;265;136;80	ENSP00000438751:Y80H;ENSP00000344233:Y265H;ENSP00000416628:Y80H	ENSP00000289014:Y136H	Y	+	1	0	LRRC43	121240760	0.000000	0.05858	0.934000	0.37439	0.988000	0.76386	0.172000	0.16704	0.039000	0.15632	0.459000	0.35465	TAC	T|0.977;C|0.023	0.023	strong		0.637	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
PRDM14	63978	hgsc.bcm.edu	37	8	70978690	70978690	+	Silent	SNP	C	C	T	rs3750227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:70978690C>T	ENST00000276594.2	-	5	1164	c.963G>A	c.(961-963)acG>acA	p.T321T		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	321	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|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(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			TCCAGTTCCCCGTACCTCCTT	0.413													C|||	810	0.161741	0.2042	0.0994	5008	,	,		18073	0.3155		0.0398	False		,,,				2504	0.1155				p.T321T	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											.	PRDM14	102	.	0			c.G963A						PASS	.	C		802,3604	322.6+/-297.7	71,660,1472	119.0	119.0	119.0		963	-11.8	0.0	8	dbSNP_107	119	386,8214	125.1+/-183.8	10,366,3924	no	coding-synonymous	PRDM14	NM_024504.2		81,1026,5396	TT,TC,CC		4.4884,18.2025,9.1342		321/572	70978690	1188,11818	2203	4300	6503	SO:0001819	synonymous_variant	63978	exon5			GTTCCCCGTACCT	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"""Zinc fingers, C2H2-type"""	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.963G>A	8.37:g.70978690C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	176	77	0.4375	NM_024504	Q86UX9	Silent	SNP	ENST00000276594.2	37	CCDS6206.1																																																																																			C|0.874;T|0.126	0.126	strong		0.413	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1		
OR10H3	26532	hgsc.bcm.edu	37	19	15852363	15852363	+	Missense_Mutation	SNP	G	G	A	rs11670007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15852363G>A	ENST00000305892.1	+	1	161	c.161G>A	c.(160-162)cGc>cAc	p.R54H		NM_013938.1	NP_039226.1	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H, member 3	54			R -> H (in dbSNP:rs11670007).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						TGGATTGAACGCAGACTCCAC	0.527													g|||	1308	0.261182	0.4319	0.2752	5008	,	,		23202	0.0119		0.3131	False		,,,				2504	0.2239				p.R54H		Atlas-SNP	.											OR10H3,caecum,carcinoma,+1,2	OR10H3	53	2	0			c.G161A						PASS	.	G	HIS/ARG	1796,2610		372,1052,779	413.0	362.0	379.0		161	-4.7	0.2	19	dbSNP_120	379	2472,6128		379,1714,2207	yes	missense	OR10H3	NM_013938.1	29	751,2766,2986	AA,AG,GG		28.7442,40.7626,32.8156	benign	54/317	15852363	4268,8738	2203	4300	6503	SO:0001583	missense	26532	exon1			TTGAACGCAGACT		CCDS12334.1	19p13.1	2012-08-09				ENSG00000171936		"""GPCR / Class A : Olfactory receptors"""	8174	protein-coding gene	gene with protein product							Standard	NM_013938		Approved		uc010xoq.2	O60404		ENST00000305892.1:c.161G>A	19.37:g.15852363G>A	ENSP00000307130:p.Arg54His	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	308	138	0.448052	NM_013938	Q2HIZ3|Q6IFQ0	Missense_Mutation	SNP	ENST00000305892.1	37	CCDS12334.1	563	0.25778388278388276	198	0.4024390243902439	115	0.31767955801104975	11	0.019230769230769232	239	0.3153034300791557	.	0.009	-1.816832	0.00595	0.407626	0.287442	ENSG00000171936	ENST00000305892	T	0.01084	5.36	2.35	-4.7	0.03288	GPCR, rhodopsin-like superfamily (1);	0.910830	0.09011	N	0.861532	T	0.00012	0.0000	N	0.04820	-0.15	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.27468	-1.0073	9	0.10636	T	0.68	.	6.0643	0.19854	0.213:0.265:0.522:0.0	rs11670007;rs52827169;rs61232867;rs11670007	54	O60404	O10H3_HUMAN	H	54	ENSP00000307130:R54H	ENSP00000307130:R54H	R	+	2	0	OR10H3	15713363	0.000000	0.05858	0.225000	0.23894	0.114000	0.19823	-2.725000	0.00808	-0.961000	0.03609	-1.125000	0.01998	CGC	G|0.700;A|0.300	0.300	strong		0.527	OR10H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460918.1		
TELO2	9894	hgsc.bcm.edu	37	16	1547477	1547477	+	Silent	SNP	T	T	C	rs2745108	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1547477T>C	ENST00000262319.6	+	5	1077	c.798T>C	c.(796-798)gcT>gcC	p.A266A		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	266					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)				CCATGGAGGCTGTGCTGACCG	0.697													N|||	1398	0.279153	0.5136	0.268	5008	,	,		17144	0.251		0.1113	False		,,,				2504	0.1718				p.A266A		Atlas-SNP	.											.	TELO2	44	.	0			c.T798C						PASS	.			1949,2381		427,1095,643	11.0	12.0	12.0		798	-10.1	0.0	16	dbSNP_100	12	868,7674		48,772,3451	no	coding-synonymous	TELO2	NM_016111.3		475,1867,4094	CC,CT,TT		10.1616,45.0115,21.8847		266/838	1547477	2817,10055	2165	4271	6436	SO:0001819	synonymous_variant	9894	exon5			GGAGGCTGTGCTG	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.798T>C	16.37:g.1547477T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Silent	SNP	ENST00000262319.6	37	CCDS32363.1																																																																																			T|0.754;C|0.246	0.246	strong		0.697	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
MUC16	94025	hgsc.bcm.edu	37	19	9070079	9070079	+	Silent	SNP	C	C	G	rs1559170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	209	0	0		WXS	Illumina HiSeq	Phase_I	185	83	0.448649	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	
TMEM120B	144404	hgsc.bcm.edu	37	12	122186317	122186317	+	Missense_Mutation	SNP	G	G	A	rs28655666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122186317G>A	ENST00000449592.2	+	3	375	c.274G>A	c.(274-276)Gac>Aac	p.D92N		NM_001080825.2	NP_001074294.2	A0PK00	T120B_HUMAN	transmembrane protein 120B	92				D -> N (in Ref. 2; AAI27770). {ECO:0000305}.		integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		CGTCTTCTTCGACATGGAGGC	0.612													G|||	2133	0.425919	0.2103	0.4481	5008	,	,		18243	0.5179		0.5467	False		,,,				2504	0.4826				p.D92N		Atlas-SNP	.											TMEM120B_ENST00000449592,brain,glioma,0,2	TMEM120B	43	2	0			c.G274A						PASS	.	G	ASN/ASP	1071,3125		161,749,1188	57.0	62.0	60.0		274	3.5	1.0	12	dbSNP_125	60	4584,3818		1263,2058,880	yes	missense	TMEM120B	NM_001080825.2	23	1424,2807,2068	AA,AG,GG		45.4416,25.5243,44.8881	benign	92/340	122186317	5655,6943	2098	4201	6299	SO:0001583	missense	144404	exon3			TTCTTCGACATGG	BC127768	CCDS41852.1	12q24.31	2007-08-01			ENSG00000188735	ENSG00000188735			32008	protein-coding gene	gene with protein product							Standard	NM_001080825		Approved		uc001ubc.4	A0PK00	OTTHUMG00000169076	ENST00000449592.2:c.274G>A	12.37:g.122186317G>A	ENSP00000404991:p.Asp92Asn	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	202	90	0.445545	NM_001080825	A0PK01|B3KX33	Missense_Mutation	SNP	ENST00000449592.2	37	CCDS41852.1	1017	0.46565934065934067	112	0.22764227642276422	172	0.47513812154696133	310	0.541958041958042	423	0.558047493403694	G	16.64	3.180210	0.57800	0.255243	0.545584	ENSG00000188735	ENST00000449592;ENST00000541467	T;T	0.36340	1.26;1.26	5.31	3.45	0.39498	.	0.145167	0.64402	D	0.000012	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	1.0	B	0.13145	0.007	B	0.18561	0.022	T	0.44283	-0.9338	9	0.54805	T	0.06	-29.1623	11.9916	0.53178	0.1553:0.0:0.8447:0.0	rs28655666	92	A0PK00	T120B_HUMAN	N	92;71	ENSP00000404991:D92N;ENSP00000442105:D71N	ENSP00000345152:D92N	D	+	1	0	TMEM120B	120670700	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	5.310000	0.65780	1.384000	0.46424	-0.250000	0.11733	GAC	G|0.502;A|0.498	0.498	strong		0.612	TMEM120B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402158.1	NM_001080825	
COL28A1	340267	hgsc.bcm.edu	37	7	7413149	7413149	+	Silent	SNP	T	T	C	rs61744841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:7413149T>C	ENST00000399429.3	-	32	2528	c.2388A>G	c.(2386-2388)ccA>ccG	p.P796P		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	796					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCAGCTCTAGTGGAGTCTCTT	0.448													T|||	549	0.109625	0.3389	0.0418	5008	,	,		18200	0.001		0.0487	False		,,,				2504	0.0225				p.P796P		Atlas-SNP	.											COL28A1,NS,carcinoma,-1,1	COL28A1	113	1	0			c.A2388G						PASS	.	T		1053,2679		154,745,967	75.0	77.0	77.0		2388	-8.9	0.0	7	dbSNP_129	77	395,7803		10,375,3714	no	coding-synonymous	COL28A1	NM_001037763.2		164,1120,4681	CC,CT,TT		4.8182,28.2154,12.1375		796/1126	7413149	1448,10482	1866	4099	5965	SO:0001819	synonymous_variant	340267	exon32			CTCTAGTGGAGTC	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2388A>G	7.37:g.7413149T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	37	CCDS43553.1																																																																																			T|0.927;C|0.073	0.073	strong		0.448	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
NCLN	56926	hgsc.bcm.edu	37	19	3186085	3186085	+	Silent	SNP	G	G	T	rs11551095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	47	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	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	
BANK1	55024	hgsc.bcm.edu	37	4	102751076	102751076	+	Missense_Mutation	SNP	G	G	A	rs10516487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:102751076G>A	ENST00000322953.4	+	2	456	c.182G>A	c.(181-183)cGc>cAc	p.R61H	BANK1_ENST00000428908.1_Intron|BANK1_ENST00000504592.1_Missense_Mutation_p.R46H|BANK1_ENST00000444316.2_Missense_Mutation_p.R31H|BANK1_ENST00000508653.1_Intron	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	61	Interaction with ITPR2.		R -> H (influences susceptibility to SLE; dbSNP:rs10516487). {ECO:0000269|PubMed:18204447}.		B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		CTGTTATATCGCTTGGAGAAT	0.353													G|||	1094	0.21845	0.2239	0.1859	5008	,	,		16221	0.1875		0.2972	False		,,,				2504	0.1851				p.R61H		Atlas-SNP	.											.	BANK1	95	.	0			c.G182A	GRCh37	CM080095	BANK1	M	rs10516487	PASS	.	G	HIS/ARG,,HIS/ARG	1075,3331	385.8+/-325.9	139,797,1267	77.0	78.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	92,,182	-1.2	0.0	4	dbSNP_119	78	2610,5990	420.8+/-353.5	395,1820,2085	yes	missense,intron,missense	BANK1	NM_001083907.2,NM_001127507.2,NM_017935.4	29,,29	534,2617,3352	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	30.3488,24.3985,28.3331	benign,,benign	31/756,,61/786	102751076	3685,9321	2203	4300	6503	SO:0001583	missense	55024	exon2			TATATCGCTTGGA	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"""Ankyrin repeat domain containing"""	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.182G>A	4.37:g.102751076G>A	ENSP00000320509:p.Arg61His	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	490	0.22435897435897437	115	0.23373983739837398	74	0.20441988950276244	84	0.14685314685314685	217	0.2862796833773087	G	11.15	1.553737	0.27739	0.243985	0.303488	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000444316	T;T;T	0.09445	2.98;2.98;2.98	5.18	-1.16	0.09678	.	0.869969	0.09740	N	0.762056	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.21753	0.06;0.06	B;B	0.15870	0.014;0.014	T	0.47799	-0.9089	9	0.42905	T	0.14	.	2.2057	0.03935	0.4512:0.1608:0.2727:0.1153	rs10516487;rs17200720;rs56600798;rs56700821;rs10516487	61;46	Q8NDB2;Q8NDB2-2	BANK1_HUMAN;.	H	46;61;31	ENSP00000421443:R46H;ENSP00000320509:R61H;ENSP00000388817:R31H	ENSP00000320509:R61H	R	+	2	0	BANK1	102970099	0.002000	0.14202	0.001000	0.08648	0.909000	0.53808	0.550000	0.23345	-0.749000	0.04747	0.650000	0.86243	CGC	G|0.748;A|0.252	0.252	strong		0.353	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	
CSMD3	114788	hgsc.bcm.edu	37	8	113668453	113668453	+	Silent	SNP	A	A	G	rs11992014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:113668453A>G	ENST00000297405.5	-	18	3178	c.2934T>C	c.(2932-2934)agT>agC	p.S978S	CSMD3_ENST00000343508.3_Silent_p.S938S|CSMD3_ENST00000352409.3_Silent_p.S978S|CSMD3_ENST00000455883.2_Silent_p.S874S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	978	CUB 5. {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						ATATAAAATTACTGCTACTAA	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	156	0.0311502	0.1112	0.0115	5008	,	,		12832	0.0		0.001	False		,,,				2504	0.0				p.S978S		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,-2,2	CSMD3	2325	2	0			c.T2934C						PASS	.	A	,,	382,4024	189.5+/-215.6	17,348,1838	67.0	74.0	72.0		2622,2934,2814	2.5	1.0	8	dbSNP_120	72	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	17,353,6133	GG,GA,AA		0.0581,8.67,2.9755	,,	874/3539,978/3708,938/3668	113668453	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon18			AAAATTACTGCTA	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.2934T>C	8.37:g.113668453A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.971;G|0.029	0.029	strong		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
TG	7038	hgsc.bcm.edu	37	8	133980214	133980214	+	Splice_Site	SNP	A	A	G	rs16904799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133980214A>G	ENST00000220616.4	+	31	5902	c.5862A>G	c.(5860-5862)aaA>aaG	p.K1954K	TG_ENST00000519543.1_Splice_Site_p.K108K|TG_ENST00000542445.1_Splice_Site_p.K324K|TG_ENST00000377869.1_Splice_Site_p.K1897K	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1954					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)		TCCGGAAGAAAGGTGAGCACT	0.458													A|||	286	0.0571086	0.1967	0.0274	5008	,	,		17565	0.0		0.006	False		,,,				2504	0.001				p.K1954K		Atlas-SNP	.											.	TG	416	.	0			c.A5862G						PASS	.	A		720,3686	266.8+/-267.5	53,614,1536	68.0	61.0	64.0		5862	3.2	1.0	8	dbSNP_123	64	27,8573	15.3+/-51.7	0,27,4273	yes	coding-synonymous-near-splice	TG	NM_003235.4		53,641,5809	GG,GA,AA		0.314,16.3414,5.7435		1954/2769	133980214	747,12259	2203	4300	6503	SO:0001630	splice_region_variant	7038	exon31			GAAGAAAGGTGAG	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.5863+1A>G	8.37:g.133980214A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	95	0.043498168498168496	83	0.16869918699186992	9	0.024861878453038673	0	0.0	3	0.00395778364116095	A	5.120	0.207815	0.09704	0.163414	0.00314	ENSG00000042832	ENST00000519178	.	.	.	5.65	3.25	0.37280	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00353	-1.1795	4	.	.	.	.	5.0621	0.14562	0.7544:0.0:0.0856:0.16	rs16904799;rs16904799	.	.	.	G	410	.	.	S	+	1	0	TG	134049396	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	1.350000	0.34010	0.495000	0.27882	0.533000	0.62120	AGT	A|0.949;G|0.051	0.051	strong		0.458	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	Silent
GPR123	84435	hgsc.bcm.edu	37	10	134942166	134942166	+	Silent	SNP	A	A	G	rs2806452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134942166A>G	ENST00000392607.3	+	7	1270	c.834A>G	c.(832-834)tcA>tcG	p.S278S	GPR123_ENST00000392606.2_Silent_p.S181S|GPR123_ENST00000607359.1_Silent_p.S997S	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	278					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		TGGCGGTGTCACAGGGCCACT	0.652													G|||	2450	0.489217	0.4826	0.621	5008	,	,		13237	0.5357		0.4145	False		,,,				2504	0.4335				p.S278S		Atlas-SNP	.											.	GPR123	118	.	0			c.A834G						PASS	.	G		2082,2306		513,1056,625	29.0	22.0	25.0		834	-9.5	0.1	10	dbSNP_100	25	3242,5342		623,1996,1673	no	coding-synonymous	GPR123	NM_001083909.1		1136,3052,2298	GG,GA,AA		37.7679,47.4476,41.0422		278/561	134942166	5324,7648	2194	4292	6486	SO:0001819	synonymous_variant	84435	exon7			GGTGTCACAGGGC	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"""-"", ""GPCR / Class B : Orphans"""	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.834A>G	10.37:g.134942166A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	37	CCDS41580.1																																																																																			A|0.559;G|0.441	0.441	strong		0.652	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2		
PPP2R2C	5522	hgsc.bcm.edu	37	4	6374263	6374263	+	Silent	SNP	G	G	A	rs35410672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6374263G>A	ENST00000382599.4	-	5	828	c.612C>T	c.(610-612)acC>acT	p.T204T	PPP2R2C_ENST00000314348.8_5'UTR|PPP2R2C_ENST00000515571.1_Silent_p.T187T|PPP2R2C_ENST00000335585.5_Silent_p.T204T|PPP2R2C_ENST00000506140.1_Silent_p.T197T|PPP2R2C_ENST00000507294.1_Silent_p.T197T			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	204					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						AGCTCCTGTCGGTGATGGCCA	0.582													G|||	153	0.0305511	0.1051	0.0101	5008	,	,		20869	0.0		0.0	False		,,,				2504	0.0072				p.T204T		Atlas-SNP	.											.	PPP2R2C	63	.	0			c.C612T						PASS	.	G	,,,	362,4044	185.7+/-212.7	20,322,1861	152.0	122.0	132.0		591,591,561,612	-3.2	1.0	4	dbSNP_126	132	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP2R2C	NM_001206994.1,NM_001206995.1,NM_001206996.1,NM_181876.2	,,,	20,327,6156	AA,AG,GG		0.0581,8.2161,2.8218	,,,	197/441,197/441,187/431,204/448	6374263	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	5522	exon5			CCTGTCGGTGATG	AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9306	protein-coding gene	gene with protein product	"""PP2A subunit B isoform gamma"""	605997	"""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform"""			10574460, 10945473	Standard	NM_020416		Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.612C>T	4.37:g.6374263G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	148	60	0.405405	NM_181876	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Silent	SNP	ENST00000382599.4	37																																																																																				G|0.973;A|0.027	0.027	strong		0.582	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876	
OR4K15	81127	hgsc.bcm.edu	37	14	20443872	20443872	+	Silent	SNP	C	C	G	rs4499148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20443872C>G	ENST00000305051.5	+	1	270	c.195C>G	c.(193-195)ggC>ggG	p.G65G		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTCTGTTGGGCAACTTTCTCA	0.443													C|||	1880	0.375399	0.7451	0.2017	5008	,	,		21174	0.1498		0.2435	False		,,,				2504	0.3671				p.G65G		Atlas-SNP	.											OR4K15,NS,carcinoma,+1,1	OR4K15	82	1	0			c.C195G						scavenged	.	C		3038,1368		1038,962,203	100.0	115.0	109.0		195	-4.4	0.7	14	dbSNP_111	109	2426,6172		333,1760,2206	no	coding-synonymous	OR4K15	NM_001005486.1		1371,2722,2409	GG,GC,CC		28.2159,31.0486,42.0178		65/349	20443872	5464,7540	2203	4299	6502	SO:0001819	synonymous_variant	81127	exon1			GTTGGGCAACTTT		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.195C>G	14.37:g.20443872C>G		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	192	190	0.989583	NM_001005486	B9EIL3|Q6IEZ4	Silent	SNP	ENST00000305051.5	37	CCDS32026.1																																																																																			.	.	weak		0.443	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
TRIOBP	11078	hgsc.bcm.edu	37	22	38164106	38164106	+	Silent	SNP	C	C	T	rs4821708	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38164106C>T	ENST00000406386.3	+	19	6753	c.6498C>T	c.(6496-6498)taC>taT	p.Y2166Y	TRIOBP_ENST00000403663.2_Silent_p.Y453Y	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	2166					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					AGAAGGCCTACCAGGAAGAGC	0.612													C|||	1326	0.264776	0.0408	0.2997	5008	,	,		18755	0.2927		0.336	False		,,,				2504	0.4407				p.Y2166Y		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	0			c.C6498T						PASS	.	C	,	303,3729		11,281,1724	33.0	37.0	35.0		6498,1359	1.0	1.0	22	dbSNP_111	35	2561,5783		367,1827,1978	no	coding-synonymous,coding-synonymous	TRIOBP	NM_001039141.2,NM_007032.5	,	378,2108,3702	TT,TC,CC		30.6927,7.5149,23.1416	,	2166/2366,453/653	38164106	2864,9512	2016	4172	6188	SO:0001819	synonymous_variant	11078	exon19			GGCCTACCAGGAA	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.6498C>T	22.37:g.38164106C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	60	0.550459	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.739;T|0.261	0.261	strong		0.612	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
VPS13A	23230	hgsc.bcm.edu	37	9	79936579	79936579	+	Missense_Mutation	SNP	G	G	A	rs73467962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79936579G>A	ENST00000360280.3	+	44	6007	c.5747G>A	c.(5746-5748)aGt>aAt	p.S1916N	VPS13A_ENST00000357409.5_Missense_Mutation_p.S1916N|VPS13A_ENST00000376636.3_Missense_Mutation_p.S1877N|VPS13A_ENST00000376634.4_Missense_Mutation_p.S1916N	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1916					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						GAAAGTTTAAGTATGGATTAT	0.343													G|||	72	0.014377	0.0537	0.0014	5008	,	,		16144	0.0		0.0	False		,,,				2504	0.0				p.S1916N		Atlas-SNP	.											.	VPS13A	735	.	0			c.G5747A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER	183,4223	118.4+/-156.1	3,177,2023	84.0	82.0	82.0		5630,5747,5747,5747	1.9	1.0	9	dbSNP_130	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	46,46,46,46	3,178,6322	AA,AG,GG		0.0116,4.1534,1.4147	benign,benign,benign,benign	1877/3136,1916/3070,1916/3096,1916/3175	79936579	184,12822	2203	4300	6503	SO:0001583	missense	23230	exon44			GTTTAAGTATGGA	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.5747G>A	9.37:g.79936579G>A	ENSP00000353422:p.Ser1916Asn	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	125	75	0.6	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	19|19	0.0086996336996337|0.0086996336996337	19|19	0.03861788617886179|0.03861788617886179	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	6.184|6.184	0.402055|0.402055	0.11696|0.11696	0.041534|0.041534	1.16E-4|1.16E-4	ENSG00000197969|ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409|ENST00000419472	T;T;T;T|.	0.47869|.	1.0;0.83;0.91;1.0|.	5.8|5.8	1.87|1.87	0.25490|0.25490	.|.	0.321368|.	0.38111|.	N|.	0.001815|.	T|T	0.08044|0.08044	0.0201|0.0201	N|N	0.11560|0.11560	0.145|0.145	0.80722|0.80722	D|D	1|1	B;B;B;B;B|.	0.16802|.	0.004;0.005;0.019;0.019;0.019|.	B;B;B;B;B|.	0.18871|.	0.006;0.012;0.01;0.023;0.023|.	T|T	0.01899|0.01899	-1.1251|-1.1251	10|5	0.37606|.	T|.	0.19|.	.|.	5.1895|5.1895	0.15203|0.15203	0.3604:0.1441:0.4955:0.0|0.3604:0.1441:0.4955:0.0	.|.	168;1877;1916;1916;1916|.	B1ALW4;Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4|.	.;.;VP13A_HUMAN;.;.|.	N|I	1916;1877;1916;1916|169	ENSP00000365821:S1916N;ENSP00000365823:S1877N;ENSP00000353422:S1916N;ENSP00000349985:S1916N|.	ENSP00000349985:S1916N|.	S|V	+|+	2|1	0|0	VPS13A|VPS13A	79126399|79126399	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.867000|0.867000	0.49689|0.49689	1.688000|1.688000	0.37690|0.37690	0.347000|0.347000	0.23924|0.23924	-0.373000|-0.373000	0.07131|0.07131	AGT|GTA	G|0.987;A|0.013	0.013	strong		0.343	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
SEMA7A	8482	hgsc.bcm.edu	37	15	74709975	74709975	+	Silent	SNP	G	G	A	rs2075589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:74709975G>A	ENST00000261918.4	-	5	1055	c.507C>T	c.(505-507)taC>taT	p.Y169Y	SEMA7A_ENST00000542748.1_Silent_p.Y4Y|SEMA7A_ENST00000543145.2_Silent_p.Y155Y	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	169	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						TGAAGGGGGCGTAGCCTCTCA	0.607													A|||	1107	0.221046	0.3631	0.0893	5008	,	,		20035	0.3046		0.1103	False		,,,				2504	0.1503				p.Y169Y		Atlas-SNP	.											.	SEMA7A	58	.	0			c.C507T						PASS	.	A	,,	1463,2931	677.2+/-403.4	239,985,973	46.0	45.0	45.0		465,12,507	3.5	1.0	15	dbSNP_96	45	977,7615	771.7+/-407.7	51,875,3370	no	coding-synonymous,coding-synonymous,coding-synonymous	SEMA7A	NM_001146029.1,NM_001146030.1,NM_003612.3	,,	290,1860,4343	AA,AG,GG		11.371,33.2954,18.7895	,,	155/653,4/502,169/667	74709975	2440,10546	2197	4296	6493	SO:0001819	synonymous_variant	8482	exon5			GGGGGCGTAGCCT	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"""Semaphorins"", ""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10741	protein-coding gene	gene with protein product	"""John Milton Hagen blood group"", ""H-Sema K1"""	607961	"""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A"", ""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"""	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.507C>T	15.37:g.74709975G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Silent	SNP	ENST00000261918.4	37	CCDS10262.1																																																																																			G|0.799;A|0.201	0.201	strong		0.607	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612	
ANKS3	124401	hgsc.bcm.edu	37	16	4748825	4748825	+	Silent	SNP	C	C	T	rs841214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4748825C>T	ENST00000304283.4	-	13	1821	c.1527G>A	c.(1525-1527)caG>caA	p.Q509Q	ANKS3_ENST00000585773.1_Silent_p.Q436Q|ANKS3_ENST00000446014.2_Silent_p.Q380Q	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	509										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						TGGCGAGCTCCTGCATCTCAG	0.667													C|||	2028	0.404952	0.146	0.4611	5008	,	,		13432	0.624		0.4602	False		,,,				2504	0.4325				p.Q509Q		Atlas-SNP	.											ANKS3,NS,carcinoma,0,1	ANKS3	44	1	0			c.G1527A						PASS	.	C	,	955,3437		106,743,1347	49.0	61.0	57.0		1206,1527	2.2	1.0	16	dbSNP_86	57	4020,4576		994,2032,1272	no	coding-synonymous,coding-synonymous	ANKS3	NM_001242929.1,NM_133450.3	,	1100,2775,2619	TT,TC,CC		46.7659,21.7441,38.3046	,	402/550,509/657	4748825	4975,8013	2196	4298	6494	SO:0001819	synonymous_variant	124401	exon13			GAGCTCCTGCATC	AK057329	CCDS10520.1, CCDS73820.1	16p13.3	2013-01-10			ENSG00000168096	ENSG00000168096		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	29422	protein-coding gene	gene with protein product						11853319	Standard	NM_133450		Approved	KIAA1977, FLJ32345, FLJ32767	uc002cxj.2	Q6ZW76	OTTHUMG00000129478	ENST00000304283.4:c.1527G>A	16.37:g.4748825C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_133450	B4DWU4|D3DUE2|Q8TF25	Silent	SNP	ENST00000304283.4	37	CCDS10520.1																																																																																			C|0.602;T|0.398	0.398	strong		0.667	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450	
FHL5	9457	hgsc.bcm.edu	37	6	97052754	97052754	+	Silent	SNP	C	C	T	rs2064947	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:97052754C>T	ENST00000326771.2	+	4	668	c.288C>T	c.(286-288)aaC>aaT	p.N96N	FHL5_ENST00000541107.1_Silent_p.N96N	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	96	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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)		GCTATTCTAACGAGTGCTCCT	0.502													C|||	682	0.136182	0.1135	0.1801	5008	,	,		17088	0.0357		0.2117	False		,,,				2504	0.1616				p.N96N		Atlas-SNP	.											.	FHL5	73	.	0			c.C288T						PASS	.	C	,	483,3923	225.2+/-241.2	23,437,1743	118.0	107.0	111.0		288,288	-10.7	0.2	6	dbSNP_94	111	1671,6929	306.8+/-308.1	174,1323,2803	no	coding-synonymous,coding-synonymous	FHL5	NM_001170807.1,NM_020482.4	,	197,1760,4546	TT,TC,CC		19.4302,10.9623,16.5616	,	96/285,96/285	97052754	2154,10852	2203	4300	6503	SO:0001819	synonymous_variant	9457	exon4			TTCTAACGAGTGC	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.288C>T	6.37:g.97052754C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Silent	SNP	ENST00000326771.2	37	CCDS5035.1																																																																																			C|0.849;T|0.151	0.151	strong		0.502	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
SPEF2	79925	hgsc.bcm.edu	37	5	35694454	35694454	+	Missense_Mutation	SNP	A	A	G	rs12332369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:35694454A>G	ENST00000356031.3	+	13	2118	c.1964A>G	c.(1963-1965)gAa>gGa	p.E655G	SPEF2_ENST00000509059.1_Intron|SPEF2_ENST00000440995.2_Intron|CTD-2113L7.1_ENST00000510433.1_RNA	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	655			E -> G (in dbSNP:rs12332369).		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)			ACAGAAGGTGAAACAATGCTT	0.368													A|||	114	0.0227636	0.0832	0.0058	5008	,	,		17502	0.0		0.0	False		,,,				2504	0.0				p.E655G		Atlas-SNP	.											.	SPEF2	324	.	0			c.A1964G						PASS	.	A	GLY/GLU	258,3442		10,238,1602	93.0	86.0	88.0		1964	3.7	0.9	5	dbSNP_120	88	1,8215		0,1,4107	yes	missense	SPEF2	NM_024867.3	98	10,239,5709	GG,GA,AA		0.0122,6.973,2.1735	benign	655/1823	35694454	259,11657	1850	4108	5958	SO:0001583	missense	79925	exon13			AAGGTGAAACAAT	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.1964A>G	5.37:g.35694454A>G	ENSP00000348314:p.Glu655Gly	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	180	89	0.494444	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	A	11.23	1.576102	0.28092	0.06973	1.22E-4	ENSG00000152582	ENST00000356031	T	0.06449	3.3	3.74	3.74	0.42951	.	0.984296	0.08306	N	0.966202	T	0.00300	0.0009	N	0.22421	0.69	0.80722	D	1	B	0.16166	0.016	B	0.09377	0.004	T	0.46965	-0.9153	10	0.33940	T	0.23	.	9.1268	0.36821	1.0:0.0:0.0:0.0	rs12332369;rs52800439;rs12332369	655	Q9C093	SPEF2_HUMAN	G	655	ENSP00000348314:E655G	ENSP00000348314:E655G	E	+	2	0	SPEF2	35730211	0.746000	0.28272	0.862000	0.33874	0.140000	0.21249	2.047000	0.41269	1.941000	0.56285	0.260000	0.18958	GAA	A|0.973;G|0.027	0.027	strong		0.368	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
SLC7A4	6545	hgsc.bcm.edu	37	22	21384578	21384578	+	Missense_Mutation	SNP	C	C	T	rs2270384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21384578C>T	ENST00000382932.2	-	3	1112	c.1045G>A	c.(1045-1047)Gcc>Acc	p.A349T	AC002472.11_ENST00000450652.1_RNA|SLC7A4_ENST00000403586.1_Missense_Mutation_p.A349T	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	349			A -> T (in dbSNP:rs2270384). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.		basic amino acid transport (GO:0015802)|cellular amino acid metabolic process (GO:0006520)|transport (GO:0006810)	integral component of membrane (GO:0016021)	basic amino acid transmembrane transporter activity (GO:0015174)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	AGCCCATCGGCGGCCATGGCA	0.647													C|||	1654	0.330272	0.3381	0.2522	5008	,	,		18900	0.5456		0.1093	False		,,,				2504	0.3804				p.A349T		Atlas-SNP	.											.	SLC7A4	50	.	0			c.G1045A						PASS	.	C	THR/ALA	1310,3096	430.6+/-342.6	193,924,1086	48.0	43.0	45.0		1045	2.6	0.0	22	dbSNP_100	45	880,7716	194.9+/-240.2	57,766,3475	yes	missense	SLC7A4	NM_004173.2	58	250,1690,4561	TT,TC,CC		10.2373,29.7322,16.8436	benign	349/636	21384578	2190,10812	2203	4298	6501	SO:0001583	missense	6545	exon3			CATCGGCGGCCAT	AJ000730	CCDS33608.1	22q11.21	2013-07-19	2013-07-19		ENSG00000099960	ENSG00000099960		"""Solute carriers"""	11062	protein-coding gene	gene with protein product		603752	"""solute carrier family 7 (cationic amino acid transporter, y+ system), member 4"", ""solute carrier family 7 (orphan transporter), member 4"""			9598310, 11665818	Standard	NM_004173		Approved	HCAT3, CAT-4, VH	uc002zud.3	O43246	OTTHUMG00000150896	ENST00000382932.2:c.1045G>A	22.37:g.21384578C>T	ENSP00000372390:p.Ala349Thr	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	213	113	0.530516	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Missense_Mutation	SNP	ENST00000382932.2	37	CCDS33608.1	589	0.2696886446886447	149	0.30284552845528456	80	0.22099447513812154	285	0.4982517482517482	75	0.09894459102902374	C	8.121	0.780865	0.16120	0.297322	0.102373	ENSG00000099960	ENST00000403586;ENST00000382932	D;D	0.89415	-2.51;-2.51	4.94	2.62	0.31277	Amino acid permease domain (1);	0.320496	0.32624	N	0.005858	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.37709	-0.9694	9	0.23302	T	0.38	.	9.2769	0.37705	0.0:0.8083:0.0:0.1917	rs2270384;rs17212409;rs58937775;rs2270384	349	O43246	CTR4_HUMAN	T	349	ENSP00000384278:A349T;ENSP00000372390:A349T	ENSP00000372390:A349T	A	-	1	0	SLC7A4	19714578	0.001000	0.12720	0.001000	0.08648	0.099000	0.18886	0.335000	0.19806	0.671000	0.31185	0.561000	0.74099	GCC	C|0.775;T|0.225	0.225	strong		0.647	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173	
OR6P1	128366	hgsc.bcm.edu	37	1	158533219	158533219	+	Missense_Mutation	SNP	A	A	C	rs114956415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158533219A>C	ENST00000334632.1	-	1	175	c.176T>G	c.(175-177)aTg>aGg	p.M59R		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	59						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						GAAAAAGTACATGGGACGATG	0.448													A|||	79	0.0157748	0.0582	0.0029	5008	,	,		20152	0.0		0.0	False		,,,				2504	0.0				p.M59R		Atlas-SNP	.											.	OR6P1	47	.	0			c.T176G						PASS	.	A	ARG/MET	78,1306		3,72,617	41.0	47.0	45.0		176	5.0	1.0	1	dbSNP_132	45	1,3181		0,1,1590	yes	missense	OR6P1	NM_001160325.1	91	3,73,2207	CC,CA,AA		0.0314,5.6358,1.7302	probably-damaging	59/318	158533219	79,4487	692	1591	2283	SO:0001583	missense	128366	exon1			AAGTACATGGGAC	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.176T>G	1.37:g.158533219A>C	ENSP00000334721:p.Met59Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001160325	Q6IFR9	Missense_Mutation	SNP	ENST00000334632.1	37	CCDS53391.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	A	14.53	2.561606	0.45590	0.056358	3.14E-4	ENSG00000186440	ENST00000334632	T	0.09911	2.93	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000027	T	0.28101	0.0693	H	0.98426	4.23	0.52099	D	0.999948	P	0.51351	0.944	P	0.48114	0.567	T	0.54476	-0.8288	10	0.87932	D	0	.	13.8199	0.63313	1.0:0.0:0.0:0.0	.	59	Q8NGX9	OR6P1_HUMAN	R	59	ENSP00000334721:M59R	ENSP00000334721:M59R	M	-	2	0	OR6P1	156799843	1.000000	0.71417	1.000000	0.80357	0.061000	0.15899	8.965000	0.93393	2.100000	0.63781	0.482000	0.46254	ATG	A|0.987;C|0.013	0.013	strong		0.448	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
CLIP4	79745	hgsc.bcm.edu	37	2	29356567	29356567	+	Silent	SNP	G	G	C	rs17749904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29356567G>C	ENST00000320081.5	+	5	669	c.414G>C	c.(412-414)ctG>ctC	p.L138L	CLIP4_ENST00000401605.1_Silent_p.L138L|CLIP4_ENST00000404424.1_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	83	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	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	
GALNT12	79695	hgsc.bcm.edu	37	9	101594219	101594219	+	Silent	SNP	A	A	G	rs16917929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101594219A>G	ENST00000375011.3	+	4	897	c.897A>G	c.(895-897)caA>caG	p.Q299Q		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	299					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)				TACGGATGCAATCCCCCGTCG	0.572													A|||	206	0.0411342	0.1513	0.0086	5008	,	,		14266	0.0		0.0	False		,,,				2504	0.0				p.Q299Q		Atlas-SNP	.											.	GALNT12	37	.	0			c.A897G						PASS	.	A		592,3814	257.7+/-262.0	43,506,1654	65.0	49.0	54.0		897	-4.0	0.6	9	dbSNP_123	54	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GALNT12	NM_024642.4		43,509,5951	GG,GA,AA		0.0349,13.4362,4.5748		299/582	101594219	595,12411	2203	4300	6503	SO:0001819	synonymous_variant	79695	exon4			GATGCAATCCCCC	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.897A>G	9.37:g.101594219A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	89	56	0.629214	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Silent	SNP	ENST00000375011.3	37	CCDS6737.1																																																																																			A|0.954;G|0.046	0.046	strong		0.572	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642	
HIST3H3	8290	hgsc.bcm.edu	37	1	228612994	228612994	+	Silent	SNP	T	T	C	rs61741017	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228612994T>C	ENST00000366696.1	-	1	32	c.33A>G	c.(31-33)tcA>tcG	p.S11S		NM_003493.2	NP_003484.1	Q16695	H31T_HUMAN	histone cluster 3, H3	11					telomere maintenance (GO:0000723)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(2)|prostate(2)|skin(1)	6		Prostate(94;0.0724)				TGCCACCCGTTGACTTGCGCG	0.652													c|||	80	0.0159744	0.0567	0.0058	5008	,	,		14474	0.0		0.001	False		,,,				2504	0.0				p.S11S		Atlas-SNP	.											.	HIST3H3	20	.	0			c.A33G						PASS	.	C		249,4147	735.3+/-410.7	1,247,1950	42.0	50.0	47.0		33	-7.2	0.0	1	dbSNP_129	47	0,8592		0,0,4296	no	coding-synonymous	HIST3H3	NM_003493.2		1,247,6246	CC,CT,TT		0.0,5.6642,1.9172		11/137	228612994	249,12739	2198	4296	6494	SO:0001819	synonymous_variant	8290	exon1			ACCCGTTGACTTG	Z49861	CCDS1572.1	1q42.13	2012-09-19	2006-10-11	2003-02-21	ENSG00000168148	ENSG00000168148		"""Histones / Replication-dependent"""	4778	protein-coding gene	gene with protein product		602820	"""H3 histone family, member T"", ""histone 3, H3"""	H3FT		8834248, 12408966	Standard	NM_003493		Approved	H3t, H3/g, H3.4	uc001hsx.1	Q16695	OTTHUMG00000040044	ENST00000366696.1:c.33A>G	1.37:g.228612994T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	143	64	0.447552	NM_003493	B2R5K3|Q6FGU4	Silent	SNP	ENST00000366696.1	37	CCDS1572.1																																																																																			T|0.984;C|0.016	0.016	strong		0.652	HIST3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096595.2	NM_003493	
MT-CYB	4519	hgsc.bcm.edu	37	M	14911	14911	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:14911C>T	ENST00000361789.2	+	1	165	c.165C>T	c.(163-165)taC>taT	p.Y55Y	MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	55					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						GCCATACACTACTCACCAGAC	0.532																																					p.Y55Y		Atlas-SNP	.											.	.	.	.	0			c.C165T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			GCACTACTCACCA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.165C>T	M.37:g.14911C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Silent	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.532	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
CDC27	996	hgsc.bcm.edu	37	17	45234411	45234411	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45234411G>T	ENST00000066544.3	-	7	803	c.710C>A	c.(709-711)tCa>tAa	p.S237*	CDC27_ENST00000446365.2_Nonsense_Mutation_p.S176*|CDC27_ENST00000527547.1_Nonsense_Mutation_p.S237*|CDC27_ENST00000531206.1_Nonsense_Mutation_p.S237*|CDC27_ENST00000528748.1_5'Flank	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	237					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						AATTACAGCTGAATCAATATA	0.338																																					p.S237X		Atlas-SNP	.											CDC27_ENST00000531206,caecum,carcinoma,0,2	CDC27	337	2	0			c.C710A						scavenged	.						39.0	44.0	42.0					17																	45234411		2188	4290	6478	SO:0001587	stop_gained	996	exon7			ACAGCTGAATCAA	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.710C>A	17.37:g.45234411G>T	ENSP00000066544:p.Ser237*	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	47	5	0.106383	NM_001114091	G3V1C4|Q16349|Q96F35	Nonsense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028766	0.75504	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	.	.	.	5.44	5.44	0.79542	.	0.068298	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.6807	16.7505	0.85484	0.0:0.0:1.0:0.0	.	.	.	.	X	237;237;176;237;237	.	ENSP00000066544:S237X	S	-	2	0	CDC27	42589410	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.255000	0.95524	2.555000	0.86185	0.460000	0.39030	TCA	.	.	none		0.338	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
ST6GAL1	6480	hgsc.bcm.edu	37	3	186793423	186793423	+	Silent	SNP	C	C	T	rs7629263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186793423C>T	ENST00000169298.3	+	8	1727	c.1053C>T	c.(1051-1053)gaC>gaT	p.D351D	ST6GAL1_ENST00000448044.1_Silent_p.D351D|ST6GAL1_ENST00000457772.2_Silent_p.D120D	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	351					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		GCAAGACTGACGTGTGCTACT	0.507													C|||	382	0.076278	0.2005	0.1124	5008	,	,		20306	0.0089		0.001	False		,,,				2504	0.0297				p.D351D		Atlas-SNP	.											.	ST6GAL1	36	.	0			c.C1053T						PASS	.	C	,,	799,3607	321.5+/-297.2	68,663,1472	147.0	121.0	130.0		1053,1053,360	-9.7	0.0	3	dbSNP_116	130	31,8569	20.4+/-63.3	0,31,4269	no	coding-synonymous,coding-synonymous,coding-synonymous	ST6GAL1	NM_003032.2,NM_173216.2,NM_173217.2	,,	68,694,5741	TT,TC,CC		0.3605,18.1344,6.3817	,,	351/407,351/407,120/176	186793423	830,12176	2203	4300	6503	SO:0001819	synonymous_variant	6480	exon7			GACTGACGTGTGC	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"""ST6Gal I"""	109675	"""sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"""	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.1053C>T	3.37:g.186793423C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	192	87	0.453125	NM_003032	A8KA14|B2R513|D3DNV3	Silent	SNP	ENST00000169298.3	37	CCDS3285.1																																																																																			C|0.922;T|0.078	0.078	strong		0.507	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216	
D2HGDH	728294	hgsc.bcm.edu	37	2	242674803	242674803	+	Missense_Mutation	SNP	G	G	A	rs77940364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242674803G>A	ENST00000321264.4	+	2	373	c.164G>A	c.(163-165)cGg>cAg	p.R55Q	D2HGDH_ENST00000403782.1_Intron|D2HGDH_ENST00000537090.1_Missense_Mutation_p.R55Q|AC114730.8_ENST00000400768.2_RNA|D2HGDH_ENST00000342518.6_Missense_Mutation_p.R55Q	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	55				R -> Q (in Ref. 3; AAH36604). {ECO:0000305}.	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)		TACCCCGTGCGGCGCTTGCCG	0.741													G|||	1134	0.226438	0.1914	0.2017	5008	,	,		13600	0.1617		0.3191	False		,,,				2504	0.2628				p.R55Q		Atlas-SNP	.											.	D2HGDH	39	.	0			c.G164A						PASS	.	G	GLN/ARG	788,3316		84,620,1348	7.0	9.0	9.0		164	-6.4	0.4	2	dbSNP_131	9	2638,5780		471,1696,2042	yes	missense	D2HGDH	NM_152783.3	43	555,2316,3390	AA,AG,GG		31.3376,19.2008,27.3598	benign	55/522	242674803	3426,9096	2052	4209	6261	SO:0001583	missense	728294	exon2			CCGTGCGGCGCTT	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.164G>A	2.37:g.242674803G>A	ENSP00000315351:p.Arg55Gln	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	37	CCDS33426.1	474	0.21703296703296704	84	0.17073170731707318	74	0.20441988950276244	77	0.1346153846153846	239	0.3153034300791557	G	11.38	1.622085	0.28889	0.192008	0.313376	ENSG00000180902	ENST00000537090;ENST00000321264;ENST00000342518	D;D;D	0.88277	-2.36;-1.97;-2.36	4.13	-6.41	0.01938	.	0.966165	0.08381	N	0.954463	T	0.00012	0.0000	N	0.25992	0.78	0.80722	P	0.0	B	0.18968	0.032	B	0.19148	0.024	T	0.03524	-1.1028	9	0.15952	T	0.53	.	13.5346	0.61641	0.7652:0.0:0.2348:0.0	.	55	Q8N465	D2HDH_HUMAN	Q	55	ENSP00000442796:R55Q;ENSP00000315351:R55Q;ENSP00000339536:R55Q	ENSP00000315351:R55Q	R	+	2	0	D2HGDH	242323476	0.045000	0.20229	0.395000	0.26283	0.607000	0.37147	-0.267000	0.08619	-1.798000	0.01250	0.297000	0.19635	CGG	G|0.785;A|0.215	0.215	strong		0.741	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
BST1	683	hgsc.bcm.edu	37	4	15733454	15733454	+	Silent	SNP	A	A	C	rs1058212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	142	0	0		WXS	Illumina HiSeq	Phase_I	173	73	0.421965	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	
TOX3	27324	hgsc.bcm.edu	37	16	52497872	52497872	+	Missense_Mutation	SNP	C	C	T	rs16951186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:52497872C>T	ENST00000219746.9	-	3	666	c.382G>A	c.(382-384)Gtg>Atg	p.V128M	TOX3_ENST00000407228.3_Missense_Mutation_p.V123M	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	128			V -> M (in dbSNP:rs16951186).		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)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						CTATGAAGCACGCCATCTTGT	0.423													C|||	306	0.0611022	0.1974	0.0259	5008	,	,		20000	0.0		0.007	False		,,,				2504	0.0204				p.V128M		Atlas-SNP	.											.	TOX3	121	.	0			c.G382A						PASS	.	C	MET/VAL,MET/VAL	732,3088		69,594,1247	86.0	91.0	89.0		382,367	5.0	1.0	16	dbSNP_123	89	80,8166		0,80,4043	yes	missense,missense	TOX3	NM_001080430.2,NM_001146188.1	21,21	69,674,5290	TT,TC,CC		0.9702,19.1623,6.7297	benign,benign	128/577,123/572	52497872	812,11254	1910	4123	6033	SO:0001583	missense	27324	exon3			GAAGCACGCCATC	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.382G>A	16.37:g.52497872C>T	ENSP00000219746:p.Val128Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	NM_001080430	B4DRD0|B5MCW4	Missense_Mutation	SNP	ENST00000219746.9	37	CCDS54009.1	105	0.04807692307692308	90	0.18292682926829268	10	0.027624309392265192	0	0.0	5	0.006596306068601583	C	8.683	0.905489	0.17760	0.191623	0.009702	ENSG00000103460	ENST00000219746;ENST00000407228	T;T	0.43688	0.94;0.94	5.9	4.96	0.65561	.	0.213630	0.39475	N	0.001341	T	0.00039	0.0001	L	0.34521	1.04	0.36377	P	0.13831300000000002	B;B	0.24721	0.046;0.11	B;B	0.09377	0.004;0.004	T	0.05468	-1.0883	9	0.33940	T	0.23	.	15.3622	0.74487	0.0:0.9332:0.0:0.0668	rs16951186;rs52806498;rs16951186	123;128	B4DRD0;O15405	.;TOX3_HUMAN	M	128;123	ENSP00000219746:V128M;ENSP00000385705:V123M	ENSP00000219746:V128M	V	-	1	0	TOX3	51055373	0.102000	0.21896	0.992000	0.48379	0.646000	0.38490	0.664000	0.25068	1.524000	0.49035	-0.126000	0.14955	GTG	C|0.938;T|0.062	0.062	strong		0.423	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037	
GALNT2	2590	hgsc.bcm.edu	37	1	230391058	230391058	+	Silent	SNP	G	G	A	rs75919037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230391058G>A	ENST00000366672.4	+	11	1176	c.1104G>A	c.(1102-1104)acG>acA	p.T368T	GALNT2_ENST00000541865.1_Missense_Mutation_p.V244I|GALNT2_ENST00000543760.1_Silent_p.T330T	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	368					cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				ACCCCTACACGTTCCCGGGTG	0.587													G|||	10	0.00199681	0.0076	0.0	5008	,	,		19672	0.0		0.0	False		,,,				2504	0.0				p.T368T		Atlas-SNP	.											GALNT2,ear,carcinoma,+1,1	GALNT2	83	1	0			c.G1104A						PASS	.	G		42,4364	45.3+/-79.5	0,42,2161	173.0	129.0	144.0		1104	-8.4	0.7	1	dbSNP_132	144	0,8600		0,0,4300	no	coding-synonymous	GALNT2	NM_004481.3		0,42,6461	AA,AG,GG		0.0,0.9532,0.3229		368/572	230391058	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	2590	exon11			CTACACGTTCCCG	BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4124	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 2"""	602274	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"""			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.1104G>A	1.37:g.230391058G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	115	69	0.6	NM_004481	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Silent	SNP	ENST00000366672.4	37	CCDS1582.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	2.687	-0.274072	0.05679	0.009532	0.0	ENSG00000143641	ENST00000541865	T	0.41065	1.01	4.97	-8.41	0.00961	.	.	.	.	.	T	0.19525	0.0469	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35847	-0.9772	6	0.59425	D	0.04	.	1.101	0.01683	0.1909:0.2919:0.1871:0.3301	.	.	.	.	I	244	ENSP00000444346:V244I	ENSP00000444346:V244I	V	+	1	0	GALNT2	228457681	0.000000	0.05858	0.694000	0.30210	0.977000	0.68977	-2.466000	0.00994	-1.729000	0.01364	-0.244000	0.11960	GTT	G|0.996;A|0.004	0.004	strong		0.587	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	
DVL2	1856	hgsc.bcm.edu	37	17	7133609	7133609	+	Silent	SNP	G	G	A	rs2074216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7133609G>A	ENST00000005340.5	-	3	687	c.405C>T	c.(403-405)tcC>tcT	p.S135S	DVL2_ENST00000574642.1_5'UTR|DVL2_ENST00000575458.1_Silent_p.S135S	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	135					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						CTCACTGGAAGGATGGAGGCC	0.622													G|||	1666	0.332668	0.267	0.268	5008	,	,		17320	0.3859		0.3777	False		,,,				2504	0.3661				p.S135S		Atlas-SNP	.											.	DVL2	49	.	0			c.C405T						PASS	.	G		1167,3239	403.3+/-332.7	152,863,1188	88.0	97.0	94.0		405	-0.9	1.0	17	dbSNP_96	94	3061,5539	463.4+/-366.0	548,1965,1787	no	coding-synonymous	DVL2	NM_004422.2		700,2828,2975	AA,AG,GG		35.593,26.4866,32.5081		135/737	7133609	4228,8778	2203	4300	6503	SO:0001819	synonymous_variant	1856	exon3			CTGGAAGGATGGA	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.405C>T	17.37:g.7133609G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_004422	D3DTN3|Q53XM0	Silent	SNP	ENST00000005340.5	37	CCDS11091.1																																																																																			G|0.674;A|0.326	0.326	strong		0.622	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415608	105415608	+	Missense_Mutation	SNP	G	G	C	rs11850848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105415608G>C	ENST00000333244.5	-	7	6299	c.6180C>G	c.(6178-6180)caC>caG	p.H2060Q	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2060						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)			CCTCGGGCACGTGGCCCTCCG	0.627													.|||	1818	0.363019	0.562	0.3329	5008	,	,		11574	0.3333		0.1163	False		,,,				2504	0.3998				p.H2060Q		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C6180G						PASS	.	G	GLN/HIS	1936,1626		688,560,533	90.0	72.0	79.0		6180	-2.5	0.0	14	dbSNP_120	79	629,5089		217,195,2447	no	missense	AHNAK2	NM_138420.2	24	905,755,2980	CC,CG,GG		11.0003,45.6485,27.6401	benign	2060/5796	105415608	2565,6715	1781	2859	4640	SO:0001583	missense	113146	exon7			GGGCACGTGGCCC	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.6180C>G	14.37:g.105415608G>C	ENSP00000353114:p.His2060Gln	Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	253	253	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	747	0.34203296703296704	269	0.5467479674796748	152	0.4198895027624309	184	0.32167832167832167	142	0.18733509234828497	-	7.258	0.604635	0.14002	0.543515	0.110003	ENSG00000185567	ENST00000333244	T	0.00882	5.58	4.25	-2.47	0.06442	.	.	.	.	.	T	0.00012	0.0000	L	0.55017	1.72	0.80722	P	0.0	B	0.17465	0.022	B	0.20384	0.029	T	0.08289	-1.0729	8	0.12766	T	0.61	.	8.9245	0.35632	0.0:0.1777:0.6214:0.2009	rs11850848;rs60903782	2060	Q8IVF2	AHNK2_HUMAN	Q	2060	ENSP00000353114:H2060Q	ENSP00000353114:H2060Q	H	-	3	2	AHNAK2	104486653	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-5.080000	0.00153	-0.084000	0.12595	-0.494000	0.04653	CAC	G|0.698;C|0.302	0.302	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MST1L	11223	hgsc.bcm.edu	37	1	17084057	17084057	+	RNA	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17084057C>T	ENST00000455405.2	-	0	655							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GTGCACATCTCGCTCTCCCGC	0.587																																					p.E622K		Atlas-SNP	.											.	.	.	.	0			c.G1864A						PASS	.																																					11223	exon14			ACATCTCGCTCTC	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.17084057C>T		Somatic	1115	0	0		WXS	Illumina HiSeq	Phase_I	1363	118	0.0865737	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	15.05	2.717424	0.48622	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.42420	D	0.000706	T	0.65943	0.2740	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.71196	-0.4664	6	0.56958	D	0.05	.	6.7402	0.23431	0.0:0.9998:0.0:2.0E-4	.	622;648	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	K	622;648	.	ENSP00000439273:E622K	E	-	1	0	MST1P9	16956644	1.000000	0.71417	0.477000	0.27303	0.000000	0.00434	4.380000	0.59581	0.502000	0.28037	0.000000	0.15137	GAG	.	.	none		0.587	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
COMMD10	51397	hgsc.bcm.edu	37	5	115469773	115469773	+	Silent	SNP	C	C	T	rs1129496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:115469773C>T	ENST00000274458.4	+	5	470	c.408C>T	c.(406-408)acC>acT	p.T136T	COMMD10_ENST00000515539.1_Silent_p.T122T	NM_016144.2	NP_057228.1	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10	136	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.							p.T136T(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)		AGCTAGAGACCGTTGGATGGC	0.413													G|||	2166	0.432508	0.1415	0.536	5008	,	,		16338	0.3839		0.6571	False		,,,				2504	0.5716				p.T136T		Atlas-SNP	.											COMMD10,NS,carcinoma,0,1	COMMD10	18	1	1	Substitution - coding silent(1)	stomach(1)	c.C408T						PASS	.	G		996,3408		118,760,1324	107.0	88.0	95.0		408	-12.0	0.1	5	dbSNP_94	95	5526,3074		1780,1966,554	no	coding-synonymous	COMMD10	NM_016144.2		1898,2726,1878	TT,TC,CC		35.7442,22.6158,49.8462		136/203	115469773	6522,6482	2202	4300	6502	SO:0001819	synonymous_variant	51397	exon5			AGAGACCGTTGGA	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.408C>T	5.37:g.115469773C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_016144	D3DT07|Q9P077	Silent	SNP	ENST00000274458.4	37	CCDS34215.1																																																																																			C|0.523;T|0.477	0.477	strong		0.413	COMMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371033.1	NM_016144	
MUC17	140453	hgsc.bcm.edu	37	7	100678407	100678407	+	Missense_Mutation	SNP	G	G	A	rs4729649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678407G>A	ENST00000306151.4	+	3	3774	c.3710G>A	c.(3709-3711)aGc>aAc	p.S1237N		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1237	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)					TCTGAGGCTAGCACCCTTTCA	0.527													G|||	989	0.197484	0.2663	0.0893	5008	,	,		29474	0.2212		0.1083	False		,,,				2504	0.2485				p.S1237N		Atlas-SNP	.											MUC17,caecum,carcinoma,0,1	MUC17	804	1	0			c.G3710A						PASS	.	G	ASN/SER	354,4052	149.2+/-183.4	0,354,1849	303.0	291.0	295.0		3710	-1.7	0.0	7	dbSNP_111	295	220,8380	66.0+/-128.3	0,220,4080	no	missense	MUC17	NM_001040105.1	46	0,574,5929	AA,AG,GG		2.5581,8.0345,4.4133	benign	1237/4494	100678407	574,12432	2203	4300	6503	SO:0001583	missense	140453	exon3			AGGCTAGCACCCT	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.3710G>A	7.37:g.100678407G>A	ENSP00000302716:p.Ser1237Asn	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	154	26	0.168831	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.984	-0.696233	0.03279	0.080345	0.025581	ENSG00000169876	ENST00000306151	T	0.02606	4.23	0.838	-1.68	0.08212	.	.	.	.	.	T	0.00144	0.0004	L	0.29908	0.895	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.47235	-0.9133	9	0.26408	T	0.33	.	2.9027	0.05711	0.0:0.3166:0.4155:0.2679	rs4729649	1237	Q685J3	MUC17_HUMAN	N	1237	ENSP00000302716:S1237N	ENSP00000302716:S1237N	S	+	2	0	MUC17	100465127	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-2.728000	0.00807	-1.139000	0.02881	0.134000	0.15878	AGC	G|0.948;A|0.052	0.052	strong		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
IFNA7	3444	hgsc.bcm.edu	37	9	21201703	21201703	+	Silent	SNP	T	T	C	rs76644201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21201703T>C	ENST00000239347.3	-	1	501	c.462A>G	c.(460-462)ctA>ctG	p.L154L		NM_021057.2	NP_066401.2	P01567	IFNA7_HUMAN	interferon, alpha 7	154					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(6)	12				GBM - Glioblastoma multiforme(5;4.75e-197)|Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		TCTTCTCCATTAGATAAAGAG	0.433																																					p.L154L		Atlas-SNP	.											.	IFNA7	24	.	0			c.A462G						PASS	.	T		252,4154	136.1+/-172.1	7,238,1958	245.0	252.0	250.0		462	-1.0	0.0	9	dbSNP_131	250	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	IFNA7	NM_021057.2		7,245,6251	CC,CT,TT		0.0814,5.7195,1.9914		154/190	21201703	259,12747	2203	4300	6503	SO:0001819	synonymous_variant	3444	exon1			CTCCATTAGATAA		CCDS34995.1	9p22	2010-12-10			ENSG00000214042	ENSG00000214042		"""Interferons"""	5428	protein-coding gene	gene with protein product		147567				1385305	Standard	NM_021057		Approved	IFNA-J, IFN-alphaJ	uc003zop.1	P01567	OTTHUMG00000019662	ENST00000239347.3:c.462A>G	9.37:g.21201703T>C		Somatic	378	0	0		WXS	Illumina HiSeq	Phase_I	368	177	0.480978	NM_021057	Q14607|Q5VV14	Silent	SNP	ENST00000239347.3	37	CCDS34995.1																																																																																			T|0.976;C|0.024	0.024	strong		0.433	IFNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051891.1	NM_021057	
CAPN12	147968	hgsc.bcm.edu	37	19	39234723	39234723	+	Missense_Mutation	SNP	C	C	T	rs112433506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39234723C>T	ENST00000328867.4	-	1	391	c.83G>A	c.(82-84)cGg>cAg	p.R28Q	CAPN12_ENST00000601953.1_Intron	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	28					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GCTCTGGCCCCGAAAAAGCTG	0.632													c|||	11	0.00219649	0.0083	0.0	5008	,	,		14500	0.0		0.0	False		,,,				2504	0.0				p.R28Q		Atlas-SNP	.											.	CAPN12	43	.	0			c.G83A						PASS	.	C	GLN/ARG	26,4380	29.9+/-59.1	0,26,2177	61.0	57.0	58.0		83	3.7	0.3	19	dbSNP_132	58	0,8600		0,0,4300	yes	missense	CAPN12	NM_144691.3	43	0,26,6477	TT,TC,CC		0.0,0.5901,0.1999	benign	28/720	39234723	26,12980	2203	4300	6503	SO:0001583	missense	147968	exon1			TGGCCCCGAAAAA	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.83G>A	19.37:g.39234723C>T	ENSP00000331636:p.Arg28Gln	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_144691		Missense_Mutation	SNP	ENST00000328867.4	37	CCDS12519.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	12.17	1.858222	0.32791	0.005901	0.0	ENSG00000182472	ENST00000328867	T	0.41065	1.01	4.74	3.7	0.42460	Peptidase C2, calpain, catalytic domain (1);	0.749962	0.11830	N	0.525296	T	0.18087	0.0434	L	0.39898	1.24	0.09310	N	1	P	0.37997	0.614	B	0.27887	0.084	T	0.07616	-1.0763	10	0.13853	T	0.58	.	5.2383	0.15458	0.2025:0.6908:0.0:0.1066	.	28	Q6ZSI9	CAN12_HUMAN	Q	28	ENSP00000331636:R28Q	ENSP00000331636:R28Q	R	-	2	0	CAPN12	43926563	0.001000	0.12720	0.349000	0.25694	0.717000	0.41224	-0.261000	0.08694	1.204000	0.43247	0.457000	0.33378	CGG	C|0.998;T|0.002	0.002	strong		0.632	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
MUC17	140453	hgsc.bcm.edu	37	7	100677415	100677415	+	Silent	SNP	T	T	C	rs57597607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677415T>C	ENST00000306151.4	+	3	2782	c.2718T>C	c.(2716-2718)ccT>ccC	p.P906P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	906	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)					GTTCGTCTCCTACAACTTCTG	0.527																																					p.P906P		Atlas-SNP	.											.	MUC17	804	.	0			c.T2718C						PASS	.	T		24,4382	21.2+/-45.6	0,24,2179	323.0	305.0	311.0		2718	-2.2	0.0	7	dbSNP_129	311	10,8590	2.2+/-6.3	0,10,4290	no	coding-synonymous	MUC17	NM_001040105.1		0,34,6469	CC,CT,TT		0.1163,0.5447,0.2614		906/4494	100677415	34,12972	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			GTCTCCTACAACT	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.2718T>C	7.37:g.100677415T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	169	37	0.218935	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.933;C|0.067	0.067	strong		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CERS4	79603	hgsc.bcm.edu	37	19	8321946	8321946	+	Silent	SNP	T	T	C	rs36247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8321946T>C	ENST00000251363.5	+	9	1026	c.726T>C	c.(724-726)tcT>tcC	p.S242S	CERS4_ENST00000558331.1_Silent_p.S191S|CERS4_ENST00000559450.1_Silent_p.S242S|CERS4_ENST00000559336.1_Silent_p.S242S|CERS4_ENST00000595722.1_3'UTR	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	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	146	146	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	
TRANK1	9881	hgsc.bcm.edu	37	3	36887863	36887863	+	Silent	SNP	G	G	A	rs142584752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:36887863G>A	ENST00000429976.2	-	16	5182	c.4935C>T	c.(4933-4935)acC>acT	p.T1645T	TRANK1_ENST00000428977.2_Silent_p.T1095T|TRANK1_ENST00000463984.1_5'UTR|TRANK1_ENST00000301807.6_Silent_p.T1095T	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1645							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						GTGTGATGGCGGTGTACAGCT	0.448													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18174	0.0		0.0	False		,,,				2504	0.0				p.T1645T		Atlas-SNP	.											.	TRANK1	398	.	0			c.C4935T						PASS	.	G		30,3826		1,28,1899	56.0	54.0	55.0		4935	-10.3	0.4	3	dbSNP_134	55	1,8267		0,1,4133	no	coding-synonymous	TRANK1	NM_014831.2		1,29,6032	AA,AG,GG		0.0121,0.778,0.2557		1645/2926	36887863	31,12093	1928	4134	6062	SO:0001819	synonymous_variant	9881	exon16			GATGGCGGTGTAC	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.4935C>T	3.37:g.36887863G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	224	92	0.410714	NM_014831	Q8N8K0	Silent	SNP	ENST00000429976.2	37	CCDS46789.2																																																																																			G|0.998;A|0.002	0.002	strong		0.448	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
DNASE2B	58511	hgsc.bcm.edu	37	1	84878228	84878228	+	Splice_Site	SNP	C	C	T	rs7511984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:84878228C>T	ENST00000370665.3	+	5	777	c.744C>T	c.(742-744)gaC>gaT	p.D248D	DNASE2B_ENST00000370662.3_Splice_Site_p.D40D	NM_021233.2	NP_067056.2	Q8WZ79	DNS2B_HUMAN	deoxyribonuclease II beta	248					apoptotic DNA fragmentation (GO:0006309)	extracellular region (GO:0005576)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)			endometrium(1)|lung(4)|skin(1)	6				all cancers(265;0.00303)|Epithelial(280;0.0112)|OV - Ovarian serous cystadenocarcinoma(397;0.0808)		CTTTTCTTGACGGTATGAAAG	0.438													C|||	679	0.135583	0.2012	0.0937	5008	,	,		18374	0.0119		0.1889	False		,,,				2504	0.1493				p.D248D	Pancreas(54;788 1175 11852 16034 30034)	Atlas-SNP	.											.	DNASE2B	40	.	0			c.C744T						PASS	.	C	,	889,3517	342.3+/-307.1	96,697,1410	71.0	71.0	71.0		744,120	-10.2	0.5	1	dbSNP_116	71	1518,7082	285.5+/-297.2	135,1248,2917	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	DNASE2B	NM_021233.2,NM_058248.1	,	231,1945,4327	TT,TC,CC		17.6512,20.177,18.5068	,	248/362,40/154	84878228	2407,10599	2203	4300	6503	SO:0001630	splice_region_variant	58511	exon5			TCTTGACGGTATG	AF274571	CCDS694.1, CCDS44167.1	1p22.3	2008-02-05			ENSG00000137976	ENSG00000137976			28875	protein-coding gene	gene with protein product		608057				12594037, 11376952	Standard	NM_021233		Approved	DLAD	uc001djt.1	Q8WZ79	OTTHUMG00000009860	ENST00000370665.3:c.745+1C>T	1.37:g.84878228C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	65	22	0.338462	NM_021233	Q5VXD0|Q5VXD1|Q8WZ80|Q9NQW3	Silent	SNP	ENST00000370665.3	37	CCDS44167.1																																																																																			C|0.841;T|0.159	0.159	strong		0.438	DNASE2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027248.1	NM_021233	Silent
NT5DC3	51559	hgsc.bcm.edu	37	12	104186995	104186995	+	Silent	SNP	G	G	A	rs61748068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:104186995G>A	ENST00000392876.3	-	9	1006	c.966C>T	c.(964-966)ttC>ttT	p.F322F		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	322						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						TGACCACATCGAACAGGTCCC	0.423													G|||	561	0.112021	0.0038	0.1585	5008	,	,		21006	0.2639		0.0974	False		,,,				2504	0.0838				p.F322F		Atlas-SNP	.											.	NT5DC3	113	.	0			c.C966T						PASS	.	G		97,4309	80.4+/-118.8	0,97,2106	196.0	205.0	202.0		966	-3.5	0.9	12	dbSNP_129	202	842,7758	194.1+/-239.6	49,744,3507	no	coding-synonymous	NT5DC3	NM_001031701.2		49,841,5613	AA,AG,GG		9.7907,2.2015,7.2197		322/549	104186995	939,12067	2203	4300	6503	SO:0001819	synonymous_variant	51559	exon9			CACATCGAACAGG	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.966C>T	12.37:g.104186995G>A		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	224	100	0.446429	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Silent	SNP	ENST00000392876.3	37	CCDS41824.1																																																																																			G|0.908;A|0.092	0.092	strong		0.423	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575	
LY6G6F	259215	hgsc.bcm.edu	37	6	31675501	31675501	+	Missense_Mutation	SNP	G	G	A	rs9267547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31675501G>A	ENST00000375832.4	+	2	341	c.319G>A	c.(319-321)Gct>Act	p.A107T	LY6G6F_ENST00000556581.1_Missense_Mutation_p.A107T|XXbac-BPG32J3.20_ENST00000461287.1_Intron|MEGT1_ENST00000503322.1_Missense_Mutation_p.A107T	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	107	Ig-like V-type.		A -> T (in dbSNP:rs9267547). {ECO:0000269|PubMed:14574404}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A107T(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	12						GTACTGGTGCGCTGTGCTAGG	0.577													G|||	755	0.150759	0.2882	0.1182	5008	,	,		20295	0.0893		0.0875	False		,,,				2504	0.1166				p.A107T		Atlas-SNP	.											LY6G6F,NS,lymphoid_neoplasm,0,1	LY6G6F	23	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G319A						PASS	.	G	THR/ALA	1077,3329	391.7+/-328.2	126,825,1252	70.0	61.0	64.0		319	0.9	0.0	6	dbSNP_118	64	791,7809	185.0+/-232.9	41,709,3550	yes	missense	LY6G6F	NM_001003693.1	58	167,1534,4802	AA,AG,GG		9.1977,24.4439,14.3626	benign	107/298	31675501	1868,11138	2203	4300	6503	SO:0001583	missense	259215	exon2			TGGTGCGCTGTGC		CCDS34403.1	6p21	2013-01-11	2008-05-21	2008-05-21		ENSG00000204424		"""Immunoglobulin superfamily / V-set domain containing"""	13933	protein-coding gene	gene with protein product		611404	"""chromosome 6 open reading frame 21"""	LY6G6D, C6orf21		12852788	Standard	NM_001003693		Approved	G6f, NG32	uc003nwa.1	Q5SQ64	OTTHUMG00000031252	ENST00000375832.4:c.319G>A	6.37:g.31675501G>A	ENSP00000364992:p.Ala107Thr	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	192	113	0.588542	NM_001003693	B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Missense_Mutation	SNP	ENST00000375832.4	37	CCDS34403.1	314	0.14377289377289376	150	0.3048780487804878	45	0.12430939226519337	50	0.08741258741258741	69	0.09102902374670185	G	11.78	1.740009	0.30865	0.244439	0.091977	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	T;T;T	0.67865	-0.29;-0.29;-0.29	5.51	0.936	0.19488	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.333539	0.25584	N	0.029665	T	0.29028	0.0721	L	0.42245	1.32	0.80722	P	0.0	B;B	0.24576	0.106;0.106	B;B	0.17979	0.02;0.02	T	0.02326	-1.1176	9	0.29301	T	0.29	-0.0497	3.1427	0.06461	0.2529:0.0:0.4535:0.2936	rs9267547;rs17207364;rs59072028;rs9267547	107;107	Q9NZJ1;Q5SQ64	.;LY66F_HUMAN	T	107	ENSP00000452432:A107T;ENSP00000364992:A107T;ENSP00000421232:A107T	ENSP00000364992:A107T	A	+	1	0	XXbac-BPG32J3.19;LY6G6F	31783480	0.000000	0.05858	0.030000	0.17652	0.983000	0.72400	0.004000	0.13106	0.585000	0.29608	0.591000	0.81541	GCT	G|0.854;A|0.146	0.146	strong		0.577	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489708	32489708	+	Missense_Mutation	SNP	C	C	A	rs41556512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32489708C>A	ENST00000374975.3	-	2	406	c.344G>T	c.(343-345)gGt>gTt	p.G115V		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						GAAGCTCTCACCAACCCCGTA	0.622													g|||	1201	0.239816	0.2247	0.2911	5008	,	,		5472	0.2242		0.2416	False		,,,				2504	0.2382				p.G115V		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.G344T						PASS	.						38.0	32.0	34.0					6																	32489708		2155	4217	6372	SO:0001583	missense	3127	exon2			CTCTCACCAACCC		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.344G>T	6.37:g.32489708C>A	ENSP00000364114:p.Gly115Val	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	2.829	-0.243055	0.05906	.	.	ENSG00000198502	ENST00000374975	T	0.00231	8.49	4.6	-8.98	0.00754	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);	135.341000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.05510	-0.035	0.09310	N	1	B;B	0.20459	0.045;0.0	B;B	0.33890	0.172;0.003	T	0.29671	-1.0004	10	0.05833	T	0.94	.	0.8795	0.01231	0.351:0.2704:0.2004:0.1782	rs41556512	42;115	Q29973;Q30154	.;DRB5_HUMAN	V	115	ENSP00000364114:G115V	ENSP00000364114:G115V	G	-	2	0	HLA-DRB5	32597686	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.921000	0.00049	-1.717000	0.01385	-4.769000	0.00003	GGT	.	.	weak		0.622	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
KCNV2	169522	hgsc.bcm.edu	37	9	2729686	2729686	+	Missense_Mutation	SNP	C	C	G	rs12352254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2729686C>G	ENST00000382082.3	+	2	1835	c.1597C>G	c.(1597-1599)Ctt>Gtt	p.L533V		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	533			L -> V (in dbSNP:rs12352254). {ECO:0000269|PubMed:16909397}.		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)		TGAGTGTTTGCTTGGAAGCAA	0.458													G|||	714	0.142572	0.3699	0.1369	5008	,	,		20155	0.0218		0.0696	False		,,,				2504	0.0389				p.L533V		Atlas-SNP	.											.	KCNV2	72	.	0			c.C1597G						PASS	.	G	VAL/LEU	1413,2993	686.4+/-404.7	221,971,1011	104.0	96.0	98.0		1597	0.1	0.0	9	dbSNP_120	98	641,7959	790.4+/-407.6	20,601,3679	yes	missense	KCNV2	NM_133497.3	32	241,1572,4690	GG,GC,CC		7.4535,32.0699,15.7927	benign	533/546	2729686	2054,10952	2203	4300	6503	SO:0001583	missense	169522	exon2			TGTTTGCTTGGAA	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.1597C>G	9.37:g.2729686C>G	ENSP00000371514:p.Leu533Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	283	0.1295787545787546	172	0.34959349593495936	50	0.13812154696132597	9	0.015734265734265736	52	0.06860158311345646	G	2.188	-0.385859	0.04966	0.320699	0.074535	ENSG00000168263	ENST00000382082	D	0.96619	-4.07	5.47	0.0575	0.14323	.	0.977578	0.08281	N	0.969886	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	0.10941	-1.0608	9	0.24483	T	0.36	.	3.6427	0.08173	0.1241:0.1016:0.3402:0.4342	rs12352254;rs52829818;rs12352254	533	Q8TDN2	KCNV2_HUMAN	V	533	ENSP00000371514:L533V	ENSP00000371514:L533V	L	+	1	0	KCNV2	2719686	0.661000	0.27430	0.017000	0.16124	0.244000	0.25665	0.045000	0.14013	-0.158000	0.11040	-0.824000	0.03097	CTT	C|0.857;G|0.143	0.143	strong		0.458	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
MT-ND5	4540	hgsc.bcm.edu	37	M	12540	12540	+	Nonstop_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:12540A>G	ENST00000361567.2	+	1	204	c.204A>G	c.(202-204)tgA>tgG	p.*68W	MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	68					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AACTGACACTGAGCCACAACC	0.408																																					p.W68W		Atlas-SNP	.											.	.	.	.	0			c.A204G						PASS	.																																			SO:0001578	stop_lost	0	exon1			ACACTGAGCCACA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.204A>G	M.37:g.12540A>G	Exception_encountered	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.408	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
DDX11	1663	hgsc.bcm.edu	37	12	31249861	31249861	+	Missense_Mutation	SNP	C	C	G	rs2075322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:31249861C>G	ENST00000407793.2	+	17	1950	c.1699C>G	c.(1699-1701)Caa>Gaa	p.Q567E	DDX11_ENST00000350437.4_Missense_Mutation_p.Q567E|DDX11_ENST00000539673.1_3'UTR|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000228264.6_Missense_Mutation_p.Q541E|DDX11_ENST00000545668.1_Missense_Mutation_p.Q567E|DDX11_ENST00000542838.1_Missense_Mutation_p.Q567E	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	567			Q -> E (in dbSNP:rs2075322). {ECO:0000269|PubMed:9013641, ECO:0000269|Ref.3}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GATGCACATCCAAGGCTTCCT	0.622										Multiple Myeloma(12;0.14)			G|||	3211	0.641174	0.708	0.6066	5008	,	,		19076	0.8294		0.4284	False		,,,				2504	0.6002				p.Q567E		Atlas-SNP	.											.	DDX11	188	.	0			c.C1699G						PASS	.	G	GLU/GLN,GLU/GLN,GLU/GLN	3015,1391	454.4+/-350.6	1029,957,217	45.0	47.0	46.0		1699,1699,1699	2.6	0.4	12	dbSNP_96	46	3876,4724	606.1+/-395.1	890,2096,1314	yes	missense,missense,missense	DDX11	NM_004399.2,NM_030653.3,NM_152438.1	29,29,29	1919,3053,1531	GG,GC,CC		45.0698,31.5706,47.0168	benign,benign,benign	567/857,567/907,567/971	31249861	6891,6115	2203	4300	6503	SO:0001583	missense	1663	exon17			CACATCCAAGGCT	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1699C>G	12.37:g.31249861C>G	ENSP00000384703:p.Gln567Glu	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	175	77	0.44	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	1393	0.6378205128205128	370	0.7520325203252033	213	0.5883977900552486	485	0.8479020979020979	325	0.4287598944591029	G	0.756	-0.770984	0.02974	0.684294	0.450698	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000404673;ENST00000228264;ENST00000545668;ENST00000350437	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	3.56	2.6	0.31112	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999919	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.40136	-0.9579	8	0.02654	T	1	.	10.8246	0.46625	0.0:0.3716:0.6284:0.0	rs2075322	541;567;567;567	Q96FC9-3;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	E	567;567;292;541;567;567	ENSP00000443426:Q567E;ENSP00000384703:Q567E;ENSP00000228264:Q541E;ENSP00000440402:Q567E;ENSP00000309965:Q567E	ENSP00000228264:Q541E	Q	+	1	0	DDX11	31141128	1.000000	0.71417	0.418000	0.26571	0.770000	0.43624	5.344000	0.65981	0.170000	0.19704	-0.293000	0.09583	CAA	C|0.436;G|0.564	0.564	strong		0.622	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
PADI6	353238	hgsc.bcm.edu	37	1	17727847	17727847	+	RNA	SNP	T	T	C	rs183565903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17727847T>C	ENST00000434762.2	+	0	2049							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)	ACTTTGACTGTTACCTGACAG	0.552													T|||	4	0.000798722	0.0015	0.0029	5008	,	,		19527	0.0		0.0	False		,,,				2504	0.0				p.C666C		Atlas-SNP	.											.	PADI6	51	.	0			c.T1998C						PASS	.	T		5,3961		0,5,1978	60.0	64.0	63.0		1999	-1.8	0.9	1		63	0,8346		0,0,4173	no	coding-synonymous	PADI6	NM_207421.3		0,5,6151	CC,CT,TT		0.0,0.1261,0.0406		666/695	17727847	5,12307	1983	4173	6156			353238	exon17			TGACTGTTACCTG	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.17727847T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	121	52	0.429752	NM_207421	Q330K5|Q70SX3	Silent	SNP	ENST00000434762.2	37																																																																																				T|1.000;C|0.000	0.000	strong		0.552	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421	
C3orf58	205428	hgsc.bcm.edu	37	3	143691756	143691756	+	Silent	SNP	T	T	C	rs139703156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:143691756T>C	ENST00000315691.3	+	1	1117	c.582T>C	c.(580-582)ctT>ctC	p.L194L	C3orf58_ENST00000493396.1_3'UTR|C3orf58_ENST00000495414.1_5'Flank|C3orf58_ENST00000441925.2_5'Flank	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	194					cardiac muscle cell proliferation (GO:0060038)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	COPI vesicle coat (GO:0030126)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCTTCCTGCTTCGCAACCTCA	0.692													C|||	5	0.000998403	0.0038	0.0	5008	,	,		15454	0.0		0.0	False		,,,				2504	0.0				p.L194L		Atlas-SNP	.											.	C3orf58	36	.	0			c.T582C						PASS	.	C		15,4325		0,15,2155	10.0	10.0	10.0		582	-0.7	1.0	3	dbSNP_134	10	1,8483		0,1,4241	no	coding-synonymous	C3orf58	NM_173552.3		0,16,6396	CC,CT,TT		0.0118,0.3456,0.1248		194/431	143691756	16,12808	2170	4242	6412	SO:0001819	synonymous_variant	205428	exon1			CCTGCTTCGCAAC	AK095161	CCDS3130.1, CCDS46929.1	3q24	2013-12-06			ENSG00000181744	ENSG00000181744			28490	protein-coding gene	gene with protein product	"""deleted in autism 1"", ""hypoxia and Akt induced stem cell factor"""	612200				21283809, 23784961, 24269490	Standard	NM_173552		Approved	MGC33365, DIA1, HASF	uc003evo.3	Q8NDZ4	OTTHUMG00000159380	ENST00000315691.3:c.582T>C	3.37:g.143691756T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_173552	B2RCF2|B7Z1W3	Silent	SNP	ENST00000315691.3	37	CCDS3130.1																																																																																			T|0.999;C|0.001	0.001	strong		0.692	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552	
FMO2	2327	hgsc.bcm.edu	37	1	171176912	171176912	+	Missense_Mutation	SNP	T	T	G	rs2020865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171176912T>G	ENST00000209929.7	+	8	1397	c.1239T>G	c.(1237-1239)aaT>aaG	p.N413K	FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Missense_Mutation_p.N413K|RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445909.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	412					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TCAAAAGGAATGAAAAAAGAA	0.343													T|||	569	0.113618	0.3343	0.0504	5008	,	,		18765	0.002		0.0467	False		,,,				2504	0.044				p.N413K		Atlas-SNP	.											.	FMO2	66	.	0			c.T1239G	GRCh37	CM033903	FMO2	M	rs2020865	PASS	.	T	LYS/ASN	1230,3176	409.5+/-335.0	183,864,1156	83.0	89.0	87.0		1239	-1.1	1.0	1	dbSNP_98	87	422,8178	131.0+/-188.9	13,396,3891	yes	missense	FMO2	NM_001460.2	94	196,1260,5047	GG,GT,TT		4.907,27.9165,12.7018	benign	413/472	171176912	1652,11354	2203	4300	6503	SO:0001583	missense	2327	exon8			AAGGAATGAAAAA	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.1239T>G	1.37:g.171176912T>G	ENSP00000209929:p.Asn413Lys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	143	77	0.538462	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	219	0.10027472527472528	169	0.3434959349593496	18	0.049723756906077346	0	0.0	32	0.04221635883905013	T	0.158	-1.084576	0.01888	0.279165	0.04907	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.57273	0.41;0.41	5.8	-1.15	0.09709	.	0.538750	0.22135	N	0.064122	T	0.03011	0.0089	N	0.00583	-1.355	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.28427	-1.0044	9	0.02654	T	1	-7.7681	1.9158	0.03297	0.1215:0.1799:0.3758:0.3228	rs2020865;rs2266708;rs52799084;rs61598461;rs2020865	413	Q99518	FMO2_HUMAN	K	413	ENSP00000209929:N413K;ENSP00000405905:N413K	ENSP00000209929:N413K	N	+	3	2	FMO2	169443536	0.666000	0.27475	0.973000	0.42090	0.473000	0.32948	0.082000	0.14847	0.140000	0.18849	0.528000	0.53228	AAT	T|0.887;G|0.113	0.113	strong		0.343	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
OBSCN	84033	hgsc.bcm.edu	37	1	228505739	228505739	+	Missense_Mutation	SNP	G	G	A	rs3795801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228505739G>A	ENST00000422127.1	+	53	14040	c.13996G>A	c.(13996-13998)Ggt>Agt	p.G4666S	OBSCN_ENST00000284548.11_Missense_Mutation_p.G4666S|OBSCN_ENST00000570156.2_Missense_Mutation_p.G5623S|OBSCN_ENST00000366709.4_Missense_Mutation_p.G1785S|OBSCN_ENST00000366707.4_Missense_Mutation_p.G2300S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4666	Ig-like 47.		G -> S (in dbSNP:rs3795801).		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)				CATCCAGCCCGGTGGGCGGTT	0.627													g|||	867	0.173123	0.2216	0.2435	5008	,	,		18063	0.1518		0.159	False		,,,				2504	0.0941				p.G5623S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G16867A						PASS	.		SER/GLY,SER/GLY	1019,3243		112,795,1224	87.0	97.0	94.0		13996,13996	-5.4	0.0	1	dbSNP_107	94	1469,6999		133,1203,2898	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	56,56	245,1998,4122	AA,AG,GG		17.3477,23.909,19.5444	benign,benign	4666/7969,4666/6621	228505739	2488,10242	2131	4234	6365	SO:0001583	missense	84033	exon64			CAGCCCGGTGGGC	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.13996G>A	1.37:g.228505739G>A	ENSP00000409493:p.Gly4666Ser	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	257	124	0.48249	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	393	0.17994505494505494	94	0.1910569105691057	89	0.24585635359116023	87	0.1520979020979021	123	0.16226912928759896	g	13.43	2.235989	0.39498	0.23909	0.173477	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	4.51	-5.37	0.02681	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.102050	0.06837	N	0.794996	T	0.00012	0.0000	N	0.17800	0.525	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.09377	0.004;0.002	T	0.41484	-0.9506	9	0.07175	T	0.84	.	20.2526	0.98410	0.1567:0.0:0.8433:0.0	rs3795801;rs52803091;rs58512327;rs3795801	4666;4666	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	4666;4666;2300;1785	ENSP00000284548:G4666S;ENSP00000409493:G4666S;ENSP00000355668:G2300S;ENSP00000355670:G1785S	ENSP00000284548:G4666S	G	+	1	0	OBSCN	226572362	0.020000	0.18652	0.000000	0.03702	0.151000	0.21798	0.239000	0.18023	-1.559000	0.01688	-0.565000	0.04167	GGT	G|0.828;A|0.172	0.172	strong		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
KIAA1551	55196	hgsc.bcm.edu	37	12	32137852	32137852	+	Silent	SNP	C	C	G	rs3759297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	71	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	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	
C1orf127	148345	hgsc.bcm.edu	37	1	11009703	11009703	+	Missense_Mutation	SNP	C	C	T	rs1281012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11009703C>T	ENST00000377008.4	-	10	1213	c.767G>A	c.(766-768)cGg>cAg	p.R256Q	C1orf127_ENST00000377004.4_Missense_Mutation_p.R423Q			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	256	Pro-rich.		R -> Q (in dbSNP:rs1281012).							NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		GTCGGAAGGCCGGTGCAGGAG	0.622													C|||	347	0.0692891	0.2042	0.0144	5008	,	,		17273	0.004		0.0427	False		,,,				2504	0.0204				p.R423Q		Atlas-SNP	.											.	C1orf127	134	.	0			c.G1268A						PASS	.	C	GLN/ARG	725,3675		66,593,1541	40.0	34.0	36.0		1268	-6.4	0.0	1	dbSNP_87	36	333,8267		4,325,3971	yes	missense	C1orf127	NM_001170754.1	43	70,918,5512	TT,TC,CC		3.8721,16.4773,8.1385	benign	423/824	11009703	1058,11942	2200	4300	6500	SO:0001583	missense	148345	exon11			GAAGGCCGGTGCA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.767G>A	1.37:g.11009703C>T	ENSP00000366207:p.Arg256Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		167|167	0.07646520146520147|0.07646520146520147	123|123	0.25|0.25	4|4	0.011049723756906077|0.011049723756906077	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	C|C	1.843|1.843	-0.467033|-0.467033	0.04476|0.04476	0.164773|0.164773	0.038721|0.038721	ENSG00000175262|ENSG00000175262	ENST00000418570|ENST00000377004;ENST00000377008	.|T;T	.|0.29142	.|1.58;1.58	3.98|3.98	-6.39|-6.39	0.01951|0.01951	.|.	.|6.202500	.|0.00166	.|N	.|0.000011	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.09022	.|0.002;0.002	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.18999|0.18999	-1.0319|-1.0319	4|9	.|0.23891	.|T	.|0.37	.|.	2.3424|2.3424	0.04263|0.04263	0.1182:0.3558:0.1181:0.4079|0.1182:0.3558:0.1181:0.4079	rs1281012;rs1281012|rs1281012;rs1281012	.|274;256	.|B7ZLG7;Q8N9H9	.|.;CA127_HUMAN	S|Q	258|423;256	.|ENSP00000366203:R423Q;ENSP00000366207:R256Q	.|ENSP00000366203:R423Q	G|R	-|-	1|2	0|0	C1orf127|C1orf127	10932290|10932290	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.451000|-1.451000	0.02387|0.02387	-1.615000|-1.615000	0.01573|0.01573	-1.314000|-1.314000	0.01303|0.01303	GGC|CGG	C|0.907;T|0.093	0.093	strong		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
SPAG17	200162	hgsc.bcm.edu	37	1	118598362	118598362	+	Missense_Mutation	SNP	A	A	G	rs138706127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118598362A>G	ENST00000336338.5	-	19	2781	c.2716T>C	c.(2716-2718)Tct>Cct	p.S906P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	906						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TTACTTTTAGATTCTTTAATG	0.303													A|||	23	0.00459265	0.0174	0.0	5008	,	,		16823	0.0		0.0	False		,,,				2504	0.0				p.S906P		Atlas-SNP	.											SPAG17,NS,haematopoietic_neoplasm,0,1	SPAG17	263	1	0			c.T2716C						scavenged	.	A	PRO/SER	93,4307	73.6+/-111.7	1,91,2108	67.0	68.0	68.0		2716	4.4	1.0	1	dbSNP_134	68	1,8595	1.2+/-3.3	0,1,4297	yes	missense	SPAG17	NM_206996.2	74	1,92,6405	GG,GA,AA		0.0116,2.1136,0.7233	possibly-damaging	906/2224	118598362	94,12902	2200	4298	6498	SO:0001583	missense	200162	exon19			TTTTAGATTCTTT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.2716T>C	1.37:g.118598362A>G	ENSP00000337804:p.Ser906Pro	Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	60	38	0.633333	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	13.34	2.206952	0.39003	0.021136	1.16E-4	ENSG00000155761	ENST00000336338	T	0.30981	1.51	5.55	4.42	0.53409	.	0.557030	0.19693	N	0.108216	T	0.14787	0.0357	L	0.59436	1.845	0.27117	N	0.962222	B	0.18166	0.026	B	0.19391	0.025	T	0.18304	-1.0341	10	0.72032	D	0.01	.	9.3895	0.38363	0.9185:0.0:0.0815:0.0	.	906	Q6Q759	SPG17_HUMAN	P	906	ENSP00000337804:S906P	ENSP00000337804:S906P	S	-	1	0	SPAG17	118399885	1.000000	0.71417	0.999000	0.59377	0.166000	0.22503	2.832000	0.48152	1.112000	0.41740	0.477000	0.44152	TCT	A|0.993;G|0.007	0.007	strong		0.303	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
XCL1	6375	hgsc.bcm.edu	37	1	168549325	168549325	+	Missense_Mutation	SNP	A	A	G	rs61546281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:168549325A>G	ENST00000367818.3	+	2	251	c.86A>G	c.(85-87)aAg>aGg	p.K29R		NM_002995.2	NP_002986.1	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1	29					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)					GTCTCAGATAAGAGGACCTGT	0.443													A|||	162	0.0323482	0.1165	0.0029	5008	,	,		19121	0.001		0.005	False		,,,				2504	0.0				p.K29R		Atlas-SNP	.											.	XCL1	16	.	0			c.A86G						PASS	.	A	ARG/LYS	158,4248		35,88,2080	131.0	134.0	133.0		86	-0.5	0.0	1	dbSNP_129	133	2,8598		0,2,4298	no	missense	XCL1	NM_002995.2	26	35,90,6378	GG,GA,AA		0.0233,3.586,1.2302	benign	29/115	168549325	160,12846	2203	4300	6503	SO:0001583	missense	6375	exon2			CAGATAAGAGGAC	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.86A>G	1.37:g.168549325A>G	ENSP00000356792:p.Lys29Arg	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	170	68	0.4	NM_002995	Q52MA8	Missense_Mutation	SNP	ENST00000367818.3	37	CCDS1274.1	41	0.018772893772893772	35	0.07113821138211382	1	0.0027624309392265192	1	0.0017482517482517483	4	0.005277044854881266	A	4.417	0.077069	0.08485	0.03586	2.33E-4	ENSG00000143184	ENST00000367818	T	0.04809	3.55	4.36	-0.539	0.11865	Chemokine interleukin-8-like domain (3);	0.562682	0.17985	N	0.155390	T	0.00936	0.0031	N	0.26162	0.8	0.25269	N	0.989532	B	0.10296	0.003	B	0.08055	0.003	T	0.48317	-0.9046	9	0.16896	T	0.51	-0.7914	7.4105	0.27016	0.483:0.0:0.517:0.0	rs61546281	29	P47992	XCL1_HUMAN	R	29	ENSP00000356792:K29R	ENSP00000356792:K29R	K	+	2	0	XCL1	166815949	0.000000	0.05858	0.002000	0.10522	0.518000	0.34316	-0.858000	0.04281	0.011000	0.14865	0.533000	0.62120	AAG	A|0.981;G|0.019	0.019	strong		0.443	XCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083612.1	NM_002995	
TRIM71	131405	hgsc.bcm.edu	37	3	32933036	32933036	+	Silent	SNP	G	G	A	rs13096271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:32933036G>A	ENST00000383763.5	+	4	2403	c.2340G>A	c.(2338-2340)tcG>tcA	p.S780S		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	780					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ACTGCCAGTCGGCACGCTTTC	0.612													G|||	719	0.14357	0.1044	0.0836	5008	,	,		18483	0.2907		0.0855	False		,,,				2504	0.1472				p.S780S		Atlas-SNP	.											TRIM71,NS,meningioma,+1,1	TRIM71	73	1	0			c.G2340A						PASS	.	G		352,3574		27,298,1638	39.0	41.0	41.0		2340	-11.9	0.0	3	dbSNP_121	41	815,7499		39,737,3381	no	coding-synonymous	TRIM71	NM_001039111.1		66,1035,5019	AA,AG,GG		9.8027,8.9659,9.5343		780/869	32933036	1167,11073	1963	4157	6120	SO:0001819	synonymous_variant	131405	exon4			CCAGTCGGCACGC		CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	32669	protein-coding gene	gene with protein product			"""tripartite motif-containing 71"", ""tripartite motif containing 71"""				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.2340G>A	3.37:g.32933036G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_001039111		Silent	SNP	ENST00000383763.5	37	CCDS43060.1																																																																																			G|0.873;A|0.127	0.127	strong		0.612	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111	
PLXNB1	5364	hgsc.bcm.edu	37	3	48454018	48454018	+	Silent	SNP	C	C	T	rs34555887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48454018C>T	ENST00000358536.4	-	26	5135	c.4866G>A	c.(4864-4866)acG>acA	p.T1622T	PLXNB1_ENST00000296440.6_Silent_p.T1622T|PLXNB1_ENST00000465117.1_5'Flank|PLXNB1_ENST00000448774.2_Silent_p.T233T|PLXNB1_ENST00000358459.4_Silent_p.T1439T|PLXNB1_ENST00000456774.1_Silent_p.T1439T	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1622					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)		GGCTCTCCAGCGTGTGGATGA	0.592													C|||	68	0.0135783	0.0484	0.0058	5008	,	,		19223	0.0		0.0	False		,,,				2504	0.0				p.T1622T		Atlas-SNP	.											.	PLXNB1	150	.	0			c.G4866A						PASS	.	C	,	194,4212	121.3+/-158.8	6,182,2015	43.0	44.0	43.0		4866,4866	-8.7	0.7	3	dbSNP_126	43	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PLXNB1	NM_001130082.1,NM_002673.4	,	6,183,6314	TT,TC,CC		0.0116,4.4031,1.4993	,	1622/2136,1622/2136	48454018	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	5364	exon26			CTCCAGCGTGTGG	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.4866G>A	3.37:g.48454018C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	37	CCDS2765.1																																																																																			C|0.985;T|0.015	0.015	strong		0.592	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	
PABPC1	26986	hgsc.bcm.edu	37	8	101719004	101719004	+	Missense_Mutation	SNP	G	G	A	rs62513924		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101719004G>A	ENST00000318607.5	-	11	2605	c.1477C>T	c.(1477-1479)Cgt>Tgt	p.R493C	PABPC1_ENST00000519004.1_Missense_Mutation_p.R448C|PABPC1_ENST00000522387.1_Missense_Mutation_p.R461C|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_Intron	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	493					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			GCTGCAGGACGTGGACCCATT	0.423																																					p.R493C		Atlas-SNP	.											.	PABPC1	76	.	0			c.C1477T						PASS	.						47.0	45.0	46.0					8																	101719004		2203	4300	6503	SO:0001583	missense	26986	exon11			CAGGACGTGGACC	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.1477C>T	8.37:g.101719004G>A	ENSP00000313007:p.Arg493Cys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	138	42	0.304348	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	G	18.94	3.729404	0.69074	.	.	ENSG00000070756	ENST00000318607;ENST00000519004;ENST00000522387;ENST00000517990;ENST00000522658	T;T;T;T	0.51574	1.52;1.45;2.5;0.7	5.3	5.3	0.74995	Polyadenylate-binding protein/Hyperplastic disc protein (1);	0.000000	0.64402	D	0.000004	T	0.51092	0.1654	L	0.49513	1.565	0.80722	D	1	B;B;B	0.34399	0.452;0.452;0.452	B;B;B	0.39531	0.027;0.302;0.302	T	0.53830	-0.8383	10	0.62326	D	0.03	.	19.3206	0.94237	0.0:0.0:1.0:0.0	rs62513924	461;493;493	E7ERJ7;B3KT93;P11940	.;.;PABP1_HUMAN	C	493;448;461;2;40	ENSP00000313007:R493C;ENSP00000429594:R448C;ENSP00000429395:R461C;ENSP00000428840:R40C	ENSP00000313007:R493C	R	-	1	0	PABPC1	101788180	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.248000	0.78268	2.658000	0.90341	0.591000	0.81541	CGT	.	.	strong		0.423	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
CYP2F1	1572	hgsc.bcm.edu	37	19	41628014	41628014	+	Missense_Mutation	SNP	G	G	C	rs75405062		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41628014G>C	ENST00000331105.2	+	6	870	c.798G>C	c.(796-798)caG>caC	p.Q266H		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	266			Q -> H (in allele CYP2F1*3). {ECO:0000269|PubMed:11827709}.		naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						ACTTCATCCAGTGCTTCCTCA	0.572																																					p.Q266H		Atlas-SNP	.											CYP2F1,NS,carcinoma,+2,1	CYP2F1	60	1	0			c.G798C						scavenged	.	C	HIS/GLN	162,3888		1,160,1864	50.0	48.0	48.0		798	-4.7	0.4	19	dbSNP_132	48	113,8171		0,113,4029	no	missense	CYP2F1	NM_000774.3	24	1,273,5893	CC,CG,GG		1.3641,4.0,2.2296	benign	266/492	41628014	275,12059	2025	4142	6167	SO:0001583	missense	1572	exon6			CATCCAGTGCTTC	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"""Cytochrome P450s"""	2632	protein-coding gene	gene with protein product		124070	"""cytochrome P450, subfamily IIF, polypeptide 1"""	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.798G>C	19.37:g.41628014G>C	ENSP00000333534:p.Gln266His	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	68	14	0.205882	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	37	CCDS12572.1	449	0.20558608058608058	107	0.21747967479674796	82	0.2265193370165746	109	0.19055944055944055	151	0.19920844327176782	N	5.932	0.355925	0.11239	0.04	0.013641	ENSG00000197446	ENST00000331105	T	0.12569	2.67	3.27	-4.65	0.03339	.	0.052380	0.64402	U	0.000001	T	0.00012	0.0000	N	0.02247	-0.625	0.51767	P	6.20000000000065E-5	D;B;B	0.64830	0.994;0.227;0.021	P;B;B	0.59595	0.86;0.017;0.007	T	0.42310	-0.9459	9	0.87932	D	0	.	8.662	0.34099	0.0:0.6997:0.1315:0.1688	.	52;266;266	B4DL83;Q32MN5;P24903	.;.;CP2F1_HUMAN	H	266	ENSP00000333534:Q266H	ENSP00000333534:Q266H	Q	+	3	2	CYP2F1	46319854	0.006000	0.16342	0.412000	0.26496	0.011000	0.07611	0.096000	0.15147	-1.780000	0.01279	-2.252000	0.00282	CAG	G|0.250;C|0.750	0.750	weak		0.572	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
OR51Q1	390061	hgsc.bcm.edu	37	11	5443442	5443442	+	Silent	SNP	G	G	C	rs2736590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5443442G>C	ENST00000300778.4	+	1	102	c.12G>C	c.(10-12)gtG>gtC	p.V4V	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTCCCAGGTGACTAACACCA	0.453													G|||	2382	0.475639	0.3623	0.4006	5008	,	,		22376	0.7024		0.3986	False		,,,				2504	0.5276				p.V4V		Atlas-SNP	.											.	OR51Q1	79	.	0			c.G12C						PASS	.	G		1585,2817	495.5+/-363.3	287,1011,903	199.0	150.0	167.0		12	-1.0	0.0	11	dbSNP_100	167	3379,5215	500.2+/-375.2	680,2019,1598	no	coding-synonymous	OR51Q1	NM_001004757.2		967,3030,2501	CC,CG,GG		39.3181,36.0064,38.1964		4/318	5443442	4964,8032	2201	4297	6498	SO:0001819	synonymous_variant	390061	exon1			CCAGGTGACTAAC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.12G>C	11.37:g.5443442G>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	209	208	0.995215	NM_001004757	B2RNN1	Silent	SNP	ENST00000300778.4	37	CCDS31381.1																																																																																			G|0.587;C|0.413	0.413	strong		0.453	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
APOH	350	hgsc.bcm.edu	37	17	64216854	64216854	+	Missense_Mutation	SNP	A	A	G	rs52797880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:64216854A>G	ENST00000205948.6	-	5	459	c.422T>C	c.(421-423)aTc>aCc	p.I141T		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	141	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			TGGAGGGCAGATGATGGCTGG	0.368													G|||	352	0.0702875	0.115	0.0418	5008	,	,		18261	0.0516		0.0696	False		,,,				2504	0.0501				p.I141T	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.T422C						PASS	.	G	THR/ILE	397,4009		17,363,1823	85.0	85.0	85.0		422	3.4	0.1	17	dbSNP_128	85	560,8040		17,526,3757	yes	missense	APOH	NM_000042.2	89	34,889,5580	GG,GA,AA		6.5116,9.0104,7.3581	benign	141/346	64216854	957,12049	2203	4300	6503	SO:0001583	missense	350	exon5			GGGCAGATGATGG		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.422T>C	17.37:g.64216854A>G	ENSP00000205948:p.Ile141Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	34	0.333333	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	167	0.07646520146520147	62	0.12601626016260162	16	0.04419889502762431	35	0.06118881118881119	54	0.0712401055408971	N	1.071	-0.670004	0.03403	0.090104	0.065116	ENSG00000091583	ENST00000205948	T	0.22743	1.94	5.4	3.37	0.38596	Complement control module (1);Sushi/SCR/CCP (1);	0.221461	0.46145	N	0.000314	T	0.00039	0.0001	N	0.00223	-1.815	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34179	-0.9839	9	0.02654	T	1	.	5.9326	0.19148	0.1474:0.0:0.5803:0.2723	rs52797880	141	P02749	APOH_HUMAN	T	141	ENSP00000205948:I141T	ENSP00000205948:I141T	I	-	2	0	APOH	61647316	1.000000	0.71417	0.060000	0.19600	0.045000	0.14185	1.743000	0.38258	0.253000	0.21552	-0.229000	0.12294	ATC	A|0.927;G|0.073	0.073	strong		0.368	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
C1orf127	148345	hgsc.bcm.edu	37	1	11008341	11008341	+	Silent	SNP	G	G	A	rs10864483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11008341G>A	ENST00000377008.4	-	11	1796	c.1350C>T	c.(1348-1350)tgC>tgT	p.C450C	C1orf127_ENST00000377004.4_Silent_p.C617C			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	450										NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CCGTTCCAGAGCACGTTTCCT	0.657													G|||	890	0.177716	0.3699	0.1254	5008	,	,		16984	0.2093		0.0557	False		,,,				2504	0.0481				p.C617C		Atlas-SNP	.											.	C1orf127	134	.	0			c.C1851T						PASS	.	G		1463,2943	459.2+/-352.2	244,975,984	59.0	68.0	65.0		1851	-0.2	0.0	1	dbSNP_120	65	364,8236	120.1+/-179.3	7,350,3943	no	coding-synonymous	C1orf127	NM_001170754.1		251,1325,4927	AA,AG,GG		4.2326,33.2047,14.0474		617/824	11008341	1827,11179	2203	4300	6503	SO:0001819	synonymous_variant	148345	exon12			TCCAGAGCACGTT	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1350C>T	1.37:g.11008341G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		381	0.17445054945054944	180	0.36585365853658536	41	0.1132596685082873	115	0.20104895104895104	45	0.059366754617414245	G	3.870	-0.028045	0.07589	0.332047	0.042326	ENSG00000175262	ENST00000418570;ENST00000520253	.	.	.	3.9	-0.204	0.13200	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44375	-0.9332	3	.	.	.	-0.1999	1.0939	0.01669	0.2064:0.1773:0.4339:0.1824	rs10864483;rs10864483	.	.	.	V	452;569	.	.	A	-	2	0	C1orf127	10930928	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.046000	0.11983	-0.020000	0.14032	0.491000	0.48974	GCT	G|0.844;A|0.156	0.156	strong		0.657	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
ALMS1	7840	hgsc.bcm.edu	37	2	73676189	73676189	+	Silent	SNP	C	C	T	rs77517267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73676189C>T	ENST00000264448.6	+	8	2643	c.2532C>T	c.(2530-2532)gaC>gaT	p.D844D	ALMS1_ENST00000377715.1_Silent_p.D844D|ALMS1_ENST00000409009.1_Silent_p.D802D	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	844	34 X 47 AA approximate tandem repeat.				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						GACCAGCTGACGGAAAGACTG	0.507													C|||	183	0.0365415	0.1324	0.0115	5008	,	,		19422	0.0		0.0	False		,,,				2504	0.0				p.D844D		Atlas-SNP	.											ALMS1,NS,carcinoma,+2,1	ALMS1	384	1	0			c.C2532T						PASS	.	C		414,3376		30,354,1511	76.0	79.0	78.0		2532	-6.5	0.0	2	dbSNP_132	78	3,8219		0,3,4108	no	coding-synonymous	ALMS1	NM_015120.4		30,357,5619	TT,TC,CC		0.0365,10.9235,3.4715		844/4168	73676189	417,11595	1895	4111	6006	SO:0001819	synonymous_variant	7840	exon8			AGCTGACGGAAAG	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.2532C>T	2.37:g.73676189C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	157	79	0.503185	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			C|0.976;T|0.024	0.024	strong		0.507	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
ZNF814	730051	hgsc.bcm.edu	37	19	58386314	58386314	+	Silent	SNP	G	G	A	rs111313171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58386314G>A	ENST00000435989.2	-	3	678	c.444C>T	c.(442-444)taC>taT	p.Y148Y	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	148					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)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						CACTCCCTCTGTAGGGTTTCT	0.483													.|||	397	0.0792732	0.2821	0.0331	5008	,	,		22387	0.0		0.001	False		,,,				2504	0.0				p.Y148Y		Atlas-SNP	.											.	ZNF814	93	.	0			c.C444T						PASS	.	G		365,1019		52,261,379	59.0	50.0	53.0		444	-5.5	0.0	19	dbSNP_132	53	7,3173		0,7,1583	no	coding-synonymous	ZNF814	NM_001144989.1		52,268,1962	AA,AG,GG		0.2201,26.3728,8.1507		148/856	58386314	372,4192	692	1590	2282	SO:0001819	synonymous_variant	730051	exon3			CCCTCTGTAGGGT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.444C>T	19.37:g.58386314G>A		Somatic	744	1	0.00134409		WXS	Illumina HiSeq	Phase_I	779	332	0.426187	NM_001144989	A6NF35	Silent	SNP	ENST00000435989.2	37	CCDS46212.1																																																																																			G|0.941;A|0.059	0.059	strong		0.483	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
SEC61A2	55176	hgsc.bcm.edu	37	10	12200092	12200092	+	Silent	SNP	A	A	G	rs61731911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:12200092A>G	ENST00000298428.9	+	9	1052	c.963A>G	c.(961-963)ctA>ctG	p.L321L	SEC61A2_ENST00000379020.4_Intron|SEC61A2_ENST00000495368.1_3'UTR|SEC61A2_ENST00000379033.3_Silent_p.L299L|SEC61A2_ENST00000304267.8_Silent_p.L321L	NM_018144.3	NP_060614.2	Q9H9S3	S61A2_HUMAN	Sec61 alpha 2 subunit (S. cerevisiae)	321					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)				TAAATTTACTAGGACAGTGGG	0.373													A|||	91	0.0181709	0.0651	0.0072	5008	,	,		16175	0.0		0.0	False		,,,				2504	0.0				p.L321L		Atlas-SNP	.											.	SEC61A2	48	.	0			c.A963G						PASS	.	A	,,	258,4148	145.7+/-180.5	6,246,1951	83.0	77.0	79.0		963,897,963	-1.3	1.0	10	dbSNP_129	79	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	SEC61A2	NM_001142627.1,NM_001142628.1,NM_018144.3	,,	6,246,6251	GG,GA,AA		0.0,5.8557,1.9837	,,	321/438,299/455,321/477	12200092	258,12748	2203	4300	6503	SO:0001819	synonymous_variant	55176	exon9			TTTACTAGGACAG	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.963A>G	10.37:g.12200092A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	142	82	0.577465	NM_001142627	A8K8D0|B4DX72|F8W773	Silent	SNP	ENST00000298428.9	37	CCDS7088.1																																																																																			A|0.974;G|0.026	0.026	strong		0.373	SEC61A2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046795.1	NM_018144	
ADAM21	8747	hgsc.bcm.edu	37	14	70924955	70924955	+	Missense_Mutation	SNP	A	A	C	rs114864695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:70924955A>C	ENST00000603540.1	+	2	997	c.739A>C	c.(739-741)Aag>Cag	p.K247Q	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.K247Q	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	247	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.			K -> Q (in Ref. 1; AAD55255 and 3; AAI09025/AAI09026). {ECO:0000305}.	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)	p.K247Q(1)		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)		TTCCATGTATAAGCAGTTAGG	0.358													A|||	1381	0.275759	0.3495	0.147	5008	,	,		18988	0.5218		0.1292	False		,,,				2504	0.1646				p.K247Q		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	1	Substitution - Missense(1)	stomach(1)	c.A739C						PASS	.						65.0	76.0	72.0					14																	70924955		2202	4300	6502	SO:0001583	missense	8747	exon2			ATGTATAAGCAGT	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.739A>C	14.37:g.70924955A>C	ENSP00000474385:p.Lys247Gln	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	542	0.24816849816849818	119	0.241869918699187	54	0.14917127071823205	272	0.4755244755244755	97	0.1279683377308707	A	0	-2.595304	0.00125	.	.	ENSG00000139985	ENST00000267499	T	0.64260	-0.09	3.86	-1.13	0.09775	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.883079	0.09333	N	0.816565	T	0.00012	0.0000	N	0.12920	0.275	0.80722	P	0.0	B	0.12013	0.005	B	0.14023	0.01	T	0.44436	-0.9328	9	0.10636	T	0.68	.	8.183	0.31322	0.508:0.3282:0.1639:0.0	.	247	Q9UKJ8	ADA21_HUMAN	Q	247	ENSP00000267499:K247Q	ENSP00000267499:K247Q	K	+	1	0	ADAM21	69994708	0.000000	0.05858	0.354000	0.25760	0.155000	0.21991	-0.543000	0.06084	-0.012000	0.14223	-1.611000	0.00801	AAG	.	.	weak		0.358	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
DNAH9	1770	hgsc.bcm.edu	37	17	11865462	11865462	+	Missense_Mutation	SNP	G	G	A	rs1990236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11865462G>A	ENST00000262442.4	+	68	13190	c.13122G>A	c.(13120-13122)atG>atA	p.M4374I	DNAH9_ENST00000608377.1_Missense_Mutation_p.M686I|DNAH9_ENST00000396001.2_3'UTR|RP11-1096G20.5_ENST00000580270.1_RNA|DNAH9_ENST00000454412.2_Missense_Mutation_p.M4298I	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4374			M -> I (in dbSNP:rs1990236). {ECO:0000269|Ref.1}.		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)		TGGACCAGATGGCCCTGCAAT	0.562													G|||	802	0.160144	0.1021	0.2392	5008	,	,		19654	0.1815		0.1948	False		,,,				2504	0.1247				p.M4374I		Atlas-SNP	.											.	DNAH9	695	.	0			c.G13122A						PASS	.	G	ILE/MET,ILE/MET	555,3851	249.3+/-256.8	35,485,1683	71.0	69.0	70.0		13122,2058	4.1	1.0	17	dbSNP_92	70	1538,7062	289.8+/-299.5	140,1258,2902	yes	missense,missense	DNAH9	NM_001372.3,NM_004662.2	10,10	175,1743,4585	AA,AG,GG		17.8837,12.5965,16.0926	benign,benign	4374/4487,686/799	11865462	2093,10913	2203	4300	6503	SO:0001583	missense	1770	exon68			CCAGATGGCCCTG	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.13122G>A	17.37:g.11865462G>A	ENSP00000262442:p.Met4374Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	394	0.1804029304029304	41	0.08333333333333333	87	0.24033149171270718	102	0.17832167832167833	164	0.21635883905013192	G	15.07	2.725497	0.48833	0.125965	0.178837	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001	T;T;T	0.08458	3.09;3.09;3.09	5.04	4.05	0.47172	Dynein heavy chain (1);	0.040348	0.85682	D	0.000000	T	0.00012	0.0000	L	0.41236	1.265	0.09310	P	0.99999780763	B	0.31989	0.35	B	0.41202	0.35	T	0.47471	-0.9115	9	0.59425	D	0.04	.	13.8943	0.63761	0.0747:0.0:0.9253:0.0	rs1990236;rs12949339;rs17410772;rs52815919;rs56617954;rs61662056;rs1990236	4374	Q9NYC9	DYH9_HUMAN	I	4374;4298;2880;686	ENSP00000262442:M4374I;ENSP00000414874:M4298I;ENSP00000379323:M686I	ENSP00000262442:M4374I	M	+	3	0	DNAH9	11806187	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.366000	0.73095	2.618000	0.88619	0.655000	0.94253	ATG	G|0.834;A|0.166	0.166	strong		0.562	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
ALMS1	7840	hgsc.bcm.edu	37	2	73786188	73786188	+	Missense_Mutation	SNP	A	A	G	rs34071195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73786188A>G	ENST00000264448.6	+	15	10411	c.10300A>G	c.(10300-10302)Aaa>Gaa	p.K3434E	ALMS1_ENST00000409009.1_Missense_Mutation_p.K3392E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3434			K -> E (in dbSNP:rs34071195).		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						CATTACACAGAAAGAGGAGAT	0.468													A|||	92	0.0183706	0.0658	0.0072	5008	,	,		16247	0.0		0.0	False		,,,				2504	0.0				p.K3434E		Atlas-SNP	.											.	ALMS1	384	.	0			c.A10300G						PASS	.	A	GLU/LYS	195,3577		8,179,1699	101.0	101.0	101.0		10300	3.8	1.0	2	dbSNP_126	101	2,8234		0,2,4116	yes	missense	ALMS1	NM_015120.4	56	8,181,5815	GG,GA,AA		0.0243,5.1697,1.6406	probably-damaging	3434/4168	73786188	197,11811	1886	4118	6004	SO:0001583	missense	7840	exon15			ACACAGAAAGAGG	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.10300A>G	2.37:g.73786188A>G	ENSP00000264448:p.Lys3434Glu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	A	18.42	3.620149	0.66787	0.051697	2.43E-4	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.07327	3.2;3.2	3.75	3.75	0.43078	.	0.162704	0.29239	N	0.012727	T	0.02848	0.0085	L	0.48642	1.525	0.80722	D	1	P;D;P	0.64830	0.886;0.994;0.932	P;D;P	0.72982	0.55;0.979;0.546	T	0.00158	-1.1976	10	0.72032	D	0.01	.	9.1435	0.36919	1.0:0.0:0.0:0.0	rs34071195	3434;3392;3434	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	E	3392;3434	ENSP00000386627:K3392E;ENSP00000264448:K3434E	ENSP00000264448:K3434E	K	+	1	0	ALMS1	73639696	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	2.265000	0.43311	1.946000	0.56461	0.377000	0.23210	AAA	A|0.991;G|0.009	0.009	strong		0.468	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
ZSCAN31	64288	hgsc.bcm.edu	37	6	28294550	28294550	+	Missense_Mutation	SNP	T	T	C	rs853684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28294550T>C	ENST00000414429.1	-	8	1517	c.614A>G	c.(613-615)aAa>aGa	p.K205R	ZSCAN31_ENST00000344279.6_Missense_Mutation_p.K205R|ZSCAN31_ENST00000439158.1_Missense_Mutation_p.K205R|ZSCAN31_ENST00000481934.1_5'Flank|ZSCAN31_ENST00000446474.1_Missense_Mutation_p.K46R|ZSCAN31_ENST00000396838.2_Missense_Mutation_p.K205R			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	205			K -> R (in dbSNP:rs853684).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TCTTTGGAGTTTGCTATCCCC	0.418													C|||	3083	0.615615	0.9531	0.4899	5008	,	,		21109	0.6042		0.3807	False		,,,				2504	0.502				p.K205R		Atlas-SNP	.											.	.	.	.	0			c.A614G						PASS	.	C	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	3733,673	283.7+/-277.2	1594,545,64	85.0	87.0	86.0		614,614,614,614	-0.8	0.0	6	dbSNP_86	86	3302,5298	645.1+/-400.1	639,2024,1637	yes	missense,missense,missense,missense	ZNF323	NM_001135215.1,NM_001135216.1,NM_030899.4,NM_145909.2	26,26,26,26	2233,2569,1701	CC,CT,TT		38.3953,15.2746,45.9096	benign,benign,benign,benign	205/407,205/407,205/407,205/407	28294550	7035,5971	2203	4300	6503	SO:0001583	missense	64288	exon4			TGGAGTTTGCTAT		CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"""-"", ""Zinc fingers, C2H2-type"""	14097	protein-coding gene	gene with protein product		610794	"""zinc finger protein 310 pseudogene"", ""zinc finger protein 323"""	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.614A>G	6.37:g.28294550T>C	ENSP00000390076:p.Lys205Arg	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_030899	Q6P178|Q8WWS5	Missense_Mutation	SNP	ENST00000414429.1	37	CCDS4649.1	1265	0.5792124542124543	464	0.943089430894309	176	0.4861878453038674	348	0.6083916083916084	277	0.3654353562005277	C	4.994	0.184589	0.09495	0.847254	0.383953	ENSG00000235109	ENST00000396838;ENST00000439158;ENST00000414429;ENST00000446474;ENST00000344279;ENST00000435857;ENST00000414431;ENST00000453745	T;T;T;T;T;T;T;T	0.05855	3.43;3.43;3.43;3.38;3.43;3.45;5.95;4.41	4.32	-0.837	0.10766	.	.	.	.	.	T	0.00440	0.0014	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44143	-0.9347	8	0.10377	T	0.69	.	0.317	0.00297	0.3355:0.2437:0.1293:0.2916	rs853684;rs52811904;rs61223141;rs853684	205	Q96LW9	ZN323_HUMAN	R	205;205;205;46;205;46;46;205	ENSP00000380050:K205R;ENSP00000413705:K205R;ENSP00000390076:K205R;ENSP00000402937:K46R;ENSP00000345339:K205R;ENSP00000391235:K46R;ENSP00000407529:K46R;ENSP00000389479:K205R	ENSP00000345339:K205R	K	-	2	0	ZNF323	28402529	0.004000	0.15560	0.015000	0.15790	0.021000	0.10359	-0.260000	0.08708	-0.197000	0.10350	-1.201000	0.01664	AAA	T|0.428;C|0.572	0.572	strong		0.418	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899	
SORBS2	8470	hgsc.bcm.edu	37	4	186545346	186545346	+	Missense_Mutation	SNP	A	A	T	rs61736043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:186545346A>T	ENST00000284776.7	-	13	1734	c.1225T>A	c.(1225-1227)Tta>Ata	p.L409I	SORBS2_ENST00000355634.5_Missense_Mutation_p.L509I|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000431808.1_Missense_Mutation_p.L409I|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.L313I|SORBS2_ENST00000498125.1_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	409					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)		TCCTCACATAACAGGGAGCCC	0.577													A|||	57	0.0113818	0.0416	0.0029	5008	,	,		18529	0.0		0.0	False		,,,				2504	0.0				p.L509I	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.T1525A						PASS	.	A	ILE/LEU,ILE/LEU,,,,,,	170,4236	112.5+/-150.6	2,166,2035	63.0	58.0	60.0		937,1225,,,,,,	-10.1	0.0	4	dbSNP_129	60	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,intron,intron,intron,intron,intron,intron	SORBS2	NM_001145674.1,NM_021069.4,NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145675.1,NM_003603.5	5,5,,,,,,	2,167,6334	TT,TA,AA		0.0116,3.8584,1.3148	probably-damaging,probably-damaging,,,,,,	313/1005,409/1101,,,,,,	186545346	171,12835	2203	4300	6503	SO:0001583	missense	8470	exon16			CACATAACAGGGA		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.1225T>A	4.37:g.186545346A>T	ENSP00000284776:p.Leu409Ile	Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	253	121	0.478261	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	A	11.06	1.528292	0.27299	0.038584	1.16E-4	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.37411	1.31;1.31;1.2;1.29	5.72	-10.1	0.00402	.	0.248771	0.33180	N	0.005188	T	0.14399	0.0348	L	0.42245	1.32	0.09310	N	1	D;D;D	0.71674	0.998;0.998;0.995	D;D;P	0.75020	0.985;0.984;0.792	T	0.63470	-0.6630	10	0.45353	T	0.12	-2.604	18.4155	0.90568	0.2035:0.0853:0.7112:0.0	rs61736043	313;509;409	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	I	409;409;313;509	ENSP00000284776:L409I;ENSP00000411764:L409I;ENSP00000397482:L313I;ENSP00000347852:L509I	ENSP00000284776:L409I	L	-	1	2	SORBS2	186782340	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.844000	0.04345	-2.307000	0.00653	-0.479000	0.04858	TTA	A|0.977;T|0.023	0.023	strong		0.577	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
TLR5	7100	hgsc.bcm.edu	37	1	223285042	223285042	+	Silent	SNP	G	G	A	rs5744169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:223285042G>A	ENST00000540964.1	-	4	1793	c.1332C>T	c.(1330-1332)ctC>ctT	p.L444L	TLR5_ENST00000342210.6_Silent_p.L444L			O60602	TLR5_HUMAN	toll-like receptor 5	444			Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1). {ECO:0000269|PubMed:14623910}.		cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		GTACCCGTAGGAGAAAGTAGA	0.418													G|||	101	0.0201677	0.0734	0.0029	5008	,	,		19084	0.0		0.002	False		,,,				2504	0.0				p.L444L		Atlas-SNP	.											.	TLR5	86	.	0			c.C1332T						PASS	.	G		315,4091	163.3+/-195.1	11,293,1899	82.0	85.0	84.0		1332	-2.9	0.9	1	dbSNP_114	84	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	TLR5	NM_003268.5		11,296,6196	AA,AG,GG		0.0349,7.1493,2.445		444/859	223285042	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	7100	exon6			CCGTAGGAGAAAG		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"""Toll/interleukin-1 receptor-like protein 3"""	603031	"""systemic lupus erythematosus susceptibility 1"""	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.1332C>T	1.37:g.223285042G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	143	63	0.440559	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Silent	SNP	ENST00000540964.1	37	CCDS31033.1																																																																																			G|0.976;A|0.024	0.024	strong		0.418	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268	
ZNFX1	57169	hgsc.bcm.edu	37	20	47865784	47865784	+	Missense_Mutation	SNP	C	C	T	rs6512577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47865784C>T	ENST00000396105.1	-	14	4023	c.3777G>A	c.(3775-3777)atG>atA	p.M1259I	ZNFX1_ENST00000371752.1_Missense_Mutation_p.M1259I|ZNFX1_ENST00000371754.4_Intron	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1259			M -> I (in dbSNP:rs6512577).				metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			AGAGCCGGAGCATGGGGCCTA	0.532													C|||	671	0.133986	0.1778	0.1686	5008	,	,		20164	0.0427		0.2018	False		,,,				2504	0.0746				p.M1259I		Atlas-SNP	.											.	ZNFX1	194	.	0			c.G3777A						PASS	.	C	ILE/MET	753,3653	308.8+/-290.8	62,629,1512	71.0	71.0	71.0		3777	-12.3	0.0	20	dbSNP_116	71	1926,6674	340.3+/-323.5	203,1520,2577	yes	missense	ZNFX1	NM_021035.2	10	265,2149,4089	TT,TC,CC		22.3953,17.0903,20.5982	benign	1259/1919	47865784	2679,10327	2203	4300	6503	SO:0001583	missense	57169	exon14			CCGGAGCATGGGG	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.3777G>A	20.37:g.47865784C>T	ENSP00000379412:p.Met1259Ile	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	225	106	0.471111	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	335	0.1533882783882784	91	0.18495934959349594	64	0.17679558011049723	28	0.04895104895104895	152	0.20052770448548812	C	1.356	-0.590167	0.03799	0.170903	0.223953	ENSG00000124201	ENST00000371752;ENST00000396105	D;D	0.86030	-2.06;-2.06	6.17	-12.3	0.00002	.	0.790063	0.12288	N	0.482275	T	0.00039	0.0001	N	0.02539	-0.55	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.13495	-1.0507	9	0.22706	T	0.39	-0.0137	7.3514	0.26693	0.0641:0.3567:0.3897:0.1895	rs6512577;rs17778787;rs52817512;rs57225169;rs6512577	1259	Q9P2E3	ZNFX1_HUMAN	I	1259	ENSP00000360817:M1259I;ENSP00000379412:M1259I	ENSP00000360817:M1259I	M	-	3	0	ZNFX1	47299191	0.000000	0.05858	0.000000	0.03702	0.301000	0.27625	-2.653000	0.00856	-3.493000	0.00153	-0.150000	0.13652	ATG	C|0.824;T|0.176	0.176	strong		0.532	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035	
PKD1L1	168507	hgsc.bcm.edu	37	7	47933494	47933494	+	Missense_Mutation	SNP	C	C	T	rs17131915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47933494C>T	ENST00000289672.2	-	15	2484	c.2434G>A	c.(2434-2436)Gac>Aac	p.D812N		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	812	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		D -> N (in dbSNP:rs17131915).		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						GCCCCAGGGTCGTCAGGGTCG	0.612													T|||	104	0.0207668	0.0741	0.0014	5008	,	,		17811	0.005		0.0	False		,,,				2504	0.0				p.D812N		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G2434A						PASS	.	T	ASN/ASP	237,4169		5,227,1971	47.0	36.0	40.0		2434	-8.5	0.0	7	dbSNP_123	40	0,8600		0,0,4300	yes	missense	PKD1L1	NM_138295.3	23	5,227,6271	TT,TC,CC		0.0,5.379,1.8222	benign	812/2850	47933494	237,12769	2203	4300	6503	SO:0001583	missense	168507	exon15			CAGGGTCGTCAGG	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.2434G>A	7.37:g.47933494C>T	ENSP00000289672:p.Asp812Asn	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	46	0.021062271062271064	41	0.08333333333333333	1	0.0027624309392265192	4	0.006993006993006993	0	0.0	N	8.513	0.867001	0.17250	0.05379	0.0	ENSG00000158683	ENST00000289672	T	0.69306	-0.39	5.12	-8.54	0.00912	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	1.892900	0.03306	N	0.189835	T	0.01254	0.0041	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09143	-1.0688	10	0.26408	T	0.33	-0.013	0.2929	0.00261	0.2928:0.2218:0.2594:0.226	rs17131915;rs52800675;rs17131915	812	Q8TDX9	PK1L1_HUMAN	N	812	ENSP00000289672:D812N	ENSP00000289672:D812N	D	-	1	0	PKD1L1	47900019	0.000000	0.05858	0.002000	0.10522	0.571000	0.35966	-3.364000	0.00496	-1.993000	0.00974	-0.389000	0.06534	GAC	C|0.974;T|0.026	0.026	strong		0.612	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
KIAA0196	9897	hgsc.bcm.edu	37	8	126087351	126087351	+	Silent	SNP	T	T	G	rs79464415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:126087351T>G	ENST00000318410.7	-	8	1216	c.867A>C	c.(865-867)gtA>gtC	p.V289V	KIAA0196_ENST00000517845.1_Silent_p.V141V	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	289					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)			AAATACTAATTACCTGAAAGA	0.363													T|||	36	0.0071885	0.0272	0.0	5008	,	,		18432	0.0		0.0	False		,,,				2504	0.0				p.V289V		Atlas-SNP	.											.	KIAA0196	90	.	0			c.A867C						PASS	.	T		72,4334	64.7+/-102.0	0,72,2131	106.0	106.0	106.0		867	-3.3	1.0	8	dbSNP_131	106	1,8599		0,1,4299	no	coding-synonymous	KIAA0196	NM_014846.3		0,73,6430	GG,GT,TT		0.0116,1.6341,0.5613		289/1160	126087351	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	9897	exon8			ACTAATTACCTGA		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.867A>C	8.37:g.126087351T>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	71	39	0.549296	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1																																																																																			T|0.994;G|0.006	0.006	strong		0.363	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
P2RX2	22953	hgsc.bcm.edu	37	12	133196596	133196596	+	Silent	SNP	T	T	C	rs7964634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133196596T>C	ENST00000389110.3	+	5	505	c.468T>C	c.(466-468)acT>acC	p.T156T	P2RX2_ENST00000351222.4_Silent_p.T64T|P2RX2_ENST00000348800.5_Silent_p.T156T|P2RX2_ENST00000449132.2_Intron|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	56	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	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		
KIF19	124602	hgsc.bcm.edu	37	17	72340965	72340965	+	Silent	SNP	G	G	A	rs34914485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72340965G>A	ENST00000389916.4	+	7	786	c.648G>A	c.(646-648)acG>acA	p.T216T		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	216	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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						CCAACCAGACGTCCTCCCGCT	0.662													G|||	182	0.0363419	0.1278	0.0144	5008	,	,		16134	0.0		0.0	False		,,,				2504	0.0031				p.T216T		Atlas-SNP	.											.	KIF19	102	.	0			c.G648A						PASS	.	G		498,3906	217.4+/-235.8	20,458,1724	38.0	40.0	39.0		648	-4.4	1.0	17	dbSNP_126	39	10,8588	6.4+/-24.3	0,10,4289	no	coding-synonymous	KIF19	NM_153209.3		20,468,6013	AA,AG,GG		0.1163,11.3079,3.9071		216/999	72340965	508,12494	2202	4299	6501	SO:0001819	synonymous_variant	124602	exon7			CCAGACGTCCTCC	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.648G>A	17.37:g.72340965G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	156	80	0.512821	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			G|0.965;A|0.035	0.035	strong		0.662	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
OR51B6	390058	hgsc.bcm.edu	37	11	5372863	5372863	+	Silent	SNP	T	T	A	rs10837882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5372863T>A	ENST00000380219.1	+	1	126	c.126T>A	c.(124-126)acT>acA	p.T42T	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	42					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)		GCAATGGCACTCTTCTCTTTC	0.468													T|||	750	0.14976	0.0658	0.0937	5008	,	,		22274	0.2351		0.1193	False		,,,				2504	0.2464				p.T42T		Atlas-SNP	.											.	OR51B6	53	.	0			c.T126A						PASS	.	T		412,3990	202.1+/-225.0	19,374,1808	175.0	139.0	151.0		126	-5.6	0.1	11	dbSNP_120	151	1090,7504	228.0+/-263.2	80,930,3287	no	coding-synonymous	OR51B6	NM_001004750.1		99,1304,5095	AA,AT,TT		12.6833,9.3594,11.5574		42/313	5372863	1502,11494	2201	4297	6498	SO:0001819	synonymous_variant	390058	exon1			TGGCACTCTTCTC		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.126T>A	11.37:g.5372863T>A		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	306	304	0.993464	NM_001004750		Silent	SNP	ENST00000380219.1	37	CCDS31379.1																																																																																			T|0.871;A|0.129	0.129	strong		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
TET2	54790	hgsc.bcm.edu	37	4	106190862	106190862	+	Silent	SNP	T	T	C	rs3733609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:106190862T>C	ENST00000540549.1	+	9	5000	c.4140T>C	c.(4138-4140)caT>caC	p.H1380H	TET2_ENST00000380013.4_Silent_p.H1380H|TET2_ENST00000513237.1_Silent_p.H1401H|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1380					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TCTGTGCTCATGCCCACAGAG	0.498			"""Mis N, F"""		MDS								T|||	560	0.111821	0.3578	0.0202	5008	,	,		19165	0.0615		0.0089	False		,,,				2504	0.002				p.H1380H		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2,NS,haematopoietic_neoplasm,+2,8	TET2	1762	8	0			c.T4140C						scavenged	.	T		467,917		82,303,307	101.0	87.0	91.0		4140	-8.0	0.7	4	dbSNP_107	91	6,3176		0,6,1585	no	coding-synonymous	TET2	NM_001127208.2		82,309,1892	CC,CT,TT		0.1886,33.7428,10.3592		1380/2003	106190862	473,4093	692	1591	2283	SO:0001819	synonymous_variant	54790	exon9			TGCTCATGCCCAC	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.4140T>C	4.37:g.106190862T>C		Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	183	84	0.459016	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	37	CCDS47120.1																																																																																			T|0.866;C|0.134	0.134	strong		0.498	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
NOS1	4842	hgsc.bcm.edu	37	12	117657991	117657991	+	Silent	SNP	G	G	T	rs2293044	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117657991G>T	ENST00000338101.4	-	27	4165	c.4161C>A	c.(4159-4161)gtC>gtA	p.V1387V	NOS1_ENST00000317775.6_Silent_p.V1353V|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CGTCCCCACAGACGTATATGT	0.597													G|||	195	0.0389377	0.062	0.0202	5008	,	,		20316	0.0585		0.0099	False		,,,				2504	0.0307				p.V1387V	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C4161A						PASS	.	G	,,,	291,4107	147.3+/-181.8	6,279,1914	142.0	153.0	149.0		4059,3051,3051,4161	-2.7	0.6	12	dbSNP_100	149	51,8547	31.7+/-84.0	0,51,4248	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	6,330,6162	TT,TG,GG		0.5932,6.6166,2.6316	,,,	1353/1435,1017/1099,1017/1099,1387/1469	117657991	342,12654	2199	4299	6498	SO:0001819	synonymous_variant	4842	exon28			CCCACAGACGTAT		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.4161C>A	12.37:g.117657991G>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	56	21	0.375	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.966;T|0.034	0.034	strong		0.597	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
PCDHB12	56124	hgsc.bcm.edu	37	5	140589738	140589738	+	Missense_Mutation	SNP	C	C	T	rs2910327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	205	0	0		WXS	Illumina HiSeq	Phase_I	193	92	0.476684	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	
TEKT4	150483	hgsc.bcm.edu	37	2	95537622	95537622	+	Missense_Mutation	SNP	A	A	G	rs11164112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:95537622A>G	ENST00000295201.4	+	1	435	c.298A>G	c.(298-300)Agc>Ggc	p.S100G	TEKT4_ENST00000427593.2_Missense_Mutation_p.S100G|AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	100			S -> G (in dbSNP:rs11164112).		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						GGACACGCACAGCTGGAAGTC	0.687													.|||	2141	0.427516	0.5166	0.4467	5008	,	,		17318	0.4881		0.3419	False		,,,				2504	0.319				p.S100G		Atlas-SNP	.											.	TEKT4	72	.	0			c.A298G						PASS	.	G	GLY/SER	2150,2232		542,1066,583	15.0	14.0	15.0		298	-0.6	0.3	2	dbSNP_120	15	3138,5444		576,1986,1729	no	missense	TEKT4	NM_144705.2	56	1118,3052,2312	GG,GA,AA		36.5649,49.0644,40.7899	benign	100/436	95537622	5288,7676	2191	4291	6482	SO:0001583	missense	150483	exon1			ACGCACAGCTGGA	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.298A>G	2.37:g.95537622A>G	ENSP00000295201:p.Ser100Gly	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_144705		Missense_Mutation	SNP	ENST00000295201.4	37	CCDS2005.1	891	0.40796703296703296	246	0.5	139	0.3839779005524862	261	0.4562937062937063	245	0.3232189973614776	.	0.056	-1.235674	0.01505	0.490644	0.365649	ENSG00000163060	ENST00000295201;ENST00000427593	T;T	0.02579	4.24;4.24	1.97	-0.615	0.11587	.	0.633849	0.15549	N	0.256532	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	0.17776	-1.0358	9	0.27082	T	0.32	-5.0599	3.6684	0.08265	0.1555:0.0:0.2897:0.5547	rs11164112	100	Q8WW24	TEKT4_HUMAN	G	100	ENSP00000295201:S100G;ENSP00000407596:S100G	ENSP00000295201:S100G	S	+	1	0	TEKT4	94901349	0.608000	0.26966	0.328000	0.25416	0.040000	0.13550	0.388000	0.20735	-0.228000	0.09869	-1.144000	0.01866	AGC	A|0.602;G|0.398	0.398	strong		0.687	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
KDM1A	23028	hgsc.bcm.edu	37	1	23409674	23409674	+	Silent	SNP	G	G	A	rs137940710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23409674G>A	ENST00000356634.3	+	19	2525	c.2376G>A	c.(2374-2376)ccG>ccA	p.P792P	KDM1A_ENST00000542151.1_Silent_p.P816P|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.P816P	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	792	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|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)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						TAAAATAGCCGATTCCACGAC	0.438													G|||	21	0.00419329	0.0144	0.0029	5008	,	,		19038	0.0		0.0	False		,,,				2504	0.0				p.P816P		Atlas-SNP	.											.	KDM1A	49	.	0			c.G2448A						PASS	.	G	,	24,4382	30.8+/-60.4	0,24,2179	75.0	71.0	72.0		2448,2376	-1.3	1.0	1	dbSNP_134	72	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KDM1A	NM_001009999.2,NM_015013.3	,	0,24,6479	AA,AG,GG		0.0,0.5447,0.1845	,	816/877,792/853	23409674	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	23028	exon21			ATAGCCGATTCCA	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"""Chromatin-modifying enzymes / K-demethylases"""	29079	protein-coding gene	gene with protein product		609132	"""amine oxidase (flavin containing) domain 2"", ""lysine (K)-specific demethylase 1"""	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.2376G>A	1.37:g.23409674G>A		Somatic	318	1	0.00314465		WXS	Illumina HiSeq	Phase_I	279	140	0.501792	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																			G|0.999;A|0.001	0.001	strong		0.438	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013	
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346594	39346594	+	Silent	SNP	C	C	T	rs377187211|rs148036927		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39346594C>T	ENST00000398470.1	+	1	456	c.456C>T	c.(454-456)acC>acT	p.T152T	KRTAP9-1_ENST00000377723.3_Intron|KRTAP9-1_ENST00000318329.5_Silent_p.T69T	NM_001190460.1	NP_001177389.1	A8MXZ3	KRA91_HUMAN	keratin associated protein 9-1	152	30 X 5 AA repeats of C-C-[CGSVRQH]- [SQTNP]-[PTSI].					keratin filament (GO:0045095)		p.T152_C153>S(2)		breast(1)|lung(3)	4						GCCAGCCCACCTGCTGTGGGT	0.582																																					p.T152T		Atlas-SNP	.											KRTAP9-1_ENST00000398470,colon,carcinoma,+2,2	KRTAP9-1	34	2	2	Complex - deletion inframe(2)	breast(2)	c.C456T						scavenged	.																																			SO:0001819	synonymous_variant	728318	exon1			GCCCACCTGCTGT	AC006070	CCDS56029.1	17q21.2	2010-06-03			ENSG00000240542	ENSG00000240542		"""Keratin associated proteins"""	18912	protein-coding gene	gene with protein product			"""keratin associated protein 9-like 3"""	KRTAP9L3			Standard	NM_001190460		Approved	KAP9.1	uc021txf.1	A8MXZ3	OTTHUMG00000133636	ENST00000398470.1:c.456C>T	17.37:g.39346594C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	111	8	0.0720721	NM_001190460		Silent	SNP	ENST00000398470.1	37	CCDS56029.1																																																																																			.	.	none		0.582	KRTAP9-1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257781.1		
PRKACG	5568	hgsc.bcm.edu	37	9	71628207	71628207	+	Missense_Mutation	SNP	G	G	C	rs3730386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:71628207G>C	ENST00000377276.2	-	1	832	c.802C>G	c.(802-804)Cat>Gat	p.H268D		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	268	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		H -> D (in dbSNP:rs3730386). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:2342480, ECO:0000269|Ref.3}.		activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|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)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						CGCAGCAGATGCTTGAGGTCA	0.592													C|||	1609	0.321286	0.3752	0.1772	5008	,	,		17415	0.3145		0.2684	False		,,,				2504	0.4121				p.H268D	Esophageal Squamous(110;2236 2623 32146)	Atlas-SNP	.											.	PRKACG	65	.	0			c.C802G						PASS	.	C	ASP/HIS	1596,2810	665.1+/-401.5	295,1006,902	89.0	89.0	89.0		802	1.6	0.0	9	dbSNP_107	89	2203,6397	710.5+/-405.8	275,1653,2372	yes	missense	PRKACG	NM_002732.3	81	570,2659,3274	CC,CG,GG		25.6163,36.2233,29.2096	benign	268/352	71628207	3799,9207	2203	4300	6503	SO:0001583	missense	5568	exon1			GCAGATGCTTGAG	M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.802C>G	9.37:g.71628207G>C	ENSP00000366488:p.His268Asp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_002732	O60850|Q5VZ02|Q86YI1	Missense_Mutation	SNP	ENST00000377276.2	37	CCDS6625.1	599	0.2742673992673993	179	0.3638211382113821	68	0.1878453038674033	159	0.27797202797202797	193	0.2546174142480211	C	0.149	-1.093767	0.01858	0.362233	0.256163	ENSG00000165059	ENST00000377276	T	0.05139	3.49	1.62	1.62	0.23740	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.00049	-2.415	0.51482	P	7.299999999998974E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.44757	-0.9307	8	0.02654	T	1	.	7.527	0.27660	0.0:0.7289:0.2711:0.0	rs3730386;rs3730386	268	P22612	KAPCG_HUMAN	D	268	ENSP00000366488:H268D	ENSP00000366488:H268D	H	-	1	0	PRKACG	70818027	1.000000	0.71417	0.001000	0.08648	0.024000	0.10985	2.604000	0.46274	0.027000	0.15297	-0.224000	0.12420	CAT	G|0.707;C|0.293	0.293	strong		0.592	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1		
TNC	3371	hgsc.bcm.edu	37	9	117846580	117846580	+	Missense_Mutation	SNP	T	T	C	rs1061494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117846580T>C	ENST00000350763.4	-	4	2450	c.2039A>G	c.(2038-2040)cAg>cGg	p.Q680R	TNC_ENST00000535648.1_Missense_Mutation_p.Q680R|TNC_ENST00000341037.4_Missense_Mutation_p.Q680R|TNC_ENST00000423613.2_Missense_Mutation_p.Q680R|TNC_ENST00000537320.1_Missense_Mutation_p.Q680R|TNC_ENST00000542877.1_Missense_Mutation_p.Q680R|TNC_ENST00000340094.3_Missense_Mutation_p.Q680R|TNC_ENST00000346706.3_Missense_Mutation_p.Q680R|TNC_ENST00000345230.3_Missense_Mutation_p.Q680R	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	680	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Q -> R (in dbSNP:rs1061494). {ECO:0000269|PubMed:1707164}.		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)	p.Q680R(1)		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						CTCCAGCTCCTGGATGATGGT	0.572													C|||	2252	0.449681	0.6014	0.5519	5008	,	,		19356	0.2857		0.4423	False		,,,				2504	0.3487				p.Q680R		Atlas-SNP	.											TNC,NS,carcinoma,0,1	TNC	282	1	1	Substitution - Missense(1)	stomach(1)	c.A2039G						PASS	.	C	ARG/GLN	2489,1917	547.8+/-377.4	707,1075,421	98.0	93.0	95.0		2039	1.0	1.0	9	dbSNP_86	95	3764,4836	615.5+/-396.4	833,2098,1369	yes	missense	TNC	NM_002160.3	43	1540,3173,1790	CC,CT,TT		43.7674,43.5089,48.0778	benign	680/2202	117846580	6253,6753	2203	4300	6503	SO:0001583	missense	3371	exon4			AGCTCCTGGATGA		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.2039A>G	9.37:g.117846580T>C	ENSP00000265131:p.Gln680Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	970	0.4441391941391941	288	0.5853658536585366	188	0.5193370165745856	153	0.2674825174825175	341	0.449868073878628	C	2.031	-0.422463	0.04734	0.564911	0.437674	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44;0.44;0.44;0.44;0.44	5.93	1.04	0.20106	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.436137	0.23700	N	0.045439	T	0.00012	0.0000	N	0.02685	-0.53	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.002	T	0.47071	-0.9145	9	0.02654	T	1	.	12.0326	0.53406	0.0:0.608:0.0:0.392	rs1061494;rs1757112;rs3202586;rs16932200;rs59848703;rs1061494	680;680	E9PC84;P24821	.;TENA_HUMAN	R	680	ENSP00000344400:Q680R;ENSP00000438152:Q680R;ENSP00000344555:Q680R;ENSP00000345861:Q680R;ENSP00000265131:Q680R;ENSP00000339553:Q680R;ENSP00000411406:Q680R;ENSP00000443478:Q680R;ENSP00000442242:Q680R	ENSP00000344400:Q680R	Q	-	2	0	TNC	116886401	0.000000	0.05858	0.977000	0.42913	0.958000	0.62258	-0.363000	0.07593	-0.273000	0.09246	-0.119000	0.15052	CAG	T|0.531;C|0.469	0.469	strong		0.572	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150284	39150284	+	Silent	SNP	A	A	G	rs2010201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39150284A>G	ENST00000391586.1	-	1	101	c.66T>C	c.(64-66)tcT>tcC	p.S22S		NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	22	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			lung(2)|prostate(2)	4		Breast(137;0.00043)				AGGATTTGTCAGAGGAGCAGA	0.582													A|||	2379	0.47504	0.6377	0.4784	5008	,	,		17574	0.5		0.2913	False		,,,				2504	0.4162				p.S22S		Atlas-SNP	.											.	KRTAP3-3	11	.	0			c.T66C						PASS	.	A		2510,1896	625.1+/-394.5	720,1070,413	90.0	90.0	90.0		66	-11.2	0.0	17	dbSNP_92	90	2274,6318	374.7+/-337.5	295,1684,2317	no	coding-synonymous	KRTAP3-3	NM_033185.2		1015,2754,2730	GG,GA,AA		26.4665,43.0322,36.8057		22/99	39150284	4784,8214	2203	4296	6499	SO:0001819	synonymous_variant	85293	exon1			TTTGTCAGAGGAG	AJ406933	CCDS32643.1	17q21.2	2013-06-25			ENSG00000212899	ENSG00000212899		"""Keratin associated proteins"""	18890	protein-coding gene	gene with protein product						11279113	Standard	NM_033185		Approved	KAP3.3	uc002hvr.1	Q9BYR6	OTTHUMG00000133591	ENST00000391586.1:c.66T>C	17.37:g.39150284A>G		Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	355	207	0.583099	NM_033185	Q52LP0|Q6NTD4	Silent	SNP	ENST00000391586.1	37	CCDS32643.1																																																																																			A|0.598;G|0.402	0.402	strong		0.582	KRTAP3-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257695.1		
RNF213	57674	hgsc.bcm.edu	37	17	78263634	78263634	+	Silent	SNP	A	A	G	rs141921176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78263634A>G	ENST00000582970.1	+	6	1253	c.1110A>G	c.(1108-1110)gcA>gcG	p.A370A	RNF213_ENST00000508628.2_Silent_p.A419A|RNF213_ENST00000319921.4_Silent_p.A370A|RNF213_ENST00000456466.1_Silent_p.A370A	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	370					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)			AAGTGAAGGCAAGGTAGGGAT	0.567													A|||	17	0.00339457	0.0129	0.0	5008	,	,		17512	0.0		0.0	False		,,,				2504	0.0				p.A370A		Atlas-SNP	.											.	RNF213	766	.	0			c.A1110G						PASS	.	A	,	61,4345	54.9+/-90.9	0,61,2142	63.0	66.0	65.0		1257,1110	-6.5	0.0	17	dbSNP_134	65	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	RNF213	NM_020914.4,NM_020954.2	,	0,63,6440	GG,GA,AA		0.0233,1.3845,0.4844	,	419/5257,370/1064	78263634	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon6			GAAGGCAAGGTAG	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.1110A>G	17.37:g.78263634A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			A|0.995;G|0.005	0.005	strong		0.567	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
LRRK1	79705	hgsc.bcm.edu	37	15	101529594	101529594	+	Silent	SNP	G	G	A	rs376627461|rs2412000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:101529594G>A	ENST00000388948.3	+	6	1112	c.753G>A	c.(751-753)ccG>ccA	p.P251P	LRRK1_ENST00000532029.2_Silent_p.P251P|LRRK1_ENST00000284395.5_Silent_p.P248P	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)			GCAGTTATCCGGGAAAAACAG	0.443													g|||	699	0.139577	0.4183	0.0677	5008	,	,		20838	0.0099		0.0398	False		,,,				2504	0.0501				p.P251P		Atlas-SNP	.											.	LRRK1	310	.	0			c.G753A						PASS	.	A		1231,2547		192,847,850	81.0	80.0	80.0		753	-5.2	0.0	15	dbSNP_100	80	420,7828		13,394,3717	no	coding-synonymous	LRRK1	NM_024652.3		205,1241,4567	AA,AG,GG		5.0921,32.5834,13.7286		251/2016	101529594	1651,10375	1889	4124	6013	SO:0001819	synonymous_variant	79705	exon6			TTATCCGGGAAAA	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.753G>A	15.37:g.101529594G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			G|0.871;A|0.129	0.129	strong		0.443	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
AR	367	hgsc.bcm.edu	37	X	66765164	66765164	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:66765164A>T	ENST00000374690.3	+	1	700	c.176A>T	c.(175-177)cAg>cTg	p.Q59L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q59L|AR_ENST00000504326.1_Missense_Mutation_p.Q59L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	59	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CTGCTgcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q59L		Atlas-SNP	.											.	AR	249	.	0			c.A176T						PASS	.						7.0	10.0	9.0					X																	66765164		2055	4063	6118	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	TGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.176A>T	X.37:g.66765164A>T	ENSP00000363822:p.Gln59Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	68	4	0.0588235	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	12.32	1.901651	0.33535	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.69175	-0.38;-0.38;-0.38	.	.	.	.	1.117170	0.06949	N	0.814177	T	0.47060	0.1425	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.34313	0.448;0.448	B;B	0.36534	0.227;0.227	T	0.31724	-0.9933	8	0.13108	T	0.6	.	.	.	.	.	59;59	E7EVX6;D3YPQ2	.;.	L	59	ENSP00000363822:Q59L;ENSP00000421155:Q59L;ENSP00000379359:Q59L	ENSP00000363822:Q59L	Q	+	2	0	AR	66681889	0.995000	0.38212	0.864000	0.33941	0.503000	0.33858	0.245000	0.18142	0.000000	0.14550	0.000000	0.15137	CAG	.	.	none		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
UNC5D	137970	hgsc.bcm.edu	37	8	35583815	35583815	+	Silent	SNP	G	G	C	rs6996645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:35583815G>C	ENST00000404895.2	+	10	1777	c.1449G>C	c.(1447-1449)gtG>gtC	p.V483V	UNC5D_ENST00000453357.2_Silent_p.V478V|UNC5D_ENST00000420357.1_Silent_p.V416V|UNC5D_ENST00000287272.2_Silent_p.V414V|UNC5D_ENST00000416672.1_Silent_p.V488V|UNC5D_ENST00000449677.1_Silent_p.V59V	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	483					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		ACATCAAAGTGAAAGTCCAGA	0.517													C|||	1034	0.20647	0.5	0.1499	5008	,	,		17632	0.1002		0.0199	False		,,,				2504	0.1513				p.V483V		Atlas-SNP	.											.	UNC5D	393	.	0			c.G1449C						PASS	.	C		1844,2562	634.9+/-396.3	370,1104,729	67.0	66.0	66.0		1449	5.2	1.0	8	dbSNP_116	66	148,8452	812.4+/-407.1	3,142,4155	no	coding-synonymous	UNC5D	NM_080872.2		373,1246,4884	CC,CG,GG		1.7209,41.852,15.316		483/954	35583815	1992,11014	2203	4300	6503	SO:0001819	synonymous_variant	137970	exon10			CAAAGTGAAAGTC	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"""Immunoglobulin superfamily / I-set domain containing"""	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.1449G>C	8.37:g.35583815G>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_080872	Q8WYP7	Silent	SNP	ENST00000404895.2	37	CCDS6093.2																																																																																			G|0.839;C|0.161	0.161	strong		0.517	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2		
PTPN2	5771	hgsc.bcm.edu	37	18	12817348	12817348	+	Missense_Mutation	SNP	G	G	T	rs78174797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:12817348G>T	ENST00000309660.5	-	6	605	c.512C>A	c.(511-513)aCa>aAa	p.T171K	PTPN2_ENST00000353319.4_Missense_Mutation_p.T171K|PTPN2_ENST00000591497.1_Missense_Mutation_p.T142K|PTPN2_ENST00000591115.1_Missense_Mutation_p.T194K|PTPN2_ENST00000327283.3_Missense_Mutation_p.T171K	NM_002828.3	NP_002819.2	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type 2	171	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)				GTGAGATATTGTTCTGGTTTC	0.338													G|||	67	0.0133786	0.0477	0.0043	5008	,	,		17923	0.0		0.001	False		,,,				2504	0.0				p.T194K		Atlas-SNP	.											.	PTPN2	37	.	0			c.C581A						PASS	.	G	LYS/THR,LYS/THR,LYS/THR,LYS/THR	222,4184	119.2+/-156.9	3,216,1984	52.0	54.0	53.0		581,512,512,512	3.1	1.0	18	dbSNP_131	53	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	PTPN2	NM_001207013.1,NM_002828.3,NM_080422.2,NM_080423.2	78,78,78,78	3,217,6283	TT,TG,GG		0.0116,5.0386,1.7146	benign,benign,benign,benign	194/411,171/416,171/388,171/354	12817348	223,12783	2203	4300	6503	SO:0001583	missense	5771	exon7			GATATTGTTCTGG	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.512C>A	18.37:g.12817348G>T	ENSP00000311857:p.Thr171Lys	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	252	109	0.43254	NM_001207013	A8K955|A8MXU3|K7ENG3|Q96AU5|Q96HR2	Missense_Mutation	SNP	ENST00000309660.5	37	CCDS11865.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	10.90	1.481893	0.26598	0.050386	1.16E-4	ENSG00000175354	ENST00000327283;ENST00000353319;ENST00000341361;ENST00000309660	D;D;D	0.83419	-1.72;-1.72;-1.72	5.25	3.09	0.35607	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.369486	0.22569	N	0.058367	T	0.14787	0.0357	N	0.21240	0.645	0.31241	N	0.695115	B;B;B;B;B	0.24132	0.025;0.013;0.098;0.055;0.016	B;B;B;B;B	0.18263	0.009;0.008;0.021;0.009;0.014	T	0.50775	-0.8788	10	0.49607	T	0.09	.	4.6107	0.12401	0.1352:0.0:0.4911:0.3736	.	171;171;148;171;171	P17706;P17706-2;Q59F91;Q96AU5;A8K3N4	PTN2_HUMAN;.;.;.;.	K	171;171;148;171	ENSP00000320298:T171K;ENSP00000320546:T171K;ENSP00000311857:T171K	ENSP00000311857:T171K	T	-	2	0	PTPN2	12807348	1.000000	0.71417	0.987000	0.45799	0.981000	0.71138	2.804000	0.47931	1.186000	0.42985	0.591000	0.81541	ACA	G|0.981;T|0.019	0.019	strong		0.338	PTPN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254613.3	NM_002828, NM_080422, NM_080423	
EXOC4	60412	hgsc.bcm.edu	37	7	133749077	133749077	+	Silent	SNP	C	C	T	rs139944066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:133749077C>T	ENST00000253861.4	+	18	2750	c.2721C>T	c.(2719-2721)gaC>gaT	p.D907D	EXOC4_ENST00000545148.1_Silent_p.D517D|EXOC4_ENST00000541309.1_Silent_p.D195D|EXOC4_ENST00000539845.1_Silent_p.D806D	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	907					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)				ACACAGCTGACGAGCTCCTGA	0.577													C|||	11	0.00219649	0.0083	0.0	5008	,	,		21152	0.0		0.0	False		,,,				2504	0.0				p.D907D		Atlas-SNP	.											.	EXOC4	118	.	0			c.C2721T						PASS	.	C		21,4385	28.1+/-56.4	0,21,2182	90.0	76.0	81.0		2721	-8.4	0.4	7	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous	EXOC4	NM_021807.3		0,21,6482	TT,TC,CC		0.0,0.4766,0.1615		907/975	133749077	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	60412	exon18			AGCTGACGAGCTC	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.2721C>T	7.37:g.133749077C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	118	52	0.440678	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	37	CCDS5829.1																																																																																			C|0.997;T|0.003	0.003	strong		0.577	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
CD109	135228	hgsc.bcm.edu	37	6	74493432	74493432	+	Missense_Mutation	SNP	A	A	C	rs10455097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74493432A>C	ENST00000287097.5	+	19	2220	c.2108A>C	c.(2107-2109)tAc>tCc	p.Y703S	CD109_ENST00000422508.2_Missense_Mutation_p.Y626S|CD109_ENST00000437994.2_Missense_Mutation_p.Y703S			Q6YHK3	CD109_HUMAN	CD109 molecule	703			Y -> S (in allele Gov(b); dbSNP:rs10455097). {ECO:0000269|PubMed:11861285, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14980714, ECO:0000269|PubMed:16754747, ECO:0000269|PubMed:17974005}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GACTTCAGTTACAGGATTTAC	0.333													C|||	2582	0.515575	0.6551	0.5072	5008	,	,		16327	0.5268		0.495	False		,,,				2504	0.3425				p.Y703S		Atlas-SNP	.											.	CD109	170	.	0			c.A2108C	GRCh37	CM020385	CD109	M	rs10455097	PASS	.	C	SER/TYR,SER/TYR,SER/TYR	2841,1565	490.3+/-361.7	914,1013,276	95.0	86.0	89.0		2108,1877,2108	5.2	0.7	6	dbSNP_119	89	4395,4205	568.4+/-389.0	1142,2111,1047	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	144,144,144	2056,3124,1323	CC,CA,AA		48.8953,35.5197,44.3641	benign,benign,benign	703/1429,626/1369,703/1446	74493432	7236,5770	2203	4300	6503	SO:0001583	missense	135228	exon19			TCAGTTACAGGAT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2108A>C	6.37:g.74493432A>C	ENSP00000287097:p.Tyr703Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	1183	0.5416666666666666	332	0.6747967479674797	187	0.5165745856353591	298	0.5209790209790209	366	0.48284960422163586	C	0.007	-1.977407	0.00452	0.644803	0.511047	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.23348	1.91;1.91;1.91	5.16	5.16	0.70880	Alpha-2-macroglobulin (1);	1.522320	0.04338	N	0.353567	T	0.02342	0.0072	N	0.00459	-1.475	0.52501	P	4.499999999996174E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.36187	-0.9758	9	0.12430	T	0.62	.	10.6226	0.45489	0.1331:0.7968:0.0:0.0701	rs10455097;rs52799109;rs56864921;rs10455097	626;703;703	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	S	703;626;703	ENSP00000388062:Y703S;ENSP00000404475:Y626S;ENSP00000287097:Y703S	ENSP00000287097:Y703S	Y	+	2	0	CD109	74550153	0.936000	0.31750	0.680000	0.29994	0.003000	0.03518	0.728000	0.26013	1.413000	0.46997	-0.127000	0.14921	TAC	A|0.454;C|0.546	0.546	strong		0.333	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
ATN1	1822	hgsc.bcm.edu	37	12	7045939	7045939	+	Missense_Mutation	SNP	T	T	G	rs146578563		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7045939T>G	ENST00000356654.4	+	5	1746	c.1509T>G	c.(1507-1509)caT>caG	p.H503Q	ATN1_ENST00000396684.2_Missense_Mutation_p.H503Q	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	503					cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						agcagcagcaTCACGGAAACT	0.637																																					p.H503Q		Atlas-SNP	.											ATN1,colon,carcinoma,0,1	ATN1	95	1	0			c.T1509G						PASS	.						55.0	62.0	60.0					12																	7045939		2203	4300	6503	SO:0001583	missense	1822	exon5			GCAGCATCACGGA	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"""dentatorubral-pallidoluysian atrophy (atrophin-1)"""	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.1509T>G	12.37:g.7045939T>G	ENSP00000349076:p.His503Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	91	8	0.0879121	NM_001007026	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	37	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	t	0.009	-1.812787	0.00600	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325;ENST00000229279	T;T;T	0.37235	1.21;1.21;1.21	3.27	-0.797	0.10909	.	.	.	.	.	T	0.21881	0.0527	L	0.29908	0.895	0.09310	N	0.999995	B	0.23058	0.079	B	0.26770	0.073	T	0.27806	-1.0063	9	0.26408	T	0.33	.	4.3098	0.10965	0.0:0.4586:0.2199:0.3215	.	503	P54259	ATN1_HUMAN	Q	503;503;503;88	ENSP00000349076:H503Q;ENSP00000379915:H503Q;ENSP00000441744:H503Q	ENSP00000229279:H88Q	H	+	3	2	ATN1	6916200	0.000000	0.05858	0.721000	0.30653	0.342000	0.28953	-1.515000	0.02252	0.069000	0.16605	0.473000	0.43528	CAT	C|0.001;G|0.000;T|0.999	0.000	strong		0.637	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940	
MBD6	114785	hgsc.bcm.edu	37	12	57920368	57920368	+	Silent	SNP	T	T	C	rs34551572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57920368T>C	ENST00000355673.3	+	7	1796	c.1440T>C	c.(1438-1440)gcT>gcC	p.A480A	MBD6_ENST00000431731.2_Silent_p.A480A	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	480	Pro-rich.					chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						CCCCACCAGCTGCCTCCAAAG	0.632													T|||	469	0.0936502	0.3328	0.0389	5008	,	,		15994	0.0		0.001	False		,,,				2504	0.001				p.A480A		Atlas-SNP	.											.	MBD6	99	.	0			c.T1440C						PASS	.	T		1234,3172		199,836,1168	51.0	66.0	61.0		1440	2.8	1.0	12	dbSNP_126	61	14,8586		0,14,4286	no	coding-synonymous	MBD6	NM_052897.3		199,850,5454	CC,CT,TT		0.1628,28.0073,9.5956		480/1004	57920368	1248,11758	2203	4300	6503	SO:0001819	synonymous_variant	114785	exon7			ACCAGCTGCCTCC	AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.1440T>C	12.37:g.57920368T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	NM_052897	Q8N3M0|Q8NA81|Q96Q00	Silent	SNP	ENST00000355673.3	37	CCDS8944.1																																																																																			T|0.893;C|0.107	0.107	strong		0.632	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1		
CYP3A43	64816	hgsc.bcm.edu	37	7	99463556	99463556	+	Missense_Mutation	SNP	A	A	T	rs540214188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99463556A>T	ENST00000354829.2	+	13	1547	c.1444A>T	c.(1444-1446)Att>Ttt	p.I482F	CYP3A43_ENST00000222382.5_Missense_Mutation_p.I483F|CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000342499.4_3'UTR|CYP3A43_ENST00000415413.1_Missense_Mutation_p.I271F|CYP3A43_ENST00000417625.1_Missense_Mutation_p.I372F|CYP3A43_ENST00000312017.5_3'UTR|CYP3A43_ENST00000444905.1_3'UTR	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	482			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)	CAATCTACCAATTCTTCAACC	0.338													A|||	292	0.0583067	0.2035	0.0216	5008	,	,		18384	0.001		0.002	False		,,,				2504	0.0051				p.I483F		Atlas-SNP	.											.	CYP3A43	52	.	0			c.A1447T						PASS	.						87.0	97.0	93.0					7																	99463556		2184	4300	6484	SO:0001583	missense	64816	exon13			CTACCAATTCTTC	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.1444A>T	7.37:g.99463556A>T	ENSP00000346887:p.Ile482Phe	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	75	12	0.16	NM_022820	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	37	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.321913	0.23994	.	.	ENSG00000021461	ENST00000354829;ENST00000417625;ENST00000415413;ENST00000222382	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	3.17	-6.34	0.01982	.	0.885559	0.09500	N	0.793766	T	0.24928	0.0605	N	0.01019	-1.045	0.22127	N	0.999348	B;B;B	0.11235	0.002;0.001;0.004	B;B;B	0.15052	0.003;0.006;0.012	T	0.16541	-1.0399	10	0.23891	T	0.37	.	0.423	0.00459	0.3831:0.1534:0.2286:0.2349	.	372;483;482	Q495Y1;Q75MK2;Q9HB55	.;.;CP343_HUMAN	F	482;372;271;483	ENSP00000346887:I482F;ENSP00000416581:I372F;ENSP00000401521:I271F;ENSP00000222382:I483F	ENSP00000222382:I483F	I	+	1	0	CYP3A43	99301492	0.000000	0.05858	0.000000	0.03702	0.483000	0.33249	-8.694000	0.00017	-2.343000	0.00623	0.172000	0.16884	ATT	.	.	none		0.338	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1		
KRT72	140807	hgsc.bcm.edu	37	12	52986187	52986187	+	Missense_Mutation	SNP	T	T	C	rs12833456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52986187T>C	ENST00000537672.2	-	4	801	c.791A>G	c.(790-792)tAt>tGt	p.Y264C	KRT72_ENST00000354310.4_Missense_Mutation_p.Y264C|KRT72_ENST00000293745.2_Missense_Mutation_p.Y264C|KRT72_ENST00000398066.3_Missense_Mutation_p.Y76C	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	264	Coil 1B.|Rod.		Y -> C (in dbSNP:rs12833456). {ECO:0000269|PubMed:14702039}.			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)		TACCCCTTCATAAAGGCACTT	0.498													T|||	1867	0.372804	0.1914	0.2406	5008	,	,		19422	0.5675		0.3638	False		,,,				2504	0.5204				p.Y264C		Atlas-SNP	.											.	KRT72	70	.	0			c.A791G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR	1138,3268	405.3+/-333.4	156,826,1221	97.0	87.0	91.0		791,791,791	3.7	1.0	12	dbSNP_121	91	3281,5319	491.9+/-373.2	598,2085,1617	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	194,194,194	754,2911,2838	CC,CT,TT		38.1512,25.8284,33.9766	benign,benign,benign	264/512,264/470,264/512	52986187	4419,8587	2203	4300	6503	SO:0001583	missense	140807	exon4			CCTTCATAAAGGC	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.791A>G	12.37:g.52986187T>C	ENSP00000441160:p.Tyr264Cys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	100	57	0.57	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	785	0.35943223443223443	104	0.21138211382113822	83	0.2292817679558011	308	0.5384615384615384	290	0.38258575197889183	T	13.46	2.243523	0.39697	0.258284	0.381512	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.64	4.85	3.67	0.42095	Filament (1);	0.439409	0.19225	N	0.119562	T	0.00012	0.0000	H	0.95187	3.635	0.40029	P	0.024499999999999966	B	0.15473	0.013	B	0.29077	0.098	T	0.18085	-1.0348	9	0.72032	D	0.01	.	11.0777	0.48040	0.1435:0.0:0.0:0.8565	rs12833456;rs52803577;rs58274768;rs12833456	264	Q14CN4	K2C72_HUMAN	C	264;264;264;76	ENSP00000441160:Y264C;ENSP00000293745:Y264C;ENSP00000346269:Y264C;ENSP00000446151:Y76C	ENSP00000293745:Y264C	Y	-	2	0	KRT72	51272454	0.053000	0.20554	0.979000	0.43373	0.908000	0.53690	0.153000	0.16323	0.914000	0.36822	0.482000	0.46254	TAT	C|0.351;N|0.000	0.351	strong		0.498	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
POLD1	5424	hgsc.bcm.edu	37	19	50916772	50916772	+	Silent	SNP	T	T	C	rs1274607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50916772T>C	ENST00000440232.2	+	18	2297	c.2244T>C	c.(2242-2244)agT>agC	p.S748S	POLD1_ENST00000599857.1_Silent_p.S748S|POLD1_ENST00000595904.1_Silent_p.S774S|CTD-2545M3.6_ENST00000599632.1_5'Flank	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	748					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		ACAGCACCAGTGCCAAGGTCG	0.652								DNA polymerases (catalytic subunits)					c|||	593	0.118411	0.3722	0.0562	5008	,	,		16316	0.002		0.003	False		,,,				2504	0.0583				p.S748S		Atlas-SNP	.											.	POLD1	174	.	0			c.T2244C						PASS	.			1403,3003	659.8+/-400.6	223,957,1023	56.0	45.0	49.0		2244	-8.6	0.0	19	dbSNP_87	49	18,8582	794.9+/-407.5	0,18,4282	no	coding-synonymous	POLD1	NM_002691.2		223,975,5305	CC,CT,TT		0.2093,31.8429,10.9257		748/1108	50916772	1421,11585	2203	4300	6503	SO:0001819	synonymous_variant	5424	exon18			CACCAGTGCCAAG		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2244T>C	19.37:g.50916772T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_002691	Q8NER3|Q96H98	Silent	SNP	ENST00000440232.2	37	CCDS12795.1																																																																																			T|0.877;C|0.123	0.123	strong		0.652	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
DHRS2	10202	hgsc.bcm.edu	37	14	24114483	24114483	+	3'UTR	SNP	T	T	C	rs7156794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24114483T>C	ENST00000250383.6	+	0	1340				DHRS2_ENST00000344777.7_Missense_Mutation_p.V292A	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2						C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		GGCGGCTGCGTAGCTGTGGTC	0.602													c|||	572	0.114217	0.4153	0.0303	5008	,	,		17144	0.0		0.002	False		,,,				2504	0.0				p.V292A		Atlas-SNP	.											.	DHRS2	78	.	0			c.T875C						PASS	.		,ALA/VAL	1524,2882	480.3+/-358.8	279,966,958	61.0	62.0	61.0		,875	-2.1	0.0	14	dbSNP_116	61	19,8581	12.6+/-44.7	0,19,4281	yes	utr-3,missense	DHRS2	NM_005794.3,NM_182908.4	,64	279,985,5239	CC,CT,TT		0.2209,34.5892,11.8638	,benign	,292/301	24114483	1543,11463	2203	4300	6503	SO:0001624	3_prime_UTR_variant	10202	exon9			GCTGCGTAGCTGT		CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18349	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 1"""	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.*21T>C	14.37:g.24114483T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	ENST00000250383.6	37	CCDS9604.1	198	0.09065934065934066	183	0.3719512195121951	14	0.03867403314917127	0	0.0	1	0.0013192612137203166	t	0.018	-1.479180	0.01035	0.345892	0.002209	ENSG00000100867	ENST00000344777	D	0.82984	-1.67	2.22	-2.14	0.07123	.	2.958940	0.01651	N	0.024553	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22068	-1.0227	8	0.87932	D	0	.	0.3421	0.00335	0.2015:0.3173:0.1984:0.2828	rs7156794;rs60193895	270	Q13268-2	.	A	292	ENSP00000344674:V292A	ENSP00000344674:V292A	V	+	2	0	DHRS2	23184323	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.227000	0.09126	-0.620000	0.05641	-0.251000	0.11542	GTA	T|0.941;C|0.059	0.059	strong		0.602	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908	
SCN1B	6324	hgsc.bcm.edu	37	19	35524824	35524824	+	Intron	SNP	T	T	C	rs55742440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35524824T>C	ENST00000262631.5	+	3	585				SCN1B_ENST00000596348.1_Intron|CTD-2527I21.9_ENST00000601692.1_RNA|SCN1B_ENST00000595652.1_Intron|SCN1B_ENST00000415950.3_Missense_Mutation_p.L210P	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)	CCTCTGTTTCTCTCCAGCCCA	0.657													C|||	1891	0.377596	0.5378	0.389	5008	,	,		17595	0.2411		0.3897	False		,,,				2504	0.2812				p.L210P		Atlas-SNP	.											.	SCN1B	32	.	0			c.T629C						PASS	.	C	,PRO/LEU	1290,1244		337,616,314	24.0	33.0	30.0		,629	-1.9	0.0	19	dbSNP_129	30	1675,2827		323,1029,899	yes	intron,missense	SCN1B	NM_001037.4,NM_199037.3	,98	660,1645,1213	CC,CT,TT		37.2057,49.0923,42.1404	,probably-damaging	,210/269	35524824	2965,4071	1267	2251	3518	SO:0001627	intron_variant	6324	exon3			TGTTTCTCTCCAG		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+181T>C	19.37:g.35524824T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	88	55	0.625	NM_199037	Q5TZZ4|Q6TN97	Missense_Mutation	SNP	ENST00000262631.5	37	CCDS12441.1	830	0.38003663003663	265	0.5386178861788617	143	0.39502762430939226	129	0.22552447552447552	293	0.3865435356200528	C	8.351	0.830987	0.16820	0.509077	0.372057	ENSG00000105711	ENST00000415950	D	0.90900	-2.75	3.94	-1.91	0.07641	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34477	-0.9827	6	.	.	.	-33.9385	8.8207	0.35025	0.0:0.3335:0.0:0.6665	rs55742440	210	Q07699-2	.	P	210	ENSP00000396915:L210P	.	L	+	2	0	SCN1B	40216664	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.005000	0.13129	-0.396000	0.07703	-1.016000	0.02456	CTC	T|0.619;C|0.381	0.381	strong		0.657	SCN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461567.1		
ADAM28	10863	hgsc.bcm.edu	37	8	24207438	24207438	+	Missense_Mutation	SNP	G	G	A	rs7829965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24207438G>A	ENST00000265769.4	+	19	2162	c.2052G>A	c.(2050-2052)atG>atA	p.M684I	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000397649.3_Missense_Mutation_p.G433S|RP11-624C23.1_ENST00000518988.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	684			M -> I (in dbSNP:rs7829965).		spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TGGTTGCTATGGTAATCCGGC	0.488													A|||	400	0.0798722	0.1059	0.0202	5008	,	,		13242	0.1062		0.0298	False		,,,				2504	0.1115				p.M684I	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.G2052A						PASS	.	A	ILE/MET	443,3963	786.0+/-414.8	20,403,1780	161.0	156.0	157.0		2052	-0.6	0.0	8	dbSNP_116	157	237,8363	808.9+/-407.2	3,231,4066	yes	missense	ADAM28	NM_014265.4	10	23,634,5846	AA,AG,GG		2.7558,10.0545,5.2284	benign	684/776	24207438	680,12326	2203	4300	6503	SO:0001583	missense	10863	exon19			TGCTATGGTAATC	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.2052G>A	8.37:g.24207438G>A	ENSP00000265769:p.Met684Ile	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	162|162	0.07417582417582418|0.07417582417582418	72|72	0.14634146341463414|0.14634146341463414	6|6	0.016574585635359115|0.016574585635359115	58|58	0.10139860139860139|0.10139860139860139	26|26	0.03430079155672823|0.03430079155672823	A|A	0.007|0.007	-2.009414|-2.009414	0.00426|0.00426	0.100545|0.100545	0.027558|0.027558	ENSG00000042980|ENSG00000042980	ENST00000397649;ENST00000521629;ENST00000518326|ENST00000265769	T|T	0.01548|0.01397	4.78|4.94	5.34|5.34	-0.579|-0.579	0.11720|0.11720	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01729|0.01729	-0.75|-0.75	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.42224|0.42224	-0.9464|-0.9464	6|8	0.20519|0.09590	T|T	0.43|0.72	.|.	0.637|0.637	0.00804|0.00804	0.4466:0.1332:0.1609:0.2593|0.4466:0.1332:0.1609:0.2593	rs7829965;rs58612661;rs7829965|rs7829965;rs58612661;rs7829965	.|684;684	.|B2RMV5;Q9UKQ2	.|.;ADA28_HUMAN	S|I	433;317;110|684	ENSP00000380770:G433S|ENSP00000265769:M684I	ENSP00000380770:G433S|ENSP00000265769:M684I	G|M	+|+	1|3	0|0	ADAM28|ADAM28	24263383|24263383	0.434000|0.434000	0.25570|0.25570	0.022000|0.022000	0.16811|0.16811	0.022000|0.022000	0.10575|0.10575	0.059000|0.059000	0.14322|0.14322	-0.185000|-0.185000	0.10550|0.10550	-0.661000|-0.661000	0.03856|0.03856	GGT|ATG	G|0.931;A|0.069	0.069	strong		0.488	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
RBM42	79171	hgsc.bcm.edu	37	19	36124822	36124822	+	Silent	SNP	C	C	A	rs147020112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36124822C>A	ENST00000262633.4	+	7	1023	c.918C>A	c.(916-918)cgC>cgA	p.R306R	RBM42_ENST00000589559.1_Silent_p.R277R|RBM42_ENST00000586618.1_Intron|RBM42_ENST00000588161.1_Silent_p.R276R|RBM42_ENST00000589871.1_Silent_p.R284R|RBM42_ENST00000360475.4_Silent_p.R277R|RBM42_ENST00000592202.1_Silent_p.R252R	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	306	Necessary for interaction with HNRNPK. {ECO:0000250}.|Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(7)|lung(9)|prostate(1)	21	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			AGGTCGTCCGCGGCCTCCTGC	0.731													C|||	79	0.0157748	0.0598	0.0	5008	,	,		14671	0.0		0.0	False		,,,				2504	0.0				p.R306R		Atlas-SNP	.											.	RBM42	40	.	0			c.C918A						PASS	.	C		157,4183		3,151,2016	7.0	9.0	8.0		918	-10.2	0.1	19	dbSNP_134	8	2,8482		0,2,4240	no	coding-synonymous	RBM42	NM_024321.3		3,153,6256	AA,AC,CC		0.0236,3.6175,1.2399		306/481	36124822	159,12665	2170	4242	6412	SO:0001819	synonymous_variant	79171	exon7			CGTCCGCGGCCTC	BC004204	CCDS12468.1	19q13.12	2013-02-12				ENSG00000126254		"""RNA binding motif (RRM) containing"""	28117	protein-coding gene	gene with protein product		613232				12477932	Standard	NM_024321		Approved	MGC10433	uc002oan.3	Q9BTD8		ENST00000262633.4:c.918C>A	19.37:g.36124822C>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_024321	O00320|Q8N5R7|Q9BU66	Silent	SNP	ENST00000262633.4	37	CCDS12468.1																																																																																			C|0.990;A|0.010	0.010	strong		0.731	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321	
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56702323	56702323	+	Missense_Mutation	SNP	C	C	T	rs4801296	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56702323C>T	ENST00000586855.2	-	4	935	c.622G>A	c.(622-624)Gta>Ata	p.V208I	ZSCAN5B_ENST00000358992.3_Missense_Mutation_p.V208I			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	208			V -> I (in dbSNP:rs4801296).		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)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TCACCTGTTACGTCAATACTC	0.502													C|||	2419	0.483027	0.739	0.4294	5008	,	,		19896	0.4067		0.3767	False		,,,				2504	0.363				p.V208I		Atlas-SNP	.											.	ZSCAN5B	160	.	0			c.G622A						PASS	.	C	ILE/VAL	3010,1396	458.4+/-352.0	1025,960,218	159.0	146.0	150.0		622	-2.6	0.0	19	dbSNP_111	150	3149,5451	655.7+/-401.3	569,2011,1720	no	missense	ZSCAN5B	NM_001080456.2	29	1594,2971,1938	TT,TC,CC		36.6163,31.6841,47.3551	benign	208/496	56702323	6159,6847	2203	4300	6503	SO:0001583	missense	342933	exon3			CTGTTACGTCAAT		CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"""-"", ""Zinc fingers, C2H2-type"""	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.622G>A	19.37:g.56702323C>T	ENSP00000466072:p.Val208Ile	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	302	300	0.993378	NM_001080456		Missense_Mutation	SNP	ENST00000586855.2	37	CCDS46203.1	1015	0.46474358974358976	352	0.7154471544715447	148	0.4088397790055249	225	0.39335664335664333	290	0.38258575197889183	T	1.338	-0.594838	0.03771	0.683159	0.366163	ENSG00000197213	ENST00000358992	T	0.05717	3.4	1.3	-2.6	0.06190	.	.	.	.	.	T	0.00012	0.0000	N	0.04043	-0.29	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16571	-1.0398	8	0.31617	T	0.26	.	4.4466	0.11600	0.0:0.4858:0.2045:0.3096	rs4801296;rs4801296	208	A6NJL1	ZSA5B_HUMAN	I	208	ENSP00000351883:V208I	ENSP00000351883:V208I	V	-	1	0	ZSCAN5B	61394135	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.563000	0.05943	-2.131000	0.00815	-1.028000	0.02416	GTA	C|0.531;T|0.469	0.469	strong		0.502	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456	
SLC35A5	55032	hgsc.bcm.edu	37	3	112292765	112292765	+	Silent	SNP	C	C	T	rs61732187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112292765C>T	ENST00000492406.1	+	5	673	c.390C>T	c.(388-390)agC>agT	p.S130S	SLC35A5_ENST00000460713.1_3'UTR	NM_017945.2	NP_060415.1	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5	130					nucleotide-sugar transport (GO:0015780)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)|sugar:proton symporter activity (GO:0005351)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|skin(1)	11						CAAATTTTAGCATTATAACAA	0.353													C|||	119	0.023762	0.0832	0.013	5008	,	,		18592	0.0		0.0	False		,,,				2504	0.0				p.S130S		Atlas-SNP	.											.	SLC35A5	40	.	0			c.C390T						PASS	.	C		278,4128	156.6+/-189.7	8,262,1933	191.0	205.0	200.0		390	5.9	1.0	3	dbSNP_129	200	0,8600		0,0,4300	no	coding-synonymous	SLC35A5	NM_017945.2		8,262,6233	TT,TC,CC		0.0,6.3096,2.1375		130/425	112292765	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	55032	exon5			TTTTAGCATTATA	AK000737	CCDS2967.1	3q13.13	2013-05-22			ENSG00000138459	ENSG00000138459		"""Solute carriers"""	20792	protein-coding gene	gene with protein product							Standard	NM_017945		Approved	FLJ20730	uc003dze.4	Q9BS91	OTTHUMG00000159263	ENST00000492406.1:c.390C>T	3.37:g.112292765C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	183	183	1	NM_017945	D3DN66|Q69YY6|Q6ZMD6|Q9NWM9	Silent	SNP	ENST00000492406.1	37	CCDS2967.1																																																																																			C|0.976;T|0.024	0.024	strong		0.353	SLC35A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354184.1	NM_017945	
DDX51	317781	hgsc.bcm.edu	37	12	132626425	132626425	+	Missense_Mutation	SNP	G	G	A	rs60927391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132626425G>A	ENST00000397333.3	-	6	1003	c.965C>T	c.(964-966)gCc>gTc	p.A322V	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	322	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		A -> V (in dbSNP:rs60927391). {ECO:0000269|PubMed:14702039}.		rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		CTGCTCCTTGGCCAGAGACTT	0.572													G|||	1433	0.286142	0.5446	0.2017	5008	,	,		18216	0.1786		0.1809	False		,,,				2504	0.2157				p.A322V		Atlas-SNP	.											.	DDX51	33	.	0			c.C965T						PASS	.	G	VAL/ALA	1871,2029		446,979,525	63.0	64.0	64.0		965	3.1	1.0	12	dbSNP_129	64	1520,6764		168,1184,2790	yes	missense	DDX51	NM_175066.3	64	614,2163,3315	AA,AG,GG		18.3486,47.9744,27.8316	benign	322/667	132626425	3391,8793	1950	4142	6092	SO:0001583	missense	317781	exon6			TCCTTGGCCAGAG	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"""DEAD-boxes"""	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.965C>T	12.37:g.132626425G>A	ENSP00000380495:p.Ala322Val	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	166	75	0.451807	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	37	CCDS41865.1	573	0.2623626373626374	258	0.524390243902439	68	0.1878453038674033	110	0.19230769230769232	137	0.18073878627968337	G	12.78	2.039785	0.35989	0.479744	0.183486	ENSG00000185163	ENST00000397333	T	0.17528	2.27	4.95	3.06	0.35304	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.247526	0.40144	N	0.001173	T	0.00012	0.0000	N	0.13198	0.31	0.26266	P	0.9785098	B	0.24186	0.099	B	0.31751	0.135	T	0.42882	-0.9425	9	0.19590	T	0.45	-15.3121	6.5455	0.22404	0.3132:0.0:0.6868:0.0	rs60927391;rs61729148	322	Q8N8A6	DDX51_HUMAN	V	322	ENSP00000380495:A322V	ENSP00000380495:A322V	A	-	2	0	DDX51	131192378	1.000000	0.71417	0.997000	0.53966	0.764000	0.43329	3.027000	0.49697	0.445000	0.26639	0.491000	0.48974	GCC	G|0.765;A|0.235	0.235	strong		0.572	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
LONRF3	79836	hgsc.bcm.edu	37	X	118148229	118148229	+	Silent	SNP	A	A	G	rs2278954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:118148229A>G	ENST00000371628.3	+	10	2065	c.2034A>G	c.(2032-2034)gcA>gcG	p.A678A	LONRF3_ENST00000472173.1_3'UTR|LONRF3_ENST00000422289.2_Silent_p.A422A|LONRF3_ENST00000304778.7_Silent_p.A637A	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	678	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						ATCAGCAAGCATCATTGTGGT	0.433													G|||	1746	0.462517	0.6021	0.2421	3775	,	,		17899	0.1359		0.2843	False		,,,				2504	0.3671				p.A678A		Atlas-SNP	.											.	LONRF3	138	.	0			c.A2034G						PASS	.	G	,	2781,1054		871,616,423,145,148	306.0	249.0	268.0		2034,1911	-6.8	0.0	X	dbSNP_100	268	2550,4178		359,1101,731,968,1141	no	coding-synonymous,coding-synonymous	LONRF3	NM_001031855.1,NM_024778.4	,	1230,1717,1154,1113,1289	GG,GA,G,AA,A		37.9013,27.4837,49.5314	,	678/760,637/719	118148229	5331,5232	2203	4300	6503	SO:0001819	synonymous_variant	79836	exon10			GCAAGCATCATTG	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"""RING-type (C3HC4) zinc fingers"""	21152	protein-coding gene	gene with protein product			"""ring finger protein 127"""	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.2034A>G	X.37:g.118148229A>G		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Silent	SNP	ENST00000371628.3	37	CCDS35374.1	673	0.405666063893912	200	0.6329113924050633	62	0.2108843537414966	52	0.09961685823754789	141	0.2288961038961039	G	7.787	0.710819	0.15239	0.725163	0.379013	ENSG00000175556	ENST00000439603	.	.	.	5.7	-6.8	0.01709	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999580202	.	.	.	.	.	.	T	0.28744	-1.0034	3	.	.	.	-63.1	2.3441	0.04267	0.5401:0.1472:0.1646:0.148	rs2278954;rs17326906;rs56528694;rs60466076;rs2278954	.	.	.	V	444	.	.	I	+	1	0	LONRF3	118032257	0.000000	0.05858	0.006000	0.13384	0.809000	0.45718	-3.583000	0.00423	-2.585000	0.00460	-0.871000	0.02989	ATC	0|0.014;G|0.475	0.475	strong		0.433	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778	
EXD3	54932	hgsc.bcm.edu	37	9	140247103	140247103	+	Missense_Mutation	SNP	C	C	T	rs115998217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140247103C>T	ENST00000340951.4	-	11	1201	c.1006G>A	c.(1006-1008)Gtg>Atg	p.V336M	EXD3_ENST00000342129.4_Missense_Mutation_p.V16M	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CGGAGTTCCACAGCCACCGCA	0.701													C|||	163	0.0325479	0.1142	0.0101	5008	,	,		8184	0.001		0.004	False		,,,				2504	0.0				p.V336M		Atlas-SNP	.											.	EXD3	86	.	0			c.G1006A						PASS	.	C	MET/VAL	259,3395		3,253,1571	5.0	7.0	6.0		1006	-0.7	0.0	9	dbSNP_132	6	35,7739		0,35,3852	yes	missense	EXD3	NM_017820.3	21	3,288,5423	TT,TC,CC		0.4502,7.0881,2.5726	benign	336/877	140247103	294,11134	1827	3887	5714	SO:0001583	missense	54932	exon11			GTTCCACAGCCAC		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.1006G>A	9.37:g.140247103C>T	ENSP00000340474:p.Val336Met	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	78	29	0.371795	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	84	0.038461538461538464	78	0.15853658536585366	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	10.88	1.476873	0.26511	0.070881	0.004502	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.64085	-0.08;0.68	3.69	-0.678	0.11353	.	0.954002	0.08598	N	0.921938	T	0.00210	0.0006	N	0.22421	0.69	0.80722	P	0.0	P;P	0.46327	0.876;0.831	B;B	0.41036	0.346;0.254	T	0.01848	-1.1261	9	0.54805	T	0.06	.	4.8317	0.13443	0.0:0.5455:0.1562:0.2983	.	16;336	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	M	16;336	ENSP00000343705:V16M;ENSP00000340474:V336M	ENSP00000340474:V336M	V	-	1	0	EXD3	139366924	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.999000	0.03697	-0.415000	0.07484	-0.494000	0.04653	GTG	C|0.960;T|0.040	0.040	strong		0.701	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
COL14A1	7373	hgsc.bcm.edu	37	8	121256150	121256150	+	Silent	SNP	T	T	C	rs2305603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:121256150T>C	ENST00000297848.3	+	20	2652	c.2382T>C	c.(2380-2382)ctT>ctC	p.L794L	COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000247781.3_Silent_p.L699L|COL14A1_ENST00000309791.4_Silent_p.L794L	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			ACAACCTCCTTCTGAAGCCTC	0.488													T|||	935	0.186701	0.1362	0.219	5008	,	,		18729	0.4067		0.0258	False		,,,				2504	0.1708				p.L794L		Atlas-SNP	.											.	COL14A1	292	.	0			c.T2382C						PASS	.	T		585,3821	257.4+/-261.8	41,503,1659	190.0	186.0	187.0		2382	-0.4	1.0	8	dbSNP_100	187	306,8294	110.6+/-171.0	3,300,3997	no	coding-synonymous	COL14A1	NM_021110.1		44,803,5656	CC,CT,TT		3.5581,13.2773,6.8507		794/1797	121256150	891,12115	2203	4300	6503	SO:0001819	synonymous_variant	7373	exon20			CCTCCTTCTGAAG		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.2382T>C	8.37:g.121256150T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_021110		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																			T|0.882;C|0.118	0.118	strong		0.488	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
FKBP11	51303	hgsc.bcm.edu	37	12	49315821	49315821	+	Silent	SNP	T	T	C	rs148302547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49315821T>C	ENST00000550765.1	-	6	950	c.552A>G	c.(550-552)aaA>aaG	p.K184K	FKBP11_ENST00000444214.2_Silent_p.K82K|AC073610.5_ENST00000537495.1_3'UTR|RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Intron	NM_016594.2	NP_057678.1	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11, 19 kDa	184					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			kidney(1)|large_intestine(3)|lung(1)	5						TTTTGGAGACTTTGGGTCTAT	0.403													T|||	8	0.00159744	0.0053	0.0014	5008	,	,		18104	0.0		0.0	False		,,,				2504	0.0				p.K184K		Atlas-SNP	.											FKBP11,colon,carcinoma,-1,1	FKBP11	12	1	0			c.A552G						PASS	.	T	,	15,4391	15.5+/-35.6	0,15,2188	90.0	91.0	91.0		246,552	4.7	1.0	12	dbSNP_134	91	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	FKBP11	NM_001143781.1,NM_016594.2	,	0,16,6487	CC,CT,TT		0.0116,0.3404,0.123	,	82/100,184/202	49315821	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	51303	exon6			GGAGACTTTGGGT	AF238079	CCDS8773.1, CCDS44870.1, CCDS44871.1	12q13.12	2008-08-04	2002-08-29			ENSG00000134285			18624	protein-coding gene	gene with protein product		610571	"""FK506 binding protein 11 (19 kDa)"""			12036304, 16596453	Standard	NM_016594		Approved	FKBP19	uc001rsp.3	Q9NYL4		ENST00000550765.1:c.552A>G	12.37:g.49315821T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_016594	B4DWB7	Silent	SNP	ENST00000550765.1	37	CCDS8773.1																																																																																			T|0.999;C|0.001	0.001	strong		0.403	FKBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408927.1	NM_016594	
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22960654	22960654	+	Missense_Mutation	SNP	C	C	T	rs10107826|rs374790272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22960654C>T	ENST00000356864.3	+	1	552	c.20C>T	c.(19-21)aCc>aTc	p.T7I	TNFRSF10C_ENST00000520607.1_Intron|TNFRSF10C_ENST00000540813.1_5'UTR|TNFRSF10C_ENST00000397703.2_Missense_Mutation_p.T47I	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	7					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)		ATCCCCAAGACCCTAAAGTTC	0.711													C|||	208	0.0415335	0.149	0.0101	5008	,	,		14783	0.0		0.004	False		,,,				2504	0.0				p.T7I		Atlas-SNP	.											.	TNFRSF10C	30	.	0			c.C20T						PASS	.	C	ILE/THR	443,3961	170.9+/-201.2	25,393,1784	79.0	59.0	66.0		20	0.6	0.0	8	dbSNP_119	66	12,8584	5.7+/-21.5	0,12,4286	yes	missense	TNFRSF10C	NM_003841.3	89	25,405,6070	TT,TC,CC		0.1396,10.059,3.5	probably-damaging	7/260	22960654	455,12545	2202	4298	6500	SO:0001583	missense	8794	exon1			CCAAGACCCTAAA	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.20C>T	8.37:g.22960654C>T	ENSP00000349324:p.Thr7Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	56	0.02564102564102564	50	0.1016260162601626	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	4.995	0.184796	0.09495	0.10059	0.001396	ENSG00000173535	ENST00000397703;ENST00000356864;ENST00000544885	T	0.62364	0.03	1.76	0.639	0.17747	.	2.630870	0.02547	U	0.095275	T	0.01627	0.0052	N	0.19112	0.55	0.52099	P	5.100000000002325E-5	B	0.21225	0.053	B	0.06405	0.002	T	0.08186	-1.0734	9	0.52906	T	0.07	.	4.4054	0.11407	0.0:0.717:0.0:0.283	rs10107826;rs10107826	7	O14798	TR10C_HUMAN	I	47;7;7	ENSP00000349324:T7I	ENSP00000349324:T7I	T	+	2	0	TNFRSF10C	23016599	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-0.737000	0.04877	-0.010000	0.14271	0.205000	0.17691	ACC	C|0.958;T|0.042	0.042	strong		0.711	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
PABPC1	26986	hgsc.bcm.edu	37	8	101727716	101727716	+	Missense_Mutation	SNP	C	C	T	rs201157005		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101727716C>T	ENST00000318607.5	-	4	1745	c.617G>A	c.(616-618)cGc>cAc	p.R206H	PABPC1_ENST00000519004.1_Missense_Mutation_p.R161H|PABPC1_ENST00000522387.1_Missense_Mutation_p.R174H|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	206	CSDE1-binding.|RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			ATCCTTAAGGCGCTCATCATC	0.353																																					p.R206H		Atlas-SNP	.											PABPC1,NS,carcinoma,-1,1	PABPC1	76	1	0			c.G617A						scavenged	.																																			SO:0001583	missense	26986	exon4			TTAAGGCGCTCAT	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.617G>A	8.37:g.101727716C>T	ENSP00000313007:p.Arg206His	Somatic	79	1	0.0126582		WXS	Illumina HiSeq	Phase_I	115	5	0.0434783	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	130|130	0.05952380952380952|0.05952380952380952	45|45	0.09146341463414634|0.09146341463414634	8|8	0.022099447513812154|0.022099447513812154	29|29	0.050699300699300696|0.050699300699300696	48|48	0.0633245382585752|0.0633245382585752	C|C	15.89|15.89	2.967520|2.967520	0.53507|0.53507	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519100|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|D;D;T	.|0.84370	.|-1.84;-1.84;2.38	5.03|5.03	5.03|5.03	0.67393|0.67393	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.56097	.|D	.|0.000024	T|T	0.14184|0.14184	0.0343|0.0343	N|N	0.25647|0.25647	0.755|0.755	0.44736|0.44736	D|D	0.997731|0.997731	.|B;B;B	.|0.24920	.|0.005;0.053;0.114	.|B;B;B	.|0.20384	.|0.008;0.029;0.026	T|T	0.56890|0.56890	-0.7904|-0.7904	5|10	.|0.49607	.|T	.|0.09	.|.	18.734|18.734	0.91748|0.91748	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|174;206;206	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	T|H	78|206;206;161;174	.|ENSP00000313007:R206H;ENSP00000429594:R161H;ENSP00000429395:R174H	.|ENSP00000313007:R206H	A|R	-|-	1|2	0|0	PABPC1|PABPC1	101796892|101796892	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.004000|6.004000	0.70709|0.70709	2.482000|2.482000	0.83794|0.83794	0.585000|0.585000	0.79938|0.79938	GCC|CGC	C|0.940;T|0.060	0.060	strong		0.353	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
LEPR	3953	hgsc.bcm.edu	37	1	66102257	66102257	+	Silent	SNP	G	G	A	rs1805096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:66102257G>A	ENST00000349533.6	+	20	3242	c.3057G>A	c.(3055-3057)ccG>ccA	p.P1019P	LEPR_ENST00000406510.3_Silent_p.P86P	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		AAAATTCTCCGTTGAAGGATT	0.413													A|||	2653	0.529752	0.4478	0.4841	5008	,	,		18263	0.869		0.3797	False		,,,				2504	0.4775				p.P1019P		Atlas-SNP	.											.	LEPR	284	.	0			c.G3057A						PASS	.	A		2073,2329		506,1061,634	66.0	72.0	70.0		3057	-11.9	0.0	1	dbSNP_89	70	3222,5370		624,1974,1698	no	coding-synonymous	LEPR	NM_002303.5		1130,3035,2332	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	37.5,47.0922,40.7496		1019/1166	66102257	5295,7699	2201	4296	6497	SO:0001819	synonymous_variant	3953	exon20			TTCTCCGTTGAAG	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.3057G>A	1.37:g.66102257G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	94	52	0.553191	NM_002303	Q6FHL5	Silent	SNP	ENST00000349533.6	37	CCDS631.1																																																																																			G|0.516;A|0.484	0.484	strong		0.413	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
TMC3	342125	hgsc.bcm.edu	37	15	81625028	81625028	+	Missense_Mutation	SNP	C	C	T	rs8031046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81625028C>T	ENST00000359440.5	-	22	3170	c.3035G>A	c.(3034-3036)aGa>aAa	p.R1012K	RP11-761I4.3_ENST00000559781.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.R1013K|RP11-761I4.3_ENST00000560851.1_RNA|RP11-761I4.3_ENST00000560973.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						TCGTGGCTTTCTGGGCACATA	0.582													T|||	836	0.166933	0.4728	0.062	5008	,	,		16882	0.0952		0.0517	False		,,,				2504	0.0204				p.R1012K		Atlas-SNP	.											.	TMC3	112	.	0			c.G3035A						PASS	.	T	LYS/ARG	1592,2362		345,902,730	35.0	40.0	39.0		3035	-9.0	0.0	15	dbSNP_116	39	440,7886		12,416,3735	yes	missense	TMC3	NM_001080532.1	26	357,1318,4465	TT,TC,CC		5.2847,40.263,16.5472	benign	1012/1101	81625028	2032,10248	1977	4163	6140	SO:0001583	missense	342125	exon22			GGCTTTCTGGGCA	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.3035G>A	15.37:g.81625028C>T	ENSP00000352413:p.Arg1012Lys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	168	93	0.553571	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	363	0.1662087912087912	240	0.4878048780487805	25	0.06906077348066299	61	0.10664335664335664	37	0.048812664907651716	T	4.161	0.028403	0.08054	0.40263	0.052847	ENSG00000188869	ENST00000359440	T	0.62232	0.04	5.42	-9.03	0.00737	.	0.406919	0.19362	N	0.116103	T	0.00012	0.0000	N	0.01742	-0.745	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31916	-0.9926	9	0.02654	T	1	-0.4035	21.2883	0.99950	0.0:0.656:0.0:0.344	rs8031046;rs52825478;rs59441739;rs8031046	1012	Q7Z5M5	TMC3_HUMAN	K	1012	ENSP00000352413:R1012K	ENSP00000352413:R1012K	R	-	2	0	TMC3	79412083	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.956000	0.03865	-2.591000	0.00456	-1.213000	0.01624	AGA	C|0.811;T|0.189	0.189	strong		0.582	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841	
FGD2	221472	hgsc.bcm.edu	37	6	36995222	36995222	+	Silent	SNP	G	G	A	rs2274587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36995222G>A	ENST00000274963.8	+	15	1794	c.1623G>A	c.(1621-1623)acG>acA	p.T541T		NM_173558.3	NP_775829.2	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	541					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						CCTCAGCCACGCCTGACCAGA	0.612													G|||	1139	0.227436	0.2035	0.2248	5008	,	,		19191	0.501		0.1054	False		,,,				2504	0.1053				p.T541T		Atlas-SNP	.											.	FGD2	65	.	0			c.G1623A						PASS	.	G		782,3624	315.8+/-294.3	78,626,1499	108.0	109.0	109.0		1623	-1.0	0.0	6	dbSNP_100	109	778,7822	185.0+/-232.9	36,706,3558	no	coding-synonymous	FGD2	NM_173558.3		114,1332,5057	AA,AG,GG		9.0465,17.7485,11.9945		541/656	36995222	1560,11446	2203	4300	6503	SO:0001819	synonymous_variant	221472	exon15			AGCCACGCCTGAC	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.1623G>A	6.37:g.36995222G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	170	94	0.552941	NM_173558	Q5T8I1|Q6P6A8|Q6ZNL5|Q8IZ32|Q8N868|Q9H7M2	Silent	SNP	ENST00000274963.8	37	CCDS4829.1																																																																																			G|0.824;A|0.175	0.175	strong		0.612	FGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040398.2	NM_173558	
CDK16	5127	hgsc.bcm.edu	37	X	47084037	47084037	+	Silent	SNP	A	A	G	rs5952422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47084037A>G	ENST00000357227.4	+	4	781	c.357A>G	c.(355-357)tcA>tcG	p.S119S	CDK16_ENST00000457458.2_Silent_p.S125S|CDK16_ENST00000276052.6_Silent_p.S193S|CDK16_ENST00000518022.1_Silent_p.S119S	NM_006201.4	NP_006192.1	Q00536	CDK16_HUMAN	cyclin-dependent kinase 16	119					exocytosis (GO:0006887)|growth hormone secretion (GO:0030252)|neuron projection development (GO:0031175)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|spermatogenesis (GO:0007283)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule cytoskeleton (GO:0015630)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)	11						AGCGCCTATCACTACCAGCTG	0.577													G|||	320	0.0847682	0.233	0.0173	3775	,	,		13696	0.0		0.0	False		,,,				2504	0.0				p.S193S		Atlas-SNP	.											.	CDK16	59	.	0			c.A579G						PASS	.	G	,,	962,2873		129,568,136,935,435	88.0	78.0	81.0		579,357,375	-3.8	0.2	X	dbSNP_114	81	13,6715		0,9,4,2419,1868	no	coding-synonymous,coding-synonymous,coding-synonymous	CDK16	NM_001170460.1,NM_006201.4,NM_033018.3	,,	129,577,140,3354,2303	GG,GA,G,AA,A		0.1932,25.0847,9.2303	,,	193/571,119/497,125/503	47084037	975,9588	2203	4300	6503	SO:0001819	synonymous_variant	5127	exon4			CCTATCACTACCA		CCDS14276.1, CCDS48101.1, CCDS55408.1	Xp11	2011-11-08	2009-12-16	2009-12-16	ENSG00000102225	ENSG00000102225		"""Cyclin-dependent kinases"""	8749	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase"""	311550	"""PCTAIRE protein kinase 1"""	PCTK1		1437147, 19884882	Standard	NM_033018		Approved	PCTAIRE, PCTAIRE1, PCTGAIRE, FLJ16665	uc011mll.2	Q00536	OTTHUMG00000021438	ENST00000357227.4:c.357A>G	X.37:g.47084037A>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	120	47	0.391667	NM_001170460	A8K280|B7Z7C8|J3KN74|J3KQP7	Silent	SNP	ENST00000357227.4	37	CCDS14276.1	139	0.08378541289933696	94	0.22926829268292684	3	0.00847457627118644	0	0.0	0	0.0	G	2.829	-0.243121	0.05906	0.250847	0.001932	ENSG00000102225	ENST00000523034	.	.	.	5.75	-3.78	0.04333	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999715269	.	.	.	.	.	.	T	0.26677	-1.0096	3	.	.	.	-6.5972	8.755	0.34639	0.4318:0.1598:0.4084:0.0	rs5952422;rs5952422	.	.	.	A	79	.	.	T	+	1	0	CDK16	46968981	0.000000	0.05858	0.170000	0.22879	0.433000	0.31745	-3.209000	0.00557	-0.772000	0.04602	-0.858000	0.03015	ACT	A|0.873;0|0.013	.	strong		0.577	CDK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056406.2	NM_006201	
FNDC1	84624	hgsc.bcm.edu	37	6	159672542	159672542	+	Silent	SNP	C	C	T	rs550443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159672542C>T	ENST00000297267.9	+	17	5243	c.5043C>T	c.(5041-5043)gcC>gcT	p.A1681A	FNDC1_ENST00000340366.6_Silent_p.A1618A	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1681	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		GGGACAAAGCCACCCCAGGAG	0.527													C|||	1100	0.219649	0.1899	0.1772	5008	,	,		22776	0.3353		0.1382	False		,,,				2504	0.2546				p.A1681A		Atlas-SNP	.											.	FNDC1	250	.	0			c.C5043T						PASS	.	C		735,3337		54,627,1355	51.0	49.0	50.0		5043	0.6	0.4	6	dbSNP_83	50	1091,7281		78,935,3173	no	coding-synonymous	FNDC1	NM_032532.2		132,1562,4528	TT,TC,CC		13.0315,18.0501,14.6737		1681/1895	159672542	1826,10618	2036	4186	6222	SO:0001819	synonymous_variant	84624	exon17			CAAAGCCACCCCA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.5043C>T	6.37:g.159672542C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	476	0.21794871794871795	115	0.23373983739837398	59	0.16298342541436464	202	0.3531468531468531	100	0.13192612137203166	C	9.638	1.138209	0.21123	0.180501	0.130315	ENSG00000164694	ENST00000329629	.	.	.	5.51	0.589	0.17452	.	.	.	.	.	T	0.14743	0.0356	.	.	.	0.09310	P	0.9999999799344	.	.	.	.	.	.	T	0.17623	-1.0363	3	.	.	.	-19.5874	4.8442	0.13505	0.1405:0.4502:0.0:0.4093	rs550443;rs3814447;rs59986709;rs550443	.	.	.	Y	1577	.	.	H	+	1	0	FNDC1	159592532	0.008000	0.16893	0.405000	0.26409	0.997000	0.91878	0.181000	0.16880	0.028000	0.15324	0.585000	0.79938	CAC	C|0.789;T|0.211	0.211	strong		0.527	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
C1QTNF9	338872	hgsc.bcm.edu	37	13	24890157	24890157	+	Missense_Mutation	SNP	C	C	T	rs1974332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:24890157C>T	ENST00000382071.2	+	2	101	c.16C>T	c.(16-18)Ctt>Ttt	p.L6F	C1QTNF9_ENST00000332018.4_Missense_Mutation_p.L6F|C1QTNF9-AS1_ENST00000449656.1_RNA|RP11-307N16.6_ENST00000382141.4_3'UTR			P0C862	C1T9A_HUMAN	C1q and tumor necrosis factor related protein 9	6			L -> F (in dbSNP:rs1974332).			collagen trimer (GO:0005581)|extracellular region (GO:0005576)				endometrium(1)|kidney(2)|lung(6)	9		all_cancers(29;3.55e-20)|all_epithelial(30;4.25e-17)|all_lung(29;1.04e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.00565)|Epithelial(112;0.027)|OV - Ovarian serous cystadenocarcinoma(117;0.115)|Lung(94;0.159)		GATCTGGTGGCTTCTGCTTGC	0.522													T|||	1322	0.263978	0.3585	0.17	5008	,	,		21412	0.2748		0.1372	False		,,,				2504	0.3221				p.L6F		Atlas-SNP	.											.	C1QTNF9	22	.	0			c.C16T						PASS	.	T	PHE/LEU	1458,2948	680.4+/-403.8	236,986,981	88.0	83.0	85.0		16	0.8	0.6	13	dbSNP_92	85	1358,7242	755.2+/-407.5	115,1128,3057	yes	missense	C1QTNF9	NM_178540.3	22	351,2114,4038	TT,TC,CC		15.7907,33.0912,21.6515	possibly-damaging	6/334	24890157	2816,10190	2203	4300	6503	SO:0001583	missense	338872	exon2			TGGTGGCTTCTGC	BC040438	CCDS9306.1	13q12.12	2010-08-18			ENSG00000240654	ENSG00000240654			28732	protein-coding gene	gene with protein product		614285				12975309, 18787108	Standard	NM_178540		Approved	MGC48915, CTRP9, C1QTNF9A, AQL1	uc001upj.3	P0C862	OTTHUMG00000016576	ENST00000382071.2:c.16C>T	13.37:g.24890157C>T	ENSP00000371503:p.Leu6Phe	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	247	113	0.45749	NM_178540	A2A3T6|Q0VGC5|Q5VX65|Q5VX66|Q8IUU4	Missense_Mutation	SNP	ENST00000382071.2	37	CCDS9306.1	527	0.2413003663003663	177	0.3597560975609756	69	0.19060773480662985	175	0.30594405594405594	106	0.13984168865435356	t	3.336	-0.135678	0.06711	0.330912	0.157907	ENSG00000240654	ENST00000382071;ENST00000332018;ENST00000382066	D;D	0.90788	-2.73;-2.73	3.85	0.772	0.18510	.	0.688766	0.12312	N	0.480104	T	0.00012	0.0000	L	0.48642	1.525	0.53688	P	2.5000000000052758E-5	B	0.21905	0.062	B	0.24006	0.05	T	0.04593	-1.0940	9	0.42905	T	0.14	.	4.5436	0.12071	0.1275:0.44:0.339:0.0936	rs1974332;rs57507910	6	P0C862	C1T9A_HUMAN	F	6	ENSP00000371503:L6F;ENSP00000333737:L6F	ENSP00000333737:L6F	L	+	1	0	C1QTNF9	23788157	0.428000	0.25522	0.626000	0.29213	0.183000	0.23260	-0.508000	0.06344	0.076000	0.16826	-1.265000	0.01443	CTT	C|0.782;T|0.218	0.218	strong		0.522	C1QTNF9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044177.1	NM_178540	
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69100200	69100200	+	Silent	SNP	A	A	G	rs4431295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:69100200A>G	ENST00000332644.5	-	5	611	c.450T>C	c.(448-450)ccT>ccC	p.P150P		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	150	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						TAATGGAAGCAGGAACTGCAT	0.328													G|||	141	0.028155	0.1006	0.0086	5008	,	,		17100	0.0		0.0	False		,,,				2504	0.002				p.P150P		Atlas-SNP	.											.	TMPRSS11B	66	.	0			c.T450C						PASS	.	G		351,4055	794.2+/-415.3	20,311,1872	108.0	104.0	106.0		450	-8.9	0.0	4	dbSNP_111	106	14,8586	818.7+/-406.8	0,14,4286	no	coding-synonymous	TMPRSS11B	NM_182502.3		20,325,6158	GG,GA,AA		0.1628,7.9664,2.8064		150/417	69100200	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	132724	exon5			GGAAGCAGGAACT	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.450T>C	4.37:g.69100200A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_182502	A8K4D9	Silent	SNP	ENST00000332644.5	37	CCDS3521.1																																																																																			A|0.970;G|0.030	0.030	strong		0.328	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502	
CMKLR1	1240	hgsc.bcm.edu	37	12	108686008	108686008	+	Silent	SNP	C	C	G	rs1057401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:108686008C>G	ENST00000312143.7	-	3	1095	c.732G>C	c.(730-732)gtG>gtC	p.V244V	CMKLR1_ENST00000412676.1_Silent_p.V244V|CMKLR1_ENST00000552995.1_Silent_p.V242V|CMKLR1_ENST00000397688.2_Silent_p.V242V|CMKLR1_ENST00000550402.1_Silent_p.V244V	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	244					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						GCAGTTTGCACACGATGGTGA	0.552													G|||	1855	0.370407	0.6513	0.3156	5008	,	,		21024	0.0119		0.4473	False		,,,				2504	0.32				p.V244V		Atlas-SNP	.											CMKLR1,NS,carcinoma,-2,1	CMKLR1	67	1	0			c.G732C						PASS	.		,,,	2563,1707		803,957,375	69.0	76.0	74.0		732,732,732,726	4.5	1.0	12	dbSNP_86	74	3973,4507		948,2077,1215	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CMKLR1	NM_001142343.1,NM_001142344.1,NM_001142345.1,NM_004072.2	,,,	1751,3034,1590	GG,GC,CC		46.8514,39.9766,48.7373	,,,	244/374,244/374,244/374,242/372	108686008	6536,6214	2135	4240	6375	SO:0001819	synonymous_variant	1240	exon3			TTTGCACACGATG	U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"""GPCR / Class A : Resolvin receptors"""	2121	protein-coding gene	gene with protein product	"""resolvin E1 receptor"", ""chemerin receptor"""	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.732G>C	12.37:g.108686008C>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Silent	SNP	ENST00000312143.7	37	CCDS44965.1																																																																																			C|0.627;G|0.373	0.373	strong		0.552	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1		
ETFB	2109	hgsc.bcm.edu	37	19	51857738	51857738	+	Intron	SNP	G	G	A	rs79338777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51857738G>A	ENST00000309244.4	-	2	149				CTD-2616J11.11_ENST00000600067.1_Intron|CTD-2616J11.9_ENST00000600974.1_RNA|ETFB_ENST00000354232.4_Missense_Mutation_p.P52L	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		tgtaggcagGGGCAGGTCACC	0.582													g|||	387	0.0772764	0.0439	0.0403	5008	,	,		16395	0.1181		0.0696	False		,,,				2504	0.1145				p.P52L		Atlas-SNP	.											.	ETFB	46	.	0			c.C155T						PASS	.	G	LEU/PRO,	196,4210	122.5+/-159.9	3,190,2010	79.0	72.0	74.0		155,	-5.5	0.0	19	dbSNP_131	74	591,8009	156.7+/-210.5	22,547,3731	yes	missense,intron	ETFB	NM_001014763.1,NM_001985.2	98,	25,737,5741	AA,AG,GG		6.8721,4.4485,6.0511	probably-damaging,	52/347,	51857738	787,12219	2203	4300	6503	SO:0001627	intron_variant	2109	exon1			GGCAGGGGCAGGT	X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379			3482	protein-coding gene	gene with protein product		130410					Standard	NM_001014763		Approved		uc002pwg.3	P38117		ENST00000309244.4:c.58-176C>T	19.37:g.51857738G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	31	0.356322	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	156	0.07142857142857142	23	0.046747967479674794	13	0.03591160220994475	69	0.12062937062937062	51	0.06728232189973615	g	12.18	1.860517	0.32884	0.044485	0.068721	ENSG00000105379	ENST00000354232	D	0.85955	-2.05	2.77	-5.53	0.02552	.	.	.	.	.	T	0.01905	0.0060	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.15954	-1.0419	6	.	.	.	.	1.673	0.02816	0.2749:0.125:0.4452:0.1549	.	52	P38117-2	.	L	52	ENSP00000346173:P52L	.	P	-	2	0	ETFB	56549550	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.733000	0.00803	-1.622000	0.01560	-0.290000	0.09829	CCC	G|0.937;A|0.063	0.063	strong		0.582	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
DCANP1	140947	hgsc.bcm.edu	37	5	134782443	134782443	+	Missense_Mutation	SNP	T	T	C	rs113429044	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134782443T>C	ENST00000503143.2	-	1	595	c.356A>G	c.(355-357)aAg>aGg	p.K119R	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		119						nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGGCCTGTCTTCCTTCTGCT	0.547													T|||	452	0.0902556	0.3033	0.0418	5008	,	,		19866	0.0		0.0179	False		,,,				2504	0.0041				p.K119R		Atlas-SNP	.											.	C5orf20	16	.	0			c.A356G						PASS	.	T	ARG/LYS	1160,3246	410.9+/-335.5	154,852,1197	112.0	120.0	117.0		356	0.2	0.0	5	dbSNP_132	117	119,8481	61.7+/-123.6	1,117,4182	yes	missense	C5orf20	NM_130848.2	26	155,969,5379	CC,CT,TT		1.3837,26.3277,9.8339	benign	119/245	134782443	1279,11727	2203	4300	6503	SO:0001583	missense	140947	exon1			CCTGTCTTCCTTC																												ENST00000503143.2:c.356A>G	5.37:g.134782443T>C	ENSP00000421871:p.Lys119Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	170	0.07783882783882784	139	0.28252032520325204	14	0.03867403314917127	0	0.0	17	0.022427440633245383	T	5.813	0.334340	0.11013	0.263277	0.013837	ENSG00000251380	ENST00000503143	T	0.37915	1.17	2.78	0.236	0.15471	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.16603	0.018	B	0.08055	0.003	T	0.36089	-0.9762	8	0.87932	D	0	.	3.1238	0.06400	0.5045:0.2511:0.0:0.2444	.	119	Q8TF63	DCNP1_HUMAN	R	119	ENSP00000421871:K119R	ENSP00000421871:K119R	K	-	2	0	C5orf20	134810342	0.000000	0.05858	0.013000	0.15412	0.047000	0.14425	-0.373000	0.07494	0.043000	0.15746	-0.669000	0.03829	AAG	T|0.902;C|0.098	0.098	strong		0.547	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
PMP2	5375	hgsc.bcm.edu	37	8	82357112	82357112	+	Silent	SNP	T	T	C	rs2229015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:82357112T>C	ENST00000256103.2	-	2	322	c.186A>G	c.(184-186)gaA>gaG	p.E62E	RP11-157I4.4_ENST00000524085.2_RNA|PMP2_ENST00000519260.1_Intron	NM_002677.3	NP_002668.1	P02689	MYP2_HUMAN	peripheral myelin protein 2	62					membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cholesterol binding (GO:0015485)|fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			Epithelial(68;0.186)			TGAAGGAGATTTCTGTATTTT	0.398													C|||	1760	0.351438	0.357	0.3285	5008	,	,		19779	0.748		0.1412	False		,,,				2504	0.1677				p.E62E		Atlas-SNP	.											.	PMP2	21	.	0			c.A186G						PASS	.	C		1469,2937	678.9+/-403.6	258,953,992	142.0	140.0	141.0		186	4.6	1.0	8	dbSNP_98	141	1449,7151	750.6+/-407.4	131,1187,2982	no	coding-synonymous	PMP2	NM_002677.3		389,2140,3974	CC,CT,TT		16.8488,33.3409,22.4358		62/133	82357112	2918,10088	2203	4300	6503	SO:0001819	synonymous_variant	5375	exon2			GGAGATTTCTGTA	X62167	CCDS6229.1	8q21.3-q22.1	2013-03-01			ENSG00000147588	ENSG00000147588		"""Fatty acid binding protein family"""	9117	protein-coding gene	gene with protein product		170715				1720307, 8288226	Standard	NM_002677		Approved	MP2, FABP8, M-FABP	uc003ycb.1	P02689	OTTHUMG00000164600	ENST00000256103.2:c.186A>G	8.37:g.82357112T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_002677	Q6FHL4	Silent	SNP	ENST00000256103.2	37	CCDS6229.1																																																																																			T|0.706;C|0.294	0.294	strong		0.398	PMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379365.1	NM_002677	
WDR93	56964	hgsc.bcm.edu	37	15	90274756	90274756	+	Silent	SNP	C	C	T	rs35502270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90274756C>T	ENST00000268130.7	+	12	1394	c.1293C>T	c.(1291-1293)tgC>tgT	p.C431C	WDR93_ENST00000444934.2_Silent_p.C148C|WDR93_ENST00000560294.1_Silent_p.C431C	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	431					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TGCTGGCCTGCGAGGATGGTG	0.617													C|||	134	0.0267572	0.0998	0.0029	5008	,	,		18890	0.0		0.0	False		,,,				2504	0.0				p.C431C		Atlas-SNP	.											.	WDR93	63	.	0			c.C1293T						PASS	.	C		363,4037	184.7+/-212.0	14,335,1851	208.0	181.0	190.0		1293	-4.6	0.9	15	dbSNP_126	190	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous	WDR93	NM_020212.1		14,338,6147	TT,TC,CC		0.0349,8.25,2.8158		431/687	90274756	366,12632	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon12			GGCCTGCGAGGAT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1293C>T	15.37:g.90274756C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			C|0.973;T|0.027	0.027	strong		0.617	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
SELP	6403	hgsc.bcm.edu	37	1	169566313	169566313	+	Missense_Mutation	SNP	C	C	T	rs6127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169566313C>T	ENST00000263686.6	-	11	1844	c.1807G>A	c.(1807-1809)Gac>Aac	p.D603N	SELP_ENST00000367791.2_Intron|SELP_ENST00000367786.2_Missense_Mutation_p.D541N|SELP_ENST00000458599.2_Intron|SELP_ENST00000367788.2_Missense_Mutation_p.D541N|SELP_ENST00000367794.2_Missense_Mutation_p.D541N|SELP_ENST00000367792.2_Intron|SELP_ENST00000367793.2_Missense_Mutation_p.D541N	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	199	0	0		WXS	Illumina HiSeq	Phase_I	190	190	1	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	
LAMA1	284217	hgsc.bcm.edu	37	18	6977844	6977844	+	Missense_Mutation	SNP	A	A	G	rs671871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6977844A>G	ENST00000389658.3	-	44	6320	c.6227T>C	c.(6226-6228)aTt>aCt	p.I2076T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2076	Domain II and I.		I -> T (in dbSNP:rs671871).		axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GTTGGCTTGAATTTCCACGTC	0.418													G|||	1372	0.273962	0.6309	0.2089	5008	,	,		20170	0.0893		0.172	False		,,,				2504	0.1329				p.I2076T		Atlas-SNP	.											.	LAMA1	458	.	0			c.T6227C						PASS	.	G	THR/ILE	2401,2005	560.5+/-380.5	669,1063,471	60.0	58.0	58.0		6227	2.2	0.9	18	dbSNP_83	58	1522,7078	746.3+/-407.3	130,1262,2908	yes	missense	LAMA1	NM_005559.3	89	799,2325,3379	GG,GA,AA		17.6977,45.5061,30.163	benign	2076/3076	6977844	3923,9083	2203	4300	6503	SO:0001583	missense	284217	exon44			GCTTGAATTTCCA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6227T>C	18.37:g.6977844A>G	ENSP00000374309:p.Ile2076Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	553	0.2532051282051282	294	0.5975609756097561	71	0.19613259668508287	59	0.10314685314685315	129	0.17018469656992086	G	5.574	0.290674	0.10567	0.544939	0.176977	ENSG00000101680	ENST00000389658	T	0.41400	1.0	5.1	2.15	0.27550	Laminin II (1);	0.565454	0.17247	N	0.181313	T	0.00012	0.0000	N	0.00926	-1.1	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.42849	-0.9427	9	0.15952	T	0.53	.	5.0817	0.14661	0.3013:0.0:0.5527:0.1461	rs671871;rs56554268;rs58305327;rs671871	2076	P25391	LAMA1_HUMAN	T	2076	ENSP00000374309:I2076T	ENSP00000374309:I2076T	I	-	2	0	LAMA1	6967844	0.989000	0.36119	0.949000	0.38748	0.939000	0.58152	1.200000	0.32247	0.209000	0.20645	-0.119000	0.15052	ATT	A|0.717;G|0.283	0.283	strong		0.418	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
REEP6	92840	hgsc.bcm.edu	37	19	1495327	1495327	+	Silent	SNP	C	C	T	rs79574672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1495327C>T	ENST00000233596.3	+	2	254	c.150C>T	c.(148-150)ttC>ttT	p.F50F		NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6	50					regulation of intracellular transport (GO:0032386)	apical part of cell (GO:0045177)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				lung(1)|ovary(1)	2		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATCTGCTGTTCGGCTACGGAG	0.657													C|||	120	0.0239617	0.09	0.0014	5008	,	,		18573	0.0		0.0	False		,,,				2504	0.0				p.F50F		Atlas-SNP	.											REEP6_ENST00000395484,NS,carcinoma,-2,1	REEP6	21	1	0			c.C150T						PASS	.	C		322,4080	171.2+/-201.5	7,308,1886	114.0	100.0	105.0		150	1.9	1.0	19	dbSNP_131	105	0,8598		0,0,4299	no	coding-synonymous	REEP6	NM_138393.1		7,308,6185	TT,TC,CC		0.0,7.3149,2.4769		50/185	1495327	322,12678	2201	4299	6500	SO:0001819	synonymous_variant	92840	exon2			GCTGTTCGGCTAC	BC008201	CCDS12070.1	19p13.3	2012-12-20	2006-02-08	2006-02-07	ENSG00000115255	ENSG00000115255		"""Receptor accessory proteins"""	30078	protein-coding gene	gene with protein product	"""polyposis locus protein 1-like 1"", ""deleted in polyposis 1-like 1"""	609346	"""chromosome 19 open reading frame 32"""	C19orf32		16271481, 15550249	Standard	NM_138393		Approved	DP1L1, FLJ25383	uc002ltc.3	Q96HR9	OTTHUMG00000180072	ENST00000233596.3:c.150C>T	19.37:g.1495327C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	182	85	0.467033	NM_138393	B2RE01|D6W5Z0|Q96LM0	Silent	SNP	ENST00000233596.3	37	CCDS12070.1	51	0.023351648351648352	51	0.10365853658536585	0	0.0	0	0.0	0	0.0	C	12.63	1.996371	0.35226	0.073149	0.0	ENSG00000115255	ENST00000395484	.	.	.	4.61	1.93	0.25924	.	.	.	.	.	T	0.03783	0.0107	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.11299	-1.0593	5	0.87932	D	0	-9.0609	8.2387	0.31645	0.0:0.6717:0.0:0.3283	.	.	.	.	W	118	.	ENSP00000378865:R118W	R	+	1	2	REEP6	1446327	0.890000	0.30428	0.982000	0.44146	0.017000	0.09413	-0.058000	0.11750	0.846000	0.35142	-0.354000	0.07668	CGG	C|0.974;T|0.026	0.026	strong		0.657	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393	
CD83	9308	hgsc.bcm.edu	37	6	14135394	14135394	+	Missense_Mutation	SNP	G	G	A	rs2230193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:14135394G>A	ENST00000379153.3	+	5	716	c.545G>A	c.(544-546)cGa>cAa	p.R182Q		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	182			R -> Q (in dbSNP:rs2230193).		defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				GGCATGGAACGAGCTTTTCTC	0.403													.|||	74	0.0147764	0.0545	0.0014	5008	,	,		21026	0.0		0.0	False		,,,				2504	0.001				p.R182Q		Atlas-SNP	.											.	CD83	23	.	0			c.G545A						PASS	.	G	GLN/ARG,GLN/ARG	202,4204	126.1+/-163.2	4,194,2005	103.0	105.0	104.0		542,545	-4.0	0.0	6	dbSNP_98	104	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	CD83	NM_001040280.1,NM_004233.3	43,43	4,200,6299	AA,AG,GG		0.0698,4.5847,1.5993	benign,benign	181/205,182/206	14135394	208,12798	2203	4300	6503	SO:0001583	missense	9308	exon5			TGGAACGAGCTTT	Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1703	protein-coding gene	gene with protein product		604534	"""CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)"", ""CD83 molecule """			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.545G>A	6.37:g.14135394G>A	ENSP00000368450:p.Arg182Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_004233	Q5THX9	Missense_Mutation	SNP	ENST00000379153.3	37	CCDS4532.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	9.394	1.076332	0.20227	0.045847	6.98E-4	ENSG00000112149	ENST00000379153	T	0.48201	0.82	5.0	-3.99	0.04069	.	1.449440	0.04161	N	0.322989	T	0.09862	0.0242	N	0.17082	0.46	0.09310	N	1	B	0.21147	0.052	B	0.10450	0.005	T	0.10200	-1.0640	10	0.25106	T	0.35	-23.8615	5.7782	0.18292	0.4997:0.2613:0.239:0.0	rs2230193;rs16874698;rs52804483;rs16874698	182	Q01151	CD83_HUMAN	Q	182	ENSP00000368450:R182Q	ENSP00000368450:R182Q	R	+	2	0	CD83	14243373	0.210000	0.23517	0.017000	0.16124	0.481000	0.33189	0.050000	0.14120	-0.988000	0.03489	-0.150000	0.13652	CGA	G|0.982;A|0.018	0.018	strong		0.403	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1		
CPEB3	22849	hgsc.bcm.edu	37	10	93999850	93999850	+	Silent	SNP	A	A	G	rs3824734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:93999850A>G	ENST00000265997.4	-	2	430	c.258T>C	c.(256-258)ccT>ccC	p.P86P	CPEB3_ENST00000412050.4_Silent_p.P86P	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	86	Pro-rich.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|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)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				GCTGCTGAGGAGGCTGATGGA	0.721													G|||	3298	0.658546	0.9501	0.745	5008	,	,		9820	0.499		0.6173	False		,,,				2504	0.41				p.P86P		Atlas-SNP	.											.	CPEB3	43	.	0			c.T258C						PASS	.	G	,	3896,456		1755,386,35	13.0	15.0	14.0		258,258	-0.1	1.0	10	dbSNP_107	14	5207,3285		1622,1963,661	no	coding-synonymous,coding-synonymous	CPEB3	NM_001178137.1,NM_014912.4	,	3377,2349,696	GG,GA,AA		38.6835,10.4779,29.1264	,	86/685,86/699	93999850	9103,3741	2176	4246	6422	SO:0001819	synonymous_variant	22849	exon2			CTGAGGAGGCTGA	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"""RNA binding motif (RRM) containing"""	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.258T>C	10.37:g.93999850A>G		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Silent	SNP	ENST00000265997.4	37	CCDS31246.1																																																																																			A|0.307;G|0.693	0.693	strong		0.721	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912	
SGK223	157285	hgsc.bcm.edu	37	8	8176051	8176051	+	Silent	SNP	G	G	A	rs114220337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8176051G>A	ENST00000520004.1	-	6	4098	c.3834C>T	c.(3832-3834)taC>taT	p.Y1278Y	SGK223_ENST00000330777.4_Silent_p.Y1278Y			Q86YV5	SG223_HUMAN		1282	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CCTCCTGCCGGTAGTCTCTCT	0.647													G|||	123	0.0245607	0.0885	0.0072	5008	,	,		10988	0.0		0.001	False		,,,				2504	0.0				p.Y1278Y	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											SgK223,caecum,carcinoma,0,2	.	.	2	0			c.C3834T						PASS	.	G		299,3693		13,273,1710	16.0	21.0	19.0		3834	2.7	1.0	8	dbSNP_132	19	0,8286		0,0,4143	no	coding-synonymous	SGK223	NM_001080826.1		13,273,5853	AA,AG,GG		0.0,7.49,2.4353		1278/1403	8176051	299,11979	1996	4143	6139	SO:0001819	synonymous_variant	0	exon5			CTGCCGGTAGTCT																												ENST00000520004.1:c.3834C>T	8.37:g.8176051G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	44	27	0.613636	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			G|0.980;A|0.020	0.020	strong		0.647	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
PABPC1	26986	hgsc.bcm.edu	37	8	101718968	101718968	+	Missense_Mutation	SNP	C	C	T	rs62513922		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101718968C>T	ENST00000318607.5	-	11	2641	c.1513G>A	c.(1513-1515)Gtc>Atc	p.V505I	PABPC1_ENST00000519004.1_Missense_Mutation_p.V460I|PABPC1_ENST00000522387.1_Missense_Mutation_p.V473I|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_Intron	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	505					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			ACGGTGCGGACAGCAGGAGTA	0.443																																					p.V505I		Atlas-SNP	.											.	PABPC1	76	.	0			c.G1513A						PASS	.						60.0	56.0	58.0					8																	101718968		2203	4300	6503	SO:0001583	missense	26986	exon11			TGCGGACAGCAGG	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.1513G>A	8.37:g.101718968C>T	ENSP00000313007:p.Val505Ile	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	214	73	0.341121	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.873827	0.91664	.	.	ENSG00000070756	ENST00000318607;ENST00000519004;ENST00000522387;ENST00000517990;ENST00000522658	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95	5.4	5.4	0.78164	Polyadenylate-binding protein/Hyperplastic disc protein (1);	0.000000	0.52532	D	0.000070	T	0.44159	0.1280	M	0.63843	1.955	0.54753	D	0.999987	B;B;B	0.10296	0.001;0.001;0.003	B;B;B	0.12837	0.008;0.008;0.008	T	0.30534	-0.9975	10	0.22109	T	0.4	.	19.5279	0.95213	0.0:1.0:0.0:0.0	rs62513922	473;505;505	E7ERJ7;B3KT93;P11940	.;.;PABP1_HUMAN	I	505;460;473;14;52	ENSP00000313007:V505I;ENSP00000429594:V460I;ENSP00000429395:V473I;ENSP00000428030:V14I;ENSP00000428840:V52I	ENSP00000313007:V505I	V	-	1	0	PABPC1	101788144	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.233000	0.78125	2.706000	0.92434	0.655000	0.94253	GTC	.	.	weak		0.443	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
EPB41L4B	54566	hgsc.bcm.edu	37	9	112017883	112017883	+	Silent	SNP	A	A	G	rs73529389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:112017883A>G	ENST00000374566.3	-	11	1594	c.1077T>C	c.(1075-1077)gtT>gtC	p.V359V	EPB41L4B_ENST00000374557.4_Silent_p.V359V	NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	359	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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						CGTGGTGCTCAACTGCACACT	0.532													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		20496	0.0		0.0	False		,,,				2504	0.0				p.V359V		Atlas-SNP	.											.	EPB41L4B	111	.	0			c.T1077C						PASS	.	G	,	79,3947		0,79,1934	131.0	125.0	127.0		1077,1077	-11.6	0.0	9	dbSNP_130	127	0,8322		0,0,4161	no	coding-synonymous,coding-synonymous	EPB41L4B	NM_018424.2,NM_019114.3	,	0,79,6095	GG,GA,AA		0.0,1.9622,0.6398	,	359/519,359/901	112017883	79,12269	2013	4161	6174	SO:0001819	synonymous_variant	54566	exon11			GTGCTCAACTGCA	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.1077T>C	9.37:g.112017883A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	116	34	0.293103	NM_019114	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Silent	SNP	ENST00000374566.3	37	CCDS43859.1																																																																																			A|0.997;G|0.003	0.003	strong		0.532	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424	
COL1A2	1278	hgsc.bcm.edu	37	7	94057007	94057007	+	Silent	SNP	C	C	T	rs34691365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:94057007C>T	ENST00000297268.6	+	49	3807	c.3336C>T	c.(3334-3336)taC>taT	p.Y1112Y		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1112					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)	ACTTTGGTTACGATGGAGACT	0.547										HNSCC(75;0.22)			C|||	27	0.00539137	0.0197	0.0	5008	,	,		18009	0.0		0.001	False		,,,				2504	0.0				p.Y1112Y		Atlas-SNP	.											.	COL1A2	240	.	0			c.C3336T						PASS	.	C		58,4348	56.2+/-92.4	1,56,2146	96.0	97.0	97.0		3336	-4.7	0.1	7	dbSNP_126	97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL1A2	NM_000089.3		1,57,6445	TT,TC,CC		0.0116,1.3164,0.4536		1112/1367	94057007	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	1278	exon49			TGGTTACGATGGA	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.3336C>T	7.37:g.94057007C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	132	67	0.507576	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																																																																																			C|0.995;T|0.005	0.005	strong		0.547	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
TLR10	81793	hgsc.bcm.edu	37	4	38776491	38776491	+	Missense_Mutation	SNP	T	T	G	rs11096957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38776491T>G	ENST00000308973.4	-	4	1326	c.721A>C	c.(721-723)Aat>Cat	p.N241H	TLR10_ENST00000506111.1_Missense_Mutation_p.N241H|TLR10_ENST00000361424.2_Missense_Mutation_p.N241H|TLR10_ENST00000508334.1_Missense_Mutation_p.N241H|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	241			N -> H (in dbSNP:rs11096957). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						GTCTTAGCATTTTCTAAACTA	0.328													T|||	2504	0.5	0.5492	0.4179	5008	,	,		21745	0.5546		0.3976	False		,,,				2504	0.5409				p.N241H		Atlas-SNP	.											.	TLR10	87	.	0			c.A721C	GRCh37	CM057765	TLR10	M	rs11096957	PASS	.	T	HIS/ASN,HIS/ASN,HIS/ASN,HIS/ASN,HIS/ASN	2231,2175	586.8+/-386.5	551,1129,523	60.0	59.0	59.0		721,721,721,679,721	4.9	0.4	4	dbSNP_120	59	2951,5649	456.0+/-363.9	524,1903,1873	yes	missense,missense,missense,missense,missense	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	68,68,68,68,68	1075,3032,2396	GG,GT,TT		34.314,49.3645,39.8431	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	241/812,241/812,241/812,227/798,241/812	38776491	5182,7824	2203	4300	6503	SO:0001583	missense	81793	exon2			TAGCATTTTCTAA	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.721A>C	4.37:g.38776491T>G	ENSP00000308925:p.Asn241His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	CCDS3445.1	1057	0.483974358974359	271	0.5508130081300813	150	0.4143646408839779	353	0.6171328671328671	283	0.3733509234828496	T	9.059	0.993939	0.19043	0.506355	0.34314	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73	4.91	4.91	0.64330	.	0.121673	0.34291	N	0.004086	T	0.00012	0.0000	M	0.74881	2.28	0.80722	P	0.0	P	0.45672	0.864	P	0.51415	0.669	T	0.46965	-0.9153	9	0.66056	D	0.02	.	14.5438	0.68015	0.0:0.0:0.0:1.0	rs11096957;rs58322425;rs11096957	241	Q9BXR5	TLR10_HUMAN	H	241	ENSP00000308925:N241H;ENSP00000421483:N241H;ENSP00000354459:N241H;ENSP00000424923:N241H	ENSP00000308925:N241H	N	-	1	0	TLR10	38452886	0.010000	0.17322	0.431000	0.26735	0.145000	0.21501	0.982000	0.29539	1.841000	0.53522	0.533000	0.62120	AAT	T|0.541;G|0.459	0.459	strong		0.328	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
AHNAK	79026	hgsc.bcm.edu	37	11	62295149	62295149	+	Missense_Mutation	SNP	T	T	G	rs61524789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62295149T>G	ENST00000378024.4	-	5	7014	c.6740A>C	c.(6739-6741)aAa>aCa	p.K2247T	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2247			K -> T (in dbSNP:rs61524789).		protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CTTGGGCATTTTCATCTTAGG	0.522													T|||	148	0.0295527	0.1051	0.0101	5008	,	,		20293	0.0		0.002	False		,,,				2504	0.0				p.K2247T		Atlas-SNP	.											.	AHNAK	532	.	0			c.A6740C						PASS	.	T	THR/LYS,	378,4026	192.6+/-218.0	16,346,1840	305.0	305.0	305.0		6740,	3.4	1.0	11	dbSNP_129	305	3,8595	2.2+/-6.3	0,3,4296	no	missense,intron	AHNAK	NM_001620.1,NM_024060.2	78,	16,349,6136	GG,GT,TT		0.0349,8.5831,2.9303	probably-damaging,	2247/5891,	62295149	381,12621	2202	4299	6501	SO:0001583	missense	79026	exon5			GGCATTTTCATCT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.6740A>C	11.37:g.62295149T>G	ENSP00000367263:p.Lys2247Thr	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	274	131	0.478102	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	73	0.033424908424908424	68	0.13821138211382114	3	0.008287292817679558	0	0.0	2	0.002638522427440633	T	16.14	3.038892	0.55003	0.085831	3.49E-4	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.12147	2.71	3.38	3.38	0.38709	.	0.000000	0.39083	U	0.001465	T	0.00440	0.0014	H	0.95470	3.675	0.44660	D	0.997647	D	0.69078	0.997	D	0.77557	0.99	T	0.01743	-1.1283	10	0.62326	D	0.03	.	12.0108	0.53286	0.0:0.0:0.0:1.0	rs61524789	2247	Q09666	AHNK_HUMAN	T	336;2247	ENSP00000367263:K2247T	ENSP00000244934:K336T	K	-	2	0	AHNAK	62051725	1.000000	0.71417	0.997000	0.53966	0.777000	0.43975	5.886000	0.69743	1.546000	0.49388	0.242000	0.17961	AAA	T|0.965;G|0.035	0.035	strong		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
FKBPL	63943	hgsc.bcm.edu	37	6	32096528	32096528	+	Silent	SNP	G	G	A	rs61747172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32096528G>A	ENST00000375156.3	-	2	1300	c.1030C>T	c.(1030-1032)Ctg>Ttg	p.L344L	ATF6B_ENST00000375201.4_5'Flank|ATF6B_ENST00000375203.3_5'Flank|ATF6B_ENST00000468502.1_5'Flank	NM_022110.3	NP_071393.2	Q9UIM3	FKBPL_HUMAN	FK506 binding protein like	344					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)|response to radiation (GO:0009314)	endoplasmic reticulum membrane (GO:0005789)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)										ATCTTGCGCAGACCCTGAGCC	0.537													G|||	10	0.00199681	0.0068	0.0014	5008	,	,		19239	0.0		0.0	False		,,,				2504	0.0				p.L344L		Atlas-SNP	.											.	FKBPL	25	.	0			c.C1030T						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	191.0	203.0	199.0		1030	3.1	0.9	6	dbSNP_129	199	0,8600		0,0,4300	no	coding-synonymous	FKBPL	NM_022110.3		0,14,6489	AA,AG,GG		0.0,0.3177,0.1076		344/350	32096528	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	63943	exon2			TGCGCAGACCCTG	AF139374	CCDS4738.1	6p21.3	2013-12-13	2001-11-28		ENSG00000204315	ENSG00000204315		"""Tetratricopeptide (TTC) repeat domain containing"""	13949	protein-coding gene	gene with protein product	"""WAF-1/CIP1 stabilizing protein 39"""		"""FK506-binding protein like"""			9056895	Standard	NM_022110		Approved	DIR1, NG7, WISp39	uc003nzr.3	Q9UIM3	OTTHUMG00000031129	ENST00000375156.3:c.1030C>T	6.37:g.32096528G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	160	83	0.51875	NM_022110	A8K5V3|B0UYX8|Q9H5G3	Silent	SNP	ENST00000375156.3	37	CCDS4738.1																																																																																			G|0.998;A|0.002	0.002	strong		0.537	FKBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076221.2		
C2CD2	25966	hgsc.bcm.edu	37	21	43327856	43327856	+	Silent	SNP	A	A	G	rs3746906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43327856A>G	ENST00000380486.3	-	9	1297	c.1056T>C	c.(1054-1056)ttT>ttC	p.F352F	C2CD2_ENST00000329623.7_Silent_p.F197F	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	352						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						GCTGCTTCTTAAATAAGTCCA	0.622													A|||	3042	0.607428	0.6248	0.5159	5008	,	,		17172	0.5923		0.6491	False		,,,				2504	0.6217				p.F352F		Atlas-SNP	.											.	C2CD2	47	.	0			c.T1056C						PASS	.	A	,	2707,1699	639.3+/-397.1	838,1031,334	34.0	38.0	37.0		1056,591	-0.9	0.9	21	dbSNP_107	37	5543,3057	645.7+/-400.2	1784,1975,541	no	coding-synonymous,coding-synonymous	C2CD2	NM_015500.1,NM_199050.2	,	2622,3006,875	GG,GA,AA		35.5465,38.5611,36.5677	,	352/697,197/542	43327856	8250,4756	2203	4300	6503	SO:0001819	synonymous_variant	25966	exon9			CTTCTTAAATAAG	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"""TMEM24-like"""		"""chromosome 21 open reading frame 25"""	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1056T>C	21.37:g.43327856A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Silent	SNP	ENST00000380486.3	37	CCDS42933.1																																																																																			A|0.367;G|0.633	0.633	strong		0.622	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
ST3GAL1	6482	hgsc.bcm.edu	37	8	134478178	134478178	+	Silent	SNP	A	A	G	rs112787936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134478178A>G	ENST00000319914.5	-	5	1489	c.462T>C	c.(460-462)tcT>tcC	p.S154S	ST3GAL1_ENST00000399640.2_Silent_p.S154S|ST3GAL1_ENST00000521180.1_Silent_p.S154S|ST3GAL1_ENST00000522652.1_Silent_p.S154S			Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	154					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein phosphorylation (GO:0006468)|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)			endometrium(3)|large_intestine(2)|lung(11)|prostate(1)	17	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			GCCCATAAGAAGACTCCCTCA	0.622													A|||	75	0.014976	0.0552	0.0029	5008	,	,		18246	0.0		0.0	False		,,,				2504	0.0				p.S154S		Atlas-SNP	.											.	ST3GAL1	39	.	0			c.T462C						PASS	.	A	,	201,4205	123.7+/-161.0	5,191,2007	94.0	93.0	93.0		462,462	1.8	0.3	8	dbSNP_132	93	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ST3GAL1	NM_003033.3,NM_173344.2	,	5,193,6305	GG,GA,AA		0.0233,4.562,1.5608	,	154/341,154/341	134478178	203,12803	2203	4300	6503	SO:0001819	synonymous_variant	6482	exon6			ATAAGAAGACTCC	L29555	CCDS6373.1	8q24.22	2013-03-01	2003-01-14	2005-02-07	ENSG00000008513	ENSG00000008513	2.4.99.4	"""Sialyltransferases"""	10862	protein-coding gene	gene with protein product	"""ST3Gal I"""	607187	"""sialyltransferase 4A (beta-galactosidase alpha-2,3-sialytransferase)"""	SIAT4A		10504389, 7655169	Standard	NM_003033		Approved	ST3O, SIATFL, ST3GalA.1	uc003yuk.2	Q11201	OTTHUMG00000164534	ENST00000319914.5:c.462T>C	8.37:g.134478178A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	160	82	0.5125	NM_173344	O60677|Q9UN51	Silent	SNP	ENST00000319914.5	37	CCDS6373.1																																																																																			A|0.984;G|0.016	0.016	strong		0.622	ST3GAL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379132.1	NM_003033	
NUP188	23511	hgsc.bcm.edu	37	9	131755891	131755891	+	Silent	SNP	C	C	T	rs17485583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131755891C>T	ENST00000372577.2	+	27	2956	c.2935C>T	c.(2935-2937)Ctg>Ttg	p.L979L		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	979					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						GTGCCCACCCCTGCTGCATCG	0.562													C|||	169	0.033746	0.1203	0.0115	5008	,	,		20683	0.0		0.002	False		,,,				2504	0.0				p.L979L		Atlas-SNP	.											.	NUP188	140	.	0			c.C2935T						PASS	.	C		452,3954	218.1+/-236.3	17,418,1768	169.0	137.0	148.0		2935	5.6	1.0	9	dbSNP_123	148	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	NUP188	NM_015354.1		17,424,6062	TT,TC,CC		0.0698,10.2587,3.5215		979/1750	131755891	458,12548	2203	4300	6503	SO:0001819	synonymous_variant	23511	exon27			CCACCCCTGCTGC	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.2935C>T	9.37:g.131755891C>T		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	218	140	0.642202	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			C|0.962;T|0.038	0.038	strong		0.562	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
ESPNL	339768	hgsc.bcm.edu	37	2	239010690	239010690	+	Silent	SNP	C	C	A	rs34878344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239010690C>A	ENST00000343063.3	+	2	666	c.403C>A	c.(403-405)Cgg>Agg	p.R135R	ESPNL_ENST00000409169.1_Silent_p.R135R	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	135										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)		GCTAGAGACCCGGGAGGGAGC	0.697													C|||	677	0.135184	0.0469	0.1744	5008	,	,		13903	0.0298		0.1581	False		,,,				2504	0.3119				p.R135R		Atlas-SNP	.											.	ESPNL	63	.	0			c.C403A						PASS	.	C		323,4055		19,285,1885	11.0	14.0	13.0		403	3.7	0.3	2	dbSNP_126	13	1275,7291		87,1101,3095	no	coding-synonymous	ESPNL	NM_194312.2		106,1386,4980	AA,AC,CC		14.8844,7.3778,12.3455		135/1006	239010690	1598,11346	2189	4283	6472	SO:0001819	synonymous_variant	339768	exon2			GAGACCCGGGAGG	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.403C>A	2.37:g.239010690C>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	74	46	0.621622	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			C|0.882;A|0.118	0.118	strong		0.697	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
PTX4	390667	hgsc.bcm.edu	37	16	1537874	1537874	+	Missense_Mutation	SNP	G	G	A	rs7202502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1537874G>A	ENST00000447419.2	-	2	264	c.239C>T	c.(238-240)gCg>gTg	p.A80V	PTX4_ENST00000440447.2_Missense_Mutation_p.A80V|PTX4_ENST00000293922.1_Missense_Mutation_p.A75V			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	86	0	0		WXS	Illumina HiSeq	Phase_I	99	37	0.373737	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	
GRIK1	2897	hgsc.bcm.edu	37	21	31062070	31062070	+	Silent	SNP	T	T	G	rs363538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31062070T>G	ENST00000399907.1	-	3	933	c.522A>C	c.(520-522)acA>acC	p.T174T	GRIK1_ENST00000399914.1_Silent_p.T174T|GRIK1_ENST00000399913.1_Silent_p.T174T|GRIK1_ENST00000399909.1_Silent_p.T174T|GRIK1_ENST00000309434.7_Silent_p.T174T|GRIK1_ENST00000535441.1_Silent_p.T174T|GRIK1_ENST00000472429.1_5'UTR|GRIK1_ENST00000389125.3_Silent_p.T174T|GRIK1_ENST00000389124.2_Silent_p.T174T|GRIK1_ENST00000327783.4_Silent_p.T174T	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	174					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)	CATACACCACTGTCACTGTTT	0.428													G|||	1704	0.340256	0.6755	0.2925	5008	,	,		18444	0.3393		0.1163	False		,,,				2504	0.1524				p.T174T		Atlas-SNP	.											.	GRIK1	293	.	0			c.A522C						PASS	.	G	,	2527,1879	542.2+/-376.0	732,1063,408	216.0	207.0	210.0		522,522	-10.0	0.0	21	dbSNP_79	210	973,7627	774.7+/-407.7	62,849,3389	no	coding-synonymous,coding-synonymous	GRIK1	NM_000830.3,NM_175611.2	,	794,1912,3797	GG,GT,TT		11.314,42.6464,26.9107	,	174/919,174/906	31062070	3500,9506	2203	4300	6503	SO:0001819	synonymous_variant	2897	exon3			CACCACTGTCACT		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.522A>C	21.37:g.31062070T>G		Somatic	294	1	0.00340136		WXS	Illumina HiSeq	Phase_I	280	280	1	NM_175611	Q13001|Q86SU9	Silent	SNP	ENST00000399907.1	37	CCDS42913.1																																																																																			T|0.690;G|0.310	0.310	strong		0.428	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1		
CDYL2	124359	hgsc.bcm.edu	37	16	80642076	80642076	+	Silent	SNP	C	C	T	rs117351184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:80642076C>T	ENST00000570137.2	-	6	1430	c.1275G>A	c.(1273-1275)agG>agA	p.R425R	CDYL2_ENST00000562812.1_Silent_p.R426R|CDYL2_ENST00000566173.1_Silent_p.R426R|CDYL2_ENST00000563890.1_Silent_p.R426R	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	425						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						ACACCAGCCCCCTGCTGCAGG	0.617													C|||	27	0.00539137	0.0	0.0029	5008	,	,		6251	0.0		0.0239	False		,,,				2504	0.001				p.R425R		Atlas-SNP	.											.	CDYL2	66	.	0			c.G1275A						PASS	.	C		15,4385		0,15,2185	36.0	26.0	30.0		1275	-5.3	0.9	16	dbSNP_132	30	120,8478		0,120,4179	no	coding-synonymous	CDYL2	NM_152342.2		0,135,6364	TT,TC,CC		1.3957,0.3409,1.0386		425/507	80642076	135,12863	2200	4299	6499	SO:0001819	synonymous_variant	124359	exon6			CAGCCCCCTGCTG	AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"""chromodomain Y-like protein 2"""			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.1275G>A	16.37:g.80642076C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	NM_152342	Q7Z5I8	Silent	SNP	ENST00000570137.2	37	CCDS32493.1																																																																																			C|0.990;T|0.010	0.010	strong		0.617	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342	
KRT33B	3884	hgsc.bcm.edu	37	17	39521517	39521517	+	Silent	SNP	C	C	T	rs553149537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39521517C>T	ENST00000251646.3	-	5	835	c.786G>A	c.(784-786)tcG>tcA	p.S262S		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	262	Coil 2.|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)	p.S262S(1)		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)				GCAGCTGCTCCGAGCTGGATA	0.617													C|||	4	0.000798722	0.0008	0.0	5008	,	,		18679	0.0		0.0	False		,,,				2504	0.0031				p.S262S		Atlas-SNP	.											KRT33B,caecum,carcinoma,0,1	KRT33B	46	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G786A						scavenged	.						51.0	51.0	51.0					17																	39521517		2189	4298	6487	SO:0001819	synonymous_variant	3884	exon5			CTGCTCCGAGCTG	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.786G>A	17.37:g.39521517C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	254	23	0.0905512	NM_002279	O76010	Silent	SNP	ENST00000251646.3	37	CCDS11389.1																																																																																			.	.	none		0.617	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
PROP1	5626	hgsc.bcm.edu	37	5	177422908	177422908	+	Silent	SNP	A	A	G	rs1135320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:177422908A>G	ENST00000308304.2	-	1	335	c.27T>C	c.(25-27)gcT>gcC	p.A9A		NM_006261.4	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	9					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)			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)			TTGGCTTCTCAGCCTGGCGCC	0.622													G|||	2242	0.447684	0.2481	0.4942	5008	,	,		14630	0.5595		0.4712	False		,,,				2504	0.545				p.A9A		Atlas-SNP	.											.	PROP1	28	.	0			c.T27C						PASS	.	G		1262,3144		181,900,1122	75.0	67.0	70.0		27	-0.8	0.0	5	dbSNP_86	70	3850,4750		887,2076,1337	no	coding-synonymous	PROP1	NM_006261.4		1068,2976,2459	GG,GA,AA		44.7674,28.6428,39.3049		9/227	177422908	5112,7894	2203	4300	6503	SO:0001819	synonymous_variant	5626	exon1			CTTCTCAGCCTGG	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.27T>C	5.37:g.177422908A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_006261		Silent	SNP	ENST00000308304.2	37	CCDS4430.1																																																																																			A|0.580;G|0.420	0.420	strong		0.622	PROP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253472.1	NM_006261	
LRP2	4036	hgsc.bcm.edu	37	2	170034473	170034473	+	Silent	SNP	G	G	A	rs139363553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170034473G>A	ENST00000263816.3	-	53	10518	c.10233C>T	c.(10231-10233)ttC>ttT	p.F3411F	LRP2_ENST00000461418.1_5'UTR	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3411					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)"""	TGGTAATAGCGAAAGGGTGAG	0.433													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20637	0.0		0.0	False		,,,				2504	0.0				p.F3411F		Atlas-SNP	.											.	LRP2	751	.	0			c.C10233T						PASS	.	G		25,4381	31.7+/-61.6	0,25,2178	169.0	146.0	154.0		10233	2.0	1.0	2	dbSNP_134	154	0,8600		0,0,4300	no	coding-synonymous	LRP2	NM_004525.2		0,25,6478	AA,AG,GG		0.0,0.5674,0.1922		3411/4656	170034473	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon53			AATAGCGAAAGGG		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.10233C>T	2.37:g.170034473G>A		Somatic	346	1	0.00289017		WXS	Illumina HiSeq	Phase_I	268	116	0.432836	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			G|0.999;A|0.001	0.001	strong		0.433	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32551949	32551949	+	Missense_Mutation	SNP	C	C	G	rs16822805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32551949C>G	ENST00000360004.5	-	2	412	c.307G>C	c.(307-309)Gcg>Ccg	p.A103P		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	103	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						GTGTCCACCGCGGCCCGCGCC	0.682										Multiple Myeloma(14;0.17)																											p.A103P		Atlas-SNP	.											HLA-DRB1,brain,glioma,+1,2	HLA-DRB1	41	2	0			c.G307C						scavenged	.						26.0	27.0	27.0					6																	32551949		2139	4247	6386	SO:0001583	missense	3123	exon2			CCACCGCGGCCCG	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.307G>C	6.37:g.32551949C>G	ENSP00000353099:p.Ala103Pro	Somatic	31	4	0.129032		WXS	Illumina HiSeq	Phase_I	11	11	1	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	10.42	1.344005	0.24339	.	.	ENSG00000196126	ENST00000360004	T	0.00289	8.28	3.52	0.631	0.17699	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	2.651270	0.02020	N	0.047686	T	0.00039	0.0001	N	0.16743	0.435	0.09310	N	1	B	0.29115	0.233	B	0.34824	0.19	T	0.22591	-1.0212	10	0.52906	T	0.07	.	3.4895	0.07632	0.1726:0.559:0.1675:0.1009	rs16822805;rs17878887;rs28993506;rs36102664	103	P01911	2B1F_HUMAN	P	103	ENSP00000353099:A103P	ENSP00000353099:A103P	A	-	1	0	HLA-DRB1	32659927	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	-6.420000	0.00066	0.007000	0.14760	-1.585000	0.00851	GCG	G|0.114;C|0.886	0.114	strong		0.682	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ABCA4	24	hgsc.bcm.edu	37	1	94505604	94505604	+	Missense_Mutation	SNP	A	A	C	rs61750126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:94505604A>C	ENST00000370225.3	-	24	3688	c.3602T>G	c.(3601-3603)cTg>cGg	p.L1201R		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1201			L -> R (in STGD1; may predispose to develop retinal toxicity after treatment with chloroquine and hydroxychloroquine; dbSNP:rs61750126). {ECO:0000269|PubMed:11384574, ECO:0000269|PubMed:11527935}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CTTACCATCCAGGACTTGTTC	0.547											OREG0013610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	146	0.0291534	0.1051	0.0101	5008	,	,		20682	0.0		0.0	False		,,,				2504	0.0				p.L1201R		Atlas-SNP	.											.	ABCA4	275	.	0			c.T3602G	GRCh37	CM990042	ABCA4	M	rs61750126	PASS	.	A	ARG/LEU	412,3994	189.5+/-215.6	25,362,1816	131.0	106.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3602	5.5	1.0	1	dbSNP_129	115	4,8596	2.2+/-6.3	0,4,4296	yes	missense	ABCA4	NM_000350.2	102	25,366,6112	CC,CA,AA		0.0465,9.3509,3.1985	probably-damaging	1201/2274	94505604	416,12590	2203	4300	6503	SO:0001583	missense	24	exon24			CCATCCAGGACTT	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.3602T>G	1.37:g.94505604A>C	ENSP00000359245:p.Leu1201Arg	Somatic	92	0	0	1306	WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	A	12.19	1.864956	0.32977	0.093509	4.65E-4	ENSG00000198691	ENST00000370225	D	0.86562	-2.14	5.54	5.54	0.83059	.	0.077785	0.50627	D	0.000119	T	0.76983	0.4064	L	0.53249	1.67	0.80722	A	1	B	0.18863	0.031	B	0.24269	0.052	T	0.73228	-0.4049	9	0.27082	T	0.32	.	13.1677	0.59581	1.0:0.0:0.0:0.0	rs61750126	1201	P78363	ABCA4_HUMAN	R	1201	ENSP00000359245:L1201R	ENSP00000359245:L1201R	L	-	2	0	ABCA4	94278192	1.000000	0.71417	0.997000	0.53966	0.864000	0.49448	4.771000	0.62318	2.326000	0.78906	0.533000	0.62120	CTG	A|0.968;C|0.032	0.032	strong		0.547	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
HABP4	22927	hgsc.bcm.edu	37	9	99250463	99250463	+	Silent	SNP	C	C	T	rs7030316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99250463C>T	ENST00000375249.4	+	7	1167	c.1092C>T	c.(1090-1092)ctC>ctT	p.L364L	HABP4_ENST00000375251.3_Silent_p.L259L|HABP4_ENST00000466976.1_3'UTR	NM_014282.2	NP_055097.2			hyaluronan binding protein 4											NS(1)|cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)				TTGGTAACCTCCCTCGTCCTG	0.547													C|||	940	0.1877	0.444	0.1066	5008	,	,		19743	0.0248		0.165	False		,,,				2504	0.09				p.L364L		Atlas-SNP	.											.	HABP4	25	.	0			c.C1092T						PASS	.	C		1820,2586	531.5+/-373.2	377,1066,760	147.0	141.0	143.0		1092	0.8	1.0	9	dbSNP_116	143	1552,7048	291.6+/-300.4	147,1258,2895	no	coding-synonymous	HABP4	NM_014282.2		524,2324,3655	TT,TC,CC		18.0465,41.3073,25.9265		364/414	99250463	3372,9634	2203	4300	6503	SO:0001819	synonymous_variant	22927	exon7			TAACCTCCCTCGT	AF241831	CCDS6719.1	9q22.3-q31	2008-02-05			ENSG00000130956	ENSG00000130956			17062	protein-coding gene	gene with protein product						9523163, 10887182	Standard	XM_005251812		Approved	IHABP4, SERBP1L	uc010msg.3	Q5JVS0	OTTHUMG00000020298	ENST00000375249.4:c.1092C>T	9.37:g.99250463C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	21	0.238636	NM_014282		Silent	SNP	ENST00000375249.4	37	CCDS6719.1																																																																																			C|0.771;T|0.229	0.229	strong		0.547	HABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053269.1	NM_014282	
MZT2A	653784	hgsc.bcm.edu	37	2	132241704	132241704	+	Missense_Mutation	SNP	C	C	T	rs11553182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:132241704C>T	ENST00000309451.6	-	3	452	c.407G>A	c.(406-408)cGc>cAc	p.R136H	MZT2A_ENST00000410036.2_5'UTR	NM_001085365.1	NP_001078834.1	Q6P582	MZT2A_HUMAN	mitotic spindle organizing protein 2A	136						centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				breast(1)|lung(1)	2						GCTGGGCTGGCGTGGCATCCT	0.647													.|||	841	0.167931	0.4607	0.1037	5008	,	,		15889	0.004		0.0924	False		,,,				2504	0.0644				p.R136H		Atlas-SNP	.											.	MZT2A	6	.	0			c.G407A						PASS	.	C	HIS/ARG	1752,2648		365,1022,813	51.0	63.0	59.0		407	2.4	1.0	2	dbSNP_120	59	785,7813		41,703,3555	no	missense	MZT2A	NM_001085365.1	29	406,1725,4368	TT,TC,CC		9.13,39.8182,19.5184	probably-damaging	136/159	132241704	2537,10461	2200	4299	6499	SO:0001583	missense	653784	exon3			GGCTGGCGTGGCA	BC018206	CCDS42758.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000173272	ENSG00000173272			33187	protein-coding gene	gene with protein product	"""mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A"""	613449	"""family with sequence similarity 128, member A"""	FAM128A		20360068	Standard	NM_001085365		Approved	MOZART2A	uc002tsw.4	Q6P582	OTTHUMG00000153606	ENST00000309451.6:c.407G>A	2.37:g.132241704C>T	ENSP00000311500:p.Arg136His	Somatic	271	1	0.00369004		WXS	Illumina HiSeq	Phase_I	286	142	0.496504	NM_001085365	Q3SWV8|Q8WVB2	Missense_Mutation	SNP	ENST00000309451.6	37	CCDS42758.1	338	0.15476190476190477	236	0.4796747967479675	39	0.10773480662983426	2	0.0034965034965034965	61	0.08047493403693931	c	12.99	2.104319	0.37145	0.398182	0.0913	ENSG00000173272	ENST00000309451	T	0.47177	0.85	2.4	2.4	0.29515	.	0.062472	0.64402	D	0.000008	T	0.00012	0.0000	M	0.63843	1.955	0.23238	P	0.99806022	B	0.22604	0.072	B	0.15052	0.012	T	0.44513	-0.9323	9	0.48119	T	0.1	-9.6738	10.5091	0.44851	0.0:1.0:0.0:0.0	rs11553182;rs61686750	136	Q6P582	MZT2A_HUMAN	H	136	ENSP00000311500:R136H	ENSP00000311500:R136H	R	-	2	0	MZT2A	131958174	1.000000	0.71417	0.985000	0.45067	0.062000	0.15995	3.776000	0.55356	1.337000	0.45525	0.430000	0.28490	CGC	C|0.872;T|0.128	0.128	strong		0.647	MZT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331811.2		
CACNA1G	8913	hgsc.bcm.edu	37	17	48653144	48653144	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48653144C>T	ENST00000359106.5	+	8	1381	c.1381C>T	c.(1381-1383)Cgg>Tgg	p.R461W	CACNA1G_ENST00000502264.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000507510.2_Missense_Mutation_p.R461W|CACNA1G_ENST00000510366.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000514717.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000514181.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000513964.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000515765.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000512389.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000360761.4_Missense_Mutation_p.R461W|CACNA1G_ENST00000515165.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000507896.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000358244.5_Missense_Mutation_p.R461W|CACNA1G_ENST00000442258.2_Missense_Mutation_p.R461W|CACNA1G_ENST00000354983.4_Missense_Mutation_p.R461W|CACNA1G_ENST00000507336.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000510115.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000416767.4_Missense_Mutation_p.R461W|CACNA1G_ENST00000515411.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000514079.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000429973.2_Missense_Mutation_p.R461W|CACNA1G_ENST00000507609.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000505165.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000503485.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000352832.5_Missense_Mutation_p.R461W|CACNA1G_ENST00000513689.2_Missense_Mutation_p.R461W	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	461					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AGCAGGTGTGCGGGTTGGGCT	0.672																																					p.R461W		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C1381T						PASS	.																																			SO:0001583	missense	8913	exon8			GGTGTGCGGGTTG	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.1381C>T	17.37:g.48653144C>T	ENSP00000352011:p.Arg461Trp	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	c	11.34	1.610132	0.28712	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97352	-4.2;-4.21;-4.35;-4.14;-4.2;-4.19;-4.23;-4.28;-4.25;-4.27;-4.28;-4.16;-4.16;-4.22;-4.2;-4.14;-4.23;-4.18;-4.15;-4.23;-4.2;-4.16;-4.22;-4.15;-4.22;-4.22	5.15	5.15	0.70609	.	0.317948	0.29783	N	0.011202	D	0.97241	0.9098	L	0.42632	1.34	0.37962	D	0.932991	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;B;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.998;1.0;1.0;0.999;0.999;1.0;0.997;1.0;0.999;1.0;1.0;1.0;0.999;1.0;0.999;0.013;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;B;D	0.83275	0.991;0.918;0.984;0.996;0.959;0.984;0.994;0.959;0.994;0.918;0.947;0.975;0.945;0.947;0.994;0.918;0.965;0.926;0.959;0.991;0.988;0.945;0.947;0.918;0.003;0.985	D	0.98292	1.0514	10	0.66056	D	0.02	.	11.91	0.52733	0.2981:0.7019:0.0:0.0	.	461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	W	461	ENSP00000353990:R461W;ENSP00000339302:R461W;ENSP00000392390:R461W;ENSP00000347078:R461W;ENSP00000409759:R461W;ENSP00000425522:R461W;ENSP00000426261:R461W;ENSP00000425451:R461W;ENSP00000422407:R461W;ENSP00000426814:R461W;ENSP00000427238:R461W;ENSP00000423112:R461W;ENSP00000420918:R461W;ENSP00000426172:R461W;ENSP00000423045:R461W;ENSP00000427173:R461W;ENSP00000426098:R461W;ENSP00000425698:R461W;ENSP00000426232:R461W;ENSP00000423317:R461W;ENSP00000350979:R461W;ENSP00000352011:R461W;ENSP00000414388:R461W;ENSP00000423155:R461W;ENSP00000422268:R461W;ENSP00000421518:R461W	ENSP00000339302:R461W	R	+	1	2	CACNA1G	46008143	0.991000	0.36638	0.995000	0.50966	0.137000	0.21094	2.463000	0.45058	2.388000	0.81334	0.655000	0.94253	CGG	.	.	none		0.672	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
MKI67	4288	hgsc.bcm.edu	37	10	129901726	129901726	+	Missense_Mutation	SNP	C	C	T	rs10082533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129901726C>T	ENST00000368654.3	-	13	8753	c.8378G>A	c.(8377-8379)aGt>aAt	p.S2793N	MKI67_ENST00000368653.3_Missense_Mutation_p.S2433N	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2793	16 X 122 AA approximate repeats.		S -> N (in dbSNP:rs10082533).		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)				GGCTTGGGCACTTTCCCTGGG	0.493													T|||	1163	0.232228	0.3404	0.2277	5008	,	,		16851	0.2599		0.1581	False		,,,				2504	0.137				p.S2793N		Atlas-SNP	.											.	MKI67	363	.	0			c.G8378A						PASS	.	T	ASN/SER,ASN/SER	1359,3047	690.3+/-405.2	207,945,1051	93.0	88.0	90.0		7298,8378	-0.3	0.0	10	dbSNP_119	90	1489,7111	747.2+/-407.3	137,1215,2948	no	missense,missense	MKI67	NM_001145966.1,NM_002417.4	46,46	344,2160,3999	TT,TC,CC		17.314,30.8443,21.8976	benign,benign	2433/2897,2793/3257	129901726	2848,10158	2203	4300	6503	SO:0001583	missense	4288	exon13			TGGGCACTTTCCC	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.8378G>A	10.37:g.129901726C>T	ENSP00000357643:p.Ser2793Asn	Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	232	103	0.443966	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	489	0.2239010989010989	147	0.29878048780487804	68	0.1878453038674033	150	0.26223776223776224	124	0.16358839050131926	T	3.636	-0.074525	0.07184	0.308443	0.17314	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02103	4.45;4.45	3.93	-0.274	0.12910	.	.	.	.	.	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	0.36841	-0.9731	8	0.17832	T	0.49	.	4.2767	0.10813	0.0:0.365:0.1847:0.4503	rs10082533;rs59377110	2792;2433;2793	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	N	2793;2433;2792	ENSP00000357643:S2793N;ENSP00000357642:S2433N	ENSP00000357642:S2433N	S	-	2	0	MKI67	129791716	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.151000	0.10175	-0.437000	0.07243	-0.982000	0.02568	AGT	C|0.784;T|0.216	0.216	strong		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
DLK2	65989	hgsc.bcm.edu	37	6	43418733	43418733	+	Silent	SNP	G	G	A	rs1214749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43418733G>A	ENST00000357338.3	-	6	1396	c.696C>T	c.(694-696)caC>caT	p.H232H	DLK2_ENST00000372488.3_Silent_p.H232H|DLK2_ENST00000414245.1_Silent_p.H226H|DLK2_ENST00000372485.1_Silent_p.H226H	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	232	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	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)			AGTCGAAGTCGTGGACACGGT	0.627													A|||	1397	0.278954	0.5424	0.2147	5008	,	,		18721	0.0804		0.2863	False		,,,				2504	0.1656				p.H232H		Atlas-SNP	.											.	DLK2	22	.	0			c.C696T						PASS	.	A	,	2216,2190	577.0+/-384.4	559,1098,546	60.0	64.0	62.0		696,696	-5.8	0.8	6	dbSNP_87	62	2675,5925	675.2+/-403.2	424,1827,2049	no	coding-synonymous,coding-synonymous	DLK2	NM_023932.2,NM_206539.1	,	983,2925,2595	AA,AG,GG		31.1047,49.7049,37.6057	,	232/384,232/384	43418733	4891,8115	2203	4300	6503	SO:0001819	synonymous_variant	65989	exon6			GAAGTCGTGGACA	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"""EGF-like-domain, multiple 9"""	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.696C>T	6.37:g.43418733G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Silent	SNP	ENST00000357338.3	37	CCDS4897.1	577	0.2641941391941392	247	0.5020325203252033	81	0.22375690607734808	41	0.07167832167832168	208	0.27440633245382584	A	4.262	0.047770	0.08243	0.502951	0.311047	ENSG00000171462	ENST00000430324	.	.	.	4.94	-5.77	0.02369	.	.	.	.	.	T	0.18002	0.0432	.	.	.	0.09310	P	0.9999999602075	.	.	.	.	.	.	T	0.18808	-1.0325	3	.	.	.	.	9.4542	0.38745	0.2896:0.2188:0.4916:0.0	rs1214749;rs1674841;rs1214749	.	.	.	M	138	.	.	T	-	2	0	DLK2	43526711	0.338000	0.24775	0.835000	0.33067	0.653000	0.38743	-0.286000	0.08399	-1.278000	0.02408	-1.390000	0.01156	ACG	G|0.662;A|0.338	0.338	strong		0.627	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932	
USP40	55230	hgsc.bcm.edu	37	2	234398065	234398065	+	Missense_Mutation	SNP	G	G	A	rs34026756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234398065G>A	ENST00000427112.2	-	26	3109	c.3074C>T	c.(3073-3075)aCg>aTg	p.T1025M	USP40_ENST00000450966.1_Missense_Mutation_p.T1037M|USP40_ENST00000251722.6_Missense_Mutation_p.T1025M|USP40_ENST00000496298.1_5'UTR			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1025			T -> M (in dbSNP:rs34026756).		ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CCTCTCCACCGTCCAGGCTCT	0.572													G|||	90	0.0179712	0.0658	0.0043	5008	,	,		17455	0.0		0.0	False		,,,				2504	0.0				p.T1037M		Atlas-SNP	.											USP40_ENST00000450966,NS,carcinoma,+1,2	USP40	174	2	0			c.C3110T						PASS	.	G	MET/THR	242,3748		6,230,1759	34.0	38.0	36.0		3110	4.6	0.9	2	dbSNP_126	36	2,8304		0,2,4151	yes	missense	USP40	NM_018218.2	81	6,232,5910	AA,AG,GG		0.0241,6.0652,1.9844	probably-damaging	1037/1248	234398065	244,12052	1995	4153	6148	SO:0001583	missense	55230	exon26			TCCACCGTCCAGG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3074C>T	2.37:g.234398065G>A	ENSP00000387898:p.Thr1025Met	Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	200	102	0.51	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	35|35	0.016025641025641024|0.016025641025641024	34|34	0.06910569105691057|0.06910569105691057	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	19.02|19.02	3.746166|3.746166	0.69418|0.69418	0.060652|0.060652	2.41E-4|2.41E-4	ENSG00000085982|ENSG00000085982	ENST00000454354;ENST00000430158|ENST00000450966;ENST00000251722;ENST00000427112	.|T;T;T	.|0.05580	.|3.42;3.42;3.42	5.5|5.5	4.57|4.57	0.56435|0.56435	.|.	.|0.947819	.|0.08861	.|N	.|0.883028	T|T	0.01730|0.01730	0.0055|0.0055	M|M	0.66939|0.66939	2.045|2.045	0.32511|0.32511	N|N	0.537508|0.537508	.|D;D	.|0.89917	.|1.0;0.999	.|D;P	.|0.63957	.|0.92;0.878	T|T	0.00967|0.00967	-1.1497|-1.1497	5|10	.|0.59425	.|D	.|0.04	.|.	15.0977|15.0977	0.72247|0.72247	0.0:0.0:0.8577:0.1423|0.0:0.0:0.8577:0.1423	rs34026756|rs34026756	.|1037;685	.|Q9NVE5-3;B4DN96	.|.;.	W|M	15;201|1037;1025;1025	.|ENSP00000415434:T1037M;ENSP00000251722:T1025M;ENSP00000387898:T1025M	.|ENSP00000251722:T1025M	R|T	-|-	1|2	2|0	USP40|USP40	234062804|234062804	1.000000|1.000000	0.71417|0.71417	0.945000|0.945000	0.38365|0.38365	0.606000|0.606000	0.37113|0.37113	3.308000|3.308000	0.51896|0.51896	2.571000|2.571000	0.86741|0.86741	0.650000|0.650000	0.86243|0.86243	CGG|ACG	G|0.985;A|0.015	0.015	strong		0.572	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
PIGB	9488	hgsc.bcm.edu	37	15	55647617	55647617	+	Missense_Mutation	SNP	A	A	C	rs2444042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55647617A>C	ENST00000164305.5	+	12	1943	c.1652A>C	c.(1651-1653)aAg>aCg	p.K551T	PIGB_ENST00000539642.1_Missense_Mutation_p.K356T|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000310958.6_3'UTR|CCPG1_ENST00000442196.3_3'UTR	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	551			K -> T (in dbSNP:rs2444042).		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|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)	mannosyltransferase activity (GO:0000030)			endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		TTCAACATGAAGATGAAATTC	0.368													A|||	96	0.0191693	0.0719	0.0014	5008	,	,		17374	0.0		0.0	False		,,,				2504	0.0				p.K551T		Atlas-SNP	.											.	PIGB	36	.	0			c.A1652C						PASS	.	A	,,,THR/LYS,	239,3401		7,225,1588	89.0	89.0	89.0		,,,1652,	3.4	0.3	15	dbSNP_100	89	2,8126		0,2,4062	yes	utr-3,utr-3,utr-3,missense,utr-3	CCPG1,PIGB	NM_001204450.1,NM_001204451.1,NM_004748.4,NM_004855.4,NM_020739.3	,,,78,	7,227,5650	CC,CA,AA		0.0246,6.5659,2.0479	,,,benign,	,,,551/555,	55647617	241,11527	1820	4064	5884	SO:0001583	missense	9488	exon12			ACATGAAGATGAA	D42138	CCDS61641.1	15q21.3	2013-02-26	2006-06-28		ENSG00000069943	ENSG00000069943		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	8959	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 3"", ""dol-P-Man dependent GPI mannosyltransferase"""	604122	"""phosphatidylinositol glycan, class B"""			8861954	Standard	NM_004855		Approved		uc002act.3	Q92521	OTTHUMG00000172654	ENST00000164305.5:c.1652A>C	15.37:g.55647617A>C	ENSP00000164305:p.Lys551Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_004855	Q53FF9|Q8WVN7	Missense_Mutation	SNP	ENST00000164305.5	37		32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	A	7.554	0.663207	0.14710	0.065659	2.46E-4	ENSG00000069943	ENST00000164305;ENST00000539642	T;T	0.59638	0.51;0.25	5.67	3.39	0.38822	.	3.113960	0.00954	N	0.003003	T	0.03827	0.0108	N	0.03608	-0.345	0.80722	D	1	B	0.31318	0.319	B	0.30029	0.11	T	0.02668	-1.1126	10	0.66056	D	0.02	9.0326	8.6085	0.33789	0.8432:0.0:0.1568:0.0	rs2444042;rs52826750;rs2444042	551	Q92521	PIGB_HUMAN	T	551;356	ENSP00000164305:K551T;ENSP00000438963:K356T	ENSP00000164305:K551T	K	+	2	0	PIGB	53434909	0.999000	0.42202	0.263000	0.24496	0.257000	0.26127	1.168000	0.31859	0.452000	0.26830	0.482000	0.46254	AAG	A|0.977;C|0.023	0.023	strong		0.368	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855	
ASB15	142685	hgsc.bcm.edu	37	7	123267200	123267200	+	Missense_Mutation	SNP	C	C	T	rs73718440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:123267200C>T	ENST00000451558.1	+	11	1255	c.734C>T	c.(733-735)tCg>tTg	p.S245L	RP11-390E23.3_ENST00000451016.1_RNA|ASB15_ENST00000275699.3_Missense_Mutation_p.S245L|RP11-390E23.3_ENST00000422401.1_RNA|ASB15_ENST00000540573.1_Missense_Mutation_p.S245L|RP11-390E23.3_ENST00000429396.1_RNA|RP11-390E23.3_ENST00000440504.1_RNA|ASB15_ENST00000451215.1_Missense_Mutation_p.S245L|RP11-390E23.3_ENST00000418409.1_RNA|ASB15_ENST00000434204.1_Missense_Mutation_p.S245L			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	245					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						GATGGGGCGTCGGTGCTGTTT	0.488													C|||	39	0.00778754	0.0295	0.0	5008	,	,		17121	0.0		0.0	False		,,,				2504	0.0				p.S245L		Atlas-SNP	.											.	ASB15	94	.	0			c.C734T						PASS	.	C	LEU/SER	96,4310	78.8+/-117.2	0,96,2107	178.0	141.0	153.0		734	5.6	0.8	7	dbSNP_130	153	1,8599		0,1,4299	yes	missense	ASB15	NM_080928.3	145	0,97,6406	TT,TC,CC		0.0116,2.1788,0.7458	probably-damaging	245/589	123267200	97,12909	2203	4300	6503	SO:0001583	missense	142685	exon7			GGGCGTCGGTGCT	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.734C>T	7.37:g.123267200C>T	ENSP00000397655:p.Ser245Leu	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	315	149	0.473016	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	37	CCDS34742.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	C	19.14	3.770300	0.69992	0.021788	1.16E-4	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000275699	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	5.57	5.57	0.84162	Ankyrin repeat-containing domain (4);	0.000000	0.56097	D	0.000022	T	0.16557	0.0398	L	0.48642	1.525	0.46317	D	0.99898	D	0.89917	1.0	D	0.81914	0.995	T	0.00964	-1.1498	10	0.87932	D	0	-24.7501	19.5537	0.95331	0.0:1.0:0.0:0.0	.	245	Q8WXK1	ASB15_HUMAN	L	245;245;245;245;34;245	ENSP00000397655:S245L;ENSP00000390963:S245L;ENSP00000416433:S245L;ENSP00000438643:S245L;ENSP00000275699:S245L	ENSP00000275699:S245L	S	+	2	0	ASB15	123054436	0.989000	0.36119	0.802000	0.32245	0.453000	0.32348	3.285000	0.51716	2.614000	0.88457	0.557000	0.71058	TCG	C|0.993;T|0.007	0.007	strong		0.488	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1		
DUOX1	53905	hgsc.bcm.edu	37	15	45442896	45442896	+	Missense_Mutation	SNP	T	T	C	rs16939743	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45442896T>C	ENST00000321429.4	+	23	3292	c.2885T>C	c.(2884-2886)aTc>aCc	p.I962T	DUOX1_ENST00000389037.3_Missense_Mutation_p.I962T|DUOX1_ENST00000561166.1_Missense_Mutation_p.I608T|CTD-2651B20.1_ENST00000558039.1_lincRNA	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	962	Interaction with TXNDC11. {ECO:0000250}.		I -> T (in dbSNP:rs16939743).		cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CAGGATATGATCTGGTGAGCA	0.607													T|||	421	0.0840655	0.1929	0.0216	5008	,	,		19232	0.1359		0.002	False		,,,				2504	0.0123				p.I962T		Atlas-SNP	.											DUOX1,caecum,carcinoma,0,2	DUOX1	125	2	0			c.T2885C						PASS	.	T	THR/ILE,THR/ILE	887,3509	342.8+/-307.3	87,713,1398	47.0	45.0	46.0		2885,2885	4.5	1.0	15	dbSNP_123	46	7,8589	5.7+/-21.5	0,7,4291	yes	missense,missense	DUOX1	NM_017434.3,NM_175940.1	89,89	87,720,5689	CC,CT,TT		0.0814,20.1774,6.8812	benign,benign	962/1552,962/1552	45442896	894,12098	2198	4298	6496	SO:0001583	missense	53905	exon23			ATATGATCTGGTG	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.2885T>C	15.37:g.45442896T>C	ENSP00000317997:p.Ile962Thr	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	37	CCDS32221.1	166	0.076007326007326	81	0.16463414634146342	9	0.024861878453038673	75	0.13111888111888112	1	0.0013192612137203166	T	7.582	0.668850	0.14776	0.201774	8.14E-4	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	D;D	0.85484	-1.99;-1.99	5.63	4.49	0.54785	.	0.588884	0.17161	N	0.184694	T	0.00210	0.0006	N	0.22421	0.69	0.32591	P	0.527243	B;B	0.13145	0.007;0.0	B;B	0.10450	0.005;0.001	T	0.09292	-1.0681	9	0.13853	T	0.58	-13.4693	10.0575	0.42255	0.0:0.0:0.3267:0.6733	rs16939743;rs61445119;rs16939743	95;962	Q9NT13;Q9NRD9	.;DUOX1_HUMAN	T	962	ENSP00000317997:I962T;ENSP00000373689:I962T	ENSP00000317997:I962T	I	+	2	0	DUOX1	43230188	0.998000	0.40836	0.986000	0.45419	0.333000	0.28666	3.586000	0.53950	0.935000	0.37341	0.459000	0.35465	ATC	T|0.927;C|0.073	0.073	strong		0.607	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
TYW3	127253	hgsc.bcm.edu	37	1	75214441	75214441	+	Missense_Mutation	SNP	A	A	G	rs1133891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:75214441A>G	ENST00000370867.3	+	4	450	c.361A>G	c.(361-363)Atg>Gtg	p.M121V	TYW3_ENST00000421739.2_Intron|TYW3_ENST00000479111.1_Start_Codon_SNP_p.M1V|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	277	0	0		WXS	Illumina HiSeq	Phase_I	283	136	0.480565	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	
SEMA3C	10512	hgsc.bcm.edu	37	7	80387766	80387766	+	Silent	SNP	C	C	T	rs1058425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	112	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	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	
UBASH3B	84959	hgsc.bcm.edu	37	11	122678778	122678778	+	Missense_Mutation	SNP	A	A	G	rs35343548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:122678778A>G	ENST00000284273.5	+	13	2081	c.1706A>G	c.(1705-1707)aAt>aGt	p.N569S		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	569	Protein tyrosine phosphatase. {ECO:0000250}.		N -> S (in dbSNP:rs35343548).		negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		CCCCCAGGAAATAACATCCTG	0.473													A|||	33	0.00658946	0.0242	0.0014	5008	,	,		18186	0.0		0.0	False		,,,				2504	0.0				p.N569S		Atlas-SNP	.											.	UBASH3B	73	.	0			c.A1706G						PASS	.	A	SER/ASN	74,4330	66.4+/-103.9	0,74,2128	336.0	327.0	330.0		1706	4.7	1.0	11	dbSNP_126	330	2,8596		0,2,4297	yes	missense	UBASH3B	NM_032873.4	46	0,76,6425	GG,GA,AA		0.0233,1.6803,0.5845	benign	569/650	122678778	76,12926	2202	4299	6501	SO:0001583	missense	84959	exon13			CAGGAAATAACAT	AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"""SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"""	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.1706A>G	11.37:g.122678778A>G	ENSP00000284273:p.Asn569Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	130	49	0.376923	NM_032873	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Missense_Mutation	SNP	ENST00000284273.5	37	CCDS31694.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	A	15.55	2.865578	0.51588	0.016803	2.33E-4	ENSG00000154127	ENST00000284273	T	0.27890	1.64	5.85	4.74	0.60224	Histidine phosphatase superfamily, clade-1 (1);	0.130095	0.64402	N	0.000002	T	0.10423	0.0255	L	0.27053	0.805	0.46376	D	0.999012	B	0.06786	0.001	B	0.08055	0.003	T	0.03514	-1.1029	10	0.48119	T	0.1	-8.6767	7.823	0.29298	0.7888:0.1392:0.072:0.0	rs35343548	569	Q8TF42	UBS3B_HUMAN	S	569	ENSP00000284273:N569S	ENSP00000284273:N569S	N	+	2	0	UBASH3B	122183988	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.395000	0.52558	1.061000	0.40601	0.533000	0.62120	AAT	A|0.992;G|0.008	0.008	strong		0.473	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873	
DMKN	93099	hgsc.bcm.edu	37	19	36002394	36002394	+	Silent	SNP	G	G	A	rs56743379|rs146822312		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002394G>A	ENST00000339686.3	-	5	1013	c.837C>T	c.(835-837)ggC>ggT	p.G279G	DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000418261.1_Silent_p.G279G|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000440396.1_Silent_p.G279G|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_Silent_p.G279G|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000424570.2_Silent_p.G279G|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000447113.2_Silent_p.G279G|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000414866.2_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	279	Gly-rich.			G -> GSSSG (in Ref. 4; AAQ88778). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			cactgctgccgccactgctgc	0.637																																					p.G279G		Atlas-SNP	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.C837T						PASS	.						26.0	20.0	22.0					19																	36002394		2165	4212	6377	SO:0001819	synonymous_variant	93099	exon5			GCTGCCGCCACTG	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.837C>T	19.37:g.36002394G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	89	30	0.337079	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1																																																																																			G|0.933;A|0.067	0.067	strong		0.637	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
NCAPD3	23310	hgsc.bcm.edu	37	11	134055275	134055275	+	Missense_Mutation	SNP	C	C	T	rs61744119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134055275C>T	ENST00000534548.2	-	17	2256	c.2192G>A	c.(2191-2193)aGg>aAg	p.R731K	RP11-700F16.3_ENST00000531710.1_RNA	NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	731					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		GTAGTCCAGCCTGGGTGAGGA	0.433													c|||	20	0.00399361	0.0136	0.0029	5008	,	,		16996	0.0		0.0	False		,,,				2504	0.0				p.R731K		Atlas-SNP	.											.	NCAPD3	141	.	0			c.G2192A						PASS	.	T	LYS/ARG	55,4347	52.3+/-87.9	0,55,2146	67.0	64.0	65.0		2192	-2.9	0.6	11	dbSNP_129	65	0,8594		0,0,4297	yes	missense	NCAPD3	NM_015261.2	26	0,55,6443	TT,TC,CC		0.0,1.2494,0.4232	benign	731/1499	134055275	55,12941	2201	4297	6498	SO:0001583	missense	23310	exon17			TCCAGCCTGGGTG	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.2192G>A	11.37:g.134055275C>T	ENSP00000433681:p.Arg731Lys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	134	74	0.552239	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	c	0.387	-0.925700	0.02377	0.012494	0.0	ENSG00000151503	ENST00000534548	T	0.16743	2.32	5.95	-2.94	0.05581	Armadillo-like helical (1);Armadillo-type fold (1);	0.333488	0.38164	N	0.001795	T	0.01387	0.0045	N	0.00104	-2.125	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45026	-0.9289	10	0.02654	T	1	-5.8849	6.0997	0.20041	0.087:0.072:0.1785:0.6625	.	731	P42695	CNDD3_HUMAN	K	731	ENSP00000433681:R731K	ENSP00000431612:R731K	R	-	2	0	NCAPD3	133560485	0.426000	0.25506	0.571000	0.28486	0.014000	0.08584	0.322000	0.19576	-1.200000	0.02662	-1.563000	0.00883	AGG	C|0.995;T|0.005	0.005	strong		0.433	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	
PRB1	5542	hgsc.bcm.edu	37	12	11506288	11506288	+	Missense_Mutation	SNP	T	T	C	rs140825288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11506288T>C	ENST00000500254.2	-	4	387	c.350A>G	c.(349-351)aAa>aGa	p.K117R	PRB1_ENST00000546254.1_Missense_Mutation_p.K117R|PRB1_ENST00000545626.1_Intron	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1	0	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].		Missing (in allele M).|Missing (in clone CP-4).|Missing (in clone CP-5).			extracellular region (GO:0005576)		p.K117R(2)		NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			ACCTTGAGGTTTGTTGCCTCC	0.612													t|||	39	0.00778754	0.0106	0.0086	5008	,	,		16399	0.0079		0.0099	False		,,,				2504	0.001				p.K117R		Atlas-SNP	.											PRB1,NS,carcinoma,0,2	PRB1	33	2	2	Substitution - Missense(2)	prostate(1)|central_nervous_system(1)	c.A350G						scavenged	.						92.0	112.0	105.0					12																	11506288		2098	4245	6343	SO:0001583	missense	5542	exon4			TGAGGTTTGTTGC		CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.350A>G	12.37:g.11506288T>C	ENSP00000420826:p.Lys117Arg	Somatic	238	2	0.00840336		WXS	Illumina HiSeq	Phase_I	764	15	0.0196335	NM_199353	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Missense_Mutation	SNP	ENST00000500254.2	37	CCDS8642.1	.	.	.	.	.	.	.	.	.	.	.	0.021	-1.431560	0.01108	.	.	ENSG00000251655	ENST00000500254;ENST00000546254	T;T	0.04119	3.7;3.7	1.29	-1.39	0.08997	.	.	.	.	.	T	0.03871	0.0109	L	0.39147	1.195	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.08055	0.002;0.003	T	0.44544	-0.9321	8	.	.	.	.	5.2744	0.15641	0.0:0.2701:0.0:0.7299	.	257;117	Q86YA1;G3V1M9	.;.	R	117	ENSP00000420826:K117R;ENSP00000442127:K117R	.	K	-	2	0	PRB1	11397555	0.003000	0.15002	0.000000	0.03702	0.007000	0.05969	0.188000	0.17018	-0.320000	0.08640	0.113000	0.15668	AAA	.	.	weak		0.612	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039	
CYBB	1536	hgsc.bcm.edu	37	X	37663234	37663234	+	Silent	SNP	G	G	A	rs2228117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37663234G>A	ENST00000378588.4	+	9	1069	c.1002G>A	c.(1000-1002)aaG>aaA	p.K334K	TM4SF2_ENST00000465127.1_Intron|CYBB_ENST00000492288.1_3'UTR|CYBB_ENST00000545017.1_Silent_p.K302K|CYBB_ENST00000536160.1_Silent_p.K67K	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	334	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|rough endoplasmic reticulum (GO:0005791)	flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|prostate(2)|skin(2)	32					Dextromethorphan(DB00514)	AGGTGTCCAAGCTGGAGTGGC	0.483													G|||	110	0.0291391	0.0719	0.0216	3775	,	,		14198	0.0		0.0	False		,,,				2504	0.0				p.K334K		Atlas-SNP	.											.	CYBB	62	.	0			c.G1002A						PASS	.	G		707,3126		70,466,101,1095,470	110.0	99.0	103.0		1002	-2.1	0.2	X	dbSNP_98	103	2,6726		0,2,0,2426,1872	no	coding-synonymous	CYBB	NM_000397.3		70,468,101,3521,2342	AA,AG,A,GG,G		0.0297,18.4451,6.7134		334/571	37663234	709,9852	2202	4300	6502	SO:0001819	synonymous_variant	1536	exon9			GTCCAAGCTGGAG	X04011	CCDS14242.1	Xp21.1	2014-09-17	2008-07-29		ENSG00000165168	ENSG00000165168		"""Cytochrome b genes"""	2578	protein-coding gene	gene with protein product		300481	"""chronic granulomatous disease"""	CGD			Standard	NM_000397		Approved	GP91-PHOX, NOX2	uc004ddr.2	P04839	OTTHUMG00000033175	ENST00000378588.4:c.1002G>A	X.37:g.37663234G>A		Somatic	324	1	0.00308642		WXS	Illumina HiSeq	Phase_I	367	190	0.517711	NM_000397	A8K138|Q2PP16	Silent	SNP	ENST00000378588.4	37	CCDS14242.1																																																																																			0|0.006;A|0.061	0.061	strong		0.483	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1		
MICALL2	79778	hgsc.bcm.edu	37	7	1488317	1488317	+	Silent	SNP	G	G	A	rs78897087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1488317G>A	ENST00000297508.7	-	3	448	c.273C>T	c.(271-273)gaC>gaT	p.D91D	MICALL2_ENST00000405088.4_Intron	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	91	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.|Forms an intramolecular interaction with the C-terminal coiled coil domain 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)		TGCTCAGCCGGTCAGGCACCT	0.657													G|||	158	0.0315495	0.1135	0.0115	5008	,	,		15745	0.0		0.0	False		,,,				2504	0.0				p.D91D		Atlas-SNP	.											.	MICALL2	63	.	0			c.C273T						PASS	.			390,4016	190.9+/-216.7	20,350,1833	97.0	89.0	92.0		273	3.2	1.0	7	dbSNP_132	92	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous	MICALL2	NM_182924.3		20,354,6128	AA,AG,GG		0.0465,8.8516,3.0298		91/905	1488317	394,12610	2203	4299	6502	SO:0001819	synonymous_variant	79778	exon3			CAGCCGGTCAGGC	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.273C>T	7.37:g.1488317G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Silent	SNP	ENST00000297508.7	37	CCDS5324.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
SSX3	10214	hgsc.bcm.edu	37	X	48213485	48213485	+	Missense_Mutation	SNP	T	T	C	rs150370741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48213485T>C	ENST00000298396.2	-	4	281	c.229A>G	c.(229-231)Aca>Gca	p.T77A	SSX3_ENST00000376893.3_Missense_Mutation_p.T77A|SSX3_ENST00000376895.1_5'Flank	NM_021014.2	NP_066294.1	Q99909	SSX3_HUMAN	synovial sarcoma, X breakpoint 3	77	KRAB-related. {ECO:0000255|PROSITE- ProRule:PRU00120}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(1)|lung(9)	13						TGGAAGTCTGTGACCCGTTTA	0.478													C|||	164	0.0434437	0.1195	0.0086	3775	,	,		12958	0.0		0.0	False		,,,				2504	0.0				p.T77A	Colon(37;227 826 19399 40970 48007)	Atlas-SNP	.											.	SSX3	64	.	0			c.A229G						PASS	.	C	ALA/THR,ALA/THR	623,3212		38,455,92,1139,479	143.0	128.0	133.0		229,229	-2.5	0.0	X	dbSNP_134	133	4,6724		0,4,0,2424,1872	no	missense,missense	SSX3	NM_021014.2,NM_175711.1	58,58	38,459,92,3563,2351	CC,CT,C,TT,T		0.0595,16.2451,5.9358	benign,benign	77/189,77/171	48213485	627,9936	2203	4300	6503	SO:0001583	missense	10214	exon4			AGTCTGTGACCCG	U90840	CCDS14291.1	Xp11.23	2009-06-17			ENSG00000165584	ENSG00000165584			11337	protein-coding gene	gene with protein product		300325				8697803, 9378559	Standard	NM_021014		Approved	CT5.3	uc004djd.1	Q99909	OTTHUMG00000021489	ENST00000298396.2:c.229A>G	X.37:g.48213485T>C	ENSP00000298396:p.Thr77Ala	Somatic	713	0	0		WXS	Illumina HiSeq	Phase_I	760	357	0.469737	NM_021014	O60223|Q5JQZ3|Q9BRW7	Missense_Mutation	SNP	ENST00000298396.2	37	CCDS14291.1	82	0.04942736588306208	53	0.12045454545454545	2	0.005555555555555556	0	0.0	0	0.0	t	0.036	-1.308354	0.01342	0.162451	5.95E-4	ENSG00000165584	ENST00000298396;ENST00000376893	T;T	0.07567	3.19;3.18	1.52	-2.54	0.06307	Krueppel-associated box (2);Krueppel-associated box-related (1);	1.846180	0.02818	N	0.125151	T	0.00039	0.0001	L	0.33710	1.025	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.39354	-0.9618	9	0.07644	T	0.81	.	5.6519	0.17620	0.0:0.3735:0.0:0.6265	.	77;77	Q9BRW7;Q99909	.;SSX3_HUMAN	A	77	ENSP00000298396:T77A;ENSP00000366090:T77A	ENSP00000298396:T77A	T	-	1	0	SSX3	48098429	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.278000	0.00529	-1.051000	0.03226	-2.666000	0.00145	ACA	T|0.940;C|0.060	0.060	strong		0.478	SSX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056486.1	NM_021014	
SPAG4	6676	hgsc.bcm.edu	37	20	34205080	34205080	+	Silent	SNP	C	C	T	rs116016997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34205080C>T	ENST00000374273.3	+	2	439	c.327C>T	c.(325-327)gtC>gtT	p.V109V	SPAG4_ENST00000462896.1_3'UTR	NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	109					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			CTCCAGTAGTCTCTGAGGAGC	0.637													C|||	107	0.0213658	0.0779	0.0058	5008	,	,		11937	0.0		0.0	False		,,,				2504	0.0				p.V109V		Atlas-SNP	.											.	SPAG4	36	.	0			c.C327T						PASS	.	C		232,4174		2,228,1973	24.0	26.0	25.0		327	2.1	0.8	20	dbSNP_132	25	3,8595		0,3,4296	no	coding-synonymous	SPAG4	NM_003116.1		2,231,6269	TT,TC,CC		0.0349,5.2655,1.8071		109/438	34205080	235,12769	2203	4299	6502	SO:0001819	synonymous_variant	6676	exon2			AGTAGTCTCTGAG	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.327C>T	20.37:g.34205080C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_003116	O43648	Silent	SNP	ENST00000374273.3	37	CCDS13259.1																																																																																			C|0.982;T|0.018	0.018	strong		0.637	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116	
FLG	2312	hgsc.bcm.edu	37	1	152284497	152284497	+	Silent	SNP	A	A	G	rs144437056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284497A>G	ENST00000368799.1	-	3	2900	c.2865T>C	c.(2863-2865)caT>caC	p.H955H	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	955	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)			AGTCTTCTGAATGTCCCTCAC	0.572									Ichthyosis				-|||	257	0.0513179	0.177	0.0029	5008	,	,		21925	0.0089		0.004	False		,,,				2504	0.0082				p.H955H		Atlas-SNP	.											.	FLG	900	.	0			c.T2865C						PASS	.	G		23,4383		0,23,2180	287.0	275.0	279.0		2865	-8.1	0.0	1	dbSNP_134	279	0,8600		0,0,4300	no	coding-synonymous	FLG	NM_002016.1		0,23,6480	GG,GA,AA		0.0,0.522,0.1768		955/4062	152284497	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTCTGAATGTCCC	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.2865T>C	1.37:g.152284497A>G		Somatic	455	1	0.0021978		WXS	Illumina HiSeq	Phase_I	640	161	0.251563	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.972;G|0.028	0.028	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CAND2	23066	hgsc.bcm.edu	37	3	12859004	12859004	+	Missense_Mutation	SNP	A	A	C	rs3732678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:12859004A>C	ENST00000456430.2	+	10	2614	c.2573A>C	c.(2572-2574)cAc>cCc	p.H858P	CAND2_ENST00000295989.5_Missense_Mutation_p.H765P	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	858			H -> P (in dbSNP:rs3732678). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GGGCCAGGCCACCAGCGGGAG	0.672													C|||	2866	0.572284	0.9713	0.4755	5008	,	,		18610	0.2897		0.6382	False		,,,				2504	0.3252				p.H858P	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.A2573C						PASS	.	C	PRO/HIS,PRO/HIS	3695,385		1677,341,22	42.0	52.0	49.0		2573,2294	3.9	1.0	3	dbSNP_107	49	5012,3388		1488,2036,676	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	77,77	3165,2377,698	CC,CA,AA		40.3333,9.4363,30.2324	benign,benign	858/1237,765/1120	12859004	8707,3773	2040	4200	6240	SO:0001583	missense	23066	exon10			CAGGCCACCAGCG		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.2573A>C	3.37:g.12859004A>C	ENSP00000387641:p.His858Pro	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1251	0.5728021978021978	464	0.943089430894309	168	0.46408839779005523	148	0.25874125874125875	471	0.6213720316622692	C	6.595	0.478073	0.12521	0.905637	0.596667	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.64618	-0.11;-0.11	4.83	3.88	0.44766	Armadillo-like helical (1);Armadillo-type fold (1);	0.556756	0.16689	N	0.203605	T	0.00012	0.0000	N	0.01576	-0.805	0.09310	P	0.99999999053269	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31971	-0.9924	9	0.29301	T	0.29	-12.7469	10.5248	0.44941	0.4804:0.5196:0.0:0.0	rs3732678;rs57480491	858;765	O75155;O75155-2	CAND2_HUMAN;.	P	765;858	ENSP00000295989:H765P;ENSP00000387641:H858P	ENSP00000295989:H765P	H	+	2	0	CAND2	12834004	0.991000	0.36638	1.000000	0.80357	0.980000	0.70556	2.850000	0.48294	1.150000	0.42419	-0.217000	0.12591	CAC	A|0.402;C|0.597;G|0.000	0.597	strong		0.672	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
C7orf31	136895	hgsc.bcm.edu	37	7	25182405	25182405	+	Missense_Mutation	SNP	G	G	T	rs11984293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:25182405G>T	ENST00000409280.1	-	8	1021	c.713C>A	c.(712-714)cCa>cAa	p.P238Q	C7orf31_ENST00000283905.3_Missense_Mutation_p.P238Q			Q8N865	CG031_HUMAN	chromosome 7 open reading frame 31	238			P -> Q (in dbSNP:rs11984293). {ECO:0000269|PubMed:15489334}.							autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	14						GTAGAATACTGGCTTATTTTT	0.368													G|||	1043	0.208267	0.416	0.1167	5008	,	,		17166	0.1587		0.167	False		,,,				2504	0.0859				p.P238Q		Atlas-SNP	.											.	C7orf31	53	.	0			c.C713A						PASS	.	G	GLN/PRO	1721,2685	514.7+/-368.7	366,989,848	84.0	90.0	88.0		713	4.6	1.0	7	dbSNP_120	88	1219,7381	243.9+/-273.3	71,1077,3152	yes	missense	C7orf31	NM_138811.3	76	437,2066,4000	TT,TG,GG		14.1744,39.0604,22.605	benign	238/591	25182405	2940,10066	2203	4300	6503	SO:0001583	missense	136895	exon8			AATACTGGCTTAT	AK097248	CCDS5394.1	7p15.2	2011-11-24			ENSG00000153790	ENSG00000153790			21722	protein-coding gene	gene with protein product							Standard	NM_138811		Approved		uc003sxn.1	Q8N865	OTTHUMG00000128497	ENST00000409280.1:c.713C>A	7.37:g.25182405G>T	ENSP00000386604:p.Pro238Gln	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	141	49	0.347518	NM_138811	A4D165|Q6MZV8|Q6P989|Q7LE28|Q86XK1|Q8N1H5|Q96BN4	Missense_Mutation	SNP	ENST00000409280.1	37	CCDS5394.1	467	0.21382783882783882	199	0.40447154471544716	46	0.1270718232044199	93	0.16258741258741258	129	0.17018469656992086	G	8.678	0.904534	0.17760	0.390604	0.141744	ENSG00000153790	ENST00000409280;ENST00000283905	T;T	0.06068	3.35;3.35	5.51	4.55	0.56014	.	0.233450	0.33895	N	0.004443	T	0.00012	0.0000	N	0.20986	0.625	0.35616	P	0.19092600000000004	P	0.35745	0.518	B	0.32533	0.147	T	0.30475	-0.9977	9	0.06365	T	0.9	-43.9912	7.4526	0.27248	0.0:0.1327:0.5487:0.3186	rs11984293;rs52799441;rs58679665;rs11984293	238	Q8N865	CG031_HUMAN	Q	238	ENSP00000386604:P238Q;ENSP00000283905:P238Q	ENSP00000283905:P238Q	P	-	2	0	C7orf31	25148930	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	3.457000	0.53007	2.594000	0.87642	0.484000	0.47621	CCA	G|0.777;T|0.223	0.223	strong		0.368	C7orf31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326929.1	NM_138811	
WDR38	401551	hgsc.bcm.edu	37	9	127616537	127616537	+	Silent	SNP	A	A	G	rs12375547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127616537A>G	ENST00000373574.1	+	2	179	c.123A>G	c.(121-123)gaA>gaG	p.E41E		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	41					hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CAGGCTCAGAAGATGGCTGCG	0.612													G|||	2267	0.452676	0.4803	0.3573	5008	,	,		18063	0.5804		0.4324	False		,,,				2504	0.3722				p.K10R		Atlas-SNP	.											.	WDR38	21	.	0			c.A29G						PASS	.	G		1968,2132		475,1018,557	125.0	134.0	131.0		123	-6.9	0.2	9	dbSNP_120	131	3636,4778		832,1972,1403	yes	coding-synonymous	WDR38	NM_001045476.1		1307,2990,1960	GG,GA,AA		43.2137,48.0,44.7818		41/315	127616537	5604,6910	2050	4207	6257	SO:0001819	synonymous_variant	401551	exon2			CTCAGAAGATGGC		CCDS43876.1, CCDS75898.1, CCDS75899.1	9q33.3	2013-01-09			ENSG00000136918	ENSG00000136918		"""WD repeat domain containing"""	23745	protein-coding gene	gene with protein product							Standard	NM_001276375		Approved		uc011lzo.3	Q5JTN6	OTTHUMG00000020664	ENST00000373574.1:c.123A>G	9.37:g.127616537A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	107	79	0.738318	NM_001276376	A0PK24	Missense_Mutation	SNP	ENST00000373574.1	37	CCDS43876.1																																																																																			A|0.541;G|0.459	0.459	strong		0.612	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476	
CLCN6	1185	hgsc.bcm.edu	37	1	11876692	11876692	+	Silent	SNP	G	G	A	rs57044879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11876692G>A	ENST00000346436.6	+	4	286	c.234G>A	c.(232-234)gcG>gcA	p.A78A	CLCN6_ENST00000376496.3_Silent_p.A78A|CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376497.3_Silent_p.A78A|CLCN6_ENST00000312413.6_Silent_p.A78A|CLCN6_ENST00000376487.3_Silent_p.A56A	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	78					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	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;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		GATATGAGGCGGTGAAGTGGA	0.532													G|||	135	0.0269569	0.0938	0.0058	5008	,	,		19754	0.004		0.001	False		,,,				2504	0.002				p.A78A		Atlas-SNP	.											.	CLCN6	77	.	0			c.G234A						PASS	.	G	,,,	483,3923	220.7+/-238.1	24,435,1744	134.0	103.0	114.0		234,234,234,234	1.6	1.0	1	dbSNP_129	114	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLCN6	NM_001286.2,NM_021735.2,NM_021736.2,NM_021737.2	,,,	24,443,6036	AA,AG,GG		0.093,10.9623,3.7752	,,,	78/870,78/321,78/354,78/309	11876692	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	1185	exon4			TGAGGCGGTGAAG	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.234G>A	1.37:g.11876692G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	192	111	0.578125	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Silent	SNP	ENST00000346436.6	37	CCDS138.1																																																																																			G|0.971;A|0.029	0.029	strong		0.532	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
TMPRSS2	7113	hgsc.bcm.edu	37	21	42866296	42866296	+	Silent	SNP	T	T	C	rs3787950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:42866296T>C	ENST00000332149.5	-	3	359	c.225A>G	c.(223-225)acA>acG	p.T75T	TMPRSS2_ENST00000458356.1_Silent_p.T75T|TMPRSS2_ENST00000497881.1_Intron|TMPRSS2_ENST00000398585.3_Silent_p.T112T	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	75					positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.T75T(1)	TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				AGGTGCACACTGTCCCGGATG	0.602			T	"""ERG, ETV1, ETV4, ETV5"""	prostate								T|||	816	0.162939	0.2179	0.0605	5008	,	,		18021	0.1548		0.0785	False		,,,				2504	0.2566				p.T112T		Atlas-SNP	.		Dom	yes		21	21q22.3	7113	"""transmembrane protease, serine 2"""		E	TMPRSS2_ENST00000332149,NS,carcinoma,0,1	TMPRSS2	148	1	1	Substitution - coding silent(1)	stomach(1)	c.A336G						PASS	.	T	,	831,3575	325.6+/-299.2	91,649,1463	47.0	46.0	46.0		336,225	-9.0	0.0	21	dbSNP_107	46	700,7900	167.4+/-219.2	38,624,3638	no	coding-synonymous,coding-synonymous	TMPRSS2	NM_001135099.1,NM_005656.3	,	129,1273,5101	CC,CT,TT		8.1395,18.8606,11.7715	,	112/530,75/493	42866296	1531,11475	2203	4300	6503	SO:0001819	synonymous_variant	7113	exon3			GCACACTGTCCCG	U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"""Serine peptidases / Transmembrane"""	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.225A>G	21.37:g.42866296T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	111	64	0.576577	NM_001135099	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Silent	SNP	ENST00000332149.5	37	CCDS33564.1																																																																																			C|0.135;N|0.001	0.135	strong		0.602	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1		
FAT3	120114	hgsc.bcm.edu	37	11	92624276	92624276	+	Silent	SNP	G	G	A	rs371790138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92624276G>A	ENST00000298047.6	+	27	13784	c.13767G>A	c.(13765-13767)gtG>gtA	p.V4589V	FAT3_ENST00000525166.1_Silent_p.V4439V|FAT3_ENST00000409404.2_Silent_p.V4557V|FAT3_ENST00000533797.1_Silent_p.V892V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4589					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)				AGACTCAAGTGTAGACATCAC	0.507										TCGA Ovarian(4;0.039)			G|||	3	0.000599042	0.0023	0.0	5008	,	,		20727	0.0		0.0	False		,,,				2504	0.0				p.V4557V		Atlas-SNP	.											.	FAT3	1822	.	0			c.G13671A						PASS	.	G		9,4135		0,9,2063	43.0	45.0	44.0		13671	3.8	1.0	11		44	0,8398		0,0,4199	no	coding-synonymous	FAT3	NM_001008781.2		0,9,6262	AA,AG,GG		0.0,0.2172,0.0718		4557/4558	92624276	9,12533	2072	4199	6271	SO:0001819	synonymous_variant	120114	exon25			TCAAGTGTAGACA	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.13767G>A	11.37:g.92624276G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	weak		0.507	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
GFM2	84340	hgsc.bcm.edu	37	5	74037369	74037369	+	Silent	SNP	C	C	T	rs35565659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:74037369C>T	ENST00000296805.3	-	11	1372	c.915G>A	c.(913-915)ttG>ttA	p.L305L	GFM2_ENST00000427854.2_Silent_p.L305L|GFM2_ENST00000509430.1_Silent_p.L305L|GFM2_ENST00000345239.2_Silent_p.L305L	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(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;1.86e-56)		CAGCTGGTAACAAATCAAAAT	0.303													C|||	152	0.0303514	0.1097	0.0101	5008	,	,		15822	0.0		0.0	False		,,,				2504	0.0				p.L305L		Atlas-SNP	.											.	GFM2	38	.	0			c.G915A						PASS	.	C	,,	392,4000		12,368,1816	42.0	44.0	43.0		915,915,915	3.1	1.0	5	dbSNP_126	43	5,8569		0,5,4282	no	coding-synonymous,coding-synonymous,coding-synonymous	GFM2	NM_032380.3,NM_170681.1,NM_170691.1	,,	12,373,6098	TT,TC,CC		0.0583,8.9253,3.0619	,,	305/780,305/514,305/733	74037369	397,12569	2196	4287	6483	SO:0001819	synonymous_variant	84340	exon11			TGGTAACAAATCA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.915G>A	5.37:g.74037369C>T		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	247	110	0.445344	NM_032380		Silent	SNP	ENST00000296805.3	37	CCDS4023.1																																																																																			C|0.976;T|0.024	0.024	strong		0.303	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
TBATA	219793	hgsc.bcm.edu	37	10	72536936	72536936	+	Silent	SNP	A	A	G	rs2254433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.	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	49	1	0.0204082		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	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	
ZNF366	167465	hgsc.bcm.edu	37	5	71740073	71740073	+	Missense_Mutation	SNP	A	A	T	rs116305374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71740073A>T	ENST00000318442.5	-	5	2235	c.1745T>A	c.(1744-1746)cTg>cAg	p.L582Q	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	582	Interaction with CTBP1.|Interaction with NRIP1.				negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		CAGACTCCTCAGGACACCGGC	0.607													A|||	9	0.00179712	0.0068	0.0	5008	,	,		15362	0.0		0.0	False		,,,				2504	0.0				p.L582Q		Atlas-SNP	.											.	ZNF366	108	.	0			c.T1745A						PASS	.	A	GLN/LEU	17,4379		0,17,2181	36.0	44.0	41.0		1745	5.9	1.0	5	dbSNP_133	41	0,8588		0,0,4294	yes	missense	ZNF366	NM_152625.1	113	0,17,6475	TT,TA,AA		0.0,0.3867,0.1309	probably-damaging	582/745	71740073	17,12967	2198	4294	6492	SO:0001583	missense	167465	exon5			CTCCTCAGGACAC	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.1745T>A	5.37:g.71740073A>T	ENSP00000313158:p.Leu582Gln	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	102	42	0.411765	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	37	CCDS4015.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	20.9	4.063034	0.76187	0.003867	0.0	ENSG00000178175	ENST00000318442	T	0.09723	2.95	5.87	5.87	0.94306	.	0.000000	0.52532	D	0.000062	T	0.17023	0.0409	L	0.36672	1.1	0.47737	D	0.999503	D	0.63880	0.993	D	0.62955	0.909	T	0.07616	-1.0763	10	0.07482	T	0.82	-37.1713	11.6024	0.51010	0.931:0.0:0.069:0.0	.	582	Q8N895	ZN366_HUMAN	Q	582	ENSP00000313158:L582Q	ENSP00000313158:L582Q	L	-	2	0	ZNF366	71775829	1.000000	0.71417	0.992000	0.48379	0.753000	0.42808	6.038000	0.70964	2.371000	0.80710	0.533000	0.62120	CTG	A|0.999;T|0.001	0.001	strong		0.607	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
C17orf85	55421	hgsc.bcm.edu	37	17	3749411	3749411	+	Missense_Mutation	SNP	T	T	G	rs12449334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3749411T>G	ENST00000389005.4	-	1	134	c.107A>C	c.(106-108)gAg>gCg	p.E36A	C17orf85_ENST00000158149.3_5'UTR	NM_001114118.2	NP_001107590.1	Q53F19	CQ085_HUMAN	chromosome 17 open reading frame 85	36							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (3;0.0725)		GGGCTCCGGCTCGCCACGGTC	0.736													T|||	346	0.0690895	0.1339	0.0101	5008	,	,		10338	0.123		0.006	False		,,,				2504	0.0327				p.E36A		Atlas-SNP	.											.	C17orf85	66	.	0			c.A107C						PASS	.	T	ALA/GLU,	160,1220		6,148,536	11.0	14.0	13.0		107,	4.3	1.0	17	dbSNP_120	13	15,3167		0,15,1576	yes	missense,utr-5	C17orf85	NM_001114118.1,NM_018553.3	107,	6,163,2112	GG,GT,TT		0.4714,11.5942,3.836	probably-damaging,	36/621,	3749411	175,4387	690	1591	2281	SO:0001583	missense	55421	exon1			TCCGGCTCGCCAC		CCDS45578.1	17p13.2	2012-10-23			ENSG00000074356	ENSG00000074356			24612	protein-coding gene	gene with protein product	"""ELG protein"""					11412301	Standard	NM_001114118		Approved	HSA277841, ELG	uc010ckl.2	Q53F19	OTTHUMG00000177672	ENST00000389005.4:c.107A>C	17.37:g.3749411T>G	ENSP00000373657:p.Glu36Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_001114118	B3KWG7|Q7L406|Q96FK1|Q9NXZ4	Missense_Mutation	SNP	ENST00000389005.4	37	CCDS45578.1	119	0.05448717948717949	55	0.11178861788617886	3	0.008287292817679558	59	0.10314685314685315	2	0.002638522427440633	T	26.4	4.738297	0.89573	0.115942	0.004714	ENSG00000074356	ENST00000389005	.	.	.	4.27	4.27	0.50696	.	0.058567	0.64402	D	0.000002	T	0.01489	0.0048	N	0.24115	0.695	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.05666	-1.0871	9	0.62326	D	0.03	-16.2075	12.0236	0.53358	0.0:0.0:0.0:1.0	rs12449334;rs57228453;rs12449334	36	Q53F19	CQ085_HUMAN	A	36	.	ENSP00000373657:E36A	E	-	2	0	C17orf85	3696160	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.869000	0.69613	2.169000	0.68431	0.374000	0.22700	GAG	T|0.949;G|0.051	0.051	strong		0.736	C17orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438385.1	NM_018553	
CEP112	201134	hgsc.bcm.edu	37	17	63822357	63822357	+	Intron	SNP	T	T	C	rs62065084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:63822357T>C	ENST00000392769.2	-	21	2613				CEP112_ENST00000535342.2_Intron|CEP112_ENST00000580482.1_Intron|CEP112_ENST00000317442.8_Missense_Mutation_p.I21V|CEP112_ENST00000541355.1_Intron|CEP112_ENST00000537949.1_Intron	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa						receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						CTCATCTCTATCAGTCTCAGG	0.463													T|||	1074	0.214457	0.2368	0.2262	5008	,	,		21080	0.125		0.2207	False		,,,				2504	0.2618				p.I21V		Atlas-SNP	.											.	CEP112	192	.	0			c.A61G						PASS	.	T	VAL/ILE,,	1069,3337	390.7+/-327.8	141,787,1275	259.0	258.0	258.0		61,,	-0.8	0.0	17	dbSNP_129	258	2066,6534	359.0+/-331.4	238,1590,2472	yes	missense,intron,intron	CEP112	NM_001037325.2,NM_001199165.1,NM_145036.3	29,,	379,2377,3747	CC,CT,TT		24.0233,24.2624,24.1043	,,	21/212,,	63822357	3135,9871	2203	4300	6503	SO:0001627	intron_variant	201134	exon1			TCTCTATCAGTCT	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"""coiled-coil domain containing 46"""	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.2394+25564A>G	17.37:g.63822357T>C		Somatic	348	0	0		WXS	Illumina HiSeq	Phase_I	395	176	0.44557	NM_001037325	Q6PIB5|Q8NCR4|Q8NFR4	Missense_Mutation	SNP	ENST00000392769.2	37	CCDS32710.1	440	0.20146520146520147	115	0.23373983739837398	86	0.23756906077348067	77	0.1346153846153846	162	0.21372031662269128	T	8.616	0.890231	0.17613	0.242624	0.240233	ENSG00000154240	ENST00000317442	.	.	.	3.01	-0.831	0.10789	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.32981	-0.9886	6	0.24483	T	0.36	.	4.3253	0.11038	0.0:0.1211:0.4057:0.4732	rs62065084	21	Q8N8E3-2	.	V	21	.	ENSP00000320592:I21V	I	-	1	0	CEP112	61252819	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.252000	0.08806	-0.210000	0.10140	0.454000	0.30748	ATA	T|0.765;C|0.235	0.235	strong		0.463	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12856087	12856087	+	Missense_Mutation	SNP	C	C	T	rs141070565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12856087C>T	ENST00000332296.7	+	4	1470	c.1367C>T	c.(1366-1368)cCc>cTc	p.P456L	PRAMEF1_ENST00000400814.3_Missense_Mutation_p.P211L	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	456					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.P456L(4)		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)		GGCCCCACCCCCTGCCCTTCC	0.557																																					p.P456L		Atlas-SNP	.											PRAMEF1,trunk,malignant_melanoma,0,4	PRAMEF1	78	4	4	Substitution - Missense(4)	skin(4)	c.C1367T						scavenged	.	C	LEU/PRO	154,4248		0,154,2047	61.0	69.0	66.0		1367	-2.3	0.0	1	dbSNP_134	66	288,8300		0,288,4006	no	missense	PRAMEF1	NM_023013.2	98	0,442,6053	TT,TC,CC		3.3535,3.4984,3.4026	probably-damaging	456/475	12856087	442,12548	2201	4294	6495	SO:0001583	missense	65121	exon4			CCACCCCCTGCCC	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.1367C>T	1.37:g.12856087C>T	ENSP00000332134:p.Pro456Leu	Somatic	699	0	0		WXS	Illumina HiSeq	Phase_I	835	136	0.162874	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	10.30	1.313050	0.23908	0.034984	0.033535	ENSG00000116721	ENST00000332296;ENST00000400814	T;T	0.51071	0.72;0.72	1.56	-2.32	0.06745	.	1.064360	0.07319	N	0.877252	T	0.20292	0.0488	L	0.58810	1.83	0.09310	N	1	P	0.50819	0.939	P	0.51135	0.66	T	0.19943	-1.0290	10	0.17832	T	0.49	.	0.4517	0.00502	0.2326:0.3128:0.2565:0.1982	.	456	O95521	PRAM1_HUMAN	L	456;211	ENSP00000332134:P456L;ENSP00000383616:P211L	ENSP00000332134:P456L	P	+	2	0	PRAMEF1	12778674	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.486000	0.06513	-0.706000	0.05028	0.205000	0.17691	CCC	C|0.968;T|0.032	0.032	strong		0.557	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
POM121L2	94026	hgsc.bcm.edu	37	6	27277051	27277051	+	Missense_Mutation	SNP	C	C	T	rs41269255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27277051C>T	ENST00000444565.1	-	1	2898	c.2899G>A	c.(2899-2901)Gcc>Acc	p.A967T	POM121L2_ENST00000377451.2_Missense_Mutation_p.A903T	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	967										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						GCAATGGGGGCCATAGTCTTT	0.572													C|||	537	0.107228	0.0817	0.1009	5008	,	,		17356	0.0813		0.1392	False		,,,				2504	0.1401				p.A967T		Atlas-SNP	.											POM121L2,colon,carcinoma,0,1	POM121L2	61	1	0			c.G2899A						PASS	.	C	THR/ALA	109,1275		6,97,589	51.0	51.0	51.0		2899	-0.0	0.0	6	dbSNP_127	51	359,2823		21,317,1253	yes	missense	POM121L2	NM_033482.3	58	27,414,1842	TT,TC,CC		11.2822,7.8757,10.2497	possibly-damaging	967/1036	27277051	468,4098	692	1591	2283	SO:0001583	missense	94026	exon1			TGGGGGCCATAGT	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.2899G>A	6.37:g.27277051C>T	ENSP00000392726:p.Ala967Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	231	0.10576923076923077	47	0.09552845528455285	37	0.10220994475138122	41	0.07167832167832168	106	0.13984168865435356	C	7.174	0.588193	0.13812	0.078757	0.112822	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.12984	2.65;2.63	3.68	-0.0238	0.13941	.	.	.	.	.	T	0.02230	0.0069	L	0.29908	0.895	0.80722	P	0.0	B	0.25312	0.123	B	0.16289	0.015	T	0.46843	-0.9162	8	0.23891	T	0.37	.	4.333	0.11073	0.0:0.5773:0.2256:0.1971	rs41269255;rs61736080	967	C9J1I7	.	T	903;967	ENSP00000366671:A903T;ENSP00000392726:A967T	ENSP00000366671:A903T	A	-	1	0	POM121L2	27385030	0.001000	0.12720	0.000000	0.03702	0.076000	0.17211	-0.104000	0.10923	-0.014000	0.14175	0.305000	0.20034	GCC	C|0.891;T|0.109	0.109	strong		0.572	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
FCRL5	83416	hgsc.bcm.edu	37	1	157514091	157514091	+	Missense_Mutation	SNP	C	C	T	rs12036228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157514091C>T	ENST00000361835.3	-	5	962	c.805G>A	c.(805-807)Gtc>Atc	p.V269I	FCRL5_ENST00000368191.3_Missense_Mutation_p.V184I|FCRL5_ENST00000368190.3_Missense_Mutation_p.V269I|FCRL5_ENST00000356953.4_Missense_Mutation_p.V269I|FCRL5_ENST00000368189.3_Missense_Mutation_p.V269I	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	269	Ig-like C2-type 2.		V -> I (in dbSNP:rs12036228). {ECO:0000269|PubMed:11493702, ECO:0000269|PubMed:15489334}.		negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				TCAGATATGACGCTGTAAGGC	0.512													T|||	990	0.197684	0.295	0.1729	5008	,	,		20744	0.0784		0.2376	False		,,,				2504	0.1656				p.V269I		Atlas-SNP	.											.	FCRL5	177	.	0			c.G805A						PASS	.	T	ILE/VAL,ILE/VAL	1295,3111	699.1+/-406.4	182,931,1090	154.0	152.0	153.0		805,805	-1.6	0.0	1	dbSNP_120	153	1842,6758	731.3+/-406.8	195,1452,2653	yes	missense,missense	FCRL5	NM_001195388.1,NM_031281.2	29,29	377,2383,3743	TT,TC,CC		21.4186,29.3917,24.1196	benign,benign	269/999,269/978	157514091	3137,9869	2203	4300	6503	SO:0001583	missense	83416	exon5			ATATGACGCTGTA	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.805G>A	1.37:g.157514091C>T	ENSP00000354691:p.Val269Ile	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	156	75	0.480769	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	457	0.20924908424908426	151	0.30691056910569103	74	0.20441988950276244	46	0.08041958041958042	186	0.24538258575197888	T	7.167	0.586880	0.13749	0.293917	0.214186	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191;ENST00000368189	T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7	4.0	-1.58	0.08479	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02230	0.0069	N	0.20685	0.6	0.80722	P	0.0	B;B;B;B;B;B	0.28605	0.032;0.1;0.026;0.217;0.114;0.045	B;B;B;B;B;B	0.29524	0.053;0.057;0.049;0.084;0.037;0.103	T	0.47341	-0.9125	8	0.13853	T	0.58	.	10.5466	0.45064	0.0:0.5765:0.0:0.4235	rs12036228;rs12036228	300;184;269;269;269;269	B4DW39;F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9-4;Q96RD9	.;.;.;.;.;FCRL5_HUMAN	I	269;269;269;184;269	ENSP00000354691:V269I;ENSP00000349434:V269I;ENSP00000357173:V269I;ENSP00000357174:V184I;ENSP00000357172:V269I	ENSP00000349434:V269I	V	-	1	0	FCRL5	155780715	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.680000	0.00837	-0.792000	0.04480	-1.361000	0.01213	GTC	C|0.772;T|0.228	0.228	strong		0.512	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
MCM8	84515	hgsc.bcm.edu	37	20	5935303	5935303	+	Missense_Mutation	SNP	A	A	C	rs6117014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5935303A>C	ENST00000378896.3	+	4	680	c.303A>C	c.(301-303)aaA>aaC	p.K101N	MCM8_ENST00000265187.4_Missense_Mutation_p.K101N|MCM8_ENST00000378883.1_Missense_Mutation_p.K101N|MCM8_ENST00000378886.2_Missense_Mutation_p.K101N	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	101			K -> N (in dbSNP:rs6117014).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						CATTTGAAAAATTTTTCACAA	0.373													A|||	351	0.0700879	0.1626	0.1009	5008	,	,		19997	0.001		0.0199	False		,,,				2504	0.046				p.K101N		Atlas-SNP	.											.	MCM8	125	.	0			c.A303C						PASS	.	A	ASN/LYS,ASN/LYS	652,3750	276.0+/-272.9	51,550,1600	101.0	97.0	98.0		303,303	-10.4	0.5	20	dbSNP_114	98	183,8417	83.1+/-145.7	2,179,4119	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	94,94	53,729,5719	CC,CA,AA		2.1279,14.8114,6.4221	benign,benign	101/841,101/825	5935303	835,12167	2201	4300	6501	SO:0001583	missense	84515	exon4			TGAAAAATTTTTC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.303A>C	20.37:g.5935303A>C	ENSP00000368174:p.Lys101Asn	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	145	0.06639194139194139	92	0.18699186991869918	29	0.08011049723756906	2	0.0034965034965034965	22	0.029023746701846966	A	11.02	1.515159	0.27123	0.148114	0.021279	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000399350;ENST00000378886;ENST00000265187	T;T;T;T	0.04119	3.7;3.7;3.7;3.7	5.37	-10.4	0.00318	Nucleic acid-binding, OB-fold-like (1);	0.302307	0.39475	N	0.001357	T	0.00012	0.0000	L	0.29908	0.895	0.27511	P	0.9516967	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.002;0.001	T	0.38265	-0.9669	9	0.11485	T	0.65	-1.2423	2.7834	0.05367	0.2356:0.137:0.3949:0.2325	rs6117014;rs52802444;rs6117014	101;101;101;101	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	N	101	ENSP00000368174:K101N;ENSP00000368161:K101N;ENSP00000368164:K101N;ENSP00000265187:K101N	ENSP00000265187:K101N	K	+	3	2	MCM8	5883303	0.041000	0.20044	0.522000	0.27862	0.993000	0.82548	-1.262000	0.02852	-1.754000	0.01321	-0.250000	0.11733	AAA	A|0.936;C|0.064	0.064	strong		0.373	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
ECM1	1893	hgsc.bcm.edu	37	1	150484016	150484016	+	Silent	SNP	G	G	A	rs78194273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150484016G>A	ENST00000369047.4	+	7	917	c.792G>A	c.(790-792)gaG>gaA	p.E264E	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Silent_p.E291E|ECM1_ENST00000346569.6_Intron	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	264	2 X approximate repeats.				angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GGCAGGGGGAGGCTCGGTTCT	0.632													G|||	82	0.0163738	0.0582	0.0072	5008	,	,		16846	0.0		0.0	False		,,,				2504	0.0				p.E291E	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											.	ECM1	96	.	0			c.G873A						PASS	.	G	,,	207,4199	127.4+/-164.3	7,193,2003	52.0	50.0	51.0		873,792,	4.5	1.0	1	dbSNP_132	51	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,intron	ECM1	NM_001202858.1,NM_004425.3,NM_022664.2	,,	7,196,6300	AA,AG,GG		0.0349,4.6981,1.6146	,,	291/568,264/541,	150484016	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	1893	exon7			GGGGGAGGCTCGG	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.792G>A	1.37:g.150484016G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	99	54	0.545455	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Silent	SNP	ENST00000369047.4	37	CCDS953.1																																																																																			G|0.984;A|0.016	0.016	strong		0.632	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
FLNB	2317	hgsc.bcm.edu	37	3	58139172	58139172	+	Silent	SNP	G	G	A	rs60599272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:58139172G>A	ENST00000295956.4	+	39	6603	c.6438G>A	c.(6436-6438)gtG>gtA	p.V2146V	FLNB_ENST00000493452.1_Silent_p.V1953V|FLNB_ENST00000490882.1_Silent_p.V2177V|FLNB_ENST00000348383.5_Silent_p.V2105V|FLNB_ENST00000429972.2_Silent_p.V2135V|FLNB_ENST00000419752.2_Silent_p.V1966V|FLNB_ENST00000358537.3_Silent_p.V2122V|FLNB_ENST00000357272.4_3'UTR	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	2146	Interaction with FLNA 1.|Interaction with INPPL1.|Interaction with the cytoplasmic tail of GP1BA.				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)		CAGAGATTGTGCCCATGGGGA	0.612													G|||	122	0.024361	0.0877	0.0086	5008	,	,		22137	0.0		0.0	False		,,,				2504	0.0				p.V2177V		Atlas-SNP	.											.	FLNB	430	.	0			c.G6531A						PASS	.	G	,,,	425,3981	206.5+/-228.1	26,373,1804	98.0	89.0	92.0		6531,6405,6366,6438	0.2	1.0	3	dbSNP_129	92	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	26,377,6100	AA,AG,GG		0.0465,9.6459,3.2985	,,,	2177/2634,2135/2592,2122/2579,2146/2603	58139172	429,12577	2203	4300	6503	SO:0001819	synonymous_variant	2317	exon40			GATTGTGCCCATG	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.6438G>A	3.37:g.58139172G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1	45	0.020604395604395604	43	0.08739837398373984	2	0.0055248618784530384	0	0.0	0	0.0	G	4.692	0.128591	0.08981	0.096459	4.65E-4	ENSG00000136068	ENST00000466455	.	.	.	5.77	0.231	0.15377	.	.	.	.	.	T	0.01222	0.0040	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06716	-1.0811	4	.	.	.	.	0.8171	0.01105	0.2853:0.1233:0.3429:0.2485	rs60599272	.	.	.	T	70	.	.	A	+	1	0	FLNB	58114212	0.055000	0.20627	0.979000	0.43373	0.529000	0.34654	-0.906000	0.04071	0.087000	0.17167	-1.151000	0.01829	GCC	G|0.971;A|0.029	0.029	strong		0.612	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
LRP2	4036	hgsc.bcm.edu	37	2	170038097	170038097	+	Missense_Mutation	SNP	C	C	T	rs137983840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170038097C>T	ENST00000263816.3	-	52	10315	c.10030G>A	c.(10030-10032)Gca>Aca	p.A3344T	LRP2_ENST00000461418.1_5'UTR	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3344					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)"""	CCAATGTATGCGCGGTGACCC	0.483													C|||	8	0.00159744	0.0053	0.0014	5008	,	,		18886	0.0		0.0	False		,,,				2504	0.0				p.A3344T		Atlas-SNP	.											LRP2,NS,carcinoma,0,1	LRP2	751	1	0			c.G10030A						PASS	.	C	THR/ALA	23,4383	29.9+/-59.1	0,23,2180	151.0	123.0	132.0		10030	4.8	0.8	2	dbSNP_134	132	1,8599	1.2+/-3.3	0,1,4299	yes	missense	LRP2	NM_004525.2	58	0,24,6479	TT,TC,CC		0.0116,0.522,0.1845	probably-damaging	3344/4656	170038097	24,12982	2203	4300	6503	SO:0001583	missense	4036	exon52			TGTATGCGCGGTG		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.10030G>A	2.37:g.170038097C>T	ENSP00000263816:p.Ala3344Thr	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	183	82	0.448087	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	C	17.25	3.341348	0.60963	0.00522	1.16E-4	ENSG00000081479	ENST00000263816;ENST00000536293	D	0.97811	-4.55	5.66	4.76	0.60689	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.170562	0.52532	D	0.000080	D	0.98327	0.9445	M	0.92169	3.28	0.80722	D	1	D	0.76494	0.999	P	0.62184	0.899	D	0.96079	0.9052	10	0.59425	D	0.04	.	16.2936	0.82761	0.0:0.7787:0.2213:0.0	.	3344	P98164	LRP2_HUMAN	T	3344;39	ENSP00000263816:A3344T	ENSP00000263816:A3344T	A	-	1	0	LRP2	169746343	0.991000	0.36638	0.788000	0.31933	0.219000	0.24729	2.604000	0.46274	2.661000	0.90470	0.655000	0.94253	GCA	C|0.999;T|0.001	0.001	strong		0.483	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
CD83	9308	hgsc.bcm.edu	37	6	14131854	14131854	+	Missense_Mutation	SNP	A	A	G	rs35118414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:14131854A>G	ENST00000379153.3	+	3	428	c.257A>G	c.(256-258)aAt>aGt	p.N86S		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	86	Ig-like V-type.				defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				GACGCCCCCAATGAAAGGCCC	0.547													A|||	194	0.038738	0.0643	0.0375	5008	,	,		20463	0.0198		0.0288	False		,,,				2504	0.0348				p.N86S		Atlas-SNP	.											.	CD83	23	.	0			c.A257G						PASS	.	A	SER/ASN,SER/ASN	258,4148	149.2+/-183.4	6,246,1951	130.0	121.0	124.0		257,257	-1.2	0.0	6	dbSNP_126	124	333,8267	116.1+/-175.8	5,323,3972	yes	missense,missense	CD83	NM_001040280.1,NM_004233.3	46,46	11,569,5923	GG,GA,AA		3.8721,5.8557,4.5441	benign,benign	86/205,86/206	14131854	591,12415	2203	4300	6503	SO:0001583	missense	9308	exon3			CCCCCAATGAAAG	Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1703	protein-coding gene	gene with protein product		604534	"""CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)"", ""CD83 molecule """			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.257A>G	6.37:g.14131854A>G	ENSP00000368450:p.Asn86Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_004233	Q5THX9	Missense_Mutation	SNP	ENST00000379153.3	37	CCDS4532.1	88	0.040293040293040296	33	0.06707317073170732	15	0.04143646408839779	16	0.027972027972027972	24	0.0316622691292876	A	1.969	-0.437052	0.04636	0.058557	0.038721	ENSG00000112149	ENST00000379153	T	0.60920	0.15	5.39	-1.24	0.09435	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.293720	0.01187	N	0.007226	T	0.05090	0.0136	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13308	-1.0514	10	0.08179	T	0.78	-14.691	2.083	0.03639	0.3074:0.122:0.4459:0.1246	rs35118414;rs61761633	86	Q01151	CD83_HUMAN	S	86	ENSP00000368450:N86S	ENSP00000368450:N86S	N	+	2	0	CD83	14239833	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.293000	0.08320	-0.146000	0.11274	-0.146000	0.13790	AAT	A|0.956;G|0.044	0.044	strong		0.547	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1		
RAET1L	154064	hgsc.bcm.edu	37	6	150342232	150342232	+	Missense_Mutation	SNP	G	G	A	rs61730071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:150342232G>A	ENST00000367341.1	-	3	439	c.440C>T	c.(439-441)aCc>aTc	p.T147I	RAET1L_ENST00000286380.2_Missense_Mutation_p.T147I			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	147	MHC class I alpha-2 like. {ECO:0000250}.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		GAGTAGGAAGGTCTGTCCATC	0.502													A|||	1648	0.329073	0.3033	0.2925	5008	,	,		19640	0.2401		0.4394	False		,,,				2504	0.3681				p.T147I		Atlas-SNP	.											.	RAET1L	21	.	0			c.C440T						PASS	.	A	ILE/THR	1375,3031		217,941,1045	284.0	245.0	258.0		440	-0.8	0.0	6	dbSNP_129	258	3839,4761		854,2131,1315	yes	missense	RAET1L	NM_130900.2	89	1071,3072,2360	AA,AG,GG		44.6395,31.2074,40.0892	benign	147/247	150342232	5214,7792	2203	4300	6503	SO:0001583	missense	154064	exon3			AGGAAGGTCTGTC	AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918			16798	protein-coding gene	gene with protein product		611047				11827464	Standard	NM_130900		Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.440C>T	6.37:g.150342232G>A	ENSP00000356310:p.Thr147Ile	Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	391	199	0.508951	NM_130900	A3KME4|Q8TE74	Missense_Mutation	SNP	ENST00000367341.1	37	CCDS5224.1	739	0.3383699633699634	153	0.31097560975609756	122	0.3370165745856354	125	0.21853146853146854	339	0.4472295514511873	N	0.003	-2.509455	0.00153	0.312074	0.446395	ENSG00000155918	ENST00000367341;ENST00000286380	T;T	0.00717	5.79;5.79	1.91	-0.819	0.10829	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00144	0.0004	N	0.04203	-0.255	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.17806	-1.0357	8	0.27082	T	0.32	.	2.1695	0.03846	0.4177:0.0:0.3358:0.2465	.	147	Q5VY80	RET1L_HUMAN	I	147	ENSP00000356310:T147I;ENSP00000286380:T147I	ENSP00000286380:T147I	T	-	2	0	RAET1L	150383925	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.278000	0.02809	-0.646000	0.05452	-1.305000	0.01319	ACC	G|0.611;A|0.389	0.389	strong		0.502	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042676.1	NM_130900	
CDT1	81620	hgsc.bcm.edu	37	16	88871908	88871908	+	Silent	SNP	A	A	G	rs1834065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88871908A>G	ENST00000301019.4	+	4	1168	c.549A>G	c.(547-549)ggA>ggG	p.G183G		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)		GCCTGCCGGGACTCGTGCTGC	0.662													G|||	683	0.136382	0.351	0.0821	5008	,	,		15455	0.003		0.0567	False		,,,				2504	0.1043				p.G183G	Melanoma(159;511 3380 30971)	Atlas-SNP	.											.	CDT1	30	.	0			c.A549G						PASS	.	G		1370,3026	663.6+/-401.2	221,928,1049	43.0	49.0	47.0		549	1.5	0.4	16	dbSNP_92	47	614,7982	778.8+/-407.7	16,582,3700	no	coding-synonymous	CDT1	NM_030928.3		237,1510,4749	GG,GA,AA		7.1429,31.1647,15.2709		183/547	88871908	1984,11008	2198	4298	6496	SO:0001819	synonymous_variant	81620	exon4			GCCGGGACTCGTG	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.549A>G	16.37:g.88871908A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_030928		Silent	SNP	ENST00000301019.4	37	CCDS32510.1																																																																																			A|0.864;G|0.136	0.136	strong		0.662	CDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423215.1	NM_030928	
TCEB3	6924	hgsc.bcm.edu	37	1	24077554	24077554	+	Silent	SNP	T	T	C	rs35397069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24077554T>C	ENST00000418390.2	+	4	808	c.537T>C	c.(535-537)gaT>gaC	p.D179D	TCEB3_ENST00000609199.1_Silent_p.D153D	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	179					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)		AGAGGAGAGATGAGAGAAAGA	0.498													C|||	487	0.0972444	0.351	0.0303	5008	,	,		19697	0.0		0.001	False		,,,				2504	0.001				p.D179D		Atlas-SNP	.											.	TCEB3	61	.	0			c.T537C						PASS	.	C		1242,3164	704.4+/-407.1	172,898,1133	105.0	97.0	100.0		537	-11.1	0.1	1	dbSNP_126	100	22,8578	818.3+/-406.9	0,22,4278	no	coding-synonymous	TCEB3	NM_003198.2		172,920,5411	CC,CT,TT		0.2558,28.1888,9.7186		179/799	24077554	1264,11742	2203	4300	6503	SO:0001819	synonymous_variant	6924	exon4			GAGAGATGAGAGA	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.537T>C	1.37:g.24077554T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	159	68	0.427673	NM_003198	B2R7Q8|Q8IXH1	Silent	SNP	ENST00000418390.2	37	CCDS239.2																																																																																			T|0.913;C|0.087	0.087	strong		0.498	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198	
VCAN	1462	hgsc.bcm.edu	37	5	82836912	82836912	+	Missense_Mutation	SNP	G	G	A	rs61733389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82836912G>A	ENST00000265077.3	+	8	8655	c.8090G>A	c.(8089-8091)cGt>cAt	p.R2697H	VCAN_ENST00000343200.5_Missense_Mutation_p.R1710H|VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2697	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CCAATTCCTCGTAAGTCTGCC	0.453													A|||	154	0.0307508	0.1097	0.0086	5008	,	,		22255	0.0		0.003	False		,,,				2504	0.0				p.R2697H		Atlas-SNP	.											.	VCAN	498	.	0			c.G8090A						PASS	.	A	,HIS/ARG,,HIS/ARG	375,4031	781.0+/-414.5	12,351,1840	87.0	82.0	84.0		,5129,,8090	3.4	0.0	5	dbSNP_129	84	4,8596	806.0+/-407.3	0,4,4296	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,29,,29	12,355,6136	AA,AG,GG		0.0465,8.5111,2.914	,benign,,benign	,1710/2410,,2697/3397	82836912	379,12627	2203	4300	6503	SO:0001583	missense	1462	exon8			TTCCTCGTAAGTC	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.8090G>A	5.37:g.82836912G>A	ENSP00000265077:p.Arg2697His	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	87	51	0.586207	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	59	0.027014652014652016	57	0.11585365853658537	2	0.0055248618784530384	0	0.0	0	0.0	A	3.518	-0.098356	0.07010	0.085111	4.65E-4	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.30714	1.52;1.52	6.17	3.43	0.39272	.	0.411591	0.25929	N	0.027400	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.19031	-1.0318	10	0.33940	T	0.23	.	9.0379	0.36300	0.1951:0.1117:0.6933:0.0	rs61733389	1710;2697	P13611-2;P13611	.;CSPG2_HUMAN	H	2697;1710	ENSP00000265077:R2697H;ENSP00000340062:R1710H	ENSP00000265077:R2697H	R	+	2	0	VCAN	82872668	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.225000	0.09151	0.183000	0.20059	-1.569000	0.00873	CGT	G|0.967;A|0.033	0.033	strong		0.453	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
C12orf43	64897	hgsc.bcm.edu	37	12	121442833	121442833	+	Missense_Mutation	SNP	C	C	T	rs34543757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121442833C>T	ENST00000288757.3	-	5	447	c.425G>A	c.(424-426)cGc>cAc	p.R142H	C12orf43_ENST00000366211.2_Missense_Mutation_p.R100H|C12orf43_ENST00000536407.2_Intron|C12orf43_ENST00000539736.1_Missense_Mutation_p.R131H|C12orf43_ENST00000537817.1_Missense_Mutation_p.R143H|C12orf43_ENST00000445832.3_Missense_Mutation_p.R112H	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	142										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TCGCTTTCGGCGGGGTTGGGG	0.527													.|||	31	0.0061901	0.0227	0.0	5008	,	,		13357	0.0		0.0	False		,,,				2504	0.001				p.R142H		Atlas-SNP	.											.	C12orf43	30	.	0			c.G425A						PASS	.	C	HIS/ARG	121,4283		2,117,2083	64.0	67.0	66.0		425	-0.7	0.0	12	dbSNP_126	66	0,8594		0,0,4297	yes	missense	C12orf43	NM_022895.1	29	2,117,6380	TT,TC,CC		0.0,2.7475,0.9309	benign	142/263	121442833	121,12877	2202	4297	6499	SO:0001583	missense	64897	exon5			TTTCGGCGGGGTT	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.425G>A	12.37:g.121442833C>T	ENSP00000288757:p.Arg142His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	100	57	0.57	NM_022895	Q53HF0|Q9H9Z7	Missense_Mutation	SNP	ENST00000288757.3	37	CCDS9210.1	15|15	0.006868131868131868|0.006868131868131868	15|15	0.03048780487804878|0.03048780487804878	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	10.27|10.27	1.304130|1.304130	0.23736|0.23736	0.027475|0.027475	0.0|0.0	ENSG00000157895|ENSG00000157895	ENST00000546272|ENST00000445832;ENST00000288757;ENST00000537817;ENST00000366211;ENST00000539736;ENST00000538296;ENST00000535367	.|T;T;T;T;T	.|0.49432	.|0.81;0.78;0.81;0.84;0.83	5.65|5.65	-0.735|-0.735	0.11137|0.11137	.|.	.|1.534110	.|0.03428	.|N	.|0.207380	T|T	0.11067|0.11067	0.0270|0.0270	N|N	0.21142|0.21142	0.635|0.635	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B	.|0.19817	.|0.017;0.039;0.003;0.017;0.001	.|B;B;B;B;B	.|0.15052	.|0.007;0.012;0.003;0.007;0.002	T|T	0.03514|0.03514	-1.1029|-1.1029	5|10	.|0.17832	.|T	.|0.49	0.9065|0.9065	2.1|2.1	0.03677|0.03677	0.1243:0.427:0.2412:0.2075|0.1243:0.427:0.2412:0.2075	.|.	.|131;100;143;131;142	.|G5EA44;F6TFQ5;F5H7W8;B4DWJ9;Q96C57	.|.;.;.;.;CL043_HUMAN	T|H	95|112;142;143;100;131;79;96	.|ENSP00000409788:R112H;ENSP00000288757:R142H;ENSP00000442224:R143H;ENSP00000437803:R131H;ENSP00000442041:R79H	.|ENSP00000288757:R142H	A|R	-|-	1|2	0|0	C12orf43|C12orf43	119927216|119927216	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.008000|-0.008000	0.12788|0.12788	-0.335000|-0.335000	0.08451|0.08451	-0.158000|-0.158000	0.13435|0.13435	GCC|CGC	C|0.990;G|0.000;T|0.009	0.009	strong		0.527	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
SLC6A11	6538	hgsc.bcm.edu	37	3	10885920	10885920	+	Silent	SNP	T	T	C	rs2304725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	127	0	0		WXS	Illumina HiSeq	Phase_I	158	70	0.443038	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	
PRSS27	83886	hgsc.bcm.edu	37	16	2762637	2762637	+	Missense_Mutation	SNP	A	A	G	rs61734617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2762637A>G	ENST00000302641.3	-	6	911	c.857T>C	c.(856-858)tTg>tCg	p.L286S	AC092117.1_ENST00000410123.1_RNA	NM_031948.3	NP_114154.1	Q9BQR3	PRS27_HUMAN	protease, serine 27	286						extracellular region (GO:0005576)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8						CTGGCCGCCCAACCTCGCTGG	0.662													g|||	240	0.0479233	0.174	0.0101	5008	,	,		14544	0.0		0.003	False		,,,				2504	0.0				p.L286S		Atlas-SNP	.											.	PRSS27	20	.	0			c.T857C						PASS	.	G	SER/LEU	609,3777		37,535,1621	42.0	37.0	38.0		857	-2.0	0.0	16	dbSNP_129	38	4,8592		0,4,4294	yes	missense	PRSS27	NM_031948.3	145	37,539,5915	GG,GA,AA		0.0465,13.8851,4.7219	benign	286/291	2762637	613,12369	2193	4298	6491	SO:0001583	missense	83886	exon6			CCGCCCAACCTCG	AB056161	CCDS10476.1	16p13.3	2010-05-07			ENSG00000172382	ENSG00000172382		"""Serine peptidases / Serine peptidases"""	15475	protein-coding gene	gene with protein product		608018					Standard	NM_031948		Approved	MPN, pancreasin, CAPH2, marapsin	uc002crf.3	Q9BQR3	OTTHUMG00000128929	ENST00000302641.3:c.857T>C	16.37:g.2762637A>G	ENSP00000306390:p.Leu286Ser	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	171	82	0.479532	NM_031948		Missense_Mutation	SNP	ENST00000302641.3	37	CCDS10476.1	93	0.042582417582417584	90	0.18292682926829268	3	0.008287292817679558	0	0.0	0	0.0	.	2.610	-0.290913	0.05568	0.138851	4.65E-4	ENSG00000172382	ENST00000302641;ENST00000543965	D	0.88586	-2.4	4.96	-2.0	0.07433	.	5.046650	0.00575	N	0.000311	T	0.00412	0.0013	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	0.50676	-0.8800	9	0.06625	T	0.88	.	2.0974	0.03671	0.3642:0.1178:0.3973:0.1207	.	286;250	Q9BQR3;B3KP25	PRS27_HUMAN;.	S	286;250	ENSP00000306390:L286S	ENSP00000306390:L286S	L	-	2	0	PRSS27	2702638	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.040000	0.13905	-1.081000	0.03105	-1.147000	0.01851	TTG	A|0.948;G|0.052	0.052	strong		0.662	PRSS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250908.1	NM_031948	
CDAN1	146059	hgsc.bcm.edu	37	15	43023482	43023482	+	Missense_Mutation	SNP	T	T	C	rs12917189	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43023482T>C	ENST00000356231.3	-	12	1810	c.1787A>G	c.(1786-1788)cAg>cGg	p.Q596R		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	596			Q -> R (in dbSNP:rs12917189).		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)		ATTGAGCTCCTGGATCTTCAA	0.517													C|||	2272	0.453674	0.9531	0.1729	5008	,	,		18714	0.2589		0.2068	False		,,,				2504	0.4325				p.Q596R		Atlas-SNP	.											.	CDAN1	70	.	0			c.A1787G						PASS	.	C	ARG/GLN	3608,798	320.7+/-296.8	1488,632,83	94.0	93.0	93.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1787	4.1	1.0	15	dbSNP_121	93	1805,6793	732.8+/-406.9	203,1399,2697	yes	missense	CDAN1	NM_138477.2	43	1691,2031,2780	CC,CT,TT		20.9933,18.1117,41.6257	benign	596/1228	43023482	5413,7591	2203	4299	6502	SO:0001583	missense	146059	exon12			AGCTCCTGGATCT	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.1787A>G	15.37:g.43023482T>C	ENSP00000348564:p.Gln596Arg	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	218	217	0.995413	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	844	0.38644688644688646	465	0.9451219512195121	65	0.17955801104972377	144	0.2517482517482518	170	0.22427440633245382	C	5.952	0.359651	0.11239	0.818883	0.209933	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.86297	-2.1	5.92	4.05	0.47172	.	0.271850	0.36815	N	0.002396	T	0.00012	0.0000	N	0.01003	-1.06	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42565	-0.9444	9	0.06365	T	0.9	-10.1082	4.6587	0.12632	0.1737:0.5317:0.0:0.2946	rs12917189;rs52826213;rs61456383;rs12917189	596	Q8IWY9	CDAN1_HUMAN	R	596;594	ENSP00000348564:Q596R	ENSP00000267892:Q594R	Q	-	2	0	CDAN1	40810774	0.988000	0.35896	0.992000	0.48379	0.979000	0.70002	2.077000	0.41557	0.421000	0.25980	-0.119000	0.15052	CAG	C|0.419;N|0.000	0.419	strong		0.517	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
NF1	4763	hgsc.bcm.edu	37	17	29553485	29553485	+	Silent	SNP	G	G	A	rs2285892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:29553485G>A	ENST00000358273.4	+	18	2417	c.2034G>A	c.(2032-2034)ccG>ccA	p.P678P	NF1_ENST00000356175.3_Silent_p.P678P	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	678			P -> L (in dbSNP:rs17881753). {ECO:0000269|Ref.7}.		actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.I679fs*21(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GAACCCCCCCGATTTGCCGAC	0.483			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			G|||	2488	0.496805	0.7428	0.4683	5008	,	,		17568	0.5258		0.2803	False		,,,				2504	0.3773				p.P678P		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	13	Whole gene deletion(8)|Unknown(4)|Insertion - Frameshift(1)	soft_tissue(7)|central_nervous_system(3)|autonomic_ganglia(2)|lung(1)	c.G2034A						PASS	.	G	,	2929,1477	677.5+/-403.4	983,963,257	56.0	63.0	61.0		2034,2034	-9.9	0.4	17	dbSNP_100	61	2486,6114	407.2+/-349.1	357,1772,2171	no	coding-synonymous,coding-synonymous	NF1	NM_000267.3,NM_001042492.2	,	1340,2735,2428	AA,AG,GG		28.907,33.5225,41.6346	,	678/2819,678/2840	29553485	5415,7591	2203	4300	6503	SO:0001819	synonymous_variant	4763	exon18	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CCCCCCGATTTGC		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.2034G>A	17.37:g.29553485G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_000267	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																			G|0.568;A|0.432	0.432	strong		0.483	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
CECR6	27439	hgsc.bcm.edu	37	22	17600977	17600977	+	Silent	SNP	G	G	A	rs5994165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17600977G>A	ENST00000331437.3	-	1	1166	c.1041C>T	c.(1039-1041)ttC>ttT	p.F347F	AC006946.15_ENST00000441544.1_5'Flank|CECR6_ENST00000399875.1_5'UTR	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	36	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	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	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274161	39274161	+	Missense_Mutation	SNP	T	T	C	rs200329167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39274161T>C	ENST00000391413.2	-	1	445	c.407A>G	c.(406-408)cAc>cGc	p.H136R		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	136	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gcagctggggtggcagcaggt	0.662													t|||	497	0.0992412	0.174	0.1124	5008	,	,		19473	0.1478		0.0179	False		,,,				2504	0.0225				p.H136R		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,3	KRTAP4-11	94	3	0			c.A407G						scavenged	.						8.0	14.0	12.0					17																	39274161		684	1586	2270	SO:0001583	missense	653240	exon1			CTGGGGTGGCAGC	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.407A>G	17.37:g.39274161T>C	ENSP00000375232:p.His136Arg	Somatic	143	6	0.041958		WXS	Illumina HiSeq	Phase_I	129	52	0.403101	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	6.053	0.378142	0.11466	.	.	ENSG00000212721	ENST00000391413	T	0.01203	5.18	4.43	-4.18	0.03846	.	606.472000	0.01656	U	0.024837	T	0.00241	0.0007	N	0.00030	-2.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.53365	-0.8449	10	0.02654	T	1	.	0.2042	0.00148	0.2921:0.2622:0.1441:0.3015	.	136	Q9BYQ6	KR411_HUMAN	R	136	ENSP00000375232:H136R	ENSP00000375232:H136R	H	-	2	0	KRTAP4-11	36527687	0.000000	0.05858	0.005000	0.12908	0.909000	0.53808	-1.036000	0.03560	-0.298000	0.08921	-0.540000	0.04249	CAC	T|0.500;C|0.500	0.500	weak		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
SLC4A2	6522	hgsc.bcm.edu	37	7	150768849	150768849	+	Silent	SNP	C	C	T	rs11542749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150768849C>T	ENST00000485713.1	+	15	3305	c.2265C>T	c.(2263-2265)tgC>tgT	p.C755C	SLC4A2_ENST00000310317.5_Silent_p.C673C|SLC4A2_ENST00000413384.2_Silent_p.C755C|SLC4A2_ENST00000392826.2_Silent_p.C746C|SLC4A2_ENST00000461735.1_Silent_p.C741C|RP11-148K1.12_ENST00000485974.1_RNA	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	755	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGGTCTTCTGCCTGCTGGGTG	0.617													C|||	332	0.0662939	0.2027	0.036	5008	,	,		15252	0.0		0.0298	False		,,,				2504	0.0092				p.C755C		Atlas-SNP	.											.	SLC4A2	98	.	0			c.C2265T						PASS	.	C	,,,	593,3813	259.8+/-263.3	40,513,1650	83.0	90.0	88.0		2265,2238,2223,2265	1.9	1.0	7	dbSNP_120	88	256,8344	100.1+/-161.6	4,248,4048	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	,,,	44,761,5698	TT,TC,CC		2.9767,13.4589,6.5278	,,,	755/1242,746/1233,741/1228,755/1242	150768849	849,12157	2203	4300	6503	SO:0001819	synonymous_variant	6522	exon15			CTTCTGCCTGCTG		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.2265C>T	7.37:g.150768849C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Silent	SNP	ENST00000485713.1	37	CCDS5917.1																																																																																			C|0.927;T|0.073	0.073	strong		0.617	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
ZNF645	158506	hgsc.bcm.edu	37	X	22291606	22291606	+	Missense_Mutation	SNP	C	C	A	rs5951426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:22291606C>A	ENST00000323684.1	+	1	542	c.498C>A	c.(496-498)gaC>gaA	p.D166E		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	166			D -> E (in dbSNP:rs5951426). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20657603}.		protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						AAATCTCTGACATCCCTAAAA	0.463													A|||	1533	0.406093	0.5802	0.2954	3775	,	,		14986	0.3393		0.0845	False		,,,				2504	0.137				p.D166E		Atlas-SNP	.											.	ZNF645	67	.	0			c.C498A						PASS	.	A	GLU/ASP	2605,1230		768,679,390,185,181	93.0	90.0	91.0		498	0.8	0.0	X	dbSNP_114	91	752,5976		39,471,203,1918,1669	yes	missense	ZNF645	NM_152577.3	45	807,1150,593,2103,1850	AA,AC,A,CC,C		11.1772,32.073,31.7807	benign	166/426	22291606	3357,7206	2203	4300	6503	SO:0001583	missense	158506	exon1			CTCTGACATCCCT	AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.498C>A	X.37:g.22291606C>A	ENSP00000323348:p.Asp166Glu	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	272	135	0.496324	NM_152577	A0AV29|A0AV31|E3SBK4|Q6DJY9	Missense_Mutation	SNP	ENST00000323684.1	37	CCDS14205.1	635	0.38276069921639544	201	0.6165644171779141	70	0.2229299363057325	125	0.2880184331797235	41	0.05742296918767507	A	3.325	-0.137835	0.06711	0.67927	0.111772	ENSG00000175809	ENST00000323684	T	0.32272	1.46	3.32	0.836	0.18891	.	0.285432	0.29253	N	0.012685	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40213	-0.9575	9	0.06365	T	0.9	.	0.5068	0.00588	0.3297:0.1861:0.1164:0.3678	rs5951426;rs6528101;rs60426202;rs5951426	166	Q8N7E2	ZN645_HUMAN	E	166	ENSP00000323348:D166E	ENSP00000323348:D166E	D	+	3	2	ZNF645	22201527	0.047000	0.20315	0.000000	0.03702	0.001000	0.01503	-0.180000	0.09754	-0.203000	0.10251	-1.309000	0.01313	GAC	C|0.602;0|0.023	.	strong		0.463	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577	
CGNL1	84952	hgsc.bcm.edu	37	15	57839587	57839587	+	Missense_Mutation	SNP	A	A	G	rs16977594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:57839587A>G	ENST00000281282.5	+	19	3886	c.3808A>G	c.(3808-3810)Atg>Gtg	p.M1270V		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	1270	Poly-Asp.|Tail.		M -> V (in dbSNP:rs16977594).			myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)	p.M1270V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		GCTGGATGACATGGATGACGA	0.557													A|||	531	0.10603	0.2753	0.0274	5008	,	,		19217	0.0308		0.0159	False		,,,				2504	0.1033				p.M1270V		Atlas-SNP	.											CGNL1,NS,carcinoma,0,1	CGNL1	125	1	1	Substitution - Missense(1)	stomach(1)	c.A3808G						PASS	.	A	VAL/MET	950,3434	360.1+/-315.1	108,734,1350	157.0	163.0	161.0		3808	-5.2	0.5	15	dbSNP_123	161	138,8446	69.0+/-131.5	3,132,4157	yes	missense	CGNL1	NM_032866.3	21	111,866,5507	GG,GA,AA		1.6076,21.6697,8.3899	benign	1270/1303	57839587	1088,11880	2192	4292	6484	SO:0001583	missense	84952	exon19			GATGACATGGATG	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.3808A>G	15.37:g.57839587A>G	ENSP00000281282:p.Met1270Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	169	0.07738095238095238	133	0.2703252032520325	11	0.03038674033149171	15	0.026223776223776224	10	0.013192612137203167	A	4.077	0.012131	0.07912	0.216697	0.016076	ENSG00000128849	ENST00000281282	T	0.75154	-0.91	4.79	-5.17	0.02849	.	0.693382	0.13085	N	0.415016	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	0.12066	-1.0562	9	0.40728	T	0.16	-4.3624	3.2421	0.06784	0.1762:0.1697:0.4551:0.199	rs16977594;rs52812772;rs56614646;rs61651064;rs16977594	1270	Q0VF96	CGNL1_HUMAN	V	1270	ENSP00000281282:M1270V	ENSP00000281282:M1270V	M	+	1	0	CGNL1	55626879	0.000000	0.05858	0.539000	0.28077	0.406000	0.30931	-0.660000	0.05317	-0.788000	0.04504	0.379000	0.24179	ATG	A|0.914;G|0.086	0.086	strong		0.557	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	
LIPE	3991	hgsc.bcm.edu	37	19	42931004	42931004	+	Missense_Mutation	SNP	A	A	G	rs16975750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42931004A>G	ENST00000244289.4	-	1	574	c.298T>C	c.(298-300)Tac>Cac	p.Y100H	LIPE-AS1_ENST00000593740.2_RNA|LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|CTB-50E14.4_ENST00000596781.1_RNA|LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000594624.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	100			Y -> H (in dbSNP:rs16975750). {ECO:0000269|Ref.3}.		cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				CTTTGGATGTAAGGTGATTGC	0.502													G|||	393	0.0784744	0.2799	0.0288	5008	,	,		19320	0.0		0.003	False		,,,				2504	0.0				p.Y100H		Atlas-SNP	.											.	LIPE	83	.	0			c.T298C						PASS	.	G	HIS/TYR	997,3409	730.3+/-410.1	128,741,1334	167.0	172.0	171.0		298	-1.8	0.0	19	dbSNP_123	171	18,8582	818.6+/-406.8	0,18,4282	yes	missense	LIPE	NM_005357.2	83	128,759,5616	GG,GA,AA		0.2093,22.6282,7.8041	benign	100/1077	42931004	1015,11991	2203	4300	6503	SO:0001583	missense	3991	exon1			GGATGTAAGGTGA	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.298T>C	19.37:g.42931004A>G	ENSP00000244289:p.Tyr100His	Somatic	434	1	0.00230415		WXS	Illumina HiSeq	Phase_I	434	193	0.4447	NM_005357	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	152	0.0695970695970696	136	0.2764227642276423	13	0.03591160220994475	0	0.0	3	0.00395778364116095	G	0.044	-1.272008	0.01421	0.226282	0.002093	ENSG00000079435	ENST00000244289	T	0.21361	2.01	4.4	-1.76	0.08006	.	0.581795	0.14398	N	0.322096	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	0.42327	-0.9458	9	0.12430	T	0.62	-3.0127	1.9171	0.03299	0.4826:0.1392:0.2367:0.1415	rs16975750;rs52836316;rs58365984;rs16975750	100	Q05469	LIPS_HUMAN	H	100	ENSP00000244289:Y100H	ENSP00000244289:Y100H	Y	-	1	0	LIPE	47622844	0.018000	0.18449	0.025000	0.17156	0.087000	0.18053	-0.426000	0.07008	-0.446000	0.07149	-0.213000	0.12676	TAC	A|0.915;G|0.085	0.085	strong		0.502	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357	
ZNF71	58491	hgsc.bcm.edu	37	19	57132879	57132879	+	Missense_Mutation	SNP	G	G	A	rs79950845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57132879G>A	ENST00000328070.6	+	3	458	c.224G>A	c.(223-225)tGt>tAt	p.C75Y		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	75					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)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		GTACCCGCATGTCATGAACTG	0.622													G|||	99	0.0197684	0.0741	0.0014	5008	,	,		17597	0.0		0.0	False		,,,				2504	0.0				p.C75Y		Atlas-SNP	.											.	ZNF71	69	.	0			c.G224A						PASS	.	G	TYR/CYS	263,4143	149.5+/-183.7	5,253,1945	57.0	54.0	55.0		224	2.9	0.0	19	dbSNP_131	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF71	NM_021216.4	194	5,254,6244	AA,AG,GG		0.0116,5.9691,2.0298	possibly-damaging	75/490	57132879	264,12742	2203	4300	6503	SO:0001583	missense	58491	exon3			CCGCATGTCATGA	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"""Zinc fingers, C2H2-type"""	13141	protein-coding gene	gene with protein product		194545	"""zinc finger protein 71 (Cos26)"""			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.224G>A	19.37:g.57132879G>A	ENSP00000328245:p.Cys75Tyr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_021216	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	37	CCDS12947.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	G	13.10	2.134948	0.37728	0.059691	1.16E-4	ENSG00000197951	ENST00000328070	T	0.07114	3.22	2.91	2.91	0.33838	.	.	.	.	.	T	0.00815	0.0027	M	0.91249	3.19	0.09310	N	1	B	0.26318	0.146	B	0.22753	0.041	T	0.04203	-1.0969	9	0.62326	D	0.03	.	9.5203	0.39131	0.0:0.0:1.0:0.0	.	75	Q9NQZ8	ZNF71_HUMAN	Y	75	ENSP00000328245:C75Y	ENSP00000328245:C75Y	C	+	2	0	ZNF71	61824691	0.006000	0.16342	0.002000	0.10522	0.001000	0.01503	0.648000	0.24828	1.942000	0.56320	0.561000	0.74099	TGT	G|0.976;A|0.024	0.024	strong		0.622	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216	
CD200R1	131450	hgsc.bcm.edu	37	3	112648222	112648222	+	Missense_Mutation	SNP	T	T	C	rs2171509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112648222T>C	ENST00000471858.1	-	3	498	c.266A>G	c.(265-267)aAg>aGg	p.K89R	CD200R1_ENST00000308611.3_Missense_Mutation_p.K112R|CD200R1_ENST00000440122.2_Missense_Mutation_p.K112R|CD200R1_ENST00000490004.1_Missense_Mutation_p.K89R|CD200R1_ENST00000295863.4_Missense_Mutation_p.K67R	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	89	Ig-like V-type.		R -> K (in allele 2; dbSNP:rs2171509). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.7}.		regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TGTTTCTTTCTTGTAGGCTTT	0.433													t|||	3262	0.651358	0.7216	0.6066	5008	,	,		18096	0.7024		0.5328	False		,,,				2504	0.6575				p.K112R		Atlas-SNP	.											.	CD200R1	91	.	0			c.A335G						PASS	.	C	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	3010,1396	686.0+/-404.6	1023,964,216	155.0	150.0	151.0		335,335,266,266	-0.6	0.0	3	dbSNP_96	151	4576,4024	595.6+/-393.5	1224,2128,948	no	missense,missense,missense,missense	CD200R1	NM_138806.3,NM_138939.2,NM_138940.2,NM_170780.2	26,26,26,26	2247,3092,1164	CC,CT,TT		46.7907,31.6841,41.6731	benign,benign,benign,benign	112/349,112/189,89/166,89/326	112648222	7586,5420	2203	4300	6503	SO:0001583	missense	131450	exon4			TCTTTCTTGTAGG	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.266A>G	3.37:g.112648222T>C	ENSP00000418928:p.Lys89Arg	Somatic	388	0	0		WXS	Illumina HiSeq	Phase_I	419	407	0.97136	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	37	CCDS2970.1	1375	0.6295787545787546	342	0.6951219512195121	222	0.6132596685082873	398	0.6958041958041958	413	0.5448548812664907	t	0.209	-1.038495	0.02013	0.683159	0.532093	ENSG00000163606	ENST00000471858;ENST00000308611;ENST00000295863;ENST00000440122;ENST00000490004	T;T;T;T;T	0.10192	2.9;2.9;2.9;2.9;2.9	5.36	-0.585	0.11698	.	0.626649	0.16488	N	0.212239	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.33420	-0.9869	6	0.02654	T	1	.	5.1545	0.15027	0.1331:0.4271:0.0:0.4398	rs2171509;rs3844660;rs57074545;rs2171509	.	.	.	R	89;112;67;112;89	ENSP00000418928:K89R;ENSP00000311035:K112R;ENSP00000295863:K67R;ENSP00000405733:K112R;ENSP00000418801:K89R	ENSP00000295863:K67R	K	-	2	0	CD200R1	114130912	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.319000	0.02702	-0.863000	0.04084	-2.009000	0.00441	AAG	.	.	weak		0.433	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
MT-ND5	4540	hgsc.bcm.edu	37	M	13105	13105	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:13105A>G	ENST00000361567.2	+	1	769	c.769A>G	c.(769-771)Atc>Gtc	p.I257V	MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	257			I -> V (in dbSNP:rs2853501). {ECO:0000269|PubMed:11553319, ECO:0000269|PubMed:7530363}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TTGTAGCAGGAATCTTCTTAC	0.517																																					p.I257V		Atlas-SNP	.											.	.	.	.	0			c.A769G						PASS	.																																			SO:0001583	missense	0	exon1			GCAGGAATCTTCT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.769A>G	M.37:g.13105A>G	ENSP00000354813:p.Ile257Val	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.517	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
LILRA6	79168	hgsc.bcm.edu	37	19	54745659	54745659	+	Missense_Mutation	SNP	G	G	C	rs200657736		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54745659G>C	ENST00000396365.2	-	4	490	c.451C>G	c.(451-453)Cac>Gac	p.H151D	LILRA6_ENST00000419410.2_Missense_Mutation_p.H151D|LILRA6_ENST00000270464.5_Missense_Mutation_p.H151D|LILRA6_ENST00000245621.5_Missense_Mutation_p.H151D|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Missense_Mutation_p.H151D|LILRA6_ENST00000391735.3_Missense_Mutation_p.H151D	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	151					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACAAAATGGTGATATCCCTTC	0.592																																					p.H151D		Atlas-SNP	.											LILRA6,NS,carcinoma,0,2	LILRA6	75	2	0			c.C451G						scavenged	.						23.0	37.0	32.0					19																	54745659		2100	4266	6366	SO:0001583	missense	79168	exon4			AATGGTGATATCC	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.451C>G	19.37:g.54745659G>C	ENSP00000379651:p.His151Asp	Somatic	500	1	0.002		WXS	Illumina HiSeq	Phase_I	875	120	0.137143	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.647560	0.00111	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;4.04;2.82;2.82	2.64	-5.28	0.02755	Immunoglobulin-like fold (1);	2.010510	0.02119	N	0.055507	T	0.01870	0.0059	N	0.00237	-1.79	0.09310	N	1	B;B;B;B;B;B	0.09022	0.002;0.0;0.002;0.0;0.0;0.0	B;B;B;B;B;B	0.08055	0.003;0.0;0.003;0.001;0.002;0.001	T	0.25537	-1.0129	10	0.02654	T	1	.	3.0381	0.06129	0.2388:0.2899:0.373:0.0983	.	151;151;151;151;151;151	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	D	151	ENSP00000390120:H151D;ENSP00000270464:H151D;ENSP00000411227:H151D;ENSP00000375615:H151D;ENSP00000379651:H151D;ENSP00000245621:H151D	ENSP00000245621:H151D	H	-	1	0	LILRA6	59437471	.	.	0.000000	0.03702	0.020000	0.10135	.	.	-3.099000	0.00245	-1.962000	0.00476	CAC	G|0.999;C|0.001	0.001	weak		0.592	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
RAET1G	353091	hgsc.bcm.edu	37	6	150239330	150239330	+	Silent	SNP	C	C	T	rs17079029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:150239330C>T	ENST00000367360.2	-	4	889	c.822G>A	c.(820-822)agG>agA	p.R274R	RAET1E-AS1_ENST00000605899.1_RNA|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000446954.2_RNA	NM_001001788.2	NP_001001788.2			retinoic acid early transcript 1G											NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|urinary_tract(1)	13		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		AAAGGACTCTCCTCAGCAGCC	0.597													N|||	1137	0.227037	0.1021	0.111	5008	,	,		21265	0.5367		0.1511	False		,,,				2504	0.2372				p.R274R		Atlas-SNP	.											.	RAET1G	31	.	0			c.G822A						PASS	.	C		489,3917	227.8+/-242.9	24,441,1738	102.0	109.0	106.0		822	-4.1	0.0	6	dbSNP_123	106	1131,7469	233.9+/-267.0	83,965,3252	no	coding-synonymous	RAET1G	NM_001001788.2		107,1406,4990	TT,TC,CC		13.1512,11.0985,12.4558		274/335	150239330	1620,11386	2203	4300	6503	SO:0001819	synonymous_variant	353091	exon4			GACTCTCCTCAGC	AY172579	CCDS43514.1	6q24.1-25.1	2009-04-29	2004-11-22		ENSG00000203722	ENSG00000203722			16795	protein-coding gene	gene with protein product		609244	"""retinoic acid early transcript 1G pseudogene"""			11827464, 15240696	Standard	NM_001001788		Approved	ULBP5	uc010kii.1	Q6H3X3	OTTHUMG00000015802	ENST00000367360.2:c.822G>A	6.37:g.150239330C>T		Somatic	467	0	0		WXS	Illumina HiSeq	Phase_I	422	214	0.507109	NM_001001788		Silent	SNP	ENST00000367360.2	37	CCDS43514.1																																																																																			C|0.785;T|0.215	0.215	strong		0.597	RAET1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042668.2		
DKK4	27121	hgsc.bcm.edu	37	8	42231786	42231786	+	Silent	SNP	G	G	A	rs2073664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	143	0	0		WXS	Illumina HiSeq	Phase_I	170	168	0.988235	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		
CPB1	1360	hgsc.bcm.edu	37	3	148545789	148545789	+	Splice_Site	SNP	C	C	T	rs80013498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148545789C>T	ENST00000491148.1	+	3	406	c.72C>T	c.(70-72)ggC>ggT	p.G24G	CPB1_ENST00000282957.4_Splice_Site_p.G24G			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	24						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			CATTATTCAGCGAGAAGGTGT	0.408													C|||	50	0.00998403	0.0356	0.0029	5008	,	,		21398	0.001		0.0	False		,,,				2504	0.0				p.G24G		Atlas-SNP	.											.	CPB1	74	.	0			c.C72T						PASS	.	C		163,4243	110.4+/-148.6	2,159,2042	101.0	103.0	102.0		72	-7.2	0.1	3	dbSNP_131	102	0,8600		0,0,4300	yes	coding-synonymous-near-splice	CPB1	NM_001871.2		2,159,6342	TT,TC,CC		0.0,3.6995,1.2533		24/418	148545789	163,12843	2203	4300	6503	SO:0001630	splice_region_variant	1360	exon2			ATTCAGCGAGAAG	AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"""pancreatic carboxypeptidase B"", ""tissue carboxypeptidase B"", ""protaminase"""	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.72-1C>T	3.37:g.148545789C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_001871	O60834|Q53XJ0|Q96BQ8	Silent	SNP	ENST00000491148.1	37	CCDS33874.1																																																																																			C|0.986;T|0.014	0.014	strong		0.408	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871	Silent
DTHD1	401124	hgsc.bcm.edu	37	4	36340753	36340753	+	Missense_Mutation	SNP	G	G	A	rs9654132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:36340753G>A	ENST00000456874.2	+	8	2043	c.1985G>A	c.(1984-1986)cGt>cAt	p.R662H	DTHD1_ENST00000357504.3_Missense_Mutation_p.R497H|DTHD1_ENST00000503528.1_Intron|RP11-431M7.2_ENST00000504344.1_RNA|DTHD1_ENST00000507598.1_Missense_Mutation_p.R702H	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	662			R -> H (in dbSNP:rs9654132). {ECO:0000269|PubMed:14702039}.		signal transduction (GO:0007165)			p.R497H(3)|p.R662H(2)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						TTAATCAACCGTCCACAGAGT	0.348													g|||	984	0.196486	0.1831	0.1873	5008	,	,		17837	0.127		0.2624	False		,,,				2504	0.2249				p.R662H		Atlas-SNP	.											DTHD1_ENST00000456874,NS,carcinoma,0,5	DTHD1	63	5	5	Substitution - Missense(5)	kidney(4)|stomach(1)	c.G1985A						PASS	.	A	HIS/ARG,HIS/ARG	277,1107		32,213,447	232.0	186.0	200.0		1490,1985	2.2	1.0	4	dbSNP_119	200	733,2449		77,579,935	yes	missense,missense	DTHD1	NM_001136536.3,NM_001170700.1	29,29	109,792,1382	AA,AG,GG		23.0358,20.0145,22.12	benign,benign	497/617,662/782	36340753	1010,3556	692	1591	2283	SO:0001583	missense	401124	exon8			TCAACCGTCCACA	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.1985G>A	4.37:g.36340753G>A	ENSP00000401597:p.Arg662His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_001170700	B2RXK4|B4E2N7	Missense_Mutation	SNP	ENST00000456874.2	37	CCDS54754.1	405	0.18543956043956045	80	0.16260162601626016	54	0.14917127071823205	72	0.1258741258741259	199	0.262532981530343	g	12.44	1.937584	0.34189	0.200145	0.230358	ENSG00000197057	ENST00000357504;ENST00000507598;ENST00000456874	T;T;T	0.78816	-1.21;-1.21;-1.21	5.04	2.18	0.27775	.	0.329059	0.32503	N	0.006013	T	0.00012	0.0000	L	0.27053	0.805	0.39370	P	0.03393400000000002	B	0.31640	0.333	B	0.25506	0.061	T	0.05099	-1.0906	9	0.46703	T	0.11	-2.3523	9.6835	0.40085	0.2531:0.0:0.7469:0.0	rs9654132;rs57110323;rs9654132	497	Q6ZMT9-2	.	H	497;702;662	ENSP00000350103:R497H;ENSP00000424426:R702H;ENSP00000401597:R662H	ENSP00000350103:R497H	R	+	2	0	DTHD1	36017148	0.984000	0.35163	1.000000	0.80357	0.975000	0.68041	0.817000	0.27281	0.732000	0.32470	-0.215000	0.12644	CGT	G|0.809;A|0.191	0.191	strong		0.348	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
APLF	200558	hgsc.bcm.edu	37	2	68753240	68753240	+	Missense_Mutation	SNP	T	T	A	rs35002937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:68753240T>A	ENST00000303795.4	+	6	841	c.670T>A	c.(670-672)Tcc>Acc	p.S224T		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	224			S -> T (in dbSNP:rs35002937).		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						CAAAGATAAATCCCAGCTAAA	0.348													A|||	1150	0.229633	0.5991	0.1182	5008	,	,		16373	0.0367		0.1213	False		,,,				2504	0.1196				p.S224T		Atlas-SNP	.											APLF,colon,carcinoma,0,1	APLF	69	1	0			c.T670A						PASS	.	A	THR/SER	2385,2021	561.6+/-380.8	667,1051,485	85.0	88.0	87.0		670	3.6	0.1	2	dbSNP_126	87	1147,7453	766.1+/-407.6	81,985,3234	yes	missense	APLF	NM_173545.2	58	748,2036,3719	AA,AT,TT		13.3372,45.8693,27.1567	benign	224/512	68753240	3532,9474	2203	4300	6503	SO:0001583	missense	200558	exon6			GATAAATCCCAGC	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.670T>A	2.37:g.68753240T>A	ENSP00000307004:p.Ser224Thr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	142	57	0.401408	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	447	0.20467032967032966	290	0.5894308943089431	43	0.11878453038674033	22	0.038461538461538464	92	0.12137203166226913	a	0.004	-2.284029	0.00251	0.541307	0.133372	ENSG00000169621	ENST00000303795	T	0.22336	1.96	4.75	3.6	0.41247	.	0.790106	0.11661	N	0.541829	T	0.00012	0.0000	N	0.00119	-2.075	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.45687	-0.9244	9	0.02654	T	1	.	4.1048	0.10032	0.7239:0.0:0.0962:0.1799	rs35002937	224;224	F8WET0;Q8IW19	.;APLF_HUMAN	T	224	ENSP00000307004:S224T	ENSP00000307004:S224T	S	+	1	0	APLF	68606744	0.270000	0.24152	0.145000	0.22337	0.037000	0.13140	0.150000	0.16263	0.421000	0.25980	-0.344000	0.07964	TCC	T|0.754;A|0.246	0.246	strong		0.348	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
TEKT5	146279	hgsc.bcm.edu	37	16	10769873	10769873	+	Silent	SNP	G	G	A	rs115325161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:10769873G>A	ENST00000283025.2	-	5	1100	c.1029C>T	c.(1027-1029)aaC>aaT	p.N343N		NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	343						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						AGATGCGGGCGTTGAAGGCCA	0.602													A|||	25	0.00499201	0.0174	0.0029	5008	,	,		21091	0.0		0.0	False		,,,				2504	0.0				p.N343N		Atlas-SNP	.											.	TEKT5	66	.	0			c.C1029T						PASS	.	A		72,4322	818.8+/-416.3	1,70,2126	153.0	126.0	135.0		1029	-3.3	0.1	16	dbSNP_132	135	0,8600		0,0,4300	no	coding-synonymous	TEKT5	NM_144674.1		1,70,6426	AA,AG,GG		0.0,1.6386,0.5541		343/486	10769873	72,12922	2197	4300	6497	SO:0001819	synonymous_variant	146279	exon5			GCGGGCGTTGAAG		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.1029C>T	16.37:g.10769873G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	101	56	0.554455	NM_144674	A1L3Z3	Silent	SNP	ENST00000283025.2	37	CCDS10542.1																																																																																			G|0.995;A|0.005	0.005	strong		0.602	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
MYBPH	4608	hgsc.bcm.edu	37	1	203143725	203143725	+	Splice_Site	SNP	G	G	C	rs2642531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:203143725G>C	ENST00000255416.4	-	3	398	c.341C>G	c.(340-342)gCc>gGc	p.A114G		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H	114	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		A -> G (in dbSNP:rs2642531).		cell adhesion (GO:0007155)|regulation of striated muscle contraction (GO:0006942)	myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			endometrium(5)|large_intestine(6)|lung(7)|skin(1)|urinary_tract(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.153)	Colorectal(1306;0.0306)		CCACTCCGAGGCTGAGGGGAT	0.612													g|||	1271	0.253794	0.528	0.2522	5008	,	,		17735	0.1468		0.1352	False		,,,				2504	0.1166				p.A114G	NSCLC(32;174 1025 14462 23899 42933)	Atlas-SNP	.											.	MYBPH	41	.	0			c.C341G						PASS	.	C	GLY/ALA	2143,2263		534,1075,594	28.0	23.0	25.0		341	4.6	1.0	1	dbSNP_100	25	1124,7476		86,952,3262	yes	missense-near-splice	MYBPH	NM_004997.2	60	620,2027,3856	CC,CG,GG		13.0698,48.6382,25.1192	benign	114/478	203143725	3267,9739	2203	4300	6503	SO:0001630	splice_region_variant	4608	exon3			TCCGAGGCTGAGG	BC044226	CCDS30975.1	1q32.1	2013-02-11	2001-11-28		ENSG00000133055	ENSG00000133055		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7552	protein-coding gene	gene with protein product		160795	"""myosin-binding protein H"""			8486381	Standard	NM_004997		Approved		uc001gzh.1	Q13203	OTTHUMG00000042121	ENST00000255416.4:c.341-1C>G	1.37:g.203143725G>C		Somatic	416	0	0		WXS	Illumina HiSeq	Phase_I	487	243	0.498973	NM_004997	Q16886|Q86YC5	Missense_Mutation	SNP	ENST00000255416.4	37	CCDS30975.1	536	0.2454212454212454	263	0.5345528455284553	85	0.23480662983425415	91	0.1590909090909091	97	0.1279683377308707	g	10.09	1.255596	0.22965	0.486382	0.130698	ENSG00000133055	ENST00000255416	T	0.54866	0.55	5.53	4.62	0.57501	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.133482	0.34245	N	0.004140	T	0.00012	0.0000	N	0.17872	0.535	0.30470	P	0.773413	B	0.20780	0.048	B	0.25614	0.062	T	0.45600	-0.9250	9	0.45353	T	0.12	.	12.5921	0.56449	0.0:0.1669:0.8331:0.0	rs2642531;rs3820146;rs59912116;rs2642531	114	Q13203	MYBPH_HUMAN	G	114	ENSP00000255416:A114G	ENSP00000255416:A114G	A	-	2	0	MYBPH	201410348	0.997000	0.39634	1.000000	0.80357	0.037000	0.13140	1.982000	0.40638	1.346000	0.45694	-0.121000	0.15023	GCC	G|0.736;C|0.264	0.264	strong		0.612	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	NM_004997	Missense_Mutation
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28219695	28219695	+	Missense_Mutation	SNP	G	G	A	rs62638680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28219695G>A	ENST00000377294.2	-	1	307	c.64C>T	c.(64-66)Ctc>Ttc	p.L22F	ZKSCAN4_ENST00000423974.2_Intron	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	22					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)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						ACGGTCAGGAGCCCCGTCTGG	0.637													G|||	179	0.0357428	0.1082	0.0187	5008	,	,		15084	0.006		0.0139	False		,,,				2504	0.0031				p.L22F		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.C64T						PASS	.	G	PHE/LEU	433,3917		24,385,1766	63.0	69.0	67.0		64	-0.6	0.1	6	dbSNP_129	67	51,8447		0,51,4198	yes	missense	ZKSCAN4	NM_019110.3	22	24,436,5964	AA,AG,GG		0.6001,9.954,3.7671	benign	22/546	28219695	484,12364	2175	4249	6424	SO:0001583	missense	387032	exon1			TCAGGAGCCCCGT	AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13854	protein-coding gene	gene with protein product		611643	"""zinc finger protein 307"", ""zinc finger protein 427"""	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.64C>T	6.37:g.28219695G>A	ENSP00000366509:p.Leu22Phe	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	102	101	0.990196	NM_019110	B2RE32|Q5U7L4	Missense_Mutation	SNP	ENST00000377294.2	37	CCDS4647.1	77	0.035256410256410256	52	0.10569105691056911	9	0.024861878453038673	5	0.008741258741258742	11	0.014511873350923483	G	16.83	3.231677	0.58777	0.09954	0.006001	ENSG00000187626	ENST00000377294	T	0.08896	3.04	4.21	-0.602	0.11634	.	.	.	.	.	T	0.02047	0.0064	L	0.27053	0.805	0.09310	N	0.999995	P	0.46706	0.883	P	0.44732	0.459	T	0.39901	-0.9591	9	0.46703	T	0.11	.	3.0342	0.06116	0.0972:0.1668:0.458:0.278	.	22	Q969J2	ZKSC4_HUMAN	F	22	ENSP00000366509:L22F	ENSP00000366509:L22F	L	-	1	0	ZKSCAN4	28327674	0.000000	0.05858	0.050000	0.19076	0.678000	0.39670	-0.612000	0.05616	0.044000	0.15775	0.563000	0.77884	CTC	G|0.968;A|0.032	0.032	strong		0.637	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110	
PKD1L1	168507	hgsc.bcm.edu	37	7	47927650	47927650	+	Missense_Mutation	SNP	G	G	A	rs79105203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47927650G>A	ENST00000289672.2	-	17	2824	c.2774C>T	c.(2773-2775)cCg>cTg	p.P925L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	925	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						AGACAGATTCGGTATTTCACT	0.398													G|||	230	0.0459265	0.1641	0.0115	5008	,	,		21650	0.0		0.004	False		,,,				2504	0.001				p.P925L		Atlas-SNP	.											PKD1L1,colon,carcinoma,0,1	PKD1L1	328	1	0			c.C2774T						scavenged	.	G	LEU/PRO	738,3668	302.1+/-287.2	68,602,1533	123.0	115.0	118.0		2774	-4.2	0.0	7	dbSNP_132	118	85,8515	48.1+/-107.5	1,83,4216	yes	missense	PKD1L1	NM_138295.3	98	69,685,5749	AA,AG,GG		0.9884,16.7499,6.3278	benign	925/2850	47927650	823,12183	2203	4300	6503	SO:0001583	missense	168507	exon17			AGATTCGGTATTT	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.2774C>T	7.37:g.47927650G>A	ENSP00000289672:p.Pro925Leu	Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	100	0.045787545787545784	92	0.18699186991869918	5	0.013812154696132596	0	0.0	3	0.00395778364116095	G	7.863	0.726477	0.15439	0.167499	0.009884	ENSG00000158683	ENST00000289672	T	0.69306	-0.39	5.65	-4.17	0.03857	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	1.960750	0.02041	N	0.049260	T	0.00109	0.0003	L	0.27053	0.805	0.80722	P	0.0	B	0.17268	0.021	B	0.10450	0.005	T	0.04635	-1.0937	9	0.37606	T	0.19	0.0986	5.9318	0.19142	0.1912:0.0:0.3612:0.4476	.	925	Q8TDX9	PK1L1_HUMAN	L	925	ENSP00000289672:P925L	ENSP00000289672:P925L	P	-	2	0	PKD1L1	47894175	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.980000	0.01492	-0.571000	0.06014	-0.978000	0.02582	CCG	G|0.945;A|0.055	0.055	strong		0.398	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4448590	4448590	+	Silent	SNP	C	C	T	rs9911631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4448590C>T	ENST00000254718.4	-	16	2430	c.2124G>A	c.(2122-2124)acG>acA	p.T708T	MYBBP1A_ENST00000381556.2_Silent_p.T708T			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	708					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						CAGAATCGTCCGTCACCACCA	0.667													C|||	367	0.0732827	0.2602	0.0231	5008	,	,		11832	0.0		0.007	False		,,,				2504	0.0				p.T708T		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G2124A						PASS	.	C	,	1006,3400	373.4+/-320.8	117,772,1314	109.0	101.0	104.0		2124,2124	-10.3	0.0	17	dbSNP_119	104	13,8587	8.4+/-32.0	0,13,4287	no	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	117,785,5601	TT,TC,CC		0.1512,22.8325,7.8348	,	708/1333,708/1329	4448590	1019,11987	2203	4300	6503	SO:0001819	synonymous_variant	10514	exon16			ATCGTCCGTCACC	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.2124G>A	17.37:g.4448590C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			C|0.931;T|0.069	0.069	strong		0.667	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
RRAGC	64121	hgsc.bcm.edu	37	1	39325136	39325136	+	Silent	SNP	C	C	T	rs112925356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39325136C>T	ENST00000373001.3	-	1	359	c.183G>A	c.(181-183)aaG>aaA	p.K61K	RP5-864K19.4_ENST00000456813.1_RNA|RP5-864K19.4_ENST00000433671.2_RNA	NM_022157.2	NP_071440.1			Ras-related GTP binding C											endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)	10	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)				GAATCCTCGGCTTGGAGCTGT	0.726													C|||	139	0.0277556	0.0658	0.0086	5008	,	,		6031	0.001		0.001	False		,,,				2504	0.045				p.K61K		Atlas-SNP	.											.	RRAGC	28	.	0			c.G183A						PASS	.	C		156,3314		2,152,1581	7.0	8.0	7.0		183	5.0	1.0	1	dbSNP_132	7	12,6612		0,12,3300	no	coding-synonymous	RRAGC	NM_022157.2		2,164,4881	TT,TC,CC		0.1812,4.4957,1.6644		61/400	39325136	168,9926	1735	3312	5047	SO:0001819	synonymous_variant	64121	exon1			CCTCGGCTTGGAG	AF323609	CCDS430.1	1p34	2008-02-05			ENSG00000116954	ENSG00000116954			19902	protein-coding gene	gene with protein product		608267				11073942	Standard	NM_022157		Approved	GTR2, FLJ13311	uc001ccq.3	Q9HB90	OTTHUMG00000000490	ENST00000373001.3:c.183G>A	1.37:g.39325136C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_001271851		Silent	SNP	ENST00000373001.3	37	CCDS430.1																																																																																			C|0.978;T|0.022	0.022	strong		0.726	RRAGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001222.2	NM_022157	
ARSG	22901	hgsc.bcm.edu	37	17	66416511	66416511	+	Silent	SNP	C	C	T	rs35268505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66416511C>T	ENST00000448504.2	+	12	2281	c.1485C>T	c.(1483-1485)aaC>aaT	p.N495N	ARSG_ENST00000452479.2_Silent_p.N331N|RP11-120M18.2_ENST00000592030.1_RNA|WIPI1_ENST00000589459.1_5'Flank|ARSG_ENST00000582154.1_3'UTR	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	495					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)			ACATTGCCAACGACAACATCT	0.552													C|||	79	0.0157748	0.0575	0.0043	5008	,	,		20902	0.0		0.0	False		,,,				2504	0.0				p.N495N		Atlas-SNP	.											.	ARSG	55	.	0			c.C1485T						PASS	.	C		231,4175	136.5+/-172.5	2,227,1974	189.0	180.0	183.0		1485	-11.8	0.0	17	dbSNP_126	183	0,8600		0,0,4300	no	coding-synonymous	ARSG	NM_014960.3		2,227,6274	TT,TC,CC		0.0,5.2429,1.7761		495/526	66416511	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	22901	exon12			TGCCAACGACAAC	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.1485C>T	17.37:g.66416511C>T		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	240	125	0.520833	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	37	CCDS11676.1																																																																																			C|0.981;T|0.019	0.019	strong		0.552	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
ACTN4	81	hgsc.bcm.edu	37	19	39212226	39212226	+	Missense_Mutation	SNP	C	C	T	rs140271107		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39212226C>T	ENST00000252699.2	+	12	1416	c.1340C>T	c.(1339-1341)tCg>tTg	p.S447L	ACTN4_ENST00000424234.2_Intron|ACTN4_ENST00000390009.3_Missense_Mutation_p.S228L	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	447					actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GCCACACTATCGGACATCAAA	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		20965	0.0		0.001	False		,,,				2504	0.0				p.S447L	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.C1340T						PASS	.						125.0	101.0	109.0					19																	39212226		2203	4300	6503	SO:0001583	missense	81	exon12			CACTATCGGACAT	D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"""EF-hand domain containing"""	166	protein-coding gene	gene with protein product		604638	"""focal segmental glomerulosclerosis 1"""	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.1340C>T	19.37:g.39212226C>T	ENSP00000252699:p.Ser447Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_004924	A4K467|D6PXK4|O76048	Missense_Mutation	SNP	ENST00000252699.2	37	CCDS12518.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.50	3.636731	0.67130	.	.	ENSG00000130402	ENST00000252699;ENST00000445727;ENST00000390009	T;T	0.51325	0.71;0.71	4.21	4.21	0.49690	.	0.194257	0.34959	N	0.003557	T	0.54271	0.1848	M	0.65498	2.005	0.80722	D	1	B;B	0.32382	0.091;0.368	B;B	0.40636	0.335;0.154	T	0.61133	-0.7124	10	0.59425	D	0.04	.	15.8417	0.78852	0.0:1.0:0.0:0.0	.	447;447	E7EV83;O43707	.;ACTN4_HUMAN	L	447;447;228	ENSP00000252699:S447L;ENSP00000439497:S228L	ENSP00000252699:S447L	S	+	2	0	ACTN4	43904066	1.000000	0.71417	0.962000	0.40283	0.599000	0.36880	7.651000	0.83577	2.340000	0.79590	0.462000	0.41574	TCG	C|1.000;T|0.000	0.000	strong		0.632	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1		
TMEM19	55266	hgsc.bcm.edu	37	12	72094627	72094627	+	Missense_Mutation	SNP	C	C	G	rs74104122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72094627C>G	ENST00000266673.5	+	6	1457	c.863C>G	c.(862-864)aCt>aGt	p.T288S		NM_018279.3	NP_060749.2	Q96HH6	TMM19_HUMAN	transmembrane protein 19	288						integral component of membrane (GO:0016021)				large_intestine(1)|lung(8)	9		Breast(359;0.0889)		GBM - Glioblastoma multiforme(134;0.044)		GATGAAAGCACTGGCATGGTG	0.358													C|||	126	0.0251597	0.09	0.0086	5008	,	,		17302	0.0		0.001	False		,,,				2504	0.0				p.T288S		Atlas-SNP	.											.	TMEM19	35	.	0			c.C863G						PASS	.	C	SER/THR	319,4087	170.9+/-201.2	13,293,1897	195.0	174.0	181.0		863	5.0	1.0	12	dbSNP_130	181	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TMEM19	NM_018279.3	58	13,296,6194	GG,GC,CC		0.0349,7.2401,2.4758	possibly-damaging	288/337	72094627	322,12684	2203	4300	6503	SO:0001583	missense	55266	exon6			AAAGCACTGGCAT	BC008596	CCDS9002.1	12q15	2004-03-04				ENSG00000139291			25605	protein-coding gene	gene with protein product						12477932	Standard	NM_018279		Approved	FLJ10936	uc001sws.3	Q96HH6	OTTHUMG00000169558	ENST00000266673.5:c.863C>G	12.37:g.72094627C>G	ENSP00000266673:p.Thr288Ser	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	NM_018279	B2RDL2|Q53FY3|Q9NV41	Missense_Mutation	SNP	ENST00000266673.5	37	CCDS9002.1	45|45	0.020604395604395604|0.020604395604395604	43|43	0.08739837398373984|0.08739837398373984	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	10.59|10.59	1.393752|1.393752	0.25205|0.25205	0.072401|0.072401	3.49E-4|3.49E-4	ENSG00000139291|ENSG00000139291	ENST00000550787|ENST00000266673;ENST00000546795	.|.	.|.	.|.	5.93|5.93	5.03|5.03	0.67393|0.67393	.|.	.|0.100553	.|0.64402	.|N	.|0.000002	T|T	0.02649|0.02649	0.0080|0.0080	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	.|P	.|0.51537	.|0.946	.|P	.|0.48952	.|0.596	T|T	0.04165|0.04165	-1.0972|-1.0972	5|9	.|0.08837	.|T	.|0.75	-22.104|-22.104	12.1152|12.1152	0.53861|0.53861	0.0:0.8121:0.1216:0.0663|0.0:0.8121:0.1216:0.0663	.|.	.|288	.|Q96HH6	.|TMM19_HUMAN	Q|S	103|288;132	.|.	.|ENSP00000266673:T288S	H|T	+|+	3|2	2|0	TMEM19|TMEM19	70380894|70380894	0.990000|0.990000	0.36364|0.36364	0.993000|0.993000	0.49108|0.49108	0.973000|0.973000	0.67179|0.67179	1.858000|1.858000	0.39408|0.39408	1.463000|1.463000	0.47967|0.47967	0.655000|0.655000	0.94253|0.94253	CAC|ACT	C|0.976;G|0.024	0.024	strong		0.358	TMEM19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404801.1	NM_018279	
TMC2	117532	hgsc.bcm.edu	37	20	2582839	2582839	+	Missense_Mutation	SNP	T	T	A	rs140733869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2582839T>A	ENST00000358864.1	+	11	1320	c.1305T>A	c.(1303-1305)ttT>ttA	p.F435L	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	435					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						TGGCCAACTTTCTCATCATCT	0.388													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		20141	0.0		0.0	False		,,,				2504	0.0				p.F435L		Atlas-SNP	.											.	TMC2	121	.	0			c.T1305A						PASS	.	T	LEU/PHE	26,4380	32.6+/-62.9	0,26,2177	199.0	174.0	182.0		1305	-4.7	1.0	20	dbSNP_134	182	0,8600		0,0,4300	yes	missense	TMC2	NM_080751.2	22	0,26,6477	AA,AT,TT		0.0,0.5901,0.1999	possibly-damaging	435/907	2582839	26,12980	2203	4300	6503	SO:0001583	missense	117532	exon11			CAACTTTCTCATC	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.1305T>A	20.37:g.2582839T>A	ENSP00000351732:p.Phe435Leu	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	245	137	0.559184	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	37	CCDS13029.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	17.98	3.520320	0.64747	0.005901	0.0	ENSG00000149488	ENST00000358864	T	0.80994	-1.44	5.58	-4.7	0.03288	.	0.171732	0.56097	D	0.000039	T	0.64811	0.2632	L	0.60845	1.875	0.39342	D	0.965601	B;B;P;P	0.45986	0.382;0.209;0.866;0.87	B;B;P;P	0.50570	0.064;0.031;0.644;0.542	T	0.76044	-0.3103	10	0.09084	T	0.74	-13.3661	15.7824	0.78272	0.0:0.7271:0.0:0.2729	.	266;267;435;435	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	L	435	ENSP00000351732:F435L	ENSP00000351732:F435L	F	+	3	2	TMC2	2530839	0.062000	0.20869	0.972000	0.41901	0.959000	0.62525	-0.545000	0.06069	-0.718000	0.04949	-1.151000	0.01829	TTT	T|0.997;A|0.003	0.003	strong		0.388	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464487	39464487	+	Missense_Mutation	SNP	G	G	C	rs2074285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39464487G>C	ENST00000391352.1	-	1	1018	c.1019C>G	c.(1018-1020)cCt>cGt	p.P340R		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	340						keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						GCAGACAGAAGGACAGCGCTT	0.567													C|||	1899	0.379193	0.6135	0.2435	5008	,	,		22005	0.3968		0.2992	False		,,,				2504	0.2229				p.P340R		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.C1019G						PASS	.																																			SO:0001583	missense	100505753	exon1			ACAGAAGGACAGC	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.1019C>G	17.37:g.39464487G>C	ENSP00000375147:p.Pro340Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001146182		Missense_Mutation	SNP	ENST00000391352.1	37	CCDS56032.1	833	0.3814102564102564	290	0.5894308943089431	99	0.27348066298342544	216	0.3776223776223776	228	0.3007915567282322	C	0.001	-2.912640	0.00056	.	.	ENSG00000212657	ENST00000391352	T	0.00646	6.0	5.26	-3.19	0.05171	.	.	.	.	.	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	.	.	.	.	.	.	T	0.02214	-1.1194	6	0.14656	T	0.56	.	7.4869	0.27439	0.0:0.2194:0.1205:0.66	rs2074285;rs2074285	.	.	.	R	340	ENSP00000375147:P340R	ENSP00000375147:P340R	P	-	2	0	KRTAP16-1	36718013	0.000000	0.05858	0.003000	0.11579	0.049000	0.14656	-1.700000	0.01905	-0.730000	0.04869	-0.322000	0.08575	CCT	G|0.614;C|0.386	0.386	strong		0.567	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
ZNF665	79788	hgsc.bcm.edu	37	19	53668549	53668549	+	Silent	SNP	T	T	G	rs10409924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53668549T>G	ENST00000600412.1	-	2	1114	c.999A>C	c.(997-999)ggA>ggC	p.G333G	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Silent_p.G398G			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	333					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(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		AAGGCTTTTCTCCGGTATGGA	0.393													T|||	1081	0.215855	0.4304	0.1484	5008	,	,		23571	0.0972		0.1342	False		,,,				2504	0.18				p.G398G		Atlas-SNP	.											.	ZNF665	136	.	0			c.A1194C						PASS	.	T		1573,2833	468.3+/-355.1	286,1001,916	96.0	101.0	99.0		1194	-2.4	0.0	19	dbSNP_119	99	1325,7269	255.4+/-280.3	99,1127,3071	no	coding-synonymous	ZNF665	NM_024733.3		385,2128,3987	GG,GT,TT		15.4177,35.7013,22.2923		398/679	53668549	2898,10102	2203	4297	6500	SO:0001819	synonymous_variant	79788	exon4			CTTTTCTCCGGTA		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"""Zinc fingers, C2H2-type"", ""-"""	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.999A>C	19.37:g.53668549T>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_024733	A8K5T8	Silent	SNP	ENST00000600412.1	37																																																																																				T|0.774;G|0.226	0.226	strong		0.393	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733	
TRPV6	55503	hgsc.bcm.edu	37	7	142573332	142573332	+	Silent	SNP	C	C	T	rs4987664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142573332C>T	ENST00000359396.3	-	8	1256	c.1011G>A	c.(1009-1011)ctG>ctA	p.L337L	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	337					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					TGATGTACAGCAGATATATGG	0.597													C|||	105	0.0209665	0.0726	0.013	5008	,	,		18895	0.0		0.0	False		,,,				2504	0.0				p.L337L		Atlas-SNP	.											.	TRPV6	108	.	0			c.G1011A						PASS	.	C		312,4094	167.3+/-198.3	17,278,1908	150.0	147.0	148.0		1011	1.6	0.4	7	dbSNP_113	148	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRPV6	NM_018646.2		17,280,6206	TT,TC,CC		0.0233,7.0813,2.4143		337/726	142573332	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	55503	exon8			GTACAGCAGATAT	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.1011G>A	7.37:g.142573332C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	37	CCDS5874.1																																																																																			C|0.971;T|0.029	0.029	strong		0.597	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	
OR1D2	4991	hgsc.bcm.edu	37	17	2995572	2995572	+	Missense_Mutation	SNP	G	G	A	rs4300683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2995572G>A	ENST00000331459.1	-	1	718	c.719C>T	c.(718-720)aCc>aTc	p.T240I		NM_002548.2	NP_002539.2	P34982	OR1D2_HUMAN	olfactory receptor, family 1, subfamily D, member 2	240			T -> I (in dbSNP:rs4300683).		cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|protein import into nucleus, translocation (GO:0000060)|sensory perception of smell (GO:0007608)|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)			kidney(2)|large_intestine(2)|lung(10)|ovary(1)	15						GGAGGCACAGGTGGAGAAGGC	0.468													.|||	766	0.152955	0.3835	0.1945	5008	,	,		23660	0.0258		0.0567	False		,,,				2504	0.0419				p.T240I		Atlas-SNP	.											.	OR1D2	39	.	0			c.C719T						PASS	.	G	ILE/THR	1365,3041	452.8+/-350.1	211,943,1049	102.0	103.0	103.0		719	3.2	1.0	17	dbSNP_111	103	554,8046	150.9+/-205.7	19,516,3765	yes	missense	OR1D2	NM_002548.2	89	230,1459,4814	AA,AG,GG		6.4419,30.9805,14.7547	probably-damaging	240/313	2995572	1919,11087	2203	4300	6503	SO:0001583	missense	4991	exon1			GCACAGGTGGAGA	U04678	CCDS11019.1	17p13.3	2012-08-09			ENSG00000184166	ENSG00000184166		"""GPCR / Class A : Olfactory receptors"""	8183	protein-coding gene	gene with protein product		164342		OLFR1		1370859, 1840504	Standard	NM_002548		Approved	OR17-4	uc010vrb.2	P34982	OTTHUMG00000090619	ENST00000331459.1:c.719C>T	17.37:g.2995572G>A	ENSP00000327585:p.Thr240Ile	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	157	69	0.43949	NM_002548	Q6IFL8|Q96RA4|Q9UM78	Missense_Mutation	SNP	ENST00000331459.1	37	CCDS11019.1	343	0.15705128205128205	218	0.44308943089430897	64	0.17679558011049723	13	0.022727272727272728	48	0.0633245382585752	g	15.69	2.908840	0.52439	0.309805	0.064419	ENSG00000184166	ENST00000331459	T	0.42513	0.97	3.21	3.21	0.36854	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.90198	3.095	0.26668	P	0.9717891	D	0.89917	1.0	D	0.97110	1.0	T	0.39761	-0.9598	8	0.72032	D	0.01	.	13.0776	0.59095	0.0:0.0:1.0:0.0	rs4300683;rs52819117;rs60483420;rs4300683	240	P34982	OR1D2_HUMAN	I	240	ENSP00000327585:T240I	ENSP00000327585:T240I	T	-	2	0	OR1D2	2942322	1.000000	0.71417	0.998000	0.56505	0.404000	0.30871	5.143000	0.64826	1.606000	0.50161	0.543000	0.68304	ACC	G|0.842;A|0.158	0.158	strong		0.468	OR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207207.1	NM_002548	
PKD1L2	114780	hgsc.bcm.edu	37	16	81211548	81211548	+	RNA	SNP	G	G	A	rs9934605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81211548G>A	ENST00000527937.1	-	0	319				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000531391.1_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						GCACAGTGCTGATCACATAGG	0.602													G|||	1112	0.222045	0.3328	0.1772	5008	,	,		18192	0.1032		0.172	False		,,,				2504	0.2781				p.I767I		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2301T						PASS	.	G	,	1176,2894		174,828,1033	56.0	56.0	56.0		2301,2301	3.9	0.9	16	dbSNP_119	56	1410,6994		121,1168,2913	no	coding-synonymous,coding-synonymous	PKD1L2	NM_001076780.1,NM_052892.3	,	295,1996,3946	AA,AG,GG		16.7777,28.8943,20.7311	,	767/992,767/2460	81211548	2586,9888	2035	4202	6237			114780	exon14			AGTGCTGATCACA	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.81211548G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000527937.1	37		392	0.1794871794871795	154	0.3130081300813008	61	0.1685082872928177	53	0.09265734265734266	124	0.16358839050131926	G	3.327	-0.137495	0.06711	0.288943	0.167777	ENSG00000166473	ENST00000526632	.	.	.	4.89	3.94	0.45596	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999992	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.4679	10.5049	0.44828	0.0916:0.0:0.9084:0.0	rs9934605;rs9934605	.	.	.	X	295	.	.	Q	-	1	0	PKD1L2	79769049	1.000000	0.71417	0.921000	0.36526	0.235000	0.25334	1.823000	0.39062	1.088000	0.41272	0.549000	0.68633	CAG	G|0.813;A|0.187	0.187	strong		0.602	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
TAS2R9	50835	hgsc.bcm.edu	37	12	10962115	10962115	+	Missense_Mutation	SNP	A	A	G	rs3741845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	102	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	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		
SPEN	23013	hgsc.bcm.edu	37	1	16255644	16255644	+	Missense_Mutation	SNP	C	C	T	rs848208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16255644C>T	ENST00000375759.3	+	11	3113	c.2909C>T	c.(2908-2910)gCa>gTa	p.A970V		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	970			A -> V (in dbSNP:rs848208).		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)		GAGCAGCCTGCAGATGGGGTA	0.488													C|||	605	0.120807	0.0212	0.2392	5008	,	,		18453	0.2222		0.0984	False		,,,				2504	0.09				p.A970V		Atlas-SNP	.											.	SPEN	374	.	0			c.C2909T						PASS	.	C	VAL/ALA	182,4224	112.1+/-150.2	6,170,2027	52.0	59.0	57.0		2909	3.6	0.0	1	dbSNP_86	57	870,7730	196.1+/-241.1	47,776,3477	yes	missense	SPEN	NM_015001.2	64	53,946,5504	TT,TC,CC		10.1163,4.1307,8.0886	benign	970/3665	16255644	1052,11954	2203	4300	6503	SO:0001583	missense	23013	exon11			AGCCTGCAGATGG		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.2909C>T	1.37:g.16255644C>T	ENSP00000364912:p.Ala970Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	308	0.14102564102564102	14	0.028455284552845527	79	0.21823204419889503	134	0.23426573426573427	81	0.10686015831134564	C	0.047	-1.261392	0.01445	0.041307	0.101163	ENSG00000065526	ENST00000375759	T	0.52754	0.65	5.5	3.64	0.41730	.	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.12630	0.006	B	0.10450	0.005	T	0.10451	-1.0629	8	0.31617	T	0.26	-4.831	8.8436	0.35157	0.0:0.7413:0.1231:0.1356	rs848208;rs1628610;rs52836456;rs60485173;rs848208	970	Q96T58	MINT_HUMAN	V	970	ENSP00000364912:A970V	ENSP00000364912:A970V	A	+	2	0	SPEN	16128231	0.000000	0.05858	0.014000	0.15608	0.004000	0.04260	0.584000	0.23864	0.889000	0.36185	0.655000	0.94253	GCA	C|0.896;T|0.104	0.104	strong		0.488	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
ZNF407	55628	hgsc.bcm.edu	37	18	72347482	72347482	+	Silent	SNP	T	T	C	rs12327359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:72347482T>C	ENST00000299687.5	+	1	4507	c.4507T>C	c.(4507-4509)Tta>Cta	p.L1503L	ZNF407_ENST00000309902.6_Silent_p.L1503L|ZNF407_ENST00000582337.1_Silent_p.L1503L|ZNF407_ENST00000577538.1_Silent_p.L1503L	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1503					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L1503L(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAATTTATTTTTACATATTAA	0.473													C|||	2123	0.423922	0.7201	0.3271	5008	,	,		19354	0.1845		0.4175	False		,,,				2504	0.3456				p.L1503L		Atlas-SNP	.											ZNF407,NS,carcinoma,0,1	ZNF407	231	1	1	Substitution - coding silent(1)	prostate(1)	c.T4507C						PASS	.	C	,,	2571,1165		885,801,182	41.0	43.0	43.0		4507,4507,4507	4.8	0.9	18	dbSNP_120	43	3538,4686		754,2030,1328	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	1639,2831,1510	CC,CT,TT		43.0204,31.1831,48.9214	,,	1503/1816,1503/1661,1503/2249	72347482	6109,5851	1868	4112	5980	SO:0001819	synonymous_variant	55628	exon1			TTATTTTTACATA	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.4507T>C	18.37:g.72347482T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			T|0.567;C|0.433	0.433	strong		0.473	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
PARVG	64098	hgsc.bcm.edu	37	22	44586519	44586519	+	Missense_Mutation	SNP	C	C	A	rs3842780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44586519C>A	ENST00000444313.3	+	7	961	c.477C>A	c.(475-477)aaC>aaA	p.N159K	PARVG_ENST00000422871.1_Missense_Mutation_p.N159K|PARVG_ENST00000415224.1_Missense_Mutation_p.N159K	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	159					actin cytoskeleton reorganization (GO:0031532)|cell-matrix adhesion (GO:0007160)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)	17		Ovarian(80;0.024)|all_neural(38;0.0299)				TCCCAACCAACGTCCAGGTGG	0.602													C|||	70	0.0139776	0.053	0.0	5008	,	,		19412	0.0		0.0	False		,,,				2504	0.0				p.N159K		Atlas-SNP	.											PARVG,NS,carcinoma,0,1	PARVG	41	1	0			c.C477A						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN	218,4188	133.7+/-170.0	2,214,1987	89.0	71.0	77.0		477,477,477	-2.7	0.0	22	dbSNP_107	77	0,8600		0,0,4300	yes	missense,missense,missense	PARVG	NM_001137605.1,NM_001137606.1,NM_022141.5	94,94,94	2,214,6287	AA,AC,CC		0.0,4.9478,1.6761	probably-damaging,probably-damaging,probably-damaging	159/332,159/332,159/332	44586519	218,12788	2203	4300	6503	SO:0001583	missense	64098	exon7			AACCAACGTCCAG	AF237772	CCDS14057.1	22q13.31	2013-01-24			ENSG00000138964	ENSG00000138964		"""Parvins"""	14654	protein-coding gene	gene with protein product		608122				11171322	Standard	NM_022141		Approved		uc003bep.4	Q9HBI0	OTTHUMG00000150473	ENST00000444313.3:c.477C>A	22.37:g.44586519C>A	ENSP00000391583:p.Asn159Lys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_001137606	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Missense_Mutation	SNP	ENST00000444313.3	37	CCDS14057.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	11.29	1.594965	0.28445	0.049478	0.0	ENSG00000138964	ENST00000422871;ENST00000444313;ENST00000415224	T;T;T	0.58506	0.33;0.33;0.33	3.46	-2.74	0.05932	Calponin homology domain (1);	0.347388	0.28130	N	0.016483	T	0.17450	0.0419	M	0.77313	2.365	0.30861	N	0.733509	P	0.50819	0.939	P	0.46253	0.509	T	0.53795	-0.8388	10	0.56958	D	0.05	-1.8351	8.7897	0.34843	0.0:0.5205:0.0:0.4795	rs3842780	159	Q9HBI0	PARVG_HUMAN	K	159	ENSP00000391453:N159K;ENSP00000391583:N159K;ENSP00000416761:N159K	ENSP00000349378:N159K	N	+	3	2	PARVG	42917852	0.015000	0.18098	0.018000	0.16275	0.401000	0.30781	-0.744000	0.04839	-0.298000	0.08921	0.561000	0.74099	AAC	C|0.985;A|0.015	0.015	strong		0.602	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141	
ACOX2	8309	hgsc.bcm.edu	37	3	58512237	58512237	+	Silent	SNP	A	A	G	rs1127745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:58512237A>G	ENST00000302819.5	-	10	1593	c.1302T>C	c.(1300-1302)tgT>tgC	p.C434C	ACOX2_ENST00000459701.2_Silent_p.C420C	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	434					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		CCTCGTAGGTACAGGAGGCCG	0.612													G|||	1418	0.283147	0.6982	0.1599	5008	,	,		18520	0.2262		0.0775	False		,,,				2504	0.0798				p.C434C		Atlas-SNP	.											.	ACOX2	53	.	0			c.T1302C						PASS	.	G		2761,1645	504.9+/-366.0	877,1007,319	82.0	66.0	71.0		1302	0.2	0.8	3	dbSNP_86	71	847,7753	780.1+/-407.7	37,773,3490	no	coding-synonymous	ACOX2	NM_003500.3		914,1780,3809	GG,GA,AA		9.8488,37.3355,27.741		434/682	58512237	3608,9398	2203	4300	6503	SO:0001819	synonymous_variant	8309	exon10			GTAGGTACAGGAG	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.1302T>C	3.37:g.58512237A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	166	68	0.409639	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			A|0.718;G|0.282	0.282	strong		0.612	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
EVC	2121	hgsc.bcm.edu	37	4	5795412	5795412	+	Silent	SNP	C	C	T	rs11737221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:5795412C>T	ENST00000264956.6	+	13	2038	c.1854C>T	c.(1852-1854)ggC>ggT	p.G618G	EVC_ENST00000515113.1_3'UTR|EVC_ENST00000382674.2_Silent_p.G618G	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	618					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)				CCATCCGCGGCGTCTTGGGCC	0.642													C|||	1672	0.333866	0.0681	0.2896	5008	,	,		14377	0.5278		0.3091	False		,,,				2504	0.5501				p.G618G		Atlas-SNP	.											EVC,caecum,carcinoma,0,1	EVC	90	1	0			c.C1854T						scavenged	.	C		409,3917		26,357,1780	19.0	19.0	19.0		1854	-8.3	0.0	4	dbSNP_120	19	2408,5964		361,1686,2139	no	coding-synonymous	EVC	NM_153717.2		387,2043,3919	TT,TC,CC		28.7625,9.4545,22.1846		618/993	5795412	2817,9881	2163	4186	6349	SO:0001819	synonymous_variant	2121	exon13			CCGCGGCGTCTTG	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.1854C>T	4.37:g.5795412C>T		Somatic	187	2	0.0106952		WXS	Illumina HiSeq	Phase_I	211	90	0.42654	NM_153717		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			C|0.742;T|0.258	0.258	strong		0.642	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
CKAP2L	150468	hgsc.bcm.edu	37	2	113509891	113509891	+	Missense_Mutation	SNP	T	T	C	rs36046436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113509891T>C	ENST00000302450.6	-	5	1633	c.1555A>G	c.(1555-1557)Agt>Ggt	p.S519G	CKAP2L_ENST00000541405.1_Missense_Mutation_p.S354G	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	519			S -> G (in dbSNP:rs36046436).			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						TTAATTTTACTGGACAGTTCG	0.348													T|||	66	0.0131789	0.0492	0.0014	5008	,	,		17493	0.0		0.0	False		,,,				2504	0.0				p.S519G		Atlas-SNP	.											.	CKAP2L	54	.	0			c.A1555G						PASS	.	T	GLY/SER	207,4199	127.8+/-164.7	5,197,2001	253.0	252.0	252.0		1555	0.2	0.0	2	dbSNP_126	252	0,8600		0,0,4300	yes	missense	CKAP2L	NM_152515.3	56	5,197,6301	CC,CT,TT		0.0,4.6981,1.5916	benign	519/746	113509891	207,12799	2203	4300	6503	SO:0001583	missense	150468	exon5			TTTTACTGGACAG	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.1555A>G	2.37:g.113509891T>C	ENSP00000305204:p.Ser519Gly	Somatic	396	0	0		WXS	Illumina HiSeq	Phase_I	382	184	0.481675	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Missense_Mutation	SNP	ENST00000302450.6	37	CCDS2100.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	T	5.135	0.210489	0.09757	0.046981	0.0	ENSG00000169607	ENST00000541405;ENST00000302450	T;T	0.22945	1.93;1.93	5.61	0.251	0.15540	.	0.735060	0.14028	N	0.346338	T	0.01730	0.0055	N	0.22421	0.69	0.09310	N	1	B;B	0.24426	0.034;0.103	B;B	0.25140	0.04;0.058	T	0.23583	-1.0184	10	0.21014	T	0.42	0.2974	1.8328	0.03133	0.1345:0.1548:0.1396:0.5711	rs36046436	108;519	Q8IYA6-2;Q8IYA6	.;CKP2L_HUMAN	G	354;519	ENSP00000438763:S354G;ENSP00000305204:S519G	ENSP00000305204:S519G	S	-	1	0	CKAP2L	113226362	0.001000	0.12720	0.041000	0.18516	0.163000	0.22366	0.999000	0.29757	0.391000	0.25143	-0.481000	0.04817	AGT	T|0.983;C|0.017	0.017	strong		0.348	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45518396	45518396	+	Silent	SNP	G	G	A	rs115989144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45518396G>A	ENST00000291574.4	+	21	3502	c.3327G>A	c.(3325-3327)tcG>tcA	p.S1109S		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	1109					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						AGCATTTTTCGACAAAGCTTA	0.527													G|||	12	0.00239617	0.0091	0.0	5008	,	,		20869	0.0		0.0	False		,,,				2504	0.0				p.S1109S		Atlas-SNP	.											TRAPPC10,colon,carcinoma,+1,1	TRAPPC10	109	1	0			c.G3327A						PASS	.	G		35,4371	40.8+/-73.8	0,35,2168	103.0	103.0	103.0		3327	-11.1	0.0	21	dbSNP_132	103	0,8600		0,0,4300	no	coding-synonymous	TRAPPC10	NM_003274.4		0,35,6468	AA,AG,GG		0.0,0.7944,0.2691		1109/1260	45518396	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	7109	exon21			TTTTTCGACAAAG	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.3327G>A	21.37:g.45518396G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	37	CCDS13704.1																																																																																			G|0.996;A|0.004	0.004	strong		0.527	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
BOD1	91272	hgsc.bcm.edu	37	5	173036394	173036394	+	Missense_Mutation	SNP	C	C	T	rs72822197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:173036394C>T	ENST00000311086.4	-	3	629	c.406G>A	c.(406-408)Gtg>Atg	p.V136M	BOD1_ENST00000285908.5_Intron|BOD1_ENST00000480951.1_Intron|BOD1_ENST00000471339.1_5'Flank	NM_138369.2	NP_612378.1	Q96IK1	BOD1_HUMAN	biorientation of chromosomes in cell division 1	136					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|kinetochore (GO:0000776)				endometrium(1)|large_intestine(2)|lung(2)|ovary(2)	7						GGATCCACCACCTGAGAAATA	0.468																																					p.V136M		Atlas-SNP	.											.	BOD1	15	.	0			c.G406A						PASS	.						150.0	136.0	141.0					5																	173036394		2203	4300	6503	SO:0001583	missense	91272	exon3			CCACCACCTGAGA	AY303777	CCDS4389.1, CCDS54951.1	5q35.2	2013-10-11	2009-03-04	2009-03-04	ENSG00000145919	ENSG00000145919			25114	protein-coding gene	gene with protein product	"""biorientation defective 1"""		"""family with sequence similarity 44, member B"""	FAM44B		17938248	Standard	NM_138369		Approved		uc003mcq.2	Q96IK1	OTTHUMG00000130540	ENST00000311086.4:c.406G>A	5.37:g.173036394C>T	ENSP00000309644:p.Val136Met	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	306	39	0.127451	NM_138369	B4DXH8|Q9BTW1	Missense_Mutation	SNP	ENST00000311086.4	37	CCDS4389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.1|27.1	4.803392|4.803392	0.90623|0.90623	.|.	.|.	ENSG00000145919|ENSG00000145919	ENST00000477985|ENST00000311086;ENST00000462674	.|.	.|.	.|.	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.71367|0.71367	0.3331|0.3331	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	.|P	.|0.46987	.|0.888	.|P	.|0.46825	.|0.528	T|T	0.75470|0.75470	-0.3306|-0.3306	5|9	.|0.72032	.|D	.|0.01	-25.5605|-25.5605	19.7198|19.7198	0.96137|0.96137	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|136	.|Q96IK1	.|BOD1_HUMAN	D|M	68|136;31	.|.	.|ENSP00000309644:V136M	G|V	-|-	2|1	0|0	BOD1|BOD1	172969000|172969000	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.474000|7.474000	0.81024|0.81024	2.668000|2.668000	0.90789|0.90789	0.655000|0.655000	0.94253|0.94253	GGT|GTG	C|0.946;T|0.054	0.054	strong		0.468	BOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252963.1	NM_138369	
LRRC23	10233	hgsc.bcm.edu	37	12	7021957	7021957	+	Silent	SNP	G	G	A	rs3759353		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7021957G>A	ENST00000007969.8	+	7	1042	c.822G>A	c.(820-822)gcG>gcA	p.A274A	LRRC23_ENST00000436789.1_Intron|LRRC23_ENST00000429740.1_Intron|LRRC23_ENST00000323702.5_Intron|ENO2_ENST00000229277.1_5'Flank|ENO2_ENST00000535366.1_5'Flank|ENO2_ENST00000544774.1_5'Flank|LRRC23_ENST00000443597.2_Silent_p.A274A|ENO2_ENST00000545045.2_5'Flank|ENO2_ENST00000541477.1_5'Flank|ENO2_ENST00000538763.1_5'Flank	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	274								p.A274A(2)		NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						AGCTGCGAGCGTTGGTGCTGC	0.587													G|||	234	0.0467252	0.0	0.0	5008	,	,		-128	0.2163		0.0	False		,,,				2504	0.0164				p.A274A		Atlas-SNP	.											LRRC23,colon,carcinoma,0,2	LRRC23	46	2	2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	c.G822A						PASS	.	G	,,	4,4402	8.1+/-20.4	0,4,2199	106.0	102.0	103.0		822,,822	-2.4	0.1	12	dbSNP_107	103	0,8600		0,0,4300	no	coding-synonymous,intron,coding-synonymous	LRRC23	NM_001135217.1,NM_006992.3,NM_201650.2	,,	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	,,	274/344,,274/344	7021957	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	10233	exon7			GCGAGCGTTGGTG	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.822G>A	12.37:g.7021957G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_001135217	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Silent	SNP	ENST00000007969.8	37	CCDS8569.1																																																																																			G|0.967;A|0.033	0.033	strong		0.587	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992	
GRHL3	57822	hgsc.bcm.edu	37	1	24664220	24664220	+	Missense_Mutation	SNP	G	G	A	rs145470039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24664220G>A	ENST00000350501.5	+	6	908	c.781G>A	c.(781-783)Gtc>Atc	p.V261I	GRHL3_ENST00000236255.4_Missense_Mutation_p.V266I|GRHL3_ENST00000342072.4_Missense_Mutation_p.V168I|GRHL3_ENST00000361548.4_Missense_Mutation_p.V261I|GRHL3_ENST00000356046.2_Missense_Mutation_p.V215I	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	261					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.V266I(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)		GTTCTACCCCGTCACCCTGCG	0.587													G|||	9	0.00179712	0.0061	0.0014	5008	,	,		20270	0.0		0.0	False		,,,				2504	0.0				p.V266I		Atlas-SNP	.											GRHL3_ENST00000350501,NS,carcinoma,0,4	GRHL3	69	4	1	Substitution - Missense(1)	ovary(1)	c.G796A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	16,4390	23.3+/-48.9	0,16,2187	98.0	84.0	89.0		781,781,796,643	4.1	0.8	1	dbSNP_134	89	0,8600		0,0,4300	yes	missense,missense,missense,missense	GRHL3	NM_198174.2,NM_198173.2,NM_021180.3,NM_001195010.1	29,29,29,29	0,16,6487	AA,AG,GG		0.0,0.3631,0.123	benign,benign,benign,benign	261/627,261/603,266/608,215/557	24664220	16,12990	2203	4300	6503	SO:0001583	missense	57822	exon6			TACCCCGTCACCC	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.781G>A	1.37:g.24664220G>A	ENSP00000288955:p.Val261Ile	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_021180	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	4.028	0.002793	0.07866	0.003631	0.0	ENSG00000158055	ENST00000361548;ENST00000342072;ENST00000350501;ENST00000356046;ENST00000236255	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.97	4.12	0.48240	.	0.237878	0.42964	N	0.000623	T	0.03390	0.0098	N	0.02103	-0.685	0.32683	N	0.515251	B;B;B	0.18310	0.013;0.003;0.027	B;B;B	0.14578	0.008;0.006;0.011	T	0.30937	-0.9961	10	0.02654	T	1	-28.162	9.5371	0.39229	0.2343:0.0:0.7657:0.0	.	215;266;261	A2A297;Q8TE85-2;G3XAF0	.;.;.	I	261;168;261;215;266	ENSP00000354943:V261I;ENSP00000340543:V168I;ENSP00000288955:V261I;ENSP00000348333:V215I;ENSP00000236255:V266I	ENSP00000236255:V266I	V	+	1	0	GRHL3	24536807	0.796000	0.28864	0.822000	0.32727	0.992000	0.81027	1.375000	0.34295	0.868000	0.35678	0.655000	0.94253	GTC	G|0.997;A|0.003	0.003	strong		0.587	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
SLC39A8	64116	hgsc.bcm.edu	37	4	103228734	103228734	+	Silent	SNP	C	C	T	rs35411892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:103228734C>T	ENST00000394833.2	-	3	887	c.411G>A	c.(409-411)acG>acA	p.T137T	SLC39A8_ENST00000510255.1_5'UTR|SLC39A8_ENST00000424970.2_Silent_p.T137T|SLC39A8_ENST00000356736.4_Silent_p.T137T	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	137					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		GATTAATAATCGTCACTGACA	0.393													C|||	821	0.163938	0.1604	0.1844	5008	,	,		18210	0.1171		0.1551	False		,,,				2504	0.2117				p.T137T		Atlas-SNP	.											.	SLC39A8	24	.	0			c.G411A						PASS	.	C	,,,	688,3718	280.8+/-275.6	49,590,1564	97.0	106.0	103.0		411,411,210,411	-11.1	0.0	4	dbSNP_126	103	1514,7086	284.2+/-296.5	122,1270,2908	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC39A8	NM_001135146.1,NM_001135147.1,NM_001135148.1,NM_022154.5	,,,	171,1860,4472	TT,TC,CC		17.6047,15.6151,16.9306	,,,	137/461,137/445,70/394,137/461	103228734	2202,10804	2203	4300	6503	SO:0001819	synonymous_variant	64116	exon3			AATAATCGTCACT		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"""Solute carriers"""	20862	protein-coding gene	gene with protein product		608732	"""solute carrier family 39 (metal ion transporter), member 8"""			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.411G>A	4.37:g.103228734C>T		Somatic	239	1	0.0041841		WXS	Illumina HiSeq	Phase_I	318	147	0.462264	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Silent	SNP	ENST00000394833.2	37	CCDS3656.1																																																																																			C|0.841;T|0.159	0.159	strong		0.393	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154	
DNAH8	1769	hgsc.bcm.edu	37	6	38743649	38743649	+	Silent	SNP	A	A	G	rs149534667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:38743649A>G	ENST00000359357.3	+	11	1487	c.1233A>G	c.(1231-1233)caA>caG	p.Q411Q	DNAH8_ENST00000441566.1_Silent_p.Q411Q|DNAH8_ENST00000449981.2_Silent_p.Q628Q			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	411					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						AGAAAAAGCAATATGACATTC	0.303													A|||	21	0.00419329	0.0151	0.0014	5008	,	,		17047	0.0		0.0	False		,,,				2504	0.0				p.Q628Q		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A1884G						PASS	.	A		49,4355	48.2+/-83.0	1,47,2154	84.0	97.0	93.0		1884	-3.2	0.9	6	dbSNP_134	93	3,8565	3.0+/-9.4	0,3,4281	no	coding-synonymous	DNAH8	NM_001206927.1		1,50,6435	GG,GA,AA		0.035,1.1126,0.4009		628/4708	38743649	52,12920	2202	4284	6486	SO:0001819	synonymous_variant	1769	exon13			AAAGCAATATGAC	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.1233A>G	6.37:g.38743649A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	149	59	0.395973	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				A|0.995;G|0.005	0.005	strong		0.303	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
ZNF679	168417	hgsc.bcm.edu	37	7	63721251	63721251	+	Missense_Mutation	SNP	A	A	G	rs12154540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:63721251A>G	ENST00000421025.1	+	4	475	c.206A>G	c.(205-207)gAg>gGg	p.E69G	ZNF679_ENST00000255746.4_Missense_Mutation_p.E69G	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		E -> G (in dbSNP:rs12154540).		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.E69G(1)		endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						ACCTGTCTGGAGCAAAATAAA	0.383													.|||	992	0.198083	0.2511	0.2478	5008	,	,		15258	0.0099		0.2575	False		,,,				2504	0.2239				p.E69G		Atlas-SNP	.											ZNF679,NS,carcinoma,0,1	ZNF679	80	1	1	Substitution - Missense(1)	kidney(1)	c.A206G						PASS	.	A	GLY/GLU	333,1051		37,259,396	120.0	105.0	110.0		206	0.2	0.1	7	dbSNP_120	110	880,2302		106,668,817	no	missense	ZNF679	NM_153363.2	98	143,927,1213	GG,GA,AA		27.6556,24.0607,26.5659	benign	69/412	63721251	1213,3353	692	1591	2283	SO:0001583	missense	168417	exon4			GTCTGGAGCAAAA	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"""Zinc fingers, C2H2-type"", ""-"""	28650	protein-coding gene	gene with protein product	"""hypothetical protein MGC42415"""					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.206A>G	7.37:g.63721251A>G	ENSP00000416809:p.Glu69Gly	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	416	0.19047619047619047	127	0.258130081300813	98	0.27071823204419887	3	0.005244755244755245	188	0.24802110817941952	A	5.271	0.235343	0.10023	0.240607	0.276556	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.01159	5.25;5.25	0.235	0.235	0.15431	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	M	0.89353	3.025	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.22591	-1.0212	7	0.72032	D	0.01	.	.	.	.	rs12154540;rs12154540	69	Q8IYX0	ZN679_HUMAN	G	69	ENSP00000416809:E69G;ENSP00000255746:E69G	ENSP00000255746:E69G	E	+	2	0	ZNF679	63358686	0.130000	0.22417	0.059000	0.19551	0.062000	0.15995	1.689000	0.37700	0.263000	0.21812	0.260000	0.18958	GAG	A|0.805;G|0.195	0.195	strong		0.383	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363	
PPWD1	23398	hgsc.bcm.edu	37	5	64881936	64881936	+	Silent	SNP	A	A	G	rs27141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:64881936A>G	ENST00000261308.5	+	10	1797	c.1725A>G	c.(1723-1725)ccA>ccG	p.P575P	PPWD1_ENST00000535264.1_Silent_p.P545P|PPWD1_ENST00000538977.1_Silent_p.P419P	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	575	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		ATGACAGGCCATACACACTCA	0.413													G|||	2897	0.578474	0.6309	0.5115	5008	,	,		20230	0.4137		0.6203	False		,,,				2504	0.682				p.P575P		Atlas-SNP	.											.	PPWD1	47	.	0			c.A1725G						PASS	.	G		2741,1665	507.6+/-366.7	852,1037,314	145.0	130.0	135.0		1725	-5.6	0.8	5	dbSNP_76	135	5584,3016	465.8+/-366.6	1800,1984,516	yes	coding-synonymous	PPWD1	NM_015342.2		2652,3021,830	GG,GA,AA		35.0698,37.7894,35.9911		575/647	64881936	8325,4681	2203	4300	6503	SO:0001819	synonymous_variant	23398	exon10			CAGGCCATACACA	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"""WD repeat domain containing"""	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.1725A>G	5.37:g.64881936A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	83	0.549669	NM_015342	B4DWR9|Q15002|Q7KZ89	Silent	SNP	ENST00000261308.5	37	CCDS3985.1																																																																																			A|0.396;G|0.604	0.604	strong		0.413	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342	
C4A	720	hgsc.bcm.edu	37	6	31963780	31963780	+	Silent	SNP	A	A	G	rs371801898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31963780A>G	ENST00000428956.2	+	26	3363	c.3279A>G	c.(3277-3279)gtA>gtG	p.V1093V	C4A_ENST00000498271.1_Silent_p.V1093V	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1093					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	AGGAGCAGGTAGGAGGCTCGC	0.567													A|||	7	0.00139776	0.0053	0.0	5008	,	,		18057	0.0		0.0	False		,,,				2504	0.0				p.V1093V		Atlas-SNP	.											.	C4A	15	.	0			c.A3279G						PASS	.	A		6,3114		0,6,1554	19.0	17.0	18.0		3279	0.3	0.6	6		18	0,6998		0,0,3499	no	coding-synonymous	C4A	NM_007293.2		0,6,5053	GG,GA,AA		0.0,0.1923,0.0593		1093/1745	31963780	6,10112	1560	3499	5059	SO:0001819	synonymous_variant	720	exon26			GCAGGTAGGAGGC	L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731		"""Blood group antigens"", ""Complement system"""	1323	protein-coding gene	gene with protein product		120810	"""complement component 4A"""				Standard	NM_001252204		Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.3279A>G	6.37:g.31963780A>G		Somatic	927	2	0.0021575		WXS	Illumina HiSeq	Phase_I	867	299	0.344867	NM_007293	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	Silent	SNP	ENST00000428956.2	37	CCDS47404.1																																																																																			.	.	weak		0.567	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293	
IGSF10	285313	hgsc.bcm.edu	37	3	151155197	151155197	+	Silent	SNP	T	T	C	rs141741834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151155197T>C	ENST00000282466.3	-	6	7151	c.7152A>G	c.(7150-7152)caA>caG	p.Q2384Q	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2384	Ig-like C2-type 10.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACTGATAACTTTGTGGTCCAT	0.403													T|||	44	0.00878594	0.0333	0.0	5008	,	,		21182	0.0		0.0	False		,,,				2504	0.0				p.Q2384Q		Atlas-SNP	.											.	IGSF10	279	.	0			c.A7152G						PASS	.	T	,,	84,4322	70.9+/-108.8	0,84,2119	124.0	124.0	124.0		1233,1089,7152	-11.2	0.0	3	dbSNP_134	124	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	0,84,6419	CC,CT,TT		0.0,1.9065,0.6459	,,	411/651,363/603,2384/2624	151155197	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			ATAACTTTGTGGT	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.7152A>G	3.37:g.151155197T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	129	71	0.550388	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			T|0.993;C|0.007	0.007	strong		0.403	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
CRAMP1L	57585	hgsc.bcm.edu	37	16	1706480	1706480	+	Silent	SNP	C	C	G	rs80154657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1706480C>G	ENST00000397412.3	+	10	1821	c.1722C>G	c.(1720-1722)ccC>ccG	p.P574P	CRAMP1L_ENST00000436138.3_Silent_p.P571P|LA16c-431H6.6_ENST00000454337.1_Intron|CRAMP1L_ENST00000293925.5_Silent_p.P574P|CRAMP1L_ENST00000262317.4_Intron			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	574						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						TCATTGTCCCCGAGCAGTGCC	0.677													C|||	98	0.0195687	0.0726	0.0029	5008	,	,		15682	0.0		0.0	False		,,,				2504	0.0				p.P574P		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.C1722G						PASS	.	C		168,3706		3,162,1772	15.0	16.0	16.0		1722	-10.0	0.0	16	dbSNP_132	16	1,8121		0,1,4060	no	coding-synonymous	CRAMP1L	NM_020825.3		3,163,5832	GG,GC,CC		0.0123,4.3366,1.4088		574/1270	1706480	169,11827	1937	4061	5998	SO:0001819	synonymous_variant	57585	exon9			TGTCCCCGAGCAG	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.1722C>G	16.37:g.1706480C>G		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	24	9	0.375	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Silent	SNP	ENST00000397412.3	37	CCDS10440.2																																																																																			C|0.979;G|0.021	0.021	strong		0.677	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		
SLC35G6	643664	hgsc.bcm.edu	37	17	7386300	7386300	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7386300G>A	ENST00000412468.2	+	2	1112	c.997G>A	c.(997-999)Gaa>Aaa	p.E333K	POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	333						integral component of membrane (GO:0016021)											CTGTGAGAGGGAAGGGAAGGT	0.557																																					p.E333K		Atlas-SNP	.											POLR2A_ENST00000412468,NS,carcinoma,-1,1	.	.	1	0			c.G997A						scavenged	.						60.0	59.0	59.0					17																	7386300		2203	4300	6503	SO:0001583	missense	643664	exon2			GAGAGGGAAGGGA		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.997G>A	17.37:g.7386300G>A	ENSP00000396523:p.Glu333Lys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	175	5	0.0285714	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.322479	0.01320	.	.	ENSG00000181222	ENST00000412468	T	0.26518	1.73	4.69	1.44	0.22558	.	.	.	.	.	T	0.14056	0.0340	L	0.36672	1.1	0.09310	N	1	B	0.18013	0.025	B	0.15870	0.014	T	0.37526	-0.9702	9	0.02654	T	1	-0.2286	4.7772	0.13185	0.2637:0.1728:0.5636:0.0	.	333	P0C7Q6	S35G6_HUMAN	K	333	ENSP00000396523:E333K	ENSP00000396523:E333K	E	+	1	0	SLC35G6	7327024	1.000000	0.71417	0.321000	0.25320	0.451000	0.32288	4.403000	0.59729	0.499000	0.27970	-0.225000	0.12378	GAA	.	.	none		0.557	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
SLC5A10	125206	hgsc.bcm.edu	37	17	18918396	18918396	+	Silent	SNP	G	G	C	rs2074279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18918396G>C	ENST00000395645.3	+	11	1143	c.1125G>C	c.(1123-1125)gcG>gcC	p.A375A	SLC5A10_ENST00000417251.2_Silent_p.A339A|SLC5A10_ENST00000395643.2_Silent_p.A348A|SLC5A10_ENST00000395647.2_Silent_p.A391A|SLC5A10_ENST00000395642.1_Silent_p.A308A|SLC5A10_ENST00000317977.6_Silent_p.A308A	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	375					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						TGATGCTGGCGGCGCTCATGT	0.677													C|||	997	0.199081	0.3336	0.0663	5008	,	,		12776	0.3413		0.0288	False		,,,				2504	0.1401				p.A391A		Atlas-SNP	.											.	SLC5A10	55	.	0			c.G1173C						PASS	.	C	,	1209,3197	706.8+/-407.4	151,907,1145	60.0	49.0	53.0		1125,1173	-4.3	0.8	17	dbSNP_96	53	187,8413	810.1+/-407.1	2,183,4115	no	coding-synonymous,coding-synonymous	SLC5A10	NM_001042450.1,NM_152351.3	,	153,1090,5260	CC,CG,GG		2.1744,27.4399,10.7335	,	375/597,391/613	18918396	1396,11610	2203	4300	6503	SO:0001819	synonymous_variant	125206	exon11			GCTGGCGGCGCTC		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"""Solute carriers"""	23155	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 10"""				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.1125G>C	17.37:g.18918396G>C		Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	348	172	0.494253	NM_152351	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Silent	SNP	ENST00000395645.3	37	CCDS42275.1																																																																																			G|0.872;C|0.128	0.128	strong		0.677	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351	
OR5I1	10798	hgsc.bcm.edu	37	11	55703728	55703728	+	Missense_Mutation	SNP	A	A	G	rs4367963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55703728A>G	ENST00000301532.3	-	1	148	c.149T>C	c.(148-150)tTg>tCg	p.L50S		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	50			L -> S (in dbSNP:rs4367963).		signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L50S(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						AATCCTGATCAACAGCATCAA	0.398													A|||	457	0.091254	0.1286	0.0418	5008	,	,		16386	0.0903		0.0954	False		,,,				2504	0.0726				p.L50S		Atlas-SNP	.											OR5I1,caecum,carcinoma,+1,2	OR5I1	110	2	1	Substitution - Missense(1)	stomach(1)	c.T149C						PASS	.	A	SER/LEU	502,3900	229.1+/-243.8	32,438,1731	70.0	69.0	69.0		149	5.1	0.2	11	dbSNP_111	69	720,7872	174.2+/-224.5	31,658,3607	yes	missense	OR5I1	NM_006637.1	145	63,1096,5338	GG,GA,AA		8.3799,11.4039,9.4043	probably-damaging	50/315	55703728	1222,11772	2201	4296	6497	SO:0001583	missense	10798	exon1			CTGATCAACAGCA	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.149T>C	11.37:g.55703728A>G	ENSP00000301532:p.Leu50Ser	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	37	CCDS7949.1	202	0.0924908424908425	73	0.1483739837398374	18	0.049723756906077346	44	0.07692307692307693	67	0.08839050131926121	A	18.62	3.663270	0.67700	0.114039	0.083799	ENSG00000167825	ENST00000301532	T	0.02837	4.14	5.05	5.05	0.67936	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36703	N	0.002444	T	0.00073	0.0002	M	0.65498	2.005	0.52501	P	4.4000000000044004E-5	D	0.76494	0.999	D	0.80764	0.994	T	0.08186	-1.0734	9	0.87932	D	0	.	13.0502	0.58950	1.0:0.0:0.0:0.0	rs4367963;rs52814279;rs57530320;rs4367963	50	Q13606	OR5I1_HUMAN	S	50	ENSP00000301532:L50S	ENSP00000301532:L50S	L	-	2	0	OR5I1	55460304	0.186000	0.23225	0.247000	0.24249	0.903000	0.53119	4.378000	0.59568	2.020000	0.59435	0.519000	0.50382	TTG	A|0.901;G|0.099	0.099	strong		0.398	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557477	32557477	+	Silent	SNP	G	G	A	rs150644773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32557477G>A	ENST00000360004.5	-	1	148	c.43C>T	c.(43-45)Ctg>Ttg	p.L15L		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	15					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						GTCACTGTCAGCGCTGTCATG	0.592										Multiple Myeloma(14;0.17)																											p.L15L		Atlas-SNP	.											HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	0			c.C43T						PASS	.						87.0	106.0	99.0					6																	32557477		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon1			CTGTCAGCGCTGT	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.43C>T	6.37:g.32557477G>A		Somatic	390	0	0		WXS	Illumina HiSeq	Phase_I	268	24	0.0895522	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.868;A|0.132	0.132	strong		0.592	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
PITRM1	10531	hgsc.bcm.edu	37	10	3180316	3180316	+	Splice_Site	SNP	T	T	C	rs11414|rs397705014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3180316T>C	ENST00000224949.4	-	27	3055	c.3021A>G	c.(3019-3021)agA>agG	p.R1007R	PITRM1_ENST00000380994.1_Splice_Site_p.R565R|PITRM1_ENST00000451104.2_Splice_Site_p.R909R|PITRM1_ENST00000464395.1_5'UTR|PITRM1_ENST00000380989.2_Splice_Site_p.R1008R			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	1007					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.R1008R(1)		breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TGCCGAGGTATCTGAGAGGAA	0.612													C|||	3054	0.609824	0.677	0.621	5008	,	,		17615	0.5327		0.6292	False		,,,				2504	0.5706				p.R1008R		Atlas-SNP	.											PITRM1,NS,carcinoma,0,1	PITRM1	109	1	1	Substitution - coding silent(1)	stomach(1)	c.A3024G						PASS	.	C	,,	2938,1330		1054,830,250	44.0	48.0	47.0		3024,2727,3021	2.9	1.0	10	dbSNP_52	47	4997,3501		1488,2021,740	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	,,	2542,2851,990	CC,CT,TT		41.1979,31.1621,37.8427	,,	1008/1039,909/940,1007/1038	3180316	7935,4831	2134	4249	6383	SO:0001630	splice_region_variant	10531	exon27			GAGGTATCTGAGA	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.3021-1A>G	10.37:g.3180316T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent	SNP	ENST00000224949.4	37	CCDS59208.1																																																																																			T|0.393;G|0.000;C|0.607	0.607	strong		0.612	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		Silent
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919064	12919064	+	Missense_Mutation	SNP	T	T	G	rs3204790	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919064T>G	ENST00000240189.2	+	2	287	c.200T>G	c.(199-201)gTa>gGa	p.V67G		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	67			V -> G (in dbSNP:rs3204790).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.V67G(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTCCCTCTGGTATCGCTGATG	0.557													.|||	934	0.186502	0.1437	0.1297	5008	,	,		22643	0.3333		0.1531	False		,,,				2504	0.1677				p.V67G		Atlas-SNP	.											PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	1	Substitution - Missense(1)	prostate(1)	c.T200G						scavenged	.	G	GLY/VAL	705,3697	757.4+/-412.7	76,553,1572	144.0	150.0	148.0		200	0.8	0.1	1	dbSNP_105	148	1295,7297	751.5+/-407.4	117,1061,3118	no	missense	PRAMEF2	NM_023014.1	109	193,1614,4690	GG,GT,TT		15.0722,16.0154,15.3917	benign	67/475	12919064	2000,10994	2201	4296	6497	SO:0001583	missense	65122	exon2			CTCTGGTATCGCT		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.200T>G	1.37:g.12919064T>G	ENSP00000240189:p.Val67Gly	Somatic	323	4	0.0123839		WXS	Illumina HiSeq	Phase_I	392	180	0.459184	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	480	0.21978021978021978	76	0.15447154471544716	59	0.16298342541436464	188	0.32867132867132864	157	0.20712401055408972	G	0.004	-2.285905	0.00251	0.160154	0.150722	ENSG00000120952	ENST00000240189	T	0.04049	3.72	0.842	0.842	0.18927	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00004	-3.36	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.37220	-0.9715	9	0.02654	T	1	.	4.0419	0.09755	0.0:0.0:0.5905:0.4095	rs3204790;rs17038653	67	O60811	PRAM2_HUMAN	G	67	ENSP00000240189:V67G	ENSP00000240189:V67G	V	+	2	0	PRAMEF2	12841651	0.017000	0.18338	0.148000	0.22405	0.037000	0.13140	-0.608000	0.05641	-0.047000	0.13423	-1.044000	0.02363	GTA	T|0.824;G|0.176	0.176	strong		0.557	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
DOCK8	81704	hgsc.bcm.edu	37	9	368030	368030	+	Silent	SNP	T	T	C	rs10972587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:368030T>C	ENST00000453981.1	+	15	1804	c.1692T>C	c.(1690-1692)taT>taC	p.Y564Y	DOCK8_ENST00000382329.1_5'UTR|DOCK8_ENST00000382331.1_5'UTR|DOCK8_ENST00000469391.1_Silent_p.Y496Y|DOCK8_ENST00000432829.2_Silent_p.Y496Y			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	144	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	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	
MUC16	94025	hgsc.bcm.edu	37	19	9070186	9070186	+	Missense_Mutation	SNP	C	C	T	rs1559171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9070186C>T	ENST00000397910.4	-	3	17463	c.17260G>A	c.(17260-17262)Gcc>Acc	p.A5754T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5756	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						TCCCCCATGGCGAAGGTGATA	0.468													t|||	100	0.0199681	0.0734	0.0043	5008	,	,		22084	0.0		0.0	False		,,,				2504	0.0				p.A5754T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G17260A						PASS	.	T	THR/ALA	251,3819		11,229,1795	161.0	152.0	155.0		17260	-3.5	0.0	19	dbSNP_88	155	5,8383		0,5,4189	yes	missense	MUC16	NM_024690.2	58	11,234,5984	TT,TC,CC		0.0596,6.1671,2.0549	benign	5754/14508	9070186	256,12202	2035	4194	6229	SO:0001583	missense	94025	exon3			CCATGGCGAAGGT	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.17260G>A	19.37:g.9070186C>T	ENSP00000381008:p.Ala5754Thr	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	282	132	0.468085	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	t	4.044	0.005793	0.07866	0.061671	5.96E-4	ENSG00000181143	ENST00000397910	T	0.20069	2.1	1.73	-3.46	0.04767	.	.	.	.	.	T	0.00724	0.0024	N	0.03608	-0.345	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.26503	-1.0101	8	0.87932	D	0	.	1.5797	0.02632	0.2079:0.4205:0.1629:0.2087	rs1559171;rs1559171	5754	B5ME49	.	T	5754	ENSP00000381008:A5754T	ENSP00000381008:A5754T	A	-	1	0	MUC16	8931186	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.346000	0.07760	-2.492000	0.00516	-0.521000	0.04368	GCC	C|0.987;T|0.013	0.013	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
C10orf113	387638	hgsc.bcm.edu	37	10	21414892	21414892	+	Missense_Mutation	SNP	C	C	G	rs625223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:21414892C>G	ENST00000534331.1	-	2	378	c.328G>C	c.(328-330)Gat>Cat	p.D110H	C10orf113_ENST00000377118.4_Missense_Mutation_p.D100H|NEBL_ENST00000417816.2_Intron|C10orf113_ENST00000529198.1_3'UTR	NM_001010896.2	NP_001010896.2	Q5VZT2	CJ113_HUMAN	chromosome 10 open reading frame 113	110			D -> H (in dbSNP:rs625223). {ECO:0000269|PubMed:15489334}.							endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|pancreas(1)	7						TTGCCTGGATCTGGTTCAGGA	0.542													C|||	2719	0.542931	0.6657	0.3847	5008	,	,		16457	0.7063		0.3181	False		,,,				2504	0.5521				p.D110H		Atlas-SNP	.											.	C10orf113	32	.	0			c.G328C						PASS	.	C	,,,HIS/ASP	2636,1770	644.5+/-398.0	789,1058,356	67.0	69.0	68.0		,,,328	2.6	0.8	10	dbSNP_83	68	2896,5704	454.0+/-363.4	507,1882,1911	yes	intron,utr-3,intron,missense	NEBL,C10orf113	NM_001173484.1,NM_001177483.1,NM_213569.2,NM_001010896.2	,,,81	1296,2940,2267	GG,GC,CC		33.6744,40.1725,42.5342	,,,benign	,,,110/156	21414892	5532,7474	2203	4300	6503	SO:0001583	missense	387638	exon2			CTGGATCTGGTTC		CCDS31162.1, CCDS31162.2, CCDS53496.1	10p12.31	2012-06-12			ENSG00000204683	ENSG00000204683			31447	protein-coding gene	gene with protein product							Standard	NM_001010896		Approved	bA165O3.1	uc001iqm.3	Q5VZT2	OTTHUMG00000017786	ENST00000534331.1:c.328G>C	10.37:g.21414892C>G	ENSP00000433646:p.Asp110His	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_001010896	B9EIM9|E9PRX7	Missense_Mutation	SNP	ENST00000534331.1	37	CCDS31162.2	1069	0.48946886446886445	317	0.6443089430894309	127	0.35082872928176795	389	0.6800699300699301	236	0.3113456464379947	C	11.97	1.796893	0.31777	0.598275	0.336744	ENSG00000204683	ENST00000534331;ENST00000377118	T;T	0.41065	1.01;1.01	4.51	2.6	0.31112	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.52099	P	5.299999999996974E-5	B	0.23735	0.09	B	0.20767	0.031	T	0.33163	-0.9879	8	0.87932	D	0	-0.1856	10.9676	0.47421	0.0:0.5718:0.4282:0.0	rs625223;rs979004;rs52825206;rs625223	110	Q5VZT2	CJ113_HUMAN	H	110;100	ENSP00000433646:D110H;ENSP00000366322:D100H	ENSP00000366322:D100H	D	-	1	0	C10orf113	21454898	0.969000	0.33509	0.775000	0.31657	0.991000	0.79684	0.708000	0.25719	0.589000	0.29677	0.460000	0.39030	GAT	C|0.539;G|0.461	0.461	strong		0.542	C10orf113-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047108.3	NM_001010896	
REXO1	57455	hgsc.bcm.edu	37	19	1827565	1827565	+	Missense_Mutation	SNP	A	A	G	rs10415018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1827565A>G	ENST00000170168.4	-	2	1317	c.1223T>C	c.(1222-1224)gTg>gCg	p.V408A	REXO1_ENST00000587524.1_5'Flank	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	408			V -> A (in dbSNP:rs10415018).			nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|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)		GGGCTTCTCCACAGGCCGCCC	0.662													.|||	1236	0.246805	0.3669	0.3458	5008	,	,		13078	0.2629		0.1054	False		,,,				2504	0.1431				p.V408A		Atlas-SNP	.											REXO1,NS,carcinoma,0,1	REXO1	55	1	0			c.T1223C						PASS	.	G	ALA/VAL	1444,2932		232,980,976	15.0	17.0	17.0		1223	-0.9	0.0	19	dbSNP_119	17	857,7703		47,763,3470	no	missense	REXO1	NM_020695.3	64	279,1743,4446	GG,GA,AA		10.0117,32.9982,17.7876	benign	408/1222	1827565	2301,10635	2188	4280	6468	SO:0001583	missense	57455	exon2			TTCTCCACAGGCC	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.1223T>C	19.37:g.1827565A>G	ENSP00000170168:p.Val408Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	112	38	0.339286	NM_020695	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	37	CCDS32866.1	534	0.2445054945054945	196	0.3983739837398374	107	0.2955801104972376	158	0.2762237762237762	73	0.09630606860158311	G	0.006	-2.052309	0.00394	0.329982	0.100117	ENSG00000079313	ENST00000170168	T	0.10860	2.83	3.97	-0.92	0.10475	.	1.467800	0.03856	N	0.273126	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45629	-0.9248	9	0.08599	T	0.76	1.2749	0.6493	0.00824	0.2097:0.2826:0.2637:0.2441	rs10415018;rs10415018	408	Q8N1G1	REXO1_HUMAN	A	408	ENSP00000170168:V408A	ENSP00000170168:V408A	V	-	2	0	REXO1	1778565	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.507000	0.06352	-0.526000	0.06383	-1.272000	0.01410	GTG	A|0.781;G|0.219	0.219	strong		0.662	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
CTSC	1075	hgsc.bcm.edu	37	11	88027393	88027393	+	Silent	SNP	A	A	C	rs17594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:88027393A>C	ENST00000227266.5	-	7	1287	c.1173T>G	c.(1171-1173)acT>acG	p.T391T		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	391					aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)			large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTCTTAGACCAGTGTGGTGGT	0.488													A|||	429	0.0856629	0.0802	0.1023	5008	,	,		19653	0.1151		0.0507	False		,,,				2504	0.0869				p.T391T		Atlas-SNP	.											.	CTSC	46	.	0			c.T1173G						PASS	.	A		302,4100	163.6+/-195.4	11,280,1910	140.0	113.0	122.0		1173	-5.8	1.0	11	dbSNP_63	122	326,8272	114.6+/-174.5	5,316,3978	no	coding-synonymous	CTSC	NM_001814.4		16,596,5888	CC,CA,AA		3.7916,6.8605,4.8308		391/464	88027393	628,12372	2201	4299	6500	SO:0001819	synonymous_variant	1075	exon7			TAGACCAGTGTGG	AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"""Cathepsins"""	2528	protein-coding gene	gene with protein product	"""dipeptidyl peptidase 1"""	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.1173T>G	11.37:g.88027393A>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	192	79	0.411458	NM_001814	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Silent	SNP	ENST00000227266.5	37	CCDS8282.1																																																																																			A|0.942;C|0.058	0.058	strong		0.488	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814	
MCTP2	55784	hgsc.bcm.edu	37	15	94858808	94858808	+	Silent	SNP	G	G	A	rs146431277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:94858808G>A	ENST00000357742.4	+	3	579	c.579G>A	c.(577-579)gcG>gcA	p.A193A	MCTP2_ENST00000543482.1_Silent_p.A193A|MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Silent_p.A193A	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	193	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			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)			GCCCTTTTGCGTACCTCCTCA	0.547													g|||	8	0.00159744	0.0053	0.0	5008	,	,		17286	0.0		0.0	False		,,,				2504	0.001				p.A193A		Atlas-SNP	.											MCTP2,NS,adenoma,0,1	MCTP2	122	1	0			c.G579A						PASS	.	A	,	28,4366	34.3+/-65.2	0,28,2169	150.0	121.0	131.0		579,579	-12.1	0.0	15	dbSNP_134	131	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	MCTP2	NM_001159643.1,NM_018349.3	,	0,29,6466	AA,AG,GG		0.0116,0.6372,0.2232	,	193/824,193/879	94858808	29,12961	2197	4298	6495	SO:0001819	synonymous_variant	55784	exon3			TTTTGCGTACCTC	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.579G>A	15.37:g.94858808G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	203	105	0.517241	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	37	CCDS32338.1																																																																																			G|0.998;A|0.002	0.002	strong		0.547	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	
PSG5	5673	hgsc.bcm.edu	37	19	43680147	43680147	+	Missense_Mutation	SNP	C	C	T	rs17856402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43680147C>T	ENST00000366175.3	-	3	714	c.584G>A	c.(583-585)cGa>cAa	p.R195Q	PSG5_ENST00000407356.1_Missense_Mutation_p.R195Q|PSG5_ENST00000342951.6_Missense_Mutation_p.R195Q|PSG5_ENST00000599812.1_Missense_Mutation_p.R288Q|PSG5_ENST00000404580.1_Missense_Mutation_p.R195Q|PSG5_ENST00000407568.1_Intron			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	195	Ig-like C2-type 1.			R -> Q (in Ref. 1; no nucleotide entry and 5; AAH12607). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.R195Q(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				TTCAATGGGTCGCTTTACCCT	0.493													C|||	1629	0.32528	0.18	0.255	5008	,	,		21769	0.5962		0.1541	False		,,,				2504	0.4683				p.R195Q		Atlas-SNP	.											PSG5,NS,carcinoma,0,1	PSG5	58	1	1	Substitution - Missense(1)	stomach(1)	c.G584A						PASS	.	C	GLN/ARG,GLN/ARG	831,3569	314.7+/-293.7	110,611,1479	100.0	108.0	105.0		584,584	-2.2	0.0	19	dbSNP_123	105	1452,7100	267.6+/-287.4	146,1160,2970	no	missense,missense	PSG5	NM_001130014.1,NM_002781.3	43,43	256,1771,4449	TT,TC,CC		16.9785,18.8864,17.6266	possibly-damaging,possibly-damaging	195/336,195/336	43680147	2283,10669	2200	4276	6476	SO:0001583	missense	5673	exon3			ATGGGTCGCTTTA		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.584G>A	19.37:g.43680147C>T	ENSP00000382334:p.Arg195Gln	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	104	29	0.278846	NM_002781	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	638	0.29212454212454214	111	0.22560975609756098	85	0.23480662983425415	321	0.5611888111888111	121	0.15963060686015831	c	6.800	0.516679	0.12944	0.188864	0.169785	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000342951;ENST00000404580	T;T;T;T	0.01203	5.21;5.21;5.21;5.18	1.08	-2.17	0.07059	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.22414	0.069	B	0.26202	0.067	T	0.26467	-1.0102	8	0.87932	D	0	.	1.9424	0.03349	0.4382:0.2855:0.0:0.2763	rs17856402;rs60589884	195	Q15238	PSG5_HUMAN	Q	195	ENSP00000382334:R195Q;ENSP00000386008:R195Q;ENSP00000344413:R195Q;ENSP00000385250:R195Q	ENSP00000344413:R195Q	R	-	2	0	PSG5	48371987	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.531000	0.23052	-1.812000	0.01227	-1.109000	0.02080	CGA	.	.	weak		0.493	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
ADCK2	90956	hgsc.bcm.edu	37	7	140374482	140374482	+	Silent	SNP	G	G	C	rs142577491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140374482G>C	ENST00000072869.4	+	2	1183	c.1005G>C	c.(1003-1005)ctG>ctC	p.L335L	ADCK2_ENST00000476491.1_Silent_p.L335L	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	335	Protein kinase.					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)					GCCGAGTCCTGGGAGTTTTGC	0.542													C|||	6	0.00119808	0.0038	0.0014	5008	,	,		18388	0.0		0.0	False		,,,				2504	0.0				p.L335L		Atlas-SNP	.											.	ADCK2	37	.	0			c.G1005C						PASS	.	C		15,4391	823.8+/-416.5	0,15,2188	113.0	95.0	101.0		1005	-11.2	0.0	7	dbSNP_134	101	0,8600		0,0,4300	no	coding-synonymous	ADCK2	NM_052853.3		0,15,6488	CC,CG,GG		0.0,0.3404,0.1153		335/627	140374482	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	90956	exon2			AGTCCTGGGAGTT	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.1005G>C	7.37:g.140374482G>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	124	71	0.572581	NM_052853	Q96CN6|Q9Y6T5	Silent	SNP	ENST00000072869.4	37	CCDS5861.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	C	8.385	0.838441	0.16891	0.003404	0.0	ENSG00000133597	ENST00000483369	.	.	.	5.61	-11.2	0.00127	.	.	.	.	.	T	0.57755	0.2075	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71537	-0.4563	4	.	.	.	-48.0441	14.5211	0.67851	0.0:0.1623:0.6463:0.1913	.	.	.	.	R	173	.	.	G	+	1	0	ADCK2	140020951	0.066000	0.20996	0.001000	0.08648	0.874000	0.50279	-0.756000	0.04777	-2.611000	0.00445	-1.093000	0.02169	GGG	G|0.999;C|0.001	0.001	strong		0.542	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853	
KRT84	3890	hgsc.bcm.edu	37	12	52777439	52777439	+	Silent	SNP	A	A	G	rs1614888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52777439A>G	ENST00000257951.3	-	2	756	c.690T>C	c.(688-690)agT>agC	p.S230S	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	230	Coil 1B.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGGCCTGATCACTGACCAGCA	0.557													a|||	1663	0.332069	0.6172	0.3199	5008	,	,		20368	0.1954		0.2058	False		,,,				2504	0.226				p.S230S		Atlas-SNP	.											.	KRT84	61	.	0			c.T690C						PASS	.	G		2467,1939	621.9+/-393.8	717,1033,453	70.0	67.0	68.0		690	-10.6	0.0	12	dbSNP_89	68	1804,6796	324.3+/-316.4	180,1444,2676	no	coding-synonymous	KRT84	NM_033045.3		897,2477,3129	GG,GA,AA		20.9767,44.0082,32.8387		230/601	52777439	4271,8735	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon2			CTGATCACTGACC	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.690T>C	12.37:g.52777439A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.686;G|0.314	0.314	strong		0.557	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
RGPD8	727851	hgsc.bcm.edu	37	2	113147666	113147666	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113147666C>A	ENST00000302558.3	-	20	3047	c.2856G>T	c.(2854-2856)agG>agT	p.R952S	RGPD8_ENST00000409750.1_Missense_Mutation_p.R812S	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	952					protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)			endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						TCTTCCGGCCCCTAATATCCT	0.413																																					p.R952S		Atlas-SNP	.											RGPD8_ENST00000302558,NS,carcinoma,-1,2	RGPD8	81	2	0			c.G2856T						scavenged	.						170.0	130.0	143.0					2																	113147666		688	1572	2260	SO:0001583	missense	727851	exon20			CCGGCCCCTAATA	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"""Tetratricopeptide (TTC) repeat domain containing"""	9849	protein-coding gene	gene with protein product		602752	"""RAN binding protein 2-like 1"""	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.2856G>T	2.37:g.113147666C>A	ENSP00000306637:p.Arg952Ser	Somatic	1391	2	0.00143781		WXS	Illumina HiSeq	Phase_I	1597	126	0.0788979	NM_001164463	Q5CZA8	Missense_Mutation	SNP	ENST00000302558.3	37	CCDS46394.1	.	.	.	.	.	.	.	.	.	.	-	0.001	-3.797847	0.00004	.	.	ENSG00000169629	ENST00000302558;ENST00000409750	T;T	0.36340	1.26;1.26	2.33	2.33	0.28932	.	.	.	.	.	T	0.05410	0.0143	N	0.00067	-2.295	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	9	0.05525	T	0.97	-3.6976	3.1911	0.06618	0.5145:0.2459:0.0:0.2395	.	952	O14715	RGPD8_HUMAN	S	952;812	ENSP00000306637:R952S;ENSP00000386511:R812S	ENSP00000306637:R952S	R	-	3	2	RGPD8	112864137	0.000000	0.05858	0.012000	0.15200	0.011000	0.07611	0.325000	0.19628	0.153000	0.19213	-1.882000	0.00544	AGG	C|0.500;A|0.500	0.500	weak		0.413	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279	
DOCK2	1794	hgsc.bcm.edu	37	5	169504743	169504743	+	Silent	SNP	T	T	C	rs1045168	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:169504743T>C	ENST00000256935.8	+	48	4976	c.4896T>C	c.(4894-4896)cgT>cgC	p.R1632R	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Silent_p.R1124R|DOCK2_ENST00000540750.1_Silent_p.R693R	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1632					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.R1632R(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAGTGGGCCGTCCCAGGTCTA	0.577													C|||	1458	0.291134	0.3782	0.2579	5008	,	,		15757	0.1071		0.334	False		,,,				2504	0.3425				p.R1632R		Atlas-SNP	.											DOCK2,NS,carcinoma,0,3	DOCK2	389	3	1	Substitution - coding silent(1)	stomach(1)	c.T4896C						PASS	.	C		1660,2746	658.5+/-400.4	303,1054,846	132.0	119.0	124.0		4896	-5.4	0.9	5	dbSNP_86	124	2650,5950	685.7+/-404.1	414,1822,2064	no	coding-synonymous	DOCK2	NM_004946.2		717,2876,2910	CC,CT,TT		30.814,37.6759,33.1386		1632/1831	169504743	4310,8696	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon48			GGGCCGTCCCAGG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4896T>C	5.37:g.169504743T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			A|0.000;C|0.311;T|0.689	0.311	strong		0.577	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
ZNF488	118738	hgsc.bcm.edu	37	10	48370595	48370595	+	Silent	SNP	G	G	A	rs11204210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	73	0	0		WXS	Illumina HiSeq	Phase_I	87	29	0.333333	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	
SVEP1	79987	hgsc.bcm.edu	37	9	113208250	113208250	+	Missense_Mutation	SNP	T	T	G	rs7863519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113208250T>G	ENST00000401783.2	-	26	4666	c.4330A>C	c.(4330-4332)Atg>Ctg	p.M1444L	SVEP1_ENST00000374469.1_Missense_Mutation_p.M1421L|SVEP1_ENST00000302728.8_Missense_Mutation_p.M1444L|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1444	Pentaxin.		M -> L (in dbSNP:rs7863519).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.M1444L(2)		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						GATGGGAGCATGCCATCTAGC	0.438													C|||	1701	0.339657	0.4569	0.2205	5008	,	,		20843	0.4504		0.1918	False		,,,				2504	0.3037				p.M1444L		Atlas-SNP	.											SVEP1,NS,carcinoma,0,2	SVEP1	326	2	2	Substitution - Missense(2)	prostate(2)	c.A4330C						PASS	.	C	LEU/MET	1478,2424		275,928,748	119.0	114.0	116.0		4330	3.6	0.0	9	dbSNP_116	116	1600,6712		164,1272,2720	yes	missense	SVEP1	NM_153366.3	15	439,2200,3468	GG,GT,TT		19.2493,37.878,25.2006	benign	1444/3572	113208250	3078,9136	1951	4156	6107	SO:0001583	missense	79987	exon26			GGAGCATGCCATC	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.4330A>C	9.37:g.113208250T>G	ENSP00000384917:p.Met1444Leu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	153	46	0.300654	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	699	0.32005494505494503	228	0.4634146341463415	80	0.22099447513812154	241	0.42132867132867136	150	0.19788918205804748	C	0.025	-1.378392	0.01204	0.37878	0.192493	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	T;T;T	0.71817	3.35;3.35;-0.6	5.5	3.62	0.41486	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.301359	0.35466	N	0.003189	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.08055	0.0;0.003	T	0.41197	-0.9522	9	0.10377	T	0.69	.	8.2245	0.31560	0.0:0.6915:0.1135:0.195	rs7863519;rs52830057;rs60340468;rs7863519	1444;1444	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	L	1444;1421;1444	ENSP00000384917:M1444L;ENSP00000363593:M1421L;ENSP00000304118:M1444L	ENSP00000304118:M1444L	M	-	1	0	SVEP1	112248071	0.004000	0.15560	0.023000	0.16930	0.138000	0.21146	0.095000	0.15127	0.361000	0.24292	-0.119000	0.15052	ATG	T|0.684;G|0.316	0.316	strong		0.438	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ZBTB40	9923	hgsc.bcm.edu	37	1	22835677	22835677	+	Missense_Mutation	SNP	A	A	G	rs209729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:22835677A>G	ENST00000375647.4	+	9	1991	c.1784A>G	c.(1783-1785)tAc>tGc	p.Y595C	ZBTB40_ENST00000404138.1_Missense_Mutation_p.Y595C|ZBTB40_ENST00000374651.4_Missense_Mutation_p.Y483C	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	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	172	171	0.994186	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	
CDC14A	8556	hgsc.bcm.edu	37	1	100949860	100949860	+	Silent	SNP	G	G	A	rs2270694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100949860G>A	ENST00000336454.3	+	11	1345	c.990G>A	c.(988-990)tcG>tcA	p.S330S	RP5-837M10.4_ENST00000432210.1_RNA|CDC14A_ENST00000370124.3_Silent_p.S330S|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000544534.1_Silent_p.S330S|CDC14A_ENST00000542213.1_Silent_p.S272S|CDC14A_ENST00000361544.6_Silent_p.S330S	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	330	B.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		AACAAGCATCGTTGTGGGTCC	0.328													G|||	442	0.0882588	0.059	0.0965	5008	,	,		17962	0.0625		0.1441	False		,,,				2504	0.091				p.S330S		Atlas-SNP	.											.	CDC14A	65	.	0			c.G990A						PASS	.	G	,,	257,4145	131.4+/-167.9	6,245,1950	39.0	36.0	37.0		990,990,990	-6.6	0.1	1	dbSNP_100	37	1144,7452	220.1+/-257.9	79,986,3233	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	85,1231,5183	AA,AG,GG		13.3085,5.8383,10.7786	,,	330/595,330/624,330/384	100949860	1401,11597	2201	4298	6499	SO:0001819	synonymous_variant	8556	exon11			AGCATCGTTGTGG	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1718	protein-coding gene	gene with protein product		603504	"""CDC10 (cell division cycle 10, S. cerevisiae, homolog)"", ""CDC14 cell division cycle 14 homolog A (S. cerevisiae)"""			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.990G>A	1.37:g.100949860G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			G|0.905;A|0.095	0.095	strong		0.328	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	
DRICH1	51233	hgsc.bcm.edu	37	22	23974200	23974200	+	Missense_Mutation	SNP	A	A	G	rs3827318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	195	0	0		WXS	Illumina HiSeq	Phase_I	209	95	0.454545	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		
C15orf43	145645	hgsc.bcm.edu	37	15	45250685	45250685	+	Missense_Mutation	SNP	T	T	G	rs147135555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45250685T>G	ENST00000340827.3	+	3	278	c.261T>G	c.(259-261)atT>atG	p.I87M		NM_152448.2	NP_689661.1	Q8NHR7	CO043_HUMAN	chromosome 15 open reading frame 43	87										NS(1)|breast(2)|large_intestine(1)|lung(2)|skin(2)	8		all_cancers(109;3.68e-08)|all_epithelial(112;1.05e-06)|Lung NSC(122;1.42e-05)|all_lung(180;0.000112)|Melanoma(134;0.0192)		all cancers(107;7.64e-17)|GBM - Glioblastoma multiforme(94;2.03e-06)		GTCATTTCATTCTTCCTCCTG	0.408													T|||	18	0.00359425	0.0136	0.0	5008	,	,		18466	0.0		0.0	False		,,,				2504	0.0				p.I87M		Atlas-SNP	.											.	C15orf43	19	.	0			c.T261G						PASS	.	T	MET/ILE	52,4344	52.3+/-87.9	1,50,2147	79.0	74.0	75.0		261	-2.2	1.0	15	dbSNP_134	75	0,8596		0,0,4298	yes	missense	C15orf43	NM_152448.1	10	1,50,6445	GG,GT,TT		0.0,1.1829,0.4002	benign	87/221	45250685	52,12940	2198	4298	6496	SO:0001583	missense	145645	exon3			TTTCATTCTTCCT	BC029537	CCDS10115.1	15q21.1	2006-02-03			ENSG00000167014	ENSG00000167014			28520	protein-coding gene	gene with protein product							Standard	NM_152448		Approved	MGC33951	uc001zuk.4	Q8NHR7	OTTHUMG00000131264	ENST00000340827.3:c.261T>G	15.37:g.45250685T>G	ENSP00000340644:p.Ile87Met	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	NM_152448		Missense_Mutation	SNP	ENST00000340827.3	37	CCDS10115.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	t	12.26	1.883358	0.33255	0.011829	0.0	ENSG00000167014	ENST00000340827	T	0.55234	0.53	4.45	-2.18	0.07037	.	0.349419	0.23496	N	0.047553	T	0.21881	0.0527	N	0.19112	0.55	0.22185	N	0.999309	B	0.15141	0.012	B	0.13407	0.009	T	0.08513	-1.0718	10	0.52906	T	0.07	.	5.0719	0.14611	0.0:0.4003:0.1728:0.4268	.	87	Q8NHR7	CO043_HUMAN	M	87	ENSP00000340644:I87M	ENSP00000340644:I87M	I	+	3	3	C15orf43	43037977	0.971000	0.33674	0.971000	0.41717	0.977000	0.68977	0.016000	0.13377	-0.254000	0.09500	0.523000	0.50628	ATT	T|0.997;G|0.003	0.003	strong		0.408	C15orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254032.1	NM_152448	
SIDT1	54847	hgsc.bcm.edu	37	3	113286405	113286405	+	Silent	SNP	C	C	T	rs2292511	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	112	0	0		WXS	Illumina HiSeq	Phase_I	131	77	0.587786	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	
DUPD1	338599	hgsc.bcm.edu	37	10	76797660	76797660	+	Silent	SNP	C	C	T	rs1868624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76797660C>T	ENST00000338487.5	-	3	596	c.597G>A	c.(595-597)caG>caA	p.Q199Q		NM_001003892.1	NP_001003892.1	Q68J44	DUPD1_HUMAN	dual specificity phosphatase and pro isomerase domain containing 1	199	Tyrosine-protein phosphatase.				protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(2)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					GCTGCACCAGCTGCTTGTCCA	0.657													C|||	34	0.00678914	0.0227	0.0058	5008	,	,		21195	0.0		0.0	False		,,,				2504	0.0				p.Q199Q		Atlas-SNP	.											.	DUPD1	30	.	0			c.G597A						PASS	.	C		89,4317	74.1+/-112.3	0,89,2114	60.0	60.0	60.0		597	4.1	1.0	10	dbSNP_92	60	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	DUPD1	NM_001003892.1		0,91,6412	TT,TC,CC		0.0233,2.02,0.6997		199/221	76797660	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	338599	exon3			CACCAGCTGCTTG		CCDS31223.1	10q22.3	2011-06-09			ENSG00000188716	ENSG00000188716		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	23481	protein-coding gene	gene with protein product							Standard	NM_001003892		Approved	DUSP27	uc001jwq.1	Q68J44	OTTHUMG00000018512	ENST00000338487.5:c.597G>A	10.37:g.76797660C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_001003892	B2RP93	Silent	SNP	ENST00000338487.5	37	CCDS31223.1																																																																																			C|0.959;T|0.041	0.041	strong		0.657	DUPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048777.2	XM_291741	
AMPD3	272	hgsc.bcm.edu	37	11	10526179	10526179	+	Silent	SNP	C	C	T	rs375685508		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:10526179C>T	ENST00000396554.3	+	14	2468	c.2127C>T	c.(2125-2127)agC>agT	p.S709S	AMPD3_ENST00000530864.1_3'UTR|AMPD3_ENST00000444303.2_Silent_p.S541S	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	700					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		CCAGGAACAGCGTGCTGCAGA	0.587																																					p.S709S		Atlas-SNP	.											.	AMPD3	68	.	0			c.C2127T						PASS	.	C	,,,,	0,4402		0,0,2201	177.0	141.0	154.0		2127,2100,2121,2100,1623	-9.7	0.5	11		154	1,8587	1.2+/-3.3	0,1,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMPD3	NM_000480.2,NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1	,,,,	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	,,,,	709/777,700/768,707/775,700/768,541/609	10526179	1,12989	2201	4294	6495	SO:0001819	synonymous_variant	272	exon14			GAACAGCGTGCTG	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.2127C>T	11.37:g.10526179C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	120	43	0.358333	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	37	CCDS7802.1																																																																																			.	.	weak		0.587	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
POLQ	10721	hgsc.bcm.edu	37	3	121207083	121207083	+	Missense_Mutation	SNP	C	C	A	rs3218639	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121207083C>A	ENST00000264233.5	-	16	4823	c.4695G>T	c.(4693-4695)caG>caT	p.Q1565H		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1565					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)		CTTCAACCATCTGAACAGAAT	0.338								DNA polymerases (catalytic subunits)					C|||	23	0.00459265	0.0159	0.0029	5008	,	,		20878	0.0		0.0	False		,,,				2504	0.0				p.Q1565H	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G4695T						PASS	.	C	HIS/GLN	75,4331	65.8+/-103.3	1,73,2129	73.0	72.0	73.0		4695	5.3	1.0	3	dbSNP_106	73	0,8600		0,0,4300	yes	missense	POLQ	NM_199420.3	24	1,73,6429	AA,AC,CC		0.0,1.7022,0.5767	probably-damaging	1565/2591	121207083	75,12931	2203	4300	6503	SO:0001583	missense	10721	exon16			AACCATCTGAACA	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.4695G>T	3.37:g.121207083C>A	ENSP00000264233:p.Gln1565His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	14.28	2.488609	0.44249	0.017022	0.0	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.57436	0.4	6.17	5.3	0.74995	.	0.354292	0.29205	N	0.012838	T	0.41880	0.1178	L	0.36672	1.1	0.26824	N	0.968735	D;P	0.71674	0.998;0.865	D;B	0.66084	0.941;0.391	T	0.46190	-0.9209	10	0.48119	T	0.1	.	8.7602	0.34669	0.0:0.6832:0.1822:0.1345	rs3218639;rs52804917;rs3218639	1565;737	O75417;O75417-2	DPOLQ_HUMAN;.	H	1188;1565;1701	ENSP00000264233:Q1565H	ENSP00000264233:Q1565H	Q	-	3	2	POLQ	122689773	1.000000	0.71417	1.000000	0.80357	0.578000	0.36192	1.322000	0.33689	1.632000	0.50472	-0.140000	0.14226	CAG	C|0.993;A|0.007	0.007	strong		0.338	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
SERPINA10	51156	hgsc.bcm.edu	37	14	94754804	94754804	+	Missense_Mutation	SNP	C	C	T	rs2232708	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94754804C>T	ENST00000393096.1	-	3	1276	c.811G>A	c.(811-813)Ggt>Agt	p.G271S	SERPINA10_ENST00000261994.4_Missense_Mutation_p.G271S|SERPINA10_ENST00000554173.1_Missense_Mutation_p.G271S|SERPINA10_ENST00000554723.1_Missense_Mutation_p.G311S	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	271			G -> S (in dbSNP:rs2232708). {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)		TTGCCTGCACCGTACATCATG	0.493													C|||	166	0.033147	0.1044	0.0144	5008	,	,		22206	0.0		0.006	False		,,,				2504	0.0123				p.G271S		Atlas-SNP	.											.	SERPINA10	83	.	0			c.G811A						PASS	.	C	SER/GLY,SER/GLY	381,4025	193.6+/-218.7	22,337,1844	127.0	111.0	117.0		811,811	-2.3	0.0	14	dbSNP_98	117	70,8530	42.6+/-100.3	0,70,4230	yes	missense,missense	SERPINA10	NM_001100607.1,NM_016186.2	56,56	22,407,6074	TT,TC,CC		0.814,8.6473,3.4676	benign,benign	271/445,271/445	94754804	451,12555	2203	4300	6503	SO:0001583	missense	51156	exon3			CTGCACCGTACAT	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.811G>A	14.37:g.94754804C>T	ENSP00000376809:p.Gly271Ser	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	143	66	0.461538	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Missense_Mutation	SNP	ENST00000393096.1	37	CCDS9923.1	64	0.029304029304029304	56	0.11382113821138211	5	0.013812154696132596	0	0.0	3	0.00395778364116095	C	7.239	0.600804	0.13939	0.086473	0.00814	ENSG00000140093	ENST00000554723;ENST00000393096;ENST00000261994;ENST00000554173	D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76	5.37	-2.29	0.06805	Serpin domain (3);	0.905436	0.09297	N	0.821441	T	0.02119	0.0066	N	0.03608	-0.345	0.09310	N	1	B	0.24618	0.107	B	0.14578	0.011	T	0.05305	-1.0893	10	0.54805	T	0.06	.	7.1697	0.25712	0.0:0.1453:0.4539:0.4008	rs2232708;rs52801294;rs60234914;rs2232708	271	Q9UK55	ZPI_HUMAN	S	311;271;271;271	ENSP00000450896:G311S;ENSP00000376809:G271S;ENSP00000261994:G271S;ENSP00000450971:G271S	ENSP00000261994:G271S	G	-	1	0	SERPINA10	93824557	0.254000	0.23992	0.002000	0.10522	0.080000	0.17528	0.415000	0.21181	-0.291000	0.09012	0.313000	0.20887	GGT	C|0.961;T|0.039	0.039	strong		0.493	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186	
STPG2	285555	hgsc.bcm.edu	37	4	99049593	99049593	+	Missense_Mutation	SNP	A	A	G	rs17558193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:99049593A>G	ENST00000295268.3	-	3	462	c.373T>C	c.(373-375)Tac>Cac	p.Y125H		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	125			Y -> H (in dbSNP:rs17558193).														TGAGGTTTGTAGTATGCTGGA	0.318													A|||	1879	0.3752	0.4425	0.2882	5008	,	,		16898	0.2748		0.4026	False		,,,				2504	0.4213				p.Y125H		Atlas-SNP	.											.	.	.	.	0			c.T373C						PASS	.	A	HIS/TYR	1973,2433	553.7+/-378.8	454,1065,684	65.0	62.0	63.0		373	5.2	0.7	4	dbSNP_123	63	3409,5189	501.0+/-375.3	694,2021,1584	yes	missense	C4orf37	NM_174952.2	83	1148,3086,2268	GG,GA,AA		39.6488,44.7798,41.3873	probably-damaging	125/460	99049593	5382,7622	2203	4299	6502	SO:0001583	missense	285555	exon3			GTTTGTAGTATGC	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.373T>C	4.37:g.99049593A>G	ENSP00000295268:p.Tyr125His	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	194	92	0.474227	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	759	0.3475274725274725	192	0.3902439024390244	106	0.292817679558011	161	0.28146853146853146	300	0.39577836411609496	A	17.14	3.312649	0.60414	0.447798	0.396488	ENSG00000163116	ENST00000295268	T	0.28666	1.6	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66939	2.045	0.28965	P	0.8896	D	0.89917	1.0	D	0.91635	0.999	T	0.47824	-0.9087	9	0.87932	D	0	-19.6536	12.8257	0.57718	1.0:0.0:0.0:0.0	rs17558193;rs52818476;rs17558193	125	Q8N412	CD037_HUMAN	H	125	ENSP00000295268:Y125H	ENSP00000295268:Y125H	Y	-	1	0	C4orf37	99268616	1.000000	0.71417	0.696000	0.30242	0.819000	0.46315	4.980000	0.63812	2.064000	0.61679	0.533000	0.62120	TAC	A|0.611;G|0.389	0.389	strong		0.318	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
HAS1	3036	hgsc.bcm.edu	37	19	52222552	52222552	+	Silent	SNP	G	G	A	rs11084112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52222552G>A	ENST00000222115.1	-	2	643	c.609C>T	c.(607-609)cgC>cgT	p.R203R	HAS1_ENST00000540069.2_Silent_p.R202R|HAS1_ENST00000594621.1_Silent_p.R57R|HAS1_ENST00000601714.1_Silent_p.R210R	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	203					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)	p.R203R(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		ACACGCACCTGCGAGTCCTCA	0.706													g|||	1797	0.358826	0.4206	0.4251	5008	,	,		14038	0.2113		0.334	False		,,,				2504	0.4059				p.R203R	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											HAS1,NS,lymphoid_neoplasm,0,1	HAS1	61	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C609T						PASS	.	G		1890,2514		429,1032,741	29.0	27.0	28.0		609	1.3	0.9	19	dbSNP_120	28	2798,5784		448,1902,1941	no	coding-synonymous	HAS1	NM_001523.2		877,2934,2682	AA,AG,GG		32.6031,42.9155,36.1004		203/579	52222552	4688,8298	2202	4291	6493	SO:0001819	synonymous_variant	3036	exon2			GCACCTGCGAGTC	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.609C>T	19.37:g.52222552G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_001523	Q14470|Q9NS49	Silent	SNP	ENST00000222115.1	37	CCDS12838.1																																																																																			G|0.658;A|0.342	0.342	strong		0.706	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
ZNF638	27332	hgsc.bcm.edu	37	2	71631109	71631109	+	Missense_Mutation	SNP	A	A	G	rs3732235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71631109A>G	ENST00000409544.1	+	17	3569	c.2939A>G	c.(2938-2940)aAc>aGc	p.N980S	ZNF638_ENST00000264447.4_Missense_Mutation_p.N980S|ZNF638_ENST00000355812.3_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	138	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	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	
PIEZO1	9780	hgsc.bcm.edu	37	16	88780603	88780603	+	IGR	SNP	C	C	G	rs73262673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88780603C>G	ENST00000301015.9	-	0	8072				CTU2_ENST00000378384.3_Silent_p.T268T|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000453996.2_Silent_p.T355T|CTU2_ENST00000312060.5_Silent_p.T355T|CTU2_ENST00000567949.1_Silent_p.T426T	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						GGCTGCAGACCCAGTTCCCCT	0.632													C|||	245	0.0489217	0.177	0.0159	5008	,	,		16241	0.0		0.0	False		,,,				2504	0.0				p.T355T		Atlas-SNP	.											.	CTU2	66	.	0			c.C1065G						PASS	.	C	,	604,3774	262.8+/-265.1	38,528,1623	84.0	76.0	79.0		1065,1065	0.1	1.0	16	dbSNP_130	79	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous,coding-synonymous	CTU2	NM_001012759.1,NM_001012762.1	,	38,533,5914	GG,GC,CC		0.0582,13.7963,4.6955	,	355/516,355/486	88780603	609,12361	2189	4296	6485	SO:0001628	intergenic_variant	348180	exon10			GCAGACCCAGTTC	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.88780603C>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1																																																																																			C|0.960;G|0.040	0.040	strong		0.632	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
TPRX1	284355	hgsc.bcm.edu	37	19	48305626	48305626	+	Silent	SNP	T	T	C	rs62130757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48305626T>C	ENST00000322175.3	-	2	797	c.642A>G	c.(640-642)ccA>ccG	p.P214P	TPRX1_ENST00000535759.1_Silent_p.P311P|TPRX1_ENST00000543508.1_Silent_p.P204P	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	87	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	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	
TNS1	7145	hgsc.bcm.edu	37	2	218683154	218683154	+	Missense_Mutation	SNP	A	A	G	rs2571445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218683154A>G	ENST00000171887.4	-	24	4041	c.3589T>C	c.(3589-3591)Tgg>Cgg	p.W1197R	TNS1_ENST00000419504.1_Missense_Mutation_p.W1184R|TNS1_ENST00000430930.1_Missense_Mutation_p.W1176R	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1197			W -> R (in dbSNP:rs2571445). {ECO:0000269|PubMed:11023826, ECO:0000269|PubMed:18088087, ECO:0000269|PubMed:18220336, ECO:0000269|PubMed:18669648, ECO:0000269|PubMed:20068231}.		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)		ATGGCCCGCCAGCCGAAGCCA	0.632													G|||	3300	0.658946	0.8351	0.6167	5008	,	,		16545	0.621		0.5905	False		,,,				2504	0.5603				p.W1197R		Atlas-SNP	.											.	TNS1	251	.	0			c.T3589C						PASS	.	G	ARG/TRP	3530,876	334.1+/-303.3	1408,714,81	53.0	58.0	56.0	http://www.ncbi.nlm.nih.gov/pubmed?term	3589	3.7	0.9	2	dbSNP_100	56	5284,3316	484.0+/-371.3	1631,2022,647	yes	missense	TNS1	NM_022648.4	101	3039,2736,728	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	38.5581,19.882,32.2313	benign	1197/1736	218683154	8814,4192	2203	4300	6503	SO:0001583	missense	7145	exon24			CCCGCCAGCCGAA	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.3589T>C	2.37:g.218683154A>G	ENSP00000171887:p.Trp1197Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	1443	0.6607142857142857	401	0.8150406504065041	230	0.6353591160220995	354	0.6188811188811189	458	0.604221635883905	G	0.067	-1.210360	0.01555	0.80118	0.614419	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;T;D;D	0.89746	-2.55;2.52;-2.55;-2.56	4.61	3.71	0.42584	.	0.371203	0.23941	N	0.043060	T	0.00012	0.0000	N	0.00583	-1.355	0.09310	P	0.9999999999999779	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42447	-0.9451	9	0.07482	T	0.82	.	7.287	0.26344	0.0778:0.0:0.6235:0.2986	rs2571445;rs17732777;rs60680731;rs2571445	1197;1176;1184	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	R	1197;335;1184;1176	ENSP00000171887:W1197R;ENSP00000394171:W335R;ENSP00000408724:W1184R;ENSP00000406016:W1176R	ENSP00000171887:W1197R	W	-	1	0	TNS1	218391399	0.963000	0.33076	0.928000	0.36995	0.702000	0.40608	1.368000	0.34216	0.552000	0.29026	-0.213000	0.12676	TGG	A|0.321;G|0.679	0.679	strong		0.632	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
ZFPM2	23414	hgsc.bcm.edu	37	8	106815286	106815286	+	Silent	SNP	T	T	C	rs1442320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:106815286T>C	ENST00000407775.2	+	8	3226	c.2976T>C	c.(2974-2976)taT>taC	p.Y992Y	RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000378472.4_Silent_p.Y723Y|ZFPM2_ENST00000520492.1_Silent_p.Y860Y|ZFPM2_ENST00000517361.1_Silent_p.Y860Y|RP11-152P17.2_ENST00000509144.2_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	992					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			CAAGTGATTATATTTCTGGTT	0.423													T|||	333	0.0664936	0.1725	0.0403	5008	,	,		19586	0.0069		0.0268	False		,,,				2504	0.044				p.Y992Y		Atlas-SNP	.											.	ZFPM2	219	.	0			c.T2976C						PASS	.	T		498,3248		33,432,1408	48.0	45.0	46.0		2976	-7.7	0.7	8	dbSNP_88	46	189,8027		2,185,3921	no	coding-synonymous	ZFPM2	NM_012082.3		35,617,5329	CC,CT,TT		2.3004,13.2942,5.7432		992/1152	106815286	687,11275	1873	4108	5981	SO:0001819	synonymous_variant	23414	exon8			TGATTATATTTCT	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.2976T>C	8.37:g.106815286T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Silent	SNP	ENST00000407775.2	37	CCDS47908.1																																																																																			T|0.939;C|0.061	0.061	strong		0.423	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
PGR	5241	hgsc.bcm.edu	37	11	100909991	100909991	+	Silent	SNP	T	T	C	rs500760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:100909991T>C	ENST00000325455.5	-	8	4111	c.2658A>G	c.(2656-2658)caA>caG	p.Q886Q	PGR_ENST00000534013.1_Silent_p.Q292Q|PGR_ENST00000263463.5_Silent_p.Q784Q	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	886	Steroid-binding.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	ACAGATGAAGTTGTTTGACAA	0.323													T|||	1310	0.261581	0.413	0.2651	5008	,	,		14650	0.2133		0.2525	False		,,,				2504	0.1135				p.Q886Q	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.A2658G						PASS	.	T	,	1679,2727	506.9+/-366.5	327,1025,851	85.0	82.0	83.0		2658,2166	-3.0	1.0	11	dbSNP_83	83	2102,6496	361.3+/-332.3	264,1574,2461	no	coding-synonymous,coding-synonymous	PGR	NM_000926.4,NM_001202474.1	,	591,2599,3312	CC,CT,TT		24.4475,38.1071,29.0757	,	886/934,722/770	100909991	3781,9223	2203	4299	6502	SO:0001819	synonymous_variant	5241	exon8			ATGAAGTTGTTTG	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.2658A>G	11.37:g.100909991T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Silent	SNP	ENST00000325455.5	37	CCDS8310.1																																																																																			T|0.704;C|0.296	0.296	strong		0.323	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
FREM2	341640	hgsc.bcm.edu	37	13	39263646	39263646	+	Missense_Mutation	SNP	G	G	A	rs58363253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39263646G>A	ENST00000280481.7	+	1	2381	c.2165G>A	c.(2164-2166)aGg>aAg	p.R722K		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	722			R -> K (in dbSNP:rs58363253).		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)		ACACCACTGAGGAAGAAGTGG	0.552													G|||	315	0.0628994	0.208	0.0231	5008	,	,		19051	0.001		0.0089	False		,,,				2504	0.0143				p.R722K		Atlas-SNP	.											.	FREM2	385	.	0			c.G2165A						PASS	.	G	LYS/ARG	745,3661	305.5+/-289.0	68,609,1526	67.0	64.0	65.0		2165	5.1	1.0	13	dbSNP_129	65	88,8512	49.8+/-109.6	1,86,4213	yes	missense	FREM2	NM_207361.4	26	69,695,5739	AA,AG,GG		1.0233,16.9088,6.4047	benign	722/3170	39263646	833,12173	2203	4300	6503	SO:0001583	missense	341640	exon1			CACTGAGGAAGAA	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.2165G>A	13.37:g.39263646G>A	ENSP00000280481:p.Arg722Lys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	96	0.04395604395604396	82	0.16666666666666666	9	0.024861878453038673	0	0.0	5	0.006596306068601583	G	11.87	1.768801	0.31320	0.169088	0.010233	ENSG00000150893	ENST00000280481	T	0.28255	1.62	5.97	5.13	0.70059	.	0.088825	0.64402	N	0.000001	T	0.00073	0.0002	L	0.49513	1.565	0.18873	P	0.9999848891	B	0.02656	0.0	B	0.06405	0.002	T	0.12708	-1.0537	9	0.17832	T	0.49	.	14.9829	0.71324	0.0679:0.0:0.932:0.0	rs58363253;rs61734231	722	Q5SZK8	FREM2_HUMAN	K	722	ENSP00000280481:R722K	ENSP00000280481:R722K	R	+	2	0	FREM2	38161646	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.884000	0.48562	1.541000	0.49316	0.655000	0.94253	AGG	G|0.949;A|0.051	0.051	strong		0.552	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
TMEM106B	54664	hgsc.bcm.edu	37	7	12269417	12269417	+	Missense_Mutation	SNP	C	C	G	rs3173615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12269417C>G	ENST00000396667.3	+	6	876	c.554C>G	c.(553-555)aCc>aGc	p.T185S	TMEM106B_ENST00000396668.3_Missense_Mutation_p.T185S	NM_018374.3	NP_060844.2	Q9NUM4	T106B_HUMAN	transmembrane protein 106B	185			T -> S (in dbSNP:rs3173615). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:23742080}.		cell death (GO:0008219)|dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(8)|large_intestine(2)|lung(7)	18				UCEC - Uterine corpus endometrioid carcinoma (126;0.185)		AACAACATAACCATTATTGGT	0.308													C|||	2980	0.595048	0.6808	0.5692	5008	,	,		18287	0.6508		0.4016	False		,,,				2504	0.6391				p.T185S		Atlas-SNP	.											TMEM106B,NS,adenoma,0,1	TMEM106B	34	1	0			c.C554G						PASS	.	C	SER/THR,SER/THR	2897,1509	673.6+/-402.8	965,967,271	69.0	70.0	69.0		554,554	5.4	1.0	7	dbSNP_105	69	3587,5009	516.1+/-378.7	780,2027,1491	yes	missense,missense	TMEM106B	NM_001134232.1,NM_018374.3	58,58	1745,2994,1762	GG,GC,CC		41.7287,34.2488,49.8693	possibly-damaging,possibly-damaging	185/275,185/275	12269417	6484,6518	2203	4298	6501	SO:0001583	missense	54664	exon5			ACATAACCATTAT	BC033901	CCDS5358.1	7p21.3	2012-06-06			ENSG00000106460	ENSG00000106460			22407	protein-coding gene	gene with protein product		613413				20154673, 22511793	Standard	NM_018374		Approved	MGC33727, FLJ11273	uc003ssh.3	Q9NUM4	OTTHUMG00000125537	ENST00000396667.3:c.554C>G	7.37:g.12269417C>G	ENSP00000379901:p.Thr185Ser	Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	271	271	1	NM_001134232	A4D108|Q53FL9|Q8N4L0	Missense_Mutation	SNP	ENST00000396667.3	37	CCDS5358.1	1198	0.5485347985347986	324	0.6585365853658537	184	0.5082872928176796	384	0.6713286713286714	306	0.40369393139841686	C	14.51	2.557596	0.45590	0.657512	0.417287	ENSG00000106460	ENST00000396668;ENST00000396667	T;T	0.22539	1.95;1.95	5.36	5.36	0.76844	.	0.048857	0.85682	D	0.000000	T	0.00012	0.0000	L	0.50333	1.59	0.22330	P	0.99919789	B	0.20261	0.043	B	0.17098	0.017	T	0.38178	-0.9673	9	0.54805	T	0.06	-15.6842	12.7762	0.57451	0.0:0.9247:0.0:0.0753	rs3173615;rs10348977;rs11546466;rs17149904;rs17853942;rs52789343;rs59821228;rs3173615	185	Q9NUM4	T106B_HUMAN	S	185	ENSP00000379902:T185S;ENSP00000379901:T185S	ENSP00000379901:T185S	T	+	2	0	TMEM106B	12235942	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	5.898000	0.69838	2.689000	0.91719	0.655000	0.94253	ACC	C|0.481;G|0.519	0.519	strong		0.308	TMEM106B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246870.3	NM_018374	
APLF	200558	hgsc.bcm.edu	37	2	68729992	68729992	+	Missense_Mutation	SNP	A	A	G	rs11902811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	139	0	0		WXS	Illumina HiSeq	Phase_I	142	69	0.485915	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	
ZNF205	7755	hgsc.bcm.edu	37	16	3169321	3169321	+	Silent	SNP	C	C	T	rs59049520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3169321C>T	ENST00000382192.3	+	7	865	c.660C>T	c.(658-660)ccC>ccT	p.P220P	RP11-473M20.14_ENST00000575139.1_RNA|ZNF205_ENST00000219091.4_Silent_p.P220P|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	220					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						ATGTGAAGCCCTTCAGAACCA	0.657													C|||	281	0.0561102	0.2065	0.0101	5008	,	,		15886	0.0		0.001	False		,,,				2504	0.0				p.P220P		Atlas-SNP	.											.	ZNF205	42	.	0			c.C660T						PASS	.	C	,	701,3651		60,581,1535	41.0	37.0	38.0		660,660	1.8	0.2	16	dbSNP_129	38	8,8474		0,8,4233	no	coding-synonymous,coding-synonymous	ZNF205	NM_001042428.1,NM_003456.2	,	60,589,5768	TT,TC,CC		0.0943,16.1075,5.5244	,	220/555,220/555	3169321	709,12125	2176	4241	6417	SO:0001819	synonymous_variant	7755	exon7			GAAGCCCTTCAGA	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.660C>T	16.37:g.3169321C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	83	52	0.626506	NM_003456	A8MZK0|D3DUB4|Q9BU95	Silent	SNP	ENST00000382192.3	37	CCDS10494.2																																																																																			C|0.944;T|0.056	0.056	strong		0.657	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456	
EMC1	23065	hgsc.bcm.edu	37	1	19565338	19565338	+	Missense_Mutation	SNP	C	C	T	rs709682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19565338C>T	ENST00000477853.1	-	10	1082	c.1040G>A	c.(1039-1041)aGt>aAt	p.S347N	RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375208.3_Missense_Mutation_p.S325N|EMC1_ENST00000375199.3_Missense_Mutation_p.S346N	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						scavenged	.	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	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	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	
ATP9A	10079	hgsc.bcm.edu	37	20	50310559	50310559	+	Silent	SNP	G	G	A	rs2031344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50310559G>A	ENST00000338821.5	-	7	894	c.630C>T	c.(628-630)ctC>ctT	p.L210L	ATP9A_ENST00000402822.1_Intron|ATP9A_ENST00000311637.5_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	210					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						CGGCCGTGGGGAGCCTCTGCG	0.627													G|||	70	0.0139776	0.0499	0.0043	5008	,	,		14542	0.0		0.001	False		,,,				2504	0.0				p.L210L		Atlas-SNP	.											.	ATP9A	135	.	0			c.C630T						PASS	.	G		171,4235	96.7+/-135.4	3,165,2035	42.0	45.0	44.0		630	-3.0	1.0	20	dbSNP_94	44	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATP9A	NM_006045.1		3,166,6334	AA,AG,GG		0.0116,3.8811,1.3225		210/1048	50310559	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	10079	exon7			CGTGGGGAGCCTC	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.630C>T	20.37:g.50310559G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	188	82	0.43617	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	37	CCDS33489.1																																																																																			G|0.985;A|0.015	0.015	strong		0.627	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
CENPE	1062	hgsc.bcm.edu	37	4	104080217	104080217	+	Missense_Mutation	SNP	A	A	C	rs75568479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:104080217A>C	ENST00000265148.3	-	22	2640	c.2551T>G	c.(2551-2553)Tct>Gct	p.S851A	CENPE_ENST00000380026.3_Missense_Mutation_p.S826A	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	851					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		GCTTCTTTAGAGAGATTAACT	0.373													A|||	53	0.0105831	0.0318	0.0101	5008	,	,		17002	0.0		0.001	False		,,,				2504	0.0031				p.S851A		Atlas-SNP	.											.	CENPE	253	.	0			c.T2551G						PASS	.	A	ALA/SER	160,4246	105.6+/-144.1	4,152,2047	77.0	74.0	75.0		2551	4.9	0.1	4	dbSNP_131	75	15,8585	9.8+/-36.6	0,15,4285	yes	missense	CENPE	NM_001813.2	99	4,167,6332	CC,CA,AA		0.1744,3.6314,1.3455	probably-damaging	851/2702	104080217	175,12831	2203	4300	6503	SO:0001583	missense	1062	exon22			CTTTAGAGAGATT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.2551T>G	4.37:g.104080217A>C	ENSP00000265148:p.Ser851Ala	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	204	107	0.52451	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	24	0.01098901098901099	20	0.04065040650406504	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	11.57	1.679425	0.29783	0.036314	0.001744	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	T;T;T	0.81163	-1.46;-1.46;-1.46	4.94	4.94	0.65067	.	.	.	.	.	T	0.51024	0.1650	M	0.62723	1.935	0.18873	N	0.999984	P;P	0.48089	0.732;0.905	B;B	0.41988	0.372;0.369	T	0.61471	-0.7056	9	0.32370	T	0.25	.	14.9037	0.70699	1.0:0.0:0.0:0.0	.	826;851	Q02224-3;Q02224	.;CENPE_HUMAN	A	851;851;826;851	ENSP00000265148:S851A;ENSP00000369365:S826A;ENSP00000423981:S851A	ENSP00000265148:S851A	S	-	1	0	CENPE	104299666	0.997000	0.39634	0.084000	0.20598	0.866000	0.49608	2.194000	0.42668	1.971000	0.57363	0.477000	0.44152	TCT	A|0.985;C|0.015	0.015	strong		0.373	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CCDC114	93233	hgsc.bcm.edu	37	19	48806977	48806977	+	Silent	SNP	G	G	A	rs2242463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48806977G>A	ENST00000315396.7	-	8	1489	c.807C>T	c.(805-807)gaC>gaT	p.D269D		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	269					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)		TATTCAGGGCGTCCTCGTAGC	0.632													G|||	768	0.153355	0.1354	0.0965	5008	,	,		17099	0.126		0.1998	False		,,,				2504	0.1984				p.D269D		Atlas-SNP	.											.	CCDC114	100	.	0			c.C807T						PASS	.	G		727,3679	301.0+/-286.6	63,601,1539	93.0	90.0	91.0		807	-6.0	0.5	19	dbSNP_98	91	1599,7001	298.6+/-304.0	164,1271,2865	no	coding-synonymous	CCDC114	NM_144577.3		227,1872,4404	AA,AG,GG		18.593,16.5002,17.8841		269/671	48806977	2326,10680	2203	4300	6503	SO:0001819	synonymous_variant	93233	exon8			CAGGGCGTCCTCG	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.807C>T	19.37:g.48806977G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	160	158	0.9875	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Silent	SNP	ENST00000315396.7	37	CCDS12714.2																																																																																			G|0.817;A|0.183	0.183	strong		0.632	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
SLC35G6	643664	hgsc.bcm.edu	37	17	7385661	7385661	+	Missense_Mutation	SNP	A	A	G	rs192630658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7385661A>G	ENST00000412468.2	+	2	473	c.358A>G	c.(358-360)Agt>Ggt	p.S120G	POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000572844.1_5'Flank|ZBTB4_ENST00000380599.4_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	120	EamA 1.					integral component of membrane (GO:0016021)											ATGTGCCTACAGTGCGGTTCA	0.617													A|||	183	0.0365415	0.1309	0.013	5008	,	,		18822	0.0		0.001	False		,,,				2504	0.0				p.S120G		Atlas-SNP	.											.	.	.	.	0			c.A358G						PASS	.	A	GLY/SER,	467,3939	220.4+/-237.8	34,399,1770	139.0	139.0	139.0		358,	4.2	1.0	17		139	4,8596	3.7+/-12.6	0,4,4296	no	missense,intron	ZBTB4,SLC35G6	NM_001102614.1,NM_020899.3	56,	34,403,6066	GG,GA,AA		0.0465,10.5992,3.6214	possibly-damaging,	120/339,	7385661	471,12535	2203	4300	6503	SO:0001583	missense	643664	exon2			GCCTACAGTGCGG		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.358A>G	17.37:g.7385661A>G	ENSP00000396523:p.Ser120Gly	Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	220	119	0.540909	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	63	0.028846153846153848	57	0.11585365853658537	5	0.013812154696132596	1	0.0017482517482517483	0	0.0	A	14.87	2.665416	0.47677	0.105992	4.65E-4	ENSG00000181222	ENST00000412468	T	0.52057	0.68	4.19	4.19	0.49359	.	.	.	.	.	T	0.00524	0.0017	N	0.24115	0.695	0.43740	D	0.996233	B	0.27286	0.174	B	0.33846	0.171	T	0.01925	-1.1246	9	0.27082	T	0.32	-4.3505	12.5602	0.56277	1.0:0.0:0.0:0.0	.	120	P0C7Q6	S35G6_HUMAN	G	120	ENSP00000396523:S120G	ENSP00000396523:S120G	S	+	1	0	SLC35G6	7326385	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	4.149000	0.58091	1.671000	0.50874	0.460000	0.39030	AGT	A|0.977;G|0.023	0.023	strong		0.617	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
GBA2	57704	hgsc.bcm.edu	37	9	35749845	35749845	+	5'Flank	SNP	G	G	C	rs2236288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35749845G>C	ENST00000378103.3	-	0	0				RGP1_ENST00000378078.4_Silent_p.P31P|RGP1_ENST00000456972.2_Silent_p.P71P|GBA2_ENST00000378094.4_5'Flank|GBA2_ENST00000545786.1_5'UTR	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ACCCCCTTCCGCCCACGGCCA	0.602													C|||	1579	0.315296	0.4811	0.232	5008	,	,		17770	0.4018		0.2127	False		,,,				2504	0.1667				p.P31P		Atlas-SNP	.											.	RGP1	60	.	0			c.G93C						PASS	.	C		1713,2251		386,941,655	51.0	55.0	54.0		93	0.4	0.7	9	dbSNP_98	54	1743,6575		184,1375,2600	no	coding-synonymous	RGP1	NM_001080496.2		570,2316,3255	CC,CG,GG		20.9546,43.2139,28.1387		31/392	35749845	3456,8826	1982	4159	6141	SO:0001631	upstream_gene_variant	9827	exon2			CCTTCCGCCCACG	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"""bile acid beta-glucosidase"", ""non-lysosomal glucosylceramidase"""	609471	"""spastic paraplegia 46 (autosomal recessive)"""	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		9.37:g.35749845G>C	Exception_encountered	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	124	68	0.548387	NM_001080496	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Silent	SNP	ENST00000378103.3	37	CCDS6589.1																																																																																			G|0.688;C|0.312	0.312	strong		0.602	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944	
SF3B1	23451	hgsc.bcm.edu	37	2	198266834	198266834	+	Missense_Mutation	SNP	T	T	C	rs559063155		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:198266834T>C	ENST00000335508.6	-	15	2189	c.2098A>G	c.(2098-2100)Aaa>Gaa	p.K700E	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'UTR	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	700					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.K700E(179)|p.Q699_K700del(2)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTCCGAACTTTCTGCTGCTCA	0.408			Mis		myelodysplastic syndrome								T|||	1	0.000199681	0.0	0.0	5008	,	,		17946	0.0		0.0	False		,,,				2504	0.001				p.K700E		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	SF3B1,NS,haematopoietic_neoplasm,0,263	SF3B1	1038	263	181	Substitution - Missense(179)|Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(153)|NS(20)|breast(5)|pancreas(2)|central_nervous_system(1)	c.A2098G						PASS	.																																			SO:0001583	missense	23451	exon15			GAACTTTCTGCTG	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2098A>G	2.37:g.198266834T>C	ENSP00000335321:p.Lys700Glu	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	214	70	0.327103	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	33	5.243295	0.95272	.	.	ENSG00000115524	ENST00000335508	T	0.63580	-0.05	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85609	0.5736	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89820	0.3988	10	0.87932	D	0	.	16.542	0.84395	0.0:0.0:0.0:1.0	.	700	O75533	SF3B1_HUMAN	E	700	ENSP00000335321:K700E	ENSP00000335321:K700E	K	-	1	0	SF3B1	197975079	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.555000	0.82223	2.304000	0.77564	0.528000	0.53228	AAA	.	.	none		0.408	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
RASGEF1A	221002	hgsc.bcm.edu	37	10	43696279	43696279	+	Silent	SNP	A	A	G	rs41301585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:43696279A>G	ENST00000395809.1	-	5	3023	c.517T>C	c.(517-519)Ttg>Ctg	p.L173L	RASGEF1A_ENST00000374459.1_Silent_p.L181L|RASGEF1A_ENST00000472864.1_5'UTR|RASGEF1A_ENST00000395810.1_Silent_p.L173L			Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A	173					cell migration (GO:0016477)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.L120L(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)	11						CGGGCAGCCAAGGACAGCAAC	0.617													G|||	407	0.08127	0.0424	0.0317	5008	,	,		20684	0.1002		0.0646	False		,,,				2504	0.1667				p.L173L		Atlas-SNP	.											RASGEF1A,NS,carcinoma,0,1	RASGEF1A	66	1	1	Substitution - coding silent(1)	ovary(1)	c.T517C						PASS	.	G		192,4214	807.3+/-415.9	6,180,2017	98.0	92.0	94.0		517	5.2	1.0	10	dbSNP_127	94	516,8084	795.8+/-407.5	22,472,3806	no	coding-synonymous	RASGEF1A	NM_145313.2		28,652,5823	GG,GA,AA		6.0,4.3577,5.4436		173/482	43696279	708,12298	2203	4300	6503	SO:0001819	synonymous_variant	221002	exon5			CAGCCAAGGACAG	AK095136	CCDS7202.2, CCDS60517.1	10q11.21	2006-01-11			ENSG00000198915	ENSG00000198915			24246	protein-coding gene	gene with protein product		614531				12477932	Standard	XM_005271808		Approved	CG4853, FLJ37817	uc001jap.1	Q8N9B8	OTTHUMG00000018025	ENST00000395809.1:c.517T>C	10.37:g.43696279A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_145313	Q8TBF1	Silent	SNP	ENST00000395809.1	37	CCDS7202.2	172	0.07875457875457875	36	0.07317073170731707	19	0.052486187845303865	70	0.12237762237762238	47	0.06200527704485488	G	10.29	1.308387	0.23821	0.043577	0.06	ENSG00000198915	ENST00000374455	.	.	.	5.18	5.18	0.71444	.	0.000000	0.56097	D	0.000025	T	0.01835	0.0058	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.23797	-1.0178	4	.	.	.	.	13.9492	0.64106	0.0733:0.0:0.9267:0.0	rs41301585;rs61749172	.	.	.	P	74	.	.	L	-	2	0	RASGEF1A	43016285	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	3.180000	0.50895	1.191000	0.43056	-0.215000	0.12644	CTT	A|0.937;G|0.063	0.063	strong		0.617	RASGEF1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313989.1	NM_145313	
CCDC171	203238	hgsc.bcm.edu	37	9	15744683	15744683	+	Missense_Mutation	SNP	G	G	A	rs34816651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:15744683G>A	ENST00000380701.3	+	17	2790	c.2462G>A	c.(2461-2463)tGt>tAt	p.C821Y	CCDC171_ENST00000297641.3_Missense_Mutation_p.C821Y	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	821			C -> Y (in dbSNP:rs34816651).														GGCCAATCATGTGCCTCTCTT	0.393													G|||	494	0.0986422	0.1452	0.0418	5008	,	,		19632	0.125		0.006	False		,,,				2504	0.1442				p.C821Y		Atlas-SNP	.											.	.	.	.	0			c.G2462A						PASS	.	G	TYR/CYS	458,3948	216.1+/-234.9	19,420,1764	66.0	65.0	65.0		2462	4.5	1.0	9	dbSNP_126	65	63,8537	39.8+/-96.3	1,61,4238	yes	missense	C9orf93	NM_173550.2	194	20,481,6002	AA,AG,GG		0.7326,10.3949,4.0058	probably-damaging	821/1327	15744683	521,12485	2203	4300	6503	SO:0001583	missense	203238	exon17			AATCATGTGCCTC	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.2462G>A	9.37:g.15744683G>A	ENSP00000370077:p.Cys821Tyr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	159|159	0.07280219780219781|0.07280219780219781	71|71	0.1443089430894309|0.1443089430894309	12|12	0.03314917127071823|0.03314917127071823	72|72	0.1258741258741259|0.1258741258741259	4|4	0.005277044854881266|0.005277044854881266	G|G	14.09|14.09	2.430553|2.430553	0.43122|0.43122	0.103949|0.103949	0.007326|0.007326	ENSG00000164989|ENSG00000164989	ENST00000297641;ENST00000380689;ENST00000380701|ENST00000449575	T;T|.	0.15017|.	2.46;2.46|.	5.46|5.46	4.51|4.51	0.55191|0.55191	.|.	0.150760|.	0.64402|.	D|.	0.000010|.	T|T	0.00356|0.00356	0.0011|0.0011	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	P|P	0.999999999999942|0.999999999999942	B;B;B;B|.	0.18461|.	0.028;0.028;0.016;0.028|.	B;B;B;B|.	0.17433|.	0.011;0.018;0.003;0.006|.	T|T	0.05733|0.05733	-1.0867|-1.0867	9|4	0.25751|.	T|.	0.34|.	-8.6083|-8.6083	9.9483|9.9483	0.41623|0.41623	0.0785:0.2222:0.6993:0.0|0.0785:0.2222:0.6993:0.0	rs34816651;rs61661263|rs34816651;rs61661263	829;821;88;821|.	B7ZM22;Q6TFL3-3;A6NK04;Q6TFL3|.	.;.;.;CI093_HUMAN|.	Y|M	821;88;821|61	ENSP00000297641:C821Y;ENSP00000370077:C821Y|.	ENSP00000297641:C821Y|.	C|V	+|+	2|1	0|0	C9orf93|C9orf93	15734683|15734683	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	1.663000|1.663000	0.37429|0.37429	2.733000|2.733000	0.93635|0.93635	0.467000|0.467000	0.42956|0.42956	TGT|GTG	G|0.951;A|0.049	0.049	strong		0.393	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
FTHL17	53940	hgsc.bcm.edu	37	X	31089873	31089873	+	Missense_Mutation	SNP	A	A	T	rs73617043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:31089873A>T	ENST00000359202.3	-	1	297	c.198T>A	c.(196-198)caT>caA	p.H66Q		NM_031894.2	NP_114100.1	Q9BXU8	FHL17_HUMAN	ferritin, heavy polypeptide-like 17	66	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)		ferric iron binding (GO:0008199)			endometrium(2)|large_intestine(2)|liver(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	23						GCTTCTGGGCATGCTCCATTT	0.592													A|||	11	0.00291391	0.0083	0.0	3775	,	,		13041	0.0		0.0	False		,,,				2504	0.0				p.H66Q		Atlas-SNP	.											.	FTHL17	99	.	0			c.T198A						PASS	.	A	GLN/HIS	31,3802		0,27,4,1604,567	73.0	66.0	69.0		198	-3.3	0.0	X	dbSNP_130	69	0,6728		0,0,0,2428,1872	yes	missense	FTHL17	NM_031894.2	24	0,27,4,4032,2439	TT,TA,T,AA,A		0.0,0.8088,0.2935	benign	66/184	31089873	31,10530	2202	4300	6502	SO:0001583	missense	53940	exon1			CTGGGCATGCTCC	AF285592	CCDS14227.1	Xp21.2	2010-07-06			ENSG00000132446	ENSG00000132446			3987	protein-coding gene	gene with protein product	"""cancer/testis antigen 38"""	300308				11279525	Standard	NM_031894		Approved	CT38	uc004dcl.1	Q9BXU8	OTTHUMG00000021332	ENST00000359202.3:c.198T>A	X.37:g.31089873A>T	ENSP00000368207:p.His66Gln	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	186	87	0.467742	NM_031894	Q6NT24|Q6NTE2	Missense_Mutation	SNP	ENST00000359202.3	37	CCDS14227.1	8	0.004822182037371911	5	0.0102880658436214	0	0.0	0	0.0	0	0.0	A	10.22	1.290499	0.23478	0.008088	0.0	ENSG00000132446	ENST00000359202	T	0.72051	-0.62	3.44	-3.29	0.05017	Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);Ferritin/DPS protein domain (1);Ferritin-like (1);	0.401704	0.26156	N	0.026011	T	0.48804	0.1520	M	0.70595	2.14	0.21220	N	0.999756	B	0.32800	0.385	B	0.29353	0.101	T	0.48822	-0.9001	10	0.59425	D	0.04	.	1.8231	0.03115	0.4037:0.1354:0.331:0.1299	.	66	Q9BXU8	FHL17_HUMAN	Q	66	ENSP00000368207:H66Q	ENSP00000368207:H66Q	H	-	3	2	FTHL17	30999794	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-1.291000	0.02775	-1.082000	0.03101	-1.413000	0.01118	CAT	A|0.996;T|0.004	0.004	strong		0.592	FTHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056178.1	NM_031894	
TPRX1	284355	hgsc.bcm.edu	37	19	48305674	48305674	+	Silent	SNP	T	T	C	rs78381908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48305674T>C	ENST00000322175.3	-	2	749	c.594A>G	c.(592-594)ccA>ccG	p.P198P	TPRX1_ENST00000535759.1_Silent_p.P295P|TPRX1_ENST00000543508.1_Silent_p.P188P	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	106	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	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	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125854404	125854404	+	Silent	SNP	C	C	T	rs114109734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125854404C>T	ENST00000393434.2	-	12	1795	c.1446G>A	c.(1444-1446)gcG>gcA	p.A482A	ALDH1L1_ENST00000452905.2_Silent_p.A381A|ALDH1L1_ENST00000472186.1_Silent_p.A482A|ALDH1L1_ENST00000273450.3_Silent_p.A492A|ALDH1L1_ENST00000393431.2_Silent_p.A482A	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	482	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)	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)	CCCGGTCCCGCGCACTGATCT	0.632													C|||	15	0.00299521	0.0106	0.0014	5008	,	,		15773	0.0		0.0	False		,,,				2504	0.0				p.A492A		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.G1476A						PASS	.	C		49,4357	50.9+/-86.3	0,49,2154	136.0	102.0	114.0		1446	-7.5	0.0	3	dbSNP_133	114	0,8600		0,0,4300	no	coding-synonymous	ALDH1L1	NM_012190.2		0,49,6454	TT,TC,CC		0.0,1.1121,0.3767		482/903	125854404	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	10840	exon12			GTCCCGCGCACTG	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.1446G>A	3.37:g.125854404C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_001270364	B4DG36|E9PBX3|Q68CS1	Silent	SNP	ENST00000393434.2	37	CCDS3034.1																																																																																			C|0.996;T|0.004	0.004	strong		0.632	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
PVR	5817	hgsc.bcm.edu	37	19	45161070	45161070	+	Missense_Mutation	SNP	G	G	A	rs35365841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45161070G>A	ENST00000425690.3	+	5	1182	c.883G>A	c.(883-885)Gcc>Acc	p.A295T	PVR_ENST00000406449.4_Missense_Mutation_p.A295T|PVR_ENST00000403059.4_Missense_Mutation_p.A295T|PVR_ENST00000344956.4_Missense_Mutation_p.A295T|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	295	Ig-like C2-type 2.		A -> T (in dbSNP:rs35365841).		adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		GGCCCAGGGCGCCCAGCTCCT	0.587											OREG0025540	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	257	0.0513179	0.1755	0.0259	5008	,	,		18444	0.0		0.001	False		,,,				2504	0.0061				p.A295T		Atlas-SNP	.											.	PVR	23	.	0			c.G883A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	656,3750	279.9+/-275.1	61,534,1608	61.0	53.0	55.0		883,883,883,883	-10.2	0.0	19	dbSNP_126	55	8,8592	5.7+/-21.5	0,8,4292	yes	missense,missense,missense,missense	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	58,58,58,58	61,542,5900	AA,AG,GG		0.093,14.8888,5.1053	benign,benign,benign,benign	295/373,295/365,295/393,295/418	45161070	664,12342	2203	4300	6503	SO:0001583	missense	5817	exon5			CAGGGCGCCCAGC	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9705	protein-coding gene	gene with protein product	"""nectin-like 5"""	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.883G>A	19.37:g.45161070G>A	ENSP00000402060:p.Ala295Thr	Somatic	84	0	0	929	WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	37	CCDS12640.1	116	0.05311355311355311	101	0.20528455284552846	14	0.03867403314917127	0	0.0	1	0.0013192612137203166	G	10.75	1.438622	0.25900	0.148888	9.3E-4	ENSG00000073008	ENST00000344956;ENST00000425690;ENST00000406449;ENST00000403059	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.08	-10.2	0.00374	Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	2.148170	0.02353	N	0.076098	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B;B;B;B	0.30361	0.038;0.154;0.097;0.277	B;B;B;B	0.28305	0.027;0.049;0.031;0.088	T	0.22765	-1.0207	9	0.14252	T	0.57	.	1.6961	0.02862	0.118:0.3407:0.2586:0.2827	rs35365841	295;295;295;295	P15151-2;P15151-3;P15151-4;P15151	.;.;.;PVR_HUMAN	T	295	ENSP00000340870:A295T;ENSP00000402060:A295T;ENSP00000383907:A295T;ENSP00000385344:A295T	ENSP00000340870:A295T	A	+	1	0	PVR	49852910	0.000000	0.05858	0.000000	0.03702	0.123000	0.20343	-2.189000	0.01248	-2.865000	0.00325	-0.165000	0.13383	GCC	G|0.951;A|0.049	0.049	strong		0.587	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505	
ZNF804B	219578	hgsc.bcm.edu	37	7	88964162	88964162	+	Missense_Mutation	SNP	T	T	G	rs150870900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88964162T>G	ENST00000333190.4	+	4	2475	c.1866T>G	c.(1864-1866)gaT>gaG	p.D622E		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	622							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ATGATATAGATGAGGACCTAT	0.383										HNSCC(36;0.09)			T|||	31	0.0061901	0.0204	0.0058	5008	,	,		19603	0.0		0.0	False		,,,				2504	0.0				p.D622E		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T1866G						PASS	.	T	GLU/ASP	63,4343	59.3+/-96.0	0,63,2140	74.0	78.0	77.0		1866	-1.2	0.0	7	dbSNP_134	77	0,8600		0,0,4300	yes	missense	ZNF804B	NM_181646.2	45	0,63,6440	GG,GT,TT		0.0,1.4299,0.4844	benign	622/1350	88964162	63,12943	2203	4300	6503	SO:0001583	missense	219578	exon4			TATAGATGAGGAC	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1866T>G	7.37:g.88964162T>G	ENSP00000329638:p.Asp622Glu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	T	0.048	-1.259050	0.01445	0.014299	0.0	ENSG00000182348	ENST00000333190	T	0.04454	3.62	5.49	-1.24	0.09435	.	0.337088	0.29376	N	0.012335	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.46205	-0.9208	10	0.02654	T	1	-6.4004	6.3638	0.21443	0.0:0.1906:0.325:0.4844	.	622	A4D1E1	Z804B_HUMAN	E	622	ENSP00000329638:D622E	ENSP00000329638:D622E	D	+	3	2	ZNF804B	88802098	0.211000	0.23529	0.002000	0.10522	0.037000	0.13140	-0.303000	0.08210	-0.334000	0.08463	0.533000	0.62120	GAT	T|0.996;G|0.004	0.004	strong		0.383	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
DNAH10	196385	hgsc.bcm.edu	37	12	124360037	124360037	+	Splice_Site	SNP	C	C	T	rs61732737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124360037C>T	ENST00000409039.3	+	46	7869	c.7844C>T	c.(7843-7845)tCg>tTg	p.S2615L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2615	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)		GGCCACACCTCGGTAACTTGA	0.448													C|||	125	0.0249601	0.034	0.0086	5008	,	,		18069	0.0526		0.007	False		,,,				2504	0.0143				p.S2615L		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7844T						PASS	.	C	LEU/SER	112,3600		3,106,1747	100.0	93.0	95.0		7844	3.3	1.0	12	dbSNP_129	95	57,8131		0,57,4037	yes	missense-near-splice	DNAH10	NM_207437.3	145	3,163,5784	TT,TC,CC		0.6961,3.0172,1.4202	benign	2615/4472	124360037	169,11731	1856	4094	5950	SO:0001630	splice_region_variant	196385	exon46			ACACCTCGGTAAC	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.7845+1C>T	12.37:g.124360037C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	64	0.029304029304029304	20	0.04065040650406504	3	0.008287292817679558	37	0.06468531468531469	4	0.005277044854881266	C	12.26	1.884048	0.33255	0.030172	0.006961	ENSG00000197653	ENST00000409039	T	0.39787	1.06	5.41	3.3	0.37823	.	2.437090	0.02760	N	0.118428	T	0.05640	0.0148	L	0.41415	1.275	0.80722	D	1	B	0.22080	0.064	B	0.16289	0.015	T	0.03524	-1.1028	10	0.34782	T	0.22	.	10.3793	0.44101	0.1914:0.7324:0.0:0.0762	rs61732737	2615	Q8IVF4	DYH10_HUMAN	L	2615	ENSP00000386770:S2615L	ENSP00000386770:S2615L	S	+	2	0	DNAH10	122925990	0.862000	0.29867	0.998000	0.56505	0.927000	0.56198	0.469000	0.22067	1.425000	0.47237	0.558000	0.71614	TCG	C|0.976;T|0.024	0.024	strong		0.448	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		Missense_Mutation
USP13	8975	hgsc.bcm.edu	37	3	179371154	179371154	+	Silent	SNP	C	C	T	rs2276803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:179371154C>T	ENST00000263966.3	+	1	612	c.141C>T	c.(139-141)aaC>aaT	p.N47N	USP13_ENST00000482333.1_3'UTR|USP13_ENST00000496897.1_5'Flank	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	47					autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TCTACAAGAACGAGTGCGCCT	0.687													C|||	1052	0.210064	0.3767	0.1499	5008	,	,		10066	0.1002		0.1541	False		,,,				2504	0.1984				p.N47N		Atlas-SNP	.											.	USP13	117	.	0			c.C141T						PASS	.	C		1382,2976		225,932,1022	38.0	29.0	32.0		141	1.6	1.0	3	dbSNP_100	32	1320,7238		111,1098,3070	no	coding-synonymous	USP13	NM_003940.2		336,2030,4092	TT,TC,CC		15.4242,31.7118,20.9198		47/864	179371154	2702,10214	2179	4279	6458	SO:0001819	synonymous_variant	8975	exon1			CAAGAACGAGTGC	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"""Ubiquitin-specific peptidases"""	12611	protein-coding gene	gene with protein product		603591	"""ubiquitin specific protease 13 (isopeptidase T-3)"""			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.141C>T	3.37:g.179371154C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_003940	A8K2S3|B4DYF3|D3DNS2|Q96B25	Silent	SNP	ENST00000263966.3	37	CCDS3235.1																																																																																			C|0.795;T|0.205	0.205	strong		0.687	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1		
SLC9A4	389015	hgsc.bcm.edu	37	2	103142761	103142761	+	Missense_Mutation	SNP	A	A	T	rs115217520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:103142761A>T	ENST00000295269.4	+	11	2451	c.1994A>T	c.(1993-1995)aAt>aTt	p.N665I		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	665					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CCCTACGGGAATCCTCAGTCT	0.498													A|||	11	0.00219649	0.0083	0.0	5008	,	,		15709	0.0		0.0	False		,,,				2504	0.0				p.N665I		Atlas-SNP	.											.	SLC9A4	115	.	0			c.A1994T						PASS	.	A	ILE/ASN	27,4379	33.5+/-64.1	0,27,2176	126.0	118.0	121.0		1994	3.4	0.0	2	dbSNP_133	121	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SLC9A4	NM_001011552.3	149	0,29,6474	TT,TA,AA		0.0233,0.6128,0.223	benign	665/799	103142761	29,12977	2203	4300	6503	SO:0001583	missense	389015	exon11			ACGGGAATCCTCA		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.1994A>T	2.37:g.103142761A>T	ENSP00000295269:p.Asn665Ile	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	131	59	0.450382	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	37	CCDS33264.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	12.38	1.919817	0.33908	0.006128	2.33E-4	ENSG00000180251	ENST00000295269	T	0.46451	0.87	5.8	3.38	0.38709	.	2.143600	0.02112	N	0.054895	T	0.33294	0.0858	L	0.44542	1.39	0.09310	N	1	B	0.22604	0.072	B	0.26517	0.07	T	0.26292	-1.0107	10	0.42905	T	0.14	.	8.6644	0.34112	0.8465:0.0:0.1535:0.0	.	665	Q6AI14	SL9A4_HUMAN	I	665	ENSP00000295269:N665I	ENSP00000295269:N665I	N	+	2	0	SLC9A4	102509193	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.084000	0.14891	0.438000	0.26450	0.533000	0.62120	AAT	A|0.997;T|0.003	0.003	strong		0.498	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
KRT14	3861	hgsc.bcm.edu	37	17	39741280	39741280	+	Silent	SNP	A	A	G	rs35849957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39741280A>G	ENST00000167586.6	-	2	641	c.555T>C	c.(553-555)aaT>aaC	p.N185N		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	185	Coil 1B.|Rod.				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)				GCAGAAGGACATTGGCATTGT	0.507													.|||	299	0.0597045	0.2118	0.0216	5008	,	,		20159	0.0		0.004	False		,,,				2504	0.0				p.N185N		Atlas-SNP	.											.	KRT14	65	.	0			c.T555C						PASS	.	G		794,3612	751.1+/-412.2	71,652,1480	101.0	82.0	89.0		555	-7.0	0.0	17	dbSNP_126	89	6,8594	818.5+/-406.9	0,6,4294	no	coding-synonymous	KRT14	NM_000526.4		71,658,5774	GG,GA,AA		0.0698,18.0209,6.151		185/473	39741280	800,12206	2203	4300	6503	SO:0001819	synonymous_variant	3861	exon2			AAGGACATTGGCA	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.555T>C	17.37:g.39741280A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Silent	SNP	ENST00000167586.6	37	CCDS11400.1																																																																																			A|0.944;G|0.056	0.056	strong		0.507	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
LRRC43	254050	hgsc.bcm.edu	37	12	122674780	122674780	+	Missense_Mutation	SNP	C	C	A	rs11060094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122674780C>A	ENST00000339777.4	+	5	794	c.766C>A	c.(766-768)Cag>Aag	p.Q256K	LRRC43_ENST00000425921.1_Missense_Mutation_p.Q71K	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	256			Q -> K (in dbSNP:rs11060094). {ECO:0000269|PubMed:14702039}.							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)		CCTGGTGCTGCAGGGAAACCC	0.637													C|||	671	0.133986	0.0953	0.2666	5008	,	,		20331	0.0357		0.2038	False		,,,				2504	0.1217				p.Q256K		Atlas-SNP	.											.	LRRC43	105	.	0			c.C766A						PASS	.	C	LYS/GLN,LYS/GLN	436,3902		20,396,1753	91.0	103.0	99.0		766,211	4.9	1.0	12	dbSNP_120	99	1763,6753		199,1365,2694	yes	missense,missense	LRRC43	NM_001098519.1,NM_152759.4	53,53	219,1761,4447	AA,AC,CC		20.7022,10.0507,17.1075	benign,benign	256/657,71/472	122674780	2199,10655	2169	4258	6427	SO:0001583	missense	254050	exon5			GTGCTGCAGGGAA	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.766C>A	12.37:g.122674780C>A	ENSP00000344233:p.Gln256Lys	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	37	CCDS45001.1	303	0.13873626373626374	49	0.09959349593495935	98	0.27071823204419887	15	0.026223776223776224	141	0.18601583113456466	C	22.3	4.268532	0.80469	0.100507	0.207022	ENSG00000158113	ENST00000537729;ENST00000339777;ENST00000289014;ENST00000425921	T;T;T	0.23348	1.91;1.91;1.91	4.95	4.95	0.65309	.	0.068949	0.64402	D	0.000017	T	0.00012	0.0000	M	0.63208	1.945	0.26746	P	0.9702966	D	0.58268	0.982	D	0.70227	0.968	T	0.01294	-1.1393	9	0.48119	T	0.1	-55.8197	17.807	0.88604	0.0:1.0:0.0:0.0	rs11060094;rs57783714;rs11060094	256	Q8N309	LRC43_HUMAN	K	71;256;127;71	ENSP00000438751:Q71K;ENSP00000344233:Q256K;ENSP00000416628:Q71K	ENSP00000289014:Q127K	Q	+	1	0	LRRC43	121240733	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.532000	0.60608	2.309000	0.77851	0.561000	0.74099	CAG	C|0.865;A|0.135	0.135	strong		0.637	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
NKX3-2	579	hgsc.bcm.edu	37	4	13545610	13545610	+	Silent	SNP	C	C	T	rs10032202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:13545610C>T	ENST00000382438.5	-	1	1064	c.429G>A	c.(427-429)gcG>gcA	p.A143A	AC006445.8_ENST00000501050.1_lincRNA	NM_001189.3	NP_001180.1	P78367	NKX32_HUMAN	NK3 homeobox 2	143					determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|intestinal epithelial cell development (GO:0060576)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|organ formation (GO:0048645)|pancreas development (GO:0031016)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|spleen development (GO:0048536)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(1)|lung(4)|prostate(1)	7						CGCTCCGGCCCGCGGCTTCCT	0.731													C|||	196	0.0391374	0.1437	0.0058	5008	,	,		11648	0.0		0.002	False		,,,				2504	0.0				p.A143A		Atlas-SNP	.											.	NKX3-2	15	.	0			c.G429A						PASS	.	C		260,3434		1,258,1588	3.0	4.0	4.0		429	3.1	1.0	4	dbSNP_119	4	10,7596		0,10,3793	no	coding-synonymous	NKX3-2	NM_001189.3		1,268,5381	TT,TC,CC		0.1315,7.0384,2.3894		143/334	13545610	270,11030	1847	3803	5650	SO:0001819	synonymous_variant	579	exon1			CCGGCCCGCGGCT	AF009801	CCDS3410.1	4p16.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000109705	ENSG00000109705		"""Homeoboxes / ANTP class : NKL subclass"""	951	protein-coding gene	gene with protein product		602183	"""bagpipe homeobox homolog 1 (Drosophila)"""	BAPX1		9344671	Standard	NM_001189		Approved	NKX3B, NKX3.2	uc003gmx.2	P78367	OTTHUMG00000090657	ENST00000382438.5:c.429G>A	4.37:g.13545610C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_001189	Q2M2I7	Silent	SNP	ENST00000382438.5	37	CCDS3410.1																																																																																			C|0.964;T|0.036	0.036	strong		0.731	NKX3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207317.3		
RUFY4	285180	hgsc.bcm.edu	37	2	218940259	218940259	+	Silent	SNP	C	C	T	rs7423696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218940259C>T	ENST00000344321.7	+	9	1562	c.1044C>T	c.(1042-1044)ccC>ccT	p.P348P	RUFY4_ENST00000441828.2_3'UTR|RUFY4_ENST00000374155.3_Silent_p.P368P|RUFY4_ENST00000463872.1_3'UTR	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	348							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)		TGCTGATGCCCAGCCCCAGAG	0.617													C|||	1161	0.231829	0.034	0.3444	5008	,	,		16738	0.2312		0.3052	False		,,,				2504	0.3446				p.P348P		Atlas-SNP	.											.	RUFY4	59	.	0			c.C1044T						PASS	.	C		292,3696		15,262,1717	31.0	36.0	34.0		1044	2.8	0.1	2	dbSNP_116	34	2412,5996		348,1716,2140	no	coding-synonymous	RUFY4	NM_198483.3		363,1978,3857	TT,TC,CC		28.687,7.322,21.8135		348/572	218940259	2704,9692	1994	4204	6198	SO:0001819	synonymous_variant	285180	exon9			GATGCCCAGCCCC	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.1044C>T	2.37:g.218940259C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	157	65	0.414013	NM_198483	Q6ZR96	Silent	SNP	ENST00000344321.7	37																																																																																				C|0.769;T|0.231	0.231	strong		0.617	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483	
PER3	8863	hgsc.bcm.edu	37	1	7887234	7887234	+	Missense_Mutation	SNP	C	C	T	rs35687686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:7887234C>T	ENST00000361923.2	+	17	2396	c.2221C>T	c.(2221-2223)Cgg>Tgg	p.R741W	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.R749W	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	741	CSNK1E binding domain. {ECO:0000250}.				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)		GAAGCACAAGCGGAAGAAGCT	0.597													C|||	30	0.00599042	0.0197	0.0058	5008	,	,		15161	0.0		0.0	False		,,,				2504	0.0				p.R741W		Atlas-SNP	.											PER3,colon,carcinoma,0,1	PER3	95	1	0			c.C2221T						PASS	.	C	TRP/ARG	70,4246		1,68,2089	19.0	24.0	22.0		2221	1.6	0.1	1	dbSNP_126	22	1,8501		0,1,4250	yes	missense	PER3	NM_016831.1	101	1,69,6339	TT,TC,CC		0.0118,1.6219,0.5539	probably-damaging	741/1202	7887234	71,12747	2158	4251	6409	SO:0001583	missense	8863	exon17			CACAAGCGGAAGA	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.2221C>T	1.37:g.7887234C>T	ENSP00000355031:p.Arg741Trp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	12	0.005494505494505495	10	0.02032520325203252	2	0.0055248618784530384	0	0.0	0	0.0	C	10.54	1.377888	0.24944	0.016219	1.18E-4	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.13778	2.56;2.6	4.52	1.64	0.23874	.	2.148170	0.02588	N	0.099653	T	0.06188	0.0160	L	0.42529	1.33	0.09310	N	1	B;P;P;B	0.40180	0.179;0.581;0.705;0.179	B;B;B;B	0.31686	0.019;0.063;0.134;0.019	T	0.32161	-0.9917	10	0.87932	D	0	.	7.6166	0.28160	0.0:0.7331:0.0:0.2669	rs35687686	741;749;749;741	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	W	749;741	ENSP00000366755:R749W;ENSP00000355031:R741W	ENSP00000355031:R741W	R	+	1	2	PER3	7809821	0.991000	0.36638	0.061000	0.19648	0.054000	0.15201	0.501000	0.22578	0.181000	0.19994	0.561000	0.74099	CGG	C|0.993;T|0.007	0.007	strong		0.597	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
UBR4	23352	hgsc.bcm.edu	37	1	19518855	19518855	+	Silent	SNP	T	T	C	rs147313932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19518855T>C	ENST00000375254.3	-	11	1248	c.1221A>G	c.(1219-1221)caA>caG	p.Q407Q	UBR4_ENST00000375226.2_Silent_p.Q407Q|UBR4_ENST00000375217.2_Silent_p.Q407Q|UBR4_ENST00000375267.2_Silent_p.Q407Q	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	407					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)			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)		CACCCAGCAATTGGAAATTCT	0.428													T|||	15	0.00299521	0.0106	0.0	5008	,	,		19894	0.001		0.0	False		,,,				2504	0.0				p.Q407Q		Atlas-SNP	.											.	UBR4	415	.	0			c.A1221G						PASS	.	T		13,4393	21.2+/-45.6	0,13,2190	79.0	81.0	80.0		1221	-11.2	0.0	1	dbSNP_134	80	0,8600		0,0,4300	no	coding-synonymous	UBR4	NM_020765.2		0,13,6490	CC,CT,TT		0.0,0.2951,0.1		407/5184	19518855	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon11			CAGCAATTGGAAA	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.1221A>G	1.37:g.19518855T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			T|0.999;C|0.001	0.001	strong		0.428	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
C17orf105	284067	hgsc.bcm.edu	37	17	41857869	41857869	+	Silent	SNP	C	C	T	rs73987086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41857869C>T	ENST00000449302.3	+	1	67	c.39C>T	c.(37-39)atC>atT	p.I13I	DUSP3_ENST00000226004.3_5'Flank|RP5-905N1.2_ENST00000591540.1_RNA|DUSP3_ENST00000591618.1_5'Flank|DUSP3_ENST00000397937.2_5'Flank	NM_001136483.1	NP_001129955.1	B2RV13	CQ105_HUMAN	chromosome 17 open reading frame 105	13																	ACCCTGTTATCGTCTCTAATC	0.443													C|||	262	0.0523163	0.1868	0.0202	5008	,	,		19742	0.0		0.001	False		,,,				2504	0.0				p.I13I		Atlas-SNP	.											.	C17orf105	3	.	0			c.C39T						PASS	.						159.0	137.0	144.0					17																	41857869		692	1591	2283	SO:0001819	synonymous_variant	284067	exon1			TGTTATCGTCTCT		CCDS45695.1	17q21.31	2012-10-23			ENSG00000231256	ENSG00000231256			37241	protein-coding gene	gene with protein product							Standard	NM_001136483		Approved		uc002ieg.3	B2RV13	OTTHUMG00000180890	ENST00000449302.3:c.39C>T	17.37:g.41857869C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	139	67	0.482014	NM_001136483		Silent	SNP	ENST00000449302.3	37	CCDS45695.1																																																																																			C|0.953;T|0.047	0.047	strong		0.443	C17orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453508.1	NM_001136483	
MBP	4155	hgsc.bcm.edu	37	18	74701984	74701984	+	Silent	SNP	G	G	A	rs470797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:74701984G>A	ENST00000397869.3	-	2	256	c.210C>T	c.(208-210)taC>taT	p.Y70Y	MBP_ENST00000382582.3_Silent_p.Y96Y|MBP_ENST00000359645.3_Silent_p.Y96Y|MBP_ENST00000397875.3_Silent_p.Y70Y|MBP_ENST00000354542.4_Intron|MBP_ENST00000526111.1_Silent_p.Y48Y|MBP_ENST00000578193.1_Silent_p.Y70Y|MBP_ENST00000528160.1_Intron|MBP_ENST00000527041.1_Silent_p.Y70Y|MBP_ENST00000355994.2_Silent_p.Y203Y|MBP_ENST00000580402.1_Silent_p.Y203Y|MBP_ENST00000397866.4_Silent_p.Y70Y|MBP_ENST00000397865.5_Silent_p.Y70Y|MBP_ENST00000579129.1_Silent_p.Y203Y			P13727	PRG2_HUMAN	myelin basic protein	0					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)	p.Y203Y(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)	Sargramostim(DB00020)	GCAGGGAGCCGTAGTGAGCAG	0.567													G|||	1166	0.232827	0.2368	0.1916	5008	,	,		17334	0.3204		0.1372	False		,,,				2504	0.2648				p.Y203Y	NSCLC(17;72 1131 19392)	Atlas-SNP	.											MBP,colon,carcinoma,0,2	MBP	45	2	1	Substitution - coding silent(1)	stomach(1)	c.C609T						PASS	.	G	,,,,	909,3497	349.3+/-310.3	98,713,1392	135.0	122.0	126.0		288,210,210,609,288	-5.9	1.0	18	dbSNP_83	126	1322,7278	259.9+/-283.0	102,1118,3080	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MBP	NM_001025081.1,NM_001025090.1,NM_001025092.1,NM_001025101.1,NM_002385.2	,,,,	200,1831,4472	AA,AG,GG		15.3721,20.631,17.1536	,,,,	96/198,70/172,70/161,203/305,96/187	74701984	2231,10775	2203	4300	6503	SO:0001819	synonymous_variant	4155	exon5			GGAGCCGTAGTGA		CCDS12011.1, CCDS32847.1, CCDS42448.1, CCDS42449.1, CCDS42450.1	18q23	2008-08-01			ENSG00000197971	ENSG00000197971			6925	protein-coding gene	gene with protein product		159430				2425357	Standard	XM_005266699		Approved		uc010xfd.2	P02686	OTTHUMG00000132874	ENST00000397869.3:c.210C>T	18.37:g.74701984G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	136	66	0.485294	NM_001025101	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Silent	SNP	ENST00000397869.3	37																																																																																				A|0.185;C|0.000;G|0.815;T|0.000	0.185	strong		0.567	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1	NM_001025081	
VAMP5	10791	hgsc.bcm.edu	37	2	85818886	85818886	+	Silent	SNP	C	C	T	rs14976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85818886C>T	ENST00000306384.4	+	2	125	c.42C>T	c.(40-42)aaC>aaT	p.N14N		NM_006634.2	NP_006625.1	O95183	VAMP5_HUMAN	vesicle-associated membrane protein 5	14	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				cell differentiation (GO:0030154)|Golgi to plasma membrane protein transport (GO:0043001)|muscle organ development (GO:0007517)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|large_intestine(3)|lung(1)	5						AGCAGGCGAACGAGGTGACGG	0.607													C|||	963	0.192292	0.152	0.2003	5008	,	,		18936	0.0883		0.2813	False		,,,				2504	0.2566				p.N14N		Atlas-SNP	.											.	VAMP5	13	.	0			c.C42T						PASS	.	C		692,3714	290.7+/-281.1	51,590,1562	132.0	113.0	119.0		42	-3.7	0.5	2	dbSNP_52	119	2410,6190	401.2+/-347.1	335,1740,2225	no	coding-synonymous	VAMP5	NM_006634.2		386,2330,3787	TT,TC,CC		28.0233,15.7059,23.8505		14/117	85818886	3102,9904	2203	4300	6503	SO:0001819	synonymous_variant	10791	exon2			GGCGAACGAGGTG	AF054825	CCDS1980.1	2p11.2	2013-02-13	2012-10-17		ENSG00000168899	ENSG00000168899		"""Vesicle-associated membrane proteins"""	12646	protein-coding gene	gene with protein product	"""myobrevin"""	607029				9725904	Standard	NM_006634		Approved		uc002spu.1	O95183	OTTHUMG00000130169	ENST00000306384.4:c.42C>T	2.37:g.85818886C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	248	135	0.544355	NM_006634	Q9P0T2	Silent	SNP	ENST00000306384.4	37	CCDS1980.1																																																																																			C|0.797;T|0.203	0.203	strong		0.607	VAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252484.2	NM_006634	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592312	1592312	+	Intron	SNP	T	T	C	rs72484087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1592312T>C	ENST00000381605.4	-	1	141				SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Missense_Mutation_p.I42V|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000568365.1_Missense_Mutation_p.I42V	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						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						GCAACTGATATGGACTTGTCA	0.557													N|||	3317	0.66234	0.7352	0.5245	5008	,	,		6786	0.7639		0.5149	False		,,,				2504	0.7086				p.I42V		Atlas-SNP	.											.	SIRPB1	83	.	0			c.A124G						PASS	.						42.0	52.0	50.0					20																	1592312		444	1336	1780	SO:0001627	intron_variant	10326	exon2			CTGATATGGACTT	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.76+8202A>G	20.37:g.1592312T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	140	40	0.285714	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	1213	0.5554029304029304	332	0.6747967479674797	169	0.46685082872928174	390	0.6818181818181818	322	0.42480211081794195	.	0.004	-2.307917	0.00240	.	.	ENSG00000101307	ENST00000279477;ENST00000381596	T	0.61510	0.1	2.61	0.574	0.17368	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00972	-1.085	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.42632	-0.9440	8	0.02654	T	1	.	5.5118	0.16884	0.0:0.5769:0.0:0.4231	.	42	Q5TFQ8	SIRBL_HUMAN	V	42	ENSP00000279477:I42V	ENSP00000279477:I42V	I	-	1	0	SIRPB1	1540312	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	0.670000	0.25157	-0.280000	0.09154	-2.568000	0.00172	ATA	T|0.465;C|0.535	0.535	strong		0.557	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
DNAH9	1770	hgsc.bcm.edu	37	17	11583245	11583245	+	Silent	SNP	G	G	A	rs8070788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11583245G>A	ENST00000262442.4	+	18	3593	c.3525G>A	c.(3523-3525)ttG>ttA	p.L1175L	DNAH9_ENST00000454412.2_Silent_p.L1175L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1175	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)		CTATTGAATTGCTGAAGACCT	0.398													G|||	56	0.0111821	0.0408	0.0029	5008	,	,		19789	0.0		0.0	False		,,,				2504	0.0				p.L1175L		Atlas-SNP	.											.	DNAH9	695	.	0			c.G3525A						PASS	.	G		163,4243	111.2+/-149.4	6,151,2046	115.0	110.0	112.0		3525	4.6	1.0	17	dbSNP_116	112	1,8599		0,1,4299	no	coding-synonymous	DNAH9	NM_001372.3		6,152,6345	AA,AG,GG		0.0116,3.6995,1.261		1175/4487	11583245	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon18			TGAATTGCTGAAG	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.3525G>A	17.37:g.11583245G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.988;A|0.012	0.012	strong		0.398	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
CSPG5	10675	hgsc.bcm.edu	37	3	47619025	47619025	+	Missense_Mutation	SNP	G	G	C	rs35863063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47619025G>C	ENST00000383738.2	-	2	2589	c.491C>G	c.(490-492)gCt>gGt	p.A164G	CSPG5_ENST00000456150.1_Missense_Mutation_p.A26G|CSPG5_ENST00000465441.1_5'Flank|CSPG5_ENST00000264723.4_Missense_Mutation_p.A164G	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	164					axon regeneration (GO:0031103)|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)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GAGTTCAGAAGCTGGGCTCAG	0.652													G|||	97	0.019369	0.0696	0.0072	5008	,	,		14217	0.0		0.0	False		,,,				2504	0.0				p.A164G		Atlas-SNP	.											.	CSPG5	46	.	0			c.C491G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	266,4134		10,246,1944	27.0	34.0	32.0		77,491,491,77,491	-4.3	0.0	3	dbSNP_126	32	1,8597		0,1,4298	yes	missense,missense,missense,missense,missense	CSPG5	NM_001206942.1,NM_001206943.1,NM_001206944.1,NM_001206945.1,NM_006574.3	60,60,60,60,60	10,247,6242	CC,CG,GG		0.0116,6.0455,2.0542	benign,benign,benign,benign,benign	26/402,164/567,164/478,26/429,164/540	47619025	267,12731	2200	4299	6499	SO:0001583	missense	10675	exon2			TCAGAAGCTGGGC	AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.491C>G	3.37:g.47619025G>C	ENSP00000373244:p.Ala164Gly	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_006574	Q71M39|Q71M40	Missense_Mutation	SNP	ENST00000383738.2	37	CCDS56253.1	38	0.0173992673992674	34	0.06910569105691057	4	0.011049723756906077	0	0.0	0	0.0	G	0.369	-0.934853	0.02340	0.060455	1.16E-4	ENSG00000114646	ENST00000456150;ENST00000383738;ENST00000264723	T;T;T	0.41400	1.0;1.0;1.0	3.92	-4.28	0.03732	Chondroitin sulphate attachment (1);	0.534137	0.14716	N	0.302660	T	0.00815	0.0027	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.17289	-1.0374	10	0.09590	T	0.72	-0.5678	0.8637	0.01198	0.2327:0.2926:0.2766:0.1981	rs35863063	164;164	O95196;O95196-2	CSPG5_HUMAN;.	G	26;164;164	ENSP00000392096:A26G;ENSP00000373244:A164G;ENSP00000264723:A164G	ENSP00000264723:A164G	A	-	2	0	CSPG5	47594029	0.002000	0.14202	0.001000	0.08648	0.453000	0.32348	-1.165000	0.03132	-0.599000	0.05798	0.579000	0.79373	GCT	G|0.981;C|0.019	0.019	strong		0.652	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574	
KMT2C	58508	hgsc.bcm.edu	37	7	151874498	151874498	+	Silent	SNP	C	C	T	rs10252263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151874498C>T	ENST00000262189.6	-	38	8258	c.8040G>A	c.(8038-8040)caG>caA	p.Q2680Q	KMT2C_ENST00000355193.2_Silent_p.Q2680Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2680					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)										CATCAGAAGGCTGGGTGGTTA	0.433													T|||	792	0.158147	0.3442	0.1052	5008	,	,		20439	0.1587		0.0119	False		,,,				2504	0.0941				p.Q2680Q		Atlas-SNP	.											.	MLL3	1564	.	0			c.G8040A						PASS	.	T		1367,3039	687.1+/-404.8	219,929,1055	77.0	76.0	76.0		8040	-1.9	0.0	7	dbSNP_119	76	148,8452	806.1+/-407.2	1,146,4153	no	coding-synonymous	MLL3	NM_170606.2		220,1075,5208	TT,TC,CC		1.7209,31.0259,11.6485		2680/4912	151874498	1515,11491	2203	4300	6503	SO:0001819	synonymous_variant	58508	exon38			AGAAGGCTGGGTG	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.8040G>A	7.37:g.151874498C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	166	60	0.361446	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1	307	0.14056776556776557	171	0.3475609756097561	35	0.09668508287292818	93	0.16258741258741258	8	0.010554089709762533	T	0.007	-1.998027	0.00435	0.310259	0.017209	ENSG00000055609	ENST00000360104	.	.	.	5.63	-1.92	0.07618	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.31308	-0.9948	3	.	.	.	.	13.3278	0.60469	0.0:0.6024:0.0:0.3976	rs10252263;rs58157666;rs10252263	.	.	.	T	186	.	.	A	-	1	0	MLL3	151505431	0.058000	0.20735	0.003000	0.11579	0.113000	0.19764	-0.070000	0.11523	-0.689000	0.05149	-1.859000	0.00561	GCC	C|0.865;T|0.135	0.135	strong		0.433	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
ZNF488	118738	hgsc.bcm.edu	37	10	48370747	48370747	+	Missense_Mutation	SNP	C	C	T	rs35618062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:48370747C>T	ENST00000395702.2	+	2	442	c.215C>T	c.(214-216)gCg>gTg	p.A72V	ZNF488_ENST00000494156.1_Intron|ZNF488_ENST00000586537.1_Intron			Q96MN9	ZN488_HUMAN	zinc finger protein 488	72			A -> V (in dbSNP:rs35618062).		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						GTGGGCAGTGCGGAGCTGGCA	0.701													c|||	444	0.0886581	0.0666	0.0764	5008	,	,		12714	0.0724		0.1183	False		,,,				2504	0.1135				p.A72V		Atlas-SNP	.											.	ZNF488	38	.	0			c.C215T						PASS	.	C	VAL/ALA	388,4012		22,344,1834	25.0	31.0	29.0		215	3.0	0.0	10	dbSNP_126	29	1252,7344		73,1106,3119	yes	missense	ZNF488	NM_153034.2	64	95,1450,4953	TT,TC,CC		14.5649,8.8182,12.6193	benign	72/341	48370747	1640,11356	2200	4298	6498	SO:0001583	missense	118738	exon2			GCAGTGCGGAGCT	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.215C>T	10.37:g.48370747C>T	ENSP00000379054:p.Ala72Val	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_153034	Q05CE0	Missense_Mutation	SNP	ENST00000395702.2	37	CCDS7217.1	189	0.08653846153846154	23	0.046747967479674794	29	0.08011049723756906	43	0.07517482517482517	94	0.12401055408970976	C	11.25	1.583609	0.28268	0.088182	0.145649	ENSG00000165388	ENST00000395702;ENST00000433077;ENST00000436850;ENST00000412534;ENST00000444585;ENST00000425196	T;T;T;T;T;T	0.58210	1.79;0.53;0.53;0.35;1.21;1.19	4.85	2.98	0.34508	.	1.107820	0.06849	U	0.796999	T	0.00328	0.0010	L	0.54323	1.7	0.58432	P	1.0000000000287557E-6	B	0.22683	0.073	B	0.14578	0.011	T	0.05099	-1.0906	9	0.49607	T	0.09	.	8.3626	0.32367	0.0:0.705:0.1375:0.1575	rs35618062	72	Q96MN9	ZN488_HUMAN	V	72	ENSP00000379054:A72V;ENSP00000401469:A72V;ENSP00000415923:A72V;ENSP00000406508:A72V;ENSP00000410326:A72V;ENSP00000412898:A72V	ENSP00000379054:A72V	A	+	2	0	ZNF488	47990753	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.140000	0.16056	0.201000	0.20466	-2.110000	0.00354	GCG	C|0.890;T|0.110	0.110	strong		0.701	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034	
CCDC186	55088	hgsc.bcm.edu	37	10	115910928	115910928	+	Missense_Mutation	SNP	G	G	T	rs7095762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	183	0	0		WXS	Illumina HiSeq	Phase_I	175	64	0.365714	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		
TSHZ1	10194	hgsc.bcm.edu	37	18	73000131	73000131	+	Silent	SNP	G	G	A	rs35073557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:73000131G>A	ENST00000580243.1	+	2	3117	c.2769G>A	c.(2767-2769)ccG>ccA	p.P923P	TSHZ1_ENST00000322038.5_Silent_p.P878P			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	923					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		ACTTGGGCCCGCAGGAGAGGG	0.592													G|||	69	0.013778	0.0477	0.0086	5008	,	,		19023	0.0		0.0	False		,,,				2504	0.0				p.P878P		Atlas-SNP	.											.	TSHZ1	104	.	0			c.G2634A						PASS	.	G		230,4176	136.5+/-172.5	6,218,1979	56.0	53.0	54.0		2634	-9.1	1.0	18	dbSNP_126	54	0,8600		0,0,4300	no	coding-synonymous	TSHZ1	NM_005786.4		6,218,6279	AA,AG,GG		0.0,5.2202,1.7684		878/1033	73000131	230,12776	2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			GGGCCCGCAGGAG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2769G>A	18.37:g.73000131G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				G|0.981;A|0.019	0.019	strong		0.592	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254184	39254184	+	Silent	SNP	T	T	C	rs7217470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39254184T>C	ENST00000333822.4	-	1	209	c.153A>G	c.(151-153)agA>agG	p.R51R		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	51	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						AGCACTGGGGTCTGCAGCAGC	0.652													T|||	241	0.048123	0.1732	0.0159	5008	,	,		15501	0.0		0.001	False		,,,				2504	0.0				p.R51R		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	0			c.A153G						scavenged	.	T		192,1192		14,164,514	14.0	17.0	16.0		153	-5.2	0.0	17	dbSNP_116	16	2,3172		0,2,1585	no	coding-synonymous	KRTAP4-8	NM_031960.2		14,166,2099	CC,CT,TT		0.063,13.8728,4.2563		51/186	39254184	194,4364	692	1587	2279	SO:0001819	synonymous_variant	728224	exon1			CTGGGGTCTGCAG	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.153A>G	17.37:g.39254184T>C		Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	146	83	0.568493	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			T|0.820;C|0.180	0.180	strong		0.652	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
ADAM18	8749	hgsc.bcm.edu	37	8	39537616	39537616	+	Silent	SNP	C	C	T	rs28454772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39537616C>T	ENST00000265707.5	+	16	1737	c.1692C>T	c.(1690-1692)gaC>gaT	p.D564D	ADAM18_ENST00000541111.1_5'UTR|ADAM18_ENST00000379866.1_Silent_p.D540D	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	564	Cys-rich.				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)			ATAAAAGTGACGCTCAATCTA	0.383													c|||	402	0.0802716	0.2723	0.0317	5008	,	,		19440	0.002		0.0099	False		,,,				2504	0.0082				p.D564D		Atlas-SNP	.											ADAM18,colon,carcinoma,0,1	ADAM18	169	1	0			c.C1692T						PASS	.	A		1031,3375	381.6+/-324.1	128,775,1300	113.0	101.0	105.0		1692	0.3	0.0	8	dbSNP_125	105	60,8540	35.9+/-90.5	0,60,4240	no	coding-synonymous	ADAM18	NM_014237.2		128,835,5540	TT,TC,CC		0.6977,23.3999,8.3884		564/740	39537616	1091,11915	2203	4300	6503	SO:0001819	synonymous_variant	8749	exon16			AAGTGACGCTCAA	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.1692C>T	8.37:g.39537616C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Silent	SNP	ENST00000265707.5	37	CCDS6113.1																																																																																			C|0.914;T|0.086	0.086	strong		0.383	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
MUC16	94025	hgsc.bcm.edu	37	19	9005719	9005719	+	Silent	SNP	A	A	G	rs4804375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9005719A>G	ENST00000397910.4	-	46	39890	c.39687T>C	c.(39685-39687)gaT>gaC	p.D13229D	MUC16_ENST00000380951.5_5'Flank	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13231	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						TGGCTACTCCATCCTTCTCAG	0.557													-|||	3672	0.733227	0.705	0.8098	5008	,	,		19779	0.7361		0.7187	False		,,,				2504	0.729				p.D13229D		Atlas-SNP	.											.	MUC16	4315	.	0			c.T39687C						PASS	.	A		2968,1080		1091,786,147	59.0	56.0	57.0		39687	-4.1	0.0	19	dbSNP_111	57	6228,2118		2340,1548,285	no	coding-synonymous	MUC16	NM_024690.2		3431,2334,432	GG,GA,AA		25.3774,26.6798,25.8028		13229/14508	9005719	9196,3198	2024	4173	6197	SO:0001819	synonymous_variant	94025	exon46			TACTCCATCCTTC	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.39687T>C	19.37:g.9005719A>G		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	205	204	0.995122	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	1626	0.7445054945054945	349	0.709349593495935	287	0.7928176795580111	461	0.8059440559440559	529	0.6978891820580475	.	3.132	-0.178229	0.06380	0.733202	0.746226	ENSG00000181143	ENST00000542240	.	.	.	3.51	-4.1	0.03940	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.28038	-1.0056	3	.	.	.	-0.7111	3.1733	0.06560	0.2639:0.0:0.2323:0.5038	rs4804375;rs35899515;rs4804375	.	.	.	T	69	.	.	M	-	2	0	MUC16	8866719	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.802000	0.04545	-0.691000	0.05135	-0.475000	0.04921	ATG	A|0.267;G|0.733	0.733	strong		0.557	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NDUFAF7	55471	hgsc.bcm.edu	37	2	37459308	37459308	+	Missense_Mutation	SNP	C	C	G	rs2714473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37459308C>G	ENST00000002125.4	+	2	155	c.115C>G	c.(115-117)Ccg>Gcg	p.P39A	CEBPZ_ENST00000234170.5_5'Flank|NDUFAF7_ENST00000483999.1_Intron|NDUFAF7_ENST00000336237.6_Missense_Mutation_p.P39A	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	39			P -> A (in dbSNP:rs2714473).		methylation (GO:0032259)|mitochondrial respiratory chain complex I assembly (GO:0032981)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|methyltransferase activity (GO:0008168)										TGCAGAAAACCCGGTGACGCC	0.463													C|||	361	0.0720847	0.2564	0.0303	5008	,	,		19737	0.0		0.001	False		,,,				2504	0.0				p.P39A		Atlas-SNP	.											.	.	.	.	0			c.C115G						PASS	.	C	ALA/PRO,ALA/PRO	982,3424	366.1+/-317.7	113,756,1334	110.0	105.0	107.0		115,115	2.7	0.0	2	dbSNP_100	107	14,8586	8.4+/-32.0	0,14,4286	yes	missense,missense	C2orf56	NM_001083946.1,NM_144736.4	27,27	113,770,5620	GG,GC,CC		0.1628,22.2878,7.658	benign,benign	39/344,39/442	37459308	996,12010	2203	4300	6503	SO:0001583	missense	55471	exon2			GAAAACCCGGTGA		CCDS1788.1, CCDS42673.1	2p22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000003509	ENSG00000003509		"""Mitochondrial respiratory chain complex assembly factors"""	28816	protein-coding gene	gene with protein product	"""mitochondrial dysfunction protein A homolog"""	615898	"""chromosome 2 open reading frame 56"""	C2orf56			Standard	NM_144736		Approved	PRO1853, MidA	uc002rqa.4	Q7L592	OTTHUMG00000128468	ENST00000002125.4:c.115C>G	2.37:g.37459308C>G	ENSP00000002125:p.Pro39Ala	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_001083946	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	37	CCDS1788.1	107	0.04899267399267399	98	0.1991869918699187	9	0.024861878453038673	0	0.0	0	0.0	C	7.698	0.692572	0.15039	0.222878	0.001628	ENSG00000003509	ENST00000002125;ENST00000336237	T;T	0.40225	1.05;1.04	5.51	2.68	0.31781	.	1.761130	0.02616	N	0.102632	T	0.00012	0.0000	N	0.05467	-0.045	0.80722	P	0.0	B;B;B;B	0.15930	0.001;0.009;0.015;0.0	B;B;B;B	0.12837	0.003;0.004;0.008;0.004	T	0.17745	-1.0359	9	0.08599	T	0.76	0.7393	3.0899	0.06290	0.2362:0.4978:0.1281:0.1379	rs2714473;rs52835713;rs2714473	39;39;39;39	E7EUC2;B4DQY3;Q7L592-2;Q7L592	.;.;.;MIDA_HUMAN	A	39	ENSP00000002125:P39A;ENSP00000337431:P39A	ENSP00000002125:P39A	P	+	1	0	C2orf56	37312812	0.000000	0.05858	0.006000	0.13384	0.962000	0.63368	0.599000	0.24089	0.268000	0.21939	-0.319000	0.08680	CCG	C|0.931;G|0.069	0.069	strong		0.463	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736	
CYBRD1	79901	hgsc.bcm.edu	37	2	172411273	172411273	+	Missense_Mutation	SNP	G	G	A	rs10455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:172411273G>A	ENST00000321348.4	+	4	995	c.797G>A	c.(796-798)aGt>aAt	p.S266N	CYBRD1_ENST00000409484.1_Missense_Mutation_p.S208N|CYBRD1_ENST00000375252.3_3'UTR	NM_024843.3	NP_079119.3	Q53TN4	CYBR1_HUMAN	cytochrome b reductase 1	266			S -> N (in dbSNP:rs10455). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		cellular iron ion homeostasis (GO:0006879)|response to iron ion (GO:0010039)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|oxidoreductase activity, oxidizing metal ions (GO:0016722)			endometrium(1)|kidney(1)|large_intestine(3)|liver(2)|lung(3)	10						GAGTTAAACAGTGAAGTAGCA	0.443													A|||	3421	0.683107	0.9327	0.6009	5008	,	,		21456	0.3958		0.666	False		,,,				2504	0.7178				p.S266N		Atlas-SNP	.											.	CYBRD1	16	.	0			c.G797A						PASS	.	A	,ASN/SER	3875,531	239.9+/-250.9	1704,467,32	74.0	71.0	72.0		,797	-3.3	0.3	2	dbSNP_52	72	5670,2930	458.4+/-364.6	1889,1892,519	yes	utr-3,missense	CYBRD1	NM_001127383.1,NM_024843.3	,46	3593,2359,551	AA,AG,GG		34.0698,12.0517,26.6108	,benign	,266/287	172411273	9545,3461	2203	4300	6503	SO:0001583	missense	79901	exon4			TAAACAGTGAAGT	AK027115	CCDS2244.1, CCDS46449.1, CCDS58736.1	2q31	2013-03-14			ENSG00000071967	ENSG00000071967		"""Cytochrome b genes"""	20797	protein-coding gene	gene with protein product	"""ferric-chelate reductase 3"", ""cytochrome b561 family, member A2"""	605745				11230685	Standard	NM_001127383		Approved	DCYTB, FLJ23462, FRRS3, CYB561A2	uc002ugy.4	Q53TN4	OTTHUMG00000132260	ENST00000321348.4:c.797G>A	2.37:g.172411273G>A	ENSP00000319141:p.Ser266Asn	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_024843	B2RE79|B4DWD7|Q6KC16|Q6KC17|Q6P147|Q6ZR51|Q9H0Q8|Q9H5G5	Missense_Mutation	SNP	ENST00000321348.4	37	CCDS2244.1	1417	0.6488095238095238	448	0.9105691056910569	233	0.643646408839779	215	0.3758741258741259	521	0.6873350923482849	A	5.162	0.215404	0.09810	0.879483	0.659302	ENSG00000071967	ENST00000409484;ENST00000321348	T;T	0.57595	0.39;0.4	5.16	-3.33	0.04958	.	0.669254	0.14511	N	0.315126	T	0.00012	0.0000	N	0.12961	0.28	0.29769	P	0.834894	B	0.02656	0.0	B	0.04013	0.001	T	0.45440	-0.9261	9	0.11794	T	0.64	0.0168	20.0263	0.97523	0.0846:0.0866:0.8288:0.0	rs10455;rs3172057;rs16859492;rs17846696;rs17859796;rs52827505;rs58982019;rs10455	266	Q53TN4	CYBR1_HUMAN	N	208;266	ENSP00000386739:S208N;ENSP00000319141:S266N	ENSP00000319141:S266N	S	+	2	0	CYBRD1	172119519	0.000000	0.05858	0.269000	0.24586	0.822000	0.46500	-1.717000	0.01876	-1.628000	0.01548	-0.972000	0.02603	AGT	A|0.688;C|0.004	0.688	strong		0.443	CYBRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255344.2	NM_024843	
ERC2	26059	hgsc.bcm.edu	37	3	56026204	56026204	+	Silent	SNP	C	C	T	rs61732592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:56026204C>T	ENST00000288221.6	-	11	2391	c.2136G>A	c.(2134-2136)gcG>gcA	p.A712A		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	712						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		GGTAGTAAGACGCCTCTTTAT	0.458													C|||	44	0.00878594	0.0325	0.0014	5008	,	,		19132	0.0		0.0	False		,,,				2504	0.0				p.A712A		Atlas-SNP	.											ERC2_ENST00000288221,caecum,carcinoma,-1,2	ERC2	221	2	0			c.G2136A						PASS	.	C		77,3739		2,73,1833	195.0	189.0	191.0		2136	1.6	1.0	3	dbSNP_129	191	1,8253		0,1,4126	no	coding-synonymous	ERC2	NM_015576.1		2,74,5959	TT,TC,CC		0.0121,2.0178,0.6462		712/958	56026204	78,11992	1908	4127	6035	SO:0001819	synonymous_variant	26059	exon11			GTAAGACGCCTCT	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2136G>A	3.37:g.56026204C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	231	118	0.510823	NM_015576	Q2T9F6|Q86TK4	Silent	SNP	ENST00000288221.6	37	CCDS46851.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	C	6.971	0.549089	0.13312	0.020178	1.21E-4	ENSG00000187672	ENST00000492584	.	.	.	5.47	1.64	0.23874	.	.	.	.	.	T	0.15652	0.0377	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06144	-1.0843	4	.	.	.	-11.4437	5.8817	0.18858	0.0:0.2089:0.3824:0.4087	.	.	.	.	H	363	.	.	R	-	2	0	ERC2	56001244	0.126000	0.22350	1.000000	0.80357	0.978000	0.69477	-0.482000	0.06544	0.039000	0.15632	-0.469000	0.05056	CGT	C|0.988;T|0.012	0.012	strong		0.458	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576	
GJB4	127534	hgsc.bcm.edu	37	1	35227466	35227466	+	Missense_Mutation	SNP	A	A	C	rs3738346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35227466A>C	ENST00000339480.1	+	2	981	c.611A>C	c.(610-612)gAa>gCa	p.E204A	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	204			E -> A (may be associated with deafness; dbSNP:rs3738346). {ECO:0000269|PubMed:11933201}.		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)				AACCTCAGTGAAGTCTTCTAC	0.587													A|||	543	0.108427	0.2481	0.1081	5008	,	,		22129	0.12		0.0099	False		,,,				2504	0.0092				p.E204A		Atlas-SNP	.											.	GJB4	51	.	0			c.A611C						PASS	.	A	ALA/GLU	831,3575	327.7+/-300.2	86,659,1458	73.0	67.0	69.0		611	5.8	1.0	1	dbSNP_107	69	35,8565	24.0+/-70.4	1,33,4266	yes	missense	GJB4	NM_153212.2	107	87,692,5724	CC,CA,AA		0.407,18.8606,6.6585	probably-damaging	204/267	35227466	866,12140	2203	4300	6503	SO:0001583	missense	127534	exon2			TCAGTGAAGTCTT		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.611A>C	1.37:g.35227466A>C	ENSP00000345868:p.Glu204Ala	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_153212	B3KQ82	Missense_Mutation	SNP	ENST00000339480.1	37	CCDS383.1	221	0.10119047619047619	99	0.20121951219512196	29	0.08011049723756906	84	0.14685314685314685	9	0.011873350923482849	A	27.7	4.858062	0.91433	0.188606	0.00407	ENSG00000189433	ENST00000339480	D	0.98120	-4.73	5.78	5.78	0.91487	Gap junction protein, cysteine-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.12817	0.0311	H	0.94847	3.59	0.20926	P	0.999823228	D	0.89917	1.0	D	0.97110	1.0	T	0.00000	-1.5297	9	0.87932	D	0	.	15.8436	0.78871	1.0:0.0:0.0:0.0	rs3738346;rs3738346	204	Q9NTQ9	CXB4_HUMAN	A	204	ENSP00000345868:E204A	ENSP00000345868:E204A	E	+	2	0	GJB4	35000053	1.000000	0.71417	0.972000	0.41901	0.995000	0.86356	6.246000	0.72405	2.222000	0.72286	0.529000	0.55759	GAA	A|0.915;C|0.085	0.085	strong		0.587	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
MYH6	4624	hgsc.bcm.edu	37	14	23874507	23874507	+	Silent	SNP	G	G	T	rs2277473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23874507G>T	ENST00000356287.3	-	4	456	c.427C>A	c.(427-429)Cgg>Agg	p.R143R	MYH6_ENST00000405093.3_Silent_p.R143R			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	143	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TTCTTGCCCCGGTAGGCGGCC	0.612													G|||	389	0.0776757	0.0129	0.085	5008	,	,		18374	0.0675		0.1044	False		,,,				2504	0.1431				p.R143R		Atlas-SNP	.											.	MYH6	274	.	0			c.C427A						PASS	.	G		110,4296		1,108,2094	108.0	110.0	110.0		427	1.2	1.0	14	dbSNP_100	110	942,7658		54,834,3412	no	coding-synonymous	MYH6	NM_002471.3		55,942,5506	TT,TG,GG		10.9535,2.4966,8.0886		143/1940	23874507	1052,11954	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon5			TGCCCCGGTAGGC	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.427C>A	14.37:g.23874507G>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	188	100	0.531915	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			A|0.000;C|0.007	.	strong		0.612	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
FAM193A	8603	hgsc.bcm.edu	37	4	2661342	2661342	+	Missense_Mutation	SNP	A	A	G	rs17164077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2661342A>G	ENST00000324666.5	+	7	925	c.574A>G	c.(574-576)Atg>Gtg	p.M192V	FAM193A_ENST00000505311.1_Missense_Mutation_p.M192V|FAM193A_ENST00000502458.1_Missense_Mutation_p.M216V|FAM193A_ENST00000382839.3_Missense_Mutation_p.M192V|FAM193A_ENST00000545951.1_Missense_Mutation_p.M192V	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	192			M -> V (in dbSNP:rs17164077). {ECO:0000269|PubMed:9734812}.							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						CATGAGGCACATGTTATCGTC	0.488													A|||	339	0.0676917	0.2443	0.0202	5008	,	,		20584	0.0		0.002	False		,,,				2504	0.0				p.M216V		Atlas-SNP	.											FAM193A,colon,carcinoma,0,1	FAM193A	103	1	0			c.A646G						PASS	.	A	VAL/MET	918,3488	354.9+/-312.8	96,726,1381	97.0	91.0	93.0		574	-2.5	0.0	4	dbSNP_123	93	7,8593	4.3+/-15.6	0,7,4293	yes	missense	FAM193A	NM_003704.3	21	96,733,5674	GG,GA,AA		0.0814,20.8352,7.1121	benign	192/1225	2661342	925,12081	2203	4300	6503	SO:0001583	missense	8603	exon8			AGGCACATGTTAT	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.574A>G	4.37:g.2661342A>G	ENSP00000324587:p.Met192Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_001256667	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	37	CCDS58875.1	109	0.04990842490842491	101	0.20528455284552846	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	A	12.59	1.983129	0.34942	0.208352	8.14E-4	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350	T;T;T;T;T	0.35048	1.41;1.82;1.4;1.43;1.33	5.82	-2.52	0.06346	.	0.074856	0.85682	N	0.000000	T	0.00039	0.0001	L	0.56769	1.78	0.23314	P	0.99792346	B;B;B;B;B	0.09022	0.001;0.001;0.002;0.001;0.001	B;B;B;B;B	0.06405	0.002;0.002;0.002;0.002;0.002	T	0.12863	-1.0531	9	0.56958	D	0.05	-7.4139	11.1394	0.48394	0.5558:0.0:0.4442:0.0	rs17164077	192;216;192;216;192	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	V	192;192;192;216;46	ENSP00000372290:M192V;ENSP00000324587:M192V;ENSP00000443617:M192V;ENSP00000427505:M216V;ENSP00000427260:M46V	ENSP00000324587:M192V	M	+	1	0	FAM193A	2631140	0.995000	0.38212	0.043000	0.18650	0.738000	0.42128	2.222000	0.42926	-0.672000	0.05266	0.459000	0.35465	ATG	A|0.937;G|0.063	0.063	strong		0.488	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704	
NOL11	25926	hgsc.bcm.edu	37	17	65735054	65735054	+	Silent	SNP	A	A	G	rs151002760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65735054A>G	ENST00000253247.4	+	15	1885	c.1770A>G	c.(1768-1770)gcA>gcG	p.A590A	SNORA38B_ENST00000363524.1_RNA|NOL11_ENST00000535137.1_Silent_p.A408A	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	590					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			TAAGTAATGCAATTCTTCATT	0.333													A|||	6	0.00119808	0.0045	0.0	5008	,	,		19461	0.0		0.0	False		,,,				2504	0.0				p.A590A		Atlas-SNP	.											.	NOL11	48	.	0			c.A1770G						PASS	.	A		45,4361	48.2+/-83.0	0,45,2158	165.0	150.0	155.0		1770	3.9	1.0	17	dbSNP_134	155	0,8600		0,0,4300	no	coding-synonymous	NOL11	NM_015462.3		0,45,6458	GG,GA,AA		0.0,1.0213,0.346		590/720	65735054	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	25926	exon15			TAATGCAATTCTT	AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.1770A>G	17.37:g.65735054A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_015462	B7Z5V9|Q7L5S1|Q9UG18	Silent	SNP	ENST00000253247.4	37	CCDS11671.1																																																																																			A|0.997;G|0.003	0.003	strong		0.333	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807938	18807938	+	Missense_Mutation	SNP	C	C	A	rs2992754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:18807938C>A	ENST00000400664.1	+	1	515	c.463C>A	c.(463-465)Cct>Act	p.P155T		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	155						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)		TAACCCTGACCCTCCCCATTT	0.652													C|||	1336	0.266773	0.174	0.2464	5008	,	,		17697	0.623		0.1252	False		,,,				2504	0.1851				p.P155T		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C463A						PASS	.	C	THR/PRO	797,3361		75,647,1357	32.0	38.0	36.0		463	5.4	0.0	1	dbSNP_101	36	1208,7214		80,1048,3083	yes	missense	KLHDC7A	NM_152375.2	38	155,1695,4440	AA,AC,CC		14.3434,19.1679,15.938	benign	155/778	18807938	2005,10575	2079	4211	6290	SO:0001583	missense	127707	exon1			CCTGACCCTCCCC	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.463C>A	1.37:g.18807938C>A	ENSP00000383505:p.Pro155Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	632	0.2893772893772894	95	0.19308943089430894	90	0.24861878453038674	355	0.6206293706293706	92	0.12137203166226913	C	15.27	2.784993	0.49997	0.191679	0.143434	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.74421	-0.84	5.4	5.4	0.78164	.	2.160560	0.03659	U	0.242324	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.44877	0.845	B	0.43478	0.421	T	0.33879	-0.9851	9	0.18710	T	0.47	.	16.2414	0.82409	0.0:1.0:0.0:0.0	rs2992754	155	Q5VTJ3	KLD7A_HUMAN	T	155;92	ENSP00000383505:P155T	ENSP00000383505:P155T	P	+	1	0	KLHDC7A	18680525	0.005000	0.15991	0.023000	0.16930	0.269000	0.26545	2.052000	0.41316	2.680000	0.91292	0.591000	0.81541	CCT	C|0.770;A|0.230	0.230	strong		0.652	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
ERMARD	55780	hgsc.bcm.edu	37	6	170155460	170155460	+	Missense_Mutation	SNP	C	C	A	rs61735516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170155460C>A	ENST00000366773.3	+	3	290	c.257C>A	c.(256-258)aCc>aAc	p.T86N	ERMARD_ENST00000392095.4_5'UTR|ERMARD_ENST00000366772.2_Missense_Mutation_p.T86N|ERMARD_ENST00000418781.3_Missense_Mutation_p.T86N|ERMARD_ENST00000588451.1_5'UTR	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	86					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TTATCTCTGACCAAGGGGCAA	0.458													C|||	45	0.00898562	0.0318	0.0043	5008	,	,		16421	0.0		0.0	False		,,,				2504	0.0				p.T86N		Atlas-SNP	.											.	C6orf70	63	.	0			c.C257A						PASS	.	C	ASN/THR	167,4239	111.2+/-149.4	1,165,2037	152.0	142.0	146.0		257	2.9	0.1	6	dbSNP_129	146	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C6orf70	NM_018341.1	65	1,167,6335	AA,AC,CC		0.0233,3.7903,1.2994	possibly-damaging	86/679	170155460	169,12837	2203	4300	6503	SO:0001583	missense	55780	exon3			CTCTGACCAAGGG	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"""chromosome 6 open reading frame 70"""	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.257C>A	6.37:g.170155460C>A	ENSP00000355735:p.Thr86Asn	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	297	149	0.501683	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	9.157	1.017709	0.19355	0.037903	2.33E-4	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781	T	0.48201	0.82	5.72	2.91	0.33838	.	0.384232	0.25050	N	0.033534	T	0.26846	0.0657	L	0.56769	1.78	0.35175	D	0.771965	B;B	0.20052	0.041;0.006	B;B	0.16722	0.016;0.007	T	0.07731	-1.0757	10	0.56958	D	0.05	.	11.748	0.51832	0.1294:0.6211:0.2494:0.0	rs61735516	86;86	Q5T6L9-2;Q5T6L9	.;CF070_HUMAN	N	86	ENSP00000355735:T86N	ENSP00000355734:T86N	T	+	2	0	C6orf70	169897385	0.815000	0.29118	0.085000	0.20634	0.078000	0.17371	0.775000	0.26689	0.308000	0.22923	-0.310000	0.09108	ACC	C|0.987;A|0.013	0.013	strong		0.458	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
AMPH	273	hgsc.bcm.edu	37	7	38431436	38431436	+	Silent	SNP	C	C	T	rs1058656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:38431436C>T	ENST00000356264.2	-	19	2006	c.1791G>A	c.(1789-1791)acG>acA	p.T597T	AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000325590.5_Silent_p.T555T|AMPH_ENST00000428293.2_Silent_p.T555T	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	597					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						GTGCAGAAGGCGTGGGCTGAG	0.612													C|||	896	0.178914	0.2322	0.2248	5008	,	,		13855	0.127		0.1759	False		,,,				2504	0.1309				p.T597T		Atlas-SNP	.											.	AMPH	157	.	0			c.G1791A						PASS	.	C	,	948,3458	360.1+/-315.1	99,750,1354	52.0	49.0	50.0		1791,1665	-1.8	0.0	7	dbSNP_86	50	1860,6740	330.3+/-319.2	197,1466,2637	no	coding-synonymous,coding-synonymous	AMPH	NM_001635.3,NM_139316.2	,	296,2216,3991	TT,TC,CC		21.6279,21.5161,21.59	,	597/696,555/654	38431436	2808,10198	2203	4300	6503	SO:0001819	synonymous_variant	273	exon19			AGAAGGCGTGGGC		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1791G>A	7.37:g.38431436C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	132	64	0.484848	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Silent	SNP	ENST00000356264.2	37	CCDS5456.1	395	0.18086080586080586	105	0.21341463414634146	74	0.20441988950276244	73	0.12762237762237763	143	0.18865435356200527	C	5.413	0.261367	0.10239	0.215161	0.216279	ENSG00000078053	ENST00000441628	.	.	.	5.34	-1.8	0.07907	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.29761	-1.0001	3	.	.	.	0.6258	3.0635	0.06207	0.106:0.3229:0.3573:0.2139	rs1058656;rs3199302;rs11553335;rs56947214	.	.	.	T	480	.	.	A	-	1	0	AMPH	38397961	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.475000	0.06599	-0.035000	0.13691	0.591000	0.81541	GCC	C|0.804;T|0.196	0.196	strong		0.612	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
ZSCAN22	342945	hgsc.bcm.edu	37	19	58850341	58850341	+	Silent	SNP	G	G	C	rs59054150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58850341G>C	ENST00000329665.4	+	3	1272	c.1125G>C	c.(1123-1125)acG>acC	p.T375T		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	375					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)		GGGTGCACACGGGGGAGCGGC	0.587													G|||	671	0.133986	0.208	0.1383	5008	,	,		19806	0.0982		0.0606	False		,,,				2504	0.1431				p.T375T		Atlas-SNP	.											.	ZSCAN22	47	.	0			c.G1125C						PASS	.	G		796,3610	313.0+/-292.9	58,680,1465	63.0	61.0	62.0		1125	-7.6	0.0	19	dbSNP_129	62	412,8188	125.8+/-184.4	13,386,3901	no	coding-synonymous	ZSCAN22	NM_181846.2		71,1066,5366	CC,CG,GG		4.7907,18.0663,9.288		375/492	58850341	1208,11798	2203	4300	6503	SO:0001819	synonymous_variant	342945	exon3			GCACACGGGGGAG	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.1125G>C	19.37:g.58850341G>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_181846	Q15922|Q7Z3L8	Silent	SNP	ENST00000329665.4	37	CCDS12975.1																																																																																			G|0.905;C|0.095	0.095	strong		0.587	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846	
SSPO	23145	hgsc.bcm.edu	37	7	149509079	149509079	+	RNA	SNP	T	T	C	rs73727633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149509079T>C	ENST00000378016.2	+	0	9625							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)			TCGGCACCGGTTCTGTGCCAG	0.682													T|||	330	0.0658946	0.211	0.0245	5008	,	,		14885	0.004		0.005	False		,,,				2504	0.0256				p.F3209L		Atlas-SNP	.											.	.	.	.	0			c.T9625C						PASS	.	T		726,3278		63,600,1339	29.0	33.0	32.0		9635	3.4	0.9	7	dbSNP_130	32	51,8273		0,51,4111	yes	coding-notMod3	SSPO	NM_198455.2		63,651,5450	CC,CT,TT		0.6127,18.1319,6.3027			149509079	777,11551	2002	4162	6164			23145	exon68			CACCGGTTCTGTG	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.149509079T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.957;C|0.043	0.043	strong		0.682	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
MYO7B	4648	hgsc.bcm.edu	37	2	128367556	128367556	+	Missense_Mutation	SNP	G	G	A	rs199654311	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128367556G>A	ENST00000409816.2	+	23	3189	c.3157G>A	c.(3157-3159)Ggt>Agt	p.G1053S	MYO7B_ENST00000428314.1_Missense_Mutation_p.G1053S|MYO7B_ENST00000389524.4_Missense_Mutation_p.G1053S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1053	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CAGGGAGCACGGTGCCCAGGT	0.642													G|||	13	0.00259585	0.0098	0.0	5008	,	,		17986	0.0		0.0	False		,,,				2504	0.0				p.G1053S		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3157A						PASS	.	G	SER/GLY	32,4284		0,32,2126	29.0	33.0	32.0		3157	-6.9	0.0	2		32	0,8518		0,0,4259	yes	missense	MYO7B	NM_001080527.1	56	0,32,6385	AA,AG,GG		0.0,0.7414,0.2493	benign	1053/2117	128367556	32,12802	2158	4259	6417	SO:0001583	missense	4648	exon24			GAGCACGGTGCCC		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3157G>A	2.37:g.128367556G>A	ENSP00000386461:p.Gly1053Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	8.095	0.775454	0.16051	0.007414	0.0	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.86164	-2.08;-2.08;-2.08	5.17	-6.92	0.01644	MyTH4 domain (2);	1.887620	0.02507	N	0.091055	T	0.52885	0.1762	N	0.00841	-1.15	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.64101	-0.6486	10	0.07030	T	0.85	.	10.025	0.42066	0.4891:0.1097:0.4012:0.0	.	1053	Q6PIF6	MYO7B_HUMAN	S	1053	ENSP00000374175:G1053S;ENSP00000415090:G1053S;ENSP00000386461:G1053S	ENSP00000374175:G1053S	G	+	1	0	MYO7B	128084026	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.438000	0.06905	-1.703000	0.01409	-0.140000	0.14226	GGT	G|0.999;A|0.001	0.001	strong		0.642	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
FBXW8	26259	hgsc.bcm.edu	37	12	117387465	117387465	+	Missense_Mutation	SNP	A	A	G	rs36021180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117387465A>G	ENST00000309909.5	+	4	713	c.631A>G	c.(631-633)Aca>Gca	p.T211A	FBXW8_ENST00000455858.2_Missense_Mutation_p.T145A			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	211			T -> A (in dbSNP:rs36021180).		cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|labyrinthine layer blood vessel development (GO:0060716)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|spongiotrophoblast layer development (GO:0060712)	Cul7-RING ubiquitin ligase complex (GO:0031467)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)				endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		TGTTCCTGACACAGTTTTGTG	0.517													G|||	64	0.0127796	0.0454	0.0029	5008	,	,		24536	0.0		0.002	False		,,,				2504	0.0				p.T211A		Atlas-SNP	.											.	FBXW8	53	.	0			c.A631G						PASS	.	G	ALA/THR,ALA/THR	214,4192	806.9+/-415.9	6,202,1995	331.0	238.0	270.0		433,631	4.1	0.3	12	dbSNP_126	270	33,8567	817.8+/-406.9	0,33,4267	yes	missense,missense	FBXW8	NM_012174.1,NM_153348.2	58,58	6,235,6262	GG,GA,AA		0.3837,4.857,1.8991	benign,benign	145/533,211/599	117387465	247,12759	2203	4300	6503	SO:0001583	missense	26259	exon4			CCTGACACAGTTT	AF176707	CCDS9182.1, CCDS44988.1	12q24.23	2013-01-09	2007-02-08	2003-06-13				"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13597	protein-coding gene	gene with protein product		609073	"""F-box only protein 29"", ""F-box and WD-40 domain protein 8"""	FBXO29		10531035, 10531037	Standard	NM_012174		Approved	FBX29, FBW6, FBW8	uc001twg.1	Q8N3Y1	OTTHUMG00000169329	ENST00000309909.5:c.631A>G	12.37:g.117387465A>G	ENSP00000310686:p.Thr211Ala	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	153	85	0.555556	NM_153348	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	37	CCDS9182.1	26	0.011904761904761904	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	0.527	-0.859427	0.02610	0.04857	0.003837	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.04454	3.62;3.62	5.05	4.09	0.47781	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.116916	0.53938	N	0.000041	T	0.00328	0.0010	N	0.02011	-0.69	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48670	-0.9015	10	0.14656	T	0.56	-3.3319	4.7195	0.12912	0.3949:0.0:0.6051:0.0	rs36021180;rs61748073	211;145	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	A	211;145;145	ENSP00000310686:T211A;ENSP00000389144:T145A	ENSP00000310686:T211A	T	+	1	0	FBXW8	115871848	0.960000	0.32886	0.276000	0.24689	0.163000	0.22366	4.018000	0.57174	1.377000	0.46286	-0.227000	0.12334	ACA	A|0.983;G|0.017	0.017	strong		0.517	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174	
ECE2	9718	hgsc.bcm.edu	37	3	183976108	183976108	+	Intron	SNP	T	T	C	rs902415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183976108T>C	ENST00000402825.3	+	2	480				ECE2_ENST00000324557.4_Silent_p.F171F|EIF2B5_ENST00000444495.1_Intron	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2						brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GAGGCCGGTTTATCTCAATGA	0.552													C|||	1629	0.32528	0.4818	0.2536	5008	,	,		19663	0.3393		0.2455	False		,,,				2504	0.2321				p.F171F		Atlas-SNP	.											.	ECE2	303	.	0			c.T513C						PASS	.	C	,	1812,2594	639.0+/-397.0	394,1024,785	146.0	138.0	141.0		,513	3.2	1.0	3	dbSNP_86	141	1974,6626	723.8+/-406.5	226,1522,2552	no	intron,coding-synonymous	ECE2	NM_014693.3,NM_032331.3	,	620,2546,3337	CC,CT,TT		22.9535,41.1257,29.1096	,	,171/256	183976108	3786,9220	2203	4300	6503	SO:0001627	intron_variant	9718	exon3			CCGGTTTATCTCA	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.480+564T>C	3.37:g.183976108T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	176	81	0.460227	NM_032331	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Silent	SNP	ENST00000402825.3	37	CCDS3256.2																																																																																			T|0.697;C|0.303	0.303	strong		0.552	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
PACS2	23241	hgsc.bcm.edu	37	14	105821457	105821457	+	Silent	SNP	G	G	A	rs61738367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105821457G>A	ENST00000325438.8	+	4	870	c.366G>A	c.(364-366)aaG>aaA	p.K122K	PACS2_ENST00000458164.2_Silent_p.K122K|PACS2_ENST00000447393.1_Silent_p.K122K|PACS2_ENST00000430725.2_Silent_p.K55K|PACS2_ENST00000547217.1_Silent_p.K92K			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	122					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)		AGCGCTACAAGAACAGAACCA	0.602													G|||	56	0.0111821	0.0416	0.0	5008	,	,		19971	0.0		0.001	False		,,,				2504	0.0				p.K122K		Atlas-SNP	.											.	PACS2	75	.	0			c.G366A						PASS	.	G	,	200,4206	123.3+/-160.7	7,186,2010	78.0	64.0	69.0		366,366	-3.3	0.9	14	dbSNP_129	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PACS2	NM_001100913.2,NM_015197.3	,	7,187,6309	AA,AG,GG		0.0116,4.5393,1.5454	,	122/894,122/890	105821457	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	23241	exon4			CTACAAGAACAGA	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.366G>A	14.37:g.105821457G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Silent	SNP	ENST00000325438.8	37	CCDS32168.1																																																																																			G|0.986;A|0.014	0.014	strong		0.602	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355	
MUC4	4585	hgsc.bcm.edu	37	3	195515199	195515199	+	Silent	SNP	A	A	C	rs201720234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515199A>C	ENST00000463781.3	-	2	3711	c.3252T>G	c.(3250-3252)ggT>ggG	p.G1084G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.G1084G	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	516					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)		GGGTGGTGTCACCTGTGGATG	0.567													.|||	158	0.0315495	0.1082	0.013	5008	,	,		18430	0.001		0.004	False		,,,				2504	0.001				p.G1084G		Atlas-SNP	.											.	MUC4	1505	.	0			c.T3252G						PASS	.																																			SO:0001819	synonymous_variant	4585	exon2			GGTGTCACCTGTG	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.3252T>G	3.37:g.195515199A>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	384	45	0.117188	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|0.994;C|0.006	0.006	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TM9SF3	56889	hgsc.bcm.edu	37	10	98282083	98282083	+	Silent	SNP	C	C	T	rs35359279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98282083C>T	ENST00000371142.4	-	15	1923	c.1707G>A	c.(1705-1707)gcG>gcA	p.A569A		NM_020123.3	NP_064508.3	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3	569						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)	15		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		TGTAACCAATCGCTCCTGCAA	0.338													C|||	47	0.00938498	0.0356	0.0	5008	,	,		18641	0.0		0.0	False		,,,				2504	0.0				p.A569A		Atlas-SNP	.											.	TM9SF3	45	.	0			c.G1707A						PASS	.	C		106,4300	82.9+/-121.4	3,100,2100	98.0	101.0	100.0		1707	-2.1	1.0	10	dbSNP_126	100	3,8595		0,3,4296	no	coding-synonymous	TM9SF3	NM_020123.3		3,103,6396	TT,TC,CC		0.0349,2.4058,0.8382		569/590	98282083	109,12895	2203	4299	6502	SO:0001819	synonymous_variant	56889	exon15			ACCAATCGCTCCT	AF160213, AF269150	CCDS7450.1	10q24.2	2006-04-12			ENSG00000077147	ENSG00000077147			21529	protein-coding gene	gene with protein product						11530251, 11595169	Standard	NM_020123		Approved	SMBP	uc001kmm.4	Q9HD45	OTTHUMG00000018834	ENST00000371142.4:c.1707G>A	10.37:g.98282083C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	95	35	0.368421	NM_020123	Q5TB57|Q6UWE7|Q9NWL8|Q9P0G9|Q9UHW8	Silent	SNP	ENST00000371142.4	37	CCDS7450.1																																																																																			C|0.990;T|0.010	0.010	strong		0.338	TM9SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049610.2	NM_020123	
DNAH10	196385	hgsc.bcm.edu	37	12	124387574	124387574	+	Silent	SNP	G	G	A	rs58411567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124387574G>A	ENST00000409039.3	+	56	9400	c.9375G>A	c.(9373-9375)gaG>gaA	p.E3125E		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3125	Stalk. {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)		CCGAGGCCGAGACGACCCTGG	0.567													G|||	1681	0.335663	0.5318	0.2925	5008	,	,		19920	0.2788		0.2495	False		,,,				2504	0.2485				p.E3125E		Atlas-SNP	.											.	DNAH10	888	.	0			c.G9375A						PASS	.	G		1934,2272		429,1076,598	58.0	69.0	65.0		9375	3.1	0.8	12	dbSNP_129	65	1868,6574		218,1432,2571	no	coding-synonymous	DNAH10	NM_207437.3		647,2508,3169	AA,AG,GG		22.1275,45.9819,30.0601		3125/4472	124387574	3802,8846	2103	4221	6324	SO:0001819	synonymous_variant	196385	exon56			GGCCGAGACGACC	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.9375G>A	12.37:g.124387574G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	79	45	0.56962	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			G|0.697;A|0.303	0.303	strong		0.567	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
TBC1D9B	23061	hgsc.bcm.edu	37	5	179297262	179297262	+	Silent	SNP	T	T	C	rs407437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179297262T>C	ENST00000356834.3	-	16	2755	c.2718A>G	c.(2716-2718)acA>acG	p.T906T	TBC1D9B_ENST00000519746.1_Silent_p.T82T|TBC1D9B_ENST00000355235.3_Silent_p.T906T|TBC1D9B_ENST00000444477.2_Silent_p.T64T	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	906	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.					integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CACTCATCCCTGTCACGAACT	0.602													C|||	622	0.124201	0.444	0.0432	5008	,	,		19694	0.0		0.005	False		,,,				2504	0.0				p.T906T		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.A2718G						PASS	.	C	,	1539,2867	670.9+/-402.4	283,973,947	104.0	111.0	109.0		2718,2718	-10.3	0.5	5	dbSNP_80	109	15,8585	818.5+/-406.9	0,15,4285	no	coding-synonymous,coding-synonymous	TBC1D9B	NM_015043.3,NM_198868.2	,	283,988,5232	CC,CT,TT		0.1744,34.9296,11.9483	,	906/1234,906/1251	179297262	1554,11452	2203	4300	6503	SO:0001819	synonymous_variant	23061	exon16			CATCCCTGTCACG	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"""EF-hand domain containing"""	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.2718A>G	5.37:g.179297262T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	37	CCDS43408.1																																																																																			T|0.882;C|0.118	0.118	strong		0.602	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043	
MIER2	54531	hgsc.bcm.edu	37	19	334474	334474	+	Silent	SNP	T	T	G	rs11084956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:334474T>G	ENST00000264819.4	-	3	179	c.169A>C	c.(169-171)Agg>Cgg	p.R57R	MIER2_ENST00000592722.1_5'UTR	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	57					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)		CACTCCCCCCTAACACTGTAG	0.597													G|||	941	0.187899	0.466	0.2147	5008	,	,		18155	0.0248		0.1143	False		,,,				2504	0.0368				p.R57R		Atlas-SNP	.											.	MIER2	51	.	0			c.A169C						PASS	.	G		1732,2674		336,1060,807	138.0	117.0	124.0		169	3.6	0.0	19	dbSNP_120	124	814,7786		38,738,3524	no	coding-synonymous	MIER2	NM_017550.1		374,1798,4331	GG,GT,TT		9.4651,39.31,19.5756		57/546	334474	2546,10460	2203	4300	6503	SO:0001819	synonymous_variant	54531	exon3			CCCCCCTAACACT	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.169A>C	19.37:g.334474T>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_017550	Q9ULM7	Silent	SNP	ENST00000264819.4	37	CCDS32855.1																																																																																			T|0.793;G|0.207	0.207	strong		0.597	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843	
ARMC9	80210	hgsc.bcm.edu	37	2	232072912	232072912	+	Silent	SNP	T	T	C	rs11558174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:232072912T>C	ENST00000349938.4	+	3	318	c.124T>C	c.(124-126)Ttg>Ctg	p.L42L	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	42						extracellular vesicular exosome (GO:0070062)		p.L42L(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)		AGGAAAACCATTGTGTAAAAC	0.299													T|||	1242	0.248003	0.3563	0.2349	5008	,	,		18620	0.1409		0.2853	False		,,,				2504	0.183				p.L42L		Atlas-SNP	.											ARMC9_ENST00000359743,NS,carcinoma,0,2	ARMC9	129	2	2	Substitution - coding silent(2)	stomach(2)	c.T124C						PASS	.	T		1601,2803	494.6+/-363.0	285,1031,886	80.0	81.0	80.0		124	-2.8	0.0	2	dbSNP_120	80	2199,6401	374.2+/-337.3	281,1637,2382	no	coding-synonymous	ARMC9	NM_025139.3		566,2668,3268	CC,CT,TT		25.5698,36.3533,29.2218		42/666	232072912	3800,9204	2202	4300	6502	SO:0001819	synonymous_variant	80210	exon3			AAACCATTGTGTA	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.124T>C	2.37:g.232072912T>C		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	227	109	0.480176	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Silent	SNP	ENST00000349938.4	37	CCDS2484.1																																																																																			T|0.713;C|0.287	0.287	strong		0.299	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139	
DLC1	10395	hgsc.bcm.edu	37	8	13356807	13356807	+	Silent	SNP	C	C	T	rs62637614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:13356807C>T	ENST00000276297.4	-	2	1183	c.774G>A	c.(772-774)ttG>ttA	p.L258L	DLC1_ENST00000316609.5_Silent_p.L258L|DLC1_ENST00000511869.1_Silent_p.L258L	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	258					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						AAGGAGTATCCAAGAACTCAT	0.438													C|||	142	0.0283546	0.0507	0.0331	5008	,	,		16429	0.0		0.0239	False		,,,				2504	0.0286				p.L258L		Atlas-SNP	.											.	DLC1	411	.	0			c.G774A						PASS	.	C	,	234,4172	138.0+/-173.8	2,230,1971	156.0	159.0	158.0		774,774	-2.2	0.0	8	dbSNP_129	158	179,8421	80.4+/-143.0	1,177,4122	no	coding-synonymous,coding-synonymous	DLC1	NM_024767.3,NM_182643.2	,	3,407,6093	TT,TC,CC		2.0814,5.3109,3.1755	,	258/464,258/1529	13356807	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	10395	exon2			AGTATCCAAGAAC	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.774G>A	8.37:g.13356807C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	113	49	0.433628	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																			C|0.968;T|0.032	0.032	strong		0.438	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
PALD1	27143	hgsc.bcm.edu	37	10	72324139	72324139	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72324139C>T	ENST00000263563.6	+	19	2550	c.2282C>T	c.(2281-2283)gCg>gTg	p.A761V		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	761						cytosol (GO:0005829)											GCGAAAGAGGCGCAAGAAATG	0.617																																					p.A761V		Atlas-SNP	.											KIAA1274,NS,carcinoma,-1,1	.	.	1	0			c.C2282T						PASS	.						77.0	75.0	76.0					10																	72324139		2203	4300	6503	SO:0001583	missense	27143	exon19			AAGAGGCGCAAGA	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.2282C>T	10.37:g.72324139C>T	ENSP00000263563:p.Ala761Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	.	.	.	.	.	.	.	.	.	.	c	10.63	1.404595	0.25378	.	.	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.29917	1.55	4.9	2.42	0.29668	.	0.426837	0.24803	N	0.035474	T	0.24547	0.0595	L	0.47716	1.5	0.26423	N	0.976068	B	0.18610	0.029	B	0.12156	0.007	T	0.16158	-1.0412	10	0.40728	T	0.16	-12.6907	8.4465	0.32845	0.3575:0.52:0.0:0.1225	.	761	Q9ULE6	PALD_HUMAN	V	761;737	ENSP00000263563:A761V	ENSP00000263563:A761V	A	+	2	0	KIAA1274	71994145	1.000000	0.71417	0.147000	0.22382	0.613000	0.37349	1.533000	0.36040	0.168000	0.19655	-0.410000	0.06199	GCG	.	.	none		0.617	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
ZNF135	7694	hgsc.bcm.edu	37	19	58579464	58579464	+	Missense_Mutation	SNP	A	A	G	rs73938600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58579464A>G	ENST00000313434.5	+	5	1713	c.1612A>G	c.(1612-1614)Att>Gtt	p.I538V	ZNF135_ENST00000506786.1_Missense_Mutation_p.I496V|ZNF135_ENST00000359978.6_Intron|ZNF135_ENST00000439855.2_Missense_Mutation_p.I538V|RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000511556.1_Missense_Mutation_p.I550V|ZNF135_ENST00000401053.4_Missense_Mutation_p.I562V	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	538					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		TGCTCCCCTCATTCAGCATCA	0.542													A|||	23	0.00459265	0.0159	0.0014	5008	,	,		19819	0.0		0.001	False		,,,				2504	0.0				p.I562V		Atlas-SNP	.											.	ZNF135	159	.	0			c.A1684G						PASS	.	A	,,VAL/ILE,VAL/ILE	74,4332	66.4+/-103.9	2,70,2131	80.0	76.0	77.0		,,1648,1684	3.4	1.0	19	dbSNP_130	77	2,8592	2.2+/-6.3	0,2,4295	no	utr-3,intron,missense,missense	ZNF135	NM_001164529.1,NM_001164530.1,NM_003436.3,NM_007134.1	,,29,29	2,72,6426	GG,GA,AA		0.0233,1.6795,0.5846	,,benign,benign	,,550/671,562/683	58579464	76,12924	2203	4297	6500	SO:0001583	missense	7694	exon4			CCCCTCATTCAGC	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"""Zinc fingers, C2H2-type"", ""-"""	12919	protein-coding gene	gene with protein product		604077	"""zinc finger protein 61"", ""zinc finger protein 135 (clone pHZ-17)"""	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.1612A>G	19.37:g.58579464A>G	ENSP00000321406:p.Ile538Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	37		8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	A	3.025	-0.200904	0.06219	0.016795	2.33E-4	ENSG00000176293	ENST00000401053;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	T;T;T;T;T	0.35605	4.1;4.1;4.1;4.1;1.3	3.37	3.37	0.38596	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13030	0.0316	N	0.11364	0.135	0.09310	N	1	P;P	0.43287	0.591;0.802	B;P	0.48873	0.437;0.593	T	0.04650	-1.0936	9	0.23891	T	0.37	.	6.8432	0.23975	0.8839:0.0:0.1161:0.0	.	550;538	E9PEV2;P52742	.;ZN135_HUMAN	V	562;538;538;550;496	ENSP00000441410:I562V;ENSP00000444828:I538V;ENSP00000321406:I538V;ENSP00000422074:I550V;ENSP00000427691:I496V	ENSP00000321406:I538V	I	+	1	0	ZNF135	63271276	0.000000	0.05858	1.000000	0.80357	0.831000	0.47069	-1.095000	0.03356	1.545000	0.49373	0.455000	0.32223	ATT	.	.	weak		0.542	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436	
COLEC11	78989	hgsc.bcm.edu	37	2	3691548	3691548	+	Missense_Mutation	SNP	A	A	G	rs7567833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:3691548A>G	ENST00000349077.4	+	7	759	c.656A>G	c.(655-657)cAc>cGc	p.H219R	COLEC11_ENST00000236693.7_Missense_Mutation_p.H216R|COLEC11_ENST00000402922.1_Missense_Mutation_p.H169R|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000402794.1_Missense_Mutation_p.H169R|COLEC11_ENST00000404205.1_Missense_Mutation_p.H145R|COLEC11_ENST00000418971.2_Missense_Mutation_p.H233R|COLEC11_ENST00000403096.3_Missense_Mutation_p.H193R|COLEC11_ENST00000382062.2_Missense_Mutation_p.H195R	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	219	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		H -> R (in dbSNP:rs7567833). {ECO:0000269|PubMed:14702039}.		developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		TACTCTGACCACTCCCCCATG	0.637													G|||	1223	0.244209	0.7436	0.0908	5008	,	,		18858	0.0218		0.0348	False		,,,				2504	0.1227				p.H233R		Atlas-SNP	.											.	COLEC11	93	.	0			c.A698G						PASS	.	G	ARG/HIS,ARG/HIS	2910,1496	476.1+/-357.5	979,952,272	63.0	75.0	71.0		656,647	5.3	1.0	2	dbSNP_116	71	279,8321	807.0+/-407.2	5,269,4026	yes	missense,missense	COLEC11	NM_024027.3,NM_199235.1	29,29	984,1221,4298	GG,GA,AA		3.2442,33.9537,24.5195	benign,benign	219/272,216/269	3691548	3189,9817	2203	4300	6503	SO:0001583	missense	78989	exon8			CTGACCACTCCCC	BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"""Collectins"""	17213	protein-coding gene	gene with protein product	"""Collectin K1"""	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.656A>G	2.37:g.3691548A>G	ENSP00000339168:p.His219Arg	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001255985	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Missense_Mutation	SNP	ENST00000349077.4	37	CCDS1649.1	419	0.19184981684981686	364	0.7398373983739838	31	0.0856353591160221	6	0.01048951048951049	18	0.023746701846965697	G	5.512	0.279351	0.10458	0.660463	0.032442	ENSG00000118004	ENST00000382062;ENST00000236693;ENST00000349077;ENST00000418971;ENST00000403096;ENST00000402794;ENST00000404205;ENST00000402922	T;T;T;T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34;2.34;2.34;2.34	5.3	5.3	0.74995	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.273464	0.41396	N	0.000893	T	0.00012	0.0000	N	0.00621	-1.32	0.58432	P	5.000000000032756E-6	B;B;B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B;B;B;B	0.06405	0.0;0.001;0.001;0.0;0.001;0.0;0.001;0.001;0.002	T	0.13872	-1.0493	9	0.41790	T	0.15	-15.7946	13.2666	0.60137	0.0767:0.0:0.9233:0.0	rs7567833;rs60526563;rs7567833	145;169;169;193;171;195;195;219;216	Q9BWP8-8;Q9BWP8-7;Q9BWP8-6;Q9BWP8-4;Q9BWP8-5;Q9BWP8-3;Q9BWP8-2;Q9BWP8;Q9BWP8-9	.;.;.;.;.;.;.;COL11_HUMAN;.	R	195;216;219;233;193;169;145;169	ENSP00000371494:H195R;ENSP00000236693:H216R;ENSP00000339168:H219R;ENSP00000411770:H233R;ENSP00000385130:H193R;ENSP00000384882:H169R;ENSP00000385827:H145R;ENSP00000385653:H169R	ENSP00000236693:H216R	H	+	2	0	COLEC11	3669423	1.000000	0.71417	0.992000	0.48379	0.002000	0.02628	4.613000	0.61176	1.240000	0.43803	-0.349000	0.07799	CAC	A|0.765;G|0.235	0.235	strong		0.637	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027	
SYTL4	94121	hgsc.bcm.edu	37	X	99955925	99955925	+	Silent	SNP	T	T	C	rs16983588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:99955925T>C	ENST00000372989.1	-	7	838	c.507A>G	c.(505-507)agA>agG	p.R169R	SYTL4_ENST00000372981.1_Silent_p.R169R|SYTL4_ENST00000454200.2_Silent_p.R169R|SYTL4_ENST00000263033.5_Silent_p.R169R|SYTL4_ENST00000455616.1_Silent_p.R169R|SYTL4_ENST00000276141.6_Silent_p.R169R	NM_080737.2	NP_542775.2	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	169					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|multivesicular body sorting pathway (GO:0071985)|negative regulation of insulin secretion (GO:0046676)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	neurexin family protein binding (GO:0042043)|phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(2)	27					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GAATGATCTTTCTTCCTGGCC	0.408													t|||	572	0.151523	0.4077	0.0432	3775	,	,		13506	0.0		0.002	False		,,,				2504	0.001				p.R169R		Atlas-SNP	.											.	SYTL4	72	.	0			c.A507G						PASS	.		,,	1688,2147		321,777,269,534,302	142.0	127.0	133.0		507,507,507	3.4	1.0	X	dbSNP_123	133	24,6704		0,19,5,2409,1867	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL4	NM_001129896.2,NM_001174068.1,NM_080737.2	,,	321,796,274,2943,2169	CC,CT,C,TT,T		0.3567,44.0156,16.2075	,,	169/672,169/672,169/672	99955925	1712,8851	2203	4300	6503	SO:0001819	synonymous_variant	94121	exon6			GATCTTTCTTCCT		CCDS14472.1	Xq21.33	2008-07-31	2008-07-31		ENSG00000102362	ENSG00000102362			15588	protein-coding gene	gene with protein product	"""granuphilin-a"", ""exophilin-2"""	300723					Standard	NM_080737		Approved		uc010nnc.3	Q96C24	OTTHUMG00000022004	ENST00000372989.1:c.507A>G	X.37:g.99955925T>C		Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	269	269	1	NM_001129896	Q5H9J3|Q5JPG8|Q8N9P4|Q9H4R0|Q9H4R1	Silent	SNP	ENST00000372989.1	37	CCDS14472.1																																																																																			0|0.004;C|0.166	0.166	strong		0.408	SYTL4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057488.1	NM_080737	
XIRP1	165904	hgsc.bcm.edu	37	3	39225549	39225549	+	Silent	SNP	G	G	C	rs36091974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39225549G>C	ENST00000340369.3	-	2	5616	c.5388C>G	c.(5386-5388)ccC>ccG	p.P1796P	XIRP1_ENST00000421646.1_Silent_p.P479P|XIRP1_ENST00000396251.1_3'UTR	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1796	Interaction with FLNC.				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)		CTGGGTTCCTGGGTGGCTCTG	0.602													G|||	121	0.0241613	0.0862	0.0086	5008	,	,		20643	0.0		0.001	False		,,,				2504	0.0				p.P1796P		Atlas-SNP	.											.	XIRP1	173	.	0			c.C5388G						PASS	.	G	,	362,4044	186.4+/-213.3	17,328,1858	126.0	132.0	130.0		,5388	2.4	0.0	3	dbSNP_126	130	3,8597	3.0+/-9.4	0,3,4297	yes	utr-3,coding-synonymous	XIRP1	NM_001198621.1,NM_194293.2	,	17,331,6155	CC,CG,GG		0.0349,8.2161,2.8064	,	,1796/1844	39225549	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	165904	exon2			GTTCCTGGGTGGC	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.5388C>G	3.37:g.39225549G>C		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	214	107	0.5	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Silent	SNP	ENST00000340369.3	37	CCDS2683.1																																																																																			G|0.973;C|0.027	0.027	strong		0.602	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
TXLNB	167838	hgsc.bcm.edu	37	6	139563914	139563914	+	Missense_Mutation	SNP	C	C	G	rs9495391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139563914C>G	ENST00000358430.3	-	10	2036	c.1804G>C	c.(1804-1806)Gcg>Ccg	p.A602P	RP1-225E12.3_ENST00000585874.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	602			A -> P (in dbSNP:rs9495391). {ECO:0000269|PubMed:17974005}.			cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		TTCCAGGACGCCTGATCAGCC	0.612													G|||	2423	0.483826	0.9062	0.3588	5008	,	,		18081	0.2351		0.3638	False		,,,				2504	0.3814				p.A602P		Atlas-SNP	.											TXLNB,caecum,carcinoma,+2,2	TXLNB	96	2	0			c.G1804C						PASS	.	G	PRO/ALA	3565,841	325.9+/-299.3	1449,667,87	62.0	72.0	69.0		1804	2.6	0.0	6	dbSNP_119	69	3162,5438	651.3+/-400.8	566,2030,1704	yes	missense	TXLNB	NM_153235.3	27	2015,2697,1791	GG,GC,CC		36.7674,19.0876,48.2777	benign	602/685	139563914	6727,6279	2203	4300	6503	SO:0001583	missense	167838	exon10			AGGACGCCTGATC		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"""chromosome 6 open reading frame 198"""	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.1804G>C	6.37:g.139563914C>G	ENSP00000351206:p.Ala602Pro	Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Missense_Mutation	SNP	ENST00000358430.3	37	CCDS34545.1	929	0.42536630036630035	406	0.8252032520325203	129	0.356353591160221	130	0.22727272727272727	264	0.3482849604221636	G	10.58	1.391441	0.25118	0.809124	0.367674	ENSG00000164440	ENST00000358430	T	0.14516	2.5	3.49	2.59	0.31030	.	1.531680	0.03515	N	0.220216	T	0.02267	0.0070	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39121	-0.9629	8	.	.	.	-2.1905	9.6776	0.40050	0.0:0.4166:0.5834:0.0	rs9495391;rs52790733;rs57864218;rs9495391	602	Q8N3L3	TXLNB_HUMAN	P	602	ENSP00000351206:A602P	.	A	-	1	0	TXLNB	139605607	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	-0.219000	0.09228	0.291000	0.22468	-0.120000	0.15030	GCG	C|0.511;G|0.489	0.489	strong		0.612	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235	
ATL1	51062	hgsc.bcm.edu	37	14	51054598	51054598	+	Silent	SNP	A	A	G	rs35014209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:51054598A>G	ENST00000358385.6	+	2	325	c.84A>G	c.(82-84)ccA>ccG	p.P28P	ATL1_ENST00000357032.3_Silent_p.P28P|ATL1_ENST00000354525.4_Silent_p.P28P|ATL1_ENST00000556478.2_3'UTR|ATL1_ENST00000441560.2_Silent_p.P28P	NM_015915.4	NP_056999.2	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	28					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)			central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						AGGAGGAGCCAGTGAAAAAGG	0.453													A|||	822	0.164137	0.3623	0.1225	5008	,	,		20809	0.0655		0.1282	False		,,,				2504	0.0644				p.P28P		Atlas-SNP	.											.	ATL1	46	.	0			c.A84G						PASS	.	A	,,	1384,3022	456.1+/-351.2	209,966,1028	109.0	105.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	84,84,84	-1.2	1.0	14	dbSNP_126	107	1236,7364	247.4+/-275.4	96,1044,3160	no	coding-synonymous,coding-synonymous,coding-synonymous	ATL1	NM_001127713.1,NM_015915.4,NM_181598.3	,,	305,2010,4188	GG,GA,AA		14.3721,31.4117,20.1445	,,	28/554,28/559,28/554	51054598	2620,10386	2203	4300	6503	SO:0001819	synonymous_variant	51062	exon2			GGAGCCAGTGAAA	AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513			11231	protein-coding gene	gene with protein product	"""atlastin"""	606439	"""spastic paraplegia 3A (autosomal dominant)"""	SPG3, SPG3A		8252041, 7825576	Standard	NM_015915		Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000358385.6:c.84A>G	14.37:g.51054598A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_015915	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Silent	SNP	ENST00000358385.6	37	CCDS9700.1																																																																																			A|0.807;G|0.193	0.193	strong		0.453	ATL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276884.2		
MKI67	4288	hgsc.bcm.edu	37	10	129913960	129913960	+	Missense_Mutation	SNP	A	A	T	rs7095325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129913960A>T	ENST00000368654.3	-	7	1087	c.712T>A	c.(712-714)Tgg>Agg	p.W238R	MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	238			W -> R (in dbSNP:rs7095325).		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)				TAAAGCTTCCAAAAGGGAGAT	0.348													T|||	1269	0.253395	0.3026	0.2522	5008	,	,		21557	0.247		0.2455	False		,,,				2504	0.2025				p.W238R		Atlas-SNP	.											.	MKI67	363	.	0			c.T712A						PASS	.	T	,ARG/TRP	1385,3021	687.4+/-404.8	218,949,1036	70.0	68.0	69.0		,712	-0.7	0.0	10	dbSNP_116	69	2140,6460	713.8+/-406.0	280,1580,2440	yes	intron,missense	MKI67	NM_001145966.1,NM_002417.4	,101	498,2529,3476	TT,TA,AA		24.8837,31.4344,27.1029	,benign	,238/3257	129913960	3525,9481	2203	4300	6503	SO:0001583	missense	4288	exon7			GCTTCCAAAAGGG	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.712T>A	10.37:g.129913960A>T	ENSP00000357643:p.Trp238Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	531	0.24313186813186813	126	0.25609756097560976	75	0.20718232044198895	144	0.2517482517482518	186	0.24538258575197888	T	0.147	-1.095509	0.01858	0.314344	0.248837	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.20069	2.1	3.69	-0.736	0.11133	.	0.696409	0.13509	N	0.382650	T	0.00012	0.0000	N	0.01576	-0.805	0.30494	P	0.7710440000000001	B	0.02656	0.0	B	0.01281	0.0	T	0.44636	-0.9315	8	.	.	.	.	1.3191	0.02113	0.1504:0.1432:0.3532:0.3531	rs7095325;rs52812070;rs57013021;rs7095325	238	P46013	KI67_HUMAN	R	238	ENSP00000357643:W238R	.	W	-	1	0	MKI67	129803950	0.838000	0.29461	0.022000	0.16811	0.971000	0.66376	0.172000	0.16704	-0.415000	0.07484	-0.257000	0.10917	TGG	A|0.739;T|0.261	0.261	strong		0.348	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238672703	238672703	+	Missense_Mutation	SNP	C	C	G	rs3739038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238672703C>G	ENST00000392000.4	+	11	2464	c.2347C>G	c.(2347-2349)Cac>Gac	p.H783D	LRRFIP1_ENST00000289175.6_Missense_Mutation_p.H727D|LRRFIP1_ENST00000244815.5_Missense_Mutation_p.H759D|LRRFIP1_ENST00000308482.9_Intron	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	783			H -> D (in dbSNP:rs3739038).		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)		AGAGCCAGGGCACTTCAATCC	0.512													G|||	1803	0.360024	0.3563	0.3026	5008	,	,		20722	0.505		0.2495	False		,,,				2504	0.3701				p.H783D		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.C2347G						PASS	.	G	,,ASP/HIS,ASP/HIS,ASP/HIS	1635,2771	659.0+/-400.5	319,997,887	78.0	77.0	77.0		,,2347,2179,2275	1.5	0.0	2	dbSNP_107	77	2004,6596	721.6+/-406.4	219,1566,2515	yes	intron,intron,missense,missense,missense	LRRFIP1	NM_001137550.1,NM_001137551.1,NM_001137552.1,NM_001137553.1,NM_004735.3	,,81,81,81	538,2563,3402	GG,GC,CC		23.3023,37.1085,27.9794	,,benign,benign,benign	,,783/809,727/753,759/785	238672703	3639,9367	2203	4300	6503	SO:0001583	missense	9208	exon11			CCAGGGCACTTCA	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.2347C>G	2.37:g.238672703C>G	ENSP00000375857:p.His783Asp	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	137	57	0.416058	NM_001137552	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	37	CCDS46552.1	811	0.37133699633699635	198	0.4024390243902439	115	0.31767955801104975	318	0.5559440559440559	180	0.23746701846965698	G	0.088	-1.172355	0.01646	0.371085	0.233023	ENSG00000124831	ENST00000289175;ENST00000244815;ENST00000392000	T;T;T	0.06768	3.27;3.27;3.26	5.34	1.5	0.22942	.	8.116580	0.00166	N	0.000000	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45629	-0.9248	9	0.02654	T	1	-13.1981	1.2179	0.01918	0.3763:0.1334:0.3364:0.1539	rs3739038;rs52824301;rs58509875;rs3739038	727;783;759	Q32MZ4-3;Q32MZ4;Q32MZ4-2	.;LRRF1_HUMAN;.	D	727;759;783	ENSP00000289175:H727D;ENSP00000244815:H759D;ENSP00000375857:H783D	ENSP00000244815:H759D	H	+	1	0	LRRFIP1	238337442	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.219000	0.17641	0.268000	0.21939	-0.120000	0.15030	CAC	C|0.687;G|0.312	0.312	strong		0.512	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
RALGAPA1	253959	hgsc.bcm.edu	37	14	36153177	36153177	+	Missense_Mutation	SNP	T	T	C	rs2274068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:36153177T>C	ENST00000389698.3	-	20	3181	c.2791A>G	c.(2791-2793)Acc>Gcc	p.T931A	RALGAPA1_ENST00000307138.6_Missense_Mutation_p.T931A|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.T978A|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.T944A	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	931			T -> A (in dbSNP:rs2274068). {ECO:0000269|PubMed:19520869}.		activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CCAGTGTCGGTTCCAAAGCCA	0.393													C|||	2373	0.473842	0.7557	0.2277	5008	,	,		16999	0.5804		0.1918	False		,,,				2504	0.4479				p.T931A		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.A2791G						PASS	.	C	ALA/THR,ALA/THR	2911,1495	472.0+/-356.2	977,957,269	44.0	54.0	51.0		2791,2791	1.6	1.0	14	dbSNP_100	51	1527,7073	744.4+/-407.2	155,1217,2928	yes	missense,missense	RALGAPA1	NM_014990.1,NM_194301.2	58,58	1132,2174,3197	CC,CT,TT		17.7558,33.931,34.1227	benign,benign	931/2037,931/2084	36153177	4438,8568	2203	4300	6503	SO:0001583	missense	253959	exon20			TGTCGGTTCCAAA	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.2791A>G	14.37:g.36153177T>C	ENSP00000374348:p.Thr931Ala	Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	175	175	1	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	953	0.43635531135531136	353	0.717479674796748	106	0.292817679558011	350	0.6118881118881119	144	0.18997361477572558	C	0.993	-0.693402	0.03303	0.66069	0.177558	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	D;D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.26;-3.27	5.46	1.57	0.23409	.	0.641598	0.15948	N	0.236867	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0	T	0.45775	-0.9238	9	0.16420	T	0.52	-0.4299	6.214	0.20646	0.0:0.4158:0.1279:0.4563	rs2274068;rs52819701;rs57932556;rs2274068	978;944;978;931;931	Q6GYQ0-6;B9EK38;Q6GYQ0-3;Q6GYQ0-2;Q6GYQ0	.;.;.;.;RGPA1_HUMAN	A	931;931;931;978;944;978	ENSP00000374348:T931A;ENSP00000302647:T931A;ENSP00000258840:T978A;ENSP00000371803:T944A;ENSP00000451877:T978A	ENSP00000258840:T978A	T	-	1	0	RALGAPA1	35222928	0.959000	0.32827	0.984000	0.44739	0.864000	0.49448	0.203000	0.17315	0.025000	0.15241	-0.197000	0.12766	ACC	T|0.603;C|0.397	0.397	strong		0.393	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	
LRRC7	57554	hgsc.bcm.edu	37	1	70460304	70460304	+	Missense_Mutation	SNP	A	A	G	rs72676879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:70460304A>G	ENST00000035383.5	+	9	908	c.878A>G	c.(877-879)aAt>aGt	p.N293S	LRRC7_ENST00000415775.2_5'UTR|LRRC7_ENST00000310961.5_Missense_Mutation_p.N298S	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	293						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						ATGCTACCCAATACAATTGGA	0.328													A|||	35	0.00698882	0.0182	0.0058	5008	,	,		16545	0.0		0.007	False		,,,				2504	0.0				p.N293S		Atlas-SNP	.											.	LRRC7	400	.	0			c.A878G						PASS	.	A	SER/ASN	57,4349	56.2+/-92.4	0,57,2146	105.0	109.0	108.0		878	5.4	1.0	1	dbSNP_130	108	56,8544	34.8+/-89.0	2,52,4246	yes	missense	LRRC7	NM_020794.2	46	2,109,6392	GG,GA,AA		0.6512,1.2937,0.8688	benign	293/1538	70460304	113,12893	2203	4300	6503	SO:0001583	missense	57554	exon9			TACCCAATACAAT		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.878A>G	1.37:g.70460304A>G	ENSP00000035383:p.Asn293Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	11	0.005036630036630037	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	17.60	3.430936	0.62844	0.012937	0.006512	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000370957	T;T	0.23950	2.03;1.88	5.4	5.4	0.78164	.	0.100641	0.64402	D	0.000003	T	0.08223	0.0205	N	0.05306	-0.075	0.80722	D	1	B	0.32365	0.367	B	0.38020	0.263	T	0.25187	-1.0139	10	0.33940	T	0.23	.	14.8941	0.70630	1.0:0.0:0.0:0.0	.	293	Q96NW7	LRRC7_HUMAN	S	298;293;116	ENSP00000309245:N298S;ENSP00000035383:N293S	ENSP00000035383:N293S	N	+	2	0	LRRC7	70232892	1.000000	0.71417	0.997000	0.53966	0.559000	0.35586	8.517000	0.90555	2.178000	0.69098	0.533000	0.62120	AAT	A|0.991;G|0.009	0.009	strong		0.328	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794	
LAMA1	284217	hgsc.bcm.edu	37	18	7012123	7012123	+	Silent	SNP	A	A	G	rs9946794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:7012123A>G	ENST00000389658.3	-	24	3471	c.3378T>C	c.(3376-3378)ggT>ggC	p.G1126G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1126	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGCACTGAGGACCAAAGACAT	0.512													G|||	2104	0.420128	0.851	0.3833	5008	,	,		15427	0.0536		0.3648	False		,,,				2504	0.2986				p.G1126G		Atlas-SNP	.											LAMA1,NS,carcinoma,0,1	LAMA1	458	1	0			c.T3378C						PASS	.	G		3346,1060	383.0+/-324.7	1264,818,121	42.0	42.0	42.0		3378	-0.9	0.8	18	dbSNP_119	42	3349,5251	640.8+/-399.6	663,2023,1614	no	coding-synonymous	LAMA1	NM_005559.3		1927,2841,1735	GG,GA,AA		38.9419,24.0581,48.5238		1126/3076	7012123	6695,6311	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon24			CTGAGGACCAAAG	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.3378T>C	18.37:g.7012123A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			A|0.528;G|0.472	0.472	strong		0.512	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
PLCE1	51196	hgsc.bcm.edu	37	10	96058298	96058298	+	Missense_Mutation	SNP	C	C	T	rs3765524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:96058298C>T	ENST00000371380.3	+	23	5565	c.5330C>T	c.(5329-5331)aCc>aTc	p.T1777I	PLCE1_ENST00000371375.1_Missense_Mutation_p.T1469I|PLCE1_ENST00000260766.3_Missense_Mutation_p.T1777I|PLCE1_ENST00000371385.3_Missense_Mutation_p.T1469I			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1777	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.		T -> I (in dbSNP:rs3765524). {ECO:0000269|PubMed:11022048, ECO:0000269|Ref.8}.		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)				CAGAAACTGACCCAGCACACC	0.522													T|||	1542	0.307907	0.4561	0.2104	5008	,	,		16656	0.2381		0.3091	False		,,,				2504	0.2474				p.T1777I		Atlas-SNP	.											.	PLCE1	543	.	0			c.C5330T						PASS	.	T	ILE/THR,ILE/THR	1593,2455		327,939,758	82.0	83.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4406,5330	5.6	1.0	10	dbSNP_107	83	2378,5946		316,1746,2100	yes	missense,missense	PLCE1	NM_001165979.1,NM_016341.3	89,89	643,2685,2858	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	28.568,39.3528,32.0967	benign,benign	1469/1995,1777/2303	96058298	3971,8401	2024	4162	6186	SO:0001583	missense	51196	exon24			AACTGACCCAGCA		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.5330C>T	10.37:g.96058298C>T	ENSP00000360431:p.Thr1777Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	144	75	0.520833	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	614	0.28113553113553114	207	0.42073170731707316	79	0.21823204419889503	110	0.19230769230769232	218	0.287598944591029	T	6.575	0.474472	0.12521	0.393528	0.28568	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.6	5.6	0.85130	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00446	-1.495	0.49483	P	2.0500000000001073E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.40308	-0.9570	9	0.02654	T	1	.	11.3769	0.49733	0.0:0.0715:0.0:0.9285	rs3765524;rs52790405;rs56794598;rs3765524	1761;1469;1777	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	I	1777;1777;1469;1469	ENSP00000260766:T1777I;ENSP00000360431:T1777I;ENSP00000360438:T1469I;ENSP00000360426:T1469I	ENSP00000260766:T1777I	T	+	2	0	PLCE1	96048288	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.148000	0.64857	0.968000	0.38212	-0.254000	0.11334	ACC	C|0.684;T|0.316	0.316	strong		0.522	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
PTPRQ	374462	hgsc.bcm.edu	37	12	80935365	80935365	+	Silent	SNP	C	C	T	rs61729275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:80935365C>T	ENST00000266688.5	+	26	3174	c.3174C>T	c.(3172-3174)taC>taT	p.Y1058Y				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1104	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						ACCTGACTTACGAATCCATTT	0.403													C|||	133	0.0265575	0.0023	0.0317	5008	,	,		15586	0.0		0.0487	False		,,,				2504	0.0603				p.Y890Y		Atlas-SNP	.											.	PTPRQ	119	.	0			c.C2670T						PASS	.	C		16,1368		0,16,676	123.0	101.0	107.0		2732	-8.6	0.1	12	dbSNP_129	107	196,2986		7,182,1402	no	coding-synonymous	PTPRQ	NM_001145026.1		7,198,2078	TT,TC,CC		6.1596,1.1561,4.643		1062/2300	80935365	212,4354	692	1591	2283	SO:0001819	synonymous_variant	374462	exon18			GACTTACGAATCC	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.3174C>T	12.37:g.80935365C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_001145026		Silent	SNP	ENST00000266688.5	37		45	0.020604395604395604	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	32	0.04221635883905013	C	5.175	0.217904	0.09810	0.011561	0.061596	ENSG00000139304	ENST00000532722	.	.	.	5.89	-8.57	0.00900	.	.	.	.	.	T	0.14743	0.0356	.	.	.	0.34350	D	0.689758	.	.	.	.	.	.	T	0.61501	-0.7050	4	.	.	.	.	19.7787	0.96409	0.0:0.1114:0.0:0.8886	rs61729275	.	.	.	M	759	.	.	T	+	2	0	PTPRQ	79459496	0.016000	0.18221	0.124000	0.21820	0.950000	0.60333	-1.282000	0.02799	-1.668000	0.01471	-1.105000	0.02106	ACG	C|0.977;T|0.023	0.023	strong		0.403	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
RIF1	55183	hgsc.bcm.edu	37	2	152321618	152321618	+	Missense_Mutation	SNP	G	G	A	rs2444258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152321618G>A	ENST00000243326.5	+	29	6067	c.5584G>A	c.(5584-5586)Gtt>Att	p.V1862I	RIF1_ENST00000430328.2_Missense_Mutation_p.V1862I|RIF1_ENST00000428287.2_Missense_Mutation_p.V1862I|RIF1_ENST00000453091.2_Missense_Mutation_p.V1862I|RIF1_ENST00000444746.2_Missense_Mutation_p.V1862I			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TTTTAAAACTGTTGGCCCGTG	0.368													G|||	370	0.0738818	0.2617	0.0317	5008	,	,		17559	0.0		0.002	False		,,,				2504	0.0				p.V1862I		Atlas-SNP	.											.	RIF1	244	.	0			c.G5584A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	986,3420	359.6+/-314.9	101,784,1318	57.0	63.0	61.0		5584,5584,5584,5584	-4.0	0.0	2	dbSNP_100	61	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense,missense	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	29,29,29,29	101,789,5613	AA,AG,GG		0.0581,22.3786,7.6196	benign,benign,benign,benign	1862/2447,1862/2447,1862/2447,1862/2473	152321618	991,12015	2203	4300	6503	SO:0001583	missense	55183	exon30			AAAACTGTTGGCC	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.5584G>A	2.37:g.152321618G>A	ENSP00000243326:p.Val1862Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	29	0.298969	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	146	0.06684981684981685	137	0.2784552845528455	9	0.024861878453038673	0	0.0	0	0.0	G	10.51	1.369197	0.24771	0.223786	5.81E-4	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.09723	2.96;2.95;2.95;2.96;2.95	5.68	-3.96	0.04106	.	1.726510	0.02579	N	0.098634	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.29988	0.172;0.264	B;B	0.24269	0.023;0.052	T	0.41342	-0.9514	9	0.31617	T	0.26	0.8111	4.8656	0.13607	0.4276:0.089:0.3932:0.0902	rs2444258;rs52808590;rs60545876;rs2444258	1862;1862	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	I	1862	ENSP00000390181:V1862I;ENSP00000414615:V1862I;ENSP00000415691:V1862I;ENSP00000243326:V1862I;ENSP00000416123:V1862I	ENSP00000243326:V1862I	V	+	1	0	RIF1	152029864	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	0.006000	0.13152	-0.725000	0.04901	0.650000	0.86243	GTT	G|0.918;A|0.082	0.082	strong		0.368	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
GRIN3B	116444	hgsc.bcm.edu	37	19	1004740	1004740	+	Missense_Mutation	SNP	T	T	C	rs2240157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1004740T>C	ENST00000234389.3	+	3	1259	c.1240T>C	c.(1240-1242)Tgg>Cgg	p.W414R	GRIN3B_ENST00000588335.1_Intron|AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	414			W -> R (in dbSNP:rs2240157).		ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGCCCAGGTCTGGCCCAAGCT	0.692													N|||	3413	0.68151	0.8048	0.5403	5008	,	,		12051	0.501		0.7157	False		,,,				2504	0.7658				p.W414R		Atlas-SNP	.											.	GRIN3B	46	.	0			c.T1240C						PASS	.	C	ARG/TRP	3447,941		1354,739,101	28.0	29.0	29.0		1240	3.3	0.0	19	dbSNP_98	29	6108,2472		2186,1736,368	yes	missense	GRIN3B	NM_138690.1	101	3540,2475,469	CC,CT,TT		28.8112,21.4448,26.3186	benign	414/1044	1004740	9555,3413	2194	4290	6484	SO:0001583	missense	116444	exon3			CAGGTCTGGCCCA		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.1240T>C	19.37:g.1004740T>C	ENSP00000234389:p.Trp414Arg	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	1417	0.6488095238095238	390	0.7926829268292683	217	0.5994475138121547	273	0.4772727272727273	537	0.7084432717678101	C	0.103	-1.149021	0.01714	0.785552	0.711888	ENSG00000116032	ENST00000234389	T	0.46063	0.88	4.41	3.35	0.38373	.	0.406531	0.26492	N	0.024067	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	0.33266	-0.9875	9	0.15066	T	0.55	.	9.8165	0.40856	0.0:0.8221:0.0:0.1779	rs2240157	414	O60391	NMD3B_HUMAN	R	414	ENSP00000234389:W414R	ENSP00000234389:W414R	W	+	1	0	GRIN3B	955740	0.047000	0.20315	0.002000	0.10522	0.005000	0.04900	0.585000	0.23879	0.880000	0.35969	-0.354000	0.07668	TGG	T|0.304;C|0.696	0.696	strong		0.692	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
CROCC	9696	hgsc.bcm.edu	37	1	17295764	17295764	+	Missense_Mutation	SNP	A	A	G	rs56278097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17295764A>G	ENST00000375541.5	+	32	5299	c.5230A>G	c.(5230-5232)Agc>Ggc	p.S1744G		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)		CAGCCTCAACAGCACCCGGGA	0.662													A|||	471	0.0940495	0.2867	0.0403	5008	,	,		16898	0.001		0.0507	False		,,,				2504	0.0123				p.S1744G		Atlas-SNP	.											.	CROCC	185	.	0			c.A5230G						PASS	.	A	GLY/SER	951,3455	337.0+/-304.7	110,731,1362	27.0	29.0	29.0		5230	1.9	1.0	1	dbSNP_129	29	442,8158	127.0+/-185.4	7,428,3865	no	missense	CROCC	NM_014675.3	56	117,1159,5227	GG,GA,AA		5.1395,21.5842,10.7104	possibly-damaging	1744/2018	17295764	1393,11613	2203	4300	6503	SO:0001583	missense	9696	exon32			CTCAACAGCACCC	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.5230A>G	1.37:g.17295764A>G	ENSP00000364691:p.Ser1744Gly	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	260	123	0.473077	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	194	0.08882783882783883	139	0.28252032520325204	16	0.04419889502762431	0	0.0	39	0.051451187335092345	A	14.49	2.550629	0.45383	0.215842	0.051395	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.11495	2.77	4.62	1.85	0.25348	.	.	.	.	.	T	0.00012	0.0000	L	0.60455	1.87	0.31354	P	0.6821699999999999	P;P;P	0.41188	0.672;0.544;0.741	P;B;B	0.45506	0.483;0.439;0.37	T	0.42531	-0.9446	8	0.34782	T	0.22	.	4.6643	0.12657	0.6908:0.0:0.1019:0.2073	rs56278097;rs61661078	1625;1047;1744	B1AKD8;Q5TZA2-2;Q5TZA2	.;.;CROCC_HUMAN	G	1744;1625	ENSP00000364691:S1744G	ENSP00000364691:S1744G	S	+	1	0	CROCC	17168351	0.018000	0.18449	0.995000	0.50966	0.969000	0.65631	1.184000	0.32053	0.742000	0.32697	0.402000	0.26972	AGC	A|0.901;G|0.099	0.099	strong		0.662	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
TLR1	7096	hgsc.bcm.edu	37	4	38799710	38799710	+	Missense_Mutation	SNP	T	T	C	rs4833095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38799710T>C	ENST00000502213.2	-	3	972	c.743A>G	c.(742-744)aAt>aGt	p.N248S	TLR1_ENST00000308979.2_Missense_Mutation_p.N248S			Q15399	TLR1_HUMAN	toll-like receptor 1	248			N -> S (may confer susceptibility to leprosy; dbSNP:rs4833095). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21618349, ECO:0000269|PubMed:9435236}.		cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						TAAGGTAAGATTTGATAACTT	0.333													C|||	2878	0.574681	0.8797	0.4726	5008	,	,		21271	0.5992		0.2803	False		,,,				2504	0.5123				p.N248S	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.A743G						PASS	.	C	SER/ASN	3424,982	331.5+/-302.0	1332,760,111	60.0	66.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743	-3.2	0.0	4	dbSNP_111	64	2141,6457	702.3+/-405.3	278,1585,2436	yes	missense	TLR1	NM_003263.3	46	1610,2345,2547	CC,CT,TT		24.9011,22.2878,42.7945	benign	248/787	38799710	5565,7439	2203	4299	6502	SO:0001583	missense	7096	exon4			GTAAGATTTGATA	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.743A>G	4.37:g.38799710T>C	ENSP00000421259:p.Asn248Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Missense_Mutation	SNP	ENST00000502213.2	37	CCDS33973.1	1156	0.5293040293040293	436	0.8861788617886179	160	0.4419889502762431	377	0.6590909090909091	183	0.24142480211081793	C	1.852	-0.464903	0.04476	0.777122	0.249011	ENSG00000174125	ENST00000308979;ENST00000502213	T;T	0.29917	1.55;1.55	4.69	-3.18	0.05186	.	0.539821	0.18243	N	0.147178	T	0.00012	0.0000	L	0.31207	0.915	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.20739	-1.0266	9	0.30078	T	0.28	.	11.4828	0.50335	0.0:0.3819:0.0:0.6181	rs4833095;rs58946512;rs4833095	248	Q15399	TLR1_HUMAN	S	248	ENSP00000354932:N248S;ENSP00000421259:N248S	ENSP00000354932:N248S	N	-	2	0	TLR1	38476105	0.001000	0.12720	0.013000	0.15412	0.001000	0.01503	-0.228000	0.09114	-1.061000	0.03185	-1.073000	0.02249	AAT	T|0.512;C|0.488	0.488	strong		0.333	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
DCHS2	54798	hgsc.bcm.edu	37	4	155156875	155156875	+	Missense_Mutation	SNP	T	T	G	rs61746101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155156875T>G	ENST00000357232.4	-	25	7563	c.7564A>C	c.(7564-7566)Aat>Cat	p.N2522H		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2522	Cadherin 22. {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)		AAAGACACATTCACAAAAACA	0.408													T|||	214	0.0427316	0.1558	0.0086	5008	,	,		18956	0.0		0.002	False		,,,				2504	0.0				p.N2522H		Atlas-SNP	.											.	DCHS2	594	.	0			c.A7564C						PASS	.	T	HIS/ASN	567,3839	253.0+/-259.1	26,515,1662	81.0	82.0	82.0		7564	5.7	1.0	4	dbSNP_129	82	9,8591	6.4+/-24.3	0,9,4291	yes	missense	DCHS2	NM_017639.3	68	26,524,5953	GG,GT,TT		0.1047,12.8688,4.4287	probably-damaging	2522/2917	155156875	576,12430	2203	4300	6503	SO:0001583	missense	54798	exon25			ACACATTCACAAA	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.7564A>C	4.37:g.155156875T>G	ENSP00000349768:p.Asn2522His	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	72	0.03296703296703297	71	0.1443089430894309	1	0.0027624309392265192	0	0.0	0	0.0	T	18.70	3.680330	0.68042	0.128688	0.001047	ENSG00000197410	ENST00000357232	T	0.60672	0.17	5.71	5.71	0.89125	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.01320	0.0043	L	0.58669	1.825	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.04495	-1.0947	10	0.56958	D	0.05	.	15.9843	0.80138	0.0:0.0:0.0:1.0	.	2522	Q6V1P9	PCD23_HUMAN	H	2522	ENSP00000349768:N2522H	ENSP00000349768:N2522H	N	-	1	0	DCHS2	155376325	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.229000	0.58625	2.176000	0.68965	0.383000	0.25322	AAT	T|0.959;G|0.041	0.041	strong		0.408	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
OR5L2	26338	hgsc.bcm.edu	37	11	55595401	55595401	+	Missense_Mutation	SNP	A	A	G	rs148148644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55595401A>G	ENST00000378397.1	+	1	707	c.707A>G	c.(706-708)aAa>aGa	p.K236R		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	236						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)				AGCAGGCACAAAGCTTTCTCC	0.488										HNSCC(27;0.073)			N|||	7	0.00139776	0.0053	0.0	5008	,	,		17988	0.0		0.0	False		,,,				2504	0.0				p.K236R		Atlas-SNP	.											.	OR5L2	135	.	0			c.A707G						PASS	.	A	ARG/LYS	43,4357		0,43,2157	177.0	150.0	159.0		707	5.2	1.0	11	dbSNP_134	159	0,8592		0,0,4296	yes	missense	OR5L2	NM_001004739.1	26	0,43,6453	GG,GA,AA		0.0,0.9773,0.331	benign	236/312	55595401	43,12949	2200	4296	6496	SO:0001583	missense	26338	exon1			GGCACAAAGCTTT	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.707A>G	11.37:g.55595401A>G	ENSP00000367650:p.Lys236Arg	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	159	73	0.459119	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	.	13.65	2.300050	0.40694	0.009773	0.0	ENSG00000205030	ENST00000378397	T	0.00360	7.86	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.110656	0.40640	N	0.001045	T	0.00300	0.0009	M	0.62723	1.935	0.39567	D	0.969221	B	0.31581	0.329	B	0.37304	0.246	T	0.77520	-0.2557	10	0.66056	D	0.02	-6.4806	14.3209	0.66487	1.0:0.0:0.0:0.0	.	236	Q8NGL0	OR5L2_HUMAN	R	236	ENSP00000367650:K236R	ENSP00000367650:K236R	K	+	2	0	OR5L2	55351977	1.000000	0.71417	0.998000	0.56505	0.029000	0.11900	2.879000	0.48522	2.115000	0.64714	0.514000	0.50259	AAA	A|0.997;G|0.003	0.003	strong		0.488	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
PRLR	5618	hgsc.bcm.edu	37	5	35065551	35065551	+	Silent	SNP	G	G	A	rs368647716		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:35065551G>A	ENST00000382002.5	-	10	1935	c.1509C>T	c.(1507-1509)tcC>tcT	p.S503S	PRLR_ENST00000511486.1_Silent_p.S402S|PRLR_ENST00000397391.3_Intron|PRLR_ENST00000231423.3_Intron|PRLR_ENST00000310101.5_Intron|PRLR_ENST00000348262.3_Intron|PRLR_ENST00000509934.1_5'Flank|PRLR_ENST00000542609.1_Intron|PRLR_ENST00000513753.1_Intron|PRLR_ENST00000342362.5_Silent_p.S402S	NM_000949.5	NP_000940.1	P16471	PRLR_HUMAN	prolactin receptor	503					activation of JAK2 kinase activity (GO:0042977)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell surface receptor signaling pathway (GO:0007166)|embryo implantation (GO:0007566)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|prolactin signaling pathway (GO:0038161)|steroid biosynthetic process (GO:0006694)|T cell activation (GO:0042110)	cell surface (GO:0009986)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|ornithine decarboxylase activator activity (GO:0042978)|peptide hormone binding (GO:0017046)|prolactin receptor activity (GO:0004925)|protein homodimerization activity (GO:0042803)	p.S503S(1)		central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Fluoxymesterone(DB01185)|Somatropin recombinant(DB00052)	AGGGTTTAGCGGAGCCAAAGG	0.517																																					p.S503S		Atlas-SNP	.											PRLR,pharynx,carcinoma,0,1	PRLR	90	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C1509T						scavenged	.	G	,,,,,	0,4406		0,0,2203	87.0	94.0	92.0		1509,1206,,,,	3.4	0.0	5		92	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron	PRLR	NM_000949.5,NM_001204314.1,NM_001204315.1,NM_001204316.1,NM_001204317.1,NM_001204318.1	,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,	503/623,402/522,,,,	35065551	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5618	exon10			TTTAGCGGAGCCA		CCDS3909.1, CCDS56358.1, CCDS56359.1, CCDS56360.1, CCDS56361.1, CCDS56362.1	5p14-p13	2013-02-27			ENSG00000113494	ENSG00000113494			9446	protein-coding gene	gene with protein product		176761					Standard	NM_001204315		Approved		uc003jjm.3	P16471	OTTHUMG00000090789	ENST00000382002.5:c.1509C>T	5.37:g.35065551G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	214	3	0.0140187	NM_000949	B2R882|D1MDP1|Q16354|Q8TD75|Q8TD78|Q96P35|Q96P36|Q9BX87|Q9UHJ5	Silent	SNP	ENST00000382002.5	37	CCDS3909.1																																																																																			.	.	weak		0.517	PRLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207575.2		
IQSEC2	23096	hgsc.bcm.edu	37	X	53263764	53263764	+	Silent	SNP	C	C	T	rs184087864		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:53263764C>T	ENST00000375368.5	-	14	4274	c.4074G>A	c.(4072-4074)ctG>ctA	p.L1358L	IQSEC2_ENST00000375365.2_3'UTR|IQSEC2_ENST00000396435.3_Silent_p.L1368L			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1358	Pro-rich.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						TGTACAGGGGCAGTGGGGATG	0.672													c|||	294	0.0778808	0.2133	0.0173	3775	,	,		4478	0.0		0.0	False		,,,				2504	0.0				p.L1368L		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G4104A						PASS	.						10.0	11.0	10.0					X																	53263764		689	1580	2269	SO:0001819	synonymous_variant	23096	exon15			CAGGGGCAGTGGG	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"""mental retardation, X-linked 1 (non-dysmorphic)"""	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.4074G>A	X.37:g.53263764C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	222	97	0.436937	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Silent	SNP	ENST00000375368.5	37																																																																																				C|0.937;T|0.063	0.063	strong		0.672	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345	
PARP12	64761	hgsc.bcm.edu	37	7	139724555	139724555	+	Silent	SNP	C	C	G	rs3735352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139724555C>G	ENST00000263549.3	-	12	2784	c.1911G>C	c.(1909-1911)ccG>ccC	p.P637P		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	637	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					CCTTGGCCGGCGGACGGACAA	0.592													G|||	368	0.0734824	0.205	0.0389	5008	,	,		19852	0.0		0.0408	False		,,,				2504	0.0297				p.P637P		Atlas-SNP	.											.	PARP12	59	.	0			c.G1911C						PASS	.						111.0	93.0	99.0					7																	139724555		2203	4300	6503	SO:0001819	synonymous_variant	64761	exon12			GGCCGGCGGACGG	AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	21919	protein-coding gene	gene with protein product		612481	"""zinc finger CCCH-type domain containing 1"""	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1911G>C	7.37:g.139724555C>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	NM_022750	Q9H610|Q9NP36|Q9NTI3	Silent	SNP	ENST00000263549.3	37	CCDS5857.1																																																																																			T|0.364;G|0.008;C|0.628	0.008	strong		0.592	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750	
HSH2D	84941	hgsc.bcm.edu	37	19	16265241	16265241	+	Silent	SNP	C	C	T	rs36088948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16265241C>T	ENST00000253680.6	+	7	945	c.414C>T	c.(412-414)ctC>ctT	p.L138L	HSH2D_ENST00000593154.2_Silent_p.L138L|HSH2D_ENST00000588246.1_Silent_p.L138L|HSH2D_ENST00000397372.4_Silent_p.L49L			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	138					negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(2)	4						ACGAGGATCTCTTCCTCTACT	0.617													C|||	324	0.0646965	0.149	0.0476	5008	,	,		18037	0.001		0.0746	False		,,,				2504	0.0184				p.L138L		Atlas-SNP	.											.	HSH2D	16	.	0			c.C414T						PASS	.	C		497,3377		25,447,1465	26.0	29.0	28.0		414	1.7	1.0	19	dbSNP_126	28	494,7612		15,464,3574	no	coding-synonymous	HSH2D	NM_032855.2		40,911,5039	TT,TC,CC		6.0943,12.8291,8.2721		138/353	16265241	991,10989	1937	4053	5990	SO:0001819	synonymous_variant	84941	exon7			GGATCTCTTCCTC	AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684		"""SH2 domain containing"""	24920	protein-coding gene	gene with protein product		608349				11700021	Standard	NM_032855		Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000253680.6:c.414C>T	19.37:g.16265241C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	45	26	0.577778	NM_032855	B5ME72|Q6ZNG7	Silent	SNP	ENST00000253680.6	37																																																																																				C|0.927;T|0.073	0.073	strong		0.617	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855	
PPIB	5479	hgsc.bcm.edu	37	15	64455123	64455123	+	Silent	SNP	G	G	T	rs4904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:64455123G>T	ENST00000300026.3	-	1	281	c.63C>A	c.(61-63)tcC>tcA	p.S21S	PPIB_ENST00000558492.1_5'UTR	NM_000942.4	NP_000933.1	P23284	PPIB_HUMAN	peptidylprolyl isomerase B (cyclophilin B)	21					bone development (GO:0060348)|chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|positive regulation of multicellular organism growth (GO:0040018)|protein peptidyl-prolyl isomerization (GO:0000413)|protein stabilization (GO:0050821)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)	peptide binding (GO:0042277)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(6)	10					L-Proline(DB00172)	GGAAGAAGACGGACCCCGCGA	0.647													G|||	243	0.0485224	0.0212	0.1916	5008	,	,		10062	0.0357		0.0229	False		,,,				2504	0.0235				p.S21S	GBM(105;399 1481 32889 33051 36637)	Atlas-SNP	.											.	PPIB	20	.	0			c.C63A						PASS	.	G		96,4310	73.6+/-111.7	1,94,2108	25.0	29.0	28.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	63	0.8	1.0	15	dbSNP_52	28	166,8432	72.6+/-135.2	1,164,4134	no	coding-synonymous	PPIB	NM_000942.4		2,258,6242	TT,TG,GG		1.9307,2.1788,2.0148		21/217	64455123	262,12742	2203	4299	6502	SO:0001819	synonymous_variant	5479	exon1			GAAGACGGACCCC		CCDS10191.1	15q21-q22	2014-09-17			ENSG00000166794	ENSG00000166794	5.2.1.8		9255	protein-coding gene	gene with protein product		123841				2000394, 20089953	Standard	NM_000942		Approved	CYPB, OI9	uc002and.3	P23284	OTTHUMG00000133018	ENST00000300026.3:c.63C>A	15.37:g.64455123G>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	189	100	0.529101	NM_000942	A8K534|Q6IBH5|Q9BVK5	Silent	SNP	ENST00000300026.3	37	CCDS10191.1																																																																																			G|0.969;T|0.031	0.031	strong		0.647	PPIB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256604.1		
TERF2	7014	hgsc.bcm.edu	37	16	69401085	69401085	+	Missense_Mutation	SNP	G	G	T	rs34014829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69401085G>T	ENST00000254942.3	-	7	981	c.965C>A	c.(964-966)cCa>cAa	p.P322Q	TERF2_ENST00000603068.1_Missense_Mutation_p.P280Q|TERF2_ENST00000569611.2_5'Flank	NM_005652.3	NP_005643.2	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2	322					age-dependent telomere shortening (GO:0001309)|cell cycle (GO:0007049)|cellular senescence (GO:0090398)|in utero embryonic development (GO:0001701)|negative regulation of telomere maintenance (GO:0032205)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|positive regulation of telomere maintenance (GO:0032206)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|telomere capping (GO:0016233)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)|telomeric loop formation (GO:0031627)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded telomeric DNA binding (GO:0003691)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			NS(2)|breast(1)|large_intestine(3)|lung(1)	7		Ovarian(137;0.101)				AATGGTGGTTGGAGGATTCCG	0.453													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		18068	0.0		0.0	False		,,,				2504	0.0				p.P322Q	Ovarian(13;63 524 30420 31710 34037)	Atlas-SNP	.											.	TERF2	24	.	0			c.C965A						PASS	.	G	GLN/PRO	80,4316	68.1+/-105.8	1,78,2119	49.0	50.0	49.0		839	6.2	1.0	16	dbSNP_126	49	0,8600		0,0,4300	yes	missense	TERF2	NM_005652.3	76	1,78,6419	TT,TG,GG		0.0,1.8198,0.6156	probably-damaging	280/501	69401085	80,12916	2198	4300	6498	SO:0001583	missense	7014	exon7			GTGGTTGGAGGAT		CCDS10879.1, CCDS10879.2	16q22.1	2008-02-05			ENSG00000132604	ENSG00000132604			11729	protein-coding gene	gene with protein product		602027		TRBF2		9326950, 10226653	Standard	NM_005652		Approved	TRF2	uc002exd.4	Q15554	OTTHUMG00000137566	ENST00000254942.3:c.965C>A	16.37:g.69401085G>T	ENSP00000254942:p.Pro322Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_005652		Missense_Mutation	SNP	ENST00000254942.3	37		15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	G	19.48	3.834956	0.71373	0.018198	0.0	ENSG00000132604	ENST00000254942	.	.	.	6.17	6.17	0.99709	.	0.265458	0.37761	N	0.001941	T	0.53270	0.1786	L	0.53249	1.67	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62101	-0.6925	9	0.31617	T	0.26	-7.4119	16.3795	0.83443	0.0:0.0:1.0:0.0	rs34014829	280	Q15554	TERF2_HUMAN	Q	280	.	ENSP00000254942:P280Q	P	-	2	0	TERF2	67958586	1.000000	0.71417	0.998000	0.56505	0.894000	0.52154	3.792000	0.55476	2.941000	0.99782	0.655000	0.94253	CCA	G|0.991;T|0.009	0.009	strong		0.453	TERF2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000268944.2		
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036951	33036951	+	Missense_Mutation	SNP	A	A	G	rs386699855|rs2308930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33036951A>G	ENST00000419277.1	-	4	602	c.473T>C	c.(472-474)cTg>cCg	p.L158P	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.L158P|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						CTCAGTGACCAGCTCCCCGTT	0.567													G|||	2199	0.439097	0.5802	0.2839	5008	,	,		19044	0.6796		0.1899	False		,,,				2504	0.3671				p.L158P		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.T473C						PASS	.	G	PRO/LEU,PRO/LEU,PRO/LEU	1408,1610		327,754,428	163.0	188.0	179.0		473,473,473	1.5	0.0	6	dbSNP_126	179	937,4479		72,793,1843	no	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	98,98,98	399,1547,2271	GG,GA,AA		17.3006,46.6534,27.8041	benign,benign,benign	158/261,158/261,158/261	33036951	2345,6089	1509	2708	4217	SO:0001583	missense	3113	exon3			GTGACCAGCTCCC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.473T>C	6.37:g.33036951A>G	ENSP00000393566:p.Leu158Pro	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	830	0.38003663003663	264	0.5365853658536586	80	0.22099447513812154	364	0.6363636363636364	122	0.16094986807387862	G	0.004	-2.279822	0.00254	0.466534	0.173006	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.02656	4.21;4.21;4.21	3.4	1.52	0.23074	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.841204	0.10189	N	0.704860	T	0.00144	0.0004	N	0.00066	-2.3	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38757	-0.9646	9	0.02654	T	1	.	3.676	0.08292	0.3205:0.0:0.5087:0.1708	rs2308930	158	P20036	DPA1_HUMAN	P	158;158;125;158	ENSP00000393566:L158P;ENSP00000402872:L158P;ENSP00000390929:L158P	ENSP00000393566:L158P	L	-	2	0	HLA-DPA1	33144929	0.000000	0.05858	0.007000	0.13788	0.408000	0.30992	-1.645000	0.02000	-0.065000	0.13021	-0.131000	0.14894	CTG	A|0.698;G|0.302	0.302	strong		0.567	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
PARD6G	84552	hgsc.bcm.edu	37	18	77918221	77918221	+	Silent	SNP	C	C	T	rs2280349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:77918221C>T	ENST00000353265.3	-	3	761	c.564G>A	c.(562-564)gaG>gaA	p.E188E	AC139100.2_ENST00000585422.1_Intron|AC139100.2_ENST00000589574.1_Intron|AC139100.2_ENST00000586421.1_Intron|AC139100.2_ENST00000587254.1_Intron	NM_032510.3	NP_115899.1	Q9BYG4	PAR6G_HUMAN	par-6 family cell polarity regulator gamma	188	Interaction with PARD3 and CDC42. {ECO:0000250}.|PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	8		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)		CGGGCACCTTCTCCAGCCCGT	0.701													C|||	1237	0.247005	0.1483	0.2017	5008	,	,		13276	0.494		0.0885	False		,,,				2504	0.3211				p.E188E		Atlas-SNP	.											.	PARD6G	20	.	0			c.G564A						PASS	.	C		646,3756		39,568,1594	24.0	25.0	25.0		564	2.0	1.0	18	dbSNP_100	25	538,8058		16,506,3776	no	coding-synonymous	PARD6G	NM_032510.3		55,1074,5370	TT,TC,CC		6.2587,14.6751,9.1091		188/377	77918221	1184,11814	2201	4298	6499	SO:0001819	synonymous_variant	84552	exon3			CACCTTCTCCAGC		CCDS12022.1	18q23	2013-08-28	2013-08-28		ENSG00000178184	ENSG00000178184			16076	protein-coding gene	gene with protein product		608976	"""par-6 (partitioning defective 6, C.elegans) homolog gamma"", ""par-6 partitioning defective 6 homolog gamma (C. elegans)"""			11260256	Standard	NM_032510		Approved	PAR-6G, PAR6gamma	uc002lny.3	Q9BYG4	OTTHUMG00000132922	ENST00000353265.3:c.564G>A	18.37:g.77918221C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_032510	A8QM57	Silent	SNP	ENST00000353265.3	37	CCDS12022.1																																																																																			C|0.871;T|0.129	0.129	strong		0.701	PARD6G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256435.2	NM_032510	
CFTR	1080	hgsc.bcm.edu	37	7	117199533	117199533	+	Missense_Mutation	SNP	G	G	A	rs213950|rs397508204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:117199533G>A	ENST00000003084.6	+	11	1540	c.1408G>A	c.(1408-1410)Gtg>Atg	p.V470M	AC000111.3_ENST00000441019.1_RNA|CFTR_ENST00000454343.1_Missense_Mutation_p.V409M	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	470	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		V -> M (in dbSNP:rs213950). {ECO:0000269|PubMed:10651488, ECO:0000269|PubMed:1710598, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:2475911, ECO:0000269|Ref.3}.		cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	ACTTCTAATGGTGATTATGGG	0.393									Cystic Fibrosis				A|||	2915	0.582069	0.9349	0.513	5008	,	,		17643	0.3869		0.4384	False		,,,				2504	0.5031				p.V470M		Atlas-SNP	.											.	CFTR	171	.	0			c.G1408A	GRCh37	CM034388	CFTR	M	rs213950	PASS	.	A	MET/VAL	3747,659		1586,575,42	102.0	111.0	108.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1408	3.0	1.0	7	dbSNP_79	108	4026,4574		1025,1976,1299	yes	missense	CFTR	NM_000492.3	21	2611,2551,1341	AA,AG,GG		46.814,14.9569,40.2353	benign	470/1481	117199533	7773,5233	2203	4300	6503	SO:0001583	missense	1080	exon11	Familial Cancer Database	CF	CTAATGGTGATTA	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.1408G>A	7.37:g.117199533G>A	ENSP00000003084:p.Val470Met	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	1180	0.5402930402930403	449	0.9126016260162602	192	0.5303867403314917	202	0.3531468531468531	337	0.4445910290237467	A	2.095	-0.407418	0.04832	0.850431	0.46814	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.94280	-3.39;-3.39;-3.39	5.47	3.05	0.35203	ABC transporter, transmembrane domain, type 1 (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.113641	0.85682	N	0.000000	T	0.00012	0.0000	N	0.11341	0.13	0.46279	P	0.0010339999999999794	B	0.02656	0.0	B	0.06405	0.002	T	0.42032	-0.9475	9	0.16420	T	0.52	-17.102	2.8388	0.05523	0.5314:0.1098:0.0703:0.2886	rs213950;rs10360044;rs34570734;rs52833540;rs57055567;rs213950	470	P13569	CFTR_HUMAN	M	470;409;440	ENSP00000003084:V470M;ENSP00000403677:V409M;ENSP00000389119:V440M	ENSP00000003084:V470M	V	+	1	0	CFTR	116986769	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.608000	0.46308	0.103000	0.17682	-0.269000	0.10298	GTG	G|0.436;A|0.564	0.564	strong		0.393	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
MYOM3	127294	hgsc.bcm.edu	37	1	24383873	24383873	+	Missense_Mutation	SNP	T	T	C	rs59805085	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24383873T>C	ENST00000374434.3	-	37	4457	c.4295A>G	c.(4294-4296)aAg>aGg	p.K1432R	MYOM3_ENST00000338909.5_Missense_Mutation_p.K325R|MYOM3_ENST00000330966.7_Missense_Mutation_p.K1435R|RP11-293P20.2_ENST00000439239.2_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1432						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)		CTTCAGCTCCTTGGGCTCGTC	0.577													T|||	277	0.0553115	0.2005	0.0159	5008	,	,		21478	0.0		0.001	False		,,,				2504	0.0				p.K1432R		Atlas-SNP	.											.	MYOM3	131	.	0			c.A4295G						PASS	.	T	ARG/LYS	524,3714		36,452,1631	75.0	74.0	74.0		4295	2.9	1.0	1	dbSNP_129	74	9,8473		0,9,4232	yes	missense	MYOM3	NM_152372.3	26	36,461,5863	CC,CT,TT		0.1061,12.3643,4.1903	benign	1432/1438	24383873	533,12187	2119	4241	6360	SO:0001583	missense	127294	exon37			AGCTCCTTGGGCT	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.4295A>G	1.37:g.24383873T>C	ENSP00000363557:p.Lys1432Arg	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	158	83	0.525316	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	85	0.03891941391941392	77	0.1565040650406504	8	0.022099447513812154	0	0.0	0	0.0	T	1.496	-0.553376	0.03996	0.123643	0.001061	ENSG00000142661	ENST00000338909;ENST00000374434;ENST00000330966;ENST00000374442	T;T;T	0.56103	0.48;0.56;0.56	5.24	2.88	0.33553	.	0.543380	0.19217	N	0.119765	T	0.00109	0.0003	N	0.22421	0.69	0.41520	P	0.01160899999999998	B;B	0.20459	0.01;0.045	B;B	0.17722	0.004;0.019	T	0.09707	-1.0662	9	0.06494	T	0.89	.	3.3931	0.07297	0.1436:0.0766:0.1321:0.6476	rs59805085	1432;325	Q5VTT5;Q5VTT5-3	MYOM3_HUMAN;.	R	325;1432;1435;326	ENSP00000342689:K325R;ENSP00000363557:K1432R;ENSP00000332670:K1435R	ENSP00000332670:K1435R	K	-	2	0	MYOM3	24256460	0.000000	0.05858	0.997000	0.53966	0.370000	0.29829	0.160000	0.16462	0.795000	0.33922	0.533000	0.62120	AAG	T|0.975;C|0.025	0.025	strong		0.577	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
RTKN2	219790	hgsc.bcm.edu	37	10	63964653	63964653	+	Silent	SNP	C	C	T	rs41274060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:63964653C>T	ENST00000373789.3	-	10	1245	c.1149G>A	c.(1147-1149)aaG>aaA	p.K383K	RTKN2_ENST00000395265.1_Silent_p.K404K|RTKN2_ENST00000315289.2_Silent_p.K185K	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	383	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					CTTCCATCCACTTCTGAAGAT	0.358													C|||	704	0.140575	0.295	0.1066	5008	,	,		17023	0.005		0.16	False		,,,				2504	0.0757				p.K383K		Atlas-SNP	.											.	RTKN2	68	.	0			c.G1149A						PASS	.	C		1173,3233	412.4+/-336.1	170,833,1200	77.0	79.0	78.0		1149	0.4	1.0	10	dbSNP_127	78	1355,7245	264.9+/-285.8	114,1127,3059	no	coding-synonymous	RTKN2	NM_145307.2		284,1960,4259	TT,TC,CC		15.7558,26.6228,19.4372		383/610	63964653	2528,10478	2203	4300	6503	SO:0001819	synonymous_variant	219790	exon10			CATCCACTTCTGA	BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"""Pleckstrin homology (PH) domain containing"""	19364	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family K member 1"""	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.1149G>A	10.37:g.63964653C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_145307	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	Silent	SNP	ENST00000373789.3	37	CCDS7263.1																																																																																			C|0.821;T|0.179	0.179	strong		0.358	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307	
MCM8	84515	hgsc.bcm.edu	37	20	5943985	5943985	+	Silent	SNP	G	G	A	rs35102646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5943985G>A	ENST00000378896.3	+	8	1232	c.855G>A	c.(853-855)acG>acA	p.T285T	MCM8_ENST00000265187.4_Silent_p.T285T|Y_RNA_ENST00000384650.1_RNA|MCM8_ENST00000378883.1_Silent_p.T285T|MCM8_ENST00000378886.2_Silent_p.T285T	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	285					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						TCACAGTTACGATGGACTGGC	0.408													A|||	49	0.00978435	0.0363	0.0014	5008	,	,		16509	0.0		0.0	False		,,,				2504	0.0				p.T285T		Atlas-SNP	.											.	MCM8	125	.	0			c.G855A						PASS	.	A	,	87,4319	818.4+/-416.3	0,87,2116	123.0	107.0	112.0		855,855	-8.8	0.0	20	dbSNP_126	112	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MCM8	NM_032485.4,NM_182802.1	,	0,87,6416	AA,AG,GG		0.0,1.9746,0.6689	,	285/841,285/825	5943985	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	84515	exon8			AGTTACGATGGAC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.855G>A	20.37:g.5943985G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Silent	SNP	ENST00000378896.3	37	CCDS13094.1																																																																																			G|0.992;A|0.008	0.008	strong		0.408	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
C6orf201	404220	hgsc.bcm.edu	37	6	4122279	4122279	+	Splice_Site	SNP	A	A	G	rs17137678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4122279A>G	ENST00000380175.4	+	4	1146	c.381A>G	c.(379-381)acA>acG	p.T127T	C6orf201_ENST00000333388.5_Splice_Site_p.T130T|C6orf201_ENST00000430835.2_Splice_Site_p.T127T|ECI2_ENST00000413766.2_Intron|ECI2_ENST00000380125.2_Intron|ECI2_ENST00000380118.3_Intron|ECI2_ENST00000361538.2_Intron|ECI2_ENST00000465828.1_Intron	NM_001085401.2	NP_001078870.1	Q7Z4U5	CF201_HUMAN	chromosome 6 open reading frame 201	127										central_nervous_system(1)|endometrium(3)|lung(2)	6	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GGACACAAACAGGTACATGCA	0.418													A|||	125	0.0249601	0.09	0.0086	5008	,	,		15796	0.0		0.0	False		,,,				2504	0.0				p.T127T		Atlas-SNP	.											.	C6orf201	17	.	0			c.A381G						PASS	.	A	,,,	308,3458		23,262,1598	63.0	61.0	62.0		381,,,	3.2	0.2	6	dbSNP_123	62	4,8226		0,4,4111	yes	coding-synonymous-near-splice,intron,intron,intron	ECI2,C6orf201	NM_001085401.1,NM_001166010.1,NM_006117.2,NM_206836.2	,,,	23,266,5709	GG,GA,AA		0.0486,8.1784,2.6009	,,,	127/141,,,	4122279	312,11684	1883	4115	5998	SO:0001630	splice_region_variant	404220	exon4			ACAAACAGGTACA	BC047663	CCDS43419.1	6p25.2	2012-02-21			ENSG00000185689	ENSG00000185689			21620	protein-coding gene	gene with protein product							Standard	NM_001085401		Approved	dJ1013A10.5	uc003mwa.4	Q7Z4U5	OTTHUMG00000014160	ENST00000380175.4:c.382+1A>G	6.37:g.4122279A>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	210	114	0.542857	NM_001085401	A6NLI6|Q6NXN5	Silent	SNP	ENST00000380175.4	37	CCDS43419.1																																																																																			A|0.978;G|0.022	0.022	strong		0.418	C6orf201-001	KNOWN	NMD_exception|basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000314019.2	NM_001085401	Silent
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84539619	84539619	+	Missense_Mutation	SNP	C	C	G	rs4144691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:84539619C>G	ENST00000286744.5	+	9	1092	c.868C>G	c.(868-870)Ctc>Gtc	p.L290V	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.L290V	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	290			L -> V (in dbSNP:rs4144691). {ECO:0000269|PubMed:14667842}.			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)			CGGCGTCTTTCTCGTAGAAAA	0.388													G|||	4044	0.807508	0.9629	0.9078	5008	,	,		15806	0.7232		0.7833	False		,,,				2504	0.638				p.L290V		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.C868G						PASS	.	G	VAL/LEU	4133,273	150.7+/-184.7	1945,243,15	62.0	68.0	66.0		868	1.7	0.0	15	dbSNP_110	66	6900,1700	308.6+/-309.0	2754,1392,154	yes	missense	ADAMTSL3	NM_207517.2	32	4699,1635,169	GG,GC,CC		19.7674,6.1961,15.1699	benign	290/1692	84539619	11033,1973	2203	4300	6503	SO:0001583	missense	57188	exon9			GTCTTTCTCGTAG	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.868C>G	15.37:g.84539619C>G	ENSP00000286744:p.Leu290Val	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	1787	0.8182234432234432	467	0.9491869918699187	320	0.8839779005524862	414	0.7237762237762237	586	0.7730870712401056	G	0	-2.816932	0.00072	0.938039	0.802326	ENSG00000156218	ENST00000286744	T	0.63744	-0.06	4.69	1.68	0.24146	.	1.092520	0.07042	N	0.830385	T	0.00012	0.0000	N	0.05414	-0.055	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39623	-0.9605	9	0.02654	T	1	.	5.542	0.17043	0.3257:0.1359:0.5384:0.0	rs4144691;rs17841183;rs52823048;rs59718593;rs4144691	290;290	P82987-2;P82987	.;ATL3_HUMAN	V	290	ENSP00000286744:L290V	ENSP00000286744:L290V	L	+	1	0	ADAMTSL3	82330623	0.998000	0.40836	0.002000	0.10522	0.021000	0.10359	1.054000	0.30455	-0.175000	0.10725	-0.357000	0.07601	CTC	C|0.164;G|0.836	0.836	strong		0.388	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
USP39	10713	hgsc.bcm.edu	37	2	85852667	85852667	+	Silent	SNP	G	G	A	rs2304564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85852667G>A	ENST00000323701.6	+	5	586	c.576G>A	c.(574-576)gtG>gtA	p.V192V	USP39_ENST00000409766.3_Silent_p.V192V|USP39_ENST00000409025.1_Silent_p.V192V|USP39_ENST00000459775.1_3'UTR|USP39_ENST00000450066.2_Silent_p.V89V|USP39_ENST00000409470.1_Silent_p.V192V	NM_006590.3	NP_006581.2	Q53GS9	SNUT2_HUMAN	ubiquitin specific peptidase 39	192					cell cycle (GO:0007049)|cell division (GO:0051301)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|ubiquitin-dependent protein catabolic process (GO:0006511)	spliceosomal complex (GO:0005681)	ubiquitinyl hydrolase activity (GO:0036459)|zinc ion binding (GO:0008270)	p.V192V(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	19						TGCAGTATGTGTTGAAGCCCA	0.408													G|||	664	0.132588	0.1967	0.049	5008	,	,		21760	0.2847		0.0338	False		,,,				2504	0.0501				p.V192V		Atlas-SNP	.											USP39,NS,carcinoma,0,1	USP39	33	1	1	Substitution - coding silent(1)	stomach(1)	c.G576A						PASS	.	G		737,3669	303.8+/-288.1	49,639,1515	125.0	114.0	118.0		576	-2.0	1.0	2	dbSNP_100	118	173,8427	79.5+/-142.1	1,171,4128	no	coding-synonymous	USP39	NM_006590.2		50,810,5643	AA,AG,GG		2.0116,16.7272,6.9968		192/566	85852667	910,12096	2203	4300	6503	SO:0001819	synonymous_variant	10713	exon5			GTATGTGTTGAAG	AF132955	CCDS33234.1, CCDS58716.1, CCDS58717.1, CCDS74534.1	2p11.2	2009-01-06	2005-08-08		ENSG00000168883	ENSG00000168883		"""Ubiquitin-specific peptidases"""	20071	protein-coding gene	gene with protein product	"""snRNP assembly defective 1 homolog (S.cerevisiae)"", ""small nuclear ribonucleoprotein 65kDa (U4/U6.U5)"""	611594	"""ubiquitin specific protease 39"""			12838346	Standard	NM_006590		Approved	SAD1, CGI-21, SNRNP65	uc002sqg.4	Q53GS9	OTTHUMG00000153090	ENST00000323701.6:c.576G>A	2.37:g.85852667G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_001256725	A8K086|B3KM40|B4DHT4|D6W5L4|G5E9H0|Q6NX47|Q96RK9|Q9BV89|Q9H381|Q9P050|Q9Y310	Silent	SNP	ENST00000323701.6	37	CCDS33234.1																																																																																			G|0.889;A|0.111	0.111	strong		0.408	USP39-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329892.1	NM_006590	
IL1R2	7850	hgsc.bcm.edu	37	2	102626187	102626187	+	Silent	SNP	G	G	A	rs2230401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102626187G>A	ENST00000332549.3	+	3	460	c.231G>A	c.(229-231)acG>acA	p.T77T	IL1R2_ENST00000441002.1_Silent_p.T77T|IL1R2_ENST00000393414.2_Silent_p.T77T	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	77	Ig-like C2-type 1.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						CTGCTAGGACGGTCCCAGGAG	0.597													G|||	215	0.0429313	0.1551	0.013	5008	,	,		18355	0.0		0.001	False		,,,				2504	0.0				p.T77T	Pancreas(106;189 1628 2302 5133 12295)	Atlas-SNP	.											.	IL1R2	58	.	0			c.G231A						PASS	.	G	,	507,3899	234.6+/-247.4	31,445,1727	157.0	164.0	161.0		231,231	-3.7	0.0	2	dbSNP_98	161	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	IL1R2	NM_004633.3,NM_173343.1	,	31,457,6015	AA,AG,GG		0.1395,11.507,3.9905	,	77/399,77/399	102626187	519,12487	2203	4300	6503	SO:0001819	synonymous_variant	7850	exon3			TAGGACGGTCCCA	X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.231G>A	2.37:g.102626187G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_001261419	D3DVJ5|Q6LCE6|Q9UE68	Silent	SNP	ENST00000332549.3	37	CCDS2054.1																																																																																			G|0.958;A|0.042	0.042	strong		0.597	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633	
SLCO6A1	133482	hgsc.bcm.edu	37	5	101748741	101748741	+	Missense_Mutation	SNP	G	G	C	rs10073333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:101748741G>C	ENST00000506729.1	-	9	1750	c.1579C>G	c.(1579-1581)Ccc>Gcc	p.P527A	SLCO6A1_ENST00000389019.3_Missense_Mutation_p.P465A|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.P274A|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.P527A|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.P274A			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	527	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.		P -> A (in dbSNP:rs10073333).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		GCAAAGCAGGGAGAAAAATAT	0.289													G|||	370	0.0738818	0.1172	0.1052	5008	,	,		11914	0.0159		0.0736	False		,,,				2504	0.0532				p.P527A		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.C1579G						PASS	.	G	ALA/PRO	430,3968	182.2+/-210.1	23,384,1792	29.0	30.0	30.0		1579	2.5	1.0	5	dbSNP_119	30	510,8082	138.1+/-194.9	17,476,3803	yes	missense	SLCO6A1	NM_173488.3	27	40,860,5595	CC,CG,GG		5.9358,9.7772,7.2363	probably-damaging	527/720	101748741	940,12050	2199	4296	6495	SO:0001583	missense	133482	exon9			AGCAGGGAGAAAA	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"""Solute carriers"""	23613	protein-coding gene	gene with protein product	"""cancer/testis antigen 48"""	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1579C>G	5.37:g.101748741G>C	ENSP00000421339:p.Pro527Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	161	85	0.52795	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	173	0.07921245421245421	57	0.11585365853658537	45	0.12430939226519337	13	0.022727272727272728	58	0.07651715039577836	G	13.67	2.305522	0.40795	0.097772	0.059358	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.03951	3.75;3.75;3.75;3.75;3.75	5.25	2.48	0.30137	Major facilitator superfamily domain, general substrate transporter (1);Protease inhibitor, Kazal-type (1);	0.421858	0.22619	N	0.057724	T	0.00178	0.0005	L	0.50333	1.59	0.25923	P	0.9830903	D;P;D	0.69078	0.976;0.872;0.997	P;P;D	0.66716	0.797;0.888;0.946	T	0.25950	-1.0117	9	0.29301	T	0.29	.	6.2915	0.21063	0.1674:0.1526:0.68:0.0	rs10073333;rs10073333	465;274;527	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	A	527;527;465;274;274	ENSP00000421339:P527A;ENSP00000369135:P527A;ENSP00000373671:P465A;ENSP00000421990:P274A;ENSP00000369138:P274A	ENSP00000369135:P527A	P	-	1	0	SLCO6A1	101776640	1.000000	0.71417	0.998000	0.56505	0.359000	0.29487	1.692000	0.37731	0.348000	0.23949	0.655000	0.94253	CCC	G|0.932;C|0.068	0.068	strong		0.289	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
AZU1	566	hgsc.bcm.edu	37	19	831811	831811	+	Silent	SNP	C	C	T	rs588442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:831811C>T	ENST00000233997.2	+	5	711	c.690C>T	c.(688-690)acC>acT	p.T230T		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	230	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		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;0.000172)|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)		ACTTCTTCACCCGAGTGGCGC	0.711													C|||	405	0.0808706	0.2935	0.0216	5008	,	,		12838	0.0		0.002	False		,,,				2504	0.0				p.T230T		Atlas-SNP	.											.	AZU1	31	.	0			c.C690T						PASS	.	C		1054,3346		120,814,1266	32.0	36.0	35.0		690	0.8	0.1	19	dbSNP_83	35	6,8588		0,6,4291	no	coding-synonymous	AZU1	NM_001700.3		120,820,5557	TT,TC,CC		0.0698,23.9545,8.1576		230/252	831811	1060,11934	2200	4297	6497	SO:0001819	synonymous_variant	566	exon5			CTTCACCCGAGTG	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.690C>T	19.37:g.831811C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Silent	SNP	ENST00000233997.2	37	CCDS12044.1																																																																																			C|0.897;T|0.103	0.103	strong		0.711	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
ZNF717	100131827	hgsc.bcm.edu	37	3	75790797	75790797	+	De_novo_Start_InFrame	SNP	C	C	T	rs147946451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:75790797C>T	ENST00000478296.1	-	0	274				ZNF717_ENST00000400845.3_Missense_Mutation_p.V43M|ZNF717_ENST00000422325.1_Missense_Mutation_p.V50M|ZNF717_ENST00000477374.1_Missense_Mutation_p.V50M|ZNF717_ENST00000491507.1_5'UTR			Q9BY31	ZN717_HUMAN	zinc finger protein 717						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TCCAGCATCACGTCCCTGTAC	0.502																																					p.V50M		Atlas-SNP	.											ZNF717,NS,malignant_melanoma,0,1	ZNF717	160	1	0			c.G148A						scavenged	.						16.0	13.0	14.0					3																	75790797		444	1237	1681			100131827	exon3			GCATCACGTCCCT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965		3.37:g.75790797C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	77	13	0.168831	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		562	0.2573260073260073	83	0.16869918699186992	111	0.30662983425414364	134	0.23426573426573427	234	0.3087071240105541	.	14.80	2.645039	0.47258	.	.	ENSG00000227124	ENST00000477374;ENST00000422325;ENST00000400845;ENST00000468296	T;T;T;T	0.04015	3.73;3.73;3.73;3.73	1.97	1.97	0.26223	.	.	.	.	.	T	0.00012	0.0000	M	0.92833	3.35	0.36926	P	0.10836100000000004	D	0.89917	1.0	D	0.64776	0.929	T	0.22417	-1.0217	8	0.72032	D	0.01	.	9.6897	0.40120	0.0:1.0:0.0:0.0	.	50	C9JSV9	.	M	50;50;43;50	ENSP00000417902:V50M;ENSP00000409514:V50M;ENSP00000383643:V43M;ENSP00000418187:V50M	ENSP00000383643:V43M	V	-	1	0	ZNF717	75873487	0.243000	0.23878	0.981000	0.43875	0.552000	0.35366	1.184000	0.32053	1.127000	0.42034	0.545000	0.68477	GTG	C|0.753;T|0.247	0.247	strong		0.502	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
KIAA0020	9933	hgsc.bcm.edu	37	9	2811522	2811522	+	Missense_Mutation	SNP	T	T	A	rs60717199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2811522T>A	ENST00000397885.2	-	15	1680	c.1474A>T	c.(1474-1476)Agc>Tgc	p.S492C		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	492	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		TGCAGGTAGCTTAACAAAGCT	0.473													T|||	109	0.0217652	0.0764	0.0101	5008	,	,		19686	0.0		0.001	False		,,,				2504	0.0				p.S492C		Atlas-SNP	.											.	KIAA0020	56	.	0			c.A1474T						PASS	.	T	CYS/SER	263,4143	148.8+/-183.1	7,249,1947	148.0	137.0	140.0		1474	4.8	0.8	9	dbSNP_129	140	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KIAA0020	NM_014878.4	112	7,252,6244	AA,AT,TT		0.0349,5.9691,2.0452	probably-damaging	492/649	2811522	266,12740	2203	4300	6503	SO:0001583	missense	9933	exon15			GGTAGCTTAACAA	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.1474A>T	9.37:g.2811522T>A	ENSP00000380982:p.Ser492Cys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	102	42	0.411765	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	T	19.38	3.816861	0.70912	0.059691	3.49E-4	ENSG00000080608	ENST00000397885	T	0.46063	0.88	5.97	4.84	0.62591	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.452768	0.30676	N	0.009106	T	0.07773	0.0195	M	0.63843	1.955	0.29221	N	0.87392	P;P	0.43607	0.544;0.812	P;P	0.54856	0.656;0.762	T	0.18147	-1.0346	10	0.66056	D	0.02	-29.6696	9.6157	0.39690	0.0:0.1502:0.0:0.8498	rs60717199	352;492	B2RDG4;Q15397	.;K0020_HUMAN	C	492	ENSP00000380982:S492C	ENSP00000380982:S492C	S	-	1	0	KIAA0020	2801522	1.000000	0.71417	0.841000	0.33234	0.884000	0.51177	2.579000	0.46059	1.089000	0.41292	0.533000	0.62120	AGC	T|0.980;A|0.020	0.020	strong		0.473	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
ANKRD18A	253650	hgsc.bcm.edu	37	9	38588602	38588602	+	Missense_Mutation	SNP	T	T	C	rs2799163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:38588602T>C	ENST00000399703.5	-	11	2437	c.2063A>G	c.(2062-2064)tAt>tGt	p.Y688C		NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	688			Y -> C (in dbSNP:rs2799163).							NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						GTCCGCAGTATAGTTCAGTAA	0.274													t|||	1964	0.392173	0.6021	0.3718	5008	,	,		16295	0.4772		0.2744	False		,,,				2504	0.1564				p.Y688C		Atlas-SNP	.											ANKRD18A,NS,carcinoma,0,1	ANKRD18A	49	1	0			c.A2063G						PASS	.						71.0	61.0	64.0					9																	38588602		692	1575	2267	SO:0001583	missense	253650	exon11			GCAGTATAGTTCA	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.2063A>G	9.37:g.38588602T>C	ENSP00000382610:p.Tyr688Cys	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	216	88	0.407407	NM_147195	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	Missense_Mutation	SNP	ENST00000399703.5	37	CCDS55311.1	916	0.4194139194139194	333	0.676829268292683	125	0.3453038674033149	240	0.4195804195804196	218	0.287598944591029	T	6.894	0.534440	0.13188	.	.	ENSG00000180071	ENST00000399703	T	0.28666	1.6	1.39	0.0723	0.14386	.	.	.	.	.	T	0.00012	0.0000	L	0.37630	1.12	0.80722	P	0.0	D	0.62365	0.991	P	0.46389	0.515	T	0.37549	-0.9701	8	0.38643	T	0.18	.	2.3016	0.04163	0.2838:0.0:0.2876:0.4286	rs2799163;rs52796725;rs59755233;rs2799163	688	Q8IVF6	AN18A_HUMAN	C	688	ENSP00000382610:Y688C	ENSP00000382610:Y688C	Y	-	2	0	ANKRD18A	38578602	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.520000	0.06252	0.006000	0.14734	0.145000	0.16022	TAT	T|0.588;C|0.412	0.412	strong		0.274	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052506.3		
AHNAK2	113146	hgsc.bcm.edu	37	14	105416621	105416621	+	Missense_Mutation	SNP	T	T	C	rs11848082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416621T>C	ENST00000333244.5	-	7	5286	c.5167A>G	c.(5167-5169)Aac>Gac	p.N1723D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1723						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)			AGTTTCACGTTCACTTGGCCA	0.627													.|||	217	0.0433307	0.152	0.013	5008	,	,		15030	0.002		0.001	False		,,,				2504	0.0041				p.N1723D		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A5167G						PASS	.	C	ASP/ASN	470,3246		77,316,1465	94.0	111.0	106.0		5167	4.0	0.0	14	dbSNP_120	106	6,8110		1,4,4053	no	missense	AHNAK2	NM_138420.2	23	78,320,5518	CC,CT,TT		0.0739,12.648,4.023	benign	1723/5796	105416621	476,11356	1858	4058	5916	SO:0001583	missense	113146	exon7			TCACGTTCACTTG	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.5167A>G	14.37:g.105416621T>C	ENSP00000353114:p.Asn1723Asp	Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	254	109	0.429134	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	52	0.023809523809523808	46	0.09349593495934959	5	0.013812154696132596	1	0.0017482517482517483	0	0.0	N	0.748	-0.773884	0.02951	0.12648	7.39E-4	ENSG00000185567	ENST00000333244	T	0.00591	6.35	3.97	3.97	0.46021	.	.	.	.	.	T	0.00012	0.0000	N	0.00159	-1.955	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31503	-0.9941	9	0.06757	T	0.87	.	7.908	0.29774	0.0:0.7962:0.0:0.2038	rs60164864	1723	Q8IVF2	AHNK2_HUMAN	D	1723	ENSP00000353114:N1723D	ENSP00000353114:N1723D	N	-	1	0	AHNAK2	104487666	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.259000	0.18405	0.665000	0.31066	-0.459000	0.05422	AAC	T|0.977;C|0.023	0.023	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
KLHL13	90293	hgsc.bcm.edu	37	X	117053499	117053499	+	Silent	SNP	C	C	T	rs6645994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:117053499C>T	ENST00000262820.3	-	4	1464	c.555G>A	c.(553-555)gtG>gtA	p.V185V	KLHL13_ENST00000371882.1_Silent_p.V134V|KLHL13_ENST00000545703.1_Silent_p.V143V|KLHL13_ENST00000539496.1_Silent_p.V188V|KLHL13_ENST00000541812.1_Silent_p.V169V|KLHL13_ENST00000371878.1_Silent_p.V134V|KLHL13_ENST00000469946.1_Silent_p.V134V|KLHL13_ENST00000371876.1_Silent_p.V134V|KLHL13_ENST00000540167.1_Silent_p.V169V	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	185					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						ATATGAGAAACACTTTACAGA	0.403													T|||	956	0.253245	0.6142	0.0793	3775	,	,		12883	0.0		0.0537	False		,,,				2504	0.0358				p.V188V		Atlas-SNP	.											.	KLHL13	87	.	0			c.G564A						PASS	.	T	,,,,,	2628,1207		767,687,407,178,164	72.0	84.0	80.0		564,537,507,507,429,555	-7.5	0.6	X	dbSNP_116	80	513,6215		22,320,149,2086,1723	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KLHL13	NM_001168299.1,NM_001168300.1,NM_001168301.1,NM_001168302.1,NM_001168303.1,NM_033495.3	,,,,,	789,1007,556,2264,1887	TT,TC,T,CC,C		7.6249,31.4733,29.7359	,,,,,	188/659,179/650,169/640,169/640,143/614,185/656	117053499	3141,7422	2203	4300	6503	SO:0001819	synonymous_variant	90293	exon5			GAGAAACACTTTA	AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"""Kelch-like"", ""BTB/POZ domain containing"""	22931	protein-coding gene	gene with protein product		300655	"""BTB and kelch domain containing 2, KIAA1309"", ""kelch-like 13 (Drosophila)"""	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.555G>A	X.37:g.117053499C>T		Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	270	270	1	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Silent	SNP	ENST00000262820.3	37	CCDS14571.1																																																																																			C|0.688;0|0.003	.	strong		0.403	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495	
HELQ	113510	hgsc.bcm.edu	37	4	84361071	84361071	+	Missense_Mutation	SNP	G	G	A	rs6817280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84361071G>A	ENST00000295488.3	-	8	1915	c.1753C>T	c.(1753-1755)Cct>Tct	p.P585S	HELQ_ENST00000510985.1_Missense_Mutation_p.P518S	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	585	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		P -> S (in dbSNP:rs6817280).		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						TTCTTACTAGGACAAAAAACT	0.303								Other identified genes with known or suspected DNA repair function					G|||	422	0.0842652	0.3026	0.0303	5008	,	,		16565	0.0		0.001	False		,,,				2504	0.0				p.P585S		Atlas-SNP	.											.	HELQ	95	.	0			c.C1753T						PASS	.	G	SER/PRO	1127,3279	391.0+/-327.9	138,851,1214	64.0	67.0	66.0		1753	5.7	1.0	4	dbSNP_116	66	14,8584	9.1+/-34.3	0,14,4285	yes	missense	HELQ	NM_133636.2	74	138,865,5499	AA,AG,GG		0.1628,25.5788,8.7742	possibly-damaging	585/1102	84361071	1141,11863	2203	4299	6502	SO:0001583	missense	113510	exon8			TACTAGGACAAAA	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.1753C>T	4.37:g.84361071G>A	ENSP00000295488:p.Pro585Ser	Somatic	335	1	0.00298507		WXS	Illumina HiSeq	Phase_I	376	192	0.510638	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	134	0.06135531135531135	122	0.24796747967479674	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	G	21.9	4.217196	0.79352	0.255788	0.001628	ENSG00000163312	ENST00000295488;ENST00000510985	T;D	0.91686	-0.57;-2.89	5.68	5.68	0.88126	Helicase, C-terminal (1);	0.051961	0.85682	D	0.000000	T	0.00144	0.0004	L	0.28694	0.88	0.09310	P	0.99999999573404	D;P	0.71674	0.998;0.855	D;P	0.64687	0.928;0.474	T	0.42361	-0.9456	9	0.11485	T	0.65	.	19.7785	0.96405	0.0:0.0:1.0:0.0	rs6817280;rs6817280	518;585	E3W980;Q8TDG4	.;HELQ_HUMAN	S	585;518	ENSP00000295488:P585S;ENSP00000424539:P518S	ENSP00000295488:P585S	P	-	1	0	HELQ	84580095	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.458000	0.66679	2.675000	0.91044	0.655000	0.94253	CCT	G|0.916;A|0.084	0.084	strong		0.303	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
WNK4	65266	hgsc.bcm.edu	37	17	40939855	40939855	+	Missense_Mutation	SNP	G	G	T	rs55781437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40939855G>T	ENST00000246914.5	+	8	1822	c.1801G>T	c.(1801-1803)Gcc>Tcc	p.A601S	WNK4_ENST00000587705.1_Intron	NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	601			A -> S (in dbSNP:rs55781437).		chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CTCAGACCCTGCCCTTCAGCC	0.622													G|||	514	0.102636	0.2549	0.0231	5008	,	,		17169	0.0387		0.004	False		,,,				2504	0.1207				p.A601S	Esophageal Squamous(6;201 374 4964 23855 42828)	Atlas-SNP	.											WNK4_ENST00000246914,NS,carcinoma,0,2	WNK4	182	2	0			c.G1801T						PASS	.	G	SER/ALA	890,3420		90,710,1355	39.0	42.0	41.0		1801	4.1	1.0	17	dbSNP_129	41	10,8456		0,10,4223	yes	missense	WNK4	NM_032387.4	99	90,720,5578	TT,TG,GG		0.1181,20.6497,7.0445	benign	601/1244	40939855	900,11876	2155	4233	6388	SO:0001583	missense	65266	exon8			GACCCTGCCCTTC	AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.1801G>T	17.37:g.40939855G>T	ENSP00000246914:p.Ala601Ser	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Missense_Mutation	SNP	ENST00000246914.5	37	CCDS11439.1	144	0.06593406593406594	112	0.22764227642276422	7	0.019337016574585635	22	0.038461538461538464	3	0.00395778364116095	G	11.42	1.633369	0.29068	0.206497	0.001181	ENSG00000126562	ENST00000246914;ENST00000316085	T	0.69926	-0.44	5.11	4.07	0.47477	.	0.146668	0.31542	N	0.007471	T	0.00039	0.0001	N	0.22421	0.69	0.40049	P	0.024248999999999965	B;B;B	0.21520	0.05;0.057;0.057	B;B;B	0.23574	0.047;0.02;0.02	T	0.04191	-1.0970	9	0.19147	T	0.46	-16.9249	7.9074	0.29769	0.0:0.1744:0.6453:0.1803	rs55781437;rs61755596	601;601;601	Q96J92-3;B0LPI0;Q96J92	.;.;WNK4_HUMAN	S	601;373	ENSP00000246914:A601S	ENSP00000246914:A601S	A	+	1	0	WNK4	38193381	0.733000	0.28132	1.000000	0.80357	0.957000	0.61999	1.160000	0.31761	2.381000	0.81170	0.555000	0.69702	GCC	G|0.929;T|0.071	0.071	strong		0.622	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
LAMA2	3908	hgsc.bcm.edu	37	6	129691132	129691132	+	Silent	SNP	C	C	G	rs17057184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:129691132C>G	ENST00000421865.2	+	34	5005	c.4956C>G	c.(4954-4956)acC>acG	p.T1652T		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1652	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		AGCTGCTGACCAGGGTAAGGT	0.448													C|||	484	0.0966454	0.1104	0.1484	5008	,	,		18463	0.0466		0.0706	False		,,,				2504	0.1196				p.T1652T		Atlas-SNP	.											.	LAMA2	481	.	0			c.C4956G						PASS	.	C	,	498,3908	231.4+/-245.2	31,436,1736	65.0	66.0	65.0		4956,4956	2.1	1.0	6	dbSNP_123	65	529,8071	148.3+/-203.6	19,491,3790	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	50,927,5526	GG,GC,CC		6.1512,11.3028,7.8964	,	1652/3123,1652/3119	129691132	1027,11979	2203	4300	6503	SO:0001819	synonymous_variant	3908	exon34			GCTGACCAGGGTA	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.4956C>G	6.37:g.129691132C>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			C|0.919;G|0.081	0.081	strong		0.448	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
IDH3B	3420	hgsc.bcm.edu	37	20	2639162	2639162	+	3'UTR	SNP	T	T	C	rs8296	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2639162T>C	ENST00000380843.4	-	0	1423				IDH3B_ENST00000380851.5_Missense_Mutation_p.T360A|IDH3B_ENST00000488299.1_5'UTR|SNORD86_ENST00000391196.1_RNA|SNORD56_ENST00000413522.1_RNA|SNORD57_ENST00000448188.1_RNA	NM_006899.3	NP_008830.2	O43837	IDH3B_HUMAN	isocitrate dehydrogenase 3 (NAD+) beta						2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|isocitrate metabolic process (GO:0006102)|NADH metabolic process (GO:0006734)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			breast(1)|endometrium(3)|kidney(2)|lung(7)|prostate(1)	14						ATGTCAGAGGTTCGAACCTGT	0.557													T|||	350	0.0698882	0.2481	0.0288	5008	,	,		20020	0.0		0.002	False		,,,				2504	0.0				p.T360A		Atlas-SNP	.											.	IDH3B	25	.	0			c.A1078G						PASS	.	T	,ALA/THR,	794,3612	318.0+/-295.4	68,658,1477	88.0	80.0	83.0		,1078,	5.8	1.0	20	dbSNP_52	83	10,8590	7.1+/-27.0	0,10,4290	yes	utr-3,missense,utr-3	IDH3B	NM_006899.2,NM_174855.1,NM_174856.1	,58,	68,668,5767	CC,CT,TT		0.1163,18.0209,6.1818	,,	,360/384,	2639162	804,12202	2203	4300	6503	SO:0001624	3_prime_UTR_variant	3420	exon12			CAGAGGTTCGAAC		CCDS13031.1, CCDS13032.1, CCDS74696.1	20p13	2013-02-14			ENSG00000101365	ENSG00000101365	1.1.1.41		5385	protein-coding gene	gene with protein product		604526				10575215	Standard	NM_006899		Approved	RP46	uc002wgp.4	O43837	OTTHUMG00000031699	ENST00000380843.4:c.*235A>G	20.37:g.2639162T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	142	76	0.535211	NM_174855	B2RDR1|D3DVX2|D3DVX3|O95106|Q5JXS8|Q9NQ06|Q9NQ07|Q9NUZ0|Q9UEX0|Q9UG99	Missense_Mutation	SNP	ENST00000380843.4	37	CCDS13032.1	131	0.059981684981684984	122	0.24796747967479674	7	0.019337016574585635	0	0.0	2	0.002638522427440633	T	24.2	4.508529	0.85282	0.180209	0.001163	ENSG00000101365	ENST00000380851	T	0.75154	-0.91	5.83	5.83	0.93111	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	D	0.89917	1.0	D	0.97110	1.0	T	0.00144	-1.1994	7	0.87932	D	0	.	14.1519	0.65392	0.0:0.0:0.0:1.0	rs8296;rs3171331;rs52803478;rs8296	360	O43837-2	.	A	360	ENSP00000370232:T360A	ENSP00000370232:T360A	T	-	1	0	IDH3B	2587162	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.857000	0.75455	2.224000	0.72417	0.477000	0.44152	ACC	T|0.938;C|0.062	0.062	strong		0.557	IDH3B-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077613.1		
ACADL	33	hgsc.bcm.edu	37	2	211060050	211060050	+	Missense_Mutation	SNP	T	T	G	rs2286963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:211060050T>G	ENST00000233710.3	-	9	1224	c.997A>C	c.(997-999)Aaa>Caa	p.K333Q	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	333			K -> Q (in dbSNP:rs2286963). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.7}.		carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		TCTGCTAATTTATGTTGCACT	0.353													T|||	1057	0.211062	0.0893	0.2248	5008	,	,		18082	0.1865		0.3131	False		,,,				2504	0.2863				p.K333Q		Atlas-SNP	.											.	ACADL	38	.	0			c.A997C						PASS	.	T	GLN/LYS	661,3745	280.5+/-275.4	53,555,1595	90.0	86.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	997	5.8	1.0	2	dbSNP_100	88	2936,5664	456.2+/-364.0	488,1960,1852	yes	missense	ACADL	NM_001608.3	53	541,2515,3447	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	34.1395,15.0023,27.6565	probably-damaging	333/431	211060050	3597,9409	2203	4300	6503	SO:0001583	missense	33	exon9			CTAATTTATGTTG	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"""acyl-Coenzyme A dehydrogenase, long chain"""			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.997A>C	2.37:g.211060050T>G	ENSP00000233710:p.Lys333Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	115	62	0.53913	NM_001608	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	37	CCDS2389.1	500	0.22893772893772893	55	0.11178861788617886	100	0.27624309392265195	105	0.18356643356643357	240	0.316622691292876	T	18.22	3.576473	0.65878	0.150023	0.341395	ENSG00000115361	ENST00000233710	D	0.96232	-3.95	5.77	5.77	0.91146	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.041576	0.85682	D	0.000000	T	0.00039	0.0001	L	0.57130	1.785	0.09310	P	0.99999853838	D	0.56968	0.978	P	0.58577	0.841	T	0.00000	-1.5769	9	0.31617	T	0.26	.	16.1475	0.81580	0.0:0.0:0.0:1.0	rs2286963;rs17769161;rs56601090;rs59503505;rs2286963	333	P28330	ACADL_HUMAN	Q	333	ENSP00000233710:K333Q	ENSP00000233710:K333Q	K	-	1	0	ACADL	210768295	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	6.842000	0.75379	2.213000	0.71641	0.529000	0.55759	AAA	G|0.250;N|0.000	0.250	strong		0.353	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766474	27766474	+	Missense_Mutation	SNP	G	G	A	rs375048390		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:27766474G>A	ENST00000451261.2	+	5	1861	c.1462G>A	c.(1462-1464)Ggt>Agt	p.G488S		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	488										central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						TGTAGTGAGCGGTAGTGATTG	0.438													G|||	1	0.000264901	0.0008	0.0	3775	,	,		15465	0.0		0.0	False		,,,				2504	0.0				p.G488S		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G1462A						PASS	.	G	SER/GLY	2,1207		0,1,1,516,174	86.0	63.0	70.0		1462	3.8	0.8	X		70	0,2391		0,0,0,800,791	no	missense	DCAF8L2	NM_001136533.1	56	0,1,1,1316,965	AA,AG,A,GG,G		0.0,0.1654,0.0556	probably-damaging	488/632	27766474	2,3598	692	1591	2283	SO:0001583	missense	347442	exon1			GTGAGCGGTAGTG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1462G>A	X.37:g.27766474G>A	ENSP00000462745:p.Gly488Ser	Somatic	295	1	0.00338983		WXS	Illumina HiSeq	Phase_I	250	138	0.552	NM_001136533	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			.	.	weak		0.438	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
BZRAP1	9256	hgsc.bcm.edu	37	17	56389631	56389631	+	Missense_Mutation	SNP	A	A	G	rs9905604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56389631A>G	ENST00000343736.4	-	17	2714	c.2551T>C	c.(2551-2553)Tgg>Cgg	p.W851R	BZRAP1_ENST00000268893.6_Missense_Mutation_p.W791R|BZRAP1_ENST00000355701.3_Missense_Mutation_p.W851R			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	851	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		W -> R (in dbSNP:rs9905604). {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)					GGCCCGGCCCACAGGTCCAGG	0.672													G|||	555	0.110823	0.1498	0.0735	5008	,	,		15498	0.1329		0.0716	False		,,,				2504	0.1022				p.W851R		Atlas-SNP	.											.	BZRAP1	287	.	0			c.T2551C						PASS	.	G	ARG/TRP,ARG/TRP	630,3772		45,540,1616	16.0	19.0	18.0		2551,2371	4.8	0.9	17	dbSNP_119	18	600,7988		22,556,3716	no	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	101,101	67,1096,5332	GG,GA,AA		6.9865,14.3117,9.4688	benign,benign	851/1858,791/1798	56389631	1230,11760	2201	4294	6495	SO:0001583	missense	9256	exon17			CGGCCCACAGGTC	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.2551T>C	17.37:g.56389631A>G	ENSP00000345824:p.Trp851Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	233	0.10668498168498168	71	0.1443089430894309	24	0.06629834254143646	80	0.13986013986013987	58	0.07651715039577836	G	0.107	-1.144254	0.01728	0.143117	0.069865	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.03801	3.8;3.8;3.8	4.85	4.85	0.62838	Fibronectin, type III (2);	0.779586	0.12696	N	0.446731	T	0.00012	0.0000	N	0.00347	-1.61	0.58432	P	5.999999999950489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34775	-0.9815	9	0.08837	T	0.75	.	7.5473	0.27775	0.0799:0.0:0.6493:0.2709	rs9905604;rs9905604	851;791;851	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	R	851;851;791	ENSP00000347929:W851R;ENSP00000345824:W851R;ENSP00000268893:W791R	ENSP00000268893:W791R	W	-	1	0	BZRAP1	53744630	0.083000	0.21467	0.895000	0.35142	0.758000	0.43043	1.008000	0.29872	1.189000	0.43028	-0.374000	0.07098	TGG	A|0.901;G|0.099	0.099	strong		0.672	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
OR2D3	120775	hgsc.bcm.edu	37	11	6942695	6942695	+	Missense_Mutation	SNP	C	C	T	rs12806437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	301	0	0		WXS	Illumina HiSeq	Phase_I	335	168	0.501493	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	
SMCO1	255798	hgsc.bcm.edu	37	3	196235191	196235191	+	Missense_Mutation	SNP	A	A	G	rs73891273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196235191A>G	ENST00000397537.2	-	3	368	c.212T>C	c.(211-213)aTg>aCg	p.M71T		NM_001077657.1	NP_001071125.1	Q147U7	SMCO1_HUMAN	single-pass membrane protein with coiled-coil domains 1	71						integral component of membrane (GO:0016021)											ATTCAATTCCATTGAAGTGAG	0.358													.|||	265	0.0529153	0.1876	0.0231	5008	,	,		16968	0.0		0.001	False		,,,				2504	0.0				p.M71T		Atlas-SNP	.											C3orf43,NS,carcinoma,+1,1	C3orf43	25	1	0			c.T212C						PASS	.	A	THR/MET	559,3137		45,469,1334	62.0	60.0	60.0		212	5.5	1.0	3	dbSNP_130	60	5,8181		0,5,4088	yes	missense	C3orf43	NM_001077657.1	81	45,474,5422	GG,GA,AA		0.0611,15.1245,4.7467	possibly-damaging	71/215	196235191	564,11318	1848	4093	5941	SO:0001583	missense	255798	exon3			AATTCCATTGAAG	AK123917	CCDS43192.1	3q29	2013-03-08	2013-03-08	2013-03-08	ENSG00000214097	ENSG00000214097			27407	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 43"""	C3orf43			Standard	NM_001077657		Approved	FLJ41923, DKFZp313B0440		Q147U7	OTTHUMG00000155581	ENST00000397537.2:c.212T>C	3.37:g.196235191A>G	ENSP00000380671:p.Met71Thr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_001077657	B3KW20	Missense_Mutation	SNP	ENST00000397537.2	37	CCDS43192.1	97	0.044413919413919416	90	0.18292682926829268	7	0.019337016574585635	0	0.0	0	0.0	A	14.07	2.425685	0.43020	0.151245	6.11E-4	ENSG00000214097	ENST00000397537	T	0.36699	1.24	5.46	5.46	0.80206	.	.	.	.	.	T	0.00073	0.0002	L	0.34521	1.04	0.30114	P	0.806335	B;B	0.32160	0.358;0.358	B;B	0.32762	0.152;0.152	T	0.11179	-1.0598	8	0.59425	D	0.04	-16.9577	13.0552	0.58975	1.0:0.0:0.0:0.0	.	71;63	Q147U7;E9PGG7	CC043_HUMAN;.	T	71	ENSP00000380671:M71T	ENSP00000380671:M71T	M	-	2	0	C3orf43	197719588	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.753000	0.62183	2.062000	0.61559	0.533000	0.62120	ATG	A|0.971;G|0.029	0.029	strong		0.358	SMCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340776.1	NM_001006109	
ZNF224	7767	hgsc.bcm.edu	37	19	44611162	44611162	+	Silent	SNP	G	G	T	rs13346417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44611162G>T	ENST00000336976.6	+	6	1103	c.849G>T	c.(847-849)acG>acT	p.T283T	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	283					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.T283T(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)				GAATCCATACGGGGGAGAAGC	0.428													G|||	697	0.139177	0.3147	0.1859	5008	,	,		22095	0.0833		0.0229	False		,,,				2504	0.046				p.T283T		Atlas-SNP	.											ZNF224,NS,carcinoma,0,1	ZNF224	70	1	1	Substitution - coding silent(1)	stomach(1)	c.G849T						PASS	.	G		1119,3287	397.9+/-330.6	156,807,1240	131.0	134.0	133.0		849	-6.9	0.0	19	dbSNP_121	133	87,8513	48.1+/-107.5	2,83,4215	no	coding-synonymous	ZNF224	NM_013398.2		158,890,5455	TT,TG,GG		1.0116,25.3972,9.2726		283/708	44611162	1206,11800	2203	4300	6503	SO:0001819	synonymous_variant	7767	exon6			CCATACGGGGGAG	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.849G>T	19.37:g.44611162G>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	137	63	0.459854	NM_013398	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Silent	SNP	ENST00000336976.6	37	CCDS33046.1																																																																																			G|0.904;T|0.096	0.096	strong		0.428	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398	
DAAM1	23002	hgsc.bcm.edu	37	14	59789892	59789892	+	Silent	SNP	G	G	T	rs17096074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:59789892G>T	ENST00000395125.1	+	5	746	c.723G>T	c.(721-723)ctG>ctT	p.L241L	DAAM1_ENST00000360909.3_Silent_p.L241L|DAAM1_ENST00000351081.1_Silent_p.L241L	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	241	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AGAAGGTTCTGCAGGCCATGC	0.552													G|||	147	0.029353	0.0053	0.0375	5008	,	,		18273	0.0109		0.0865	False		,,,				2504	0.0164				p.L241L		Atlas-SNP	.											DAAM1,NS,carcinoma,+2,1	DAAM1	95	1	0			c.G723T						scavenged	.	G		67,4339	64.1+/-101.4	0,67,2136	26.0	26.0	26.0		723	5.1	1.0	14	dbSNP_123	26	784,7816	180.3+/-229.3	32,720,3548	no	coding-synonymous	DAAM1	NM_014992.1		32,787,5684	TT,TG,GG		9.1163,1.5207,6.5431		241/1079	59789892	851,12155	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon6			GGTTCTGCAGGCC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.723G>T	14.37:g.59789892G>T		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	116	63	0.543103	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.945;T|0.055	0.055	strong		0.552	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
ZNF142	7701	hgsc.bcm.edu	37	2	219515109	219515109	+	Missense_Mutation	SNP	T	T	G	rs61733648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219515109T>G	ENST00000449707.1	-	5	842	c.421A>C	c.(421-423)Aaa>Caa	p.K141Q	ZNF142_ENST00000411696.2_Missense_Mutation_p.K141Q	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	141					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(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CCTTGGCCTTTATCCACAGCC	0.527													T|||	67	0.0133786	0.0492	0.0029	5008	,	,		19332	0.0		0.0	False		,,,				2504	0.0				p.K141Q	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.A421C						PASS	.	T	GLN/LYS	162,3762		0,162,1800	230.0	233.0	232.0		421	4.1	0.0	2	dbSNP_129	232	1,8297		0,1,4148	yes	missense	ZNF142	NM_001105537.1	53	0,163,5948	GG,GT,TT		0.0121,4.1284,1.3337	possibly-damaging	141/1688	219515109	163,12059	1962	4149	6111	SO:0001583	missense	7701	exon5			GGCCTTTATCCAC	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"""Zinc fingers, C2H2-type"""	12927	protein-coding gene	gene with protein product		604083	"""zinc finger protein 142 (clone pHZ-49)"""				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.421A>C	2.37:g.219515109T>G	ENSP00000408643:p.Lys141Gln	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	191	96	0.502618	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	37	CCDS42817.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	T	8.836	0.941010	0.18281	0.041284	1.21E-4	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.12984	2.63;2.63	5.2	4.05	0.47172	.	0.711144	0.13741	N	0.365968	T	0.02193	0.0068	L	0.44542	1.39	0.09310	N	1	P	0.39282	0.666	B	0.35859	0.212	T	0.21999	-1.0229	10	0.21014	T	0.42	-0.251	7.4012	0.26965	0.0:0.0962:0.0:0.9038	.	141	P52746	ZN142_HUMAN	Q	141	ENSP00000408643:K141Q;ENSP00000398798:K141Q	ENSP00000398798:K141Q	K	-	1	0	ZNF142	219223353	0.172000	0.23043	0.048000	0.18961	0.098000	0.18820	1.797000	0.38804	1.011000	0.39340	0.533000	0.62120	AAA	T|0.990;G|0.010	0.010	strong		0.527	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626790	140626790	+	Silent	SNP	A	A	C	rs3096082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	141	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	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	
MORN4	118812	hgsc.bcm.edu	37	10	99376092	99376092	+	Silent	SNP	T	T	C	rs3814555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99376092T>C	ENST00000307450.6	-	5	532	c.369A>G	c.(367-369)cgA>cgG	p.R123R	PI4K2A_ENST00000555577.1_Intron|PI4K2A_ENST00000370649.3_Intron|MORN4_ENST00000478953.1_3'UTR|MORN4_ENST00000335628.3_Silent_p.R181R	NM_001098831.1|NM_178832.3	NP_001092301.1|NP_849154.1	Q8NDC4	MORN4_HUMAN	MORN repeat containing 4	123								p.R123R(2)		large_intestine(1)|lung(1)|stomach(2)	4						ACTTCTCACGTCGCAGCAGCT	0.532													C|||	1497	0.298922	0.4864	0.2507	5008	,	,		19837	0.2817		0.1978	False		,,,				2504	0.2014				p.R123R		Atlas-SNP	.											MORN4_ENST00000307450,NS,carcinoma,0,4	MORN4	24	4	2	Substitution - coding silent(2)	stomach(2)	c.A369G						PASS	.	C	,	1921,2485	625.6+/-394.6	423,1075,705	61.0	58.0	59.0		369,369	-1.8	0.5	10	dbSNP_107	59	1886,6714	728.0+/-406.7	195,1496,2609	no	coding-synonymous,coding-synonymous	MORN4	NM_001098831.1,NM_178832.3	,	618,2571,3314	CC,CT,TT		21.9302,43.5996,29.2711	,	123/147,123/147	99376092	3807,9199	2203	4300	6503	SO:0001819	synonymous_variant	118812	exon5			CTCACGTCGCAGC	AJ431726	CCDS7468.1	10q24.2	2008-06-23	2008-06-23	2008-06-23	ENSG00000171160	ENSG00000171160			24001	protein-coding gene	gene with protein product	"""44050 protein"""		"""chromosome 10 open reading frame 83"""	C10orf83		12477932	Standard	NM_178832		Approved	bA548K23.4, FLJ25925	uc001koe.3	Q8NDC4	OTTHUMG00000018861	ENST00000307450.6:c.369A>G	10.37:g.99376092T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	92	36	0.391304	NM_001098831	Q86Y54	Silent	SNP	ENST00000307450.6	37	CCDS7468.1																																																																																			T|0.703;C|0.297	0.297	strong		0.532	MORN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049730.1	NM_178832	
PRICKLE4	29964	hgsc.bcm.edu	37	6	41753136	41753136	+	Missense_Mutation	SNP	G	G	A	rs35880970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41753136G>A	ENST00000394260.1	+	3	320	c.320G>A	c.(319-321)cGc>cAc	p.R107H	PRICKLE4_ENST00000458694.1_Missense_Mutation_p.R147H|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000394259.1_Missense_Mutation_p.R107H|PRICKLE4_ENST00000394263.1_Missense_Mutation_p.R147H|PRICKLE4_ENST00000359201.5_Missense_Mutation_p.R147H|TOMM6_ENST00000398884.3_5'Flank|PRICKLE4_ENST00000463606.1_3'UTR			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	107	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.					nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GGGGAACAGCGCTGCTGGCAC	0.602													G|||	81	0.0161741	0.0537	0.0072	5008	,	,		17211	0.0		0.001	False		,,,				2504	0.0041				p.R147H		Atlas-SNP	.											.	PRICKLE4	29	.	0			c.G440A						PASS	.	G	HIS/ARG	225,4181	134.1+/-170.4	6,213,1984	51.0	50.0	50.0		440	2.9	0.6	6	dbSNP_126	50	17,8583	11.2+/-40.8	0,17,4283	yes	missense	PRICKLE4	NM_013397.5	29	6,230,6267	AA,AG,GG		0.1977,5.1067,1.8607	benign	147/385	41753136	242,12764	2203	4300	6503	SO:0001583	missense	29964	exon6			AACAGCGCTGCTG	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"""chromosome 6 open reading frame 49"""	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.320G>A	6.37:g.41753136G>A	ENSP00000377803:p.Arg107His	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	79	77	0.974684	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Missense_Mutation	SNP	ENST00000394260.1	37		32	0.014652014652014652	28	0.056910569105691054	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	1.735	-0.493181	0.04322	0.051067	0.001977	ENSG00000124593	ENST00000458694;ENST00000359201;ENST00000394263;ENST00000394259;ENST00000394260	D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26;-2.26	4.71	2.91	0.33838	.	0.859014	0.09926	N	0.737859	T	0.63988	0.2558	L	0.35542	1.07	0.09310	N	1	B	0.25169	0.119	B	0.22601	0.04	T	0.55817	-0.8081	10	0.42905	T	0.14	-6.1033	4.9115	0.13823	0.084:0.1478:0.6159:0.1523	rs35880970	147	Q2TBC4-3	.	H	147;147;147;107;107	ENSP00000404911:R147H;ENSP00000352128:R147H;ENSP00000377806:R147H;ENSP00000377802:R107H;ENSP00000377803:R107H	ENSP00000335185:R147H	R	+	2	0	PRICKLE4	41861114	0.024000	0.19004	0.631000	0.29282	0.275000	0.26752	0.519000	0.22862	0.587000	0.29643	-0.258000	0.10820	CGC	G|0.982;A|0.018	0.018	strong		0.602	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397	
KIF26B	55083	hgsc.bcm.edu	37	1	245775265	245775265	+	Silent	SNP	C	C	T	rs61741293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:245775265C>T	ENST00000407071.2	+	9	2525	c.2085C>T	c.(2083-2085)agC>agT	p.S695S	RP11-522M21.2_ENST00000418402.1_RNA|KIF26B_ENST00000366518.4_Silent_p.S314S	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	695	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)			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)			TGGAGAAGAGCGGGAAAGGGG	0.587													C|||	71	0.0141773	0.0514	0.0029	5008	,	,		17393	0.0		0.001	False		,,,				2504	0.0				p.S695S		Atlas-SNP	.											.	KIF26B	343	.	0			c.C2085T						PASS	.	C		149,3979		1,147,1916	55.0	62.0	60.0		2085	0.9	1.0	1	dbSNP_129	60	4,8378		0,4,4187	no	coding-synonymous	KIF26B	NM_018012.3		1,151,6103	TT,TC,CC		0.0477,3.6095,1.223		695/2109	245775265	153,12357	2064	4191	6255	SO:0001819	synonymous_variant	55083	exon9			GAAGAGCGGGAAA	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.2085C>T	1.37:g.245775265C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	111	43	0.387387	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																			C|0.989;T|0.011	0.011	strong		0.587	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
DPH1	1801	hgsc.bcm.edu	37	17	1943525	1943525	+	Missense_Mutation	SNP	A	A	G	rs200693145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1943525A>G	ENST00000263083.6	+	8	823	c.778A>G	c.(778-780)Agc>Ggc	p.S260G	OVCA2_ENST00000572195.1_5'Flank|DPH1_ENST00000570477.1_Missense_Mutation_p.S180G|RP11-667K14.4_ENST00000572404.1_RNA	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	260					cell proliferation (GO:0008283)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	17						TGACCCATATAGCAAAGTCCT	0.557													A|||	6	0.00119808	0.0045	0.0	5008	,	,		19386	0.0		0.0	False		,,,				2504	0.0				p.S260G		Atlas-SNP	.											.	DPH1	32	.	0			c.A778G						PASS	.	A	GLY/SER	13,4155		0,13,2071	86.0	87.0	87.0		778	4.0	1.0	17		87	0,8422		0,0,4211	yes	missense	DPH1	NM_001383.3	56	0,13,6282	GG,GA,AA		0.0,0.3119,0.1033	benign	260/444	1943525	13,12577	2084	4211	6295	SO:0001583	missense	1801	exon8			CCATATAGCAAAG	S81752	CCDS42228.1	17p13.3	2013-05-02	2013-05-02	2005-06-03	ENSG00000108963	ENSG00000108963			3003	protein-coding gene	gene with protein product	"""ovarian tumor suppressor candidate 1"""	603527	"""diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (S. cerevisiae)"", ""DPH-like 1 (S. cerevisiae)"", ""DPH1 homolog (S. cerevisiae)"""	DPH2L, DPH2L1		8603384, 15485916, 22869748	Standard	NM_001383		Approved	OVCA1	uc002fts.3	Q9BZG8	OTTHUMG00000177724	ENST00000263083.6:c.778A>G	17.37:g.1943525A>G	ENSP00000263083:p.Ser260Gly	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	51	34	0.666667	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Missense_Mutation	SNP	ENST00000263083.6	37	CCDS42228.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	10.42	1.346368	0.24426	0.003119	0.0	ENSG00000108963	ENST00000263083	T	0.49720	0.77	5.15	4.03	0.46877	.	0.040549	0.85682	N	0.000000	T	0.48241	0.1489	M	0.74647	2.275	0.50467	D	0.999871	B;B;B	0.14805	0.011;0.011;0.003	B;B;B	0.23852	0.049;0.049;0.033	T	0.43410	-0.9393	10	0.46703	T	0.11	-13.6359	10.1501	0.42788	0.9183:0.0:0.0817:0.0	.	270;270;260	E7ENH3;B4DNK0;Q9BZG8	.;.;DPH1_HUMAN	G	260	ENSP00000263083:S260G	ENSP00000263083:S260G	S	+	1	0	DPH1	1890275	1.000000	0.71417	0.990000	0.47175	0.054000	0.15201	4.836000	0.62789	0.748000	0.32831	0.459000	0.35465	AGC	A|1.000;G|0.000	0.000	strong		0.557	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416784	105416784	+	Silent	SNP	A	A	G	rs59373922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416784A>G	ENST00000333244.5	-	7	5123	c.5004T>C	c.(5002-5004)ttT>ttC	p.F1668F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1668						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)			CCGACACCCCAAATGATGGCA	0.602													.|||	1298	0.259185	0.3563	0.1081	5008	,	,		17171	0.3462		0.1044	False		,,,				2504	0.3047				p.F1668F		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T5004C						PASS	.	G		1080,2792		259,562,1115	198.0	234.0	223.0		5004	-6.9	0.0	14	dbSNP_129	223	900,7304		141,618,3343	no	coding-synonymous	AHNAK2	NM_138420.2		400,1180,4458	GG,GA,AA		10.9703,27.8926,16.3962		1668/5796	105416784	1980,10096	1936	4102	6038	SO:0001819	synonymous_variant	113146	exon7			CACCCCAAATGAT	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.5004T>C	14.37:g.105416784A>G		Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	216	79	0.365741	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.835;G|0.165	0.165	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OR10G4	390264	hgsc.bcm.edu	37	11	123886822	123886822	+	Missense_Mutation	SNP	C	C	T	rs1893764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123886822C>T	ENST00000320891.4	+	1	541	c.541C>T	c.(541-543)Ccg>Tcg	p.P181S		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	181			P -> S (in dbSNP:rs1893764).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P181S(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CTGTGACGCACCGCCCATCCT	0.532													c|||	398	0.0794728	0.0787	0.147	5008	,	,		22538	0.1478		0.007	False		,,,				2504	0.0368				p.P181S		Atlas-SNP	.											OR10G4,rectum,carcinoma,-2,8	OR10G4	77	8	1	Substitution - Missense(1)	stomach(1)	c.C541T						PASS	.	C	SER/PRO	287,4115	159.2+/-191.8	8,271,1922	200.0	167.0	178.0		541	3.3	0.2	11	dbSNP_92	178	25,8569	17.3+/-56.4	0,25,4272	no	missense	OR10G4	NM_001004462.1	74	8,296,6194	TT,TC,CC		0.2909,6.5198,2.4007	probably-damaging	181/312	123886822	312,12684	2201	4297	6498	SO:0001583	missense	390264	exon1			GACGCACCGCCCA	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.541C>T	11.37:g.123886822C>T	ENSP00000325076:p.Pro181Ser	Somatic	501	0	0		WXS	Illumina HiSeq	Phase_I	482	266	0.551867	NM_001004462	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	192	0.08791208791208792	41	0.08333333333333333	59	0.16298342541436464	86	0.15034965034965034	6	0.0079155672823219	c	7.944	0.743428	0.15642	0.065198	0.002909	ENSG00000254737	ENST00000320891	T	0.00202	8.56	3.33	3.33	0.38152	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	D	0.000296	T	0.00012	0.0000	L	0.58510	1.815	0.80722	P	0.0	D	0.55605	0.972	D	0.65233	0.933	T	0.73940	-0.3824	9	0.41790	T	0.15	.	11.0054	0.47631	0.0:0.81:0.19:0.0	rs1893764;rs1893764	181	Q8NGN3	O10G4_HUMAN	S	181	ENSP00000325076:P181S	ENSP00000325076:P181S	P	+	1	0	OR10G4	123392032	0.000000	0.05858	0.168000	0.22838	0.011000	0.07611	-1.190000	0.03058	1.878000	0.54408	0.580000	0.79431	CCG	C|0.907;T|0.093	0.093	strong		0.532	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
DHX40	79665	hgsc.bcm.edu	37	17	57652789	57652789	+	Silent	SNP	C	C	T	rs77178464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:57652789C>T	ENST00000251241.4	+	7	1077	c.930C>T	c.(928-930)ctC>ctT	p.L310L	DHX40_ENST00000451169.2_Silent_p.L211L|DHX40_ENST00000425628.3_Silent_p.L233L	NM_024612.4	NP_078888.4	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	310	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(7)|large_intestine(6)|lung(6)|prostate(1)	20	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					ATACCACCCTCGATGGCTTGT	0.303													C|||	263	0.052516	0.1914	0.013	5008	,	,		16582	0.001		0.0	False		,,,				2504	0.0				p.L310L		Atlas-SNP	.											.	DHX40	40	.	0			c.C930T						PASS	.	C	,	569,3837	254.3+/-259.9	34,501,1668	112.0	107.0	109.0		699,930	-4.6	1.0	17	dbSNP_131	109	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	DHX40	NM_001166301.1,NM_024612.4	,	34,501,5967	TT,TC,CC		0.0,12.9142,4.3756	,	233/703,310/780	57652789	569,12435	2203	4299	6502	SO:0001819	synonymous_variant	79665	exon7			CACCCTCGATGGC	AF260270	CCDS11617.1, CCDS54150.1	17q22	2014-01-28	2003-06-13	2003-06-20		ENSG00000108406		"""DEAH-boxes"""	18018	protein-coding gene	gene with protein product		607570	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 40 (RNA helicase)"""	DDX40			Standard	NM_024612		Approved	ARG147, PAD, FLJ22060	uc002ixn.2	Q8IX18		ENST00000251241.4:c.930C>T	17.37:g.57652789C>T		Somatic	392	1	0.00255102		WXS	Illumina HiSeq	Phase_I	386	201	0.520725	NM_024612	B3KTJ5|C9JR60|Q5JPH4|Q8TC86|Q8WY53|Q9BXM1|Q9H6M9	Silent	SNP	ENST00000251241.4	37	CCDS11617.1																																																																																			C|0.957;T|0.043	0.043	strong		0.303	DHX40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446095.1	NM_024612	
SLC30A4	7782	hgsc.bcm.edu	37	15	45814306	45814306	+	Silent	SNP	A	A	G	rs61756712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45814306A>G	ENST00000261867.4	-	2	561	c.247T>C	c.(247-249)Ttg>Ctg	p.L83L	HMGN2P46_ENST00000409454.1_RNA|SLC30A4_ENST00000559667.1_5'UTR	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	83	Asp-rich (acidic).				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)		CTGTTGGTCAAAGGTAAGTCT	0.547													A|||	489	0.0976438	0.3427	0.0259	5008	,	,		19317	0.0149		0.002	False		,,,				2504	0.001				p.L83L		Atlas-SNP	.											.	SLC30A4	25	.	0			c.T247C						PASS	.	A		1255,3141	431.6+/-343.0	195,865,1138	159.0	150.0	153.0		247	-5.2	0.0	15	dbSNP_129	153	11,8585	7.7+/-29.5	0,11,4287	no	coding-synonymous	SLC30A4	NM_013309.4		195,876,5425	GG,GA,AA		0.128,28.5487,9.7445		83/430	45814306	1266,11726	2198	4298	6496	SO:0001819	synonymous_variant	7782	exon2			TGGTCAAAGGTAA		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.247T>C	15.37:g.45814306A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	NM_013309	Q8TC39	Silent	SNP	ENST00000261867.4	37	CCDS10125.1																																																																																			A|0.912;G|0.088	0.088	strong		0.547	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1		
CDH23	64072	hgsc.bcm.edu	37	10	73199595	73199595	+	Missense_Mutation	SNP	C	C	T	rs7902757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73199595C>T	ENST00000224721.6	+	1	12	c.7C>T	c.(7-9)Cgc>Tgc	p.R3C	CDH23_ENST00000398842.3_Missense_Mutation_p.R3C|CDH23_ENST00000461841.3_Missense_Mutation_p.R48C|CDH23_ENST00000299366.7_Missense_Mutation_p.R48C|CDH23_ENST00000398809.4_Missense_Mutation_p.R3C	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	3			R -> C (in dbSNP:rs7902757). {ECO:0000269|PubMed:11138009, ECO:0000269|PubMed:12075507, ECO:0000269|PubMed:12975309}.		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						AGCCATGGGGCGCCATGTTGC	0.617													T|||	686	0.136981	0.4266	0.0504	5008	,	,		18630	0.002		0.0318	False		,,,				2504	0.0542				p.R3C		Atlas-SNP	.											.	CDH23	365	.	0			c.C7T						PASS	.	T	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	1330,2752		216,898,927	44.0	49.0	47.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7,7,7,7,7	0.5	1.0	10	dbSNP_116	47	202,8132		5,192,3970	yes	missense,missense,missense,missense,missense	CDH23	NM_001171930.1,NM_001171931.1,NM_001171932.1,NM_022124.5,NM_052836.3	180,180,180,180,180	221,1090,4897	TT,TC,CC		2.4238,32.5821,12.3389	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	3/1382,3/1062,3/407,3/3355,3/531	73199595	1532,10884	2041	4167	6208	SO:0001583	missense	64072	exon2			ATGGGGCGCCATG	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.7C>T	10.37:g.73199595C>T	ENSP00000224721:p.Arg3Cys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		241	0.11034798534798534	199	0.40447154471544716	18	0.049723756906077346	3	0.005244755244755245	21	0.027704485488126648	T	6.746	0.506418	0.12883	0.325821	0.024238	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721	T;T	0.59502	0.26;0.31	4.59	0.539	0.17156	.	0.664336	0.13012	N	0.420749	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.999999999868258	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.39603	-0.9606	9	0.48119	T	0.1	.	4.2952	0.10897	0.0:0.1904:0.3357:0.4739	rs7902757;rs60485232;rs7902757	3;3;3	A5D6V9;Q9H251;Q9H251-5	.;CAD23_HUMAN;.	C	3	ENSP00000381789:R3C;ENSP00000381822:R3C	ENSP00000224721:R3C	R	+	1	0	CDH23	72869601	0.978000	0.34361	0.987000	0.45799	0.212000	0.24457	-0.053000	0.11846	-0.351000	0.08249	-0.817000	0.03123	CGC	C|0.895;T|0.105	0.105	strong		0.617	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
EPPK1	83481	hgsc.bcm.edu	37	8	144942934	144942934	+	Silent	SNP	C	C	T	rs114155737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144942934C>T	ENST00000525985.1	-	2	4559	c.4488G>A	c.(4486-4488)gcG>gcA	p.A1496A				P58107	EPIPL_HUMAN	epiplakin 1	1496						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)			GCCGCAGGGCCGCAGCCCTCC	0.672													C|||	59	0.0117812	0.0416	0.0043	5008	,	,		17427	0.0		0.001	False		,,,				2504	0.0				p.A1496A		Atlas-SNP	.											.	EPPK1	199	.	0			c.G4488A						PASS	.	C		163,4153		2,159,1997	19.0	22.0	21.0		4488	-9.0	0.0	8	dbSNP_132	21	4,8516		0,4,4256	no	coding-synonymous	EPPK1	NM_031308.1		2,163,6253	TT,TC,CC		0.0469,3.7766,1.301		1496/2420	144942934	167,12669	2158	4260	6418	SO:0001819	synonymous_variant	83481	exon1			CAGGGCCGCAGCC	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.4488G>A	8.37:g.144942934C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	25	16	0.64	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				C|0.987;T|0.013	0.013	strong		0.672	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
SLC9A4	389015	hgsc.bcm.edu	37	2	103095494	103095494	+	Silent	SNP	C	C	T	rs61731285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:103095494C>T	ENST00000295269.4	+	2	910	c.453C>T	c.(451-453)ttC>ttT	p.F151F		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	151					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CCCGGCCCTTCTTTGAGAACA	0.587													C|||	205	0.0409345	0.0787	0.0086	5008	,	,		17344	0.0873		0.001	False		,,,				2504	0.0061				p.F151F		Atlas-SNP	.											.	SLC9A4	115	.	0			c.C453T						PASS	.	C		384,4022	191.9+/-217.4	14,356,1833	59.0	56.0	57.0		453	2.5	1.0	2	dbSNP_129	57	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	SLC9A4	NM_001011552.3		14,359,6130	TT,TC,CC		0.0349,8.7154,2.9755		151/799	103095494	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	389015	exon2			GCCCTTCTTTGAG		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.453C>T	2.37:g.103095494C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001011552	Q69YK0	Silent	SNP	ENST00000295269.4	37	CCDS33264.1																																																																																			C|0.965;T|0.035	0.035	strong		0.587	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
FNDC9	408263	hgsc.bcm.edu	37	5	156770209	156770209	+	Silent	SNP	G	G	A	rs10214194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156770209G>A	ENST00000312349.4	-	2	523	c.336C>T	c.(334-336)tcC>tcT	p.S112S	CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000541131.1_Intron|CYFIP2_ENST00000521420.1_Intron|CYFIP2_ENST00000377576.3_Intron|CYFIP2_ENST00000442283.2_Intron|CYFIP2_ENST00000318218.6_Intron|CYFIP2_ENST00000347377.6_Intron|CYFIP2_ENST00000435847.2_Intron	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9	112						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						GCACCCAAAGGGAGATCTGGG	0.587											OREG0016977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1367	0.272963	0.3911	0.1556	5008	,	,		20194	0.2986		0.171	False		,,,				2504	0.2751				p.S112S		Atlas-SNP	.											.	FNDC9	22	.	0			c.C336T						PASS	.	G	,,,	1515,2891	482.3+/-359.4	242,1031,930	74.0	76.0	75.0		336,,,	0.4	1.0	5	dbSNP_119	75	1391,7209	269.8+/-288.6	109,1173,3018	no	coding-synonymous,intron,intron,intron	CYFIP2,FNDC9	NM_001001343.3,NM_001037332.2,NM_001037333.1,NM_014376.2	,,,	351,2204,3948	AA,AG,GG		16.1744,34.3849,22.3435	,,,	112/225,,,	156770209	2906,10100	2203	4300	6503	SO:0001819	synonymous_variant	408263	exon2			CCAAAGGGAGATC	BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"""Fibronectin type III domain containing"""	33547	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 40"""	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248	ENST00000312349.4:c.336C>T	5.37:g.156770209G>A		Somatic	105	1	0.00952381	1781	WXS	Illumina HiSeq	Phase_I	145	144	0.993103	NM_001001343	A8K0Y6	Silent	SNP	ENST00000312349.4	37	CCDS4337.1																																																																																			G|0.764;A|0.236	0.236	strong		0.587	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343	
BRDT	676	hgsc.bcm.edu	37	1	92467626	92467626	+	Missense_Mutation	SNP	A	A	G	rs78267346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:92467626A>G	ENST00000362005.3	+	17	2726	c.2308A>G	c.(2308-2310)Aat>Gat	p.N770D	BRDT_ENST00000402388.1_Missense_Mutation_p.N770D|BRDT_ENST00000399546.2_Missense_Mutation_p.N770D|BRDT_ENST00000394530.3_Missense_Mutation_p.N724D|BRDT_ENST00000370389.2_Missense_Mutation_p.N697D	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	770					cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		ACAGCTCTCAAATGGCATAAC	0.333													A|||	56	0.0111821	0.0401	0.0029	5008	,	,		17569	0.0		0.001	False		,,,				2504	0.0				p.N774D		Atlas-SNP	.											.	BRDT	133	.	0			c.A2320G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN	113,4293	86.8+/-125.4	2,109,2092	113.0	101.0	105.0		2308,2320,2170,2170,2089,2308,2308	1.3	0.0	1	dbSNP_132	105	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	23,23,23,23,23,23,23	2,109,6392	GG,GA,AA		0.0,2.5647,0.8688	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	770/948,774/952,724/902,724/902,697/875,770/948,770/948	92467626	113,12893	2203	4300	6503	SO:0001583	missense	676	exon16			CTCTCAAATGGCA	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.2308A>G	1.37:g.92467626A>G	ENSP00000354568:p.Asn770Asp	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	297	159	0.535354	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	A	8.950	0.968040	0.18659	0.025647	0.0	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000394530;ENST00000402388	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	3.71	1.32	0.21799	.	0.438833	0.21441	N	0.074491	T	0.18341	0.0440	L	0.56769	1.78	0.09310	N	1	B;B;B;B	0.33694	0.421;0.421;0.16;0.421	B;B;B;B	0.29862	0.108;0.108;0.045;0.055	T	0.14504	-1.0470	10	0.18710	T	0.47	-3.342	3.8025	0.08764	0.6439:0.235:0.1211:0.0	.	724;724;774;770	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	D	770;697;770;724;770	ENSP00000354568:N770D;ENSP00000359416:N697D;ENSP00000387822:N770D;ENSP00000378038:N724D;ENSP00000384051:N770D	ENSP00000354568:N770D	N	+	1	0	BRDT	92240214	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.214000	0.17541	0.274000	0.22072	0.533000	0.62120	AAT	A|0.988;G|0.012	0.012	strong		0.333	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
CLDN14	23562	hgsc.bcm.edu	37	21	37833361	37833361	+	Silent	SNP	G	G	A	rs61745291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:37833361G>A	ENST00000399137.1	-	3	1499	c.633C>T	c.(631-633)taC>taT	p.Y211Y	AP000695.4_ENST00000454980.1_RNA|CLDN14_ENST00000399135.1_Silent_p.Y211Y|AP000695.6_ENST00000429588.1_RNA|AP000695.4_ENST00000428667.1_RNA|CLDN14_ENST00000399136.1_Silent_p.Y211Y|CLDN14_ENST00000342108.2_Silent_p.Y211Y|CLDN14_ENST00000399139.1_Silent_p.Y211Y	NM_144492.2	NP_652763.1	O95500	CLD14_HUMAN	claudin 14	211					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						CTGGTGGCTGGTAGGCAGGTG	0.657													G|||	118	0.0235623	0.0862	0.0043	5008	,	,		17127	0.0		0.001	False		,,,				2504	0.0				p.Y211Y		Atlas-SNP	.											.	CLDN14	25	.	0			c.C633T						PASS	.	G	,,,,	278,4128	154.4+/-187.8	11,256,1936	96.0	86.0	90.0		633,633,633,633,633	4.8	0.8	21	dbSNP_129	90	2,8598	2.2+/-6.3	0,2,4298	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	,,,,	11,258,6234	AA,AG,GG		0.0233,6.3096,2.1529	,,,,	211/240,211/240,211/240,211/240,211/240	37833361	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	23562	exon3			TGGCTGGTAGGCA	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.633C>T	21.37:g.37833361G>A		Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	419	228	0.544153	NM_144492		Silent	SNP	ENST00000399137.1	37	CCDS13645.1																																																																																			G|0.976;A|0.024	0.024	strong		0.657	CLDN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194697.1	NM_144492	
CEP250	11190	hgsc.bcm.edu	37	20	34084415	34084415	+	Silent	SNP	G	G	C	rs224376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34084415G>C	ENST00000397527.1	+	25	3897	c.3177G>C	c.(3175-3177)ctG>ctC	p.L1059L	CEP250_ENST00000342580.4_Silent_p.L1003L	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1059	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)			GCCTGACTCTGTCACTGATGG	0.453													G|||	31	0.0061901	0.0234	0.0	5008	,	,		19409	0.0		0.0	False		,,,				2504	0.0				p.L1059L		Atlas-SNP	.											.	CEP250	141	.	0			c.G3177C						PASS	.	G		131,4275	95.7+/-134.4	2,127,2074	72.0	68.0	69.0		3177	3.8	1.0	20	dbSNP_79	69	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CEP250	NM_007186.3		2,130,6371	CC,CG,GG		0.0349,2.9732,1.0303		1059/2443	34084415	134,12872	2203	4300	6503	SO:0001819	synonymous_variant	11190	exon25			GACTCTGTCACTG	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.3177G>C	20.37:g.34084415G>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																			G|0.991;C|0.009	0.009	strong		0.453	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
SERPINI2	5276	hgsc.bcm.edu	37	3	167167126	167167126	+	Silent	SNP	A	A	G	rs61750372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:167167126A>G	ENST00000476257.1	-	8	1327	c.1029T>C	c.(1027-1029)ggT>ggC	p.G343G	SERPINI2_ENST00000264677.4_Silent_p.G343G|SERPINI2_ENST00000471111.1_Silent_p.G343G|SERPINI2_ENST00000461846.1_Silent_p.G343G			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	343					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						CAGCTTCACTACCATCTTCAT	0.378													G|||	297	0.0593051	0.2148	0.0144	5008	,	,		15155	0.0		0.002	False		,,,				2504	0.001				p.G353G		Atlas-SNP	.											.	SERPINI2	85	.	0			c.T1059C						PASS	.	G		876,3530	743.2+/-411.4	94,688,1421	129.0	111.0	117.0		1029	-0.8	0.1	3	dbSNP_129	117	21,8579	817.9+/-406.9	0,21,4279	no	coding-synonymous	SERPINI2	NM_006217.3		94,709,5700	GG,GA,AA		0.2442,19.882,6.8968		343/406	167167126	897,12109	2203	4300	6503	SO:0001819	synonymous_variant	5276	exon8			TTCACTACCATCT	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.1029T>C	3.37:g.167167126A>G		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	219	117	0.534247	NM_001012303		Silent	SNP	ENST00000476257.1	37	CCDS3200.1																																																																																			A|0.931;G|0.069	0.069	strong		0.378	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
BTBD11	121551	hgsc.bcm.edu	37	12	107712880	107712880	+	Silent	SNP	C	C	T	rs10082935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:107712880C>T	ENST00000280758.5	+	1	691	c.163C>T	c.(163-165)Cta>Tta	p.L55L	BTBD11_ENST00000420571.2_Silent_p.L55L|BTBD11_ENST00000490090.2_Silent_p.L55L	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	55						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						CTGGCCGCCTCTAGCTGACTC	0.647													C|||	493	0.0984425	0.0484	0.1758	5008	,	,		12283	0.0		0.1799	False		,,,				2504	0.1288				p.L55L		Atlas-SNP	.											.	BTBD11	122	.	0			c.C163T						PASS	.	C		316,4090		9,298,1896	29.0	30.0	30.0		163	4.0	1.0	12	dbSNP_119	30	1585,7009		143,1299,2855	no	coding-synonymous	BTBD11	NM_001018072.1		152,1597,4751	TT,TC,CC		18.4431,7.172,14.6231		55/1105	107712880	1901,11099	2203	4297	6500	SO:0001819	synonymous_variant	121551	exon1			CCGCCTCTAGCTG	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.163C>T	12.37:g.107712880C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	37	CCDS31893.1																																																																																			C|0.868;T|0.132	0.132	strong		0.647	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
NSUN3	63899	hgsc.bcm.edu	37	3	93845062	93845062	+	Missense_Mutation	SNP	A	A	G	rs61730354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:93845062A>G	ENST00000314622.4	+	6	962	c.751A>G	c.(751-753)Att>Gtt	p.I251V		NM_022072.3	NP_071355.1	Q9H649	NSUN3_HUMAN	NOP2/Sun domain family, member 3	251							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	18						CAGGTCTGCAATTAAGGCCTT	0.388													A|||	89	0.0177716	0.0537	0.0115	5008	,	,		18150	0.0		0.007	False		,,,				2504	0.0031				p.I251V		Atlas-SNP	.											.	NSUN3	33	.	0			c.A751G						PASS	.	A	VAL/ILE	193,4213	120.4+/-158.0	6,181,2016	52.0	49.0	50.0		751	3.3	1.0	3	dbSNP_129	50	93,8507	51.9+/-112.3	0,93,4207	yes	missense	NSUN3	NM_022072.3	29	6,274,6223	GG,GA,AA		1.0814,4.3804,2.199	benign	251/341	93845062	286,12720	2203	4300	6503	SO:0001583	missense	63899	exon6			TCTGCAATTAAGG	BC020602	CCDS2927.1	3q11.2	2009-11-23	2009-11-23		ENSG00000178694	ENSG00000178694		"""NOP2/Sun domain containing"""	26208	protein-coding gene	gene with protein product			"""NOL1/NOP2/Sun domain family 3"", ""NOL1/NOP2/Sun domain family, member 3"""			12477932	Standard	NM_022072		Approved	FLJ22609	uc003drl.1	Q9H649	OTTHUMG00000159025	ENST00000314622.4:c.751A>G	3.37:g.93845062A>G	ENSP00000318986:p.Ile251Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	150	82	0.546667	NM_022072	Q6PG41|Q8IXG9|Q9H6M2	Missense_Mutation	SNP	ENST00000314622.4	37	CCDS2927.1	25	0.011446886446886446	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	9.012	0.982684	0.18889	0.043804	0.010814	ENSG00000178694	ENST00000314622	T	0.25579	1.79	5.64	3.29	0.37713	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.121362	0.64402	D	0.000015	T	0.03136	0.0092	N	0.17723	0.515	0.35580	D	0.806204	B	0.21821	0.061	B	0.23574	0.047	T	0.16453	-1.0402	10	0.25751	T	0.34	-12.7984	7.4732	0.27361	0.6633:0.0:0.3367:0.0	rs61730354	251	Q9H649	NSUN3_HUMAN	V	251	ENSP00000318986:I251V	ENSP00000318986:I251V	I	+	1	0	NSUN3	95327752	0.993000	0.37304	1.000000	0.80357	0.720000	0.41350	0.754000	0.26390	0.964000	0.38108	0.377000	0.23210	ATT	A|0.982;G|0.018	0.018	strong		0.388	NSUN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352934.1	NM_022072	
DTHD1	401124	hgsc.bcm.edu	37	4	36317970	36317970	+	Silent	SNP	T	T	C	rs9995922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:36317970T>C	ENST00000456874.2	+	7	1885	c.1827T>C	c.(1825-1827)agT>agC	p.S609S	DTHD1_ENST00000357504.3_Silent_p.S444S|RP11-431M7.2_ENST00000504344.1_RNA|DTHD1_ENST00000507598.1_Silent_p.S649S	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	609					signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						GAAACTATAGTTGCCCTCATT	0.368													C|||	1794	0.358227	0.5287	0.3804	5008	,	,		17459	0.2153		0.3648	False		,,,				2504	0.2526				p.S609S		Atlas-SNP	.											.	DTHD1	63	.	0			c.T1827C						PASS	.	C	,	691,693		174,343,175	110.0	103.0	105.0		1332,1827	2.9	1.0	4	dbSNP_119	105	1155,2027		209,737,645	no	coding-synonymous,coding-synonymous	DTHD1	NM_001136536.3,NM_001170700.1	,	383,1080,820	CC,CT,TT		36.2979,49.9277,40.4293	,	444/617,609/782	36317970	1846,2720	692	1591	2283	SO:0001819	synonymous_variant	401124	exon7			CTATAGTTGCCCT	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.1827T>C	4.37:g.36317970T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_001170700	B2RXK4|B4E2N7	Silent	SNP	ENST00000456874.2	37	CCDS54754.1																																																																																			T|0.642;C|0.358	0.358	strong		0.368	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
KIF19	124602	hgsc.bcm.edu	37	17	72351024	72351024	+	Missense_Mutation	SNP	T	T	C	rs9891620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72351024T>C	ENST00000389916.4	+	19	2948	c.2810T>C	c.(2809-2811)cTg>cCg	p.L937P	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	937			L -> P (in dbSNP:rs9891620).		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						ATCCGGCATCTGGGAAAGGTC	0.632													T|||	847	0.169129	0.3041	0.1729	5008	,	,		18686	0.0397		0.1342	False		,,,				2504	0.1534				p.L937P		Atlas-SNP	.											.	KIF19	102	.	0			c.T2810C						PASS	.	T	PRO/LEU	1116,2870		151,814,1028	25.0	28.0	27.0		2810	0.1	0.4	17	dbSNP_119	27	1074,7220		63,948,3136	yes	missense	KIF19	NM_153209.3	98	214,1762,4164	CC,CT,TT		12.9491,27.998,17.8339	benign	937/999	72351024	2190,10090	1993	4147	6140	SO:0001583	missense	124602	exon19			GGCATCTGGGAAA	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.2810T>C	17.37:g.72351024T>C	ENSP00000374566:p.Leu937Pro	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	37	CCDS32718.2	350	0.16025641025641027	141	0.2865853658536585	66	0.18232044198895028	27	0.0472027972027972	116	0.15303430079155672	T	3.804	-0.041038	0.07452	0.27998	0.129491	ENSG00000196169	ENST00000389916	T	0.70045	-0.45	5.03	0.0507	0.14294	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.11690	-1.0577	8	0.37606	T	0.19	.	4.4225	0.11488	0.0:0.3067:0.1675:0.5258	rs9891620;rs59029600;rs9891620	937	Q2TAC6	KIF19_HUMAN	P	937	ENSP00000374566:L937P	ENSP00000374566:L937P	L	+	2	0	KIF19	69862619	0.000000	0.05858	0.423000	0.26634	0.051000	0.14879	-0.122000	0.10627	0.295000	0.22570	-0.387000	0.06579	CTG	T|0.855;C|0.145	0.145	strong		0.632	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
PRICKLE1	144165	hgsc.bcm.edu	37	12	42862431	42862431	+	Silent	SNP	G	G	A	rs74081707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:42862431G>A	ENST00000455697.1	-	5	870	c.585C>T	c.(583-585)gaC>gaT	p.D195D	RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000345127.3_Silent_p.D195D|PRICKLE1_ENST00000552240.1_Silent_p.D195D|PRICKLE1_ENST00000445766.2_Silent_p.D195D|PRICKLE1_ENST00000548696.1_Silent_p.D195D	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	195	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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)		TTTTTACCTCGTCACATGCTG	0.403													G|||	153	0.0305511	0.1097	0.0115	5008	,	,		20234	0.0		0.0	False		,,,				2504	0.0				p.D195D		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.C585T						PASS	.	G	,,,	477,3929	223.9+/-240.3	23,431,1749	82.0	82.0	82.0		585,585,585,585	-6.4	0.9	12	dbSNP_130	82	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRICKLE1	NM_001144881.1,NM_001144882.1,NM_001144883.1,NM_153026.2	,,,	23,434,6046	AA,AG,GG		0.0349,10.8261,3.6906	,,,	195/832,195/832,195/832,195/832	42862431	480,12526	2203	4300	6503	SO:0001819	synonymous_variant	144165	exon5			TACCTCGTCACAT	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.585C>T	12.37:g.42862431G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_001144882	Q14C83|Q71QF8|Q96N00	Silent	SNP	ENST00000455697.1	37	CCDS8742.1																																																																																			G|0.967;A|0.033	0.033	strong		0.403	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1		
C5orf42	65250	hgsc.bcm.edu	37	5	37244669	37244669	+	Silent	SNP	C	C	T	rs73750958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37244669C>T	ENST00000508244.1	-	4	471	c.378G>A	c.(376-378)ggG>ggA	p.G126G	C5orf42_ENST00000274258.7_5'UTR|RN7SL37P_ENST00000490461.2_RNA|C5orf42_ENST00000425232.2_Silent_p.G126G			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	126						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CAATTCTTTTCCCATTTCCAG	0.348													C|||	153	0.0305511	0.1127	0.0043	5008	,	,		18071	0.0		0.001	False		,,,				2504	0.0				p.G126G		Atlas-SNP	.											.	C5orf42	422	.	0			c.G378A						PASS	.	C		145,1239		8,129,555	70.0	61.0	64.0		378	1.9	1.0	5	dbSNP_130	64	0,3182		0,0,1591	no	coding-synonymous	C5orf42	NM_023073.3		8,129,2146	TT,TC,CC		0.0,10.4769,3.1756		126/3198	37244669	145,4421	692	1591	2283	SO:0001819	synonymous_variant	65250	exon5			TCTTTTCCCATTT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.378G>A	5.37:g.37244669C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	136	49	0.360294	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			C|0.980;T|0.020	0.020	strong		0.348	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
GTF3C3	9330	hgsc.bcm.edu	37	2	197662526	197662526	+	Missense_Mutation	SNP	T	T	C	rs11559078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:197662526T>C	ENST00000263956.3	-	2	298	c.209A>G	c.(208-210)aAt>aGt	p.N70S	GTF3C3_ENST00000409364.3_Missense_Mutation_p.N70S	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	70			N -> S (in dbSNP:rs11559078). {ECO:0000269|PubMed:15489334}.		5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|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)	p.N70S(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CATACCTTCATTGACATCTTT	0.353													T|||	578	0.115415	0.1944	0.0735	5008	,	,		20174	0.0327		0.0775	False		,,,				2504	0.1626				p.N70S		Atlas-SNP	.											GTF3C3,NS,carcinoma,0,1	GTF3C3	96	1	1	Substitution - Missense(1)	stomach(1)	c.A209G						PASS	.	T	SER/ASN,SER/ASN	750,3656	306.9+/-289.7	68,614,1521	137.0	132.0	134.0		209,209	0.4	0.1	2	dbSNP_120	134	603,7997	158.9+/-212.3	27,549,3724	yes	missense,missense	GTF3C3	NM_001206774.1,NM_012086.3	46,46	95,1163,5245	CC,CT,TT		7.0116,17.0222,10.4029	benign,benign	70/414,70/887	197662526	1353,11653	2203	4300	6503	SO:0001583	missense	9330	exon2			CCTTCATTGACAT	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"""General transcription factors"", ""Tetratricopeptide (TTC) repeat domain containing"""	4666	protein-coding gene	gene with protein product		604888	"""general transcription factor IIIC, polypeptide 3 (102kD)"""			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.209A>G	2.37:g.197662526T>C	ENSP00000263956:p.Asn70Ser	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	156	70	0.448718	NM_001206774	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	37	CCDS2316.1	188	0.08608058608058608	72	0.14634146341463414	32	0.08839779005524862	24	0.04195804195804196	60	0.079155672823219	T	9.807	1.182136	0.21787	0.170222	0.070116	ENSG00000119041	ENST00000263956;ENST00000409364	T;T	0.40476	1.03;1.05	5.42	0.442	0.16582	.	0.494468	0.21745	N	0.069768	T	0.00039	0.0001	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.23048	-1.0199	9	0.05620	T	0.96	-2.65	5.0385	0.14447	0.0:0.3307:0.1551:0.5142	rs11559078;rs17384126;rs17854287;rs52816855;rs17384126	70;70	Q9Y5Q9-2;Q9Y5Q9	.;TF3C3_HUMAN	S	70	ENSP00000263956:N70S;ENSP00000386465:N70S	ENSP00000263956:N70S	N	-	2	0	GTF3C3	197370771	0.056000	0.20664	0.132000	0.22025	0.885000	0.51271	-0.003000	0.12901	-0.055000	0.13244	-0.263000	0.10527	AAT	T|0.737;G|0.020;C|0.079;N|0.000;A|0.164	0.079	strong		0.353	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1		
PPCS	79717	hgsc.bcm.edu	37	1	42925501	42925501	+	Silent	SNP	A	A	G	rs142078638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:42925501A>G	ENST00000372561.3	+	3	847	c.840A>G	c.(838-840)ctA>ctG	p.L280L	PPCS_ENST00000372556.3_3'UTR|PPCS_ENST00000455780.1_Silent_p.L107L|PPCS_ENST00000372562.1_Silent_p.L107L|PPCS_ENST00000472013.1_3'UTR	NM_024664.2	NP_078940.2	Q9HAB8	PPCS_HUMAN	phosphopantothenoylcysteine synthetase	280					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)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	phosphopantothenate--cysteine ligase activity (GO:0004632)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|skin(3)	12	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGTTATTGCTATCAGAGGAAG	0.388													A|||	6	0.00119808	0.0015	0.0	5008	,	,		17283	0.004		0.0	False		,,,				2504	0.0				p.L280L		Atlas-SNP	.											.	PPCS	30	.	0			c.A840G						PASS	.	A	,	7,3669		0,7,1831	102.0	98.0	99.0		321,840	-10.5	0.6	1	dbSNP_134	99	0,8184		0,0,4092	no	coding-synonymous,coding-synonymous	PPCS	NM_001077447.1,NM_024664.2	,	0,7,5923	GG,GA,AA		0.0,0.1904,0.059	,	107/139,280/312	42925501	7,11853	1838	4092	5930	SO:0001819	synonymous_variant	79717	exon3			ATTGCTATCAGAG	AK021900	CCDS41311.1, CCDS41312.1	1p34.2	2008-02-05			ENSG00000127125	ENSG00000127125	6.3.2.5		25686	protein-coding gene	gene with protein product		609853				11923312	Standard	NM_024664		Approved	FLJ11838	uc001chl.3	Q9HAB8	OTTHUMG00000007332	ENST00000372561.3:c.840A>G	1.37:g.42925501A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_024664	Q3KQT2|Q5VVM0	Silent	SNP	ENST00000372561.3	37	CCDS41311.1																																																																																			A|0.998;G|0.002	0.002	strong		0.388	PPCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019166.1	NM_024664	
NSUN5	55695	hgsc.bcm.edu	37	7	72719048	72719048	+	Missense_Mutation	SNP	G	G	A	rs34913552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:72719048G>A	ENST00000252594.6	-	5	562	c.547C>T	c.(547-549)Ccc>Tcc	p.P183S	NSUN5_ENST00000310326.8_Missense_Mutation_p.P183S|NSUN5_ENST00000438747.2_Missense_Mutation_p.P183S|NSUN5_ENST00000428206.1_Missense_Mutation_p.P145S			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	183			P -> S (in dbSNP:rs34913552).		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)				GGCATCAAGGGGTCCAGGAGA	0.567													g|||	189	0.0377396	0.1377	0.0101	5008	,	,		19720	0.0		0.0	False		,,,				2504	0.0				p.P183S		Atlas-SNP	.											.	NSUN5	47	.	0			c.C547T						PASS	.	A	SER/PRO,SER/PRO,SER/PRO,SER/PRO	445,3961	174.4+/-204.0	16,413,1774	19.0	20.0	20.0		547,433,547,547	-2.3	0.1	7	dbSNP_126	20	1,8579		0,1,4289	no	missense,missense,missense,missense	NSUN5	NM_001168347.1,NM_001168348.1,NM_018044.3,NM_148956.2	74,74,74,74	16,414,6063	AA,AG,GG		0.0117,10.0999,3.4345	benign,benign,benign,benign	183/471,145/392,183/430,183/467	72719048	446,12540	2203	4290	6493	SO:0001583	missense	55695	exon5			TCAAGGGGTCCAG	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.547C>T	7.37:g.72719048G>A	ENSP00000252594:p.Pro183Ser	Somatic	568	0	0		WXS	Illumina HiSeq	Phase_I	496	155	0.3125	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Missense_Mutation	SNP	ENST00000252594.6	37	CCDS5547.1	70	0.03205128205128205	59	0.11991869918699187	4	0.011049723756906077	3	0.005244755244755245	4	0.005277044854881266	g	0.011	-1.725772	0.00694	0.100999	1.17E-4	ENSG00000130305	ENST00000428206;ENST00000252594;ENST00000438747;ENST00000310326	T;T;T;T	0.09911	2.93;2.93;2.93;2.93	4.31	-2.31	0.06765	.	0.500976	0.23395	N	0.048648	T	0.00144	0.0004	M	0.69463	2.115	0.09310	N	1	B;B;B;B	0.23185	0.002;0.066;0.081;0.017	B;B;B;B	0.20384	0.01;0.029;0.021;0.018	T	0.42189	-0.9466	10	0.13853	T	0.58	.	7.9291	0.29891	0.3346:0.1027:0.5626:0.0	rs34913552	183;145;183;183	B4DP79;G3V0G9;Q96P11;Q96P11-2	.;.;NSUN5_HUMAN;.	S	145;183;183;183	ENSP00000393081:P145S;ENSP00000252594:P183S;ENSP00000388464:P183S;ENSP00000309126:P183S	ENSP00000252594:P183S	P	-	1	0	NSUN5	72356984	0.893000	0.30496	0.076000	0.20297	0.032000	0.12392	0.935000	0.28924	-0.731000	0.04862	-1.478000	0.00992	CCC	G|0.971;A|0.029	0.029	strong		0.567	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
SLC37A1	54020	hgsc.bcm.edu	37	21	43954850	43954850	+	Missense_Mutation	SNP	G	G	A	rs115669950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43954850G>A	ENST00000352133.2	+	4	1163	c.181G>A	c.(181-183)Gtc>Atc	p.V61I	SLC37A1_ENST00000398341.3_Missense_Mutation_p.V61I			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	61					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						TGAAGCTGACGTCAGGTTCAG	0.602													G|||	91	0.0181709	0.0673	0.0029	5008	,	,		19958	0.0		0.0	False		,,,				2504	0.0				p.V61I		Atlas-SNP	.											.	SLC37A1	48	.	0			c.G181A						PASS	.	G	ILE/VAL	215,4191	130.6+/-167.2	6,203,1994	98.0	90.0	93.0		181	1.4	0.0	21	dbSNP_132	93	0,8600		0,0,4300	yes	missense	SLC37A1	NM_018964.3	29	6,203,6294	AA,AG,GG		0.0,4.8797,1.6531	benign	61/534	43954850	215,12791	2203	4300	6503	SO:0001583	missense	54020	exon5			GCTGACGTCAGGT	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"""Solute carriers"""	11024	protein-coding gene	gene with protein product		608094	"""solute carrier family 37 (glycerol-3-phosphate transporter), member 1"""			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.181G>A	21.37:g.43954850G>A	ENSP00000344648:p.Val61Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	118	68	0.576271	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	37	CCDS13689.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	G	3.524	-0.097237	0.07010	0.048797	0.0	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.22743	1.94;1.94	4.36	1.44	0.22558	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.175660	0.06063	N	0.658658	T	0.01353	0.0044	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.34428	-0.9829	10	0.22706	T	0.39	-15.6473	2.5906	0.04841	0.1086:0.2627:0.4637:0.165	.	61	P57057	GLPT_HUMAN	I	61	ENSP00000381383:V61I;ENSP00000344648:V61I	ENSP00000344648:V61I	V	+	1	0	SLC37A1	42827919	0.009000	0.17119	0.000000	0.03702	0.010000	0.07245	1.076000	0.30729	0.170000	0.19704	0.655000	0.94253	GTC	G|0.984;A|0.016	0.016	strong		0.602	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
UNC5C	8633	hgsc.bcm.edu	37	4	96123981	96123981	+	Silent	SNP	C	C	T	rs3733212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:96123981C>T	ENST00000453304.1	-	12	2385	c.2037G>A	c.(2035-2037)gcG>gcA	p.A679A		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	679					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)		TGAGGCGCTTCGCAGCCGCTT	0.602													C|||	2926	0.584265	0.73	0.5375	5008	,	,		19095	0.3601		0.7167	False		,,,				2504	0.5153				p.A679A		Atlas-SNP	.											.	UNC5C	141	.	0			c.G2037A						PASS	.	C		3146,1260	701.8+/-406.8	1121,904,178	114.0	109.0	111.0		2037	-10.7	0.0	4	dbSNP_107	111	5962,2638	687.1+/-404.2	2073,1816,411	no	coding-synonymous	UNC5C	NM_003728.3		3194,2720,589	TT,TC,CC		30.6744,28.5974,29.9708		679/932	96123981	9108,3898	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon12			GCGCTTCGCAGCC	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.2037G>A	4.37:g.96123981C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	207	207	1	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			C|0.347;T|0.653	0.653	strong		0.602	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
SVEP1	79987	hgsc.bcm.edu	37	9	113169631	113169631	+	Missense_Mutation	SNP	G	G	A	rs71492888|rs7030192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113169631G>A	ENST00000401783.2	-	38	8585	c.8249C>T	c.(8248-8250)gCa>gTa	p.A2750V	SVEP1_ENST00000374469.1_Missense_Mutation_p.A2727V|SVEP1_ENST00000297826.5_Missense_Mutation_p.A676V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2750	Sushi 22. {ECO:0000255|PROSITE- ProRule:PRU00302}.		A -> V (in dbSNP:rs7030192). {ECO:0000269|PubMed:14702039}.		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						GTCAGAGCCTGCTAGAATGTG	0.458													A|||	2138	0.426917	0.5726	0.3256	5008	,	,		22620	0.4365		0.328	False		,,,				2504	0.3937				p.A2750V		Atlas-SNP	.											.	SVEP1	326	.	0			c.C8249T						PASS	.	A	VAL/ALA	1929,2047		465,999,524	75.0	79.0	78.0		8249	4.7	0.1	9	dbSNP_116	78	2601,5709		391,1819,1945	yes	missense	SVEP1	NM_153366.3	64	856,2818,2469	AA,AG,GG		31.2996,48.5161,36.8712	benign	2750/3572	113169631	4530,7756	1988	4155	6143	SO:0001583	missense	79987	exon38			GAGCCTGCTAGAA	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.8249C>T	9.37:g.113169631G>A	ENSP00000384917:p.Ala2750Val	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	239	65	0.271967	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	742	0.33974358974358976	212	0.43089430894308944	108	0.2983425414364641	213	0.3723776223776224	209	0.2757255936675462	A	0	-2.739132	0.00088	0.485161	0.312996	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	T;T;T	0.62364	0.03;0.03;0.03	5.87	4.71	0.59529	Complement control module (2);Sushi/SCR/CCP (3);	0.717443	0.14280	N	0.329611	T	0.00012	0.0000	N	0.00205	-1.85	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45934	-0.9227	9	0.25106	T	0.35	.	6.1143	0.20117	0.568:0.0:0.0664:0.3656	rs7030192;rs60576083;rs7030192	2750	Q4LDE5	SVEP1_HUMAN	V	2750;2727;676;422	ENSP00000384917:A2750V;ENSP00000363593:A2727V;ENSP00000297826:A676V	ENSP00000297826:A676V	A	-	2	0	SVEP1	112209452	0.005000	0.15991	0.139000	0.22197	0.028000	0.11728	1.821000	0.39041	0.451000	0.26802	-0.352000	0.07741	GCA	A|0.380;G|0.620	0.380	strong		0.458	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
GTSE1	51512	hgsc.bcm.edu	37	22	46719100	46719100	+	Missense_Mutation	SNP	C	C	G	rs6008684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	169	0	0		WXS	Illumina HiSeq	Phase_I	153	86	0.562092	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	
RBM19	9904	hgsc.bcm.edu	37	12	114374887	114374887	+	Missense_Mutation	SNP	T	T	A	rs2290787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114374887T>A	ENST00000545145.2	-	16	2071	c.1993A>T	c.(1993-1995)Aca>Tca	p.T665S	RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.T665S|RBM19_ENST00000392561.3_Missense_Mutation_p.T665S	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	665			T -> A (in dbSNP:rs2290787). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T665A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TGTGGGGCTGTGCTGGAGAAG	0.527													C|||	386	0.0770767	0.2731	0.0317	5008	,	,		17578	0.0		0.003	False		,,,				2504	0.0				p.T665S		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - Missense(1)	stomach(1)	c.A1993T						PASS	.						130.0	129.0	129.0					12																	114374887		2203	4300	6503	SO:0001583	missense	9904	exon16			GGGCTGTGCTGGA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1993A>T	12.37:g.114374887T>A	ENSP00000442053:p.Thr665Ser	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	188	85	0.452128	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	127	0.05815018315018315	112	0.22764227642276422	13	0.03591160220994475	0	0.0	2	0.002638522427440633	C	8.267	0.812524	0.16537	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05025	3.51;3.51;3.51	4.5	-7.42	0.01388	Nucleotide-binding, alpha-beta plait (1);	0.638273	0.16199	N	0.225012	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	0.33701	-0.9858	9	0.08599	T	0.76	0.174	2.1166	0.03715	0.1533:0.1255:0.303:0.4182	rs2290787;rs17856103;rs17856172	665	Q9Y4C8	RBM19_HUMAN	S	665	ENSP00000442053:T665S;ENSP00000376344:T665S;ENSP00000261741:T665S	ENSP00000261741:T665S	T	-	1	0	RBM19	112859270	0.076000	0.21285	0.052000	0.19188	0.226000	0.24999	-0.181000	0.09740	-2.257000	0.00695	-1.557000	0.00889	ACA	A|0.076;C|0.019;T|0.905	0.076	strong		0.527	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
KIAA1731	85459	hgsc.bcm.edu	37	11	93412587	93412587	+	Missense_Mutation	SNP	C	C	T	rs111783199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:93412587C>T	ENST00000325212.6	+	7	796	c.634C>T	c.(634-636)Cgt>Tgt	p.R212C	KIAA1731_ENST00000344196.4_5'UTR|KIAA1731_ENST00000411936.1_Missense_Mutation_p.R212C			Q9C0D2	K1731_HUMAN	KIAA1731	212						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)				GCCAGATGCTCGTTTGGCTGC	0.383													C|||	58	0.0115815	0.0431	0.0014	5008	,	,		16817	0.0		0.0	False		,,,				2504	0.0				p.R212C		Atlas-SNP	.											.	KIAA1731	173	.	0			c.C634T						PASS	.	C	CYS/ARG	33,1351		0,33,659	106.0	105.0	105.0		634	5.3	1.0	11	dbSNP_132	105	0,3182		0,0,1591	yes	missense	KIAA1731	NM_033395.1	180	0,33,2250	TT,TC,CC		0.0,2.3844,0.7227	probably-damaging	212/2602	93412587	33,4533	692	1591	2283	SO:0001583	missense	85459	exon7			GATGCTCGTTTGG	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.634C>T	11.37:g.93412587C>T	ENSP00000316681:p.Arg212Cys	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	132	75	0.568182	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	37	CCDS44708.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	C	17.45	3.393403	0.62066	0.023844	0.0	ENSG00000166004	ENST00000325212;ENST00000411936	T;T	0.11821	2.74;2.74	5.29	5.29	0.74685	.	0.165985	0.28889	N	0.013812	T	0.07863	0.0197	N	0.22421	0.69	0.80722	D	1	D	0.63880	0.993	P	0.47705	0.555	T	0.01480	-1.1344	10	0.46703	T	0.11	-2.4017	19.2977	0.94129	0.0:1.0:0.0:0.0	.	212	Q9C0D2	K1731_HUMAN	C	212	ENSP00000316681:R212C;ENSP00000406505:R212C	ENSP00000316681:R212C	R	+	1	0	KIAA1731	93052235	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.205000	0.65186	2.627000	0.88993	0.563000	0.77884	CGT	C|0.995;T|0.005	0.005	strong		0.383	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
COL12A1	1303	hgsc.bcm.edu	37	6	75848181	75848181	+	Missense_Mutation	SNP	A	A	G	rs240736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:75848181A>G	ENST00000322507.8	-	29	5522	c.5213T>C	c.(5212-5214)aTt>aCt	p.I1738T	COL12A1_ENST00000416123.2_Missense_Mutation_p.I1738T|COL12A1_ENST00000345356.6_Missense_Mutation_p.I574T|COL12A1_ENST00000483888.2_Missense_Mutation_p.I1738T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1738	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> T (in dbSNP:rs240736).		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CTCACTGCCAATCAGGTCATC	0.373													A|||	1327	0.264976	0.3487	0.2911	5008	,	,		19678	0.1548		0.2883	False		,,,				2504	0.2229				p.I1738T		Atlas-SNP	.											.	COL12A1	385	.	0			c.T5213C						PASS	.	A	THR/ILE,THR/ILE	1179,2649		179,821,914	95.0	88.0	90.0		5213,1721	-11.6	0.0	6	dbSNP_79	90	2364,5942		327,1710,2116	yes	missense,missense	COL12A1	NM_004370.5,NM_080645.2	89,89	506,2531,3030	GG,GA,AA		28.4614,30.7994,29.1989	benign,benign	1738/3064,574/1900	75848181	3543,8591	1914	4153	6067	SO:0001583	missense	1303	exon29			CTGCCAATCAGGT	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.5213T>C	6.37:g.75848181A>G	ENSP00000325146:p.Ile1738Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	66	0.52381	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	563	0.25778388278388276	169	0.3434959349593496	102	0.281767955801105	86	0.15034965034965034	206	0.2717678100263852	A	6.073	0.381789	0.11524	0.307994	0.284614	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	D;D;D;D	0.86769	-2.13;-2.17;-2.14;-2.11	5.79	-11.6	0.00059	Fibronectin, type III (2);	1.352220	0.04630	N	0.403531	T	0.44138	0.1279	N	0.05306	-0.075	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42103	-0.9471	9	0.12766	T	0.61	.	11.4509	0.50151	0.6276:0.2382:0.1342:0.0	rs240736;rs1758118;rs52807243;rs60846728;rs240736	574;1738	Q99715-2;Q99715	.;COCA1_HUMAN	T	1738;1738;574;1738;1738	ENSP00000325146:I1738T;ENSP00000305147:I574T;ENSP00000412864:I1738T;ENSP00000421216:I1738T	ENSP00000325146:I1738T	I	-	2	0	COL12A1	75904901	0.004000	0.15560	0.002000	0.10522	0.480000	0.33159	0.400000	0.20932	-2.627000	0.00436	-1.074000	0.02243	ATT	A|0.734;G|0.266	0.266	strong		0.373	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
TG	7038	hgsc.bcm.edu	37	8	134108459	134108459	+	Missense_Mutation	SNP	G	G	C	rs61730222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134108459G>C	ENST00000220616.4	+	43	7454	c.7414G>C	c.(7414-7416)Gtg>Ctg	p.V2472L	SLA_ENST00000524345.1_Intron|TG_ENST00000519543.1_Missense_Mutation_p.V605L|SLA_ENST00000517648.1_Intron|SLA_ENST00000518565.1_Intron|SLA_ENST00000395352.3_Intron|SLA_ENST00000338087.5_Intron|TG_ENST00000542445.1_Missense_Mutation_p.V842L|TG_ENST00000377869.1_Missense_Mutation_p.V2415L	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2472					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)		p.V2472M(1)		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)		GCTCCTGGCCGTGAGTGGCCC	0.502													G|||	90	0.0179712	0.0658	0.0043	5008	,	,		21243	0.0		0.0	False		,,,				2504	0.0				p.V2472L		Atlas-SNP	.											TG,colon,carcinoma,0,2	TG	416	2	1	Substitution - Missense(1)	large_intestine(1)	c.G7414C						PASS	.	G	,,LEU/VAL	250,4156	146.9+/-181.5	5,240,1958	171.0	160.0	164.0		,,7414	3.4	1.0	8	dbSNP_129	164	2,8598	1.2+/-3.3	0,2,4298	no	intron,intron,missense	SLA,TG	NM_001045556.2,NM_001045557.2,NM_003235.4	,,32	5,242,6256	CC,CG,GG		0.0233,5.6741,1.9376	,,possibly-damaging	,,2472/2769	134108459	252,12754	2203	4300	6503	SO:0001583	missense	7038	exon43			CTGGCCGTGAGTG	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.7414G>C	8.37:g.134108459G>C	ENSP00000220616:p.Val2472Leu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	181	85	0.469613	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	42|42	0.019230769230769232|0.019230769230769232	39|39	0.07926829268292683|0.07926829268292683	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	19.35|19.35	3.810956|3.810956	0.70797|0.70797	0.056741|0.056741	2.33E-4|2.33E-4	ENSG00000042832|ENSG00000042832	ENST00000519178|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	.|T;T;T;T	.|0.66815	.|-0.23;-0.23;-0.23;-0.23	5.46|5.46	3.42|3.42	0.39159|0.39159	.|Carboxylesterase, type B (1);	.|0.800184	.|0.11276	.|N	.|0.580893	T|T	0.05318|0.05318	0.0141|0.0141	L|L	0.33137|0.33137	0.985|0.985	0.80722|0.80722	D|D	1|1	.|P;B;P	.|0.45283	.|0.855;0.142;0.526	.|B;B;B	.|0.41571	.|0.36;0.014;0.172	T|T	0.11867|0.11867	-1.0570|-1.0570	5|10	.|0.66056	.|D	.|0.02	.|.	5.3896|5.3896	0.16237|0.16237	0.2809:0.0:0.7191:0.0|0.2809:0.0:0.7191:0.0	rs61730222|rs61730222	.|605;842;2472	.|E7EVM0;F5GWW5;P01266	.|.;.;THYG_HUMAN	P|L	927|2415;1278;2472;842;605	.|ENSP00000367100:V2415L;ENSP00000220616:V2472L;ENSP00000441693:V842L;ENSP00000430430:V605L	.|ENSP00000220616:V2472L	R|V	+|+	2|1	0|0	TG|TG	134177641|134177641	0.999000|0.999000	0.42202|0.42202	0.989000|0.989000	0.46669|0.46669	0.954000|0.954000	0.61252|0.61252	4.049000|4.049000	0.57397|0.57397	1.300000|1.300000	0.44818|0.44818	0.655000|0.655000	0.94253|0.94253	CGT|GTG	G|0.978;C|0.022	0.022	strong		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
SYTL2	54843	hgsc.bcm.edu	37	11	85436500	85436500	+	Intron	SNP	T	T	C	rs580459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:85436500T>C	ENST00000528231.1	-	7	1737				SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000359152.5_Missense_Mutation_p.M858V|SYTL2_ENST00000354566.3_Missense_Mutation_p.M334V|SYTL2_ENST00000525423.1_Missense_Mutation_p.M334V|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000524452.1_Intron	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TCTGCAGCCATCTGAATCAAA	0.463													T|||	3338	0.666534	0.8812	0.5706	5008	,	,		19951	0.6012		0.6551	False		,,,				2504	0.5235				p.M334V		Atlas-SNP	.											.	SYTL2	231	.	0			c.A1000G						PASS	.	T	,,,VAL/MET,VAL/MET	3631,775	753.6+/-412.4	1499,633,71	95.0	96.0	96.0		,,,1000,1000	1.7	0.0	11	dbSNP_83	96	5650,2948	668.6+/-402.6	1881,1888,530	yes	intron,intron,intron,missense,missense	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,21,21	3380,2521,601	CC,CT,TT		34.287,17.5897,28.6297	,,,benign,benign	,,,334/1273,334/1257	85436500	9281,3723	2203	4299	6502	SO:0001627	intron_variant	54843	exon1			CAGCCATCTGAAT	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2438A>G	11.37:g.85436500T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	1480	0.6776556776556777	428	0.8699186991869918	223	0.6160220994475138	326	0.5699300699300699	503	0.6635883905013192	T	7.460	0.644420	0.14451	0.824103	0.65713	ENSG00000137501	ENST00000359152;ENST00000354566;ENST00000525423	T;T;T	0.26660	1.72;1.73;1.73	5.43	1.74	0.24563	.	0.842935	0.10717	N	0.642187	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.16802	0.019;0.019;0.019	B;B;B	0.12156	0.007;0.007;0.007	T	0.15292	-1.0442	8	.	.	.	-0.0784	3.4297	0.07424	0.1717:0.2449:0.0:0.5834	rs580459;rs17810970;rs52803235;rs59688999;rs580459	334;334;334	Q9HCH5-11;Q9HCH5-7;Q9HCH5-8	.;.;.	V	858;334;334	ENSP00000352065:M858V;ENSP00000346576:M334V;ENSP00000432694:M334V	.	M	-	1	0	SYTL2	85114148	0.000000	0.05858	0.030000	0.17652	0.963000	0.63663	-2.079000	0.01369	0.490000	0.27771	0.533000	0.62120	ATG	T|0.304;C|0.696	0.696	strong		0.463	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
ALOX15B	247	hgsc.bcm.edu	37	17	7942785	7942785	+	Missense_Mutation	SNP	C	C	G	rs78230493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7942785C>G	ENST00000380183.4	+	2	368	c.229C>G	c.(229-231)Ccc>Gcc	p.P77A	ALOX15B_ENST00000573359.1_Missense_Mutation_p.P77A|ALOX15B_ENST00000572022.1_Missense_Mutation_p.P77A|ALOX15B_ENST00000380173.2_Missense_Mutation_p.P77A	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	77	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						CCCAGTGCTGCCCCTGCTGGG	0.692													C|||	175	0.0349441	0.1241	0.0144	5008	,	,		9830	0.0		0.001	False		,,,				2504	0.0				p.P77A		Atlas-SNP	.											.	ALOX15B	66	.	0			c.C229G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	282,4080		13,256,1912	8.0	9.0	9.0		229,229,229	-0.4	0.0	17	dbSNP_131	9	3,8557		0,3,4277	no	missense,missense,missense	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	27,27,27	13,259,6189	GG,GC,CC		0.035,6.4649,2.2055	possibly-damaging,possibly-damaging,possibly-damaging	77/648,77/603,77/677	7942785	285,12637	2181	4280	6461	SO:0001583	missense	247	exon2			GTGCTGCCCCTGC	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.229C>G	17.37:g.7942785C>G	ENSP00000369530:p.Pro77Ala	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	22	15	0.681818	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	C	10.09	1.253985	0.22965	0.064649	3.5E-4	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	T;T	0.20738	2.05;2.05	4.15	-0.36	0.12568	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	2.042930	0.02987	N	0.146355	T	0.00144	0.0004	N	0.08118	0	0.09310	N	1	B;B;B;B	0.22800	0.075;0.061;0.061;0.075	B;B;B;B	0.29524	0.071;0.043;0.043;0.103	T	0.31806	-0.9930	10	0.40728	T	0.16	-4.4415	7.6122	0.28137	0.0:0.6248:0.0:0.3752	.	77;77;77;77	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	A	77	ENSP00000369520:P77A;ENSP00000369530:P77A	ENSP00000344337:P77A	P	+	1	0	ALOX15B	7883510	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.527000	0.06200	-0.237000	0.09739	0.591000	0.81541	CCC	C|0.966;G|0.034	0.034	strong		0.692	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
VILL	50853	hgsc.bcm.edu	37	3	38038982	38038982	+	Silent	SNP	T	T	C	rs6809649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38038982T>C	ENST00000283713.6	+	7	836	c.570T>C	c.(568-570)gcT>gcC	p.A190A	VILL_ENST00000383759.2_Silent_p.A190A|VILL_ENST00000465644.1_Intron			O15195	VILL_HUMAN	villin-like	190					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		AGGGGCTGGCTTTGACCTACA	0.607													C|||	1182	0.236022	0.4304	0.1398	5008	,	,		18461	0.0863		0.1441	False		,,,				2504	0.2904				p.A190A		Atlas-SNP	.											.	VILL	61	.	0			c.T570C						PASS	.	C		1760,2646	641.1+/-397.4	346,1068,789	62.0	61.0	61.0		570	3.5	0.7	3	dbSNP_116	61	1488,7112	747.8+/-407.3	125,1238,2937	no	coding-synonymous	VILL	NM_015873.3		471,2306,3726	CC,CT,TT		17.3023,39.9455,24.9731		190/857	38038982	3248,9758	2203	4300	6503	SO:0001819	synonymous_variant	50853	exon6			GCTGGCTTTGACC		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.570T>C	3.37:g.38038982T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Silent	SNP	ENST00000283713.6	37	CCDS2670.2																																																																																			T|0.768;C|0.232	0.232	strong		0.607	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
SMC2	10592	hgsc.bcm.edu	37	9	106896809	106896809	+	Silent	SNP	G	G	A	rs7872034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:106896809G>A	ENST00000286398.7	+	23	3510	c.3222G>A	c.(3220-3222)ttG>ttA	p.L1074L	SMC2_ENST00000374787.3_Silent_p.L1074L|SMC2_ENST00000303219.8_Silent_p.L1074L|SMC2_ENST00000374793.3_Silent_p.L1074L	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	1074					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						AGGTTGCCTTGGGAAATACCT	0.393													A|||	2532	0.505591	0.7943	0.4063	5008	,	,		15029	0.2044		0.5746	False		,,,				2504	0.4254				p.L1074L		Atlas-SNP	.											.	SMC2	127	.	0			c.G3222A						PASS	.	A	,,	3270,1136	404.2+/-333.0	1211,848,144	111.0	116.0	114.0		3222,3222,3222	3.6	1.0	9	dbSNP_116	114	4843,3757	534.0+/-382.5	1403,2037,860	no	coding-synonymous,coding-synonymous,coding-synonymous	SMC2	NM_001042550.1,NM_001042551.1,NM_006444.2	,,	2614,2885,1004	AA,AG,GG		43.686,25.783,37.6211	,,	1074/1198,1074/1198,1074/1198	106896809	8113,4893	2203	4300	6503	SO:0001819	synonymous_variant	10592	exon23			TGCCTTGGGAAAT	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"""Structural maintenance of chromosomes proteins"""	14011	protein-coding gene	gene with protein product		605576	"""SMC2 (structural maintenance of chromosomes 2, yeast)-like 1"", ""SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"""	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.3222G>A	9.37:g.106896809G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_006444	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	37	CCDS35086.1																																																																																			G|0.502;A|0.498	0.498	strong		0.393	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1		
TMEM104	54868	hgsc.bcm.edu	37	17	72784931	72784931	+	Silent	SNP	C	C	T	rs62638676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72784931C>T	ENST00000335464.5	+	4	333	c.171C>T	c.(169-171)ttC>ttT	p.F57F	TMEM104_ENST00000582773.1_Silent_p.F57F|TMEM104_ENST00000417024.2_Silent_p.F70F|TMEM104_ENST00000582330.1_Silent_p.F57F	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	57						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					CCCTCAGCTTCGTGACCACCA	0.587													c|||	157	0.0313498	0.115	0.0072	5008	,	,		18997	0.0		0.0	False		,,,				2504	0.0				p.F57F		Atlas-SNP	.											.	TMEM104	49	.	0			c.C171T						PASS	.	T		423,3983	206.2+/-227.9	22,379,1802	69.0	59.0	62.0		171	-9.1	0.2	17	dbSNP_129	62	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	TMEM104	NM_017728.3		22,382,6099	TT,TC,CC		0.0349,9.6005,3.2754		57/497	72784931	426,12580	2203	4300	6503	SO:0001819	synonymous_variant	54868	exon4			CAGCTTCGTGACC	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.171C>T	17.37:g.72784931C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Silent	SNP	ENST00000335464.5	37	CCDS32723.1																																																																																			C|0.968;T|0.032	0.032	strong		0.587	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728	
DMXL2	23312	hgsc.bcm.edu	37	15	51791559	51791559	+	Missense_Mutation	SNP	A	A	G	rs12102203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51791559A>G	ENST00000251076.5	-	18	4149	c.3862T>C	c.(3862-3864)Tct>Cct	p.S1288P	RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000449909.3_Intron|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	141	0	0		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	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	
MSTN	2660	hgsc.bcm.edu	37	2	190925077	190925077	+	Missense_Mutation	SNP	T	T	C	rs1805086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	141	0	0		WXS	Illumina HiSeq	Phase_I	139	77	0.553957	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	
LMTK2	22853	hgsc.bcm.edu	37	7	97822990	97822990	+	Silent	SNP	G	G	A	rs56064038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:97822990G>A	ENST00000297293.5	+	11	3506	c.3213G>A	c.(3211-3213)ccG>ccA	p.P1071P		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1071					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					CTCCCAACCCGGTCATTGTCA	0.632													G|||	76	0.0151757	0.0567	0.0014	5008	,	,		17179	0.0		0.0	False		,,,				2504	0.0				p.P1071P		Atlas-SNP	.											.	LMTK2	228	.	0			c.G3213A						PASS	.	G		192,4214	118.8+/-156.5	3,186,2014	34.0	33.0	34.0		3213	-10.7	0.1	7	dbSNP_129	34	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	LMTK2	NM_014916.3		3,189,6311	AA,AG,GG		0.0349,4.3577,1.4993		1071/1504	97822990	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	22853	exon11			CAACCCGGTCATT	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.3213G>A	7.37:g.97822990G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_014916	A4D272|Q75MG7|Q9UPS3	Silent	SNP	ENST00000297293.5	37	CCDS5654.1																																																																																			G|0.985;A|0.015	0.015	strong		0.632	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
SLC35F3	148641	hgsc.bcm.edu	37	1	234041422	234041422	+	Silent	SNP	G	G	C	rs57010808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:234041422G>C	ENST00000366618.3	+	2	346	c.201G>C	c.(199-201)ccG>ccC	p.P67P		NM_173508.2	NP_775779.1	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	408					thiamine transport (GO:0015888)	integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			CCAGCGGGCCGGTGGGGCTCA	0.622													C|||	2257	0.450679	0.4387	0.3127	5008	,	,		16969	0.4474		0.4742	False		,,,				2504	0.544				p.P67P		Atlas-SNP	.											.	SLC35F3	81	.	0			c.G201C						PASS	.	C		1996,2410	611.4+/-391.8	451,1094,658	69.0	69.0	69.0		201	-10.5	0.5	1	dbSNP_129	69	4459,4141	563.0+/-388.1	1156,2147,997	no	coding-synonymous	SLC35F3	NM_173508.2		1607,3241,1655	CC,CG,GG		48.1512,45.3019,49.6309		67/491	234041422	6455,6551	2203	4300	6503	SO:0001819	synonymous_variant	148641	exon2			CGGGCCGGTGGGG		CCDS1600.1, CCDS73050.1	1q42.3	2013-05-22			ENSG00000183780	ENSG00000183780		"""Solute carriers"""	23616	protein-coding gene	gene with protein product							Standard	XM_005273070		Approved	FLJ37712	uc001hvy.1	Q8IY50	OTTHUMG00000037929	ENST00000366618.3:c.201G>C	1.37:g.234041422G>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_173508	Q5TDD6|Q8N9C9	Silent	SNP	ENST00000366618.3	37	CCDS1600.1																																																																																			G|0.531;C|0.469	0.469	strong		0.622	SLC35F3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092579.2	NM_173508	
RPGR	6103	hgsc.bcm.edu	37	X	38144856	38144856	+	Intron	SNP	G	G	A	rs12687163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38144856G>A	ENST00000339363.3	-	14	2688				RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000378505.2_Silent_p.N1132N|RPGR_ENST00000342811.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						CTGATGGCCCGTTTTTTAAAA	0.378													G|||	986	0.261192	0.0787	0.1556	3775	,	,		12241	0.4573		0.0626	False		,,,				2504	0.2556				p.N1132N		Atlas-SNP	.											.	RPGR	175	.	0			c.C3396T						PASS	.		,	402,3431		17,292,76,1322,495	201.0	183.0	190.0		,3396	-0.1	0.0	X	dbSNP_120	190	583,6145		16,400,151,2012,1721	no	intron,coding-synonymous	RPGR	NM_000328.2,NM_001034853.1	,	33,692,227,3334,2216	AA,AG,A,GG,G		8.6653,10.4879,9.3268	,	,1132/1153	38144856	985,9576	2202	4300	6502	SO:0001627	intron_variant	6103	exon15			TGGCCCGTTTTTT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+1490C>T	X.37:g.38144856G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	194	88	0.453608	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Silent	SNP	ENST00000339363.3	37																																																																																				G|0.844;A|0.156	0.156	strong		0.378	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595106	140595106	+	Missense_Mutation	SNP	C	C	G	rs2910329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140595106C>G	ENST00000341948.4	+	1	1598	c.1411C>G	c.(1411-1413)Cgc>Ggc	p.R471G		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	471	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> G (in dbSNP:rs2910329).		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)			CCTGCACATCCGCAGCGTCAG	0.642																																					p.R471G		Atlas-SNP	.											.	PCDHB13	142	.	0			c.C1411G						PASS	.	G	GLY/ARG	2957,1447		987,983,232	103.0	114.0	110.0		1411	2.8	0.3	5	dbSNP_101	110	3007,5587		534,1939,1824	no	missense	PCDHB13	NM_018933.2	125	1521,2922,2056	GG,GC,CC		34.9895,32.8565,45.884	benign	471/799	140595106	5964,7034	2202	4297	6499	SO:0001583	missense	56123	exon1			CACATCCGCAGCG	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.1411C>G	5.37:g.140595106C>G	ENSP00000345491:p.Arg471Gly	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_018933	A8K9V6	Missense_Mutation	SNP	ENST00000341948.4	37	CCDS4255.1	730	0.3342490842490842	324	0.6585365853658537	116	0.32044198895027626	68	0.11888111888111888	222	0.2928759894459103	N	0.012	-1.682679	0.00745	0.671435	0.349895	ENSG00000187372	ENST00000341948;ENST00000430318;ENST00000419217	T	0.00753	5.74	3.67	2.78	0.32641	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00006	-3.25	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18335	-1.0340	8	0.02654	T	1	.	8.0096	0.30344	0.0:0.1564:0.5207:0.3228	rs2910329;rs3733685;rs17844611;rs2910329	471	Q9Y5F0	PCDBD_HUMAN	G	471	ENSP00000345491:R471G	ENSP00000345491:R471G	R	+	1	0	PCDHB13	140575290	0.345000	0.24835	0.324000	0.25361	0.611000	0.37282	1.343000	0.33930	0.185000	0.20105	-0.702000	0.03669	CGC	C|0.532;G|0.468	0.468	strong		0.642	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
ZP2	7783	hgsc.bcm.edu	37	16	21222672	21222672	+	Missense_Mutation	SNP	C	C	A	rs2075520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:21222672C>A	ENST00000574002.1	-	3	589	c.107G>T	c.(106-108)gGg>gTg	p.G36V	ZP2_ENST00000574091.1_Missense_Mutation_p.G36V|ZP2_ENST00000219593.4_Missense_Mutation_p.G36V			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	36			G -> V (in dbSNP:rs2075520). {ECO:0000269|PubMed:15489334}.		binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		TATGGAGTTCCCTGAAGTCAC	0.453													A|||	2244	0.448083	0.6717	0.4524	5008	,	,		22005	0.4444		0.2555	False		,,,				2504	0.3446				p.G36V		Atlas-SNP	.											.	ZP2	92	.	0			c.G107T						PASS	.	A	VAL/GLY	2677,1721	516.7+/-369.2	831,1015,353	143.0	142.0	142.0		107	2.4	0.4	16	dbSNP_96	142	2398,6202	700.3+/-405.1	332,1734,2234	yes	missense	ZP2	NM_003460.1	109	1163,2749,2587	AA,AC,CC		27.8837,39.1314,39.0445	benign	36/746	21222672	5075,7923	2199	4300	6499	SO:0001583	missense	7783	exon2			GAGTTCCCTGAAG	M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"""Zona pellucida glycoproteins"""	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.107G>T	16.37:g.21222672C>A	ENSP00000460971:p.Gly36Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	918	0.42032967032967034	319	0.6483739837398373	129	0.356353591160221	263	0.4597902097902098	207	0.27308707124010556	A	0.005	-2.221557	0.00283	0.608686	0.278837	ENSG00000103310	ENST00000219593	T	0.21361	2.01	4.73	2.42	0.29668	.	0.617242	0.15139	N	0.278368	T	0.00012	0.0000	N	0.00049	-2.42	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.40739	-0.9547	9	0.02654	T	1	-3.0493	5.3241	0.15896	0.5579:0.3491:0.093:0.0	rs2075520;rs59742566;rs2075520	36;36;36	B4DEV1;Q4VAP1;Q05996	.;.;ZP2_HUMAN	V	36	ENSP00000219593:G36V	ENSP00000219593:G36V	G	-	2	0	ZP2	21130173	0.012000	0.17670	0.414000	0.26521	0.204000	0.24138	0.668000	0.25127	0.059000	0.16252	-0.256000	0.11100	GGG	C|0.593;A|0.407	0.407	strong		0.453	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
CEP55	55165	hgsc.bcm.edu	37	10	95259979	95259979	+	Missense_Mutation	SNP	C	C	G	rs3740370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	47	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	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	
SARDH	1757	hgsc.bcm.edu	37	9	136595253	136595253	+	Silent	SNP	C	C	T	rs35457000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136595253C>T	ENST00000371872.4	-	5	1004	c.747G>A	c.(745-747)gtG>gtA	p.V249V	SARDH_ENST00000298628.5_Silent_p.V249V|SARDH_ENST00000371867.1_Silent_p.V160V|SARDH_ENST00000422262.2_Silent_p.V81V|SARDH_ENST00000439388.1_Silent_p.V249V	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	249					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CGACCCGCCGCACCCCAAAAT	0.577													C|||	82	0.0163738	0.0598	0.0043	5008	,	,		17220	0.0		0.0	False		,,,				2504	0.0				p.V249V		Atlas-SNP	.											.	SARDH	112	.	0			c.G747A						PASS	.	C	,	174,4232	114.6+/-152.6	5,164,2034	92.0	85.0	88.0		747,747	3.1	1.0	9	dbSNP_126	88	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	5,166,6332	TT,TC,CC		0.0233,3.9492,1.3532	,	249/919,249/919	136595253	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon5			CCGCCGCACCCCA		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.747G>A	9.37:g.136595253C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	113	40	0.353982	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			C|0.985;T|0.015	0.015	strong		0.577	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
PRR3	80742	hgsc.bcm.edu	37	6	30529816	30529816	+	Silent	SNP	G	G	A	rs3888777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30529816G>A	ENST00000376560.3	+	3	834	c.375G>A	c.(373-375)aaG>aaA	p.K125K	PRR3_ENST00000376557.3_Silent_p.K104K|PRR3_ENST00000498336.1_3'UTR	NM_025263.3	NP_079539.2	P79522	PRR3_HUMAN	proline rich 3	125							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						GCTTTCACAAGGAACAGAGAA	0.557													.|||	355	0.0708866	0.149	0.0288	5008	,	,		16653	0.0804		0.0139	False		,,,				2504	0.044				p.K125K		Atlas-SNP	.											.	PRR3	5	.	0			c.G375A						PASS	.	A	,	249,2083		16,217,933	72.0	76.0	75.0		312,375	2.5	1.0	6	dbSNP_108	75	73,4919		0,73,2423	no	coding-synonymous,coding-synonymous	PRR3	NM_001077497.2,NM_025263.3	,	16,290,3356	AA,AG,GG		1.4623,10.6775,4.3965	,	104/168,125/189	30529816	322,7002	1166	2496	3662	SO:0001819	synonymous_variant	80742	exon3			TCACAAGGAACAG	AK074531	CCDS43440.1, CCDS43441.1	6p21.32	2013-01-18	2004-05-27		ENSG00000204576	ENSG00000204576		"""Zinc fingers, CCCH-type domain containing"""	21149	protein-coding gene	gene with protein product			"""proline-rich polpeptide 3"""				Standard	NM_025263		Approved	CAT56, Em:AB014077.1, Em:AB023052.2	uc003nqi.2	P79522	OTTHUMG00000031037	ENST00000376560.3:c.375G>A	6.37:g.30529816G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_025263	A1A4H4|Q5RJB5|Q5STN6	Silent	SNP	ENST00000376560.3	37	CCDS43440.1																																																																																			G|0.952;A|0.048	0.048	strong		0.557	PRR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076033.2	NM_025263	
SPATA22	84690	hgsc.bcm.edu	37	17	3343519	3343519	+	Silent	SNP	T	T	C	rs17822627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3343519T>C	ENST00000573128.1	-	9	1497	c.1014A>G	c.(1012-1014)gaA>gaG	p.E338E	SPATA22_ENST00000572969.1_Silent_p.E338E|SPATA22_ENST00000397168.3_Silent_p.E338E|SPATA22_ENST00000541913.1_Silent_p.E322E|SPATA22_ENST00000355380.4_Silent_p.E295E|SPATA22_ENST00000575375.1_Silent_p.E338E			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	338					fertilization (GO:0009566)|gamete generation (GO:0007276)|meiotic DNA repair synthesis (GO:0000711)|regulation of meiotic cell cycle (GO:0051445)|reproductive system development (GO:0061458)|synapsis (GO:0007129)	chromosome (GO:0005694)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)	19						AAGTTTTTTGTTCAGAAACAG	0.368													T|||	1319	0.263379	0.2095	0.3501	5008	,	,		15510	0.4147		0.1809	False		,,,				2504	0.2035				p.E338E		Atlas-SNP	.											.	SPATA22	49	.	0			c.A1014G						PASS	.	T	,,,,,	1048,3358	375.9+/-321.8	128,792,1283	66.0	73.0	70.0		1014,885,1014,1014,,1014	3.5	1.0	17	dbSNP_123	70	1585,7015	294.4+/-301.9	145,1295,2860	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous	SPATA22	NM_001170695.1,NM_001170696.1,NM_001170697.1,NM_001170698.1,NM_001170699.1,NM_032598.4	,,,,,	273,2087,4143	CC,CT,TT		18.4302,23.7857,20.2445	,,,,,	338/364,295/321,338/364,338/364,,338/364	3343519	2633,10373	2203	4300	6503	SO:0001819	synonymous_variant	84690	exon9			TTTTTGTTCAGAA	AY035868	CCDS11027.1, CCDS54066.1, CCDS54067.1	17p13.3	2005-12-19							30705	protein-coding gene	gene with protein product						12477932	Standard	NM_001170696		Approved	NYD-SP20	uc002fvn.3	Q8NHS9		ENST00000573128.1:c.1014A>G	17.37:g.3343519T>C		Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	318	159	0.5	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Silent	SNP	ENST00000573128.1	37	CCDS11027.1																																																																																			T|0.774;C|0.226	0.226	strong		0.368	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598	
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346595	39346595	+	Missense_Mutation	SNP	T	T	A	rs377187211|rs148036927|rs11283848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39346595T>A	ENST00000398470.1	+	1	457	c.457T>A	c.(457-459)Tgc>Agc	p.C153S	KRTAP9-1_ENST00000377723.3_Intron|KRTAP9-1_ENST00000318329.5_Missense_Mutation_p.C70S	NM_001190460.1	NP_001177389.1	A8MXZ3	KRA91_HUMAN	keratin associated protein 9-1	153	30 X 5 AA repeats of C-C-[CGSVRQH]- [SQTNP]-[PTSI].					keratin filament (GO:0045095)		p.T152_C153>S(2)		breast(1)|lung(3)	4						CCAGCCCACCTGCTGTGGGTC	0.582																																					p.C153S		Atlas-SNP	.											KRTAP9-1_ENST00000398470,rectum,carcinoma,0,2	KRTAP9-1	34	2	2	Complex - deletion inframe(2)	breast(2)	c.T457A						PASS	.																																			SO:0001583	missense	728318	exon1			CCCACCTGCTGTG	AC006070	CCDS56029.1	17q21.2	2010-06-03			ENSG00000240542	ENSG00000240542		"""Keratin associated proteins"""	18912	protein-coding gene	gene with protein product			"""keratin associated protein 9-like 3"""	KRTAP9L3			Standard	NM_001190460		Approved	KAP9.1	uc021txf.1	A8MXZ3	OTTHUMG00000133636	ENST00000398470.1:c.457T>A	17.37:g.39346595T>A	ENSP00000381488:p.Cys153Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	110	9	0.0818182	NM_001190460		Missense_Mutation	SNP	ENST00000398470.1	37	CCDS56029.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.796850	0.31777	.	.	ENSG00000240542	ENST00000398470;ENST00000318329	T;T	0.02085	4.46;6.06	3.56	2.46	0.29980	.	.	.	.	.	T	0.06234	0.0161	M	0.73430	2.235	0.09310	N	0.999998	.	.	.	.	.	.	T	0.15636	-1.0430	7	0.51188	T	0.08	.	7.8228	0.29296	0.1856:0.0:0.0:0.8144	.	.	.	.	S	153;70	ENSP00000381488:C153S;ENSP00000325023:C70S	ENSP00000325023:C70S	C	+	1	0	KRTAP9-1	36600121	0.004000	0.15560	0.064000	0.19789	0.084000	0.17831	0.909000	0.28558	0.705000	0.31890	0.338000	0.21704	TGC	.	.	none		0.582	KRTAP9-1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257781.1		
RFX7	64864	hgsc.bcm.edu	37	15	56387859	56387859	+	Silent	SNP	T	T	C	rs3803459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56387859T>C	ENST00000559447.2	-	9	2047	c.1776A>G	c.(1774-1776)aaA>aaG	p.K592K	RFX7_ENST00000317318.6_Silent_p.K689K|RFX7_ENST00000422057.1_Silent_p.K592K|RFX7_ENST00000423270.1_Silent_p.K689K			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	592					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CACTGCCTTGTTTCTGCCCTT	0.453													T|||	1140	0.227636	0.0635	0.1513	5008	,	,		22128	0.494		0.1123	False		,,,				2504	0.3476				p.K689K		Atlas-SNP	.											.	RFX7	170	.	0			c.A2067G						PASS	.	T		330,3478		13,304,1587	121.0	112.0	115.0		2067	2.1	1.0	15	dbSNP_107	115	1063,7185		72,919,3133	no	coding-synonymous	RFX7	NM_022841.5		85,1223,4720	CC,CT,TT		12.888,8.666,11.5544		689/1461	56387859	1393,10663	1904	4124	6028	SO:0001819	synonymous_variant	64864	exon9			GCCTTGTTTCTGC			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.1776A>G	15.37:g.56387859T>C		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	254	102	0.401575	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																				T|0.799;C|0.201	0.201	strong		0.453	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
PPP1R26	9858	hgsc.bcm.edu	37	9	138376972	138376972	+	Missense_Mutation	SNP	A	A	G	rs3928777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138376972A>G	ENST00000356818.2	+	4	1165	c.616A>G	c.(616-618)Aag>Gag	p.K206E	PPP1R26_ENST00000604351.1_Missense_Mutation_p.K206E|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Missense_Mutation_p.K206E|PPP1R26_ENST00000605286.1_Missense_Mutation_p.K206E|PPP1R26_ENST00000401470.3_Missense_Mutation_p.K206E	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	206			K -> E (in dbSNP:rs3928777). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGGATCCAGCAAGGACCAGGG	0.607													G|||	2059	0.411142	0.2927	0.4899	5008	,	,		17027	0.6319		0.2107	False		,,,				2504	0.4939				p.K206E		Atlas-SNP	.											.	.	.	.	0			c.A616G						PASS	.	G	GLU/LYS	1123,3281		138,847,1217	48.0	57.0	54.0		616	-5.0	0.0	9	dbSNP_108	54	1779,6809		195,1389,2710	yes	missense	KIAA0649	NM_014811.3	56	333,2236,3927	GG,GA,AA		20.715,25.4995,22.3368	benign	206/1210	138376972	2902,10090	2202	4294	6496	SO:0001583	missense	9858	exon4			TCCAGCAAGGACC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.616A>G	9.37:g.138376972A>G	ENSP00000349274:p.Lys206Glu	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	56	39	0.696429	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	825	0.37774725274725274	124	0.25203252032520324	158	0.43646408839779005	385	0.6730769230769231	158	0.20844327176781002	G	1.359	-0.589194	0.03799	0.254995	0.20715	ENSG00000196422	ENST00000356818	T	0.08370	3.1	5.4	-4.97	0.03029	.	1.900700	0.02781	N	0.120907	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	0.38134	-0.9675	9	0.02654	T	1	0.0044	4.3603	0.11199	0.2545:0.4099:0.2528:0.0828	rs3928777;rs17846423;rs17859469;rs56846731	206	Q5T8A7	PPR26_HUMAN	E	206	ENSP00000349274:K206E	ENSP00000349274:K206E	K	+	1	0	KIAA0649	137516793	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.040000	0.12104	-2.103000	0.00844	-2.245000	0.00285	AAG	A|0.724;G|0.276	0.276	strong		0.607	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
MUC4	4585	hgsc.bcm.edu	37	3	195513010	195513010	+	Missense_Mutation	SNP	G	G	A	rs559958622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513010G>A	ENST00000463781.3	-	2	5900	c.5441C>T	c.(5440-5442)cCt>cTt	p.P1814L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1814L	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)		TGCTGAGGAAGGGCTGGTGAC	0.587													.|||	18	0.00359425	0.0129	0.0014	5008	,	,		34904	0.0		0.0	False		,,,				2504	0.0				p.P1814L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C5441T						scavenged	.						81.0	71.0	74.0					3																	195513010		691	1591	2282	SO:0001583	missense	4585	exon2			GAGGAAGGGCTGG	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.5441C>T	3.37:g.195513010G>A	ENSP00000417498:p.Pro1814Leu	Somatic	645	5	0.00775194		WXS	Illumina HiSeq	Phase_I	508	14	0.0275591	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	.	.	.	.	.	.	.	.	.	.	-	4.067	0.010265	0.07912	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26518	1.73;1.8	0.423	0.423	0.16463	.	.	.	.	.	T	0.09949	0.0244	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.34378	-0.9831	8	.	.	.	.	2.9333	0.05807	0.389:0.0:0.611:0.0	.	1814	E7ESK3	.	L	1814	ENSP00000417498:P1814L;ENSP00000420243:P1814L	.	P	-	2	0	MUC4	196997405	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	-0.287000	0.08388	0.494000	0.27859	0.089000	0.15464	CCT	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR2Y1	134083	hgsc.bcm.edu	37	5	180166141	180166141	+	Silent	SNP	C	C	T	rs9329115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180166141C>T	ENST00000307832.2	-	1	958	c.918G>A	c.(916-918)agG>agA	p.R306R		NM_001001657.1	NP_001001657.1	Q8NGV0	OR2Y1_HUMAN	olfactory receptor, family 2, subfamily Y, member 1	306						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R306R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(89;1.25e-05)|all_epithelial(37;4.36e-06)|Renal(175;0.000159)|Lung NSC(126;0.00317)|all_lung(126;0.0041)|Breast(19;0.114)	all_cancers(40;0.0834)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGTCCCTGCCCCTCCATAGTA	0.428													C|||	477	0.0952476	0.2383	0.0576	5008	,	,		18154	0.1012		0.006	False		,,,				2504	0.0143				p.R306R		Atlas-SNP	.											OR2Y1,NS,carcinoma,0,1	OR2Y1	49	1	1	Substitution - coding silent(1)	stomach(1)	c.G918A						PASS	.	C		1033,3373	368.6+/-318.7	129,775,1299	85.0	95.0	91.0		918	-4.2	0.0	5	dbSNP_119	91	150,8450	73.2+/-135.9	2,146,4152	no	coding-synonymous	OR2Y1	NM_001001657.1		131,921,5451	TT,TC,CC		1.7442,23.4453,9.0958		306/312	180166141	1183,11823	2203	4300	6503	SO:0001819	synonymous_variant	134083	exon1			CCTGCCCCTCCAT	AB065676	CCDS34323.1	5q35	2012-08-09			ENSG00000174339	ENSG00000174339		"""GPCR / Class A : Olfactory receptors"""	14837	protein-coding gene	gene with protein product							Standard	NM_001001657		Approved		uc003mmf.1	Q8NGV0	OTTHUMG00000162237	ENST00000307832.2:c.918G>A	5.37:g.180166141C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	47	31	0.659574	NM_001001657	B9EIP1|Q6IFB1|Q96R16	Silent	SNP	ENST00000307832.2	37	CCDS34323.1																																																																																			C|0.913;T|0.087	0.087	strong		0.428	OR2Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368059.2	XM_068682	
EMCN	51705	hgsc.bcm.edu	37	4	101386643	101386643	+	Missense_Mutation	SNP	C	C	T	rs78403369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:101386643C>T	ENST00000296420.4	-	4	491	c.313G>A	c.(313-315)Gta>Ata	p.V105I	EMCN_ENST00000511970.1_Missense_Mutation_p.V105I|EMCN_ENST00000305864.3_Missense_Mutation_p.V105I|EMCN_ENST00000502327.1_5'UTR	NM_001159694.1|NM_016242.3	NP_001153166.1|NP_057326.2	Q9ULC0	MUCEN_HUMAN	endomucin	105	Thr-rich.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)		GTTACTGTTACGTTTGAAATG	0.363													C|||	82	0.0163738	0.0582	0.0043	5008	,	,		18744	0.0		0.002	False		,,,				2504	0.0				p.V105I		Atlas-SNP	.											.	EMCN	37	.	0			c.G313A						PASS	.	C	ILE/VAL,ILE/VAL	256,4150	146.1+/-180.8	8,240,1955	193.0	169.0	177.0		313,313	-5.4	0.0	4	dbSNP_132	177	32,8568	21.0+/-64.5	0,32,4268	yes	missense,missense	EMCN	NM_001159694.1,NM_016242.3	29,29	8,272,6223	TT,TC,CC		0.3721,5.8103,2.2144	possibly-damaging,possibly-damaging	105/249,105/262	101386643	288,12718	2203	4300	6503	SO:0001583	missense	51705	exon4			CTGTTACGTTTGA	AF205940	CCDS3655.1, CCDS54782.1	4q22.1	2008-02-05			ENSG00000164035	ENSG00000164035		"""Mucins"""	16041	protein-coding gene	gene with protein product		608350				11418125, 11594763	Standard	NM_016242		Approved	MUC14	uc003hvr.3	Q9ULC0	OTTHUMG00000131051	ENST00000296420.4:c.313G>A	4.37:g.101386643C>T	ENSP00000296420:p.Val105Ile	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_001159694	A8K716|B4E347|Q8NEY5|Q8WWE7|Q9NRM8	Missense_Mutation	SNP	ENST00000296420.4	37	CCDS3655.1	37	0.01694139194139194	33	0.06707317073170732	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	5.591	0.293797	0.10567	0.058103	0.003721	ENSG00000164035	ENST00000296420;ENST00000305864;ENST00000506300;ENST00000511970;ENST00000502569	.	.	.	3.93	-5.39	0.02664	.	5.984870	0.00541	N	0.000223	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B;B;B	0.25667	0.107;0.131;0.131	B;B;B	0.17098	0.01;0.017;0.017	T	0.06481	-1.0824	9	0.19590	T	0.45	0.1434	13.3485	0.60589	0.0:0.2287:0.0:0.7713	.	105;105;105	Q9ULC0-2;B4E347;Q9ULC0	.;.;MUCEN_HUMAN	I	105;105;32;105;105	.	ENSP00000296420:V105I	V	-	1	0	EMCN	101605666	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.676000	0.00840	-1.586000	0.01632	-0.150000	0.13652	GTA	C|0.980;T|0.020	0.020	strong		0.363	EMCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253699.2	NM_016242	
MKI67	4288	hgsc.bcm.edu	37	10	129905429	129905429	+	Missense_Mutation	SNP	C	C	T	rs7918199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129905429C>T	ENST00000368654.3	-	13	5050	c.4675G>A	c.(4675-4677)Gtg>Atg	p.V1559M	MKI67_ENST00000368653.3_Missense_Mutation_p.V1199M	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1559	16 X 122 AA approximate repeats.		V -> M (in dbSNP:rs7918199).		cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.V1559M(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				AGTTTCTGCACTGGAGTTCCC	0.498													C|||	515	0.102835	0.0666	0.1556	5008	,	,		20762	0.1359		0.0785	False		,,,				2504	0.1053				p.V1559M		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - Missense(1)	stomach(1)	c.G4675A						PASS	.	C	MET/VAL,MET/VAL	296,4110	162.5+/-194.5	11,274,1918	278.0	249.0	259.0		3595,4675	-2.0	0.0	10	dbSNP_116	259	771,7829	183.7+/-231.9	39,693,3568	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	21,21	50,967,5486	TT,TC,CC		8.9651,6.7181,8.2039	possibly-damaging,possibly-damaging	1199/2897,1559/3257	129905429	1067,11939	2203	4300	6503	SO:0001583	missense	4288	exon13			TCTGCACTGGAGT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.4675G>A	10.37:g.129905429C>T	ENSP00000357643:p.Val1559Met	Somatic	394	0	0		WXS	Illumina HiSeq	Phase_I	369	186	0.504065	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	209	0.09569597069597069	33	0.06707317073170732	39	0.10773480662983426	79	0.1381118881118881	58	0.07651715039577836	C	10.76	1.440781	0.25900	0.067181	0.089651	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02258	4.37;4.37	4.21	-1.95	0.07548	.	1.347280	0.05153	N	0.496442	T	0.00039	0.0001	L	0.44542	1.39	0.80722	P	0.0	B;P;P	0.48503	0.128;0.911;0.56	B;P;B	0.49953	0.033;0.627;0.446	T	0.42464	-0.9450	9	0.46703	T	0.11	.	9.7412	0.40420	0.0:0.5379:0.0:0.4621	rs7918199;rs52813597;rs60630618;rs7918199	1558;1199;1559	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	M	1559;1199;1558	ENSP00000357643:V1559M;ENSP00000357642:V1199M	ENSP00000357642:V1199M	V	-	1	0	MKI67	129795419	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.562000	0.00920	-0.576000	0.05974	0.462000	0.41574	GTG	C|0.914;T|0.086	0.086	strong		0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
FBN1	2200	hgsc.bcm.edu	37	15	48734008	48734008	+	Missense_Mutation	SNP	C	C	A	rs113577372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:48734008C>A	ENST00000316623.5	-	50	6528	c.6073G>T	c.(6073-6075)Gcc>Tcc	p.A2025S		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2025	EGF-like 35; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GTGCCCAGGGCACAAATTTCT	0.448													C|||	10	0.00199681	0.0076	0.0	5008	,	,		19650	0.0		0.0	False		,,,				2504	0.0				p.A2025S		Atlas-SNP	.											.	FBN1	310	.	0			c.G6073T						PASS	.	C	SER/ALA	21,4375	29.0+/-57.7	0,21,2177	137.0	135.0	136.0		6073	5.9	1.0	15	dbSNP_132	136	0,8592		0,0,4296	yes	missense	FBN1	NM_000138.4	99	0,21,6473	AA,AC,CC		0.0,0.4777,0.1617	possibly-damaging	2025/2872	48734008	21,12967	2198	4296	6494	SO:0001583	missense	2200	exon50			CCAGGGCACAAAT	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.6073G>T	15.37:g.48734008C>A	ENSP00000325527:p.Ala2025Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	12.59	1.982249	0.34942	0.004777	0.0	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.91996	-2.95	5.94	5.94	0.96194	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.098253	0.64402	D	0.000001	T	0.77552	0.4147	N	0.01800	-0.715	0.80722	D	1	B	0.25850	0.136	B	0.29942	0.109	T	0.76753	-0.2843	10	0.17832	T	0.49	.	19.9452	0.97179	0.0:1.0:0.0:0.0	.	2025	P35555	FBN1_HUMAN	S	2025;593;915	ENSP00000325527:A2025S	ENSP00000325527:A2025S	A	-	1	0	FBN1	46521300	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.864000	0.39469	2.807000	0.96579	0.650000	0.86243	GCC	C|0.998;A|0.002	0.002	strong		0.448	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487229	32487229	+	Silent	SNP	C	C	T	rs148633289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32487229C>T	ENST00000374975.3	-	3	632	c.570G>A	c.(568-570)ctG>ctA	p.L190L		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						GAACTGTTTCCAGCATCACCA	0.557													C|||	1286	0.256789	0.3495	0.2305	5008	,	,		13332	0.2232		0.2425	False		,,,				2504	0.1994				p.L190L		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	0			c.G570A						scavenged	.						60.0	66.0	64.0					6																	32487229		1865	3705	5570	SO:0001819	synonymous_variant	3127	exon3			TGTTTCCAGCATC		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.570G>A	6.37:g.32487229C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	125	91	0.728	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			C|0.781;T|0.219	0.219	strong		0.557	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
INADL	10207	hgsc.bcm.edu	37	1	62393420	62393420	+	Missense_Mutation	SNP	C	C	T	rs61743112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62393420C>T	ENST00000371158.2	+	27	3703	c.3589C>T	c.(3589-3591)Ccg>Tcg	p.P1197S	INADL_ENST00000316485.6_Missense_Mutation_p.P1197S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1197					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						AACTGCTCCACCGCCAATGAA	0.398													C|||	199	0.0397364	0.1415	0.0173	5008	,	,		17651	0.0		0.0	False		,,,				2504	0.0				p.P1197S		Atlas-SNP	.											.	INADL	179	.	0			c.C3589T						PASS	.	C	SER/PRO	478,3928	224.9+/-240.9	21,436,1746	102.0	94.0	97.0		3589	4.4	0.6	1	dbSNP_129	97	2,8598	2.2+/-6.3	0,2,4298	yes	missense	INADL	NM_176877.2	74	21,438,6044	TT,TC,CC		0.0233,10.8488,3.6906	possibly-damaging	1197/1802	62393420	480,12526	2203	4300	6503	SO:0001583	missense	10207	exon27			GCTCCACCGCCAA	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.3589C>T	1.37:g.62393420C>T	ENSP00000360200:p.Pro1197Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	86	0.039377289377289376	81	0.16463414634146342	5	0.013812154696132596	0	0.0	0	0.0	C	11.14	1.550134	0.27652	0.108488	2.33E-4	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513	T;T	0.16073	2.44;2.37	4.45	4.45	0.53987	.	0.000000	0.64402	D	0.000002	T	0.00144	0.0004	M	0.74258	2.255	0.09310	P	1.0	D;P;D	0.89917	0.959;0.726;1.0	P;B;D	0.79108	0.897;0.205;0.992	T	0.09335	-1.0679	9	0.08381	T	0.77	.	12.8308	0.57744	0.0:1.0:0.0:0.0	rs61743112	1197;1197;1197	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	S	1197	ENSP00000360200:P1197S;ENSP00000326199:P1197S	ENSP00000326199:P1197S	P	+	1	0	INADL	62166008	0.949000	0.32298	0.641000	0.29422	0.012000	0.07955	3.927000	0.56499	2.465000	0.83290	0.650000	0.86243	CCG	C|0.959;T|0.041	0.041	strong		0.398	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238668802	238668802	+	Silent	SNP	A	A	G	rs3213868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238668802A>G	ENST00000392000.4	+	10	960	c.843A>G	c.(841-843)acA>acG	p.T281T	LRRFIP1_ENST00000289175.6_Silent_p.T225T|LRRFIP1_ENST00000244815.5_Silent_p.T257T|LRRFIP1_ENST00000308482.9_Silent_p.T471T	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	281					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)		CCAAGATGACAAAAGAAGAGT	0.448													G|||	1813	0.362021	0.3487	0.3012	5008	,	,		20595	0.505		0.2515	False		,,,				2504	0.3896				p.T471T		Atlas-SNP	.											LRRFIP1_ENST00000392000,colon,carcinoma,+1,3	LRRFIP1	171	3	0			c.A1413G						PASS	.	G	,,,,	1561,2845	669.1+/-402.1	299,963,941	105.0	100.0	102.0		1413,675,843,675,771	-10.8	0.0	2	dbSNP_106	102	2000,6600	722.2+/-406.4	218,1564,2518	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LRRFIP1	NM_001137550.1,NM_001137551.1,NM_001137552.1,NM_001137553.1,NM_004735.3	,,,,	517,2527,3459	GG,GA,AA		23.2558,35.429,27.3797	,,,,	471/641,225/395,281/809,225/753,257/785	238668802	3561,9445	2203	4300	6503	SO:0001819	synonymous_variant	9208	exon19			GATGACAAAAGAA	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.843A>G	2.37:g.238668802A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	104	37	0.355769	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Silent	SNP	ENST00000392000.4	37	CCDS46552.1																																																																																			A|0.676;G|0.324	0.324	strong		0.448	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
EXPH5	23086	hgsc.bcm.edu	37	11	108383676	108383676	+	Missense_Mutation	SNP	A	A	G	rs10749920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108383676A>G	ENST00000265843.4	-	6	2668	c.2558T>C	c.(2557-2559)cTg>cCg	p.L853P	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000443411.1_Missense_Mutation_p.L665P|EXPH5_ENST00000428840.1_Missense_Mutation_p.L777P|EXPH5_ENST00000525344.1_Missense_Mutation_p.L846P	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	853			L -> P (in dbSNP:rs10749920).		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AGTATCAGTCAGTGCAGAGCT	0.403													G|||	1795	0.358427	0.6876	0.1844	5008	,	,		19778	0.2093		0.1909	False		,,,				2504	0.363				p.L853P		Atlas-SNP	.											.	EXPH5	193	.	0			c.T2558C						PASS	.	G	PRO/LEU	2667,1735	518.5+/-369.7	837,993,371	235.0	228.0	231.0		2558	1.3	0.0	11	dbSNP_120	231	1594,7002	743.4+/-407.2	166,1262,2870	yes	missense	EXPH5	NM_015065.2	98	1003,2255,3241	GG,GA,AA		18.5435,39.4139,32.782	benign	853/1990	108383676	4261,8737	2201	4298	6499	SO:0001583	missense	23086	exon6			TCAGTCAGTGCAG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.2558T>C	11.37:g.108383676A>G	ENSP00000265843:p.Leu853Pro	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	650	0.2976190476190476	324	0.6585365853658537	61	0.1685082872928177	132	0.23076923076923078	133	0.17546174142480211	G	0.483	-0.879129	0.02550	0.605861	0.185435	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.03801	4.39;4.32;4.16;4.39;4.25;3.8	5.4	1.31	0.21738	.	0.983285	0.08319	N	0.964210	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	0.35525	-0.9785	9	0.05620	T	0.96	0.8463	2.5384	0.04720	0.1563:0.2705:0.4337:0.1395	rs10749920;rs12786084;rs17108124;rs52803067;rs58088271;rs10749920	853	Q8NEV8	EXPH5_HUMAN	P	853;777;665;846;777;665	ENSP00000265843:L853P;ENSP00000391966:L777P;ENSP00000411390:L665P;ENSP00000432546:L846P;ENSP00000432683:L777P;ENSP00000446434:L665P	ENSP00000265843:L853P	L	-	2	0	EXPH5	107888886	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.200000	0.09478	-0.133000	0.11537	-0.213000	0.12676	CTG	A|0.676;G|0.324	0.324	strong		0.403	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
ZNF594	84622	hgsc.bcm.edu	37	17	5085806	5085806	+	Silent	SNP	G	G	A	rs114624606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085806G>A	ENST00000399604.4	-	1	1886	c.1746C>T	c.(1744-1746)gaC>gaT	p.D582D	ZNF594_ENST00000575779.1_Silent_p.D582D			Q96JF6	ZN594_HUMAN	zinc finger protein 594	582					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)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GTCTGATGAGGTCTGAGCTGC	0.453																																					p.D582D		Atlas-SNP	.											.	ZNF594	89	.	0			c.C1746T						PASS	.	G		95,3919		4,87,1916	149.0	144.0	145.0		1746	-2.1	0.0	17	dbSNP_132	145	1,8411		0,1,4205	no	coding-synonymous	ZNF594	NM_032530.1		4,88,6121	AA,AG,GG		0.0119,2.3667,0.7726		582/808	5085806	96,12330	2007	4206	6213	SO:0001819	synonymous_variant	84622	exon2			GATGAGGTCTGAG	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.1746C>T	17.37:g.5085806G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_032530	Q6RFS0	Silent	SNP	ENST00000399604.4	37	CCDS42241.1																																																																																			G|0.990;A|0.010	0.010	strong		0.453	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
TMC8	147138	hgsc.bcm.edu	37	17	76127746	76127746	+	Missense_Mutation	SNP	T	T	C	rs145016347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76127746T>C	ENST00000318430.5	+	2	451	c.77T>C	c.(76-78)aTg>aCg	p.M26T	TMC6_ENST00000589553.1_5'Flank|TMC8_ENST00000589691.1_Intron|TMC6_ENST00000590602.1_5'Flank|TMC6_ENST00000322933.4_5'Flank|TMC6_ENST00000322914.3_Intron	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	26					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)			GAGGCAGAGATGGAGCGGCTG	0.726													T|||	145	0.0289537	0.0038	0.0216	5008	,	,		12067	0.006		0.0229	False		,,,				2504	0.0982				p.M26T		Atlas-SNP	.											.	TMC8	44	.	0			c.T77C						PASS	.	T	,THR/MET	15,4205		0,15,2095	7.0	9.0	9.0		,77	3.1	1.0	17	dbSNP_134	9	218,8122		2,214,3954	no	intron,missense	TMC6,TMC8	NM_007267.6,NM_152468.4	,81	2,229,6049	CC,CT,TT		2.6139,0.3555,1.8551	,benign	,26/727	76127746	233,12327	2110	4170	6280	SO:0001583	missense	147138	exon2			CAGAGATGGAGCG	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.77T>C	17.37:g.76127746T>C	ENSP00000325561:p.Met26Thr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Missense_Mutation	SNP	ENST00000318430.5	37	CCDS32749.1	32	0.014652014652014652	2	0.0040650406504065045	9	0.024861878453038673	2	0.0034965034965034965	19	0.025065963060686015	T	11.47	1.648700	0.29336	0.003555	0.026139	ENSG00000167895	ENST00000318430;ENST00000301627	T	0.74947	-0.89	3.13	3.13	0.36017	.	1.015750	0.07922	U	0.975995	T	0.40297	0.1111	L	0.34521	1.04	0.80722	D	1	B;B	0.24823	0.112;0.005	B;B	0.23574	0.047;0.004	T	0.54159	-0.8335	10	0.52906	T	0.07	-11.5249	7.8883	0.29663	0.0:0.0:0.0:1.0	.	26;26	B4E0S0;Q8IU68	.;TMC8_HUMAN	T	26	ENSP00000325561:M26T	ENSP00000301627:M26T	M	+	2	0	TMC8	73639341	1.000000	0.71417	0.997000	0.53966	0.666000	0.39218	1.811000	0.38942	1.422000	0.47177	0.379000	0.24179	ATG	T|0.985;C|0.015	0.015	strong		0.726	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3		
DDR2	4921	hgsc.bcm.edu	37	1	162737116	162737116	+	Silent	SNP	C	C	G	rs2298258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:162737116C>G	ENST00000367922.3	+	12	1698	c.1260C>G	c.(1258-1260)ctC>ctG	p.L420L	DDR2_ENST00000367921.3_Silent_p.L420L	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	420					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	TCATCATCCTCTGGAGGCAGT	0.473													C|||	1745	0.348442	0.5023	0.353	5008	,	,		20143	0.4077		0.1461	False		,,,				2504	0.2843				p.L420L	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											DDR2_ENST00000367922,NS,carcinoma,+2,1	DDR2	228	1	0			c.C1260G						PASS	.	C	,	2082,2324	572.6+/-383.4	502,1078,623	117.0	107.0	110.0		1260,1260	1.6	1.0	1	dbSNP_100	110	1264,7336	252.6+/-278.6	103,1058,3139	no	coding-synonymous,coding-synonymous	DDR2	NM_001014796.1,NM_006182.2	,	605,2136,3762	GG,GC,CC		14.6977,47.2537,25.7266	,	420/856,420/856	162737116	3346,9660	2203	4300	6503	SO:0001819	synonymous_variant	4921	exon12			CATCCTCTGGAGG	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"""discoidin domain receptor family, member 2"""	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.1260C>G	1.37:g.162737116C>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	199	89	0.447236	NM_001014796	Q7Z730	Silent	SNP	ENST00000367922.3	37	CCDS1241.1	705	0.3228021978021978	253	0.5142276422764228	113	0.31215469613259667	237	0.4143356643356643	102	0.1345646437994723	C	9.562	1.118647	0.20877	0.472537	0.146977	ENSG00000162733	ENST00000433757	T	0.74315	-0.83	5.79	1.65	0.23941	.	0.000000	0.85682	D	0.000000	T	0.67420	0.2891	.	.	.	0.31024	P	0.717955	.	.	.	.	.	.	T	0.68010	-0.5522	6	0.87932	D	0	.	9.3142	0.37924	0.0:0.5761:0.2821:0.1418	rs2298258;rs2298258	.	.	.	V	13	ENSP00000396864:L13V	ENSP00000396864:L13V	L	+	1	2	DDR2	161003740	0.991000	0.36638	0.998000	0.56505	0.995000	0.86356	0.218000	0.17622	0.034000	0.15491	0.655000	0.94253	CTG	C|0.718;G|0.282	0.282	strong		0.473	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182	
OR2L2	26246	hgsc.bcm.edu	37	1	248202344	248202344	+	Missense_Mutation	SNP	G	G	C	rs6658141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248202344G>C	ENST00000366479.2	+	1	871	c.775G>C	c.(775-777)Gta>Cta	p.V259L	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	259			V -> L (in dbSNP:rs6658141).			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(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	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;0.0278)			TTATACCTATGTACGTCCAAG	0.507													N|||	1728	0.345048	0.7799	0.1484	5008	,	,		20898	0.3036		0.1551	False		,,,				2504	0.135				p.V259L		Atlas-SNP	.											.	OR2L2	115	.	0			c.G775C						PASS	.	C	LEU/VAL,	3005,1401		1027,951,225	157.0	141.0	146.0		775,	1.9	0.0	1	dbSNP_116	146	1249,7351		91,1067,3142	no	missense,intron	OR2L2,OR2L13	NM_001004686.2,NM_175911.2	32,	1118,2018,3367	CC,CG,GG		14.5233,31.7975,32.708	benign,	259/313,	248202344	4254,8752	2203	4300	6503	SO:0001583	missense	26246	exon1			ACCTATGTACGTC	X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"""GPCR / Class A : Olfactory receptors"""	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.775G>C	1.37:g.248202344G>C	ENSP00000355435:p.Val259Leu	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	226	119	0.526549	NM_001004686	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	37	CCDS31103.1	751	0.34386446886446886	381	0.774390243902439	58	0.16022099447513813	201	0.3513986013986014	111	0.14643799472295516	.	0.161	-1.081535	0.01888	0.682025	0.145233	ENSG00000203663	ENST00000366479	T	0.33654	1.4	1.9	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	0.000000	0.26055	N	0.026610	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.32771	-0.9894	8	0.12103	T	0.63	.	3.3465	0.07137	0.0:0.5:0.2296:0.2703	rs6658141;rs6658141	259	Q8NH16	OR2L2_HUMAN	L	259	ENSP00000355435:V259L	ENSP00000355435:V259L	V	+	1	0	OR2L2	246268967	0.000000	0.05858	0.007000	0.13788	0.132000	0.20833	-3.472000	0.00459	0.046000	0.15833	-1.041000	0.02371	GTA	G|0.650;C|0.350	0.350	strong		0.507	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604564	140604564	+	Missense_Mutation	SNP	G	G	C	rs61997246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604564G>C	ENST00000239449.4	+	1	1487	c.1487G>C	c.(1486-1488)cGg>cCg	p.R496P	PCDHB14_ENST00000515856.2_Missense_Mutation_p.R343P	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	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)|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)			CCCCAGGACCGGCACCTGCCC	0.637													c|||	418	0.0834665	0.2769	0.0548	5008	,	,		15681	0.0		0.0139	False		,,,				2504	0.0				p.R496P	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G1487C						PASS	.	C	PRO/ARG	990,3416		110,770,1323	89.0	99.0	96.0		1487	-0.2	0.1	5	dbSNP_129	96	120,8480		0,120,4180	no	missense	PCDHB14	NM_018934.2	103	110,890,5503	CC,CG,GG		1.3953,22.4694,8.5345	benign	496/799	140604564	1110,11896	2203	4300	6503	SO:0001583	missense	56122	exon1			AGGACCGGCACCT	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.1487G>C	5.37:g.140604564G>C	ENSP00000239449:p.Arg496Pro	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	275	135	0.490909	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	162	0.07417582417582418	133	0.2703252032520325	20	0.055248618784530384	0	0.0	9	0.011873350923482849	-	0.001	-3.069461	0.00036	0.224694	0.013953	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.01745	4.66;4.66	4.15	-0.219	0.13135	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.16066	0.365	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.42649	-0.9439	8	0.02654	T	1	.	2.8274	0.05489	0.2732:0.2374:0.3928:0.0965	rs61997246	496	Q9Y5E9	PCDBE_HUMAN	P	343;496	ENSP00000444518:R343P;ENSP00000239449:R496P	ENSP00000239449:R496P	R	+	2	0	PCDHB14	140584748	0.000000	0.05858	0.073000	0.20177	0.022000	0.10575	0.082000	0.14847	0.031000	0.15407	-0.223000	0.12442	CGG	G|0.918;C|0.082	0.082	strong		0.637	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84683428	84683428	+	Missense_Mutation	SNP	A	A	G	rs17158450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:84683428A>G	ENST00000286744.5	+	24	4332	c.4108A>G	c.(4108-4110)Acc>Gcc	p.T1370A	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.T1370A	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1370	Ig-like C2-type 3.		T -> A (in dbSNP:rs17158450).			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)			CTGCATAGCCACCAATGCTCT	0.443													A|||	240	0.0479233	0.1717	0.0187	5008	,	,		20971	0.0		0.0	False		,,,				2504	0.0				p.T1370A		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.A4108G						PASS	.	A	ALA/THR	680,3726	286.6+/-278.8	50,580,1573	134.0	125.0	128.0		4108	2.7	1.0	15	dbSNP_123	128	7,8591	6.4+/-24.3	0,7,4292	yes	missense	ADAMTSL3	NM_207517.2	58	50,587,5865	GG,GA,AA		0.0814,15.4335,5.283	benign	1370/1692	84683428	687,12317	2203	4299	6502	SO:0001583	missense	57188	exon24			ATAGCCACCAATG	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.4108A>G	15.37:g.84683428A>G	ENSP00000286744:p.Thr1370Ala	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	159	63	0.396226	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	94	0.04304029304029304	86	0.17479674796747968	8	0.022099447513812154	0	0.0	0	0.0	A	2.759	-0.258227	0.05791	0.154335	8.14E-4	ENSG00000156218	ENST00000286744	T	0.68903	-0.36	5.03	2.73	0.32206	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.188900	0.26149	N	0.026056	T	0.00210	0.0006	L	0.46741	1.465	0.30564	P	0.7641979999999999	B;B	0.17465	0.002;0.022	B;B	0.19946	0.01;0.027	T	0.06991	-1.0796	9	0.10111	T	0.7	.	8.0282	0.30448	0.7665:0.0:0.2335:0.0	rs17158450;rs52789838;rs17158450	1370;1370	P82987-2;P82987	.;ATL3_HUMAN	A	1370	ENSP00000286744:T1370A	ENSP00000286744:T1370A	T	+	1	0	ADAMTSL3	82474432	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.012000	0.29924	0.760000	0.33108	0.454000	0.30748	ACC	A|0.943;G|0.057	0.057	strong		0.443	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
CWF19L1	55280	hgsc.bcm.edu	37	10	101993024	101993024	+	Missense_Mutation	SNP	C	C	T	rs7922946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101993024C>T	ENST00000354105.4	-	14	1663	c.1577G>A	c.(1576-1578)cGg>cAg	p.R526Q	CWF19L1_ENST00000478047.1_5'UTR|RP11-316M21.6_ENST00000444359.1_RNA|CWF19L1_ENST00000370379.1_Missense_Mutation_p.R241Q	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	526			R -> Q (in dbSNP:rs7922946).				catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		AAAGTCTTTCCGGAAGCGGCG	0.448													C|||	34	0.00678914	0.0257	0.0	5008	,	,		16484	0.0		0.0	False		,,,				2504	0.0				p.R526Q		Atlas-SNP	.											.	CWF19L1	39	.	0			c.G1577A						PASS	.	C	GLN/ARG	107,4299	83.4+/-121.9	1,105,2097	85.0	90.0	88.0		1577	2.5	1.0	10	dbSNP_116	88	0,8600		0,0,4300	yes	missense	CWF19L1	NM_018294.4	43	1,105,6397	TT,TC,CC		0.0,2.4285,0.8227	probably-damaging	526/539	101993024	107,12899	2203	4300	6503	SO:0001583	missense	55280	exon14			TCTTTCCGGAAGC	AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.1577G>A	10.37:g.101993024C>T	ENSP00000326411:p.Arg526Gln	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	37	CCDS7489.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	21.5	4.159440	0.78226	0.024285	0.0	ENSG00000095485	ENST00000354105;ENST00000370379	T;T	0.30714	1.52;1.52	5.38	2.55	0.30701	Histidine triad motif (1);Cwf19-like protein, C-terminal domain-2 (1);	0.099847	0.64402	N	0.000004	T	0.31104	0.0786	M	0.79475	2.455	0.43168	D	0.994968	P;D;D	0.76494	0.815;0.993;0.999	B;P;P	0.60173	0.394;0.596;0.87	T	0.19063	-1.0317	10	0.41790	T	0.15	-3.3822	9.1705	0.37078	0.0:0.7604:0.0:0.2396	rs7922946;rs7922946	230;389;526	Q69YN2-2;Q69YN2-3;Q69YN2	.;.;C19L1_HUMAN	Q	526;241	ENSP00000326411:R526Q;ENSP00000359405:R241Q	ENSP00000326411:R526Q	R	-	2	0	CWF19L1	101983014	1.000000	0.71417	0.999000	0.59377	0.652000	0.38707	4.389000	0.59639	0.262000	0.21774	-0.219000	0.12488	CGG	C|0.993;T|0.007	0.007	strong		0.448	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
SRF	6722	hgsc.bcm.edu	37	6	43146105	43146105	+	Silent	SNP	G	G	T	rs140883192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43146105G>T	ENST00000265354.4	+	5	1594	c.1236G>T	c.(1234-1236)ccG>ccT	p.P412P	SRF_ENST00000457278.2_Silent_p.P208P	NM_003131.2	NP_003122.1	P11831	SRF_HUMAN	serum response factor (c-fos serum response element-binding transcription factor)	412					angiogenesis involved in wound healing (GO:0060055)|associative learning (GO:0008306)|cardiac myofibril assembly (GO:0055003)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular senescence (GO:0090398)|contractile actin filament bundle assembly (GO:0030038)|developmental growth (GO:0048589)|dorsal aorta morphogenesis (GO:0035912)|epithelial cell-cell adhesion (GO:0090136)|epithelial structure maintenance (GO:0010669)|erythrocyte development (GO:0048821)|eyelid development in camera-type eye (GO:0061029)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|hematopoietic stem cell differentiation (GO:0060218)|hippocampus development (GO:0021766)|long term synaptic depression (GO:0060292)|long-term memory (GO:0007616)|megakaryocyte development (GO:0035855)|mesoderm formation (GO:0001707)|morphogenesis of an epithelial sheet (GO:0002011)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet formation (GO:0030220)|positive regulation of cell differentiation (GO:0045597)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription by glucose (GO:0046016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive thymic T cell selection (GO:0045059)|primitive streak formation (GO:0090009)|regulation of cell adhesion (GO:0030155)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of water loss via skin (GO:0033561)|response to cytokine (GO:0034097)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|sarcomere organization (GO:0045214)|skin morphogenesis (GO:0043589)|stress fiber assembly (GO:0043149)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|tight junction assembly (GO:0070830)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|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 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)|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)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	12			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.011)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			ACCCTAGCCCGCATGCGGTGA	0.607													G|||	31	0.0061901	0.0219	0.0014	5008	,	,		20467	0.0		0.001	False		,,,				2504	0.0				p.P412P		Atlas-SNP	.											.	SRF	24	.	0			c.G1236T						PASS	.	G		57,4349	55.5+/-91.7	0,57,2146	102.0	75.0	84.0		1236	4.7	1.0	6	dbSNP_134	84	0,8600		0,0,4300	no	coding-synonymous	SRF	NM_003131.2		0,57,6446	TT,TG,GG		0.0,1.2937,0.4383		412/509	43146105	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	6722	exon5			TAGCCCGCATGCG	J03161	CCDS4889.1	6p	2008-02-05			ENSG00000112658	ENSG00000112658			11291	protein-coding gene	gene with protein product		600589				3203386	Standard	NM_003131		Approved	MCM1	uc003oui.3	P11831	OTTHUMG00000014722	ENST00000265354.4:c.1236G>T	6.37:g.43146105G>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_003131	Q5T648	Silent	SNP	ENST00000265354.4	37	CCDS4889.1																																																																																			G|0.997;T|0.003	0.003	strong		0.607	SRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040581.1	NM_003131	
CARD14	79092	hgsc.bcm.edu	37	17	78176193	78176193	+	Silent	SNP	G	G	A	rs35692270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78176193G>A	ENST00000573882.1	+	17	2729	c.2193G>A	c.(2191-2193)gcG>gcA	p.A731A	RP11-334C17.5_ENST00000570309.1_RNA|RP11-334C17.5_ENST00000576824.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|CARD14_ENST00000570421.1_Silent_p.A731A|CARD14_ENST00000344227.2_Silent_p.A731A|CARD14_ENST00000392434.2_3'UTR|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	731					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			ATACTGCCGCGCACGGCACCA	0.632													G|||	32	0.00638978	0.0227	0.0029	5008	,	,		17093	0.0		0.0	False		,,,				2504	0.0				p.A731A		Atlas-SNP	.											.	CARD14	98	.	0			c.G2193A						PASS	.	G		115,4291	88.2+/-126.9	2,111,2090	51.0	41.0	44.0		2193	-4.0	0.0	17	dbSNP_126	44	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CARD14	NM_024110.3		2,114,6387	AA,AG,GG		0.0349,2.6101,0.9073		731/1005	78176193	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	79092	exon15			TGCCGCGCACGGC	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2193G>A	17.37:g.78176193G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_024110	B8QQJ3|Q9BVB5	Silent	SNP	ENST00000573882.1	37	CCDS11768.1																																																																																			G|0.992;A|0.008	0.008	strong		0.632	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
TRIM49C	642612	hgsc.bcm.edu	37	11	89774236	89774236	+	Missense_Mutation	SNP	C	C	G	rs74584169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:89774236C>G	ENST00000448984.1	+	8	1206	c.877C>G	c.(877-879)Cat>Gat	p.H293D	TRIM49C_ENST00000432771.1_Intron	NM_001195234.1	NP_001182163.1	P0CI26	TR49C_HUMAN	tripartite motif containing 49C	293	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|lung(4)	8						TACTCTGCATCATGAAGAAGC	0.313																																					p.H293D		Atlas-SNP	.											.	TRIM49C	48	.	0			c.C877G						PASS	.																																			SO:0001583	missense	642612	exon8			CTGCATCATGAAG	BC126470	CCDS53694.1	11q14.3	2014-02-17	2012-05-18	2012-05-18	ENSG00000204449	ENSG00000204449		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	38877	protein-coding gene	gene with protein product			"""tripartite motif containing 49-like 2"""	TRIM49L2			Standard	NM_001195234		Approved		uc010rua.2	P0CI26		ENST00000448984.1:c.877C>G	11.37:g.89774236C>G	ENSP00000388299:p.His293Asp	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	164	82	0.5	NM_001195234	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Missense_Mutation	SNP	ENST00000448984.1	37	CCDS53694.1	815	0.3731684981684982	211	0.42886178861788615	159	0.43922651933701656	224	0.3916083916083916	221	0.29155672823219	C	1.349	-0.591968	0.03799	.	.	ENSG00000204449	ENST00000448984	T	0.60672	0.17	0.823	0.823	0.18812	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.53005	P	3.399999999997849E-5	B	0.14438	0.01	B	0.13407	0.009	T	0.43442	-0.9391	7	.	.	.	.	4.9575	0.14050	0.0:1.0:0.0:0.0	.	293	P0CI26	T49L2_HUMAN	D	293	ENSP00000388299:H293D	.	H	+	1	0	TRIM49L2	89413884	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	-1.205000	0.03014	0.742000	0.32697	0.305000	0.20034	CAT	C|0.658;G|0.342	0.342	strong		0.313	TRIM49C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395455.1	NM_001195234	
SPINK2	6691	hgsc.bcm.edu	37	4	57687719	57687719	+	Intron	SNP	C	C	T	rs781544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57687719C>T	ENST00000248701.4	-	1	135				SPINK2_ENST00000506738.1_Missense_Mutation_p.G37E|SPINK2_ENST00000504762.1_Missense_Mutation_p.G37E	NM_021114.2	NP_066937.1	P20155	ISK2_HUMAN	serine peptidase inhibitor, Kazal type 2 (acrosin-trypsin inhibitor)						negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(1)|lung(2)	4	Glioma(25;0.08)|all_neural(26;0.181)					GGTCTGACTCCCAAACCCGCT	0.711													C|||	1104	0.220447	0.5651	0.2421	5008	,	,		11543	0.0913		0.0616	False		,,,				2504	0.0358				p.G37E		Atlas-SNP	.											.	SPINK2	12	.	0			c.G110A						PASS	.						4.0	8.0	7.0					4																	57687719		624	1506	2130	SO:0001627	intron_variant	6691	exon1			TGACTCCCAAACC	BC022514	CCDS3508.1, CCDS63971.1, CCDS63972.1, CCDS75128.1	4q12	2011-08-31	2005-08-17		ENSG00000128040	ENSG00000128040		"""Serine peptidase inhibitors, Kazal type"""	11245	protein-coding gene	gene with protein product		605753	"""serine protease inhibitor, Kazal type 2 (acrosin-trypsin inhibitor)"""			8428671	Standard	NM_001271718		Approved	HUSI-II	uc031sep.1	P20155	OTTHUMG00000128769	ENST00000248701.4:c.55+54G>A	4.37:g.57687719C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	35	12	0.342857	NM_001271722	Q6FGH2	Missense_Mutation	SNP	ENST00000248701.4	37	CCDS3508.1	454	0.2078754578754579	259	0.5264227642276422	79	0.21823204419889503	66	0.11538461538461539	50	0.06596306068601583	C	12.16	1.855248	0.32791	.	.	ENSG00000128040	ENST00000506738;ENST00000504762	D;T	0.81908	-1.55;-1.48	2.47	-0.106	0.13596	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.34976	-0.9807	5	0.49607	T	0.09	.	1.9144	0.03294	0.2844:0.4279:0.0:0.2877	rs781544	.	.	.	E	37	ENSP00000425961:G37E;ENSP00000423858:G37E	ENSP00000423858:G37E	G	-	2	0	SPINK2	57382476	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	-0.427000	0.06999	-0.042000	0.13535	0.313000	0.20887	GGG	C|0.791;T|0.209	0.209	strong		0.711	SPINK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250690.2	NM_021114	
LGALS2	3957	hgsc.bcm.edu	37	22	37966314	37966314	+	Missense_Mutation	SNP	C	C	T	rs2235339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37966314C>T	ENST00000215886.4	-	4	529	c.355G>A	c.(355-357)Gta>Ata	p.V119I		NM_006498.2	NP_006489.1	P05162	LEG2_HUMAN	lectin, galactoside-binding, soluble, 2	119	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.		V -> I (in dbSNP:rs2235339). {ECO:0000269|PubMed:3020551}.				carbohydrate binding (GO:0030246)|galactoside binding (GO:0016936)	p.V119I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|stomach(1)	11	Melanoma(58;0.0574)					CCGCCCCTTACGCTCAGGTAG	0.502													c|||	273	0.0545128	0.1634	0.0101	5008	,	,		20669	0.0427		0.002	False		,,,				2504	0.0051				p.V119I	GBM(193;1840 2185 13711 20676 24505)	Atlas-SNP	.											LGALS2,NS,carcinoma,0,1	LGALS2	16	1	1	Substitution - Missense(1)	stomach(1)	c.G355A						PASS	.	T	ILE/VAL	553,3853	248.1+/-256.1	38,477,1688	89.0	93.0	92.0		355	-0.0	0.0	22	dbSNP_98	92	3,8597	3.7+/-12.6	0,3,4297	yes	missense	LGALS2	NM_006498.2	29	38,480,5985	TT,TC,CC		0.0349,12.5511,4.275	benign	119/133	37966314	556,12450	2203	4300	6503	SO:0001583	missense	3957	exon4			CCCTTACGCTCAG		CCDS13950.1	22q13.1	2011-08-04	2007-02-01		ENSG00000100079	ENSG00000100079		"""Lectins, galactoside-binding"""	6562	protein-coding gene	gene with protein product	"""galectin 2"""	150571				1988031, 15356130	Standard	NM_006498		Approved	HL14	uc003ata.3	P05162	OTTHUMG00000150590	ENST00000215886.4:c.355G>A	22.37:g.37966314C>T	ENSP00000215886:p.Val119Ile	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	127	54	0.425197	NM_006498	Q6FGY4	Missense_Mutation	SNP	ENST00000215886.4	37	CCDS13950.1	103	0.04716117216117216	68	0.13821138211382114	6	0.016574585635359115	28	0.04895104895104895	1	0.0013192612137203166	c	9.643	1.139575	0.21205	0.125511	3.49E-4	ENSG00000100079	ENST00000215886	T	0.06608	3.28	5.69	-0.0117	0.13991	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.409539	0.27331	N	0.019843	T	0.00039	0.0001	N	0.13272	0.32	0.80722	P	0.0	B	0.26445	0.149	B	0.25614	0.062	T	0.44097	-0.9350	9	0.02654	T	1	-9.3003	5.5936	0.17315	0.0:0.4847:0.1354:0.3798	rs2235339;rs2235339	119	P05162	LEG2_HUMAN	I	119	ENSP00000215886:V119I	ENSP00000215886:V119I	V	-	1	0	LGALS2	36296260	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	-0.060000	0.11712	0.056000	0.16144	-0.927000	0.02713	GTA	C|0.948;T|0.052	0.052	strong		0.502	LGALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318991.1	NM_006498	
RTP5	285093	hgsc.bcm.edu	37	2	242815157	242815157	+	Missense_Mutation	SNP	C	C	T	rs77317868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242815157C>T	ENST00000343216.3	+	2	1478	c.1450C>T	c.(1450-1452)Cgc>Tgc	p.R484C		NM_173821.2	NP_776182.2																					TGTCATAAAGCGCAAGGGCGG	0.627													C|||	168	0.0335463	0.121	0.0086	5008	,	,		15580	0.0		0.002	False		,,,				2504	0.0				p.R484C		Atlas-SNP	.											.	.	.	.	0			c.C1450T						PASS	.	C	CYS/ARG	469,3695		27,415,1640	69.0	80.0	76.0		1450	-3.6	0.0	2	dbSNP_131	76	4,8400		0,4,4198	yes	missense	C2orf85	NM_173821.2	180	27,419,5838	TT,TC,CC		0.0476,11.2632,3.7635	benign	484/573	242815157	473,12095	2082	4202	6284	SO:0001583	missense	285093	exon2			ATAAAGCGCAAGG																												ENST00000343216.3:c.1450C>T	2.37:g.242815157C>T	ENSP00000345374:p.Arg484Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_173821		Missense_Mutation	SNP	ENST00000343216.3	37	CCDS42843.1	49	0.022435897435897436	44	0.08943089430894309	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	.	7.258	0.604519	0.14002	0.112632	4.76E-4	ENSG00000188011	ENST00000343216	T	0.22539	1.95	2.14	-3.6	0.04570	.	.	.	.	.	T	0.00144	0.0004	N	0.03608	-0.345	0.09310	N	1	B	0.21225	0.053	B	0.06405	0.002	T	0.32322	-0.9911	9	0.87932	D	0	-7.0233	0.6619	0.00844	0.4047:0.248:0.1829:0.1644	.	484	Q14D33	CB085_HUMAN	C	484	ENSP00000345374:R484C	ENSP00000345374:R484C	R	+	1	0	C2orf85	242463830	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-1.257000	0.02866	-0.945000	0.03681	0.196000	0.17591	CGC	C|0.973;T|0.027	0.027	strong		0.627	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
ZNF20	7568	hgsc.bcm.edu	37	19	12244624	12244624	+	Missense_Mutation	SNP	G	G	A	rs61743205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12244624G>A	ENST00000334213.5	-	4	601	c.377C>T	c.(376-378)gCt>gTt	p.A126V	ZNF625-ZNF20_ENST00000430024.1_3'UTR|ZNF20_ENST00000600335.1_Intron|ZNF20_ENST00000485451.1_5'UTR	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	126					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)|lung(6)	8						TCCAGTGTCAGCTCTGATATG	0.408													G|||	103	0.0205671	0.0764	0.0029	5008	,	,		20665	0.0		0.0	False		,,,				2504	0.0				p.A126V		Atlas-SNP	.											.	ZNF20	86	.	0			c.C377T						PASS	.	G	VAL/ALA,VAL/ALA	196,4082		3,190,1946	248.0	252.0	251.0		368,377	-0.3	0.0	19	dbSNP_129	251	1,8541		0,1,4270	yes	missense,missense	ZNF20	NM_001203250.1,NM_021143.3	64,64	3,191,6216	AA,AG,GG		0.0117,4.5816,1.5367	possibly-damaging,possibly-damaging	123/530,126/533	12244624	197,12623	2139	4271	6410	SO:0001583	missense	7568	exon4			GTGTCAGCTCTGA	X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"""Zinc fingers, C2H2-type"", ""-"""	12992	protein-coding gene	gene with protein product		194557	"""zinc finger protein 20 (KOX 13)"""				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.377C>T	19.37:g.12244624G>A	ENSP00000335437:p.Ala126Val	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	182	88	0.483516	NM_021143	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	37	CCDS45986.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	G	4.410	0.075745	0.08485	0.045816	1.17E-4	ENSG00000132010	ENST00000334213;ENST00000292241;ENST00000418866	T;T	0.13420	3.41;2.59	0.94	-0.349	0.12609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.	.	.	.	T	0.00241	0.0007	N	0.04148	-0.265	0.09310	N	1	P	0.44627	0.839	B	0.33454	0.164	T	0.38607	-0.9653	9	0.21540	T	0.41	.	4.7244	0.12935	0.0:0.4015:0.5985:0.0	.	126	P17024	ZNF20_HUMAN	V	126;126;123	ENSP00000335437:A126V;ENSP00000390115:A123V	ENSP00000292241:A126V	A	-	2	0	ZNF20	12105624	0.000000	0.05858	0.029000	0.17559	0.267000	0.26476	-1.626000	0.02035	-0.066000	0.12998	0.313000	0.20887	GCT	G|0.981;A|0.019	0.019	strong		0.408	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143	
VWA3B	200403	hgsc.bcm.edu	37	2	98779418	98779418	+	Missense_Mutation	SNP	G	G	A	rs77092382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98779418G>A	ENST00000477737.1	+	8	1297	c.1093G>A	c.(1093-1095)Gac>Aac	p.D365N	VWA3B_ENST00000435344.1_Missense_Mutation_p.D365N|VWA3B_ENST00000451075.2_Missense_Mutation_p.D215N	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	365										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						TCCCAAGCCCGACGTGGCCAC	0.567													G|||	132	0.0263578	0.0946	0.0101	5008	,	,		16753	0.0		0.0	False		,,,				2504	0.0				p.D365N		Atlas-SNP	.											.	VWA3B	138	.	0			c.G1093A						PASS	.	G	ASN/ASP	319,3775		17,285,1745	56.0	64.0	62.0		1093	-9.4	0.0	2	dbSNP_131	62	4,8420		0,4,4208	no	missense	VWA3B	NM_144992.4	23	17,289,5953	AA,AG,GG		0.0475,7.7919,2.5803	benign	365/1295	98779418	323,12195	2047	4212	6259	SO:0001583	missense	200403	exon8			AAGCCCGACGTGG	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.1093G>A	2.37:g.98779418G>A	ENSP00000417955:p.Asp365Asn	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	139	60	0.431655	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	35	0.016025641025641024	33	0.06707317073170732	2	0.0055248618784530384	0	0.0	0	0.0	G	10.25	1.297516	0.23650	0.077919	4.75E-4	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.23147	1.92;3.36;2.47	4.68	-9.37	0.00626	.	2.270810	0.02023	N	0.047965	T	0.00496	0.0016	N	0.04959	-0.14	0.09310	N	1	B;B;B	0.12630	0.006;0.001;0.002	B;B;B	0.04013	0.001;0.001;0.001	T	0.11179	-1.0598	10	0.34782	T	0.22	.	4.1345	0.10164	0.5431:0.1901:0.1706:0.0961	.	215;365;365	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	N	365;365;215	ENSP00000401959:D365N;ENSP00000417955:D365N;ENSP00000389463:D215N	ENSP00000411168:D365N	D	+	1	0	VWA3B	98145850	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.018000	0.01444	-2.385000	0.00590	-0.781000	0.03364	GAC	G|0.981;A|0.019	0.019	strong		0.567	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
CSNK1G1	53944	hgsc.bcm.edu	37	15	64592522	64592522	+	Silent	SNP	T	T	C	rs7163558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:64592522T>C	ENST00000303052.7	-	2	600	c.177A>G	c.(175-177)agA>agG	p.R59R	CSNK1G1_ENST00000303032.6_Silent_p.R59R|CSNK1G1_ENST00000607537.1_Silent_p.R59R|CTD-2116N17.1_ENST00000606793.1_5'UTR|CTD-2116N17.1_ENST00000558783.1_5'Flank	NM_022048.3	NP_071331.2	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	59	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	13						GCTTACCTAATCTGAGCTCTC	0.448													T|||	153	0.0305511	0.115	0.0014	5008	,	,		19957	0.0		0.0	False		,,,				2504	0.0				p.R59R		Atlas-SNP	.											.	CSNK1G1	56	.	0			c.A177G						PASS	.	T		401,4005	199.1+/-222.7	18,365,1820	253.0	243.0	246.0		177	5.4	1.0	15	dbSNP_116	246	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	CSNK1G1	NM_022048.3		18,372,6113	CC,CT,TT		0.0814,9.1012,3.137		59/423	64592522	408,12598	2203	4300	6503	SO:0001819	synonymous_variant	53944	exon2			ACCTAATCTGAGC	AB042562	CCDS10192.2	15q22.1-q22.31	2013-01-17			ENSG00000169118	ENSG00000169118			2454	protein-coding gene	gene with protein product		606274				11124537	Standard	NM_022048		Approved	CK1gamma1	uc002anf.3	Q9HCP0	OTTHUMG00000133019	ENST00000303052.7:c.177A>G	15.37:g.64592522T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	190	91	0.478947	NM_022048	Q5JPH1|Q96AE9|Q9HCP1	Silent	SNP	ENST00000303052.7	37	CCDS10192.2																																																																																			T|0.968;C|0.032	0.032	strong		0.448	CSNK1G1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256605.1	NM_022048	
SEC14L3	266629	hgsc.bcm.edu	37	22	30864545	30864545	+	Missense_Mutation	SNP	T	T	A	rs115380280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30864545T>A	ENST00000215812.4	-	5	463	c.373A>T	c.(373-375)Atg>Ttg	p.M125L	SEC14L3_ENST00000539629.1_Missense_Mutation_p.M66L|SEC14L3_ENST00000540910.1_Missense_Mutation_p.M48L|SEC14L3_ENST00000402286.1_Missense_Mutation_p.M48L|SEC14L3_ENST00000403066.1_Missense_Mutation_p.M66L|SEC14L3_ENST00000415957.2_Missense_Mutation_p.M66L|SEC14L3_ENST00000401751.1_Missense_Mutation_p.M66L	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	125	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					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)	CAGTCCCTCATCTTGGTCTTG	0.602													T|||	18	0.00359425	0.0129	0.0014	5008	,	,		18253	0.0		0.0	False		,,,				2504	0.0				p.M125L	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.A373T						PASS	.	T	LEU/MET	33,4373	39.2+/-71.8	0,33,2170	176.0	130.0	145.0		373	4.6	1.0	22	dbSNP_132	145	0,8600		0,0,4300	yes	missense	SEC14L3	NM_174975.4	15	0,33,6470	AA,AT,TT		0.0,0.749,0.2537	benign	125/401	30864545	33,12973	2203	4300	6503	SO:0001583	missense	266629	exon5			CCCTCATCTTGGT	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.373A>T	22.37:g.30864545T>A	ENSP00000215812:p.Met125Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	2|2	9.157509157509158E-4|9.157509157509158E-4	2|2	0.0040650406504065045|0.0040650406504065045	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	T|T	10.11|10.11	1.260683|1.260683	0.23051|0.23051	0.00749|0.00749	0.0|0.0	ENSG00000100012|ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910|ENST00000435069	T;T;T;T;T;T;T|.	0.72835|.	-0.69;-0.69;-0.69;-0.69;-0.69;-0.69;-0.69|.	4.55|4.55	4.55|4.55	0.56014|0.56014	Cellular retinaldehyde-binding/triple function, C-terminal (5);|.	0.222920|.	0.48286|.	D|.	0.000195|.	T|T	0.25754|0.25754	0.0627|0.0627	N|N	0.05592|0.05592	-0.015|-0.015	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.08055|.	0.003;0.003|.	T|T	0.11251|0.11251	-1.0595|-1.0595	10|5	0.15952|.	T|.	0.53|.	-18.6063|-18.6063	9.2656|9.2656	0.37639|0.37639	0.205:0.0:0.0:0.795|0.205:0.0:0.0:0.795	.|.	48;125|.	E9PE57;Q9UDX4|.	.;S14L3_HUMAN|.	L|S	66;66;125;48;66;66;48|90	ENSP00000385941:M66L;ENSP00000401864:M66L;ENSP00000215812:M125L;ENSP00000385004:M48L;ENSP00000383896:M66L;ENSP00000444691:M66L;ENSP00000439752:M48L|.	ENSP00000215812:M125L|.	M|R	-|-	1|3	0|2	SEC14L3|SEC14L3	29194545|29194545	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.513000|3.513000	0.53414|0.53414	1.810000|1.810000	0.52873|0.52873	0.519000|0.519000	0.50382|0.50382	ATG|AGA	T|0.998;A|0.002	0.002	strong		0.602	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370605	26370605	+	Silent	SNP	T	T	C	rs9379860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26370605T>C	ENST00000356386.2	+	5	677	c.489T>C	c.(487-489)caT>caC	p.H163H	BTN3A2_ENST00000396934.3_Silent_p.H140H|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000377708.2_Silent_p.H163H|BTN3A2_ENST00000396948.1_Silent_p.H163H|BTN3A2_ENST00000508906.2_Silent_p.H121H|BTN3A2_ENST00000527422.1_Silent_p.H163H	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	163					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						GAGGGATCCATCTGGAGTGCA	0.522													T|||	1755	0.350439	0.4266	0.3098	5008	,	,		18970	0.2232		0.4135	False		,,,				2504	0.3425				p.H163H		Atlas-SNP	.											.	BTN3A2	44	.	0			c.T489C						PASS	.	T	,,,,	1865,2541	540.1+/-375.4	382,1101,720	115.0	102.0	107.0		489,489,420,363,489	-4.6	0.0	6	dbSNP_119	107	3406,5194	503.8+/-376.0	658,2090,1552	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	1040,3191,2272	CC,CT,TT		39.6047,42.3286,40.5274	,,,,	163/335,163/335,140/312,121/293,163/335	26370605	5271,7735	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon3			GATCCATCTGGAG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.489T>C	6.37:g.26370605T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	169	84	0.497041	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			T|0.614;C|0.386	0.386	strong		0.522	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
ZNF676	163223	hgsc.bcm.edu	37	19	22364322	22364322	+	Missense_Mutation	SNP	A	A	G	rs62000438	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22364322A>G	ENST00000397121.2	-	3	514	c.197T>C	c.(196-198)aTg>aCg	p.M66T		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	66					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TCTCAATATCATTTTTTGGAA	0.303													A|||	203	0.0405351	0.1475	0.0101	5008	,	,		17799	0.0		0.001	False		,,,				2504	0.0				p.M66T		Atlas-SNP	.											ZNF676,NS,carcinoma,+1,1	ZNF676	146	1	0			c.T197C						PASS	.	A	THR/MET	503,3277		31,441,1418	59.0	53.0	55.0		197	0.8	0.0	19	dbSNP_129	55	11,8297		0,11,4143	yes	missense	ZNF676	NM_001001411.2	81	31,452,5561	GG,GA,AA		0.1324,13.3069,4.2522	benign	66/589	22364322	514,11574	1890	4154	6044	SO:0001583	missense	163223	exon3			AATATCATTTTTT	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.197T>C	19.37:g.22364322A>G	ENSP00000380310:p.Met66Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	37	CCDS42539.1	79	0.036172161172161175	77	0.1565040650406504	2	0.0055248618784530384	0	0.0	0	0.0	.	4.684	0.127192	0.08981	0.133069	0.001324	ENSG00000196109	ENST00000397121	T	0.06608	3.28	0.814	0.814	0.18756	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.12630	0.006	B	0.04013	0.001	T	0.46373	-0.9196	8	0.33940	T	0.23	.	3.7226	0.08462	1.0:0.0:0.0:0.0	.	66	Q8N7Q3	ZN676_HUMAN	T	66	ENSP00000380310:M66T	ENSP00000380310:M66T	M	-	2	0	ZNF676	22156162	0.000000	0.05858	0.033000	0.17914	0.033000	0.12548	0.541000	0.23207	0.158000	0.19367	0.156000	0.16432	ATG	A|0.974;G|0.026	0.026	strong		0.303	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
IGSF5	150084	hgsc.bcm.edu	37	21	41165462	41165462	+	Splice_Site	SNP	C	C	A	rs2837225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	124	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	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
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458200	39458200	+	Missense_Mutation	SNP	C	C	T	rs115643796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39458200C>T	ENST00000391353.1	-	1	903	c.904G>A	c.(904-906)Ggc>Agc	p.G302S		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	302	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											GATTTGCAGCCACTCTGGTTA	0.512													C|||	77	0.0153754	0.056	0.0043	5008	,	,		22736	0.0		0.0	False		,,,				2504	0.0				p.G302S		Atlas-SNP	.											.	KRTAP29-1	2	.	0			c.G904A						PASS	.																																			SO:0001583	missense	100533177	exon1			TGCAGCCACTCTG		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.904G>A	17.37:g.39458200C>T	ENSP00000375148:p.Gly302Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_001257309		Missense_Mutation	SNP	ENST00000391353.1	37		28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	C	11.47	1.648830	0.29336	.	.	ENSG00000212658	ENST00000391353	.	.	.	4.25	3.28	0.37604	.	.	.	.	.	T	0.02888	0.0086	.	.	.	.	.	.	.	.	.	.	.	.	T	0.16928	-1.0386	4	0.05959	T	0.93	.	7.7986	0.29162	0.0:0.8855:0.0:0.1145	.	.	.	.	S	302	.	ENSP00000375148:G302S	G	-	1	0	KRTAP29-1	36711726	0.008000	0.16893	0.746000	0.31095	0.834000	0.47266	0.971000	0.29396	0.995000	0.38917	0.455000	0.32223	GGC	C|0.987;T|0.013	0.013	strong		0.512	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
CAMSAP1	157922	hgsc.bcm.edu	37	9	138742077	138742077	+	Silent	SNP	C	C	G	rs35981196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138742077C>G	ENST00000389532.4	-	7	1015	c.951G>C	c.(949-951)ccG>ccC	p.P317P	CAMSAP1_ENST00000312405.6_Silent_p.P39P|CAMSAP1_ENST00000409386.3_Silent_p.P328P	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	317	CH.				cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		CCATAACATTCGGCTAAAAGA	0.378													C|||	609	0.121605	0.2057	0.0879	5008	,	,		18956	0.0		0.1322	False		,,,				2504	0.1462				p.P317P		Atlas-SNP	.											.	CAMSAP1	142	.	0			c.G951C						PASS	.	C		884,3522	337.3+/-304.8	105,674,1424	44.0	42.0	43.0		951	-10.7	0.0	9	dbSNP_126	43	1523,7077	283.9+/-296.4	134,1255,2911	no	coding-synonymous	CAMSAP1	NM_015447.3		239,1929,4335	GG,GC,CC		17.7093,20.0635,18.5068		317/1603	138742077	2407,10599	2203	4300	6503	SO:0001819	synonymous_variant	157922	exon7			AACATTCGGCTAA	AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.951G>C	9.37:g.138742077C>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	82	30	0.365854	NM_015447	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Silent	SNP	ENST00000389532.4	37	CCDS35176.2																																																																																			C|0.836;G|0.164	0.164	strong		0.378	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055024.2	XM_351857	
SVIL	6840	hgsc.bcm.edu	37	10	29840038	29840038	+	Silent	SNP	A	A	G	rs3740003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:29840038A>G	ENST00000355867.4	-	6	1067	c.315T>C	c.(313-315)atT>atC	p.I105I	SVIL_ENST00000375400.3_Silent_p.I105I|SVIL_ENST00000375398.2_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						PASS	.	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	177	0	0		WXS	Illumina HiSeq	Phase_I	184	82	0.445652	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		
FRAS1	80144	hgsc.bcm.edu	37	4	79455733	79455733	+	Silent	SNP	C	C	T	rs4975139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79455733C>T	ENST00000264895.6	+	71	11496	c.11056C>T	c.(11056-11058)Cta>Tta	p.L3686L		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3682					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						TGATATGTCACTAGCAGAAAT	0.438													C|||	2579	0.514976	0.3086	0.4395	5008	,	,		21167	0.7758		0.4632	False		,,,				2504	0.6319				p.L3686L		Atlas-SNP	.											.	FRAS1	779	.	0			c.C11056T						PASS	.	C		1271,2491		214,843,824	104.0	93.0	97.0		11056	2.4	1.0	4	dbSNP_111	97	3591,4647		790,2011,1318	no	coding-synonymous	FRAS1	NM_025074.6		1004,2854,2142	TT,TC,CC		43.5907,33.7852,40.5167		3686/4013	79455733	4862,7138	1881	4119	6000	SO:0001819	synonymous_variant	80144	exon71			ATGTCACTAGCAG	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.11056C>T	4.37:g.79455733C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	1143	0.5233516483516484	172	0.34959349593495936	163	0.45027624309392267	453	0.791958041958042	355	0.4683377308707124	C	5.004	0.186442	0.09495	0.337852	0.435907	ENSG00000138759	ENST00000512123	.	.	.	5.05	2.41	0.29592	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999856936	.	.	.	.	.	.	T	0.20940	-1.0260	3	.	.	.	.	6.0073	0.19553	0.1323:0.6491:0.0:0.2186	rs4975139;rs58497218;rs4975139	.	.	.	I	1914	.	.	T	+	2	0	FRAS1	79674757	0.602000	0.26916	0.987000	0.45799	0.774000	0.43823	1.126000	0.31344	0.174000	0.19809	-0.216000	0.12614	ACT	C|0.484;T|0.516	0.516	strong		0.438	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
DZIP1L	199221	hgsc.bcm.edu	37	3	137787173	137787173	+	Missense_Mutation	SNP	G	G	A	rs11917468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:137787173G>A	ENST00000327532.2	-	13	2014	c.1652C>T	c.(1651-1653)gCc>gTc	p.A551V	DZIP1L_ENST00000488595.1_5'UTR	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	551			A -> V (in dbSNP:rs11917468).		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						CTTTGGCTGGGCCTCTCTGGT	0.577											OREG0015830	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	262	0.0523163	0.1868	0.0202	5008	,	,		16312	0.0		0.001	False		,,,				2504	0.0				p.A551V		Atlas-SNP	.											.	DZIP1L	88	.	0			c.C1652T						PASS	.	G	VAL/ALA	707,3699	290.1+/-280.8	50,607,1546	71.0	78.0	75.0		1652	-2.2	0.0	3	dbSNP_120	75	12,8588	9.1+/-34.3	0,12,4288	yes	missense	DZIP1L	NM_173543.2	64	50,619,5834	AA,AG,GG		0.1395,16.0463,5.5282	benign	551/768	137787173	719,12287	2203	4300	6503	SO:0001583	missense	199221	exon13			GGCTGGGCCTCTC	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.1652C>T	3.37:g.137787173G>A	ENSP00000332148:p.Ala551Val	Somatic	209	0	0	1636	WXS	Illumina HiSeq	Phase_I	166	77	0.463855	NM_173543	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	72	0.03296703296703297	66	0.13414634146341464	6	0.016574585635359115	0	0.0	0	0.0	G	3.102	-0.184558	0.06340	0.160463	0.001395	ENSG00000158163	ENST00000327532	T	0.39056	1.1	4.91	-2.15	0.07102	.	1.124280	0.06592	N	0.752174	T	0.00073	0.0002	N	0.02011	-0.69	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.17379	-1.0371	10	0.20046	T	0.44	0.1447	9.7913	0.40708	0.6267:0.0:0.3733:0.0	rs11917468;rs52808108;rs11917468	551	Q8IYY4	DZI1L_HUMAN	V	551	ENSP00000332148:A551V	ENSP00000332148:A551V	A	-	2	0	DZIP1L	139269863	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-0.062000	0.11674	-0.389000	0.07786	0.650000	0.86243	GCC	G|0.948;A|0.052	0.052	strong		0.577	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
LTN1	26046	hgsc.bcm.edu	37	21	30318207	30318207	+	Silent	SNP	T	T	C	rs2250574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:30318207T>C	ENST00000361371.5	-	21	3769	c.3690A>G	c.(3688-3690)ctA>ctG	p.L1230L	LTN1_ENST00000389194.2_Silent_p.L1276L			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	1230					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						ATTTCAGAAATAGGGAAAGAA	0.388													T|||	567	0.113219	0.084	0.1196	5008	,	,		18596	0.1667		0.0974	False		,,,				2504	0.1094				p.L1276L		Atlas-SNP	.											.	LTN1	141	.	0			c.A3828G						PASS	.	T		435,3971	210.5+/-231.0	27,381,1795	103.0	110.0	108.0		3828	-3.7	0.9	21	dbSNP_100	108	797,7803	187.4+/-234.7	42,713,3545	no	coding-synonymous	LTN1	NM_015565.2		69,1094,5340	CC,CT,TT		9.2674,9.8729,9.4726		1276/1813	30318207	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	26046	exon21			CAGAAATAGGGAA	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.3690A>G	21.37:g.30318207T>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	198	110	0.555556	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Silent	SNP	ENST00000361371.5	37																																																																																				A|0.007;C|0.102	0.102	strong		0.388	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
PIN1	5300	hgsc.bcm.edu	37	19	9949152	9949152	+	Silent	SNP	G	G	A	rs2233682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9949152G>A	ENST00000247970.4	+	2	121	c.99G>A	c.(97-99)caG>caA	p.Q33Q	PIN1_ENST00000380889.6_3'UTR|PIN1_ENST00000587625.1_Silent_p.Q33Q|PIN1_ENST00000588695.1_Silent_p.Q33Q	NM_006221.3	NP_006212.1	Q13526	PIN1_HUMAN	peptidylprolyl cis/trans isomerase, NIMA-interacting 1	33	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cell cycle (GO:0007049)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|negative regulation of cell motility (GO:2000146)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of cytokinesis (GO:0032465)|regulation of mitosis (GO:0007088)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTPase activating protein binding (GO:0032794)|mitogen-activated protein kinase kinase binding (GO:0031434)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)			skin(3)	3						ACGCCAGCCAGTGGGAGCGGC	0.647													G|||	420	0.0838658	0.1989	0.1095	5008	,	,		17028	0.0387		0.005	False		,,,				2504	0.0378				p.Q33Q		Atlas-SNP	.											PIN1,ear,carcinoma,+2,1	PIN1	7	1	0			c.G99A						PASS	.	G		733,3669		65,603,1533	17.0	19.0	19.0		99	1.0	1.0	19	dbSNP_98	19	73,8519		0,73,4223	no	coding-synonymous	PIN1	NM_006221.3		65,676,5756	AA,AG,GG		0.8496,16.6515,6.2029		33/164	9949152	806,12188	2201	4296	6497	SO:0001819	synonymous_variant	5300	exon2			CAGCCAGTGGGAG		CCDS12220.1	19p13	2014-09-17	2008-03-25		ENSG00000127445	ENSG00000127445			8988	protein-coding gene	gene with protein product		601052	"""protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1"""			8606777	Standard	NM_006221		Approved	dod	uc002mml.2	Q13526		ENST00000247970.4:c.99G>A	19.37:g.9949152G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	140	77	0.55	NM_006221	A8K4V9|Q53X75	Silent	SNP	ENST00000247970.4	37	CCDS12220.1																																																																																			G|0.936;A|0.064	0.064	strong		0.647	PIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451107.1		
FAT4	79633	hgsc.bcm.edu	37	4	126241335	126241335	+	Missense_Mutation	SNP	C	C	G	rs36052762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	102	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	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	
MUC4	4585	hgsc.bcm.edu	37	3	195511237	195511237	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511237T>C	ENST00000463781.3	-	2	7673	c.7214A>G	c.(7213-7215)gAc>gGc	p.D2405G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D2405G	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)		TGAGGAAGTGTCGGTGACAGG	0.587																																					p.D2405G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	0			c.A7214G						scavenged	.																																			SO:0001583	missense	4585	exon2			GAAGTGTCGGTGA	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.7214A>G	3.37:g.195511237T>C	ENSP00000417498:p.Asp2405Gly	Somatic	635	6	0.00944882		WXS	Illumina HiSeq	Phase_I	233	18	0.0772532	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	5.343	0.248518	0.10130	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.48;1.46	.	.	.	.	.	.	.	.	T	0.28732	0.0712	N	0.19112	0.55	0.09310	N	0.999999	P	0.52170	0.951	D	0.65443	0.935	T	0.12993	-1.0526	7	.	.	.	.	1.4125	0.02295	0.3443:0.3266:0.0:0.3291	.	2405	E7ESK3	.	G	2405	ENSP00000417498:D2405G;ENSP00000420243:D2405G	.	D	-	2	0	MUC4	196995632	0.000000	0.05858	0.003000	0.11579	0.080000	0.17528	-0.862000	0.04263	-0.437000	0.07243	0.000000	0.15137	GAC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TSPAN18	90139	hgsc.bcm.edu	37	11	44931308	44931308	+	Missense_Mutation	SNP	C	C	T	rs34282417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44931308C>T	ENST00000520358.2	+	5	531	c.116C>T	c.(115-117)aCc>aTc	p.T39I	TSPAN18_ENST00000340160.3_Missense_Mutation_p.T39I			Q96SJ8	TSN18_HUMAN	tetraspanin 18	39						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						GTGGACCCCACCGGCTTCCGG	0.667													C|||	17	0.00339457	0.0121	0.0014	5008	,	,		14867	0.0		0.0	False		,,,				2504	0.0				p.T39I		Atlas-SNP	.											.	TSPAN18	38	.	0			c.C116T						PASS	.	C	ILE/THR	46,4360	47.5+/-82.1	0,46,2157	45.0	49.0	48.0		116	5.0	1.0	11	dbSNP_126	48	0,8598		0,0,4299	yes	missense	TSPAN18	NM_130783.4	89	0,46,6456	TT,TC,CC		0.0,1.044,0.3537	probably-damaging	39/249	44931308	46,12958	2203	4299	6502	SO:0001583	missense	90139	exon4			ACCCCACCGGCTT	AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"""Tetraspanins"""	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.116C>T	11.37:g.44931308C>T	ENSP00000429993:p.Thr39Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_130783	Q6UY44|Q8NBI9	Missense_Mutation	SNP	ENST00000520358.2	37	CCDS7910.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	C	18.20	3.570526	0.65765	0.01044	0.0	ENSG00000157570	ENST00000533786;ENST00000533202;ENST00000520358;ENST00000520999;ENST00000340160;ENST00000520837	T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.67859	0.2938	M	0.67517	2.055	0.80722	D	1	B;P	0.40050	0.143;0.7	B;B	0.42882	0.228;0.401	T	0.76041	-0.3104	10	0.40728	T	0.16	.	18.2971	0.90150	0.0:1.0:0.0:0.0	rs34282417	39;39	Q8WUV1;Q96SJ8	.;TSN18_HUMAN	I	39;39;39;49;39;49	ENSP00000433592:T39I;ENSP00000434625:T39I;ENSP00000429993:T39I;ENSP00000427942:T49I;ENSP00000339820:T39I;ENSP00000430343:T49I	ENSP00000339820:T39I	T	+	2	0	TSPAN18	44887884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.845000	0.62853	2.319000	0.78375	0.561000	0.74099	ACC	C|0.995;T|0.005	0.005	strong		0.667	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783	
ATP13A4	84239	hgsc.bcm.edu	37	3	193120459	193120459	+	Silent	SNP	G	G	A	rs9863164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:193120459G>A	ENST00000342695.4	-	30	3895	c.3573C>T	c.(3571-3573)agC>agT	p.S1191S	ATP13A4_ENST00000482964.1_5'UTR|ATP13A4_ENST00000392443.3_Silent_p.S1172S|ATP13A4_ENST00000400270.2_Silent_p.S207S	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1191						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		GTTCTTCATTGCTCTCAAATA	0.438													G|||	110	0.0219649	0.0802	0.0058	5008	,	,		18998	0.0		0.0	False		,,,				2504	0.0				p.S1191S		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C3573T						PASS	.	G		302,4104	165.1+/-196.6	13,276,1914	91.0	89.0	90.0		3573	4.1	1.0	3	dbSNP_119	90	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ATP13A4	NM_032279.2		13,280,6210	AA,AG,GG		0.0465,6.8543,2.3528		1191/1197	193120459	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon30			TTCATTGCTCTCA	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.3573C>T	3.37:g.193120459G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			G|0.974;A|0.026	0.026	strong		0.438	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
ZNF516	9658	hgsc.bcm.edu	37	18	74090931	74090931	+	Silent	SNP	C	C	T	rs690353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:74090931C>T	ENST00000443185.2	-	5	3455	c.3138G>A	c.(3136-3138)ccG>ccA	p.P1046P	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	1046					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)		CCTCGGCCACCGGCTCCTGTT	0.657													C|||	541	0.108027	0.3548	0.0476	5008	,	,		14366	0.0		0.0219	False		,,,				2504	0.0174				p.P1046P		Atlas-SNP	.											.	ZNF516	102	.	0			c.G3138A						PASS	.	C		1036,2930		145,746,1092	43.0	51.0	48.0		3139	-4.1	0.9	18	dbSNP_83	48	140,8156		4,132,4012	yes	coding-synonymous	ZNF516	NM_014643.3		149,878,5104	TT,TC,CC		1.6876,26.122,9.5906		1046/1164	74090931	1176,11086	1983	4148	6131	SO:0001819	synonymous_variant	9658	exon5			GGCCACCGGCTCC	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.3138G>A	18.37:g.74090931C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_014643		Silent	SNP	ENST00000443185.2	37																																																																																				C|0.903;T|0.097	0.097	strong		0.657	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
PTOV1	53635	hgsc.bcm.edu	37	19	50361874	50361874	+	Silent	SNP	A	A	G	rs35389621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50361874A>G	ENST00000601675.1	+	10	1109	c.1005A>G	c.(1003-1005)acA>acG	p.T335T	PTOV1_ENST00000221557.9_Silent_p.T303T|AC018766.5_ENST00000601893.1_RNA|AC018766.4_ENST00000596624.1_RNA|AC018766.5_ENST00000599259.1_RNA|PTOV1_ENST00000391842.1_Silent_p.T335T|PTOV1_ENST00000600603.1_Silent_p.T303T|PTOV1_ENST00000599732.1_Silent_p.T335T|PTOV1_ENST00000601638.1_Silent_p.T303T|PTOV1_ENST00000598325.1_3'UTR|AC018766.5_ENST00000593654.1_RNA			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	335	Interaction with FLOT1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(5)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)	16		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		ACCTGGAGACACTGAAGAGCC	0.667													A|||	48	0.00958466	0.034	0.0043	5008	,	,		16455	0.0		0.0	False		,,,				2504	0.0				p.T335T		Atlas-SNP	.											.	PTOV1	41	.	0			c.A1005G						PASS	.	A		125,4277	87.3+/-125.9	2,121,2078	43.0	30.0	35.0		1005	-5.7	0.3	19	dbSNP_126	35	0,8598		0,0,4299	no	coding-synonymous	PTOV1	NM_017432.3		2,121,6377	GG,GA,AA		0.0,2.8396,0.9615		335/417	50361874	125,12875	2201	4299	6500	SO:0001819	synonymous_variant	53635	exon10			GGAGACACTGAAG	AF238381	CCDS12782.1	19q13.33	2014-08-28	2008-09-12		ENSG00000104960	ENSG00000104960			9632	protein-coding gene	gene with protein product		610195				12598323, 15713644	Standard	XM_005258998		Approved		uc002pqf.1	Q86YD1	OTTHUMG00000183162	ENST00000601675.1:c.1005A>G	19.37:g.50361874A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Silent	SNP	ENST00000601675.1	37	CCDS12782.1																																																																																			A|0.990;G|0.010	0.010	strong		0.667	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432	
SSPO	23145	hgsc.bcm.edu	37	7	149485987	149485987	+	RNA	SNP	T	T	A	rs893597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149485987T>A	ENST00000378016.2	+	0	4206							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)			AGGACGACTGTGGCGATGGCT	0.582													T|||	131	0.0261581	0.0946	0.0086	5008	,	,		22616	0.0		0.0	False		,,,				2504	0.0				p.C1402X		Atlas-SNP	.											.	.	.	.	0			c.T4206A						PASS	.	T		277,4091		10,257,1917	83.0	87.0	86.0		4210	1.2	1.0	7	dbSNP_86	86	4,8564		0,4,4280	yes	coding-notMod3	SSPO	NM_198455.2		10,261,6197	AA,AT,TT		0.0467,6.3416,2.1722			149485987	281,12655	2184	4284	6468			23145	exon29			CGACTGTGGCGAT	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.149485987T>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	190	90	0.473684	NM_198455	Q76B61	Nonsense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.977;A|0.023	0.023	strong		0.582	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
IPPK	64768	hgsc.bcm.edu	37	9	95411816	95411816	+	Silent	SNP	G	G	A	rs16908484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95411816G>A	ENST00000287996.3	-	5	609	c.333C>T	c.(331-333)taC>taT	p.Y111Y		NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	111					inositol phosphate metabolic process (GO:0043647)|inositol phosphorylation (GO:0052746)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|inositol pentakisphosphate 2-kinase activity (GO:0035299)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(2)|urinary_tract(1)	15						GGCACATAGCGTAACCACTGA	0.512													G|||	59	0.0117812	0.0424	0.0043	5008	,	,		19264	0.0		0.0	False		,,,				2504	0.0				p.Y111Y		Atlas-SNP	.											.	IPPK	34	.	0			c.C333T						PASS	.	G		156,4250	106.0+/-144.5	1,154,2048	165.0	127.0	140.0		333	-1.9	1.0	9	dbSNP_123	140	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	IPPK	NM_022755.5		1,155,6347	AA,AG,GG		0.0116,3.5406,1.2071		111/492	95411816	157,12849	2203	4300	6503	SO:0001819	synonymous_variant	64768	exon5			CATAGCGTAACCA	AK023225	CCDS6699.1	9q22.31	2010-12-02	2005-10-20	2005-10-20	ENSG00000127080	ENSG00000127080			14645	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 12"""	C9orf12		12084730	Standard	NM_022755		Approved	INSP5K2, FLJ13163, IP5K, IPK1	uc004asl.1	Q9H8X2	OTTHUMG00000020231	ENST00000287996.3:c.333C>T	9.37:g.95411816G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	69	0.594828	NM_022755	Q5T9F7|Q9H7V8	Silent	SNP	ENST00000287996.3	37	CCDS6699.1																																																																																			G|0.986;A|0.014	0.014	strong		0.512	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755	
C16orf58	64755	hgsc.bcm.edu	37	16	31519174	31519174	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31519174G>C	ENST00000327237.2	-	2	365	c.326C>G	c.(325-327)tCc>tGc	p.S109C	C16orf58_ENST00000570164.1_Missense_Mutation_p.S109C|RP11-452L6.7_ENST00000569782.1_RNA|C16orf58_ENST00000567994.1_Missense_Mutation_p.S64C|C16orf58_ENST00000430477.2_Intron			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	109						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)	14						GGTGGCTAGGGAGCCGGAGAG	0.587																																					p.G109G		Atlas-SNP	.											.	C16orf58	28	.	0			c.G326G						PASS	.						32.0	27.0	29.0					16																	31519174		2189	4291	6480	SO:0001583	missense	64755	exon2			GCTAGGGAGCCGG	AK023930	CCDS10715.1	16p11.2	2013-03-04			ENSG00000140688	ENSG00000140688			25848	protein-coding gene	gene with protein product							Standard	NM_022744		Approved	FLJ13868	uc002eci.3	Q96GQ5	OTTHUMG00000132466	ENST00000327237.2:c.326C>G	16.37:g.31519174G>C	ENSP00000317579:p.Ser109Cys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Silent	SNP	ENST00000327237.2	37	CCDS10715.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.018996	0.93462	.	.	ENSG00000140688	ENST00000327237;ENST00000452223;ENST00000541442	T	0.43294	0.95	5.45	5.45	0.79879	.	0.158717	0.56097	D	0.000026	T	0.59905	0.2228	M	0.74881	2.28	0.80722	D	1	P	0.45531	0.86	P	0.55667	0.781	T	0.62817	-0.6774	10	0.66056	D	0.02	-3.0354	14.7866	0.69808	0.0:0.0:1.0:0.0	.	109	Q96GQ5	CP058_HUMAN	C	109;63;109	ENSP00000317579:S109C	ENSP00000317579:S109C	S	-	2	0	C16orf58	31426675	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.068000	0.76748	2.559000	0.86315	0.655000	0.94253	TCC	.	.	none		0.587	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744	
FAT4	79633	hgsc.bcm.edu	37	4	126411594	126411594	+	Silent	SNP	G	G	A	rs62312781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:126411594G>A	ENST00000394329.3	+	17	13630	c.13617G>A	c.(13615-13617)gaG>gaA	p.E4539E	FAT4_ENST00000335110.5_Silent_p.E2780E	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4539					branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATCCCAAAGAGGAGAAGAAAC	0.522													G|||	786	0.156949	0.236	0.2349	5008	,	,		19314	0.0		0.1819	False		,,,				2504	0.1309				p.E4539E		Atlas-SNP	.											.	FAT4	1752	.	0			c.G13617A						PASS	.	G		916,3490	348.2+/-309.8	108,700,1395	69.0	72.0	71.0		13617	1.8	0.9	4	dbSNP_129	71	1587,7013	293.9+/-301.6	145,1297,2858	no	coding-synonymous	FAT4	NM_024582.4		253,1997,4253	AA,AG,GG		18.4535,20.7898,19.245		4539/4982	126411594	2503,10503	2203	4300	6503	SO:0001819	synonymous_variant	79633	exon17			CAAAGAGGAGAAG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.13617G>A	4.37:g.126411594G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			G|0.825;A|0.175	0.175	strong		0.522	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
RIPK4	54101	hgsc.bcm.edu	37	21	43176832	43176832	+	Silent	SNP	A	A	G	rs2277791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43176832A>G	ENST00000352483.2	-	2	391	c.327T>C	c.(325-327)gcT>gcC	p.A109A	RIPK4_ENST00000544709.1_Silent_p.A46A|RIPK4_ENST00000332512.3_Silent_p.A109A|RIPK4_ENST00000542057.1_Silent_p.A46A			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	109	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						ATGGCTCCGAAGCCAGCAGCT	0.607													G|||	631	0.125998	0.171	0.0879	5008	,	,		19419	0.0417		0.1302	False		,,,				2504	0.1748				p.A109A		Atlas-SNP	.											.	RIPK4	151	.	0			c.T327C						PASS	.	G		749,3657	756.2+/-412.6	61,627,1515	81.0	76.0	78.0		327	0.9	0.0	21	dbSNP_100	78	1160,7440	765.2+/-407.6	86,988,3226	no	coding-synonymous	RIPK4	NM_020639.2		147,1615,4741	GG,GA,AA		13.4884,16.9995,14.6778		109/785	43176832	1909,11097	2203	4300	6503	SO:0001819	synonymous_variant	54101	exon2			CTCCGAAGCCAGC	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.327T>C	21.37:g.43176832A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_020639	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				A|0.872;G|0.128	0.128	strong		0.607	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
PCMTD1	115294	hgsc.bcm.edu	37	8	52733214	52733214	+	Missense_Mutation	SNP	A	A	C	rs200377849		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:52733214A>C	ENST00000360540.5	-	7	1177	c.771T>G	c.(769-771)aaT>aaG	p.N257K	PCMTD1_ENST00000544451.1_Missense_Mutation_p.N181K|PCMTD1_ENST00000522514.1_Missense_Mutation_p.N257K|PCMTD1_ENST00000519559.1_5'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	257						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)	p.N257K(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)				CATTTATGAAATTTCTAAGTG	0.388																																					p.N257K		Atlas-SNP	.											PCMTD1,trunk,malignant_melanoma,0,1	PCMTD1	73	1	1	Substitution - Missense(1)	skin(1)	c.T771G						scavenged	.						78.0	81.0	80.0					8																	52733214		2203	4300	6503	SO:0001583	missense	115294	exon6			TATGAAATTTCTA		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.771T>G	8.37:g.52733214A>C	ENSP00000353739:p.Asn257Lys	Somatic	290	2	0.00689655		WXS	Illumina HiSeq	Phase_I	307	8	0.0260586	NM_052937	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	A	12.61	1.991059	0.35131	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.47528	0.84;0.84;0.84	5.56	-0.996	0.10218	.	0.046341	0.85682	D	0.000000	T	0.38983	0.1061	N	0.20530	0.585	0.53005	D	0.999961	P;D;B	0.65815	0.651;0.995;0.002	B;P;B	0.60886	0.122;0.88;0.002	T	0.41556	-0.9502	10	0.02654	T	1	-22.28	11.477	0.50304	0.3747:0.0:0.6253:0.0	.	127;181;257	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	K	257;181;257	ENSP00000353739:N257K;ENSP00000444026:N181K;ENSP00000428099:N257K	ENSP00000353739:N257K	N	-	3	2	PCMTD1	52895767	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	3.249000	0.51437	-0.122000	0.11766	-0.250000	0.11733	AAT	.	.	weak		0.388	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
C4B	721	hgsc.bcm.edu	37	6	31996524	31996524	+	Silent	SNP	C	C	A	rs406658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31996524C>A	ENST00000435363.2	+	26	3369	c.3285C>A	c.(3283-3285)ggC>ggA	p.G1095G	C4B_ENST00000425700.2_Silent_p.G1095G	NM_001002029.3	NP_001002029.3	P0C0L5	CO4B_HUMAN	complement component 4B (Chido blood group)	1095					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|detection of molecule of bacterial origin (GO:0032490)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|complement binding (GO:0001848)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	AGGTAGGAGGCTCGCCTGAGA	0.562													C|||	1123	0.224241	0.385	0.1643	5008	,	,		17136	0.1448		0.1412	False		,,,				2504	0.2168				p.G1095G		Atlas-SNP	.											.	C4A	15	.	0			c.C3285A						PASS	.						18.0	17.0	18.0					6																	31996524		1530	3498	5028	SO:0001819	synonymous_variant	720	exon26			AGGAGGCTCGCCT	AF019413	CCDS47405.1	6p21.3	2014-09-17	2009-01-06		ENSG00000224389	ENSG00000224389		"""Blood group antigens"", ""Complement system"""	1324	protein-coding gene	gene with protein product		120820	"""complement component 4B"""				Standard	NM_001002029		Approved	CPAMD3, C4F, CO4, C4B1, C4B3, CH	uc011jpm.2	P0C0L5	OTTHUMG00000031187	ENST00000435363.2:c.3285C>A	6.37:g.31996524C>A		Somatic	570	1	0.00175439		WXS	Illumina HiSeq	Phase_I	823	321	0.390036	NM_007293	A2BHY4|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q6U2E9|Q6U2G1|Q6U2I5|Q6U2L1|Q6U2L7|Q6U2L9|Q6U2M5|Q6VCV8|Q96SA7|Q9NPK5|Q9UIP5	Silent	SNP	ENST00000435363.2	37	CCDS47405.1																																																																																			.	.	weak		0.562	C4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076368.5	NM_001002029	
EEF1D	1936	hgsc.bcm.edu	37	8	144662353	144662353	+	Silent	SNP	G	G	A	rs1062391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144662353G>A	ENST00000529272.1	-	7	1036	c.636C>T	c.(634-636)gcC>gcT	p.A212A	EEF1D_ENST00000528610.1_Silent_p.A188A|NAPRT1_ENST00000449291.2_5'Flank|EEF1D_ENST00000419152.2_Silent_p.A212A|NAPRT1_ENST00000276844.7_5'Flank|EEF1D_ENST00000532400.1_Intron|EEF1D_ENST00000531621.1_Silent_p.A169A|EEF1D_ENST00000532741.1_Silent_p.A628A|EEF1D_ENST00000526838.1_Silent_p.A193A|EEF1D_ENST00000524624.1_Silent_p.A188A|EEF1D_ENST00000442189.2_Silent_p.A578A|RP11-661A12.9_ENST00000531730.1_RNA|EEF1D_ENST00000423316.2_Silent_p.A578A|RP11-661A12.7_ENST00000529247.1_RNA|EEF1D_ENST00000317198.6_Silent_p.A212A|NAPRT1_ENST00000435154.3_5'Flank|EEF1D_ENST00000395119.3_Silent_p.A212A|NAPRT1_ENST00000426292.3_5'Flank			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	212	Catalytic (GEF).				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	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)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			CCTCCAGCTGGGCCATGTCCG	0.617													G|||	1873	0.374002	0.0983	0.4539	5008	,	,		18011	0.3998		0.6163	False		,,,				2504	0.4141				p.A578A		Atlas-SNP	.											.	EEF1D	48	.	0			c.C1734T						PASS	.	G	,,,,,,	763,3643	301.3+/-286.8	75,613,1515	30.0	34.0	32.0		1734,636,564,636,579,636,1734	-0.8	1.0	8	dbSNP_86	32	5359,3239	638.1+/-399.3	1697,1965,637	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EEF1D	NM_001130053.2,NM_001130055.2,NM_001130056.2,NM_001130057.2,NM_001195203.1,NM_001960.4,NM_032378.4	,,,,,,	1772,2578,2152	AA,AG,GG		37.6716,17.3173,47.0778	,,,,,,	578/648,212/282,188/258,212/282,193/263,212/282,578/648	144662353	6122,6882	2203	4299	6502	SO:0001819	synonymous_variant	1936	exon9			CAGCTGGGCCATG	AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.636C>T	8.37:g.144662353G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	160	91	0.56875	NM_001130053	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Silent	SNP	ENST00000529272.1	37	CCDS6405.1	939	0.42994505494505497	73	0.1483739837398374	193	0.5331491712707183	206	0.36013986013986016	467	0.6160949868073878	G	11.05	1.524662	0.27299	0.173173	0.623284	ENSG00000104529	ENST00000530109	.	.	.	4.84	-0.8	0.10897	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999881695	.	.	.	.	.	.	T	0.43310	-0.9399	3	.	.	.	.	4.35	0.11151	0.0701:0.2956:0.3294:0.3049	rs1062391;rs1563149;rs2070239;rs3203458;rs1062391	.	.	.	S	87	.	.	P	-	1	0	EEF1D	144733496	0.056000	0.20664	0.991000	0.47740	0.956000	0.61745	-0.747000	0.04823	-0.058000	0.13177	-0.237000	0.12165	CCA	G|0.563;A|0.437	0.437	strong		0.617	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378	
ABCA8	10351	hgsc.bcm.edu	37	17	66938141	66938141	+	Missense_Mutation	SNP	G	G	C	rs35643726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66938141G>C	ENST00000269080.2	-	2	172	c.35C>G	c.(34-36)aCt>aGt	p.T12S	ABCA8_ENST00000586539.1_Missense_Mutation_p.T12S|ABCA8_ENST00000430352.2_Missense_Mutation_p.T12S	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	12					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)					TAAGGCCCAAGTTTGTTGACA	0.294													G|||	102	0.0203674	0.0719	0.0072	5008	,	,		20789	0.0		0.0	False		,,,				2504	0.002				p.T12S		Atlas-SNP	.											ABCA8,NS,carcinoma,+1,2	ABCA8	213	2	0			c.C35G						scavenged	.	G	SER/THR	291,4115	160.0+/-192.4	10,271,1922	193.0	187.0	189.0		35	4.8	0.9	17	dbSNP_126	189	7,8589	5.7+/-21.5	0,7,4291	yes	missense	ABCA8	NM_007168.2	58	10,278,6213	CC,CG,GG		0.0814,6.6046,2.292	probably-damaging	12/1582	66938141	298,12704	2203	4298	6501	SO:0001583	missense	10351	exon2			GCCCAAGTTTGTT	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.35C>G	17.37:g.66938141G>C	ENSP00000269080:p.Thr12Ser	Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	36	0.016483516483516484	32	0.06504065040650407	4	0.011049723756906077	0	0.0	0	0.0	G	16.70	3.195689	0.58126	0.066046	8.14E-4	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000428549	D;D	0.86694	-2.15;-2.16	4.84	4.84	0.62591	.	0.167779	0.28760	N	0.014225	T	0.64283	0.2584	M	0.87456	2.885	0.29290	N	0.869437	D;D;D;D	0.89917	0.996;1.0;0.999;0.999	D;D;D;D	0.72338	0.91;0.977;0.975;0.945	T	0.75422	-0.3323	10	0.66056	D	0.02	.	13.2834	0.60228	0.0:0.0:1.0:0.0	rs35643726	12;12;12;12	A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;ABCA8_HUMAN	S	12	ENSP00000269080:T12S;ENSP00000402814:T12S	ENSP00000269080:T12S	T	-	2	0	ABCA8	64449736	0.998000	0.40836	0.892000	0.35008	0.606000	0.37113	3.507000	0.53371	2.505000	0.84491	0.650000	0.86243	ACT	G|0.980;C|0.020	0.020	strong		0.294	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
SELP	6403	hgsc.bcm.edu	37	1	169580885	169580885	+	Missense_Mutation	SNP	C	C	T	rs6131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169580885C>T	ENST00000263686.6	-	7	1029	c.992G>A	c.(991-993)aGt>aAt	p.S331N	SELP_ENST00000367791.2_Intron|SELP_ENST00000367786.2_Intron|SELP_ENST00000458599.2_Intron|SELP_ENST00000367788.2_Missense_Mutation_p.S269N|SELP_ENST00000367794.2_Intron|SELP_ENST00000367792.2_Intron|SELP_ENST00000367793.2_Missense_Mutation_p.S269N	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	331	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.		S -> N (in dbSNP:rs6131). {ECO:0000269|PubMed:10391209, 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)	GGTTCCTTCACTGGGGGCTTC	0.512													T|||	1197	0.239018	0.3389	0.1412	5008	,	,		20808	0.2024		0.1859	False		,,,				2504	0.2658				p.S331N		Atlas-SNP	.											.	SELP	132	.	0			c.G992A	GRCh37	CM055538	SELP	M	rs6131	PASS	.	T	ASN/SER	1336,3070	694.5+/-405.8	194,948,1061	109.0	109.0	109.0		992	-4.5	0.0	1	dbSNP_52	109	1618,6982	742.6+/-407.2	154,1310,2836	yes	missense	SELP	NM_003005.3	46	348,2258,3897	TT,TC,CC		18.814,30.3223,22.7126	benign	331/831	169580885	2954,10052	2203	4300	6503	SO:0001583	missense	6403	exon7			CCTTCACTGGGGG	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.992G>A	1.37:g.169580885C>T	ENSP00000263686:p.Ser331Asn	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	146	144	0.986301	NM_003005	Q5R344|Q8IVD1	Missense_Mutation	SNP	ENST00000263686.6	37	CCDS1282.1	467	0.21382783882783882	150	0.3048780487804878	66	0.18232044198895028	106	0.1853146853146853	145	0.19129287598944592	T	6.193	0.403756	0.11754	0.303223	0.18814	ENSG00000174175	ENST00000367790;ENST00000426706;ENST00000263686;ENST00000544572;ENST00000367793;ENST00000367788	T;T;T	0.73897	-0.79;1.84;1.84	4.9	-4.53	0.03462	Complement control module (2);Sushi/SCR/CCP (2);	1.893840	0.02037	N	0.049019	T	0.34135	0.0887	L	0.41124	1.26	0.80722	P	0.0	B;B;B	0.14438	0.01;0.006;0.002	B;B;B	0.15052	0.012;0.008;0.003	T	0.10683	-1.0619	9	0.18710	T	0.47	4.4267	1.6575	0.02785	0.1151:0.2666:0.2292:0.3892	rs6131;rs17845837;rs17858806;rs58906495;rs6131	331;331;331	Q6NUL9;P16109;G3V1U2	.;LYAM3_HUMAN;.	N	331;330;331;331;269;269	ENSP00000263686:S331N;ENSP00000356767:S269N;ENSP00000356762:S269N	ENSP00000263686:S331N	S	-	2	0	SELP	167847509	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.365000	0.01079	-1.171000	0.02765	-0.723000	0.03601	AGT	C|0.778;T|0.221	0.221	strong		0.512	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005	
ZC3H12D	340152	hgsc.bcm.edu	37	6	149777914	149777914	+	Missense_Mutation	SNP	G	G	T	rs200917878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:149777914G>T	ENST00000409806.3	-	4	886	c.568C>A	c.(568-570)Cag>Aag	p.Q190K	ZC3H12D_ENST00000542614.1_Missense_Mutation_p.Q190K|ZC3H12D_ENST00000389942.5_Missense_Mutation_p.Q190K|ZC3H12D_ENST00000416573.2_Missense_Mutation_p.Q190K			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	190					negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)		ACGCCGTCCTGCTCGTAGGCC	0.627													G|||	13	0.00259585	0.0076	0.0029	5008	,	,		12923	0.001		0.0	False		,,,				2504	0.0				p.Q190K		Atlas-SNP	.											.	ZC3H12D	21	.	0			c.C568A						PASS	.	G	LYS/GLN	63,4247		1,61,2093	85.0	95.0	92.0		568	1.6	1.0	6		92	1,8539		0,1,4269	yes	missense	ZC3H12D	NM_207360.2	53	1,62,6362	TT,TG,GG		0.0117,1.4617,0.4981	benign	190/528	149777914	64,12786	2155	4270	6425	SO:0001583	missense	340152	exon4			CGTCCTGCTCGTA			6q25.1	2012-07-05	2005-06-30	2005-06-30	ENSG00000178199	ENSG00000178199		"""Zinc fingers, CCCH-type domain containing"""	21175	protein-coding gene	gene with protein product	"""MCP induced protein 4"""	611106	"""chromosome 6 open reading frame 95"""	C6orf95		18178554	Standard	NM_207360		Approved	dJ281H8.1, MCPIP4	uc010kid.3	A2A288	OTTHUMG00000015786	ENST00000409806.3:c.568C>A	6.37:g.149777914G>T	ENSP00000386616:p.Gln190Lys	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_207360	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	Missense_Mutation	SNP	ENST00000409806.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.37|10.37	1.330416|1.330416	0.24167|0.24167	0.014617|0.014617	1.17E-4|1.17E-4	ENSG00000178199|ENSG00000178199	ENST00000458251|ENST00000389942;ENST00000416573;ENST00000409806;ENST00000542614	.|T;T;T;T	.|0.38560	.|1.13;1.13;1.13;1.13	4.84|4.84	1.63|1.63	0.23807|0.23807	.|Ribonuclease Zc3h12a-like (1);	.|0.660796	.|0.14612	.|N	.|0.308967	T|T	0.01387|0.01387	0.0045|0.0045	N|N	0.00035|0.00035	-2.545|-2.545	0.20403|0.20403	N|N	0.999907|0.999907	.|B;B	.|0.10296	.|0.003;0.0	.|B;B	.|0.08055	.|0.003;0.001	T|T	0.47328|0.47328	-0.9126|-0.9126	5|10	.|0.02654	.|T	.|1	-11.5336|-11.5336	5.6416|5.6416	0.17567|0.17567	0.183:0.0:0.4125:0.4045|0.183:0.0:0.4125:0.4045	.|.	.|190;190	.|A2A288;B7WNU7	.|ZC12D_HUMAN;.	E|K	31|190	.|ENSP00000374592:Q190K;ENSP00000408686:Q190K;ENSP00000386616:Q190K;ENSP00000440813:Q190K	.|ENSP00000374592:Q190K	A|Q	-|-	2|1	0|0	ZC3H12D|ZC3H12D	149819607|149819607	0.890000|0.890000	0.30428|0.30428	0.999000|0.999000	0.59377|0.59377	0.998000|0.998000	0.95712|0.95712	1.503000|1.503000	0.35715|0.35715	0.574000|0.574000	0.29417|0.29417	0.561000|0.561000	0.74099|0.74099	GCA|CAG	.	.	weak		0.627	ZC3H12D-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000286400.2	NM_207360	
LGALS2	3957	hgsc.bcm.edu	37	22	37966409	37966409	+	Missense_Mutation	SNP	G	G	A	rs73884090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37966409G>A	ENST00000215886.4	-	4	434	c.260C>T	c.(259-261)aCc>aTc	p.T87I		NM_006498.2	NP_006489.1	P05162	LEG2_HUMAN	lectin, galactoside-binding, soluble, 2	87	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.						carbohydrate binding (GO:0030246)|galactoside binding (GO:0016936)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|stomach(1)	11	Melanoma(58;0.0574)					ACTCTCAAAGGTCACTGTGAA	0.577													G|||	170	0.0339457	0.1225	0.0086	5008	,	,		18900	0.0		0.002	False		,,,				2504	0.0				p.T87I	GBM(193;1840 2185 13711 20676 24505)	Atlas-SNP	.											.	LGALS2	16	.	0			c.C260T						PASS	.	G	ILE/THR	393,4013	195.3+/-220.0	22,349,1832	80.0	77.0	78.0		260	2.4	0.4	22	dbSNP_130	78	2,8598	2.2+/-6.3	0,2,4298	yes	missense	LGALS2	NM_006498.2	89	22,351,6130	AA,AG,GG		0.0233,8.9197,3.0371	probably-damaging	87/133	37966409	395,12611	2203	4300	6503	SO:0001583	missense	3957	exon4			TCAAAGGTCACTG		CCDS13950.1	22q13.1	2011-08-04	2007-02-01		ENSG00000100079	ENSG00000100079		"""Lectins, galactoside-binding"""	6562	protein-coding gene	gene with protein product	"""galectin 2"""	150571				1988031, 15356130	Standard	NM_006498		Approved	HL14	uc003ata.3	P05162	OTTHUMG00000150590	ENST00000215886.4:c.260C>T	22.37:g.37966409G>A	ENSP00000215886:p.Thr87Ile	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	177	82	0.463277	NM_006498	Q6FGY4	Missense_Mutation	SNP	ENST00000215886.4	37	CCDS13950.1	53	0.024267399267399268	47	0.09552845528455285	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	G	22.0	4.233869	0.79688	0.089197	2.33E-4	ENSG00000100079	ENST00000215886	T	0.05855	3.38	5.83	2.41	0.29592	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.524912	0.21727	N	0.070021	T	0.00328	0.0010	L	0.54908	1.71	0.27707	N	0.945575	D	0.56287	0.975	P	0.57152	0.814	T	0.05273	-1.0895	10	0.54805	T	0.06	-3.1337	7.5839	0.27980	0.0801:0.0:0.4258:0.4941	.	87	P05162	LEG2_HUMAN	I	87	ENSP00000215886:T87I	ENSP00000215886:T87I	T	-	2	0	LGALS2	36296355	0.996000	0.38824	0.359000	0.25824	0.610000	0.37248	1.438000	0.35002	0.771000	0.33359	0.561000	0.74099	ACC	G|0.973;A|0.027	0.027	strong		0.577	LGALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318991.1	NM_006498	
EIF2S3	1968	hgsc.bcm.edu	37	X	24073785	24073785	+	Silent	SNP	A	A	G	rs56229020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24073785A>G	ENST00000253039.4	+	2	376	c.123A>G	c.(121-123)acA>acG	p.T41T		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	41	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						GACAAGCCACAATTAACATAG	0.348													A|||	10	0.00264901	0.0061	0.0014	3775	,	,		16856	0.0		0.001	False		,,,				2504	0.0				p.T41T		Atlas-SNP	.											.	EIF2S3	31	.	0			c.A123G						PASS	.	A		20,3815		0,19,1,1613,570	86.0	71.0	76.0		123	0.8	1.0	X	dbSNP_129	76	3,6725		0,2,1,2426,1871	no	coding-synonymous	EIF2S3	NM_001415.3		0,21,2,4039,2441	GG,GA,G,AA,A		0.0446,0.5215,0.2177		41/473	24073785	23,10540	2203	4300	6503	SO:0001819	synonymous_variant	1968	exon2			AGCCACAATTAAC	L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741			3267	protein-coding gene	gene with protein product	"""eukaryotic translation initiation factor 2G"""	300161	"""eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)"""	EIF2G		8106381, 9736774	Standard	NM_001415		Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.123A>G	X.37:g.24073785A>G		Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	370	169	0.456757	NM_001415	B5BTZ4	Silent	SNP	ENST00000253039.4	37	CCDS14210.1	4	0.0024110910186859553	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	9.881	1.201486	0.22121	0.005215	4.46E-4	ENSG00000130741	ENST00000423068	.	.	.	4.68	0.75	0.18387	.	.	.	.	.	T	0.42877	0.1222	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29458	-1.0011	4	.	.	.	.	4.9157	0.13844	0.6333:0.0:0.2319:0.1348	rs56229020	.	.	.	D	41	.	.	N	+	1	0	EIF2S3	23983706	0.992000	0.36948	1.000000	0.80357	0.903000	0.53119	0.389000	0.20751	0.110000	0.17919	0.339000	0.21740	AAT	A|0.998;G|0.002	0.002	strong		0.348	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415	
MUC2	4583	hgsc.bcm.edu	37	11	1103876	1103876	+	Silent	SNP	C	C	T	rs41532344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1103876C>T	ENST00000441003.2	+	48	8202	c.8175C>T	c.(8173-8175)gcC>gcT	p.A2725A		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5087					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)	TTTCGTACGCCGGCTGCACCA	0.657													c|||	531	0.10603	0.1331	0.0548	5008	,	,		15043	0.1448		0.0447	False		,,,				2504	0.1288				p.A2721A		Atlas-SNP	.											.	MUC2	614	.	0			c.C8163T						PASS	.	T		408,3738		18,372,1683	26.0	30.0	28.0		8160	-4.7	0.0	11	dbSNP_127	28	311,8061		4,303,3879	no	coding-synonymous	MUC2	NM_002457.2		22,675,5562	TT,TC,CC		3.7148,9.8408,5.7437		2720/2813	1103876	719,11799	2073	4186	6259	SO:0001819	synonymous_variant	4583	exon49			GTACGCCGGCTGC	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.8175C>T	11.37:g.1103876C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.898;T|0.102	0.102	strong		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921127	12921127	+	Silent	SNP	A	A	G	rs12139549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12921127A>G	ENST00000240189.2	+	4	1005	c.918A>G	c.(916-918)ttA>ttG	p.L306L		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	306					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)		GCAACCTATTAGAAGAGGACT	0.483													.|||	1616	0.322684	0.4349	0.2421	5008	,	,		21674	0.3472		0.2604	False		,,,				2504	0.2669				p.L306L		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.A918G						PASS	.	G		1793,2611	639.8+/-397.2	399,995,808	122.0	125.0	124.0		918	-1.0	0.0	1	dbSNP_120	124	2196,6398	708.6+/-405.7	339,1518,2440	no	coding-synonymous	PRAMEF2	NM_023014.1		738,2513,3248	GG,GA,AA		25.5527,40.713,30.6893		306/475	12921127	3989,9009	2202	4297	6499	SO:0001819	synonymous_variant	65122	exon4			CCTATTAGAAGAG		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.918A>G	1.37:g.12921127A>G		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	233	232	0.995708	NM_023014		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			A|0.699;G|0.301	0.301	strong		0.483	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238705	71238705	+	Missense_Mutation	SNP	G	G	A	rs536797652		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71238705G>A	ENST00000398536.4	+	1	393	c.359G>A	c.(358-360)tGc>tAc	p.C120Y		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	120	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.C120Y(2)		breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						tgtaagccctgctgctgccag	0.607													g|||	1	0.000199681	0.0008	0.0	5008	,	,		20154	0.0		0.0	False		,,,				2504	0.0				p.C120Y		Atlas-SNP	.											KRTAP5-7,NS,carcinoma,0,3	KRTAP5-7	23	3	2	Substitution - Missense(2)	kidney(2)	c.G359A						scavenged	.						129.0	139.0	136.0					11																	71238705		2200	4294	6494	SO:0001583	missense	440050	exon1			AGCCCTGCTGCTG	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"""Keratin associated proteins"""	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.359G>A	11.37:g.71238705G>A	ENSP00000417330:p.Cys120Tyr	Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	262	7	0.0267176	NM_001012503	B2RNM3|Q701N5	Missense_Mutation	SNP	ENST00000398536.4	37	CCDS41682.1	.	.	.	.	.	.	.	.	.	.	N	4.462	0.085611	0.08583	.	.	ENSG00000244411	ENST00000398536	T	0.01304	5.03	1.87	1.87	0.25490	.	.	.	.	.	T	0.01421	0.0046	L	0.60455	1.87	0.26143	N	0.980242	B	0.12630	0.006	B	0.08055	0.003	T	0.51733	-0.8668	9	0.02654	T	1	.	4.3831	0.11304	0.201:0.0:0.799:0.0	.	120	Q6L8G8	KRA57_HUMAN	Y	120	ENSP00000417330:C120Y	ENSP00000417330:C120Y	C	+	2	0	KRTAP5-7	70916353	0.718000	0.27976	0.999000	0.59377	0.075000	0.17131	2.143000	0.42187	1.367000	0.46095	0.289000	0.19496	TGC	.	.	none		0.607	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1		
UCN3	114131	hgsc.bcm.edu	37	10	5416027	5416027	+	Missense_Mutation	SNP	C	C	G	rs201708420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5416027C>G	ENST00000380433.3	+	2	572	c.344C>G	c.(343-345)cCc>cGc	p.P115R		NM_053049.2	NP_444277.2	Q969E3	UCN3_HUMAN	urocortin 3	115					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|digestion (GO:0007586)|positive regulation of insulin secretion (GO:0032024)|positive regulation of membrane potential (GO:0045838)|response to corticosterone (GO:0051412)|response to glucose (GO:0009749)|response to immobilization stress (GO:0035902)|response to starvation (GO:0042594)	axon terminus (GO:0043679)|extracellular space (GO:0005615)|varicosity (GO:0043196)				endometrium(1)|large_intestine(1)	2						GCCAAGAGTCCCCACCGCACC	0.642													.|||	4	0.000798722	0.003	0.0	5008	,	,		10358	0.0		0.0	False		,,,				2504	0.0				p.P115R		Atlas-SNP	.											.	UCN3	13	.	0			c.C344G						PASS	.	C	ARG/PRO	4,4402	8.1+/-20.4	0,4,2199	74.0	76.0	76.0		344	1.7	0.0	10		76	0,8600		0,0,4300	yes	missense	UCN3	NM_053049.2	103	0,4,6499	GG,GC,CC		0.0,0.0908,0.0308	possibly-damaging	115/162	5416027	4,13002	2203	4300	6503	SO:0001583	missense	114131	exon2			AGAGTCCCCACCG	AF361943	CCDS7065.1	10p15.1	2013-02-28	2012-10-17		ENSG00000178473	ENSG00000178473		"""Endogenous ligands"""	17781	protein-coding gene	gene with protein product	"""stresscopin"", ""prepro-urocortin 3"""	605901				11416224	Standard	NM_053049		Approved	UCNIII, SPC	uc001ihx.1	Q969E3	OTTHUMG00000017594	ENST00000380433.3:c.344C>G	10.37:g.5416027C>G	ENSP00000369798:p.Pro115Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_053049	Q496H2|Q5SR91	Missense_Mutation	SNP	ENST00000380433.3	37	CCDS7065.1	.	.	.	.	.	.	.	.	.	.	C	6.795	0.515627	0.12944	9.08E-4	0.0	ENSG00000178473	ENST00000380433	T	0.30182	1.54	5.49	1.67	0.24075	.	0.332477	0.29884	N	0.010946	T	0.18045	0.0433	N	0.22421	0.69	0.23144	N	0.998221	B	0.23490	0.086	B	0.21360	0.034	T	0.16630	-1.0396	10	0.59425	D	0.04	-11.4379	7.1327	0.25510	0.6324:0.291:0.0767:0.0	.	115	Q969E3	UCN3_HUMAN	R	115	ENSP00000369798:P115R	ENSP00000369798:P115R	P	+	2	0	UCN3	5406027	1.000000	0.71417	0.003000	0.11579	0.007000	0.05969	3.203000	0.51075	0.390000	0.25115	-0.500000	0.04577	CCC	.	.	weak		0.642	UCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046547.1	NM_053049	
RAD51B	5890	hgsc.bcm.edu	37	14	68292187	68292187	+	Silent	SNP	T	T	C	rs114131734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:68292187T>C	ENST00000487270.1	+	3	139	c.91T>C	c.(91-93)Tta>Cta	p.L31L	RAD51B_ENST00000471583.1_Silent_p.L31L|RAD51B_ENST00000390683.3_Silent_p.L31L|RAD51B_ENST00000488612.1_Silent_p.L31L|RAD51B_ENST00000487861.1_Silent_p.L31L	NM_133509.3	NP_598193.2	O15315	RA51B_HUMAN	RAD51 paralog B	31	Interaction with RAD51C.				ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)		HMGA2/RAD51B(11)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11						TTAGGACTTTTTATGTCTTTC	0.383								Direct reversal of damage					T|||	45	0.00898562	0.0325	0.0029	5008	,	,		16807	0.0		0.0	False		,,,				2504	0.0				p.L31L		Atlas-SNP	.											.	RAD51B	80	.	0			c.T91C						PASS	.	T	,,	162,4244	111.6+/-149.8	3,156,2044	118.0	113.0	115.0		91,91,91	0.4	1.0	14	dbSNP_132	115	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	RAD51B	NM_002877.5,NM_133509.3,NM_133510.3	,,	3,158,6342	CC,CT,TT		0.0233,3.6768,1.261	,,	31/351,31/385,31/351	68292187	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	5890	exon3			GACTTTTTATGTC	U84138	CCDS9789.1, CCDS9790.1	14q23-q24.2	2013-07-02	2013-07-02	2011-07-01	ENSG00000182185	ENSG00000182185			9822	protein-coding gene	gene with protein product		602948	"""RAD51 (S. cerevisiae)-like 1"", ""RAD51-like 1 (S. cerevisiae)"", ""RAD51 homolog B (S. cerevisiae)"""	RAD51L1		6261043, 9207106	Standard	NM_002877		Approved	REC2, hREC2, R51H2	uc001xkf.2	O15315	OTTHUMG00000157530	ENST00000487270.1:c.91T>C	14.37:g.68292187T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_133509	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	Silent	SNP	ENST00000487270.1	37	CCDS9789.1																																																																																			T|0.991;C|0.009	0.009	strong		0.383	RAD51B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349063.1		
SRPX	8406	hgsc.bcm.edu	37	X	38033415	38033415	+	Missense_Mutation	SNP	T	T	C	rs35474361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38033415T>C	ENST00000378533.3	-	3	453	c.347A>G	c.(346-348)aAa>aGa	p.K116R	SRPX_ENST00000544439.1_Missense_Mutation_p.K96R|TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000538295.1_Missense_Mutation_p.K116R|SRPX_ENST00000432886.2_Missense_Mutation_p.K116R|SRPX_ENST00000343800.6_Missense_Mutation_p.K103R	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	116	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						CTACTCACGTTTGCAGATGAC	0.493													T|||	274	0.0725828	0.1952	0.0231	3775	,	,		15221	0.0		0.0	False		,,,				2504	0.0				p.K116R		Atlas-SNP	.											.	SRPX	53	.	0			c.A347G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	901,2932		90,578,143,963,428	127.0	98.0	108.0		287,347,347,347	5.7	1.0	X	dbSNP_126	108	6,6722		0,5,1,2423,1871	yes	missense,missense,missense,missense	SRPX	NM_001170750.1,NM_001170751.1,NM_001170752.1,NM_006307.4	26,26,26,26	90,583,144,3386,2299	CC,CT,C,TT,T		0.0892,23.5064,8.5882	benign,benign,benign,benign	96/445,116/406,116/380,116/465	38033415	907,9654	2202	4300	6502	SO:0001583	missense	8406	exon3			TCACGTTTGCAGA	U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.347A>G	X.37:g.38033415T>C	ENSP00000367794:p.Lys116Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_001170751	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Missense_Mutation	SNP	ENST00000378533.3	37	CCDS14245.1	83	0.050030138637733576	51	0.11486486486486487	7	0.019444444444444445	0	0.0	0	0.0	T	1.424	-0.572093	0.03882	0.235064	8.92E-4	ENSG00000101955	ENST00000544439;ENST00000432886;ENST00000538295;ENST00000378533;ENST00000343800	T;T;T;T;T	0.73897	1.88;-0.79;1.88;1.88;1.87	5.7	5.7	0.88788	Complement control module (1);Sushi/SCR/CCP (1);	0.137867	0.64402	D	0.000003	T	0.00039	0.0001	N	0.13043	0.29	0.24140	P	0.99573811	B;B;B;B	0.24618	0.007;0.107;0.058;0.071	B;B;B;B	0.27262	0.043;0.078;0.022;0.038	T	0.04281	-1.0963	9	0.07644	T	0.81	-13.8523	14.935	0.70948	0.0:0.0:0.0:1.0	rs35474361	116;116;96;116	F5H4D7;B4DQH5;G3V1L0;P78539	.;.;.;SRPX_HUMAN	R	96;116;116;116;103	ENSP00000440758:K96R;ENSP00000411165:K116R;ENSP00000445034:K116R;ENSP00000367794:K116R;ENSP00000339211:K103R	ENSP00000339211:K103R	K	-	2	0	SRPX	37918359	1.000000	0.71417	1.000000	0.80357	0.385000	0.30292	3.342000	0.52159	1.909000	0.55274	0.486000	0.48141	AAA	T|0.921;C|0.079	0.079	strong		0.493	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307	
MIDN	90007	hgsc.bcm.edu	37	19	1250397	1250397	+	Silent	SNP	C	C	T	rs3746107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1250397C>T	ENST00000591446.2	+	1	511	c.102C>T	c.(100-102)gcC>gcT	p.A34A	MIDN_ENST00000300952.2_Silent_p.A34A			Q504T8	MIDN_HUMAN	midnolin	34	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					cytosol (GO:0005829)|nucleolus (GO:0005730)				NS(1)|endometrium(3)|kidney(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		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)		TGAGCCTCGCCATCCACAGCA	0.786													c|||	925	0.184704	0.5325	0.0389	5008	,	,		3815	0.1002		0.0159	False		,,,				2504	0.0787				p.A34A		Atlas-SNP	.											.	MIDN	34	.	0			c.C102T						PASS	.			1831,2463		402,1027,718	9.0	9.0	9.0		102	0.3	1.0	19	dbSNP_107	9	104,8314		2,100,4107	no	coding-synonymous	MIDN	NM_177401.4		404,1127,4825	TT,TC,CC		1.2354,42.6409,15.2218		34/469	1250397	1935,10777	2147	4209	6356	SO:0001819	synonymous_variant	90007	exon2			CCTCGCCATCCAC	AC004221	CCDS32864.1	19p13.3	2013-09-20			ENSG00000167470	ENSG00000167470			16298	protein-coding gene	gene with protein product		606700				10974535	Standard	XM_005259671		Approved		uc002lrp.3	Q504T8	OTTHUMG00000180144	ENST00000591446.2:c.102C>T	19.37:g.1250397C>T		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_177401	Q96BW8	Silent	SNP	ENST00000591446.2	37	CCDS32864.1																																																																																			C|0.846;T|0.154	0.154	strong		0.786	MIDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449965.2		
ZC3H4	23211	hgsc.bcm.edu	37	19	47584869	47584869	+	Silent	SNP	C	C	T	rs73943616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47584869C>T	ENST00000253048.5	-	11	1378	c.1341G>A	c.(1339-1341)ccG>ccA	p.P447P	RN7SL533P_ENST00000584468.1_RNA|ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	447							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		ACAGCTTACACGGGAAATCAC	0.522													C|||	133	0.0265575	0.093	0.0115	5008	,	,		20932	0.0		0.002	False		,,,				2504	0.0				p.P447P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G1341A						PASS	.	C		287,3833		14,259,1787	120.0	121.0	121.0		1341	-11.4	0.2	19	dbSNP_130	121	30,8360		0,30,4165	no	coding-synonymous	ZC3H4	NM_015168.1		14,289,5952	TT,TC,CC		0.3576,6.966,2.534		447/1304	47584869	317,12193	2060	4195	6255	SO:0001819	synonymous_variant	23211	exon11			CTTACACGGGAAA	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1341G>A	19.37:g.47584869C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	144	84	0.583333	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			C|0.986;T|0.014	0.014	strong		0.522	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
CD93	22918	hgsc.bcm.edu	37	20	23066338	23066338	+	Silent	SNP	G	G	C	rs6048539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23066338G>C	ENST00000246006.4	-	1	639	c.492C>G	c.(490-492)ccC>ccG	p.P164P		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	164	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GGCTCCCACAGGGGCCCTCAG	0.652													G|||	474	0.0946486	0.1422	0.0836	5008	,	,		13028	0.0933		0.0944	False		,,,				2504	0.0399				p.P164P		Atlas-SNP	.											.	CD93	84	.	0			c.C492G						PASS	.	G		629,3777		37,555,1611	29.0	36.0	34.0		492	-11.0	0.1	20	dbSNP_114	34	773,7827		40,693,3567	no	coding-synonymous	CD93	NM_012072.3		77,1248,5178	CC,CG,GG		8.9884,14.276,10.7796		164/653	23066338	1402,11604	2203	4300	6503	SO:0001819	synonymous_variant	22918	exon1			CCCACAGGGGCCC	U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"""CD molecules"""	15855	protein-coding gene	gene with protein product		120577	"""matrix-remodelling associated 4"", ""complement component 1, q subcomponent, receptor 1"", ""CD93 antigen"""	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.492C>G	20.37:g.23066338G>C		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_012072	O00274	Silent	SNP	ENST00000246006.4	37	CCDS13149.1																																																																																			G|0.889;C|0.111	0.111	strong		0.652	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072	
ZNF695	57116	hgsc.bcm.edu	37	1	247150631	247150631	+	Missense_Mutation	SNP	T	T	C	rs77178548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247150631T>C	ENST00000339986.7	-	4	1333	c.1186A>G	c.(1186-1188)Att>Gtt	p.I396V	ZNF695_ENST00000487338.2_Intron|ZNF695_ENST00000498046.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	396					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)			TTATGCTGAATAAGGTATGAG	0.398													T|||	157	0.0313498	0.1165	0.0043	5008	,	,		21162	0.0		0.0	False		,,,				2504	0.0				p.I396V		Atlas-SNP	.											.	ZNF695	55	.	0			c.A1186G						PASS	.	T	,VAL/ILE	387,3903		17,353,1775	51.0	55.0	53.0		,1186	0.6	0.0	1	dbSNP_132	53	3,8535		0,3,4266	no	intron,missense	ZNF695	NM_001204221.1,NM_020394.4	,29	17,356,6041	CC,CT,TT		0.0351,9.021,3.0402	,benign	,396/516	247150631	390,12438	2145	4269	6414	SO:0001583	missense	57116	exon4			GCTGAATAAGGTA		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.1186A>G	1.37:g.247150631T>C	ENSP00000341236:p.Ile396Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	37	CCDS44344.1	54	0.024725274725274724	52	0.10569105691056911	2	0.0055248618784530384	0	0.0	0	0.0	T	11.16	1.556933	0.27827	0.09021	3.51E-4	ENSG00000197472	ENST00000339986	T	0.07216	3.21	0.642	0.642	0.17765	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	N	0.02111	-0.68	0.09310	N	1	B	0.17465	0.022	B	0.08055	0.003	T	0.44742	-0.9308	9	0.66056	D	0.02	.	5.509	0.16870	0.0:1.0E-4:0.0:0.9999	.	396	Q8IW36	ZN695_HUMAN	V	396	ENSP00000341236:I396V	ENSP00000341236:I396V	I	-	1	0	ZNF695	245217254	0.000000	0.05858	0.009000	0.14445	0.744000	0.42396	-0.039000	0.12124	0.534000	0.28695	0.172000	0.16884	ATT	T|0.968;C|0.032	0.032	strong		0.398	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394	
ZNF883	169834	hgsc.bcm.edu	37	9	115760381	115760381	+	lincRNA	SNP	G	G	A	rs113877750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:115760381G>A	ENST00000427548.1	-	0	1432							P0CG24	ZN883_HUMAN	zinc finger protein 883						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										CAAGATTACTGTTCCGGGTAA	0.373													G|||	51	0.0101837	0.0371	0.0029	5008	,	,		18831	0.0		0.0	False		,,,				2504	0.0				p.N53N		Atlas-SNP	.											.	.	.	.	0			c.C159T						PASS	.	G		108,4228		3,102,2063	59.0	65.0	63.0		159	-0.9	0.0	9	dbSNP_132	63	1,8557		0,1,4278	no	coding-synonymous	ZNF883	NM_001101338.1		3,103,6341	AA,AG,GG		0.0117,2.4908,0.8454		53/380	115760381	109,12785	2168	4279	6447			169834	exon5			ATTACTGTTCCGG	AK095843		9q32	2010-07-23			ENSG00000228623	ENSG00000228623		"""Zinc fingers, C2H2-type"""	27271	protein-coding gene	gene with protein product							Standard	NM_001101338		Approved		uc011lwy.2	P0CG24	OTTHUMG00000020514		9.37:g.115760381G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	93	34	0.365591	NM_001101338		Silent	SNP	ENST00000427548.1	37																																																																																				G|0.991;A|0.009	0.009	strong		0.373	ZNF883-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000053704.1	NM_001101338	
ZDHHC2	51201	hgsc.bcm.edu	37	8	17067959	17067959	+	Missense_Mutation	SNP	C	C	G	rs190630185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17067959C>G	ENST00000262096.8	+	10	1615	c.920C>G	c.(919-921)aCt>aGt	p.T307S		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	307					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|recycling endosome membrane (GO:0055038)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|pancreas(1)|stomach(1)	8				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		CAAGCATCTACTCCTGCAGGG	0.328													C|||	8	0.00159744	0.0	0.0	5008	,	,		16046	0.0		0.008	False		,,,				2504	0.0				p.T307S		Atlas-SNP	.											.	ZDHHC2	25	.	0			c.C920G						PASS	.	C	SER/THR	1,3667		0,1,1833	69.0	64.0	65.0		920	5.5	1.0	8		65	28,8156		0,28,4064	yes	missense	ZDHHC2	NM_016353.4	58	0,29,5897	GG,GC,CC		0.3421,0.0273,0.2447	benign	307/368	17067959	29,11823	1834	4092	5926	SO:0001583	missense	51201	exon10			CATCTACTCCTGC	AB023584	CCDS47810.1	8p22	2008-05-15			ENSG00000104219	ENSG00000104219		"""Zinc fingers, DHHC-type"""	18469	protein-coding gene	gene with protein product						10918388	Standard	NM_016353		Approved	ZNF372	uc003wxe.3	Q9UIJ5	OTTHUMG00000163860	ENST00000262096.8:c.920C>G	8.37:g.17067959C>G	ENSP00000262096:p.Thr307Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_016353	D3DSP5	Missense_Mutation	SNP	ENST00000262096.8	37	CCDS47810.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	8.049	0.765606	0.15914	2.73E-4	0.003421	ENSG00000104219	ENST00000262096	T	0.41758	0.99	5.53	5.53	0.82687	.	0.075692	0.51477	D	0.000086	T	0.23210	0.0561	N	0.22421	0.69	0.43160	D	0.994945	B	0.11235	0.004	B	0.08055	0.003	T	0.13710	-1.0499	10	0.08179	T	0.78	-3.0288	19.8416	0.96692	0.0:1.0:0.0:0.0	.	307	Q9UIJ5	ZDHC2_HUMAN	S	307	ENSP00000262096:T307S	ENSP00000262096:T307S	T	+	2	0	ZDHHC2	17112330	0.998000	0.40836	0.996000	0.52242	0.427000	0.31564	4.020000	0.57189	2.774000	0.95407	0.585000	0.79938	ACT	C|0.997;G|0.003	0.003	strong		0.328	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	NM_016353	
HELT	391723	hgsc.bcm.edu	37	4	185940952	185940952	+	Missense_Mutation	SNP	C	C	G	rs1078461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:185940952C>G	ENST00000515777.1	+	3	272	c.184C>G	c.(184-186)Ctg>Gtg	p.L62V	HELT_ENST00000505610.1_Missense_Mutation_p.L62V|HELT_ENST00000338875.4_Missense_Mutation_p.L147V			A6NFD8	HELT_HUMAN	helt bHLH transcription factor	62	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.		L -> V (in dbSNP:rs1078461).		central nervous system development (GO:0007417)|GABAergic neuron differentiation in basal ganglia (GO:0021858)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	14		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;8.92e-26)|Epithelial(43;3.02e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-11)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		CGTTCAGTACCTGAGAGCACT	0.642													c|||	559	0.111621	0.0862	0.1354	5008	,	,		16083	0.1885		0.0924	False		,,,				2504	0.0695				p.L147V		Atlas-SNP	.											.	HELT	34	.	0			c.C439G						PASS	.	C	VAL/LEU	425,3981	193.3+/-218.5	21,383,1799	30.0	31.0	31.0		439	3.1	1.0	4	dbSNP_86	31	819,7781	180.6+/-229.5	39,741,3520	yes	missense	HELT	NM_001029887.1	32	60,1124,5319	GG,GC,CC		9.5233,9.6459,9.5648	probably-damaging	147/328	185940952	1244,11762	2203	4300	6503	SO:0001583	missense	391723	exon3			CAGTACCTGAGAG	BC144567	CCDS75214.1, CCDS75215.1	4q35.1	2014-07-17	2011-09-12		ENSG00000187821	ENSG00000187821		"""Basic helix-loop-helix proteins"""	33783	protein-coding gene	gene with protein product	"""megane bHLH factor"", ""HES-like"""		"""Hey-like transcription factor (zebrafish)"", ""HES/HEY-like transcription factor"""			14764602, 17611227	Standard	XM_005262989		Approved	HESL, HCM1228, Mgn, bHLHb44, MEGANE	uc011ckq.2	A6NFD8	OTTHUMG00000160484	ENST00000515777.1:c.184C>G	4.37:g.185940952C>G	ENSP00000426033:p.Leu62Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	155	80	0.516129	NM_001029887	B2RTS5|B7ZMI7|B7ZMI8	Missense_Mutation	SNP	ENST00000515777.1	37		264	0.12087912087912088	41	0.08333333333333333	41	0.1132596685082873	109	0.19055944055944055	73	0.09630606860158311	C	19.49	3.837382	0.71373	0.096459	0.095233	ENSG00000187821	ENST00000505610;ENST00000515777;ENST00000338875	D;D;D	0.98060	-4.69;-4.69;-4.69	4.89	3.12	0.35913	Helix-loop-helix DNA-binding (5);	0.000000	0.64402	D	0.000010	T	0.04770	0.0129	L	0.39566	1.225	0.20975	P	0.999819995	D;P;P	0.57899	0.981;0.937;0.923	P;P;P	0.59948	0.866;0.794;0.69	T	0.05852	-1.0860	9	0.56958	D	0.05	.	9.7352	0.40384	0.0:0.7691:0.0:0.2309	rs1078461;rs4359954;rs17631598;rs1078461	147;62;62	A6NFD8;B7ZMI7;A6NFD8-2	HELT_HUMAN;.;.	V	62;62;147	ENSP00000422140:L62V;ENSP00000426033:L62V;ENSP00000343464:L147V	ENSP00000343464:L147V	L	+	1	2	HELT	186177946	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.880000	0.48530	1.288000	0.44600	0.561000	0.74099	CTG	C|0.898;G|0.102	0.102	strong		0.642	HELT-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000360792.1	NM_001300781	
CWC25	54883	hgsc.bcm.edu	37	17	36963226	36963226	+	Silent	SNP	G	G	T	rs3785452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36963226G>T	ENST00000225428.5	-	7	991	c.694C>A	c.(694-696)Cgg>Agg	p.R232R	CWC25_ENST00000536127.1_Silent_p.R169R	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	232										central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						TCAGAGTTCCGGACCTACATC	0.512													T|||	805	0.160743	0.4849	0.049	5008	,	,		18783	0.0556		0.0109	False		,,,				2504	0.0644				p.R232R		Atlas-SNP	.											.	CWC25	24	.	0			c.C694A						PASS	.	T		1555,2235		324,907,664	83.0	78.0	80.0		694	3.0	0.4	17	dbSNP_107	80	121,8119		0,121,3999	no	coding-synonymous	CWC25	NM_017748.3		324,1028,4663	TT,TG,GG		1.4684,41.029,13.9318		232/426	36963226	1676,10354	1895	4120	6015	SO:0001819	synonymous_variant	54883	exon7			AGTTCCGGACCTA	AK000298	CCDS45663.1	17q12	2010-01-26	2010-01-26	2010-01-26		ENSG00000273559			25989	protein-coding gene	gene with protein product			"""coiled-coil domain containing 49"""	CCDC49		19941820	Standard	NM_017748		Approved	FLJ20291	uc002hqu.4	Q9NXE8		ENST00000225428.5:c.694C>A	17.37:g.36963226G>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_017748	A0JLM3|Q68DK5	Silent	SNP	ENST00000225428.5	37	CCDS45663.1																																																																																			G|0.860;T|0.140	0.140	strong		0.512	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442186.6	NM_017748	
CCSER1	401145	hgsc.bcm.edu	37	4	91230407	91230407	+	Silent	SNP	T	T	C	rs34445159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:91230407T>C	ENST00000509176.1	+	2	1260	c.972T>C	c.(970-972)taT>taC	p.Y324Y	CCSER1_ENST00000333691.8_Silent_p.Y324Y|CCSER1_ENST00000432775.2_Silent_p.Y324Y	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	324																	CTGGGAAATATAGGTTAGAGG	0.413													T|||	23	0.00459265	0.0166	0.0014	5008	,	,		20571	0.0		0.0	False		,,,				2504	0.0				p.Y324Y		Atlas-SNP	.											.	.	.	.	0			c.T972C						PASS	.	T	,	68,3690		1,66,1812	124.0	117.0	119.0		972,972	1.3	1.0	4	dbSNP_126	119	1,8211		0,1,4105	no	coding-synonymous,coding-synonymous	FAM190A	NM_001145065.1,NM_207491.2	,	1,67,5917	CC,CT,TT		0.0122,1.8095,0.5764	,	324/901,324/678	91230407	69,11901	1879	4106	5985	SO:0001819	synonymous_variant	401145	exon2			GAAATATAGGTTA		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"""family with sequence similarity 190, member A"""	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.972T>C	4.37:g.91230407T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	218	92	0.422018	NM_001145065	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	37	CCDS47099.1																																																																																			T|0.995;C|0.005	0.005	strong		0.413	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065	
MAP4	4134	hgsc.bcm.edu	37	3	47956424	47956424	+	Missense_Mutation	SNP	C	C	T	rs1137524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47956424C>T	ENST00000360240.6	-	8	2400	c.1882G>A	c.(1882-1884)Gtc>Atc	p.V628I	MAP4_ENST00000426837.2_Missense_Mutation_p.V645I|MAP4_ENST00000395734.3_Missense_Mutation_p.V628I|MAP4_ENST00000383737.4_Intron	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	111	0	0		WXS	Illumina HiSeq	Phase_I	138	70	0.507246	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	
FAM71C	196472	hgsc.bcm.edu	37	12	100042163	100042163	+	Missense_Mutation	SNP	A	A	G	rs11109969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:100042163A>G	ENST00000324341.1	+	1	633	c.211A>G	c.(211-213)Atg>Gtg	p.M71V	ANKS1B_ENST00000547776.2_Intron|ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	71			M -> V (in dbSNP:rs11109969).							breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		AATGGTAACAATGGGCATCGT	0.532													G|||	1082	0.216054	0.298	0.1772	5008	,	,		19135	0.0992		0.2903	False		,,,				2504	0.1769				p.M71V		Atlas-SNP	.											.	FAM71C	48	.	0			c.A211G						PASS	.	G	,VAL/MET	1283,3123	699.8+/-406.5	165,953,1085	134.0	112.0	119.0		,211	2.0	0.2	12	dbSNP_120	119	2551,6049	691.5+/-404.5	386,1779,2135	yes	intron,missense	ANKS1B,FAM71C	NM_152788.4,NM_153364.3	,21	551,2732,3220	GG,GA,AA		29.6628,29.1194,29.4787	,benign	,71/242	100042163	3834,9172	2203	4300	6503	SO:0001583	missense	196472	exon1			GTAACAATGGGCA		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.211A>G	12.37:g.100042163A>G	ENSP00000315247:p.Met71Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	128	52	0.40625	NM_153364	B2R6Y6	Missense_Mutation	SNP	ENST00000324341.1	37	CCDS9072.1	514	0.23534798534798534	150	0.3048780487804878	74	0.20441988950276244	56	0.0979020979020979	234	0.3087071240105541	G	0.001	-2.909759	0.00056	0.291194	0.296628	ENSG00000180219	ENST00000324341	T	0.07688	3.17	3.85	1.97	0.26223	.	0.206665	0.29964	N	0.010752	T	0.00012	0.0000	N	0.02202	-0.64	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48525	-0.9028	8	.	.	.	-12.1097	6.2766	0.20983	0.1027:0.3583:0.539:0.0	rs11109969;rs56567578;rs11109969	71	Q8NEG0	FA71C_HUMAN	V	71	ENSP00000315247:M71V	.	M	+	1	0	FAM71C	98566294	0.003000	0.15002	0.214000	0.23707	0.008000	0.06430	-0.136000	0.10405	0.210000	0.20664	-1.081000	0.02215	ATG	A|0.738;G|0.262	0.262	strong		0.532	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364	
AFAP1	60312	hgsc.bcm.edu	37	4	7765495	7765495	+	Silent	SNP	G	G	T	rs2240053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:7765495G>T	ENST00000360265.4	-	16	2424	c.2190C>A	c.(2188-2190)acC>acA	p.T730T	AFAP1_ENST00000513842.1_5'UTR|AFAP1_ENST00000358461.2_Silent_p.T730T|AFAP1-AS1_ENST00000608442.1_RNA|AFAP1_ENST00000382543.3_Silent_p.T814T|AFAP1_ENST00000420658.1_Silent_p.T814T			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	730						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						CTGTCCCCTAGGTCCCGTTCT	0.572													T|||	1209	0.241414	0.2685	0.1628	5008	,	,		17435	0.3899		0.0924	False		,,,				2504	0.2607				p.T814T		Atlas-SNP	.											.	AFAP1	93	.	0			c.C2442A						PASS	.	T	,	879,3319		83,713,1303	156.0	120.0	132.0		2442,2190	-8.6	0.0	4	dbSNP_98	132	609,7517		19,571,3473	no	coding-synonymous,coding-synonymous	AFAP1	NM_001134647.1,NM_198595.2	,	102,1284,4776	TT,TG,GG		7.4945,20.9385,12.074	,	814/815,730/731	7765495	1488,10836	2099	4063	6162	SO:0001819	synonymous_variant	60312	exon18			CCCCTAGGTCCCG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.2190C>A	4.37:g.7765495G>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	137	63	0.459854	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	37	CCDS3397.1																																																																																			G|0.803;T|0.197	0.197	strong		0.572	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49967996	49967996	+	Silent	SNP	G	G	A	rs10421522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49967996G>A	ENST00000293350.4	+	12	1708	c.1545G>A	c.(1543-1545)ccG>ccA	p.P515P	ALDH16A1_ENST00000540132.1_Silent_p.P352P|ALDH16A1_ENST00000455361.2_Silent_p.P464P|ALDH16A1_ENST00000433981.2_Silent_p.P350P|CTD-3148I10.9_ENST00000599536.1_3'UTR	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	515						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)		CAACCCTGCCGGCTGGGCCTG	0.617													g|||	197	0.0393371	0.1399	0.0159	5008	,	,		14923	0.0		0.001	False		,,,				2504	0.0				p.P515P		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1545A						PASS	.	A	,	461,3945	218.4+/-236.5	24,413,1766	105.0	113.0	111.0		1392,1545	-8.9	0.0	19	dbSNP_119	111	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	24,418,6061	AA,AG,GG		0.0581,10.463,3.583	,	464/752,515/803	49967996	466,12540	2203	4300	6503	SO:0001819	synonymous_variant	126133	exon12			CCTGCCGGCTGGG	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.1545G>A	19.37:g.49967996G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			G|0.964;A|0.036	0.036	strong		0.617	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102493761	102493761	+	Silent	SNP	A	A	G	rs8010870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102493761A>G	ENST00000360184.4	+	46	9092	c.8928A>G	c.(8926-8928)ctA>ctG	p.L2976L		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2976	AAA 4. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ATGAAGATCTACGGACAGTGT	0.418													A|||	975	0.194688	0.2504	0.1484	5008	,	,		23531	0.248		0.0895	False		,,,				2504	0.2055				p.L2976L		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A8928G						PASS	.	A		976,3430	366.4+/-317.8	117,742,1344	118.0	111.0	113.0		8928	-12.1	0.0	14	dbSNP_116	113	942,7658	206.9+/-248.8	54,834,3412	no	coding-synonymous	DYNC1H1	NM_001376.4		171,1576,4756	GG,GA,AA		10.9535,22.1516,14.747		2976/4647	102493761	1918,11088	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon46			AGATCTACGGACA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.8928A>G	14.37:g.102493761A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			A|0.835;G|0.165;T|0.000	0.165	strong		0.418	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
MUC5B	727897	hgsc.bcm.edu	37	11	1276327	1276327	+	Missense_Mutation	SNP	G	G	A	rs3829224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1276327G>A	ENST00000529681.1	+	36	15779	c.15721G>A	c.(15721-15723)Gcc>Acc	p.A5241T	MUC5B_ENST00000447027.1_Missense_Mutation_p.A5244T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5241	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)		AACCACTGCCGCCAGTTGCAA	0.682													G|||	649	0.129593	0.1089	0.1282	5008	,	,		10373	0.2768		0.003	False		,,,				2504	0.137				p.A5241T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G15721A						PASS	.	G	THR/ALA	322,3860		16,290,1785	19.0	26.0	24.0		15721	-8.4	0.0	11	dbSNP_107	24	13,8351		0,13,4169	yes	missense	MUC5B	NM_002458.2	58	16,303,5954	AA,AG,GG		0.1554,7.6997,2.6702	benign	5241/5763	1276327	335,12211	2091	4182	6273	SO:0001583	missense	727897	exon36			ACTGCCGCCAGTT	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.15721G>A	11.37:g.1276327G>A	ENSP00000436812:p.Ala5241Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	160	83	0.51875	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	234	0.10714285714285714	51	0.10365853658536585	37	0.10220994475138122	144	0.2517482517482518	2	0.002638522427440633	G	9.622	1.134084	0.21123	0.076997	0.001554	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.15139	2.45;2.64	4.19	-8.39	0.00969	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.12630	0.003;0.006	B;B	0.04013	0.001;0.001	T	0.43940	-0.9360	8	0.87932	D	0	.	0.5699	0.00694	0.3961:0.1875:0.1911:0.2253	rs3829224	5578;5244	A7Y9J9;E9PBJ0	.;.	T	5241;5244;5185;140;4953	ENSP00000436812:A5241T;ENSP00000415793:A5244T	ENSP00000343037:A5185T	A	+	1	0	MUC5B	1232903	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.161000	0.01278	-1.669000	0.01470	-1.856000	0.00563	GCC	G|0.887;A|0.113	0.113	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
COQ4	51117	hgsc.bcm.edu	37	9	131088076	131088076	+	Silent	SNP	G	G	A	rs2270203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131088076G>A	ENST00000300452.3	+	4	641	c.318G>A	c.(316-318)tcG>tcA	p.S106S	COQ4_ENST00000372875.3_Silent_p.S106S	NM_016035.3	NP_057119			coenzyme Q4											endometrium(4)|large_intestine(1)|lung(4)	9						CCCGGATTTCGACATCCACCC	0.602													G|||	668	0.133387	0.2065	0.0677	5008	,	,		21989	0.1935		0.0467	False		,,,				2504	0.1084				p.S106S		Atlas-SNP	.											.	COQ4	20	.	0			c.G318A						PASS	.	G		845,3561	334.1+/-303.3	75,695,1433	89.0	80.0	83.0		318	-4.7	0.3	9	dbSNP_100	83	358,8242	120.6+/-179.8	7,344,3949	no	coding-synonymous	COQ4	NM_016035.3		82,1039,5382	AA,AG,GG		4.1628,19.1784,9.2496		106/266	131088076	1203,11803	2203	4300	6503	SO:0001819	synonymous_variant	51117	exon4			GATTTCGACATCC	AF151850	CCDS6898.1	9q34.2	2013-10-18	2013-10-18		ENSG00000167113	ENSG00000167113			19693	protein-coding gene	gene with protein product		612898	"""coenzyme Q4 homolog (yeast)"", ""coenzyme Q4 homolog (S. cerevisiae)"""			11469793, 18474229	Standard	NM_016035		Approved	CGI-92	uc004bur.4	Q9Y3A0	OTTHUMG00000020743	ENST00000300452.3:c.318G>A	9.37:g.131088076G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	146	55	0.376712	NM_016035		Silent	SNP	ENST00000300452.3	37	CCDS6898.1																																																																																			G|0.891;A|0.109	0.109	strong		0.602	COQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054427.1	NM_016035	
ENDOD1	23052	hgsc.bcm.edu	37	11	94862340	94862340	+	Missense_Mutation	SNP	A	A	T	rs188091415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94862340A>T	ENST00000278505.4	+	2	1218	c.1100A>T	c.(1099-1101)cAg>cTg	p.Q367L		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	367						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				GTTACCAAGCAGGTGATTAAT	0.438													A|||	5	0.000998403	0.0038	0.0	5008	,	,		21650	0.0		0.0	False		,,,				2504	0.0				p.Q367L		Atlas-SNP	.											.	ENDOD1	26	.	0			c.A1100T						PASS	.	A	LEU/GLN	12,3830		0,12,1909	114.0	102.0	106.0		1100	4.9	1.0	11		106	0,8256		0,0,4128	yes	missense	ENDOD1	NM_015036.2	113	0,12,6037	TT,TA,AA		0.0,0.3123,0.0992	possibly-damaging	367/501	94862340	12,12086	1921	4128	6049	SO:0001583	missense	23052	exon2			CCAAGCAGGTGAT	BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.1100A>T	11.37:g.94862340A>T	ENSP00000278505:p.Gln367Leu	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	145	89	0.613793	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	37	CCDS41699.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	13.12	2.141283	0.37825	0.003123	0.0	ENSG00000149218	ENST00000278505	T	0.33865	1.39	6.03	4.88	0.63580	.	0.171913	0.40469	N	0.001086	T	0.26991	0.0661	M	0.67953	2.075	0.32644	N	0.52035	B	0.18461	0.028	B	0.17433	0.018	T	0.44360	-0.9333	10	0.87932	D	0	-24.9899	6.2791	0.20997	0.7766:0.0:0.0796:0.1438	.	367	O94919	ENDD1_HUMAN	L	367	ENSP00000278505:Q367L	ENSP00000278505:Q367L	Q	+	2	0	ENDOD1	94501988	0.987000	0.35691	0.993000	0.49108	0.553000	0.35397	1.425000	0.34859	1.066000	0.40716	0.455000	0.32223	CAG	A|0.998;T|0.002	0.002	strong		0.438	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036	
POLR1A	25885	hgsc.bcm.edu	37	2	86259443	86259443	+	Silent	SNP	C	C	T	rs2276626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86259443C>T	ENST00000263857.6	-	29	4602	c.4224G>A	c.(4222-4224)ggG>ggA	p.G1408G	POLR1A_ENST00000409681.1_Silent_p.G1408G			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1408					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)	p.G1408G(1)		NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						CATCGGCGTCCCCCTCCTCAG	0.582													C|||	2889	0.576877	0.8283	0.4712	5008	,	,		17574	0.3611		0.5934	False		,,,				2504	0.5174				p.G1408G		Atlas-SNP	.											POLR1A,NS,carcinoma,0,1	POLR1A	137	1	1	Substitution - coding silent(1)	stomach(1)	c.G4224A						PASS	.	C		3443,807		1386,671,68	166.0	180.0	175.0		4224	-0.6	0.9	2	dbSNP_100	175	5431,3037		1742,1947,545	no	coding-synonymous	POLR1A	NM_015425.3		3128,2618,613	TT,TC,CC		35.8644,18.9882,30.2249		1408/1721	86259443	8874,3844	2125	4234	6359	SO:0001819	synonymous_variant	25885	exon29			GGCGTCCCCCTCC	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.4224G>A	2.37:g.86259443C>T		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	225	222	0.986667	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Silent	SNP	ENST00000263857.6	37	CCDS42706.1																																																																																			T|0.595;C|0.405;A|0.000	0.595	strong		0.582	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
OR8K1	390157	hgsc.bcm.edu	37	11	56113703	56113703	+	Silent	SNP	C	C	T	rs145394503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56113703C>T	ENST00000279783.2	+	1	283	c.189C>T	c.(187-189)acC>acT	p.T63T		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	63						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					AGCTACACACCCCCATGTACT	0.433										HNSCC(65;0.19)			C|||	35	0.00698882	0.0242	0.0029	5008	,	,		19161	0.0		0.001	False		,,,				2504	0.0				p.T63T		Atlas-SNP	.											.	OR8K1	93	.	0			c.C189T						PASS	.	C		108,4294	83.9+/-122.4	2,104,2095	165.0	149.0	154.0		189	-10.0	0.0	11	dbSNP_134	154	3,8589	2.2+/-6.3	0,3,4293	no	coding-synonymous	OR8K1	NM_001002907.1		2,107,6388	TT,TC,CC		0.0349,2.4534,0.8542		63/320	56113703	111,12883	2201	4296	6497	SO:0001819	synonymous_variant	390157	exon1			ACACACCCCCATG	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.189C>T	11.37:g.56113703C>T		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	189	94	0.497355	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Silent	SNP	ENST00000279783.2	37	CCDS31528.1																																																																																			C|0.993;T|0.007	0.007	strong		0.433	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
MUC4	4585	hgsc.bcm.edu	37	3	195513756	195513756	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513756G>A	ENST00000463781.3	-	2	5154	c.4695C>T	c.(4693-4695)caC>caT	p.H1565H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.H1565H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)		GAGGGGTGGTGTGACCTGTGG	0.572																																					p.H1565H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	0			c.C4695T						scavenged	.						27.0	19.0	21.0					3																	195513756		687	1584	2271	SO:0001819	synonymous_variant	4585	exon2			GGTGGTGTGACCT	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.4695C>T	3.37:g.195513756G>A		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	255	8	0.0313726	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																																																																																			.	.	none		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PGAM4	441531	hgsc.bcm.edu	37	X	77225099	77225099	+	Missense_Mutation	SNP	C	C	T	rs6622613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:77225099C>T	ENST00000458128.1	-	1	36	c.37G>A	c.(37-39)Gag>Aag	p.E13K	ATP7A_ENST00000343533.5_Intron|ATP7A_ENST00000341514.6_Intron|ATP7A_ENST00000350425.4_Intron	NM_001029891.2	NP_001025062.1	Q8N0Y7	PGAM4_HUMAN	phosphoglycerate mutase family member 4	13					glycolytic process (GO:0006096)|positive regulation of sperm motility (GO:1902093)	extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)			endometrium(2)|lung(4)	6						CATGTGCTCTCGCCGTGCCGG	0.587													C|||	52	0.0137748	0.0363	0.0058	3775	,	,		12671	0.0		0.0	False		,,,				2504	0.0				p.E13K		Atlas-SNP	.											.	PGAM4	28	.	0			c.G37A						PASS	.	C	,LYS/GLU	101,3734		1,82,17,1549,554	55.0	54.0	54.0		,37	0.1	0.6	X	dbSNP_116	54	9,6713		0,7,2,2420,1866	no	intron,missense	ATP7A,PGAM4	NM_000052.4,NM_001029891.2	,56	1,89,19,3969,2420	TT,TC,T,CC,C		0.1339,2.6336,1.042	,possibly-damaging	,13/255	77225099	110,10447	2203	4295	6498	SO:0001583	missense	441531	exon1			TGCTCTCGCCGTG	AF465731	CCDS35338.1	Xq21.1	2011-02-09	2006-02-09		ENSG00000226784	ENSG00000226784			21731	protein-coding gene	gene with protein product		300567	"""phosphoglycerate mutase family 4"""			11961099, 9370262	Standard	NM_001029891		Approved	dJ1000K24.1, PGAM3, PGAM-B, PGAM1	uc004ecy.1	Q8N0Y7	OTTHUMG00000057865	ENST00000458128.1:c.37G>A	X.37:g.77225099C>T	ENSP00000412189:p.Glu13Lys	Somatic	470	1	0.00212766		WXS	Illumina HiSeq	Phase_I	488	248	0.508197	NM_001029891	Q5JPN2|Q8NI24|Q8NI25|Q8NI26	Missense_Mutation	SNP	ENST00000458128.1	37	CCDS35338.1	13	0.007836045810729355	4	0.008298755186721992	4	0.011111111111111112	0	0.0	0	0.0	C	17.78	3.473730	0.63737	0.026336	0.001339	ENSG00000226784	ENST00000458128	D	0.83163	-1.69	0.119	0.119	0.14685	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	U	0.000000	T	0.53916	0.1826	L	0.55743	1.74	0.22675	P	0.99886112	B	0.31077	0.307	B	0.35655	0.207	T	0.64266	-0.6448	8	.	.	.	-7.1432	6.135	0.20227	0.0:0.9996:0.0:4.0E-4	rs6622613	13	Q8N0Y7	PGAM4_HUMAN	K	13	ENSP00000412189:E13K	.	E	-	1	0	PGAM4	77111755	1.000000	0.71417	0.623000	0.29173	0.641000	0.38312	3.649000	0.54417	0.260000	0.21731	0.264000	0.19307	GAG	C|0.990;T|0.010	0.010	strong		0.587	PGAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128371.2	NM_001029891	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919267	51919267	+	Silent	SNP	A	A	G	rs7258638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51919267A>G	ENST00000339313.5	-	5	1025	c.909T>C	c.(907-909)ccT>ccC	p.P303P	SIGLEC10_ENST00000356298.5_Silent_p.P303P|SIGLEC10_ENST00000525998.1_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000439889.2_Silent_p.P245P|SIGLEC10_ENST00000353836.5_Silent_p.P303P|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000432469.2_Silent_p.P220P|SIGLEC10_ENST00000436984.2_Silent_p.P255P|SIGLEC10_ENST00000441969.3_Silent_p.P245P|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000442846.3_Intron			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	303	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CCAGGGGTCTAGGGCCCCAGG	0.677																																					p.P303P		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.T909C						PASS	.						26.0	30.0	29.0					19																	51919267		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			GGGTCTAGGGCCC	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.909T>C	19.37:g.51919267A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	177	29	0.163842	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			A|0.996;G|0.004	0.004	strong		0.677	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
TSSC4	10078	hgsc.bcm.edu	37	11	2424541	2424541	+	Missense_Mutation	SNP	C	C	G	rs2234279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2424541C>G	ENST00000333256.6	+	3	1121	c.678C>G	c.(676-678)caC>caG	p.H226Q	TSSC4_ENST00000467308.1_Intron|AC124057.5_ENST00000433035.1_RNA|TSSC4_ENST00000451491.2_Missense_Mutation_p.H226Q|TSSC4_ENST00000380996.5_Missense_Mutation_p.H162Q|TSSC4_ENST00000380992.1_Intron			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	226										endometrium(3)|large_intestine(1)|lung(4)	8		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAGCCAGACACGAGAGGAAGA	0.657													c|||	670	0.133786	0.3411	0.0735	5008	,	,		16131	0.1151		0.0258	False		,,,				2504	0.0266				p.H226Q		Atlas-SNP	.											.	TSSC4	19	.	0			c.C678G						PASS	.	T	GLN/HIS	1263,3139	418.3+/-338.2	200,863,1138	41.0	49.0	47.0		678	-7.3	0.0	11	dbSNP_98	47	259,8339	97.7+/-159.3	5,249,4045	yes	missense	TSSC4	NM_005706.2	24	205,1112,5183	GG,GC,CC		3.0123,28.6915,11.7077	benign	226/330	2424541	1522,11478	2201	4299	6500	SO:0001583	missense	10078	exon2			CAGACACGAGAGG	AF125568	CCDS7735.1, CCDS73241.1	11p15.5	2008-02-05			ENSG00000184281	ENSG00000184281			12386	protein-coding gene	gene with protein product		603852				10072438	Standard	XM_005252722		Approved		uc001lwl.3	Q9Y5U2	OTTHUMG00000009895	ENST00000333256.6:c.678C>G	11.37:g.2424541C>G	ENSP00000331087:p.His226Gln	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	183	92	0.502732	NM_005706	C9JS66|Q86VL2|Q9BRS6	Missense_Mutation	SNP	ENST00000333256.6	37	CCDS7735.1	279	0.12774725274725274	165	0.3353658536585366	30	0.08287292817679558	68	0.11888111888111888	16	0.021108179419525065	c	0.016	-1.531603	0.00951	0.286915	0.030123	ENSG00000184281	ENST00000380996;ENST00000333256;ENST00000440813;ENST00000451491	T;T;T;T	0.21191	2.3;2.56;2.02;2.56	3.67	-7.33	0.01431	.	1.177240	0.06289	U	0.698832	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	B;B	0.33379	0.41;0.41	B;B	0.30179	0.112;0.112	T	0.25293	-1.0136	9	0.32370	T	0.25	-0.1137	4.7935	0.13261	0.0803:0.2104:0.1601:0.5493	rs2234279	226;162	Q9Y5U2;Q9Y5U2-2	TSSC4_HUMAN;.	Q	162;226;162;226	ENSP00000370384:H162Q;ENSP00000331087:H226Q;ENSP00000416937:H162Q;ENSP00000411224:H226Q	ENSP00000331087:H226Q	H	+	3	2	TSSC4	2381117	0.000000	0.05858	0.001000	0.08648	0.124000	0.20399	-1.962000	0.01514	-2.708000	0.00395	-1.297000	0.01338	CAC	C|0.883;G|0.117	0.117	strong		0.657	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706	
SLFN14	342618	hgsc.bcm.edu	37	17	33880003	33880003	+	Silent	SNP	C	C	G	rs28498569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	70	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	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	
RPGR	6103	hgsc.bcm.edu	37	X	38145918	38145918	+	Intron	SNP	C	C	T	rs201730068		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145918C>T	ENST00000339363.3	-	14	2688				RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000378505.2_Silent_p.E778E|RPGR_ENST00000342811.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						ccgctctttcctcctttttcc	0.537																																					p.E778E		Atlas-SNP	.											.	RPGR	175	.	0			c.G2334A						PASS	.						315.0	191.0	233.0					X																	38145918		1858	3627	5485	SO:0001627	intron_variant	6103	exon15			TCTTTCCTCCTTT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+428G>A	X.37:g.38145918C>T		Somatic	459	0	0		WXS	Illumina HiSeq	Phase_I	294	15	0.0510204	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Silent	SNP	ENST00000339363.3	37																																																																																				.	.	none		0.537	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
UBE3A	7337	hgsc.bcm.edu	37	15	25616844	25616844	+	Silent	SNP	T	T	A	rs28528079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25616844T>A	ENST00000397954.2	-	4	485	c.486A>T	c.(484-486)gcA>gcT	p.A162A	SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000566215.1_Silent_p.A139A|UBE3A_ENST00000428984.2_Silent_p.A139A|UBE3A_ENST00000232165.3_Silent_p.A159A|UBE3A_ENST00000438097.1_Silent_p.A139A			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	162					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		TCTGTACCAATGCCTCAGCAC	0.363													T|||	167	0.0333466	0.1172	0.0144	5008	,	,		19091	0.0		0.001	False		,,,				2504	0.001				p.A162A		Atlas-SNP	.											.	UBE3A	109	.	0			c.A486T						PASS	.	T	,,	406,4000	196.0+/-220.5	19,368,1816	104.0	106.0	105.0		486,417,477	-0.7	1.0	15	dbSNP_125	105	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	UBE3A	NM_000462.3,NM_130838.1,NM_130839.2	,,	19,369,6115	AA,AT,TT		0.0116,9.2147,3.1293	,,	162/876,139/853,159/873	25616844	407,12599	2203	4300	6503	SO:0001819	synonymous_variant	7337	exon7			TACCAATGCCTCA	AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"""Angelman syndrome"""	601623	"""human papilloma virus E6-associated protein"""	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.486A>T	15.37:g.25616844T>A		Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	341	169	0.495601	NM_000462	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Silent	SNP	ENST00000397954.2	37	CCDS45192.1																																																																																			T|0.958;A|0.042	0.042	strong		0.363	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462	
FAM178B	51252	hgsc.bcm.edu	37	2	97543701	97543701	+	Missense_Mutation	SNP	G	G	A	rs34013660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:97543701G>A	ENST00000417561.3	-	20	2376	c.2377C>T	c.(2377-2379)Cgc>Tgc	p.R793C	FAM178B_ENST00000327896.3_Missense_Mutation_p.R613C|FAM178B_ENST00000490605.2_Missense_Mutation_p.R645C|FAM178B_ENST00000393526.2_Missense_Mutation_p.R85C|FAM178B_ENST00000470789.1_5'UTR			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	793			R -> C (in dbSNP:rs34013660).							large_intestine(1)|ovary(1)	2						AGCATGGTGCGGTGCATGGCC	0.672													G|||	86	0.0171725	0.0635	0.0014	5008	,	,		16465	0.0		0.001	False		,,,				2504	0.0				p.R645C		Atlas-SNP	.											FAM178B_ENST00000417561,colon,carcinoma,+1,2	FAM178B	35	2	0			c.C1933T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	256,4150	147.3+/-181.8	8,240,1955	77.0	64.0	68.0		1933,310,253	2.3	1.0	2	dbSNP_126	68	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	FAM178B	NM_001122646.2,NM_001172667.1,NM_016490.4	180,180,180	8,242,6253	AA,AG,GG		0.0233,5.8103,1.9837	probably-damaging,probably-damaging,probably-damaging	645/680,104/139,85/120	97543701	258,12748	2203	4300	6503	SO:0001583	missense	51252	exon16			TGGTGCGGTGCAT	AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.2377C>T	2.37:g.97543701G>A	ENSP00000413245:p.Arg793Cys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Missense_Mutation	SNP	ENST00000417561.3	37		30	0.013736263736263736	29	0.05894308943089431	0	0.0	0	0.0	1	0.0013192612137203166	G	16.16	3.045853	0.55110	0.058103	2.33E-4	ENSG00000168754	ENST00000417561;ENST00000327896;ENST00000393526;ENST00000490605	T;T;T;T	0.60797	0.18;0.2;0.16;0.18	5.2	2.31	0.28768	.	.	.	.	.	T	0.14830	0.0358	M	0.62723	1.935	0.41162	D	0.986107	D	0.71674	0.998	P	0.53861	0.736	T	0.33369	-0.9871	9	0.87932	D	0	-4.1547	4.8677	0.13616	0.1825:0.0:0.636:0.1815	rs34013660	793	Q8IXR5	F178B_HUMAN	C	793;613;85;645	ENSP00000413245:R793C;ENSP00000333553:R613C;ENSP00000377160:R85C;ENSP00000429896:R645C	ENSP00000333553:R613C	R	-	1	0	FAM178B	96907428	0.594000	0.26849	0.988000	0.46212	0.405000	0.30901	0.542000	0.23222	0.161000	0.19458	0.455000	0.32223	CGC	G|0.979;A|0.021	0.021	strong		0.672	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490	
C16orf58	64755	hgsc.bcm.edu	37	16	31505252	31505252	+	Silent	SNP	C	C	T	rs34231527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31505252C>T	ENST00000327237.2	-	7	747	c.708G>A	c.(706-708)acG>acA	p.T236T	C16orf58_ENST00000570164.1_Silent_p.T236T|C16orf58_ENST00000567994.1_Silent_p.T191T|C16orf58_ENST00000430477.2_Silent_p.T94T			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	236						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)	14						GGTTCACCAGCGTCTCCTGGA	0.622													C|||	36	0.0071885	0.025	0.0043	5008	,	,		16051	0.0		0.0	False		,,,				2504	0.0				p.S236S		Atlas-SNP	.											.	C16orf58	28	.	0			c.C708A						PASS	.	C		101,4291	76.8+/-115.0	1,99,2096	34.0	36.0	36.0		708	-6.7	0.8	16	dbSNP_126	36	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	C16orf58	NM_022744.2		1,100,6395	TT,TC,CC		0.0116,2.2996,0.7851		236/469	31505252	102,12890	2196	4300	6496	SO:0001819	synonymous_variant	64755	exon7			CACCAGCGTCTCC	AK023930	CCDS10715.1	16p11.2	2013-03-04			ENSG00000140688	ENSG00000140688			25848	protein-coding gene	gene with protein product							Standard	NM_022744		Approved	FLJ13868	uc002eci.3	Q96GQ5	OTTHUMG00000132466	ENST00000327237.2:c.708G>A	16.37:g.31505252C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Silent	SNP	ENST00000327237.2	37	CCDS10715.1																																																																																			C|0.991;T|0.009	0.009	strong		0.622	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744	
MICA	100507436	hgsc.bcm.edu	37	6	31378977	31378977	+	Missense_Mutation	SNP	G	G	A	rs1051792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31378977G>A	ENST00000449934.2	+	3	508	c.454G>A	c.(454-456)Gtg>Atg	p.V152M	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)				GGAATGGACAGTGCCCCAGTC	0.517													g|||	1827	0.364816	0.4788	0.4078	5008	,	,		20742	0.3006		0.3141	False		,,,				2504	0.2986				p.V152M		Atlas-SNP	.											.	MICA	21	.	0			c.G454A						PASS	.	G	MET/VAL	580,804		132,316,244	100.0	85.0	89.0		454	-0.6	0.0	6	dbSNP_86	89	919,2263		126,667,798	no	missense	MICA	NM_001177519.1	21	258,983,1042	AA,AG,GG		28.8812,41.9075,32.8296	probably-damaging	152/333	31378977	1499,3067	692	1591	2283	SO:0001583	missense	100507436	exon3			TGGACAGTGCCCC	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.454G>A	6.37:g.31378977G>A	ENSP00000413079:p.Val152Met	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	800|800	0.3663003663003663|0.3663003663003663	228|228	0.4634146341463415|0.4634146341463415	169|169	0.46685082872928174|0.46685082872928174	160|160	0.27972027972027974|0.27972027972027974	243|243	0.32058047493403696|0.32058047493403696	.|N	0.869|0.869	-0.732690|-0.732690	0.03135|0.03135	0.419075|0.419075	0.288812|0.288812	ENSG00000204520|ENSG00000204520	ENST00000399172|ENST00000364810;ENST00000449934	.|T	.|0.00730	.|5.77	1.41|1.41	-0.635|-0.635	0.11512|0.11512	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00440	.|0.0014	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|D	.|0.53462	.|0.96	.|P	.|0.51550	.|0.673	.|T	.|0.51841	.|-0.8654	.|7	.|0.40728	.|T	.|0.16	.|.	2.6169|2.6169	0.04906|0.04906	0.3636:0.2644:0.372:0.0|0.3636:0.2644:0.372:0.0	rs1051792;rs3192169;rs3819270;rs16897487;rs17845518;rs17858408;rs17885687;rs1051792|rs1051792;rs3192169;rs3819270;rs16897487;rs17845518;rs17858408;rs17885687;rs1051792	.|152	.|Q96QC4	.|.	.|M	-1|152	.|ENSP00000413079:V152M	.|ENSP00000365394:V152M	.|V	+|+	.|1	.|0	MICA|MICA	31486956|31486956	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.136000|0.136000	0.15974|0.15974	-0.189000|-0.189000	0.10482|0.10482	-0.667000|-0.667000	0.03836|0.03836	.|GTG	G|0.653;A|0.347	0.347	strong		0.517	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
CMPK2	129607	hgsc.bcm.edu	37	2	7005236	7005236	+	Missense_Mutation	SNP	G	G	T	rs575313172		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:7005236G>T	ENST00000256722.5	-	1	591	c.592C>A	c.(592-594)Ccc>Acc	p.P198T	CMPK2_ENST00000478738.1_Intron|CMPK2_ENST00000404168.1_Missense_Mutation_p.P198T|CMPK2_ENST00000458098.1_Missense_Mutation_p.P198T	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	198					cellular response to lipopolysaccharide (GO:0071222)|dTDP biosynthetic process (GO:0006233)|dUDP biosynthetic process (GO:0006227)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)|thymidylate kinase activity (GO:0004798)|UMP kinase activity (GO:0033862)			large_intestine(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TGCAGCGGGGGCTCCGGGACG	0.721													G|||	1	0.000199681	0.0008	0.0	5008	,	,		11581	0.0		0.0	False		,,,				2504	0.0				p.P198T		Atlas-SNP	.											.	CMPK2	30	.	0			c.C592A						PASS	.						3.0	5.0	4.0					2																	7005236		1735	3836	5571	SO:0001583	missense	129607	exon1			GCGGGGGCTCCGG		CCDS42648.1, CCDS58695.1, CCDS58696.1	2p25.2	2008-01-25			ENSG00000134326	ENSG00000134326	2.7.4.14		27015	protein-coding gene	gene with protein product	"""cytidylate kinase 2"""	611787				17999954	Standard	NM_207315		Approved	TYKi, UMP-CMPK2	uc002qyo.4	Q5EBM0	OTTHUMG00000151629	ENST00000256722.5:c.592C>A	2.37:g.7005236G>T	ENSP00000256722:p.Pro198Thr	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	12	6	0.5	NM_001256478	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Missense_Mutation	SNP	ENST00000256722.5	37	CCDS42648.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.547309	0.65311	.	.	ENSG00000134326	ENST00000458098;ENST00000256722;ENST00000404168	T	0.57436	0.4	4.43	3.55	0.40652	.	0.061334	0.64402	D	0.000003	T	0.55065	0.1897	L	0.29908	0.895	0.38526	D	0.948847	D;D	0.67145	0.996;0.994	P;P	0.62014	0.897;0.663	T	0.60311	-0.7288	10	0.66056	D	0.02	-21.992	10.2012	0.43084	0.0989:0.0:0.9011:0.0	.	198;198	Q5EBM0-3;Q5EBM0	.;CMPK2_HUMAN	T	198	ENSP00000256722:P198T	ENSP00000256722:P198T	P	-	1	0	CMPK2	6922687	1.000000	0.71417	0.566000	0.28421	0.894000	0.52154	2.696000	0.47052	1.069000	0.40788	0.563000	0.77884	CCC	.	.	none		0.721	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315	
LMNTD1	160492	hgsc.bcm.edu	37	12	25673001	25673001	+	Silent	SNP	C	C	G	rs76419032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25673001C>G	ENST00000282881.6	-	6	893	c.744G>C	c.(742-744)gcG>gcC	p.A248A	IFLTD1_ENST00000458174.2_Silent_p.A269A|IFLTD1_ENST00000445693.1_Silent_p.A185A|IFLTD1_ENST00000413632.2_Silent_p.A229A|IFLTD1_ENST00000539744.1_Silent_p.A151A	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		248	LTD.				cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GGGTGTACCACGCAATGGCCT	0.343													G|||	88	0.0175719	0.0628	0.0072	5008	,	,		13235	0.0		0.0	False		,,,				2504	0.0				p.A269A		Atlas-SNP	.											.	IFLTD1	121	.	0			c.G807C						PASS	.	G	,,,	248,4158	801.2+/-415.6	5,238,1960	79.0	67.0	71.0		555,807,687,744	0.9	1.0	12	dbSNP_132	71	1,8599	818.4+/-406.9	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	,,,	5,239,6259	GG,GC,CC		0.0116,5.6287,1.9145	,,,	185/326,269/410,229/370,248/389	25673001	249,12757	2203	4300	6503	SO:0001819	synonymous_variant	160492	exon7			GTACCACGCAATG																												ENST00000282881.6:c.744G>C	12.37:g.25673001C>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	112	65	0.580357	NM_001145728	B4DL27|B4DY70|Q8IY38	Silent	SNP	ENST00000282881.6	37	CCDS8704.1	20	0.009157509157509158	17	0.034552845528455285	3	0.008287292817679558	0	0.0	0	0.0	G	1.295	-0.606444	0.03717	0.056287	1.16E-4	ENSG00000152936	ENST00000543629	.	.	.	5.05	0.883	0.19177	.	.	.	.	.	T	0.06371	0.0164	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.07654	-1.0761	4	.	.	.	-5.3188	0.7606	0.01006	0.2856:0.1643:0.3812:0.1689	.	.	.	.	L	23	.	.	V	-	1	0	IFLTD1	25564268	1.000000	0.71417	0.983000	0.44433	0.110000	0.19582	0.968000	0.29357	0.060000	0.16281	-1.126000	0.01995	GTG	C|0.981;G|0.019	0.019	strong		0.343	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
ARFGAP3	26286	hgsc.bcm.edu	37	22	43195134	43195134	+	Missense_Mutation	SNP	C	C	T	rs36003980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:43195134C>T	ENST00000263245.5	-	15	1663	c.1444G>A	c.(1444-1446)Gcc>Acc	p.A482T	ARFGAP3_ENST00000429508.2_Missense_Mutation_p.A410T|ARFGAP3_ENST00000437119.2_Missense_Mutation_p.A438T	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	482			A -> T (in dbSNP:rs36003980).		intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						ATGTCGGGGGCGTTGGGCAGC	0.562													C|||	80	0.0159744	0.0575	0.0043	5008	,	,		17224	0.0		0.001	False		,,,				2504	0.0				p.A482T	GBM(58;544 1030 21460 27159 48838)	Atlas-SNP	.											.	ARFGAP3	48	.	0			c.G1444A						PASS	.	C	THR/ALA,THR/ALA	192,4214	120.8+/-158.4	4,184,2015	144.0	126.0	132.0		1312,1444	3.6	0.4	22	dbSNP_126	132	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	ARFGAP3	NM_001142293.1,NM_014570.4	58,58	4,187,6312	TT,TC,CC		0.0349,4.3577,1.4993	benign,benign	438/473,482/517	43195134	195,12811	2203	4300	6503	SO:0001583	missense	26286	exon15			CGGGGGCGTTGGG	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"""ADP-ribosylation factor GTPase activating proteins"""	661	protein-coding gene	gene with protein product		612439	"""ADP-ribosylation factor GTPase activating protein 1"""	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.1444G>A	22.37:g.43195134C>T	ENSP00000263245:p.Ala482Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_014570	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Missense_Mutation	SNP	ENST00000263245.5	37	CCDS14042.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	11.57	1.678342	0.29783	0.043577	3.49E-4	ENSG00000242247	ENST00000263245;ENST00000429508;ENST00000437119	T;T;T	0.07021	3.4;3.23;3.35	4.65	3.63	0.41609	.	0.000000	0.85682	D	0.000000	T	0.01092	0.0036	L	0.48260	1.515	0.53005	D	0.999964	B;B	0.33212	0.066;0.402	B;B	0.20184	0.028;0.027	T	0.31943	-0.9925	10	0.51188	T	0.08	0.0519	11.8638	0.52482	0.0:0.9119:0.0:0.0881	rs36003980	438;482	E9PB03;Q9NP61	.;ARFG3_HUMAN	T	482;410;438	ENSP00000263245:A482T;ENSP00000393959:A410T;ENSP00000388791:A438T	ENSP00000263245:A482T	A	-	1	0	ARFGAP3	41525078	1.000000	0.71417	0.437000	0.26809	0.135000	0.20990	4.958000	0.63660	0.951000	0.37770	-0.137000	0.14449	GCC	C|0.983;T|0.017	0.017	strong		0.562	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570	
MUC6	4588	hgsc.bcm.edu	37	11	1017316	1017316	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017316G>T	ENST00000421673.2	-	31	5535	c.5485C>A	c.(5485-5487)Cca>Aca	p.P1829T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1829	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			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)		GGGTGTGATGGGGTTGGATAG	0.547																																					p.P1829T		Atlas-SNP	.											MUC6_ENST00000421673,right_upper_lobe,carcinoma,+1,2	MUC6	408	2	0			c.C5485A						scavenged	.																																			SO:0001583	missense	4588	exon31			GTGATGGGGTTGG	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.5485C>A	11.37:g.1017316G>T	ENSP00000406861:p.Pro1829Thr	Somatic	1180	17	0.0144068		WXS	Illumina HiSeq	Phase_I	1388	64	0.0461095	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	10.38	1.335327	0.24253	.	.	ENSG00000184956	ENST00000421673	T	0.24723	1.84	3.21	-0.343	0.12632	.	.	.	.	.	T	0.30355	0.0762	L	0.52126	1.63	0.09310	N	1	D	0.54964	0.969	P	0.61477	0.889	T	0.17531	-1.0366	9	0.02654	T	1	.	7.2552	0.26173	0.0:0.2939:0.4065:0.2996	.	1829	Q6W4X9	MUC6_HUMAN	T	1829	ENSP00000406861:P1829T	ENSP00000406861:P1829T	P	-	1	0	MUC6	1007316	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.664000	0.05292	-0.177000	0.10690	0.313000	0.20887	CCA	.	.	none		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
HIST1H2BE	8344	hgsc.bcm.edu	37	6	26184082	26184082	+	Missense_Mutation	SNP	C	C	G	rs61978632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26184082C>G	ENST00000356530.3	+	1	125	c.59C>G	c.(58-60)aCc>aGc	p.T20S		NM_003523.2	NP_003514.2	P62807	H2B1C_HUMAN	histone cluster 1, H2be	20					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(1)	4						AAGGCCGTGACCAAGGCGCAG	0.557													C|||	202	0.0403355	0.1339	0.0216	5008	,	,		19019	0.0		0.002	False		,,,				2504	0.0082				p.T20S		Atlas-SNP	.											.	HIST1H2BE	10	.	0			c.C59G						PASS	.	C	SER/THR	444,3962		21,402,1780	121.0	113.0	116.0		59	5.1	1.0	6	dbSNP_129	116	31,8569		0,31,4269	no	missense	HIST1H2BE	NM_003523.2	58	21,433,6049	GG,GC,CC		0.3605,10.0772,3.6522	benign	20/127	26184082	475,12531	2203	4300	6503	SO:0001583	missense	8344	exon1			CCGTGACCAAGGC	Z80780	CCDS4588.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197697	ENSG00000274290		"""Histones / Replication-dependent"""	4753	protein-coding gene	gene with protein product		602805	"""H2B histone family, member H"", ""histone 1, H2be"""	H2BFH		9119399, 12408966	Standard	NM_003523		Approved	H2B/h, H2B.h	uc003ngt.3	P62807	OTTHUMG00000014427	ENST00000356530.3:c.59C>G	6.37:g.26184082C>G	ENSP00000348924:p.Thr20Ser	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	213	105	0.492958	NM_003523	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000356530.3	37	CCDS4588.1	72	0.03296703296703297	64	0.13008130081300814	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	.	17.23	3.336510	0.60963	0.100772	0.003605	ENSG00000197697	ENST00000356530	T	0.22539	1.95	5.08	5.08	0.68730	.	0.000000	0.35040	U	0.003493	T	0.34308	0.0893	.	.	.	0.25861	P	0.9838228	.	.	.	.	.	.	T	0.09100	-1.0690	6	0.59425	D	0.04	.	17.8237	0.88657	0.0:1.0:0.0:0.0	rs61978632	.	.	.	S	20	ENSP00000348924:T20S	ENSP00000348924:T20S	T	+	2	0	HIST1H2BE	26292061	1.000000	0.71417	1.000000	0.80357	0.377000	0.30045	5.752000	0.68728	2.526000	0.85167	0.603000	0.83216	ACC	C|0.965;G|0.035	0.035	strong		0.557	HIST1H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040090.1	NM_003523	
ITGB3	3690	hgsc.bcm.edu	37	17	45360730	45360730	+	Missense_Mutation	SNP	T	T	C	rs5918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45360730T>C	ENST00000559488.1	+	3	192	c.176T>C	c.(175-177)cTg>cCg	p.L59P	ITGB3_ENST00000571680.1_Missense_Mutation_p.L59P|ITGB3_ENST00000435993.2_Missense_Mutation_p.L12P|ITGB3_ENST00000560629.1_Silent_p.S47S	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	59			L -> P (in alloantigen HPA-1B; dbSNP:rs5918). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:2565345, ECO:0000269|Ref.13}.		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)	GCCCTGCCTCTGGGCTCACCT	0.552													T|||	445	0.0888578	0.0915	0.1023	5008	,	,		19719	0.0089		0.1322	False		,,,				2504	0.1135				p.L59P		Atlas-SNP	.											.	ITGB3	157	.	0			c.T176C	GRCh37	CM890078	ITGB3	M	rs5918	PASS	.	T	PRO/LEU	470,3936	224.6+/-240.7	28,414,1761	61.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	176	-11.8	0.0	17	dbSNP_52	57	1305,7295	257.6+/-281.6	89,1127,3084	yes	missense	ITGB3	NM_000212.2	98	117,1541,4845	CC,CT,TT		15.1744,10.6673,13.6475	benign	59/789	45360730	1775,11231	2203	4300	6503	SO:0001583	missense	3690	exon3			TGCCTCTGGGCTC		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.176T>C	17.37:g.45360730T>C	ENSP00000452786:p.Leu59Pro	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	200	0.09157509157509157	59	0.11991869918699187	35	0.09668508287292818	5	0.008741258741258742	101	0.13324538258575197	T	6.670	0.492238	0.12702	0.106673	0.151744	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.92446	-3.04	5.88	-11.8	0.00035	Integrin beta subunit, N-terminal (2);	1.063610	0.07337	N	0.880144	T	0.02193	0.0068	L	0.43152	1.355	0.58432	P	1.0000000000287557E-6	B	0.10296	0.003	B	0.10450	0.005	T	0.48490	-0.9031	9	0.20519	T	0.43	.	9.9068	0.41381	0.1749:0.5694:0.1433:0.1124	rs5918;rs5918	59	P05106	ITB3_HUMAN	P	59;12	ENSP00000407801:L12P	ENSP00000262017:L59P	L	+	2	0	C17orf57	42715729	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-1.382000	0.02546	-3.995000	0.00083	-1.117000	0.02048	CTG	T|0.884;C|0.116	0.116	strong		0.552	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
TNR	7143	hgsc.bcm.edu	37	1	175306758	175306758	+	Missense_Mutation	SNP	G	G	A	rs61731114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:175306758G>A	ENST00000367674.2	-	19	4148	c.3440C>T	c.(3439-3441)aCt>aTt	p.T1147I	RP3-518E13.2_ENST00000569593.1_RNA|TNR_ENST00000263525.2_Missense_Mutation_p.T1147I			Q92752	TENR_HUMAN	tenascin R	1147	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					CCCACTCAAAGTGTCTCCATT	0.502													G|||	49	0.00978435	0.0303	0.013	5008	,	,		21455	0.0		0.0	False		,,,				2504	0.0				p.T1147I		Atlas-SNP	.											.	TNR	399	.	0			c.C3440T						PASS	.	G	ILE/THR	137,4269	96.7+/-135.4	4,129,2070	58.0	54.0	55.0		3440	5.4	1.0	1	dbSNP_129	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TNR	NM_003285.2	89	4,130,6369	AA,AG,GG		0.0116,3.1094,1.061	benign	1147/1359	175306758	138,12868	2203	4300	6503	SO:0001583	missense	7143	exon19			CTCAAAGTGTCTC	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.3440C>T	1.37:g.175306758G>A	ENSP00000356646:p.Thr1147Ile	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	131	71	0.541985	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	24	0.01098901098901099	20	0.04065040650406504	4	0.011049723756906077	0	0.0	0	0.0	G	22.4	4.278785	0.80692	0.031094	1.16E-4	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.77229	-1.08;-1.08	5.37	5.37	0.77165	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.055231	0.64402	D	0.000001	T	0.47340	0.1440	M	0.62088	1.915	0.58432	D	0.999995	P	0.49253	0.921	B	0.43301	0.415	T	0.69997	-0.4993	10	0.59425	D	0.04	.	13.659	0.62354	0.0:0.0:0.8453:0.1547	.	1147	Q92752	TENR_HUMAN	I	1147;1147;1057	ENSP00000356646:T1147I;ENSP00000263525:T1147I	ENSP00000263525:T1147I	T	-	2	0	TNR	173573381	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	5.037000	0.64170	2.500000	0.84329	0.655000	0.94253	ACT	G|0.989;A|0.011	0.011	strong		0.502	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102469273	102469273	+	Silent	SNP	T	T	C	rs75094258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102469273T>C	ENST00000360184.4	+	23	5018	c.4854T>C	c.(4852-4854)taT>taC	p.Y1618Y		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1618	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TGGGAGAATATCTGGAAAGAG	0.458													T|||	27	0.00539137	0.0197	0.0014	5008	,	,		19492	0.0		0.0	False		,,,				2504	0.0				p.Y1618Y		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.T4854C						PASS	.	T		53,4353	52.9+/-88.7	1,51,2151	70.0	69.0	70.0		4854	4.5	1.0	14	dbSNP_132	70	0,8600		0,0,4300	no	coding-synonymous	DYNC1H1	NM_001376.4		1,51,6451	CC,CT,TT		0.0,1.2029,0.4075		1618/4647	102469273	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon23			AGAATATCTGGAA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.4854T>C	14.37:g.102469273T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			T|0.994;C|0.006	0.006	strong		0.458	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
ABTB2	25841	hgsc.bcm.edu	37	11	34226140	34226140	+	Silent	SNP	G	G	T	rs77165558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34226140G>T	ENST00000435224.2	-	2	1405	c.981C>A	c.(979-981)acC>acA	p.T327T	ABTB2_ENST00000298992.2_Silent_p.T141T|ABTB2_ENST00000530814.1_5'UTR	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	327					cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				ACTGCTCCAGGGTTCGGAGCT	0.637													G|||	142	0.0283546	0.1036	0.0072	5008	,	,		17394	0.0		0.0	False		,,,				2504	0.0				p.T327T		Atlas-SNP	.											ABTB2,NS,carcinoma,-2,1	ABTB2	101	1	0			c.C981A						PASS	.	G		392,4012	193.0+/-218.2	21,350,1831	45.0	43.0	44.0		981	-5.2	1.0	11	dbSNP_132	44	4,8592	3.0+/-9.4	0,4,4294	no	coding-synonymous	ABTB2	NM_145804.2		21,354,6125	TT,TG,GG		0.0465,8.901,3.0462		327/1026	34226140	396,12604	2202	4298	6500	SO:0001819	synonymous_variant	25841	exon2			CTCCAGGGTTCGG	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.981C>A	11.37:g.34226140G>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Silent	SNP	ENST00000435224.2	37	CCDS7890.2																																																																																			G|0.972;T|0.028	0.028	strong		0.637	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804	
KIF17	57576	hgsc.bcm.edu	37	1	21030956	21030956	+	Missense_Mutation	SNP	G	G	T	rs56750936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21030956G>T	ENST00000247986.2	-	5	1417	c.1107C>A	c.(1105-1107)agC>agA	p.S369R	KIF17_ENST00000400463.3_Missense_Mutation_p.S369R|KIF17_ENST00000375044.1_Missense_Mutation_p.S269R			Q9P2E2	KIF17_HUMAN	kinesin family member 17	369			S -> R (in dbSNP:rs56750936).		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)		GGCTGCTGGGGCTCATCTGCT	0.607													G|||	135	0.0269569	0.0961	0.0101	5008	,	,		14173	0.0		0.0	False		,,,				2504	0.001				p.S369R		Atlas-SNP	.											.	KIF17	130	.	0			c.C1107A						PASS	.	G	ARG/SER,ARG/SER	369,4037	188.5+/-214.9	14,341,1848	85.0	73.0	77.0		1107,1107	3.4	1.0	1	dbSNP_129	77	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	KIF17	NM_001122819.1,NM_020816.2	110,110	14,347,6142	TT,TG,GG		0.0698,8.3749,2.8833	benign,benign	369/1029,369/1030	21030956	375,12631	2203	4300	6503	SO:0001583	missense	57576	exon5			GCTGGGGCTCATC	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.1107C>A	1.37:g.21030956G>T	ENSP00000247986:p.Ser369Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	126	121	0.960317	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	G	2.171	-0.389993	0.04932	0.083749	6.98E-4	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986	T;T;T	0.70986	-0.53;-0.44;-0.44	5.26	3.4	0.38934	.	0.959805	0.08472	U	0.940858	T	0.01287	0.0042	N	0.22421	0.69	0.09310	N	1	B;B	0.30406	0.278;0.007	B;B	0.33960	0.173;0.011	T	0.01762	-1.1279	10	0.19590	T	0.45	.	8.9324	0.35680	0.2408:0.0:0.7592:0.0	rs56750936;rs61731590	369;369	Q9P2E2-3;Q9P2E2	.;KIF17_HUMAN	R	269;369;369	ENSP00000364184:S269R;ENSP00000383311:S369R;ENSP00000247986:S369R	ENSP00000247986:S369R	S	-	3	2	KIF17	20903543	0.011000	0.17503	0.984000	0.44739	0.078000	0.17371	0.251000	0.18257	0.733000	0.32492	-0.448000	0.05591	AGC	G|0.968;T|0.032	0.032	strong		0.607	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
EOGT	285203	hgsc.bcm.edu	37	3	69054341	69054341	+	Silent	SNP	T	T	C	rs6781612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:69054341T>C	ENST00000383701.3	-	7	1207	c.465A>G	c.(463-465)agA>agG	p.R155R	EOGT_ENST00000295571.5_Silent_p.R155R|EOGT_ENST00000540955.1_5'UTR|EOGT_ENST00000540764.1_Silent_p.R54R	NM_001278689.1	NP_001265618.1	Q5NDL2	EOGT_HUMAN	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	155					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)	protein N-acetylglucosaminyltransferase activity (GO:0016262)										GATTGGTTGCTCTGCAGTACT	0.353													T|||	1918	0.382987	0.2995	0.3804	5008	,	,		18700	0.5169		0.2873	False		,,,				2504	0.4581				p.R155R		Atlas-SNP	.											.	.	.	.	0			c.A465G						PASS	.	T		1341,3065	444.1+/-347.2	216,909,1078	124.0	124.0	124.0		465	3.7	1.0	3	dbSNP_116	124	2393,6207	398.5+/-346.1	349,1695,2256	no	coding-synonymous	C3orf64	NM_173654.1		565,2604,3334	CC,CT,TT		27.8256,30.4358,28.7098		155/444	69054341	3734,9272	2203	4300	6503	SO:0001819	synonymous_variant	285203	exon7			GGTTGCTCTGCAG	AK091089	CCDS2908.1, CCDS63684.1	3p14.1	2013-10-11	2012-05-21	2012-05-21	ENSG00000163378	ENSG00000163378	2.4.1.255		28526	protein-coding gene	gene with protein product	"""AER61 glycosyltransferase"""	614789	"""chromosome 3 open reading frame 64"""	C3orf64		22310717	Standard	NM_001278689		Approved	AER61, FLJ33770	uc003dnk.3	Q5NDL2	OTTHUMG00000156279	ENST00000383701.3:c.465A>G	3.37:g.69054341T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_173654	A8K2U1|B4DFH5|L7X1M5|Q6MZY0|Q6P985|Q6ZTV0	Silent	SNP	ENST00000383701.3	37																																																																																				T|0.701;C|0.299	0.299	strong		0.353	EOGT-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000343722.1	NM_173654	
FRAS1	80144	hgsc.bcm.edu	37	4	79396610	79396610	+	Silent	SNP	G	G	A	rs79849142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79396610G>A	ENST00000264895.6	+	54	8141	c.7701G>A	c.(7699-7701)aaG>aaA	p.K2567K		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2567	Calx-beta 1.				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						TCAGTGAGAAGGCAGGGTCTG	0.502													G|||	149	0.0297524	0.1074	0.0101	5008	,	,		22558	0.0		0.0	False		,,,				2504	0.0				p.K2567K		Atlas-SNP	.											.	FRAS1	779	.	0			c.G7701A						PASS	.	G		324,3850		17,290,1780	117.0	129.0	125.0		7701	1.3	1.0	4	dbSNP_132	125	3,8441		0,3,4219	no	coding-synonymous	FRAS1	NM_025074.6		17,293,5999	AA,AG,GG		0.0355,7.7623,2.5915		2567/4013	79396610	327,12291	2087	4222	6309	SO:0001819	synonymous_variant	80144	exon54			TGAGAAGGCAGGG	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.7701G>A	4.37:g.79396610G>A		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	220	110	0.5	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	G	9.007	0.981435	0.18812	0.077623	3.55E-4	ENSG00000138759	ENST00000512123	.	.	.	5.44	1.34	0.21922	.	.	.	.	.	T	0.02970	0.0088	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03761	-1.1006	4	.	.	.	.	1.7426	0.02955	0.3312:0.1357:0.4093:0.1237	.	.	.	.	S	796	.	.	G	+	1	0	FRAS1	79615634	0.990000	0.36364	0.999000	0.59377	0.994000	0.84299	0.287000	0.18920	0.212000	0.20703	0.591000	0.81541	GGC	G|0.984;A|0.016	0.016	strong		0.502	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PCDHA8	56140	hgsc.bcm.edu	37	5	140222430	140222430	+	Missense_Mutation	SNP	T	T	G	rs6873763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140222430T>G	ENST00000531613.1	+	1	1524	c.1524T>G	c.(1522-1524)atT>atG	p.I508M	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.I508M|PCDHA7_ENST00000525929.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	508	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(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)			CGAGCTACATTTCGGTGCACA	0.687													.|||	350	0.0698882	0.2564	0.0144	5008	,	,		12674	0.0		0.001	False		,,,				2504	0.0				p.I508M		Atlas-SNP	.											.	PCDHA8	366	.	0			c.T1524G						PASS	.	T	,,,,,,,MET/ILE,,,MET/ILE	994,3394	710.8+/-407.9	169,656,1369	62.0	70.0	67.0		,,,,,,,1524,,,1524	2.8	1.0	5	dbSNP_116	67	4,8526	800.3+/-407.4	0,4,4261	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	,,,,,,,10,,,10	169,660,5630	GG,GT,TT		0.0469,22.6527,7.7257	,,,,,,,,,,	,,,,,,,508/951,,,508/815	140222430	998,11920	2194	4265	6459	SO:0001583	missense	56140	exon1			CTACATTTCGGTG	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.1524T>G	5.37:g.140222430T>G	ENSP00000434655:p.Ile508Met	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	287	156	0.543554	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	108	0.04945054945054945	101	0.20528455284552846	7	0.019337016574585635	0	0.0	0	0.0	G	11.04	1.520541	0.27211	0.226527	4.69E-4	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.61274	0.12;0.12	3.72	2.85	0.33270	Cadherin (4);Cadherin-like (1);	0.000000	0.33199	U	0.005173	T	0.00073	0.0002	M	0.77486	2.375	0.43122	P	0.005152999999999963	P;P	0.45240	0.473;0.854	P;P	0.60068	0.868;0.729	T	0.06303	-1.0834	9	0.87932	D	0	.	8.018	0.30393	0.0:0.2626:0.4599:0.2775	rs6873763	508;508	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	M	508	ENSP00000434655:I508M;ENSP00000367363:I508M	ENSP00000367363:I508M	I	+	3	3	PCDHA8	140202614	0.030000	0.19436	1.000000	0.80357	0.083000	0.17756	-0.581000	0.05820	0.682000	0.31407	-0.741000	0.03529	ATT	T|0.933;G|0.067	0.067	strong		0.687	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
AGRN	375790	hgsc.bcm.edu	37	1	985900	985900	+	Silent	SNP	C	C	T	rs17160776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:985900C>T	ENST00000379370.2	+	29	5120	c.5070C>T	c.(5068-5070)ttC>ttT	p.F1690F		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1690	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		AGGGGGACTTCGTGTCGCTGG	0.692													C|||	224	0.0447284	0.1475	0.0173	5008	,	,		13702	0.0		0.0109	False		,,,				2504	0.0061				p.F1690F		Atlas-SNP	.											.	AGRN	110	.	0			c.C5070T						PASS	.	C		537,3869	231.7+/-245.5	40,457,1706	37.0	46.0	43.0		5070	-4.1	1.0	1	dbSNP_123	43	72,8524	41.2+/-98.3	0,72,4226	no	coding-synonymous	AGRN	NM_198576.3		40,529,5932	TT,TC,CC		0.8376,12.1879,4.6839		1690/2046	985900	609,12393	2203	4298	6501	SO:0001819	synonymous_variant	375790	exon29			GGACTTCGTGTCG	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.5070C>T	1.37:g.985900C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	154	66	0.428571	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			C|0.953;T|0.047	0.047	strong		0.692	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
PODN	127435	hgsc.bcm.edu	37	1	53527948	53527948	+	Silent	SNP	T	T	G	rs7513730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53527948T>G	ENST00000312553.5	+	1	64	c.57T>G	c.(55-57)ccT>ccG	p.P19P	PODN_ENST00000395871.2_Silent_p.P19P|PODN_ENST00000371500.3_5'UTR	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	0					negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GCGTTCGGCCTGTGGGGCGCC	0.736													G|||	2040	0.407348	0.8154	0.3934	5008	,	,		5598	0.3819		0.1024	False		,,,				2504	0.2055				p.P19P		Atlas-SNP	.											.	PODN	86	.	0			c.T57G						PASS	.	G	,,,	2348,1734		691,966,384	5.0	8.0	7.0		,,57,57	-5.1	0.0	1	dbSNP_116	7	849,7315		54,741,3287	no	utr-5,utr-5,coding-synonymous,coding-synonymous	PODN	NM_001199080.1,NM_001199081.1,NM_001199082.1,NM_153703.4	,,,	745,1707,3671	GG,GT,TT		10.3993,42.4792,26.1065	,,,	,,19/520,19/662	53527948	3197,9049	2041	4082	6123	SO:0001819	synonymous_variant	127435	exon1			TCGGCCTGTGGGG	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.57T>G	1.37:g.53527948T>G		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	26	25	0.961538	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Silent	SNP	ENST00000312553.5	37	CCDS573.1																																																																																			T|0.628;G|0.372	0.372	strong		0.736	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703	
TMPRSS11E	28983	hgsc.bcm.edu	37	4	69337325	69337325	+	Missense_Mutation	SNP	C	C	G	rs2603188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:69337325C>G	ENST00000305363.4	+	5	538	c.474C>G	c.(472-474)caC>caG	p.H158Q		NM_014058.3	NP_054777.2	Q9UL52	TM11E_HUMAN	transmembrane protease, serine 11E	158	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.			H -> Q (in Ref. 3; AC019173). {ECO:0000305}.	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						TAGATCCTCACTCAGTTAAAA	0.313													G|||	468	0.0934505	0.1248	0.0778	5008	,	,		13908	0.004		0.1551	False		,,,				2504	0.091				p.H158Q		Atlas-SNP	.											.	TMPRSS11E	40	.	0			c.C474G						PASS	.	G	GLN/HIS	470,3936	776.0+/-414.1	24,422,1757	102.0	107.0	105.0		474	-10.9	0.0	4	dbSNP_100	105	1212,7386	759.5+/-407.6	85,1042,3172	yes	missense	TMPRSS11E	NM_014058.3	24	109,1464,4929	GG,GC,CC		14.0963,10.6673,12.9345	benign	158/424	69337325	1682,11322	2203	4299	6502	SO:0001583	missense	28983	exon5			TCCTCACTCAGTT	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.474C>G	4.37:g.69337325C>G	ENSP00000307519:p.His158Gln	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	325	158	0.486154	NM_014058	A6NL71|Q14DC8|Q6UW31	Missense_Mutation	SNP	ENST00000305363.4	37	CCDS33993.1	198	0.09065934065934066	56	0.11382113821138211	27	0.07458563535911603	1	0.0017482517482517483	114	0.1503957783641161	G	0.664	-0.804394	0.02819	0.106673	0.140963	ENSG00000087128	ENST00000305363	T	0.32272	1.46	5.83	-10.9	0.00192	.	0.725069	0.12235	N	0.487060	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23226	-1.0194	9	0.27082	T	0.32	.	9.7094	0.40236	0.2174:0.3911:0.3915:0.0	.	158	Q9UL52	TM11E_HUMAN	Q	158	ENSP00000307519:H158Q	ENSP00000307519:H158Q	H	+	3	2	TMPRSS11E	69019920	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-2.211000	0.01226	-1.724000	0.01373	-2.686000	0.00141	CAC	C|0.887;G|0.113	0.113	strong		0.313	TMPRSS11E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360584.1	NM_014058	
DUOX2	50506	hgsc.bcm.edu	37	15	45392382	45392382	+	Missense_Mutation	SNP	T	T	C	rs79393107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45392382T>C	ENST00000603300.1	-	24	3252	c.3050A>G	c.(3049-3051)gAg>gGg	p.E1017G	DUOX2_ENST00000389039.6_Missense_Mutation_p.E1017G	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1017	Interaction with TXNDC11. {ECO:0000250}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CTGCATCTTCTCTTGCAGCGC	0.602													T|||	183	0.0365415	0.1293	0.0173	5008	,	,		20832	0.0		0.0	False		,,,				2504	0.0				p.E1017G		Atlas-SNP	.											.	DUOX2	137	.	0			c.A3050G						PASS	.	T	GLY/GLU	524,3872	240.6+/-251.3	40,444,1714	78.0	68.0	72.0		3050	5.4	1.0	15	dbSNP_131	72	3,8593	3.0+/-9.4	0,3,4295	yes	missense	DUOX2	NM_014080.4	98	40,447,6009	CC,CT,TT		0.0349,11.9199,4.0563	probably-damaging	1017/1549	45392382	527,12465	2198	4298	6496	SO:0001583	missense	50506	exon24			ATCTTCTCTTGCA	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.3050A>G	15.37:g.45392382T>C	ENSP00000475084:p.Glu1017Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	58	0.026556776556776556	51	0.10365853658536585	7	0.019337016574585635	0	0.0	0	0.0	T	25.5	4.644005	0.87859	0.119199	3.49E-4	ENSG00000140279	ENST00000389039	.	.	.	5.45	5.45	0.79879	.	0.105054	0.64402	D	0.000003	T	0.02727	0.0082	M	0.76328	2.33	0.58432	D	0.999998	D	0.52996	0.957	P	0.52823	0.71	T	0.06698	-1.0812	9	0.34782	T	0.22	-29.5989	14.7059	0.69189	0.0:0.0:0.0:1.0	.	1017	Q9NRD8	DUOX2_HUMAN	G	1017	.	ENSP00000373691:E1017G	E	-	2	0	DUOX2	43179674	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	3.726000	0.54977	2.080000	0.62538	0.460000	0.39030	GAG	T|0.960;C|0.040	0.040	strong		0.602	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
TXNDC2	84203	hgsc.bcm.edu	37	18	9888027	9888027	+	Silent	SNP	C	C	T	rs11664080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9888027C>T	ENST00000306084.6	+	2	1750	c.1551C>T	c.(1549-1551)tgC>tgT	p.C517C	TXNDC2_ENST00000357775.5_Silent_p.C450C|TXNDC2_ENST00000536353.2_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	517	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				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						TGAGAGAGTGCGCCATCATGT	0.488													C|||	314	0.0626997	0.0378	0.0591	5008	,	,		19964	0.0218		0.0716	False		,,,				2504	0.1319				p.C517C		Atlas-SNP	.											.	TXNDC2	168	.	0			c.C1551T						PASS	.	C	,	183,4223	117.5+/-155.4	3,177,2023	92.0	79.0	83.0		1551,1350	-4.6	0.0	18	dbSNP_120	83	668,7932	167.8+/-219.5	28,612,3660	no	coding-synonymous,coding-synonymous	TXNDC2	NM_001098529.1,NM_032243.5	,	31,789,5683	TT,TC,CC		7.7674,4.1534,6.5431	,	517/554,450/487	9888027	851,12155	2203	4300	6503	SO:0001819	synonymous_variant	84203	exon2			AGAGTGCGCCATC	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.1551C>T	18.37:g.9888027C>T		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	243	127	0.522634	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			C|0.941;T|0.059	0.059	strong		0.488	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
MUC4	4585	hgsc.bcm.edu	37	3	195511983	195511983	+	Silent	SNP	A	A	G	rs200576215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511983A>G	ENST00000463781.3	-	2	6927	c.6468T>C	c.(6466-6468)ggT>ggC	p.G2156G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.G2156G	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)		AGGTGGCGTGACCTGTGGATA	0.582																																					p.G2156G		Atlas-SNP	.											.	MUC4	1505	.	0			c.T6468C						PASS	.						13.0	10.0	11.0					3																	195511983		668	1512	2180	SO:0001819	synonymous_variant	4585	exon2			GGCGTGACCTGTG	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.6468T>C	3.37:g.195511983A>G		Somatic	453	1	0.00220751		WXS	Illumina HiSeq	Phase_I	280	79	0.282143	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|0.949;G|0.051	0.051	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PKHD1	5314	hgsc.bcm.edu	37	6	51491866	51491866	+	Missense_Mutation	SNP	A	A	T	rs2661488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:51491866A>T	ENST00000371117.3	-	66	11989	c.11714T>A	c.(11713-11715)aTt>aAt	p.I3905N		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3905			I -> N (in dbSNP:rs2661488).		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)					GTGGATATGAATATTTTGATT	0.413													T|||	193	0.0385383	0.0983	0.0259	5008	,	,		18093	0.0		0.0229	False		,,,				2504	0.0225				p.I3905N		Atlas-SNP	.											.	PKHD1	927	.	0			c.T11714A						PASS	.	T	ASN/ILE	406,4000	789.0+/-415.0	20,366,1817	260.0	260.0	260.0		11714	-1.6	0.0	6	dbSNP_100	260	218,8382	809.6+/-407.2	3,212,4085	yes	missense	PKHD1	NM_138694.3	149	23,578,5902	TT,TA,AA		2.5349,9.2147,4.7978	benign	3905/4075	51491866	624,12382	2203	4300	6503	SO:0001583	missense	5314	exon66			ATATGAATATTTT	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.11714T>A	6.37:g.51491866A>T	ENSP00000360158:p.Ile3905Asn	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	236	127	0.538136	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	64	0.029304029304029304	35	0.07113821138211382	9	0.024861878453038673	0	0.0	20	0.026385224274406333	T	0.036	-1.306934	0.01353	0.092147	0.025349	ENSG00000170927	ENST00000371117	D	0.85013	-1.93	5.19	-1.65	0.08291	.	0.956151	0.08677	N	0.910025	T	0.19765	0.0475	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06250	-1.0837	9	0.02654	T	1	.	1.6951	0.02860	0.1334:0.3104:0.1383:0.4179	rs2661488;rs52834645;rs2661488	3905	P08F94	PKHD1_HUMAN	N	3905	ENSP00000360158:I3905N	ENSP00000360158:I3905N	I	-	2	0	PKHD1	51599825	0.076000	0.21285	0.000000	0.03702	0.001000	0.01503	-0.012000	0.12699	-0.625000	0.05604	-2.677000	0.00143	ATT	A|0.959;T|0.041	0.041	strong		0.413	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
DHX37	57647	hgsc.bcm.edu	37	12	125441359	125441359	+	Silent	SNP	T	T	C	rs10773127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125441359T>C	ENST00000308736.2	-	18	2429	c.2331A>G	c.(2329-2331)acA>acG	p.T777T	DHX37_ENST00000544745.1_Silent_p.T564T	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	777							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.T777T(1)		breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		CCACGGGGAATGTGGCCATTG	0.642													C|||	1904	0.380192	0.8533	0.2536	5008	,	,		19284	0.2034		0.2058	False		,,,				2504	0.1922				p.T777T		Atlas-SNP	.											DHX37,rectum,carcinoma,0,1	DHX37	114	1	1	Substitution - coding silent(1)	large_intestine(1)	c.A2331G						PASS	.	C		3352,1054	382.3+/-324.4	1296,760,147	95.0	93.0	93.0		2331	-3.0	1.0	12	dbSNP_120	93	1821,6779	729.8+/-406.7	189,1443,2668	no	coding-synonymous	DHX37	NM_032656.3		1485,2203,2815	CC,CT,TT		21.1744,23.9219,39.774		777/1158	125441359	5173,7833	2203	4300	6503	SO:0001819	synonymous_variant	57647	exon18			GGGGAATGTGGCC	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.2331A>G	12.37:g.125441359T>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	116	46	0.396552	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1																																																																																			T|0.608;C|0.392	0.392	strong		0.642	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
PRSS1	5644	hgsc.bcm.edu	37	7	142460764	142460764	+	Missense_Mutation	SNP	G	G	A	rs200902389		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142460764G>A	ENST00000311737.7	+	5	643	c.637G>A	c.(637-639)Gtt>Att	p.V213I	PRSS1_ENST00000486171.1_Missense_Mutation_p.V227I	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	213	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	GCTCCAAGGAGTTGTCTCCTG	0.507																																					p.V213I		Atlas-SNP	.											PRSS1,NS,carcinoma,0,1	PRSS1	68	1	0			c.G637A						scavenged	.																																			SO:0001583	missense	5644	exon5			CAAGGAGTTGTCT	M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.637G>A	7.37:g.142460764G>A	ENSP00000308720:p.Val213Ile	Somatic	392	2	0.00510204		WXS	Illumina HiSeq	Phase_I	429	12	0.027972	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Missense_Mutation	SNP	ENST00000311737.7	37	CCDS5872.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.715405	0.00093	.	.	ENSG00000204983	ENST00000486171;ENST00000311737;ENST00000529243	D;D	0.92495	-3.05;-3.05	3.18	-2.69	0.06022	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.441828	0.26891	N	0.021970	T	0.73860	0.3641	N	0.04387	-0.21	0.19575	N	0.999967	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.003	T	0.65500	-0.6153	10	0.02654	T	1	.	8.608	0.33784	0.6977:0.0:0.3023:0.0	.	227;213	E7EQ64;P07477	.;TRY1_HUMAN	I	227;213;203	ENSP00000417854:V227I;ENSP00000308720:V213I	ENSP00000308720:V213I	V	+	1	0	PRSS1	142140338	0.000000	0.05858	0.014000	0.15608	0.002000	0.02628	-0.180000	0.09754	-0.675000	0.05246	-1.152000	0.01820	GTT	.	.	weak		0.507	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		
ESX1	80712	hgsc.bcm.edu	37	X	103495007	103495007	+	Missense_Mutation	SNP	G	G	C	rs78191648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:103495007G>C	ENST00000372588.4	-	4	1206	c.1123C>G	c.(1123-1125)Ctg>Gtg	p.L375V		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	375	15 X 9 AA tandem repeats of P-P-x-x-P-x- P-P-x.				labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						CTGGGTGGCAGAGGCGCCATG	0.667													T|||	187	0.0495364	0.1346	0.0101	3775	,	,		7462	0.0		0.001	False		,,,				2504	0.001				p.L375V	Pancreas(200;1705 2227 25194 28471 45274)	Atlas-SNP	.											.	ESX1	57	.	0			c.C1123G						PASS	.	T	VAL/LEU	553,3282		42,388,81,1202,490	36.0	34.0	35.0		1123	-8.3	0.0	X	dbSNP_131	35	7,6721		0,7,0,2421,1872	yes	missense	ESX1	NM_153448.3	32	42,395,81,3623,2362	CC,CG,C,GG,G		0.104,14.4198,5.3015	benign	375/407	103495007	560,10003	2203	4300	6503	SO:0001583	missense	80712	exon4			GTGGCAGAGGCGC	AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"""Homeoboxes / PRD class"""	14865	protein-coding gene	gene with protein product		300154	"""extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"""	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.1123C>G	X.37:g.103495007G>C	ENSP00000361669:p.Leu375Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	CCDS14516.1	75	0.045207956600361664	55	0.1206140350877193	1	0.002777777777777778	0	0.0	0	0.0	T	0.004	-2.247286	0.00271	0.144198	0.00104	ENSG00000123576	ENST00000372588	T	0.73152	-0.72	4.14	-8.28	0.01013	.	.	.	.	.	T	0.00356	0.0011	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10706	-1.0618	8	0.42905	T	0.14	0.5915	7.4597	0.27287	0.1697:0.6473:0.0849:0.0981	.	375	Q8N693	ESX1_HUMAN	V	375	ENSP00000361669:L375V	ENSP00000361669:L375V	L	-	1	2	ESX1	103381663	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.954000	0.00166	-3.304000	0.00192	-2.542000	0.00179	CTG	G|0.948;C|0.052	0.052	strong		0.667	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448	
PPP1R26	9858	hgsc.bcm.edu	37	9	138379059	138379059	+	Silent	SNP	G	G	T	rs3748198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138379059G>T	ENST00000356818.2	+	4	3252	c.2703G>T	c.(2701-2703)ctG>ctT	p.L901L	PPP1R26_ENST00000604351.1_Silent_p.L901L|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Silent_p.L901L|PPP1R26_ENST00000605286.1_Silent_p.L901L|PPP1R26_ENST00000401470.3_Silent_p.L901L	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	901					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TCCCACATCTGGCCGAAGGGC	0.711													G|||	908	0.18131	0.1029	0.2075	5008	,	,		15467	0.4464		0.0328	False		,,,				2504	0.1483				p.L901L		Atlas-SNP	.											.	.	.	.	0			c.G2703T						PASS	.	G		347,3887		10,327,1780	31.0	39.0	36.0		2703	-2.7	0.0	9	dbSNP_107	36	254,8026		4,246,3890	no	coding-synonymous	KIAA0649	NM_014811.3		14,573,5670	TT,TG,GG		3.0676,8.1956,4.8026		901/1210	138379059	601,11913	2117	4140	6257	SO:0001819	synonymous_variant	9858	exon4			ACATCTGGCCGAA	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.2703G>T	9.37:g.138379059G>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	49	0.690141	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																			G|0.858;T|0.142	0.142	strong		0.711	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
RFPL4A	342931	hgsc.bcm.edu	37	19	56273293	56273293	+	Missense_Mutation	SNP	G	G	A	rs2019946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	790	0	0		WXS	Illumina HiSeq	Phase_I	897	109	0.121516	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	
FUCA2	2519	hgsc.bcm.edu	37	6	143823157	143823157	+	Missense_Mutation	SNP	T	T	C	rs3762002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:143823157T>C	ENST00000002165.6	-	5	1121	c.1066A>G	c.(1066-1068)Atg>Gtg	p.M356V	RP1-20N2.6_ENST00000590703.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|RP1-20N2.6_ENST00000415586.1_RNA|RP1-20N2.6_ENST00000591189.1_RNA|FUCA2_ENST00000367585.1_5'UTR|RP1-20N2.6_ENST00000589489.1_RNA|FUCA2_ENST00000438118.2_3'UTR|RP1-20N2.6_ENST00000593045.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000593175.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	356			M -> V (in dbSNP:rs3762002). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743}.		fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		CAGGACCCCATTTGCCTCAGT	0.448													T|||	1164	0.232428	0.3396	0.1859	5008	,	,		14611	0.1687		0.2247	False		,,,				2504	0.1943				p.M356V		Atlas-SNP	.											.	FUCA2	28	.	0			c.A1066G						PASS	.	T	VAL/MET	1408,2998	462.4+/-353.2	231,946,1026	96.0	94.0	95.0		1066	6.0	1.0	6	dbSNP_107	95	1945,6655	343.2+/-324.8	216,1513,2571	yes	missense	FUCA2	NM_032020.4	21	447,2459,3597	CC,CT,TT		22.6163,31.9564,25.7804	benign	356/468	143823157	3353,9653	2203	4300	6503	SO:0001583	missense	2519	exon5			ACCCCATTTGCCT	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1066A>G	6.37:g.143823157T>C	ENSP00000002165:p.Met356Val	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	504	0.23076923076923078	164	0.3333333333333333	60	0.16574585635359115	104	0.18181818181818182	176	0.23218997361477572	T	11.97	1.797932	0.31777	0.319564	0.226163	ENSG00000001036	ENST00000002165;ENST00000451668	T;T	0.56941	0.43;0.43	5.98	5.98	0.97165	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.074659	0.85682	D	0.000000	T	0.23370	0.0565	L	0.31420	0.93	0.09310	P	1.0	B;B	0.23128	0.08;0.044	B;B	0.24006	0.05;0.034	T	0.11227	-1.0596	9	0.20046	T	0.44	-24.5233	12.26	0.54645	0.0:0.0673:0.0:0.9327	rs3762002;rs17849713;rs17854672;rs52821129;rs60454233;rs3762002	35;356	Q7Z6V2;Q9BTY2	.;FUCO2_HUMAN	V	356;35	ENSP00000002165:M356V;ENSP00000398119:M35V	ENSP00000002165:M356V	M	-	1	0	FUCA2	143864850	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.814000	0.62627	2.288000	0.76882	0.528000	0.53228	ATG	T|0.749;C|0.251	0.251	strong		0.448	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
CT47B1	643311	hgsc.bcm.edu	37	X	120008979	120008979	+	Silent	SNP	T	T	C	rs871733		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:120008979T>C	ENST00000371311.3	-	1	800	c.546A>G	c.(544-546)ccA>ccG	p.P182P		NM_001145718.1	NP_001139190.1	P0C2W7	CT47B_HUMAN	cancer/testis antigen family 47, member B1	182										breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|lung(9)|ovary(1)|skin(1)	22						CCTCGCCTTCTGGGGCTGCAG	0.711													N|||	2563	0.67894	0.7209	0.4524	3775	,	,		9784	0.5278		0.3897	False		,,,				2504	0.3804				p.P182P		Atlas-SNP	.											.	CT47B1	67	.	0			c.A546G						PASS	.	C		1084,125		424,86,150,7,25	30.0	29.0	30.0		546	-2.5	0.0	X	dbSNP_86	30	1169,1220		188,394,399,218,390	no	coding-synonymous	CT47B1	NM_001145718.1		612,480,549,225,415	CC,CT,C,TT,T		48.9326,10.3391,37.3819		182/300	120008979	2253,1345	692	1589	2281	SO:0001819	synonymous_variant	643311	exon1			GCCTTCTGGGGCT		CCDS48161.1	Xq24	2014-05-06	2011-03-24		ENSG00000236446	ENSG00000236446			33293	protein-coding gene	gene with protein product	"""cancer/testis CT47 family, member 13"""	300790				16382448	Standard	NM_001145718		Approved	CT47.13	uc011muc.2	P0C2W7	OTTHUMG00000187483	ENST00000371311.3:c.546A>G	X.37:g.120008979T>C		Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_001145718	A6NM97	Silent	SNP	ENST00000371311.3	37	CCDS48161.1																																																																																			T|0.345;C|0.655	0.655	strong		0.711	CT47B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058121.1	NM_001145718	
CYP1B1	1545	hgsc.bcm.edu	37	2	38301803	38301803	+	Silent	SNP	C	C	G	rs9341249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:38301803C>G	ENST00000260630.3	-	2	1130	c.729G>C	c.(727-729)gtG>gtC	p.V243V	CYP1B1-AS1_ENST00000431999.1_RNA|CYP1B1_ENST00000407341.1_Silent_p.V243V|CYP1B1-AS1_ENST00000589303.1_RNA|CYP1B1_ENST00000494864.1_Intron	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	243					angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	GCCAGGGCATCACGTCCACCA	0.627													c|||	383	0.0764776	0.2678	0.0159	5008	,	,		16495	0.0129		0.003	False		,,,				2504	0.002				p.V243V		Atlas-SNP	.											.	CYP1B1	39	.	0			c.G729C						PASS	.	A		917,3489	333.9+/-303.2	93,731,1379	43.0	41.0	42.0		729	1.5	1.0	2	dbSNP_119	42	21,8579	12.6+/-44.7	0,21,4279	yes	coding-synonymous	CYP1B1	NM_000104.3		93,752,5658	GG,GC,CC		0.2442,20.8125,7.2121		243/544	38301803	938,12068	2203	4300	6503	SO:0001819	synonymous_variant	1545	exon2			GGGCATCACGTCC	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"""Cytochrome P450s"""	2597	protein-coding gene	gene with protein product		601771	"""cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"""	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.729G>C	2.37:g.38301803C>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_000104	Q5TZW8|Q93089|Q9H316	Silent	SNP	ENST00000260630.3	37	CCDS1793.1																																																																																			C|0.934;G|0.066	0.066	strong		0.627	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104	
ABCA13	154664	hgsc.bcm.edu	37	7	48313757	48313757	+	Silent	SNP	G	G	A	rs77190804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:48313757G>A	ENST00000435803.1	+	17	4518	c.4494G>A	c.(4492-4494)aaG>aaA	p.K1498K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1498					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						ATTCCACAAAGCAAGTAAGGA	0.289													G|||	482	0.096246	0.143	0.0548	5008	,	,		17436	0.1498		0.0477	False		,,,				2504	0.0573				p.K1498K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G4494A						PASS	.	G		395,3233		24,347,1443	26.0	27.0	27.0		4494	1.3	0.4	7	dbSNP_131	27	469,7645		12,445,3600	no	coding-synonymous	ABCA13	NM_152701.3		36,792,5043	AA,AG,GG		5.7801,10.8875,7.3582		1498/5059	48313757	864,10878	1814	4057	5871	SO:0001819	synonymous_variant	154664	exon17			CACAAAGCAAGTA	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.4494G>A	7.37:g.48313757G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	132	55	0.416667	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			G|0.901;A|0.099	0.099	strong		0.289	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
THBS1	7057	hgsc.bcm.edu	37	15	39885301	39885301	+	Silent	SNP	T	T	C	rs2228263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39885301T>C	ENST00000260356.5	+	18	3033	c.2868T>C	c.(2866-2868)gaT>gaC	p.D956D	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	956					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		GTGAGACCGATTTCCGCCGAT	0.502													T|||	574	0.114617	0.2224	0.1037	5008	,	,		20624	0.002		0.159	False		,,,				2504	0.047				p.D956D		Atlas-SNP	.											.	THBS1	106	.	0			c.T2868C						PASS	.	T		920,3480	351.3+/-311.2	108,704,1388	81.0	69.0	73.0		2868	2.2	1.0	15	dbSNP_98	73	1461,7133	277.5+/-292.9	110,1241,2946	no	coding-synonymous	THBS1	NM_003246.2		218,1945,4334	CC,CT,TT		17.0002,20.9091,18.3238		956/1171	39885301	2381,10613	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon18			GACCGATTTCCGC		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2868T>C	15.37:g.39885301T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			T|0.841;C|0.159	0.159	strong		0.502	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
SLC12A5	57468	hgsc.bcm.edu	37	20	44680412	44680412	+	Silent	SNP	C	C	T	rs3746522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44680412C>T	ENST00000454036.2	+	18	2398	c.2349C>T	c.(2347-2349)tcC>tcT	p.S783S	SLC12A5_ENST00000243964.3_Silent_p.S760S	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	783					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	TGATCCAGTCCGGGGGCCTCG	0.592													C|||	866	0.172923	0.0121	0.1816	5008	,	,		13847	0.3393		0.2197	False		,,,				2504	0.1646				p.S783S		Atlas-SNP	.											SLC12A5,caecum,carcinoma,0,1	SLC12A5	181	1	0			c.C2349T						PASS	.	C	,	193,4213	120.0+/-157.7	6,181,2016	86.0	83.0	84.0		2349,2280	-8.4	0.8	20	dbSNP_107	84	1978,6622	347.9+/-326.8	223,1532,2545	no	coding-synonymous,coding-synonymous	SLC12A5	NM_001134771.1,NM_020708.4	,	229,1713,4561	TT,TC,CC		23.0,4.3804,16.6923	,	783/1140,760/1117	44680412	2171,10835	2203	4300	6503	SO:0001819	synonymous_variant	57468	exon18			CCAGTCCGGGGGC	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"""Solute carriers"""	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.2349C>T	20.37:g.44680412C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	37	CCDS46610.1																																																																																			C|0.824;T|0.176	0.176	strong		0.592	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
TECTA	7007	hgsc.bcm.edu	37	11	121016818	121016818	+	Silent	SNP	G	G	A	rs12275038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:121016818G>A	ENST00000392793.1	+	12	4369	c.4098G>A	c.(4096-4098)acG>acA	p.T1366T	TECTA_ENST00000478058.1_3'UTR|TECTA_ENST00000264037.2_Silent_p.T1366T			O75443	TECTA_HUMAN	tectorin alpha	1366					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)		GGAATTACACGTCCTGCAGTG	0.572													G|||	1180	0.235623	0.5499	0.1686	5008	,	,		21213	0.006		0.2097	False		,,,				2504	0.1217				p.T1366T		Atlas-SNP	.											.	TECTA	329	.	0			c.G4098A						PASS	.	G		1993,2385		473,1047,669	59.0	48.0	51.0		4098	-7.5	0.9	11	dbSNP_120	51	1766,6776		195,1376,2700	no	coding-synonymous	TECTA	NM_005422.2		668,2423,3369	AA,AG,GG		20.6743,45.5231,29.0944		1366/2156	121016818	3759,9161	2189	4271	6460	SO:0001819	synonymous_variant	7007	exon11			TTACACGTCCTGC	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.4098G>A	11.37:g.121016818G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_005422		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																			G|0.722;A|0.278	0.278	strong		0.572	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
BMP10	27302	hgsc.bcm.edu	37	2	69093312	69093312	+	Silent	SNP	A	A	G	rs2231344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69093312A>G	ENST00000295379.1	-	2	884	c.726T>C	c.(724-726)gaT>gaC	p.D242D		NM_014482.1	NP_055297.1	O95393	BMP10_HUMAN	bone morphogenetic protein 10	242					activin receptor signaling pathway (GO:0032924)|adult heart development (GO:0007512)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heart trabecula formation (GO:0060347)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction (GO:0055117)|sarcomere organization (GO:0045214)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Z disc (GO:0030018)	hormone activity (GO:0005179)|receptor serine/threonine kinase binding (GO:0033612)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(15)|ovary(2)	27						GGGCACTGGTATCTATTTCTA	0.488													G|||	710	0.141773	0.3048	0.0908	5008	,	,		21484	0.1151		0.0606	False		,,,				2504	0.0685				p.D242D		Atlas-SNP	.											.	BMP10	70	.	0			c.T726C						PASS	.	G		1168,3238	713.3+/-408.2	158,852,1193	106.0	95.0	98.0		726	3.2	1.0	2	dbSNP_98	98	570,8030	793.8+/-407.5	17,536,3747	no	coding-synonymous	BMP10	NM_014482.1		175,1388,4940	GG,GA,AA		6.6279,26.5093,13.3631		242/425	69093312	1738,11268	2203	4300	6503	SO:0001819	synonymous_variant	27302	exon2			ACTGGTATCTATT	AF101441	CCDS1890.1	2p13.2	2014-09-17			ENSG00000163217	ENSG00000163217		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	20869	protein-coding gene	gene with protein product		608748				10072785	Standard	NM_014482		Approved		uc002sez.1	O95393	OTTHUMG00000129573	ENST00000295379.1:c.726T>C	2.37:g.69093312A>G		Somatic	396	1	0.00252525		WXS	Illumina HiSeq	Phase_I	394	203	0.515228	NM_014482	Q53R17|Q6NTE0	Silent	SNP	ENST00000295379.1	37	CCDS1890.1																																																																																			A|0.870;G|0.130	0.130	strong		0.488	BMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251768.1	NM_014482	
PLIN4	729359	hgsc.bcm.edu	37	19	4511913	4511913	+	Missense_Mutation	SNP	C	C	T	rs199927982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4511913C>T	ENST00000301286.3	-	3	2016	c.2017G>A	c.(2017-2019)Gac>Aac	p.D673N		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	673	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						TTGGCCGTGTCTACACCTGTC	0.567													C|||	52	0.0103834	0.0386	0.0014	5008	,	,		29014	0.0		0.0	False		,,,				2504	0.0				p.D673N		Atlas-SNP	.											.	PLIN4	191	.	0			c.G2017A						PASS	.	G	ASN/ASP	151,4073		4,143,1965	139.0	148.0	145.0		2017	3.0	0.3	19	dbSNP_132	145	0,8444		0,0,4222	yes	missense	PLIN4	NM_001080400.1	23	4,143,6187	TT,TC,CC		0.0,3.5748,1.192	probably-damaging	673/1358	4511913	151,12517	2112	4222	6334	SO:0001583	missense	729359	exon3			CCGTGTCTACACC	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.2017G>A	19.37:g.4511913C>T	ENSP00000301286:p.Asp673Asn	Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	359	137	0.381616	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	13.17	2.155782	0.38021	0.035748	0.0	ENSG00000167676	ENST00000301286	T	0.11063	2.81	5.14	3.0	0.34707	.	0.287773	0.24191	U	0.040720	T	0.02970	0.0088	M	0.85197	2.74	0.20926	N	0.999825	P	0.49961	0.93	P	0.47044	0.535	T	0.04811	-1.0925	10	0.46703	T	0.11	-25.9696	7.1023	0.25344	0.0:0.6943:0.1443:0.1613	.	673	Q96Q06	PLIN4_HUMAN	N	673	ENSP00000301286:D673N	ENSP00000301286:D673N	D	-	1	0	PLIN4	4462913	0.000000	0.05858	0.349000	0.25694	0.008000	0.06430	-0.258000	0.08733	0.567000	0.29293	-0.757000	0.03467	GAC	C|0.988;T|0.012	0.012	strong		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
GPR20	2843	hgsc.bcm.edu	37	8	142367246	142367246	+	Missense_Mutation	SNP	G	G	A	rs36092215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:142367246G>A	ENST00000377741.3	-	2	868	c.778C>T	c.(778-780)Cgc>Tgc	p.R260C	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	260			R -> C (in dbSNP:rs36092215).		G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(3)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	15	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			GCCACTTGGCGGGCGTGGAAG	0.667													G|||	410	0.081869	0.2496	0.0331	5008	,	,		19230	0.0		0.0368	False		,,,				2504	0.0204				p.R260C		Atlas-SNP	.											.	GPR20	43	.	0			c.C778T						PASS	.	G	CYS/ARG	1014,3388	345.1+/-308.4	108,798,1295	35.0	28.0	30.0		778	4.8	1.0	8	dbSNP_126	30	335,8261	108.0+/-168.7	11,313,3974	yes	missense	GPR20	NM_005293.2	180	119,1111,5269	AA,AG,GG		3.8972,23.035,10.3785	probably-damaging	260/359	142367246	1349,11649	2201	4298	6499	SO:0001583	missense	2843	exon2			CTTGGCGGGCGTG	U66579	CCDS34949.1	8q24.3	2012-08-21				ENSG00000204882		"""GPCR / Class A : Orphans"""	4475	protein-coding gene	gene with protein product		601908				18347022	Standard	NM_005293		Approved		uc003ywf.3	Q99678		ENST00000377741.3:c.778C>T	8.37:g.142367246G>A	ENSP00000366970:p.Arg260Cys	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_005293	Q17R96	Missense_Mutation	SNP	ENST00000377741.3	37	CCDS34949.1	163	0.07463369963369963	129	0.2621951219512195	10	0.027624309392265192	0	0.0	24	0.0316622691292876	G	14.33	2.504122	0.44558	0.23035	0.038972	ENSG00000204882	ENST00000377741	T	0.72167	-0.63	4.84	4.84	0.62591	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	L	0.31926	0.97	0.26149	P	0.9801759	D	0.89917	1.0	D	0.67231	0.95	T	0.02868	-1.1100	8	0.39692	T	0.17	-28.9204	12.0917	0.53730	0.0:0.0:0.8282:0.1718	rs36092215;rs62522460	260	Q99678	GPR20_HUMAN	C	260	ENSP00000366970:R260C	ENSP00000366970:R260C	R	-	1	0	GPR20	142436428	.	.	0.998000	0.56505	0.698000	0.40448	.	.	2.234000	0.73211	0.462000	0.41574	CGC	G|0.904;A|0.096	0.096	strong		0.667	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293	
MYO15A	51168	hgsc.bcm.edu	37	17	18064730	18064730	+	Silent	SNP	C	C	T	rs8077577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	69	0	0		WXS	Illumina HiSeq	Phase_I	84	49	0.583333	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	
CBX2	84733	hgsc.bcm.edu	37	17	77755894	77755894	+	Intron	SNP	C	C	G	rs9912676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77755894C>G	ENST00000310942.4	+	4	392				CBX2_ENST00000269399.5_Missense_Mutation_p.F194L	NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2						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)			AAGCACTCTTCCCTCCCAGGG	0.592													C|||	131	0.0261581	0.0961	0.0058	5008	,	,		17679	0.0		0.0	False		,,,				2504	0.0				p.F194L		Atlas-SNP	.											.	CBX2	50	.	0			c.C582G						PASS	.	C	,LEU/PHE	365,4037		13,339,1849	36.0	41.0	39.0		,582	0.7	0.0	17	dbSNP_119	39	3,8587		0,3,4292	yes	intron,missense	CBX2	NM_005189.2,NM_032647.3	,22	13,342,6141	GG,GC,CC		0.0349,8.2917,2.8325	,	,194/212	77755894	368,12624	2201	4295	6496	SO:0001627	intron_variant	84733	exon4			ACTCTTCCCTCCC	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.288+294C>G	17.37:g.77755894C>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	116	42	0.362069	NM_032647	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	37	CCDS32757.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	C	0.251	-1.006634	0.02112	0.082917	3.49E-4	ENSG00000173894	ENST00000269399	.	.	.	2.87	0.722	0.18225	.	.	.	.	.	T	0.00815	0.0027	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13388	-1.0511	6	.	.	.	.	5.5063	0.16856	0.2264:0.553:0.2205:0.0	rs9912676	194	Q14781-2	.	L	194	.	.	F	+	3	2	CBX2	75370489	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.028000	0.13644	0.057000	0.16193	0.455000	0.32223	TTC	C|0.976;G|0.024	0.024	strong		0.592	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
COL5A1	1289	hgsc.bcm.edu	37	9	137711997	137711997	+	Silent	SNP	G	G	C	rs2228560	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:137711997G>C	ENST00000371817.3	+	58	4896	c.4482G>C	c.(4480-4482)ccG>ccC	p.P1494P		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1494	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TCGGTCCTCCGGGTGAACAGG	0.627													G|||	2044	0.408147	0.5416	0.3256	5008	,	,		21008	0.375		0.3439	False		,,,				2504	0.3865				p.P1494P		Atlas-SNP	.											.	COL5A1	323	.	0			c.G4482C						PASS	.	G		2257,2149		590,1077,536	101.0	95.0	97.0		4482	-9.4	0.0	9	dbSNP_107	97	3273,5327		731,1811,1758	no	coding-synonymous	COL5A1	NM_000093.3		1321,2888,2294	CC,CG,GG		38.0581,48.7744,42.5188		1494/1839	137711997	5530,7476	2203	4300	6503	SO:0001819	synonymous_variant	1289	exon58			TCCTCCGGGTGAA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4482G>C	9.37:g.137711997G>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	123	41	0.333333	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			A|0.009;C|0.408;G|0.583	0.408	strong		0.627	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
SLC45A4	57210	hgsc.bcm.edu	37	8	142228386	142228386	+	Silent	SNP	C	C	T	rs61995881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:142228386C>T	ENST00000024061.3	-	4	1507	c.1200G>A	c.(1198-1200)ccG>ccA	p.P400P	SLC45A4_ENST00000519067.1_Silent_p.P400P|SLC45A4_ENST00000433583.2_Silent_p.P393P|SLC45A4_ENST00000517878.1_Silent_p.P451P	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			TGCTGCGCGACGGCTTGATCA	0.677													C|||	69	0.013778	0.0461	0.0086	5008	,	,		15669	0.0		0.0	False		,,,				2504	0.002				p.P400P		Atlas-SNP	.											.	SLC45A4	71	.	0			c.G1200A						PASS	.	C		212,4194	124.9+/-162.1	7,198,1998	46.0	44.0	45.0		1200	-2.3	0.9	8	dbSNP_129	45	0,8598		0,0,4299	no	coding-synonymous	SLC45A4	NM_001080431.1		7,198,6297	TT,TC,CC		0.0,4.8116,1.6303		400/799	142228386	212,12792	2203	4299	6502	SO:0001819	synonymous_variant	57210	exon4			GCGCGACGGCTTG	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"""Solute carriers"""	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.1200G>A	8.37:g.142228386C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	46	28	0.608696	NM_001080431	Q6ZRI2|Q9ULU3	Silent	SNP	ENST00000024061.3	37	CCDS34948.1																																																																																			C|0.986;T|0.014	0.014	strong		0.677	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
POMT2	29954	hgsc.bcm.edu	37	14	77786864	77786864	+	Missense_Mutation	SNP	G	G	T	rs8177536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:77786864G>T	ENST00000261534.4	-	1	363	c.161C>A	c.(160-162)gCg>gAg	p.A54E	GSTZ1_ENST00000216465.5_5'Flank|GSTZ1_ENST00000554279.1_5'Flank|GSTZ1_ENST00000557053.1_5'Flank|GSTZ1_ENST00000557639.1_5'Flank|GSTZ1_ENST00000556627.1_5'Flank|GSTZ1_ENST00000349555.3_5'Flank|GSTZ1_ENST00000393734.1_5'Flank|GSTZ1_ENST00000361389.4_5'Flank	NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	54			A -> E (in dbSNP:rs8177536).			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		CCAGCCGACCGCCTCGAAGCG	0.711													G|||	162	0.0323482	0.1188	0.0072	5008	,	,		11629	0.0		0.0	False		,,,				2504	0.0				p.A54E		Atlas-SNP	.											.	POMT2	47	.	0			c.C161A						PASS	.	G	GLU/ALA	359,3731		14,331,1700	11.0	10.0	10.0		161	-1.7	0.0	14	dbSNP_117	10	3,8235		0,3,4116	yes	missense	POMT2	NM_013382.5	107	14,334,5816	TT,TG,GG		0.0364,8.7775,2.9364	benign	54/751	77786864	362,11966	2045	4119	6164	SO:0001583	missense	29954	exon1			CCGACCGCCTCGA	AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.161C>A	14.37:g.77786864G>T	ENSP00000261534:p.Ala54Glu	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	41	27	0.658537	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	37	CCDS9857.1	72	0.03296703296703297	70	0.14227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	G	9.945	1.218430	0.22373	0.087775	3.64E-4	ENSG00000009830	ENST00000261534	T	0.76709	-1.04	5.34	-1.66	0.08265	.	0.721535	0.12751	N	0.442179	T	0.00412	0.0013	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.07271	-1.0781	9	0.02654	T	1	-1.3895	2.5294	0.04699	0.1453:0.2152:0.4208:0.2187	rs8177536;rs8177536	54	Q9UKY4	POMT2_HUMAN	E	54	ENSP00000261534:A54E	ENSP00000261534:A54E	A	-	2	0	POMT2	76856617	0.000000	0.05858	0.041000	0.18516	0.017000	0.09413	-0.222000	0.09190	-0.024000	0.13941	-0.136000	0.14681	GCG	G|0.920;T|0.080	0.080	strong		0.711	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382	
CACNA1G	8913	hgsc.bcm.edu	37	17	48703986	48703986	+	Silent	SNP	G	G	A	rs9893223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48703986G>A	ENST00000359106.5	+	38	7008	c.7008G>A	c.(7006-7008)ccG>ccA	p.P2336P	CACNA1G_ENST00000502264.1_Silent_p.P2265P|CACNA1G_ENST00000507510.2_Silent_p.P2291P|CACNA1G_ENST00000510366.1_Silent_p.P2191P|CACNA1G_ENST00000514717.1_Silent_p.P2186P|CACNA1G_ENST00000514181.1_Silent_p.P2218P|CACNA1G_ENST00000513964.1_Silent_p.P2198P|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000515765.1_Silent_p.P2280P|CACNA1G_ENST00000512389.1_Silent_p.P2232P|CACNA1G_ENST00000360761.4_Silent_p.P2220P|CACNA1G_ENST00000515165.1_Silent_p.P2243P|CACNA1G_ENST00000507896.1_Silent_p.P2153P|CACNA1G_ENST00000358244.5_Silent_p.P2130P|CACNA1G_ENST00000442258.2_Silent_p.P2202P|CACNA1G_ENST00000354983.4_Silent_p.P2302P|CACNA1G_ENST00000507336.1_Silent_p.P2325P|CACNA1G_ENST00000510115.1_Silent_p.P2257P|CACNA1G_ENST00000515411.1_Silent_p.P2273P|CACNA1G_ENST00000514079.1_Silent_p.P2250P|CACNA1G_ENST00000429973.2_Silent_p.P2225P|CACNA1G_ENST00000507609.1_Silent_p.P2236P|CACNA1G_ENST00000505165.1_Silent_p.P2164P|CACNA1G_ENST00000503485.1_Silent_p.P2209P|CACNA1G_ENST00000352832.5_Silent_p.P2209P|CACNA1G_ENST00000513689.2_Silent_p.P2246P	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2336					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GGAGGGCTCCGTCCAGCGACT	0.622											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	965	0.192692	0.3858	0.1369	5008	,	,		14554	0.0813		0.0557	False		,,,				2504	0.227				p.P2336P		Atlas-SNP	.											CACNA1G_ENST00000359106,NS,carcinoma,0,6	CACNA1G	659	6	0			c.G7008A						PASS	.	G	,,,,,,,,,,,,,	1251,2609		202,847,881	27.0	32.0	30.0		7008,6390,6939,6696,6771,6840,6660,6795,6729,6873,6675,6627,6606,6906	-8.3	0.2	17	dbSNP_119	30	423,7815		13,397,3709	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1G	NM_018896.3,NM_198376.1,NM_198377.1,NM_198378.1,NM_198379.1,NM_198380.1,NM_198382.1,NM_198383.1,NM_198384.1,NM_198385.1,NM_198386.1,NM_198387.1,NM_198388.1,NM_198396.1	,,,,,,,,,,,,,	215,1244,4590	AA,AG,GG		5.1347,32.4093,13.837	,,,,,,,,,,,,,	2336/2378,2130/2172,2313/2355,2232/2274,2257/2299,2280/2322,2220/2262,2265/2307,2243/2285,2291/2333,2225/2267,2209/2251,2202/2244,2302/2344	48703986	1674,10424	1930	4119	6049	SO:0001819	synonymous_variant	8913	exon38			GGCTCCGTCCAGC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.7008G>A	17.37:g.48703986G>A		Somatic	82	0	0	956	WXS	Illumina HiSeq	Phase_I	140	55	0.392857	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	CCDS45730.1																																																																																			G|0.876;A|0.124	0.124	strong		0.622	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
INPP4A	3631	hgsc.bcm.edu	37	2	99149946	99149946	+	Silent	SNP	G	G	A	rs2278211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99149946G>A	ENST00000523221.1	+	3	258	c.258G>A	c.(256-258)acG>acA	p.T86T	INPP4A_ENST00000409540.3_Silent_p.T86T|INPP4A_ENST00000545415.1_Silent_p.T86T|INPP4A_ENST00000409851.3_Silent_p.T86T|INPP4A_ENST00000074304.5_Silent_p.T86T|INPP4A_ENST00000409016.4_Silent_p.T86T|INPP4A_ENST00000409463.1_Intron			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	86	C2.				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						ATGCACAGACGGAGATCATTG	0.522													G|||	1154	0.230431	0.0749	0.304	5008	,	,		18892	0.2956		0.2674	False		,,,				2504	0.2832				p.T86T		Atlas-SNP	.											.	INPP4A	205	.	0			c.G258A						PASS	.	G	,,,	479,3711		32,415,1648	112.0	112.0	112.0		258,258,258,258	-2.2	1.0	2	dbSNP_100	112	2216,6242		296,1624,2309	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	328,2039,3957	AA,AG,GG		26.2,11.432,21.3077	,,,	86/978,86/973,86/955,86/939	99149946	2695,9953	2095	4229	6324	SO:0001819	synonymous_variant	3631	exon5			ACAGACGGAGATC	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.258G>A	2.37:g.99149946G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	96	59	0.614583	NM_004027	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																			G|0.779;N|0.000	.	strong		0.522	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
CD163L1	283316	hgsc.bcm.edu	37	12	7528471	7528471	+	Silent	SNP	G	G	A	rs7306824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7528471G>A	ENST00000313599.3	-	10	2568	c.2511C>T	c.(2509-2511)aaC>aaT	p.N837N	CD163L1_ENST00000416109.2_Silent_p.N847N|CD163L1_ENST00000396630.1_Silent_p.N837N|CD163L1_ENST00000544331.1_5'UTR			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	837	SRCR 8. {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						CATCTCCACAGTTTAATTCTC	0.468													A|||	2323	0.463858	0.6331	0.4841	5008	,	,		-128	0.4752		0.2714	False		,,,				2504	0.407				p.N837N		Atlas-SNP	.											CD163L1,colon,carcinoma,0,2	CD163L1	238	2	0			c.C2511T						PASS	.	A		2474,1932	549.1+/-377.7	698,1078,427	99.0	99.0	99.0		2511	-5.5	0.0	12	dbSNP_116	99	2144,6456	714.9+/-406.0	281,1582,2437	no	coding-synonymous	CD163L1	NM_174941.4		979,2660,2864	AA,AG,GG		24.9302,43.8493,35.5067		837/1454	7528471	4618,8388	2203	4300	6503	SO:0001819	synonymous_variant	283316	exon10			TCCACAGTTTAAT	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.2511C>T	12.37:g.7528471G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																			G|0.601;A|0.399	0.399	strong		0.468	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
HSD17B14	51171	hgsc.bcm.edu	37	19	49339098	49339098	+	Missense_Mutation	SNP	T	T	C	rs8110220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49339098T>C	ENST00000263278.4	-	2	357	c.91A>G	c.(91-93)Aac>Gac	p.N31D	HSD17B14_ENST00000599157.1_Missense_Mutation_p.N31D	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	31			N -> D (in dbSNP:rs8110220).		steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		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;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		GCCCCGCTGTTCACTGAGAAT	0.607											OREG0025610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	1722	0.34385	0.6165	0.2867	5008	,	,		16704	0.0893		0.2674	False		,,,				2504	0.3569				p.N31D		Atlas-SNP	.											.	HSD17B14	25	.	0			c.A91G						PASS	.		ASP/ASN	2378,2028		645,1088,470	87.0	73.0	78.0		91	-1.8	0.1	19	dbSNP_116	78	2126,6472		258,1610,2431	yes	missense	HSD17B14	NM_016246.2	23	903,2698,2901	CC,CT,TT		24.7267,46.0281,34.6355	benign	31/271	49339098	4504,8500	2203	4299	6502	SO:0001583	missense	51171	exon2			CGCTGTTCACTGA	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.91A>G	19.37:g.49339098T>C	ENSP00000263278:p.Asn31Asp	Somatic	56	0	0	961	WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_016246	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	37	CCDS12736.1	665	0.30448717948717946	285	0.5792682926829268	115	0.31767955801104975	67	0.11713286713286714	198	0.2612137203166227	-	0.019	-1.451578	0.01080	0.539719	0.247267	ENSG00000087076	ENST00000263278	T	0.21031	2.03	3.1	-1.77	0.07982	NAD(P)-binding domain (1);	0.876083	0.09791	N	0.755389	T	0.00012	0.0000	N	0.03891	-0.335	0.52099	P	5.500000000002725E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41538	-0.9503	9	0.21540	T	0.41	.	4.0567	0.09819	0.0:0.3503:0.3462:0.3035	rs8110220;rs52799828;rs61231150;rs8110220	31	Q9BPX1	DHB14_HUMAN	D	31	ENSP00000263278:N31D	ENSP00000263278:N31D	N	-	1	0	HSD17B14	54030910	0.109000	0.22037	0.063000	0.19743	0.073000	0.16967	-0.043000	0.12043	-0.518000	0.06452	-0.382000	0.06688	AAC	C|0.335;N|0.001	0.335	strong		0.607	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49376582	49376582	+	Missense_Mutation	SNP	G	G	A	rs564196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49376582G>A	ENST00000200453.5	+	2	361	c.92G>A	c.(91-93)cGc>cAc	p.R31H		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	31	Required for localization in the endoplasmic reticulum.		R -> H (in dbSNP:rs564196).		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CTCCTCAGCCGCGCCTGGAGC	0.652													G|||	1372	0.273962	0.5325	0.2262	5008	,	,		16179	0.0873		0.1501	False		,,,				2504	0.2781				p.R31H		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G92A						PASS	.	G	HIS/ARG	2111,2289		524,1063,613	25.0	28.0	27.0		92	2.2	0.9	19	dbSNP_83	27	1232,7358		75,1082,3138	yes	missense	PPP1R15A	NM_014330.3	29	599,2145,3751	AA,AG,GG		14.3423,47.9773,25.7352	probably-damaging	31/675	49376582	3343,9647	2200	4295	6495	SO:0001583	missense	23645	exon2			TCAGCCGCGCCTG	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.92G>A	19.37:g.49376582G>A	ENSP00000200453:p.Arg31His	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	499	0.22847985347985347	249	0.5060975609756098	82	0.2265193370165746	54	0.0944055944055944	114	0.1503957783641161	G	17.76	3.468799	0.63625	0.479773	0.143423	ENSG00000087074	ENST00000200453	T	0.05996	3.36	4.28	2.16	0.27623	.	0.226254	0.28606	N	0.014748	T	0.00012	0.0000	L	0.43923	1.385	0.33266	P	0.43964800000000004	D	0.76494	0.999	P	0.57846	0.828	T	0.45264	-0.9273	9	0.72032	D	0.01	-4.0888	6.5741	0.22555	0.2149:0.0:0.7851:0.0	rs564196;rs564196	31	O75807	PR15A_HUMAN	H	31	ENSP00000200453:R31H	ENSP00000200453:R31H	R	+	2	0	PPP1R15A	54068394	0.865000	0.29922	0.897000	0.35233	0.378000	0.30076	1.188000	0.32102	0.758000	0.33059	0.561000	0.74099	CGC	G|0.729;A|0.271	0.271	strong		0.652	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
CLCF1	23529	hgsc.bcm.edu	37	11	67135006	67135006	+	Silent	SNP	A	A	T	rs867193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67135006A>T	ENST00000312438.7	-	2	305	c.108T>A	c.(106-108)ccT>ccA	p.P36P	AP003419.11_ENST00000543494.1_RNA|CLCF1_ENST00000528474.1_Silent_p.P26P|CLCF1_ENST00000533438.1_Silent_p.P26P	NM_013246.2	NP_037378.1	Q9UBD9	CLCF1_HUMAN	cardiotrophin-like cytokine factor 1	36					B cell differentiation (GO:0030183)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)	CNTFR-CLCF1 complex (GO:0097059)|CRLF-CLCF1 complex (GO:0097058)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	ciliary neurotrophic factor receptor binding (GO:0005127)|cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			endometrium(1)|urinary_tract(1)	2			BRCA - Breast invasive adenocarcinoma(15;2.39e-06)			TGGAGGGGCCAGGCCCTGGGT	0.622													A|||	391	0.0780751	0.1422	0.0519	5008	,	,		16418	0.1141		0.0358	False		,,,				2504	0.0164				p.P36P		Atlas-SNP	.											.	CLCF1	15	.	0			c.T108A						PASS	.	A	,	591,3809	260.4+/-263.7	47,497,1656	123.0	103.0	110.0		78,108	-4.2	1.0	11	dbSNP_86	110	290,8300	107.2+/-168.0	7,276,4012	no	coding-synonymous,coding-synonymous	CLCF1	NM_001166212.1,NM_013246.2	,	54,773,5668	TT,TA,AA		3.376,13.4318,6.7821	,	26/216,36/226	67135006	881,12109	2200	4295	6495	SO:0001819	synonymous_variant	23529	exon2			GGGGCCAGGCCCT	BC012939	CCDS31617.1, CCDS53666.1	11q13.3	2014-01-28	2006-07-03		ENSG00000175505	ENSG00000175505			17412	protein-coding gene	gene with protein product	"""B-cell stimulating factor 3"", ""cold-induced sweating syndrome 2"", ""novel neurotrophin-1"""	607672	"""CRLF1 associated cytokine-like factor 1"""			10500198, 10448081, 16782820	Standard	NM_001166212		Approved	NNT1, BSF3, CLC, NR6, CISS2, BSF-3, NNT-1	uc010rpp.2	Q9UBD9	OTTHUMG00000167669	ENST00000312438.7:c.108T>A	11.37:g.67135006A>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	128	72	0.5625	NM_013246	B4DNT4|Q6NZA4	Silent	SNP	ENST00000312438.7	37	CCDS31617.1																																																																																			A|0.928;T|0.072	0.072	strong		0.622	CLCF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395478.1	NM_013246	
FGFR3	2261	hgsc.bcm.edu	37	4	1803704	1803704	+	Silent	SNP	T	T	C	rs2234909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1803704T>C	ENST00000260795.2	+	6	984	c.882T>C	c.(880-882)aaT>aaC	p.N294N	FGFR3_ENST00000340107.4_Silent_p.N294N|FGFR3_ENST00000352904.1_Silent_p.N294N|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000412135.2_Silent_p.N294N|FGFR3_ENST00000481110.2_Silent_p.N294N|FGFR3_ENST00000440486.2_Silent_p.N294N			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	294	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.N294N(5)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TGGAGGTGAATGGCAGCAAGG	0.672		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome				N|||	1039	0.207468	0.3707	0.1441	5008	,	,		12849	0.0744		0.17	False		,,,				2504	0.2076				p.N294N		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	FGFR3_ENST00000340107,caecum,carcinoma,+2,11	FGFR3	3320	11	5	Substitution - coding silent(5)	upper_aerodigestive_tract(3)|skin(2)	c.T882C						PASS	.	C	,,	1504,2902	654.3+/-399.7	251,1002,950	47.0	42.0	44.0		882,882,882	-6.8	0.9	4	dbSNP_98	44	1278,7320	749.7+/-407.4	98,1082,3119	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	349,2084,4069	CC,CT,TT		14.8639,34.1353,21.3934	,,	294/807,294/809,294/695	1803704	2782,10222	2203	4299	6502	SO:0001819	synonymous_variant	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GGTGAATGGCAGC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.882T>C	4.37:g.1803704T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			T|0.799;C|0.201	0.201	strong		0.672	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
KRTAP13-3	337960	hgsc.bcm.edu	37	21	31797919	31797919	+	Silent	SNP	G	G	A	rs73356706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31797919G>A	ENST00000390690.2	-	1	367	c.312C>T	c.(310-312)tcC>tcT	p.S104S		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	104						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						AGCAGCTATTGGATCCAAAAC	0.532													-|||	210	0.0419329	0.1505	0.0144	5008	,	,		18568	0.0		0.001	False		,,,				2504	0.0				p.S104S		Atlas-SNP	.											.	KRTAP13-3	47	.	0			c.C312T						PASS	.	G		432,3908		23,386,1761	51.0	57.0	55.0		312	3.4	0.3	21	dbSNP_130	55	9,8569		0,9,4280	no	coding-synonymous	KRTAP13-3	NM_181622.1		23,395,6041	AA,AG,GG		0.1049,9.9539,3.4138		104/173	31797919	441,12477	2170	4289	6459	SO:0001819	synonymous_variant	337960	exon1			GCTATTGGATCCA	AP001708	CCDS13591.1	21q22.1	2006-03-13			ENSG00000240432	ENSG00000240432		"""Keratin associated proteins"""	18925	protein-coding gene	gene with protein product						12359730	Standard	NM_181622		Approved	KAP13.3	uc002yob.1	Q3SY46	OTTHUMG00000057776	ENST00000390690.2:c.312C>T	21.37:g.31797919G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_181622	Q3LI78	Silent	SNP	ENST00000390690.2	37	CCDS13591.1																																																																																			G|0.975;A|0.025	0.025	strong		0.532	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2		
CCDC134	79879	hgsc.bcm.edu	37	22	42209767	42209767	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42209767C>T	ENST00000255784.5	+	6	609	c.505C>T	c.(505-507)Ctg>Ttg	p.L169L	CCDC134_ENST00000402061.3_Intron	NM_024821.2	NP_079097.1	Q9H6E4	CC134_HUMAN	coiled-coil domain containing 134	169						extracellular region (GO:0005576)|membrane (GO:0016020)				large_intestine(1)|lung(2)|ovary(2)|skin(1)	6						GGCCCAGGAGCTGGGGATCAG	0.532																																					p.L169L		Atlas-SNP	.											.	CCDC134	19	.	0			c.C505T						PASS	.						100.0	96.0	97.0					22																	42209767		2203	4300	6503	SO:0001819	synonymous_variant	79879	exon6			CAGGAGCTGGGGA	AL021453	CCDS33654.1	22q13.2	2010-12-24			ENSG00000100147	ENSG00000100147			26185	protein-coding gene	gene with protein product						18087676	Standard	NM_024821		Approved	FLJ22349	uc003bbh.1	Q9H6E4	OTTHUMG00000151262	ENST00000255784.5:c.505C>T	22.37:g.42209767C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_024821		Silent	SNP	ENST00000255784.5	37	CCDS33654.1																																																																																			.	.	none		0.532	CCDC134-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321964.1	NM_024821	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047348	46047348	+	Missense_Mutation	SNP	C	C	T	rs62220926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46047348C>T	ENST00000397911.3	+	1	309	c.260C>T	c.(259-261)cCg>cTg	p.P87L	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	87	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						AGCTGCCAGCCGGCTTACTGC	0.682													C|||	705	0.140775	0.3449	0.0706	5008	,	,		18902	0.0109		0.0606	False		,,,				2504	0.1309				p.P87L		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.C260T						PASS	.	C	,LEU/PRO	1393,3001		227,939,1031	62.0	80.0	74.0		,260	2.3	0.3	21	dbSNP_129	74	433,8153		10,413,3870	no	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,98	237,1352,4901	TT,TC,CC		5.0431,31.7023,14.0678	,benign	,87/293	46047348	1826,11154	2197	4293	6490	SO:0001583	missense	386676	exon1			GCCAGCCGGCTTA	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.260C>T	21.37:g.46047348C>T	ENSP00000381009:p.Pro87Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	167	67	0.401198	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	234	0.10714285714285714	154	0.3130081300813008	32	0.08839779005524862	7	0.012237762237762238	41	0.05408970976253298	c	9.773	1.173270	0.21704	0.317023	0.050431	ENSG00000221837	ENST00000397911	T	0.00873	5.59	3.34	2.33	0.28932	.	.	.	.	.	T	0.00012	0.0000	M	0.71206	2.165	0.80722	P	0.0	B	0.21753	0.06	B	0.14578	0.011	T	0.43147	-0.9409	7	.	.	.	.	3.6373	0.08154	0.2472:0.6162:0.0:0.1366	rs62220926	87	P60411	KR109_HUMAN	L	87	ENSP00000381009:P87L	.	P	+	2	0	KRTAP10-9	44871776	0.003000	0.15002	0.299000	0.25016	0.729000	0.41735	0.316000	0.19469	1.567000	0.49668	0.650000	0.86243	CCG	C|0.927;T|0.073	0.073	strong		0.682	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
GFAP	2670	hgsc.bcm.edu	37	17	42985453	42985453	+	Silent	SNP	G	G	T	rs146298944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42985453G>T	ENST00000253408.5	-	8	1301	c.1236C>A	c.(1234-1236)acC>acA	p.T412T	GFAP_ENST00000588735.1_Silent_p.T38T	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein	412	Tail.				astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				GCATCTCCACGGTCTTCACCA	0.592													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19484	0.0		0.0	False		,,,				2504	0.0				p.T412T		Atlas-SNP	.											GFAP,colon,carcinoma,0,1	GFAP	88	1	0			c.C1236A						PASS	.	G		20,4386	27.2+/-55.0	0,20,2183	231.0	198.0	209.0		1236	-10.3	0.1	17	dbSNP_134	209	0,8600		0,0,4300	no	coding-synonymous	GFAP	NM_002055.4		0,20,6483	TT,TG,GG		0.0,0.4539,0.1538		412/433	42985453	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	2670	exon8			CTCCACGGTCTTC	S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"""Intermediate filaments type III"""	4235	protein-coding gene	gene with protein product	"""intermediate filament protein"""	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.1236C>A	17.37:g.42985453G>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	149	70	0.469799	NM_002055	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Silent	SNP	ENST00000253408.5	37	CCDS11491.1																																																																																			G|0.999;T|0.001	0.001	strong		0.592	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055	
CENPF	1063	hgsc.bcm.edu	37	1	214820099	214820099	+	Missense_Mutation	SNP	A	A	G	rs3748697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:214820099A>G	ENST00000366955.3	+	13	7354	c.7186A>G	c.(7186-7188)Aat>Gat	p.N2396D		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2492	2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGAAAAAGAAAATCTGACAAA	0.323													A|||	1177	0.235024	0.0522	0.3127	5008	,	,		19895	0.122		0.4831	False		,,,				2504	0.2883				p.N2396D	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,NS,carcinoma,0,1	CENPF	321	1	0			c.A7186G						PASS	.	A	ASP/ASN	521,3881		44,433,1724	32.0	37.0	35.0		7186	4.0	0.2	1	dbSNP_107	35	4376,4224		1112,2152,1036	yes	missense	CENPF	NM_016343.3	23	1156,2585,2760	GG,GA,AA		49.1163,11.8355,37.6634	benign	2396/3115	214820099	4897,8105	2201	4300	6501	SO:0001583	missense	1063	exon13			AAAGAAAATCTGA	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.7186A>G	1.37:g.214820099A>G	ENSP00000355922:p.Asn2396Asp	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	63	0.567568	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	583	0.26694139194139194	34	0.06910569105691057	128	0.35359116022099446	63	0.11013986013986014	358	0.47229551451187335	A	3.995	-0.003637	0.07773	0.118355	0.508837	ENSG00000117724	ENST00000366955	T	0.42900	0.96	5.09	3.97	0.46021	Centromere protein Cenp-F, leucine-rich repeat-containing domain (1);	0.178649	0.27008	N	0.021399	T	0.00012	0.0000	L	0.48642	1.525	0.37429	P	0.08606100000000005	B	0.15473	0.013	B	0.17433	0.018	T	0.46816	-0.9164	9	0.10902	T	0.67	.	5.1495	0.15002	0.7373:0.0:0.0925:0.1701	rs3748697;rs17737483;rs52804761;rs61185773;rs3748697	2492	P49454	CENPF_HUMAN	D	2396	ENSP00000355922:N2396D	ENSP00000355922:N2396D	N	+	1	0	CENPF	212886722	0.000000	0.05858	0.203000	0.23512	0.176000	0.22953	0.342000	0.19926	0.969000	0.38237	0.496000	0.49642	AAT	A|0.689;G|0.311	0.311	strong		0.323	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
TMEM132B	114795	hgsc.bcm.edu	37	12	126137060	126137060	+	Missense_Mutation	SNP	C	C	T	rs61021440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						scavenged	.						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	311	3	0.0096463		WXS	Illumina HiSeq	Phase_I	316	134	0.424051	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	
UMPS	7372	hgsc.bcm.edu	37	3	124462808	124462808	+	Silent	SNP	C	C	T	rs13146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124462808C>T	ENST00000232607.2	+	6	1426	c.1320C>T	c.(1318-1320)ggC>ggT	p.G440G	UMPS_ENST00000538242.1_Silent_p.G262G|UMPS_ENST00000536109.1_Silent_p.G348G|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	114	0	0		WXS	Illumina HiSeq	Phase_I	133	58	0.43609	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	
PKDREJ	10343	hgsc.bcm.edu	37	22	46655948	46655948	+	Missense_Mutation	SNP	T	T	C	rs6008384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	127	0	0		WXS	Illumina HiSeq	Phase_I	161	79	0.490683	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	
GUCY2D	3000	hgsc.bcm.edu	37	17	7907189	7907189	+	Silent	SNP	C	C	T	rs3829789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7907189C>T	ENST00000254854.4	+	3	891	c.741C>T	c.(739-741)caC>caT	p.H247H		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	247					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				TGGTGATGCACTCGGTGCTGC	0.687													C|||	561	0.112021	0.0605	0.1037	5008	,	,		15826	0.2103		0.1034	False		,,,				2504	0.0951				p.H247H		Atlas-SNP	.											.	GUCY2D	82	.	0			c.C741T						PASS	.	C		351,4055	179.4+/-207.9	12,327,1864	47.0	43.0	44.0		741	-1.2	1.0	17	dbSNP_107	44	1059,7541	220.5+/-258.2	73,913,3314	no	coding-synonymous	GUCY2D	NM_000180.3		85,1240,5178	TT,TC,CC		12.314,7.9664,10.8412		247/1104	7907189	1410,11596	2203	4300	6503	SO:0001819	synonymous_variant	3000	exon3			GATGCACTCGGTG	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"""cone rod dystrophy 6"""	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.741C>T	17.37:g.7907189C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_000180	Q6LEA7	Silent	SNP	ENST00000254854.4	37	CCDS11127.1																																																																																			C|0.893;T|0.107	0.107	strong		0.687	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
PCDHA3	56145	hgsc.bcm.edu	37	5	140180964	140180964	+	Missense_Mutation	SNP	C	C	A	rs7731327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140180964C>A	ENST00000522353.2	+	1	182	c.182C>A	c.(181-183)cCg>cAg	p.P61Q	PCDHA3_ENST00000532566.2_Missense_Mutation_p.P61Q|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	61	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> Q (in dbSNP:rs7731327).		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)			GAGCTGGTGCCGCGCCTGTTC	0.612													.|||	285	0.0569089	0.208	0.013	5008	,	,		16771	0.0		0.001	False		,,,				2504	0.0				p.P61Q		Atlas-SNP	.											PCDHA3_ENST00000522353,NS,carcinoma,-1,2	PCDHA3	396	2	0			c.C182A						PASS	.	C	,,GLN/PRO,,GLN/PRO	789,3617		66,657,1480	51.0	63.0	59.0		,,182,,182	3.6	1.0	5	dbSNP_116	59	5,8583		0,5,4289	no	intron,intron,missense,intron,missense	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,76,,76	66,662,5769	AA,AC,CC		0.0582,17.9074,6.1105	,,,,	,,61/951,,61/825	140180964	794,12200	2203	4294	6497	SO:0001583	missense	56145	exon1			TGGTGCCGCGCCT	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.182C>A	5.37:g.140180964C>A	ENSP00000429808:p.Pro61Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	32	0.380952	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	88	0.040293040293040296	82	0.16666666666666666	6	0.016574585635359115	0	0.0	0	0.0	c	13.35	2.210033	0.39003	0.179074	5.82E-4	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.26067	1.76;1.76	4.48	3.59	0.41128	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.203527	0.23851	U	0.043957	T	0.00039	0.0001	M	0.66297	2.02	0.46798	P	8.000000000000229E-4	P;P	0.42871	0.792;0.48	B;B	0.37508	0.224;0.252	T	0.16158	-1.0412	9	0.62326	D	0.03	.	13.352	0.60607	0.0:0.9179:0.0:0.0821	rs7731327	61;61	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	Q	61	ENSP00000429808:P61Q;ENSP00000434086:P61Q	ENSP00000429808:P61Q	P	+	2	0	PCDHA3	140161148	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-0.420000	0.07062	2.228000	0.72767	0.586000	0.80456	CCG	C|0.949;A|0.051	0.051	strong		0.612	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
SORD	6652	hgsc.bcm.edu	37	15	45365724	45365724	+	Missense_Mutation	SNP	C	C	T	rs76283634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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|RP11-109D20.2_ENST00000560967.1_RNA|SORD_ENST00000559562.1_3'UTR	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	563	2	0.0035524		WXS	Illumina HiSeq	Phase_I	547	198	0.361974	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		
CHD5	26038	hgsc.bcm.edu	37	1	6204161	6204161	+	De_novo_Start_OutOfFrame	SNP	G	G	A	rs17436816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6204161G>A	ENST00000378021.1	-	0	1956				CHD5_ENST00000262450.3_Silent_p.Y619Y			O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5						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)		TGCACTGGTCGTAGGGCAGGT	0.582													G|||	414	0.0826677	0.0151	0.2089	5008	,	,		20646	0.0337		0.1203	False		,,,				2504	0.0961				p.Y619Y		Atlas-SNP	.											.	CHD5	267	.	0			c.C1857T						PASS	.	G		143,4263	98.9+/-137.6	3,137,2063	262.0	208.0	226.0		1857	-3.4	0.9	1	dbSNP_123	226	1054,7546	223.1+/-260.0	78,898,3324	no	coding-synonymous	CHD5	NM_015557.2		81,1035,5387	AA,AG,GG		12.2558,3.2456,9.2034		619/1955	6204161	1197,11809	2203	4300	6503			26038	exon12			CTGGTCGTAGGGC	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	ENST00000378021.1:c.-1573C>T	1.37:g.6204161G>A		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	257	120	0.466926	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000378021.1	37																																																																																				G|0.919;A|0.081	0.081	strong		0.582	CHD5-201	KNOWN	basic	protein_coding	protein_coding		NM_015557	
MIA2	117153	hgsc.bcm.edu	37	14	39722023	39722023	+	Missense_Mutation	SNP	G	G	C	rs10134365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:39722023G>C	ENST00000280082.3	+	5	1838	c.1639G>C	c.(1639-1641)Gat>Cat	p.D547H	RP11-407N17.3_ENST00000553728.1_Intron	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	0					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)		p.D547Y(1)		NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		ATCTTCTAAAGATAGTGATGA	0.368													G|||	1556	0.310703	0.4039	0.2032	5008	,	,		17147	0.502		0.2127	False		,,,				2504	0.1646				p.D547H		Atlas-SNP	.											MIA2,rectum,carcinoma,0,1	MIA2	82	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1639C						PASS	.	G	HIS/ASP	1763,2643	515.5+/-368.9	359,1045,799	85.0	94.0	91.0		1639	-0.7	0.5	14	dbSNP_119	91	1801,6797	320.9+/-314.9	161,1479,2659	yes	missense	MIA2	NM_054024.3	81	520,2524,3458	CC,CG,GG		20.9467,40.0136,27.407	benign	547/655	39722023	3564,9440	2203	4299	6502	SO:0001583	missense	117153	exon5			TCTAAAGATAGTG	BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.1639G>C	14.37:g.39722023G>C	ENSP00000280082:p.Asp547His	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_054024	A1L4H0|Q9H6C1	Missense_Mutation	SNP	ENST00000280082.3	37	CCDS9672.1	685	0.31364468864468864	163	0.3313008130081301	78	0.2154696132596685	292	0.5104895104895105	152	0.20052770448548812	G	7.156	0.584811	0.13749	0.400136	0.209467	ENSG00000150526	ENST00000280082	T	0.46063	0.88	4.81	-0.683	0.11335	.	0.655352	0.12592	N	0.455473	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.48525	-0.9028	7	.	.	.	.	4.2613	0.10742	0.4232:0.193:0.3839:0.0	rs10134365;rs52801113;rs60244623;rs10134365	547	Q96PC5-2	.	H	547	ENSP00000280082:D547H	.	D	+	1	0	MIA2	38791774	0.010000	0.17322	0.513000	0.27749	0.256000	0.26092	0.925000	0.28791	0.295000	0.22570	-0.438000	0.05819	GAT	G|0.714;C|0.286	0.286	strong		0.368	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024	
NOL7	51406	hgsc.bcm.edu	37	6	13615767	13615767	+	Silent	SNP	T	T	C	rs75029999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:13615767T>C	ENST00000451315.2	+	1	209	c.177T>C	c.(175-177)ttT>ttC	p.F59F	AL441883.1_ENST00000600057.1_3'UTR|RP1-223E5.4_ENST00000566170.1_RNA	NM_016167.3	NP_057251.2	Q9UMY1	NOL7_HUMAN	nucleolar protein 7, 27kDa	59						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(3)|lung(1)	5	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.135)	Epithelial(50;0.176)			ACGATGAGTTTGACGATGAGG	0.706											OREG0017200	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	40	0.00798722	0.028	0.0043	5008	,	,		15084	0.0		0.0	False		,,,				2504	0.0				p.F59F		Atlas-SNP	.											.	NOL7	18	.	0			c.T177C						PASS	.	T		71,4223		1,69,2077	8.0	10.0	9.0		177	-7.7	0.0	6	dbSNP_132	9	1,8465		0,1,4232	no	coding-synonymous	NOL7	NM_016167.3		1,70,6309	CC,CT,TT		0.0118,1.6535,0.5643		59/258	13615767	72,12688	2147	4233	6380	SO:0001819	synonymous_variant	51406	exon1			TGAGTTTGACGAT	AF172066	CCDS4528.1	6p23	2008-05-23	2004-02-10		ENSG00000225921	ENSG00000225921			21040	protein-coding gene	gene with protein product		611533	"""chromosome 6 open reading frame 90"", ""polyglutamine binding protein 3"""	C6orf90, PQBP3		16205646	Standard	NM_016167		Approved	NOP27, RARG-1, dJ223E5.2	uc003naz.3	Q9UMY1	OTTHUMG00000014277	ENST00000451315.2:c.177T>C	6.37:g.13615767T>C		Somatic	48	0	0	688	WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_016167	Q5T297|Q9Y3U7	Silent	SNP	ENST00000451315.2	37	CCDS4528.1																																																																																			T|0.994;C|0.006	0.006	strong		0.706	NOL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039904.1	NM_016167	
PABPC1	26986	hgsc.bcm.edu	37	8	101721870	101721870	+	Silent	SNP	G	G	A	rs146609644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721870G>A	ENST00000318607.5	-	8	2190	c.1062C>T	c.(1060-1062)aaC>aaT	p.N354N	PABPC1_ENST00000519004.1_Silent_p.N309N|PABPC1_ENST00000522387.1_Silent_p.N322N|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	354	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.N354N(1)		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)			CAATTCTACCGTTCATTTCTG	0.448																																					p.N354N		Atlas-SNP	.											PABPC1,rectum,carcinoma,0,1	PABPC1	76	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C1062T						scavenged	.						90.0	82.0	85.0					8																	101721870		2203	4297	6500	SO:0001819	synonymous_variant	26986	exon8			TCTACCGTTCATT	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.1062C>T	8.37:g.101721870G>A		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	272	66	0.242647	NM_002568	Q15097|Q93004	Silent	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.395|9.395	1.076506|1.076506	0.20227|0.20227	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519596|ENST00000519100	.|.	.|.	.|.	4.92|4.92	0.812|0.812	0.18744|0.18744	.|.	.|.	.|.	.|.	.|.	T|T	0.55465|0.55465	0.1922|0.1922	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.45440|0.45440	-0.9261|-0.9261	4|4	.|.	.|.	.|.	.|.	8.6459|8.6459	0.34005|0.34005	0.7462:0.0:0.2538:0.0|0.7462:0.0:0.2538:0.0	.|.	.|.	.|.	.|.	W|M	187|223	.|.	.|.	R|T	-|-	1|2	2|0	PABPC1|PABPC1	101791046|101791046	0.998000|0.998000	0.40836|0.40836	0.999000|0.999000	0.59377|0.59377	0.995000|0.995000	0.86356|0.86356	0.616000|0.616000	0.24344|0.24344	-0.042000|-0.042000	0.13535|0.13535	-0.345000|-0.345000	0.07892|0.07892	CGG|ACG	G|0.767;A|0.233	0.233	strong		0.448	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
VWDE	221806	hgsc.bcm.edu	37	7	12414314	12414314	+	Splice_Site	SNP	C	C	G	rs138469050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12414314C>G	ENST00000275358.3	-	9	1505		c.e9+1			NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains							extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						CAGAAAATTACCTGCCATCAA	0.279													C|||	57	0.0113818	0.0416	0.0029	5008	,	,		13055	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	VWDE	123	.	0			c.1316+1G>C						PASS	.	C		43,1341		1,41,650	124.0	111.0	115.0			4.0	1.0	7	dbSNP_134	115	1,3157		0,1,1578	no	splice-5	VWDE	NM_001135924.1		1,42,2228	GG,GC,CC		0.0317,3.1069,0.9687			12414314	44,4498	692	1579	2271	SO:0001630	splice_region_variant	221806	exon10			AAATTACCTGCCA		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.1316+1G>C	7.37:g.12414314C>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	171	81	0.473684	NM_001135924	B7ZM77|Q96SQ3	Splice_Site	SNP	ENST00000275358.3	37	CCDS47544.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	20.5	4.001307	0.74818	0.031069	3.17E-4	ENSG00000146530	ENST00000275358	.	.	.	4.01	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3189	0.82938	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	VWDE	12380839	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.194000	0.77789	2.073000	0.62155	0.591000	0.81541	.	C|0.994;G|0.006	0.006	strong		0.279	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	Intron
LPA	4018	hgsc.bcm.edu	37	6	161007496	161007496	+	Missense_Mutation	SNP	G	G	C	rs7765781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:161007496G>C	ENST00000316300.5	-	25	4158	c.4114C>G	c.(4114-4116)Ctt>Gtt	p.L1372V	LPA_ENST00000447678.1_Missense_Mutation_p.L1372V			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3880	Kringle 12. {ECO:0000255|PROSITE- ProRule:PRU00121}.				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)	TCAGAAGGAAGCTCTGTGCTT	0.478													C|||	2078	0.414936	0.6006	0.268	5008	,	,		20695	0.4107		0.3648	False		,,,				2504	0.3241				p.L1372V		Atlas-SNP	.											.	LPA	237	.	0			c.C4114G						PASS	.	C	VAL/LEU	2188,1720		625,938,391	116.0	112.0	114.0		4114	-2.2	0.0	6	dbSNP_116	114	2865,5499		510,1845,1827	yes	missense	LPA	NM_005577.2	32	1135,2783,2218	CC,CG,GG		34.2539,44.0123,41.175	benign	1372/2041	161007496	5053,7219	1954	4182	6136	SO:0001583	missense	4018	exon26			AAGGAAGCTCTGT	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.4114C>G	6.37:g.161007496G>C	ENSP00000321334:p.Leu1372Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	128	71	0.554688	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	940	0.43040293040293043	312	0.6341463414634146	99	0.27348066298342544	240	0.4195804195804196	289	0.3812664907651715	c	0.003	-2.485890	0.00163	0.559877	0.342539	ENSG00000198670	ENST00000316300;ENST00000447678	D;D	0.86956	-2.19;-2.19	2.39	-2.21	0.06973	Kringle (1);	.	.	.	.	T	0.34861	0.0912	N	0.01352	-0.895	0.80722	P	0.0	B	0.22683	0.073	B	0.12837	0.008	T	0.07083	-1.0791	8	0.13470	T	0.59	.	4.4369	0.11555	0.0:0.2799:0.1829:0.5372	rs7765781;rs52813570;rs7765781	3880	P08519	APOA_HUMAN	V	1372	ENSP00000321334:L1372V;ENSP00000395608:L1372V	ENSP00000321334:L1372V	L	-	1	0	LPA	160927486	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.349000	0.02627	-0.967000	0.03582	-0.444000	0.05651	CTT	G|0.582;C|0.418	0.418	strong		0.478	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
FTHL17	53940	hgsc.bcm.edu	37	X	31089628	31089628	+	Missense_Mutation	SNP	T	T	A	rs7058123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:31089628T>A	ENST00000359202.3	-	1	542	c.443A>T	c.(442-444)gAg>gTg	p.E148V		NM_031894.2	NP_114100.1	Q9BXU8	FHL17_HUMAN	ferritin, heavy polypeptide-like 17	148	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)		ferric iron binding (GO:0008199)			endometrium(2)|large_intestine(2)|liver(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	23						GCCACCCAGCTCTTTGATGGT	0.612													T|||	228	0.0603974	0.0129	0.0	3775	,	,		13717	0.1101		0.001	False		,,,				2504	0.1012				p.E148V		Atlas-SNP	.											.	FTHL17	99	.	0			c.A443T						PASS	.	T	VAL/GLU	65,3768		1,57,6,1573,565	72.0	61.0	65.0		443	3.7	0.0	X	dbSNP_116	65	4,6724		0,3,1,2425,1871	yes	missense	FTHL17	NM_031894.2	121	1,60,7,3998,2436	AA,AT,A,TT,T		0.0595,1.6958,0.6533	probably-damaging	148/184	31089628	69,10492	2202	4300	6502	SO:0001583	missense	53940	exon1			CCCAGCTCTTTGA	AF285592	CCDS14227.1	Xp21.2	2010-07-06			ENSG00000132446	ENSG00000132446			3987	protein-coding gene	gene with protein product	"""cancer/testis antigen 38"""	300308				11279525	Standard	NM_031894		Approved	CT38	uc004dcl.1	Q9BXU8	OTTHUMG00000021332	ENST00000359202.3:c.443A>T	X.37:g.31089628T>A	ENSP00000368207:p.Glu148Val	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	194	109	0.561856	NM_031894	Q6NT24|Q6NTE2	Missense_Mutation	SNP	ENST00000359202.3	37	CCDS14227.1	73	0.044002411091018684	8	0.01652892561983471	0	0.0	37	0.07142857142857142	1	0.0013192612137203166	T	18.77	3.694430	0.68386	0.016958	5.95E-4	ENSG00000132446	ENST00000359202	T	0.65916	-0.18	3.67	3.67	0.42095	Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);Ferritin/DPS protein domain (1);Ferritin-like (1);	0.182095	0.47852	D	0.000214	T	0.24586	0.0596	M	0.82630	2.6	0.09310	P	0.99999247289	D	0.76494	0.999	D	0.74023	0.982	T	0.70684	-0.4804	9	0.72032	D	0.01	.	9.8188	0.40869	0.0:0.0:0.0:1.0	rs7058123	148	Q9BXU8	FHL17_HUMAN	V	148	ENSP00000368207:E148V	ENSP00000368207:E148V	E	-	2	0	FTHL17	30999549	1.000000	0.71417	0.032000	0.17829	0.018000	0.09664	7.314000	0.78988	1.675000	0.50919	0.441000	0.28932	GAG	T|0.982;A|0.018	0.018	strong		0.612	FTHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056178.1	NM_031894	
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24256512	24256512	+	Silent	SNP	T	T	C	rs7005258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24256512T>C	ENST00000256412.4	+	9	1108	c.888T>C	c.(886-888)tcT>tcC	p.S296S	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000522298.1_Silent_p.S217S|ADAMDEC1_ENST00000538205.1_Silent_p.S217S	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	296	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		GGCACAGTTCTAACCTGGGGA	0.517													C|||	88	0.0175719	0.0635	0.0058	5008	,	,		18805	0.0		0.0	False		,,,				2504	0.0				p.S296S	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.T888C						PASS	.	C	,,	261,4145	803.2+/-415.7	11,239,1953	102.0	90.0	94.0		651,651,888	-0.3	0.0	8	dbSNP_116	94	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	11,241,6251	CC,CT,TT		0.0233,5.9237,2.0221	,,	217/392,217/392,296/471	24256512	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon9			CAGTTCTAACCTG	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.888T>C	8.37:g.24256512T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	133	56	0.421053	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			T|0.977;C|0.023	0.023	strong		0.517	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411781	105411781	+	Missense_Mutation	SNP	G	G	A	rs10438247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105411781G>A	ENST00000333244.5	-	7	10126	c.10007C>T	c.(10006-10008)cCg>cTg	p.P3336L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3336			P -> L (in dbSNP:rs10438247).			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)			CTCCGCCTTCGGCGCAGACAC	0.607													.|||	2697	0.538538	0.5855	0.5101	5008	,	,		20068	0.4137		0.5318	False		,,,				2504	0.6309				p.P3336L		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	0			c.C10007T						PASS	.	G	LEU/PRO	2594,1378		876,842,268	147.0	150.0	149.0		10007	2.9	0.0	14	dbSNP_119	149	4525,3787		1252,2021,883	no	missense	AHNAK2	NM_138420.2	98	2128,2863,1151	AA,AG,GG		45.5606,34.6928,42.0466	probably-damaging	3336/5796	105411781	7119,5165	1986	4156	6142	SO:0001583	missense	113146	exon7			GCCTTCGGCGCAG	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.10007C>T	14.37:g.105411781G>A	ENSP00000353114:p.Pro3336Leu	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	323	322	0.996904	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1116	0.510989010989011	298	0.6056910569105691	196	0.5414364640883977	221	0.38636363636363635	401	0.5290237467018469	g	17.20	3.329313	0.60743	0.653072	0.544394	ENSG00000185567	ENST00000333244	T	0.03094	4.05	3.83	2.91	0.33838	.	.	.	.	.	T	0.00012	0.0000	H	0.94808	3.585	0.80722	P	0.0	D	0.76494	0.999	D	0.62955	0.909	T	0.24404	-1.0161	8	0.52906	T	0.07	.	12.5658	0.56308	0.0:0.0:0.8325:0.1675	.	3336	Q8IVF2	AHNK2_HUMAN	L	3336	ENSP00000353114:P3336L	ENSP00000353114:P3336L	P	-	2	0	AHNAK2	104482826	0.303000	0.24463	0.001000	0.08648	0.002000	0.02628	2.160000	0.42348	0.789000	0.33779	0.491000	0.48974	CCG	G|0.479;A|0.521	0.521	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
VSTM1	284415	hgsc.bcm.edu	37	19	54561792	54561792	+	Silent	SNP	G	G	A	rs11669427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54561792G>A	ENST00000338372.2	-	3	298	c.123C>T	c.(121-123)gcC>gcT	p.A41A	VSTM1_ENST00000366170.2_Intron|VSTM1_ENST00000376626.1_Silent_p.A41A|VSTM1_ENST00000425006.2_Silent_p.A41A	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	41	Ig-like V-type.				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)		CATTGCTCTCGGCTTCAACCA	0.517													G|||	796	0.158946	0.0386	0.1888	5008	,	,		14443	0.1736		0.2336	False		,,,				2504	0.2086				p.A41A		Atlas-SNP	.											.	VSTM1	30	.	0			c.C123T						PASS	.	G		293,4113	159.6+/-192.1	8,277,1918	94.0	95.0	95.0		123	-7.0	0.0	19	dbSNP_120	95	1984,6616	347.8+/-326.7	206,1572,2522	no	coding-synonymous	VSTM1	NM_198481.3		214,1849,4440	AA,AG,GG		23.0698,6.65,17.5073		41/237	54561792	2277,10729	2203	4300	6503	SO:0001819	synonymous_variant	284415	exon3			GCTCTCGGCTTCA	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.123C>T	19.37:g.54561792G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Silent	SNP	ENST00000338372.2	37	CCDS12872.1																																																																																			G|0.824;A|0.176	0.176	strong		0.517	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481	
PRB2	653247	hgsc.bcm.edu	37	12	11546395	11546395	+	Missense_Mutation	SNP	G	G	T	rs11054277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11546395G>T	ENST00000389362.4	-	3	652	c.617C>A	c.(616-618)cCa>cAa	p.P206Q	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	206	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)		p.P185Q(1)|p.P206Q(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GCCTCCTTGTGGGGGTGGTCC	0.602													g|||	257	0.0513179	0.0091	0.062	5008	,	,		19479	0.0804		0.1113	False		,,,				2504	0.0092				p.P206Q		Atlas-SNP	.											PRB2_ENST00000389362,NS,carcinoma,0,2	PRB2	168	2	2	Substitution - Missense(2)	lung(2)	c.C617A						scavenged	.						68.0	78.0	75.0					12																	11546395		2075	4125	6200	SO:0001583	missense	653247	exon3			CCTTGTGGGGGTG	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.617C>A	12.37:g.11546395G>T	ENSP00000374013:p.Pro206Gln	Somatic	597	4	0.00670017		WXS	Illumina HiSeq	Phase_I	434	24	0.0552995	NM_006248	O00599|P02811|P04281	Missense_Mutation	SNP	ENST00000389362.4	37	CCDS41757.2	.	.	.	.	.	.	.	.	.	.	.	13.45	2.239350	0.39598	.	.	ENSG00000121335	ENST00000389362	T	0.04551	3.6	1.46	-2.65	0.06095	.	0.000000	0.35466	U	0.003186	T	0.04907	0.0132	L	0.33792	1.035	0.22888	N	0.998607	D	0.59357	0.985	P	0.52031	0.688	T	0.29882	-0.9997	10	0.42905	T	0.14	.	3.3379	0.07107	0.2091:0.2667:0.5243:0.0	.	206	P02812	PRB2_HUMAN	Q	206	ENSP00000374013:P206Q	ENSP00000374013:P206Q	P	-	2	0	PRB2	11437662	0.001000	0.12720	0.029000	0.17559	0.747000	0.42532	-0.415000	0.07106	-0.824000	0.04295	0.291000	0.19559	CCA	.	.	weak		0.602	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
HBS1L	10767	hgsc.bcm.edu	37	6	135358567	135358567	+	Intron	SNP	T	T	G	rs7742542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135358567T>G	ENST00000367837.5	-	4	637				HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.E343A|HBS1L_ENST00000367826.2_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		AACTTCAGTTTCTTTACTAGC	0.323													T|||	2338	0.466853	0.3381	0.4928	5008	,	,		19939	0.5347		0.4891	False		,,,				2504	0.5297				p.E343A		Atlas-SNP	.											.	HBS1L	75	.	0			c.A1028C						PASS	.						50.0	39.0	42.0					6																	135358567		692	1591	2283	SO:0001627	intron_variant	10767	exon5			TCAGTTTCTTTAC	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2143A>C	6.37:g.135358567T>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	140	74	0.528571	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	37	CCDS5173.1	1040	0.47619047619047616	183	0.3719512195121951	171	0.4723756906077348	311	0.5437062937062938	375	0.4947229551451187	T	0.430	-0.903663	0.02453	.	.	ENSG00000112339	ENST00000367822	.	.	.	4.7	-2.0	0.07433	.	.	.	.	.	T	0.06005	0.0156	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.11329	0.006	T	0.34725	-0.9817	6	0.28530	T	0.3	.	1.0202	0.01516	0.1539:0.1557:0.2315:0.4589	rs7742542;rs52802452;rs57741240;rs7742542	343	Q9Y450-2	.	A	343	.	ENSP00000356796:E343A	E	-	2	0	HBS1L	135400260	0.931000	0.31567	0.000000	0.03702	0.560000	0.35617	1.152000	0.31663	-0.425000	0.07371	0.533000	0.62120	GAA	T|0.538;G|0.462	0.462	strong		0.323	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
SPINK4	27290	hgsc.bcm.edu	37	9	33240225	33240225	+	Missense_Mutation	SNP	G	G	A	rs706107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:33240225G>A	ENST00000379721.3	+	1	64	c.19G>A	c.(19-21)Gta>Ata	p.V7I	SPINK4_ENST00000379725.1_Intron|SPINK4_ENST00000379723.1_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	185	0	0		WXS	Illumina HiSeq	Phase_I	215	214	0.995349	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	
MYLK	4638	hgsc.bcm.edu	37	3	123357037	123357037	+	Silent	SNP	A	A	G	rs820463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:123357037A>G	ENST00000475616.1	-	26	4841	c.4842T>C	c.(4840-4842)aaT>aaC	p.N1614N	MYLK_ENST00000360304.3_Silent_p.N1614N|MYLK_ENST00000360772.3_Silent_p.N1614N|MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000346322.5_Silent_p.N1545N|MYLK_ENST00000354792.5_Silent_p.N414N|MYLK_ENST00000359169.1_Silent_p.N1614N			Q15746	MYLK_HUMAN	myosin light chain kinase	1614	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		GAGACCCCGCATTCTCTGAAA	0.552													A|||	1875	0.374401	0.4743	0.3271	5008	,	,		20106	0.6399		0.0785	False		,,,				2504	0.3037				p.N1614N		Atlas-SNP	.											.	MYLK	224	.	0			c.T4842C						PASS	.	A	,,,	1798,2608	529.2+/-372.6	372,1054,777	57.0	58.0	58.0		4842,4635,4842,4635	-0.1	1.0	3	dbSNP_86	58	776,7824	184.5+/-232.4	41,694,3565	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	,,,	413,1748,4342	GG,GA,AA		9.0233,40.808,19.7909	,,,	1614/1915,1545/1846,1614/1864,1545/1795	123357037	2574,10432	2203	4300	6503	SO:0001819	synonymous_variant	4638	exon29			CCCCGCATTCTCT	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.4842T>C	3.37:g.123357037A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	124	49	0.395161	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|0.732;G|0.268	0.268	strong		0.552	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
SPATA20	64847	hgsc.bcm.edu	37	17	48625928	48625928	+	Missense_Mutation	SNP	C	C	G	rs8076632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48625928C>G	ENST00000356488.4	+	3	345	c.262C>G	c.(262-264)Cag>Gag	p.Q88E	SPATA20_ENST00000006658.6_Missense_Mutation_p.Q104E|SPATA20_ENST00000393244.3_Missense_Mutation_p.Q44E|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	88			Q -> E (in dbSNP:rs8076632). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CCCCTGGGGACAGGAAGCCTT	0.637													C|||	1690	0.33746	0.6831	0.2767	5008	,	,		18074	0.0625		0.3499	False		,,,				2504	0.184				p.Q104E		Atlas-SNP	.											SPATA20,NS,carcinoma,0,1	SPATA20	59	1	0			c.C310G						scavenged	.	C	GLU/GLN	2797,1607	646.3+/-398.3	904,989,309	72.0	81.0	78.0		310	4.6	1.0	17	dbSNP_116	78	3108,5492	464.2+/-366.2	561,1986,1753	yes	missense	SPATA20	NM_022827.2	29	1465,2975,2062	GG,GC,CC		36.1395,36.4896,45.4091	benign	104/803	48625928	5905,7099	2202	4300	6502	SO:0001583	missense	64847	exon4			TGGGGACAGGAAG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.262C>G	17.37:g.48625928C>G	ENSP00000348878:p.Gln88Glu	Somatic	39	1	0.025641		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	746	0.3415750915750916	324	0.6585365853658537	113	0.31215469613259667	48	0.08391608391608392	261	0.34432717678100266	C	10.44	1.351888	0.24512	0.635104	0.361395	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.35973	1.28;1.28;1.28	4.59	4.59	0.56863	Thioredoxin-like fold (2);Domain of unknown function DUF255 (1);	0.057503	0.64402	D	0.000001	T	0.00012	0.0000	N	0.00507	-1.42	0.20403	P	0.9999042779	B;B;B	0.14012	0.009;0.009;0.003	B;B;B	0.12156	0.007;0.007;0.007	T	0.39375	-0.9617	9	0.02654	T	1	-19.6545	15.7482	0.77962	0.0:1.0:0.0:0.0	rs8076632;rs11559097;rs17855972;rs57357545;rs8076632	88;88;104	B4DZC5;Q8TB22;Q8TB22-2	.;SPT20_HUMAN;.	E	104;88;44	ENSP00000006658:Q104E;ENSP00000348878:Q88E;ENSP00000376935:Q44E	ENSP00000006658:Q104E	Q	+	1	0	SPATA20	45980927	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.181000	0.65054	2.368000	0.80403	0.561000	0.74099	CAG	C|0.583;G|0.417	0.417	strong		0.637	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
MUC4	4585	hgsc.bcm.edu	37	3	195507926	195507926	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507926C>T	ENST00000463781.3	-	2	10984	c.10525G>A	c.(10525-10527)Ggc>Agc	p.G3509S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G3509S	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)		GAGGAAGCGCCGGTGACAGGA	0.602																																					p.G3509S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	0			c.G10525A						scavenged	.						41.0	37.0	38.0					3																	195507926		644	1581	2225	SO:0001583	missense	4585	exon2			AAGCGCCGGTGAC	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.10525G>A	3.37:g.195507926C>T	ENSP00000417498:p.Gly3509Ser	Somatic	445	6	0.0134831		WXS	Illumina HiSeq	Phase_I	64	17	0.265625	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	3.931	-0.016213	0.07681	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.55;1.55	0.743	-1.49	0.08718	.	.	.	.	.	T	0.10078	0.0247	N	0.03608	-0.345	0.09310	N	1	B	0.15930	0.015	B	0.09377	0.004	T	0.23261	-1.0193	8	.	.	.	.	2.5972	0.04857	0.0:0.2544:0.2715:0.4741	.	3381	E7ESK3	.	S	3509	ENSP00000417498:G3509S;ENSP00000420243:G3509S	.	G	-	1	0	MUC4	196992705	0.005000	0.15991	0.004000	0.12327	0.004000	0.04260	0.111000	0.15458	-1.791000	0.01261	-1.780000	0.00649	GGC	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
IRF2BP2	359948	hgsc.bcm.edu	37	1	234743492	234743492	+	Silent	SNP	C	C	T	rs14739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:234743492C>T	ENST00000366609.3	-	2	1185	c.1155G>A	c.(1153-1155)gaG>gaA	p.E385E	RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000491430.1_5'UTR|IRF2BP2_ENST00000366610.3_Silent_p.E369E	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			TCTTGAGCCCCTCTGTGGATG	0.597													T|||	636	0.126997	0.4508	0.0533	5008	,	,		17358	0.0		0.001	False		,,,				2504	0.002				p.E385E		Atlas-SNP	.											.	IRF2BP2	37	.	0			c.G1155A						PASS	.	T	,	1744,2662	646.1+/-398.3	337,1070,796	102.0	117.0	112.0		1107,1155	3.2	1.0	1	dbSNP_52	112	13,8587	818.4+/-406.9	0,13,4287	no	coding-synonymous,coding-synonymous	IRF2BP2	NM_001077397.1,NM_182972.2	,	337,1083,5083	TT,TC,CC		0.1512,39.5824,13.5091	,	369/572,385/588	234743492	1757,11249	2203	4300	6503	SO:0001819	synonymous_variant	359948	exon2			GAGCCCCTCTGTG	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.1155G>A	1.37:g.234743492C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	117	115	0.982906	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	37	CCDS1602.1																																																																																			C|0.863;T|0.137	0.137	strong		0.597	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972	
MT-ND5	4540	hgsc.bcm.edu	37	M	12705	12705	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:12705C>T	ENST00000361567.2	+	1	369	c.369C>T	c.(367-369)atC>atT	p.I123I	MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TL2_ENST00000387456.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	123					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TATCTACTCATTTTCCTAATT	0.373																																					p.I123I		Atlas-SNP	.											.	.	.	.	0			c.C369T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ACTCATCTTCCTA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.369C>T	M.37:g.12705C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.373	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
WFS1	7466	hgsc.bcm.edu	37	4	6303955	6303955	+	Silent	SNP	G	G	A	rs1046314	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6303955G>A	ENST00000226760.1	+	8	2603	c.2433G>A	c.(2431-2433)aaG>aaA	p.K811K	WFS1_ENST00000503569.1_Silent_p.K811K	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	811					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)		GCGAGTTCAAGAGCGTGCTGC	0.672													G|||	3271	0.653155	0.4871	0.6772	5008	,	,		17476	0.9038		0.6213	False		,,,				2504	0.635				p.K811K		Atlas-SNP	.											.	WFS1	71	.	0			c.G2433A	GRCh37	CM021365	WFS1	M	rs1046314	PASS	.	G	,	2229,2177	578.5+/-384.7	542,1145,516	42.0	46.0	44.0		2433,2433	1.2	0.1	4	dbSNP_86	44	5131,3469	623.6+/-397.5	1517,2097,686	no	coding-synonymous,coding-synonymous	WFS1	NM_001145853.1,NM_006005.3	,	2059,3242,1202	AA,AG,GG		40.3372,49.4099,43.4107	,	811/891,811/891	6303955	7360,5646	2203	4300	6503	SO:0001819	synonymous_variant	7466	exon8			GTTCAAGAGCGTG	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.2433G>A	4.37:g.6303955G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	72	42	0.583333	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	37	CCDS3386.1																																																																																			G|0.382;A|0.618	0.618	strong		0.672	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
EFTUD1	79631	hgsc.bcm.edu	37	15	82443824	82443824	+	Missense_Mutation	SNP	C	C	T	rs78664413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:82443824C>T	ENST00000268206.7	-	18	3139	c.2971G>A	c.(2971-2973)Gcc>Acc	p.A991T	EFTUD1_ENST00000359445.3_Missense_Mutation_p.A940T	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	991					GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)	p.A991T(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						TCACCAGTGGCCATGATGTCA	0.448													C|||	286	0.0571086	0.1415	0.0793	5008	,	,		22875	0.005		0.0328	False		,,,				2504	0.0061				p.A991T		Atlas-SNP	.											EFTUD1,NS,carcinoma,0,1	EFTUD1	74	1	1	Substitution - Missense(1)	pancreas(1)	c.G2971A						PASS	.	C	THR/ALA,THR/ALA	479,3505		30,419,1543	118.0	115.0	116.0		2818,2971	6.2	1.0	15	dbSNP_131	116	299,8045		5,289,3878	yes	missense,missense	EFTUD1	NM_001040610.2,NM_024580.5	58,58	35,708,5421	TT,TC,CC		3.5834,12.0231,6.3108	benign,benign	940/1070,991/1121	82443824	778,11550	1992	4172	6164	SO:0001583	missense	79631	exon18			CAGTGGCCATGAT	AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"""ribosome assembly 1 homolog (yeast)"""					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.2971G>A	15.37:g.82443824C>T	ENSP00000268206:p.Ala991Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Missense_Mutation	SNP	ENST00000268206.7	37	CCDS42071.1	141	0.06456043956043957	87	0.17682926829268292	26	0.0718232044198895	5	0.008741258741258742	23	0.030343007915567283	C	18.87	3.715333	0.68844	0.120231	0.035834	ENSG00000140598	ENST00000268206;ENST00000359445	T;T	0.62498	0.02;0.02	6.16	6.16	0.99307	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (3);	0.000000	0.45867	D	0.000334	T	0.00210	0.0006	L	0.36672	1.1	0.09310	P	0.9999999986533	P;P	0.41848	0.481;0.763	B;B	0.42522	0.263;0.39	T	0.00129	-1.2016	9	0.34782	T	0.22	-6.8926	20.8598	0.99761	0.0:1.0:0.0:0.0	.	940;991	Q7Z2Z2-2;Q7Z2Z2	.;ETUD1_HUMAN	T	991;940	ENSP00000268206:A991T;ENSP00000352418:A940T	ENSP00000268206:A991T	A	-	1	0	EFTUD1	80230879	1.000000	0.71417	1.000000	0.80357	0.745000	0.42441	4.810000	0.62598	2.937000	0.99478	0.650000	0.86243	GCC	C|0.942;T|0.058	0.058	strong		0.448	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580	
RANBP3	8498	hgsc.bcm.edu	37	19	5914605	5914605	+	IGR	SNP	A	A	G	rs7249419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5914605A>G	ENST00000340578.6	-	0	3233				CAPS_ENST00000452990.2_Missense_Mutation_p.R39G|AC104532.4_ENST00000591109.1_RNA|CAPS_ENST00000588776.1_Missense_Mutation_p.R125G|CAPS_ENST00000222125.5_Missense_Mutation_p.R39G|AC104532.2_ENST00000588891.1_3'UTR	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3						intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						GGACGGGAGCAGATCCCTGGA	0.647													A|||	326	0.0650958	0.1452	0.062	5008	,	,		17171	0.0129		0.003	False		,,,				2504	0.0767				p.R39G		Atlas-SNP	.											.	CAPS	14	.	0			c.A115G						PASS	.	A	GLY/ARG,GLY/ARG	597,3809	259.8+/-263.3	35,527,1641	66.0	68.0	67.0		115,115	0.2	0.5	19	dbSNP_116	67	35,8565	23.4+/-69.3	0,35,4265	yes	missense,missense	CAPS	NM_004058.3,NM_080590.2	125,125	35,562,5906	GG,GA,AA		0.407,13.5497,4.8593	benign,benign	39/190,39/163	5914605	632,12374	2203	4300	6503	SO:0001628	intergenic_variant	828	exon3			GGGAGCAGATCCC	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4			19.37:g.5914605A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_080590	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	37	CCDS42478.1	83	0.038003663003663	62	0.12601626016260162	14	0.03867403314917127	5	0.008741258741258742	2	0.002638522427440633	A	9.241	1.038301	0.19669	0.135497	0.00407	ENSG00000105519	ENST00000394521;ENST00000222125;ENST00000452990	T;T	0.57107	0.79;0.42	5.3	0.24	0.15489	EF-hand-like domain (1);	0.486738	0.19195	N	0.120324	T	0.00241	0.0007	L	0.35723	1.085	0.22918	N	0.998565	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.04635	-1.0937	10	0.06494	T	0.89	-2.5164	7.9602	0.30066	0.3895:0.3881:0.2224:0.0	rs7249419;rs7249419	172;39	Q8NF12;Q13938	.;CAYP1_HUMAN	G	172;39;39	ENSP00000222125:R39G;ENSP00000403263:R39G	ENSP00000222125:R39G	R	+	1	2	CAPS	5865605	0.081000	0.21417	0.537000	0.28052	0.018000	0.09664	-0.059000	0.11731	0.543000	0.28864	0.454000	0.30748	AGA	A|0.954;G|0.046	0.046	strong		0.647	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322	
GAS2L3	283431	hgsc.bcm.edu	37	12	101018061	101018061	+	Missense_Mutation	SNP	C	C	T	rs61748063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101018061C>T	ENST00000539410.1	+	9	1864	c.1478C>T	c.(1477-1479)tCa>tTa	p.S493L	GAS2L3_ENST00000266754.5_Missense_Mutation_p.S493L|GAS2L3_ENST00000547754.1_Missense_Mutation_p.S493L|GAS2L3_ENST00000537247.1_Missense_Mutation_p.S389L			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	493					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						GCTGCACATTCAAATTCATCC	0.363													C|||	17	0.00339457	0.0008	0.0086	5008	,	,		20148	0.0		0.008	False		,,,				2504	0.002				p.S493L		Atlas-SNP	.											.	GAS2L3	76	.	0			c.C1478T						PASS	.	C	LEU/SER	6,4398	11.4+/-27.6	0,6,2196	61.0	65.0	64.0		1478	-0.2	0.0	12	dbSNP_129	64	50,8550	32.8+/-85.7	0,50,4250	yes	missense	GAS2L3	NM_174942.1	145	0,56,6446	TT,TC,CC		0.5814,0.1362,0.4306	benign	493/695	101018061	56,12948	2202	4300	6502	SO:0001583	missense	283431	exon10			CACATTCAAATTC	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.1478C>T	12.37:g.101018061C>T	ENSP00000439672:p.Ser493Leu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_174942	B2RCN2	Missense_Mutation	SNP	ENST00000539410.1	37	CCDS9079.1	11	0.005036630036630037	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	5	0.006596306068601583	C	0.060	-1.227601	0.01518	0.001362	0.005814	ENSG00000139354	ENST00000266754;ENST00000547754;ENST00000537247;ENST00000539410	T;T;T;T	0.22743	1.96;1.96;1.94;1.96	4.93	-0.166	0.13351	.	1.089570	0.07116	N	0.843066	T	0.06142	0.0159	N	0.02315	-0.6	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37478	-0.9704	10	0.23302	T	0.38	-1.9276	10.8995	0.47043	0.0:0.4908:0.0:0.5092	rs61748063	493	Q86XJ1	GA2L3_HUMAN	L	493;493;389;493	ENSP00000266754:S493L;ENSP00000448955:S493L;ENSP00000442406:S389L;ENSP00000439672:S493L	ENSP00000266754:S493L	S	+	2	0	GAS2L3	99542192	0.000000	0.05858	0.000000	0.03702	0.198000	0.23893	-0.585000	0.05794	-0.113000	0.11958	-0.793000	0.03317	TCA	C|0.995;T|0.005	0.005	strong		0.363	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	
KIAA0195	9772	hgsc.bcm.edu	37	17	73488794	73488794	+	Silent	SNP	C	C	T	rs4078259	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73488794C>T	ENST00000314256.7	+	15	2230	c.1836C>T	c.(1834-1836)atC>atT	p.I612I	KIAA0195_ENST00000375248.5_Silent_p.I622I|KIAA0195_ENST00000579208.1_Silent_p.I263I	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	612						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGTGCAACATCGCCCTGCAAG	0.642													C|||	3184	0.635783	0.5257	0.5706	5008	,	,		18745	0.4673		0.8151	False		,,,				2504	0.82				p.I612I		Atlas-SNP	.											.	KIAA0195	102	.	0			c.C1836T						PASS	.	C		2485,1921	625.5+/-394.5	696,1093,414	103.0	99.0	100.0		1836	1.4	1.0	17	dbSNP_108	100	7261,1339	756.7+/-407.5	3068,1125,107	no	coding-synonymous	KIAA0195	NM_014738.4		3764,2218,521	TT,TC,CC		15.5698,43.5996,25.0654		612/1357	73488794	9746,3260	2203	4300	6503	SO:0001819	synonymous_variant	9772	exon15			CAACATCGCCCTG		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.1836C>T	17.37:g.73488794C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_014738	O75536|Q86XF1	Silent	SNP	ENST00000314256.7	37	CCDS32732.1																																																																																			C|0.295;T|0.705	0.705	strong		0.642	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
OBSCN	84033	hgsc.bcm.edu	37	1	228461055	228461055	+	Intron	SNP	T	T	C	rs113996842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228461055T>C	ENST00000422127.1	+	18	5181				OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000570156.2_Silent_p.C2023C|RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000284548.11_Intron|OBSCN_ENST00000359599.6_Silent_p.C495C|RP5-1139B12.3_ENST00000602529.1_RNA|OBSCN_ENST00000366709.4_Intron|RP5-1139B12.2_ENST00000602517.1_RNA	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)				CGCTGAGCTGTGAGGTGGCCC	0.637													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		17510	0.0		0.0	False		,,,				2504	0.0				p.C2023C		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T6069C						PASS	.																																			SO:0001627	intron_variant	84033	exon21			GAGCTGTGAGGTG	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.5138-416T>C	1.37:g.228461055T>C		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	290	140	0.482759	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																																																																																			T|0.997;C|0.003	0.003	strong		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656562	46656562	+	Silent	SNP	A	A	G	rs7287371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46656562A>G	ENST00000253255.5	-	1	2657	c.2658T>C	c.(2656-2658)taT>taC	p.Y886Y		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	886	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)		TGAGTGTTGGATAAAAACAAT	0.388													A|||	265	0.0529153	0.1899	0.0144	5008	,	,		21079	0.0		0.0	False		,,,				2504	0.0041				p.Y886Y		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T2658C						PASS	.	A		777,3629	311.9+/-292.3	72,633,1498	83.0	84.0	83.0		2658	-10.1	0.0	22	dbSNP_116	83	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	PKDREJ	NM_006071.1		72,647,5784	GG,GA,AA		0.1628,17.635,6.0818		886/2254	46656562	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			TGTTGGATAAAAA	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.2658T>C	22.37:g.46656562A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	139	74	0.532374	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.942;G|0.058	0.058	strong		0.388	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
CCDC168	643677	hgsc.bcm.edu	37	13	103388370	103388370	+	Missense_Mutation	SNP	C	C	T	rs9518825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	202	0	0		WXS	Illumina HiSeq	Phase_I	242	116	0.479339	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	
ATP11A	23250	hgsc.bcm.edu	37	13	113527967	113527967	+	Silent	SNP	G	G	A	rs1320525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113527967G>A	ENST00000487903.1	+	27	3226	c.3138G>A	c.(3136-3138)tcG>tcA	p.S1046S	ATP11A_ENST00000283558.8_Silent_p.S1046S|ATP11A_ENST00000375645.3_Silent_p.S1046S|ATP11A_ENST00000375630.2_Silent_p.S1046S			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	1046					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)				TTGTCTTTTCGCTTCTCTGGG	0.393											OREG0003854	type=REGULATORY REGION|Gene=ATP11A|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	1877	0.3748	0.298	0.3761	5008	,	,		21339	0.4742		0.3658	False		,,,				2504	0.3845				p.S1046S		Atlas-SNP	.											.	ATP11A	225	.	0			c.G3138A						PASS	.	G	,	1360,3046	451.2+/-349.6	220,920,1063	205.0	169.0	181.0		3138,3138	2.5	1.0	13	dbSNP_88	181	3364,5236	499.4+/-375.0	674,2016,1610	no	coding-synonymous,coding-synonymous	ATP11A	NM_015205.2,NM_032189.3	,	894,2936,2673	AA,AG,GG		39.1163,30.867,36.3217	,	1046/1135,1046/1192	113527967	4724,8282	2203	4300	6503	SO:0001819	synonymous_variant	23250	exon27			CTTTTCGCTTCTC	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.3138G>A	13.37:g.113527967G>A		Somatic	202	0	0	1451	WXS	Illumina HiSeq	Phase_I	188	99	0.526596	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1																																																																																			G|0.623;A|0.377	0.377	strong		0.393	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
ZNF283	284349	hgsc.bcm.edu	37	19	44352690	44352690	+	Missense_Mutation	SNP	G	G	T	rs10417624|rs386809610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44352690G>T	ENST00000324461.7	+	7	2234	c.1937G>T	c.(1936-1938)aGa>aTa	p.R646I	ZNF283_ENST00000588797.1_Missense_Mutation_p.R507I	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	646			R -> I (in dbSNP:rs10417624).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(4)	8		Prostate(69;0.0352)				GTTCATGAGAGAACTCATAGT	0.368													G|||	221	0.0441294	0.1543	0.0231	5008	,	,		19758	0.0		0.001	False		,,,				2504	0.0				p.R646I		Atlas-SNP	.											ZNF283_ENST00000324461,NS,carcinoma,+1,1	ZNF283	83	1	0			c.G1937T						PASS	.	G	ILE/ARG	480,3432		29,422,1505	91.0	97.0	95.0		1937	2.9	0.3	19	dbSNP_119	95	10,8300		0,10,4145	yes	missense	ZNF283	NM_181845.1	97	29,432,5650	TT,TG,GG		0.1203,12.2699,4.0092	benign	646/680	44352690	490,11732	1956	4155	6111	SO:0001583	missense	284349	exon7			ATGAGAGAACTCA	AK098175	CCDS46097.1, CCDS74387.1	19q13.31	2013-01-08			ENSG00000167637	ENSG00000167637		"""Zinc fingers, C2H2-type"", ""-"""	13077	protein-coding gene	gene with protein product						12743021	Standard	NM_181845		Approved		uc002oxr.4	Q8N7M2		ENST00000324461.7:c.1937G>T	19.37:g.44352690G>T	ENSP00000327314:p.Arg646Ile	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_181845	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Missense_Mutation	SNP	ENST00000324461.7	37	CCDS46097.1	79	0.036172161172161175	67	0.13617886178861788	12	0.03314917127071823	0	0.0	0	0.0	G	13.04	2.117736	0.37339	0.122699	0.001203	ENSG00000167637	ENST00000324461	T	0.47528	0.84	2.89	2.89	0.33648	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00468	0.0015	M	0.71296	2.17	0.09310	P	0.9999999999950114	P	0.42941	0.794	P	0.45119	0.47	T	0.16276	-1.0408	8	0.59425	D	0.04	.	5.8675	0.18783	0.1483:0.0:0.8517:0.0	rs10417624;rs57616204;rs10417624	646	Q8N7M2	ZN283_HUMAN	I	646	ENSP00000327314:R646I	ENSP00000327314:R646I	R	+	2	0	ZNF283	49044530	0.189000	0.23263	0.274000	0.24659	0.180000	0.23129	2.942000	0.49018	1.626000	0.50381	0.557000	0.71058	AGA	G|0.953;T|0.047	0.047	strong		0.368	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845	
TAF1	6872	hgsc.bcm.edu	37	X	70586196	70586196	+	Missense_Mutation	SNP	C	C	T	rs139510844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70586196C>T	ENST00000373790.4	+	1	83	c.32C>T	c.(31-33)aCa>aTa	p.T11I	TAF1_ENST00000449580.1_Missense_Mutation_p.T11I|TAF1_ENST00000276072.3_Missense_Mutation_p.T11I|TAF1_ENST00000423759.1_Missense_Mutation_p.T11I	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	11	Protein kinase 1.				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)				CTGCTGCGGACAGCAGCTACC	0.562													c|||	27	0.00715232	0.0189	0.0029	3775	,	,		5194	0.0		0.0	False		,,,				2504	0.0				p.T11I		Atlas-SNP	.											.	TAF1	439	.	0			c.C32T						PASS	.	C	ILE/THR,ILE/THR	98,3737		0,86,12,1546,559	66.0	56.0	59.0		32,32	-5.4	0.0	X	dbSNP_134	59	0,6728		0,0,0,2428,1872	yes	missense,missense	TAF1	NM_004606.3,NM_138923.2	89,89	0,86,12,3974,2431	TT,TC,T,CC,C		0.0,2.5554,0.9278	possibly-damaging,possibly-damaging	11/1894,11/1873	70586196	98,10465	2203	4300	6503	SO:0001583	missense	6872	exon1			TGCGGACAGCAGC		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.32C>T	X.37:g.70586196C>T	ENSP00000362895:p.Thr11Ile	Somatic	303	1	0.00330033		WXS	Illumina HiSeq	Phase_I	351	183	0.521368	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	12	0.007233273056057866	6	0.012345679012345678	1	0.002777777777777778	1	0.0017482517482517483	0	0.0	.	10.35	1.325295	0.24080	0.025554	0.0	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.08720	3.06;3.12;3.13;3.08	4.36	-5.37	0.02681	.	4.117550	0.00760	N	0.001123	T	0.01254	0.0041	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.34304	-0.9834	10	0.39692	T	0.17	.	4.0791	0.09917	0.4281:0.2007:0.0:0.3712	.	11;11	P21675;P21675-2	TAF1_HUMAN;.	I	11	ENSP00000362895:T11I;ENSP00000389000:T11I;ENSP00000406549:T11I;ENSP00000276072:T11I	ENSP00000276072:T11I	T	+	2	0	TAF1	70502921	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.175000	0.03102	-1.604000	0.01595	0.399000	0.26434	ACA	C|0.989;T|0.011	0.011	strong		0.562	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
MASP2	10747	hgsc.bcm.edu	37	1	11087687	11087687	+	Missense_Mutation	SNP	C	C	T	rs12085877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11087687C>T	ENST00000400897.3	-	11	1331	c.1316G>A	c.(1315-1317)cGc>cAc	p.R439H	RP4-635E18.8_ENST00000607145.1_RNA	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	439			R -> H (in dbSNP:rs12085877).		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)		TCCTGTTGTGCGGGCTGATAG	0.443													C|||	144	0.028754	0.1036	0.0101	5008	,	,		19654	0.0		0.0	False		,,,				2504	0.0				p.R439H	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											MASP2,NS,carcinoma,-1,1	MASP2	71	1	0			c.G1316A						PASS	.	C	HIS/ARG	413,3987		16,381,1803	59.0	62.0	61.0		1316	-0.5	0.0	1	dbSNP_120	61	3,8595		0,3,4296	yes	missense	MASP2	NM_006610.3	29	16,384,6099	TT,TC,CC		0.0349,9.3864,3.2005	benign	439/687	11087687	416,12582	2200	4299	6499	SO:0001583	missense	10747	exon11			GTTGTGCGGGCTG	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.1316G>A	1.37:g.11087687C>T	ENSP00000383690:p.Arg439His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	37	CCDS123.1	54	0.024725274725274724	50	0.1016260162601626	4	0.011049723756906077	0	0.0	0	0.0	C	11.07	1.530812	0.27387	0.093864	3.49E-4	ENSG00000009724	ENST00000400897	D	0.92858	-3.12	5.45	-0.488	0.12056	Peptidase cysteine/serine, trypsin-like (1);Complement control module (1);	0.541857	0.18692	N	0.133825	T	0.12050	0.0293	L	0.28400	0.85	0.21802	N	0.99953	B	0.11235	0.004	B	0.06405	0.002	T	0.50363	-0.8837	10	0.35671	T	0.21	.	0.5192	0.00609	0.2067:0.2927:0.1873:0.3133	rs12085877;rs52829987;rs12085877	439	O00187	MASP2_HUMAN	H	439	ENSP00000383690:R439H	ENSP00000383690:R439H	R	-	2	0	MASP2	11010274	0.000000	0.05858	0.005000	0.12908	0.027000	0.11550	-0.560000	0.05964	0.002000	0.14630	0.563000	0.77884	CGC	C|0.971;T|0.029	0.029	strong		0.443	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610	
TMEM82	388595	hgsc.bcm.edu	37	1	16069664	16069664	+	Missense_Mutation	SNP	T	T	C	rs61740067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16069664T>C	ENST00000375782.1	+	3	449	c.311T>C	c.(310-312)gTg>gCg	p.V104A	TMEM82_ENST00000465575.1_3'UTR|RP11-169K16.4_ENST00000418525.1_RNA	NM_001013641.1	NP_001013663.1	A0PJX8	TMM82_HUMAN	transmembrane protein 82	104	Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|lung(5)|prostate(1)|skin(1)	13		Colorectal(325;0.00108)|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;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTCCGGGCCGTGTCCACGCTG	0.701													T|||	115	0.0229633	0.0817	0.0101	5008	,	,		13676	0.0		0.0	False		,,,				2504	0.0				p.V104A		Atlas-SNP	.											.	TMEM82	30	.	0			c.T311C						PASS	.	T	ALA/VAL	248,4156	138.4+/-174.2	7,234,1961	39.0	37.0	38.0		311	4.4	0.8	1	dbSNP_129	38	0,8594		0,0,4297	yes	missense	TMEM82	NM_001013641.1	64	7,234,6258	CC,CT,TT		0.0,5.6312,1.908	benign	104/344	16069664	248,12750	2202	4297	6499	SO:0001583	missense	388595	exon3			GGGCCGTGTCCAC		CCDS30608.1	1p36.13	2008-02-05				ENSG00000162460			32350	protein-coding gene	gene with protein product							Standard	NM_001013641		Approved		uc001axc.4	A0PJX8		ENST00000375782.1:c.311T>C	1.37:g.16069664T>C	ENSP00000364938:p.Val104Ala	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	80	29	0.3625	NM_001013641	B2RP27|Q5VVD4	Missense_Mutation	SNP	ENST00000375782.1	37	CCDS30608.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	T	18.43	3.622000	0.66787	0.056312	0.0	ENSG00000162460	ENST00000375782	T	0.57595	0.39	4.44	4.44	0.53790	.	0.248154	0.34002	N	0.004349	T	0.01976	0.0062	M	0.72894	2.215	0.32890	D	0.511731	P	0.49559	0.925	B	0.38264	0.269	T	0.49370	-0.8947	10	0.66056	D	0.02	-21.6084	13.99	0.64359	0.0:0.0:0.0:1.0	rs61740067	104	A0PJX8	TMM82_HUMAN	A	104	ENSP00000364938:V104A	ENSP00000364938:V104A	V	+	2	0	TMEM82	15942251	0.731000	0.28111	0.774000	0.31636	0.905000	0.53344	3.834000	0.55798	1.763000	0.52060	0.459000	0.35465	GTG	T|0.982;C|0.018	0.018	strong		0.701	TMEM82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008471.2	NM_001013641	
ZNF778	197320	hgsc.bcm.edu	37	16	89289624	89289624	+	Silent	SNP	G	G	A	rs12920028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	209	0	0		WXS	Illumina HiSeq	Phase_I	181	83	0.458564	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	
OR2T2	401992	hgsc.bcm.edu	37	1	248616668	248616668	+	Silent	SNP	C	C	T	rs144808604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248616668C>T	ENST00000342927.3	+	1	592	c.570C>T	c.(568-570)tgC>tgT	p.C190C		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGTTGTCTTGCACAGACACGT	0.502													C|||	13	0.00259585	0.0	0.0072	5008	,	,		23424	0.0		0.007	False		,,,				2504	0.001				p.C190C		Atlas-SNP	.											.	OR2T2	73	.	0			c.C570T						PASS	.	C		5,4341		1,3,2169	11.0	12.0	11.0		570	-0.1	0.0	1	dbSNP_134	11	102,8330		27,48,4141	no	coding-synonymous	OR2T2	NM_001004136.1		28,51,6310	TT,TC,CC		1.2097,0.115,0.8374		190/325	248616668	107,12671	2173	4216	6389	SO:0001819	synonymous_variant	401992	exon1			GTCTTGCACAGAC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.570C>T	1.37:g.248616668C>T		Somatic	490	0	0		WXS	Illumina HiSeq	Phase_I	544	205	0.376838	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			C|0.997;T|0.003	0.003	strong		0.502	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
ZNF286B	729288	hgsc.bcm.edu	37	17	18566422	18566422	+	Missense_Mutation	SNP	C	C	T	rs146829975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18566422C>T	ENST00000545289.1	-	5	647	c.397G>A	c.(397-399)Gaa>Aaa	p.E133K	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	133					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						TTGCATGATTCTGCTTTGGAA	0.408													.|||	165	0.0329473	0.118	0.0115	5008	,	,		22416	0.0		0.001	False		,,,				2504	0.0				p.E133K		Atlas-SNP	.											.	ZNF286B	75	.	0			c.G397A						PASS	.	C	LYS/GLU	110,1274		4,102,586	90.0	80.0	83.0		397	1.6	1.0	17	dbSNP_134	83	1,3179		0,1,1589	no	missense	ZNF286B	NM_001145045.1	56	4,103,2175	TT,TC,CC		0.0314,7.948,2.4321	benign	133/523	18566422	111,4453	692	1590	2282	SO:0001583	missense	729288	exon5			ATGATTCTGCTTT		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.397G>A	17.37:g.18566422C>T	ENSP00000461413:p.Glu133Lys	Somatic	416	0	0		WXS	Illumina HiSeq	Phase_I	381	149	0.391076	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			C|0.975;T|0.025	0.025	strong		0.408	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74203789	74203789	+	Missense_Mutation	SNP	G	G	A	rs17782124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74203789G>A	ENST00000286523.5	-	3	2443	c.1661C>T	c.(1660-1662)cCt>cTt	p.P554L	ELMSAN1_ENST00000394071.2_Missense_Mutation_p.P554L|ELMSAN1_ENST00000486739.1_5'Flank	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	554			P -> L (in dbSNP:rs17782124). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										GTTCTGTTCAGGACCCTTCCC	0.607													G|||	766	0.152955	0.0507	0.1182	5008	,	,		17647	0.1409		0.1839	False		,,,				2504	0.2965				p.P554L		Atlas-SNP	.											.	.	.	.	0			c.C1661T						PASS	.	G	LEU/PRO,LEU/PRO	284,4122	157.0+/-190.0	12,260,1931	98.0	82.0	88.0		1661,1661	-0.3	0.0	14	dbSNP_123	88	1667,6933	307.6+/-308.5	164,1339,2797	yes	missense,missense	C14orf43	NM_001043318.1,NM_194278.3	98,98	176,1599,4728	AA,AG,GG		19.3837,6.4458,15.0008	benign,benign	554/1046,554/1046	74203789	1951,11055	2203	4300	6503	SO:0001583	missense	91748	exon3			TGTTCAGGACCCT	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.1661C>T	14.37:g.74203789G>A	ENSP00000286523:p.Pro554Leu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	134	68	0.507463	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	
OBSCN	84033	hgsc.bcm.edu	37	1	228412308	228412308	+	Silent	SNP	G	G	A	rs1757152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228412308G>A	ENST00000422127.1	+	9	2846	c.2802G>A	c.(2800-2802)tcG>tcA	p.S934S	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.S1026S|OBSCN_ENST00000284548.11_Silent_p.S934S|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	934	Ig-like 9.|Poly-Ser.				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)				GCTCCAGCTCGAAAGTGTGCA	0.662													G|||	2066	0.41254	0.5885	0.402	5008	,	,		19773	0.3839		0.3678	False		,,,				2504	0.2577				p.S1026S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G3078A						PASS	.	G	,	2342,1864		643,1056,404	58.0	59.0	59.0		2802,2802	-9.0	0.0	1	dbSNP_89	59	3317,5133		663,1991,1571	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1306,3047,1975	AA,AG,GG		39.2544,44.3176,44.714	,	934/7969,934/6621	228412308	5659,6997	2103	4225	6328	SO:0001819	synonymous_variant	84033	exon10			CAGCTCGAAAGTG	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.2802G>A	1.37:g.228412308G>A		Somatic	343	2	0.0058309		WXS	Illumina HiSeq	Phase_I	308	308	1	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																																																																																			G|0.567;A|0.433	0.433	strong		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
TLDC2	140711	hgsc.bcm.edu	37	20	35507542	35507542	+	Silent	SNP	G	G	A	rs3748459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:35507542G>A	ENST00000217320.3	+	3	332	c.288G>A	c.(286-288)cgG>cgA	p.R96R	TLDC2_ENST00000602922.1_Silent_p.R96R	NM_080628.1	NP_542195.1	A0PJX2	TLDC2_HUMAN	TBC/LysM-associated domain containing 2	96	TLD.																TGTACCGGCGGATGGAGGGCT	0.667													G|||	1164	0.232428	0.4092	0.2046	5008	,	,		16822	0.0069		0.2982	False		,,,				2504	0.1779				p.R96R		Atlas-SNP	.											.	C20orf118	21	.	0			c.G288A						PASS	.	G		1697,2709	511.2+/-367.7	310,1077,816	55.0	47.0	50.0		288	0.8	1.0	20	dbSNP_107	50	2360,6240	390.2+/-343.2	311,1738,2251	no	coding-synonymous	C20orf118	NM_080628.1		621,2815,3067	AA,AG,GG		27.4419,38.5157,31.1933		96/216	35507542	4057,8949	2203	4300	6503	SO:0001819	synonymous_variant	140711	exon3			CCGGCGGATGGAG	AL079335	CCDS33465.1	20q11.23	2013-03-14	2013-03-14	2013-03-14	ENSG00000101342	ENSG00000101342			16112	protein-coding gene	gene with protein product	"""hypothetical protein LOC140711"", ""TLD domain containing 2"""		"""chromosome 20 open reading frame 118"""	C20orf118			Standard	NM_080628		Approved	dJ132F21.2	uc002xgg.1	A0PJX2	OTTHUMG00000032400	ENST00000217320.3:c.288G>A	20.37:g.35507542G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_080628	B3KVU8	Silent	SNP	ENST00000217320.3	37	CCDS33465.1																																																																																			G|0.723;A|0.277	0.277	strong		0.667	TLDC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079060.2	NM_080628	
MYBL2	4605	hgsc.bcm.edu	37	20	42310449	42310449	+	Missense_Mutation	SNP	G	G	A	rs150704861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42310449G>A	ENST00000217026.4	+	3	267	c.140G>A	c.(139-141)aGg>aAg	p.R47K	MYBL2_ENST00000396863.4_Intron	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	47	HTH myb-type 1. {ECO:0000255|PROSITE- ProRule:PRU00625}.				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)			GCCCTGGTGAGGCAGTTTGGA	0.617													G|||	5	0.000998403	0.003	0.0014	5008	,	,		17008	0.0		0.0	False		,,,				2504	0.0				p.R47K		Atlas-SNP	.											.	MYBL2	82	.	0			c.G140A						PASS	.	G	LYS/ARG	11,4395	17.9+/-39.9	0,11,2192	80.0	67.0	71.0		140	3.7	1.0	20	dbSNP_134	71	0,8600		0,0,4300	yes	missense	MYBL2	NM_002466.2	26	0,11,6492	AA,AG,GG		0.0,0.2497,0.0846	benign	47/701	42310449	11,12995	2203	4300	6503	SO:0001583	missense	4605	exon3			TGGTGAGGCAGTT		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.140G>A	20.37:g.42310449G>A	ENSP00000217026:p.Arg47Lys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	122	49	0.401639	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	G	13.64	2.297518	0.40694	0.002497	0.0	ENSG00000101057	ENST00000217026	T	0.12774	2.65	5.61	3.68	0.42216	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.198434	0.53938	N	0.000054	T	0.05640	0.0148	N	0.03224	-0.385	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31503	-0.9941	10	0.35671	T	0.21	-32.0158	7.5543	0.27814	0.3171:0.0:0.6829:0.0	.	47	P10244	MYBB_HUMAN	K	47	ENSP00000217026:R47K	ENSP00000217026:R47K	R	+	2	0	MYBL2	41743863	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.841000	0.48223	0.872000	0.35775	0.655000	0.94253	AGG	G|0.998;A|0.002	0.002	strong		0.617	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735091	55735091	+	Silent	SNP	C	C	T	rs12292026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55735091C>T	ENST00000312345.2	-	1	899	c.849G>A	c.(847-849)ctG>ctA	p.L283L		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					CTTTGTTCCTCAGGGTATATA	0.328													C|||	121	0.0241613	0.0862	0.0101	5008	,	,		18729	0.0		0.0	False		,,,				2504	0.0				p.L283L		Atlas-SNP	.											.	OR10AG1	100	.	0			c.G849A						PASS	.	C		306,4096	161.4+/-193.6	17,272,1912	55.0	61.0	59.0		849	3.2	1.0	11	dbSNP_120	59	6,8586	5.7+/-21.5	0,6,4290	no	coding-synonymous	OR10AG1	NM_001005491.1		17,278,6202	TT,TC,CC		0.0698,6.9514,2.4011		283/302	55735091	312,12682	2201	4296	6497	SO:0001819	synonymous_variant	282770	exon1			GTTCCTCAGGGTA	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.849G>A	11.37:g.55735091C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_001005491	B2RNH4|Q6IEU3	Silent	SNP	ENST00000312345.2	37	CCDS31514.1																																																																																			C|0.974;T|0.026	0.026	strong		0.328	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
ST7L	54879	hgsc.bcm.edu	37	1	113068651	113068651	+	Missense_Mutation	SNP	C	C	T	rs12069022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113068651C>T	ENST00000358039.4	-	15	2016	c.1712G>A	c.(1711-1713)gGt>gAt	p.G571D	WNT2B_ENST00000369686.5_3'UTR|ST7L_ENST00000544629.1_Missense_Mutation_p.G506D|ST7L_ENST00000360743.4_Missense_Mutation_p.G540D|ST7L_ENST00000490067.1_Missense_Mutation_p.G554D|ST7L_ENST00000369669.1_Missense_Mutation_p.G388D	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	571			G -> D (in dbSNP:rs12069022).		negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				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)		agaactcaaacctaggtcttc	0.478													C|||	174	0.0347444	0.1263	0.0101	5008	,	,		18280	0.0		0.0	False		,,,				2504	0.0				p.G571D		Atlas-SNP	.											.	ST7L	31	.	0			c.G1712A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY	441,3965	212.5+/-232.4	23,395,1785	114.0	113.0	113.0		1712,1661,1619	1.9	0.1	1	dbSNP_120	113	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	ST7L	NM_017744.4,NM_138727.3,NM_138728.2	94,94,94	23,398,6082	TT,TC,CC		0.0349,10.0091,3.4138	probably-damaging,probably-damaging,probably-damaging	571/576,554/559,540/545	113068651	444,12562	2203	4300	6503	SO:0001583	missense	54879	exon15			CTCAAACCTAGGT	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.1712G>A	1.37:g.113068651C>T	ENSP00000350734:p.Gly571Asp	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_017744	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	37	CCDS848.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	C	15.95	2.984826	0.53934	0.100091	3.49E-4	ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000369673;ENST00000544629;ENST00000369669;ENST00000490067	T;T;T;T;T	0.19394	2.43;2.24;2.15;2.39;2.43	3.81	1.87	0.25490	.	1.917730	0.02054	N	0.050248	T	0.04003	0.0112	N	0.08118	0	0.20563	N	0.999889	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.001;0.0;0.0	T	0.32052	-0.9921	10	0.87932	D	0	.	5.8421	0.18639	0.0:0.7468:0.0:0.2532	rs12069022;rs12069022	506;506;554;540;571	B7Z3J2;F5H2P3;Q8TDW4-3;Q8TDW4-2;Q8TDW4	.;.;.;.;ST7L_HUMAN	D	571;540;321;506;388;554	ENSP00000350734:G571D;ENSP00000353972:G540D;ENSP00000445499:G506D;ENSP00000358683:G388D;ENSP00000417140:G554D	ENSP00000350734:G571D	G	-	2	0	ST7L	112870174	0.000000	0.05858	0.071000	0.20095	0.353000	0.29299	0.130000	0.15850	0.558000	0.29135	-0.119000	0.15052	GGT	C|0.963;T|0.037	0.037	strong		0.478	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3		
OSBPL6	114880	hgsc.bcm.edu	37	2	179226431	179226431	+	Silent	SNP	A	A	G	rs145291582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179226431A>G	ENST00000190611.4	+	13	1552	c.1176A>G	c.(1174-1176)gcA>gcG	p.A392A	OSBPL6_ENST00000409631.1_Silent_p.A392A|OSBPL6_ENST00000392505.2_Silent_p.A417A|OSBPL6_ENST00000359685.3_Silent_p.A392A|OSBPL6_ENST00000357080.4_Silent_p.A361A|OSBPL6_ENST00000409045.3_Silent_p.A361A|OSBPL6_ENST00000315022.2_Silent_p.A396A	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	392					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TGAAGTCTGCATTTAATAGCA	0.438													a|||	19	0.00379393	0.0136	0.0014	5008	,	,		20040	0.0		0.0	False		,,,				2504	0.0				p.A417A		Atlas-SNP	.											OSBPL6,NS,carcinoma,+1,1	OSBPL6	178	1	0			c.A1251G						PASS	.	A	,,,,	58,4348	55.5+/-91.7	0,58,2145	104.0	98.0	100.0		1251,1083,1176,1176,1188	-11.1	0.2	2	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSBPL6	NM_001201480.1,NM_001201481.1,NM_001201482.1,NM_032523.3,NM_145739.2	,,,,	0,58,6445	GG,GA,AA		0.0,1.3164,0.4459	,,,,	417/960,361/904,392/899,392/935,396/939	179226431	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	114880	exon14			GTCTGCATTTAAT	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1176A>G	2.37:g.179226431A>G		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	289	144	0.49827	NM_001201480	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Silent	SNP	ENST00000190611.4	37	CCDS2277.1																																																																																			A|0.995;G|0.005	0.005	strong		0.438	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523	
CD33	945	hgsc.bcm.edu	37	19	51742839	51742839	+	Missense_Mutation	SNP	A	A	G	rs35632246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51742839A>G	ENST00000262262.4	+	7	1012	c.991A>G	c.(991-993)Act>Gct	p.T331A	CD33_ENST00000600557.1_3'UTR|CD33_ENST00000421133.2_Missense_Mutation_p.T204A	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	331			T -> A (in dbSNP:rs35632246).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	TGCCGCCCCTACTGTGGAGAT	0.517													a|||	62	0.0123802	0.0454	0.0029	5008	,	,		18838	0.0		0.0	False		,,,				2504	0.0				p.T331A		Atlas-SNP	.											.	CD33	55	.	0			c.A991G						PASS	.	A	ALA/THR,ALA/THR	194,4212	121.3+/-158.8	6,182,2015	115.0	99.0	105.0		610,991	-5.0	0.0	19	dbSNP_126	105	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense	CD33	NM_001082618.1,NM_001772.3	58,58	6,184,6313	GG,GA,AA		0.0233,4.4031,1.507	benign,benign	204/238,331/365	51742839	196,12810	2203	4300	6503	SO:0001583	missense	945	exon7			GCCCCTACTGTGG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.991A>G	19.37:g.51742839A>G	ENSP00000262262:p.Thr331Ala	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	3.525	-0.096917	0.07010	0.044031	2.33E-4	ENSG00000105383	ENST00000262262;ENST00000421133	T;T	0.04758	3.56;3.56	2.51	-5.02	0.02982	.	.	.	.	.	T	0.00552	0.0018	L	0.39147	1.195	0.09310	N	1	B;B	0.15141	0.012;0.012	B;B	0.11329	0.006;0.006	T	0.44528	-0.9322	9	0.22706	T	0.39	.	3.2402	0.06778	0.2436:0.0:0.2473:0.5091	rs35632246	204;331	C9JEN7;P20138	.;CD33_HUMAN	A	331;204	ENSP00000262262:T331A;ENSP00000410126:T204A	ENSP00000262262:T331A	T	+	1	0	CD33	56434651	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.760000	0.01806	-1.514000	0.01786	0.260000	0.18958	ACT	A|0.986;G|0.014	0.014	strong		0.517	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
EPS8	2059	hgsc.bcm.edu	37	12	15776095	15776095	+	Silent	SNP	C	C	T	rs1126786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15776095C>T	ENST00000281172.5	-	20	2788	c.2352G>A	c.(2350-2352)ttG>ttA	p.L784L	EPS8_ENST00000542903.1_Silent_p.L524L|EPS8_ENST00000540613.1_Silent_p.L524L|EPS8_ENST00000543523.1_Silent_p.L784L|EPS8_ENST00000543612.1_Silent_p.L784L	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	784	Effector region. {ECO:0000250}.|Helix bundle 4. {ECO:0000250}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		GTCATACCTCCAATGCAGCTT	0.418													T|||	882	0.176118	0.5507	0.0562	5008	,	,		17316	0.0536		0.0209	False		,,,				2504	0.0409				p.L784L		Atlas-SNP	.											.	EPS8	70	.	0			c.G2352A						PASS	.	T		2128,2278	599.1+/-389.2	529,1070,604	131.0	135.0	133.0		2352	-0.9	0.7	12	dbSNP_86	133	204,8396	810.5+/-407.1	2,200,4098	no	coding-synonymous	EPS8	NM_004447.5		531,1270,4702	TT,TC,CC		2.3721,48.2978,17.9302		784/823	15776095	2332,10674	2203	4300	6503	SO:0001819	synonymous_variant	2059	exon20			TACCTCCAATGCA	U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.2352G>A	12.37:g.15776095C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Silent	SNP	ENST00000281172.5	37	CCDS31753.1																																																																																			T|0.130;G|0.153;C|0.674;A|0.042	0.130	strong		0.418	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1		
ZC3H6	376940	hgsc.bcm.edu	37	2	113090047	113090047	+	Silent	SNP	T	T	C	rs4578863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113090047T>C	ENST00000409871.1	+	12	3953	c.3552T>C	c.(3550-3552)acT>acC	p.T1184T	AC115115.2_ENST00000607612.1_RNA|ZC3H6_ENST00000343936.4_Silent_p.T1184T	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	1184							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						TTGATCCAACTGCTTCACCAT	0.423													C|||	3626	0.724042	0.966	0.6455	5008	,	,		15966	0.7421		0.5477	False		,,,				2504	0.6155				p.T1184T		Atlas-SNP	.											.	ZC3H6	93	.	0			c.T3552C						PASS	.	C		2893,339		1310,273,33	90.0	105.0	100.0		3552	-9.7	0.9	2	dbSNP_111	100	4000,3356		1138,1724,816	no	coding-synonymous	ZC3H6	NM_198581.2		2448,1997,849	CC,CT,TT		45.6226,10.4889,34.898		1184/1190	113090047	6893,3695	1616	3678	5294	SO:0001819	synonymous_variant	376940	exon12			TCCAACTGCTTCA	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.3552T>C	2.37:g.113090047T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_198581	A9JR71|Q6ZW96	Silent	SNP	ENST00000409871.1	37	CCDS46393.1																																																																																			T|0.276;C|0.724	0.724	strong		0.423	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581	
TRAF2	7186	hgsc.bcm.edu	37	9	139814931	139814931	+	Silent	SNP	G	G	T	rs17244166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139814931G>T	ENST00000247668.2	+	8	976	c.924G>T	c.(922-924)cgG>cgT	p.R308R	TRAF2_ENST00000359662.3_Silent_p.R360R|TRAF2_ENST00000536468.1_Silent_p.R308R	NM_021138.3	NP_066961.2	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	308				Missing (in Ref. 2; BAB70792). {ECO:0000305}.	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)|cellular protein complex assembly (GO:0043623)|cellular response to nitric oxide (GO:0071732)|innate immune response (GO:0045087)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron death (GO:1901215)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|programmed necrotic cell death (GO:0097300)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein complex assembly (GO:0006461)|protein heterooligomerization (GO:0051291)|protein homotrimerization (GO:0070207)|protein K63-linked ubiquitination (GO:0070534)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of immunoglobulin secretion (GO:0051023)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|membrane raft (GO:0045121)|ubiquitin ligase complex (GO:0000151)	CD40 receptor binding (GO:0005174)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein phosphatase binding (GO:0019903)|signal transducer activity (GO:0004871)|sphingolipid binding (GO:0046625)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)		GGCAGCACCGGCTGGACCAAG	0.597													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		15208	0.0		0.0	False		,,,				2504	0.0				p.R308R		Atlas-SNP	.											.	TRAF2	46	.	0			c.G924T						PASS	.	G		114,4290	85.8+/-124.5	1,112,2089	30.0	33.0	32.0		924	-1.9	1.0	9	dbSNP_123	32	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TRAF2	NM_021138.3		1,113,6388	TT,TG,GG		0.0116,2.5886,0.8843		308/502	139814931	115,12889	2202	4300	6502	SO:0001819	synonymous_variant	7186	exon8			GCACCGGCTGGAC	U12597	CCDS7013.1	9q34	2013-01-09			ENSG00000127191	ENSG00000127191		"""RING-type (C3HC4) zinc fingers"""	12032	protein-coding gene	gene with protein product		601895				7639698	Standard	NM_021138		Approved	TRAP3	uc004cjv.3	Q12933	OTTHUMG00000020952	ENST00000247668.2:c.924G>T	9.37:g.139814931G>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	77	29	0.376623	NM_021138	A8K107|B4DPJ7|Q7Z337|Q96NT2	Silent	SNP	ENST00000247668.2	37	CCDS7013.1																																																																																			G|0.989;T|0.011	0.011	strong		0.597	TRAF2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055166.1	NM_021138	
RP1L1	94137	hgsc.bcm.edu	37	8	10464474	10464474	+	Silent	SNP	G	G	T	rs113172380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10464474G>T	ENST00000382483.3	-	4	7357	c.7134C>A	c.(7132-7134)ctC>ctA	p.L2378L		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2458					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)		CGAGACTTCCGAGTGCCTGGT	0.532													G|||	15	0.00299521	0.0113	0.0	5008	,	,		17727	0.0		0.0	False		,,,				2504	0.0				p.L2378L		Atlas-SNP	.											RP1L1,NS,carcinoma,-2,1	RP1L1	453	1	0			c.C7134A						PASS	.	G		27,3811		0,27,1892	110.0	114.0	113.0		7134	-7.2	0.0	8	dbSNP_132	113	0,8234		0,0,4117	no	coding-synonymous	RP1L1	NM_178857.5		0,27,6009	TT,TG,GG		0.0,0.7035,0.2237		2378/2401	10464474	27,12045	1919	4117	6036	SO:0001819	synonymous_variant	94137	exon4			ACTTCCGAGTGCC	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.7134C>A	8.37:g.10464474G>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	68	46	0.676471	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			G|0.996;T|0.004	0.004	strong		0.532	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
WDR59	79726	hgsc.bcm.edu	37	16	75018874	75018874	+	Silent	SNP	G	G	A	rs12448858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	103	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	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	
LCN15	389812	hgsc.bcm.edu	37	9	139657900	139657900	+	Silent	SNP	C	C	G	rs11145872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139657900C>G	ENST00000316144.5	-	4	351	c.327G>C	c.(325-327)gtG>gtC	p.V109V	LCN15_ENST00000482511.1_5'UTR	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15	109					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						CCACGATGCGCACGTCCAGGT	0.642													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		8406	0.0		0.0	False		,,,				2504	0.0				p.V109V		Atlas-SNP	.											.	LCN15	11	.	0			c.G327C						PASS	.	C		56,4350	54.9+/-90.9	1,54,2148	76.0	67.0	70.0		327	3.9	1.0	9	dbSNP_120	70	0,8600		0,0,4300	no	coding-synonymous	LCN15	NM_203347.1		1,54,6448	GG,GC,CC		0.0,1.271,0.4306		109/185	139657900	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	389812	exon4			GATGCGCACGTCC		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"""Lipocalins"""	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943	ENST00000316144.5:c.327G>C	9.37:g.139657900C>G		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	32	20	0.625	NM_203347		Silent	SNP	ENST00000316144.5	37	CCDS7006.1																																																																																			C|0.994;G|0.006	0.006	strong		0.642	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347	
NRAP	4892	hgsc.bcm.edu	37	10	115409840	115409840	+	Missense_Mutation	SNP	C	C	T	rs2275799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115409840C>T	ENST00000359988.3	-	9	1088	c.844G>A	c.(844-846)Gct>Act	p.A282T	NRAP_ENST00000360478.3_Missense_Mutation_p.A282T|NRAP_ENST00000369360.3_Missense_Mutation_p.A282T|NRAP_ENST00000369358.4_Missense_Mutation_p.A282T	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)		ATGCCCTCAGCTCCAATGGCT	0.458													C|||	1341	0.267772	0.3419	0.2248	5008	,	,		18853	0.2173		0.2684	False		,,,				2504	0.2495				p.A282T		Atlas-SNP	.											.	NRAP	208	.	0			c.G844A						PASS	.	C	THR/ALA,THR/ALA	1595,2811	497.7+/-363.9	294,1007,902	184.0	168.0	174.0		844,844	5.2	1.0	10	dbSNP_100	174	2389,6211	397.6+/-345.8	334,1721,2245	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	58,58	628,2728,3147	TT,TC,CC		27.7791,36.2006,30.632	benign,benign	282/1696,282/1731	115409840	3984,9022	2203	4300	6503	SO:0001583	missense	4892	exon9			CCTCAGCTCCAAT		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.844G>A	10.37:g.115409840C>T	ENSP00000353078:p.Ala282Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	120	68	0.566667	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	584	0.2673992673992674	159	0.3231707317073171	75	0.20718232044198895	134	0.23426573426573427	216	0.2849604221635884	C	9.493	1.101124	0.20552	0.362006	0.277791	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350;ENST00000369343	T;T;T;T	0.16743	2.51;2.54;2.44;2.32	6.06	5.15	0.70609	.	0.150870	0.64402	D	0.000011	T	0.00012	0.0000	N	0.14661	0.345	0.35895	P	0.17004300000000006	B;B;B	0.27656	0.184;0.036;0.038	B;B;B	0.27262	0.078;0.06;0.02	T	0.49341	-0.8950	9	0.19590	T	0.45	.	10.3614	0.43996	0.0:0.8583:0.0:0.1417	rs2275799;rs52833940;rs60271628;rs2275799	282;282;282	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	T	282;282;282;282;11;11	ENSP00000358365:A282T;ENSP00000358367:A282T;ENSP00000353078:A282T;ENSP00000353666:A282T	ENSP00000353078:A282T	A	-	1	0	NRAP	115399830	1.000000	0.71417	1.000000	0.80357	0.115000	0.19883	1.080000	0.30779	2.876000	0.98609	0.655000	0.94253	GCT	C|0.708;T|0.292	0.292	strong		0.458	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
OR13C5	138799	hgsc.bcm.edu	37	9	107361009	107361009	+	Missense_Mutation	SNP	C	C	G	rs73508187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361009C>G	ENST00000374779.2	-	1	779	c.686G>C	c.(685-687)aGc>aCc	p.S229T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	229						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CTCCGAAGAGCTAATTTTGAA	0.428													C|||	65	0.0129792	0.0454	0.0072	5008	,	,		22160	0.0		0.0	False		,,,				2504	0.0				p.S229T		Atlas-SNP	.											.	OR13C5	60	.	0			c.G686C						PASS	.	C	THR/SER	125,4281	92.5+/-131.2	0,125,2078	122.0	115.0	117.0		686	-1.2	0.0	9	dbSNP_130	117	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR13C5	NM_001004482.1	58	0,126,6377	GG,GC,CC		0.0116,2.837,0.9688	benign	229/319	107361009	126,12880	2203	4300	6503	SO:0001583	missense	138799	exon1			GAAGAGCTAATTT		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.686G>C	9.37:g.107361009C>G	ENSP00000363911:p.Ser229Thr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	210	132	0.628571	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	C	10.96	1.499301	0.26861	0.02837	1.16E-4	ENSG00000255800	ENST00000374779	T	0.38722	1.12	4.03	-1.21	0.09524	GPCR, rhodopsin-like superfamily (1);	1.008970	0.07986	U	0.986370	T	0.05777	0.0151	L	0.29908	0.895	0.09310	N	1	B	0.22800	0.075	B	0.32022	0.139	T	0.36915	-0.9728	10	0.59425	D	0.04	.	5.1916	0.15212	0.0:0.2959:0.4158:0.2883	.	229	Q8NGS8	O13C5_HUMAN	T	229	ENSP00000363911:S229T	ENSP00000363911:S229T	S	-	2	0	OR13C5	106400830	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-5.456000	0.00121	-0.113000	0.11958	0.423000	0.28283	AGC	C|0.990;G|0.010	0.010	strong		0.428	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
NCAN	1463	hgsc.bcm.edu	37	19	19345802	19345802	+	Silent	SNP	C	C	T	rs2228600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19345802C>T	ENST00000252575.6	+	10	3246	c.3147C>T	c.(3145-3147)gaC>gaT	p.D1049D	NCAN_ENST00000538881.1_Silent_p.D500D|RNU6-1028P_ENST00000517164.1_RNA	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	1049	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|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)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	ACATTGATGACTGCCTCTGCA	0.547													C|||	504	0.100639	0.1982	0.0663	5008	,	,		18957	0.0526		0.0288	False		,,,				2504	0.1166				p.D1049D		Atlas-SNP	.											.	NCAN	277	.	0			c.C3147T						PASS	.	C		772,3634	314.7+/-293.7	66,640,1497	143.0	111.0	122.0		3147	3.5	1.0	19	dbSNP_98	122	289,8311	106.8+/-167.6	3,283,4014	no	coding-synonymous	NCAN	NM_004386.2		69,923,5511	TT,TC,CC		3.3605,17.5216,8.1578		1049/1322	19345802	1061,11945	2203	4300	6503	SO:0001819	synonymous_variant	1463	exon10			TGATGACTGCCTC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.3147C>T	19.37:g.19345802C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	119	67	0.563025	NM_004386	Q9UPK6	Silent	SNP	ENST00000252575.6	37	CCDS12397.1																																																																																			C|0.920;T|0.080	0.080	strong		0.547	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
CCDC42	146849	hgsc.bcm.edu	37	17	8647015	8647015	+	Missense_Mutation	SNP	G	G	A	rs9893451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8647015G>A	ENST00000293845.3	-	3	449	c.223C>T	c.(223-225)Cgc>Tgc	p.R75C	CCDC42_ENST00000539522.2_Missense_Mutation_p.R75C	NM_144681.2	NP_653282.2	Q96M95	CCD42_HUMAN	coiled-coil domain containing 42	75			R -> C (in dbSNP:rs9893451).							kidney(1)|large_intestine(4)|lung(3)|ovary(1)	9						TCCTCCCAGCGCAGGTTCAGG	0.582													G|||	359	0.0716853	0.2095	0.0274	5008	,	,		18849	0.002		0.0219	False		,,,				2504	0.0399				p.R75C		Atlas-SNP	.											CCDC42,caecum,carcinoma,+1,1	CCDC42	31	1	0			c.C223T						PASS	.	G	CYS/ARG,CYS/ARG	787,3619	319.9+/-296.3	75,637,1491	83.0	71.0	75.0		223,223	4.4	1.0	17	dbSNP_119	75	201,8399	87.4+/-149.7	2,197,4101	yes	missense,missense	CCDC42	NM_001158261.1,NM_144681.2	180,180	77,834,5592	AA,AG,GG		2.3372,17.862,7.5965	probably-damaging,probably-damaging	75/243,75/317	8647015	988,12018	2203	4300	6503	SO:0001583	missense	146849	exon3			CCCAGCGCAGGTT	AK057296	CCDS11145.1, CCDS54088.1	17p13.1	2012-05-28			ENSG00000161973	ENSG00000161973			26528	protein-coding gene	gene with protein product							Standard	NM_144681		Approved	FLJ32734, CCDC42A	uc002gln.3	Q96M95		ENST00000293845.3:c.223C>T	17.37:g.8647015G>A	ENSP00000293845:p.Arg75Cys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_144681	Q8N6Q0	Missense_Mutation	SNP	ENST00000293845.3	37	CCDS11145.1	109	0.04990842490842491	84	0.17073170731707318	9	0.024861878453038673	1	0.0017482517482517483	15	0.01978891820580475	G	20.5	3.996611	0.74818	0.17862	0.023372	ENSG00000161973	ENST00000293845;ENST00000539522	T;T	0.24538	1.85;1.85	4.38	4.38	0.52667	.	0.000000	0.53938	D	0.000050	T	0.00144	0.0004	M	0.73598	2.24	0.20074	P	0.9999320848	D	0.89917	1.0	D	0.85130	0.997	T	0.01252	-1.1405	9	0.87932	D	0	-14.7306	15.8885	0.79273	0.0:0.0:1.0:0.0	rs9893451;rs9893451	75	Q96M95	CCD42_HUMAN	C	75	ENSP00000293845:R75C;ENSP00000444359:R75C	ENSP00000293845:R75C	R	-	1	0	CCDC42	8587740	1.000000	0.71417	0.995000	0.50966	0.856000	0.48823	3.450000	0.52957	2.255000	0.74692	0.650000	0.86243	CGC	G|0.924;A|0.076	0.076	strong		0.582	CCDC42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442491.1	NM_144681	
NOS2	4843	hgsc.bcm.edu	37	17	26089867	26089867	+	Silent	SNP	T	T	C	rs1060826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26089867T>C	ENST00000313735.6	-	22	2990	c.2757A>G	c.(2755-2757)acA>acG	p.T919T		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	919	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GGTGGATCTCTGTGGGCGTGT	0.627													.|||	3655	0.729832	0.8041	0.6484	5008	,	,		17935	0.6696		0.6153	False		,,,				2504	0.8671				p.T919T		Atlas-SNP	.											NOS2,NS,carcinoma,0,1	NOS2	113	1	0			c.A2757G						PASS	.	C		3346,1018		1294,758,130	21.0	17.0	18.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2757	-2.6	0.0	17	dbSNP_86	18	5268,3310		1667,1934,688	no	coding-synonymous	NOS2	NM_000625.4		2961,2692,818	CC,CT,TT		38.5871,23.3272,33.4415		919/1154	26089867	8614,4328	2182	4289	6471	SO:0001819	synonymous_variant	4843	exon22			GATCTCTGTGGGC	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2757A>G	17.37:g.26089867T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																			T|0.303;C|0.697	0.697	strong		0.627	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
AQP2	359	hgsc.bcm.edu	37	12	50344958	50344958	+	Silent	SNP	C	C	T	rs60629501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50344958C>T	ENST00000199280.3	+	1	430	c.345C>T	c.(343-345)gaC>gaT	p.D115D	RP11-469H8.6_ENST00000552379.1_RNA|RP11-469H8.6_ENST00000550530.1_RNA	NM_000486.5	NP_000477.1	P41181	AQP2_HUMAN	aquaporin 2 (collecting duct)	115					actin filament depolymerization (GO:0030042)|aging (GO:0007568)|apoptotic process (GO:0006915)|cell volume homeostasis (GO:0006884)|cellular response to copper ion (GO:0071280)|cellular response to mercury ion (GO:0071288)|cellular response to water deprivation (GO:0042631)|excretion (GO:0007588)|female pregnancy (GO:0007565)|glycerol transport (GO:0015793)|hyperosmotic response (GO:0006972)|metanephric collecting duct development (GO:0072205)|positive regulation of calcium ion transport (GO:0051928)|renal water transport (GO:0003097)|response to calcium ion (GO:0051592)|response to glucagon (GO:0033762)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to salt stress (GO:0009651)|response to starvation (GO:0042594)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|recycling endosome (GO:0055037)|rough endoplasmic reticulum (GO:0005791)|trans-Golgi network (GO:0005802)|transport vesicle membrane (GO:0030658)	glycerol transmembrane transporter activity (GO:0015168)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(4)|ovary(2)	10						TCCGCGGGGACCTGGCTGTCA	0.627													C|||	61	0.0121805	0.0431	0.0058	5008	,	,		18198	0.0		0.0	False		,,,				2504	0.0				p.D115D		Atlas-SNP	.											.	AQP2	34	.	0			c.C345T						PASS	.	C		173,4225		2,169,2028	16.0	17.0	17.0		345	0.7	1.0	12	dbSNP_129	17	0,8590		0,0,4295	no	coding-synonymous	AQP2	NM_000486.5		2,169,6323	TT,TC,CC		0.0,3.9336,1.332		115/272	50344958	173,12815	2199	4295	6494	SO:0001819	synonymous_variant	359	exon1			CGGGGACCTGGCT		CCDS8792.1	12q12-q13	2014-09-17				ENSG00000167580		"""Ion channels / Aquaporins"""	634	protein-coding gene	gene with protein product		107777				7512890	Standard	NM_000486		Approved		uc001rvn.3	P41181		ENST00000199280.3:c.345C>T	12.37:g.50344958C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_000486	Q9UD68	Silent	SNP	ENST00000199280.3	37	CCDS8792.1																																																																																			C|0.988;T|0.012	0.012	strong		0.627	AQP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405540.1	NM_000486	
TRPC7	57113	hgsc.bcm.edu	37	5	135583342	135583342	+	Missense_Mutation	SNP	C	C	T	rs183404828		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:135583342C>T	ENST00000513104.1	-	7	1943	c.1661G>A	c.(1660-1662)cGc>cAc	p.R554H	TRPC7_ENST00000355180.3_Missense_Mutation_p.R493H|TRPC7_ENST00000426057.2_Missense_Mutation_p.R438H	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	554					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.R554L(2)		NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GTATGCAATGCGAGAGAAGCT	0.498													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20968	0.0		0.0	False		,,,				2504	0.0				p.R554H		Atlas-SNP	.											TRPC7,NS,carcinoma,0,2	TRPC7	126	2	2	Substitution - Missense(2)	lung(2)	c.G1661A						scavenged	.						122.0	122.0	122.0					5																	135583342		1968	4171	6139	SO:0001583	missense	57113	exon7			GCAATGCGAGAGA	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.1661G>A	5.37:g.135583342C>T	ENSP00000426070:p.Arg554His	Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	231	3	0.012987	NM_020389	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Missense_Mutation	SNP	ENST00000513104.1	37	CCDS47267.2	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	35	5.570690	0.96540	.	.	ENSG00000069018	ENST00000355180;ENST00000426057;ENST00000513104;ENST00000265193	D;D;D	0.99591	-6.24;-6.24;-6.24	5.65	5.65	0.86999	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99708	0.9888	M	0.90082	3.085	0.54753	D	0.999989	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.979;0.999;0.999	D	0.97962	1.0338	10	0.87932	D	0	-14.3984	19.9142	0.97043	0.0:1.0:0.0:0.0	.	438;493;499;554	Q8IWP7;F5H5U9;Q70T25;Q9HCX4	.;.;.;TRPC7_HUMAN	H	493;438;554;554	ENSP00000347312:R493H;ENSP00000441628:R438H;ENSP00000426070:R554H	ENSP00000265193:R554H	R	-	2	0	TRPC7	135611241	1.000000	0.71417	0.981000	0.43875	0.995000	0.86356	7.651000	0.83577	2.941000	0.99782	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	strong		0.498	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389	
RPL31	6160	hgsc.bcm.edu	37	2	101619211	101619211	+	Silent	SNP	C	C	T	rs141007382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:101619211C>T	ENST00000264258.3	+	2	649	c.48C>T	c.(46-48)gcC>gcT	p.A16A	RPL31_ENST00000409000.1_Silent_p.A16A|RPL31_ENST00000409650.1_Silent_p.A16A|RPL31_ENST00000409038.1_Silent_p.A16A|RPL31_ENST00000409733.1_Silent_p.A16A|RPL31_ENST00000409711.1_Silent_p.A16A|RPL31_ENST00000409320.3_Silent_p.A16A|AC016738.4_ENST00000452364.1_RNA|RPL31_ENST00000409028.4_Silent_p.A16A	NM_000993.4	NP_000984.1	P62899	RL31_HUMAN	ribosomal protein L31	16					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)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(3)	8						GCCGTTCTGCCATCAACGAAG	0.532													C|||	5	0.000998403	0.0038	0.0	5008	,	,		19707	0.0		0.0	False		,,,				2504	0.0				p.A16A		Atlas-SNP	.											.	RPL31	12	.	0			c.C48T						PASS	.	C	,,	13,4393	19.1+/-41.9	0,13,2190	71.0	66.0	68.0		48,48,48	2.5	1.0	2	dbSNP_134	68	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	RPL31	NM_000993.4,NM_001098577.2,NM_001099693.1	,,	0,13,6490	TT,TC,CC		0.0,0.2951,0.1	,,	16/126,16/129,16/122	101619211	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	6160	exon2			TTCTGCCATCAAC	X15940	CCDS2049.1, CCDS46373.1, CCDS46374.1	2q11.2	2011-04-06			ENSG00000071082	ENSG00000071082		"""L ribosomal proteins"""	10334	protein-coding gene	gene with protein product						2780320, 11875025	Standard	NM_000993		Approved	L31	uc010fiu.1	P62899	OTTHUMG00000130687	ENST00000264258.3:c.48C>T	2.37:g.101619211C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	219	114	0.520548	NM_001098577	B7Z4K2|D3DVJ4|P12947|Q53SQ5|Q6IRZ0|Q6LBJ6	Silent	SNP	ENST00000264258.3	37	CCDS2049.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	13.12	2.141667	0.37825	0.002951	0.0	ENSG00000071082	ENST00000441435	.	.	.	5.38	2.51	0.30379	.	.	.	.	.	T	0.56587	0.1995	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50939	-0.8768	4	.	.	.	.	8.4008	0.32586	0.1258:0.7401:0.0:0.1341	.	.	.	.	L	4	.	.	P	+	2	0	RPL31	100985643	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.039000	0.49791	0.839000	0.34971	-0.150000	0.13652	CCA	C|0.999;T|0.001	0.001	strong		0.532	RPL31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253182.3	NM_001098577	
PHYHD1	254295	hgsc.bcm.edu	37	9	131702891	131702891	+	Silent	SNP	A	A	G	rs2273866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131702891A>G	ENST00000372592.3	+	11	1533	c.600A>G	c.(598-600)agA>agG	p.R200R	RP11-101E3.5_ENST00000482796.1_5'Flank|PHYHD1_ENST00000421063.2_Silent_p.R179R|PHYHD1_ENST00000487504.1_3'UTR|PHYHD1_ENST00000308941.5_Missense_Mutation_p.E193G|PHYHD1_ENST00000353176.5_Silent_p.R179R	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	200							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.E193G(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						GTGTGTCAAGAAGGATGGTCC	0.607													A|||	1760	0.351438	0.3555	0.4251	5008	,	,		18832	0.2381		0.4095	False		,,,				2504	0.3507				p.E193G		Atlas-SNP	.											PHYHD1,NS,carcinoma,0,1	PHYHD1	29	1	1	Substitution - Missense(1)	stomach(1)	c.A578G						PASS	.	A	,,GLY/GLU	1558,2848	490.6+/-361.9	254,1050,899	108.0	100.0	103.0		600,537,578	-1.5	0.9	9	dbSNP_100	103	3247,5353	488.0+/-372.2	631,1985,1684	yes	coding-synonymous,coding-synonymous,missense	PHYHD1	NM_001100876.1,NM_001100877.1,NM_174933.3	,,98	885,3035,2583	GG,GA,AA		37.7558,35.3609,36.9445	,,	200/292,179/271,193/298	131702891	4805,8201	2203	4300	6503	SO:0001819	synonymous_variant	254295	exon10			GTCAAGAAGGATG	BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.600A>G	9.37:g.131702891A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_174933	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Missense_Mutation	SNP	ENST00000372592.3	37	CCDS43885.1	790	0.3617216117216117	198	0.4024390243902439	149	0.4116022099447514	130	0.22727272727272727	313	0.4129287598944591	A	14.23	2.473911	0.43942	0.353609	0.377558	ENSG00000175287	ENST00000308941	.	.	.	4.78	-1.45	0.08828	.	2.450790	0.02210	N	0.063064	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999990798	B	0.06786	0.001	B	0.08055	0.003	T	0.39143	-0.9628	7	0.22109	T	0.4	0.7128	8.2316	0.31601	0.2791:0.1426:0.5782:0.0	rs2273866;rs17452324;rs17455259;rs17485374;rs17850494;rs52819401;rs56896723;rs2273866	193	Q5SRE7-3	.	G	193	.	ENSP00000309515:E193G	E	+	2	0	PHYHD1	130742712	0.920000	0.31207	0.901000	0.35422	0.949000	0.60115	-0.020000	0.12525	-0.043000	0.13513	0.454000	0.30748	GAA	A|0.643;G|0.357	0.357	strong		0.607	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933	
PCDHGB3	56102	hgsc.bcm.edu	37	5	140803241	140803241	+	Intron	SNP	C	C	A	rs57195665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140803241C>A	ENST00000576222.1	+	1	2546				PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB8P_ENST00000502926.1_RNA|PCDHGA9_ENST00000573521.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB6_ENST00000520790.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGATTTATTTCTCTGCCTCCT	0.453													c|||	567	0.113219	0.1195	0.1499	5008	,	,		14734	0.1171		0.0596	False		,,,				2504	0.1299				p.S816Y		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.C2447A						PASS	.	C	,,,,,,,,,,,,,,,,,,TYR/SER,	476,3742		26,424,1659	33.0	37.0	36.0		,,,,,,,,,,,,,,,,,,2447,	-2.0	0.0	5	dbSNP_129	36	632,7882		25,582,3650	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032091.1,NM_032092.1	,,,,,,,,,,,,,,,,,,144,	51,1006,5309	AA,AC,CC		7.4231,11.285,8.7025	,,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,816/838,	140803241	1108,11624	2109	4257	6366	SO:0001627	intron_variant	56105	exon1			TTATTTCTCTGCC	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+50865C>A	5.37:g.140803241C>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	121	70	0.578512	NM_032091	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			C|0.900;A|0.100	0.100	strong		0.453	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
TMEM253	643382	hgsc.bcm.edu	37	14	21570273	21570273	+	Silent	SNP	T	T	C	rs745696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21570273T>C	ENST00000556585.2	+	4	388	c.270T>C	c.(268-270)ctT>ctC	p.L90L	ZNF219_ENST00000451119.2_Intron|TMEM253_ENST00000418511.2_Silent_p.L90L			P0C7T8	TM253_HUMAN	transmembrane protein 253	90						integral component of membrane (GO:0016021)											CACCCCGCCTTTGGAAGGTGA	0.552													C|||	3201	0.639177	0.767	0.5893	5008	,	,		22222	0.5357		0.7157	False		,,,				2504	0.5297				p.L90L		Atlas-SNP	.											.	.	.	.	0			c.T270C						PASS	.	C	,	1033,351		386,261,45	54.0	58.0	56.0		,270	1.1	1.0	14	dbSNP_86	56	2229,953		792,645,154	no	intron,coding-synonymous	ZNF219,C14orf176	NM_001102454.1,NM_001146683.1	,	1178,906,199	CC,CT,TT		29.9497,25.3613,28.5589	,	,90/218	21570273	3262,1304	692	1591	2283	SO:0001819	synonymous_variant	643382	exon5			CCGCCTTTGGAAG		CCDS53884.1	14q11.2	2012-10-24	2012-10-24	2012-10-24	ENSG00000232070	ENSG00000232070			32545	protein-coding gene	gene with protein product			"""non-protein coding RNA 220"", ""chromosome 14 open reading frame 95"", ""chromosome 14 open reading frame 176"""	NCRNA00220, C14orf95, C14orf176			Standard	NM_001146683		Approved		uc010tlo.2	P0C7T8	OTTHUMG00000171361	ENST00000556585.2:c.270T>C	14.37:g.21570273T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_001146683		Silent	SNP	ENST00000556585.2	37	CCDS53884.1																																																																																			T|0.354;C|0.646	0.646	strong		0.552	TMEM253-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413146.2	XM_926711	
MOK	5891	hgsc.bcm.edu	37	14	102700028	102700028	+	Missense_Mutation	SNP	T	T	C	rs34965156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102700028T>C	ENST00000361847.2	-	8	920	c.689A>G	c.(688-690)aAa>aGa	p.K230R	MOK_ENST00000523231.1_5'UTR|MOK_ENST00000520266.1_5'UTR|MOK_ENST00000522874.1_Missense_Mutation_p.K229R|MOK_ENST00000522867.1_5'UTR|MOK_ENST00000517966.1_5'UTR|MOK_ENST00000524370.1_5'UTR|MOK_ENST00000522534.1_5'UTR|MOK_ENST00000561150.1_5'UTR|MOK_ENST00000519058.1_5'UTR|MOK_ENST00000193029.6_5'UTR|MOK_ENST00000524214.1_Missense_Mutation_p.K200R	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	230	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> R (in dbSNP:rs34965156). {ECO:0000269|PubMed:17344846}.		protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)										TACTTACTGTTTGAACTTGGT	0.532													T|||	258	0.0515176	0.1876	0.0115	5008	,	,		19334	0.0		0.002	False		,,,				2504	0.0				p.K230R		Atlas-SNP	.											.	.	.	.	0			c.A689G						PASS	.	T	ARG/LYS	689,3717		61,567,1575	189.0	147.0	161.0		689	5.2	1.0	14	dbSNP_126	161	17,8583		0,17,4283	yes	missense	MOK	NM_014226.1	26	61,584,5858	CC,CT,TT		0.1977,15.6378,5.4283	benign	230/420	102700028	706,12300	2203	4300	6503	SO:0001583	missense	5891	exon8			TACTGTTTGAACT	AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"""renal tumor antigen"""	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.689A>G	14.37:g.102700028T>C	ENSP00000355304:p.Lys230Arg	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	225	113	0.502222	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Missense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	99	0.04532967032967033	92	0.18699186991869918	5	0.013812154696132596	0	0.0	2	0.002638522427440633	.	14.82	2.649258	0.47362	0.156378	0.001977	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	T;T;T	0.64803	-0.12;-0.12;-0.12	5.2	5.2	0.72013	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.054522	0.64402	D	0.000001	T	0.00073	0.0002	N	0.11313	0.125	0.09310	P	1.0	B;B	0.21225	0.021;0.053	B;B	0.26517	0.044;0.07	T	0.04752	-1.0929	9	0.46703	T	0.11	-1.1389	15.0926	0.72207	0.0:0.0:0.0:1.0	rs34965156	200;230	E7ERR8;Q9UQ07	.;MOK_HUMAN	R	229;230;200	ENSP00000429469:K229R;ENSP00000355304:K230R;ENSP00000428942:K200R	ENSP00000355304:K230R	K	-	2	0	RAGE	101769781	1.000000	0.71417	0.985000	0.45067	0.870000	0.49936	4.211000	0.58507	1.978000	0.57642	0.482000	0.46254	AAA	T|0.940;C|0.060	0.060	strong		0.532	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		
C2CD3	26005	hgsc.bcm.edu	37	11	73796917	73796917	+	Missense_Mutation	SNP	C	C	T	rs826058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73796917C>T	ENST00000334126.7	-	21	3882	c.3656G>A	c.(3655-3657)cGg>cAg	p.R1219Q	C2CD3_ENST00000313663.7_Missense_Mutation_p.R1219Q			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1219	C2 1.		R -> Q (in dbSNP:rs826058). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1}.		brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					AGCGGGTTCCCGTTCAGCCAA	0.493													T|||	1754	0.35024	0.5741	0.4135	5008	,	,		20841	0.1577		0.3091	False		,,,				2504	0.2434				p.R1219Q		Atlas-SNP	.											C2CD3_ENST00000334126,NS,adenoma,0,2	C2CD3	288	2	0			c.G3656A						PASS	.	T	GLN/ARG	2227,2173	585.0+/-386.2	561,1105,534	50.0	47.0	48.0		3656	4.7	1.0	11	dbSNP_86	48	2640,5946	685.7+/-404.1	410,1820,2063	yes	missense	C2CD3	NM_015531.4	43	971,2925,2597	TT,TC,CC		30.7477,49.3864,37.4788	benign	1219/1964	73796917	4867,8119	2200	4293	6493	SO:0001583	missense	26005	exon21			GGTTCCCGTTCAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.3656G>A	11.37:g.73796917C>T	ENSP00000334379:p.Arg1219Gln	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		772	0.3534798534798535	291	0.5914634146341463	138	0.3812154696132597	97	0.16958041958041958	246	0.3245382585751979	T	2.369	-0.344862	0.05208	0.506136	0.307477	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.12147	3.16;3.15;2.71	5.8	4.66	0.58398	.	0.243070	0.42053	N	0.000770	T	0.00012	0.0000	N	0.00308	-1.67	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35025	-0.9805	8	.	.	.	-2.6174	7.8745	0.29586	0.1231:0.0674:0.0:0.8096	rs826058;rs1278706;rs17244733;rs58708907;rs826058	1219	Q4AC94-1	.	Q	1219;1219;1219;27	ENSP00000334379:R1219Q;ENSP00000323339:R1219Q;ENSP00000388750:R27Q	.	R	-	2	0	C2CD3	73474565	1.000000	0.71417	1.000000	0.80357	0.253000	0.25986	2.328000	0.43867	0.447000	0.26695	-0.254000	0.11334	CGG	C|0.635;T|0.365	0.365	strong		0.493	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
FHL2	2274	hgsc.bcm.edu	37	2	106002854	106002854	+	Silent	SNP	G	G	A	rs11537578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:106002854G>A	ENST00000409807.1	-	2	454	c.120C>T	c.(118-120)tgC>tgT	p.C40C	FHL2_ENST00000409177.1_Silent_p.C156C|FHL2_ENST00000607522.1_Silent_p.C40C|FHL2_ENST00000393353.3_Silent_p.C40C|FHL2_ENST00000322142.8_Silent_p.C40C|FHL2_ENST00000408995.1_Silent_p.C40C|FHL2_ENST00000344213.4_Silent_p.C150C|FHL2_ENST00000336660.5_Silent_p.C40C|FHL2_ENST00000358129.4_Silent_p.C40C|FHL2_ENST00000393352.3_Silent_p.C40C			Q14192	FHL2_HUMAN	four and a half LIM domains 2	40	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|atrial cardiac muscle cell development (GO:0055014)|cellular lipid metabolic process (GO:0044255)|heart trabecula formation (GO:0060347)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|M band (GO:0031430)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Z disc (GO:0030018)	androgen receptor binding (GO:0050681)|identical protein binding (GO:0042802)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9						CACACTCCTCGCAGGTGTTGG	0.607													G|||	58	0.0115815	0.0416	0.0043	5008	,	,		16948	0.0		0.0	False		,,,				2504	0.0				p.C40C		Atlas-SNP	.											.	FHL2	18	.	0			c.C120T						PASS	.	G	,,,	166,4240	111.2+/-149.4	4,158,2041	71.0	66.0	68.0		120,120,120,120	-5.8	0.6	2	dbSNP_120	68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FHL2	NM_001039492.2,NM_001450.3,NM_201555.1,NM_201557.3	,,,	4,159,6340	AA,AG,GG		0.0116,3.7676,1.284	,,,	40/280,40/280,40/280,40/280	106002854	167,12839	2203	4300	6503	SO:0001819	synonymous_variant	2274	exon3			CTCCTCGCAGGTG		CCDS2070.1	2q12.2	2014-09-17			ENSG00000115641	ENSG00000115641			3703	protein-coding gene	gene with protein product		602633				8753811	Standard	NM_201557		Approved	SLIM3, DRAL	uc002tcy.3	Q14192	OTTHUMG00000153120	ENST00000409807.1:c.120C>T	2.37:g.106002854G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	138	72	0.521739	NM_001039492	Q13229|Q13644|Q2I5I4|Q5TM15|Q9P294	Silent	SNP	ENST00000409807.1	37	CCDS2070.1																																																																																			G|0.989;A|0.011	0.011	strong		0.607	FHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329654.1		
AK8	158067	hgsc.bcm.edu	37	9	135601126	135601126	+	Silent	SNP	G	G	A	rs28477720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135601126G>A	ENST00000298545.3	-	13	1910	c.1389C>T	c.(1387-1389)ttC>ttT	p.F463F	AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	463	Adenylate kinase 2.				nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						CGATGTATTCGAAGACTGTGT	0.532													G|||	151	0.0301518	0.1089	0.0086	5008	,	,		18753	0.0		0.001	False		,,,				2504	0.0				p.F463F		Atlas-SNP	.											.	AK8	45	.	0			c.C1389T						PASS	.	G		452,3954		24,404,1775	80.0	61.0	67.0		1389	-1.5	0.8	9	dbSNP_125	67	3,8597		0,3,4297	no	coding-synonymous	AK8	NM_152572.2		24,407,6072	AA,AG,GG		0.0349,10.2587,3.4984		463/480	135601126	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	158067	exon13			GTATTCGAAGACT	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"""Adenylate kinases"""	26526	protein-coding gene	gene with protein product		615365	"""chromosome 9 open reading frame 98"""	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.1389C>T	9.37:g.135601126G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	117	89	0.760684	NM_152572	A8K821|Q8N9W9	Silent	SNP	ENST00000298545.3	37	CCDS6954.1																																																																																			G|0.966;A|0.034	0.034	strong		0.532	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572	
KLC2	64837	hgsc.bcm.edu	37	11	66033430	66033430	+	Missense_Mutation	SNP	C	C	T	rs2276036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:66033430C>T	ENST00000417856.1	+	13	1792	c.1549C>T	c.(1549-1551)Cct>Tct	p.P517S	KLC2_ENST00000394065.2_Missense_Mutation_p.P378S|RAB1B_ENST00000311481.6_5'Flank|KLC2_ENST00000316924.5_Missense_Mutation_p.P517S|KLC2_ENST00000394066.2_Missense_Mutation_p.P440S|RP11-867G23.2_ENST00000533287.1_RNA|KLC2_ENST00000394078.1_Intron|RP11-867G23.1_ENST00000530805.1_RNA|RAB1B_ENST00000527397.1_5'Flank|KLC2_ENST00000421552.1_Missense_Mutation_p.P440S|KLC2_ENST00000394067.2_Missense_Mutation_p.P517S	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2	517			P -> S (in dbSNP:rs2276036).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon cargo transport (GO:0008088)|blood coagulation (GO:0007596)|microtubule-based movement (GO:0007018)	ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinesin I complex (GO:0016938)|membrane (GO:0016020)|microtubule (GO:0005874)|neuron projection (GO:0043005)|protein complex (GO:0043234)	kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						GGGTGCCGGGCCTCGGTCTGA	0.682													C|||	970	0.19369	0.1823	0.1268	5008	,	,		13064	0.2887		0.173	False		,,,				2504	0.18				p.P517S		Atlas-SNP	.											.	KLC2	50	.	0			c.C1549T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	762,3634	295.0+/-283.4	70,622,1506	36.0	43.0	41.0		1318,1549,1549,1549	0.4	1.0	11	dbSNP_100	41	1488,7096	269.1+/-288.2	137,1214,2941	yes	missense,missense,missense,missense	KLC2	NM_001134774.1,NM_001134775.1,NM_001134776.1,NM_022822.2	74,74,74,74	207,1836,4447	TT,TC,CC		17.3346,17.3339,17.3344	benign,benign,benign,benign	440/546,517/623,517/623,517/623	66033430	2250,10730	2198	4292	6490	SO:0001583	missense	64837	exon13			GCCGGGCCTCGGT	AK022449	CCDS8130.1, CCDS44653.1	11q13.1	2013-01-10			ENSG00000174996	ENSG00000174996		"""Tetratricopeptide (TTC) repeat domain containing"""	20716	protein-coding gene	gene with protein product		611729				9624122	Standard	NM_022822		Approved	FLJ12387	uc001ohb.2	Q9H0B6	OTTHUMG00000133757	ENST00000417856.1:c.1549C>T	11.37:g.66033430C>T	ENSP00000399403:p.Pro517Ser	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	236	111	0.470339	NM_022822	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Missense_Mutation	SNP	ENST00000417856.1	37	CCDS8130.1	422	0.19322344322344323	77	0.1565040650406504	49	0.13535911602209943	160	0.27972027972027974	136	0.17941952506596306	C	4.543	0.100733	0.08731	0.173339	0.173346	ENSG00000174996	ENST00000417856;ENST00000394067;ENST00000316924;ENST00000421552;ENST00000394066;ENST00000394065	T;T;T;T;T;D	0.82081	-0.94;-0.94;-0.94;-0.95;-0.95;-1.57	3.71	0.365	0.16131	.	0.603350	0.14605	N	0.309400	T	0.00012	0.0000	L	0.29908	0.895	0.34550	P	0.288802	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.03453	-1.1035	9	0.18276	T	0.48	-0.0827	7.7791	0.29054	0.0:0.6758:0.1993:0.1249	rs2276036;rs59407109;rs2276036	378;440;517	A8MZ87;A8MXL7;Q9H0B6	.;.;KLC2_HUMAN	S	517;517;517;440;440;378	ENSP00000399403:P517S;ENSP00000377631:P517S;ENSP00000314837:P517S;ENSP00000408484:P440S;ENSP00000377630:P440S;ENSP00000377629:P378S	ENSP00000314837:P517S	P	+	1	0	KLC2	65790006	0.000000	0.05858	0.986000	0.45419	0.343000	0.28985	-0.074000	0.11450	0.241000	0.21283	0.491000	0.48974	CCT	C|0.818;T|0.182	0.182	strong		0.682	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822	
ARSE	415	hgsc.bcm.edu	37	X	2867651	2867651	+	Missense_Mutation	SNP	C	C	T	rs34412194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:2867651C>T	ENST00000381134.3	-	6	614	c.548G>A	c.(547-549)cGc>cAc	p.R183H	ARSE_ENST00000540563.1_Missense_Mutation_p.R138H|ARSE_ENST00000545496.1_Missense_Mutation_p.R208H	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	183			R -> H (in dbSNP:rs34412194).		cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|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)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		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)				GAGTTCCCAGCGGGCGCAATC	0.527													c|||	39	0.0103311	0.0295	0.0	3775	,	,		15270	0.0		0.0	False		,,,				2504	0.0				p.R183H		Atlas-SNP	.											.	ARSE	43	.	0			c.G548A						PASS	.		HIS/ARG	149,3686		2,118,27,1512,544	97.0	81.0	86.0		548	-6.2	0.0	X	dbSNP_126	86	20,6708		0,16,4,2412,1868	yes	missense	ARSE	NM_000047.2	29	2,134,31,3924,2412	TT,TC,T,CC,C		0.2973,3.8853,1.5999	benign	183/590	2867651	169,10394	2203	4300	6503	SO:0001583	missense	415	exon6			TCCCAGCGGGCGC	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"""Arylsulfatase family"""	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.548G>A	X.37:g.2867651C>T	ENSP00000370526:p.Arg183His	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	211	107	0.507109	NM_000047	Q53FT2|Q53FU8	Missense_Mutation	SNP	ENST00000381134.3	37	CCDS14122.1	6	0.003616636528028933	5	0.010245901639344262	0	0.0	0	0.0	0	0.0	c	3.529	-0.096143	0.07010	0.038853	0.002973	ENSG00000157399	ENST00000540563;ENST00000545496;ENST00000381134	D;D;D	0.98649	-5.05;-5.05;-5.05	3.13	-6.25	0.02039	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	1.414780	0.04104	N	0.313410	T	0.80281	0.4594	N	0.04787	-0.16	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.82319	-0.0516	10	0.41790	T	0.15	.	0.8636	0.01198	0.1773:0.2059:0.2526:0.3642	rs34412194	138;208;183	F5H324;F5GYY5;P51690	.;.;ARSE_HUMAN	H	138;208;183	ENSP00000438198:R138H;ENSP00000441417:R208H;ENSP00000370526:R183H	ENSP00000370526:R183H	R	-	2	0	ARSE	2877651	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.031000	0.00158	-3.969000	0.00086	-2.358000	0.00240	CGC	C|0.969;0|0.016	.	strong		0.527	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047	
MIP	4284	hgsc.bcm.edu	37	12	56847384	56847384	+	Silent	SNP	G	G	A	rs36032520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56847384G>A	ENST00000257979.4	-	2	544	c.516C>T	c.(514-516)caC>caT	p.H172H	MIP_ENST00000555551.1_5'UTR	NM_012064.3	NP_036196.1	P30301	MIP_HUMAN	major intrinsic protein of lens fiber	172					canalicular bile acid transport (GO:0015722)|lens development in camera-type eye (GO:0002088)|response to stimulus (GO:0050896)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)|water transport (GO:0006833)	gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|structural constituent of eye lens (GO:0005212)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	16						CCCCAAAGAGGTGCCCCAGGG	0.562													G|||	9	0.00179712	0.0068	0.0	5008	,	,		20604	0.0		0.0	False		,,,				2504	0.0				p.H172H		Atlas-SNP	.											.	MIP	39	.	0			c.C516T						PASS	.	G		39,4367	43.8+/-77.6	0,39,2164	57.0	53.0	54.0		516	3.0	1.0	12	dbSNP_126	54	0,8600		0,0,4300	no	coding-synonymous	MIP	NM_012064.3		0,39,6464	AA,AG,GG		0.0,0.8852,0.2999		172/264	56847384	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	4284	exon2			AAAGAGGTGCCCC		CCDS8919.1	12q13	2012-10-02				ENSG00000135517		"""Ion channels / Aquaporins"""	7103	protein-coding gene	gene with protein product	aquaporin 0	154050				1840563, 7536742	Standard	NM_012064		Approved	MP26, LIM1, AQP0	uc001slh.3	P30301		ENST00000257979.4:c.516C>T	12.37:g.56847384G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_012064	Q17R41	Silent	SNP	ENST00000257979.4	37	CCDS8919.1																																																																																			G|0.998;A|0.002	0.002	strong		0.562	MIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409620.1	NM_012064	
ZNF774	342132	hgsc.bcm.edu	37	15	90902172	90902172	+	Missense_Mutation	SNP	C	C	T	rs16944267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90902172C>T	ENST00000354377.3	+	3	380	c.194C>T	c.(193-195)cCg>cTg	p.P65L	ZNF774_ENST00000379090.5_Missense_Mutation_p.P65L|ZNF774_ENST00000558115.1_3'UTR	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	65			P -> L (in dbSNP:rs16944267).		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)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AGGAAGATCCCGAGGGAAAGC	0.488													T|||	708	0.141374	0.3722	0.0735	5008	,	,		16431	0.1062		0.0089	False		,,,				2504	0.0501				p.P65L		Atlas-SNP	.											.	ZNF774	35	.	0			c.C194T						PASS	.	T	LEU/PRO	1286,3112	696.9+/-406.1	194,898,1107	65.0	60.0	61.0		194	1.4	0.0	15	dbSNP_123	61	29,8567	817.7+/-406.9	0,29,4269	yes	missense	ZNF774	NM_001004309.2	98	194,927,5376	TT,TC,CC		0.3374,29.2406,10.1201	benign	65/484	90902172	1315,11679	2199	4298	6497	SO:0001583	missense	342132	exon3			AGATCCCGAGGGA	BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"""Zinc fingers, C2H2-type"""	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.194C>T	15.37:g.90902172C>T	ENSP00000346348:p.Pro65Leu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_001004309	A8K020	Missense_Mutation	SNP	ENST00000354377.3	37	CCDS32330.1	286	0.13095238095238096	182	0.3699186991869919	25	0.06906077348066299	72	0.1258741258741259	7	0.009234828496042216	T	1.139	-0.650179	0.03506	0.292406	0.003374	ENSG00000196391	ENST00000354377;ENST00000379090	T;T	0.21191	2.02;2.02	4.99	1.38	0.22167	.	0.000000	0.27581	N	0.018739	T	0.00012	0.0000	N	0.01751	-0.74	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47824	-0.9087	9	0.18276	T	0.48	.	3.7627	0.08610	0.1708:0.3641:0.0:0.4651	rs16944267;rs52823254;rs16944267	65	Q6NX45	ZN774_HUMAN	L	65	ENSP00000346348:P65L;ENSP00000368383:P65L	ENSP00000346348:P65L	P	+	2	0	ZNF774	88703176	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.163000	0.09997	-0.027000	0.13873	-1.658000	0.00752	CCG	C|0.886;T|0.114	0.114	strong		0.488	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309	
MATN4	8785	hgsc.bcm.edu	37	20	43933163	43933163	+	Silent	SNP	T	T	C	rs2233094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43933163T>C	ENST00000372754.1	-	2	356	c.348A>G	c.(346-348)gcA>gcG	p.A116A	RBPJL_ENST00000372743.1_5'Flank|RBPJL_ENST00000372741.3_5'Flank|MATN4_ENST00000342716.4_Silent_p.A116A|MATN4_ENST00000372756.1_Silent_p.A116A|MATN4_ENST00000360607.6_Silent_p.A116A|MATN4_ENST00000353917.5_Silent_p.A116A|RBPJL_ENST00000343694.3_5'Flank|MATN4_ENST00000537548.1_Silent_p.A116A|MATN4_ENST00000372751.4_Intron			O95460	MATN4_HUMAN	matrilin 4	116	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CGTACTGGATTGCCAGTCCCG	0.687													T|||	2021	0.403554	0.2239	0.3444	5008	,	,		16128	0.755		0.2634	False		,,,				2504	0.4703				p.A116A		Atlas-SNP	.											MATN4,NS,carcinoma,0,1	MATN4	57	1	0			c.A348G						PASS	.	T	,,	985,3411		120,745,1333	19.0	16.0	17.0		348,348,348	-9.6	0.1	20	dbSNP_98	17	2373,6207		337,1699,2254	no	coding-synonymous,coding-synonymous,coding-synonymous	MATN4	NM_003833.3,NM_030590.2,NM_030592.2	,,	457,2444,3587	CC,CT,TT		27.6573,22.4067,25.8785	,,	116/582,116/541,116/500	43933163	3358,9618	2198	4290	6488	SO:0001819	synonymous_variant	8785	exon3			CTGGATTGCCAGT	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.348A>G	20.37:g.43933163T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_030592	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Silent	SNP	ENST00000372754.1	37																																																																																				T|0.676;C|0.324	0.324	strong		0.687	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1		
ARNTL2	56938	hgsc.bcm.edu	37	12	27543141	27543141	+	Missense_Mutation	SNP	G	G	C	rs74988383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27543141G>C	ENST00000266503.5	+	9	906	c.888G>C	c.(886-888)gaG>gaC	p.E296D	ARNTL2_ENST00000544915.1_Missense_Mutation_p.E262D|ARNTL2_ENST00000311001.5_Missense_Mutation_p.E282D|ARNTL2_ENST00000395901.2_Missense_Mutation_p.E259D|ARNTL2_ENST00000542388.1_Missense_Mutation_p.E211D|ARNTL2_ENST00000261178.5_Missense_Mutation_p.E248D|RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000546179.1_Missense_Mutation_p.E259D			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	296					circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|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)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					TCAAAGAAGAGCATGGATGCT	0.373													G|||	31	0.0061901	0.0227	0.0014	5008	,	,		17221	0.0		0.0	False		,,,				2504	0.0				p.E296D		Atlas-SNP	.											.	ARNTL2	54	.	0			c.G888C						PASS	.	G	ASP/GLU	136,4270	97.1+/-135.8	1,134,2068	94.0	92.0	92.0		888	-2.6	0.3	12	dbSNP_132	92	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ARNTL2	NM_020183.3	45	1,137,6365	CC,CG,GG		0.0349,3.0867,1.0687	benign	296/637	27543141	139,12867	2203	4300	6503	SO:0001583	missense	56938	exon9			AGAAGAGCATGGA	AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"""Basic helix-loop-helix proteins"""	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.888G>C	12.37:g.27543141G>C	ENSP00000266503:p.Glu296Asp	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_020183	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Missense_Mutation	SNP	ENST00000266503.5	37	CCDS8712.1	13|13	0.005952380952380952|0.005952380952380952	13|13	0.026422764227642278|0.026422764227642278	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	17.22|17.22	3.334286|3.334286	0.60853|0.60853	0.030867|0.030867	3.49E-4|3.49E-4	ENSG00000029153|ENSG00000029153	ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388|ENST00000457040	T;T;T;T;T;T;T|.	0.08720|.	3.16;3.17;3.06;3.16;3.18;3.16;3.19|.	3.71|3.71	-2.58|-2.58	0.06228|0.06228	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.37571|0.37571	0.1008|0.1008	M|M	0.70903|0.70903	2.155|2.155	0.38371|0.38371	D|D	0.944876|0.944876	P;D;P;P;B;B|.	0.53151|.	0.907;0.958;0.907;0.907;0.161;0.09|.	P;P;P;P;B;B|.	0.60345|.	0.686;0.873;0.801;0.686;0.137;0.103|.	T|T	0.58601|0.58601	-0.7608|-0.7608	10|5	0.56958|.	D|.	0.05|.	.|.	10.3192|10.3192	0.43756|0.43756	0.6174:0.0:0.3826:0.0|0.6174:0.0:0.3826:0.0	.|.	259;262;259;248;282;296|.	F5H402;Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1|.	.;.;.;.;.;BMAL2_HUMAN|.	D|T	262;259;259;282;248;296;211|248	ENSP00000442438:E262D;ENSP00000379238:E259D;ENSP00000438545:E259D;ENSP00000312247:E282D;ENSP00000261178:E248D;ENSP00000266503:E296D;ENSP00000445836:E211D|.	ENSP00000261178:E248D|.	E|S	+|+	3|2	2|0	ARNTL2|ARNTL2	27434408|27434408	0.865000|0.865000	0.29922|0.29922	0.275000|0.275000	0.24674|0.24674	0.946000|0.946000	0.59487|0.59487	-0.103000|-0.103000	0.10940|0.10940	-0.470000|-0.470000	0.06901|0.06901	0.655000|0.655000	0.94253|0.94253	GAG|AGC	G|0.991;C|0.009	0.009	strong		0.373	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183	
IGSF3	3321	hgsc.bcm.edu	37	1	117131407	117131407	+	Silent	SNP	G	G	A	rs57816525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117131407G>A	ENST00000369486.3	-	8	3114	c.2349C>T	c.(2347-2349)caC>caT	p.H783H	IGSF3_ENST00000318837.6_Silent_p.H803H|IGSF3_ENST00000369483.1_Silent_p.H803H	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	783	Ig-like C2-type 6.				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)		ACTCCTCCACGTGGCAGTAGT	0.617													g|||	237	0.0473243	0.152	0.0173	5008	,	,		15573	0.002		0.0	False		,,,				2504	0.0225				p.H803H		Atlas-SNP	.											.	IGSF3	294	.	0			c.C2409T						PASS	.	A	,	548,3854		28,492,1681	32.0	33.0	33.0		2349,2409	-3.3	1.0	1	dbSNP_129	33	14,8564		0,14,4275	no	coding-synonymous,coding-synonymous	IGSF3	NM_001007237.1,NM_001542.2	,	28,506,5956	AA,AG,GG		0.1632,12.4489,4.3297	,	783/1195,803/1215	117131407	562,12418	2201	4289	6490	SO:0001819	synonymous_variant	3321	exon9			CTCCACGTGGCAG	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.2349C>T	1.37:g.117131407G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	203	98	0.482759	NM_001542	A6NJZ6|A6NMC7	Silent	SNP	ENST00000369486.3	37	CCDS30813.1																																																																																			G|0.962;A|0.038	0.038	strong		0.617	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
CREBRF	153222	hgsc.bcm.edu	37	5	172550204	172550204	+	Splice_Site	SNP	C	C	T	rs1129146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	175	0	0		WXS	Illumina HiSeq	Phase_I	196	100	0.510204	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
CAPZA1	829	hgsc.bcm.edu	37	1	113202386	113202386	+	Silent	SNP	C	C	T	rs12074157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113202386C>T	ENST00000263168.3	+	7	1242	c.570C>T	c.(568-570)ggC>ggT	p.G190G	CAPZA1_ENST00000476936.1_3'UTR	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	190					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	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)		AGGTGGTTGGCGTGCTTAAGA	0.403													c|||	179	0.0357428	0.1301	0.0101	5008	,	,		16515	0.0		0.0	False		,,,				2504	0.0				p.G190G		Atlas-SNP	.											CAPZA1,colon,carcinoma,0,1	CAPZA1	16	1	0			c.C570T						PASS	.	C		459,3947	217.1+/-235.6	24,411,1768	94.0	89.0	91.0		570	4.4	1.0	1	dbSNP_120	91	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CAPZA1	NM_006135.2		24,414,6065	TT,TC,CC		0.0349,10.4176,3.5522		190/287	113202386	462,12544	2203	4300	6503	SO:0001819	synonymous_variant	829	exon7			GGTTGGCGTGCTT	U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.570C>T	1.37:g.113202386C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	35	0.406977	NM_006135	Q53FQ6|Q6FHD5	Silent	SNP	ENST00000263168.3	37	CCDS30805.1																																																																																			C|0.968;T|0.032	0.032	strong		0.403	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135	
INPP4B	8821	hgsc.bcm.edu	37	4	143043340	143043340	+	Silent	SNP	A	A	G	rs2270658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:143043340A>G	ENST00000513000.1	-	22	2509	c.2076T>C	c.(2074-2076)gtT>gtC	p.V692V	INPP4B_ENST00000262992.4_Silent_p.V692V|INPP4B_ENST00000508116.1_Silent_p.V692V|INPP4B_ENST00000509777.1_Silent_p.V692V|INPP4B_ENST00000308502.4_Silent_p.V692V	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	692					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					TTTTAAATGCAACTTTCTTTA	0.393													G|||	747	0.149161	0.205	0.1052	5008	,	,		18794	0.2321		0.0815	False		,,,				2504	0.089				p.V692V		Atlas-SNP	.											.	INPP4B	132	.	0			c.T2076C						PASS	.	G	,	753,3653	754.5+/-412.5	60,633,1510	130.0	121.0	124.0		2076,2076	-11.7	0.1	4	dbSNP_100	124	880,7720	778.6+/-407.7	44,792,3464	no	coding-synonymous,coding-synonymous	INPP4B	NM_001101669.1,NM_003866.2	,	104,1425,4974	GG,GA,AA		10.2326,17.0903,12.5557	,	692/925,692/925	143043340	1633,11373	2203	4300	6503	SO:0001819	synonymous_variant	8821	exon22			AAATGCAACTTTC	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.2076T>C	4.37:g.143043340A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			A|0.867;G|0.133	0.133	strong		0.393	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971108	45971108	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45971108C>T	ENST00000391621.1	-	1	280	c.234G>A	c.(232-234)tcG>tcA	p.S78S	TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	78	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						GCTGGCAGCACGAGGGCGTGC	0.687																																					p.S78S		Atlas-SNP	.											KRTAP10-2,caecum,carcinoma,-1,1	KRTAP10-2	21	1	0			c.G234A						scavenged	.						52.0	56.0	55.0					21																	45971108		2202	4293	6495	SO:0001819	synonymous_variant	386679	exon1			GCAGCACGAGGGC	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.234G>A	21.37:g.45971108C>T		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	173	18	0.104046	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			.	.	none		0.687	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
WWOX	51741	hgsc.bcm.edu	37	16	78458807	78458807	+	Missense_Mutation	SNP	C	C	G	rs7201683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:78458807C>G	ENST00000566780.1	+	7	1012	c.646C>G	c.(646-648)Cta>Gta	p.L216V	WWOX_ENST00000539474.2_Intron|WWOX_ENST00000408984.3_Missense_Mutation_p.L216V|WWOX_ENST00000402655.2_Intron|WWOX_ENST00000406884.2_Intron	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	216	Interaction with MAPT. {ECO:0000250}.|Mediates targeting to the mitochondria. {ECO:0000250}.		L -> V (in dbSNP:rs7201683).		cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)			large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		AACTTTTGCTCTACCCTGGAG	0.468													C|||	197	0.0393371	0.1218	0.0202	5008	,	,		19087	0.0		0.0089	False		,,,				2504	0.0133				p.L216V		Atlas-SNP	.											.	WWOX	98	.	0			c.C646G						PASS	.	C	VAL/LEU	370,3528		15,340,1594	281.0	282.0	282.0		646	1.1	0.0	16	dbSNP_116	282	102,8180		1,100,4040	yes	missense	WWOX	NM_016373.2	32	16,440,5634	GG,GC,CC		1.2316,9.492,3.8752	possibly-damaging	216/415	78458807	472,11708	1949	4141	6090	SO:0001583	missense	51741	exon7			TTTGCTCTACCCT	AF187015	CCDS42196.1, CCDS42197.1	16q23.3-q24.1	2012-08-15	2002-01-14		ENSG00000186153	ENSG00000186153	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	12799	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 41C, member 1"""	605131	"""WW domain-containing oxidoreductase"""			10786676, 10861292, 19027726	Standard	XR_243411		Approved	FOR, WOX1, SDR41C1	uc002ffk.3	Q9NZC7	OTTHUMG00000176851	ENST00000566780.1:c.646C>G	16.37:g.78458807C>G	ENSP00000457230:p.Leu216Val	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	196	100	0.510204	NM_016373	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	37	CCDS42196.1	79	0.036172161172161175	64	0.13008130081300814	9	0.024861878453038673	0	0.0	6	0.0079155672823219	C	0.015	-1.539831	0.00934	0.09492	0.012316	ENSG00000186153	ENST00000408984;ENST00000299644	T	0.21191	2.02	5.66	1.14	0.20703	NAD(P)-binding domain (1);	0.170005	0.43416	D	0.000569	T	0.00109	0.0003	N	0.16016	0.355	0.80722	P	0.0	B	0.14805	0.011	B	0.22601	0.04	T	0.23691	-1.0181	9	0.40728	T	0.16	.	8.0658	0.30659	0.0:0.5003:0.1647:0.335	rs7201683;rs52793545;rs7201683	216	Q9NZC7	WWOX_HUMAN	V	216;59	ENSP00000386161:L216V	ENSP00000299644:L59V	L	+	1	2	WWOX	77016308	0.006000	0.16342	0.043000	0.18650	0.121000	0.20230	0.216000	0.17585	-0.215000	0.10063	-0.797000	0.03246	CTA	C|0.956;G|0.044	0.044	strong		0.468	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1		
CD109	135228	hgsc.bcm.edu	37	6	74524757	74524757	+	Silent	SNP	T	T	G	rs58562849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74524757T>G	ENST00000287097.5	+	30	3934	c.3822T>G	c.(3820-3822)tcT>tcG	p.S1274S	CD109_ENST00000422508.2_Silent_p.S1197S|CD109_ENST00000437994.2_Silent_p.S1257S			Q6YHK3	CD109_HUMAN	CD109 molecule	1274					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						GACGAAGATCTATCCAAAATC	0.328													T|||	132	0.0263578	0.0953	0.0086	5008	,	,		14879	0.0		0.0	False		,,,				2504	0.0				p.S1274S		Atlas-SNP	.											.	CD109	170	.	0			c.T3822G						PASS	.	T	,,	323,4083	172.3+/-202.3	13,297,1893	99.0	101.0	100.0		3771,3591,3822	-5.2	0.0	6	dbSNP_129	100	5,8591	4.3+/-15.6	0,5,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	,,	13,302,6186	GG,GT,TT		0.0582,7.3309,2.5227	,,	1257/1429,1197/1369,1274/1446	74524757	328,12674	2203	4298	6501	SO:0001819	synonymous_variant	135228	exon30			AAGATCTATCCAA	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.3822T>G	6.37:g.74524757T>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																			T|0.971;G|0.029	0.029	strong		0.328	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
FHOD1	29109	hgsc.bcm.edu	37	16	67266065	67266065	+	Silent	SNP	T	T	C	rs34888644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67266065T>C	ENST00000258201.4	-	14	2326	c.2079A>G	c.(2077-2079)acA>acG	p.T693T		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	693	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.|Interaction with ROCK1.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		GGTCCAGCACTGTGGTCATTG	0.582													T|||	375	0.0748802	0.2201	0.013	5008	,	,		18790	0.003		0.003	False		,,,				2504	0.0706				p.T693T		Atlas-SNP	.											.	FHOD1	86	.	0			c.A2079G						PASS	.	T		797,3599	319.1+/-295.9	76,645,1477	147.0	122.0	131.0		2079	-0.9	1.0	16	dbSNP_126	131	8,8592	3.7+/-12.6	0,8,4292	no	coding-synonymous	FHOD1	NM_013241.2		76,653,5769	CC,CT,TT		0.093,18.1301,6.1942		693/1165	67266065	805,12191	2198	4300	6498	SO:0001819	synonymous_variant	29109	exon14			CAGCACTGTGGTC	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.2079A>G	16.37:g.67266065T>C		Somatic	418	1	0.00239234		WXS	Illumina HiSeq	Phase_I	452	223	0.493363	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Silent	SNP	ENST00000258201.4	37	CCDS10834.1																																																																																			T|0.919;C|0.081	0.081	strong		0.582	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2		
RHBDD1	84236	hgsc.bcm.edu	37	2	227860232	227860232	+	Silent	SNP	C	C	T	rs61745917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:227860232C>T	ENST00000341329.3	+	7	1184	c.942C>T	c.(940-942)agC>agT	p.S314S	RHBDD1_ENST00000493526.1_3'UTR|RHBDD1_ENST00000392062.2_Silent_p.S314S	NM_032276.3	NP_115652.2	Q8TEB9	RHBL4_HUMAN	rhomboid domain containing 1	314	VCP/p97-interacting motif (VIM). {ECO:0000250}.				apoptotic process (GO:0006915)|cellular response to unfolded protein (GO:0034620)|cellular response to UV (GO:0034644)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|membrane protein intracellular domain proteolysis (GO:0031293)|membrane protein proteolysis (GO:0033619)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein processing (GO:0010954)|positive regulation of secretion (GO:0051047)|post-translational protein modification (GO:0043687)|spermatid differentiation (GO:0048515)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			breast(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		GATTCGATAGCCAGTGAGGTG	0.448													C|||	29	0.00579073	0.0212	0.0014	5008	,	,		18839	0.0		0.0	False		,,,				2504	0.0				p.S314S		Atlas-SNP	.											.	RHBDD1	34	.	0			c.C942T						PASS	.	C	,	58,4348	57.4+/-93.9	0,58,2145	67.0	61.0	63.0		942,942	2.4	0.8	2	dbSNP_129	63	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	RHBDD1	NM_001167608.1,NM_032276.3	,	0,58,6445	TT,TC,CC		0.0,1.3164,0.4459	,	314/316,314/316	227860232	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	84236	exon9			CGATAGCCAGTGA	AK074258	CCDS2464.1	2q36.3	2012-07-09			ENSG00000144468	ENSG00000144468			23081	protein-coding gene	gene with protein product						12838346	Standard	NM_032276		Approved	DKFZp547E052	uc002voi.3	Q8TEB9	OTTHUMG00000133178	ENST00000341329.3:c.942C>T	2.37:g.227860232C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	NM_001167608	Q495B9|Q53S43|Q5EBM8|Q6P5V8|Q8IV60|Q9H057	Silent	SNP	ENST00000341329.3	37	CCDS2464.1																																																																																			C|0.996;T|0.004	0.004	strong		0.448	RHBDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256885.2		
THNSL1	79896	hgsc.bcm.edu	37	10	25312895	25312895	+	Missense_Mutation	SNP	C	C	A	rs34929144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:25312895C>A	ENST00000524413.1	+	3	1090	c.743C>A	c.(742-744)gCa>gAa	p.A248E	THNSL1_ENST00000376356.4_Missense_Mutation_p.A248E			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	248			A -> E (in dbSNP:rs34929144).			cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	AAGGTTTCAGCAAAATTCTTT	0.423													C|||	134	0.0267572	0.0015	0.0461	5008	,	,		19867	0.0		0.0368	False		,,,				2504	0.0644				p.A248E		Atlas-SNP	.											.	THNSL1	70	.	0			c.C743A						PASS	.	C	GLU/ALA	28,4378	31.7+/-61.6	0,28,2175	108.0	116.0	113.0		743	5.7	0.7	10	dbSNP_126	113	386,8214	123.9+/-182.7	10,366,3924	yes	missense	THNSL1	NM_024838.4	107	10,394,6099	AA,AC,CC		4.4884,0.6355,3.1831	benign	248/744	25312895	414,12592	2203	4300	6503	SO:0001583	missense	79896	exon3			TTTCAGCAAAATT	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"""threonine synthase-like 1 (bacterial)"""			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.743C>A	10.37:g.25312895C>A	ENSP00000434887:p.Ala248Glu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	125	48	0.384	NM_024838	B3KWL1|D3DRV3|Q5VV21	Missense_Mutation	SNP	ENST00000524413.1	37	CCDS7147.1	39	0.017857142857142856	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	22	0.029023746701846966	C	12.01	1.808256	0.31961	0.006355	0.044884	ENSG00000185875	ENST00000524413;ENST00000376356	T;T	0.28454	1.61;1.61	5.71	5.71	0.89125	Pyridoxal phosphate-dependent enzyme, beta subunit (1);	0.882556	0.09541	N	0.788227	T	0.04452	0.0122	N	0.03608	-0.345	0.23739	N	0.996979	B	0.06786	0.001	B	0.06405	0.002	T	0.14062	-1.0486	10	0.72032	D	0.01	-15.6055	15.5512	0.76155	0.1463:0.8537:0.0:0.0	rs34929144	248	Q8IYQ7	THNS1_HUMAN	E	248	ENSP00000434887:A248E;ENSP00000365534:A248E	ENSP00000365534:A248E	A	+	2	0	THNSL1	25352901	0.002000	0.14202	0.664000	0.29753	0.906000	0.53458	1.046000	0.30354	2.700000	0.92200	0.650000	0.86243	GCA	C|0.974;A|0.026	0.026	strong		0.423	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
C1orf112	55732	hgsc.bcm.edu	37	1	169796197	169796197	+	Missense_Mutation	SNP	T	T	C	rs142988055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169796197T>C	ENST00000286031.6	+	11	1554	c.854T>C	c.(853-855)tTt>tCt	p.F285S	C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Missense_Mutation_p.F285S|C1orf112_ENST00000413811.2_Missense_Mutation_p.F256S	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	285										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)					CCCAGCAAGTTTCCTCCAAGC	0.388													T|||	89	0.0177716	0.0658	0.0029	5008	,	,		14059	0.0		0.0	False		,,,				2504	0.0				p.F285S		Atlas-SNP	.											.	C1orf112	74	.	0			c.T854C						PASS	.	T	SER/PHE	258,4148	144.2+/-179.2	8,242,1953	87.0	87.0	87.0		854	5.0	1.0	1	dbSNP_134	87	0,8600		0,0,4300	yes	missense	C1orf112	NM_018186.2	155	8,242,6253	CC,CT,TT		0.0,5.8557,1.9837	probably-damaging	285/854	169796197	258,12748	2203	4300	6503	SO:0001583	missense	55732	exon11			GCAAGTTTCCTCC	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.854T>C	1.37:g.169796197T>C	ENSP00000286031:p.Phe285Ser	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	242	125	0.516529	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	37	CCDS1285.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	T	18.57	3.652833	0.67472	0.058557	0.0	ENSG00000000460	ENST00000413811;ENST00000359326;ENST00000286031	T;T;T	0.58210	0.35;0.35;0.35	5.04	5.04	0.67666	.	0.088478	0.85682	D	0.000000	T	0.64034	0.2562	M	0.78637	2.42	0.46011	D	0.998815	D;P;D	0.61080	0.979;0.91;0.989	P;P;D	0.66084	0.776;0.821;0.941	T	0.70317	-0.4905	10	0.72032	D	0.01	-12.7977	13.0228	0.58799	0.0:0.0:0.0:1.0	.	256;227;285	B4E0A9;B4DGF2;Q9NSG2	.;.;CA112_HUMAN	S	256;285;285	ENSP00000389257:F256S;ENSP00000352276:F285S;ENSP00000286031:F285S	ENSP00000286031:F285S	F	+	2	0	C1orf112	168062821	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	3.338000	0.52128	2.002000	0.58637	0.528000	0.53228	TTT	T|0.984;C|0.016	0.016	strong		0.388	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
CEACAM21	90273	hgsc.bcm.edu	37	19	42083673	42083673	+	Silent	SNP	T	T	C	rs7247842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42083673T>C	ENST00000401445.2	+	2	212	c.186T>C	c.(184-186)ctT>ctC	p.L62L	CEACAM21_ENST00000187608.9_Silent_p.L62L|CEACAM21_ENST00000482870.2_3'UTR|CEACAM21_ENST00000407170.2_5'UTR			Q3KPI0	CEA21_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 21	62						integral component of membrane (GO:0016021)		p.L62L(1)		endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	13						CCGAGAATCTTTACAGCTATG	0.502													t|||	1154	0.230431	0.41	0.0807	5008	,	,		21314	0.3562		0.0537	False		,,,				2504	0.1462				p.L62L		Atlas-SNP	.											CEACAM21_ENST00000401445,NS,carcinoma,0,1	CEACAM21	52	1	1	Substitution - coding silent(1)	stomach(1)	c.T186C						PASS	.	T	,	1293,2713		202,889,912	72.0	74.0	74.0		186,186	0.4	0.0	19	dbSNP_116	74	297,8119		4,289,3915	no	coding-synonymous,coding-synonymous	CEACAM21	NM_001098506.1,NM_033543.3	,	206,1178,4827	CC,CT,TT		3.529,32.2766,12.7999	,	62/294,62/293	42083673	1590,10832	2003	4208	6211	SO:0001819	synonymous_variant	90273	exon2			GAATCTTTACAGC	AK023602	CCDS46086.1, CCDS46087.1, CCDS74373.1	19q13.2	2013-01-29			ENSG00000007129	ENSG00000007129		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28834	protein-coding gene	gene with protein product						12477932	Standard	XM_005278397		Approved	R29124_1, FLJ13540	uc002ore.4	Q3KPI0	OTTHUMG00000151062	ENST00000401445.2:c.186T>C	19.37:g.42083673T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	180	179	0.994444	NM_033543	B7WNQ6|O75296|Q6UY47|Q96ER7	Silent	SNP	ENST00000401445.2	37	CCDS46086.1																																																																																			T|0.766;C|0.234	0.234	strong		0.502	CEACAM21-005	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321140.1	NM_033543	
MUC5B	727897	hgsc.bcm.edu	37	11	1265786	1265786	+	Missense_Mutation	SNP	C	C	T	rs60787297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1265786C>T	ENST00000529681.1	+	31	7734	c.7676C>T	c.(7675-7677)aCg>aTg	p.T2559M	MUC5B_ENST00000447027.1_Missense_Mutation_p.T2562M|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2559	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.		T -> M (in dbSNP:rs2860722).	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)		ACCACACCCACGGCCACCATG	0.637													C|||	2056	0.410543	0.295	0.4539	5008	,	,		18934	0.5774		0.3837	False		,,,				2504	0.3916				p.T2559M		Atlas-SNP	.											.	MUC5B	473	.	0			c.C7676T						PASS	.						19.0	29.0	26.0					11																	1265786		1879	4070	5949	SO:0001583	missense	727897	exon31			CACCCACGGCCAC	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.7676C>T	11.37:g.1265786C>T	ENSP00000436812:p.Thr2559Met	Somatic	506	1	0.00197628		WXS	Illumina HiSeq	Phase_I	607	202	0.332784	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.373|5.373	0.254033|0.254033	0.10185|0.10185	.|.	.|.	ENSG00000117983|ENSG00000117983	ENST00000537836|ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	.|T;T	.|0.17854	.|2.25;2.44	2.96|2.96	-3.82|-3.82	0.04281|0.04281	.|.	.|.	.|.	.|.	.|.	T|T	0.08268|0.08268	0.0206|0.0206	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	P|P	0.0|0.0	.|P;P	.|0.44260	.|0.83;0.83	.|B;B	.|0.28139	.|0.086;0.086	T|T	0.13683|0.13683	-1.0500|-1.0500	5|8	0.59425|0.87932	D|D	0.04|0	.|.	1.3164|1.3164	0.02108|0.02108	0.1479:0.4211:0.1448:0.2861|0.1479:0.4211:0.1448:0.2861	rs2860722;rs4046522;rs4046525;rs2860722|rs2860722;rs4046522;rs4046525;rs2860722	.|3197;2562	.|A7Y9J9;E9PBJ0	.|.;.	W|M	103|2559;2562;2531;2574	.|ENSP00000436812:T2559M;ENSP00000415793:T2562M	ENSP00000440615:R103W|ENSP00000343037:T2531M	R|T	+|+	1|2	2|0	MUC5B|MUC5B	1222362|1222362	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	0.051000|0.051000	0.14141|0.14141	-1.007000|-1.007000	0.03408|0.03408	0.195000|0.195000	0.17529|0.17529	CGG|ACG	C|0.500;T|0.500	0.500	strong		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
FAM221B	392307	hgsc.bcm.edu	37	9	35826058	35826058	+	Missense_Mutation	SNP	T	T	C	rs13294256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	114	0	0	858	WXS	Illumina HiSeq	Phase_I	97	39	0.402062	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	
BCAR1	9564	hgsc.bcm.edu	37	16	75269730	75269730	+	Missense_Mutation	SNP	G	G	A	rs61729593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75269730G>A	ENST00000162330.5	-	5	1193	c.1067C>T	c.(1066-1068)cCg>cTg	p.P356L	BCAR1_ENST00000393420.6_Missense_Mutation_p.P374L|BCAR1_ENST00000546196.1_Missense_Mutation_p.P327L|BCAR1_ENST00000393422.2_Missense_Mutation_p.P374L|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000418647.3_Missense_Mutation_p.P402L|BCAR1_ENST00000542031.2_Missense_Mutation_p.P354L|BCAR1_ENST00000535626.2_Missense_Mutation_p.P208L|BCAR1_ENST00000538440.2_Missense_Mutation_p.P356L|BCAR1_ENST00000420641.3_Missense_Mutation_p.P374L	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	356	Substrate for kinases. {ECO:0000250}.				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)		CTCGGCCGGCGGGGAGTCTGG	0.716													G|||	36	0.0071885	0.0257	0.0029	5008	,	,		14012	0.0		0.0	False		,,,				2504	0.0				p.P402L		Atlas-SNP	.											.	BCAR1	184	.	0			c.C1205T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	38,4262		0,38,2112	7.0	8.0	8.0		1205,1121,1121,1121,1067,1061,623,437,1067	3.3	0.3	16	dbSNP_129	8	2,8398		0,2,4198	no	missense,missense,missense,missense,missense,missense,missense,missense,missense	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	98,98,98,98,98,98,98,98,98	0,40,6310	AA,AG,GG		0.0238,0.8837,0.315	benign,benign,benign,benign,benign,benign,benign,benign,benign	402/917,374/889,374/889,374/889,356/871,354/869,208/723,146/661,356/871	75269730	40,12660	2150	4200	6350	SO:0001583	missense	9564	exon6			GCCGGCGGGGAGT	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.1067C>T	16.37:g.75269730G>A	ENSP00000162330:p.Pro356Leu	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Missense_Mutation	SNP	ENST00000162330.5	37	CCDS10915.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	G	8.927	0.962569	0.18583	0.008837	2.38E-4	ENSG00000050820	ENST00000162330;ENST00000393422;ENST00000420641;ENST00000538440;ENST00000418647;ENST00000535626;ENST00000393420;ENST00000542031;ENST00000546196	T;T;T;T;T;T;T;T;T	0.41065	1.12;1.66;1.47;1.23;1.4;1.01;1.3;1.13;2.9	4.29	3.29	0.37713	.	0.858926	0.10058	N	0.721285	T	0.14399	0.0348	L	0.47716	1.5	0.29586	N	0.848804	B;B;B;B;B;B;B;B;B	0.10296	0.001;0.003;0.002;0.001;0.002;0.0;0.0;0.001;0.0	B;B;B;B;B;B;B;B;B	0.09377	0.0;0.004;0.001;0.002;0.001;0.0;0.002;0.001;0.001	T	0.18555	-1.0333	10	0.21014	T	0.42	-13.6226	9.512	0.39082	0.113:0.0:0.887:0.0	.	374;208;402;354;374;374;356;356;146	B4DIW5;F5GXV6;E9PCL5;F5GXA2;F8WA69;E9PCV2;F5H7Z0;P56945;B3KWE2	.;.;.;.;.;.;.;BCAR1_HUMAN;.	L	356;374;374;356;402;208;374;354;327	ENSP00000162330:P356L;ENSP00000377074:P374L;ENSP00000392708:P374L;ENSP00000443841:P356L;ENSP00000391669:P402L;ENSP00000440370:P208L;ENSP00000377072:P374L;ENSP00000440415:P354L;ENSP00000442161:P327L	ENSP00000162330:P356L	P	-	2	0	BCAR1	73827231	0.006000	0.16342	0.262000	0.24481	0.052000	0.14988	1.241000	0.32743	0.871000	0.35750	0.558000	0.71614	CCG	G|0.991;A|0.009	0.009	strong		0.716	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
OR10H4	126541	hgsc.bcm.edu	37	19	16060453	16060453	+	Silent	SNP	T	T	C	rs115548355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16060453T>C	ENST00000322107.1	+	1	636	c.636T>C	c.(634-636)tgT>tgC	p.C212C		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	212						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(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						TGATAGGCTGTTTATTCCTCA	0.488													.|||	43	0.00858626	0.0318	0.0014	5008	,	,		23791	0.0		0.0	False		,,,				2504	0.0				p.C212C		Atlas-SNP	.											.	OR10H4	48	.	0			c.T636C						PASS	.	T		200,4206	125.7+/-162.9	6,188,2009	295.0	266.0	276.0		636	-0.8	0.8	19	dbSNP_132	276	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR10H4	NM_001004465.1		6,189,6308	CC,CT,TT		0.0116,4.5393,1.5454		212/317	16060453	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	126541	exon1			AGGCTGTTTATTC	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"""GPCR / Class A : Olfactory receptors"""	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.636T>C	19.37:g.16060453T>C		Somatic	389	1	0.00257069		WXS	Illumina HiSeq	Phase_I	390	196	0.502564	NM_001004465	Q6IFJ2|Q96R57	Silent	SNP	ENST00000322107.1	37	CCDS32941.1																																																																																			T|0.988;C|0.012	0.012	strong		0.488	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1		
OR51Q1	390061	hgsc.bcm.edu	37	11	5444061	5444061	+	Missense_Mutation	SNP	G	G	A	rs2736586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5444061G>A	ENST00000300778.4	+	1	721	c.631G>A	c.(631-633)Gtg>Atg	p.V211M	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	211			V -> M (in dbSNP:rs2736586).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATTATTATCGTGGATCCTCT	0.498													A|||	2272	0.453674	0.2799	0.3991	5008	,	,		22644	0.7024		0.3986	False		,,,				2504	0.5276				p.V211M		Atlas-SNP	.											.	OR51Q1	79	.	0			c.G631A						PASS	.	A	MET/VAL	1332,3070	694.1+/-405.8	203,926,1072	176.0	150.0	159.0		631	-6.4	0.0	11	dbSNP_100	159	3373,5221	641.9+/-399.7	676,2021,1600	yes	missense	OR51Q1	NM_001004757.2	21	879,2947,2672	AA,AG,GG		39.2483,30.259,36.2034	benign	211/318	5444061	4705,8291	2201	4297	6498	SO:0001583	missense	390061	exon1			ATTATCGTGGATC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.631G>A	11.37:g.5444061G>A	ENSP00000300778:p.Val211Met	Somatic	276	2	0.00724638		WXS	Illumina HiSeq	Phase_I	223	220	0.986547	NM_001004757	B2RNN1	Missense_Mutation	SNP	ENST00000300778.4	37	CCDS31381.1	966	0.4423076923076923	139	0.28252032520325204	148	0.4088397790055249	395	0.6905594405594405	284	0.37467018469656993	A	1.024	-0.684014	0.03353	0.30259	0.392483	ENSG00000167360	ENST00000300778	T	0.40225	1.04	5.0	-6.36	0.01969	GPCR, rhodopsin-like superfamily (1);	0.797893	0.10688	N	0.645565	T	0.00012	0.0000	N	0.16066	0.365	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.41893	-0.9483	9	0.34782	T	0.22	.	2.3076	0.04178	0.162:0.4157:0.2302:0.1921	rs2736586;rs17359689;rs56459839;rs60685018;rs2736586	211	Q8NH59	O51Q1_HUMAN	M	211	ENSP00000300778:V211M	ENSP00000300778:V211M	V	+	1	0	OR51Q1	5400637	0.000000	0.05858	0.034000	0.17996	0.033000	0.12548	-3.921000	0.00334	-1.154000	0.02825	-1.540000	0.00911	GTG	G|0.599;A|0.401	0.401	strong		0.498	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
ZNF254	9534	hgsc.bcm.edu	37	19	24310074	24310074	+	Silent	SNP	T	T	C	rs61737179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:24310074T>C	ENST00000357002.4	+	4	1387	c.1272T>C	c.(1270-1272)caT>caC	p.H424H	ZNF254_ENST00000342944.6_Silent_p.H339H	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	424					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)				TTACTACACATAAGATAATTC	0.338													T|||	119	0.023762	0.0862	0.0072	5008	,	,		21190	0.0		0.0	False		,,,				2504	0.0				p.H424H		Atlas-SNP	.											.	ZNF254	88	.	0			c.T1272C						PASS	.	T		243,4161	134.9+/-171.1	7,229,1966	37.0	40.0	39.0		1272	1.1	0.1	19	dbSNP_129	39	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF254	NM_203282.2		7,230,6265	CC,CT,TT		0.0116,5.5177,1.8763		424/660	24310074	244,12760	2202	4300	6502	SO:0001819	synonymous_variant	9534	exon4			TACACATAAGATA	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.1272T>C	19.37:g.24310074T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_203282	A4QPC0|Q86XL7	Silent	SNP	ENST00000357002.4	37	CCDS32983.1																																																																																			T|0.979;C|0.021	0.021	strong		0.338	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876	
BAIAP3	8938	hgsc.bcm.edu	37	16	1391132	1391132	+	Silent	SNP	C	C	T	rs11866635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1391132C>T	ENST00000324385.5	+	7	734	c.576C>T	c.(574-576)gcC>gcT	p.A192A	BAIAP3_ENST00000562208.1_Silent_p.A134A|BAIAP3_ENST00000568887.1_Silent_p.A129A|BAIAP3_ENST00000426824.3_Silent_p.A157A|BAIAP3_ENST00000397489.1_Silent_p.A174A|BAIAP3_ENST00000421665.2_Silent_p.A157A|BAIAP3_ENST00000397488.2_Silent_p.A174A	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	192	C2 1. {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)				GTCCACAGGCCCCCACGTATG	0.672													C|||	440	0.0878594	0.2156	0.0346	5008	,	,		17155	0.0069		0.0318	False		,,,				2504	0.0941				p.A192A		Atlas-SNP	.											.	BAIAP3	88	.	0			c.C576T						PASS	.	C	,,,,	795,3601	313.6+/-293.2	68,659,1471	55.0	53.0	54.0		471,471,402,387,576	-0.7	1.0	16	dbSNP_120	54	218,8380	91.4+/-153.5	5,208,4086	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	,,,,	73,867,5557	TT,TC,CC		2.5355,18.0846,7.7959	,,,,	157/1117,157/1153,134/1130,129/1125,192/1188	1391132	1013,11981	2198	4299	6497	SO:0001819	synonymous_variant	8938	exon7			ACAGGCCCCCACG	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.576C>T	16.37:g.1391132C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	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|0.927;T|0.073	0.073	strong		0.672	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240560	39240560	+	Silent	SNP	T	T	C	rs200090467		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39240560T>C	ENST00000391417.4	+	1	102	c.102T>C	c.(100-102)tgT>tgC	p.C34C		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	34	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.C34C(2)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						AGACCACCTGTTGCAGGACCA	0.647																																					p.C34C		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-7	49	2	2	Substitution - coding silent(2)	endometrium(2)	c.T102C						scavenged	.						15.0	23.0	20.0					17																	39240560		691	1591	2282	SO:0001819	synonymous_variant	100132476	exon1			CACCTGTTGCAGG	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.102T>C	17.37:g.39240560T>C		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	127	14	0.110236	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	37	CCDS45673.1																																																																																			T|0.995;C|0.005	0.005	weak		0.647	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324190	39324190	+	Missense_Mutation	SNP	A	A	G	rs377224840		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324190A>G	ENST00000391356.2	-	1	234	c.235T>C	c.(235-237)Tgc>Cgc	p.C79R		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	79	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				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)			ggcctgcagcaactggaaatg	0.612																																					p.C79R		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.T235C						PASS	.	A	ARG/CYS	147,2777		0,147,1315	3.0	5.0	4.0		235	4.6	1.0	17		4	1,6765		0,1,3382	no	missense	KRTAP4-3	NM_033187.1	180	0,148,4697	GG,GA,AA		0.0148,5.0274,1.5273	possibly-damaging	79/196	39324190	148,9542	1462	3383	4845	SO:0001583	missense	85290	exon1			TGCAGCAACTGGA	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.235T>C	17.37:g.39324190A>G	ENSP00000375151:p.Cys79Arg	Somatic	392	1	0.00255102		WXS	Illumina HiSeq	Phase_I	166	73	0.439759	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	12.37	1.918720	0.33908	0.050274	1.48E-4	ENSG00000196156	ENST00000391356	T	0.03689	3.84	4.57	4.57	0.56435	.	0.000000	0.34362	U	0.004039	T	0.01523	0.0049	M	0.94142	3.5	0.48571	D	0.999674	P	0.38827	0.649	B	0.39185	0.293	T	0.00288	-1.1845	10	0.66056	D	0.02	.	7.092	0.25289	0.8963:0.0:0.1037:0.0	.	79	Q9BYR4	KRA43_HUMAN	R	79	ENSP00000375151:C79R	ENSP00000375151:C79R	C	-	1	0	KRTAP4-3	36577716	0.718000	0.27976	0.995000	0.50966	0.018000	0.09664	1.969000	0.40510	1.799000	0.52666	0.496000	0.49642	TGC	.	.	weak		0.612	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
VWDE	221806	hgsc.bcm.edu	37	7	12443312	12443312	+	Missense_Mutation	SNP	C	C	T	rs139879021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12443312C>T	ENST00000275358.3	-	1	219	c.31G>A	c.(31-33)Gcg>Acg	p.A11T		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	11						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						AACATCAGCGCGATCACCAGC	0.721													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		14305	0.0		0.0	False		,,,				2504	0.0				p.A11T		Atlas-SNP	.											.	VWDE	123	.	0			c.G31A						PASS	.	C	THR/ALA	33,1351		1,31,660	20.0	27.0	25.0		31	2.4	0.0	7	dbSNP_134	25	1,3181		0,1,1590	yes	missense	VWDE	NM_001135924.1	58	1,32,2250	TT,TC,CC		0.0314,2.3844,0.7446	benign	11/1591	12443312	34,4532	692	1591	2283	SO:0001583	missense	221806	exon1			TCAGCGCGATCAC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.31G>A	7.37:g.12443312C>T	ENSP00000275358:p.Ala11Thr	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	C	13.20	2.164755	0.38217	0.023844	3.14E-4	ENSG00000146530	ENST00000275358;ENST00000541006	D	0.82344	-1.6	3.28	2.38	0.29361	.	1.817110	0.02839	N	0.127729	T	0.58293	0.2112	L	0.36672	1.1	0.09310	N	1	P	0.43431	0.807	B	0.29663	0.105	T	0.61431	-0.7064	10	0.37606	T	0.19	.	7.8381	0.29382	0.2478:0.7522:0.0:0.0	.	11	Q8N2E2	VWDE_HUMAN	T	11	ENSP00000275358:A11T	ENSP00000275358:A11T	A	-	1	0	VWDE	12409837	0.001000	0.12720	0.005000	0.12908	0.107000	0.19398	0.623000	0.24447	0.953000	0.37825	0.491000	0.48974	GCG	C|0.996;T|0.004	0.004	strong		0.721	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
RGS8	85397	hgsc.bcm.edu	37	1	182640851	182640851	+	5'UTR	SNP	T	T	G	rs569956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182640851T>G	ENST00000483095.2	-	0	95				RGS8_ENST00000367557.4_5'UTR|RGS8_ENST00000367556.1_5'UTR|RGS8_ENST00000258302.4_Silent_p.R7R|RGS8_ENST00000491420.2_5'UTR			P57771	RGS8_HUMAN	regulator of G-protein signaling 8						positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.R7R(1)		haematopoietic_and_lymphoid_tissue(1)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	5						CAGAGAGGCTTCGGGTTAAGG	0.498													G|||	783	0.15635	0.3396	0.1297	5008	,	,		20102	0.1399		0.0408	False		,,,				2504	0.0634				p.R7R	Ovarian(189;1262 3804 41973)	Atlas-SNP	.											RGS8,NS,carcinoma,0,1	RGS8	51	1	1	Substitution - coding silent(1)	stomach(1)	c.A21C						PASS	.	G	,	1164,3242	712.2+/-408.1	159,846,1198	171.0	173.0	173.0		,21	4.3	1.0	1	dbSNP_83	173	368,8232	802.8+/-407.3	6,356,3938	no	utr-5,coding-synonymous	RGS8	NM_001102450.1,NM_033345.2	,	165,1202,5136	GG,GT,TT		4.2791,26.4185,11.7792	,	,7/199	182640851	1532,11474	2203	4300	6503	SO:0001623	5_prime_UTR_variant	85397	exon2			GAGGCTTCGGGTT	AF297015	CCDS1349.1, CCDS41443.1	1q25	2008-07-18	2007-08-14		ENSG00000135824	ENSG00000135824		"""Regulators of G-protein signaling"""	16810	protein-coding gene	gene with protein product		607189	"""regulator of G-protein signalling 8"""			11318611	Standard	NM_001102450		Approved	MGC119067, MGC119068, MGC119069	uc001gpm.1	P57771	OTTHUMG00000035219	ENST00000483095.2:c.-163A>C	1.37:g.182640851T>G		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	217	83	0.382488	NM_033345	B4DGL9|Q3SYD2	Silent	SNP	ENST00000483095.2	37	CCDS41443.1																																																																																			T|0.880;G|0.120	0.120	strong		0.498	RGS8-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358979.1	NM_033345	
BAG6	7917	hgsc.bcm.edu	37	6	31615514	31615514	+	Silent	SNP	T	T	C	rs10484558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31615514T>C	ENST00000375964.6	-	7	973	c.660A>G	c.(658-660)acA>acG	p.T220T	BAG6_ENST00000404765.2_Silent_p.T214T|BAG6_ENST00000211379.5_Silent_p.T214T|BAG6_ENST00000375976.4_Silent_p.T214T|BAG6_ENST00000439687.2_Silent_p.T214T|BAG6_ENST00000362049.6_Silent_p.T214T	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	220	Pro-rich.				brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						CTGGTTCTGATGTTTGAGAGC	0.647													T|||	272	0.0543131	0.1278	0.0692	5008	,	,		15125	0.0179		0.0219	False		,,,				2504	0.0153				p.T220T		Atlas-SNP	.											.	BAG6	73	.	0			c.A660G						PASS	.	T	,,,,,	321,2699		16,289,1205	130.0	165.0	153.0		642,642,642,660,642,642	-3.1	0.3	6	dbSNP_119	153	150,5266		1,148,2559	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAG6	NM_001098534.1,NM_001199697.1,NM_001199698.1,NM_004639.3,NM_080702.2,NM_080703.2	,,,,,	17,437,3764	CC,CT,TT		2.7696,10.6291,5.5832	,,,,,	214/1127,214/904,214/1078,220/1133,214/1127,214/1127	31615514	471,7965	1510	2708	4218	SO:0001819	synonymous_variant	7917	exon7			TTCTGATGTTTGA	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"""HLA-B associated transcript 3"""	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.660A>G	6.37:g.31615514T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	108	51	0.472222	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Silent	SNP	ENST00000375964.6	37	CCDS47403.1																																																																																			T|0.937;C|0.063	0.063	strong		0.647	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703	
PAPOLB	56903	hgsc.bcm.edu	37	7	4901385	4901385	+	Missense_Mutation	SNP	A	A	C	rs3750009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:4901385A>C	ENST00000404991.1	-	1	240	c.54T>G	c.(52-54)aaT>aaG	p.N18K	RADIL_ENST00000399583.3_Intron|RADIL_ENST00000536091.1_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	26	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	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	
PYROXD2	84795	hgsc.bcm.edu	37	10	100148176	100148176	+	Missense_Mutation	SNP	A	A	G	rs2147896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	113	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	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	
MZF1	7593	hgsc.bcm.edu	37	19	59074429	59074429	+	Silent	SNP	C	C	T	rs2228162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:59074429C>T	ENST00000215057.2	-	6	1775	c.1215G>A	c.(1213-1215)acG>acA	p.T405T	AC016629.8_ENST00000600726.1_RNA|MZF1_ENST00000599369.1_Silent_p.T405T|MZF1_ENST00000594234.1_3'UTR|AC016629.8_ENST00000600534.1_RNA|AC016629.8_ENST00000593642.1_RNA	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	405					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		CCTCGGTGTGCGTAAGCTGGT	0.677													.|||	966	0.192891	0.4198	0.1916	5008	,	,		15967	0.1121		0.0457	False		,,,				2504	0.1217				p.T405T		Atlas-SNP	.											.	MZF1	37	.	0			c.G1215A						PASS	.	C	,	1606,2782		300,1006,888	17.0	17.0	17.0		1215,1215	-3.0	0.9	19	dbSNP_98	17	332,8206		13,306,3950	no	coding-synonymous,coding-synonymous	MZF1	NM_003422.2,NM_198055.1	,	313,1312,4838	TT,TC,CC		3.8885,36.5998,14.993	,	405/735,405/735	59074429	1938,10988	2194	4269	6463	SO:0001819	synonymous_variant	7593	exon6			GGTGTGCGTAAGC	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"""-"", ""Zinc fingers, C2H2-type"""	13108	protein-coding gene	gene with protein product		194550	"""zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"""	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.1215G>A	19.37:g.59074429C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	25	11	0.44	NM_198055	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Silent	SNP	ENST00000215057.2	37	CCDS12988.1																																																																																			C|0.839;T|0.161	0.161	strong		0.677	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055	
TNXB	7148	hgsc.bcm.edu	37	6	32046832	32046832	+	Silent	SNP	C	C	T	rs61998180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32046832C>T	ENST00000375244.3	-	11	4554	c.4353G>A	c.(4351-4353)ccG>ccA	p.P1451P	TNXB_ENST00000375247.2_Silent_p.P1451P|RNA5SP206_ENST00000516703.1_RNA			P22105	TENX_HUMAN	tenascin XB	1538					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.P1538P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CGGCGGACACCGGGCCCACGC	0.662													C|||	18	0.00359425	0.0129	0.0014	5008	,	,		15860	0.0		0.0	False		,,,				2504	0.0				p.P1451P		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,0,1	TNXB	553	1	1	Substitution - coding silent(1)	breast(1)	c.G4353A						PASS	.	C		11,2573		0,11,1281	38.0	43.0	41.0		4353	-2.3	0.8	6	dbSNP_129	41	0,5136		0,0,2568	no	coding-synonymous	TNXB	NM_019105.6		0,11,3849	TT,TC,CC		0.0,0.4257,0.1425		1451/4243	32046832	11,7709	1292	2568	3860	SO:0001819	synonymous_variant	7148	exon11			GGACACCGGGCCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.4353G>A	6.37:g.32046832C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	137	71	0.518248	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				C|0.987;T|0.013	0.013	weak		0.662	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
PGLYRP3	114771	hgsc.bcm.edu	37	1	153276449	153276449	+	Missense_Mutation	SNP	T	T	C	rs41264632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153276449T>C	ENST00000290722.1	-	4	465	c.413A>G	c.(412-414)gAg>gGg	p.E138G		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	138					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.E138G(1)		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)			GATCAGACCCTCTGCAGCTGA	0.527													T|||	203	0.0405351	0.0371	0.0432	5008	,	,		20460	0.1062		0.004	False		,,,				2504	0.0133				p.E138G		Atlas-SNP	.											PGLYRP3,NS,carcinoma,0,1	PGLYRP3	55	1	1	Substitution - Missense(1)	stomach(1)	c.A413G						scavenged	.	T	GLY/GLU	113,4293	83.9+/-122.4	1,111,2091	66.0	67.0	67.0		413	2.9	0.9	1	dbSNP_127	67	32,8568	19.8+/-62.0	1,30,4269	yes	missense	PGLYRP3	NM_052891.1	98	2,141,6360	CC,CT,TT		0.3721,2.5647,1.1149	probably-damaging	138/342	153276449	145,12861	2203	4300	6503	SO:0001583	missense	114771	exon4			AGACCCTCTGCAG	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.413A>G	1.37:g.153276449T>C	ENSP00000290722:p.Glu138Gly	Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_052891	A1A4U8|Q5SY65	Missense_Mutation	SNP	ENST00000290722.1	37	CCDS1035.1	90	0.04120879120879121	12	0.024390243902439025	11	0.03038674033149171	64	0.11188811188811189	3	0.00395778364116095	T	12.84	2.059855	0.36373	0.025647	0.003721	ENSG00000159527	ENST00000290722	T	0.14516	2.5	4.15	2.91	0.33838	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.127266	0.35677	N	0.003057	T	0.05731	0.0150	L	0.61218	1.895	0.25854	N	0.983909	B	0.19935	0.04	B	0.26969	0.075	T	0.27606	-1.0069	10	0.66056	D	0.02	-60.0862	5.5581	0.17127	0.0:0.1501:0.0:0.8499	rs41264632	138	Q96LB9	PGRP3_HUMAN	G	138	ENSP00000290722:E138G	ENSP00000290722:E138G	E	-	2	0	PGLYRP3	151543073	0.000000	0.05858	0.941000	0.38009	0.882000	0.50991	0.086000	0.14935	0.721000	0.32231	0.528000	0.53228	GAG	T|0.982;C|0.018	0.018	strong		0.527	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891	
WDR4	10785	hgsc.bcm.edu	37	21	44283574	44283574	+	Silent	SNP	C	C	T	rs11911090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	187	102	0.545455	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		
INTS3	65123	hgsc.bcm.edu	37	1	153740285	153740285	+	Silent	SNP	G	G	A	rs61736048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153740285G>A	ENST00000318967.2	+	21	2794	c.2226G>A	c.(2224-2226)acG>acA	p.T742T	INTS3_ENST00000512605.1_Silent_p.T536T|INTS3_ENST00000435409.2_Silent_p.T742T|INTS3_ENST00000456435.1_Silent_p.T536T|INTS3_ENST00000476843.1_3'UTR	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	743					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GCCACCTCACGCCCTCCATCT	0.592													G|||	61	0.0121805	0.0446	0.0029	5008	,	,		18290	0.0		0.0	False		,,,				2504	0.0				p.T742T		Atlas-SNP	.											.	INTS3	83	.	0			c.G2226A						PASS	.	G		170,4236	112.9+/-151.0	2,166,2035	91.0	75.0	81.0		2226	-11.7	0.1	1	dbSNP_129	81	0,8600		0,0,4300	no	coding-synonymous	INTS3	NM_023015.3		2,166,6335	AA,AG,GG		0.0,3.8584,1.3071		742/1043	153740285	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	65123	exon21			CCTCACGCCCTCC	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.2226G>A	1.37:g.153740285G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Silent	SNP	ENST00000318967.2	37	CCDS1052.1																																																																																			G|0.983;A|0.017	0.017	strong		0.592	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
PTRF	284119	hgsc.bcm.edu	37	17	40556951	40556951	+	Silent	SNP	C	C	T	rs112332573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40556951C>T	ENST00000357037.5	-	2	1346	c.927G>A	c.(925-927)gcG>gcA	p.A309A		NM_012232.5	NP_036364.2			polymerase I and transcript release factor											breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		TCTTGGAGCGCGCGTACACCA	0.647													C|||	92	0.0183706	0.0696	0.0	5008	,	,		12868	0.0		0.0	False		,,,				2504	0.0				p.A309A		Atlas-SNP	.											.	PTRF	48	.	0			c.G927A						PASS	.	C		259,4147	148.4+/-182.8	10,239,1954	104.0	89.0	94.0		927	0.5	1.0	17	dbSNP_132	94	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	PTRF	NM_012232.5		10,244,6249	TT,TC,CC		0.0581,5.8783,2.0298		309/391	40556951	264,12742	2203	4300	6503	SO:0001819	synonymous_variant	284119	exon2			GGAGCGCGCGTAC	AF000421	CCDS11425.1	17q21.31	2011-04-20				ENSG00000177469			9688	protein-coding gene	gene with protein product		603198				9582279	Standard	NM_012232		Approved	cavin-1, CAVIN1	uc002hzo.3	Q6NZI2		ENST00000357037.5:c.927G>A	17.37:g.40556951C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	172	92	0.534884	NM_012232		Silent	SNP	ENST00000357037.5	37	CCDS11425.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232	
TTC16	158248	hgsc.bcm.edu	37	9	130485476	130485476	+	Missense_Mutation	SNP	A	A	C	rs115363266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130485476A>C	ENST00000373289.3	+	7	816	c.736A>C	c.(736-738)Aag>Cag	p.K246Q	TTC16_ENST00000489226.1_3'UTR|PTRH1_ENST00000429848.1_Intron|TTC16_ENST00000393748.4_Missense_Mutation_p.K70Q|PTRH1_ENST00000419060.1_Intron	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	246										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						GCTGCTCCAGAAGATGGTGGC	0.662													A|||	136	0.0271565	0.0983	0.0086	5008	,	,		19586	0.0		0.0	False		,,,				2504	0.0				p.K246Q		Atlas-SNP	.											.	TTC16	55	.	0			c.A736C						PASS	.	A	GLN/LYS	459,3947	211.5+/-231.7	30,399,1774	55.0	56.0	55.0		736	0.1	0.1	9	dbSNP_132	55	0,8600		0,0,4300	yes	missense	TTC16	NM_144965.1	53	30,399,6074	CC,CA,AA		0.0,10.4176,3.5291	benign	246/874	130485476	459,12547	2203	4300	6503	SO:0001583	missense	158248	exon7			CTCCAGAAGATGG	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.736A>C	9.37:g.130485476A>C	ENSP00000362386:p.Lys246Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	100	62	0.62	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	37	CCDS6875.1	69|69	0.03159340659340659|0.03159340659340659	66|66	0.13414634146341464|0.13414634146341464	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	A|A	7.212|7.212	0.595622|0.595622	0.13875|0.13875	0.104176|0.104176	0.0|0.0	ENSG00000167094|ENSG00000167094	ENST00000373288|ENST00000373289;ENST00000393748;ENST00000316259	.|T	.|0.54866	.|0.55	5.08|5.08	0.119|0.119	0.14685|0.14685	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.|1.102050	.|0.06828	.|N	.|0.793373	T|T	0.00637|0.00637	0.0021|0.0021	L|L	0.53249|0.53249	1.67|1.67	0.09310|0.09310	N|N	1|1	.|P;B;P	.|0.51351	.|0.944;0.022;0.944	.|B;B;B	.|0.44044	.|0.439;0.013;0.439	T|T	0.02491|0.02491	-1.1151|-1.1151	6|10	0.87932|0.46703	D|T	0|0.11	-1.776|-1.776	7.3747|7.3747	0.26821|0.26821	0.6016:0.0:0.3984:0.0|0.6016:0.0:0.3984:0.0	.|.	.|233;198;246	.|B4DZ42;B4DH05;Q8NEE8	.|.;.;TTC16_HUMAN	A|Q	71|246;70;191	.|ENSP00000362386:K246Q	ENSP00000362385:E71A|ENSP00000319048:K191Q	E|K	+|+	2|1	0|0	TTC16|TTC16	129525297|129525297	0.005000|0.005000	0.15991|0.15991	0.113000|0.113000	0.21522|0.21522	0.358000|0.358000	0.29455|0.29455	0.441000|0.441000	0.21611|0.21611	-0.113000|-0.113000	0.11958|0.11958	0.374000|0.374000	0.22700|0.22700	GAA|AAG	A|0.962;C|0.038	0.038	strong		0.662	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
TAS1R3	83756	hgsc.bcm.edu	37	1	1269488	1269488	+	Missense_Mutation	SNP	G	G	A	rs112507608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1269488G>A	ENST00000339381.5	+	6	2235	c.2203G>A	c.(2203-2205)Gcc>Acc	p.A735T		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	735					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)		CCTAGCGCACGCCACCAATGC	0.677													g|||	299	0.0597045	0.2148	0.0202	5008	,	,		18080	0.0		0.001	False		,,,				2504	0.0				p.A735T		Atlas-SNP	.											.	TAS1R3	39	.	0			c.G2203A						PASS	.	G	THR/ALA	825,3533		76,673,1430	31.0	17.0	22.0		2203	-1.0	0.0	1	dbSNP_132	22	6,8566		0,6,4280	yes	missense	TAS1R3	NM_152228.1	58	76,679,5710	AA,AG,GG		0.07,18.9307,6.4269	benign	735/853	1269488	831,12099	2179	4286	6465	SO:0001583	missense	83756	exon6			GCGCACGCCACCA	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.2203G>A	1.37:g.1269488G>A	ENSP00000344411:p.Ala735Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_152228	Q5TA49|Q8NGW9	Missense_Mutation	SNP	ENST00000339381.5	37	CCDS30556.1	110	0.05036630036630037	102	0.2073170731707317	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	G	5.972	0.363238	0.11296	0.189307	7.0E-4	ENSG00000169962	ENST00000339381	D	0.88741	-2.42	4.35	-1.05	0.10036	GPCR, family 3, C-terminal (2);	0.499914	0.20112	N	0.098990	T	0.00210	0.0006	L	0.33485	1.01	0.80722	P	0.0	B	0.18166	0.026	B	0.14578	0.011	T	0.24119	-1.0169	9	0.62326	D	0.03	.	9.7028	0.40198	0.4805:0.0:0.5195:0.0	.	735	Q7RTX0	TS1R3_HUMAN	T	735	ENSP00000344411:A735T	ENSP00000344411:A735T	A	+	1	0	TAS1R3	1259351	0.001000	0.12720	0.001000	0.08648	0.011000	0.07611	0.420000	0.21263	-0.093000	0.12396	0.456000	0.33151	GCC	G|0.933;A|0.067	0.067	strong		0.677	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1		
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609806	32609806	+	Missense_Mutation	SNP	C	C	T	rs707952	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	196	0	0		WXS	Illumina HiSeq	Phase_I	254	254	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	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	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261778	39261778	+	Silent	SNP	A	A	G	rs556157666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39261778A>G	ENST00000391415.1	+	1	195	c.138A>G	c.(136-138)gtA>gtG	p.V46V		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	46	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						GCTGTTGTGTATCCAGCTGCT	0.652													G|||	380	0.0758786	0.171	0.0749	5008	,	,		16398	0.0714		0.0119	False		,,,				2504	0.0184				p.V46V		Atlas-SNP	.											KRTAP4-9,NS,carcinoma,0,1	KRTAP4-9	110	1	0			c.A138G						scavenged	.						15.0	22.0	20.0					17																	39261778		690	1591	2281	SO:0001819	synonymous_variant	100132386	exon1			TTGTGTATCCAGC	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.138A>G	17.37:g.39261778A>G		Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	85	23	0.270588	NM_001146041		Silent	SNP	ENST00000391415.1	37	CCDS54124.1																																																																																			.	.	none		0.652	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
TOP2B	7155	hgsc.bcm.edu	37	3	25679738	25679738	+	Silent	SNP	T	T	C	rs60422476	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:25679738T>C	ENST00000264331.4	-	5	458	c.459A>G	c.(457-459)gtA>gtG	p.V153V	TOP2B_ENST00000435706.2_Silent_p.V148V	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	153					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)	AAACTTTCTCTACCTTGTGTT	0.279													T|||	1682	0.335863	0.3933	0.3689	5008	,	,		12520	0.3095		0.2763	False		,,,				2504	0.3231				p.V148V		Atlas-SNP	.											.	TOP2B	98	.	0			c.A444G						PASS	.	T		1450,2128		290,870,629	60.0	57.0	58.0		444	3.8	1.0	3	dbSNP_129	58	2011,6063		255,1501,2281	no	coding-synonymous	TOP2B	NM_001068.2		545,2371,2910	CC,CT,TT		24.9071,40.5254,29.7031		148/1622	25679738	3461,8191	1789	4037	5826	SO:0001819	synonymous_variant	7155	exon5			TTTCTCTACCTTG	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.459A>G	3.37:g.25679738T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	222	123	0.554054	NM_001068	Q13600|Q9UMG8|Q9UQP8	Silent	SNP	ENST00000264331.4	37																																																																																				T|0.700;C|0.300	0.300	strong		0.279	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
PABPC1	26986	hgsc.bcm.edu	37	8	101721705	101721705	+	Missense_Mutation	SNP	G	G	T	rs201017624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721705G>T	ENST00000318607.5	-	8	2355	c.1227C>A	c.(1225-1227)ttC>ttA	p.F409L	PABPC1_ENST00000519004.1_Missense_Mutation_p.F364L|PABPC1_ENST00000522387.1_Missense_Mutation_p.F377L|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	409					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TAGCTGCCATGAAGTAACCTG	0.488													g|||	1288	0.257188	0.2943	0.2089	5008	,	,		21380	0.2649		0.2107	False		,,,				2504	0.2812				p.F409L		Atlas-SNP	.											.	PABPC1	76	.	0			c.C1227A						PASS	.						101.0	92.0	95.0					8																	101721705		2203	4300	6503	SO:0001583	missense	26986	exon8			TGCCATGAAGTAA	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.1227C>A	8.37:g.101721705G>T	ENSP00000313007:p.Phe409Leu	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	264	48	0.181818	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	g|g|g	17.00|17.00|17.00	3.276204|3.276204|3.276204	0.59649|0.59649|0.59649	.|.|.	.|.|.	ENSG00000070756|ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387|ENST00000519596|ENST00000517403;ENST00000519100	T;T;T|.|.	0.29142|.|.	1.67;1.58;2.65|.|.	5.37|5.37|5.37	4.5|4.5|4.5	0.54988|0.54988|0.54988	.|.|.	0.000000|.|.	0.64402|.|.	D|.|.	0.000001|.|.	T|T|.	0.61160|0.61160|.	0.2325|0.2325|.	L|L|L	0.46819|0.46819|0.46819	1.47|1.47|1.47	0.58432|0.58432|0.58432	D|D|D	0.999997|0.999997|0.999997	B;B;B|.|.	0.23937|.|.	0.094;0.024;0.009|.|.	B;B;B|.|.	0.19946|.|.	0.027;0.01;0.013|.|.	T|T|.	0.58747|0.58747|.	-0.7582|-0.7582|.	10|5|.	0.49607|.|.	T|.|.	0.09|.|.	.|.|.	14.6297|14.6297|14.6297	0.68647|0.68647|0.68647	0.0702:0.0:0.9298:0.0|0.0702:0.0:0.9298:0.0|0.0702:0.0:0.9298:0.0	.|.|.	377;409;409|.|.	E7ERJ7;B3KT93;P11940|.|.	.;.;PABP1_HUMAN|.|.	L|N|X	409;409;364;377|242|62;278	ENSP00000313007:F409L;ENSP00000429594:F364L;ENSP00000429395:F377L|.|.	ENSP00000313007:F409L|.|.	F|H|S	-|-|-	3|1|2	2|0|0	PABPC1|PABPC1|PABPC1	101790881|101790881|101790881	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.996000|0.996000|0.996000	0.88848|0.88848|0.88848	7.998000|7.998000|7.998000	0.88491|0.88491|0.88491	1.419000|1.419000|1.419000	0.47118|0.47118|0.47118	-0.119000|-0.119000|-0.119000	0.15052|0.15052|0.15052	TTC|CAT|TCA	G|0.944;T|0.057	0.057	strong		0.488	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
RFX4	5992	hgsc.bcm.edu	37	12	107114548	107114548	+	Silent	SNP	G	G	A	rs73391388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:107114548G>A	ENST00000392842.1	+	13	1659	c.1245G>A	c.(1243-1245)aaG>aaA	p.K415K	RP11-482D24.3_ENST00000552415.1_RNA|RFX4_ENST00000357881.4_Silent_p.K424K|RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000229387.5_Silent_p.K321K	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	415	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						TGGCTGCCAAGAGACAAGGGT	0.493													G|||	53	0.0105831	0.0378	0.0043	5008	,	,		20153	0.0		0.0	False		,,,				2504	0.0				p.K424K		Atlas-SNP	.											.	RFX4	218	.	0			c.G1272A						PASS	.	G	,,	175,4231	115.4+/-153.4	2,171,2030	89.0	81.0	84.0		1272,963,1245	5.6	1.0	12	dbSNP_130	84	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	RFX4	NM_001206691.1,NM_032491.5,NM_213594.2	,,	2,178,6323	AA,AG,GG		0.0814,3.9719,1.3994	,,	424/745,321/642,415/736	107114548	182,12824	2203	4300	6503	SO:0001819	synonymous_variant	5992	exon13			TGCCAAGAGACAA	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.1245G>A	12.37:g.107114548G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	156	66	0.423077	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	37	CCDS9106.1																																																																																			G|0.988;A|0.012	0.012	strong		0.493	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
UGT1A4	54657	hgsc.bcm.edu	37	2	234627992	234627992	+	Missense_Mutation	SNP	A	A	T	rs45540231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234627992A>T	ENST00000373409.3	+	1	569	c.526A>T	c.(526-528)Att>Ttt	p.I176F	UGT1A10_ENST00000344644.5_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron	NM_007120.2	NP_009051.1	P22310	UD14_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A4	176			I -> F (in dbSNP:rs45540231).		cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	26		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;3.49e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000504)|Lung(119;0.0026)|LUSC - Lung squamous cell carcinoma(224;0.00624)	Asenapine(DB06216)|Clozapine(DB00363)|Ezogabine(DB04953)|Lamotrigine(DB00555)|Midazolam(DB00683)|Paricalcitol(DB00910)|Tamoxifen(DB00675)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)	TTGGAGGTACATTCCATGTGA	0.453													A|||	120	0.0239617	0.0862	0.0072	5008	,	,		22076	0.0		0.001	False		,,,				2504	0.0				p.I176F	Melanoma(99;1011 1962 13201 26492)	Atlas-SNP	.											.	UGT1A4	63	.	0			c.A526T						PASS	.	A	,PHE/ILE,,,,,,	269,4137	151.4+/-185.3	8,253,1942	179.0	173.0	175.0		,526,,,,,,	-6.9	0.0	2	dbSNP_127	175	4,8596	3.7+/-12.6	0,4,4296	no	intron,missense,intron,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4	NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_021027.2,NM_205862.1	,21,,,,,,	8,257,6238	TT,TA,AA		0.0465,6.1053,2.099	,,,,,,,	,176/535,,,,,,	234627992	273,12733	2203	4300	6503	SO:0001583	missense	54657	exon1			AGGTACATTCCAT	M84128	CCDS33405.1	2q37.1	2014-01-10	2005-07-20		ENSG00000244474	ENSG00000244474		"""UDP glucuronosyltransferases"""	12536	other	complex locus constituent		606429	"""UDP glycosyltransferase 1 family, polypeptide A4"""			9295054, 1339448	Standard	NM_007120		Approved	HUG-BR2, UGT1D	uc002vux.3	P22310	OTTHUMG00000059119	ENST00000373409.3:c.526A>T	2.37:g.234627992A>T	ENSP00000362508:p.Ile176Phe	Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	411	215	0.523114	NM_007120	B2R937|B8K288|Q5DT00	Missense_Mutation	SNP	ENST00000373409.3	37	CCDS33405.1	43	0.019688644688644688	40	0.08130081300813008	3	0.008287292817679558	0	0.0	0	0.0	A	9.158	1.017991	0.19355	0.061053	4.65E-4	ENSG00000244474	ENST00000373409	T	0.60299	0.2	4.49	-6.89	0.01660	.	.	.	.	.	T	0.02119	0.0066	N	0.05124	-0.11	0.09310	N	1	B;P	0.49447	0.327;0.924	B;P	0.52823	0.187;0.71	T	0.04165	-1.0972	9	0.09590	T	0.72	.	7.3186	0.26515	0.2629:0.5035:0.2335:0.0	rs45540231	176;176	B8K288;P22310	.;UD14_HUMAN	F	176	ENSP00000362508:I176F	ENSP00000362508:I176F	I	+	1	0	UGT1A4	234292731	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.458000	0.00464	-1.016000	0.03371	-0.619000	0.04042	ATT	A|0.980;T|0.020	0.020	strong		0.453	UGT1A4-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130984.1	NM_007120	
PMEPA1	56937	hgsc.bcm.edu	37	20	56227514	56227514	+	Silent	SNP	T	T	C	rs6025698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:56227514T>C	ENST00000341744.3	-	4	778	c.459A>G	c.(457-459)tcA>tcG	p.S153S	PMEPA1_ENST00000265626.4_Silent_p.S103S|PMEPA1_ENST00000395814.1_Silent_p.S103S|PMEPA1_ENST00000395816.3_Silent_p.S103S|PMEPA1_ENST00000347215.4_Silent_p.S118S	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	153					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)	p.S153S(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						CCTCCCCGTCTGACAGCGAGA	0.701													C|||	1558	0.311102	0.5484	0.1801	5008	,	,		14970	0.3661		0.1451	False		,,,				2504	0.1973				p.S153S		Atlas-SNP	.											PMEPA1,NS,lymphoid_neoplasm,0,1	PMEPA1	29	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.A459G						PASS	.	C	,,,	2058,2348	599.9+/-389.4	507,1044,652	34.0	37.0	36.0		459,354,309,309	-6.5	0.5	20	dbSNP_114	36	1471,7129	742.0+/-407.2	137,1197,2966	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PMEPA1	NM_020182.3,NM_199169.1,NM_199170.1,NM_199171.1	,,,	644,2241,3618	CC,CT,TT		17.1047,46.709,27.1336	,,,	153/288,118/253,103/238,103/238	56227514	3529,9477	2203	4300	6503	SO:0001819	synonymous_variant	56937	exon4			CCCGTCTGACAGC	AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"""solid tumor-associated 1"""	606564	"""transmembrane, prostate androgen induced RNA"""	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.459A>G	20.37:g.56227514T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_020182	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Silent	SNP	ENST00000341744.3	37	CCDS13463.1																																																																																			T|0.715;C|0.285	0.285	strong		0.701	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182	
SUPV3L1	6832	hgsc.bcm.edu	37	10	70940052	70940052	+	Missense_Mutation	SNP	C	C	T	rs33998366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70940052C>T	ENST00000359655.4	+	1	65	c.5C>T	c.(4-6)tCc>tTc	p.S2F	SUPV3L1_ENST00000483572.1_3'UTR	NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	2			S -> F (in dbSNP:rs33998366).		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						GCCTCGATGTCCTTCTCCCGT	0.692													C|||	218	0.0435304	0.1573	0.013	5008	,	,		16089	0.0		0.001	False		,,,				2504	0.0				p.S2F		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.C5T						PASS	.	C	PHE/SER	537,3867	208.5+/-229.5	33,471,1698	25.0	29.0	28.0		5	4.9	1.0	10	dbSNP_126	28	2,8596	2.2+/-6.3	0,2,4297	yes	missense	SUPV3L1	NM_003171.3	155	33,473,5995	TT,TC,CC		0.0233,12.1935,4.1455	probably-damaging	2/787	70940052	539,12463	2202	4299	6501	SO:0001583	missense	6832	exon1			CGATGTCCTTCTC	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.5C>T	10.37:g.70940052C>T	ENSP00000352678:p.Ser2Phe	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_003171	A8K301|O43630	Missense_Mutation	SNP	ENST00000359655.4	37	CCDS7287.1	89	0.04075091575091575	81	0.16463414634146342	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	22.0	4.227112	0.79576	0.121935	2.33E-4	ENSG00000156502	ENST00000359655;ENST00000422378	T;T	0.35973	1.43;1.28	5.78	4.88	0.63580	.	0.080168	0.50627	N	0.000116	T	0.00073	0.0002	N	0.22421	0.69	0.31663	N	0.645286	P	0.35077	0.483	B	0.33392	0.163	T	0.02789	-1.1110	10	0.87932	D	0	-0.6733	8.3656	0.32385	0.1559:0.7643:0.0:0.0797	rs33998366	2	Q8IYB8	SUV3_HUMAN	F	2	ENSP00000352678:S2F;ENSP00000409072:S2F	ENSP00000352678:S2F	S	+	2	0	SUPV3L1	70610058	0.672000	0.27530	1.000000	0.80357	0.919000	0.55068	1.022000	0.30052	2.729000	0.93468	0.655000	0.94253	TCC	C|0.961;T|0.039	0.039	strong		0.692	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415469	105415469	+	Missense_Mutation	SNP	T	T	C	rs11846918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105415469T>C	ENST00000333244.5	-	7	6438	c.6319A>G	c.(6319-6321)Atg>Gtg	p.M2107V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2107			M -> V (in dbSNP:rs11846918).			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)			GGGACTCTCATTTCCACCTTG	0.597													.|||	2244	0.448083	0.6369	0.4323	5008	,	,		14687	0.374		0.2724	False		,,,				2504	0.4611				p.M2107V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A6319G						PASS	.	C	VAL/MET	2269,1485		794,681,402	138.0	94.0	111.0		6319	-2.2	0.0	14	dbSNP_120	111	720,5004		240,240,2382	yes	missense	AHNAK2	NM_138420.2	21	1034,921,2784	CC,CT,TT		12.5786,39.5578,31.5362	benign	2107/5796	105415469	2989,6489	1877	2862	4739	SO:0001583	missense	113146	exon7			CTCTCATTTCCAC	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.6319A>G	14.37:g.105415469T>C	ENSP00000353114:p.Met2107Val	Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	359	357	0.994429	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	935	0.4281135531135531	323	0.6565040650406504	180	0.4972375690607735	201	0.3513986013986014	231	0.30474934036939316	N	0.013	-1.627804	0.00813	0.604422	0.125786	ENSG00000185567	ENST00000333244	T	0.01119	5.31	3.75	-2.21	0.06973	.	.	.	.	.	T	0.00012	0.0000	N	0.00119	-2.075	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.19647	-1.0299	8	0.02654	T	1	.	5.9469	0.19223	0.0:0.3584:0.3864:0.2551	rs11846918	2107	Q8IVF2	AHNK2_HUMAN	V	2107	ENSP00000353114:M2107V	ENSP00000353114:M2107V	M	-	1	0	AHNAK2	104486514	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-3.969000	0.00323	-1.017000	0.03367	-0.665000	0.03846	ATG	T|0.581;C|0.419	0.419	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
BAIAP3	8938	hgsc.bcm.edu	37	16	1391419	1391419	+	Silent	SNP	T	T	C	rs73485660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1391419T>C	ENST00000324385.5	+	8	923	c.765T>C	c.(763-765)ccT>ccC	p.P255P	BAIAP3_ENST00000562208.1_Silent_p.P197P|BAIAP3_ENST00000568887.1_Silent_p.P192P|BAIAP3_ENST00000426824.3_Silent_p.P220P|BAIAP3_ENST00000397489.1_Silent_p.P237P|BAIAP3_ENST00000421665.2_Silent_p.P220P|BAIAP3_ENST00000397488.2_Silent_p.P237P	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	255	C2 1. {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)				GACCCCTGCCTGCCAAGTGCA	0.677													C|||	42	0.00838658	0.031	0.0014	5008	,	,		17741	0.0		0.0	False		,,,				2504	0.0				p.P255P		Atlas-SNP	.											.	BAIAP3	88	.	0			c.T765C						PASS	.	C	,,,,	113,4283		0,113,2085	61.0	56.0	58.0		660,660,591,576,765	-9.4	0.1	16	dbSNP_130	58	0,8594		0,0,4297	yes	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	,,,,	0,113,6382	CC,CT,TT		0.0,2.5705,0.8699	,,,,	220/1117,220/1153,197/1130,192/1125,255/1188	1391419	113,12877	2198	4297	6495	SO:0001819	synonymous_variant	8938	exon8			CCTGCCTGCCAAG	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.765T>C	16.37:g.1391419T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	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																																																																																			T|0.989;C|0.011	0.011	strong		0.677	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
MT-ND4	4538	hgsc.bcm.edu	37	M	10792	10792	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10792A>G	ENST00000361381.2	+	1	33	c.33A>G	c.(31-33)ttA>ttG	p.L11L	MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TS2_ENST00000387449.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	11					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						ACAATTATATTACTACCACTG	0.383																																					p.L11L		Atlas-SNP	.											.	.	.	.	0			c.A33G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TATATTACTACCA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.33A>G	M.37:g.10792A>G		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.383	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
SOS1	6654	hgsc.bcm.edu	37	2	39294787	39294787	+	Silent	SNP	T	T	G	rs7609455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:39294787T>G	ENST00000426016.1	-	3	281	c.195A>C	c.(193-195)cgA>cgC	p.R65R	SOS1_ENST00000395038.2_Silent_p.R65R|SOS1_ENST00000428721.2_Silent_p.R8R|SOS1_ENST00000402219.2_Silent_p.R65R			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	65					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)				CTGAAGCACTTCGGGGCTGAG	0.363									Noonan syndrome				t|||	249	0.0497204	0.1286	0.0576	5008	,	,		16835	0.0288		0.001	False		,,,				2504	0.0092				p.R65R		Atlas-SNP	.											.	SOS1	134	.	0			c.A195C						PASS	.	T		512,3894	233.3+/-246.5	27,458,1718	135.0	151.0	146.0		195	3.1	1.0	2	dbSNP_116	146	5,8595	2.2+/-6.3	0,5,4295	no	coding-synonymous	SOS1	NM_005633.3		27,463,6013	GG,GT,TT		0.0581,11.6205,3.9751		65/1334	39294787	517,12489	2203	4300	6503	SO:0001819	synonymous_variant	6654	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	AGCACTTCGGGGC	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.195A>C	2.37:g.39294787T>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	159	75	0.471698	NM_005633	A8K2G3|B4DXG2	Silent	SNP	ENST00000426016.1	37	CCDS1802.1																																																																																			T|0.952;G|0.048	0.048	strong		0.363	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633	
ZNF354C	30832	hgsc.bcm.edu	37	5	178507069	178507069	+	Missense_Mutation	SNP	T	T	C	rs1445846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:178507069T>C	ENST00000315475.6	+	5	1942	c.1636T>C	c.(1636-1638)Ttt>Ctt	p.F546L		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	546			F -> L (in dbSNP:rs1445846).		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(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|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;0.247)		TCAGAGATTTTTTAAAGGAGA	0.368													C|||	3886	0.775958	0.7368	0.7406	5008	,	,		17548	0.8879		0.666	False		,,,				2504	0.8517				p.F546L		Atlas-SNP	.											.	ZNF354C	77	.	0			c.T1636C						PASS	.	C	LEU/PHE	3148,1250		1120,908,171	57.0	62.0	60.0		1636	1.5	0.0	5	dbSNP_88	60	5797,2797		1974,1849,474	yes	missense	ZNF354C	NM_014594.1	22	3094,2757,645	CC,CT,TT		32.546,28.422,31.1499	benign	546/555	178507069	8945,4047	2199	4297	6496	SO:0001583	missense	30832	exon5			AGATTTTTTAAAG		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.1636T>C	5.37:g.178507069T>C	ENSP00000324064:p.Phe546Leu	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	278	118	0.42446	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	1668	0.7637362637362637	367	0.7459349593495935	271	0.7486187845303868	512	0.8951048951048951	518	0.683377308707124	C	15.59	2.878252	0.51801	0.71578	0.67454	ENSG00000177932	ENST00000315475	T	0.04502	3.61	4.37	1.48	0.22813	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04090	-0.28	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06110	-1.0845	8	0.72032	D	0.01	0.0	2.6352	0.04956	0.1495:0.5339:0.1451:0.1715	rs1445846;rs17666360;rs57491175;rs1445846	546	Q86Y25	Z354C_HUMAN	L	546	ENSP00000324064:F546L	ENSP00000324064:F546L	F	+	1	0	ZNF354C	178439675	0.001000	0.12720	0.000000	0.03702	0.876000	0.50452	0.686000	0.25392	-0.044000	0.13491	-0.186000	0.12905	TTT	T|0.268;C|0.731	0.731	strong		0.368	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
SLC9C2	284525	hgsc.bcm.edu	37	1	173516903	173516903	+	Silent	SNP	A	A	G	rs10494490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	122	0	0		WXS	Illumina HiSeq	Phase_I	104	40	0.384615	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	
KCNK15	60598	hgsc.bcm.edu	37	20	43374694	43374694	+	Missense_Mutation	SNP	T	T	C	rs144556326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43374694T>C	ENST00000372861.3	+	1	274	c.143T>C	c.(142-144)cTc>cCc	p.L48P	RP11-445H22.4_ENST00000445420.1_RNA|RP11-445H22.4_ENST00000427303.1_RNA	NM_022358.3	NP_071753.2	Q9H427	KCNKF_HUMAN	potassium channel, subfamily K, member 15	48					regulation of ion transmembrane transport (GO:0034765)	integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)			NS(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(2)	10		Myeloproliferative disorder(115;0.0122)				CGGGGCGCTCTCCGGAGGAAG	0.706													T|||	106	0.0211661	0.0726	0.0144	5008	,	,		11543	0.0		0.0	False		,,,				2504	0.0				p.L48P		Atlas-SNP	.											.	KCNK15	19	.	0			c.T143C						PASS	.	T	PRO/LEU	166,4206		2,162,2022	10.0	15.0	13.0		143	2.9	0.9	20	dbSNP_134	13	6,8538		0,6,4266	yes	missense	KCNK15	NM_022358.3	98	2,168,6288	CC,CT,TT		0.0702,3.7969,1.3317	probably-damaging	48/331	43374694	172,12744	2186	4272	6458	SO:0001583	missense	60598	exon1			GCGCTCTCCGGAG	AF257081	CCDS13337.1	20q13.12	2012-03-07			ENSG00000124249	ENSG00000124249		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	13814	protein-coding gene	gene with protein product		607368		KCNK11, KCNK14		11409881, 11431495, 16382106	Standard	NM_022358		Approved	K2p15.1, dJ781B1.1, KT3.3, KIAA0237, TASK5, TASK-5	uc002xmr.3	Q9H427	OTTHUMG00000032544	ENST00000372861.3:c.143T>C	20.37:g.43374694T>C	ENSP00000361952:p.Leu48Pro	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_022358	Q52LL3|Q9HBC8	Missense_Mutation	SNP	ENST00000372861.3	37	CCDS13337.1	43	0.019688644688644688	36	0.07317073170731707	7	0.019337016574585635	0	0.0	0	0.0	T	14.77	2.635968	0.47049	0.037969	7.02E-4	ENSG00000124249	ENST00000372861	T	0.17854	2.25	4.04	2.91	0.33838	.	0.349704	0.29892	N	0.010923	T	0.03827	0.0108	M	0.87180	2.865	0.80722	D	1	D	0.63880	0.993	P	0.61070	0.883	T	0.00295	-1.1839	10	0.87932	D	0	.	8.6904	0.34262	0.1705:0.0:0.0:0.8295	.	48	Q9H427	KCNKF_HUMAN	P	48	ENSP00000361952:L48P	ENSP00000361952:L48P	L	+	2	0	KCNK15	42808108	0.968000	0.33430	0.914000	0.36105	0.012000	0.07955	4.497000	0.60367	0.577000	0.29470	0.455000	0.32223	CTC	T|0.981;C|0.019	0.019	strong		0.706	KCNK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079378.2	NM_022358	
ZNF286B	729288	hgsc.bcm.edu	37	17	18565915	18565915	+	Missense_Mutation	SNP	G	G	A	rs73291461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18565915G>A	ENST00000545289.1	-	5	1154	c.904C>T	c.(904-906)Cgt>Tgt	p.R302C	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	302					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						TTACATTCACGGCATTCAAAG	0.398													.|||	424	0.0846645	0.3071	0.0202	5008	,	,		21283	0.0		0.002	False		,,,				2504	0.002				p.R302C		Atlas-SNP	.											.	ZNF286B	75	.	0			c.C904T						PASS	.	T	CYS/ARG	317,1067		31,255,406	74.0	66.0	69.0		904	0.1	0.9	17	dbSNP_130	69	13,3169		0,13,1578	no	missense	ZNF286B	NM_001145045.1	180	31,268,1984	AA,AG,GG		0.4085,22.9046,7.2273	benign	302/523	18565915	330,4236	692	1591	2283	SO:0001583	missense	729288	exon5			ATTCACGGCATTC		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.904C>T	17.37:g.18565915G>A	ENSP00000461413:p.Arg302Cys	Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	299	130	0.434783	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.943;A|0.057	0.057	strong		0.398	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
ANXA2	302	hgsc.bcm.edu	37	15	60690089	60690089	+	Intron	SNP	A	A	G	rs12904657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:60690089A>G	ENST00000396024.3	-	1	44				ANXA2_ENST00000421017.2_Intron|ANXA2_ENST00000557937.1_Intron|ANXA2_ENST00000451270.2_Intron|ANXA2_ENST00000332680.4_Silent_p.C8C	NM_001136015.2	NP_001129487.1	P07355	ANXA2_HUMAN	annexin A2						angiogenesis (GO:0001525)|body fluid secretion (GO:0007589)|cellular response to acid chemical (GO:0071229)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|membrane budding (GO:0006900)|membrane raft assembly (GO:0001765)|negative regulation of catalytic activity (GO:0043086)|osteoclast development (GO:0036035)|positive regulation of binding (GO:0051099)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vesicle fusion (GO:0031340)|protein heterotetramerization (GO:0051290)|protein targeting to plasma membrane (GO:0072661)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell surface (GO:0009986)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|late endosome membrane (GO:0031902)|lipid particle (GO:0005811)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)|midbody (GO:0030496)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|sarcolemma (GO:0042383)|Schmidt-Lanterman incisure (GO:0043220)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phospholipase A2 inhibitor activity (GO:0019834)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)	p.C8C(1)		kidney(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9					Tenecteplase(DB00031)	CAGCGTCTCCACACCCCGCTA	0.741													g|||	3978	0.794329	0.7859	0.7752	5008	,	,		7804	0.9087		0.7187	False		,,,				2504	0.7791				p.C8C		Atlas-SNP	.											ANXA2,rectum,carcinoma,0,1	ANXA2	28	1	1	Substitution - coding silent(1)	prostate(1)	c.T24C						scavenged	.		,,,	3229,943		1289,651,146	5.0	7.0	6.0		,24,,	-5.9	0.0	15	dbSNP_121	6	5975,2181		2248,1479,351	no	intron,coding-synonymous,intron,intron	ANXA2	NM_001002857.1,NM_001002858.2,NM_001136015.2,NM_004039.2	,,,	3537,2130,497	GG,GA,AA		26.741,22.6031,25.3407	,,,	,8/358,,	60690089	9204,3124	2086	4078	6164	SO:0001627	intron_variant	302	exon1			GTCTCCACACCCC	D00017	CCDS10175.1, CCDS32256.1	15q22.2	2012-10-02			ENSG00000182718	ENSG00000182718		"""Annexins"""	537	protein-coding gene	gene with protein product	"""annexin II"""	151740		ANX2, ANX2L4, CAL1H, LPC2D		7961821	Standard	NM_001136015		Approved	LIP2	uc002agm.3	P07355	OTTHUMG00000132763	ENST00000396024.3:c.115+52T>C	15.37:g.60690089A>G		Somatic	11	1	0.0909091		WXS	Illumina HiSeq	Phase_I	15	4	0.266667	NM_001002858	Q567R4|Q6N0B3|Q8TBV2|Q96DD5|Q9UDH8	Silent	SNP	ENST00000396024.3	37	CCDS10175.1																																																																																			A|0.203;G|0.797	0.797	strong		0.741	ANXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256135.1	NM_001002857	
TBC1D13	54662	hgsc.bcm.edu	37	9	131565554	131565554	+	Missense_Mutation	SNP	T	T	C	rs1572912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131565554T>C	ENST00000372648.5	+	8	719	c.569T>C	c.(568-570)gTg>gCg	p.V190A	TBC1D13_ENST00000539497.1_Missense_Mutation_p.V9A|TBC1D13_ENST00000466056.1_3'UTR|TBC1D13_ENST00000223865.8_Intron	NM_018201.3	NP_060671.3	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13	190	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		V -> A (in dbSNP:rs1572912). {ECO:0000269|PubMed:15489334}.				Rab GTPase activator activity (GO:0005097)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	6						AAGAACTCTGTGCCATCATCC	0.552													C|||	2520	0.503195	0.9206	0.2637	5008	,	,		19402	0.3571		0.2863	False		,,,				2504	0.4826				p.V190A		Atlas-SNP	.											.	TBC1D13	27	.	0			c.T569C						PASS	.	C	ALA/VAL	3576,830	328.3+/-300.5	1455,666,82	102.0	93.0	96.0		569	2.5	0.0	9	dbSNP_88	96	2434,6166	698.7+/-405.0	322,1790,2188	yes	missense	TBC1D13	NM_018201.3	64	1777,2456,2270	CC,CT,TT		28.3023,18.8379,46.2094	benign	190/401	131565554	6010,6996	2203	4300	6503	SO:0001583	missense	54662	exon8			ACTCTGTGCCATC	AK001605	CCDS6911.1, CCDS69677.1	9q34.13	2013-07-09			ENSG00000107021	ENSG00000107021			25571	protein-coding gene	gene with protein product						22762500	Standard	XM_005252060		Approved	FLJ10743	uc010myj.3	Q9NVG8	OTTHUMG00000020760	ENST00000372648.5:c.569T>C	9.37:g.131565554T>C	ENSP00000361731:p.Val190Ala	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	166	163	0.981928	NM_018201	A7E2E7|B3KW04|B9EGJ8|Q5T270|Q5T271	Missense_Mutation	SNP	ENST00000372648.5	37	CCDS6911.1	928	0.4249084249084249	435	0.8841463414634146	103	0.2845303867403315	206	0.36013986013986016	184	0.24274406332453827	C	0.579	-0.838026	0.02692	0.811621	0.283023	ENSG00000107021	ENST00000372648;ENST00000539497	T;T	0.41758	0.99;1.55	5.36	2.49	0.30216	Rab-GAP/TBC domain (3);	0.812882	0.11683	N	0.539641	T	0.00012	0.0000	N	0.16656	0.425	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37430	-0.9706	9	0.07030	T	0.85	0.5411	6.3238	0.21232	0.0:0.6384:0.1326:0.229	rs1572912;rs52793555;rs60746730;rs1572912	190	Q9NVG8	TBC13_HUMAN	A	190;9	ENSP00000361731:V190A;ENSP00000437751:V9A	ENSP00000361731:V190A	V	+	2	0	TBC1D13	130605375	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.664000	0.25068	0.013000	0.14918	-1.536000	0.00914	GTG	T|0.535;C|0.464	0.464	strong		0.552	TBC1D13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054496.1	NM_018201	
EXD3	54932	hgsc.bcm.edu	37	9	140218212	140218212	+	Missense_Mutation	SNP	G	G	A	rs56750318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140218212G>A	ENST00000340951.4	-	19	2344	c.2149C>T	c.(2149-2151)Cgt>Tgt	p.R717C	EXD3_ENST00000342129.4_Missense_Mutation_p.R368C	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						TGGGTGACACGCACGTTGAAA	0.672													G|||	343	0.0684904	0.2504	0.0159	5008	,	,		15324	0.0		0.001	False		,,,				2504	0.0				p.R717C		Atlas-SNP	.											.	EXD3	86	.	0			c.C2149T						PASS	.	G	CYS/ARG	794,3434		61,672,1381	49.0	56.0	54.0		2149	2.0	0.0	9	dbSNP_129	54	14,8456		0,14,4221	yes	missense	EXD3	NM_017820.3	180	61,686,5602	AA,AG,GG		0.1653,18.7796,6.3632	benign	717/877	140218212	808,11890	2114	4235	6349	SO:0001583	missense	54932	exon19			TGACACGCACGTT		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.2149C>T	9.37:g.140218212G>A	ENSP00000340474:p.Arg717Cys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	97	29	0.298969	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	118	0.05402930402930403	114	0.23170731707317074	4	0.011049723756906077	0	0.0	0	0.0	G	7.535	0.659472	0.14645	0.187796	0.001653	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.66280	-0.2;0.56	3.9	2.01	0.26516	.	0.304355	0.32802	N	0.005624	T	0.00039	0.0001	L	0.38531	1.155	0.33825	P	0.37048099999999995	B;B	0.32781	0.384;0.274	B;B	0.23275	0.023;0.045	T	0.04708	-1.0932	9	0.56958	D	0.05	.	7.7883	0.29106	0.2171:0.0:0.7829:0.0	rs56750318	368;717	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	C	368;717	ENSP00000343705:R368C;ENSP00000340474:R717C	ENSP00000340474:R717C	R	-	1	0	EXD3	139338033	0.009000	0.17119	0.004000	0.12327	0.090000	0.18270	1.489000	0.35562	0.136000	0.18733	0.305000	0.20034	CGT	G|0.957;A|0.043	0.043	strong		0.672	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
UBXN6	80700	hgsc.bcm.edu	37	19	4446164	4446164	+	Missense_Mutation	SNP	G	G	A	rs34179017	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4446164G>A	ENST00000301281.6	-	10	1206	c.1082C>T	c.(1081-1083)gCg>gTg	p.A361V	MIR4746_ENST00000579802.1_RNA|CTB-50L17.7_ENST00000588798.1_RNA|UBXN6_ENST00000394765.3_Missense_Mutation_p.A308V	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	361	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					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						CCCGTACACCGCCCCCAGCCG	0.711													G|||	32	0.00638978	0.0242	0.0	5008	,	,		14161	0.0		0.0	False		,,,				2504	0.0				p.A361V		Atlas-SNP	.											.	UBXN6	27	.	0			c.C1082T						PASS	.	G	VAL/ALA,VAL/ALA	76,4324		1,74,2125	15.0	19.0	18.0		923,1082	-1.2	0.0	19	dbSNP_126	18	0,8590		0,0,4295	yes	missense,missense	UBXN6	NM_001171091.1,NM_025241.2	64,64	1,74,6420	AA,AG,GG		0.0,1.7273,0.5851	benign,benign	308/389,361/442	4446164	76,12914	2200	4295	6495	SO:0001583	missense	80700	exon10			TACACCGCCCCCA	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.1082C>T	19.37:g.4446164G>A	ENSP00000301281:p.Ala361Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	37	CCDS12129.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	5.191	0.220842	0.09863	0.017273	0.0	ENSG00000167671	ENST00000301281;ENST00000394765	T;T	0.44881	0.91;0.91	5.15	-1.23	0.09465	UBX (3);	0.540957	0.20913	N	0.083423	T	0.14399	0.0348	L	0.48260	1.515	0.09310	N	0.999999	B;B	0.23540	0.047;0.087	B;B	0.22880	0.013;0.042	T	0.10019	-1.0648	10	0.25106	T	0.35	-7.5495	4.4434	0.11586	0.2944:0.0:0.4642:0.2414	rs34179017;rs34179017	308;361	Q9BZV1-2;Q9BZV1	.;UBXN6_HUMAN	V	361;308	ENSP00000301281:A361V;ENSP00000378246:A308V	ENSP00000301281:A361V	A	-	2	0	UBXN6	4397164	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.189000	0.17037	-0.230000	0.09840	0.561000	0.74099	GCG	G|0.992;A|0.008	0.008	strong		0.711	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
RAB17	64284	hgsc.bcm.edu	37	2	238494742	238494742	+	Missense_Mutation	SNP	A	A	G	rs3751112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238494742A>G	ENST00000264601.3	-	2	685	c.56T>C	c.(55-57)gTg>gCg	p.V19A	RAB17_ENST00000538644.1_5'UTR|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	19			V -> A (in dbSNP:rs3751112). {ECO:0000269|Ref.3}.		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)		CAGCTTGAACACACGGGGCTG	0.597													A|||	1486	0.296725	0.553	0.2075	5008	,	,		18090	0.1667		0.1561	False		,,,				2504	0.2924				p.V19A	Colon(56;987 1029 6466 13943 27336)	Atlas-SNP	.											.	RAB17	17	.	0			c.T56C						PASS	.	A	ALA/VAL	2239,2167	591.2+/-387.5	574,1091,538	54.0	56.0	55.0		56	0.6	0.0	2	dbSNP_107	55	1451,7149	276.1+/-292.1	126,1199,2975	yes	missense	RAB17	NM_022449.3	64	700,2290,3513	GG,GA,AA		16.8721,49.1829,28.3715	benign	19/213	238494742	3690,9316	2203	4300	6503	SO:0001583	missense	64284	exon2			TTGAACACACGGG	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.56T>C	2.37:g.238494742A>G	ENSP00000264601:p.Val19Ala	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	138	79	0.572464	NM_022449	Q53QV6|Q6IA73|Q6PJZ0|Q9BVU1|Q9H9U9	Missense_Mutation	SNP	ENST00000264601.3	37	CCDS2520.1	539|539	0.2467948717948718|0.2467948717948718	256|256	0.5203252032520326|0.5203252032520326	76|76	0.20994475138121546|0.20994475138121546	93|93	0.16258741258741258|0.16258741258741258	114|114	0.1503957783641161|0.1503957783641161	A|A	1.105|1.105	-0.660007|-0.660007	0.03454|0.03454	0.508171|0.508171	0.168721|0.168721	ENSG00000124839|ENSG00000124839	ENST00000430445|ENST00000264601;ENST00000411462	.|T;T	.|0.80214	.|-1.35;-1.35	4.69|4.69	0.644|0.644	0.17776|0.17776	.|.	.|0.727711	.|0.11443	.|N	.|0.563575	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.12637|0.12637	0.245|0.245	0.51233|0.51233	P|P	8.20000000000265E-5|8.20000000000265E-5	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.42447|0.42447	-0.9451|-0.9451	4|9	.|0.23891	.|T	.|0.37	-6.0609|-6.0609	5.1932|5.1932	0.15220|0.15220	0.6565:0.0:0.1256:0.2178|0.6565:0.0:0.1256:0.2178	rs3751112;rs52805492;rs58005530;rs3751112|rs3751112;rs52805492;rs58005530;rs3751112	.|19	.|Q9H0T7	.|RAB17_HUMAN	R|A	1|19	.|ENSP00000264601:V19A;ENSP00000400240:V19A	.|ENSP00000264601:V19A	C|V	-|-	1|2	0|0	RAB17|RAB17	238159481|238159481	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.034000|0.034000	0.12701|0.12701	0.886000|0.886000	0.28241|0.28241	-0.081000|-0.081000	0.12662|0.12662	-2.649000|-2.649000	0.00149|0.00149	TGT|GTG	A|0.726;G|0.274	0.274	strong		0.597	RAB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257084.2		
OR51F1	256892	hgsc.bcm.edu	37	11	4791012	4791012	+	Missense_Mutation	SNP	C	C	T	rs146706676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4791012C>T	ENST00000380383.1	-	1	156	c.157G>A	c.(157-159)Gtg>Atg	p.V53M	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.V46M			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	53						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)		AACAGGATCACGCTGTTCCCA	0.478													C|||	4	0.000798722	0.003	0.0	5008	,	,		20537	0.0		0.0	False		,,,				2504	0.0				p.V46M		Atlas-SNP	.											.	OR51F1	60	.	0			c.G136A						PASS	.	C	MET/VAL	15,4387	22.3+/-47.3	0,15,2186	66.0	63.0	64.0		136	1.0	1.0	11	dbSNP_134	64	0,8596		0,0,4298	yes	missense	OR51F1	NM_001004752.1	21	0,15,6484	TT,TC,CC		0.0,0.3408,0.1154	benign	46/313	4791012	15,12983	2201	4298	6499	SO:0001583	missense	256892	exon1			GGATCACGCTGTT	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.157G>A	11.37:g.4791012C>T	ENSP00000369744:p.Val53Met	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		.	.	.	.	.	.	.	.	.	.	C	0.094	-1.162853	0.01673	0.003408	0.0	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00451	7.35;7.35	4.81	1.05	0.20165	GPCR, rhodopsin-like superfamily (1);	0.193258	0.36234	N	0.002716	T	0.00109	0.0003	N	0.00595	-1.35	0.22762	N	0.998768	B	0.02656	0.0	B	0.01281	0.0	T	0.26916	-1.0089	10	0.18710	T	0.47	.	3.1994	0.06645	0.1376:0.0783:0.1435:0.6405	.	53	A6NGY5	O51F1_HUMAN	M	46;53	ENSP00000345163:V46M;ENSP00000369744:V53M	ENSP00000345163:V46M	V	-	1	0	OR51F1	4747588	0.000000	0.05858	0.993000	0.49108	0.775000	0.43874	-1.227000	0.02950	0.008000	0.14787	-0.385000	0.06624	GTG	C|0.999;T|0.001	0.001	strong		0.478	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
MYO9B	4650	hgsc.bcm.edu	37	19	17283657	17283657	+	Silent	SNP	C	C	T	rs2279006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17283657C>T	ENST00000594824.1	+	13	2172	c.2025C>T	c.(2023-2025)atC>atT	p.I675I	MYO9B_ENST00000595618.1_Silent_p.I675I|MYO9B_ENST00000397274.2_Silent_p.I675I			Q13459	MYO9B_HUMAN	myosin IXB	675	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						GGGAGCTCATCGGCATGGACC	0.692													C|||	708	0.141374	0.2927	0.0865	5008	,	,		15230	0.0933		0.0785	False		,,,				2504	0.09				p.I675I		Atlas-SNP	.											.	MYO9B	264	.	0			c.C2025T						PASS	.	C	,	1119,3123		130,859,1132	52.0	60.0	57.0		2025,2025	-9.0	0.7	19	dbSNP_100	57	624,7820		20,584,3618	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	150,1443,4750	TT,TC,CC		7.3899,26.3791,13.7396	,	675/2023,675/2158	17283657	1743,10943	2121	4222	6343	SO:0001819	synonymous_variant	4650	exon13			GCTCATCGGCATG		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.2025C>T	19.37:g.17283657C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	48	30	0.625	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				C|0.845;T|0.155	0.155	strong		0.692	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
KIRREL2	84063	hgsc.bcm.edu	37	19	36349721	36349721	+	Silent	SNP	G	G	A	rs57079408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36349721G>A	ENST00000360202.5	+	4	675	c.477G>A	c.(475-477)ctG>ctA	p.L159L	KIRREL2_ENST00000592409.1_Silent_p.L159L|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Silent_p.L109L|KIRREL2_ENST00000262625.7_Silent_p.L159L	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	159	Ig-like C2-type 2.				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)			CTGAATTGCTGTGGTTCCGAG	0.592													G|||	35	0.00698882	0.0242	0.0043	5008	,	,		18517	0.0		0.0	False		,,,				2504	0.0				p.L159L		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G477A						PASS	.	G	,,	87,4319	72.0+/-110.0	0,87,2116	107.0	103.0	104.0		477,327,477	2.1	1.0	19	dbSNP_129	104	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	,,	0,87,6416	AA,AG,GG		0.0,1.9746,0.6689	,,	159/634,109/584,159/709	36349721	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	84063	exon4			ATTGCTGTGGTTC	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.477G>A	19.37:g.36349721G>A		Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	215	104	0.483721	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	37	CCDS12481.1																																																																																			G|0.994;A|0.006	0.006	strong		0.592	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
CKAP2L	150468	hgsc.bcm.edu	37	2	113514180	113514180	+	Silent	SNP	T	T	C	rs17042342	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113514180T>C	ENST00000302450.6	-	4	846	c.768A>G	c.(766-768)gtA>gtG	p.V256V	CKAP2L_ENST00000481732.1_5'Flank|CKAP2L_ENST00000541405.1_Silent_p.V91V	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	256						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						GCTGTGATTTTACTGGGAAAG	0.418													T|||	370	0.0738818	0.2073	0.0461	5008	,	,		20522	0.0		0.0497	False		,,,				2504	0.0143				p.V256V		Atlas-SNP	.											.	CKAP2L	54	.	0			c.A768G						PASS	.	T		760,3646	304.9+/-288.7	60,640,1503	121.0	122.0	122.0		768	-9.1	0.0	2	dbSNP_123	122	453,8147	135.1+/-192.4	15,423,3862	no	coding-synonymous	CKAP2L	NM_152515.3		75,1063,5365	CC,CT,TT		5.2674,17.2492,9.3265		256/746	113514180	1213,11793	2203	4300	6503	SO:0001819	synonymous_variant	150468	exon4			TGATTTTACTGGG	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.768A>G	2.37:g.113514180T>C		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	143	66	0.461538	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Silent	SNP	ENST00000302450.6	37	CCDS2100.1																																																																																			T|0.919;C|0.081	0.081	strong		0.418	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515	
SCGB1D2	10647	hgsc.bcm.edu	37	11	62010863	62010863	+	Missense_Mutation	SNP	C	C	T	rs2232950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	224	0	0		WXS	Illumina HiSeq	Phase_I	197	112	0.568528	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	
MBOAT2	129642	hgsc.bcm.edu	37	2	9013424	9013424	+	Missense_Mutation	SNP	C	C	T	rs34573615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:9013424C>T	ENST00000305997.3	-	8	895	c.697G>A	c.(697-699)Gtt>Att	p.V233I	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	233					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTCTGAACAACCGCAGTCTGA	0.398													C|||	71	0.0141773	0.0212	0.0086	5008	,	,		19264	0.003		0.004	False		,,,				2504	0.0307				p.V233I	Ovarian(194;1699 3813 22401)	Atlas-SNP	.											.	MBOAT2	36	.	0			c.G697A						PASS	.	C	ILE/VAL	69,4337	62.3+/-99.4	1,67,2135	83.0	81.0	82.0		697	5.2	0.1	2	dbSNP_126	82	13,8587	9.8+/-36.6	0,13,4287	yes	missense	MBOAT2	NM_138799.2	29	1,80,6422	TT,TC,CC		0.1512,1.566,0.6305	probably-damaging	233/521	9013424	82,12924	2203	4300	6503	SO:0001583	missense	129642	exon8			GAACAACCGCAGT	BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"""O-acyltransferase (membrane bound) domain containing 2"""	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.697G>A	2.37:g.9013424C>T	ENSP00000302177:p.Val233Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	95	61	0.642105	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Missense_Mutation	SNP	ENST00000305997.3	37	CCDS1660.1	20	0.009157509157509158	14	0.028455284552845527	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	26.8	4.769230	0.90020	0.01566	0.001512	ENSG00000143797	ENST00000305997	T	0.72615	-0.67	5.22	5.22	0.72569	.	0.173169	0.50627	D	0.000119	T	0.71888	0.3393	M	0.88775	2.98	0.80722	D	1	D;D	0.61697	0.99;0.99	D;D	0.64506	0.92;0.926	D	0.83693	0.0178	10	0.72032	D	0.01	-23.1005	18.7799	0.91928	0.0:1.0:0.0:0.0	rs34573615	233;233	B7Z3I3;Q6ZWT7	.;MBOA2_HUMAN	I	233	ENSP00000302177:V233I	ENSP00000302177:V233I	V	-	1	0	MBOAT2	8930875	1.000000	0.71417	0.062000	0.19696	0.024000	0.10985	7.292000	0.78731	2.418000	0.82041	0.460000	0.39030	GTT	C|0.994;T|0.006	0.006	strong		0.398	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799	
MYOM1	8736	hgsc.bcm.edu	37	18	3215030	3215030	+	Silent	SNP	C	C	A	rs9964300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	15	0	0		WXS	Illumina HiSeq	Phase_I	32	20	0.625	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	
SMARCA2	6595	hgsc.bcm.edu	37	9	2029196	2029196	+	Silent	SNP	G	G	A	rs10964470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2029196G>A	ENST00000382203.1	+	2	383	c.174G>A	c.(172-174)ccG>ccA	p.P58P	SMARCA2_ENST00000349721.2_Silent_p.P58P|SMARCA2_ENST00000382194.1_Silent_p.P58P|SMARCA2_ENST00000357248.2_Silent_p.P58P			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	58					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|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)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		ATCCTATGCCGACGATGGGGT	0.527													G|||	245	0.0489217	0.1778	0.0115	5008	,	,		19068	0.0		0.002	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G174A						PASS	.	G	,	635,3771	271.0+/-269.9	44,547,1612	42.0	36.0	38.0		174,174	-11.2	0.0	9	dbSNP_120	38	2,8598	1.2+/-3.3	0,2,4298	yes	coding-synonymous,coding-synonymous	SMARCA2	NM_003070.3,NM_139045.2	,	44,549,5910	AA,AG,GG		0.0233,14.4122,4.8977	,	58/1591,58/1573	2029196	637,12369	2203	4300	6503	SO:0001819	synonymous_variant	6595	exon2			TATGCCGACGATG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.174G>A	9.37:g.2029196G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			G|0.950;A|0.050	0.050	strong		0.527	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
IRF4	3662	hgsc.bcm.edu	37	6	393330	393330	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:393330C>A	ENST00000380956.4	+	2	304	c.178C>A	c.(178-180)Cag>Aag	p.Q60K	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	60					cytokine-mediated signaling pathway (GO:0019221)|defense response to protozoan (GO:0042832)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of DNA binding (GO:0043388)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of interleukin-13 biosynthetic process (GO:0045368)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of T-helper cell differentiation (GO:0045622)|T cell activation (GO:0042110)|T-helper 17 cell lineage commitment (GO:0072540)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear nucleosome (GO:0000788)|nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.Q60K(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		CGCGGGCAAGCAGGACTACAA	0.692			T	IGH@	MM																																p.Q60K		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	IRF4_ENST00000380956,NS,lymphoid_neoplasm,-2,2	IRF4	65	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C178A						PASS	.						29.0	26.0	27.0					6																	393330		2201	4300	6501	SO:0001583	missense	3662	exon2			GGCAAGCAGGACT	U52682	CCDS4469.1	6p25-p23	2008-08-29			ENSG00000137265	ENSG00000137265			6119	protein-coding gene	gene with protein product		601900		MUM1		8921401, 18417578	Standard	NM_002460		Approved	LSIRF	uc003msz.4	Q15306	OTTHUMG00000016294	ENST00000380956.4:c.178C>A	6.37:g.393330C>A	ENSP00000370343:p.Gln60Lys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	34	5.402639	0.96030	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.97505	-4.41	4.58	4.58	0.56647	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.115641	0.64402	D	0.000010	D	0.97297	0.9116	L	0.53561	1.675	0.80722	D	1	P;P;D	0.69078	0.852;0.624;0.997	P;P;D	0.74348	0.813;0.61;0.983	D	0.96246	0.9179	10	0.30854	T	0.27	-22.6787	17.6301	0.88104	0.0:1.0:0.0:0.0	.	60;60;60	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	K	60;90	ENSP00000370343:Q60K	ENSP00000370343:Q60K	Q	+	1	0	IRF4	338330	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.909000	0.75735	2.399000	0.81585	0.306000	0.20318	CAG	.	.	none		0.692	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1		
POPDC2	64091	hgsc.bcm.edu	37	3	119378872	119378872	+	Silent	SNP	G	G	A	rs1880040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119378872G>A	ENST00000264231.3	-	1	565	c.399C>T	c.(397-399)tgC>tgT	p.C133C	POPDC2_ENST00000474523.1_5'UTR|POPDC2_ENST00000538678.1_Silent_p.C133C|POPDC2_ENST00000493094.1_Silent_p.C133C|POPDC2_ENST00000468801.1_Silent_p.C133C	NM_022135.2	NP_071418.2	Q9HBU9	POPD2_HUMAN	popeye domain containing 2	133					regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sinoatrial node cell development (GO:0060931)	integral component of membrane (GO:0016021)	cAMP binding (GO:0030552)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.242)		CCTGCTCCTCGCAGCAGTGAA	0.572													G|||	2008	0.400958	0.2912	0.4611	5008	,	,		21497	0.3323		0.4304	False		,,,				2504	0.547				p.C133C		Atlas-SNP	.											.	POPDC2	36	.	0			c.C399T						PASS	.	G		1394,3012	457.5+/-351.6	223,948,1032	150.0	144.0	146.0		399	-2.1	0.4	3	dbSNP_92	146	3806,4794	538.3+/-383.4	840,2126,1334	no	coding-synonymous	POPDC2	NM_022135.2		1063,3074,2366	AA,AG,GG		44.2558,31.6387,39.9815		133/365	119378872	5200,7806	2203	4300	6503	SO:0001819	synonymous_variant	64091	exon1			CTCCTCGCAGCAG	AF204173	CCDS2992.1	3q13.33	2004-01-15			ENSG00000121577	ENSG00000121577			17648	protein-coding gene	gene with protein product		605823				10882522	Standard	NM_022135		Approved	POP2	uc031sbc.1	Q9HBU9	OTTHUMG00000159438	ENST00000264231.3:c.399C>T	3.37:g.119378872G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	149	63	0.422819	NM_022135	Q86UE7	Silent	SNP	ENST00000264231.3	37	CCDS2992.1																																																																																			G|0.616;A|0.384	0.384	strong		0.572	POPDC2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355378.1	NM_022135	
ACOT1	641371	hgsc.bcm.edu	37	14	74008304	74008304	+	Missense_Mutation	SNP	G	G	A	rs146335256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74008304G>A	ENST00000311148.4	+	2	873	c.565G>A	c.(565-567)Gct>Act	p.A189T	HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000553558.1_Intron|ACOT1_ENST00000557556.1_Missense_Mutation_p.A189T|HEATR4_ENST00000334988.2_Intron	NM_001037161.1	NP_001032238.1	Q86TX2	ACOT1_HUMAN	acyl-CoA thioesterase 1	189					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		GATGGCTCTGGCTTACTATAA	0.527													-|||	78	0.0155751	0.0552	0.0072	5008	,	,		9026	0.0		0.0	False		,,,				2504	0.0				p.A189T		Atlas-SNP	.											.	ACOT1	12	.	0			c.G565A						PASS	.	G	THR/ALA,,	147,3835		36,75,1880	224.0	174.0	192.0		565,,	3.6	1.0	14	dbSNP_134	192	2,7196		1,0,3598	no	missense,intron,intron	HEATR4,ACOT1	NM_001037161.1,NM_001220484.1,NM_203309.2	58,,	37,75,5478	AA,AG,GG		0.0278,3.6916,1.3327	,,	189/422,,	74008304	149,11031	1991	3599	5590	SO:0001583	missense	641371	exon2			GCTCTGGCTTACT	DQ082754	CCDS32117.1	14q24.3	2013-09-20			ENSG00000184227	ENSG00000184227		"""Acyl CoA thioesterases"""	33128	protein-coding gene	gene with protein product		614313				16103133, 16940157	Standard	NM_001037161		Approved	ACH2, CTE-1, LACH2		Q86TX2	OTTHUMG00000171607	ENST00000311148.4:c.565G>A	14.37:g.74008304G>A	ENSP00000311224:p.Ala189Thr	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	258	257	0.996124	NM_001037161	A1L173|Q3I5F9	Missense_Mutation	SNP	ENST00000311148.4	37	CCDS32117.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	-	15.12	2.737774	0.49045	0.036916	2.78E-4	ENSG00000184227	ENST00000311148;ENST00000557556	T;T	0.42513	0.97;0.97	3.61	3.61	0.41365	.	0.149549	0.64402	D	0.000013	T	0.42743	0.1216	H	0.94345	3.525	0.54753	D	0.999987	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.75634	-0.3250	10	0.87932	D	0	-10.4661	15.853	0.78947	0.0:0.0:1.0:0.0	.	189;189	E9KL42;Q86TX2	.;ACOT1_HUMAN	T	189	ENSP00000311224:A189T;ENSP00000451764:A189T	ENSP00000311224:A189T	A	+	1	0	ACOT1	73078057	1.000000	0.71417	1.000000	0.80357	0.046000	0.14306	5.637000	0.67854	2.022000	0.59522	0.423000	0.28283	GCT	G|0.989;A|0.011	0.011	strong		0.527	ACOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414432.1	NM_001037161	
SIGLEC9	27180	hgsc.bcm.edu	37	19	51628622	51628622	+	Missense_Mutation	SNP	A	A	C	rs16988910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51628622A>C	ENST00000250360.3	+	1	458	c.391A>C	c.(391-393)Aaa>Caa	p.K131Q	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.K131Q	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	131	Ig-like V-type.		K -> Q (in dbSNP:rs16988910).		cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		ATGGAATTATAAACATCACCG	0.498													.|||	482	0.096246	0.3495	0.0288	5008	,	,		19570	0.0		0.0	False		,,,				2504	0.0				p.K131Q		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.A391C						PASS	.	A	GLN/LYS,GLN/LYS	1306,3100		197,912,1094	54.0	54.0	54.0		391,391	-6.1	0.0	19	dbSNP_123	54	9,8591		0,9,4291	yes	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	53,53	197,921,5385	CC,CA,AA		0.1047,29.6414,10.1107	benign,benign	131/480,131/464	51628622	1315,11691	2203	4300	6503	SO:0001583	missense	27180	exon1			AATTATAAACATC	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.391A>C	19.37:g.51628622A>C	ENSP00000250360:p.Lys131Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	177	0.08104395604395605	167	0.3394308943089431	10	0.027624309392265192	0	0.0	0	0.0	.	2.109	-0.404270	0.04832	0.296414	0.001047	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.45668	0.89;0.89	3.03	-6.06	0.02165	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.634600	0.01116	N	0.005689	T	0.00012	0.0000	L	0.35542	1.07	0.80722	P	0.0	B	0.13145	0.007	B	0.11329	0.006	T	0.28138	-1.0053	9	0.19147	T	0.46	.	0.854	0.01178	0.2909:0.3232:0.227:0.1589	rs16988910;rs57111846;rs16988910	131	Q9Y336	SIGL9_HUMAN	Q	131	ENSP00000413861:K131Q;ENSP00000250360:K131Q	ENSP00000250360:K131Q	K	+	1	0	SIGLEC9	56320434	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.430000	0.02434	-1.179000	0.02737	-0.476000	0.04901	AAA	A|0.895;C|0.105	0.105	strong		0.498	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441	
RSBN1L	222194	hgsc.bcm.edu	37	7	77325919	77325919	+	Missense_Mutation	SNP	G	G	A	rs79095281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:77325919G>A	ENST00000334955.8	+	1	160	c.133G>A	c.(133-135)Gtc>Atc	p.V45I	RSBN1L-AS1_ENST00000440088.1_lincRNA|RSBN1L_ENST00000445288.1_5'Flank	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	45						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CGCCAAGAAGGTCCGGACTGA	0.677													G|||	139	0.0277556	0.1029	0.0043	5008	,	,		14173	0.0		0.0	False		,,,				2504	0.0				p.V45I		Atlas-SNP	.											.	RSBN1L	74	.	0			c.G133A						PASS	.	G	ILE/VAL	329,3439		19,291,1574	34.0	45.0	41.0		133	2.1	1.0	7	dbSNP_131	41	3,8221		0,3,4109	yes	missense	RSBN1L	NM_198467.2	29	19,294,5683	AA,AG,GG		0.0365,8.7314,2.7685	benign	45/847	77325919	332,11660	1884	4112	5996	SO:0001583	missense	222194	exon1			AAGAAGGTCCGGA	AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.133G>A	7.37:g.77325919G>A	ENSP00000334040:p.Val45Ile	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	67	39	0.58209	NM_198467	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Missense_Mutation	SNP	ENST00000334955.8	37	CCDS43607.1	47	0.02152014652014652	45	0.09146341463414634	2	0.0055248618784530384	0	0.0	0	0.0	G	12.96	2.095669	0.36952	0.087314	3.65E-4	ENSG00000187257	ENST00000334955	.	.	.	4.02	2.14	0.27477	.	0.551396	0.14695	N	0.303893	T	0.01124	0.0037	N	0.14661	0.345	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.03184	-1.1063	9	0.19147	T	0.46	-2.8559	7.0249	0.24934	0.2286:0.0:0.7714:0.0	.	45	Q6PCB5	RSBNL_HUMAN	I	45	.	ENSP00000334040:V45I	V	+	1	0	RSBN1L	77163855	0.998000	0.40836	0.998000	0.56505	0.557000	0.35523	0.398000	0.20899	0.421000	0.25980	0.313000	0.20887	GTC	G|0.973;A|0.027	0.027	strong		0.677	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467	
C14orf2	9556	hgsc.bcm.edu	37	14	104381502	104381502	+	Missense_Mutation	SNP	T	T	C	rs1053419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:104381502T>C	ENST00000554880.1	-	2	178	c.25A>G	c.(25-27)Ata>Gta	p.I9V	C14orf2_ENST00000557040.1_Missense_Mutation_p.I9V|C14orf2_ENST00000553449.1_Intron|C14orf2_ENST00000555030.1_Missense_Mutation_p.I9V|C14orf2_ENST00000414262.2_Missense_Mutation_p.I26V|C14orf2_ENST00000286953.3_Missense_Mutation_p.I9V|C14orf2_ENST00000554713.1_Missense_Mutation_p.I9V|C14orf2_ENST00000553430.1_Missense_Mutation_p.I9V			P56378	68MP_HUMAN	chromosome 14 open reading frame 2	9			I -> V (in dbSNP:rs1053419).			integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)				kidney(1)	1				Epithelial(152;0.223)		GGGATCCATATGTTTTTAATA	0.358													T|||	918	0.183307	0.4281	0.1009	5008	,	,		16886	0.0496		0.0855	False		,,,				2504	0.1493				p.I26V		Atlas-SNP	.											.	C14orf2	7	.	0			c.A76G						PASS	.	T	VAL/ILE,VAL/ILE	1780,2626	523.3+/-371.0	370,1040,793	82.0	81.0	81.0		76,25	1.6	0.0	14	dbSNP_86	81	741,7859	177.8+/-227.3	36,669,3595	yes	missense,missense	C14orf2	NM_001127393.1,NM_004894.2	29,29	406,1709,4388	CC,CT,TT		8.6163,40.3995,19.3834	benign,benign	26/76,9/59	104381502	2521,10485	2203	4300	6503	SO:0001583	missense	9556	exon3			TCCATATGTTTTT	AF054175	CCDS9986.1, CCDS45169.1	14q32.33	2013-02-18			ENSG00000156411	ENSG00000156411			1188	protein-coding gene	gene with protein product	"""6.8 kDa mitochondrial proteolipid"""	604573				9653160	Standard	NM_001127393		Approved	MP68	uc001yoi.4	P56378	OTTHUMG00000171601	ENST00000554880.1:c.25A>G	14.37:g.104381502T>C	ENSP00000452133:p.Ile9Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_001127393	B2R588|G3V5Q3|Q86TT7	Missense_Mutation	SNP	ENST00000554880.1	37	CCDS9986.1	360	0.16483516483516483	219	0.4451219512195122	42	0.11602209944751381	38	0.06643356643356643	61	0.08047493403693931	T	0	-2.619437	0.00118	0.403995	0.086163	ENSG00000156411	ENST00000286953;ENST00000554880;ENST00000555030;ENST00000414262;ENST00000553430;ENST00000557040;ENST00000554713	T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06	5.5	1.56	0.23342	.	0.528786	0.15725	N	0.247738	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45338	-0.9268	8	0.02654	T	1	.	4.7772	0.13185	0.1482:0.6035:0.0:0.2483	rs1053419;rs1802294;rs3168859;rs52835603;rs59140229;rs1053419	9;9;9	G3V556;G3V5Q3;P56378	.;.;68MP_HUMAN	V	9;9;9;26;9;9;9	ENSP00000286953:I9V;ENSP00000452133:I9V;ENSP00000452186:I9V;ENSP00000401770:I26V;ENSP00000452462:I9V;ENSP00000450894:I9V;ENSP00000451500:I9V	ENSP00000286953:I9V	I	-	1	0	C14orf2	103451255	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	0.199000	0.17237	0.281000	0.22233	-0.766000	0.03442	ATA	T|0.809;C|0.191;A|0.000	0.191	strong		0.358	C14orf2-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414398.1	NM_001127393	
LRPPRC	10128	hgsc.bcm.edu	37	2	44172496	44172496	+	Silent	SNP	T	T	C	rs145963884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44172496T>C	ENST00000260665.7	-	22	2328	c.2271A>G	c.(2269-2271)gtA>gtG	p.V757V		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	757					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GCTTTGCCAATACTCTTACAA	0.378													T|||	5	0.000998403	0.0038	0.0	5008	,	,		22524	0.0		0.0	False		,,,				2504	0.0				p.V757V		Atlas-SNP	.											.	LRPPRC	105	.	0			c.A2271G						PASS	.	T		7,4399	12.9+/-30.5	0,7,2196	137.0	122.0	127.0		2271	-0.7	1.0	2	dbSNP_134	127	0,8598		0,0,4299	no	coding-synonymous	LRPPRC	NM_133259.3		0,7,6495	CC,CT,TT		0.0,0.1589,0.0538		757/1395	44172496	7,12997	2203	4299	6502	SO:0001819	synonymous_variant	10128	exon22			TGCCAATACTCTT	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.2271A>G	2.37:g.44172496T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	130	54	0.415385	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			T|0.999;C|0.001	0.001	strong		0.378	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
MUC17	140453	hgsc.bcm.edu	37	7	100675512	100675512	+	Missense_Mutation	SNP	G	G	A	rs10259584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100675512G>A	ENST00000306151.4	+	3	879	c.815G>A	c.(814-816)gGa>gAa	p.G272E		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	272	59 X approximate tandem repeats.|Ser-rich.		G -> E (in dbSNP:rs10259584).		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)					GCTCCTAGTGGAGGAAGCACT	0.507													A|||	683	0.136382	0.2519	0.085	5008	,	,		24177	0.0665		0.1173	False		,,,				2504	0.1084				p.G272E		Atlas-SNP	.											.	MUC17	804	.	0			c.G815A						PASS	.	A	GLU/GLY	970,3436	733.4+/-410.5	105,760,1338	148.0	146.0	147.0		815	0.4	0.0	7	dbSNP_119	147	986,7614	774.1+/-407.7	56,874,3370	yes	missense	MUC17	NM_001040105.1	98	161,1634,4708	AA,AG,GG		11.4651,22.0154,15.0392	benign	272/4494	100675512	1956,11050	2203	4300	6503	SO:0001583	missense	140453	exon3			CTAGTGGAGGAAG	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.815G>A	7.37:g.100675512G>A	ENSP00000302716:p.Gly272Glu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	248	0.11355311355311355	98	0.1991869918699187	34	0.09392265193370165	29	0.050699300699300696	87	0.11477572559366754	A	0.489	-0.876341	0.02550	0.220154	0.114651	ENSG00000169876	ENST00000306151	T	0.03553	3.89	0.429	0.429	0.16506	.	.	.	.	.	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	0.48502	-0.9030	8	0.02654	T	1	.	4.4758	0.11739	0.428:0.0:0.572:0.0	rs10259584;rs10259584	272	Q685J3	MUC17_HUMAN	E	272	ENSP00000302716:G272E	ENSP00000302716:G272E	G	+	2	0	MUC17	100462232	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.655000	0.00854	-1.479000	0.01867	-1.958000	0.00481	GGA	G|0.868;A|0.132	0.132	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FBXW9	84261	hgsc.bcm.edu	37	19	12805525	12805525	+	Silent	SNP	G	G	C	rs10416965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12805525G>C	ENST00000380339.3	-	3	597	c.561C>G	c.(559-561)ctC>ctG	p.L187L	FBXW9_ENST00000393261.3_Silent_p.L187L|FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000587955.1_Silent_p.L177L			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	187					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CCGACAGACAGAGTGACCCAC	0.632													G|||	749	0.149561	0.5348	0.0461	5008	,	,		18468	0.0		0.0099	False		,,,				2504	0.0				p.L187L		Atlas-SNP	.											.	FBXW9	30	.	0			c.C561G						PASS	.	G		1693,2405		363,967,719	62.0	68.0	66.0		561	-2.5	0.1	19	dbSNP_119	66	131,8263		1,129,4067	no	coding-synonymous	FBXW9	NM_032301.2		364,1096,4786	CC,CG,GG		1.5606,41.3128,14.6013		187/459	12805525	1824,10668	2049	4197	6246	SO:0001819	synonymous_variant	84261	exon3			CAGACAGAGTGAC	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.561C>G	19.37:g.12805525G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_032301	B3KVP7|Q9BT89	Silent	SNP	ENST00000380339.3	37																																																																																				G|0.921;C|0.079	0.079	strong		0.632	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
TAF1C	9013	hgsc.bcm.edu	37	16	84212779	84212779	+	Missense_Mutation	SNP	G	G	A	rs2230131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84212779G>A	ENST00000567759.1	-	14	2560	c.2378C>T	c.(2377-2379)cCg>cTg	p.P793L	TAF1C_ENST00000570117.1_Missense_Mutation_p.P461L|TAF1C_ENST00000566732.1_Missense_Mutation_p.P767L|TAF1C_ENST00000378541.4_Missense_Mutation_p.P793L|TAF1C_ENST00000541676.1_Missense_Mutation_p.P700L|TAF1C_ENST00000341690.6_Missense_Mutation_p.P699L	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	793			P -> L (in dbSNP:rs2230131). {ECO:0000269|PubMed:14702039, 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						CTGGGAGGGCGGGGTCGTGGG	0.647													G|||	795	0.158746	0.208	0.0648	5008	,	,		14150	0.1508		0.1103	False		,,,				2504	0.2168				p.P793L		Atlas-SNP	.											.	TAF1C	60	.	0			c.C2378T						PASS	.	G	LEU/PRO,LEU/PRO	861,3537		79,703,1417	20.0	17.0	18.0		2378,2096	2.2	0.0	16	dbSNP_98	18	804,7788		46,712,3538	yes	missense,missense	TAF1C	NM_005679.3,NM_139353.2	98,98	125,1415,4955	AA,AG,GG		9.3575,19.5771,12.8176	possibly-damaging,possibly-damaging	793/870,699/776	84212779	1665,11325	2199	4296	6495	SO:0001583	missense	9013	exon14			GAGGGCGGGGTCG	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.2378C>T	16.37:g.84212779G>A	ENSP00000455265:p.Pro793Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	37	CCDS32496.1	296	0.13553113553113552	105	0.21341463414634146	29	0.08011049723756906	78	0.13636363636363635	84	0.11081794195250659	G	11.18	1.563138	0.27915	0.195771	0.093575	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000544090	T;T;T	0.02579	4.24;4.24;4.24	5.3	2.21	0.28008	.	0.366869	0.21074	N	0.080606	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B;B;B;B	0.32717	0.078;0.381;0.007;0.032	B;B;B;B	0.26202	0.014;0.067;0.006;0.01	T	0.45220	-0.9276	9	0.72032	D	0.01	-8.6675	4.7623	0.13113	0.1809:0.0:0.6479:0.1712	rs2230131;rs3743641	767;316;793;699	Q15572-6;F5H0H4;Q15572;Q15572-2	.;.;TAF1C_HUMAN;.	L	793;700;699;316	ENSP00000367802:P793L;ENSP00000437900:P700L;ENSP00000345305:P699L	ENSP00000345305:P699L	P	-	2	0	TAF1C	82770280	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	1.120000	0.31271	0.219000	0.20840	-0.136000	0.14681	CCG	G|0.840;A|0.160	0.160	strong		0.647	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
MYOM2	9172	hgsc.bcm.edu	37	8	2050564	2050564	+	Silent	SNP	G	G	A	rs34460811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2050564G>A	ENST00000262113.4	+	21	2868	c.2727G>A	c.(2725-2727)gcG>gcA	p.A909A	MYOM2_ENST00000523438.1_Silent_p.A334A	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	909	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.|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)		TGGTAGAGGCGAGACCAGGTA	0.498													G|||	45	0.00898562	0.0333	0.0014	5008	,	,		21003	0.0		0.0	False		,,,				2504	0.0				p.A909A		Atlas-SNP	.											.	MYOM2	251	.	0			c.G2727A						PASS	.	G		115,4291	86.8+/-125.4	2,111,2090	61.0	53.0	55.0		2727	-7.8	0.2	8	dbSNP_126	55	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MYOM2	NM_003970.2		2,112,6389	AA,AG,GG		0.0116,2.6101,0.8919		909/1466	2050564	116,12890	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon21			AGAGGCGAGACCA		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.2727G>A	8.37:g.2050564G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			G|0.991;A|0.009	0.009	strong		0.498	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
PFN4	375189	hgsc.bcm.edu	37	2	24342505	24342505	+	Silent	SNP	T	T	C	rs1056122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:24342505T>C	ENST00000313213.4	-	4	674	c.303A>G	c.(301-303)gtA>gtG	p.V101V	PFN4_ENST00000465360.1_5'UTR	NM_199346.1	NP_955378.1	Q8NHR9	PROF4_HUMAN	profilin family, member 4	101					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)					TGTAAGTTGCTACCAGAAGAT	0.453													C|||	1387	0.276957	0.2133	0.2075	5008	,	,		18510	0.1528		0.3738	False		,,,				2504	0.4407				p.V101V		Atlas-SNP	.											.	PFN4	16	.	0			c.A303G						PASS	.	C		1091,3315	721.9+/-409.2	129,833,1241	137.0	124.0	129.0		303	5.4	1.0	2	dbSNP_86	129	3051,5549	661.9+/-401.9	537,1977,1786	no	coding-synonymous	PFN4	NM_199346.1		666,2810,3027	CC,CT,TT		35.4767,24.7617,31.8468		101/130	24342505	4142,8864	2203	4300	6503	SO:0001819	synonymous_variant	375189	exon4			AGTTGCTACCAGA	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.303A>G	2.37:g.24342505T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_199346	Q53TL9	Silent	SNP	ENST00000313213.4	37	CCDS1709.1																																																																																			T|0.709;C|0.291	0.291	strong		0.453	PFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207617.2	NM_199346	
OR2T4	127074	hgsc.bcm.edu	37	1	248525285	248525285	+	Missense_Mutation	SNP	T	T	C	rs58006779|rs28637620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248525285T>C	ENST00000366475.1	+	1	403	c.403T>C	c.(403-405)Ttc>Ctc	p.F135L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, 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)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCAGATGTTCTTCTACGTGAC	0.522													t|||	1679	0.335264	0.3464	0.2824	5008	,	,		20303	0.4514		0.1928	False		,,,				2504	0.3845				p.F135L		Atlas-SNP	.											.	OR2T4	126	.	0			c.T403C						PASS	.						171.0	168.0	169.0					1																	248525285		2203	4299	6502	SO:0001583	missense	127074	exon1			ATGTTCTTCTACG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.403T>C	1.37:g.248525285T>C	ENSP00000355431:p.Phe135Leu	Somatic	964	1	0.00103734		WXS	Illumina HiSeq	Phase_I	914	373	0.408096	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	536	0.2454212454212454	113	0.22967479674796748	84	0.23204419889502761	216	0.3776223776223776	123	0.16226912928759896	T	0.004	-2.337549	0.00224	.	.	ENSG00000196944	ENST00000366475	T	0.02236	4.38	3.48	1.54	0.23209	GPCR, rhodopsin-like superfamily (1);	0.170893	0.28093	N	0.016632	T	0.00012	0.0000	L	0.27944	0.81	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46105	-0.9215	9	0.02654	T	1	.	6.7611	0.23540	0.0:0.6788:0.0:0.3212	rs28637620	135	Q8NH00	OR2T4_HUMAN	L	135	ENSP00000355431:F135L	ENSP00000355431:F135L	F	+	1	0	OR2T4	246591908	0.000000	0.05858	0.055000	0.19348	0.230000	0.25150	-0.558000	0.05978	0.021000	0.15133	-0.390000	0.06520	TTC	T|0.811;C|0.189	0.189	strong		0.522	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
OAS3	4940	hgsc.bcm.edu	37	12	113386950	113386950	+	Silent	SNP	T	T	C	rs2285932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113386950T>C	ENST00000228928.7	+	6	1493	c.1314T>C	c.(1312-1314)atT>atC	p.I438I	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	438	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						AAAAGGCCATTGACATCATCT	0.567													C|||	4219	0.842452	0.9902	0.8012	5008	,	,		18302	0.9117		0.672	False		,,,				2504	0.7761				p.I438I		Atlas-SNP	.											.	OAS3	63	.	0			c.T1314C						PASS	.	C		3978,248		1869,240,4	55.0	61.0	59.0		1314	-8.1	0.0	12	dbSNP_100	59	5776,2698		1975,1826,436	no	coding-synonymous	OAS3	NM_006187.2		3844,2066,440	CC,CT,TT		31.8386,5.8684,23.1969		438/1088	113386950	9754,2946	2113	4237	6350	SO:0001819	synonymous_variant	4940	exon6			GGCCATTGACATC	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.1314T>C	12.37:g.113386950T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_006187	Q2HJ14|Q9H3P5	Silent	SNP	ENST00000228928.7	37	CCDS44981.1																																																																																			T|0.189;C|0.811	0.811	strong		0.567	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
ADAM28	10863	hgsc.bcm.edu	37	8	24184088	24184088	+	Silent	SNP	G	G	T	rs113950884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24184088G>T	ENST00000265769.4	+	10	1022	c.912G>T	c.(910-912)acG>acT	p.T304T	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000518516.1_3'UTR|ADAM28_ENST00000397649.3_Silent_p.T51T|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000437154.2_Silent_p.T304T|ADAM28_ENST00000540823.1_Silent_p.T71T	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	304	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TTGCTGGAACGACTGTGGGTC	0.348													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17957	0.0		0.0	False		,,,				2504	0.0				p.T304T	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.G912T						PASS	.	G	,	20,4386	27.2+/-55.0	0,20,2183	316.0	276.0	289.0		912,912	-11.0	0.0	8	dbSNP_132	289	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	0,20,6483	TT,TG,GG		0.0,0.4539,0.1538	,	304/776,304/541	24184088	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon10			TGGAACGACTGTG	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.912G>T	8.37:g.24184088G>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	216	106	0.490741	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																			G|0.998;T|0.002	0.002	strong		0.348	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
CACNA1H	8912	hgsc.bcm.edu	37	16	1255206	1255206	+	Silent	SNP	C	C	T	rs28365123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1255206C>T	ENST00000348261.5	+	11	2792	c.2544C>T	c.(2542-2544)ggC>ggT	p.G848G	CACNA1H_ENST00000565831.1_Silent_p.G848G|CACNA1H_ENST00000358590.4_Silent_p.G848G|RP11-616M22.3_ENST00000564700.1_RNA	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	848			G -> S (in ECA6). {ECO:0000269|PubMed:12891677}.		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)	TGGCCTGCGGCCCTCTGGGCT	0.612													c|||	290	0.0579073	0.2057	0.0216	5008	,	,		14068	0.0		0.003	False		,,,				2504	0.0				p.G848G		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2544T						PASS	.		,	677,3501		66,545,1478	74.0	79.0	77.0		2544,2544	1.9	0.9	16	dbSNP_126	77	5,8423		0,5,4209	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	66,550,5687	TT,TC,CC		0.0593,16.2039,5.4101	,	848/2348,848/2354	1255206	682,11924	2089	4214	6303	SO:0001819	synonymous_variant	8912	exon11			CTGCGGCCCTCTG	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.2544C>T	16.37:g.1255206C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	65	38	0.584615	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.953;T|0.047	0.047	strong		0.612	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
SPSB2	84727	hgsc.bcm.edu	37	12	6982162	6982162	+	Splice_Site	SNP	C	C	T	rs11064437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6982162C>T	ENST00000524270.1	-	2	91		c.e2-1		SPSB2_ENST00000523102.1_Intron|LRRC23_ENST00000433346.1_5'Flank|SPSB2_ENST00000519357.1_Splice_Site|RPL13P5_ENST00000412023.1_RNA|SPSB2_ENST00000437851.1_5'Flank	NM_032641.3	NP_116030.1	Q99619	SPSB2_HUMAN	splA/ryanodine receptor domain and SOCS box containing 2						intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				kidney(2)|lung(2)|upper_aerodigestive_tract(1)	5						TGGAAGGGAGCTGGGAGAAAA	0.592											OREG0021639	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	786	0.156949	0.3101	0.1081	5008	,	,		-128	0.2768		0.008	False		,,,				2504	0.0143				.		Atlas-SNP	.											.	SPSB2	11	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	84727	.			AGGGAGCTGGGAG	AF403027	CCDS8567.1	12p13.31	2008-02-05				ENSG00000111671			29522	protein-coding gene	gene with protein product		611658				8723724, 12076535	Standard	NM_001146316		Approved	GRCC9, SSB-2	uc001qrl.3	Q99619		ENST00000524270.1:c.96-1G>A	12.37:g.6982162C>T		Somatic	41	0	0	638	WXS	Illumina HiSeq	Phase_I	43	43	1	.	B7Z4W1|D3DUT0	Splice_Site	SNP	ENST00000524270.1	37	CCDS8567.1																																																																																			C|0.840;T|0.160	0.160	strong		0.592	SPSB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375721.1	NM_032641	Intron
INTS1	26173	hgsc.bcm.edu	37	7	1533513	1533513	+	Silent	SNP	A	A	G	rs2251226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1533513A>G	ENST00000404767.3	-	15	2030	c.1945T>C	c.(1945-1947)Ttg>Ctg	p.L649L	INTS1_ENST00000389470.4_Silent_p.L777L	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	649					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GTGTCCTCCAAAATGGGCACC	0.677													G|||	3083	0.615615	0.8419	0.4236	5008	,	,		16908	0.7123		0.4662	False		,,,				2504	0.5				p.L649L		Atlas-SNP	.											.	INTS1	145	.	0			c.T1945C						PASS	.			3083,975		1206,671,152	17.0	24.0	22.0		1945	2.8	1.0	7	dbSNP_100	22	3480,4846		768,1944,1451	no	coding-synonymous	INTS1	NM_001080453.2		1974,2615,1603	GG,GA,AA		41.7968,24.0266,47.0042		649/2191	1533513	6563,5821	2029	4163	6192	SO:0001819	synonymous_variant	26173	exon15			CCTCCAAAATGGG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.1945T>C	7.37:g.1533513A>G		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	240	240	1	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																			A|0.379;G|0.621	0.621	strong		0.677	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
TREML1	340205	hgsc.bcm.edu	37	6	41117586	41117586	+	Missense_Mutation	SNP	T	T	G	rs34254490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41117586T>G	ENST00000426005.2	-	6	735	c.692A>C	c.(691-693)cAc>cCc	p.H231P	TREML1_ENST00000437044.2_Missense_Mutation_p.H120P|TREML1_ENST00000373127.4_3'UTR	NM_178174.2	NP_835468.1	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid cells-like 1	231	Pro-rich.		H -> P (in dbSNP:rs34254490).		calcium-mediated signaling (GO:0019722)|innate immune response (GO:0045087)|platelet activation (GO:0030168)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)				breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					AAGCCTAATGTGTGGTACATC	0.507													T|||	138	0.0275559	0.1029	0.0029	5008	,	,		19751	0.0		0.0	False		,,,				2504	0.0				p.H231P		Atlas-SNP	.											.	TREML1	20	.	0			c.A692C						PASS	.	T	PRO/HIS	347,4059	175.9+/-205.1	18,311,1874	174.0	154.0	161.0		692	4.5	0.0	6	dbSNP_126	161	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TREML1	NM_178174.2	77	18,312,6173	GG,GT,TT		0.0116,7.8756,2.6757	benign	231/312	41117586	348,12658	2203	4300	6503	SO:0001583	missense	340205	exon6			CTAATGTGTGGTA	AF534822	CCDS4851.1, CCDS64420.1, CCDS64421.1	6p21.1	2013-01-11			ENSG00000161911	ENSG00000161911		"""Immunoglobulin superfamily / V-set domain containing"""	20434	protein-coding gene	gene with protein product	"""TREM-like transcript 1"""	609714				12393607, 12645956	Standard	NM_178174		Approved	TLT1, dJ238O23.3	uc011duc.3	Q86YW5	OTTHUMG00000016231	ENST00000426005.2:c.692A>C	6.37:g.41117586T>G	ENSP00000402855:p.His231Pro	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_178174	Q496B3|Q8IWY1|Q8IWY2	Missense_Mutation	SNP	ENST00000426005.2	37	CCDS4851.1	49	0.022435897435897436	49	0.09959349593495935	0	0.0	0	0.0	0	0.0	T	12.67	2.007412	0.35415	0.078756	1.16E-4	ENSG00000161911	ENST00000373127;ENST00000437044	T	0.46819	0.86	5.71	4.52	0.55395	.	0.532842	0.17347	N	0.177556	T	0.16385	0.0394	N	0.19112	0.55	0.09310	N	1	B;B	0.22683	0.073;0.072	B;B	0.25405	0.06;0.027	T	0.18053	-1.0349	10	0.66056	D	0.02	.	9.718	0.40286	0.0:0.0:0.1745:0.8255	rs34254490;rs60023904	120;231	Q86YW5-3;Q86YW5	.;TRML1_HUMAN	P	231;120	ENSP00000400405:H120P	ENSP00000362219:H231P	H	-	2	0	TREML1	41225564	0.001000	0.12720	0.001000	0.08648	0.184000	0.23303	0.517000	0.22832	0.954000	0.37851	0.533000	0.62120	CAC	T|0.975;G|0.025	0.025	strong		0.507	TREML1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043538.2	NM_178174	
EPHA7	2045	hgsc.bcm.edu	37	6	93982100	93982100	+	Silent	SNP	C	C	T	rs34302170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:93982100C>T	ENST00000369303.4	-	6	1549	c.1365G>A	c.(1363-1365)ctG>ctA	p.L455L		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	455	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CACTCCGCTGCAGTACTCTCT	0.438													C|||	206	0.0411342	0.152	0.0029	5008	,	,		18429	0.0		0.003	False		,,,				2504	0.0				p.L455L		Atlas-SNP	.											.	EPHA7	251	.	0			c.G1365A						PASS	.	C		517,3889	237.7+/-249.4	30,457,1716	204.0	194.0	197.0		1365	5.7	1.0	6	dbSNP_126	197	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	EPHA7	NM_004440.3		30,464,6009	TT,TC,CC		0.0814,11.734,4.0289		455/999	93982100	524,12482	2203	4300	6503	SO:0001819	synonymous_variant	2045	exon6			CCGCTGCAGTACT	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3390	protein-coding gene	gene with protein product		602190	"""EphA7"""			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.1365G>A	6.37:g.93982100C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	174	92	0.528736	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Silent	SNP	ENST00000369303.4	37	CCDS5031.1																																																																																			C|0.963;T|0.037	0.037	strong		0.438	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
TSPYL1	7259	hgsc.bcm.edu	37	6	116600774	116600774	+	Missense_Mutation	SNP	C	C	G	rs3749895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116600774C>G	ENST00000368608.3	-	1	292	c.220G>C	c.(220-222)Gcc>Ccc	p.A74P	DSE_ENST00000540275.1_Intron|RP1-93H18.1_ENST00000449314.1_lincRNA|DSE_ENST00000452085.3_5'Flank	NM_003309.3	NP_003300.1	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	74			A -> P (in dbSNP:rs3749895). {ECO:0000269|PubMed:11230166}.		nucleosome assembly (GO:0006334)	nucleus (GO:0005634)	enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(3)|urinary_tract(1)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)		CGGCCCGCGGCATCCTGGGGT	0.711													G|||	2325	0.464257	0.348	0.3847	5008	,	,		14160	0.6448		0.3082	False		,,,				2504	0.6524				p.A74P		Atlas-SNP	.											TSPYL1,NS,carcinoma,0,1	TSPYL1	28	1	0			c.G220C						PASS	.	G	PRO/ALA	1399,2907		244,911,998	25.0	29.0	27.0		220	1.4	0.0	6	dbSNP_107	27	2333,6069		345,1643,2213	no	missense	TSPYL1	NM_003309.3	27	589,2554,3211	GG,GC,CC		27.7672,32.4895,29.3673	benign	74/438	116600774	3732,8976	2153	4201	6354	SO:0001583	missense	7259	exon1			CCGCGGCATCCTG	AF042181	CCDS34518.1	6q22.1	2014-09-17	2004-04-05	2004-04-07	ENSG00000189241	ENSG00000189241			12382	protein-coding gene	gene with protein product		604714	"""TSPY-like"""	TSPYL		9730615	Standard	NM_003309		Approved		uc003pwp.4	Q9H0U9	OTTHUMG00000015427	ENST00000368608.3:c.220G>C	6.37:g.116600774C>G	ENSP00000357597:p.Ala74Pro	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_003309	O75885|Q5TFE6	Missense_Mutation	SNP	ENST00000368608.3	37	CCDS34518.1	887	0.40613553113553114	157	0.31910569105691056	131	0.36187845303867405	370	0.6468531468531469	229	0.3021108179419525	G	2.250	-0.371714	0.05034	0.324895	0.277672	ENSG00000189241	ENST00000368608;ENST00000545830	T	0.20738	2.05	4.22	1.42	0.22433	.	.	.	.	.	T	0.00998	0.0033	N	0.00554	-1.385	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46952	-0.9154	8	0.02654	T	1	-0.2268	4.9149	0.13840	0.1909:0.3357:0.4734:0.0	rs3749895;rs56769178;rs3749895	74	Q9H0U9	TSYL1_HUMAN	P	74	ENSP00000357597:A74P	ENSP00000357597:A74P	A	-	1	0	TSPYL1	116707467	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.032000	0.13732	0.050000	0.15949	-0.120000	0.15030	GCC	C|0.657;G|0.343	0.343	strong		0.711	TSPYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041929.1		
NFAM1	150372	hgsc.bcm.edu	37	22	42793873	42793873	+	Silent	SNP	A	A	G	rs5996153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42793873A>G	ENST00000329021.5	-	4	691	c.654T>C	c.(652-654)tcT>tcC	p.S218S		NM_145912.5	NP_666017.1	Q8NET5	NFAM1_HUMAN	NFAT activating protein with ITAM motif 1	218	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cytokine production (GO:0001819)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of B cell differentiation (GO:0045577)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(3)	4						CTGTGTAGACAGATTCTGAAG	0.597													G|||	645	0.128794	0.2126	0.1988	5008	,	,		16255	0.001		0.1431	False		,,,				2504	0.0828				p.S218S		Atlas-SNP	.											.	NFAM1	12	.	0			c.T654C						PASS	.	G		951,3455	736.1+/-410.7	110,731,1362	103.0	99.0	100.0		654	-4.4	0.0	22	dbSNP_114	100	1337,7263	757.1+/-407.5	97,1143,3060	no	coding-synonymous	NFAM1	NM_145912.5		207,1874,4422	GG,GA,AA		15.5465,21.5842,17.5919		218/271	42793873	2288,10718	2203	4300	6503	SO:0001819	synonymous_variant	150372	exon4			GTAGACAGATTCT	BC038241	CCDS14034.1	22q13.2	2005-02-01			ENSG00000235568	ENSG00000235568			29872	protein-coding gene	gene with protein product		608740				12615919	Standard	NM_145912		Approved	CNAIP	uc003bcn.4	Q8NET5	OTTHUMG00000150923	ENST00000329021.5:c.654T>C	22.37:g.42793873A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_145912	B0QYD0|Q20WL2|Q5JZ96|Q8IUY8|Q8TEM8	Silent	SNP	ENST00000329021.5	37	CCDS14034.1																																																																																			A|0.848;G|0.152	0.152	strong		0.597	NFAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320541.1	NM_145912	
CACTIN	58509	hgsc.bcm.edu	37	19	3614538	3614538	+	Silent	SNP	C	C	T	rs60651483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3614538C>T	ENST00000429344.2	-	7	1264	c.1212G>A	c.(1210-1212)tcG>tcA	p.S404S	CACTIN-AS1_ENST00000592274.1_RNA|CACTIN_ENST00000248420.5_Silent_p.S404S|CACTIN_ENST00000221899.3_Silent_p.S336S	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	404					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CCTTGAACACCGACTGCACAT	0.637													C|||	692	0.138179	0.1921	0.0375	5008	,	,		15802	0.2341		0.0388	False		,,,				2504	0.1401				p.S404S		Atlas-SNP	.											.	.	.	.	0			c.G1212A						PASS	.	C	,	670,3476		51,568,1454	67.0	74.0	72.0		1212,1212	-8.2	0.9	19	dbSNP_129	72	334,8064		2,330,3867	no	coding-synonymous,coding-synonymous	C19orf29	NM_001080543.1,NM_021231.1	,	53,898,5321	TT,TC,CC		3.9771,16.1602,8.0038	,	404/759,404/759	3614538	1004,11540	2073	4199	6272	SO:0001819	synonymous_variant	58509	exon7			GAACACCGACTGC	BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"""NY REN 24 antigen"", ""functional spliceosome-associated protein c"", ""cactin homolog (Drosophila)"""		"""chromosome 19 open reading frame 29"""	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.1212G>A	19.37:g.3614538C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	179	107	0.597765	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Silent	SNP	ENST00000429344.2	37	CCDS45920.1																																																																																			C|0.890;T|0.110	0.110	strong		0.637	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2		
WRAP73	49856	hgsc.bcm.edu	37	1	3548136	3548136	+	Silent	SNP	T	T	C	rs2760321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3548136T>C	ENST00000270708.7	-	11	1207	c.1134A>G	c.(1132-1134)gcA>gcG	p.A378A	WRAP73_ENST00000378322.3_Silent_p.A378A	NM_017818.3	NP_060288.3	Q9P2S5	WRP73_HUMAN	WD repeat containing, antisense to TP73	378						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)	12						CCCACTGAAATGCGCGCACTG	0.642													C|||	4538	0.90615	0.8926	0.8458	5008	,	,		15672	0.995		0.836	False		,,,				2504	0.9479				p.A378A		Atlas-SNP	.											.	WRAP73	43	.	0			c.A1134G						PASS	.	C		3857,545	238.4+/-249.8	1693,471,37	38.0	37.0	38.0		1134	-10.9	0.0	1	dbSNP_100	38	7201,1399	265.0+/-285.9	3016,1169,115	no	coding-synonymous	WRAP73	NM_017818.3		4709,1640,152	CC,CT,TT		16.2674,12.3807,14.9515		378/461	3548136	11058,1944	2201	4300	6501	SO:0001819	synonymous_variant	49856	exon11			CTGAAATGCGCGC	AB034912, EF494669	CCDS48.1	1p36.3	2013-05-21	2011-04-13	2011-04-13	ENSG00000116213	ENSG00000116213		"""WD repeat domain containing"""	12759	protein-coding gene	gene with protein product		606040	"""WD repeat domain 8"""	WDR8			Standard	NM_017818		Approved		uc001ako.3	Q9P2S5	OTTHUMG00000000612	ENST00000270708.7:c.1134A>G	1.37:g.3548136T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_017818	Q5T0D6|Q9BUH7|Q9NTK7|Q9NX56	Silent	SNP	ENST00000270708.7	37	CCDS48.1																																																																																			T|0.138;C|0.862	0.862	strong		0.642	WRAP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001470.1		
CCT8L2	150160	hgsc.bcm.edu	37	22	17071899	17071899	+	Silent	SNP	G	G	A	rs547801677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17071899G>A	ENST00000359963.3	-	1	1801	c.1542C>T	c.(1540-1542)ctC>ctT	p.L514L		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	514					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CTACAGTCACGAGCTGTAGCA	0.498													g|||	3	0.000599042	0.0	0.0	5008	,	,		18283	0.003		0.0	False		,,,				2504	0.0				p.L514L		Atlas-SNP	.											CCT8L2,NS,carcinoma,-2,2	CCT8L2	150	2	0			c.C1542T						PASS	.						103.0	96.0	98.0					22																	17071899		2203	4298	6501	SO:0001819	synonymous_variant	150160	exon1			AGTCACGAGCTGT	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.1542C>T	22.37:g.17071899G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	173	94	0.543353	NM_014406	A4QPH3|Q9UJS3	Silent	SNP	ENST00000359963.3	37	CCDS13738.1																																																																																			.	.	none		0.498	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1		
EMC1	23065	hgsc.bcm.edu	37	1	19570146	19570146	+	Silent	SNP	G	G	A	rs6661253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19570146G>A	ENST00000477853.1	-	4	384	c.342C>T	c.(340-342)atC>atT	p.I114I	RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375208.3_Silent_p.I92I|EMC1_ENST00000375199.3_Silent_p.I114I	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	114						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											TCAGGCCCCCGATGTTAGTCT	0.498													G|||	191	0.038139	0.1241	0.0288	5008	,	,		21352	0.0069		0.0	False		,,,				2504	0.0				p.I114I		Atlas-SNP	.											.	.	.	.	0			c.C342T						PASS	.	G		513,3893	236.1+/-248.4	39,435,1729	124.0	128.0	126.0		342	-11.3	0.3	1	dbSNP_116	126	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	KIAA0090	NM_015047.1		39,441,6023	AA,AG,GG		0.0698,11.6432,3.9905		114/994	19570146	519,12487	2203	4300	6503	SO:0001819	synonymous_variant	23065	exon4			GCCCCCGATGTTA		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.342C>T	1.37:g.19570146G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	256	129	0.503906	NM_001271427	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Silent	SNP	ENST00000477853.1	37	CCDS190.1																																																																																			G|0.959;A|0.041	0.041	strong		0.498	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047	
KIAA1324	57535	hgsc.bcm.edu	37	1	109740128	109740128	+	Silent	SNP	C	C	G	rs61756684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109740128C>G	ENST00000369939.3	+	16	2337	c.2154C>G	c.(2152-2154)gtC>gtG	p.V718V	KIAA1324_ENST00000369938.1_3'UTR|KIAA1324_ENST00000529753.1_Silent_p.V631V	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	718					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		CCGACAATGTCACTGACCTCC	0.537													C|||	127	0.0253594	0.0885	0.013	5008	,	,		18314	0.0		0.001	False		,,,				2504	0.0				p.V718V		Atlas-SNP	.											.	KIAA1324	77	.	0			c.C2154G						PASS	.	C		339,4067	176.9+/-206.0	9,321,1873	93.0	95.0	94.0		2154	6.1	1.0	1	dbSNP_129	94	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	KIAA1324	NM_020775.3		9,325,6169	GG,GC,CC		0.0465,7.6941,2.6372		718/1014	109740128	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	57535	exon16			CAATGTCACTGAC	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"""estrogen induced gene 121"""	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.2154C>G	1.37:g.109740128C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	24	0.333333	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	37	CCDS794.1																																																																																			C|0.975;G|0.025	0.025	strong		0.537	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	
TCOF1	6949	hgsc.bcm.edu	37	5	149755340	149755340	+	Silent	SNP	G	G	T	rs7701163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149755340G>T	ENST00000504761.2	+	12	1761	c.1761G>T	c.(1759-1761)ggG>ggT	p.G587G	TCOF1_ENST00000394269.3_Silent_p.G587G|TCOF1_ENST00000451292.1_Silent_p.G587G|TCOF1_ENST00000445265.2_Silent_p.G510G|TCOF1_ENST00000513346.1_Silent_p.G587G|TCOF1_ENST00000323668.7_Silent_p.G510G|TCOF1_ENST00000439160.2_Silent_p.G587G|TCOF1_ENST00000377797.3_Silent_p.G587G			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	587					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGCCAAGGGGCCCCCTCAGA	0.612													G|||	363	0.072484	0.1415	0.0548	5008	,	,		18897	0.0228		0.0636	False		,,,				2504	0.0521				p.G587G		Atlas-SNP	.											.	TCOF1	154	.	0			c.G1761T						PASS	.	G	,,,,,	654,3752	271.9+/-270.5	48,558,1597	86.0	98.0	94.0		1530,1761,1761,1761,1530,1761	-9.9	0.0	5	dbSNP_116	94	658,7942	163.5+/-216.0	18,622,3660	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	,,,,,	66,1180,5257	TT,TG,GG		7.6512,14.8434,10.0877	,,,,,	510/1412,587/959,587/1489,587/1452,510/1413,587/1451	149755340	1312,11694	2203	4300	6503	SO:0001819	synonymous_variant	6949	exon12			CAAGGGGCCCCCT		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.1761G>T	5.37:g.149755340G>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Silent	SNP	ENST00000504761.2	37	CCDS54936.1																																																																																			G|0.910;T|0.090	0.090	strong		0.612	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
PLOD1	5351	hgsc.bcm.edu	37	1	12024235	12024235	+	Silent	SNP	C	C	T	rs1130529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	63	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	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	
PKD1	5310	hgsc.bcm.edu	37	16	2156021	2156021	+	Silent	SNP	A	A	G	rs28575767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2156021A>G	ENST00000262304.4	-	20	7916	c.7708T>C	c.(7708-7710)Ttg>Ctg	p.L2570L	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Silent_p.L2570L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2570	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				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						GTGATGGCCAAAGACCTACGA	0.701													g|||	890	0.177716	0.5212	0.1383	5008	,	,		15830	0.0		0.0905	False		,,,				2504	0.0143				p.L2570L		Atlas-SNP	.											PKD1,right_upper_lobe,carcinoma,+2,1	PKD1	184	1	0			c.T7708C						scavenged	.						23.0	36.0	31.0					16																	2156021		1407	2607	4014	SO:0001819	synonymous_variant	5310	exon20			TGGCCAAAGACCT	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.7708T>C	16.37:g.2156021A>G		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			A|0.873;G|0.127	0.127	strong		0.701	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
ZNF354C	30832	hgsc.bcm.edu	37	5	178505831	178505831	+	Missense_Mutation	SNP	A	A	G	rs57271258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:178505831A>G	ENST00000315475.6	+	5	704	c.398A>G	c.(397-399)gAg>gGg	p.E133G		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	133					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.E133G(1)		endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|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;0.247)		TTTGAGAGCGAGATAGAAGAA	0.378													G|||	122	0.024361	0.0862	0.0115	5008	,	,		20349	0.0		0.0	False		,,,				2504	0.0				p.E133G		Atlas-SNP	.											ZNF354C,caecum,carcinoma,0,1	ZNF354C	77	1	1	Substitution - Missense(1)	large_intestine(1)	c.A398G						PASS	.	G	GLY/GLU	312,4094	788.4+/-414.9	9,294,1900	90.0	95.0	93.0		398	1.0	0.0	5	dbSNP_129	93	0,8600		0,0,4300	yes	missense	ZNF354C	NM_014594.1	98	9,294,6200	GG,GA,AA		0.0,7.0813,2.3989	benign	133/555	178505831	312,12694	2203	4300	6503	SO:0001583	missense	30832	exon5			AGAGCGAGATAGA		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.398A>G	5.37:g.178505831A>G	ENSP00000324064:p.Glu133Gly	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	179	99	0.553073	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	30	0.013736263736263736	27	0.054878048780487805	3	0.008287292817679558	0	0.0	0	0.0	G	7.305	0.613748	0.14066	0.070813	0.0	ENSG00000177932	ENST00000315475	T	0.05786	3.39	3.87	1.04	0.20106	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48747	-0.9008	9	0.16896	T	0.51	1.603	3.2954	0.06964	0.3129:0.0:0.505:0.182	rs57271258	133	Q86Y25	Z354C_HUMAN	G	133	ENSP00000324064:E133G	ENSP00000324064:E133G	E	+	2	0	ZNF354C	178438437	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.082000	0.03400	-0.148000	0.11234	-0.930000	0.02707	GAG	A|0.974;G|0.026	0.026	strong		0.378	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
ZNF444	55311	hgsc.bcm.edu	37	19	56671359	56671359	+	Missense_Mutation	SNP	C	C	G	rs145075834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56671359C>G	ENST00000337080.3	+	5	1140	c.773C>G	c.(772-774)aCc>aGc	p.T258S	ZNF444_ENST00000592949.1_Missense_Mutation_p.T257S	NM_001253792.1|NM_018337.3	NP_001240721.1|NP_060807.2	Q8N0Y2	ZN444_HUMAN	zinc finger protein 444	258					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)			NS(1)|endometrium(1)|lung(5)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0531)		TGTGGCAAGACCTTCTACTGG	0.746													C|||	62	0.0123802	0.0461	0.0014	5008	,	,		9131	0.0		0.0	False		,,,				2504	0.0				p.T258S		Atlas-SNP	.											.	ZNF444	15	.	0			c.C773G						PASS	.	C	SER/THR	95,3577		0,95,1741	3.0	2.0	3.0		773	3.4	1.0	19	dbSNP_134	3	0,7290		0,0,3645	yes	missense	ZNF444	NM_018337.2	58	0,95,5386	GG,GC,CC		0.0,2.5871,0.8666	probably-damaging	258/328	56671359	95,10867	1836	3645	5481	SO:0001583	missense	55311	exon5			GCAAGACCTTCTA	AB052954	CCDS12939.1, CCDS59426.1	19q13.43	2013-01-09			ENSG00000167685	ENSG00000167685		"""-"", ""Zinc fingers, C2H2-type"""	16052	protein-coding gene	gene with protein product		607874				11978792, 19760602	Standard	NM_001253792		Approved	ZSCAN17, FLJ11137, EZF2	uc002qmm.3	Q8N0Y2		ENST00000337080.3:c.773C>G	19.37:g.56671359C>G	ENSP00000338860:p.Thr258Ser	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_018337	Q8TEQ9|Q8WU35|Q9NUU1	Missense_Mutation	SNP	ENST00000337080.3	37	CCDS12939.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	13.37	2.215791	0.39102	0.025871	0.0	ENSG00000167685	ENST00000337080	T	0.27402	1.67	3.43	3.43	0.39272	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.203463	0.24681	N	0.036467	T	0.01454	0.0047	N	0.01473	-0.845	0.24823	N	0.992574	B;P	0.48089	0.106;0.905	B;P	0.47118	0.047;0.538	T	0.07986	-1.0744	10	0.21540	T	0.41	.	12.7548	0.57328	0.0:1.0:0.0:0.0	.	257;258	Q8N0Y2-2;Q8N0Y2	.;ZN444_HUMAN	S	258	ENSP00000338860:T258S	ENSP00000338860:T258S	T	+	2	0	ZNF444	61363171	0.072000	0.21174	1.000000	0.80357	0.965000	0.64279	0.403000	0.20982	1.938000	0.56188	0.455000	0.32223	ACC	C|0.987;G|0.013	0.013	strong		0.746	ZNF444-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457503.1	NM_018337	
GPR112	139378	hgsc.bcm.edu	37	X	135431358	135431358	+	Silent	SNP	C	C	T	rs5930933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:135431358C>T	ENST00000394143.1	+	6	5784	c.5493C>T	c.(5491-5493)ccC>ccT	p.P1831P	GPR112_ENST00000370652.1_Silent_p.P1831P|GPR112_ENST00000412101.1_Silent_p.P1626P|GPR112_ENST00000287534.4_Silent_p.P1768P|GPR112_ENST00000394141.1_Silent_p.P1626P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1831					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CAACTCTACCCTCTTTGACAT	0.433													c|||	1787	0.473377	0.4236	0.3573	3775	,	,		16215	0.2778		0.3797	False		,,,				2504	0.3241				p.P1831P		Atlas-SNP	.											.	GPR112	459	.	0			c.C5493T						PASS	.			2112,1723		495,811,311,326,260	143.0	125.0	131.0		5493	0.4	0.0	X	dbSNP_114	131	3228,3500		567,1180,914,681,958	yes	coding-synonymous	GPR112	NM_153834.3		1062,1991,1225,1007,1218	TT,TC,T,CC,C		47.9786,44.9283,49.4462		1831/3081	135431358	5340,5223	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			TCTACCCTCTTTG	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5493C>T	X.37:g.135431358C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	167	98	0.586826	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			C|0.507;0|0.003	.	strong		0.433	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
OR4A47	403253	hgsc.bcm.edu	37	11	48510777	48510777	+	Missense_Mutation	SNP	G	G	A	rs7103992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48510777G>A	ENST00000446524.1	+	1	509	c.433G>A	c.(433-435)Gtg>Atg	p.V145M		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	145			V -> M (in dbSNP:rs7103992).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						GCTGCTGGTAGTGTCCTGGGT	0.448													G|||	2406	0.480431	0.3767	0.5922	5008	,	,		20789	0.4474		0.6451	False		,,,				2504	0.4059				p.V145M		Atlas-SNP	.											.	OR4A47	72	.	0			c.G433A						PASS	.	G	MET/VAL	1939,2463		433,1073,695	126.0	109.0	115.0		433	2.7	0.0	11	dbSNP_116	115	5358,3238		1665,2028,605	no	missense	OR4A47	NM_001005512.2	21	2098,3101,1300	AA,AG,GG		37.6687,44.0482,43.8606	benign	145/310	48510777	7297,5701	2201	4298	6499	SO:0001583	missense	403253	exon1			CTGGTAGTGTCCT	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"""GPCR / Class A : Olfactory receptors"""	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.433G>A	11.37:g.48510777G>A	ENSP00000412752:p.Val145Met	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	297	155	0.521886	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	1175	0.538003663003663	182	0.3699186991869919	224	0.6187845303867403	282	0.493006993006993	487	0.6424802110817942	N	6.195	0.404118	0.11754	0.440482	0.623313	ENSG00000237388	ENST00000446524	T	0.39592	1.07	4.84	2.74	0.32292	GPCR, rhodopsin-like superfamily (1);	0.464403	0.18016	N	0.154387	T	0.00012	0.0000	L	0.49350	1.555	0.80722	P	0.0	P	0.44090	0.826	P	0.44359	0.447	T	0.41734	-0.9492	9	0.39692	T	0.17	.	4.9609	0.14066	0.1014:0.0:0.5026:0.396	rs7103992	145	Q6IF82	O4A47_HUMAN	M	145	ENSP00000412752:V145M	ENSP00000412752:V145M	V	+	1	0	OR4A47	48467353	0.000000	0.05858	0.004000	0.12327	0.007000	0.05969	-0.261000	0.08694	0.948000	0.37687	0.511000	0.50034	GTG	G|0.441;A|0.559	0.559	strong		0.448	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512	
KNOP1	400506	hgsc.bcm.edu	37	16	19726124	19726124	+	Silent	SNP	G	G	A	rs58543897	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19726124G>A	ENST00000219837.7	-	2	312	c.234C>T	c.(232-234)tgC>tgT	p.C78C	AC002550.5_ENST00000565916.1_RNA|KNOP1_ENST00000568230.1_5'Flank|IQCK_ENST00000320394.6_5'Flank	NM_001012991.2	NP_001013009.2	Q1ED39	KNOP1_HUMAN	lysine-rich nucleolar protein 1	78	Lys-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CATGCTCCTCGCAAAGGGTGC	0.542													G|||	271	0.0541134	0.1906	0.0245	5008	,	,		18472	0.0		0.002	False		,,,				2504	0.0				p.C78C		Atlas-SNP	.											.	C16orf88	41	.	0			c.C234T						PASS	.	G		700,3352		55,590,1381	65.0	64.0	64.0		234	-9.2	0.0	16	dbSNP_129	64	22,8366		0,22,4172	no	coding-synonymous	C16orf88	NM_001012991.2		55,612,5553	AA,AG,GG		0.2623,17.2754,5.8039		78/459	19726124	722,11718	2026	4194	6220	SO:0001819	synonymous_variant	400506	exon2			CTCCTCGCAAAGG	BC047010	CCDS42127.1	16p12.3	2013-03-12	2013-03-12	2013-03-12	ENSG00000103550	ENSG00000103550			34404	protein-coding gene	gene with protein product	"""family with sequence similarity 191, member A"", ""testis-specific gene 118"""		"""chromosome 16 open reading frame 88"""	C16orf88			Standard	NM_001012991		Approved	101F10.1, FAM191A, TSG118	uc002dgq.3	Q1ED39		ENST00000219837.7:c.234C>T	16.37:g.19726124G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_001012991	O43328|Q5FWF3	Silent	SNP	ENST00000219837.7	37	CCDS42127.1																																																																																			G|0.972;A|0.028	0.028	strong		0.542	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2	NM_001012991	
PYROXD2	84795	hgsc.bcm.edu	37	10	100147060	100147060	+	Silent	SNP	A	A	G	rs4345897	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	84	32	0.380952	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	
TUBA3C	7278	hgsc.bcm.edu	37	13	19753479	19753479	+	Splice_Site	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:19753479A>G	ENST00000400113.3	-	2	331		c.e2+1		RP11-408E5.4_ENST00000382988.2_5'Flank	NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c						'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		CCGAGCACCTACCGACCACAG	0.587																																					.		Atlas-SNP	.											TUBA3C,NS,carcinoma,-2,1	TUBA3C	166	1	0			c.226+2T>C						scavenged	.						96.0	84.0	88.0					13																	19753479		2203	4300	6503	SO:0001630	splice_region_variant	7278	exon3			GCACCTACCGACC	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.226+1T>C	13.37:g.19753479A>G		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	258	3	0.0116279	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Splice_Site	SNP	ENST00000400113.3	37	CCDS9284.1	.	.	.	.	.	.	.	.	.	.	A	8.724	0.914994	0.17907	.	.	ENSG00000198033	ENST00000400113;ENST00000360801	.	.	.	1.37	1.37	0.22104	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.8515	0.24018	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TUBA3C	18651479	1.000000	0.71417	0.902000	0.35471	0.345000	0.29048	7.649000	0.83500	0.885000	0.36088	0.163000	0.16589	.	.	.	none		0.587	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	Intron
DNAJC30	84277	hgsc.bcm.edu	37	7	73097720	73097720	+	Missense_Mutation	SNP	G	G	C	rs113424906|rs28494095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73097720G>C	ENST00000395176.2	-	1	63	c.34C>G	c.(34-36)Ctg>Gtg	p.L12V	WBSCR22_ENST00000423497.1_5'Flank|WBSCR22_ENST00000265758.2_5'Flank|WBSCR22_ENST00000423166.2_5'Flank|WBSCR22_ENST00000464615.1_Intron	NM_032317.2	NP_115693.2	Q96LL9	DJC30_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 30	12						mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(1)	4						CAAGGTAACAGCCGCTGCCAC	0.597													G|||	480	0.0958466	0.171	0.1239	5008	,	,		13737	0.0198		0.0785	False		,,,				2504	0.0706				p.L12V		Atlas-SNP	.											.	DNAJC30	12	.	0			c.C34G						PASS	.	G	VAL/LEU	652,3630		56,540,1545	29.0	36.0	33.0		34	-9.1	0.0	7	dbSNP_125	33	593,7767		25,543,3612	yes	missense	DNAJC30	NM_032317.2	32	81,1083,5157	CC,CG,GG		7.0933,15.2265,9.8481	benign	12/227	73097720	1245,11397	2141	4180	6321	SO:0001583	missense	84277	exon1			GTAACAGCCGCTG	AF412025	CCDS5556.1	7q11.23	2011-09-02	2008-06-17	2008-06-17	ENSG00000176410	ENSG00000176410		"""Heat shock proteins / DNAJ (HSP40)"""	16410	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 18"""	WBSCR18		12073013	Standard	NM_032317		Approved		uc003tys.1	Q96LL9	OTTHUMG00000023290	ENST00000395176.2:c.34C>G	7.37:g.73097720G>C	ENSP00000378605:p.Leu12Val	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	44	26	0.590909	NM_032317	Q9BSG8	Missense_Mutation	SNP	ENST00000395176.2	37	CCDS5556.1	190	0.08699633699633699	74	0.15040650406504066	42	0.11602209944751381	11	0.019230769230769232	63	0.08311345646437995	G	13.10	2.135786	0.37728	0.152265	0.070933	ENSG00000176410	ENST00000395176;ENST00000539255	T	0.59224	0.28	4.96	-9.05	0.00730	.	2.390160	0.03370	N	0.198845	T	0.00210	0.0006	N	0.24115	0.695	0.58432	P	4.000000000004E-6	B	0.09022	0.002	B	0.10450	0.005	T	0.02208	-1.1195	9	0.35671	T	0.21	-0.2085	3.7048	0.08397	0.5398:0.2013:0.1573:0.1016	rs28494095	12	Q96LL9	DJC30_HUMAN	V	12;9	ENSP00000378605:L12V	ENSP00000378605:L12V	L	-	1	2	DNAJC30	72735656	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.088000	0.03379	-2.087000	0.00862	-0.345000	0.07892	CTG	G|0.897;C|0.103	0.103	strong		0.597	DNAJC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252304.2		
JSRP1	126306	hgsc.bcm.edu	37	19	2255311	2255311	+	Start_Codon_SNP	SNP	C	C	G	rs7250822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	145	0	0		WXS	Illumina HiSeq	Phase_I	196	82	0.418367	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
MYO1B	4430	hgsc.bcm.edu	37	2	192256874	192256874	+	Missense_Mutation	SNP	G	G	A	rs200814325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:192256874G>A	ENST00000392318.3	+	19	2270	c.2023G>A	c.(2023-2025)Gtg>Atg	p.V675M	MYO1B_ENST00000392316.1_Missense_Mutation_p.V675M|MYO1B_ENST00000304164.4_Missense_Mutation_p.V675M|MYO1B_ENST00000439065.2_5'UTR|MYO1B_ENST00000339514.4_Missense_Mutation_p.V675M	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	675	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.V675M(1)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			AGAAATTCCCGTGGAAGAATA	0.323													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17281	0.0		0.0	False		,,,				2504	0.0				p.V675M		Atlas-SNP	.											MYO1B_ENST00000392318,rectum,carcinoma,-1,3	MYO1B	160	3	1	Substitution - Missense(1)	central_nervous_system(1)	c.G2023A						scavenged	.	G	MET/VAL,MET/VAL,MET/VAL	4,4402	6.2+/-15.9	0,4,2199	66.0	73.0	70.0		2023,2023,2023	2.6	1.0	2		70	0,8598		0,0,4299	no	missense,missense,missense	MYO1B	NM_001130158.1,NM_001161819.1,NM_012223.3	21,21,21	0,4,6498	AA,AG,GG		0.0,0.0908,0.0308	benign,benign,benign	675/1137,675/1137,675/1079	192256874	4,13000	2203	4299	6502	SO:0001583	missense	4430	exon19			ATTCCCGTGGAAG	L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"""Myosins / Myosin superfamily : Class I"""	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.2023G>A	2.37:g.192256874G>A	ENSP00000376132:p.Val675Met	Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	183	3	0.0163934	NM_012223	O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.936012	0.34189	9.08E-4	0.0	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316	T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58	5.71	2.61	0.31194	Myosin head, motor domain (2);	0.411684	0.25894	N	0.027618	T	0.53722	0.1814	L	0.27053	0.805	0.39497	D	0.96813	B;B	0.09022	0.002;0.002	B;B	0.11329	0.006;0.006	T	0.55761	-0.8090	10	0.62326	D	0.03	.	7.2207	0.25985	0.068:0.1232:0.6813:0.1275	.	675;675	O43795;O43795-2	MYO1B_HUMAN;.	M	675	ENSP00000341903:V675M;ENSP00000376132:V675M;ENSP00000306382:V675M;ENSP00000376130:V675M	ENSP00000306382:V675M	V	+	1	0	MYO1B	191965119	0.032000	0.19561	0.983000	0.44433	0.875000	0.50365	0.265000	0.18515	1.422000	0.47177	0.557000	0.71058	GTG	G|0.999;A|0.001	0.001	weak		0.323	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223	
TDP1	55775	hgsc.bcm.edu	37	14	90429858	90429858	+	Missense_Mutation	SNP	G	G	A	rs28365054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:90429858G>A	ENST00000335725.4	+	3	650	c.400G>A	c.(400-402)Gcc>Acc	p.A134T	TDP1_ENST00000393454.2_Missense_Mutation_p.A134T|TDP1_ENST00000555565.1_Intron|TDP1_ENST00000357382.3_5'UTR|TDP1_ENST00000393452.3_Missense_Mutation_p.A134T|TDP1_ENST00000555880.1_Missense_Mutation_p.A134T	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	134			A -> T (in dbSNP:rs28365054). {ECO:0000269|Ref.3}.		cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		TGGCGCTCCCGCCTGCCACAG	0.527								Repair of DNA-protein crosslinks					G|||	530	0.105831	0.3336	0.0447	5008	,	,		20317	0.0089		0.0199	False		,,,				2504	0.0297				p.A134T		Atlas-SNP	.											.	TDP1	47	.	0			c.G400A						PASS	.	G	THR/ALA,THR/ALA	1239,3167	411.7+/-335.8	181,877,1145	48.0	45.0	46.0		400,400	-2.6	0.0	14	dbSNP_126	46	179,8421	80.1+/-142.7	3,173,4124	yes	missense,missense	TDP1	NM_001008744.1,NM_018319.3	58,58	184,1050,5269	AA,AG,GG		2.0814,28.1207,10.9027	benign,benign	134/609,134/609	90429858	1418,11588	2203	4300	6503	SO:0001583	missense	55775	exon3			GCTCCCGCCTGCC	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.400G>A	14.37:g.90429858G>A	ENSP00000337353:p.Ala134Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	99	54	0.545455	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	37	CCDS9888.1	195	0.08928571428571429	155	0.3150406504065041	19	0.052486187845303865	8	0.013986013986013986	13	0.017150395778364115	G	6.023	0.372548	0.11409	0.281207	0.020814	ENSG00000042088	ENST00000393452;ENST00000554180;ENST00000393454;ENST00000553617;ENST00000335725;ENST00000556867;ENST00000553527;ENST00000553989;ENST00000556498;ENST00000555880	T;T;T;T;T;T;T;T;T;T	0.30981	1.51;2.25;1.75;2.22;1.75;1.87;1.87;1.87;1.91;1.52	5.36	-2.62	0.06152	.	1.082140	0.06853	N	0.797624	T	0.00012	0.0000	N	0.13043	0.29	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.09022	0.001;0.001;0.001;0.002	B;B;B;B	0.06405	0.001;0.001;0.002;0.0	T	0.44390	-0.9331	9	0.13108	T	0.6	-10.0622	5.7326	0.18049	0.4341:0.0:0.4386:0.1273	rs28365054;rs35332925;rs28365054	134;134;134;134	G3V2F4;E7EPD8;G3V4W8;Q9NUW8	.;.;.;TYDP1_HUMAN	T	134;134;134;35;134;134;134;134;134;134	ENSP00000377098:A134T;ENSP00000450872:A134T;ENSP00000377099:A134T;ENSP00000450708:A35T;ENSP00000337353:A134T;ENSP00000452279:A134T;ENSP00000451358:A134T;ENSP00000452333:A134T;ENSP00000452183:A134T;ENSP00000450628:A134T	ENSP00000337353:A134T	A	+	1	0	TDP1	89499611	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.012000	0.13287	-0.617000	0.05664	-1.300000	0.01332	GCC	G|0.892;A|0.108	0.108	strong		0.527	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319	
HOXD9	3235	hgsc.bcm.edu	37	2	176988765	176988765	+	Silent	SNP	C	C	T	rs35649704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:176988765C>T	ENST00000249499.6	+	2	1330	c.921C>T	c.(919-921)aaC>aaT	p.N307N	HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	307					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal system morphogenesis (GO:0048704)|hindlimb morphogenesis (GO:0035137)|mammary gland development (GO:0030879)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		TCCTCTTCAACATGTACCTCA	0.537													C|||	83	0.0165735	0.0613	0.0029	5008	,	,		17944	0.0		0.0	False		,,,				2504	0.0				p.N307N	GBM(47;924 952 7959 9248 12176)	Atlas-SNP	.											.	HOXD9	49	.	0			c.C921T						PASS	.	C		186,4220	118.8+/-156.5	4,178,2021	94.0	105.0	101.0		921	3.9	1.0	2	dbSNP_126	101	0,8600		0,0,4300	no	coding-synonymous	HOXD9	NM_014213.3		4,178,6321	TT,TC,CC		0.0,4.2215,1.4301		307/353	176988765	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	3235	exon2			CTTCAACATGTAC		CCDS2267.2	2q31.1	2011-06-20	2005-12-22		ENSG00000128709	ENSG00000128709		"""Homeoboxes / ANTP class : HOXL subclass"""	5140	protein-coding gene	gene with protein product		142982	"""homeo box D9"""	HOX4C, HOX4		1973146, 1358459	Standard	NM_014213		Approved		uc010zex.2	P28356	OTTHUMG00000132516	ENST00000249499.6:c.921C>T	2.37:g.176988765C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	170	86	0.505882	NM_014213	Q86ST1	Silent	SNP	ENST00000249499.6	37	CCDS2267.2																																																																																			C|0.987;T|0.013	0.013	strong		0.537	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255698.4		
LRRC38	126755	hgsc.bcm.edu	37	1	13802373	13802373	+	Missense_Mutation	SNP	G	G	A	rs2940315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:13802373G>A	ENST00000376085.3	-	2	1280	c.826C>T	c.(826-828)Ctc>Ttc	p.L276F		NM_001010847.1	NP_001010847.1	Q5VT99	LRC38_HUMAN	leucine rich repeat containing 38	276			L -> F (in dbSNP:rs2940315).		ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CACCTCTGGAGGCACTGCACC	0.577													A|||	291	0.058107	0.1899	0.0202	5008	,	,		19997	0.0		0.0189	False		,,,				2504	0.0072				p.L276F		Atlas-SNP	.											.	LRRC38	12	.	0			c.C826T						PASS	.																																			SO:0001583	missense	126755	exon2			TCTGGAGGCACTG	BC016048	CCDS53269.1	1p36.21	2008-02-05			ENSG00000162494	ENSG00000162494			27005	protein-coding gene	gene with protein product		615212				12477932	Standard	NM_001010847		Approved		uc001avb.3	Q5VT99	OTTHUMG00000007918	ENST00000376085.3:c.826C>T	1.37:g.13802373G>A	ENSP00000365253:p.Leu276Phe	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_001010847	Q96B32	Missense_Mutation	SNP	ENST00000376085.3	37	CCDS53269.1	96	0.04395604395604396	80	0.16260162601626016	3	0.008287292817679558	0	0.0	13	0.017150395778364115	.	7.327	0.618183	0.14129	.	.	ENSG00000162494	ENST00000376085	T	0.61627	0.09	5.25	5.25	0.73442	.	0.000000	0.85682	N	0.000000	T	0.00073	0.0002	N	0.00101	-2.135	0.50467	P	1.2299999999998423E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.14062	-1.0486	9	0.02654	T	1	.	10.1313	0.42680	0.9207:0.0:0.0793:0.0	rs2940315;rs52806058;rs57128796;rs2940315	276	Q5VT99	LRC38_HUMAN	F	276	ENSP00000365253:L276F	ENSP00000365253:L276F	L	-	1	0	LRRC38	13674960	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.092000	0.76930	0.841000	0.35020	-0.361000	0.07541	CTC	G|0.944;A|0.056	0.056	strong		0.577	LRRC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021793.1		
CR1L	1379	hgsc.bcm.edu	37	1	207890818	207890818	+	Missense_Mutation	SNP	G	G	A	rs113806677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207890818G>A	ENST00000508064.2	+	11	1484	c.1424G>A	c.(1423-1425)tGt>tAt	p.C475Y		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	475	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GAAATCTTTTGTCCAAATCCT	0.388													g|||	139	0.0277556	0.1014	0.0072	5008	,	,		18100	0.0		0.0	False		,,,				2504	0.0				p.C475Y		Atlas-SNP	.											CR1L_ENST00000508064,NS,carcinoma,-1,1	CR1L	97	1	0			c.G1424A						PASS	.	G	TYR/CYS	344,3278		18,308,1485	80.0	74.0	76.0		1424	3.0	0.1	1	dbSNP_132	76	1,8137		0,1,4068	yes	missense	CR1L	NM_175710.1	194	18,309,5553	AA,AG,GG		0.0123,9.4975,2.9337	probably-damaging	475/570	207890818	345,11415	1811	4069	5880	SO:0001583	missense	1379	exon11			TCTTTTGTCCAAA	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1424G>A	1.37:g.207890818G>A	ENSP00000421736:p.Cys475Tyr	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	210	112	0.533333	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	.	14.21	2.467416	0.43839	0.094975	1.23E-4	ENSG00000197721	ENST00000508064	D	0.99784	-6.74	3.01	3.01	0.34805	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	D	0.95401	0.8507	H	0.99719	4.725	0.25098	N	0.99081	D	0.89917	1.0	D	0.97110	1.0	T	0.80630	-0.1297	9	0.87932	D	0	.	10.1225	0.42630	0.0:0.0:1.0:0.0	.	475	Q2VPA4	CR1L_HUMAN	Y	475	ENSP00000421736:C475Y	ENSP00000421736:C475Y	C	+	2	0	CR1L	205957441	0.981000	0.34729	0.142000	0.22268	0.288000	0.27193	4.125000	0.57931	1.639000	0.50556	0.305000	0.20034	TGT	G|0.976;A|0.024	0.024	strong		0.388	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
TRIM56	81844	hgsc.bcm.edu	37	7	100732321	100732321	+	Silent	SNP	C	C	T	rs11760747	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100732321C>T	ENST00000306085.6	+	3	2025	c.1728C>T	c.(1726-1728)aaC>aaT	p.N576N		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	576					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)					TCAACCCCAACGGCGAAGTGC	0.726													C|||	906	0.180911	0.3366	0.1052	5008	,	,		15445	0.1379		0.1312	False		,,,				2504	0.1196				p.N576N	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.C1728T						PASS	.	C		1162,3026		169,824,1101	56.0	62.0	60.0		1728	-7.4	0.0	7	dbSNP_120	60	996,7416		54,888,3264	no	coding-synonymous	TRIM56	NM_030961.1		223,1712,4365	TT,TC,CC		11.8402,27.7459,17.127		576/756	100732321	2158,10442	2094	4206	6300	SO:0001819	synonymous_variant	81844	exon3			CCCCAACGGCGAA	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.1728C>T	7.37:g.100732321C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																			C|0.857;T|0.143	0.143	strong		0.726	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961	
PSMC3IP	29893	hgsc.bcm.edu	37	17	40725379	40725379	+	Missense_Mutation	SNP	A	A	T	rs2292754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40725379A>T	ENST00000393795.3	-	6	595	c.487T>A	c.(487-489)Tac>Aac	p.Y163N	PSMC3IP_ENST00000253789.5_Missense_Mutation_p.Y151N|PSMC3IP_ENST00000590760.1_Missense_Mutation_p.Y38N|PSMC3IP_ENST00000587209.1_Missense_Mutation_p.Y100N	NM_001256015.1|NM_001256016.1|NM_016556.3	NP_001242944.1|NP_001242945.1|NP_057640.1	Q9P2W1	HOP2_HUMAN	PSMC3 interacting protein	163	DNA binding. {ECO:0000250}.		Y -> N (in dbSNP:rs2292754).		DNA recombination (GO:0006310)|meiotic nuclear division (GO:0007126)|regulation of RNA biosynthetic process (GO:2001141)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			endometrium(2)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(2)	7		all_cancers(22;0.00426)|Breast(137;0.00116)|all_epithelial(22;0.0395)		BRCA - Breast invasive adenocarcinoma(366;0.13)		CTCTCTCTGTACACCTAGAAG	0.537													A|||	450	0.0898562	0.1293	0.0331	5008	,	,		21171	0.1855		0.005	False		,,,				2504	0.0654				p.Y163N		Atlas-SNP	.											.	PSMC3IP	23	.	0			c.T487A						PASS	.	A	ASN/TYR,ASN/TYR	442,3964	212.8+/-232.6	29,384,1790	184.0	146.0	159.0		451,487	4.8	0.8	17	dbSNP_100	159	36,8564	24.6+/-71.5	0,36,4264	yes	missense,missense	PSMC3IP	NM_013290.5,NM_016556.2	143,143	29,420,6054	TT,TA,AA		0.4186,10.0318,3.6752	benign,benign	151/206,163/218	40725379	478,12528	2203	4300	6503	SO:0001583	missense	29893	exon6			CTCTGTACACCTA	AB030304, NM_013290, BC008792	CCDS11431.1, CCDS45688.1, CCDS59289.1	17q21.2	2012-04-10				ENSG00000131470		"""Proteasome (prosome, macropain) subunits"""	17928	protein-coding gene	gene with protein product	"""TBP-1 interacting protein"""	608665				7490091, 10806355, 11739747	Standard	NM_016556		Approved	TBPIP, GT198, HUMGT198A	uc002iai.3	Q9P2W1		ENST00000393795.3:c.487T>A	17.37:g.40725379A>T	ENSP00000377384:p.Tyr163Asn	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	201	89	0.442786	NM_016556	C5ILB7|Q14458|Q8WXG2|Q96HA2	Missense_Mutation	SNP	ENST00000393795.3	37	CCDS45688.1	171	0.0782967032967033	74	0.15040650406504066	3	0.008287292817679558	90	0.15734265734265734	4	0.005277044854881266	A	12.06	1.825009	0.32237	0.100318	0.004186	ENSG00000131470	ENST00000393795;ENST00000253789	T;T	0.42131	0.98;0.98	5.93	4.84	0.62591	.	0.111391	0.64402	D	0.000006	T	0.00178	0.0005	L	0.60957	1.885	0.09310	P	0.99999819491	B;B	0.18461	0.023;0.028	B;B	0.20384	0.017;0.029	T	0.10428	-1.0630	9	0.15952	T	0.53	-4.7468	13.3644	0.60676	0.8684:0.1316:0.0:0.0	rs2292754;rs52820455;rs2292754	151;163	Q9P2W1-2;Q9P2W1	.;HOP2_HUMAN	N	163;151	ENSP00000377384:Y163N;ENSP00000253789:Y151N	ENSP00000253789:Y151N	Y	-	1	0	PSMC3IP	37978905	0.928000	0.31464	0.786000	0.31890	0.516000	0.34256	2.116000	0.41930	1.043000	0.40175	0.460000	0.39030	TAC	A|0.948;T|0.052	0.052	strong		0.537	PSMC3IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450427.1	NM_013290	
SH3D19	152503	hgsc.bcm.edu	37	4	152065197	152065197	+	Silent	SNP	C	C	T	rs3736502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:152065197C>T	ENST00000409252.2	-	12	2024	c.1317G>A	c.(1315-1317)ggG>ggA	p.G439G	SH3D19_ENST00000514152.1_Silent_p.G416G|SH3D19_ENST00000304527.4_Silent_p.G439G|RP11-372K14.2_ENST00000603472.1_RNA|SH3D19_ENST00000409598.4_Silent_p.G416G|SH3D19_ENST00000427414.2_Silent_p.G380G|SH3D19_ENST00000424281.1_Silent_p.G380G|SH3D19_ENST00000455740.1_Silent_p.G416G			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	439	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cytoskeleton organization (GO:0007010)|membrane organization (GO:0061024)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of cell morphogenesis (GO:0022604)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(1)|skin(3)|urinary_tract(1)	20	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				CAAGTACATCCCCACGCTGCA	0.363													C|||	486	0.0970447	0.152	0.0259	5008	,	,		18817	0.1944		0.0249	False		,,,				2504	0.047				p.G439G		Atlas-SNP	.											.	SH3D19	54	.	0			c.G1317A						PASS	.	C	,,	605,3801	262.5+/-264.9	42,521,1640	127.0	118.0	121.0		1317,1248,1140	1.6	1.0	4	dbSNP_107	121	296,8304	107.6+/-168.3	6,284,4010	no	coding-synonymous,coding-synonymous,coding-synonymous	SH3D19	NM_001009555.3,NM_001128923.1,NM_001128924.1	,,	48,805,5650	TT,TC,CC		3.4419,13.7313,6.9276	,,	439/791,416/768,380/732	152065197	901,12105	2203	4300	6503	SO:0001819	synonymous_variant	152503	exon13			TACATCCCCACGC	BX647422	CCDS34077.2, CCDS47143.1, CCDS47144.1	4q31.3	2009-03-05	2009-03-05	2009-03-05	ENSG00000109686	ENSG00000109686			30418	protein-coding gene	gene with protein product	"""EEN binding protein"""	608674				12477932	Standard	NM_001009555		Approved	DKFZp434D0215, EVE1, EBP, Kryn, SH3P19	uc010ipl.1	Q5HYK7	OTTHUMG00000154051	ENST00000409252.2:c.1317G>A	4.37:g.152065197C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_001009555	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Silent	SNP	ENST00000409252.2	37	CCDS34077.2																																																																																			C|0.913;T|0.087	0.087	strong		0.363	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555	
RTP5	285093	hgsc.bcm.edu	37	2	242814463	242814463	+	Silent	SNP	A	A	T	rs28523279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242814463A>T	ENST00000343216.3	+	2	784	c.756A>T	c.(754-756)tcA>tcT	p.S252S		NM_173821.2	NP_776182.2																					CTGGGGATTCAGTGGCCATGC	0.682													T|||	1562	0.311901	0.3638	0.3199	5008	,	,		16443	0.6012		0.1064	False		,,,				2504	0.1493				p.S252S		Atlas-SNP	.											.	.	.	.	0			c.A756T						PASS	.			1180,2618		196,788,915	26.0	30.0	29.0		756	-0.2	0.0	2	dbSNP_125	29	739,7481		41,657,3412	no	coding-synonymous	C2orf85	NM_173821.2		237,1445,4327	TT,TA,AA		8.9903,31.069,15.9677		252/573	242814463	1919,10099	1899	4110	6009	SO:0001819	synonymous_variant	285093	exon2			GGATTCAGTGGCC																												ENST00000343216.3:c.756A>T	2.37:g.242814463A>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	133	71	0.533835	NM_173821		Silent	SNP	ENST00000343216.3	37	CCDS42843.1																																																																																			A|0.731;T|0.269	0.269	strong		0.682	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
C1orf168	199920	hgsc.bcm.edu	37	1	57186000	57186000	+	Silent	SNP	G	G	A	rs76493848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57186000G>A	ENST00000343433.6	-	18	2057	c.1977C>T	c.(1975-1977)taC>taT	p.Y659Y		NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	659										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						TCTCTTTGTCGTACTGAAATG	0.303													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		15674	0.0		0.0	False		,,,				2504	0.0				p.Y659Y		Atlas-SNP	.											.	C1orf168	102	.	0			c.C1977T						PASS	.	G		207,4199	122.5+/-159.9	2,203,1998	52.0	52.0	52.0		1977	-0.1	0.6	1	dbSNP_132	52	3,8587	1.2+/-3.3	0,3,4292	no	coding-synonymous	C1orf168	NM_001004303.4		2,206,6290	AA,AG,GG		0.0349,4.6981,1.6159		659/729	57186000	210,12786	2203	4295	6498	SO:0001819	synonymous_variant	199920	exon18			TTTGTCGTACTGA	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.1977C>T	1.37:g.57186000G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001004303	Q63HM3|Q6ZUY6	Silent	SNP	ENST00000343433.6	37	CCDS30729.1																																																																																			G|0.987;A|0.013	0.013	strong		0.303	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303	
FREM1	158326	hgsc.bcm.edu	37	9	14801738	14801738	+	Missense_Mutation	SNP	G	G	C	rs16932300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14801738G>C	ENST00000380880.3	-	20	4389	c.3606C>G	c.(3604-3606)agC>agG	p.S1202R	FREM1_ENST00000380881.4_Missense_Mutation_p.S1203R|FREM1_ENST00000422223.2_Missense_Mutation_p.S1202R			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1202			S -> R (in dbSNP:rs16932300).		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)		AGAAGTCTTTGCTAAACCCCC	0.517													G|||	820	0.163738	0.3578	0.098	5008	,	,		18063	0.1002		0.0795	False		,,,				2504	0.1002				p.S1202R		Atlas-SNP	.											.	FREM1	261	.	0			c.C3606G						PASS	.	G	ARG/SER	1213,2779		181,851,964	147.0	145.0	145.0		3606	-2.4	0.0	9	dbSNP_123	145	542,7814		13,516,3649	yes	missense	FREM1	NM_144966.5	110	194,1367,4613	CC,CG,GG		6.4864,30.3858,14.2128	benign	1202/2180	14801738	1755,10593	1996	4178	6174	SO:0001583	missense	158326	exon21			GTCTTTGCTAAAC	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.3606C>G	9.37:g.14801738G>C	ENSP00000370262:p.Ser1202Arg	Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	311	167	0.536977	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	341	0.15613553113553114	176	0.35772357723577236	38	0.10497237569060773	65	0.11363636363636363	62	0.08179419525065963	G	1.832	-0.469514	0.04445	0.303858	0.064864	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.54279	0.58;0.58;0.58	5.51	-2.39	0.06602	.	0.432154	0.30068	N	0.010492	T	0.00012	0.0000	N	0.25144	0.715	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.38542	-0.9656	9	0.22706	T	0.39	-4.1075	4.321	0.11016	0.1358:0.304:0.4434:0.1168	rs16932300;rs58105230;rs16932300	1202	Q5H8C1	FREM1_HUMAN	R	1203;1202;1202	ENSP00000370263:S1203R;ENSP00000412940:S1202R;ENSP00000370262:S1202R	ENSP00000370257:S1205R	S	-	3	2	FREM1	14791738	0.104000	0.21937	0.001000	0.08648	0.023000	0.10783	0.018000	0.13422	-0.241000	0.09681	-0.282000	0.10007	AGC	G|0.839;C|0.161	0.161	strong		0.517	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
SRP68	6730	hgsc.bcm.edu	37	17	74060168	74060168	+	Silent	SNP	T	T	C	rs58471646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74060168T>C	ENST00000307877.2	-	4	611	c.450A>G	c.(448-450)cgA>cgG	p.R150R	SRP68_ENST00000355113.5_Silent_p.R49R|SRP68_ENST00000539137.1_Silent_p.R112R	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	150					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						GAAACCGTTTTCGGGGTTCAG	0.502													T|||	393	0.0784744	0.2806	0.0317	5008	,	,		19465	0.0		0.0	False		,,,				2504	0.0				p.R150R		Atlas-SNP	.											SRP68,rectum,carcinoma,-1,1	SRP68	61	1	0			c.A450G						scavenged	.	T		1023,3383	380.2+/-323.6	119,785,1299	189.0	162.0	171.0		450	0.2	1.0	17	dbSNP_129	171	19,8581	11.2+/-40.8	0,19,4281	no	coding-synonymous	SRP68	NM_014230.2		119,804,5580	CC,CT,TT		0.2209,23.2183,8.0117		150/628	74060168	1042,11964	2203	4300	6503	SO:0001819	synonymous_variant	6730	exon4			CCGTTTTCGGGGT	AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"""signal recognition particle 68kD"""			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.450A>G	17.37:g.74060168T>C		Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	273	115	0.421245	NM_014230	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Silent	SNP	ENST00000307877.2	37	CCDS11738.1																																																																																			T|0.925;C|0.075	0.075	strong		0.502	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230	
FMN2	56776	hgsc.bcm.edu	37	1	240371328	240371328	+	Silent	SNP	G	G	A	rs71646895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:240371328G>A	ENST00000319653.9	+	5	3446	c.3216G>A	c.(3214-3216)gcG>gcA	p.A1072A		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1072	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)			TACCCGGAGCGGGCATACCCC	0.736																																					p.A1072A		Atlas-SNP	.											FMN2,colon,carcinoma,0,2	FMN2	451	2	0			c.G3216A						scavenged	.						2.0	3.0	3.0					1																	240371328		1326	2694	4020	SO:0001819	synonymous_variant	56776	exon5			CGGAGCGGGCATA	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.3216G>A	1.37:g.240371328G>A		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	178	50	0.280899	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			G|0.835;A|0.165	0.165	strong		0.736	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
KCNK4	50801	hgsc.bcm.edu	37	11	64066999	64066999	+	Missense_Mutation	SNP	C	C	T	rs953778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64066999C>T	ENST00000539216.1	+	6	1343	c.983C>T	c.(982-984)cCg>cTg	p.P328L	KCNK4_ENST00000422670.2_Missense_Mutation_p.P328L|KCNK4_ENST00000394525.2_Missense_Mutation_p.P328L|RP11-783K16.10_ENST00000539086.1_RNA|TEX40_ENST00000539943.1_5'Flank|KCNK4_ENST00000538767.1_Silent_p.A212A|TEX40_ENST00000328404.6_5'Flank			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	32	0	0		WXS	Illumina HiSeq	Phase_I	28	17	0.607143	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	
HMHA1	23526	hgsc.bcm.edu	37	19	1079968	1079968	+	Silent	SNP	G	G	A	rs34047143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1079968G>A	ENST00000313093.2	+	13	1785	c.1554G>A	c.(1552-1554)gcG>gcA	p.A518A	HMHA1_ENST00000539243.2_Silent_p.A534A|HMHA1_ENST00000590577.1_Silent_p.A153A|HMHA1_ENST00000586866.1_Silent_p.A522A|HMHA1_ENST00000590214.1_Silent_p.A545A|HMHA1_ENST00000536472.1_Silent_p.A358A|HMHA1_ENST00000543365.1_Silent_p.A401A	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	518					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)		TGCAGACGGCGCCGCTGCCCG	0.672													G|||	176	0.0351438	0.1309	0.0043	5008	,	,		15158	0.0		0.0	False		,,,				2504	0.0				p.A534A		Atlas-SNP	.											.	HMHA1	78	.	0			c.G1602A						PASS	.	G		481,3925	223.3+/-239.8	28,425,1750	74.0	80.0	78.0		1554	-6.9	1.0	19	dbSNP_126	78	0,8600		0,0,4300	no	coding-synonymous	HMHA1	NM_012292.2		28,425,6050	AA,AG,GG		0.0,10.9169,3.6983		518/1137	1079968	481,12525	2203	4300	6503	SO:0001819	synonymous_variant	23526	exon13			GACGGCGCCGCTG	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.1554G>A	19.37:g.1079968G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			G|0.962;A|0.038	0.038	strong		0.672	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
GNMT	27232	hgsc.bcm.edu	37	6	42930877	42930877	+	Silent	SNP	G	G	A	rs147291064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42930877G>A	ENST00000372808.3	+	4	529	c.519G>A	c.(517-519)ctG>ctA	p.L173L		NM_018960.4	NP_061833.1	Q14749	GNMT_HUMAN	glycine N-methyltransferase	173					cellular protein modification process (GO:0006464)|glycogen metabolic process (GO:0005977)|methionine metabolic process (GO:0006555)|one-carbon metabolic process (GO:0006730)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|S-adenosylmethionine metabolic process (GO:0046500)	cytoplasm (GO:0005737)	folic acid binding (GO:0005542)|glycine binding (GO:0016594)|glycine N-methyltransferase activity (GO:0017174)			kidney(2)|large_intestine(1)|lung(1)	4	Colorectal(47;0.196)		all cancers(41;0.00196)|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;0.0461)		Glycine(DB00145)|S-Adenosylmethionine(DB00118)	GGGGCCTACTGGTCATTGATC	0.602													G|||	47	0.00938498	0.034	0.0029	5008	,	,		11061	0.0		0.0	False		,,,				2504	0.0				p.L173L		Atlas-SNP	.											.	GNMT	13	.	0			c.G519A						PASS	.	G		88,4318	74.7+/-112.8	0,88,2115	42.0	40.0	41.0		519	3.9	1.0	6	dbSNP_134	41	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GNMT	NM_018960.4		0,91,6412	AA,AG,GG		0.0349,1.9973,0.6997		173/296	42930877	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	27232	exon4			CCTACTGGTCATT	AF101475	CCDS4876.1	6p12	2008-02-05			ENSG00000124713	ENSG00000124713			4415	protein-coding gene	gene with protein product		606628				10843803, 9495250	Standard	NM_018960		Approved		uc003otd.3	Q14749	OTTHUMG00000014712	ENST00000372808.3:c.519G>A	6.37:g.42930877G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_018960	Q5T8W2|Q9NNZ1|Q9NS24	Silent	SNP	ENST00000372808.3	37	CCDS4876.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	GNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040568.1	NM_018960	
LPP	4026	hgsc.bcm.edu	37	3	188327555	188327555	+	Missense_Mutation	SNP	T	T	C	rs7645635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:188327555T>C	ENST00000312675.4	+	6	1282	c.1036T>C	c.(1036-1038)Tat>Cat	p.Y346H	LPP_ENST00000543006.1_Missense_Mutation_p.Y346H|LPP_ENST00000448637.1_Missense_Mutation_p.Y346H|LPP_ENST00000471917.1_3'UTR	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	346	Pro-rich.		Y -> H (in dbSNP:rs7645635).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TCCTGGGATGTATCCAGTCAC	0.522			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								T|||	1002	0.20008	0.7126	0.0764	5008	,	,		18753	0.0		0.005	False		,,,				2504	0.002				p.Y346H		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	LPP	72	.	0			c.T1036C						PASS	.	T	HIS/TYR,,HIS/TYR	2581,1825		769,1043,391	42.0	42.0	42.0		1036,,1036	6.2	0.9	3	dbSNP_116	42	34,8564		0,34,4265	yes	missense,intron,missense	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	83,,83	769,1077,4656	CC,CT,TT		0.3954,41.4208,20.1092	probably-damaging,,probably-damaging	346/613,,346/613	188327555	2615,10389	2203	4299	6502	SO:0001583	missense	4026	exon6			GGGATGTATCCAG	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1036T>C	3.37:g.188327555T>C	ENSP00000318089:p.Tyr346His	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	37	CCDS3291.1	360	0.16483516483516483	328	0.6666666666666666	28	0.07734806629834254	0	0.0	4	0.005277044854881266	T	16.16	3.043406	0.55003	0.585792	0.003954	ENSG00000145012	ENST00000448637;ENST00000312675;ENST00000543006;ENST00000415906	T;T;T;T	0.54866	1.79;0.55;0.55;1.41	6.17	6.17	0.99709	.	0.188754	0.37348	N	0.002140	T	0.00012	0.0000	M	0.66939	2.045	0.22050	P	0.999392708	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.965	T	0.47611	-0.9104	9	0.15499	T	0.54	.	16.0034	0.80327	0.0:0.0:0.0:1.0	rs7645635;rs52823079;rs57290235;rs7645635	346;346	C9JUT4;Q93052	.;LPP_HUMAN	H	346;346;346;183	ENSP00000393602:Y346H;ENSP00000318089:Y346H;ENSP00000438891:Y346H;ENSP00000393008:Y183H	ENSP00000318089:Y346H	Y	+	1	0	LPP	189810249	1.000000	0.71417	0.850000	0.33497	0.194000	0.23727	5.358000	0.66064	2.371000	0.80710	0.533000	0.62120	TAT	T|0.786;C|0.214	0.214	strong		0.522	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
VN1R4	317703	hgsc.bcm.edu	37	19	53770746	53770746	+	Missense_Mutation	SNP	C	C	A	rs140031028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53770746C>A	ENST00000311170.4	-	1	226	c.173G>T	c.(172-174)cGc>cTc	p.R58L	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	58			R -> L (in allele VN1R4*4). {ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)	p.R58L(1)		central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	22				GBM - Glioblastoma multiforme(134;0.00294)		TCCTTTACAGCGGAGAGCTAA	0.453										HNSCC(26;0.072)																											p.R58L		Atlas-SNP	.											VN1R4,mouth,carcinoma,0,1	VN1R4	65	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G173T						PASS	.						37.0	38.0	38.0					19																	53770746		2203	4297	6500	SO:0001583	missense	317703	exon1			TTACAGCGGAGAG	AY114733	CCDS33099.1	19q13.42	2012-08-22			ENSG00000228567	ENSG00000228567		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19871	protein-coding gene	gene with protein product						12123587	Standard	NM_173857		Approved	V1RL4	uc010ydu.2	Q7Z5H5		ENST00000311170.4:c.173G>T	19.37:g.53770746C>A	ENSP00000310856:p.Arg58Leu	Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	301	178	0.591362	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	
TRMU	55687	hgsc.bcm.edu	37	22	46731689	46731689	+	Missense_Mutation	SNP	G	G	T	rs11090865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46731689G>T	ENST00000290846.4	+	1	368	c.28G>T	c.(28-30)Gcc>Tcc	p.A10S	TRMU_ENST00000424260.2_5'Flank|TRMU_ENST00000381019.3_Missense_Mutation_p.A10S	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	13	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	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	
BCO1	53630	hgsc.bcm.edu	37	16	81301571	81301571	+	Silent	SNP	A	A	G	rs7202895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81301571A>G	ENST00000258168.2	+	6	1139	c.678A>G	c.(676-678)ccA>ccG	p.P226P	BCMO1_ENST00000425577.2_Silent_p.P157P	NM_017429.2	NP_059125.2														breast(2)|endometrium(1)|large_intestine(4)|lung(9)|prostate(3)|skin(3)|stomach(1)	23						GCTCCATCCCATCCCGCTCCC	0.522													a|||	711	0.141973	0.4312	0.062	5008	,	,		19057	0.0099		0.0447	False		,,,				2504	0.044				p.P226P		Atlas-SNP	.											.	BCMO1	53	.	0			c.A678G						PASS	.			1551,2853	487.4+/-360.9	274,1003,925	134.0	105.0	115.0		678	-0.9	0.9	16	dbSNP_116	115	345,8255	117.2+/-176.8	11,323,3966	no	coding-synonymous	BCMO1	NM_017429.2		285,1326,4891	GG,GA,AA		4.0116,35.218,14.5801		226/548	81301571	1896,11108	2202	4300	6502	SO:0001819	synonymous_variant	53630	exon6			CATCCCATCCCGC																												ENST00000258168.2:c.678A>G	16.37:g.81301571A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	115	49	0.426087	NM_017429		Silent	SNP	ENST00000258168.2	37	CCDS10934.1																																																																																			A|0.850;G|0.150	0.150	strong		0.522	BCMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269056.1		
MYO7B	4648	hgsc.bcm.edu	37	2	128378009	128378009	+	Missense_Mutation	SNP	G	G	A	rs199900811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128378009G>A	ENST00000409816.2	+	25	3447	c.3415G>A	c.(3415-3417)Ggc>Agc	p.G1139S	MYO7B_ENST00000428314.1_Missense_Mutation_p.G1139S|MYO7B_ENST00000389524.4_Missense_Mutation_p.G1139S|MYO7B_ENST00000409090.1_5'UTR			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1139	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CCTCTGCCTCGGCTGCTTCCC	0.607													G|||	13	0.00259585	0.0098	0.0	5008	,	,		14187	0.0		0.0	False		,,,				2504	0.0				p.G1139S		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3415A						PASS	.	G	SER/GLY	30,3642		0,30,1806	33.0	36.0	35.0		3415	4.2	1.0	2		35	0,8174		0,0,4087	yes	missense	MYO7B	NM_001080527.1	56	0,30,5893	AA,AG,GG		0.0,0.817,0.2533	probably-damaging	1139/2117	128378009	30,11816	1836	4087	5923	SO:0001583	missense	4648	exon26			TGCCTCGGCTGCT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3415G>A	2.37:g.128378009G>A	ENSP00000386461:p.Gly1139Ser	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	236	120	0.508475	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	6	0.0027472527472527475	2	0.0040650406504065045	0	0.0	3	0.005244755244755245	1	0.0013192612137203166	.	26.3	4.726017	0.89298	0.00817	0.0	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.91407	-2.84;-2.84;-2.84	4.16	4.16	0.48862	MyTH4 domain (3);	0.000000	0.85682	D	0.000000	D	0.91074	0.7191	L	0.48986	1.54	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.89742	0.3934	10	0.25106	T	0.35	.	17.0488	0.86513	0.0:0.0:1.0:0.0	.	1139	Q6PIF6	MYO7B_HUMAN	S	1139	ENSP00000374175:G1139S;ENSP00000415090:G1139S;ENSP00000386461:G1139S	ENSP00000374175:G1139S	G	+	1	0	MYO7B	128094479	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	8.993000	0.93524	2.318000	0.78349	0.456000	0.33151	GGC	G|0.997;A|0.003	0.003	strong		0.607	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
SPTA1	6708	hgsc.bcm.edu	37	1	158623092	158623092	+	Missense_Mutation	SNP	T	T	A	rs145054175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158623092T>A	ENST00000368147.4	-	22	3340	c.3160A>T	c.(3160-3162)Acc>Tcc	p.T1054S		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1054					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)					TGGCGCTGGGTGATGTTTCCT	0.517													T|||	25	0.00499201	0.0182	0.0014	5008	,	,		15465	0.0		0.0	False		,,,				2504	0.0				p.T1054S		Atlas-SNP	.											SPTA1,NS,carcinoma,+1,1	SPTA1	720	1	0			c.A3160T						scavenged	.	T	SER/THR	56,3900		0,56,1922	118.0	122.0	120.0		3160	-1.3	0.2	1	dbSNP_134	120	0,8344		0,0,4172	yes	missense	SPTA1	NM_003126.2	58	0,56,6094	AA,AT,TT		0.0,1.4156,0.4553	benign	1054/2420	158623092	56,12244	1978	4172	6150	SO:0001583	missense	6708	exon22			GCTGGGTGATGTT	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.3160A>T	1.37:g.158623092T>A	ENSP00000357129:p.Thr1054Ser	Somatic	137	2	0.0145985		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	12.06	1.823290	0.32237	0.014156	0.0	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.65916	-0.18;-0.18	5.15	-1.33	0.09172	Src homology-3 domain (1);	2.011270	0.03053	N	0.154860	T	0.13457	0.0326	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.07790	-1.0754	10	0.10636	T	0.68	.	8.2403	0.31656	0.0:0.5787:0.1365:0.2848	.	1054	P02549	SPTA1_HUMAN	S	1054	ENSP00000357130:T1054S;ENSP00000357129:T1054S	ENSP00000357129:T1054S	T	-	1	0	SPTA1	156889716	0.008000	0.16893	0.150000	0.22450	0.671000	0.39405	0.091000	0.15046	-0.379000	0.07906	-1.139000	0.01908	ACC	T|0.996;A|0.004	0.004	strong		0.517	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
SIGLEC12	89858	hgsc.bcm.edu	37	19	51994926	51994926	+	Missense_Mutation	SNP	T	T	C	rs7245807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51994926T>C	ENST00000291707.3	-	8	1812	c.1757A>G	c.(1756-1758)tAt>tGt	p.Y586C	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.Y468C	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	586			Y -> C (in dbSNP:rs7245807).		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)		GGAGTACTCATAGCCGATGGC	0.572													t|||	234	0.0467252	0.1437	0.0144	5008	,	,		14528	0.0327		0.001	False		,,,				2504	0.0				p.Y586C		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.A1757G						PASS	.	T	CYS/TYR,CYS/TYR	523,3883		36,451,1716	122.0	106.0	111.0		1403,1757	-4.5	0.0	19	dbSNP_116	111	5,8595		0,5,4295	yes	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	194,194	36,456,6011	CC,CT,TT		0.0581,11.8702,4.0597	benign,benign	468/478,586/596	51994926	528,12478	2203	4300	6503	SO:0001583	missense	89858	exon8			TACTCATAGCCGA	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.1757A>G	19.37:g.51994926T>C	ENSP00000291707:p.Tyr586Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	124	71	0.572581	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	91	0.041666666666666664	66	0.13414634146341464	6	0.016574585635359115	19	0.033216783216783216	0	0.0	.	0.031	-1.337170	0.01287	0.118702	5.81E-4	ENSG00000254521	ENST00000291707	T	0.04654	3.58	2.23	-4.47	0.03525	.	.	.	.	.	T	0.00039	0.0001	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	0.39502	-0.9611	9	0.44086	T	0.13	.	0.9451	0.01364	0.1876:0.1548:0.2634:0.3942	rs7245807;rs59181054;rs7245807	586;468	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	C	586	ENSP00000291707:Y586C	ENSP00000291707:Y586C	Y	-	2	0	SIGLEC12	56686738	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.806000	0.00361	-5.302000	0.00017	-1.158000	0.01797	TAT	T|0.956;C|0.044	0.044	strong		0.572	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
LONRF2	164832	hgsc.bcm.edu	37	2	100916306	100916306	+	Silent	SNP	A	A	G	rs2033748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:100916306A>G	ENST00000393437.3	-	5	1779	c.1140T>C	c.(1138-1140)ttT>ttC	p.F380F	LONRF2_ENST00000409647.1_Silent_p.F137F	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	380							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						TATCCTCTTCAAAGTGTAGAC	0.418													A|||	3863	0.771366	0.8911	0.7349	5008	,	,		13826	0.9405		0.673	False		,,,				2504	0.5624				p.F380F		Atlas-SNP	.											.	LONRF2	62	.	0			c.T1140C						PASS	.	A		3669,737	757.4+/-412.7	1525,619,59	69.0	67.0	68.0		1140	-4.1	0.0	2	dbSNP_94	68	5543,3057	662.6+/-402.0	1797,1949,554	no	coding-synonymous	LONRF2	NM_198461.3		3322,2568,613	GG,GA,AA		35.5465,16.7272,29.1712		380/755	100916306	9212,3794	2203	4300	6503	SO:0001819	synonymous_variant	164832	exon5			CTCTTCAAAGTGT	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"""RING-type (C3HC4) zinc fingers"""	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1140T>C	2.37:g.100916306A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_198461	B9A006|Q6ZSR4	Silent	SNP	ENST00000393437.3	37	CCDS2046.2																																																																																			A|0.270;G|0.730	0.730	strong		0.418	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461	
PTPN7	5778	hgsc.bcm.edu	37	1	202129826	202129826	+	5'Flank	SNP	T	T	C	rs4309039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:202129826T>C	ENST00000308986.5	-	0	0				PTPN7_ENST00000544762.1_5'Flank|PTPN7_ENST00000309017.3_Missense_Mutation_p.Q37R|PTPN7_ENST00000543735.1_5'Flank|PTPN7_ENST00000492977.1_5'Flank|PTPN7_ENST00000367279.4_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	175	0	0		WXS	Illumina HiSeq	Phase_I	162	73	0.450617	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	
DNAH10	196385	hgsc.bcm.edu	37	12	124401117	124401117	+	Silent	SNP	C	C	T	rs61749063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124401117C>T	ENST00000409039.3	+	62	10507	c.10482C>T	c.(10480-10482)aaC>aaT	p.N3494N		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3494	AAA 5. {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)		TGATTGACAACGTCTTAGAAA	0.428													c|||	327	0.0652955	0.2322	0.0231	5008	,	,		21228	0.0		0.003	False		,,,				2504	0.001				p.N3494N		Atlas-SNP	.											.	DNAH10	888	.	0			c.C10482T						PASS	.	T		695,3101		58,579,1261	95.0	95.0	95.0		10482	-6.3	0.0	12	dbSNP_129	95	41,8179		1,39,4070	no	coding-synonymous	DNAH10	NM_207437.3		59,618,5331	TT,TC,CC		0.4988,18.3087,6.1252		3494/4472	124401117	736,11280	1898	4110	6008	SO:0001819	synonymous_variant	196385	exon62			TGACAACGTCTTA	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.10482C>T	12.37:g.124401117C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.957;T|0.043	0.043	strong		0.428	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
PRNP	5621	hgsc.bcm.edu	37	20	4680217	4680217	+	Silent	SNP	A	A	G	rs8124214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:4680217A>G	ENST00000379440.4	+	2	638	c.351A>G	c.(349-351)gcA>gcG	p.A117A	PRNP_ENST00000430350.2_Silent_p.A117A	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)				central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	14						GTGCTGCAGCAGCTGGGGCAG	0.577													A|||	195	0.0389377	0.0961	0.0274	5008	,	,		17693	0.0		0.0328	False		,,,				2504	0.0164				p.A117A		Atlas-SNP	.											.	PRNP	31	.	0			c.A351G						PASS	.	A	,,,,	360,4042		16,328,1857	56.0	48.0	51.0		351,351,351,351,351	-10.4	0.1	20	dbSNP_116	51	286,8310		5,276,4017	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRNP	NM_000311.3,NM_001080121.1,NM_001080122.1,NM_001080123.1,NM_183079.2	,,,,	21,604,5874	GG,GA,AA		3.3271,8.1781,4.97	,,,,	117/254,117/254,117/254,117/254,117/254	4680217	646,12352	2201	4298	6499	SO:0001819	synonymous_variant	5621	exon2			TGCAGCAGCTGGG	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.351A>G	20.37:g.4680217A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	127	70	0.551181	NM_000311		Silent	SNP	ENST00000379440.4	37	CCDS13080.1																																																																																			A|0.956;G|0.044	0.044	strong		0.577	PRNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077820.2	NM_000311	
PDIA6	10130	hgsc.bcm.edu	37	2	10942687	10942687	+	Silent	SNP	C	C	T	rs4758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10942687C>T	ENST00000272227.3	-	2	246	c.99G>A	c.(97-99)tcG>tcA	p.S33S	PDIA6_ENST00000404371.2_Silent_p.S85S|PDIA6_ENST00000404824.2_Silent_p.S81S|PDIA6_ENST00000540494.1_Silent_p.S30S|PDIA6_ENST00000489662.1_5'UTR|PDIA6_ENST00000381611.4_Silent_p.S38S	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	33	Thioredoxin 1. {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)		GGTTGAAATTCGATGGAGTTA	0.358													T|||	2303	0.459864	0.1989	0.5245	5008	,	,		19515	0.4613		0.5835	False		,,,				2504	0.638				p.S33S	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											.	PDIA6	31	.	0			c.G99A						PASS	.	T		1192,3214	710.4+/-407.9	179,834,1190	91.0	84.0	86.0		99	-6.5	0.8	2	dbSNP_52	86	5117,3483	510.2+/-377.4	1506,2105,689	no	coding-synonymous	PDIA6	NM_005742.2		1685,2939,1879	TT,TC,CC		40.5,27.054,48.5084		33/441	10942687	6309,6697	2203	4300	6503	SO:0001819	synonymous_variant	10130	exon2			GAAATTCGATGGA	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.99G>A	2.37:g.10942687C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	175	87	0.497143	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	37	CCDS1675.1																																																																																			C|0.523;T|0.477	0.477	strong		0.358	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742	
SDR42E1	93517	hgsc.bcm.edu	37	16	82034435	82034435	+	Missense_Mutation	SNP	C	C	G	rs6564956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:82034435C>G	ENST00000328945.5	-	2	156	c.29G>C	c.(28-30)aGt>aCt	p.S10T	SDR42E1_ENST00000534209.1_5'UTR	NM_145168.2	NP_660151.2	Q8WUS8	D42E1_HUMAN	short chain dehydrogenase/reductase family 42E, member 1	10			S -> T (in dbSNP:rs6564956).		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						AATGAGGACACTTTCCTTTTG	0.383													G|||	717	0.143171	0.4198	0.0389	5008	,	,		20442	0.0516		0.005	False		,,,				2504	0.0798				p.S10T		Atlas-SNP	.											.	SDR42E1	26	.	0			c.G29C						PASS	.	G	THR/SER	1212,2514		204,804,855	87.0	88.0	87.0		29	2.5	0.1	16	dbSNP_116	87	68,8134		0,68,4033	yes	missense	SDR42E1	NM_145168.2	58	204,872,4888	GG,GC,CC		0.8291,32.5282,10.7311	benign	10/394	82034435	1280,10648	1863	4101	5964	SO:0001583	missense	93517	exon2			AGGACACTTTCCT	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.29G>C	16.37:g.82034435C>G	ENSP00000332407:p.Ser10Thr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_145168	B2RDS1|Q9P0D1	Missense_Mutation	SNP	ENST00000328945.5	37	CCDS42205.1	228	0.1043956043956044	198	0.4024390243902439	12	0.03314917127071823	16	0.027972027972027972	2	0.002638522427440633	G	0.018	-1.478217	0.01035	0.325282	0.008291	ENSG00000184860	ENST00000328945	D	0.86769	-2.17	5.59	2.47	0.30058	NAD(P)-binding domain (1);	0.307447	0.39475	N	0.001352	T	0.00012	0.0000	N	0.04724	-0.175	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08785	-1.0705	9	0.06891	T	0.86	-2.5276	9.095	0.36634	0.1292:0.3298:0.541:0.0	rs6564956;rs52804854;rs57510790;rs6564956	10	Q8WUS8	D42E1_HUMAN	T	10	ENSP00000332407:S10T	ENSP00000332407:S10T	S	-	2	0	SDR42E1	80591936	0.025000	0.19082	0.098000	0.21074	0.467000	0.32768	0.397000	0.20883	0.286000	0.22352	-0.127000	0.14921	AGT	C|0.924;G|0.076	0.076	strong		0.383	SDR42E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388081.2	NM_145168	
XRCC1	7515	hgsc.bcm.edu	37	19	44047550	44047550	+	Silent	SNP	T	T	C	rs3547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44047550T>C	ENST00000262887.5	-	17	2443	c.1896A>G	c.(1894-1896)caA>caG	p.Q632Q	XRCC1_ENST00000543982.1_Silent_p.Q601Q			P18887	XRCC1_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 1	632					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|hippocampus development (GO:0021766)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to organic substance (GO:0010033)|single strand break repair (GO:0000012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Prostate(69;0.0153)				TACTTCAGGCTTGCGGCACCA	0.493								Other BER factors					C|||	3559	0.710663	0.674	0.7853	5008	,	,		15005	0.8849		0.5934	False		,,,				2504	0.6483				p.Q632Q		Atlas-SNP	.											.	XRCC1	47	.	0			c.A1896G						PASS	.	C		2878,1528	483.9+/-359.9	933,1012,258	96.0	83.0	87.0		1896	2.7	1.0	19	dbSNP_36	87	5023,3577	518.4+/-379.2	1466,2091,743	no	coding-synonymous	XRCC1	NM_006297.2		2399,3103,1001	CC,CT,TT		41.593,34.68,39.2511		632/634	44047550	7901,5105	2203	4300	6503	SO:0001819	synonymous_variant	7515	exon17			TCAGGCTTGCGGC	M36089	CCDS12624.1	19q13.2	2014-09-17				ENSG00000073050			12828	protein-coding gene	gene with protein product		194360		RCC		2247054	Standard	NM_006297		Approved		uc002owt.2	P18887		ENST00000262887.5:c.1896A>G	19.37:g.44047550T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_006297	Q6IBS4|Q9HCB1	Silent	SNP	ENST00000262887.5	37	CCDS12624.1																																																																																			T|0.344;C|0.656	0.656	strong		0.493	XRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463194.1	NM_006297	
TCF20	6942	hgsc.bcm.edu	37	22	42610099	42610099	+	Missense_Mutation	SNP	T	T	C	rs34030679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42610099T>C	ENST00000359486.3	-	1	1349	c.1213A>G	c.(1213-1215)Atg>Gtg	p.M405V	TCF20_ENST00000335626.4_Missense_Mutation_p.M405V	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	405			M -> V (in dbSNP:rs34030679).		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						CTGGAACCCATAGGCACACTG	0.502													T|||	431	0.0860623	0.1324	0.062	5008	,	,		21046	0.0308		0.0815	False		,,,				2504	0.1022				p.M405V		Atlas-SNP	.											.	TCF20	164	.	0			c.A1213G						PASS	.	T	VAL/MET,VAL/MET	607,3799	264.7+/-266.2	45,517,1641	131.0	129.0	130.0		1213,1213	3.7	1.0	22	dbSNP_126	130	788,7812	186.4+/-233.9	41,706,3553	yes	missense,missense	TCF20	NM_005650.1,NM_181492.1	21,21	86,1223,5194	CC,CT,TT		9.1628,13.7767,10.7258	benign,benign	405/1961,405/1939	42610099	1395,11611	2203	4300	6503	SO:0001583	missense	6942	exon1			AACCCATAGGCAC	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.1213A>G	22.37:g.42610099T>C	ENSP00000352463:p.Met405Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	164	88	0.536585	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	37	CCDS14033.1	161	0.07371794871794872	67	0.13617886178861788	26	0.0718232044198895	12	0.02097902097902098	56	0.07387862796833773	T	0.009	-1.837371	0.00573	0.137767	0.091628	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.30448	1.53;1.53	5.95	3.74	0.42951	.	0.186652	0.48767	N	0.000178	T	0.00144	0.0004	L	0.40543	1.245	0.09310	P	0.9999999999668289	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20306	-1.0279	9	0.02654	T	1	-1.6351	5.6675	0.17702	0.0:0.1404:0.2615:0.5981	rs34030679	405;405	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	V	405	ENSP00000352463:M405V;ENSP00000335561:M405V	ENSP00000335561:M405V	M	-	1	0	TCF20	40940043	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.197000	0.32211	1.084000	0.41184	0.533000	0.62120	ATG	T|0.901;C|0.099	0.099	strong		0.502	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
PTGFR	5737	hgsc.bcm.edu	37	1	78959081	78959081	+	Missense_Mutation	SNP	T	T	C	rs115994459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:78959081T>C	ENST00000370757.3	+	2	890	c.653T>C	c.(652-654)tTg>tCg	p.L218S	PTGFR_ENST00000370758.1_Missense_Mutation_p.L218S|PTGFR_ENST00000370756.3_Missense_Mutation_p.L218S	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	218					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)			breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	GTTTCATTGTTGTGCAATGCA	0.378													T|||	22	0.00439297	0.0129	0.0058	5008	,	,		20200	0.0		0.001	False		,,,				2504	0.0				p.L218S		Atlas-SNP	.											.	PTGFR	121	.	0			c.T653C						PASS	.	T	SER/LEU,SER/LEU	58,4348	58.1+/-94.6	1,56,2146	62.0	65.0	64.0		653,653	4.7	0.6	1	dbSNP_132	64	0,8600		0,0,4300	yes	missense,missense	PTGFR	NM_000959.3,NM_001039585.1	145,145	1,56,6446	CC,CT,TT		0.0,1.3164,0.4459	benign,benign	218/360,218/298	78959081	58,12948	2203	4300	6503	SO:0001583	missense	5737	exon2			CATTGTTGTGCAA	AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"""GPCR / Class A : Prostanoid receptors"""	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.653T>C	1.37:g.78959081T>C	ENSP00000359793:p.Leu218Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	142	61	0.429577	NM_000959	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Missense_Mutation	SNP	ENST00000370757.3	37	CCDS686.1	9	0.004120879120879121	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	12.84	2.059053	0.36373	0.013164	0.0	ENSG00000122420	ENST00000370758;ENST00000370757;ENST00000370756	T;T;T	0.38887	1.11;1.11;1.11	5.85	4.73	0.59995	GPCR, rhodopsin-like superfamily (1);	0.414998	0.24801	N	0.035481	T	0.12817	0.0311	N	0.16903	0.455	0.34244	D	0.677948	B;B	0.16166	0.001;0.016	B;B	0.17433	0.008;0.018	T	0.05784	-1.0864	10	0.33940	T	0.23	-2.4004	11.3546	0.49609	0.0:0.0715:0.0:0.9285	.	218;218	P43088;P43088-2	PF2R_HUMAN;.	S	218	ENSP00000359794:L218S;ENSP00000359793:L218S;ENSP00000359792:L218S	ENSP00000359792:L218S	L	+	2	0	PTGFR	78731669	1.000000	0.71417	0.551000	0.28230	0.878000	0.50629	3.960000	0.56752	1.168000	0.42723	0.533000	0.62120	TTG	T|0.995;C|0.005	0.005	strong		0.378	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959	
CEMP1	752014	hgsc.bcm.edu	37	16	2580912	2580912	+	Missense_Mutation	SNP	T	T	C	rs13331643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2580912T>C	ENST00000567119.1	-	1	497	c.163A>G	c.(163-165)Aag>Gag	p.K55E	CEMP1_ENST00000565480.1_Intron|CEMP1_ENST00000382350.1_Missense_Mutation_p.K55E|AMDHD2_ENST00000413459.3_3'UTR|AMDHD2_ENST00000302956.4_3'UTR|AMDHD2_ENST00000565570.1_3'UTR|MIR3178_ENST00000581887.1_RNA	NM_001048212.3	NP_001041677.1	Q6PRD7	CEMP1_HUMAN	cementum protein 1	55			K -> E (in dbSNP:rs13331643).			cytoplasm (GO:0005737)				lung(1)|skin(1)	2						GCGCACCCCTTAGGAAGTGGC	0.657													C|||	358	0.0714856	0.2564	0.0231	5008	,	,		20272	0.0		0.002	False		,,,				2504	0.001				p.K55E		Atlas-SNP	.											.	CEMP1	17	.	0			c.A163G						PASS	.	C	,GLU/LYS	839,3203		88,663,1270	36.0	42.0	40.0		,163	-0.1	0.0	16	dbSNP_121	40	12,8334		0,12,4161	yes	utr-3,missense	AMDHD2,CEMP1	NM_001145815.1,NM_001048212.3	,56	88,675,5431	CC,CT,TT		0.1438,20.7571,6.8696	,benign	,55/248	2580912	851,11537	2021	4173	6194	SO:0001583	missense	752014	exon1			ACCCCTTAGGAAG	AY584596	CCDS42108.1	16p13.3	2006-09-22							32553	protein-coding gene	gene with protein product	"""cementum protein-23"""	611113				16263347	Standard	NM_001048212		Approved	CP-23	uc002cqr.3	Q6PRD7		ENST00000567119.1:c.163A>G	16.37:g.2580912T>C	ENSP00000457380:p.Lys55Glu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_001048212	B2RUY1	Missense_Mutation	SNP	ENST00000567119.1	37	CCDS42108.1	124	0.056776556776556776	118	0.23983739837398374	6	0.016574585635359115	0	0.0	0	0.0	C	4.436	0.080653	0.08533	0.207571	0.001438	ENSG00000205923	ENST00000382350	T	0.54675	0.56	0.977	-0.126	0.13515	.	.	.	.	.	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	0.18681	-1.0329	8	0.87932	D	0	.	1.8024	0.03073	0.3218:0.4366:0.0:0.2416	rs13331643;rs13331643	55	Q6PRD7	CEMP1_HUMAN	E	55	ENSP00000371787:K55E	ENSP00000371787:K55E	K	-	1	0	CEMP1	2520913	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.745000	0.04834	-0.526000	0.06383	-1.124000	0.02001	AAG	T|0.955;C|0.045	0.045	strong		0.657	CEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435686.1	NM_001048212	
KIF5C	3800	hgsc.bcm.edu	37	2	149799216	149799216	+	Silent	SNP	T	T	C	rs61734995	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	138	0	0		WXS	Illumina HiSeq	Phase_I	113	37	0.327434	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	
CGN	57530	hgsc.bcm.edu	37	1	151496718	151496718	+	Missense_Mutation	SNP	C	C	T	rs16833336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151496718C>T	ENST00000271636.7	+	7	1418	c.1285C>T	c.(1285-1287)Cgc>Tgc	p.R429C		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	423	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GAACATGAAGCGCCTCTTGGA	0.433													C|||	189	0.0377396	0.1377	0.0058	5008	,	,		20806	0.0		0.003	False		,,,				2504	0.0				p.R429C		Atlas-SNP	.											CGN,colon,carcinoma,-1,2	CGN	106	2	0			c.C1285T						PASS	.	C	CYS/ARG	482,3924	225.6+/-241.4	29,424,1750	72.0	67.0	69.0		1285	4.0	1.0	1	dbSNP_123	69	6,8594	4.3+/-15.6	0,6,4294	yes	missense	CGN	NM_020770.2	180	29,430,6044	TT,TC,CC		0.0698,10.9396,3.7521	benign	429/1204	151496718	488,12518	2203	4300	6503	SO:0001583	missense	57530	exon7			ATGAAGCGCCTCT	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.1285C>T	1.37:g.151496718C>T	ENSP00000271636:p.Arg429Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	79	0.036172161172161175	77	0.1565040650406504	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	15.65	2.896561	0.52121	0.109396	6.98E-4	ENSG00000143375	ENST00000271636	T	0.63417	-0.04	4.95	4.02	0.46733	.	0.429980	0.25004	N	0.033881	T	0.19248	0.0462	N	0.08118	0	0.26850	N	0.96819	P	0.46327	0.876	B	0.34452	0.183	T	0.04781	-1.0927	10	0.72032	D	0.01	0.3796	10.5107	0.44860	0.1942:0.8058:0.0:0.0	rs16833336;rs16833336	423	Q9P2M7	CING_HUMAN	C	429	ENSP00000271636:R429C	ENSP00000271636:R429C	R	+	1	0	CGN	149763342	0.706000	0.27856	0.997000	0.53966	0.893000	0.52053	0.899000	0.28417	1.041000	0.40125	0.491000	0.48974	CGC	C|0.961;T|0.039	0.039	strong		0.433	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
CD109	135228	hgsc.bcm.edu	37	6	74521948	74521948	+	Silent	SNP	G	G	T	rs61063525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74521948G>T	ENST00000287097.5	+	29	3835	c.3723G>T	c.(3721-3723)acG>acT	p.T1241T	CD109_ENST00000422508.2_Silent_p.T1164T|CD109_ENST00000437994.2_Silent_p.T1224T			Q6YHK3	CD109_HUMAN	CD109 molecule	1241			T -> M (in dbSNP:rs2917862). {ECO:0000269|PubMed:11861284, 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						TACAGCCAACGGCAGTTAATA	0.328													T|||	132	0.0263578	0.0953	0.0086	5008	,	,		20405	0.0		0.0	False		,,,				2504	0.0				p.T1241T		Atlas-SNP	.											.	CD109	170	.	0			c.G3723T						PASS	.	T	,,	324,4082	796.3+/-415.4	13,298,1892	146.0	139.0	142.0		3672,3492,3723	0.0	0.0	6	dbSNP_129	142	5,8595	818.7+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	,,	13,303,6187	TT,TG,GG		0.0581,7.3536,2.5296	,,	1224/1429,1164/1369,1241/1446	74521948	329,12677	2203	4300	6503	SO:0001819	synonymous_variant	135228	exon29			GCCAACGGCAGTT	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.3723G>T	6.37:g.74521948G>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	193	84	0.435233	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																			G|0.971;T|0.029	0.029	strong		0.328	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
PDZRN4	29951	hgsc.bcm.edu	37	12	41966699	41966699	+	Silent	SNP	A	A	G	rs78683283	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:41966699A>G	ENST00000402685.2	+	10	2126	c.2118A>G	c.(2116-2118)ggA>ggG	p.G706G	PDZRN4_ENST00000298919.7_Silent_p.G446G|PDZRN4_ENST00000539469.2_Silent_p.G448G	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	706							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				ATGATGGAGGATTCCGGAATT	0.443													A|||	140	0.0279553	0.0378	0.0086	5008	,	,		22417	0.0585		0.0139	False		,,,				2504	0.0112				p.G706G		Atlas-SNP	.											.	PDZRN4	346	.	0			c.A2118G						PASS	.	A	,	191,4215	121.7+/-159.2	7,177,2019	99.0	100.0	99.0		2118,1344	-3.1	1.0	12	dbSNP_131	99	123,8477	64.2+/-126.4	1,121,4178	no	coding-synonymous,coding-synonymous	PDZRN4	NM_001164595.1,NM_013377.3	,	8,298,6197	GG,GA,AA		1.4302,4.335,2.4143	,	706/1037,448/779	41966699	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	29951	exon10			TGGAGGATTCCGG	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2118A>G	12.37:g.41966699A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	37	CCDS53777.1																																																																																			A|0.974;G|0.026	0.026	strong		0.443	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
OGT	8473	hgsc.bcm.edu	37	X	70777435	70777435	+	Silent	SNP	G	G	A	rs34739713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70777435G>A	ENST00000373719.3	+	12	1732	c.1515G>A	c.(1513-1515)gtG>gtA	p.V505V	OGT_ENST00000373701.3_Silent_p.V495V	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	505					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					TGCCTTCTGTGCATCCTCATC	0.433													G|||	160	0.0423841	0.1127	0.0144	3775	,	,		14352	0.0		0.001	False		,,,				2504	0.0				p.V505V		Atlas-SNP	.											.	OGT	207	.	0			c.G1515A						PASS	.	G	,	533,3302		27,404,75,1201,496	158.0	104.0	122.0		1515,1485	1.5	1.0	X	dbSNP_126	122	2,6726		0,2,0,2426,1872	no	coding-synonymous,coding-synonymous	OGT	NM_181672.2,NM_181673.2	,	27,406,75,3627,2368	AA,AG,A,GG,G		0.0297,13.8983,5.0648	,	505/1047,495/1037	70777435	535,10028	2203	4300	6503	SO:0001819	synonymous_variant	8473	exon12			TTCTGTGCATCCT	U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"""Tetratricopeptide (TTC) repeat domain containing"""	8127	protein-coding gene	gene with protein product	"""UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"""	300255	"""O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"""			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.1515G>A	X.37:g.70777435G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	185	90	0.486486	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Silent	SNP	ENST00000373719.3	37	CCDS14414.1																																																																																			G|0.947;A|0.053	0.053	strong		0.433	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672	
WDR64	128025	hgsc.bcm.edu	37	1	241886717	241886717	+	Silent	SNP	C	C	T	rs10926547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241886717C>T	ENST00000366552.2	+	9	1350	c.1143C>T	c.(1141-1143)gtC>gtT	p.V381V	WDR64_ENST00000437684.2_Silent_p.V381V	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	381										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			ATCAACATGTCGTCAGCCTTT	0.403													c|||	332	0.0662939	0.2405	0.0159	5008	,	,		19323	0.0		0.003	False		,,,				2504	0.0				p.V381V		Atlas-SNP	.											.	WDR64	234	.	0			c.C1143T						PASS	.	G		976,3430	366.1+/-317.7	123,730,1350	84.0	79.0	81.0		1143	-0.9	0.4	1	dbSNP_120	81	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	WDR64	NM_144625.4		123,737,5643	TT,TC,CC		0.0814,22.1516,7.5581		381/1082	241886717	983,12023	2203	4300	6503	SO:0001819	synonymous_variant	128025	exon9			ACATGTCGTCAGC	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"""WD repeat domain containing"""	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1143C>T	1.37:g.241886717C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	134	56	0.41791	NM_144625	B1ANT0|Q7Z573|Q96LY9	Silent	SNP	ENST00000366552.2	37																																																																																				C|0.922;T|0.078	0.078	strong		0.403	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625	
FTHL17	53940	hgsc.bcm.edu	37	X	31089629	31089629	+	Nonsense_Mutation	SNP	C	C	A	rs7057057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:31089629C>A	ENST00000359202.3	-	1	541	c.442G>T	c.(442-444)Gag>Tag	p.E148*		NM_031894.2	NP_114100.1	Q9BXU8	FHL17_HUMAN	ferritin, heavy polypeptide-like 17	148	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)		ferric iron binding (GO:0008199)			endometrium(2)|large_intestine(2)|liver(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	23						CCACCCAGCTCTTTGATGGTC	0.617													C|||	228	0.0603974	0.0129	0.0	3775	,	,		13756	0.1101		0.001	False		,,,				2504	0.1012				p.E148X		Atlas-SNP	.											.	FTHL17	99	.	0			c.G442T						PASS	.	C	stop/GLU	66,3767		1,58,6,1572,565	72.0	61.0	65.0		442	1.8	0.0	X	dbSNP_116	65	4,6724		0,3,1,2425,1871	yes	stop-gained	FTHL17	NM_031894.2		1,61,7,3997,2436	AA,AC,A,CC,C		0.0595,1.7219,0.6628		148/184	31089629	70,10491	2202	4300	6502	SO:0001587	stop_gained	53940	exon1			CCAGCTCTTTGAT	AF285592	CCDS14227.1	Xp21.2	2010-07-06			ENSG00000132446	ENSG00000132446			3987	protein-coding gene	gene with protein product	"""cancer/testis antigen 38"""	300308				11279525	Standard	NM_031894		Approved	CT38	uc004dcl.1	Q9BXU8	OTTHUMG00000021332	ENST00000359202.3:c.442G>T	X.37:g.31089629C>A	ENSP00000368207:p.Glu148*	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	194	109	0.561856	NM_031894	Q6NT24|Q6NTE2	Nonsense_Mutation	SNP	ENST00000359202.3	37	CCDS14227.1	72	0.0433996383363472	7	0.014462809917355372	0	0.0	37	0.07142857142857142	1	0.0013192612137203166	C	16.88	3.245665	0.59103	0.017219	5.95E-4	ENSG00000132446	ENST00000359202	.	.	.	3.67	1.78	0.24846	.	0.182095	0.47852	D	0.000214	.	.	.	.	.	.	0.09310	P	0.999999999993751	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	.	10.7889	0.46422	0.0:0.6803:0.3197:0.0	rs7057057	.	.	.	X	148	.	ENSP00000368207:E148X	E	-	1	0	FTHL17	30999550	0.006000	0.16342	0.016000	0.15963	0.017000	0.09413	0.069000	0.14552	0.335000	0.23614	0.544000	0.68410	GAG	C|0.982;A|0.018	0.018	strong		0.617	FTHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056178.1	NM_031894	
CYP2D6	1565	hgsc.bcm.edu	37	22	42523558	42523558	+	Missense_Mutation	SNP	T	T	C	rs202102799		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42523558T>C	ENST00000360608.5	-	7	1178	c.1064A>G	c.(1063-1065)tAc>tGc	p.Y355C	NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.Y355C|CYP2D6_ENST00000359033.4_Missense_Mutation_p.Y304C|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	355					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GGCAGTGGTGTAGGGCATGTG	0.607																																					p.Y355C		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,2	CYP2D6	104	2	0			c.A1064G						scavenged	.						106.0	82.0	90.0					22																	42523558		2202	4300	6502	SO:0001583	missense	1565	exon7			GTGGTGTAGGGCA	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1064A>G	22.37:g.42523558T>C	ENSP00000353820:p.Tyr355Cys	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	228	11	0.0482456	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.884011	0.51908	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.76186	-1.0;-1.0;-1.0	4.93	-8.43	0.00953	.	0.656947	0.15234	N	0.273223	D	0.88265	0.6390	H	0.96518	3.835	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.81914	0.995;0.976;0.995	D	0.91542	0.5250	10	0.87932	D	0	.	18.217	0.89889	0.1595:0.0:0.0:0.8405	.	355;304;355	C1ID54;Q6NXU8;Q6NWU0	.;.;.	C	355;355;301;304;304	ENSP00000353820:Y355C;ENSP00000374620:Y355C;ENSP00000351927:Y304C	ENSP00000351927:Y304C	Y	-	2	0	CYP2D6	40853502	0.995000	0.38212	0.872000	0.34217	0.407000	0.30961	0.270000	0.18607	-1.565000	0.01676	-0.509000	0.04479	TAC	T|0.999;C|0.001	0.001	weak		0.607	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
FLG	2312	hgsc.bcm.edu	37	1	152276603	152276603	+	Missense_Mutation	SNP	C	C	T	rs111939167		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276603C>T	ENST00000368799.1	-	3	10794	c.10759G>A	c.(10759-10761)Ggt>Agt	p.G3587S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3587	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)			TGCCCGTGACCGGCTCTGTCT	0.562									Ichthyosis																												p.G3587S		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.G10759A						PASS	.						176.0	237.0	216.0					1																	152276603		2200	4294	6494	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGTGACCGGCTCT	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.10759G>A	1.37:g.152276603C>T	ENSP00000357789:p.Gly3587Ser	Somatic	609	0	0		WXS	Illumina HiSeq	Phase_I	581	297	0.511188	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	3.513	-0.099425	0.07010	.	.	ENSG00000143631	ENST00000368799	T	0.00902	5.56	3.24	-6.48	0.01896	.	.	.	.	.	T	0.00144	0.0004	N	0.25890	0.77	0.09310	N	1	P	0.47106	0.89	B	0.41646	0.362	T	0.48790	-0.9004	9	0.05436	T	0.98	.	1.8762	0.03219	0.2398:0.387:0.2291:0.1442	.	3587	P20930	FILA_HUMAN	S	3587	ENSP00000357789:G3587S	ENSP00000357789:G3587S	G	-	1	0	FLG	150543227	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.237000	0.00545	-3.276000	0.00198	-0.507000	0.04495	GGT	T|1.000;|0.000	1.000	weak		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
BRD4	23476	hgsc.bcm.edu	37	19	15355540	15355540	+	Missense_Mutation	SNP	G	G	A	rs149185763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15355540G>A	ENST00000263377.2	-	12	2413	c.2192C>T	c.(2191-2193)cCc>cTc	p.P731L		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	731					cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			CTCCCTCCCGGGGTGCCCCTT	0.582			T	C15orf55	lethal midline carcinoma of young people								G|||	13	0.00259585	0.0098	0.0	5008	,	,		13894	0.0		0.0	False		,,,				2504	0.0				p.P731L		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.C2192T						PASS	.	G	LEU/PRO	16,4390	23.3+/-48.9	0,16,2187	144.0	141.0	142.0		2192	3.4	0.8	19	dbSNP_134	142	0,8600		0,0,4300	yes	missense	BRD4	NM_058243.2	98	0,16,6487	AA,AG,GG		0.0,0.3631,0.123	probably-damaging	731/1363	15355540	16,12990	2203	4300	6503	SO:0001583	missense	23476	exon12			CTCCCGGGGTGCC	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"""chromosome-associated protein"""	608749	"""bromodomain-containing 4"""			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.2192C>T	19.37:g.15355540G>A	ENSP00000263377:p.Pro731Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	37	CCDS12328.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	14.84	2.654846	0.47467	0.003631	0.0	ENSG00000141867	ENST00000263377	T	0.07216	3.21	4.48	3.43	0.39272	.	1.004540	0.08020	N	0.991771	T	0.08980	0.0222	L	0.36672	1.1	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.07751	-1.0756	10	0.42905	T	0.14	-1.3945	10.1453	0.42760	0.1003:0.0:0.8997:0.0	.	731	O60885	BRD4_HUMAN	L	731	ENSP00000263377:P731L	ENSP00000263377:P731L	P	-	2	0	BRD4	15216540	1.000000	0.71417	0.803000	0.32268	0.934000	0.57294	6.710000	0.74670	0.868000	0.35678	0.561000	0.74099	CCC	A|0.001;G|0.999	0.001	strong		0.582	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243	
CSMD2	114784	hgsc.bcm.edu	37	1	34174737	34174737	+	Silent	SNP	A	A	G	rs10914765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:34174737A>G	ENST00000373380.1	-	1	367	c.147T>C	c.(145-147)atT>atC	p.I49I	CSMD2_ENST00000373381.4_Silent_p.I1176I|CSMD2_ENST00000373388.2_5'UTR			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1136	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CTTTCAGCTGAATTCCCTTCC	0.453													A|||	205	0.0409345	0.087	0.0101	5008	,	,		20724	0.0		0.001	False		,,,				2504	0.0838				p.I1136I		Atlas-SNP	.											.	CSMD2	946	.	0			c.T3408C						PASS	.	A		313,4093	170.1+/-200.6	10,293,1900	132.0	124.0	127.0		3408	4.4	1.0	1	dbSNP_120	127	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CSMD2	NM_052896.3		10,297,6196	GG,GA,AA		0.0465,7.1039,2.4373		1136/3488	34174737	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	114784	exon22			CAGCTGAATTCCC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.147T>C	1.37:g.34174737A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373380.1	37																																																																																				A|0.972;G|0.028	0.028	strong		0.453	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	
CYP2C8	1558	hgsc.bcm.edu	37	10	96818106	96818106	+	Missense_Mutation	SNP	T	T	A	rs11572103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:96818106T>A	ENST00000371270.3	-	5	899	c.805A>T	c.(805-807)Atc>Ttc	p.I269F	CYP2C8_ENST00000539050.1_Missense_Mutation_p.I183F|CYP2C8_ENST00000535898.1_Missense_Mutation_p.I167F	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	269			I -> F (in allele CYP2C8*2; only found in African-Americans; dbSNP:rs11572103). {ECO:0000269|PubMed:11668219, ECO:0000269|PubMed:12429347, ECO:0000269|PubMed:15469410, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	TCCATTTTGATCAGGAAGCAA	0.358													T|||	274	0.0547125	0.1891	0.0115	5008	,	,		17668	0.0		0.004	False		,,,				2504	0.0123				p.I269F		Atlas-SNP	.											.	CYP2C8	73	.	0			c.A805T	GRCh37	CM016067	CYP2C8	M	rs11572103	PASS	.	T	PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE	690,3716	289.5+/-280.5	68,554,1581	156.0	139.0	145.0		805,595,499,595	4.2	0.8	10	dbSNP_120	145	30,8570	21.0+/-64.5	0,30,4270	yes	missense,missense,missense,missense	CYP2C8	NM_000770.3,NM_001198853.1,NM_001198854.1,NM_001198855.1	21,21,21,21	68,584,5851	AA,AT,TT		0.3488,15.6605,5.5359	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	269/491,199/421,167/389,199/421	96818106	720,12286	2203	4300	6503	SO:0001583	missense	1558	exon5			TTTTGATCAGGAA	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"""Cytochrome P450s"""	2622	protein-coding gene	gene with protein product		601129	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"""			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.805A>T	10.37:g.96818106T>A	ENSP00000360317:p.Ile269Phe	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	85	0.03891941391941392	82	0.16666666666666666	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	13.62	2.290753	0.40494	0.156605	0.003488	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.68624	-0.34;-0.34;-0.34	4.17	4.17	0.49024	.	0.225081	0.35235	U	0.003341	T	0.00524	0.0017	M	0.66378	2.025	0.23903	P	0.99651506	P;D;D;D	0.59767	0.898;0.961;0.986;0.961	P;P;P;P	0.57101	0.622;0.675;0.795;0.813	T	0.32134	-0.9918	9	0.72032	D	0.01	.	11.4277	0.50020	0.0:0.0:0.0:1.0	rs11572103;rs52833642;rs58027822;rs11572103	183;167;237;269	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	F	269;236;167;183	ENSP00000360317:I269F;ENSP00000445062:I167F;ENSP00000442343:I183F	ENSP00000360317:I269F	I	-	1	0	CYP2C8	96808096	0.980000	0.34600	0.793000	0.32043	0.156000	0.22039	1.316000	0.33620	1.642000	0.50584	0.254000	0.18369	ATC	T|0.950;A|0.050	0.050	strong		0.358	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770	
NCOA5	57727	hgsc.bcm.edu	37	20	44691350	44691350	+	Silent	SNP	T	T	G	rs1537028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	304	0	0		WXS	Illumina HiSeq	Phase_I	273	124	0.454212	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	
RREB1	6239	hgsc.bcm.edu	37	6	7231736	7231736	+	Missense_Mutation	SNP	G	G	T	rs116295722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7231736G>T	ENST00000349384.6	+	10	3718	c.3404G>T	c.(3403-3405)aGc>aTc	p.S1135I	RREB1_ENST00000379933.3_Missense_Mutation_p.S1135I|RREB1_ENST00000379938.2_Missense_Mutation_p.S1135I|RREB1_ENST00000334984.6_Missense_Mutation_p.S1135I	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1135					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)				CCAGCCAGCAGCCCAGAGGCT	0.687													G|||	12	0.00239617	0.0091	0.0	5008	,	,		13021	0.0		0.0	False		,,,				2504	0.0				p.S1135I		Atlas-SNP	.											.	RREB1	242	.	0			c.G3404T						PASS	.	G	ILE/SER,ILE/SER,ILE/SER,ILE/SER	17,4291		0,17,2137	8.0	12.0	11.0		3404,3404,3404,3404	5.7	1.0	6	dbSNP_132	11	1,8493		0,1,4246	yes	missense,missense,missense,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	142,142,142,142	0,18,6383	TT,TG,GG		0.0118,0.3946,0.1406	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1135/1688,1135/1743,1135/1477,1135/1688	7231736	18,12784	2154	4247	6401	SO:0001583	missense	6239	exon10			CCAGCAGCCCAGA	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.3404G>T	6.37:g.7231736G>T	ENSP00000305560:p.Ser1135Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	17.76	3.469337	0.63625	0.003946	1.18E-4	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.13307	2.6;2.7;2.6;2.6	5.73	5.73	0.89815	.	0.089674	0.47455	D	0.000240	T	0.21186	0.0510	M	0.62723	1.935	0.38993	D	0.959191	D;D;D	0.67145	0.993;0.993;0.996	P;P;D	0.65010	0.9;0.855;0.931	T	0.00778	-1.1570	10	0.72032	D	0.01	-50.0022	10.0245	0.42063	0.1544:0.0:0.8456:0.0	.	1135;1135;1135	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	I	1135	ENSP00000369265:S1135I;ENSP00000369270:S1135I;ENSP00000305560:S1135I;ENSP00000335574:S1135I	ENSP00000335574:S1135I	S	+	2	0	RREB1	7176735	0.693000	0.27728	0.999000	0.59377	0.626000	0.37791	1.532000	0.36029	2.695000	0.91970	0.655000	0.94253	AGC	G|0.997;T|0.003	0.003	strong		0.687	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
PZP	5858	hgsc.bcm.edu	37	12	9312951	9312951	+	Missense_Mutation	SNP	G	G	A	rs57006764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9312951G>A	ENST00000261336.2	-	24	3036	c.3008C>T	c.(3007-3009)aCg>aTg	p.T1003M	PZP_ENST00000539983.1_5'Flank|PZP_ENST00000381997.2_Missense_Mutation_p.T789M	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1003			T -> M (in dbSNP:rs57006764).		female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GATCTCCTGCGTCAGCTGCTG	0.428													G|||	1356	0.270767	0.1619	0.2695	5008	,	,		-128	0.4762		0.1909	False		,,,				2504	0.2894				p.T1003M	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											PZP_ENST00000381997,NS,carcinoma,+1,2	PZP	422	2	0			c.C3008T						PASS	.	G	MET/THR	710,3696	293.6+/-282.7	68,574,1561	130.0	119.0	123.0		3008	3.7	0.0	12	dbSNP_129	123	1456,7144	278.2+/-293.3	116,1224,2960	yes	missense	PZP	NM_002864.2	81	184,1798,4521	AA,AG,GG		16.9302,16.1144,16.6539	probably-damaging	1003/1483	9312951	2166,10840	2203	4300	6503	SO:0001583	missense	5858	exon24			TCCTGCGTCAGCT	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.3008C>T	12.37:g.9312951G>A	ENSP00000261336:p.Thr1003Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	577	0.2641941391941392	105	0.21341463414634146	92	0.2541436464088398	253	0.4423076923076923	127	0.16754617414248021	G	11.01	1.514300	0.27123	0.161144	0.169302	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.40225	1.04;1.04	4.56	3.67	0.42095	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.075423	0.48286	U	0.000182	T	0.00012	0.0000	M	0.90369	3.11	0.43203	P	0.004940999999999973	D;D	0.89917	1.0;1.0	D;D	0.83275	0.951;0.996	T	0.38090	-0.9677	9	0.87932	D	0	.	8.6441	0.33994	0.0835:0.1509:0.7656:0.0	rs57006764;rs61740800	789;1003	P20742-2;P20742	.;PZP_HUMAN	M	1003;789	ENSP00000261336:T1003M;ENSP00000371427:T789M	ENSP00000261336:T1003M	T	-	2	0	PZP	9204218	0.993000	0.37304	0.031000	0.17742	0.009000	0.06853	2.458000	0.45014	1.044000	0.40200	0.563000	0.77884	ACG	G|0.805;A|0.195	0.195	strong		0.428	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
OR8B4	283162	hgsc.bcm.edu	37	11	124294703	124294703	+	Missense_Mutation	SNP	T	T	C	rs10750270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124294703T>C	ENST00000356130.3	-	1	86	c.65A>G	c.(64-66)gAg>gGg	p.E22G		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	22			E -> G (in dbSNP:rs10750270).			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)		GAGCTGGAGCTCTGGCTGTTC	0.483													T|||	1735	0.346446	0.2874	0.3242	5008	,	,		19677	0.5952		0.3121	False		,,,				2504	0.2209				p.E22G		Atlas-SNP	.											.	OR8B4	60	.	0			c.A65G						PASS	.	T	GLY/GLU	1209,3193	413.0+/-336.3	176,857,1168	53.0	52.0	52.0		65	2.2	0.0	11	dbSNP_120	52	2675,5923	416.8+/-352.2	419,1837,2043	yes	missense	OR8B4	NM_001005196.1	98	595,2694,3211	CC,CT,TT		31.1119,27.4648,29.8769	benign	22/310	124294703	3884,9116	2201	4299	6500	SO:0001583	missense	283162	exon1			TGGAGCTCTGGCT	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.65A>G	11.37:g.124294703T>C	ENSP00000348449:p.Glu22Gly	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	832	0.38095238095238093	123	0.25	125	0.3453038674033149	352	0.6153846153846154	232	0.30606860158311344	t	2.515	-0.312118	0.05422	0.274648	0.311119	ENSG00000198657	ENST00000356130	T	0.00444	7.4	4.62	2.16	0.27623	.	0.264994	0.26899	N	0.021931	T	0.00012	0.0000	L	0.39467	1.215	0.80722	P	0.0	B	0.12630	0.006	B	0.15052	0.012	T	0.02743	-1.1116	9	0.37606	T	0.19	.	11.1631	0.48526	0.0:0.0:0.2894:0.7106	rs10750270;rs52830364;rs58760348;rs10750270	22	Q96RC9	OR8B4_HUMAN	G	22	ENSP00000348449:E22G	ENSP00000348449:E22G	E	-	2	0	OR8B4	123799913	0.000000	0.05858	0.014000	0.15608	0.159000	0.22180	0.167000	0.16602	0.337000	0.23665	0.533000	0.62120	GAG	T|0.675;C|0.325	0.325	strong		0.483	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
SCARB2	950	hgsc.bcm.edu	37	4	77102148	77102148	+	Missense_Mutation	SNP	G	G	C	rs143558324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77102148G>C	ENST00000264896.2	-	3	731	c.382C>G	c.(382-384)Cct>Gct	p.P128A	SCARB2_ENST00000452464.2_Intron	NM_005506.3	NP_005497.1	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2	128					cell adhesion (GO:0007155)|protein targeting to lysosome (GO:0006622)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(3)|prostate(2)|skin(1)	22			Lung(101;0.196)			TCAATTTTAGGGTCTCCAACA	0.323													G|||	6	0.00119808	0.0045	0.0	5008	,	,		15540	0.0		0.0	False		,,,				2504	0.0				p.P128A		Atlas-SNP	.											.	SCARB2	47	.	0			c.C382G						PASS	.	G	,ALA/PRO	19,4383	26.2+/-53.5	0,19,2182	103.0	104.0	104.0		,382	3.2	0.9	4	dbSNP_134	104	0,8598		0,0,4299	yes	intron,missense	SCARB2	NM_001204255.1,NM_005506.3	,27	0,19,6481	CC,CG,GG		0.0,0.4316,0.1462	,benign	,128/479	77102148	19,12981	2201	4299	6500	SO:0001583	missense	950	exon3			TTTTAGGGTCTCC	D12676	CCDS3577.1, CCDS56335.1	4q21.1	2014-07-11	2002-09-06	2002-09-06	ENSG00000138760	ENSG00000138760			1665	protein-coding gene	gene with protein product		602257	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2 (lysosomal integral membrane protein II)"""	CD36L2		1374238	Standard	NM_005506		Approved	HLGP85, LIMPII, SR-BII, LIMP-2	uc003hju.2	Q14108	OTTHUMG00000130099	ENST00000264896.2:c.382C>G	4.37:g.77102148G>C	ENSP00000264896:p.Pro128Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_005506	B4DKD8|E7EM68|Q53Y63	Missense_Mutation	SNP	ENST00000264896.2	37	CCDS3577.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.857612	0.32791	0.004316	0.0	ENSG00000138760	ENST00000264896	T	0.72282	-0.64	5.87	3.17	0.36434	.	0.189182	0.64402	N	0.000018	T	0.75034	0.3795	M	0.71206	2.165	0.80722	D	1	B	0.29481	0.245	B	0.43575	0.424	T	0.66697	-0.5858	10	0.09590	T	0.72	.	16.5946	0.84792	0.0:0.3673:0.6327:0.0	.	128	Q14108	SCRB2_HUMAN	A	128	ENSP00000264896:P128A	ENSP00000264896:P128A	P	-	1	0	SCARB2	77321172	1.000000	0.71417	0.946000	0.38457	0.282000	0.26991	3.001000	0.49488	0.452000	0.26830	-0.176000	0.13171	CCT	G|0.999;C|0.001	0.001	strong		0.323	SCARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252403.1	NM_005506	
MAS1L	116511	hgsc.bcm.edu	37	6	29455333	29455333	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29455333A>G	ENST00000377127.3	-	1	405	c.347T>C	c.(346-348)gTc>gCc	p.V116A		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	116					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						GTCAGCAGCGACCAGGTGGAG	0.512																																					p.V116A	NSCLC(153;755 1987 3859 11251 32945)	Atlas-SNP	.											MAS1L,NS,carcinoma,+1,1	MAS1L	66	1	0			c.T347C						scavenged	.						72.0	67.0	68.0					6																	29455333		2203	4300	6503	SO:0001583	missense	116511	exon1			GCAGCGACCAGGT	S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"""GPCR / Class A : Orphans"""	13961	protein-coding gene	gene with protein product		607235	"""MAS1 oncogene-like"""				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.347T>C	6.37:g.29455333A>G	ENSP00000366331:p.Val116Ala	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	83	3	0.0361446	NM_052967	Q5SUN5	Missense_Mutation	SNP	ENST00000377127.3	37	CCDS4661.1	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.514934	0.00975	.	.	ENSG00000204687	ENST00000377127	T	0.21734	1.99	2.6	1.42	0.22433	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00724	0.0024	N	0.00080	-2.225	0.18873	N	0.999983	B	0.18013	0.025	B	0.12837	0.008	T	0.47484	-0.9114	9	0.02654	T	1	.	6.5045	0.22188	0.2161:0.0:0.7839:0.0	.	116	P35410	MAS1L_HUMAN	A	116	ENSP00000366331:V116A	ENSP00000366331:V116A	V	-	2	0	MAS1L	29563312	0.426000	0.25506	0.013000	0.15412	0.008000	0.06430	1.700000	0.37815	0.188000	0.20168	-0.569000	0.04157	GTC	.	.	none		0.512	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967	
TCHHL1	126637	hgsc.bcm.edu	37	1	152060495	152060495	+	Missense_Mutation	SNP	C	C	T	rs76137589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152060495C>T	ENST00000368806.1	-	2	189	c.125G>A	c.(124-126)gGg>gAg	p.G42E		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	42							calcium ion binding (GO:0005509)			breast(4)|endometrium(1)|kidney(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(1)|skin(7)|stomach(1)	60	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			AAAAAAGTCCCCAAACTCGCC	0.458													c|||	59	0.0117812	0.0431	0.0029	5008	,	,		19439	0.0		0.0	False		,,,				2504	0.0				p.G42E		Atlas-SNP	.											.	TCHHL1	132	.	0			c.G125A						PASS	.	C	GLU/GLY	196,4210		8,180,2015	183.0	181.0	182.0		125	-0.3	0.9	1	dbSNP_131	182	0,8600		0,0,4300	yes	missense	TCHHL1	NM_001008536.1	98	8,180,6315	TT,TC,CC		0.0,4.4485,1.507	possibly-damaging	42/905	152060495	196,12810	2203	4300	6503	SO:0001583	missense	126637	exon2			AAGTCCCCAAACT		CCDS30857.1	1q21.3	2011-10-11	2004-10-05	2006-01-27	ENSG00000182898	ENSG00000182898		"""S100 calcium binding proteins"""	31796	protein-coding gene	gene with protein product			"""S100 calcium binding protein A17"""	S100A17, THHL1			Standard	NM_001008536		Approved		uc001ezo.1	Q5QJ38	OTTHUMG00000013058	ENST00000368806.1:c.125G>A	1.37:g.152060495C>T	ENSP00000357796:p.Gly42Glu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	120	51	0.425	NM_001008536	B2RPK8|Q5VTJ9	Missense_Mutation	SNP	ENST00000368806.1	37	CCDS30857.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	.	11.72	1.721614	0.30503	0.044485	0.0	ENSG00000182898	ENST00000368806	T	0.10573	2.86	6.0	-0.34	0.12643	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.624434	0.13321	N	0.396729	T	0.05593	0.0147	L	0.58969	1.84	0.29774	N	0.834538	D	0.56746	0.977	P	0.51324	0.666	T	0.28004	-1.0057	10	0.20519	T	0.43	-1.2812	5.8572	0.18727	0.0:0.5081:0.1244:0.3675	.	42	Q5QJ38	TCHL1_HUMAN	E	42	ENSP00000357796:G42E	ENSP00000357796:G42E	G	-	2	0	TCHHL1	150327119	0.666000	0.27475	0.918000	0.36340	0.264000	0.26372	-0.095000	0.11077	-0.059000	0.13154	-0.136000	0.14681	GGG	C|0.985;T|0.015	0.015	strong		0.458	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104	
GPATCH4	54865	hgsc.bcm.edu	37	1	156565389	156565389	+	Silent	SNP	C	C	T	rs145851878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156565389C>T	ENST00000438976.2	-	8	774	c.744G>A	c.(742-744)aaG>aaA	p.K248K	GPATCH4_ENST00000497287.1_5'Flank|GPATCH4_ENST00000368232.4_Silent_p.K243K			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	243							poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(3)|stomach(1)	17	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GTCGCCTTTTCTTCTTCTTGC	0.468													C|||	68	0.0135783	0.0499	0.0029	5008	,	,		22178	0.0		0.0	False		,,,				2504	0.0				p.K248K		Atlas-SNP	.											.	GPATCH4	34	.	0			c.G744A						PASS	.	C	,	172,4234	115.4+/-153.4	4,164,2035	332.0	314.0	320.0		744,729	1.0	0.4	1	dbSNP_134	320	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GPATCH4	NM_015590.3,NM_182679.2	,	4,164,6335	TT,TC,CC		0.0,3.9038,1.3225	,	248/376,243/371	156565389	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	54865	exon8			CCTTTTCTTCTTC	BC056904	CCDS1146.1, CCDS44245.1	1q22	2013-01-28		2006-12-13	ENSG00000160818	ENSG00000160818		"""G patch domain containing"""	25982	protein-coding gene	gene with protein product				GPATC4		12477932	Standard	NM_015590		Approved	FLJ20249, DKFZP434F1735	uc001fpl.3	Q5T3I0	OTTHUMG00000033203	ENST00000438976.2:c.744G>A	1.37:g.156565389C>T		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	284	130	0.457746	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Silent	SNP	ENST00000438976.2	37	CCDS44245.1																																																																																			C|0.988;T|0.012	0.012	strong		0.468	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725	
NCAN	1463	hgsc.bcm.edu	37	19	19338942	19338942	+	Missense_Mutation	SNP	G	G	A	rs10426537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19338942G>A	ENST00000252575.6	+	8	2612	c.2513G>A	c.(2512-2514)aGt>aAt	p.S838N	NCAN_ENST00000538881.1_Missense_Mutation_p.S289N	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	838					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|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)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	CCGGCCCCCAGTGATGCTAGT	0.537													G|||	197	0.0393371	0.0885	0.0043	5008	,	,		17947	0.0526		0.001	False		,,,				2504	0.0235				p.S838N		Atlas-SNP	.											.	NCAN	277	.	0			c.G2513A						PASS	.	G	ASN/SER	325,4081	171.6+/-201.8	10,305,1888	55.0	57.0	56.0		2513	0.2	0.0	19	dbSNP_119	56	4,8596	3.0+/-9.4	0,4,4296	yes	missense	NCAN	NM_004386.2	46	10,309,6184	AA,AG,GG		0.0465,7.3763,2.5296	probably-damaging	838/1322	19338942	329,12677	2203	4300	6503	SO:0001583	missense	1463	exon8			CCCCCAGTGATGC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.2513G>A	19.37:g.19338942G>A	ENSP00000252575:p.Ser838Asn	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_004386	Q9UPK6	Missense_Mutation	SNP	ENST00000252575.6	37	CCDS12397.1	78	0.03571428571428571	42	0.08536585365853659	1	0.0027624309392265192	34	0.05944055944055944	1	0.0013192612137203166	G	13.54	2.268686	0.40095	0.073763	4.65E-4	ENSG00000130287	ENST00000539499;ENST00000252575;ENST00000538881	D;D	0.87256	-1.89;-2.23	3.75	0.2	0.15181	.	0.531595	0.16158	N	0.226911	T	0.10035	0.0246	L	0.29908	0.895	0.09310	N	1	P;B	0.37466	0.596;0.244	B;B	0.29267	0.1;0.074	T	0.30327	-0.9982	10	0.46703	T	0.11	.	6.052	0.19790	0.0:0.1739:0.3924:0.4337	rs10426537	852;838	Q4LE67;O14594	.;NCAN_HUMAN	N	852;838;289	ENSP00000252575:S838N;ENSP00000442202:S289N	ENSP00000252575:S838N	S	+	2	0	NCAN	19199942	0.001000	0.12720	0.000000	0.03702	0.823000	0.46562	0.745000	0.26259	0.131000	0.18576	0.491000	0.48974	AGT	G|0.973;A|0.027	0.027	strong		0.537	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
TRIB1	10221	hgsc.bcm.edu	37	8	126448674	126448674	+	Missense_Mutation	SNP	G	G	T	rs16900603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:126448674G>T	ENST00000519576.1	+	2	650	c.387G>T	c.(385-387)gaG>gaT	p.E129D	TRIB1_ENST00000311922.3_Missense_Mutation_p.E360D|TRIB1_ENST00000520847.1_Missense_Mutation_p.E194D					tribbles pseudokinase 1											NS(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8	all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			TTGTTCCAGAGTACCAGGAGG	0.473													G|||	147	0.029353	0.1051	0.0101	5008	,	,		20227	0.0		0.001	False		,,,				2504	0.0				p.E360D		Atlas-SNP	.											.	TRIB1	73	.	0			c.G1080T						PASS	.	G	ASP/GLU	353,4053	181.5+/-209.5	15,323,1865	83.0	85.0	84.0		1080	2.7	1.0	8	dbSNP_123	84	4,8596	3.7+/-12.6	0,4,4296	yes	missense	TRIB1	NM_025195.2	45	15,327,6161	TT,TG,GG		0.0465,8.0118,2.7449	benign	360/373	126448674	357,12649	2203	4300	6503	SO:0001583	missense	10221	exon3			TCCAGAGTACCAG	AF205437	CCDS6357.1, CCDS64971.1	8q24.13	2013-10-03	2013-10-03			ENSG00000173334			16891	protein-coding gene	gene with protein product		609461	"""tribbles homolog 1 (Drosophila)"""			9342215, 16715410	Standard	NM_001282985		Approved	C8FW, GIG2, TRB1	uc003yrx.3	Q96RU8		ENST00000519576.1:c.387G>T	8.37:g.126448674G>T	ENSP00000428879:p.Glu129Asp	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	134	75	0.559702	NM_025195		Missense_Mutation	SNP	ENST00000519576.1	37		39	0.017857142857142856	35	0.07113821138211382	4	0.011049723756906077	0	0.0	0	0.0	G	0.601	-0.829096	0.02734	0.080118	4.65E-4	ENSG00000173334	ENST00000311922;ENST00000520847;ENST00000519576	T;T;T	0.47177	0.88;0.85;1.12	5.88	2.65	0.31530	.	0.241181	0.21003	N	0.081838	T	0.00936	0.0031	N	0.08118	0	0.23903	N	0.996519	B	0.11235	0.004	B	0.10450	0.005	T	0.17410	-1.0370	10	0.02654	T	1	-15.0092	5.2841	0.15692	0.0985:0.2463:0.5295:0.1257	rs16900603;rs52815805;rs16900603	360	Q96RU8	TRIB1_HUMAN	D	360;194;129	ENSP00000312150:E360D;ENSP00000429063:E194D;ENSP00000428879:E129D	ENSP00000312150:E360D	E	+	3	2	TRIB1	126517856	0.026000	0.19158	0.998000	0.56505	0.850000	0.48378	-0.005000	0.12855	0.811000	0.34303	-0.305000	0.09177	GAG	G|0.974;T|0.026	0.026	strong		0.473	TRIB1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000381433.1	NM_025195	
TEP1	7011	hgsc.bcm.edu	37	14	20844383	20844383	+	Silent	SNP	C	C	T	rs2228042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20844383C>T	ENST00000262715.5	-	42	6169	c.6129G>A	c.(6127-6129)acG>acA	p.T2043T	TEP1_ENST00000545983.1_Silent_p.T381T|TEP1_ENST00000556935.1_Silent_p.T1935T	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2043					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)		TGTGTGGCCGCGTCAGCAGCT	0.582													C|||	188	0.0375399	0.0083	0.0346	5008	,	,		18923	0.002		0.0676	False		,,,				2504	0.0849				p.T2043T		Atlas-SNP	.											.	TEP1	224	.	0			c.G6129A						PASS	.	C		93,4313	75.7+/-113.9	0,93,2110	51.0	51.0	51.0		6129	-11.6	0.0	14	dbSNP_98	51	567,8033	153.1+/-207.6	18,531,3751	no	coding-synonymous	TEP1	NM_007110.4		18,624,5861	TT,TC,CC		6.593,2.1108,5.0746		2043/2628	20844383	660,12346	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon42			TGGCCGCGTCAGC		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.6129G>A	14.37:g.20844383C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	244	129	0.528689	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			T|0.040;G|0.128;C|0.828;A|0.004	0.040	strong		0.582	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
NAPG	8774	hgsc.bcm.edu	37	18	10539774	10539774	+	Missense_Mutation	SNP	C	C	T	rs2228300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:10539774C>T	ENST00000322897.6	+	6	343	c.274C>T	c.(274-276)Cca>Tca	p.P92S	NAPG_ENST00000542979.1_Missense_Mutation_p.P10S	NM_003826.2	NP_003817.1	Q99747	SNAG_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, gamma	92			P -> S (in dbSNP:rs16974765).		intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)				large_intestine(2)|lung(2)	4						GCAGAAACTACCAGAGGCCGT	0.438													C|||	217	0.0433307	0.1573	0.013	5008	,	,		17838	0.0		0.0	False		,,,				2504	0.0				p.P92S		Atlas-SNP	.											.	NAPG	18	.	0			c.C274T						PASS	.	C	SER/PRO	498,3326		28,442,1442	64.0	64.0	64.0		274	4.1	0.1	18	dbSNP_123	64	1,8233		0,1,4116	yes	missense	NAPG	NM_003826.2	74	28,443,5558	TT,TC,CC		0.0121,13.023,4.1383	possibly-damaging	92/313	10539774	499,11559	1912	4117	6029	SO:0001583	missense	8774	exon6			AAACTACCAGAGG	U78107	CCDS45827.1	18p11.21	2013-02-28			ENSG00000134265	ENSG00000134265			7642	protein-coding gene	gene with protein product	"""gamma SNAP"""	603216				9269766	Standard	NM_003826		Approved		uc002kon.3	Q99747	OTTHUMG00000179119	ENST00000322897.6:c.274C>T	18.37:g.10539774C>T	ENSP00000324628:p.Pro92Ser	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_003826	B4DFC9|Q9BUV1	Missense_Mutation	SNP	ENST00000322897.6	37	CCDS45827.1	74	0.03388278388278388	69	0.1402439024390244	5	0.013812154696132596	0	0.0	0	0.0	C	10.89	1.479069	0.26511	0.13023	1.21E-4	ENSG00000134265	ENST00000322897;ENST00000542979	T;T	0.75050	-0.9;-0.9	5.82	4.06	0.47325	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.00580	0.0019	L	0.34521	1.04	0.09310	P	0.99999957713	P	0.37101	0.582	B	0.25987	0.065	T	0.28650	-1.0037	9	0.06625	T	0.88	-10.0671	11.8346	0.52316	0.0:0.8645:0.0:0.1355	rs2228300	92	Q99747	SNAG_HUMAN	S	92;10	ENSP00000324628:P92S;ENSP00000442849:P10S	ENSP00000324628:P92S	P	+	1	0	NAPG	10529774	1.000000	0.71417	0.125000	0.21846	0.551000	0.35334	5.446000	0.66600	0.820000	0.34516	0.561000	0.74099	CCA	C|0.965;T|0.035	0.035	strong		0.438	NAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444873.1	NM_003826	
RIMS2	9699	hgsc.bcm.edu	37	8	105263979	105263979	+	Silent	SNP	C	C	T	rs10461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:105263979C>T	ENST00000436393.2	+	28	4276	c.4035C>T	c.(4033-4035)gcC>gcT	p.A1345A	RIMS2_ENST00000339750.2_Silent_p.A263A|RIMS2_ENST00000507740.1_Silent_p.A1141A|RIMS2_ENST00000406091.3_Silent_p.A1327A|RIMS2_ENST00000262231.10_Silent_p.A1166A			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1389	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			CAACCTTGGCCCCTCTGACAA	0.448										HNSCC(12;0.0054)			C|||	2394	0.478035	0.5227	0.536	5008	,	,		16632	0.6498		0.3529	False		,,,				2504	0.3282				p.A1327A		Atlas-SNP	.											.	RIMS2	1357	.	0			c.C3981T						PASS	.	C	,	1859,1877		476,907,485	149.0	149.0	149.0		3981,3423	0.4	1.0	8	dbSNP_52	149	2858,5328		525,1808,1760	no	coding-synonymous,coding-synonymous	RIMS2	NM_001100117.2,NM_014677.4	,	1001,2715,2245	TT,TC,CC		34.9133,49.7591,39.5655	,	1327/1350,1141/1164	105263979	4717,7205	1868	4093	5961	SO:0001819	synonymous_variant	9699	exon24			CTTGGCCCCTCTG	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.4035C>T	8.37:g.105263979C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	166	74	0.445783	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000436393.2	37																																																																																				C|0.553;T|0.447	0.447	strong		0.448	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117	
GPRASP2	114928	hgsc.bcm.edu	37	X	101970662	101970662	+	Missense_Mutation	SNP	A	A	G	rs113336462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101970662A>G	ENST00000535209.1	+	4	1696	c.865A>G	c.(865-867)Agc>Ggc	p.S289G	GPRASP2_ENST00000543253.1_Missense_Mutation_p.S289G|GPRASP2_ENST00000332262.5_Missense_Mutation_p.S289G			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	289						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						GGATGAGGCCAGCAACCCATT	0.507													.|||	50	0.013245	0.0371	0.0014	3775	,	,		14521	0.0		0.0	False		,,,				2504	0.0				p.S289G		Atlas-SNP	.											.	GPRASP2	89	.	0			c.A865G						PASS	.	G	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	148,3687		2,116,28,1514,543	112.0	111.0	112.0		865,865,865,865,865,865	1.3	0.0	X	dbSNP_132	112	0,6728		0,0,0,2428,1872	yes	missense,missense,missense,missense,missense,missense	GPRASP2,ARMCX5-GPRASP2	NM_001004051.3,NM_001184874.2,NM_001184875.2,NM_001184876.2,NM_001199818.1,NM_138437.5	56,56,56,56,56,56	2,116,28,3942,2415	GG,GA,G,AA,A		0.0,3.8592,1.4011	benign,benign,benign,benign,benign,benign	289/839,289/839,289/839,289/839,289/839,289/839	101970662	148,10415	2203	4300	6503	SO:0001583	missense	114928	exon4			GAGGCCAGCAACC	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"""Armadillo repeat containing"""	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.865A>G	X.37:g.101970662A>G	ENSP00000437394:p.Ser289Gly	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	157	64	0.407643	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	37	CCDS14501.1	15	0.009041591320072333	11	0.022727272727272728	0	0.0	0	0.0	0	0.0	G	0.001	-3.165628	0.00028	0.038592	0.0	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.06218	3.33;3.33;3.33	4.2	1.33	0.21861	.	0.304465	0.24078	N	0.041755	T	0.00524	0.0017	N	0.02539	-0.55	0.18873	N	0.999988	B	0.02656	0.0	B	0.01281	0.0	T	0.46373	-0.9196	10	0.22706	T	0.39	-0.1711	4.5595	0.12152	0.2852:0.0:0.5594:0.1554	.	289	Q96D09	GASP2_HUMAN	G	289	ENSP00000437872:S289G;ENSP00000437394:S289G;ENSP00000339057:S289G	ENSP00000339057:S289G	S	+	1	0	GPRASP2	101857318	0.826000	0.29277	0.037000	0.18230	0.001000	0.01503	0.260000	0.18424	-0.074000	0.12820	-0.834000	0.03071	AGC	A|0.986;G|0.014	0.014	strong		0.507	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
ZSWIM4	65249	hgsc.bcm.edu	37	19	13936385	13936385	+	Missense_Mutation	SNP	C	C	T	rs62620757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	146	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	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	
ADCY7	113	hgsc.bcm.edu	37	16	50344627	50344627	+	Silent	SNP	C	C	T	rs140505854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50344627C>T	ENST00000394697.2	+	19	2530	c.2190C>T	c.(2188-2190)ttC>ttT	p.F730F	ADCY7_ENST00000254235.3_Silent_p.F730F			P51828	ADCY7_HUMAN	adenylate cyclase 7	730					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)		TCCTGGGCTTCATCGCCTGCT	0.617													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18686	0.0		0.0	False		,,,				2504	0.0				p.F730F		Atlas-SNP	.											.	ADCY7	90	.	0			c.C2190T						PASS	.	C		4,4392	8.1+/-20.4	0,4,2194	107.0	78.0	88.0		2190	1.1	0.2	16	dbSNP_134	88	0,8600		0,0,4300	no	coding-synonymous	ADCY7	NM_001114.3		0,4,6494	TT,TC,CC		0.0,0.091,0.0308		730/1081	50344627	4,12992	2198	4300	6498	SO:0001819	synonymous_variant	113	exon18			GGGCTTCATCGCC	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.2190C>T	16.37:g.50344627C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_001114	A0AVA6	Silent	SNP	ENST00000394697.2	37	CCDS10741.1																																																																																			C|1.000;T|0.000	0.000	weak		0.617	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3		
SMYD4	114826	hgsc.bcm.edu	37	17	1703982	1703982	+	Missense_Mutation	SNP	C	C	T	rs9913923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1703982C>T	ENST00000305513.7	-	5	873	c.706G>A	c.(706-708)Ggc>Agc	p.G236S		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	236	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		G -> S (in dbSNP:rs9913923).				metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						ACGCATAAGCCGATGGATGAT	0.502													C|||	654	0.130591	0.2451	0.0735	5008	,	,		12317	0.0635		0.0805	False		,,,				2504	0.137				p.G236S		Atlas-SNP	.											.	SMYD4	50	.	0			c.G706A						PASS	.	C	SER/GLY	976,3430	367.1+/-318.1	107,762,1334	171.0	165.0	167.0		706	-6.1	0.2	17	dbSNP_119	167	828,7772	190.7+/-237.1	35,758,3507	yes	missense	SMYD4	NM_052928.2	56	142,1520,4841	TT,TC,CC		9.6279,22.1516,13.8705	benign	236/805	1703982	1804,11202	2203	4300	6503	SO:0001583	missense	114826	exon5			ATAAGCCGATGGA	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.706G>A	17.37:g.1703982C>T	ENSP00000304360:p.Gly236Ser	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	207	100	0.483092	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	266	0.12179487179487179	134	0.27235772357723576	31	0.0856353591160221	48	0.08391608391608392	53	0.06992084432717678	C	0.014	-1.582771	0.00879	0.221516	0.096279	ENSG00000186532	ENST00000305513	T	0.08896	3.04	5.99	-6.05	0.02172	SET domain (1);	0.750916	0.14769	N	0.299484	T	0.00012	0.0000	N	0.02103	-0.685	0.58432	P	1.999999999946489E-6	B	0.12630	0.006	B	0.04013	0.001	T	0.34428	-0.9829	9	0.02654	T	1	-0.033	10.6048	0.45388	0.0:0.2418:0.5253:0.2329	rs9913923;rs52828951;rs56419688;rs59448424;rs9913923	236	Q8IYR2	SMYD4_HUMAN	S	236	ENSP00000304360:G236S	ENSP00000304360:G236S	G	-	1	0	SMYD4	1650732	0.002000	0.14202	0.177000	0.23020	0.001000	0.01503	-0.797000	0.04570	-0.727000	0.04888	-0.302000	0.09304	GGC	C|0.863;T|0.137	0.137	strong		0.502	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305775	39305775	+	Missense_Mutation	SNP	T	T	C	rs535144703|rs141265645|rs58117746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305775T>C	ENST00000343246.4	-	1	279	c.245A>G	c.(244-246)cAg>cGg	p.Q82R		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	82	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)			gcaggtggtctggcagcagca	0.657																																					p.Q82R		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	1	0			c.A245G						PASS	.						14.0	21.0	18.0					17																	39305775		2102	4214	6316	SO:0001583	missense	85289	exon1			GTGGTCTGGCAGC	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.245A>G	17.37:g.39305775T>C	ENSP00000340546:p.Gln82Arg	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	87	53	0.609195	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	1.564	-0.535892	0.04082	.	.	ENSG00000198271	ENST00000343246	T	0.00581	6.42	2.44	-3.27	0.05048	.	.	.	.	.	T	0.00271	0.0008	N	0.04260	-0.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35001	-0.9806	9	0.11794	T	0.64	.	3.3098	0.07013	0.2034:0.3821:0.0:0.4145	.	87	Q9BYR2	KRA45_HUMAN	R	82	ENSP00000340546:Q82R	ENSP00000340546:Q82R	Q	-	2	0	KRTAP4-5	36559301	0.000000	0.05858	0.009000	0.14445	0.001000	0.01503	-1.539000	0.02202	-0.998000	0.03446	-1.710000	0.00715	CAG	.	.	weak		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
HMHB1	57824	hgsc.bcm.edu	37	5	143200053	143200053	+	Missense_Mutation	SNP	C	C	T	rs161557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:143200053C>T	ENST00000289448.2	+	2	153	c.46C>T	c.(46-48)Cat>Tat	p.H16Y	CTB-57H20.1_ENST00000503323.1_RNA	NM_021182.1	NP_067005	O97980	HMHB1_HUMAN	histocompatibility (minor) HB-1	16	Loss of recognition by cytotoxic T lymphocyte (CTL).		H -> Y (in allele HB-1Y; loss of CTL recognition for epitope HB-1. No influence on HLA-B/HLA-B44 binding, nor on the processing by the proteasome; dbSNP:rs161557). {ECO:0000269|PubMed:9892612}.		immune system process (GO:0002376)								Acute lymphoblastic leukemia(2;0.0236)|all_hematologic(2;0.041)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AGGTTCTCTGCATGTTTGGAA	0.393													C|||	1464	0.292332	0.295	0.3343	5008	,	,		16673	0.3889		0.2227	False		,,,				2504	0.2311				p.H16Y		Atlas-SNP	.											.	HMHB1	3	.	0			c.C46T						PASS	.	C	TYR/HIS	950,2776		114,722,1027	257.0	232.0	239.0		46	-2.3	0.0	5	dbSNP_79	239	1797,6417		203,1391,2513	yes	missense	HMHB1	NM_021182.1	83	317,2113,3540	TT,TC,CC		21.8773,25.4965,23.0067	benign	16/42	143200053	2747,9193	1863	4107	5970	SO:0001583	missense	57824	exon2			TCTCTGCATGTTT	AF103884	CCDS43376.1	5q32	2006-07-20			ENSG00000158497	ENSG00000158497			29677	protein-coding gene	gene with protein product		609961				9892612	Standard	NM_021182		Approved	HB-1	uc003lnj.3	O97980	OTTHUMG00000163173	ENST00000289448.2:c.46C>T	5.37:g.143200053C>T	ENSP00000289448:p.His16Tyr	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	192	83	0.432292	NM_021182	Q9MY25	Missense_Mutation	SNP	ENST00000289448.2	37	CCDS43376.1	610	0.2793040293040293	133	0.2703252032520325	93	0.2569060773480663	228	0.3986013986013986	156	0.20580474934036938	C	8.763	0.924004	0.18056	0.254965	0.218773	ENSG00000158497	ENST00000289448	T	0.62498	0.02	5.38	-2.32	0.06745	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25166	P	0.990314	B	0.17268	0.021	B	0.12156	0.007	T	0.39860	-0.9593	7	0.87932	D	0	.	0.1886	0.00131	0.3003:0.2066:0.1481:0.345	rs161557;rs52812230;rs61290874;rs161557	16	O97980	HMHB1_HUMAN	Y	16	ENSP00000289448:H16Y	ENSP00000289448:H16Y	H	+	1	0	HMHB1	143180246	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.312000	0.08113	-0.226000	0.09899	0.563000	0.77884	CAT	C|0.720;T|0.280	0.280	strong		0.393	HMHB1-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371899.1	NM_021182	
MTMR4	9110	hgsc.bcm.edu	37	17	56584508	56584508	+	Missense_Mutation	SNP	T	T	C	rs2302190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	157	0	0		WXS	Illumina HiSeq	Phase_I	148	60	0.405405	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	
MUC17	140453	hgsc.bcm.edu	37	7	100678560	100678560	+	Missense_Mutation	SNP	C	C	A	rs77199586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678560C>A	ENST00000306151.4	+	3	3927	c.3863C>A	c.(3862-3864)aCg>aAg	p.T1288K		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1288	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)					GTCAGCACCACGCTGGTGACC	0.473																																					p.T1288K		Atlas-SNP	.											MUC17,NS,carcinoma,-1,2	MUC17	804	2	0			c.C3863A						PASS	.	C	LYS/THR	768,3638		0,768,1435	272.0	261.0	265.0		3863	-0.9	0.0	7	dbSNP_131	265	553,8047		0,553,3747	no	missense	MUC17	NM_001040105.1	78	0,1321,5182	AA,AC,CC		6.4302,17.4308,10.1569	possibly-damaging	1288/4494	100678560	1321,11685	2203	4300	6503	SO:0001583	missense	140453	exon3			GCACCACGCTGGT	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.3863C>A	7.37:g.100678560C>A	ENSP00000302716:p.Thr1288Lys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	142	30	0.211268	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.025	-1.376343	0.01214	0.174308	0.064302	ENSG00000169876	ENST00000306151	T	0.02421	4.3	0.471	-0.942	0.10398	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	N	1	P	0.47302	0.893	B	0.35727	0.209	T	0.40683	-0.9550	8	0.25106	T	0.35	.	.	.	.	.	1288	Q685J3	MUC17_HUMAN	K	1288	ENSP00000302716:T1288K	ENSP00000302716:T1288K	T	+	2	0	MUC17	100465280	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.039000	0.13884	-1.561000	0.01684	-2.053000	0.00404	ACG	C|0.936;A|0.064	0.064	strong		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
OR8H3	390152	hgsc.bcm.edu	37	11	55890066	55890066	+	Missense_Mutation	SNP	G	G	A	rs140843028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55890066G>A	ENST00000313472.3	+	1	218	c.218G>A	c.(217-219)aGt>aAt	p.S73N		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	73						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)					ATTGACCTCAGTTACTCAACT	0.448													G|||	73	0.0145767	0.0499	0.0101	5008	,	,		20989	0.0		0.0	False		,,,				2504	0.0				p.S73N		Atlas-SNP	.											.	OR8H3	92	.	0			c.G218A						PASS	.	G	ASN/SER	175,4227	115.0+/-153.0	4,167,2030	255.0	252.0	253.0		218	-0.2	0.9	11	dbSNP_134	253	4,8582	4.3+/-15.6	0,4,4289	no	missense	OR8H3	NM_001005201.1	46	4,171,6319	AA,AG,GG		0.0466,3.9755,1.3782	possibly-damaging	73/313	55890066	179,12809	2201	4293	6494	SO:0001583	missense	390152	exon1			ACCTCAGTTACTC	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.218G>A	11.37:g.55890066G>A	ENSP00000323928:p.Ser73Asn	Somatic	368	0	0		WXS	Illumina HiSeq	Phase_I	390	160	0.410256	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	26	0.011904761904761904	22	0.044715447154471545	4	0.011049723756906077	0	0.0	0	0.0	G	11.76	1.735059	0.30774	0.039755	4.66E-4	ENSG00000181761	ENST00000313472	T	0.01359	4.98	3.44	-0.164	0.13359	GPCR, rhodopsin-like superfamily (1);	0.421176	0.23038	N	0.052645	T	0.00875	0.0029	M	0.86864	2.845	0.09310	N	1	D	0.56287	0.975	P	0.52267	0.694	T	0.26849	-1.0091	10	0.87932	D	0	.	3.7935	0.08730	0.0939:0.291:0.4667:0.1484	.	73	Q8N146	OR8H3_HUMAN	N	73	ENSP00000323928:S73N	ENSP00000323928:S73N	S	+	2	0	OR8H3	55646642	0.006000	0.16342	0.902000	0.35471	0.267000	0.26476	1.600000	0.36762	0.075000	0.16796	0.173000	0.16961	AGT	G|0.986;A|0.014	0.014	weak		0.448	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
FEZ2	9637	hgsc.bcm.edu	37	2	36810586	36810586	+	Silent	SNP	T	T	C	rs14291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:36810586T>C	ENST00000405912.3	-	3	401	c.402A>G	c.(400-402)acA>acG	p.T134T	FEZ2_ENST00000305852.7_5'UTR|FEZ2_ENST00000379245.4_Silent_p.T134T	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	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	106	106	1	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		
JAK1	3716	hgsc.bcm.edu	37	1	65300305	65300305	+	Silent	SNP	T	T	C	rs369143723		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:65300305T>C	ENST00000342505.4	-	25	3653	c.3405A>G	c.(3403-3405)caA>caG	p.Q1135Q		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	1135	Protein kinase 2. {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)	GATTGGATGGTTGGAATTCCC	0.313			Mis		ALL																																p.Q1135Q		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A3405G						PASS	.	T		1,3603		0,1,1801	104.0	98.0	100.0		3405	-4.4	0.6	1		100	0,8148		0,0,4074	no	coding-synonymous	JAK1	NM_002227.2		0,1,5875	CC,CT,TT		0.0,0.0277,0.0085		1135/1155	65300305	1,11751	1802	4074	5876	SO:0001819	synonymous_variant	3716	exon25			GGATGGTTGGAAT	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.3405A>G	1.37:g.65300305T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	166	78	0.46988	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																			.	.	none		0.313	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
SPEF2	79925	hgsc.bcm.edu	37	5	35779447	35779447	+	Splice_Site	SNP	A	A	C	rs2277044	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:35779447A>C	ENST00000356031.3	+	30	4600	c.4446A>C	c.(4444-4446)aaA>aaC	p.K1482N	SPEF2_ENST00000440995.2_Splice_Site_p.K1477N|SPEF2_ENST00000303129.4_5'UTR|CTD-2113L7.1_ENST00000510433.1_RNA	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1482			K -> N (in dbSNP:rs2277044).		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)			TGGCACCTAAAGGTAGGAAAA	0.388													C|||	384	0.0766773	0.1505	0.0058	5008	,	,		18939	0.0397		0.0	False		,,,				2504	0.1442				p.K1482N		Atlas-SNP	.											SPEF2_ENST00000356031,NS,carcinoma,+1,1	SPEF2	324	1	0			c.A4446C						PASS	.	C	ASN/LYS	608,3096		55,498,1299	57.0	50.0	52.0		4446	4.5	1.0	5	dbSNP_100	52	16,8190		0,16,4087	yes	missense-near-splice	SPEF2	NM_024867.3	94	55,514,5386	CC,CA,AA		0.195,16.4147,5.2393	probably-damaging	1482/1823	35779447	624,11286	1852	4103	5955	SO:0001630	splice_region_variant	79925	exon30			ACCTAAAGGTAGG	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.4447+1A>C	5.37:g.35779447A>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	104	0.047619047619047616	83	0.16869918699186992	2	0.0055248618784530384	19	0.033216783216783216	0	0.0	C	17.66	3.445688	0.63178	0.164147	0.00195	ENSG00000152582	ENST00000356031;ENST00000440995	T;T	0.64085	-0.08;-0.08	5.64	4.48	0.54585	.	0.370098	0.30419	N	0.009667	T	0.00384	0.0012	L	0.38175	1.15	0.09310	P	1.0	D;D	0.76494	0.999;0.995	D;P	0.68192	0.956;0.722	T	0.10314	-1.0635	9	0.25751	T	0.34	.	11.6457	0.51259	0.8515:0.1485:0.0:0.0	rs2277044;rs2277044	1477;1482	Q9C093-2;Q9C093	.;SPEF2_HUMAN	N	1482;1477	ENSP00000348314:K1482N;ENSP00000412125:K1477N	ENSP00000348314:K1482N	K	+	3	2	SPEF2	35815204	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	2.266000	0.43320	1.153000	0.42468	-0.264000	0.10439	AAA	A|0.949;C|0.051	0.051	strong		0.388	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	Missense_Mutation
PLEKHG7	440107	hgsc.bcm.edu	37	12	93150102	93150102	+	Missense_Mutation	SNP	T	T	C	rs924326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:93150102T>C	ENST00000344636.3	+	8	819	c.635T>C	c.(634-636)aTg>aCg	p.M212T		NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	212			M -> T (in dbSNP:rs924326).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						AAAGAACACATGGCAGAAAAC	0.353													t|||	3243	0.647564	0.5628	0.7017	5008	,	,		22869	0.8919		0.4871	False		,,,				2504	0.637				p.M212T		Atlas-SNP	.											.	PLEKHG7	38	.	0			c.T635C						PASS	.	T	THR/MET	2374,2032	564.2+/-381.4	630,1114,459	86.0	87.0	86.0		635	1.1	1.0	12	dbSNP_86	86	4215,4385	582.5+/-391.4	1040,2135,1125	yes	missense	PLEKHG7	NM_001004330.2	81	1670,3249,1584	CC,CT,TT		49.0116,46.1189,49.3388	benign	212/380	93150102	6589,6417	2203	4300	6503	SO:0001583	missense	440107	exon8			AACACATGGCAGA	AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"""Pleckstrin homology (PH) domain containing"""	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.635T>C	12.37:g.93150102T>C	ENSP00000344961:p.Met212Thr	Somatic	396	2	0.00505051		WXS	Illumina HiSeq	Phase_I	331	327	0.987915	NM_001004330	B2RNR7	Missense_Mutation	SNP	ENST00000344636.3	37	CCDS31873.1	1401	0.6414835164835165	268	0.5447154471544715	246	0.6795580110497238	516	0.9020979020979021	371	0.4894459102902375	C	0.014	-1.585935	0.00872	0.538811	0.490116	ENSG00000187510	ENST00000344636	T	0.29655	1.56	4.92	1.11	0.20524	Pleckstrin homology-type (1);	0.450495	0.26742	N	0.022734	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.42327	-0.9458	9	0.02654	T	1	-0.012	1.0247	0.01525	0.2402:0.1579:0.1232:0.4787	rs924326;rs52824540;rs60008903;rs924326	212	Q6ZR37	PKHG7_HUMAN	T	212	ENSP00000344961:M212T	ENSP00000344961:M212T	M	+	2	0	PLEKHG7	91674233	0.000000	0.05858	0.983000	0.44433	0.272000	0.26649	-0.625000	0.05534	-0.061000	0.13110	-1.280000	0.01385	ATG	T|0.427;C|0.573	0.573	strong		0.353	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330	
NTAN1	123803	hgsc.bcm.edu	37	16	15133889	15133889	+	Silent	SNP	T	T	G	rs14347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:15133889T>G	ENST00000287706.3	-	8	668	c.576A>C	c.(574-576)gcA>gcC	p.A192A	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	192					adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						CTTGAAAGGATGCTCTGTAAA	0.458													G|||	1726	0.344649	0.1846	0.5331	5008	,	,		20562	0.372		0.3072	False		,,,				2504	0.4376				p.A192A		Atlas-SNP	.											.	NTAN1	21	.	0			c.A576C						PASS	.	G		1000,3394	729.0+/-410.0	121,758,1318	115.0	121.0	119.0		576	-1.8	0.9	16	dbSNP_52	119	2588,6012	689.3+/-404.4	360,1868,2072	no	coding-synonymous	NTAN1	NM_173474.2		481,2626,3390	GG,GT,TT		30.093,22.7583,27.6127		192/311	15133889	3588,9406	2197	4300	6497	SO:0001819	synonymous_variant	123803	exon8			AAAGGATGCTCTG	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.576A>C	16.37:g.15133889T>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_173474	Q7Z4Z0	Silent	SNP	ENST00000287706.3	37	CCDS10558.1																																																																																			T|0.710;G|0.290	0.290	strong		0.458	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474	
PLXND1	23129	hgsc.bcm.edu	37	3	129293256	129293256	+	Missense_Mutation	SNP	T	T	C	rs2255703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129293256T>C	ENST00000324093.4	-	12	2786	c.2608A>G	c.(2608-2610)Atg>Gtg	p.M870V	PLXND1_ENST00000393239.1_Missense_Mutation_p.M870V	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	870			M -> V (in dbSNP:rs2255703).		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						TCACTCCACATGCACAGGTGA	0.677													C|||	2564	0.511981	0.7247	0.3559	5008	,	,		16048	0.5109		0.4115	False		,,,				2504	0.4397				p.M870V	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											PLXND1,colon,carcinoma,0,1	PLXND1	149	1	0			c.A2608G						PASS	.	C	VAL/MET	2954,1450		1003,948,251	22.0	25.0	24.0		2608	0.9	0.7	3	dbSNP_100	24	3368,5228		673,2022,1603	yes	missense	PLXND1	NM_015103.2	21	1676,2970,1854	CC,CT,TT		39.181,32.9246,48.6308	benign	870/1926	129293256	6322,6678	2202	4298	6500	SO:0001583	missense	23129	exon12			TCCACATGCACAG	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.2608A>G	3.37:g.129293256T>C	ENSP00000317128:p.Met870Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	1045	0.4784798534798535	334	0.6788617886178862	131	0.36187845303867405	275	0.4807692307692308	305	0.4023746701846966	C	0.004	-2.338084	0.00224	0.670754	0.39181	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.29142	1.63;1.58	4.32	0.907	0.19321	.	0.700883	0.13388	N	0.391612	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	0.32295	-0.9912	9	0.19590	T	0.45	.	2.0191	0.03505	0.1277:0.3212:0.1259:0.4252	rs2255703;rs52797788;rs60959372;rs2255703	870	Q9Y4D7	PLXD1_HUMAN	V	870	ENSP00000317128:M870V;ENSP00000376931:M870V	ENSP00000317128:M870V	M	-	1	0	PLXND1	130775946	0.011000	0.17503	0.724000	0.30704	0.025000	0.11179	0.079000	0.14782	0.076000	0.16826	-1.183000	0.01708	ATG	T|0.496;C|0.504	0.504	strong		0.677	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
ARHGAP23	57636	hgsc.bcm.edu	37	17	36623157	36623157	+	Silent	SNP	G	G	A	rs12326006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36623157G>A	ENST00000431231.2	+	7	1301	c.1233G>A	c.(1231-1233)ctG>ctA	p.L411L	ARHGAP23_ENST00000443378.1_Silent_p.L317L|ARHGAP23_ENST00000437668.3_Silent_p.L411L	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	411					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(8)|kidney(6)|lung(1)|skin(1)|stomach(2)	20						TGCAGGGCCTGGATGACCTCG	0.706													G|||	273	0.0545128	0.1974	0.0173	5008	,	,		13202	0.0		0.0	False		,,,				2504	0.0				p.L411L		Atlas-SNP	.											.	ARHGAP23	48	.	0			c.G1233A						PASS	.						3.0	4.0	4.0					17																	36623157		622	1470	2092	SO:0001819	synonymous_variant	57636	exon7			GGGCCTGGATGAC	AB040934	CCDS56027.1	17q12	2014-05-06			ENSG00000225485	ENSG00000275832		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	29293	protein-coding gene	gene with protein product		610590				10819331, 15254754	Standard	NM_001199417		Approved	KIAA1501	uc021twd.1	Q9P227	OTTHUMG00000188547	ENST00000431231.2:c.1233G>A	17.37:g.36623157G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_001199417		Silent	SNP	ENST00000431231.2	37	CCDS56027.1																																																																																			G|0.964;A|0.036	0.036	strong		0.706	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1	XM_290799	
PRR25	388199	hgsc.bcm.edu	37	16	855732	855732	+	Missense_Mutation	SNP	C	C	T	rs115484509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:855732C>T	ENST00000301698.1	+	1	290	c.290C>T	c.(289-291)gCg>gTg	p.A97V		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	97										large_intestine(1)|lung(1)|skin(1)	3						TCAGGAACAGCGCAGCCGCTC	0.652													C|||	129	0.0257588	0.0938	0.0072	5008	,	,		17511	0.0		0.0	False		,,,				2504	0.0				p.A97V		Atlas-SNP	.											PRR25,NS,carcinoma,+1,1	PRR25	27	1	0			c.C290T						PASS	.	C	VAL/ALA	307,3571		16,275,1648	21.0	28.0	26.0		290	-0.5	0.0	16	dbSNP_132	26	1,8279		0,1,4139	yes	missense	PRR25	NM_001013638.1	64	16,276,5787	TT,TC,CC		0.0121,7.9165,2.5333	possibly-damaging	97/403	855732	308,11850	1939	4140	6079	SO:0001583	missense	388199	exon1			GAACAGCGCAGCC	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.290C>T	16.37:g.855732C>T	ENSP00000301698:p.Ala97Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001013638		Missense_Mutation	SNP	ENST00000301698.1	37	CCDS45372.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	C	8.111	0.778895	0.16120	0.079165	1.21E-4	ENSG00000167945	ENST00000301698	T	0.38401	1.14	0.701	-0.467	0.12150	.	.	.	.	.	T	0.00815	0.0027	N	0.19112	0.55	0.09310	N	1	P	0.39964	0.697	B	0.29440	0.102	T	0.07121	-1.0789	8	0.87932	D	0	.	.	.	.	.	97	Q96S07	PRR25_HUMAN	V	97	ENSP00000301698:A97V	ENSP00000301698:A97V	A	+	2	0	PRR25	795733	0.000000	0.05858	0.013000	0.15412	0.030000	0.12068	-0.594000	0.05733	-0.199000	0.10317	0.313000	0.20887	GCG	C|0.977;T|0.023	0.023	strong		0.652	PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638	
SLC38A10	124565	hgsc.bcm.edu	37	17	79220224	79220224	+	Missense_Mutation	SNP	G	G	C	rs2725405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	47	0	0		WXS	Illumina HiSeq	Phase_I	51	30	0.588235	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	
MKI67	4288	hgsc.bcm.edu	37	10	129906903	129906903	+	Silent	SNP	C	C	T	rs3740424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129906903C>T	ENST00000368654.3	-	13	3576	c.3201G>A	c.(3199-3201)acG>acA	p.T1067T	MKI67_ENST00000484853.1_5'Flank|MKI67_ENST00000368653.3_Silent_p.T707T	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1067	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)				ACTCCTTAAACGTTCTGATGC	0.547													C|||	360	0.071885	0.031	0.0029	5008	,	,		19029	0.1548		0.0149	False		,,,				2504	0.1493				p.T1067T		Atlas-SNP	.											.	MKI67	363	.	0			c.G3201A						PASS	.	C	,	111,4295	86.3+/-125.0	0,111,2092	232.0	209.0	217.0		2121,3201	-3.4	0.0	10	dbSNP_107	217	65,8535	40.3+/-97.0	1,63,4236	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	1,174,6328	TT,TC,CC		0.7558,2.5193,1.3532	,	707/2897,1067/3257	129906903	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			CTTAAACGTTCTG	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.3201G>A	10.37:g.129906903C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	223	107	0.479821	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			C|0.970;T|0.030	0.030	strong		0.547	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
WDR87	83889	hgsc.bcm.edu	37	19	38375666	38375666	+	Missense_Mutation	SNP	C	C	T	rs73027451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38375666C>T	ENST00000303868.5	-	6	8752	c.8528G>A	c.(8527-8529)cGg>cAg	p.R2843Q	WDR87_ENST00000447313.2_Missense_Mutation_p.R2882Q	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2843										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						GATCCCATACCGGGCAATGCC	0.557													C|||	830	0.165735	0.1573	0.1455	5008	,	,		19065	0.12		0.1938	False		,,,				2504	0.2096				p.R2843Q		Atlas-SNP	.											.	WDR87	191	.	0			c.G8528A						PASS	.	C	GLN/ARG	252,1132		27,198,467	34.0	34.0	34.0		8528	2.5	0.9	19	dbSNP_130	34	550,2632		43,464,1084	yes	missense	WDR87	NM_031951.3	43	70,662,1551	TT,TC,CC		17.2847,18.2081,17.5646	benign	2843/2874	38375666	802,3764	692	1591	2283	SO:0001583	missense	83889	exon6			CCATACCGGGCAA	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.8528G>A	19.37:g.38375666C>T	ENSP00000368025:p.Arg2843Gln	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	340	0.15567765567765568	65	0.13211382113821138	51	0.1408839779005525	73	0.12762237762237763	151	0.19920844327176782	C	10.23	1.292736	0.23564	0.182081	0.172847	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.09538	2.97;2.97	4.67	2.45	0.29901	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.51012	P	9.40000000000385E-5	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.44772	-0.9306	8	0.02654	T	1	.	5.7628	0.18209	0.0:0.2157:0.0:0.7843	.	2843;2882	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	Q	2882;2843	ENSP00000405012:R2882Q;ENSP00000368025:R2843Q	ENSP00000368025:R2843Q	R	-	2	0	WDR87	43067506	0.783000	0.28701	0.943000	0.38184	0.496000	0.33645	0.953000	0.29162	0.905000	0.36596	-0.693000	0.03709	CGG	C|0.835;T|0.166	0.166	strong		0.557	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
PSG8	440533	hgsc.bcm.edu	37	19	43269704	43269704	+	Silent	SNP	T	T	C	rs71337226|rs34129574|rs62112127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43269704T>C	ENST00000306511.4	-	1	127	c.30A>G	c.(28-30)acA>acG	p.T10T	PSG8_ENST00000406636.3_Silent_p.T10T|PSG8_ENST00000404209.4_Silent_p.T10T|PSG8_ENST00000401467.2_Intron	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	10				TQR -> MQH (in Ref. 2; CAH18672). {ECO:0000305}.		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)				TGATGCGCTGTGTGCAGGGAG	0.597													.|||	1834	0.366214	0.7322	0.2781	5008	,	,		17082	0.0933		0.3241	False		,,,				2504	0.2587				p.T10T		Atlas-SNP	.											.	PSG8	101	.	0			c.A30G						PASS	.	C	,,	1742,1280		670,402,439	120.0	120.0	120.0		30,30,30	-1.0	0.0	19	dbSNP_129	120	1357,4061		286,785,1638	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	,,	956,1187,2077	CC,CT,TT		25.0461,42.3561,36.718	,,	10/420,10/298,10/427	43269704	3099,5341	1511	2709	4220	SO:0001819	synonymous_variant	440533	exon1			GCGCTGTGTGCAG	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.30A>G	19.37:g.43269704T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001130168	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Silent	SNP	ENST00000306511.4	37	CCDS33037.1																																																																																			T|0.624;C|0.376	0.376	strong		0.597	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
KIF21B	23046	hgsc.bcm.edu	37	1	200978412	200978412	+	Silent	SNP	C	C	T	rs7556510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200978412C>T	ENST00000422435.2	-	2	562	c.246G>A	c.(244-246)acG>acA	p.T82T	KIF21B_ENST00000332129.2_Silent_p.T82T|KIF21B_ENST00000461742.2_Silent_p.T82T|KIF21B_ENST00000360529.5_Silent_p.T82T	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	82	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						AGGCCAGCACCGTGGCATTAT	0.557													C|||	399	0.0796725	0.2897	0.0202	5008	,	,		21098	0.0		0.001	False		,,,				2504	0.001				p.T82T		Atlas-SNP	.											.	KIF21B	208	.	0			c.G246A						PASS	.	C		1105,3301	396.5+/-330.1	120,865,1218	99.0	88.0	92.0		246	-3.9	1.0	1	dbSNP_116	92	42,8558	28.5+/-78.6	1,40,4259	no	coding-synonymous	KIF21B	NM_017596.2		121,905,5477	TT,TC,CC		0.4884,25.0794,8.819		82/1625	200978412	1147,11859	2203	4300	6503	SO:0001819	synonymous_variant	23046	exon2			CAGCACCGTGGCA	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.246G>A	1.37:g.200978412C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	142	62	0.43662	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	37	CCDS58056.1																																																																																			C|0.922;T|0.078	0.078	strong		0.557	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
CRELD2	79174	hgsc.bcm.edu	37	22	50315971	50315971	+	Intron	SNP	C	C	G	rs377640443|rs71805922|rs386822608|rs386822607|rs73891177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50315971C>G	ENST00000328268.4	+	6	666				CRELD2_ENST00000403427.3_Intron|CRELD2_ENST00000407217.3_Intron|CRELD2_ENST00000404488.3_Missense_Mutation_p.P207A|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)		CGATTCTTACCCGCCTTGCTG	0.612													C|||	553	0.110423	0.3419	0.0231	5008	,	,		14622	0.0367		0.0149	False		,,,				2504	0.0337				p.P207A		Atlas-SNP	.											.	CRELD2	57	.	0			c.C619G						PASS	.						28.0	31.0	30.0					22																	50315971		1548	3578	5126	SO:0001627	intron_variant	79174	exon6			TCTTACCCGCCTT	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.593-289C>G	22.37:g.50315971C>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Missense_Mutation	SNP	ENST00000328268.4	37	CCDS14082.1	177	0.08104395604395605	136	0.2764227642276423	7	0.019337016574585635	22	0.038461538461538464	12	0.0158311345646438	C	0.266	-0.996275	0.02145	.	.	ENSG00000184164	ENST00000404488	T	0.51071	0.72	1.32	-2.64	0.06114	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	N	1	B	0.14805	0.011	B	0.08055	0.003	T	0.21314	-1.0249	8	0.13470	T	0.59	.	4.967	0.14096	0.2351:0.5907:0.0:0.1742	.	207	Q6UXH1-5	.	A	207	ENSP00000383938:P207A	ENSP00000383938:P207A	P	+	1	0	CRELD2	48701975	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.308000	0.01131	-2.211000	0.00737	-1.172000	0.01736	CCG	C|0.933;G|0.067	0.067	strong		0.612	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
USP35	57558	hgsc.bcm.edu	37	11	77920563	77920563	+	Silent	SNP	G	G	T	rs2510045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000530535.1_3'UTR|USP35_ENST00000441408.2_Silent_p.P140P	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	118	0	0		WXS	Illumina HiSeq	Phase_I	161	79	0.490683	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	
ALDH3A1	218	hgsc.bcm.edu	37	17	19642952	19642952	+	Missense_Mutation	SNP	G	G	C	rs2228100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19642952G>C	ENST00000457500.2	-	7	1314	c.985C>G	c.(985-987)Ccg>Gcg	p.P329A	RP11-311F12.2_ENST00000580884.1_RNA|ALDH3A1_ENST00000395555.3_Intron|ALDH3A1_ENST00000444455.1_Missense_Mutation_p.P329A|ALDH3A1_ENST00000494157.2_Missense_Mutation_p.P256A|ALDH3A1_ENST00000225740.6_Missense_Mutation_p.P329A|ALDH3A1_ENST00000485231.1_5'Flank	NM_001135168.1	NP_001128640.1	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3 family, member A1	329			P -> A (in allele ALDH3A1*2; dbSNP:rs2228100). {ECO:0000269|PubMed:9250352}.		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)		TGCATCACCGGGGACTGGGGG	0.637													G|||	1903	0.379992	0.4758	0.3098	5008	,	,		18858	0.4395		0.2396	False		,,,				2504	0.3834				p.P329A		Atlas-SNP	.											.	ALDH3A1	40	.	0			c.C985G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO	2033,2373	555.8+/-379.4	453,1127,623	50.0	45.0	47.0		985,985,985	2.6	0.9	17	dbSNP_98	47	2160,6440	363.6+/-333.2	266,1628,2406	yes	missense,missense,missense	ALDH3A1	NM_000691.4,NM_001135167.1,NM_001135168.1	27,27,27	719,2755,3029	CC,CG,GG		25.1163,46.1416,32.239	benign,benign,benign	329/454,329/454,329/454	19642952	4193,8813	2203	4300	6503	SO:0001583	missense	218	exon7			TCACCGGGGACTG	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.985C>G	17.37:g.19642952G>C	ENSP00000411821:p.Pro329Ala	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_001135168	A8K828|Q9BT37	Missense_Mutation	SNP	ENST00000457500.2	37	CCDS11212.1	759	0.3475274725274725	230	0.46747967479674796	109	0.3011049723756906	247	0.4318181818181818	173	0.22823218997361477	G	9.982	1.228526	0.22542	0.461416	0.251163	ENSG00000108602	ENST00000225740;ENST00000379258;ENST00000444455;ENST00000457500;ENST00000457844;ENST00000439102	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	4.82	2.57	0.30868	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.459276	0.24947	N	0.034329	T	0.00012	0.0000	N	0.11756	0.17	0.31477	P	0.667686	B;B;B	0.18310	0.0;0.027;0.0	B;B;B	0.17722	0.0;0.019;0.0	T	0.39313	-0.9620	9	0.29301	T	0.29	-36.1848	11.1793	0.48618	0.0:0.0:0.6212:0.3788	rs2228100;rs3744696;rs56956419;rs2228100	329;446;329	A8K828;Q8N9T9;P30838	.;.;AL3A1_HUMAN	A	329;387;329;329;256;329	ENSP00000225740:P329A;ENSP00000388469:P329A;ENSP00000411821:P329A;ENSP00000389766:P329A	ENSP00000225740:P329A	P	-	1	0	ALDH3A1	19583544	0.256000	0.24012	0.947000	0.38551	0.652000	0.38707	0.843000	0.27640	2.232000	0.73038	0.655000	0.94253	CCG	G|0.662;C|0.338	0.338	strong		0.637	ALDH3A1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132265.4	NM_000691	
GSTM5	2949	hgsc.bcm.edu	37	1	110257831	110257831	+	Missense_Mutation	SNP	T	T	C	rs2227963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110257831T>C	ENST00000256593.3	+	7	594	c.536T>C	c.(535-537)cTa>cCa	p.L179P	GSTM5_ENST00000369813.1_Missense_Mutation_p.L138P|GSTM5_ENST00000492718.1_3'UTR|GSTM5_ENST00000369812.5_Missense_Mutation_p.L198P	NM_000851.3	NP_000842.2	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5	179	GST C-terminal.		L -> P (in dbSNP:rs2227963).		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)	p.L179P(4)		NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	GACGCCTTCCTAAACTTGAAG	0.478													T|||	703	0.140375	0.3941	0.0663	5008	,	,		19912	0.001		0.0845	False		,,,				2504	0.0511				p.L179P		Atlas-SNP	.											GSTM5,scalp,carcinoma,0,13	GSTM5	89	13	4	Substitution - Missense(4)	central_nervous_system(3)|skin(1)	c.T536C						PASS	.	T	PRO/LEU	1097,3309		276,545,1382	189.0	205.0	199.0		536	3.1	0.7	1	dbSNP_98	199	399,8201		16,367,3917	yes	missense	GSTM5	NM_000851.3	98	292,912,5299	CC,CT,TT		4.6395,24.8979,11.5024	benign	179/219	110257831	1496,11510	2203	4300	6503	SO:0001583	missense	2949	exon7			CCTTCCTAAACTT	L02321	CCDS811.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134201	ENSG00000134201	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4637	protein-coding gene	gene with protein product		138385	"""glutathione S-transferase M5"""			8473333	Standard	NM_000851		Approved		uc001dyn.3	P46439	OTTHUMG00000011644	ENST00000256593.3:c.536T>C	1.37:g.110257831T>C	ENSP00000256593:p.Leu179Pro	Somatic	545	1	0.00183486		WXS	Illumina HiSeq	Phase_I	585	287	0.490598	NM_000851	A8K0V8|Q6PD78	Missense_Mutation	SNP	ENST00000256593.3	37	CCDS811.1	295	0.13507326007326007	204	0.4146341463414634	26	0.0718232044198895	0	0.0	65	0.08575197889182058	t	0.004	-2.358658	0.00214	0.248979	0.046395	ENSG00000134201	ENST00000256593;ENST00000369813;ENST00000369812	T;T;T	0.00691	5.84;5.84;5.84	5.02	3.11	0.35812	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.335277	0.25598	N	0.029571	T	0.00039	0.0001	N	0.00005	-3.3	0.27811	P	0.9421374	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.07673	-1.0760	9	0.02654	T	1	.	6.4549	0.21924	0.317:0.597:0.0:0.0859	rs2227963;rs61309452	138;179	Q5T8Q9;P46439	.;GSTM5_HUMAN	P	179;138;198	ENSP00000256593:L179P;ENSP00000358828:L138P;ENSP00000358827:L198P	ENSP00000256593:L179P	L	+	2	0	GSTM5	110059354	0.997000	0.39634	0.702000	0.30337	0.065000	0.16274	3.314000	0.51943	0.584000	0.29591	-0.206000	0.12725	CTA	T|0.847;C|0.153	0.153	strong		0.478	GSTM5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032200.1	NM_000851	
SYTL2	54843	hgsc.bcm.edu	37	11	85436868	85436868	+	Intron	SNP	G	G	C	rs597480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:85436868G>C	ENST00000528231.1	-	7	1737				SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000359152.5_Missense_Mutation_p.A735G|SYTL2_ENST00000354566.3_Missense_Mutation_p.A211G|SYTL2_ENST00000525423.1_Missense_Mutation_p.A211G|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000389960.4_Intron	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CTCAGTATCAGCAAAATCTGT	0.398													G|||	2613	0.521765	0.4077	0.4986	5008	,	,		21672	0.5972		0.6282	False		,,,				2504	0.5051				p.A211G		Atlas-SNP	.											.	SYTL2	231	.	0			c.C632G						PASS	.	G	,,,GLY/ALA,GLY/ALA	1927,2479	547.8+/-377.4	436,1055,712	147.0	133.0	138.0		,,,632,632	3.0	0.0	11	dbSNP_83	138	5436,3162	655.2+/-401.2	1734,1968,597	yes	intron,intron,intron,missense,missense	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,60,60	2170,3023,1309	CC,CG,GG		36.776,43.7358,43.379	,,,possibly-damaging,possibly-damaging	,,,211/1273,211/1257	85436868	7363,5641	2203	4299	6502	SO:0001627	intron_variant	54843	exon1			GTATCAGCAAAAT	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2070C>G	11.37:g.85436868G>C		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	200	200	1	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	1202	0.5503663003663004	207	0.42073170731707316	195	0.5386740331491713	323	0.5646853146853147	477	0.6292875989445911	G	11.68	1.709859	0.30322	0.437358	0.63224	ENSG00000137501	ENST00000359152;ENST00000354566;ENST00000525423	T;T;T	0.33654	1.4;1.41;1.41	6.03	2.97	0.34412	.	0.135236	0.33792	N	0.004544	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;P;P	0.37370	0.592;0.592;0.592	B;B;B	0.40199	0.322;0.322;0.322	T	0.37337	-0.9710	8	.	.	.	-0.2866	5.1608	0.15060	0.2405:0.1501:0.6094:0.0	rs597480;rs17810982;rs56612956;rs597480	211;211;211	Q9HCH5-11;Q9HCH5-7;Q9HCH5-8	.;.;.	G	735;211;211	ENSP00000352065:A735G;ENSP00000346576:A211G;ENSP00000432694:A211G	.	A	-	2	0	SYTL2	85114516	0.000000	0.05858	0.009000	0.14445	0.899000	0.52679	0.469000	0.22067	0.849000	0.35215	0.655000	0.94253	GCT	G|0.491;C|0.509	0.509	strong		0.398	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
SLC3A1	6519	hgsc.bcm.edu	37	2	44547672	44547672	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44547672A>G	ENST00000260649.6	+	10	2028	c.1952A>G	c.(1951-1953)aAc>aGc	p.N651S	PREPL_ENST00000409957.1_3'UTR|PREPL_ENST00000541738.1_3'UTR|SLC3A1_ENST00000409380.1_Missense_Mutation_p.N373S|PREPL_ENST00000409411.1_3'UTR|PREPL_ENST00000409936.1_3'UTR|SLC3A1_ENST00000409740.3_Missense_Mutation_p.N282S	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	651					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)	TTTGAACACAACACGAAGAAT	0.418																																					p.N651S		Atlas-SNP	.											SLC3A1,NS,carcinoma,-1,1	SLC3A1	62	1	0			c.A1952G						scavenged	.						104.0	89.0	94.0					2																	44547672		2203	4300	6503	SO:0001583	missense	6519	exon10			AACACAACACGAA		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.1952A>G	2.37:g.44547672A>G	ENSP00000260649:p.Asn651Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	130	3	0.0230769	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Missense_Mutation	SNP	ENST00000260649.6	37	CCDS1819.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508605	0.27036	.	.	ENSG00000138079	ENST00000260649;ENST00000540334;ENST00000409380;ENST00000409740	D;D;D	0.99023	-5.34;-4.77;-4.42	5.99	0.419	0.16438	.	0.636516	0.17209	N	0.182836	D	0.93906	0.8050	N	0.11927	0.2	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	D	0.87273	0.2287	10	0.07175	T	0.84	-2.2702	6.9945	0.24774	0.5478:0.1428:0.3094:0.0	.	651	Q07837	SLC31_HUMAN	S	651;587;373;282	ENSP00000260649:N651S;ENSP00000386709:N373S;ENSP00000386677:N282S	ENSP00000260649:N651S	N	+	2	0	SLC3A1	44401176	0.020000	0.18652	0.054000	0.19295	0.868000	0.49771	0.316000	0.19469	0.131000	0.18576	0.533000	0.62120	AAC	.	.	none		0.418	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	
CTSG	1511	hgsc.bcm.edu	37	14	25045386	25045386	+	Missense_Mutation	SNP	C	C	G	rs61737123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:25045386C>G	ENST00000216336.2	-	1	80	c.44G>C	c.(43-45)gGg>gCg	p.G15A		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	15					angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|defense response to fungus (GO:0050832)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|negative regulation of growth of symbiont in host (GO:0044130)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|positive regulation of immune response (GO:0050778)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	heparin binding (GO:0008201)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(265;0.0269)		TGCCTCAGCCCCAGTGGGTAG	0.527													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		18510	0.0		0.0	False		,,,				2504	0.0				p.G15A		Atlas-SNP	.											.	CTSG	63	.	0			c.G44C						PASS	.	C	ALA/GLY	228,4178	128.6+/-165.4	7,214,1982	63.0	54.0	57.0		44	1.1	0.0	14	dbSNP_129	57	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CTSG	NM_001911.2	60	7,216,6280	GG,GC,CC		0.0233,5.1748,1.7684	probably-damaging	15/256	25045386	230,12776	2203	4300	6503	SO:0001583	missense	1511	exon1			TCAGCCCCAGTGG	M16117	CCDS9631.1	14q12	2013-02-25			ENSG00000100448	ENSG00000100448		"""Cathepsins"", ""Endogenous ligands"""	2532	protein-coding gene	gene with protein product		116830				2569462	Standard	NM_001911		Approved	CG	uc001wpq.3	P08311	OTTHUMG00000140182	ENST00000216336.2:c.44G>C	14.37:g.25045386C>G	ENSP00000216336:p.Gly15Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_001911	Q6IBJ6|Q9UCA5|Q9UCU6	Missense_Mutation	SNP	ENST00000216336.2	37	CCDS9631.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	c	11.21	1.572963	0.28092	0.051748	2.33E-4	ENSG00000100448	ENST00000216336	D	0.92752	-3.1	5.29	1.14	0.20703	Peptidase cysteine/serine, trypsin-like (1);	0.801389	0.10545	N	0.662150	T	0.49406	0.1555	L	0.28400	0.85	0.09310	N	1	B	0.25312	0.123	B	0.21360	0.034	T	0.57774	-0.7753	10	0.06236	T	0.91	.	6.4789	0.22051	0.0:0.6773:0.1397:0.1829	rs61737123	15	P08311	CATG_HUMAN	A	15	ENSP00000216336:G15A	ENSP00000216336:G15A	G	-	2	0	CTSG	24115226	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.884000	0.28214	0.309000	0.22966	0.655000	0.94253	GGG	C|0.969;G|0.031	0.031	strong		0.527	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2	NM_001911	
FREM2	341640	hgsc.bcm.edu	37	13	39264083	39264083	+	Missense_Mutation	SNP	C	C	G	rs7329939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39264083C>G	ENST00000280481.7	+	1	2818	c.2602C>G	c.(2602-2604)Ctc>Gtc	p.L868V		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	868			L -> V (in dbSNP:rs7329939).		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)		CTCTTTCACTCTCACTCAGGC	0.507													C|||	315	0.0628994	0.208	0.0231	5008	,	,		21471	0.001		0.0089	False		,,,				2504	0.0143				p.L868V		Atlas-SNP	.											.	FREM2	385	.	0			c.C2602G						PASS	.	C	VAL/LEU	745,3661	306.3+/-289.4	68,609,1526	101.0	88.0	92.0		2602	5.8	1.0	13	dbSNP_116	92	88,8512	49.8+/-109.6	1,86,4213	yes	missense	FREM2	NM_207361.4	32	69,695,5739	GG,GC,CC		1.0233,16.9088,6.4047	benign	868/3170	39264083	833,12173	2203	4300	6503	SO:0001583	missense	341640	exon1			TTCACTCTCACTC	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.2602C>G	13.37:g.39264083C>G	ENSP00000280481:p.Leu868Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	114	64	0.561404	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	96	0.04395604395604396	82	0.16666666666666666	9	0.024861878453038673	0	0.0	5	0.006596306068601583	C	10.04	1.240711	0.22711	0.169088	0.010233	ENSG00000150893	ENST00000280481	T	0.43294	0.95	5.8	5.8	0.92144	.	0.062991	0.64402	D	0.000004	T	0.00109	0.0003	N	0.25647	0.755	0.19575	P	0.9999648898	B	0.30824	0.296	B	0.27262	0.078	T	0.03068	-1.1076	9	0.33940	T	0.23	.	20.0609	0.97674	0.0:1.0:0.0:0.0	rs7329939;rs52807873;rs7329939	868	Q5SZK8	FREM2_HUMAN	V	868	ENSP00000280481:L868V	ENSP00000280481:L868V	L	+	1	0	FREM2	38162083	0.038000	0.19896	1.000000	0.80357	0.329000	0.28539	0.383000	0.20651	2.755000	0.94549	0.655000	0.94253	CTC	C|0.947;G|0.053	0.053	strong		0.507	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
SGSM1	129049	hgsc.bcm.edu	37	22	25270455	25270455	+	Silent	SNP	G	G	C	rs9624633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25270455G>C	ENST00000400359.4	+	13	1372	c.1365G>C	c.(1363-1365)cgG>cgC	p.R455R	SGSM1_ENST00000400358.4_Intron	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	455						Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						CTGCAGGCCGGTCCATGCTGG	0.607													G|||	708	0.141374	0.0825	0.1369	5008	,	,		18657	0.1548		0.0944	False		,,,				2504	0.2587				p.R455R		Atlas-SNP	.											.	SGSM1	150	.	0			c.G1365C						PASS	.	G	,,,	317,3787		14,289,1749	42.0	45.0	44.0		1365,,,1365	1.1	0.2	22	dbSNP_119	44	930,7466		49,832,3317	no	coding-synonymous,intron,intron,coding-synonymous	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	,,,	63,1121,5066	CC,CG,GG		11.0767,7.7242,9.976	,,,	455/1149,,,455/1088	25270455	1247,11253	2052	4198	6250	SO:0001819	synonymous_variant	129049	exon13			AGGCCGGTCCATG	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.1365G>C	22.37:g.25270455G>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	157	81	0.515924	NM_133454	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																			G|0.883;C|0.117	0.117	strong		0.607	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
OR8B2	26595	hgsc.bcm.edu	37	11	124253042	124253042	+	Silent	SNP	G	G	A	rs142893914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124253042G>A	ENST00000375013.2	-	1	216	c.198C>T	c.(196-198)ctC>ctT	p.L66L		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	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)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CAATGAAGGAGAGATTGAAGA	0.398													g|||	90	0.0179712	0.0605	0.0115	5008	,	,		22840	0.0		0.002	False		,,,				2504	0.0				p.L66L		Atlas-SNP	.											.	OR8B2	42	.	0			c.C198T						PASS	.	G		271,4131	153.7+/-187.2	8,255,1938	154.0	143.0	147.0		198	-8.4	0.0	11	dbSNP_134	147	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous	OR8B2	NM_001005468.1		8,260,6229	AA,AG,GG		0.0582,6.1563,2.1241		66/314	124253042	276,12718	2201	4296	6497	SO:0001819	synonymous_variant	26595	exon1			GAAGGAGAGATTG	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"""GPCR / Class A : Olfactory receptors"""	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.198C>T	11.37:g.124253042G>A		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	175	87	0.497143	NM_001005468	Q8NGH2	Silent	SNP	ENST00000375013.2	37	CCDS31708.1																																																																																			.	.	weak		0.398	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468	
RHBDF1	64285	hgsc.bcm.edu	37	16	113027	113027	+	Missense_Mutation	SNP	G	G	A	rs78541046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:113027G>A	ENST00000262316.6	-	5	758	c.616C>T	c.(616-618)Cgc>Tgc	p.R206C	RHBDF1_ENST00000454039.2_Missense_Mutation_p.R206C	NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	206					cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				TCTCGCTTGCGCCGCCGCGGG	0.701													G|||	19	0.00379393	0.0144	0.0	5008	,	,		13623	0.0		0.0	False		,,,				2504	0.0				p.R206C		Atlas-SNP	.											.	RHBDF1	54	.	0			c.C616T						PASS	.	G	CYS/ARG	46,4332		1,44,2144	27.0	32.0	30.0		616	5.1	1.0	16	dbSNP_131	30	0,8578		0,0,4289	yes	missense	RHBDF1	NM_022450.3	180	1,44,6433	AA,AG,GG		0.0,1.0507,0.355	probably-damaging	206/856	113027	46,12910	2189	4289	6478	SO:0001583	missense	64285	exon5			GCTTGCGCCGCCG	BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"""chromosome 16 open reading frame 8"", ""rhomboid family 1 (Drosophila)"""	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.616C>T	16.37:g.113027G>A	ENSP00000262316:p.Arg206Cys	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	140	80	0.571429	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Missense_Mutation	SNP	ENST00000262316.6	37	CCDS32344.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	.	24.2	4.509855	0.85282	0.010507	0.0	ENSG00000007384	ENST00000262316;ENST00000454039	T;T	0.80304	-1.36;-1.36	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.86406	0.5925	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.994;0.998;0.999	D	0.88684	0.3204	10	0.62326	D	0.03	-33.0545	17.4836	0.87682	0.0:0.0:1.0:0.0	.	206;229;206	F5GWL4;B4E3Q0;Q96CC6	.;.;RHDF1_HUMAN	C	206	ENSP00000262316:R206C;ENSP00000392133:R206C	ENSP00000262316:R206C	R	-	1	0	RHBDF1	53027	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.266000	0.65525	2.354000	0.79902	0.462000	0.41574	CGC	G|0.996;A|0.004	0.004	strong		0.701	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450	
OR51V1	283111	hgsc.bcm.edu	37	11	5221132	5221132	+	Missense_Mutation	SNP	G	G	A	rs61736992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5221132G>A	ENST00000321255.1	-	1	798	c.799C>T	c.(799-801)Ctc>Ttc	p.L267F		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	267					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(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCATTGTGAGGCTAATGATA	0.483													G|||	126	0.0251597	0.0378	0.0086	5008	,	,		19744	0.0		0.0189	False		,,,				2504	0.0521				p.L267F		Atlas-SNP	.											.	OR51V1	77	.	0			c.C799T						PASS	.	G	PHE/LEU	182,4220	116.3+/-154.2	1,180,2020	134.0	117.0	123.0		799	1.4	0.0	11	dbSNP_129	123	209,8387	89.4+/-151.6	4,201,4093	yes	missense	OR51V1	NM_001004760.2	22	5,381,6113	AA,AG,GG		2.4314,4.1345,3.0082	probably-damaging	267/322	5221132	391,12607	2201	4298	6499	SO:0001583	missense	283111	exon1			TTGTGAGGCTAAT	BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"""GPCR / Class A : Olfactory receptors"""	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.799C>T	11.37:g.5221132G>A	ENSP00000321729:p.Leu267Phe	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	104	58	0.557692	NM_001004760		Missense_Mutation	SNP	ENST00000321255.1	37	CCDS31375.1	32	0.014652014652014652	15	0.03048780487804878	6	0.016574585635359115	0	0.0	11	0.014511873350923483	G	10.05	1.243241	0.22796	0.041345	0.024314	ENSG00000176742	ENST00000321255	T	0.72835	-0.69	5.27	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40144	N	0.001163	T	0.56992	0.2023	M	0.85373	2.75	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63972	-0.6516	10	0.87932	D	0	.	8.363	0.32369	0.3867:0.0:0.6133:0.0	.	267	Q9H2C8	O51V1_HUMAN	F	267	ENSP00000321729:L267F	ENSP00000321729:L267F	L	-	1	0	OR51V1	5177708	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.502000	0.06390	0.103000	0.17682	0.655000	0.94253	CTC	G|0.975;A|0.025	0.025	strong		0.483	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760	
LILRA6	79168	hgsc.bcm.edu	37	19	54744722	54744722	+	Missense_Mutation	SNP	T	T	C	rs56257556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54744722T>C	ENST00000396365.2	-	5	979	c.940A>G	c.(940-942)Aac>Gac	p.N314D	LILRA6_ENST00000419410.2_Missense_Mutation_p.N314D|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000245621.5_Missense_Mutation_p.N314D|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Missense_Mutation_p.N314D|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	314	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ATCAGGATGTTCAGGGGGTCG	0.682																																					p.N314D		Atlas-SNP	.											LILRA6,NS,carcinoma,+2,1	LILRA6	75	1	0			c.A940G						scavenged	.						22.0	32.0	29.0					19																	54744722		2100	4147	6247	SO:0001583	missense	79168	exon5			GGATGTTCAGGGG	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.940A>G	19.37:g.54744722T>C	ENSP00000379651:p.Asn314Asp	Somatic	273	1	0.003663		WXS	Illumina HiSeq	Phase_I	302	20	0.0662252	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	207	0.09478021978021978	73	0.1483739837398374	41	0.1132596685082873	19	0.033216783216783216	74	0.09762532981530343	T	0	-2.690915	0.00100	.	.	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	2.16	1.1	0.20463	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.389073	0.18849	N	0.129445	T	0.00012	0.0000	N	0.00022	-2.725	0.80722	D	1	B;B;B;B	0.17852	0.002;0.024;0.0;0.0	B;B;B;B	0.28385	0.002;0.089;0.0;0.001	T	0.46020	-0.9221	10	0.02654	T	1	.	5.0417	0.14462	0.0:0.8181:0.0:0.1819	rs56257556	314;314;314;314	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	D	314	ENSP00000390120:N314D;ENSP00000411227:N314D;ENSP00000379651:N314D;ENSP00000245621:N314D	ENSP00000245621:N314D	N	-	1	0	LILRA6	59436534	0.686000	0.27661	0.905000	0.35620	0.042000	0.13812	1.191000	0.32138	0.467000	0.27218	-1.232000	0.01568	AAC	CATCAGGATGTT|0.500;GATCAGGATGTC|0.500	.	alt		0.682	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
UBE2L3	7332	hgsc.bcm.edu	37	22	21965298	21965298	+	Silent	SNP	C	C	G	rs61133050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21965298C>G	ENST00000342192.4	+	3	474	c.276C>G	c.(274-276)gcC>gcG	p.A92A	UBE2L3_ENST00000458578.2_Silent_p.A150A|UBE2L3_ENST00000545681.1_Silent_p.A60A	NM_003347.3	NP_003338.1	P68036	UB2L3_HUMAN	ubiquitin-conjugating enzyme E2L 3	92					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein K11-linked ubiquitination (GO:0070979)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)|ubiquitin-protein transferase activity (GO:0004842)		UBE2L3/KRAS(2)	large_intestine(4)	4	Colorectal(54;0.105)					TAATTAGTGCCGAAAACTGGA	0.512													T|||	162	0.0323482	0.1172	0.0101	5008	,	,		17052	0.0		0.0	False		,,,				2504	0.0				p.A150A		Atlas-SNP	.											.	UBE2L3	11	.	0			c.C450G						PASS	.	T		393,4013		18,357,1828	38.0	38.0	38.0		276	4.6	1.0	22	dbSNP_129	38	4,8596		0,4,4296	no	coding-synonymous	UBE2L3	NM_003347.2		18,361,6124	GG,GC,CC		0.0465,8.9197,3.0524		92/155	21965298	397,12609	2203	4300	6503	SO:0001819	synonymous_variant	7332	exon3			TAGTGCCGAAAAC	AJ000519	CCDS13790.1, CCDS58795.1, CCDS58796.1	22q11.2	2007-02-05			ENSG00000185651	ENSG00000185651		"""Ubiquitin-conjugating enzymes E2"""	12488	protein-coding gene	gene with protein product		603721				8672131, 9693040	Standard	NM_001256356		Approved	UBCH7	uc031rxe.1	P68036	OTTHUMG00000150823	ENST00000342192.4:c.276C>G	22.37:g.21965298C>G		Somatic	446	0	0		WXS	Illumina HiSeq	Phase_I	459	203	0.442266	NM_001256355	B2R4A7|B4DDG1|B4DSZ4|E7EWS7|P51966|P70653|Q9HAV1	Silent	SNP	ENST00000342192.4	37	CCDS13790.1																																																																																			C|0.964;G|0.036	0.036	strong		0.512	UBE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320219.1	NM_198157	
SIRPA	140885	hgsc.bcm.edu	37	20	1902301	1902301	+	Missense_Mutation	SNP	G	G	A	rs199733185		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1902301G>A	ENST00000358771.4	+	3	849	c.697G>A	c.(697-699)Gtc>Atc	p.V233I	SIRPA_ENST00000356025.3_Missense_Mutation_p.V233I|SIRPA_ENST00000400068.3_Missense_Mutation_p.V233I	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	233	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.V233I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GGTGGCCCACGTCACCTTGCA	0.617																																					p.V233I	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA_ENST00000400068,NS,carcinoma,0,5	SIRPA	83	5	1	Substitution - Missense(1)	lung(1)	c.G697A						scavenged	.						67.0	60.0	62.0					20																	1902301		2203	4296	6499	SO:0001583	missense	140885	exon4			GCCCACGTCACCT	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.697G>A	20.37:g.1902301G>A	ENSP00000351621:p.Val233Ile	Somatic	510	0	0		WXS	Illumina HiSeq	Phase_I	550	18	0.0327273	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	G	10.55	1.382458	0.24944	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02863	4.13;4.13;4.13	4.86	-7.7	0.01259	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	2.216010	0.01765	N	0.030825	T	0.02727	0.0082	L	0.27053	0.805	0.09310	N	1	B;B;B	0.14805	0.002;0.011;0.008	B;B;B	0.12156	0.002;0.007;0.006	T	0.30765	-0.9967	10	0.20519	T	0.43	.	13.8982	0.63785	0.7446:0.0:0.2554:0.0	.	213;233;233	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	I	233	ENSP00000382941:V233I;ENSP00000348307:V233I;ENSP00000351621:V233I	ENSP00000348307:V233I	V	+	1	0	SIRPA	1850301	0.000000	0.05858	0.000000	0.03702	0.766000	0.43426	-2.041000	0.01415	-1.573000	0.01659	-0.355000	0.07637	GTC	.	.	weak		0.617	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
CYP11B1	1584	hgsc.bcm.edu	37	8	143958291	143958291	+	Silent	SNP	C	C	T	rs61751154		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143958291C>T	ENST00000292427.4	-	4	638	c.606G>A	c.(604-606)ttG>ttA	p.L202L	CYP11B1_ENST00000517471.1_Silent_p.L202L|CYP11B1_ENST00000377675.3_Silent_p.L273L	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	202					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	CAAAAAGAGCCAAGTTGCTGG	0.642									Familial Hyperaldosteronism type I				.|||	1	0.000199681	0.0008	0.0	5008	,	,		19690	0.0		0.0	False		,,,				2504	0.0				p.L202L		Atlas-SNP	.											CYP11B1,right_lower_lobe,carcinoma,0,1	CYP11B1	128	1	0			c.G606A						scavenged	.						37.0	38.0	38.0					8																	143958291		2203	4300	6503	SO:0001819	synonymous_variant	1584	exon4	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	AAGAGCCAAGTTG	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"""Cytochrome P450s"""	2591	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	610613	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"""	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.606G>A	8.37:g.143958291C>T		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	184	24	0.130435	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	37	CCDS6392.1																																																																																			C|0.025;T|0.975	0.975	strong		0.642	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		
ANKRD50	57182	hgsc.bcm.edu	37	4	125592065	125592065	+	Silent	SNP	C	C	A	rs10018651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	185	0	0		WXS	Illumina HiSeq	Phase_I	203	93	0.458128	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	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209190649	209190649	+	Silent	SNP	A	A	G	rs999891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	103	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	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	
RNF151	146310	hgsc.bcm.edu	37	16	2018580	2018580	+	Missense_Mutation	SNP	G	G	A	rs62038784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2018580G>A	ENST00000569714.1	+	4	400	c.392G>A	c.(391-393)cGg>cAg	p.R131Q	RNF151_ENST00000321392.3_Missense_Mutation_p.R130Q|RNF151_ENST00000569210.2_3'UTR	NM_174903.4	NP_777563.2	Q2KHN1	RN151_HUMAN	ring finger protein 151	131					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)	2						GCAGAGCACCGGCAGCATTGC	0.706													G|||	204	0.0407348	0.118	0.0159	5008	,	,		15035	0.0069		0.0179	False		,,,				2504	0.0123				p.R131Q		Atlas-SNP	.											.	RNF151	12	.	0			c.G392A						PASS	.	G	GLN/ARG	323,3615		11,301,1657	10.0	10.0	10.0		392	-6.3	0.0	16	dbSNP_129	10	101,8157		1,99,4029	no	missense	RNF151	NM_174903.4	43	12,400,5686	AA,AG,GG		1.2231,8.2021,3.4765	benign	131/246	2018580	424,11772	1969	4129	6098	SO:0001583	missense	146310	exon4			AGCACCGGCAGCA	BC029501	CCDS58405.1	16p13.3	2013-01-09			ENSG00000179580	ENSG00000179580		"""RING-type (C3HC4) zinc fingers"""	23235	protein-coding gene	gene with protein product						12477932	Standard	NM_174903		Approved		uc002cnt.1	Q2KHN1	OTTHUMG00000176852	ENST00000569714.1:c.392G>A	16.37:g.2018580G>A	ENSP00000456566:p.Arg131Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_174903	Q8NHS5	Missense_Mutation	SNP	ENST00000569714.1	37	CCDS58405.1	67	0.030677655677655676	49	0.09959349593495935	6	0.016574585635359115	4	0.006993006993006993	8	0.010554089709762533	g	1.782	-0.481785	0.04383	0.082021	0.012231	ENSG00000179580	ENST00000321392	T	0.29142	1.58	5.25	-6.3	0.02007	Zinc finger, TRAF-type (1);TRAF-like (1);Zinc finger, SIAH-type (1);	0.679770	0.13596	N	0.376216	T	0.00384	0.0012	L	0.33485	1.01	0.09310	N	1	B	0.22683	0.073	B	0.16289	0.015	T	0.22138	-1.0225	10	0.12430	T	0.62	-5.4708	7.1367	0.25533	0.5424:0.0:0.3431:0.1145	rs62038784	131	Q2KHN1	RN151_HUMAN	Q	130	ENSP00000325794:R130Q	ENSP00000325794:R130Q	R	+	2	0	RNF151	1958581	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.062000	0.11674	-1.696000	0.01421	-1.119000	0.02030	CGG	G|0.970;A|0.030	0.030	strong		0.706	RNF151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434030.1	NM_174903	
FKRP	79147	hgsc.bcm.edu	37	19	47258842	47258842	+	Silent	SNP	C	C	T	rs2287717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47258842C>T	ENST00000318584.5	+	4	432	c.135C>T	c.(133-135)gcC>gcT	p.A45A	FKRP_ENST00000391909.3_Silent_p.A45A|FKRP_ENST00000600646.1_Intron	NM_001039885.2|NM_024301.4	NP_001034974.1|NP_077277.1	Q9H9S5	FKRP_HUMAN	fukutin related protein	45					glycoprotein biosynthetic process (GO:0009101)|protein processing (GO:0016485)	dystrophin-associated glycoprotein complex (GO:0016010)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|rough endoplasmic reticulum (GO:0005791)|sarcolemma (GO:0042383)	transferase activity (GO:0016740)			NS(1)|large_intestine(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_epithelial(76;5.08e-05)|Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000541)|all cancers(93;0.00128)|Epithelial(262;0.0207)|GBM - Glioblastoma multiforme(486;0.0336)		CCTCTGCTGCCGGCCCCCGTG	0.667													C|||	752	0.15016	0.1664	0.1311	5008	,	,		13153	0.1319		0.1431	False		,,,				2504	0.1677				p.A45A		Atlas-SNP	.											.	FKRP	16	.	0			c.C135T						PASS	.	C	,	625,3773		46,533,1620	22.0	21.0	21.0		135,135	-5.0	0.0	19	dbSNP_100	21	1218,7374		91,1036,3169	no	coding-synonymous,coding-synonymous	FKRP	NM_001039885.2,NM_024301.4	,	137,1569,4789	TT,TC,CC		14.176,14.211,14.1878	,	45/496,45/496	47258842	1843,11147	2199	4296	6495	SO:0001819	synonymous_variant	79147	exon4			TGCTGCCGGCCCC	AJ314847	CCDS12691.1	19q13.32	2014-09-17			ENSG00000181027	ENSG00000181027			17997	protein-coding gene	gene with protein product		606596				11592034, 11741828	Standard	NM_024301		Approved	LGMD2I, MDC1C	uc002pfp.2	Q9H9S5		ENST00000318584.5:c.135C>T	19.37:g.47258842C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	136	71	0.522059	NM_024301	A8K5G7	Silent	SNP	ENST00000318584.5	37	CCDS12691.1																																																																																			C|0.859;T|0.141	0.141	strong		0.667	FKRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465473.1	NM_024301	
TMCO3	55002	hgsc.bcm.edu	37	13	114175004	114175004	+	Silent	SNP	C	C	T	rs2260334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114175004C>T	ENST00000434316.2	+	8	1658	c.1299C>T	c.(1297-1299)gcC>gcT	p.A433A	TMCO3_ENST00000375391.1_Intron|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	433						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			TCTTCATGGCCGTCATGCCGA	0.517													C|||	1223	0.244209	0.4213	0.1499	5008	,	,		16761	0.2728		0.1571	False		,,,				2504	0.1319				p.A433A		Atlas-SNP	.											.	TMCO3	77	.	0			c.C1299T						PASS	.	C		1559,2847	490.6+/-361.9	275,1009,919	89.0	82.0	84.0		1299	-8.5	0.0	13	dbSNP_100	84	1266,7334	251.2+/-277.8	88,1090,3122	no	coding-synonymous	TMCO3	NM_017905.4		363,2099,4041	TT,TC,CC		14.7209,35.3836,21.7207		433/678	114175004	2825,10181	2203	4300	6503	SO:0001819	synonymous_variant	55002	exon8			CATGGCCGTCATG	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.1299C>T	13.37:g.114175004C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	141	67	0.475177	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																			C|0.768;T|0.232	0.232	strong		0.517	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
CYFIP1	23191	hgsc.bcm.edu	37	15	22925851	22925851	+	Silent	SNP	C	C	T	rs4134802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:22925851C>T	ENST00000313077.7	+	2	194	c.69C>T	c.(67-69)ccC>ccT	p.P23P	CYFIP1_ENST00000560848.1_Silent_p.P23P	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		TGCCCCTGCCCGACCAGCAGC	0.667													C|||	886	0.176917	0.3427	0.1412	5008	,	,		15649	0.003		0.2207	False		,,,				2504	0.1125				p.P23P		Atlas-SNP	.											.	CYFIP1	159	.	0			c.C69T						PASS	.	C		1456,2950	467.2+/-354.7	231,994,978	42.0	41.0	41.0		69	-10.9	0.0	15	dbSNP_108	41	1820,6780	325.8+/-317.1	185,1450,2665	no	coding-synonymous	CYFIP1	NM_014608.2		416,2444,3643	TT,TC,CC		21.1628,33.0458,25.1884		23/1254	22925851	3276,9730	2203	4300	6503	SO:0001819	synonymous_variant	23191	exon2			CCTGCCCGACCAG	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.69C>T	15.37:g.22925851C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	57	0.553398	NM_014608		Silent	SNP	ENST00000313077.7	37	CCDS10009.1																																																																																			C|0.769;T|0.231	0.231	strong		0.667	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
DHDDS	79947	hgsc.bcm.edu	37	1	26786627	26786627	+	Missense_Mutation	SNP	G	G	A	rs3816539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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|DHDDS_ENST00000525682.2_Missense_Mutation_p.V219M|RP3-476K8.3_ENST00000423060.1_RNA|DHDDS_ENST00000360009.2_Missense_Mutation_p.V253M			Q86SQ9	DHDDS_HUMAN	dehydrodolichyl diphosphate synthase	253			V -> M (in dbSNP:rs3816539). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20736409}.		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)	p.V253M(1)		breast(5)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	15		all_cancers(24;2.04e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)		GAACCATAGCGTGCTTCAGGT	0.493													G|||	2280	0.455272	0.4811	0.3069	5008	,	,		21309	0.7093		0.2346	False		,,,				2504	0.4908				p.V253M		Atlas-SNP	.											DHDDS,NS,carcinoma,0,2	DHDDS	33	2	1	Substitution - Missense(1)	stomach(1)	c.G757A						scavenged	.	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	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	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	
DNAI2	64446	hgsc.bcm.edu	37	17	72306239	72306239	+	Silent	SNP	C	C	G	rs144035254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72306239C>G	ENST00000311014.6	+	11	1498	c.1431C>G	c.(1429-1431)acC>acG	p.T477T	AC103809.1_ENST00000516976.1_RNA|RP11-647F2.2_ENST00000585167.1_RNA|DNAI2_ENST00000579490.1_Silent_p.T534T|DNAI2_ENST00000446837.2_Silent_p.T477T|DNAI2_ENST00000582036.1_Silent_p.T465T|DNAI2_ENST00000307504.5_Silent_p.T334T			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	477					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						GGACAACCACCCTGCTGGAGG	0.627									Kartagener syndrome				C|||	27	0.00539137	0.0204	0.0	5008	,	,		12200	0.0		0.0	False		,,,				2504	0.0				p.T477T		Atlas-SNP	.											.	DNAI2	102	.	0			c.C1431G						PASS	.	C	,	65,4341	61.1+/-98.1	1,63,2139	53.0	49.0	50.0		1395,1431	-4.8	0.9	17	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	DNAI2	NM_001172810.1,NM_023036.4	,	1,64,6438	GG,GC,CC		0.0116,1.4753,0.5075	,	465/594,477/606	72306239	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	64446	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AACCACCCTGCTG	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.1431C>G	17.37:g.72306239C>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_023036	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																			C|0.996;G|0.004	0.004	strong		0.627	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
KCNA7	3743	hgsc.bcm.edu	37	19	49573518	49573518	+	Silent	SNP	G	G	A	rs3810188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49573518G>A	ENST00000221444.1	-	2	1528	c.1173C>T	c.(1171-1173)ccC>ccT	p.P391P		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	391					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	AGACAATGACGGGCACTGGCA	0.567													G|||	723	0.144369	0.2988	0.1354	5008	,	,		19724	0.0476		0.0875	False		,,,				2504	0.1002				p.P391P	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											.	KCNA7	30	.	0			c.C1173T						PASS	.	G		1129,3277	403.7+/-332.8	128,873,1202	74.0	66.0	69.0		1173	-9.3	0.1	19	dbSNP_107	69	806,7794	188.0+/-235.1	42,722,3536	no	coding-synonymous	KCNA7	NM_031886.2		170,1595,4738	AA,AG,GG		9.3721,25.6241,14.8777		391/457	49573518	1935,11071	2203	4300	6503	SO:0001819	synonymous_variant	3743	exon2			AATGACGGGCACT	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.1173C>T	19.37:g.49573518G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_031886	A1KYX7|Q9BYS4	Silent	SNP	ENST00000221444.1	37	CCDS12755.1																																																																																			G|0.856;A|0.144	0.144	strong		0.567	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886	
CACNA1H	8912	hgsc.bcm.edu	37	16	1245062	1245062	+	Silent	SNP	C	C	T	rs59794024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1245062C>T	ENST00000348261.5	+	3	638	c.390C>T	c.(388-390)tcC>tcT	p.S130S	CACNA1H_ENST00000565831.1_Silent_p.S130S|CACNA1H_ENST00000358590.4_Silent_p.S130S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	130					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)	AGTGCGGCTCCGAGCGCTGCA	0.647											OREG0023543	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	215	0.0429313	0.1551	0.0144	5008	,	,		8995	0.0		0.0	False		,,,				2504	0.0				p.S130S		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C390T						PASS	.		,	470,3718		28,414,1652	79.0	86.0	84.0		390,390	-9.0	0.7	16	dbSNP_129	84	3,8407		0,3,4202	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	28,417,5854	TT,TC,CC		0.0357,11.2225,3.7546	,	130/2348,130/2354	1245062	473,12125	2094	4205	6299	SO:0001819	synonymous_variant	8912	exon3			CGGCTCCGAGCGC	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.390C>T	16.37:g.1245062C>T		Somatic	80	0	0	594	WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.967;T|0.033	0.033	strong		0.647	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
MAPK4	5596	hgsc.bcm.edu	37	18	48248453	48248453	+	Silent	SNP	T	T	C	rs16952476	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:48248453T>C	ENST00000400384.2	+	4	1873	c.837T>C	c.(835-837)ccT>ccC	p.P279P	MAPK4_ENST00000540640.1_Silent_p.P68P|MAPK4_ENST00000592595.1_Intron	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	279	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		AGCTGCTCCCTGAAGTGAACA	0.612													t|||	209	0.0417332	0.0787	0.0101	5008	,	,		20179	0.0883		0.004	False		,,,				2504	0.0051				p.P279P		Atlas-SNP	.											.	MAPK4	75	.	0			c.T837C						PASS	.	C		243,3865		11,221,1822	55.0	61.0	59.0		837	-11.4	0.0	18	dbSNP_123	59	5,8377		0,5,4186	no	coding-synonymous	MAPK4	NM_002747.3		11,226,6008	CC,CT,TT		0.0597,5.9153,1.9856		279/588	48248453	248,12242	2054	4191	6245	SO:0001819	synonymous_variant	5596	exon4			GCTCCCTGAAGTG	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.837T>C	18.37:g.48248453T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_002747	A1A4C4|Q0VG04	Silent	SNP	ENST00000400384.2	37	CCDS42437.1																																																																																			T|0.971;C|0.029	0.029	strong		0.612	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448631.2	NM_002747	
LSM14A	26065	hgsc.bcm.edu	37	19	34706531	34706531	+	Missense_Mutation	SNP	A	A	G	rs73929373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:34706531A>G	ENST00000433627.5	+	6	821	c.746A>G	c.(745-747)aAt>aGt	p.N249S	LSM14A_ENST00000544216.3_Missense_Mutation_p.N249S|LSM14A_ENST00000540746.2_Missense_Mutation_p.N208S	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	249					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					AGGCCAGAAAATGAGCAACTC	0.348													A|||	598	0.119409	0.2526	0.1859	5008	,	,		17565	0.0268		0.0249	False		,,,				2504	0.0849				p.N249S		Atlas-SNP	.											.	LSM14A	44	.	0			c.A746G						PASS	.	A	SER/ASN,SER/ASN	942,3464	357.6+/-314.0	111,720,1372	105.0	99.0	101.0		746,746	3.5	1.0	19	dbSNP_130	101	283,8317	105.4+/-166.3	8,267,4025	yes	missense,missense	LSM14A	NM_001114093.1,NM_015578.2	46,46	119,987,5397	GG,GA,AA		3.2907,21.3799,9.4187	benign,benign	249/464,249/464	34706531	1225,11781	2203	4300	6503	SO:0001583	missense	26065	exon6			CAGAAAATGAGCA	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"""chromosome 19 open reading frame 13"", ""family with sequence similarity 61, member A"", ""LSM14 homolog A (SCD6, S. cerevisiae)"""	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.746A>G	19.37:g.34706531A>G	ENSP00000413964:p.Asn249Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Missense_Mutation	SNP	ENST00000433627.5	37	CCDS46040.1	203	0.09294871794871795	126	0.25609756097560976	50	0.13812154696132597	10	0.017482517482517484	17	0.022427440633245383	a	11.36	1.614331	0.28712	0.213799	0.032907	ENSG00000257103	ENST00000544216;ENST00000433627;ENST00000540746	T;T;T	0.32988	1.44;1.43;1.51	5.67	3.45	0.39498	.	0.584793	0.21286	N	0.077070	T	0.00012	0.0000	L	0.34521	1.04	0.32771	P	0.503819	B;B;B	0.10296	0.0;0.003;0.001	B;B;B	0.14023	0.002;0.01;0.001	T	0.30995	-0.9959	9	0.07325	T	0.83	-9.8271	7.9304	0.29899	0.6192:0.3076:0.0732:0.0	.	208;249;249	B4DTG6;Q8ND56;Q8ND56-2	.;LS14A_HUMAN;.	S	249;249;208	ENSP00000446271:N249S;ENSP00000413964:N249S;ENSP00000446451:N208S	ENSP00000314768:N249S	N	+	2	0	LSM14A	39398371	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.253000	0.32886	1.085000	0.41206	0.533000	0.62120	AAT	A|0.908;G|0.092	0.092	strong		0.348	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578	
B9D2	80776	hgsc.bcm.edu	37	19	41858921	41858921	+	IGR	SNP	G	G	A	rs1800470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41858921G>A	ENST00000243578.3	-	0	1027				TMEM91_ENST00000604123.1_5'Flank|TMEM91_ENST00000539627.1_Intron|CTC-435M10.3_ENST00000604424.1_Intron|TGFB1_ENST00000221930.5_Missense_Mutation_p.P10L	NM_030578.3	NP_085055.2	Q9BPU9	B9D2_HUMAN	B9 protein domain 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						tagcagcagcggcagcagccg	0.731													G|||	2731	0.545327	0.5862	0.4942	5008	,	,		11309	0.4454		0.6183	False		,,,				2504	0.5542				p.P10L		Atlas-SNP	.											.	TGFB1	27	.	0			c.C29T	GRCh37	CM002115	TGFB1	M	rs1800470	PASS	.						4.0	3.0	4.0					19																	41858921		1381	2874	4255	SO:0001628	intergenic_variant	7040	exon1			AGCAGCGGCAGCA	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			19.37:g.41858921G>A		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_000660		Missense_Mutation	SNP	ENST00000243578.3	37	CCDS12579.1	1213	0.5554029304029304	288	0.5853658536585366	194	0.5359116022099447	276	0.4825174825174825	455	0.600263852242744	G	15.42	2.828179	0.50845	.	.	ENSG00000105329	ENST00000221930	T	0.26518	1.73	3.88	1.45	0.22620	.	1.172640	0.06054	N	0.657121	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999585855	.	.	.	.	.	.	T	0.42413	-0.9453	6	0.11794	T	0.64	1.3735	6.0338	0.19694	0.1381:0.2095:0.6524:0.0	rs1800470;rs1982073;rs3745293;rs17849267;rs17849435;rs17851976;rs60195696;rs1982073	.	.	.	L	10	ENSP00000221930:P10L	ENSP00000221930:P10L	P	-	2	0	TGFB1	46550761	0.991000	0.36638	1.000000	0.80357	0.984000	0.73092	0.753000	0.26376	0.757000	0.33036	0.462000	0.41574	CCG	G|0.436;A|0.564	0.564	strong		0.731	B9D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463489.1	NM_030578	
LRIT1	26103	hgsc.bcm.edu	37	10	85992390	85992390	+	Missense_Mutation	SNP	G	G	T	rs12262099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85992390G>T	ENST00000372105.3	-	4	1186	c.1165C>A	c.(1165-1167)Ccc>Acc	p.P389T		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	389			P -> T (in dbSNP:rs12262099).			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						AGGACAGCGGGTTTGGGAATC	0.617													G|||	968	0.193291	0.5507	0.1081	5008	,	,		19158	0.0417		0.0378	False		,,,				2504	0.0869				p.P389T		Atlas-SNP	.											.	LRIT1	73	.	0			c.C1165A						PASS	.	G	THR/PRO	2073,2333	545.5+/-376.8	497,1079,627	59.0	48.0	51.0		1165	2.8	0.0	10	dbSNP_120	51	381,8219	122.4+/-181.4	4,373,3923	yes	missense	LRIT1	NM_015613.2	38	501,1452,4550	TT,TG,GG		4.4302,47.0495,18.8682	benign	389/624	85992390	2454,10552	2203	4300	6503	SO:0001583	missense	26103	exon4			CAGCGGGTTTGGG	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.1165C>A	10.37:g.85992390G>T	ENSP00000361177:p.Pro389Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	143	56	0.391608	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	37	CCDS7373.1	370	0.16941391941391942	260	0.5284552845528455	42	0.11602209944751381	26	0.045454545454545456	42	0.055408970976253295	G	0.586	-0.834861	0.02713	0.470495	0.044302	ENSG00000148602	ENST00000372105	T	0.35236	1.32	5.66	2.78	0.32641	.	0.653998	0.15885	N	0.239854	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.19445	0.036	B	0.06405	0.002	T	0.45116	-0.9283	9	0.05525	T	0.97	.	9.0016	0.36085	0.3071:0.0:0.6929:0.0	rs12262099;rs52819914;rs57593568;rs12262099	389	Q9P2V4	LRIT1_HUMAN	T	389	ENSP00000361177:P389T	ENSP00000361177:P389T	P	-	1	0	LRIT1	85982370	0.000000	0.05858	0.002000	0.10522	0.041000	0.13682	-0.135000	0.10420	0.317000	0.23160	0.655000	0.94253	CCC	G|0.815;T|0.185	0.185	strong		0.617	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
GPR176	11245	hgsc.bcm.edu	37	15	40094431	40094431	+	Silent	SNP	C	C	T	rs76578471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40094431C>T	ENST00000561100.1	-	3	1315	c.450G>A	c.(448-450)ctG>ctA	p.L150L	GPR176_ENST00000543580.1_Silent_p.L105L|GPR176_ENST00000560729.1_5'UTR|GPR176_ENST00000299092.3_Silent_p.L149L|RP11-37C7.1_ENST00000558616.1_RNA	NM_007223.1	NP_009154.1	Q14439	GP176_HUMAN	G protein-coupled receptor 176	150					G-protein coupled receptor signaling pathway (GO:0007186)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(9)|ovary(2)|pancreas(1)|skin(2)	23		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)		TTTTCCTCTCCAGTGGATAGA	0.438											OREG0023053	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	67	0.0133786	0.0477	0.0058	5008	,	,		21801	0.0		0.0	False		,,,				2504	0.0				p.L150L		Atlas-SNP	.											.	GPR176	41	.	0			c.G450A						PASS	.	C		112,4294	86.3+/-125.0	0,112,2091	70.0	61.0	64.0		450	4.8	1.0	15	dbSNP_132	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPR176	NM_007223.1		0,113,6390	TT,TC,CC		0.0116,2.542,0.8688		150/516	40094431	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	11245	exon3			CCTCTCCAGTGGA	BC067106	CCDS10051.1, CCDS61588.1, CCDS61589.1	15q14-q15.1	2012-08-21			ENSG00000166073	ENSG00000166073		"""GPCR / Class A : Orphans"""	32370	protein-coding gene	gene with protein product		612183				7893747	Standard	NM_007223		Approved	Gm1012	uc010uck.2	Q14439	OTTHUMG00000129873	ENST00000561100.1:c.450G>A	15.37:g.40094431C>T		Somatic	39	0	0	890	WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_007223	Q6NXF6	Silent	SNP	ENST00000561100.1	37	CCDS10051.1																																																																																			C|0.989;T|0.011	0.011	strong		0.438	GPR176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252117.2	NM_007223	
DHRS1	115817	hgsc.bcm.edu	37	14	24768220	24768220	+	Silent	SNP	G	G	T	rs150092528		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24768220G>T	ENST00000288111.7	-	2	369	c.93C>A	c.(91-93)ggC>ggA	p.G31G	NOP9_ENST00000396802.3_5'Flank|NOP9_ENST00000267425.3_5'Flank|DHRS1_ENST00000396813.1_Silent_p.G31G	NM_001136050.2	NP_001129522.1	Q96LJ7	DHRS1_HUMAN	dehydrogenase/reductase (SDR family) member 1	31						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)		AAACTGTGGCGCCTGCTTTGC	0.582																																					p.G31G		Atlas-SNP	.											.	DHRS1	21	.	0			c.C93A						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	67.0	60.0	63.0		93,93	-8.8	0.9	14	dbSNP_134	63	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DHRS1	NM_001136050.2,NM_138452.2	,	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	,	31/314,31/314	24768220	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	115817	exon2			TGTGGCGCCTGCT	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.93C>A	14.37:g.24768220G>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	25	0.362319	NM_138452	D3DS71|Q8NDG3|Q96B59|Q96CQ5	Silent	SNP	ENST00000288111.7	37	CCDS9623.1																																																																																			G|1.000;T|0.000	0.000	weak		0.582	DHRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073168.4	NM_138452	
TAPT1	202018	hgsc.bcm.edu	37	4	16215451	16215451	+	Silent	SNP	C	C	T	rs6823623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:16215451C>T	ENST00000405303.2	-	2	353	c.270G>A	c.(268-270)aaG>aaA	p.K90K	TAPT1_ENST00000399920.3_Intron|TAPT1_ENST00000508888.1_5'UTR	NM_153365.2	NP_699196.2	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation 1	90					embryonic skeletal system development (GO:0048706)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|post-embryonic development (GO:0009791)	integral component of membrane (GO:0016021)	growth hormone-releasing hormone receptor activity (GO:0016520)			NS(1)|breast(2)|cervix(1)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)	10						TTTCTGTATACTTGGCCTCAT	0.348													C|||	729	0.145567	0.475	0.0418	5008	,	,		18664	0.0417		0.005	False		,,,				2504	0.0256				p.K90K		Atlas-SNP	.											TAPT1,colon,carcinoma,-1,1	TAPT1	31	1	0			c.G270A						PASS	.	C		1457,2221		292,873,674	157.0	155.0	155.0		270	3.4	1.0	4	dbSNP_116	155	23,8155		0,23,4066	no	coding-synonymous	TAPT1	NM_153365.2		292,896,4740	TT,TC,CC		0.2812,39.6139,12.4831		90/568	16215451	1480,10376	1839	4089	5928	SO:0001819	synonymous_variant	202018	exon2			TGTATACTTGGCC	AK074494	CCDS47030.1	4p15.32	2014-01-28			ENSG00000169762	ENSG00000169762			26887	protein-coding gene	gene with protein product		612758				12477932	Standard	NM_153365		Approved	FLJ90013	uc010ied.1	Q6NXT6	OTTHUMG00000160177	ENST00000405303.2:c.270G>A	4.37:g.16215451C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	142	61	0.429577	NM_153365	Q8N2S3|Q9NZK9	Silent	SNP	ENST00000405303.2	37	CCDS47030.1																																																																																			C|0.863;T|0.137	0.137	strong		0.348	TAPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359568.1	NM_153365	
OR2T6	254879	hgsc.bcm.edu	37	1	248550970	248550970	+	Missense_Mutation	SNP	A	A	G	rs7417616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248550970A>G	ENST00000355728.2	+	1	61	c.61A>G	c.(61-63)Aat>Gat	p.N21D		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	21			N -> D (in dbSNP:rs7417616).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTTCACTCACAATAAATGCTC	0.433													g|||	1890	0.377396	0.5234	0.3156	5008	,	,		15093	0.4375		0.1769	False		,,,				2504	0.3681				p.N21D		Atlas-SNP	.											.	OR2T6	101	.	0			c.A61G						PASS	.	G	ASP/ASN	2003,2403	615.1+/-392.5	466,1071,666	148.0	142.0	144.0		61	-6.2	0.0	1	dbSNP_116	144	1299,7301	758.8+/-407.5	92,1115,3093	yes	missense	OR2T6	NM_001005471.1	23	558,2186,3759	GG,GA,AA		15.1047,45.4607,25.3883	benign	21/309	248550970	3302,9704	2203	4300	6503	SO:0001583	missense	254879	exon1			ACTCACAATAAAT	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"""GPCR / Class A : Olfactory receptors"""	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.61A>G	1.37:g.248550970A>G	ENSP00000347965:p.Asn21Asp	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	125	72	0.576	NM_001005471	A6NE36	Missense_Mutation	SNP	ENST00000355728.2	37	CCDS31114.1	744	0.34065934065934067	262	0.532520325203252	96	0.26519337016574585	243	0.42482517482517484	143	0.18865435356200527	G	11.81	1.749870	0.30955	0.454607	0.151047	ENSG00000198104	ENST00000355728	T	0.02974	4.09	4.48	-6.15	0.02105	.	1.525930	0.03801	N	0.264518	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41070	-0.9529	9	0.62326	D	0.03	.	4.0254	0.09685	0.4105:0.1039:0.3836:0.102	rs7417616;rs60973717;rs7417616	21	Q8NHC8	OR2T6_HUMAN	D	21	ENSP00000347965:N21D	ENSP00000347965:N21D	N	+	1	0	OR2T6	246617593	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-3.757000	0.00374	-1.171000	0.02765	-1.555000	0.00892	AAT	A|0.702;G|0.298	0.298	strong		0.433	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471	
FER	2241	hgsc.bcm.edu	37	5	108281862	108281862	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:108281862C>T	ENST00000281092.4	+	11	1652	c.1268C>T	c.(1267-1269)tCt>tTt	p.S423F	FER_ENST00000536402.1_Silent_p.L319L|FER_ENST00000438717.2_Missense_Mutation_p.S248F	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	423					actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		AAATTTGAATCTATTCGTCAT	0.373																																					p.S423F	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.C1268T						PASS	.						129.0	134.0	132.0					5																	108281862		2202	4300	6502	SO:0001583	missense	2241	exon11			TTGAATCTATTCG	J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	3655	protein-coding gene	gene with protein product	"""phosphoprotein NCP94"", ""protein phosphatase 1, regulatory subunit 74"""	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.1268C>T	5.37:g.108281862C>T	ENSP00000281092:p.Ser423Phe	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	70	4	0.0571429	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	37	CCDS4098.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.859764	0.71834	.	.	ENSG00000151422	ENST00000281092;ENST00000438717	T;T	0.75367	-0.92;-0.93	5.45	5.45	0.79879	.	0.045955	0.85682	D	0.000000	T	0.68842	0.3045	N	0.22421	0.69	0.49213	D	0.999767	P	0.37955	0.612	B	0.41088	0.347	T	0.72261	-0.4345	10	0.66056	D	0.02	-12.8969	19.6346	0.95724	0.0:1.0:0.0:0.0	.	423	P16591	FER_HUMAN	F	423;248	ENSP00000281092:S423F;ENSP00000394297:S248F	ENSP00000281092:S423F	S	+	2	0	FER	108309761	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.910000	0.75741	2.720000	0.93068	0.491000	0.48974	TCT	.	.	none		0.373	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
ZCCHC14	23174	hgsc.bcm.edu	37	16	87451273	87451273	+	Silent	SNP	G	G	T	rs56283442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:87451273G>T	ENST00000268616.4	-	8	982	c.765C>A	c.(763-765)tcC>tcA	p.S255S		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	255							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AGGGGGCGGCGGAGCCGGCCG	0.697													T|||	746	0.148962	0.5053	0.0533	5008	,	,		15812	0.0		0.0358	False		,,,				2504	0.0051				p.S255S		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.C765A						PASS	.	T		1774,2622	627.4+/-394.9	360,1054,784	43.0	51.0	49.0		765	-11.1	0.0	16	dbSNP_129	49	220,8378	798.3+/-407.4	1,218,4080	no	coding-synonymous	ZCCHC14	NM_015144.2		361,1272,4864	TT,TG,GG		2.5587,40.3549,15.3455		255/950	87451273	1994,11000	2198	4299	6497	SO:0001819	synonymous_variant	23174	exon8			GGCGGCGGAGCCG	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.765C>A	16.37:g.87451273G>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	26	17	0.653846	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Silent	SNP	ENST00000268616.4	37	CCDS10961.1																																																																																			G|0.859;T|0.141	0.141	strong		0.697	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
CEBPZ	10153	hgsc.bcm.edu	37	2	37454998	37454998	+	Silent	SNP	A	A	G	rs1803251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37454998A>G	ENST00000234170.5	-	2	1483	c.1338T>C	c.(1336-1338)aaT>aaC	p.N446N		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	446					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)				GAGCCATTTGATTTAAAAAGC	0.343													A|||	451	0.0900559	0.32	0.0389	5008	,	,		21260	0.0		0.001	False		,,,				2504	0.0				p.N446N		Atlas-SNP	.											.	CEBPZ	68	.	0			c.T1338C						PASS	.	A		1241,3163	393.3+/-328.8	184,873,1145	69.0	70.0	70.0		1338	3.0	1.0	2	dbSNP_89	70	15,8585	8.4+/-32.0	0,15,4285	no	coding-synonymous	CEBPZ	NM_005760.2		184,888,5430	GG,GA,AA		0.1744,28.1789,9.6586		446/1055	37454998	1256,11748	2202	4300	6502	SO:0001819	synonymous_variant	10153	exon2			CATTTGATTTAAA	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.1338T>C	2.37:g.37454998A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_005760	Q8NE75	Silent	SNP	ENST00000234170.5	37	CCDS1787.1																																																																																			A|0.912;G|0.088	0.088	strong		0.343	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760	
FNDC1	84624	hgsc.bcm.edu	37	6	159672419	159672419	+	Silent	SNP	G	G	C	rs551392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159672419G>C	ENST00000297267.9	+	17	5120	c.4920G>C	c.(4918-4920)ctG>ctC	p.L1640L	FNDC1_ENST00000340366.6_Silent_p.L1577L	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1640					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TGGACAGCCTGGATGAAATCA	0.532													G|||	1099	0.219449	0.1899	0.1772	5008	,	,		22374	0.3343		0.1382	False		,,,				2504	0.2546				p.L1640L		Atlas-SNP	.											.	FNDC1	250	.	0			c.G4920C						PASS	.	G		716,3384		53,610,1387	75.0	72.0	73.0		4920	3.7	1.0	6	dbSNP_83	73	1094,7302		78,938,3182	no	coding-synonymous	FNDC1	NM_032532.2		131,1548,4569	CC,CG,GG		13.03,17.4634,14.4846		1640/1895	159672419	1810,10686	2050	4198	6248	SO:0001819	synonymous_variant	84624	exon17			CAGCCTGGATGAA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.4920G>C	6.37:g.159672419G>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	149	67	0.449664	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	475	0.2174908424908425	115	0.23373983739837398	59	0.16298342541436464	201	0.3513986013986014	100	0.13192612137203166	G	8.942	0.966161	0.18659	0.174634	0.1303	ENSG00000164694	ENST00000329629	.	.	.	5.51	3.7	0.42460	.	.	.	.	.	T	0.33876	0.0878	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.15206	-1.0445	3	.	.	.	-18.2795	8.6871	0.34245	0.0739:0.0:0.603:0.3231	rs551392;rs3814445;rs61299761;rs551392	.	.	.	R	1536	.	.	G	+	1	0	FNDC1	159592409	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.993000	0.49425	0.683000	0.31428	0.585000	0.79938	GGA	G|0.777;C|0.222	0.222	strong		0.532	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
CR1	1378	hgsc.bcm.edu	37	1	207753621	207753621	+	Missense_Mutation	SNP	A	A	G	rs2274567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207753621A>G	ENST00000367049.4	+	30	4973	c.4973A>G	c.(4972-4974)cAt>cGt	p.H1658R	CR1_ENST00000367052.1_Missense_Mutation_p.H1208R|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367051.1_Missense_Mutation_p.H1208R|CR1_ENST00000400960.2_Missense_Mutation_p.H1208R|CR1_ENST00000367053.1_Missense_Mutation_p.H1208R|RP11-78B10.2_ENST00000596003.1_RNA	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1208	Sushi 26. {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						CATGGTGAGCATACCCCAAGC	0.522													A|||	1474	0.294329	0.2186	0.2709	5008	,	,		18110	0.3274		0.1819	False		,,,				2504	0.4949				p.H1658R		Atlas-SNP	.											.	CR1	354	.	0			c.A4973G						PASS	.	A	ARG/HIS,ARG/HIS	875,3049		94,687,1181	126.0	127.0	126.0		3623,4973	0.2	0.0	1	dbSNP_100	126	1524,6788		129,1266,2761	no	missense,missense	CR1	NM_000573.3,NM_000651.4	29,29	223,1953,3942	GG,GA,AA		18.3349,22.2987,19.6061	probably-damaging,probably-damaging	1208/2040,1658/2490	207753621	2399,9837	1962	4156	6118	SO:0001583	missense	1378	exon30			GTGAGCATACCCC	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.4973A>G	1.37:g.207753621A>G	ENSP00000356016:p.His1658Arg	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	227	120	0.528634	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	487	0.222985347985348	114	0.23170731707317074	108	0.2983425414364641	134	0.23426573426573427	131	0.17282321899736147	A	0.454	-0.892160	0.02491	0.222987	0.183349	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03;-0.03	4.34	0.182	0.15077	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B;B;D	0.65815	0.147;0.08;0.995	B;B;D	0.74674	0.168;0.049;0.984	T	0.09907	-1.0653	8	0.25106	T	0.35	.	1.2006	0.01884	0.5248:0.1803:0.1191:0.1757	rs2274567;rs3860293;rs17047280;rs52826014;rs60859711;rs2274567	1208;1208;1658	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	R	1208;1208;1208;1208;758;1658	ENSP00000356019:H1208R;ENSP00000356018:H1208R;ENSP00000356020:H1208R;ENSP00000383744:H1208R;ENSP00000436139:H758R;ENSP00000356016:H1658R	ENSP00000356016:H1658R	H	+	2	0	CR1	205820244	0.000000	0.05858	0.001000	0.08648	0.091000	0.18340	0.814000	0.27239	0.164000	0.19529	0.529000	0.55759	CAT	A|0.785;G|0.214	0.214	strong		0.522	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
ATXN1L	342371	hgsc.bcm.edu	37	16	71885423	71885423	+	Missense_Mutation	SNP	A	A	G	rs61747555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71885423A>G	ENST00000427980.2	+	3	2073	c.1780A>G	c.(1780-1782)Agc>Ggc	p.S594G	ATXN1L_ENST00000569119.1_Intron	NM_001137675.3	NP_001131147.1	P0C7T5	ATX1L_HUMAN	ataxin 1-like	594					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)	4						TTCTCAGGCCAGCTGTGCTCC	0.567													A|||	848	0.169329	0.0189	0.2219	5008	,	,		18533	0.2927		0.1889	False		,,,				2504	0.1881				p.S594G		Atlas-SNP	.											.	ATXN1L	18	.	0			c.A1780G						PASS	.	A	GLY/SER	46,1338		2,42,648	34.0	39.0	37.0		1780	3.0	1.0	16	dbSNP_129	37	650,2532		57,536,998	yes	missense	ATXN1L	NM_001137675.2	56	59,578,1646	GG,GA,AA		20.4274,3.3237,15.2431	benign	594/690	71885423	696,3870	692	1591	2283	SO:0001583	missense	342371	exon3			CAGGCCAGCTGTG		CCDS45523.1	16q22.2	2014-09-04			ENSG00000224470	ENSG00000224470			33279	protein-coding gene	gene with protein product	"""brother of ataxin 1"""	614301				16121196, 17322884, 21475249	Standard	NM_001137675		Approved	BOAT1	uc002fbd.3	P0C7T5	OTTHUMG00000176872	ENST00000427980.2:c.1780A>G	16.37:g.71885423A>G	ENSP00000415822:p.Ser594Gly	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_001137675		Missense_Mutation	SNP	ENST00000427980.2	37	CCDS45523.1	377	0.17261904761904762	12	0.024390243902439025	68	0.1878453038674033	158	0.2762237762237762	139	0.18337730870712401	A	8.360	0.832987	0.16820	0.033237	0.204274	ENSG00000224470	ENST00000427980	T	0.32988	1.43	5.61	3.01	0.34805	.	.	.	.	.	T	0.00012	0.0000	N	0.04959	-0.14	0.30424	P	0.777807	B	0.02656	0.0	B	0.04013	0.001	T	0.41016	-0.9532	8	0.22109	T	0.4	-0.0444	9.8813	0.41236	0.8169:0.0:0.1831:0.0	rs61747555	594	P0C7T5	ATX1L_HUMAN	G	594	ENSP00000415822:S594G	ENSP00000415822:S594G	S	+	1	0	ATXN1L	70442924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.465000	0.53064	1.040000	0.40099	0.454000	0.30748	AGC	A|0.828;G|0.172	0.172	strong		0.567	ATXN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434171.1	NM_001137675.2	
OR5H15	403274	hgsc.bcm.edu	37	3	97887970	97887970	+	Missense_Mutation	SNP	C	C	T	rs72933946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	509	3	0.00589391		WXS	Illumina HiSeq	Phase_I	514	16	0.0311284	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		
BCL2A1	597	hgsc.bcm.edu	37	15	80263345	80263345	+	Missense_Mutation	SNP	A	A	C	rs1138358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80263345A>C	ENST00000267953.3	-	1	443	c.117T>G	c.(115-117)aaT>aaG	p.N39K	BCL2A1_ENST00000335661.6_Missense_Mutation_p.N39K	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	39			N -> K (in dbSNP:rs1138358). {ECO:0000269|Ref.6}.		extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						AGAACGCAACATTTTGTAGCA	0.443													a|||	2298	0.458866	0.6377	0.3127	5008	,	,		21936	0.5367		0.2624	False		,,,				2504	0.4427				p.N39K		Atlas-SNP	.											.	BCL2A1	28	.	0			c.T117G						PASS	.	A	LYS/ASN,LYS/ASN	2472,1934	623.5+/-394.1	688,1096,419	139.0	127.0	131.0		117,117	-10.2	0.0	15	dbSNP_86	131	2248,6352	381.2+/-339.9	276,1696,2328	yes	missense,missense	BCL2A1	NM_001114735.1,NM_004049.3	94,94	964,2792,2747	CC,CA,AA		26.1395,43.8947,36.2909	benign,benign	39/164,39/176	80263345	4720,8286	2203	4300	6503	SO:0001583	missense	597	exon1			CGCAACATTTTGT		CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.117T>G	15.37:g.80263345A>C	ENSP00000267953:p.Asn39Lys	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	210	87	0.414286	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	950	0.434981684981685	308	0.6260162601626016	135	0.3729281767955801	312	0.5454545454545454	195	0.25725593667546176	a	4.156	0.027388	0.08054	0.561053	0.261395	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.15834	2.39;2.39	5.63	-10.2	0.00374	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (2);	0.950099	0.08840	N	0.885950	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B	0.21147	0.052;0.001	B;B	0.16722	0.016;0.004	T	0.46331	-0.9199	9	0.08179	T	0.78	-1.1102	1.5289	0.02531	0.3591:0.2423:0.2488:0.1498	rs1138358;rs2070263;rs3202147;rs3743426;rs52805955;rs57940215;rs1138358	39;39	Q86W13;Q16548	.;B2LA1_HUMAN	K	39	ENSP00000267953:N39K;ENSP00000335250:N39K	ENSP00000267953:N39K	N	-	3	2	BCL2A1	78050400	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.817000	0.00359	-1.753000	0.01323	-1.967000	0.00467	AAT	A|0.600;C|0.400	0.400	strong		0.443	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049	
TNXB	7148	hgsc.bcm.edu	37	6	32035634	32035634	+	Silent	SNP	G	G	A	rs143840297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32035634G>A	ENST00000375244.3	-	18	6549	c.6348C>T	c.(6346-6348)acC>acT	p.T2116T	TNXB_ENST00000375247.2_Silent_p.T2116T			P22105	TENX_HUMAN	tenascin XB	2188	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCTGGGGGACGGTCCAGGAGA	0.677													G|||	89	0.0177716	0.0144	0.0187	5008	,	,		14419	0.0565		0.0	False		,,,				2504	0.0				p.T2116T		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,-2,2	TNXB	553	2	0			c.C6348T						PASS	.	G		18,3658		0,18,1820	29.0	33.0	32.0		6348	-3.2	0.9	6	dbSNP_134	32	0,8082		0,0,4041	no	coding-synonymous	TNXB	NM_019105.6		0,18,5861	AA,AG,GG		0.0,0.4897,0.1531		2116/4243	32035634	18,11740	1838	4041	5879	SO:0001819	synonymous_variant	7148	exon18			GGGGACGGTCCAG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.6348C>T	6.37:g.32035634G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	231	115	0.497835	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				G|0.987;A|0.013	0.013	weak		0.677	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
RAI1	10743	hgsc.bcm.edu	37	17	17700573	17700573	+	Silent	SNP	T	T	C	rs4925112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17700573T>C	ENST00000353383.1	+	3	4780	c.4311T>C	c.(4309-4311)ccT>ccC	p.P1437P	RAI1_ENST00000261641.6_Silent_p.P1437P	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1437					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CCCTGCAGCCTGGGGGGACTG	0.587													C|||	474	0.0946486	0.2655	0.0447	5008	,	,		16820	0.0069		0.0577	False		,,,				2504	0.0276				p.P1437P		Atlas-SNP	.											.	RAI1	121	.	0			c.T4311C						PASS	.	C		1089,3317	685.0+/-404.5	142,805,1256	30.0	35.0	33.0		4311	-1.9	0.0	17	dbSNP_111	33	518,8082	771.5+/-407.7	19,480,3801	no	coding-synonymous	RAI1	NM_030665.3		161,1285,5057	CC,CT,TT		6.0233,24.7163,12.3558		1437/1907	17700573	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	10743	exon3			GCAGCCTGGGGGG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.4311T>C	17.37:g.17700573T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			T|0.888;C|0.112	0.112	strong		0.587	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
MATN4	8785	hgsc.bcm.edu	37	20	43926573	43926573	+	Missense_Mutation	SNP	C	C	T	rs2227275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43926573C>T	ENST00000372754.1	-	8	1695	c.1687G>A	c.(1687-1689)Ggc>Agc	p.G563S	MATN4_ENST00000342716.4_Missense_Mutation_p.G522S|MATN4_ENST00000372756.1_Missense_Mutation_p.G522S|MATN4_ENST00000360607.6_Missense_Mutation_p.G481S|MATN4_ENST00000353917.5_Missense_Mutation_p.G440S|MATN4_ENST00000537548.1_Missense_Mutation_p.G522S|MATN4_ENST00000372751.4_Missense_Mutation_p.G373S			O95460	MATN4_HUMAN	matrilin 4	563				G -> S (in Ref. 2; BAC11083). {ECO:0000305}.	extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CAGATGCTGCCTCTGAGGTTC	0.622													C|||	1095	0.21865	0.261	0.3415	5008	,	,		17973	0.1121		0.2773	False		,,,				2504	0.1237				p.G522S		Atlas-SNP	.											.	MATN4	57	.	0			c.G1564A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	1121,3285	398.3+/-330.8	136,849,1218	76.0	78.0	78.0		1564,1441,1318	4.6	1.0	20	dbSNP_98	78	2126,6474	366.3+/-334.3	262,1602,2436	yes	missense,missense,missense	MATN4	NM_003833.3,NM_030590.2,NM_030592.2	56,56,56	398,2451,3654	TT,TC,CC		24.7209,25.4426,24.9654	benign,benign,benign	522/582,481/541,440/500	43926573	3247,9759	2203	4300	6503	SO:0001583	missense	8785	exon8			TGCTGCCTCTGAG	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.1687G>A	20.37:g.43926573C>T	ENSP00000361840:p.Gly563Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_003833	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Missense_Mutation	SNP	ENST00000372754.1	37		542	0.24816849816849818	138	0.2804878048780488	114	0.3149171270718232	78	0.13636363636363635	212	0.2796833773087071	C	11.07	1.530132	0.27387	0.254426	0.247209	ENSG00000124159	ENST00000372753;ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132;ENST00000372751	T;T;T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06	5.64	4.64	0.57946	.	0.164448	0.29002	N	0.013458	T	0.00012	0.0000	N	0.11427	0.14	0.32213	P	0.576256	B;B;B	0.20550	0.002;0.045;0.046	B;B;B	0.23574	0.024;0.047;0.041	T	0.02282	-1.1183	9	0.11182	T	0.66	.	13.0781	0.59099	0.0:0.6907:0.3093:0.0	rs2227275;rs17426884;rs52795698;rs56588055;rs59660933;rs2227275	440;481;522	A6NNA4;O95460-4;O95460-2	.;.;.	S	373;563;522;440;481;522;522;563;373	ENSP00000361839:G373S;ENSP00000361840:G563S;ENSP00000361842:G522S;ENSP00000243983:G440S;ENSP00000353819:G481S;ENSP00000343164:G522S;ENSP00000440328:G522S;ENSP00000361837:G373S	ENSP00000255132:G563S	G	-	1	0	MATN4	43359987	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	1.529000	0.35996	2.661000	0.90470	0.644000	0.83932	GGC	C|0.757;T|0.243	0.243	strong		0.622	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1		
NSMCE1	197370	hgsc.bcm.edu	37	16	27268779	27268779	+	Missense_Mutation	SNP	G	G	C	rs7195194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27268779G>C	ENST00000361439.4	-	2	212	c.113C>G	c.(112-114)aCg>aGg	p.T38R		NM_145080.3	NP_659547.2	Q8WV22	NSE1_HUMAN	non-SMC element 1 homolog (S. cerevisiae)	38	Interaction with NDNL2.		T -> R (in dbSNP:rs7195194).		DNA recombination (GO:0006310)|DNA repair (GO:0006281)|intracellular signal transduction (GO:0035556)|positive regulation of response to DNA damage stimulus (GO:2001022)|protein ubiquitination (GO:0016567)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)	7						GTAGCAGTGCGTCTGCAAGCG	0.557													C|||	453	0.0904553	0.3124	0.0447	5008	,	,		18274	0.0		0.008	False		,,,				2504	0.001				p.T38R		Atlas-SNP	.											NSMCE1,NS,carcinoma,0,1	NSMCE1	28	1	0			c.C113G						PASS	.	C	ARG/THR	1012,3224		115,782,1221	117.0	125.0	122.0		113	1.0	1.0	16	dbSNP_116	122	110,8326		2,106,4110	yes	missense	NSMCE1	NM_145080.3	71	117,888,5331	CC,CG,GG		1.3039,23.8905,8.8542	benign	38/267	27268779	1122,11550	2118	4218	6336	SO:0001583	missense	197370	exon2			CAGTGCGTCTGCA	AF161451	CCDS10628.2	16p12.1	2010-03-23	2006-07-05		ENSG00000169189	ENSG00000169189			29897	protein-coding gene	gene with protein product						11927594	Standard	XM_005255163		Approved	NSE1	uc002doi.1	Q8WV22	OTTHUMG00000131674	ENST00000361439.4:c.113C>G	16.37:g.27268779G>C	ENSP00000355077:p.Thr38Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_145080	D3DWF6|Q9P045|Q9P049	Missense_Mutation	SNP	ENST00000361439.4	37	CCDS10628.2	173	0.07921245421245421	153	0.31097560975609756	16	0.04419889502762431	0	0.0	4	0.005277044854881266	C	0.325	-0.959541	0.02267	0.238905	0.013039	ENSG00000169189	ENST00000361439	T	0.29917	1.55	4.85	0.995	0.19838	.	0.349466	0.31188	N	0.008096	T	0.00012	0.0000	N	0.01874	-0.695	0.54753	P	1.0999999999983245E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41998	-0.9477	9	0.08599	T	0.76	.	3.9853	0.09513	0.0:0.3662:0.2003:0.4335	rs7195194;rs11553889;rs17845594;rs17858499;rs7195194	38	Q8WV22	NSE1_HUMAN	R	38	ENSP00000355077:T38R	ENSP00000355077:T38R	T	-	2	0	NSMCE1	27176280	0.233000	0.23772	0.974000	0.42286	0.526000	0.34562	-0.508000	0.06344	0.033000	0.15463	-1.389000	0.01157	ACG	G|0.913;C|0.087	0.087	strong		0.557	NSMCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254577.3	NM_145080	
ME2	4200	hgsc.bcm.edu	37	18	48458662	48458662	+	Missense_Mutation	SNP	G	G	A	rs649224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:48458662G>A	ENST00000321341.5	+	13	1621	c.1349G>A	c.(1348-1350)gGg>gAg	p.G450E	ME2_ENST00000585680.1_3'UTR|ME2_ENST00000382927.3_Missense_Mutation_p.G450E	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	450			G -> E (in dbSNP:rs649224).		malate metabolic process (GO:0006108)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(3)	23		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)		AGTCCATTTGGGCCAGTGAAA	0.368													G|||	782	0.15615	0.3517	0.1023	5008	,	,		14058	0.0942		0.0726	False		,,,				2504	0.0798				p.G450E		Atlas-SNP	.											.	ME2	49	.	0			c.G1349A						PASS	.	G	GLU/GLY,GLU/GLY	1257,3149	430.6+/-342.6	174,909,1120	128.0	125.0	126.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1349,1349	-4.5	0.9	18	dbSNP_83	126	661,7939	167.7+/-219.4	22,617,3661	yes	missense,missense	ME2	NM_001168335.1,NM_002396.4	98,98	196,1526,4781	AA,AG,GG		7.686,28.5293,14.747	benign,benign	450/480,450/585	48458662	1918,11088	2203	4300	6503	SO:0001583	missense	4200	exon13			CATTTGGGCCAGT	M55905	CCDS11948.1, CCDS54187.1	18q21	2012-10-02			ENSG00000082212	ENSG00000082212	1.1.1.40		6984	protein-coding gene	gene with protein product		154270				1993674	Standard	NM_002396		Approved		uc002ley.3	P23368	OTTHUMG00000132694	ENST00000321341.5:c.1349G>A	18.37:g.48458662G>A	ENSP00000321070:p.Gly450Glu	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	266	266	1	NM_001168335	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	37	CCDS11948.1	330	0.1510989010989011	173	0.3516260162601626	40	0.11049723756906077	69	0.12062937062937062	48	0.0633245382585752	G	9.596	1.127309	0.20959	0.285293	0.07686	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.40476	1.03;1.03	5.18	-4.53	0.03462	Malic enzyme, NAD-binding (2);NAD(P)-binding domain (1);	0.586195	0.19418	N	0.114769	T	0.00012	0.0000	N	0.04275	-0.24	0.40955	P	0.015429000000000026	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.40905	-0.9538	9	0.20046	T	0.44	-0.0013	15.3934	0.74767	0.765:0.0:0.235:0.0	rs649224;rs52805686;rs61056684;rs649224	450;450	Q9BWL6;P23368	.;MAOM_HUMAN	E	450	ENSP00000321070:G450E;ENSP00000372384:G450E	ENSP00000321070:G450E	G	+	2	0	ME2	46712660	0.037000	0.19845	0.913000	0.36048	0.961000	0.63080	0.038000	0.13862	-0.931000	0.03746	-0.291000	0.09656	GGG	G|0.838;A|0.162	0.162	strong		0.368	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396	
EGFL7	51162	hgsc.bcm.edu	37	9	139564668	139564668	+	Missense_Mutation	SNP	G	G	A	rs2297538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139564668G>A	ENST00000371699.1	+	7	1368	c.457G>A	c.(457-459)Gtc>Atc	p.V153I	EGFL7_ENST00000371698.3_Missense_Mutation_p.V153I|EGFL7_ENST00000492002.1_3'UTR|EGFL7_ENST00000406555.3_Missense_Mutation_p.V153I|EGFL7_ENST00000308874.7_Missense_Mutation_p.V153I|MIR126_ENST00000362291.1_RNA			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	153	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		V -> I (in dbSNP:rs2297538). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		angiogenesis (GO:0001525)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|negative regulation of cell migration (GO:0030336)|negative regulation of Notch signaling pathway (GO:0045746)|positive regulation of endothelial cell proliferation (GO:0001938)|vasculogenesis (GO:0001570)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)			kidney(2)|ovary(1)|prostate(2)|urinary_tract(1)	6	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		CCAGCGCTGCGTCAACACCGC	0.672													g|||	843	0.168331	0.2073	0.1945	5008	,	,		17073	0.1349		0.2087	False		,,,				2504	0.09				p.V153I		Atlas-SNP	.											.	EGFL7	11	.	0			c.G457A						PASS	.	G	ILE/VAL,ILE/VAL	967,3427		108,751,1338	35.0	38.0	37.0		457,457	0.5	0.9	9	dbSNP_100	37	1757,6825		169,1419,2703	yes	missense,missense	EGFL7	NM_016215.4,NM_201446.2	29,29	277,2170,4041	AA,AG,GG		20.4731,22.0073,20.9926	benign,benign	153/274,153/274	139564668	2724,10252	2197	4291	6488	SO:0001583	missense	51162	exon8			CGCTGCGTCAACA	AF186111	CCDS7002.1	9q34.3	2008-02-05			ENSG00000172889	ENSG00000172889			20594	protein-coding gene	gene with protein product		608582					Standard	NM_016215		Approved	ZNEU1	uc004cih.3	Q9UHF1	OTTHUMG00000020938	ENST00000371699.1:c.457G>A	9.37:g.139564668G>A	ENSP00000360764:p.Val153Ile	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	100	30	0.3	NM_016215	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	ENST00000371699.1	37	CCDS7002.1	407	0.18635531135531136	118	0.23983739837398374	66	0.18232044198895028	68	0.11888111888111888	155	0.20448548812664907	G	6.763	0.509711	0.12883	0.220073	0.204731	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.05	0.508	0.16972	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);	0.447530	0.23342	N	0.049234	T	0.00012	0.0000	N	0.05230	-0.09	0.26060	P	0.9813663	B	0.15473	0.013	B	0.12837	0.008	T	0.40384	-0.9566	9	0.27082	T	0.32	-17.081	9.6192	0.39710	0.4213:0.0:0.5787:0.0	rs2297538;rs17850906;rs61338841;rs2297538	153	Q9UHF1	EGFL7_HUMAN	I	153	ENSP00000360764:V153I;ENSP00000307843:V153I;ENSP00000385639:V153I;ENSP00000360763:V153I	ENSP00000307843:V153I	V	+	1	0	EGFL7	138684489	0.020000	0.18652	0.857000	0.33713	0.266000	0.26442	-0.001000	0.12947	0.173000	0.19788	-0.254000	0.11334	GTC	G|0.800;A|0.200	0.200	strong		0.672	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215	
NELFA	7469	hgsc.bcm.edu	37	4	1985668	1985668	+	Silent	SNP	G	G	A	rs2234574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1985668G>A	ENST00000411638.2	-	9	1224	c.1209C>T	c.(1207-1209)gtC>gtT	p.V403V	MIR943_ENST00000401286.1_RNA|NELFA_ENST00000382882.3_Silent_p.V414V|NELFA_ENST00000542778.1_Silent_p.V268V	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A	403					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)										TGGTAGGGGCGACAGCCGGAG	0.682													G|||	137	0.0273562	0.0825	0.013	5008	,	,		13899	0.0129		0.002	False		,,,				2504	0.0041				p.V414V		Atlas-SNP	.											.	.	.	.	0			c.C1242T						PASS	.	G		286,4120	156.6+/-189.7	5,276,1922	42.0	45.0	44.0		1242	-2.0	0.0	4	dbSNP_98	44	13,8585	9.1+/-34.3	0,13,4286	no	coding-synonymous	WHSC2	NM_005663.4		5,289,6208	AA,AG,GG		0.1512,6.4911,2.2993		414/540	1985668	299,12705	2203	4299	6502	SO:0001819	synonymous_variant	7469	exon9			AGGGGCGACAGCC	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.1209C>T	4.37:g.1985668G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	126	66	0.52381	NM_005663	A2A2T1|O95392	Silent	SNP	ENST00000411638.2	37																																																																																				G|0.977;A|0.023	0.023	strong		0.682	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663	
CLDN23	137075	hgsc.bcm.edu	37	8	8559917	8559917	+	Silent	SNP	G	G	A	rs61754917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8559917G>A	ENST00000519106.1	+	1	470	c.9G>A	c.(7-9)acG>acA	p.T3T		NM_194284.2	NP_919260.2	Q96B33	CLD23_HUMAN	claudin 23	3					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	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(2)	2		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.071)|READ - Rectum adenocarcinoma(644;0.238)		GGATGCGGACGCCGGTGGTGA	0.736													G|||	31	0.0061901	0.0219	0.0029	5008	,	,		12030	0.0		0.0	False		,,,				2504	0.0				p.T3T		Atlas-SNP	.											.	CLDN23	5	.	0			c.G9A						PASS	.	G		90,3868		0,90,1889	9.0	13.0	11.0		9	2.2	1.0	8	dbSNP_129	11	0,8248		0,0,4124	no	coding-synonymous	CLDN23	NM_194284.2		0,90,6013	AA,AG,GG		0.0,2.2739,0.7373		3/293	8559917	90,12116	1979	4124	6103	SO:0001819	synonymous_variant	137075	exon1			GCGGACGCCGGTG	AK123547	CCDS55195.1	8p23.1	2006-04-12				ENSG00000253958		"""Claudins"""	17591	protein-coding gene	gene with protein product		609203				12736707	Standard	NM_194284		Approved	CLDNL	uc003wsi.3	Q96B33		ENST00000519106.1:c.9G>A	8.37:g.8559917G>A		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	7	6	0.857143	NM_194284	Q08AJ3	Silent	SNP	ENST00000519106.1	37	CCDS55195.1																																																																																			G|0.995;A|0.005	0.005	strong		0.736	CLDN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374721.1	NM_194284	
CELSR1	9620	hgsc.bcm.edu	37	22	46761497	46761497	+	Missense_Mutation	SNP	C	C	G	rs12165943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	101	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	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	
OR4K15	81127	hgsc.bcm.edu	37	14	20444026	20444026	+	Missense_Mutation	SNP	T	T	G	rs3861513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20444026T>G	ENST00000305051.5	+	1	424	c.349T>G	c.(349-351)Tct>Gct	p.S117A		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	117			S -> A (in dbSNP:rs3861513). {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)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CAAGACTATTTCTTTTGATGC	0.433													T|||	1093	0.218251	0.2141	0.1715	5008	,	,		22872	0.123		0.2227	False		,,,				2504	0.3507				p.S117A		Atlas-SNP	.											.	OR4K15	82	.	0			c.T349G						PASS	.	T	ALA/SER	1058,3348		122,814,1267	134.0	137.0	136.0		349	3.8	0.8	14	dbSNP_108	136	2283,6313		291,1701,2306	no	missense	OR4K15	NM_001005486.1	99	413,2515,3573	GG,GT,TT		26.5589,24.0127,25.696	probably-damaging	117/349	20444026	3341,9661	2203	4298	6501	SO:0001583	missense	81127	exon1			ACTATTTCTTTTG		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.349T>G	14.37:g.20444026T>G	ENSP00000304077:p.Ser117Ala	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	191	191	1	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	400	0.18315018315018314	95	0.19308943089430894	65	0.17955801104972377	66	0.11538461538461539	174	0.22955145118733508	.	15.40	2.823282	0.50739	0.240127	0.265589	ENSG00000169488	ENST00000305051	T	0.00700	5.82	3.8	3.8	0.43715	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000117	T	0.00012	0.0000	M	0.92459	3.31	0.40068	P	0.024025999999999992	D	0.71674	0.998	P	0.60286	0.872	T	0.31971	-0.9924	9	0.72032	D	0.01	.	10.5358	0.45002	0.0:0.0:0.0:1.0	rs3861513;rs58615739;rs3861513	117	Q8NH41	OR4KF_HUMAN	A	117	ENSP00000304077:S117A	ENSP00000304077:S117A	S	+	1	0	OR4K15	19513866	0.833000	0.29383	0.755000	0.31263	0.388000	0.30384	1.743000	0.38258	1.578000	0.49821	0.477000	0.44152	TCT	T|0.767;G|0.233	0.233	strong		0.433	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
ELP2	55250	hgsc.bcm.edu	37	18	33744465	33744465	+	Missense_Mutation	SNP	A	A	G	rs73428967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:33744465A>G	ENST00000358232.6	+	18	1852	c.1789A>G	c.(1789-1791)Att>Gtt	p.I597V	ELP2_ENST00000351393.6_Missense_Mutation_p.I571V|ELP2_ENST00000350494.6_Missense_Mutation_p.I592V|ELP2_ENST00000442325.2_Missense_Mutation_p.I662V|ELP2_ENST00000542050.1_3'UTR|ELP2_ENST00000542824.1_Missense_Mutation_p.I527V|ELP2_ENST00000423854.2_Missense_Mutation_p.I527V	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	597					chromatin organization (GO:0006325)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)				NS(1)|breast(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|urinary_tract(2)	30						TGCAGCTATCATTCTTTGGAA	0.368													A|||	15	0.00299521	0.0113	0.0	5008	,	,		19841	0.0		0.0	False		,,,				2504	0.0				p.I662V		Atlas-SNP	.											.	ELP2	70	.	0			c.A1984G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	52,4354	52.3+/-87.9	1,50,2152	118.0	113.0	115.0		1984,1774,1711,1579,1579,1789	5.8	1.0	18	dbSNP_130	115	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	ELP2	NM_001242875.1,NM_001242876.1,NM_001242877.1,NM_001242878.1,NM_001242879.1,NM_018255.2	29,29,29,29,29,29	1,50,6452	GG,GA,AA		0.0,1.1802,0.3998	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	662/892,592/822,571/801,527/757,527/757,597/827	33744465	52,12954	2203	4300	6503	SO:0001583	missense	55250	exon19			GCTATCATTCTTT	AK001741	CCDS11918.1, CCDS56065.1, CCDS56066.1, CCDS56067.1, CCDS56068.1, CCDS56069.1	18q12.1	2013-01-10	2012-08-08	2007-04-20	ENSG00000134759	ENSG00000134759		"""Elongator acetyltransferase complex subunits"", ""WD repeat domain containing"""	18248	protein-coding gene	gene with protein product			"""signal transducer and activator of transcription 3 interacting protein 1"", ""elongation protein 2 homolog (S. cerevisiae)"""	STATIP1		11714725, 10954736	Standard	NM_001242875		Approved	FLJ10879, StIP	uc002kzk.2	Q6IA86	OTTHUMG00000132589	ENST00000358232.6:c.1789A>G	18.37:g.33744465A>G	ENSP00000350967:p.Ile597Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	176	80	0.454545	NM_001242875	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Missense_Mutation	SNP	ENST00000358232.6	37	CCDS11918.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	18.12	3.554080	0.65425	0.011802	0.0	ENSG00000134759	ENST00000358232;ENST00000351393;ENST00000442325;ENST00000423854;ENST00000350494;ENST00000542824	T;T;T;T;T;T	0.65364	-0.15;2.26;1.09;2.26;0.0;-0.15	5.79	5.79	0.91817	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.103034	0.64402	D	0.000005	T	0.62756	0.2454	M	0.67625	2.065	0.54753	D	0.999986	P;P;P;P;P;P	0.49090	0.879;0.879;0.881;0.919;0.619;0.868	P;P;P;P;P;P	0.52031	0.688;0.688;0.527;0.672;0.511;0.472	T	0.66308	-0.5956	10	0.33940	T	0.23	-26.4385	14.0849	0.64949	1.0:0.0:0.0:0.0	.	592;662;527;527;571;597	B4DTG0;E7EP23;E9PCX0;Q6IA86-2;Q6IA86-3;Q6IA86	.;.;.;.;.;ELP2_HUMAN	V	597;571;662;527;592;527	ENSP00000350967:I597V;ENSP00000257191:I571V;ENSP00000414851:I662V;ENSP00000391202:I527V;ENSP00000316051:I592V;ENSP00000443800:I527V	ENSP00000316051:I592V	I	+	1	0	ELP2	31998463	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.037000	0.49775	2.208000	0.71279	0.533000	0.62120	ATT	A|0.997;G|0.003	0.003	strong		0.368	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255	
SLC39A14	23516	hgsc.bcm.edu	37	8	22273687	22273687	+	Silent	SNP	T	T	C	rs6558052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22273687T>C	ENST00000381237.1	+	7	1160	c.1041T>C	c.(1039-1041)caT>caC	p.H347H	SLC39A14_ENST00000359741.5_Silent_p.H347H|SLC39A14_ENST00000240095.6_Silent_p.H347H|SLC39A14_ENST00000289952.5_Silent_p.H347H	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	347					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		ACGGCCTCCATAATTTCATCG	0.557													C|||	1434	0.286342	0.7247	0.121	5008	,	,		21035	0.1915		0.0517	False		,,,				2504	0.1503				p.H347H		Atlas-SNP	.											SLC39A14_ENST00000381237,NS,malignant_melanoma,+2,2	SLC39A14	59	2	0			c.T1041C						PASS	.	C	,,,	2620,1786	527.4+/-372.1	791,1038,374	103.0	96.0	99.0		1041,1041,1041,1041	4.2	1.0	8	dbSNP_116	99	465,8135	798.8+/-407.4	10,445,3845	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC39A14	NM_001128431.2,NM_001135153.1,NM_001135154.1,NM_015359.4	,,,	801,1483,4219	CC,CT,TT		5.407,40.5356,23.7198	,,,	347/493,347/493,347/482,347/493	22273687	3085,9921	2203	4300	6503	SO:0001819	synonymous_variant	23516	exon7			CCTCCATAATTTC	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"""Solute carriers"""	20858	protein-coding gene	gene with protein product		608736	"""solute carrier family 39 (metal ion transporter), member 14"""			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.1041T>C	8.37:g.22273687T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	164	75	0.457317	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Silent	SNP	ENST00000381237.1	37	CCDS47823.1																																																																																			T|0.748;C|0.252	0.252	strong		0.557	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677	
SHC2	25759	hgsc.bcm.edu	37	19	422229	422229	+	Missense_Mutation	SNP	C	C	T	rs61750917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:422229C>T	ENST00000264554.6	-	11	1536	c.1537G>A	c.(1537-1539)Gtc>Atc	p.V513I		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	513	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-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)		GGGTTGGTGACGCTGTCTCGC	0.672													C|||	93	0.0185703	0.0651	0.0086	5008	,	,		14638	0.0		0.001	False		,,,				2504	0.0				p.V513I		Atlas-SNP	.											SHC2,colon,carcinoma,0,1	SHC2	47	1	0			c.G1537A						PASS	.	C	ILE/VAL	310,4082		12,286,1898	23.0	29.0	27.0		1537	-1.1	1.0	19	dbSNP_129	27	2,8592		0,2,4295	yes	missense	SHC2	NM_012435.2	29	12,288,6193	TT,TC,CC		0.0233,7.0583,2.4026	benign	513/583	422229	312,12674	2196	4297	6493	SO:0001583	missense	25759	exon11			TGGTGACGCTGTC	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"""SH2 domain containing"""	29869	protein-coding gene	gene with protein product	"""neuronal Shc adaptor homolog"""	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.1537G>A	19.37:g.422229C>T	ENSP00000264554:p.Val513Ile	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_012435	O60230|Q9NPL5|Q9UCX4	Missense_Mutation	SNP	ENST00000264554.6	37	CCDS45891.1	37	0.01694139194139194	34	0.06910569105691057	3	0.008287292817679558	0	0.0	0	0.0	C	8.377	0.836675	0.16891	0.070583	2.33E-4	ENSG00000129946	ENST00000264554	D	0.88431	-2.38	4.76	-1.12	0.09808	SH2 motif (5);	0.368945	0.29624	N	0.011635	T	0.16642	0.0400	N	0.02985	-0.445	0.24255	N	0.995303	B	0.12630	0.006	B	0.14023	0.01	T	0.49351	-0.8949	10	0.37606	T	0.19	-39.6557	8.286	0.31928	0.0:0.4041:0.0:0.5959	.	513	P98077	SHC2_HUMAN	I	513	ENSP00000264554:V513I	ENSP00000264554:V513I	V	-	1	0	SHC2	373229	0.748000	0.28294	0.991000	0.47740	0.309000	0.27889	-0.010000	0.12743	0.029000	0.15352	-0.812000	0.03155	GTC	C|0.981;T|0.019	0.019	strong		0.672	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3		
DCAF4L2	138009	hgsc.bcm.edu	37	8	88885256	88885256	+	Missense_Mutation	SNP	G	G	A	rs146716352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:88885256G>A	ENST00000319675.3	-	1	1040	c.944C>T	c.(943-945)tCc>tTc	p.S315F		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	315										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						TAGGTAGGCGGAGTTATTCAC	0.542													G|||	11	0.00219649	0.0083	0.0	5008	,	,		19579	0.0		0.0	False		,,,				2504	0.0				p.S315F		Atlas-SNP	.											.	DCAF4L2	187	.	0			c.C944T						PASS	.	G	PHE/SER	45,4361	46.7+/-81.2	0,45,2158	108.0	102.0	104.0		944	0.1	0.0	8	dbSNP_134	104	0,8600		0,0,4300	yes	missense	DCAF4L2	NM_152418.3	155	0,45,6458	AA,AG,GG		0.0,1.0213,0.346	benign	315/396	88885256	45,12961	2203	4300	6503	SO:0001583	missense	138009	exon1			TAGGCGGAGTTAT	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"""WD repeat domain containing"""	26657	protein-coding gene	gene with protein product			"""WD repeat domain 21C"""	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.944C>T	8.37:g.88885256G>A	ENSP00000316496:p.Ser315Phe	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	185	87	0.47027	NM_152418		Missense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	14.00	2.405976	0.42715	0.010213	0.0	ENSG00000176566	ENST00000319675	T	0.22945	1.93	1.39	0.0752	0.14398	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.113194	0.64402	D	0.000008	T	0.07773	0.0195	N	0.14661	0.345	0.22096	N	0.999368	B	0.25521	0.128	B	0.25614	0.062	T	0.24548	-1.0157	10	0.22706	T	0.39	.	5.3547	0.16055	0.0:0.0:0.3197:0.6803	.	315	Q8NA75	DC4L2_HUMAN	F	315	ENSP00000316496:S315F	ENSP00000316496:S315F	S	-	2	0	DCAF4L2	88954372	1.000000	0.71417	0.009000	0.14445	0.009000	0.06853	2.530000	0.45641	-0.175000	0.10725	-0.518000	0.04402	TCC	G|0.997;A|0.003	0.003	strong		0.542	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418	
KIAA1671	85379	hgsc.bcm.edu	37	22	25570285	25570285	+	Silent	SNP	C	C	T	rs56351192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25570285C>T	ENST00000406486.4	+	9	5115	c.4728C>T	c.(4726-4728)tcC>tcT	p.S1576S	KIAA1671_ENST00000358431.3_Silent_p.S1576S|KIAA1671_ENST00000401395.1_Silent_p.S83S			Q9BY89	K1671_HUMAN	KIAA1671	1576										autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						CTTCTCTGTCCTCCCAAACGG	0.602													C|||	111	0.0221645	0.0779	0.0086	5008	,	,		17838	0.0		0.002	False		,,,				2504	0.0				p.S1576S		Atlas-SNP	.											.	KIAA1671	28	.	0			c.C4728T						PASS	.						27.0	31.0	30.0					22																	25570285		692	1591	2283	SO:0001819	synonymous_variant	85379	exon6			TCTGTCCTCCCAA		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.4728C>T	22.37:g.25570285C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			C|0.981;T|0.019	0.019	strong		0.602	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	
RANBP3	8498	hgsc.bcm.edu	37	19	5914625	5914625	+	IGR	SNP	G	G	A	rs7248090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:5914625G>A	ENST00000340578.6	-	0	3233				CAPS_ENST00000452990.2_Silent_p.E45E|AC104532.4_ENST00000591109.1_RNA|CAPS_ENST00000588776.1_Silent_p.E131E|CAPS_ENST00000222125.5_Silent_p.E45E|AC104532.2_ENST00000588891.1_3'UTR	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3						intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						ACGCTGATGAGTTCCGGCAGG	0.652													G|||	328	0.0654952	0.1467	0.062	5008	,	,		17780	0.0129		0.003	False		,,,				2504	0.0767				p.E45E		Atlas-SNP	.											.	CAPS	14	.	0			c.G135A						PASS	.	G	,	604,3802	263.1+/-265.3	33,538,1632	72.0	74.0	73.0		135,135	1.9	0.3	19	dbSNP_116	73	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous,coding-synonymous	CAPS	NM_004058.3,NM_080590.2	,	33,573,5897	AA,AG,GG		0.407,13.7086,4.9131	,	45/190,45/163	5914625	639,12367	2203	4300	6503	SO:0001628	intergenic_variant	828	exon3			TGATGAGTTCCGG	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4			19.37:g.5914625G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_080590	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Silent	SNP	ENST00000340578.6	37	CCDS42478.1																																																																																			G|0.953;A|0.047	0.047	strong		0.652	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322	
BPIFB4	149954	hgsc.bcm.edu	37	20	31678534	31678534	+	Silent	SNP	T	T	C	rs2070326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31678534T>C	ENST00000375483.3	+	8	1072	c.1072T>C	c.(1072-1074)Ttg>Ctg	p.L358L		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	358						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCTGGGGATATTGGGAAGTGT	0.592													T|||	1090	0.217652	0.1732	0.3127	5008	,	,		19342	0.1607		0.2366	False		,,,				2504	0.2495				p.L358L		Atlas-SNP	.											.	.	.	.	0			c.T1072C						PASS	.	T		858,3548	334.9+/-303.7	95,668,1440	119.0	96.0	104.0		1072	0.4	1.0	20	dbSNP_96	104	2000,6600	349.3+/-327.4	222,1556,2522	no	coding-synonymous	BPIFB4	NM_182519.2		317,2224,3962	CC,CT,TT		23.2558,19.4734,21.9745		358/615	31678534	2858,10148	2203	4300	6503	SO:0001819	synonymous_variant	149954	exon8			GGGATATTGGGAA	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.1072T>C	20.37:g.31678534T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	37	CCDS13213.2																																																																																			T|0.784;C|0.216	0.216	strong		0.592	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
DDX24	57062	hgsc.bcm.edu	37	14	94526812	94526812	+	Silent	SNP	C	C	T	rs11845400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94526812C>T	ENST00000330836.5	-	5	1676	c.1545G>A	c.(1543-1545)caG>caA	p.Q515Q	DDX24_ENST00000555054.1_Silent_p.Q472Q|DDX24_ENST00000544005.1_Silent_p.Q265Q	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	515	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		GAGCAGGAGCCTGATGCACCA	0.473													C|||	202	0.0403355	0.1483	0.0043	5008	,	,		21521	0.0		0.002	False		,,,				2504	0.001				p.Q515Q		Atlas-SNP	.											.	DDX24	82	.	0			c.G1545A						PASS	.	C		558,3848	249.6+/-257.0	33,492,1678	192.0	177.0	182.0		1545	-1.5	1.0	14	dbSNP_120	182	39,8561	26.3+/-74.7	0,39,4261	no	coding-synonymous	DDX24	NM_020414.3		33,531,5939	TT,TC,CC		0.4535,12.6645,4.5902		515/860	94526812	597,12409	2203	4300	6503	SO:0001819	synonymous_variant	57062	exon5			AGGAGCCTGATGC	AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"""DEAD-boxes"""	13266	protein-coding gene	gene with protein product		606181	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"""			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.1545G>A	14.37:g.94526812C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	228	118	0.517544	NM_020414	E7EMJ4|Q4V9L5	Silent	SNP	ENST00000330836.5	37	CCDS9918.1																																																																																			C|0.952;T|0.048	0.048	strong		0.473	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414	
SYCE1	93426	hgsc.bcm.edu	37	10	135369532	135369532	+	Missense_Mutation	SNP	T	T	C	rs3747881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135369532T>C	ENST00000343131.5	-	9	652	c.548A>G	c.(547-549)aAg>aGg	p.K183R	SYCE1_ENST00000432597.2_Missense_Mutation_p.K147R|SPRN_ENST00000541506.1_Intron|SYCE1_ENST00000368517.3_Missense_Mutation_p.K147R	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	183			K -> R (in dbSNP:rs3747881). {ECO:0000269|PubMed:15489334}.		synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		ACAAATCTCCTTTGCCAGCCG	0.552													C|||	988	0.197284	0.1997	0.1844	5008	,	,		21691	0.2698		0.1093	False		,,,				2504	0.2188				p.K183R		Atlas-SNP	.											.	SYCE1	81	.	0			c.A548G						PASS	.	C	ARG/LYS,ARG/LYS,ARG/LYS	722,3684	748.4+/-411.9	41,640,1522	99.0	87.0	91.0		548,548,440	-3.9	0.0	10	dbSNP_107	91	807,7793	779.6+/-407.7	45,717,3538	yes	missense,missense,missense	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	26,26,26	86,1357,5060	CC,CT,TT		9.3837,16.3867,11.7561	benign,benign,benign	183/319,183/352,147/283	135369532	1529,11477	2203	4300	6503	SO:0001583	missense	93426	exon9			ATCTCCTTTGCCA	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.548A>G	10.37:g.135369532T>C	ENSP00000341282:p.Lys183Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	37	CCDS44501.1	404	0.184981684981685	93	0.18902439024390244	68	0.1878453038674033	153	0.2674825174825175	90	0.11873350923482849	C	0.855	-0.737129	0.03111	0.163867	0.093837	ENSG00000171772	ENST00000303903;ENST00000432597;ENST00000368517;ENST00000343131	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	4.38	-3.92	0.04155	.	0.864322	0.10196	N	0.704037	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.28996	-1.0026	9	0.05959	T	0.93	-9.816	7.6589	0.28392	0.133:0.1995:0.0:0.6675	rs3747881;rs17857025;rs52827544;rs60545805;rs3747881	55;183;147	Q8N0S2-3;Q8N0S2;Q8N0S2-2	.;SYCE1_HUMAN;.	R	183;147;147;183	ENSP00000303978:K183R;ENSP00000411779:K147R;ENSP00000357503:K147R;ENSP00000341282:K183R	ENSP00000303978:K183R	K	-	2	0	SYCE1	135219522	0.001000	0.12720	0.005000	0.12908	0.017000	0.09413	-1.544000	0.02192	-1.244000	0.02516	-0.119000	0.15052	AAG	T|0.851;C|0.149	0.149	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
MDC1	9656	hgsc.bcm.edu	37	6	30672342	30672342	+	Missense_Mutation	SNP	A	A	G	rs3130645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30672342A>G	ENST00000376406.3	-	10	5265	c.4618T>C	c.(4618-4620)Tcc>Ccc	p.S1540P	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Missense_Mutation_p.S1276P	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1540	Interaction with the PRKDC complex.		S -> P (in dbSNP:rs3130645). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18669648, ECO:0000269|PubMed:8724849, ECO:0000269|Ref.3}.		DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						GTGGAGGTGGAAGGCTGGAGC	0.577								Other conserved DNA damage response genes					A|||	657	0.13119	0.3056	0.134	5008	,	,		21158	0.0635		0.0596	False		,,,				2504	0.0368				p.S1540P		Atlas-SNP	.											.	MDC1	218	.	0			c.T4618C						PASS	.	A	PRO/SER	1223,3183	409.3+/-334.9	174,875,1154	119.0	139.0	132.0		4618	-8.4	0.0	6	dbSNP_103	132	519,8081	141.9+/-198.1	21,477,3802	no	missense	MDC1	NM_014641.2	74	195,1352,4956	GG,GA,AA		6.0349,27.7576,13.3938	probably-damaging	1540/2090	30672342	1742,11264	2203	4300	6503	SO:0001583	missense	9656	exon10			AGGTGGAAGGCTG	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.4618T>C	6.37:g.30672342A>G	ENSP00000365588:p.Ser1540Pro	Somatic	392	1	0.00255102		WXS	Illumina HiSeq	Phase_I	416	201	0.483173	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	269	0.12316849816849818	136	0.2764227642276423	52	0.143646408839779	43	0.07517482517482517	38	0.05013192612137203	A	10.58	1.389410	0.25118	0.277576	0.060349	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.11169	2.8;2.8	4.26	-8.4	0.00965	.	.	.	.	.	T	0.02455	0.0075	M	0.68593	2.085	0.80722	P	0.0	B;B	0.17852	0.024;0.002	B;B	0.18561	0.022;0.001	T	0.39603	-0.9606	8	0.30078	T	0.28	.	2.3277	0.04227	0.2323:0.1232:0.4035:0.241	rs3130645;rs13219132;rs52796082;rs61323254;rs3130645	1276;1540	Q14676-2;Q14676	.;MDC1_HUMAN	P	1540;1276;1253;1106	ENSP00000365588:S1540P;ENSP00000365587:S1276P	ENSP00000365587:S1276P	S	-	1	0	MDC1	30780321	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.052000	0.00305	-1.785000	0.01271	-1.251000	0.01509	TCC	A|0.872;G|0.128	0.128	strong		0.577	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
NCOA3	8202	hgsc.bcm.edu	37	20	46264805	46264805	+	Missense_Mutation	SNP	C	C	T	rs2230781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:46264805C>T	ENST00000371998.3	+	12	1866	c.1675C>T	c.(1675-1677)Cca>Tca	p.P559S	NCOA3_ENST00000341724.6_Missense_Mutation_p.P569S|NCOA3_ENST00000372004.3_Missense_Mutation_p.P559S|NCOA3_ENST00000371997.3_Missense_Mutation_p.P569S			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	559	Ser-rich.		P -> S (in dbSNP:rs2230781). {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						TATTACCCAACCAAGTAAAGT	0.443													C|||	96	0.0191693	0.0651	0.0101	5008	,	,		17392	0.0		0.003	False		,,,				2504	0.0				p.P569S		Atlas-SNP	.											.	NCOA3	156	.	0			c.C1705T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	246,4160	143.1+/-178.2	7,232,1964	90.0	89.0	89.0		1675,1705,1675,1675	3.7	0.8	20	dbSNP_98	89	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense,missense	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	74,74,74,74	7,236,6260	TT,TC,CC		0.0465,5.5833,1.9222	benign,benign,benign,benign	559/1424,569/1416,559/1421,559/1425	46264805	250,12756	2203	4300	6503	SO:0001583	missense	8202	exon12			ACCCAACCAAGTA	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.1675C>T	20.37:g.46264805C>T	ENSP00000361066:p.Pro559Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	155	87	0.56129	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	38	0.0173992673992674	33	0.06707317073170732	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	8.392	0.839981	0.16891	0.055833	4.65E-4	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.72	3.7	0.42460	.	0.351919	0.27627	N	0.018540	T	0.01061	0.0035	L	0.44542	1.39	0.26797	N	0.969286	B;B;B;B;B;B	0.25312	0.088;0.123;0.088;0.088;0.029;0.038	B;B;B;B;B;B	0.30572	0.103;0.117;0.103;0.103;0.098;0.071	T	0.24870	-1.0148	10	0.05833	T	0.94	-3.6234	16.0462	0.80722	0.0:0.7459:0.2541:0.0	rs2230781;rs52817019;rs2230781	559;569;563;559;559;559	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	S	559;569;559;559;569	ENSP00000342123:P569S;ENSP00000361073:P559S;ENSP00000361066:P559S;ENSP00000361065:P569S	ENSP00000345671:P559S	P	+	1	0	NCOA3	45698212	0.993000	0.37304	0.828000	0.32881	0.927000	0.56198	1.799000	0.38824	0.693000	0.31634	0.655000	0.94253	CCA	C|0.981;T|0.019	0.019	strong		0.443	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
SPTBN1	6711	hgsc.bcm.edu	37	2	54844790	54844790	+	Silent	SNP	C	C	T	rs2229506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:54844790C>T	ENST00000356805.4	+	6	893	c.612C>T	c.(610-612)gaC>gaT	p.D204D	SPTBN1_ENST00000333896.5_Silent_p.D191D	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	204	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GCTGGAGGGACGGCATGGCCT	0.458													C|||	568	0.113419	0.1165	0.1052	5008	,	,		19328	0.0506		0.167	False		,,,				2504	0.1247				p.D204D		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C612T						PASS	.	C	,	533,3873	241.5+/-251.9	35,463,1705	179.0	144.0	156.0		612,573	-3.5	1.0	2	dbSNP_98	156	1334,7266	262.4+/-284.4	116,1102,3082	no	coding-synonymous,coding-synonymous	SPTBN1	NM_003128.2,NM_178313.2	,	151,1565,4787	TT,TC,CC		15.5116,12.0971,14.3549	,	204/2365,191/2156	54844790	1867,11139	2203	4300	6503	SO:0001819	synonymous_variant	6711	exon6			GAGGGACGGCATG		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.612C>T	2.37:g.54844790C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	201	97	0.482587	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			C|0.859;G|0.000;T|0.140	0.140	strong		0.458	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
PYCR2	29920	hgsc.bcm.edu	37	1	226108200	226108200	+	Silent	SNP	C	C	T	rs73131849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226108200C>T	ENST00000343818.6	-	7	1066	c.918G>A	c.(916-918)ggG>ggA	p.G306G	RP4-559A3.7_ENST00000432920.2_Intron|PYCR2_ENST00000478402.1_5'UTR	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	116	0	0		WXS	Illumina HiSeq	Phase_I	126	67	0.531746	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	
PPFIA2	8499	hgsc.bcm.edu	37	12	81769581	81769581	+	Silent	SNP	C	C	T	rs10862301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:81769581C>T	ENST00000549396.1	-	10	1285	c.1125G>A	c.(1123-1125)ctG>ctA	p.L375L	PPFIA2_ENST00000549325.1_Silent_p.L357L|PPFIA2_ENST00000443686.3_Silent_p.L276L|RP11-315E17.1_ENST00000546936.1_RNA|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000550359.2_Silent_p.L222L|PPFIA2_ENST00000552948.1_Silent_p.L375L|PPFIA2_ENST00000407050.4_Silent_p.L301L|PPFIA2_ENST00000548586.1_Silent_p.L375L|PPFIA2_ENST00000333447.7_Silent_p.L357L|PPFIA2_ENST00000550584.2_Silent_p.L375L	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	375	Glu-rich.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						GAACCTGCCGCAGGATAGCTT	0.403													T|||	2232	0.445687	0.5673	0.402	5008	,	,		16197	0.5387		0.2724	False		,,,				2504	0.3947				p.L375L		Atlas-SNP	.											.	PPFIA2	207	.	0			c.G1125A						PASS	.	T	,,,,,,	1778,2016		402,974,521	150.0	147.0	148.0		1125,1071,1125,1125,903,828,1125	-5.7	0.8	12	dbSNP_120	148	2059,6149		257,1545,2302	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPFIA2	NM_001220473.1,NM_001220474.1,NM_001220475.1,NM_001220476.1,NM_001220477.1,NM_001220478.1,NM_003625.3	,,,,,,	659,2519,2823	TT,TC,CC		25.0853,46.8635,31.9697	,,,,,,	375/1248,357/1233,375/1237,375/1252,301/1157,276/1153,375/1258	81769581	3837,8165	1897	4104	6001	SO:0001819	synonymous_variant	8499	exon9			CTGCCGCAGGATA	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9246	protein-coding gene	gene with protein product	"""Liprin-alpha2"""	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.1125G>A	12.37:g.81769581C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	176	82	0.465909	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		
LGALS16	148003	hgsc.bcm.edu	37	19	40148584	40148584	+	Missense_Mutation	SNP	T	T	C	rs10403702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40148584T>C	ENST00000392051.3	+	2	145	c.77T>C	c.(76-78)cTg>cCg	p.L26P		NM_001190441.1	NP_001177370.1			lectin, galactoside-binding, soluble, 16																		AAAGGGACACTGATCGACTCT	0.478													.|||	304	0.0607029	0.2209	0.0159	5008	,	,		23871	0.0		0.001	False		,,,				2504	0.0				p.L26P		Atlas-SNP	.											.	LGALS16	6	.	0			c.T77C						PASS	.																																			SO:0001583	missense	148003	exon2			GGACACTGATCGA		CCDS54267.1	19q13.2	2011-08-04			ENSG00000249861	ENSG00000249861		"""Lectins, galactoside-binding"""	40039	protein-coding gene	gene with protein product						19497882	Standard	NM_001190441		Approved		uc021uun.1	A8MUM7		ENST00000392051.3:c.77T>C	19.37:g.40148584T>C	ENSP00000375904:p.Leu26Pro	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	71	0.577236	NM_001190441		Missense_Mutation	SNP	ENST00000392051.3	37	CCDS54267.1	132	0.06043956043956044	124	0.25203252032520324	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	.	0.003	-2.453243	0.00175	.	.	ENSG00000249861	ENST00000392051	T	0.04194	3.68	1.21	0.065	0.14355	.	.	.	.	.	T	0.00012	0.0000	N	0.00510	-1.415	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45673	-0.9245	8	0.42905	T	0.14	.	3.8659	0.09016	0.0:0.4602:0.0:0.5398	rs10403702;rs10403702	26	A8MUM7	LEG16_HUMAN	P	26	ENSP00000375904:L26P	ENSP00000375904:L26P	L	+	2	0	LGALS16	44840424	0.000000	0.05858	0.007000	0.13788	0.200000	0.23975	-0.442000	0.06871	-0.172000	0.10779	-1.033000	0.02402	CTG	T|0.912;C|0.088	0.088	strong		0.478	LGALS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465022.1		
PTCHD2	57540	hgsc.bcm.edu	37	1	11561164	11561164	+	Missense_Mutation	SNP	G	G	A	rs41274528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11561164G>A	ENST00000294484.6	+	2	253	c.115G>A	c.(115-117)Ggg>Agg	p.G39R	PTCHD2_ENST00000389575.3_Missense_Mutation_p.G39R	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	39			G -> R (in dbSNP:rs41274528).		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)		GCCCCAACCTGGGGCAGGGGG	0.642													G|||	915	0.182708	0.407	0.0764	5008	,	,		16504	0.0476		0.0577	False		,,,				2504	0.2229				p.G39R		Atlas-SNP	.											.	PTCHD2	193	.	0			c.G115A						PASS	.	G	ARG/GLY	1260,2476		219,822,827	40.0	46.0	44.0		115	4.8	0.1	1	dbSNP_127	44	543,7639		19,505,3567	yes	missense	PTCHD2	NM_020780.1	125	238,1327,4394	AA,AG,GG		6.6365,33.7259,15.1284	benign	39/1393	11561164	1803,10115	1868	4091	5959	SO:0001583	missense	57540	exon2			CAACCTGGGGCAG	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.115G>A	1.37:g.11561164G>A	ENSP00000294484:p.Gly39Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	136	67	0.492647	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	288	0.13186813186813187	189	0.38414634146341464	34	0.09392265193370165	19	0.033216783216783216	46	0.06068601583113457	G	0.229	-1.022663	0.02061	0.337259	0.066365	ENSG00000204624	ENST00000294484;ENST00000389575	T;T	0.22336	1.96;1.96	5.78	4.85	0.62838	.	2.107450	0.02625	U	0.103649	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40794	-0.9544	9	0.32370	T	0.25	-3.5197	14.1249	0.65213	0.0:0.1499:0.8501:0.0	rs41274528;rs61744903	39	Q9P2K9	PTHD2_HUMAN	R	39	ENSP00000294484:G39R;ENSP00000374226:G39R	ENSP00000294484:G39R	G	+	1	0	PTCHD2	11483751	0.843000	0.29541	0.105000	0.21289	0.006000	0.05464	1.320000	0.33666	1.402000	0.46780	0.563000	0.77884	GGG	G|0.885;A|0.115	0.115	strong		0.642	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
ANKRD24	170961	hgsc.bcm.edu	37	19	4216829	4216829	+	Missense_Mutation	SNP	G	G	A	rs61738959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4216829G>A	ENST00000600132.1	+	18	1948	c.1672G>A	c.(1672-1674)Gga>Aga	p.G558R	ANKRD24_ENST00000262970.5_Missense_Mutation_p.G648R|ANKRD24_ENST00000318934.4_Missense_Mutation_p.G558R	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	558										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		CAAAGTTAACGGAGCCGAGAC	0.592													G|||	102	0.0203674	0.0749	0.0043	5008	,	,		18749	0.0		0.0	False		,,,				2504	0.0				p.G558R		Atlas-SNP	.											.	ANKRD24	180	.	0			c.G1672A						PASS	.	G	ARG/GLY	191,3851		8,175,1838	19.0	21.0	21.0		1672	3.5	0.0	19	dbSNP_129	21	4,8382		0,4,4189	yes	missense	ANKRD24	NM_133475.1	125	8,179,6027	AA,AG,GG		0.0477,4.7254,1.569	probably-damaging	558/1147	4216829	195,12233	2021	4193	6214	SO:0001583	missense	170961	exon18			GTTAACGGAGCCG	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1672G>A	19.37:g.4216829G>A	ENSP00000471252:p.Gly558Arg	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	g	17.79	3.476233	0.63737	0.047254	4.77E-4	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.39406	1.08;1.12	3.54	3.54	0.40534	.	0.251067	0.20840	N	0.084734	T	0.04998	0.0134	L	0.29908	0.895	0.26508	N	0.974647	D;D	0.67145	0.993;0.996	P;P	0.62089	0.794;0.898	T	0.01834	-1.1264	10	0.15952	T	0.53	-12.2673	12.9066	0.58156	0.0:0.0:1.0:0.0	rs61738959	558;648	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	R	558;648	ENSP00000321731:G558R;ENSP00000262970:G648R	ENSP00000262970:G648R	G	+	1	0	ANKRD24	4167829	0.332000	0.24722	0.008000	0.14137	0.088000	0.18126	0.933000	0.28897	2.288000	0.76882	0.313000	0.20887	GGA	G|0.982;A|0.018	0.018	strong		0.592	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
CASS4	57091	hgsc.bcm.edu	37	20	55027509	55027509	+	Missense_Mutation	SNP	C	C	T	rs34899200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:55027509C>T	ENST00000360314.3	+	6	1502	c.1277C>T	c.(1276-1278)tCg>tTg	p.S426L	CASS4_ENST00000371336.3_Missense_Mutation_p.S426L|CASS4_ENST00000434344.1_Intron	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	426	Ser-rich.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						AGCTCTTCCTCGGAGGAGTCA	0.572													C|||	94	0.01877	0.0681	0.0043	5008	,	,		20870	0.0		0.001	False		,,,				2504	0.0				p.S426L		Atlas-SNP	.											CASS4,rectum,adenoma,-1,1	CASS4	121	1	0			c.C1277T						PASS	.	C	LEU/SER,,LEU/SER,LEU/SER	242,4164	137.7+/-173.5	9,224,1970	44.0	40.0	41.0		1115,,1277,1277	2.7	0.0	20	dbSNP_126	41	5,8593	4.3+/-15.6	0,5,4294	yes	missense,intron,missense,missense	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	145,,145,145	9,229,6264	TT,TC,CC		0.0582,5.4925,1.8994	possibly-damaging,,possibly-damaging,possibly-damaging	372/733,,426/787,426/787	55027509	247,12757	2203	4299	6502	SO:0001583	missense	57091	exon5			CTTCCTCGGAGGA	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.1277C>T	20.37:g.55027509C>T	ENSP00000353462:p.Ser426Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	37	CCDS33492.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	15.20	2.762107	0.49468	0.054925	5.82E-4	ENSG00000087589	ENST00000360314;ENST00000371336	T;T	0.16597	2.33;2.33	5.6	2.65	0.31530	.	0.315398	0.35708	N	0.003026	T	0.01940	0.0061	M	0.76002	2.32	0.09310	N	1	B;B;B	0.31640	0.225;0.333;0.225	B;B;B	0.25506	0.028;0.061;0.028	T	0.04537	-1.0944	10	0.42905	T	0.14	-1.5677	11.146	0.48430	0.0:0.8005:0.0:0.1995	rs34899200	372;426;426	B4DII4;Q9NQ75-2;Q9NQ75	.;.;CASS4_HUMAN	L	426	ENSP00000353462:S426L;ENSP00000360387:S426L	ENSP00000353462:S426L	S	+	2	0	CASS4	54460916	0.617000	0.27043	0.002000	0.10522	0.864000	0.49448	2.043000	0.41231	0.416000	0.25844	-0.157000	0.13467	TCG	C|0.984;T|0.016	0.016	strong		0.572	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
PCDHGA9	56107	hgsc.bcm.edu	37	5	140783596	140783596	+	Silent	SNP	C	C	T	rs1363448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140783596C>T	ENST00000573521.1	+	1	1077	c.1077C>T	c.(1075-1077)gaC>gaT	p.D359D	PCDHGA8_ENST00000398604.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	359	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAGAGAAGACGCACCTCAGG	0.428													.|||	2713	0.541733	0.8427	0.6182	5008	,	,		18694	0.3274		0.4235	False		,,,				2504	0.4233				p.D359D		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.C1077T						PASS	.	T	,,,,,,,,,,,,,,	3199,771		1305,589,91	76.0	78.0	77.0		,,,,,,,,1077,,,,,,1077	-1.5	0.5	5	dbSNP_88	77	3605,4723		774,2057,1333	no	intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032089.1	,,,,,,,,,,,,,,	2079,2646,1424	TT,TC,CC		43.2877,19.4207,44.6739	,,,,,,,,,,,,,,	,,,,,,,,359/933,,,,,,359/829	140783596	6804,5494	1985	4164	6149	SO:0001819	synonymous_variant	56107	exon1			AGAAGACGCACCT	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.1077C>T	5.37:g.140783596C>T		Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_032089	A2RU65|Q9Y5C9	Silent	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			C|0.540;T|0.460	0.460	strong		0.428	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84582124	84582124	+	Missense_Mutation	SNP	G	G	T	rs4842838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:84582124G>T	ENST00000286744.5	+	16	2205	c.1981G>T	c.(1981-1983)Gtg>Ttg	p.V661L	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.V661L	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	661			V -> L (in dbSNP:rs4842838). {ECO:0000269|PubMed:14667842}.			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)			AGCAACATGCGTGGGAGGTAT	0.498													T|||	3434	0.685703	0.8306	0.7248	5008	,	,		18879	0.7202		0.5318	False		,,,				2504	0.5849				p.V661L		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.G1981T						PASS	.	T	LEU/VAL	3420,986	364.6+/-317.1	1332,756,115	36.0	40.0	38.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1981	-1.8	0.0	15	dbSNP_111	38	4620,3980	547.3+/-385.1	1250,2120,930	yes	missense	ADAMTSL3	NM_207517.2	32	2582,2876,1045	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	46.2791,22.3786,38.1824	benign	661/1692	84582124	8040,4966	2203	4300	6503	SO:0001583	missense	57188	exon16			ACATGCGTGGGAG	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.1981G>T	15.37:g.84582124G>T	ENSP00000286744:p.Val661Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	1469	0.6726190476190477	404	0.8211382113821138	248	0.6850828729281768	413	0.722027972027972	404	0.5329815303430079	T	9.774	1.173578	0.21704	0.776214	0.537209	ENSG00000156218	ENST00000286744	T	0.60424	0.19	5.05	-1.79	0.07932	.	1.774700	0.02812	N	0.124530	T	0.00012	0.0000	N	0.00174	-1.93	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37291	-0.9712	9	0.09590	T	0.72	.	2.979	0.05947	0.1094:0.3784:0.224:0.2883	rs4842838;rs61613424;rs4842838	661;661	P82987-2;P82987	.;ATL3_HUMAN	L	661	ENSP00000286744:V661L	ENSP00000286744:V661L	V	+	1	0	ADAMTSL3	82373128	0.387000	0.25188	0.038000	0.18304	0.967000	0.64934	0.155000	0.16362	-0.598000	0.05806	-0.362000	0.07510	GTG	G|0.348;T|0.652	0.652	strong		0.498	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
LPP	4026	hgsc.bcm.edu	37	3	188327461	188327461	+	Silent	SNP	C	C	T	rs1059380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:188327461C>T	ENST00000312675.4	+	6	1188	c.942C>T	c.(940-942)gaC>gaT	p.D314D	LPP_ENST00000543006.1_Silent_p.D314D|LPP_ENST00000448637.1_Silent_p.D314D|LPP_ENST00000471917.1_3'UTR	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	314	Pro-rich.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		ATGACTCTGACCCTACCTATG	0.562			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								T|||	2937	0.586462	0.7322	0.5591	5008	,	,		18456	0.4355		0.5726	False		,,,				2504	0.5787				p.D314D		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	LPP	72	.	0			c.C942T						PASS	.	T	,,	3082,1324	443.9+/-347.2	1084,914,205	64.0	59.0	61.0		942,,942	-1.5	0.8	3	dbSNP_86	61	5048,3552	516.5+/-378.8	1489,2070,741	no	coding-synonymous,intron,coding-synonymous	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	,,	2573,2984,946	TT,TC,CC		41.3023,30.0499,37.4904	,,	314/613,,314/613	188327461	8130,4876	2203	4300	6503	SO:0001819	synonymous_variant	4026	exon6			CTCTGACCCTACC	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.942C>T	3.37:g.188327461C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	37	CCDS3291.1																																																																																			C|0.403;T|0.597	0.597	strong		0.562	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
ARNTL2	56938	hgsc.bcm.edu	37	12	27543028	27543028	+	Splice_Site	SNP	G	G	A	rs113615248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27543028G>A	ENST00000266503.5	+	9	793		c.e9-1		ARNTL2_ENST00000544915.1_Splice_Site|ARNTL2_ENST00000311001.5_Splice_Site|ARNTL2_ENST00000395901.2_Splice_Site|ARNTL2_ENST00000542388.1_Splice_Site|ARNTL2_ENST00000261178.5_Splice_Site|RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000546179.1_Splice_Site			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2						circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|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)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					CTGCACGAAAGCTGGTTTGCA	0.383													G|||	31	0.0061901	0.0227	0.0014	5008	,	,		17019	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	ARNTL2	54	.	0			c.665-1G>A						PASS	.	G		135,4271	96.7+/-135.4	1,133,2069	153.0	151.0	152.0			2.2	0.2	12	dbSNP_132	152	3,8597	3.0+/-9.4	0,3,4297	yes	splice-3	ARNTL2	NM_020183.3		1,136,6366	AA,AG,GG		0.0349,3.064,1.061			27543028	138,12868	2203	4300	6503	SO:0001630	splice_region_variant	56938	exon7			ACGAAAGCTGGTT	AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"""Basic helix-loop-helix proteins"""	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.776-1G>A	12.37:g.27543028G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	151	78	0.516556	NM_001248005	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Splice_Site	SNP	ENST00000266503.5	37	CCDS8712.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	17.45	3.393650	0.62066	0.03064	3.49E-4	ENSG00000029153	ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000457040;ENST00000542388	.	.	.	3.14	2.25	0.28309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6704	0.34147	0.1092:0.0:0.8908:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARNTL2	27434295	1.000000	0.71417	0.181000	0.23098	0.664000	0.39144	7.551000	0.82182	0.675000	0.31264	0.655000	0.94253	.	G|0.991;A|0.009	0.009	strong		0.383	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183	Intron
PELI2	57161	hgsc.bcm.edu	37	14	56763743	56763743	+	Silent	SNP	G	G	T	rs112097284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:56763743G>T	ENST00000267460.4	+	6	1408	c.1122G>T	c.(1120-1122)tcG>tcT	p.S374S		NM_021255.2	NP_067078.1	Q9HAT8	PELI2_HUMAN	pellino E3 ubiquitin protein ligase family member 2	374					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein phosphorylation (GO:0001934)|protein ubiquitination (GO:0016567)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)	ligase activity (GO:0016874)			kidney(6)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	22						ACGTGTGCTCGGAGAAGTCTG	0.547													G|||	114	0.0227636	0.084	0.0043	5008	,	,		20479	0.0		0.0	False		,,,				2504	0.0				p.S374S		Atlas-SNP	.											.	PELI2	55	.	0			c.G1122T						PASS	.	G		307,4099	164.7+/-196.3	15,277,1911	170.0	147.0	155.0		1122	-4.0	1.0	14	dbSNP_132	155	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	PELI2	NM_021255.2		15,279,6209	TT,TG,GG		0.0233,6.9678,2.3758		374/421	56763743	309,12697	2203	4300	6503	SO:0001819	synonymous_variant	57161	exon6			GTGCTCGGAGAAG	AF302502	CCDS9726.1	14q21	2012-02-23	2012-02-23		ENSG00000139946	ENSG00000139946		"""Pellino homologs"""	8828	protein-coding gene	gene with protein product		614798	"""pellino (Drosophila) homolog 2"", ""pellino homolog 2 (Drosophila)"""			11306823, 12860405	Standard	XM_006720211		Approved		uc001xch.3	Q9HAT8	OTTHUMG00000152336	ENST00000267460.4:c.1122G>T	14.37:g.56763743G>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_021255	B2RDY5	Silent	SNP	ENST00000267460.4	37	CCDS9726.1																																																																																			G|0.979;T|0.021	0.021	strong		0.547	PELI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276925.1		
ZNF860	344787	hgsc.bcm.edu	37	3	32031024	32031024	+	Silent	SNP	C	C	T	rs4449357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:32031024C>T	ENST00000360311.4	+	2	1002	c.453C>T	c.(451-453)atC>atT	p.I151I		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						ACAAGCCTATCAAAGATCAGC	0.398													T|||	2149	0.429113	0.7912	0.3573	5008	,	,		20480	0.3006		0.1928	False		,,,				2504	0.3661				p.I151I		Atlas-SNP	.											.	ZNF860	96	.	0			c.C453T						PASS	.	T		922,462		315,292,85	67.0	49.0	54.0		453	0.3	0.0	3	dbSNP_111	54	608,2574		58,492,1041	no	coding-synonymous	ZNF860	NM_001137674.2		373,784,1126	TT,TC,CC		19.1075,33.3815,33.5085		151/633	32031024	1530,3036	692	1591	2283	SO:0001819	synonymous_variant	344787	exon2			GCCTATCAAAGAT	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.453C>T	3.37:g.32031024C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	208	98	0.471154	NM_001137674	B4DFA4	Silent	SNP	ENST00000360311.4	37	CCDS46784.1																																																																																			C|0.655;T|0.345	0.345	strong		0.398	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
CPM	1368	hgsc.bcm.edu	37	12	69326547	69326547	+	Missense_Mutation	SNP	C	C	T	rs7978197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:69326547C>T	ENST00000551568.1	-	2	131	c.71G>A	c.(70-72)cGc>cAc	p.R24H	CPM_ENST00000338356.3_Missense_Mutation_p.R24H|CPM_ENST00000546373.1_Missense_Mutation_p.R24H	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	24			R -> H (in dbSNP:rs7978197).		anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			CCCTTCCTGGCGGTGGTAGTT	0.473													T|||	908	0.18131	0.6021	0.0677	5008	,	,		19760	0.003		0.0159	False		,,,				2504	0.047				p.R24H		Atlas-SNP	.											CPM,NS,carcinoma,-1,1	CPM	30	1	0			c.G71A						PASS	.	T	HIS/ARG,HIS/ARG,HIS/ARG	2145,2261	596.6+/-388.7	506,1133,564	116.0	114.0	114.0		71,71,71	4.1	1.0	12	dbSNP_116	114	147,8453	813.0+/-407.0	1,145,4154	yes	missense,missense,missense	CPM	NM_001005502.2,NM_001874.4,NM_198320.3	29,29,29	507,1278,4718	TT,TC,CC		1.7093,48.6836,17.6226	benign,benign,benign	24/444,24/444,24/444	69326547	2292,10714	2203	4300	6503	SO:0001583	missense	1368	exon2			TCCTGGCGGTGGT	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"""renal carboxypeptidase"", ""urinary carboxypeptidase B"""	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.71G>A	12.37:g.69326547C>T	ENSP00000448517:p.Arg24His	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_001005502	B2R800|Q9H2K9	Missense_Mutation	SNP	ENST00000551568.1	37	CCDS8987.1	330	0.1510989010989011	292	0.5934959349593496	22	0.06077348066298342	2	0.0034965034965034965	14	0.018469656992084433	T	10.68	1.419258	0.25552	0.486836	0.017093	ENSG00000135678	ENST00000551568;ENST00000338356;ENST00000546373;ENST00000548954;ENST00000548262;ENST00000549781	T;T;T;T;T;T	0.03441	3.93;3.93;3.93;3.93;3.93;3.93	4.14	4.14	0.48551	Peptidase M14, carboxypeptidase A (1);	0.172860	0.48767	N	0.000166	T	0.00012	0.0000	N	0.02142	-0.665	0.53005	P	3.900000000001125E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.11616	-1.0580	8	.	.	.	-11.6919	7.6907	0.28567	0.0:0.1:0.0:0.9	rs7978197;rs52829589;rs59228977;rs7978197	24	P14384	CBPM_HUMAN	H	24	ENSP00000448517:R24H;ENSP00000339157:R24H;ENSP00000447255:R24H;ENSP00000446799:R24H;ENSP00000449911:R24H;ENSP00000448078:R24H	.	R	-	2	0	CPM	67612814	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.963000	0.49184	0.736000	0.32559	-0.360000	0.07572	CGC	C|0.819;T|0.181	0.181	strong		0.473	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320	
OR10T2	128360	hgsc.bcm.edu	37	1	158369025	158369025	+	Missense_Mutation	SNP	T	T	C	rs6662597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158369025T>C	ENST00000334438.1	-	1	231	c.232A>G	c.(232-234)Atc>Gtc	p.I78V		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	78			I -> V (in dbSNP:rs6662597).			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)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					TGAGGGATGATGACAAAAGTG	0.502													T|||	63	0.0125799	0.0477	0.0	5008	,	,		20910	0.0		0.0	False		,,,				2504	0.0				p.I78V		Atlas-SNP	.											.	OR10T2	76	.	0			c.A232G						PASS	.	T	VAL/ILE	143,4263	99.4+/-138.0	3,137,2063	96.0	95.0	96.0		232	4.7	1.0	1	dbSNP_116	96	0,8600		0,0,4300	yes	missense	OR10T2	NM_001004475.1	29	3,137,6363	CC,CT,TT		0.0,3.2456,1.0995	possibly-damaging	78/315	158369025	143,12863	2203	4300	6503	SO:0001583	missense	128360	exon1			GGATGATGACAAA	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.232A>G	1.37:g.158369025T>C	ENSP00000334115:p.Ile78Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	91	53	0.582418	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	T	16.66	3.184032	0.57800	0.032456	0.0	ENSG00000186306	ENST00000334438	T	0.00611	6.23	4.73	4.73	0.59995	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39759	U	0.001269	T	0.00271	0.0008	L	0.41573	1.285	0.09310	N	0.999995	P	0.36282	0.546	B	0.31442	0.13	T	0.50668	-0.8801	10	0.37606	T	0.19	.	13.3352	0.60515	0.0:0.0:0.0:1.0	rs6662597;rs52820437;rs56418545;rs6662597	78	Q8NGX3	O10T2_HUMAN	V	78	ENSP00000334115:I78V	ENSP00000334115:I78V	I	-	1	0	OR10T2	156635649	0.969000	0.33509	1.000000	0.80357	0.999000	0.98932	2.867000	0.48428	1.973000	0.57446	0.528000	0.53228	ATC	T|0.985;C|0.015	0.015	strong		0.502	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
ZFPM2	23414	hgsc.bcm.edu	37	8	106813518	106813518	+	Missense_Mutation	SNP	C	C	G	rs11993776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:106813518C>G	ENST00000407775.2	+	8	1458	c.1208C>G	c.(1207-1209)gCa>gGa	p.A403G	RP11-152P17.2_ENST00000524045.2_RNA|ZFPM2_ENST00000517361.1_Missense_Mutation_p.A271G|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|ZFPM2_ENST00000522296.1_3'UTR|ZFPM2_ENST00000520492.1_Missense_Mutation_p.A271G|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000378472.4_Missense_Mutation_p.A134G|RP11-152P17.2_ENST00000509144.2_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	403			A -> G (in dbSNP:rs11993776). {ECO:0000269|PubMed:24549039}.		blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			TCTCCAAGTGCAACTGAAGAC	0.517													G|||	968	0.193291	0.441	0.1023	5008	,	,		19753	0.131		0.1024	False		,,,				2504	0.0808				p.A403G		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C1208G						PASS	.	G	GLY/ALA	1423,2563		257,909,827	87.0	86.0	86.0		1208	4.0	0.0	8	dbSNP_120	86	787,7573		40,707,3433	yes	missense	ZFPM2	NM_012082.3	60	297,1616,4260	GG,GC,CC		9.4139,35.6999,17.9005	benign	403/1152	106813518	2210,10136	1993	4180	6173	SO:0001583	missense	23414	exon8			CAAGTGCAACTGA	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.1208C>G	8.37:g.106813518C>G	ENSP00000384179:p.Ala403Gly	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	136	48	0.352941	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	410	0.18772893772893773	209	0.4247967479674797	34	0.09392265193370165	83	0.1451048951048951	84	0.11081794195250659	G	0.020	-1.443220	0.01089	0.356999	0.094139	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.19532	2.14;2.63;2.63;3.84	5.87	4.01	0.46588	.	0.152514	0.64402	N	0.000017	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	8.000000000008E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46965	-0.9153	9	0.06625	T	0.88	.	13.3304	0.60483	0.0:0.388:0.4991:0.1129	rs11993776;rs57100171;rs11993776	403	Q8WW38	FOG2_HUMAN	G	403;271;271;134	ENSP00000384179:A403G;ENSP00000430757:A271G;ENSP00000428720:A271G;ENSP00000367733:A134G	ENSP00000367733:A134G	A	+	2	0	ZFPM2	106882694	1.000000	0.71417	0.024000	0.17045	0.590000	0.36582	4.021000	0.57196	0.318000	0.23185	-0.120000	0.15030	GCA	C|0.817;G|0.183	0.183	strong		0.517	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
LMNTD1	160492	hgsc.bcm.edu	37	12	25672945	25672945	+	Missense_Mutation	SNP	T	T	C	rs34326830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672945T>C	ENST00000282881.6	-	6	949	c.800A>G	c.(799-801)gAa>gGa	p.E267G	IFLTD1_ENST00000458174.2_Missense_Mutation_p.E288G|IFLTD1_ENST00000445693.1_Missense_Mutation_p.E204G|IFLTD1_ENST00000413632.2_Missense_Mutation_p.E248G|IFLTD1_ENST00000539744.1_Missense_Mutation_p.E170G	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		267			E -> G (in dbSNP:rs34326830).		cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					TCTGTTAAATTCAACGTCAGC	0.388													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13538	0.0		0.0	False		,,,				2504	0.0				p.E288G		Atlas-SNP	.											.	IFLTD1	121	.	0			c.A863G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	251,4155	144.6+/-179.5	5,241,1957	138.0	121.0	126.0		611,863,743,800	5.1	1.0	12	dbSNP_126	126	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	98,98,98,98	5,242,6256	CC,CT,TT		0.0116,5.6968,1.9376	probably-damaging,probably-damaging,probably-damaging,probably-damaging	204/326,288/410,248/370,267/389	25672945	252,12754	2203	4300	6503	SO:0001583	missense	160492	exon7			TTAAATTCAACGT																												ENST00000282881.6:c.800A>G	12.37:g.25672945T>C	ENSP00000282881:p.Glu267Gly	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	155	81	0.522581	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	19.78|19.78	3.891505|3.891505	0.72524|0.72524	0.056968|0.056968	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000545543|ENST00000543629	T;T;T;T;T;T|.	0.18502|.	2.35;2.43;2.33;2.38;2.28;2.21|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	.|.	.|.	.|.	.|.	T|.	0.05410|.	0.0143|.	L|L	0.32530|0.32530	0.975|0.975	0.29530|0.29530	N|N	0.852852|0.852852	P;P;D;D|.	0.76494|.	0.734;0.946;0.972;0.999|.	B;P;P;D|.	0.64144|.	0.421;0.637;0.723;0.922|.	T|.	0.04635|.	-1.0937|.	9|.	0.87932|.	D|.	0|.	4.219|4.219	11.112|11.112	0.48239|0.48239	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs34326830|rs34326830	204;288;248;267|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	G|W	267;170;288;204;248;97|41	ENSP00000282881:E267G;ENSP00000443132:E170G;ENSP00000407353:E288G;ENSP00000407043:E204G;ENSP00000393150:E248G;ENSP00000443596:E97G|.	ENSP00000282881:E267G|.	E|X	-|-	2|3	0|0	IFLTD1|IFLTD1	25564212|25564212	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.842000|0.842000	0.47809|0.47809	3.758000|3.758000	0.55220|0.55220	2.134000|2.134000	0.65973|0.65973	0.477000|0.477000	0.44152|0.44152	GAA|TGA	T|0.980;C|0.020	0.020	strong		0.388	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
CYP4F12	66002	hgsc.bcm.edu	37	19	15793238	15793238	+	Silent	SNP	C	C	T	rs144258147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15793238C>T	ENST00000550308.1	+	6	945	c.565C>T	c.(565-567)Ctg>Ttg	p.L189L	CYP4F12_ENST00000324632.10_Silent_p.L189L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	189					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)	p.L189V(1)		NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CAGCAGTTGTCTGGACATGTT	0.557													.|||	31	0.0061901	0.0227	0.0	5008	,	,		20398	0.0		0.001	False		,,,				2504	0.0				p.L189L		Atlas-SNP	.											.	CYP4F12	89	.	1	Substitution - Missense(1)	urinary_tract(1)	c.C565T						PASS	.						81.0	78.0	79.0					19																	15793238		2203	4300	6503	SO:0001819	synonymous_variant	66002	exon6			AGTTGTCTGGACA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.565C>T	19.37:g.15793238C>T		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	342	74	0.216374	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			C|0.990;T|0.010	0.010	strong		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
CC2D1A	54862	hgsc.bcm.edu	37	19	14030689	14030689	+	Silent	SNP	T	T	C	rs10410239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14030689T>C	ENST00000318003.7	+	12	1522	c.1281T>C	c.(1279-1281)ggT>ggC	p.G427G	CC2D1A_ENST00000589606.1_Silent_p.G427G	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	427					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			GTCTGGTGGGTGTCCTGGAGA	0.622													C|||	2110	0.421326	0.8154	0.3256	5008	,	,		14061	0.3016		0.2078	False		,,,				2504	0.2996				p.G427G		Atlas-SNP	.											.	CC2D1A	67	.	0			c.T1281C						PASS	.	C		2729,1057		992,745,156	50.0	58.0	55.0		1281	-9.9	0.4	19	dbSNP_119	55	1706,6544		180,1346,2599	no	coding-synonymous	CC2D1A	NM_017721.4		1172,2091,2755	CC,CT,TT		20.6788,27.9186,36.8478		427/952	14030689	4435,7601	1893	4125	6018	SO:0001819	synonymous_variant	54862	exon12			GGTGGGTGTCCTG	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.1281T>C	19.37:g.14030689T>C		Somatic	242	1	0.00413223		WXS	Illumina HiSeq	Phase_I	219	217	0.990868	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Silent	SNP	ENST00000318003.7	37	CCDS42512.1																																																																																			T|0.665;C|0.335	0.335	strong		0.622	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
ZNF211	10520	hgsc.bcm.edu	37	19	58152182	58152182	+	Missense_Mutation	SNP	G	G	A	rs34897843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58152182G>A	ENST00000347302.3	+	3	507	c.328G>A	c.(328-330)Gac>Aac	p.D110N	ZNF211_ENST00000240731.4_Missense_Mutation_p.D123N|ZNF211_ENST00000391703.3_Missense_Mutation_p.D49N|ZNF211_ENST00000541801.1_Missense_Mutation_p.D101N|ZNF211_ENST00000544273.1_Missense_Mutation_p.D122N|ZNF211_ENST00000254182.7_Missense_Mutation_p.D101N|ZNF211_ENST00000420680.1_Missense_Mutation_p.D114N|ZNF211_ENST00000299871.5_Missense_Mutation_p.D175N	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	110			D -> N (in dbSNP:rs34897843).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CCAGAATGCCGACTCCTGTGA	0.453													g|||	32	0.00638978	0.0204	0.0043	5008	,	,		21518	0.0		0.001	False		,,,				2504	0.001				p.D175N		Atlas-SNP	.											.	ZNF211	78	.	0			c.G523A						PASS	.	A	ASN/ASP,ASN/ASP	123,4283	91.1+/-129.8	1,121,2081	98.0	98.0	98.0		367,328	-0.9	0.0	19	dbSNP_126	98	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	ZNF211	NM_006385.3,NM_198855.2	23,23	1,122,6380	AA,AG,GG		0.0116,2.7916,0.9534	benign,benign	123/578,110/565	58152182	124,12882	2203	4300	6503	SO:0001583	missense	10520	exon5			AATGCCGACTCCT	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.328G>A	19.37:g.58152182G>A	ENSP00000339562:p.Asp110Asn	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	242	115	0.475207	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Missense_Mutation	SNP	ENST00000347302.3	37	CCDS12957.1	13|13	0.005952380952380952|0.005952380952380952	11|11	0.022357723577235773|0.022357723577235773	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	10.25|10.25	1.298596|1.298596	0.23650|0.23650	0.027916|0.027916	1.16E-4|1.16E-4	ENSG00000121417|ENSG00000121417	ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731|ENST00000407202	T;T;T;T;T;T;T;T|.	0.06768|.	3.31;3.33;3.26;3.27;3.26;3.37;3.33;3.33|.	3.7|3.7	-0.942|-0.942	0.10398|0.10398	.|.	.|.	.|.	.|.	.|.	T|T	0.02304|0.02304	0.0071|0.0071	N|N	0.01493|0.01493	-0.835|-0.835	0.09310|0.09310	N|N	1|1	B;B;B;P;B;B|.	0.39060|.	0.091;0.038;0.001;0.657;0.011;0.011|.	B;B;B;B;B;B|.	0.31812|.	0.013;0.008;0.0;0.136;0.004;0.006|.	T|T	0.30297|0.30297	-0.9983|-0.9983	9|5	0.20519|.	T|.	0.43|.	.|.	0.6887|0.6887	0.00887|0.00887	0.1784:0.3318:0.1832:0.3066|0.1784:0.3318:0.1832:0.3066	rs34897843|rs34897843	114;122;175;101;110;123|.	Q13398-4;Q13398-3;F8WDV2;Q13398-2;Q13398;B9ZVW1|.	.;.;.;.;ZN211_HUMAN;.|.	N|Q	114;110;101;49;101;175;122;123|113	ENSP00000399193:D114N;ENSP00000339562:D110N;ENSP00000254182:D101N;ENSP00000375584:D49N;ENSP00000442601:D101N;ENSP00000299871:D175N;ENSP00000441386:D122N;ENSP00000240731:D123N|.	ENSP00000240731:D123N|.	D|R	+|+	1|2	0|0	ZNF211|ZNF211	62843994|62843994	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.248000|0.248000	0.25809|0.25809	-0.035000|-0.035000	0.12205|0.12205	-0.041000|-0.041000	0.13558|0.13558	-1.230000|-1.230000	0.01575|0.01575	GAC|CGA	G|0.991;A|0.009	0.009	strong		0.453	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
CDH19	28513	hgsc.bcm.edu	37	18	64235877	64235877	+	Missense_Mutation	SNP	G	G	A	rs114375304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:64235877G>A	ENST00000540086.1	-	3	512	c.266C>T	c.(265-267)aCt>aTt	p.T89I	CDH19_ENST00000262150.2_Missense_Mutation_p.T89I	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	190	Cadherin 1. {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)				AATGATAAAAGTACTTCCAGC	0.398													G|||	71	0.0141773	0.0499	0.0072	5008	,	,		16014	0.0		0.0	False		,,,				2504	0.0				p.T89I		Atlas-SNP	.											CDH19,NS,carcinoma,-1,1	CDH19	141	1	0			c.C266T						PASS	.	G	ILE/THR	266,4140	150.3+/-184.3	15,236,1952	94.0	93.0	94.0		266	1.9	0.1	18	dbSNP_132	94	2,8594	2.2+/-6.3	0,2,4296	yes	missense	CDH19	NM_021153.2	89	15,238,6248	AA,AG,GG		0.0233,6.0372,2.0612	benign	89/773	64235877	268,12734	2203	4298	6501	SO:0001583	missense	28513	exon3			ATAAAAGTACTTC	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	ENST00000540086.1:c.266C>T	18.37:g.64235877G>A	ENSP00000439593:p.Thr89Ile	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_021153	O15098	Missense_Mutation	SNP	ENST00000540086.1	37	CCDS59325.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	G	9.972	1.225826	0.22542	0.060372	2.33E-4	ENSG00000071991	ENST00000262150;ENST00000540086;ENST00000454642	T;T	0.51817	0.69;0.69	5.48	1.91	0.25777	Cadherin (5);Cadherin-like (1);	0.572976	0.18606	N	0.136310	T	0.01661	0.0053	N	0.02665	-0.54	0.22127	N	0.999345	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.19943	-1.0290	10	0.02654	T	1	.	7.9396	0.29950	0.7547:0.0:0.2453:0.0	.	89;89	F5H1K0;Q9H159	.;CAD19_HUMAN	I	89;89;34	ENSP00000262150:T89I;ENSP00000439593:T89I	ENSP00000262150:T89I	T	-	2	0	CDH19	62386857	0.762000	0.28451	0.145000	0.22337	0.830000	0.47004	3.161000	0.50747	0.396000	0.25283	-0.469000	0.05056	ACT	G|0.980;A|0.020	0.020	strong		0.398	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153	
CASZ1	54897	hgsc.bcm.edu	37	1	10713765	10713765	+	Silent	SNP	T	T	C	rs284294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:10713765T>C	ENST00000377022.3	-	11	2666	c.2349A>G	c.(2347-2349)tcA>tcG	p.S783S	CASZ1_ENST00000344008.5_Silent_p.S783S|RP4-734G22.3_ENST00000606802.1_RNA	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	57	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	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	
SLC12A4	6560	hgsc.bcm.edu	37	16	67984589	67984589	+	Silent	SNP	A	A	G	rs11542821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67984589A>G	ENST00000316341.3	-	11	1562	c.1422T>C	c.(1420-1422)ggT>ggC	p.G474G	SLC12A4_ENST00000537830.2_Silent_p.G468G|SLC12A4_ENST00000541864.2_Silent_p.G443G|SLC12A4_ENST00000572037.1_Silent_p.G426G|SLC12A4_ENST00000422611.2_Silent_p.G476G|SLC12A4_ENST00000338335.3_Silent_p.G474G|SLC12A4_ENST00000572010.1_5'Flank|SLC12A4_ENST00000576616.1_Silent_p.G474G	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	474					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CAATGCAGGCACCAAAGAGAA	0.622													G|||	743	0.148363	0.4312	0.0793	5008	,	,		18579	0.006		0.0467	False		,,,				2504	0.0665				p.G476G		Atlas-SNP	.											.	SLC12A4	81	.	0			c.T1428C						PASS	.	G	,,,,	1615,2781	637.4+/-396.7	303,1009,886	108.0	97.0	100.0		1422,1428,1404,1329,1422	-5.9	1.0	16	dbSNP_120	100	431,8169	780.6+/-407.7	13,405,3882	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC12A4	NM_001145961.1,NM_001145962.1,NM_001145963.1,NM_001145964.1,NM_005072.4	,,,,	316,1414,4768	GG,GA,AA		5.0116,36.7379,15.7433	,,,,	474/1080,476/1088,468/1080,443/1055,474/1086	67984589	2046,10950	2198	4300	6498	SO:0001819	synonymous_variant	6560	exon10			GCAGGCACCAAAG		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"""Solute carriers"""	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.1422T>C	16.37:g.67984589A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	161	78	0.484472	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Silent	SNP	ENST00000316341.3	37	CCDS10855.1																																																																																			A|0.851;G|0.149	0.149	strong		0.622	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072	
ADD1	118	hgsc.bcm.edu	37	4	2896419	2896419	+	Silent	SNP	G	G	A	rs112813723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2896419G>A	ENST00000398129.1	+	5	722	c.702G>A	c.(700-702)gtG>gtA	p.V234V	ADD1_ENST00000398125.1_Silent_p.V234V|ADD1_ENST00000355842.3_Silent_p.V234V|ADD1_ENST00000446856.1_Silent_p.V234V|ADD1_ENST00000513328.2_Silent_p.V234V|ADD1_ENST00000264758.7_Silent_p.V234V|ADD1_ENST00000398123.2_Silent_p.V234V|ADD1_ENST00000503455.2_Silent_p.V234V			P35611	ADDA_HUMAN	adducin 1 (alpha)	234					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GCCCGGACGTGAAGTGCGTCG	0.542													G|||	49	0.00978435	0.0356	0.0014	5008	,	,		14014	0.0		0.001	False		,,,				2504	0.0				p.V234V	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.G702A						PASS	.	G	,,,	140,4266	98.9+/-137.6	3,134,2066	63.0	54.0	57.0		702,702,702,702	-4.3	0.1	4	dbSNP_132	57	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADD1	NM_001119.4,NM_014189.3,NM_014190.3,NM_176801.2	,,,	3,136,6364	AA,AG,GG		0.0233,3.1775,1.0918	,,,	234/738,234/769,234/632,234/663	2896419	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	118	exon6			GGACGTGAAGTGC	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.702G>A	4.37:g.2896419G>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	294	148	0.503401	NM_014190	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Silent	SNP	ENST00000398129.1	37	CCDS43205.1																																																																																			G|0.988;A|0.012	0.012	strong		0.542	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189	
PLEKHO2	80301	hgsc.bcm.edu	37	15	65157482	65157482	+	Missense_Mutation	SNP	C	C	T	rs2010875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65157482C>T	ENST00000323544.4	+	6	996	c.868C>T	c.(868-870)Ccg>Tcg	p.P290S	AC069368.3_ENST00000437723.1_Intron	NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	290	Pro-rich.		P -> S (in dbSNP:rs2010875). {ECO:0000269|PubMed:15498874}.							NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						GAGTGCAGAACCGTCCCAGGC	0.617													C|||	1518	0.303115	0.1581	0.2983	5008	,	,		17993	0.7589		0.1461	False		,,,				2504	0.1943				p.P290S		Atlas-SNP	.											.	PLEKHO2	50	.	0			c.C868T						PASS	.	C	SER/PRO,SER/PRO	673,3731	275.7+/-272.7	50,573,1579	49.0	52.0	51.0		718,868	1.8	0.0	15	dbSNP_92	51	1310,7286	250.0+/-277.0	100,1110,3088	yes	missense,missense	PLEKHO2	NM_001195059.1,NM_025201.4	74,74	150,1683,4667	TT,TC,CC		15.2396,15.2816,15.2538	benign,benign	240/441,290/491	65157482	1983,11017	2202	4298	6500	SO:0001583	missense	80301	exon6			GCAGAACCGTCCC	AF318373	CCDS10196.1, CCDS73739.1	15q22.31	2013-01-10	2007-12-14	2007-12-14	ENSG00000241839	ENSG00000241839		"""Pleckstrin homology (PH) domain containing"""	30026	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family Q member 1"""	PLEKHQ1		12477932	Standard	NM_025201		Approved	DKFZp761K2312, PP1628, pp9099	uc002anv.3	Q8TD55	OTTHUMG00000133050	ENST00000323544.4:c.868C>T	15.37:g.65157482C>T	ENSP00000326706:p.Pro290Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_025201	Q7L4H4|Q8WYS8	Missense_Mutation	SNP	ENST00000323544.4	37	CCDS10196.1	730	0.3342490842490842	69	0.1402439024390244	97	0.26795580110497236	451	0.7884615384615384	113	0.14907651715039577	C	0.003	-2.482521	0.00163	0.152816	0.152396	ENSG00000241839	ENST00000323544	T	0.29142	1.58	5.33	1.78	0.24846	.	1.654450	0.02961	N	0.143106	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.40059	-0.9583	9	0.06236	T	0.91	.	2.3278	0.04227	0.1592:0.2521:0.4516:0.1371	rs2010875;rs3809502;rs12911443;rs16948324;rs52791051;rs57577084;rs2010875	240;290	Q8TD55-2;Q8TD55	.;PKHO2_HUMAN	S	290	ENSP00000326706:P290S	ENSP00000326706:P290S	P	+	1	0	PLEKHO2	62944535	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	0.212000	0.17497	0.593000	0.29745	0.655000	0.94253	CCG	T|0.220;G|0.000;C|0.779	0.220	strong		0.617	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1	NM_025201	
C8A	731	hgsc.bcm.edu	37	1	57378150	57378150	+	Silent	SNP	C	C	T	rs386631447|rs1620073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57378150C>T	ENST00000361249.3	+	10	1551	c.1455C>T	c.(1453-1455)cgC>cgT	p.R485R		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	485	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.		R -> L (in dbSNP:rs1620075).		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						ACCTGCGCCGCGCCTTGGACC	0.617													C|||	683	0.136382	0.261	0.134	5008	,	,		17547	0.0407		0.0477	False		,,,				2504	0.1595				p.R485R		Atlas-SNP	.											C8A,NS,carcinoma,+2,1	C8A	103	1	0			c.C1455T						PASS	.	C		863,3543		90,683,1430	69.0	72.0	71.0		1455	0.6	0.0	1	dbSNP_89	71	370,8230		8,354,3938	no	coding-synonymous	C8A	NM_000562.2		98,1037,5368	TT,TC,CC		4.3023,19.5869,9.4802		485/585	57378150	1233,11773	2203	4300	6503	SO:0001819	synonymous_variant	731	exon10			GCGCCGCGCCTTG	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"""Complement system"""	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1455C>T	1.37:g.57378150C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	221	110	0.497738	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Silent	SNP	ENST00000361249.3	37	CCDS606.1																																																																																			C|0.905;T|0.095	0.095	strong		0.617	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
MCM5	4174	hgsc.bcm.edu	37	22	35802661	35802661	+	Missense_Mutation	SNP	C	C	G	rs2307340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:35802661C>G	ENST00000216122.4	+	5	693	c.539C>G	c.(538-540)aCc>aGc	p.T180S	MCM5_ENST00000382011.5_Missense_Mutation_p.T137S	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	180			T -> S (in dbSNP:rs2307340). {ECO:0000269|Ref.5}.		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						AACACCCTCACCAACATTGCC	0.637													C|||	208	0.0415335	0.0234	0.0288	5008	,	,		21179	0.006		0.0855	False		,,,				2504	0.0665				p.T180S		Atlas-SNP	.											.	MCM5	54	.	0			c.C539G						PASS	.	C	SER/THR	121,4285	91.1+/-129.8	3,115,2085	75.0	55.0	61.0		539	0.2	1.0	22	dbSNP_100	61	735,7865	177.3+/-227.0	27,681,3592	yes	missense	MCM5	NM_006739.3	58	30,796,5677	GG,GC,CC		8.5465,2.7463,6.5816	benign	180/735	35802661	856,12150	2203	4300	6503	SO:0001583	missense	4174	exon5			CCCTCACCAACAT		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"""minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)"", ""MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"""	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.539C>G	22.37:g.35802661C>G	ENSP00000216122:p.Thr180Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_006739	O60785|Q14578|Q9BTJ4|Q9BWL8	Missense_Mutation	SNP	ENST00000216122.4	37	CCDS13915.1	90	0.04120879120879121	14	0.028455284552845527	9	0.024861878453038673	3	0.005244755244755245	64	0.08443271767810026	C	5.317	0.243830	0.10077	0.027463	0.085465	ENSG00000100297	ENST00000216122;ENST00000382011;ENST00000444582;ENST00000416905;ENST00000444778	T;T;T;T	0.04654	3.58;3.58;3.58;3.58	3.94	0.199	0.15175	Nucleic acid-binding, OB-fold-like (1);	0.558871	0.18678	N	0.134238	T	0.00109	0.0003	N	0.11255	0.115	0.24550	N	0.994025	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.49163	-0.8968	10	0.10636	T	0.68	-30.8481	8.3315	0.32189	0.302:0.3613:0.3367:0.0	rs2307340;rs17720368;rs52837575;rs2307340	137;180	B1AHB1;P33992	.;MCM5_HUMAN	S	180;137;89;212;37	ENSP00000216122:T180S;ENSP00000371441:T137S;ENSP00000393977:T212S;ENSP00000408705:T37S	ENSP00000216122:T180S	T	+	2	0	MCM5	34132661	0.701000	0.27806	1.000000	0.80357	0.998000	0.95712	-0.180000	0.09754	0.397000	0.25310	0.561000	0.74099	ACC	C|0.945;G|0.055	0.055	strong		0.637	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3		
SPOCD1	90853	hgsc.bcm.edu	37	1	32279629	32279629	+	Missense_Mutation	SNP	G	G	A	rs6669563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:32279629G>A	ENST00000360482.2	-	2	1435	c.1306C>T	c.(1306-1308)Cgg>Tgg	p.R436W	SPOCD1_ENST00000533231.1_Missense_Mutation_p.R436W|SPOCD1_ENST00000373648.2_Missense_Mutation_p.R436W|SPOCD1_ENST00000257100.3_Intron	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	436			R -> W (in dbSNP:rs6669563).		negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)			p.R436W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		TCTGTGCCCCGGTCTTGGGCA	0.592													G|||	1734	0.346246	0.1876	0.4957	5008	,	,		18940	0.4226		0.4374	False		,,,				2504	0.2822				p.R436W		Atlas-SNP	.											SPOCD1,NS,carcinoma,0,2	SPOCD1	109	2	1	Substitution - Missense(1)	stomach(1)	c.C1306T						PASS	.	G	TRP/ARG	990,3416	365.9+/-317.6	118,754,1331	59.0	62.0	61.0		1306	0.2	0.0	1	dbSNP_116	61	3765,4835	527.7+/-381.2	804,2157,1339	yes	missense	SPOCD1	NM_144569.4	101	922,2911,2670	AA,AG,GG		43.7791,22.4694,36.56	probably-damaging	436/1217	32279629	4755,8251	2203	4300	6503	SO:0001583	missense	90853	exon2			TGCCCCGGTCTTG	AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 146"""					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.1306C>T	1.37:g.32279629G>A	ENSP00000353670:p.Arg436Trp	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	865	0.39606227106227104	106	0.21544715447154472	161	0.4447513812154696	260	0.45454545454545453	338	0.44591029023746703	G	10.09	1.254901	0.22965	0.224694	0.437791	ENSG00000134668	ENST00000360482;ENST00000373648;ENST00000533231	T;T;T	0.34275	1.84;1.37;1.84	3.25	0.152	0.14893	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P	0.44044	0.825;0.733	B;B	0.36959	0.237;0.12	T	0.45011	-0.9290	8	0.87932	D	0	9.782	3.8093	0.08791	0.2419:0.202:0.556:0.0	rs6669563;rs6669563	436;436	Q6ZMY3-2;Q6ZMY3	.;SPOC1_HUMAN	W	436	ENSP00000353670:R436W;ENSP00000362752:R436W;ENSP00000435851:R436W	ENSP00000353670:R436W	R	-	1	2	SPOCD1	32052216	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	0.049000	0.14099	0.044000	0.15775	0.455000	0.32223	CGG	G|0.624;A|0.376	0.376	strong		0.592	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569	
SPATA22	84690	hgsc.bcm.edu	37	17	3352294	3352294	+	Missense_Mutation	SNP	A	A	G	rs1488689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3352294A>G	ENST00000573128.1	-	6	962	c.479T>C	c.(478-480)aTa>aCa	p.I160T	SPATA22_ENST00000572969.1_Missense_Mutation_p.I160T|SPATA22_ENST00000397168.3_Missense_Mutation_p.I160T|SPATA22_ENST00000541913.1_Missense_Mutation_p.I144T|SPATA22_ENST00000268981.5_Missense_Mutation_p.I160T|SPATA22_ENST00000355380.4_Missense_Mutation_p.I117T|SPATA22_ENST00000575375.1_Missense_Mutation_p.I160T			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	160			I -> T (in dbSNP:rs1488689). {ECO:0000269|PubMed:15489334}.		fertilization (GO:0009566)|gamete generation (GO:0007276)|meiotic DNA repair synthesis (GO:0000711)|regulation of meiotic cell cycle (GO:0051445)|reproductive system development (GO:0061458)|synapsis (GO:0007129)	chromosome (GO:0005694)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)	19						AGGTTCAGGTATTCTTAATTG	0.383													a|||	1337	0.266973	0.2209	0.3501	5008	,	,		15352	0.4187		0.1809	False		,,,				2504	0.2025				p.I160T		Atlas-SNP	.											.	SPATA22	49	.	0			c.T479C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE	1088,3318	393.5+/-328.9	136,816,1251	268.0	258.0	261.0		479,350,479,479,479,479	2.8	0.0	17	dbSNP_88	261	1586,7014	296.9+/-303.1	144,1298,2858	yes	missense,missense,missense,missense,missense,missense	SPATA22	NM_001170695.1,NM_001170696.1,NM_001170697.1,NM_001170698.1,NM_001170699.1,NM_032598.4	89,89,89,89,89,89	280,2114,4109	GG,GA,AA		18.4419,24.6936,20.5597	benign,benign,benign,benign,benign,benign	160/364,117/321,160/364,160/364,160/270,160/364	3352294	2674,10332	2203	4300	6503	SO:0001583	missense	84690	exon6			TCAGGTATTCTTA	AY035868	CCDS11027.1, CCDS54066.1, CCDS54067.1	17p13.3	2005-12-19							30705	protein-coding gene	gene with protein product						12477932	Standard	NM_001170696		Approved	NYD-SP20	uc002fvn.3	Q8NHS9		ENST00000573128.1:c.479T>C	17.37:g.3352294A>G	ENSP00000459580:p.Ile160Thr	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	273	135	0.494505	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Missense_Mutation	SNP	ENST00000573128.1	37	CCDS11027.1	593	0.2715201465201465	108	0.21951219512195122	127	0.35082872928176795	219	0.38286713286713286	139	0.18337730870712401	a	0.254	-1.004215	0.02112	0.246936	0.184419	ENSG00000141255	ENST00000355380;ENST00000397168;ENST00000268981;ENST00000541913	T;T;T;T	0.17370	2.28;2.3;2.31;2.29	3.87	2.79	0.32731	.	1.568880	0.03690	N	0.246975	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B	0.13145	0.001;0.0;0.007;0.001	B;B;B;B	0.08055	0.003;0.002;0.003;0.003	T	0.44651	-0.9314	9	0.19590	T	0.45	-1.2633	6.7352	0.23405	0.8841:0.0:0.1159:0.0	rs1488689;rs17845887;rs17858862;rs61019090;rs1488689	144;160;117;160	F5GWB9;B4DXB1;Q8NHS9-2;Q8NHS9	.;.;.;SPT22_HUMAN	T	117;160;160;144	ENSP00000347541:I117T;ENSP00000380354:I160T;ENSP00000268981:I160T;ENSP00000441920:I144T	ENSP00000268981:I160T	I	-	2	0	SPATA22	3299044	0.025000	0.19082	0.003000	0.11579	0.010000	0.07245	0.736000	0.26130	0.851000	0.35264	0.454000	0.30748	ATA	A|0.769;G|0.231	0.231	strong		0.383	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598	
NOC3L	64318	hgsc.bcm.edu	37	10	96098373	96098373	+	Missense_Mutation	SNP	C	C	T	rs17517578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:96098373C>T	ENST00000371361.3	-	18	2183	c.2083G>A	c.(2083-2085)Gct>Act	p.A695T	NOC3L_ENST00000371350.1_Missense_Mutation_p.A695T|NOC3L_ENST00000543788.1_Missense_Mutation_p.A433T	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	695			A -> T (in dbSNP:rs17517578).		fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				ACCCGCAGAGCATGCAGTTCC	0.438													C|||	553	0.110423	0.1059	0.111	5008	,	,		16705	0.003		0.1839	False		,,,				2504	0.1513				p.A695T		Atlas-SNP	.											.	NOC3L	67	.	0			c.G2083A						PASS	.	C	THR/ALA	493,3913	230.7+/-244.8	24,445,1734	100.0	98.0	99.0		2083	3.8	0.2	10	dbSNP_123	99	1376,7224	267.6+/-287.4	103,1170,3027	yes	missense	NOC3L	NM_022451.9	58	127,1615,4761	TT,TC,CC		16.0,11.1893,14.3703	benign	695/801	96098373	1869,11137	2203	4300	6503	SO:0001583	missense	64318	exon18			GCAGAGCATGCAG	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"""chromosome 10 open reading frame 117"""	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.2083G>A	10.37:g.96098373C>T	ENSP00000360412:p.Ala695Thr	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	233	105	0.450644	NM_022451	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	222	0.10164835164835165	45	0.09146341463414634	41	0.1132596685082873	1	0.0017482517482517483	135	0.17810026385224276	C	0.836	-0.743469	0.03088	0.111893	0.16	ENSG00000173145	ENST00000543788;ENST00000371361;ENST00000371350	T;T;T	0.21734	1.99;1.99;1.99	5.63	3.77	0.43336	CCAAT-binding factor (1);	0.744226	0.13218	N	0.404571	T	0.00039	0.0001	N	0.20574	0.59	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.34477	-0.9827	9	0.25751	T	0.34	-1.7679	3.1464	0.06473	0.123:0.5555:0.1192:0.2023	rs17517578;rs52814170;rs17517578	695	Q8WTT2	NOC3L_HUMAN	T	433;695;695	ENSP00000437838:A433T;ENSP00000360412:A695T;ENSP00000360401:A695T	ENSP00000360401:A695T	A	-	1	0	NOC3L	96088363	0.004000	0.15560	0.176000	0.23000	0.002000	0.02628	0.359000	0.20233	0.844000	0.35094	-0.136000	0.14681	GCT	C|0.868;T|0.132	0.132	strong		0.438	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451	
DNAH17	8632	hgsc.bcm.edu	37	17	76447617	76447617	+	Silent	SNP	A	A	G	rs34002770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76447617A>G	ENST00000585328.1	-	66	10777	c.10653T>C	c.(10651-10653)gaT>gaC	p.D3551D	DNAH17_ENST00000389840.5_Silent_p.D3542D|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3542	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(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)			CCTCGAGTCCATCCCTGGTGA	0.562													A|||	146	0.0291534	0.1044	0.0086	5008	,	,		21631	0.0		0.002	False		,,,				2504	0.0				p.D3556D		Atlas-SNP	.											.	DNAH17	347	.	0			c.T10668C						PASS	.	A		376,4030	191.9+/-217.4	17,342,1844	301.0	246.0	265.0		10668	-3.6	0.8	17	dbSNP_126	265	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	DNAH17	NM_173628.3		17,346,6140	GG,GA,AA		0.0465,8.5338,2.9217		3556/4463	76447617	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	8632	exon66			GAGTCCATCCCTG	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.10653T>C	17.37:g.76447617A>G		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	267	125	0.468165	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				A|0.969;G|0.031	0.031	strong		0.562	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
MUC4	4585	hgsc.bcm.edu	37	3	195515726	195515726	+	Missense_Mutation	SNP	G	G	C	rs55697302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515726G>C	ENST00000463781.3	-	2	3184	c.2725C>G	c.(2725-2727)Cag>Gag	p.Q909E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.Q909E	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	914	Ser-rich.				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)		CTCTGAGTCTGGGCCATCCGG	0.602													.|||	462	0.0922524	0.3018	0.0202	5008	,	,		19609	0.002		0.007	False		,,,				2504	0.0409				p.Q909E		Atlas-SNP	.											.	MUC4	1505	.	0			c.C2725G						PASS	.		,,GLU/GLN	1021,3177		130,761,1208	113.0	115.0	114.0		,,2725	1.9	0.0	3	dbSNP_129	114	46,8360		0,46,4157	yes	intron,intron,missense	MUC4	NM_004532.5,NM_138297.4,NM_018406.6	,,29	130,807,5365	CC,CG,GG		0.5472,24.3211,8.4656	,,benign	,,909/5413	195515726	1067,11537	2099	4203	6302	SO:0001583	missense	4585	exon2			GAGTCTGGGCCAT	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.2725C>G	3.37:g.195515726G>C	ENSP00000417498:p.Gln909Glu	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	275	136	0.494545	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	154	0.07051282051282051	139	0.28252032520325204	10	0.027624309392265192	1	0.0017482517482517483	4	0.005277044854881266	g	3.831	-0.035685	0.07497	0.243211	0.005472	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.42513	0.97;0.99	2.78	1.9	0.25705	.	1.330860	0.05376	N	0.536212	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.29508	0.141;0.246	B;B	0.20955	0.031;0.032	T	0.17992	-1.0351	9	0.06891	T	0.86	-1.2845	4.3272	0.11046	0.1349:0.2358:0.6293:0.0	rs55697302	909;914	E7ESK3;Q99102	.;MUC4_HUMAN	E	909;909;883	ENSP00000417498:Q909E;ENSP00000420243:Q909E	ENSP00000376209:Q883E	Q	-	1	0	MUC4	197000121	0.001000	0.12720	0.002000	0.10522	0.010000	0.07245	0.850000	0.27737	0.742000	0.32697	0.579000	0.79373	CAG	G|0.942;C|0.058	0.058	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PLA2G3	50487	hgsc.bcm.edu	37	22	31535995	31535995	+	Missense_Mutation	SNP	C	C	G	rs2074734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31535995C>G	ENST00000215885.3	-	1	598	c.346G>C	c.(346-348)Gag>Cag	p.E116Q		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	116			E -> Q (in dbSNP:rs2074734).		acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						CGGCATGCCTCCCACTGACTC	0.637													C|||	801	0.159944	0.1747	0.134	5008	,	,		17339	0.3909		0.0467	False		,,,				2504	0.0368				p.E116Q		Atlas-SNP	.											.	PLA2G3	85	.	0			c.G346C						PASS	.	C	GLN/GLU	516,3890	219.4+/-237.2	34,448,1721	49.0	49.0	49.0		346	4.3	1.0	22	dbSNP_96	49	452,8148	128.5+/-186.7	12,428,3860	yes	missense	PLA2G3	NM_015715.3	29	46,876,5581	GG,GC,CC		5.2558,11.7113,7.4427	benign	116/510	31535995	968,12038	2203	4300	6503	SO:0001583	missense	50487	exon1			ATGCCTCCCACTG	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.346G>C	22.37:g.31535995C>G	ENSP00000215885:p.Glu116Gln	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	156	82	0.525641	NM_015715	O95768	Missense_Mutation	SNP	ENST00000215885.3	37	CCDS13889.1	401	0.18360805860805862	94	0.1910569105691057	47	0.1298342541436464	230	0.4020979020979021	30	0.0395778364116095	C	15.79	2.936043	0.52972	0.117113	0.052558	ENSG00000100078	ENST00000215885	T	0.12465	2.68	5.35	4.27	0.50696	.	1.012140	0.07912	N	0.974456	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	D	0.56521	0.976	P	0.47864	0.559	T	0.48559	-0.9025	9	0.38643	T	0.18	-21.121	11.1801	0.48623	0.0:0.8144:0.1856:0.0	rs2074734;rs17820743;rs60301489;rs2074734	116	Q9NZ20	PA2G3_HUMAN	Q	116	ENSP00000215885:E116Q	ENSP00000215885:E116Q	E	-	1	0	PLA2G3	29865995	0.000000	0.05858	0.994000	0.49952	0.714000	0.41099	-0.106000	0.10890	2.513000	0.84729	0.591000	0.81541	GAG	C|0.889;G|0.111	0.111	strong		0.637	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715	
NUP133	55746	hgsc.bcm.edu	37	1	229635521	229635521	+	Silent	SNP	A	A	G	rs10916495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229635521A>G	ENST00000261396.3	-	5	649	c.558T>C	c.(556-558)taT>taC	p.Y186Y	NUP133_ENST00000537506.1_Silent_p.Y170Y|NUP133_ENST00000366678.3_Silent_p.Y186Y	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	186					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 organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|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)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.Y186Y(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GGCTTGGCCAATAGCGGATAG	0.453													A|||	883	0.176318	0.1369	0.2896	5008	,	,		17612	0.1577		0.2028	False		,,,				2504	0.1411				p.Y186Y		Atlas-SNP	.											NUP133,NS,carcinoma,0,1	NUP133	111	1	1	Substitution - coding silent(1)	stomach(1)	c.T558C						PASS	.	A		650,3756	276.0+/-272.9	50,550,1603	94.0	91.0	92.0		558	-2.6	1.0	1	dbSNP_120	92	1811,6789	325.4+/-316.9	190,1431,2679	no	coding-synonymous	NUP133	NM_018230.2		240,1981,4282	GG,GA,AA		21.0581,14.7526,18.922		186/1157	229635521	2461,10545	2203	4300	6503	SO:0001819	synonymous_variant	55746	exon5			TGGCCAATAGCGG		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.558T>C	1.37:g.229635521A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	128	74	0.578125	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	37	CCDS1579.1																																																																																			A|0.813;G|0.187	0.187	strong		0.453	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
ZNF230	7773	hgsc.bcm.edu	37	19	44514859	44514859	+	Missense_Mutation	SNP	C	C	T	rs147553354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44514859C>T	ENST00000429154.2	+	5	896	c.668C>T	c.(667-669)cCa>cTa	p.P223L		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	223					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)				GGAGAGAAACCATTCAAATGT	0.428													C|||	11	0.00219649	0.0083	0.0	5008	,	,		22817	0.0		0.0	False		,,,				2504	0.0				p.P223L	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.C668T						PASS	.	C	LEU/PRO	37,4369	40.0+/-72.8	0,37,2166	101.0	103.0	103.0		668	2.7	0.1	19	dbSNP_134	103	0,8600		0,0,4300	yes	missense	ZNF230	NM_006300.3	98	0,37,6466	TT,TC,CC		0.0,0.8398,0.2845	benign	223/475	44514859	37,12969	2203	4300	6503	SO:0001583	missense	7773	exon5			AGAAACCATTCAA	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.668C>T	19.37:g.44514859C>T	ENSP00000409318:p.Pro223Leu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	120	50	0.416667	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Missense_Mutation	SNP	ENST00000429154.2	37	CCDS33044.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.17	2.158672	0.38119	0.008398	0.0	ENSG00000159882	ENST00000429154	T	0.27557	1.66	2.67	2.67	0.31697	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29256	0.0728	M	0.80422	2.495	0.80722	D	1	B	0.25105	0.118	B	0.26310	0.068	T	0.44697	-0.9311	9	0.66056	D	0.02	.	12.4612	0.55733	0.0:1.0:0.0:0.0	.	223	Q9UIE0	ZN230_HUMAN	L	223	ENSP00000409318:P223L	ENSP00000409318:P223L	P	+	2	0	ZNF230	49206699	0.016000	0.18221	0.064000	0.19789	0.067000	0.16453	1.315000	0.33608	1.468000	0.48064	0.407000	0.27541	CCA	C|0.998;T|0.002	0.002	strong		0.428	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1		
DHRS4L1	728635	hgsc.bcm.edu	37	14	24505722	24505722	+	RNA	SNP	C	C	G	rs8005834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	104	0	0		WXS	Illumina HiSeq	Phase_I	98	36	0.367347	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		
OR4D9	390199	hgsc.bcm.edu	37	11	59282960	59282960	+	Missense_Mutation	SNP	C	C	G	rs113146895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59282960C>G	ENST00000329328.3	+	1	575	c.575C>G	c.(574-576)aCc>aGc	p.T192S		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	192						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(14)|prostate(5)|upper_aerodigestive_tract(1)	26						TGCACTGACACCTTCACTCTG	0.453													C|||	108	0.0215655	0.0802	0.0029	5008	,	,		21548	0.0		0.0	False		,,,				2504	0.0				p.T192S		Atlas-SNP	.											.	OR4D9	47	.	0			c.C575G						PASS	.	C	SER/THR	263,4139	149.5+/-183.7	9,245,1947	189.0	162.0	171.0		575	3.5	0.1	11	dbSNP_132	171	1,8589		0,1,4294	yes	missense	OR4D9	NM_001004711.1	58	9,246,6241	GG,GC,CC		0.0116,5.9746,2.032	possibly-damaging	192/315	59282960	264,12728	2201	4295	6496	SO:0001583	missense	390199	exon1			CTGACACCTTCAC	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"""GPCR / Class A : Olfactory receptors"""	15178	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily D, member 9 pseudogene"""				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.575C>G	11.37:g.59282960C>G	ENSP00000328563:p.Thr192Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	169	82	0.485207	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	C	11.61	1.689273	0.29962	0.059746	1.16E-4	ENSG00000172742	ENST00000329328	T	0.00207	8.55	4.44	3.52	0.40303	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	U	0.000628	T	0.00012	0.0000	M	0.78916	2.43	0.09310	N	1	D	0.53151	0.958	P	0.59825	0.864	T	0.37174	-0.9717	10	0.72032	D	0.01	-12.673	11.2423	0.48977	0.0:0.9081:0.0:0.0919	.	192	Q8NGE8	OR4D9_HUMAN	S	192	ENSP00000328563:T192S	ENSP00000328563:T192S	T	+	2	0	OR4D9	59039536	0.004000	0.15560	0.109000	0.21407	0.328000	0.28507	0.698000	0.25571	0.977000	0.38444	0.557000	0.71058	ACC	C|0.979;G|0.021	0.021	strong		0.453	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711	
SSPO	23145	hgsc.bcm.edu	37	7	149498893	149498893	+	RNA	SNP	A	A	G	rs77858430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149498893A>G	ENST00000378016.2	+	0	7345							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)			GCCCTTCATGATGCCTACCAT	0.612													G|||	671	0.133986	0.2753	0.072	5008	,	,		18169	0.0833		0.0636	False		,,,				2504	0.1115				p.M2449V		Atlas-SNP	.											.	.	.	.	0			c.A7345G						PASS	.	G		903,3281		93,717,1282	56.0	57.0	57.0		7349	2.9	0.3	7	dbSNP_132	57	534,7920		26,482,3719	yes	coding-notMod3	SSPO	NM_198455.2		119,1199,5001	GG,GA,AA		6.3165,21.5822,11.3705			149498893	1437,11201	2092	4227	6319			23145	exon50			TTCATGATGCCTA	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.149498893A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				A|0.897;G|0.103	0.103	strong		0.612	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
DNAH12	201625	hgsc.bcm.edu	37	3	57528503	57528503	+	Missense_Mutation	SNP	A	A	G	rs9311651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:57528503A>G	ENST00000351747.2	-	2	275	c.95T>C	c.(94-96)gTt>gCt	p.V32A	DNAH12_ENST00000311202.6_Missense_Mutation_p.V32A|DNAH12_ENST00000389536.4_Missense_Mutation_p.V32A	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	32	Stem. {ECO:0000250}.		V -> A (in dbSNP:rs9311651). {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(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TGGTGTATCAACGCCTATGTT	0.398													A|||	1084	0.216454	0.5477	0.1715	5008	,	,		17572	0.003		0.1461	False		,,,				2504	0.093				p.V32A		Atlas-SNP	.											.	DNAH12	182	.	0			c.T95C						PASS	.	A	ALA/VAL,ALA/VAL	2164,2242	585.5+/-386.3	531,1102,570	147.0	138.0	141.0		95,95	-2.9	0.2	3	dbSNP_119	141	1302,7298	257.9+/-281.7	102,1098,3100	yes	missense,missense	DNAH12	NM_178504.4,NM_198564.3	64,64	633,2200,3670	GG,GA,AA		15.1395,49.1148,26.6492	possibly-damaging,possibly-damaging	32/3093,32/458	57528503	3466,9540	2203	4300	6503	SO:0001583	missense	201625	exon2			GTATCAACGCCTA	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.95T>C	3.37:g.57528503A>G	ENSP00000295937:p.Val32Ala	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	108	46	0.425926	NM_198564	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		453	0.20741758241758243	273	0.5548780487804879	72	0.19889502762430938	1	0.0017482517482517483	107	0.14116094986807387	A	1.215	-0.628672	0.03610	0.491148	0.151395	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536;ENST00000311202	T;T;T;T	0.20200	2.24;2.09;3.76;3.21	5.75	-2.94	0.05581	.	0.438335	0.19737	N	0.107210	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.47548	-0.9109	9	0.09338	T	0.73	.	3.9621	0.09415	0.3715:0.0:0.3074:0.3211	rs9311651;rs52837959;rs9311651	32;32	Q6ZR08-4;Q6ZR08	.;DYH12_HUMAN	A	32	ENSP00000295937:V32A;ENSP00000418137:V32A;ENSP00000374187:V32A;ENSP00000312554:V32A	ENSP00000312554:V32A	V	-	2	0	DNAH12	57503543	0.002000	0.14202	0.229000	0.23960	0.644000	0.38419	0.065000	0.14466	-0.116000	0.11893	-0.274000	0.10170	GTT	A|0.760;G|0.240	0.240	strong		0.398	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919145	12919145	+	Missense_Mutation	SNP	G	G	A	rs149655365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919145G>A	ENST00000240189.2	+	2	368	c.281G>A	c.(280-282)cGc>cAc	p.R94H		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	94					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)		CAGAAGGATCGCCCCAGGTGA	0.552													.|||	204	0.0407348	0.1498	0.0086	5008	,	,		23772	0.0		0.0	False		,,,				2504	0.0				p.R94H		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G281A						PASS	.	G	HIS/ARG	545,3857	236.1+/-248.4	53,439,1709	141.0	155.0	150.0		281	-0.6	0.0	1	dbSNP_134	150	3,8583	2.2+/-6.3	0,3,4290	no	missense	PRAMEF2	NM_023014.1	29	53,442,5999	AA,AG,GG		0.0349,12.3807,4.2193	benign	94/475	12919145	548,12440	2201	4293	6494	SO:0001583	missense	65122	exon2			AGGATCGCCCCAG		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.281G>A	1.37:g.12919145G>A	ENSP00000240189:p.Arg94His	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	195	100	0.512821	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	77	0.035256410256410256	72	0.14634146341463414	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	4.603	0.111991	0.08831	0.123807	3.49E-4	ENSG00000120952	ENST00000240189	T	0.04758	3.56	0.842	-0.64	0.11493	.	1.317630	0.05044	N	0.476841	T	0.00039	0.0001	L	0.42632	1.34	0.09310	N	1	B	0.21309	0.054	B	0.17979	0.02	T	0.46884	-0.9159	10	0.13853	T	0.58	.	3.5838	0.07963	0.0:0.0:0.5309:0.4691	.	94	O60811	PRAM2_HUMAN	H	94	ENSP00000240189:R94H	ENSP00000240189:R94H	R	+	2	0	PRAMEF2	12841732	0.000000	0.05858	0.040000	0.18447	0.062000	0.15995	-5.853000	0.00094	-0.190000	0.10465	0.194000	0.17425	CGC	G|0.957;A|0.043	0.043	strong		0.552	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
CDPF1	150383	hgsc.bcm.edu	37	22	46644168	46644168	+	Missense_Mutation	SNP	A	A	G	rs9627281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46644168A>G	ENST00000314567.3	-	2	437	c.14T>C	c.(13-15)gTa>gCa	p.V5A	CDPF1_ENST00000404583.1_Missense_Mutation_p.V5A|CDPF1_ENST00000475605.1_Intron|CDPF1_ENST00000404744.1_Missense_Mutation_p.V5A	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	55	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	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	
UBB	7314	hgsc.bcm.edu	37	17	16285491	16285491	+	Silent	SNP	C	C	T	rs16962973		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16285491C>T	ENST00000395837.1	+	2	451	c.270C>T	c.(268-270)acC>acT	p.T90T	UBB_ENST00000535788.1_Intron|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000302182.3_Silent_p.T90T|UBB_ENST00000578649.1_Intron|UBB_ENST00000395839.1_Silent_p.T90T	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	90	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|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)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|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)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|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 epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|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)|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 transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|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)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AGACCATCACCCTGGAAGTGG	0.552																																					p.T90T	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,bladder,carcinoma,0,2	UBB	30	2	0			c.C270T						scavenged	.						75.0	76.0	75.0					17																	16285491		2203	4297	6500	SO:0001819	synonymous_variant	7314	exon2			CATCACCCTGGAA		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.270C>T	17.37:g.16285491C>T		Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	220	5	0.0227273	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			C|0.996;T|0.004	0.004	strong		0.552	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
SEPT9	10801	hgsc.bcm.edu	37	17	75471762	75471762	+	Intron	SNP	G	G	A	rs312821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:75471762G>A	ENST00000427177.1	+	4	847				SEPT9_ENST00000591088.1_Intron|RP11-75C10.9_ENST00000591110.1_RNA|SEPT9_ENST00000585930.1_Intron|SEPT9_ENST00000592420.1_Intron|SEPT9_ENST00000427674.2_Intron|SEPT9_ENST00000590294.1_Intron|SEPT9_ENST00000590917.1_Intron|SEPT9_ENST00000588690.1_Intron|SEPT9_ENST00000423034.2_Intron|SEPT9_ENST00000592481.1_Intron|SEPT9_ENST00000329047.8_Intron|SEPT9_ENST00000449803.2_Intron|SEPT9_ENST00000427180.1_Silent_p.T54T|SEPT9_ENST00000591198.1_Intron|SEPT9_ENST00000541152.2_Intron|SEPT9_ENST00000592951.1_Intron|SEPT9_ENST00000431235.2_Intron	NM_001113491.1	NP_001106963.1	Q9UHD8	SEPT9_HUMAN	septin 9						cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|protein heterooligomerization (GO:0051291)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)	16			BRCA - Breast invasive adenocarcinoma(99;0.153)			CTGGGCCCACGCTGGGCCGGG	0.642													G|||	387	0.0772764	0.2799	0.0231	5008	,	,		18847	0.0		0.001	False		,,,				2504	0.0				p.T54T		Atlas-SNP	.											.	SEPT9	105	.	0			c.G162A						PASS	.	G	,,,,,,	718,2418		83,552,933	35.0	38.0	37.0		,,,,162,,	-1.7	0.0	17	dbSNP_79	37	18,7146		0,18,3564	no	intron,intron,intron,intron,coding-synonymous,intron,intron	SEPT9	NM_001113491.1,NM_001113492.1,NM_001113493.1,NM_001113494.1,NM_001113495.1,NM_001113496.1,NM_006640.4	,,,,,,	83,570,4497	AA,AG,GG		0.2513,22.8954,7.1456	,,,,,,	,,,,54/475,,	75471762	736,9564	1568	3582	5150	SO:0001627	intron_variant	10801	exon1			GCCCACGCTGGGC	AB023208	CCDS45790.1, CCDS45791.1, CCDS45792.1, CCDS45793.1, CCDS45794.1, CCDS45795.1, CCDS74166.1	17q25.3	2014-09-17	2005-01-11	2005-01-12	ENSG00000184640	ENSG00000184640		"""Septins"""	7323	protein-coding gene	gene with protein product	"""Ov/Br septin"""	604061	"""MLL septin-like fusion"""	MSF		10339604, 10485469	Standard	NM_006640		Approved	MSF1, KIAA0991, PNUTL4, AF17q25, SeptD1	uc002jts.4	Q9UHD8		ENST00000427177.1:c.722-6464G>A	17.37:g.75471762G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_001113495	A8K2V3|B3KPM0|B4DTL9|B4E0N2|B4E274|B7Z654|Q96QF3|Q96QF4|Q96QF5|Q9HA04|Q9UG40|Q9Y5W4	Silent	SNP	ENST00000427177.1	37	CCDS45790.1																																																																																			G|0.937;A|0.063	0.063	strong		0.642	SEPT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436304.2	NM_006640	
MRPL46	26589	hgsc.bcm.edu	37	15	89008072	89008072	+	Silent	SNP	T	T	G	rs16941885	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89008072T>G	ENST00000312475.4	-	3	492	c.451A>C	c.(451-453)Agg>Cgg	p.R151R	MRPS11_ENST00000325844.4_5'Flank|MRPL46_ENST00000559538.1_5'Flank|MRPS11_ENST00000353598.6_5'Flank	NM_022163.3	NP_071446.2	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46	151						mitochondrion (GO:0005739)|ribosome (GO:0005840)	hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			TCTAGCTTCCTGTTCAGGGAT	0.512													G|||	378	0.0754792	0.2587	0.0173	5008	,	,		17989	0.006		0.001	False		,,,				2504	0.0174				p.R151R		Atlas-SNP	.											.	MRPL46	13	.	0			c.A451C						PASS	.	G		1001,3401	729.1+/-410.0	124,753,1324	135.0	132.0	133.0		451	1.4	1.0	15	dbSNP_123	133	8,8590	818.9+/-406.8	0,8,4291	yes	coding-synonymous	MRPL46	NM_022163.3		124,761,5615	GG,GT,TT		0.093,22.7397,7.7615		151/280	89008072	1009,11991	2201	4299	6500	SO:0001819	synonymous_variant	26589	exon3			GCTTCCTGTTCAG	AF210056	CCDS10341.1	15q25.3	2012-10-08	2001-12-10	2001-12-14	ENSG00000259494	ENSG00000259494		"""Mitochondrial ribosomal proteins / large subunits"""	1192	protein-coding gene	gene with protein product		611851	"""chromosome 15 open reading frame 4"""	C15orf4		11761714, 11551941	Standard	NM_022163		Approved	LIECG2, P2ECSL	uc002bmj.2	Q9H2W6	OTTHUMG00000148683	ENST00000312475.4:c.451A>C	15.37:g.89008072T>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	146	73	0.5	NM_022163	B2RD75|Q9HBU8	Silent	SNP	ENST00000312475.4	37	CCDS10341.1																																																																																			T|0.925;G|0.075	0.075	strong		0.512	MRPL46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309073.1	NM_022163	
FAT3	120114	hgsc.bcm.edu	37	11	92616006	92616006	+	Silent	SNP	C	C	T	rs58474174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92616006C>T	ENST00000298047.6	+	23	12401	c.12384C>T	c.(12382-12384)taC>taT	p.Y4128Y	FAT3_ENST00000525166.1_Silent_p.Y3978Y|FAT3_ENST00000409404.2_Silent_p.Y4128Y|FAT3_ENST00000533797.1_Silent_p.Y463Y			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4128	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)				CGCCGGGCTACGTGGGCCAGT	0.632										TCGA Ovarian(4;0.039)			C|||	182	0.0363419	0.1309	0.0115	5008	,	,		15044	0.0		0.001	False		,,,				2504	0.0				p.Y4128Y		Atlas-SNP	.											.	FAT3	1822	.	0			c.C12384T						PASS	.	C		392,3806		19,354,1726	62.0	79.0	73.0		12384	1.9	1.0	11	dbSNP_129	73	2,8424		0,2,4211	no	coding-synonymous	FAT3	NM_001008781.2		19,356,5937	TT,TC,CC		0.0237,9.3378,3.121		4128/4558	92616006	394,12230	2099	4213	6312	SO:0001819	synonymous_variant	120114	exon23			GGGCTACGTGGGC	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.12384C>T	11.37:g.92616006C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	115	47	0.408696	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.976;T|0.024	0.024	strong		0.632	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
CDH23	64072	hgsc.bcm.edu	37	10	73551088	73551088	+	Silent	SNP	G	G	A	rs55964031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73551088G>A	ENST00000224721.6	+	46	6269	c.6264G>A	c.(6262-6264)ccG>ccA	p.P2088P		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2083	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.P2088P(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						AGAACTGCCCGCCTGGTAAGC	0.627													G|||	135	0.0269569	0.0976	0.0072	5008	,	,		16895	0.0		0.001	False		,,,				2504	0.0				p.P2083P		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - coding silent(1)	prostate(1)	c.G6249A						scavenged	.	G		276,3814		11,254,1780	42.0	43.0	43.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6249	-8.6	1.0	10	dbSNP_129	43	4,8364		0,4,4180	no	coding-synonymous	CDH23	NM_022124.5		11,258,5960	AA,AG,GG		0.0478,6.7482,2.2476		2083/3355	73551088	280,12178	2045	4184	6229	SO:0001819	synonymous_variant	64072	exon45			CTGCCCGCCTGGT	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.6264G>A	10.37:g.73551088G>A		Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				G|0.974;A|0.026	0.026	strong		0.627	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
PPFIA1	8500	hgsc.bcm.edu	37	11	70200529	70200529	+	Silent	SNP	C	C	T	rs17853270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:70200529C>T	ENST00000253925.7	+	17	2501	c.2286C>T	c.(2284-2286)gtC>gtT	p.V762V	PPFIA1_ENST00000389547.3_Silent_p.V762V|AP000487.6_ENST00000528607.1_RNA	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	49	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	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	
LPA	4018	hgsc.bcm.edu	37	6	160977167	160977167	+	Silent	SNP	G	G	T	rs375904594		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160977167G>T	ENST00000316300.5	-	30	4907	c.4863C>A	c.(4861-4863)ggC>ggA	p.G1621G	LPA_ENST00000447678.1_Silent_p.G1621G			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4129	Kringle 15. {ECO:0000255|PROSITE- ProRule:PRU00121}.				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)	GATAACTCTGGCCATTACCAT	0.483																																					p.G1621G		Atlas-SNP	.											LPA,right_upper_lobe,carcinoma,-1,1	LPA	237	1	0			c.C4863A						scavenged	.	T		0,4376		0,0,2188	154.0	156.0	155.0		4863	-5.5	0.0	6		155	1,8599		0,1,4299	no	coding-synonymous	LPA	NM_005577.2		0,1,6487	TT,TG,GG		0.0116,0.0,0.0077		1621/2041	160977167	1,12975	2188	4300	6488	SO:0001819	synonymous_variant	4018	exon31			ACTCTGGCCATTA	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.4863C>A	6.37:g.160977167G>T		Somatic	342	2	0.00584795		WXS	Illumina HiSeq	Phase_I	361	33	0.0914127	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																			.	.	weak		0.483	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
APTX	54840	hgsc.bcm.edu	37	9	32984803	32984803	+	Missense_Mutation	SNP	C	C	T	rs150886026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:32984803C>T	ENST00000379819.1	-	6	637	c.638G>A	c.(637-639)cGt>cAt	p.R213H	APTX_ENST00000468275.1_Missense_Mutation_p.R199H|APTX_ENST00000436040.2_Intron|APTX_ENST00000476858.1_Missense_Mutation_p.R159H|APTX_ENST00000397172.3_Missense_Mutation_p.R141H|APTX_ENST00000379817.2_Missense_Mutation_p.R199H|APTX_ENST00000379813.3_Missense_Mutation_p.R199H|APTX_ENST00000309615.3_Missense_Mutation_p.R213H|APTX_ENST00000463596.1_Missense_Mutation_p.R199H|APTX_ENST00000379825.2_Missense_Mutation_p.R213H			Q7Z2E3	APTX_HUMAN	aprataxin	213	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.		R -> H (in AOA; dbSNP:rs150886026). {ECO:0000269|PubMed:11586300}.		cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|dephosphorylation (GO:0016311)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA ligation (GO:0006266)|double-strand break repair (GO:0006302)|polynucleotide 3' dephosphorylation (GO:0098506)|regulation of protein stability (GO:0031647)|response to hydrogen peroxide (GO:0042542)|single strand break repair (GO:0000012)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA 5'-adenosine monophosphate hydrolase activity (GO:0033699)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|phosphoglycolate phosphatase activity (GO:0008967)|phosphoprotein binding (GO:0051219)|polynucleotide 3'-phosphatase activity (GO:0046403)|protein N-terminus binding (GO:0047485)			endometrium(1)|lung(1)|ovary(2)|prostate(2)	6			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)		CCAATGGTAACGGGCCTTTGG	0.473								Editing and processing nucleases					C|||	31	0.0061901	0.0197	0.0058	5008	,	,		21579	0.0		0.0	False		,,,				2504	0.001				p.R213H		Atlas-SNP	.											.	APTX	44	.	0			c.G638A	GRCh37	CM012895	APTX	M	rs150886026	PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	80,4326	69.2+/-107.0	0,80,2123	162.0	146.0	152.0		638,596,476,596,422,434,638,596	4.0	0.8	9	dbSNP_134	152	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense	APTX	NM_001195248.1,NM_001195249.1,NM_001195250.1,NM_001195251.1,NM_001195252.1,NM_001195254.1,NM_175069.2,NM_175073.2	29,29,29,29,29,29,29,29	0,80,6423	TT,TC,CC		0.0,1.8157,0.6151	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	213/357,199/343,159/303,199/293,141/285,145/289,213/307,199/343	32984803	80,12926	2203	4300	6503	SO:0001583	missense	54840	exon6			TGGTAACGGGCCT	AK000164	CCDS47956.1, CCDS56568.1, CCDS75827.1	9p13.3	2014-01-28	2003-04-03		ENSG00000137074	ENSG00000137074			15984	protein-coding gene	gene with protein product		606350	"""ataxia 1, early onset with hypoalbuminemia"""	AXA1		11586299, 11586300	Standard	NM_175069		Approved	FLJ20157, AOA, AOA1, EAOH, EOAHA	uc003zry.3	Q7Z2E3	OTTHUMG00000019759	ENST00000379819.1:c.638G>A	9.37:g.32984803C>T	ENSP00000369147:p.Arg213His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	112	63	0.5625	NM_001195248	A8MTN4|D3DRK9|D3DRL0|Q0P662|Q5T781|Q5T782|Q5T784|Q6JV81|Q6JV82|Q6JV85|Q7Z2F3|Q7Z336|Q7Z5R5|Q7Z6V7|Q7Z6V8|Q9NXM5	Missense_Mutation	SNP	ENST00000379819.1	37		9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	C	13.81	2.348650	0.41599	0.018157	0.0	ENSG00000137074	ENST00000379825;ENST00000309615;ENST00000397172;ENST00000379817;ENST00000379819;ENST00000468275;ENST00000463596;ENST00000476858;ENST00000344355;ENST00000379813;ENST00000379812;ENST00000473221;ENST00000477119	D;D;D;D;D;D;D;D;D;D;D;D	0.95656	-3.77;-3.77;-2.86;-2.86;-2.86;-2.86;-2.86;-2.86;-2.86;-3.77;-3.77;-3.77	5.81	3.96	0.45880	Histidine triad motif (1);Histidine triad-like motif (1);	0.047355	0.85682	D	0.000000	D	0.92257	0.7544	M	0.64170	1.965	0.80722	D	1	D;P;P;P;P	0.64830	0.994;0.864;0.632;0.769;0.632	P;B;B;B;B	0.55785	0.784;0.304;0.288;0.352;0.288	D	0.91337	0.5094	10	0.52906	T	0.07	-11.4381	11.0972	0.48152	0.0:0.8459:0.0:0.1541	.	159;141;213;145;213	C9JZ40;Q7Z2E3-3;Q5T782;Q7Z2E3-5;Q7Z2E3	.;.;.;.;APTX_HUMAN	H	213;213;141;199;213;199;199;159;194;199;141;159;145	ENSP00000369153:R213H;ENSP00000311547:R213H;ENSP00000380357:R141H;ENSP00000369145:R199H;ENSP00000369147:R213H;ENSP00000420263:R199H;ENSP00000419846:R199H;ENSP00000419042:R159H;ENSP00000369141:R199H;ENSP00000369140:R141H;ENSP00000419020:R159H;ENSP00000417649:R145H	ENSP00000311547:R213H	R	-	2	0	APTX	32974803	1.000000	0.71417	0.798000	0.32154	0.012000	0.07955	6.082000	0.71318	1.451000	0.47736	0.655000	0.94253	CGT	C|0.994;T|0.006	0.006	strong		0.473	APTX-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000052028.2	NM_017692	
ZNF324	25799	hgsc.bcm.edu	37	19	58982447	58982447	+	Silent	SNP	A	A	G	rs61742224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58982447A>G	ENST00000536459.2	+	4	1297	c.588A>G	c.(586-588)aaA>aaG	p.K196K	ZNF446_ENST00000596341.1_5'Flank|ZNF324_ENST00000196482.3_Silent_p.K196K|ZNF324_ENST00000535298.1_5'UTR			O75467	Z324A_HUMAN	zinc finger protein 324	196					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)		AGCGGCAGAAACCATGTGCAC	0.652													A|||	292	0.0583067	0.1891	0.0288	5008	,	,		9263	0.005		0.001	False		,,,				2504	0.0164				p.K196K		Atlas-SNP	.											ZNF324,NS,carcinoma,0,1	ZNF324	46	1	0			c.A588G						scavenged	.	A		786,3620	295.3+/-283.6	63,660,1480	36.0	43.0	40.0		588	-0.2	0.0	19	dbSNP_129	40	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	ZNF324	NM_014347.2		63,671,5769	GG,GA,AA		0.1279,17.8393,6.1279		196/554	58982447	797,12209	2203	4300	6503	SO:0001819	synonymous_variant	25799	exon4			GCAGAAACCATGT	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.588A>G	19.37:g.58982447A>G		Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_014347	B3KRX1	Silent	SNP	ENST00000536459.2	37	CCDS12981.1																																																																																			A|0.942;G|0.058	0.058	strong		0.652	ZNF324-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467044.1	NM_014347	
GALNT18	374378	hgsc.bcm.edu	37	11	11292700	11292700	+	Silent	SNP	G	G	C	rs10831567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:11292700G>C	ENST00000227756.4	-	11	2226	c.1815C>G	c.(1813-1815)ctC>ctG	p.L605L		NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	605					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)	p.L605L(1)									GTCAGGACGCGAGGCTCCTCA	0.612													c|||	2005	0.400359	0.32	0.5058	5008	,	,		14500	0.38		0.4294	False		,,,				2504	0.4254				p.L605L		Atlas-SNP	.											GALNTL4,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C1815G						PASS	.			1557,2845	668.4+/-402.0	272,1013,916	59.0	56.0	57.0		1815	4.8	1.0	11	dbSNP_120	57	3659,4929	622.1+/-397.3	765,2129,1400	no	coding-synonymous	GALNTL4	NM_198516.2		1037,3142,2316	CC,CG,GG		42.606,35.3703,40.154		605/608	11292700	5216,7774	2201	4294	6495	SO:0001819	synonymous_variant	374378	exon11			GGACGCGAGGCTC	AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	30488	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 18"""	615136	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"""	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.1815C>G	11.37:g.11292700G>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_198516	O95903|Q8NDY9	Silent	SNP	ENST00000227756.4	37	CCDS7807.1																																																																																			G|0.596;C|0.404	0.404	strong		0.612	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516	
SMTN	6525	hgsc.bcm.edu	37	22	31478942	31478942	+	Intron	SNP	G	G	A	rs73408133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31478942G>A	ENST00000347557.2	+	2	138				RP3-412A9.16_ENST00000609017.1_RNA|SMTN_ENST00000358743.1_Intron|SMTN_ENST00000475548.1_Intron|SMTN_ENST00000333137.7_Intron	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin						muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						gcagactggcggccaagctgg	0.612											OREG0026470	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	217	0.0433307	0.1596	0.0086	5008	,	,		16659	0.0		0.0	False		,,,				2504	0.0				p.A12A		Atlas-SNP	.											.	SMTN	219	.	0			c.G36A						PASS	.																																			SO:0001627	intron_variant	6525	exon1			ACTGGCGGCCAAG	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.-80-223G>A	22.37:g.31478942G>A		Somatic	76	0	0	825	WXS	Illumina HiSeq	Phase_I	100	38	0.38	NM_001207017	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Silent	SNP	ENST00000347557.2	37	CCDS13886.1																																																																																			G|0.963;A|0.037	0.037	strong		0.612	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270	
SCN4A	6329	hgsc.bcm.edu	37	17	62018164	62018164	+	Silent	SNP	A	A	C	rs2227906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62018164A>C	ENST00000435607.1	-	24	5554	c.5478T>G	c.(5476-5478)acT>acG	p.T1826T	SCN4A_ENST00000578147.1_Silent_p.T1826T	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1826					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)	CTGGGCGCACAGTCTGCCCTG	0.677													C|||	928	0.185304	0.6694	0.0476	5008	,	,		17911	0.002		0.005	False		,,,				2504	0.0031				p.T1826T		Atlas-SNP	.											.	SCN4A	205	.	0			c.T5478G						PASS	.	C		2118,1974		567,984,495	36.0	46.0	42.0		5478	-8.6	0.0	17	dbSNP_98	42	23,8359		0,23,4168	no	coding-synonymous	SCN4A	NM_000334.4		567,1007,4663	CC,CA,AA		0.2744,48.2405,17.1637		1826/1837	62018164	2141,10333	2046	4191	6237	SO:0001819	synonymous_variant	6329	exon24			GCGCACAGTCTGC	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.5478T>G	17.37:g.62018164A>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			A|0.808;C|0.192	0.192	strong		0.677	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242184	81242184	+	RNA	SNP	T	T	C	rs9927930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81242184T>C	ENST00000525539.1	-	0	671				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						CCACCTGGCATGACTGTAGCT	0.562													T|||	184	0.0367412	0.1339	0.0101	5008	,	,		20552	0.0		0.0	False		,,,				2504	0.0				p.S224S		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A672G						PASS	.	T	,	433,3807		22,389,1709	75.0	73.0	74.0		672,672	-8.6	0.6	16	dbSNP_119	74	3,8453		0,3,4225	no	coding-synonymous,coding-synonymous	PKD1L2	NM_001076780.1,NM_052892.3	,	22,392,5934	CC,CT,TT		0.0355,10.2123,3.4342	,	224/992,224/2460	81242184	436,12260	2120	4228	6348			114780	exon4			CTGGCATGACTGT	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.81242184T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	37																																																																																				T|0.951;C|0.049	0.049	strong		0.562	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
CDRT1	374286	hgsc.bcm.edu	37	17	15496730	15496730	+	Missense_Mutation	SNP	A	A	G	rs8078150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15496730A>G	ENST00000395906.3	-	11	1926	c.1927T>C	c.(1927-1929)Ttc>Ctc	p.F643L	RP11-385D13.1_ENST00000455584.2_Intron|CDRT1_ENST00000354433.3_Missense_Mutation_p.F143L|CDRT1_ENST00000583965.1_Intron	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	643			F -> L (in dbSNP:rs8078150). {ECO:0000269|PubMed:9403059}.							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)		TTCCCATTGAAGAAATTGTAA	0.512													.|||	1806	0.360623	0.4675	0.33	5008	,	,		17454	0.3819		0.2346	False		,,,				2504	0.3456				p.F643L		Atlas-SNP	.											.	CDRT1	83	.	0			c.T1927C						PASS	.	G	LEU/PHE	1972,2434		457,1058,688	221.0	234.0	230.0		1927	2.5	1.0	17	dbSNP_116	230	2187,6413		277,1633,2390	no	missense	CDRT1	NM_006382.3	22	734,2691,3078	GG,GA,AA		25.4302,44.7571,31.9775	benign	643/753	15496730	4159,8847	2203	4300	6503	SO:0001583	missense	374286	exon11			CATTGAAGAAATT	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.1927T>C	17.37:g.15496730A>G	ENSP00000379242:p.Phe643Leu	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	241	240	0.995851	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	744	0.34065934065934067	228	0.4634146341463415	114	0.3149171270718232	212	0.3706293706293706	190	0.25065963060686014	N	4.048	0.006554	0.07866	0.447571	0.254302	ENSG00000241322;ENSG00000251537;ENSG00000251537	ENST00000354433;ENST00000261644;ENST00000395906	T;T	0.17054	2.3;2.3	4.74	2.47	0.30058	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.00210	-1.845	0.09310	P	0.9999999999997713	B	0.02656	0.0	B	0.01281	0.0	T	0.43475	-0.9389	7	.	.	.	.	4.2827	0.10839	0.3871:0.1734:0.4395:0.0	rs8078150	643	O95170	CDRT1_HUMAN	L	143;673;643	ENSP00000346416:F143L;ENSP00000379242:F643L	.	F	-	1	0	CDRT1;RP11-385D13.1	15437455	1.000000	0.71417	0.990000	0.47175	0.914000	0.54420	2.533000	0.45667	0.301000	0.22738	-0.128000	0.14901	TTC	A|0.688;G|0.312	0.312	strong		0.512	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
AKAP2	11217	hgsc.bcm.edu	37	9	112811038	112811038	+	Missense_Mutation	SNP	C	C	T	rs78923754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:112811038C>T	ENST00000374525.1	+	1	63	c.59C>T	c.(58-60)cCg>cTg	p.P20L	AKAP2_ENST00000555236.1_Intron|AKAP2_ENST00000434623.2_Missense_Mutation_p.P20L|PALM2-AKAP2_ENST00000302798.7_Intron|AKAP2_ENST00000510514.5_Intron|PALM2-AKAP2_ENST00000374530.3_Intron	NM_001004065.4	NP_001004065.2	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	374										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						CCTGGACCCCCGGAGTCTCCT	0.776													-|||	379	0.0756789	0.0703	0.0879	5008	,	,		9335	0.0298		0.0954	False		,,,				2504	0.1012				p.P20L		Atlas-SNP	.											.	AKAP2	98	.	0			c.C59T						PASS	.	C	LEU/PRO,LEU/PRO,,	146,2418		2,142,1138	2.0	3.0	2.0		59,59,,	0.3	0.0	9	dbSNP_132	2	557,5611		13,531,2540	no	missense,missense,intron,intron	AKAP2,PALM2-AKAP2	NM_001004065.4,NM_001198656.1,NM_007203.4,NM_147150.2	98,98,,	15,673,3678	TT,TC,CC		9.0305,5.6942,8.0508	,,,	20/949,20/962,,	112811038	703,8029	1282	3084	4366	SO:0001583	missense	11217	exon1			GACCCCCGGAGTC	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000374525.1:c.59C>T	9.37:g.112811038C>T	ENSP00000363649:p.Pro20Leu	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	12	10	0.833333	NM_001004065	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000374525.1	37	CCDS43861.1	184	0.08424908424908426	48	0.0975609756097561	42	0.11602209944751381	16	0.027972027972027972	78	0.10290237467018469	-	6.449	0.450901	0.12223	0.056942	0.090305	ENSG00000241978	ENST00000434623;ENST00000374525	T;T	0.44482	1.5;0.92	3.3	0.302	0.15786	.	.	.	.	.	T	0.00412	0.0013	.	.	.	0.58432	P	5.000000000032756E-6	B;B	0.11235	0.001;0.004	B;B	0.04013	0.001;0.001	T	0.06972	-1.0797	7	0.72032	D	0.01	-9.3294	7.3755	0.26825	0.0:0.6472:0.0:0.3528	.	20;21	Q9Y2D5-7;B1ALY1	.;.	L	20	ENSP00000404782:P20L;ENSP00000363649:P20L	ENSP00000363649:P20L	P	+	2	0	AKAP2	111850859	0.208000	0.23494	0.001000	0.08648	0.000000	0.00434	0.026000	0.13599	-0.068000	0.12953	-1.980000	0.00456	CCG	C|0.917;T|0.083	0.083	strong		0.776	AKAP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053609.3	NM_001004065	
AIP	9049	hgsc.bcm.edu	37	11	67258362	67258362	+	Silent	SNP	C	C	A	rs35665586|rs267606585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67258362C>A	ENST00000279146.3	+	6	1009	c.891C>A	c.(889-891)gcC>gcA	p.A297A	PITPNM1_ENST00000526450.1_5'Flank	NM_003977.2	NP_003968.2	O00170	AIP_HUMAN	aryl hydrocarbon receptor interacting protein	297					negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|protein maturation by protein folding (GO:0022417)|protein targeting to mitochondrion (GO:0006626)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GAF domain binding (GO:0036004)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(2)	7						TGGACCCAGCCCTGGCGCCTG	0.652									Familial Isolated Pituitary Adenoma				C|||	31	0.0061901	0.0219	0.0029	5008	,	,		16963	0.0		0.0	False		,,,				2504	0.0				p.A297A		Atlas-SNP	.											.	AIP	26	.	0			c.C891A						PASS	.	C		70,4322	61.1+/-98.1	1,68,2127	25.0	27.0	26.0		891	4.0	1.0	11	dbSNP_126	26	1,8585		0,1,4292	no	coding-synonymous	AIP	NM_003977.2		1,69,6419	AA,AC,CC		0.0116,1.5938,0.5471		297/331	67258362	71,12907	2196	4293	6489	SO:0001819	synonymous_variant	9049	exon6	Familial Cancer Database	FIPA, incl. Familial Isolated Somatotropinomas, FIS, IFS, Familial Acromegaly	CCCAGCCCTGGCG	U31913	CCDS8168.1	11q13.3	2014-09-17	2001-11-29		ENSG00000110711	ENSG00000110711			358	protein-coding gene	gene with protein product		605555	"""aryl hydrocarbon receptor-interacting protein"""			8972861, 9111057	Standard	NM_003977		Approved	XAP2, ARA9, FKBP16	uc001olv.3	O00170	OTTHUMG00000167674	ENST00000279146.3:c.891C>A	11.37:g.67258362C>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	148	70	0.472973	NM_003977	A0SZW3|A0SZW4|A0SZW5|A0SZW6|Q2M3Q2|Q99606	Silent	SNP	ENST00000279146.3	37	CCDS8168.1																																																																																			C|0.995;A|0.005	0.005	strong		0.652	AIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395516.1		
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769228	43769228	+	Silent	SNP	A	A	C	rs10506226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:43769228A>C	ENST00000389420.3	-	36	5399	c.5400T>G	c.(5398-5400)acT>acG	p.T1800T		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1800	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TGCTGAAAACAGTGTATCCAG	0.338													A|||	1114	0.222444	0.4213	0.1239	5008	,	,		17947	0.1002		0.1998	False		,,,				2504	0.1728				p.T1800T		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T5400G						PASS	.	A		1633,2773	500.1+/-364.6	310,1013,880	137.0	133.0	134.0		5400	-3.6	0.2	12	dbSNP_119	134	1768,6832	319.5+/-314.2	182,1404,2714	no	coding-synonymous	ADAMTS20	NM_025003.3		492,2417,3594	CC,CA,AA		20.5581,37.0631,26.1495		1800/1911	43769228	3401,9605	2203	4300	6503	SO:0001819	synonymous_variant	80070	exon36			GAAAACAGTGTAT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.5400T>G	12.37:g.43769228A>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	122	75	0.614754	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	CCDS31778.2																																																																																			A|0.790;C|0.210	0.210	strong		0.338	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
OR52E2	119678	hgsc.bcm.edu	37	11	5080523	5080523	+	Missense_Mutation	SNP	A	A	G	rs144077173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5080523A>G	ENST00000321522.2	-	1	334	c.335T>C	c.(334-336)aTg>aCg	p.M112T		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	112						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)		TGCTGACTCCATAAGTGTGAA	0.468													a|||	3	0.000599042	0.0	0.0	5008	,	,		22727	0.003		0.0	False		,,,				2504	0.0				p.M112T		Atlas-SNP	.											.	OR52E2	63	.	0			c.T335C						PASS	.	G	THR/MET	3,4399	8.1+/-20.4	0,3,2198	75.0	71.0	72.0		335	1.4	0.7	11	dbSNP_134	72	0,8596		0,0,4298	yes	missense	OR52E2	NM_001005164.2	81	0,3,6496	GG,GA,AA		0.0,0.0682,0.0231	benign	112/326	5080523	3,12995	2201	4298	6499	SO:0001583	missense	119678	exon1			GACTCCATAAGTG	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.335T>C	11.37:g.5080523A>G	ENSP00000322088:p.Met112Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	a	2.241	-0.373782	0.05034	6.82E-4	0.0	ENSG00000176787	ENST00000321522	T	0.01613	4.73	3.77	1.43	0.22495	GPCR, rhodopsin-like superfamily (1);	0.185074	0.38111	N	0.001815	T	0.01222	0.0040	L	0.35249	1.045	0.09310	N	1	B	0.23316	0.083	B	0.25291	0.059	T	0.44697	-0.9311	10	0.54805	T	0.06	.	7.9034	0.29748	0.8183:0.0:0.1817:0.0	.	112	Q8NGJ4	O52E2_HUMAN	T	112	ENSP00000322088:M112T	ENSP00000322088:M112T	M	-	2	0	OR52E2	5037099	0.000000	0.05858	0.673000	0.29887	0.113000	0.19764	0.661000	0.25023	0.311000	0.23014	-0.259000	0.10710	ATG	A|0.999;G|0.001	0.001	strong		0.468	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
ANKRD45	339416	hgsc.bcm.edu	37	1	173596257	173596257	+	Missense_Mutation	SNP	A	A	T	rs12059066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173596257A>T	ENST00000333279.2	-	4	598	c.538T>A	c.(538-540)Tta>Ata	p.L180I		NM_198493.2	NP_940895.1	Q5TZF3	ANR45_HUMAN	ankyrin repeat domain 45	196										NS(2)|endometrium(2)|large_intestine(4)|lung(3)|skin(1)	12						GTAACAGCTAAAGAGACTTTT	0.373													A|||	965	0.192692	0.6989	0.0504	5008	,	,		20198	0.0		0.005	False		,,,				2504	0.001				p.L180I		Atlas-SNP	.											.	ANKRD45	36	.	0			c.T538A						PASS	.	A	ILE/LEU	2539,1867	632.6+/-395.9	756,1027,420	145.0	150.0	148.0		538	-3.8	0.0	1	dbSNP_120	148	32,8568	19.8+/-62.0	0,32,4268	yes	missense	ANKRD45	NM_198493.2	5	756,1059,4688	TT,TA,AA		0.3721,42.374,19.7678	benign	180/267	173596257	2571,10435	2203	4300	6503	SO:0001583	missense	339416	exon4			CAGCTAAAGAGAC		CCDS1309.1	1q25.1	2013-01-10			ENSG00000183831	ENSG00000183831		"""Ankyrin repeat domain containing"""	24786	protein-coding gene	gene with protein product	"""cancer/testis antigen 117"""						Standard	NM_198493		Approved	FLJ45235, CT117	uc001gja.1	Q5TZF3	OTTHUMG00000040546	ENST00000333279.2:c.538T>A	1.37:g.173596257A>T	ENSP00000331268:p.Leu180Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_198493	A1A4G2|Q6ZST1	Missense_Mutation	SNP	ENST00000333279.2	37	CCDS1309.1	377	0.17261904761904762	353	0.717479674796748	20	0.055248618784530384	0	0.0	4	0.005277044854881266	A	11.25	1.583800	0.28268	0.57626	0.003721	ENSG00000183831	ENST00000333279	T	0.13778	2.56	5.35	-3.79	0.04320	.	1.555310	0.03916	N	0.282716	T	0.01870	0.0059	N	0.22421	0.69	0.80722	P	0.0	B	0.27068	0.167	B	0.19148	0.024	T	0.35895	-0.9770	9	0.36615	T	0.2	-17.7491	1.2921	0.02062	0.1379:0.3633:0.2467:0.2521	rs12059066;rs52822128;rs12059066	196	Q5TZF3	ANR45_HUMAN	I	180	ENSP00000331268:L180I	ENSP00000331268:L180I	L	-	1	2	ANKRD45	171862880	0.000000	0.05858	0.000000	0.03702	0.656000	0.38851	-0.559000	0.05971	-1.213000	0.02617	0.455000	0.32223	TTA	A|0.814;T|0.186	0.186	strong		0.373	ANKRD45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097580.2	NM_198493	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3672746	3672746	+	Silent	SNP	G	G	A	rs34921899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3672746G>A	ENST00000344754.4	-	16	4133	c.4134C>T	c.(4132-4134)gcC>gcT	p.A1378A	SIGLEC1_ENST00000202578.4_Silent_p.A1378A	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1378	Ig-like C2-type 14.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CATGAGATAGGGCCAGCTCAG	0.637													G|||	103	0.0205671	0.0772	0.0014	5008	,	,		19801	0.0		0.0	False		,,,				2504	0.0				p.A1378A		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C4134T						PASS	.	G		234,4170	138.0+/-173.8	7,220,1975	45.0	37.0	40.0		4134	1.1	0.3	20	dbSNP_126	40	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	SIGLEC1	NM_023068.3		7,224,6271	AA,AG,GG		0.0465,5.3134,1.8302		1378/1710	3672746	238,12766	2202	4300	6502	SO:0001819	synonymous_variant	6614	exon16			AGATAGGGCCAGC	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.4134C>T	20.37:g.3672746G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1	32	0.014652014652014652	31	0.06300813008130081	0	0.0	0	0.0	1	0.0013192612137203166	G	6.234	0.411258	0.11812	0.053134	4.65E-4	ENSG00000088827	ENST00000419548	.	.	.	5.5	1.12	0.20585	.	.	.	.	.	T	0.07098	0.0180	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.03193	-1.1062	4	.	.	.	.	3.0219	0.06078	0.1405:0.1464:0.5625:0.1506	rs34921899	.	.	.	S	192	.	.	P	-	1	0	SIGLEC1	3620746	0.613000	0.27009	0.313000	0.25210	0.552000	0.35366	0.539000	0.23175	-0.009000	0.14296	0.655000	0.94253	CCT	G|0.979;A|0.021	0.021	strong		0.637	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
KDM1A	23028	hgsc.bcm.edu	37	1	23395037	23395037	+	Silent	SNP	T	T	C	rs145865107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23395037T>C	ENST00000356634.3	+	9	1262	c.1113T>C	c.(1111-1113)ccT>ccC	p.P371P	KDM1A_ENST00000542151.1_Silent_p.P395P|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.P395P	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	371	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|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)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						TTCAGGTTCCTAAAGAGAAAG	0.348													T|||	22	0.00439297	0.0151	0.0029	5008	,	,		18338	0.0		0.0	False		,,,				2504	0.0				p.P395P		Atlas-SNP	.											.	KDM1A	49	.	0			c.T1185C						PASS	.	T	,	41,4365	43.8+/-77.6	0,41,2162	72.0	68.0	69.0		1185,1113	0.5	1.0	1	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KDM1A	NM_001009999.2,NM_015013.3	,	0,42,6461	CC,CT,TT		0.0116,0.9305,0.3229	,	395/877,371/853	23395037	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	23028	exon11			GGTTCCTAAAGAG	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"""Chromatin-modifying enzymes / K-demethylases"""	29079	protein-coding gene	gene with protein product		609132	"""amine oxidase (flavin containing) domain 2"", ""lysine (K)-specific demethylase 1"""	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.1113T>C	1.37:g.23395037T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	130	71	0.546154	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																			T|0.998;C|0.002	0.002	strong		0.348	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013	
CCDC157	550631	hgsc.bcm.edu	37	22	30765502	30765502	+	Silent	SNP	G	G	C	rs5749080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30765502G>C	ENST00000405659.1	+	4	1039	c.330G>C	c.(328-330)gcG>gcC	p.A110A	CCDC157_ENST00000338306.3_Silent_p.A110A			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	110										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CACAGGCTGCGGGGCCCTGCA	0.652													G|||	51	0.0101837	0.0378	0.0014	5008	,	,		17743	0.0		0.0	False		,,,				2504	0.0				p.A110A		Atlas-SNP	.											.	CCDC157	86	.	0			c.G330C						PASS	.						41.0	40.0	41.0					22																	30765502		2203	4300	6503	SO:0001819	synonymous_variant	550631	exon4			GGCTGCGGGGCCC	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.330G>C	22.37:g.30765502G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	69	0.64486	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			A|0.198;C|0.000;G|0.802	0.000	strong		0.652	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
ZDHHC20	253832	hgsc.bcm.edu	37	13	21987823	21987823	+	Missense_Mutation	SNP	G	G	A	rs151151710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:21987823G>A	ENST00000400590.3	-	4	536	c.338C>T	c.(337-339)gCt>gTt	p.A113V	ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.A113V|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.A50V|ZDHHC20_ENST00000422251.1_Missense_Mutation_p.A113V|ZDHHC20_ENST00000320220.9_Missense_Mutation_p.A113V|ZDHHC20_ENST00000415724.1_Missense_Mutation_p.A113V			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	113					protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		GATAGGTAAAGCTCTTGCTGC	0.313													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		14776	0.0		0.0	False		,,,				2504	0.0				p.A113V		Atlas-SNP	.											ZDHHC20_ENST00000382466,NS,carcinoma,0,2	ZDHHC20	36	2	0			c.C338T						PASS	.	G	VAL/ALA	66,3544		0,66,1739	117.0	101.0	106.0		338	3.1	1.0	13	dbSNP_134	106	0,8150		0,0,4075	yes	missense	ZDHHC20	NM_153251.3	64	0,66,5814	AA,AG,GG		0.0,1.8283,0.5612	benign	113/355	21987823	66,11694	1805	4075	5880	SO:0001583	missense	253832	exon4			GGTAAAGCTCTTG	AK090979	CCDS45017.1, CCDS73551.1	13q12.11	2008-10-21			ENSG00000180776	ENSG00000180776		"""Zinc fingers, DHHC-type"""	20749	protein-coding gene	gene with protein product							Standard	NM_153251		Approved	FLJ25952	uc001uoa.2	Q5W0Z9	OTTHUMG00000017410	ENST00000400590.3:c.338C>T	13.37:g.21987823G>A	ENSP00000383433:p.Ala113Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	G	10.49	1.365289	0.24684	0.018283	0.0	ENSG00000180776	ENST00000400590;ENST00000320220;ENST00000382466;ENST00000542645;ENST00000415724;ENST00000422251	T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74	5.59	3.12	0.35913	.	0.330632	0.39834	N	0.001258	T	0.06325	0.0163	N	0.10916	0.065	0.20764	N	0.999855	B;B	0.02656	0.0;0.0	B;B	0.16722	0.016;0.001	T	0.20174	-1.0283	10	0.44086	T	0.13	-10.0193	8.0652	0.30657	0.125:0.0:0.3373:0.5376	.	50;113	B4DRN8;Q5W0Z9-3	.;.	V	113;113;113;50;113;113	ENSP00000383433:A113V;ENSP00000313583:A113V;ENSP00000371905:A113V;ENSP00000443236:A50V;ENSP00000401232:A113V	ENSP00000313583:A113V	A	-	2	0	ZDHHC20	20885823	0.999000	0.42202	0.989000	0.46669	0.681000	0.39784	1.392000	0.34486	0.017000	0.15025	-1.579000	0.00862	GCT	G|0.994;A|0.006	0.006	strong		0.313	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251	
TEP1	7011	hgsc.bcm.edu	37	14	20873695	20873695	+	Missense_Mutation	SNP	A	A	G	rs148090256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20873695A>G	ENST00000262715.5	-	4	825	c.785T>C	c.(784-786)aTg>aCg	p.M262T	TEP1_ENST00000556935.1_Missense_Mutation_p.M262T	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	262	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)		TGTATTGTTCATGTTTACTTC	0.463													A|||	33	0.00658946	0.0234	0.0029	5008	,	,		21319	0.0		0.0	False		,,,				2504	0.0				p.M262T		Atlas-SNP	.											TEP1,caecum,carcinoma,0,1	TEP1	224	1	0			c.T785C						PASS	.	A	THR/MET	82,4324	70.3+/-108.2	0,82,2121	116.0	111.0	113.0		785	-2.0	0.0	14	dbSNP_134	113	0,8600		0,0,4300	yes	missense	TEP1	NM_007110.4	81	0,82,6421	GG,GA,AA		0.0,1.8611,0.6305	benign	262/2628	20873695	82,12924	2203	4300	6503	SO:0001583	missense	7011	exon4			TTGTTCATGTTTA		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.785T>C	14.37:g.20873695A>G	ENSP00000262715:p.Met262Thr	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	A	5.089	0.202155	0.09652	0.018611	0.0	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.14144	2.53;2.53	4.07	-1.99	0.07457	TROVE (2);	2.107970	0.01669	N	0.025498	T	0.05044	0.0135	L	0.29908	0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.32534	-0.9903	10	0.49607	T	0.09	15.064	5.3797	0.16183	0.594:0.1384:0.2676:0.0	.	262;262	G3V5X7;Q99973	.;TEP1_HUMAN	T	262	ENSP00000262715:M262T;ENSP00000452574:M262T	ENSP00000262715:M262T	M	-	2	0	TEP1	19943535	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.762000	0.04745	-0.429000	0.07329	0.533000	0.62120	ATG	A|0.994;G|0.006	0.006	strong		0.463	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
GATB	5188	hgsc.bcm.edu	37	4	152682046	152682046	+	Missense_Mutation	SNP	G	G	T	rs11556167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:152682046G>T	ENST00000515812.1	-	1	105	c.89C>A	c.(88-90)gCt>gAt	p.A30D	PET112_ENST00000508611.1_Missense_Mutation_p.A30D|PET112_ENST00000512306.1_Missense_Mutation_p.A30D|PET112_ENST00000263985.6_Missense_Mutation_p.A30D																breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						CCCAGTCGGAGCCCCTCTTCG	0.617													G|||	642	0.128195	0.2511	0.0807	5008	,	,		14549	0.122		0.1044	False		,,,				2504	0.0266				p.A30D		Atlas-SNP	.											.	PET112	43	.	0			c.C89A						PASS	.	G	ASP/ALA	1022,3384	378.5+/-322.9	130,762,1311	52.0	53.0	53.0		89	2.3	0.0	4	dbSNP_120	53	976,7624	211.3+/-251.9	54,868,3378	yes	missense	PET112	NM_004564.2	126	184,1630,4689	TT,TG,GG		11.3488,23.1956,15.3621	benign	30/558	152682046	1998,11008	2203	4300	6503	SO:0001583	missense	5188	exon1			GTCGGAGCCCCTC																												ENST00000515812.1:c.89C>A	4.37:g.152682046G>T	ENSP00000426859:p.Ala30Asp	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	NM_004564		Missense_Mutation	SNP	ENST00000515812.1	37		260	0.11904761904761904	105	0.21341463414634146	24	0.06629834254143646	51	0.08916083916083917	80	0.10554089709762533	G	12.60	1.986626	0.35036	0.231956	0.113488	ENSG00000059691	ENST00000263985;ENST00000515812;ENST00000512306;ENST00000508611	T;T;T;T	0.46819	0.88;0.88;0.87;0.86	5.23	2.35	0.29111	.	1.047520	0.07465	N	0.901270	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.27498	0.18;0.18	B;B	0.24701	0.055;0.055	T	0.14811	-1.0459	9	0.72032	D	0.01	-20.7822	6.1248	0.20174	0.3201:0.0:0.6799:0.0	rs11556167;rs52817867;rs58478355;rs11556167	30;30	D6RDU9;O75879	.;GATB_HUMAN	D	30	ENSP00000263985:A30D;ENSP00000426859:A30D;ENSP00000420831:A30D;ENSP00000421105:A30D	ENSP00000263985:A30D	A	-	2	0	PET112	152901496	0.002000	0.14202	0.008000	0.14137	0.650000	0.38633	0.241000	0.18065	0.776000	0.33473	0.650000	0.86243	GCT	G|0.857;T|0.143	0.143	strong		0.617	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1		
WDR87	83889	hgsc.bcm.edu	37	19	38377417	38377417	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38377417C>T	ENST00000303868.5	-	6	7001	c.6777G>A	c.(6775-6777)gaG>gaA	p.E2259E	WDR87_ENST00000447313.2_Silent_p.E2298E	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2259	Glu-rich.									NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						ttacctcctcctcctcccttt	0.483																																					p.E2259E		Atlas-SNP	.											.	WDR87	191	.	0			c.G6777A						PASS	.						58.0	46.0	50.0					19																	38377417		692	1591	2283	SO:0001819	synonymous_variant	83889	exon6			CTCCTCCTCCTCC	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.6777G>A	19.37:g.38377417C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	11	0.148649	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			.	.	none		0.483	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
SHROOM3	57619	hgsc.bcm.edu	37	4	77660550	77660550	+	Silent	SNP	T	T	C	rs61745983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77660550T>C	ENST00000296043.6	+	5	2177	c.1224T>C	c.(1222-1224)gaT>gaC	p.D408D		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	408					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)			CTAGCCTTGATCAGAAACGGC	0.577													T|||	94	0.01877	0.0681	0.0058	5008	,	,		19865	0.0		0.0	False		,,,				2504	0.0				p.D408D		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T1224C						PASS	.	T		262,4144	146.1+/-180.8	7,248,1948	45.0	45.0	45.0		1224	-1.7	1.0	4	dbSNP_129	45	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous	SHROOM3	NM_020859.3		7,249,6247	CC,CT,TT		0.0116,5.9464,2.0221		408/1997	77660550	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	57619	exon5			CCTTGATCAGAAA	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.1224T>C	4.37:g.77660550T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	132	58	0.439394	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	CCDS3579.2																																																																																			T|0.978;C|0.022	0.022	strong		0.577	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
APOH	350	hgsc.bcm.edu	37	17	64216815	64216815	+	Missense_Mutation	SNP	C	C	T	rs8178847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:64216815C>T	ENST00000205948.6	-	5	498	c.461G>A	c.(460-462)cGt>cAt	p.R154H		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	154	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.		R -> H (in dbSNP:rs8178847). {ECO:0000269|Ref.8}.		blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			CTTATAAACACGAAGTGTTGC	0.383													c|||	352	0.0702875	0.115	0.0418	5008	,	,		19173	0.0516		0.0696	False		,,,				2504	0.0501				p.R154H	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.G461A						PASS	.	T	HIS/ARG	397,4009	790.4+/-415.0	17,363,1823	116.0	113.0	114.0		461	1.6	0.0	17	dbSNP_117	114	560,8040	794.3+/-407.5	17,526,3757	yes	missense	APOH	NM_000042.2	29	34,889,5580	TT,TC,CC		6.5116,9.0104,7.3581	benign	154/346	64216815	957,12049	2203	4300	6503	SO:0001583	missense	350	exon5			TAAACACGAAGTG		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.461G>A	17.37:g.64216815C>T	ENSP00000205948:p.Arg154His	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	132	49	0.371212	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	167	0.07646520146520147	62	0.12601626016260162	16	0.04419889502762431	35	0.06118881118881119	54	0.0712401055408971	t	3.786	-0.044700	0.07452	0.090104	0.065116	ENSG00000091583	ENST00000205948	T	0.63417	-0.04	5.42	1.59	0.23543	Complement control module (2);Sushi/SCR/CCP (3);	1.273270	0.04813	N	0.435553	T	0.00356	0.0011	N	0.08118	0	0.80722	P	0.0	P	0.40731	0.728	B	0.25884	0.064	T	0.03008	-1.1083	9	0.33141	T	0.24	.	4.8598	0.13577	0.0:0.3473:0.2571:0.3956	rs8178847;rs61420267;rs8178847	154	P02749	APOH_HUMAN	H	154	ENSP00000205948:R154H	ENSP00000205948:R154H	R	-	2	0	APOH	61647277	0.000000	0.05858	0.000000	0.03702	0.150000	0.21749	0.005000	0.13129	0.492000	0.27815	-0.213000	0.12676	CGT	C|0.927;T|0.073	0.073	strong		0.383	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3425731	3425731	+	Missense_Mutation	SNP	G	G	A	rs35775829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:3425731G>A	ENST00000324266.5	+	4	1439	c.1244G>A	c.(1243-1245)gGg>gAg	p.G415E	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.G415E	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	415					vesicle-mediated transport (GO:0016192)												GGCAAGAGCGGGCTGCTCACC	0.587													G|||	30	0.00599042	0.0227	0.0	5008	,	,		18288	0.0		0.0	False		,,,				2504	0.0				p.G415E		Atlas-SNP	.											.	.	.	.	0			c.G1244A						PASS	.	G	GLU/GLY	107,4299	82.4+/-120.9	0,107,2096	32.0	31.0	31.0		1244	4.7	1.0	2	dbSNP_126	31	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TTC15	NM_016030.5	98	0,109,6394	AA,AG,GG		0.0233,2.4285,0.8381	probably-damaging	415/736	3425731	109,12897	2203	4300	6503	SO:0001583	missense	51112	exon4			AGAGCGGGCTGCT	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.1244G>A	2.37:g.3425731G>A	ENSP00000324318:p.Gly415Glu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	176	87	0.494318	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	10|10	0.004578754578754579|0.004578754578754579	10|10	0.02032520325203252|0.02032520325203252	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	28.0|28.0	4.879029|4.879029	0.91740|0.91740	0.024285|0.024285	2.33E-4|2.33E-4	ENSG00000171853|ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266|ENST00000441983	T;T|.	0.53206|.	0.63;0.63|.	4.72|4.72	4.72|4.72	0.59763|0.59763	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.61924|0.61924	0.2386|0.2386	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D;P|.	0.53312|.	0.959;0.93|.	P;P|.	0.52881|.	0.712;0.712|.	T|T	0.68462|0.68462	-0.5402|-0.5402	10|7	0.44086|0.18710	T|T	0.13|0.47	.|.	16.8604|16.8604	0.86016|0.86016	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs35775829|rs35775829	398;415|.	E7ENL7;Q8WVT3|.	.;TPC12_HUMAN|.	E|S	415;398;415|95	ENSP00000371544:G415E;ENSP00000324318:G415E|.	ENSP00000303612:G398E|ENSP00000409960:G95S	G|G	+|+	2|1	0|0	TTC15|TTC15	3404738|3404738	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	7.184000|7.184000	0.77705|0.77705	2.439000|2.439000	0.82584|0.82584	0.563000|0.563000	0.77884|0.77884	GGG|GGC	G|0.992;A|0.008	0.008	strong		0.587	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
LTN1	26046	hgsc.bcm.edu	37	21	30342933	30342933	+	Missense_Mutation	SNP	C	C	A	rs61748614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:30342933C>A	ENST00000361371.5	-	8	1195	c.1116G>T	c.(1114-1116)caG>caT	p.Q372H	LTN1_ENST00000389195.2_Missense_Mutation_p.Q418H|LTN1_ENST00000389194.2_Missense_Mutation_p.Q418H			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	372				Q -> H (in Ref. 5; BAB14589/BAA91976). {ECO:0000305}.	protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						TTGTGATGGACTGAGGGAGCT	0.388													C|||	277	0.0553115	0.0507	0.0432	5008	,	,		16416	0.1597		0.005	False		,,,				2504	0.0143				p.Q418H		Atlas-SNP	.											.	LTN1	141	.	0			c.G1254T						PASS	.	C	HIS/GLN	183,4223	116.7+/-154.6	1,181,2021	106.0	99.0	101.0		1254	3.3	1.0	21	dbSNP_129	101	81,8519	47.2+/-106.3	0,81,4219	yes	missense	LTN1	NM_015565.2	24	1,262,6240	AA,AC,CC		0.9419,4.1534,2.0298	benign	418/1813	30342933	264,12742	2203	4300	6503	SO:0001583	missense	26046	exon8			GATGGACTGAGGG	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1116G>T	21.37:g.30342933C>A	ENSP00000354977:p.Gln372His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		139	0.06364468864468864	18	0.036585365853658534	23	0.06353591160220995	93	0.16258741258741258	5	0.006596306068601583	C	11.22	1.573168	0.28092	0.041534	0.009419	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000446611;ENST00000389195	T;T;T	0.66460	3.47;3.47;-0.21	4.24	3.27	0.37495	Armadillo-type fold (1);	0.372302	0.27139	N	0.020743	T	0.00241	0.0007	L	0.28115	0.83	0.34013	P	0.348322	B	0.06786	0.001	B	0.04013	0.001	T	0.03148	-1.1067	9	0.40728	T	0.16	.	6.8119	0.23809	0.2958:0.5634:0.1407:0.0	.	372	O94822	LTN1_HUMAN	H	418;372;374;418	ENSP00000373846:Q418H;ENSP00000354977:Q372H;ENSP00000373847:Q418H	ENSP00000354977:Q372H	Q	-	3	2	LTN1	29264804	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	1.035000	0.30216	2.353000	0.79882	0.555000	0.69702	CAG	C|0.971;A|0.029	0.029	strong		0.388	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
DNAH10	196385	hgsc.bcm.edu	37	12	124288213	124288213	+	Missense_Mutation	SNP	G	G	A	rs77726895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124288213G>A	ENST00000409039.3	+	16	2291	c.2266G>A	c.(2266-2268)Ggt>Agt	p.G756S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	756	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)		CAAAGGTATCGGTGACTATAT	0.428													G|||	78	0.0155751	0.053	0.0115	5008	,	,		19141	0.0		0.0	False		,,,				2504	0.0				p.G756S		Atlas-SNP	.											.	DNAH10	888	.	0			c.G2266A						PASS	.	G	SER/GLY	261,4143	140.4+/-175.9	8,245,1949	37.0	33.0	35.0		2266	2.9	0.1	12	dbSNP_131	35	14,8584	8.4+/-32.0	0,14,4285	yes	missense	DNAH10	NM_207437.3	56	8,259,6234	AA,AG,GG		0.1628,5.9264,2.1151	benign	756/4472	124288213	275,12727	2202	4299	6501	SO:0001583	missense	196385	exon16			GGTATCGGTGACT	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.2266G>A	12.37:g.124288213G>A	ENSP00000386770:p.Gly756Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	37	23	0.621622	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	G	0.013	-1.611697	0.00835	0.059264	0.001628	ENSG00000197653	ENST00000409039	T	0.53640	0.61	4.78	2.86	0.33363	Dynein heavy chain, domain-1 (1);	0.636305	0.13044	N	0.418306	T	0.01765	0.0056	N	0.01505	-0.83	0.09310	N	1	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.09377	0.004;0.003;0.004	T	0.15925	-1.0420	10	0.08381	T	0.77	.	8.2499	0.31710	0.0747:0.0:0.6468:0.2785	.	756;631;756	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	S	756	ENSP00000386770:G756S	ENSP00000386770:G756S	G	+	1	0	DNAH10	122854166	0.000000	0.05858	0.130000	0.21974	0.029000	0.11900	0.209000	0.17435	0.475000	0.27415	0.650000	0.86243	GGT	G|0.980;A|0.020	0.020	strong		0.428	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
ECM1	1893	hgsc.bcm.edu	37	1	150484004	150484004	+	Silent	SNP	G	G	A	rs11801190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150484004G>A	ENST00000369047.4	+	7	905	c.780G>A	c.(778-780)acG>acA	p.T260T	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Silent_p.T287T|ECM1_ENST00000346569.6_Intron	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	260	2 X approximate repeats.				angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GGTGCTGCACGCGGCAGGGGG	0.632													G|||	498	0.0994409	0.2761	0.0548	5008	,	,		17764	0.001		0.0716	False		,,,				2504	0.0225				p.T287T	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											.	ECM1	96	.	0			c.G861A						PASS	.	G	,,	981,3425	366.4+/-317.8	95,791,1317	57.0	55.0	56.0		861,780,	-1.1	0.0	1	dbSNP_120	56	765,7835	180.9+/-229.7	35,695,3570	no	coding-synonymous,coding-synonymous,intron	ECM1	NM_001202858.1,NM_004425.3,NM_022664.2	,,	130,1486,4887	AA,AG,GG		8.8953,22.2651,13.4246	,,	287/568,260/541,	150484004	1746,11260	2203	4300	6503	SO:0001819	synonymous_variant	1893	exon7			CTGCACGCGGCAG	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.780G>A	1.37:g.150484004G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Silent	SNP	ENST00000369047.4	37	CCDS953.1																																																																																			G|0.878;A|0.122	0.122	strong		0.632	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
GPRC6A	222545	hgsc.bcm.edu	37	6	117114223	117114223	+	Silent	SNP	T	T	A	rs6924002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117114223T>A	ENST00000310357.3	-	6	1884	c.1863A>T	c.(1861-1863)acA>acT	p.T621T	GPRC6A_ENST00000368549.3_Silent_p.T550T|GPRC6A_ENST00000530250.1_Silent_p.T446T	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	621					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TCACAACAGGTGTGTTCAGGT	0.433													T|||	1607	0.320887	0.1989	0.3703	5008	,	,		19816	0.5228		0.3082	False		,,,				2504	0.2556				p.T621T		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A1863T						PASS	.	T		917,3489	352.1+/-311.5	94,729,1380	100.0	97.0	98.0		1863	-2.1	1.0	6	dbSNP_116	98	2837,5763	447.3+/-361.5	458,1921,1921	no	coding-synonymous	GPRC6A	NM_148963.2		552,2650,3301	AA,AT,TT		32.9884,20.8125,28.8636		621/927	117114223	3754,9252	2203	4300	6503	SO:0001819	synonymous_variant	222545	exon6			AACAGGTGTGTTC	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1863A>T	6.37:g.117114223T>A		Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	188	88	0.468085	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			T|0.683;A|0.317	0.317	strong		0.433	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
LZTS1	11178	hgsc.bcm.edu	37	8	20107325	20107325	+	Missense_Mutation	SNP	G	G	C	rs114929298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:20107325G>C	ENST00000381569.1	-	4	2056	c.1699C>G	c.(1699-1701)Ctg>Gtg	p.L567V	LZTS1_ENST00000522290.1_Missense_Mutation_p.L508V|LZTS1_ENST00000265801.6_Missense_Mutation_p.L567V			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	567					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		CCACGTGCCAGCTGCTGCAGG	0.617													g|||	19	0.00379393	0.0144	0.0	5008	,	,		18009	0.0		0.0	False		,,,				2504	0.0				p.L567V		Atlas-SNP	.											.	LZTS1	72	.	0			c.C1699G						PASS	.		VAL/LEU	46,4360	48.2+/-83.0	1,44,2158	86.0	87.0	87.0		1699	4.4	1.0	8	dbSNP_132	87	0,8600		0,0,4300	yes	missense	LZTS1	NM_021020.2	32	1,44,6458	CC,CG,GG		0.0,1.044,0.3537	probably-damaging	567/597	20107325	46,12960	2203	4300	6503	SO:0001583	missense	11178	exon3			GTGCCAGCTGCTG	AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"""F37/Esophageal cancer-related gene-coding leucine-zipper motif"""			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.1699C>G	8.37:g.20107325G>C	ENSP00000370981:p.Leu567Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	121	71	0.586777	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Missense_Mutation	SNP	ENST00000381569.1	37	CCDS6015.1	12	0.005494505494505495	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	g	13.50	2.257140	0.39896	0.01044	0.0	ENSG00000061337	ENST00000381569;ENST00000265801;ENST00000522290;ENST00000360248	T;T;T	0.31769	1.59;1.59;1.48	5.28	4.4	0.53042	.	0.075319	0.53938	D	0.000043	T	0.17408	0.0418	N	0.08118	0	0.58432	D	0.99999	P;D	0.76494	0.884;0.999	B;D	0.66847	0.41;0.947	T	0.08351	-1.0726	10	0.36615	T	0.2	-20.5699	12.9504	0.58397	0.0808:0.0:0.9192:0.0	.	508;567	Q9Y250-4;Q9Y250	.;LZTS1_HUMAN	V	567;567;508;544	ENSP00000370981:L567V;ENSP00000265801:L567V;ENSP00000429263:L508V	ENSP00000265801:L567V	L	-	1	2	LZTS1	20151605	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	3.266000	0.51569	2.454000	0.82982	0.543000	0.68304	CTG	G|0.995;C|0.005	0.005	strong		0.617	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020	
RFPL3	10738	hgsc.bcm.edu	37	22	32756807	32756807	+	Silent	SNP	G	G	C	rs78565810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32756807G>C	ENST00000249007.4	+	2	1147	c.942G>C	c.(940-942)ggG>ggC	p.G314G	RFPL3S_ENST00000382084.4_Silent_p.S48S|RFPL3S_ENST00000400234.1_Silent_p.S77S|RFPL3S_ENST00000461833.1_5'UTR|RFPL3_ENST00000382088.3_Silent_p.G285G|RFPL3_ENST00000397468.1_Silent_p.G285G	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	314							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TCCGTCCTGGGGAGGCCAAAT	0.443													g|||	99	0.0197684	0.0734	0.0029	5008	,	,		15426	0.0		0.0	False		,,,				2504	0.0				p.G314G		Atlas-SNP	.											.	RFPL3	91	.	0			c.G942C						PASS	.	G	,	237,4113		2,233,1940	44.0	48.0	47.0		942,855	-0.6	0.0	22	dbSNP_131	47	0,8528		0,0,4264	no	coding-synonymous,coding-synonymous	RFPL3	NM_001098535.1,NM_006604.2	,	2,233,6204	CC,CG,GG		0.0,5.4483,1.8403	,	314/318,285/289	32756807	237,12641	2175	4264	6439	SO:0001819	synonymous_variant	10738	exon2			TCCTGGGGAGGCC	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.942G>C	22.37:g.32756807G>C		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	216	86	0.398148	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	37	CCDS43011.1																																																																																			G|0.978;C|0.022	0.022	strong		0.443	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
RGS8	85397	hgsc.bcm.edu	37	1	182640848	182640848	+	5'UTR	SNP	G	G	A	rs115960776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182640848G>A	ENST00000483095.2	-	0	98				RGS8_ENST00000367557.4_5'UTR|RGS8_ENST00000367556.1_5'UTR|RGS8_ENST00000258302.4_Silent_p.S8S|RGS8_ENST00000491420.2_5'UTR			P57771	RGS8_HUMAN	regulator of G-protein signaling 8						positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			haematopoietic_and_lymphoid_tissue(1)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	5						GGTCAGAGAGGCTTCGGGTTA	0.502													G|||	104	0.0207668	0.0749	0.0072	5008	,	,		20143	0.0		0.0	False		,,,				2504	0.0				p.S8S	Ovarian(189;1262 3804 41973)	Atlas-SNP	.											.	RGS8	51	.	0			c.C24T						PASS	.	G	,	243,4163	142.3+/-177.5	10,223,1970	173.0	176.0	175.0		,24	4.4	1.0	1	dbSNP_132	175	5,8595	3.7+/-12.6	0,5,4295	no	utr-5,coding-synonymous	RGS8	NM_001102450.1,NM_033345.2	,	10,228,6265	AA,AG,GG		0.0581,5.5152,1.9068	,	,8/199	182640848	248,12758	2203	4300	6503	SO:0001623	5_prime_UTR_variant	85397	exon2			AGAGAGGCTTCGG	AF297015	CCDS1349.1, CCDS41443.1	1q25	2008-07-18	2007-08-14		ENSG00000135824	ENSG00000135824		"""Regulators of G-protein signaling"""	16810	protein-coding gene	gene with protein product		607189	"""regulator of G-protein signalling 8"""			11318611	Standard	NM_001102450		Approved	MGC119067, MGC119068, MGC119069	uc001gpm.1	P57771	OTTHUMG00000035219	ENST00000483095.2:c.-160C>T	1.37:g.182640848G>A		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	215	80	0.372093	NM_033345	B4DGL9|Q3SYD2	Silent	SNP	ENST00000483095.2	37	CCDS41443.1																																																																																			G|0.981;A|0.019	0.019	strong		0.502	RGS8-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358979.1	NM_033345	
HERC6	55008	hgsc.bcm.edu	37	4	89338691	89338691	+	Missense_Mutation	SNP	A	A	G	rs190243300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:89338691A>G	ENST00000264346.7	+	13	1732	c.1673A>G	c.(1672-1674)aAt>aGt	p.N558S	HERC6_ENST00000380265.5_Missense_Mutation_p.N558S	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	558					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)		GATCACTGTAATGTTAAAGCT	0.373													A|||	17	0.00339457	0.0083	0.0043	5008	,	,		17266	0.0		0.003	False		,,,				2504	0.0				p.N558S		Atlas-SNP	.											.	HERC6	104	.	0			c.A1673G						PASS	.	A	SER/ASN,SER/ASN	17,3737		0,17,1860	65.0	61.0	62.0		1673,1673	0.7	0.0	4		62	5,8207		0,5,4101	yes	missense,missense	HERC6	NM_001165136.1,NM_017912.3	46,46	0,22,5961	GG,GA,AA		0.0609,0.4529,0.1839	benign,benign	558/987,558/1023	89338691	22,11944	1877	4106	5983	SO:0001583	missense	55008	exon13			ACTGTAATGTTAA	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.1673A>G	4.37:g.89338691A>G	ENSP00000264346:p.Asn558Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Missense_Mutation	SNP	ENST00000264346.7	37	CCDS47098.1	5	0.0022893772893772895	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	6.688	0.495465	0.12762	0.004529	6.09E-4	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.38240	1.15;1.17	4.79	0.721	0.18219	.	0.377680	0.25885	N	0.027670	T	0.12220	0.0297	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.20052	0.041;0.024	B;B	0.14578	0.011;0.005	T	0.18999	-1.0319	10	0.14252	T	0.57	.	6.1186	0.20139	0.6064:0.3068:0.0867:0.0	.	558;558	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	S	558	ENSP00000369617:N558S;ENSP00000264346:N558S	ENSP00000264346:N558S	N	+	2	0	HERC6	89557714	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	0.982000	0.29539	0.414000	0.25790	-0.438000	0.05819	AAT	A|0.998;G|0.002	0.002	strong		0.373	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2		
SERPINB3	6317	hgsc.bcm.edu	37	18	61323228	61323228	+	Missense_Mutation	SNP	C	C	G	rs61748838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323228C>G	ENST00000283752.5	-	8	979	c.836G>C	c.(835-837)cGt>cCt	p.R279P	SERPINB3_ENST00000332821.8_Missense_Mutation_p.R227P|SERPINB11_ENST00000489748.1_RNA	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	279					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TAAATCGACACGTGTCTCTCT	0.413													c|||	286	0.0571086	0.205	0.0144	5008	,	,		20730	0.0		0.004	False		,,,				2504	0.001				p.R279P		Atlas-SNP	.											SERPINB3,caecum,carcinoma,0,1	SERPINB3	90	1	0			c.G836C						PASS	.	G	PRO/ARG	699,3707	292.4+/-282.0	53,593,1557	149.0	127.0	135.0		836	-0.9	0.0	18	dbSNP_129	135	15,8585	9.8+/-36.6	0,15,4285	no	missense	SERPINB3	NM_006919.2	103	53,608,5842	GG,GC,CC		0.1744,15.8647,5.4898	benign	279/391	61323228	714,12292	2203	4300	6503	SO:0001583	missense	6317	exon8			TCGACACGTGTCT	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.836G>C	18.37:g.61323228C>G	ENSP00000283752:p.Arg279Pro	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	230	121	0.526087	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	100	0.045787545787545784	92	0.18699186991869918	6	0.016574585635359115	0	0.0	2	0.002638522427440633	c	9.127	1.010414	0.19277	0.158647	0.001744	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.84944	-1.92;-1.92	3.07	-0.89	0.10577	Serpin domain (3);	4.332970	0.00769	N	0.001198	T	0.00300	0.0009	N	0.16368	0.405	0.80722	P	0.0	B;B	0.20164	0.042;0.0	B;B	0.33454	0.164;0.007	T	0.36529	-0.9744	9	0.66056	D	0.02	.	0.3718	0.00381	0.2731:0.1823:0.1396:0.405	rs61748838	227;279	P29508-2;P29508	.;SPB3_HUMAN	P	279;227	ENSP00000283752:R279P;ENSP00000329498:R227P	ENSP00000283752:R279P	R	-	2	0	SERPINB3	59474208	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.785000	0.04628	-0.480000	0.06803	-2.438000	0.00212	CGT	C|0.940;G|0.060	0.060	strong		0.413	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
BRD3	8019	hgsc.bcm.edu	37	9	136913355	136913355	+	Silent	SNP	T	T	C	rs464826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136913355T>C	ENST00000303407.7	-	6	1121	c.936A>G	c.(934-936)ctA>ctG	p.L312L	BRD3_ENST00000357885.2_Silent_p.L312L|BRD3_ENST00000371834.2_Silent_p.L312L	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3	312					chromatin modification (GO:0016568)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)		BRD3/C15orf55(3)	kidney(1)|skin(1)|stomach(4)	6				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)		CGCAGTAGCGTAGGTGCTCCG	0.647			T	C15orf55	lethal midline carcinoma of young people								C|||	3631	0.72504	0.8691	0.5418	5008	,	,		16109	0.6845		0.6759	False		,,,				2504	0.7526				p.L312L		Atlas-SNP	.		Dom	yes		9	9q34	8019	bromodomain containing 3		E	.	BRD3	82	.	0			c.A936G						PASS	.	C		3601,803	316.1+/-294.4	1471,659,72	81.0	60.0	67.0		936	3.9	1.0	9	dbSNP_80	67	5602,2998	460.7+/-365.2	1833,1936,531	no	coding-synonymous	BRD3	NM_007371.3		3304,2595,603	CC,CT,TT		34.8605,18.2334,29.2295		312/727	136913355	9203,3801	2202	4300	6502	SO:0001819	synonymous_variant	8019	exon6			GTAGCGTAGGTGC		CCDS6980.1	9q34	2010-12-23	2002-01-14		ENSG00000169925	ENSG00000169925			1104	protein-coding gene	gene with protein product	"""RING3-like"""	601541	"""bromodomain-containing 3"""			7584044, 8781126	Standard	NM_007371		Approved	RING3L, ORFX, KIAA0043	uc004cew.3	Q15059	OTTHUMG00000021004	ENST00000303407.7:c.936A>G	9.37:g.136913355T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_007371	B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645	Silent	SNP	ENST00000303407.7	37	CCDS6980.1																																																																																			T|0.288;C|0.712	0.712	strong		0.647	BRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055390.4	NM_007371	
UGGT1	56886	hgsc.bcm.edu	37	2	128870784	128870784	+	Silent	SNP	A	A	G	rs149605444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128870784A>G	ENST00000259253.6	+	6	695	c.648A>G	c.(646-648)tcA>tcG	p.S216S	UGGT1_ENST00000375990.3_Silent_p.S192S	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	216					'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						AGCTTATATCAAAAAGCAATG	0.353													A|||	25	0.00499201	0.0189	0.0	5008	,	,		15033	0.0		0.0	False		,,,				2504	0.0				p.S216S		Atlas-SNP	.											.	UGGT1	126	.	0			c.A648G						PASS	.	A		64,4342	58.1+/-94.6	1,62,2140	71.0	74.0	73.0		648	-1.1	0.1	2	dbSNP_134	73	0,8598		0,0,4299	no	coding-synonymous	UGGT1	NM_020120.3		1,62,6439	GG,GA,AA		0.0,1.4526,0.4922		216/1556	128870784	64,12940	2203	4299	6502	SO:0001819	synonymous_variant	56886	exon6			TATATCAAAAAGC	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.648A>G	2.37:g.128870784A>G		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	290	132	0.455172	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																			A|0.995;G|0.005	0.005	strong		0.353	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
AGL	178	hgsc.bcm.edu	37	1	100353654	100353654	+	Silent	SNP	A	A	C	rs34230588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100353654A>C	ENST00000294724.4	+	21	3280	c.2802A>C	c.(2800-2802)gcA>gcC	p.A934A	AGL_ENST00000361915.3_Silent_p.A934A|AGL_ENST00000361522.4_Silent_p.A917A|AGL_ENST00000370161.2_Silent_p.A918A|AGL_ENST00000370165.3_Silent_p.A934A|AGL_ENST00000370163.3_Silent_p.A934A|AGL_ENST00000361302.3_Silent_p.A918A	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	934					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TTAAATATGCAGGTCTTCAAG	0.418													A|||	27	0.00539137	0.0204	0.0	5008	,	,		17736	0.0		0.0	False		,,,				2504	0.0				p.A934A		Atlas-SNP	.											.	AGL	137	.	0			c.A2802C						PASS	.	A	,,,,,	97,4309	78.8+/-117.2	1,95,2107	121.0	115.0	117.0		2802,2802,2802,2802,2751,2754	1.8	1.0	1	dbSNP_126	117	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000645.2,NM_000646.2	,,,,,	1,95,6407	CC,CA,AA		0.0,2.2015,0.7458	,,,,,	934/1533,934/1533,934/1533,934/1533,917/1516,918/1517	100353654	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	178	exon21			ATATGCAGGTCTT	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.2802A>C	1.37:g.100353654A>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	37	CCDS759.1																																																																																			A|0.994;C|0.006	0.006	strong		0.418	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
LAIR2	3904	hgsc.bcm.edu	37	19	55019379	55019379	+	Missense_Mutation	SNP	T	T	A	rs34429135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55019379T>A	ENST00000301202.2	+	3	466	c.344T>A	c.(343-345)tTc>tAc	p.F115Y	LAIR2_ENST00000351841.2_Missense_Mutation_p.F115Y	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	115	Ig-like C2-type.		F -> Y (in dbSNP:rs34429135).			extracellular region (GO:0005576)				central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		CACAGTGACTTCCTGGAGCTG	0.577													T|||	284	0.0567093	0.2005	0.0245	5008	,	,		17434	0.0		0.002	False		,,,				2504	0.0				p.F115Y		Atlas-SNP	.											.	LAIR2	30	.	0			c.T344A						PASS	.	T	TYR/PHE,TYR/PHE	773,3633	307.7+/-290.2	60,653,1490	89.0	92.0	91.0		344,344	-7.6	0.0	19	dbSNP_126	91	14,8586	8.4+/-32.0	0,14,4286	yes	missense,missense	LAIR2	NM_002288.4,NM_021270.3	22,22	60,667,5776	AA,AT,TT		0.1628,17.5443,6.0511	benign,benign	115/153,115/136	55019379	787,12219	2203	4300	6503	SO:0001583	missense	3904	exon3			GTGACTTCCTGGA	AF013250	CCDS12897.1, CCDS12898.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167618	ENSG00000167618		"""Leukocyte-associated Ig like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6478	protein-coding gene	gene with protein product		602993	"""leukocyte-associated Ig-like receptor 2"""			9285412	Standard	XM_005277264		Approved	CD306	uc002qgc.3	Q6ISS4	OTTHUMG00000065697	ENST00000301202.2:c.344T>A	19.37:g.55019379T>A	ENSP00000301202:p.Phe115Tyr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	127	55	0.433071	NM_002288	Q6PEZ4	Missense_Mutation	SNP	ENST00000301202.2	37	CCDS12897.1	99	0.04532967032967033	87	0.17682926829268292	10	0.027624309392265192	0	0.0	2	0.002638522427440633	T	0.013	-1.619502	0.00828	0.175443	0.001628	ENSG00000167618	ENST00000301202;ENST00000351841	T;T	0.11277	2.79;2.79	3.77	-7.55	0.01327	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	8.928910	0.00166	N	0.000000	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.35822	-0.9773	8	.	.	.	.	0.0766	0.00027	0.2872:0.2456:0.1969:0.2703	rs34429135	115;115	Q6ISS4-2;Q6ISS4	.;LAIR2_HUMAN	Y	115	ENSP00000301202:F115Y;ENSP00000301203:F115Y	.	F	+	2	0	LAIR2	59711191	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.540000	0.00218	-3.651000	0.00126	-0.907000	0.02831	TTC	T|0.943;A|0.057	0.057	strong		0.577	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1		
ARSH	347527	hgsc.bcm.edu	37	X	2933057	2933057	+	Silent	SNP	T	T	C	rs143359225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:2933057T>C	ENST00000381130.2	+	4	387	c.387T>C	c.(385-387)tgT>tgC	p.C129C		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	129					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)				ATGATCACTGTTACCACCCGC	0.507													C|||	122	0.0323179	0.0877	0.0086	3775	,	,		15128	0.0		0.0	False		,,,				2504	0.0				p.C129C		Atlas-SNP	.											.	ARSH	72	.	0			c.T387C						PASS	.	C		491,3344		32,349,78,1251,493	102.0	88.0	93.0		387	2.8	0.9	X	dbSNP_134	93	6,6722		0,4,2,2424,1870	no	coding-synonymous	ARSH	NM_001011719.1		32,353,80,3675,2363	CC,CT,C,TT,T		0.0892,12.8031,4.7051		129/563	2933057	497,10066	2203	4300	6503	SO:0001819	synonymous_variant	347527	exon4			TCACTGTTACCAC	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.387T>C	X.37:g.2933057T>C		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	227	115	0.506608	NM_001011719		Silent	SNP	ENST00000381130.2	37	CCDS35198.1																																																																																			T|0.952;C|0.048	0.048	strong		0.507	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
PLXND1	23129	hgsc.bcm.edu	37	3	129275206	129275206	+	Silent	SNP	C	C	T	rs11920311	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129275206C>T	ENST00000324093.4	-	36	5905	c.5727G>A	c.(5725-5727)caG>caA	p.Q1909Q	PLXND1_ENST00000393239.1_3'UTR|PLXND1_ENST00000504689.1_Intron	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1909					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						AAGCCACCACCTGCTCAAACT	0.617													T|||	1165	0.232628	0.3306	0.2046	5008	,	,		19032	0.2103		0.1402	False		,,,				2504	0.2382				p.Q1909Q	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.G5727A						PASS	.	T		1236,3170	705.9+/-407.3	162,912,1129	206.0	184.0	192.0		5727	2.8	1.0	3	dbSNP_120	192	1147,7453	766.4+/-407.6	67,1013,3220	no	coding-synonymous	PLXND1	NM_015103.2		229,1925,4349	TT,TC,CC		13.3372,28.0527,18.3223		1909/1926	129275206	2383,10623	2203	4300	6503	SO:0001819	synonymous_variant	23129	exon36			CACCACCTGCTCA	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.5727G>A	3.37:g.129275206C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	201	106	0.527363	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			C|0.790;T|0.210	0.210	strong		0.617	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
PRKAR2B	5577	hgsc.bcm.edu	37	7	106791447	106791447	+	Silent	SNP	G	G	A	rs3729878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:106791447G>A	ENST00000265717.4	+	7	1081	c.822G>A	c.(820-822)ctG>ctA	p.L274L		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	274					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TTGAGTCACTGCCATTCCTTA	0.303													G|||	196	0.0391374	0.1422	0.0115	5008	,	,		14361	0.0		0.0	False		,,,				2504	0.0				p.L274L		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.G822A						PASS	.	G		532,3874	238.4+/-249.8	30,472,1701	72.0	74.0	73.0		822	4.6	1.0	7	dbSNP_107	73	9,8587	7.1+/-27.0	0,9,4289	no	coding-synonymous	PRKAR2B	NM_002736.2		30,481,5990	AA,AG,GG		0.1047,12.0744,4.1609		274/419	106791447	541,12461	2203	4298	6501	SO:0001819	synonymous_variant	5577	exon7			GTCACTGCCATTC		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.822G>A	7.37:g.106791447G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	209	95	0.454545	NM_002736	A4D0R9	Silent	SNP	ENST00000265717.4	37	CCDS5740.1																																																																																			G|0.953;A|0.047	0.047	strong		0.303	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
KCNH3	23416	hgsc.bcm.edu	37	12	49951377	49951377	+	Missense_Mutation	SNP	C	C	T	rs59261129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49951377C>T	ENST00000257981.6	+	15	3153	c.2893C>T	c.(2893-2895)Cgt>Tgt	p.R965C	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	965	Pro-rich.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						GCCCCACCCTCGTCCGGGGCC	0.682													C|||	367	0.0732827	0.149	0.0533	5008	,	,		16519	0.0238		0.0686	False		,,,				2504	0.0409				p.R965C		Atlas-SNP	.											.	KCNH3	88	.	0			c.C2893T						PASS	.	C	CYS/ARG	558,3848	250.0+/-257.2	37,484,1682	48.0	48.0	48.0		2893	5.1	0.9	12	dbSNP_129	48	615,7985	158.8+/-212.2	21,573,3706	yes	missense	KCNH3	NM_012284.1	180	58,1057,5388	TT,TC,CC		7.1512,12.6645,9.0189	probably-damaging	965/1084	49951377	1173,11833	2203	4300	6503	SO:0001583	missense	23416	exon15			CACCCTCGTCCGG	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.2893C>T	12.37:g.49951377C>T	ENSP00000257981:p.Arg965Cys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_012284	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	37	CCDS8786.1	156	0.07142857142857142	73	0.1483739837398374	25	0.06906077348066299	7	0.012237762237762238	51	0.06728232189973615	C	14.56	2.571254	0.45798	0.126645	0.071512	ENSG00000135519	ENST00000257981	D	0.98978	-5.29	5.09	5.09	0.68999	.	0.174710	0.28082	N	0.016664	T	0.09730	0.0239	N	0.08118	0	0.09310	P	1.0	D	0.56968	0.978	B	0.30782	0.12	T	0.70494	-0.4856	9	0.36615	T	0.2	.	13.8582	0.63542	0.0:1.0:0.0:0.0	rs59261129;rs61745869	965	Q9ULD8	KCNH3_HUMAN	C	965	ENSP00000257981:R965C	ENSP00000257981:R965C	R	+	1	0	KCNH3	48237644	0.668000	0.27493	0.935000	0.37517	0.960000	0.62799	1.494000	0.35616	2.650000	0.89964	0.561000	0.74099	CGT	C|0.914;T|0.086	0.086	strong		0.682	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45503121	45503121	+	Missense_Mutation	SNP	G	G	A	rs2071152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45503121G>A	ENST00000291574.4	+	14	2351	c.2176G>A	c.(2176-2178)Gtg>Atg	p.V726M		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	726			V -> M (common polymorphism; dbSNP:rs2071152). {ECO:0000269|PubMed:9370297}.		sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						GGGTGCCCACGTGCTGAGGTG	0.562													G|||	1974	0.394169	0.6664	0.3012	5008	,	,		19366	0.2976		0.1541	False		,,,				2504	0.4387				p.V726M		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.G2176A						PASS	.	G	MET/VAL	2696,1710	643.0+/-397.8	836,1024,343	102.0	99.0	100.0		2176	-1.1	0.0	21	dbSNP_96	100	1395,7205	264.6+/-285.7	140,1115,3045	yes	missense	TRAPPC10	NM_003274.4	21	976,2139,3388	AA,AG,GG		16.2209,38.8107,31.4547	benign	726/1260	45503121	4091,8915	2203	4300	6503	SO:0001583	missense	7109	exon14			GCCCACGTGCTGA	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.2176G>A	21.37:g.45503121G>A	ENSP00000291574:p.Val726Met	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	71	28	0.394366	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	37	CCDS13704.1	696	0.31868131868131866	313	0.6361788617886179	95	0.26243093922651933	169	0.29545454545454547	119	0.15699208443271767	G	4.979	0.181776	0.09495	0.611893	0.162209	ENSG00000160218	ENST00000291574	T	0.23348	1.91	5.73	-1.09	0.09904	.	0.504277	0.23874	N	0.043713	T	0.00012	0.0000	N	0.11560	0.145	0.45634	P	0.00143099999999996	B;B	0.17852	0.024;0.011	B;B	0.13407	0.009;0.003	T	0.35126	-0.9801	9	0.39692	T	0.17	.	6.6404	0.22906	0.3741:0.2141:0.4119:0.0	rs2071152;rs58410301;rs2071152	26;726	B4DI17;P48553	.;TPC10_HUMAN	M	726	ENSP00000291574:V726M	ENSP00000291574:V726M	V	+	1	0	TRAPPC10	44327549	0.951000	0.32395	0.013000	0.15412	0.003000	0.03518	1.941000	0.40233	-0.108000	0.12066	-0.773000	0.03387	GTG	G|0.661;A|0.339	0.339	strong		0.562	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
DRC7	84229	hgsc.bcm.edu	37	16	57758732	57758732	+	Missense_Mutation	SNP	C	C	A	rs2923144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57758732C>A	ENST00000360716.3	+	13	1964	c.1743C>A	c.(1741-1743)aaC>aaA	p.N581K	CCDC135_ENST00000336825.8_Missense_Mutation_p.N516K|CCDC135_ENST00000394337.4_Missense_Mutation_p.N581K			Q8IY82	CC135_HUMAN		581			N -> K (in dbSNP:rs2923144).		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						CAGAGTCAAACCCCCGGCCCA	0.602													.|||	450	0.0898562	0.1815	0.0634	5008	,	,		18037	0.001		0.1004	False		,,,				2504	0.0654				p.N581K		Atlas-SNP	.											.	CCDC135	97	.	0			c.C1743A						PASS	.	C	LYS/ASN	725,3669		62,601,1534	47.0	41.0	43.0		1743	-0.1	0.9	16	dbSNP_101	43	842,7756		36,770,3493	yes	missense	CCDC135	NM_032269.5	94	98,1371,5027	AA,AC,CC		9.793,16.4998,12.0613	probably-damaging	581/875	57758732	1567,11425	2197	4299	6496	SO:0001583	missense	84229	exon12			GTCAAACCCCCGG																												ENST00000360716.3:c.1743C>A	16.37:g.57758732C>A	ENSP00000353942:p.Asn581Lys	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	173	0.07921245421245421	73	0.1483739837398374	26	0.0718232044198895	1	0.0017482517482517483	73	0.09630606860158311	.	16.68	3.189813	0.57909	0.164998	0.09793	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.09445	3.14;2.98;3.14	5.2	-0.106	0.13596	.	0.296489	0.37715	N	0.001979	T	0.00109	0.0003	M	0.80183	2.485	0.24037	P	0.9960909	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.977	T	0.12167	-1.0558	9	0.18276	T	0.48	-47.579	9.4754	0.38869	0.0:0.6228:0.0:0.3772	rs2923144;rs52829900;rs59847143;rs2923144	516;581	Q8IY82-2;Q8IY82	.;CC135_HUMAN	K	581;516;581	ENSP00000377869:N581K;ENSP00000338938:N516K;ENSP00000353942:N581K	ENSP00000338938:N516K	N	+	3	2	CCDC135	56316233	0.251000	0.23961	0.949000	0.38748	0.883000	0.51084	-0.202000	0.09451	0.222000	0.20900	-0.218000	0.12543	AAC	C|0.891;A|0.109	0.109	strong		0.602	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
CDKN1B	1027	hgsc.bcm.edu	37	12	12871099	12871099	+	Missense_Mutation	SNP	T	T	G	rs2066827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:12871099T>G	ENST00000228872.4	+	1	1042	c.326T>G	c.(325-327)gTc>gGc	p.V109G	CDKN1B_ENST00000396340.1_Missense_Mutation_p.V109G|CDKN1B_ENST00000477087.1_Intron	NM_004064.3	NP_004055.1	P46527	CDN1B_HUMAN	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	109			V -> G (in dbSNP:rs2066827). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|cellular response to antibiotic (GO:0071236)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|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)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|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 cellular component movement (GO:0051271)|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 kinase activity (GO:0033673)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|potassium ion transport (GO:0006813)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein phosphatase binding (GO:0019903)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)			breast(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(5)	13		Prostate(47;0.0322)|all_epithelial(100;0.159)		BRCA - Breast invasive adenocarcinoma(232;0.0336)		AGCCAGGATGTCAGCGGGAGC	0.647													T|||	1799	0.359225	0.7837	0.2176	5008	,	,		14039	0.0556		0.2425	False		,,,				2504	0.319				p.V109G		Atlas-SNP	.											.	CDKN1B	48	.	0			c.T326G	GRCh37	CM033961	CDKN1B	M	rs2066827	PASS	.	T	GLY/VAL	3047,1349		1088,871,239	24.0	33.0	30.0		326	-0.9	1.0	12	dbSNP_94	30	2044,6552		249,1546,2503	no	missense	CDKN1B	NM_004064.3	109	1337,2417,2742	GG,GT,TT		23.7785,30.687,39.1857	benign	109/199	12871099	5091,7901	2198	4298	6496	SO:0001583	missense	1027	exon1			AGGATGTCAGCGG	AF480891	CCDS8653.1	12p13.1-p12	2008-08-04			ENSG00000111276	ENSG00000111276			1785	protein-coding gene	gene with protein product		600778				8033212	Standard	NM_004064		Approved	KIP1, P27KIP1	uc001rat.2	P46527	OTTHUMG00000149914	ENST00000228872.4:c.326T>G	12.37:g.12871099T>G	ENSP00000228872:p.Val109Gly	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_004064	Q16307|Q5U0H2|Q9BUS6	Missense_Mutation	SNP	ENST00000228872.4	37	CCDS8653.1	646	0.2957875457875458	363	0.7378048780487805	83	0.2292817679558011	23	0.04020979020979021	177	0.23350923482849603	T	12.59	1.983905	0.35036	0.69313	0.237785	ENSG00000111276	ENST00000228872;ENST00000535674;ENST00000396340	T;T	0.59364	0.27;0.27	5.51	-0.898	0.10550	.	0.693430	0.13648	N	0.372461	T	0.00012	0.0000	L	0.43152	1.355	0.23559	P	0.9974102	B	0.20671	0.047	B	0.16722	0.016	T	0.40664	-0.9551	9	0.25751	T	0.34	-18.8666	10.916	0.47137	0.0:0.4189:0.0:0.5811	rs2066827;rs17758691;rs17844936;rs17857669;rs56657003;rs2066827	109	P46527	CDN1B_HUMAN	G	109;58;109	ENSP00000228872:V109G;ENSP00000379629:V109G	ENSP00000228872:V109G	V	+	2	0	CDKN1B	12762366	0.999000	0.42202	0.977000	0.42913	0.946000	0.59487	1.199000	0.32235	-0.156000	0.11079	0.528000	0.53228	GTC	T|0.661;G|0.339	0.339	strong		0.647	CDKN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313878.2	NM_004064	
CDH23	64072	hgsc.bcm.edu	37	10	73550969	73550969	+	Missense_Mutation	SNP	G	G	A	rs10466026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73550969G>A	ENST00000224721.6	+	46	6150	c.6145G>A	c.(6145-6147)Gag>Aag	p.E2049K		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2044	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.E2049K(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GCTGCTGGCTGAGGACATCGG	0.627													G|||	1666	0.332668	0.261	0.3473	5008	,	,		20132	0.5288		0.2763	False		,,,				2504	0.2751				p.E2044K		Atlas-SNP	.											CDH23,colon,carcinoma,0,2	CDH23	365	2	1	Substitution - Missense(1)	stomach(1)	c.G6130A						scavenged	.	G	LYS/GLU	1189,3207		151,887,1160	51.0	58.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6130	5.9	1.0	10	dbSNP_119	55	2258,6330		313,1632,2349	yes	missense	CDH23	NM_022124.5	56	464,2519,3509	AA,AG,GG		26.2925,27.0473,26.5481	possibly-damaging	2044/3355	73550969	3447,9537	2198	4294	6492	SO:0001583	missense	64072	exon45			CTGGCTGAGGACA	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.6145G>A	10.37:g.73550969G>A	ENSP00000224721:p.Glu2049Lys	Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		760	0.34798534798534797	145	0.29471544715447157	108	0.2983425414364641	299	0.5227272727272727	208	0.27440633245382584	G	21.3	4.130608	0.77549	0.270473	0.262925	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	5.91	5.91	0.95273	Cadherin (3);Cadherin-like (1);	0.213542	0.38605	N	0.001630	T	0.00012	0.0000	N	0.02142	-0.665	0.09310	P	1.0	P	0.38535	0.635	B	0.40134	0.32	T	0.18840	-1.0324	8	0.08179	T	0.78	.	11.4841	0.50344	0.0683:0.1272:0.8045:0.0	rs10466026;rs58573365;rs10466026	2044	Q9H251	CAD23_HUMAN	K	2049;2044;2047	.	ENSP00000224721:E2049K	E	+	1	0	CDH23	73220975	0.996000	0.38824	1.000000	0.80357	0.837000	0.47467	2.222000	0.42926	2.793000	0.96121	0.655000	0.94253	GAG	G|0.661;A|0.339	0.339	strong		0.627	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
MESP2	145873	hgsc.bcm.edu	37	15	90320146	90320146	+	Silent	SNP	G	G	A	rs56192595|rs199821487|rs28546919		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90320146G>A	ENST00000341735.3	+	1	558	c.558G>A	c.(556-558)caG>caA	p.Q186Q	MESP2_ENST00000560219.1_Intron|MESP2_ENST00000558723.1_Intron	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	186	13 X 2 AA tandem repeats of G-Q.				mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|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)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			ggcaggggcaggggcaggggc	0.781																																					p.Q186Q		Atlas-SNP	.											.	MESP2	20	.	0			c.G558A						PASS	.						2.0	2.0	2.0					15																	90320146		1056	2363	3419	SO:0001819	synonymous_variant	145873	exon1			GGGGCAGGGGCAG		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"""Basic helix-loop-helix proteins"""	29659	protein-coding gene	gene with protein product		605195	"""mesoderm posterior 2 homolog (mouse)"""			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.558G>A	15.37:g.90320146G>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_001039958	Q7RTU2	Silent	SNP	ENST00000341735.3	37	CCDS42078.1																																																																																			A|1.000;|0.000	1.000	weak		0.781	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261	
SLC4A7	9497	hgsc.bcm.edu	37	3	27473066	27473066	+	Silent	SNP	A	A	G	rs13077400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:27473066A>G	ENST00000295736.5	-	7	916	c.846T>C	c.(844-846)ctT>ctC	p.L282L	SLC4A7_ENST00000455077.1_Intron|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000437179.1_Intron|SLC4A7_ENST00000440156.1_Silent_p.L278L|SLC4A7_ENST00000446700.1_Silent_p.L274L|SLC4A7_ENST00000428386.1_Intron|SLC4A7_ENST00000425128.2_Silent_p.L274L|SLC4A7_ENST00000435667.2_Intron|SLC4A7_ENST00000445684.1_Silent_p.L278L|SLC4A7_ENST00000454389.1_Silent_p.L291L	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	282					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	GAAGATGACCAAGAAGAAGAG	0.522													G|||	823	0.164337	0.1702	0.1772	5008	,	,		17626	0.0575		0.2276	False		,,,				2504	0.1922				p.L282L		Atlas-SNP	.											.	SLC4A7	119	.	0			c.T846C						PASS	.	G		833,3573	747.4+/-411.8	77,679,1447	89.0	97.0	94.0		846	6.0	1.0	3	dbSNP_121	94	2165,6435	713.6+/-406.0	271,1623,2406	no	coding-synonymous	SLC4A7	NM_003615.3		348,2302,3853	GG,GA,AA		25.1744,18.906,23.0509		282/1215	27473066	2998,10008	2203	4300	6503	SO:0001819	synonymous_variant	9497	exon7			ATGACCAAGAAGA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.846T>C	3.37:g.27473066A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	136	67	0.492647	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			A|0.800;G|0.200	0.200	strong		0.522	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
GPCPD1	56261	hgsc.bcm.edu	37	20	5556512	5556512	+	Missense_Mutation	SNP	G	G	A	rs2273373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5556512G>A	ENST00000379019.4	-	9	1030	c.818C>T	c.(817-819)aCt>aTt	p.T273I	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	273			T -> I (in dbSNP:rs2273373).		glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						GATGGGAAGAGTAAGAATTCC	0.443													G|||	531	0.10603	0.2322	0.0648	5008	,	,		14547	0.1022		0.0318	False		,,,				2504	0.045				p.T273I		Atlas-SNP	.											GPCPD1,NS,carcinoma,+1,1	GPCPD1	52	1	0			c.C818T						PASS	.	G	ILE/THR	925,3481	355.4+/-313.0	93,739,1371	115.0	104.0	107.0		818	5.6	1.0	20	dbSNP_100	107	379,8221	122.9+/-181.8	16,347,3937	no	missense	GPCPD1	NM_019593.3	89	109,1086,5308	AA,AG,GG		4.407,20.9941,10.0261	possibly-damaging	273/673	5556512	1304,11702	2203	4300	6503	SO:0001583	missense	56261	exon9			GGAAGAGTAAGAA		CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.818C>T	20.37:g.5556512G>A	ENSP00000368305:p.Thr273Ile	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	325	147	0.452308	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Missense_Mutation	SNP	ENST00000379019.4	37	CCDS13090.1	239	0.10943223443223443	128	0.2601626016260163	21	0.058011049723756904	64	0.11188811188811189	26	0.03430079155672823	G	22.0	4.234783	0.79800	0.209941	0.04407	ENSG00000125772	ENST00000379019	T	0.51325	0.71	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.32530	0.975	0.09310	P	0.999999629175	D	0.89917	1.0	D	0.69307	0.963	T	0.00970	-1.1496	9	0.37606	T	0.19	-17.0643	19.6443	0.95770	0.0:0.0:1.0:0.0	rs2273373	273	Q9NPB8	GPCP1_HUMAN	I	273	ENSP00000368305:T273I	ENSP00000368305:T273I	T	-	2	0	GPCPD1	5504512	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.855000	0.86950	2.634000	0.89283	0.655000	0.94253	ACT	G|0.899;A|0.101	0.101	strong		0.443	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593	
FAM135A	57579	hgsc.bcm.edu	37	6	71234960	71234960	+	Missense_Mutation	SNP	A	A	G	rs9455142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71234960A>G	ENST00000418814.2	+	15	2787	c.2173A>G	c.(2173-2175)Att>Gtt	p.I725V	FAM135A_ENST00000457062.2_Missense_Mutation_p.I512V|FAM135A_ENST00000361499.3_Missense_Mutation_p.I529V|FAM135A_ENST00000370479.3_Missense_Mutation_p.I512V|FAM135A_ENST00000505769.1_Intron|FAM135A_ENST00000505868.1_Missense_Mutation_p.I725V	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	725			I -> V (in dbSNP:rs9455142).							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						GTGTCTTTCTATTGGAGAATC	0.313													A|||	102	0.0203674	0.0726	0.0058	5008	,	,		20204	0.0		0.002	False		,,,				2504	0.0				p.I725V		Atlas-SNP	.											.	FAM135A	181	.	0			c.A2173G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	299,4105	154.8+/-188.1	6,287,1909	47.0	52.0	51.0		1585,2173,1534	-12.1	0.0	6	dbSNP_119	51	4,8590	3.0+/-9.4	0,4,4293	yes	missense,missense,missense	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	29,29,29	6,291,6202	GG,GA,AA		0.0465,6.7893,2.3311	benign,benign,benign	529/1320,725/1516,512/1303	71234960	303,12695	2202	4297	6499	SO:0001583	missense	57579	exon13			CTTTCTATTGGAG	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.2173A>G	6.37:g.71234960A>G	ENSP00000410768:p.Ile725Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	60	22	0.366667	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	A	0.009	-1.845019	0.00568	0.067893	4.65E-4	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	6.07	-12.1	0.00011	.	1.270720	0.04845	N	0.441304	T	0.06416	0.0165	N	0.03948	-0.315	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.001	T	0.38542	-0.9656	10	0.23891	T	0.37	.	18.3851	0.90464	0.7861:0.0739:0.1401:0.0	rs9455142;rs52822960;rs9455142	725;725;529;512	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	V	725;512;512;529;725	ENSP00000410768:I725V;ENSP00000359510:I512V;ENSP00000409201:I512V;ENSP00000354913:I529V;ENSP00000423307:I725V	ENSP00000354913:I529V	I	+	1	0	FAM135A	71291681	0.000000	0.05858	0.000000	0.03702	0.896000	0.52359	-0.852000	0.04308	-2.772000	0.00364	-0.959000	0.02639	ATT	A|0.974;G|0.026	0.026	strong		0.313	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
FKBP15	23307	hgsc.bcm.edu	37	9	115931703	115931703	+	Silent	SNP	G	G	A	rs3810910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:115931703G>A	ENST00000238256.3	-	26	3403	c.3286C>T	c.(3286-3288)Ctg>Ttg	p.L1096L		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1096					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						GTCAGGGACAGTCTTGTGGAG	0.577													G|||	1420	0.283546	0.3351	0.2954	5008	,	,		17925	0.1617		0.3489	False		,,,				2504	0.2638				p.L1096L		Atlas-SNP	.											.	FKBP15	128	.	0			c.C3286T						PASS	.	G		1174,2710		177,820,945	96.0	98.0	98.0		3286	3.5	0.0	9	dbSNP_107	98	2704,5574		443,1818,1878	no	coding-synonymous	FKBP15	NM_015258.1		620,2638,2823	AA,AG,GG		32.6649,30.2266,31.8862		1096/1220	115931703	3878,8284	1942	4139	6081	SO:0001819	synonymous_variant	23307	exon26			GGGACAGTCTTGT	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.3286C>T	9.37:g.115931703G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	227	225	0.991189	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			G|0.712;A|0.288	0.288	strong		0.577	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
MASTL	84930	hgsc.bcm.edu	37	10	27475444	27475444	+	Silent	SNP	T	T	C	rs10741130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:27475444T>C	ENST00000375940.4	+	12	2676	c.2619T>C	c.(2617-2619)acT>acC	p.T873T	MASTL_ENST00000477034.1_3'UTR|MASTL_ENST00000342386.6_Silent_p.T834T|MASTL_ENST00000375946.4_Silent_p.T872T			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	873	AGC-kinase C-terminal.				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						AGCACCTGACTGTATCTGGAT	0.388													C|||	2559	0.510982	0.5295	0.5231	5008	,	,		19363	0.4563		0.6103	False		,,,				2504	0.4315				p.T873T		Atlas-SNP	.											.	MASTL	81	.	0			c.T2619C						PASS	.	C	,,	2476,1930	549.0+/-377.7	689,1098,416	164.0	157.0	160.0		2619,2502,2616	-11.3	0.0	10	dbSNP_120	160	5659,2941	459.0+/-364.8	1853,1953,494	no	coding-synonymous,coding-synonymous,coding-synonymous	MASTL	NM_001172303.1,NM_001172304.1,NM_032844.3	,,	2542,3051,910	CC,CT,TT		34.1977,43.8039,37.4519	,,	873/880,834/841,872/879	27475444	8135,4871	2203	4300	6503	SO:0001819	synonymous_variant	84930	exon12			CCTGACTGTATCT	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.2619T>C	10.37:g.27475444T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_001172303	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Silent	SNP	ENST00000375940.4	37	CCDS53502.1																																																																																			T|0.404;C|0.596	0.596	strong		0.388	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844	
GPATCH1	55094	hgsc.bcm.edu	37	19	33605300	33605300	+	Missense_Mutation	SNP	A	A	G	rs10416265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33605300A>G	ENST00000170564.2	+	15	2485	c.2171A>G	c.(2170-2172)cAt>cGt	p.H724R		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	724			H -> R (in dbSNP:rs10416265). {ECO:0000269|PubMed:17974005}.		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)					GAGGAAGAGCATGCACCAGAA	0.438													G|||	2967	0.592452	0.7239	0.3386	5008	,	,		18961	0.8433		0.2475	False		,,,				2504	0.6912				p.H724R	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.A2171G						PASS	.	G	ARG/HIS	2963,1443	466.2+/-354.4	998,967,238	70.0	77.0	75.0		2171	-8.9	0.0	19	dbSNP_119	75	2340,6260	703.4+/-405.3	294,1752,2254	yes	missense	GPATCH1	NM_018025.2	29	1292,2719,2492	GG,GA,AA		27.2093,32.7508,40.7735	benign	724/932	33605300	5303,7703	2203	4300	6503	SO:0001583	missense	55094	exon15			AAGAGCATGCACC	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.2171A>G	19.37:g.33605300A>G	ENSP00000170564:p.His724Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Missense_Mutation	SNP	ENST00000170564.2	37	CCDS12428.1	1164	0.532967032967033	358	0.7276422764227642	116	0.32044198895027626	493	0.8618881118881119	197	0.2598944591029024	G	3.646	-0.072520	0.07228	0.672492	0.272093	ENSG00000076650	ENST00000170564	T	0.20332	2.08	5.32	-8.87	0.00792	.	1.955520	0.02032	N	0.048608	T	0.00012	0.0000	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	0.24764	-1.0151	9	0.14656	T	0.56	4.8647	9.3731	0.38266	0.2957:0.3351:0.3692:0.0	rs10416265;rs60644468;rs10416265	724;724	B2RDX4;Q9BRR8	.;GPTC1_HUMAN	R	724	ENSP00000170564:H724R	ENSP00000170564:H724R	H	+	2	0	GPATCH1	38297140	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.933000	0.01553	-2.702000	0.00398	-0.748000	0.03510	CAT	A|0.517;G|0.483	0.483	strong		0.438	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
CLCN5	1184	hgsc.bcm.edu	37	X	49854942	49854942	+	Silent	SNP	C	C	T	rs34173954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49854942C>T	ENST00000307367.2	+	10	1995	c.1704C>T	c.(1702-1704)ccC>ccT	p.P568P	CLCN5_ENST00000376088.3_Silent_p.P638P|CLCN5_ENST00000376091.3_Silent_p.P638P|CLCN5_ENST00000376108.3_Silent_p.P568P			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	568					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|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)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					ATGGATACCCCTTTCTTGAAG	0.512													C|||	238	0.0630464	0.1717	0.0159	3775	,	,		14843	0.0		0.0	False		,,,				2504	0.0				p.P638P		Atlas-SNP	.											.	CLCN5	137	.	0			c.C1914T						PASS	.	C	,,	792,3043		84,519,105,1029,466	114.0	95.0	101.0		1704,1914,1914	2.9	1.0	X	dbSNP_126	101	5,6723		0,4,1,2424,1871	no	coding-synonymous,coding-synonymous,coding-synonymous	CLCN5	NM_000084.2,NM_001127898.1,NM_001127899.1	,,	84,523,106,3453,2337	TT,TC,T,CC,C		0.0743,20.6519,7.5452	,,	568/747,638/817,638/817	49854942	797,9766	2203	4300	6503	SO:0001819	synonymous_variant	1184	exon13			ATACCCCTTTCTT	X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"""Ion channels / Chloride channels : Voltage-sensitive"""	2023	protein-coding gene	gene with protein product	"""Dent disease"""	300008	"""nephrolithiasis 2, X-linked"", ""nephrolithiasis 1 (X-linked)"", ""chloride channel 5"""	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.1704C>T	X.37:g.49854942C>T		Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	270	270	1	NM_001127898	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Silent	SNP	ENST00000307367.2	37	CCDS14328.1																																																																																			C|0.910;T|0.090	0.090	strong		0.512	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1		
METTL4	64863	hgsc.bcm.edu	37	18	2554836	2554836	+	Silent	SNP	A	A	G	rs16943442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2554836A>G	ENST00000574538.1	-	4	1436	c.661T>C	c.(661-663)Ttg>Ctg	p.L221L	METTL4_ENST00000319888.6_Silent_p.L221L|snoU109_ENST00000459316.1_RNA	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	221					nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						TCTTCCACCAATTGTAATGTC	0.373													A|||	614	0.122604	0.264	0.0994	5008	,	,		20201	0.1339		0.0457	False		,,,				2504	0.0153				p.L221L		Atlas-SNP	.											.	METTL4	40	.	0			c.T661C						PASS	.	A		1019,3387	375.1+/-321.5	116,787,1300	85.0	74.0	78.0		661	3.4	0.0	18	dbSNP_123	78	381,8219	124.6+/-183.3	11,359,3930	no	coding-synonymous	METTL4	NM_022840.3		127,1146,5230	GG,GA,AA		4.4302,23.1276,10.7643		221/473	2554836	1400,11606	2203	4300	6503	SO:0001819	synonymous_variant	64863	exon4			CCACCAATTGTAA		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.661T>C	18.37:g.2554836A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	152	68	0.447368	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Silent	SNP	ENST00000574538.1	37	CCDS11826.1																																																																																			A|0.881;G|0.119	0.119	strong		0.373	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840	
FAM25A	643161	hgsc.bcm.edu	37	10	88782100	88782100	+	Missense_Mutation	SNP	G	G	C	rs7079587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:88782100G>C	ENST00000343959.4	+	2	122	c.103G>C	c.(103-105)Gtg>Ctg	p.V35L	RP11-96C23.14_ENST00000444180.3_RNA	NM_001146157.2	NP_001139629.1	B3EWG3	FM25A_HUMAN	family with sequence similarity 25, member A	35			V -> L (in dbSNP:rs7079587).							stomach(1)	1						GGTGAAGGAGGTGGTGGGACA	0.622													.|||	189	0.0377396	0.0855	0.036	5008	,	,		20449	0.0		0.0388	False		,,,				2504	0.0123				p.V35L		Atlas-SNP	.											.	FAM25A	4	.	0			c.G103C						PASS	.	G	LEU/VAL	100,1284		2,96,594	42.0	39.0	40.0		103	3.9	1.0	10	dbSNP_116	40	117,3065		3,111,1477	no	missense	FAM25A	NM_001146157.2	32	5,207,2071	CC,CG,GG		3.6769,7.2254,4.7525	probably-damaging	35/90	88782100	217,4349	692	1591	2283	SO:0001583	missense	643161	exon2			AAGGAGGTGGTGG		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.103G>C	10.37:g.88782100G>C	ENSP00000342790:p.Val35Leu	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_001146157	B2RV02|Q5VTM1	Missense_Mutation	SNP	ENST00000343959.4	37	CCDS44451.1	91|91	0.041666666666666664|0.041666666666666664	48|48	0.0975609756097561|0.0975609756097561	15|15	0.04143646408839779|0.04143646408839779	2|2	0.0034965034965034965|0.0034965034965034965	26|26	0.03430079155672823|0.03430079155672823	G|G	12.56|12.56	1.974538|1.974538	0.34848|0.34848	0.072254|0.072254	0.036769|0.036769	ENSG00000188100|ENSG00000188100	ENST00000343959|ENST00000444180	.|.	.|.	.|.	3.93|3.93	3.93|3.93	0.45458|0.45458	.|.	.|0.000000	.|0.49305	.|D	.|0.000156	T|T	0.03390|0.03390	0.0098|0.0098	.|.	.|.	.|.	0.32906|0.32906	D|D	0.51392|0.51392	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49021|0.49021	-0.8982|-0.8982	4|6	.|0.59425	.|D	.|0.04	-18.7332|-18.7332	13.1877|13.1877	0.59691|0.59691	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs7079587;rs52814476;rs7079587|rs7079587;rs52814476;rs7079587	.|.	.|.	.|.	A|L	41|35	.|.	.|ENSP00000417034:V35L	G|V	+|+	2|1	0|0	FAM25A|FAM25A	88772080|88772080	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.148000|0.148000	0.21650|0.21650	4.172000|4.172000	0.58243|0.58243	2.216000|2.216000	0.71823|0.71823	0.478000|0.478000	0.44815|0.44815	GGT|GTG	G|0.964;C|0.036	0.036	strong		0.622	FAM25A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049182.2		
PANX1	24145	hgsc.bcm.edu	37	11	93913392	93913392	+	Missense_Mutation	SNP	G	G	T	rs74549886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:93913392G>T	ENST00000227638.3	+	4	1555	c.1170G>T	c.(1168-1170)gaG>gaT	p.E390D	PANX1_ENST00000436171.2_Missense_Mutation_p.E390D	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	390					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)	AGATGAGAGAGGAGCAGGGGA	0.532													G|||	180	0.0359425	0.1286	0.0115	5008	,	,		17647	0.0		0.002	False		,,,				2504	0.0				p.E390D		Atlas-SNP	.											.	PANX1	38	.	0			c.G1170T						PASS	.	G	ASP/GLU	484,3918	225.9+/-241.6	21,442,1738	68.0	64.0	66.0		1170	1.0	0.0	11	dbSNP_131	66	6,8590	4.3+/-15.6	0,6,4292	yes	missense	PANX1	NM_015368.3	45	21,448,6030	TT,TG,GG		0.0698,10.995,3.7698	benign	390/427	93913392	490,12508	2201	4298	6499	SO:0001583	missense	24145	exon4			GAGAGAGGAGCAG	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.1170G>T	11.37:g.93913392G>T	ENSP00000227638:p.Glu390Asp	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Missense_Mutation	SNP	ENST00000227638.3	37	CCDS8296.1	62	0.028388278388278388	57	0.11585365853658537	5	0.013812154696132596	0	0.0	0	0.0	G	12.51	1.958933	0.34565	0.10995	6.98E-4	ENSG00000110218	ENST00000227638;ENST00000436171	T;T	0.19250	2.17;2.16	5.22	0.965	0.19661	.	1.495480	0.03723	N	0.252178	T	0.00300	0.0009	M	0.67953	2.075	0.09310	N	1	B;B	0.32573	0.376;0.29	B;B	0.29785	0.049;0.107	T	0.16600	-1.0397	10	0.39692	T	0.17	-15.6543	4.6163	0.12428	0.3593:0.2803:0.3603:0.0	.	390;390	Q96RD7;Q96RD7-2	PANX1_HUMAN;.	D	390	ENSP00000227638:E390D;ENSP00000411461:E390D	ENSP00000227638:E390D	E	+	3	2	PANX1	93553040	0.059000	0.20769	0.005000	0.12908	0.026000	0.11368	0.183000	0.16919	0.606000	0.29965	0.655000	0.94253	GAG	G|0.968;T|0.032	0.032	strong		0.532	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368	
ACACB	32	hgsc.bcm.edu	37	12	109644616	109644616	+	Silent	SNP	C	C	T	rs17848814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109644616C>T	ENST00000338432.7	+	20	3134	c.3015C>T	c.(3013-3015)aaC>aaT	p.N1005N	ACACB_ENST00000377854.5_Silent_p.N1005N|ACACB_ENST00000377848.3_Silent_p.N1005N			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1005					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)	p.N1005N(1)		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)	ACCTCACCAACGTCATGAGTG	0.542													C|||	450	0.0898562	0.289	0.0432	5008	,	,		16239	0.0099		0.0258	False		,,,				2504	0.002				p.N1005N		Atlas-SNP	.											ACACB,NS,carcinoma,0,1	ACACB	330	1	1	Substitution - coding silent(1)	stomach(1)	c.C3015T						scavenged	.	C		1078,3328	391.2+/-328.0	119,840,1244	145.0	136.0	139.0		3015	-4.6	0.4	12	dbSNP_123	139	138,8462	69.0+/-131.5	0,138,4162	no	coding-synonymous	ACACB	NM_001093.3		119,978,5406	TT,TC,CC		1.6047,24.4666,9.3495		1005/2459	109644616	1216,11790	2203	4300	6503	SO:0001819	synonymous_variant	32	exon19			CACCAACGTCATG	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.3015C>T	12.37:g.109644616C>T		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	178	87	0.488764	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.914;T|0.086	0.086	strong		0.542	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
ILDR1	286676	hgsc.bcm.edu	37	3	121712271	121712271	+	Missense_Mutation	SNP	C	C	T	rs34883204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121712271C>T	ENST00000344209.5	-	7	1451	c.1325G>A	c.(1324-1326)cGc>cAc	p.R442H	ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Missense_Mutation_p.R353H|ILDR1_ENST00000462014.1_Missense_Mutation_p.R410H|ILDR1_ENST00000273691.3_Missense_Mutation_p.R398H	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	442	Arg-rich.				positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		CTCCTGACAGCGGCTCCTGAA	0.672													C|||	202	0.0403355	0.1452	0.0144	5008	,	,		16784	0.0		0.0	False		,,,				2504	0.0				p.R442H		Atlas-SNP	.											ILDR1_ENST00000344209,colon,carcinoma,-1,2	ILDR1	120	2	0			c.G1325A						scavenged	.	C	HIS/ARG,HIS/ARG,HIS/ARG	528,3878		24,480,1699	22.0	24.0	23.0		1325,1058,1193	-0.6	0.2	3	dbSNP_126	23	8,8592		0,8,4292	yes	missense,missense,missense	ILDR1	NM_001199799.1,NM_001199800.1,NM_175924.3	29,29,29	24,488,5991	TT,TC,CC		0.093,11.9837,4.1212	probably-damaging,probably-damaging,probably-damaging	442/547,353/458,398/503	121712271	536,12470	2203	4300	6503	SO:0001583	missense	286676	exon7			TGACAGCGGCTCC	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"""deafness, autosomal recessive 42"""	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.1325G>A	3.37:g.121712271C>T	ENSP00000345667:p.Arg442His	Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_001199799	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	37	CCDS56271.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	C	7.187	0.590696	0.13812	0.119837	9.3E-4	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000393631;ENST00000462014	T;T;D;T	0.82984	-1.18;-0.64;-1.67;-0.71	4.69	-0.554	0.11811	.	0.768774	0.12399	N	0.472300	T	0.01287	0.0042	M	0.61703	1.905	0.38075	P	0.06350900000000004	B;B;B;B	0.10296	0.003;0.001;0.003;0.003	B;B;B;B	0.06405	0.001;0.0;0.001;0.002	T	0.38156	-0.9674	9	0.45353	T	0.12	-5.2038	8.9045	0.35515	0.0:0.3969:0.0:0.6031	rs34883204	353;442;398;410	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	H	398;442;353;410	ENSP00000273691:R398H;ENSP00000345667:R442H;ENSP00000377251:R353H;ENSP00000419414:R410H	ENSP00000273691:R398H	R	-	2	0	ILDR1	123194961	0.000000	0.05858	0.161000	0.22692	0.133000	0.20885	-0.271000	0.08572	-0.338000	0.08413	-0.345000	0.07892	CGC	C|0.960;T|0.040	0.040	strong		0.672	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924	
BHMT	635	hgsc.bcm.edu	37	5	78421959	78421959	+	Missense_Mutation	SNP	G	G	A	rs3733890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:78421959G>A	ENST00000274353.5	+	6	823	c.716G>A	c.(715-717)cGa>cAa	p.R239Q	DMGDH_ENST00000520388.1_Intron|BHMT_ENST00000524080.1_Missense_Mutation_p.R86Q	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	239	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.		R -> Q (may decrease risk for coronary artery disease; dbSNP:rs3733890). {ECO:0000269|PubMed:12818402, ECO:0000269|PubMed:8798461}.		amino-acid betaine catabolic process (GO:0006579)|amino-acid betaine metabolic process (GO:0006577)|cellular nitrogen compound metabolic process (GO:0034641)|L-methionine salvage (GO:0071267)|protein methylation (GO:0006479)|regulation of homocysteine metabolic process (GO:0050666)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	betaine-homocysteine S-methyltransferase activity (GO:0047150)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	GAGGCTGCCCGACTGAAAGCT	0.512													G|||	1456	0.290735	0.2035	0.3775	5008	,	,		18501	0.3155		0.3231	False		,,,				2504	0.2883				p.R239Q		Atlas-SNP	.											.	BHMT	53	.	0			c.G716A	GRCh37	CM031139	BHMT	M	rs3733890	PASS	.	G	GLN/ARG	980,3426	368.6+/-318.7	121,738,1344	106.0	95.0	99.0		716	3.5	0.0	5	dbSNP_107	99	2584,6016	419.9+/-353.2	399,1786,2115	yes	missense	BHMT	NM_001713.2	43	520,2524,3459	AA,AG,GG		30.0465,22.2424,27.4027	benign	239/407	78421959	3564,9442	2203	4300	6503	SO:0001583	missense	635	exon6			CTGCCCGACTGAA	BC012616	CCDS4046.1	5q14.1	2012-09-20	2010-04-28		ENSG00000145692	ENSG00000145692	2.1.1.5		1047	protein-coding gene	gene with protein product	"""betaine homocysteine methyltransferase"""	602888				8798461, 9281325	Standard	NM_001713		Approved	BHMT1	uc003kfu.4	Q93088	OTTHUMG00000108157	ENST00000274353.5:c.716G>A	5.37:g.78421959G>A	ENSP00000274353:p.Arg239Gln	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	219	118	0.538813	NM_001713	Q9UNI9	Missense_Mutation	SNP	ENST00000274353.5	37	CCDS4046.1	658	0.30128205128205127	125	0.2540650406504065	125	0.3453038674033149	173	0.30244755244755245	235	0.3100263852242744	G	14.36	2.512207	0.44660	0.222424	0.300465	ENSG00000145692	ENST00000274353;ENST00000524080;ENST00000436224	T;T	0.29397	1.57;1.57	5.66	3.51	0.40186	Homocysteine S-methyltransferase (4);	0.536255	0.21754	N	0.069629	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;B	0.42456	0.78;0.0	B;B	0.25884	0.064;0.001	T	0.43893	-0.9363	9	0.28530	T	0.3	-3.8727	4.6612	0.12643	0.4122:0.0:0.5878:0.0	rs3733890;rs52838192;rs59208899;rs3733890	86;239	E5RJH0;Q93088	.;BHMT1_HUMAN	Q	239;86;86	ENSP00000274353:R239Q;ENSP00000428240:R86Q	ENSP00000274353:R239Q	R	+	2	0	BHMT	78457715	0.083000	0.21467	0.004000	0.12327	0.749000	0.42624	2.821000	0.48065	1.533000	0.49186	0.655000	0.94253	CGA	G|0.715;A|0.285	0.285	strong		0.512	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713	
SPTA1	6708	hgsc.bcm.edu	37	1	158623103	158623103	+	Missense_Mutation	SNP	G	G	A	rs116297260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158623103G>A	ENST00000368147.4	-	22	3329	c.3149C>T	c.(3148-3150)cCa>cTa	p.P1050L		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1050					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)					GATGTTTCCTGGCTCTTCTCG	0.532													G|||	40	0.00798722	0.0295	0.0014	5008	,	,		15095	0.0		0.0	False		,,,				2504	0.0				p.P1050L		Atlas-SNP	.											.	SPTA1	720	.	0			c.C3149T						PASS	.	G	LEU/PRO	81,3859		0,81,1889	116.0	119.0	118.0		3149	3.3	0.9	1	dbSNP_132	118	0,8370		0,0,4185	yes	missense	SPTA1	NM_003126.2	98	0,81,6074	AA,AG,GG		0.0,2.0558,0.658	benign	1050/2420	158623103	81,12229	1970	4185	6155	SO:0001583	missense	6708	exon22			TTTCCTGGCTCTT	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.3149C>T	1.37:g.158623103G>A	ENSP00000357129:p.Pro1050Leu	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	130	65	0.5	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	11.31	1.600501	0.28534	0.020558	0.0	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.31510	1.49;1.49	5.15	3.28	0.37604	Src homology-3 domain (1);	0.273133	0.19703	N	0.107990	T	0.06962	0.0177	N	0.22421	0.69	0.47123	D	0.999327	B	0.11235	0.004	B	0.10450	0.005	T	0.12863	-1.0531	10	0.28530	T	0.3	.	4.5022	0.11869	0.1722:0.0:0.5672:0.2606	.	1050	P02549	SPTA1_HUMAN	L	1050	ENSP00000357130:P1050L;ENSP00000357129:P1050L	ENSP00000357129:P1050L	P	-	2	0	SPTA1	156889727	1.000000	0.71417	0.878000	0.34440	0.726000	0.41606	4.176000	0.58269	0.762000	0.33152	0.655000	0.94253	CCA	G|0.995;A|0.005	0.005	strong		0.532	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
DACT1	51339	hgsc.bcm.edu	37	14	59112732	59112732	+	Missense_Mutation	SNP	C	C	T	rs17832998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	17	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	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	
KRT4	3851	hgsc.bcm.edu	37	12	53207628	53207628	+	Missense_Mutation	SNP	G	G	A	rs2638525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53207628G>A	ENST00000551956.1	-	1	707	c.215C>T	c.(214-216)gCc>gTc	p.A72V	KRT4_ENST00000293774.4_Missense_Mutation_p.A146V|KRT4_ENST00000458244.2_Missense_Mutation_p.A52V			P19013	K2C4_HUMAN	keratin 4	72	Gly-rich.|Head.		A -> V (in allele K4A1). {ECO:0000269|PubMed:7684424}.		cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CCCAAAGCAGGCACCTTGTCG	0.607													G|||	1110	0.221645	0.4576	0.1225	5008	,	,		15658	0.1091		0.1481	False		,,,				2504	0.1646				p.A72V	Pancreas(190;284 2995 41444 45903)	Atlas-SNP	.											.	KRT4	110	.	0			c.C215T						PASS	.	G	VAL/ALA	1611,2567		322,967,800	96.0	114.0	108.0		215	1.0	0.0	12	dbSNP_100	108	1480,6978		141,1198,2890	yes	missense	KRT4	NM_002272.3	64	463,2165,3690	AA,AG,GG		17.4982,38.5591,24.4619	benign	72/521	53207628	3091,9545	2089	4229	6318	SO:0001583	missense	3851	exon1			AAGCAGGCACCTT		CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.215C>T	12.37:g.53207628G>A	ENSP00000448220:p.Ala72Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_002272	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Missense_Mutation	SNP	ENST00000551956.1	37	CCDS41787.2	415	0.190018315018315	202	0.4105691056910569	52	0.143646408839779	42	0.07342657342657342	119	0.15699208443271767	G	2.781	-0.253445	0.05829	0.385591	0.174982	ENSG00000170477	ENST00000551956;ENST00000293774;ENST00000458244	D;T;D	0.88818	-2.43;2.13;-2.27	5.14	1.03	0.20045	.	0.300384	0.24229	N	0.040380	T	0.00012	0.0000	L	0.42686	1.345	0.80722	P	0.0	.	.	.	.	.	.	T	0.04165	-1.0972	7	0.36615	T	0.2	.	7.4829	0.27415	0.0695:0.4533:0.3654:0.1118	rs2638525;rs41423744;rs58915602;rs2638525	.	.	.	V	72;146;52	ENSP00000448220:A72V;ENSP00000293774:A146V;ENSP00000387904:A52V	ENSP00000293774:A146V	A	-	2	0	KRT4	51493895	0.000000	0.05858	0.025000	0.17156	0.484000	0.33280	-0.114000	0.10757	0.072000	0.16694	0.585000	0.79938	GCC	G|0.795;A|0.205	0.205	strong		0.607	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
SEMA6A	57556	hgsc.bcm.edu	37	5	115827506	115827506	+	Silent	SNP	G	G	A	rs34096390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:115827506G>A	ENST00000343348.6	-	7	1252	c.465C>T	c.(463-465)ttC>ttT	p.F155F	SEMA6A_ENST00000257414.8_Silent_p.F155F|SEMA6A_ENST00000510263.1_Silent_p.F155F|SEMA6A_ENST00000503962.1_5'UTR|CTB-118N6.3_ENST00000514214.1_RNA|CTB-118N6.3_ENST00000510682.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	155	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)		ATTCATCCCCGAATGGTTCCA	0.418													G|||	155	0.0309505	0.1112	0.0086	5008	,	,		21381	0.0		0.002	False		,,,				2504	0.0				p.F155F		Atlas-SNP	.											SEMA6A,NS,carcinoma,-2,1	SEMA6A	93	1	0			c.C465T						scavenged	.	G		326,3528		20,286,1621	120.0	118.0	118.0		465	-12.2	0.0	5	dbSNP_126	118	3,8247		0,3,4122	no	coding-synonymous	SEMA6A	NM_020796.3		20,289,5743	AA,AG,GG		0.0364,8.4587,2.7181		155/1031	115827506	329,11775	1927	4125	6052	SO:0001819	synonymous_variant	57556	exon7			ATCCCCGAATGGT	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.465C>T	5.37:g.115827506G>A		Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	228	91	0.399123	NM_020796	Q9P2H9	Silent	SNP	ENST00000343348.6	37	CCDS47256.1																																																																																			G|0.979;A|0.021	0.021	strong		0.418	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	
LY75	4065	hgsc.bcm.edu	37	2	160735775	160735775	+	Missense_Mutation	SNP	C	C	T	rs77761086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160735775C>T	ENST00000263636.4	-	9	1537	c.1510G>A	c.(1510-1512)Gat>Aat	p.D504N	LY75-CD302_ENST00000504764.1_Missense_Mutation_p.D504N|LY75_ENST00000554112.1_Missense_Mutation_p.D504N|LY75_ENST00000553424.1_Missense_Mutation_p.D504N|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.D504N	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	504	C-type lectin 3. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		CCTACCTCATCTGGAGGACAC	0.353													C|||	26	0.00519169	0.0197	0.0	5008	,	,		19467	0.0		0.0	False		,,,				2504	0.0				p.D504N		Atlas-SNP	.											.	LY75	151	.	0			c.G1510A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	59,4345	58.1+/-94.6	0,59,2143	199.0	183.0	189.0		1510,1510,1510	2.4	0.4	2	dbSNP_131	189	0,8598		0,0,4299	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	23,23,23	0,59,6442	TT,TC,CC		0.0,1.3397,0.4538	benign,benign,benign	504/1874,504/1818,504/1723	160735775	59,12943	2202	4299	6501	SO:0001583	missense	4065	exon9			CCTCATCTGGAGG	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.1510G>A	2.37:g.160735775C>T	ENSP00000263636:p.Asp504Asn	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	92	35	0.380435	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	4.816	0.151794	0.09185	0.013397	0.0	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.55413	0.52;3.0;2.98;0.52;3.0	5.4	2.44	0.29823	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (1);	1.063440	0.07525	N	0.911197	T	0.41096	0.1144	M	0.82056	2.57	0.09310	N	1	B;B;B;B	0.16603	0.001;0.018;0.018;0.007	B;B;B;B	0.22386	0.005;0.039;0.017;0.009	T	0.44221	-0.9342	10	0.34782	T	0.22	-1.7808	11.0531	0.47903	0.0:0.6813:0.0:0.3187	.	122;504;504;504	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	N	504	ENSP00000451511:D504N;ENSP00000451446:D504N;ENSP00000263636:D504N;ENSP00000423463:D504N;ENSP00000421035:D504N	ENSP00000423463:D504N	D	-	1	0	LY75;LY75-CD302	160444021	0.095000	0.21747	0.411000	0.26484	0.053000	0.15095	0.244000	0.18124	0.025000	0.15241	-1.595000	0.00837	GAT	C|0.994;T|0.006	0.006	strong		0.353	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
SENP5	205564	hgsc.bcm.edu	37	3	196613075	196613075	+	Silent	SNP	C	C	T	rs34533379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196613075C>T	ENST00000323460.5	+	2	1272	c.1023C>T	c.(1021-1023)gaC>gaT	p.D341D	SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Silent_p.D341D	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	341					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		TTAGTTTAGACGAAGCATTCC	0.502													C|||	1186	0.236821	0.3555	0.1239	5008	,	,		20943	0.1667		0.2346	False		,,,				2504	0.2311				p.D341D	Ovarian(47;891 1095 11174 13858 51271)	Atlas-SNP	.											.	SENP5	68	.	0			c.C1023T						PASS	.	C		1438,2968	466.8+/-354.6	220,998,985	91.0	79.0	83.0		1023	-6.5	0.4	3	dbSNP_126	83	1844,6756	330.7+/-319.3	200,1444,2656	no	coding-synonymous	SENP5	NM_152699.4		420,2442,3641	TT,TC,CC		21.4419,32.6373,25.2345		341/756	196613075	3282,9724	2203	4300	6503	SO:0001819	synonymous_variant	205564	exon2			TTTAGACGAAGCA	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"""SUMO1/sentrin specific protease 5"""			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1023C>T	3.37:g.196613075C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_152699	B4DY82|Q96SA5	Silent	SNP	ENST00000323460.5	37	CCDS3322.1																																																																																			C|0.751;T|0.249	0.249	strong		0.502	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699	
KRT7	3855	hgsc.bcm.edu	37	12	52636843	52636843	+	Silent	SNP	G	G	A	rs10564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52636843G>A	ENST00000331817.5	+	6	1089	c.906G>A	c.(904-906)cgG>cgA	p.R302R	RP3-416H24.1_ENST00000546686.1_RNA	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	302	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	ACGACCTCCGGAATACCCGGA	0.567													G|||	172	0.034345	0.1256	0.0086	5008	,	,		18629	0.0		0.0	False		,,,				2504	0.0				p.R302R		Atlas-SNP	.											KRT7,colon,carcinoma,+1,1	KRT7	48	1	0			c.G906A						PASS	.	G		434,3972	210.8+/-231.2	19,396,1788	74.0	69.0	70.0		906	-0.4	0.5	12	dbSNP_52	70	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KRT7	NM_005556.3		19,398,6086	AA,AG,GG		0.0233,9.8502,3.3523		302/470	52636843	436,12570	2203	4300	6503	SO:0001819	synonymous_variant	3855	exon6			CCTCCGGAATACC		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6445	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 7"", ""cytokeratin 7"", ""sarcolectin"", ""keratin, 55K type II cytoskeletal"""	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.906G>A	12.37:g.52636843G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Silent	SNP	ENST00000331817.5	37	CCDS8822.1																																																																																			G|0.964;A|0.036	0.036	strong		0.567	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556	
RCBTB1	55213	hgsc.bcm.edu	37	13	50123622	50123622	+	Silent	SNP	G	G	C	rs3751384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:50123622G>C	ENST00000378302.2	-	9	1277	c.1017C>G	c.(1015-1017)ccC>ccG	p.P339P	RCBTB1_ENST00000546015.1_Silent_p.P339P|RCBTB1_ENST00000258646.3_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	100	0	0		WXS	Illumina HiSeq	Phase_I	92	90	0.978261	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	
DIS3L2	129563	hgsc.bcm.edu	37	2	232995462	232995462	+	Silent	SNP	A	A	G	rs75061164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:232995462A>G	ENST00000409401.3	+	7	910	c.735A>G	c.(733-735)caA>caG	p.Q245Q	DIS3L2_ENST00000325385.7_Intron|DIS3L2_ENST00000273009.6_Intron|DIS3L2_ENST00000409307.1_Intron|DIS3L2_ENST00000470087.1_3'UTR|DIS3L2_ENST00000360410.4_Intron	NM_001257282.1	NP_001244211.1			DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CACGTGTCCAAATGGCTTTCA	0.408													A|||	66	0.0131789	0.0492	0.0014	5008	,	,		17265	0.0		0.0	False		,,,				2504	0.0				p.Q245Q		Atlas-SNP	.											.	DIS3L2	77	.	0			c.A735G						PASS	.	A		183,3565		5,173,1696	56.0	53.0	54.0			0.9	0.0	2	dbSNP_132	54	1,8213		0,1,4106	no	intron	DIS3L2	NM_152383.4		5,174,5802	GG,GA,AA		0.0122,4.8826,1.5382			232995462	184,11778	1874	4107	5981	SO:0001819	synonymous_variant	129563	exon7			TGTCCAAATGGCT	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"""family with sequence similarity 6, member A"", ""DIS3 mitotic control homolog (S. cerevisiae)-like 2"""	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409401.3:c.735A>G	2.37:g.232995462A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	135	72	0.533333	NM_001257282		Silent	SNP	ENST00000409401.3	37	CCDS58753.1																																																																																			A|0.984;G|0.016	0.016	strong		0.408	DIS3L2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330976.1	NM_152383	
MUC4	4585	hgsc.bcm.edu	37	3	195511212	195511212	+	Missense_Mutation	SNP	G	G	C	rs549429405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511212G>C	ENST00000463781.3	-	2	7698	c.7239C>G	c.(7237-7239)caC>caG	p.H2413Q	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H2413Q	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)		GATGGGTGGCGTGACCTGTGG	0.592																																					p.H2413Q		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	0			c.C7239G						scavenged	.						42.0	42.0	42.0					3																	195511212		668	1587	2255	SO:0001583	missense	4585	exon2			GGTGGCGTGACCT	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.7239C>G	3.37:g.195511212G>C	ENSP00000417498:p.His2413Gln	Somatic	760	4	0.00526316		WXS	Illumina HiSeq	Phase_I	269	11	0.0408922	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	5.745	0.321952	0.10900	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26810	1.71;1.75	.	.	.	.	.	.	.	.	T	0.13586	0.0329	N	0.19112	0.55	0.09310	N	1	B	0.18610	0.029	B	0.04013	0.001	T	0.30909	-0.9962	7	.	.	.	.	6.6894	0.23163	2.0E-4:0.0:0.9998:0.0	.	2413	E7ESK3	.	Q	2413	ENSP00000417498:H2413Q;ENSP00000420243:H2413Q	.	H	-	3	2	MUC4	196995607	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	0.313000	0.19415	0.482000	0.27582	0.000000	0.15137	CAC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DROSHA	29102	hgsc.bcm.edu	37	5	31526531	31526531	+	Missense_Mutation	SNP	G	G	A	rs77034974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:31526531G>A	ENST00000511367.2	-	4	753	c.509C>T	c.(508-510)cCg>cTg	p.P170L	DROSHA_ENST00000513349.1_Missense_Mutation_p.P170L|DROSHA_ENST00000344624.3_Missense_Mutation_p.P170L|DROSHA_ENST00000504361.1_5'Flank|DROSHA_ENST00000442743.1_Missense_Mutation_p.P170L	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	170	Pro-rich.			YQYPPGYSH -> RERERTSLE (in Ref. 4; CAB45133). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						AGAATAGCCCGGAGGGTACTG	0.532													G|||	179	0.0357428	0.1293	0.0115	5008	,	,		13508	0.0		0.0	False		,,,				2504	0.0				p.P170L		Atlas-SNP	.											.	DROSHA	130	.	0			c.C509T						PASS	.	G	LEU/PRO,LEU/PRO	443,3287		29,385,1451	47.0	47.0	47.0		509,509	5.1	0.2	5	dbSNP_131	47	2,8200		0,2,4099	yes	missense,missense	DROSHA	NM_001100412.1,NM_013235.4	98,98	29,387,5550	AA,AG,GG		0.0244,11.8767,3.7295	possibly-damaging,possibly-damaging	170/1338,170/1375	31526531	445,11487	1865	4101	5966	SO:0001583	missense	29102	exon4			TAGCCCGGAGGGT	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.509C>T	5.37:g.31526531G>A	ENSP00000425979:p.Pro170Leu	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	228	103	0.451754	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	55	0.025183150183150184	51	0.10365853658536585	4	0.011049723756906077	0	0.0	0	0.0	G	10.57	1.386208	0.25031	0.118767	2.44E-4	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000507438	T;T;T;T;T	0.41400	1.56;1.56;1.0;1.0;1.02	5.12	5.12	0.69794	.	0.173463	0.48767	D	0.000168	T	0.00384	0.0012	N	0.14661	0.345	0.22989	N	0.998465	B;B;B	0.28760	0.221;0.033;0.081	B;B;B	0.16722	0.016;0.007;0.007	T	0.00466	-1.1722	10	0.26408	T	0.33	-10.9681	18.5802	0.91168	0.0:0.0:1.0:0.0	.	170;170;170	Q9NRR4-2;E7EMP9;Q9NRR4	.;.;RNC_HUMAN	L	170;170;170;170;163;163;170	ENSP00000425979:P170L;ENSP00000339845:P170L;ENSP00000409335:P170L;ENSP00000424161:P170L;ENSP00000430921:P170L	ENSP00000265075:P163L	P	-	2	0	DROSHA	31562288	0.989000	0.36119	0.199000	0.23439	0.255000	0.26057	4.682000	0.61671	2.366000	0.80165	0.655000	0.94253	CCG	G|0.974;A|0.026	0.026	strong		0.532	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
PPL	5493	hgsc.bcm.edu	37	16	4952511	4952511	+	Missense_Mutation	SNP	C	C	T	rs115478590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4952511C>T	ENST00000345988.2	-	4	423	c.334G>A	c.(334-336)Gag>Aag	p.E112K	PPL_ENST00000590782.2_Missense_Mutation_p.E112K	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	112					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						GTCACACGCTCCTTCAGCTGG	0.637													C|||	16	0.00319489	0.0113	0.0014	5008	,	,		18020	0.0		0.0	False		,,,				2504	0.0				p.E112K		Atlas-SNP	.											.	PPL	168	.	0			c.G334A						PASS	.	C	LYS/GLU	47,4347	48.9+/-83.8	0,47,2150	129.0	94.0	106.0		334	5.0	1.0	16	dbSNP_132	106	0,8600		0,0,4300	yes	missense	PPL	NM_002705.4	56	0,47,6450	TT,TC,CC		0.0,1.0696,0.3617	probably-damaging	112/1757	4952511	47,12947	2197	4300	6497	SO:0001583	missense	5493	exon4			CACGCTCCTTCAG	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.334G>A	16.37:g.4952511C>T	ENSP00000340510:p.Glu112Lys	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	160	90	0.5625	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	C	25.4	4.631767	0.87660	0.010696	0.0	ENSG00000118898	ENST00000345988	T	0.36520	1.25	4.98	4.98	0.66077	.	0.126906	0.52532	D	0.000078	T	0.43523	0.1251	M	0.69823	2.125	0.45528	D	0.998484	D	0.69078	0.997	D	0.75020	0.985	T	0.58629	-0.7603	10	0.72032	D	0.01	.	16.4235	0.83790	0.0:1.0:0.0:0.0	.	112	O60437	PEPL_HUMAN	K	112	ENSP00000340510:E112K	ENSP00000340510:E112K	E	-	1	0	PPL	4892512	1.000000	0.71417	1.000000	0.80357	0.645000	0.38454	5.290000	0.65661	2.311000	0.77944	0.650000	0.86243	GAG	C|0.996;T|0.004	0.004	strong		0.637	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
CAMSAP3	57662	hgsc.bcm.edu	37	19	7682267	7682267	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7682267C>T	ENST00000160298.4	+	15	3369	c.3268C>T	c.(3268-3270)Cgg>Tgg	p.R1090W	CAMSAP3_ENST00000446248.2_Missense_Mutation_p.R1117W	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	1090					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						AAGCCGCGAACGGGACTGGGA	0.632																																					p.R1117W		Atlas-SNP	.											KIAA1543,NS,carcinoma,0,3	CAMSAP3	131	3	0			c.C3349T						scavenged	.						68.0	78.0	75.0					19																	7682267		2058	4183	6241	SO:0001583	missense	57662	exon17			CGCGAACGGGACT	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.3268C>T	19.37:g.7682267C>T	ENSP00000160298:p.Arg1090Trp	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	88	3	0.0340909	NM_001080429	Q8NDF1	Missense_Mutation	SNP	ENST00000160298.4	37	CCDS42489.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.037847	0.54896	.	.	ENSG00000076826	ENST00000446248;ENST00000160298	T;T	0.16597	2.33;2.33	5.12	2.86	0.33363	.	0.087251	0.47455	D	0.000236	T	0.33352	0.0860	M	0.66939	2.045	0.09310	N	1	D;D;D	0.89917	1.0;0.997;1.0	D;P;D	0.72625	0.95;0.798;0.978	T	0.03433	-1.1037	10	0.87932	D	0	-15.5721	6.5502	0.22429	0.2974:0.6148:0.0:0.0877	.	1101;1090;1117	D6W648;Q9P1Y5;Q9P1Y5-2	.;CAMP3_HUMAN;.	W	1117;1090	ENSP00000416797:R1117W;ENSP00000160298:R1090W	ENSP00000160298:R1090W	R	+	1	2	KIAA1543	7588267	0.729000	0.28090	0.018000	0.16275	0.462000	0.32619	3.120000	0.50430	1.161000	0.42604	0.462000	0.41574	CGG	.	.	none		0.632	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362	
DUSP27	92235	hgsc.bcm.edu	37	1	167097739	167097739	+	Missense_Mutation	SNP	C	C	A	rs2281959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167097739C>A	ENST00000361200.2	+	6	3537	c.3371C>A	c.(3370-3372)aCt>aAt	p.T1124N	DUSP27_ENST00000443333.1_Missense_Mutation_p.T1124N|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.T1124N			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	1124			T -> N (in dbSNP:rs2281959).		protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CGGAGAAGCACTGACAGGGAG	0.517													C|||	1914	0.382188	0.2776	0.2867	5008	,	,		20287	0.7431		0.3141	False		,,,				2504	0.2894				p.T1124N		Atlas-SNP	.											.	DUSP27	235	.	0			c.C3371A						PASS	.	C	ASN/THR	1248,3158	428.7+/-342.0	181,886,1136	46.0	42.0	43.0		3371	0.9	0.4	1	dbSNP_100	43	2668,5932	425.7+/-355.0	433,1802,2065	yes	missense	DUSP27	NM_001080426.1	65	614,2688,3201	AA,AC,CC		31.0233,28.325,30.1092	probably-damaging	1124/1159	167097739	3916,9090	2203	4300	6503	SO:0001583	missense	92235	exon5			GAAGCACTGACAG	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.3371C>A	1.37:g.167097739C>A	ENSP00000354483:p.Thr1124Asn	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	917	0.4198717948717949	142	0.2886178861788618	117	0.32320441988950277	435	0.7604895104895105	223	0.2941952506596306	C	5.249	0.231340	0.09969	0.28325	0.310233	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03580	3.88;3.88;3.88	5.4	0.916	0.19373	.	0.385319	0.22313	N	0.061703	T	0.01523	0.0049	M	0.63428	1.95	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.33085	-0.9882	9	0.87932	D	0	-3.2628	4.6731	0.12699	0.3827:0.4217:0.1241:0.0714	rs2281959;rs52811569;rs60867293;rs2281959	1124	Q5VZP5	DUS27_HUMAN	N	1124	ENSP00000354483:T1124N;ENSP00000271385:T1124N;ENSP00000404874:T1124N	ENSP00000271385:T1124N	T	+	2	0	DUSP27	165364363	0.002000	0.14202	0.363000	0.25875	0.335000	0.28730	0.036000	0.13819	0.198000	0.20407	-0.335000	0.08231	ACT	C|0.639;A|0.361	0.361	strong		0.517	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
PCDH7	5099	hgsc.bcm.edu	37	4	31144189	31144189	+	Silent	SNP	C	C	T	rs148629328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:31144189C>T	ENST00000543491.1	+	3	3486	c.3486C>T	c.(3484-3486)cgC>cgT	p.R1162R				O60245	PCDH7_HUMAN	protocadherin 7	0					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						TGCCGGTCCGCACTTCTCCGG	0.552													C|||	19	0.00379393	0.0144	0.0	5008	,	,		15274	0.0		0.0	False		,,,				2504	0.0				p.R1162R		Atlas-SNP	.											.	PCDH7	215	.	0			c.C3486T						PASS	.	C	,	56,3986		0,56,1965	91.0	91.0	91.0		3486,3462	2.1	1.0	4	dbSNP_134	91	2,8402		0,2,4200	no	coding-synonymous,coding-synonymous	PCDH7	NM_001173523.1,NM_032457.3	,	0,58,6165	TT,TC,CC		0.0238,1.3855,0.466	,	1162/1256,1154/1248	31144189	58,12388	2021	4202	6223	SO:0001819	synonymous_variant	5099	exon3			GGTCCGCACTTCT	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000543491.1:c.3486C>T	4.37:g.31144189C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_001173523	O60246|O60247|Q4W5C4	Silent	SNP	ENST00000543491.1	37	CCDS54753.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	5.456	0.269217	0.10349	0.013855	2.38E-4	ENSG00000169851	ENST00000511884	.	.	.	5.86	2.14	0.27477	.	.	.	.	.	T	0.51109	0.1655	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48364	-0.9042	4	.	.	.	.	10.4605	0.44577	0.0:0.731:0.0:0.269	.	.	.	.	Y	844	.	.	H	+	1	0	PCDH7	30753287	0.983000	0.35010	0.999000	0.59377	0.829000	0.46940	0.584000	0.23864	0.146000	0.19002	0.650000	0.86243	CAC	C|0.997;T|0.003	0.003	strong		0.552	PCDH7-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032457, NM_002589	
WNK4	65266	hgsc.bcm.edu	37	17	40947163	40947163	+	Silent	SNP	G	G	A	rs2290042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40947163G>A	ENST00000246914.5	+	14	2745	c.2724G>A	c.(2722-2724)ccG>ccA	p.P908P		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	908					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		TCTTTCCTCCGTGCCCCTCCA	0.572													A|||	515	0.102835	0.2557	0.0231	5008	,	,		16077	0.0387		0.004	False		,,,				2504	0.1207				p.P908P	Esophageal Squamous(6;201 374 4964 23855 42828)	Atlas-SNP	.											.	WNK4	182	.	0			c.G2724A						PASS	.	A		1002,3404	730.3+/-410.1	116,770,1317	275.0	253.0	260.0		2724	-4.8	0.0	17	dbSNP_100	260	11,8589	818.8+/-406.8	0,11,4289	no	coding-synonymous	WNK4	NM_032387.4		116,781,5606	AA,AG,GG		0.1279,22.7417,7.7887		908/1244	40947163	1013,11993	2203	4300	6503	SO:0001819	synonymous_variant	65266	exon14			TCCTCCGTGCCCC	AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.2724G>A	17.37:g.40947163G>A		Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	275	139	0.505455	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Silent	SNP	ENST00000246914.5	37	CCDS11439.1																																																																																			G|0.918;A|0.082	0.082	strong		0.572	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
PIEZO1	9780	hgsc.bcm.edu	37	16	88783449	88783449	+	Silent	SNP	C	C	G	rs8057031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88783449C>G	ENST00000301015.9	-	45	6888	c.6642G>C	c.(6640-6642)ctG>ctC	p.L2214L	RP5-1142A6.9_ENST00000564984.1_RNA|PIEZO1_ENST00000327397.7_Silent_p.L82L|MIR4722_ENST00000578292.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	2214					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						CGCCCAGCTTCAGGGTGACGG	0.622													G|||	3434	0.685703	0.7716	0.7176	5008	,	,		18796	0.8313		0.5596	False		,,,				2504	0.5266				p.L2214L		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G6642C						PASS	.	G		1035,349		392,251,49	169.0	168.0	168.0		6642	1.0	1.0	16	dbSNP_116	168	1848,1334		524,800,267	no	coding-synonymous	PIEZO1	NM_001142864.2		916,1051,316	GG,GC,CC		41.9233,25.2168,36.8594		2214/2522	88783449	2883,1683	692	1591	2283	SO:0001819	synonymous_variant	9780	exon45			CAGCTTCAGGGTG	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.6642G>C	16.37:g.88783449C>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	1539	0.7046703296703297	371	0.7540650406504065	244	0.6740331491712708	486	0.8496503496503497	438	0.5778364116094987	G	0.207	-1.040115	0.02013	0.747832	0.580767	ENSG00000103335	ENST00000451779	.	.	.	4.54	1.05	0.20165	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.17531	-1.0366	3	.	.	.	-28.0485	5.2143	0.15334	0.3531:0.1385:0.5084:0.0	rs8057031;rs11547380;rs60291860	.	.	.	Q	2160	.	.	E	-	1	0	FAM38A	87310950	1.000000	0.71417	0.992000	0.48379	0.103000	0.19146	0.982000	0.29539	-0.209000	0.10156	-0.216000	0.12614	GAA	C|0.318;G|0.682	0.682	strong		0.622	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
NRAP	4892	hgsc.bcm.edu	37	10	115392919	115392919	+	Missense_Mutation	SNP	T	T	A	rs2270182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115392919T>A	ENST00000359988.3	-	16	1800	c.1556A>T	c.(1555-1557)aAt>aTt	p.N519I	NRAP_ENST00000360478.3_Missense_Mutation_p.N484I|NRAP_ENST00000369360.3_Missense_Mutation_p.N484I|NRAP_ENST00000369358.4_Missense_Mutation_p.N519I	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		ATTCAACTTATTTTTCTCATA	0.423													T|||	1296	0.258786	0.3336	0.2248	5008	,	,		19373	0.1915		0.2714	False		,,,				2504	0.2382				p.N519I		Atlas-SNP	.											.	NRAP	208	.	0			c.A1556T						PASS	.	T	ILE/ASN,ILE/ASN	1556,2850	488.5+/-361.2	276,1004,923	139.0	118.0	125.0		1451,1556	5.7	1.0	10	dbSNP_100	125	2383,6217	394.7+/-344.8	332,1719,2249	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	149,149	608,2723,3172	AA,AT,TT		27.7093,35.3155,30.286	benign,benign	484/1696,519/1731	115392919	3939,9067	2203	4300	6503	SO:0001583	missense	4892	exon16			AACTTATTTTTCT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.1556A>T	10.37:g.115392919T>A	ENSP00000353078:p.Asn519Ile	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	204	103	0.504902	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	561	0.25686813186813184	152	0.3089430894308943	75	0.20718232044198895	117	0.20454545454545456	217	0.2862796833773087	T	17.26	3.344359	0.61073	0.353155	0.277093	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350;ENST00000369343	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.67	5.67	0.87782	.	0.097718	0.64402	D	0.000002	T	0.00012	0.0000	N	0.17082	0.46	0.32215	P	0.576051	D;P;D	0.53151	0.958;0.889;0.958	P;P;P	0.55749	0.783;0.578;0.783	T	0.38542	-0.9656	9	0.37606	T	0.19	.	11.4347	0.50062	0.0:0.0:0.2723:0.7277	rs2270182;rs60908683;rs2270182	519;484;519	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	I	519;484;519;484;248;248	ENSP00000358365:N519I;ENSP00000358367:N484I;ENSP00000353078:N519I;ENSP00000353666:N484I	ENSP00000353078:N519I	N	-	2	0	NRAP	115382909	1.000000	0.71417	0.959000	0.39883	0.989000	0.77384	2.477000	0.45180	2.159000	0.67721	0.455000	0.32223	AAT	T|0.718;A|0.282	0.282	strong		0.423	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
PSD4	23550	hgsc.bcm.edu	37	2	113941002	113941002	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113941002C>T	ENST00000245796.6	+	2	1164	c.969C>T	c.(967-969)ccC>ccT	p.P323P	PSD4_ENST00000441564.3_Silent_p.P323P	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	323					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						TCCCTGTGCCCATCTATAAAC	0.607																																					p.P323P		Atlas-SNP	.											PSD4,NS,carcinoma,+2,1	PSD4	74	1	0			c.C969T						scavenged	.						56.0	49.0	51.0					2																	113941002		2203	4300	6503	SO:0001819	synonymous_variant	23550	exon2			TGTGCCCATCTAT	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.969C>T	2.37:g.113941002C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	229	3	0.0131004	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Silent	SNP	ENST00000245796.6	37	CCDS33276.1																																																																																			.	.	none		0.607	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
PCSK5	5125	hgsc.bcm.edu	37	9	78925716	78925716	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:78925716C>T	ENST00000545128.1	+	29	4290	c.3752C>T	c.(3751-3753)cCg>cTg	p.P1251L		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1251	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						CAGATGCAGCCGGGCCACCCT	0.532																																					p.P1251L		Atlas-SNP	.											PCSK5_ENST00000545128,NS,carcinoma,-1,2	PCSK5	329	2	0			c.C3752T						scavenged	.						24.0	23.0	23.0					9																	78925716		876	1991	2867	SO:0001583	missense	5125	exon29			TGCAGCCGGGCCA		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.3752C>T	9.37:g.78925716C>T	ENSP00000446280:p.Pro1251Leu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	98	3	0.0306122	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	.	.	.	.	.	.	.	.	.	.	C	1.948	-0.442036	0.04604	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.49720	0.77;1.5	5.54	-0.713	0.11223	.	0.416740	0.24554	N	0.037532	T	0.32734	0.0839	L	0.37750	1.13	0.09310	N	1	.	.	.	.	.	.	T	0.34576	-0.9823	8	0.08381	T	0.77	-0.0018	10.5385	0.45018	0.0:0.5504:0.0:0.4496	.	.	.	.	L	1251;981;951	ENSP00000446280:P1251L;ENSP00000411654:P951L	ENSP00000365945:P981L	P	+	2	0	PCSK5	78115536	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	-0.410000	0.07151	-0.434000	0.07275	-1.731000	0.00696	CCG	.	.	none		0.532	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
BRSK1	84446	hgsc.bcm.edu	37	19	55817676	55817676	+	Silent	SNP	G	G	A	rs12973169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55817676G>A	ENST00000309383.1	+	17	2224	c.1947G>A	c.(1945-1947)aaG>aaA	p.K649K	BRSK1_ENST00000590333.1_Silent_p.K665K|BRSK1_ENST00000326848.7_Silent_p.K344K	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	649					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)		CCGAGTACAAGGCCAGTGGCG	0.642													G|||	451	0.0900559	0.1944	0.0836	5008	,	,		20548	0.0		0.1163	False		,,,				2504	0.0194				p.K649K		Atlas-SNP	.											.	BRSK1	192	.	0			c.G1947A						PASS	.	G		719,3687		68,583,1552	61.0	61.0	61.0		1947	4.1	1.0	19	dbSNP_121	61	830,7770		38,754,3508	no	coding-synonymous	BRSK1	NM_032430.1		106,1337,5060	AA,AG,GG		9.6512,16.3187,11.9099		649/779	55817676	1549,11457	2203	4300	6503	SO:0001819	synonymous_variant	84446	exon17			GTACAAGGCCAGT	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.1947G>A	19.37:g.55817676G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			G|0.889;A|0.111	0.111	strong		0.642	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
ROCK2	9475	hgsc.bcm.edu	37	2	11484212	11484212	+	Silent	SNP	C	C	A	rs368832806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11484212C>A	ENST00000315872.6	-	1	499	c.51G>T	c.(49-51)gcG>gcT	p.A17A	ROCK2_ENST00000462366.1_Intron	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	17					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		CGTCCCCCGGCGCGGTCTCGG	0.741													C|||	9	0.00179712	0.0061	0.0	5008	,	,		9307	0.001		0.0	False		,,,				2504	0.0				p.A17A		Atlas-SNP	.											ROCK2_ENST00000315872,NS,carcinoma,-2,2	ROCK2	224	2	0			c.G51T						PASS	.	C		7,3463		0,7,1728	10.0	12.0	11.0		51	-1.3	0.0	2		11	0,7918		0,0,3959	no	coding-synonymous	ROCK2	NM_004850.3		0,7,5687	AA,AC,CC		0.0,0.2017,0.0615		17/1389	11484212	7,11381	1735	3959	5694	SO:0001819	synonymous_variant	9475	exon1			CCCCGGCGCGGTC	D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.51G>T	2.37:g.11484212C>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	53	35	0.660377	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Silent	SNP	ENST00000315872.6	37	CCDS42654.1																																																																																			.	.	weak		0.741	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3		
ZNF610	162963	hgsc.bcm.edu	37	19	52869312	52869312	+	Silent	SNP	T	T	C	rs162120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52869312T>C	ENST00000403906.3	+	6	1137	c.681T>C	c.(679-681)acT>acC	p.T227T	ZNF610_ENST00000601151.1_Silent_p.T184T|ZNF610_ENST00000321287.8_Silent_p.T227T|ZNF610_ENST00000327920.8_Silent_p.T227T	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	227					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)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		TAATCCATACTGCAGAGAAAC	0.383													T|||	3940	0.786741	0.8366	0.7666	5008	,	,		19445	0.5268		0.8966	False		,,,				2504	0.8885				p.T227T		Atlas-SNP	.											.	ZNF610	84	.	0			c.T681C						PASS	.	T	,,,	3657,749	744.2+/-411.5	1515,627,61	68.0	68.0	68.0		681,681,552,681	-1.4	0.0	19	dbSNP_79	68	7507,1093	765.5+/-407.6	3276,955,69	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF610	NM_001161425.1,NM_001161426.1,NM_001161427.1,NM_173530.2	,,,	4791,1582,130	CC,CT,TT		12.7093,16.9995,14.1627	,,,	227/463,227/463,184/420,227/463	52869312	11164,1842	2203	4300	6503	SO:0001819	synonymous_variant	162963	exon6			CCATACTGCAGAG	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"""Zinc fingers, C2H2-type"", ""-"""	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.681T>C	19.37:g.52869312T>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001161426	A8K4C3|Q86YH8|Q8NDS9	Silent	SNP	ENST00000403906.3	37	CCDS12851.1																																																																																			T|0.181;C|0.819	0.819	strong		0.383	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530	
FAT3	120114	hgsc.bcm.edu	37	11	92538351	92538351	+	Silent	SNP	C	C	T	rs56843577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92538351C>T	ENST00000298047.6	+	10	8946	c.8929C>T	c.(8929-8931)Ctg>Ttg	p.L2977L	FAT3_ENST00000525166.1_Silent_p.L2827L|FAT3_ENST00000409404.2_Silent_p.L2977L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2977	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)				TGCTCTGGGCCTGGTGCAAAG	0.428										TCGA Ovarian(4;0.039)			C|||	81	0.0161741	0.059	0.0043	5008	,	,		19268	0.0		0.0	False		,,,				2504	0.0				p.L2977L		Atlas-SNP	.											.	FAT3	1822	.	0			c.C8929T						PASS	.	C		197,3563		4,189,1687	80.0	81.0	81.0		8929	5.1	1.0	11	dbSNP_129	81	0,8218		0,0,4109	no	coding-synonymous	FAT3	NM_001008781.2		4,189,5796	TT,TC,CC		0.0,5.2394,1.6447		2977/4558	92538351	197,11781	1880	4109	5989	SO:0001819	synonymous_variant	120114	exon10			CTGGGCCTGGTGC	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.8929C>T	11.37:g.92538351C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	178	81	0.455056	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.988;T|0.012	0.012	strong		0.428	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
NEURL4	84461	hgsc.bcm.edu	37	17	7226082	7226082	+	Silent	SNP	G	G	A	rs116452797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7226082G>A	ENST00000399464.2	-	16	2712	c.2697C>T	c.(2695-2697)acC>acT	p.T899T	NEURL4_ENST00000570460.1_Silent_p.T875T|NEURL4_ENST00000315614.7_Silent_p.T897T	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	899						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						AGGACTTCTCGGTGGCAGTGT	0.622													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21184	0.0		0.0	False		,,,				2504	0.0				p.T899T		Atlas-SNP	.											.	NEURL4	192	.	0			c.C2697T						PASS	.	G	,	6,4132		0,6,2063	159.0	171.0	167.0		2691,2697	-4.8	1.0	17	dbSNP_132	167	0,8428		0,0,4214	no	coding-synonymous,coding-synonymous	NEURL4	NM_001005408.1,NM_032442.2	,	0,6,6277	AA,AG,GG		0.0,0.145,0.0477	,	897/1561,899/1563	7226082	6,12560	2069	4214	6283	SO:0001819	synonymous_variant	84461	exon16			CTTCTCGGTGGCA		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.2697C>T	17.37:g.7226082G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Silent	SNP	ENST00000399464.2	37	CCDS42251.1																																																																																			G|0.999;A|0.001	0.001	strong		0.622	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	
CCDC40	55036	hgsc.bcm.edu	37	17	78032677	78032677	+	Silent	SNP	C	C	T	rs61734950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78032677C>T	ENST00000397545.4	+	9	1365	c.1338C>T	c.(1336-1338)ctC>ctT	p.L446L	CCDC40_ENST00000374876.4_Intron|CCDC40_ENST00000269318.5_Silent_p.L446L|CCDC40_ENST00000374877.3_Silent_p.L446L	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	446					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TGGACCAGCTCACCACTCGAG	0.562													C|||	292	0.0583067	0.1694	0.0159	5008	,	,		18404	0.0		0.001	False		,,,				2504	0.0573				p.L446L		Atlas-SNP	.											.	CCDC40	198	.	0			c.C1338T						PASS	.	C		578,3600		37,504,1548	87.0	91.0	90.0		1338	-3.2	0.8	17	dbSNP_129	90	3,8431		0,3,4214	no	coding-synonymous	CCDC40	NM_017950.3		37,507,5762	TT,TC,CC		0.0356,13.8344,4.6067		446/1143	78032677	581,12031	2089	4217	6306	SO:0001819	synonymous_variant	55036	exon9			CCAGCTCACCACT	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.1338C>T	17.37:g.78032677C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	103	60	0.582524	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																			C|0.972;T|0.028	0.028	strong		0.562	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082	
CAD	790	hgsc.bcm.edu	37	2	27462651	27462651	+	Silent	SNP	T	T	C	rs61741874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27462651T>C	ENST00000403525.1	+	33	5436	c.5292T>C	c.(5290-5292)acT>acC	p.T1764T	CAD_ENST00000264705.4_Silent_p.T1827T			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCCTGCCACTAGTGAGATGA	0.582													C|||	305	0.0609026	0.1089	0.0403	5008	,	,		17448	0.001		0.0626	False		,,,				2504	0.0706				p.T1827T		Atlas-SNP	.											.	CAD	199	.	0			c.T5481C						PASS	.	C		470,3936		28,414,1761	43.0	46.0	45.0		5481	4.3	0.8	2	dbSNP_129	45	538,8060		23,492,3784	no	coding-synonymous	CAD	NM_004341.3		51,906,5545	CC,CT,TT		6.2573,10.6673,7.7515		1827/2226	27462651	1008,11996	2203	4299	6502	SO:0001819	synonymous_variant	790	exon34			TGCCACTAGTGAG	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.5292T>C	2.37:g.27462651T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	37		113	0.051739926739926737	48	0.0975609756097561	19	0.052486187845303865	1	0.0017482517482517483	45	0.059366754617414245	C	3.673	-0.067097	0.07273	0.106673	0.062573	ENSG00000084774	ENST00000456311	.	.	.	5.15	4.28	0.50868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.3809	7.5674	0.27887	0.0:0.7373:0.0:0.2627	rs61741874	.	.	.	Q	115	.	.	X	+	1	0	CAD	27316155	0.912000	0.30974	0.787000	0.31911	0.424000	0.31475	0.588000	0.23924	0.582000	0.29556	-0.994000	0.02522	TAG	A|0.000;C|0.070;G|0.000;T|0.929	0.070	strong		0.582	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
C2orf16	84226	hgsc.bcm.edu	37	2	27801418	27801418	+	Missense_Mutation	SNP	C	C	A	rs1919126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27801418C>A	ENST00000408964.2	+	1	2030	c.1979C>A	c.(1978-1980)gCa>gAa	p.A660E		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	660			A -> E (in dbSNP:rs1919126).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GTGAAGTCTGCAGAATTAACC	0.393													A|||	3303	0.659545	0.7368	0.6888	5008	,	,		21677	0.8462		0.498	False		,,,				2504	0.5082				p.A660E		Atlas-SNP	.											.	C2orf16	357	.	0			c.C1979A						PASS	.	A	GLU/ALA	2621,1157		901,819,169	97.0	94.0	95.0		1979	-3.1	0.6	2	dbSNP_92	95	4093,4147		1033,2027,1060	yes	missense	C2orf16	NM_032266.3	107	1934,2846,1229	AA,AC,CC		49.6723,30.6247,44.1338	benign	660/1985	27801418	6714,5304	1889	4120	6009	SO:0001583	missense	84226	exon1			AGTCTGCAGAATT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.1979C>A	2.37:g.27801418C>A	ENSP00000386190:p.Ala660Glu	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	282	282	1	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	1446	0.6620879120879121	359	0.7296747967479674	228	0.6298342541436464	490	0.8566433566433567	369	0.4868073878627968	A	3.617	-0.078286	0.07184	0.693753	0.496723	ENSG00000221843	ENST00000408964	T	0.08807	3.05	4.83	-3.09	0.05331	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.10064	-1.0646	8	0.33141	T	0.24	.	1.8543	0.03175	0.3285:0.3785:0.1261:0.1669	rs1919126;rs17705292;rs56730508;rs1919126	660	Q68DN1	CB016_HUMAN	E	660	ENSP00000386190:A660E	ENSP00000386190:A660E	A	+	2	0	C2orf16	27654922	0.755000	0.28372	0.604000	0.28916	0.421000	0.31385	-1.056000	0.03489	-1.023000	0.03342	-0.363000	0.07495	GCA	C|0.365;A|0.635	0.635	strong		0.393	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
RDX	5962	hgsc.bcm.edu	37	11	110118459	110118459	+	Silent	SNP	T	T	C	rs139953187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:110118459T>C	ENST00000343115.4	-	10	1378	c.1059A>G	c.(1057-1059)caA>caG	p.Q353Q	RDX_ENST00000528900.1_Silent_p.Q6Q|RDX_ENST00000405097.1_Silent_p.Q353Q|RDX_ENST00000544551.1_Silent_p.Q217Q|RDX_ENST00000528498.1_Silent_p.Q353Q|RDX_ENST00000530301.1_Intron	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	353	Glu-rich.				actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		GCTCTTCAATTTGTTTTAGAC	0.308													T|||	53	0.0105831	0.0333	0.0115	5008	,	,		17959	0.0		0.001	False		,,,				2504	0.0				p.Q353Q	Esophageal Squamous(55;25 1062 11040 28755 44273)	Atlas-SNP	.											.	RDX	59	.	0			c.A1059G						PASS	.	T		107,4289	79.3+/-117.8	1,105,2092	134.0	122.0	126.0		1059	2.8	1.0	11	dbSNP_134	126	1,8587	1.2+/-3.3	0,1,4293	no	coding-synonymous	RDX	NM_002906.3		1,106,6385	CC,CT,TT		0.0116,2.434,0.8318		353/584	110118459	108,12876	2198	4294	6492	SO:0001819	synonymous_variant	5962	exon10			TTCAATTTGTTTT	BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710			9944	protein-coding gene	gene with protein product		179410	"""deafness, autosomal recessive 24"""	DFNB24		8486357, 17226784	Standard	NM_001260492		Approved		uc031qdy.1	P35241		ENST00000343115.4:c.1059A>G	11.37:g.110118459T>C		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	163	99	0.607362	NM_001260493	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Silent	SNP	ENST00000343115.4	37	CCDS8343.1																																																																																			T|0.989;C|0.011	0.011	strong		0.308	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906	
DROSHA	29102	hgsc.bcm.edu	37	5	31409252	31409252	+	Silent	SNP	A	A	G	rs2241337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:31409252A>G	ENST00000511367.2	-	32	4009	c.3765T>C	c.(3763-3765)aaT>aaC	p.N1255N	DROSHA_ENST00000513349.1_Silent_p.N1218N|DROSHA_ENST00000344624.3_Silent_p.N1255N|DROSHA_ENST00000442743.1_Silent_p.N1218N	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	1255	Necessary for interaction with DGCR8 and pri-miRNA processing activity.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						TCCAATCCTGATTCAAAATGA	0.413													A|||	1537	0.306909	0.2519	0.2839	5008	,	,		17757	0.4772		0.2137	False		,,,				2504	0.318				p.N1255N		Atlas-SNP	.											.	DROSHA	130	.	0			c.T3765C						PASS	.	A	,	890,2784		115,660,1062	62.0	58.0	59.0		3654,3765	4.1	1.0	5	dbSNP_98	59	1561,6621		151,1259,2681	no	coding-synonymous,coding-synonymous	DROSHA	NM_001100412.1,NM_013235.4	,	266,1919,3743	GG,GA,AA		19.0785,24.2243,20.6731	,	1218/1338,1255/1375	31409252	2451,9405	1837	4091	5928	SO:0001819	synonymous_variant	29102	exon32			ATCCTGATTCAAA	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.3765T>C	5.37:g.31409252A>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	248	110	0.443548	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Silent	SNP	ENST00000511367.2	37	CCDS47195.1																																																																																			A|0.696;G|0.304	0.304	strong		0.413	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
CP	1356	hgsc.bcm.edu	37	3	148901300	148901300	+	Missense_Mutation	SNP	C	C	T	rs115552500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148901300C>T	ENST00000264613.6	-	13	2640	c.2378G>A	c.(2377-2379)cGt>cAt	p.R793H	CP_ENST00000462336.1_5'Flank	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	793	F5/8 type A 3.|Plastocyanin-like 5.		R -> H. {ECO:0000269|PubMed:15557511}.		cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CACTGGAACACGGAATGTGCT	0.373													C|||	61	0.0121805	0.0234	0.013	5008	,	,		13349	0.001		0.0169	False		,,,				2504	0.0031				p.R793H		Atlas-SNP	.											.	CP	112	.	0			c.G2378A	GRCh37	CM045287	CP	M	rs115552500	PASS	.	C	HIS/ARG	89,4317	74.1+/-112.3	1,87,2115	133.0	118.0	123.0		2378	-1.8	0.0	3	dbSNP_132	123	79,8521	46.3+/-105.2	0,79,4221	yes	missense	CP	NM_000096.3	29	1,166,6336	TT,TC,CC		0.9186,2.02,1.2917	possibly-damaging	793/1066	148901300	168,12838	2203	4300	6503	SO:0001583	missense	1356	exon13			GGAACACGGAATG	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.2378G>A	3.37:g.148901300C>T	ENSP00000264613:p.Arg793His	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	25	0.011446886446886446	4	0.008130081300813009	8	0.022099447513812154	1	0.0017482517482517483	12	0.0158311345646438	C	14.94	2.684284	0.47991	0.0202	0.009186	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98937	-5.25;-5.25	5.39	-1.8	0.07907	Cupredoxin (2);	1.207680	0.05806	N	0.613068	D	0.93877	0.8041	L	0.49350	1.555	0.09310	N	1	P;P;P	0.47350	0.528;0.802;0.894	B;B;B	0.42653	0.279;0.394;0.394	D	0.90687	0.4610	10	0.42905	T	0.14	0.5473	6.2989	0.21101	0.0:0.338:0.3602:0.3019	.	793;793;793	A8K5A4;P00450;Q1L857	.;CERU_HUMAN;.	H	793;576	ENSP00000264613:R793H;ENSP00000420545:R576H	ENSP00000264613:R793H	R	-	2	0	CP	150383990	0.000000	0.05858	0.000000	0.03702	0.304000	0.27724	-0.336000	0.07863	-0.782000	0.04541	0.555000	0.69702	CGT	C|0.987;T|0.013	0.013	strong		0.373	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096	
MRPL46	26589	hgsc.bcm.edu	37	15	89002888	89002888	+	Missense_Mutation	SNP	G	G	T	rs146290179		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89002888G>T	ENST00000312475.4	-	4	837	c.796C>A	c.(796-798)Cca>Aca	p.P266T	MRPL46_ENST00000559538.1_5'UTR	NM_022163.3	NP_071446.2	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46	266						mitochondrion (GO:0005739)|ribosome (GO:0005840)	hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			AGGTATTTTGGTTTCAAATAG	0.502																																					p.P266T		Atlas-SNP	.											.	MRPL46	13	.	0			c.C796A						PASS	.	G	THR/PRO	2,4400	4.2+/-10.8	0,2,2199	119.0	101.0	107.0		796	6.0	0.5	15	dbSNP_134	107	0,8598		0,0,4299	no	missense	MRPL46	NM_022163.3	38	0,2,6498	TT,TG,GG		0.0,0.0454,0.0154	possibly-damaging	266/280	89002888	2,12998	2201	4299	6500	SO:0001583	missense	26589	exon4			ATTTTGGTTTCAA	AF210056	CCDS10341.1	15q25.3	2012-10-08	2001-12-10	2001-12-14	ENSG00000259494	ENSG00000259494		"""Mitochondrial ribosomal proteins / large subunits"""	1192	protein-coding gene	gene with protein product		611851	"""chromosome 15 open reading frame 4"""	C15orf4		11761714, 11551941	Standard	NM_022163		Approved	LIECG2, P2ECSL	uc002bmj.2	Q9H2W6	OTTHUMG00000148683	ENST00000312475.4:c.796C>A	15.37:g.89002888G>T	ENSP00000312311:p.Pro266Thr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_022163	B2RD75|Q9HBU8	Missense_Mutation	SNP	ENST00000312475.4	37	CCDS10341.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278489	0.59758	4.54E-4	0.0	ENSG00000173867	ENST00000312475	T	0.48201	0.82	5.98	5.98	0.97165	.	0.102208	0.64402	D	0.000002	T	0.47967	0.1474	M	0.62154	1.92	0.58432	D	0.999993	P	0.51653	0.947	B	0.43916	0.436	T	0.44697	-0.9311	10	0.36615	T	0.2	.	12.628	0.56640	0.0824:0.0:0.9176:0.0	.	266	Q9H2W6	RM46_HUMAN	T	266	ENSP00000312311:P266T	ENSP00000312311:P266T	P	-	1	0	MRPL46	86803892	1.000000	0.71417	0.508000	0.27688	0.542000	0.35054	4.395000	0.59678	2.835000	0.97688	0.650000	0.86243	CCA	G|1.000;T|0.000	0.000	weak		0.502	MRPL46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309073.1	NM_022163	
MASP2	10747	hgsc.bcm.edu	37	1	11106648	11106648	+	Missense_Mutation	SNP	G	G	A	rs56392418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11106648G>A	ENST00000400897.3	-	3	392	c.377C>T	c.(376-378)cCg>cTg	p.P126L	MASP2_ENST00000400898.3_Missense_Mutation_p.P126L	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	126	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.		P -> L (in MASPD; dbSNP:rs56392418). {ECO:0000269|PubMed:16029433, 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)		CCCCGTGAACGGCTTCTCGTT	0.607													G|||	181	0.0361422	0.1316	0.0101	5008	,	,		19642	0.0		0.0	False		,,,				2504	0.0				p.P126L	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											.	MASP2	71	.	0			c.C377T	GRCh37	CM073192	MASP2	M	rs56392418	PASS	.	G	LEU/PRO,LEU/PRO	505,3901	231.7+/-245.5	22,461,1720	52.0	45.0	47.0		377,377	2.8	1.0	1	dbSNP_129	47	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	MASP2	NM_006610.3,NM_139208.2	98,98	22,463,6018	AA,AG,GG		0.0233,11.4616,3.8982	possibly-damaging,possibly-damaging	126/687,126/186	11106648	507,12499	2203	4300	6503	SO:0001583	missense	10747	exon3			GTGAACGGCTTCT	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.377C>T	1.37:g.11106648G>A	ENSP00000383690:p.Pro126Leu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	130	50	0.384615	NM_139208	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	37	CCDS123.1	70	0.03205128205128205	66	0.13414634146341464	4	0.011049723756906077	0	0.0	0	0.0	G	17.33	3.361797	0.61403	0.114616	2.33E-4	ENSG00000009724	ENST00000400897;ENST00000400898	T;T	0.26660	1.72;1.72	4.87	2.75	0.32379	CUB (5);	0.752220	0.12578	N	0.456686	T	0.00178	0.0005	L	0.33485	1.01	0.49051	D	0.999741	B;P	0.36183	0.179;0.542	B;B	0.33196	0.016;0.159	T	0.18461	-1.0336	10	0.66056	D	0.02	.	7.2086	0.25921	0.0979:0.0:0.6342:0.2678	rs56392418;rs61747086	126;126	O00187-2;O00187	.;MASP2_HUMAN	L	126	ENSP00000383690:P126L;ENSP00000383691:P126L	ENSP00000383690:P126L	P	-	2	0	MASP2	11029235	0.099000	0.21834	0.984000	0.44739	0.939000	0.58152	0.769000	0.26604	1.046000	0.40249	-0.251000	0.11542	CCG	G|0.964;A|0.036	0.036	strong		0.607	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610	
FUT4	2526	hgsc.bcm.edu	37	11	94278713	94278713	+	Silent	SNP	C	C	T	rs2230274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94278713C>T	ENST00000358752.2	+	1	1697	c.1414C>T	c.(1414-1416)Ctg>Ttg	p.L472L	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_002033.3	NP_002024.1	P22083	FUT4_HUMAN	fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-specific)	472					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	cell periphery (GO:0071944)|cell surface (GO:0009986)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(2)|endometrium(2)|lung(1)|skin(2)|upper_aerodigestive_tract(1)	8		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GGCCTCGTACCTGCTTTTCCT	0.652													C|||	356	0.0710863	0.034	0.1369	5008	,	,		15600	0.0536		0.0586	False		,,,				2504	0.1053				p.L472L		Atlas-SNP	.											FUT4,NS,carcinoma,0,1	FUT4	17	1	0			c.C1414T						PASS	.	C		114,4288	83.4+/-121.9	2,110,2089	51.0	52.0	52.0		1414	2.1	1.0	11	dbSNP_98	52	472,8124	136.8+/-193.9	6,460,3832	no	coding-synonymous	FUT4	NM_002033.3		8,570,5921	TT,TC,CC		5.4909,2.5897,4.5084		472/531	94278713	586,12412	2201	4298	6499	SO:0001819	synonymous_variant	2526	exon1			TCGTACCTGCTTT		CCDS8301.1	11q21	2013-02-26			ENSG00000196371	ENSG00000196371		"""CD molecules"", ""Fucosyltransferases"""	4015	protein-coding gene	gene with protein product	"""ELAM ligand fucosyltransferase"", ""galactoside 3-L-fucosyltransferase"""	104230		CD15, FCT3A, ELFT		1702034	Standard	NM_002033		Approved	FUC-TIV	uc001pez.3	P22083	OTTHUMG00000167795	ENST00000358752.2:c.1414C>T	11.37:g.94278713C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	115	47	0.408696	NM_002033	B2RMS0	Silent	SNP	ENST00000358752.2	37	CCDS8301.1																																																																																			C|0.940;T|0.060	0.060	strong		0.652	FUT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396327.2	NM_002033	
P2RX7	5027	hgsc.bcm.edu	37	12	121622563	121622563	+	Silent	SNP	G	G	A	rs1621388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121622563G>A	ENST00000546057.1	+	13	1889	c.1746G>A	c.(1744-1746)ccG>ccA	p.P582P	P2RX7_ENST00000328963.5_Silent_p.P412P|RP11-340F14.5_ENST00000569999.1_RNA|P2RX7_ENST00000541446.1_Silent_p.P293P|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000535250.1_Silent_p.P492P	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	582					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)					AAGAGTTTCCGAAGAGTGAAG	0.607													C|||	1604	0.320288	0.4546	0.2003	5008	,	,		18772	0.1438		0.3837	False		,,,				2504	0.3405				p.P582P		Atlas-SNP	.											P2RX7,NS,carcinoma,0,1	P2RX7	53	1	0			c.G1746A						PASS	.	C		1901,2449		434,1033,708	8.0	7.0	7.0		1746	1.1	0.9	12	dbSNP_89	7	3244,5208		747,1750,1729	no	coding-synonymous	P2RX7	NM_002562.5		1181,2783,2437	AA,AG,GG		38.3814,43.7011,40.189		582/596	121622563	5145,7657	2175	4226	6401	SO:0001819	synonymous_variant	5027	exon13			GTTTCCGAAGAGT	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.1746G>A	12.37:g.121622563G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	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|0.649;A|0.351	0.351	strong		0.607	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
RBL2	5934	hgsc.bcm.edu	37	16	53504721	53504721	+	Silent	SNP	T	T	C	rs10748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53504721T>C	ENST00000262133.6	+	17	2727	c.2590T>C	c.(2590-2592)Ttg>Ctg	p.L864L	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Intron	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	864	Domain B.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TTCAGATGAATTGAGGAAAAA	0.378													C|||	2524	0.503994	0.8464	0.4049	5008	,	,		19554	0.1786		0.4662	False		,,,				2504	0.4857				p.L864L		Atlas-SNP	.											.	RBL2	115	.	0			c.T2590C						PASS	.	C		3377,1019	372.2+/-320.3	1309,759,130	128.0	136.0	133.0		2590	2.2	1.0	16	dbSNP_52	133	4177,4423	587.1+/-392.1	1029,2119,1152	no	coding-synonymous	RBL2	NM_005611.3		2338,2878,1282	CC,CT,TT		48.5698,23.1802,41.8744		864/1140	53504721	7554,5442	2198	4300	6498	SO:0001819	synonymous_variant	5934	exon17			GATGAATTGAGGA	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2590T>C	16.37:g.53504721T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Silent	SNP	ENST00000262133.6	37	CCDS10748.1																																																																																			T|0.470;C|0.530	0.530	strong		0.378	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
TCF7L1	83439	hgsc.bcm.edu	37	2	85510654	85510654	+	Missense_Mutation	SNP	T	T	A	rs115942112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85510654T>A	ENST00000282111.3	+	4	753	c.478T>A	c.(478-480)Tcc>Acc	p.S160T		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	160	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CGATGTCCCCTCCAGCGCCAC	0.507													T|||	60	0.0119808	0.0393	0.0	5008	,	,		20302	0.005		0.0	False		,,,				2504	0.0031				p.S160T		Atlas-SNP	.											.	TCF7L1	44	.	0			c.T478A						PASS	.	T	THR/SER	134,4272	97.1+/-135.8	1,132,2070	257.0	224.0	235.0		478	3.1	1.0	2	dbSNP_132	235	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TCF7L1	NM_031283.2	58	1,133,6369	AA,AT,TT		0.0116,3.0413,1.038	benign	160/589	85510654	135,12871	2203	4300	6503	SO:0001583	missense	83439	exon4			GTCCCCTCCAGCG	X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.478T>A	2.37:g.85510654T>A	ENSP00000282111:p.Ser160Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	131	57	0.435115	NM_031283	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000282111.3	37	CCDS1971.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	T	12.34	1.910078	0.33721	0.030413	1.16E-4	ENSG00000152284	ENST00000282111;ENST00000442813	D	0.98550	-4.99	5.44	3.08	0.35506	CTNNB1 binding, N-teminal (1);	0.586502	0.18208	N	0.148291	D	0.83608	0.5291	N	0.22421	0.69	0.26675	N	0.971648	B	0.33000	0.393	B	0.34536	0.185	D	0.84356	0.0535	10	0.56958	D	0.05	.	5.5742	0.17215	0.0:0.09:0.1841:0.7258	.	160	Q9HCS4	TF7L1_HUMAN	T	160;10	ENSP00000282111:S160T	ENSP00000282111:S160T	S	+	1	0	TCF7L1	85364165	0.989000	0.36119	0.998000	0.56505	0.988000	0.76386	0.065000	0.14466	0.382000	0.24878	0.533000	0.62120	TCC	T|0.989;A|0.011	0.011	strong		0.507	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283	
MUC21	394263	hgsc.bcm.edu	37	6	30955043	30955043	+	Missense_Mutation	SNP	G	G	A	rs9262385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30955043G>A	ENST00000376296.3	+	2	1332	c.1091G>A	c.(1090-1092)gGg>gAg	p.G364E	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	364	28 X 15 AA approximate tandem repeats.|Ser-rich.			G -> E (in Ref. 3; AAQ88781 and 4; CAQ08321). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACCAACTCTGGGTCCAGCACG	0.632													a|||	106	0.0211661	0.0197	0.0576	5008	,	,		18768	0.0079		0.0179	False		,,,				2504	0.0143				p.G364E		Atlas-SNP	.											MUC21,NS,neuroblastoma,0,1	MUC21	98	1	0			c.G1091A						scavenged	.	A	GLU/GLY	25,4361		2,21,2170	143.0	141.0	141.0		1091	-6.6	0.0	6	dbSNP_118	141	46,8528		4,38,4245	no	missense	MUC21	NM_001010909.2	98	6,59,6415	AA,AG,GG		0.5365,0.57,0.5478	benign	364/567	30955043	71,12889	2193	4287	6480	SO:0001583	missense	394263	exon2			ACTCTGGGTCCAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1091G>A	6.37:g.30955043G>A	ENSP00000365473:p.Gly364Glu	Somatic	152	4	0.0263158		WXS	Illumina HiSeq	Phase_I	185	10	0.0540541	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	a	0.072	-1.201075	0.01581	0.0057	0.005365	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02323	4.34	4.44	-6.61	0.01818	.	.	.	.	.	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.46830	-0.9163	9	0.02654	T	1	0.4928	3.9243	0.09257	0.1415:0.3445:0.3555:0.1585	rs9262385	364	Q5SSG8	MUC21_HUMAN	E	214;364	ENSP00000365473:G364E	ENSP00000365473:G364E	G	+	2	0	MUC21	31063022	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.474000	0.02337	-1.580000	0.01644	-2.305000	0.00258	GGG	G|0.992;A|0.008	0.008	strong		0.632	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
NUAK2	81788	hgsc.bcm.edu	37	1	205273142	205273142	+	Silent	SNP	G	G	C	rs41264881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	106	0	0		WXS	Illumina HiSeq	Phase_I	126	73	0.579365	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	
ZNF721	170960	hgsc.bcm.edu	37	4	438067	438067	+	Silent	SNP	C	C	T	rs73070365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:438067C>T	ENST00000338977.5	-	2	201	c.153G>A	c.(151-153)aaG>aaA	p.K51K	ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000511833.2_Silent_p.K63K			Q8TF20	ZN721_HUMAN	zinc finger protein 721	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)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						TATAAACTCCCTTCTGCACTT	0.308													T|||	350	0.0698882	0.1967	0.0591	5008	,	,		20712	0.0		0.0358	False		,,,				2504	0.0133				p.V63V		Atlas-SNP	.											.	ZNF721	205	.	0			c.A189A						PASS	.	T		620,3442		45,530,1456	65.0	73.0	70.0		189	0.0	0.0	4	dbSNP_130	70	305,8181		2,301,3940	no	coding-synonymous	ZNF721	NM_133474.2		47,831,5396	TT,TC,CC		3.5942,15.2634,7.3717		63/924	438067	925,11623	2031	4243	6274	SO:0001819	synonymous_variant	170960	exon3			AACTCCCTTCTGC	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.153G>A	4.37:g.438067C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	140	58	0.414286	NM_133474	Q69YG7	Silent	SNP	ENST00000338977.5	37																																																																																				C|0.943;T|0.057	0.057	strong		0.308	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474	
RNF207	388591	hgsc.bcm.edu	37	1	6267523	6267523	+	Silent	SNP	C	C	T	rs58587405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6267523C>T	ENST00000377939.4	+	3	403	c.276C>T	c.(274-276)ggC>ggT	p.G92G	RNF207_ENST00000377948.2_5'UTR|RP1-120G22.11_ENST00000455744.1_RNA	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	92						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		CAGGGGATGGCGTGGAGGCGG	0.692													C|||	152	0.0303514	0.1059	0.0144	5008	,	,		10633	0.0		0.002	False		,,,				2504	0.0				p.G92G		Atlas-SNP	.											.	RNF207	45	.	0			c.C276T						PASS	.	C		427,3971		22,383,1794	23.0	26.0	25.0		276	3.6	0.4	1	dbSNP_129	25	5,8589		0,5,4292	no	coding-synonymous	RNF207	NM_207396.2		22,388,6086	TT,TC,CC		0.0582,9.709,3.3251		92/635	6267523	432,12560	2199	4297	6496	SO:0001819	synonymous_variant	388591	exon3			GGATGGCGTGGAG	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.276C>T	1.37:g.6267523C>T		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	294	152	0.517007	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Silent	SNP	ENST00000377939.4	37	CCDS59.2																																																																																			C|0.966;T|0.034	0.034	strong		0.692	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
ASB2	51676	hgsc.bcm.edu	37	14	94401102	94401102	+	Missense_Mutation	SNP	C	C	T	rs35858830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94401102C>T	ENST00000315988.4	-	8	2152	c.1664G>A	c.(1663-1665)cGg>cAg	p.R555Q	ASB2_ENST00000555019.1_Missense_Mutation_p.R603Q	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	555	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		CTTTCGAACCCGCAGTCGGCA	0.478													C|||	42	0.00838658	0.0038	0.0144	5008	,	,		22330	0.002		0.0109	False		,,,				2504	0.0143				p.R603Q		Atlas-SNP	.											.	ASB2	71	.	0			c.G1808A						PASS	.	C	GLN/ARG,GLN/ARG	37,4369	42.3+/-75.8	1,35,2167	83.0	84.0	84.0		1808,1664	2.4	1.0	14	dbSNP_126	84	171,8429	79.2+/-141.9	1,169,4130	yes	missense,missense	ASB2	NM_001202429.1,NM_016150.4	43,43	2,204,6297	TT,TC,CC		1.9884,0.8398,1.5993	benign,benign	603/636,555/588	94401102	208,12798	2203	4300	6503	SO:0001583	missense	51676	exon10			CGAACCCGCAGTC	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.1664G>A	14.37:g.94401102C>T	ENSP00000320675:p.Arg555Gln	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	37	CCDS9915.1	17	0.007783882783882784	3	0.006097560975609756	5	0.013812154696132596	2	0.0034965034965034965	7	0.009234828496042216	C	13.32	2.201541	0.38905	0.008398	0.019884	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988	T;T	0.43688	0.94;0.94	5.44	2.36	0.29203	SOCS protein, C-terminal (3);	0.230510	0.41605	N	0.000842	T	0.10981	0.0268	N	0.11673	0.155	0.32024	N	0.600374	B;B	0.09022	0.002;0.002	B;B	0.12837	0.004;0.008	T	0.09530	-1.0670	10	0.33141	T	0.24	.	8.4054	0.32612	0.0:0.536:0.0:0.464	rs35858830	603;555	B4E166;Q96Q27	.;ASB2_HUMAN	Q	603;571;555	ENSP00000451575:R603Q;ENSP00000320675:R555Q	ENSP00000320675:R555Q	R	-	2	0	ASB2	93470855	0.012000	0.17670	0.996000	0.52242	0.974000	0.67602	-0.537000	0.06128	0.150000	0.19136	0.491000	0.48974	CGG	C|0.985;T|0.015	0.015	strong		0.478	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
KIF17	57576	hgsc.bcm.edu	37	1	21011346	21011346	+	Silent	SNP	A	A	G	rs12028811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21011346A>G	ENST00000247986.2	-	10	2497	c.2187T>C	c.(2185-2187)acT>acC	p.T729T	KIF17_ENST00000400463.3_Silent_p.T729T|KIF17_ENST00000375044.1_Silent_p.T629T|KIF17_ENST00000490034.1_5'UTR			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	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	201	91	0.452736	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	
CCDC92	80212	hgsc.bcm.edu	37	12	124421764	124421764	+	Silent	SNP	C	C	T	rs34241686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124421764C>T	ENST00000238156.3	-	5	1191	c.837G>A	c.(835-837)ccG>ccA	p.P279P	CCDC92_ENST00000545135.1_Silent_p.P262P|CCDC92_ENST00000545891.1_Silent_p.P262P|CCDC92_ENST00000544798.1_Intron|RP11-380L11.3_ENST00000602292.1_RNA|DNAH10OS_ENST00000514254.2_5'Flank	NM_025140.1	NP_079416.1	Q53HC0	CCD92_HUMAN	coiled-coil domain containing 92	279						centriole (GO:0005814)				large_intestine(5)|lung(2)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.0002)|OV - Ovarian serous cystadenocarcinoma(86;0.000222)|all cancers(50;0.00129)|BRCA - Breast invasive adenocarcinoma(302;0.242)		TTTCGCGGGCCGGGCTGTGCT	0.701													C|||	27	0.00539137	0.0197	0.0	5008	,	,		12393	0.0		0.001	False		,,,				2504	0.0				p.P279P		Atlas-SNP	.											.	CCDC92	18	.	0			c.G837A						PASS	.	C		54,4342		0,54,2144	18.0	21.0	20.0		837	-9.9	0.1	12	dbSNP_126	20	4,8578		0,4,4287	no	coding-synonymous	CCDC92	NM_025140.1		0,58,6431	TT,TC,CC		0.0466,1.2284,0.4469		279/332	124421764	58,12920	2198	4291	6489	SO:0001819	synonymous_variant	80212	exon5			GCGGGCCGGGCTG	AK026124	CCDS9256.1	12q24.31	2011-09-02			ENSG00000119242	ENSG00000119242			29563	protein-coding gene	gene with protein product	"""limkain beta 2"""					12477932	Standard	NM_025140		Approved	FLJ22471	uc001ufw.1	Q53HC0	OTTHUMG00000168725	ENST00000238156.3:c.837G>A	12.37:g.124421764C>T		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_025140	B3KNQ0|Q9H697	Silent	SNP	ENST00000238156.3	37	CCDS9256.1																																																																																			C|0.996;T|0.004	0.004	strong		0.701	CCDC92-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400780.2	NM_025140	
MICALL1	85377	hgsc.bcm.edu	37	22	38302469	38302469	+	Missense_Mutation	SNP	C	C	T	rs146549351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38302469C>T	ENST00000215957.6	+	1	166	c.40C>T	c.(40-42)Cgc>Tgc	p.R14C		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	14	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)					CTGGTGCCGCCGCCAGTGCGA	0.786													c|||	50	0.00998403	0.0371	0.0014	5008	,	,		3679	0.0		0.0	False		,,,				2504	0.0				p.R14C		Atlas-SNP	.											.	MICALL1	53	.	0			c.C40T						PASS	.		CYS/ARG	44,3156		1,42,1557	4.0	4.0	4.0		40	1.0	1.0	22	dbSNP_134	4	0,6182		0,0,3091	no	missense	MICALL1	NM_033386.3	180	1,42,4648	TT,TC,CC		0.0,1.375,0.469	probably-damaging	14/864	38302469	44,9338	1600	3091	4691	SO:0001583	missense	85377	exon1			TGCCGCCGCCAGT	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.40C>T	22.37:g.38302469C>T	ENSP00000215957:p.Arg14Cys	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	37	CCDS13961.1	128	0.05860805860805861	70	0.14227642276422764	22	0.06077348066298342	12	0.02097902097902098	24	0.0316622691292876	c	14.95	2.687334	0.48097	0.01375	0.0	ENSG00000100139	ENST00000215957	D	0.95342	-3.68	2.15	1.04	0.20106	Calponin homology domain (5);	.	.	.	.	T	0.15046	0.0363	M	0.92317	3.295	0.80722	D	1	B	0.14438	0.01	B	0.14023	0.01	T	0.69442	-0.5144	9	0.87932	D	0	.	8.698	0.34307	0.0:0.8737:0.0:0.1263	.	14	Q8N3F8	MILK1_HUMAN	C	14	ENSP00000215957:R14C	ENSP00000215957:R14C	R	+	1	0	MICALL1	36632415	1.000000	0.71417	0.985000	0.45067	0.590000	0.36582	4.587000	0.60991	0.179000	0.19938	0.165000	0.16767	CGC	C|0.942;T|0.058	0.058	strong		0.786	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386	
PAQR5	54852	hgsc.bcm.edu	37	15	69682021	69682021	+	Silent	SNP	G	G	A	rs12438855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:69682021G>A	ENST00000340965.3	+	6	1082	c.414G>A	c.(412-414)acG>acA	p.T138T	PAQR5_ENST00000395407.2_Silent_p.T138T|PAQR5_ENST00000561153.1_Silent_p.T138T|PAQR5_ENST00000561027.1_3'UTR|RP11-253M7.6_ENST00000560870.1_RNA	NM_001104554.1	NP_001098024.1	Q9NXK6	MPRG_HUMAN	progestin and adipoQ receptor family member V	138					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)|steroid binding (GO:0005496)			endometrium(3)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|skin(1)	11						CTGCATACACGTTCCCGGATG	0.582													G|||	250	0.0499201	0.0416	0.0562	5008	,	,		20434	0.1151		0.0179	False		,,,				2504	0.0225				p.T138T		Atlas-SNP	.											PAQR5,caecum,carcinoma,+1,1	PAQR5	35	1	0			c.G414A						PASS	.	G	,	169,4231	112.9+/-151.0	5,159,2036	180.0	137.0	152.0		414,414	-4.6	0.5	15	dbSNP_120	152	91,8505	53.1+/-113.8	1,89,4208	no	coding-synonymous,coding-synonymous	PAQR5	NM_001104554.1,NM_017705.3	,	6,248,6244	AA,AG,GG		1.0586,3.8409,2.0006	,	138/331,138/331	69682021	260,12736	2200	4298	6498	SO:0001819	synonymous_variant	54852	exon6			ATACACGTTCCCG		CCDS10232.1	15q22.31	2012-08-10			ENSG00000137819	ENSG00000137819			29645	protein-coding gene	gene with protein product	"""membrane progestin receptor gamma"""	607781				12574519	Standard	NM_001104554		Approved	FLJ20190, MPRG	uc002arz.2	Q9NXK6	OTTHUMG00000133322	ENST00000340965.3:c.414G>A	15.37:g.69682021G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	173	86	0.49711	NM_001104554	Q8IXU2	Silent	SNP	ENST00000340965.3	37	CCDS10232.1																																																																																			G|0.960;A|0.040	0.040	strong		0.582	PAQR5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416671.1	NM_017705	
IGLL1	3543	hgsc.bcm.edu	37	22	23917176	23917176	+	Silent	SNP	G	G	A	rs115303391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:23917176G>A	ENST00000330377.2	-	2	417	c.300C>T	c.(298-300)agC>agT	p.S100S	AP000345.2_ENST00000454863.1_RNA|AP000345.2_ENST00000458318.1_RNA|IGLL1_ENST00000249053.3_Intron	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	100	J region (By similarity to lambda light- chain).				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						GCTGGGTCCCGCTGCCAAACA	0.577													g|||	176	0.0351438	0.1263	0.0115	5008	,	,		17917	0.0		0.001	False		,,,				2504	0.0				p.S100S		Atlas-SNP	.											.	IGLL1	27	.	0			c.C300T						PASS	.	G	,	537,3869		35,467,1701	70.0	59.0	63.0		300,	-3.2	0.0	22	dbSNP_132	63	11,8589		0,11,4289	no	coding-synonymous,intron	IGLL1	NM_020070.2,NM_152855.1	,	35,478,5990	AA,AG,GG		0.1279,12.1879,4.2134	,	100/214,	23917176	548,12458	2203	4300	6503	SO:0001819	synonymous_variant	3543	exon2			GGTCCCGCTGCCA	X52204	CCDS13809.1, CCDS13810.1	22q11.23	2014-09-17			ENSG00000128322	ENSG00000128322		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	5870	protein-coding gene	gene with protein product		146770		IGLL		3139558, 2511029	Standard	NM_020070		Approved	IGVPB, IGL5, 14.1, CD179B	uc002zxd.3	P15814	OTTHUMG00000150673	ENST00000330377.2:c.300C>T	22.37:g.23917176G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	154	72	0.467532	NM_020070	Q0P681	Silent	SNP	ENST00000330377.2	37	CCDS13809.1																																																																																			G|0.965;A|0.035	0.035	strong		0.577	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1	NM_020070	
RFX6	222546	hgsc.bcm.edu	37	6	117248218	117248218	+	Silent	SNP	T	T	C	rs611349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117248218T>C	ENST00000332958.2	+	17	1930	c.1914T>C	c.(1912-1914)ggT>ggC	p.G638G		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	638					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AGATTGCTGGTCATCTGATGA	0.453													T|||	1705	0.340455	0.2958	0.2911	5008	,	,		17880	0.4226		0.2286	False		,,,				2504	0.4663				p.G638G		Atlas-SNP	.											.	RFX6	141	.	0			c.T1914C						PASS	.	T		1251,3155	428.5+/-341.9	187,877,1139	101.0	100.0	101.0		1914	-4.1	0.9	6	dbSNP_83	101	1530,7070	288.9+/-299.0	143,1244,2913	no	coding-synonymous	RFX6	NM_173560.3		330,2121,4052	CC,CT,TT		17.7907,28.3931,21.3824		638/929	117248218	2781,10225	2203	4300	6503	SO:0001819	synonymous_variant	222546	exon17			TGCTGGTCATCTG	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1914T>C	6.37:g.117248218T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_173560	Q5T6B3	Silent	SNP	ENST00000332958.2	37	CCDS5113.1																																																																																			T|0.757;C|0.243	0.243	strong		0.453	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560	
MED14	9282	hgsc.bcm.edu	37	X	40551993	40551993	+	Silent	SNP	G	G	A	rs10127014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40551993G>A	ENST00000324817.1	-	14	1930	c.1812C>T	c.(1810-1812)acC>acT	p.T604T		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	604	Interaction with SREBF1.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|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)|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)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	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 coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCTGTTTCCCGGTTTTTGTAC	0.433													G|||	105	0.0278146	0.0719	0.0029	3775	,	,		13717	0.0		0.0	False		,,,				2504	0.0082				p.T604T		Atlas-SNP	.											.	MED14	108	.	0			c.C1812T						PASS	.	G		275,3560		4,230,37,1398,534	137.0	113.0	121.0		1812	-9.3	0.0	X	dbSNP_119	121	0,6728		0,0,0,2428,1872	no	coding-synonymous	MED14	NM_004229.3		4,230,37,3826,2406	AA,AG,A,GG,G		0.0,7.1708,2.6034		604/1455	40551993	275,10288	2203	4300	6503	SO:0001819	synonymous_variant	9282	exon14			TTTCCCGGTTTTT	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.1812C>T	X.37:g.40551993G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	236	128	0.542373	NM_004229	Q4KMR7|Q9UNB3	Silent	SNP	ENST00000324817.1	37	CCDS14254.1																																																																																			G|0.966;A|0.034	0.034	strong		0.433	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229	
HAPLN2	60484	hgsc.bcm.edu	37	1	156593928	156593928	+	Missense_Mutation	SNP	G	G	T	rs149573918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156593928G>T	ENST00000255039.1	+	4	822	c.415G>T	c.(415-417)Gtg>Ttg	p.V139L	HAPLN2_ENST00000494218.1_3'UTR	NM_021817.2	NP_068589.1	Q9GZV7	HPLN2_HUMAN	hyaluronan and proteoglycan link protein 2	139	Ig-like V-type.				cell adhesion (GO:0007155)|establishment of blood-nerve barrier (GO:0008065)|extracellular matrix assembly (GO:0085029)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	7	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGACGAGAGCGTGGCGCTGAC	0.692													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		14129	0.0		0.0	False		,,,				2504	0.0				p.V139L		Atlas-SNP	.											.	HAPLN2	20	.	0			c.G415T						PASS	.	G	LEU/VAL	162,4192		4,154,2019	42.0	36.0	38.0		415	1.9	1.0	1	dbSNP_134	38	2,8482		0,2,4240	yes	missense	HAPLN2	NM_021817.2	32	4,156,6259	TT,TG,GG		0.0236,3.7207,1.2775	benign	139/341	156593928	164,12674	2177	4242	6419	SO:0001583	missense	60484	exon4			GAGAGCGTGGCGC	AB049054	CCDS1148.1	1q23.1	2013-01-11			ENSG00000132702	ENSG00000132702		"""Immunoglobulin superfamily / V-set domain containing"""	17410	protein-coding gene	gene with protein product	"""brain link protein 1"""					11027579, 11873941	Standard	NM_021817		Approved	BRAL1	uc001fpn.1	Q9GZV7	OTTHUMG00000033205	ENST00000255039.1:c.415G>T	1.37:g.156593928G>T	ENSP00000255039:p.Val139Leu	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	213	99	0.464789	NM_021817	Q5T3J0	Missense_Mutation	SNP	ENST00000255039.1	37	CCDS1148.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	G	13.59	2.283640	0.40394	0.037207	2.36E-4	ENSG00000132702	ENST00000255039;ENST00000544775;ENST00000456112	T;T	0.26957	1.7;1.7	4.04	1.89	0.25635	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.225805	0.35838	N	0.002959	T	0.05090	0.0136	N	0.17379	0.485	0.32704	N	0.512539	B	0.10296	0.003	B	0.18871	0.023	T	0.29731	-1.0002	10	0.27082	T	0.32	-15.0291	7.6488	0.28336	0.0:0.1512:0.5635:0.2853	.	139	Q9GZV7	HPLN2_HUMAN	L	139;112;139	ENSP00000255039:V139L;ENSP00000388835:V139L	ENSP00000255039:V139L	V	+	1	0	HAPLN2	154860552	0.867000	0.29959	1.000000	0.80357	0.971000	0.66376	0.920000	0.28705	0.995000	0.38917	0.655000	0.94253	GTG	G|0.986;T|0.014	0.014	strong		0.692	HAPLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081039.1	NM_021817	
ITGAM	3684	hgsc.bcm.edu	37	16	31276811	31276811	+	Missense_Mutation	SNP	G	G	A	rs1143679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31276811G>A	ENST00000287497.8	+	3	305	c.230G>A	c.(229-231)cGc>cAc	p.R77H	RNU7-199P_ENST00000517067.1_RNA|ITGAM_ENST00000544665.3_Missense_Mutation_p.R77H			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	77			R -> H (influences susceptibility to SLE; dbSNP:rs1143679). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18204448}.		activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						GAGCCCATCCGCCTGCAGGGT	0.632													G|||	426	0.0850639	0.1203	0.0893	5008	,	,		15680	0.0149		0.1312	False		,,,				2504	0.0593				p.R77H		Atlas-SNP	.											.	ITGAM	137	.	0			c.G230A	GRCh37	CM080418	ITGAM	M	rs1143679	PASS	.	G	HIS/ARG,HIS/ARG	375,3739		20,335,1702	12.0	14.0	13.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	230,230	-9.3	0.0	16	dbSNP_86	13	958,7490		66,826,3332	yes	missense,missense	ITGAM	NM_000632.3,NM_001145808.1	29,29	86,1161,5034	AA,AG,GG		11.34,9.1152,10.6114	possibly-damaging,possibly-damaging	77/1153,77/1154	31276811	1333,11229	2057	4224	6281	SO:0001583	missense	3684	exon3			CCATCCGCCTGCA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.230G>A	16.37:g.31276811G>A	ENSP00000287497:p.Arg77His	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_000632	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	192	0.08791208791208792	59	0.11991869918699187	31	0.0856353591160221	1	0.0017482517482517483	101	0.13324538258575197	G	11.69	1.714788	0.30413	0.091152	0.1134	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.72615	-0.67;-0.67	5.03	-9.33	0.00639	.	.	.	.	.	T	0.00580	0.0019	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.06162	-1.0842	9	0.41790	T	0.15	.	6.0249	0.19650	0.2214:0.5921:0.1048:0.0817	rs1143679;rs17362505	77	P11215	ITAM_HUMAN	H	77	ENSP00000441691:R77H;ENSP00000287497:R77H	ENSP00000287497:R77H	R	+	2	0	ITGAM	31184312	0.000000	0.05858	0.018000	0.16275	0.894000	0.52154	-1.319000	0.02702	-2.349000	0.00618	-0.140000	0.14226	CGC	G|0.914;A|0.086	0.086	strong		0.632	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632	
GUCA1C	9626	hgsc.bcm.edu	37	3	108627024	108627024	+	Missense_Mutation	SNP	T	T	C	rs16854916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108627024T>C	ENST00000261047.3	-	4	607	c.475A>G	c.(475-477)Atg>Gtg	p.M159V	GUCA1C_ENST00000393963.3_Missense_Mutation_p.H172R	NM_005459.3	NP_005450.3	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C	159	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.		M -> V (in dbSNP:rs16854916).		phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(2)|large_intestine(1)|liver(1)|lung(8)|pancreas(1)|skin(1)	14						TCTTTTGCCATGCCATTGATA	0.398													T|||	76	0.0151757	0.056	0.0029	5008	,	,		17705	0.0		0.0	False		,,,				2504	0.0				p.M159V	NSCLC(157;1360 1999 30631 40189 44208)	Atlas-SNP	.											.	GUCA1C	39	.	0			c.A475G						PASS	.	T	VAL/MET	184,4222	119.6+/-157.3	3,178,2022	84.0	82.0	83.0		475	-0.5	0.0	3	dbSNP_123	83	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GUCA1C	NM_005459.3	21	3,179,6321	CC,CT,TT		0.0116,4.1761,1.4224	benign	159/210	108627024	185,12821	2203	4300	6503	SO:0001583	missense	9626	exon4			TTGCCATGCCATT	AF110002	CCDS2954.1	3q13.1	2013-01-10			ENSG00000138472	ENSG00000138472		"""EF-hand domain containing"""	4680	protein-coding gene	gene with protein product	"""guanylyl cyclase-activating protein 3"""	605128				10037746, 11860507	Standard	NM_005459		Approved	GCAP3	uc003dxj.2	O95843	OTTHUMG00000159204	ENST00000261047.3:c.475A>G	3.37:g.108627024T>C	ENSP00000261047:p.Met159Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_005459	O95844|Q9UNM0	Missense_Mutation	SNP	ENST00000261047.3	37	CCDS2954.1	29|29	0.013278388278388278|0.013278388278388278	28|28	0.056910569105691054|0.056910569105691054	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	T|T	0.866|0.866	-0.733700|-0.733700	0.03111|0.03111	0.041761|0.041761	1.16E-4|1.16E-4	ENSG00000138472|ENSG00000138472	ENST00000393963|ENST00000261047	T|T	0.66638|0.71817	-0.22|-0.6	5.67|5.67	-0.534|-0.534	0.11883|0.11883	.|EF-hand-like domain (1);	.|1.183010	.|0.05826	.|N	.|0.616757	T|T	0.06508|0.06508	0.0167|0.0167	N|N	0.05280|0.05280	-0.08|-0.08	0.09310|0.09310	N|N	1|1	B|B	0.13145|0.02656	0.007|0.0	B|B	0.10450|0.01281	0.005|0.0	T|T	0.08597|0.08597	-1.0714|-1.0714	9|10	0.41790|0.07175	T|T	0.15|0.84	.|.	3.7193|3.7193	0.08450|0.08450	0.1218:0.0744:0.2242:0.5796|0.1218:0.0744:0.2242:0.5796	rs16854916;rs52837740;rs56517263;rs16854916|rs16854916;rs52837740;rs56517263;rs16854916	172|159	C9JNI2|O95843	.|GUC1C_HUMAN	R|V	172|159	ENSP00000377535:H172R|ENSP00000261047:M159V	ENSP00000377535:H172R|ENSP00000261047:M159V	H|M	-|-	2|1	0|0	GUCA1C|GUCA1C	110109714|110109714	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.322000|0.322000	0.28314|0.28314	0.442000|0.442000	0.21628|0.21628	0.073000|0.073000	0.16731|0.16731	-0.461000|-0.461000	0.05368|0.05368	CAT|ATG	T|0.982;C|0.018	0.018	strong		0.398	GUCA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353819.1	NM_005459	
C16orf82	162083	hgsc.bcm.edu	37	16	27078547	27078547	+	lincRNA	SNP	G	G	C	rs386790113|rs201942674|rs114049498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27078547G>C	ENST00000505035.1	+	0	520				RP11-673P17.2_ENST00000565783.1_RNA			Q7Z2V1	TNT_HUMAN	chromosome 16 open reading frame 82																		TGCAGCACCCGAGGCCAGAGG	0.652													C|||	228	0.0455272	0.1346	0.0086	5008	,	,		16840	0.0		0.004	False		,,,				2504	0.0409				p.P77P		Atlas-SNP	.											.	.	.	.	0			c.G231C						PASS	.	C		249,4131		11,227,1952	22.0	30.0	27.0		231	3.1	0.0	16	dbSNP_132	27	73,8505		0,73,4216	no	coding-synonymous	C16orf82	NM_001145545.1		11,300,6168	CC,CG,GG		0.851,5.6849,2.485		77/155	27078547	322,12636	2190	4289	6479			162083	exon1			GCACCCGAGGCCA	BC031257		16p12.1	2013-01-24			ENSG00000234186	ENSG00000234186			30755	other	unknown						12477932	Standard	NM_001145545		Approved	TNT	uc010vcm.2	Q7Z2V1	OTTHUMG00000161986		16.37:g.27078547G>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_001145545	B9EGC2|Q8NEF0	Silent	SNP	ENST00000505035.1	37																																																																																				G|0.968;C|0.032	0.032	strong		0.652	C16orf82-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000366634.1	NM_001145545	
BEST1	7439	hgsc.bcm.edu	37	11	61722645	61722645	+	Silent	SNP	C	C	A	rs1109748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61722645C>A	ENST00000378043.4	+	3	862	c.219C>A	c.(217-219)atC>atA	p.I73I	BEST1_ENST00000378042.3_Silent_p.I13I|BEST1_ENST00000526988.1_5'UTR|BEST1_ENST00000449131.2_Silent_p.I13I|BEST1_ENST00000534553.1_5'UTR|BEST1_ENST00000301774.9_5'UTR|BEST1_ENST00000435278.2_Silent_p.I73I	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	73			I -> N (in VMD2). {ECO:0000269|PubMed:11241846}.		chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						ACAGCTACATCCAGCTCATCC	0.602													C|||	1590	0.317492	0.0825	0.2839	5008	,	,		13980	0.6498		0.0726	False		,,,				2504	0.5685				p.I73I		Atlas-SNP	.											.	BEST1	85	.	0			c.C219A						PASS	.	C	,	366,4038	187.1+/-213.8	19,328,1855	187.0	155.0	166.0	http://www.ncbi.nlm.nih.gov/pubmed?term	39,219	3.9	1.0	11	dbSNP_86	166	629,7969	162.0+/-214.8	30,569,3700	no	coding-synonymous,coding-synonymous	BEST1	NM_001139443.1,NM_004183.3	,	49,897,5555	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	7.3157,8.3106,7.6527	,	13/605,73/586	61722645	995,12007	2202	4299	6501	SO:0001819	synonymous_variant	7439	exon3			CTACATCCAGCTC	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.219C>A	11.37:g.61722645C>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			C|0.838;A|0.162	0.162	strong		0.602	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
CDC42BPA	8476	hgsc.bcm.edu	37	1	227348245	227348245	+	Splice_Site	SNP	G	G	A	rs34614709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227348245G>A	ENST00000366769.3	-	6	1983	c.692C>T	c.(691-693)aCg>aTg	p.T231M	CDC42BPA_ENST00000535525.1_Splice_Site_p.T231M|CDC42BPA_ENST00000366766.2_Splice_Site_p.T231M|CDC42BPA_ENST00000366764.2_Splice_Site_p.T231M|CDC42BPA_ENST00000334218.5_Splice_Site_p.T231M|CDC42BPA_ENST00000366765.3_Splice_Site_p.T231M|CDC42BPA_ENST00000366767.3_Splice_Site_p.T231M	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TTTATTTACCGTTCCATCTTC	0.318													G|||	29	0.00579073	0.0219	0.0	5008	,	,		16832	0.0		0.0	False		,,,				2504	0.0				p.T231M		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.C692T						PASS	.	G	MET/THR,MET/THR	77,4329	68.7+/-106.4	1,75,2127	130.0	139.0	136.0		692,692	5.2	1.0	1	dbSNP_126	136	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,missense-near-splice	CDC42BPA	NM_003607.3,NM_014826.4	81,81	1,76,6426	AA,AG,GG		0.0116,1.7476,0.5997	probably-damaging,probably-damaging	231/1720,231/1639	227348245	78,12928	2203	4300	6503	SO:0001630	splice_region_variant	8476	exon6			TTTACCGTTCCAT	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.693+1C>T	1.37:g.227348245G>A		Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	305	136	0.445902	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	37	CCDS1558.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	25.7	4.667652	0.88348	0.017476	1.16E-4	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;-0.19;-0.19	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.60741	0.2292	L	0.55743	1.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.998;0.999	T	0.65084	-0.6254	10	0.22109	T	0.4	.	17.4674	0.87637	0.0:0.0:1.0:0.0	rs34614709	231;231;231;231	F5H5N0;Q5VT25-4;Q5VT25-3;Q5VT25-5	.;.;.;.	M	231	ENSP00000355731:T231M;ENSP00000355729:T231M;ENSP00000335341:T231M;ENSP00000355728:T231M;ENSP00000355726:T231M;ENSP00000443275:T231M;ENSP00000355727:T231M	ENSP00000335341:T231M	T	-	2	0	CDC42BPA	225414868	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.035000	0.93752	2.394000	0.81467	0.585000	0.79938	ACG	G|0.995;A|0.005	0.005	strong		0.318	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	Missense_Mutation
OR2T4	127074	hgsc.bcm.edu	37	1	248525290	248525290	+	Silent	SNP	C	C	T	rs202028348|rs141576206|rs386642002|rs374193555|rs57728407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248525290C>T	ENST00000366475.1	+	1	408	c.408C>T	c.(406-408)taC>taT	p.Y136Y		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, 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)	p.Y136*(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGTTCTTCTACGTGACACTAG	0.522													t|||	1549	0.309305	0.2678	0.2752	5008	,	,		19688	0.4405		0.1899	False		,,,				2504	0.3773				p.Y136Y		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	1	1	Substitution - Nonsense(1)	lung(1)	c.C408T						scavenged	.																																			SO:0001819	synonymous_variant	127074	exon1			CTTCTACGTGACA	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.408C>T	1.37:g.248525290C>T		Somatic	953	2	0.00209864		WXS	Illumina HiSeq	Phase_I	567	22	0.0388007	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			C|0.840;T|0.160	0.160	strong		0.522	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
MUC4	4585	hgsc.bcm.edu	37	3	195515025	195515025	+	Silent	SNP	A	A	G	rs199975352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515025A>G	ENST00000463781.3	-	2	3885	c.3426T>C	c.(3424-3426)acT>acC	p.T1142T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T1142T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	616					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.T1142T(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)		ATACTGAGGAAGTGTCGGTGA	0.562																																					p.T1142T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,4	MUC4	1505	4	1	Substitution - coding silent(1)	endometrium(1)	c.T3426C						scavenged	.						11.0	7.0	8.0					3																	195515025		677	1483	2160	SO:0001819	synonymous_variant	4585	exon2			TGAGGAAGTGTCG	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.3426T>C	3.37:g.195515025A>G		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	438	161	0.36758	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|0.960;G|0.040	0.040	strong		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PRRC2C	23215	hgsc.bcm.edu	37	1	171553209	171553209	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171553209C>T	ENST00000338920.4	+	29	7755	c.7518C>T	c.(7516-7518)tcC>tcT	p.S2506S	PRRC2C_ENST00000367742.3_Silent_p.S2508S|PRRC2C_ENST00000392078.3_Silent_p.S2508S|PRRC2C_ENST00000426496.2_Silent_p.S2441S	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2506	Gln-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AGGCACAATCCGGTCTTGCCT	0.463																																					p.S2506S		Atlas-SNP	.											.	.	.	.	0			c.C7518T						PASS	.						181.0	172.0	175.0					1																	171553209		2203	4300	6503	SO:0001819	synonymous_variant	23215	exon29			ACAATCCGGTCTT	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.7518C>T	1.37:g.171553209C>T		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	272	133	0.488971	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	C	5.989	0.366324	0.11352	.	.	ENSG00000117523	ENST00000495585	.	.	.	5.98	-12.0	0.00017	.	.	.	.	.	T	0.19805	0.0476	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54702	-0.8254	4	.	.	.	.	4.6701	0.12685	0.2829:0.418:0.1692:0.1299	.	.	.	.	L	989	.	.	P	+	2	0	PRRC2C	169819833	0.000000	0.05858	0.002000	0.10522	0.916000	0.54674	-2.380000	0.01066	-4.069000	0.00076	-2.084000	0.00378	CCG	.	.	none		0.463	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
CACNA2D4	93589	hgsc.bcm.edu	37	12	1965369	1965369	+	Silent	SNP	G	G	A	rs2286372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:1965369G>A	ENST00000382722.5	-	21	2397	c.2035C>T	c.(2035-2037)Ctg>Ttg	p.L679L	CACNA2D4_ENST00000586184.1_Silent_p.L679L|CACNA2D4_ENST00000585708.1_Silent_p.L615L|CACNA2D4_ENST00000539048.2_5'UTR|CACNA2D4_ENST00000587995.1_Silent_p.L654L|CACNA2D4_ENST00000585732.1_Silent_p.L540L|CACNA2D4_ENST00000588077.1_Silent_p.L615L	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	679					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GCCAGGGCCAGGTCTGGGTGA	0.507													G|||	871	0.173922	0.0961	0.1412	5008	,	,		21761	0.4226		0.0139	False		,,,				2504	0.2106				p.L679L	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.C2035T						PASS	.	G		337,3587		19,299,1644	141.0	143.0	143.0		2035	2.5	0.6	12	dbSNP_100	143	147,8139		3,141,3999	no	coding-synonymous	CACNA2D4	NM_172364.4		22,440,5643	AA,AG,GG		1.7741,8.5882,3.964		679/1138	1965369	484,11726	1962	4143	6105	SO:0001819	synonymous_variant	93589	exon21			GGGCCAGGTCTGG	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.2035C>T	12.37:g.1965369G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	82	49	0.597561	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Silent	SNP	ENST00000382722.5	37	CCDS44785.1																																																																																			G|0.840;A|0.160	0.160	strong		0.507	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
ALDH1L2	160428	hgsc.bcm.edu	37	12	105433523	105433523	+	Silent	SNP	T	T	A	rs4964317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	155	0	0		WXS	Illumina HiSeq	Phase_I	147	85	0.578231	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	
EFCAB12	90288	hgsc.bcm.edu	37	3	129137245	129137245	+	Missense_Mutation	SNP	T	T	G	rs116798859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129137245T>G	ENST00000505956.1	-	3	695	c.533A>C	c.(532-534)cAg>cCg	p.Q178P	EFCAB12_ENST00000326085.3_Missense_Mutation_p.Q178P	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	178							calcium ion binding (GO:0005509)										CAGCTGGAGCTGGGGCACCAT	0.607													T|||	163	0.0325479	0.1157	0.013	5008	,	,		14537	0.0		0.001	False		,,,				2504	0.0				p.Q178P		Atlas-SNP	.											.	.	.	.	0			c.A533C						PASS	.	T	PRO/GLN	316,3492		6,304,1594	31.0	30.0	30.0		533	-2.7	1.0	3	dbSNP_132	30	5,8221		0,5,4108	yes	missense	C3orf25	NM_207307.1	76	6,309,5702	GG,GT,TT		0.0608,8.2983,2.6674	probably-damaging	178/573	129137245	321,11713	1904	4113	6017	SO:0001583	missense	90288	exon3			TGGAGCTGGGGCA	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.533A>C	3.37:g.129137245T>G	ENSP00000420854:p.Gln178Pro	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	68	41	0.602941	NM_207307	Q69YX4	Missense_Mutation	SNP	ENST00000505956.1	37	CCDS54638.1	47	0.02152014652014652	41	0.08333333333333333	6	0.016574585635359115	0	0.0	0	0.0	T	13.32	2.201720	0.38905	0.082983	6.08E-4	ENSG00000172771	ENST00000505956;ENST00000326085;ENST00000503957	T;T;T	0.33438	2.47;2.47;1.41	4.82	-2.68	0.06041	.	0.623436	0.14251	N	0.331422	T	0.01353	0.0044	L	0.34521	1.04	0.23802	N	0.99681	D	0.58620	0.983	P	0.56700	0.804	T	0.02983	-1.1086	10	0.40728	T	0.16	-17.8429	1.6546	0.02779	0.4769:0.0911:0.1374:0.2946	.	178	Q6NXP0	CC025_HUMAN	P	178;178;28	ENSP00000420854:Q178P;ENSP00000324241:Q178P;ENSP00000421462:Q28P	ENSP00000324241:Q178P	Q	-	2	0	C3orf25	130619935	0.954000	0.32549	0.988000	0.46212	0.232000	0.25224	-0.068000	0.11561	-0.177000	0.10690	0.459000	0.35465	CAG	T|0.975;G|0.025	0.025	strong		0.607	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	
MYO9B	4650	hgsc.bcm.edu	37	19	17303774	17303774	+	Missense_Mutation	SNP	T	T	G	rs1545620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17303774T>G	ENST00000594824.1	+	21	3178	c.3031T>G	c.(3031-3033)Tca>Gca	p.S1011A	MYO9B_ENST00000595618.1_Missense_Mutation_p.S1011A|MYO9B_ENST00000397274.2_Missense_Mutation_p.S1011A			Q13459	MYO9B_HUMAN	myosin IXB	1011	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.|Neck or regulatory domain.			S -> A (in Ref. 1; AAC50402). {ECO:0000305}.	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						CCTCCAGGCCTCATGGAGGGG	0.677													G|||	3227	0.644369	0.7905	0.7032	5008	,	,		14650	0.7391		0.3897	False		,,,				2504	0.5695				p.S1011A		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	0			c.T3031G	GRCh37	CM066145	MYO9B	M	rs1545620	PASS	.	G	ALA/SER,ALA/SER	2939,1003		1112,715,144	12.0	17.0	15.0		3031,3031	-1.5	0.0	19	dbSNP_88	15	3377,4719		787,1803,1458	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	99,99	1899,2518,1602	GG,GT,TT		41.712,25.4439,47.5328	benign,benign	1011/2023,1011/2158	17303774	6316,5722	1971	4048	6019	SO:0001583	missense	4650	exon21			CAGGCCTCATGGA		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.3031T>G	19.37:g.17303774T>G	ENSP00000471367:p.Ser1011Ala	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	45	44	0.977778	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		1361	0.6231684981684982	382	0.7764227642276422	239	0.6602209944751382	440	0.7692307692307693	300	0.39577836411609496	G	0.005	-2.214157	0.00289	0.745561	0.41712	ENSG00000099331	ENST00000397274	T	0.21361	2.01	4.88	-1.46	0.08800	.	1.199970	0.06003	N	0.648098	T	0.00012	0.0000	N	0.00368	-1.59	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	0.43909	-0.9362	9	0.02654	T	1	.	0.9756	0.01425	0.2544:0.1088:0.337:0.2998	rs1545620;rs57113186;rs1545620	1011;1011;1017	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	A	1011	ENSP00000380444:S1011A	ENSP00000380444:S1011A	S	+	1	0	MYO9B	17164774	0.000000	0.05858	0.043000	0.18650	0.020000	0.10135	0.668000	0.25127	0.092000	0.17331	-0.721000	0.03606	TCA	T|0.363;G|0.637	0.637	strong		0.677	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
IKBKAP	8518	hgsc.bcm.edu	37	9	111641825	111641825	+	Missense_Mutation	SNP	G	G	A	rs1538660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:111641825G>A	ENST00000374647.5	-	33	3780	c.3473C>T	c.(3472-3474)cCc>cTc	p.P1158L	IKBKAP_ENST00000467959.1_5'UTR|IKBKAP_ENST00000537196.1_Missense_Mutation_p.P809L	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	1158			P -> L (in dbSNP:rs1538660). {ECO:0000269|PubMed:17974005}.		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						TTGCCCGTGGGGTACCTCATC	0.473													G|||	1227	0.245008	0.3207	0.1599	5008	,	,		17712	0.2937		0.172	False		,,,				2504	0.228				p.P1158L		Atlas-SNP	.											.	IKBKAP	122	.	0			c.C3473T						PASS	.	G	LEU/PRO	1333,3073	446.5+/-348.0	194,945,1064	98.0	79.0	86.0		3473	3.0	0.0	9	dbSNP_88	86	1423,7177	272.7+/-290.2	129,1165,3006	yes	missense	IKBKAP	NM_003640.3	98	323,2110,4070	AA,AG,GG		16.5465,30.2542,21.1902	benign	1158/1333	111641825	2756,10250	2203	4300	6503	SO:0001583	missense	8518	exon33			CCGTGGGGTACCT	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.3473C>T	9.37:g.111641825G>A	ENSP00000363779:p.Pro1158Leu	Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	202	144	0.712871	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	37	CCDS6773.1	488	0.22344322344322345	141	0.2865853658536585	49	0.13535911602209943	165	0.28846153846153844	133	0.17546174142480211	G	8.589	0.884182	0.17467	0.302542	0.165465	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.27557	2.05;1.66	5.96	2.96	0.34315	.	0.316290	0.33813	N	0.004524	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B	0.09022	0.002	B	0.11329	0.006	T	0.41413	-0.9510	9	0.15952	T	0.53	1.6491	6.3668	0.21459	0.1673:0.0:0.6873:0.1454	rs1538660;rs2230797;rs52816671;rs56685838;rs1538660	1158	O95163	ELP1_HUMAN	L	1158;809	ENSP00000363779:P1158L;ENSP00000439367:P809L	ENSP00000363779:P1158L	P	-	2	0	IKBKAP	110681646	0.982000	0.34865	0.027000	0.17364	0.657000	0.38888	3.011000	0.49567	0.334000	0.23590	-0.345000	0.07892	CCC	G|0.773;A|0.227	0.227	strong		0.473	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
ZCCHC18	644353	hgsc.bcm.edu	37	X	103359334	103359334	+	Missense_Mutation	SNP	C	C	T	rs61745269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:103359334C>T	ENST00000537356.3	+	2	1946	c.532C>T	c.(532-534)Ctt>Ttt	p.L178F	ZCCHC18_ENST00000422784.1_Intron|SLC25A53_ENST00000357421.4_Intron			P0CG32	ZCC18_HUMAN	zinc finger, CCHC domain containing 18	178							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)										CTTGCAACAGCTTCTTTTAGG	0.498													C|||	164	0.0434437	0.118	0.0101	3775	,	,		14288	0.0		0.001	False		,,,				2504	0.0				p.L178F		Atlas-SNP	.											.	.	.	.	0			c.C532T						PASS	.	C	,PHE/LEU	164,1045		12,119,21,386,154	40.0	32.0	35.0		,532	2.7	0.3	X	dbSNP_129	35	1,2390		0,1,0,799,791	yes	intron,missense	MCART6,ZCCHC18	NM_001012755.3,NM_001143978.1	,22	12,120,21,1185,945	TT,TC,T,CC,C		0.0418,13.5649,4.5833	,benign	,178/404	103359334	165,3435	692	1591	2283	SO:0001583	missense	644353	exon3			CAACAGCTTCTTT	AF086548	CCDS65304.1	Xq22.2	2013-01-31	2009-02-03		ENSG00000166707	ENSG00000166707		"""Zinc fingers, CCHC domain containing"", ""Paraneoplastic Ma antigens"""	32459	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 7B"""		"""zinc finger, CCHC domain containing 12 pseudogene 1"""				Standard	NM_001143978		Approved	SIZN2, PNMA7B	uc011msh.2	P0CG32	OTTHUMG00000022123	ENST00000537356.3:c.532C>T	X.37:g.103359334C>T	ENSP00000473824:p.Leu178Phe	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	259	148	0.571429	NM_001143978		Missense_Mutation	SNP	ENST00000537356.3	37																																																																																				C|0.962;T|0.038	0.038	strong		0.498	ZCCHC18-006	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471686.1	NM_001143978	
GPC4	2239	hgsc.bcm.edu	37	X	132438872	132438872	+	Missense_Mutation	SNP	C	C	A	rs1129980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:132438872C>A	ENST00000370828.3	-	7	1697	c.1173G>T	c.(1171-1173)gaG>gaT	p.E391D	GPC4_ENST00000535467.1_Missense_Mutation_p.E321D	NM_001448.2	NP_001439.2	O75487	GPC4_HUMAN	glypican 4	391			E -> D (in dbSNP:rs1129980). {ECO:0000269|PubMed:10814714, ECO:0000269|PubMed:9787072, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|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)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|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)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					GTTTCAGTTTCTCCTTGACAT	0.433													C|||	1732	0.458808	0.5053	0.1787	3775	,	,		15716	0.3492		0.2177	False		,,,				2504	0.3773				p.E391D		Atlas-SNP	.											.	GPC4	58	.	0			c.G1173T						PASS	.	C	ASP/GLU	2289,1546		593,784,319,255,252	178.0	150.0	160.0		1173	3.4	1.0	X	dbSNP_86	160	1986,4742		209,1010,558,1209,1314	yes	missense	GPC4	NM_001448.2	45	802,1794,877,1464,1566	AA,AC,A,CC,C		29.5184,40.3129,40.4715	benign	391/557	132438872	4275,6288	2203	4300	6503	SO:0001583	missense	2239	exon7			CAGTTTCTCCTTG	AF030186	CCDS14637.1	Xq26.1	2008-02-05			ENSG00000076716	ENSG00000076716		"""Proteoglycans / Cell Surface : Glypicans"""	4452	protein-coding gene	gene with protein product	"""glypican proteoglycan 4"""	300168				9787072	Standard	NM_001448		Approved	K-glypican	uc004exc.1	O75487	OTTHUMG00000022434	ENST00000370828.3:c.1173G>T	X.37:g.132438872C>A	ENSP00000359864:p.Glu391Asp	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	121	47	0.38843	NM_001448	B2R6J7|B4E2C0|Q6ZMA6|Q96L43|Q9NU08|Q9UJN1|Q9UPD9	Missense_Mutation	SNP	ENST00000370828.3	37	CCDS14637.1	654	0.39421338155515373	173	0.4914772727272727	50	0.15822784810126583	117	0.26	117	0.17410714285714285	C	12.01	1.808215	0.31961	0.596871	0.295184	ENSG00000076716	ENST00000370828;ENST00000536418;ENST00000535467	T;T	0.52526	0.66;0.66	5.13	3.36	0.38483	.	0.046337	0.85682	D	0.000000	T	0.00012	0.0000	L	0.43152	1.355	0.24745	P	0.99301708	B	0.24483	0.104	B	0.30782	0.12	T	0.45279	-0.9272	9	0.23891	T	0.37	-19.7874	7.2029	0.25891	0.0:0.643:0.0:0.357	rs1129980;rs1805046;rs52808097;rs57817524;rs1129980	391	O75487	GPC4_HUMAN	D	391;385;321	ENSP00000359864:E391D;ENSP00000444959:E321D	ENSP00000359864:E391D	E	-	3	2	GPC4	132266538	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.974000	0.29436	0.948000	0.37687	0.594000	0.82650	GAG	C|0.574;A|0.426	0.426	strong		0.433	GPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058338.1	NM_001448	
PPFIBP1	8496	hgsc.bcm.edu	37	12	27842052	27842052	+	Silent	SNP	G	G	A	rs61730962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27842052G>A	ENST00000318304.8	+	26	2902	c.2619G>A	c.(2617-2619)ctG>ctA	p.L873L	PPFIBP1_ENST00000537927.1_Silent_p.L720L|PPFIBP1_ENST00000542629.1_Silent_p.L842L|PPFIBP1_ENST00000228425.6_Silent_p.L867L	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	873	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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)					TCAACCTTCTGATTGGGGCTG	0.473													G|||	274	0.0547125	0.2005	0.0115	5008	,	,		18229	0.0		0.001	False		,,,				2504	0.0				p.L873L		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.G2619A						PASS	.	G	,,,	720,3686	299.0+/-285.6	56,608,1539	130.0	117.0	121.0		2160,2526,2601,2619	4.4	1.0	12	dbSNP_129	121	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPFIBP1	NM_001198915.1,NM_001198916.1,NM_003622.3,NM_177444.2	,,,	56,612,5835	AA,AG,GG		0.0465,16.3414,5.5667	,,,	720/859,842/981,867/1006,873/1012	27842052	724,12282	2203	4300	6503	SO:0001819	synonymous_variant	8496	exon26			CCTTCTGATTGGG	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.2619G>A	12.37:g.27842052G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	167	84	0.502994	NM_177444	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	37	CCDS55812.1																																																																																			G|0.949;A|0.051	0.051	strong		0.473	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
PTPRD	5789	hgsc.bcm.edu	37	9	8518143	8518143	+	Silent	SNP	T	T	C	rs7026388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:8518143T>C	ENST00000381196.4	-	18	1791	c.1248A>G	c.(1246-1248)gcA>gcG	p.A416A	PTPRD_ENST00000358503.5_Silent_p.A403A|PTPRD_ENST00000397606.3_Silent_p.A406A|PTPRD_ENST00000355233.5_Silent_p.A416A|PTPRD_ENST00000397611.3_Silent_p.A413A|PTPRD_ENST00000356435.5_Silent_p.A416A|PTPRD_ENST00000397617.3_Silent_p.A406A|PTPRD_ENST00000486161.1_Silent_p.A416A|PTPRD_ENST00000540109.1_Silent_p.A416A|PTPRD_ENST00000537002.1_Silent_p.A413A|PTPRD_ENST00000360074.4_Silent_p.A403A	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	217	0	0		WXS	Illumina HiSeq	Phase_I	250	144	0.576	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		
C8A	731	hgsc.bcm.edu	37	1	57378149	57378149	+	Missense_Mutation	SNP	G	G	T	rs1620075|rs386631447	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57378149G>T	ENST00000361249.3	+	10	1550	c.1454G>T	c.(1453-1455)cGc>cTc	p.R485L		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	485	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.		R -> L (in dbSNP:rs1620075).		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						AACCTGCGCCGCGCCTTGGAC	0.622													G|||	682	0.136182	0.261	0.1326	5008	,	,		17760	0.0407		0.0477	False		,,,				2504	0.1595				p.R485L		Atlas-SNP	.											C8A,NS,carcinoma,+1,1	C8A	103	1	0			c.G1454T						scavenged	.	G	LEU/ARG	864,3542		90,684,1429	68.0	71.0	70.0		1454	0.7	0.0	1	dbSNP_89	70	370,8230		8,354,3938	no	missense	C8A	NM_000562.2	102	98,1038,5367	TT,TG,GG		4.3023,19.6096,9.4879	probably-damaging	485/585	57378149	1234,11772	2203	4300	6503	SO:0001583	missense	731	exon10			TGCGCCGCGCCTT	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"""Complement system"""	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1454G>T	1.37:g.57378149G>T	ENSP00000354458:p.Arg485Leu	Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	218	109	0.5	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	193	0.08836996336996338	97	0.19715447154471544	36	0.09944751381215469	33	0.057692307692307696	27	0.03562005277044855	G	12.54	1.968002	0.34754	0.196096	0.043023	ENSG00000157131	ENST00000361249	D	0.85484	-1.99	5.73	0.696	0.18075	Membrane attack complex component/perforin (MACPF) domain (3);	0.258044	0.41001	D	0.000972	T	0.00637	0.0021	M	0.88906	2.99	0.80722	P	0.0	P	0.45594	0.862	P	0.49922	0.626	T	0.48547	-0.9026	9	0.66056	D	0.02	-1.8617	12.4712	0.55787	0.4218:0.0:0.5782:0.0	rs1620075;rs1620075	485	P07357	CO8A_HUMAN	L	485	ENSP00000354458:R485L	ENSP00000354458:R485L	R	+	2	0	C8A	57150737	0.000000	0.05858	0.004000	0.12327	0.363000	0.29612	0.336000	0.19823	-0.331000	0.08501	-1.731000	0.00696	CGC	T|0.096;G|0.903;A|0.001	0.096	strong		0.622	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
FLG	2312	hgsc.bcm.edu	37	1	152280614	152280614	+	Missense_Mutation	SNP	C	C	G	rs3120645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152280614C>G	ENST00000368799.1	-	3	6783	c.6748G>C	c.(6748-6750)Gag>Cag	p.E2250Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	446	0	0		WXS	Illumina HiSeq	Phase_I	495	20	0.040404	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	
ARMC1	55156	hgsc.bcm.edu	37	8	66517549	66517549	+	Silent	SNP	T	T	C	rs16932266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:66517549T>C	ENST00000276569.3	-	6	850	c.606A>G	c.(604-606)tcA>tcG	p.S202S	ARMC1_ENST00000458464.2_Silent_p.S100S	NM_018120.4	NP_060590.1	Q9NVT9	ARMC1_HUMAN	armadillo repeat containing 1	202					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)			TAACCTTGGTTGATGCTATTG	0.323													T|||	109	0.0217652	0.0257	0.0288	5008	,	,		18451	0.0248		0.0159	False		,,,				2504	0.0143				p.S202S		Atlas-SNP	.											.	ARMC1	22	.	0			c.A606G						PASS	.	T		105,4301	81.4+/-119.9	2,101,2100	114.0	110.0	111.0		606	-0.1	1.0	8	dbSNP_123	111	126,8474	65.3+/-127.6	1,124,4175	no	coding-synonymous	ARMC1	NM_018120.4		3,225,6275	CC,CT,TT		1.4651,2.3831,1.7761		202/283	66517549	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	55156	exon6			CTTGGTTGATGCT	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.606A>G	8.37:g.66517549T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	193	103	0.533679	NM_018120	B4E2W7|Q9H018|Q9H820	Silent	SNP	ENST00000276569.3	37	CCDS6181.1																																																																																			T|0.984;C|0.016	0.016	strong		0.323	ARMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378480.1	NM_018120	
PCDHGC3	5098	hgsc.bcm.edu	37	5	140857798	140857798	+	Silent	SNP	T	T	C	rs1423148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140857798T>C	ENST00000308177.3	+	1	2219	c.2115T>C	c.(2113-2115)ttT>ttC	p.F705F	PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA9_ENST00000573521.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB6_ENST00000520790.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	705					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)			CTGTGGGGTTTGTGGTCACAG	0.498											OREG0016865	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2776	0.554313	0.8903	0.6182	5008	,	,		19318	0.3264		0.4225	False		,,,				2504	0.4254				p.F705F		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.T2115C						PASS	.	C	,,,,,,,,,,,,,,,,,,,,,,	3637,769	308.8+/-290.8	1499,639,65	205.0	250.0	235.0		2115,,,,,,,,,,,,,,,,,,,,,2115,	-1.6	0.6	5	dbSNP_88	235	3681,4919	618.6+/-396.8	779,2123,1398	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	,,,,,,,,,,,,,,,,,,,,,,	2278,2762,1463	CC,CT,TT		42.8023,17.4535,43.7337	,,,,,,,,,,,,,,,,,,,,,,	705/935,,,,,,,,,,,,,,,,,,,,,705/864,	140857798	7318,5688	2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			GGGGTTTGTGGTC	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.2115T>C	5.37:g.140857798T>C		Somatic	90	0	0	1659	WXS	Illumina HiSeq	Phase_I	90	90	1	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	37	CCDS4261.1																																																																																			A|0.002;C|0.545	0.545	strong		0.498	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588	
SNAP23	8773	hgsc.bcm.edu	37	15	42820589	42820589	+	Silent	SNP	G	G	A	rs1060291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42820589G>A	ENST00000249647.3	+	6	864	c.396G>A	c.(394-396)acG>acA	p.T132T	SNAP23_ENST00000397138.1_Intron|SNAP23_ENST00000349777.1_Intron|SNAP23_ENST00000564153.1_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	91	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	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	
SFXN4	119559	hgsc.bcm.edu	37	10	120920588	120920588	+	Silent	SNP	T	T	C	rs10749291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:120920588T>C	ENST00000355697.2	-	4	277	c.258A>G	c.(256-258)caA>caG	p.Q86Q	SFXN4_ENST00000461438.1_5'UTR|SFXN4_ENST00000330036.6_Intron	NM_213649.1	NP_998814.1	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	86					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	11		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		TCCAAGCTTCTTGTATCTTAA	0.393													T|||	2476	0.494409	0.4349	0.4496	5008	,	,		17752	0.7163		0.4374	False		,,,				2504	0.4366				p.Q86Q		Atlas-SNP	.											.	SFXN4	24	.	0			c.A258G						PASS	.	T		1901,2505	541.3+/-375.7	412,1077,714	98.0	105.0	103.0		258	2.8	1.0	10	dbSNP_120	103	4171,4429	560.6+/-387.6	975,2221,1104	no	coding-synonymous	SFXN4	NM_213649.1		1387,3298,1818	CC,CT,TT		48.5,43.1457,46.6861		86/338	120920588	6072,6934	2203	4300	6503	SO:0001819	synonymous_variant	119559	exon4			AGCTTCTTGTATC		CCDS7610.1	10q26.11	2006-03-13			ENSG00000183605	ENSG00000183605		"""Sideroflexins"""	16088	protein-coding gene	gene with protein product		615564				14756423	Standard	NM_213649		Approved		uc001leb.3	Q6P4A7	OTTHUMG00000019147	ENST00000355697.2:c.258A>G	10.37:g.120920588T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_213649	Q6WSU4|Q86TD9	Silent	SNP	ENST00000355697.2	37	CCDS7610.1																																																																																			T|0.515;C|0.485	0.485	strong		0.393	SFXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050642.3	XM_058406	
UBR3	130507	hgsc.bcm.edu	37	2	170684548	170684548	+	Silent	SNP	G	G	A	rs79036304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170684548G>A	ENST00000272793.5	+	1	581	c.531G>A	c.(529-531)gtG>gtA	p.V177V	UBR3_ENST00000418381.1_Silent_p.V177V			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	177					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						ACAGCAACGTGATGCGGGAGA	0.726													g|||	320	0.0638978	0.174	0.0461	5008	,	,		9387	0.0109		0.0258	False		,,,				2504	0.0215				p.V177V		Atlas-SNP	.											.	UBR3	182	.	0			c.G531A						PASS	.						6.0	6.0	6.0					2																	170684548		685	1551	2236	SO:0001819	synonymous_variant	130507	exon1			CAACGTGATGCGG	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.531G>A	2.37:g.170684548G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																				G|0.940;A|0.060	0.060	strong		0.726	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
ZSWIM3	140831	hgsc.bcm.edu	37	20	44506418	44506418	+	Silent	SNP	G	G	A	rs1045493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	101	0	0		WXS	Illumina HiSeq	Phase_I	132	56	0.424242	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	
HSPA8	3312	hgsc.bcm.edu	37	11	122931337	122931337	+	Silent	SNP	T	T	C	rs147610984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:122931337T>C	ENST00000532636.1	-	3	494	c.375A>G	c.(373-375)acA>acG	p.T125T	SNORD14E_ENST00000364009.1_RNA|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000534624.1_Silent_p.T125T|HSPA8_ENST00000533540.1_Intron|HSPA8_ENST00000526110.1_Silent_p.T125T|HSPA8_ENST00000534319.1_5'Flank|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000227378.3_Silent_p.T125T|HSPA8_ENST00000453788.2_Silent_p.T125T|SNORD14C_ENST00000365382.1_RNA			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	125					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		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;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CCTTCATCTTTGTCAGAACCA	0.488													T|||	41	0.0081869	0.0303	0.0014	5008	,	,		19288	0.0		0.0	False		,,,				2504	0.0				p.T125T	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.A375G						PASS	.	T	,	123,4281	91.6+/-130.3	1,121,2080	94.0	97.0	96.0		375,375	-2.6	1.0	11	dbSNP_134	96	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	HSPA8	NM_006597.4,NM_153201.2	,	1,121,6379	CC,CT,TT		0.0,2.7929,0.946	,	125/647,125/494	122931337	123,12879	2202	4299	6501	SO:0001819	synonymous_variant	3312	exon3			CATCTTTGTCAGA	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.375A>G	11.37:g.122931337T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	132	56	0.424242	NM_006597	Q9H3R6	Silent	SNP	ENST00000532636.1	37	CCDS8440.1																																																																																			T|0.989;C|0.011	0.011	strong		0.488	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
SLC22A5	6584	hgsc.bcm.edu	37	5	131721174	131721174	+	Silent	SNP	A	A	G	rs274558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:131721174A>G	ENST00000245407.3	+	4	1028	c.807A>G	c.(805-807)ctA>ctG	p.L269L	SLC22A5_ENST00000435065.2_Silent_p.L293L	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	269					carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	CGGGGGTGCTATGCGTGGCAC	0.557											OREG0016766	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2435	0.486222	0.3434	0.33	5008	,	,		16426	0.6736		0.4145	False		,,,				2504	0.6708				p.L269L		Atlas-SNP	.											.	SLC22A5	34	.	0			c.A807G						PASS	.	G		1555,2851	668.4+/-402.0	264,1027,912	113.0	100.0	104.0		807	-0.8	1.0	5	dbSNP_79	104	3365,5235	642.5+/-399.8	674,2017,1609	no	coding-synonymous	SLC22A5	NM_003060.3		938,3044,2521	GG,GA,AA		39.1279,35.2928,37.8287		269/558	131721174	4920,8086	2203	4300	6503	SO:0001819	synonymous_variant	6584	exon4			GGTGCTATGCGTG	AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"""Solute carriers"""	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.807A>G	5.37:g.131721174A>G		Somatic	173	0	0	1589	WXS	Illumina HiSeq	Phase_I	147	71	0.482993	NM_003060	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Silent	SNP	ENST00000245407.3	37	CCDS4154.1																																																																																			A|0.579;G|0.421	0.421	strong		0.557	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060	
COQ5	84274	hgsc.bcm.edu	37	12	120954490	120954490	+	Missense_Mutation	SNP	C	C	T	rs3742049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	171	2	0.0116959		WXS	Illumina HiSeq	Phase_I	190	68	0.357895	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	
NOL9	79707	hgsc.bcm.edu	37	1	6614230	6614230	+	Silent	SNP	G	G	A	rs10864625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6614230G>A	ENST00000377705.5	-	1	365	c.333C>T	c.(331-333)ctC>ctT	p.L111L	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	111					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)		GTGGGATGAGGAGAGGCCGGT	0.731													G|||	942	0.188099	0.2791	0.1311	5008	,	,		11221	0.1766		0.1322	False		,,,				2504	0.1748				p.L111L		Atlas-SNP	.											.	NOL9	49	.	0			c.C333T						PASS	.	G		630,2510		41,548,981	9.0	6.0	7.0		333	-0.8	0.0	1	dbSNP_120	7	559,5725		19,521,2602	no	coding-synonymous	NOL9	NM_024654.4		60,1069,3583	AA,AG,GG		8.8956,20.0637,12.6167		111/703	6614230	1189,8235	1570	3142	4712	SO:0001819	synonymous_variant	79707	exon1			GATGAGGAGAGGC	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.333C>T	1.37:g.6614230G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_024654	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	Silent	SNP	ENST00000377705.5	37	CCDS80.1																																																																																			G|0.815;A|0.185	0.185	strong		0.731	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002625.1	NM_024654	
FLG	2312	hgsc.bcm.edu	37	1	152281007	152281007	+	Missense_Mutation	SNP	A	A	G	rs7512553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281007A>G	ENST00000368799.1	-	3	6390	c.6355T>C	c.(6355-6357)Tat>Cat	p.Y2119H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	482	1	0.00207469		WXS	Illumina HiSeq	Phase_I	974	509	0.522587	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	
ZNF433	163059	hgsc.bcm.edu	37	19	12127370	12127370	+	Silent	SNP	G	G	A	rs79787738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12127370G>A	ENST00000344980.6	-	4	482	c.312C>T	c.(310-312)tgC>tgT	p.C104C	CTD-2006C1.2_ENST00000495324.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA|ZNF433_ENST00000419886.2_Silent_p.C69C|CTD-2006C1.2_ENST00000406892.2_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	104					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						CACTGCTTTCGCATGATTTTA	0.408													G|||	15	0.00299521	0.0106	0.0014	5008	,	,		19210	0.0		0.0	False		,,,				2504	0.0				p.C104C		Atlas-SNP	.											.	ZNF433	49	.	0			c.C312T						PASS	.	G		67,4277		0,67,2105	93.0	93.0	93.0		312	-2.4	0.0	19	dbSNP_132	93	2,8572		0,2,4285	no	coding-synonymous	ZNF433	NM_001080411.1		0,69,6390	AA,AG,GG		0.0233,1.5424,0.5341		104/674	12127370	69,12849	2172	4287	6459	SO:0001819	synonymous_variant	163059	exon4			GCTTTCGCATGAT	AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647		"""Zinc fingers, C2H2-type"", ""-"""	20811	protein-coding gene	gene with protein product							Standard	NM_001080411		Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.312C>T	19.37:g.12127370G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	161	72	0.447205	NM_001080411	Q86VX3	Silent	SNP	ENST00000344980.6	37	CCDS45983.1																																																																																			G|0.994;A|0.006	0.006	strong		0.408	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403716.1	NM_152602	
VEGFA	7422	hgsc.bcm.edu	37	6	43738977	43738977	+	5'UTR	SNP	C	C	T	rs25648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43738977C>T	ENST00000523873.1	+	0	32				VEGFA_ENST00000518824.1_5'Flank|VEGFA_ENST00000520948.1_5'UTR|VEGFA_ENST00000372067.3_Silent_p.S178S|VEGFA_ENST00000417285.2_Silent_p.S178S|VEGFA_ENST00000230480.6_5'Flank|VEGFA_ENST00000372077.4_5'UTR|VEGFA_ENST00000425836.2_Silent_p.S178S|VEGFA_ENST00000482630.2_Silent_p.S178S|VEGFA_ENST00000324450.6_Silent_p.S178S|VEGFA_ENST00000523125.1_5'Flank|VEGFA_ENST00000372055.4_Silent_p.S178S|VEGFA_ENST00000523950.1_5'UTR|VEGFA_ENST00000413642.3_Silent_p.S178S|VEGFA_ENST00000518689.1_5'Flank|VEGFA_ENST00000372064.4_Silent_p.S178S|VEGFA_ENST00000457104.2_5'Flank|RP1-261G23.7_ENST00000607600.1_RNA			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	21	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	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	
ADCY8	114	hgsc.bcm.edu	37	8	132002770	132002770	+	Silent	SNP	G	G	A	rs2228950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:132002770G>A	ENST00000286355.5	-	2	3071	c.979C>T	c.(979-981)Cta>Tta	p.L327L	ADCY8_ENST00000377928.3_Silent_p.L327L	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	327					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CACATGAATAGCACTGCCTGG	0.448										HNSCC(32;0.087)			A|||	1554	0.310304	0.6921	0.2291	5008	,	,		19148	0.0774		0.168	False		,,,				2504	0.2382				p.L327L		Atlas-SNP	.											.	ADCY8	291	.	0			c.C979T						PASS	.	A		2766,1640	502.9+/-365.4	890,986,327	110.0	119.0	116.0		979	-1.1	0.0	8	dbSNP_121	116	1399,7201	753.6+/-407.5	116,1167,3017	no	coding-synonymous	ADCY8	NM_001115.2		1006,2153,3344	AA,AG,GG		16.2674,37.222,32.0237		327/1252	132002770	4165,8841	2203	4300	6503	SO:0001819	synonymous_variant	114	exon2			TGAATAGCACTGC	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.979C>T	8.37:g.132002770G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_001115		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																			G|0.701;A|0.299	0.299	strong		0.448	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
SYNGAP1	8831	hgsc.bcm.edu	37	6	33408542	33408542	+	Silent	SNP	G	G	A	rs587780472|rs411136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33408542G>A	ENST00000418600.2	+	11	1814	c.1713G>A	c.(1711-1713)tcG>tcA	p.S571S	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Silent_p.S571S|MIR5004_ENST00000579078.1_RNA|SYNGAP1_ENST00000428982.2_Silent_p.S512S	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	571	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)	p.S556S(1)|p.S571S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						TGTTTGCTTCGTGGCGGCTGC	0.632													G|||	2192	0.4377	0.2716	0.4035	5008	,	,		17633	0.6319		0.3837	False		,,,				2504	0.5419				p.S571S		Atlas-SNP	.											SYNGAP1_ENST00000293748,NS,carcinoma,0,2	SYNGAP1	202	2	2	Substitution - coding silent(2)	stomach(2)	c.G1713A						PASS	.	G		1228,3176		187,854,1161	23.0	23.0	23.0		1713	-10.5	0.2	6	dbSNP_80	23	3424,5172		694,2036,1568	no	coding-synonymous	SYNGAP1	NM_006772.2		881,2890,2729	AA,AG,GG		39.8325,27.8837,35.7846		571/1344	33408542	4652,8348	2202	4298	6500	SO:0001819	synonymous_variant	8831	exon11			TGCTTCGTGGCGG	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.1713G>A	6.37:g.33408542G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			G|0.608;A|0.392	0.392	strong		0.632	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
TBC1D9	23158	hgsc.bcm.edu	37	4	141600320	141600320	+	Silent	SNP	A	A	G	rs4956329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:141600320A>G	ENST00000442267.2	-	5	701	c.627T>C	c.(625-627)ctT>ctC	p.L209L		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	209	GRAM 1.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				CATTCTTCTCAAGCTGAGTGA	0.478													G|||	3180	0.634984	0.6884	0.6124	5008	,	,		18897	0.5655		0.668	False		,,,				2504	0.6166				p.L209L		Atlas-SNP	.											.	TBC1D9	198	.	0			c.T627C						PASS	.	G		2844,1246		983,878,184	134.0	130.0	131.0		627	-10.9	0.1	4	dbSNP_111	131	5706,2696		1964,1778,459	no	coding-synonymous	TBC1D9	NM_015130.2		2947,2656,643	GG,GA,AA		32.0876,30.4645,31.5562		209/1267	141600320	8550,3942	2045	4201	6246	SO:0001819	synonymous_variant	23158	exon5			CTTCTCAAGCTGA	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"""EF-hand domain containing"""	21710	protein-coding gene	gene with protein product			"""TBC1 domain family, member 9"""			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.627T>C	4.37:g.141600320A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	125	65	0.52	NM_015130	A6H8U8|D3DNZ1|O94958	Silent	SNP	ENST00000442267.2	37	CCDS47136.1																																																																																			A|0.352;G|0.648	0.648	strong		0.478	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130	
SSPO	23145	hgsc.bcm.edu	37	7	149486294	149486294	+	RNA	SNP	A	A	G	rs855691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149486294A>G	ENST00000378016.2	+	0	4270							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)			GATGACTTGCAGCTCCGGCCA	0.667													A|||	454	0.090655	0.1331	0.0634	5008	,	,		17034	0.0972		0.0656	False		,,,				2504	0.0716				p.S1424G		Atlas-SNP	.											.	.	.	.	0			c.A4270G						PASS	.	A		439,3871		26,387,1742	19.0	24.0	22.0		4274	2.2	1.0	7	dbSNP_86	22	530,7980		27,476,3752	yes	coding-notMod3	SSPO	NM_198455.2		53,863,5494	GG,GA,AA		6.228,10.1856,7.5585			149486294	969,11851	2155	4255	6410			23145	exon30			ACTTGCAGCTCCG	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.149486294A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.003;G|0.087	0.087	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
OR1S2	219958	hgsc.bcm.edu	37	11	57971478	57971478	+	Missense_Mutation	SNP	A	A	G	rs11229281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57971478A>G	ENST00000302592.6	-	1	175	c.176T>C	c.(175-177)aTt>aCt	p.I59T		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	59			I -> T (in dbSNP:rs11229281).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				GATAGCCACAATGATGAGCCC	0.473													A|||	438	0.0874601	0.056	0.1095	5008	,	,		21576	0.0417		0.1083	False		,,,				2504	0.1401				p.I59T		Atlas-SNP	.											.	OR1S2	119	.	0			c.T176C						PASS	.	A	THR/ILE	230,4172	137.3+/-173.1	6,218,1977	207.0	192.0	197.0		176	4.3	0.9	11	dbSNP_120	197	834,7758	192.1+/-238.2	46,742,3508	yes	missense	OR1S2	NM_001004459.1	89	52,960,5485	GG,GA,AA		9.7067,5.2249,8.1884	probably-damaging	59/326	57971478	1064,11930	2201	4296	6497	SO:0001583	missense	219958	exon1			GCCACAATGATGA	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.176T>C	11.37:g.57971478A>G	ENSP00000305469:p.Ile59Thr	Somatic	391	0	0		WXS	Illumina HiSeq	Phase_I	398	181	0.454774	NM_001004459	Q6IFG5|Q96R85	Missense_Mutation	SNP	ENST00000302592.6	37	CCDS31545.1	171	0.0782967032967033	38	0.07723577235772358	33	0.09116022099447514	22	0.038461538461538464	78	0.10290237467018469	A	11.87	1.767166	0.31320	0.052249	0.097067	ENSG00000197887	ENST00000302592	T	0.03124	4.04	4.26	4.26	0.50523	GPCR, rhodopsin-like superfamily (1);	0.274748	0.25552	N	0.029897	T	0.00384	0.0012	M	0.89414	3.03	0.44985	P	0.0019970000000000265	D	0.62365	0.991	P	0.56700	0.804	T	0.02860	-1.1101	9	0.87932	D	0	.	9.5868	0.39521	0.8241:0.1759:0.0:0.0	rs11229281	59	Q8NGQ3	OR1S2_HUMAN	T	59	ENSP00000305469:I59T	ENSP00000305469:I59T	I	-	2	0	OR1S2	57728054	0.574000	0.26684	0.928000	0.36995	0.353000	0.29299	4.177000	0.58276	1.921000	0.55644	0.533000	0.62120	ATT	A|0.913;G|0.087	0.087	strong		0.473	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
ZNF585B	92285	hgsc.bcm.edu	37	19	37697988	37697988	+	Missense_Mutation	SNP	T	T	C	rs145040657		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37697988T>C	ENST00000532828.2	-	2	277	c.26A>G	c.(25-27)cAg>cGg	p.Q9R	ZNF585B_ENST00000527838.1_Missense_Mutation_p.Q9R|CTC-454I21.3_ENST00000585860.2_Missense_Mutation_p.Q9R|ZNF585B_ENST00000534363.1_5'Flank	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	9					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGAGGATTTCTGGGGTGAGGT	0.532													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19866	0.0		0.0	False		,,,				2504	0.0				p.Q9R	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.A26G						PASS	.	T	ARG/GLN	5,4401	9.9+/-24.2	0,5,2198	120.0	104.0	109.0		26	0.6	0.0	19	dbSNP_134	109	0,8600		0,0,4300	yes	missense	ZNF585B	NM_152279.3	43	0,5,6498	CC,CT,TT		0.0,0.1135,0.0384	benign	9/770	37697988	5,13001	2203	4300	6503	SO:0001583	missense	92285	exon2			GATTTCTGGGGTG	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"""Zinc fingers, C2H2-type"", ""-"""	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.26A>G	19.37:g.37697988T>C	ENSP00000433773:p.Gln9Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	T	8.991	0.977714	0.18812	0.001135	0.0	ENSG00000245680	ENST00000532828;ENST00000527838	T;T	0.06933	3.24;6.86	1.79	0.647	0.17796	.	.	.	.	.	T	0.06690	0.0171	L	0.52573	1.65	0.09310	N	1	B	0.31655	0.334	B	0.15870	0.014	T	0.32534	-0.9903	9	0.87932	D	0	.	3.6073	0.08048	0.374:0.0:0.0:0.626	.	9	Q52M93	Z585B_HUMAN	R	9	ENSP00000433773:Q9R;ENSP00000435268:Q9R	ENSP00000432760:Q9R	Q	-	2	0	ZNF585B	42389828	0.048000	0.20356	0.004000	0.12327	0.700000	0.40528	0.118000	0.15605	0.117000	0.18138	0.260000	0.18958	CAG	T|1.000;C|0.000	0.000	strong		0.532	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279	
DEK	7913	hgsc.bcm.edu	37	6	18237661	18237661	+	Silent	SNP	C	C	T	rs1013062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:18237661C>T	ENST00000397239.3	-	8	1296	c.849G>A	c.(847-849)aaG>aaA	p.K283K	DEK_ENST00000244776.7_Silent_p.K249K	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	283					chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			TATCTGCTTTCTTAACATTGG	0.313			T	NUP214	AML								C|||	823	0.164337	0.0295	0.1124	5008	,	,		18170	0.247		0.2087	False		,,,				2504	0.2526				p.K283K		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31	.	0			c.G849A						PASS	.	C	,	280,4124	155.9+/-189.0	6,268,1928	218.0	189.0	199.0		747,849	4.0	1.0	6	dbSNP_86	199	1791,6809	322.2+/-315.5	196,1399,2705	no	coding-synonymous,coding-synonymous	DEK	NM_001134709.1,NM_003472.3	,	202,1667,4633	TT,TC,CC		20.8256,6.3579,15.9259	,	249/342,283/376	18237661	2071,10933	2202	4300	6502	SO:0001819	synonymous_variant	7913	exon8			TGCTTTCTTAACA	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"""DEK oncogene (DNA binding)"", ""DEK oncogene"""			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.849G>A	6.37:g.18237661C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	215	115	0.534884	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Silent	SNP	ENST00000397239.3	37	CCDS34344.1																																																																																			C|0.837;T|0.163	0.163	strong		0.313	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4		
SBNO1	55206	hgsc.bcm.edu	37	12	123801856	123801856	+	Silent	SNP	T	T	C	rs61751328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123801856T>C	ENST00000602398.1	-	21	2974	c.2847A>G	c.(2845-2847)caA>caG	p.Q949Q	SBNO1_ENST00000420886.2_Silent_p.Q949Q|SBNO1_ENST00000602750.1_Silent_p.Q948Q|SBNO1_ENST00000267176.4_Silent_p.Q948Q			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	949					regulation of transcription, DNA-templated (GO:0006355)					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)		TCCTATCTGCTTGTAATGAAA	0.388													T|||	489	0.0976438	0.3389	0.0447	5008	,	,		19983	0.0		0.008	False		,,,				2504	0.002				p.Q949Q		Atlas-SNP	.											.	SBNO1	138	.	0			c.A2847G						PASS	.	T	,	1176,3230	414.4+/-336.8	160,856,1187	108.0	101.0	103.0		2847,2844	5.7	1.0	12	dbSNP_129	103	122,8478	62.4+/-124.4	2,118,4180	no	coding-synonymous,coding-synonymous	SBNO1	NM_001167856.1,NM_018183.3	,	162,974,5367	CC,CT,TT		1.4186,26.6909,9.98	,	949/1394,948/1393	123801856	1298,11708	2203	4300	6503	SO:0001819	synonymous_variant	55206	exon20			ATCTGCTTGTAAT	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.2847A>G	12.37:g.123801856T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	37	CCDS53844.1																																																																																			T|0.907;C|0.093	0.093	strong		0.388	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
EOMES	8320	hgsc.bcm.edu	37	3	27758756	27758756	+	Silent	SNP	G	G	A	rs6783101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:27758756G>A	ENST00000295743.4	-	6	2069	c.1866C>T	c.(1864-1866)ccC>ccT	p.P622P	EOMES_ENST00000537516.1_Silent_p.P346P|EOMES_ENST00000461503.1_5'Flank|EOMES_ENST00000449599.1_Silent_p.P641P			O95936	EOMES_HUMAN	eomesodermin	622	Required for transcription activation. {ECO:0000250}.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						TGATGGAAGGGGGTGTCTCTA	0.463													G|||	182	0.0363419	0.1316	0.0115	5008	,	,		18478	0.0		0.0	False		,,,				2504	0.0				p.P622P		Atlas-SNP	.											.	EOMES	65	.	0			c.C1866T						PASS	.	G		548,3858	247.5+/-255.7	26,496,1681	118.0	122.0	121.0		1866	-1.7	1.0	3	dbSNP_116	121	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	EOMES	NM_005442.2		26,503,5974	AA,AG,GG		0.0814,12.4376,4.2673		622/687	27758756	555,12451	2203	4300	6503	SO:0001819	synonymous_variant	8320	exon6			GGAAGGGGGTGTC	BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"""T-boxes"""	3372	protein-coding gene	gene with protein product	"""T-box brain2"""	604615	"""eomesodermin (Xenopus laevis) homolog"""			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.1866C>T	3.37:g.27758756G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	212	99	0.466981	NM_005442	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Silent	SNP	ENST00000295743.4	37	CCDS2646.1																																																																																			G|0.963;A|0.037	0.037	strong		0.463	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442	
RAET1E	135250	hgsc.bcm.edu	37	6	150210681	150210681	+	Missense_Mutation	SNP	G	G	A	rs9371533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:150210681G>A	ENST00000357183.4	-	3	557	c.425C>T	c.(424-426)aCc>aTc	p.T142I	RAET1E-AS1_ENST00000605899.1_RNA|RAET1E_ENST00000532335.1_Missense_Mutation_p.T142I|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E_ENST00000529948.1_Missense_Mutation_p.T142I|RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000367363.3_Missense_Mutation_p.T106I	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	142	MHC class I alpha-2 like.		T -> I (in dbSNP:rs9371533).	AT -> TI (in Ref. 8; AAL76417). {ECO:0000305}.	antigen processing and presentation (GO:0019882)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			cervix(1)|kidney(2)|large_intestine(3)|lung(3)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		CTCTCCATTGGTGGCGAACTG	0.468													N|||	3435	0.685903	0.8442	0.5447	5008	,	,		21656	0.8968		0.4324	False		,,,				2504	0.6155				p.T142I		Atlas-SNP	.											RAET1E,NS,carcinoma,+1,2	RAET1E	20	2	0			c.C425T						PASS	.	A	ILE/THR	3478,928	353.3+/-312.1	1384,710,109	156.0	127.0	137.0		425	-1.8	0.0	6	dbSNP_119	137	3544,5056	631.0+/-398.4	742,2060,1498	yes	missense	RAET1E	NM_139165.2	89	2126,2770,1607	AA,AG,GG		41.2093,21.0622,46.0095	benign	142/264	150210681	7022,5984	2203	4300	6503	SO:0001583	missense	135250	exon3			CCATTGGTGGCGA	AF359243	CCDS5221.1, CCDS59042.1, CCDS59043.1, CCDS59044.1	6q24.3	2011-02-09			ENSG00000164520	ENSG00000164520			16793	protein-coding gene	gene with protein product		609243				11827464	Standard	NM_139165		Approved	LETAL, bA350J20.7, ULBP4	uc003qnl.1	Q8TD07	OTTHUMG00000015796	ENST00000357183.4:c.425C>T	6.37:g.150210681G>A	ENSP00000349709:p.Thr142Ile	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	271	118	0.435424	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Missense_Mutation	SNP	ENST00000357183.4	37	CCDS5221.1	1415	0.6478937728937729	397	0.806910569105691	200	0.5524861878453039	503	0.8793706293706294	315	0.4155672823218997	A	3.644	-0.072921	0.07228	0.789378	0.412093	ENSG00000164520	ENST00000532335;ENST00000357183;ENST00000367363;ENST00000529948	T;T;T;T	0.06068	3.35;3.35;5.85;3.35	3.68	-1.75	0.08031	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.757356	0.11741	N	0.534006	T	0.00300	0.0009	N	0.00159	-1.955	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	0.35847	-0.9772	9	0.07644	T	0.81	-6.9511	4.4433	0.11584	0.3415:0.3442:0.3142:0.0	rs9371533;rs59091272;rs9371533	142;106;142	Q8TD07;Q8TD07-2;Q8TD07-3	N2DL4_HUMAN;.;.	I	142;142;106;142	ENSP00000437067:T142I;ENSP00000349709:T142I;ENSP00000356332:T106I;ENSP00000432366:T142I	ENSP00000349709:T142I	T	-	2	0	RAET1E	150252374	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.847000	0.27696	-0.637000	0.05516	-1.330000	0.01273	ACC	G|0.403;A|0.597	0.597	strong		0.468	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165	
COG7	91949	hgsc.bcm.edu	37	16	23403744	23403744	+	Silent	SNP	A	A	G	rs8057712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23403744A>G	ENST00000307149.5	-	16	2288	c.2103T>C	c.(2101-2103)ccT>ccC	p.P701P	COG7_ENST00000569635.1_Intron	NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	701					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		GGCTCAGCTCAGGGATCTGTA	0.597													G|||	540	0.107827	0.2625	0.1268	5008	,	,		18783	0.0169		0.0258	False		,,,				2504	0.0634				p.P701P		Atlas-SNP	.											COG7,NS,malignant_melanoma,-2,1	COG7	62	1	0			c.T2103C						PASS	.	G		947,3447	733.6+/-410.5	98,751,1348	107.0	92.0	97.0		2103	-11.0	0.3	16	dbSNP_116	97	254,8346	807.9+/-407.2	4,246,4050	no	coding-synonymous	COG7	NM_153603.3		102,997,5398	GG,GA,AA		2.9535,21.5521,9.2427		701/771	23403744	1201,11793	2197	4300	6497	SO:0001819	synonymous_variant	91949	exon16			CAGCTCAGGGATC	AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"""Components of oligomeric golgi complex"""	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.2103T>C	16.37:g.23403744A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_153603	Q6UWU7	Silent	SNP	ENST00000307149.5	37	CCDS10610.1																																																																																			A|0.910;G|0.090	0.090	strong		0.597	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1		
DSCAML1	57453	hgsc.bcm.edu	37	11	117392110	117392110	+	Silent	SNP	A	A	G	rs35503235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117392110A>G	ENST00000321322.6	-	6	1129	c.1128T>C	c.(1126-1128)caT>caC	p.H376H	DSCAML1_ENST00000527706.1_Silent_p.H106H	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	316	Ig-like C2-type 4.				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)		TCAGGGTCACATGAAGGGGAT	0.587													A|||	191	0.038139	0.0711	0.0115	5008	,	,		17910	0.0258		0.0199	False		,,,				2504	0.044				p.H376H		Atlas-SNP	.											.	DSCAML1	286	.	0			c.T1128C						PASS	.	A		219,4183	128.2+/-165.1	2,215,1984	26.0	27.0	27.0		1128	-5.8	0.9	11	dbSNP_126	27	206,8386	84.8+/-147.2	1,204,4091	no	coding-synonymous	DSCAML1	NM_020693.2		3,419,6075	GG,GA,AA		2.3976,4.975,3.2707		376/2114	117392110	425,12569	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon6			GGTCACATGAAGG		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.1128T>C	11.37:g.117392110A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	28	0.35	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			A|0.969;G|0.031	0.031	strong		0.587	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
PPIAL4G	644591	hgsc.bcm.edu	37	1	143767730	143767730	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:143767730C>T	ENST00000419275.1	-	1	151	c.119G>A	c.(118-120)aGc>aAc	p.S40N		NM_001123068.1	NP_001116540.1	A2BFH1	PAL4G_HUMAN	peptidylprolyl isomerase A (cyclophilin A)-like 4G	40	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	cytoplasm (GO:0005737)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(2)|kidney(1)|lung(8)|ovary(1)|skin(1)	14						CTCTCCAGTGCTCAGAGCACG	0.473																																					p.S40N		Atlas-SNP	.											.	PPIAL4G	22	.	0			c.G119A						PASS	.						84.0	81.0	82.0					1																	143767730		1568	3562	5130	SO:0001583	missense	644591	exon1			CCAGTGCTCAGAG		CCDS41375.1, CCDS41375.2	1q21.1	2010-06-03			ENSG00000236334	ENSG00000236334			33996	protein-coding gene	gene with protein product							Standard	NM_001123068		Approved		uc001ejt.3	A2BFH1	OTTHUMG00000013629	ENST00000419275.1:c.119G>A	1.37:g.143767730C>T	ENSP00000393845:p.Ser40Asn	Somatic	1116	0	0		WXS	Illumina HiSeq	Phase_I	1225	155	0.126531	NM_001123068	A1L431	Missense_Mutation	SNP	ENST00000419275.1	37	CCDS41375.1	.	.	.	.	.	.	.	.	.	.	.	14.94	2.685463	0.47991	.	.	ENSG00000236334	ENST00000419275	T	0.44482	0.92	0.523	-0.795	0.10915	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.235838	0.42682	U	0.000663	T	0.16342	0.0393	L	0.49571	1.57	0.23010	N	0.99844	B	0.22480	0.07	B	0.35114	0.196	T	0.35475	-0.9787	10	0.35671	T	0.21	.	4.7838	0.13215	0.0:0.7163:0.0:0.2837	.	40	A2BFH1	PAL4G_HUMAN	N	40	ENSP00000393845:S40N	ENSP00000393845:S40N	S	-	2	0	PPIAL4G	142559253	1.000000	0.71417	0.814000	0.32528	0.857000	0.48899	2.074000	0.41529	-0.252000	0.09528	0.403000	0.27427	AGC	.	.	none		0.473	PPIAL4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037969.1	NM_001123068	
TMEM204	79652	hgsc.bcm.edu	37	16	1591962	1591962	+	Silent	SNP	G	G	A	rs2076443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1591962G>A	ENST00000566264.1	+	2	1024	c.321G>A	c.(319-321)acG>acA	p.T107T	TMEM204_ENST00000253934.5_Silent_p.T107T|IFT140_ENST00000426508.2_Intron	NM_024600.5	NP_078876.2	Q9BSN7	TM204_HUMAN	transmembrane protein 204	107					lymph vessel development (GO:0001945)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to stress (GO:0006950)|smooth muscle cell differentiation (GO:0051145)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|cervix(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Hepatocellular(780;0.219)				TGGTGGCCACGGCCGCGCTCA	0.701													G|||	1534	0.30631	0.4228	0.1599	5008	,	,		18178	0.3423		0.1918	False		,,,				2504	0.3333				p.T107T		Atlas-SNP	.											TMEM204,NS,carcinoma,0,1	TMEM204	29	1	0			c.G321A						PASS	.	G	,	1554,2760		288,978,891	30.0	37.0	35.0		,321	-11.5	0.2	16	dbSNP_96	35	1649,6841		166,1317,2762	no	intron,coding-synonymous	IFT140,TMEM204	NM_014714.3,NM_024600.4	,	454,2295,3653	AA,AG,GG		19.4229,36.0223,25.0156	,	,107/227	1591962	3203,9601	2157	4245	6402	SO:0001819	synonymous_variant	79652	exon2			GGCCACGGCCGCG		CCDS42098.1	16p13.3	2008-02-05	2008-01-08	2008-01-08		ENSG00000131634			14158	protein-coding gene	gene with protein product		611002	"""chromosome 16 open reading frame 30"""	C16orf30			Standard	NM_024600		Approved	FLJ20898	uc002cmc.3	Q9BSN7		ENST00000566264.1:c.321G>A	16.37:g.1591962G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_024600	D3DU76|Q3KRC1|Q9H7G5	Silent	SNP	ENST00000566264.1	37	CCDS42098.1																																																																																			G|0.746;A|0.254	0.254	strong		0.701	TMEM204-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432610.1	NM_024600	
GRM8	2918	hgsc.bcm.edu	37	7	126173902	126173902	+	Missense_Mutation	SNP	G	G	C	rs61753365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:126173902G>C	ENST00000339582.2	-	9	2342	c.1534C>G	c.(1534-1536)Ccg>Gcg	p.P512A	GRM8_ENST00000444921.2_Missense_Mutation_p.P512A|GRM8_ENST00000480995.1_Intron|GRM8_ENST00000358373.3_Missense_Mutation_p.P512A			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	512					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)			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)				ACAGACGCCGGGTGAGTATGT	0.488										HNSCC(24;0.065)			G|||	89	0.0177716	0.0635	0.0072	5008	,	,		17794	0.0		0.0	False		,,,				2504	0.0				p.P512A		Atlas-SNP	.											GRM8,NS,carcinoma,+2,1	GRM8	377	1	0			c.C1534G						scavenged	.	G	ALA/PRO,ALA/PRO	274,4132	149.2+/-183.4	11,252,1940	53.0	57.0	56.0		1534,1534	5.8	1.0	7	dbSNP_129	56	3,8597		0,3,4297	yes	missense,missense	GRM8	NM_000845.2,NM_001127323.1	27,27	11,255,6237	CC,CG,GG		0.0349,6.2188,2.1298	probably-damaging,probably-damaging	512/909,512/909	126173902	277,12729	2203	4300	6503	SO:0001583	missense	2918	exon8			ACGCCGGGTGAGT		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.1534C>G	7.37:g.126173902G>C	ENSP00000344173:p.Pro512Ala	Somatic	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	G	20.9	4.059053	0.76074	0.062188	3.49E-4	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373	D;D;D	0.92699	-3.09;-3.09;-3.09	5.8	5.8	0.92144	GPCR, family 3, nine cysteines domain (1);	0.000000	0.85682	D	0.000000	D	0.85805	0.5782	H	0.94582	3.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.86401	0.1742	10	0.87932	D	0	.	19.0428	0.93008	0.0:0.0:1.0:0.0	rs61753365	512;512	O00222-2;O00222	.;GRM8_HUMAN	A	512	ENSP00000344173:P512A;ENSP00000409790:P512A;ENSP00000351142:P512A	ENSP00000344173:P512A	P	-	1	0	GRM8	125961138	1.000000	0.71417	0.971000	0.41717	0.816000	0.46133	9.859000	0.99545	2.758000	0.94735	0.643000	0.83706	CCG	G|0.968;C|0.032	0.032	strong		0.488	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
OR6B1	135946	hgsc.bcm.edu	37	7	143701516	143701516	+	Missense_Mutation	SNP	C	C	T	rs7787378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143701516C>T	ENST00000408922.2	+	1	495	c.427C>T	c.(427-429)Cgc>Tgc	p.R143C		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	143			R -> C (in dbSNP:rs7787378).			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(3)|large_intestine(3)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	27	Melanoma(164;0.0783)					GCTCTGCTTCCGCCTCGCTCT	0.562													C|||	813	0.16234	0.0764	0.3674	5008	,	,		21958	0.2411		0.0885	False		,,,				2504	0.1278				p.R143C		Atlas-SNP	.											OR6B1,NS,carcinoma,-1,3	OR6B1	60	3	0			c.C427T						PASS	.	C	CYS/ARG	303,3985		11,281,1852	80.0	83.0	82.0		427	5.3	0.5	7	dbSNP_116	82	796,7768		49,698,3535	yes	missense	OR6B1	NM_001005281.1	180	60,979,5387	TT,TC,CC		9.2947,7.0662,8.5512	benign	143/312	143701516	1099,11753	2144	4282	6426	SO:0001583	missense	135946	exon1			TGCTTCCGCCTCG		CCDS43667.1	7q33-q35	2012-08-09			ENSG00000221813	ENSG00000221813		"""GPCR / Class A : Olfactory receptors"""	8354	protein-coding gene	gene with protein product							Standard	NM_001005281		Approved	OR7-3	uc003wdt.1	O95007	OTTHUMG00000157765	ENST00000408922.2:c.427C>T	7.37:g.143701516C>T	ENSP00000386151:p.Arg143Cys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	176	83	0.471591	NM_001005281	A4D2G2|B9EH47|Q6IFP6|Q96R38	Missense_Mutation	SNP	ENST00000408922.2	37	CCDS43667.1	358	0.16391941391941392	38	0.07723577235772358	111	0.30662983425414364	141	0.2465034965034965	68	0.08970976253298153	C	8.409	0.843804	0.16963	0.070662	0.092947	ENSG00000221813	ENST00000408922	T	0.00123	8.7	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.415982	0.17515	U	0.171466	T	0.00012	0.0000	L	0.28458	0.855	0.41184	P	0.013746000000000036	B	0.09022	0.002	B	0.18561	0.022	T	0.50955	-0.8766	9	0.34782	T	0.22	.	14.2547	0.66043	0.0:1.0:0.0:0.0	rs7787378;rs52795515;rs7787378	143	O95007	OR6B1_HUMAN	C	143	ENSP00000386151:R143C	ENSP00000386151:R143C	R	+	1	0	OR6B1	143332449	0.022000	0.18835	0.511000	0.27724	0.142000	0.21351	1.965000	0.40471	2.739000	0.93911	0.655000	0.94253	CGC	C|0.853;N|0.000	.	strong		0.562	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1		
ZNF331	55422	hgsc.bcm.edu	37	19	54080999	54080999	+	Silent	SNP	A	A	G	rs1056393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54080999A>G	ENST00000253144.9	+	7	2518	c.1185A>G	c.(1183-1185)ggA>ggG	p.G395G	ZNF331_ENST00000511154.1_Silent_p.G395G|ZNF331_ENST00000513999.1_Silent_p.G395G|ZNF331_ENST00000411977.2_Silent_p.G395G|ZNF331_ENST00000511593.2_Silent_p.G395G|ZNF331_ENST00000449416.1_Silent_p.G395G|ZNF331_ENST00000512387.1_Silent_p.G395G	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	395					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)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		TCATTTATGGATCGAGCCTCG	0.483			T	?	follicular thyroid adenoma								G|||	468	0.0934505	0.2549	0.0605	5008	,	,		19155	0.0		0.0726	False		,,,				2504	0.0164				p.G395G		Atlas-SNP	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	.	ZNF331	66	.	0			c.A1185G						PASS	.	G	,,	947,3459	735.8+/-410.7	93,761,1349	70.0	68.0	68.0		1185,1185,1185	-3.5	0.5	19	dbSNP_86	68	559,8041	794.3+/-407.5	16,527,3757	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF331	NM_001079906.1,NM_001079907.1,NM_018555.5	,,	109,1288,5106	GG,GA,AA		6.5,21.4934,11.5793	,,	395/464,395/464,395/464	54080999	1506,11500	2203	4300	6503	SO:0001819	synonymous_variant	55422	exon5			TTATGGATCGAGC	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"""Zinc fingers, C2H2-type"", ""-"""	15489	protein-coding gene	gene with protein product	"""rearranged in thyroid adenomas"""	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.1185A>G	19.37:g.54080999A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	150	79	0.526667	NM_001253801	Q96GJ4	Silent	SNP	ENST00000253144.9	37	CCDS33102.1																																																																																			A|0.890;G|0.110	0.110	strong		0.483	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555	
TMEM64	169200	hgsc.bcm.edu	37	8	91638019	91638019	+	Silent	SNP	T	T	C	rs61741096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:91638019T>C	ENST00000458549.2	-	3	1200	c.1023A>G	c.(1021-1023)gtA>gtG	p.V341V	TMEM64_ENST00000519519.1_Silent_p.V80V|TMEM64_ENST00000418210.2_Silent_p.V289V	NM_001008495.3	NP_001008495.2	Q6YI46	TMM64_HUMAN	transmembrane protein 64	341					cytosolic calcium ion homeostasis (GO:0051480)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of ATPase activity (GO:0043462)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)	2			BRCA - Breast invasive adenocarcinoma(11;0.0598)			TTTCACAAGCTACAATAGCTG	0.353													T|||	24	0.00479233	0.0174	0.0	5008	,	,		17444	0.0		0.001	False		,,,				2504	0.0				p.V341V		Atlas-SNP	.											.	TMEM64	31	.	0			c.A1023G						PASS	.	T	,	57,4349	52.9+/-88.7	0,57,2146	95.0	87.0	89.0		1023,867	0.2	1.0	8	dbSNP_129	89	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	TMEM64	NM_001008495.3,NM_001146273.1	,	0,58,6445	CC,CT,TT		0.0116,1.2937,0.4459	,	341/381,289/329	91638019	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	169200	exon3			ACAAGCTACAATA	AL834364	CCDS34920.2, CCDS55260.1	8q21.3	2005-08-09			ENSG00000180694	ENSG00000180694			25441	protein-coding gene	gene with protein product							Standard	NM_001008495		Approved	DKFZp762C1112	uc003yen.2	Q6YI46	OTTHUMG00000157185	ENST00000458549.2:c.1023A>G	8.37:g.91638019T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	151	68	0.450331	NM_001008495	B4DUC0|F5GXM4|Q2HIZ7|Q8N3G6	Silent	SNP	ENST00000458549.2	37	CCDS34920.2																																																																																			T|0.996;C|0.004	0.004	strong		0.353	TMEM64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347825.1	NM_001008495	
DNAH8	1769	hgsc.bcm.edu	37	6	38800164	38800164	+	Missense_Mutation	SNP	G	G	A	rs9357283	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:38800164G>A	ENST00000359357.3	+	29	3858	c.3604G>A	c.(3604-3606)Gaa>Aaa	p.E1202K	DNAH8_ENST00000441566.1_Missense_Mutation_p.E1202K|DNAH8_ENST00000449981.2_Missense_Mutation_p.E1419K			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1202			E -> K (in dbSNP:rs9357283). {ECO:0000269|PubMed:12297094}.		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.E1202K(1)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGAGTCTGTGGAAGTTTTTCG	0.343													G|||	913	0.182308	0.1415	0.1556	5008	,	,		20049	0.3423		0.1074	False		,,,				2504	0.1687				p.E1419K		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	1	Substitution - Missense(1)	stomach(1)	c.G4255A						PASS	.	G	LYS/GLU	638,3768	272.5+/-270.8	45,548,1610	130.0	122.0	125.0		4255	4.5	1.0	6	dbSNP_119	125	1188,7412	240.8+/-271.4	71,1046,3183	yes	missense	DNAH8	NM_001206927.1	56	116,1594,4793	AA,AG,GG		13.814,14.4803,14.0397	benign	1419/4708	38800164	1826,11180	2203	4300	6503	SO:0001583	missense	1769	exon31			TCTGTGGAAGTTT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.3604G>A	6.37:g.38800164G>A	ENSP00000352312:p.Glu1202Lys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		381	0.17445054945054944	63	0.12804878048780488	50	0.13812154696132597	195	0.3409090909090909	73	0.09630606860158311	G	8.047	0.765224	0.15914	0.144803	0.13814	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.25912	1.83;1.82;1.77	5.41	4.53	0.55603	.	0.264968	0.36066	N	0.002816	T	0.06096	0.0158	L	0.31157	0.91	0.30677	P	0.75271	B	0.02656	0.0	B	0.06405	0.002	T	0.23048	-1.0199	9	0.10377	T	0.69	.	10.1478	0.42774	0.073:0.1359:0.7911:0.0	rs9357283;rs59127177;rs9357283	1202	Q96JB1	DYH8_HUMAN	K	1407;1407;1202;1202	ENSP00000333363:E1407K;ENSP00000352312:E1202K;ENSP00000402294:E1202K	ENSP00000333363:E1407K	E	+	1	0	DNAH8	38908142	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	2.663000	0.46774	1.261000	0.44149	0.563000	0.77884	GAA	G|0.840;A|0.160	0.160	strong		0.343	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
NPY4R	5540	hgsc.bcm.edu	37	10	47087371	47087371	+	Silent	SNP	G	G	A	rs1048156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:47087371G>A	ENST00000395716.1	+	2	673	c.588G>A	c.(586-588)gcG>gcA	p.A196A	NPY4R_ENST00000374312.1_Silent_p.A196A			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	196					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)	p.A196A(1)									AGTTCCTGGCGGATAAGGTGG	0.582													g|||	639	0.127596	0.0318	0.1671	5008	,	,		42287	0.0109		0.2833	False		,,,				2504	0.1892				p.A196A		Atlas-SNP	.											PPYR1,mouth,carcinoma,0,1	PPYR1	54	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.G588A						PASS	.			267,4139		0,267,1936	190.0	159.0	169.0		588	-9.9	0.0	10	dbSNP_86	169	2052,6548		0,2052,2248	no	coding-synonymous	PPYR1	NM_005972.4		0,2319,4184	AA,AG,GG		23.8605,6.0599,17.8302		196/376	47087371	2319,10687	2203	4300	6503	SO:0001819	synonymous_variant	5540	exon3			CCTGGCGGATAAG		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"""GPCR / Class A : Neuropeptide receptors : Y"""	9329	protein-coding gene	gene with protein product		601790	"""pancreatic polypeptide receptor 1"""	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.588G>A	10.37:g.47087371G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	270	125	0.462963	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Silent	SNP	ENST00000395716.1	37	CCDS31193.1																																																																																			G|0.870;A|0.130	0.130	strong		0.582	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
LILRA3	11026	hgsc.bcm.edu	37	19	54803504	54803504	+	Missense_Mutation	SNP	A	A	C	rs6509862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54803504A>C	ENST00000251390.3	-	3	411	c.320T>G	c.(319-321)cTc>cGc	p.L107R	LILRA3_ENST00000391745.1_Missense_Mutation_p.L124R|LILRA3_ENST00000391744.3_Missense_Mutation_p.L107R	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	107	Ig-like C2-type 1.		L -> R (in dbSNP:rs6509862). {ECO:0000269|PubMed:12750859}.		defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCTCTCTGAGAGGCCTGCAGT	0.607													.|||	2181	0.435503	0.8306	0.4337	5008	,	,		12643	0.4345		0.1064	False		,,,				2504	0.2423				p.L107R		Atlas-SNP	.											.	LILRA3	65	.	0			c.T320G						PASS	.	C	ARG/LEU,ARG/LEU	3352,1036		1356,640,198	64.0	62.0	62.0		320,320	-1.5	0.0	19	dbSNP_116	62	1014,7284		203,608,3338	yes	missense,missense	LILRA3	NM_001172654.1,NM_006865.3	102,102	1559,1248,3536	CC,CA,AA		12.2198,23.6098,34.4159	,	107/376,107/440	54803504	4366,8320	2194	4149	6343	SO:0001583	missense	11026	exon3			TCTGAGAGGCCTG	U91926		19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.320T>G	19.37:g.54803504A>C	ENSP00000251390:p.Leu107Arg	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	172	90	0.523256	NM_001172654	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	37	CCDS12887.1	979	0.4482600732600733	405	0.823170731707317	125	0.3453038674033149	358	0.6258741258741258	91	0.12005277044854881	a	4.167	0.029547	0.08054	0.763902	0.122198	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.00784	5.7;5.7;5.7	2.5	-1.55	0.08558	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.31752	0.955	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.002	T	0.04191	-1.0970	8	0.42905	T	0.14	.	4.4897	0.11808	0.5563:0.3197:0.0:0.1239	rs6509862;rs59970448	107;107	E7EU74;Q8N6C8	.;LIRA3_HUMAN	R	107;107;124	ENSP00000251390:L107R;ENSP00000375624:L107R;ENSP00000375625:L124R	ENSP00000251390:L107R	L	-	2	0	LILRA3	59495316	0.033000	0.19621	0.000000	0.03702	0.001000	0.01503	-0.019000	0.12546	-0.770000	0.04614	-1.782000	0.00648	CTC	A|0.646;C|0.354	0.354	strong		0.607	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
CCDC183	84960	hgsc.bcm.edu	37	9	139694613	139694613	+	Missense_Mutation	SNP	C	C	A	rs35342663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139694613C>A	ENST00000338005.6	+	4	465	c.430C>A	c.(430-432)Ctg>Atg	p.L144M	RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.L174M|KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.18_ENST00000471502.1_RNA|RP11-216L13.19_ENST00000415992.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		144										biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		GGAGCTGCGGCTGCTGCAGGT	0.741													C|||	462	0.0922524	0.152	0.0144	5008	,	,		7965	0.1389		0.0219	False		,,,				2504	0.091				p.L144M		Atlas-SNP	.											.	KIAA1984	39	.	0			c.C430A						PASS	.	C	MET/LEU	345,2927		9,327,1300	4.0	4.0	4.0		430	-3.5	0.0	9	dbSNP_126	4	162,7194		2,158,3518	no	missense	KIAA1984	NM_001039374.4	15	11,485,4818	AA,AC,CC		2.2023,10.544,4.7704	benign	144/535	139694613	507,10121	1636	3678	5314	SO:0001583	missense	84960	exon4			CTGCGGCTGCTGC																												ENST00000338005.6:c.430C>A	9.37:g.139694613C>A	ENSP00000338013:p.Leu144Met	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	11	9	0.818182	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	155	0.07097069597069597	63	0.12804878048780488	6	0.016574585635359115	71	0.12412587412587413	15	0.01978891820580475	C	8.887	0.953003	0.18431	0.10544	0.022023	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.11604	2.76	4.69	-3.55	0.04639	.	1.415250	0.05927	U	0.634446	T	0.00073	0.0002	N	0.21448	0.665	0.80722	P	0.0	B	0.24368	0.102	B	0.23852	0.049	T	0.40098	-0.9581	9	0.45353	T	0.12	-2.6838	3.6184	0.08086	0.384:0.3008:0.0:0.3152	rs35342663;rs59016673;rs62581420	144	Q5T5S1	K1984_HUMAN	M	144	ENSP00000338013:L144M	ENSP00000338013:L144M	L	+	1	2	KIAA1984	138814434	0.000000	0.05858	0.004000	0.12327	0.449000	0.32228	-3.365000	0.00496	-1.346000	0.02211	-0.384000	0.06662	CTG	C|0.929;A|0.071	0.071	strong		0.741	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
SLX4	84464	hgsc.bcm.edu	37	16	3640893	3640893	+	Missense_Mutation	SNP	C	C	A	rs79448721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3640893C>A	ENST00000294008.3	-	12	3386	c.2746G>T	c.(2746-2748)Gcc>Tcc	p.A916S		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	916	Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GTGGTGGCGGCCTCATCTCTT	0.657								Direct reversal of damage					C|||	53	0.0105831	0.0393	0.0014	5008	,	,		15331	0.0		0.0	False		,,,				2504	0.0				p.A916S		Atlas-SNP	.											.	SLX4	173	.	0			c.G2746T						PASS	.	C	SER/ALA	146,4248	101.2+/-139.8	3,140,2054	88.0	89.0	88.0		2746	-4.9	0.0	16	dbSNP_131	88	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLX4	NM_032444.2	99	3,141,6353	AA,AC,CC		0.0116,3.3227,1.1313	benign	916/1835	3640893	147,12847	2197	4300	6497	SO:0001583	missense	84464	exon12			TGGCGGCCTCATC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2746G>T	16.37:g.3640893C>A	ENSP00000294008:p.Ala916Ser	Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	343	168	0.489796	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	C	6.127	0.391716	0.11581	0.033227	1.16E-4	ENSG00000188827	ENST00000294008	T	0.01139	5.28	5.04	-4.9	0.03094	.	1.567630	0.03656	N	0.241881	T	0.00412	0.0013	L	0.43152	1.355	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.48525	-0.9028	10	0.09843	T	0.71	.	3.8877	0.09105	0.3555:0.2957:0.0:0.3488	.	916	Q8IY92	SLX4_HUMAN	S	916	ENSP00000294008:A916S	ENSP00000294008:A916S	A	-	1	0	SLX4	3580894	0.004000	0.15560	0.000000	0.03702	0.009000	0.06853	-0.251000	0.08818	-1.230000	0.02561	0.561000	0.74099	GCC	C|0.990;A|0.010	0.010	strong		0.657	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
CDH23	64072	hgsc.bcm.edu	37	10	73377069	73377069	+	Silent	SNP	C	C	T	rs7903475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73377069C>T	ENST00000224721.6	+	10	1073	c.1068C>T	c.(1066-1068)tcC>tcT	p.S356S	CDH23_ENST00000398842.3_Silent_p.S351S|CDH23_ENST00000461841.3_Silent_p.S396S|CDH23_ENST00000299366.7_Silent_p.S396S|CDH23_ENST00000398809.4_Silent_p.S351S	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	351	Cadherin 4. {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						TCAACAGCTCCGAGTACAGCG	0.547													C|||	368	0.0734824	0.2625	0.0259	5008	,	,		21110	0.0		0.003	False		,,,				2504	0.0				p.S351S		Atlas-SNP	.											.	CDH23	365	.	0			c.C1053T						PASS	.	C	,,,,	967,3407	328.0+/-300.3	116,735,1336	83.0	86.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1053,1053,1053,1053,1053	-10.9	0.2	10	dbSNP_116	85	12,8568	7.7+/-29.5	0,12,4278	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_001171932.1,NM_022124.5,NM_052836.3	,,,,	116,747,5614	TT,TC,CC		0.1399,22.1079,7.5575	,,,,	351/1382,351/1062,351/407,351/3355,351/531	73377069	979,11975	2187	4290	6477	SO:0001819	synonymous_variant	64072	exon11			CAGCTCCGAGTAC	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.1068C>T	10.37:g.73377069C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				C|0.932;T|0.068	0.068	strong		0.547	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
AR	367	hgsc.bcm.edu	37	X	66765161	66765161	+	Missense_Mutation	SNP	A	A	T	rs200185441		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:66765161A>T	ENST00000374690.3	+	1	697	c.173A>T	c.(172-174)cAg>cTg	p.Q58L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q58L|AR_ENST00000504326.1_Missense_Mutation_p.Q58L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	58	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.Q58L(2)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CTGCTGCTgcagcagcagcag	0.667									Androgen Insensitivity Syndrome																												p.Q58L		Atlas-SNP	.											.	AR	249	.	2	Substitution - Missense(2)	lung(1)|endometrium(1)	c.A173T	GRCh37	CM033749	AR	M	rs5902610	PASS	.						8.0	11.0	10.0					X																	66765161		2116	4153	6269	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	TGCTGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.173A>T	X.37:g.66765161A>T	ENSP00000363822:p.Gln58Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	6	0.0857143	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.20	1.568808	0.28003	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.69040	-0.37;-0.37;-0.37	.	.	.	.	0.157519	0.30235	N	0.010084	T	0.46541	0.1398	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.34313	0.448;0.448	B;B	0.36534	0.227;0.227	T	0.39800	-0.9596	8	0.62326	D	0.03	.	.	.	.	.	58;58	E7EVX6;D3YPQ2	.;.	L	58	ENSP00000363822:Q58L;ENSP00000421155:Q58L;ENSP00000379359:Q58L	ENSP00000363822:Q58L	Q	+	2	0	AR	66681886	0.997000	0.39634	0.872000	0.34217	0.495000	0.33615	1.386000	0.34419	0.000000	0.14550	0.000000	0.15137	CAG	.	.	weak		0.667	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058968	79058968	+	Silent	SNP	T	T	C	rs112827102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:79058968T>C	ENST00000388820.4	-	19	3495	c.3285A>G	c.(3283-3285)acA>acG	p.T1095T	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1095					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GTGGTGGGGGTGTCCGGTCCC	0.622													t|||	553	0.110423	0.0477	0.0562	5008	,	,		13778	0.2063		0.0855	False		,,,				2504	0.1605				p.T1095T		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.A3285G						PASS	.	C		153,4213		5,143,2035	16.0	23.0	21.0		3285	-7.3	0.0	15	dbSNP_132	21	545,8023		18,509,3757	no	coding-synonymous	ADAMTS7	NM_014272.3		23,652,5792	CC,CT,TT		6.3609,3.5044,5.3966		1095/1687	79058968	698,12236	2183	4284	6467	SO:0001819	synonymous_variant	11173	exon19			TGGGGGTGTCCGG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3285A>G	15.37:g.79058968T>C		Somatic	212	2	0.00943396		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			T|0.935;C|0.065	0.065	strong		0.622	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
STARD8	9754	hgsc.bcm.edu	37	X	67938392	67938392	+	Missense_Mutation	SNP	C	C	T	rs58255923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:67938392C>T	ENST00000252336.6	+	5	1768	c.1396C>T	c.(1396-1398)Ccc>Tcc	p.P466S	STARD8_ENST00000374597.3_Missense_Mutation_p.P466S|STARD8_ENST00000374599.3_Missense_Mutation_p.P546S	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	466				P -> S (in Ref. 1; BAA11506). {ECO:0000305}.	regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	50						GGCTGCGGGGCCCCTGGCTGG	0.587													C|||	148	0.0392053	0.0991	0.0173	3775	,	,		10820	0.0		0.005	False		,,,				2504	0.0				p.P546S		Atlas-SNP	.											.	STARD8	282	.	0			c.C1636T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	468,3367		23,336,86,1273,485	46.0	39.0	41.0		1636,1396,1396	1.8	0.0	X	dbSNP_129	41	22,6706		0,15,7,2413,1865	yes	missense,missense,missense	STARD8	NM_001142503.2,NM_001142504.2,NM_014725.4	74,74,74	23,351,93,3686,2350	TT,TC,T,CC,C		0.327,12.2034,4.6388	benign,benign,benign	546/1104,466/1024,466/1024	67938392	490,10073	2203	4300	6503	SO:0001583	missense	9754	exon6			GCGGGGCCCCTGG	D80011	CCDS14390.1, CCDS48134.1	Xq13.1	2011-09-13	2007-08-16		ENSG00000130052	ENSG00000130052		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19161	protein-coding gene	gene with protein product		300689	"""START domain containing 8"""			8724849	Standard	NM_001142504		Approved	KIAA0189, ARHGAP38	uc004dxb.3	Q92502	OTTHUMG00000021748	ENST00000252336.6:c.1396C>T	X.37:g.67938392C>T	ENSP00000252336:p.Pro466Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	147	75	0.510204	NM_001142503	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Missense_Mutation	SNP	ENST00000252336.6	37	CCDS14390.1	48	0.028933092224231464	28	0.059322033898305086	5	0.014124293785310734	0	0.0	1	0.0013192612137203166	C	1.597	-0.527487	0.04141	0.122034	0.00327	ENSG00000130052	ENST00000252336;ENST00000374599;ENST00000374597	T;T;T	0.06218	3.33;3.33;3.33	4.26	1.76	0.24704	.	0.487629	0.17593	N	0.168718	T	0.00039	0.0001	N	0.00347	-1.61	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39722	-0.9600	9	0.06494	T	0.89	.	3.9538	0.09380	0.0:0.1325:0.2824:0.5851	rs58255923;rs61736965	546;466	Q92502-2;Q92502	.;STAR8_HUMAN	S	466;546;466	ENSP00000252336:P466S;ENSP00000363727:P546S;ENSP00000363725:P466S	ENSP00000252336:P466S	P	+	1	0	STARD8	67855117	0.000000	0.05858	0.002000	0.10522	0.932000	0.56968	0.017000	0.13399	0.106000	0.17784	-0.340000	0.08031	CCC	C|0.955;T|0.045	0.045	strong		0.587	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971023	45971023	+	Missense_Mutation	SNP	G	G	T	rs478967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45971023G>T	ENST00000391621.1	-	1	365	c.319C>A	c.(319-321)Cct>Act	p.P107T	TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	107	22 X 5 AA repeats of C-C-X(3).		P -> T (in dbSNP:rs478967). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CAGCACACAGGCTTGCAGCAG	0.662													g|||	1139	0.227436	0.2171	0.1585	5008	,	,		20659	0.369		0.2048	False		,,,				2504	0.1677				p.P107T		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.C319A						PASS	.	T	,THR/PRO	996,3408	350.8+/-311.0	91,814,1297	104.0	107.0	106.0		,319	0.7	0.0	21	dbSNP_83	106	1678,6922	302.0+/-305.7	148,1382,2770	no	intron,missense	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,38	239,2196,4067	TT,TG,GG		19.5116,22.6158,20.5629	,benign	,107/256	45971023	2674,10330	2202	4300	6502	SO:0001583	missense	386679	exon1			ACACAGGCTTGCA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.319C>A	21.37:g.45971023G>T	ENSP00000375479:p.Pro107Thr	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	317	125	0.394322	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	522	0.23901098901098902	101	0.20528455284552846	61	0.1685082872928177	200	0.34965034965034963	160	0.21108179419525067	g	2.743	-0.261873	0.05791	0.226158	0.195116	ENSG00000205445	ENST00000391621	T	0.04360	3.64	3.77	0.683	0.17998	.	.	.	.	.	T	0.00012	0.0000	M	0.78285	2.405	0.80722	P	0.0	B	0.25351	0.124	B	0.27887	0.084	T	0.41413	-0.9510	8	0.39692	T	0.17	.	1.2578	0.01995	0.2057:0.1724:0.4448:0.177	rs56265636	107	P60368	KR102_HUMAN	T	107	ENSP00000375479:P107T	ENSP00000375479:P107T	P	-	1	0	KRTAP10-2	44795451	0.669000	0.27502	0.004000	0.12327	0.026000	0.11368	1.776000	0.38594	0.131000	0.18576	-0.369000	0.07265	CCT	G|0.811;T|0.189	0.189	strong		0.662	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
CS	1431	hgsc.bcm.edu	37	12	56676233	56676233	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	305	0	0		WXS	Illumina HiSeq	Phase_I	265	18	0.0679245	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	
ATP2C2	9914	hgsc.bcm.edu	37	16	84492984	84492984	+	Silent	SNP	G	G	A	rs7187624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84492984G>A	ENST00000262429.4	+	23	2414	c.2325G>A	c.(2323-2325)ccG>ccA	p.P775P	ATP2C2_ENST00000420010.2_3'UTR|RP11-517C16.2_ENST00000565700.1_RNA|ATP2C2_ENST00000416219.2_Silent_p.P775P	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	775					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						ATGGGCCACCGGCGCAGAGGT	0.632													G|||	77	0.0153754	0.0514	0.0058	5008	,	,		17868	0.0		0.005	False		,,,				2504	0.0				p.P775P		Atlas-SNP	.											.	ATP2C2	75	.	0			c.G2325A						PASS	.	G		175,3791		3,169,1811	48.0	52.0	51.0		2325	-9.4	0.0	16	dbSNP_116	51	117,8201		2,113,4044	no	coding-synonymous	ATP2C2	NM_014861.2		5,282,5855	AA,AG,GG		1.4066,4.4125,2.3771		775/947	84492984	292,11992	1983	4159	6142	SO:0001819	synonymous_variant	9914	exon23			GCCACCGGCGCAG	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.2325G>A	16.37:g.84492984G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Silent	SNP	ENST00000262429.4	37	CCDS42207.1																																																																																			G|0.981;A|0.019	0.019	strong		0.632	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
MAT2A	4144	hgsc.bcm.edu	37	2	85769711	85769711	+	Silent	SNP	C	C	G	rs1078004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85769711C>G	ENST00000306434.3	+	7	915	c.792C>G	c.(790-792)cgC>cgG	p.R264R	MAT2A_ENST00000409017.1_Silent_p.R201R	NM_005911.5	NP_005902.1	P31153	METK2_HUMAN	methionine adenosyltransferase II, alpha	264					cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|methionine adenosyltransferase complex (GO:0048269)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)	p.R264R(1)		breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9					L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	TGACTGGACGCAAAATCATTG	0.453													G|||	2468	0.492812	0.7194	0.3934	5008	,	,		20209	0.3859		0.494	False		,,,				2504	0.3661				p.R264R		Atlas-SNP	.											MAT2A,NS,carcinoma,0,1	MAT2A	23	1	1	Substitution - coding silent(1)	stomach(1)	c.C792G						PASS	.	G		2978,1428	464.2+/-353.8	1016,946,241	132.0	141.0	138.0		792	2.8	1.0	2	dbSNP_86	138	3955,4645	602.6+/-394.5	911,2133,1256	yes	coding-synonymous	MAT2A	NM_005911.5		1927,3079,1497	GG,GC,CC		45.9884,32.4103,46.6938		264/396	85769711	6933,6073	2203	4300	6503	SO:0001819	synonymous_variant	4144	exon7			TGGACGCAAAATC		CCDS1977.1	2p11.2	2008-06-03			ENSG00000168906	ENSG00000168906			6904	protein-coding gene	gene with protein product		601468				1426236, 9703951	Standard	NM_005911		Approved	SAMS2, MATA2, MATII	uc002spr.3	P31153	OTTHUMG00000130174	ENST00000306434.3:c.792C>G	2.37:g.85769711C>G		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	183	99	0.540984	NM_005911	A8K511|B4DN45|D6W5L1|Q53SP5	Silent	SNP	ENST00000306434.3	37	CCDS1977.1																																																																																			C|0.483;G|0.517	0.517	strong		0.453	MAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252491.2	NM_005911	
ALG1	56052	hgsc.bcm.edu	37	16	5129756	5129756	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5129756A>G	ENST00000262374.5	+	9	940	c.909A>G	c.(907-909)gaA>gaG	p.E303E	ALG1_ENST00000544428.1_Silent_p.E192E|ALG1_ENST00000588623.1_Silent_p.E192E	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	303					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)	p.E303E(3)		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)				CAGAGTTTGAACAACTGACTC	0.443																																					p.E303E		Atlas-SNP	.											ALG1,NS,carcinoma,0,3	ALG1	35	3	3	Substitution - coding silent(3)	lung(2)|urinary_tract(1)	c.A909G						scavenged	.						89.0	85.0	87.0					16																	5129756		2197	4300	6497	SO:0001819	synonymous_variant	56052	exon9			GTTTGAACAACTG	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.909A>G	16.37:g.5129756A>G		Somatic	344	9	0.0261628		WXS	Illumina HiSeq	Phase_I	402	26	0.0646766	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Silent	SNP	ENST00000262374.5	37	CCDS10528.1																																																																																			.	.	none		0.443	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
SSPO	23145	hgsc.bcm.edu	37	7	149526071	149526071	+	RNA	SNP	G	G	A	rs142321773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149526071G>A	ENST00000378016.2	+	0	15128							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)			CCCTCTTGCCGCAGGGAGGCT	0.667													G|||	21	0.00419329	0.0159	0.0	5008	,	,		14491	0.0		0.0	False		,,,				2504	0.0				p.R5042H		Atlas-SNP	.											.	.	.	.	0			c.G15125A						PASS	.	G	HIS/ARG	46,4080		1,44,2018	42.0	53.0	49.0		15144	-1.8	0.0	7	dbSNP_134	49	1,8405		0,1,4202	no	missense	SSPO	NM_198455.2	29	1,45,6220	AA,AG,GG		0.0119,1.1149,0.375	benign	5042/5148	149526071	47,12485	2063	4203	6266			23145	exon107			CTTGCCGCAGGGA	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.149526071G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.997;A|0.003	0.003	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
RALGAPA1	253959	hgsc.bcm.edu	37	14	36191030	36191030	+	Silent	SNP	A	A	G	rs2296168	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:36191030A>G	ENST00000389698.3	-	16	2520	c.2130T>C	c.(2128-2130)gtT>gtC	p.V710V	RALGAPA1_ENST00000307138.6_Silent_p.V710V|RALGAPA1_ENST00000382366.3_Silent_p.V710V|RALGAPA1_ENST00000554704.1_5'UTR|RALGAPA1_ENST00000258840.6_Silent_p.V710V	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	710					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TGTCAACTGAAACTTTCTGAA	0.423													A|||	793	0.158347	0.1392	0.0677	5008	,	,		18289	0.3978		0.0408	False		,,,				2504	0.1227				p.V710V		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.T2130C						PASS	.	A	,	625,3781	268.6+/-268.5	43,539,1621	82.0	79.0	80.0		2130,2130	-0.2	1.0	14	dbSNP_100	80	384,8216	125.0+/-183.6	13,358,3929	no	coding-synonymous,coding-synonymous	RALGAPA1	NM_014990.1,NM_194301.2	,	56,897,5550	GG,GA,AA		4.4651,14.1852,7.758	,	710/2037,710/2084	36191030	1009,11997	2203	4300	6503	SO:0001819	synonymous_variant	253959	exon16			AACTGAAACTTTC	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.2130T>C	14.37:g.36191030A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Silent	SNP	ENST00000389698.3	37	CCDS32065.1																																																																																			A|0.890;G|0.110	0.110	strong		0.423	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	
SYTL2	54843	hgsc.bcm.edu	37	11	85435742	85435742	+	Intron	SNP	C	C	T	rs146372321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:85435742C>T	ENST00000528231.1	-	7	1737				SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000359152.5_Silent_p.K1110K|SYTL2_ENST00000354566.3_Silent_p.K586K|SYTL2_ENST00000525423.1_Silent_p.K586K|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000389960.4_Intron	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		GAGCCTCGGCCTTTTCTACTG	0.443													C|||	30	0.00599042	0.0219	0.0014	5008	,	,		18228	0.0		0.0	False		,,,				2504	0.0				p.K586K		Atlas-SNP	.											.	SYTL2	231	.	0			c.G1758A						PASS	.	C	,,,,	79,4327	62.3+/-99.4	0,79,2124	67.0	65.0	66.0		,,,1758,1758	1.0	0.1	11	dbSNP_134	66	0,8598		0,0,4299	no	intron,intron,intron,coding-synonymous,coding-synonymous	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,,	0,79,6423	TT,TC,CC		0.0,1.793,0.6075	,,,,	,,,586/1273,586/1257	85435742	79,12925	2203	4299	6502	SO:0001627	intron_variant	54843	exon1			CTCGGCCTTTTCT	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+3196G>A	11.37:g.85435742C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	117	47	0.401709	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			C|0.995;T|0.005	0.005	strong		0.443	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
MUC7	4589	hgsc.bcm.edu	37	4	71347060	71347060	+	Missense_Mutation	SNP	A	A	C	rs74904873	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71347060A>C	ENST00000304887.5	+	3	789	c.599A>C	c.(598-600)cAa>cCa	p.Q200P	MUC7_ENST00000456088.1_Missense_Mutation_p.Q200P|MUC7_ENST00000413702.1_Missense_Mutation_p.Q200P	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	200	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.Q200P(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)			GCAACTACACAAGCTCCACCA	0.597													A|||	6	0.00119808	0.0015	0.0	5008	,	,		20514	0.002		0.001	False		,,,				2504	0.001				p.Q200P		Atlas-SNP	.											MUC7,pharynx,carcinoma,0,1	MUC7	91	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.A599C						scavenged	.						489.0	395.0	427.0					4																	71347060		2203	4300	6503	SO:0001583	missense	4589	exon4			CTACACAAGCTCC	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.599A>C	4.37:g.71347060A>C	ENSP00000302021:p.Gln200Pro	Somatic	501	9	0.0179641		WXS	Illumina HiSeq	Phase_I	552	12	0.0217391	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	A	0.019	-1.465514	0.01053	.	.	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.48522	0.81;0.81;0.81	2.05	1.2	0.21068	.	.	.	.	.	T	0.20129	0.0484	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25433	-1.0132	8	.	.	.	3.0933	9.4049	0.38455	0.2401:0.7599:0.0:0.0	.	200	Q8TAX7	MUC7_HUMAN	P	200	ENSP00000407422:Q200P;ENSP00000400585:Q200P;ENSP00000302021:Q200P	.	Q	+	2	0	MUC7	71381649	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.162000	0.03141	0.022000	0.15160	-0.710000	0.03640	CAA	A|0.500;C|0.500	0.500	strong		0.597	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
KIAA1683	80726	hgsc.bcm.edu	37	19	18368748	18368748	+	Missense_Mutation	SNP	C	C	T	rs61740685		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18368748C>T	ENST00000600328.3	-	4	2978	c.2785G>A	c.(2785-2787)Gca>Aca	p.A929T	KIAA1683_ENST00000392413.4_Missense_Mutation_p.A1116T|KIAA1683_ENST00000600359.3_Missense_Mutation_p.A883T|PDE4C_ENST00000596647.1_5'Flank|PDE4C_ENST00000355502.3_5'Flank			Q9H0B3	K1683_HUMAN	KIAA1683	929	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GTGATCACTGCGAGGATGCGG	0.677													C|||	1	0.000199681	0.0	0.0	5008	,	,		16152	0.0		0.001	False		,,,				2504	0.0				p.A1116T		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G3346A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	1,4401	2.1+/-5.4	0,1,2200	58.0	57.0	57.0		3346,2647,2785	3.5	0.0	19	dbSNP_129	57	6,8590	5.0+/-18.6	0,6,4292	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	58,58,58	0,7,6492	TT,TC,CC		0.0698,0.0227,0.0539	probably-damaging,probably-damaging,probably-damaging	1116/1368,883/1135,929/1181	18368748	7,12991	2201	4298	6499	SO:0001583	missense	80726	exon4			TCACTGCGAGGAT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2785G>A	19.37:g.18368748C>T	ENSP00000470780:p.Ala929Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.27	3.587572	0.66105	2.27E-4	6.98E-4	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000392412;ENST00000411671	T;T;T	0.46819	0.86;0.86;0.86	3.5	3.5	0.40072	.	0.000000	0.32671	N	0.005798	T	0.67373	0.2886	M	0.83603	2.65	0.09310	N	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.992;0.996	T	0.57877	-0.7735	10	0.51188	T	0.08	-16.8658	10.7032	0.45939	0.0:1.0:0.0:0.0	.	1116;929	E9PDE0;Q9H0B3	.;K1683_HUMAN	T	1116;929;883;193;543	ENSP00000376213:A1116T;ENSP00000352774:A929T;ENSP00000404501:A883T	ENSP00000352774:A929T	A	-	1	0	KIAA1683	18229748	0.809000	0.29036	0.021000	0.16686	0.006000	0.05464	3.249000	0.51437	1.971000	0.57363	0.313000	0.20887	GCA	C|0.999;T|0.001	0.001	strong		0.677	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
FAM47C	442444	hgsc.bcm.edu	37	X	37028762	37028762	+	Missense_Mutation	SNP	C	C	G	rs61730910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37028762C>G	ENST00000358047.3	+	1	2331	c.2279C>G	c.(2278-2280)tCt>tGt	p.S760C		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	760										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						ACTCGCGTATCTCATCTCCGC	0.632													c|||	23	0.00609272	0.0166	0.0014	3775	,	,		11549	0.0		0.0	False		,,,				2504	0.0				p.S760C		Atlas-SNP	.											.	FAM47C	267	.	0			c.C2279G						PASS	.	C	CYS/SER	66,3767		3,52,8,1576,563	46.0	44.0	45.0		2279	0.9	0.0	X	dbSNP_129	45	0,6728		0,0,0,2428,1872	yes	missense	FAM47C	NM_001013736.2	112	3,52,8,4004,2435	GG,GC,G,CC,C		0.0,1.7219,0.6249	probably-damaging	760/1036	37028762	66,10495	2202	4300	6502	SO:0001583	missense	442444	exon1			GCGTATCTCATCT	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2279C>G	X.37:g.37028762C>G	ENSP00000367913:p.Ser760Cys	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	150	80	0.533333	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	8	0.004822182037371911	6	0.012244897959183673	1	0.0027624309392265192	0	0.0	0	0.0	-	5.654	0.305291	0.10678	0.017219	0.0	ENSG00000198173	ENST00000358047	T	0.20332	2.08	0.895	0.895	0.19247	.	.	.	.	.	T	0.21631	0.0521	M	0.81341	2.54	0.09310	N	1	D	0.58268	0.982	P	0.58873	0.847	T	0.08932	-1.0698	9	0.62326	D	0.03	.	3.8459	0.08934	0.0:0.67:0.0:0.33	rs61730910	760	Q5HY64	FA47C_HUMAN	C	760	ENSP00000367913:S760C	ENSP00000367913:S760C	S	+	2	0	FAM47C	36938683	0.005000	0.15991	0.002000	0.10522	0.002000	0.02628	0.436000	0.21526	0.163000	0.19507	0.165000	0.16767	TCT	C|0.993;G|0.007	0.007	strong		0.632	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
PPT1	5538	hgsc.bcm.edu	37	1	40535945	40535945	+	IGR	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:40535945A>G	ENST00000433473.3	-	0	2740				CAP1_ENST00000372802.1_Missense_Mutation_p.I369V|CAP1_ENST00000340450.3_Missense_Mutation_p.I369V|CAP1_ENST00000372797.3_Missense_Mutation_p.I370V|CAP1_ENST00000372805.3_Missense_Mutation_p.I370V|CAP1_ENST00000372798.1_Missense_Mutation_p.I369V|CAP1_ENST00000372792.2_Missense_Mutation_p.I370V|CAP1_ENST00000479759.1_3'UTR	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1						adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-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;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AATTAACTCCATTACAGTAGG	0.458																																					p.I370V		Atlas-SNP	.											.	CAP1	38	.	0			c.A1108G						PASS	.						81.0	77.0	78.0					1																	40535945		2020	4170	6190	SO:0001628	intergenic_variant	10487	exon10			AACTCCATTACAG	U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"""ceroid-lipofuscinosis, neuronal 1, infantile"""	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495		1.37:g.40535945A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	154	82	0.532468	NM_006367	B4DY24|Q6FGQ4	Missense_Mutation	SNP	ENST00000433473.3	37	CCDS447.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.066402	0.55539	.	.	ENSG00000131236	ENST00000372797;ENST00000372802;ENST00000372792;ENST00000538246;ENST00000372798;ENST00000340450;ENST00000372805	T;T;T;T;T;T	0.08896	3.05;3.04;3.05;3.04;3.04;3.05	5.34	5.34	0.76211	CARP motif (1);Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal (1);Adenylate cyclase-associated CAP, C-terminal (2);C-CAP/cofactor C-like domain (1);	0.000000	0.85682	D	0.000000	T	0.11707	0.0285	L	0.48986	1.54	0.80722	D	1	B;B	0.33807	0.061;0.426	B;B	0.36534	0.149;0.227	T	0.03829	-1.1000	10	0.46703	T	0.11	-17.1934	14.503	0.67734	1.0:0.0:0.0:0.0	.	317;370	E7ENY9;Q01518	.;CAP1_HUMAN	V	370;369;370;347;369;369;370	ENSP00000361883:I370V;ENSP00000361888:I369V;ENSP00000361878:I370V;ENSP00000361884:I369V;ENSP00000344832:I369V;ENSP00000361891:I370V	ENSP00000344832:I369V	I	+	1	0	CAP1	40308532	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.437000	0.80417	1.996000	0.58369	0.528000	0.53228	ATT	.	.	none		0.458	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310	
TF	7018	hgsc.bcm.edu	37	3	133474286	133474286	+	Silent	SNP	A	A	G	rs8177226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133474286A>G	ENST00000402696.3	+	5	1067	c.582A>G	c.(580-582)ccA>ccG	p.P194P	TF_ENST00000264998.3_Silent_p.P67P|TFP1_ENST00000460564.1_RNA	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	194	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)	AACTGTGTCCAGGGTGTGGCT	0.567													A|||	63	0.0125799	0.0439	0.0043	5008	,	,		20471	0.002		0.0	False		,,,				2504	0.0				p.P194P		Atlas-SNP	.											.	TF	116	.	0			c.A582G						PASS	.	A		154,4252	105.2+/-143.6	1,152,2050	111.0	96.0	101.0		582	-9.9	0.0	3	dbSNP_117	101	0,8600		0,0,4300	no	coding-synonymous	TF	NM_001063.3		1,152,6350	GG,GA,AA		0.0,3.4952,1.1841		194/699	133474286	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon5			GTGTCCAGGGTGT		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.582A>G	3.37:g.133474286A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	129	77	0.596899	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			A|0.988;G|0.012	0.012	strong		0.567	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249532	71249532	+	Missense_Mutation	SNP	C	C	G	rs532438179|rs11234084|rs369043826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249532C>G	ENST00000398534.3	+	1	462	c.431C>G	c.(430-432)tCc>tGc	p.S144C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	144	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						CCCTGCTGTTCCCAGTCCAGC	0.612																																					p.S144C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.C431G						PASS	.						148.0	160.0	156.0					11																	71249532		2200	4294	6494	SO:0001583	missense	57830	exon1			GCTGTTCCCAGTC	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.431C>G	11.37:g.71249532C>G	ENSP00000420723:p.Ser144Cys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	222	9	0.0405405	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	37	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	-	3.125	-0.179750	0.06380	.	.	ENSG00000241233	ENST00000398534	T	0.01197	5.19	1.57	-2.99	0.05497	.	.	.	.	.	T	0.00552	0.0018	N	0.02213	-0.635	0.21861	N	0.999505	B	0.02656	0.0	B	0.01281	0.0	T	0.44314	-0.9336	9	0.02654	T	1	.	12.0511	0.53507	0.0:0.7645:0.2355:0.0	rs11234084	144	O75690	KRA58_HUMAN	C	144	ENSP00000420723:S144C	ENSP00000420723:S144C	S	+	2	0	KRTAP5-8	70927180	0.000000	0.05858	0.375000	0.26029	0.014000	0.08584	-0.627000	0.05521	-0.723000	0.04915	-0.951000	0.02657	TCC	.	.	weak		0.612	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
PROM1	8842	hgsc.bcm.edu	37	4	16020162	16020162	+	Splice_Site	SNP	C	C	T	rs2286455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:16020162C>T	ENST00000510224.1	-	9	1034	c.786G>A	c.(784-786)gcG>gcA	p.A262A	PROM1_ENST00000543373.1_Splice_Site_p.A253A|PROM1_ENST00000540805.1_Splice_Site_p.A262A|PROM1_ENST00000447510.2_Splice_Site_p.A262A|PROM1_ENST00000505450.1_Splice_Site_p.A253A|PROM1_ENST00000508167.1_Splice_Site_p.A253A|PROM1_ENST00000502943.1_5'UTR|PROM1_ENST00000539194.1_Splice_Site_p.A262A			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	215	0	0		WXS	Illumina HiSeq	Phase_I	200	90	0.45	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
SLA2	84174	hgsc.bcm.edu	37	20	35242745	35242745	+	Missense_Mutation	SNP	C	C	T	rs34834764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:35242745C>T	ENST00000262866.4	-	7	1050	c.628G>A	c.(628-630)Gtg>Atg	p.V210M	SLA2_ENST00000360672.2_Missense_Mutation_p.C193Y	NM_032214.3|NM_175077.2	NP_115590.1|NP_778252.1	Q9H6Q3	SLAP2_HUMAN	Src-like-adaptor 2	210	SLA C-terminal.		V -> M (in dbSNP:rs34834764).		antigen receptor-mediated signaling pathway (GO:0050851)|B cell mediated immunity (GO:0019724)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of B cell activation (GO:0050869)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of signal transduction (GO:0009967)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|late endosome (GO:0005770)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)|SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(2)|skin(2)	5	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				GTCCTCTGCACAGTCACAGGT	0.572													C|||	149	0.0297524	0.1067	0.0115	5008	,	,		21213	0.0		0.0	False		,,,				2504	0.0				p.V210M	Ovarian(59;720 1165 26994 46188 51693)	Atlas-SNP	.											.	SLA2	12	.	0			c.G628A						PASS	.	C	MET/VAL,TYR/CYS	374,4032	191.2+/-216.9	17,340,1846	152.0	144.0	147.0		628,578	5.4	1.0	20	dbSNP_126	147	1,8599		0,1,4299	yes	missense,missense	SLA2	NM_032214.2,NM_175077.1	21,194	17,341,6145	TT,TC,CC		0.0116,8.4884,2.8833	probably-damaging,probably-damaging	210/262,193/211	35242745	375,12631	2203	4300	6503	SO:0001583	missense	84174	exon7			TCTGCACAGTCAC	AF326353	CCDS13282.1, CCDS13283.1	20q11.23	2013-02-14			ENSG00000101082	ENSG00000101082		"""SH2 domain containing"""	17329	protein-coding gene	gene with protein product		606577		C20orf156		11696592	Standard	NM_032214		Approved	FLJ21992, SLAP-2	uc002xfv.3	Q9H6Q3	OTTHUMG00000032393	ENST00000262866.4:c.628G>A	20.37:g.35242745C>T	ENSP00000262866:p.Val210Met	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	205	105	0.512195	NM_032214	A8K648|E1P5U1|E1P5U2|Q5TH27|Q5TH28|Q8WY18|Q96QI4|Q9H135	Missense_Mutation	SNP	ENST00000262866.4	37	CCDS13282.1	45|45	0.020604395604395604|0.020604395604395604	42|42	0.08536585365853659|0.08536585365853659	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	C|C	15.68|15.68	2.904261|2.904261	0.52333|0.52333	0.084884|0.084884	1.16E-4|1.16E-4	ENSG00000101082|ENSG00000101082	ENST00000360672|ENST00000262866	T|T	0.74632|0.79033	-0.86|-1.23	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	.|0.131339	.|0.49916	.|D	.|0.000132	T|T	0.09862|0.09862	0.0242|0.0242	.|.	.|.	.|.	0.26547|0.26547	N|N	0.973972|0.973972	B|B	0.14012|0.29988	0.009|0.264	B|B	0.04013|0.33846	0.001|0.171	T|T	0.36187|0.36187	-0.9758|-0.9758	8|9	0.45353|0.39692	T|T	0.12|0.17	-19.6165|-19.6165	16.7763|16.7763	0.85551|0.85551	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs34834764|rs34834764	193|210	Q9H6Q3-2|Q9H6Q3	.|SLAP2_HUMAN	Y|M	193|210	ENSP00000353890:C193Y|ENSP00000262866:V210M	ENSP00000353890:C193Y|ENSP00000262866:V210M	C|V	-|-	2|1	0|0	SLA2|SLA2	34676159|34676159	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.904000|0.904000	0.53231|0.53231	2.488000|2.488000	0.45276|0.45276	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	TGT|GTG	C|0.968;T|0.032	0.032	strong		0.572	SLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079037.2	NM_175077	
ACP5	54	hgsc.bcm.edu	37	19	11685948	11685948	+	Silent	SNP	A	A	G	rs77911902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11685948A>G	ENST00000592828.1	-	7	1257	c.855T>C	c.(853-855)acT>acC	p.T285T	ACP5_ENST00000590420.1_Missense_Mutation_p.L43P|ZNF627_ENST00000588651.1_Intron|ACP5_ENST00000218758.5_Silent_p.T285T|ACP5_ENST00000412435.2_Silent_p.T285T|ACP5_ENST00000433365.2_Silent_p.T285T	NM_001111034.1	NP_001104504.1	P13686	PPA5_HUMAN	acid phosphatase 5, tartrate resistant	285					bone morphogenesis (GO:0060349)|bone resorption (GO:0045453)|defense response to Gram-positive bacterium (GO:0050830)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of superoxide anion generation (GO:0032929)|negative regulation of tumor necrosis factor production (GO:0032720)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	acid phosphatase activity (GO:0003993)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	9						GTGAGTCTTCAGTCCCATAGT	0.572													A|||	148	0.0295527	0.1051	0.013	5008	,	,		21260	0.0		0.0	False		,,,				2504	0.0				p.T285T		Atlas-SNP	.											.	ACP5	30	.	0			c.T855C						PASS	.		,,,	478,3928	225.9+/-241.6	21,436,1746	100.0	86.0	91.0		855,855,855,855	-1.6	0.0	19	dbSNP_131	91	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACP5	NM_001111034.1,NM_001111035.1,NM_001111036.1,NM_001611.3	,,,	21,443,6039	GG,GA,AA		0.0814,10.8488,3.729	,,,	285/326,285/326,285/326,285/326	11685948	485,12521	2203	4300	6503	SO:0001819	synonymous_variant	54	exon6			GTCTTCAGTCCCA	X14618	CCDS12265.1	19p13.2	2012-10-02			ENSG00000102575	ENSG00000102575	3.1.3.2		124	protein-coding gene	gene with protein product	"""tartrate-resistant acid phosphatase"""	171640				8449511, 2338077	Standard	NM_001611		Approved	TRAP	uc002msj.4	P13686	OTTHUMG00000182036	ENST00000592828.1:c.855T>C	19.37:g.11685948A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	158	80	0.506329	NM_001111034	A8K3V2|Q2TAB1|Q6IAS6|Q9UCJ5|Q9UCJ6|Q9UCJ7	Silent	SNP	ENST00000592828.1	37	CCDS12265.1																																																																																			A|0.967;G|0.033	0.033	strong		0.572	ACP5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458881.1		
ZNF518B	85460	hgsc.bcm.edu	37	4	10445427	10445427	+	Silent	SNP	A	A	T	rs7694496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:10445427A>T	ENST00000326756.3	-	3	2964	c.2526T>A	c.(2524-2526)ccT>ccA	p.P842P		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	842					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.P842P(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						TAGGCCGCAGAGGTGTCTCGA	0.463													A|||	720	0.14377	0.3154	0.036	5008	,	,		18870	0.1597		0.003	False		,,,				2504	0.1166				p.P842P		Atlas-SNP	.											ZNF518B,NS,carcinoma,0,1	ZNF518B	116	1	1	Substitution - coding silent(1)	stomach(1)	c.T2526A						PASS	.	A		1122,3284	402.6+/-332.4	155,812,1236	90.0	86.0	88.0		2526	3.3	0.0	4	dbSNP_116	88	34,8566	24.0+/-70.4	1,32,4267	no	coding-synonymous	ZNF518B	NM_053042.2		156,844,5503	TT,TA,AA		0.3953,25.4653,8.8882		842/1075	10445427	1156,11850	2203	4300	6503	SO:0001819	synonymous_variant	85460	exon3			CCGCAGAGGTGTC	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.2526T>A	4.37:g.10445427A>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_053042	Q96LN8	Silent	SNP	ENST00000326756.3	37	CCDS33960.1																																																																																			A|0.901;T|0.099	0.099	strong		0.463	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
KHDC1	80759	hgsc.bcm.edu	37	6	74019338	74019338	+	Nonsense_Mutation	SNP	G	G	A	rs16883571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74019338G>A	ENST00000370384.3	-	1	600	c.100C>T	c.(100-102)Cag>Tag	p.Q34*	KHDC1_ENST00000484801.1_5'UTR	NM_001251874.1	NP_001238803.1	Q4VXA5	KHDC1_HUMAN	KH homology domain containing 1	34						integral component of membrane (GO:0016021)	RNA binding (GO:0003723)			large_intestine(1)|lung(4)|skin(1)	6						GCAAGGGTCTGGAGAAAGGGC	0.507											OREG0017531	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	303	0.0605032	0.1082	0.0692	5008	,	,		19499	0.0129		0.0746	False		,,,				2504	0.0245				p.Q34X		Atlas-SNP	.											.	KHDC1	10	.	0			c.C100T						PASS	.																																			SO:0001587	stop_gained	80759	exon1			GGGTCTGGAGAAA		CCDS43480.1, CCDS59027.1	6q13	2014-05-15	2007-11-13	2007-11-13	ENSG00000135314	ENSG00000135314			21366	protein-coding gene	gene with protein product		611688	"""chromosome 6 open reading frame 148"""	C6orf148		17913455	Standard	NM_030568		Approved	MGC10818, bA257K9.4, NDG1	uc003pgn.4	Q4VXA5	OTTHUMG00000015030	ENST00000370384.3:c.100C>T	6.37:g.74019338G>A	ENSP00000359411:p.Gln34*	Somatic	87	0	0	1149	WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_001251874	Q5JSQ7|Q8WTV2|Q96NQ5	Nonsense_Mutation	SNP	ENST00000370384.3	37	CCDS59027.1	144	0.06593406593406594	60	0.12195121951219512	20	0.055248618784530384	5	0.008741258741258742	59	0.07783641160949868	G	37	6.382366	0.97520	.	.	ENSG00000135314	ENST00000370384	.	.	.	1.82	1.82	0.25136	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999999086687	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	7.1384	0.25541	0.0:0.0:1.0:0.0	rs16883571;rs16883571	.	.	.	X	34	.	ENSP00000359411:Q34X	Q	-	1	0	KHDC1	74076059	0.000000	0.05858	0.003000	0.11579	0.010000	0.07245	0.205000	0.17356	1.345000	0.45676	0.407000	0.27541	CAG	G|0.934;A|0.066	0.066	strong		0.507	KHDC1-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000148103.2	NM_030568	
HBEGF	1839	hgsc.bcm.edu	37	5	139722345	139722345	+	Silent	SNP	G	G	A	rs2074611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	258	0	0		WXS	Illumina HiSeq	Phase_I	273	126	0.461538	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	
TSPEAR	54084	hgsc.bcm.edu	37	21	45929192	45929192	+	Silent	SNP	G	G	A	rs115847549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45929192G>A	ENST00000323084.4	-	10	1709	c.1644C>T	c.(1642-1644)taC>taT	p.Y548Y	TSPEAR-AS1_ENST00000451035.1_RNA|TSPEAR-AS1_ENST00000430181.1_RNA|TSPEAR_ENST00000397916.1_Silent_p.Y480Y	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	548					sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						TCTCCACATCGTAGCTGTGAC	0.537													G|||	41	0.0081869	0.0287	0.0043	5008	,	,		13812	0.0		0.0	False		,,,				2504	0.0				p.Y548Y		Atlas-SNP	.											.	TSPEAR	110	.	0			c.C1644T						PASS	.	G		138,4268	100.7+/-139.4	6,126,2071	202.0	127.0	152.0		1644	-1.0	0.9	21	dbSNP_132	152	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous	TSPEAR	NM_144991.2		6,145,6352	AA,AG,GG		0.2209,3.1321,1.2071		548/670	45929192	157,12849	2203	4300	6503	SO:0001819	synonymous_variant	54084	exon10			CACATCGTAGCTG	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"""chromosome 21 open reading frame 29"", ""deafness, autosomal recessive 98"""	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.1644C>T	21.37:g.45929192G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	184	97	0.527174	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			G|0.988;A|0.012	0.012	strong		0.537	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991	
ABCA13	154664	hgsc.bcm.edu	37	7	48317708	48317708	+	Missense_Mutation	SNP	A	A	C	rs78334925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:48317708A>C	ENST00000435803.1	+	18	6941	c.6917A>C	c.(6916-6918)aAa>aCa	p.K2306T		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2306					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						CCAAAAGATAAAATTCTAGAA	0.234													A|||	487	0.0972444	0.1452	0.0548	5008	,	,		10236	0.1508		0.0487	False		,,,				2504	0.0573				p.K2306T		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A6917C						PASS	.	A	THR/LYS	352,3094		19,314,1390	11.0	10.0	11.0		6917	3.7	0.5	7	dbSNP_131	11	426,7404		15,396,3504	yes	missense	ABCA13	NM_152701.3	78	34,710,4894	CC,CA,AA		5.4406,10.2147,6.8996	probably-damaging	2306/5059	48317708	778,10498	1723	3915	5638	SO:0001583	missense	154664	exon18			AAGATAAAATTCT	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.6917A>C	7.37:g.48317708A>C	ENSP00000411096:p.Lys2306Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	242	0.1108058608058608	81	0.16463414634146342	25	0.06906077348066299	97	0.16958041958041958	39	0.051451187335092345	A	12.75	2.032480	0.35893	0.102147	0.054406	ENSG00000179869	ENST00000435803	T	0.60040	0.22	4.88	3.68	0.42216	.	0.000000	0.52532	D	0.000070	T	0.00210	0.0006	M	0.61703	1.905	0.09310	P	0.9999999402452	B	0.27997	0.197	B	0.28638	0.092	T	0.11446	-1.0587	9	0.87932	D	0	.	8.7131	0.34395	0.8074:0.1926:0.0:0.0	.	2306	Q86UQ4	ABCAD_HUMAN	T	2306	ENSP00000411096:K2306T	ENSP00000411096:K2306T	K	+	2	0	ABCA13	48288254	0.970000	0.33590	0.509000	0.27700	0.979000	0.70002	1.860000	0.39428	0.781000	0.33589	0.528000	0.53228	AAA	A|0.900;C|0.100	0.100	strong		0.234	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
WNT9A	7483	hgsc.bcm.edu	37	1	228109696	228109696	+	Silent	SNP	G	G	A	rs112703157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228109696G>A	ENST00000272164.5	-	4	631	c.621C>T	c.(619-621)atC>atT	p.I207I		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	207					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				CCCCAGCCTTGATCACCTGGC	0.677													G|||	122	0.024361	0.0862	0.0115	5008	,	,		17033	0.0		0.0	False		,,,				2504	0.0				p.I207I		Atlas-SNP	.											.	WNT9A	39	.	0			c.C621T						PASS	.	G		318,4080		6,306,1887	34.0	35.0	34.0		621	3.4	1.0	1	dbSNP_132	34	2,8592		0,2,4295	no	coding-synonymous	WNT9A	NM_003395.2		6,308,6182	AA,AG,GG		0.0233,7.2306,2.4631		207/366	228109696	320,12672	2199	4297	6496	SO:0001819	synonymous_variant	7483	exon4			AGCCTTGATCACC	AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"""Wingless-type MMTV integration sites"""	12778	protein-coding gene	gene with protein product		602863	"""wingless-type MMTV integration site family, member 14"""	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.621C>T	1.37:g.228109696G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	84	30	0.357143	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Silent	SNP	ENST00000272164.5	37	CCDS31045.1																																																																																			G|0.977;A|0.023	0.023	strong		0.677	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395	
MAST4	375449	hgsc.bcm.edu	37	5	66461583	66461583	+	Silent	SNP	C	C	T	rs56201012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:66461583C>T	ENST00000403625.2	+	29	6871	c.6576C>T	c.(6574-6576)caC>caT	p.H2192H	MAST4_ENST00000404260.3_Silent_p.H2195H|MAST4_ENST00000403666.1_Silent_p.H2003H|MAST4_ENST00000405643.1_Silent_p.H2013H|MAST4_ENST00000261569.7_Silent_p.H1998H	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2195	Pro-rich.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GCAGCAGCCACAAGCCCCGGC	0.667													C|||	92	0.0183706	0.0673	0.0043	5008	,	,		14359	0.0		0.0	False		,,,				2504	0.0				p.H2192H		Atlas-SNP	.											.	MAST4	218	.	0			c.C6576T						PASS	.	C	,	176,3520		6,164,1678	6.0	10.0	9.0		6576,6009	1.2	0.0	5	dbSNP_129	9	0,8114		0,0,4057	no	coding-synonymous,coding-synonymous	MAST4	NM_001164664.1,NM_015183.2	,	6,164,5735	TT,TC,CC		0.0,4.7619,1.4903	,	2192/2624,2003/2435	66461583	176,11634	1848	4057	5905	SO:0001819	synonymous_variant	375449	exon29			CAGCCACAAGCCC	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.6576C>T	5.37:g.66461583C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Silent	SNP	ENST00000403625.2	37	CCDS54861.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	C	0.038	-1.299299	0.01364	0.047619	0.0	ENSG00000069020	ENST00000443808	.	.	.	5.0	1.16	0.20824	.	.	.	.	.	.	.	.	.	.	.	0.22389	N	0.999143	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.25	3.4785	0.07594	0.1768:0.386:0.0:0.4373	rs56201012;rs61910710	.	.	.	X	1249	.	.	Q	+	1	0	MAST4	66497339	0.016000	0.18221	0.007000	0.13788	0.092000	0.18411	-0.102000	0.10956	0.022000	0.15160	-0.140000	0.14226	CAA	C|0.990;T|0.010	0.010	strong		0.667	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2		
METRNL	284207	hgsc.bcm.edu	37	17	81043175	81043175	+	Missense_Mutation	SNP	G	G	T	rs72854240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:81043175G>T	ENST00000320095.7	+	2	657	c.532G>T	c.(532-534)Gcg>Tcg	p.A178S	METRNL_ENST00000571814.1_Missense_Mutation_p.A96S|METRNL_ENST00000570778.1_Missense_Mutation_p.A96S	NM_001004431.1	NP_001004431.1	Q641Q3	METRL_HUMAN	meteorin, glial cell differentiation regulator-like	178					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)			GAGGCACAGGGCGTCGGACCT	0.672													G|||	150	0.0299521	0.003	0.0476	5008	,	,		13564	0.0		0.0954	False		,,,				2504	0.0174				p.A178S		Atlas-SNP	.											METRNL,NS,carcinoma,0,2	METRNL	29	2	0			c.G532T						PASS	.	G	SER/ALA	98,4308	77.3+/-115.6	1,96,2106	49.0	56.0	54.0		532	2.1	0.0	17	dbSNP_130	54	877,7719	189.3+/-236.1	53,771,3474	yes	missense	METRNL	NM_001004431.1	99	54,867,5580	TT,TG,GG		10.2024,2.2242,7.4988	benign	178/312	81043175	975,12027	2203	4298	6501	SO:0001583	missense	284207	exon2			CACAGGGCGTCGG	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.532G>T	17.37:g.81043175G>T	ENSP00000315731:p.Ala178Ser	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	168	79	0.470238	NM_001004431	B3KSJ5|Q86VM0	Missense_Mutation	SNP	ENST00000320095.7	37	CCDS32779.1	105	0.04807692307692308	3	0.006097560975609756	18	0.049723756906077346	0	0.0	84	0.11081794195250659	g	8.856	0.945846	0.18356	0.022242	0.102024	ENSG00000176845	ENST00000320095	.	.	.	4.1	2.1	0.27182	.	1.171190	0.06246	N	0.691200	T	0.00384	0.0012	N	0.16656	0.425	0.09310	N	1	B	0.25904	0.137	B	0.25140	0.058	T	0.19321	-1.0309	8	.	.	.	-9.565	4.4948	0.11831	0.2058:0.1841:0.6101:0.0	.	178	Q641Q3	METRL_HUMAN	S	178	.	.	A	+	1	0	METRNL	78636464	0.043000	0.20138	0.000000	0.03702	0.004000	0.04260	2.535000	0.45685	0.516000	0.28340	-0.260000	0.10688	GCG	G|0.934;T|0.066	0.066	strong		0.672	METRNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438902.1	NM_001004431	
PCDHA1	56147	hgsc.bcm.edu	37	5	140167520	140167520	+	Missense_Mutation	SNP	G	G	A	rs150585640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140167520G>A	ENST00000504120.2	+	1	1645	c.1645G>A	c.(1645-1647)Gtg>Atg	p.V549M	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000378133.3_Missense_Mutation_p.V549M	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	549	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCAGCAACGTGACGCTGCA	0.672													.|||	71	0.0141773	0.053	0.0014	5008	,	,		16239	0.0		0.0	False		,,,				2504	0.0				p.V549M		Atlas-SNP	.											.	PCDHA1	387	.	0			c.G1645A						PASS	.	G	MET/VAL,MET/VAL,	233,4173	136.1+/-172.1	9,215,1979	78.0	81.0	80.0		1645,1645,	2.7	1.0	5	dbSNP_134	80	1,8589	1.2+/-3.3	0,1,4294	no	missense,missense,intron	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	21,21,	9,216,6273	AA,AG,GG		0.0116,5.2882,1.8006	,,	549/951,549/808,	140167520	234,12762	2203	4295	6498	SO:0001583	missense	56147	exon1			AGCAACGTGACGC	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1645G>A	5.37:g.140167520G>A	ENSP00000420840:p.Val549Met	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_031410	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	g	16.14	3.037929	0.54896	0.052882	1.16E-4	ENSG00000204970	ENST00000504120;ENST00000378133	T;T	0.53640	0.61;0.61	3.59	2.71	0.32032	Cadherin (5);Cadherin-like (1);	0.209202	0.23219	N	0.050600	T	0.16896	0.0406	M	0.83384	2.64	0.23997	N	0.996224	D;D	0.65815	0.995;0.988	P;P	0.50192	0.634;0.501	T	0.25847	-1.0120	10	0.66056	D	0.02	.	7.0109	0.24861	0.0968:0.1747:0.7285:0.0	.	549;549	Q9Y5I3;Q9Y5I3-3	PCDA1_HUMAN;.	M	549	ENSP00000420840:V549M;ENSP00000367373:V549M	ENSP00000367373:V549M	V	+	1	0	PCDHA1	140147704	0.967000	0.33354	0.987000	0.45799	0.935000	0.57460	2.495000	0.45337	0.621000	0.30232	0.555000	0.69702	GTG	G|0.961;A|0.039	0.039	strong		0.672	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329793	24329793	+	IGR	SNP	C	C	T	rs139232512		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24329793C>T								AC096509.1 (24999 upstream) : AC004552.1 (37132 downstream)																							AGCTGGACGGCGCCTGCTAGC	0.637													C|||	170	0.0450331	0.1218	0.013	3775	,	,		10526	0.0		0.0	False		,,,				2504	0.0				p.R547H		Atlas-SNP	.											.	.	.	.	0			c.G1640A						PASS	.	C	HIS/ARG	385,2240		27,253,78,778,431	11.0	11.0	11.0		1640	-1.0	0.0	X	dbSNP_134	11	4,5486		0,4,0,1912,1658	yes	missense	FAM48B2	NM_001136233.1	29	27,257,78,2690,2089	TT,TC,T,CC,C		0.0729,14.6667,4.7936	possibly-damaging	547/818	24329793	389,7726	1567	3574	5141	SO:0001628	intergenic_variant	170067	exon1			GGACGGCGCCTGC																													X.37:g.24329793C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	223	129	0.578475	NM_001136233		Missense_Mutation	SNP		37																																																																																				C|0.963;T|0.037	0.037	strong	0	0.637								
PCDH8	5100	hgsc.bcm.edu	37	13	53419765	53419765	+	Silent	SNP	G	G	A	rs5030686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:53419765G>A	ENST00000377942.3	-	2	2837	c.2634C>T	c.(2632-2634)ccC>ccT	p.P878P	PCDH8_ENST00000338862.4_Silent_p.P781P	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	878					cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		AGGCACCGTAGGGCTGCAGCA	0.562													G|||	259	0.0517173	0.0673	0.085	5008	,	,		15777	0.0109		0.0547	False		,,,				2504	0.046				p.P878P	GBM(36;25 841 9273 49207)	Atlas-SNP	.											.	PCDH8	95	.	0			c.C2634T						PASS	.	G	,	297,4107	143.1+/-178.2	14,269,1919	25.0	26.0	26.0		2634,2343	0.6	1.0	13	dbSNP_113	26	500,8100	133.8+/-191.2	16,468,3816	no	coding-synonymous,coding-synonymous	PCDH8	NM_002590.3,NM_032949.2	,	30,737,5735	AA,AG,GG		5.814,6.7439,6.1289	,	878/1071,781/974	53419765	797,12207	2202	4300	6502	SO:0001819	synonymous_variant	5100	exon2			ACCGTAGGGCTGC	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"""Cadherins / Protocadherins : Non-clustered"""	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.2634C>T	13.37:g.53419765G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_002590	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Silent	SNP	ENST00000377942.3	37	CCDS9438.1																																																																																			G|0.945;A|0.055	0.055	strong		0.562	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590	
CCDC180	100499483	hgsc.bcm.edu	37	9	100105735	100105735	+	Silent	SNP	T	T	C	rs1947717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100105735T>C	ENST00000357054.1	+	33	3872	c.2937T>C	c.(2935-2937)tgT>tgC	p.C979C	CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000529487.1_Silent_p.C840C|CCDC180_ENST00000460482.2_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000411667.2_Silent_p.C837C|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	114	0	0		WXS	Illumina HiSeq	Phase_I	107	72	0.672897	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	
C3	718	hgsc.bcm.edu	37	19	6709704	6709704	+	Silent	SNP	C	C	T	rs2230205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6709704C>T	ENST00000245907.6	-	14	1928	c.1836G>A	c.(1834-1836)acG>acA	p.T612T		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	612					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CCTTACTCTGCGTCAGTTTGT	0.617													c|||	1094	0.21845	0.1346	0.1066	5008	,	,		13822	0.4425		0.1372	False		,,,				2504	0.2638				p.T612T		Atlas-SNP	.											.	C3	192	.	0			c.G1836A						PASS	.			509,3897	233.6+/-246.7	19,471,1713	138.0	146.0	143.0		1836	-10.0	0.0	19	dbSNP_98	143	1117,7483	231.5+/-265.5	89,939,3272	no	coding-synonymous	C3	NM_000064.2		108,1410,4985	TT,TC,CC		12.9884,11.5524,12.5019		612/1664	6709704	1626,11380	2203	4300	6503	SO:0001819	synonymous_variant	718	exon14			ACTCTGCGTCAGT	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1836G>A	19.37:g.6709704C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	139	136	0.978417	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	37	CCDS32883.1																																																																																			C|0.836;T|0.164	0.164	strong		0.617	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
KXD1	79036	hgsc.bcm.edu	37	19	18679351	18679351	+	Silent	SNP	C	C	T	rs11086117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18679351C>T	ENST00000602094.1	+	5	1901	c.441C>T	c.(439-441)ccC>ccT	p.P147P	KXD1_ENST00000222307.4_Silent_p.P147P|KXD1_ENST00000539106.1_Silent_p.P147P|KXD1_ENST00000599319.1_Silent_p.P147P|AC005253.4_ENST00000593791.1_RNA|KXD1_ENST00000540691.1_Silent_p.P147P|KXD1_ENST00000595073.1_Silent_p.P147P|KXD1_ENST00000601630.1_Silent_p.P166P			Q9BQD3	KXDL1_HUMAN	KxDL motif containing 1	147					vesicle-mediated transport (GO:0016192)	BLOC-1 complex (GO:0031083)											CCCTGAGCCCCGGCTTCGAGG	0.657													C|||	719	0.14357	0.4856	0.0504	5008	,	,		16847	0.001		0.0318	False		,,,				2504	0.0092				p.P147P		Atlas-SNP	.											.	.	.	.	0			c.C441T						PASS	.	C	,,	1848,2558	538.4+/-375.0	399,1050,754	151.0	138.0	143.0		441,441,441	-9.8	0.1	19	dbSNP_120	143	272,8328	103.3+/-164.5	8,256,4036	no	coding-synonymous,coding-synonymous,coding-synonymous	C19orf50	NM_001171948.1,NM_001171949.1,NM_024069.3	,,	407,1306,4790	TT,TC,CC		3.1628,41.9428,16.3002	,,	147/177,147/177,147/177	18679351	2120,10886	2203	4300	6503	SO:0001819	synonymous_variant	79036	exon6			GAGCCCCGGCTTC	AK098346	CCDS12381.1	19p13.11	2011-11-24	2011-11-24	2011-11-24	ENSG00000105700	ENSG00000105700			28420	protein-coding gene	gene with protein product		615178	"""chromosome 19 open reading frame 50"""	C19orf50		21159114	Standard	NM_001171948		Approved	FLJ25480, MGC2749, KXDL	uc002njo.3	Q9BQD3		ENST00000602094.1:c.441C>T	19.37:g.18679351C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_001171948	O76098	Silent	SNP	ENST00000602094.1	37	CCDS12381.1																																																																																			A|0.000;C|0.852;G|0.000;T|0.148	0.148	strong		0.657	KXD1-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465107.1	NM_024069	
QRICH2	84074	hgsc.bcm.edu	37	17	74288422	74288422	+	Missense_Mutation	SNP	T	T	C	rs6501879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74288422T>C	ENST00000262765.5	-	4	2067	c.1888A>G	c.(1888-1890)Ata>Gta	p.I630V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	630	Gln-rich.		I -> T (in dbSNP:rs6501878).|I -> V (in dbSNP:rs6501879).					p.I630_G639delIVQRGLVQPG(3)		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						cgctgaactataccaggttgc	0.542													t|||	2361	0.471446	0.7148	0.3098	5008	,	,		23437	0.5724		0.2753	False		,,,				2504	0.3548				p.I630V		Atlas-SNP	.											.	QRICH2	143	.	3	Deletion - In frame(3)	stomach(3)	c.A1888G						PASS	.	C	VAL/ILE	1348,2456		625,98,1179	73.0	85.0	81.0		1888	-1.3	0.0	17	dbSNP_116	81	531,7855		209,113,3871	yes	missense	QRICH2	NM_032134.1	29	834,211,5050	CC,CT,TT		6.332,35.4364,15.4143	benign	630/1664	74288422	1879,10311	1902	4193	6095	SO:0001583	missense	84074	exon4			GAACTATACCAGG	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.1888A>G	17.37:g.74288422T>C	ENSP00000262765:p.Ile630Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	146	56	0.383562	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	711	0.32554945054945056	252	0.5121951219512195	85	0.23480662983425415	267	0.46678321678321677	107	0.14116094986807387	t	4.471	0.087376	0.08583	0.354364	0.06332	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.20881	2.04	4.72	-1.27	0.09347	.	.	.	.	.	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45279	-0.9272	8	0.21014	T	0.42	0.5378	6.084	0.19956	0.0:0.4089:0.1892:0.4018	rs6501879	630;630	B5MD94;Q9H0J4	.;QRIC2_HUMAN	V	630	ENSP00000262765:I630V	ENSP00000262765:I630V	I	-	1	0	QRICH2	71800017	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.408000	0.00067	-0.294000	0.08973	-2.756000	0.00123	ATA	T|0.675;C|0.325	0.325	strong		0.542	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
BCAN	63827	hgsc.bcm.edu	37	1	156621251	156621251	+	Missense_Mutation	SNP	C	C	T	rs12065791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156621251C>T	ENST00000329117.5	+	7	1403	c.1067C>T	c.(1066-1068)tCg>tTg	p.S356L	BCAN_ENST00000361588.5_Missense_Mutation_p.S356L|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	356			S -> L (in dbSNP:rs12065791).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|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 disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GCCACAGACTCGGCCCAGCCT	0.557													C|||	237	0.0473243	0.1687	0.0173	5008	,	,		18259	0.0		0.002	False		,,,				2504	0.0				p.S356L		Atlas-SNP	.											.	BCAN	174	.	0			c.C1067T						PASS	.	C	LEU/SER,LEU/SER	656,3750	268.0+/-268.2	43,570,1590	47.0	44.0	45.0		1067,1067	5.2	1.0	1	dbSNP_120	45	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	BCAN	NM_021948.4,NM_198427.1	145,145	43,574,5886	TT,TC,CC		0.0465,14.8888,5.0746	benign,benign	356/912,356/672	156621251	660,12346	2203	4300	6503	SO:0001583	missense	63827	exon7			CAGACTCGGCCCA	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1067C>T	1.37:g.156621251C>T	ENSP00000331210:p.Ser356Leu	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	88	0.040293040293040296	79	0.16056910569105692	7	0.019337016574585635	0	0.0	2	0.002638522427440633	C	9.099	1.003544	0.19121	0.148888	4.65E-4	ENSG00000132692	ENST00000329117;ENST00000361588	T;T	0.11495	2.77;2.77	5.17	5.17	0.71159	C-type lectin fold (1);C-type lectin-like (1);	0.474289	0.19636	N	0.109545	T	0.02533	0.0077	L	0.27053	0.805	0.32632	N	0.521804	P;B	0.42518	0.782;0.145	B;B	0.29077	0.098;0.041	T	0.45190	-0.9278	10	0.33141	T	0.24	-10.544	11.8228	0.52250	0.0:0.8238:0.1762:0.0	rs12065791;rs12065791	356;356	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	L	356	ENSP00000331210:S356L;ENSP00000354925:S356L	ENSP00000331210:S356L	S	+	2	0	BCAN	154887875	0.998000	0.40836	0.995000	0.50966	0.125000	0.20455	3.340000	0.52143	2.692000	0.91855	0.655000	0.94253	TCG	C|0.949;T|0.051	0.051	strong		0.557	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
SALL3	27164	hgsc.bcm.edu	37	18	76753588	76753588	+	Missense_Mutation	SNP	A	A	G	rs7240860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	0	0		WXS	Illumina HiSeq	Phase_I	11	4	0.363636	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	
RGS3	5998	hgsc.bcm.edu	37	9	116224452	116224452	+	Missense_Mutation	SNP	G	G	A	rs16933949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116224452G>A	ENST00000374140.2	+	4	595	c.386G>A	c.(385-387)aGg>aAg	p.R129K	RGS3_ENST00000350696.5_Missense_Mutation_p.R129K|RGS3_ENST00000317613.6_5'Flank	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	129			R -> K (in dbSNP:rs16933949).		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						GCCAGGAAGAGGATCACGCAT	0.537													G|||	288	0.057508	0.2088	0.0159	5008	,	,		16916	0.0		0.001	False		,,,				2504	0.0				p.R129K		Atlas-SNP	.											.	RGS3	251	.	0			c.G386A						PASS	.	G	LYS/ARG	726,3434		72,582,1426	77.0	81.0	79.0		386	-1.2	0.0	9	dbSNP_123	79	4,8432		0,4,4214	yes	missense	RGS3	NM_144488.4	26	72,586,5640	AA,AG,GG		0.0474,17.4519,5.7955	possibly-damaging	129/1199	116224452	730,11866	2080	4218	6298	SO:0001583	missense	5998	exon4			GGAAGAGGATCAC	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.386G>A	9.37:g.116224452G>A	ENSP00000363255:p.Arg129Lys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	105	72	0.685714	NM_144488	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	100	0.045787545787545784	93	0.18902439024390244	7	0.019337016574585635	0	0.0	0	0.0	G	6.337	0.430283	0.12045	0.174519	4.74E-4	ENSG00000138835	ENST00000374140;ENST00000350696	T;T	0.41065	1.01;1.01	4.39	-1.25	0.09405	.	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.15321	-1.0441	8	0.87932	D	0	.	7.8729	0.29576	0.5369:0.0:0.4631:0.0	rs16933949;rs59024905;rs16933949	129	P49796	RGS3_HUMAN	K	129	ENSP00000363255:R129K;ENSP00000259406:R129K	ENSP00000259406:R129K	R	+	2	0	RGS3	115264273	0.022000	0.18835	0.003000	0.11579	0.862000	0.49288	0.044000	0.13992	-0.349000	0.08274	0.591000	0.81541	AGG	G|0.957;A|0.043	0.043	strong		0.537	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
ATP10A	57194	hgsc.bcm.edu	37	15	25926179	25926179	+	Missense_Mutation	SNP	C	C	T	rs2076744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25926179C>T	ENST00000356865.6	-	18	3646	c.3535G>A	c.(3535-3537)Gcc>Acc	p.A1179T		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1179			A -> T (in dbSNP:rs2076744).		ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CTCTGGAAGGCGGCGTCGGCC	0.517													c|||	1413	0.282149	0.4735	0.3516	5008	,	,		19333	0.2599		0.1441	False		,,,				2504	0.1391				p.A1179T		Atlas-SNP	.											ATP10A,colon,carcinoma,0,1	ATP10A	270	1	0			c.G3535A						PASS	.	C	THR/ALA	1839,2567	535.6+/-374.3	379,1081,743	90.0	86.0	87.0		3535	0.3	0.2	15	dbSNP_96	87	1378,7222	268.2+/-287.7	103,1172,3025	yes	missense	ATP10A	NM_024490.3	58	482,2253,3768	TT,TC,CC		16.0233,41.7385,24.7347	benign	1179/1500	25926179	3217,9789	2203	4300	6503	SO:0001583	missense	57194	exon18			GGAAGGCGGCGTC	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3535G>A	15.37:g.25926179C>T	ENSP00000349325:p.Ala1179Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	637	0.2916666666666667	239	0.48577235772357724	118	0.3259668508287293	172	0.3006993006993007	108	0.1424802110817942	c	8.127	0.782181	0.16189	0.417385	0.160233	ENSG00000206190	ENST00000356865	T	0.43688	0.94	4.84	0.298	0.15766	.	0.495561	0.22824	N	0.055187	T	0.00012	0.0000	N	0.11255	0.115	0.53005	P	3.399999999997849E-5	P	0.38729	0.644	B	0.28849	0.095	T	0.47355	-0.9124	9	0.48119	T	0.1	-16.3478	1.5902	0.02653	0.2175:0.4237:0.1137:0.2452	rs2076744;rs2076744	1179	O60312	AT10A_HUMAN	T	1179	ENSP00000349325:A1179T	ENSP00000349325:A1179T	A	-	1	0	ATP10A	23477272	0.152000	0.22762	0.210000	0.23637	0.050000	0.14768	0.681000	0.25320	0.111000	0.17947	-1.349000	0.01238	GCC	C|0.734;T|0.266	0.266	strong		0.517	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
WDR90	197335	hgsc.bcm.edu	37	16	705844	705844	+	Silent	SNP	T	T	C	rs8051645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	69	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	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	
SYCP2	10388	hgsc.bcm.edu	37	20	58475307	58475307	+	Silent	SNP	G	G	A	rs6027185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58475307G>A	ENST00000357552.3	-	18	1515	c.1290C>T	c.(1288-1290)gtC>gtT	p.V430V	SYCP2_ENST00000371001.2_Silent_p.V430V			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	430					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			GCTCTTCTCCGACTGGTGAGA	0.338													G|||	417	0.0832668	0.2769	0.0259	5008	,	,		17811	0.0159		0.005	False		,,,				2504	0.0123				p.V430V		Atlas-SNP	.											.	SYCP2	204	.	0			c.C1290T						PASS	.	G		1004,3400	364.1+/-316.8	121,762,1319	75.0	70.0	72.0		1290	-10.3	0.0	20	dbSNP_114	72	47,8553	29.6+/-80.5	1,45,4254	no	coding-synonymous	SYCP2	NM_014258.2		122,807,5573	AA,AG,GG		0.5465,22.7975,8.0821		430/1531	58475307	1051,11953	2202	4300	6502	SO:0001819	synonymous_variant	10388	exon17			TTCTCCGACTGGT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1290C>T	20.37:g.58475307G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Silent	SNP	ENST00000357552.3	37	CCDS13482.1																																																																																			G|0.919;A|0.081	0.081	strong		0.338	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	
MUC6	4588	hgsc.bcm.edu	37	11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1016851T>C	ENST00000421673.2	-	31	6000	c.5950A>G	c.(5950-5952)Atg>Gtg	p.M1984V		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1984	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			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)		GTTGCAGTCATAGGACCTGTG	0.582																																					p.M1984V		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,+2,2	MUC6	408	2	0			c.A5950G						scavenged	.						1531.0	1522.0	1525.0					11																	1016851		2203	4298	6501	SO:0001583	missense	4588	exon31			CAGTCATAGGACC	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.5950A>G	11.37:g.1016851T>C	ENSP00000406861:p.Met1984Val	Somatic	1912	36	0.0188285		WXS	Illumina HiSeq	Phase_I	2182	80	0.0366636	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	1.757	-0.487796	0.04352	.	.	ENSG00000184956	ENST00000421673	T	0.17370	2.28	2.75	-1.23	0.09465	.	.	.	.	.	T	0.10809	0.0264	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45205	-0.9277	9	0.06365	T	0.9	.	7.0983	0.25321	0.0:0.1589:0.2688:0.5723	.	1984	Q6W4X9	MUC6_HUMAN	V	1984	ENSP00000406861:M1984V	ENSP00000406861:M1984V	M	-	1	0	MUC6	1006851	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.137000	0.00588	-0.732000	0.04856	-2.319000	0.00253	ATG	.	.	none		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
RBM33	155435	hgsc.bcm.edu	37	7	155530954	155530954	+	Silent	SNP	T	T	C	rs2178428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:155530954T>C	ENST00000401878.3	+	11	1792	c.1594T>C	c.(1594-1596)Ttg>Ctg	p.L532L		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	532	Pro-rich.						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)		ACGACCAGCCTTGCAGCCTCC	0.597													C|||	1590	0.317492	0.5492	0.2695	5008	,	,		17130	0.3125		0.1869	False		,,,				2504	0.1779				p.L532L		Atlas-SNP	.											.	RBM33	157	.	0			c.T1594C						PASS	.	C		2011,2151		485,1041,555	80.0	90.0	87.0		1594	1.8	0.7	7	dbSNP_96	87	1626,6790		177,1272,2759	no	coding-synonymous	RBM33	NM_053043.2		662,2313,3314	CC,CT,TT		19.3203,48.3181,28.9156		532/1171	155530954	3637,8941	2081	4208	6289	SO:0001819	synonymous_variant	155435	exon11			CCAGCCTTGCAGC	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.1594T>C	7.37:g.155530954T>C		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Silent	SNP	ENST00000401878.3	37	CCDS5941.2																																																																																			T|0.707;C|0.293	0.293	strong		0.597	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408	
FGD3	89846	hgsc.bcm.edu	37	9	95782667	95782667	+	Silent	SNP	C	C	T	rs11790517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95782667C>T	ENST00000375482.3	+	13	1951	c.1455C>T	c.(1453-1455)ttC>ttT	p.F485F	FGD3_ENST00000538555.1_Silent_p.F88F|FGD3_ENST00000416701.2_Silent_p.F485F|FGD3_ENST00000337352.6_Silent_p.F485F	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	485					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)|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)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						GTGGCGCCTTCAGCCAGGATG	0.577													C|||	1414	0.282348	0.3812	0.3876	5008	,	,		16496	0.2411		0.2903	False		,,,				2504	0.1084				p.F485F		Atlas-SNP	.											.	FGD3	116	.	0			c.C1455T						PASS	.	C	,	1536,2680		298,940,870	60.0	66.0	64.0		1455,1455	0.2	0.0	9	dbSNP_120	64	2352,6102		331,1690,2206	no	coding-synonymous,coding-synonymous	FGD3	NM_001083536.1,NM_033086.2	,	629,2630,3076	TT,TC,CC		27.8211,36.4326,30.6867	,	485/726,485/726	95782667	3888,8782	2108	4227	6335	SO:0001819	synonymous_variant	89846	exon13			CGCCTTCAGCCAG	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16027	protein-coding gene	gene with protein product			"""FGD1 family, member 3"""			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.1455C>T	9.37:g.95782667C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	86	28	0.325581	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Silent	SNP	ENST00000375482.3	37	CCDS43849.1																																																																																			C|0.684;T|0.316	0.316	strong		0.577	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086	
OR2T34	127068	hgsc.bcm.edu	37	1	248737419	248737419	+	Missense_Mutation	SNP	T	T	C	rs145854970		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248737419T>C	ENST00000328782.2	-	1	661	c.640A>G	c.(640-642)Acc>Gcc	p.T214A		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	214						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)			ATGATGGGGGTGAGAAGCATG	0.557																																					p.T214A		Atlas-SNP	.											OR2T34,NS,carcinoma,+1,2	OR2T34	72	2	0			c.A640G						scavenged	.						196.0	210.0	206.0					1																	248737419		2114	4300	6414	SO:0001583	missense	127068	exon1			TGGGGGTGAGAAG	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.640A>G	1.37:g.248737419T>C	ENSP00000330904:p.Thr214Ala	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	206	17	0.0825243	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	.	.	.	.	.	.	.	.	.	.	.	8.088	0.773777	0.16051	.	.	ENSG00000183310	ENST00000328782	T	0.36520	1.25	2.37	-2.05	0.07321	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.15609	0.0376	N	0.11818	0.18	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22208	-1.0223	9	0.59425	D	0.04	.	0.341	0.00334	0.2537:0.2468:0.1387:0.3608	.	214	Q8NGX1	O2T34_HUMAN	A	214	ENSP00000330904:T214A	ENSP00000330904:T214A	T	-	1	0	OR2T34	246804042	0.000000	0.05858	0.035000	0.18076	0.091000	0.18340	-0.914000	0.04038	-0.298000	0.08921	-1.680000	0.00737	ACC	.	.	weak		0.557	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110539186	110539186	+	Missense_Mutation	SNP	G	G	A	rs1783174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	165	0	0		WXS	Illumina HiSeq	Phase_I	200	92	0.46	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	
MATN3	4148	hgsc.bcm.edu	37	2	20205848	20205848	+	Silent	SNP	G	G	A	rs28598872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20205848G>A	ENST00000407540.3	-	2	509	c.447C>T	c.(445-447)gcC>gcT	p.A149A	AC079145.4_ENST00000416575.1_RNA|MATN3_ENST00000421259.2_Silent_p.A149A	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	149	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCGACCCACGGCCTGCTTCA	0.587													A|||	2628	0.52476	0.531	0.4625	5008	,	,		19853	0.619		0.4016	False		,,,				2504	0.59				p.A149A		Atlas-SNP	.											.	MATN3	28	.	0			c.C447T						PASS	.	A		2056,2156		528,1000,578	66.0	71.0	69.0		447	-11.7	0.1	2	dbSNP_125	69	3481,4981		723,2035,1473	no	coding-synonymous	MATN3	NM_002381.4		1251,3035,2051	AA,AG,GG		41.1368,48.8129,43.6879		149/487	20205848	5537,7137	2106	4231	6337	SO:0001819	synonymous_variant	4148	exon2			ACCCACGGCCTGC	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.447C>T	2.37:g.20205848G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	139	75	0.539568	NM_002381	B2CPU0|Q4ZG02	Silent	SNP	ENST00000407540.3	37	CCDS46226.1																																																																																			G|0.508;A|0.492	0.492	strong		0.587	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381	
ATR	545	hgsc.bcm.edu	37	3	142178144	142178144	+	Missense_Mutation	SNP	C	C	T	rs2229032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:142178144C>T	ENST00000350721.4	-	43	7395	c.7274G>A	c.(7273-7275)cGa>cAa	p.R2425Q	ATR_ENST00000383101.3_Missense_Mutation_p.R2361Q	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2425	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		R -> Q (in dbSNP:rs2229032). {ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R2425Q(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GAGAAATTCTCGGAATACTTT	0.403								Other conserved DNA damage response genes					C|||	512	0.102236	0.0658	0.1037	5008	,	,		17089	0.1012		0.172	False		,,,				2504	0.0798				p.R2425Q		Atlas-SNP	.											ATR,NS,carcinoma,0,1	ATR	285	1	1	Substitution - Missense(1)	stomach(1)	c.G7274A						PASS	.	C	GLN/ARG	388,4018	193.6+/-218.7	17,354,1832	67.0	66.0	67.0		7274	-9.1	0.4	3	dbSNP_98	67	1357,7243	264.2+/-285.4	118,1121,3061	yes	missense	ATR	NM_001184.3	43	135,1475,4893	TT,TC,CC		15.7791,8.8062,13.4169	benign	2425/2645	142178144	1745,11261	2203	4300	6503	SO:0001583	missense	545	exon43			AATTCTCGGAATA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7274G>A	3.37:g.142178144C>T	ENSP00000343741:p.Arg2425Gln	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	128	51	0.398438	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	262	0.11996336996336997	27	0.054878048780487805	39	0.10773480662983426	64	0.11188811188811189	132	0.1741424802110818	C	11.32	1.602569	0.28534	0.088062	0.157791	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.76186	-1.0;-1.0	4.58	-9.12	0.00707	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.601425	0.15707	N	0.248596	T	0.00210	0.0006	N	0.16233	0.39	0.44995	P	0.0019900000000000473	B	0.02656	0.0	B	0.04013	0.001	T	0.03278	-1.1053	9	0.16420	T	0.52	0.6971	19.1019	0.93277	0.0:0.161:0.0:0.839	rs2229032;rs17698526;rs57742124;rs2229032	2425	Q13535	ATR_HUMAN	Q	2425;2361	ENSP00000343741:R2425Q;ENSP00000372581:R2361Q	ENSP00000343741:R2425Q	R	-	2	0	ATR	143660834	0.963000	0.33076	0.437000	0.26809	0.948000	0.59901	0.044000	0.13992	-2.531000	0.00491	-1.406000	0.01132	CGA	C|0.883;T|0.117	0.117	strong		0.403	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
EEF1A2	1917	hgsc.bcm.edu	37	20	62119717	62119717	+	Silent	SNP	C	C	T	rs1042796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62119717C>T	ENST00000298049.7	-	7	1396	c.1326G>A	c.(1324-1326)gaG>gaA	p.E442E	EEF1A2_ENST00000217182.3_Silent_p.E442E			Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha 2	442					positive regulation of apoptotic process (GO:0043065)|response to inorganic substance (GO:0010035)	eukaryotic translation elongation factor 1 complex (GO:0005853)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(14)|stomach(1)	20	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			CGCTCTTCTTCTCCACGTTCT	0.746													c|||	399	0.0796725	0.1415	0.0115	5008	,	,		4527	0.002		0.0	False		,,,				2504	0.2065				p.E442E		Atlas-SNP	.											.	EEF1A2	60	.	0			c.G1326A						PASS	.			389,3539		15,359,1590	8.0	7.0	7.0		1326	2.0	1.0	20	dbSNP_86	7	5,7783		0,5,3889	no	coding-synonymous	EEF1A2	NM_001958.2		15,364,5479	TT,TC,CC		0.0642,9.9033,3.3629		442/464	62119717	394,11322	1964	3894	5858	SO:0001819	synonymous_variant	1917	exon8			CTTCTTCTCCACG	AF163763	CCDS13522.1	20q13.3	2010-06-03			ENSG00000101210	ENSG00000101210			3192	protein-coding gene	gene with protein product		602959	"""statin-like"", ""statin"""	STNL, STN		8354261, 8812466	Standard	NM_001958		Approved	EEF1AL, HS1	uc002yfe.2	Q05639	OTTHUMG00000033076	ENST00000298049.7:c.1326G>A	20.37:g.62119717C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	27	6	0.222222	NM_001958	B5BUF3|E1P5J1|P54266|Q0VGC7	Silent	SNP	ENST00000298049.7	37	CCDS13522.1																																																																																			C|0.966;T|0.034	0.034	strong		0.746	EEF1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080495.1	NM_001958	
UBE4B	10277	hgsc.bcm.edu	37	1	10218439	10218439	+	Silent	SNP	T	T	C	rs2273299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:10218439T>C	ENST00000253251.8	+	21	3404	c.2565T>C	c.(2563-2565)agT>agC	p.S855S	UBE4B_ENST00000343090.6_Silent_p.S984S|UBE4B_ENST00000377157.3_Silent_p.S739S					ubiquitination factor E4B									p.S855S(1)		NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-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;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GAGCCACCAGTGAGTTTTATG	0.398													C|||	1832	0.365815	0.8033	0.1873	5008	,	,		19632	0.2956		0.1392	False		,,,				2504	0.2065				p.S984S		Atlas-SNP	.											UBE4B,NS,carcinoma,0,1	UBE4B	233	1	1	Substitution - coding silent(1)	stomach(1)	c.T2952C						PASS	.	C	,	2942,1464	472.0+/-356.2	996,950,257	137.0	140.0	139.0		2952,2565	-0.9	1.0	1	dbSNP_100	139	1135,7465	767.0+/-407.6	81,973,3246	no	coding-synonymous,coding-synonymous	UBE4B	NM_001105562.2,NM_006048.4	,	1077,1923,3503	CC,CT,TT		13.1977,33.2274,31.3471	,	984/1303,855/1174	10218439	4077,8929	2203	4300	6503	SO:0001819	synonymous_variant	10277	exon22			CACCAGTGAGTTT	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2565T>C	1.37:g.10218439T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_001105562		Silent	SNP	ENST00000253251.8	37	CCDS110.1																																																																																			T|0.658;C|0.342	0.342	strong		0.398	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048	
UIMC1	51720	hgsc.bcm.edu	37	5	176370402	176370402	+	Missense_Mutation	SNP	A	A	G	rs13360277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176370402A>G	ENST00000377227.4	-	10	1663	c.1531T>C	c.(1531-1533)Tgc>Cgc	p.C511R	UIMC1_ENST00000511320.1_Missense_Mutation_p.C511R|UIMC1_ENST00000503273.1_5'UTR|UIMC1_ENST00000506128.1_Missense_Mutation_p.C345R|UIMC1_ENST00000377219.2_Missense_Mutation_p.C511R			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	511	Zinc-finger-like region.		C -> R (common polymorphism not associated with susceptibility to breast cancer; dbSNP:rs13360277). {ECO:0000269|PubMed:18695986}.		double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGTGGAAAGCATTGGTCACAT	0.458													G|||	844	0.16853	0.4304	0.1023	5008	,	,		19523	0.0129		0.0517	False		,,,				2504	0.1421				p.C511R		Atlas-SNP	.											.	UIMC1	55	.	0			c.T1531C						PASS	.	G	ARG/CYS,ARG/CYS,ARG/CYS	1638,2768	659.2+/-400.5	314,1010,879	268.0	239.0	249.0		1531,1531,1531	2.0	1.0	5	dbSNP_121	249	382,8218	802.3+/-407.3	13,356,3931	yes	missense,missense,missense	UIMC1	NM_001199297.1,NM_001199298.1,NM_016290.4	180,180,180	327,1366,4810	GG,GA,AA		4.4419,37.1766,15.5313	benign,benign,benign	511/720,511/720,511/720	176370402	2020,10986	2203	4300	6503	SO:0001583	missense	51720	exon10			GAAAGCATTGGTC	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"""receptor associated protein 80"""	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.1531T>C	5.37:g.176370402A>G	ENSP00000366434:p.Cys511Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Missense_Mutation	SNP	ENST00000377227.4	37	CCDS4408.1	283	0.1295787545787546	208	0.42276422764227645	28	0.07734806629834254	9	0.015734265734265736	38	0.05013192612137203	G	0.008	-1.871872	0.00542	0.371766	0.044419	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000506128;ENST00000377220;ENST00000323774	T;T;T;T	0.12569	2.67;2.67;2.67;2.67	4.78	2.0	0.26442	.	0.519717	0.18999	N	0.125398	T	0.00012	0.0000	N	0.08118	0	0.37199	P	0.09571399999999997	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.09377	0.0;0.004;0.0;0.0;0.0	T	0.47275	-0.9130	9	0.11794	T	0.64	.	4.2306	0.10601	0.1506:0.4697:0.2961:0.0837	rs13360277;rs58061296;rs13360277	511;230;345;141;433	Q96RL1;D6RCF3;C9JR12;Q96RL1-4;Q96RL1-3	UIMC1_HUMAN;.;.;.;.	R	511;511;511;345;433;141	ENSP00000366434:C511R;ENSP00000366425:C511R;ENSP00000421926:C511R;ENSP00000427480:C345R	ENSP00000314909:C141R	C	-	1	0	UIMC1	176303008	0.977000	0.34250	0.964000	0.40570	0.001000	0.01503	0.178000	0.16820	-0.007000	0.14345	-2.306000	0.00257	TGC	A|0.846;G|0.154	0.154	strong		0.458	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290	
COL27A1	85301	hgsc.bcm.edu	37	9	116958283	116958283	+	Silent	SNP	G	G	A	rs10982098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116958283G>A	ENST00000356083.3	+	7	2506	c.2115G>A	c.(2113-2115)ccG>ccA	p.P705P		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	705	Collagen-like 2.|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						CAGGACCTCCGGGACGAAAGG	0.592													G|||	39	0.00778754	0.0295	0.0	5008	,	,		19536	0.0		0.0	False		,,,				2504	0.0				p.P705P		Atlas-SNP	.											.	COL27A1	200	.	0			c.G2115A						PASS	.	G		101,4305	79.3+/-117.8	2,97,2104	160.0	134.0	143.0		2115	1.2	0.4	9	dbSNP_120	143	0,8600		0,0,4300	no	coding-synonymous	COL27A1	NM_032888.2		2,97,6404	AA,AG,GG		0.0,2.2923,0.7766		705/1861	116958283	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon7			ACCTCCGGGACGA	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.2115G>A	9.37:g.116958283G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	77	27	0.350649	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			G|0.993;A|0.007	0.007	strong		0.592	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
LRRC14	9684	hgsc.bcm.edu	37	8	145740622	145740622	+	5'Flank	SNP	C	C	T	rs34948955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145740622C>T	ENST00000292524.1	+	0	0				RECQL4_ENST00000428558.2_Silent_p.T465T|LRRC14_ENST00000529022.1_5'Flank|CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000532237.1_5'UTR	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-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;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CCTCAGCCGGCGTCTCTGCAG	0.622													C|||	8	0.00159744	0.0	0.0014	5008	,	,		20490	0.0		0.007	False		,,,				2504	0.0				p.T465T		Atlas-SNP	.											RECQL4,brain,glioma,0,2	RECQL4	75	2	0			c.G1395A						scavenged	.	C		5,4245		0,5,2120	25.0	32.0	29.0		1395	-10.8	0.0	8	dbSNP_126	29	70,8422		0,70,4176	no	coding-synonymous	RECQL4	NM_004260.3		0,75,6296	TT,TC,CC		0.8243,0.1176,0.5886		465/1209	145740622	75,12667	2125	4246	6371	SO:0001631	upstream_gene_variant	9401	exon8			AGCCGGCGTCTCT	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		8.37:g.145740622C>T	Exception_encountered	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	115	49	0.426087	NM_004260	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			C|0.997;T|0.003	0.003	strong		0.622	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
HPGD	3248	hgsc.bcm.edu	37	4	175443156	175443156	+	Silent	SNP	C	C	T	rs1050145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:175443156C>T	ENST00000296522.6	-	2	602	c.156G>A	c.(154-156)caG>caA	p.Q52Q	RP11-440I14.2_ENST00000515178.1_lincRNA|HPGD_ENST00000542498.1_Silent_p.Q52Q|HPGD_ENST00000422112.2_Silent_p.Q52Q|HPGD_ENST00000510901.1_5'UTR|HPGD_ENST00000504433.1_Silent_p.Q52Q|HPGD_ENST00000541923.1_5'UTR|HPGD_ENST00000296521.7_Silent_p.Q52Q	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	91	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	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		
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011415	46011415	+	Silent	SNP	G	G	A	rs145570198		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011415G>A	ENST00000400368.1	-	1	971	c.951C>T	c.(949-951)tgC>tgT	p.C317C	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	317	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						GGACGGGCACGCAGCAGGTGG	0.687																																					p.C317C		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C951T						PASS	.						70.0	84.0	79.0					21																	46011415		2202	4300	6502	SO:0001819	synonymous_variant	386674	exon1			GGGCACGCAGCAG	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.951C>T	21.37:g.46011415G>A		Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	261	58	0.222222	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			G|0.976;A|0.024	0.024	strong		0.687	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38610504	38610504	+	Silent	SNP	G	G	A	rs59185302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	27	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	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	
MUC17	140453	hgsc.bcm.edu	37	7	100678421	100678421	+	Missense_Mutation	SNP	T	T	A	rs200902631|rs10265276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678421T>A	ENST00000306151.4	+	3	3788	c.3724T>A	c.(3724-3726)Tct>Act	p.S1242T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1242	59 X approximate tandem repeats.|Ser-rich.		S -> T (in dbSNP:rs10265276).		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)					CCTTTCAACATCTCCCGTTGA	0.517													A|||	1177	0.235024	0.3389	0.1009	5008	,	,		29246	0.253		0.1213	False		,,,				2504	0.2883				p.S1242T		Atlas-SNP	.											MUC17,NS,carcinoma,-1,1	MUC17	804	1	0			c.T3724A						PASS	.	A	THR/SER	1322,3084	695.6+/-406.0	206,910,1087	288.0	284.0	286.0		3724	-1.7	0.0	7	dbSNP_119	286	999,7601	773.2+/-407.7	57,885,3358	no	missense	MUC17	NM_001040105.1	58	263,1795,4445	AA,AT,TT		11.6163,30.0045,17.8456	benign	1242/4494	100678421	2321,10685	2203	4300	6503	SO:0001583	missense	140453	exon3			TCAACATCTCCCG	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.3724T>A	7.37:g.100678421T>A	ENSP00000302716:p.Ser1242Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	149	83	0.557047	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	471	0.21565934065934067	160	0.3252032520325203	46	0.1270718232044199	161	0.28146853146853146	104	0.13720316622691292	A	1.120	-0.655521	0.03480	0.300045	0.116163	ENSG00000169876	ENST00000306151	T	0.02498	4.27	0.838	-1.68	0.08212	.	.	.	.	.	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	0.35871	-0.9771	8	0.09084	T	0.74	.	2.3789	0.04349	0.3049:0.2132:0.0:0.4819	rs10265276;rs59394740	1242	Q685J3	MUC17_HUMAN	T	1242	ENSP00000302716:S1242T	ENSP00000302716:S1242T	S	+	1	0	MUC17	100465141	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.179000	0.03090	-2.874000	0.00322	-1.617000	0.00794	TCT	T|0.819;A|0.181	0.181	strong		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
LILRB2	10288	hgsc.bcm.edu	37	19	54782173	54782173	+	Missense_Mutation	SNP	A	A	C	rs4993130		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782173A>C	ENST00000391749.4	-	7	1470	c.1199T>G	c.(1198-1200)cTc>cGc	p.L400R	LILRB2_ENST00000391748.1_Missense_Mutation_p.L400R|LILRB2_ENST00000391746.1_Missense_Mutation_p.L400R|LILRB2_ENST00000434421.1_Missense_Mutation_p.L284R|LILRB2_ENST00000314446.5_Missense_Mutation_p.L400R|LILRB2_ENST00000471216.1_5'Flank	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	400	Ig-like C2-type 4.				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)		GTCGGAGTTGAGTGAGCCGTA	0.582																																					p.L400R		Atlas-SNP	.											.	LILRB2	94	.	0			c.T1199G						PASS	.	C	ARG/LEU,ARG/LEU	1,4405	825.9+/-416.6	0,1,2202	113.0	105.0	107.0		1199,1199	-3.8	0.0	19	dbSNP_113	107	1,8599		0,1,4299	no	missense,missense	LILRB2	NM_005874.3,NM_001080978.2	102,102	0,2,6501	CC,CA,AA		0.0116,0.0227,0.0154	benign,benign	400/599,400/598	54782173	2,13004	2203	4300	6503	SO:0001583	missense	10288	exon7			GAGTTGAGTGAGC	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.1199T>G	19.37:g.54782173A>C	ENSP00000375629:p.Leu400Arg	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	172	77	0.447674	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.109135	0.00353	2.27E-4	1.16E-4	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00745	5.75;5.75;5.75;5.75;5.75	1.88	-3.77	0.04346	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	6.345920	0.00496	N	0.000144	T	0.00580	0.0019	N	0.05592	-0.015	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.17979	0.013;0.013;0.02	T	0.47471	-0.9115	10	0.19590	T	0.45	.	5.0707	0.14606	0.1536:0.252:0.0:0.5944	.	400;417;400	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	R	400;400;400;400;284	ENSP00000375628:L400R;ENSP00000319960:L400R;ENSP00000375629:L400R;ENSP00000375626:L400R;ENSP00000410117:L284R	ENSP00000319960:L400R	L	-	2	0	LILRB2	59473985	0.000000	0.05858	0.000000	0.03702	0.061000	0.15899	-4.942000	0.00167	-5.508000	0.00013	-3.110000	0.00062	CTC	A|1.000;C|0.000	0.000	weak		0.582	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
MUC4	4585	hgsc.bcm.edu	37	3	195507684	195507684	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507684G>A	ENST00000463781.3	-	2	11226	c.10767C>T	c.(10765-10767)gaC>gaT	p.D3589D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D3589D	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)		CTGAGGAAGCGTCGGTGACAA	0.592																																					p.D3589D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	0			c.C10767T						scavenged	.						4.0	4.0	4.0					3																	195507684		541	1355	1896	SO:0001819	synonymous_variant	4585	exon2			GGAAGCGTCGGTG	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.10767C>T	3.37:g.195507684G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	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																																																																																			.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SH3TC1	54436	hgsc.bcm.edu	37	4	8238151	8238151	+	Silent	SNP	C	C	T	rs11603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:8238151C>T	ENST00000245105.3	+	16	3619	c.3552C>T	c.(3550-3552)acC>acT	p.T1184T	SH3TC1_ENST00000539824.1_Silent_p.T1108T	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	1184										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						TCAGCATCACCCTGGGTAAGC	0.647													C|||	1407	0.28095	0.2073	0.3026	5008	,	,		17382	0.2431		0.4095	False		,,,				2504	0.272				p.T1184T	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.C3552T						PASS	.	C		843,3261		90,663,1299	30.0	26.0	28.0		3552	2.9	1.0	4	dbSNP_52	28	2674,5232		458,1758,1737	no	coding-synonymous	SH3TC1	NM_018986.3		548,2421,3036	TT,TC,CC		33.8224,20.5409,29.2839		1184/1337	8238151	3517,8493	2052	3953	6005	SO:0001819	synonymous_variant	54436	exon16			CATCACCCTGGGT	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.3552C>T	4.37:g.8238151C>T		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	258	130	0.503876	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	37	CCDS3399.1																																																																																			C|0.684;T|0.316	0.316	strong		0.647	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518422	161518422	+	Missense_Mutation	SNP	C	C	G	rs200475280		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161518422C>G	ENST00000436743.1	-	4	262	c.108G>C	c.(106-108)agG>agC	p.R36S	FCGR3A_ENST00000476031.1_5'UTR|FCGR3A_ENST00000443193.1_Missense_Mutation_p.R71S|FCGR3A_ENST00000367969.3_Missense_Mutation_p.R72S|RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000540048.1_Missense_Mutation_p.R36S	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)	36	Ig-like C2-type 1.				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)	TCTCGAGCACCCTGTACCATT	0.547																																					p.R72S		Atlas-SNP	.											FCGR3A,NS,carcinoma,-1,1	FCGR3A	38	1	0			c.G216C	GRCh37	CM061766	FCGR3A	M		scavenged	.						162.0	152.0	155.0					1																	161518422		2203	4300	6503	SO:0001583	missense	2214	exon3			GAGCACCCTGTAC	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.108G>C	1.37:g.161518422C>G	ENSP00000416607:p.Arg36Ser	Somatic	325	7	0.0215385		WXS	Illumina HiSeq	Phase_I	408	27	0.0661765	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	6.938|6.938	0.542861|0.542861	0.13250|0.13250	.|.	.|.	ENSG00000203747|ENSG00000203747	ENST00000426740|ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048;ENST00000442336	.|T;T;T;T;T;T	.|0.12255	.|2.7;2.7;2.7;2.7;2.7;2.7	4.43|4.43	-2.63|-2.63	0.06133|0.06133	.|Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.630492	.|0.14320	.|N	.|0.327075	T|T	0.03053|0.03053	0.0090|0.0090	L|L	0.35288|0.35288	1.05|1.05	0.09310|0.09310	A|A	1.56413e-08|1.56413e-08	.|D;D	.|0.58268	.|0.982;0.982	.|P;P	.|0.50570	.|0.644;0.644	T|T	0.17471|0.17471	-1.0368|-1.0368	4|9	.|0.12103	.|T	.|0.63	.|.	0.9726|0.9726	0.01419|0.01419	0.1479:0.2934:0.2902:0.2686|0.1479:0.2934:0.2902:0.2686	rs403016;rs403016|rs403016;rs403016	.|36;71	.|P08637;E9PG94	.|FCG3A_HUMAN;.	A|S	53|72;71;36;36;36;35	.|ENSP00000356946:R72S;ENSP00000392047:R71S;ENSP00000416607:R36S;ENSP00000356944:R36S;ENSP00000444971:R36S;ENSP00000396567:R35S	.|ENSP00000356944:R36S	G|R	-|-	2|3	0|2	FCGR3A|FCGR3A	159785046|159785046	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.021000|0.021000	0.10359|0.10359	-0.311000|-0.311000	0.08124|0.08124	-0.259000|-0.259000	0.09432|0.09432	0.591000|0.591000	0.81541|0.81541	GGG|AGG	G|1.000;|0.000	1.000	weak		0.547	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552060	32552060	+	Missense_Mutation	SNP	A	A	T	rs16822820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32552060A>T	ENST00000360004.5	-	2	301	c.196T>A	c.(196-198)Tcc>Acc	p.S66T		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	66	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						AAGCGCACGGACTCCTCCTGG	0.602										Multiple Myeloma(14;0.17)			A|||	876	0.17492	0.2284	0.1888	5008	,	,		9661	0.0813		0.1938	False		,,,				2504	0.1697				p.S66T		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.T196A						PASS	.						36.0	35.0	36.0					6																	32552060		2191	4284	6475	SO:0001583	missense	3123	exon2			GCACGGACTCCTC	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.196T>A	6.37:g.32552060A>T	ENSP00000353099:p.Ser66Thr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	82	28	0.341463	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	1.398	-0.578994	0.03854	.	.	ENSG00000196126	ENST00000360004	T	0.00249	8.44	3.52	-7.04	0.01578	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);	3.581920	0.00597	N	0.000377	T	0.00039	0.0001	N	0.13371	0.34	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.50074	-0.8870	9	0.49607	T	0.09	.	1.7273	0.02925	0.1198:0.2542:0.2155:0.4106	rs16822820;rs17881836	66	P01911	2B1F_HUMAN	T	66	ENSP00000353099:S66T	ENSP00000353099:S66T	S	-	1	0	HLA-DRB1	32660038	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.680000	0.01939	-5.225000	0.00019	-3.146000	0.00059	TCC	T|0.164;C|0.002;A|0.834	0.164	strong		0.602	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
CEACAM4	1089	hgsc.bcm.edu	37	19	42125709	42125709	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42125709G>A	ENST00000221954.2	-	7	839	c.729C>T	c.(727-729)gtC>gtT	p.V243V		NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	243						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						GAACCTAAGAGACCACATCTG	0.532																																					p.V243V		Atlas-SNP	.											CEACAM4,NS,neuroblastoma,0,1	CEACAM4	42	1	0			c.C729T						PASS	.						113.0	108.0	110.0					19																	42125709		2203	4300	6503	SO:0001819	synonymous_variant	1089	exon7			CTAAGAGACCACA	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"""Immunoglobulin superfamily / V-set domain containing"""	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.729C>T	19.37:g.42125709G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_001817	Q03715|Q7LDZ7	Silent	SNP	ENST00000221954.2	37	CCDS33033.1																																																																																			.	.	none		0.532	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817	
GAS2	2620	hgsc.bcm.edu	37	11	22770669	22770669	+	Silent	SNP	T	T	C	rs7122835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:22770669T>C	ENST00000454584.2	+	6	782	c.477T>C	c.(475-477)taT>taC	p.Y159Y	GAS2_ENST00000278187.3_Silent_p.Y159Y|GAS2_ENST00000433790.1_Silent_p.Y159Y	NM_001143830.1	NP_001137302.1	O43903	GAS2_HUMAN	growth arrest-specific 2	159					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|regulation of cell shape (GO:0008360)	actin filament (GO:0005884)|cytosol (GO:0005829)|membrane (GO:0016020)				breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(4)|stomach(1)	24						TTTAAAGGTATGGTGTGGAGC	0.378													t|||	80	0.0159744	0.059	0.0029	5008	,	,		18402	0.0		0.0	False		,,,				2504	0.0				p.Y159Y		Atlas-SNP	.											.	GAS2	46	.	0			c.T477C						PASS	.	C	,,	212,4194	128.6+/-165.4	5,202,1996	73.0	76.0	75.0		477,477,477	4.7	1.0	11	dbSNP_116	75	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS2	NM_001143830.1,NM_005256.3,NM_177553.2	,,	5,205,6292	CC,CT,TT		0.0349,4.8116,1.6533	,,	159/314,159/314,159/314	22770669	215,12789	2203	4299	6502	SO:0001819	synonymous_variant	2620	exon6			AAGGTATGGTGTG	BC040470	CCDS7858.1	11p14.3	2005-10-11			ENSG00000148935	ENSG00000148935			4167	protein-coding gene	gene with protein product		602835				9521882	Standard	NM_005256		Approved		uc001mqo.3	O43903	OTTHUMG00000166071	ENST00000454584.2:c.477T>C	11.37:g.22770669T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	121	56	0.46281	NM_177553	B2R9C8|D3DQZ0|Q6ICV8|Q7Z3X8	Silent	SNP	ENST00000454584.2	37	CCDS7858.1																																																																																			T|0.988;C|0.012	0.012	strong		0.378	GAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387717.1	NM_177553	
SLC24A1	9187	hgsc.bcm.edu	37	15	65917349	65917349	+	Missense_Mutation	SNP	G	G	C	rs34363823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65917349G>C	ENST00000261892.6	+	2	1218	c.931G>C	c.(931-933)Gtc>Ctc	p.V311L	SLC24A1_ENST00000399033.4_Missense_Mutation_p.V311L|SLC24A1_ENST00000546330.1_Missense_Mutation_p.V311L|SLC24A1_ENST00000339868.6_Missense_Mutation_p.V311L|SLC24A1_ENST00000544319.2_Missense_Mutation_p.V311L|SLC24A1_ENST00000537259.1_Missense_Mutation_p.V311L	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	311			V -> L (in dbSNP:rs34363823).		calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						CCAGGGAACAGTCCTGTTGCA	0.557													G|||	84	0.0167732	0.0348	0.0	5008	,	,		19814	0.002		0.005	False		,,,				2504	0.0317				p.V311L		Atlas-SNP	.											.	SLC24A1	58	.	0			c.G931C	GRCh37	CM025395	SLC24A1	M	rs34363823	PASS	.	G	LEU/VAL	116,3812		1,114,1849	71.0	76.0	74.0		931	0.3	0.0	15	dbSNP_126	74	52,8226		0,52,4087	yes	missense	SLC24A1	NM_004727.2	32	1,166,5936	CC,CG,GG		0.6282,2.9532,1.3764	benign	311/1100	65917349	168,12038	1964	4139	6103	SO:0001583	missense	9187	exon2			GGAACAGTCCTGT	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"""Solute carriers"""	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.931G>C	15.37:g.65917349G>C	ENSP00000261892:p.Val311Leu	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_004727	O43485|O75184|Q17RM9	Missense_Mutation	SNP	ENST00000261892.6	37	CCDS45284.1	26	0.011904761904761904	22	0.044715447154471545	0	0.0	0	0.0	4	0.005277044854881266	G	12.69	2.014890	0.35511	0.029532	0.006282	ENSG00000074621	ENST00000537259;ENST00000261892;ENST00000339868;ENST00000544319;ENST00000399033;ENST00000546330	T;T;T;T;T;T	0.66460	0.04;-0.19;-0.18;-0.19;-0.21;-0.18	5.47	0.277	0.15668	.	2.029760	0.02311	N	0.072094	T	0.35828	0.0945	L	0.47190	1.495	0.09310	N	1	B;B;B;P;P	0.46859	0.052;0.031;0.031;0.885;0.817	B;B;B;P;B	0.50659	0.007;0.01;0.005;0.647;0.444	T	0.40627	-0.9553	10	0.48119	T	0.1	.	4.6642	0.12657	0.2534:0.3026:0.444:0.0	rs34363823	311;311;311;311;311	O60721-2;Q17RM9;O60721;F5H127;B4E1W0	.;.;NCKX1_HUMAN;.;.	L	311	ENSP00000439693:V311L;ENSP00000261892:V311L;ENSP00000341837:V311L;ENSP00000445163:V311L;ENSP00000381991:V311L;ENSP00000439190:V311L	ENSP00000261892:V311L	V	+	1	0	SLC24A1	63704402	0.115000	0.22152	0.000000	0.03702	0.015000	0.08874	1.862000	0.39448	-0.082000	0.12640	-0.882000	0.02950	GTC	G|0.990;C|0.010	0.010	strong		0.557	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727	
PLA2G3	50487	hgsc.bcm.edu	37	22	31533967	31533967	+	Silent	SNP	G	G	A	rs2074739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31533967G>A	ENST00000215885.3	-	4	1047	c.795C>T	c.(793-795)taC>taT	p.Y265Y		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	265	Phospholipase A2-like.				acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						GCACTGTGCCGTACATCCTAC	0.637													A|||	2686	0.536342	0.472	0.4395	5008	,	,		16981	0.3948		0.5736	False		,,,				2504	0.7996				p.Y265Y		Atlas-SNP	.											.	PLA2G3	85	.	0			c.C795T						PASS	.	A		2050,2356	599.3+/-389.2	476,1098,629	37.0	43.0	41.0		795	1.6	1.0	22	dbSNP_96	41	5022,3578	506.9+/-376.7	1475,2072,753	yes	coding-synonymous	PLA2G3	NM_015715.3		1951,3170,1382	AA,AG,GG		41.6047,46.5275,45.6251		265/510	31533967	7072,5934	2203	4300	6503	SO:0001819	synonymous_variant	50487	exon4			TGTGCCGTACATC	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.795C>T	22.37:g.31533967G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_015715	O95768	Silent	SNP	ENST00000215885.3	37	CCDS13889.1																																																																																			G|0.488;N|0.000	.	strong		0.637	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715	
MID2	11043	hgsc.bcm.edu	37	X	107159291	107159291	+	Missense_Mutation	SNP	C	C	A	rs12849510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:107159291C>A	ENST00000262843.6	+	6	1681	c.1133C>A	c.(1132-1134)gCc>gAc	p.A378D	MID2_ENST00000443968.2_Missense_Mutation_p.A378D|RP6-191P20.4_ENST00000430140.1_RNA	NM_012216.3|NM_052817.2	NP_036348.2|NP_438112.2	Q9UJV3	TRIM1_HUMAN	midline 2	378	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.		A -> D (in dbSNP:rs12849510).		innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein localization to microtubule (GO:0035372)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)	19						TTTAATGATGCCTTTGAAAAC	0.343													C|||	110	0.0291391	0.0091	0.0245	3775	,	,		10993	0.002		0.0497	False		,,,				2504	0.0297				p.A378D		Atlas-SNP	.											.	MID2	122	.	0			c.C1133A						PASS	.	C	ASP/ALA,ASP/ALA	59,3776		1,50,7,1581,564	119.0	116.0	117.0		1133,1133	5.2	1.0	X	dbSNP_121	117	342,6385		6,218,112,2204,1759	yes	missense,missense	MID2	NM_012216.3,NM_052817.2	126,126	7,268,119,3785,2323	AA,AC,A,CC,C		5.084,1.5385,3.7966	benign,benign	378/736,378/706	107159291	401,10161	2203	4299	6502	SO:0001583	missense	11043	exon6			ATGATGCCTTTGA		CCDS14532.2, CCDS14533.2	Xq22.1-q22.2	2013-02-11			ENSG00000080561	ENSG00000080561		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	7096	protein-coding gene	gene with protein product		300204				10400986	Standard	NM_012216		Approved	FXY2, TRIM1, RNF60	uc004enl.3	Q9UJV3	OTTHUMG00000022171	ENST00000262843.6:c.1133C>A	X.37:g.107159291C>A	ENSP00000262843:p.Ala378Asp	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	104	59	0.567308	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	
ACAD10	80724	hgsc.bcm.edu	37	12	112121090	112121090	+	5'Flank	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:112121090T>C	ENST00000313698.4	+	0	0				ACAD10_ENST00000455480.2_5'Flank|BRAP_ENST00000419234.4_Missense_Mutation_p.E35G|BRAP_ENST00000327551.6_Missense_Mutation_p.E5G|ACAD10_ENST00000549590.1_5'Flank|ACAD10_ENST00000392636.2_5'Flank|BRAP_ENST00000539060.1_5'Flank	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10							mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						CTTTTTTATCTCCTCATCAGA	0.423																																					p.E35G		Atlas-SNP	.											BRAP,NS,carcinoma,+1,1	BRAP	42	1	0			c.A104G						scavenged	.						194.0	170.0	178.0					12																	112121090		2203	4300	6503	SO:0001631	upstream_gene_variant	8315	exon2			TTTATCTCCTCAT	AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"""acyl-Coenzyme A dehydrogenase family, member 10"""			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602		12.37:g.112121090T>C	Exception_encountered	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	233	3	0.0128755	NM_006768	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Missense_Mutation	SNP	ENST00000313698.4	37	CCDS31903.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.767532	0.49574	.	.	ENSG00000089234	ENST00000419234;ENST00000327551	T;T	0.49139	0.86;0.79	5.44	3.06	0.35304	.	0.261425	0.38326	N	0.001728	T	0.39572	0.1083	L	0.54323	1.7	0.80722	D	1	B	0.30068	0.267	B	0.25405	0.06	T	0.25641	-1.0126	10	0.87932	D	0	-9.9935	8.4818	0.33047	0.1297:0.0:0.1361:0.7343	.	35	Q7Z569	BRAP_HUMAN	G	35;5	ENSP00000403524:E35G;ENSP00000330813:E5G	ENSP00000330813:E5G	E	-	2	0	BRAP	110605473	1.000000	0.71417	0.996000	0.52242	0.874000	0.50279	3.914000	0.56401	0.361000	0.24292	0.402000	0.26972	GAG	.	.	none		0.423	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247	
SLC2A11	66035	hgsc.bcm.edu	37	22	24199704	24199704	+	Intron	SNP	C	C	T	rs16986337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24199704C>T	ENST00000345044.6	+	1	289				SLC2A11_ENST00000398356.2_Missense_Mutation_p.R10W|SLC2A11_ENST00000403208.3_Intron|SLC2A11_ENST00000405847.1_Intron|SLC2A11_ENST00000467660.1_3'UTR|SLC2A11_ENST00000316185.8_5'Flank|KB-1125A3.11_ENST00000609825.1_RNA			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11						carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						GCCGTCCTTACGGCCTCGGAC	0.687													C|||	473	0.0944489	0.298	0.0634	5008	,	,		10106	0.0		0.0298	False		,,,				2504	0.0051				p.R10W		Atlas-SNP	.											.	SLC2A11	32	.	0			c.C28T						PASS	.	C	,TRP/ARG	1204,3202	403.3+/-332.7	178,848,1177	31.0	35.0	33.0		,28	0.8	0.0	22	dbSNP_123	33	267,8333	99.3+/-160.8	6,255,4039	yes	intron,missense	SLC2A11	NM_001024938.2,NM_030807.3	,101	184,1103,5216	TT,TC,CC		3.1047,27.3264,11.3102	,	,10/504	24199704	1471,11535	2203	4300	6503	SO:0001627	intron_variant	66035	exon2			TCCTTACGGCCTC	AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"""Solute carriers"""	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.21+526C>T	22.37:g.24199704C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_030807	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Missense_Mutation	SNP	ENST00000345044.6	37	CCDS46673.1	179	0.08195970695970696	135	0.27439024390243905	26	0.0718232044198895	0	0.0	18	0.023746701846965697	C	13.09	2.132060	0.37630	0.273264	0.031047	ENSG00000133460	ENST00000398356;ENST00000398359;ENST00000407566	T	0.79247	-1.25	2.98	0.754	0.18410	.	5.998850	0.00559	N	0.000274	T	0.00039	0.0001	L	0.38175	1.15	0.58432	P	5.000000000032756E-6	D;D;D	0.69078	0.995;0.993;0.997	P;B;B	0.53722	0.733;0.296;0.332	T	0.07673	-1.0760	9	0.72032	D	0.01	.	3.539	0.07804	0.2465:0.6161:0.0:0.1374	rs16986337;rs52815520;rs16986337	10;10;10	E7ENI4;E9PH55;Q6P4C1	.;.;.	W	10	ENSP00000381399:R10W	ENSP00000381399:R10W	R	+	1	2	SLC2A11	22529704	0.000000	0.05858	0.001000	0.08648	0.054000	0.15201	-0.118000	0.10692	0.284000	0.22305	0.650000	0.86243	CGG	C|0.885;T|0.115	0.115	strong		0.687	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807	
KL	9365	hgsc.bcm.edu	37	13	33628138	33628138	+	Missense_Mutation	SNP	T	T	G	rs9536314	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33628138T>G	ENST00000380099.3	+	2	1062	c.1054T>G	c.(1054-1056)Ttt>Gtt	p.F352V	KL_ENST00000426690.2_Missense_Mutation_p.F45V|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	352	Glycosyl hydrolase-1 1.		F -> V (in allele KL-VS; associated with S-370; dbSNP:rs9536314). {ECO:0000269|PubMed:11792841, ECO:0000269|PubMed:15677572}.		acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TCTGCCTGATTTTACTGAATC	0.398													T|||	651	0.129992	0.2005	0.0821	5008	,	,		19946	0.0		0.1938	False		,,,				2504	0.137				p.F352V		Atlas-SNP	.											.	KL	106	.	0			c.T1054G	GRCh37	CM020378	KL	M	rs9536314	PASS	.	T	VAL/PHE	816,3590	325.6+/-299.2	74,668,1461	172.0	175.0	174.0		1054	5.9	0.9	13	dbSNP_119	174	1411,7189	273.9+/-290.9	116,1179,3005	yes	missense	KL	NM_004795.3	50	190,1847,4466	GG,GT,TT		16.407,18.5202,17.1229	probably-damaging	352/1013	33628138	2227,10779	2203	4300	6503	SO:0001583	missense	9365	exon2			CCTGATTTTACTG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1054T>G	13.37:g.33628138T>G	ENSP00000369442:p.Phe352Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	37	CCDS9347.1	287	0.13141025641025642	93	0.18902439024390244	41	0.1132596685082873	0	0.0	153	0.20184696569920843	T	24.2	4.501579	0.85176	0.185202	0.16407	ENSG00000133116	ENST00000426690;ENST00000380099	T;T	0.32753	1.44;1.44	5.9	5.9	0.94986	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	M	0.74467	2.265	0.09310	P	0.9999999999726445	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.00202	-1.1925	9	0.87932	D	0	-24.0951	16.3317	0.83023	0.0:0.0:0.0:1.0	rs9536314;rs52816323;rs58038499;rs9536314	352;45	Q9UEF7;B3KUJ4	KLOT_HUMAN;.	V	45;352	ENSP00000399513:F45V;ENSP00000369442:F352V	ENSP00000369442:F352V	F	+	1	0	KL	32526138	1.000000	0.71417	0.944000	0.38274	0.853000	0.48598	7.914000	0.87478	2.264000	0.75181	0.533000	0.62120	TTT	T|0.846;G|0.154	0.154	strong		0.398	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
ASB18	401036	hgsc.bcm.edu	37	2	237103548	237103548	+	Silent	SNP	G	G	A	rs10177825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:237103548G>A	ENST00000409749.3	-	6	1367	c.1368C>T	c.(1366-1368)taC>taT	p.Y456Y	ASB18_ENST00000330842.6_Silent_p.Y427Y|AC079135.1_ENST00000483218.1_RNA|AC079135.1_ENST00000415226.1_RNA	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	456	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				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)		CCAAAAGTAGGTAATTCTGCA	0.532													A|||	929	0.185503	0.4418	0.0951	5008	,	,		22038	0.002		0.1481	False		,,,				2504	0.1309				p.Y456Y		Atlas-SNP	.											.	ASB18	34	.	0			c.C1368T						PASS	.	A		1570,2464		306,958,753	54.0	64.0	60.0		1368	-0.9	0.1	2	dbSNP_119	60	1057,7313		69,919,3197	no	coding-synonymous	ASB18	NM_212556.2		375,1877,3950	AA,AG,GG		12.6284,38.9192,21.1787		456/467	237103548	2627,9777	2017	4185	6202	SO:0001819	synonymous_variant	401036	exon6			AAGTAGGTAATTC	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.1368C>T	2.37:g.237103548G>A		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_212556	B6ZDL7	Silent	SNP	ENST00000409749.3	37	CCDS46548.1																																																																																			G|0.807;A|0.193	0.193	strong		0.532	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556	
DENND5B	160518	hgsc.bcm.edu	37	12	31605044	31605044	+	Missense_Mutation	SNP	G	G	T	rs1056320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:31605044G>T	ENST00000389082.5	-	5	1723	c.1459C>A	c.(1459-1461)Cat>Aat	p.H487N	DENND5B_ENST00000536562.1_Missense_Mutation_p.H522N|DENND5B_ENST00000354285.4_Missense_Mutation_p.H509N|snoU13_ENST00000458765.1_RNA|DENND5B_ENST00000306833.6_Missense_Mutation_p.H522N	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	487			H -> N (in dbSNP:rs1056320). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TCTTCACAATGCAGTTTTAAA	0.473													G|||	888	0.177316	0.2284	0.1052	5008	,	,		19727	0.247		0.1233	False		,,,				2504	0.1431				p.H487N		Atlas-SNP	.											.	DENND5B	114	.	0			c.C1459A						PASS	.	G	ASN/HIS	770,3092		77,616,1238	167.0	167.0	167.0		1459	4.7	1.0	12	dbSNP_86	167	867,7403		54,759,3322	yes	missense	DENND5B	NM_144973.3	68	131,1375,4560	TT,TG,GG		10.4837,19.9379,13.4932	benign	487/1275	31605044	1637,10495	1931	4135	6066	SO:0001583	missense	160518	exon5			CACAATGCAGTTT	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.1459C>A	12.37:g.31605044G>T	ENSP00000373734:p.His487Asn	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	229	104	0.454148	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	394	0.1804029304029304	122	0.24796747967479674	42	0.11602209944751381	139	0.243006993006993	91	0.12005277044854881	G	10.69	1.420867	0.25639	0.199379	0.104837	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285;ENST00000546299	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	4.67	4.67	0.58626	.	0.346390	0.26804	N	0.022409	T	0.00012	0.0000	N	0.14661	0.345	0.45239	P	0.0017559999999999798	B;B;B;B	0.12630	0.001;0.006;0.0;0.0	B;B;B;B	0.19666	0.001;0.026;0.0;0.001	T	0.19516	-1.0303	9	0.19147	T	0.46	-18.0088	13.191	0.59711	0.0791:0.0:0.9209:0.0	rs1056320;rs3168408;rs16916263;rs52832424;rs58342800;rs1056320	409;509;487;522	Q6ZUT9-3;Q6ZUT9-4;Q6ZUT9;G3V1S3	.;.;DEN5B_HUMAN;.	N	487;522;522;509;439	ENSP00000373734:H487N;ENSP00000306482:H522N;ENSP00000444889:H522N;ENSP00000346238:H509N;ENSP00000442938:H439N	ENSP00000306482:H522N	H	-	1	0	DENND5B	31496311	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	5.975000	0.70475	2.421000	0.82119	0.563000	0.77884	CAT	G|0.818;T|0.182	0.182	strong		0.473	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
CEP89	84902	hgsc.bcm.edu	37	19	33439187	33439187	+	Missense_Mutation	SNP	G	G	A	rs3764633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33439187G>A	ENST00000305768.5	-	5	668	c.580C>T	c.(580-582)Cgg>Tgg	p.R194W	CEP89_ENST00000590597.2_Missense_Mutation_p.R194W	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	194			R -> W (in dbSNP:rs3764633).		cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						TGTTGTGTCCGCTGTGGTGCA	0.333													G|||	950	0.189696	0.2224	0.098	5008	,	,		15572	0.1984		0.2237	False		,,,				2504	0.1667				p.R194W		Atlas-SNP	.											.	CEP89	82	.	0			c.C580T						PASS	.	G	TRP/ARG	971,3435	359.4+/-314.8	103,765,1335	66.0	55.0	59.0		580	-9.1	0.0	19	dbSNP_107	59	1625,6975	296.7+/-303.1	139,1347,2814	yes	missense	CEP89	NM_032816.3	101	242,2112,4149	AA,AG,GG		18.8953,22.0381,19.96	probably-damaging	194/784	33439187	2596,10410	2203	4300	6503	SO:0001583	missense	84902	exon5			GTGTCCGCTGTGG	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.580C>T	19.37:g.33439187G>A	ENSP00000306105:p.Arg194Trp	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	440	0.20146520146520147	103	0.20934959349593496	37	0.10220994475138122	114	0.1993006993006993	186	0.24538258575197888	G	9.076	0.998002	0.19043	0.220381	0.188953	ENSG00000121289	ENST00000305768	T	0.32272	1.46	4.56	-9.12	0.00707	.	2.443350	0.01393	N	0.013315	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.16070	-1.0415	9	0.54805	T	0.06	8.6014	0.0598	0.00015	0.3039:0.2052:0.1707:0.3201	rs3764633;rs17527988;rs17845604;rs17858524;rs52814258;rs59062989;rs3764633	194;194	Q96ST8-3;Q96ST8	.;CEP89_HUMAN	W	194	ENSP00000306105:R194W	ENSP00000306105:R194W	R	-	1	2	CEP89	38131027	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.007000	0.01457	-1.432000	0.01979	-0.215000	0.12644	CGG	G|0.806;A|0.194	0.194	strong		0.333	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324237	39324237	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324237C>G	ENST00000391356.2	-	1	187	c.188G>C	c.(187-189)aGc>aCc	p.S63T		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	63	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				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)			cctgcagcagctgggtttgca	0.627																																					p.S63T		Atlas-SNP	.											KRTAP4-3,NS,carcinoma,-1,1	KRTAP4-3	40	1	0			c.G188C						scavenged	.						3.0	5.0	4.0					17																	39324237		1480	3536	5016	SO:0001583	missense	85290	exon1			CAGCAGCTGGGTT	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.188G>C	17.37:g.39324237C>G	ENSP00000375151:p.Ser63Thr	Somatic	420	0	0		WXS	Illumina HiSeq	Phase_I	110	18	0.163636	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	0.578	-0.838330	0.02692	.	.	ENSG00000196156	ENST00000391356	T	0.01335	5.0	4.13	-2.75	0.05914	.	.	.	.	.	T	0.01061	0.0035	N	0.20881	0.62	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.47573	-0.9107	9	0.14252	T	0.57	.	8.0489	0.30566	0.3482:0.2735:0.3783:0.0	.	63	Q9BYR4	KRA43_HUMAN	T	63	ENSP00000375151:S63T	ENSP00000375151:S63T	S	-	2	0	KRTAP4-3	36577763	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.870000	0.00346	-0.385000	0.07833	-2.956000	0.00083	AGC	.	.	none		0.627	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
FGD2	221472	hgsc.bcm.edu	37	6	36976637	36976637	+	Missense_Mutation	SNP	G	G	C	rs831510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36976637G>C	ENST00000274963.8	+	2	267	c.96G>C	c.(94-96)caG>caC	p.Q32H		NM_173558.3	NP_775829.2	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	32			Q -> H (in dbSNP:rs831510). {ECO:0000269|PubMed:15489334}.		actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.Q32H(1)		central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	25						CCAGAGGCCAGAGGCTAGAGG	0.637													C|||	1632	0.325879	0.264	0.3761	5008	,	,		18864	0.5417		0.2575	False		,,,				2504	0.2219				p.Q32H		Atlas-SNP	.											FGD2,NS,carcinoma,0,1	FGD2	65	1	1	Substitution - Missense(1)	prostate(1)	c.G96C						PASS	.	C	HIS/GLN	1276,3130	680.9+/-403.9	197,882,1124	50.0	57.0	55.0		96	2.2	0.0	6	dbSNP_86	55	2137,6463	696.1+/-404.9	281,1575,2444	yes	missense	FGD2	NM_173558.3	24	478,2457,3568	CC,CG,GG		24.8488,28.9605,26.2417	benign	32/656	36976637	3413,9593	2203	4300	6503	SO:0001583	missense	221472	exon2			AGGCCAGAGGCTA	AK097230	CCDS4829.1	6p21.2	2013-01-10	2004-08-24		ENSG00000146192	ENSG00000146192		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	3664	protein-coding gene	gene with protein product		605091	"""FGD1 family, member 2"""			10458911	Standard	NM_173558		Approved	ZFYVE4	uc010jwp.1	Q7Z6J4	OTTHUMG00000014616	ENST00000274963.8:c.96G>C	6.37:g.36976637G>C	ENSP00000274963:p.Gln32His	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	177	87	0.491525	NM_173558	Q5T8I1|Q6P6A8|Q6ZNL5|Q8IZ32|Q8N868|Q9H7M2	Missense_Mutation	SNP	ENST00000274963.8	37	CCDS4829.1	777	0.3557692307692308	142	0.2886178861788618	122	0.3370165745856354	311	0.5437062937062938	202	0.26649076517150394	C	0.024	-1.385287	0.01194	0.289605	0.248488	ENSG00000146192	ENST00000274963	T	0.58210	0.35	5.0	2.16	0.27623	.	0.767167	0.11414	N	0.566460	T	0.06142	0.0159	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33954	-0.9848	9	0.12766	T	0.61	.	4.6034	0.12364	0.0:0.5542:0.1599:0.2858	rs831510;rs17855748;rs17856702;rs52822242;rs57642495;rs831510	32;32	Q7Z6J4;F8WEZ2	FGD2_HUMAN;.	H	32	ENSP00000274963:Q32H	ENSP00000274963:Q32H	Q	+	3	2	FGD2	37084615	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.243000	0.18106	0.157000	0.19338	-0.647000	0.03941	CAG	G|0.699;C|0.301	0.301	strong		0.637	FGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040398.2	NM_173558	
STRC	161497	hgsc.bcm.edu	37	15	43892847	43892847	+	Silent	SNP	G	G	C	rs12438025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43892847G>C	ENST00000450892.2	-	26	4955	c.4878C>G	c.(4876-4878)ctC>ctG	p.L1626L	RNU6-554P_ENST00000410466.1_RNA|STRC_ENST00000541030.1_Silent_p.L853L	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	1626					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CAGAGCACTGGAGATGCAGGG	0.532													G|||	1475	0.294529	0.556	0.2032	5008	,	,		20056	0.2718		0.0994	False		,,,				2504	0.2301				p.L1626L		Atlas-SNP	.											STRC_ENST00000450892,colon,carcinoma,0,1	STRC	58	1	0			c.C4878G						PASS	.	G		2041,2359	541.9+/-375.9	485,1071,644	55.0	64.0	61.0		4878	2.9	1.0	15	dbSNP_120	61	846,7748	189.1+/-236.0	50,746,3501	no	coding-synonymous	STRC	NM_153700.2		535,1817,4145	CC,CG,GG		9.8441,46.3864,22.2179		1626/1776	43892847	2887,10107	2200	4297	6497	SO:0001819	synonymous_variant	161497	exon26			GCACTGGAGATGC	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.4878C>G	15.37:g.43892847G>C		Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	280	121	0.432143	NM_153700		Silent	SNP	ENST00000450892.2	37	CCDS10098.1																																																																																			G|0.784;C|0.216	0.216	strong		0.532	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
GALK2	2585	hgsc.bcm.edu	37	15	49574223	49574223	+	Missense_Mutation	SNP	A	A	G	rs35507772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:49574223A>G	ENST00000560031.1	+	6	851	c.544A>G	c.(544-546)Att>Gtt	p.I182V	GALK2_ENST00000561014.1_3'UTR|GALK2_ENST00000327171.3_Missense_Mutation_p.I171V|GALK2_ENST00000396509.2_Missense_Mutation_p.I158V|GALK2_ENST00000543495.1_Missense_Mutation_p.I53V|GALK2_ENST00000559454.1_Missense_Mutation_p.I158V|GALK2_ENST00000544523.1_Missense_Mutation_p.I158V			Q01415	GALK2_HUMAN	galactokinase 2	182			I -> V (in dbSNP:rs35507772).		carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		TGAGCGTTACATTGGCACTGA	0.418													A|||	31	0.0061901	0.0227	0.0014	5008	,	,		20552	0.0		0.0	False		,,,				2504	0.0				p.I182V		Atlas-SNP	.											.	GALK2	78	.	0			c.A544G						PASS	.	A	VAL/ILE,VAL/ILE	85,4307	72.0+/-110.0	0,85,2111	132.0	124.0	126.0		511,544	5.8	1.0	15	dbSNP_126	126	0,8590		0,0,4295	yes	missense,missense	GALK2	NM_001001556.1,NM_002044.2	29,29	0,85,6406	GG,GA,AA		0.0,1.9353,0.6548	benign,benign	171/448,182/459	49574223	85,12897	2196	4295	6491	SO:0001583	missense	2585	exon6			CGTTACATTGGCA		CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.544A>G	15.37:g.49574223A>G	ENSP00000453129:p.Ile182Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	134	75	0.559702	NM_002044	Q7Z4Q4	Missense_Mutation	SNP	ENST00000560031.1	37	CCDS42034.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	A	17.89	3.500334	0.64298	0.019353	0.0	ENSG00000156958	ENST00000327171;ENST00000396509;ENST00000543495;ENST00000544523	D;D;D	0.86562	-2.14;-2.14;-2.14	5.79	5.79	0.91817	Ribosomal protein S5 domain 2-type fold (1);GHMP kinase (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.043082	0.85682	D	0.000000	T	0.62245	0.2412	N	0.11870	0.19	0.80722	D	1	B;B	0.32382	0.368;0.174	B;B	0.42062	0.374;0.213	T	0.72047	-0.4408	10	0.15499	T	0.54	-14.2408	16.1193	0.81336	1.0:0.0:0.0:0.0	rs35507772	182;171	Q01415;Q7Z4Q4	GALK2_HUMAN;.	V	171;182;53;158	ENSP00000316632:I171V;ENSP00000443220:I53V;ENSP00000440312:I158V	ENSP00000316632:I171V	I	+	1	0	GALK2	47361515	1.000000	0.71417	0.999000	0.59377	0.968000	0.65278	5.983000	0.70540	2.201000	0.70794	0.533000	0.62120	ATT	A|0.992;G|0.008	0.008	strong		0.418	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1		
NADK	65220	hgsc.bcm.edu	37	1	1688719	1688719	+	Silent	SNP	C	C	A	rs78921781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1688719C>A	ENST00000341426.5	-	4	515	c.294G>T	c.(292-294)ctG>ctT	p.L98L	NADK_ENST00000341991.3_Silent_p.L98L|NADK_ENST00000492768.1_5'UTR|NADK_ENST00000378625.1_Silent_p.L202L|NADK_ENST00000342348.5_Silent_p.L66L|NADK_ENST00000344463.4_Silent_p.L202L	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	98					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)		TGTTCCACGTCAGCCGCTGGC	0.552													C|||	27	0.00539137	0.0159	0.0014	5008	,	,		10189	0.001		0.004	False		,,,				2504	0.0				p.L202L		Atlas-SNP	.											.	NADK	79	.	0			c.G606T						PASS	.	C	,,,	69,4337	62.3+/-99.4	1,67,2135	97.0	98.0	98.0		294,606,198,294	5.7	1.0	1	dbSNP_133	98	7,8593	6.4+/-24.3	1,5,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NADK	NM_001198993.1,NM_001198994.1,NM_001198995.1,NM_023018.4	,,,	2,72,6429	AA,AC,CC		0.0814,1.566,0.5843	,,,	98/447,202/592,66/415,98/447	1688719	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	65220	exon6			CCACGTCAGCCGC	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.294G>T	1.37:g.1688719C>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Silent	SNP	ENST00000341426.5	37	CCDS30565.1																																																																																			C|0.995;A|0.005	0.005	strong		0.552	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018	
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39191003	39191003	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39191003C>G	ENST00000344363.5	-	1	104	c.71G>C	c.(70-72)tGc>tCc	p.C24S		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	24						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCTGGCAGCAGCTGGAGCC	0.592																																					p.C24S		Atlas-SNP	.											KRTAP1-3,NS,carcinoma,0,1	KRTAP1-3	18	1	0			c.G71C						scavenged	.						37.0	45.0	42.0					17																	39191003		1971	4166	6137	SO:0001583	missense	81850	exon1			TGGCAGCAGCTGG	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"""Keratin associated proteins"""	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.71G>C	17.37:g.39191003C>G	ENSP00000344420:p.Cys24Ser	Somatic	234	2	0.00854701		WXS	Illumina HiSeq	Phase_I	236	18	0.0762712	NM_030966	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.535706	0.45176	.	.	ENSG00000221880	ENST00000344363	T	0.30448	1.53	4.11	3.14	0.36123	.	.	.	.	.	T	0.50292	0.1607	.	.	.	0.36497	D	0.868786	D	0.65815	0.995	D	0.73708	0.981	T	0.59445	-0.7453	8	0.72032	D	0.01	.	7.8183	0.29274	0.0:0.8874:0.0:0.1126	.	34	Q8IUG1	KRA13_HUMAN	S	24	ENSP00000344420:C24S	ENSP00000344420:C24S	C	-	2	0	KRTAP1-3	36444529	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	0.952000	0.29149	1.303000	0.44873	0.563000	0.77884	TGC	.	.	none		0.592	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1		
C2CD2	25966	hgsc.bcm.edu	37	21	43327117	43327117	+	Silent	SNP	C	C	T	rs2277795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43327117C>T	ENST00000380486.3	-	10	1543	c.1302G>A	c.(1300-1302)gcG>gcA	p.A434A	C2CD2_ENST00000329623.7_Silent_p.A279A	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	434						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						TCAGCGGGGACGCCCTCCCCA	0.582													C|||	1507	0.300919	0.5545	0.1527	5008	,	,		18310	0.2728		0.1471	False		,,,				2504	0.2505				p.A434A		Atlas-SNP	.											.	C2CD2	47	.	0			c.G1302A						PASS	.	C	,	2195,2211	587.9+/-386.8	551,1093,559	81.0	67.0	72.0		1302,837	-4.9	0.9	21	dbSNP_100	72	1278,7322	254.6+/-279.8	101,1076,3123	no	coding-synonymous,coding-synonymous	C2CD2	NM_015500.1,NM_199050.2	,	652,2169,3682	TT,TC,CC		14.8605,49.8184,26.7031	,	434/697,279/542	43327117	3473,9533	2203	4300	6503	SO:0001819	synonymous_variant	25966	exon10			CGGGGACGCCCTC	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"""TMEM24-like"""		"""chromosome 21 open reading frame 25"""	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1302G>A	21.37:g.43327117C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Silent	SNP	ENST00000380486.3	37	CCDS42933.1																																																																																			C|0.714;T|0.286	0.286	strong		0.582	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
OR4A5	81318	hgsc.bcm.edu	37	11	51411817	51411817	+	Silent	SNP	G	G	A	rs144502772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:51411817G>A	ENST00000319760.6	-	1	631	c.579C>T	c.(577-579)ggC>ggT	p.G193G		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	193						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)				CAACAGTGAGGCCTATAAAGT	0.428													.|||	30	0.00599042	0.0219	0.0014	5008	,	,		20435	0.0		0.0	False		,,,				2504	0.0				p.G193G		Atlas-SNP	.											.	OR4A5	116	.	0			c.C579T						PASS	.	G		102,4300		2,98,2101	62.0	55.0	57.0		579	-2.1	0.1	11	dbSNP_134	57	0,8590		0,0,4295	no	coding-synonymous	OR4A5	NM_001005272.3		2,98,6396	AA,AG,GG		0.0,2.3171,0.7851		193/316	51411817	102,12890	2201	4295	6496	SO:0001819	synonymous_variant	81318	exon1			AGTGAGGCCTATA	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.579C>T	11.37:g.51411817G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	37	CCDS31497.1																																																																																			G|0.993;A|0.007	0.007	strong		0.428	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
ZNF280D	54816	hgsc.bcm.edu	37	15	56959028	56959028	+	Missense_Mutation	SNP	C	C	T	rs28620278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56959028C>T	ENST00000267807.7	-	15	1918	c.1702G>A	c.(1702-1704)Gtc>Atc	p.V568I	ZNF280D_ENST00000396245.1_Missense_Mutation_p.V272I|ZNF280D_ENST00000559237.1_Missense_Mutation_p.V555I|ZNF280D_ENST00000559000.1_Missense_Mutation_p.V555I	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	568			V -> I (in dbSNP:rs28620278). {ECO:0000269|PubMed:10997877, 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(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		TTGGATTTGACTGTATTAGGT	0.333													T|||	2640	0.527157	0.7141	0.6225	5008	,	,		15602	0.3829		0.4066	False		,,,				2504	0.4796				p.V568I		Atlas-SNP	.											.	ZNF280D	82	.	0			c.G1702A						PASS	.	T	ILE/VAL,ILE/VAL	2803,1581	486.2+/-360.5	917,969,306	139.0	145.0	143.0		1663,1702	-0.9	0.0	15	dbSNP_125	143	3481,5103	631.5+/-398.5	697,2087,1508	yes	missense,missense	ZNF280D	NM_001002843.1,NM_017661.2	29,29	1614,3056,1814	TT,TC,CC		40.5522,36.063,48.4577	benign,benign	555/967,568/980	56959028	6284,6684	2192	4292	6484	SO:0001583	missense	54816	exon15			ATTTGACTGTATT	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.1702G>A	15.37:g.56959028C>T	ENSP00000267807:p.Val568Ile	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	327	182	0.556575	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Missense_Mutation	SNP	ENST00000267807.7	37	CCDS32245.1	1099	0.5032051282051282	370	0.7520325203252033	214	0.5911602209944752	225	0.39335664335664333	290	0.38258575197889183	T	1.441	-0.567698	0.03910	0.63937	0.405522	ENSG00000137871	ENST00000267807;ENST00000455329;ENST00000396245	T;T	0.03004	4.08;4.5	4.58	-0.931	0.10438	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.05305	-1.0893	8	0.17832	T	0.49	0.0847	6.768	0.23579	0.0:0.4082:0.1329:0.459	rs28620278;rs28620278	568	Q6N043	Z280D_HUMAN	I	568;555;272	ENSP00000267807:V568I;ENSP00000379545:V272I	ENSP00000267807:V568I	V	-	1	0	ZNF280D	54746320	0.059000	0.20769	0.018000	0.16275	0.511000	0.34104	-0.286000	0.08399	-0.282000	0.09128	-0.332000	0.08345	GTC	C|0.495;T|0.505	0.505	strong		0.333	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417777	105417777	+	Silent	SNP	C	C	T	rs1960092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417777C>T	ENST00000333244.5	-	7	4130	c.4011G>A	c.(4009-4011)tcG>tcA	p.S1337S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1337						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)			ACACCCCGAACGACGGCATCT	0.612													.|||	385	0.076877	0.2693	0.0173	5008	,	,		14219	0.0079		0.007	False		,,,				2504	0.002				p.S1337S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G4011A						PASS	.	G		843,2819		207,429,1195	147.0	129.0	135.0		4011	-2.5	0.0	14	dbSNP_92	135	21,6593		3,15,3289	no	coding-synonymous	AHNAK2	NM_138420.2		210,444,4484	TT,TC,CC		0.3175,23.0202,8.4079		1337/5796	105417777	864,9412	1831	3307	5138	SO:0001819	synonymous_variant	113146	exon7			CCCGAACGACGGC	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.4011G>A	14.37:g.105417777C>T		Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	255	254	0.996078	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.959;T|0.041	0.041	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OR10K1	391109	hgsc.bcm.edu	37	1	158435572	158435572	+	Missense_Mutation	SNP	C	C	T	rs78779179|rs386635902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158435572C>T	ENST00000289451.2	+	1	301	c.221C>T	c.(220-222)aCc>aTc	p.T74I		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, member 1	74						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)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					ATTTGCTATACCTTTGTCATT	0.453													C|||	189	0.0377396	0.1354	0.013	5008	,	,		24656	0.0		0.001	False		,,,				2504	0.0				p.T74I		Atlas-SNP	.											.	OR10K1	80	.	0			c.C221T						PASS	.	C	ILE/THR	501,3905	216.4+/-235.1	27,447,1729	209.0	190.0	197.0		221	4.5	1.0	1	dbSNP_131	197	8,8592	6.4+/-24.3	0,8,4292	yes	missense	OR10K1	NM_001004473.1	89	27,455,6021	TT,TC,CC		0.093,11.3709,3.9136	probably-damaging	74/314	158435572	509,12497	2203	4300	6503	SO:0001583	missense	391109	exon1			GCTATACCTTTGT	AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"""GPCR / Class A : Olfactory receptors"""	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.221C>T	1.37:g.158435572C>T	ENSP00000289451:p.Thr74Ile	Somatic	490	0	0		WXS	Illumina HiSeq	Phase_I	474	204	0.43038	NM_001004473	Q6IFS2	Missense_Mutation	SNP	ENST00000289451.2	37	CCDS30897.1	55	0.025183150183150184	49	0.09959349593495935	6	0.016574585635359115	0	0.0	0	0.0	c	13.70	2.316088	0.40996	0.113709	9.3E-4	ENSG00000173285	ENST00000289451	T	0.00444	7.4	4.5	4.5	0.54988	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	D	0.000467	T	0.00384	0.0012	L	0.49778	1.585	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.53173	-0.8476	10	0.62326	D	0.03	.	10.4216	0.44354	0.0:0.9045:0.0:0.0955	.	74	Q8NGX5	O10K1_HUMAN	I	74	ENSP00000289451:T74I	ENSP00000289451:T74I	T	+	2	0	OR10K1	156702196	0.000000	0.05858	0.999000	0.59377	0.887000	0.51463	0.237000	0.17985	2.311000	0.77944	0.557000	0.71058	ACC	C|0.966;T|0.034	0.034	strong		0.453	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1		
PAH	5053	hgsc.bcm.edu	37	12	103248924	103248924	+	Silent	SNP	C	C	T	rs1126758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:103248924C>T	ENST00000553106.1	-	6	1168	c.696G>A	c.(694-696)caG>caA	p.Q232Q	PAH_ENST00000551988.1_5'Flank|PAH_ENST00000307000.2_Silent_p.Q227Q	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	232					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	TCTGCAGGAACTGAGAAACGT	0.483													T|||	2737	0.546526	0.8011	0.6888	5008	,	,		21740	0.0794		0.5815	False		,,,				2504	0.547				p.Q232Q		Atlas-SNP	.											.	PAH	77	.	0			c.G696A						PASS	.	T		3385,1021	376.6+/-322.1	1296,793,114	120.0	110.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	696	-9.4	0.4	12	dbSNP_86	114	5115,3485	510.6+/-377.5	1510,2095,695	no	coding-synonymous	PAH	NM_000277.1		2806,2888,809	TT,TC,CC		40.5233,23.1729,34.6455		232/453	103248924	8500,4506	2203	4300	6503	SO:0001819	synonymous_variant	5053	exon6			CAGGAACTGAGAA	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.696G>A	12.37:g.103248924C>T		Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_000277	Q16717|Q8TC14	Silent	SNP	ENST00000553106.1	37	CCDS9092.1																																																																																			C|0.415;T|0.585	0.585	strong		0.483	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1		
OTUD7B	56957	hgsc.bcm.edu	37	1	149916584	149916584	+	Silent	SNP	C	C	G	rs200362140	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:149916584C>G	ENST00000369135.4	-	12	1998	c.1704G>C	c.(1702-1704)ggG>ggC	p.G568G		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	568					mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CAGGCCCATCCCCAGCTGCCT	0.572													C|||	10	0.00199681	0.0076	0.0	5008	,	,		16047	0.0		0.0	False		,,,				2504	0.0				p.G568G		Atlas-SNP	.											.	OTUD7B	76	.	0			c.G1704C						PASS	.	C		16,4136		0,16,2060	73.0	82.0	79.0		1704	0.7	1.0	1		79	0,8438		0,0,4219	no	coding-synonymous	OTUD7B	NM_020205.2		0,16,6279	GG,GC,CC		0.0,0.3854,0.1271		568/844	149916584	16,12574	2076	4219	6295	SO:0001819	synonymous_variant	56957	exon12			CCCATCCCCAGCT	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"""OTU domain containing"""	16683	protein-coding gene	gene with protein product		611748	"""zinc finger, A20 domain containing 1"", ""OTU domain containing 7B"""	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.1704G>C	1.37:g.149916584C>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Silent	SNP	ENST00000369135.4	37	CCDS41389.1																																																																																			C|0.999;G|0.001	0.001	strong		0.572	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205	
DNAH5	1767	hgsc.bcm.edu	37	5	13762972	13762972	+	Silent	SNP	T	T	C	rs6554812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13762972T>C	ENST00000265104.4	-	60	10244	c.10140A>G	c.(10138-10140)gaA>gaG	p.E3380E	DNAH5_ENST00000504001.3_5'UTR	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3380	Stalk. {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)					GACTCAAAAATTCTATCACCT	0.373									Kartagener syndrome				C|||	1554	0.310304	0.3722	0.2709	5008	,	,		21726	0.1052		0.3012	False		,,,				2504	0.4755				p.E3380E		Atlas-SNP	.											DNAH5,NS,carcinoma,-2,1	DNAH5	868	1	0			c.A10140G						PASS	.	C		1601,2805	665.6+/-401.6	294,1013,896	77.0	74.0	75.0		10140	-5.2	0.7	5	dbSNP_116	75	2272,6328	707.4+/-405.6	306,1660,2334	no	coding-synonymous	DNAH5	NM_001369.2		600,2673,3230	CC,CT,TT		26.4186,36.3368,29.7786		3380/4625	13762972	3873,9133	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon60	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAAAAATTCTATC	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.10140A>G	5.37:g.13762972T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.714;C|0.286	0.286	strong		0.373	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
PRKAR1B	5575	hgsc.bcm.edu	37	7	590199	590199	+	Silent	SNP	A	A	G	rs11545042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:590199A>G	ENST00000406797.1	-	11	1188	c.1014T>C	c.(1012-1014)acT>acC	p.T338T	AC147651.2_ENST00000517177.1_RNA|PRKAR1B_ENST00000403562.1_Silent_p.T338T|PRKAR1B_ENST00000360274.4_Silent_p.T338T|PRKAR1B_ENST00000537384.1_Silent_p.T338T|PRKAR1B_ENST00000544935.1_Silent_p.T338T	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	338					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		GGGCCACGACAGTGGCCGCCC	0.672													.|||	795	0.158746	0.2322	0.1124	5008	,	,		11673	0.2391		0.1123	False		,,,				2504	0.0573				p.T338T		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.T1014C						PASS	.	G	,,,,,	885,3459		93,699,1380	21.0	20.0	20.0		1014,1014,1014,1014,1014,1014	-2.0	1.0	7	dbSNP_120	20	967,7557		46,875,3341	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKAR1B	NM_001164758.1,NM_001164759.1,NM_001164760.1,NM_001164761.1,NM_001164762.1,NM_002735.2	,,,,,	139,1574,4721	GG,GA,AA		11.3444,20.3729,14.3923	,,,,,	338/382,338/382,338/382,338/382,338/382,338/382	590199	1852,11016	2172	4262	6434	SO:0001819	synonymous_variant	5575	exon11			CACGACAGTGGCC	M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	2.7.11.1		9390	protein-coding gene	gene with protein product		176911				1358799, 3479018	Standard	NM_002735		Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.1014T>C	7.37:g.590199A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_001164760	Q8N422	Silent	SNP	ENST00000406797.1	37	CCDS34579.1	379	0.17353479853479853	126	0.25609756097560976	44	0.12154696132596685	130	0.22727272727272727	79	0.10422163588390501	a	3.749	-0.051904	0.07362	0.203729	0.113444	ENSG00000188191	ENST00000400758	.	.	.	4.65	-1.96	0.07525	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999987	.	.	.	.	.	.	T	0.26780	-1.0093	3	.	.	.	-1.4289	8.2013	0.31426	0.5175:0.2625:0.2199:0.0	rs11545042;rs28722665	.	.	.	P	199	.	.	L	-	2	0	PRKAR1B	556725	0.000000	0.05858	0.964000	0.40570	0.529000	0.34654	-2.186000	0.01251	-0.857000	0.04115	-2.296000	0.00263	CTG	A|0.826;G|0.174	0.174	strong		0.672	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1		
PZP	5858	hgsc.bcm.edu	37	12	9317784	9317784	+	Missense_Mutation	SNP	A	A	G	rs2277413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9317784A>G	ENST00000261336.2	-	19	2466	c.2438T>C	c.(2437-2439)gTc>gCc	p.V813A	PZP_ENST00000539983.1_5'UTR|PZP_ENST00000381997.2_Missense_Mutation_p.V682A	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	813			V -> A (in dbSNP:rs2277413).		female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GAGTGTGAAGACCTCTCCACG	0.498													A|||	1934	0.386182	0.3411	0.2421	5008	,	,		-128	0.5357		0.3419	False		,,,				2504	0.4407				p.V813A	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.T2438C						PASS	.	A	ALA/VAL	1464,2942	463.4+/-353.5	261,942,1000	127.0	120.0	122.0		2438	-0.9	1.0	12	dbSNP_100	122	2537,6063	408.7+/-349.6	381,1775,2144	no	missense	PZP	NM_002864.2	64	642,2717,3144	GG,GA,AA		29.5,33.2274,30.7627	benign	813/1483	9317784	4001,9005	2203	4300	6503	SO:0001583	missense	5858	exon19			GTGAAGACCTCTC	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.2438T>C	12.37:g.9317784A>G	ENSP00000261336:p.Val813Ala	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	179	179	1	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	732	0.33516483516483514	137	0.2784552845528455	97	0.26795580110497236	282	0.493006993006993	216	0.2849604221635884	A	0.003	-2.442208	0.00180	0.332274	0.295	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.24908	1.83;1.83	3.7	-0.929	0.10444	Alpha-2-macroglobulin (1);	0.671497	0.13428	N	0.388670	T	0.00012	0.0000	N	0.02420	-0.555	0.80722	P	0.0	B;B;B	0.16802	0.001;0.019;0.001	B;B;B	0.15484	0.002;0.013;0.002	T	0.43360	-0.9396	9	0.02654	T	1	.	3.0317	0.06109	0.268:0.1205:0.4895:0.122	rs2277413;rs59075755;rs2277413	813;682;813	B2R950;P20742-2;P20742	.;.;PZP_HUMAN	A	813;682	ENSP00000261336:V813A;ENSP00000371427:V682A	ENSP00000261336:V813A	V	-	2	0	PZP	9209051	0.000000	0.05858	0.990000	0.47175	0.212000	0.24457	-1.395000	0.02516	0.004000	0.14682	-1.483000	0.00984	GTC	A|0.677;G|0.323	0.323	strong		0.498	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
SSPO	23145	hgsc.bcm.edu	37	7	149506195	149506195	+	RNA	SNP	C	C	T	rs73727627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149506195C>T	ENST00000378016.2	+	0	9187							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)			CTACAGGAACCGCACCCGAGG	0.682													C|||	125	0.0249601	0.0772	0.0115	5008	,	,		13530	0.001		0.002	False		,,,				2504	0.0123				p.R3063C		Atlas-SNP	.											.	.	.	.	0			c.C9187T						PASS	.	C		235,3871		4,227,1822	16.0	24.0	22.0		9195	5.2	1.0	7	dbSNP_130	22	32,8324		0,32,4146	no	coding-notMod3	SSPO	NM_198455.2		4,259,5968	TT,TC,CC		0.383,5.7233,2.1425			149506195	267,12195	2053	4178	6231			23145	exon63			AGGAACCGCACCC	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.149506195C>T		Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	292	154	0.527397	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.978;T|0.022	0.022	strong		0.682	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
KRT79	338785	hgsc.bcm.edu	37	12	53227803	53227803	+	Missense_Mutation	SNP	A	A	G	rs2638497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53227803A>G	ENST00000330553.5	-	1	276	c.242T>C	c.(241-243)tTg>tCg	p.L81S		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	81	Head.		L -> S (in dbSNP:rs2638497). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.			extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGCCCGCCCCAACAAGGCCCC	0.647													G|||	3704	0.739617	0.8381	0.6138	5008	,	,		12534	0.7966		0.6044	False		,,,				2504	0.7761				p.L81S		Atlas-SNP	.											KRT79,NS,carcinoma,+1,1	KRT79	78	1	0			c.T242C						PASS	.	G	SER/LEU	3514,888		1409,696,96	23.0	30.0	28.0		242	3.4	0.0	12	dbSNP_100	28	4947,3651		1447,2053,799	yes	missense	KRT79	NM_175834.2	145	2856,2749,895	GG,GA,AA		42.4634,20.1726,34.9154	benign	81/536	53227803	8461,4539	2201	4299	6500	SO:0001583	missense	338785	exon1			CGCCCCAACAAGG	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28930	protein-coding gene	gene with protein product	"""keratin 6-like"""	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.242T>C	12.37:g.53227803A>G	ENSP00000328358:p.Leu81Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	37	CCDS8839.1	1521	0.6964285714285714	405	0.823170731707317	219	0.6049723756906077	447	0.7814685314685315	450	0.5936675461741425	G	0.043	-1.278312	0.01410	0.798274	0.575366	ENSG00000185640	ENST00000330553	T	0.18502	2.21	4.28	3.39	0.38822	.	0.980624	0.08301	N	0.966946	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	0.21621	-1.0240	9	0.21014	T	0.42	.	8.5716	0.33572	0.2617:0.0:0.7383:0.0	rs2638497;rs17846647;rs17859742;rs57759231;rs2638497	81	Q5XKE5	K2C79_HUMAN	S	81	ENSP00000328358:L81S	ENSP00000328358:L81S	L	-	2	0	KRT79	51514070	0.002000	0.14202	0.002000	0.10522	0.007000	0.05969	0.450000	0.21762	0.754000	0.32968	-0.186000	0.12905	TTG	A|0.331;G|0.669	0.669	strong		0.647	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834	
TSEN2	80746	hgsc.bcm.edu	37	3	12531461	12531461	+	Silent	SNP	G	G	A	rs78685815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:12531461G>A	ENST00000284995.6	+	2	549	c.162G>A	c.(160-162)gcG>gcA	p.A54A	TSEN2_ENST00000415684.1_Silent_p.A54A|TSEN2_ENST00000402228.3_Silent_p.A54A|TSEN2_ENST00000383797.5_Silent_p.A54A|TSEN2_ENST00000444864.1_Silent_p.A54A|TSEN2_ENST00000314571.7_Silent_p.A54A|TSEN2_ENST00000454502.2_Silent_p.A54A	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	54					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)	p.A54A(1)		central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						TGAGGAATGCGGAGGACATTG	0.463													A|||	468	0.0934505	0.2103	0.0865	5008	,	,		20603	0.0298		0.0239	False		,,,				2504	0.0777				p.A54A		Atlas-SNP	.											TSEN2,NS,carcinoma,+1,2	TSEN2	46	2	1	Substitution - coding silent(1)	large_intestine(1)	c.G162A						PASS	.	A	,,,,	698,3708		41,616,1546	129.0	122.0	124.0		162,162,162,162,162	-4.3	0.0	3	dbSNP_131	124	120,8480		3,114,4183	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TSEN2	NM_001145392.1,NM_001145393.1,NM_001145394.1,NM_001145395.1,NM_025265.3	,,,,	44,730,5729	AA,AG,GG		1.3953,15.842,6.2894	,,,,	54/466,54/440,54/407,54/403,54/466	12531461	818,12188	2203	4300	6503	SO:0001819	synonymous_variant	80746	exon2			GAATGCGGAGGAC	BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"""tRNA splicing endonuclease subunits"""	28422	protein-coding gene	gene with protein product		608753	"""tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)"", ""tRNA splicing endonuclease 2 homolog (S. cerevisiae)"""			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.162G>A	3.37:g.12531461G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_001145394	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Silent	SNP	ENST00000284995.6	37	CCDS2611.1																																																																																			A|0.060;G|0.940	0.060	strong		0.463	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1	NM_025265	
EXPH5	23086	hgsc.bcm.edu	37	11	108380609	108380609	+	Silent	SNP	C	C	T	rs115867994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108380609C>T	ENST00000265843.4	-	6	5735	c.5625G>A	c.(5623-5625)agG>agA	p.R1875R	EXPH5_ENST00000443411.1_Silent_p.R1687R|EXPH5_ENST00000428840.1_Silent_p.R1799R|EXPH5_ENST00000525344.1_Silent_p.R1868R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1875					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		ATATTGCAGACCTGGGACCTG	0.418													C|||	66	0.0131789	0.0492	0.0014	5008	,	,		19501	0.0		0.0	False		,,,				2504	0.0				p.R1875R		Atlas-SNP	.											.	EXPH5	193	.	0			c.G5625A						PASS	.	C		174,4228	114.6+/-152.6	0,174,2027	62.0	63.0	63.0		5625	2.2	0.2	11	dbSNP_132	63	0,8596		0,0,4298	no	coding-synonymous	EXPH5	NM_015065.2		0,174,6325	TT,TC,CC		0.0,3.9527,1.3387		1875/1990	108380609	174,12824	2201	4298	6499	SO:0001819	synonymous_variant	23086	exon6			TGCAGACCTGGGA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.5625G>A	11.37:g.108380609C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	157	74	0.471338	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	37	CCDS8341.1																																																																																			C|0.986;T|0.014	0.014	strong		0.418	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
DLG5	9231	hgsc.bcm.edu	37	10	79616520	79616520	+	Silent	SNP	G	G	C	rs12243930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79616520G>C	ENST00000372391.2	-	3	509	c.504C>G	c.(502-504)gcC>gcG	p.A168A	DLG5_ENST00000372388.2_Silent_p.A168A	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	168					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)			GCGTAGCAAAGGCCAGGCGCT	0.592													G|||	720	0.14377	0.5197	0.0432	5008	,	,		18218	0.0		0.003	False		,,,				2504	0.0				p.A168A		Atlas-SNP	.											.	DLG5	154	.	0			c.C504G						PASS	.	G		1939,2467	545.8+/-376.9	450,1039,714	46.0	48.0	47.0		504	4.5	1.0	10	dbSNP_120	47	24,8576	14.6+/-50.1	0,24,4276	no	coding-synonymous	DLG5	NM_004747.3		450,1063,4990	CC,CG,GG		0.2791,44.0082,15.093		168/1920	79616520	1963,11043	2203	4300	6503	SO:0001819	synonymous_variant	9231	exon3			AGCAAAGGCCAGG	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.504C>G	10.37:g.79616520G>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	198	95	0.479798	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			G|0.857;C|0.143	0.143	strong		0.592	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
ANKRD2	26287	hgsc.bcm.edu	37	10	99337572	99337572	+	Missense_Mutation	SNP	G	G	A	rs7094973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99337572G>A	ENST00000307518.5	+	2	451	c.184G>A	c.(184-186)Gca>Aca	p.A62T	ANKRD2_ENST00000298808.5_Missense_Mutation_p.A62T|ANKRD2_ENST00000370655.1_Missense_Mutation_p.A35T|ANKRD2_ENST00000455090.1_Missense_Mutation_p.A35T			Q9GZV1	ANKR2_HUMAN	ankyrin repeat domain 2 (stretch responsive muscle)	62	May mediate interaction with PML, p53/TP53 and YBX1.		A -> T (in dbSNP:rs7094973). {ECO:0000269|PubMed:11444853, ECO:0000269|PubMed:11453652, ECO:0000269|PubMed:14583192, ECO:0000269|PubMed:14702039}.		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)	p.A62T(1)		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)		CCGAGGAGACGCACGCCAGAA	0.617													G|||	2274	0.454073	0.1921	0.6585	5008	,	,		15754	0.4018		0.6869	False		,,,				2504	0.4775				p.A62T		Atlas-SNP	.											ANKRD2,NS,carcinoma,0,1	ANKRD2	27	1	1	Substitution - Missense(1)	stomach(1)	c.G184A						PASS	.	G	THR/ALA,THR/ALA	1255,3145		204,847,1149	48.0	36.0	40.0		184,184	-7.9	0.0	10	dbSNP_116	40	6028,2552		2122,1784,384	yes	missense,missense	ANKRD2	NM_001129981.1,NM_020349.2	58,58	2326,2631,1533	AA,AG,GG		29.7436,28.5227,43.8906	benign,benign	62/328,62/361	99337572	7283,5697	2200	4290	6490	SO:0001583	missense	26287	exon2			GGAGACGCACGCC	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.184G>A	10.37:g.99337572G>A	ENSP00000306163:p.Ala62Thr	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_001129981	Q3B778|Q5T456|Q70EZ9|Q8WUD7|Q96MG0|Q9NQC9	Missense_Mutation	SNP	ENST00000307518.5	37	CCDS7466.1	1079	0.49404761904761907	85	0.17276422764227642	232	0.6408839779005525	233	0.40734265734265734	529	0.6978891820580475	G	6.465	0.453901	0.12283	0.285227	0.702564	ENSG00000165887	ENST00000307518;ENST00000298808;ENST00000370655;ENST00000455090	T;T;T;T	0.50277	0.98;0.77;0.93;0.75	4.65	-7.86	0.01187	.	1.506750	0.03523	N	0.221279	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.33394	-0.9870	9	0.19147	T	0.46	0.7688	2.8043	0.05423	0.4552:0.1831:0.2615:0.1001	rs7094973;rs56731722;rs7094973	62;62	Q9GZV1-2;Q9GZV1	.;ANKR2_HUMAN	T	62;62;35;35	ENSP00000306163:A62T;ENSP00000298808:A62T;ENSP00000359689:A35T;ENSP00000403114:A35T	ENSP00000298808:A62T	A	+	1	0	ANKRD2	99327562	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-2.752000	0.00791	-1.293000	0.02362	0.561000	0.74099	GCA	G|0.516;A|0.484	0.484	strong		0.617	ANKRD2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CEP250	11190	hgsc.bcm.edu	37	20	34091624	34091624	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34091624G>A	ENST00000397527.1	+	30	6147	c.5427G>A	c.(5425-5427)caG>caA	p.Q1809Q	CEP250_ENST00000342580.4_Silent_p.Q1753Q	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1809	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)			ATGAGGCCCAGAGAGCCCTAG	0.597																																					p.Q1809Q		Atlas-SNP	.											.	CEP250	141	.	0			c.G5427A						PASS	.						55.0	59.0	58.0					20																	34091624		2203	4300	6503	SO:0001819	synonymous_variant	11190	exon30			GGCCCAGAGAGCC	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.5427G>A	20.37:g.34091624G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																			.	.	none		0.597	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
CWF19L1	55280	hgsc.bcm.edu	37	10	102016044	102016044	+	Missense_Mutation	SNP	C	C	T	rs2270962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102016044C>T	ENST00000354105.4	-	5	565	c.479G>A	c.(478-480)tGt>tAt	p.C160Y	CWF19L1_ENST00000478047.1_5'Flank|RNU6-422P_ENST00000384632.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	160			C -> Y (in dbSNP:rs2270962).				catalytic activity (GO:0003824)	p.C160Y(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		GTTCCCCACACACTTGGGCCA	0.423													T|||	1257	0.250998	0.5998	0.1311	5008	,	,		18538	0.1419		0.0775	False		,,,				2504	0.1554				p.C160Y		Atlas-SNP	.											CWF19L1,NS,carcinoma,0,1	CWF19L1	39	1	1	Substitution - Missense(1)	stomach(1)	c.G479A						PASS	.	T	TYR/CYS	2270,2136	579.1+/-384.8	590,1090,523	129.0	121.0	124.0		479	4.8	1.0	10	dbSNP_100	124	569,8031	793.7+/-407.5	19,531,3750	yes	missense	CWF19L1	NM_018294.4	194	609,1621,4273	TT,TC,CC		6.6163,48.4793,21.8284	benign	160/539	102016044	2839,10167	2203	4300	6503	SO:0001583	missense	55280	exon5			CCCACACACTTGG	AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.479G>A	10.37:g.102016044C>T	ENSP00000326411:p.Cys160Tyr	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	176	82	0.465909	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	37	CCDS7489.1	475	0.2174908424908425	277	0.5630081300813008	47	0.1298342541436464	84	0.14685314685314685	67	0.08839050131926121	T	11.57	1.677721	0.29783	0.515207	0.066163	ENSG00000095485	ENST00000354105	T	0.27402	1.67	6.16	4.85	0.62838	.	0.261247	0.44483	N	0.000453	T	0.00012	0.0000	N	0.01352	-0.895	0.52501	P	4.499999999996174E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39502	-0.9611	9	0.32370	T	0.25	-3.1421	9.637	0.39814	0.0:0.1624:0.0:0.8376	rs2270962;rs52822289;rs59268290;rs2270962	23;160	Q69YN2-3;Q69YN2	.;C19L1_HUMAN	Y	160	ENSP00000326411:C160Y	ENSP00000326411:C160Y	C	-	2	0	CWF19L1	102006034	0.996000	0.38824	0.998000	0.56505	0.940000	0.58332	1.883000	0.39658	1.152000	0.42452	-0.269000	0.10298	TGT	C|0.775;T|0.225	0.225	strong		0.423	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
B3GNT2	10678	hgsc.bcm.edu	37	2	62449664	62449664	+	Silent	SNP	G	G	A	rs72893877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:62449664G>A	ENST00000301998.4	+	2	561	c.309G>A	c.(307-309)acG>acA	p.T103T	B3GNT2_ENST00000405767.1_Silent_p.T103T	NM_006577.5	NP_006568.2	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	103					axon guidance (GO:0007411)|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)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)	18	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)			TGAGGGTCACGTCGGTGGTTA	0.502													G|||	22	0.00439297	0.0151	0.0029	5008	,	,		18758	0.0		0.0	False		,,,				2504	0.0				p.T103T		Atlas-SNP	.											.	B3GNT2	34	.	0			c.G309A						PASS	.	G		63,4343	56.2+/-92.4	0,63,2140	216.0	242.0	233.0		309	-11.5	0.0	2	dbSNP_130	233	0,8600		0,0,4300	no	coding-synonymous	B3GNT2	NM_006577.5		0,63,6440	AA,AG,GG		0.0,1.4299,0.4844		103/398	62449664	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	10678	exon2			GGTCACGTCGGTG	AB049584	CCDS1870.1	2p15	2013-02-19	2006-04-12	2006-04-12	ENSG00000170340	ENSG00000170340		"""Beta 3-glycosyltransferases"""	15629	protein-coding gene	gene with protein product		605581	"""UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1"""	B3GNT1		9892646, 11042166	Standard	NM_006577		Approved	B3GNT-2, BETA3GNT, B3GN-T2, B3GN-T1	uc002sbs.3	Q9NY97	OTTHUMG00000129444	ENST00000301998.4:c.309G>A	2.37:g.62449664G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	132	76	0.575758	NM_006577	Q54AC1|Q9NQQ9|Q9NQR0|Q9NUT9	Silent	SNP	ENST00000301998.4	37	CCDS1870.1																																																																																			G|0.996;A|0.004	0.004	strong		0.502	B3GNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251606.2	NM_006577	
ENAM	10117	hgsc.bcm.edu	37	4	71510368	71510368	+	Silent	SNP	C	C	T	rs61737041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71510368C>T	ENST00000396073.3	+	9	3506	c.3225C>T	c.(3223-3225)agC>agT	p.S1075S	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	1075					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CTCCATCTAGCGATGGAAGGC	0.433													C|||	40	0.00798722	0.0295	0.0014	5008	,	,		24126	0.0		0.0	False		,,,				2504	0.0				p.S1075S		Atlas-SNP	.											.	ENAM	140	.	0			c.C3225T						PASS	.	C		106,4300	82.4+/-120.9	2,102,2099	96.0	93.0	94.0		3225	4.2	1.0	4	dbSNP_129	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ENAM	NM_031889.2		2,103,6398	TT,TC,CC		0.0116,2.4058,0.8227		1075/1143	71510368	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	10117	exon9			ATCTAGCGATGGA	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.3225C>T	4.37:g.71510368C>T		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	266	127	0.477444	NM_031889	Q17RI5|Q9H3D1	Silent	SNP	ENST00000396073.3	37	CCDS3544.2																																																																																			C|0.993;T|0.007	0.007	strong		0.433	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889	
C17orf97	400566	hgsc.bcm.edu	37	17	263643	263643	+	Missense_Mutation	SNP	C	C	A	rs71369083|rs71145728		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:263643C>A	ENST00000360127.6	+	2	1025	c.1009C>A	c.(1009-1011)Ccc>Acc	p.P337T	C17orf97_ENST00000571106.1_Intron|AC108004.3_ENST00000466740.2_RNA	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	367	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.									breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						GGGCTTCCACCCCGACCCCGA	0.697																																					p.P337T		Atlas-SNP	.											C17orf97_ENST00000360127,NS,carcinoma,0,2	C17orf97	76	2	0			c.C1009A						scavenged	.																																			SO:0001583	missense	400566	exon2			TTCCACCCCGACC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.1009C>A	17.37:g.263643C>A	ENSP00000353245:p.Pro337Thr	Somatic	321	8	0.0249221		WXS	Illumina HiSeq	Phase_I	310	14	0.0451613	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Missense_Mutation	SNP	ENST00000360127.6	37	CCDS32519.2	.	.	.	.	.	.	.	.	.	.	c	0.001	-3.987809	0.00002	.	.	ENSG00000187624	ENST00000360127	T	0.31247	1.5	2.05	-4.1	0.03940	.	.	.	.	.	T	0.13329	0.0323	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35400	-0.9790	9	0.13853	T	0.58	.	10.5042	0.44823	0.1779:0.7067:0.1154:0.0	.	337	Q6ZQX7-4	.	T	337	ENSP00000353245:P337T	ENSP00000353245:P337T	P	+	1	0	C17orf97	263989	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.281000	0.00260	-5.715000	0.00010	-5.246000	0.00001	CCC	C|0.981;A|0.019	0.019	strong		0.697	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
DMKN	93099	hgsc.bcm.edu	37	19	36002488	36002488	+	Missense_Mutation	SNP	C	C	A	rs57760262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002488C>A	ENST00000339686.3	-	5	919	c.743G>T	c.(742-744)aGc>aTc	p.S248I	DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.S248I|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.S248I|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.S248I|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000424570.2_Missense_Mutation_p.S248I|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.S248I|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000414866.2_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	248	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CTGTGAGCCGCTGCCTCCCTG	0.637													C|||	173	0.0345447	0.1241	0.0101	5008	,	,		18431	0.0		0.002	False		,,,				2504	0.0				p.S248I		Atlas-SNP	.											DMKN,NS,carcinoma,+1,1	DMKN	116	1	0			c.G743T						PASS	.	C	ILE/SER,ILE/SER,ILE/SER,ILE/SER,ILE/SER,,	365,4041	183.6+/-211.2	14,337,1852	34.0	31.0	32.0		743,743,743,743,743,,	2.7	0.7	19	dbSNP_129	32	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense,missense,missense,intron,intron	DMKN	NM_001126057.2,NM_001126058.2,NM_001190348.1,NM_001190349.1,NM_033317.4,NM_001126056.2,NM_001190347.1	142,142,142,142,142,,	14,341,6148	AA,AC,CC		0.0465,8.2842,2.8372	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,	248/399,248/387,248/437,248/370,248/477,,	36002488	369,12637	2203	4300	6503	SO:0001583	missense	93099	exon5			GAGCCGCTGCCTC	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.743G>T	19.37:g.36002488C>A	ENSP00000342012:p.Ser248Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	62	0.028388278388278388	56	0.11382113821138211	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	13.09	2.132916	0.37630	0.082842	4.65E-4	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77	3.78	2.73	0.32206	.	0.880319	0.09618	N	0.777875	T	0.02012	0.0063	L	0.52573	1.65	0.24630	N	0.993629	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.997	D;D;D;D;P	0.69479	0.964;0.964;0.964;0.964;0.899	T	0.01078	-1.1459	10	0.72032	D	0.01	-3.8258	7.2516	0.26152	0.0:0.8755:0.0:0.1245	rs57760262	248;248;248;248;248	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	I	248	ENSP00000342012:S248I;ENSP00000394908:S248I;ENSP00000415277:S248I;ENSP00000414743:S248I;ENSP00000388404:S248I;ENSP00000409513:S248I	ENSP00000342012:S248I	S	-	2	0	DMKN	40694328	0.006000	0.16342	0.659000	0.29680	0.091000	0.18340	0.717000	0.25851	0.948000	0.37687	0.561000	0.74099	AGC	C|0.967;A|0.033	0.033	strong		0.637	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
TMEM232	642987	hgsc.bcm.edu	37	5	109961032	109961032	+	Missense_Mutation	SNP	C	C	T	rs61730863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:109961032C>T	ENST00000455884.2	-	7	754	c.704G>A	c.(703-705)cGt>cAt	p.R235H	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Missense_Mutation_p.R235H			C9JQI7	TM232_HUMAN	transmembrane protein 232	235						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						GGATTCAGAACGGAGTTCTCT	0.378													C|||	149	0.0297524	0.1104	0.0029	5008	,	,		17282	0.0		0.001	False		,,,				2504	0.0				p.R235H		Atlas-SNP	.											.	TMEM232	57	.	0			c.G704A						PASS	.	C	HIS/ARG	111,1273		6,99,587	227.0	195.0	204.0		704	-9.4	0.0	5	dbSNP_129	204	0,3182		0,0,1591	yes	missense	TMEM232	NM_001039763.3	29	6,99,2178	TT,TC,CC		0.0,8.0202,2.431	benign	235/658	109961032	111,4455	692	1591	2283	SO:0001583	missense	642987	exon7			TCAGAACGGAGTT	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.704G>A	5.37:g.109961032C>T	ENSP00000401477:p.Arg235His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	168	89	0.529762	NM_001039763	B4DKF4	Missense_Mutation	SNP	ENST00000455884.2	37	CCDS47253.2	50	0.022893772893772892	49	0.09959349593495935	1	0.0027624309392265192	0	0.0	0	0.0	C	9.585	1.124637	0.20959	0.080202	0.0	ENSG00000186952	ENST00000429839;ENST00000455884;ENST00000511883	.	.	.	4.72	-9.44	0.00603	.	1.502430	0.03762	N	0.258267	T	0.00356	0.0011	N	0.05383	-0.06	0.09310	N	1	B;B;B	0.12630	0.006;0.002;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.06338	-1.0832	8	.	.	.	4.4953	4.058	0.09826	0.1922:0.274:0.4192:0.1145	.	235;235;117	C9JQI7;C9JQI7-2;E9PFK0	TM232_HUMAN;.;.	H	235	.	.	R	-	2	0	TMEM232	109988931	0.000000	0.05858	0.000000	0.03702	0.099000	0.18886	-2.983000	0.00661	-2.769000	0.00366	-0.340000	0.08031	CGT	C|0.975;T|0.025	0.025	strong		0.378	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316870	39316870	+	Missense_Mutation	SNP	T	T	C	rs385055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39316870T>C	ENST00000390661.3	-	1	113	c.74A>G	c.(73-75)tAc>tGc	p.Y25C		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	25	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		Y -> C (in dbSNP:rs385055).			keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GGTCTGGCAGTAGCTGGGACG	0.637													C|||	641	0.127995	0.466	0.0331	5008	,	,		19142	0.0		0.002	False		,,,				2504	0.0				p.Y25C		Atlas-SNP	.											KRTAP4-4,NS,carcinoma,-1,1	KRTAP4-4	21	1	0			c.A74G						PASS	.	C	CYS/TYR	1640,2760		330,980,890	50.0	68.0	62.0		74	4.6	0.9	17	dbSNP_80	62	10,8590		0,10,4290	no	missense	KRTAP4-4	NM_032524.1	194	330,990,5180	CC,CT,TT		0.1163,37.2727,12.6923	benign	25/167	39316870	1650,11350	2200	4300	6500	SO:0001583	missense	84616	exon1			TGGCAGTAGCTGG	AJ406936	CCDS11383.1	17q21.2	2013-06-25			ENSG00000171396	ENSG00000171396		"""Keratin associated proteins"""	16928	protein-coding gene	gene with protein product			"""keratin associated protein 4-13"""	KRTAP4-13		11279113	Standard	NM_032524		Approved	KAP4.4, KAP4.13	uc002hwc.3	Q9BYR3	OTTHUMG00000133428	ENST00000390661.3:c.74A>G	17.37:g.39316870T>C	ENSP00000375076:p.Tyr25Cys	Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_032524	Q9BYU7	Missense_Mutation	SNP	ENST00000390661.3	37	CCDS11383.1	231	0.10576923076923077	218	0.44308943089430897	13	0.03591160220994475	0	0.0	0	0.0	.	0.052	-1.247813	0.01469	0.372727	0.001163	ENSG00000171396	ENST00000390661	T	0.00571	6.5	4.62	4.62	0.57501	.	0.157197	0.29868	N	0.010999	T	0.00012	0.0000	N	0.00005	-3.295	0.42889	P	0.005808000000000035	B	0.02656	0.0	B	0.01281	0.0	T	0.19647	-1.0299	9	0.02654	T	1	.	10.7732	0.46336	0.0:0.9051:0.0:0.0949	rs385055;rs59740078	25	Q9BYR3	KRA44_HUMAN	C	25	ENSP00000375076:Y25C	ENSP00000375076:Y25C	Y	-	2	0	KRTAP4-4	36570396	0.010000	0.17322	0.851000	0.33527	0.345000	0.29048	0.694000	0.25512	0.943000	0.37553	-0.227000	0.12334	TAC	T|0.890;C|0.110	0.110	strong		0.637	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1		
ALMS1	7840	hgsc.bcm.edu	37	2	73717103	73717103	+	Missense_Mutation	SNP	G	G	C	rs2017116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73717103G>C	ENST00000264448.6	+	10	8125	c.8014G>C	c.(8014-8016)Gat>Cat	p.D2672H	ALMS1_ENST00000409009.1_Missense_Mutation_p.D2630H|AC096546.1_ENST00000408160.1_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2672			D -> H (in dbSNP:rs2017116). {ECO:0000269|PubMed:15489334}.		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						AATGCCATTCGATGAAAAGAT	0.393													C|||	681	0.135982	0.1135	0.0663	5008	,	,		20771	0.2034		0.1262	False		,,,				2504	0.1564				p.D2672H		Atlas-SNP	.											.	ALMS1	384	.	0			c.G8014C						PASS	.	C	HIS/ASP	451,3261		27,397,1432	144.0	134.0	137.0		8014	2.6	0.0	2	dbSNP_92	137	1081,7089		67,947,3071	yes	missense	ALMS1	NM_015120.4	81	94,1344,4503	CC,CG,GG		13.2313,12.1498,12.8935	benign	2672/4168	73717103	1532,10350	1856	4085	5941	SO:0001583	missense	7840	exon10			CCATTCGATGAAA	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.8014G>C	2.37:g.73717103G>C	ENSP00000264448:p.Asp2672His	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	129	72	0.55814	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	320	0.14652014652014653	56	0.11382113821138211	30	0.08287292817679558	134	0.23426573426573427	100	0.13192612137203166	C	0.011	-1.711987	0.00712	0.121498	0.132313	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.05580	3.42;3.42	4.45	2.64	0.31445	.	0.412634	0.21037	N	0.081226	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	0.45086	-0.9285	9	0.02654	T	1	.	6.5992	0.22691	0.0:0.5521:0.3527:0.0952	rs2017116;rs3738849;rs17349615;rs17846124;rs17848862;rs17859129;rs17859507;rs52812860;rs2017116	2672;2630;2672	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	H	2630;2672	ENSP00000386627:D2630H;ENSP00000264448:D2672H	ENSP00000264448:D2672H	D	+	1	0	ALMS1	73570611	0.002000	0.14202	0.049000	0.19019	0.916000	0.54674	0.444000	0.21661	0.383000	0.24910	-0.127000	0.14921	GAT	G|0.852;C|0.148	0.148	strong		0.393	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
OR1N2	138882	hgsc.bcm.edu	37	9	125315778	125315778	+	Silent	SNP	G	G	C	rs1411271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125315778G>C	ENST00000373688.2	+	1	388	c.330G>C	c.(328-330)tcG>tcC	p.S110S		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						AGATCATCTCGTATTCTGGGT	0.483													C|||	2802	0.559505	0.5953	0.5908	5008	,	,		25005	0.6677		0.4791	False		,,,				2504	0.4601				p.S110S		Atlas-SNP	.											.	OR1N2	51	.	0			c.G330C						PASS	.	C		2529,1877	541.3+/-375.7	715,1099,389	232.0	227.0	229.0		330	3.5	1.0	9	dbSNP_88	229	4211,4389	583.4+/-391.5	1011,2189,1100	no	coding-synonymous	OR1N2	NM_001004457.1		1726,3288,1489	CC,CG,GG		48.9651,42.601,48.1778		110/331	125315778	6740,6266	2203	4300	6503	SO:0001819	synonymous_variant	138882	exon1			CATCTCGTATTCT		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.330G>C	9.37:g.125315778G>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	174	64	0.367816	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Silent	SNP	ENST00000373688.2	37	CCDS35123.1																																																																																			G|0.468;C|0.532	0.532	strong		0.483	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
SLC26A10	65012	hgsc.bcm.edu	37	12	58019388	58019388	+	Missense_Mutation	SNP	C	C	T	rs114079678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:58019388C>T	ENST00000320442.4	+	14	1863	c.1552C>T	c.(1552-1554)Cgg>Tgg	p.R518W	SLC26A10_ENST00000490243.1_Intron|SLC26A10_ENST00000379218.2_3'UTR	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	518	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.					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)					GACACTGACCCGGGTAGGACT	0.587													C|||	6	0.00119808	0.0045	0.0	5008	,	,		19242	0.0		0.0	False		,,,				2504	0.0				p.R518W		Atlas-SNP	.											.	SLC26A10	89	.	0			c.C1552T						PASS	.	C	TRP/ARG	21,4385		0,21,2182	63.0	58.0	60.0		1552	1.2	0.8	12	dbSNP_133	60	1,8599		0,1,4299	yes	missense	SLC26A10	NM_133489.2	101	0,22,6481	TT,TC,CC		0.0116,0.4766,0.1692	probably-damaging	518/564	58019388	22,12984	2203	4300	6503	SO:0001583	missense	65012	exon14			CTGACCCGGGTAG		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.1552C>T	12.37:g.58019388C>T	ENSP00000320217:p.Arg518Trp	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Missense_Mutation	SNP	ENST00000320442.4	37	CCDS8949.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	9.455	1.091629	0.20471	0.004766	1.16E-4	ENSG00000135502	ENST00000320442	D	0.89343	-2.5	4.62	1.25	0.21368	Sulphate transporter/antisigma-factor antagonist STAS (4);	.	.	.	.	T	0.81531	0.4842	L	0.56199	1.76	0.41713	D	0.989468	B	0.27316	0.175	B	0.14023	0.01	T	0.76225	-0.3037	9	0.87932	D	0	.	1.6978	0.02866	0.2061:0.4624:0.1995:0.132	.	518	Q8NG04	S2610_HUMAN	W	518	ENSP00000320217:R518W	ENSP00000320217:R518W	R	+	1	2	SLC26A10	56305655	0.903000	0.30736	0.796000	0.32109	0.255000	0.26057	0.125000	0.15749	0.554000	0.29061	0.557000	0.71058	CGG	C|0.999;T|0.001	0.001	strong		0.587	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2		
ITPKC	80271	hgsc.bcm.edu	37	19	41223387	41223387	+	Missense_Mutation	SNP	A	A	T	rs145275994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41223387A>T	ENST00000263370.2	+	1	380	c.347A>T	c.(346-348)gAc>gTc	p.D116V	ADCK4_ENST00000243583.6_5'Flank|ADCK4_ENST00000324464.3_5'Flank|ADCK4_ENST00000450541.1_5'Flank	NM_025194.2	NP_079470.1	Q96DU7	IP3KC_HUMAN	inositol-trisphosphate 3-kinase C	116					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)			ACGGAGCCAGACAGGTCCAGC	0.602													A|||	17	0.00339457	0.0121	0.0014	5008	,	,		13975	0.0		0.0	False		,,,				2504	0.0				p.D116V		Atlas-SNP	.											.	ITPKC	36	.	0			c.A347T						PASS	.	A	VAL/ASP	41,4363	43.1+/-76.7	0,41,2161	52.0	59.0	57.0		347	1.9	0.0	19	dbSNP_134	57	0,8600		0,0,4300	yes	missense	ITPKC	NM_025194.2	152	0,41,6461	TT,TA,AA		0.0,0.931,0.3153	benign	116/684	41223387	41,12963	2202	4300	6502	SO:0001583	missense	80271	exon1			AGCCAGACAGGTC	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.347A>T	19.37:g.41223387A>T	ENSP00000263370:p.Asp116Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_025194	Q9UE25|Q9Y475	Missense_Mutation	SNP	ENST00000263370.2	37	CCDS12563.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	A	2.482	-0.319454	0.05386	0.00931	0.0	ENSG00000086544	ENST00000263370	.	.	.	4.07	1.93	0.25924	.	0.659632	0.13336	N	0.395559	T	0.17789	0.0427	N	0.19112	0.55	0.19775	N	0.999958	B	0.17667	0.023	B	0.15870	0.014	T	0.17107	-1.0380	9	0.27785	T	0.31	-3.0482	6.4104	0.21688	0.7762:0.0:0.2238:0.0	.	116	Q96DU7	IP3KC_HUMAN	V	116	.	ENSP00000263370:D116V	D	+	2	0	ITPKC	45915227	0.122000	0.22280	0.001000	0.08648	0.323000	0.28346	0.708000	0.25719	0.248000	0.21435	0.397000	0.26171	GAC	A|0.997;T|0.003	0.003	strong		0.602	ITPKC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463104.1	NM_025194	
SCLY	51540	hgsc.bcm.edu	37	2	239006879	239006879	+	Silent	SNP	C	C	T	rs12993309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239006879C>T	ENST00000555827.1	+	12	1285	c.1221C>T	c.(1219-1221)ttC>ttT	p.F407F	SCLY_ENST00000429612.2_Silent_p.F201F|SCLY_ENST00000422984.2_Silent_p.F313F|SCLY_ENST00000254663.6_Silent_p.F415F|ESPNL_ENST00000409169.1_5'Flank|ESPNL_ENST00000343063.3_5'Flank			Q96I15	SCLY_HUMAN	selenocysteine lyase	407					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		GTGTCCCCTTCGACGTGGCCA	0.706													C|||	1231	0.245807	0.2337	0.2161	5008	,	,		15225	0.2341		0.1968	False		,,,				2504	0.3456				p.F415F	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	Atlas-SNP	.											SCLY,NS,carcinoma,0,2	SCLY	51	2	0			c.C1245T						PASS	.	C		1169,3237	388.9+/-327.1	157,855,1191	36.0	35.0	35.0		1245	-6.8	0.0	2	dbSNP_121	35	1661,6937	287.4+/-298.2	156,1349,2794	no	coding-synonymous	SCLY	NM_016510.5		313,2204,3985	TT,TC,CC		19.3184,26.532,21.7625		415/454	239006879	2830,10174	2203	4299	6502	SO:0001819	synonymous_variant	51540	exon12			CCCCTTCGACGTG	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.1221C>T	2.37:g.239006879C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Silent	SNP	ENST00000555827.1	37																																																																																				C|0.785;T|0.215	0.215	strong		0.706	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
FRMD6	122786	hgsc.bcm.edu	37	14	52182081	52182081	+	Silent	SNP	T	T	A	rs731715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:52182081T>A	ENST00000344768.5	+	10	1084	c.888T>A	c.(886-888)tcT>tcA	p.S296S	FRMD6_ENST00000356218.4_Silent_p.S288S|FRMD6_ENST00000395718.2_Silent_p.S288S|FRMD6_ENST00000554167.1_Silent_p.S219S|FRMD6_ENST00000553556.1_5'Flank			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	296	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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)					GCTTGCCTTCTGCCCGGAAGC	0.488													A|||	3353	0.669529	0.6899	0.6888	5008	,	,		16553	0.628		0.7187	False		,,,				2504	0.6207				p.S296S		Atlas-SNP	.											FRMD6,NS,carcinoma,+1,1	FRMD6	100	1	0			c.T888A						PASS	.	A	,	3028,1378	457.6+/-351.7	1045,938,220	58.0	61.0	60.0		864,864	-11.9	0.2	14	dbSNP_86	60	6086,2514	412.1+/-350.7	2156,1774,370	no	coding-synonymous,coding-synonymous	FRMD6	NM_001042481.1,NM_152330.3	,	3201,2712,590	AA,AT,TT		29.2326,31.2755,29.9247	,	288/615,288/615	52182081	9114,3892	2203	4300	6503	SO:0001819	synonymous_variant	122786	exon10			GCCTTCTGCCCGG	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.888T>A	14.37:g.52182081T>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_001267046	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Silent	SNP	ENST00000344768.5	37	CCDS58318.1																																																																																			T|0.309;A|0.691	0.691	strong		0.488	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330	
EMC1	23065	hgsc.bcm.edu	37	1	19549250	19549250	+	Missense_Mutation	SNP	C	C	T	rs371524055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19549250C>T	ENST00000477853.1	-	20	2497	c.2455G>A	c.(2455-2457)Gcc>Acc	p.A819T	RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000480380.1_5'Flank|EMC1_ENST00000375208.3_Missense_Mutation_p.A797T|EMC1_ENST00000375199.3_Missense_Mutation_p.A818T	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	819						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											AAGGCGGTGGCGTTGTATTGC	0.602													C|||	4	0.000798722	0.003	0.0	5008	,	,		18529	0.0		0.0	False		,,,				2504	0.0				p.A819T		Atlas-SNP	.											.	.	.	.	0			c.G2455A						PASS	.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	121.0	107.0	111.0		2455	6.0	1.0	1		111	0,8600		0,0,4300	no	missense	KIAA0090	NM_015047.1	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	819/994	19549250	1,13005	2203	4300	6503	SO:0001583	missense	23065	exon20			CGGTGGCGTTGTA		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.2455G>A	1.37:g.19549250C>T	ENSP00000420608:p.Ala819Thr	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	199	105	0.527638	NM_015047	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	37	CCDS190.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.93|14.93	2.680976|2.680976	0.47886|0.47886	2.27E-4|2.27E-4	0.0|0.0	ENSG00000127463|ENSG00000127463	ENST00000477853;ENST00000375199;ENST00000375208;ENST00000486405|ENST00000375197	T;T;T|.	0.24723|.	1.84;1.84;1.84|.	5.98|5.98	5.98|5.98	0.97165|0.97165	Domain of unknown function DUF1620 (1);|.	0.085825|.	0.85682|.	D|.	0.000000|.	T|T	0.51856|0.51856	0.1699|0.1699	N|N	0.26092|0.26092	0.79|0.79	0.80722|0.80722	D|D	1|1	B;B;P;P|.	0.39520|.	0.334;0.101;0.625;0.676|.	B;B;B;B|.	0.32289|.	0.063;0.063;0.088;0.143|.	T|T	0.45160|0.45160	-0.9280|-0.9280	10|5	0.21014|.	T|.	0.42|.	-26.1445|-26.1445	12.3448|12.3448	0.55114|0.55114	0.0:0.9228:0.0:0.0772|0.0:0.9228:0.0:0.0772	.|.	797;818;818;819|.	Q8N766-4;Q8N766-2;Q8N766-3;Q8N766|.	.;.;.;K0090_HUMAN|.	T|H	819;818;797;64|552	ENSP00000420608:A819T;ENSP00000364345:A818T;ENSP00000364354:A797T|.	ENSP00000364345:A818T|.	A|R	-|-	1|2	0|0	KIAA0090|KIAA0090	19421837|19421837	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.732000|0.732000	0.41865|0.41865	5.405000|5.405000	0.66351|0.66351	2.838000|2.838000	0.97847|0.97847	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.	none		0.602	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412009	105412009	+	Missense_Mutation	SNP	A	A	G	rs28714612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105412009A>G	ENST00000333244.5	-	7	9898	c.9779T>C	c.(9778-9780)aTg>aCg	p.M3260T	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3260						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)			CGTCACATCCATCTTCGGGCC	0.617													.|||	1929	0.385184	0.3896	0.389	5008	,	,		16305	0.1905		0.496	False		,,,				2504	0.4632				p.M3260T		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,neuroblastoma,0,2	AHNAK2	719	2	0			c.T9779C						PASS	.						100.0	73.0	82.0					14																	105412009		1854	4017	5871	SO:0001583	missense	113146	exon7			ACATCCATCTTCG	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.9779T>C	14.37:g.105412009A>G	ENSP00000353114:p.Met3260Thr	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	324	69	0.212963	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	1.452	-0.564730	0.03939	.	.	ENSG00000185567	ENST00000333244	T	0.00892	5.57	3.09	-4.72	0.03269	.	.	.	.	.	T	0.00580	0.0019	N	0.16368	0.405	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.45542	-0.9254	8	0.14252	T	0.57	.	3.5943	0.08000	0.4733:0.1389:0.3022:0.0856	rs28714612	3260	Q8IVF2	AHNK2_HUMAN	T	3260	ENSP00000353114:M3260T	ENSP00000353114:M3260T	M	-	2	0	AHNAK2	104483054	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	1.604000	0.36804	-1.025000	0.03334	-3.622000	0.00027	ATG	A|0.454;G|0.546	0.546	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OR52L1	338751	hgsc.bcm.edu	37	11	6007992	6007992	+	Silent	SNP	A	A	G	rs115266467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6007992A>G	ENST00000332249.4	-	1	223	c.169T>C	c.(169-171)Tta>Cta	p.L57L		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, 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)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGCCCACTAAAGCAAGGAGG	0.512													.|||	116	0.0231629	0.0809	0.013	5008	,	,		22867	0.0		0.0	False		,,,				2504	0.0				p.L57L	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											.	OR52L1	100	.	0			c.T169C						PASS	.	G		204,3818		9,186,1816	75.0	75.0	75.0		169	0.5	0.9	11	dbSNP_132	75	6,8360		0,6,4177	no	coding-synonymous	OR52L1	NM_001005173.2		9,192,5993	GG,GA,AA		0.0717,5.0721,1.6952		57/330	6007992	210,12178	2011	4183	6194	SO:0001819	synonymous_variant	338751	exon1			CCACTAAAGCAAG	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"""GPCR / Class A : Olfactory receptors"""	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.169T>C	11.37:g.6007992A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	163	74	0.453988	NM_001005173	B2RPA6|Q6IFK9	Silent	SNP	ENST00000332249.4	37	CCDS44529.1																																																																																			A|0.989;G|0.011	0.011	strong		0.512	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173	
PCDHB16	57717	hgsc.bcm.edu	37	5	140563550	140563550	+	Silent	SNP	C	C	T	rs56237941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140563550C>T	ENST00000361016.2	+	1	2571	c.1416C>T	c.(1414-1416)agC>agT	p.S472S		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	472	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)	p.S472S(1)		breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACATCGGCAGCGTCAGCGCCA	0.627													c|||	59	0.0117812	0.0439	0.0014	5008	,	,		13762	0.0		0.0	False		,,,				2504	0.0				p.S472S		Atlas-SNP	.											PCDHB16,NS,carcinoma,0,1	PCDHB16	159	1	1	Substitution - coding silent(1)	prostate(1)	c.C1416T						PASS	.	T		152,4254	99.4+/-138.0	3,146,2054	73.0	70.0	71.0		1416	0.4	0.9	5	dbSNP_129	71	1,8591		0,1,4295	no	coding-synonymous	PCDHB16	NM_020957.1		3,147,6349	TT,TC,CC		0.0116,3.4498,1.1771		472/777	140563550	153,12845	2203	4296	6499	SO:0001819	synonymous_variant	57717	exon1			CGGCAGCGTCAGC	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1416C>T	5.37:g.140563550C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	114	70	0.614035	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Silent	SNP	ENST00000361016.2	37	CCDS4251.1																																																																																			C|0.992;T|0.008	0.008	strong		0.627	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
SLC25A42	284439	hgsc.bcm.edu	37	19	19217081	19217081	+	Silent	SNP	C	C	A	rs61740506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19217081C>A	ENST00000318596.7	+	6	535	c.384C>A	c.(382-384)gcC>gcA	p.A128A	SLC25A42_ENST00000600275.1_3'UTR	NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	128					ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|coenzyme A transmembrane transport (GO:0035349)|metabolic process (GO:0008152)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	adenosine-diphosphatase activity (GO:0043262)|ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|coenzyme A transmembrane transporter activity (GO:0015228)			cervix(1)|large_intestine(2)|lung(3)	6			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)			TGTTCAGAGCCCTGCCCCCTT	0.682													C|||	113	0.0225639	0.0749	0.0072	5008	,	,		14862	0.0		0.005	False		,,,				2504	0.0041				p.A128A		Atlas-SNP	.											.	SLC25A42	18	.	0			c.C384A						PASS	.	C		360,4046	184.0+/-211.4	12,336,1855	80.0	85.0	83.0		384	0.3	1.0	19	dbSNP_129	83	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous	SLC25A42	NM_178526.3		12,370,6121	AA,AC,CC		0.3953,8.1707,3.0294		128/319	19217081	394,12612	2203	4300	6503	SO:0001819	synonymous_variant	284439	exon6			CAGAGCCCTGCCC		CCDS32966.1	19p13.11	2013-05-22			ENSG00000181035	ENSG00000181035		"""Solute carriers"""	28380	protein-coding gene	gene with protein product		610823				16949250, 19429682	Standard	NM_178526		Approved	MGC26694	uc002nlf.3	Q86VD7		ENST00000318596.7:c.384C>A	19.37:g.19217081C>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_178526	D2T2J5|O14553|O43378	Silent	SNP	ENST00000318596.7	37	CCDS32966.1																																																																																			C|0.976;A|0.024	0.024	strong		0.682	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526	
ZBTB38	253461	hgsc.bcm.edu	37	3	141163705	141163705	+	Silent	SNP	G	G	A	rs3732868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141163705G>A	ENST00000514251.1	+	4	2754	c.2475G>A	c.(2473-2475)ccG>ccA	p.P825P	ZBTB38_ENST00000321464.5_Silent_p.P826P|ZBTB38_ENST00000441582.2_Silent_p.P825P					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						CTGCTCTGCCGGGAACCTCCA	0.408													G|||	119	0.023762	0.0461	0.0014	5008	,	,		21124	0.0298		0.003	False		,,,				2504	0.0245				p.P825P		Atlas-SNP	.											.	ZBTB38	92	.	0			c.G2475A						PASS	.	G		187,3519		7,173,1673	61.0	58.0	59.0		2475	-11.1	0.0	3	dbSNP_107	59	23,8155		0,23,4066	no	coding-synonymous	ZBTB38	NM_001080412.2		7,196,5739	AA,AG,GG		0.2812,5.0459,1.7671		825/1196	141163705	210,11674	1853	4089	5942	SO:0001819	synonymous_variant	253461	exon8			TCTGCCGGGAACC	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.2475G>A	3.37:g.141163705G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_001080412		Silent	SNP	ENST00000514251.1	37	CCDS43157.1																																																																																			G|0.980;A|0.020	0.020	strong		0.408	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
PI4KA	5297	hgsc.bcm.edu	37	22	21064203	21064203	+	Missense_Mutation	SNP	G	G	A	rs535848772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	742	6	0.00808625		WXS	Illumina HiSeq	Phase_I	757	10	0.01321	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	
CD109	135228	hgsc.bcm.edu	37	6	74524724	74524724	+	Silent	SNP	G	G	A	rs59555720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74524724G>A	ENST00000287097.5	+	30	3901	c.3789G>A	c.(3787-3789)gtG>gtA	p.V1263V	CD109_ENST00000437994.2_Silent_p.V1246V|CD109_ENST00000422508.2_Silent_p.V1186V			Q6YHK3	CD109_HUMAN	CD109 molecule	1263					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						TATATAATGTGAAGGCTTCTG	0.308													G|||	132	0.0263578	0.0953	0.0086	5008	,	,		15195	0.0		0.0	False		,,,				2504	0.0				p.V1263V		Atlas-SNP	.											.	CD109	170	.	0			c.G3789A						PASS	.	G	,,	321,4085	168.7+/-199.5	13,295,1895	80.0	87.0	84.0		3738,3558,3789	5.4	1.0	6	dbSNP_129	84	5,8593	4.3+/-15.6	0,5,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	,,	13,300,6189	AA,AG,GG		0.0582,7.2855,2.5069	,,	1246/1429,1186/1369,1263/1446	74524724	326,12678	2203	4299	6502	SO:0001819	synonymous_variant	135228	exon30			TAATGTGAAGGCT	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.3789G>A	6.37:g.74524724G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																			G|0.971;A|0.029	0.029	strong		0.308	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
LMNB2	84823	hgsc.bcm.edu	37	19	2432450	2432450	+	Silent	SNP	C	C	G	rs11882908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2432450C>G	ENST00000582871.1	-	9	1580	c.1494G>C	c.(1492-1494)acG>acC	p.T498T	LMNB2_ENST00000475819.1_5'Flank|LMNB2_ENST00000325327.3_Silent_p.T518T	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	498	LTD.|Tail.					lamin filament (GO:0005638)|nuclear inner membrane (GO:0005637)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		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)		TGTACTTGGGCGTGAACTTGT	0.632													C|||	143	0.0285543	0.1059	0.0043	5008	,	,		14898	0.0		0.0	False		,,,				2504	0.0				p.T518T		Atlas-SNP	.											LMNB2,NS,carcinoma,0,2	LMNB2	40	2	0			c.G1554C						scavenged	.	C		491,3915	228.5+/-243.3	26,439,1738	300.0	225.0	250.0		1494	-8.2	0.9	19	dbSNP_120	250	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	LMNB2	NM_032737.2		26,442,6035	GG,GC,CC		0.0349,11.1439,3.7982		498/601	2432450	494,12512	2203	4300	6503	SO:0001819	synonymous_variant	84823	exon9			CTTGGGCGTGAAC	M94362	CCDS12090.1, CCDS12090.2	19p13.3	2013-01-16			ENSG00000176619	ENSG00000176619		"""Intermediate filaments type V, lamins"""	6638	protein-coding gene	gene with protein product		150341		LMN2		1630457	Standard	NM_032737		Approved		uc002lvy.4	Q03252	OTTHUMG00000150626	ENST00000582871.1:c.1494G>C	19.37:g.2432450C>G		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_032737	O75292|Q14734|Q96DF6	Silent	SNP	ENST00000582871.1	37																																																																																				C|0.960;G|0.040	0.040	strong		0.632	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737	
NFIA	4774	hgsc.bcm.edu	37	1	61869783	61869783	+	Silent	SNP	G	G	A	rs2236059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:61869783G>A	ENST00000403491.3	+	8	1567	c.1083G>A	c.(1081-1083)ccG>ccA	p.P361P	NFIA_ENST00000371187.3_Silent_p.P361P|NFIA_ENST00000357977.5_Silent_p.P9P|NFIA_ENST00000371185.2_Silent_p.P339P|NFIA_ENST00000407417.3_Silent_p.P353P|NFIA_ENST00000371189.4_Silent_p.P406P|NFIA_ENST00000371184.2_Silent_p.P232P|NFIA_ENST00000371191.1_Silent_p.P384P|NFIA_ENST00000479364.1_3'UTR|NFIA_ENST00000485903.2_Silent_p.P318P	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	361					DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						CAGCAAGTCCGCATGCAACAC	0.483													G|||	1772	0.353834	0.289	0.3761	5008	,	,		19329	0.5625		0.2853	False		,,,				2504	0.2812				p.P406P		Atlas-SNP	.											.	NFIA	76	.	0			c.G1218A						PASS	.	G	,,,	1259,3147	433.3+/-343.5	179,901,1123	175.0	160.0	165.0		1083,1059,1218,1083	-10.5	0.6	1	dbSNP_98	165	2299,6301	387.1+/-342.1	331,1637,2332	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFIA	NM_001134673.3,NM_001145511.1,NM_001145512.1,NM_005595.4	,,,	510,2538,3455	AA,AG,GG		26.7326,28.5747,27.3566	,,,	361/510,353/502,406/555,361/499	61869783	3558,9448	2203	4300	6503	SO:0001819	synonymous_variant	4774	exon9			AAGTCCGCATGCA	U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599			7784	protein-coding gene	gene with protein product		600727				7590749	Standard	NM_001134673		Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.1083G>A	1.37:g.61869783G>A		Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	289	142	0.491349	NM_001145512	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	Silent	SNP	ENST00000403491.3	37	CCDS44156.1																																																																																			G|0.699;A|0.301	0.301	strong		0.483	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023799.3	NM_005595	
CCDC158	339965	hgsc.bcm.edu	37	4	77288833	77288833	+	Missense_Mutation	SNP	C	C	T	rs17001824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77288833C>T	ENST00000388914.3	-	11	1596	c.1444G>A	c.(1444-1446)Gaa>Aaa	p.E482K		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	482										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						GTCAACTCTTCTACTACTTTG	0.453													C|||	103	0.0205671	0.0734	0.0086	5008	,	,		19288	0.0		0.0	False		,,,				2504	0.0				p.E482K		Atlas-SNP	.											.	CCDC158	114	.	0			c.G1444A						PASS	.	C	LYS/GLU	235,3573		12,211,1681	72.0	70.0	70.0		1444	5.7	1.0	4	dbSNP_123	70	8,8232		1,6,4113	yes	missense	CCDC158	NM_001042784.1	56	13,217,5794	TT,TC,CC		0.0971,6.1712,2.0169	possibly-damaging	482/1114	77288833	243,11805	1904	4120	6024	SO:0001583	missense	339965	exon11			ACTCTTCTACTAC	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.1444G>A	4.37:g.77288833C>T	ENSP00000373566:p.Glu482Lys	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	37	CCDS43242.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	C	26.5	4.747697	0.89663	0.061712	9.71E-4	ENSG00000163749	ENST00000388914	T	0.78364	-1.17	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000019	T	0.36826	0.0981	N	0.19112	0.55	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.66077	-0.6013	9	.	.	.	.	17.6416	0.88138	0.0:1.0:0.0:0.0	rs17001824;rs17001824	482	Q5M9N0	CD158_HUMAN	K	482	ENSP00000373566:E482K	.	E	-	1	0	CCDC158	77507857	0.999000	0.42202	0.963000	0.40424	0.995000	0.86356	5.178000	0.65037	2.711000	0.92665	0.563000	0.77884	GAA	C|0.981;T|0.019	0.019	strong		0.453	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
PCDHB7	56129	hgsc.bcm.edu	37	5	140553919	140553919	+	Silent	SNP	C	C	A	rs17844456|rs386692906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140553919C>A	ENST00000231137.3	+	1	1677	c.1503C>A	c.(1501-1503)gcC>gcA	p.A501A		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	501	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(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)			TGCCCCTCGCCTCCCTGGTCT	0.672													C|||	759	0.151558	0.2572	0.1902	5008	,	,		16995	0.0417		0.1531	False		,,,				2504	0.093				p.A501A		Atlas-SNP	.											.	PCDHB7	231	.	0			c.C1503A						PASS	.	C		1021,3385	360.1+/-315.1	113,795,1295	86.0	89.0	88.0		1503	3.5	0.0	5	dbSNP_123	88	1409,7191	257.0+/-281.3	121,1167,3012	no	coding-synonymous	PCDHB7	NM_018940.2		234,1962,4307	AA,AC,CC		16.3837,23.1729,18.6837		501/794	140553919	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	56129	exon1			CCTCGCCTCCCTG	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.1503C>A	5.37:g.140553919C>A		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	273	116	0.424908	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			C|0.826;A|0.174	0.174	strong		0.672	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
KIAA0020	9933	hgsc.bcm.edu	37	9	2837218	2837218	+	Missense_Mutation	SNP	T	T	C	rs112185565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2837218T>C	ENST00000397885.2	-	3	472	c.266A>G	c.(265-267)aAc>aGc	p.N89S		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	89						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)		TCTCTTCTTGTTGAATTTATT	0.433													T|||	2	0.000399361	0.0015	0.0	5008	,	,		18588	0.0		0.0	False		,,,				2504	0.0				p.N89S		Atlas-SNP	.											.	KIAA0020	56	.	0			c.A266G						PASS	.	T	SER/ASN	6,3742		0,6,1868	226.0	222.0	223.0		266	-3.1	0.8	9	dbSNP_132	223	0,8196		0,0,4098	yes	missense	KIAA0020	NM_014878.4	46	0,6,5966	CC,CT,TT		0.0,0.1601,0.0502	benign	89/649	2837218	6,11938	1874	4098	5972	SO:0001583	missense	9933	exon3			TTCTTGTTGAATT	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.266A>G	9.37:g.2837218T>C	ENSP00000380982:p.Asn89Ser	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	246	110	0.447154	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	2.871	-0.234057	0.05983	0.001601	0.0	ENSG00000080608	ENST00000397885	T	0.11277	2.79	3.73	-3.09	0.05331	.	1.455670	0.03867	N	0.274933	T	0.06554	0.0168	N	0.22421	0.69	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.38394	-0.9663	10	0.09084	T	0.74	-4.4541	7.1421	0.25562	0.0:0.4276:0.1305:0.4419	.	89	Q15397	K0020_HUMAN	S	89	ENSP00000380982:N89S	ENSP00000380982:N89S	N	-	2	0	KIAA0020	2827218	0.005000	0.15991	0.824000	0.32777	0.991000	0.79684	-0.410000	0.07151	-0.634000	0.05538	-0.263000	0.10527	AAC	T|0.999;C|0.001	0.001	strong		0.433	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
ACTA1	58	hgsc.bcm.edu	37	1	229567384	229567384	+	Silent	SNP	G	G	T	rs74897770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229567384G>T	ENST00000366684.3	-	7	1098	c.996C>A	c.(994-996)atC>atA	p.I332I	ACTA1_ENST00000366683.2_Silent_p.I244I	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	332					cell growth (GO:0016049)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to extracellular stimulus (GO:0009991)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to steroid hormone (GO:0048545)|skeletal muscle fiber adaptation (GO:0043503)|skeletal muscle fiber development (GO:0048741)|skeletal muscle thin filament assembly (GO:0030240)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|striated muscle thin filament (GO:0005865)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|myosin binding (GO:0017022)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|large_intestine(4)|lung(18)|prostate(1)|urinary_tract(1)	28	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)				CCGGCGGGGCGATGATCTGCA	0.652													G|||	99	0.0197684	0.0734	0.0014	5008	,	,		13992	0.0		0.001	False		,,,				2504	0.0				p.I332I		Atlas-SNP	.											.	ACTA1	65	.	0			c.C996A						PASS	.	G		253,4153	146.5+/-181.1	10,233,1960	85.0	86.0	86.0		996	0.8	1.0	1	dbSNP_131	86	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ACTA1	NM_001100.3		10,235,6258	TT,TG,GG		0.0233,5.7422,1.9606		332/378	229567384	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	58	exon7			CGGGGCGATGATC	J00068	CCDS1578.1	1q42.13	2014-09-17			ENSG00000143632	ENSG00000143632			129	protein-coding gene	gene with protein product	"""nemaline myopathy type 3"""	102610		ACTA		10072583, 6865942	Standard	NM_001100		Approved	NEM3	uc001htm.3	P68133	OTTHUMG00000038006	ENST00000366684.3:c.996C>A	1.37:g.229567384G>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_001100	P02568|P99020|Q5T8M9	Silent	SNP	ENST00000366684.3	37	CCDS1578.1																																																																																			G|0.982;T|0.018	0.018	strong		0.652	ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	NM_001100	
SPCS2	9789	hgsc.bcm.edu	37	11	74688086	74688086	+	Nonstop_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:74688086T>C	ENST00000263672.6	+	5	718	c.679T>C	c.(679-681)Tag>Cag	p.*227Q	SPCS2_ENST00000528265.1_Intron|SPCS2_ENST00000526361.1_Nonstop_Mutation_p.*88Q|SPCS2_ENST00000530257.1_Nonstop_Mutation_p.*158Q	NM_014752.2	NP_055567.2	Q15005	SPCS2_HUMAN	signal peptidase complex subunit 2 homolog (S. cerevisiae)	0					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)			breast(1)	1						AAAAATAAAGTAGCCAATTCT	0.418																																					p.X227Q		Atlas-SNP	.											SPCS2_ENST00000263672,colon,carcinoma,-2,1	SPCS2	17	1	0			c.T679C						scavenged	.						6.0	6.0	6.0					11																	74688086		1717	3855	5572	SO:0001578	stop_lost	9789	exon5			ATAAAGTAGCCAA	D14658	CCDS44681.1	11q13.4	2008-02-05			ENSG00000118363	ENSG00000118363			28962	protein-coding gene	gene with protein product						7788527	Standard	NM_014752		Approved	KIAA0102	uc001ovu.2	Q15005	OTTHUMG00000165517	ENST00000263672.6:c.679T>C	11.37:g.74688086T>C	ENSP00000263672:p.*227Glnext*27	Somatic	365	0	0		WXS	Illumina HiSeq	Phase_I	378	4	0.010582	NM_014752	Q15507|Q3KQT0|Q641R4|Q6FG65|Q6IRX0|Q6P1P4|Q96HU9	Missense_Mutation	SNP	ENST00000263672.6	37	CCDS44681.1	.	.	.	.	.	.	.	.	.	.	.	12.05	1.821118	0.32237	.	.	ENSG00000118363	ENST00000263672;ENST00000530257;ENST00000526361;ENST00000532972	.	.	.	5.36	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.554	0.39328	0.0:0.0839:0.0:0.9161	.	.	.	.	Q	227;158;88;258	.	.	X	+	1	0	SPCS2	74365734	1.000000	0.71417	0.932000	0.37286	0.229000	0.25112	7.129000	0.77225	0.986000	0.38683	0.533000	0.62120	TAG	.	.	none		0.418	SPCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384587.1	NM_014752	
ETAA1	54465	hgsc.bcm.edu	37	2	67631541	67631541	+	Missense_Mutation	SNP	T	T	C	rs145096592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:67631541T>C	ENST00000272342.5	+	5	1857	c.1727T>C	c.(1726-1728)tTc>tCc	p.F576S	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	576						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						GTAGGTTCTTTCTTTGATGAT	0.363													T|||	4	0.000798722	0.003	0.0	5008	,	,		20046	0.0		0.0	False		,,,				2504	0.0				p.F576S		Atlas-SNP	.											.	ETAA1	88	.	0			c.T1727C						PASS	.	T	SER/PHE	14,4392	20.2+/-43.8	0,14,2189	80.0	84.0	83.0		1727	2.9	1.0	2	dbSNP_134	83	1,8597	1.2+/-3.3	0,1,4298	yes	missense	ETAA1	NM_019002.3	155	0,15,6487	CC,CT,TT		0.0116,0.3177,0.1153	benign	576/927	67631541	15,12989	2203	4299	6502	SO:0001583	missense	54465	exon5			GTTCTTTCTTTGA	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1727T>C	2.37:g.67631541T>C	ENSP00000272342:p.Phe576Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	9.471	1.095577	0.20471	0.003177	1.16E-4	ENSG00000143971	ENST00000272342	T	0.19669	2.13	5.3	2.91	0.33838	.	0.634419	0.15834	N	0.242376	T	0.09686	0.0238	L	0.39898	1.24	0.26563	N	0.973703	P	0.42518	0.782	B	0.37650	0.255	T	0.07809	-1.0753	10	0.10902	T	0.67	-36.4777	8.156	0.31169	0.0:0.1631:0.0:0.8369	.	576	Q9NY74	ETAA1_HUMAN	S	576	ENSP00000272342:F576S	ENSP00000272342:F576S	F	+	2	0	ETAA1	67485045	0.146000	0.22672	0.998000	0.56505	0.629000	0.37895	1.768000	0.38511	1.046000	0.40249	0.533000	0.62120	TTC	T|0.999;C|0.001	0.001	strong		0.363	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002	
GANC	2595	hgsc.bcm.edu	37	15	42644235	42644235	+	Silent	SNP	A	A	G	rs145163630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42644235A>G	ENST00000318010.8	+	24	2883	c.2643A>G	c.(2641-2643)aaA>aaG	p.K881K	CAPN3_ENST00000356316.3_5'UTR|RP11-164J13.1_ENST00000495723.1_RNA	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	881					carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	TAGATGGTAAAGATCAGCCTG	0.408													A|||	2	0.000399361	0.0015	0.0	5008	,	,		19780	0.0		0.0	False		,,,				2504	0.0				p.K881K		Atlas-SNP	.											.	GANC	57	.	0			c.A2643G						PASS	.	A		12,4394	16.8+/-37.8	0,12,2191	134.0	117.0	123.0		2643	1.8	0.2	15	dbSNP_134	123	0,8598		0,0,4299	no	coding-synonymous	GANC	NM_198141.2		0,12,6490	GG,GA,AA		0.0,0.2724,0.0923		881/915	42644235	12,12992	2203	4299	6502	SO:0001819	synonymous_variant	2595	exon24			TGGTAAAGATCAG	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.2643A>G	15.37:g.42644235A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	192	85	0.442708	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Silent	SNP	ENST00000318010.8	37	CCDS10084.1																																																																																			A|0.999;G|0.001	0.001	strong		0.408	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
MEGF6	1953	hgsc.bcm.edu	37	1	3428160	3428160	+	Silent	SNP	T	T	G	rs2820999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3428160T>G	ENST00000356575.4	-	9	1294	c.1068A>C	c.(1066-1068)acA>acC	p.T356T	MEGF6_ENST00000294599.4_Silent_p.T251T	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	356	EGF-like 6. {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)		CGCGGGGACATGTGCACAGGG	0.642													G|||	2504	0.5	0.7511	0.4049	5008	,	,		17510	0.6409		0.2863	False		,,,				2504	0.3027				p.T356T	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.A1068C						PASS	.	G		2799,1351		950,899,226	46.0	62.0	57.0		1068	3.9	1.0	1	dbSNP_100	57	2487,5913		395,1697,2108	no	coding-synonymous	MEGF6	NM_001409.3		1345,2596,2334	GG,GT,TT		29.6071,32.5542,42.1195		356/1542	3428160	5286,7264	2075	4200	6275	SO:0001819	synonymous_variant	1953	exon9			GGGACATGTGCAC	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.1068A>C	1.37:g.3428160T>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	37	CCDS41237.1																																																																																			T|0.574;G|0.426	0.426	strong		0.642	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
KLHL20	27252	hgsc.bcm.edu	37	1	173725101	173725101	+	Silent	SNP	G	G	A	rs16846395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173725101G>A	ENST00000209884.4	+	6	1027	c.891G>A	c.(889-891)ccG>ccA	p.P297P	KLHL20_ENST00000546011.1_Silent_p.P108P	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	297					cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)			breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						TCCTATTGCCGCAAGAACGAC	0.403													G|||	472	0.0942492	0.3404	0.0274	5008	,	,		18997	0.0		0.003	False		,,,				2504	0.0				p.P297P	GBM(159;862 2695 6559 23041)	Atlas-SNP	.											.	KLHL20	54	.	0			c.G891A						PASS	.	G		1110,3296	397.2+/-330.3	139,832,1232	108.0	99.0	102.0		891	1.2	1.0	1	dbSNP_123	102	23,8577	15.3+/-51.7	0,23,4277	no	coding-synonymous	KLHL20	NM_014458.3		139,855,5509	AA,AG,GG		0.2674,25.1929,8.7114		297/610	173725101	1133,11873	2203	4300	6503	SO:0001819	synonymous_variant	27252	exon6			ATTGCCGCAAGAA	AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"""Kelch-like"", ""BTB/POZ domain containing"""	25056	protein-coding gene	gene with protein product			"""kelch-like 20 (Drosophila)"""			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.891G>A	1.37:g.173725101G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	NM_014458	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Silent	SNP	ENST00000209884.4	37	CCDS1310.1																																																																																			G|0.899;A|0.101	0.101	strong		0.403	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458	
RDH5	5959	hgsc.bcm.edu	37	12	56117700	56117700	+	Silent	SNP	C	C	G	rs13193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56117700C>G	ENST00000257895.5	+	4	752	c.600C>G	c.(598-600)gtC>gtG	p.V200V	RDH5_ENST00000547072.1_Silent_p.V103V|RDH5_ENST00000548082.1_Silent_p.V200V|RP11-644F5.10_ENST00000550412.1_3'UTR	NM_001199771.1|NM_002905.3	NP_001186700.1|NP_002896.2	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis/9-cis)	200				V -> E (in Ref. 2; AAB93668). {ECO:0000305}.	phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)	12					Vitamin A(DB00162)	GGATACGAGTCTCCATCGTGG	0.592													C|||	700	0.139776	0.3616	0.1239	5008	,	,		19146	0.0248		0.0457	False		,,,				2504	0.0665				p.V200V		Atlas-SNP	.											RDH5,NS,carcinoma,0,1	RDH5	25	1	0			c.C600G						PASS	.	C	,	1459,2947	470.5+/-355.8	242,975,986	73.0	67.0	69.0		600,600	5.1	1.0	12	dbSNP_52	69	260,8340	101.2+/-162.5	6,248,4046	no	coding-synonymous,coding-synonymous	RDH5	NM_001199771.1,NM_002905.3	,	248,1223,5032	GG,GC,CC		3.0233,33.1139,13.217	,	200/319,200/319	56117700	1719,11287	2203	4300	6503	SO:0001819	synonymous_variant	5959	exon4			ACGAGTCTCCATC	U89717	CCDS31829.1	12q13-q14	2013-06-03	2006-05-09			ENSG00000135437	1.1.1.105	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	9940	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 9C, member 5"""	601617	"""retinol dehydrogenase 5 (11-cis and 9-cis)"""	RDH1		9115228, 8884265, 19027726	Standard	NM_002905		Approved	HSD17B9, SDR9C5	uc001shl.3	Q92781	OTTHUMG00000170126	ENST00000257895.5:c.600C>G	12.37:g.56117700C>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_001199771	O00179|Q8TAI2	Silent	SNP	ENST00000257895.5	37	CCDS31829.1																																																																																			C|0.876;G|0.124	0.124	strong		0.592	RDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407493.1	NM_002905	
KDM2B	84678	hgsc.bcm.edu	37	12	121877739	121877739	+	Silent	SNP	G	G	A	rs35674891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121877739G>A	ENST00000377071.4	-	22	3822	c.3750C>T	c.(3748-3750)caC>caT	p.H1250H	KDM2B_ENST00000542973.1_Silent_p.H618H|KDM2B_ENST00000377069.4_Silent_p.H1181H|KDM2B_ENST00000536437.1_Intron	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1250					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						GGTCGGTGACGTGGTTACAGT	0.602													G|||	75	0.014976	0.0567	0.0	5008	,	,		17032	0.0		0.0	False		,,,				2504	0.0				p.H1250H		Atlas-SNP	.											.	KDM2B	218	.	0			c.C3750T						PASS	.	G	,	235,4127		6,223,1952	123.0	146.0	138.0		3543,3750	-0.6	0.6	12	dbSNP_126	138	2,8542		0,2,4270	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	6,225,6222	AA,AG,GG		0.0234,5.3874,1.8364	,	1181/1266,1250/1337	121877739	237,12669	2181	4272	6453	SO:0001819	synonymous_variant	84678	exon22			GGTGACGTGGTTA	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.3750C>T	12.37:g.121877739G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	122	54	0.442623	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			G|0.990;A|0.010	0.010	strong		0.602	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
DACT1	51339	hgsc.bcm.edu	37	14	59113430	59113430	+	Missense_Mutation	SNP	G	G	A	rs698025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:59113430G>A	ENST00000335867.4	+	4	2113	c.2089G>A	c.(2089-2091)Ggt>Agt	p.G697S	DACT1_ENST00000541264.2_Missense_Mutation_p.G416S|DACT1_ENST00000556859.1_Missense_Mutation_p.G416S|DACT1_ENST00000395153.3_Missense_Mutation_p.G660S			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	697			G -> S (in dbSNP:rs698025).		dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						GGCCCGGCGCGGTCGCCGGGA	0.672													G|||	1353	0.270168	0.4281	0.3343	5008	,	,		11210	0.1508		0.1958	False		,,,				2504	0.2106				p.G697S		Atlas-SNP	.											.	DACT1	119	.	0			c.G2089A						PASS	.	G	SER/GLY,SER/GLY	1574,2826		289,996,915	19.0	22.0	21.0		1978,2089	0.9	0.0	14	dbSNP_86	21	1642,6942		150,1342,2800	yes	missense,missense	DACT1	NM_001079520.1,NM_016651.5	56,56	439,2338,3715	AA,AG,GG		19.1286,35.7727,24.7689	benign,benign	660/800,697/837	59113430	3216,9768	2200	4292	6492	SO:0001583	missense	51339	exon4			CGGCGCGGTCGCC	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.2089G>A	14.37:g.59113430G>A	ENSP00000337439:p.Gly697Ser	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	35	23	0.657143	NM_016651	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	37	CCDS9736.1	548	0.2509157509157509	206	0.4186991869918699	115	0.31767955801104975	80	0.13986013986013987	147	0.19393139841688653	G	0.306	-0.970599	0.02232	0.357727	0.191286	ENSG00000165617	ENST00000556859;ENST00000395151;ENST00000395153;ENST00000335867;ENST00000541264	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	5.32	0.845	0.18950	.	1.464120	0.03992	N	0.294976	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.39522	-0.9610	9	0.10636	T	0.68	-0.416	0.7972	0.01068	0.3771:0.1634:0.2964:0.1632	rs698025	660;697	A8MYJ2;Q9NYF0	.;DACT1_HUMAN	S	416;416;660;697;416	ENSP00000451598:G416S;ENSP00000378581:G416S;ENSP00000378582:G660S;ENSP00000337439:G697S;ENSP00000442850:G416S	ENSP00000337439:G697S	G	+	1	0	DACT1	58183183	0.077000	0.21312	0.000000	0.03702	0.242000	0.25591	1.550000	0.36223	-0.056000	0.13221	-0.244000	0.11960	GGT	G|0.747;T|0.005	.	strong		0.672	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
XPR1	9213	hgsc.bcm.edu	37	1	180772708	180772708	+	Silent	SNP	T	T	C	rs12078050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:180772708T>C	ENST00000367590.4	+	4	606	c.408T>C	c.(406-408)agT>agC	p.S136S	XPR1_ENST00000367589.3_Silent_p.S136S	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	136	SPX. {ECO:0000255|PROSITE- ProRule:PRU00714}.				G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						TGGCCTTCAGTGAGTTCTACC	0.408													C|||	258	0.0515176	0.1808	0.0259	5008	,	,		19232	0.0		0.001	False		,,,				2504	0.0				p.S136S		Atlas-SNP	.											.	XPR1	76	.	0			c.T408C						PASS	.	C	,	636,3770	767.9+/-413.5	45,546,1612	119.0	123.0	121.0		408,408	0.9	1.0	1	dbSNP_120	121	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous,coding-synonymous	XPR1	NM_001135669.1,NM_004736.3	,	45,550,5908	CC,CT,TT		0.0465,14.4349,4.9208	,	136/632,136/697	180772708	640,12366	2203	4300	6503	SO:0001819	synonymous_variant	9213	exon4			CTTCAGTGAGTTC	AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.408T>C	1.37:g.180772708T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	37	CCDS1340.1																																																																																			T|0.942;C|0.058	0.058	strong		0.408	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736	
HMCN1	83872	hgsc.bcm.edu	37	1	186026366	186026366	+	Splice_Site	SNP	C	C	T	rs140744695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186026366C>T	ENST00000271588.4	+	46	7374	c.7145C>T	c.(7144-7146)gCt>gTt	p.A2382V	HMCN1_ENST00000367492.2_Splice_Site_p.A2382V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2382					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGTCTTACAGCTCCTCCAAGC	0.363													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17150	0.0		0.0	False		,,,				2504	0.0				p.A2382V		Atlas-SNP	.											.	HMCN1	797	.	0			c.C7145T						PASS	.	C	VAL/ALA	5,4401	9.9+/-24.2	0,5,2198	77.0	77.0	77.0		7145	-2.6	0.7	1	dbSNP_134	77	0,8598		0,0,4299	yes	missense-near-splice	HMCN1	NM_031935.2	64	0,5,6497	TT,TC,CC		0.0,0.1135,0.0384	benign	2382/5636	186026366	5,12999	2203	4299	6502	SO:0001630	splice_region_variant	83872	exon46			TTACAGCTCCTCC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7145-1C>T	1.37:g.186026366C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	1.308	-0.602865	0.03744	0.001135	0.0	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.72167	-0.63;-0.63	5.8	-2.64	0.06114	Immunoglobulin-like fold (1);	0.288142	0.38058	N	0.001832	T	0.32285	0.0824	N	0.00746	-1.225	0.34659	D	0.722457	B	0.09022	0.002	B	0.06405	0.002	T	0.31024	-0.9958	9	.	.	.	.	12.1208	0.53889	0.0:0.2184:0.0:0.7816	.	2382	Q96RW7	HMCN1_HUMAN	V	2382	ENSP00000271588:A2382V;ENSP00000356462:A2382V	.	A	+	2	0	HMCN1	184292989	0.973000	0.33851	0.699000	0.30290	0.417000	0.31264	1.939000	0.40213	-0.338000	0.08413	-0.142000	0.14014	GCT	C|0.999;T|0.001	0.001	strong		0.363	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	Missense_Mutation
PDE4DIP	9659	hgsc.bcm.edu	37	1	144873983	144873983	+	Silent	SNP	T	T	C	rs148165371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144873983T>C	ENST00000369354.3	-	31	5163	c.4974A>G	c.(4972-4974)ccA>ccG	p.P1658P	PDE4DIP_ENST00000369356.4_Silent_p.P1658P|PDE4DIP_ENST00000313382.9_Silent_p.P1614P|RP4-791M13.5_ENST00000531288.1_RNA|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369359.4_Silent_p.P1794P			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1658					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)		TGGTTGATGATGGTTTAGAAG	0.473			T	PDGFRB	MPD								.|||	3	0.000599042	0.0023	0.0	5008	,	,		42684	0.0		0.0	False		,,,				2504	0.0				p.P1658P		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A4974G						PASS	.	T	,,	11,4395	17.9+/-39.9	0,11,2192	417.0	423.0	421.0		4842,4974,4974	5.3	1.0	1	dbSNP_134	421	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,11,6489	CC,CT,TT		0.0,0.2497,0.0846	,,	1614/2241,1658/2363,1658/2347	144873983	11,12989	2203	4297	6500	SO:0001819	synonymous_variant	9659	exon31			TGATGATGGTTTA	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.4974A>G	1.37:g.144873983T>C		Somatic	355	0	0		WXS	Illumina HiSeq	Phase_I	418	111	0.26555	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1																																																																																			T|0.999;C|0.001	0.001	strong		0.473	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
LAMB3	3914	hgsc.bcm.edu	37	1	209797061	209797061	+	Missense_Mutation	SNP	C	C	T	rs114174766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:209797061C>T	ENST00000356082.4	-	16	2281	c.2147G>A	c.(2146-2148)cGg>cAg	p.R716Q	LAMB3_ENST00000391911.1_Missense_Mutation_p.R716Q|MIR4260_ENST00000583107.1_RNA|LAMB3_ENST00000367030.3_Missense_Mutation_p.R716Q	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	716	Domain II.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GCTCAGCATCCGGAAGGCTCC	0.652													c|||	9	0.00179712	0.0061	0.0014	5008	,	,		19113	0.0		0.0	False		,,,				2504	0.0				p.R716Q		Atlas-SNP	.											.	LAMB3	136	.	0			c.G2147A						PASS	.	T	GLN/ARG,GLN/ARG,GLN/ARG	23,4383	29.0+/-57.7	0,23,2180	31.0	31.0	31.0		2147,2147,2147	1.2	0.7	1	dbSNP_132	31	0,8600		0,0,4300	yes	missense,missense,missense	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	43,43,43	0,23,6480	TT,TC,CC		0.0,0.522,0.1768	benign,benign,benign	716/1173,716/1173,716/1173	209797061	23,12983	2203	4300	6503	SO:0001583	missense	3914	exon16			AGCATCCGGAAGG	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.2147G>A	1.37:g.209797061C>T	ENSP00000348384:p.Arg716Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	c	6.857	0.527355	0.13066	0.00522	0.0	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.35789	1.29;1.29;1.29	5.15	1.19	0.21007	.	0.666644	0.15639	N	0.251967	T	0.15435	0.0372	L	0.35723	1.085	0.18873	N	0.999981	B	0.16802	0.019	B	0.06405	0.002	T	0.23904	-1.0175	10	0.14252	T	0.57	.	4.7578	0.13093	0.1382:0.5549:0.0:0.3069	.	716	Q13751	LAMB3_HUMAN	Q	716	ENSP00000375778:R716Q;ENSP00000348384:R716Q;ENSP00000355997:R716Q	ENSP00000348384:R716Q	R	-	2	0	LAMB3	207863684	0.020000	0.18652	0.733000	0.30861	0.335000	0.28730	-0.012000	0.12699	0.043000	0.15746	-0.365000	0.07479	CGG	C|0.998;T|0.002	0.002	strong		0.652	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
PIGT	51604	hgsc.bcm.edu	37	20	44054349	44054349	+	Silent	SNP	T	T	C	rs707577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44054349T>C	ENST00000279036.6	+	12	1700	c.1620T>C	c.(1618-1620)taT>taC	p.Y540Y	PIGT_ENST00000341555.5_Silent_p.Y346Y|PIGT_ENST00000279035.9_Silent_p.Y438Y|PIGT_ENST00000545755.1_Silent_p.Y278Y|PIGT_ENST00000535404.1_Silent_p.Y385Y|PIGT_ENST00000543458.2_Silent_p.Y484Y|PIGT_ENST00000372689.5_Silent_p.Y473Y	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	113	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	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	
METTL4	64863	hgsc.bcm.edu	37	18	2555005	2555005	+	Silent	SNP	C	C	T	rs61730027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2555005C>T	ENST00000574538.1	-	4	1267	c.492G>A	c.(490-492)caG>caA	p.Q164Q	METTL4_ENST00000319888.6_Silent_p.Q164Q|snoU109_ENST00000459316.1_RNA	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	164					nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						CCTGGATCAACTGTAAAGATC	0.368													c|||	613	0.122404	0.264	0.0994	5008	,	,		19475	0.1329		0.0457	False		,,,				2504	0.0153				p.Q164Q		Atlas-SNP	.											.	METTL4	40	.	0			c.G492A						PASS	.	T		999,3407	350.5+/-310.9	116,767,1320	112.0	131.0	125.0		492	-1.4	0.8	18	dbSNP_129	125	373,8227	118.6+/-178.1	10,353,3937	no	coding-synonymous	METTL4	NM_022840.3		126,1120,5257	TT,TC,CC		4.3372,22.6736,10.549		164/473	2555005	1372,11634	2203	4300	6503	SO:0001819	synonymous_variant	64863	exon4			GATCAACTGTAAA		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.492G>A	18.37:g.2555005C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Silent	SNP	ENST00000574538.1	37	CCDS11826.1																																																																																			C|0.895;T|0.105	0.105	strong		0.368	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840	
MUC17	140453	hgsc.bcm.edu	37	7	100678405	100678405	+	Silent	SNP	T	T	C	rs4729648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678405T>C	ENST00000306151.4	+	3	3772	c.3708T>C	c.(3706-3708)gcT>gcC	p.A1236A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1236	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)					GTTCTGAGGCTAGCACCCTTT	0.522													T|||	989	0.197484	0.2663	0.0893	5008	,	,		30674	0.2212		0.1083	False		,,,				2504	0.2485				p.A1236A		Atlas-SNP	.											MUC17,caecum,carcinoma,0,1	MUC17	804	1	0			c.T3708C						PASS	.	T		340,4066	144.2+/-179.2	0,340,1863	305.0	293.0	297.0		3708	-0.9	0.0	7	dbSNP_111	297	209,8391	66.0+/-128.3	0,209,4091	no	coding-synonymous	MUC17	NM_001040105.1		0,549,5954	CC,CT,TT		2.4302,7.7167,4.2211		1236/4494	100678405	549,12457	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TGAGGCTAGCACC	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.3708T>C	7.37:g.100678405T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	155	27	0.174194	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.936;C|0.064	0.064	strong		0.522	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
VSTM4	196740	hgsc.bcm.edu	37	10	50315893	50315893	+	Missense_Mutation	SNP	A	A	G	rs13088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50315893A>G	ENST00000332853.4	-	2	226	c.203T>C	c.(202-204)tTc>tCc	p.F68S	VSTM4_ENST00000298454.3_Missense_Mutation_p.F68S	NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	68	Ig-like.		F -> S (in dbSNP:rs13088). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						CTGGGAGTCGAAGGAGTGTGC	0.607													G|||	2485	0.496206	0.7753	0.4827	5008	,	,		19434	0.2401		0.3907	False		,,,				2504	0.501				p.F68S		Atlas-SNP	.											.	VSTM4	83	.	0			c.T203C						PASS	.	G	SER/PHE,SER/PHE	3121,1285	438.0+/-345.2	1116,889,198	61.0	61.0	61.0		203,203	1.8	0.0	10	dbSNP_52	61	3376,5224	640.7+/-399.6	676,2024,1600	yes	missense,missense	VSTM4	NM_001031746.3,NM_144984.2	155,155	1792,2913,1798	GG,GA,AA		39.2558,29.1648,49.9539	benign,benign	68/321,68/192	50315893	6497,6509	2203	4300	6503	SO:0001583	missense	196740	exon2			GAGTCGAAGGAGT	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"""Immunoglobulin superfamily / V-set domain containing"""	26470	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 72"""	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.203T>C	10.37:g.50315893A>G	ENSP00000331062:p.Phe68Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_144984	B4DNI6|Q96MX7	Missense_Mutation	SNP	ENST00000332853.4	37	CCDS31198.1	954	0.4368131868131868	374	0.7601626016260162	170	0.4696132596685083	121	0.21153846153846154	289	0.3812664907651715	G	0.006	-2.068113	0.00382	0.708352	0.392558	ENSG00000165633	ENST00000332853;ENST00000298454	T;T	0.62941	-0.01;-0.01	1.75	1.75	0.24633	.	0.284997	0.21139	N	0.079509	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46414	-0.9193	9	0.02654	T	1	.	4.4037	0.11399	0.2404:0.0:0.7596:0.0	rs13088;rs1137471;rs3201257;rs17857253;rs52807236;rs61590125;rs13088	68;68	Q8IW00-2;Q8IW00	.;VSTM4_HUMAN	S	68	ENSP00000331062:F68S;ENSP00000298454:F68S	ENSP00000298454:F68S	F	-	2	0	VSTM4	49985899	0.001000	0.12720	0.001000	0.08648	0.046000	0.14306	-0.111000	0.10807	-0.651000	0.05415	-0.642000	0.03964	TTC	A|0.518;G|0.482	0.482	strong		0.607	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984	
AK8	158067	hgsc.bcm.edu	37	9	135753629	135753629	+	Missense_Mutation	SNP	A	A	G	rs2231400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135753629A>G	ENST00000298545.3	-	1	535	c.14T>C	c.(13-15)aTc>aCc	p.I5T	C9orf9_ENST00000372136.3_5'UTR|C9orf9_ENST00000350499.6_5'Flank|C9orf9_ENST00000356311.5_5'Flank|AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	5			I -> T (in dbSNP:rs2231400).		nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						GTGCGGGGCGATAGTGGCGTC	0.701													G|||	587	0.117212	0.3555	0.0605	5008	,	,		12654	0.002		0.0427	False		,,,				2504	0.0307				p.I5T		Atlas-SNP	.											.	AK8	45	.	0			c.T14C						PASS	.	G	THR/ILE	1329,3077		228,873,1102	37.0	33.0	35.0		14	1.5	0.0	9	dbSNP_98	35	382,8216		14,354,3931	yes	missense	AK8	NM_152572.2	89	242,1227,5033	GG,GA,AA		4.4429,30.1634,13.1575	benign	5/480	135753629	1711,11293	2203	4299	6502	SO:0001583	missense	158067	exon1			GGGGCGATAGTGG	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"""Adenylate kinases"""	26526	protein-coding gene	gene with protein product		615365	"""chromosome 9 open reading frame 98"""	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.14T>C	9.37:g.135753629A>G	ENSP00000298545:p.Ile5Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_152572	A8K821|Q8N9W9	Missense_Mutation	SNP	ENST00000298545.3	37	CCDS6954.1	209	0.09569597069597069	153	0.31097560975609756	21	0.058011049723756904	0	0.0	35	0.04617414248021108	G	0.022	-1.414199	0.01145	0.301634	0.044429	ENSG00000165695	ENST00000298545	T	0.65178	-0.14	4.62	1.49	0.22878	.	0.932048	0.09057	N	0.854846	T	0.00012	0.0000	N	0.00538	-1.39	0.58432	P	4.000000000004E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29518	-1.0009	9	0.10111	T	0.7	-4.0202	11.827	0.52273	0.0741:0.4465:0.4795:0.0	rs2231400;rs2231400	5;5	Q8N9Z7;Q96MA6	.;KAD8_HUMAN	T	5	ENSP00000298545:I5T	ENSP00000298545:I5T	I	-	2	0	AK8	134743450	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.520000	0.22878	-0.182000	0.10602	-3.955000	0.00015	ATC	A|0.871;G|0.129	0.129	strong		0.701	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572	
BCAM	4059	hgsc.bcm.edu	37	19	45316804	45316804	+	Silent	SNP	C	C	T	rs3810141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45316804C>T	ENST00000270233.6	+	6	733	c.711C>T	c.(709-711)tgC>tgT	p.C237C	BCAM_ENST00000589651.1_Silent_p.C237C	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	237	Ig-like V-type 2.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GCTTCCACTGCGCCGCCCACT	0.692													C|||	501	0.10004	0.087	0.0893	5008	,	,		14090	0.0466		0.0815	False		,,,				2504	0.1994				p.C237C		Atlas-SNP	.											.	BCAM	53	.	0			c.C711T	GRCh37	CM973376	BCAM	M	rs3810141	PASS	.	C	,	401,4001		20,361,1820	39.0	45.0	43.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	711,711	-3.5	0.1	19	dbSNP_107	43	526,8060		18,490,3785	no	coding-synonymous,coding-synonymous	BCAM	NM_001013257.1,NM_005581.3	,	38,851,5605	TT,TC,CC		6.1263,9.1095,7.1374	,	237/589,237/629	45316804	927,12061	2201	4293	6494	SO:0001819	synonymous_variant	4059	exon6			CCACTGCGCCGCC	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6722	protein-coding gene	gene with protein product		612773	"""Lutheran blood group (Auberger b antigen included)"", ""basal cell adhesion molecule (Lu and Au blood groups)"""	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.711C>T	19.37:g.45316804C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	116	64	0.551724	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Silent	SNP	ENST00000270233.6	37	CCDS12644.1																																																																																			T|0.064;C|0.936	0.064	strong		0.692	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	
COL27A1	85301	hgsc.bcm.edu	37	9	116930194	116930194	+	Missense_Mutation	SNP	A	A	G	rs2567706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	62	0	0		WXS	Illumina HiSeq	Phase_I	63	45	0.714286	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	
SYTL2	54843	hgsc.bcm.edu	37	11	85456703	85456703	+	Silent	SNP	T	T	C	rs647912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:85456703T>C	ENST00000528231.1	-	3	643	c.366A>G	c.(364-366)gaA>gaG	p.E122E	SYTL2_ENST00000527523.1_Silent_p.E74E|SYTL2_ENST00000524452.1_Silent_p.E122E|SYTL2_ENST00000316356.4_Silent_p.E122E|SYTL2_ENST00000389960.4_Silent_p.E122E	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	122					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		GTGCTGCATCTTCTTCTGGCT	0.532													T|||	2738	0.546725	0.4788	0.5029	5008	,	,		18212	0.6141		0.6342	False		,,,				2504	0.5102				p.E122E		Atlas-SNP	.											.	SYTL2	231	.	0			c.A366G						PASS	.	T	,,	2233,2173	591.1+/-387.5	572,1089,542	167.0	149.0	155.0		366,366,366	-1.5	0.9	11	dbSNP_83	155	5457,3141	656.9+/-401.4	1741,1975,583	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3	,,	2313,3064,1125	CC,CT,TT		36.5318,49.3191,40.8643	,,	122/935,122/936,122/911	85456703	7690,5314	2203	4299	6502	SO:0001819	synonymous_variant	54843	exon4			TGCATCTTCTTCT	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.366A>G	11.37:g.85456703T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_032943	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			T|0.426;C|0.574	0.574	strong		0.532	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
SNX18	112574	hgsc.bcm.edu	37	5	53814736	53814736	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:53814736G>C	ENST00000326277.3	+	1	1144	c.954G>C	c.(952-954)tgG>tgC	p.W318C	SNX18_ENST00000343017.6_Missense_Mutation_p.W318C|SNX18_ENST00000381410.4_Missense_Mutation_p.W318C	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	318	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)				ACTTCGACTGGCTGTACGCGC	0.622																																					p.W318C		Atlas-SNP	.											.	SNX18	102	.	0			c.G954C						PASS	.						48.0	45.0	46.0					5																	53814736		2203	4300	6503	SO:0001583	missense	112574	exon1			CGACTGGCTGTAC	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.954G>C	5.37:g.53814736G>C	ENSP00000317332:p.Trp318Cys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	138	15	0.108696	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Missense_Mutation	SNP	ENST00000326277.3	37	CCDS3962.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.740451	0.49045	.	.	ENSG00000178996	ENST00000343017;ENST00000381410;ENST00000326277	T;T;T	0.41400	1.0;1.0;1.0	4.8	3.94	0.45596	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	M	0.91612	3.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.77598	-0.2528	10	0.87932	D	0	-9.487	13.0976	0.59202	0.0771:0.0:0.9229:0.0	.	318;318	Q96RF0;Q96RF0-2	SNX18_HUMAN;.	C	318	ENSP00000342276:W318C;ENSP00000370817:W318C;ENSP00000317332:W318C	ENSP00000317332:W318C	W	+	3	0	SNX18	53850493	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	9.638000	0.98445	1.250000	0.43966	-0.259000	0.10710	TGG	.	.	none		0.622	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
DPPA4	55211	hgsc.bcm.edu	37	3	109049507	109049507	+	Silent	SNP	A	A	G	rs16834356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:109049507A>G	ENST00000335658.6	-	5	597	c.543T>C	c.(541-543)aaT>aaC	p.N181N	DPPA4_ENST00000478791.1_5'UTR	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	181					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						GAGCAGTGGAATTTTCCAGGG	0.547													A|||	41	0.0081869	0.028	0.0043	5008	,	,		15162	0.0		0.001	False		,,,				2504	0.0				p.N181N		Atlas-SNP	.											.	DPPA4	56	.	0			c.T543C						PASS	.	A		122,4284	93.0+/-131.7	3,116,2084	71.0	77.0	75.0		543	-8.2	0.0	3	dbSNP_123	75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DPPA4	NM_018189.3		3,117,6383	GG,GA,AA		0.0116,2.769,0.9457		181/305	109049507	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	55211	exon5			AGTGGAATTTTCC	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.543T>C	3.37:g.109049507A>G		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	204	204	1	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Silent	SNP	ENST00000335658.6	37	CCDS33814.1																																																																																			A|0.991;G|0.009	0.009	strong		0.547	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189	
CELSR1	9620	hgsc.bcm.edu	37	22	46805007	46805007	+	Silent	SNP	G	G	A	rs35717986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46805007G>A	ENST00000262738.3	-	9	5111	c.5112C>T	c.(5110-5112)gaC>gaT	p.D1704D		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1704	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)		TGATGTTCAGGTCACTCCAGG	0.627													G|||	562	0.11222	0.3192	0.0576	5008	,	,		16776	0.0		0.0666	False		,,,				2504	0.0337				p.D1704D		Atlas-SNP	.											.	CELSR1	242	.	0			c.C5112T						PASS	.	G		1173,3233	409.1+/-334.9	151,871,1181	97.0	87.0	90.0		5112	0.7	1.0	22	dbSNP_126	90	480,8120	140.0+/-196.6	10,460,3830	no	coding-synonymous	CELSR1	NM_014246.1		161,1331,5011	AA,AG,GG		5.5814,26.6228,12.7095		1704/3015	46805007	1653,11353	2203	4300	6503	SO:0001819	synonymous_variant	9620	exon9			GTTCAGGTCACTC	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.5112C>T	22.37:g.46805007G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			G|0.882;A|0.118	0.118	strong		0.627	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
KCNA6	3742	hgsc.bcm.edu	37	12	4919267	4919267	+	Silent	SNP	A	A	G	rs758534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:4919267A>G	ENST00000280684.3	+	1	926	c.60A>G	c.(58-60)ggA>ggG	p.G20G	RP11-234B24.4_ENST00000542988.1_lincRNA|KCNA6_ENST00000433855.1_Silent_p.G20G			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	20					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	GGCCGGAGGGAGAGCAACAGG	0.697										HNSCC(72;0.22)			G|||	2239	0.447085	0.4576	0.4121	5008	,	,		11913	0.4395		0.4433	False		,,,				2504	0.4693				p.G20G		Atlas-SNP	.											.	KCNA6	122	.	0			c.A60G						PASS	.	G		1862,2530		435,992,769	19.0	27.0	24.0		60	0.2	0.8	12	dbSNP_86	24	3511,5075		791,1929,1573	no	coding-synonymous	KCNA6	NM_002235.3		1226,2921,2342	GG,GA,AA		40.8922,42.3953,41.4008		20/530	4919267	5373,7605	2196	4293	6489	SO:0001819	synonymous_variant	3742	exon1			GGAGGGAGAGCAA	X17622	CCDS8534.1	12p13	2014-06-12						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6225	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 96"""	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.60A>G	12.37:g.4919267A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	40	39	0.975	NM_002235		Silent	SNP	ENST00000280684.3	37	CCDS8534.1																																																																																			A|0.580;G|0.420	0.420	strong		0.697	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235	
ARHGAP4	393	hgsc.bcm.edu	37	X	153176284	153176284	+	Silent	SNP	C	C	T	rs62620965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153176284C>T	ENST00000350060.5	-	15	1727	c.1686G>A	c.(1684-1686)gaG>gaA	p.E562E	ARHGAP4_ENST00000370016.1_Silent_p.E541E|ARHGAP4_ENST00000467421.1_5'UTR|ARHGAP4_ENST00000537206.1_Silent_p.E539E|ARHGAP4_ENST00000393721.1_Silent_p.E384E|ARHGAP4_ENST00000370028.3_Silent_p.E602E	NM_001666.4	NP_001657.3	P98171	RHG04_HUMAN	Rho GTPase activating protein 4	562	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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)					CCAGTGGGTCCTCCCCTGCAG	0.701											OREG0003617	type=REGULATORY REGION|Gene=ARHGAP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	77	0.0203974	0.0015	0.0202	3775	,	,		6248	0.0		0.0586	False		,,,				2504	0.002				p.E602E		Atlas-SNP	.											.	ARHGAP4	103	.	0			c.G1806A						PASS	.	C	,	50,3731		0,45,5,1570,546	12.0	14.0	13.0		1806,1686	1.9	1.0	X	dbSNP_129	13	524,6159		19,358,128,2039,1723	no	coding-synonymous,coding-synonymous	ARHGAP4	NM_001164741.1,NM_001666.4	,	19,403,133,3609,2269	TT,TC,T,CC,C		7.8408,1.3224,5.4855	,	602/987,562/947	153176284	574,9890	2166	4267	6433	SO:0001819	synonymous_variant	393	exon16			TGGGTCCTCCCCT	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.1686G>A	X.37:g.153176284C>T		Somatic	70	0	0	1753	WXS	Illumina HiSeq	Phase_I	78	45	0.576923	NM_001164741	Q14144|Q86UY3	Silent	SNP	ENST00000350060.5	37	CCDS14736.1	60	0.03616636528028933	2	0.004081632653061225	3	0.008522727272727272	0	0.0	40	0.05420054200542006	C	5.744	0.321708	0.10845	0.013224	0.078408	ENSG00000089820	ENST00000454164;ENST00000442172	.	.	.	4.61	1.88	0.25563	.	.	.	.	.	T	0.02807	0.0084	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17653	-1.0362	3	.	.	.	.	7.0854	0.25254	0.0:0.5108:0.0:0.4892	rs62620965	.	.	.	K	62;51	.	.	R	-	2	0	ARHGAP4	152829478	0.906000	0.30813	0.999000	0.59377	0.588000	0.36517	-0.008000	0.12788	0.082000	0.17018	-0.195000	0.12781	AGG	C|0.957;T|0.043	0.043	strong		0.701	ARHGAP4-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061119.1	NM_001666	
VWA2	340706	hgsc.bcm.edu	37	10	116049199	116049199	+	Silent	SNP	C	C	T	rs148020287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116049199C>T	ENST00000392982.3	+	12	2323	c.2073C>T	c.(2071-2073)taC>taT	p.Y691Y	VWA2_ENST00000603594.1_Silent_p.Y691Y			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	691	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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)		TGGCAGCTTACGCCGACCTGC	0.642													C|||	29	0.00579073	0.0212	0.0014	5008	,	,		18395	0.0		0.0	False		,,,				2504	0.0				p.Y691Y		Atlas-SNP	.											VWA2,caecum,carcinoma,0,1	VWA2	64	1	0			c.C2073T						PASS	.	C		62,4344	58.7+/-95.3	0,62,2141	126.0	100.0	109.0		2073	-0.5	0.1	10	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous	VWA2	NM_198496.1		0,62,6441	TT,TC,CC		0.0,1.4072,0.4767		691/726	116049199	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	340706	exon12			AGCTTACGCCGAC	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.2073C>T	10.37:g.116049199C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	162	93	0.574074	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Silent	SNP	ENST00000392982.3	37																																																																																				C|0.994;T|0.006	0.006	strong		0.642	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
OR51G1	79324	hgsc.bcm.edu	37	11	4945196	4945196	+	Missense_Mutation	SNP	T	T	G	rs1378739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	50	0	0		WXS	Illumina HiSeq	Phase_I	51	50	0.980392	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	
NMT2	9397	hgsc.bcm.edu	37	10	15170387	15170387	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:15170387T>C	ENST00000378165.4	-	8	1041	c.961A>G	c.(961-963)Act>Gct	p.T321A	RPP38_ENST00000451677.1_Intron|NMT2_ENST00000540259.1_Missense_Mutation_p.T133A|NMT2_ENST00000535341.1_Missense_Mutation_p.T308A|NMT2_ENST00000378150.1_Missense_Mutation_p.T308A	NM_004808.2	NP_004799.1	O60551	NMT2_HUMAN	N-myristoyltransferase 2	321					intracellular transport of virus (GO:0075733)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(3)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(3)	21						CTCTGTAAAGTCATATTTCTA	0.328																																					p.T321A	Melanoma(117;1345 1645 4130 12688 30625)	Atlas-SNP	.											.	NMT2	44	.	0			c.A961G						PASS	.						85.0	88.0	87.0					10																	15170387		2202	4300	6502	SO:0001583	missense	9397	exon8			GTAAAGTCATATT	AF043325	CCDS7109.1	10p13	2006-07-11			ENSG00000152465	ENSG00000152465			7858	protein-coding gene	gene with protein product		603801				9506952	Standard	NM_004808		Approved		uc001inz.1	O60551	OTTHUMG00000017723	ENST00000378165.4:c.961A>G	10.37:g.15170387T>C	ENSP00000367407:p.Thr321Ala	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	149	6	0.0402685	NM_004808	B0YJ49|Q53Y38|Q5VUC8|Q9BRB4	Missense_Mutation	SNP	ENST00000378165.4	37	CCDS7109.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582566	0.86748	.	.	ENSG00000152465	ENST00000378165;ENST00000378150;ENST00000378143;ENST00000540259;ENST00000535341	T	0.50813	0.73	5.58	5.58	0.84498	Acyl-CoA N-acyltransferase (2);Myristoyl-CoA:protein N-myristoyltransferase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77928	0.4204	H	0.95437	3.67	0.80722	D	1	D;D;D	0.65815	0.992;0.995;0.992	D;D;D	0.75020	0.985;0.985;0.985	D	0.85108	0.0961	10	0.87932	D	0	-19.6603	15.7488	0.77967	0.0:0.0:0.0:1.0	.	321;308;321	B2RCF3;Q5VUC6;O60551	.;.;NMT2_HUMAN	A	321;308;352;133;308	ENSP00000367407:T321A	ENSP00000367385:T352A	T	-	1	0	NMT2	15210393	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.115000	0.64714	0.533000	0.62120	ACT	.	.	none		0.328	NMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046958.2	NM_004808	
FAT3	120114	hgsc.bcm.edu	37	11	92534829	92534829	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92534829G>A	ENST00000298047.6	+	9	8667	c.8650G>A	c.(8650-8652)Gag>Aag	p.E2884K	FAT3_ENST00000525166.1_Missense_Mutation_p.E2734K|FAT3_ENST00000409404.2_Missense_Mutation_p.E2884K			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2884	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)	p.E2884K(1)		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)				CCTAGATCACGAGACAGACCC	0.512										TCGA Ovarian(4;0.039)																											p.E2884K		Atlas-SNP	.											FAT3_ENST00000409404,extremity,malignant_melanoma,0,1	FAT3	1822	1	1	Substitution - Missense(1)	skin(1)	c.G8650A						scavenged	.						89.0	93.0	92.0					11																	92534829		2109	4228	6337	SO:0001583	missense	120114	exon9			GATCACGAGACAG	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.8650G>A	11.37:g.92534829G>A	ENSP00000298047:p.Glu2884Lys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	117	2	0.017094	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	28.6	4.931088	0.92389	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.72394	-0.65;-0.65;-0.65	6.04	6.04	0.98038	.	.	.	.	.	D	0.89591	0.6759	H	0.95151	3.63	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.89840	0.4002	9	0.42905	T	0.14	.	20.5948	0.99439	0.0:0.0:1.0:0.0	.	2884	Q8TDW7-3	.	K	2884;2884;2734	ENSP00000298047:E2884K;ENSP00000387040:E2884K;ENSP00000432586:E2734K	ENSP00000298047:E2884K	E	+	1	0	FAT3	92174477	1.000000	0.71417	0.973000	0.42090	0.907000	0.53573	9.787000	0.99055	2.873000	0.98535	0.563000	0.77884	GAG	.	.	none		0.512	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
KRT84	3890	hgsc.bcm.edu	37	12	52774158	52774158	+	Silent	SNP	G	G	A	rs951772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52774158G>A	ENST00000257951.3	-	7	1479	c.1413C>T	c.(1411-1413)ggC>ggT	p.G471G	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	471	Coil 2.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGCTCTCCTCGCCCTCCAGCA	0.577											OREG0021848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1657	0.330871	0.6165	0.317	5008	,	,		18924	0.1994		0.2068	False		,,,				2504	0.2178				p.G471G		Atlas-SNP	.											.	KRT84	61	.	0			c.C1413T						PASS	.	G		2449,1953		711,1027,463	37.0	39.0	38.0		1413	0.8	1.0	12	dbSNP_86	38	1798,6800		184,1430,2685	no	coding-synonymous	KRT84	NM_033045.3		895,2457,3148	AA,AG,GG		20.9118,44.3662,32.6692		471/601	52774158	4247,8753	2201	4299	6500	SO:0001819	synonymous_variant	3890	exon7			CTCCTCGCCCTCC	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.1413C>T	12.37:g.52774158G>A		Somatic	131	0	0	987	WXS	Illumina HiSeq	Phase_I	125	124	0.992	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			G|0.688;A|0.312	0.312	strong		0.577	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
PSME4	23198	hgsc.bcm.edu	37	2	54115904	54115904	+	Silent	SNP	A	A	G	rs805400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:54115904A>G	ENST00000404125.1	-	38	4397	c.4342T>C	c.(4342-4344)Ttg>Ctg	p.L1448L	PSME4_ENST00000421748.2_Silent_p.L592L|PSME4_ENST00000476586.1_5'Flank	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1448					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)			GGTGATTCCAACAGCAGTTCA	0.368													A|||	1763	0.352037	0.2201	0.2579	5008	,	,		17217	0.4742		0.3072	False		,,,				2504	0.5174				p.L1448L		Atlas-SNP	.											.	PSME4	247	.	0			c.T4342C						PASS	.	A		949,3457	360.6+/-315.3	91,767,1345	126.0	123.0	124.0		4342	2.0	0.8	2	dbSNP_86	124	2667,5933	428.8+/-356.0	401,1865,2034	no	coding-synonymous	PSME4	NM_014614.2		492,2632,3379	GG,GA,AA		31.0116,21.5388,27.8026		1448/1844	54115904	3616,9390	2203	4300	6503	SO:0001819	synonymous_variant	23198	exon38			ATTCCAACAGCAG	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.4342T>C	2.37:g.54115904A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																			A|0.711;G|0.289	0.289	strong		0.368	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
TBC1D10C	374403	hgsc.bcm.edu	37	11	67171736	67171736	+	Silent	SNP	C	C	T	rs2514256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67171736C>T	ENST00000542590.1	+	1	77	c.63C>T	c.(61-63)tcC>tcT	p.S21S	PPP1CA_ENST00000532446.1_5'Flank|PPP1CA_ENST00000358239.4_5'Flank|TBC1D10C_ENST00000312390.5_Silent_p.S21S|TBC1D10C_ENST00000526387.1_Silent_p.S21S|PPP1CA_ENST00000376745.4_5'Flank|PPP1CA_ENST00000312989.7_5'Flank			Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	21					retrograde transport, endosome to Golgi (GO:0042147)	filopodium membrane (GO:0031527)|membrane (GO:0016020)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			ACTCCAGCTCCTTGGGGTCCG	0.667													T|||	1762	0.351837	0.8283	0.4049	5008	,	,		15412	0.2589		0.0785	False		,,,				2504	0.047				p.S21S		Atlas-SNP	.											TBC1D10C,NS,carcinoma,0,1	TBC1D10C	42	1	0			c.C63T						scavenged	.	T		2948,1446		1011,926,260	17.0	19.0	18.0		63	-4.5	0.5	11	dbSNP_100	18	633,7937		24,585,3676	no	coding-synonymous	TBC1D10C	NM_198517.2		1035,1511,3936	TT,TC,CC		7.3862,32.9085,27.6226		21/447	67171736	3581,9383	2197	4285	6482	SO:0001819	synonymous_variant	374403	exon2			CAGCTCCTTGGGG	BC035630	CCDS8162.1, CCDS58150.1	11q13.1	2013-07-09			ENSG00000175463	ENSG00000175463			24702	protein-coding gene	gene with protein product		610831				17230191, 20404108	Standard	NM_001256508		Approved	FLJ00332, Carabin, EPI64C	uc001ola.4	Q8IV04	OTTHUMG00000167139	ENST00000542590.1:c.63C>T	11.37:g.67171736C>T		Somatic	79	1	0.0126582		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_001256508	G3V1D6	Silent	SNP	ENST00000542590.1	37	CCDS8162.1																																																																																			C|0.683;T|0.317	0.317	strong		0.667	TBC1D10C-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395492.2	NM_198517	
MCF2L	23263	hgsc.bcm.edu	37	13	113741590	113741590	+	Silent	SNP	G	G	A	rs9604022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113741590G>A	ENST00000375608.3	+	23	2563	c.2505G>A	c.(2503-2505)tcG>tcA	p.S835S	MCF2L_ENST00000375604.2_Silent_p.S862S|MCF2L_ENST00000375601.3_Silent_p.S809S|MCF2L_ENST00000535094.2_Silent_p.S805S|MCF2L_ENST00000397030.1_Silent_p.S838S|MCF2L_ENST00000421756.1_Silent_p.S809S|MCF2L_ENST00000423482.2_Silent_p.S803S|MCF2L_ENST00000434480.2_Silent_p.S811S|MCF2L_ENST00000375597.4_Silent_p.S803S|MCF2L_ENST00000442652.2_Silent_p.S835S			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	835	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 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)				TGCAGGGCTCGTTCAGCGTCT	0.637													g|||	812	0.162141	0.2466	0.1311	5008	,	,		19303	0.005		0.1571	False		,,,				2504	0.2372				p.S805S		Atlas-SNP	.											.	MCF2L	182	.	0			c.G2415A						PASS	.	G	,	950,3456	357.4+/-313.9	119,712,1372	68.0	59.0	62.0		2415,2409	-2.3	1.0	13	dbSNP_119	62	1427,7171	273.7+/-290.8	128,1171,3000	no	coding-synonymous,coding-synonymous	MCF2L	NM_001112732.2,NM_024979.4	,	247,1883,4372	AA,AG,GG		16.5969,21.5615,18.279	,	805/1126,803/1124	113741590	2377,10627	2203	4299	6502	SO:0001819	synonymous_variant	23263	exon22			GGGCTCGTTCAGC	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.2505G>A	13.37:g.113741590G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37		284|284	0.13003663003663005|0.13003663003663005	123|123	0.25|0.25	53|53	0.1464088397790055|0.1464088397790055	5|5	0.008741258741258742|0.008741258741258742	103|103	0.1358839050131926|0.1358839050131926	G|G	2.941|2.941	-0.218814|-0.218814	0.06101|0.06101	0.215615|0.215615	0.165969|0.165969	ENSG00000126217|ENSG00000126217	ENST00000413354|ENST00000397017	.|.	.|.	.|.	4.34|4.34	-2.28|-2.28	0.06826|0.06826	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.34502|0.34502	-0.9826|-0.9826	3|3	.|.	.|.	.|.	.|.	1.8524|1.8524	0.03172|0.03172	0.3428:0.2912:0.2297:0.1363|0.3428:0.2912:0.2297:0.1363	rs9604022;rs9604022|rs9604022;rs9604022	.|.	.|.	.|.	H|I	35|466	.|.	.|.	R|V	+|+	2|1	0|0	MCF2L|MCF2L	112789591|112789591	0.006000|0.006000	0.16342|0.16342	0.956000|0.956000	0.39512|0.39512	0.324000|0.324000	0.28378|0.28378	-1.073000|-1.073000	0.03430|0.03430	-0.924000|-0.924000	0.03780|0.03780	-2.416000|-2.416000	0.00220|0.00220	CGT|GTT	G|0.832;A|0.168	0.168	strong		0.637	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
SLC30A4	7782	hgsc.bcm.edu	37	15	45779810	45779810	+	Silent	SNP	G	G	A	rs2453531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45779810G>A	ENST00000261867.4	-	6	1229	c.915C>T	c.(913-915)gaC>gaT	p.D305D	RP11-519G16.3_ENST00000560647.1_RNA|RP11-519G16.3_ENST00000558536.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	305					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)		TACAGATGGGGTCAGCAATCT	0.328													A|||	3810	0.760783	0.9092	0.6095	5008	,	,		17991	0.7034		0.7177	False		,,,				2504	0.771				p.D305D		Atlas-SNP	.											.	SLC30A4	25	.	0			c.C915T						PASS	.	A		3821,575	257.7+/-262.0	1665,491,42	124.0	134.0	131.0		915	2.5	1.0	15	dbSNP_100	131	6015,2581	418.0+/-352.6	2104,1807,387	no	coding-synonymous	SLC30A4	NM_013309.4		3769,2298,429	AA,AG,GG		30.0256,13.0801,24.2919		305/430	45779810	9836,3156	2198	4298	6496	SO:0001819	synonymous_variant	7782	exon6			GATGGGGTCAGCA		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.915C>T	15.37:g.45779810G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_013309	Q8TC39	Silent	SNP	ENST00000261867.4	37	CCDS10125.1																																																																																			G|0.240;A|0.760	0.760	strong		0.328	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1		
TBC1D10C	374403	hgsc.bcm.edu	37	11	67172911	67172911	+	Silent	SNP	C	C	T	rs61734600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67172911C>T	ENST00000542590.1	+	3	308	c.294C>T	c.(292-294)cgC>cgT	p.R98R	TBC1D10C_ENST00000312390.5_Silent_p.R98R|TBC1D10C_ENST00000526387.1_Silent_p.R98R			Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	98	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				retrograde transport, endosome to Golgi (GO:0042147)	filopodium membrane (GO:0031527)|membrane (GO:0016020)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CTGCCCTGCGCGCCCGATGCT	0.652													C|||	303	0.0605032	0.0794	0.0461	5008	,	,		18421	0.1141		0.0348	False		,,,				2504	0.0164				p.R98R		Atlas-SNP	.											.	TBC1D10C	42	.	0			c.C294T						PASS	.	C		323,4077	166.9+/-198.0	16,291,1893	47.0	44.0	45.0		294	-3.7	0.9	11	dbSNP_129	45	284,8306	106.2+/-167.1	7,270,4018	no	coding-synonymous	TBC1D10C	NM_198517.2		23,561,5911	TT,TC,CC		3.3062,7.3409,4.6728		98/447	67172911	607,12383	2200	4295	6495	SO:0001819	synonymous_variant	374403	exon4			CCTGCGCGCCCGA	BC035630	CCDS8162.1, CCDS58150.1	11q13.1	2013-07-09			ENSG00000175463	ENSG00000175463			24702	protein-coding gene	gene with protein product		610831				17230191, 20404108	Standard	NM_001256508		Approved	FLJ00332, Carabin, EPI64C	uc001ola.4	Q8IV04	OTTHUMG00000167139	ENST00000542590.1:c.294C>T	11.37:g.67172911C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	122	77	0.631148	NM_001256508	G3V1D6	Silent	SNP	ENST00000542590.1	37	CCDS8162.1																																																																																			C|0.948;T|0.052	0.052	strong		0.652	TBC1D10C-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395492.2	NM_198517	
ECI2	10455	hgsc.bcm.edu	37	6	4119492	4119492	+	Silent	SNP	T	T	C	rs10708	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4119492T>C	ENST00000380118.3	-	8	849	c.813A>G	c.(811-813)ccA>ccG	p.P271P	C6orf201_ENST00000333388.5_Intron|C6orf201_ENST00000430835.2_Intron|ECI2_ENST00000413766.2_Silent_p.P104P|ECI2_ENST00000380125.2_Silent_p.P241P|ECI2_ENST00000361538.2_Silent_p.P241P|ECI2_ENST00000465828.1_Silent_p.P241P|C6orf201_ENST00000380175.4_Intron			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	271	ECH-like.				fatty acid catabolic process (GO:0009062)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|fatty-acyl-CoA binding (GO:0000062)|receptor binding (GO:0005102)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	11						GGTGACTAAATGGTGTATGAA	0.378													T|||	214	0.0427316	0.1536	0.0159	5008	,	,		18618	0.0		0.0	False		,,,				2504	0.0				p.P271P		Atlas-SNP	.											.	ECI2	59	.	0			c.A813G						PASS	.	T	,,,	590,3816	258.9+/-262.7	51,488,1664	77.0	79.0	78.0		,723,723,813	-5.8	0.7	6	dbSNP_130	78	6,8594	5.0+/-18.6	0,6,4294	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECI2,C6orf201	NM_001085401.1,NM_001166010.1,NM_006117.2,NM_206836.2	,,,	51,494,5958	CC,CT,TT		0.0698,13.3908,4.5825	,,,	,241/365,241/365,271/395	4119492	596,12410	2203	4300	6503	SO:0001819	synonymous_variant	10455	exon8			ACTAAATGGTGTA	AF069301	CCDS4490.1, CCDS43420.1, CCDS43420.2	6p24.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000198721	ENSG00000198721			14601	protein-coding gene	gene with protein product	"""acyl-Coenzyme A binding domain containing 2"", "" Hepatocellular carcinoma-associated antigen 88"""	608024	"""peroxisomal D3,D2-enoyl-CoA isomerase"""	PECI		10419495	Standard	NM_206836		Approved	ACBD2, DRS1, HCA88	uc003mwf.3	O75521	OTTHUMG00000014158	ENST00000380118.3:c.813A>G	6.37:g.4119492T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_206836	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Silent	SNP	ENST00000380118.3	37	CCDS43420.2																																																																																			T|0.962;C|0.038	0.038	strong		0.378	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117	
POLE	5426	hgsc.bcm.edu	37	12	133201327	133201327	+	Missense_Mutation	SNP	T	T	A	rs73481453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133201327T>A	ENST00000320574.5	-	49	6860	c.6817A>T	c.(6817-6819)Acc>Tcc	p.T2273S	POLE_ENST00000535270.1_Missense_Mutation_p.T2246S	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	2273					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)	CACTCCAGGGTCTCCAGGAGG	0.612								DNA polymerases (catalytic subunits)					T|||	25	0.00499201	0.0189	0.0	5008	,	,		18347	0.0		0.0	False		,,,				2504	0.0				p.T2273S		Atlas-SNP	.											.	POLE	416	.	0			c.A6817T						PASS	.	T	SER/THR	62,4344	58.7+/-95.3	2,58,2143	81.0	82.0	82.0		6817	2.4	1.0	12	dbSNP_130	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense	POLE	NM_006231.2	58	2,59,6442	AA,AT,TT		0.0116,1.4072,0.4844	benign	2273/2287	133201327	63,12943	2203	4300	6503	SO:0001583	missense	5426	exon49			CCAGGGTCTCCAG		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.6817A>T	12.37:g.133201327T>A	ENSP00000322570:p.Thr2273Ser	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	154	72	0.467532	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	T	16.01	3.000426	0.54147	0.014072	1.16E-4	ENSG00000177084	ENST00000434528;ENST00000320574;ENST00000455752;ENST00000320557;ENST00000535270	T;T;T	0.02944	4.11;4.1;4.11	4.89	2.43	0.29744	.	0.285116	0.38436	N	0.001689	T	0.02193	0.0068	M	0.77103	2.36	0.41149	D	0.98601	B;B	0.12630	0.001;0.006	B;B	0.18263	0.005;0.021	T	0.20405	-1.0276	10	0.59425	D	0.04	.	7.0622	0.25131	0.1316:0.0728:0.0:0.7956	.	2273;483	Q07864;B3KS74	DPOE1_HUMAN;.	S	483;2273;2284;243;2246	ENSP00000322570:T2273S;ENSP00000406383:T2284S;ENSP00000445753:T2246S	ENSP00000322473:T243S	T	-	1	0	POLE	131711400	1.000000	0.71417	0.954000	0.39281	0.840000	0.47671	4.700000	0.61803	0.325000	0.23359	0.459000	0.35465	ACC	T|0.995;A|0.005	0.005	strong		0.612	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
GPRASP1	9737	hgsc.bcm.edu	37	X	101912118	101912118	+	Missense_Mutation	SNP	C	C	T	rs2235804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101912118C>T	ENST00000361600.5	+	5	4078	c.3277C>T	c.(3277-3279)Cca>Tca	p.P1093S	RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000415986.1_Missense_Mutation_p.P1093S|GPRASP1_ENST00000537097.1_Missense_Mutation_p.P1093S|GPRASP1_ENST00000444152.1_Missense_Mutation_p.P1093S	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	1093	OPRD1-binding.		P -> S (in dbSNP:rs2235804).		endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)		p.P1093S(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						GGTACTTAGCCCAGAAGGGGA	0.478													C|||	592	0.156821	0.1589	0.0447	3775	,	,		14834	0.1032		0.005	False		,,,				2504	0.2474				p.P1093S		Atlas-SNP	.											.	GPRASP1	140	.	1	Substitution - Missense(1)	stomach(1)	c.C3277T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,,SER/PRO	735,3100		59,510,107,1063,464	133.0	130.0	131.0		3277,3277,3277,,3277	0.8	0.0	X	dbSNP_98	131	22,6706		0,16,6,2412,1866	yes	missense,missense,missense,intron,missense	GPRASP1,ARMCX5-GPRASP2	NM_001099410.1,NM_001099411.1,NM_001184727.1,NM_001199818.1,NM_014710.4	74,74,74,,74	59,526,113,3475,2330	TT,TC,T,CC,C		0.327,19.1656,7.1665	benign,benign,benign,,benign	1093/1396,1093/1396,1093/1396,,1093/1396	101912118	757,9806	2203	4300	6503	SO:0001583	missense	9737	exon3			CTTAGCCCAGAAG	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"""Armadillo repeat containing"""	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.3277C>T	X.37:g.101912118C>T	ENSP00000355146:p.Pro1093Ser	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	245	145	0.591837	NM_001099411	O43168|Q96LA1	Missense_Mutation	SNP	ENST00000361600.5	37	CCDS35352.1	168	0.10126582278481013	65	0.14772727272727273	7	0.020114942528735632	41	0.0762081784386617	4	0.005291005291005291	C	1.907	-0.451569	0.04572	0.191656	0.00327	ENSG00000198932	ENST00000415986;ENST00000444152;ENST00000361600;ENST00000537097	T;T;T;T	0.08458	3.09;3.09;3.09;3.09	2.84	0.79	0.18613	.	.	.	.	.	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B	0.22346	0.068	B	0.15870	0.014	T	0.42068	-0.9473	8	0.40728	T	0.16	0.0	4.3522	0.11160	0.2628:0.4836:0.2536:0.0	rs2235804;rs2235804	1093	Q5JY77	GASP1_HUMAN	S	1093	ENSP00000393691:P1093S;ENSP00000409420:P1093S;ENSP00000355146:P1093S;ENSP00000445683:P1093S	ENSP00000355146:P1093S	P	+	1	0	GPRASP1	101798774	0.000000	0.05858	0.006000	0.13384	0.851000	0.48451	-1.173000	0.03108	0.084000	0.17077	0.284000	0.19432	CCA	C|0.895;T|0.105	0.105	strong		0.478	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710	
GREB1	9687	hgsc.bcm.edu	37	2	11706693	11706693	+	Missense_Mutation	SNP	T	T	C	rs4669751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11706693T>C	ENST00000381486.2	+	4	665	c.365T>C	c.(364-366)gTc>gCc	p.V122A	GREB1_ENST00000234142.5_Missense_Mutation_p.V122A|GREB1_ENST00000263834.5_Missense_Mutation_p.V122A|GREB1_ENST00000381483.2_Missense_Mutation_p.V122A|GREB1_ENST00000389825.3_Missense_Mutation_p.V12A	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	122			V -> A (in dbSNP:rs4669751).			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)		CTCGTGGGGGTCAAGTCCCCC	0.597													C|||	1719	0.343251	0.7663	0.1499	5008	,	,		16677	0.2401		0.1093	False		,,,				2504	0.2556				p.V122A	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.T365C						PASS	.	C	ALA/VAL,ALA/VAL,ALA/VAL	2710,1696	512.1+/-368.0	853,1004,346	105.0	95.0	99.0		365,365,365	4.6	1.0	2	dbSNP_111	99	921,7679	777.5+/-407.7	51,819,3430	yes	missense,missense,missense	GREB1	NM_014668.3,NM_033090.2,NM_148903.2	64,64,64	904,1823,3776	CC,CT,TT		10.7093,38.493,27.9179	benign,benign,benign	122/1950,122/458,122/410	11706693	3631,9375	2203	4300	6503	SO:0001583	missense	9687	exon4			TGGGGGTCAAGTC		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.365T>C	2.37:g.11706693T>C	ENSP00000370896:p.Val122Ala	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	643	0.2944139194139194	358	0.7276422764227642	58	0.16022099447513813	144	0.2517482517482518	83	0.10949868073878628	C	6.279	0.419512	0.11928	0.61507	0.107093	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000389825;ENST00000381483;ENST00000234142	T;T;T;T;T	0.39787	3.46;2.37;1.06;2.39;3.46	5.51	4.63	0.57726	.	0.069830	0.64402	N	0.000020	T	0.00012	0.0000	N	0.00841	-1.15	0.41610	P	0.011090999999999962	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	0.43653	-0.9378	9	0.02654	T	1	-40.3849	9.3506	0.38136	0.0:0.7832:0.0:0.2168	rs4669751;rs57292736;rs4669751	122;12;122;122	Q4ZG55-2;F8W6E5;Q4ZG55-3;Q4ZG55	.;.;.;GREB1_HUMAN	A	122;122;12;122;122	ENSP00000370896:V122A;ENSP00000263834:V122A;ENSP00000374475:V12A;ENSP00000370892:V122A;ENSP00000234142:V122A	ENSP00000234142:V122A	V	+	2	0	GREB1	11624144	0.950000	0.32346	1.000000	0.80357	0.984000	0.73092	1.195000	0.32186	0.709000	0.31976	-0.119000	0.15052	GTC	T|0.700;C|0.300	0.300	strong		0.597	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
PDXDC1	23042	hgsc.bcm.edu	37	16	15129970	15129970	+	Silent	SNP	A	A	G	rs7200543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:15129970A>G	ENST00000396410.4	+	23	2302	c.2205A>G	c.(2203-2205)ctA>ctG	p.L735L	PDXDC1_ENST00000447912.2_Silent_p.L644L|PDXDC1_ENST00000563679.1_Silent_p.L753L|PDXDC1_ENST00000569715.1_Silent_p.L708L|PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000325823.7_Silent_p.L720L|PDXDC1_ENST00000450288.2_Silent_p.L707L	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	735					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						TGGAGCGCCTATCCAGTGGGC	0.582													G|||	1728	0.345048	0.1846	0.5331	5008	,	,		18589	0.371		0.3062	False		,,,				2504	0.4417				p.L735L		Atlas-SNP	.											.	PDXDC1	59	.	0			c.A2205G						PASS	.	G		989,3405	730.4+/-410.2	119,751,1327	120.0	120.0	120.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2205	4.7	0.1	16	dbSNP_116	120	2587,6013	689.7+/-404.4	359,1869,2072	yes	coding-synonymous	PDXDC1	NM_015027.2		478,2620,3399	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	30.0814,22.508,27.5204		735/789	15129970	3576,9418	2197	4300	6497	SO:0001819	synonymous_variant	23042	exon23			GCGCCTATCCAGT	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.2205A>G	16.37:g.15129970A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	37	CCDS32393.1																																																																																			A|0.706;G|0.294	0.294	strong		0.582	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
JMY	133746	hgsc.bcm.edu	37	5	78596044	78596044	+	Silent	SNP	T	T	C	rs10514159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	92	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	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	
TPTE	7179	hgsc.bcm.edu	37	21	10944728	10944728	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:10944728A>G	ENST00000361285.4	-	11	835	c.506T>C	c.(505-507)cTt>cCt	p.L169P	TPTE_ENST00000298232.7_Missense_Mutation_p.L151P|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Missense_Mutation_p.L131P	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	169					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AACCAGCAGAAGAATCACAAT	0.313																																					p.L169P		Atlas-SNP	.											TPTE_ENST00000361285,NS,carcinoma,-1,2	TPTE	513	2	0			c.T506C						scavenged	.						161.0	169.0	167.0					21																	10944728		2203	4298	6501	SO:0001583	missense	7179	exon11			AGCAGAAGAATCA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.506T>C	21.37:g.10944728A>G	ENSP00000355208:p.Leu169Pro	Somatic	368	1	0.00271739		WXS	Illumina HiSeq	Phase_I	345	5	0.0144928	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	1.636	-0.517838	0.04171	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.98249	-4.82;-4.82;-4.82	2.31	-0.692	0.11301	Ion transport (1);	0.059488	0.64402	N	0.000003	D	0.89567	0.6752	N	0.01352	-0.895	0.09310	N	1	B;B;B	0.09022	0.0;0.0;0.002	B;B;B	0.11329	0.0;0.0;0.006	D	0.84102	0.0396	10	0.37606	T	0.19	-7.6157	6.5741	0.22555	0.4737:0.0:0.5263:0.0	.	131;151;169	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	P	151;169;131	ENSP00000298232:L151P;ENSP00000355208:L169P;ENSP00000344441:L131P	ENSP00000298232:L151P	L	-	2	0	TPTE	9966599	0.685000	0.27652	0.000000	0.03702	0.016000	0.09150	0.204000	0.17335	-0.554000	0.06150	-2.843000	0.00104	CTT	.	.	none		0.313	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
TG	7038	hgsc.bcm.edu	37	8	134108546	134108546	+	Missense_Mutation	SNP	T	T	C	rs2069569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134108546T>C	ENST00000220616.4	+	43	7541	c.7501T>C	c.(7501-7503)Tgg>Cgg	p.W2501R	SLA_ENST00000524345.1_Intron|TG_ENST00000519543.1_Missense_Mutation_p.W634R|SLA_ENST00000517648.1_Intron|SLA_ENST00000518565.1_Intron|SLA_ENST00000395352.3_Intron|SLA_ENST00000338087.5_Intron|TG_ENST00000542445.1_Missense_Mutation_p.W871R|TG_ENST00000377869.1_Missense_Mutation_p.W2444R	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2501			W -> R (in dbSNP:rs2069569). {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)		GAGGTCTTTATGGGTAGAGGT	0.587													C|||	2616	0.522364	0.8275	0.5086	5008	,	,		19240	0.2302		0.5328	False		,,,				2504	0.41				p.W2501R		Atlas-SNP	.											.	TG	416	.	0			c.T7501C						PASS	.	C	,,ARG/TRP	3462,944	362.9+/-316.3	1362,738,103	158.0	154.0	156.0		,,7501	2.0	0.0	8	dbSNP_96	156	4533,4067	560.0+/-387.5	1215,2103,982	yes	intron,intron,missense	SLA,TG	NM_001045556.2,NM_001045557.2,NM_003235.4	,,101	2577,2841,1085	CC,CT,TT		47.2907,21.4253,38.5284	,,benign	,,2501/2769	134108546	7995,5011	2203	4300	6503	SO:0001583	missense	7038	exon43			TCTTTATGGGTAG	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.7501T>C	8.37:g.134108546T>C	ENSP00000220616:p.Trp2501Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	1131|1131	0.5178571428571429|0.5178571428571429	412|412	0.8373983739837398|0.8373983739837398	192|192	0.5303867403314917|0.5303867403314917	122|122	0.21328671328671328|0.21328671328671328	405|405	0.5343007915567283|0.5343007915567283	C|C	0.017|0.017	-1.494739|-1.494739	0.01009|0.01009	0.785747|0.785747	0.527093|0.527093	ENSG00000042832|ENSG00000042832	ENST00000519178|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	.|T;T;T;T	.|0.66280	.|-0.2;-0.2;-0.2;-0.2	5.26|5.26	2.0|2.0	0.26442|0.26442	.|Carboxylesterase, type B (1);	.|0.795765	.|0.10645	.|N	.|0.650544	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01242|0.01242	-0.935|-0.935	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	0.29882|0.29882	-0.9997|-0.9997	4|9	.|0.28530	.|T	.|0.3	.|.	5.2901|5.2901	0.15721|0.15721	0.293:0.5391:0.0:0.168|0.293:0.5391:0.0:0.168	rs56541861;rs59673778|rs56541861;rs59673778	.|634;871;2501	.|E7EVM0;F5GWW5;P01266	.|.;.;THYG_HUMAN	T|R	956|2444;1307;2501;871;634	.|ENSP00000367100:W2444R;ENSP00000220616:W2501R;ENSP00000441693:W871R;ENSP00000430430:W634R	.|ENSP00000220616:W2501R	M|W	+|+	2|1	0|0	TG|TG	134177728|134177728	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.018000|-0.018000	0.12568|0.12568	0.197000|0.197000	0.20387|0.20387	-0.716000|-0.716000	0.03619|0.03619	ATG|TGG	C|0.598;N|0.002	0.598	strong		0.587	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
FOCAD	54914	hgsc.bcm.edu	37	9	20978439	20978439	+	Missense_Mutation	SNP	A	A	C	rs149031092		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:20978439A>C	ENST00000380249.1	+	39	4727	c.4363A>C	c.(4363-4365)Atc>Ctc	p.I1455L	FOCAD_ENST00000605086.1_Missense_Mutation_p.I891L|FOCAD_ENST00000338382.6_Missense_Mutation_p.I1455L	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1455						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											ACCACCACTGATCCACAGTCT	0.458													A|||	1	0.000199681	0.0008	0.0	5008	,	,		19302	0.0		0.0	False		,,,				2504	0.0				p.I1455L		Atlas-SNP	.											.	.	.	.	0			c.A4363C						PASS	.	A	LEU/ILE	3,4403	6.2+/-15.9	0,3,2200	77.0	71.0	73.0		4363	-1.0	0.1	9	dbSNP_134	73	0,8600		0,0,4300	no	missense	KIAA1797	NM_017794.3	5	0,3,6500	CC,CA,AA		0.0,0.0681,0.0231	benign	1455/1802	20978439	3,13003	2203	4300	6503	SO:0001583	missense	54914	exon39			CCACTGATCCACA	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.4363A>C	9.37:g.20978439A>C	ENSP00000369599:p.Ile1455Leu	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	152	80	0.526316	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	12.27	1.888125	0.33348	6.81E-4	0.0	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.21543	2.0;2.0	6.06	-0.993	0.10228	.	0.598323	0.18257	N	0.146776	T	0.15435	0.0372	L	0.51422	1.61	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.16897	-1.0387	10	0.39692	T	0.17	-0.8041	5.9075	0.19008	0.399:0.252:0.349:0.0	.	1455	Q5VW36	K1797_HUMAN	L	1455	ENSP00000369599:I1455L;ENSP00000344307:I1455L	ENSP00000344307:I1455L	I	+	1	0	KIAA1797	20968439	0.409000	0.25368	0.067000	0.19924	0.828000	0.46876	0.494000	0.22467	-0.159000	0.11021	0.533000	0.62120	ATC	A|1.000;C|0.000	0.000	strong		0.458	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
PABPC1	26986	hgsc.bcm.edu	37	8	101721839	101721839	+	Missense_Mutation	SNP	C	C	A	rs202074479		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721839C>A	ENST00000318607.5	-	8	2221	c.1093G>T	c.(1093-1095)Gta>Tta	p.V365L	PABPC1_ENST00000519004.1_Missense_Mutation_p.V320L|PABPC1_ENST00000522387.1_Missense_Mutation_p.V333L|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	365	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)			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)			GCTAAAGCTACATACAATGGC	0.463																																					p.V365L		Atlas-SNP	.											.	PABPC1	76	.	0			c.G1093T						PASS	.						120.0	104.0	109.0					8																	101721839		2203	4300	6503	SO:0001583	missense	26986	exon8			AAGCTACATACAA	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.1093G>T	8.37:g.101721839C>A	ENSP00000313007:p.Val365Leu	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	294	88	0.29932	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	30|30|30	5.056922|5.056922|5.056922	0.93846|0.93846|0.93846	.|.|.	.|.|.	ENSG00000070756|ENSG00000070756|ENSG00000070756	ENST00000519596|ENST00000519100|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|.|T;T;T	.|.|0.08720	.|.|3.06;3.06;3.06	5.05|5.05|5.05	5.05|5.05|5.05	0.67936|0.67936|0.67936	.|.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	.|.|0.000000	.|.|0.56097	.|.|D	.|.|0.000031	T|T|T	0.29256|0.29256|0.29256	0.0728|0.0728|0.0728	M|M|M	0.74647|0.74647|0.74647	2.275|2.275|2.275	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|P;D;D	.|.|0.54772	.|.|0.757;0.968;0.968	.|.|B;D;P	.|.|0.63283	.|.|0.299;0.913;0.587	T|T|T	0.01925|0.01925|0.01925	-1.1246|-1.1246|-1.1246	5|5|10	.|.|0.87932	.|.|D	.|.|0	.|.|.	18.7718|18.7718|18.7718	0.91894|0.91894|0.91894	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|.|333;365;365	.|.|E7ERJ7;B3KT93;P11940	.|.|.;.;PABP1_HUMAN	F|I|L	197|233|365;365;320;333	.|.|ENSP00000313007:V365L;ENSP00000429594:V320L;ENSP00000429395:V333L	.|.|ENSP00000313007:V365L	C|M|V	-|-|-	2|3|1	0|0|0	PABPC1|PABPC1|PABPC1	101791015|101791015|101791015	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	7.748000|7.748000|7.748000	0.85085|0.85085|0.85085	2.507000|2.507000|2.507000	0.84556|0.84556|0.84556	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	TGT|ATG|GTA	.	.	weak		0.463	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
AKNA	80709	hgsc.bcm.edu	37	9	117103900	117103900	+	Missense_Mutation	SNP	T	T	C	rs2787344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117103900T>C	ENST00000307564.4	-	21	4141	c.3980A>G	c.(3979-3981)tAt>tGt	p.Y1327C	AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374075.5_Missense_Mutation_p.Y1246C|AKNA_ENST00000374079.4_Missense_Mutation_p.Y272C|AKNA_ENST00000374088.3_Missense_Mutation_p.Y1327C|AKNA_ENST00000223791.3_Missense_Mutation_p.Y787C	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1327			Y -> C (in dbSNP:rs2787344).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TGTTGCCAGATACCACAGTCC	0.622													T|||	395	0.0788738	0.2897	0.0173	5008	,	,		15911	0.0		0.0	False		,,,				2504	0.0				p.Y1327C		Atlas-SNP	.											.	AKNA	119	.	0			c.A3980G						PASS	.	T	CYS/TYR	981,3425	369.1+/-318.9	102,777,1324	56.0	62.0	60.0		3980	5.5	1.0	9	dbSNP_100	60	6,8594	4.3+/-15.6	0,6,4294	yes	missense	AKNA	NM_030767.4	194	102,783,5618	CC,CT,TT		0.0698,22.2651,7.5888	probably-damaging	1327/1440	117103900	987,12019	2203	4300	6503	SO:0001583	missense	80709	exon21			GCCAGATACCACA	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3980A>G	9.37:g.117103900T>C	ENSP00000303769:p.Tyr1327Cys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	126	40	0.31746	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	141|141	0.06456043956043957|0.06456043956043957	135|135	0.27439024390243905|0.27439024390243905	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	0|0	0.0|0.0	T|T	16.55|16.55	3.154873|3.154873	0.57259|0.57259	0.222651|0.222651	6.98E-4|6.98E-4	ENSG00000106948|ENSG00000106948	ENST00000320310|ENST00000307564;ENST00000374079;ENST00000374088;ENST00000223791;ENST00000374075	.|T;T;T;T;T	.|0.39592	.|1.99;1.07;1.99;1.73;1.97	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.000000	.|0.53938	.|D	.|0.000059	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.27590|0.27590	P|P	0.9492969|0.9492969	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.998;0.999	T|T	0.10567|0.10567	-1.0624|-1.0624	5|9	0.51188|0.72032	T|D	0.08|0.01	-18.4356|-18.4356	12.2902|12.2902	0.54815|0.54815	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs2787344;rs2787344|rs2787344;rs2787344	.|1327;1246	.|Q7Z591;Q7Z591-2	.|AKNA_HUMAN;.	V|C	338|1327;272;1327;787;1246	.|ENSP00000303769:Y1327C;ENSP00000363192:Y272C;ENSP00000363201:Y1327C;ENSP00000223791:Y787C;ENSP00000363188:Y1246C	ENSP00000314538:I338V|ENSP00000223791:Y787C	I|Y	-|-	1|2	0|0	AKNA|AKNA	116143721|116143721	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.450000|0.450000	0.32258|0.32258	4.341000|4.341000	0.59335|0.59335	2.209000|2.209000	0.71365|0.71365	0.533000|0.533000	0.62120|0.62120	ATC|TAT	T|0.919;C|0.081	0.081	strong		0.622	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595343	140595343	+	Missense_Mutation	SNP	G	G	C	rs56309578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140595343G>C	ENST00000341948.4	+	1	1835	c.1648G>C	c.(1648-1650)Gtg>Ctg	p.V550L		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	550	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)			GGTGCGCGTGGTGGTGCTGGA	0.721													C|||	343	0.0684904	0.1377	0.0663	5008	,	,		16063	0.003		0.0795	False		,,,				2504	0.0327				p.V550L		Atlas-SNP	.											.	PCDHB13	142	.	0			c.G1648C						PASS	.	C	LEU/VAL	522,3882		26,470,1706	33.0	38.0	36.0		1648	-3.5	0.0	5	dbSNP_129	36	734,7862		41,652,3605	no	missense	PCDHB13	NM_018933.2	32	67,1122,5311	CC,CG,GG		8.5389,11.8529,9.6615	benign	550/799	140595343	1256,11744	2202	4298	6500	SO:0001583	missense	56123	exon1			CGCGTGGTGGTGC	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.1648G>C	5.37:g.140595343G>C	ENSP00000345491:p.Val550Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	153	84	0.54902	NM_018933	A8K9V6	Missense_Mutation	SNP	ENST00000341948.4	37	CCDS4255.1	129	0.059065934065934064	67	0.13617886178861788	18	0.049723756906077346	2	0.0034965034965034965	42	0.055408970976253295	-	0.028	-1.351816	0.01256	0.118529	0.085389	ENSG00000187372	ENST00000341948;ENST00000430318;ENST00000419217	T	0.01745	4.66	3.0	-3.54	0.04653	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.12611	0.24	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.41395	-0.9511	9	0.02654	T	1	.	4.891	0.13726	0.0975:0.2484:0.4784:0.1756	rs56309578	550	Q9Y5F0	PCDBD_HUMAN	L	550;550;496	ENSP00000345491:V550L	ENSP00000345491:V550L	V	+	1	0	PCDHB13	140575527	0.000000	0.05858	0.005000	0.12908	0.004000	0.04260	-2.965000	0.00670	-1.078000	0.03117	-1.279000	0.01387	GTG	G|0.921;C|0.079	0.079	strong		0.721	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
TTN	7273	hgsc.bcm.edu	37	2	179613962	179613962	+	Intron	SNP	C	C	T	rs72648903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179613962C>T	ENST00000591111.1	-	45	10585				TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.V4389I			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)			TTAATAGTGACATCACTGAAA	0.343													C|||	95	0.0189696	0.0703	0.0029	5008	,	,		19175	0.0		0.0	False		,,,				2504	0.0				p.V4389I		Atlas-SNP	.											TTN_ENST00000360870,rectum,carcinoma,+1,1	TTN	18412	1	0			c.G13165A						PASS	.	C	,,ILE/VAL,,	221,4179	123.7+/-161.0	6,209,1985	57.0	62.0	60.0		,,13165,,	3.4	0.0	2	dbSNP_130	60	6,8586	3.7+/-12.6	0,6,4290	yes	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,29,,	6,215,6275	TT,TC,CC		0.0698,5.0227,1.7472	,,,,	,,4389/5605,,	179613962	227,12765	2200	4296	6496	SO:0001627	intron_variant	7273	exon46			TAGTGACATCACT	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.10360+3888G>A	2.37:g.179613962C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	28	0.337349	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	C	10.23	1.293061	0.23564	0.050227	6.98E-4	ENSG00000155657	ENST00000360870	T	0.60672	0.17	5.23	3.42	0.39159	.	.	.	.	.	T	0.04452	0.0122	N	0.24115	0.695	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.02126	-1.1209	9	0.16420	T	0.52	.	13.5505	0.61730	0.0:0.8613:0.0:0.1387	.	4389	Q8WZ42-6	.	I	4389	ENSP00000354117:V4389I	ENSP00000354117:V4389I	V	-	1	0	TTN	179322207	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	1.120000	0.31271	0.434000	0.26340	-2.010000	0.00438	GTC	C|0.980;T|0.020	0.020	strong		0.343	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
JMY	133746	hgsc.bcm.edu	37	5	78610174	78610174	+	Missense_Mutation	SNP	A	A	G	rs16876657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:78610174A>G	ENST00000396137.4	+	9	2621	c.2159A>G	c.(2158-2160)cAt>cGt	p.H720R	JMY_ENST00000412001.1_Intron	NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	720			H -> R (in dbSNP:rs16876657).		'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)		CAAGAGGATCATTGTGACTCT	0.453													A|||	389	0.0776757	0.1725	0.0159	5008	,	,		14532	0.0863		0.0169	False		,,,				2504	0.047				p.H720R		Atlas-SNP	.											.	JMY	82	.	0			c.A2159G						PASS	.	A	ARG/HIS	567,3465		34,499,1483	77.0	79.0	78.0		2159	0.7	0.0	5	dbSNP_123	78	108,8300		0,108,4096	yes	missense	JMY	NM_152405.4	29	34,607,5579	GG,GA,AA		1.2845,14.0625,5.426	benign	720/989	78610174	675,11765	2016	4204	6220	SO:0001583	missense	133746	exon9			AGGATCATTGTGA	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.2159A>G	5.37:g.78610174A>G	ENSP00000379441:p.His720Arg	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	120	54	0.45	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	37	CCDS4047.3	156	0.07142857142857142	71	0.1443089430894309	6	0.016574585635359115	66	0.11538461538461539	13	0.017150395778364115	A	1.854	-0.464379	0.04476	0.140625	0.012845	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.73152	-0.72	4.57	0.684	0.18003	.	0.879298	0.09693	N	0.768068	T	0.00328	0.0010	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06516	-1.0822	9	0.15499	T	0.54	.	6.7725	0.23601	0.6326:0.2899:0.0775:0.0	rs16876657;rs52832545;rs16876657	720	Q8N9B5	JMY_HUMAN	R	720	ENSP00000379441:H720R	ENSP00000282259:H720R	H	+	2	0	JMY	78645930	0.141000	0.22595	0.021000	0.16686	0.344000	0.29017	1.567000	0.36407	0.121000	0.18284	0.477000	0.44152	CAT	A|0.926;G|0.074	0.074	strong		0.453	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405	
NQO1	1728	hgsc.bcm.edu	37	16	69745145	69745145	+	Missense_Mutation	SNP	G	G	A	rs1800566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69745145G>A	ENST00000320623.5	-	6	1070	c.559C>T	c.(559-561)Cct>Tct	p.P187S	NQO1_ENST00000379046.2_Missense_Mutation_p.P149S|snoU13_ENST00000459361.1_RNA|NQO1_ENST00000379047.3_Missense_Mutation_p.P153S|NQO1_ENST00000561500.1_Missense_Mutation_p.P149S|CTD-2033A16.1_ENST00000562696.1_RNA|NQO1_ENST00000564043.1_Missense_Mutation_p.P166S|NQO1_ENST00000439109.2_Missense_Mutation_p.P115S	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	125	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	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		
SSTR3	6753	hgsc.bcm.edu	37	22	37603744	37603744	+	Silent	SNP	C	C	T	rs86583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	110	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	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		
ZNHIT1	10467	hgsc.bcm.edu	37	7	100866015	100866015	+	Silent	SNP	C	C	T	rs142012618		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100866015C>T	ENST00000305105.2	+	2	681	c.153C>T	c.(151-153)ctC>ctT	p.L51L	ZNHIT1_ENST00000492315.1_3'UTR	NM_006349.2	NP_006340.1	O43257	ZNHI1_HUMAN	zinc finger, HIT-type containing 1	51					negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of histone deacetylation (GO:0031063)|regulation of T cell proliferation (GO:0042129)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)	11	Lung NSC(181;0.168)|all_lung(186;0.215)					TCCCTCAGCTCGGCAAGAGAC	0.657													C|||	1	0.000199681	0.0	0.0	5008	,	,		16246	0.0		0.001	False		,,,				2504	0.0				p.L51L		Atlas-SNP	.											.	ZNHIT1	21	.	0			c.C153T						PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	57.0	53.0	54.0		153	-10.3	0.1	7	dbSNP_134	54	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	ZNHIT1	NM_006349.2		0,17,6486	TT,TC,CC		0.1163,0.1589,0.1307		51/155	100866015	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	10467	exon2			TCAGCTCGGCAAG	AF093571	CCDS5716.1	7q22.1	2010-09-15	2010-09-15	2003-08-08	ENSG00000106400	ENSG00000106400		"""Zinc fingers, HIT-type"""	21688	protein-coding gene	gene with protein product	"""putative cyclin G1 interacting protein"""		"""zinc finger protein, subfamily 4A (HIT domain containing), member 1"", ""zinc finger, HIT domain containing 1"""	ZNFN4A1			Standard	NM_006349		Approved	CG1I, H_DJ0747G18.14	uc003uye.3	O43257	OTTHUMG00000157113	ENST00000305105.2:c.153C>T	7.37:g.100866015C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	173	84	0.485549	NM_006349	Q6IB12	Silent	SNP	ENST00000305105.2	37	CCDS5716.1																																																																																			C|0.999;T|0.001	0.001	strong		0.657	ZNHIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347488.1	NM_006349	
SCN9A	6335	hgsc.bcm.edu	37	2	167142979	167142979	+	Missense_Mutation	SNP	C	C	T	rs58022607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:167142979C>T	ENST00000409435.1	-	10	1468	c.1469G>A	c.(1468-1470)aGt>aAt	p.S490N	SCN9A_ENST00000303354.6_Missense_Mutation_p.S491N|SCN9A_ENST00000409672.1_Missense_Mutation_p.S490N|SCN9A_ENST00000375387.4_Missense_Mutation_p.S491N|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	490			S -> N (in dbSNP:rs58022607). {ECO:0000269|PubMed:19763161}.		behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTCCTCTCCACTGGAGAGCTT	0.423													C|||	230	0.0459265	0.1551	0.0187	5008	,	,		19535	0.0		0.004	False		,,,				2504	0.0082				p.S490N		Atlas-SNP	.											.	SCN9A	296	.	0			c.G1469A						PASS	.	C	ASN/SER	464,3260		28,408,1426	111.0	104.0	106.0		1469	4.0	1.0	2	dbSNP_129	106	44,8140		3,38,4051	yes	missense	SCN9A	NM_002977.3	46	31,446,5477	TT,TC,CC		0.5376,12.4597,4.266	benign	490/1978	167142979	508,11400	1862	4092	5954	SO:0001583	missense	6335	exon11			TCTCCACTGGAGA	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1469G>A	2.37:g.167142979C>T	ENSP00000386330:p.Ser490Asn	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	181	181	1	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	95	0.043498168498168496	85	0.17276422764227642	8	0.022099447513812154	0	0.0	2	0.002638522427440633	C	11.89	1.773085	0.31411	0.124597	0.005376	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435;ENST00000454569;ENST00000452182	D;D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75;-2.75	5.82	4.01	0.46588	Domain of unknown function DUF3451 (1);	0.994312	0.08172	N	0.986830	T	0.01592	0.0051	M	0.66939	2.045	0.40162	P	0.022926000000000002	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.003;0.003	T	0.53599	-0.8416	9	0.31617	T	0.26	.	6.4457	0.21875	0.2587:0.6092:0.0:0.1321	rs58022607	490;490;491	E7EUN6;Q15858;E9PF08	.;SCN9A_HUMAN;.	N	490;491;491;490;355;355	ENSP00000386306:S490N;ENSP00000364536:S491N;ENSP00000304748:S491N;ENSP00000386330:S490N;ENSP00000413212:S355N;ENSP00000393141:S355N	ENSP00000304748:S491N	S	-	2	0	SCN9A	166851225	0.956000	0.32656	1.000000	0.80357	0.897000	0.52465	0.338000	0.19858	1.468000	0.48064	0.484000	0.47621	AGT	C|0.964;T|0.036	0.036	strong		0.423	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417286	105417286	+	Missense_Mutation	SNP	G	G	A	rs149840830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417286G>A	ENST00000333244.5	-	7	4621	c.4502C>T	c.(4501-4503)cCg>cTg	p.P1501L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1501						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)			CCCGAACGACGGCATCTTGAA	0.607													.|||	272	0.0543131	0.2027	0.0058	5008	,	,		14935	0.0		0.0	False		,,,				2504	0.0				p.P1501L		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,0,1	AHNAK2	719	1	0			c.C4502T						PASS	.	G	LEU/PRO	600,3288		124,352,1468	194.0	134.0	153.0		4502	4.2	0.9	14	dbSNP_134	153	13,8061		4,5,4028	no	missense	AHNAK2	NM_138420.2	98	128,357,5496	AA,AG,GG		0.161,15.4321,5.1246	probably-damaging	1501/5796	105417286	613,11349	1944	4037	5981	SO:0001583	missense	113146	exon7			AACGACGGCATCT	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.4502C>T	14.37:g.105417286G>A	ENSP00000353114:p.Pro1501Leu	Somatic	370	0	0		WXS	Illumina HiSeq	Phase_I	355	337	0.949296	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	92	0.04212454212454213	90	0.18292682926829268	2	0.0055248618784530384	0	0.0	0	0.0	g	14.95	2.687349	0.48097	0.154321	0.00161	ENSG00000185567	ENST00000333244	T	0.03065	4.06	4.16	4.16	0.48862	.	.	.	.	.	T	0.00073	0.0002	H	0.95043	3.615	0.27144	P	0.9615793	D	0.89917	1.0	D	0.91635	0.999	T	0.05305	-1.0893	8	0.87932	D	0	-29.3229	16.1243	0.81382	0.0:0.0:1.0:0.0	.	1501	Q8IVF2	AHNK2_HUMAN	L	1501	ENSP00000353114:P1501L	ENSP00000353114:P1501L	P	-	2	0	AHNAK2	104488331	0.035000	0.19736	0.884000	0.34674	0.008000	0.06430	0.923000	0.28757	1.867000	0.54127	0.485000	0.47835	CCG	G|0.966;A|0.034	0.034	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
NRIP1	8204	hgsc.bcm.edu	37	21	16337538	16337538	+	Silent	SNP	G	G	A	rs28587162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:16337538G>A	ENST00000400202.1	-	3	3688	c.2976C>T	c.(2974-2976)agC>agT	p.S992S	NRIP1_ENST00000318948.4_Silent_p.S992S|NRIP1_ENST00000400199.1_Silent_p.S992S|AF127577.10_ENST00000446301.1_RNA			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	992	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)		CCATGCAACTGCTGGGCTGAG	0.428													G|||	112	0.0223642	0.0787	0.0115	5008	,	,		21468	0.0		0.0	False		,,,				2504	0.0				p.S992S		Atlas-SNP	.											.	NRIP1	103	.	0			c.C2976T						PASS	.	G		334,4072	175.9+/-205.1	15,304,1884	70.0	62.0	65.0		2976	4.0	0.0	21	dbSNP_125	65	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	NRIP1	NM_003489.3		15,305,6182	AA,AG,GG		0.0116,7.5806,2.5761		992/1159	16337538	335,12669	2203	4299	6502	SO:0001819	synonymous_variant	8204	exon4			GCAACTGCTGGGC	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.2976C>T	21.37:g.16337538G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	37	CCDS13568.1																																																																																			G|0.979;A|0.021	0.021	strong		0.428	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
TRPM5	29850	hgsc.bcm.edu	37	11	2439767	2439767	+	Missense_Mutation	SNP	T	T	C	rs886277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2439767T>C	ENST00000155858.6	-	5	712	c.704A>G	c.(703-705)aAc>aGc	p.N235S	TRPM5_ENST00000528453.1_Missense_Mutation_p.N235S|TRPM5_ENST00000533060.1_Missense_Mutation_p.N235S|TRPM5_ENST00000452833.1_Missense_Mutation_p.N237S	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)		CTCCAAGGTGTTGGGATCACC	0.667													C|||	2691	0.53734	0.6407	0.5375	5008	,	,		17424	0.6607		0.3678	False		,,,				2504	0.4448				p.N235S	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.A704G						PASS	.	C	SER/ASN	2693,1703	488.7+/-361.3	839,1015,344	41.0	39.0	40.0		704	1.4	1.0	11	dbSNP_86	40	3312,5282	624.2+/-397.5	650,2012,1635	yes	missense	TRPM5	NM_014555.3	46	1489,3027,1979	CC,CT,TT		38.5385,38.7398,46.2279	benign	235/1166	2439767	6005,6985	2198	4297	6495	SO:0001583	missense	29850	exon5			AAGGTGTTGGGAT	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.704A>G	11.37:g.2439767T>C	ENSP00000155858:p.Asn235Ser	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	190	190	1	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	1160	0.5311355311355311	307	0.6239837398373984	192	0.5303867403314917	381	0.666083916083916	280	0.36939313984168864	C	0.011	-1.713757	0.00706	0.612602	0.385385	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	3.41	1.44	0.22558	.	0.358275	0.27336	N	0.019824	T	0.00012	0.0000	L	0.39898	1.24	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	0.43294	-0.9400	9	0.07813	T	0.8	-17.7773	7.5438	0.27755	0.0:0.6853:0.0:0.3147	rs886277;rs56695969;rs886277	235;237;235	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	S	229;235;237;235;235;235	ENSP00000434383:N229S;ENSP00000155858:N235S;ENSP00000387965:N237S;ENSP00000434121:N235S;ENSP00000436809:N235S	ENSP00000155858:N235S	N	-	2	0	TRPM5	2396343	0.874000	0.30092	1.000000	0.80357	0.459000	0.32528	0.252000	0.18278	0.262000	0.21774	-0.320000	0.08662	AAC	T|0.506;C|0.494	0.494	strong		0.667	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
TMEM132E	124842	hgsc.bcm.edu	37	17	32962004	32962004	+	Silent	SNP	C	C	T	rs73988752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:32962004C>T	ENST00000321639.5	+	8	1933	c.1605C>T	c.(1603-1605)acC>acT	p.T535T		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	535						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TGGAGGTCACCGACCTAGTCA	0.622													C|||	435	0.086861	0.1929	0.0303	5008	,	,		15370	0.005		0.0358	False		,,,				2504	0.1207				p.T535T		Atlas-SNP	.											.	TMEM132E	122	.	0			c.C1605T						PASS	.	C		745,3661	300.4+/-286.3	61,623,1519	90.0	69.0	76.0		1605	-8.0	1.0	17	dbSNP_130	76	276,8324	104.6+/-165.6	4,268,4028	no	coding-synonymous	TMEM132E	NM_207313.1		65,891,5547	TT,TC,CC		3.2093,16.9088,7.8502		535/985	32962004	1021,11985	2203	4300	6503	SO:0001819	synonymous_variant	124842	exon8			GGTCACCGACCTA	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1605C>T	17.37:g.32962004C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_207313	Q8WUF4|Q8WVA5	Silent	SNP	ENST00000321639.5	37	CCDS11283.1																																																																																			C|0.929;T|0.071	0.071	strong		0.622	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
ZNF208	7757	hgsc.bcm.edu	37	19	22155434	22155434	+	Missense_Mutation	SNP	T	T	C	rs139351235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22155434T>C	ENST00000397126.4	-	4	2550	c.2402A>G	c.(2401-2403)gAt>gGt	p.D801G	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	801					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)				GGGTTTCTCATCAGTATGAAT	0.363													N|||	152	0.0303514	0.1089	0.0115	5008	,	,		20788	0.0		0.0	False		,,,				2504	0.0				p.D801G		Atlas-SNP	.											.	ZNF208	817	.	0			c.A2402G						PASS	.	C	GLY/ASP	404,3794		23,358,1718	57.0	66.0	63.0		2402	2.6	0.1	19	dbSNP_134	63	3,8493		0,3,4245	no	missense	ZNF208	NM_007153.3	94	23,361,5963	CC,CT,TT		0.0353,9.6236,3.2062	benign	801/1281	22155434	407,12287	2099	4248	6347	SO:0001583	missense	7757	exon4			TTCTCATCAGTAT	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.2402A>G	19.37:g.22155434T>C	ENSP00000380315:p.Asp801Gly	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	26	16	0.615385	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	t	0.001	-2.962685	0.00049	0.096236	3.53E-4	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.11277	2.79	2.57	2.57	0.30868	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.43327	-0.9398	7	0.02654	T	1	.	5.0553	0.14529	0.0:0.6551:0.213:0.1319	.	701	O43345	ZN208_HUMAN	G	801;701	ENSP00000380315:D801G	ENSP00000380315:D801G	D	-	2	0	ZNF208	21947274	0.000000	0.05858	0.123000	0.21794	0.158000	0.22134	-0.473000	0.06615	0.123000	0.18342	-1.171000	0.01739	GAT	T|0.972;C|0.028	0.028	strong		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
DSCAML1	57453	hgsc.bcm.edu	37	11	117329597	117329597	+	Silent	SNP	G	G	C	rs115831160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117329597G>C	ENST00000321322.6	-	19	3622	c.3621C>G	c.(3619-3621)acC>acG	p.T1207T	DSCAML1_ENST00000527706.1_Silent_p.T937T	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1147	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		GCTCCCGCGTGGTGGTGATGT	0.652													G|||	5	0.000998403	0.0038	0.0	5008	,	,		20355	0.0		0.0	False		,,,				2504	0.0				p.T1207T		Atlas-SNP	.											.	DSCAML1	286	.	0			c.C3621G						PASS	.	G		14,4388	22.3+/-47.3	0,14,2187	104.0	95.0	98.0		3621	-7.8	0.7	11	dbSNP_132	98	2,8590	2.2+/-6.3	0,2,4294	no	coding-synonymous	DSCAML1	NM_020693.2		0,16,6481	CC,CG,GG		0.0233,0.318,0.1231		1207/2114	117329597	16,12978	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon19			CCGCGTGGTGGTG		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.3621C>G	11.37:g.117329597G>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			G|0.999;C|0.001	0.001	strong		0.652	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
MYZAP	100820829	hgsc.bcm.edu	37	15	57925873	57925873	+	Missense_Mutation	SNP	G	G	C	rs148672365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:57925873G>C	ENST00000267853.5	+	8	961	c.867G>C	c.(865-867)gaG>gaC	p.E289D	GCOM1_ENST00000380569.2_Missense_Mutation_p.E289D|GCOM1_ENST00000587652.1_Missense_Mutation_p.E289D|GCOM1_ENST00000380561.2_Missense_Mutation_p.E258D|POLR2M_ENST00000380563.2_5'UTR|MYZAP_ENST00000380565.4_Missense_Mutation_p.E289D|GCOM1_ENST00000572390.1_Missense_Mutation_p.E289D|GCOM1_ENST00000396180.1_Missense_Mutation_p.E258D|GCOM1_ENST00000380568.3_Missense_Mutation_p.E289D|GCOM1_ENST00000380560.2_Missense_Mutation_p.E220D|GCOM1_ENST00000574161.1_Missense_Mutation_p.E289D			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	289					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											AAGCAGCAGAGATCAGCCTAG	0.478													G|||	20	0.00399361	0.0144	0.0014	5008	,	,		18055	0.0		0.0	False		,,,				2504	0.0				p.E289D		Atlas-SNP	.											.	GCOM1	66	.	0			c.G867C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	70,4314	64.7+/-102.0	0,70,2122	128.0	127.0	128.0		867,867,867,867	3.5	1.0	15	dbSNP_134	128	0,8584		0,0,4292	yes	missense,missense,missense,missense	GCOM1	NM_001018090.3,NM_001018091.3,NM_001018100.3,NM_152451.6	45,45,45,45	0,70,6414	CC,CG,GG		0.0,1.5967,0.5398	probably-damaging,probably-damaging,probably-damaging,probably-damaging	289/551,289/446,289/467,289/439	57925873	70,12898	2192	4292	6484	SO:0001583	missense	145781	exon8			AGCAGAGATCAGC	FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"""myocardium-enriched zonula adherens protein"""	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.867G>C	15.37:g.57925873G>C	ENSP00000267853:p.Glu289Asp	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	162	79	0.487654	NM_001018090	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	37	CCDS10162.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	18.62	3.663734	0.67700	0.015967	0.0	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568;ENST00000461709	T;T;T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41	5.68	3.46	0.39613	.	0.000000	0.85682	D	0.000000	T	0.37019	0.0988	M	0.75615	2.305	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.87578	0.995;0.993;0.995;0.998	T	0.51911	-0.8645	10	0.62326	D	0.03	-34.0747	12.4064	0.55443	0.1663:0.0:0.8337:0.0	.	289;289;289;289	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	D	289;258;258;220;289;289;289;4	ENSP00000369943:E289D;ENSP00000369935:E258D;ENSP00000379483:E258D;ENSP00000369933:E220D;ENSP00000267853:E289D;ENSP00000369939:E289D;ENSP00000369942:E289D;ENSP00000431396:E4D	ENSP00000267853:E289D	E	+	3	2	GCOM1	55713165	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	1.551000	0.36233	1.394000	0.46624	0.563000	0.77884	GAG	G|0.994;C|0.006	0.006	strong		0.478	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100	
TANC1	85461	hgsc.bcm.edu	37	2	160019901	160019901	+	Missense_Mutation	SNP	C	C	T	rs55929944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160019901C>T	ENST00000263635.6	+	8	1027	c.790C>T	c.(790-792)Cgc>Tgc	p.R264C	TANC1_ENST00000454300.1_Missense_Mutation_p.R158C	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	264					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GCTTCATGACCGCAGGGCAGA	0.522													C|||	163	0.0325479	0.1172	0.0086	5008	,	,		19708	0.0		0.002	False		,,,				2504	0.0				p.R264C		Atlas-SNP	.											.	TANC1	157	.	0			c.C790T						PASS	.	C	CYS/ARG,CYS/ARG	436,3492		33,370,1561	74.0	79.0	77.0		787,790	6.0	1.0	2	dbSNP_129	77	2,8292		0,2,4145	yes	missense,missense	TANC1	NM_001145909.1,NM_033394.2	180,180	33,372,5706	TT,TC,CC		0.0241,11.0998,3.5837	probably-damaging,probably-damaging	263/1391,264/1862	160019901	438,11784	1964	4147	6111	SO:0001583	missense	85461	exon8			CATGACCGCAGGG	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.790C>T	2.37:g.160019901C>T	ENSP00000263635:p.Arg264Cys	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	278	165	0.593525	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	62	0.028388278388278388	57	0.11585365853658537	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	15.63	2.890072	0.52014	0.110998	2.41E-4	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.70869	-0.51;-0.52	6.04	6.04	0.98038	.	0.113037	0.64402	D	0.000007	T	0.02455	0.0075	L	0.54323	1.7	0.80722	D	1	B;B	0.24721	0.066;0.11	B;B	0.17722	0.01;0.019	T	0.25710	-1.0124	10	0.66056	D	0.02	.	20.5948	0.99439	0.0:1.0:0.0:0.0	rs55929944	263;264	B9EK39;Q9C0D5	.;TANC1_HUMAN	C	158;264	ENSP00000396339:R158C;ENSP00000263635:R264C	ENSP00000263635:R264C	R	+	1	0	TANC1	159728147	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.696000	0.54757	2.873000	0.98535	0.563000	0.77884	CGC	C|0.971;T|0.029	0.029	strong		0.522	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
PCSK7	9159	hgsc.bcm.edu	37	11	117078702	117078702	+	Silent	SNP	A	A	C	rs200068220		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117078702A>C	ENST00000320934.3	-	14	2400	c.1770T>G	c.(1768-1770)ctT>ctG	p.L590L	PCSK7_ENST00000529458.1_5'UTR|PCSK7_ENST00000540028.1_Silent_p.L231L	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	590					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.L590L(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CCCTGATGACAAGCCTGTAGG	0.567			T	IGH@	MLCLS																																p.L590L		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	PCSK7,NS,carcinoma,0,1	PCSK7	59	1	1	Substitution - coding silent(1)	ovary(1)	c.T1770G						scavenged	.						2.0	2.0	2.0					11																	117078702		1345	2817	4162	SO:0001819	synonymous_variant	9159	exon14			GATGACAAGCCTG	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.1770T>G	11.37:g.117078702A>C		Somatic	923	221	0.239437		WXS	Illumina HiSeq	Phase_I	750	335	0.446667	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			.	.	weak		0.567	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
MAP3K9	4293	hgsc.bcm.edu	37	14	71204973	71204973	+	Silent	SNP	C	C	T	rs7153601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:71204973C>T	ENST00000554752.2	-	8	1832	c.1833G>A	c.(1831-1833)tcG>tcA	p.S611S	MAP3K9_ENST00000553414.1_Silent_p.S353S|MAP3K9_ENST00000555993.2_Silent_p.S611S|MAP3K9_ENST00000554146.1_Silent_p.S348S|MAP3K9_ENST00000381250.4_Silent_p.S611S	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	611					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		CTTCATCTCCCGAGGCAAGCT	0.493													C|||	1084	0.216454	0.1573	0.2565	5008	,	,		19782	0.3363		0.167	False		,,,				2504	0.1953				p.S611S	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.G1833A						PASS	.	C		698,3708	293.3+/-282.5	57,584,1562	131.0	118.0	122.0		1833	-6.1	1.0	14	dbSNP_116	122	1399,7201	270.4+/-288.9	109,1181,3010	no	coding-synonymous	MAP3K9	NM_033141.2		166,1765,4572	TT,TC,CC		16.2674,15.842,16.1233		611/1119	71204973	2097,10909	2203	4300	6503	SO:0001819	synonymous_variant	4293	exon8			ATCTCCCGAGGCA	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.1833G>A	14.37:g.71204973C>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	192	89	0.463542	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Silent	SNP	ENST00000554752.2	37																																																																																				C|0.823;T|0.177	0.177	strong		0.493	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2		
RIN3	79890	hgsc.bcm.edu	37	14	93154540	93154540	+	Silent	SNP	C	C	T	rs71461983|rs570458246|rs68153141|rs71698059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:93154540C>T	ENST00000216487.7	+	10	3060	c.2901C>T	c.(2899-2901)ggC>ggT	p.G967G	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	967	Poly-Gly.				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)				ACGGTGGTGGCGGCGGCGGCG	0.736													-|||	66	0.0131789	0.0068	0.0159	5008	,	,		9928	0.0099		0.0298	False		,,,				2504	0.0061				p.G967G		Atlas-SNP	.											.	RIN3	81	.	0			c.C2901T						PASS	.						5.0	7.0	7.0					14																	93154540		1961	3940	5901	SO:0001819	synonymous_variant	79890	exon10			TGGTGGCGGCGGC	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.2901C>T	14.37:g.93154540C>T		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	15	12	0.8	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Silent	SNP	ENST00000216487.7	37	CCDS32144.1																																																																																			C|0.974;T|0.026	0.026	strong		0.736	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
MTSS1	9788	hgsc.bcm.edu	37	8	125575047	125575047	+	Silent	SNP	G	G	T	rs16899702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:125575047G>T	ENST00000518547.1	-	10	1484	c.1011C>A	c.(1009-1011)ccC>ccA	p.P337P	MTSS1_ENST00000378017.3_Silent_p.P337P|MTSS1_ENST00000395508.2_Silent_p.P71P|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000325064.5_Silent_p.P341P|MTSS1_ENST00000431961.2_Silent_p.P137P|MTSS1_ENST00000354184.4_Silent_p.P137P|MTSS1_ENST00000524090.1_Silent_p.P227P	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	337	Ser-rich.				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)			CTGGCGGCATGGGGGATGGTG	0.607													G|||	305	0.0609026	0.2201	0.0144	5008	,	,		18723	0.001		0.003	False		,,,				2504	0.0				p.P337P	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.C1011A						PASS	.	G		702,3704	291.8+/-281.7	69,564,1570	58.0	55.0	56.0		1011	-1.0	1.0	8	dbSNP_123	56	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous	MTSS1	NM_014751.4		69,583,5851	TT,TG,GG		0.2209,15.9328,5.5436		337/756	125575047	721,12285	2203	4300	6503	SO:0001819	synonymous_variant	9788	exon10			CGGCATGGGGGAT	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.1011C>A	8.37:g.125575047G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Silent	SNP	ENST00000518547.1	37	CCDS6353.1	116	0.05311355311355311	107	0.21747967479674796	8	0.022099447513812154	1	0.0017482517482517483	0	0.0	G	1.045	-0.677528	0.03378	0.159328	0.002209	ENSG00000170873	ENST00000519168;ENST00000523179	.	.	.	5.6	-0.986	0.10252	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.26780	-1.0093	3	.	.	.	-14.8982	2.3089	0.04181	0.1747:0.1927:0.435:0.1977	rs16899702;rs16899702	.	.	.	N	85;185	.	.	H	-	1	0	MTSS1	125644228	0.683000	0.27633	0.995000	0.50966	0.047000	0.14425	-0.264000	0.08658	-0.095000	0.12351	-0.156000	0.13503	CAT	G|0.936;T|0.064	0.064	strong		0.607	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	
BTBD3	22903	hgsc.bcm.edu	37	20	11903654	11903654	+	Silent	SNP	G	G	A	rs35364034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:11903654G>A	ENST00000405977.1	+	5	1534	c.909G>A	c.(907-909)gcG>gcA	p.A303A	BTBD3_ENST00000399006.2_Silent_p.A242A|BTBD3_ENST00000254977.3_Silent_p.A242A|BTBD3_ENST00000378226.2_Silent_p.A303A	NM_001282550.1|NM_001282552.1|NM_001282554.1	NP_001269479.1|NP_001269481.1|NP_001269483.1	Q9Y2F9	BTBD3_HUMAN	BTB (POZ) domain containing 3	303					cerebral cortex development (GO:0021987)|dendrite morphogenesis (GO:0048813)	cytosol (GO:0005829)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(18)|ovary(3)|skin(2)	34						AAGATCTGGCGTTGAGCATTG	0.448													G|||	478	0.0954473	0.0371	0.0706	5008	,	,		22219	0.2054		0.0368	False		,,,				2504	0.1391				p.A303A		Atlas-SNP	.											BTBD3,caecum,carcinoma,+1,4	BTBD3	92	4	0			c.G909A						scavenged	.	G	,	186,4220	118.4+/-156.1	4,178,2021	106.0	106.0	106.0		909,726	-2.5	0.1	20	dbSNP_126	106	424,8176	131.8+/-189.6	10,404,3886	no	coding-synonymous,coding-synonymous	BTBD3	NM_014962.2,NM_181443.1	,	14,582,5907	AA,AG,GG		4.9302,4.2215,4.6901	,	303/523,242/462	11903654	610,12396	2203	4300	6503	SO:0001819	synonymous_variant	22903	exon4			TCTGGCGTTGAGC	AB023169	CCDS13113.1, CCDS13114.1	20p12.2	2013-01-08			ENSG00000132640	ENSG00000132640		"""BTB/POZ domain containing"""	15854	protein-coding gene	gene with protein product		615566					Standard	NM_001282551		Approved	KIAA0952, dJ742J24.1	uc002wnz.3	Q9Y2F9	OTTHUMG00000031889	ENST00000405977.1:c.909G>A	20.37:g.11903654G>A		Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	157	87	0.55414	NM_014962	D3DW19|Q5JY73	Silent	SNP	ENST00000405977.1	37	CCDS13113.1																																																																																			G|0.944;A|0.056	0.056	strong		0.448	BTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078021.3		
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919934	12919934	+	Missense_Mutation	SNP	A	A	G	rs3204805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919934A>G	ENST00000240189.2	+	3	761	c.674A>G	c.(673-675)tAt>tGt	p.Y225C		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	225			Y -> C (in dbSNP:rs3204805).		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)		AGAAAGCTTTATTGTTACCTG	0.383													.|||	849	0.169529	0.1437	0.1095	5008	,	,		22588	0.3125		0.1352	False		,,,				2504	0.135				p.Y225C		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.A674G						PASS	.	G	CYS/TYR	714,3690	758.0+/-412.8	77,560,1565	101.0	106.0	104.0		674	-1.7	0.0	1	dbSNP_105	104	1254,7330	756.9+/-407.5	112,1030,3150	no	missense	PRAMEF2	NM_023014.1	194	189,1590,4715	GG,GA,AA		14.6086,16.2125,15.1524	benign	225/475	12919934	1968,11020	2202	4292	6494	SO:0001583	missense	65122	exon3			AGCTTTATTGTTA		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.674A>G	1.37:g.12919934A>G	ENSP00000240189:p.Tyr225Cys	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	138	79	0.572464	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	372	0.17032967032967034	50	0.1016260162601626	46	0.1270718232044199	165	0.28846153846153844	111	0.14643799472295516	G	1.447	-0.566127	0.03910	0.162125	0.146086	ENSG00000120952	ENST00000240189	T	0.14766	2.48	0.842	-1.68	0.08212	.	0.335847	0.28688	N	0.014461	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.17465	0.022	B	0.26202	0.067	T	0.48103	-0.9064	9	0.66056	D	0.02	.	3.4172	0.07380	0.4582:0.2964:0.2453:0.0	rs3204805;rs17038687;rs52806752;rs3204805	225	O60811	PRAM2_HUMAN	C	225	ENSP00000240189:Y225C	ENSP00000240189:Y225C	Y	+	2	0	PRAMEF2	12842521	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.549000	0.02182	-2.688000	0.00405	-2.828000	0.00107	TAT	A|0.846;G|0.154	0.154	strong		0.383	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
ADH4	127	hgsc.bcm.edu	37	4	100047812	100047812	+	Silent	SNP	G	G	A	rs1126672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100047812G>A	ENST00000265512.7	-	8	1125	c.1051C>T	c.(1051-1053)Ctg>Ttg	p.L351L	ADH4_ENST00000508393.1_Silent_p.L370L|ADH4_ENST00000505590.1_Silent_p.L370L|RP11-696N14.1_ENST00000500358.2_RNA|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	134	0	0		WXS	Illumina HiSeq	Phase_I	136	75	0.551471	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	
MED26	9441	hgsc.bcm.edu	37	19	16687870	16687870	+	Silent	SNP	G	G	A	rs61734286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16687870G>A	ENST00000263390.3	-	3	1033	c.771C>T	c.(769-771)gaC>gaT	p.D257D	CTC-429P9.4_ENST00000593962.1_5'Flank|CTD-3222D19.2_ENST00000409035.1_Silent_p.D265D	NM_004831.3	NP_004822.2	O95402	MED26_HUMAN	mediator complex subunit 26	257	Pro-rich.				gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	8						CCGGAGTCTCGTCCACCCTGT	0.677													G|||	165	0.0329473	0.121	0.0072	5008	,	,		14022	0.0		0.0	False		,,,				2504	0.0				p.D257D		Atlas-SNP	.											.	MED26	25	.	0			c.C771T						PASS	.	G		407,3999	185.0+/-212.2	21,365,1817	30.0	32.0	31.0		771	-9.5	0.1	19	dbSNP_129	31	2,8598		0,2,4298	no	coding-synonymous	MED26	NM_004831.3		21,367,6115	AA,AG,GG		0.0233,9.2374,3.1447		257/601	16687870	409,12597	2203	4300	6503	SO:0001819	synonymous_variant	9441	exon3			AGTCTCGTCCACC	AF104253	CCDS12347.1	19p13.11	2008-02-05	2007-07-30	2007-07-30		ENSG00000105085			2376	protein-coding gene	gene with protein product		605043	"""cofactor required for Sp1 transcriptional activation, subunit 7, 70kDa"""	CRSP7		9989412	Standard	NM_004831		Approved	CRSP70	uc002nen.1	O95402		ENST00000263390.3:c.771C>T	19.37:g.16687870G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_004831	A1A4S3|Q0VGB6	Silent	SNP	ENST00000263390.3	37	CCDS12347.1																																																																																			G|0.967;A|0.033	0.033	strong		0.677	MED26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461178.1	NM_004831	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256275	140256275	+	Silent	SNP	G	G	A	rs73793508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140256275G>A	ENST00000398631.2	+	1	1218	c.1218G>A	c.(1216-1218)tcG>tcA	p.S406S	PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	406	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(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)			ATTACTACTCGTTGGTGCTGG	0.607													.|||	65	0.0129792	0.0484	0.0014	5008	,	,		20801	0.0		0.0	False		,,,				2504	0.0				p.S406S	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,NS,carcinoma,+1,1	PCDHA12	196	1	0			c.G1218A						PASS	.	G	,,,,,,,,,,,,,,,	143,4263	102.1+/-140.7	3,137,2063	190.0	183.0	185.0		,,,1218,,,,,,,,,,,,1218	-9.9	0.0	5	dbSNP_130	185	0,8596		0,0,4298	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	,,,,,,,,,,,,,,,	3,137,6361	AA,AG,GG		0.0,3.2456,1.0998	,,,,,,,,,,,,,,,	,,,406/942,,,,,,,,,,,,406/793	140256275	143,12859	2203	4298	6501	SO:0001819	synonymous_variant	56137	exon1			CTACTCGTTGGTG	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.1218G>A	5.37:g.140256275G>A		Somatic	307	1	0.00325733		WXS	Illumina HiSeq	Phase_I	312	151	0.483974	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			G|0.990;A|0.010	0.010	strong		0.607	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
RIPK4	54101	hgsc.bcm.edu	37	21	43176799	43176799	+	Silent	SNP	T	T	G	rs13049286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43176799T>G	ENST00000352483.2	-	2	424	c.360A>C	c.(358-360)cgA>cgC	p.R120R	RIPK4_ENST00000544709.1_Silent_p.R57R|RIPK4_ENST00000332512.3_Silent_p.R120R|RIPK4_ENST00000542057.1_Silent_p.R57R			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	120	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CGTGGATGATTCGGAACCGGA	0.627													G|||	633	0.126398	0.171	0.0893	5008	,	,		16787	0.0417		0.1312	False		,,,				2504	0.1748				p.R120R		Atlas-SNP	.											.	RIPK4	151	.	0			c.A360C						PASS	.	G		748,3658	756.3+/-412.6	61,626,1516	80.0	72.0	75.0		360	-5.7	0.0	21	dbSNP_121	75	1160,7440	765.2+/-407.6	87,986,3227	no	coding-synonymous	RIPK4	NM_020639.2		148,1612,4743	GG,GT,TT		13.4884,16.9768,14.6702		120/785	43176799	1908,11098	2203	4300	6503	SO:0001819	synonymous_variant	54101	exon2			GATGATTCGGAAC	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.360A>C	21.37:g.43176799T>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_020639	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				T|0.869;G|0.131	0.131	strong		0.627	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
PSG5	5673	hgsc.bcm.edu	37	19	43689004	43689004	+	Silent	SNP	G	G	A	rs2302112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43689004G>A	ENST00000366175.3	-	2	490	c.360C>T	c.(358-360)taC>taT	p.Y120Y	PSG5_ENST00000407356.1_Silent_p.Y120Y|PSG5_ENST00000342951.6_Silent_p.Y120Y|PSG5_ENST00000599812.1_Silent_p.Y120Y|PSG5_ENST00000404580.1_Silent_p.Y120Y|PSG5_ENST00000401992.1_5'UTR|PSG5_ENST00000407568.1_Silent_p.Y120Y			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	120	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.Y120Y(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				TGTGTAAGGTGTAGGATCCTG	0.443													G|||	1626	0.324681	0.1793	0.2536	5008	,	,		21945	0.5952		0.1541	False		,,,				2504	0.4683				p.Y120Y		Atlas-SNP	.											PSG5,NS,carcinoma,0,1	PSG5	58	1	1	Substitution - coding silent(1)	stomach(1)	c.C360T						scavenged	.	G	,	834,3572		112,610,1481	344.0	312.0	323.0		360,360	1.6	0.1	19	dbSNP_100	323	1468,7122		149,1170,2976	no	coding-synonymous,coding-synonymous	PSG5	NM_001130014.1,NM_002781.3	,	261,1780,4457	AA,AG,GG		17.0896,18.9287,17.7131	,	120/336,120/336	43689004	2302,10694	2203	4295	6498	SO:0001819	synonymous_variant	5673	exon2			TAAGGTGTAGGAT		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.360C>T	19.37:g.43689004G>A		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	271	110	0.405904	NM_002781	Q15239|Q96QJ1|Q9UQ75	Silent	SNP	ENST00000366175.3	37	CCDS12617.1																																																																																			G|0.795;A|0.205	0.205	strong		0.443	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
SLC7A1	6541	hgsc.bcm.edu	37	13	30107067	30107067	+	Silent	SNP	G	G	C	rs2277451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:30107067G>C	ENST00000380752.5	-	4	809	c.423C>G	c.(421-423)ggC>ggG	p.G141G		NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	141					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)	p.G141G(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|stomach(1)|urinary_tract(2)	24		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CGATGGGTCTGCCTATCAGCT	0.552													G|||	1246	0.248802	0.152	0.2723	5008	,	,		17784	0.6052		0.0517	False		,,,				2504	0.1984				p.G141G		Atlas-SNP	.											SLC7A1,NS,carcinoma,0,1	SLC7A1	64	1	1	Substitution - coding silent(1)	stomach(1)	c.C423G						PASS	.	G		650,3756	276.0+/-272.9	46,558,1599	85.0	81.0	82.0		423	2.0	1.0	13	dbSNP_100	82	462,8138	137.6+/-194.5	14,434,3852	no	coding-synonymous	SLC7A1	NM_003045.4		60,992,5451	CC,CG,GG		5.3721,14.7526,8.5499		141/630	30107067	1112,11894	2203	4300	6503	SO:0001819	synonymous_variant	6541	exon4			GGGTCTGCCTATC	AF078107	CCDS9333.1	13q12.3	2013-05-22			ENSG00000139514	ENSG00000139514		"""Solute carriers"""	11057	protein-coding gene	gene with protein product	"""ecotropic retroviral receptor"", ""amino acid transporter, cationic 1"""	104615		ERR, ATRC1		1348489	Standard	NM_003045		Approved	CAT-1, HCAT1, REC1L	uc001uso.3	P30825	OTTHUMG00000016658	ENST00000380752.5:c.423C>G	13.37:g.30107067G>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	157	60	0.382166	NM_003045	Q5JR50	Silent	SNP	ENST00000380752.5	37	CCDS9333.1																																																																																			G|0.860;C|0.140	0.140	strong		0.552	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045	
FLG	2312	hgsc.bcm.edu	37	1	152281290	152281290	+	Silent	SNP	A	A	G	rs80353812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281290A>G	ENST00000368799.1	-	3	6107	c.6072T>C	c.(6070-6072)caT>caC	p.H2024H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	246	0	0		WXS	Illumina HiSeq	Phase_I	505	246	0.487129	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	
SEZ6	124925	hgsc.bcm.edu	37	17	27286851	27286851	+	Missense_Mutation	SNP	T	T	C	rs1976165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27286851T>C	ENST00000317338.12	-	8	2064	c.1636A>G	c.(1636-1638)Aca>Gca	p.T546A	SEZ6_ENST00000442608.3_Missense_Mutation_p.T546A|SEZ6_ENST00000360295.9_Missense_Mutation_p.T546A|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000335960.6_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	546	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.		T -> A (in dbSNP:rs1976165).		adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|negative regulation of dendrite development (GO:2000171)|positive regulation of dendrite development (GO:1900006)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	apical dendrite (GO:0097440)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	29	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			TAGGTGGGTGTGCTGCTGCTG	0.577													C|||	1805	0.360423	0.4977	0.317	5008	,	,		20834	0.244		0.2525	False		,,,				2504	0.4366				p.T546A		Atlas-SNP	.											.	SEZ6	61	.	0			c.A1636G	GRCh37	CM073339	SEZ6	M	rs1976165	PASS	.	C	ALA/THR,ALA/THR	1790,2384		381,1028,678	62.0	70.0	68.0		1636,1636	5.1	0.9	17	dbSNP_92	68	2162,6318		280,1602,2358	yes	missense,missense	SEZ6	NM_001098635.1,NM_178860.4	58,58	661,2630,3036	CC,CT,TT		25.4953,42.8845,31.2312	benign,benign	546/994,546/995	27286851	3952,8702	2087	4240	6327	SO:0001583	missense	124925	exon8			TGGGTGTGCTGCT	AY038048	CCDS45638.1, CCDS45639.1	17q11.2	2008-03-06	2001-11-28		ENSG00000063015	ENSG00000063015			15955	protein-coding gene	gene with protein product			"""seizure related gene 6 (mouse) homolog"""			17086543	Standard	NM_178860		Approved		uc002hdp.2	Q53EL9	OTTHUMG00000168010	ENST00000317338.12:c.1636A>G	17.37:g.27286851T>C	ENSP00000312942:p.Thr546Ala	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_001098635	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Missense_Mutation	SNP	ENST00000317338.12	37	CCDS45639.1	677	0.309981684981685	243	0.49390243902439024	113	0.31215469613259667	145	0.2534965034965035	176	0.23218997361477572	C	12.14	1.848110	0.32699	0.428845	0.254953	ENSG00000063015	ENST00000442608;ENST00000360295;ENST00000317338;ENST00000541381	T;T	0.63744	-0.06;-0.06	5.07	5.07	0.68467	Complement control module (2);Sushi/SCR/CCP (3);	0.135388	0.48767	N	0.000180	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43245	-0.9403	9	0.30854	T	0.27	.	11.8833	0.52587	0.0:0.9138:0.0:0.0862	rs1976165;rs52834488;rs60868464;rs1976165	546;546	Q53EL9-3;Q53EL9	.;SEZ6_HUMAN	A	546;546;421;546	ENSP00000403784:T546A;ENSP00000353440:T546A	ENSP00000312942:T421A	T	-	1	0	SEZ6	24310977	1.000000	0.71417	0.865000	0.33974	0.752000	0.42762	5.780000	0.68956	1.281000	0.44480	-0.215000	0.12644	ACA	T|0.664;C|0.336	0.336	strong		0.577	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3		
PDHX	8050	hgsc.bcm.edu	37	11	34938269	34938269	+	Missense_Mutation	SNP	C	C	T	rs1049306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34938269C>T	ENST00000227868.4	+	1	151	c.67C>T	c.(67-69)Cgc>Tgc	p.R23C	PDHX_ENST00000430469.2_Missense_Mutation_p.R23C|PDHX_ENST00000448838.3_Intron|APIP_ENST00000278359.5_5'Flank|APIP_ENST00000395787.3_5'Flank|APIP_ENST00000527830.1_5'Flank			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	23			R -> C (in dbSNP:rs1049306). {ECO:0000269|PubMed:9242632}.		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)			CTTCCCCGGCCGCCGAAGCGT	0.642													C|||	964	0.192492	0.4395	0.1037	5008	,	,		12243	0.0873		0.1173	False		,,,				2504	0.1074				p.R23C		Atlas-SNP	.											.	PDHX	40	.	0			c.C67T						PASS	.	C	,CYS/ARG,CYS/ARG	1727,2677	490.1+/-361.7	352,1023,827	31.0	35.0	34.0		,67,67	-0.6	0.0	11	dbSNP_86	34	947,7649	199.7+/-243.7	56,835,3407	no	intron,missense,missense	PDHX	NM_001135024.1,NM_001166158.1,NM_003477.2	,180,180	408,1858,4234	TT,TC,CC		11.0168,39.2144,20.5692	,benign,benign	,23/275,23/502	34938269	2674,10326	2202	4298	6500	SO:0001583	missense	8050	exon1			CCCGGCCGCCGAA	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.67C>T	11.37:g.34938269C>T	ENSP00000227868:p.Arg23Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	37	CCDS7896.1	387	0.1771978021978022	195	0.39634146341463417	41	0.1132596685082873	63	0.11013986013986014	88	0.11609498680738786	C	10.40	1.340934	0.24339	0.392144	0.110168	ENSG00000110435	ENST00000227868;ENST00000430469;ENST00000533262	T;T;T	0.40225	1.87;1.04;1.76	5.26	-0.622	0.11560	.	0.878589	0.10162	N	0.708207	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.0	T	0.44817	-0.9303	8	0.37606	T	0.19	0.1283	7.7318	0.28791	0.0:0.4515:0.38:0.1685	rs1049306;rs3189450;rs3818399;rs17173964;rs1049306	23;23	E9PBP7;O00330	.;ODPX_HUMAN	C	23	ENSP00000227868:R23C;ENSP00000415695:R23C;ENSP00000432277:R23C	ENSP00000227868:R23C	R	+	1	0	PDHX	34894845	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.080000	0.11339	-0.171000	0.10797	-1.134000	0.01955	CGC	C|0.802;T|0.198	0.198	strong		0.642	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
SSTR5	6755	hgsc.bcm.edu	37	16	1129023	1129023	+	Missense_Mutation	SNP	C	C	T	rs4988484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1129023C>T	ENST00000293897.4	+	1	243	c.155C>T	c.(154-156)gCg>gTg	p.A52V	SSTR5_ENST00000562758.1_Missense_Mutation_p.A52V|SSTR5_ENST00000397547.2_Missense_Mutation_p.A52V|SSTR5-AS1_ENST00000569832.1_RNA	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	52			A -> V (in dbSNP:rs4988484).		G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytokinesis (GO:0032467)|regulation of insulin secretion (GO:0050796)|somatostatin signaling pathway (GO:0038170)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			endometrium(2)|lung(5)|prostate(1)|skin(1)	9		Hepatocellular(780;0.00369)			Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	CTGGTGTGTGCGGCCGGGCTG	0.677													C|||	458	0.0914537	0.177	0.0447	5008	,	,		13756	0.005		0.0427	False		,,,				2504	0.1483				p.A52V		Atlas-SNP	.											.	SSTR5	36	.	0			c.C155T						PASS	.	C	VAL/ALA,VAL/ALA	590,3768		39,512,1628	48.0	35.0	39.0		155,155	-1.7	0.0	16	dbSNP_113	39	335,8239		6,323,3958	yes	missense,missense	SSTR5	NM_001053.3,NM_001172560.1	64,64	45,835,5586	TT,TC,CC		3.9072,13.5383,7.1528	benign,benign	52/365,52/365	1129023	925,12007	2179	4287	6466	SO:0001583	missense	6755	exon2			TGTGTGCGGCCGG	D16827	CCDS10429.1	16p13.3	2012-08-08			ENSG00000162009	ENSG00000162009		"""GPCR / Class A : Somatostatin receptors"""	11334	protein-coding gene	gene with protein product		182455				7607700	Standard	NM_001053		Approved		uc021taf.1	P35346	OTTHUMG00000047842	ENST00000293897.4:c.155C>T	16.37:g.1129023C>T	ENSP00000293897:p.Ala52Val	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	25	10	0.4	NM_001172560	P34988|Q541E0|Q9UJI5	Missense_Mutation	SNP	ENST00000293897.4	37	CCDS10429.1	133	0.060897435897435896	86	0.17479674796747968	19	0.052486187845303865	0	0.0	28	0.036939313984168866	C	0.010	-1.745934	0.00669	0.135383	0.039072	ENSG00000162009	ENST00000397547;ENST00000293897;ENST00000539762	T;T	0.16897	2.31;2.31	4.56	-1.72	0.08107	.	1.327860	0.05379	N	0.536760	T	0.00039	0.0001	N	0.16602	0.42	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.38520	-0.9657	9	0.02654	T	1	.	10.3765	0.44085	0.0:0.5086:0.0:0.4914	rs4988484	52	P35346	SSR5_HUMAN	V	52	ENSP00000380680:A52V;ENSP00000293897:A52V	ENSP00000293897:A52V	A	+	2	0	SSTR5	1069024	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.484000	0.22308	-0.162000	0.10964	0.491000	0.48974	GCG	C|0.930;T|0.070	0.070	strong		0.677	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1		
C12orf50	160419	hgsc.bcm.edu	37	12	88380094	88380094	+	Missense_Mutation	SNP	T	T	C	rs10777084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:88380094T>C	ENST00000298699.2	-	10	1097	c.917A>G	c.(916-918)cAg>cGg	p.Q306R	C12orf50_ENST00000550553.1_Missense_Mutation_p.Q267R	NM_152589.1	NP_689802.1	Q8NA57	CL050_HUMAN	chromosome 12 open reading frame 50	306			Q -> R (in dbSNP:rs10777084).							NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|urinary_tract(2)	34						CTTACCTCTCTGCATTCCAGA	0.313													T|||	1518	0.303115	0.8147	0.1383	5008	,	,		15823	0.0565		0.0994	False		,,,				2504	0.1922				p.Q306R		Atlas-SNP	.											.	C12orf50	70	.	0			c.A917G						PASS	.	T	ARG/GLN	3042,1364	688.1+/-404.9	1048,946,209	94.0	95.0	95.0		917	-0.2	0.0	12	dbSNP_120	95	1006,7592	214.9+/-254.4	63,880,3356	yes	missense	C12orf50	NM_152589.1	43	1111,1826,3565	CC,CT,TT		11.7004,30.9578,31.1289	benign	306/415	88380094	4048,8956	2203	4299	6502	SO:0001583	missense	160419	exon10			CCTCTCTGCATTC	AK093140	CCDS9031.1	12q21.32	2006-02-03				ENSG00000165805			26665	protein-coding gene	gene with protein product						12477932	Standard	NM_152589		Approved	FLJ35821	uc001tam.1	Q8NA57	OTTHUMG00000169869	ENST00000298699.2:c.917A>G	12.37:g.88380094T>C	ENSP00000298699:p.Gln306Arg	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_152589	Q6P674	Missense_Mutation	SNP	ENST00000298699.2	37	CCDS9031.1	524	0.23992673992673993	384	0.7804878048780488	47	0.1298342541436464	25	0.043706293706293704	68	0.08970976253298153	T	0.001	-3.085134	0.00035	0.690422	0.117004	ENSG00000165805	ENST00000298699;ENST00000550553;ENST00000551944	T;T	0.27720	1.65;1.65	6.01	-0.245	0.13027	.	0.522728	0.18993	N	0.125548	T	0.00012	0.0000	N	0.01668	-0.77	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.25117	-1.0141	9	0.07813	T	0.8	.	6.5806	0.22591	0.0:0.4556:0.116:0.4284	rs10777084;rs52816943;rs59302935;rs10777084	321;306	G3V208;Q8NA57	.;CL050_HUMAN	R	306;267;321	ENSP00000298699:Q306R;ENSP00000448344:Q267R	ENSP00000298699:Q306R	Q	-	2	0	C12orf50	86904225	0.000000	0.05858	0.022000	0.16811	0.001000	0.01503	-0.089000	0.11180	-0.326000	0.08564	-1.748000	0.00681	CAG	T|0.704;C|0.296	0.296	strong		0.313	C12orf50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406328.1	NM_152589	
GNG12	55970	hgsc.bcm.edu	37	1	68171215	68171215	+	Silent	SNP	A	A	G	rs17130202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:68171215A>G	ENST00000370982.3	-	4	337	c.138T>C	c.(136-138)caT>caC	p.H46H		NM_018841.5	NP_061329.3	Q9UBI6	GBG12_HUMAN	guanine nucleotide binding protein (G protein), gamma 12	46					cellular response to glucagon stimulus (GO:0071377)|cerebral cortex development (GO:0021987)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)			lung(3)	3						CACTCCTGGCATGTTCCTCAC	0.393													A|||	54	0.0107827	0.0386	0.0043	5008	,	,		20621	0.0		0.0	False		,,,				2504	0.0				p.H46H		Atlas-SNP	.											.	GNG12	11	.	0			c.T138C						PASS	.	A		138,4268	99.4+/-138.0	2,134,2067	128.0	119.0	122.0		138	-4.2	1.0	1	dbSNP_123	122	0,8600		0,0,4300	no	coding-synonymous	GNG12	NM_018841.5		2,134,6367	GG,GA,AA		0.0,3.1321,1.061		46/73	68171215	138,12868	2203	4300	6503	SO:0001819	synonymous_variant	55970	exon4			CCTGGCATGTTCC	AF119663	CCDS30749.1	1p31.2	2008-02-05			ENSG00000172380	ENSG00000172380			19663	protein-coding gene	gene with protein product		615405				10819326	Standard	NM_018841		Approved		uc001dea.2	Q9UBI6	OTTHUMG00000009545	ENST00000370982.3:c.138T>C	1.37:g.68171215A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_018841	Q69YP5|Q9BRV5	Silent	SNP	ENST00000370982.3	37	CCDS30749.1																																																																																			A|0.991;G|0.009	0.009	strong		0.393	GNG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026355.2		
PINX1	54984	hgsc.bcm.edu	37	8	10623138	10623138	+	Missense_Mutation	SNP	T	T	A	rs1078543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10623138T>A	ENST00000314787.3	-	7	879	c.760A>T	c.(760-762)Agc>Tgc	p.S254C	CTD-2135J3.3_ENST00000519568.1_RNA|PINX1_ENST00000426190.2_3'UTR|CTD-2135J3.3_ENST00000506149.2_RNA|SOX7_ENST00000554914.1_Intron|PINX1_ENST00000519088.1_3'UTR|SOX7_ENST00000553390.1_Intron	NM_017884.4	NP_060354.4	Q96BK5	PINX1_HUMAN	PIN2/TERF1 interacting, telomerase inhibitor 1	254	Telomerase inhibitory domain (TID).		S -> C (in dbSNP:rs1078543). {ECO:0000269|PubMed:11701125}.		mitotic metaphase plate congression (GO:0007080)|negative regulation of cell proliferation (GO:0008285)|negative regulation of telomerase activity (GO:0051974)|regulation of telomerase activity (GO:0051972)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|spindle (GO:0005819)	telomerase inhibitor activity (GO:0010521)|telomeric RNA binding (GO:0070034)			kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17				Kidney(29;0.0595)|COAD - Colon adenocarcinoma(149;0.105)|KIRC - Kidney renal clear cell carcinoma(542;0.201)		GCTGGCGCGCTCTTCTTCTTG	0.632													T|||	943	0.188299	0.438	0.1124	5008	,	,		14708	0.0288		0.1372	False		,,,				2504	0.1217				p.S254C		Atlas-SNP	.											PINX1,NS,carcinoma,+2,1	PINX1	38	1	0			c.A760T						PASS	.	T	CYS/SER	1441,2431		260,921,755	47.0	52.0	50.0		760	4.1	0.5	8	dbSNP_86	50	1075,7201		51,973,3114	yes	missense	PINX1	NM_017884.4	112	311,1894,3869	AA,AT,TT		12.9894,37.2159,20.7112		254/329	10623138	2516,9632	1936	4138	6074	SO:0001583	missense	54984	exon7			GCGCGCTCTTCTT	AF418553	CCDS47801.1, CCDS64825.1	8p23	2013-01-28				ENSG00000254093		"""G patch domain containing"""	30046	protein-coding gene	gene with protein product	"""PIN2 interacting protein 1"", ""liver-related putative tumor suppressor"""	606505				11003615, 11701125	Standard	NM_001284356		Approved	PinX1, LPTL, LPTS, FLJ20565, MGC8850		Q96BK5		ENST00000314787.3:c.760A>T	8.37:g.10623138T>A	ENSP00000318966:p.Ser254Cys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	114	111	0.973684	NM_017884	B2R9B1|Q548A5|Q6QWG9|Q7Z7J8|Q96QD7|Q9HBU7|Q9NWW2	Missense_Mutation	SNP	ENST00000314787.3	37	CCDS47801.1	368	0.1684981684981685	208	0.42276422764227645	39	0.10773480662983426	20	0.03496503496503497	101	0.13324538258575197	T	11.99	1.803132	0.31869	0.372159	0.129894	ENSG00000254093	ENST00000314787	T	0.18960	2.18	5.27	4.13	0.48395	.	0.753612	0.12935	N	0.427064	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.999999999540518	P	0.48640	0.913	B	0.43103	0.408	T	0.48317	-0.9046	9	0.49607	T	0.09	.	7.5449	0.27761	0.0:0.094:0.0:0.906	rs1078543;rs2280046;rs1078543	254	Q96BK5	PINX1_HUMAN	C	254	ENSP00000318966:S254C	ENSP00000318966:S254C	S	-	1	0	PINX1	10660548	0.030000	0.19436	0.489000	0.27452	0.075000	0.17131	0.167000	0.16602	1.033000	0.39918	0.533000	0.62120	AGC	T|0.831;A|0.169	0.169	strong		0.632	PINX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375683.1	NM_017884	
OR10G8	219869	hgsc.bcm.edu	37	11	123900968	123900968	+	Missense_Mutation	SNP	A	A	G	rs146815262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123900968A>G	ENST00000431524.1	+	1	672	c.639A>G	c.(637-639)atA>atG	p.I213M		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	213						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)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		TTGTCCTGATAGTGCTGTCCT	0.552													A|||	5	0.000998403	0.0038	0.0	5008	,	,		21238	0.0		0.0	False		,,,				2504	0.0				p.I213M		Atlas-SNP	.											.	OR10G8	132	.	0			c.A639G						PASS	.	A	MET/ILE	11,4391	17.9+/-39.9	0,11,2190	187.0	162.0	171.0		639	0.0	0.8	11	dbSNP_134	171	0,8598		0,0,4299	yes	missense	OR10G8	NM_001004464.1	10	0,11,6489	GG,GA,AA		0.0,0.2499,0.0846	probably-damaging	213/312	123900968	11,12989	2201	4299	6500	SO:0001583	missense	219869	exon1			CCTGATAGTGCTG	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"""GPCR / Class A : Olfactory receptors"""	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.639A>G	11.37:g.123900968A>G	ENSP00000389072:p.Ile213Met	Somatic	437	0	0		WXS	Illumina HiSeq	Phase_I	406	224	0.551724	NM_001004464	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	8.778	0.927449	0.18056	0.002499	0.0	ENSG00000234560	ENST00000431524	T	0.00333	8.07	2.91	0.0166	0.14109	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000074	T	0.00754	0.0025	M	0.89601	3.045	0.22571	N	0.998971	D	0.89917	1.0	D	0.97110	1.0	T	0.36089	-0.9762	10	0.72032	D	0.01	.	7.3929	0.26919	0.3109:0.0:0.0:0.6891	.	213	Q8NGN5	O10G8_HUMAN	M	213	ENSP00000389072:I213M	ENSP00000389072:I213M	I	+	3	3	OR10G8	123406178	0.000000	0.05858	0.808000	0.32385	0.060000	0.15804	-2.286000	0.01152	0.282000	0.22254	0.455000	0.32223	ATA	A|0.999;G|0.001	0.001	strong		0.552	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464	
CELSR1	9620	hgsc.bcm.edu	37	22	46761135	46761135	+	Silent	SNP	G	G	T	rs9627424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46761135G>T	ENST00000262738.3	-	32	8546	c.8547C>A	c.(8545-8547)acC>acA	p.T2849T		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2849					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)		CACCTTTGGGGGTGCTGTGGA	0.652													G|||	441	0.0880591	0.3177	0.0259	5008	,	,		17157	0.001		0.001	False		,,,				2504	0.001				p.T2849T		Atlas-SNP	.											.	CELSR1	242	.	0			c.C8547A						PASS	.	G		1269,3107	414.6+/-336.9	175,919,1094	28.0	27.0	27.0		8547	4.9	1.0	22	dbSNP_119	27	26,8564	16.6+/-54.9	0,26,4269	no	coding-synonymous	CELSR1	NM_014246.1		175,945,5363	TT,TG,GG		0.3027,28.9991,9.9877		2849/3015	46761135	1295,11671	2188	4295	6483	SO:0001819	synonymous_variant	9620	exon32			TTTGGGGGTGCTG	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.8547C>A	22.37:g.46761135G>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			G|0.911;T|0.089	0.089	strong		0.652	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
SVIL	6840	hgsc.bcm.edu	37	10	29843833	29843833	+	Silent	SNP	C	C	T	rs1547169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:29843833C>T	ENST00000355867.4	-	5	791	c.39G>A	c.(37-39)ggG>ggA	p.G13G	SVIL_ENST00000375400.3_Silent_p.G13G|SVIL_ENST00000375398.2_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	113	0	0		WXS	Illumina HiSeq	Phase_I	111	63	0.567568	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		
IGSF22	283284	hgsc.bcm.edu	37	11	18737095	18737095	+	Missense_Mutation	SNP	C	C	T	rs4424652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18737095C>T	ENST00000513874.1	-	11	1554	c.1415G>A	c.(1414-1416)cGa>cAa	p.R472Q	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	472	Ig-like 3.		R -> Q (in dbSNP:rs4424652). {ECO:0000269|PubMed:14702039}.							NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CAGCTCTGCTCGCTTGCCCTC	0.537													C|||	3753	0.749401	0.829	0.7032	5008	,	,		22546	0.8125		0.7734	False		,,,				2504	0.5849				p.R472Q		Atlas-SNP	.											.	IGSF22	211	.	0			c.G1415A						PASS	.	C	GLN/ARG	3470,926	703.4+/-407.0	1375,720,103	132.0	128.0	130.0		1415	2.5	0.8	11	dbSNP_111	130	6358,2218	695.6+/-404.8	2352,1654,282	yes	missense	IGSF22	NM_173588.3	43	3727,2374,385	TT,TC,CC		25.8629,21.0646,24.2368	probably-damaging	472/1327	18737095	9828,3144	2198	4288	6486	SO:0001583	missense	283284	exon11			TCTGCTCGCTTGC	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1415G>A	11.37:g.18737095C>T	ENSP00000421191:p.Arg472Gln	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	179	179	1	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	1712	0.7838827838827839	405	0.823170731707317	264	0.7292817679558011	461	0.8059440559440559	582	0.7678100263852242	C	8.657	0.899532	0.17686	0.789354	0.741371	ENSG00000179057	ENST00000513874	T	0.67523	-0.27	4.79	2.53	0.30540	.	0.000000	0.32785	N	0.005652	T	0.00012	0.0000	L	0.33293	1	0.47905	P	4.509999999999792E-4	P	0.34800	0.469	B	0.21546	0.035	T	0.33701	-0.9858	9	0.31617	T	0.26	.	5.0144	0.14328	0.0:0.6128:0.1612:0.226	rs4424652;rs52801068;rs4424652	472	D6RGV7	.	Q	472	ENSP00000421191:R472Q	ENSP00000322422:R472Q	R	-	2	0	IGSF22	18693671	0.967000	0.33354	0.814000	0.32528	0.595000	0.36748	1.983000	0.40648	0.249000	0.21456	0.455000	0.32223	CGA	C|0.231;N|0.000	.	strong		0.537	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919963	12919963	+	Missense_Mutation	SNP	T	T	G	rs72472699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919963T>G	ENST00000240189.2	+	3	790	c.703T>G	c.(703-705)Tgc>Ggc	p.C235G		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	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)					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)		GAAGACTCTTTGCAAACTCGT	0.428													.|||	689	0.13758	0.1422	0.1614	5008	,	,		22517	0.1438		0.1302	False		,,,				2504	0.1155				p.C235G		Atlas-SNP	.											PRAMEF2,lymph_node,lymphoid_neoplasm,0,1	PRAMEF2	85	1	0			c.T703G						PASS	.						109.0	113.0	112.0					1																	12919963		2203	4299	6502	SO:0001583	missense	65122	exon3			ACTCTTTGCAAAC		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.703T>G	1.37:g.12919963T>G	ENSP00000240189:p.Cys235Gly	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	171	103	0.602339	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	561	0.25686813186813184	106	0.21544715447154472	76	0.20994475138121546	148	0.25874125874125875	231	0.30474934036939316	G	2.175	-0.388896	0.04932	.	.	ENSG00000120952	ENST00000240189	T	0.14516	2.5	0.842	-0.163	0.13363	.	2.817050	0.01348	N	0.011788	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	0.44847	-0.9301	9	0.42905	T	0.14	.	2.5682	0.04788	0.0:0.4409:0.318:0.2411	.	235	O60811	PRAM2_HUMAN	G	235	ENSP00000240189:C235G	ENSP00000240189:C235G	C	+	1	0	PRAMEF2	12842550	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.855000	0.04295	-0.611000	0.05709	-3.628000	0.00027	TGC	T|0.756;G|0.244	0.244	strong		0.428	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
OR7D4	125958	hgsc.bcm.edu	37	19	9324863	9324863	+	Silent	SNP	G	G	A	rs8109935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9324863G>A	ENST00000308682.2	-	1	679	c.651C>T	c.(649-651)tcC>tcT	p.S217S		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	217						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						TCTGAGAGTAGGAGAAGAGGA	0.512													G|||	880	0.175719	0.3578	0.134	5008	,	,		21686	0.0407		0.0626	False		,,,				2504	0.2147				p.S217S		Atlas-SNP	.											OR7D4,NS,malignant_melanoma,-1,2	OR7D4	66	2	0			c.C651T						PASS	.	G		1368,3038	446.3+/-348.0	212,944,1047	82.0	77.0	79.0		651	-1.2	0.0	19	dbSNP_116	79	677,7923	169.3+/-220.7	31,615,3654	no	coding-synonymous	OR7D4	NM_001005191.2		243,1559,4701	AA,AG,GG		7.8721,31.0486,15.7235		217/313	9324863	2045,10961	2203	4300	6503	SO:0001819	synonymous_variant	125958	exon1			AGAGTAGGAGAAG		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.651C>T	19.37:g.9324863G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Silent	SNP	ENST00000308682.2	37	CCDS32901.1																																																																																			G|0.833;A|0.167	0.167	strong		0.512	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1		
CLCNKA	1187	hgsc.bcm.edu	37	1	16354394	16354394	+	Missense_Mutation	SNP	C	C	T	rs200268763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16354394C>T	ENST00000331433.4	+	9	879	c.860C>T	c.(859-861)gCg>gTg	p.A287V	CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000420078.1_Missense_Mutation_p.A287V|CLCNKA_ENST00000375692.1_Missense_Mutation_p.A287V|CLCNKA_ENST00000439316.2_Missense_Mutation_p.A244V			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	702	85	0.121083		WXS	Illumina HiSeq	Phase_I	708	399	0.563559	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		
ITGA11	22801	hgsc.bcm.edu	37	15	68650913	68650913	+	Silent	SNP	G	G	A	rs61729771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68650913G>A	ENST00000315757.7	-	6	569	c.483C>T	c.(481-483)acC>acT	p.T161T	ITGA11_ENST00000423218.2_Silent_p.T161T|ITGA11_ENST00000562826.1_5'UTR	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	161					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)			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						TGTCCATGTAGGTCTGGCACC	0.483													G|||	259	0.0517173	0.1853	0.0202	5008	,	,		22319	0.0		0.0	False		,,,				2504	0.0				p.T161T		Atlas-SNP	.											.	ITGA11	110	.	0			c.C483T						PASS	.	G		686,3688	269.5+/-269.1	42,602,1543	73.0	75.0	74.0		483	2.1	1.0	15	dbSNP_129	74	4,8592	3.7+/-12.6	0,4,4294	no	coding-synonymous	ITGA11	NM_001004439.1		42,606,5837	AA,AG,GG		0.0465,15.6836,5.32		161/1189	68650913	690,12280	2187	4298	6485	SO:0001819	synonymous_variant	22801	exon6			CATGTAGGTCTGG	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.483C>T	15.37:g.68650913G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			G|0.956;A|0.044	0.044	strong		0.483	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
GBP7	388646	hgsc.bcm.edu	37	1	89615023	89615023	+	Missense_Mutation	SNP	C	C	G	rs74098339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89615023C>G	ENST00000294671.2	-	7	1242	c.1104G>C	c.(1102-1104)atG>atC	p.M368I		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	368						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		AGGAGTACTCCATGAAGACTG	0.453													C|||	43	0.00858626	0.0303	0.0043	5008	,	,		17526	0.0		0.0	False		,,,				2504	0.0				p.M368I		Atlas-SNP	.											.	GBP7	57	.	0			c.G1104C						PASS	.	C	ILE/MET	143,4263	99.8+/-138.5	3,137,2063	97.0	93.0	95.0		1104	3.5	1.0	1	dbSNP_130	95	0,8600		0,0,4300	no	missense	GBP7	NM_207398.2	10	3,137,6363	GG,GC,CC		0.0,3.2456,1.0995	possibly-damaging	368/639	89615023	143,12863	2203	4300	6503	SO:0001583	missense	388646	exon7			GTACTCCATGAAG	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1104G>C	1.37:g.89615023C>G	ENSP00000294671:p.Met368Ile	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	235	120	0.510638	NM_207398		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	8.920	0.960823	0.18583	0.032456	0.0	ENSG00000213512	ENST00000294671	T	0.02369	4.32	3.54	3.54	0.40534	Guanylate-binding protein, C-terminal (3);	0.154247	0.56097	D	0.000024	T	0.02649	0.0080	M	0.70903	2.155	0.34498	D	0.705737	B	0.32324	0.364	B	0.37943	0.261	T	0.22765	-1.0207	10	0.45353	T	0.12	.	12.621	0.56603	0.0:1.0:0.0:0.0	.	368	Q8N8V2	GBP7_HUMAN	I	368	ENSP00000294671:M368I	ENSP00000294671:M368I	M	-	3	0	GBP7	89387611	0.368000	0.25031	1.000000	0.80357	0.063000	0.16089	0.647000	0.24812	1.819000	0.53055	0.523000	0.50628	ATG	C|0.988;G|0.012	0.012	strong		0.453	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
LAMA1	284217	hgsc.bcm.edu	37	18	7017322	7017322	+	Silent	SNP	A	A	G	rs539713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:7017322A>G	ENST00000389658.3	-	20	2856	c.2763T>C	c.(2761-2763)tgT>tgC	p.C921C		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	921	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GTTTGCAGTCACAGAGCCCGG	0.488													A|||	2742	0.547524	0.9168	0.4135	5008	,	,		19361	0.2262		0.5368	False		,,,				2504	0.4857				p.C921C		Atlas-SNP	.											.	LAMA1	458	.	0			c.T2763C						PASS	.	A		3707,699	760.4+/-413.0	1563,581,59	168.0	126.0	140.0		2763	-5.0	0.5	18	dbSNP_83	140	4601,3999	598.7+/-394.0	1254,2093,953	no	coding-synonymous	LAMA1	NM_005559.3		2817,2674,1012	GG,GA,AA		46.5,15.8647,36.1218		921/3076	7017322	8308,4698	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon20			GCAGTCACAGAGC	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.2763T>C	18.37:g.7017322A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			A|0.392;G|0.608	0.608	strong		0.488	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
ATP8B3	148229	hgsc.bcm.edu	37	19	1811603	1811603	+	Missense_Mutation	SNP	C	C	T	rs7250872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1811603C>T	ENST00000310127.6	-	2	371	c.133G>A	c.(133-135)Gga>Aga	p.G45R	ATP8B3_ENST00000526092.2_5'UTR|ATP8B3_ENST00000539485.1_Missense_Mutation_p.G45R|ATP8B3_ENST00000525591.1_5'UTR	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	45			G -> R (in dbSNP:rs7250872).		binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCTCACCTCCGCGGATGCCA	0.657													c|||	1984	0.396166	0.5068	0.4481	5008	,	,		14880	0.374		0.3141	False		,,,				2504	0.317				p.G45R		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G133A						PASS	.	C	,ARG/GLY	1898,2254		457,984,635	53.0	61.0	58.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,133	1.4	0.0	19	dbSNP_116	58	2506,5894		375,1756,2069	yes	utr-5,missense	ATP8B3	NM_001178002.1,NM_138813.2	,125	832,2740,2704	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	29.8333,45.7129,35.086	,probably-damaging	,45/1301	1811603	4404,8148	2076	4200	6276	SO:0001583	missense	148229	exon2			CACCTCCGCGGAT	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.133G>A	19.37:g.1811603C>T	ENSP00000311336:p.Gly45Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	859	0.3933150183150183	246	0.5	149	0.4116022099447514	221	0.38636363636363635	243	0.32058047493403696	c	13.83	2.353566	0.41700	0.457129	0.298333	ENSG00000130270	ENST00000310127;ENST00000539485	T;T	0.74421	-0.84;-0.84	2.42	1.37	0.22104	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15473	0.013	B	0.08055	0.003	T	0.40869	-0.9540	8	0.51188	T	0.08	.	5.1659	0.15084	0.0:0.8303:0.0:0.1697	rs7250872;rs12985801;rs16990936;rs58934279;rs7250872	45	O60423	AT8B3_HUMAN	R	45	ENSP00000311336:G45R;ENSP00000443574:G45R	ENSP00000311336:G45R	G	-	1	0	ATP8B3	1762603	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-0.497000	0.06428	0.589000	0.29677	-0.258000	0.10820	GGA	C|0.614;T|0.386	0.386	strong		0.657	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
GDPGP1	390637	hgsc.bcm.edu	37	15	90784862	90784862	+	Missense_Mutation	SNP	G	G	A	rs75296384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90784862G>A	ENST00000558017.1	+	4	1142	c.722G>A	c.(721-723)gGa>gAa	p.G241E	GDPGP1_ENST00000329600.6_Missense_Mutation_p.G241E	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	241					glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)	GDP-D-glucose phosphorylase activity (GO:0080048)|guanyl-nucleotide exchange factor activity (GO:0005085)|hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|nucleotidyltransferase activity (GO:0016779)										CTGGACCCTGGAGGCCATTTG	0.617													G|||	174	0.0347444	0.1248	0.013	5008	,	,		17261	0.0		0.0	False		,,,				2504	0.0				p.G241E		Atlas-SNP	.											.	.	.	.	0			c.G722A						PASS	.	G	GLU/GLY	608,3790	264.4+/-266.0	41,526,1632	47.0	43.0	45.0		722	-2.9	0.0	15	dbSNP_131	45	9,8587	7.1+/-27.0	0,9,4289	yes	missense	C15orf58	NM_001013657.2	98	41,535,5921	AA,AG,GG		0.1047,13.8245,4.7483	benign	241/386	90784862	617,12377	2199	4298	6497	SO:0001583	missense	390637	exon4			ACCCTGGAGGCCA		CCDS32327.1	15q26.1	2012-05-04	2012-05-04	2012-05-04	ENSG00000183208	ENSG00000183208	2.7.7.78		34360	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 58"""	C15orf58		21507950	Standard	NM_001013657		Approved		uc002bpc.3	Q6ZNW5		ENST00000558017.1:c.722G>A	15.37:g.90784862G>A	ENSP00000452793:p.Gly241Glu	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	50	18	0.36	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	64	0.029304029304029304	57	0.11585365853658537	7	0.019337016574585635	0	0.0	0	0.0	G	0.008	-1.878262	0.00537	0.138245	0.001047	ENSG00000183208	ENST00000329600	T	0.25579	1.79	5.95	-2.86	0.05717	.	1.014510	0.07864	N	0.966806	T	0.00109	0.0003	L	0.35341	1.055	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34229	-0.9837	10	0.10902	T	0.67	0.0023	2.465	0.04550	0.4479:0.2093:0.2364:0.1065	.	241	Q6ZNW5	VTC2_HUMAN	E	241	ENSP00000368405:G241E	ENSP00000368405:G241E	G	+	2	0	C15orf58	88585866	0.000000	0.05858	0.000000	0.03702	0.142000	0.21351	0.507000	0.22675	-0.510000	0.06523	-0.150000	0.13652	GGA	G|0.962;A|0.038	0.038	strong		0.617	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657	
MKI67	4288	hgsc.bcm.edu	37	10	129899543	129899543	+	Silent	SNP	C	C	T	rs10082504	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129899543C>T	ENST00000368654.3	-	14	10059	c.9684G>A	c.(9682-9684)agG>agA	p.R3228R	MKI67_ENST00000368653.3_Silent_p.R2868R	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3228					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.R3228R(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTTCTGCACACCTCTTGACAC	0.433													C|||	519	0.103634	0.0666	0.1556	5008	,	,		21188	0.1389		0.0785	False		,,,				2504	0.1063				p.R3228R		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - coding silent(1)	stomach(1)	c.G9684A						scavenged	.	C	,	301,4105	164.4+/-196.0	13,275,1915	130.0	121.0	124.0		8604,9684	-0.4	0.0	10	dbSNP_119	124	803,7797	188.0+/-235.1	40,723,3537	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	53,998,5452	TT,TC,CC		9.3372,6.8316,8.4884	,	2868/2897,3228/3257	129899543	1104,11902	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon14			TGCACACCTCTTG	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.9684G>A	10.37:g.129899543C>T		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	161	73	0.453416	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			C|0.913;T|0.087	0.087	strong		0.433	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
VTN	7448	hgsc.bcm.edu	37	17	26694483	26694483	+	Silent	SNP	A	A	G	rs2227728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26694483A>G	ENST00000226218.4	-	8	1962	c.1344T>C	c.(1342-1344)aaT>aaC	p.N448N	VTN_ENST00000536498.1_Missense_Mutation_p.I32T|TMEM199_ENST00000509083.1_Intron|SARM1_ENST00000379061.4_Intron|VTN_ENST00000438614.1_Missense_Mutation_p.I32T|CTB-96E2.2_ENST00000555059.2_Silent_p.N106N|CTB-96E2.3_ENST00000591482.1_RNA|VTN_ENST00000431468.1_5'Flank	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	448					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)	GTGTGCGAAGATTGACTCGGT	0.602													G|||	779	0.155551	0.1596	0.0821	5008	,	,		19913	0.245		0.0785	False		,,,				2504	0.1892				p.N448N		Atlas-SNP	.											.	VTN	45	.	0			c.T1344C						PASS	.	G		647,3759	762.5+/-413.1	50,547,1606	128.0	106.0	113.0		1344	3.3	1.0	17	dbSNP_98	113	701,7899	786.9+/-407.6	31,639,3630	no	coding-synonymous	VTN	NM_000638.3		81,1186,5236	GG,GA,AA		8.1512,14.6845,10.3644		448/479	26694483	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	7448	exon8			GCGAAGATTGACT	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.1344T>C	17.37:g.26694483A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	176	80	0.454545	NM_000638	B2R7G0|P01141|Q9BSH7	Silent	SNP	ENST00000226218.4	37	CCDS11229.1	278	0.12728937728937728	87	0.17682926829268292	36	0.09944751381215469	100	0.17482517482517482	55	0.07255936675461741	G	9.371	1.070412	0.20147	0.146845	0.081512	ENSG00000109072;ENSG00000109072;ENSG00000258852	ENST00000536498;ENST00000438614;ENST00000555059	D;D	0.91351	-2.83;-2.83	5.27	3.28	0.37604	.	.	.	.	.	T	0.00580	0.0019	.	.	.	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.21280	-1.0250	7	0.13108	T	0.6	-46.27	8.5936	0.33701	0.2913:0.0:0.7087:0.0	rs2227728;rs57255300;rs2227728	32	C9JDG5	.	T	32;32;58	ENSP00000444503:I32T;ENSP00000395142:I32T	ENSP00000395142:I32T	I	-	2	0	VTN;CTB-96E2.2	23718610	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.941000	0.40233	0.381000	0.24851	-0.186000	0.12905	ATC	A|0.881;G|0.119	0.119	strong		0.602	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638	
NPTN	27020	hgsc.bcm.edu	37	15	73862606	73862606	+	Silent	SNP	C	C	T	rs35100473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:73862606C>T	ENST00000345330.4	-	6	1196	c.999G>A	c.(997-999)gtG>gtA	p.V333V	NPTN_ENST00000564551.1_5'Flank|NPTN_ENST00000287226.8_Missense_Mutation_p.C317Y|NPTN_ENST00000545878.1_Silent_p.V333V|NPTN_ENST00000542234.1_Silent_p.V128V|NPTN_ENST00000562924.1_Silent_p.V217V|NPTN_ENST00000563691.1_Silent_p.V333V|NPTN_ENST00000351217.6_Silent_p.V217V	NM_001161363.1|NM_012428.3	NP_001154835.1|NP_036560.1	Q9Y639	NPTN_HUMAN	neuroplastin	333					homophilic cell adhesion (GO:0007156)|long-term synaptic potentiation (GO:0060291)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein phosphorylation (GO:0001934)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)	cell adhesion molecule binding (GO:0050839)|type 1 fibroblast growth factor receptor binding (GO:0005105)			breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	13						GGTGGCTCCGCACCCTGAGGA	0.522													C|||	57	0.0113818	0.0393	0.0043	5008	,	,		16485	0.0		0.002	False		,,,				2504	0.0				p.V333V	Pancreas(101;1519 1568 9459 19537 41286)|Esophageal Squamous(143;1278 1787 35254 36835 44843)	Atlas-SNP	.											.	NPTN	35	.	0			c.G999A						PASS	.	C	,,,	139,4257	100.3+/-138.9	3,133,2062	80.0	75.0	76.0		999,651,999,651	0.3	1.0	15	dbSNP_126	76	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPTN	NM_001161363.1,NM_001161364.1,NM_012428.3,NM_017455.3	,,,	3,133,6359	TT,TC,CC		0.0,3.162,1.0701	,,,	333/395,217/279,333/399,217/283	73862606	139,12851	2198	4297	6495	SO:0001819	synonymous_variant	27020	exon6			GCTCCGCACCCTG	AF035287	CCDS10249.1, CCDS10250.1, CCDS58379.1, CCDS58380.1	15q24.1	2013-01-29	2006-02-22	2006-02-22	ENSG00000156642	ENSG00000156642		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17867	protein-coding gene	gene with protein product		612820	"""stromal cell derived factor receptor 1"""	SDFR1		8619474, 9110174	Standard	NM_012428		Approved	SDR1, GP55, GP65, np65, np55	uc002avs.3	Q9Y639	OTTHUMG00000137586	ENST00000345330.4:c.999G>A	15.37:g.73862606C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	187	103	0.550802	NM_001161363	B2RAL7|B7Z4D3|B7ZLL2|Q17R52|Q59EJ9|Q6NVX7|Q9Y640	Silent	SNP	ENST00000345330.4	37	CCDS10249.1	21	0.009615384615384616	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	16.12	3.034197	0.54896	0.03162	0.0	ENSG00000156642	ENST00000287226	T	0.67171	-0.25	5.6	0.321	0.15883	.	.	.	.	.	T	0.33411	0.0862	.	.	.	0.52501	D	0.999955	.	.	.	.	.	.	T	0.54516	-0.8282	6	0.87932	D	0	.	3.2099	0.06678	0.1208:0.4314:0.1233:0.3246	rs35100473	.	.	.	Y	317	ENSP00000287226:C317Y	ENSP00000287226:C317Y	C	-	2	0	NPTN	71649659	0.657000	0.27393	1.000000	0.80357	0.994000	0.84299	-0.201000	0.09464	0.055000	0.16094	-0.345000	0.07892	TGC	C|0.988;G|0.000;T|0.012	0.012	strong		0.522	NPTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268980.1	NM_012428	
CCDC160	347475	hgsc.bcm.edu	37	X	133378851	133378851	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:133378851C>T	ENST00000517294.1	+	3	404	c.21C>T	c.(19-21)caC>caT	p.H7H	CCDC160_ENST00000370809.4_Silent_p.H7H			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	7										endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						GAAGAAAACACTGGAAGGAGA	0.373																																					p.H7H		Atlas-SNP	.											.	CCDC160	38	.	0			c.C21T						PASS	.						20.0	18.0	19.0					X																	133378851		1825	4074	5899	SO:0001819	synonymous_variant	347475	exon2			AAAACACTGGAAG	BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.21C>T	X.37:g.133378851C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	146	91	0.623288	NM_001101357		Silent	SNP	ENST00000517294.1	37	CCDS48171.1																																																																																			.	.	none		0.373	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1	NM_001101357	
ZNF439	90594	hgsc.bcm.edu	37	19	11976987	11976987	+	Missense_Mutation	SNP	C	C	T	rs10421552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11976987C>T	ENST00000304030.2	+	1	216	c.16C>T	c.(16-18)Ccc>Tcc	p.P6S	ZNF439_ENST00000455282.1_Intron|ZNF439_ENST00000592534.1_Intron	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	6			P -> S (in dbSNP:rs10421552).		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						GTCACTCTCACCCATCCTCCT	0.498													c|||	85	0.0169728	0.0628	0.0029	5008	,	,		16172	0.0		0.0	False		,,,				2504	0.0				p.P6S		Atlas-SNP	.											.	ZNF439	67	.	0			c.C16T						PASS	.	C	SER/PRO	294,4112	161.8+/-193.9	10,274,1919	116.0	115.0	115.0		16	-0.9	0.0	19	dbSNP_119	115	5,8595	3.7+/-12.6	0,5,4295	no	missense	ZNF439	NM_152262.2	74	10,279,6214	TT,TC,CC		0.0581,6.6727,2.2989	probably-damaging	6/500	11976987	299,12707	2203	4300	6503	SO:0001583	missense	90594	exon1			CTCTCACCCATCC	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.16C>T	19.37:g.11976987C>T	ENSP00000305077:p.Pro6Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	103	61	0.592233	NM_152262	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	49	0.022435897435897436	47	0.09552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	c	5.148	0.212963	0.09757	0.066727	5.81E-4	ENSG00000171291	ENST00000304030	T	0.06608	3.28	0.566	-0.848	0.10727	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.04013	0.001	T	0.46261	-0.9204	8	0.35671	T	0.21	.	.	.	.	rs10421552;rs52808667;rs10421552	6	Q8NDP4	ZN439_HUMAN	S	6	ENSP00000305077:P6S	ENSP00000305077:P6S	P	+	1	0	ZNF439	11837987	0.000000	0.05858	0.001000	0.08648	0.088000	0.18126	-0.512000	0.06313	-0.358000	0.08162	0.184000	0.17185	CCC	C|0.975;T|0.025	0.025	strong		0.498	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1		
TPSD1	23430	hgsc.bcm.edu	37	16	1306680	1306680	+	Silent	SNP	C	C	T	rs1969653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1306680C>T	ENST00000211076.3	+	2	394	c.246C>T	c.(244-246)tgC>tgT	p.C82C	TPSD1_ENST00000397534.2_Silent_p.C75C|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	82	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CGGCGCACTGCGTGGAACCGT	0.706													-|||	857	0.171126	0.289	0.2522	5008	,	,		17255	0.122		0.0994	False		,,,				2504	0.0787				p.C82C		Atlas-SNP	.											.	TPSD1	47	.	0			c.C246T						PASS	.	C		1176,3222		169,838,1192	39.0	48.0	45.0		246	-3.0	0.0	16	dbSNP_92	45	797,7799		30,737,3531	no	coding-synonymous	TPSD1	NM_012217.2		199,1575,4723	TT,TC,CC		9.2718,26.7394,15.1839		82/243	1306680	1973,11021	2199	4298	6497	SO:0001819	synonymous_variant	23430	exon2			GCACTGCGTGGAA	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.246C>T	16.37:g.1306680C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	187	77	0.411765	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			C|0.850;T|0.150	0.150	strong		0.706	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
ZNF442	79973	hgsc.bcm.edu	37	19	12462873	12462873	+	Nonsense_Mutation	SNP	C	C	A	rs73507958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12462873C>A	ENST00000242804.4	-	5	799	c.217G>T	c.(217-219)Gaa>Taa	p.E73*	ZNF442_ENST00000438182.1_Nonsense_Mutation_p.E4*	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	73	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(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TTTGTGTCTTCCCATTTCATT	0.353													C|||	39	0.00778754	0.0287	0.0014	5008	,	,		16758	0.0		0.0	False		,,,				2504	0.0				p.E73X		Atlas-SNP	.											.	ZNF442	102	.	0			c.G217T						PASS	.	C	stop/GLU	83,4323	71.4+/-109.4	1,81,2121	123.0	111.0	115.0		217	-1.0	0.1	19	dbSNP_130	115	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	ZNF442	NM_030824.2		1,82,6420	AA,AC,CC		0.0116,1.8838,0.6459		73/628	12462873	84,12922	2203	4300	6503	SO:0001587	stop_gained	79973	exon5			TGTCTTCCCATTT	AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"""Zinc fingers, C2H2-type"", ""-"""	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.217G>T	19.37:g.12462873C>A	ENSP00000242804:p.Glu73*	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_030824	B4DJ48	Nonsense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	13.54	2.268178	0.40095	0.018838	1.16E-4	ENSG00000198342	ENST00000242804;ENST00000438182;ENST00000424168	.	.	.	1.51	-0.994	0.10225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	.	3.7481	0.08556	0.0:0.4674:0.0:0.5326	.	.	.	.	X	73;4;4	.	ENSP00000242804:E73X	E	-	1	0	ZNF442	12323873	0.001000	0.12720	0.062000	0.19696	0.439000	0.31926	-0.419000	0.07071	-0.071000	0.12886	0.313000	0.20887	GAA	C|0.993;A|0.007	0.007	strong		0.353	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824	
ATP8A1	10396	hgsc.bcm.edu	37	4	42457545	42457545	+	Silent	SNP	G	G	A	rs61735691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:42457545G>A	ENST00000381668.5	-	28	2922	c.2691C>T	c.(2689-2691)aaC>aaT	p.N897N	ATP8A1_ENST00000264449.10_Silent_p.N882N	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	897					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	AACTTACCACGTTATAGAGAC	0.388													G|||	740	0.147764	0.3903	0.098	5008	,	,		20154	0.0397		0.0457	False		,,,				2504	0.0716				p.N897N		Atlas-SNP	.											.	ATP8A1	206	.	0			c.C2691T						PASS	.	G	,	1472,2934	469.6+/-355.5	239,994,970	90.0	90.0	90.0		2646,2691	-6.3	0.9	4	dbSNP_129	90	377,8223	123.9+/-182.7	13,351,3936	no	coding-synonymous,coding-synonymous	ATP8A1	NM_001105529.1,NM_006095.2	,	252,1345,4906	AA,AG,GG		4.3837,33.409,14.2165	,	882/1150,897/1165	42457545	1849,11157	2203	4300	6503	SO:0001819	synonymous_variant	10396	exon28			TACCACGTTATAG	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"""ATPases / P-type"""	13531	protein-coding gene	gene with protein product		609542	"""ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"""			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.2691C>T	4.37:g.42457545G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	186	90	0.483871	NM_006095	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Silent	SNP	ENST00000381668.5	37	CCDS3466.1																																																																																			G|0.866;A|0.134	0.134	strong		0.388	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095	
TIMM10B	26515	hgsc.bcm.edu	37	11	6502780	6502780	+	Silent	SNP	C	C	A	rs11555935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6502780C>A	ENST00000254616.6	+	1	104	c.34C>A	c.(34-36)Cga>Aga	p.R12R	ARFIP2_ENST00000445086.2_5'Flank|ARFIP2_ENST00000254584.2_5'Flank|ARFIP2_ENST00000396777.3_5'Flank|ARFIP2_ENST00000423813.2_5'Flank|TIMM10B_ENST00000472836.1_Silent_p.R12R|ARFIP2_ENST00000525235.1_5'Flank|TIMM10B_ENST00000530751.1_Silent_p.R12R	NM_012192.3	NP_036324.1	Q9Y5J6	T10B_HUMAN	translocase of inner mitochondrial membrane 10 homolog B (yeast)	12					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial intermembrane space protein transporter complex (GO:0042719)	metal ion binding (GO:0046872)										acagcaACTGCGAAACGTAAG	0.607													A|||	837	0.167133	0.2118	0.1686	5008	,	,		17547	0.0327		0.1839	False		,,,				2504	0.227				p.R12R		Atlas-SNP	.											.	.	.	.	0			c.C34A						PASS	.	A		910,3492	721.9+/-409.2	93,724,1384	98.0	67.0	78.0		34	2.9	0.9	11	dbSNP_120	78	1667,6925	727.2+/-406.6	170,1327,2799	no	coding-synonymous	FXC1	NM_012192.3		263,2051,4183	AA,AC,CC		19.4018,20.6724,19.8322		12/104	6502780	2577,10417	2201	4296	6497	SO:0001819	synonymous_variant	26515	exon1			CAACTGCGAAACG	AF150105	CCDS7766.1	11p15.4	2012-12-07	2012-12-07	2012-12-07	ENSG00000132286	ENSG00000132286			4022	protein-coding gene	gene with protein product		607388	"""fracture callus 1 (rat) homolog"", ""fracture callus 1 homolog (rat)"""	FXC1		10552927	Standard	NM_012192		Approved	Tim9b, TIM10B	uc001mdn.4	Q9Y5J6	OTTHUMG00000133400	ENST00000254616.6:c.34C>A	11.37:g.6502780C>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_012192	Q96FF3	Silent	SNP	ENST00000254616.6	37	CCDS7766.1																																																																																			A|0.180;C|0.820;G|0.000;T|0.000	0.180	strong		0.607	TIMM10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257257.2	NM_012192	
TUBB8	347688	hgsc.bcm.edu	37	10	94562	94562	+	Silent	SNP	G	G	A	rs145350711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:94562G>A	ENST00000309812.4	-	3	332	c.270C>T	c.(268-270)ttC>ttT	p.F90F	TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000447903.2_Silent_p.F18F|TUBB8_ENST00000332708.5_Missense_Mutation_p.S54L	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	90					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)		CACCGAAGATGAAGTTGTCTG	0.637													g|||	2	0.000399361	0.0015	0.0	5008	,	,		15565	0.0		0.0	False		,,,				2504	0.0				p.F90F	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.C270T						PASS	.	G		16,4386	21.2+/-45.6	0,16,2185	42.0	52.0	49.0		270	0.1	0.0	10	dbSNP_134	49	0,8596		0,0,4298	no	coding-synonymous	TUBB8	NM_177987.2		0,16,6483	AA,AG,GG		0.0,0.3635,0.1231		90/445	94562	16,12982	2201	4298	6499	SO:0001819	synonymous_variant	347688	exon3			GAAGATGAAGTTG	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.270C>T	10.37:g.94562G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	111	62	0.558559	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	G	6.257	0.415577	0.11870	0.003635	0.0	ENSG00000173876	ENST00000332708	.	.	.	0.109	0.109	0.14578	.	.	.	.	.	T	0.55497	0.1924	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55598	-0.8116	5	0.87932	D	0	.	2.6667	0.05054	0.4741:0.0:0.5259:0.0	.	.	.	.	L	54	.	ENSP00000371071:S54L	S	-	2	0	RP11-631M21.2	84562	0.988000	0.35896	0.031000	0.17742	0.032000	0.12392	0.081000	0.14823	0.181000	0.19994	0.184000	0.17185	TCA	G|0.999;A|0.001	0.001	strong		0.637	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
HSPBAP1	79663	hgsc.bcm.edu	37	3	122496628	122496628	+	Missense_Mutation	SNP	A	A	C	rs16833517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122496628A>C	ENST00000306103.2	-	2	333	c.190T>G	c.(190-192)Tcg>Gcg	p.S64A	HSPBAP1_ENST00000465044.1_5'UTR|HSPBAP1_ENST00000383659.1_Missense_Mutation_p.S64A	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	64			S -> A (in dbSNP:rs16833517).			cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(114;0.0531)		AGGACCTGCGAAAGGTATTTA	0.413													A|||	256	0.0511182	0.1831	0.0202	5008	,	,		20190	0.0		0.0	False		,,,				2504	0.0				p.S64A		Atlas-SNP	.											HSPBAP1,NS,carcinoma,+1,1	HSPBAP1	32	1	0			c.T190G						PASS	.	A	ALA/SER	634,3772	274.0+/-271.7	39,556,1608	188.0	169.0	175.0		190	2.8	0.9	3	dbSNP_123	175	3,8597	3.0+/-9.4	0,3,4297	yes	missense	HSPBAP1	NM_024610.5	99	39,559,5905	CC,CA,AA		0.0349,14.3895,4.8977	benign	64/489	122496628	637,12369	2203	4300	6503	SO:0001583	missense	79663	exon2			CCTGCGAAAGGTA	AF400663	CCDS3017.1	3q21.1	2008-07-18	2002-08-29		ENSG00000169087	ENSG00000169087			16389	protein-coding gene	gene with protein product		608263	"""HSPB (heat shock 27kD) associated protein 1"""			11978969	Standard	NM_024610		Approved	FLJ22623, PASS1	uc003efu.2	Q96EW2	OTTHUMG00000159550	ENST00000306103.2:c.190T>G	3.37:g.122496628A>C	ENSP00000302562:p.Ser64Ala	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	346	191	0.552023	NM_024610	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	Missense_Mutation	SNP	ENST00000306103.2	37	CCDS3017.1	75	0.034340659340659344	67	0.13617886178861788	8	0.022099447513812154	0	0.0	0	0.0	A	9.139	1.013317	0.19277	0.143895	3.49E-4	ENSG00000169087	ENST00000383659;ENST00000306103	T;T	0.69040	-0.37;3.02	5.32	2.8	0.32819	.	0.105878	0.64402	N	0.000002	T	0.00496	0.0016	L	0.43757	1.38	0.37348	D	0.910665	B;B	0.28324	0.124;0.207	B;B	0.29353	0.057;0.101	T	0.02093	-1.1215	10	0.11485	T	0.65	.	6.8743	0.24139	0.6936:0.1567:0.0:0.1497	rs16833517;rs57105676;rs16833517	64;64	Q96EW2-2;Q96EW2	.;HBAP1_HUMAN	A	64	ENSP00000373155:S64A;ENSP00000302562:S64A	ENSP00000302562:S64A	S	-	1	0	HSPBAP1	123979318	1.000000	0.71417	0.943000	0.38184	0.390000	0.30446	2.466000	0.45084	0.405000	0.25532	0.528000	0.53228	TCG	A|0.951;C|0.049	0.049	strong		0.413	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610	
OPN1LW	5956	hgsc.bcm.edu	37	X	153418524	153418524	+	Missense_Mutation	SNP	C	C	T	rs149897670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153418524C>T	ENST00000369951.4	+	3	581	c.521C>T	c.(520-522)gCc>gTc	p.A174V	OPN1LW_ENST00000463296.1_3'UTR	NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	174			A -> V (in dbSNP:rs731613).		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)					GTGGGCATTGCCTTCTCCTGG	0.582													C|||	509	0.134834	0.1725	0.098	3775	,	,		13280	0.0536		0.0636	False		,,,				2504	0.0971				p.A174V		Atlas-SNP	.											.	OPN1LW	87	.	0			c.C521T						PASS	.	C	VAL/ALA	773,3029		92,471,118,1067,424	235.0	142.0	175.0		521	-0.0	0.2	X	dbSNP_134	175	485,5896		66,226,127,2083,1504	no	missense	OPN1LW	NM_020061.4	64	158,697,245,3150,1928	TT,TC,T,CC,C		7.6007,20.3314,12.3539	benign	174/365	153418524	1258,8925	2172	4006	6178	SO:0001583	missense	5956	exon3			GCATTGCCTTCTC	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.521C>T	X.37:g.153418524C>T	ENSP00000358967:p.Ala174Val	Somatic	439	0	0		WXS	Illumina HiSeq	Phase_I	1010	311	0.307921	NM_020061		Missense_Mutation	SNP	ENST00000369951.4	37	CCDS14742.1	174	0.10488245931283906	50	0.10775862068965517	26	0.07602339181286549	18	0.031578947368421054	64	0.08767123287671233	C	0.005	-2.119635	0.00346	0.203314	0.076007	ENSG00000102076	ENST00000369951;ENST00000442922	T;T	0.38077	1.16;1.16	4.57	-0.00794	0.14007	GPCR, rhodopsin-like superfamily (1);	0.553654	0.19908	N	0.103358	T	0.00012	0.0000	N	0.02854	-0.475	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.35674	-0.9779	9	0.02654	T	1	.	9.3456	0.38107	0.0:0.4905:0.0:0.5095	.	174	P04000	OPSR_HUMAN	V	174;37	ENSP00000358967:A174V;ENSP00000402493:A37V	ENSP00000358967:A174V	A	+	2	0	OPN1LW	153071718	0.000000	0.05858	0.238000	0.24106	0.026000	0.11368	-0.589000	0.05767	-0.099000	0.12263	-0.818000	0.03119	GCC	C|0.830;T|0.170	0.170	strong		0.582	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011544	46011544	+	Silent	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011544G>C	ENST00000400368.1	-	1	842	c.822C>G	c.(820-822)gtC>gtG	p.V274V	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	274	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CCCCAGAGCAGACGGGCACAC	0.647																																					p.V274V		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C822G						PASS	.						112.0	115.0	114.0					21																	46011544		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			AGAGCAGACGGGC	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.822C>G	21.37:g.46011544G>C		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	327	33	0.100917	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.647	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
GOLPH3	64083	hgsc.bcm.edu	37	5	32126441	32126441	+	Silent	SNP	G	G	A	rs34212503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32126441G>A	ENST00000265070.6	-	4	1089	c.774C>T	c.(772-774)gaC>gaT	p.D258D	GOLPH3_ENST00000512668.1_5'Flank	NM_022130.3	NP_071413.1	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3 (coat-protein)	258					cell adhesion molecule production (GO:0060352)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|gene expression (GO:0010467)|glycoprotein biosynthetic process (GO:0009101)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|Golgi vesicle budding (GO:0048194)|lamellipodium assembly (GO:0030032)|leukocyte tethering or rolling (GO:0050901)|positive regulation of protein secretion (GO:0050714)|positive regulation of TOR signaling (GO:0032008)|protein retention in Golgi apparatus (GO:0045053)|protein secretion (GO:0009306)|regulation of mitochondrion organization (GO:0010821)	cytosol (GO:0005829)|endosome (GO:0005768)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	enzyme binding (GO:0019899)|phosphatidylinositol-4-phosphate binding (GO:0070273)			kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11						CATACTGCTCGTCCAGAAGAG	0.557													G|||	219	0.04373	0.1604	0.0072	5008	,	,		19268	0.0		0.002	False		,,,				2504	0.0				p.D258D		Atlas-SNP	.											.	GOLPH3	25	.	0			c.C774T						PASS	.	G		495,3911	231.7+/-245.5	32,431,1740	103.0	86.0	92.0		774	-7.3	0.7	5	dbSNP_126	92	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	GOLPH3	NM_022130.3		32,439,6032	AA,AG,GG		0.093,11.2347,3.8674		258/299	32126441	503,12503	2203	4300	6503	SO:0001819	synonymous_variant	64083	exon4			CTGCTCGTCCAGA	AK075156	CCDS3896.1	5p13.2	2008-07-18			ENSG00000113384	ENSG00000113384			15452	protein-coding gene	gene with protein product	"""golgi peripheral membrane protein 1, 34 kDa"", ""golgi protein"", ""coat-protein"", ""golgi-associated protein"""	612207				11042173, 16263763	Standard	NM_022130		Approved	GPP34, GOPP1, MIDAS	uc003jhp.1	Q9H4A6	OTTHUMG00000090679	ENST00000265070.6:c.774C>T	5.37:g.32126441G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	NM_022130	Q9UIW5	Silent	SNP	ENST00000265070.6	37	CCDS3896.1																																																																																			G|0.966;A|0.034	0.034	strong		0.557	GOLPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207363.2	NM_022130	
PRPF4	9128	hgsc.bcm.edu	37	9	116041316	116041316	+	Silent	SNP	T	T	C	rs146246780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116041316T>C	ENST00000374198.4	+	3	402	c.300T>C	c.(298-300)aaT>aaC	p.N100N	PRPF4_ENST00000374199.4_Silent_p.N99N	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	100				HISERQAEVLAEFERRKRARQINVST -> ISASDRQKYWL SLREGSEPGRSMFPP (in Ref. 3; AAC02261). {ECO:0000305}.	gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						GGCAGATCAATGTTTCCACAG	0.473													T|||	7	0.00139776	0.0045	0.0014	5008	,	,		15580	0.0		0.0	False		,,,				2504	0.0				p.N100N		Atlas-SNP	.											.	PRPF4	56	.	0			c.T300C						PASS	.	T		14,4392	21.2+/-45.6	0,14,2189	95.0	91.0	92.0		300	0.2	1.0	9	dbSNP_134	92	0,8600		0,0,4300	no	coding-synonymous	PRPF4	NM_004697.3		0,14,6489	CC,CT,TT		0.0,0.3177,0.1076		100/523	116041316	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9128	exon3			GATCAATGTTTCC	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"""WD repeat domain containing"""	17349	protein-coding gene	gene with protein product	"""PRP4/STK/WD splicing factor"", ""U4/U6 small nuclear ribonucleoprotein Prp4"""	607795	"""PRP4 pre-mRNA processing factor 4 homolog (yeast)"""			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.300T>C	9.37:g.116041316T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Silent	SNP	ENST00000374198.4	37	CCDS6791.1																																																																																			T|0.999;C|0.001	0.001	strong		0.473	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697	
RNF39	80352	hgsc.bcm.edu	37	6	30043486	30043486	+	Silent	SNP	T	T	C	rs11758516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30043486T>C	ENST00000244360.6	-	1	178	c.81A>G	c.(79-81)aaA>aaG	p.K27K	RNF39_ENST00000376751.3_Silent_p.K27K	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	27						cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										CCGCATTAACTTTTGCCGCTT	0.602													t|||	682	0.136182	0.2337	0.1138	5008	,	,		16597	0.1339		0.0398	False		,,,				2504	0.1217				p.K27K	NSCLC(8;188 360 1520 20207 31481)	Atlas-SNP	.											.	RNF39	27	.	0			c.A81G						PASS	.	T	,	848,3558	316.6+/-294.7	88,672,1443	51.0	53.0	52.0		81,81	-0.4	0.0	6	dbSNP_120	52	427,8173	129.0+/-187.1	13,401,3886	no	coding-synonymous,coding-synonymous	RNF39	NM_025236.3,NM_170769.2	,	101,1073,5329	CC,CT,TT		4.9651,19.2465,9.8032	,	27/421,27/355	30043486	1275,11731	2203	4300	6503	SO:0001819	synonymous_variant	80352	exon1			ATTAACTTTTGCC	AF238315	CCDS4673.1, CCDS4674.1	6p21.3	2013-01-09			ENSG00000204618	ENSG00000204618		"""RING-type (C3HC4) zinc fingers"""	18064	protein-coding gene	gene with protein product		607524				11130983, 11716498	Standard	NM_170769		Approved	HZFw1, LIRF	uc003npe.3	Q9H2S5	OTTHUMG00000031288	ENST00000244360.6:c.81A>G	6.37:g.30043486T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	162	77	0.475309	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Silent	SNP	ENST00000244360.6	37	CCDS4673.1																																																																																			T|0.897;C|0.103	0.103	strong		0.602	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769	
OMP	4975	hgsc.bcm.edu	37	11	76814110	76814110	+	Silent	SNP	G	G	A	rs2233549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:76814110G>A	ENST00000529803.1	+	1	225	c.225G>A	c.(223-225)ccG>ccA	p.P75P	CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000529629.1_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						PASS	.	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	118	0	0		WXS	Illumina HiSeq	Phase_I	136	75	0.551471	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	
RPAP1	26015	hgsc.bcm.edu	37	15	41827757	41827757	+	Missense_Mutation	SNP	T	T	A	rs2297382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41827757T>A	ENST00000304330.4	-	5	610	c.494A>T	c.(493-495)aAg>aTg	p.K165M	RPAP1_ENST00000561603.1_Missense_Mutation_p.K165M|RPAP1_ENST00000568413.1_5'Flank	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	165			K -> M (in dbSNP:rs2297382).			nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TGATGGGCCCTTGGCTTCAGC	0.522													T|||	712	0.142173	0.4017	0.0922	5008	,	,		19046	0.0149		0.0537	False		,,,				2504	0.0491				p.K165M		Atlas-SNP	.											.	RPAP1	111	.	0			c.A494T						PASS	.	T	MET/LYS	1534,2872	485.8+/-360.4	251,1032,920	88.0	89.0	89.0		494	-2.5	0.0	15	dbSNP_100	89	517,8083	145.1+/-200.9	12,493,3795	yes	missense	RPAP1	NM_015540.2	95	263,1525,4715	AA,AT,TT		6.0116,34.8162,15.7696	benign	165/1394	41827757	2051,10955	2203	4300	6503	SO:0001583	missense	26015	exon5			GGGCCCTTGGCTT	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.494A>T	15.37:g.41827757T>A	ENSP00000306123:p.Lys165Met	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	279	0.12774725274725274	196	0.3983739837398374	34	0.09392265193370165	10	0.017482517482517484	39	0.051451187335092345	T	15.70	2.909962	0.52439	0.348162	0.060116	ENSG00000103932	ENST00000304330	T	0.12672	2.66	5.26	-2.47	0.06442	.	1.431580	0.03677	N	0.244940	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.31040	0.305	B	0.33295	0.161	T	0.46091	-0.9216	9	0.72032	D	0.01	-12.1361	5.4209	0.16400	0.1357:0.3919:0.0:0.4725	rs2297382;rs57017522;rs2297382	165	Q9BWH6	RPAP1_HUMAN	M	165	ENSP00000306123:K165M	ENSP00000306123:K165M	K	-	2	0	RPAP1	39615049	0.003000	0.15002	0.000000	0.03702	0.532000	0.34746	-0.115000	0.10741	-0.316000	0.08690	-0.696000	0.03686	AAG	T|0.855;A|0.145	0.145	strong		0.522	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
CNTN5	53942	hgsc.bcm.edu	37	11	100226900	100226900	+	Silent	SNP	G	G	A	rs34539243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:100226900G>A	ENST00000524871.1	+	25	3542	c.3252G>A	c.(3250-3252)tcG>tcA	p.S1084S	CNTN5_ENST00000524560.1_3'UTR|CNTN5_ENST00000418526.2_Silent_p.S1010S|CNTN5_ENST00000279463.3_Silent_p.S1084S|CNTN5_ENST00000528682.1_Silent_p.S1084S	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	1084					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)		CCACATCTTCGTCATCAGTCA	0.418													G|||	88	0.0175719	0.0651	0.0	5008	,	,		20062	0.0		0.002	False		,,,				2504	0.0				p.S1084S		Atlas-SNP	.											.	CNTN5	324	.	0			c.G3252A						PASS	.	G	,	209,3773		7,195,1789	143.0	139.0	140.0		3252,3030	-4.7	0.0	11	dbSNP_126	140	5,8327		0,5,4161	no	coding-synonymous,coding-synonymous	CNTN5	NM_014361.3,NM_175566.2	,	7,200,5950	AA,AG,GG		0.06,5.2486,1.7379	,	1084/1101,1010/1027	100226900	214,12100	1991	4166	6157	SO:0001819	synonymous_variant	53942	exon24			ATCTTCGTCATCA	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.3252G>A	11.37:g.100226900G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	94	56	0.595745	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Silent	SNP	ENST00000524871.1	37	CCDS53696.1																																																																																			G|0.988;A|0.012	0.012	strong		0.418	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
LEFTY1	10637	hgsc.bcm.edu	37	1	226074436	226074436	+	Silent	SNP	G	G	C	rs35684337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226074436G>C	ENST00000272134.5	-	4	1171	c.1092C>G	c.(1090-1092)ctC>ctG	p.L364L	RP4-559A3.7_ENST00000432920.2_3'UTR|LEFTY1_ENST00000492457.1_5'Flank	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	364					cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					CCTATGGCTGGAGCCTCCTTG	0.602													G|||	195	0.0389377	0.1354	0.0216	5008	,	,		18096	0.0		0.0	False		,,,				2504	0.001				p.L364L		Atlas-SNP	.											.	LEFTY1	30	.	0			c.C1092G						PASS	.	G		556,3840		26,504,1668	60.0	62.0	61.0		1092	1.1	0.8	1	dbSNP_126	61	0,8598		0,0,4299	no	coding-synonymous	LEFTY1	NM_020997.3		26,504,5967	CC,CG,GG		0.0,12.6479,4.2789		364/367	226074436	556,12438	2198	4299	6497	SO:0001819	synonymous_variant	10637	exon4			TGGCTGGAGCCTC	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"""left-right determination, factor B"""	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.1092C>G	1.37:g.226074436G>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	198	109	0.550505	NM_020997	B2R7U0|Q53H67|Q5TE94	Silent	SNP	ENST00000272134.5	37	CCDS1548.1																																																																																			G|0.963;C|0.037	0.037	strong		0.602	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997	
SCN10A	6336	hgsc.bcm.edu	37	3	38770198	38770198	+	Missense_Mutation	SNP	T	T	G	rs146028829		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38770198T>G	ENST00000449082.2	-	15	2474	c.2475A>C	c.(2473-2475)gaA>gaC	p.E825D		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	825					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.E825D(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)	GGGGCCAGTCTTCATGGGGCG	0.517													T|||	1	0.000199681	0.0	0.0	5008	,	,		18556	0.0		0.001	False		,,,				2504	0.0				p.E825D		Atlas-SNP	.											SCN10A,NS,carcinoma,0,2	SCN10A	359	2	1	Substitution - Missense(1)	kidney(1)	c.A2475C						PASS	.	T	ASP/GLU	2,4404	4.2+/-10.8	0,2,2201	121.0	117.0	118.0		2475	-9.4	0.0	3	dbSNP_134	118	19,8581	14.6+/-50.1	0,19,4281	yes	missense	SCN10A	NM_006514.2	45	0,21,6482	GG,GT,TT		0.2209,0.0454,0.1615	benign	825/1957	38770198	21,12985	2203	4300	6503	SO:0001583	missense	6336	exon15			CCAGTCTTCATGG	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.2475A>C	3.37:g.38770198T>G	ENSP00000390600:p.Glu825Asp	Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	347	160	0.461095	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	3.068	-0.191656	0.06299	4.54E-4	0.002209	ENSG00000185313	ENST00000449082	D	0.98531	-4.98	4.73	-9.45	0.00600	Ion transport (1);	1.276660	0.04859	N	0.443792	D	0.93058	0.7790	N	0.16478	0.41	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	D	0.86553	0.1836	10	0.45353	T	0.12	.	6.9757	0.24674	0.0871:0.3789:0.4161:0.1179	.	825	Q9Y5Y9	SCNAA_HUMAN	D	825	ENSP00000390600:E825D	ENSP00000390600:E825D	E	-	3	2	SCN10A	38745202	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-1.935000	0.01550	-2.903000	0.00311	0.533000	0.62120	GAA	T|0.999;G|0.001	0.001	strong		0.517	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
MTFR2	113115	hgsc.bcm.edu	37	6	136560948	136560948	+	Silent	SNP	G	G	A	rs10484485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:136560948G>A	ENST00000420702.1	-	6	914	c.525C>T	c.(523-525)ggC>ggT	p.G175G	MTFR2_ENST00000451457.2_Silent_p.G175G	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	175					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											CGTCACTCAAGCCAAAGGAAC	0.428													G|||	293	0.0585064	0.208	0.0231	5008	,	,		19229	0.0		0.002	False		,,,				2504	0.0				p.G175G		Atlas-SNP	.											.	.	.	.	0			c.C525T						PASS	.	G	,	786,3620	311.6+/-292.2	74,638,1491	38.0	33.0	35.0		525,525	1.3	0.0	6	dbSNP_119	35	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	FAM54A	NM_001099286.1,NM_138419.3	,	74,643,5786	AA,AG,GG		0.0581,17.8393,6.0818	,	175/386,175/386	136560948	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	113115	exon6			ACTCAAGCCAAAG	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"""DUF729 domain containing 1"", ""family with sequence similarity 54, member A"""	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.525C>T	6.37:g.136560948G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Silent	SNP	ENST00000420702.1	37	CCDS5176.1																																																																																			G|0.939;A|0.061	0.061	strong		0.428	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419	
CSMD3	114788	hgsc.bcm.edu	37	8	113662508	113662508	+	Silent	SNP	A	A	G	rs7839690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:113662508A>G	ENST00000297405.5	-	19	3319	c.3075T>C	c.(3073-3075)gaT>gaC	p.D1025D	CSMD3_ENST00000343508.3_Silent_p.D985D|CSMD3_ENST00000352409.3_Silent_p.D1025D|CSMD3_ENST00000455883.2_Silent_p.D921D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1025	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					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						CAATGGAGAAATCATGACCAT	0.433										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	132	0.0263578	0.0968	0.0058	5008	,	,		14812	0.0		0.0	False		,,,				2504	0.0				p.D1025D		Atlas-SNP	.											CSMD3_ENST00000343508,colon,carcinoma,-2,2	CSMD3	2325	2	0			c.T3075C						PASS	.	A	,,	311,4095	166.2+/-197.5	10,291,1902	147.0	147.0	147.0		2763,3075,2955	2.3	1.0	8	dbSNP_116	147	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	10,296,6197	GG,GA,AA		0.0581,7.0586,2.4296	,,	921/3539,1025/3708,985/3668	113662508	316,12690	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon19			GGAGAAATCATGA	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.3075T>C	8.37:g.113662508A>G		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	219	90	0.410959	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.972;G|0.028	0.028	strong		0.433	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
ZNF792	126375	hgsc.bcm.edu	37	19	35450229	35450229	+	Missense_Mutation	SNP	C	C	T	rs2651079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35450229C>T	ENST00000404801.1	-	4	916	c.530G>A	c.(529-531)cGg>cAg	p.R177Q	ZNF792_ENST00000605484.1_Missense_Mutation_p.R110Q	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	177			R -> Q (in dbSNP:rs2651079). {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)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CACCTGTTTCCGGGGAAGGTT	0.507													T|||	3136	0.626198	0.9123	0.3991	5008	,	,		21491	0.5942		0.5149	False		,,,				2504	0.5481				p.R177Q	GBM(1;7 183 21053 22581 22847)	Atlas-SNP	.											.	ZNF792	46	.	0			c.G530A						PASS	.	T	GLN/ARG	3665,741	301.5+/-286.9	1531,603,69	252.0	246.0	248.0		530	-0.2	0.0	19	dbSNP_100	248	4068,4532	594.2+/-393.3	969,2130,1201	yes	missense	ZNF792	NM_175872.4	43	2500,2733,1270	TT,TC,CC		47.3023,16.818,40.5428	benign	177/633	35450229	7733,5273	2203	4300	6503	SO:0001583	missense	126375	exon4			TGTTTCCGGGGAA	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.530G>A	19.37:g.35450229C>T	ENSP00000385099:p.Arg177Gln	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	330	327	0.990909	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Missense_Mutation	SNP	ENST00000404801.1	37	CCDS12440.2	1362	0.6236263736263736	454	0.9227642276422764	168	0.46408839779005523	355	0.6206293706293706	385	0.5079155672823219	t	0.114	-1.134845	0.01742	0.83182	0.473023	ENSG00000180884	ENST00000404801	T	0.04862	3.54	3.16	-0.202	0.13208	.	.	.	.	.	T	0.00012	0.0000	N	0.01431	-0.87	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23904	-1.0175	8	0.02654	T	1	.	2.9579	0.05882	0.3482:0.3338:0.0:0.3179	rs2651079;rs52801030;rs58153206;rs2651079	177	Q3KQV3	ZN792_HUMAN	Q	177	ENSP00000385099:R177Q	ENSP00000385099:R177Q	R	-	2	0	ZNF792	40142069	0.000000	0.05858	0.003000	0.11579	0.024000	0.10985	-0.565000	0.05929	-0.420000	0.07427	-0.516000	0.04426	CGG	C|0.367;T|0.633	0.633	strong		0.507	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
SLC35E4	339665	hgsc.bcm.edu	37	22	31032881	31032881	+	Silent	SNP	G	G	A	rs8136373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31032881G>A	ENST00000343605.4	+	1	1243	c.444G>A	c.(442-444)ctG>ctA	p.L148L	SLC35E4_ENST00000406566.1_Silent_p.L148L|SLC35E4_ENST00000300385.8_Silent_p.L148L	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	148	EamA.|Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						TGTTCACCCTGGCCCTGTCGG	0.677													G|||	440	0.0878594	0.2988	0.0303	5008	,	,		14087	0.0		0.0149	False		,,,				2504	0.0092				p.L148L		Atlas-SNP	.											.	SLC35E4	22	.	0			c.G444A						PASS	.	G		1219,3185	391.9+/-328.3	165,889,1148	65.0	36.0	46.0		444	5.2	1.0	22	dbSNP_116	46	171,8429	72.9+/-135.5	1,169,4130	no	coding-synonymous	SLC35E4	NM_001001479.2		166,1058,5278	AA,AG,GG		1.9884,27.6794,10.689		148/351	31032881	1390,11614	2202	4300	6502	SO:0001819	synonymous_variant	339665	exon1			CACCCTGGCCCTG		CCDS13882.1	22q12.2	2013-05-22			ENSG00000100036	ENSG00000100036		"""Solute carriers"""	17058	protein-coding gene	gene with protein product							Standard	NM_001001479		Approved		uc003ais.1	Q6ICL7	OTTHUMG00000151110	ENST00000343605.4:c.444G>A	22.37:g.31032881G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	39	38	0.974359	NM_001001479	Q567P0	Silent	SNP	ENST00000343605.4	37	CCDS13882.1																																																																																			G|0.900;A|0.100	0.100	strong		0.677	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973	
ZNF678	339500	hgsc.bcm.edu	37	1	227842516	227842516	+	Missense_Mutation	SNP	G	G	C	rs61744724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227842516G>C	ENST00000343776.5	+	4	910	c.565G>C	c.(565-567)Gtt>Ctt	p.V189L	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.V244L	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	189					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				ATGTGACAAAGTTTTTAATTG	0.373													G|||	82	0.0163738	0.059	0.0043	5008	,	,		18566	0.0		0.001	False		,,,				2504	0.0				p.V244L		Atlas-SNP	.											.	ZNF678	137	.	0			c.G730C						PASS	.	G	LEU/VAL	213,4193	124.5+/-161.8	3,207,1993	88.0	103.0	98.0		730	1.2	0.1	1	dbSNP_129	98	1,8597	1.2+/-3.3	0,1,4298	no	missense	ZNF678	NM_178549.3	32	3,208,6291	CC,CG,GG		0.0116,4.8343,1.6456	benign	244/581	227842516	214,12790	2203	4299	6502	SO:0001583	missense	339500	exon4			GACAAAGTTTTTA	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"""Zinc fingers, C2H2-type"", ""-"""	28652	protein-coding gene	gene with protein product	"""hypothetical protein MGC42493"""					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.565G>C	1.37:g.227842516G>C	ENSP00000344828:p.Val189Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		27	0.012362637362637362	22	0.044715447154471545	1	0.0027624309392265192	4	0.006993006993006993	0	0.0	G	10.75	1.437218	0.25900	0.048343	1.16E-4	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.35605	1.3;1.3	1.21	1.21	0.21127	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04724	0.0128	L	0.41415	1.275	0.19945	N	0.999946	P	0.36171	0.541	B	0.36608	0.229	T	0.09100	-1.0690	9	0.72032	D	0.01	.	5.6119	0.17410	0.0:0.3493:0.6507:0.0	rs61744724	189	Q5SXM1	ZN678_HUMAN	L	189;244	ENSP00000344828:V189L;ENSP00000440403:V244L	ENSP00000344828:V189L	V	+	1	0	ZNF678	225909139	0.001000	0.12720	0.092000	0.20876	0.083000	0.17756	-0.016000	0.12613	0.502000	0.28037	0.505000	0.49811	GTT	G|0.987;C|0.013	0.013	strong		0.373	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549	
CAPN9	10753	hgsc.bcm.edu	37	1	230916057	230916057	+	Missense_Mutation	SNP	T	T	G	rs79844715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230916057T>G	ENST00000271971.2	+	10	1360	c.1247T>G	c.(1246-1248)cTg>cGg	p.L416R	RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000412344.1_RNA|RP11-99J16__A.2_ENST00000452640.1_RNA|CAPN9_ENST00000366666.2_Missense_Mutation_p.L353R|CAPN9_ENST00000354537.1_Missense_Mutation_p.L390R	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	416	Domain III.				digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				GCCAATGTGCTGACAATCGGC	0.483													T|||	7	0.00139776	0.0045	0.0014	5008	,	,		17721	0.0		0.0	False		,,,				2504	0.0				p.L416R		Atlas-SNP	.											.	CAPN9	116	.	0			c.T1247G						PASS	.	T	ARG/LEU,ARG/LEU	23,4383	29.9+/-59.1	0,23,2180	124.0	112.0	116.0		1247,1169	5.5	1.0	1	dbSNP_131	116	0,8600		0,0,4300	yes	missense,missense	CAPN9	NM_006615.2,NM_016452.1	102,102	0,23,6480	GG,GT,TT		0.0,0.522,0.1768	probably-damaging,probably-damaging	416/691,390/665	230916057	23,12983	2203	4300	6503	SO:0001583	missense	10753	exon10			ATGTGCTGACAAT	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1247T>G	1.37:g.230916057T>G	ENSP00000271971:p.Leu416Arg	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	37	CCDS1586.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	10.03	1.239188	0.22711	0.00522	0.0	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	D;D;D	0.88586	-2.4;-2.4;-2.4	5.54	5.54	0.83059	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.197529	0.44483	D	0.000444	D	0.92691	0.7677	M	0.88241	2.94	0.58432	D	0.999996	D;D;D	0.67145	0.996;0.991;0.993	D;P;P	0.64410	0.925;0.793;0.869	D	0.92319	0.5864	10	0.31617	T	0.26	.	15.3798	0.74645	0.0:0.0:0.0:1.0	.	353;390;416	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	R	416;390;353	ENSP00000271971:L416R;ENSP00000346538:L390R;ENSP00000355626:L353R	ENSP00000271971:L416R	L	+	2	0	CAPN9	228982680	1.000000	0.71417	0.998000	0.56505	0.017000	0.09413	3.833000	0.55790	2.112000	0.64535	0.524000	0.50904	CTG	T|0.998;G|0.002	0.002	strong		0.483	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
ZNF10	7556	hgsc.bcm.edu	37	12	133732512	133732512	+	Missense_Mutation	SNP	A	A	G	rs11147259	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133732512A>G	ENST00000248211.6	+	5	902	c.680A>G	c.(679-681)cAg>cGg	p.Q227R	ZNF10_ENST00000426665.2_Missense_Mutation_p.Q227R|ZNF10_ENST00000402932.2_Intron|ZNF268_ENST00000416488.1_Intron|CTD-2140B24.4_ENST00000540096.2_Intron	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	227			Q -> R (in dbSNP:rs11147259).	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)		CACCTTATTCAGTTTGCAAGA	0.358													A|||	337	0.0672923	0.1944	0.0303	5008	,	,		22500	0.002		0.0398	False		,,,				2504	0.0174				p.Q227R		Atlas-SNP	.											ZNF10,bladder,carcinoma,+1,1	ZNF10	58	1	0			c.A680G						PASS	.	A	ARG/GLN	711,3695	295.6+/-283.7	54,603,1546	111.0	102.0	105.0		680	4.2	0.9	12	dbSNP_120	105	366,8234	121.8+/-180.9	6,354,3940	yes	missense	ZNF10	NM_015394.4	43	60,957,5486	GG,GA,AA		4.2558,16.1371,8.2808	possibly-damaging	227/574	133732512	1077,11929	2203	4300	6503	SO:0001583	missense	7556	exon5			TTATTCAGTTTGC	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.680A>G	12.37:g.133732512A>G	ENSP00000248211:p.Gln227Arg	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	121	50	0.413223	NM_015394	B2RBS1|Q8TC91	Missense_Mutation	SNP	ENST00000248211.6	37	CCDS9283.1	137	0.06272893772893773	98	0.1991869918699187	8	0.022099447513812154	0	0.0	31	0.040897097625329816	A	6.062	0.379830	0.11466	0.161371	0.042558	ENSG00000256223	ENST00000248211;ENST00000426665;ENST00000537119	T;T;T	0.59364	0.27;0.27;4.7	4.22	4.22	0.49857	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36234	N	0.002714	T	0.00039	0.0001	N	0.05574	-0.02	0.09310	P	0.99999835466	B	0.30326	0.276	B	0.27796	0.083	T	0.09930	-1.0652	8	.	.	.	.	9.4701	0.38837	0.8219:0.1781:0.0:0.0	rs11147259;rs58328991;rs11147259	227	P21506	ZNF10_HUMAN	R	227;227;185	ENSP00000248211:Q227R;ENSP00000393814:Q227R;ENSP00000437397:Q185R	.	Q	+	2	0	ZNF10	132242585	0.000000	0.05858	0.916000	0.36221	0.450000	0.32258	0.710000	0.25748	1.896000	0.54893	0.533000	0.62120	CAG	A|0.918;G|0.082	0.082	strong		0.358	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394	
PPFIBP2	8495	hgsc.bcm.edu	37	11	7662732	7662732	+	Silent	SNP	C	C	T	rs4643071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7662732C>T	ENST00000299492.4	+	16	1786	c.1398C>T	c.(1396-1398)gaC>gaT	p.D466D	PPFIBP2_ENST00000533792.1_Silent_p.D308D|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000528883.1_Silent_p.D354D|PPFIBP2_ENST00000530181.1_Silent_p.D323D	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	466					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		GTGGCTGGGACGACACTGCTG	0.527													T|||	3338	0.666534	0.7905	0.6182	5008	,	,		17093	0.5813		0.6431	False		,,,				2504	0.6452				p.D466D		Atlas-SNP	.											PPFIBP2,NS,carcinoma,+1,1	PPFIBP2	87	1	0			c.C1398T						PASS	.	T		3471,931	354.6+/-312.7	1360,751,90	123.0	107.0	112.0		1398	-1.0	0.8	11	dbSNP_111	112	5725,2867	450.1+/-362.3	1916,1893,487	no	coding-synonymous	PPFIBP2	NM_003621.2		3276,2644,577	TT,TC,CC		33.3682,21.1495,29.2289		466/877	7662732	9196,3798	2201	4296	6497	SO:0001819	synonymous_variant	8495	exon16			CTGGGACGACACT	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.1398C>T	11.37:g.7662732C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	129	74	0.573643	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Silent	SNP	ENST00000299492.4	37	CCDS31419.1	1468	0.6721611721611722	389	0.790650406504065	229	0.6325966850828729	357	0.6241258741258742	493	0.6503957783641161	T	0.184	-1.059576	0.01950	0.788505	0.666318	ENSG00000166387	ENST00000534409	.	.	.	5.93	-1.04	0.10068	.	.	.	.	.	.	.	.	.	.	.	0.27699	P	0.9458467	.	.	.	.	.	.	.	.	.	.	.	.	.	-9.4907	6.3408	0.21322	0.1535:0.4429:0.0:0.4036	rs4643071;rs17851926;rs58264303;rs4643071	.	.	.	X	157	.	.	R	+	1	2	PPFIBP2	7619308	0.093000	0.21703	0.812000	0.32479	0.138000	0.21146	-0.815000	0.04481	-0.495000	0.06659	-0.972000	0.02603	CGA	C|0.307;T|0.693	0.693	strong		0.527	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
AHNAK2	113146	hgsc.bcm.edu	37	14	105410827	105410827	+	Missense_Mutation	SNP	C	C	T	rs28380382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105410827C>T	ENST00000333244.5	-	7	11080	c.10961G>A	c.(10960-10962)gGg>gAg	p.G3654E	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3654			G -> E (in dbSNP:rs28380382).			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)			CATGGACTTCCCTGGGGCCGA	0.577													.|||	2767	0.552516	0.6316	0.513	5008	,	,		19166	0.4127		0.5348	False		,,,				2504	0.636				p.G3654E		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G10961A						PASS	.	C	GLU/GLY	2649,1289		906,837,226	171.0	182.0	178.0		10961	0.8	0.0	14	dbSNP_125	178	4501,3781		1240,2021,880	no	missense	AHNAK2	NM_138420.2	98	2146,2858,1106	TT,TC,CC		45.6532,32.7324,41.4894	probably-damaging	3654/5796	105410827	7150,5070	1969	4141	6110	SO:0001583	missense	113146	exon7			GACTTCCCTGGGG	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.10961G>A	14.37:g.105410827C>T	ENSP00000353114:p.Gly3654Glu	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	272	272	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1144	0.5238095238095238	320	0.6504065040650406	199	0.5497237569060773	223	0.38986013986013984	402	0.5303430079155673	c	13.14	2.147422	0.37923	0.672676	0.543468	ENSG00000185567	ENST00000333244	T	0.02525	4.26	3.77	0.827	0.18835	.	.	.	.	.	T	0.00012	0.0000	M	0.86028	2.79	0.80722	P	0.0	B	0.33044	0.395	B	0.33121	0.158	T	0.50491	-0.8822	8	0.02654	T	1	.	1.7266	0.02923	0.1685:0.4793:0.1636:0.1885	rs28380382;rs59092583	3654	Q8IVF2	AHNK2_HUMAN	E	3654	ENSP00000353114:G3654E	ENSP00000353114:G3654E	G	-	2	0	AHNAK2	104481872	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	0.000000	0.12993	-0.015000	0.14150	-0.326000	0.08463	GGG	C|0.468;T|0.532	0.532	strong		0.577	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SNAP91	9892	hgsc.bcm.edu	37	6	84303273	84303273	+	Silent	SNP	G	G	A	rs181491904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84303273G>A	ENST00000439399.2	-	18	1936	c.1620C>T	c.(1618-1620)acC>acT	p.T540T	SNAP91_ENST00000428679.2_Silent_p.T540T|SNAP91_ENST00000521743.1_Silent_p.T540T|SNAP91_ENST00000520302.1_Silent_p.T538T|SNAP91_ENST00000437520.1_Intron|SNAP91_ENST00000369694.2_Silent_p.T540T|SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000195649.6_Silent_p.T540T|SNAP91_ENST00000521485.1_Silent_p.T540T	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	540	Ala-rich.|Thr-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		tggcagcggcggtggcagcag	0.577													G|||	20	0.00399361	0.0151	0.0	5008	,	,		15737	0.0		0.0	False		,,,				2504	0.0				p.T540T		Atlas-SNP	.											.	SNAP91	199	.	0			c.C1620T						PASS	.	G	,,,	20,4206		0,20,2093	15.0	21.0	19.0		1620,1614,,1620	2.3	0.1	6		19	1,8333		0,1,4166	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	SNAP91	NM_001242792.1,NM_001242793.1,NM_001242794.1,NM_014841.2	,,,	0,21,6259	AA,AG,GG		0.012,0.4733,0.1672	,,,	540/908,538/878,,540/908	84303273	21,12539	2113	4167	6280	SO:0001819	synonymous_variant	9892	exon17			AGCGGCGGTGGCA	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"""synaptosomal-associated protein, 91 kDa (mouse) homolog"", ""synaptosomal-associated protein, 91kDa homolog (mouse)"""			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1620C>T	6.37:g.84303273G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Silent	SNP	ENST00000439399.2	37	CCDS47455.1																																																																																			G|0.995;A|0.005	0.005	strong		0.577	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1		
OR10AG1	282770	hgsc.bcm.edu	37	11	55735343	55735343	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55735343C>T	ENST00000312345.2	-	1	647	c.597G>A	c.(595-597)acG>acA	p.T199T		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T199T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					GAAATGGCACCGTGATAAACA	0.408																																					p.T199T		Atlas-SNP	.											OR10AG1,NS,carcinoma,0,1	OR10AG1	100	1	1	Substitution - coding silent(1)	lung(1)	c.G597A						scavenged	.						80.0	80.0	80.0					11																	55735343		2201	4296	6497	SO:0001819	synonymous_variant	282770	exon1			TGGCACCGTGATA	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.597G>A	11.37:g.55735343C>T		Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	226	3	0.0132743	NM_001005491	B2RNH4|Q6IEU3	Silent	SNP	ENST00000312345.2	37	CCDS31514.1																																																																																			.	.	none		0.408	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
AFAP1L2	84632	hgsc.bcm.edu	37	10	116056779	116056779	+	Silent	SNP	C	C	T	rs62641713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116056779C>T	ENST00000304129.4	-	18	2417	c.2388G>A	c.(2386-2388)tcG>tcA	p.S796S	AFAP1L2_ENST00000369271.3_Silent_p.S792S|AFAP1L2_ENST00000491814.1_5'UTR|AFAP1L2_ENST00000545353.1_Silent_p.S849S			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	796					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)		TGACCACGACCGAGAGAGGCC	0.567													C|||	206	0.0411342	0.1467	0.0115	5008	,	,		19382	0.001		0.003	False		,,,				2504	0.0				p.S796S		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.G2388A						PASS	.	C	,	664,3742	280.8+/-275.6	62,540,1601	180.0	157.0	164.0		2388,2376	-10.9	0.1	10	dbSNP_129	164	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous	AFAP1L2	NM_001001936.1,NM_032550.2	,	62,547,5894	TT,TC,CC		0.0814,15.0704,5.1592	,	796/819,792/815	116056779	671,12335	2203	4300	6503	SO:0001819	synonymous_variant	84632	exon18			CACGACCGAGAGA	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.2388G>A	10.37:g.116056779C>T		Somatic	297	1	0.003367		WXS	Illumina HiSeq	Phase_I	337	337	1	NM_001001936	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																			C|0.953;T|0.047	0.047	strong		0.567	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
C5	727	hgsc.bcm.edu	37	9	123725971	123725971	+	Silent	SNP	C	C	T	rs12237774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:123725971C>T	ENST00000223642.1	-	34	4295	c.4266G>A	c.(4264-4266)gcG>gcA	p.A1422A		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1422					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	TGTCCATCACCGCATGAGAGG	0.358													C|||	534	0.106629	0.1936	0.0375	5008	,	,		17051	0.1994		0.0109	False		,,,				2504	0.0409				p.A1422A		Atlas-SNP	.											.	C5	124	.	0			c.G4266A						PASS	.	C		824,3582	329.1+/-300.9	77,670,1456	79.0	76.0	77.0		4266	-2.5	1.0	9	dbSNP_120	77	107,8493	57.2+/-118.5	0,107,4193	no	coding-synonymous	C5	NM_001735.2		77,777,5649	TT,TC,CC		1.2442,18.7018,7.1582		1422/1677	123725971	931,12075	2203	4300	6503	SO:0001819	synonymous_variant	727	exon34			CATCACCGCATGA	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.4266G>A	9.37:g.123725971C>T		Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	279	101	0.362007	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	37	CCDS6826.1																																																																																			C|0.914;T|0.086	0.086	strong		0.358	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
KANK2	25959	hgsc.bcm.edu	37	19	11289073	11289073	+	Missense_Mutation	SNP	C	C	T	rs115473443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11289073C>T	ENST00000586659.1	-	6	1782	c.1468G>A	c.(1468-1470)Gca>Aca	p.A490T	KANK2_ENST00000589894.1_Missense_Mutation_p.A490T|KANK2_ENST00000355150.5_Missense_Mutation_p.A490T|KANK2_ENST00000589359.1_Missense_Mutation_p.A498T|KANK2_ENST00000432929.2_Missense_Mutation_p.A498T			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	490					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GTGGGGTCTGCAACCTCCTCT	0.667													c|||	79	0.0157748	0.0575	0.0043	5008	,	,		10474	0.0		0.0	False		,,,				2504	0.0				p.A498T		Atlas-SNP	.											.	KANK2	47	.	0			c.G1492A						PASS	.		THR/ALA,THR/ALA	194,4212	115.9+/-153.8	4,186,2013	24.0	27.0	26.0		1468,1492	-3.0	0.0	19	dbSNP_132	26	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	58,58	4,190,6309	TT,TC,CC		0.0465,4.4031,1.5224	benign,benign	490/852,498/860	11289073	198,12808	2203	4300	6503	SO:0001583	missense	25959	exon4			GGTCTGCAACCTC	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	29300	protein-coding gene	gene with protein product		614610	"""matrix-remodelling associated 3"", ""ankyrin repeat domain 25"""	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.1468G>A	19.37:g.11289073C>T	ENSP00000465650:p.Ala490Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	C	6.571	0.473652	0.12521	0.044031	4.65E-4	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.39406	1.08;1.1	5.45	-3.0	0.05480	.	0.449602	0.22279	N	0.062158	T	0.03348	0.0097	L	0.27053	0.805	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.08186	-1.0734	10	0.23891	T	0.37	-18.7177	6.2347	0.20756	0.1484:0.1981:0.0:0.6536	.	490;498	Q63ZY3;Q63ZY3-2	KANK2_HUMAN;.	T	498;490	ENSP00000395650:A498T;ENSP00000347276:A490T	ENSP00000347276:A490T	A	-	1	0	KANK2	11150073	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.342000	0.02645	-0.503000	0.06586	-0.144000	0.13903	GCA	C|0.985;T|0.015	0.015	strong		0.667	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
ALK	238	hgsc.bcm.edu	37	2	29416750	29416750	+	Silent	SNP	A	A	G	rs55772745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29416750A>G	ENST00000389048.3	-	29	5109	c.4203T>C	c.(4201-4203)taT>taC	p.Y1401Y	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1401					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)	CAAGTGGACCATATTCTATCG	0.488			"""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				A|||	114	0.0227636	0.0847	0.0029	5008	,	,		17238	0.0		0.0	False		,,,				2504	0.0				p.Y1401Y		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.T4203C						PASS	.			255,4149		7,241,1954	43.0	47.0	45.0		4203	-10.6	0.0	2	dbSNP_129	45	1,8599		0,1,4299	no	coding-synonymous	ALK	NM_004304.4		7,242,6253	GG,GA,AA		0.0116,5.7902,1.9686		1401/1621	29416750	256,12748	2202	4300	6502	SO:0001819	synonymous_variant	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TGGACCATATTCT	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.4203T>C	2.37:g.29416750A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	133	78	0.586466	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			A|0.979;G|0.021	0.021	strong		0.488	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
KCNH3	23416	hgsc.bcm.edu	37	12	49951232	49951232	+	Silent	SNP	T	T	C	rs2241418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49951232T>C	ENST00000257981.6	+	15	3008	c.2748T>C	c.(2746-2748)ggT>ggC	p.G916G	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	916					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						ACAGGGAGGGTCCGTGCCCTC	0.662													C|||	1036	0.206869	0.5151	0.1081	5008	,	,		16526	0.0833		0.1054	False		,,,				2504	0.092				p.G916G		Atlas-SNP	.											.	KCNH3	88	.	0			c.T2748C						PASS	.	C		1914,2490	586.8+/-386.5	429,1056,717	24.0	27.0	26.0		2748	2.4	0.5	12	dbSNP_98	26	900,7698	752.9+/-407.4	56,788,3455	no	coding-synonymous	KCNH3	NM_012284.1		485,1844,4172	CC,CT,TT		10.4676,43.4605,21.6428		916/1084	49951232	2814,10188	2202	4299	6501	SO:0001819	synonymous_variant	23416	exon15			GGAGGGTCCGTGC	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.2748T>C	12.37:g.49951232T>C		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_012284	Q9UQ06	Silent	SNP	ENST00000257981.6	37	CCDS8786.1																																																																																			T|0.792;C|0.208	0.208	strong		0.662	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
PCSK5	5125	hgsc.bcm.edu	37	9	78938186	78938186	+	Missense_Mutation	SNP	G	G	C	rs2803429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:78938186G>C	ENST00000545128.1	+	31	4778	c.4240G>C	c.(4240-4242)Gag>Cag	p.E1414Q		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1414	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						TTATGAAAAGGAGACTAAGGA	0.532													G|||	1611	0.321685	0.4667	0.2392	5008	,	,		15651	0.1369		0.3529	False		,,,				2504	0.3425				p.E1414Q		Atlas-SNP	.											.	PCSK5	329	.	0			c.G4240C						PASS	.	G	GLN/GLU	791,961		189,413,274	57.0	55.0	56.0		4240	-5.4	0.0	9	dbSNP_100	56	1344,2638		235,874,882	yes	missense	PCSK5	NM_001190482.1	29	424,1287,1156	CC,CG,GG		33.7519,45.1484,37.234	benign	1414/1861	78938186	2135,3599	876	1991	2867	SO:0001583	missense	5125	exon31			GAAAAGGAGACTA		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.4240G>C	9.37:g.78938186G>C	ENSP00000446280:p.Glu1414Gln	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	112	66	0.589286	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	686	0.3141025641025641	239	0.48577235772357724	99	0.27348066298342544	76	0.13286713286713286	272	0.35883905013192613	G	4.588	0.109191	0.08780	0.451484	0.337519	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.28666	1.6;1.67	5.35	-5.44	0.02624	.	1.452020	0.03812	N	0.266049	T	0.00012	0.0000	L	0.31804	0.96	0.80722	P	0.0	.	.	.	.	.	.	T	0.43750	-0.9372	7	0.14656	T	0.56	0.7389	2.3399	0.04257	0.3703:0.298:0.2304:0.1014	rs2803429;rs17777849;rs61513592;rs2803429	.	.	.	Q	1414;1144;1114	ENSP00000446280:E1414Q;ENSP00000411654:E1114Q	ENSP00000365945:E1144Q	E	+	1	0	PCSK5	78128006	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.431000	0.21444	-1.152000	0.02832	-0.859000	0.03014	GAG	G|0.675;C|0.325	0.325	strong		0.532	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PKD1	5310	hgsc.bcm.edu	37	16	2162810	2162810	+	Missense_Mutation	SNP	G	G	A	rs147910505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2162810G>A	ENST00000262304.4	-	13	3348	c.3140C>T	c.(3139-3141)tCg>tTg	p.S1047L	PKD1_ENST00000423118.1_Missense_Mutation_p.S1047L|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1047	PKD 5. {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						CTCCACGGCCGAGTCCACCAG	0.682													g|||	5	0.000998403	0.003	0.0014	5008	,	,		9360	0.0		0.0	False		,,,				2504	0.0				p.S1047L		Atlas-SNP	.											.	PKD1	184	.	0			c.C3140T	GRCh37	CM074435	PKD1	M	rs147910505	PASS	.	G	LEU/SER,LEU/SER	16,4376	22.3+/-47.3	0,16,2180	50.0	53.0	52.0		3140,3140	5.0	1.0	16	dbSNP_134	52	0,8586		0,0,4293	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	145,145	0,16,6473	AA,AG,GG		0.0,0.3643,0.1233	possibly-damaging,possibly-damaging	1047/4303,1047/4304	2162810	16,12962	2196	4293	6489	SO:0001583	missense	5310	exon13			ACGGCCGAGTCCA	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.3140C>T	16.37:g.2162810G>A	ENSP00000262304:p.Ser1047Leu	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	26	11	0.423077	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	g	15.48	2.845291	0.51164	0.003643	0.0	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.62105	0.05;0.05	4.99	4.99	0.66335	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (2);	0.207794	0.41500	D	0.000864	T	0.74261	0.3693	M	0.68952	2.095	0.40941	D	0.984461	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.915	T	0.70506	-0.4853	10	0.02654	T	1	.	18.2979	0.90153	0.0:0.0:1.0:0.0	.	1047;1047	P98161-3;P98161	.;PKD1_HUMAN	L	1047;1047;762	ENSP00000262304:S1047L;ENSP00000399501:S1047L	ENSP00000262304:S1047L	S	-	2	0	PKD1	2102811	1.000000	0.71417	0.969000	0.41365	0.444000	0.32077	5.507000	0.66999	2.321000	0.78463	0.645000	0.84053	TCG	G|0.999;A|0.001	0.001	strong		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
CRELD1	78987	hgsc.bcm.edu	37	3	9984855	9984855	+	Splice_Site	SNP	C	C	T	rs79223485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9984855C>T	ENST00000383811.3	+	8	1511	c.912C>T	c.(910-912)ctC>ctT	p.L304L	CRELD1_ENST00000452070.1_Splice_Site_p.L304L|CRELD1_ENST00000326434.5_Splice_Site_p.L304L|CRELD1_ENST00000397170.3_Splice_Site_p.L304L|CRELD1_ENST00000489674.1_3'UTR	NM_015513.4	NP_056328	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1	304					cardiac septum development (GO:0003279)|endocardial cushion development (GO:0003197)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			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						CCAAGTGTCTCGGTGAGTCTC	0.612													C|||	106	0.0211661	0.0772	0.0058	5008	,	,		19596	0.0		0.0	False		,,,				2504	0.0				p.L304L		Atlas-SNP	.											.	CRELD1	48	.	0			c.C912T						PASS	.	C	,,	289,4117	156.6+/-189.7	12,265,1926	45.0	47.0	46.0		912,912,912	-1.4	1.0	3	dbSNP_132	46	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	CRELD1	NM_001031717.3,NM_001077415.2,NM_015513.4	,,	12,268,6223	TT,TC,CC		0.0349,6.5592,2.2451	,,	304/423,304/421,304/421	9984855	292,12714	2203	4300	6503	SO:0001630	splice_region_variant	78987	exon9			GTGTCTCGGTGAG	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.913+1C>T	3.37:g.9984855C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	102	43	0.421569	NM_001077415	A8MX90|B2RAA9|Q6I9X5|Q8NFT4|Q9Y409	Silent	SNP	ENST00000383811.3	37	CCDS2593.1																																																																																			C|0.975;T|0.025	0.025	strong		0.612	CRELD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250533.1	NM_015513	Silent
ZSCAN25	221785	hgsc.bcm.edu	37	7	99227172	99227172	+	Silent	SNP	A	A	G	rs1859690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99227172A>G	ENST00000394152.2	+	8	1491	c.1164A>G	c.(1162-1164)gaA>gaG	p.E388E	ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000262941.6_Silent_p.E316E|ZSCAN25_ENST00000334715.3_Silent_p.E388E	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	388					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)										CCCTGAGAGAATACCTGATGA	0.557													G|||	1736	0.346645	0.6899	0.1902	5008	,	,		19138	0.3046		0.0547	False		,,,				2504	0.3374				p.E388E		Atlas-SNP	.											.	.	.	.	0			c.A1164G						PASS	.	G		2507,1899	544.9+/-376.7	712,1083,408	78.0	75.0	76.0		1164	2.1	0.9	7	dbSNP_92	76	597,8003	793.0+/-407.5	26,545,3729	yes	coding-synonymous	ZNF498	NM_145115.2		738,1628,4137	GG,GA,AA		6.9419,43.1003,23.8659		388/545	99227172	3104,9902	2203	4300	6503	SO:0001819	synonymous_variant	221785	exon8			GAGAGAATACCTG	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"""-"", ""Zinc fingers, C2H2-type"""	21961	protein-coding gene	gene with protein product			"""zinc finger protein 498"""	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.1164A>G	7.37:g.99227172A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Silent	SNP	ENST00000394152.2	37	CCDS5671.2																																																																																			A|0.737;G|0.263	0.263	strong		0.557	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115	
ANKRD36B	57730	hgsc.bcm.edu	37	2	98197010	98197010	+	RNA	SNP	G	G	A	rs2922614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98197010G>A	ENST00000443455.1	-	0	650							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		CTCACAGCAAGTAACAGTGGC	0.303													.|||	57	0.0113818	0.0401	0.0043	5008	,	,		20283	0.001		0.0	False		,,,				2504	0.0				p.L158F		Atlas-SNP	.											.	.	.	.	0			c.C472T						PASS	.	G	PHE/LEU	51,1333		1,49,642	161.0	125.0	136.0		472	-0.4	0.0	2	dbSNP_101	136	0,3182		0,0,1591	no	missense	ANKRD36B	NM_025190.3	22	1,49,2233	AA,AG,GG		0.0,3.685,1.117	benign	158/1354	98197010	51,4515	692	1591	2283			57730	exon4			CAGCAAGTAACAG	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98197010G>A		Somatic	533	0	0		WXS	Illumina HiSeq	Phase_I	517	223	0.431335	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				G|0.984;A|0.016	0.016	strong		0.303	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
ARVCF	421	hgsc.bcm.edu	37	22	19968971	19968971	+	Missense_Mutation	SNP	G	G	A	rs2073748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19968971G>A	ENST00000263207.3	-	5	950	c.659C>T	c.(658-660)cCa>cTa	p.P220L	ARVCF_ENST00000401994.1_Missense_Mutation_p.P157L|ARVCF_ENST00000344269.3_Missense_Mutation_p.P157L|ARVCF_ENST00000406259.1_Missense_Mutation_p.P220L|ARVCF_ENST00000406522.1_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	9	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	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	
OTUD1	220213	hgsc.bcm.edu	37	10	23729361	23729361	+	Silent	SNP	C	C	G	rs141182498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:23729361C>G	ENST00000376495.3	+	1	1164	c.975C>G	c.(973-975)gtC>gtG	p.V325V		NM_001145373.2	NP_001138845.1	Q5VV17	OTUD1_HUMAN	OTU deubiquitinase 1	325	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				protein K63-linked deubiquitination (GO:0070536)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)	5						ACCGAGCTGTCAGCAAGACGG	0.572													C|||	37	0.00738818	0.0008	0.0216	5008	,	,		18005	0.0		0.0179	False		,,,				2504	0.0031				p.V325V		Atlas-SNP	.											.	OTUD1	9	.	0			c.C975G						PASS	.						44.0	48.0	47.0					10																	23729361		692	1591	2283	SO:0001819	synonymous_variant	220213	exon1			AGCTGTCAGCAAG	AK096389	CCDS44366.1	10p12.31	2014-02-24	2014-02-24		ENSG00000165312	ENSG00000165312		"""OTU domain containing"""	27346	protein-coding gene	gene with protein product		612022	"""OTU domain containing 1"""	OTDC1		23827681	Standard	NM_001145373		Approved	DUBA7	uc001irr.2	Q5VV17	OTTHUMG00000017819	ENST00000376495.3:c.975C>G	10.37:g.23729361C>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_001145373		Silent	SNP	ENST00000376495.3	37	CCDS44366.1																																																																																			C|0.989;G|0.011	0.011	strong		0.572	OTUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047215.1	XM_166659	
EPM2AIP1	9852	hgsc.bcm.edu	37	3	37033348	37033348	+	Silent	SNP	A	A	G	rs200289425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37033348A>G	ENST00000322716.5	-	1	1447	c.1221T>C	c.(1219-1221)gcT>gcC	p.A407A	MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000539477.1_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	407					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						GGTCAAAGGCAGCAGCAGCAA	0.383													A|||	4	0.000798722	0.003	0.0	5008	,	,		19336	0.0		0.0	False		,,,				2504	0.0				p.A407A		Atlas-SNP	.											.	EPM2AIP1	47	.	0			c.T1221C						PASS	.	A		4,3784		0,4,1890	93.0	95.0	95.0		1221	-2.3	1.0	3		95	0,8210		0,0,4105	no	coding-synonymous	EPM2AIP1	NM_014805.3		0,4,5995	GG,GA,AA		0.0,0.1056,0.0333		407/608	37033348	4,11994	1894	4105	5999	SO:0001819	synonymous_variant	9852	exon1			AAAGGCAGCAGCA	AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.1221T>C	3.37:g.37033348A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_014805	O94866|Q9H3L3	Silent	SNP	ENST00000322716.5	37	CCDS46790.1																																																																																			A|0.999;G|0.001	0.001	strong		0.383	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805	
KLHDC7B	113730	hgsc.bcm.edu	37	22	50988193	50988193	+	Missense_Mutation	SNP	A	A	G	rs131779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50988193A>G	ENST00000395676.2	+	1	1732	c.1598A>G	c.(1597-1599)cAc>cGc	p.H533R	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	533										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)		GCCCCACTGCACTGCACCACC	0.692													G|||	2906	0.580272	0.5681	0.5288	5008	,	,		11564	0.5942		0.6421	False		,,,				2504	0.5552				p.H533R		Atlas-SNP	.											KLHDC7B,NS,carcinoma,0,1	KLHDC7B	39	1	0			c.A1598G						PASS	.	G	ARG/HIS	2536,1834		770,996,419	10.0	12.0	11.0		1598	3.3	0.3	22	dbSNP_78	11	5522,3022		1823,1876,573	yes	missense	KLHDC7B	NM_138433.3	29	2593,2872,992	GG,GA,AA		35.3699,41.968,37.6026	benign	533/595	50988193	8058,4856	2185	4272	6457	SO:0001583	missense	113730	exon1			CACTGCACTGCAC	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.1598A>G	22.37:g.50988193A>G	ENSP00000379034:p.His533Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_138433		Missense_Mutation	SNP	ENST00000395676.2	37	CCDS14097.2	1292	0.5915750915750916	279	0.5670731707317073	192	0.5303867403314917	338	0.5909090909090909	483	0.637203166226913	G	0.009	-1.806562	0.00606	0.58032	0.646301	ENSG00000130487	ENST00000395676	T	0.12879	2.64	5.45	3.31	0.37934	Kelch-type beta propeller (1);	0.341271	0.21124	N	0.079762	T	0.00012	0.0000	N	0.01482	-0.84	0.36922	P	0.10854399999999997	B	0.02656	0.0	B	0.04013	0.001	T	0.19679	-1.0298	9	0.21014	T	0.42	.	8.3074	0.32051	0.2773:0.0:0.7227:0.0	rs131779;rs3747274;rs57664384;rs131779	533	Q96G42	KLD7B_HUMAN	R	533	ENSP00000379034:H533R	ENSP00000379034:H533R	H	+	2	0	KLHDC7B	49335059	0.998000	0.40836	0.311000	0.25182	0.013000	0.08279	3.906000	0.56340	0.244000	0.21351	-0.320000	0.08662	CAC	A|0.413;G|0.587	0.587	strong		0.692	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433	
OGFR	11054	hgsc.bcm.edu	37	20	61444693	61444693	+	Missense_Mutation	SNP	G	G	A	rs35813009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61444693G>A	ENST00000290291.6	+	7	1751	c.1726G>A	c.(1726-1728)Gag>Aag	p.E576K	OGFR_ENST00000370461.1_Missense_Mutation_p.E524K	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	576	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].			E -> K (in Ref. 1; AAF64406, 2 and 5; BAB15775). {ECO:0000305}.	opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CGAGCCAGCCGAGAGCCCATC	0.751													G|||	1063	0.21226	0.2927	0.2349	5008	,	,		8783	0.1677		0.2555	False		,,,				2504	0.089				p.E576K		Atlas-SNP	.											OGFR,rectum,carcinoma,0,2	OGFR	63	2	0			c.G1726A						scavenged	.						3.0	7.0	6.0					20																	61444693		1480	3390	4870	SO:0001583	missense	11054	exon7			CCAGCCGAGAGCC	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1726G>A	20.37:g.61444693G>A	ENSP00000290291:p.Glu576Lys	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	13	8	0.615385	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	491	0.22481684981684982	137	0.2784552845528455	84	0.23204419889502761	78	0.13636363636363635	192	0.2532981530343008	g	9.066	0.995706	0.19043	.	.	ENSG00000060491	ENST00000290291;ENST00000357163;ENST00000370469;ENST00000370461	T;T	0.52983	0.64;0.64	1.49	-2.99	0.05497	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.27765	0.188;0.188	B;B	0.13407	0.009;0.009	T	0.32295	-0.9912	8	0.18710	T	0.47	.	6.4368	0.21827	0.3151:0.0:0.6849:0.0	rs35813009;rs60843362	576;576	B3KMQ6;Q9NZT2	.;OGFR_HUMAN	K	576;556;411;524	ENSP00000290291:E576K;ENSP00000359491:E524K	ENSP00000290291:E576K	E	+	1	0	OGFR	60915138	0.004000	0.15560	0.000000	0.03702	0.003000	0.03518	1.586000	0.36611	-1.508000	0.01800	-1.863000	0.00559	GAG	G|0.780;A|0.220	0.220	strong		0.751	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
CNTROB	116840	hgsc.bcm.edu	37	17	7849087	7849087	+	Silent	SNP	C	C	G	rs4462665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7849087C>G	ENST00000563694.1	+	13	2701	c.1776C>G	c.(1774-1776)ccC>ccG	p.P592P	CNTROB_ENST00000380262.3_Silent_p.P592P|CNTROB_ENST00000380255.3_Missense_Mutation_p.P538R|CNTROB_ENST00000565740.1_Silent_p.P592P	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	592	Pro-rich.|Required for centrosome localization.				centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				CTCAGGAGCCCGAGAAGGAGG	0.602													G|||	3160	0.63099	0.5424	0.67	5008	,	,		16148	0.8016		0.4493	False		,,,				2504	0.7342				p.P592P		Atlas-SNP	.											CNTROB,colon,carcinoma,0,1	CNTROB	61	1	0			c.C1776G						PASS	.	G	,	2443,1963	552.7+/-378.6	670,1103,430	57.0	59.0	59.0		1776,1776	-5.3	0.0	17	dbSNP_111	59	3953,4647	599.3+/-394.1	915,2123,1262	no	coding-synonymous,coding-synonymous	CNTROB	NM_001037144.5,NM_053051.3	,	1585,3226,1692	GG,GC,CC		45.9651,44.5529,49.1773	,	592/926,592/904	7849087	6396,6610	2203	4300	6503	SO:0001819	synonymous_variant	116840	exon13			GGAGCCCGAGAAG	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.1776C>G	17.37:g.7849087C>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Silent	SNP	ENST00000563694.1	37	CCDS11126.1	1270	0.5815018315018315	277	0.5630081300813008	222	0.6132596685082873	424	0.7412587412587412	347	0.4577836411609499	G	0.238	-1.015843	0.02078	0.554471	0.459651	ENSG00000170037	ENST00000380255	T	0.46451	0.87	5.48	-5.31	0.02730	.	0.553031	0.16472	N	0.212908	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.13980	-1.0489	6	0.27082	T	0.32	0.0029	7.964	0.30087	0.3758:0.2132:0.411:0.0	rs4462665;rs59940402;rs4462665	.	.	.	R	538	ENSP00000369605:P538R	ENSP00000369605:P538R	P	+	2	0	CNTROB	7789812	0.000000	0.05858	0.002000	0.10522	0.109000	0.19521	-1.603000	0.02077	-1.742000	0.01342	-2.784000	0.00117	CCG	C|0.474;G|0.526	0.526	strong		0.602	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	
NET1	10276	hgsc.bcm.edu	37	10	5498102	5498102	+	Missense_Mutation	SNP	C	C	T	rs34658946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5498102C>T	ENST00000355029.4	+	11	1392	c.1250C>T	c.(1249-1251)aCa>aTa	p.T417I	NET1_ENST00000380359.3_Missense_Mutation_p.T363I|NET1_ENST00000542715.1_Missense_Mutation_p.T236I|NET1_ENST00000484741.1_3'UTR	NM_001047160.2	NP_001040625.1	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming 1	417	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		T -> I (in dbSNP:rs34658946).		apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|myoblast migration (GO:0051451)|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 substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|kidney(2)|large_intestine(9)|lung(5)|prostate(2)|skin(1)	23						CGGCCCGTCACACGGAACGAA	0.473													C|||	76	0.0151757	0.056	0.0029	5008	,	,		18225	0.0		0.0	False		,,,				2504	0.0				p.T417I		Atlas-SNP	.											.	NET1	82	.	0			c.C1250T						PASS	.	C	ILE/THR,ILE/THR	177,4229	115.4+/-153.4	4,169,2030	88.0	90.0	89.0		1250,1088	4.7	1.0	10	dbSNP_126	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	NET1	NM_001047160.1,NM_005863.3	89,89	4,170,6329	TT,TC,CC		0.0116,4.0172,1.3686	benign,benign	417/597,363/543	5498102	178,12828	2203	4300	6503	SO:0001583	missense	10276	exon11			CCGTCACACGGAA	AJ010046	CCDS7067.1, CCDS41483.1	10p15	2013-01-10	2008-09-12		ENSG00000173848	ENSG00000173848		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14592	protein-coding gene	gene with protein product		606450				8649828	Standard	NR_073040		Approved	ARHGEF8, NET1A	uc001iia.4	Q7Z628	OTTHUMG00000017596	ENST00000355029.4:c.1250C>T	10.37:g.5498102C>T	ENSP00000347134:p.Thr417Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	55	20	0.363636	NM_001047160	Q12773|Q96D82|Q99903|Q9UEN6	Missense_Mutation	SNP	ENST00000355029.4	37	CCDS41483.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	C	15.93	2.978394	0.53720	0.040172	1.16E-4	ENSG00000173848	ENST00000355029;ENST00000542715;ENST00000380359	T;T;T	0.31510	1.49;1.49;1.49	5.78	4.69	0.59074	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.43110	D	0.000603	T	0.06050	0.0157	L	0.49350	1.555	0.58432	D	0.999994	B;B	0.23490	0.048;0.086	B;B	0.34138	0.153;0.176	T	0.02491	-1.1151	10	0.48119	T	0.1	-20.9971	10.7957	0.46459	0.0:0.8395:0.0:0.1605	rs34658946	363;417	Q5SQI7;Q7Z628	.;ARHG8_HUMAN	I	417;236;363	ENSP00000347134:T417I;ENSP00000446452:T236I;ENSP00000369717:T363I	ENSP00000347134:T417I	T	+	2	0	NET1	5488102	0.967000	0.33354	0.997000	0.53966	0.951000	0.60555	2.640000	0.46579	2.735000	0.93741	0.557000	0.71058	ACA	C|0.984;T|0.016	0.016	strong		0.473	NET1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046553.3	NM_005863	
SYNPO2	171024	hgsc.bcm.edu	37	4	119952589	119952589	+	Missense_Mutation	SNP	G	G	A	rs115012720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:119952589G>A	ENST00000429713.2	+	4	2841	c.2659G>A	c.(2659-2661)Gtg>Atg	p.V887M	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000434046.2_Missense_Mutation_p.V887M|SYNPO2_ENST00000307142.4_Missense_Mutation_p.V887M	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	887						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						GGAGAAGTATGTGGTCGATTC	0.562													G|||	28	0.00559105	0.0212	0.0	5008	,	,		20471	0.0		0.0	False		,,,				2504	0.0				p.V887M		Atlas-SNP	.											.	SYNPO2	353	.	0			c.G2659A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	100,4306	80.4+/-118.8	1,98,2104	126.0	118.0	121.0		2659,2659,2659	5.8	1.0	4	dbSNP_132	121	3,8597	1.2+/-3.3	0,3,4297	yes	missense,missense,missense	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	21,21,21	1,101,6401	AA,AG,GG		0.0349,2.2696,0.7919	probably-damaging,probably-damaging,probably-damaging	887/1094,887/1110,887/1262	119952589	103,12903	2203	4300	6503	SO:0001583	missense	171024	exon4			AAGTATGTGGTCG	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.2659G>A	4.37:g.119952589G>A	ENSP00000395143:p.Val887Met	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	8|8	0.003663003663003663|0.003663003663003663	8|8	0.016260162601626018|0.016260162601626018	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	18.38|18.38	3.611213|3.611213	0.66558|0.66558	0.022696|0.022696	3.49E-4|3.49E-4	ENSG00000172403|ENSG00000172403	ENST00000504178|ENST00000307142;ENST00000429713;ENST00000434046	.|T;T;T	.|0.25085	.|1.82;1.87;1.88	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	.|0.000000	.|0.56097	.|D	.|0.000026	T|T	0.39200|0.39200	0.1069|0.1069	M|M	0.79258|0.79258	2.445|2.445	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.999	.|D;D;D;D	.|0.87578	.|0.998;0.994;0.986;0.99	T|T	0.43972|0.43972	-0.9358|-0.9358	5|9	.|.	.|.	.|.	-20.0199|-20.0199	19.9596|19.9596	0.97236|0.97236	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|887;887;887;887	.|B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6	.|.;.;.;SYNP2_HUMAN	Y|M	838|887	.|ENSP00000306015:V887M;ENSP00000395143:V887M;ENSP00000390965:V887M	.|.	C|V	+|+	2|1	0|0	SYNPO2|SYNPO2	120172037|120172037	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.948000|0.948000	0.59901|0.59901	5.790000|5.790000	0.69038|0.69038	2.726000|2.726000	0.93360|0.93360	0.655000|0.655000	0.94253|0.94253	TGT|GTG	G|0.993;A|0.007	0.007	strong		0.562	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
LUZP1	7798	hgsc.bcm.edu	37	1	23419914	23419914	+	Missense_Mutation	SNP	G	G	A	rs142425004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23419914G>A	ENST00000302291.4	-	4	1642	c.841C>T	c.(841-843)Cgc>Tgc	p.R281C	LUZP1_ENST00000314174.5_Missense_Mutation_p.R281C|LUZP1_ENST00000418342.1_Missense_Mutation_p.R281C|LUZP1_ENST00000374623.3_Missense_Mutation_p.R281C			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	281					artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		TCCTGATTGCGGTTCTTTTCA	0.388													G|||	20	0.00399361	0.0106	0.0014	5008	,	,		20491	0.005		0.0	False		,,,				2504	0.0				p.R281C		Atlas-SNP	.											LUZP1,NS,carcinoma,+1,1	LUZP1	83	1	0			c.C841T						PASS	.	G	CYS/ARG,CYS/ARG	28,4378	35.2+/-66.4	0,28,2175	217.0	203.0	208.0		841,841	4.1	1.0	1	dbSNP_134	208	0,8600		0,0,4300	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	180,180	0,28,6475	AA,AG,GG		0.0,0.6355,0.2153	probably-damaging,probably-damaging	281/1077,281/1077	23419914	28,12978	2203	4300	6503	SO:0001583	missense	7798	exon4			GATTGCGGTTCTT	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.841C>T	1.37:g.23419914G>A	ENSP00000303758:p.Arg281Cys	Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	313	147	0.469649	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	16.53	3.149333	0.57151	0.006355	0.0	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.15372	2.64;2.64;2.64;2.43	6.08	4.13	0.48395	.	0.000000	0.39909	N	0.001226	T	0.08980	0.0222	L	0.42245	1.32	0.42205	D	0.991782	P;P	0.41929	0.765;0.765	B;B	0.28139	0.086;0.086	T	0.08046	-1.0741	10	0.44086	T	0.13	.	13.9909	0.64367	0.0:0.0:0.5289:0.4711	.	281;281	Q86V48-2;Q86V48	.;LUZP1_HUMAN	C	281	ENSP00000393460:R281C;ENSP00000363752:R281C;ENSP00000303758:R281C;ENSP00000313705:R281C	ENSP00000303758:R281C	R	-	1	0	LUZP1	23292501	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.802000	0.38853	1.554000	0.49487	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.388	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631	
C16orf89	146556	hgsc.bcm.edu	37	16	5115811	5115811	+	Silent	SNP	G	G	A	rs35751409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5115811G>A	ENST00000315997.5	-	1	300	c.99C>T	c.(97-99)gcC>gcT	p.A33A	C16orf89_ENST00000350219.4_Silent_p.A71A|C16orf89_ENST00000472572.3_Silent_p.A33A|C16orf89_ENST00000474471.3_Silent_p.A33A|C16orf89_ENST00000422873.1_Silent_p.A71A|ALG1_ENST00000588623.1_Intron	NM_152459.4	NP_689672.4	Q6UX73	CP089_HUMAN	chromosome 16 open reading frame 89	33						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						CTGCAATGGTGGCTTTACTTT	0.602													G|||	35	0.00698882	0.0265	0.0	5008	,	,		19948	0.0		0.0	False		,,,				2504	0.0				p.A33A		Atlas-SNP	.											.	C16orf89	64	.	0			c.C99T						PASS	.	G	,	111,4137		1,109,2014	61.0	66.0	64.0		99,99	-0.5	0.5	16	dbSNP_126	64	0,8502		0,0,4251	no	coding-synonymous,coding-synonymous	C16orf89	NM_001098514.2,NM_152459.4	,	1,109,6265	AA,AG,GG		0.0,2.613,0.8706	,	33/362,33/403	5115811	111,12639	2124	4251	6375	SO:0001819	synonymous_variant	146556	exon1			AATGGTGGCTTTA		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.99C>T	16.37:g.5115811G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	143	61	0.426573	NM_001098514	B4DUM5|Q8N2I3|Q8N4T1	Silent	SNP	ENST00000315997.5	37	CCDS42116.2																																																																																			G|0.990;A|0.010	0.010	strong		0.602	C16orf89-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354524.1	NM_152459	
CDK2AP1	8099	hgsc.bcm.edu	37	12	123749834	123749834	+	Silent	SNP	G	G	A	rs76783415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123749834G>A	ENST00000261692.2	-	3	710	c.189C>T	c.(187-189)taC>taT	p.Y63Y	CDK2AP1_ENST00000542174.1_Silent_p.Y35Y|CDK2AP1_ENST00000538446.1_Silent_p.Y35Y|CDK2AP1_ENST00000535979.1_Silent_p.Y35Y|CDK2AP1_ENST00000544658.1_Silent_p.Y35Y|RP11-282O18.7_ENST00000602352.1_RNA	NM_001270433.1|NM_001270434.1|NM_004642.3	NP_001257362.1|NP_001257363.1|NP_004633.1	O14519	CDKA1_HUMAN	cyclin-dependent kinase 2 associated protein 1	63					cell cycle (GO:0007049)|DNA-dependent DNA replication (GO:0006261)|positive regulation of protein phosphorylation (GO:0001934)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA polymerase binding (GO:0070182)			lung(2)|stomach(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000554)|Epithelial(86;0.00178)		GCAGCTCCGCGTATTTGCTTT	0.582													G|||	152	0.0303514	0.1112	0.0072	5008	,	,		18220	0.0		0.0	False		,,,				2504	0.0				p.Y63Y		Atlas-SNP	.											.	CDK2AP1	8	.	0			c.C189T						PASS	.	G		443,3963	214.1+/-233.5	22,399,1782	137.0	129.0	132.0		189	-7.6	0.1	12	dbSNP_132	132	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	CDK2AP1	NM_004642.2		22,405,6076	AA,AG,GG		0.0698,10.0545,3.4523		63/116	123749834	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	8099	exon3			CTCCGCGTATTTG	AB006077	CCDS9245.1, CCDS58289.1	12q24	2008-11-04	2008-11-04		ENSG00000111328	ENSG00000111328			14002	protein-coding gene	gene with protein product		602198	"""CDK2-associated protein 1"""			9331572, 9506968	Standard	NM_004642		Approved	DORC1, doc-1, DOC1, ST19, p12DOC-1	uc001ueq.4	O14519	OTTHUMG00000168854	ENST00000261692.2:c.189C>T	12.37:g.123749834G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_004642	F5GYA4	Silent	SNP	ENST00000261692.2	37	CCDS9245.1																																																																																			G|0.970;A|0.030	0.030	strong		0.582	CDK2AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401387.1	NM_004642	
C7orf71	285941	hgsc.bcm.edu	37	7	26678856	26678856	+	Silent	SNP	A	A	G	rs57000259	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:26678856A>G	ENST00000409974.3	+	2	809	c.93A>G	c.(91-93)agA>agG	p.R31R		NM_001145531.1	NP_001139003.1	A4D174	CG071_HUMAN	chromosome 7 open reading frame 71	31																	cagagacaagacacatgagga	0.547													G|||	1990	0.397364	0.7526	0.2536	5008	,	,		17132	0.3393		0.2763	False		,,,				2504	0.2035				p.R31R		Atlas-SNP	.											.	C7orf71	6	.	0			c.A93G						PASS	.	G		943,441		314,315,63	69.0	85.0	80.0		93	0.4	0.1	7	dbSNP_129	80	965,2217		150,665,776	no	coding-synonymous	C7orf71	NM_001145531.1		464,980,839	GG,GA,AA		30.3268,31.8642,41.7871		31/170	26678856	1908,2658	692	1591	2283	SO:0001819	synonymous_variant	285941	exon2			GACAAGACACATG		CCDS47565.1	7p15.2	2009-09-11			ENSG00000222004	ENSG00000222004			22364	protein-coding gene	gene with protein product							Standard	NM_001145531		Approved		uc003syb.3	A4D174	OTTHUMG00000152860	ENST00000409974.3:c.93A>G	7.37:g.26678856A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_001145531		Silent	SNP	ENST00000409974.3	37	CCDS47565.1																																																																																			A|0.601;G|0.399	0.399	strong		0.547	C7orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328272.1	NM_001145531	
GPR97	222487	hgsc.bcm.edu	37	16	57722328	57722328	+	Silent	SNP	C	C	T	rs12444859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57722328C>T	ENST00000333493.4	+	12	1766	c.1605C>T	c.(1603-1605)tcC>tcT	p.S535S	GPR97_ENST00000327655.6_Intron|GPR97_ENST00000450388.3_Silent_p.S415S|RP11-405F3.4_ENST00000563062.1_RNA	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	535					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CAGTCTCCTCCTCTACTGCAA	0.557													c|||	1740	0.347444	0.441	0.3127	5008	,	,		20043	0.3274		0.3221	False		,,,				2504	0.2924				p.S535S		Atlas-SNP	.											.	GPR97	74	.	0			c.C1605T						PASS	.	C		1895,2501	544.0+/-376.4	427,1041,730	182.0	162.0	169.0		1605	-7.1	0.0	16	dbSNP_120	169	2658,5942	428.2+/-355.8	412,1834,2054	no	coding-synonymous	GPR97	NM_170776.4		839,2875,2784	TT,TC,CC		30.907,43.1074,35.0339		535/550	57722328	4553,8443	2198	4300	6498	SO:0001819	synonymous_variant	222487	exon12			CTCCTCCTCTACT	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.1605C>T	16.37:g.57722328C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	136	65	0.477941	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Silent	SNP	ENST00000333493.4	37	CCDS10786.1																																																																																			C|0.646;T|0.354	0.354	strong		0.557	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
TATDN2	9797	hgsc.bcm.edu	37	3	10311939	10311939	+	Missense_Mutation	SNP	C	C	T	rs2075352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	67	0	0		WXS	Illumina HiSeq	Phase_I	120	71	0.591667	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	
CBY1	25776	hgsc.bcm.edu	37	22	39069181	39069181	+	Silent	SNP	T	T	C	rs3747174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39069181T>C	ENST00000216029.3	+	5	455	c.321T>C	c.(319-321)gcT>gcC	p.A107A	RP3-508I15.9_ENST00000431924.2_RNA|RP3-508I15.9_ENST00000412067.1_RNA|RP3-508I15.9_ENST00000444381.1_RNA|RP3-508I15.9_ENST00000422408.2_RNA	NM_015373.3	NP_056188.1	Q9Y3M2	CBY1_HUMAN	chibby homolog 1 (Drosophila)	107	Minimal region for the interaction with PKD2.				cardiac muscle cell differentiation (GO:0055007)|cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|protein localization (GO:0008104)	ciliary basal body (GO:0036064)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	beta-catenin binding (GO:0008013)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|ovary(1)	4	Melanoma(58;0.04)					AGTCCACTGCTGAATCCCACT	0.498													C|||	1431	0.285743	0.2897	0.2032	5008	,	,		20300	0.3502		0.2932	False		,,,				2504	0.2648				p.A150A		Atlas-SNP	.											.	CBY1	10	.	0			c.T450C						PASS	.	C	,	1279,3127	700.4+/-406.6	186,907,1110	71.0	65.0	67.0		321,321	-10.1	0.1	22	dbSNP_107	67	2514,6086	693.3+/-404.6	362,1790,2148	no	coding-synonymous,coding-synonymous	CBY1	NM_001002880.1,NM_015373.3	,	548,2697,3258	CC,CT,TT		29.2326,29.0286,29.1635	,	107/127,107/127	39069181	3793,9213	2203	4300	6503	SO:0001819	synonymous_variant	25776	exon6			CACTGCTGAATCC	BK005534	CCDS13974.1, CCDS74861.1	22q12	2014-02-06	2007-01-26	2007-01-26	ENSG00000100211	ENSG00000100211			1307	protein-coding gene	gene with protein product	"""chibby CTNNB1-mediated transcription inhibitor"""	607757	"""chromosome 22 open reading frame 2"", ""PKD2 interactor, golgi and endoplasmic reticulum associated 1"""	C22orf2, PGEA1		10591208, 15194699	Standard	NM_015373		Approved	PIGEA14, PIGEA-14, Chibby, Cby	uc003awb.4	Q9Y3M2	OTTHUMG00000150990	ENST00000216029.3:c.321T>C	22.37:g.39069181T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_001002880	B2R4S2|Q66GT6|Q9UIK9	Silent	SNP	ENST00000216029.3	37	CCDS13974.1																																																																																			T|0.702;C|0.298	0.298	strong		0.498	CBY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320832.1	NM_015373	
HPSE2	60495	hgsc.bcm.edu	37	10	100219374	100219374	+	Missense_Mutation	SNP	T	T	A	rs10883100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:100219374T>A	ENST00000370552.3	-	12	1795	c.1736A>T	c.(1735-1737)tAt>tTt	p.Y579F	HPSE2_ENST00000370549.1_Missense_Mutation_p.Y521F|HPSE2_ENST00000370546.1_3'UTR|HPSE2_ENST00000404542.1_Missense_Mutation_p.Y467F	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						PASS	.	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	108	0	0		WXS	Illumina HiSeq	Phase_I	103	48	0.466019	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	
BSPRY	54836	hgsc.bcm.edu	37	9	116131916	116131916	+	Missense_Mutation	SNP	G	G	A	rs377189582		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116131916G>A	ENST00000374183.4	+	6	742	c.703G>A	c.(703-705)Gat>Aat	p.D235N	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	235	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						CATACGGATCGATGAGAGGAC	0.562																																					p.D235N		Atlas-SNP	.											.	BSPRY	21	.	0			c.G703A						PASS	.						85.0	85.0	85.0					9																	116131916		2012	4204	6216	SO:0001583	missense	54836	exon6			CGGATCGATGAGA	AJ276691	CCDS43868.1	9q33.1	2008-02-05			ENSG00000119411	ENSG00000119411			18232	protein-coding gene	gene with protein product						10978534, 11099500	Standard	NM_017688		Approved	FLJ20150	uc004bhg.4	Q5W0U4	OTTHUMG00000021006	ENST00000374183.4:c.703G>A	9.37:g.116131916G>A	ENSP00000363298:p.Asp235Asn	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	50	0.746269	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Missense_Mutation	SNP	ENST00000374183.4	37	CCDS43868.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868407	0.72065	.	.	ENSG00000119411	ENST00000374183	T	0.61274	0.12	5.6	4.7	0.59300	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.047007	0.85682	D	0.000000	T	0.67951	0.2948	M	0.92317	3.295	0.58432	D	0.999992	P	0.44195	0.828	B	0.41174	0.349	T	0.76429	-0.2962	10	0.59425	D	0.04	-17.9828	13.9619	0.64185	0.0733:0.0:0.9267:0.0	.	235	Q5W0U4	BSPRY_HUMAN	N	235	ENSP00000363298:D235N	ENSP00000363298:D235N	D	+	1	0	BSPRY	115171737	1.000000	0.71417	0.645000	0.29479	0.973000	0.67179	4.224000	0.58593	1.355000	0.45865	0.561000	0.74099	GAT	.	.	alt		0.562	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688	
TNIP2	79155	hgsc.bcm.edu	37	4	2747194	2747194	+	Silent	SNP	C	C	T	rs61734614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2747194C>T	ENST00000315423.7	-	3	722	c.636G>A	c.(634-636)ctG>ctA	p.L212L	TNIP2_ENST00000510267.1_Silent_p.L105L|TNIP2_ENST00000505186.1_5'UTR|TNIP2_ENST00000503235.1_Silent_p.L212L	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TCTGTTTTAACAGTCGATTTT	0.458													C|||	47	0.00938498	0.0008	0.0187	5008	,	,		22935	0.0		0.0288	False		,,,				2504	0.0041				p.L212L		Atlas-SNP	.											.	TNIP2	28	.	0			c.G636A						PASS	.	C	,	18,4388	26.2+/-53.5	0,18,2185	147.0	125.0	132.0		315,636	1.2	0.0	4	dbSNP_129	132	199,8401	86.6+/-149.0	2,195,4103	no	coding-synonymous,coding-synonymous	TNIP2	NM_001161527.1,NM_024309.3	,	2,213,6288	TT,TC,CC		2.314,0.4085,1.6685	,	105/323,212/430	2747194	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	79155	exon3			TTTTAACAGTCGA	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.636G>A	4.37:g.2747194C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	144	77	0.534722	NM_024309		Silent	SNP	ENST00000315423.7	37	CCDS3362.1																																																																																			C|0.984;T|0.016	0.016	strong		0.458	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309	
PKDREJ	10343	hgsc.bcm.edu	37	22	46652737	46652737	+	Silent	SNP	G	G	A	rs6008362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46652737G>A	ENST00000253255.5	-	1	6482	c.6483C>T	c.(6481-6483)tgC>tgT	p.C2161C		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	2161					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)		TGATCAAGACGCAGATCATCA	0.438													G|||	1202	0.240016	0.6604	0.1297	5008	,	,		22415	0.001		0.16	False		,,,				2504	0.0787				p.C2161C		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C6483T						PASS	.	G		2569,1837	635.7+/-396.4	749,1071,383	68.0	65.0	66.0		6483	-2.1	0.2	22	dbSNP_114	66	1256,7344	251.2+/-277.8	88,1080,3132	no	coding-synonymous	PKDREJ	NM_006071.1		837,2151,3515	AA,AG,GG		14.6047,41.6931,29.4095		2161/2254	46652737	3825,9181	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			CAAGACGCAGATC	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.6483C>T	22.37:g.46652737G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	121	67	0.553719	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			G|0.737;A|0.263	0.263	strong		0.438	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
TRIT1	54802	hgsc.bcm.edu	37	1	40349131	40349131	+	Silent	SNP	G	G	A	rs3845570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:40349131G>A	ENST00000316891.5	-	1	47	c.33C>T	c.(31-33)ccC>ccT	p.P11P	TRIT1_ENST00000541099.1_5'Flank|TRIT1_ENST00000545233.1_5'Flank|TRIT1_ENST00000491865.1_5'UTR|Y_RNA_ENST00000365352.1_RNA|TRIT1_ENST00000372818.1_Silent_p.P11P|TRIT1_ENST00000537440.1_5'Flank|TRIT1_ENST00000537223.1_5'Flank|TRIT1_ENST00000544981.1_Silent_p.P11P|TRIT1_ENST00000441669.2_Silent_p.P11P	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	11					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)			breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-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;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CACTGCCCACGGGAACTGCTC	0.662													A|||	2547	0.508586	0.6157	0.4107	5008	,	,		13891	0.5933		0.3946	False		,,,				2504	0.4632				p.P11P		Atlas-SNP	.											TRIT1,NS,carcinoma,0,2	TRIT1	40	2	0			c.C33T						PASS	.	A		2498,1908		718,1062,423	22.0	27.0	26.0		33	-1.0	0.0	1	dbSNP_108	26	3379,5219		654,2071,1574	no	coding-synonymous	TRIT1	NM_017646.4		1372,3133,1997	AA,AG,GG		39.2998,43.3046,45.1938		11/468	40349131	5877,7127	2203	4299	6502	SO:0001819	synonymous_variant	54802	exon1			GCCCACGGGAACT	AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	2.5.1.8		20286	protein-coding gene	gene with protein product						11111046, 15870694	Standard	NM_017646		Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.33C>T	1.37:g.40349131G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_017646	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	Silent	SNP	ENST00000316891.5	37	CCDS30681.1																																																																																			G|0.541;A|0.459	0.459	strong		0.662	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025627.2	NM_017646	
UMODL1	89766	hgsc.bcm.edu	37	21	43524188	43524188	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43524188C>T	ENST00000408910.2	+	9	1510	c.1510C>T	c.(1510-1512)Cgc>Tgc	p.R504C	C21orf128_ENST00000329015.2_Intron|UMODL1_ENST00000408989.2_Missense_Mutation_p.R504C|UMODL1_ENST00000400424.2_Missense_Mutation_p.R432C|UMODL1_ENST00000400427.1_Missense_Mutation_p.R432C	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	504	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						GCAGGGGACACGCGTGCAAGG	0.587																																					p.R504C	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C1510T						PASS	.						48.0	50.0	49.0					21																	43524188		2203	4300	6503	SO:0001583	missense	89766	exon9			GGGACACGCGTGC		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.1510C>T	21.37:g.43524188C>T	ENSP00000386147:p.Arg504Cys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	7	0.148936	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	C	8.034	0.762462	0.15914	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	D;T;D;T	0.82167	-1.58;-0.65;-1.58;-0.67	3.67	0.744	0.18353	.	4.413020	0.00541	N	0.000220	D	0.85331	0.5672	L	0.47716	1.5	0.09310	N	0.999994	D;D;P	0.67145	0.98;0.996;0.939	P;P;P	0.59703	0.711;0.862;0.513	T	0.67321	-0.5700	10	0.37606	T	0.19	0.2373	4.6354	0.12521	0.0:0.4456:0.3484:0.206	.	432;504;504	Q5DID0-3;Q5DID0-2;Q5DID0	.;.;UROL1_HUMAN	C	432;432;504;504	ENSP00000383279:R432C;ENSP00000383276:R432C;ENSP00000386126:R504C;ENSP00000386147:R504C	ENSP00000383276:R432C	R	+	1	0	UMODL1	42397257	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.543000	0.06084	0.140000	0.18849	0.655000	0.94253	CGC	.	.	none		0.587	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
TAS2R20	259295	hgsc.bcm.edu	37	12	11150214	11150214	+	Silent	SNP	G	G	A	rs11054142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11150214G>A	ENST00000538986.1	-	1	260	c.261C>T	c.(259-261)gcC>gcT	p.A87A	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	87					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)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						TTACTGCCCAGGCATTAGAAA	0.343													G|||	2118	0.422923	0.0651	0.3847	5008	,	,		19034	0.755		0.3817	False		,,,				2504	0.6339				p.A87A		Atlas-SNP	.											.	TAS2R20	17	.	0			c.C261T						PASS	.	G		431,3969		22,387,1791	57.0	63.0	61.0		261	-0.3	0.0	12	dbSNP_120	61	2982,5612		533,1916,1848	no	coding-synonymous	TAS2R20	NM_176889.2		555,2303,3639	AA,AG,GG		34.6986,9.7955,26.266		87/310	11150214	3413,9581	2200	4297	6497	SO:0001819	synonymous_variant	259295	exon1			TGCCCAGGCATTA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.261C>T	12.37:g.11150214G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	40	0.373832	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Silent	SNP	ENST00000538986.1	37	CCDS8639.1																																																																																			G|0.672;A|0.328	0.328	strong		0.343	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
SNAI1	6615	hgsc.bcm.edu	37	20	48600809	48600809	+	Silent	SNP	G	G	A	rs1063210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48600809G>A	ENST00000244050.2	+	2	592	c.531G>A	c.(529-531)acG>acA	p.T177T		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	177	Required for nuclear localization and interaction with KPNB1, NOTCH1 and PARP1.				cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|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 regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			GAAGCCACACGCTGCCCTGCG	0.612													G|||	1466	0.292732	0.7171	0.232	5008	,	,		19108	0.0913		0.1262	False		,,,				2504	0.1411				p.T177T		Atlas-SNP	.											.	SNAI1	28	.	0			c.G531A						PASS	.	G		2738,1668	643.3+/-397.8	874,990,339	33.0	32.0	32.0		531	-9.0	0.7	20	dbSNP_86	32	1060,7540	218.7+/-257.0	65,930,3305	no	coding-synonymous	SNAI1	NM_005985.3		939,1920,3644	AA,AG,GG		12.3256,37.8575,29.2019		177/265	48600809	3798,9208	2203	4300	6503	SO:0001819	synonymous_variant	6615	exon2			CCACACGCTGCCC	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	11128	protein-coding gene	gene with protein product		604238	"""snail 1 (drosophila homolog), zinc finger protein"", ""snail homolog 1 (Drosophila)"""			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.531G>A	20.37:g.48600809G>A		Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_005985	B2R842|Q9P113|Q9UBP7|Q9UHH7	Silent	SNP	ENST00000244050.2	37	CCDS13423.1																																																																																			G|0.726;A|0.274	0.274	strong		0.612	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1		
SYNE3	161176	hgsc.bcm.edu	37	14	95921722	95921722	+	Missense_Mutation	SNP	G	G	A	rs74079986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95921722G>A	ENST00000334258.5	-	5	1143	c.1129C>T	c.(1129-1131)Cgc>Tgc	p.R377C	SYNE3_ENST00000554873.1_Missense_Mutation_p.R134C|SYNE3_ENST00000557275.1_Missense_Mutation_p.R377C|SYNE3_ENST00000553340.1_Missense_Mutation_p.R377C	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	377					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						ACCGAGTAGCGTCTCCAGTGT	0.647													G|||	60	0.0119808	0.0439	0.0029	5008	,	,		17289	0.0		0.0	False		,,,				2504	0.0				p.R377C		Atlas-SNP	.											.	SYNE3	130	.	0			c.C1129T						PASS	.	G	CYS/ARG	174,4232	108.6+/-147.0	5,164,2034	29.0	32.0	31.0		1129	3.0	0.5	14	dbSNP_130	31	1,8597	1.2+/-3.3	0,1,4298	yes	missense	C14orf49	NM_152592.3	180	5,165,6332	AA,AG,GG		0.0116,3.9492,1.3457	possibly-damaging	377/976	95921722	175,12829	2203	4299	6502	SO:0001583	missense	161176	exon5			AGTAGCGTCTCCA	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.1129C>T	14.37:g.95921722G>A	ENSP00000334308:p.Arg377Cys	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	G	13.55	2.271639	0.40194	0.039492	1.16E-4	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.37058	3.5;1.22;3.49;2.9	4.99	2.96	0.34315	.	1.317840	0.05603	N	0.576684	T	0.09730	0.0239	N	0.22421	0.69	0.25690	N	0.985697	D;D;D	0.64830	0.994;0.994;0.989	P;P;B	0.50617	0.646;0.646;0.443	T	0.12502	-1.0545	10	0.66056	D	0.02	-0.0728	5.3201	0.15876	0.1091:0.0:0.5537:0.3371	.	377;377;377	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	C	377;134;377;377	ENSP00000334308:R377C;ENSP00000452154:R134C;ENSP00000450562:R377C;ENSP00000450774:R377C	ENSP00000334308:R377C	R	-	1	0	C14orf49	94991475	0.999000	0.42202	0.468000	0.27192	0.258000	0.26162	3.690000	0.54713	1.110000	0.41699	0.455000	0.32223	CGC	G|0.988;A|0.012	0.012	strong		0.647	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416010	105416010	+	Silent	SNP	T	T	C	rs2582511	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416010T>C	ENST00000333244.5	-	7	5897	c.5778A>G	c.(5776-5778)acA>acG	p.T1926T	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1926						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)			CCTTAACATCTGTCTGGGGGC	0.622													.|||	2922	0.583466	0.7057	0.4755	5008	,	,		16374	0.3998		0.6014	False		,,,				2504	0.6656				p.T1926T		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-1,1	AHNAK2	719	1	0			c.A5778G						PASS	.	C		2698,1050		1055,588,231	126.0	138.0	134.0		5778	-2.6	0.0	14	dbSNP_100	134	4926,3192		1693,1540,826	no	coding-synonymous	AHNAK2	NM_138420.2		2748,2128,1057	CC,CT,TT		39.32,28.0149,35.7492		1926/5796	105416010	7624,4242	1874	4059	5933	SO:0001819	synonymous_variant	113146	exon7			AACATCTGTCTGG	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.5778A>G	14.37:g.105416010T>C		Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	267	266	0.996255	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			T|0.428;C|0.572	0.572	strong		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
DSC1	1823	hgsc.bcm.edu	37	18	28712639	28712639	+	Silent	SNP	T	T	C	rs16961338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28712639T>C	ENST00000257198.5	-	14	2391	c.2130A>G	c.(2128-2130)acA>acG	p.T710T	RP11-408H20.2_ENST00000581836.1_RNA|DSC1_ENST00000257197.3_Silent_p.T710T|RP11-408H20.3_ENST00000582307.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	710					homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CACAGAAACATGTAAACAGAA	0.318													T|||	149	0.0297524	0.1097	0.0058	5008	,	,		17598	0.0		0.0	False		,,,				2504	0.0				p.T710T		Atlas-SNP	.											.	DSC1	240	.	0			c.A2130G						PASS	.	T	,	391,4013	195.7+/-220.2	15,361,1826	76.0	72.0	73.0		2130,2130	-3.4	1.0	18	dbSNP_123	73	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	15,363,6124	CC,CT,TT		0.0233,8.8783,3.0221	,	710/841,710/895	28712639	393,12611	2202	4300	6502	SO:0001819	synonymous_variant	1823	exon14			GAAACATGTAAAC	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.2130A>G	18.37:g.28712639T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			T|0.959;C|0.041	0.041	strong		0.318	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
CEP89	84902	hgsc.bcm.edu	37	19	33457328	33457328	+	Silent	SNP	C	C	T	rs150504912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33457328C>T	ENST00000305768.5	-	2	172	c.84G>A	c.(82-84)ccG>ccA	p.P28P	CEP89_ENST00000591863.1_5'Flank|CEP89_ENST00000590597.2_Silent_p.P28P	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	28					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CAGCTGCCTTCGGAGCAACGC	0.557													c|||	2	0.000399361	0.0008	0.0	5008	,	,		20181	0.001		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											CEP89,caecum,carcinoma,0,1	CEP89	82	1	0			c.G84A						scavenged	.	C		3,4403	6.2+/-15.9	0,3,2200	98.0	78.0	85.0		84	-7.9	1.0	19	dbSNP_134	85	0,8600		0,0,4300	no	coding-synonymous	CEP89	NM_032816.3		0,3,6500	TT,TC,CC		0.0,0.0681,0.0231		28/784	33457328	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	84902	exon2			TGCCTTCGGAGCA	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.84G>A	19.37:g.33457328C>T		Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	94	50	0.531915	NM_032816	B9EGA6|Q8N5J8	Silent	SNP	ENST00000305768.5	37	CCDS32987.1																																																																																			C|1.000;T|0.000	0.000	weak		0.557	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
KIAA1456	57604	hgsc.bcm.edu	37	8	12878755	12878755	+	Silent	SNP	C	C	T	rs61736893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:12878755C>T	ENST00000524591.2	+	5	1056	c.567C>T	c.(565-567)ccC>ccT	p.P189P	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	189							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						GAGGCCATCCCTACCATCCTC	0.522													C|||	193	0.0385383	0.1415	0.0058	5008	,	,		18661	0.001		0.001	False		,,,				2504	0.0				p.P189P		Atlas-SNP	.											.	KIAA1456	20	.	0			c.C567T						PASS	.	C	,	493,3461		23,447,1507	117.0	111.0	113.0		189,567	-0.9	0.0	8	dbSNP_129	113	6,8282		0,6,4138	no	coding-synonymous,coding-synonymous	KIAA1456	NM_001099677.1,NM_020844.2	,	23,453,5645	TT,TC,CC		0.0724,12.4684,4.0761	,	63/329,189/455	12878755	499,11743	1977	4144	6121	SO:0001819	synonymous_variant	57604	exon5			CCATCCCTACCAT	BC035082	CCDS47808.1	8p22	2013-10-04	2011-02-23	2011-02-23	ENSG00000250305	ENSG00000250305			26725	protein-coding gene	gene with protein product		615666	"""chromosome 8 open reading frame 79"""	C8orf79		23381944	Standard	NM_020844		Approved	FLJ36980	uc010lsq.3	Q8N9K7	OTTHUMG00000165477	ENST00000524591.2:c.567C>T	8.37:g.12878755C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	94	37	0.393617	NM_020844	Q96AW6	Silent	SNP	ENST00000524591.2	37	CCDS47808.1																																																																																			C|0.978;T|0.022	0.022	strong		0.522	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677	
MUC4	4585	hgsc.bcm.edu	37	3	195512768	195512768	+	Missense_Mutation	SNP	T	T	A	rs2688553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512768T>A	ENST00000463781.3	-	2	6142	c.5683A>T	c.(5683-5685)Aac>Tac	p.N1895Y	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.N1895Y	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		GATGCTGAGTTAGTGTCGGTG	0.572																																					p.N1895Y		Atlas-SNP	.											.	MUC4	1505	.	0			c.A5683T						PASS	.						30.0	30.0	30.0					3																	195512768		682	1590	2272	SO:0001583	missense	4585	exon2			CTGAGTTAGTGTC	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.5683A>T	3.37:g.195512768T>A	ENSP00000417498:p.Asn1895Tyr	Somatic	370	1	0.0027027		WXS	Illumina HiSeq	Phase_I	287	177	0.616725	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	.	.	.	.	.	.	.	.	.	.	-	6.116	0.389611	0.11581	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.39787	1.06;1.27	0.423	0.423	0.16463	.	.	.	.	.	T	0.17874	0.0429	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.27806	-1.0063	7	.	.	.	.	3.7386	0.08521	0.671:0.0:0.0:0.329	.	1895	E7ESK3	.	Y	1895	ENSP00000417498:N1895Y;ENSP00000420243:N1895Y	.	N	-	1	0	MUC4	196997163	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-4.091000	0.00297	-1.671000	0.01466	-2.263000	0.00279	AAC	T|0.934;A|0.066	0.066	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ACOX3	8310	hgsc.bcm.edu	37	4	8390948	8390948	+	Missense_Mutation	SNP	C	C	T	rs13434465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:8390948C>T	ENST00000356406.5	-	13	1566	c.1489G>A	c.(1489-1491)Gac>Aac	p.D497N	ACOX3_ENST00000503233.1_Missense_Mutation_p.D497N|ACOX3_ENST00000413009.2_Missense_Mutation_p.D497N	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	497			D -> N (in dbSNP:rs13434465).		cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						AACTTCTGGTCAAGGATGCCG	0.552													C|||	197	0.0393371	0.0749	0.0259	5008	,	,		19260	0.0		0.0388	False		,,,				2504	0.0419				p.D497N		Atlas-SNP	.											.	ACOX3	70	.	0			c.G1489A						PASS	.	C	ASN/ASP,ASN/ASP	254,4152	146.9+/-181.5	7,240,1956	82.0	77.0	79.0		1489,1489	0.8	0.0	4	dbSNP_121	79	327,8273	113.9+/-173.9	9,309,3982	yes	missense,missense	ACOX3	NM_001101667.1,NM_003501.2	23,23	16,549,5938	TT,TC,CC		3.8023,5.7649,4.4672	benign,benign	497/625,497/701	8390948	581,12425	2203	4300	6503	SO:0001583	missense	8310	exon13			TCTGGTCAAGGAT	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"""acyl-Coenzyme A oxidase 3, pristanoyl"""			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.1489G>A	4.37:g.8390948C>T	ENSP00000348775:p.Asp497Asn	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	47	0.51087	NM_001101667	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	37	CCDS3401.1	86	0.039377289377289376	46	0.09349593495934959	11	0.03038674033149171	0	0.0	29	0.03825857519788918	C	0.658	-0.806939	0.02819	0.057649	0.038023	ENSG00000087008	ENST00000413009;ENST00000356406;ENST00000503233	D;D;D	0.92249	-2.98;-3.0;-3.0	3.49	0.77	0.18497	Acyl-CoA dehydrogenase/oxidase C-terminal (1);	1.100970	0.06825	N	0.792987	T	0.15132	0.0365	N	0.08118	0	0.19775	N	0.99996	B;B;B	0.14438	0.003;0.01;0.003	B;B;B	0.16289	0.007;0.015;0.007	T	0.49688	-0.8913	10	0.14252	T	0.57	-9.2626	3.9431	0.09336	0.1667:0.5265:0.0:0.3068	rs13434465;rs13434465	497;497;497	B2R856;O15254-2;O15254	.;.;ACOX3_HUMAN	N	497	ENSP00000413994:D497N;ENSP00000348775:D497N;ENSP00000421625:D497N	ENSP00000348775:D497N	D	-	1	0	ACOX3	8441848	0.005000	0.15991	0.001000	0.08648	0.035000	0.12851	0.020000	0.13466	-0.069000	0.12931	-0.140000	0.14226	GAC	C|0.954;T|0.046	0.046	strong		0.552	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4		
DCAF12L2	340578	hgsc.bcm.edu	37	X	125298690	125298690	+	Silent	SNP	G	G	A	rs3761552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:125298690G>A	ENST00000360028.2	-	1	1244	c.1218C>T	c.(1216-1218)tgC>tgT	p.C406C	DCAF12L2_ENST00000538699.1_Silent_p.C406C			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	406										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						AGCCTCTGCCGCAGGCAAGCT	0.607													A|||	2113	0.559735	0.6293	0.4294	3775	,	,		13019	0.3859		0.2525	False		,,,				2504	0.3476				p.C406C		Atlas-SNP	.											.	DCAF12L2	157	.	0			c.C1218T						PASS	.	A		2961,874		976,573,436,83,135	86.0	91.0	89.0		1218	1.8	0.9	X	dbSNP_107	89	2000,4728		221,987,571,1220,1301	no	coding-synonymous	DCAF12L2	NM_001013628.2		1197,1560,1007,1303,1436	AA,AG,A,GG,G		29.7265,22.7901,46.9658		406/464	125298690	4961,5602	2203	4300	6503	SO:0001819	synonymous_variant	340578	exon1			TCTGCCGCAGGCA	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"""WD repeat domain containing"""	32950	protein-coding gene	gene with protein product			"""WD repeat domain 40C"""	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.1218C>T	X.37:g.125298690G>A		Somatic	310	1	0.00322581		WXS	Illumina HiSeq	Phase_I	388	387	0.997423	NM_001013628	B2RN42	Silent	SNP	ENST00000360028.2	37	CCDS43991.1																																																																																			G|0.437;A|0.563	0.563	strong		0.607	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628	
DNAH3	55567	hgsc.bcm.edu	37	16	21078693	21078693	+	Silent	SNP	T	T	A	rs861424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:21078693T>A	ENST00000261383.3	-	24	3428	c.3429A>T	c.(3427-3429)gcA>gcT	p.A1143A	DNAH3_ENST00000415178.1_Silent_p.A1143A	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1143	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GAAGCTTCTCTGCCATCCGTG	0.468													G|||	115	0.0229633	0.0817	0.0086	5008	,	,		17763	0.0		0.0	False		,,,				2504	0.001				p.A1143A		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A3429T						PASS	.						85.0	86.0	86.0					16																	21078693		2201	4300	6501	SO:0001819	synonymous_variant	55567	exon24			CTTCTCTGCCATC	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.3429A>T	16.37:g.21078693T>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			G|0.438;T|0.562	.	strong		0.468	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24331328	24331328	+	IGR	SNP	A	A	G	rs150934306		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24331328A>G								AC096509.1 (26534 upstream) : AC004552.1 (35597 downstream)																							TTTCCTGCAGAGTTTTTCCCG	0.418													A|||	233	0.0617219	0.1452	0.0403	3775	,	,		14543	0.001		0.0099	False		,,,				2504	0.002				p.T35T		Atlas-SNP	.											.	.	.	.	0			c.T105C						PASS	.	A		461,2166		36,299,90,724,419	79.0	72.0	74.0		105	-1.7	0.0	X	dbSNP_134	74	115,5383		0,82,33,1834,1633	no	coding-synonymous	FAM48B2	NM_001136233.1		36,381,123,2558,2052	GG,GA,G,AA,A		2.0917,17.5485,7.0892		35/818	24331328	576,7549	1568	3582	5150	SO:0001628	intergenic_variant	170067	exon1			CTGCAGAGTTTTT																													X.37:g.24331328A>G		Somatic	524	2	0.00381679		WXS	Illumina HiSeq	Phase_I	562	221	0.393238	NM_001136233		Silent	SNP		37																																																																																				A|0.947;G|0.053	0.053	strong	0	0.418								
KCNQ2	3785	hgsc.bcm.edu	37	20	62078184	62078184	+	Silent	SNP	G	G	C	rs145415996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62078184G>C	ENST00000359125.2	-	2	477	c.303C>G	c.(301-303)ctC>ctG	p.L101L	KCNQ2_ENST00000359689.1_Silent_p.L101L|KCNQ2_ENST00000357249.2_Silent_p.L101L|RP11-358D14.2_ENST00000436263.1_RNA|KCNQ2_ENST00000360480.3_Silent_p.L101L|KCNQ2_ENST00000344462.4_Silent_p.L101L|KCNQ2_ENST00000354587.3_Silent_p.L101L|KCNQ2_ENST00000344425.5_Silent_p.L101L|KCNQ2_ENST00000370224.1_Silent_p.L101L	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	101					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	AGAAAACCAGGAGGAACCTGG	0.632													G|||	7	0.00139776	0.0053	0.0	5008	,	,		11541	0.0		0.0	False		,,,				2504	0.0				p.L101L		Atlas-SNP	.											.	KCNQ2	201	.	0			c.C303G						PASS	.	G	,,,,	22,4384	29.0+/-57.7	0,22,2181	80.0	75.0	77.0		303,303,303,303,303	0.6	1.0	20	dbSNP_134	77	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNQ2	NM_004518.4,NM_172106.1,NM_172107.2,NM_172108.3,NM_172109.1	,,,,	0,24,6479	CC,CG,GG		0.0233,0.4993,0.1845	,,,,	101/845,101/855,101/873,101/842,101/394	62078184	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	3785	exon2			AACCAGGAGGAAC	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.303C>G	20.37:g.62078184G>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_172106	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	ENST00000359125.2	37	CCDS13520.1																																																																																			G|0.998;C|0.002	0.002	strong		0.632	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	
CHIA	27159	hgsc.bcm.edu	37	1	111854859	111854859	+	Missense_Mutation	SNP	C	C	T	rs61752461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111854859C>T	ENST00000369740.1	+	4	206	c.103C>T	c.(103-105)Cgg>Tgg	p.R35W	CHIA_ENST00000483391.1_Intron|CHIA_ENST00000343320.6_Missense_Mutation_p.R35W|CHIA_ENST00000353665.6_Intron|CHIA_ENST00000451398.2_Intron|CHIA_ENST00000430615.1_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	35					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)		GGCCCAGTACCGGCCAGGCCT	0.582													C|||	58	0.0115815	0.0393	0.0086	5008	,	,		18399	0.0		0.0	False		,,,				2504	0.0				p.R35W		Atlas-SNP	.											CHIA_ENST00000369740,NS,carcinoma,-2,1	CHIA	115	1	0			c.C103T						PASS	.	C	,TRP/ARG	170,4018		2,166,1926	70.0	74.0	73.0		,103	-0.2	0.2	1	dbSNP_129	73	0,8432		0,0,4216	yes	intron,missense	CHIA	NM_021797.2,NM_201653.2	,101	2,166,6142	TT,TC,CC		0.0,4.0592,1.3471	,probably-damaging	,35/477	111854859	170,12450	2094	4216	6310	SO:0001583	missense	27159	exon4			CAGTACCGGCCAG	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.103C>T	1.37:g.111854859C>T	ENSP00000358755:p.Arg35Trp	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	197	92	0.467005	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	26	0.011904761904761904	23	0.046747967479674794	3	0.008287292817679558	0	0.0	0	0.0	C	17.72	3.459828	0.63401	0.040592	0.0	ENSG00000134216	ENST00000369740;ENST00000343320	T;T	0.06933	3.24;3.24	5.08	-0.166	0.13351	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.47852	U	0.000201	T	0.17874	0.0429	H	0.95294	3.65	0.80722	D	1	P	0.47484	0.896	P	0.51453	0.67	T	0.41998	-0.9477	10	0.66056	D	0.02	-8.6166	13.0776	0.59095	0.7282:0.2718:0.0:0.0	rs61752461	35	Q9BZP6	CHIA_HUMAN	W	35	ENSP00000358755:R35W;ENSP00000341828:R35W	ENSP00000341828:R35W	R	+	1	2	CHIA	111656382	0.000000	0.05858	0.241000	0.24154	0.789000	0.44602	-0.273000	0.08548	0.179000	0.19938	0.655000	0.94253	CGG	C|0.988;T|0.012	0.012	strong		0.582	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
MUC4	4585	hgsc.bcm.edu	37	3	195512455	195512455	+	Missense_Mutation	SNP	G	G	T	rs202241172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512455G>T	ENST00000463781.3	-	2	6455	c.5996C>A	c.(5995-5997)aCc>aAc	p.T1999N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1999N	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)		CGGAAGAGGGGTGGCATGACC	0.607													.|||	176	0.0351438	0.0938	0.013	5008	,	,		26657	0.002		0.0159	False		,,,				2504	0.0256				p.T1999N		Atlas-SNP	.											.	MUC4	1505	.	0			c.C5996A						PASS	.	G	,,ASN/THR	144,1222		19,106,558	39.0	40.0	39.0		,,5996		0.0	3	dbSNP_134	39	56,3122		1,54,1534	no	intron,intron,missense	MUC4	NM_004532.5,NM_138297.4,NM_018406.6	,,65	20,160,2092	TT,TG,GG		1.7621,10.5417,4.4014	,,benign	,,1999/5413	195512455	200,4344	683	1589	2272	SO:0001583	missense	4585	exon2			AGAGGGGTGGCAT	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.5996C>A	3.37:g.195512455G>T	ENSP00000417498:p.Thr1999Asn	Somatic	390	0	0		WXS	Illumina HiSeq	Phase_I	209	109	0.521531	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	5.697	0.313136	0.10789	0.105417	0.017621	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37752	1.18;1.27	.	.	.	.	.	.	.	.	T	0.00356	0.0011	N	0.19112	0.55	0.09310	N	0.999997	B	0.22909	0.077	B	0.14023	0.01	T	0.16335	-1.0406	6	.	.	.	.	.	.	.	.	1999	E7ESK3	.	N	1999	ENSP00000417498:T1999N;ENSP00000420243:T1999N	.	T	-	2	0	MUC4	196996850	0.896000	0.30565	0.032000	0.17829	0.076000	0.17211	1.532000	0.36029	0.488000	0.27723	0.064000	0.15345	ACC	G|0.993;T|0.007	0.007	strong		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CCDC151	115948	hgsc.bcm.edu	37	19	11537006	11537006	+	Silent	SNP	G	G	A	rs61739937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11537006G>A	ENST00000356392.4	-	7	1008	c.921C>T	c.(919-921)cgC>cgT	p.R307R	CCDC151_ENST00000545100.1_Silent_p.R253R|CCDC151_ENST00000591179.1_Silent_p.R247R|CCDC151_ENST00000586836.1_Silent_p.R116R	NM_145045.4	NP_659482.3	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	307										endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	12						TCTCCTCGGCGCGCTTCTTGC	0.627													G|||	129	0.0257588	0.09	0.0072	5008	,	,		14915	0.004		0.001	False		,,,				2504	0.0				p.R307R		Atlas-SNP	.											.	CCDC151	44	.	0			c.C921T						PASS	.	G		295,3731		14,267,1732	41.0	43.0	42.0		921	-8.9	0.1	19	dbSNP_129	42	2,8354		0,2,4176	no	coding-synonymous	CCDC151	NM_145045.4		14,269,5908	AA,AG,GG		0.0239,7.3274,2.3986		307/596	11537006	297,12085	2013	4178	6191	SO:0001819	synonymous_variant	115948	exon7			CTCGGCGCGCTTC		CCDS42501.1	19p13.2	2014-02-20				ENSG00000198003			28303	protein-coding gene	gene with protein product		615956				24067530	Standard	NM_145045		Approved	MGC20983	uc002mrs.3	A5D8V7		ENST00000356392.4:c.921C>T	19.37:g.11537006G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_145045	B4DXT0|Q96CG5	Silent	SNP	ENST00000356392.4	37	CCDS42501.1																																																																																			G|0.986;A|0.014	0.014	strong		0.627	CCDC151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458800.1	NM_145045	
NLRP4	147945	hgsc.bcm.edu	37	19	56369668	56369668	+	Silent	SNP	C	C	T	rs112565033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56369668C>T	ENST00000301295.6	+	3	1331	c.909C>T	c.(907-909)aaC>aaT	p.N303N	NLRP4_ENST00000346986.5_Silent_p.N303N|NLRP4_ENST00000587891.1_Silent_p.N228N	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	303	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)		GGGGATTCAACGAGAGTGATA	0.507													C|||	26	0.00519169	0.0189	0.0014	5008	,	,		18203	0.0		0.0	False		,,,				2504	0.0				p.N303N		Atlas-SNP	.											.	NLRP4	331	.	0			c.C909T						PASS	.	C		56,4350	56.2+/-92.4	0,56,2147	73.0	78.0	76.0		909	-8.2	0.0	19	dbSNP_132	76	0,8600		0,0,4300	yes	coding-synonymous	NLRP4	NM_134444.4		0,56,6447	TT,TC,CC		0.0,1.271,0.4306		303/995	56369668	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			ATTCAACGAGAGT	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.909C>T	19.37:g.56369668C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	143	78	0.545455	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.994;T|0.006	0.006	strong		0.507	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
TMEM132D	121256	hgsc.bcm.edu	37	12	129559086	129559086	+	Missense_Mutation	SNP	C	C	A	rs555131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:129559086C>A	ENST00000422113.2	-	9	2960	c.2634G>T	c.(2632-2634)ttG>ttT	p.L878F	TMEM132D_ENST00000389441.4_Missense_Mutation_p.L416F	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	878			L -> F (in dbSNP:rs555131).		negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GGATGGTCTGCAAGTGGCTGT	0.557													C|||	269	0.0537141	0.1672	0.0231	5008	,	,		19621	0.001		0.0278	False		,,,				2504	0.0031				p.L878F		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G2634T						PASS	.	C	PHE/LEU	548,3858	247.2+/-255.5	40,468,1695	86.0	85.0	86.0		2634	-1.8	0.0	12	dbSNP_83	86	255,8345	100.1+/-161.6	1,253,4046	yes	missense	TMEM132D	NM_133448.2	22	41,721,5741	AA,AC,CC		2.9651,12.4376,6.1741	benign	878/1100	129559086	803,12203	2203	4300	6503	SO:0001583	missense	121256	exon9			GGTCTGCAAGTGG	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.2634G>T	12.37:g.129559086C>A	ENSP00000408581:p.Leu878Phe	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	117	0.05357142857142857	87	0.17682926829268292	7	0.019337016574585635	1	0.0017482517482517483	22	0.029023746701846966	C	0.653	-0.808627	0.02819	0.124376	0.029651	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.10382	2.88;3.68	4.2	-1.75	0.08031	.	0.435538	0.18481	N	0.139921	T	0.00012	0.0000	L	0.49455	1.56	0.58432	P	6.999999999979245E-6	B;B	0.14012	0.001;0.009	B;B	0.11329	0.004;0.006	T	0.37753	-0.9692	8	.	.	.	-0.3828	1.8639	0.03194	0.3467:0.3649:0.1333:0.1552	rs555131;rs52800417;rs61225719;rs555131	878;416	Q14C87;Q14C87-2	T132D_HUMAN;.	F	416;878	ENSP00000374092:L416F;ENSP00000408581:L878F	.	L	-	3	2	TMEM132D	128125039	0.000000	0.05858	0.020000	0.16555	0.020000	0.10135	-0.759000	0.04761	-0.287000	0.09064	0.462000	0.41574	TTG	C|0.938;A|0.062	0.062	strong		0.557	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
EDIL3	10085	hgsc.bcm.edu	37	5	83433087	83433087	+	Silent	SNP	G	G	A	rs58219060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:83433087G>A	ENST00000296591.5	-	5	859	c.441C>T	c.(439-441)ggC>ggT	p.G147G	EDIL3_ENST00000380138.3_Silent_p.G137G	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	147	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		CCATAAATTCGCCTGGGCACT	0.393													G|||	159	0.0317492	0.118	0.0029	5008	,	,		16170	0.0		0.001	False		,,,				2504	0.0				p.G147G		Atlas-SNP	.											.	EDIL3	94	.	0			c.C441T						PASS	.	G		465,3941	220.7+/-238.1	23,419,1761	175.0	153.0	160.0		441	-4.0	1.0	5	dbSNP_129	160	4,8596	3.7+/-12.6	0,4,4296	yes	coding-synonymous	EDIL3	NM_005711.3		23,423,6057	AA,AG,GG		0.0465,10.5538,3.606		147/481	83433087	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	10085	exon5			AAATTCGCCTGGG	U70312	CCDS4062.1, CCDS64195.1	5q14	2008-02-05			ENSG00000164176	ENSG00000164176			3173	protein-coding gene	gene with protein product		606018				9420328	Standard	NM_005711		Approved	DEL1	uc003kio.1	O43854	OTTHUMG00000119047	ENST00000296591.5:c.441C>T	5.37:g.83433087G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_005711	B2R763|O43855|Q5D094|Q8N610	Silent	SNP	ENST00000296591.5	37	CCDS4062.1																																																																																			G|0.965;A|0.035	0.035	strong		0.393	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711	
TPMT	7172	hgsc.bcm.edu	37	6	18139214	18139214	+	Silent	SNP	G	G	A	rs2842934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:18139214G>A	ENST00000309983.4	-	6	559	c.474C>T	c.(472-474)atC>atT	p.I158I		NM_000367.2	NP_000358.1	P51580	TPMT_HUMAN	thiopurine S-methyltransferase	158					methylation (GO:0032259)|nucleobase-containing compound metabolic process (GO:0006139)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	thiopurine S-methyltransferase activity (GO:0008119)			large_intestine(2)|lung(1)	3	Ovarian(93;0.016)|Breast(50;0.0245)	all_hematologic(90;0.146)	all cancers(50;0.06)|Epithelial(50;0.0654)		Azathioprine(DB00993)|Bendroflumethiazide(DB00436)|Cefazolin(DB01327)|Mercaptopurine(DB01033)|Olsalazine(DB01250)|Trichlormethiazide(DB01021)	CACCTGGATTGATGGCAACTA	0.313													A|||	3771	0.752995	0.8101	0.7767	5008	,	,		19152	0.7619		0.7763	False		,,,				2504	0.6258				p.I158I	Colon(190;1381 2791 16728 32493)	Atlas-SNP	.											.	TPMT	17	.	0			c.C474T						PASS	.	A		3558,846	332.0+/-302.3	1434,690,78	82.0	83.0	83.0		474	-2.0	0.1	6	dbSNP_100	83	6771,1829	328.9+/-318.5	2670,1431,199	no	coding-synonymous	TPMT	NM_000367.2		4104,2121,277	AA,AG,GG		21.2674,19.2098,20.5706		158/246	18139214	10329,2675	2202	4300	6502	SO:0001819	synonymous_variant	7172	exon6			TGGATTGATGGCA		CCDS4543.1	6p22.3	2014-09-17			ENSG00000137364	ENSG00000137364	2.1.1.67		12014	protein-coding gene	gene with protein product		187680				8316220	Standard	NM_000367		Approved		uc003ncm.3	P51580	OTTHUMG00000014317	ENST00000309983.4:c.474C>T	6.37:g.18139214G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	262	132	0.503817	NM_000367	O14806|O15423|O15424|O15425|O15426|O15515|O15548|O43213|Q5VUK6|Q9UBE6|Q9UBT8|Q9UE62	Silent	SNP	ENST00000309983.4	37	CCDS4543.1																																																																																			G|0.250;A|0.750	0.750	strong		0.313	TPMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039960.1		
XPA	7507	hgsc.bcm.edu	37	9	100449436	100449436	+	Missense_Mutation	SNP	A	A	G	rs143374902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100449436A>G	ENST00000375128.4	-	4	561	c.497T>C	c.(496-498)gTg>gCg	p.V166A		NM_000380.3	NP_000371.1	P23025	XPA_HUMAN	xeroderma pigmentosum, complementation group A	166					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)|nucleotide-excision repair, DNA damage removal (GO:0000718)|response to oxidative stress (GO:0006979)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(4)|large_intestine(1)|lung(4)|prostate(1)	11		Acute lymphoblastic leukemia(62;0.158)				ATTCTTCTTCACAATAAATTT	0.313			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				A|||	10	0.00199681	0.0076	0.0	5008	,	,		15259	0.0		0.0	False		,,,				2504	0.0				p.V166A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (A)	9	9q22.3	7507	"""xeroderma pigmentosum, complementation group A"""		E	.	XPA	21	.	0			c.T497C						PASS	.	A	ALA/VAL	48,4358	48.9+/-83.8	0,48,2155	119.0	126.0	123.0		497	5.4	1.0	9	dbSNP_134	123	0,8596		0,0,4298	yes	missense	XPA	NM_000380.3	64	0,48,6453	GG,GA,AA		0.0,1.0894,0.3692	benign	166/274	100449436	48,12954	2203	4298	6501	SO:0001583	missense	7507	exon4	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TTCTTCACAATAA	D14533	CCDS6729.1	9q22.3	2014-09-17			ENSG00000136936	ENSG00000136936			12814	protein-coding gene	gene with protein product		611153					Standard	NM_000380		Approved	XPAC, XP1	uc004axr.4	P23025	OTTHUMG00000020330	ENST00000375128.4:c.497T>C	9.37:g.100449436A>G	ENSP00000364270:p.Val166Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	71	55	0.774648	NM_000380	Q5T1U9|Q6LCW7|Q6LD02	Missense_Mutation	SNP	ENST00000375128.4	37	CCDS6729.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	15.65	2.896170	0.52121	0.010894	0.0	ENSG00000136936	ENST00000375128	T	0.59224	0.28	5.42	5.42	0.78866	DNA binding domain, putative (1);XPA C- terminal (1);	0.212392	0.44483	D	0.000454	T	0.48624	0.1510	L	0.48362	1.52	0.45852	D	0.998718	B	0.24426	0.103	B	0.36766	0.232	T	0.53063	-0.8491	10	0.40728	T	0.16	.	13.2937	0.60284	1.0:0.0:0.0:0.0	.	166	P23025	XPA_HUMAN	A	166	ENSP00000364270:V166A	ENSP00000364270:V166A	V	-	2	0	XPA	99489257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.905000	0.92613	2.196000	0.70406	0.533000	0.62120	GTG	A|0.996;G|0.004	0.004	strong		0.313	XPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053332.1	NM_000380	
BZRAP1	9256	hgsc.bcm.edu	37	17	56388238	56388238	+	Missense_Mutation	SNP	C	C	G	rs2680704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56388238C>G	ENST00000343736.4	-	19	3581	c.3418G>C	c.(3418-3420)Gca>Cca	p.A1140P	BZRAP1_ENST00000268893.6_Missense_Mutation_p.A1080P|BZRAP1_ENST00000355701.3_Missense_Mutation_p.A1140P			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	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	125	124	0.992	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	
LBP	3929	hgsc.bcm.edu	37	20	37001761	37001761	+	Missense_Mutation	SNP	T	T	C	rs2232618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:37001761T>C	ENST00000217407.2	+	13	1467	c.1306T>C	c.(1306-1308)Ttc>Ctc	p.F436L		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	436			F -> L (in dbSNP:rs2232618). {ECO:0000269|PubMed:2402637, ECO:0000269|PubMed:9240454, ECO:0000269|Ref.5}.		acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				CCTTAACACCTTCTACCCCAA	0.463													C|||	629	0.125599	0.2201	0.0591	5008	,	,		19471	0.0565		0.0726	False		,,,				2504	0.1708				p.F436L		Atlas-SNP	.											.	LBP	60	.	0			c.T1306C						PASS	.	C	LEU/PHE	843,3563	746.2+/-411.7	82,679,1442	112.0	102.0	106.0		1306	-1.0	0.0	20	dbSNP_98	106	774,7826	784.1+/-407.6	25,724,3551	yes	missense	LBP	NM_004139.2	22	107,1403,4993	CC,CT,TT		9.0,19.133,12.4327	benign	436/482	37001761	1617,11389	2203	4300	6503	SO:0001583	missense	3929	exon13			AACACCTTCTACC		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.1306T>C	20.37:g.37001761T>C	ENSP00000217407:p.Phe436Leu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	188	0.08608058608058608	81	0.16463414634146342	26	0.0718232044198895	33	0.057692307692307696	48	0.0633245382585752	C	0.006	-2.060426	0.00386	0.19133	0.09	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.05925	3.37	4.82	-0.996	0.10218	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.415593	0.22646	N	0.057383	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	0.41360	-0.9513	9	0.18276	T	0.48	-12.5231	1.2193	0.01921	0.2711:0.3029:0.2646:0.1614	rs2232618;rs3197421;rs17422694;rs52812841;rs58745877;rs2232618	436	P18428	LBP_HUMAN	L	436	ENSP00000217407:F436L	ENSP00000217407:F436L	F	+	1	0	LBP	36435175	0.002000	0.14202	0.005000	0.12908	0.001000	0.01503	-0.516000	0.06282	-0.466000	0.06943	-1.473000	0.01005	TTC	T|0.884;C|0.116	0.116	strong		0.463	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
CCDC83	220047	hgsc.bcm.edu	37	11	85627108	85627108	+	Silent	SNP	T	T	C	rs7927222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:85627108T>C	ENST00000342404.3	+	10	1128	c.912T>C	c.(910-912)agT>agC	p.S304S	RP11-90K17.2_ENST00000531414.1_RNA|CCDC83_ENST00000280245.4_Silent_p.S335S|CCDC83_ENST00000376067.1_Silent_p.S204S			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	304										breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				AAGTAGAAAGTAGAGACTTGA	0.323													T|||	631	0.125998	0.1399	0.1585	5008	,	,		19840	0.0		0.2604	False		,,,				2504	0.0757				p.S335S		Atlas-SNP	.											.	CCDC83	48	.	0			c.T1005C						PASS	.	T		662,3744	280.8+/-275.6	57,548,1598	113.0	114.0	114.0		1005	-10.3	0.0	11	dbSNP_116	114	2106,6492	363.6+/-333.2	275,1556,2468	no	coding-synonymous	CCDC83	NM_173556.3		332,2104,4066	CC,CT,TT		24.4941,15.025,21.2858		335/445	85627108	2768,10236	2203	4299	6502	SO:0001819	synonymous_variant	220047	exon11			AGAAAGTAGAGAC	AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.912T>C	11.37:g.85627108T>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	172	78	0.453488	NM_173556	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Silent	SNP	ENST00000342404.3	37		320	0.14652014652014653	61	0.12398373983739837	64	0.17679558011049723	0	0.0	195	0.25725593667546176	T	4.888	0.165049	0.09339	0.15025	0.244941	ENSG00000150676	ENST00000526729	.	.	.	5.17	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.15867	-1.0422	3	.	.	.	0.2638	4.5566	0.12140	0.2081:0.4914:0.1158:0.1848	rs7927222;rs17744860;rs57862723;rs7927222	.	.	.	A	209	.	.	V	+	2	0	CCDC83	85304756	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.837000	0.01689	-1.808000	0.01234	-0.468000	0.05107	GTA	T|0.812;C|0.188	0.188	strong		0.323	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556	
LMNTD1	160492	hgsc.bcm.edu	37	12	25672877	25672877	+	Missense_Mutation	SNP	C	C	T	rs34074522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672877C>T	ENST00000282881.6	-	6	1017	c.868G>A	c.(868-870)Gct>Act	p.A290T	IFLTD1_ENST00000458174.2_Missense_Mutation_p.A311T|IFLTD1_ENST00000445693.1_Missense_Mutation_p.A227T|IFLTD1_ENST00000413632.2_Missense_Mutation_p.A271T|IFLTD1_ENST00000539744.1_Missense_Mutation_p.A193T	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		290			A -> T (in dbSNP:rs34074522).		cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GTTATTGTAGCTGTAGATGCT	0.383													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13260	0.0		0.0	False		,,,				2504	0.0				p.A311T		Atlas-SNP	.											IFLTD1_ENST00000458174,NS,carcinoma,+1,2	IFLTD1	121	2	0			c.G931A						PASS	.	T	THR/ALA,THR/ALA,THR/ALA,THR/ALA	251,4155	802.9+/-415.7	5,241,1957	210.0	187.0	195.0		679,931,811,868	-0.6	0.0	12	dbSNP_126	195	1,8599	818.9+/-406.8	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	58,58,58,58	5,242,6256	TT,TC,CC		0.0116,5.6968,1.9376	benign,benign,benign,benign	227/326,311/410,271/370,290/389	25672877	252,12754	2203	4300	6503	SO:0001583	missense	160492	exon7			TTGTAGCTGTAGA																												ENST00000282881.6:c.868G>A	12.37:g.25672877C>T	ENSP00000282881:p.Ala290Thr	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	119	50	0.420168	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	0.198|0.198	-1.047307|-1.047307	0.01981|0.01981	0.056968|0.056968	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000539523;ENST00000545543|ENST00000543629	T;T;T;T;T;T;T|.	0.22336|.	2.67;2.68;2.67;2.66;2.53;1.96;2.54|.	4.68|4.68	-0.618|-0.618	0.11576|0.11576	.|.	.|.	.|.	.|.	.|.	T|T	0.00875|0.00875	0.0029|0.0029	N|N	0.01874|0.01874	-0.695|-0.695	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.0;0.0;0.0|.	T|T	0.30179|0.30179	-0.9987|-0.9987	9|5	0.08599|.	T|.	0.76|.	-1.4413|-1.4413	4.4653|4.4653	0.11685|0.11685	0.1606:0.3771:0.0:0.4623|0.1606:0.3771:0.0:0.4623	rs34074522|rs34074522	227;311;271;290|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	T|N	290;193;311;227;271;7;120|64	ENSP00000282881:A290T;ENSP00000443132:A193T;ENSP00000407353:A311T;ENSP00000407043:A227T;ENSP00000393150:A271T;ENSP00000438160:A7T;ENSP00000443596:A120T|.	ENSP00000282881:A290T|.	A|S	-|-	1|2	0|0	IFLTD1|IFLTD1	25564144|25564144	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-0.752000|-0.752000	0.04797|0.04797	-0.241000|-0.241000	0.09681|0.09681	-1.163000|-1.163000	0.01768|0.01768	GCT|AGC	C|0.980;T|0.020	0.020	strong		0.383	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
OR10G7	390265	hgsc.bcm.edu	37	11	123909637	123909637	+	Silent	SNP	G	G	T	rs4936889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909637G>T	ENST00000330487.5	-	1	80	c.72C>A	c.(70-72)ccC>ccA	p.P24P		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P24P(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		TTCCAAAGAGGGGGGCGTCCA	0.567																																					p.P24P		Atlas-SNP	.											OR10G7,NS,carcinoma,0,1	OR10G7	103	1	1	Substitution - coding silent(1)	stomach(1)	c.C72A						PASS	.						95.0	92.0	93.0					11																	123909637		2200	4299	6499	SO:0001819	synonymous_variant	390265	exon1			AAAGAGGGGGGCG	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.72C>A	11.37:g.123909637G>T		Somatic	412	0	0		WXS	Illumina HiSeq	Phase_I	228	114	0.5	NM_001004463	Q6IFE8	Silent	SNP	ENST00000330487.5	37	CCDS31705.1																																																																																			.	.	weak		0.567	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
OR1N1	138883	hgsc.bcm.edu	37	9	125288893	125288893	+	Missense_Mutation	SNP	C	C	T	rs58226717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125288893C>T	ENST00000304880.2	-	1	679	c.680G>A	c.(679-681)cGa>cAa	p.R227Q		NM_012363.1	NP_036495.1	Q8NGS0	OR1N1_HUMAN	olfactory receptor, family 1, subfamily N, member 1	227			R -> Q (in dbSNP:rs58226717).			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						ACCACGGGTTCGGACCCTCAG	0.537													C|||	483	0.0964457	0.0734	0.0187	5008	,	,		22785	0.2798		0.0149	False		,,,				2504	0.0777				p.R227Q		Atlas-SNP	.											OR1N1,NS,carcinoma,-1,2	OR1N1	38	2	0			c.G680A						PASS	.	C	GLN/ARG	263,4143	149.2+/-183.4	7,249,1947	86.0	73.0	78.0		680	-7.5	0.0	9	dbSNP_129	78	114,8486	60.6+/-122.4	2,110,4188	yes	missense	OR1N1	NM_012363.1	43	9,359,6135	TT,TC,CC		1.3256,5.9691,2.8987	benign	227/312	125288893	377,12629	2203	4300	6503	SO:0001583	missense	138883	exon1			CGGGTTCGGACCC	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.680G>A	9.37:g.125288893C>T	ENSP00000306974:p.Arg227Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	31	0.303922	NM_012363	A3KFM1|O43870|Q6IF16|Q96R93	Missense_Mutation	SNP	ENST00000304880.2	37	CCDS6844.1	241	0.11034798534798534	32	0.06504065040650407	7	0.019337016574585635	193	0.3374125874125874	9	0.011873350923482849	C	11.08	1.533018	0.27387	0.059691	0.013256	ENSG00000171505	ENST00000304880	T	0.37915	1.17	3.75	-7.49	0.01355	GPCR, rhodopsin-like superfamily (1);	0.293204	0.17403	U	0.175464	T	0.00012	0.0000	N	0.17278	0.47	0.80722	P	0.0	B	0.20671	0.047	B	0.10450	0.005	T	0.32587	-0.9901	9	0.72032	D	0.01	.	6.5113	0.22224	0.0849:0.0918:0.4865:0.3368	rs58226717	227	Q8NGS0	OR1N1_HUMAN	Q	227	ENSP00000306974:R227Q	ENSP00000306974:R227Q	R	-	2	0	OR1N1	124328714	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-6.175000	0.00077	-2.251000	0.00700	0.545000	0.68477	CGA	C|0.949;T|0.051	0.051	strong		0.537	OR1N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053938.1		
MUC4	4585	hgsc.bcm.edu	37	3	195514969	195514969	+	Missense_Mutation	SNP	G	G	A	rs192133475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195514969G>A	ENST00000463781.3	-	2	3941	c.3482C>T	c.(3481-3483)gCa>gTa	p.A1161V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1161V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	639	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				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)		ACCTGTGGATGCTGAGGAAGC	0.567																																					p.A1161V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	0			c.C3482T						scavenged	.						5.0	4.0	4.0					3																	195514969		588	1352	1940	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	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.3482C>T	3.37:g.195514969G>A	ENSP00000417498:p.Ala1161Val	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	354	163	0.460452	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	352	0.16117216117216118	205	0.4166666666666667	36	0.09944751381215469	12	0.02097902097902098	99	0.13060686015831136	-	7.142	0.581942	0.13749	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26067	1.77;1.76	0.534	-1.07	0.09968	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.17667	0.023	B	0.08055	0.003	T	0.48937	-0.8990	7	.	.	.	.	4.0801	0.09922	0.5247:0.0:0.4753:0.0	.	1161	E7ESK3	.	V	1161	ENSP00000417498:A1161V;ENSP00000420243:A1161V	.	A	-	2	0	MUC4	196999364	0.005000	0.15991	0.001000	0.08648	0.011000	0.07611	1.044000	0.30329	-0.319000	0.08652	-2.092000	0.00371	GCA	G|0.855;A|0.145	0.145	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
APOBEC4	403314	hgsc.bcm.edu	37	1	183616884	183616884	+	Missense_Mutation	SNP	C	C	T	rs10911390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:183616884C>T	ENST00000308641.4	-	2	1304	c.1033G>A	c.(1033-1035)Gtg>Atg	p.V345M	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)	345			V -> M (in dbSNP:rs10911390).		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						GTGATTTCCACTATCTCCACT	0.413													C|||	473	0.0944489	0.18	0.036	5008	,	,		21617	0.1091		0.0318	False		,,,				2504	0.0695				p.V345M		Atlas-SNP	.											.	APOBEC4	45	.	0			c.G1033A						PASS	.	C	,MET/VAL	668,3738	282.8+/-276.7	46,576,1581	138.0	142.0	141.0		,1033	3.3	0.1	1	dbSNP_120	141	242,8358	96.1+/-157.9	1,240,4059	yes	intron,missense	RGL1,APOBEC4	NM_015149.3,NM_203454.2	,21	47,816,5640	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	2.814,15.1611,6.9968	,possibly-damaging	,345/368	183616884	910,12096	2203	4300	6503	SO:0001583	missense	403314	exon2			TTTCCACTATCTC	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.1033G>A	1.37:g.183616884C>T	ENSP00000310622:p.Val345Met	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	150	68	0.453333	NM_203454	Q8N7F6	Missense_Mutation	SNP	ENST00000308641.4	37	CCDS1358.1	155	0.07097069597069597	73	0.1483739837398374	16	0.04419889502762431	43	0.07517482517482517	23	0.030343007915567283	C	4.474	0.087922	0.08583	0.151611	0.02814	ENSG00000173627	ENST00000308641	T	0.13538	2.58	5.15	3.29	0.37713	.	0.441213	0.17487	N	0.172495	T	0.00073	0.0002	L	0.29908	0.895	0.41539	P	0.01149599999999995	B	0.23591	0.088	B	0.21151	0.033	T	0.15925	-1.0420	9	0.66056	D	0.02	-12.8583	10.5051	0.44828	0.0:0.8391:0.0:0.1609	rs10911390;rs52834070;rs57489946;rs10911390	345	Q8WW27	ABEC4_HUMAN	M	345	ENSP00000310622:V345M	ENSP00000310622:V345M	V	-	1	0	APOBEC4	181883507	0.000000	0.05858	0.087000	0.20705	0.069000	0.16628	0.120000	0.15647	0.575000	0.29434	0.655000	0.94253	GTG	C|0.929;T|0.071	0.071	strong		0.413	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454	
MORN4	118812	hgsc.bcm.edu	37	10	99376152	99376152	+	Silent	SNP	A	A	G	rs3814556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99376152A>G	ENST00000307450.6	-	5	472	c.309T>C	c.(307-309)ccT>ccC	p.P103P	PI4K2A_ENST00000555577.1_Intron|PI4K2A_ENST00000370649.3_Intron|MORN4_ENST00000478953.1_Nonstop_Mutation_p.*67R|MORN4_ENST00000335628.3_Silent_p.P161P	NM_001098831.1|NM_178832.3	NP_001092301.1|NP_849154.1	Q8NDC4	MORN4_HUMAN	MORN repeat containing 4	103								p.P103P(2)		large_intestine(1)|lung(1)|stomach(2)	4						GAGAACCATCAGGGAAAGTCA	0.493													G|||	1675	0.334465	0.6142	0.2608	5008	,	,		21271	0.2837		0.1978	False		,,,				2504	0.2014				p.P103P		Atlas-SNP	.											MORN4_ENST00000307450,NS,carcinoma,0,2	MORN4	24	2	2	Substitution - coding silent(2)	stomach(2)	c.T309C						PASS	.	G	,	2385,2021	560.3+/-380.4	650,1085,468	45.0	44.0	44.0		309,309	-10.1	0.1	10	dbSNP_107	44	1889,6711	724.4+/-406.5	195,1499,2606	no	coding-synonymous,coding-synonymous	MORN4	NM_001098831.1,NM_178832.3	,	845,2584,3074	GG,GA,AA		21.9651,45.8693,32.8618	,	103/147,103/147	99376152	4274,8732	2203	4300	6503	SO:0001819	synonymous_variant	118812	exon5			ACCATCAGGGAAA	AJ431726	CCDS7468.1	10q24.2	2008-06-23	2008-06-23	2008-06-23	ENSG00000171160	ENSG00000171160			24001	protein-coding gene	gene with protein product	"""44050 protein"""		"""chromosome 10 open reading frame 83"""	C10orf83		12477932	Standard	NM_178832		Approved	bA548K23.4, FLJ25925	uc001koe.3	Q8NDC4	OTTHUMG00000018861	ENST00000307450.6:c.309T>C	10.37:g.99376152A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_001098831	Q86Y54	Silent	SNP	ENST00000307450.6	37	CCDS7468.1	697	0.3191391941391941	298	0.6056910569105691	95	0.26243093922651933	161	0.28146853146853146	143	0.18865435356200527	G	1.553	-0.538700	0.04053	0.541307	0.219651	ENSG00000171160	ENST00000478953	.	.	.	5.03	-10.1	0.00402	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999911	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.3015	3.4743	0.07578	0.3815:0.164:0.3555:0.0991	rs3814556;rs17850630;rs60361165;rs3814556	.	.	.	R	67	.	.	X	-	1	0	MORN4	99366142	0.000000	0.05858	0.146000	0.22360	0.884000	0.51177	-2.921000	0.00693	-3.319000	0.00188	-1.163000	0.01768	TGA	A|0.673;G|0.327	0.327	strong		0.493	MORN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049730.1	NM_178832	
PEAK1	79834	hgsc.bcm.edu	37	15	77407516	77407516	+	Missense_Mutation	SNP	G	G	T	rs56079860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:77407516G>T	ENST00000560626.2	-	7	4698	c.4223C>A	c.(4222-4224)cCa>cAa	p.P1408Q	PEAK1_ENST00000312493.4_Missense_Mutation_p.P1408Q			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1408	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> Q (in dbSNP:rs56079860). {ECO:0000269|PubMed:17344846}.		cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										AGGGTCATCTGGATCCTCCCA	0.507													G|||	139	0.0277556	0.0802	0.0043	5008	,	,		21618	0.0238		0.002	False		,,,				2504	0.0041				p.P1408Q		Atlas-SNP	.											.	.	.	.	0			c.C4223A						PASS	.	G	GLN/PRO	259,3599		9,241,1679	106.0	99.0	101.0		4223	4.4	0.9	15	dbSNP_129	101	7,8289		0,7,4141	yes	missense	PEAK1	NM_024776.3	76	9,248,5820	TT,TG,GG		0.0844,6.7133,2.1886	probably-damaging	1408/1747	77407516	266,11888	1929	4148	6077	SO:0001583	missense	0	exon8			TCATCTGGATCCT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.4223C>A	15.37:g.77407516G>T	ENSP00000452796:p.Pro1408Gln	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	171	76	0.444444	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	54	0.024725274725274724	31	0.06300813008130081	1	0.0027624309392265192	21	0.03671328671328671	1	0.0013192612137203166	G	7.667	0.686201	0.14973	0.067133	8.44E-4	ENSG00000173517	ENST00000312493	T	0.69435	-0.4	5.29	4.36	0.52297	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.768243	0.11101	U	0.599654	T	0.06917	0.0176	N	0.22421	0.69	0.33285	D	0.562754	P	0.41265	0.744	B	0.36666	0.23	T	0.47045	-0.9147	10	0.62326	D	0.03	-8.3706	9.7816	0.40651	0.0743:0.0:0.7851:0.1406	rs56079860	1408	Q9H792	PEAK1_HUMAN	Q	1408	ENSP00000309230:P1408Q	ENSP00000309230:P1408Q	P	-	2	0	AC087465.1	75194571	1.000000	0.71417	0.947000	0.38551	0.054000	0.15201	3.778000	0.55371	2.492000	0.84095	0.561000	0.74099	CCA	G|0.984;T|0.016	0.016	strong		0.507	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
DNAH10	196385	hgsc.bcm.edu	37	12	124288212	124288212	+	Silent	SNP	C	C	T	rs80041527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124288212C>T	ENST00000409039.3	+	16	2290	c.2265C>T	c.(2263-2265)atC>atT	p.I755I		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	755	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)		tCAAAGGTATCGGTGACTATA	0.428													T|||	838	0.167332	0.4728	0.0807	5008	,	,		19257	0.0466		0.0408	False		,,,				2504	0.0706				p.I755I		Atlas-SNP	.											.	DNAH10	888	.	0			c.C2265T						PASS	.	T		1830,2572	612.2+/-391.9	400,1030,771	36.0	32.0	33.0		2265	0.7	0.1	12	dbSNP_131	33	379,8219	770.6+/-407.7	5,369,3925	no	coding-synonymous	DNAH10	NM_207437.3		405,1399,4696	TT,TC,CC		4.408,41.572,16.9923		755/4472	124288212	2209,10791	2201	4299	6500	SO:0001819	synonymous_variant	196385	exon16			AGGTATCGGTGAC	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.2265C>T	12.37:g.124288212C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	37	14	0.378378	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.827;T|0.173	0.173	strong		0.428	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
PTCHD3	374308	hgsc.bcm.edu	37	10	27702688	27702688	+	Silent	SNP	C	C	T	rs7087552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	102	101	0.990196	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	
SLC5A2	6524	hgsc.bcm.edu	37	16	31501642	31501642	+	Missense_Mutation	SNP	C	C	T	rs61746400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31501642C>T	ENST00000330498.3	+	14	1824	c.1805C>T	c.(1804-1806)cCg>cTg	p.P602L	C16orf58_ENST00000570164.1_3'UTR|C16orf58_ENST00000567994.1_3'UTR|C16orf58_ENST00000327237.2_3'UTR|AC026471.6_ENST00000565137.1_RNA|SLC5A2_ENST00000564197.1_Intron	NM_003041.3	NP_003032.1	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 2	602					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-affinity glucose:sodium symporter activity (GO:0005362)			endometrium(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	25					Canagliflozin(DB08907)|Dapagliflozin(DB06292)	CCCCAGGCCCCGGCACCAAGC	0.632													c|||	44	0.00878594	0.0325	0.0014	5008	,	,		16541	0.0		0.0	False		,,,				2504	0.0				p.P602L		Atlas-SNP	.											.	SLC5A2	58	.	0			c.C1805T						PASS	.	T	LEU/PRO,	75,4319		2,71,2124	16.0	18.0	18.0		1805,	-0.1	0.0	16	dbSNP_129	18	0,8600		0,0,4300	yes	missense,utr-3	SLC5A2,C16orf58	NM_003041.3,NM_022744.2	98,	2,71,6424	TT,TC,CC		0.0,1.7069,0.5772	benign,	602/673,	31501642	75,12919	2197	4300	6497	SO:0001583	missense	6524	exon14			AGGCCCCGGCACC		CCDS10714.1	16p11.2	2013-05-22			ENSG00000140675	ENSG00000140675		"""Solute carriers"""	11037	protein-coding gene	gene with protein product		182381		SGLT2		8244402	Standard	NM_003041		Approved		uc002ecf.4	P31639	OTTHUMG00000176620	ENST00000330498.3:c.1805C>T	16.37:g.31501642C>T	ENSP00000327943:p.Pro602Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_003041	A2RRD2	Missense_Mutation	SNP	ENST00000330498.3	37	CCDS10714.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	c	3.253	-0.152863	0.06585	0.017069	0.0	ENSG00000140675	ENST00000330498	D	0.91740	-2.9	5.22	-0.0727	0.13738	.	1.172050	0.06093	N	0.663966	T	0.68118	0.2966	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.65903	-0.6055	10	0.49607	T	0.09	.	8.1774	0.31289	0.0:0.5827:0.0:0.4173	rs61746400	602	P31639	SC5A2_HUMAN	L	602	ENSP00000327943:P602L	ENSP00000327943:P602L	P	+	2	0	SLC5A2	31409143	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.493000	0.22451	-0.230000	0.09840	-0.993000	0.02533	CCG	C|0.992;T|0.008	0.008	strong		0.632	SLC5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255627.2		
CCHCR1	54535	hgsc.bcm.edu	37	6	31112737	31112737	+	Missense_Mutation	SNP	C	C	A	rs130079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31112737C>A	ENST00000376266.5	-	14	1845	c.1723G>T	c.(1723-1725)Ggc>Tgc	p.G575C	CCHCR1_ENST00000451521.2_Missense_Mutation_p.G628C|CCHCR1_ENST00000396263.2_Missense_Mutation_p.G522C|CCHCR1_ENST00000396268.3_Missense_Mutation_p.G664C	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	575			G -> C (in allele HCR*WWCC; associated with psoriasis; dbSNP:rs130079). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:10888604, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						TCCTGCTGGCCCTGGCGTGCT	0.652													C|||	710	0.141773	0.1649	0.1383	5008	,	,		17573	0.0377		0.2018	False		,,,				2504	0.1585				p.G664C		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G1990T						PASS	.	C	CYS/GLY,CYS/GLY,CYS/GLY	835,3571	330.4+/-301.5	89,657,1457	59.0	58.0	59.0		1882,1990,1723	1.5	1.0	6	dbSNP_78	59	2031,6569	351.3+/-328.2	247,1537,2516	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	159,159,159	336,2194,3973	AA,AC,CC		23.6163,18.9514,22.036	benign,benign,benign	628/836,664/872,575/783	31112737	2866,10140	2203	4300	6503	SO:0001583	missense	54535	exon14			GCTGGCCCTGGCG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1723G>T	6.37:g.31112737C>A	ENSP00000365442:p.Gly575Cys	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	329	0.15064102564102563	90	0.18292682926829268	51	0.1408839779005525	26	0.045454545454545456	162	0.21372031662269128	C	12.17	1.857747	0.32791	0.189514	0.236163	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521	T;T;T;T	0.10477	2.87;2.87;2.87;2.87	4.79	1.49	0.22878	.	0.872767	0.09696	N	0.767660	T	0.05502	0.0145	M	0.65975	2.015	0.36574	P	0.12684600000000001	B;B;B;B;B	0.25206	0.077;0.01;0.029;0.12;0.099	B;B;B;B;B	0.29663	0.064;0.015;0.041;0.105;0.064	T	0.24297	-1.0164	9	0.51188	T	0.08	-4.183	7.474	0.27365	0.0:0.6716:0.0:0.3284	rs130079;rs1265077;rs16898850;rs17840016;rs52811991;rs57918849;rs130079	575;575;575;628;664	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	C	664;575;522;575;628	ENSP00000379566:G664C;ENSP00000365442:G575C;ENSP00000379561:G522C;ENSP00000401039:G628C	ENSP00000365442:G575C	G	-	1	0	CCHCR1	31220716	1.000000	0.71417	0.998000	0.56505	0.804000	0.45430	1.297000	0.33400	0.446000	0.26666	0.448000	0.29417	GGC	C|0.801;A|0.199	0.199	strong		0.652	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
ILK	3611	hgsc.bcm.edu	37	11	6629665	6629665	+	Silent	SNP	C	C	T	rs1043388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6629665C>T	ENST00000396751.2	+	3	753	c.297C>T	c.(295-297)caC>caT	p.H99H	ILK_ENST00000528995.1_Silent_p.H99H|ILK_ENST00000537806.1_5'UTR|TAF10_ENST00000531760.1_5'Flank|RP11-732A19.2_ENST00000527398.1_RNA|ILK_ENST00000299421.4_Silent_p.H99H|ILK_ENST00000420936.2_Silent_p.H99H	NM_001014795.1	NP_001014795.1	Q13418	ILK_HUMAN	integrin-linked kinase	99	Interaction with LIMS1.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell junction assembly (GO:0034329)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|extracellular fibril organization (GO:0043206)|fibroblast migration (GO:0010761)|integrin-mediated signaling pathway (GO:0007229)|myelin assembly (GO:0032288)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|peptidyl-serine phosphorylation (GO:0018105)|platelet aggregation (GO:0070527)|positive regulation of axon extension (GO:0045773)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)		TGAATGAACACGGGAATGTGC	0.483													T|||	1576	0.314696	0.4153	0.2608	5008	,	,		24191	0.3512		0.2535	False		,,,				2504	0.2423				p.H99H		Atlas-SNP	.											.	ILK	41	.	0			c.C297T						PASS	.	T	,,	1685,2717	654.2+/-399.7	315,1055,831	138.0	118.0	124.0		297,297,297	2.4	1.0	11	dbSNP_86	124	2148,6444	713.9+/-406.0	260,1628,2408	no	coding-synonymous,coding-synonymous,coding-synonymous	ILK	NM_001014794.1,NM_001014795.1,NM_004517.2	,,	575,2683,3239	TT,TC,CC		25.0,38.2781,29.4982	,,	99/453,99/453,99/453	6629665	3833,9161	2201	4296	6497	SO:0001819	synonymous_variant	3611	exon4			TGAACACGGGAAT	U40282	CCDS7768.1, CCDS60712.1, CCDS60713.1	11p15.4	2014-09-17			ENSG00000166333	ENSG00000166333		"""Ankyrin repeat domain containing"""	6040	protein-coding gene	gene with protein product		602366				8538749	Standard	NM_004517		Approved		uc001mef.3	Q13418	OTTHUMG00000133407	ENST00000396751.2:c.297C>T	11.37:g.6629665C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	168	85	0.505952	NM_001014794	B7Z1I0|B7Z418|D3DQU0|P57043|Q68DZ3	Silent	SNP	ENST00000396751.2	37	CCDS7768.1																																																																																			C|0.690;T|0.310	0.310	strong		0.483	ILK-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384519.1	NM_004517	
OR13C5	138799	hgsc.bcm.edu	37	9	107361038	107361038	+	Silent	SNP	C	C	T	rs75872480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361038C>T	ENST00000374779.2	-	1	750	c.657G>A	c.(655-657)acG>acA	p.T219T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AAATGATTAACGTGTAAGAGA	0.428													C|||	14	0.00279553	0.0106	0.0	5008	,	,		22708	0.0		0.0	False		,,,				2504	0.0				p.T219T		Atlas-SNP	.											OR13C5,NS,haematopoietic_neoplasm,-1,1	OR13C5	60	1	0			c.G657A						PASS	.	C		24,4382	30.8+/-60.4	0,24,2179	131.0	124.0	127.0		657	-8.1	0.0	9	dbSNP_131	127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR13C5	NM_001004482.1		0,25,6478	TT,TC,CC		0.0116,0.5447,0.1922		219/319	107361038	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	138799	exon1			GATTAACGTGTAA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.657G>A	9.37:g.107361038C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	212	134	0.632075	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			C|0.998;T|0.002	0.002	strong		0.428	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
EDEM2	55741	hgsc.bcm.edu	37	20	33706509	33706509	+	Silent	SNP	G	G	A	rs3192415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33706509G>A	ENST00000374492.3	-	10	1233	c.1128C>T	c.(1126-1128)agC>agT	p.S376S	SNORD56_ENST00000364281.1_RNA|EDEM2_ENST00000542871.1_Silent_p.S100S|EDEM2_ENST00000374491.3_Silent_p.S339S|EDEM2_ENST00000540582.1_Silent_p.S335S|EDEM2_ENST00000541621.1_Silent_p.S155S	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	376					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			GGTACATTGCGCTTTCAATAA	0.547													G|||	559	0.111621	0.4032	0.0346	5008	,	,		21110	0.0		0.002	False		,,,				2504	0.0				p.S376S	Esophageal Squamous(51;906 1021 24535 36410 39145)	Atlas-SNP	.											.	EDEM2	46	.	0			c.C1128T						PASS	.	G	,	1436,2970	466.6+/-354.6	226,984,993	97.0	93.0	94.0		1017,1128	-7.1	0.6	20	dbSNP_116	94	18,8582	11.2+/-40.8	0,18,4282	no	coding-synonymous,coding-synonymous	EDEM2	NM_001145025.1,NM_018217.2	,	226,1002,5275	AA,AG,GG		0.2093,32.5919,11.1795	,	339/542,376/579	33706509	1454,11552	2203	4300	6503	SO:0001819	synonymous_variant	55741	exon10			CATTGCGCTTTCA	AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"""chromosome 20 open reading frame 31"""	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.1128C>T	20.37:g.33706509G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_018217	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Silent	SNP	ENST00000374492.3	37	CCDS13247.1																																																																																			G|0.886;A|0.114	0.114	strong		0.547	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217	
DCAF4L2	138009	hgsc.bcm.edu	37	8	88886059	88886059	+	Silent	SNP	G	G	A	rs142584363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:88886059G>A	ENST00000319675.3	-	1	237	c.141C>T	c.(139-141)cgC>cgT	p.R47R		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	47										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						CACGCAGCTCGCGAGCTATAC	0.498													G|||	11	0.00219649	0.0083	0.0	5008	,	,		20270	0.0		0.0	False		,,,				2504	0.0				p.R47R		Atlas-SNP	.											DCAF4L2,NS,carcinoma,-1,2	DCAF4L2	187	2	0			c.C141T						scavenged	.	G		32,4374	36.8+/-68.6	0,32,2171	101.0	91.0	94.0		141	-3.8	0.0	8	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	DCAF4L2	NM_152418.3		0,32,6471	AA,AG,GG		0.0,0.7263,0.246		47/396	88886059	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	138009	exon1			CAGCTCGCGAGCT	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"""WD repeat domain containing"""	26657	protein-coding gene	gene with protein product			"""WD repeat domain 21C"""	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.141C>T	8.37:g.88886059G>A		Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	283	3	0.0106007	NM_152418		Silent	SNP	ENST00000319675.3	37	CCDS6245.1																																																																																			G|0.998;A|0.002	0.002	strong		0.498	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418	
CARD17	440068	hgsc.bcm.edu	37	11	104971257	104971257	+	Missense_Mutation	SNP	G	G	A	rs12806837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:104971257G>A	ENST00000375707.1	-	2	273	c.257C>T	c.(256-258)aCg>aTg	p.T86M	CASP1_ENST00000594519.1_Intron|CASP1_ENST00000598974.1_Intron|CASP1_ENST00000415981.2_Intron|CARD16_ENST00000525374.1_Intron|CASP1_ENST00000593315.1_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	200	0	0		WXS	Illumina HiSeq	Phase_I	210	66	0.314286	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	
AGRN	375790	hgsc.bcm.edu	37	1	979748	979748	+	Missense_Mutation	SNP	A	A	T	rs113288277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:979748A>T	ENST00000379370.2	+	12	2233	c.2183A>T	c.(2182-2184)gAg>gTg	p.E728V		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	728	Kazal-like 8. {ECO:0000255|PROSITE- ProRule:PRU00798}.		E -> V (in dbSNP:rs113288277). {ECO:0000269|PubMed:19631309}.		axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		TACAGCACCGAGTGTGAGCTG	0.692													A|||	92	0.0183706	0.0008	0.0159	5008	,	,		14997	0.0079		0.0467	False		,,,				2504	0.0256				p.E728V		Atlas-SNP	.											.	AGRN	110	.	0			c.A2183T						PASS	.	A	VAL/GLU	38,4366	40.0+/-72.8	0,38,2164	40.0	39.0	39.0		2183	4.6	1.0	1	dbSNP_132	39	366,8232	121.1+/-180.3	10,346,3943	yes	missense	AGRN	NM_198576.3	121	10,384,6107	TT,TA,AA		4.2568,0.8629,3.1072	probably-damaging	728/2046	979748	404,12598	2202	4299	6501	SO:0001583	missense	375790	exon12			GCACCGAGTGTGA	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.2183A>T	1.37:g.979748A>T	ENSP00000368678:p.Glu728Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	164	84	0.512195	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	42	0.019230769230769232	1	0.0020325203252032522	7	0.019337016574585635	2	0.0034965034965034965	32	0.04221635883905013	A	15.76	2.929878	0.52759	0.008629	0.042568	ENSG00000188157	ENST00000379370	T	0.04758	3.56	4.58	4.58	0.56647	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.000000	0.64402	D	0.000004	T	0.04952	0.0133	M	0.78637	2.42	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	T	0.00119	-1.2032	10	0.56958	D	0.05	-27.4006	13.9535	0.64133	1.0:0.0:0.0:0.0	.	728	O00468	AGRIN_HUMAN	V	728	ENSP00000368678:E728V	ENSP00000368678:E728V	E	+	2	0	AGRN	969611	1.000000	0.71417	0.964000	0.40570	0.122000	0.20287	5.688000	0.68227	1.686000	0.51046	0.533000	0.62120	GAG	A|0.975;T|0.025	0.025	strong		0.692	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
SSC5D	284297	hgsc.bcm.edu	37	19	56001665	56001665	+	Splice_Site	SNP	C	C	T	rs114976626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56001665C>T	ENST00000389623.6	+	5	499	c.476C>T	c.(475-477)gCc>gTc	p.A159V	SSC5D_ENST00000587166.1_Splice_Site_p.A159V	NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	159					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						CCACTCCCAGCCCCCCGCCCA	0.697													c|||	213	0.0425319	0.1256	0.0187	5008	,	,		9907	0.005		0.0239	False		,,,				2504	0.0051				p.A159V		Atlas-SNP	.											.	SSC5D	65	.	0			c.C476T						PASS	.						14.0	26.0	23.0					19																	56001665		688	1586	2274	SO:0001630	splice_region_variant	284297	exon5			TCCCAGCCCCCCG		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.476-1C>T	19.37:g.56001665C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_001195267	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Missense_Mutation	SNP	ENST00000389623.6	37	CCDS46196.1	85	0.03891941391941392	59	0.11991869918699187	10	0.027624309392265192	1	0.0017482517482517483	15	0.01978891820580475	.	11.12	1.546179	0.27652	.	.	ENSG00000179954	ENST00000389623;ENST00000541230	T	0.01246	5.11	4.14	-0.852	0.10713	.	.	.	.	.	T	0.00039	0.0001	N	0.24115	0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	7	.	.	.	.	6.7603	0.23536	0.0:0.5487:0.2728:0.1785	.	159	A1L4H1	SRCRL_HUMAN	V	159	ENSP00000374274:A159V	.	A	+	2	0	SSC5D	60693477	0.001000	0.12720	0.011000	0.14972	0.006000	0.05464	-0.249000	0.08842	-0.593000	0.05844	-2.185000	0.00314	GCC	C|0.956;T|0.044	0.044	strong		0.697	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	Missense_Mutation
EPHB2	2048	hgsc.bcm.edu	37	1	23222008	23222008	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23222008C>T	ENST00000400191.3	+	8	1653	c.1635C>T	c.(1633-1635)atC>atT	p.I545I	EPHB2_ENST00000374630.3_Silent_p.I545I|EPHB2_ENST00000374632.3_Silent_p.I545I|EPHB2_ENST00000465676.1_3'UTR|EPHB2_ENST00000374627.1_Silent_p.I540I	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	545					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		CACTCATCATCGGCTCCTCGG	0.592																																					p.I545I		Atlas-SNP	.											.	EPHB2	257	.	0			c.C1635T						PASS	.						139.0	120.0	126.0					1																	23222008		2203	4300	6503	SO:0001819	synonymous_variant	2048	exon8			CATCATCGGCTCC	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3393	protein-coding gene	gene with protein product		600997	"""EphB2"""	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1635C>T	1.37:g.23222008C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Silent	SNP	ENST00000400191.3	37																																																																																				.	.	none		0.592	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449	
OSER1	51526	hgsc.bcm.edu	37	20	42826350	42826350	+	Missense_Mutation	SNP	A	A	C	rs9346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42826350A>C	ENST00000372970.2	-	6	401	c.221T>G	c.(220-222)gTg>gGg	p.V74G	OSER1_ENST00000255174.2_Missense_Mutation_p.V74G			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	74			V -> G (in dbSNP:rs9346).		cellular response to hydrogen peroxide (GO:0070301)												CTGAGTTCTCACTGCTCCTCG	0.423													A|||	1771	0.353634	0.5862	0.1354	5008	,	,		22691	0.4196		0.1531	False		,,,				2504	0.3323				p.V74G		Atlas-SNP	.											.	C20orf111	28	.	0			c.T221G						PASS	.	A	GLY/VAL	2235,2171	589.5+/-387.1	574,1087,542	59.0	57.0	58.0		221	1.0	1.0	20	dbSNP_52	58	1215,7385	243.9+/-273.3	80,1055,3165	yes	missense	C20orf111	NM_016470.7	109	654,2142,3707	CC,CA,AA		14.1279,49.2737,26.5262	benign	74/293	42826350	3450,9556	2203	4300	6503	SO:0001583	missense	51526	exon4			GTTCTCACTGCTC	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"""peroxide-inducible transcript 1"", ""oxidative stress-responsive 1"""		"""chromosome 20 open reading frame 111"""	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.221T>G	20.37:g.42826350A>C	ENSP00000362061:p.Val74Gly	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Missense_Mutation	SNP	ENST00000372970.2	37	CCDS13327.1	718	0.32875457875457875	294	0.5975609756097561	58	0.16022099447513813	242	0.4230769230769231	124	0.16358839050131926	A	12.62	1.992149	0.35131	0.507263	0.141279	ENSG00000132823	ENST00000255174;ENST00000372970	T;T	0.54479	0.57;0.57	5.72	1.03	0.20045	.	0.636671	0.16840	N	0.197362	T	0.00012	0.0000	L	0.53249	1.67	0.09310	P	0.9999999260926	B	0.21905	0.062	B	0.30716	0.119	T	0.43845	-0.9366	9	0.66056	D	0.02	-0.5225	9.1613	0.37023	0.7244:0.0:0.2756:0.0	rs9346;rs1049822;rs3171228;rs52815417;rs58950417;rs9346	74	Q9NX31	CT111_HUMAN	G	74	ENSP00000255174:V74G;ENSP00000362061:V74G	ENSP00000255174:V74G	V	-	2	0	C20orf111	42259764	0.533000	0.26354	0.992000	0.48379	0.919000	0.55068	1.618000	0.36954	0.116000	0.18110	0.383000	0.25322	GTG	T|0.004;G|0.002	.	strong		0.423	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470	
MYO7A	4647	hgsc.bcm.edu	37	11	76853783	76853783	+	Missense_Mutation	SNP	T	T	C	rs1052030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:76853783T>C	ENST00000409709.3	+	3	319	c.47T>C	c.(46-48)tTg>tCg	p.L16S	MYO7A_ENST00000458637.2_Missense_Mutation_p.L16S|MYO7A_ENST00000409619.2_Missense_Mutation_p.L5S|MYO7A_ENST00000409893.1_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	142	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	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	
UAP1	6675	hgsc.bcm.edu	37	1	162560209	162560209	+	Silent	SNP	G	G	A	rs61743694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:162560209G>A	ENST00000367925.1	+	7	1298	c.1266G>A	c.(1264-1266)agG>agA	p.R422R	UAP1_ENST00000367924.1_Silent_p.R422R|UAP1_ENST00000271469.3_Silent_p.R422R|RP11-359K18.4_ENST00000609669.1_RNA|UAP1_ENST00000367926.4_Silent_p.R422R			Q16222	UAP1_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1	422					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)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|UDP-N-acetylglucosamine diphosphorylase activity (GO:0003977)			breast(2)|cervix(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)|skin(2)|stomach(1)	22	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			CTACTGCAAGGCATGCTTTGA	0.458													G|||	119	0.023762	0.0877	0.0043	5008	,	,		19084	0.0		0.0	False		,,,				2504	0.0				p.R422R		Atlas-SNP	.											.	UAP1	47	.	0			c.G1266A						PASS	.	G		377,4029	191.2+/-216.9	15,347,1841	174.0	159.0	164.0		1266	1.0	0.6	1	dbSNP_129	164	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	UAP1	NM_003115.4		15,355,6133	AA,AG,GG		0.093,8.5565,2.9602		422/506	162560209	385,12621	2203	4300	6503	SO:0001819	synonymous_variant	6675	exon8			TGCAAGGCATGCT	AB011004	CCDS1240.1	1q23.2	2014-07-31	2014-07-31		ENSG00000117143	ENSG00000117143	2.7.7.23		12457	protein-coding gene	gene with protein product		602862		SPAG2		9603950, 8025165	Standard	NM_003115		Approved	AGX1, AgX	uc001gce.4	Q16222	OTTHUMG00000034419	ENST00000367925.1:c.1266G>A	1.37:g.162560209G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	162	88	0.54321	NM_003115	B2R6R8|Q5VTA9|Q5VTB0|Q5VTB1|Q96GM2	Silent	SNP	ENST00000367925.1	37																																																																																				G|0.969;A|0.031	0.031	strong		0.458	UAP1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000083203.1	NM_003115	
EPPK1	83481	hgsc.bcm.edu	37	8	144940540	144940540	+	Silent	SNP	G	G	A	rs56034452		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144940540G>A	ENST00000525985.1	-	2	6953	c.6882C>T	c.(6880-6882)ggC>ggT	p.G2294G				P58107	EPIPL_HUMAN	epiplakin 1	2294						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)			CCTGGATCTCGCCGCCCACCA	0.706																																					p.G2294G		Atlas-SNP	.											EPPK1,NS,carcinoma,0,3	EPPK1	199	3	0			c.C6882T						scavenged	.						90.0	89.0	90.0					8																	144940540		2176	4252	6428	SO:0001819	synonymous_variant	83481	exon1			GATCTCGCCGCCC	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.6882C>T	8.37:g.144940540G>A		Somatic	42	1	0.0238095		WXS	Illumina HiSeq	Phase_I	47	12	0.255319	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.500;A|0.500	0.500	weak		0.706	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
CHAF1B	8208	hgsc.bcm.edu	37	21	37787615	37787615	+	Missense_Mutation	SNP	A	A	C	rs74900401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:37787615A>C	ENST00000314103.5	+	13	1667	c.1516A>C	c.(1516-1518)Aag>Cag	p.K506Q		NM_005441.2	NP_005432.1	Q13112	CAF1B_HUMAN	chromatin assembly factor 1, subunit B (p60)	506			K -> Q (in dbSNP:rs2230638).		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						AACACCCTTAAAGACGGACAC	0.358													A|||	94	0.01877	0.0666	0.0086	5008	,	,		18323	0.0		0.0	False		,,,				2504	0.0				p.K506Q		Atlas-SNP	.											.	CHAF1B	47	.	0			c.A1516C						PASS	.	A	GLN/LYS	231,4175	137.7+/-173.5	11,209,1983	94.0	93.0	94.0		1516	5.3	1.0	21	dbSNP_131	94	3,8597	2.2+/-6.3	0,3,4297	no	missense	CHAF1B	NM_005441.2	53	11,212,6280	CC,CA,AA		0.0349,5.2429,1.7992	benign	506/560	37787615	234,12772	2203	4300	6503	SO:0001583	missense	8208	exon13			CCCTTAAAGACGG	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.1516A>C	21.37:g.37787615A>C	ENSP00000315700:p.Lys506Gln	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	NM_005441	Q99548	Missense_Mutation	SNP	ENST00000314103.5	37	CCDS13644.1	31	0.014194139194139194	27	0.054878048780487805	4	0.011049723756906077	0	0.0	0	0.0	A	15.24	2.773669	0.49786	0.052429	3.49E-4	ENSG00000159259	ENST00000314103	T	0.56444	0.46	5.27	5.27	0.74061	.	0.467856	0.25244	N	0.032064	T	0.09949	0.0244	L	0.34521	1.04	0.41488	D	0.988205	P	0.46706	0.883	B	0.41571	0.36	T	0.02868	-1.1100	10	0.28530	T	0.3	-21.6711	13.7766	0.63057	1.0:0.0:0.0:0.0	rs2230638;rs16994063;rs52813568;rs16994063	506	Q13112	CAF1B_HUMAN	Q	506	ENSP00000315700:K506Q	ENSP00000315700:K506Q	K	+	1	0	CHAF1B	36709485	1.000000	0.71417	0.995000	0.50966	0.553000	0.35397	5.445000	0.66594	1.991000	0.58162	0.533000	0.62120	AAG	A|0.984;C|0.016;T|0.000	0.016	strong		0.358	CHAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194616.2	NM_005441	
EPHA10	284656	hgsc.bcm.edu	37	1	38184470	38184470	+	Silent	SNP	C	C	G	rs610213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38184470C>G	ENST00000373048.4	-	16	2774	c.2775G>C	c.(2773-2775)gcG>gcC	p.A925A	EPHA10_ENST00000540011.1_3'UTR|EPHA10_ENST00000427468.2_Silent_p.A925A|EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000330210.7_Silent_p.A420A	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	925					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGGCACGGTCCGCTAGTGGGG	0.677													C|||	561	0.112021	0.1793	0.0865	5008	,	,		17325	0.001		0.1551	False		,,,				2504	0.1094				p.A925A		Atlas-SNP	.											.	EPHA10	120	.	0			c.G2775C						PASS	.	C		702,3364		57,588,1388	19.0	24.0	22.0		2775	-3.1	1.0	1	dbSNP_83	22	1373,6981		115,1143,2919	no	coding-synonymous	EPHA10	NM_001099439.1		172,1731,4307	GG,GC,CC		16.4352,17.2651,16.7069		925/1009	38184470	2075,10345	2033	4177	6210	SO:0001819	synonymous_variant	284656	exon16			ACGGTCCGCTAGT	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2775G>C	1.37:g.38184470C>G		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	224	101	0.450893	NM_001099439	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	37	CCDS41305.1																																																																																			C|0.889;G|0.111	0.111	strong		0.677	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
TMEM254	80195	hgsc.bcm.edu	37	10	81838864	81838864	+	Intron	SNP	A	A	G	rs61748824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:81838864A>G	ENST00000372281.3	+	1	117				TMEM254-AS1_ENST00000448729.2_RNA|TMEM254-AS1_ENST00000432070.2_RNA|TMEM254_ENST00000372275.1_Intron|TMEM254-AS1_ENST00000412298.1_RNA|TMEM254_ENST00000372277.3_Intron|TMEM254_ENST00000372274.1_Intron	NM_001270372.1|NM_025125.3	NP_001257301.1|NP_079401.2	Q8TBM7	TM254_HUMAN	transmembrane protein 254							integral component of membrane (GO:0016021)											GAGGCCAGCAATGCGGCTACC	0.627													.|||	97	0.019369	0.0514	0.0144	5008	,	,		14740	0.001		0.004	False		,,,				2504	0.0143				p.N28S		Atlas-SNP	.											.	TMEM254	1	.	0			c.A83G						PASS	.																																			SO:0001627	intron_variant	80195	exon1			CCAGCAATGCGGC	BC022252	CCDS7363.1, CCDS58086.1, CCDS58087.1, CCDS73157.1	10q23.1	2012-11-06	2012-11-06	2012-11-06	ENSG00000133678	ENSG00000133678			25804	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 57"""	C10orf57		14702039	Standard	NM_025125		Approved	FLJ13263, bA369J21.6	uc010qlw.3	Q8TBM7	OTTHUMG00000018602	ENST00000372281.3:c.87+322A>G	10.37:g.81838864A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	232	120	0.517241	NM_001270368	D3DWC8|Q53HP4|Q5JTC0|Q5JTC1|Q6IA45|Q9H8S6	Missense_Mutation	SNP	ENST00000372281.3	37	CCDS7363.1	24	0.01098901098901099	16	0.032520325203252036	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	A	1.201	-0.632572	0.03584	.	.	ENSG00000133678	ENST00000372273	.	.	.	4.56	-2.15	0.07102	.	.	.	.	.	T	0.08313	0.0207	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.24584	-1.0156	4	.	.	.	-2.0324	4.9974	0.14247	0.458:0.1525:0.3894:0.0	rs61748824	.	.	.	V	25	.	.	M	+	1	0	C10orf57	81828844	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.359000	0.20233	-0.336000	0.08438	-0.959000	0.02639	ATG	A|0.988;G|0.012	0.012	strong		0.627	TMEM254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049030.1	NM_025125	
FBN3	84467	hgsc.bcm.edu	37	19	8171068	8171068	+	Silent	SNP	G	G	A	rs7258713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8171068G>A	ENST00000600128.1	-	38	5151	c.4737C>T	c.(4735-4737)tgC>tgT	p.C1579C	FBN3_ENST00000601739.1_Silent_p.C1579C|FBN3_ENST00000270509.2_Silent_p.C1579C			Q75N90	FBN3_HUMAN	fibrillin 3	1579	EGF-like 24; 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						ACGTGTTGACGCAGTCACCCC	0.572													G|||	366	0.0730831	0.2428	0.0202	5008	,	,		20054	0.0		0.003	False		,,,				2504	0.0286				p.C1579C		Atlas-SNP	.											.	FBN3	300	.	0			c.C4737T						PASS	.	G		836,3570	331.5+/-302.0	86,664,1453	120.0	85.0	97.0		4737	0.9	0.8	19	dbSNP_116	97	25,8575	17.9+/-57.8	0,25,4275	no	coding-synonymous	FBN3	NM_032447.3		86,689,5728	AA,AG,GG		0.2907,18.9741,6.62		1579/2810	8171068	861,12145	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon37			GTTGACGCAGTCA		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.4737C>T	19.37:g.8171068G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.925;A|0.075	0.075	strong		0.572	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
ADAM33	80332	hgsc.bcm.edu	37	20	3651742	3651742	+	Silent	SNP	C	C	G	rs528557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	174	173	0.994253	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	
BUB1B	701	hgsc.bcm.edu	37	15	40512906	40512906	+	Silent	SNP	A	A	G	rs35611758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40512906A>G	ENST00000287598.6	+	23	3294	c.3099A>G	c.(3097-3099)aaA>aaG	p.K1033K	PAK6_ENST00000453867.1_Intron|BUB1B_ENST00000412359.3_Silent_p.K1047K|RP11-133K1.2_ENST00000558658.1_Intron|PAK6_ENST00000441369.1_Intron	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	1033	Protein kinase.				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)		ACCTGAACAAAGCCTTATGGA	0.468			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				A|||	480	0.0958466	0.3502	0.0245	5008	,	,		19233	0.0		0.0	False		,,,				2504	0.0				p.K1033K		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.A3099G						PASS	.	A	,,	1160,3246	411.9+/-335.9	151,858,1194	139.0	133.0	135.0		,,3099	5.3	1.0	15	dbSNP_126	135	18,8582	13.3+/-46.6	0,18,4282	no	intron,intron,coding-synonymous	BUB1B,PAK6	NM_001128628.1,NM_001128629.1,NM_001211.5	,,	151,876,5476	GG,GA,AA		0.2093,26.3277,9.0574	,,	,,1033/1051	40512906	1178,11828	2203	4300	6503	SO:0001819	synonymous_variant	701	exon23	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GAACAAAGCCTTA	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.3099A>G	15.37:g.40512906A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	137	73	0.532847	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			A|0.915;G|0.085	0.085	strong		0.468	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
C5orf45	51149	hgsc.bcm.edu	37	5	179285781	179285781	+	Missense_Mutation	SNP	G	G	A	rs199537217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179285781G>A	ENST00000292586.6	-	1	106	c.16C>T	c.(16-18)Cgt>Tgt	p.R6C	CTC-241N9.1_ENST00000499601.2_5'Flank|C5orf45_ENST00000520698.1_Missense_Mutation_p.R6C|C5orf45_ENST00000376931.2_Missense_Mutation_p.R6C|C5orf45_ENST00000518235.1_Missense_Mutation_p.R6C|C5orf45_ENST00000518219.1_Missense_Mutation_p.R6C|C5orf45_ENST00000523084.1_5'UTR|C5orf45_ENST00000403396.2_Missense_Mutation_p.A21V|C5orf45_ENST00000521333.1_Missense_Mutation_p.R6C	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	6										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						ACCCGAGAACGCTGAAGCGAC	0.721													G|||	4	0.000798722	0.003	0.0	5008	,	,		14523	0.0		0.0	False		,,,				2504	0.0				p.R6C		Atlas-SNP	.											.	C5orf45	23	.	0			c.C16T						PASS	.	G	CYS/ARG,CYS/ARG	7,3989		0,7,1991	12.0	14.0	13.0		16,16	3.4	0.0	5		13	0,7610		0,0,3805	yes	missense,missense	C5orf45	NM_001017987.2,NM_016175.3	180,180	0,7,5796	AA,AG,GG		0.0,0.1752,0.0603	probably-damaging,probably-damaging	6/289,6/344	179285781	7,11599	1998	3805	5803	SO:0001583	missense	51149	exon1			GAGAACGCTGAAG		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.16C>T	5.37:g.179285781G>A	ENSP00000292586:p.Arg6Cys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	37	CCDS34319.1	3|3	0.0013736263736263737|0.0013736263736263737	3|3	0.006097560975609756|0.006097560975609756	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.22|13.22	2.172040|2.172040	0.38315|0.38315	0.001752|0.001752	0.0|0.0	ENSG00000161010|ENSG00000161010	ENST00000403396|ENST00000518235;ENST00000520698;ENST00000376931;ENST00000518219;ENST00000292586;ENST00000521333	T|T;D;D;D;T;D	0.28454|0.82619	1.61|3.13;-1.63;-1.63;-1.63;3.13;-1.63	3.43|3.43	3.43|3.43	0.39272|0.39272	.|.	.|1.497770	.|0.04096	.|N	.|0.312148	T|T	0.70945|0.70945	0.3282|0.3282	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|D;D;D;D	.|0.60160	.|0.968;0.968;0.987;0.986	.|B;B;B;B	.|0.43809	.|0.432;0.335;0.432;0.432	T|T	0.67841|0.67841	-0.5566|-0.5566	7|10	0.87932|0.87932	D|D	0|0	-1.0479|-1.0479	10.2343|10.2343	0.43273|0.43273	0.1009:0.0:0.8991:0.0|0.1009:0.0:0.8991:0.0	.|.	.|6;6;6;6	.|E7EMV9;B7Z1T6;E9PAK6;Q6NTE8	.|.;.;.;CE045_HUMAN	V|C	21|6	ENSP00000384599:A21V|ENSP00000430298:R6C;ENSP00000427849:R6C;ENSP00000366130:R6C;ENSP00000428460:R6C;ENSP00000292586:R6C;ENSP00000429651:R6C	ENSP00000384599:A21V|ENSP00000292586:R6C	A|R	-|-	2|1	0|0	C5orf45|C5orf45	179218387|179218387	0.016000|0.016000	0.18221|0.18221	0.007000|0.007000	0.13788|0.13788	0.001000|0.001000	0.01503|0.01503	1.350000|1.350000	0.34010|0.34010	2.211000|2.211000	0.71520|0.71520	0.561000|0.561000	0.74099|0.74099	GCG|CGT	G|0.999;A|0.001	0.001	strong		0.721	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	
OR6F1	343169	hgsc.bcm.edu	37	1	247875415	247875415	+	Missense_Mutation	SNP	A	A	G	rs2282316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247875415A>G	ENST00000302084.2	-	1	690	c.643T>C	c.(643-645)Ttt>Ctt	p.F215L	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	215			F -> L (in dbSNP:rs2282316).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F215L(1)		breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	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;0.0168)			TAGGAGACAAAGGTGATGAGG	0.552													G|||	1763	0.352037	0.6929	0.2017	5008	,	,		22569	0.2401		0.2058	False		,,,				2504	0.2638				p.F215L		Atlas-SNP	.											OR6F1,NS,carcinoma,0,1	OR6F1	88	1	1	Substitution - Missense(1)	stomach(1)	c.T643C						PASS	.	G	LEU/PHE	2663,1743	519.4+/-370.0	775,1113,315	132.0	116.0	122.0		643	-1.8	0.0	1	dbSNP_100	122	1976,6624	722.5+/-406.4	219,1538,2543	yes	missense	OR6F1	NM_001005286.1	22	994,2651,2858	GG,GA,AA		22.9767,39.5597,35.6682	benign	215/309	247875415	4639,8367	2203	4300	6503	SO:0001583	missense	343169	exon1			AGACAAAGGTGAT	BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"""GPCR / Class A : Olfactory receptors"""	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.643T>C	1.37:g.247875415A>G	ENSP00000305640:p.Phe215Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_001005286	B2RNV6|Q6IF02|Q96R39	Missense_Mutation	SNP	ENST00000302084.2	37	CCDS31095.1	708	0.3241758241758242	342	0.6951219512195121	88	0.2430939226519337	130	0.22727272727272727	148	0.19525065963060687	G	0.007	-1.995955	0.00435	0.604403	0.229767	ENSG00000169214	ENST00000302084	T	0.00017	9.09	3.72	-1.83	0.07833	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34268	N	0.004102	T	0.00012	0.0000	N	0.00329	-1.635	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.50541	-0.8816	9	0.15066	T	0.55	-10.0518	2.2613	0.04068	0.3244:0.121:0.4315:0.1232	rs2282316;rs56501180;rs60719956;rs2282316	215	Q8NGZ6	OR6F1_HUMAN	L	215	ENSP00000305640:F215L	ENSP00000305640:F215L	F	-	1	0	OR6F1	245942038	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.023000	0.03607	-0.547000	0.06207	-1.054000	0.02325	TTT	A|0.635;G|0.365	0.365	strong		0.552	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286	
SGK223	157285	hgsc.bcm.edu	37	8	8234218	8234218	+	Silent	SNP	C	C	T	rs4840954|rs373458829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8234218C>T	ENST00000520004.1	-	3	1965	c.1701G>A	c.(1699-1701)ccG>ccA	p.P567P	SGK223_ENST00000330777.4_Silent_p.P567P			Q86YV5	SG223_HUMAN		569							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GGTCAGCCAGCGGTGACACTG	0.662													C|||	2272	0.453674	0.3896	0.4323	5008	,	,		16883	0.6409		0.3002	False		,,,				2504	0.5204				p.P567P	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G1701A						PASS	.	C		1303,2737		237,829,954	24.0	29.0	27.0		1701	-9.8	0.0	8	dbSNP_127	27	2269,6033		341,1587,2223	no	coding-synonymous	SGK223	NM_001080826.1		578,2416,3177	TT,TC,CC		27.3308,32.2525,28.9418		567/1403	8234218	3572,8770	2020	4151	6171	SO:0001819	synonymous_variant	0	exon2			AGCCAGCGGTGAC																												ENST00000520004.1:c.1701G>A	8.37:g.8234218C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			C|0.631;T|0.369	0.369	strong		0.662	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
ATP6V1G3	127124	hgsc.bcm.edu	37	1	198498234	198498234	+	Missense_Mutation	SNP	C	C	G	rs16843254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:198498234C>G	ENST00000367382.1	-	2	244	c.160G>C	c.(160-162)Gag>Cag	p.E54Q	ATP6V1G3_ENST00000367381.1_Missense_Mutation_p.E60Q|ATP6V1G3_ENST00000489986.1_Missense_Mutation_p.E60Q|ATP6V1G3_ENST00000309309.7_3'UTR|ATP6V1G3_ENST00000281087.2_Missense_Mutation_p.E54Q			Q96LB4	VATG3_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G3	54			E -> Q (in dbSNP:rs16843254).		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						AGTCGAAACTCTTTATCTCTC	0.323													C|||	155	0.0309505	0.1142	0.0058	5008	,	,		9490	0.0		0.0	False		,,,				2504	0.0				p.E54Q		Atlas-SNP	.											.	ATP6V1G3	26	.	0			c.G160C						PASS	.	C	GLN/GLU,	460,3944	219.4+/-237.2	26,408,1768	148.0	140.0	143.0		160,	3.3	0.0	1	dbSNP_123	143	5,8593	3.7+/-12.6	0,5,4294	yes	missense,utr-3	ATP6V1G3	NM_133262.2,NM_133326.1	29,	26,413,6062	GG,GC,CC		0.0582,10.445,3.5764	possibly-damaging,	54/119,	198498234	465,12537	2202	4299	6501	SO:0001583	missense	127124	exon3			GAAACTCTTTATC	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.160G>C	1.37:g.198498234C>G	ENSP00000356352:p.Glu54Gln	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	100	58	0.58	NM_133262	Q495K2|Q495K4|Q5T9L6	Missense_Mutation	SNP	ENST00000367382.1	37	CCDS1395.1	62	0.028388278388278388	61	0.12398373983739837	1	0.0027624309392265192	0	0.0	0	0.0	C	8.216	0.801462	0.16397	0.10445	5.82E-4	ENSG00000151418	ENST00000367382;ENST00000367381;ENST00000281087;ENST00000489986	T;T;T;T	0.50548	0.74;0.79;0.74;0.79	5.19	3.31	0.37934	.	0.194878	0.53938	N	0.000054	T	0.01254	0.0041	L	0.53729	1.69	0.31164	N	0.704056	D;D	0.67145	0.996;0.989	P;P	0.60473	0.801;0.875	T	0.15780	-1.0425	10	0.15499	T	0.54	-20.9559	15.1522	0.72709	0.0:0.732:0.268:0.0	rs16843254;rs16843254	60;54	Q96LB4-4;Q96LB4	.;VATG3_HUMAN	Q	54;60;54;60	ENSP00000356352:E54Q;ENSP00000356351:E60Q;ENSP00000281087:E54Q;ENSP00000417171:E60Q	ENSP00000281087:E54Q	E	-	1	0	ATP6V1G3	196764857	1.000000	0.71417	0.044000	0.18714	0.074000	0.17049	3.337000	0.52120	0.682000	0.31407	-0.127000	0.14921	GAG	C|0.959;G|0.041	0.041	strong		0.323	ATP6V1G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086559.1	NM_133326	
POLE4	56655	hgsc.bcm.edu	37	2	75185856	75185856	+	Missense_Mutation	SNP	G	G	T	rs12366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:75185856G>T	ENST00000483063.1	+	1	238	c.50G>T	c.(49-51)gGa>gTa	p.G17V	POLE4_ENST00000459636.1_3'UTR	NM_019896.2	NP_063949.2	Q9NR33	DPOE4_HUMAN	polymerase (DNA-directed), epsilon 4, accessory subunit	17			G -> V (in dbSNP:rs12366). {ECO:0000269|PubMed:10801849, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17525332}.		DNA-dependent DNA replication (GO:0006261)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|epsilon DNA polymerase complex (GO:0008622)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|sequence-specific DNA binding (GO:0043565)			lung(1)	1					Cladribine(DB00242)	GAGGAGGAGGGACCTGCTGGG	0.751													G|||	1711	0.341653	0.2965	0.3545	5008	,	,		9775	0.4206		0.3917	False		,,,				2504	0.2607				p.G17V		Atlas-SNP	.											.	POLE4	2	.	0			c.G50T						PASS	.	G	VAL/GLY	1078,2746		168,742,1002	6.0	8.0	7.0		50	3.6	0.8	2	dbSNP_52	7	2577,4845		504,1569,1638	no	missense	POLE4	NM_019896.2	109	672,2311,2640	TT,TG,GG		34.7211,28.1904,32.5004	possibly-damaging	17/118	75185856	3655,7591	1912	3711	5623	SO:0001583	missense	56655	exon1			AGGAGGGACCTGC	AF261688	CCDS1957.1	2p12	2012-05-18	2012-05-18		ENSG00000115350	ENSG00000115350		"""DNA polymerases"""	18755	protein-coding gene	gene with protein product		607269	"""polymerase (DNA-directed), epsilon 4 (p12 subunit)"""			10801849	Standard	NM_019896		Approved	p12	uc002snf.3	Q9NR33	OTTHUMG00000129971	ENST00000483063.1:c.50G>T	2.37:g.75185856G>T	ENSP00000420176:p.Gly17Val	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_019896	Q53TR2	Missense_Mutation	SNP	ENST00000483063.1	37	CCDS1957.1	827	0.37866300366300365	124	0.25203252032520324	145	0.4005524861878453	253	0.4423076923076923	305	0.4023746701846966	G	11.83	1.756056	0.31137	0.281904	0.347211	ENSG00000115350	ENST00000483063	T	0.30981	1.51	5.41	3.58	0.41010	Histone-fold (1);	0.159172	0.56097	D	0.000033	T	0.00012	0.0000	N	0.12182	0.205	0.18873	P	0.9999885704	P	0.34780	0.468	B	0.39503	0.301	T	0.46414	-0.9193	9	0.49607	T	0.09	-6.284	7.1936	0.25839	0.0936:0.18:0.7264:0.0	rs12366;rs3171885;rs17296293;rs17845953;rs17858934	17	Q9NR33	DPOE4_HUMAN	V	17	ENSP00000420176:G17V	ENSP00000420176:G17V	G	+	2	0	POLE4	75039364	0.978000	0.34361	0.787000	0.31911	0.697000	0.40408	2.026000	0.41069	0.631000	0.30412	0.591000	0.81541	GGA	G|0.638;T|0.362	0.362	strong		0.751	POLE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252237.2	NM_019896	
UBALD2	283991	hgsc.bcm.edu	37	17	74266322	74266322	+	Silent	SNP	T	T	C	rs712833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74266322T>C	ENST00000327490.6	+	3	535	c.231T>C	c.(229-231)gaT>gaC	p.D77D	UBALD2_ENST00000589240.1_Silent_p.D17D	NM_182565.3	NP_872371.1	Q8IYN6	UBAD2_HUMAN	UBA-like domain containing 2	77																	ACTTCCCCGATGCGCTGGCCA	0.682													C|||	623	0.124401	0.3601	0.0476	5008	,	,		9337	0.0387		0.0239	False		,,,				2504	0.0521				p.D77D		Atlas-SNP	.											.	.	.	.	0			c.T231C						PASS	.	C		1320,3082		200,920,1081	28.0	29.0	28.0		231	-5.1	0.2	17	dbSNP_86	28	163,8435		1,161,4137	no	coding-synonymous	FAM100B	NM_182565.3		201,1081,5218	CC,CT,TT		1.8958,29.9864,11.4077		77/165	74266322	1483,11517	2201	4299	6500	SO:0001819	synonymous_variant	283991	exon3			CCCCGATGCGCTG		CCDS11742.1	17q25.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000185262	ENSG00000185262			28438	protein-coding gene	gene with protein product			"""family with sequence similarity 100, member B"""	FAM100B			Standard	NM_182565		Approved	MGC29814	uc010wsy.1	Q8IYN6	OTTHUMG00000132666	ENST00000327490.6:c.231T>C	17.37:g.74266322T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_182565		Silent	SNP	ENST00000327490.6	37	CCDS11742.1																																																																																			T|0.888;C|0.112	0.112	strong		0.682	UBALD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255920.1	NM_182565	
KRT8	3856	hgsc.bcm.edu	37	12	53294381	53294381	+	Silent	SNP	T	T	C	rs8608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53294381T>C	ENST00000552551.1	-	5	1113	c.681A>G	c.(679-681)ctA>ctG	p.L227L	KRT8_ENST00000546897.1_Silent_p.L227L|KRT8_ENST00000293308.6_Silent_p.L227L|KRT8_ENST00000552150.1_Silent_p.L255L			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	60	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	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	
APOL5	80831	hgsc.bcm.edu	37	22	36122930	36122930	+	Missense_Mutation	SNP	C	C	T	rs2076671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36122930C>T	ENST00000249044.2	+	3	815	c.815C>T	c.(814-816)aCg>aTg	p.T272M		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	272			T -> M (in dbSNP:rs2076671).		lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|skin(2)|urinary_tract(1)	19						CCTTTCTGGACGGCTAGAGGG	0.527													G|||	1935	0.386382	0.32	0.2349	5008	,	,		18520	0.5962		0.2903	False		,,,				2504	0.4663				p.T272M		Atlas-SNP	.											.	APOL5	45	.	0			c.C815T						PASS	.	G	MET/THR	1410,2996		245,920,1038	139.0	146.0	144.0		815	-0.3	0.0	22	dbSNP_96	144	2663,5937		437,1789,2074	yes	missense	APOL5	NM_030642.1	81	682,2709,3112	TT,TC,CC		30.9651,32.0018,31.3163	probably-damaging	272/434	36122930	4073,8933	2203	4300	6503	SO:0001583	missense	80831	exon3			TCTGGACGGCTAG	AY014878	CCDS13920.1	22q12.3	2013-01-24			ENSG00000128313	ENSG00000128313		"""Apolipoproteins"""	14869	protein-coding gene	gene with protein product		607255				11374903	Standard	NM_030642		Approved	APOLV	uc003aof.3	Q9BWW9	OTTHUMG00000150588	ENST00000249044.2:c.815C>T	22.37:g.36122930C>T	ENSP00000249044:p.Thr272Met	Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_030642	Q5TFL9|Q9UGW5	Missense_Mutation	SNP	ENST00000249044.2	37	CCDS13920.1	796	0.36446886446886445	156	0.3170731707317073	89	0.24585635359116023	335	0.5856643356643356	216	0.2849604221635884	G	18.41	3.617524	0.66787	0.320018	0.309651	ENSG00000128313	ENST00000249044	T	0.03607	3.87	3.8	-0.258	0.12975	.	2.147360	0.02570	U	0.097668	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P	0.45283	0.855	B	0.35770	0.21	T	0.40515	-0.9559	9	0.62326	D	0.03	.	2.6112	0.04891	0.1212:0.2999:0.4272:0.1518	rs2076671;rs52791490;rs57567438;rs2076671	272	Q9BWW9	APOL5_HUMAN	M	272	ENSP00000249044:T272M	ENSP00000249044:T272M	T	+	2	0	APOL5	34452876	0.008000	0.16893	0.000000	0.03702	0.009000	0.06853	0.057000	0.14279	-0.784000	0.04528	-1.137000	0.01932	ACG	C|0.663;T|0.337	0.337	strong		0.527	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
RTP5	285093	hgsc.bcm.edu	37	2	242814778	242814778	+	Silent	SNP	C	C	T	rs7597435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242814778C>T	ENST00000343216.3	+	2	1099	c.1071C>T	c.(1069-1071)acC>acT	p.T357T		NM_173821.2	NP_776182.2																					CGGAGCCCACCGATGGCCCTG	0.612													C|||	204	0.0407348	0.1475	0.0101	5008	,	,		19528	0.0		0.002	False		,,,				2504	0.0				p.T357T		Atlas-SNP	.											.	.	.	.	0			c.C1071T						PASS	.	C		534,3442		35,464,1489	29.0	34.0	32.0		1071	-4.3	0.0	2	dbSNP_116	32	3,8279		0,3,4138	no	coding-synonymous	C2orf85	NM_173821.2		35,467,5627	TT,TC,CC		0.0362,13.4306,4.3808		357/573	242814778	537,11721	1988	4141	6129	SO:0001819	synonymous_variant	285093	exon2			GCCCACCGATGGC																												ENST00000343216.3:c.1071C>T	2.37:g.242814778C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	198	88	0.444444	NM_173821		Silent	SNP	ENST00000343216.3	37	CCDS42843.1																																																																																			C|0.963;T|0.037	0.037	strong		0.612	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
REG4	83998	hgsc.bcm.edu	37	1	120341193	120341193	+	Missense_Mutation	SNP	C	C	T	rs75358916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120341193C>T	ENST00000354219.1	-	6	775	c.336G>A	c.(334-336)atG>atA	p.M112I	REG4_ENST00000530654.1_Intron|REG4_ENST00000256585.5_Missense_Mutation_p.M112I	NM_001159352.1	NP_001152824.1	Q9BYZ8	REG4_HUMAN	regenerating islet-derived family, member 4	112	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|mannan binding (GO:2001065)			central_nervous_system(1)|large_intestine(1)|lung(8)|ovary(2)|prostate(1)|skin(2)	15	all_cancers(5;4.81e-10)|all_epithelial(5;7.98e-11)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;8.1e-07)|Lung NSC(69;5.89e-06)|all_epithelial(167;0.000959)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0588)		TGTACAGATACATGGCCCCAT	0.532													C|||	42	0.00838658	0.031	0.0014	5008	,	,		17162	0.0		0.0	False		,,,				2504	0.0				p.M112I		Atlas-SNP	.											.	REG4	36	.	0			c.G336A						PASS	.	C	ILE/MET,ILE/MET	128,4278	93.4+/-132.2	2,124,2077	201.0	185.0	190.0		336,336	-7.1	0.0	1	dbSNP_131	190	0,8600		0,0,4300	yes	missense,missense	REG4	NM_001159352.1,NM_032044.3	10,10	2,124,6377	TT,TC,CC		0.0,2.9051,0.9842	benign,benign	112/159,112/159	120341193	128,12878	2203	4300	6503	SO:0001583	missense	83998	exon5			CAGATACATGGCC	AY007243	CCDS906.1, CCDS53354.1	1p13.1-p12	2008-02-05			ENSG00000134193	ENSG00000134193			22977	protein-coding gene	gene with protein product	"""regenerating gene type IV"", "" gastrointestinal secretory protein"""	609846				11311942, 12455032	Standard	NM_032044		Approved	REG-IV, RELP, GISP	uc001eif.3	Q9BYZ8	OTTHUMG00000012175	ENST00000354219.1:c.336G>A	1.37:g.120341193C>T	ENSP00000346158:p.Met112Ile	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	225	120	0.533333	NM_032044	Q8NER6|Q8NER7	Missense_Mutation	SNP	ENST00000354219.1	37	CCDS906.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	C	9.514	1.106451	0.20632	0.029051	0.0	ENSG00000134193	ENST00000354219;ENST00000256585	T;T	0.07216	3.21;3.21	5.02	-7.05	0.01573	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.458410	0.04405	N	0.364865	T	0.01156	0.0038	N	0.11756	0.17	0.09310	N	1	B	0.02656	0.0	B	0.11329	0.006	T	0.43523	-0.9386	10	0.32370	T	0.25	0.8924	7.2514	0.26152	0.0:0.1828:0.4589:0.3583	.	112	Q9BYZ8	REG4_HUMAN	I	112	ENSP00000346158:M112I;ENSP00000256585:M112I	ENSP00000256585:M112I	M	-	3	0	REG4	120142716	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.742000	0.01835	-1.675000	0.01459	-0.893000	0.02921	ATG	C|0.991;T|0.009	0.009	strong		0.532	REG4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033675.1	NM_032044	
COBL	23242	hgsc.bcm.edu	37	7	51096974	51096974	+	Missense_Mutation	SNP	C	C	T	rs2240090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	210	0	0		WXS	Illumina HiSeq	Phase_I	259	257	0.992278	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	
C19orf45	374877	hgsc.bcm.edu	37	19	7573225	7573225	+	Missense_Mutation	SNP	C	C	T	rs141790796		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7573225C>T	ENST00000361664.2	+	9	1568	c.1427C>T	c.(1426-1428)cCc>cTc	p.P476L	CTD-2207O23.12_ENST00000599312.1_Intron	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	476										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						GGCTTCGTGCCCCTGGGCACG	0.582																																					p.P476L		Atlas-SNP	.											.	C19orf45	36	.	0			c.C1427T						PASS	.						42.0	41.0	41.0					19																	7573225		2203	4300	6503	SO:0001583	missense	374877	exon9			TCGTGCCCCTGGG	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.1427C>T	19.37:g.7573225C>T	ENSP00000355241:p.Pro476Leu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	139	10	0.0719424	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530201	0.45073	.	.	ENSG00000198723	ENST00000361664	T	0.49139	0.79	4.15	3.09	0.35607	.	0.235290	0.36444	N	0.002596	T	0.43211	0.1237	M	0.63843	1.955	0.46798	D	0.999203	P	0.41597	0.756	B	0.39805	0.31	T	0.45702	-0.9243	10	0.87932	D	0	-24.0027	8.3255	0.32153	0.0:0.8889:0.0:0.1111	.	476	Q8NA69	CS045_HUMAN	L	476	ENSP00000355241:P476L	ENSP00000355241:P476L	P	+	2	0	C19orf45	7479225	0.647000	0.27304	0.555000	0.28281	0.064000	0.16182	1.178000	0.31981	1.090000	0.41315	0.462000	0.41574	CCC	C|1.000;A|0.000	.	alt		0.582	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
VIT	5212	hgsc.bcm.edu	37	2	37035934	37035934	+	Missense_Mutation	SNP	A	A	G	rs2072526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37035934A>G	ENST00000389975.3	+	14	1966	c.1664A>G	c.(1663-1665)aAg>aGg	p.K555R	VIT_ENST00000379241.3_Missense_Mutation_p.K533R|VIT_ENST00000379242.3_Missense_Mutation_p.K570R|VIT_ENST00000401530.1_Missense_Mutation_p.K534R|VIT_ENST00000404084.1_Missense_Mutation_p.K507R|VIT_ENST00000497382.1_Missense_Mutation_p.K224R	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	555	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.		K -> R (in dbSNP:rs2072526). {ECO:0000269|PubMed:15489334}.		extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				TACAGCAGCAAGCCTGACATC	0.582													A|||	903	0.180312	0.2958	0.0706	5008	,	,		19800	0.245		0.0477	False		,,,				2504	0.1718				p.K570R		Atlas-SNP	.											.	VIT	138	.	0			c.A1709G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	1086,3320	394.0+/-329.1	118,850,1235	91.0	85.0	87.0		1664,1601,1598,1709	4.1	0.4	2	dbSNP_96	87	292,8308	108.0+/-168.7	7,278,4015	yes	missense,missense,missense,missense	VIT	NM_001177969.1,NM_001177970.1,NM_001177971.1,NM_053276.3	26,26,26,26	125,1128,5250	GG,GA,AA		3.3953,24.6482,10.5951	benign,benign,benign,benign	555/679,534/658,533/657,570/694	37035934	1378,11628	2203	4300	6503	SO:0001583	missense	5212	exon15			GCAGCAAGCCTGA	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.1664A>G	2.37:g.37035934A>G	ENSP00000374625:p.Lys555Arg	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	178	92	0.516854	NM_053276	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	37	CCDS54347.1	338	0.15476190476190477	142	0.2886178861788618	16	0.04419889502762431	146	0.25524475524475526	34	0.044854881266490766	A	13.97	2.396815	0.42512	0.246482	0.033953	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000497382;ENST00000404084;ENST00000379241;ENST00000401530	D;D;D;D;D;D	0.85013	-1.93;-1.93;-1.93;-1.93;-1.93;-1.93	5.27	4.12	0.48240	von Willebrand factor, type A (3);	0.094893	0.64402	D	0.000001	T	0.00039	0.0001	L	0.55213	1.73	0.23459	P	0.99763814	D;D;D;B	0.76494	0.999;0.999;0.997;0.005	D;D;D;B	0.73708	0.97;0.981;0.949;0.016	T	0.02087	-1.1216	9	0.45353	T	0.12	-21.3083	7.29	0.26360	0.7995:0.0:0.0717:0.1288	rs2072526;rs52832758;rs2072526	534;533;555;570	E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4	.;.;VITRN_HUMAN;.	R	570;555;224;507;533;534	ENSP00000368544:K570R;ENSP00000374625:K555R;ENSP00000417874:K224R;ENSP00000384154:K507R;ENSP00000368543:K533R;ENSP00000385658:K534R	ENSP00000368543:K533R	K	+	2	0	VIT	36889438	1.000000	0.71417	0.442000	0.26870	0.104000	0.19210	7.485000	0.81204	0.850000	0.35239	0.455000	0.32223	AAG	G|0.137;N|0.000	0.137	strong		0.582	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			
C5orf42	65250	hgsc.bcm.edu	37	5	37182940	37182940	+	Silent	SNP	T	T	A	rs73750949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37182940T>A	ENST00000508244.1	-	25	5436	c.5343A>T	c.(5341-5343)acA>acT	p.T1781T	C5orf42_ENST00000274258.7_Silent_p.T662T|C5orf42_ENST00000425232.2_Silent_p.T1781T			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1781						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GAATGGCAGCTGTAGAGGTCT	0.363													T|||	144	0.028754	0.1067	0.0043	5008	,	,		18465	0.0		0.0	False		,,,				2504	0.0				p.T1781T		Atlas-SNP	.											.	C5orf42	422	.	0			c.A5343T						PASS	.	T		416,3990	203.1+/-225.7	20,376,1807	83.0	77.0	79.0		5343	1.2	1.0	5	dbSNP_130	79	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C5orf42	NM_023073.3		20,377,6106	AA,AT,TT		0.0116,9.4417,3.2062		1781/3198	37182940	417,12589	2203	4300	6503	SO:0001819	synonymous_variant	65250	exon26			GGCAGCTGTAGAG		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.5343A>T	5.37:g.37182940T>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			T|0.973;A|0.027	0.027	strong		0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
TXK	7294	hgsc.bcm.edu	37	4	48096101	48096101	+	Silent	SNP	A	A	G	rs73151620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:48096101A>G	ENST00000264316.4	-	8	787	c.702T>C	c.(700-702)aaT>aaC	p.N234N	TXK_ENST00000510457.1_5'UTR	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	234	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						TACCGGCTGCATTGTGCTGGT	0.473													A|||	174	0.0347444	0.1263	0.0101	5008	,	,		17952	0.0		0.0	False		,,,				2504	0.0				p.N234N		Atlas-SNP	.											.	TXK	58	.	0			c.T702C						PASS	.	A		544,3862	245.6+/-254.5	32,480,1691	131.0	130.0	130.0		702	-9.1	0.2	4	dbSNP_130	130	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous	TXK	NM_003328.2		32,483,5988	GG,GA,AA		0.0349,12.3468,4.2058		234/528	48096101	547,12459	2203	4300	6503	SO:0001819	synonymous_variant	7294	exon8			GGCTGCATTGTGC	L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"""SH2 domain containing"""	12434	protein-coding gene	gene with protein product		600058	"""PTK4 protein tyrosine kinase 4"""	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.702T>C	4.37:g.48096101A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_003328	Q14220	Silent	SNP	ENST00000264316.4	37	CCDS3480.1																																																																																			A|0.959;G|0.041	0.041	strong		0.473	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328	
F5	2153	hgsc.bcm.edu	37	1	169529973	169529973	+	Silent	SNP	C	C	T	rs6029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169529973C>T	ENST00000367797.3	-	4	606	c.405G>A	c.(403-405)gcG>gcA	p.A135A	F5_ENST00000367796.3_Silent_p.A135A|F5_ENST00000546081.1_5'UTR	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	151	0	0		WXS	Illumina HiSeq	Phase_I	160	80	0.5	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	
TAS2R20	259295	hgsc.bcm.edu	37	12	11150319	11150319	+	Silent	SNP	T	T	C	rs11054143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11150319T>C	ENST00000538986.1	-	1	155	c.156A>G	c.(154-156)gcA>gcG	p.A52A	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	52					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)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						CTCTGGAGACTGCCAGAGCAG	0.343													C|||	2118	0.422923	0.0651	0.3847	5008	,	,		18136	0.755		0.3817	False		,,,				2504	0.6339				p.A52A		Atlas-SNP	.											.	TAS2R20	17	.	0			c.A156G						PASS	.	C		433,3971	729.6+/-410.1	18,397,1787	40.0	46.0	44.0		156	-5.5	0.0	12	dbSNP_120	44	3001,5597	650.8+/-400.8	539,1923,1837	no	coding-synonymous	TAS2R20	NM_176889.2		557,2320,3624	CC,CT,TT		34.9035,9.832,26.4113		52/310	11150319	3434,9568	2202	4299	6501	SO:0001819	synonymous_variant	259295	exon1			GGAGACTGCCAGA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.156A>G	12.37:g.11150319T>C		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	262	121	0.461832	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Silent	SNP	ENST00000538986.1	37	CCDS8639.1																																																																																			T|0.678;C|0.322	0.322	strong		0.343	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
CPNE7	27132	hgsc.bcm.edu	37	16	89655120	89655120	+	Missense_Mutation	SNP	G	G	A	rs28568523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89655120G>A	ENST00000268720.5	+	12	1320	c.1190G>A	c.(1189-1191)cGg>cAg	p.R397Q	CPNE7_ENST00000319518.8_Missense_Mutation_p.R322Q	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	397	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		R -> Q (in dbSNP:rs28568523).		lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		GGAGACCCGCGGAACAGCTGC	0.647													G|||	28	0.00559105	0.0144	0.0	5008	,	,		15442	0.002		0.007	False		,,,				2504	0.0				p.R397Q		Atlas-SNP	.											.	CPNE7	56	.	0			c.G1190A						PASS	.	G	GLN/ARG,GLN/ARG	43,4353	46.7+/-81.2	0,43,2155	129.0	98.0	108.0		1190,965	3.8	0.8	16	dbSNP_125	108	51,8549	33.3+/-86.6	0,51,4249	yes	missense,missense	CPNE7	NM_014427.4,NM_153636.2	43,43	0,94,6404	AA,AG,GG		0.593,0.9782,0.7233	probably-damaging,probably-damaging	397/634,322/559	89655120	94,12902	2198	4300	6498	SO:0001583	missense	27132	exon12			ACCCGCGGAACAG	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.1190G>A	16.37:g.89655120G>A	ENSP00000268720:p.Arg397Gln	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	58	41	0.706897	NM_014427		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	10	0.004578754578754579	3	0.006097560975609756	0	0.0	1	0.0017482517482517483	6	0.0079155672823219	G	18.57	3.653381	0.67472	0.009782	0.00593	ENSG00000178773	ENST00000319518;ENST00000268720;ENST00000529800	T;T;T	0.18174	2.45;2.41;2.23	3.75	3.75	0.43078	von Willebrand factor, type A (2);	0.000000	0.85682	D	0.000000	T	0.18130	0.0435	M	0.64676	1.99	0.49798	D	0.999823	P;P	0.52316	0.907;0.952	P;B	0.46299	0.511;0.259	T	0.06481	-1.0824	10	0.49607	T	0.09	-8.211	15.5036	0.75719	0.0:0.0:1.0:0.0	rs28568523;rs28568523	322;397	Q9UBL6-2;Q9UBL6	.;CPNE7_HUMAN	Q	322;397;42	ENSP00000317374:R322Q;ENSP00000268720:R397Q;ENSP00000435876:R42Q	ENSP00000268720:R397Q	R	+	2	0	CPNE7	88182621	0.993000	0.37304	0.844000	0.33320	0.161000	0.22273	7.195000	0.77798	1.776000	0.52262	0.313000	0.20887	CGG	G|0.992;A|0.008	0.008	strong		0.647	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
KIAA1755	85449	hgsc.bcm.edu	37	20	36856579	36856579	+	Silent	SNP	G	G	A	rs74723843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36856579G>A	ENST00000279024.4	-	6	2206	c.1935C>T	c.(1933-1935)ccC>ccT	p.P645P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	645										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)				TGACCAGACCGGGCTGTGGGG	0.602													g|||	114	0.0227636	0.0794	0.0101	5008	,	,		17204	0.0		0.0	False		,,,				2504	0.002				p.P645P		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C1935T						PASS	.	G		301,4103	160.0+/-192.4	14,273,1915	36.0	37.0	37.0		1935	-9.6	0.0	20	dbSNP_131	37	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA1755	NM_001029864.1		14,274,6214	AA,AG,GG		0.0116,6.8347,2.3224		645/1201	36856579	302,12702	2202	4300	6502	SO:0001819	synonymous_variant	85449	exon6			CAGACCGGGCTGT	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.1935C>T	20.37:g.36856579G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.974;A|0.026	0.026	strong		0.602	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
PCDHB2	56133	hgsc.bcm.edu	37	5	140475958	140475958	+	Silent	SNP	G	G	T	rs371176940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140475958G>T	ENST00000194155.4	+	1	1732	c.1584G>T	c.(1582-1584)gcG>gcT	p.A528A		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTGCAGGCGTTCGAGTTCC	0.706													g|||	5	0.000998403	0.0	0.0	5008	,	,		15707	0.0		0.0	False		,,,				2504	0.0051				p.A528A		Atlas-SNP	.											.	PCDHB2	163	.	0			c.G1584T						PASS	.						68.0	75.0	73.0					5																	140475958		2203	4299	6502	SO:0001819	synonymous_variant	56133	exon1			GCAGGCGTTCGAG	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1584G>T	5.37:g.140475958G>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	205	10	0.0487805	NM_018936	Q4KMU1	Silent	SNP	ENST00000194155.4	37	CCDS4244.1																																																																																			.	.	alt		0.706	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
TRIM15	89870	hgsc.bcm.edu	37	6	30131515	30131515	+	Silent	SNP	C	C	A	rs2523733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30131515C>A	ENST00000376694.4	+	1	523	c.54C>A	c.(52-54)ctC>ctA	p.L18L	TRIM15_ENST00000376688.1_Silent_p.L18L|TRIM10_ENST00000449742.2_5'Flank|TRIM10_ENST00000376704.3_5'Flank	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	18					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						CCTGTACCCTCTGTGCGGGGC	0.687													C|||	912	0.182109	0.2655	0.1354	5008	,	,		17556	0.0952		0.1272	False		,,,				2504	0.2485				p.L18L		Atlas-SNP	.											.	TRIM15	34	.	0			c.C54A						PASS	.	C		690,2332		82,526,903	51.0	45.0	47.0		54	-0.3	0.0	6	dbSNP_100	47	720,4696		45,630,2033	no	coding-synonymous	TRIM15	NM_033229.2		127,1156,2936	AA,AC,CC		13.2939,22.8326,16.7101		18/466	30131515	1410,7028	1511	2708	4219	SO:0001819	synonymous_variant	89870	exon1			TACCCTCTGTGCG	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.54C>A	6.37:g.30131515C>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Silent	SNP	ENST00000376694.4	37	CCDS4677.1																																																																																			C|0.820;A|0.180	0.180	strong		0.687	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229	
CC2D2B	387707	hgsc.bcm.edu	37	10	97779510	97779510	+	Missense_Mutation	SNP	T	T	C	rs9943393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:97779510T>C	ENST00000344386.3	+	8	873	c.709T>C	c.(709-711)Tat>Cat	p.Y237H	ENTPD1-AS1_ENST00000454638.1_RNA|CC2D2B_ENST00000410012.2_Missense_Mutation_p.Y237H|CC2D2B_ENST00000371198.2_Intron|ENTPD1-AS1_ENST00000458228.1_RNA|RP11-690P14.4_ENST00000475252.2_Intron|ENTPD1-AS1_ENST00000452728.1_RNA|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1-AS1_ENST00000449197.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B	237			Y -> H (in dbSNP:rs9943393).							large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		ATTTTTTGACTATTCAAAGGA	0.338													T|||	67	0.0133786	0.0477	0.0043	5008	,	,		17685	0.0		0.001	False		,,,				2504	0.0				p.Y237H		Atlas-SNP	.											.	CC2D2B	46	.	0			c.T709C						PASS	.	T	HIS/TYR,HIS/TYR	124,3472		7,110,1681	105.0	107.0	106.0		709,709	3.7	1.0	10	dbSNP_119	106	3,8137		0,3,4067	yes	missense,missense	CC2D2B	NM_001001732.3,NM_001159747.1	83,83	7,113,5748	CC,CT,TT		0.0369,3.4483,1.0821	possibly-damaging,possibly-damaging	237/323,237/402	97779510	127,11609	1798	4070	5868	SO:0001583	missense	387707	exon8			TTTGACTATTCAA	BC075861	CCDS41555.1, CCDS53560.1	10q23.33	2008-11-06	2007-10-19	2007-10-19	ENSG00000188649	ENSG00000188649			31666	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 130"""	C10orf130			Standard	NM_001001732		Approved	bA248J23.4	uc010qop.2	Q6DHV5	OTTHUMG00000018820	ENST00000344386.3:c.709T>C	10.37:g.97779510T>C	ENSP00000343747:p.Tyr237His	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	288	127	0.440972	NM_001001732	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Missense_Mutation	SNP	ENST00000344386.3	37	CCDS41555.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	14.01	2.407470	0.42715	0.034483	3.69E-4	ENSG00000188649	ENST00000451649;ENST00000410012;ENST00000344386	T;T	0.70399	-0.48;-0.48	4.93	3.73	0.42828	.	.	.	.	.	T	0.22166	0.0534	L	0.44542	1.39	0.26525	N	0.974358	P;B	0.44195	0.828;0.392	B;B	0.42593	0.392;0.141	T	0.31194	-0.9952	9	0.39692	T	0.17	.	7.3082	0.26459	0.2619:0.0:0.0:0.7381	rs9943393;rs9943393	237;237	E9PCC3;Q6DHV5	.;C2D2B_HUMAN	H	237	ENSP00000386988:Y237H;ENSP00000343747:Y237H	ENSP00000343747:Y237H	Y	+	1	0	CC2D2B	97769500	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	2.130000	0.42064	2.072000	0.62099	0.454000	0.30748	TAT	T|0.988;C|0.012	0.012	strong		0.338	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732	
GLIS1	148979	hgsc.bcm.edu	37	1	54060107	54060107	+	Missense_Mutation	SNP	A	A	G	rs34961060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54060107A>G	ENST00000312233.2	-	3	1035	c.469T>C	c.(469-471)Ttt>Ctt	p.F157L		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						TGAGGCCCAAAGAGCTCTGAA	0.657													A|||	183	0.0365415	0.1362	0.0029	5008	,	,		14987	0.0		0.001	False		,,,				2504	0.0				p.F157L		Atlas-SNP	.											.	GLIS1	52	.	0			c.T469C						PASS	.	A	LEU/PHE	429,3963		23,383,1790	15.0	18.0	17.0		469	2.4	0.8	1	dbSNP_126	17	4,8562		0,4,4279	yes	missense	GLIS1	NM_147193.2	22	23,387,6069	GG,GA,AA		0.0467,9.7678,3.3416	possibly-damaging	157/621	54060107	433,12525	2196	4283	6479	SO:0001583	missense	148979	exon3			GCCCAAAGAGCTC	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.469T>C	1.37:g.54060107A>G	ENSP00000309653:p.Phe157Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	79	0.036172161172161175	77	0.1565040650406504	2	0.0055248618784530384	0	0.0	0	0.0	A	16.69	3.192807	0.58017	0.097678	4.67E-4	ENSG00000174332	ENST00000312233	T	0.10573	2.86	5.07	2.43	0.29744	.	0.105911	0.41605	N	0.000847	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.39313	-0.9620	9	0.02654	T	1	.	7.8454	0.29422	0.7801:0.0:0.2199:0.0	rs34961060	157	Q8NBF1	GLIS1_HUMAN	L	157	ENSP00000309653:F157L	ENSP00000309653:F157L	F	-	1	0	GLIS1	53832695	1.000000	0.71417	0.814000	0.32528	0.822000	0.46500	2.049000	0.41288	0.888000	0.36160	0.379000	0.24179	TTT	A|0.968;G|0.032	0.032	strong		0.657	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
ZNF227	7770	hgsc.bcm.edu	37	19	44740602	44740602	+	Silent	SNP	G	G	A	rs3810137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44740602G>A	ENST00000313040.7	+	6	2224	c.2019G>A	c.(2017-2019)tcG>tcA	p.S673S	ZNF235_ENST00000589799.1_3'UTR|ZNF227_ENST00000391961.2_Silent_p.S622S|ZNF227_ENST00000589005.1_Silent_p.S622S	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S673S(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				GATACAGTTCGCAGTTTATAT	0.463													G|||	872	0.174121	0.4516	0.2046	5008	,	,		21632	0.1012		0.0179	False		,,,				2504	0.0133				p.S673S		Atlas-SNP	.											ZNF227,NS,carcinoma,+1,2	ZNF227	62	2	1	Substitution - coding silent(1)	stomach(1)	c.G2019A						PASS	.	G		1792,2614	527.3+/-372.1	365,1062,776	73.0	77.0	76.0		2019	-3.7	0.0	19	dbSNP_107	76	64,8536	36.9+/-92.0	2,60,4238	no	coding-synonymous	ZNF227	NM_182490.1		367,1122,5014	AA,AG,GG		0.7442,40.6718,14.2703		673/800	44740602	1856,11150	2203	4300	6503	SO:0001819	synonymous_variant	7770	exon6			CAGTTCGCAGTTT	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.2019G>A	19.37:g.44740602G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_182490	B3KRU7|B7Z5P9	Silent	SNP	ENST00000313040.7	37	CCDS12636.1																																																																																			G|0.861;A|0.139	0.139	strong		0.463	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490	
CELSR1	9620	hgsc.bcm.edu	37	22	46786315	46786315	+	Missense_Mutation	SNP	T	T	C	rs4044210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	72	0	0	941	WXS	Illumina HiSeq	Phase_I	59	29	0.491525	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	
PRRG2	5639	hgsc.bcm.edu	37	19	50091798	50091798	+	Missense_Mutation	SNP	G	G	T	rs2288920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	94	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	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	
DNAJC17	55192	hgsc.bcm.edu	37	15	41068409	41068409	+	Missense_Mutation	SNP	C	C	T	rs73398528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41068409C>T	ENST00000220496.4	-	6	493	c.463G>A	c.(463-465)Gac>Aac	p.D155N		NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	155					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)		nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|skin(1)	6		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		AACCTCTGGTCACGCTCCTGG	0.622													C|||	294	0.0587061	0.2141	0.0144	5008	,	,		16797	0.001		0.0	False		,,,				2504	0.0				p.D155N		Atlas-SNP	.											.	DNAJC17	18	.	0			c.G463A						PASS	.	C	ASN/ASP	781,3625	315.2+/-294.0	55,671,1477	104.0	84.0	91.0		463	4.4	0.3	15	dbSNP_130	91	3,8597	2.2+/-6.3	0,3,4297	yes	missense	DNAJC17	NM_018163.2	23	55,674,5774	TT,TC,CC		0.0349,17.7258,6.028	benign	155/305	41068409	784,12222	2203	4300	6503	SO:0001583	missense	55192	exon6			TCTGGTCACGCTC	AK001496	CCDS10065.1	15q15.1	2014-02-12			ENSG00000104129	ENSG00000104129		"""Heat shock proteins / DNAJ (HSP40)"", ""RNA binding motif (RRM) containing"""	25556	protein-coding gene	gene with protein product						12477932	Standard	NM_018163		Approved	FLJ10634	uc001zms.2	Q9NVM6	OTTHUMG00000130065	ENST00000220496.4:c.463G>A	15.37:g.41068409C>T	ENSP00000220496:p.Asp155Asn	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_018163		Missense_Mutation	SNP	ENST00000220496.4	37	CCDS10065.1	103	0.04716117216117216	95	0.19308943089430894	7	0.019337016574585635	1	0.0017482517482517483	0	0.0	C	6.900	0.535565	0.13188	0.177258	3.49E-4	ENSG00000104129	ENST00000220496	T	0.18338	2.22	4.41	4.41	0.53225	.	0.289804	0.36444	N	0.002600	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	0.38394	-0.9663	9	0.21540	T	0.41	.	13.7416	0.62852	0.0:0.8449:0.1551:0.0	.	155	Q9NVM6	DJC17_HUMAN	N	155	ENSP00000220496:D155N	ENSP00000220496:D155N	D	-	1	0	DNAJC17	38855701	0.959000	0.32827	0.332000	0.25469	0.105000	0.19272	3.571000	0.53841	2.300000	0.77407	0.561000	0.74099	GAC	C|0.947;T|0.053	0.053	strong		0.622	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163	
KIF21B	23046	hgsc.bcm.edu	37	1	200945910	200945910	+	Silent	SNP	G	G	A	rs61740477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200945910G>A	ENST00000422435.2	-	32	4753	c.4437C>T	c.(4435-4437)taC>taT	p.Y1479Y	KIF21B_ENST00000332129.2_Silent_p.Y1466Y|KIF21B_ENST00000461742.2_Silent_p.Y1479Y|KIF21B_ENST00000360529.5_Silent_p.Y1466Y	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1479					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						GTACCTTAACGTAGTGGTCCT	0.577													G|||	390	0.0778754	0.0968	0.0504	5008	,	,		17521	0.1349		0.005	False		,,,				2504	0.0879				p.Y1479Y		Atlas-SNP	.											.	KIF21B	208	.	0			c.C4437T						PASS	.	G		432,3974	209.5+/-230.2	22,388,1793	52.0	43.0	46.0		4398	-2.7	0.8	1	dbSNP_129	46	22,8578	14.6+/-50.1	0,22,4278	no	coding-synonymous	KIF21B	NM_017596.2		22,410,6071	AA,AG,GG		0.2558,9.8048,3.4907		1466/1625	200945910	454,12552	2203	4300	6503	SO:0001819	synonymous_variant	23046	exon32			CTTAACGTAGTGG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.4437C>T	1.37:g.200945910G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_001252102	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	37	CCDS58056.1																																																																																			G|0.958;A|0.042	0.042	strong		0.577	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
ZNF208	7757	hgsc.bcm.edu	37	19	22155520	22155520	+	Silent	SNP	A	A	G	rs7258270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22155520A>G	ENST00000397126.4	-	4	2464	c.2316T>C	c.(2314-2316)acT>acC	p.T772T	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	772					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)				GTTTCTCTACAGTATGAATTT	0.358													a|||	1100	0.219649	0.3343	0.2233	5008	,	,		21120	0.1885		0.1113	False		,,,				2504	0.2055				p.T772T		Atlas-SNP	.											ZNF208_ENST00000428290,NS,carcinoma,-1,3	ZNF208	817	3	0			c.T2316C						PASS	.	A		1151,2855		175,801,1027	31.0	35.0	34.0		2316	-0.1	0.0	19	dbSNP_116	34	1121,7271		74,973,3149	no	coding-synonymous	ZNF208	NM_007153.3		249,1774,4176	GG,GA,AA		13.358,28.7319,18.3255		772/1281	22155520	2272,10126	2003	4196	6199	SO:0001819	synonymous_variant	7757	exon4			CTCTACAGTATGA	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.2316T>C	19.37:g.22155520A>G		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	17	6	0.352941	NM_007153		Silent	SNP	ENST00000397126.4	37	CCDS54240.1																																																																																			A|0.814;G|0.186	0.186	strong		0.358	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
OR4B1	119765	hgsc.bcm.edu	37	11	48239071	48239071	+	Missense_Mutation	SNP	C	C	A	rs12292056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48239071C>A	ENST00000309562.2	+	1	728	c.710C>A	c.(709-711)aCc>aAc	p.T237N		NM_001005470.1	NP_001005470.1	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B, member 1	237			T -> N (in dbSNP:rs12292056).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T237N(1)		breast(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						GCCCTCTCCACCTGTGCTTCT	0.463													c|||	485	0.096845	0.1967	0.0605	5008	,	,		22492	0.0605		0.0785	False		,,,				2504	0.044				p.T237N		Atlas-SNP	.											OR4B1,NS,carcinoma,0,1	OR4B1	52	1	1	Substitution - Missense(1)	stomach(1)	c.C710A						PASS	.	C	ASN/THR	837,3565	331.8+/-302.1	85,667,1449	151.0	117.0	129.0		710	5.5	1.0	11	dbSNP_120	129	550,8046	150.6+/-205.5	17,516,3765	yes	missense	OR4B1	NM_001005470.1	65	102,1183,5214	AA,AC,CC		6.3983,19.0141,10.6709	probably-damaging	237/310	48239071	1387,11611	2201	4298	6499	SO:0001583	missense	119765	exon1			TCTCCACCTGTGC	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.710C>A	11.37:g.48239071C>A	ENSP00000311605:p.Thr237Asn	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	245	125	0.510204	NM_001005470	Q6IF75|Q96R64	Missense_Mutation	SNP	ENST00000309562.2	37	CCDS31485.1	215	0.09844322344322344	109	0.22154471544715448	24	0.06629834254143646	31	0.05419580419580419	51	0.06728232189973615	C	23.3	4.393877	0.83011	0.190141	0.063983	ENSG00000175619	ENST00000309562	T	0.40476	1.03	5.5	5.5	0.81552	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000035	T	0.00144	0.0004	H	0.98786	4.33	0.21553	P	0.999645381	D	0.89917	1.0	D	0.97110	1.0	T	0.41945	-0.9480	9	0.87932	D	0	.	16.9603	0.86271	0.0:1.0:0.0:0.0	rs12292056;rs52837392;rs57096167;rs12292056	237	Q8NGF8	OR4B1_HUMAN	N	237	ENSP00000311605:T237N	ENSP00000311605:T237N	T	+	2	0	OR4B1	48195647	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	5.906000	0.69900	2.595000	0.87683	0.502000	0.49764	ACC	C|0.890;A|0.110	0.110	strong		0.463	OR4B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390554.1	NM_001005470	
LNP1	348801	hgsc.bcm.edu	37	3	100170600	100170600	+	Missense_Mutation	SNP	A	A	T	rs386663873|rs76354691|rs71132521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	143	0	0		WXS	Illumina HiSeq	Phase_I	135	12	0.0888889	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		
SMYD2	56950	hgsc.bcm.edu	37	1	214507580	214507580	+	Missense_Mutation	SNP	A	A	G	rs34259050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:214507580A>G	ENST00000366957.5	+	11	1172	c.1150A>G	c.(1150-1152)Atg>Gtg	p.M384V	SMYD2_ENST00000491455.1_3'UTR|SMYD2_ENST00000415093.2_3'UTR	NM_020197.2	NP_064582.2	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	384					negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|RNA polymerase II core binding (GO:0000993)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		CGTGGCCTCCATGTGGTTGAA	0.542													A|||	54	0.0107827	0.0098	0.0115	5008	,	,		20709	0.001		0.0209	False		,,,				2504	0.0112				p.M384V		Atlas-SNP	.											.	SMYD2	40	.	0			c.A1150G						PASS	.	A	VAL/MET	31,4375	36.0+/-67.5	0,31,2172	241.0	230.0	234.0		1150	5.1	1.0	1	dbSNP_126	234	199,8401	87.1+/-149.5	2,195,4103	yes	missense	SMYD2	NM_020197.2	21	2,226,6275	GG,GA,AA		2.314,0.7036,1.7684	benign	384/434	214507580	230,12776	2203	4300	6503	SO:0001583	missense	56950	exon11			GCCTCCATGTGGT	AF226053	CCDS31022.1	1q32.3	2011-07-01			ENSG00000143499	ENSG00000143499		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20982	protein-coding gene	gene with protein product		610663					Standard	NM_020197		Approved	HSKM-B, ZMYND14, KMT3C	uc021pix.1	Q9NRG4	OTTHUMG00000037066	ENST00000366957.5:c.1150A>G	1.37:g.214507580A>G	ENSP00000355924:p.Met384Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	179	86	0.480447	NM_020197	B2R9P9|I6L9H7|Q4V765|Q5VSH9|Q96AI4	Missense_Mutation	SNP	ENST00000366957.5	37	CCDS31022.1	22	0.010073260073260074	4	0.008130081300813009	5	0.013812154696132596	1	0.0017482517482517483	12	0.0158311345646438	A	14.03	2.413182	0.42817	0.007036	0.02314	ENSG00000143499	ENST00000366957	T	0.61392	0.11	6.17	5.05	0.67936	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.30572	0.0769	L	0.48362	1.52	0.80722	D	1	B	0.26512	0.151	B	0.17979	0.02	T	0.21143	-1.0254	10	0.14656	T	0.56	-5.5028	12.297	0.54854	0.9345:0.0:0.0655:0.0	rs34259050	384	Q9NRG4	SMYD2_HUMAN	V	384	ENSP00000355924:M384V	ENSP00000355924:M384V	M	+	1	0	SMYD2	212574203	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.874000	0.48483	1.158000	0.42547	0.533000	0.62120	ATG	A|0.983;G|0.017	0.017	strong		0.542	SMYD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089998.1	NM_020197	
WDR90	197335	hgsc.bcm.edu	37	16	717544	717544	+	Silent	SNP	G	G	C	rs3752492	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:717544G>C	ENST00000293879.4	+	41	5202	c.5202G>C	c.(5200-5202)acG>acC	p.T1734T	WDR90_ENST00000315764.4_Silent_p.T285T|WDR90_ENST00000549091.1_Silent_p.T1736T|WDR90_ENST00000547944.1_Silent_p.T333T|RHOT2_ENST00000315082.4_5'Flank			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	66	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	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	
CIC	23152	hgsc.bcm.edu	37	19	42795554	42795554	+	Silent	SNP	T	T	C	rs10410185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42795554T>C	ENST00000575354.2	+	10	2674	c.2634T>C	c.(2632-2634)gcT>gcC	p.A878A	CIC_ENST00000572681.2_Silent_p.A1787A|CIC_ENST00000160740.3_Silent_p.A878A	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	878	Pro-rich.				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)				AAGTCCTGGCTGCCACTGCAC	0.692			"""Mis, F, S"""		oligodendroglioma								C|||	435	0.086861	0.087	0.0951	5008	,	,		15967	0.0536		0.0586	False		,,,				2504	0.1442				p.A878A		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.T2634C						PASS	.	C		320,4026		10,300,1863	47.0	41.0	43.0		2634	-5.3	0.7	19	dbSNP_119	43	450,8094		14,422,3836	no	coding-synonymous	CIC	NM_015125.3		24,722,5699	CC,CT,TT		5.2669,7.3631,5.9736		878/1609	42795554	770,12120	2173	4272	6445	SO:0001819	synonymous_variant	23152	exon10			CCTGGCTGCCACT	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.2634T>C	19.37:g.42795554T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	132	71	0.537879	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Silent	SNP	ENST00000575354.2	37	CCDS12601.1																																																																																			T|0.924;C|0.076	0.076	strong		0.692	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2		
COL1A1	1277	hgsc.bcm.edu	37	17	48263786	48263786	+	Silent	SNP	G	G	A	rs34940368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48263786G>A	ENST00000225964.5	-	49	4015	c.3897C>T	c.(3895-3897)tgC>tgT	p.C1299C		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	1299	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	TGGGGTACACGCAGGTCTCAC	0.562			T	"""PDGFB, USP6"""	"""dermatofibrosarcoma protuberans, aneurysmal bone cyst """		Osteogenesis imperfecta						G|||	32	0.00638978	0.0227	0.0029	5008	,	,		22768	0.0		0.0	False		,,,				2504	0.0				p.C1299C		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"""collagen, type I, alpha 1"""	yes	M	COL1A1,rectum,carcinoma,0,1	COL1A1	158	1	0			c.C3897T	GRCh37	CM012085	COL1A1	M	rs34940368	scavenged	.	G		75,4331	66.4+/-103.9	0,75,2128	160.0	143.0	149.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3897	-0.3	1.0	17	dbSNP_126	149	0,8600		0,0,4300	no	coding-synonymous	COL1A1	NM_000088.3		0,75,6428	AA,AG,GG		0.0,1.7022,0.5767		1299/1465	48263786	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	1277	exon49			GTACACGCAGGTC	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"""Collagens"""	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.3897C>T	17.37:g.48263786G>A		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	141	63	0.446809	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	37	CCDS11561.1																																																																																			G|0.994;A|0.006	0.006	strong		0.562	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2		
EPC2	26122	hgsc.bcm.edu	37	2	149528738	149528738	+	Missense_Mutation	SNP	A	A	G	rs34444151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:149528738A>G	ENST00000258484.6	+	10	1536	c.1502A>G	c.(1501-1503)aAt>aGt	p.N501S		NM_015630.3	NP_056445.3	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2 (Drosophila)	501					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0516)		TCTCGGACCAATGCTTCCAGT	0.378													A|||	43	0.00858626	0.0265	0.0029	5008	,	,		19522	0.0		0.0	False		,,,				2504	0.0061				p.N501S		Atlas-SNP	.											.	EPC2	57	.	0			c.A1502G						PASS	.	A	SER/ASN	71,3607		1,69,1769	55.0	54.0	54.0		1502	5.4	1.0	2	dbSNP_126	54	4,8166		0,4,4081	yes	missense	EPC2	NM_015630.3	46	1,73,5850	GG,GA,AA		0.049,1.9304,0.633	benign	501/808	149528738	75,11773	1839	4085	5924	SO:0001583	missense	26122	exon10			GGACCAATGCTTC	AF286904	CCDS46422.1	2q23	2008-02-05			ENSG00000135999	ENSG00000135999			24543	protein-coding gene	gene with protein product		611000					Standard	NM_015630		Approved	DKFZP566F2124	uc010zbt.2	Q52LR7	OTTHUMG00000153739	ENST00000258484.6:c.1502A>G	2.37:g.149528738A>G	ENSP00000258484:p.Asn501Ser	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	181	96	0.530387	NM_015630	B3KWT7|D3DP89|Q7L9J1|Q96RR7|Q9NUT8|Q9NVR1|Q9UFM9	Missense_Mutation	SNP	ENST00000258484.6	37	CCDS46422.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	A	14.04	2.415328	0.42817	0.019304	4.9E-4	ENSG00000135999	ENST00000258484	T	0.16324	2.35	5.36	5.36	0.76844	.	0.097920	0.64402	D	0.000002	T	0.05777	0.0151	L	0.40543	1.245	0.80722	D	1	B	0.25521	0.128	B	0.23018	0.043	T	0.01863	-1.1258	10	0.54805	T	0.06	-4.6206	15.6403	0.76993	1.0:0.0:0.0:0.0	rs34444151	501	Q52LR7	EPC2_HUMAN	S	501	ENSP00000258484:N501S	ENSP00000258484:N501S	N	+	2	0	EPC2	149245208	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.325000	0.59234	2.140000	0.66376	0.460000	0.39030	AAT	A|0.992;G|0.008	0.008	strong		0.378	EPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332278.1	NM_015630	
TRIM72	493829	hgsc.bcm.edu	37	16	31235548	31235548	+	Silent	SNP	G	G	C	rs58585879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31235548G>C	ENST00000322122.3	+	7	1190	c.906G>C	c.(904-906)ctG>ctC	p.L302L	RP11-388M20.9_ENST00000576745.1_lincRNA	NM_001008274.3	NP_001008275.2			tripartite motif containing 72, E3 ubiquitin protein ligase											breast(1)|endometrium(2)|large_intestine(2)|lung(9)|skin(1)	15						ACCCGAGCCTGGTGGTGTCTT	0.677													G|||	154	0.0307508	0.1067	0.0086	5008	,	,		12224	0.0		0.002	False		,,,				2504	0.0051				p.L302L		Atlas-SNP	.											.	TRIM72	32	.	0			c.G906C						PASS	.	G		414,3970		20,374,1798	22.0	23.0	23.0		906	2.3	1.0	16	dbSNP_129	23	6,8568		0,6,4281	no	coding-synonymous	TRIM72	NM_001008274.3		20,380,6079	CC,CG,GG		0.07,9.4434,3.2412		302/478	31235548	420,12538	2192	4287	6479	SO:0001819	synonymous_variant	493829	exon7			GAGCCTGGTGGTG	AK090695	CCDS32437.1	16p11.2	2014-02-10	2014-02-10					"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	32671	protein-coding gene	gene with protein product	"""mitsugumin 53"""	613288	"""tripartite motif-containing 72"", ""tripartite motif containing 72"""			20399744, 23354051	Standard	NM_001008274		Approved	MG53	uc002ebn.2	Q6ZMU5		ENST00000322122.3:c.906G>C	16.37:g.31235548G>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	33	10	0.30303	NM_001008274		Silent	SNP	ENST00000322122.3	37	CCDS32437.1																																																																																			G|0.966;C|0.034	0.034	strong		0.677	TRIM72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433567.1	NM_001008274	
KCNQ1	3784	hgsc.bcm.edu	37	11	2683252	2683252	+	Silent	SNP	C	C	T	rs17215465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2683252C>T	ENST00000155840.5	+	11	1563	c.1455C>T	c.(1453-1455)ttC>ttT	p.F485F	KCNQ1_ENST00000335475.5_Silent_p.F358F|KCNQ1OT1_ENST00000597346.1_RNA	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	485					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	CCAACAGCTTCGCCGAGGACC	0.577													C|||	78	0.0155751	0.0514	0.0029	5008	,	,		17275	0.0		0.001	False		,,,				2504	0.0072				p.F485F		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1455T						PASS	.	C	,	211,4193	128.6+/-165.4	4,203,1995	170.0	158.0	162.0		1455,1074	-5.4	0.0	11	dbSNP_125	162	7,8591	5.0+/-18.6	0,7,4292	no	coding-synonymous,coding-synonymous	KCNQ1	NM_000218.2,NM_181798.1	,	4,210,6287	TT,TC,CC		0.0814,4.7911,1.6767	,	485/677,358/550	2683252	218,12784	2202	4299	6501	SO:0001819	synonymous_variant	3784	exon11			CAGCTTCGCCGAG	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6294	protein-coding gene	gene with protein product	"""Jervell and Lange-Nielsen syndrome 1"""	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.1455C>T	11.37:g.2683252C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	150	83	0.553333	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			C|0.983;T|0.017	0.017	strong		0.577	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
MAPK6	5597	hgsc.bcm.edu	37	15	52350879	52350879	+	Silent	SNP	T	T	C	rs2306793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52350879T>C	ENST00000261845.5	+	4	1557	c.750T>C	c.(748-750)gtT>gtC	p.V250V	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	250	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		CTATTCCTGTTGTACATGAGG	0.378													t|||	550	0.109824	0.2458	0.1513	5008	,	,		20218	0.0813		0.006	False		,,,				2504	0.0327				p.V250V		Atlas-SNP	.											.	MAPK6	70	.	0			c.T750C						PASS	.	C		833,3557	329.9+/-301.2	84,665,1446	59.0	54.0	56.0		750	1.6	1.0	15	dbSNP_100	56	109,8477	59.1+/-120.7	0,109,4184	no	coding-synonymous	MAPK6	NM_002748.3		84,774,5630	CC,CT,TT		1.2695,18.9749,7.2596		250/722	52350879	942,12034	2195	4293	6488	SO:0001819	synonymous_variant	5597	exon4			TCCTGTTGTACAT	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"""Mitogen-activated protein kinase cascade / Kinases"""	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.750T>C	15.37:g.52350879T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Silent	SNP	ENST00000261845.5	37	CCDS10147.1																																																																																			T|0.921;C|0.079	0.079	strong		0.378	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748	
TEX11	56159	hgsc.bcm.edu	37	X	69772000	69772000	+	Silent	SNP	A	A	G	rs16991177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:69772000A>G	ENST00000395889.2	-	29	2696	c.2541T>C	c.(2539-2541)gaT>gaC	p.D847D	TEX11_ENST00000374333.2_Silent_p.D832D|TEX11_ENST00000374320.2_Silent_p.D522D|TEX11_ENST00000344304.3_Silent_p.D847D	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	847					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					GGCTCAGAGCATCTTCAAAAT	0.398													.|||	505	0.133775	0.0953	0.1859	3775	,	,		13175	0.0942		0.0278	False		,,,				2504	0.1299				p.D847D		Atlas-SNP	.											.	TEX11	132	.	0			c.T2541C						PASS	.	A	,	396,3439		16,296,68,1320,503	84.0	73.0	77.0		2541,2496	2.5	0.7	X	dbSNP_123	77	287,6441		5,194,83,2229,1789	no	coding-synonymous,coding-synonymous	TEX11	NM_001003811.1,NM_031276.2	,	21,490,151,3549,2292	GG,GA,G,AA,A		4.2658,10.3259,6.466	,	847/941,832/926	69772000	683,9880	2203	4300	6503	SO:0001819	synonymous_variant	56159	exon29			CAGAGCATCTTCA	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"""testis expressed sequence 11"""			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.2541T>C	X.37:g.69772000A>G		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	203	90	0.44335	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Silent	SNP	ENST00000395889.2	37	CCDS35323.1																																																																																			A|0.896;0|0.017	.	strong		0.398	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1		
PSPH	5723	hgsc.bcm.edu	37	7	56085002	56085002	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:56085002C>T	ENST00000395471.3	-	6	1151	c.346G>A	c.(346-348)Gta>Ata	p.V116I	PSPH_ENST00000275605.3_Missense_Mutation_p.V116I|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	116					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)	p.V116I(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			ACATGCTCTACAATACTCCTA	0.393																																					p.V116I		Atlas-SNP	.											PSPH,NS,carcinoma,0,2	PSPH	23	2	1	Substitution - Missense(1)	lung(1)	c.G346A						scavenged	.						87.0	75.0	79.0					7																	56085002		2203	4300	6503	SO:0001583	missense	5723	exon6			GCTCTACAATACT	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.346G>A	7.37:g.56085002C>T	ENSP00000378854:p.Val116Ile	Somatic	482	5	0.0103734		WXS	Illumina HiSeq	Phase_I	507	7	0.0138067	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.432510	0.25813	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626	D;D;D	0.81908	-1.55;-1.55;-1.55	4.85	4.85	0.62838	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.65228	0.2671	N	0.05124	-0.11	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.18263	0.021;0.021	T	0.62992	-0.6736	10	0.02654	T	1	-16.2549	17.1115	0.86676	0.0:1.0:0.0:0.0	.	116;116	Q53EY1;P78330	.;SERB_HUMAN	I	116	ENSP00000275605:V116I;ENSP00000378854:V116I;ENSP00000398653:V116I	ENSP00000275605:V116I	V	-	1	0	PSPH	56052496	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.551000	0.82182	2.297000	0.77311	0.579000	0.79373	GTA	.	.	none		0.393	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
ZNF708	7562	hgsc.bcm.edu	37	19	21476912	21476912	+	Missense_Mutation	SNP	C	C	T	rs112819776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21476912C>T	ENST00000356929.3	-	4	1053	c.856G>A	c.(856-858)Ggc>Agc	p.G286S		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	222					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.G286C(1)		breast(1)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						AAAGCTTTGCCACATTCTTCA	0.383													C|||	27	0.00539137	0.0197	0.0014	5008	,	,		20573	0.0		0.0	False		,,,				2504	0.0				p.G286S		Atlas-SNP	.											ZNF708,NS,carcinoma,0,1	ZNF708	66	1	1	Substitution - Missense(1)	lung(1)	c.G856A						PASS	.	C	SER/GLY	64,4332		0,64,2134	51.0	55.0	54.0		856	1.0	0.6	19	dbSNP_132	54	1,8595		0,1,4297	no	missense	ZNF708	NM_021269.2	56	0,65,6431	TT,TC,CC		0.0116,1.4559,0.5003	possibly-damaging	286/564	21476912	65,12927	2198	4298	6496	SO:0001583	missense	7562	exon4			CTTTGCCACATTC	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"""Zinc fingers, C2H2-type"", ""-"""	12945	protein-coding gene	gene with protein product			"""zinc finger protein 15-like 1 (KOX 8)"", ""zinc finger protein 708"", ""zinc finger protein 708 (KOX8)"""	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.856G>A	19.37:g.21476912C>T	ENSP00000349401:p.Gly286Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	23	9	0.391304	NM_021269	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	.	13.82	2.351563	0.41700	0.014559	1.16E-4	ENSG00000182141	ENST00000356929	T	0.01455	4.87	1.05	1.05	0.20165	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01558	0.0050	L	0.43701	1.375	0.35437	D	0.794531	D	0.76494	0.999	D	0.81914	0.995	T	0.45614	-0.9249	9	0.62326	D	0.03	.	8.9689	0.35894	0.0:1.0:0.0:0.0	.	286	P17019	ZN708_HUMAN	S	286	ENSP00000349401:G286S	ENSP00000349401:G286S	G	-	1	0	ZNF708	21268752	0.049000	0.20398	0.552000	0.28243	0.491000	0.33493	0.979000	0.29500	0.482000	0.27582	0.485000	0.47835	GGC	C|0.994;T|0.006	0.006	strong		0.383	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269	
DNAH14	127602	hgsc.bcm.edu	37	1	225393828	225393828	+	Missense_Mutation	SNP	A	A	G	rs143058170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225393828A>G	ENST00000445597.2	+	27	4852	c.4852A>G	c.(4852-4854)Aat>Gat	p.N1618D	DNAH14_ENST00000439375.2_Missense_Mutation_p.N2023D|DNAH14_ENST00000430092.1_Missense_Mutation_p.N2023D			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1618					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TGAAGTGGACAATCTCTCTCA	0.363													a|||	28	0.00559105	0.0204	0.0014	5008	,	,		16357	0.0		0.0	False		,,,				2504	0.0				p.N2023D		Atlas-SNP	.											.	DNAH14	300	.	0			c.A6067G						PASS	.	A	ASP/ASN	41,1343		0,41,651	74.0	68.0	70.0		6067	4.4	0.3	1	dbSNP_134	70	0,3182		0,0,1591	no	missense	DNAH14	NM_001373.1	23	0,41,2242	GG,GA,AA		0.0,2.9624,0.8979	benign	2023/4516	225393828	41,4525	692	1591	2283	SO:0001583	missense	127602	exon39			GTGGACAATCTCT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.4852A>G	1.37:g.225393828A>G	ENSP00000409472:p.Asn1618Asp	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	A	6.311	0.425409	0.11987	0.029624	0.0	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	D;D;D	0.82893	-1.66;-1.66;-1.66	5.59	4.44	0.53790	.	.	.	.	.	T	0.35393	0.0930	N	0.03917	-0.325	0.80722	D	1	B	0.11235	0.004	B	0.16289	0.015	T	0.50021	-0.8876	9	0.02654	T	1	.	11.2778	0.49176	0.8633:0.0:0.0:0.1367	.	2023	Q0VDD8-4	.	D	1618;2023;2023	ENSP00000409472:N1618D;ENSP00000414402:N2023D;ENSP00000392061:N2023D	ENSP00000414402:N2023D	N	+	1	0	DNAH14	223460451	0.983000	0.35010	0.324000	0.25361	0.992000	0.81027	2.175000	0.42491	0.907000	0.36646	0.481000	0.45027	AAT	A|0.993;G|0.007	0.007	strong		0.363	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
ALPK1	80216	hgsc.bcm.edu	37	4	113352899	113352899	+	Missense_Mutation	SNP	G	G	A	rs2074379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:113352899G>A	ENST00000458497.1	+	11	2475	c.2196G>A	c.(2194-2196)atG>atA	p.M732I	ALPK1_ENST00000177648.9_Missense_Mutation_p.M732I|ALPK1_ENST00000504176.2_Missense_Mutation_p.M654I	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	732			M -> I (in dbSNP:rs2074379). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.5}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CCAAGAATATGGGCACACATC	0.453													G|||	3139	0.626797	0.7224	0.5576	5008	,	,		19724	0.6359		0.6173	False		,,,				2504	0.547				p.M732I		Atlas-SNP	.											.	ALPK1	125	.	0			c.G2196A						PASS	.	G	ILE/MET,ILE/MET	3083,1323	694.3+/-405.8	1074,935,194	63.0	67.0	66.0		2196,2196	3.3	0.0	4	dbSNP_96	66	5420,3180	650.9+/-400.8	1705,2010,585	yes	missense,missense	ALPK1	NM_001102406.1,NM_025144.3	10,10	2779,2945,779	AA,AG,GG		36.9767,30.0272,34.6225	benign,benign	732/1245,732/1245	113352899	8503,4503	2203	4300	6503	SO:0001583	missense	80216	exon11			GAATATGGGCACA	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.2196G>A	4.37:g.113352899G>A	ENSP00000398048:p.Met732Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	1394	0.6382783882783882	343	0.6971544715447154	200	0.5524861878453039	376	0.6573426573426573	475	0.6266490765171504	G	6.077	0.382466	0.11524	0.699728	0.630233	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.02177	4.48;4.48;4.41	5.22	3.31	0.37934	.	0.909044	0.09685	N	0.769236	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.11916	-1.0568	9	0.06099	T	0.92	-2.2316	10.9258	0.47189	0.0846:0.1407:0.7747:0.0	rs2074379;rs52812592;rs60193682;rs2074379	654;732	F5H138;Q96QP1	.;ALPK1_HUMAN	I	732;732;654	ENSP00000398048:M732I;ENSP00000177648:M732I;ENSP00000426044:M654I	ENSP00000177648:M732I	M	+	3	0	ALPK1	113572348	0.005000	0.15991	0.002000	0.10522	0.023000	0.10783	0.648000	0.24828	1.141000	0.42275	0.655000	0.94253	ATG	G|0.353;A|0.647	0.647	strong		0.453	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
LRRC8E	80131	hgsc.bcm.edu	37	19	7963976	7963976	+	Missense_Mutation	SNP	T	T	C	rs2115108	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7963976T>C	ENST00000306708.6	+	3	670	c.569T>C	c.(568-570)aTg>aCg	p.M190T	AC010336.1_ENST00000539278.1_3'UTR	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	190			M -> T (in dbSNP:rs2115108). {ECO:0000269|PubMed:17974005}.		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						ATAGTGGCCATGGCAGGGACC	0.652													C|||	1407	0.28095	0.3563	0.2046	5008	,	,		17043	0.2629		0.325	False		,,,				2504	0.2065				p.M190T		Atlas-SNP	.											.	LRRC8E	67	.	0			c.T569C						PASS	.	C	THR/MET	1520,2864		277,966,949	28.0	36.0	33.0		569	-0.7	0.0	19	dbSNP_96	33	2638,5940		427,1784,2078	no	missense	LRRC8E	NM_025061.3	81	704,2750,3027	CC,CT,TT		30.7531,34.6715,32.0784	benign	190/797	7963976	4158,8804	2192	4289	6481	SO:0001583	missense	80131	exon4			TGGCCATGGCAGG		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.569T>C	19.37:g.7963976T>C	ENSP00000306524:p.Met190Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Missense_Mutation	SNP	ENST00000306708.6	37	CCDS12189.1	659	0.3017399267399267	195	0.39634146341463417	73	0.20165745856353592	155	0.270979020979021	236	0.3113456464379947	C	0.004	-2.370692	0.00209	0.346715	0.307531	ENSG00000171017	ENST00000306708	T	0.24908	1.83	5.19	-0.706	0.11249	.	1.138340	0.06349	N	0.709546	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	0.47368	-0.9123	9	0.13108	T	0.6	.	1.9981	0.03461	0.1299:0.4175:0.1272:0.3253	rs2115108;rs3745381;rs60796256	190	Q6NSJ5	LRC8E_HUMAN	T	190	ENSP00000306524:M190T	ENSP00000306524:M190T	M	+	2	0	LRRC8E	7869976	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.295000	0.19065	-0.101000	0.12219	-0.735000	0.03563	ATG	T|0.676;C|0.324	0.324	strong		0.652	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
ZNF614	80110	hgsc.bcm.edu	37	19	52520518	52520518	+	Silent	SNP	T	T	C	rs73934728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52520518T>C	ENST00000270649.6	-	5	877	c.333A>G	c.(331-333)agA>agG	p.R111R	ZNF614_ENST00000356322.6_Silent_p.R111R	NM_025040.3	NP_079316.2	Q8N883	ZN614_HUMAN	zinc finger protein 614	111					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(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00513)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GTACAATATTTCTAAGTGTAT	0.358													T|||	241	0.048123	0.121	0.0317	5008	,	,		18990	0.006		0.0408	False		,,,				2504	0.0123				p.R111R		Atlas-SNP	.											.	ZNF614	58	.	0			c.A333G						PASS	.	T		400,4006	196.7+/-221.0	13,374,1816	86.0	82.0	83.0		333	2.8	0.5	19	dbSNP_130	83	217,8383	89.4+/-151.6	2,213,4085	no	coding-synonymous	ZNF614	NM_025040.3		15,587,5901	CC,CT,TT		2.5233,9.0785,4.744		111/586	52520518	617,12389	2203	4300	6503	SO:0001819	synonymous_variant	80110	exon5			AATATTTCTAAGT	BC022246	CCDS12847.1	19q13.41	2013-01-08				ENSG00000142556		"""Zinc fingers, C2H2-type"", ""-"""	24722	protein-coding gene	gene with protein product						12477932	Standard	NM_025040		Approved	FLJ21941	uc002pyj.3	Q8N883		ENST00000270649.6:c.333A>G	19.37:g.52520518T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	150	87	0.58	NM_025040	Q494T8|Q8TCF4|Q9BSN8	Silent	SNP	ENST00000270649.6	37	CCDS12847.1																																																																																			T|0.949;C|0.051	0.051	strong		0.358	ZNF614-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462407.1	NM_025040	
ATP11AUN	400165	hgsc.bcm.edu	37	13	113333809	113333809	+	Missense_Mutation	SNP	G	G	A	rs114091399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113333809G>A	ENST00000356049.1	+	2	874	c.116G>A	c.(115-117)gGt>gAt	p.G39D		NM_207440.1	NP_997323.1	Q6ZP68	ATPUN_HUMAN		39										breast(1)|lung(2)|ovary(1)|prostate(1)	5	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(43;0.201)			GACCCGGCAGGTCTGGAGGGA	0.602													G|||	71	0.0141773	0.0507	0.0058	5008	,	,		14668	0.0		0.0	False		,,,				2504	0.0				p.G39D		Atlas-SNP	.											.	C13orf35	13	.	0			c.G116A						PASS	.	G	ASP/GLY	194,4212	122.5+/-159.9	3,188,2012	38.0	40.0	40.0		116	-0.7	0.0	13	dbSNP_132	40	9,8591	7.1+/-27.0	0,9,4291	yes	missense	C13orf35	NM_207440.1	94	3,197,6303	AA,AG,GG		0.1047,4.4031,1.5608	benign	39/122	113333809	203,12803	2203	4300	6503	SO:0001583	missense	400165	exon2			CGGCAGGTCTGGA																												ENST00000356049.1:c.116G>A	13.37:g.113333809G>A	ENSP00000348337:p.Gly39Asp	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	108	51	0.472222	NM_207440		Missense_Mutation	SNP	ENST00000356049.1	37	CCDS9526.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	2.915	-0.224514	0.06061	0.044031	0.001047	ENSG00000197595	ENST00000356049	.	.	.	1.24	-0.688	0.11317	.	.	.	.	.	T	0.03390	0.0098	N	0.08118	0	0.09310	N	1	D	0.54601	0.967	P	0.46629	0.522	T	0.07597	-1.0764	8	0.87932	D	0	.	1.9567	0.03378	0.2212:0.0:0.4635:0.3153	.	39	Q6ZP68	CM035_HUMAN	D	39	.	ENSP00000348337:G39D	G	+	2	0	C13orf35	112381810	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.464000	0.02359	-0.287000	0.09064	-0.372000	0.07161	GGT	G|0.985;A|0.015	0.015	strong		0.602	C13orf35-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000126522.2		
MYLIP	29116	hgsc.bcm.edu	37	6	16145325	16145325	+	Missense_Mutation	SNP	A	A	G	rs9370867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:16145325A>G	ENST00000356840.3	+	6	1223	c.1025A>G	c.(1024-1026)aAc>aGc	p.N342S	MYLIP_ENST00000349606.4_Missense_Mutation_p.N161S	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	342			N -> S (in dbSNP:rs9370867). {ECO:0000269|PubMed:10593918, ECO:0000269|PubMed:11042152, ECO:0000269|PubMed:15498874, ECO:0000269|Ref.2}.		cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			GTTTCAAGAAACAACCAGAGC	0.517													G|||	3856	0.769968	0.9652	0.6945	5008	,	,		22511	0.9435		0.4861	False		,,,				2504	0.6728				p.N342S		Atlas-SNP	.											.	MYLIP	44	.	0			c.A1025G						PASS	.	G	SER/ASN	3906,500	231.7+/-245.5	1738,430,35	100.0	103.0	102.0		1025	3.8	0.0	6	dbSNP_119	102	4094,4506	593.3+/-393.1	967,2160,1173	yes	missense	MYLIP	NM_013262.3	46	2705,2590,1208	GG,GA,AA		47.6047,11.3482,38.4899	benign	342/446	16145325	8000,5006	2203	4300	6503	SO:0001583	missense	29116	exon6			CAAGAAACAACCA	AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"""	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.1025A>G	6.37:g.16145325A>G	ENSP00000349298:p.Asn342Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_013262	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Missense_Mutation	SNP	ENST00000356840.3	37	CCDS4536.1	1620	0.7417582417582418	469	0.9532520325203252	239	0.6602209944751382	541	0.9458041958041958	371	0.4894459102902375	G	0.035	-1.312768	0.01331	0.886518	0.476047	ENSG00000007944	ENST00000356840;ENST00000349606	D;T	0.81908	-1.55;1.16	5.65	3.85	0.44370	.	0.514420	0.25666	N	0.029102	T	0.39200	0.1069	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08868	-1.0701	9	0.02654	T	1	.	9.9368	0.41556	0.1268:0.1148:0.7584:0.0	rs9370867;rs59084742;rs9370867	342	Q8WY64	MYLIP_HUMAN	S	342;161	ENSP00000349298:N342S;ENSP00000008686:N161S	ENSP00000008686:N161S	N	+	2	0	MYLIP	16253304	0.018000	0.18449	0.000000	0.03702	0.446000	0.32137	1.572000	0.36461	0.415000	0.25817	-0.119000	0.15052	AAC	A|0.313;G|0.687	0.687	strong		0.517	MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043864.1	NM_013262	
CAPN12	147968	hgsc.bcm.edu	37	19	39227889	39227889	+	Silent	SNP	C	C	T	rs202082771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39227889C>T	ENST00000328867.4	-	10	1577	c.1269G>A	c.(1267-1269)aaG>aaA	p.K423K	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Silent_p.K274K	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	423	Domain III.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GGACCGTGCACTTGGGCGTGC	0.692													C|||	11	0.00219649	0.0083	0.0	5008	,	,		5252	0.0		0.0	False		,,,				2504	0.0				p.K423K		Atlas-SNP	.											.	CAPN12	43	.	0			c.G1269A						PASS	.	C		14,4130		0,14,2058	15.0	13.0	14.0		1269	0.4	1.0	19		14	0,8264		0,0,4132	yes	coding-synonymous	CAPN12	NM_144691.3		0,14,6190	TT,TC,CC		0.0,0.3378,0.1128		423/720	39227889	14,12394	2072	4132	6204	SO:0001819	synonymous_variant	147968	exon10			CGTGCACTTGGGC	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1269G>A	19.37:g.39227889C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			.	.	weak		0.692	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
FOSB	2354	hgsc.bcm.edu	37	19	45971961	45971961	+	Silent	SNP	C	C	G	rs2282695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45971961C>G	ENST00000353609.3	+	1	709	c.117C>G	c.(115-117)gcC>gcG	p.A39A	FOSB_ENST00000417353.2_Silent_p.A39A|FOSB_ENST00000443841.2_Silent_p.A39A|FOSB_ENST00000592436.1_Silent_p.A39A|FOSB_ENST00000591858.1_Silent_p.A39A|FOSB_ENST00000590335.1_Silent_p.A39A|FOSB_ENST00000586615.1_5'Flank|FOSB_ENST00000585836.1_Silent_p.A39A|FOSB_ENST00000592811.1_5'Flank|ERCC1_ENST00000423698.2_Intron	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	55	0	0		WXS	Illumina HiSeq	Phase_I	55	54	0.981818	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	
BHLHB9	80823	hgsc.bcm.edu	37	X	102005371	102005371	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102005371A>T	ENST00000372735.1	+	4	2033	c.1448A>T	c.(1447-1449)aAt>aTt	p.N483I	BHLHB9_ENST00000447531.1_Missense_Mutation_p.N483I|BHLHB9_ENST00000361229.4_Missense_Mutation_p.N483I|BHLHB9_ENST00000448867.1_Missense_Mutation_p.N483I|BHLHB9_ENST00000457056.1_Missense_Mutation_p.N483I			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	483					learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GACATGATCAATATGAAGGCA	0.363																																					p.N483I		Atlas-SNP	.											.	BHLHB9	60	.	0			c.A1448T						PASS	.						120.0	119.0	119.0					X																	102005371		2203	4300	6503	SO:0001583	missense	80823	exon2			TGATCAATATGAA	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"""Basic helix-loop-helix proteins"", ""Armadillo repeat containing"""	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.1448A>T	X.37:g.102005371A>T	ENSP00000361820:p.Asn483Ile	Somatic	438	0	0		WXS	Illumina HiSeq	Phase_I	429	59	0.137529	NM_001142530	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	37	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.240331	0.39598	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46	4.24	1.84	0.25277	Armadillo-like helical (1);Armadillo-type fold (1);	0.647734	0.13738	N	0.366174	T	0.23210	0.0561	N	0.08118	0	0.09310	N	1	D	0.53462	0.96	P	0.57101	0.813	T	0.08411	-1.0723	9	.	.	.	-29.9634	5.1019	0.14764	0.7516:0.0:0.2484:0.0	.	483	Q6PI77	BHLH9_HUMAN	I	483	ENSP00000403226:N483I;ENSP00000354675:N483I;ENSP00000405893:N483I;ENSP00000391722:N483I;ENSP00000361820:N483I	.	N	+	2	0	BHLHB9	101892027	0.006000	0.16342	0.005000	0.12908	0.995000	0.86356	0.712000	0.25779	0.262000	0.21774	0.339000	0.21740	AAT	.	.	none		0.363	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639	
OR8G5	219865	hgsc.bcm.edu	37	11	124135143	124135143	+	Missense_Mutation	SNP	G	G	A	rs200012972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124135143G>A	ENST00000524943.2	+	1	421	c.421G>A	c.(421-423)Gtt>Att	p.V141I	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	141						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		CTTCTTCCTCGTTTTTGCTAT	0.463													g|||	27	0.00539137	0.0197	0.0014	5008	,	,		23436	0.0		0.0	False		,,,				2504	0.0				p.V141I	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.G421A						PASS	.	G	ILE/VAL	38,4260		0,38,2111	165.0	155.0	158.0		421	-7.2	0.0	11		158	0,8562		0,0,4281	no	missense	OR8G5	NM_001005198.1	29	0,38,6392	AA,AG,GG		0.0,0.8841,0.2955		141/347	124135143	38,12822	2149	4281	6430	SO:0001583	missense	219865	exon1			TTCCTCGTTTTTG	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.421G>A	11.37:g.124135143G>A	ENSP00000477014:p.Val141Ile	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	258	127	0.492248	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	37																																																																																				.	.	weak		0.463	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
POTEB2	100287399	hgsc.bcm.edu	37	15	21071492	21071492	+	Missense_Mutation	SNP	G	G	T	rs536533463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:21071492G>T	ENST00000454856.4	-	1	151	c.119C>A	c.(118-120)aCg>aAg	p.T40K		NM_001277303.1	NP_001264232.1	H3BUK9	POTB2_HUMAN	POTE ankyrin domain family, member B2	40																	CACATTGCTCGTGCCGCTCCC	0.582													G|||	2239	0.447085	0.4206	0.513	5008	,	,		15782	0.4742		0.4274	False		,,,				2504	0.4284				p.T40K		Atlas-SNP	.											ENSG00000230031,NS,carcinoid-endocrine_tumour,0,1	POTEB	22	1	0			c.C119A						scavenged	.																																			SO:0001583	missense	339010	exon1			TTGCTCGTGCCGC		CCDS59248.1	15q11.2	2014-01-29			ENSG00000230031	ENSG00000230031		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	48327	protein-coding gene	gene with protein product							Standard	NM_001277303		Approved			H3BUK9	OTTHUMG00000185829	ENST00000454856.4:c.119C>A	15.37:g.21071492G>T	ENSP00000456953:p.Thr40Lys	Somatic	325	101	0.310769		WXS	Illumina HiSeq	Phase_I	465	145	0.311828	NM_207355		Missense_Mutation	SNP	ENST00000454856.4	37	CCDS59248.1																																																																																			.	.	weak		0.582	POTEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471435.1		
NDUFV2	4729	hgsc.bcm.edu	37	18	9117899	9117899	+	Missense_Mutation	SNP	G	G	A	rs75362221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9117899G>A	ENST00000318388.6	+	2	232	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	RP11-143J12.3_ENST00000579467.1_RNA|NDUFV2_ENST00000400033.1_Missense_Mutation_p.V43M|RP11-21J18.1_ENST00000579126.1_RNA	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	40					cardiac muscle tissue development (GO:0048738)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|nervous system development (GO:0007399)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|lung(4)|ovary(1)|stomach(1)	7						AGCTTTATTTGTGGTAAGTAA	0.289													G|||	20	0.00399361	0.0151	0.0	5008	,	,		17599	0.0		0.0	False		,,,				2504	0.0				p.V40M		Atlas-SNP	.											.	NDUFV2	17	.	0			c.G118A						PASS	.	G	MET/VAL	48,4358	45.3+/-79.5	0,48,2155	54.0	59.0	57.0		118	5.5	1.0	18	dbSNP_131	57	0,8588		0,0,4294	yes	missense	NDUFV2	NM_021074.4	21	0,48,6449	AA,AG,GG		0.0,1.0894,0.3694	benign	40/250	9117899	48,12946	2203	4294	6497	SO:0001583	missense	4729	exon2			TTATTTGTGGTAA	X84421	CCDS11842.1	18p11.22	2011-07-04	2002-08-29		ENSG00000178127	ENSG00000178127	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7717	protein-coding gene	gene with protein product	"""complex I 24kDa subunit"", ""NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial"""	600532	"""NADH dehydrogenase (ubiquinone) flavoprotein 2 (24kD)"""			9763677, 7607668	Standard	NM_021074		Approved	CI-24k	uc002knu.3	P19404	OTTHUMG00000131593	ENST00000318388.6:c.118G>A	18.37:g.9117899G>A	ENSP00000327268:p.Val40Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_021074	Q9BV41	Missense_Mutation	SNP	ENST00000318388.6	37	CCDS11842.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	G	17.70	3.453208	0.63290	0.010894	0.0	ENSG00000178127	ENST00000318388;ENST00000400033	T;T	0.52057	0.69;0.68	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	M	0.89478	3.035	0.80722	D	1	B	0.30406	0.278	B	0.32677	0.15	T	0.59595	-0.7425	10	0.72032	D	0.01	-16.8798	14.9056	0.70715	0.0709:0.0:0.9291:0.0	.	40	P19404	NDUV2_HUMAN	M	40;43	ENSP00000327268:V40M;ENSP00000382908:V43M	ENSP00000327268:V40M	V	+	1	0	NDUFV2	9107899	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.872000	0.69636	2.738000	0.93877	0.585000	0.79938	GTG	G|0.996;A|0.004	0.004	strong		0.289	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254475.2	NM_021074	
GOLGA1	2800	hgsc.bcm.edu	37	9	127661645	127661645	+	Missense_Mutation	SNP	G	G	A	rs634710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127661645G>A	ENST00000373555.4	-	14	1607	c.1274C>T	c.(1273-1275)aCg>aTg	p.T425M	AL354928.1_ENST00000580940.1_RNA	NM_002077.3	NP_002068	Q92805	GOGA1_HUMAN	golgin A1	425	Gln-rich.		T -> M (in dbSNP:rs634710). {ECO:0000269|PubMed:15489334}.		protein targeting to Golgi (GO:0000042)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)				NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	20						AGCTGCCCGCGTTCTCTCCAG	0.637													G|||	2004	0.40016	0.2965	0.353	5008	,	,		17342	0.5694		0.4254	False		,,,				2504	0.3732				p.T425M		Atlas-SNP	.											.	GOLGA1	60	.	0			c.C1274T						PASS	.	G	MET/THR	1359,2935		238,883,1026	44.0	36.0	39.0		1274	3.5	0.0	9	dbSNP_83	39	3473,4877		832,1809,1534	yes	missense	GOLGA1	NM_002077.3	81	1070,2692,2560	AA,AG,GG		41.5928,31.6488,38.2158	possibly-damaging	425/768	127661645	4832,7812	2147	4175	6322	SO:0001583	missense	2800	exon14			GCCCGCGTTCTCT	U51587	CCDS6860.1	9q34.11	2010-02-12	2010-02-12		ENSG00000136935	ENSG00000136935			4424	protein-coding gene	gene with protein product		602502	"""golgi autoantigen, golgin subfamily a, 1"""			9324025	Standard	NM_002077		Approved	golgin-97, MGC33154	uc004bpc.3	Q92805	OTTHUMG00000020665	ENST00000373555.4:c.1274C>T	9.37:g.127661645G>A	ENSP00000362656:p.Thr425Met	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	46	0.666667	NM_002077	Q5T164|Q8IYZ9	Missense_Mutation	SNP	ENST00000373555.4	37	CCDS6860.1	921	0.4217032967032967	150	0.3048780487804878	130	0.35911602209944754	339	0.5926573426573427	302	0.39841688654353563	G	11.28	1.590714	0.28357	0.316488	0.415928	ENSG00000136935	ENST00000373555	T	0.22539	1.95	5.36	3.5	0.40072	.	0.913583	0.09089	U	0.850191	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	D	0.54772	0.968	B	0.35182	0.197	T	0.38693	-0.9649	9	0.51188	T	0.08	-0.0077	7.3442	0.26654	0.0889:0.1684:0.7427:0.0	rs634710;rs3816271;rs16927715;rs17855565;rs52820334;rs56548659;rs58712407;rs634710	425	Q92805	GOGA1_HUMAN	M	425	ENSP00000362656:T425M	ENSP00000362656:T425M	T	-	2	0	GOLGA1	126701466	0.024000	0.19004	0.001000	0.08648	0.002000	0.02628	1.416000	0.34759	0.800000	0.34041	-0.150000	0.13652	ACG	G|0.595;T|0.005	.	strong		0.637	GOLGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054049.1	NM_002077	
SLC9A3	6550	hgsc.bcm.edu	37	5	476353	476353	+	Silent	SNP	C	C	T	rs2230437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:476353C>T	ENST00000264938.3	-	13	2040	c.2031G>A	c.(2029-2031)gcG>gcA	p.A677A	CTD-2228K2.7_ENST00000606319.1_RNA|SLC9A3_ENST00000514375.1_Silent_p.A668A|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	677					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)	p.A677A(1)		NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			ACAGCTTGGCCGCCTTCTTGT	0.642													C|||	1062	0.212061	0.1377	0.3112	5008	,	,		16387	0.0347		0.4115	False		,,,				2504	0.2198				p.A677A		Atlas-SNP	.											SLC9A3,NS,carcinoma,0,1	SLC9A3	89	1	1	Substitution - coding silent(1)	prostate(1)	c.G2031A						PASS	.	C		788,3616	316.3+/-294.6	73,642,1487	61.0	60.0	61.0		2031	-9.5	0.0	5	dbSNP_98	61	3384,5216	499.2+/-374.9	689,2006,1605	no	coding-synonymous	SLC9A3	NM_004174.2		762,2648,3092	TT,TC,CC		39.3488,17.8928,32.0824		677/835	476353	4172,8832	2202	4300	6502	SO:0001819	synonymous_variant	6550	exon13			CTTGGCCGCCTTC		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"""Solute carriers"""	11073	protein-coding gene	gene with protein product		182307	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3"""	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.2031G>A	5.37:g.476353C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																			C|0.706;T|0.294	0.294	strong		0.642	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	
KRT72	140807	hgsc.bcm.edu	37	12	52992812	52992812	+	Missense_Mutation	SNP	T	T	C	rs11170187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52992812T>C	ENST00000537672.2	-	2	521	c.511A>G	c.(511-513)Aac>Gac	p.N171D	KRT72_ENST00000354310.4_Missense_Mutation_p.N171D|KRT72_ENST00000293745.2_Missense_Mutation_p.N171D|KRT72_ENST00000398066.3_5'UTR|RP11-641A6.2_ENST00000551089.1_RNA	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	171	Linker 1.|Rod.		N -> D (in dbSNP:rs11170187). {ECO:0000269|PubMed:14702039}.			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)		GGCTCCAGGTTCTTCCTGCAG	0.557													T|||	1864	0.372204	0.1906	0.2406	5008	,	,		19466	0.5655		0.3638	False		,,,				2504	0.5204				p.N171D		Atlas-SNP	.											.	KRT72	70	.	0			c.A511G						PASS	.	T	ASP/ASN,ASP/ASN,ASP/ASN	1139,3267	405.5+/-333.5	156,827,1220	152.0	139.0	143.0		511,511,511	4.1	0.7	12	dbSNP_120	143	3282,5318	492.0+/-373.2	599,2084,1617	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	23,23,23	755,2911,2837	CC,CT,TT		38.1628,25.8511,33.992	benign,benign,benign	171/512,171/470,171/512	52992812	4421,8585	2203	4300	6503	SO:0001583	missense	140807	exon2			CCAGGTTCTTCCT	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.511A>G	12.37:g.52992812T>C	ENSP00000441160:p.Asn171Asp	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	218	116	0.53211	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	784|784	0.358974358974359|0.358974358974359	103|103	0.20934959349593496|0.20934959349593496	83|83	0.2292817679558011|0.2292817679558011	308|308	0.5384615384615384|0.5384615384615384	290|290	0.38258575197889183|0.38258575197889183	T|T	15.93|15.93	2.978363|2.978363	0.53720|0.53720	0.258511|0.258511	0.381628|0.381628	ENSG00000170486|ENSG00000170486	ENST00000549979|ENST00000537672;ENST00000293745;ENST00000354310	.|T;T;T	.|0.71698	.|-0.59;-0.59;-0.59	5.25|5.25	4.08|4.08	0.47627|0.47627	.|Filament (1);	.|0.394845	.|0.21341	.|N	.|0.076127	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.84948|0.84948	2.725|2.725	0.09310|0.09310	P|P	0.9999999999996898|0.9999999999996898	.|B	.|0.15141	.|0.012	.|B	.|0.22880	.|0.042	T|T	0.38628|0.38628	-0.9652|-0.9652	4|9	.|0.62326	.|D	.|0.03	.|.	8.6797|8.6797	0.34201|0.34201	0.1276:0.0:0.1335:0.7389|0.1276:0.0:0.1335:0.7389	rs11170187;rs11170187|rs11170187;rs11170187	.|171	.|Q14CN4	.|K2C72_HUMAN	G|D	167|171	.|ENSP00000441160:N171D;ENSP00000293745:N171D;ENSP00000346269:N171D	.|ENSP00000293745:N171D	E|N	-|-	2|1	0|0	KRT72|KRT72	51279079|51279079	0.988000|0.988000	0.35896|0.35896	0.702000|0.702000	0.30337|0.30337	0.982000|0.982000	0.71751|0.71751	2.780000|2.780000	0.47742|0.47742	1.065000|1.065000	0.40693|0.40693	0.459000|0.459000	0.35465|0.35465	GAA|AAC	T|0.649;C|0.351	0.351	strong		0.557	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
ZFP28	140612	hgsc.bcm.edu	37	19	57066013	57066013	+	Missense_Mutation	SNP	C	C	T	rs10409531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57066013C>T	ENST00000301318.3	+	8	1930	c.1859C>T	c.(1858-1860)gCg>gTg	p.A620V	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	620			A -> V (in dbSNP:rs10409531).		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.A620V(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)		TTTGAATGTGCGGAGTGTGGA	0.428													C|||	2048	0.408946	0.5953	0.304	5008	,	,		20994	0.2986		0.3509	False		,,,				2504	0.4049				p.A620V	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											ZFP28,NS,carcinoma,0,1	ZFP28	99	1	1	Substitution - Missense(1)	stomach(1)	c.C1859T						PASS	.	C	VAL/ALA	2432,1974	616.5+/-392.8	666,1100,437	97.0	107.0	103.0		1859	0.9	1.0	19	dbSNP_119	103	2867,5733	449.6+/-362.1	497,1873,1930	yes	missense	ZFP28	NM_020828.1	64	1163,2973,2367	TT,TC,CC		33.3372,44.8025,40.7427	benign	620/869	57066013	5299,7707	2203	4300	6503	SO:0001583	missense	140612	exon8			AATGTGCGGAGTG		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.1859C>T	19.37:g.57066013C>T	ENSP00000301318:p.Ala620Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	818	0.37454212454212454	284	0.5772357723577236	112	0.30939226519337015	160	0.27972027972027974	262	0.34564643799472294	C	11.19	1.566773	0.28003	0.551975	0.333372	ENSG00000196867	ENST00000301318	T	0.07688	3.17	4.23	0.896	0.19253	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.303860	0.23997	N	0.042507	T	0.00012	0.0000	N	0.17872	0.535	0.58432	P	4.000000000004E-6	B	0.29909	0.261	B	0.31614	0.133	T	0.26430	-1.0103	9	0.44086	T	0.13	.	6.5728	0.22549	0.1344:0.5349:0.3307:0.0	rs10409531;rs17305444;rs52820939;rs56805806;rs10409531	620	Q8NHY6	ZFP28_HUMAN	V	620	ENSP00000301318:A620V	ENSP00000301318:A620V	A	+	2	0	ZFP28	61757825	0.000000	0.05858	0.988000	0.46212	0.984000	0.73092	-1.939000	0.01545	0.536000	0.28733	-0.235000	0.12190	GCG	C|0.594;T|0.406	0.406	strong		0.428	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
NFATC3	4775	hgsc.bcm.edu	37	16	68225197	68225197	+	Silent	SNP	C	C	T	rs140991156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:68225197C>T	ENST00000346183.3	+	9	2649	c.2625C>T	c.(2623-2625)acC>acT	p.T875T	NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Silent_p.T875T|SNORA48_ENST00000391143.1_RNA|NFATC3_ENST00000329524.4_Silent_p.T875T|NFATC3_ENST00000349223.5_Silent_p.T875T	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	875					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|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)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		CTGTGCATACCCTGCCTCATC	0.443																																					p.T875T		Atlas-SNP	.											.	NFATC3	190	.	0			c.C2625T						PASS	.	C	,,	4,4392	8.1+/-20.4	0,4,2194	199.0	181.0	187.0		2625,2625,2625	-1.8	0.4	16	dbSNP_134	187	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	NFATC3	NM_004555.3,NM_173163.2,NM_173165.2	,,	0,4,6494	TT,TC,CC		0.0,0.091,0.0308	,,	875/1069,875/1066,875/1076	68225197	4,12992	2198	4300	6498	SO:0001819	synonymous_variant	4775	exon9			GCATACCCTGCCT	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.2625C>T	16.37:g.68225197C>T		Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	251	125	0.498008	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Silent	SNP	ENST00000346183.3	37	CCDS10860.1																																																																																			C|1.000;T|0.000	0.000	strong		0.443	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555	
MUC17	140453	hgsc.bcm.edu	37	7	100683067	100683067	+	Silent	SNP	C	C	T	rs112360991		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100683067C>T	ENST00000306151.4	+	3	8434	c.8370C>T	c.(8368-8370)tcC>tcT	p.S2790S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2790	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)					AAGCCAGTTCCTCTCCTACAA	0.507																																					p.S2790S		Atlas-SNP	.											.	MUC17	804	.	0			c.C8370T						PASS	.						257.0	254.0	255.0					7																	100683067		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CAGTTCCTCTCCT	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.8370C>T	7.37:g.100683067C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	181	21	0.116022	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			C|0.500;T|0.500	0.500	weak		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
BCOR	54880	hgsc.bcm.edu	37	X	39932907	39932907	+	Silent	SNP	T	T	C	rs6520618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:39932907T>C	ENST00000378444.4	-	4	1920	c.1692A>G	c.(1690-1692)gcA>gcG	p.A564A	BCOR_ENST00000378455.4_Silent_p.A564A|BCOR_ENST00000397354.3_Silent_p.A564A|BCOR_ENST00000342274.4_Silent_p.A564A	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	564					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						CTGGGCGGCCTGCACTCGACA	0.592			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic						t|||	1978	0.523974	0.6884	0.1657	3775	,	,		13235	0.5258		0.0765	False		,,,				2504	0.3538				p.A564A		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.A1692G						PASS	.	C	,,,	3052,781		1053,500,446,78,125	81.0	64.0	70.0		1692,1692,1692,1692	-11.2	0.0	X	dbSNP_116	70	766,5962		38,467,223,1923,1649	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCOR	NM_001123383.1,NM_001123384.1,NM_001123385.1,NM_017745.5	,,,	1091,967,669,2001,1774	CC,CT,C,TT,T		11.3853,20.3757,36.1519	,,,	564/1722,564/1704,564/1756,564/1722	39932907	3818,6743	2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			GCGGCCTGCACTC	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.1692A>G	X.37:g.39932907T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			0|0.003;C|0.438	0.438	strong		0.592	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
CEACAM8	1088	hgsc.bcm.edu	37	19	43087428	43087428	+	Missense_Mutation	SNP	A	A	C	rs8103051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43087428A>C	ENST00000244336.5	-	5	1121	c.1020T>G	c.(1018-1020)atT>atG	p.I340M	CEACAM8_ENST00000599005.1_Missense_Mutation_p.I42M|LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000594624.2_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	340			I -> M (in dbSNP:rs8103051).		immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				CCAGTACTCCAATCATGATGC	0.458													A|||	359	0.0716853	0.2572	0.0231	5008	,	,		21532	0.0		0.003	False		,,,				2504	0.0				p.I340M		Atlas-SNP	.											.	CEACAM8	44	.	0			c.T1020G						PASS	.	A	MET/ILE	878,3528	342.0+/-307.0	92,694,1417	99.0	89.0	93.0		1020	0.6	0.1	19	dbSNP_116	93	18,8582	10.5+/-38.8	0,18,4282	no	missense	CEACAM8	NM_001816.3	10	92,712,5699	CC,CA,AA		0.2093,19.9274,6.8891	probably-damaging	340/350	43087428	896,12110	2203	4300	6503	SO:0001583	missense	1088	exon5			TACTCCAATCATG	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.1020T>G	19.37:g.43087428A>C	ENSP00000244336:p.Ile340Met	Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	318	157	0.493711	NM_001816	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	37	CCDS12610.1	124	0.056776556776556776	110	0.22357723577235772	11	0.03038674033149171	0	0.0	3	0.00395778364116095	a	11.22	1.574497	0.28092	0.199274	0.002093	ENSG00000124469	ENST00000244336	T	0.21734	1.99	1.7	0.575	0.17374	.	.	.	.	.	T	0.00039	0.0001	M	0.78049	2.395	0.80722	P	0.0	D	0.76494	0.999	D	0.63488	0.915	T	0.05750	-1.0866	8	0.87932	D	0	.	3.7257	0.08474	0.6637:0.0:0.0:0.3363	rs8103051;rs8103051	340	P31997	CEAM8_HUMAN	M	340	ENSP00000244336:I340M	ENSP00000244336:I340M	I	-	3	3	CEACAM8	47779268	0.002000	0.14202	0.069000	0.20011	0.113000	0.19764	-0.125000	0.10579	0.101000	0.17610	0.254000	0.18369	ATT	A|0.937;C|0.063	0.063	strong		0.458	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
BTN3A2	11118	hgsc.bcm.edu	37	6	26374571	26374571	+	Silent	SNP	G	G	A	rs115820857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26374571G>A	ENST00000356386.2	+	9	1169	c.981G>A	c.(979-981)tcG>tcA	p.S327S	BTN3A2_ENST00000396934.3_Silent_p.S304S|BTN3A2_ENST00000377708.2_Silent_p.S327S|BTN3A2_ENST00000396948.1_Silent_p.S327S|BTN3A2_ENST00000508906.2_Silent_p.S285S|BTN3A2_ENST00000527422.1_Silent_p.S327S	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	327				S -> L (in Ref. 2; AAC02655). {ECO:0000305}.	interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						AGGAGTCTTCGTCCGATACCA	0.473													G|||	75	0.014976	0.0552	0.0029	5008	,	,		16013	0.0		0.0	False		,,,				2504	0.0				p.S327S		Atlas-SNP	.											.	BTN3A2	44	.	0			c.G981A						PASS	.	G	,,,,	168,4238	110.8+/-149.0	1,166,2036	196.0	161.0	173.0		981,981,912,855,981	-1.2	0.0	6	dbSNP_132	173	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	1,178,6324	AA,AG,GG		0.1395,3.813,1.384	,,,,	327/335,327/335,304/312,285/293,327/335	26374571	180,12826	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon7			GTCTTCGTCCGAT	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.981G>A	6.37:g.26374571G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	216	96	0.444444	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			G|0.988;A|0.012	0.012	strong		0.473	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
TUBB8	347688	hgsc.bcm.edu	37	10	95169	95169	+	Missense_Mutation	SNP	T	T	G	rs199817418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:95169T>G	ENST00000309812.4	-	1	72	c.10A>C	c.(10-12)Atc>Ctc	p.I4L	TUBB8_ENST00000413237.3_Intron|TUBB8_ENST00000447903.2_Intron|TUBB8_ENST00000332708.5_Missense_Mutation_p.I4L	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	4					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		GTGAGCACGATCTCCCTCATG	0.667																																					p.I4L	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,colon,carcinoma,0,2	TUBB8	62	2	0			c.A10C						scavenged	.						18.0	17.0	17.0					10																	95169		2196	4294	6490	SO:0001583	missense	347688	exon1			GCACGATCTCCCT	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.10A>C	10.37:g.95169T>G	ENSP00000311042:p.Ile4Leu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	148	10	0.0675676	NM_177987	Q5SQX9|Q8WZ78	Missense_Mutation	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	T	7.968	0.748352	0.15710	.	.	ENSG00000173876	ENST00000440680;ENST00000328974;ENST00000309812;ENST00000332708	T;T	0.75704	-0.96;-0.76	0.109	0.109	0.14578	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.64402	U	0.000017	T	0.73938	0.3651	M	0.88450	2.955	0.80722	D	1	B;B	0.09022	0.0;0.002	B;B	0.27608	0.001;0.081	T	0.68334	-0.5436	10	0.87932	D	0	.	4.6217	0.12455	0.0:4.0E-4:0.0:0.9996	.	4;4	C9JAA5;Q3ZCM7	.;TBB8_HUMAN	L	4	ENSP00000311042:I4L;ENSP00000371071:I4L	ENSP00000311042:I4L	I	-	1	0	RP11-631M21.2	85169	1.000000	0.71417	0.020000	0.16555	0.020000	0.10135	2.326000	0.43849	0.156000	0.19299	0.155000	0.16302	ATC	T|0.980;G|0.020	0.020	strong		0.667	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
POM121L12	285877	hgsc.bcm.edu	37	7	53103371	53103371	+	Missense_Mutation	SNP	G	G	T	rs72598684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:53103371G>T	ENST00000408890.4	+	1	23	c.7G>T	c.(7-9)Gct>Tct	p.A3S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	3										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						AGCCATGGGCGCTGCAGCTCC	0.706													G|||	1509	0.301318	0.1377	0.2334	5008	,	,		13585	0.4315		0.2833	False		,,,				2504	0.455				p.A3S		Atlas-SNP	.											.	POM121L12	146	.	0			c.G7T						PASS	.	G	SER/ALA	555,3451		48,459,1496	6.0	9.0	8.0		7	-0.3	0.0	7	dbSNP_130	8	1999,6175		239,1521,2327	no	missense	POM121L12	NM_182595.3	99	287,1980,3823	TT,TG,GG		24.4556,13.8542,20.9688	benign	3/297	53103371	2554,9626	2003	4087	6090	SO:0001583	missense	285877	exon1			ATGGGCGCTGCAG		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.7G>T	7.37:g.53103371G>T	ENSP00000386133:p.Ala3Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	70	42	0.6	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	624	0.2857142857142857	70	0.14227642276422764	94	0.2596685082872928	250	0.4370629370629371	210	0.2770448548812665	G	9.531	1.110853	0.20714	0.138542	0.244556	ENSG00000221900	ENST00000408890	T	0.29397	1.57	1.66	-0.285	0.12866	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.59357	0.985	P	0.55824	0.785	T	0.43637	-0.9379	8	0.41790	T	0.15	.	4.0677	0.09868	0.421:0.0:0.579:0.0	.	3	Q8N7R1	P1L12_HUMAN	S	3	ENSP00000386133:A3S	ENSP00000386133:A3S	A	+	1	0	POM121L12	53070865	0.000000	0.05858	0.003000	0.11579	0.008000	0.06430	-1.106000	0.03319	-0.090000	0.12462	0.462000	0.41574	GCT	G|0.715;T|0.285	0.285	strong		0.706	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
PRUNE	58497	hgsc.bcm.edu	37	1	150997155	150997155	+	Missense_Mutation	SNP	G	G	A	rs56805474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150997155G>A	ENST00000271620.3	+	4	560	c.404G>A	c.(403-405)tGc>tAc	p.C135Y	PRUNE_ENST00000368934.1_5'Flank|PRUNE_ENST00000368937.1_Intron|PRUNE_ENST00000368935.1_Intron|PRUNE_ENST00000368936.1_5'UTR|RNU6-884P_ENST00000363889.1_RNA|PRUNE_ENST00000271619.8_Intron|PRUNE_ENST00000467771.1_3'UTR	NM_021222.1	NP_067045.1	Q86TP1	PRUNE_HUMAN	prune exopolyphosphatase	135						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)			CCGAAACACTGCCCTCCCTGC	0.577											OREG0013792	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	156	0.0311502	0.1142	0.0043	5008	,	,		17672	0.0		0.002	False		,,,				2504	0.0				p.C135Y		Atlas-SNP	.											.	PRUNE	40	.	0			c.G404A						PASS	.	G	TYR/CYS	427,3979	208.8+/-229.8	19,389,1795	103.0	89.0	94.0		404	3.8	1.0	1	dbSNP_129	94	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PRUNE	NM_021222.1	194	19,391,6093	AA,AG,GG		0.0233,9.6913,3.2985	possibly-damaging	135/454	150997155	429,12577	2203	4300	6503	SO:0001583	missense	58497	exon4			AACACTGCCCTCC	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.404G>A	1.37:g.150997155G>A	ENSP00000271620:p.Cys135Tyr	Somatic	106	0	0	1737	WXS	Illumina HiSeq	Phase_I	100	33	0.33	NM_021222	B2RCH8|B4DFL7|Q5SZF9|Q659E5|Q6P4E0|Q8N654|Q96JU5|Q9C071|Q9C072|Q9UIV0	Missense_Mutation	SNP	ENST00000271620.3	37	CCDS977.1	58	0.026556776556776556	57	0.11585365853658537	1	0.0027624309392265192	0	0.0	0	0.0	g	8.084	0.773045	0.16051	0.096913	2.33E-4	ENSG00000143363	ENST00000271620;ENST00000302413	T	0.30182	1.54	5.76	3.84	0.44239	Phosphoesterase, RecJ-like (1);	0.361754	0.29362	N	0.012374	T	0.09247	0.0228	N	0.22421	0.69	0.80722	D	1	D	0.53151	0.958	P	0.48334	0.574	T	0.06250	-1.0837	10	0.02654	T	1	.	9.1856	0.37168	0.0892:0.1831:0.7278:0.0	rs56805474	135	Q86TP1	PRUNE_HUMAN	Y	135;68	ENSP00000271620:C135Y	ENSP00000271620:C135Y	C	+	2	0	PRUNE	149263779	0.975000	0.34042	0.998000	0.56505	0.961000	0.63080	2.512000	0.45485	1.436000	0.47453	0.645000	0.84053	TGC	G|0.965;A|0.035	0.035	strong		0.577	PRUNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084885.1	NM_021222	
FAM83G	644815	hgsc.bcm.edu	37	17	18907029	18907029	+	Missense_Mutation	SNP	A	A	G	rs2074283	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18907029A>G	ENST00000388995.6	-	2	549	c.326T>C	c.(325-327)aTc>aCc	p.I109T	FAM83G_ENST00000585154.2_Missense_Mutation_p.I109T|SLC5A10_ENST00000395645.3_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|FAM83G_ENST00000345041.4_Missense_Mutation_p.I109T			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	109			I -> T (in dbSNP:rs2074283).		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						CTCGGCCTCGATGGGGACCCC	0.736													G|||	1417	0.282947	0.3797	0.1297	5008	,	,		12145	0.3998		0.0298	False		,,,				2504	0.4008				p.I109T		Atlas-SNP	.											.	FAM83G	51	.	0			c.T326C						PASS	.	G	THR/ILE,,	1168,2718		184,800,959	10.0	13.0	12.0		326,,	1.4	0.0	17	dbSNP_96	12	215,8003		2,211,3896	no	missense,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	89,,	186,1011,4855	GG,GA,AA		2.6162,30.0566,11.426	benign,,	109/824,,	18907029	1383,10721	1943	4109	6052	SO:0001583	missense	644815	exon2			GCCTCGATGGGGA	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.326T>C	17.37:g.18907029A>G	ENSP00000373647:p.Ile109Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	467	0.21382783882783882	178	0.3617886178861789	51	0.1408839779005525	218	0.3811188811188811	20	0.026385224274406333	G	6.063	0.379857	0.11466	0.300566	0.026162	ENSG00000188522	ENST00000388995;ENST00000345041;ENST00000399096	T;T	0.10668	2.85;2.85	4.8	1.39	0.22231	.	1.609950	0.03601	N	0.233476	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	0.47169	-0.9138	9	0.13470	T	0.59	-0.9574	2.3661	0.04319	0.0981:0.1653:0.3978:0.3389	rs2074283;rs58892823;rs2074283	109	A6ND36	FA83G_HUMAN	T	109	ENSP00000373647:I109T;ENSP00000343279:I109T	ENSP00000343279:I109T	I	-	2	0	FAM83G	18847754	0.012000	0.17670	0.001000	0.08648	0.426000	0.31534	0.082000	0.14847	0.093000	0.17368	-0.320000	0.08662	ATC	A|0.778;G|0.222	0.222	strong		0.736	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
TMEM8B	51754	hgsc.bcm.edu	37	9	35845998	35845998	+	Silent	SNP	G	G	C	rs34807292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35845998G>C	ENST00000377991.4	+	8	1321	c.306G>C	c.(304-306)acG>acC	p.T102T	TMEM8B_ENST00000473947.1_3'UTR|TMEM8B_ENST00000377996.1_Silent_p.T102T|TMEM8B_ENST00000439587.2_Silent_p.T102T|TMEM8B_ENST00000377988.2_Silent_p.T102T	NM_001042589.2	NP_001036054.1	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B	102					cell-matrix adhesion (GO:0007160)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle (GO:0007346)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	7						AAAACGTGACGGTGTTTGGAT	0.617													G|||	127	0.0253594	0.0908	0.0072	5008	,	,		16083	0.0		0.002	False		,,,				2504	0.0				p.T102T		Atlas-SNP	.											.	TMEM8B	53	.	0			c.G306C						PASS	.	G	,,	386,4020	191.9+/-217.4	17,352,1834	114.0	95.0	102.0		306,306,306	-2.7	1.0	9	dbSNP_126	102	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM8B	NM_001042589.1,NM_001042590.1,NM_016446.3	,,	17,353,6133	CC,CG,GG		0.0116,8.7608,2.9755	,,	102/473,102/473,102/339	35845998	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	51754	exon7			CGTGACGGTGTTT	BC043384	CCDS6595.1, CCDS43800.1	9p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000137103	ENSG00000137103			21427	protein-coding gene	gene with protein product	"""nasopharyngeal carcinoma expressed 6"""		"""chromosome 9 open reading frame 127"""	C9orf127		12918109, 8619474	Standard	NM_016446		Approved	NAG-5, NGX6	uc003zym.4	A6NDV4	OTTHUMG00000019885	ENST00000377991.4:c.306G>C	9.37:g.35845998G>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_001042590	B3KQF3|O75539|Q49AB1|Q4KMX5|Q5TCW5|Q9HBY2|Q9P0U7	Silent	SNP	ENST00000377991.4	37	CCDS43800.1																																																																																			G|0.969;C|0.031	0.031	strong		0.617	TMEM8B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052388.2	NM_016446	
DPYS	1807	hgsc.bcm.edu	37	8	105478933	105478933	+	Silent	SNP	G	G	A	rs2298840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:105478933G>A	ENST00000351513.2	-	1	348	c.216C>T	c.(214-216)ttC>ttT	p.F72F		NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	72					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CCATGAAGGGGAACTGCATGT	0.736													G|||	1160	0.231629	0.2867	0.2133	5008	,	,		9267	0.3085		0.175	False		,,,				2504	0.1493				p.F72F		Atlas-SNP	.											.	DPYS	107	.	0			c.C216T						PASS	.	G		728,2942		64,600,1171	18.0	11.0	14.0		216	3.0	1.0	8	dbSNP_100	14	1026,5972		73,880,2546	no	coding-synonymous	DPYS	NM_001385.2		137,1480,3717	AA,AG,GG		14.6613,19.8365,16.4417		72/520	105478933	1754,8914	1835	3499	5334	SO:0001819	synonymous_variant	1807	exon1			GAAGGGGAACTGC	D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.216C>T	8.37:g.105478933G>A		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	19	13	0.684211	NM_001385		Silent	SNP	ENST00000351513.2	37	CCDS6302.1																																																																																			G|0.763;A|0.237	0.237	strong		0.736	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385	
ASNSD1	54529	hgsc.bcm.edu	37	2	190531615	190531615	+	Silent	SNP	T	T	C	rs3828267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:190531615T>C	ENST00000260952.4	+	4	1170	c.757T>C	c.(757-759)Ttg>Ctg	p.L253L	ASNSD1_ENST00000607062.1_Intron	NM_019048.2	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1	253					asparagine biosynthetic process (GO:0006529)|glutamine metabolic process (GO:0006541)		asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(3)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)			ACAAGCTGCATTGGAGACTCA	0.383													T|||	750	0.14976	0.3525	0.1066	5008	,	,		20913	0.12		0.0447	False		,,,				2504	0.045				p.L253L		Atlas-SNP	.											.	ASNSD1	63	.	0			c.T757C						PASS	.	T		1400,2998	412.4+/-336.1	224,952,1023	94.0	98.0	97.0		757	-8.7	0.0	2	dbSNP_107	97	393,8205	123.6+/-182.4	6,381,3912	yes	coding-synonymous	ASNSD1	NM_019048.2		230,1333,4935	CC,CT,TT		4.5708,31.8327,13.7966		253/644	190531615	1793,11203	2199	4299	6498	SO:0001819	synonymous_variant	54529	exon4			GCTGCATTGGAGA	AY116969	CCDS2300.1	2q32.2	2012-09-20			ENSG00000138381	ENSG00000138381			24910	protein-coding gene	gene with protein product							Standard	NM_019048		Approved	NS3TP1, FLJ20752, NBLA00058	uc002uqt.3	Q9NWL6	OTTHUMG00000132665	ENST00000260952.4:c.757T>C	2.37:g.190531615T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_019048	D3DPH6|Q3LIC3|Q4ZG45	Silent	SNP	ENST00000260952.4	37	CCDS2300.1																																																																																			T|0.870;C|0.130	0.130	strong		0.383	ASNSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255919.3	NM_019048	
DNAI2	64446	hgsc.bcm.edu	37	17	72278080	72278080	+	Missense_Mutation	SNP	G	G	A	rs151176313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72278080G>A	ENST00000311014.6	+	2	191	c.124G>A	c.(124-126)Gtg>Atg	p.V42M	DNAI2_ENST00000579490.1_Missense_Mutation_p.V99M|DNAI2_ENST00000446837.2_Missense_Mutation_p.V42M|DNAI2_ENST00000582036.1_Missense_Mutation_p.V42M|DNAI2_ENST00000307504.5_5'UTR			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	42					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						CGAGCAGTTCGTGGAGCGGAA	0.632									Kartagener syndrome				G|||	23	0.00459265	0.0083	0.0	5008	,	,		18520	0.0089		0.0	False		,,,				2504	0.0031				p.V42M		Atlas-SNP	.											.	DNAI2	102	.	0			c.G124A						PASS	.	G	MET/VAL,MET/VAL	47,4359	48.9+/-83.8	0,47,2156	136.0	117.0	123.0		124,124	2.1	1.0	17	dbSNP_134	123	0,8600		0,0,4300	yes	missense,missense	DNAI2	NM_001172810.1,NM_023036.4	21,21	0,47,6456	AA,AG,GG		0.0,1.0667,0.3614	benign,benign	42/594,42/606	72278080	47,12959	2203	4300	6503	SO:0001583	missense	64446	exon2	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAGTTCGTGGAGC	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.124G>A	17.37:g.72278080G>A	ENSP00000308312:p.Val42Met	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	152	75	0.493421	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Missense_Mutation	SNP	ENST00000311014.6	37	CCDS11697.1	11	0.005036630036630037	5	0.01016260162601626	0	0.0	6	0.01048951048951049	0	0.0	G	13.85	2.360905	0.41801	0.010667	0.0	ENSG00000171595	ENST00000311014;ENST00000446837	T;T	0.68903	-0.36;-0.36	5.22	2.1	0.27182	.	0.434461	0.25319	N	0.031531	T	0.48995	0.1531	L	0.55103	1.725	0.80722	D	1	B	0.25609	0.13	B	0.18561	0.022	T	0.51212	-0.8734	10	0.56958	D	0.05	-34.5277	8.8263	0.35057	0.449:0.0:0.551:0.0	.	42	Q9GZS0	DNAI2_HUMAN	M	42	ENSP00000308312:V42M;ENSP00000400252:V42M	ENSP00000308312:V42M	V	+	1	0	DNAI2	69789675	0.064000	0.20934	0.991000	0.47740	0.995000	0.86356	0.516000	0.22817	0.338000	0.23692	0.644000	0.83932	GTG	G|0.996;A|0.004	0.004	strong		0.632	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
LAMA5	3911	hgsc.bcm.edu	37	20	60909316	60909316	+	Missense_Mutation	SNP	C	C	T	rs6062223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60909316C>T	ENST00000252999.3	-	22	2731	c.2665G>A	c.(2665-2667)Gtg>Atg	p.V889M	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	889	Domain IV 1 (domain IV B).		V -> M (in dbSNP:rs6062223). {ECO:0000269|PubMed:11572484}.		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)			CCAAAGCGCACGGCGTGACCC	0.682													c|||	545	0.108826	0.2693	0.1369	5008	,	,		16259	0.0427		0.0209	False		,,,				2504	0.0307				p.V889M		Atlas-SNP	.											.	LAMA5	268	.	0			c.G2665A						PASS	.		MET/VAL	1016,3388	360.6+/-315.3	119,778,1305	35.0	37.0	36.0		2665	1.4	0.0	20	dbSNP_114	36	195,8403	82.9+/-145.4	5,185,4109	yes	missense	LAMA5	NM_005560.3	21	124,963,5414	TT,TC,CC		2.268,23.0699,9.314	probably-damaging	889/3696	60909316	1211,11791	2202	4299	6501	SO:0001583	missense	3911	exon22			AGCGCACGGCGTG	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.2665G>A	20.37:g.60909316C>T	ENSP00000252999:p.Val889Met	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	192	0.08791208791208792	113	0.22967479674796748	48	0.13259668508287292	16	0.027972027972027972	15	0.01978891820580475	c	9.983	1.228672	0.22542	0.230699	0.02268	ENSG00000130702	ENST00000252999	T	0.23754	1.89	4.47	1.42	0.22433	.	0.134600	0.49916	U	0.000125	T	0.00012	0.0000	M	0.70595	2.14	0.09310	P	0.9999999999975331	D	0.63880	0.993	P	0.52554	0.702	T	0.07046	-1.0793	9	0.54805	T	0.06	.	6.1753	0.20441	0.1383:0.6535:0.1333:0.0749	rs6062223;rs59553737;rs6062223	889	O15230	LAMA5_HUMAN	M	889	ENSP00000252999:V889M	ENSP00000252999:V889M	V	-	1	0	LAMA5	60342711	0.993000	0.37304	0.048000	0.18961	0.012000	0.07955	3.085000	0.50151	0.105000	0.17753	-1.153000	0.01818	GTG	C|0.902;T|0.098	0.098	strong		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
FAM111B	374393	hgsc.bcm.edu	37	11	58892558	58892558	+	Silent	SNP	C	C	T	rs35732637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58892558C>T	ENST00000343597.3	+	4	1179	c.988C>T	c.(988-990)Cta>Tta	p.L330L	FAM111B_ENST00000411426.1_Silent_p.L300L|FAM111B_ENST00000529618.1_Silent_p.L300L	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	330							catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						ACCTCAGGATCTAAGCCATTA	0.373													C|||	538	0.107428	0.2005	0.0605	5008	,	,		17210	0.1786		0.004	False		,,,				2504	0.0481				p.L330L		Atlas-SNP	.											.	FAM111B	84	.	0			c.C988T						PASS	.	C	,,	595,3793		38,519,1637	71.0	84.0	79.0		898,898,988	-3.4	0.0	11	dbSNP_126	79	25,8561		0,25,4268	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM111B	NM_001142703.1,NM_001142704.1,NM_198947.3	,,	38,544,5905	TT,TC,CC		0.2912,13.5597,4.7788	,,	300/705,300/705,330/735	58892558	620,12354	2194	4293	6487	SO:0001819	synonymous_variant	374393	exon4			CAGGATCTAAGCC	BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.988C>T	11.37:g.58892558C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_198947	B4E2G2|Q6P661	Silent	SNP	ENST00000343597.3	37	CCDS7972.1																																																																																			C|0.940;T|0.060	0.060	strong		0.373	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947	
ZNF843	283933	hgsc.bcm.edu	37	16	31448168	31448168	+	Start_Codon_SNP	SNP	C	C	T	rs150789330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31448168C>T	ENST00000315678.5	-	2	727	c.3G>A	c.(1-3)atG>atA	p.M1I	ZNF843_ENST00000564218.1_Start_Codon_SNP_p.M1I	NM_001136509.1	NP_001129981.1	Q8N446	ZN843_HUMAN	zinc finger protein 843	1							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|large_intestine(1)|prostate(1)	4						GGAGGCTTCTCATGAGCAGGG	0.627													C|||	12	0.00239617	0.0091	0.0	5008	,	,		18756	0.0		0.0	False		,,,				2504	0.0				p.M1I		Atlas-SNP	.											.	ZNF843	14	.	0			c.G3A						PASS	.	C	ILE/MET	18,1366		1,16,675	37.0	36.0	36.0		3	0.7	0.0	16	dbSNP_134	36	1,3181		0,1,1590	yes	missense	ZNF843	NM_001136509.1	10	1,17,2265	TT,TC,CC		0.0314,1.3006,0.4161	benign	1/349	31448168	19,4547	692	1591	2283	SO:0001582	initiator_codon_variant	283933	exon2			GCTTCTCATGAGC	BC036762	CCDS45471.1	16p11.2	2013-01-11			ENSG00000176723	ENSG00000176723		"""Zinc fingers, C2H2-type"""	28710	protein-coding gene	gene with protein product						12477932	Standard	NM_001136509		Approved	MGC46336	uc010vfm.1	Q8N446		ENST00000315678.5:c.3G>A	16.37:g.31448168C>T	ENSP00000322899:p.Met1Ile	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_001136509	A8K4U8	Missense_Mutation	SNP	ENST00000315678.5	37	CCDS45471.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	7.728	0.698715	0.15106	0.013006	3.14E-4	ENSG00000176723	ENST00000315678	T	0.01099	5.34	1.72	0.701	0.18104	.	.	.	.	.	T	0.00815	0.0027	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55854	-0.8075	8	0.87932	D	0	.	5.7668	0.18231	0.0:0.8075:0.0:0.1925	.	1	Q8N446	ZN843_HUMAN	I	1	ENSP00000322899:M1I	ENSP00000322899:M1I	M	-	3	0	ZNF843	31355669	0.903000	0.30736	0.004000	0.12327	0.005000	0.04900	2.394000	0.44450	0.055000	0.16094	0.411000	0.27672	ATG	C|0.999;T|0.001	0.001	strong		0.627	ZNF843-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432843.1	NM_001136509	Missense_Mutation
UBA7	7318	hgsc.bcm.edu	37	3	49840843	49840843	+	IGR	SNP	T	T	C	rs115355405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49840843T>C	ENST00000333486.3	-	0	3299				FAM212A_ENST00000333323.4_Silent_p.L8L|MIR5193_ENST00000584510.1_RNA	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7						cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCGCTCGGCTTGACAGCTTCC	0.701													T|||	43	0.00858626	0.0008	0.0187	5008	,	,		9656	0.0		0.0249	False		,,,				2504	0.0041				p.L8L		Atlas-SNP	.											.	.	.	.	0			c.T24C						PASS	.	T		12,4368		0,12,2178	33.0	32.0	32.0		24	-0.2	1.0	3	dbSNP_132	32	194,8378		6,182,4098	no	coding-synonymous	C3orf54	NM_203370.1		6,194,6276	CC,CT,TT		2.2632,0.274,1.5905		8/288	49840843	206,12746	2190	4286	6476	SO:0001628	intergenic_variant	389119	exon1			TCGGCTTGACAGC	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"""Ubiquitin-like modifier activating enzymes"""	12471	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)"", ""UBA7, ubiquitin-activating enzyme E1"""	191325	"""ubiquitin-activating enzyme E1-like"""	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267		3.37:g.49840843T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	150	87	0.58	NM_203370	Q9BRB2	Silent	SNP	ENST00000333486.3	37	CCDS2805.1																																																																																			T|0.984;C|0.016	0.016	strong		0.701	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335	
RAB40AL	282808	hgsc.bcm.edu	37	X	102192372	102192372	+	Silent	SNP	G	G	A	rs61745023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192372G>A	ENST00000218249.5	+	1	173	c.126G>A	c.(124-126)ccG>ccA	p.P42P	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	42					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						CCGAGTCCCCGTACAGTCACC	0.622													.|||	67	0.0177483	0.0477	0.0058	3775	,	,		11299	0.0		0.0	False		,,,				2504	0.0				p.P42P		Atlas-SNP	.											.	RAB40AL	33	.	0			c.G126A						PASS	.	G		213,3622		4,171,34,1457,537	115.0	109.0	111.0		126	-1.7	0.0	X	dbSNP_129	111	0,6728		0,0,0,2428,1872	no	coding-synonymous	RAB40AL	NM_001031834.1		4,171,34,3885,2409	AA,AG,A,GG,G		0.0,5.5541,2.0165		42/279	102192372	213,10350	2203	4300	6503	SO:0001819	synonymous_variant	282808	exon1			GTCCCCGTACAGT	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"""Ras like GTPase"""	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.126G>A	X.37:g.102192372G>A		Somatic	507	0	0		WXS	Illumina HiSeq	Phase_I	455	145	0.318681	NM_001031834	Q495H3	Silent	SNP	ENST00000218249.5	37	CCDS35353.1																																																																																			G|0.981;A|0.019	0.019	strong		0.622	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834	
KRT4	3851	hgsc.bcm.edu	37	12	53205757	53205757	+	Missense_Mutation	SNP	T	T	C	rs7959052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53205757T>C	ENST00000551956.1	-	2	959	c.467A>G	c.(466-468)cAg>cGg	p.Q156R	KRT4_ENST00000293774.4_Missense_Mutation_p.Q230R|KRT4_ENST00000458244.2_Missense_Mutation_p.Q136R			P19013	K2C4_HUMAN	keratin 4	170	Coil 1A.|Rod.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CTCTAAGAACTGCACCTGTGT	0.542													C|||	1352	0.269968	0.643	0.1254	5008	,	,		19076	0.1052		0.1491	False		,,,				2504	0.1626				p.Q156R	Pancreas(190;284 2995 41444 45903)	Atlas-SNP	.											.	KRT4	110	.	0			c.A467G						PASS	.	C	ARG/GLN	2297,1913		622,1053,430	56.0	60.0	59.0		467	4.4	1.0	12	dbSNP_116	59	1511,6981		146,1219,2881	yes	missense	KRT4	NM_002272.3	43	768,2272,3311	CC,CT,TT		17.7932,45.4394,29.9795	benign	156/521	53205757	3808,8894	2105	4246	6351	SO:0001583	missense	3851	exon2			AAGAACTGCACCT		CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.467A>G	12.37:g.53205757T>C	ENSP00000448220:p.Gln156Arg	Somatic	310	1	0.00322581		WXS	Illumina HiSeq	Phase_I	281	141	0.501779	NM_002272	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Missense_Mutation	SNP	ENST00000551956.1	37	CCDS41787.2	510	0.23351648351648352	295	0.5995934959349594	53	0.1464088397790055	42	0.07342657342657342	120	0.158311345646438	C	9.302	1.053361	0.19907	0.545606	0.177932	ENSG00000170477	ENST00000551956;ENST00000293774;ENST00000458244	D;D;D	0.84223	-1.82;-1.82;-1.82	4.41	4.41	0.53225	Filament (1);	0.000000	0.43416	N	0.000566	T	0.00012	0.0000	N	0.00025	-2.685	0.50039	P	1.60000000000049E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.44772	-0.9306	9	0.02654	T	1	.	13.6387	0.62237	0.0:0.9237:0.0:0.0763	rs7959052;rs11538841;rs61013411;rs7959052	170	P19013	K2C4_HUMAN	R	156;230;136	ENSP00000448220:Q156R;ENSP00000293774:Q230R;ENSP00000387904:Q136R	ENSP00000293774:Q230R	Q	-	2	0	KRT4	51492024	0.998000	0.40836	1.000000	0.80357	0.981000	0.71138	3.970000	0.56824	1.477000	0.48234	-0.215000	0.12644	CAG	C|0.245;N|0.000	0.245	strong		0.542	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
KALRN	8997	hgsc.bcm.edu	37	3	124418879	124418879	+	Splice_Site	SNP	T	T	C	rs56047676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124418879T>C	ENST00000291478.5	+	23	3067	c.2904T>C	c.(2902-2904)taT>taC	p.Y968Y	AC080008.1_ENST00000584173.1_RNA|KALRN_ENST00000360013.3_Splice_Site_p.Y2665Y|KALRN_ENST00000428018.2_Splice_Site_p.Y936Y	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2664					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						TTCCAGAATATGGTGAGTCCC	0.602													T|||	553	0.110423	0.1415	0.1182	5008	,	,		17183	0.0843		0.1024	False		,,,				2504	0.0982				p.Y2665Y		Atlas-SNP	.											.	KALRN	556	.	0			c.T7995C						PASS	.	T	,	662,3744	281.9+/-276.2	50,562,1591	109.0	101.0	104.0		7995,2904	-3.8	0.9	3	dbSNP_129	104	1047,7553	221.3+/-258.8	63,921,3316	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	KALRN	NM_001024660.3,NM_007064.3	,	113,1483,4907	CC,CT,TT		12.1744,15.025,13.1401	,	2665/2987,968/1290	124418879	1709,11297	2203	4300	6503	SO:0001630	splice_region_variant	8997	exon56			AGAATATGGTGAG	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	ENST00000291478.5:c.2905+1T>C	3.37:g.124418879T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	37	CCDS3028.1	227	0.10393772893772894	71	0.1443089430894309	46	0.1270718232044199	41	0.07167832167832168	69	0.09102902374670185	T	9.021	0.984823	0.18889	0.15025	0.121744	ENSG00000160145	ENST00000354186	.	.	.	6.17	-3.82	0.04281	.	.	.	.	.	T	0.00468	0.0015	.	.	.	0.09310	P	0.9999999999869995	.	.	.	.	.	.	T	0.43972	-0.9358	3	.	.	.	.	16.0872	0.81065	0.0:0.3113:0.0:0.6887	rs56047676	.	.	.	T	2634	.	.	M	+	2	0	KALRN	125901569	0.000000	0.05858	0.941000	0.38009	0.974000	0.67602	-3.477000	0.00458	-0.618000	0.05656	-0.290000	0.09829	ATG	T|0.879;C|0.121	0.121	strong		0.602	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947	Silent
TRABD2A	129293	hgsc.bcm.edu	37	2	85059205	85059205	+	Silent	SNP	G	G	A	rs60429698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85059205G>A	ENST00000409520.2	-	5	1098	c.1056C>T	c.(1054-1056)caC>caT	p.H352H	TRABD2A_ENST00000479944.1_5'UTR|TRABD2A_ENST00000335459.5_Silent_p.H303H	NM_001277053.1	NP_001263982.1	Q86V40	TIKI1_HUMAN	TraB domain containing 2A	352					head development (GO:0060322)|metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|Wnt-protein binding (GO:0017147)										CAGCAGGGGCGTGTTCTACCT	0.562													G|||	104	0.0207668	0.0772	0.0029	5008	,	,		19501	0.0		0.0	False		,,,				2504	0.0				p.A303A		Atlas-SNP	.											.	.	.	.	0			c.C909T						PASS	.	G		216,3844		7,202,1821	134.0	134.0	134.0		909	-0.3	1.0	2	dbSNP_129	134	2,8402		0,2,4200	no	coding-synonymous	C2orf89	NM_001080824.1		7,204,6021	AA,AG,GG		0.0238,5.3202,1.749		303/457	85059205	218,12246	2030	4202	6232	SO:0001819	synonymous_variant	129293	exon4			AGGGGCGTGTTCT	BC049209	CCDS46349.1, CCDS62946.1	2p11.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000186854	ENSG00000186854			27013	protein-coding gene	gene with protein product		614912	"""chromosome 2 open reading frame 89"""	C2orf89		12477932	Standard	NM_001080824		Approved		uc010ysl.3	Q86V40	OTTHUMG00000152922	ENST00000409520.2:c.1056C>T	2.37:g.85059205G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001080824	B4DKK8|I6UMB9	Silent	SNP	ENST00000409520.2	37																																																																																				G|0.982;A|0.018	0.018	strong		0.562	TRABD2A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001080824	
ZNF750	79755	hgsc.bcm.edu	37	17	80788465	80788465	+	Silent	SNP	T	T	C	rs12938126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80788465T>C	ENST00000269394.3	-	3	2558	c.1725A>G	c.(1723-1725)gcA>gcG	p.A575A	TBCD_ENST00000355528.4_Intron|TBCD_ENST00000397466.2_Intron|ZNF750_ENST00000572562.1_Silent_p.A176A|TBCD_ENST00000539345.2_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	575					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			CAGCAGGTTCTGCAGCTCGTG	0.627													T|||	1849	0.369209	0.4017	0.3343	5008	,	,		16310	0.3522		0.4195	False		,,,				2504	0.316				p.A575A		Atlas-SNP	.											.	ZNF750	60	.	0			c.A1725G						PASS	.	T	,	1764,2642	519.9+/-370.1	364,1036,803	56.0	60.0	59.0		,1725	-6.2	0.0	17	dbSNP_121	59	3532,5068	510.5+/-377.5	715,2102,1483	no	intron,coding-synonymous	TBCD,ZNF750	NM_005993.4,NM_024702.2	,	1079,3138,2286	CC,CT,TT		41.0698,40.0363,40.7197	,	,575/724	80788465	5296,7710	2203	4300	6503	SO:0001819	synonymous_variant	79755	exon3			AGGTTCTGCAGCT	AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.1725A>G	17.37:g.80788465T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	161	83	0.515528	NM_024702	Q9H899	Silent	SNP	ENST00000269394.3	37	CCDS11819.1																																																																																			T|0.600;C|0.400	0.400	strong		0.627	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702	
LILRA1	11024	hgsc.bcm.edu	37	19	55105743	55105743	+	Splice_Site	SNP	A	A	G	rs1974982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55105743A>G	ENST00000251372.3	+	2	216	c.34A>G	c.(34-36)Agg>Ggg	p.R12G	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000418536.2_Intron|LILRA1_ENST00000473156.1_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Splice_Site_p.R12G	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	12			R -> G (in dbSNP:rs1974982). {ECO:0000269|PubMed:9548455}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		GATCTGTCTCAGTGAGATTTG	0.592													N|||	1467	0.292931	0.5174	0.2723	5008	,	,		16145	0.2778		0.1034	False		,,,				2504	0.2147				p.R12G		Atlas-SNP	.											.	LILRA1	105	.	0			c.A34G						PASS	.	G	GLY/ARG	1261,3145		429,403,1371	81.0	105.0	97.0		34	2.4	0.1	19	dbSNP_92	97	268,8332		49,170,4081	no	missense-near-splice	LILRA1	NM_006863.1	125	478,573,5452	GG,GA,AA		3.1163,28.6201,11.7561	benign	12/490	55105743	1529,11477	2203	4300	6503	SO:0001630	splice_region_variant	11024	exon2			TGTCTCAGTGAGA	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.34+1A>G	19.37:g.55105743A>G		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	455	0.20833333333333334	180	0.36585365853658536	81	0.22375690607734808	140	0.24475524475524477	54	0.0712401055408971	G	0.048	-1.260465	0.01445	0.286201	0.031163	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.00468	7.24;7.22	2.42	2.42	0.29668	.	0.324020	0.22200	N	0.063246	T	0.00012	0.0000	N	0.00001	-3.745	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32534	-0.9903	9	0.02654	T	1	.	5.9171	0.19061	0.1712:0.0:0.8288:0.0	rs1974982	12;12	O75019-2;O75019	.;LIRA1_HUMAN	G	12	ENSP00000251372:R12G;ENSP00000413715:R12G	ENSP00000251372:R12G	R	+	1	2	LILRA1	59797555	0.981000	0.34729	0.053000	0.19242	0.025000	0.11179	2.181000	0.42547	0.331000	0.23511	-1.032000	0.02404	AGG	A|0.864;G|0.136	0.136	strong		0.592	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	Missense_Mutation
PASK	23178	hgsc.bcm.edu	37	2	242046785	242046785	+	Missense_Mutation	SNP	A	A	C	rs1131293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242046785A>C	ENST00000405260.1	-	17	4495	c.3797T>G	c.(3796-3798)tTt>tGt	p.F1266C	PASK_ENST00000234040.4_Missense_Mutation_p.F1266C|PASK_ENST00000539818.1_Missense_Mutation_p.F1050C|PASK_ENST00000544142.1_Missense_Mutation_p.F1080C|PASK_ENST00000358649.4_Missense_Mutation_p.F1273C|PASK_ENST00000475666.1_5'Flank	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	1266			F -> C (in dbSNP:rs1131293). {ECO:0000269|PubMed:11459942, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8590280}.		negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GTTTACTCGAAACACCTCTTC	0.542													C|||	1617	0.322883	0.5802	0.2594	5008	,	,		20031	0.4286		0.1064	False		,,,				2504	0.1339				p.F1273C		Atlas-SNP	.											.	PASK	230	.	0			c.T3818G						PASS	.	C	CYS/PHE	2171,2235	592.5+/-387.8	557,1057,589	168.0	155.0	159.0		3797	3.2	1.0	2	dbSNP_86	159	836,7764	781.4+/-407.6	38,760,3502	yes	missense	PASK	NM_015148.2	205	595,1817,4091	CC,CA,AA		9.7209,49.2737,23.1201	benign	1266/1324	242046785	3007,9999	2203	4300	6503	SO:0001583	missense	23178	exon17			ACTCGAAACACCT	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.3797T>G	2.37:g.242046785A>C	ENSP00000384016:p.Phe1266Cys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	152	76	0.5	NM_001252119	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	683	0.31272893772893773	274	0.556910569105691	84	0.23204419889502761	248	0.43356643356643354	77	0.10158311345646438	C	0.513	-0.865544	0.02590	0.492737	0.097209	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818	T;T;T;T;T	0.41758	1.84;1.84;1.84;0.99;1.84	5.05	3.23	0.37069	Protein kinase-like domain (1);	0.219452	0.32386	N	0.006176	T	0.00012	0.0000	N	0.00230	-1.795	0.58432	P	9.000000000036756E-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	0.44982	-0.9292	9	0.13853	T	0.58	.	3.9373	0.09311	0.3446:0.3793:0.0:0.2761	rs1131293;rs3191065;rs6761641;rs52811271;rs61332862;rs1131293	1231;1080;1273;1266	B7Z7R6;F5GYW7;Q96RG2-2;Q96RG2	.;.;.;PASK_HUMAN	C	1266;1080;1266;1273;1050	ENSP00000234040:F1266C;ENSP00000441374:F1080C;ENSP00000384016:F1266C;ENSP00000351475:F1273C;ENSP00000443083:F1050C	ENSP00000234040:F1266C	F	-	2	0	PASK	241695458	0.009000	0.17119	0.967000	0.41034	0.732000	0.41865	0.018000	0.13422	0.551000	0.29008	-0.121000	0.15023	TTT	C|0.280;N|0.000	0.280	strong		0.542	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
PHYHIP	9796	hgsc.bcm.edu	37	8	22084503	22084503	+	Silent	SNP	C	C	T	rs11547656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22084503C>T	ENST00000321613.3	-	4	657	c.201G>A	c.(199-201)ccG>ccA	p.P67P	PHYHIP_ENST00000454243.2_Silent_p.P67P	NM_001099335.1	NP_001092805.1	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein	67	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.									endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	10				Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)		TCATGGGCAGCGGCACTGCCT	0.622													C|||	1615	0.322484	0.2398	0.3401	5008	,	,		20345	0.2044		0.4304	False		,,,				2504	0.4325				p.P67P		Atlas-SNP	.											.	PHYHIP	24	.	0			c.G201A						PASS	.	C	,	1098,3244		154,790,1227	51.0	60.0	57.0		201,201	-11.4	0.4	8	dbSNP_120	57	3514,5002		728,2058,1472	no	coding-synonymous,coding-synonymous	PHYHIP	NM_001099335.1,NM_014759.3	,	882,2848,2699	TT,TC,CC		41.2635,25.2879,35.8687	,	67/331,67/331	22084503	4612,8246	2171	4258	6429	SO:0001819	synonymous_variant	9796	exon3			GGGCAGCGGCACT	D87463	CCDS43723.1	8p21.2	2010-02-17	2006-01-09		ENSG00000168490	ENSG00000168490			16865	protein-coding gene	gene with protein product		608511	"""phytanoyl-CoA hydroxylase interacting protein"", ""DYRK1A interacting protein 3"""	DYRK1AP3		9039502, 10686344	Standard	NM_014759		Approved	KIAA0273, PAHX-AP	uc003xbj.4	Q92561	OTTHUMG00000163776	ENST00000321613.3:c.201G>A	8.37:g.22084503C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	49	15	0.306122	NM_014759	D3DSR1|Q8N4I9	Silent	SNP	ENST00000321613.3	37	CCDS43723.1																																																																																			T|0.357;G|0.000;C|0.642	0.357	strong		0.622	PHYHIP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375388.1	NM_014759	
LILRB4	11006	hgsc.bcm.edu	37	19	55179342	55179342	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55179342C>T	ENST00000391736.1	+	14	1534	c.1219C>T	c.(1219-1221)Ccc>Tcc	p.P407S	LILRB4_ENST00000391734.3_Missense_Mutation_p.P354S|LILRB4_ENST00000430952.2_Missense_Mutation_p.P406S|LILRB4_ENST00000391733.3_Missense_Mutation_p.P408S|LILRB4_ENST00000270452.2_Missense_Mutation_p.P407S	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	407					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.P407S(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)		ATCTGAAGCCCCCCAGGATGT	0.647																																					p.P407S		Atlas-SNP	.											LILRB4,NS,carcinoma,0,1	LILRB4	86	1	1	Substitution - Missense(1)	lung(1)	c.C1219T						scavenged	.						62.0	67.0	66.0					19																	55179342		2203	4300	6503	SO:0001583	missense	11006	exon12			GAAGCCCCCCAGG	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.1219C>T	19.37:g.55179342C>T	ENSP00000375616:p.Pro407Ser	Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	378	11	0.0291005	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	C	11.16	1.556618	0.27827	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733	T;T;T;T;T	0.00505	7.11;7.11;7.11;6.93;7.12	2.07	2.07	0.26955	.	.	.	.	.	T	0.00906	0.0030	L	0.48935	1.535	0.20764	N	0.999854	D;D;B;B	0.76494	0.999;0.999;0.007;0.001	D;D;B;B	0.76575	0.972;0.988;0.01;0.001	T	0.57946	-0.7723	9	0.22706	T	0.39	.	7.5752	0.27931	0.0:1.0:0.0:0.0	.	354;408;406;407	A8MUE1;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	S	407;407;406;354;408	ENSP00000375616:P407S;ENSP00000270452:P407S;ENSP00000408995:P406S;ENSP00000375614:P354S;ENSP00000375613:P408S	ENSP00000270452:P407S	P	+	1	0	LILRB4	59871154	0.007000	0.16637	0.721000	0.30653	0.421000	0.31385	0.250000	0.18235	1.166000	0.42689	0.407000	0.27541	CCC	.	.	none		0.647	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
MUC2	4583	hgsc.bcm.edu	37	11	1093228	1093228	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1093228A>G	ENST00000441003.2	+	30	5074	c.5047A>G	c.(5047-5049)Acg>Gcg	p.T1683A	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1650A	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)	caccaccactacGGTGacccc	0.632																																					p.T1683A		Atlas-SNP	.											.	MUC2	614	.	0			c.A5047G						PASS	.						85.0	148.0	126.0					11																	1093228		1822	3322	5144	SO:0001583	missense	4583	exon30			ACCACTACGGTGA	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.5047A>G	11.37:g.1093228A>G	ENSP00000415183:p.Thr1683Ala	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	13	0.19697	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	A	3.524	-0.097228	0.07010	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12465	2.97;2.68	1.75	0.234	0.15390	.	0.000000	0.34750	U	0.003714	T	0.04497	0.0123	.	.	.	0.09310	N	1	B	0.28933	0.228	B	0.21546	0.035	T	0.37126	-0.9719	9	0.11485	T	0.65	.	3.3046	0.06996	0.6291:0.0:0.0:0.3709	.	1683	E7EUV1	.	A	1683;1650	ENSP00000415183:T1683A;ENSP00000351956:T1650A	ENSP00000351956:T1650A	T	+	1	0	MUC2	1083228	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.225000	0.09151	0.813000	0.34350	0.155000	0.16302	ACG	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
TBP	6908	hgsc.bcm.edu	37	6	170871058	170871058	+	Silent	SNP	G	G	A	rs113440919		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170871058G>A	ENST00000392092.2	+	3	513	c.234G>A	c.(232-234)caG>caA	p.Q78Q	TBP_ENST00000540980.1_Silent_p.Q58Q|TBP_ENST00000230354.6_Silent_p.Q78Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	78	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.577																																					p.Q78Q		Atlas-SNP	.											TBP,caecum,carcinoma,0,1	TBP	58	1	0			c.G234A						PASS	.						13.0	18.0	16.0					6																	170871058		1927	3786	5713	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAGCAG	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.234G>A	6.37:g.170871058G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	70	18	0.257143	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			G|0.500;A|0.500	0.500	weak		0.577	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
JSRP1	126306	hgsc.bcm.edu	37	19	2253641	2253641	+	Silent	SNP	G	G	T	rs200918439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2253641G>T	ENST00000300961.6	-	5	478	c.414C>A	c.(412-414)ggC>ggA	p.G138G	JSRP1_ENST00000586471.2_Silent_p.G138G|MIR4321_ENST00000592276.1_RNA	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	138	Pro-rich.				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)		GGAAAGCCGAGCCCAGCAGCG	0.716													G|||	54	0.0107827	0.0363	0.0072	5008	,	,		13645	0.0		0.001	False		,,,				2504	0.0				p.G138G		Atlas-SNP	.											.	JSRP1	18	.	0			c.C414A						PASS	.	G		103,3903		0,103,1900	6.0	10.0	9.0		414	1.9	1.0	19		9	8,7862		0,8,3927	no	coding-synonymous	JSRP1	NM_144616.3		0,111,5827	TT,TG,GG		0.1017,2.5711,0.9347		138/332	2253641	111,11765	2003	3935	5938	SO:0001819	synonymous_variant	126306	exon5			AGCCGAGCCCAGC	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.414C>A	19.37:g.2253641G>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_144616		Silent	SNP	ENST00000300961.6	37	CCDS12086.1																																																																																			G|0.996;T|0.004	0.004	strong		0.716	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616	
VCAN	1462	hgsc.bcm.edu	37	5	82837631	82837631	+	Missense_Mutation	SNP	G	G	T	rs160277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82837631G>T	ENST00000265077.3	+	8	9374	c.8809G>T	c.(8809-8811)Gat>Tat	p.D2937Y	VCAN_ENST00000343200.5_Missense_Mutation_p.D1950Y|VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2937	GAG-beta.		D -> Y (in dbSNP:rs160277).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AAACAAAACCGATGGTCAAGT	0.398													G|||	1806	0.360623	0.357	0.4597	5008	,	,		18764	0.3234		0.4254	False		,,,				2504	0.2669				p.D2937Y		Atlas-SNP	.											.	VCAN	498	.	0			c.G8809T						PASS	.	G	,TYR/ASP,,TYR/ASP	1625,2781	482.4+/-359.4	296,1033,874	80.0	85.0	83.0		,5848,,8809	0.8	0.0	5	dbSNP_79	83	3433,5167	503.3+/-375.9	700,2033,1567	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,160,,160	996,3066,2441	TT,TG,GG		39.9186,36.8815,38.8897	,possibly-damaging,,possibly-damaging	,1950/2410,,2937/3397	82837631	5058,7948	2203	4300	6503	SO:0001583	missense	1462	exon8			AAAACCGATGGTC	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.8809G>T	5.37:g.82837631G>T	ENSP00000265077:p.Asp2937Tyr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	37	0.397849	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	837	0.38324175824175827	145	0.29471544715447157	168	0.46408839779005523	203	0.3548951048951049	321	0.4234828496042216	G	12.91	2.079124	0.36662	0.368815	0.399186	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.18338	2.22;2.22	5.99	0.819	0.18785	.	1.042050	0.07483	N	0.904317	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D;D	0.60160	0.987;0.979	P;P	0.52672	0.706;0.607	T	0.46748	-0.9169	9	0.59425	D	0.04	.	2.3966	0.04391	0.5352:0.1193:0.2293:0.1161	rs160277;rs310482;rs496670;rs3734093;rs52794243;rs60765899;rs160277	1950;2937	P13611-2;P13611	.;CSPG2_HUMAN	Y	2937;1950	ENSP00000265077:D2937Y;ENSP00000340062:D1950Y	ENSP00000265077:D2937Y	D	+	1	0	VCAN	82873387	0.001000	0.12720	0.001000	0.08648	0.083000	0.17756	0.638000	0.24674	0.540000	0.28808	-0.312000	0.09012	GAT	G|0.618;T|0.382	0.382	strong		0.398	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
PASK	23178	hgsc.bcm.edu	37	2	242051777	242051777	+	Silent	SNP	G	G	A	rs2074824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242051777G>A	ENST00000405260.1	-	15	4109	c.3411C>T	c.(3409-3411)gcC>gcT	p.A1137A	PASK_ENST00000234040.4_Silent_p.A1137A|PASK_ENST00000539818.1_Silent_p.A921A|PASK_ENST00000544142.1_Silent_p.A951A|PASK_ENST00000358649.4_Silent_p.A1144A|PASK_ENST00000475666.1_5'UTR	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	1137	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		TGAAGTCCTCGGCGATCACGA	0.502													G|||	1617	0.322883	0.5802	0.2594	5008	,	,		17008	0.4286		0.1064	False		,,,				2504	0.1339				p.A1144A		Atlas-SNP	.											.	PASK	230	.	0			c.C3432T						PASS	.	G		2172,2234	584.5+/-386.0	558,1056,589	80.0	72.0	75.0		3411	-11.8	0.0	2	dbSNP_96	75	837,7763	192.0+/-238.1	38,761,3501	no	coding-synonymous	PASK	NM_015148.2		596,1817,4090	AA,AG,GG		9.7326,49.2964,23.1355		1137/1324	242051777	3009,9997	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon15			GTCCTCGGCGATC	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.3411C>T	2.37:g.242051777G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	116	64	0.551724	NM_001252119	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			G|0.727;A|0.273	0.273	strong		0.502	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
SPANXN1	494118	hgsc.bcm.edu	37	X	144337286	144337286	+	Silent	SNP	G	G	A	rs75090998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:144337286G>A	ENST00000370493.3	+	2	930	c.171G>A	c.(169-171)agG>agA	p.R57R		NM_001009614.2	NP_001009614.1	Q5VSR9	SPXN1_HUMAN	SPANX family, member N1	57										endometrium(2)|kidney(2)|lung(8)|prostate(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;6.56e-05)					TTTGCTACAGGAAAGCTAAGA	0.443													G|||	280	0.0741722	0.208	0.0072	3775	,	,		15977	0.0		0.0	False		,,,				2504	0.0				p.R57R		Atlas-SNP	.											.	SPANXN1	23	.	0			c.G171A						PASS	.	G		826,3009		83,540,120,1009,451	186.0	161.0	170.0		171	1.5	0.0	X	dbSNP_131	170	9,6716		1,5,2,2422,1867	no	coding-synonymous	SPANXN1	NM_001009614.2		84,545,122,3431,2318	AA,AG,A,GG,G		0.1338,21.5385,7.9072		57/73	144337286	835,9725	2203	4297	6500	SO:0001819	synonymous_variant	494118	exon2			CTACAGGAAAGCT		CCDS35421.1	Xq27.3	2009-03-25				ENSG00000203923			33174	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 6"""	300664				14973187, 17012309	Standard	NM_001009614		Approved	SPANX-N1, CT11.6	uc004fcb.2	Q5VSR9		ENST00000370493.3:c.171G>A	X.37:g.144337286G>A		Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	365	363	0.994521	NM_001009614		Silent	SNP	ENST00000370493.3	37	CCDS35421.1																																																																																			G|0.919;A|0.081	0.081	strong		0.443	SPANXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058631.2	NM_001009614	
USP42	84132	hgsc.bcm.edu	37	7	6189780	6189780	+	Silent	SNP	T	T	C	rs3764814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6189780T>C	ENST00000306177.5	+	13	2111	c.1953T>C	c.(1951-1953)ctT>ctC	p.L651L		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	651					cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		CGCACGAGCTTCAAGAACCCA	0.577													C|||	1416	0.282748	0.4349	0.1844	5008	,	,		19683	0.4276		0.0885	False		,,,				2504	0.1973				p.L651L		Atlas-SNP	.											.	USP42	138	.	0			c.T1953C						PASS	.	C		1484,2590		263,958,816	34.0	40.0	38.0		1953	-6.2	0.0	7	dbSNP_107	38	596,7796		34,528,3634	no	coding-synonymous	USP42	NM_032172.2		297,1486,4450	CC,CT,TT		7.102,36.4261,16.6854		651/1317	6189780	2080,10386	2037	4196	6233	SO:0001819	synonymous_variant	84132	exon13			CGAGCTTCAAGAA	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.1953T>C	7.37:g.6189780T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	72	42	0.583333	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Silent	SNP	ENST00000306177.5	37	CCDS47535.1																																																																																			T|0.728;C|0.272	0.272	strong		0.577	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
SPTA1	6708	hgsc.bcm.edu	37	1	158631106	158631106	+	Missense_Mutation	SNP	G	G	C	rs35121052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158631106G>C	ENST00000368147.4	-	18	2738	c.2558C>G	c.(2557-2559)aCa>aGa	p.T853R		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	853			T -> R (in dbSNP:rs35121052).		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)					TCCCCTTTCTGTTATCTCTTG	0.438													G|||	531	0.10603	0.382	0.0331	5008	,	,		17472	0.0		0.003	False		,,,				2504	0.0				p.T853R		Atlas-SNP	.											.	SPTA1	720	.	0			c.C2558G						PASS	.	G	ARG/THR	1121,2763		177,767,998	266.0	264.0	265.0		2558	3.9	1.0	1	dbSNP_126	265	21,8275		0,21,4127	yes	missense	SPTA1	NM_003126.2	71	177,788,5125	CC,CG,GG		0.2531,28.862,9.376	benign	853/2420	158631106	1142,11038	1942	4148	6090	SO:0001583	missense	6708	exon18			CTTTCTGTTATCT	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.2558C>G	1.37:g.158631106G>C	ENSP00000357129:p.Thr853Arg	Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	338	165	0.488166	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	192	0.08791208791208792	181	0.3678861788617886	11	0.03038674033149171	0	0.0	0	0.0	G	16.67	3.187725	0.57909	0.28862	0.002531	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.52057	0.68;0.68	4.81	3.9	0.45041	.	.	.	.	.	T	0.39145	0.1067	M	0.64997	1.995	0.23076	P	0.99833702	P	0.44659	0.84	P	0.51550	0.673	T	0.29243	-1.0018	8	0.18710	T	0.47	.	11.9273	0.52827	0.0851:0.0:0.9149:0.0	rs35121052;rs61126478	853	P02549	SPTA1_HUMAN	R	853	ENSP00000357130:T853R;ENSP00000357129:T853R	ENSP00000357129:T853R	T	-	2	0	SPTA1	156897730	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	5.076000	0.64413	1.249000	0.43950	0.650000	0.86243	ACA	G|0.933;C|0.067	0.067	strong		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
SHD	56961	hgsc.bcm.edu	37	19	4288332	4288332	+	Missense_Mutation	SNP	A	A	G	rs888930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4288332A>G	ENST00000543264.2	+	5	2272	c.809A>G	c.(808-810)aAc>aGc	p.N270S	SHD_ENST00000599689.1_Intron	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	270	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		N -> S (in dbSNP:rs888930). {ECO:0000269|PubMed:14702039}.					p.N270S(1)		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)		AGTGAGACCAACCCCCAGGAC	0.582													G|||	2424	0.484026	0.6203	0.5591	5008	,	,		18076	0.3393		0.3787	False		,,,				2504	0.5041				p.N270S		Atlas-SNP	.											SHD,NS,carcinoma,0,3	SHD	33	3	1	Substitution - Missense(1)	stomach(1)	c.A809G						PASS	.	G	SER/ASN	2534,1872	537.6+/-374.8	745,1044,414	78.0	66.0	70.0		809	4.0	1.0	19	dbSNP_86	70	3154,5446	653.7+/-401.1	567,2020,1713	yes	missense	SHD	NM_020209.3	46	1312,3064,2127	GG,GA,AA		36.6744,42.4875,43.7337	benign	270/341	4288332	5688,7318	2203	4300	6503	SO:0001583	missense	56961	exon5			AGACCAACCCCCA	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.809A>G	19.37:g.4288332A>G	ENSP00000446058:p.Asn270Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	60	22	0.366667	NM_020209	Q96NC2	Missense_Mutation	SNP	ENST00000543264.2	37	CCDS12125.1	1011	0.46291208791208793	331	0.6727642276422764	197	0.5441988950276243	198	0.34615384615384615	285	0.3759894459102902	G	7.008	0.556285	0.13436	0.575125	0.366744	ENSG00000105251	ENST00000543264;ENST00000221852	D	0.88046	-2.33	5.02	3.99	0.46301	SH2 motif (4);	0.262943	0.40554	N	0.001075	T	0.00012	0.0000	N	0.02181	-0.65	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.41752	-0.9491	9	0.02654	T	1	-4.3447	9.4055	0.38460	0.1725:0.0:0.8275:0.0	rs888930;rs1043817;rs3170373;rs52826654;rs59490546;rs888930	270	Q96IW2	SHD_HUMAN	S	270;185	ENSP00000446058:N270S	ENSP00000221852:N185S	N	+	2	0	SHD	4239332	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	5.276000	0.65580	0.738000	0.32606	-0.222000	0.12452	AAC	A|0.552;G|0.446	0.446	strong		0.582	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209	
MLXIP	22877	hgsc.bcm.edu	37	12	122618417	122618417	+	Missense_Mutation	SNP	G	G	T	rs34702867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122618417G>T	ENST00000319080.7	+	9	1747	c.1615G>T	c.(1615-1617)Gtg>Ttg	p.V539L	MLXIP_ENST00000538698.1_Missense_Mutation_p.V146L|MLXIP_ENST00000377037.2_Missense_Mutation_p.V129L					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)		GTTAACTTTTGTGCACCCCAA	0.607													G|||	194	0.038738	0.1422	0.0086	5008	,	,		14499	0.0		0.0	False		,,,				2504	0.0				p.V539L	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.G1615T						PASS	.	G	LEU/VAL	448,3490		28,392,1549	22.0	26.0	25.0		1205	4.2	1.0	12	dbSNP_126	25	6,8264		0,6,4129	yes	missense	MLXIP	NM_014938.3	32	28,398,5678	TT,TG,GG		0.0726,11.3763,3.7189	benign	539/920	122618417	454,11754	1969	4135	6104	SO:0001583	missense	22877	exon9			ACTTTTGTGCACC	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.1615G>T	12.37:g.122618417G>T	ENSP00000312834:p.Val539Leu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_014938		Missense_Mutation	SNP	ENST00000319080.7	37		73	0.033424908424908424	70	0.14227642276422764	3	0.008287292817679558	0	0.0	0	0.0	G	14.85	2.657247	0.47467	0.113763	7.26E-4	ENSG00000175727	ENST00000319080;ENST00000538698;ENST00000539039;ENST00000377037	D;D;D	0.84516	-1.86;-1.86;-1.86	5.09	4.19	0.49359	.	0.332806	0.28784	N	0.014156	T	0.02012	0.0063	.	.	.	0.24861	N	0.992344	B;B	0.31318	0.319;0.1	B;B	0.34301	0.179;0.03	T	0.00812	-1.1556	9	0.28530	T	0.3	-11.9952	12.6399	0.56705	0.0813:0.0:0.9187:0.0	rs34702867	539;539	Q9HAP2-3;Q9HAP2	.;MLXIP_HUMAN	L	539;146;146;129	ENSP00000312834:V539L;ENSP00000440769:V146L;ENSP00000366236:V129L	ENSP00000312834:V539L	V	+	1	0	MLXIP	121184370	1.000000	0.71417	0.977000	0.42913	0.967000	0.64934	4.310000	0.59141	1.097000	0.41459	0.655000	0.94253	GTG	G|0.973;T|0.027	0.027	strong		0.607	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938	
ZNF610	162963	hgsc.bcm.edu	37	19	52869022	52869022	+	Missense_Mutation	SNP	G	G	T	rs2241586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52869022G>T	ENST00000403906.3	+	6	847	c.391G>T	c.(391-393)Gca>Tca	p.A131S	ZNF610_ENST00000601151.1_Missense_Mutation_p.A88S|ZNF610_ENST00000321287.8_Missense_Mutation_p.A131S|ZNF610_ENST00000327920.8_Missense_Mutation_p.A131S	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	131			A -> S (in dbSNP:rs2241586). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15057824}.		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)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		AACCCTTGAGGCACATCTGTC	0.388													T|||	4129	0.824481	0.857	0.8012	5008	,	,		18847	0.6538		0.9006	False		,,,				2504	0.8947				p.A131S		Atlas-SNP	.											.	ZNF610	84	.	0			c.G391T						PASS	.	T	SER/ALA,SER/ALA,SER/ALA,SER/ALA	3729,677	286.3+/-278.7	1576,577,50	117.0	127.0	123.0		391,391,262,391	-2.2	0.0	19	dbSNP_98	123	7532,1068	224.3+/-260.7	3295,942,63	yes	missense,missense,missense,missense	ZNF610	NM_001161425.1,NM_001161426.1,NM_001161427.1,NM_173530.2	99,99,99,99	4871,1519,113	TT,TG,GG		12.4186,15.3654,13.4169	benign,benign,benign,benign	131/463,131/463,88/420,131/463	52869022	11261,1745	2203	4300	6503	SO:0001583	missense	162963	exon6			CTTGAGGCACATC	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"""Zinc fingers, C2H2-type"", ""-"""	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.391G>T	19.37:g.52869022G>T	ENSP00000383922:p.Ala131Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001161426	A8K4C3|Q86YH8|Q8NDS9	Missense_Mutation	SNP	ENST00000403906.3	37	CCDS12851.1	1744	0.7985347985347986	410	0.8333333333333334	301	0.8314917127071824	354	0.6188811188811189	679	0.895778364116095	T	0.001	-4.565087	0.00000	0.846346	0.875814	ENSG00000167554	ENST00000403906;ENST00000321287;ENST00000327920	T;T	0.04809	3.55;3.55	1.11	-2.21	0.06973	.	.	.	.	.	T	0.00012	0.0000	N	0.00642	-1.3	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39522	-0.9610	8	0.02654	T	1	.	5.3289	0.15922	0.0:0.1387:0.4761:0.3852	rs2241586;rs17836031;rs17857206;rs57199826;rs2241586	88;131	Q8N9Z0-2;Q8N9Z0	.;ZN610_HUMAN	S	131;88;131	ENSP00000383922:A131S;ENSP00000327597:A131S	ENSP00000324441:A88S	A	+	1	0	ZNF610	57560834	0.002000	0.14202	0.000000	0.03702	0.010000	0.07245	-0.736000	0.04882	-3.448000	0.00161	-2.491000	0.00194	GCA	G|0.164;T|0.836	0.836	strong		0.388	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530	
GPC1	2817	hgsc.bcm.edu	37	2	241404914	241404914	+	Silent	SNP	C	C	T	rs2228329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241404914C>T	ENST00000264039.2	+	8	1541	c.1293C>T	c.(1291-1293)gaC>gaT	p.D431D		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	431					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)		TCATGGGTGACGGCCTGGCCA	0.612													C|||	59	0.0117812	0.0416	0.0058	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.D431D		Atlas-SNP	.											.	GPC1	32	.	0			c.C1293T						PASS	.	C		128,4278	93.0+/-131.7	2,124,2077	92.0	77.0	82.0		1293	-2.5	1.0	2	dbSNP_98	82	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPC1	NM_002081.2		2,125,6376	TT,TC,CC		0.0116,2.9051,0.9918		431/559	241404914	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	2817	exon8			GGGTGACGGCCTG	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.1293C>T	2.37:g.241404914C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	C	2.512	-0.312638	0.05422	0.029051	1.16E-4	ENSG00000063660	ENST00000420138;ENST00000455111	.	.	.	3.56	-2.52	0.06346	.	.	.	.	.	T	0.29389	0.0732	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40459	-0.9562	4	.	.	.	-27.9108	9.046	0.36347	0.0:0.2401:0.0:0.7599	rs2228329;rs2228329	.	.	.	W	471;183	.	.	R	+	1	2	GPC1	241053587	0.000000	0.05858	0.965000	0.40720	0.315000	0.28087	-3.267000	0.00533	-0.465000	0.06953	-0.269000	0.10298	CGG	C|0.991;T|0.009	0.009	strong		0.612	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
NPR2	4882	hgsc.bcm.edu	37	9	35792423	35792423	+	Silent	SNP	T	T	C	rs2228580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	82	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	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		
DNHD1	144132	hgsc.bcm.edu	37	11	6541225	6541225	+	Missense_Mutation	SNP	C	C	G	rs11603869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6541225C>G	ENST00000527990.2	+	7	1678	c.1678C>G	c.(1678-1680)Cag>Gag	p.Q560E	DNHD1_ENST00000254579.6_Missense_Mutation_p.Q560E|DNHD1_ENST00000354685.3_Missense_Mutation_p.Q560E			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	560			Q -> E (in dbSNP:rs11603869).		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)		TCTCTCATCACAGCTGGTCTT	0.488													C|||	714	0.142572	0.1233	0.1628	5008	,	,		20440	0.0327		0.1909	False		,,,				2504	0.2178				p.Q560E		Atlas-SNP	.											.	DNHD1	198	.	0			c.C1678G						PASS	.	C	GLU/GLN,GLU/GLN	545,3857	247.2+/-255.5	36,473,1692	161.0	149.0	153.0		1678,1678	3.6	0.2	11	dbSNP_120	153	1840,6752	328.8+/-318.4	201,1438,2657	yes	missense,missense	DNHD1	NM_144666.2,NM_173589.3	29,29	237,1911,4349	GG,GC,CC		21.4153,12.3807,18.3546	possibly-damaging,possibly-damaging	560/4754,560/598	6541225	2385,10609	2201	4296	6497	SO:0001583	missense	144132	exon8			TCATCACAGCTGG	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.1678C>G	11.37:g.6541225C>G	ENSP00000436180:p.Gln560Glu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	291	0.13324175824175824	65	0.13211382113821138	52	0.143646408839779	25	0.043706293706293704	149	0.19656992084432717	C	10.69	1.420306	0.25552	0.123807	0.214153	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.25579	1.79;2.79;1.79	5.7	3.63	0.41609	.	0.813344	0.10962	N	0.614855	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B;B	0.32467	0.001;0.372	B;B	0.27796	0.002;0.083	T	0.13019	-1.0525	9	0.02654	T	1	.	9.8502	0.41053	0.1636:0.695:0.1414:0.0	rs11603869;rs11603869	560;560	Q96M86;Q96M86-4	DNHD1_HUMAN;.	E	560	ENSP00000254579:Q560E;ENSP00000346716:Q560E;ENSP00000436180:Q560E	ENSP00000254579:Q560E	Q	+	1	0	DNHD1	6497801	0.348000	0.24861	0.198000	0.23420	0.556000	0.35491	1.531000	0.36018	1.401000	0.46761	0.561000	0.74099	CAG	C|0.836;G|0.164	0.164	strong		0.488	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
MYL2	4633	hgsc.bcm.edu	37	12	111353556	111353556	+	Silent	SNP	A	A	G	rs2301610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:111353556A>G	ENST00000228841.8	-	3	179	c.132T>C	c.(130-132)atT>atC	p.I44I	MYL2_ENST00000548438.1_Intron	NM_000432.3	NP_000423.2	P10916	MLRV_HUMAN	myosin, light chain 2, regulatory, cardiac, slow	44	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cardiac muscle contraction (GO:0060048)|cardiac myofibril assembly (GO:0055003)|heart contraction (GO:0060047)|muscle cell fate specification (GO:0042694)|muscle fiber development (GO:0048747)|muscle filament sliding (GO:0030049)|negative regulation of cell growth (GO:0030308)|post-embryonic development (GO:0009791)|regulation of striated muscle contraction (GO:0006942)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|myofibril (GO:0030016)|myosin complex (GO:0016459)|sarcomere (GO:0030017)	actin monomer binding (GO:0003785)|calcium ion binding (GO:0005509)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)	12						CGTTCTTGTCAATGAAGCCAT	0.522													G|||	577	0.115216	0.0522	0.0317	5008	,	,		19995	0.2024		0.0895	False		,,,				2504	0.1963				p.I44I	GBM(14;268 426 18829 21617 25540)	Atlas-SNP	.											.	MYL2	31	.	0			c.T132C						PASS	.	G		305,4101	798.8+/-415.5	6,293,1904	248.0	213.0	225.0		132	-1.1	1.0	12	dbSNP_100	225	689,7911	788.2+/-407.6	25,639,3636	no	coding-synonymous	MYL2	NM_000432.3		31,932,5540	GG,GA,AA		8.0116,6.9224,7.6426		44/167	111353556	994,12012	2203	4300	6503	SO:0001819	synonymous_variant	4633	exon3			CTTGTCAATGAAG		CCDS31901.1	12q24.11	2014-09-17	2006-09-29		ENSG00000111245	ENSG00000111245		"""Myosins / Light chain"", ""EF-hand domain containing"""	7583	protein-coding gene	gene with protein product	"""cardiac ventricular myosin light chain 2"""	160781	"""myosin, light polypeptide 2, regulatory, cardiac, slow"""			1386340	Standard	NM_000432		Approved	CMH10	uc001try.4	P10916	OTTHUMG00000169535	ENST00000228841.8:c.132T>C	12.37:g.111353556A>G		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	319	147	0.460815	NM_000432	Q16123	Silent	SNP	ENST00000228841.8	37	CCDS31901.1																																																																																			A|0.911;G|0.089	0.089	strong		0.522	MYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404677.2	NM_000432	
CPT1A	1374	hgsc.bcm.edu	37	11	68529027	68529027	+	Silent	SNP	A	A	G	rs2228503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:68529027A>G	ENST00000265641.5	-	16	2158	c.2004T>C	c.(2002-2004)gcT>gcC	p.A668A	CPT1A_ENST00000539743.1_Silent_p.A668A|CPT1A_ENST00000376618.2_Silent_p.A668A|CPT1A_ENST00000540367.1_Silent_p.A668A|CPT1A_ENST00000537756.2_5'Flank	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	668					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)	p.A668A(1)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	GGGACTCCACAGCGAGATATT	0.473													G|||	63	0.0125799	0.0461	0.0014	5008	,	,		19324	0.0		0.001	False		,,,				2504	0.0				p.A668A		Atlas-SNP	.											CPT1A,colon,carcinoma,0,1	CPT1A	89	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T2004C						PASS	.	G	,	117,4283	815.3+/-416.2	2,113,2085	176.0	173.0	174.0		2004,2004	-11.3	0.0	11	dbSNP_132	174	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous	CPT1A	NM_001031847.2,NM_001876.3	,	2,113,6379	GG,GA,AA		0.0,2.6591,0.9008	,	668/757,668/774	68529027	117,12871	2200	4294	6494	SO:0001819	synonymous_variant	1374	exon16			CTCCACAGCGAGA	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.2004T>C	11.37:g.68529027A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_001876	Q8TCU0|Q9BWK0	Silent	SNP	ENST00000265641.5	37	CCDS8185.1																																																																																			A|0.991;G|0.009	0.009	strong		0.473	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876	
KRT23	25984	hgsc.bcm.edu	37	17	39081713	39081713	+	Silent	SNP	A	A	G	rs8037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39081713A>G	ENST00000209718.3	-	7	1459	c.1035T>C	c.(1033-1035)caT>caC	p.H345H	KRT23_ENST00000436344.3_Silent_p.H208H|AC004231.2_ENST00000418393.1_RNA	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)	345	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000301)|Ovarian(249;0.15)				GCTCCAGTTCATGGCGTAGCT	0.532													G|||	2859	0.570887	0.5643	0.6081	5008	,	,		21238	0.7083		0.4056	False		,,,				2504	0.5818				p.H345H		Atlas-SNP	.											.	KRT23	59	.	0			c.T1035C						PASS	.	G		2354,2052	568.7+/-382.4	628,1098,477	209.0	156.0	174.0		1035	-4.4	0.4	17	dbSNP_52	174	3382,5218	641.7+/-399.7	687,2008,1605	no	coding-synonymous	KRT23	NM_015515.3		1315,3106,2082	GG,GA,AA		39.3256,46.5729,44.1027		345/423	39081713	5736,7270	2203	4300	6503	SO:0001819	synonymous_variant	25984	exon7			CAGTTCATGGCGT	AF102848	CCDS11380.1, CCDS62182.1	17q21.2	2013-01-16			ENSG00000108244	ENSG00000108244		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6438	protein-coding gene	gene with protein product		606194				11135429, 16831889	Standard	NM_015515		Approved	K23, DKFZP434G032, HAIK1, CK23, MGC26158	uc002hvm.1	Q9C075	OTTHUMG00000133376	ENST00000209718.3:c.1035T>C	17.37:g.39081713A>G		Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	258	258	1	NM_015515	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Silent	SNP	ENST00000209718.3	37	CCDS11380.1																																																																																			A|0.501;G|0.499	0.499	strong		0.532	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1		
VPS52	6293	hgsc.bcm.edu	37	6	33235755	33235755	+	Silent	SNP	G	G	A	rs213199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33235755G>A	ENST00000445902.2	-	9	1038	c.820C>T	c.(820-822)Ctg>Ttg	p.L274L	VPS52_ENST00000482399.1_3'UTR|VPS52_ENST00000436044.2_Silent_p.L149L|VPS52_ENST00000478934.1_5'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	274					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						TCATTGCCCAGCAGAAACTGA	0.507													G|||	2227	0.444688	0.4501	0.3761	5008	,	,		19882	0.5823		0.3847	False		,,,				2504	0.4059				p.L274L		Atlas-SNP	.											.	VPS52	56	.	0			c.C820T						PASS	.	G		1291,1731		266,759,486	153.0	160.0	158.0		820	3.1	1.0	6	dbSNP_79	158	1948,3470		348,1252,1109	yes	coding-synonymous	VPS52	NM_022553.4		614,2011,1595	AA,AG,GG		35.9542,42.7201,38.3768		274/724	33235755	3239,5201	1511	2709	4220	SO:0001819	synonymous_variant	6293	exon9			TGCCCAGCAGAAA	AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"""SAC2 suppressor of actin mutations 2-like (yeast)"", ""vacuolar protein sorting 52 (yeast)"""	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.820C>T	6.37:g.33235755G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																			G|0.576;A|0.424	0.424	strong		0.507	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553	
PASK	23178	hgsc.bcm.edu	37	2	242065624	242065624	+	Silent	SNP	A	A	G	rs2240541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242065624A>G	ENST00000405260.1	-	10	3404	c.2706T>C	c.(2704-2706)gaT>gaC	p.D902D	PASK_ENST00000234040.4_Silent_p.D902D|PASK_ENST00000539818.1_Silent_p.D686D|PASK_ENST00000544142.1_Silent_p.D716D|PASK_ENST00000403638.3_Silent_p.D902D|PASK_ENST00000358649.4_Silent_p.D902D	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	902					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GCCGTAAGCCATCTCGATGGT	0.642													G|||	872	0.174121	0.4244	0.1153	5008	,	,		17498	0.124		0.0696	False		,,,				2504	0.0368				p.D902D		Atlas-SNP	.											.	PASK	230	.	0			c.T2706C						PASS	.	G		1774,2632	637.0+/-396.7	365,1044,794	63.0	49.0	54.0		2706	-3.9	0.0	2	dbSNP_98	54	648,7952	785.7+/-407.6	25,598,3677	no	coding-synonymous	PASK	NM_015148.2		390,1642,4471	GG,GA,AA		7.5349,40.2633,18.6222		902/1324	242065624	2422,10584	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon10			TAAGCCATCTCGA	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2706T>C	2.37:g.242065624A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			A|0.812;G|0.188	0.188	strong		0.642	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
MKL1	57591	hgsc.bcm.edu	37	22	40814594	40814594	+	Silent	SNP	C	C	T	rs56211152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:40814594C>T	ENST00000355630.3	-	12	2438	c.1848G>A	c.(1846-1848)ccG>ccA	p.P616P	MKL1_ENST00000407029.1_Silent_p.P616P|MKL1_ENST00000402042.1_Silent_p.P566P|MKL1_ENST00000396617.3_Silent_p.P616P	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	616	Pro-rich.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						ACGGGGGCCCCGGGGCCACAG	0.716			T	RBM15	acute megakaryocytic leukemia								C|||	1050	0.209665	0.3147	0.1599	5008	,	,		9970	0.0694		0.1581	False		,,,				2504	0.3006				p.P616P		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1	69	.	0			c.G1848A						PASS	.	C		1350,2998		209,932,1033	12.0	17.0	15.0		1848	-9.2	0.0	22	dbSNP_129	15	1449,7081		140,1169,2956	no	coding-synonymous	MKL1	NM_020831.3		349,2101,3989	TT,TC,CC		16.9871,31.0488,21.7347		616/932	40814594	2799,10079	2174	4265	6439	SO:0001819	synonymous_variant	57591	exon12			GGGCCCCGGGGCC	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.1848G>A	22.37:g.40814594C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Silent	SNP	ENST00000355630.3	37	CCDS14003.1																																																																																			C|0.833;T|0.167	0.167	strong		0.716	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831	
SYT2	127833	hgsc.bcm.edu	37	1	202569555	202569555	+	Silent	SNP	C	C	T	rs907699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:202569555C>T	ENST00000367267.1	-	7	1041	c.849G>A	c.(847-849)acG>acA	p.T283T	SYT2_ENST00000367268.4_Silent_p.T283T	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	283	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|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)	GCTTCCCGGCCGTGGGCACAT	0.607											OREG0014101	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	419	0.0836661	0.3011	0.0245	5008	,	,		20029	0.0		0.003	False		,,,				2504	0.001				p.T283T		Atlas-SNP	.											.	SYT2	51	.	0			c.G849A						PASS	.	C	,	1168,3238	411.7+/-335.8	150,868,1185	86.0	83.0	84.0		849,849	-4.4	0.7	1	dbSNP_86	84	45,8555	30.1+/-81.4	0,45,4255	no	coding-synonymous,coding-synonymous	SYT2	NM_001136504.1,NM_177402.4	,	150,913,5440	TT,TC,CC		0.5233,26.5093,9.3265	,	283/420,283/420	202569555	1213,11793	2203	4300	6503	SO:0001819	synonymous_variant	127833	exon7			CCCGGCCGTGGGC	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.849G>A	1.37:g.202569555C>T		Somatic	87	0	0	2130	WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_177402	Q496K5|Q8NBE5	Silent	SNP	ENST00000367267.1	37	CCDS1427.1																																																																																			C|0.917;T|0.083	0.083	strong		0.607	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402	
FCGBP	8857	hgsc.bcm.edu	37	19	40399385	40399385	+	Missense_Mutation	SNP	C	C	T	rs201168964		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40399385C>T	ENST00000221347.6	-	13	6317	c.6310G>A	c.(6310-6312)Gga>Aga	p.G2104R		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2104	VWFD 5. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AAGGGTGGTCCGTGGCAGGGT	0.597																																					p.G2104R		Atlas-SNP	.											FCGBP,NS,carcinoma,0,2	FCGBP	416	2	0			c.G6310A						scavenged	.						9.0	12.0	11.0					19																	40399385		1085	2084	3169	SO:0001583	missense	8857	exon13			GTGGTCCGTGGCA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.6310G>A	19.37:g.40399385C>T	ENSP00000221347:p.Gly2104Arg	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	252	50	0.198413	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	0.241	-1.013596	0.02095	.	.	ENSG00000090920	ENST00000221347	T	0.59083	0.29	3.01	0.723	0.18231	von Willebrand factor, type D domain (3);	.	.	.	.	T	0.43389	0.1245	L	0.43923	1.385	0.09310	N	1	B	0.19445	0.036	B	0.10450	0.005	T	0.26780	-1.0093	9	0.28530	T	0.3	.	5.6999	0.17877	0.0:0.5011:0.0:0.4989	.	2104	Q9Y6R7	FCGBP_HUMAN	R	2104	ENSP00000221347:G2104R	ENSP00000221347:G2104R	G	-	1	0	FCGBP	45091225	0.000000	0.05858	0.002000	0.10522	0.254000	0.26022	-2.133000	0.01308	0.480000	0.27534	0.298000	0.19748	GGA	C|0.500;T|0.500	0.500	strong		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
SLC36A3	285641	hgsc.bcm.edu	37	5	150664183	150664183	+	Silent	SNP	G	G	C	rs17111902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	119	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	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	
SLC25A23	79085	hgsc.bcm.edu	37	19	6454651	6454651	+	Silent	SNP	T	T	C	rs8103745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6454651T>C	ENST00000301454.4	-	5	667	c.561A>G	c.(559-561)aaA>aaG	p.K187K	SLC25A23_ENST00000414491.2_Silent_p.K4K|SLC25A23_ENST00000334510.5_Silent_p.K187K	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	187					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CCACCAGCTGTTTCCACCACA	0.612													C|||	924	0.184505	0.5983	0.0576	5008	,	,		18809	0.0		0.0268	False		,,,				2504	0.0675				p.K187K		Atlas-SNP	.											.	SLC25A23	43	.	0			c.A561G						PASS	.	C		2286,2120	576.0+/-384.1	590,1106,507	54.0	49.0	51.0		561	0.6	1.0	19	dbSNP_116	51	357,8243	802.2+/-407.3	6,345,3949	no	coding-synonymous	SLC25A23	NM_024103.2		596,1451,4456	CC,CT,TT		4.1512,48.1162,20.3214		187/469	6454651	2643,10363	2203	4300	6503	SO:0001819	synonymous_variant	79085	exon5			CAGCTGTTTCCAC	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"""Solute carriers"", ""EF-hand domain containing"""	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.561A>G	19.37:g.6454651T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Silent	SNP	ENST00000301454.4	37	CCDS32882.1																																																																																			T|0.820;C|0.180	0.180	strong		0.612	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103	
SNAI1	6615	hgsc.bcm.edu	37	20	48600557	48600557	+	Silent	SNP	T	T	C	rs4647959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48600557T>C	ENST00000244050.2	+	2	340	c.279T>C	c.(277-279)gaT>gaC	p.D93D		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	93	Ser-rich.				cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|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 regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			CCCTGTCAGATGAGGACAGTG	0.642													C|||	1466	0.292732	0.7171	0.232	5008	,	,		15499	0.0913		0.1262	False		,,,				2504	0.1411				p.D93D		Atlas-SNP	.											.	SNAI1	28	.	0			c.T279C						PASS	.	C		2735,1671	501.0+/-364.9	874,987,342	47.0	57.0	53.0		279	-7.4	0.6	20	dbSNP_111	53	1059,7541	760.8+/-407.6	65,929,3306	no	coding-synonymous	SNAI1	NM_005985.3		939,1916,3648	CC,CT,TT		12.314,37.9256,29.1712		93/265	48600557	3794,9212	2203	4300	6503	SO:0001819	synonymous_variant	6615	exon2			GTCAGATGAGGAC	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	11128	protein-coding gene	gene with protein product		604238	"""snail 1 (drosophila homolog), zinc finger protein"", ""snail homolog 1 (Drosophila)"""			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.279T>C	20.37:g.48600557T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_005985	B2R842|Q9P113|Q9UBP7|Q9UHH7	Silent	SNP	ENST00000244050.2	37	CCDS13423.1																																																																																			T|0.712;C|0.288	0.288	strong		0.642	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1		
CXorf36	79742	hgsc.bcm.edu	37	X	45011018	45011018	+	Missense_Mutation	SNP	C	C	A	rs143817529		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:45011018C>A	ENST00000398000.2	-	5	1255	c.1181G>T	c.(1180-1182)cGc>cTc	p.R394L	CXorf36_ENST00000477281.1_5'UTR	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	394						extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						TGGGTCTGGGCGGATGCTGTC	0.572													C||||C|||	161|161	0.042649|0.042649	0.1188|0.1188	0.0043|0.0043	3775|3775	,|,	,|,		12325|12325	0.0|0.0		0.001|0.001	False|False		,,,|,,,				2504|2504	0.0|0.0				p.R394L		Atlas-SNP	.											.	CXorf36	53	.	0			c.G1181T						PASS	.	C	LEU/ARG	336,2291		19,221,77,819,432	63.0	57.0	59.0		1181	0.3	0.0	X	dbSNP_134	59	0,5498		0,0,0,1916,1666	yes	missense	CXorf36	NM_176819.3	102	19,221,77,2735,2098	AA,AC,A,CC,C		0.0,12.7903,4.1354	benign	394/434	45011018	336,7789	1568	3582	5150	SO:0001583	missense	79742	exon5			TCTGGGCGGATGC	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.1181G>T	X.37:g.45011018C>A	ENSP00000381086:p.Arg394Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Missense_Mutation	SNP	ENST00000398000.2	37	CCDS48096.1	50	0.030138637733574444	36	0.07692307692307693	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	1.583	-0.531173	0.04112	0.127903	0.0	ENSG00000147113	ENST00000398000	T	0.28895	1.59	5.17	0.326	0.15908	.	1.193830	0.06015	N	0.650241	T	0.00178	0.0005	N	0.16307	0.4	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.24476	-1.0159	9	0.27082	T	0.32	.	3.0329	0.06112	0.3241:0.4237:0.0931:0.1592	.	394	Q9H7Y0	CX036_HUMAN	L	394	ENSP00000381086:R394L	ENSP00000381086:R394L	R	-	2	0	CXorf36	44895962	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	-0.848000	0.04326	-0.006000	0.14370	-0.215000	0.12644	CGC	C|0.970;A|0.030	0.030	strong		0.572	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689	
WBSCR27	155368	hgsc.bcm.edu	37	7	73254871	73254871	+	Silent	SNP	A	A	G	rs61741292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73254871A>G	ENST00000297873.4	-	4	310	c.261T>C	c.(259-261)gcT>gcC	p.A87A		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	87										NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				GGAAGCCTGGAGCCCGCAGCT	0.672													A|||	173	0.0345447	0.1263	0.0072	5008	,	,		14138	0.0		0.001	False		,,,				2504	0.0				p.A87A		Atlas-SNP	.											.	WBSCR27	21	.	0			c.T261C						PASS	.	A		341,3999		14,313,1843	14.0	17.0	16.0		261	-0.2	1.0	7	dbSNP_129	16	2,8534		0,2,4266	no	coding-synonymous	WBSCR27	NM_152559.2		14,315,6109	GG,GA,AA		0.0234,7.8571,2.6639		87/246	73254871	343,12533	2170	4268	6438	SO:0001819	synonymous_variant	155368	exon4			GCCTGGAGCCCGC	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.261T>C	7.37:g.73254871A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_152559		Silent	SNP	ENST00000297873.4	37	CCDS5561.1																																																																																			A|0.974;G|0.026	0.026	strong		0.672	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559	
PABPC3	5042	hgsc.bcm.edu	37	13	25671742	25671742	+	Missense_Mutation	SNP	G	G	A	rs140135080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25671742G>A	ENST00000281589.3	+	1	1443	c.1406G>A	c.(1405-1407)cGa>cAa	p.R469Q		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	469					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		CAGGTTCCACGAGTCATGTCA	0.547																																					p.R469Q		Atlas-SNP	.											PABPC3,NS,carcinoma,+1,1	PABPC3	129	1	0			c.G1406A						PASS	.						104.0	96.0	98.0					13																	25671742		2203	4300	6503	SO:0001583	missense	5042	exon1			TTCCACGAGTCAT	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1406G>A	13.37:g.25671742G>A	ENSP00000281589:p.Arg469Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	120	6	0.05	NM_030979	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	6.381	0.438497	0.12104	.	.	ENSG00000151846	ENST00000281589	T	0.26223	1.75	0.875	-0.195	0.13236	.	0.000000	0.40064	U	0.001189	T	0.13114	0.0318	L	0.35288	1.05	0.42075	D	0.991227	B	0.06786	0.001	B	0.06405	0.002	T	0.20638	-1.0269	10	0.10902	T	0.67	.	5.1429	0.14969	0.252:0.0:0.748:0.0	.	469	Q9H361	PABP3_HUMAN	Q	469	ENSP00000281589:R469Q	ENSP00000281589:R469Q	R	+	2	0	PABPC3	24569742	1.000000	0.71417	0.977000	0.42913	0.138000	0.21146	3.032000	0.49736	-0.094000	0.12374	0.313000	0.20887	CGA	G|0.919;A|0.081	0.081	strong		0.547	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
RNF213	57674	hgsc.bcm.edu	37	17	78261805	78261805	+	Silent	SNP	A	A	G	rs7215243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78261805A>G	ENST00000582970.1	+	4	596	c.453A>G	c.(451-453)ccA>ccG	p.P151P	RNF213_ENST00000508628.2_Silent_p.P200P|RNF213_ENST00000319921.4_Silent_p.P151P|RNF213_ENST00000456466.1_Silent_p.P151P	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	151					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCCAGCCCCCAGGCACAGCCA	0.692													G|||	1481	0.295727	0.5885	0.1873	5008	,	,		12591	0.131		0.1988	False		,,,				2504	0.2464				p.P151P		Atlas-SNP	.											RNF213_ENST00000456466,NS,carcinoma,0,3	RNF213	766	3	0			c.A453G						PASS	.	G	,	2141,2209		550,1041,584	11.0	13.0	12.0		600,453	-4.2	0.0	17	dbSNP_116	12	1773,6779		200,1373,2703	no	coding-synonymous,coding-synonymous	RNF213	NM_020914.4,NM_020954.2	,	750,2414,3287	GG,GA,AA		20.732,49.2184,30.3364	,	200/5257,151/1064	78261805	3914,8988	2175	4276	6451	SO:0001819	synonymous_variant	57674	exon4			GCCCCCAGGCACA	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.453A>G	17.37:g.78261805A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			A|0.731;G|0.269	0.269	strong		0.692	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
TRPM8	79054	hgsc.bcm.edu	37	2	234915540	234915540	+	Silent	SNP	C	C	G	rs11563071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234915540C>G	ENST00000324695.4	+	23	3214	c.3174C>G	c.(3172-3174)gtC>gtG	p.V1058V	TRPM8_ENST00000433712.2_Silent_p.V636V	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	1058					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	GGGAGGGTGTCATGAAGGAAA	0.418													C|||	632	0.126198	0.1989	0.1484	5008	,	,		21661	0.1081		0.0815	False		,,,				2504	0.0767				p.V1058V		Atlas-SNP	.											.	TRPM8	146	.	0			c.C3174G						PASS	.	C		782,3624	314.7+/-293.7	73,636,1494	132.0	109.0	117.0		3174	2.9	1.0	2	dbSNP_120	117	831,7769	191.7+/-237.8	34,763,3503	no	coding-synonymous	TRPM8	NM_024080.4		107,1399,4997	GG,GC,CC		9.6628,17.7485,12.402		1058/1105	234915540	1613,11393	2203	4300	6503	SO:0001819	synonymous_variant	79054	exon23			GGGTGTCATGAAG	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.3174C>G	2.37:g.234915540C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	89	58	0.651685	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Silent	SNP	ENST00000324695.4	37	CCDS33407.1																																																																																			C|0.880;G|0.120	0.120	strong		0.418	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
SPAG17	200162	hgsc.bcm.edu	37	1	118634297	118634297	+	Missense_Mutation	SNP	A	A	C	rs150596428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118634297A>C	ENST00000336338.5	-	10	1356	c.1291T>G	c.(1291-1293)Tat>Gat	p.Y431D		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	431						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TTCAGCAAATAATTGTAATAT	0.383													C|||	6	0.00119808	0.0045	0.0	5008	,	,		18256	0.0		0.0	False		,,,				2504	0.0				p.Y431D		Atlas-SNP	.											.	SPAG17	263	.	0			c.T1291G						PASS	.	C	ASP/TYR	28,4376	822.7+/-416.5	1,26,2175	89.0	85.0	86.0		1291	5.6	1.0	1	dbSNP_134	86	0,8600		0,0,4300	yes	missense	SPAG17	NM_206996.2	160	1,26,6475	CC,CA,AA		0.0,0.6358,0.2153	benign	431/2224	118634297	28,12976	2202	4300	6502	SO:0001583	missense	200162	exon10			GCAAATAATTGTA		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.1291T>G	1.37:g.118634297A>C	ENSP00000337804:p.Tyr431Asp	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	145	59	0.406897	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	7.275	0.607874	0.14002	0.006358	0.0	ENSG00000155761	ENST00000336338	T	0.67171	-0.25	5.59	5.59	0.84812	.	0.259606	0.43747	N	0.000525	T	0.07863	0.0197	N	0.00043	-2.47	0.26007	N	0.982046	B	0.02656	0.0	B	0.01281	0.0	T	0.33317	-0.9873	10	0.02654	T	1	.	16.0877	0.81070	0.1351:0.8649:0.0:0.0	.	431	Q6Q759	SPG17_HUMAN	D	431	ENSP00000337804:Y431D	ENSP00000337804:Y431D	Y	-	1	0	SPAG17	118435820	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.779000	0.47734	1.387000	0.46486	-0.127000	0.14921	TAT	A|0.997;C|0.003	0.003	strong		0.383	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
MAD1L1	8379	hgsc.bcm.edu	37	7	2275177	2275177	+	5'Flank	SNP	G	G	A	rs11547272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2275177G>A	ENST00000406869.1	-	0	0				MAD1L1_ENST00000399654.2_5'Flank|FTSJ2_ENST00000486040.1_5'UTR|FTSJ2_ENST00000407040.1_Silent_p.F13F|MAD1L1_ENST00000265854.7_5'Flank|FTSJ2_ENST00000440306.2_Missense_Mutation_p.S142L|FTSJ2_ENST00000242257.8_Silent_p.F107F|MAD1L1_ENST00000402746.1_5'Flank			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)						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)		CCCCAAGCACGAAGCCAACAG	0.448													G|||	73	0.0145767	0.0537	0.0029	5008	,	,		22055	0.0		0.0	False		,,,				2504	0.0				p.F107F		Atlas-SNP	.											.	FTSJ2	22	.	0			c.C321T						PASS	.	G		246,4160	136.9+/-172.8	7,232,1964	49.0	47.0	48.0		321	-5.2	0.8	7	dbSNP_120	48	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	FTSJ2	NM_013393.1		7,235,6261	AA,AG,GG		0.0349,5.5833,1.9145		107/247	2275177	249,12757	2203	4300	6503	SO:0001631	upstream_gene_variant	29960	exon3			AAGCACGAAGCCA	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		7.37:g.2275177G>A	Exception_encountered	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	42	29	0.690476	NM_013393	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Silent	SNP	ENST00000406869.1	37	CCDS43539.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	G	15.89	2.967220	0.53507	0.055833	3.49E-4	ENSG00000122687	ENST00000440306	T	0.30714	1.52	5.47	-5.18	0.02840	.	.	.	.	.	T	0.05181	0.0138	.	.	.	0.22710	N	0.99883	.	.	.	.	.	.	T	0.39961	-0.9588	6	0.87932	D	0	.	14.6466	0.68764	0.5757:0.0:0.4243:0.0	rs11547272	.	.	.	L	142	ENSP00000392343:S142L	ENSP00000392343:S142L	S	-	2	0	FTSJ2	2241703	0.001000	0.12720	0.835000	0.33067	0.981000	0.71138	-1.403000	0.02497	-1.417000	0.02017	-0.137000	0.14449	TCG	G|0.982;C|0.000;A|0.018	0.018	strong		0.448	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550	
MUC17	140453	hgsc.bcm.edu	37	7	100678610	100678610	+	Missense_Mutation	SNP	A	A	T	rs78010183	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678610A>T	ENST00000306151.4	+	3	3977	c.3913A>T	c.(3913-3915)Act>Tct	p.T1305S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1305	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)					TCCTGTTGACACTAAAGGTCC	0.458																																					p.T1305S		Atlas-SNP	.											.	MUC17	804	.	0			c.A3913T						PASS	.						240.0	230.0	233.0					7																	100678610		2203	4300	6503	SO:0001583	missense	140453	exon3			GTTGACACTAAAG	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.3913A>T	7.37:g.100678610A>T	ENSP00000302716:p.Thr1305Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	126	21	0.166667	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	0.022	-1.413760	0.01145	.	.	ENSG00000169876	ENST00000306151	T	0.02323	4.34	0.471	-0.942	0.10398	.	.	.	.	.	T	0.01870	0.0059	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.49670	-0.8915	8	0.18710	T	0.47	.	.	.	.	.	1305	Q685J3	MUC17_HUMAN	S	1305	ENSP00000302716:T1305S	ENSP00000302716:T1305S	T	+	1	0	MUC17	100465330	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.508000	0.06344	-3.256000	0.00203	-4.074000	0.00012	ACT	A|0.943;T|0.057	0.057	strong		0.458	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SSPO	23145	hgsc.bcm.edu	37	7	149479335	149479335	+	RNA	SNP	G	G	C	rs855680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149479335G>C	ENST00000378016.2	+	0	1848							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)			GGAGCTGCCTGCACGCCATCT	0.637													C|||	829	0.165535	0.3782	0.0807	5008	,	,		18920	0.0972		0.0696	False		,,,				2504	0.1074				p.L616L		Atlas-SNP	.											.	.	.	.	0			c.G1848C						PASS	.	C		1349,2911		218,913,999	34.0	41.0	38.0		1850	3.1	0.9	7	dbSNP_86	38	588,7880		31,526,3677	yes	coding-notMod3	SSPO	NM_198455.2		249,1439,4676	CC,CG,GG		6.9438,31.6667,15.2184			149479335	1937,10791	2130	4234	6364			23145	exon14			CTGCCTGCACGCC	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.149479335G>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				G|0.868;C|0.132	0.132	strong		0.637	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
GLRA3	8001	hgsc.bcm.edu	37	4	175598280	175598280	+	Silent	SNP	A	A	G	rs12648678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:175598280A>G	ENST00000274093.3	-	7	1378	c.876T>C	c.(874-876)acT>acC	p.T292T	GLRA3_ENST00000340217.5_Silent_p.T292T	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	292					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)	p.T292T(1)		endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)|Ivermectin(DB00602)|Lindane(DB00431)	TCGTTAGCACAGTGGTTATCC	0.458													A|||	1084	0.216454	0.1589	0.2305	5008	,	,		17324	0.3651		0.1769	False		,,,				2504	0.1718				p.T292T		Atlas-SNP	.											GLRA3,NS,carcinoma,0,1	GLRA3	76	1	1	Substitution - coding silent(1)	stomach(1)	c.T876C						PASS	.	A	,	723,3683	297.3+/-284.7	60,603,1540	113.0	91.0	98.0		876,876	-8.1	0.9	4	dbSNP_120	98	1487,7113	282.8+/-295.8	117,1253,2930	no	coding-synonymous,coding-synonymous	GLRA3	NM_001042543.1,NM_006529.2	,	177,1856,4470	GG,GA,AA		17.2907,16.4094,16.9922	,	292/450,292/465	175598280	2210,10796	2203	4300	6503	SO:0001819	synonymous_variant	8001	exon7			TAGCACAGTGGTT	AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"""Ligand-gated ion channels / Glycine receptors"""	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.876T>C	4.37:g.175598280A>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	188	86	0.457447	NM_001042543	D3DP44|O75816|Q5D0E3	Silent	SNP	ENST00000274093.3	37	CCDS3822.1																																																																																			A|0.807;G|0.193	0.193	strong		0.458	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1		
C2orf54	79919	hgsc.bcm.edu	37	2	241831005	241831005	+	Silent	SNP	C	C	T	rs10195453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241831005C>T	ENST00000388934.4	-	2	848	c.690G>A	c.(688-690)agG>agA	p.R230R	C2orf54_ENST00000307486.8_Silent_p.R81R|C2orf54_ENST00000402775.2_Silent_p.R62R	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	230										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		GGCTGAGGATCCTTCTCAAGC	0.667													C|||	2637	0.526558	0.7784	0.3473	5008	,	,		18639	0.4405		0.5179	False		,,,				2504	0.411				p.R230R		Atlas-SNP	.											.	C2orf54	14	.	0			c.G690A						PASS	.	C	,	2972,1046		1107,758,144	49.0	58.0	55.0		690,186	0.1	0.0	2	dbSNP_119	55	4121,4201		1036,2049,1076	no	coding-synonymous,coding-synonymous	C2orf54	NM_001085437.1,NM_024861.2	,	2143,2807,1220	TT,TC,CC		49.5193,26.0329,42.5203	,	230/448,62/280	241831005	7093,5247	2009	4161	6170	SO:0001819	synonymous_variant	79919	exon2			GAGGATCCTTCTC	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.690G>A	2.37:g.241831005C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	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	
PTPRQ	374462	hgsc.bcm.edu	37	12	80900348	80900348	+	Splice_Site	SNP	T	T	G	rs7965277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	23	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	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
CYP3A43	64816	hgsc.bcm.edu	37	7	99447241	99447241	+	Silent	SNP	T	T	C	rs800667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99447241T>C	ENST00000354829.2	+	7	697	c.594T>C	c.(592-594)aaT>aaC	p.N198N	CYP3A43_ENST00000222382.5_Silent_p.N198N|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000342499.4_Missense_Mutation_p.S61P|CYP3A43_ENST00000415413.1_Intron|CYP3A43_ENST00000417625.1_Intron|CYP3A43_ENST00000312017.5_Silent_p.N198N|CYP3A43_ENST00000444905.1_Intron	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	198			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)	CTCTCAACAATCCACAAGATC	0.333													C|||	975	0.194688	0.5938	0.1009	5008	,	,		18347	0.001		0.0616	False		,,,				2504	0.0583				p.N198N		Atlas-SNP	.											.	CYP3A43	52	.	0			c.T594C						PASS	.	C	,,	2230,2176	585.0+/-386.2	552,1126,525	140.0	132.0	135.0		594,594,594	-3.2	0.6	7	dbSNP_86	135	593,8007	792.7+/-407.5	24,545,3731	no	coding-synonymous,coding-synonymous,coding-synonymous	CYP3A43	NM_022820.3,NM_057095.1,NM_057096.2	,,	576,1671,4256	CC,CT,TT		6.8953,49.3872,21.7054	,,	198/505,198/504,198/421	99447241	2823,10183	2203	4300	6503	SO:0001819	synonymous_variant	64816	exon7			CAACAATCCACAA	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.594T>C	7.37:g.99447241T>C		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	195	86	0.441026	NM_057096	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Silent	SNP	ENST00000354829.2	37	CCDS5676.1	393	0.17994505494505494	306	0.6219512195121951	38	0.10497237569060773	1	0.0017482517482517483	48	0.0633245382585752	C	0.203	-1.042775	0.01997	0.506128	0.068953	ENSG00000021461	ENST00000342499;ENST00000379654	T	0.75477	-0.94	3.14	-3.15	0.05233	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.52501	P	4.8000000000048004E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43829	-0.9367	7	0.87932	D	0	.	6.0388	0.19722	0.1468:0.2312:0.0:0.622	rs800667;rs1403189;rs17161960;rs58499684;rs800667	61	F8W6L8	.	P	61;92	ENSP00000345351:S61P	ENSP00000345351:S61P	S	+	1	0	CYP3A43	99285177	0.411000	0.25384	0.601000	0.28877	0.201000	0.24016	-0.433000	0.06948	-0.896000	0.03915	-2.949000	0.00084	TCC	T|0.798;G|0.002	.	strong		0.333	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1		
SPHK2	56848	hgsc.bcm.edu	37	19	49133020	49133020	+	Missense_Mutation	SNP	G	G	A	rs11881285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49133020G>A	ENST00000245222.4	+	7	2321	c.1955G>A	c.(1954-1956)cGg>cAg	p.R652Q	SPHK2_ENST00000600537.1_Missense_Mutation_p.R593Q|SPHK2_ENST00000599748.1_Missense_Mutation_p.R616Q|SPHK2_ENST00000598088.1_Missense_Mutation_p.R652Q|SPHK2_ENST00000599029.1_Intron|SPHK2_ENST00000443164.1_Intron|SPHK2_ENST00000340932.3_Missense_Mutation_p.R614Q	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	652			R -> Q (in dbSNP:rs11881285).		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)		TGCCCGGGGCGGGAGCCCTGA	0.657													G|||	274	0.0547125	0.1959	0.0216	5008	,	,		14281	0.0		0.0	False		,,,				2504	0.0				p.R652Q		Atlas-SNP	.											.	SPHK2	62	.	0			c.G1955A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	687,3701		44,599,1551	13.0	14.0	13.0		1955,1847,1955,1778	0.8	0.0	19	dbSNP_120	13	3,8561		0,3,4279	yes	missense,missense,missense,missense	SPHK2	NM_020126.4,NM_001204160.2,NM_001204159.2,NM_001204158.2	43,43,43,43	44,602,5830	AA,AG,GG		0.035,15.6563,5.3274	benign,benign,benign,benign	652/655,616/619,652/655,593/596	49133020	690,12262	2194	4282	6476	SO:0001583	missense	56848	exon7			CGGGGCGGGAGCC	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.1955G>A	19.37:g.49133020G>A	ENSP00000245222:p.Arg652Gln	Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Missense_Mutation	SNP	ENST00000245222.4	37	CCDS12727.1	94	0.04304029304029304	84	0.17073170731707318	10	0.027624309392265192	0	0.0	0	0.0	G	13.95	2.389587	0.42410	0.156563	3.5E-4	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000340932	T;T	0.26067	2.04;1.76	4.57	0.757	0.18427	.	1.133370	0.06720	N	0.774700	T	0.00039	0.0001	N	0.00926	-1.1	0.09310	N	1	B;B	0.10296	0.001;0.003	B;B	0.01281	0.0;0.0	T	0.29882	-0.9997	10	0.87932	D	0	.	4.2933	0.10888	0.1758:0.4248:0.3994:0.0	rs11881285;rs11881285	593;652	B4DU87;Q9NRA0	.;SPHK2_HUMAN	Q	652;625;614	ENSP00000245222:R652Q;ENSP00000341091:R614Q	ENSP00000245222:R652Q	R	+	2	0	SPHK2	53824832	0.005000	0.15991	0.003000	0.11579	0.039000	0.13416	0.222000	0.17699	0.076000	0.16826	0.555000	0.69702	CGG	G|0.942;A|0.058	0.058	strong		0.657	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
DGKA	1606	hgsc.bcm.edu	37	12	56346891	56346891	+	Silent	SNP	C	C	T	rs199663532		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56346891C>T	ENST00000331886.5	+	22	2464	c.2010C>T	c.(2008-2010)acC>acT	p.T670T	DGKA_ENST00000394147.1_Silent_p.T670T|DGKA_ENST00000551156.1_Silent_p.T670T|DGKA_ENST00000549079.2_3'UTR	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	670					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)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	AAATCTATACCAAGCTCAAGA	0.532																																					p.T670T		Atlas-SNP	.											.	DGKA	70	.	0			c.C2010T						PASS	.						112.0	109.0	110.0					12																	56346891		2203	4300	6503	SO:0001819	synonymous_variant	1606	exon22			CTATACCAAGCTC	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"""EF-hand domain containing"""	2849	protein-coding gene	gene with protein product		125855	"""diacylglycerol kinase, alpha (80kD)"""	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.2010C>T	12.37:g.56346891C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Silent	SNP	ENST00000331886.5	37	CCDS8896.1																																																																																			.	.	none		0.532	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1		
SIRPA	140885	hgsc.bcm.edu	37	20	1895889	1895889	+	Missense_Mutation	SNP	G	G	C	rs72620874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1895889G>C	ENST00000358771.4	+	2	376	c.224G>C	c.(223-225)gGc>gCc	p.G75A	SIRPA_ENST00000356025.3_Missense_Mutation_p.G75A|SIRPA_ENST00000400068.3_Missense_Mutation_p.G75A	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	75	Ig-like V-type.		G -> A (in dbSNP:rs1057114). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.G75A(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GCTGGACCAGGCCGGGAATTA	0.537													G|||	2164	0.432109	0.298	0.4553	5008	,	,		14136	0.6369		0.3588	False		,,,				2504	0.4611				p.G75A	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,right_upper_lobe,carcinoma,+1,3	SIRPA	83	3	1	Substitution - Missense(1)	pancreas(1)	c.G224C						PASS	.						68.0	62.0	64.0					20																	1895889		2203	4297	6500	SO:0001583	missense	140885	exon3			GACCAGGCCGGGA	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.224G>C	20.37:g.1895889G>C	ENSP00000351621:p.Gly75Ala	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	211	27	0.127962	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	952	0.4358974358974359	153	0.31097560975609756	151	0.4171270718232044	373	0.6520979020979021	275	0.3627968337730871	G	8.882	0.951948	0.18431	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.66995	-0.24;-0.24;-0.24	5.11	-1.44	0.08856	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.281220	0.04967	N	0.463081	T	0.00012	0.0000	L	0.60957	1.885	0.80722	P	0.0	B;B;B	0.22851	0.0;0.076;0.001	B;B;B	0.26416	0.02;0.069;0.012	T	0.48514	-0.9029	9	0.37606	T	0.19	.	8.9336	0.35686	0.7056:0.0:0.2944:0.0	.	55;75;75	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	A	75	ENSP00000382941:G75A;ENSP00000348307:G75A;ENSP00000351621:G75A	ENSP00000348307:G75A	G	+	2	0	SIRPA	1843889	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.791000	0.04599	-0.225000	0.09913	-0.266000	0.10368	GGC	G|0.689;C|0.311	0.311	strong		0.537	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
KCNJ4	3761	hgsc.bcm.edu	37	22	38822905	38822905	+	Silent	SNP	C	C	T	rs105153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38822905C>T	ENST00000303592.3	-	2	1491	c.1233G>A	c.(1231-1233)gcG>gcA	p.A411A	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	411					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					GGATGATGCCCGCCTCCTCCT	0.677													C|||	308	0.0615016	0.1846	0.0187	5008	,	,		13455	0.0		0.0159	False		,,,				2504	0.0358				p.A411A		Atlas-SNP	.											.	KCNJ4	74	.	0			c.G1233A						PASS	.	C	,	746,3654	286.9+/-279.0	60,626,1514	53.0	61.0	58.0		1233,1233	-3.4	1.0	22	dbSNP_79	58	173,8427	77.8+/-140.4	2,169,4129	no	coding-synonymous,coding-synonymous	KCNJ4	NM_004981.1,NM_152868.1	,	62,795,5643	TT,TC,CC		2.0116,16.9545,7.0692	,	411/446,411/446	38822905	919,12081	2200	4300	6500	SO:0001819	synonymous_variant	3761	exon2			GATGCCCGCCTCC	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.1233G>A	22.37:g.38822905C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	151	82	0.543046	NM_004981	Q14D44	Silent	SNP	ENST00000303592.3	37	CCDS13971.1																																																																																			C|0.929;T|0.071	0.071	strong		0.677	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981	
BRSK1	84446	hgsc.bcm.edu	37	19	55815072	55815072	+	Silent	SNP	C	C	T	rs17851414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55815072C>T	ENST00000309383.1	+	12	1441	c.1164C>T	c.(1162-1164)agC>agT	p.S388S	BRSK1_ENST00000590333.1_Silent_p.S404S|BRSK1_ENST00000326848.7_Silent_p.S83S	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	388					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)		CCATGCTGAGCCGTCACGGGA	0.617													C|||	156	0.0311502	0.115	0.0058	5008	,	,		15985	0.0		0.0	False		,,,				2504	0.0				p.S388S		Atlas-SNP	.											.	BRSK1	192	.	0			c.C1164T						PASS	.	C		400,4006		19,362,1822	63.0	72.0	69.0		1164	4.0	1.0	19	dbSNP_123	69	3,8597		0,3,4297	no	coding-synonymous	BRSK1	NM_032430.1		19,365,6119	TT,TC,CC		0.0349,9.0785,3.0986		388/779	55815072	403,12603	2203	4300	6503	SO:0001819	synonymous_variant	84446	exon12			GCTGAGCCGTCAC	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.1164C>T	19.37:g.55815072C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			C|0.969;T|0.031	0.031	strong		0.617	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18473928	18473928	+	Silent	SNP	T	T	C	rs12309666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18473928T>C	ENST00000266497.5	+	6	1208	c.1170T>C	c.(1168-1170)aaT>aaC	p.N390N	PIK3C2G_ENST00000535651.1_Silent_p.N390N|PIK3C2G_ENST00000433979.1_Silent_p.N390N|PIK3C2G_ENST00000538779.1_Silent_p.N390N|RERGL_ENST00000541632.1_5'Flank			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	390					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)	p.N390N(1)		breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TTTATCTGAATCAACTTCTAG	0.318													C|||	1121	0.223842	0.4145	0.2233	5008	,	,		16827	0.2312		0.1083	False		,,,				2504	0.0777				p.N390N		Atlas-SNP	.											PIK3C2G,NS,carcinoma,0,1	PIK3C2G	315	1	1	Substitution - coding silent(1)	stomach(1)	c.T1170C						PASS	.	C		1472,2130		299,874,628	52.0	51.0	51.0		1170	1.7	1.0	12	dbSNP_120	51	688,7436		22,644,3396	no	coding-synonymous	PIK3C2G	NM_004570.4		321,1518,4024	CC,CT,TT		8.4687,40.8662,18.4206		390/1446	18473928	2160,9566	1801	4062	5863	SO:0001819	synonymous_variant	5288	exon7			TCTGAATCAACTT	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1170T>C	12.37:g.18473928T>C		Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	245	244	0.995918	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																			T|0.786;C|0.214	0.214	strong		0.318	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
CDH26	60437	hgsc.bcm.edu	37	20	58558073	58558073	+	Silent	SNP	C	C	T	rs6015610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58558073C>T	ENST00000244047.5	+	5	800	c.489C>T	c.(487-489)ccC>ccT	p.P163P	CDH26_ENST00000348616.4_Silent_p.P163P			Q8IXH8	CAD26_HUMAN	cadherin 26	163	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			ATCATGCACCCCAGTTTCCAG	0.463													C|||	389	0.0776757	0.2844	0.0144	5008	,	,		18540	0.0		0.003	False		,,,				2504	0.0				p.P163P		Atlas-SNP	.											.	CDH26	229	.	0			c.C489T						PASS	.	C		976,3430	367.6+/-318.3	104,768,1331	153.0	159.0	157.0		489	2.7	0.0	20	dbSNP_114	157	16,8584	11.2+/-40.8	0,16,4284	no	coding-synonymous	CDH26	NM_177980.2		104,784,5615	TT,TC,CC		0.186,22.1516,7.6272		163/833	58558073	992,12014	2203	4300	6503	SO:0001819	synonymous_variant	60437	exon5			TGCACCCCAGTTT	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"""Cadherins / Major cadherins"""	15902	protein-coding gene	gene with protein product			"""cadherin-like 26"""				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.489C>T	20.37:g.58558073C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	153	76	0.496732	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Silent	SNP	ENST00000244047.5	37																																																																																				C|0.915;T|0.085	0.085	strong		0.463	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	
PKD1L2	114780	hgsc.bcm.edu	37	16	81208348	81208348	+	RNA	SNP	G	G	T	rs745211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81208348G>T	ENST00000527937.1	-	0	636				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000531391.1_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						TCTATGCTCAGTGACTGTCCT	0.622													G|||	336	0.0670927	0.2443	0.0187	5008	,	,		18559	0.0		0.0	False		,,,				2504	0.0				p.L919M		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2755A						PASS	.	G	MET/LEU,MET/LEU	897,3165		103,691,1237	55.0	54.0	54.0		2755,2755	4.3	0.0	16	dbSNP_86	54	8,8374		0,8,4183	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	15,15	103,699,5420	TT,TG,GG		0.0954,22.0827,7.2726	probably-damaging,probably-damaging	919/992,919/2460	81208348	905,11539	2031	4191	6222			114780	exon16			TGCTCAGTGACTG	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.81208348G>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	118	67	0.567797	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		139|139	0.06364468864468864|0.06364468864468864	134|134	0.27235772357723576|0.27235772357723576	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	15.20|15.20	2.762411|2.762411	0.49468|0.49468	0.220827|0.220827	9.54E-4|9.54E-4	ENSG00000166473|ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937|ENST00000526632	T;T;T|.	0.34667|.	2.35;4.96;1.35|.	4.33|4.33	4.33|4.33	0.51752|0.51752	Egg jelly receptor, REJ-like (1);|.	1.304660|.	0.05138|.	N|.	0.493678|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	D;D;B|.	0.89917|.	0.999;1.0;0.329|.	D;D;B|.	0.74348|.	0.967;0.983;0.077|.	T|T	0.03086|0.03086	-1.1074|-1.1074	8|3	0.87932|.	D|.	0|.	-5.2934|-5.2934	14.1184|14.1184	0.65169|0.65169	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs745211;rs52837063;rs745211|rs745211;rs52837063;rs745211	175;919;919|.	Q7Z442-6;Q7Z442-3;Q7Z442|.	.;.;PK1L2_HUMAN|.	M|N	234;919;175|446	ENSP00000436309:L234M;ENSP00000337397:L919M;ENSP00000432818:L175M|.	ENSP00000337397:L919M|.	L|T	-|-	1|2	2|0	PKD1L2|PKD1L2	79765849|79765849	0.108000|0.108000	0.22018|0.22018	0.003000|0.003000	0.11579|0.11579	0.003000|0.003000	0.03518|0.03518	3.794000|3.794000	0.55492|0.55492	2.116000|2.116000	0.64780|0.64780	0.555000|0.555000	0.69702|0.69702	CTG|ACT	G|0.924;T|0.076	0.076	strong		0.622	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
PLIN4	729359	hgsc.bcm.edu	37	19	4512661	4512661	+	Silent	SNP	G	G	A	rs58830758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512661G>A	ENST00000301286.3	-	3	1268	c.1269C>T	c.(1267-1269)tgC>tgT	p.C423C		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	423	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						TCACCCCACTGCAGACGGTGT	0.557													G|||	863	0.172324	0.5303	0.0663	5008	,	,		19302	0.001		0.0507	False		,,,				2504	0.0654				p.C423C		Atlas-SNP	.											PLIN4_ENST00000301286,caecum,carcinoma,0,2	PLIN4	191	2	0			c.C1269T						scavenged	.	G		1457,2509		459,539,985	94.0	133.0	120.0		1269	0.1	0.0	19	dbSNP_129	120	204,8150		32,140,4005	no	coding-synonymous	PLIN4	NM_001080400.1		491,679,4990	AA,AG,GG		2.4419,36.7373,13.4821		423/1358	4512661	1661,10659	1983	4177	6160	SO:0001819	synonymous_variant	729359	exon3			CCCACTGCAGACG	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.1269C>T	19.37:g.4512661G>A		Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	163	32	0.196319	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			G|0.927;A|0.073	0.073	strong		0.557	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
SPECC1	92521	hgsc.bcm.edu	37	17	20163529	20163529	+	Silent	SNP	A	A	G	rs2703791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:20163529A>G	ENST00000261503.5	+	12	2913	c.2862A>G	c.(2860-2862)gcA>gcG	p.A954A	SPECC1_ENST00000395530.2_Silent_p.A873A|SPECC1_ENST00000536879.1_Silent_p.A294A|SPECC1_ENST00000395527.4_Silent_p.A954A|AC004702.2_ENST00000580225.1_lincRNA	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	954					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)		ACCCTCTGGCAGCCTTGGCCC	0.448													G|||	4103	0.819289	0.9713	0.6686	5008	,	,		19738	0.9861		0.5716	False		,,,				2504	0.8037				p.A954A		Atlas-SNP	.											.	SPECC1	100	.	0			c.A2862G						PASS	.	G	,	4007,399	197.4+/-221.5	1822,363,18	97.0	99.0	98.0		2862,2619	-4.7	0.9	17	dbSNP_100	98	4962,3638	523.1+/-380.3	1439,2084,777	no	coding-synonymous,coding-synonymous	SPECC1	NM_001033553.2,NM_001033555.2	,	3261,2447,795	GG,GA,AA		42.3023,9.0558,31.0395	,	954/1069,873/988	20163529	8969,4037	2203	4300	6503	SO:0001819	synonymous_variant	92521	exon12			TCTGGCAGCCTTG	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.2862A>G	17.37:g.20163529A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Silent	SNP	ENST00000261503.5	37	CCDS32590.1																																																																																			A|0.284;G|0.716	0.716	strong		0.448	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
CDC27	996	hgsc.bcm.edu	37	17	45214527	45214527	+	Missense_Mutation	SNP	T	T	C	rs62075618|rs200720095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45214527T>C	ENST00000066544.3	-	14	1997	c.1904A>G	c.(1903-1905)tAt>tGt	p.Y635C	CDC27_ENST00000446365.2_Missense_Mutation_p.Y574C|CDC27_ENST00000527547.1_Missense_Mutation_p.Y634C|CDC27_ENST00000531206.1_Missense_Mutation_p.Y641C	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	635					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CCATGCATTATAATGTCTAGG	0.338																																					p.Y641C		Atlas-SNP	.											CDC27_ENST00000531206,colon,carcinoma,-1,2	CDC27	337	2	0			c.A1922G						scavenged	.						35.0	35.0	35.0					17																	45214527		2203	4300	6503	SO:0001583	missense	996	exon14			GCATTATAATGTC	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1904A>G	17.37:g.45214527T>C	ENSP00000066544:p.Tyr635Cys	Somatic	26	2	0.0769231		WXS	Illumina HiSeq	Phase_I	34	6	0.176471	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.004463	0.93287	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	5.98	5.98	0.97165	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.80798	0.4692	H	0.96943	3.91	0.09310	P	0.999999999633698	D;D;D;D	0.59357	0.985;0.982;0.982;0.969	P;P;P;P	0.56042	0.79;0.753;0.753;0.727	D	0.88807	0.3289	9	0.87932	D	0	-24.5847	14.4087	0.67101	0.0:0.0:0.0:1.0	rs62075618	574;634;641;635	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	C	635;641;574;634	ENSP00000066544:Y635C;ENSP00000434614:Y641C;ENSP00000392802:Y574C;ENSP00000437339:Y634C	ENSP00000066544:Y635C	Y	-	2	0	CDC27	42569526	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.308000	0.72820	2.293000	0.77203	0.477000	0.44152	TAT	T|0.500;C|0.500	0.500	strong		0.338	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
PSMF1	9491	hgsc.bcm.edu	37	20	1106143	1106143	+	Silent	SNP	G	G	A	rs35517343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1106143G>A	ENST00000335877.6	+	2	308	c.132G>A	c.(130-132)ccG>ccA	p.P44P	PSMF1_ENST00000333082.3_Silent_p.P44P|PSMF1_ENST00000438768.2_Silent_p.P44P|PSMF1_ENST00000246015.4_Silent_p.P44P|PSMF1_ENST00000381898.4_5'UTR	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	44	Important for homodimerization and interaction with FBXO7.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						CTTCCCAGCCGGGTCCCAATG	0.458													G|||	15	0.00299521	0.0113	0.0	5008	,	,		21820	0.0		0.0	False		,,,				2504	0.0				p.P44P		Atlas-SNP	.											.	PSMF1	27	.	0			c.G132A						PASS	.	G	,	61,4345	58.7+/-95.3	0,61,2142	77.0	70.0	72.0		132,132	-3.1	0.1	20	dbSNP_126	72	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	PSMF1	NM_006814.3,NM_178578.2	,	0,62,6441	AA,AG,GG		0.0116,1.3845,0.4767	,	44/272,44/272	1106143	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	9491	exon2			CCAGCCGGGTCCC	D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"""Proteasome (prosome, macropain) subunits"""	9571	protein-coding gene	gene with protein product	"""proteasome inhibitor hP131 subunit"""					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.132G>A	20.37:g.1106143G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_006814	A0AVQ9|D3DVW3|Q9H4I1	Silent	SNP	ENST00000335877.6	37	CCDS13010.1																																																																																			G|0.995;A|0.005	0.005	strong		0.458	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578	
TRAF1	7185	hgsc.bcm.edu	37	9	123671613	123671613	+	Silent	SNP	C	C	T	rs112060909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:123671613C>T	ENST00000373887.3	-	7	3372	c.927G>A	c.(925-927)ctG>ctA	p.L309L	TRAF1_ENST00000540010.1_Silent_p.L309L|TRAF1_ENST00000546084.1_Silent_p.L187L	NM_005658.4	NP_005649.1	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	309	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein complex assembly (GO:0006461)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(4)|pancreas(1)|skin(2)	22						CATTCAGGTACAGCCGCAGGC	0.547													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		20674	0.0		0.0	False		,,,				2504	0.0				p.L309L		Atlas-SNP	.											.	TRAF1	42	.	0			c.G927A						PASS	.	C	,,	179,4227	117.1+/-155.0	3,173,2027	173.0	163.0	167.0		927,561,927	-0.2	1.0	9	dbSNP_132	167	6,8594	5.7+/-21.5	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	TRAF1	NM_001190945.1,NM_001190947.1,NM_005658.4	,,	3,179,6321	TT,TC,CC		0.0698,4.0626,1.4224	,,	309/417,187/295,309/417	123671613	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	7185	exon7			CAGGTACAGCCGC	AK090468	CCDS6825.1, CCDS55335.1	9q33-q34	2008-02-05			ENSG00000056558	ENSG00000056558			12031	protein-coding gene	gene with protein product		601711				8069916	Standard	NM_001190945		Approved	EBI6	uc010mvl.2	Q13077	OTTHUMG00000020578	ENST00000373887.3:c.927G>A	9.37:g.123671613C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	127	48	0.377953	NM_005658	B4DJ77|Q658U1|Q8NF13	Silent	SNP	ENST00000373887.3	37	CCDS6825.1																																																																																			C|0.983;T|0.017	0.017	strong		0.547	TRAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053843.1	NM_005658	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55341589	55341589	+	Silent	SNP	C	C	T	rs112943025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55341589C>T	ENST00000391728.4	+	9	1227	c.1194C>T	c.(1192-1194)taC>taT	p.Y398Y	KIR3DL1_ENST00000541392.1_Silent_p.Y381Y|KIR3DL1_ENST00000358178.4_Silent_p.Y303Y|KIR2DS4_ENST00000339924.8_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000538269.1_Silent_p.Y398Y|KIR3DL1_ENST00000326542.7_Silent_p.Y381Y	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	398					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)		AGGTGACATACGCACAGTTGG	0.517													.|||	324	0.0646965	0.0658	0.0274	5008	,	,		15673	0.1101		0.0457	False		,,,				2504	0.0624				p.Y398Y		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.C1194T						PASS	.	T		332,4010		56,220,1895	261.0	237.0	245.0		1194	-1.4	0.0	19	dbSNP_132	245	316,8024		64,188,3918	no	coding-synonymous	KIR3DL1	NM_013289.2		120,408,5813	TT,TC,CC		3.789,7.6462,5.1096		398/445	55341589	648,12034	2171	4170	6341	SO:0001819	synonymous_variant	3811	exon9			GACATACGCACAG	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.1194C>T	19.37:g.55341589C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	114	45	0.394737	NM_013289	O43473|Q14946|Q16541	Silent	SNP	ENST00000391728.4	37	CCDS42621.1																																																																																			C|0.946;T|0.054	0.054	strong		0.517	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
ESPL1	9700	hgsc.bcm.edu	37	12	53662624	53662624	+	Missense_Mutation	SNP	C	C	A	rs6580942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53662624C>A	ENST00000257934.4	+	2	165	c.74C>A	c.(73-75)gCc>gAc	p.A25D	ESPL1_ENST00000552462.1_Missense_Mutation_p.A25D	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	25				A -> D (in Ref. 1; AAR18247). {ECO:0000305}.	apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TTGCTGCCCGCCTTGAAGGTG	0.527													A|||	4449	0.888379	0.9841	0.7954	5008	,	,		17314	0.999		0.673	False		,,,				2504	0.9325				p.A25D	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C74A						PASS	.	A	ASP/ALA	4135,271	151.0+/-185.0	1946,243,14	35.0	34.0	34.0	http://omim.org/entry/606257	74	4.8	0.1	12	dbSNP_116	34	5835,2765	433.7+/-357.5	1997,1841,462	yes	missense	ESPL1	NM_012291.4	126	3943,2084,476	AA,AC,CC		32.1512,6.1507,23.3431	benign	25/2121	53662624	9970,3036	2203	4300	6503	SO:0001583	missense	9700	exon2			TGCCCGCCTTGAA	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.74C>A	12.37:g.53662624C>A	ENSP00000257934:p.Ala25Asp	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	1822	0.8342490842490843	475	0.9654471544715447	281	0.7762430939226519	572	1.0	494	0.6517150395778364	A	1.127	-0.653471	0.03480	0.938493	0.678488	ENSG00000135476	ENST00000257934;ENST00000552462	T;T	0.10668	2.85;2.85	5.95	4.79	0.61399	.	0.227922	0.36519	N	0.002552	T	0.00012	0.0000	N	0.00116	-2.08	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37753	-0.9692	9	0.02654	T	1	.	11.3037	0.49323	0.7081:0.2919:0.0:0.0	rs6580942;rs17750752;rs52806931;rs60259413;rs6580942	25	Q14674	ESPL1_HUMAN	D	25	ENSP00000257934:A25D;ENSP00000449831:A25D	ENSP00000257934:A25D	A	+	2	0	ESPL1	51948891	0.995000	0.38212	0.137000	0.22149	0.354000	0.29330	3.448000	0.52943	0.492000	0.27815	-0.256000	0.11100	GCC	C|0.192;A|0.808	0.808	strong		0.527	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
VILL	50853	hgsc.bcm.edu	37	3	38047954	38047954	+	Missense_Mutation	SNP	G	G	C	rs9816693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38047954G>C	ENST00000283713.6	+	19	2486	c.2220G>C	c.(2218-2220)ttG>ttC	p.L740F	VILL_ENST00000465644.1_Missense_Mutation_p.L458F|VILL_ENST00000383759.2_Missense_Mutation_p.L740F			O15195	VILL_HUMAN	villin-like	740			L -> F (in dbSNP:rs9816693).		actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)	p.L740F(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		TCAACAACTTGCGGCTATCCA	0.617													C|||	1164	0.232428	0.4168	0.1383	5008	,	,		17942	0.0863		0.1441	False		,,,				2504	0.2914				p.L740F		Atlas-SNP	.											VILL,NS,carcinoma,0,1	VILL	61	1	1	Substitution - Missense(1)	stomach(1)	c.G2220C						scavenged	.	C	PHE/LEU	1635,2753		309,1017,868	74.0	88.0	83.0		2220	2.3	0.5	3	dbSNP_119	83	1448,7118		121,1206,2956	yes	missense	VILL	NM_015873.3	22	430,2223,3824	CC,CG,GG		16.904,37.2607,23.7996	benign	740/857	38047954	3083,9871	2194	4283	6477	SO:0001583	missense	50853	exon18			CAACTTGCGGCTA		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.2220G>C	3.37:g.38047954G>C	ENSP00000283713:p.Leu740Phe	Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Missense_Mutation	SNP	ENST00000283713.6	37	CCDS2670.2	389	0.17811355311355312	194	0.3943089430894309	44	0.12154696132596685	45	0.07867132867132867	106	0.13984168865435356	C	0.885	-0.727332	0.03158	0.372607	0.16904	ENSG00000136059	ENST00000283713;ENST00000383759;ENST00000356246;ENST00000465644	T;T;T	0.14516	2.58;2.58;2.5	3.14	2.26	0.28386	.	0.479810	0.20403	N	0.093008	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45716	-0.9242	9	0.44086	T	0.13	-11.3814	4.5018	0.11867	0.0:0.6389:0.2314:0.1297	rs9816693;rs58692772;rs9816693	740	O15195	VILL_HUMAN	F	740;740;726;458	ENSP00000283713:L740F;ENSP00000373266:L740F;ENSP00000422096:L458F	ENSP00000283713:L740F	L	+	3	2	VILL	38022958	0.001000	0.12720	0.499000	0.27577	0.691000	0.40173	-0.005000	0.12855	0.379000	0.24794	-0.357000	0.07601	TTG	G|0.800;C|0.200	0.200	strong		0.617	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
TTN	7273	hgsc.bcm.edu	37	2	179610619	179610619	+	Intron	SNP	C	C	G	rs16866489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179610619C>G	ENST00000591111.1	-	46	10585				TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.S5503T			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)			TTCAAAAAAACTGTCTGTGTA	0.378													C|||	29	0.00579073	0.0204	0.0029	5008	,	,		21580	0.0		0.0	False		,,,				2504	0.0				p.S5503T		Atlas-SNP	.											.	TTN	18412	.	0			c.G16508C						PASS	.	C	,,THR/SER,,	80,4326	70.9+/-108.8	0,80,2123	114.0	111.0	112.0		,,16508,,	5.1	1.0	2	dbSNP_123	112	2,8596	1.2+/-3.3	0,2,4297	yes	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,58,,	0,82,6420	GG,GC,CC		0.0233,1.8157,0.6306	,,,,	,,5503/5605,,	179610619	82,12922	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			AAAAAACTGTCTG	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.10361-3971G>C	2.37:g.179610619C>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	118	66	0.559322	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	C	12.68	2.011534	0.35511	0.018157	2.33E-4	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.58210	0.35	5.94	5.06	0.68205	.	.	.	.	.	T	0.22704	0.0548	L	0.27053	0.805	0.80722	D	1	P	0.35272	0.493	B	0.33620	0.167	T	0.06770	-1.0808	9	0.30078	T	0.28	.	12.1518	0.54053	0.0:0.9185:0.0:0.0815	rs16866489;rs16866489	5503	Q8WZ42-6	.	T	5503;784	ENSP00000354117:S5503T	ENSP00000304714:S784T	S	-	2	0	TTN	179318864	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	2.864000	0.48404	2.816000	0.96949	0.563000	0.77884	AGT	C|0.992;G|0.008	0.008	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
EPHB3	2049	hgsc.bcm.edu	37	3	184299068	184299068	+	Silent	SNP	G	G	A	rs9881589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184299068G>A	ENST00000330394.2	+	15	3212	c.2760G>A	c.(2758-2760)acG>acA	p.T920T	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	920					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TGGACCGCACGGTCCCAGATT	0.567													G|||	788	0.157348	0.1377	0.1095	5008	,	,		19897	0.1597		0.1899	False		,,,				2504	0.182				p.T920T		Atlas-SNP	.											.	EPHB3	114	.	0			c.G2760A						PASS	.	G		645,3761	274.9+/-272.2	47,551,1605	117.0	109.0	112.0		2760	-6.0	0.8	3	dbSNP_119	112	1517,7083	287.1+/-298.1	150,1217,2933	no	coding-synonymous	EPHB3	NM_004443.3		197,1768,4538	AA,AG,GG		17.6395,14.6391,16.6231		920/999	184299068	2162,10844	2203	4300	6503	SO:0001819	synonymous_variant	2049	exon15			CCGCACGGTCCCA	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.2760G>A	3.37:g.184299068G>A		Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	282	150	0.531915	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			G|0.834;A|0.166	0.166	strong		0.567	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
PIK3C2A	5286	hgsc.bcm.edu	37	11	17118687	17118687	+	Missense_Mutation	SNP	T	T	C	rs11604561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:17118687T>C	ENST00000265970.7	-	26	4242	c.4243A>G	c.(4243-4245)Aca>Gca	p.T1415A	PIK3C2A_ENST00000531428.1_5'UTR|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.T1035A	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1415			T -> A (in dbSNP:rs11604561).		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						AAGGAGTATGTTTTAGGTGAA	0.348													T|||	402	0.0802716	0.0968	0.1081	5008	,	,		19717	0.0109		0.1243	False		,,,				2504	0.0644				p.T1415A		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.A4243G						PASS	.	T	ALA/THR	431,3969	209.8+/-230.5	24,383,1793	121.0	117.0	118.0		4243	5.0	1.0	11	dbSNP_120	118	1075,7511	225.5+/-261.6	73,929,3291	yes	missense	PIK3C2A	NM_002645.2	58	97,1312,5084	CC,CT,TT		12.5204,9.7955,11.5971	benign	1415/1687	17118687	1506,11480	2200	4293	6493	SO:0001583	missense	5286	exon26			AGTATGTTTTAGG	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.4243A>G	11.37:g.17118687T>C	ENSP00000265970:p.Thr1415Ala	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	185	0.08470695970695971	43	0.08739837398373984	48	0.13259668508287292	6	0.01048951048951049	88	0.11609498680738786	T	15.83	2.950077	0.53186	0.097955	0.125204	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.63580	-0.05;0.37	6.07	4.96	0.65561	.	0.042928	0.85682	D	0.000000	T	0.00967	0.0032	M	0.71581	2.175	0.09310	P	0.999996412	B	0.16603	0.018	B	0.15052	0.012	T	0.30822	-0.9965	9	0.33141	T	0.24	-17.7599	11.6847	0.51479	0.0:0.0683:0.0:0.9317	rs11604561;rs17640755;rs57703026;rs11604561	1415	O00443	P3C2A_HUMAN	A	1415;1035	ENSP00000265970:T1415A;ENSP00000438687:T1035A	ENSP00000265970:T1415A	T	-	1	0	PIK3C2A	17075263	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.121000	0.57904	2.326000	0.78906	0.533000	0.62120	ACA	T|0.898;C|0.102	0.102	strong		0.348	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
RYR3	6263	hgsc.bcm.edu	37	15	34030767	34030767	+	Silent	SNP	G	G	T	rs115185294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34030767G>T	ENST00000389232.4	+	50	7702	c.7632G>T	c.(7630-7632)ggG>ggT	p.G2544G	RYR3_ENST00000415757.3_Silent_p.G2544G	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2544	4 X approximate repeats.				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)		TTTTCTGGGGGATTTTTGACT	0.473											OREG0023032	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	36	0.0071885	0.025	0.0043	5008	,	,		18919	0.0		0.0	False		,,,				2504	0.0				p.G2544G		Atlas-SNP	.											.	RYR3	760	.	0			c.G7632T						PASS	.	G		61,3703		1,59,1822	96.0	104.0	102.0		7632	0.4	1.0	15	dbSNP_132	102	1,8205		0,1,4102	no	coding-synonymous	RYR3	NM_001036.3		1,60,5924	TT,TG,GG		0.0122,1.6206,0.518		2544/4871	34030767	62,11908	1882	4103	5985	SO:0001819	synonymous_variant	6263	exon50			CTGGGGGATTTTT		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.7632G>T	15.37:g.34030767G>T		Somatic	65	0	0	844	WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.994;T|0.006	0.006	strong		0.473	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
RFFL	117584	hgsc.bcm.edu	37	17	33348541	33348541	+	Missense_Mutation	SNP	C	C	T	rs34747500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33348541C>T	ENST00000315249.7	-	3	662	c.440G>A	c.(439-441)cGt>cAt	p.R147H	RFFL_ENST00000413582.2_Missense_Mutation_p.R147H|RFFL_ENST00000268850.7_Missense_Mutation_p.R147H|RAD51L3-RFFL_ENST00000593039.1_Intron|RFFL_ENST00000378516.2_Missense_Mutation_p.R147H|RFFL_ENST00000415395.2_Missense_Mutation_p.R147H|RFFL_ENST00000447669.2_Missense_Mutation_p.R147H|RFFL_ENST00000394597.2_Missense_Mutation_p.R147H|RFFL_ENST00000584655.1_Missense_Mutation_p.R147H					ring finger and FYVE-like domain containing E3 ubiquitin protein ligase											kidney(1)|large_intestine(2)|lung(3)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		GGTGGAGGCACGAGTCCTGTC	0.582													C|||	68	0.0135783	0.0356	0.0029	5008	,	,		19710	0.0188		0.0	False		,,,				2504	0.0				p.R147H		Atlas-SNP	.											.	RFFL	27	.	0			c.G440A						PASS	.	C	HIS/ARG	124,4282	91.6+/-130.3	3,118,2082	81.0	65.0	70.0		440	-4.3	0.4	17	dbSNP_126	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RFFL	NM_001017368.1	29	3,119,6381	TT,TC,CC		0.0116,2.8143,0.9611	benign	147/364	33348541	125,12881	2203	4300	6503	SO:0001583	missense	117584	exon3			GAGGCACGAGTCC	AF434816	CCDS11286.1	17q12	2012-02-23	2012-02-23		ENSG00000092871	ENSG00000092871		"""RING-type (C3HC4) zinc fingers"""	24821	protein-coding gene	gene with protein product		609735	"""ring finger and FYVE-like domain containing"""			15229288	Standard	NR_037713		Approved	rififylin, fring, RNF189, RNF34L	uc002hin.1	Q8WZ73	OTTHUMG00000132933	ENST00000315249.7:c.440G>A	17.37:g.33348541C>T	ENSP00000326170:p.Arg147His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	138	65	0.471014	NM_001017368		Missense_Mutation	SNP	ENST00000315249.7	37	CCDS11286.1	31	0.014194139194139194	16	0.032520325203252036	1	0.0027624309392265192	14	0.024475524475524476	0	0.0	C	7.587	0.669935	0.14776	0.028143	1.16E-4	ENSG00000092871	ENST00000315249;ENST00000394597;ENST00000378516;ENST00000268850;ENST00000413582;ENST00000415395	T;T;T;T;T;T	0.46451	0.87;0.87;0.89;0.91;0.89;0.87	5.65	-4.35	0.03656	.	1.494590	0.03679	N	0.245226	T	0.14184	0.0343	L	0.46157	1.445	0.19300	N	0.999975	B;B;B;B	0.10296	0.003;0.003;0.002;0.003	B;B;B;B	0.10450	0.005;0.003;0.001;0.001	T	0.33497	-0.9866	10	0.45353	T	0.12	-0.0021	7.6995	0.28615	0.1025:0.4344:0.0:0.4631	rs34747500	147;147;147;147	C9JN73;Q8WZ73-3;Q8WZ73;Q8WZ73-2	.;.;RFFL_HUMAN;.	H	147	ENSP00000326170:R147H;ENSP00000378096:R147H;ENSP00000367777:R147H;ENSP00000268850:R147H;ENSP00000408513:R147H;ENSP00000412322:R147H	ENSP00000268850:R147H	R	-	2	0	RFFL	30372654	0.000000	0.05858	0.450000	0.26969	0.123000	0.20343	-1.166000	0.03129	-0.526000	0.06383	-0.940000	0.02684	CGT	C|0.986;T|0.014	0.014	strong		0.582	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256460.2	NM_057178	
PDIA2	64714	hgsc.bcm.edu	37	16	335373	335373	+	Missense_Mutation	SNP	C	C	T	rs2685127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:335373C>T	ENST00000219406.6	+	6	875	c.857C>T	c.(856-858)aCg>aTg	p.T286M	PDIA2_ENST00000404312.1_Missense_Mutation_p.T283M|PDIA2_ENST00000462950.1_3'UTR	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	286			T -> M (in dbSNP:rs2685127).		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)				GTCAACCAGACGCTGGCTGCG	0.662													c|||	406	0.0810703	0.1679	0.0562	5008	,	,		12621	0.0069		0.1183	False		,,,				2504	0.0194				p.T286M		Atlas-SNP	.											.	PDIA2	51	.	0			c.C857T						PASS	.		MET/THR	587,3477		37,513,1482	35.0	40.0	38.0		857	3.9	0.7	16	dbSNP_100	38	995,7375		70,855,3260	yes	missense	PDIA2	NM_006849.2	81	107,1368,4742	TT,TC,CC		11.8877,14.4439,12.7232	probably-damaging	286/526	335373	1582,10852	2032	4185	6217	SO:0001583	missense	64714	exon6			ACCAGACGCTGGC	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.857C>T	16.37:g.335373C>T	ENSP00000219406:p.Thr286Met	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	119	78	0.655462	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	202	0.0924908424908425	92	0.18699186991869918	23	0.06353591160220995	3	0.005244755244755245	84	0.11081794195250659	c	11.79	1.742809	0.30865	0.144439	0.118877	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312	T;T	0.14640	2.49;2.49	3.87	3.87	0.44632	Thioredoxin-like fold (1);	0.188317	0.44097	D	0.000499	T	0.00039	0.0001	M	0.61703	1.905	0.24573	P	0.99391392	P	0.51240	0.943	P	0.52386	0.697	T	0.08391	-1.0724	9	0.72032	D	0.01	.	14.7294	0.69368	0.0:1.0:0.0:0.0	rs2685127;rs60535328;rs2685127	286	Q13087	PDIA2_HUMAN	M	286;255;283	ENSP00000219406:T286M;ENSP00000384410:T283M	ENSP00000219406:T286M	T	+	2	0	PDIA2	275374	0.941000	0.31946	0.732000	0.30844	0.062000	0.15995	2.599000	0.46231	2.013000	0.59113	0.486000	0.48141	ACG	C|0.898;T|0.102	0.102	strong		0.662	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
TNC	3371	hgsc.bcm.edu	37	9	117849314	117849314	+	Silent	SNP	T	T	C	rs2992147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117849314T>C	ENST00000350763.4	-	3	1107	c.696A>G	c.(694-696)gtA>gtG	p.V232V	TNC_ENST00000340094.3_Silent_p.V232V|TNC_ENST00000537320.1_Silent_p.V232V|TNC_ENST00000346706.3_Silent_p.V232V|TNC_ENST00000542877.1_Silent_p.V232V|TNC_ENST00000345230.3_Silent_p.V232V|TNC_ENST00000535648.1_Silent_p.V232V|TNC_ENST00000341037.4_Silent_p.V232V|TNC_ENST00000423613.2_Silent_p.V232V	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	232	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						AGACTCCATTTACGCACTTGC	0.602													C|||	2255	0.45028	0.6021	0.5533	5008	,	,		21340	0.2857		0.4423	False		,,,				2504	0.3497				p.V232V		Atlas-SNP	.											.	TNC	282	.	0			c.A696G						PASS	.	C		2489,1917	547.8+/-377.4	707,1075,421	93.0	76.0	81.0		696	0.7	0.0	9	dbSNP_101	81	3766,4834	614.8+/-396.3	834,2098,1368	no	coding-synonymous	TNC	NM_002160.3		1541,3173,1789	CC,CT,TT		43.7907,43.5089,48.0932		232/2202	117849314	6255,6751	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon3			TCCATTTACGCAC		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.696A>G	9.37:g.117849314T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																			T|0.532;C|0.468	0.468	strong		0.602	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
RALBP1	10928	hgsc.bcm.edu	37	18	9517221	9517221	+	Missense_Mutation	SNP	G	G	A	rs28552921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9517221G>A	ENST00000019317.4	+	3	846	c.623G>A	c.(622-624)cGg>cAg	p.R208Q	RP11-61L19.3_ENST00000609094.1_RNA|RNU2-27P_ENST00000516185.1_RNA|RALBP1_ENST00000383432.3_Missense_Mutation_p.R208Q			Q15311	RBP1_HUMAN	ralA binding protein 1	208	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				ATP catabolic process (GO:0006200)|chemotaxis (GO:0006935)|positive regulation of Cdc42 GTPase activity (GO:0043089)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|transport (GO:0006810)	cytosol (GO:0005829)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ATPase activity, coupled to movement of substances (GO:0043492)|GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	14					Carbamazepine(DB00564)|Doxorubicin(DB00997)|Sorafenib(DB00398)|Vincristine(DB00541)	GATGGCATTCGGCTGCCAGCC	0.458													G|||	21	0.00419329	0.0159	0.0	5008	,	,		18073	0.0		0.0	False		,,,				2504	0.0				p.R208Q		Atlas-SNP	.											.	RALBP1	48	.	0			c.G623A						PASS	.	G	GLN/ARG	41,4365	45.3+/-79.5	0,41,2162	71.0	66.0	67.0		623	4.2	0.9	18	dbSNP_125	67	0,8600		0,0,4300	yes	missense	RALBP1	NM_006788.3	43	0,41,6462	AA,AG,GG		0.0,0.9305,0.3152	benign	208/656	9517221	41,12965	2203	4300	6503	SO:0001583	missense	10928	exon3			GCATTCGGCTGCC	L42542	CCDS11845.1	18p11.22	2006-04-22			ENSG00000017797	ENSG00000017797			9841	protein-coding gene	gene with protein product		605801				7673236	Standard	NM_006788		Approved	RLIP76, RIP1, RIP	uc002koc.3	Q15311	OTTHUMG00000131596	ENST00000019317.4:c.623G>A	18.37:g.9517221G>A	ENSP00000019317:p.Arg208Gln	Somatic	366	1	0.00273224		WXS	Illumina HiSeq	Phase_I	380	179	0.471053	NM_006788	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	37	CCDS11845.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	11.16	1.558039	0.27827	0.009305	0.0	ENSG00000017797	ENST00000019317;ENST00000383432;ENST00000458039	T;T	0.22134	1.97;1.97	5.1	4.22	0.49857	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.120124	0.56097	D	0.000026	T	0.04724	0.0128	N	0.04768	-0.165	0.43489	D	0.995729	B	0.15473	0.013	B	0.04013	0.001	T	0.14476	-1.0471	10	0.14252	T	0.57	-0.6029	13.6511	0.62312	0.0752:0.0:0.9248:0.0	rs28552921	208	Q15311	RBP1_HUMAN	Q	208	ENSP00000019317:R208Q;ENSP00000372924:R208Q	ENSP00000019317:R208Q	R	+	2	0	RALBP1	9507221	0.992000	0.36948	0.879000	0.34478	0.997000	0.91878	3.800000	0.55537	1.264000	0.44198	0.655000	0.94253	CGG	G|0.996;A|0.004	0.004	strong		0.458	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788	
OR10G2	26534	hgsc.bcm.edu	37	14	22102315	22102315	+	Silent	SNP	A	A	G	rs61753931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:22102315A>G	ENST00000542433.1	-	1	781	c.684T>C	c.(682-684)caT>caC	p.H228H		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		TCAGGATGGCATGGACTATGT	0.532													.|||	70	0.0139776	0.053	0.0	5008	,	,		17587	0.0		0.0	False		,,,				2504	0.0				p.H228H		Atlas-SNP	.											.	OR10G2	35	.	0			c.T684C						PASS	.	A		210,4082		33,144,1969	52.0	52.0	52.0		684	-1.2	0.9	14	dbSNP_129	52	4,8380		1,2,4189	no	coding-synonymous	OR10G2	NM_001005466.1		34,146,6158	GG,GA,AA		0.0477,4.8928,1.6882		228/311	22102315	214,12462	2146	4192	6338	SO:0001819	synonymous_variant	26534	exon1			GATGGCATGGACT		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"""GPCR / Class A : Olfactory receptors"""	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.684T>C	14.37:g.22102315A>G		Somatic	375	0	0		WXS	Illumina HiSeq	Phase_I	356	173	0.485955	NM_001005466	B2RPD0	Silent	SNP	ENST00000542433.1	37	CCDS32047.1																																																																																			A|0.983;G|0.017	0.017	strong		0.532	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1		
OR10G4	390264	hgsc.bcm.edu	37	11	123886984	123886984	+	Missense_Mutation	SNP	A	A	G	rs4936880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123886984A>G	ENST00000320891.4	+	1	703	c.703A>G	c.(703-705)Aga>Gga	p.R235G		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	235			R -> G (in dbSNP:rs4936880).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		TGGGAGGCGCAGAGCCTTTCA	0.537													a|||	2140	0.427316	0.4682	0.5014	5008	,	,		20938	0.3591		0.4404	False		,,,				2504	0.3763				p.R235G		Atlas-SNP	.											.	OR10G4	77	.	0			c.A703G						PASS	.	A	GLY/ARG	2096,2306	573.2+/-383.5	510,1076,615	179.0	145.0	157.0		703	3.3	1.0	11	dbSNP_111	157	3917,4681	546.9+/-385.1	872,2173,1254	yes	missense	OR10G4	NM_001004462.1	125	1382,3249,1869	GG,GA,AA		45.5571,47.6147,46.2538	probably-damaging	235/312	123886984	6013,6987	2201	4299	6500	SO:0001583	missense	390264	exon1			AGGCGCAGAGCCT	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.703A>G	11.37:g.123886984A>G	ENSP00000325076:p.Arg235Gly	Somatic	363	1	0.00275482		WXS	Illumina HiSeq	Phase_I	340	340	1	NM_001004462	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	978	0.4478021978021978	221	0.4491869918699187	195	0.5386740331491713	232	0.40559440559440557	330	0.43535620052770446	a	15.39	2.819021	0.50633	0.476147	0.455571	ENSG00000254737	ENST00000320891	T	0.00169	8.63	3.33	3.33	0.38152	GPCR, rhodopsin-like superfamily (1);	0.135740	0.32161	N	0.006484	T	0.00012	0.0000	M	0.87381	2.88	0.37292	P	0.09169000000000005	P	0.46578	0.88	P	0.58660	0.843	T	0.00673	-1.1616	9	0.87932	D	0	.	11.8736	0.52534	1.0:0.0:0.0:0.0	rs4936880;rs4936880	235	Q8NGN3	O10G4_HUMAN	G	235	ENSP00000325076:R235G	ENSP00000325076:R235G	R	+	1	2	OR10G4	123392194	0.370000	0.25047	0.977000	0.42913	0.770000	0.43624	2.582000	0.46085	1.529000	0.49120	0.473000	0.43528	AGA	A|0.538;G|0.462	0.462	strong		0.537	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
IL4R	3566	hgsc.bcm.edu	37	16	27374180	27374180	+	Missense_Mutation	SNP	T	T	C	rs1805015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27374180T>C	ENST00000395762.2	+	11	1766	c.1507T>C	c.(1507-1509)Tcc>Ccc	p.S503P	IL4R_ENST00000543915.2_Missense_Mutation_p.S503P|IL4R_ENST00000380922.3_Missense_Mutation_p.S488P|IL4R_ENST00000170630.2_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	87	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	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		
ZC3H13	23091	hgsc.bcm.edu	37	13	46584500	46584500	+	Silent	SNP	G	G	A	rs79878411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:46584500G>A	ENST00000242848.4	-	7	1077	c.729C>T	c.(727-729)ccC>ccT	p.P243P	ZC3H13_ENST00000282007.3_Silent_p.P243P|ZC3H13_ENST00000470308.1_5'UTR			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	243							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			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)		GGTCCAACAGGGGAGAAGATA	0.403													G|||	41	0.0081869	0.031	0.0	5008	,	,		15604	0.0		0.0	False		,,,				2504	0.0				p.P243P	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-SNP	.											.	ZC3H13	197	.	0			c.C729T						PASS	.	G		117,4289	87.8+/-126.4	1,115,2087	107.0	99.0	102.0		729	-1.8	0.5	13	dbSNP_132	102	0,8600		0,0,4300	no	coding-synonymous	ZC3H13	NM_015070.3		1,115,6387	AA,AG,GG		0.0,2.6555,0.8996		243/1565	46584500	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	23091	exon7			CAACAGGGGAGAA	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.729C>T	13.37:g.46584500G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	162	70	0.432099	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Silent	SNP	ENST00000242848.4	37																																																																																				G|0.990;A|0.010	0.010	strong		0.403	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070	
TRPM2	7226	hgsc.bcm.edu	37	21	45856963	45856963	+	Silent	SNP	T	T	C	rs11910471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45856963T>C	ENST00000397928.1	+	29	4525	c.4080T>C	c.(4078-4080)gaT>gaC	p.D1360D	TRPM2_ENST00000300481.9_Silent_p.D1306D|snoZ6_ENST00000583496.1_RNA|TRPM2_ENST00000300482.5_Silent_p.D1360D|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Silent_p.D1410D|snoZ6_ENST00000581669.1_RNA	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1360	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GGAACGAGGATGGAGCCATCT	0.687													C|||	432	0.086262	0.3109	0.0288	5008	,	,		14340	0.0		0.001	False		,,,				2504	0.0				p.D1360D		Atlas-SNP	.											.	TRPM2	196	.	0			c.T4080C						PASS	.	C		892,2978		106,680,1149	92.0	66.0	75.0		4080	-6.6	0.2	21	dbSNP_120	75	8,7486		0,8,3739	no	coding-synonymous	TRPM2	NM_003307.3		106,688,4888	CC,CT,TT		0.1068,23.0491,7.9197		1360/1504	45856963	900,10464	1935	3747	5682	SO:0001819	synonymous_variant	7226	exon29			CGAGGATGGAGCC	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.4080T>C	21.37:g.45856963T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																			T|0.901;C|0.099	0.099	strong		0.687	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
CYP4F12	66002	hgsc.bcm.edu	37	19	15807305	15807305	+	Silent	SNP	T	T	C	rs688755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15807305T>C	ENST00000550308.1	+	12	1760	c.1380T>C	c.(1378-1380)ccT>ccC	p.P460P	CYP4F12_ENST00000324632.10_Silent_p.P460P	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	460					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CTTTTATTCCTTTCTCCGCAG	0.562													t|||	1209	0.241414	0.4024	0.2421	5008	,	,		18267	0.0139		0.2763	False		,,,				2504	0.2219				p.P460P		Atlas-SNP	.											.	CYP4F12	89	.	0			c.T1380C						PASS	.	G		1685,2719		320,1045,837	122.0	115.0	117.0		1380	-2.6	0.9	19	dbSNP_83	117	2117,6483		294,1529,2477	no	coding-synonymous	CYP4F12	NM_023944.3		614,2574,3314	CC,CT,TT		24.6163,38.2607,29.2372		460/525	15807305	3802,9202	2202	4300	6502	SO:0001819	synonymous_variant	66002	exon12			TATTCCTTTCTCC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1380T>C	19.37:g.15807305T>C		Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	305	212	0.695082	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			T|0.764;C|0.236	0.236	strong		0.562	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
EXOC3L1	283849	hgsc.bcm.edu	37	16	67221494	67221494	+	Missense_Mutation	SNP	C	C	T	rs79820293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67221494C>T	ENST00000314586.6	-	5	914	c.674G>A	c.(673-675)cGt>cAt	p.R225H	EXOC3L1_ENST00000562887.1_Intron	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	225	Mediates interaction with EXOC2, EXOC4 and EXOC5. {ECO:0000250}.				exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						CTCCGCCACACGCACAGCAGC	0.687													C|||	107	0.0213658	0.0772	0.0043	5008	,	,		16224	0.0		0.002	False		,,,				2504	0.0				p.R225H		Atlas-SNP	.											.	EXOC3L1	52	.	0			c.G674A						PASS	.	C	HIS/ARG	242,4152		8,226,1963	28.0	33.0	32.0		674	5.8	1.0	16	dbSNP_131	32	1,8597		0,1,4298	yes	missense	EXOC3L1	NM_178516.3	29	8,227,6261	TT,TC,CC		0.0116,5.5075,1.8704	probably-damaging	225/747	67221494	243,12749	2197	4299	6496	SO:0001583	missense	283849	exon5			GCCACACGCACAG	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"""exocyst complex component 3-like"""	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.674G>A	16.37:g.67221494C>T	ENSP00000325674:p.Arg225His	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	49	0.022435897435897436	47	0.09552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	26.0	4.691637	0.88735	0.055075	1.16E-4	ENSG00000179044	ENST00000314586;ENST00000545725;ENST00000314553	T;T	0.34472	3.05;1.36	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.03695	0.0105	M	0.74881	2.28	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.998;0.999	T	0.04454	-1.0950	10	0.59425	D	0.04	-11.3738	18.7162	0.91677	0.0:1.0:0.0:0.0	.	164;164;225	F5H4W1;B7Z6U0;Q86VI1	.;.;EX3L1_HUMAN	H	225;164;169	ENSP00000325674:R225H;ENSP00000439910:R164H	ENSP00000325008:R169H	R	-	2	0	EXOC3L1	65778995	0.997000	0.39634	1.000000	0.80357	0.982000	0.71751	4.142000	0.58044	2.763000	0.94921	0.650000	0.86243	CGT	C|0.978;T|0.022	0.022	strong		0.687	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
ING1	3621	hgsc.bcm.edu	37	13	111368023	111368023	+	Missense_Mutation	SNP	C	C	G	rs56682720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:111368023C>G	ENST00000375774.3	+	1	695	c.233C>G	c.(232-234)tCc>tGc	p.S78C	ING1_ENST00000464141.1_Intron|CARS2_ENST00000535398.1_5'Flank|ING1_ENST00000375775.3_Intron|ING1_ENST00000338450.7_Intron|ING1_ENST00000333219.7_Intron	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	78					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CCGTGCTCTTCCGCCCTGCGG	0.672													C|||	189	0.0377396	0.1362	0.0101	5008	,	,		13851	0.0		0.002	False		,,,				2504	0.0				p.S78C		Atlas-SNP	.											.	ING1	106	.	0			c.C233G						PASS	.	C	CYS/SER,,,	544,3856		29,486,1685	69.0	63.0	65.0		233,,,	-8.2	0.0	13	dbSNP_129	65	6,8592		0,6,4293	yes	missense,intron,intron,intron	ING1	NM_005537.3,NM_198217.1,NM_198218.1,NM_198219.1	112,,,	29,492,5978	GG,GC,CC		0.0698,12.3636,4.2314	benign,,,	78/423,,,	111368023	550,12448	2200	4299	6499	SO:0001583	missense	3621	exon1			GCTCTTCCGCCCT		CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"""Zinc fingers, PHD-type"""	6062	protein-coding gene	gene with protein product	"""inhibitor of growth 1"", ""tumor suppressor ING1"", ""growth inhibitor ING1"", ""growth inhibitory protein ING1"""	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.233C>G	13.37:g.111368023C>G	ENSP00000364929:p.Ser78Cys	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_005537	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Missense_Mutation	SNP	ENST00000375774.3	37	CCDS9517.1	51	0.023351648351648352	49	0.09959349593495935	2	0.0055248618784530384	0	0.0	0	0.0	C	14.45	2.539810	0.45176	0.123636	6.98E-4	ENSG00000153487	ENST00000375774	T	0.35421	1.31	4.11	-8.22	0.01037	.	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	P	0.43352	0.804	B	0.36959	0.237	T	0.15607	-1.0431	8	0.87932	D	0	0.3496	0.192	0.00135	0.2844:0.1541:0.2434:0.318	rs56682720	78	Q9UK53	ING1_HUMAN	C	78	ENSP00000364929:S78C	ENSP00000364929:S78C	S	+	2	0	ING1	110166024	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.050000	0.00628	-2.327000	0.00636	-1.083000	0.02208	TCC	C|0.961;G|0.039	0.039	strong		0.672	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377319	49377319	+	Missense_Mutation	SNP	A	A	G	rs610308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49377319A>G	ENST00000200453.5	+	2	1098	c.829A>G	c.(829-831)Aaa>Gaa	p.K277E		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	277	Glu-rich.		K -> E (in dbSNP:rs610308). {ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		AAAGGCACACAAAGAAACTGG	0.612													G|||	2228	0.444888	0.8033	0.3444	5008	,	,		17948	0.1141		0.3539	False		,,,				2504	0.4663				p.K277E		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.A829G						PASS	.	G	GLU/LYS	3295,1111	388.4+/-326.9	1232,831,140	63.0	78.0	73.0		829	-3.1	0.0	19	dbSNP_83	73	3002,5598	652.0+/-400.9	527,1948,1825	yes	missense	PPP1R15A	NM_014330.3	56	1759,2779,1965	GG,GA,AA		34.907,25.2156,48.4161	benign	277/675	49377319	6297,6709	2203	4300	6503	SO:0001583	missense	23645	exon2			GCACACAAAGAAA	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.829A>G	19.37:g.49377319A>G	ENSP00000200453:p.Lys277Glu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	844	0.38644688644688646	383	0.7784552845528455	127	0.35082872928176795	68	0.11888111888111888	266	0.35092348284960423	G	0.655	-0.808008	0.02819	0.747844	0.34907	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05382	3.45	3.8	-3.11	0.05299	.	2.747870	0.01207	N	0.007758	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	0.33675	-0.9859	9	0.02654	T	1	2.7997	5.5496	0.17083	0.5438:0.1519:0.3044:0.0	rs610308;rs3745701;rs52824100;rs58566411;rs610308	277	O75807	PR15A_HUMAN	E	277;117;235	ENSP00000200453:K277E	ENSP00000200453:K277E	K	+	1	0	PPP1R15A	54069131	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.530000	0.06179	-0.994000	0.03463	-1.110000	0.02074	AAA	A|0.546;G|0.454	0.454	strong		0.612	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
SPAG4	6676	hgsc.bcm.edu	37	20	34204168	34204168	+	Silent	SNP	G	G	A	rs115161777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34204168G>A	ENST00000374273.3	+	1	355	c.243G>A	c.(241-243)gcG>gcA	p.A81A		NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	81					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			AGAAGCCAGCGCCTCGGAGCC	0.731													G|||	107	0.0213658	0.0779	0.0058	5008	,	,		8847	0.0		0.0	False		,,,				2504	0.0				p.A81A		Atlas-SNP	.											.	SPAG4	36	.	0			c.G243A						PASS	.	G		185,3729		2,181,1774	5.0	8.0	7.0		243	4.6	1.0	20	dbSNP_132	7	4,7996		0,4,3996	no	coding-synonymous	SPAG4	NM_003116.1		2,185,5770	AA,AG,GG		0.05,4.7266,1.5864		81/438	34204168	189,11725	1957	4000	5957	SO:0001819	synonymous_variant	6676	exon1			GCCAGCGCCTCGG	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.243G>A	20.37:g.34204168G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_003116	O43648	Silent	SNP	ENST00000374273.3	37	CCDS13259.1																																																																																			G|0.980;A|0.020	0.020	strong		0.731	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116	
SCRN1	9805	hgsc.bcm.edu	37	7	29980471	29980471	+	Missense_Mutation	SNP	C	C	T	rs35960711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:29980471C>T	ENST00000426154.1	-	5	742	c.566G>A	c.(565-567)aGt>aAt	p.S189N	SCRN1_ENST00000416113.2_Intron|SCRN1_ENST00000242059.5_Missense_Mutation_p.S189N|SCRN1_ENST00000425819.2_Missense_Mutation_p.S121N|SCRN1_ENST00000409497.1_Missense_Mutation_p.S189N|SCRN1_ENST00000434476.2_Missense_Mutation_p.S209N	NM_001145513.1	NP_001138985.1	Q12765	SCRN1_HUMAN	secernin 1	189			S -> N (in dbSNP:rs35960711).		exocytosis (GO:0006887)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	dipeptidase activity (GO:0016805)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(2)|prostate(2)|skin(2)	25						CGAAAGCTGACTGCAAATGCA	0.453													T|||	345	0.0688898	0.1029	0.0432	5008	,	,		18985	0.0645		0.0388	False		,,,				2504	0.0767				p.S209N		Atlas-SNP	.											.	SCRN1	85	.	0			c.G626A						PASS	.	T	ASN/SER,ASN/SER,ASN/SER,ASN/SER	456,3950	783.9+/-414.7	17,422,1764	115.0	115.0	115.0		566,626,362,566	3.0	0.8	7	dbSNP_126	115	353,8247	803.4+/-407.3	7,339,3954	yes	missense,missense,missense,missense	SCRN1	NM_001145513.1,NM_001145514.1,NM_001145515.1,NM_014766.4	46,46,46,46	24,761,5718	TT,TC,CC		4.1047,10.3495,6.2202	benign,benign,benign,benign	189/415,209/435,121/347,189/415	29980471	809,12197	2203	4300	6503	SO:0001583	missense	9805	exon5			AGCTGACTGCAAA	D83777	CCDS5422.1, CCDS47567.1, CCDS47568.1	7p14.3-p14.1	2006-09-06			ENSG00000136193	ENSG00000136193			22192	protein-coding gene	gene with protein product		614965				12221138	Standard	NM_014766		Approved	KIAA0193	uc011kaa.2	Q12765	OTTHUMG00000097093	ENST00000426154.1:c.566G>A	7.37:g.29980471C>T	ENSP00000409068:p.Ser189Asn	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_001145514	A8K0E9|B4DHM0|B4DIP5|C9JPG0|Q25QX7|Q8IWD1	Missense_Mutation	SNP	ENST00000426154.1	37	CCDS5422.1	133	0.060897435897435896	36	0.07317073170731707	16	0.04419889502762431	51	0.08916083916083917	30	0.0395778364116095	T	3.443	-0.113555	0.06881	0.103495	0.041047	ENSG00000136193	ENST00000242059;ENST00000426154;ENST00000425819;ENST00000409497;ENST00000434476;ENST00000421434	T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94	5.58	3.05	0.35203	.	0.145037	0.46758	N	0.000263	T	0.00073	0.0002	N	0.00003	-3.405	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30937	-0.9961	9	.	.	.	-15.3602	6.1577	0.20346	0.0:0.1478:0.1352:0.717	rs35960711	209;189	C9JPG0;Q12765	.;SCRN1_HUMAN	N	189;189;121;189;209;189	ENSP00000242059:S189N;ENSP00000409068:S189N;ENSP00000414245:S121N;ENSP00000386872:S189N;ENSP00000388942:S209N;ENSP00000413184:S189N	.	S	-	2	0	SCRN1	29946996	1.000000	0.71417	0.756000	0.31282	0.734000	0.41952	2.621000	0.46418	0.395000	0.25257	-0.332000	0.08345	AGT	C|0.936;T|0.064	0.064	strong		0.453	SCRN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214231.2	NM_014766	
STXBP2	6813	hgsc.bcm.edu	37	19	7711221	7711221	+	Silent	SNP	T	T	C	rs10001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7711221T>C	ENST00000221283.5	+	16	1474	c.1443T>C	c.(1441-1443)gaT>gaC	p.D481D	STXBP2_ENST00000602355.1_Silent_p.D16D|STXBP2_ENST00000441779.2_Silent_p.D492D|STXBP2_ENST00000414284.2_Silent_p.D478D	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	481					leukocyte mediated cytotoxicity (GO:0001909)|neutrophil degranulation (GO:0043312)|protein transport (GO:0015031)|regulation of mast cell degranulation (GO:0043304)|vesicle docking involved in exocytosis (GO:0006904)	azurophil granule (GO:0042582)|cytolytic granule (GO:0044194)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin-3 binding (GO:0030348)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	23						TCATCAAGGATGTAATGGAGG	0.667													C|||	2525	0.504193	0.5356	0.4669	5008	,	,		17100	0.7034		0.4036	False		,,,				2504	0.3865				p.D492D		Atlas-SNP	.											STXBP2,NS,adenoma,0,1	STXBP2	63	1	0			c.T1476C						scavenged	.	C	,	2187,2217		534,1119,549	35.0	29.0	31.0		1434,1443	-3.7	0.9	19	dbSNP_52	31	3217,5383		585,2047,1668	no	coding-synonymous,coding-synonymous	STXBP2	NM_001127396.1,NM_006949.2	,	1119,3166,2217	CC,CT,TT		37.407,49.6594,41.5564	,	478/591,481/594	7711221	5404,7600	2202	4300	6502	SO:0001819	synonymous_variant	6813	exon16			CAAGGATGTAATG	U63533	CCDS12181.1, CCDS45948.1, CCDS62522.1	19p13.3-p13.2	2014-09-17				ENSG00000076944			11445	protein-coding gene	gene with protein product		601717				8921365	Standard	NM_001127396		Approved	UNC18B, Hunc18b	uc010xjr.3	Q15833		ENST00000221283.5:c.1443T>C	19.37:g.7711221T>C		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_001272034	B4E175|E7EQD5|Q9BU65	Silent	SNP	ENST00000221283.5	37	CCDS12181.1																																																																																			T|0.548;C|0.452	0.452	strong		0.667	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949	
ARHGEF39	84904	hgsc.bcm.edu	37	9	35665153	35665153	+	Missense_Mutation	SNP	C	C	A	rs45567235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35665153C>A	ENST00000378387.3	-	1	131	c.14G>T	c.(13-15)tGc>tTc	p.C5F	ARHGEF39_ENST00000378395.2_Intron|ARHGEF39_ENST00000490970.1_5'UTR|ARHGEF39_ENST00000343259.3_Missense_Mutation_p.C5F	NM_032818.2	NP_116207.2	Q8N4T4	ARG39_HUMAN	Rho guanine nucleotide exchange factor (GEF) 39	5			C -> F (in dbSNP:rs45567235).		positive regulation of cell migration (GO:0030335)	plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)										CGAACCGGGGCAGGAGAGCTC	0.711													C|||	343	0.0684904	0.0991	0.0648	5008	,	,		14392	0.0278		0.0924	False		,,,				2504	0.047				p.C5F		Atlas-SNP	.											.	.	.	.	0			c.G14T						PASS	.	C	PHE/CYS	403,3887		8,387,1750	6.0	8.0	7.0		14	-1.6	0.0	9	dbSNP_127	7	802,7598		36,730,3434	yes	missense	C9orf100	NM_032818.2	205	44,1117,5184	AA,AC,CC		9.5476,9.3939,9.4957	benign	5/336	35665153	1205,11485	2145	4200	6345	SO:0001583	missense	84904	exon1			CCGGGGCAGGAGA	AK001187	CCDS6584.2	9p13.3	2012-08-08	2012-08-08	2012-08-08	ENSG00000137135	ENSG00000137135			25909	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 100"""	C9orf100		22327280	Standard	XR_242516		Approved	FLJ14642	uc003zxm.1	Q8N4T4	OTTHUMG00000019869	ENST00000378387.3:c.14G>T	9.37:g.35665153C>A	ENSP00000367638:p.Cys5Phe	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_032818	Q49AG0|Q6TPQ2|Q96ST6	Missense_Mutation	SNP	ENST00000378387.3	37	CCDS6584.2	159	0.07280219780219781	47	0.09552845528455285	21	0.058011049723756904	16	0.027972027972027972	75	0.09894459102902374	C	4.235	0.042612	0.08196	0.093939	0.095476	ENSG00000137135	ENST00000378387;ENST00000343259	T;T	0.72835	-0.69;1.93	5.34	-1.63	0.08345	Dbl homology (DH) domain (1);	0.709155	0.14661	N	0.305961	T	0.01454	0.0047	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.02121	-1.1210	10	0.46703	T	0.11	-19.2451	6.681	0.23119	0.0:0.4122:0.3454:0.2424	rs45567235;rs61752948	5;5	B4E0T1;Q8N4T4	.;CI100_HUMAN	F	5	ENSP00000367638:C5F;ENSP00000344922:C5F	ENSP00000344922:C5F	C	-	2	0	C9orf100	35655153	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.686000	0.05161	-0.641000	0.05487	-0.813000	0.03139	TGC	C|0.927;A|0.073	0.073	strong		0.711	ARHGEF39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052330.1	NM_032818	
DCTD	1635	hgsc.bcm.edu	37	4	183814234	183814234	+	Silent	SNP	G	G	A	rs369366826		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:183814234G>A	ENST00000438320.2	-	5	698	c.408C>T	c.(406-408)gaC>gaT	p.D136D	DCTD_ENST00000357067.3_Silent_p.D147D|DCTD_ENST00000510370.1_Silent_p.D136D	NM_001921.2	NP_001912.2	P32321	DCTD_HUMAN	dCMP deaminase	136					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)	CAGTTGCCTCGTCACTATCAT	0.507													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17184	0.0		0.0	False		,,,				2504	0.0				p.D147D		Atlas-SNP	.											.	DCTD	30	.	0			c.C441T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	72.0	67.0	69.0		441,408	-10.8	0.0	4		69	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DCTD	NM_001012732.1,NM_001921.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	147/190,136/179	183814234	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1635	exon5			TGCCTCGTCACTA	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.408C>T	4.37:g.183814234G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	233	110	0.472103	NM_001012732	B2R836|D3DP49|D3DP50|Q5M7Z8|Q9BVD8	Silent	SNP	ENST00000438320.2	37	CCDS3831.1																																																																																			.	.	weak		0.507	DCTD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361743.2		
GIMAP7	168537	hgsc.bcm.edu	37	7	150217089	150217089	+	Silent	SNP	G	G	A	rs7800829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150217089G>A	ENST00000313543.4	+	2	184	c.27G>A	c.(25-27)ctG>ctA	p.L9L		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	9	AIG1-type G.				GTP catabolic process (GO:0006184)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACCGCTCCCTGAGGATCGTTC	0.502													G|||	1338	0.267173	0.4856	0.111	5008	,	,		19967	0.3819		0.0676	False		,,,				2504	0.1697				p.L9L		Atlas-SNP	.											.	GIMAP7	47	.	0			c.G27A						PASS	.	G		1735,2671	514.1+/-368.5	340,1055,808	64.0	59.0	61.0		27	3.8	1.0	7	dbSNP_116	61	585,8015	156.7+/-210.5	16,553,3731	no	coding-synonymous	GIMAP7	NM_153236.3		356,1608,4539	AA,AG,GG		6.8023,39.3781,17.8379		9/301	150217089	2320,10686	2203	4300	6503	SO:0001819	synonymous_variant	168537	exon2			CTCCCTGAGGATC	BC027613	CCDS5903.1	7q36.1	2014-04-04			ENSG00000179144	ENSG00000179144		"""GTPases, IMAP"""	22404	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 7"""					15474311	Standard	NM_153236		Approved	MGC27027, IAN7	uc003whk.3	Q8NHV1	OTTHUMG00000157626	ENST00000313543.4:c.27G>A	7.37:g.150217089G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_153236		Silent	SNP	ENST00000313543.4	37	CCDS5903.1																																																																																			G|0.776;A|0.224	0.224	strong		0.502	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236	
CIITA	4261	hgsc.bcm.edu	37	16	11001770	11001770	+	Silent	SNP	G	G	T	rs34654419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11001770G>T	ENST00000324288.8	+	11	2554	c.2421G>T	c.(2419-2421)ctG>ctT	p.L807L	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	807					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)	p.L807L(1)		central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						GGCAGCTGCTGGAGCTGCTGC	0.687			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								G|||	1081	0.215855	0.2057	0.3876	5008	,	,		12685	0.1329		0.1869	False		,,,				2504	0.2229				p.L807L		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	CIITA_ENST00000324288,NS,lymphoid_neoplasm,0,1	CIITA	92	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2421T						PASS	.	G		828,3494		88,652,1421	19.0	27.0	24.0		2421	2.8	1.0	16	dbSNP_126	24	1706,6752		189,1328,2712	no	coding-synonymous	CIITA	NM_000246.3		277,1980,4133	TT,TG,GG		20.1703,19.1578,19.8279		807/1131	11001770	2534,10246	2161	4229	6390	SO:0001819	synonymous_variant	4261	exon11			GCTGCTGGAGCTG	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.2421G>T	16.37:g.11001770G>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			T|0.193;G|0.806;C|0.000	0.193	strong		0.687	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
SGTA	6449	hgsc.bcm.edu	37	19	2762585	2762585	+	Silent	SNP	A	A	C	rs2302491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	88	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	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	
IFT140	9742	hgsc.bcm.edu	37	16	1608082	1608082	+	Silent	SNP	A	A	G	rs2076436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1608082A>G	ENST00000426508.2	-	19	2616	c.2253T>C	c.(2251-2253)ccT>ccC	p.P751P	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	751					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)		p.P751P(1)		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)				ACACCATCTGAGGGATGTGGT	0.547													A|||	1740	0.347444	0.5507	0.1844	5008	,	,		18218	0.3433		0.2087	False		,,,				2504	0.3354				p.P751P		Atlas-SNP	.											IFT140,NS,carcinoma,0,1	IFT140	128	1	1	Substitution - coding silent(1)	stomach(1)	c.T2253C						scavenged	.	A		2135,2263	579.6+/-385.0	518,1099,582	146.0	144.0	145.0		2253	0.7	0.3	16	dbSNP_96	145	1861,6739	333.7+/-320.7	197,1467,2636	no	coding-synonymous	IFT140	NM_014714.3		715,2566,3218	GG,GA,AA		21.6395,48.5448,30.7432		751/1463	1608082	3996,9002	2199	4300	6499	SO:0001819	synonymous_variant	9742	exon19			CATCTGAGGGATG	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.2253T>C	16.37:g.1608082A>G		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	188	93	0.494681	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																			A|0.687;G|0.313	0.313	strong		0.547	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
CNOT1	23019	hgsc.bcm.edu	37	16	58575489	58575489	+	Silent	SNP	G	G	A	rs11540994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58575489G>A	ENST00000317147.5	-	34	5048	c.4716C>T	c.(4714-4716)taC>taT	p.Y1572Y	CNOT1_ENST00000569240.1_Silent_p.Y1567Y|CNOT1_ENST00000245138.4_Silent_p.Y423Y	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1572	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				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)		CAAACTCTTCGTAAACAGCCA	0.398													G|||	2430	0.485224	0.6687	0.2983	5008	,	,		18050	0.5704		0.3211	False		,,,				2504	0.4509				p.Y1572Y		Atlas-SNP	.											.	CNOT1	359	.	0			c.C4716T						PASS	.	G		2658,1738	646.7+/-398.4	835,988,375	106.0	101.0	103.0		4716	3.7	1.0	16	dbSNP_120	103	2516,6084	411.9+/-350.6	380,1756,2164	no	coding-synonymous	CNOT1	NM_016284.3		1215,2744,2539	AA,AG,GG		29.2558,39.5359,39.8122		1572/2377	58575489	5174,7822	2198	4300	6498	SO:0001819	synonymous_variant	23019	exon34			CTCTTCGTAAACA	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.4716C>T	16.37:g.58575489G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_016284	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	37	CCDS10799.1																																																																																			G|0.584;A|0.416	0.416	strong		0.398	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605257	32605257	+	Missense_Mutation	SNP	C	C	A	rs1047989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	174	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	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	
TNIP1	10318	hgsc.bcm.edu	37	5	150436503	150436503	+	Missense_Mutation	SNP	G	G	C	rs2233290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150436503G>C	ENST00000389378.2	-	6	1039	c.451C>G	c.(451-453)Ccc>Gcc	p.P151A	TNIP1_ENST00000521591.1_Missense_Mutation_p.P151A|TNIP1_ENST00000524280.1_Missense_Mutation_p.P151A|TNIP1_ENST00000520931.1_Missense_Mutation_p.P98A|TNIP1_ENST00000523200.1_Missense_Mutation_p.P151A|TNIP1_ENST00000523338.1_Missense_Mutation_p.P151A|TNIP1_ENST00000522226.1_Missense_Mutation_p.P151A|TNIP1_ENST00000315050.7_Missense_Mutation_p.P151A|TNIP1_ENST00000518977.1_Missense_Mutation_p.P151A	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	151	Interacts with Nef.		P -> A (in dbSNP:rs2233290).		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)	p.P151A(1)		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)			TCCTCACGGGGCAGGGGGCCC	0.657													G|||	477	0.0952476	0.2133	0.0908	5008	,	,		18189	0.003		0.0825	False		,,,				2504	0.047				p.P151A		Atlas-SNP	.											TNIP1,NS,lymphoid_neoplasm,0,1	TNIP1	51	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C451G						PASS	.	G	ALA/PRO	793,3609		79,635,1487	21.0	23.0	22.0		451	4.1	0.9	5	dbSNP_98	22	759,7831		37,685,3573	yes	missense	TNIP1	NM_006058.3	27	116,1320,5060	CC,CG,GG		8.8359,18.0145,11.9458	probably-damaging	151/637	150436503	1552,11440	2201	4295	6496	SO:0001583	missense	10318	exon6			CACGGGGCAGGGG	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.451C>G	5.37:g.150436503G>C	ENSP00000374029:p.Pro151Ala	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Missense_Mutation	SNP	ENST00000389378.2	37	CCDS34280.1	211	0.09661172161172162	110	0.22357723577235772	37	0.10220994475138122	1	0.0017482517482517483	63	0.08311345646437995	G	15.15	2.748460	0.49257	0.180145	0.088359	ENSG00000145901	ENST00000520931;ENST00000389378;ENST00000315050;ENST00000523338;ENST00000544828;ENST00000417127;ENST00000539213;ENST00000522226;ENST00000521591;ENST00000518977;ENST00000524280;ENST00000523200;ENST00000545840;ENST00000522100	T;T;T;T;T;T;T;T;T;T	0.19806	2.34;2.4;2.4;2.4;2.4;2.4;2.4;2.43;2.43;2.12	5.03	4.14	0.48551	.	0.055087	0.85682	N	0.000000	T	0.00039	0.0001	M	0.77103	2.36	0.19575	P	0.9999685735	D;D;D;D;D;D	0.89917	0.978;1.0;0.978;0.978;0.999;0.999	P;D;P;P;D;D	0.85130	0.908;0.997;0.908;0.908;0.984;0.984	T	0.01436	-1.1355	9	0.39692	T	0.17	-16.4867	15.5862	0.76485	0.0:0.1385:0.8615:0.0	rs2233290	105;105;151;151;151;151	A4F1X9;A4F1X7;E7EPY1;E7ET96;A4F1W9;Q15025	.;.;.;.;.;TNIP1_HUMAN	A	98;151;151;151;108;108;113;151;151;151;151;151;108;98	ENSP00000429891:P98A;ENSP00000374029:P151A;ENSP00000317891:P151A;ENSP00000428243:P151A;ENSP00000428187:P151A;ENSP00000430760:P151A;ENSP00000430971:P151A;ENSP00000429912:P151A;ENSP00000431105:P151A;ENSP00000428487:P98A	ENSP00000317891:P151A	P	-	1	0	TNIP1	150416696	1.000000	0.71417	0.862000	0.33874	0.156000	0.22039	6.324000	0.72896	1.209000	0.43321	0.655000	0.94253	CCC	G|0.885;C|0.115	0.115	strong		0.657	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
RIN1	9610	hgsc.bcm.edu	37	11	66099888	66099888	+	Silent	SNP	C	C	T	rs61547186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:66099888C>T	ENST00000311320.4	-	10	2337	c.2211G>A	c.(2209-2211)ggG>ggA	p.G737G	RIN1_ENST00000524804.1_5'Flank|RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000424433.2_Intron|RIN1_ENST00000530056.1_Silent_p.G571G	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	737					associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						CCCCAGCATCCCCATCTCCCT	0.647													C|||	153	0.0305511	0.1104	0.0101	5008	,	,		17960	0.0		0.0	False		,,,				2504	0.0				p.G737G		Atlas-SNP	.											.	RIN1	64	.	0			c.G2211A						PASS	.	C		437,3963	211.5+/-231.7	17,403,1780	156.0	151.0	153.0		2211	-2.9	0.0	11	dbSNP_129	153	2,8588	1.2+/-3.3	0,2,4293	no	coding-synonymous	RIN1	NM_004292.2		17,405,6073	TT,TC,CC		0.0233,9.9318,3.3795		737/784	66099888	439,12551	2200	4295	6495	SO:0001819	synonymous_variant	9610	exon10			AGCATCCCCATCT	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.2211G>A	11.37:g.66099888C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	182	182	1	NM_004292	O15010|Q00427|Q96CC8	Silent	SNP	ENST00000311320.4	37	CCDS31614.1																																																																																			C|0.969;T|0.031	0.031	strong		0.647	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292	
FAM83F	113828	hgsc.bcm.edu	37	22	40417780	40417780	+	Silent	SNP	C	C	T	rs5995793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:40417780C>T	ENST00000333407.6	+	4	1360	c.1266C>T	c.(1264-1266)aaC>aaT	p.N422N	FAM83F_ENST00000473717.1_Silent_p.N254N	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	422										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						CCAGCCGAAACGGCATGGGAG	0.667													T|||	1443	0.288139	0.3979	0.1628	5008	,	,		15282	0.0853		0.2873	False		,,,				2504	0.4387				p.N422N		Atlas-SNP	.											.	FAM83F	29	.	0			c.C1266T						PASS	.	T		1481,2919		256,969,975	21.0	20.0	21.0		1266	-6.0	0.1	22	dbSNP_114	21	2483,6113		342,1799,2157	no	coding-synonymous	FAM83F	NM_138435.2		598,2768,3132	TT,TC,CC		28.8855,33.6591,30.5017		422/501	40417780	3964,9032	2200	4298	6498	SO:0001819	synonymous_variant	113828	exon4			CCGAAACGGCATG		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.1266C>T	22.37:g.40417780C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_138435	Q96FD6	Silent	SNP	ENST00000333407.6	37	CCDS14000.2																																																																																			C|0.719;T|0.281	0.281	strong		0.667	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
ME3	10873	hgsc.bcm.edu	37	11	86267633	86267633	+	Silent	SNP	C	C	T	rs17211115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:86267633C>T	ENST00000393324.3	-	3	682	c.429G>A	c.(427-429)ctG>ctA	p.L143L	ME3_ENST00000543262.1_Silent_p.L143L|ME3_ENST00000323418.6_Silent_p.L81L|ME3_ENST00000359636.2_Silent_p.L143L|RP11-317J19.1_ENST00000524610.1_RNA	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	143					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)				GCTGACAGGCCAGCCCCACGG	0.582													C|||	1380	0.275559	0.1921	0.3487	5008	,	,		18963	0.5317		0.1799	False		,,,				2504	0.1708				p.L143L		Atlas-SNP	.											.	ME3	70	.	0			c.G429A						PASS	.	C	,,	819,3585	325.6+/-299.2	67,685,1450	75.0	60.0	65.0		429,429,429	5.1	1.0	11	dbSNP_123	65	1448,7150	276.9+/-292.6	110,1228,2961	no	coding-synonymous,coding-synonymous,coding-synonymous	ME3	NM_001014811.1,NM_001161586.1,NM_006680.2	,,	177,1913,4411	TT,TC,CC		16.8411,18.5967,17.4358	,,	143/605,143/605,143/605	86267633	2267,10735	2202	4299	6501	SO:0001819	synonymous_variant	10873	exon4			ACAGGCCAGCCCC	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.429G>A	11.37:g.86267633C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_006680	B7Z6V0|Q8TBJ0	Silent	SNP	ENST00000393324.3	37	CCDS8277.1																																																																																			C|0.784;T|0.216	0.216	strong		0.582	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2		
NCR2	9436	hgsc.bcm.edu	37	6	41318578	41318578	+	Silent	SNP	T	T	C	rs115509322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41318578T>C	ENST00000373089.5	+	5	895	c.807T>C	c.(805-807)gaT>gaC	p.D269D	NCR2_ENST00000373086.3_3'UTR|NCR2_ENST00000373083.4_3'UTR	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	269	Poly-Asp.				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)					agataagcgatgatgatgatg	0.398													T|||	43	0.00858626	0.0272	0.0058	5008	,	,		22654	0.0		0.003	False		,,,				2504	0.0				p.D269D		Atlas-SNP	.											.	NCR2	44	.	0			c.T807C						PASS	.	T	,,	118,4288	89.7+/-128.4	1,116,2086	95.0	89.0	91.0		,,807	-2.5	0.0	6	dbSNP_132	91	17,8583	12.6+/-44.7	0,17,4283	no	utr-3,utr-3,coding-synonymous	NCR2	NM_001199509.1,NM_001199510.1,NM_004828.3	,,	1,133,6369	CC,CT,TT		0.1977,2.6782,1.038	,,	,,269/277	41318578	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	9436	exon5			AAGCGATGATGAT	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.807T>C	6.37:g.41318578T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_004828	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Silent	SNP	ENST00000373089.5	37	CCDS4855.1																																																																																			T|0.990;C|0.010	0.010	strong		0.398	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3		
PSG6	5675	hgsc.bcm.edu	37	19	43411150	43411150	+	Silent	SNP	G	G	A	rs78024453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43411150G>A	ENST00000292125.2	-	5	1208	c.1164C>T	c.(1162-1164)agC>agT	p.S388S	PSG6_ENST00000187910.2_Silent_p.S388S|PSG6_ENST00000402603.4_Silent_p.S295S	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	388	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				CATAGAGCCCGCTATGATTTG	0.458													.|||	116	0.0231629	0.0825	0.0101	5008	,	,		19776	0.0		0.0	False		,,,				2504	0.0				p.S388S		Atlas-SNP	.											.	PSG6	89	.	0			c.C1164T						PASS	.	T	,	343,4059		23,297,1881	192.0	203.0	199.0		1164,1164	-3.1	0.0	19	dbSNP_131	199	2,8596		0,2,4297	no	coding-synonymous,coding-synonymous	PSG6	NM_001031850.2,NM_002782.3	,	23,299,6178	AA,AG,GG		0.0233,7.7919,2.6538	,	388/425,388/436	43411150	345,12655	2201	4299	6500	SO:0001819	synonymous_variant	5675	exon5			GAGCCCGCTATGA		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.1164C>T	19.37:g.43411150G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	171	70	0.409357	NM_001031850	O75244|Q15224|Q15235|Q549K1	Silent	SNP	ENST00000292125.2	37	CCDS12613.1																																																																																			G|0.976;A|0.024	0.024	strong		0.458	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
COL19A1	1310	hgsc.bcm.edu	37	6	70733547	70733547	+	Missense_Mutation	SNP	C	C	G	rs2273426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	82	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	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		
KRI1	65095	hgsc.bcm.edu	37	19	10672493	10672493	+	Missense_Mutation	SNP	C	C	T	rs12984043|rs34229707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10672493C>T	ENST00000312962.6	-	5	449	c.430G>A	c.(430-432)Ggg>Agg	p.G144R	KRI1_ENST00000537964.1_5'UTR|KRI1_ENST00000361821.5_Missense_Mutation_p.G140R	NM_023008.3	NP_075384.3	Q8N9T8	KRI1_HUMAN	KRI1 homolog (S. cerevisiae)	138	Glu-rich.					nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.G144R(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			GAAGTCTCCCCGTCTGAGTTC	0.592													C|||	1310	0.261581	0.1362	0.2522	5008	,	,		11668	0.2034		0.4036	False		,,,				2504	0.3517				p.G144R		Atlas-SNP	.											KRI1,NS,carcinoma,0,1	KRI1	65	1	1	Substitution - Missense(1)	stomach(1)	c.G430A						PASS	.	C	ARG/GLY	756,3650	307.7+/-290.2	61,634,1508	80.0	88.0	85.0		430	1.7	0.4	19	dbSNP_121	85	3265,5335	487.5+/-372.1	594,2077,1629	yes	missense	KRI1	NM_023008.3	125	655,2711,3137	TT,TC,CC		37.9651,17.1584,30.9165	benign	144/710	10672493	4021,8985	2203	4300	6503	SO:0001583	missense	65095	exon5			TCTCCCCGTCTGA		CCDS12242.1	19p13.2	2008-02-05			ENSG00000129347	ENSG00000129347			25769	protein-coding gene	gene with protein product						12878157	Standard	NM_023008		Approved	FLJ12949	uc002moy.1	Q8N9T8	OTTHUMG00000150343	ENST00000312962.6:c.430G>A	19.37:g.10672493C>T	ENSP00000320917:p.Gly144Arg	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_023008	Q2M1R5|Q2M1R7|Q7L5J7|Q96G92|Q9BU50|Q9H6I1|Q9H978	Missense_Mutation	SNP	ENST00000312962.6	37	CCDS12242.1	586	0.2683150183150183	69	0.1402439024390244	109	0.3011049723756906	107	0.18706293706293706	301	0.3970976253298153	C	6.809	0.518267	0.13005	0.171584	0.379651	ENSG00000129347	ENST00000312962;ENST00000361821;ENST00000541101;ENST00000539027	T;T;T	0.32023	1.47;1.47;1.47	4.05	1.67	0.24075	.	0.426594	0.23189	N	0.050931	T	0.00012	0.0000	L	0.59436	1.845	0.41381	P	0.012442999999999982	B;B	0.20988	0.028;0.05	B;B	0.10450	0.005;0.005	T	0.44605	-0.9317	9	0.21540	T	0.41	-36.7837	8.1253	0.30995	0.1643:0.6526:0.1831:0.0	rs12984043;rs17677304;rs52822002;rs56722461;rs12984043	144;140	Q8N9T8;D3YTE0	KRI1_HUMAN;.	R	144;140;144;135	ENSP00000320917:G144R;ENSP00000355366:G140R;ENSP00000445789:G135R	ENSP00000320917:G144R	G	-	1	0	KRI1	10533493	0.956000	0.32656	0.384000	0.26145	0.042000	0.13812	3.193000	0.50997	0.888000	0.36160	-0.521000	0.04368	GGG	C|0.715;T|0.285	0.285	strong		0.592	KRI1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317705.1	NM_023008	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036959	33036959	+	Silent	SNP	G	G	A	rs201076982|rs2308929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33036959G>A	ENST00000419277.1	-	4	594	c.465C>T	c.(463-465)aaC>aaT	p.N155N	HLA-DPA1_ENST00000428995.1_Silent_p.N155N|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	155	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CCAGCTCCCCGTTGCACAGCC	0.567													G|||	2199	0.439097	0.5802	0.2839	5008	,	,		18975	0.6796		0.1899	False		,,,				2504	0.3671				p.N155N		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C465T						PASS	.	G	,,	1420,1600		327,766,417	156.0	180.0	172.0		465,465,465	-6.8	0.0	6	dbSNP_126	172	962,4454		72,818,1818	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	399,1584,2235	AA,AG,GG		17.7622,47.0199,28.2361	,,	155/261,155/261,155/261	33036959	2382,6054	1510	2708	4218	SO:0001819	synonymous_variant	3113	exon3			CTCCCCGTTGCAC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.465C>T	6.37:g.33036959G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1	864	0.3956043956043956	274	0.556910569105691	89	0.24585635359116023	371	0.6486013986013986	130	0.17150395778364116	G	3.309	-0.141181	0.06669	0.470199	0.177622	ENSG00000231389	ENST00000437811	.	.	.	3.4	-6.81	0.01704	.	.	.	.	.	T	0.19604	0.0471	.	.	.	0.18873	P	0.9999892507	.	.	.	.	.	.	T	0.14755	-1.0461	3	.	.	.	.	11.6574	0.51325	0.4795:0.0:0.5205:0.0	rs2308929;rs17850580	.	.	.	W	23	.	.	R	-	1	2	HLA-DPA1	33144937	0.958000	0.32768	0.019000	0.16419	0.560000	0.35617	0.053000	0.14184	-1.606000	0.01591	-0.481000	0.04817	CGG	G|0.695;A|0.305	0.305	strong		0.567	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
IVL	3713	hgsc.bcm.edu	37	1	152883711	152883711	+	Missense_Mutation	SNP	G	G	C	rs7545520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152883711G>C	ENST00000368764.3	+	2	1502	c.1438G>C	c.(1438-1440)Gtg>Ctg	p.V480L	IVL_ENST00000392667.2_Missense_Mutation_p.V334L			P07476	INVO_HUMAN	involucrin	480	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].		V -> L (in dbSNP:rs7545520).		isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGAGGGCCAGGTGAAGCACCT	0.617													C|||	2065	0.41234	0.6808	0.2997	5008	,	,		18908	0.5615		0.1083	False		,,,				2504	0.2883				p.V480L		Atlas-SNP	.											.	IVL	100	.	0			c.G1438C						PASS	.	C	LEU/VAL	2393,1961		673,1047,457	53.0	57.0	56.0		1438	-0.1	0.0	1	dbSNP_116	56	744,7794		37,670,3562	yes	missense	IVL	NM_005547.2	32	710,1717,4019	CC,CG,GG		8.714,45.039,24.3329	benign	480/586	152883711	3137,9755	2177	4269	6446	SO:0001583	missense	3713	exon2			GGCCAGGTGAAGC	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1438G>C	1.37:g.152883711G>C	ENSP00000357753:p.Val480Leu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	190	189	0.994737	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	856	0.39194139194139194	342	0.6951219512195121	101	0.27900552486187846	333	0.5821678321678322	80	0.10554089709762533	C	0.006	-2.019429	0.00418	0.54961	0.08714	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.10668	3.1;2.85	2.3	-0.118	0.13547	.	.	.	.	.	T	0.00666	0.0022	N	0.00321	-1.65	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.46442	-0.9191	8	0.25751	T	0.34	.	6.9492	0.24536	0.1867:0.3029:0.5104:0.0	rs7545520;rs52815615	480	P07476	INVO_HUMAN	L	480;334	ENSP00000357753:V480L;ENSP00000376435:V334L	ENSP00000357753:V480L	V	+	1	0	IVL	151150335	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.407000	0.07178	-0.629000	0.05575	-1.481000	0.00988	GTG	G|0.646;C|0.354	0.354	strong		0.617	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
POR	5447	hgsc.bcm.edu	37	7	75583325	75583325	+	Silent	SNP	A	A	G	rs10262966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75583325A>G	ENST00000461988.1	+	2	120	c.15A>G	c.(13-15)ggA>ggG	p.G5G	POR_ENST00000419840.1_5'UTR|POR_ENST00000394893.1_Silent_p.G5G	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	2					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)	TCAACATGGGAGACTCCCACG	0.552													G|||	524	0.104633	0.3011	0.0303	5008	,	,		20069	0.005		0.005	False		,,,				2504	0.0971				p.G5G		Atlas-SNP	.											.	POR	46	.	0			c.A15G						PASS	.	G		982,3060		130,722,1169	77.0	75.0	75.0		15	3.4	0.9	7	dbSNP_119	75	37,8319		0,37,4141	no	coding-synonymous	POR	NM_000941.2		130,759,5310	GG,GA,AA		0.4428,24.2949,8.2191		5/681	75583325	1019,11379	2021	4178	6199	SO:0001819	synonymous_variant	5447	exon2			CATGGGAGACTCC	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.15A>G	7.37:g.75583325A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	116	46	0.396552	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Silent	SNP	ENST00000461988.1	37	CCDS5579.1																																																																																			A|0.934;G|0.066	0.066	strong		0.552	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941	
OTOP2	92736	hgsc.bcm.edu	37	17	72926879	72926879	+	Silent	SNP	T	T	C	rs16967162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72926879T>C	ENST00000580223.1	+	5	1179	c.1149T>C	c.(1147-1149)tcT>tcC	p.S383S	OTOP2_ENST00000331427.4_Silent_p.S383S			Q7RTS6	OTOP2_HUMAN	otopetrin 2	383						integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|prostate(4)|skin(1)|urinary_tract(2)	39	all_lung(278;0.172)|Lung NSC(278;0.207)					ACGCCATCTCTTACTACTCCA	0.637													C|||	334	0.0666933	0.2428	0.0187	5008	,	,		18213	0.0		0.0	False		,,,				2504	0.0				p.S383S		Atlas-SNP	.											.	OTOP2	81	.	0			c.T1149C						PASS	.	C		1004,3402	729.1+/-410.0	132,740,1331	72.0	63.0	66.0		1149	4.3	1.0	17	dbSNP_123	66	16,8584	818.5+/-406.9	0,16,4284	no	coding-synonymous	OTOP2	NM_178160.2		132,756,5615	CC,CT,TT		0.186,22.7871,7.8425		383/563	72926879	1020,11986	2203	4300	6503	SO:0001819	synonymous_variant	92736	exon6			CATCTCTTACTAC	BK000567	CCDS11708.1	17q25.3	2006-09-20				ENSG00000183034			19657	protein-coding gene	gene with protein product		607827				12651873	Standard	NM_178160		Approved		uc010wrp.2	Q7RTS6		ENST00000580223.1:c.1149T>C	17.37:g.72926879T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_178160		Silent	SNP	ENST00000580223.1	37	CCDS11708.1																																																																																			T|0.925;C|0.075	0.075	strong		0.637	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160	
VWDE	221806	hgsc.bcm.edu	37	7	12409197	12409197	+	Missense_Mutation	SNP	C	C	G	rs78231473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12409197C>G	ENST00000275358.3	-	12	2923	c.2735G>C	c.(2734-2736)aGt>aCt	p.S912T		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	912						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						GTCATAGGAACTAAAGCTTGG	0.383													C|||	93	0.0185703	0.0688	0.0029	5008	,	,		20375	0.0		0.0	False		,,,				2504	0.0				p.S912T		Atlas-SNP	.											VWDE_ENST00000275358,NS,carcinoma,+1,2	VWDE	123	2	0			c.G2735C						PASS	.	C	THR/SER	59,1325		1,57,634	84.0	68.0	73.0		2735	3.0	0.4	7	dbSNP_132	73	1,3181		0,1,1590	yes	missense	VWDE	NM_001135924.1	58	1,58,2224	GG,GC,CC		0.0314,4.263,1.3141	possibly-damaging	912/1591	12409197	60,4506	692	1591	2283	SO:0001583	missense	221806	exon12			TAGGAACTAAAGC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.2735G>C	7.37:g.12409197C>G	ENSP00000275358:p.Ser912Thr	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	138	66	0.478261	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	0.328	-0.957594	0.02267	0.04263	3.14E-4	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.82081	-1.57	4.83	3.03	0.35002	.	0.711350	0.14327	N	0.326598	T	0.27697	0.0681	L	0.42245	1.32	0.19575	N	0.999962	B	0.02656	0.0	B	0.06405	0.002	T	0.26573	-1.0099	10	0.12430	T	0.62	.	9.9581	0.41680	0.0:0.7396:0.12:0.1404	.	912	Q8N2E2	VWDE_HUMAN	T	912;366	ENSP00000275358:S912T	ENSP00000275358:S912T	S	-	2	0	VWDE	12375722	0.723000	0.28027	0.393000	0.26258	0.040000	0.13550	2.936000	0.48971	0.262000	0.21774	-0.795000	0.03280	AGT	C|0.986;G|0.014	0.014	strong		0.383	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
TEX14	56155	hgsc.bcm.edu	37	17	56636908	56636908	+	Silent	SNP	T	T	C	rs9903050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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|RP11-112H10.4_ENST00000578022.1_RNA|TEX14_ENST00000389934.3_Silent_p.K1431K|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	497	0	0		WXS	Illumina HiSeq	Phase_I	505	267	0.528713	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		
SREK1IP1	285672	hgsc.bcm.edu	37	5	64020241	64020241	+	Silent	SNP	T	T	C	rs16879016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:64020241T>C	ENST00000513458.4	-	5	605	c.438A>G	c.(436-438)acA>acG	p.T146T		NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	146					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						AACTATTAGGTGTAGAAGAAT	0.294													C|||	724	0.144569	0.4924	0.0519	5008	,	,		18873	0.0238		0.0109	False		,,,				2504	0.002				p.T146T		Atlas-SNP	.											.	SREK1IP1	28	.	0			c.A438G						PASS	.	C		1770,2634	619.0+/-393.3	360,1050,792	34.0	34.0	34.0		438	-9.1	0.0	5	dbSNP_123	34	59,8533	801.1+/-407.4	0,59,4237	no	coding-synonymous	SREK1IP1	NM_173829.3		360,1109,5029	CC,CT,TT		0.6867,40.1907,14.0736		146/156	64020241	1829,11167	2202	4296	6498	SO:0001819	synonymous_variant	285672	exon5			ATTAGGTGTAGAA	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.438A>G	5.37:g.64020241T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	180	90	0.5	NM_173829	Q32NC8	Silent	SNP	ENST00000513458.4	37	CCDS34171.1																																																																																			T|0.886;C|0.114	0.114	strong		0.294	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829	
LARP6	55323	hgsc.bcm.edu	37	15	71128691	71128691	+	Silent	SNP	G	G	A	rs78188777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:71128691G>A	ENST00000299213.8	-	2	424	c.354C>T	c.(352-354)caC>caT	p.H118H		NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	118	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.				regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						TCCTCCTCACGTGTTTTAGCA	0.453													G|||	79	0.0157748	0.0567	0.0058	5008	,	,		20033	0.0		0.0	False		,,,				2504	0.0				p.H118H		Atlas-SNP	.											.	LARP6	43	.	0			c.C354T						PASS	.	G		219,4179	132.1+/-168.6	5,209,1985	124.0	123.0	123.0		354	-3.1	1.0	15	dbSNP_132	123	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	LARP6	NM_018357.2		5,210,6281	AA,AG,GG		0.0116,4.9795,1.6933		118/492	71128691	220,12772	2199	4297	6496	SO:0001819	synonymous_variant	55323	exon2			CCTCACGTGTTTT	BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"""La ribonucleoprotein domain containing"""	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.354C>T	15.37:g.71128691G>A		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	206	93	0.451456	NM_018357	Q5XKE4|Q8N3N2|Q9NUR0	Silent	SNP	ENST00000299213.8	37	CCDS32281.1																																																																																			G|0.984;A|0.016	0.016	strong		0.453	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357	
MOGAT2	80168	hgsc.bcm.edu	37	11	75431049	75431049	+	Missense_Mutation	SNP	C	C	T	rs35828061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:75431049C>T	ENST00000198801.5	+	2	174	c.104C>T	c.(103-105)aCt>aTt	p.T35I	MOGAT2_ENST00000526712.1_5'UTR	NM_025098.2	NP_079374.2	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	35					diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|intestinal absorption (GO:0050892)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|acetyltransferase activity (GO:0016407)			NS(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	20	Ovarian(111;0.103)					GAGATCTGCACTGTGGGCTTC	0.592													C|||	122	0.024361	0.0908	0.0	5008	,	,		19209	0.0		0.002	False		,,,				2504	0.0				p.T35I		Atlas-SNP	.											MOGAT2,NS,carcinoma,+1,1	MOGAT2	49	1	0			c.C104T						PASS	.	C	ILE/THR	311,4089	169.8+/-200.3	8,295,1897	165.0	143.0	150.0		104	-7.3	0.0	11	dbSNP_126	150	6,8580	4.3+/-15.6	0,6,4287	yes	missense	MOGAT2	NM_025098.2	89	8,301,6184	TT,TC,CC		0.0699,7.0682,2.4411	benign	35/335	75431049	317,12669	2200	4293	6493	SO:0001583	missense	80168	exon2			TCTGCACTGTGGG	AY157608	CCDS8240.1	11q13.5	2008-02-05			ENSG00000166391	ENSG00000166391			23248	protein-coding gene	gene with protein product		610270				14970677	Standard	NM_025098		Approved	MGAT2, DGAT2L5, FLJ22644	uc010rru.2	Q3SYC2	OTTHUMG00000165341	ENST00000198801.5:c.104C>T	11.37:g.75431049C>T	ENSP00000198801:p.Thr35Ile	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_025098	A8K7I3|Q3SYC1|Q6ZQZ2|Q86UH6|Q9H630	Missense_Mutation	SNP	ENST00000198801.5	37	CCDS8240.1	37	0.01694139194139194	37	0.07520325203252033	0	0.0	0	0.0	0	0.0	C	2.919	-0.223665	0.06061	0.070682	6.99E-4	ENSG00000166391	ENST00000198801	T	0.09163	3.01	4.99	-7.32	0.01436	.	1.133530	0.06466	N	0.730377	T	0.00241	0.0007	N	0.04959	-0.14	0.20307	N	0.999911	B;B	0.06786	0.0;0.001	B;B	0.09377	0.0;0.004	T	0.42716	-0.9435	10	0.05833	T	0.94	2.7006	8.1687	0.31241	0.201:0.487:0.0:0.3121	rs35828061;rs61085918	35;35	Q3SYC2;Q3SYC2-3	MOGT2_HUMAN;.	I	35	ENSP00000198801:T35I	ENSP00000198801:T35I	T	+	2	0	MOGAT2	75108697	0.000000	0.05858	0.000000	0.03702	0.551000	0.35334	-2.562000	0.00920	-1.376000	0.02126	-1.300000	0.01332	ACT	C|0.974;T|0.026	0.026	strong		0.592	MOGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383520.1	NM_025098	
ACOT7	11332	hgsc.bcm.edu	37	1	6324747	6324747	+	Silent	SNP	G	G	A	rs61739537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6324747G>A	ENST00000377855.2	-	9	1199	c.1053C>T	c.(1051-1053)acC>acT	p.T351T	ACOT7_ENST00000608083.1_Silent_p.T309T|ACOT7_ENST00000545482.1_Silent_p.T236T|ACOT7_ENST00000377842.3_Silent_p.T300T|ACOT7_ENST00000377845.3_Silent_p.T321T|ACOT7_ENST00000361521.4_Silent_p.T341T	NM_181864.2	NP_863654.1	O00154	BACH_HUMAN	acyl-CoA thioesterase 7	351					coenzyme A biosynthetic process (GO:0015937)|fatty acid catabolic process (GO:0009062)|long-chain fatty-acyl-CoA catabolic process (GO:0036116)|medium-chain fatty acid biosynthetic process (GO:0051792)|medium-chain fatty-acyl-CoA catabolic process (GO:0036114)|palmitic acid biosynthetic process (GO:1900535)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)	carboxylic ester hydrolase activity (GO:0052689)|fatty-acyl-CoA binding (GO:0000062)|long-chain fatty acyl-CoA binding (GO:0036042)|palmitoyl-CoA hydrolase activity (GO:0016290)|protein homodimerization activity (GO:0042803)	p.T341T(1)		kidney(1)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	16	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		TCTCGTCCTCGGTCTCGGGCT	0.647													G|||	99	0.0197684	0.062	0.0086	5008	,	,		19936	0.0		0.0089	False		,,,				2504	0.002				p.T351T	GBM(74;673 1226 4974 11850 13190)	Atlas-SNP	.											ACOT7,NS,carcinoma,0,1	ACOT7	71	1	1	Substitution - coding silent(1)	pancreas(1)	c.C1053T						PASS	.	G	,,,	244,4160	138.4+/-174.2	9,226,1967	143.0	102.0	116.0		1023,1053,963,900	-7.1	0.9	1	dbSNP_129	116	69,8531	40.3+/-97.0	1,67,4232	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACOT7	NM_007274.3,NM_181864.2,NM_181865.2,NM_181866.2	,,,	10,293,6199	AA,AG,GG		0.8023,5.5404,2.407	,,,	341/371,351/381,321/351,300/330	6324747	313,12691	2202	4300	6502	SO:0001819	synonymous_variant	11332	exon9			GTCCTCGGTCTCG	AB074417	CCDS65.1, CCDS66.1, CCDS67.1, CCDS30573.1	1p36	2008-08-14			ENSG00000097021	ENSG00000097021		"""Acyl CoA thioesterases"""	24157	protein-coding gene	gene with protein product	"""brain acyl CoA hydrolase"""	602587				10578051, 16103133, 16940157	Standard	XM_005263427		Approved	BACH, ACH1, ACT, CTE-II, LACH1, MGC1126, hBACH	uc001amt.3	O00154	OTTHUMG00000001295	ENST00000377855.2:c.1053C>T	1.37:g.6324747G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_181864	A8K0K7|A8K232|A8K6B8|A8K837|B3KQ12|O43703|Q53Y78|Q5JYL2|Q5JYL3|Q5JYL4|Q5JYL5|Q5JYL6|Q5TGR4|Q9UJM9|Q9Y539|Q9Y540	Silent	SNP	ENST00000377855.2	37	CCDS65.1																																																																																			G|0.972;A|0.028	0.028	strong		0.647	ACOT7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003773.1	NM_007274	
CD3G	917	hgsc.bcm.edu	37	11	118221350	118221350	+	Missense_Mutation	SNP	G	G	T	rs71469175|rs3753058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118221350G>T	ENST00000532917.1	+	4	459	c.391G>T	c.(391-393)Gtt>Ttt	p.V131F	CD3G_ENST00000532903.1_3'UTR|CD3G_ENST00000392883.2_Intron	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN	CD3g molecule, gamma (CD3-TCR complex)	131			V -> F (in dbSNP:rs3753058).		cell surface receptor signaling pathway (GO:0007166)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|regulation of immune response (GO:0050776)|regulation of lymphocyte apoptotic process (GO:0070228)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|receptor signaling complex scaffold activity (GO:0030159)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	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)	Muromonab(DB00075)	CGTCCTTGCTGTTGGGGTCTA	0.473													G|||	1490	0.297524	0.1611	0.1124	5008	,	,		19740	0.5119		0.1789	False		,,,				2504	0.5143				p.V131F		Atlas-SNP	.											.	CD3G	31	.	0			c.G391T						PASS	.	G	PHE/VAL	19,4381		7,5,2188	193.0	167.0	176.0		391	1.6	1.0	11	dbSNP_107	176	38,8554		10,18,4268	yes	missense	CD3G	NM_000073.2	50	17,23,6456	TT,TG,GG		0.4423,0.4318,0.4387	probably-damaging	131/183	118221350	57,12935	2200	4296	6496	SO:0001583	missense	917	exon4			CTTGCTGTTGGGG	X60491	CCDS8395.1	11q23	2014-09-17	2006-03-28		ENSG00000160654	ENSG00000160654		"""CD molecules"""	1675	protein-coding gene	gene with protein product		186740	"""CD3g antigen, gamma polypeptide (TiT3 complex)"""				Standard	NM_000073		Approved		uc001psu.2	P09693	OTTHUMG00000166971	ENST00000532917.1:c.391G>T	11.37:g.118221350G>T	ENSP00000431445:p.Val131Phe	Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	195	102	0.523077	NM_000073	Q2HIZ6	Missense_Mutation	SNP	ENST00000532917.1	37	CCDS8395.1	451	0.2065018315018315	49	0.09959349593495935	41	0.1132596685082873	256	0.44755244755244755	105	0.13852242744063326	G	20.7	4.042038	0.75732	0.004318	0.004423	ENSG00000160654	ENST00000532917	T	0.63255	-0.03	5.76	1.63	0.23807	.	0.332375	0.31495	N	0.007550	T	0.00012	0.0000	M	0.72894	2.215	0.09310	P	0.999999999950223	D	0.59767	0.986	P	0.51415	0.669	T	0.39603	-0.9606	9	0.49607	T	0.09	.	9.2037	0.37275	0.0784:0.4192:0.5024:0.0	rs3753058	131	P09693	CD3G_HUMAN	F	131	ENSP00000431445:V131F	ENSP00000431445:V131F	V	+	1	0	CD3G	117726560	0.999000	0.42202	0.994000	0.49952	0.986000	0.74619	0.322000	0.19576	0.046000	0.15833	0.655000	0.94253	GTT	G|0.828;T|0.172	0.172	strong		0.473	CD3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392135.1	NM_000073	
SUV39H2	79723	hgsc.bcm.edu	37	10	14939067	14939067	+	Silent	SNP	A	A	C	rs45473500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:14939067A>C	ENST00000354919.6	+	3	400	c.400A>C	c.(400-402)Agg>Cgg	p.R134R	SUV39H2_ENST00000313519.5_Silent_p.R74R|SUV39H2_ENST00000378325.3_Intron	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	134					cell differentiation (GO:0030154)|chromatin assembly or disassembly (GO:0006333)|chromatin remodeling (GO:0006338)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|male meiosis (GO:0007140)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nuclear heterochromatin (GO:0005720)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						GGCTAAACAAAGGATAGCTCT	0.368													A|||	29	0.00579073	0.0	0.0086	5008	,	,		20305	0.0		0.0199	False		,,,				2504	0.0031				p.R134R		Atlas-SNP	.											.	SUV39H2	72	.	0			c.A400C						PASS	.	A	,,,,	21,4385	28.1+/-56.4	0,21,2182	71.0	67.0	69.0		400,220,,,220	5.9	1.0	10	dbSNP_127	69	141,8459	70.3+/-132.9	4,133,4163	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	SUV39H2	NM_001193424.1,NM_001193425.1,NM_001193426.1,NM_001193427.1,NM_024670.3	,,,,	4,154,6345	CC,CA,AA		1.6395,0.4766,1.2456	,,,,	134/411,74/351,,,74/351	14939067	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	79723	exon3			AAACAAAGGATAG	AK027067	CCDS7104.1, CCDS53493.1, CCDS53494.1	10p13	2011-07-01			ENSG00000152455	ENSG00000152455		"""Chromatin-modifying enzymes / K-methyltransferases"""	17287	protein-coding gene	gene with protein product		606503				11094092	Standard	NM_001193424		Approved	FLJ23414, KMT1B	uc021png.1	Q9H5I1	OTTHUMG00000017718	ENST00000354919.6:c.400A>C	10.37:g.14939067A>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_001193424	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Silent	SNP	ENST00000354919.6	37	CCDS53494.1																																																																																			A|0.990;C|0.010	0.010	strong		0.368	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670	
CNTN2	6900	hgsc.bcm.edu	37	1	205033518	205033518	+	Missense_Mutation	SNP	C	C	G	rs79431021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:205033518C>G	ENST00000331830.4	+	11	1593	c.1309C>G	c.(1309-1311)Ctt>Gtt	p.L437V	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	437	Ig-like C2-type 5.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GGGAGAGATCCTTATCCCCTG	0.627													G|||	176	0.0351438	0.1112	0.0202	5008	,	,		13924	0.0		0.0129	False		,,,				2504	0.002				p.L437V	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.C1309G						PASS	.	G	VAL/LEU	380,4026	787.3+/-414.9	19,342,1842	91.0	107.0	101.0		1309	-7.0	0.0	1	dbSNP_132	101	148,8452	809.3+/-407.2	1,146,4153	yes	missense	CNTN2	NM_005076.3	32	20,488,5995	GG,GC,CC		1.7209,8.6246,4.0597	benign	437/1041	205033518	528,12478	2203	4300	6503	SO:0001583	missense	6900	exon11			GAGATCCTTATCC	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.1309C>G	1.37:g.205033518C>G	ENSP00000330633:p.Leu437Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	161	82	0.509317	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	76	0.0347985347985348	59	0.11991869918699187	7	0.019337016574585635	0	0.0	10	0.013192612137203167	G	0.460	-0.889703	0.02511	0.086246	0.017209	ENSG00000184144	ENST00000331830	T	0.66460	-0.21	5.33	-6.97	0.01616	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.302220	0.05908	N	0.631129	T	0.00496	0.0016	N	0.02985	-0.445	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.05241	-1.0897	10	0.15952	T	0.53	.	8.1491	0.31130	0.7102:0.0949:0.1004:0.0945	.	437;328	Q02246;Q68DA2	CNTN2_HUMAN;.	V	437	ENSP00000330633:L437V	ENSP00000330633:L437V	L	+	1	0	CNTN2	203300141	0.000000	0.05858	0.000000	0.03702	0.366000	0.29705	0.009000	0.13219	-1.704000	0.01407	-0.978000	0.02582	CTT	C|0.962;G|0.038	0.038	strong		0.627	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076	
ZNF736	728927	hgsc.bcm.edu	37	7	63808867	63808867	+	Missense_Mutation	SNP	C	C	A	rs11976837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:63808867C>A	ENST00000423484.2	+	4	748	c.626C>A	c.(625-627)gCg>gAg	p.A209E	ZNF736_ENST00000355095.4_Missense_Mutation_p.A209E			B4DX44	ZN736_HUMAN	zinc finger protein 736	209					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(6)|stomach(1)|urinary_tract(1)	9						TGTGGCAAAGCGTTTAAAAAG	0.363													c|||	1722	0.34385	0.5257	0.2824	5008	,	,		20536	0.3651		0.2873	False		,,,				2504	0.1779				p.A209E		Atlas-SNP	.											.	ZNF736	33	.	0			c.C626A						PASS	.	C	GLU/ALA	658,726		161,336,195	21.0	20.0	20.0		626	1.1	0.0	7	dbSNP_120	20	906,2274		121,664,805	no	missense	ZNF736	NM_001170905.1	107	282,1000,1000	AA,AC,CC		28.4906,47.5434,34.2682	probably-damaging	209/428	63808867	1564,3000	692	1590	2282	SO:0001583	missense	728927	exon5			GCAAAGCGTTTAA		CCDS55114.1	7q11.21	2013-01-08			ENSG00000234444	ENSG00000234444		"""Zinc fingers, C2H2-type"", ""-"""	32467	protein-coding gene	gene with protein product							Standard	XM_006716104		Approved		uc011kdo.2	B4DX44	OTTHUMG00000156537	ENST00000423484.2:c.626C>A	7.37:g.63808867C>A	ENSP00000400852:p.Ala209Glu	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_001170905		Missense_Mutation	SNP	ENST00000423484.2	37	CCDS55114.1	778	0.35622710622710624	230	0.46747967479674796	107	0.2955801104972376	220	0.38461538461538464	221	0.29155672823219	C	12.34	1.908165	0.33721	0.475434	0.284906	ENSG00000234444	ENST00000355095;ENST00000423484	T;T	0.00840	5.63;5.63	1.15	1.15	0.20763	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.56199	1.76	0.80722	P	0.0	D	0.69078	0.997	P	0.62435	0.902	T	0.49051	-0.8979	8	0.87932	D	0	.	5.1222	0.14865	0.0:0.6209:0.3791:0.0	rs11976837;rs57515600;rs11976837	209	B4DX44	ZN736_HUMAN	E	209	ENSP00000347210:A209E;ENSP00000400852:A209E	ENSP00000347210:A209E	A	+	2	0	ZNF736	63446302	0.000000	0.05858	0.003000	0.11579	0.119000	0.20118	-0.368000	0.07543	0.555000	0.29079	0.305000	0.20034	GCG	.	.	weak		0.363	ZNF736-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000344559.2	NM_001170905	
PDIA6	10130	hgsc.bcm.edu	37	2	10930903	10930903	+	Missense_Mutation	SNP	T	T	C	rs4807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10930903T>C	ENST00000272227.3	-	7	788	c.641A>G	c.(640-642)aAa>aGa	p.K214R	PDIA6_ENST00000404371.2_Missense_Mutation_p.K266R|PDIA6_ENST00000404824.2_Missense_Mutation_p.K262R|PDIA6_ENST00000540494.1_Missense_Mutation_p.K211R|PDIA6_ENST00000381611.4_Missense_Mutation_p.K219R	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	214	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.		K -> R (in dbSNP:rs4807). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9110174}.		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)		CAGTTTCACTTTTCCTTTCGT	0.438													T|||	1409	0.28135	0.1059	0.3372	5008	,	,		22101	0.3948		0.2654	False		,,,				2504	0.3783				p.K214R	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											PDIA6,colon,carcinoma,0,1	PDIA6	31	1	0			c.A641G						PASS	.	T	ARG/LYS	547,3859	246.2+/-254.9	35,477,1691	153.0	148.0	150.0		641	4.6	0.9	2	dbSNP_52	150	2453,6147	404.7+/-348.2	368,1717,2215	yes	missense	PDIA6	NM_005742.2	26	403,2194,3906	CC,CT,TT		28.5233,12.4149,23.0663	possibly-damaging	214/441	10930903	3000,10006	2203	4300	6503	SO:0001583	missense	10130	exon7			TTCACTTTTCCTT	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.641A>G	2.37:g.10930903T>C	ENSP00000272227:p.Lys214Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	154	77	0.5	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Missense_Mutation	SNP	ENST00000272227.3	37	CCDS1675.1	592	0.27106227106227104	57	0.11585365853658537	130	0.35911602209944754	202	0.3531468531468531	203	0.2678100263852243	T	17.41	3.381466	0.61845	0.124149	0.285233	ENSG00000143870	ENST00000272227;ENST00000404371;ENST00000404824;ENST00000540494;ENST00000381611	T;T;T;T;T	0.03524	3.9;3.9;3.9;3.9;3.9	5.71	4.56	0.56223	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.044045	0.85682	N	0.000000	T	0.00012	0.0000	L	0.39467	1.215	0.09310	P	0.99999999214648	B;B;B;B	0.20887	0.049;0.014;0.007;0.003	P;B;B;B	0.45099	0.469;0.084;0.033;0.027	T	0.51733	-0.8668	9	0.54805	T	0.06	.	11.426	0.50012	0.0:0.07:0.0:0.93	rs4807;rs1059775;rs3200587;rs3732109;rs52800710;rs60679704;rs4807	211;262;266;214	B7Z254;B5MCQ5;Q15084-2;Q15084	.;.;.;PDIA6_HUMAN	R	214;266;262;211;219	ENSP00000272227:K214R;ENSP00000385385:K266R;ENSP00000384459:K262R;ENSP00000438778:K211R;ENSP00000371024:K219R	ENSP00000272227:K214R	K	-	2	0	PDIA6	10848354	1.000000	0.71417	0.930000	0.37139	0.986000	0.74619	5.144000	0.64832	1.016000	0.39470	0.533000	0.62120	AAA	T|0.748;C|0.252	0.252	strong		0.438	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742	
AP5B1	91056	hgsc.bcm.edu	37	11	65547775	65547775	+	Silent	SNP	C	C	T	rs114368095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65547775C>T	ENST00000532090.2	-	2	399	c.189G>A	c.(187-189)caG>caA	p.Q63Q		NM_138368.4	NP_612377.4	Q2VPB7	AP5B1_HUMAN	adaptor-related protein complex 5, beta 1 subunit	63					endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-type membrane coat adaptor complex (GO:0030119)|lysosomal membrane (GO:0005765)				lung(1)	1						CGGGCCACAGCTGCGCAGGGT	0.667													C|||	130	0.0259585	0.0893	0.0173	5008	,	,		13769	0.0		0.0	False		,,,				2504	0.0				p.Q63Q		Atlas-SNP	.											.	AP5B1	40	.	0			c.G189A						PASS	.	C		220,3598		0,220,1689	5.0	7.0	6.0		18	3.2	1.0	11	dbSNP_132	6	4,8094		0,4,4045	no	coding-synonymous	DKFZp761E198	NM_138368.3		0,224,5734	TT,TC,CC		0.0494,5.7622,1.8798		6/822	65547775	224,11692	1909	4049	5958	SO:0001819	synonymous_variant	91056	exon2			CCACAGCTGCGCA	JQ313135	CCDS58146.1	11q13.1	2012-02-29			ENSG00000254470	ENSG00000254470			25104	protein-coding gene	gene with protein product		614367				22022230	Standard	NM_138368		Approved	PP1030, AP-5, DKFZp761E198	uc031qbm.1	Q2VPB7	OTTHUMG00000166593	ENST00000532090.2:c.189G>A	11.37:g.65547775C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_138368	A1L0S6|H6WUK2|Q0D2Q2|Q8N3J7|Q8WYH6	Silent	SNP	ENST00000532090.2	37	CCDS58146.1																																																																																			C|0.975;T|0.025	0.025	strong		0.667	AP5B1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390636.2	NM_138368	
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744287	31744287	+	Missense_Mutation	SNP	C	C	T	rs113360916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31744287C>T	ENST00000399889.2	-	1	270	c.245G>A	c.(244-246)cGc>cAc	p.R82H		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	82	5 X 10 AA approximate repeats.					intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						GGTTCTGGGGCGGTAGCAGGA	0.607													C|||	41	0.0081869	0.0295	0.0029	5008	,	,		19842	0.0		0.0	False		,,,				2504	0.0				p.R82H		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.G245A						PASS	.	C	HIS/ARG	124,4282	92.0+/-130.7	0,124,2079	59.0	59.0	59.0		245	1.4	0.1	21	dbSNP_132	59	2,8598	2.2+/-6.3	0,2,4298	yes	missense	KRTAP13-2	NM_181621.3	29	0,126,6377	TT,TC,CC		0.0233,2.8143,0.9688	benign	82/176	31744287	126,12880	2203	4300	6503	SO:0001583	missense	337959	exon1			CTGGGGCGGTAGC	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"""Keratin associated proteins"""	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.245G>A	21.37:g.31744287C>T	ENSP00000382777:p.Arg82His	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	182	86	0.472527	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	7.773	0.707941	0.15239	0.028143	2.33E-4	ENSG00000182816	ENST00000399889	T	0.03496	3.91	4.26	1.36	0.22044	.	0.161204	0.28871	N	0.013862	T	0.00906	0.0030	L	0.39326	1.205	0.09310	N	1	B	0.24258	0.1	B	0.22601	0.04	T	0.46978	-0.9152	10	0.18710	T	0.47	.	4.1563	0.10263	0.1829:0.6128:0.0:0.2043	.	82	Q52LG2	KR132_HUMAN	H	82	ENSP00000382777:R82H	ENSP00000382777:R82H	R	-	2	0	KRTAP13-2	30666158	0.000000	0.05858	0.054000	0.19295	0.994000	0.84299	-1.818000	0.01717	0.138000	0.18790	0.655000	0.94253	CGC	C|0.990;T|0.010	0.010	strong		0.607	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1		
DCDC2	51473	hgsc.bcm.edu	37	6	24175021	24175021	+	Missense_Mutation	SNP	T	T	A	rs9460973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24175021T>A	ENST00000378454.3	-	10	1669	c.1368A>T	c.(1366-1368)aaA>aaT	p.K456N	DCDC2_ENST00000378450.3_Missense_Mutation_p.K209N	NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	456			K -> N (in dbSNP:rs9460973).		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)				GACTGGTAATTTTTACTTCTG	0.378													T|||	717	0.143171	0.4947	0.0548	5008	,	,		14734	0.0		0.0249	False		,,,				2504	0.0				p.K456N		Atlas-SNP	.											.	DCDC2	53	.	0			c.A1368T						PASS	.	T	ASN/LYS,ASN/LYS	1840,2566	536.5+/-374.5	383,1074,746	180.0	158.0	165.0		1368,1368	3.3	1.0	6	dbSNP_119	165	246,8354	98.4+/-159.9	5,236,4059	yes	missense,missense	DCDC2	NM_001195610.1,NM_016356.3	94,94	388,1310,4805	AA,AT,TT		2.8605,41.7612,16.0388	benign,benign	456/477,456/477	24175021	2086,10920	2203	4300	6503	SO:0001583	missense	51473	exon11			GGTAATTTTTACT	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.1368A>T	6.37:g.24175021T>A	ENSP00000367715:p.Lys456Asn	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Missense_Mutation	SNP	ENST00000378454.3	37	CCDS4550.1	287	0.13141025641025642	245	0.49796747967479676	24	0.06629834254143646	0	0.0	18	0.023746701846965697	T	15.60	2.881600	0.51908	0.417612	0.028605	ENSG00000146038	ENST00000378454;ENST00000378450	T;T	0.52526	4.1;0.66	5.67	3.29	0.37713	.	0.447465	0.21854	N	0.068137	T	0.23688	0.0573	L	0.27053	0.805	0.47698	P	5.060000000000064E-4	P;P	0.50369	0.839;0.934	B;P	0.50490	0.351;0.642	T	0.07214	-1.0784	9	0.36615	T	0.2	-10.8947	7.2128	0.25943	0.0:0.1737:0.0:0.8263	rs9460973;rs52810021;rs9460973	456;209	Q9UHG0;Q9UHG0-2	DCDC2_HUMAN;.	N	456;209	ENSP00000367715:K456N;ENSP00000367711:K209N	ENSP00000367711:K209N	K	-	3	2	DCDC2	24283000	0.987000	0.35691	0.979000	0.43373	0.984000	0.73092	1.093000	0.30939	0.440000	0.26502	0.533000	0.62120	AAA	T|0.853;A|0.147	0.147	strong		0.378	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356	
FBXO42	54455	hgsc.bcm.edu	37	1	16577948	16577948	+	Silent	SNP	G	G	A	rs61731119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16577948G>A	ENST00000375592.3	-	10	1587	c.1371C>T	c.(1369-1371)gaC>gaT	p.D457D		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	457										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)		GTACAGGACTGTCCAAAGAAG	0.552													G|||	149	0.0297524	0.1074	0.0101	5008	,	,		17306	0.0		0.0	False		,,,				2504	0.0				p.D457D		Atlas-SNP	.											.	FBXO42	53	.	0			c.C1371T						PASS	.	G		386,4020	179.7+/-208.2	17,352,1834	29.0	33.0	32.0		1371	5.5	1.0	1	dbSNP_129	32	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	FBXO42	NM_018994.1		17,356,6130	AA,AG,GG		0.0465,8.7608,2.9986		457/718	16577948	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	54455	exon10			AGGACTGTCCAAA	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.1371C>T	1.37:g.16577948G>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	159	87	0.54717	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Silent	SNP	ENST00000375592.3	37	CCDS30613.1																																																																																			G|0.973;A|0.027	0.027	strong		0.552	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
GPRC5B	51704	hgsc.bcm.edu	37	16	19883364	19883364	+	Silent	SNP	G	G	A	rs61742688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19883364G>A	ENST00000300571.2	-	2	995	c.804C>T	c.(802-804)aaC>aaT	p.N268N	GPRC5B_ENST00000569847.1_Silent_p.N268N|GPRC5B_ENST00000569479.1_Silent_p.N268N|GPRC5B_ENST00000535671.1_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	64	0	0		WXS	Illumina HiSeq	Phase_I	74	44	0.594595	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		
KLF12	11278	hgsc.bcm.edu	37	13	74387412	74387412	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:74387412G>A	ENST00000377669.2	-	4	709	c.683C>T	c.(682-684)cCc>cTc	p.P228L	KLF12_ENST00000472022.1_5'UTR|KLF12_ENST00000377666.4_Missense_Mutation_p.P228L	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	228					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		TAGGCCTCGGGGGTCCATTTG	0.433																																					p.P228L		Atlas-SNP	.											KLF12,right_upper_lobe,carcinoma,+1,1	KLF12	42	1	0			c.C683T						scavenged	.						161.0	148.0	153.0					13																	74387412		2203	4300	6503	SO:0001583	missense	11278	exon5			CCTCGGGGGTCCA	AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6346	protein-coding gene	gene with protein product	"""KLF12 zinc finger transcriptional repressor"", ""AP-2rep transcription factor"", ""AP-2 repressor"""	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.683C>T	13.37:g.74387412G>A	ENSP00000366897:p.Pro228Leu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	165	2	0.0121212	NM_007249	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Missense_Mutation	SNP	ENST00000377669.2	37	CCDS9449.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.875808	0.51695	.	.	ENSG00000118922	ENST00000377669;ENST00000342812;ENST00000377666	T;T	0.01455	4.87;4.87	5.47	5.47	0.80525	.	0.167885	0.53938	D	0.000050	T	0.02156	0.0067	N	0.19112	0.55	0.58432	D	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.61053	-0.7140	10	0.59425	D	0.04	.	18.6836	0.91556	0.0:0.0:1.0:0.0	.	228	Q9Y4X4	KLF12_HUMAN	L	228	ENSP00000366897:P228L;ENSP00000366894:P228L	ENSP00000344057:P228L	P	-	2	0	KLF12	73285413	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	6.113000	0.71553	2.721000	0.93114	0.655000	0.94253	CCC	.	.	none		0.433	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249	
MUC4	4585	hgsc.bcm.edu	37	3	195512603	195512603	+	Missense_Mutation	SNP	T	T	C	rs79969373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512603T>C	ENST00000463781.3	-	2	6307	c.5848A>G	c.(5848-5850)Acc>Gcc	p.T1950A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1950A	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)		AGAGGGGTGGTGTGACCTGAG	0.597																																					p.T1950A		Atlas-SNP	.											.	MUC4	1505	.	0			c.A5848G						PASS	.						49.0	44.0	45.0					3																	195512603		691	1589	2280	SO:0001583	missense	4585	exon2			GGGTGGTGTGACC	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.5848A>G	3.37:g.195512603T>C	ENSP00000417498:p.Thr1950Ala	Somatic	384	0	0		WXS	Illumina HiSeq	Phase_I	240	60	0.25	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	.	.	.	.	.	.	.	.	.	.	-	3.349	-0.132926	0.06711	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26810	1.82;1.71	.	.	.	.	.	.	.	.	T	0.09818	0.0241	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.04013	0.001	T	0.34502	-0.9826	7	.	.	.	.	2.8304	0.05498	3.0E-4:2.0E-4:0.4983:0.5012	.	1950	E7ESK3	.	A	1950	ENSP00000417498:T1950A;ENSP00000420243:T1950A	.	T	-	1	0	MUC4	196996998	0.028000	0.19301	0.042000	0.18584	0.032000	0.12392	-0.278000	0.08490	0.056000	0.16144	0.055000	0.15244	ACC	T|0.989;C|0.011	0.011	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RNF213	57674	hgsc.bcm.edu	37	17	78319380	78319380	+	Silent	SNP	G	G	C	rs4890012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78319380G>C	ENST00000582970.1	+	29	7388	c.7245G>C	c.(7243-7245)ccG>ccC	p.P2415P	RNF213_ENST00000508628.2_Silent_p.P2464P|RNF213_ENST00000336301.6_Silent_p.P488P	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2415					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)			GTGGGATCCCGGTTATCATCA	0.527													G|||	2370	0.473243	0.407	0.3948	5008	,	,		22033	0.378		0.668	False		,,,				2504	0.5164				p.P2415P		Atlas-SNP	.											.	RNF213	766	.	0			c.G7245C						PASS	.	G		1946,2460	551.4+/-378.3	452,1042,709	82.0	80.0	81.0		7392	-10.2	0.0	17	dbSNP_111	81	5500,3100	658.6+/-401.6	1772,1956,572	no	coding-synonymous	RNF213	NM_020914.4		2224,2998,1281	CC,CG,GG		36.0465,44.167,42.7495		2464/5257	78319380	7446,5560	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon29			GATCCCGGTTATC	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.7245G>C	17.37:g.78319380G>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	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																																																																																			G|0.447;C|0.553	0.553	strong		0.527	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
PKD1L2	114780	hgsc.bcm.edu	37	16	81211496	81211496	+	RNA	SNP	C	C	A	rs9935113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81211496C>A	ENST00000527937.1	-	0	319				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000531391.1_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	69	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	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		
ABHD12	26090	hgsc.bcm.edu	37	20	25288632	25288632	+	Silent	SNP	G	G	A	rs6107027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:25288632G>A	ENST00000339157.5	-	9	1109	c.837C>T	c.(835-837)cgC>cgT	p.R279R	ABHD12_ENST00000376542.3_Silent_p.R279R|ABHD12_ENST00000481556.1_5'UTR	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	279					adult walking behavior (GO:0007628)|phosphatidylserine catabolic process (GO:0006660)|response to auditory stimulus (GO:0010996)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)	acylglycerol lipase activity (GO:0047372)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	12						TAGCTTCTTCGCGGATATTAG	0.368													g|||	1683	0.336062	0.211	0.5836	5008	,	,		13675	0.0228		0.5089	False		,,,				2504	0.4744				p.R279R		Atlas-SNP	.											.	ABHD12	46	.	0			c.C837T						PASS	.	A	,	1183,3223	415.2+/-337.1	157,869,1177	73.0	72.0	72.0		837,837	-11.1	0.0	20	dbSNP_114	72	4470,4130	589.2+/-392.5	1153,2164,983	no	coding-synonymous,coding-synonymous	ABHD12	NM_001042472.2,NM_015600.4	,	1310,3033,2160	AA,AG,GG		48.0233,26.8498,43.4646	,	279/399,279/405	25288632	5653,7353	2203	4300	6503	SO:0001819	synonymous_variant	26090	exon9			TTCTTCGCGGATA	AL117442	CCDS13172.1, CCDS42857.1	20p11.21	2007-04-24	2006-03-10	2006-03-10	ENSG00000100997	ENSG00000100997		"""Abhydrolase domain containing"""	15868	protein-coding gene	gene with protein product		613599	"""chromosome 20 open reading frame 22"""	C20orf22			Standard	NM_015600		Approved	DKFZP434P106, dJ965G21.2, BEM46L2, ABHD12A	uc002wuq.3	Q8N2K0	OTTHUMG00000032121	ENST00000339157.5:c.837C>T	20.37:g.25288632G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Silent	SNP	ENST00000339157.5	37	CCDS42857.1																																																																																			G|0.608;A|0.392	0.392	strong		0.368	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600	
CSRNP1	64651	hgsc.bcm.edu	37	3	39185077	39185077	+	Silent	SNP	G	G	A	rs1274957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39185077G>A	ENST00000273153.5	-	5	1416	c.1239C>T	c.(1237-1239)agC>agT	p.S413S	CSRNP1_ENST00000514182.1_Silent_p.S413S	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	413					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						GGTTCCCCACGCTCCCTTCCT	0.582													A|||	2460	0.491214	0.115	0.6239	5008	,	,		21304	0.5724		0.6551	False		,,,				2504	0.6534				p.S413S		Atlas-SNP	.											.	CSRNP1	59	.	0			c.C1239T						PASS	.	A		870,3536	741.0+/-411.2	86,698,1419	64.0	66.0	65.0		1239	-7.5	0.0	3	dbSNP_87	65	5594,3006	460.9+/-365.3	1824,1946,530	no	coding-synonymous	CSRNP1	NM_033027.3		1910,2644,1949	AA,AG,GG		34.9535,19.7458,49.7001		413/590	39185077	6464,6542	2203	4300	6503	SO:0001819	synonymous_variant	64651	exon5			CCCCACGCTCCCT	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.1239C>T	3.37:g.39185077G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	168	71	0.422619	NM_033027	Q69YY5	Silent	SNP	ENST00000273153.5	37	CCDS2682.1																																																																																			G|0.495;A|0.505	0.505	strong		0.582	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027	
RNF112	7732	hgsc.bcm.edu	37	17	19319374	19319374	+	Silent	SNP	T	T	C	rs76138388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19319374T>C	ENST00000461366.1	+	14	1997	c.1782T>C	c.(1780-1782)gcT>gcC	p.A594A	CTB-187M2.2_ENST00000579897.1_RNA|AC004448.2_ENST00000437646.1_lincRNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	594						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	12						CAGGGGCCGCTGTGGTTGGGG	0.687													.|||	1150	0.229633	0.4228	0.085	5008	,	,		10555	0.2847		0.008	False		,,,				2504	0.2423				p.A594A		Atlas-SNP	.											RNF112,NS,haematopoietic_neoplasm,0,1	RNF112	37	1	0			c.T1782C						PASS	.	C		811,2571		72,667,952	3.0	4.0	4.0		1782	-7.5	0.0	17	dbSNP_132	4	89,7169		1,87,3541	no	coding-synonymous	RNF112	NM_007148.4		73,754,4493	CC,CT,TT		1.2262,23.9799,8.4586		594/632	19319374	900,9740	1691	3629	5320	SO:0001819	synonymous_variant	7732	exon14			GGCCGCTGTGGTT	AF054587	CCDS58529.1	17p11.2	2013-01-16	2008-06-13	2008-06-13	ENSG00000128482	ENSG00000128482		"""RING-type (C3HC4) zinc fingers"""	12968	protein-coding gene	gene with protein product		601237	"""zinc finger protein 179"""	ZNF179		8660987, 9806830	Standard	NM_007148		Approved	BFP	uc010vyw.2	Q9ULX5	OTTHUMG00000059601	ENST00000461366.1:c.1782T>C	17.37:g.19319374T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_007148	O60633|Q7Z5V9	Silent	SNP	ENST00000461366.1	37	CCDS58529.1																																																																																			T|0.829;C|0.171	0.171	strong		0.687	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148	
NRN1L	123904	hgsc.bcm.edu	37	16	67919930	67919930	+	Missense_Mutation	SNP	A	A	C	rs73593844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67919930A>C	ENST00000339176.3	+	3	365	c.266A>C	c.(265-267)gAg>gCg	p.E89A	CTC-479C5.10_ENST00000572067.1_lincRNA|NRN1L_ENST00000576147.1_Silent_p.R16R	NM_198443.1	NP_940845.1	Q496H8	NRN1L_HUMAN	neuritin 1-like	89					nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)		GGCTGTCCGGAGGAGGCAGCT	0.582													A|||	314	0.0626997	0.1982	0.0159	5008	,	,		16226	0.001		0.003	False		,,,				2504	0.0378				p.E89A		Atlas-SNP	.											.	NRN1L	13	.	0			c.A266C						PASS	.	A	ALA/GLU	810,3586	319.6+/-296.2	76,658,1464	61.0	55.0	57.0		266	4.9	0.9	16	dbSNP_130	57	9,8591	4.3+/-15.6	0,9,4291	yes	missense	NRN1L	NM_198443.1	107	76,667,5755	CC,CA,AA		0.1047,18.4258,6.3019	probably-damaging	89/166	67919930	819,12177	2198	4300	6498	SO:0001583	missense	123904	exon3			GTCCGGAGGAGGC	AY358782	CCDS10850.1	16q22.1	2008-02-05			ENSG00000188038	ENSG00000188038			29811	protein-coding gene	gene with protein product						12975309	Standard	NM_198443		Approved	UNQ2446, MRCC2446	uc002euu.3	Q496H8	OTTHUMG00000137541	ENST00000339176.3:c.266A>C	16.37:g.67919930A>C	ENSP00000342411:p.Glu89Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_198443	Q6UWH7	Missense_Mutation	SNP	ENST00000339176.3	37	CCDS10850.1	102	0.046703296703296704	97	0.19715447154471544	5	0.013812154696132596	0	0.0	0	0.0	A	19.67	3.871364	0.72065	0.184258	0.001047	ENSG00000188038	ENST00000339176	.	.	.	4.86	4.86	0.63082	.	0.470389	0.20557	N	0.089986	T	0.00109	0.0003	M	0.77820	2.39	0.09310	P	0.99999999389136	P	0.36837	0.571	B	0.33960	0.173	T	0.16041	-1.0416	8	0.66056	D	0.02	.	12.9814	0.58567	1.0:0.0:0.0:0.0	.	89	Q496H8	NRN1L_HUMAN	A	89	.	ENSP00000342411:E89A	E	+	2	0	NRN1L	66477431	1.000000	0.71417	0.851000	0.33527	0.690000	0.40134	2.938000	0.48987	1.953000	0.56701	0.379000	0.24179	GAG	A|0.944;C|0.056	0.056	strong		0.582	NRN1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268872.2	NM_198443	
OSGIN1	29948	hgsc.bcm.edu	37	16	83999000	83999000	+	Silent	SNP	C	C	G	rs3743627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:83999000C>G	ENST00000343939.2	+	7	1454	c.1071C>G	c.(1069-1071)gcC>gcG	p.A357A	OSGIN1_ENST00000393306.1_Silent_p.A274A|OSGIN1_ENST00000361711.3_Silent_p.A274A			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	357					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						CCCTGGAGGCCGCCACAAGGG	0.706													G|||	648	0.129393	0.2806	0.0548	5008	,	,		15108	0.0446		0.0626	False		,,,				2504	0.1339				p.A274A		Atlas-SNP	.											.	OSGIN1	33	.	0			c.C822G						PASS	.	G	,,	965,3361		108,749,1306	19.0	24.0	22.0		1071,822,822	-3.2	0.2	16	dbSNP_107	22	450,8000		12,426,3787	yes	coding-synonymous,coding-synonymous,coding-synonymous	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	,,	120,1175,5093	GG,GC,CC		5.3254,22.307,11.0755	,,	357/561,274/478,274/478	83999000	1415,11361	2163	4225	6388	SO:0001819	synonymous_variant	29948	exon6			GGAGGCCGCCACA	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.1071C>G	16.37:g.83999000C>G		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Silent	SNP	ENST00000343939.2	37																																																																																				C|0.896;G|0.104	0.104	strong		0.706	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
SARS2	54938	hgsc.bcm.edu	37	19	39416935	39416935	+	Silent	SNP	C	C	T	rs144229840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39416935C>T	ENST00000221431.6	-	2	432	c.273G>A	c.(271-273)tcG>tcA	p.S91S	SARS2_ENST00000448145.2_Silent_p.S91S|SARS2_ENST00000430193.3_Silent_p.S91S|SARS2_ENST00000600042.1_Silent_p.S91S|SARS2_ENST00000594171.1_5'UTR|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.D161N	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	91					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)	p.S91S(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CCTGCCATGTCGAGATCTGGG	0.612													C|||	38	0.00758786	0.0265	0.0029	5008	,	,		19704	0.0		0.001	False		,,,				2504	0.0				p.S91S		Atlas-SNP	.											SARS2,rectum,carcinoma,0,1	SARS2	33	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G273A						PASS	.	C	,	75,4331	65.3+/-102.7	1,73,2129	50.0	42.0	45.0		273,273	-8.9	0.0	19	dbSNP_134	45	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	SARS2	NM_001145901.1,NM_017827.3	,	1,76,6426	TT,TC,CC		0.0349,1.7022,0.5997	,	91/521,91/519	39416935	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	54938	exon2			CCATGTCGAGATC	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"""Aminoacyl tRNA synthetases / Class II"""	17697	protein-coding gene	gene with protein product	"""serine tRNA ligase 2, mitochondrial"""	612804	"""serine-tRNA ligase, mitochondrial"", ""seryl-tRNA synthetase 2"""	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.273G>A	19.37:g.39416935C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	37	CCDS33017.1																																																																																			C|0.995;T|0.005	0.005	strong		0.612	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827	
EIF2A	83939	hgsc.bcm.edu	37	3	150280445	150280445	+	Missense_Mutation	SNP	C	C	G	rs1132979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150280445C>G	ENST00000460851.1	+	4	399	c.290C>G	c.(289-291)aCt>aGt	p.T97S	EIF2A_ENST00000273435.5_Missense_Mutation_p.T92S|EIF2A_ENST00000406576.3_Missense_Mutation_p.T97S|SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000487799.1_Missense_Mutation_p.T72S			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	97			T -> S (in dbSNP:rs1132979). {ECO:0000269|PubMed:12133843, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3, ECO:0000269|Ref.4, ECO:0000269|Ref.6}.		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)	p.T72S(1)		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)			CAGCCTTACACTAGTAAGTAT	0.403													C|||	1774	0.354233	0.1611	0.3631	5008	,	,		16648	0.4861		0.3588	False		,,,				2504	0.4683				p.T97S		Atlas-SNP	.											EIF2A_ENST00000487799,NS,carcinoma,0,1	EIF2A	59	1	1	Substitution - Missense(1)	stomach(1)	c.C290G						PASS	.	C	SER/THR	631,3103		45,541,1281	67.0	61.0	63.0		290	5.9	1.0	3	dbSNP_86	63	2865,5335		508,1849,1743	yes	missense	EIF2A	NM_032025.3	58	553,2390,3024	GG,GC,CC		34.939,16.8988,29.2945	benign	97/586	150280445	3496,8438	1867	4100	5967	SO:0001583	missense	83939	exon4			CTTACACTAGTAA	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.290C>G	3.37:g.150280445C>G	ENSP00000417229:p.Thr97Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Missense_Mutation	SNP	ENST00000460851.1	37	CCDS46935.1	797	0.3649267399267399	90	0.18292682926829268	141	0.38950276243093923	287	0.5017482517482518	279	0.36807387862796836	C	13.40	2.226881	0.39399	0.168988	0.34939	ENSG00000144895	ENST00000487799;ENST00000460851;ENST00000406576;ENST00000482093;ENST00000273435	T;T;T;T;T	0.54071	0.9;0.9;0.59;0.9;0.9	5.86	5.86	0.93980	WD40/YVTN repeat-like-containing domain (1);	0.266752	0.40222	N	0.001157	T	0.00012	0.0000	N	0.05012	-0.13	0.09310	P	1.0	B;B;B	0.13145	0.007;0.001;0.004	B;B;B	0.12156	0.007;0.002;0.003	T	0.43228	-0.9404	9	0.10902	T	0.67	-6.8954	20.1894	0.98226	0.0:1.0:0.0:0.0	rs1132979;rs2049228;rs3194341;rs11537792;rs16862740;rs17418293;rs52804311;rs1132979	97;72;97	B4DF96;B4DQ14;Q9BY44	.;.;EIF2A_HUMAN	S	72;97;97;97;92	ENSP00000420537:T72S;ENSP00000417229:T97S;ENSP00000385292:T97S;ENSP00000418698:T97S;ENSP00000273435:T92S	ENSP00000273435:T92S	T	+	2	0	EIF2A	151763135	0.999000	0.42202	1.000000	0.80357	0.933000	0.57130	2.755000	0.47540	2.781000	0.95711	0.591000	0.81541	ACT	C|0.635;G|0.365	0.365	strong		0.403	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025	
SPTAN1	6709	hgsc.bcm.edu	37	9	131395568	131395568	+	Silent	SNP	C	C	T	rs2228952	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131395568C>T	ENST00000372731.4	+	56	7484	c.7374C>T	c.(7372-7374)acC>acT	p.T2458T	WDR34_ENST00000483181.1_5'Flank|SPTAN1_ENST00000372739.3_Silent_p.T2463T|SPTAN1_ENST00000358161.5_Silent_p.T2463T	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	2458					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						AGCTCCCCACCGCGTTCGACT	0.632													C|||	116	0.0231629	0.0817	0.0101	5008	,	,		17940	0.0		0.001	False		,,,				2504	0.0				p.T2463T	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.C7389T						PASS	.	C	,,	348,4058	182.9+/-210.6	11,326,1866	83.0	72.0	76.0		7389,7314,7374	-10.7	0.0	9	dbSNP_98	76	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	11,331,6161	TT,TC,CC		0.0581,7.8983,2.7141	,,	2463/2478,2438/2453,2458/2473	131395568	353,12653	2203	4300	6503	SO:0001819	synonymous_variant	6709	exon57			CCCCACCGCGTTC	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.7374C>T	9.37:g.131395568C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	52	0.675325	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																			C|0.967;T|0.033	0.033	strong		0.632	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
TH	7054	hgsc.bcm.edu	37	11	2190951	2190951	+	Missense_Mutation	SNP	C	C	T	rs6356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2190951C>T	ENST00000381178.1	-	3	352	c.334G>A	c.(334-336)Gtg>Atg	p.V112M	TH_ENST00000381175.1_Missense_Mutation_p.V108M|TH_ENST00000352909.3_Missense_Mutation_p.V81M|TH_ENST00000333684.5_Missense_Mutation_p.V85M	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	112			V -> M (common polymorphism; dbSNP:rs6356). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21940685, ECO:0000269|PubMed:7789962, ECO:0000269|PubMed:9613851}.		anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	AGGTTTAGCACGGCCTTCCCC	0.697													C|||	2156	0.430511	0.1014	0.3919	5008	,	,		15378	0.7877		0.4026	False		,,,				2504	0.5634				p.V112M		Atlas-SNP	.											.	TH	43	.	0			c.G334A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	623,3779	265.6+/-266.7	36,551,1614	58.0	60.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	241,334,322	-1.8	0.0	11	dbSNP_52	60	3121,5477	472.4+/-368.3	569,1983,1747	yes	missense,missense,missense	TH	NM_000360.3,NM_199292.2,NM_199293.2	21,21,21	605,2534,3361	TT,TC,CC		36.2991,14.1527,28.8	benign,benign,benign	81/498,112/529,108/525	2190951	3744,9256	2201	4299	6500	SO:0001583	missense	7054	exon3			TTAGCACGGCCTT	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.334G>A	11.37:g.2190951C>T	ENSP00000370571:p.Val112Met	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	179	94	0.52514	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Missense_Mutation	SNP	ENST00000381178.1	37	CCDS7731.1	913	0.41804029304029305	52	0.10569105691056911	127	0.35082872928176795	443	0.7744755244755245	291	0.3839050131926121	C	13.68	2.310931	0.40895	0.141527	0.362991	ENSG00000180176	ENST00000381178;ENST00000381175;ENST00000352909;ENST00000333684	D;D;D;D	0.98419	-4.92;-4.92;-4.92;-4.92	3.59	-1.8	0.07907	.	0.577810	0.17552	N	0.170143	T	0.00012	0.0000	L	0.31664	0.95	0.80722	P	0.0	B;B;B;B;B	0.24576	0.037;0.037;0.044;0.016;0.106	B;B;B;B;B	0.21151	0.006;0.006;0.02;0.005;0.033	T	0.41662	-0.9496	9	0.33141	T	0.24	.	4.7289	0.12955	0.0:0.2915:0.2918:0.4167	rs6356;rs57599796;rs6356	85;81;81;112;108	Q0PWM2;Q0PWM3;P07101-3;P07101;P07101-2	.;.;.;TY3H_HUMAN;.	M	112;108;81;85	ENSP00000370571:V112M;ENSP00000370567:V108M;ENSP00000325951:V81M;ENSP00000328814:V85M	ENSP00000328814:V85M	V	-	1	0	TH	2147527	0.000000	0.05858	0.000000	0.03702	0.948000	0.59901	-0.327000	0.07955	-0.189000	0.10482	0.491000	0.48974	GTG	C|0.652;T|0.348	0.348	strong		0.697	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
C19orf57	79173	hgsc.bcm.edu	37	19	14006300	14006300	+	Missense_Mutation	SNP	C	C	A	rs58722011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14006300C>A	ENST00000586783.1	-	2	90	c.91G>T	c.(91-93)Gac>Tac	p.D31Y	C19orf57_ENST00000591586.1_Missense_Mutation_p.D31Y|C19orf57_ENST00000454313.1_Missense_Mutation_p.D31Y|C19orf57_ENST00000346736.2_Missense_Mutation_p.D31Y			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	31					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)			CTCTGGGGGTCCCCATAGAAG	0.547													C|||	160	0.0319489	0.118	0.0058	5008	,	,		17727	0.0		0.0	False		,,,				2504	0.0				p.D31Y		Atlas-SNP	.											.	C19orf57	34	.	0			c.G91T						PASS	.	C	TYR/ASP	352,4054	182.9+/-210.6	15,322,1866	171.0	183.0	179.0		91	-1.8	0.0	19	dbSNP_129	179	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C19orf57	NM_024323.3	160	15,323,6165	AA,AC,CC		0.0116,7.9891,2.7141	probably-damaging	31/638	14006300	353,12653	2203	4300	6503	SO:0001583	missense	79173	exon3			GGGGGTCCCCATA	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.91G>T	19.37:g.14006300C>A	ENSP00000465822:p.Asp31Tyr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	174	79	0.454023	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		60	0.027472527472527472	59	0.11991869918699187	1	0.0027624309392265192	0	0.0	0	0.0	C	12.10	1.837639	0.32513	0.079891	1.16E-4	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.38401	1.14;1.14	4.12	-1.78	0.07957	.	1.528260	0.04542	N	0.388298	T	0.00300	0.0009	N	0.19112	0.55	0.09310	N	1	P	0.42620	0.785	B	0.37346	0.247	T	0.06661	-1.0814	10	0.56958	D	0.05	0.0377	4.2284	0.10590	0.0:0.4118:0.1831:0.4051	rs58722011	31	Q0VDD7-2	.	Y	31	ENSP00000404382:D31Y;ENSP00000254336:D31Y	ENSP00000254336:D31Y	D	-	1	0	C19orf57	13867300	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.800000	0.04555	-0.166000	0.10890	-0.743000	0.03520	GAC	C|0.974;A|0.026	0.026	strong		0.547	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	
IRF2BP1	26145	hgsc.bcm.edu	37	19	46387503	46387503	+	Silent	SNP	T	T	C	rs3745926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46387503T>C	ENST00000302165.3	-	1	1873	c.1530A>G	c.(1528-1530)ctA>ctG	p.L510L		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	510	Cys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		GGGTGTCTTCTAGCCGCTCCC	0.701													C|||	1610	0.321486	0.5764	0.3127	5008	,	,		13341	0.3125		0.169	False		,,,				2504	0.1493				p.L510L		Atlas-SNP	.											.	IRF2BP1	23	.	0			c.A1530G						PASS	.	C		2131,2247		538,1055,596	18.0	18.0	18.0		1530	1.3	1.0	19	dbSNP_107	18	1602,6944		164,1274,2835	no	coding-synonymous	IRF2BP1	NM_015649.1		702,2329,3431	CC,CT,TT		18.7456,48.6752,28.8842		510/585	46387503	3733,9191	2189	4273	6462	SO:0001819	synonymous_variant	26145	exon1			GTCTTCTAGCCGC	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.1530A>G	19.37:g.46387503T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_015649	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Silent	SNP	ENST00000302165.3	37	CCDS12678.1																																																																																			T|0.681;C|0.319	0.319	strong		0.701	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649	
HTATSF1	27336	hgsc.bcm.edu	37	X	135593167	135593167	+	Silent	SNP	G	G	A	rs1058376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:135593167G>A	ENST00000218364.4	+	9	1437	c.1263G>A	c.(1261-1263)gcG>gcA	p.A421A	HTATSF1_ENST00000535601.1_Silent_p.A421A	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	421	Mediates interaction with the P-TEFb complex.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					CTGGAATGGCGTTTGAAGAAC	0.448													g|||	513	0.135894	0.329	0.0447	3775	,	,		14100	0.0337		0.0089	False		,,,				2504	0.0041				p.A421A		Atlas-SNP	.											.	HTATSF1	66	.	0			c.G1263A						PASS	.	A	,	1427,2408		222,748,235,662,336	115.0	126.0	123.0		1263,1263	-3.1	0.0	X	dbSNP_86	123	73,6655		0,49,24,2379,1848	no	coding-synonymous,coding-synonymous	HTATSF1	NM_001163280.1,NM_014500.4	,	222,797,259,3041,2184	AA,AG,A,GG,G		1.085,37.2099,14.2005	,	421/756,421/756	135593167	1500,9063	2203	4300	6503	SO:0001819	synonymous_variant	27336	exon10			AATGGCGTTTGAA	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"""RNA binding motif (RRM) containing"""	5276	protein-coding gene	gene with protein product		300346	"""HIV TAT specific factor 1"""			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.1263G>A	X.37:g.135593167G>A		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	252	251	0.996032	NM_001163280	D3DWG9|Q59G06|Q99730	Silent	SNP	ENST00000218364.4	37	CCDS14657.1																																																																																			0|0.004;A|0.148	0.148	strong		0.448	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500	
PABPC1	26986	hgsc.bcm.edu	37	8	101721709	101721709	+	Missense_Mutation	SNP	T	T	A	rs146200489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721709T>A	ENST00000318607.5	-	8	2351	c.1223A>T	c.(1222-1224)tAc>tTc	p.Y408F	PABPC1_ENST00000519004.1_Missense_Mutation_p.Y363F|PABPC1_ENST00000522387.1_Missense_Mutation_p.Y376F|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	408					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TGCCATGAAGTAACCTGAAGG	0.493																																					p.Y408F		Atlas-SNP	.											PABPC1,NS,carcinoma,0,1	PABPC1	76	1	0			c.A1223T						PASS	.						103.0	93.0	96.0					8																	101721709		2203	4300	6503	SO:0001583	missense	26986	exon8			ATGAAGTAACCTG	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.1223A>T	8.37:g.101721709T>A	ENSP00000313007:p.Tyr408Phe	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	281	58	0.206406	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	17.26|17.26|17.26	3.344254|3.344254|3.344254	0.61073|0.61073|0.61073	.|.|.	.|.|.	ENSG00000070756|ENSG00000070756|ENSG00000070756	ENST00000519596|ENST00000517403;ENST00000519100|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|.|T;T;T	.|.|0.29917	.|.|1.64;1.55;2.61	5.37|5.37|5.37	5.37|5.37|5.37	0.77165|0.77165|0.77165	.|.|.	.|.|0.000000	.|.|0.64402	.|.|D	.|.|0.000016	T|T|T	0.31796|0.31796|0.31796	0.0808|0.0808|0.0808	L|L|L	0.54908|0.54908|0.54908	1.71|1.71|1.71	0.53688|0.53688|0.53688	D|D|D	0.999979|0.999979|0.999979	.|.|B;B;B	.|.|0.09022	.|.|0.0;0.002;0.002	.|.|B;B;B	.|.|0.10450	.|.|0.005;0.003;0.005	T|T|T	0.05257|0.05257|0.05257	-1.0896|-1.0896|-1.0896	5|5|10	.|.|0.33141	.|.|T	.|.|0.24	.|.|.	15.6695|15.6695|15.6695	0.77262|0.77262|0.77262	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|.|376;408;408	.|.|E7ERJ7;B3KT93;P11940	.|.|.;.;PABP1_HUMAN	F|S|F	240|61;277|408;408;363;376	.|.|ENSP00000313007:Y408F;ENSP00000429594:Y363F;ENSP00000429395:Y376F	.|.|ENSP00000313007:Y408F	L|T|Y	-|-|-	3|1|2	2|0|0	PABPC1|PABPC1|PABPC1	101790885|101790885|101790885	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	8.010000|8.010000|8.010000	0.88615|0.88615|0.88615	2.163000|2.163000|2.163000	0.67991|0.67991|0.67991	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	TTA|ACT|TAC	T|0.899;A|0.101	0.101	strong		0.493	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
HK3	3101	hgsc.bcm.edu	37	5	176315822	176315822	+	Silent	SNP	G	G	T	rs61749652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176315822G>T	ENST00000292432.5	-	9	1049	c.958C>A	c.(958-960)Cgg>Agg	p.R320R		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	320	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)			AGCACCAGCCGCACCAGCTCA	0.637													G|||	79	0.0157748	0.0144	0.0072	5008	,	,		16439	0.0		0.0268	False		,,,				2504	0.0286				p.R320R		Atlas-SNP	.											HK3_ENST00000292432,NS,carcinoma,0,2	HK3	210	2	0			c.C958A						PASS	.	G		108,4298	83.4+/-121.9	1,106,2096	46.0	49.0	48.0		958	3.5	1.0	5	dbSNP_129	48	170,8430	78.6+/-141.3	6,158,4136	no	coding-synonymous	HK3	NM_002115.2		7,264,6232	TT,TG,GG		1.9767,2.4512,2.1375		320/924	176315822	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	3101	exon9			CCAGCCGCACCAG		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.958C>A	5.37:g.176315822G>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_002115	Q8N1E7	Silent	SNP	ENST00000292432.5	37	CCDS4407.1																																																																																			G|0.979;T|0.021	0.021	strong		0.637	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
UNC5B	219699	hgsc.bcm.edu	37	10	72972771	72972771	+	Missense_Mutation	SNP	C	C	T	rs61757569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72972771C>T	ENST00000335350.6	+	1	445	c.29C>T	c.(28-30)gCg>gTg	p.A10V	AL359832.1_ENST00000401185.1_RNA|UNC5B_ENST00000373192.4_Missense_Mutation_p.A10V	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	10					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						GCTCGGGGCGCGCTGCTGCTG	0.746													c|||	77	0.0153754	0.0537	0.0072	5008	,	,		10870	0.0		0.001	False		,,,				2504	0.0				p.A10V		Atlas-SNP	.											.	UNC5B	123	.	0			c.C29T						PASS	.	C	VAL/ALA	40,4190		3,34,2078	6.0	8.0	7.0		29	2.5	1.0	10	dbSNP_129	7	2,8386		0,2,4192	yes	missense	UNC5B	NM_170744.4	64	3,36,6270	TT,TC,CC		0.0238,0.9456,0.3329	benign	10/946	72972771	42,12576	2115	4194	6309	SO:0001583	missense	219699	exon1			GGGGCGCGCTGCT	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.29C>T	10.37:g.72972771C>T	ENSP00000334329:p.Ala10Val	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_001244889	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	26	0.011904761904761904	22	0.044715447154471545	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	c	11.78	1.740401	0.30865	0.009456	2.38E-4	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.48836	0.87;0.8	4.39	2.52	0.30459	.	0.385350	0.22088	U	0.064791	T	0.07638	0.0192	L	0.29908	0.895	0.30473	N	0.773157	B;B	0.20459	0.045;0.027	B;B	0.12837	0.008;0.003	T	0.08472	-1.0720	10	0.17832	T	0.49	-12.4358	6.2386	0.20776	0.0:0.771:0.0:0.229	rs61757569	10;10	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	V	10	ENSP00000334329:A10V;ENSP00000362288:A10V	ENSP00000334329:A10V	A	+	2	0	UNC5B	72642777	1.000000	0.71417	1.000000	0.80357	0.265000	0.26407	1.192000	0.32150	0.853000	0.35312	-0.701000	0.03672	GCG	C|0.986;T|0.014	0.014	strong		0.746	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
DCC	1630	hgsc.bcm.edu	37	18	50976898	50976898	+	Silent	SNP	G	G	A	rs35891220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:50976898G>A	ENST00000442544.2	+	23	3874	c.3258G>A	c.(3256-3258)ccG>ccA	p.P1086P	DCC_ENST00000581580.1_Silent_p.P721P	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1086					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)		TGCACCCCCCGCATGGCAGTG	0.507													g|||	203	0.0405351	0.1172	0.0231	5008	,	,		17120	0.006		0.0119	False		,,,				2504	0.0143				p.P1086P		Atlas-SNP	.											DCC,colon,carcinoma,0,1	DCC	360	1	0			c.G3258A						scavenged	.	A		458,3948	219.1+/-236.9	22,414,1767	104.0	89.0	94.0		3258	-9.3	0.3	18	dbSNP_126	94	30,8570	19.8+/-62.0	0,30,4270	no	coding-synonymous	DCC	NM_005215.3		22,444,6037	AA,AG,GG		0.3488,10.3949,3.7521		1086/1448	50976898	488,12518	2203	4300	6503	SO:0001819	synonymous_variant	1630	exon23			CCCCCCGCATGGC	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.3258G>A	18.37:g.50976898G>A		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	127	64	0.503937	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																			G|0.966;A|0.034	0.034	strong		0.507	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
LILRA1	11024	hgsc.bcm.edu	37	19	55107869	55107869	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55107869T>G	ENST00000251372.3	+	7	1356	c.1174T>G	c.(1174-1176)Tcg>Gcg	p.S392A	LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000418536.2_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000453777.1_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	392	Ig-like C2-type 4.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.S392T(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CTCAGCCCACTCGGGGACCTA	0.587																																					p.S392A		Atlas-SNP	.											LILRA1,NS,carcinoma,0,2	LILRA1	105	2	1	Substitution - Missense(1)	lung(1)	c.T1174G						scavenged	.						144.0	135.0	138.0					19																	55107869		2203	4300	6503	SO:0001583	missense	11024	exon7			GCCCACTCGGGGA	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.1174T>G	19.37:g.55107869T>G	ENSP00000251372:p.Ser392Ala	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	254	14	0.0551181	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.088474	0.00367	.	.	ENSG00000104974	ENST00000251372	T	0.03553	3.89	1.8	-3.59	0.04583	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.846833	0.09755	N	0.760012	T	0.00608	0.0020	N	0.00123	-2.06	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.33292	-0.9874	10	0.02654	T	1	.	0.6627	0.00845	0.4001:0.1718:0.2547:0.1734	.	392	O75019	LIRA1_HUMAN	A	392	ENSP00000251372:S392A	ENSP00000251372:S392A	S	+	1	0	LILRA1	59799681	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.554000	0.02172	-1.875000	0.01132	-0.982000	0.02568	TCG	.	.	none		0.587	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
SORCS1	114815	hgsc.bcm.edu	37	10	108380213	108380213	+	Silent	SNP	G	G	A	rs4917481	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:108380213G>A	ENST00000263054.6	-	20	2776	c.2769C>T	c.(2767-2769)taC>taT	p.Y923Y	SORCS1_ENST00000344440.6_Silent_p.Y923Y|SORCS1_ENST00000369698.1_Silent_p.Y458Y|SORCS1_ENST00000478809.2_5'Flank	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	923					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)		ACCACCACACGTAAGTGAGGG	0.547													A|||	1883	0.375998	0.4682	0.2435	5008	,	,		12097	0.5069		0.171	False		,,,				2504	0.4213				p.Y923Y		Atlas-SNP	.											.	SORCS1	534	.	0			c.C2769T						PASS	.	A	,,,,,	1883,2523	630.4+/-395.5	403,1077,723	170.0	136.0	147.0		2769,2769,2769,2769,2769,2769	-3.2	0.8	10	dbSNP_111	147	1450,7150	751.3+/-407.4	117,1216,2967	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	,,,,,	520,2293,3690	AA,AG,GG		16.8605,42.7372,25.6266	,,,,,	923/1199,923/1180,923/1131,923/1160,923/1180,923/1169	108380213	3333,9673	2203	4300	6503	SO:0001819	synonymous_variant	114815	exon20			CCACACGTAAGTG	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.2769C>T	10.37:g.108380213G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1																																																																																			G|0.707;A|0.293	0.293	strong		0.547	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
CDAN1	146059	hgsc.bcm.edu	37	15	43028207	43028207	+	Silent	SNP	G	G	C	rs143391538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43028207G>C	ENST00000356231.3	-	3	662	c.639C>G	c.(637-639)acC>acG	p.T213T		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	213					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)		AGGTGAAGCAGGTCTTGGGCT	0.592													G|||	10	0.00199681	0.0076	0.0	5008	,	,		16376	0.0		0.0	False		,,,				2504	0.0				p.T213T		Atlas-SNP	.											.	CDAN1	70	.	0			c.C639G						PASS	.	G		15,4391	22.3+/-47.3	0,15,2188	107.0	124.0	118.0		639	-0.6	1.0	15	dbSNP_134	118	0,8598		0,0,4299	no	coding-synonymous	CDAN1	NM_138477.2		0,15,6487	CC,CG,GG		0.0,0.3404,0.1153		213/1228	43028207	15,12989	2203	4299	6502	SO:0001819	synonymous_variant	146059	exon3			GAAGCAGGTCTTG	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.639C>G	15.37:g.43028207G>C		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	166	83	0.5	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Silent	SNP	ENST00000356231.3	37	CCDS32209.1																																																																																			G|0.998;C|0.002	0.002	strong		0.592	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036853	33036853	+	Missense_Mutation	SNP	A	A	C	rs1042308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33036853A>C	ENST00000419277.1	-	4	700	c.571T>G	c.(571-573)Ttc>Gtc	p.F191V	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.F191V|HLA-DPA1_ENST00000463066.1_5'Flank	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	191	Alpha-2.|Ig-like C1-type.		F -> V (in allele DPA1*02:01, allele DPA1*02:02 and allele DPA1*04:01; dbSNP:rs1042308).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CAGTCATAGAAGTCCTCTGCT	0.547													A|||	2194	0.438099	0.5802	0.2839	5008	,	,		19836	0.6786		0.1889	False		,,,				2504	0.364				p.F191V		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.T571G						PASS	.	A	VAL/PHE,VAL/PHE,VAL/PHE	1427,1593		327,773,410	196.0	217.0	209.0		571,571,571	-3.7	0.0	6	dbSNP_86	209	960,4458		72,816,1821	yes	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	50,50,50	399,1589,2231	CC,CA,AA		17.7187,47.2517,28.2887	benign,benign,benign	191/261,191/261,191/261	33036853	2387,6051	1510	2709	4219	SO:0001583	missense	3113	exon3			CATAGAAGTCCTC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.571T>G	6.37:g.33036853A>C	ENSP00000393566:p.Phe191Val	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	169	167	0.988166	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	864|864	0.3956043956043956|0.3956043956043956	275|275	0.5589430894308943|0.5589430894308943	89|89	0.24585635359116023|0.24585635359116023	371|371	0.6486013986013986|0.6486013986013986	129|129	0.17018469656992086|0.17018469656992086	A|A	0.003|0.003	-2.491932|-2.491932	0.00161|0.00161	0.472517|0.472517	0.177187|0.177187	ENSG00000231389|ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337|ENST00000437811	T;T;T|.	0.02579|.	4.24;4.24;4.24|.	3.4|3.4	-3.7|-3.7	0.04437|0.04437	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);|.	0.524360|.	0.17386|.	N|.	0.176127|.	T|T	0.02380|0.02380	0.0073|0.0073	N|N	0.00738|0.00738	-1.235|-1.235	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.43426|0.43426	-0.9392|-0.9392	9|4	0.02654|.	T|.	1|.	.|.	8.0008|8.0008	0.30295|0.30295	0.7188:0.1825:0.0:0.0987|0.7188:0.1825:0.0:0.0987	rs1042308;rs2308933;rs45587632;rs52831627|rs1042308;rs2308933;rs45587632;rs52831627	191|.	P20036|.	DPA1_HUMAN|.	V|R	191;191;158;191|58	ENSP00000393566:F191V;ENSP00000402872:F191V;ENSP00000390929:F191V|.	ENSP00000393566:F191V|.	F|L	-|-	1|2	0|0	HLA-DPA1|HLA-DPA1	33144831|33144831	0.003000|0.003000	0.15002|0.15002	0.003000|0.003000	0.11579|0.11579	0.001000|0.001000	0.01503|0.01503	-0.160000|-0.160000	0.10041|0.10041	-0.501000|-0.501000	0.06605|0.06605	-0.178000|-0.178000	0.13098|0.13098	TTC|CTT	T|0.000;G|0.000;C|0.321;N|0.000;A|0.679	0.321	strong		0.547	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
RPUSD4	84881	hgsc.bcm.edu	37	11	126074192	126074192	+	Silent	SNP	A	A	G	rs2276312	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	41	0	0		WXS	Illumina HiSeq	Phase_I	39	29	0.74359	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	
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138417682	138417682	+	Silent	SNP	G	G	A	rs143883618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:138417682G>A	ENST00000310018.2	-	17	2130	c.1848C>T	c.(1846-1848)ttC>ttT	p.F616F	ATP6V0A4_ENST00000393054.1_Silent_p.F616F|ATP6V0A4_ENST00000353492.4_Silent_p.F616F	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	616					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|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 part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|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)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						ACATGTTGATGAAGTGGATGA	0.398													G|||	24	0.00479233	0.0182	0.0	5008	,	,		17290	0.0		0.0	False		,,,				2504	0.0				p.F616F		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.C1848T						PASS	.	G	,,	74,4332	65.3+/-102.7	0,74,2129	116.0	110.0	112.0		1848,1848,1848	2.8	1.0	7	dbSNP_134	112	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	,,	0,74,6429	AA,AG,GG		0.0,1.6795,0.569	,,	616/841,616/841,616/841	138417682	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	50617	exon16			GTTGATGAAGTGG	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"""ATPases / V-type"""	866	protein-coding gene	gene with protein product		605239	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 4"", ""ATPase, H+ transporting, lysosomal V0 subunit A4"""	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1848C>T	7.37:g.138417682G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_130841	A4D1R4|A8KA80|Q32M47	Silent	SNP	ENST00000310018.2	37	CCDS5849.1																																																																																			G|0.995;A|0.005	0.005	strong		0.398	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632	
TBC1D2	55357	hgsc.bcm.edu	37	9	100995758	100995758	+	Missense_Mutation	SNP	G	G	T	rs879368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100995758G>T	ENST00000375064.1	-	4	759	c.721C>A	c.(721-723)Cca>Aca	p.P241T	TBC1D2_ENST00000375066.5_Missense_Mutation_p.P241T|TBC1D2_ENST00000342112.5_Missense_Mutation_p.P23T	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	106	0	0		WXS	Illumina HiSeq	Phase_I	131	81	0.618321	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	
CPAMD8	27151	hgsc.bcm.edu	37	19	17088319	17088319	+	Missense_Mutation	SNP	G	G	T	rs3745335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17088319G>T	ENST00000443236.1	-	15	1789	c.1758C>A	c.(1756-1758)gaC>gaA	p.D586E	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	539						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						TCACACACACGTCGACCTCAG	0.597													g|||	1748	0.349042	0.503	0.3012	5008	,	,		17953	0.2837		0.2863	False		,,,				2504	0.3067				p.D586E		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C1758A						PASS	.	G	GLU/ASP	1694,2282		352,990,646	31.0	38.0	36.0		1758	-4.9	0.0	19	dbSNP_107	36	2249,6059		294,1661,2199	yes	missense	CPAMD8	NM_015692.2	45	646,2651,2845	TT,TG,GG		27.0703,42.6056,32.0987	benign	586/1933	17088319	3943,8341	1988	4154	6142	SO:0001583	missense	27151	exon15			ACACACGTCGACC	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.1758C>A	19.37:g.17088319G>T	ENSP00000402505:p.Asp586Glu	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	749|749	0.34294871794871795|0.34294871794871795	244|244	0.4959349593495935|0.4959349593495935	114|114	0.3149171270718232|0.3149171270718232	167|167	0.291958041958042|0.291958041958042	224|224	0.2955145118733509|0.2955145118733509	g|g	1.841|1.841	-0.467320|-0.467320	0.04476|0.04476	0.426056|0.426056	0.270703|0.270703	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|T	.|0.63744	.|-0.06	2.45|2.45	-4.91|-4.91	0.03085|0.03085	Alpha-2-macroglobulin, N-terminal 2 (1);|.	1.225170|.	0.06333|.	U|.	0.706515|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.16307|0.16307	0.4|0.4	0.27253|0.27253	P|P	0.9588331|0.9588331	B|.	0.09022|.	0.002|.	B|.	0.18871|.	0.023|.	T|T	0.38650|0.38650	-0.9651|-0.9651	8|5	0.05620|.	T|.	0.96|.	.|.	1.0551|1.0551	0.01588|0.01588	0.1807:0.1571:0.437:0.2253|0.1807:0.1571:0.437:0.2253	rs3745335;rs57288934;rs3745335|rs3745335;rs57288934;rs3745335	539|.	Q8IZJ3|.	CPMD8_HUMAN|.	E|K	586|597	.|ENSP00000402505:T597K	ENSP00000291440:D586E|.	D|T	-|-	3|2	2|0	CPAMD8|CPAMD8	16949319|16949319	0.133000|0.133000	0.22466|0.22466	0.028000|0.028000	0.17463|0.17463	0.151000|0.151000	0.21798|0.21798	-0.780000|-0.780000	0.04654|0.04654	-2.316000|-2.316000	0.00645|0.00645	-1.631000|-1.631000	0.00782|0.00782	GAC|ACG	.	.	weak		0.597	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
ERCC1	2067	hgsc.bcm.edu	37	19	45923653	45923653	+	Silent	SNP	A	A	G	rs11615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45923653A>G	ENST00000300853.3	-	4	945	c.354T>C	c.(352-354)aaT>aaC	p.N118N	ERCC1_ENST00000013807.5_Silent_p.N118N|ERCC1_ENST00000591636.1_Silent_p.N118N|ERCC1_ENST00000340192.7_Silent_p.N118N|ERCC1_ENST00000589165.1_Silent_p.N118N|ERCC1_ENST00000423698.2_Silent_p.N46N	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	118					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)		CCCAGGGCACATTGCGCACGA	0.597								Nucleotide excision repair (NER)					G|||	3350	0.66893	0.9629	0.6124	5008	,	,		17729	0.7381		0.3777	False		,,,				2504	0.5399				p.N118N		Atlas-SNP	.											.	ERCC1	46	.	0			c.T354C						PASS	.	A	,,	3823,583	770.6+/-413.7	1657,509,37	110.0	83.0	92.0		354,354,354	-10.5	0.4	19	dbSNP_52	92	3201,5399	480.4+/-370.4	582,2037,1681	yes	coding-synonymous,coding-synonymous,coding-synonymous	ERCC1	NM_001166049.1,NM_001983.3,NM_202001.2	,,	2239,2546,1718	GG,GA,AA		37.2209,13.232,45.9942	,,	118/274,118/298,118/324	45923653	7024,5982	2203	4300	6503	SO:0001819	synonymous_variant	2067	exon4			GGGCACATTGCGC		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.354T>C	19.37:g.45923653A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Silent	SNP	ENST00000300853.3	37	CCDS12662.1																																																																																			A|0.403;G|0.597	0.597	strong		0.597	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983	
ADCY3	109	hgsc.bcm.edu	37	2	25141434	25141434	+	Silent	SNP	G	G	A	rs61732745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:25141434G>A	ENST00000260600.5	-	1	1274	c.423C>T	c.(421-423)taC>taT	p.Y141Y		NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	141					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					GCCACAGCACGTAGGGCAGCA	0.622													G|||	506	0.101038	0.2179	0.0865	5008	,	,		20124	0.0446		0.0835	False		,,,				2504	0.0297				p.Y141Y		Atlas-SNP	.											.	ADCY3	114	.	0			c.C423T						PASS	.	G		912,3494	353.8+/-312.3	101,710,1392	77.0	84.0	82.0		423	2.6	1.0	2	dbSNP_129	82	782,7818	184.2+/-232.2	38,706,3556	no	coding-synonymous	ADCY3	NM_004036.3		139,1416,4948	AA,AG,GG		9.093,20.699,13.0248		141/1145	25141434	1694,11312	2203	4300	6503	SO:0001819	synonymous_variant	109	exon1			CAGCACGTAGGGC	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.423C>T	2.37:g.25141434G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	169	73	0.431953	NM_004036	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	37	CCDS1715.1																																																																																			G|0.885;A|0.115	0.115	strong		0.622	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
MST1L	11223	hgsc.bcm.edu	37	1	17085046	17085046	+	RNA	SNP	C	C	G	rs200838083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17085046C>G	ENST00000455405.2	-	0	142							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										TCCAGCCGATCCACCCTCTTG	0.607																																					p.D477H		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,2	.	.	2	0			c.G1429C						PASS	.																																					11223	exon11			GCCGATCCACCCT	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.17085046C>G		Somatic	742	0	0		WXS	Illumina HiSeq	Phase_I	878	78	0.0888383	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	10.75	1.438605	0.25900	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);	0.703897	0.12141	N	0.495839	T	0.52370	0.1730	.	.	.	.	.	.	D;D	0.76494	0.999;0.996	D;P	0.64595	0.927;0.885	T	0.56774	-0.7923	6	0.20046	T	0.44	.	6.8326	0.23919	0.0:0.9999:0.0:1.0E-4	.	477;477	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	H	446;477;477	.	ENSP00000439273:D477H	D	-	1	0	MST1P9	16957633	0.998000	0.40836	0.000000	0.03702	0.000000	0.00434	4.846000	0.62860	-0.000000	0.14550	0.000000	0.15137	GAT	C|0.994;G|0.006	0.006	strong		0.607	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
KCNV2	169522	hgsc.bcm.edu	37	9	2729705	2729705	+	Missense_Mutation	SNP	T	T	C	rs112673841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2729705T>C	ENST00000382082.3	+	2	1854	c.1616T>C	c.(1615-1617)cTc>cCc	p.L539P		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	539					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)		AACCCACAGCTCACCCCAAGA	0.433													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		19814	0.0		0.0	False		,,,				2504	0.0				p.L539P		Atlas-SNP	.											.	KCNV2	72	.	0			c.T1616C						PASS	.	C	PRO/LEU	195,4211	808.3+/-415.9	2,191,2010	92.0	87.0	89.0		1616	3.5	0.0	9	dbSNP_132	89	4,8596	819.1+/-406.8	0,4,4296	yes	missense	KCNV2	NM_133497.3	98	2,195,6306	CC,CT,TT		0.0465,4.4258,1.5301	benign	539/546	2729705	199,12807	2203	4300	6503	SO:0001583	missense	169522	exon2			CACAGCTCACCCC	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.1616T>C	9.37:g.2729705T>C	ENSP00000371514:p.Leu539Pro	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	175	0.08012820512820513	58	0.11788617886178862	16	0.04419889502762431	36	0.06293706293706294	65	0.08575197889182058	C	0.271	-0.992832	0.02162	0.044258	4.65E-4	ENSG00000168263	ENST00000382082	D	0.96716	-4.1	5.47	3.52	0.40303	.	5.982730	0.00424	N	0.000068	T	0.08980	0.0222	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.70938	-0.4736	10	0.23302	T	0.38	.	5.3373	0.15965	0.2188:0.5872:0.1183:0.0758	.	539	Q8TDN2	KCNV2_HUMAN	P	539	ENSP00000371514:L539P	ENSP00000371514:L539P	L	+	2	0	KCNV2	2719705	0.000000	0.05858	0.010000	0.14722	0.081000	0.17604	0.370000	0.20433	1.461000	0.47929	-0.119000	0.15052	CTC	T|0.962;C|0.038	0.038	strong		0.433	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
ZNF699	374879	hgsc.bcm.edu	37	19	9407468	9407468	+	Silent	SNP	G	G	A	rs189167193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9407468G>A	ENST00000591998.1	-	6	840	c.612C>T	c.(610-612)ttC>ttT	p.F204F	CTC-325H20.4_ENST00000591336.1_RNA|ZNF699_ENST00000308650.3_Silent_p.F204F			Q32M78	ZN699_HUMAN	zinc finger protein 699	204					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(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AATGATCCACGAAGGCCTTTC	0.428													G|||	15	0.00299521	0.0113	0.0	5008	,	,		19156	0.0		0.0	False		,,,				2504	0.0				p.F204F		Atlas-SNP	.											.	ZNF699	67	.	0			c.C612T						PASS	.	G		36,3990		0,36,1977	154.0	140.0	145.0		612	-0.2	0.0	19		145	1,8385		0,1,4192	no	coding-synonymous	ZNF699	NM_198535.1		0,37,6169	AA,AG,GG		0.0119,0.8942,0.2981		204/643	9407468	37,12375	2013	4193	6206	SO:0001819	synonymous_variant	374879	exon5			ATCCACGAAGGCC	BC109268	CCDS42495.1	19p13.2	2013-01-08				ENSG00000196110		"""Zinc fingers, C2H2-type"", ""-"""	24750	protein-coding gene	gene with protein product	hangover homolog (Drosophila)	609571				16940975	Standard	NM_198535		Approved	FLJ38144, hang	uc002mlc.1	Q32M78		ENST00000591998.1:c.612C>T	19.37:g.9407468G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	153	89	0.581699	NM_198535	Q8N9A1	Silent	SNP	ENST00000591998.1	37	CCDS42495.1																																																																																			G|0.998;A|0.002	0.002	strong		0.428	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535	
PEX14	5195	hgsc.bcm.edu	37	1	10684422	10684422	+	Silent	SNP	C	C	A	rs35046754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:10684422C>A	ENST00000356607.4	+	7	593	c.513C>A	c.(511-513)gcC>gcA	p.A171A	PEX14_ENST00000538836.1_Silent_p.A107A	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	171					microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		CGACCCTCGCCTCCGTCCAGG	0.622													C|||	63	0.0125799	0.0469	0.0014	5008	,	,		15967	0.0		0.0	False		,,,				2504	0.0				p.A171A		Atlas-SNP	.											.	PEX14	40	.	0			c.C513A						PASS	.	C		209,4197	127.4+/-164.3	9,191,2003	75.0	76.0	76.0		513	2.9	1.0	1	dbSNP_126	76	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PEX14	NM_004565.2		9,193,6301	AA,AC,CC		0.0233,4.7435,1.6223		171/378	10684422	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	5195	exon7			CCTCGCCTCCGTC	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.513C>A	1.37:g.10684422C>A		Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	314	171	0.544586	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Silent	SNP	ENST00000356607.4	37	CCDS30582.1																																																																																			C|0.986;A|0.014	0.014	strong		0.622	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		
PARM1	25849	hgsc.bcm.edu	37	4	75938179	75938179	+	Silent	SNP	G	G	A	rs3775527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:75938179G>A	ENST00000307428.7	+	2	800	c.588G>A	c.(586-588)ccG>ccA	p.P196P	PARM1_ENST00000513238.1_Intron|RP11-44F21.2_ENST00000513770.1_RNA	NM_015393.3	NP_056208.2	Q6UWI2	PARM1_HUMAN	prostate androgen-regulated mucin-like protein 1	196					positive regulation of telomerase activity (GO:0051973)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)		p.P196P(1)		cervix(1)|endometrium(2)|lung(4)|ovary(1)	8						CAGAGTCCCCGACAGAGGAGT	0.567													G|||	1599	0.319289	0.2542	0.2637	5008	,	,		19672	0.1627		0.4523	False		,,,				2504	0.4714				p.P196P		Atlas-SNP	.											PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	1	Substitution - coding silent(1)	stomach(1)	c.G588A						PASS	.	G		1183,3093		180,823,1135	161.0	175.0	171.0		588	-5.0	0.0	4	dbSNP_107	171	3600,4922		772,2056,1433	no	coding-synonymous	PARM1	NM_015393.3		952,2879,2568	AA,AG,GG		42.2436,27.666,37.373		196/311	75938179	4783,8015	2138	4261	6399	SO:0001819	synonymous_variant	25849	exon2			GTCCCCGACAGAG	AK022311	CCDS47077.1	4q13.3-q21.3	2010-02-17	2009-09-28		ENSG00000169116	ENSG00000169116			24536	protein-coding gene	gene with protein product	"""Prostatic androgen-repressed message 1"", ""Castration-induced prostatic apoptosis-related protein 1"", ""WSC4, cell wall integrity and stress response component 4 homolog (S. cerevisiae)"""					10499539, 12772192, 18027867	Standard	NM_015393		Approved	DKFZP564O0823, Cipar1, WSC4	uc003hih.2	Q6UWI2	OTTHUMG00000160827	ENST00000307428.7:c.588G>A	4.37:g.75938179G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	160	97	0.60625	NM_015393	B3KMQ9|Q96DV8|Q9Y4S1	Silent	SNP	ENST00000307428.7	37	CCDS47077.1																																																																																			G|0.698;A|0.302	0.302	strong		0.567	PARM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362494.1	NM_015393	
PLXND1	23129	hgsc.bcm.edu	37	3	129286413	129286413	+	Silent	SNP	G	G	C	rs2245285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129286413G>C	ENST00000324093.4	-	22	4186	c.4008C>G	c.(4006-4008)ctC>ctG	p.L1336L	PLXND1_ENST00000393239.1_Silent_p.L1336L	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1336					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GCTCCTTGGTGAGATCTGTCA	0.622													C|||	2594	0.517971	0.6044	0.379	5008	,	,		18165	0.7431		0.3519	False		,,,				2504	0.4387				p.L1336L	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C4008G						PASS	.	C		2429,1977	549.3+/-377.7	655,1119,429	71.0	55.0	60.0		4008	3.5	1.0	3	dbSNP_100	60	2783,5817	668.9+/-402.6	459,1865,1976	no	coding-synonymous	PLXND1	NM_015103.2		1114,2984,2405	CC,CG,GG		32.3605,44.8706,40.0738		1336/1926	129286413	5212,7794	2203	4300	6503	SO:0001819	synonymous_variant	23129	exon22			CTTGGTGAGATCT	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.4008C>G	3.37:g.129286413G>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			G|0.549;C|0.451	0.451	strong		0.622	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
TJP2	9414	hgsc.bcm.edu	37	9	71844124	71844124	+	Missense_Mutation	SNP	G	G	A	rs41277901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:71844124G>A	ENST00000377245.4	+	10	1686	c.1478G>A	c.(1477-1479)aGa>aAa	p.R493K	TJP2_ENST00000535702.1_Missense_Mutation_p.R497K|TJP2_ENST00000539225.1_Missense_Mutation_p.R524K|TJP2_ENST00000348208.4_Missense_Mutation_p.R493K|TJP2_ENST00000265384.7_Missense_Mutation_p.R493K|TJP2_ENST00000453658.2_Missense_Mutation_p.R470K	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	493					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GCAGCCCCGAGAACTTTTCTT	0.393													G|||	60	0.0119808	0.0356	0.0115	5008	,	,		19298	0.0		0.005	False		,,,				2504	0.0				p.R524K		Atlas-SNP	.											.	TJP2	120	.	0			c.G1571A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	153,4253	106.5+/-144.9	0,153,2050	215.0	200.0	205.0		1409,1490,1571,1478,1478,1478	4.0	0.3	9	dbSNP_127	205	14,8586	11.2+/-40.8	0,14,4286	yes	missense,missense,missense,missense,missense,missense	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	26,26,26,26,26,26	0,167,6336	AA,AG,GG		0.1628,3.4725,1.284	benign,benign,benign,benign,benign,benign	470/1021,497/1158,524/1222,493/994,493/1191,493/1044	71844124	167,12839	2203	4300	6503	SO:0001583	missense	9414	exon10			CCCCGAGAACTTT	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1478G>A	9.37:g.71844124G>A	ENSP00000366453:p.Arg493Lys	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	254	70	0.275591	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	19	0.0086996336996337	13	0.026422764227642278	3	0.008287292817679558	0	0.0	3	0.00395778364116095	G	13.41	2.227582	0.39399	0.034725	0.001628	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.08807	3.06;3.06;3.05;3.05;3.08;3.11	5.85	4.02	0.46733	PDZ/DHR/GLGF (1);	0.162144	0.56097	D	0.000036	T	0.01870	0.0059	L	0.29908	0.895	0.33647	D	0.608025	B;B;B;B;B	0.29136	0.234;0.007;0.004;0.007;0.021	B;B;B;B;B	0.28465	0.09;0.01;0.003;0.004;0.018	T	0.29731	-1.0002	10	0.24483	T	0.36	.	9.1425	0.36912	0.2159:0.0:0.7841:0.0	rs41277901;rs61731595	524;497;493;493;493	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	K	470;493;493;493;497;524	ENSP00000392178:R470K;ENSP00000366453:R493K;ENSP00000345893:R493K;ENSP00000265384:R493K;ENSP00000442090:R497K;ENSP00000438262:R524K	ENSP00000265384:R493K	R	+	2	0	TJP2	71033944	1.000000	0.71417	0.285000	0.24819	0.979000	0.70002	4.172000	0.58243	1.481000	0.48307	0.557000	0.71058	AGA	G|0.988;A|0.012	0.012	strong		0.393	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
COG2	22796	hgsc.bcm.edu	37	1	230810756	230810756	+	Missense_Mutation	SNP	T	T	A	rs6681346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230810756T>A	ENST00000366669.4	+	9	1027	c.912T>A	c.(910-912)aaT>aaA	p.N304K	COG2_ENST00000535166.1_Missense_Mutation_p.N188K|COG2_ENST00000534989.1_Missense_Mutation_p.N245K|COG2_ENST00000366668.3_Missense_Mutation_p.N304K	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	304			N -> K (in dbSNP:rs6681346).		Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				AAAAAGGCAATACTGTTCCTG	0.368													T|||	475	0.0948482	0.2156	0.0231	5008	,	,		16747	0.0625		0.0159	False		,,,				2504	0.0971				p.N304K		Atlas-SNP	.											.	COG2	61	.	0			c.T912A						PASS	.	T	LYS/ASN,LYS/ASN	793,3613	316.9+/-294.8	78,637,1488	127.0	136.0	133.0		912,912	-2.2	0.3	1	dbSNP_116	133	90,8510	51.1+/-111.2	1,88,4211	yes	missense,missense	COG2	NM_001145036.1,NM_007357.2	94,94	79,725,5699	AA,AT,TT		1.0465,17.9982,6.7892	benign,benign	304/738,304/739	230810756	883,12123	2203	4300	6503	SO:0001583	missense	22796	exon9			AGGCAATACTGTT	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.912T>A	1.37:g.230810756T>A	ENSP00000355629:p.Asn304Lys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_007357	Q86U99	Missense_Mutation	SNP	ENST00000366669.4	37	CCDS1584.1	154	0.07051282051282051	104	0.21138211382113822	8	0.022099447513812154	34	0.05944055944055944	8	0.010554089709762533	T	11.50	1.658121	0.29425	0.179982	0.010465	ENSG00000135775	ENST00000366669;ENST00000535166;ENST00000366668;ENST00000534989	T;T;T;T	0.27256	1.68;1.68;1.68;1.68	5.92	-2.23	0.06930	.	0.182059	0.56097	D	0.000023	T	0.00012	0.0000	L	0.47716	1.5	0.21355	P	0.999712339	B;B	0.26195	0.144;0.045	B;B	0.18263	0.021;0.021	T	0.40021	-0.9585	9	0.07990	T	0.79	-16.6064	11.4718	0.50272	0.0:0.3913:0.0:0.6087	rs6681346;rs17848117;rs52807515;rs6681346	304;304	Q86U99;Q14746	.;COG2_HUMAN	K	304;188;304;245	ENSP00000355629:N304K;ENSP00000445724:N188K;ENSP00000355628:N304K;ENSP00000440349:N245K	ENSP00000355628:N304K	N	+	3	2	COG2	228877379	0.753000	0.28349	0.277000	0.24703	0.994000	0.84299	0.099000	0.15210	-0.398000	0.07679	0.533000	0.62120	AAT	T|0.922;A|0.078	0.078	strong		0.368	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
ESPNL	339768	hgsc.bcm.edu	37	2	239025630	239025630	+	Silent	SNP	T	T	C	rs11904159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239025630T>C	ENST00000343063.3	+	5	1205	c.942T>C	c.(940-942)caT>caC	p.H314H	ESPNL_ENST00000409169.1_Intron	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	314										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)		CGGAGTACCATGGACACCGGG	0.687													C|||	983	0.196286	0.2867	0.1412	5008	,	,		17120	0.2302		0.1322	False		,,,				2504	0.1442				p.H314H		Atlas-SNP	.											.	ESPNL	63	.	0			c.T942C						PASS	.	C		1121,3279	705.9+/-407.3	174,773,1253	69.0	55.0	59.0		942	-2.8	0.9	2	dbSNP_120	59	1415,7177	748.6+/-407.3	129,1157,3010	no	coding-synonymous	ESPNL	NM_194312.2		303,1930,4263	CC,CT,TT		16.4688,25.4773,19.5197		314/1006	239025630	2536,10456	2200	4296	6496	SO:0001819	synonymous_variant	339768	exon5			GTACCATGGACAC	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.942T>C	2.37:g.239025630T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			T|0.803;C|0.197	0.197	strong		0.687	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
AHSP	51327	hgsc.bcm.edu	37	16	31539934	31539934	+	Silent	SNP	G	G	T	rs17677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31539934G>T	ENST00000302312.4	+	3	334	c.231G>T	c.(229-231)ctG>ctT	p.L77L	AHSP_ENST00000569954.1_3'UTR	NM_016633.2	NP_057717.1	Q9NZD4	AHSP_HUMAN	alpha hemoglobin stabilizing protein	77					hemoglobin metabolic process (GO:0020027)|hemopoiesis (GO:0030097)|protein folding (GO:0006457)|protein stabilization (GO:0050821)	hemoglobin complex (GO:0005833)	hemoglobin binding (GO:0030492)|unfolded protein binding (GO:0051082)			lung(2)	2						TGAACACTCTGGCCAACCCTT	0.587													G|||	1590	0.317492	0.4667	0.1311	5008	,	,		18109	0.2222		0.1541	False		,,,				2504	0.5143				p.L77L		Atlas-SNP	.											.	AHSP	10	.	0			c.G231T						PASS	.	G		1786,2608	525.5+/-371.6	374,1038,785	63.0	57.0	59.0		231	1.0	0.0	16	dbSNP_63	59	1411,7189	270.7+/-289.1	121,1169,3010	no	coding-synonymous	AHSP	NM_016633.2		495,2207,3795	TT,TG,GG		16.407,40.6463,24.6037		77/103	31539934	3197,9797	2197	4300	6497	SO:0001819	synonymous_variant	51327	exon3			CACTCTGGCCAAC	AF208865	CCDS10716.1	16p11.1	2009-10-07	2009-10-07	2009-10-07	ENSG00000169877	ENSG00000169877			18075	protein-coding gene	gene with protein product	"""alpha hemoglobin stabilising protein"""	605821	"""erythroid associated factor"""	ERAF		11231637, 12066189	Standard	XM_005255352		Approved	EDRF	uc002ecj.3	Q9NZD4	OTTHUMG00000132461	ENST00000302312.4:c.231G>T	16.37:g.31539934G>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_016633	Q8TD01	Silent	SNP	ENST00000302312.4	37	CCDS10716.1																																																																																			G|0.755;T|0.245	0.245	strong		0.587	AHSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255624.1	NM_016633	
IFIH1	64135	hgsc.bcm.edu	37	2	163128883	163128883	+	Silent	SNP	G	G	A	rs13418718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:163128883G>A	ENST00000263642.2	-	13	2864	c.2469C>T	c.(2467-2469)gcC>gcT	p.A823A		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	823	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						CATCAGCTCTGGCTCGACCAC	0.428													G|||	473	0.0944489	0.3374	0.0389	5008	,	,		19695	0.0		0.0	False		,,,				2504	0.0				p.A823A		Atlas-SNP	.											.	IFIH1	102	.	0			c.C2469T						PASS	.	G		1416,2990	462.1+/-353.1	226,964,1013	80.0	70.0	74.0		2469	1.3	1.0	2	dbSNP_121	74	7,8593	3.7+/-12.6	0,7,4293	no	coding-synonymous	IFIH1	NM_022168.2		226,971,5306	AA,AG,GG		0.0814,32.138,10.9411		823/1026	163128883	1423,11583	2203	4300	6503	SO:0001819	synonymous_variant	64135	exon13			AGCTCTGGCTCGA	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.2469C>T	2.37:g.163128883G>A		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	188	106	0.56383	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Silent	SNP	ENST00000263642.2	37	CCDS2217.1																																																																																			G|0.888;A|0.112	0.112	strong		0.428	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168	
ITIH3	3699	hgsc.bcm.edu	37	3	52840325	52840325	+	Silent	SNP	C	C	T	rs34397833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52840325C>T	ENST00000449956.2	+	18	1965	c.1959C>T	c.(1957-1959)caC>caT	p.H653H	ITIH3_ENST00000416872.2_Intron	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	653					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				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)		GGGATCCCCACTTCATCATCC	0.582													C|||	219	0.04373	0.1581	0.013	5008	,	,		15639	0.0		0.0	False		,,,				2504	0.001				p.H653H		Atlas-SNP	.											.	ITIH3	132	.	0			c.C1959T						PASS	.	C		412,3666		24,364,1651	53.0	55.0	55.0		1959	4.6	1.0	3	dbSNP_126	55	1,8389		0,1,4194	no	coding-synonymous	ITIH3	NM_002217.3		24,365,5845	TT,TC,CC		0.0119,10.103,3.3125		653/891	52840325	413,12055	2039	4195	6234	SO:0001819	synonymous_variant	3699	exon18			TCCCCACTTCATC		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"""pre-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha-trypsin inhibitor heavy chain H3"""	146650	"""inter-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha (globulin) inhibitor H3"""			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.1959C>T	3.37:g.52840325C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Silent	SNP	ENST00000449956.2	37	CCDS46845.1	75	0.034340659340659344	71	0.1443089430894309	4	0.011049723756906077	0	0.0	0	0.0	C	3.086	-0.187992	0.06299	0.10103	1.19E-4	ENSG00000162267	ENST00000398670;ENST00000536431	.	.	.	5.48	4.61	0.57282	.	.	.	.	.	T	0.00580	0.0019	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00478	-1.1715	5	0.15952	T	0.53	-32.6536	13.5864	0.61933	0.0:0.9234:0.0:0.0766	rs34397833;rs61654726	.	.	.	F	654;642	.	ENSP00000381662:L654F	L	+	1	0	ITIH3	52815365	1.000000	0.71417	1.000000	0.80357	0.441000	0.31987	1.124000	0.31320	1.457000	0.47850	0.561000	0.74099	CTT	C|0.971;T|0.029	0.029	strong		0.582	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217	
VPS33A	65082	hgsc.bcm.edu	37	12	122720423	122720423	+	Silent	SNP	G	G	A	rs34461198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122720423G>A	ENST00000267199.4	-	11	1462	c.1350C>T	c.(1348-1350)gcC>gcT	p.A450A	RP11-512M8.5_ENST00000535844.1_Silent_p.A411A	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	450					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of developmental pigmentation (GO:0048070)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	28	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		TCAGCAGGCCGGCCTTCTCCA	0.478													G|||	232	0.0463259	0.1702	0.0086	5008	,	,		18772	0.0		0.001	False		,,,				2504	0.0				p.A450A		Atlas-SNP	.											.	VPS33A	61	.	0			c.C1350T						PASS	.	G		696,3710	291.8+/-281.7	53,590,1560	208.0	192.0	197.0		1350	-11.7	0.0	12	dbSNP_126	197	17,8583	11.9+/-42.8	0,17,4283	no	coding-synonymous	VPS33A	NM_022916.4		53,607,5843	AA,AG,GG		0.1977,15.7966,5.4821		450/597	122720423	713,12293	2203	4300	6503	SO:0001819	synonymous_variant	65082	exon11			CAGGCCGGCCTTC	AK026048	CCDS9231.1	12q24.31	2008-06-23	2006-04-04		ENSG00000139719	ENSG00000139719			18179	protein-coding gene	gene with protein product		610034	"""vacuolar protein sorting 33A (yeast)"""			11250079	Standard	NM_022916		Approved		uc001ucd.3	Q96AX1	OTTHUMG00000168920	ENST00000267199.4:c.1350C>T	12.37:g.122720423G>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	253	125	0.494071	NM_022916	Q547V4|Q9H5Q0	Silent	SNP	ENST00000267199.4	37	CCDS9231.1																																																																																			G|0.944;A|0.056	0.056	strong		0.478	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401607.2		
CRIPAK	285464	hgsc.bcm.edu	37	4	1388759	1388759	+	Missense_Mutation	SNP	C	C	T	rs112233131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1388759C>T	ENST00000324803.4	+	1	3420	c.460C>T	c.(460-462)Cgg>Tgg	p.R154W		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	154					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)		p.R154W(2)		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)			CGTGCCCATGCGGAGTGCCCG	0.701																																					p.R154W		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,3	CRIPAK	185	3	2	Substitution - Missense(2)	NS(1)|skin(1)	c.C460T						scavenged	.						84.0	72.0	76.0					4																	1388759		2202	4282	6484	SO:0001583	missense	285464	exon1			CCCATGCGGAGTG	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.460C>T	4.37:g.1388759C>T	ENSP00000323978:p.Arg154Trp	Somatic	28	1	0.0357143		WXS	Illumina HiSeq	Phase_I	80	14	0.175	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.074|0.074	-1.196289|-1.196289	0.01594|0.01594	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000382944|ENST00000324803	.|T	.|0.19806	.|2.12	0.948|0.948	-1.9|-1.9	0.07665|0.07665	.|.	.|.	.|.	.|.	.|.	T|T	0.07908|0.07908	0.0198|0.0198	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.22851	.|0.076	.|B	.|0.04013	.|0.001	T|T	0.18116|0.18116	-1.0347|-1.0347	6|9	0.02654|0.49607	T|T	1|0.09	.|.	0.8279|0.8279	0.01124|0.01124	0.1649:0.1747:0.3249:0.3355|0.1649:0.1747:0.3249:0.3355	.|.	.|154	.|Q8N1N5	.|CRPAK_HUMAN	V|W	137|154	.|ENSP00000323978:R154W	ENSP00000372402:A137V|ENSP00000323978:R154W	A|R	+|+	2|1	0|2	CRIPAK|CRIPAK	1378759|1378759	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.017000|0.017000	0.09413|0.09413	-2.063000|-2.063000	0.01388|0.01388	-3.215000|-3.215000	0.00213|0.00213	-1.709000|-1.709000	0.00716|0.00716	GCG|CGG	C|0.966;T|0.034	0.034	strong		0.701	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
SPAM1	6677	hgsc.bcm.edu	37	7	123594206	123594206	+	Silent	SNP	G	G	A	rs2285996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:123594206G>A	ENST00000439500.1	+	4	1195	c.582G>A	c.(580-582)aaG>aaA	p.K194K	SPAM1_ENST00000223028.7_Silent_p.K194K|SPAM1_ENST00000402183.2_Silent_p.K194K|SPAM1_ENST00000460182.1_Silent_p.K194K|SPAM1_ENST00000340011.5_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	102	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	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		
OR2F1	26211	hgsc.bcm.edu	37	7	143657473	143657473	+	Missense_Mutation	SNP	A	A	G	rs2072165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143657473A>G	ENST00000392899.1	+	1	447	c.410A>G	c.(409-411)cAt>cGt	p.H137R	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	137			H -> R (in dbSNP:rs2072165).		signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					GCCATCATGCATGGAGGGCTG	0.567													A|||	1132	0.226038	0.4463	0.2378	5008	,	,		21578	0.1627		0.1093	False		,,,				2504	0.1053				p.H137R		Atlas-SNP	.											.	OR2F1	71	.	0			c.A410G						PASS	.	A	ARG/HIS	1711,2695	515.5+/-368.9	335,1041,827	154.0	132.0	140.0		410	3.2	0.6	7	dbSNP_96	140	776,7824	183.3+/-231.6	34,708,3558	yes	missense	OR2F1	NM_012369.2	29	369,1749,4385	GG,GA,AA		9.0233,38.8334,19.1219	benign	137/318	143657473	2487,10519	2203	4300	6503	SO:0001583	missense	26211	exon1			TCATGCATGGAGG	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"""GPCR / Class A : Olfactory receptors"""	8246	protein-coding gene	gene with protein product		608497	"""olfactory receptor, family 2, subfamily F, member 1"""	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.410A>G	7.37:g.143657473A>G	ENSP00000376633:p.His137Arg	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	275	137	0.498182	NM_012369	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	37	CCDS5887.1	476	0.21794871794871795	202	0.4105691056910569	88	0.2430939226519337	102	0.17832167832167833	84	0.11081794195250659	A	2.960	-0.214763	0.06101	0.388334	0.090233	ENSG00000213215	ENST00000392899	T	0.35421	1.31	5.53	3.17	0.36434	GPCR, rhodopsin-like superfamily (1);	0.229512	0.30911	N	0.008621	T	0.00012	0.0000	N	0.20483	0.58	0.46499	P	9.299999999999864E-4	B	0.06786	0.001	B	0.06405	0.002	T	0.43294	-0.9400	9	0.56958	D	0.05	-7.694	7.008	0.24848	0.7489:0.0:0.2511:0.0	rs2072165;rs60798611	137	Q13607	OR2F1_HUMAN	R	137	ENSP00000376633:H137R	ENSP00000376633:H137R	H	+	2	0	OR2F1	143288406	0.000000	0.05858	0.568000	0.28447	0.033000	0.12548	0.163000	0.16520	0.524000	0.28502	-0.256000	0.11100	CAT	A|0.807;G|0.193	0.193	strong		0.567	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1		
OVGP1	5016	hgsc.bcm.edu	37	1	111957721	111957721	+	Missense_Mutation	SNP	C	C	T	rs115512535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111957721C>T	ENST00000369732.3	-	11	1457	c.1402G>A	c.(1402-1404)Gga>Aga	p.G468R		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	468					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)		GTCTTCTCTCCTAGAGCTACA	0.498													C|||	11	0.00219649	0.0083	0.0	5008	,	,		20915	0.0		0.0	False		,,,				2504	0.0				p.G468R		Atlas-SNP	.											.	OVGP1	177	.	0			c.G1402A						PASS	.	C	ARG/GLY	57,4349	55.5+/-91.7	0,57,2146	121.0	104.0	110.0		1402	-0.9	0.0	1	dbSNP_132	110	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OVGP1	NM_002557.3	125	0,58,6445	TT,TC,CC		0.0116,1.2937,0.4459	possibly-damaging	468/679	111957721	58,12948	2203	4300	6503	SO:0001583	missense	5016	exon11			TCTCTCCTAGAGC	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.1402G>A	1.37:g.111957721C>T	ENSP00000358747:p.Gly468Arg	Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	300	134	0.446667	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	17.36	3.368778	0.61624	0.012937	1.16E-4	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.04317	3.65	4.86	-0.95	0.10372	.	0.931884	0.09108	N	0.847418	T	0.01489	0.0048	L	0.39898	1.24	0.09310	N	1	P;P	0.48764	0.675;0.915	B;B	0.41946	0.131;0.371	T	0.45977	-0.9224	10	0.40728	T	0.16	-0.097	5.5535	0.17103	0.0:0.5337:0.1411:0.3252	.	468;532	Q12889;Q59HH5	OVGP1_HUMAN;.	R	468;532;276	ENSP00000358747:G468R	ENSP00000358743:G532R	G	-	1	0	OVGP1	111759244	0.000000	0.05858	0.000000	0.03702	0.895000	0.52256	0.199000	0.17237	-0.209000	0.10156	0.585000	0.79938	GGA	C|0.997;T|0.003	0.003	strong		0.498	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85492658	85492658	+	Missense_Mutation	SNP	A	A	C	rs139758674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:85492658A>C	ENST00000393217.2	+	13	3156	c.3095A>C	c.(3094-3096)gAg>gCg	p.E1032A		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1032										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		CCATCCTTGGAGAATCTTGTT	0.299													A|||	43	0.00858626	0.031	0.0029	5008	,	,		11103	0.0		0.0	False		,,,				2504	0.0				p.E1032A		Atlas-SNP	.											LRRIQ1_ENST00000393217,NS,carcinoma,-1,2	LRRIQ1	512	2	0			c.A3095C						scavenged	.	A	ALA/GLU	79,4325	69.8+/-107.6	1,77,2124	75.0	78.0	77.0		3095	0.4	0.0	12	dbSNP_134	77	2,8586	2.2+/-6.3	0,2,4292	yes	missense	LRRIQ1	NM_001079910.1	107	1,79,6416	CC,CA,AA		0.0233,1.7938,0.6235	benign	1032/1723	85492658	81,12911	2202	4294	6496	SO:0001583	missense	84125	exon13			CCTTGGAGAATCT	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.3095A>C	12.37:g.85492658A>C	ENSP00000376910:p.Glu1032Ala	Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	6.385	0.439095	0.12104	0.017938	2.33E-4	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.23348	1.91	5.18	0.447	0.16608	.	1.889910	0.03114	N	0.162924	T	0.08537	0.0212	N	0.20574	0.59	0.09310	N	1	B;B	0.25667	0.063;0.131	B;B	0.22386	0.039;0.039	T	0.21211	-1.0252	10	0.56958	D	0.05	.	4.26	0.10737	0.6323:0.0:0.2269:0.1408	.	1032;1007	Q96JM4;C9JI57	LRIQ1_HUMAN;.	A	1032;1007;1032	ENSP00000376910:E1032A	ENSP00000256007:E1032A	E	+	2	0	LRRIQ1	84016789	0.569000	0.26643	0.003000	0.11579	0.778000	0.44026	1.102000	0.31050	-0.162000	0.10964	0.477000	0.44152	GAG	A|0.995;C|0.005	0.005	strong		0.299	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
SCML4	256380	hgsc.bcm.edu	37	6	108026455	108026455	+	Silent	SNP	A	A	G	rs1546960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:108026455A>G	ENST00000369020.3	-	8	1439	c.1194T>C	c.(1192-1194)ccT>ccC	p.P398P	SCML4_ENST00000369022.2_Silent_p.P340P|SCML4_ENST00000369025.2_Silent_p.P156P	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	398					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		GTTTCAGTGCAGGTCCCAGCT	0.458											OREG0017598	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	4505	0.899561	0.8328	0.928	5008	,	,		17797	0.8998		0.9274	False		,,,				2504	0.9407				p.P398P		Atlas-SNP	.											.	SCML4	65	.	0			c.T1194C						PASS	.	G		1162,222		490,182,20	148.0	116.0	126.0		1194	-5.4	0.3	6	dbSNP_88	126	2909,273		1331,247,13	no	coding-synonymous	SCML4	NM_198081.3		1821,429,33	GG,GA,AA		8.5795,16.0405,10.841		398/415	108026455	4071,495	692	1591	2283	SO:0001819	synonymous_variant	256380	exon8			CAGTGCAGGTCCC		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.1194T>C	6.37:g.108026455A>G		Somatic	128	1	0.0078125	1409	WXS	Illumina HiSeq	Phase_I	104	104	1	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Silent	SNP	ENST00000369020.3	37	CCDS5060.2																																																																																			A|0.095;G|0.905	0.905	strong		0.458	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
C2CD2	25966	hgsc.bcm.edu	37	21	43319214	43319214	+	Silent	SNP	C	C	T	rs9985096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43319214C>T	ENST00000380486.3	-	13	2059	c.1818G>A	c.(1816-1818)ctG>ctA	p.L606L	C2CD2_ENST00000329623.7_Silent_p.L451L	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	606						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						AGCTCTCTGACAGCTCATCAC	0.637													C|||	301	0.0601038	0.1445	0.0288	5008	,	,		17253	0.0387		0.0239	False		,,,				2504	0.0276				p.L606L		Atlas-SNP	.											.	C2CD2	47	.	0			c.G1818A						PASS	.	C	,	628,3778	265.6+/-266.7	57,514,1632	46.0	51.0	49.0		1818,1353	3.3	1.0	21	dbSNP_119	49	134,8466	66.0+/-128.3	0,134,4166	no	coding-synonymous,coding-synonymous	C2CD2	NM_015500.1,NM_199050.2	,	57,648,5798	TT,TC,CC		1.5581,14.2533,5.8588	,	606/697,451/542	43319214	762,12244	2203	4300	6503	SO:0001819	synonymous_variant	25966	exon13			CTCTGACAGCTCA	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"""TMEM24-like"""		"""chromosome 21 open reading frame 25"""	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1818G>A	21.37:g.43319214C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Silent	SNP	ENST00000380486.3	37	CCDS42933.1	130	0.05952380952380952	84	0.17073170731707318	10	0.027624309392265192	24	0.04195804195804196	12	0.0158311345646438	C	5.943	0.357917	0.11239	0.142533	0.015581	ENSG00000157617	ENST00000449165	.	.	.	5.09	3.26	0.37387	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.06338	-1.0832	3	.	.	.	-22.8353	11.306	0.49336	0.0:0.7926:0.0:0.2074	rs9985096;rs9985096	.	.	.	I	92	.	.	V	-	1	0	C2CD2	42192283	0.869000	0.29996	0.986000	0.45419	0.498000	0.33706	-0.031000	0.12287	0.643000	0.30638	-0.217000	0.12591	GTC	C|0.938;T|0.062	0.062	strong		0.637	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
MUC4	4585	hgsc.bcm.edu	37	3	195515027	195515027	+	Missense_Mutation	SNP	T	T	C	rs552771790	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515027T>C	ENST00000463781.3	-	2	3883	c.3424A>G	c.(3424-3426)Act>Gct	p.T1142A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1142A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	616					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)		ACTGAGGAAGTGTCGGTGACA	0.567													.|||	4	0.000798722	0.0015	0.0	5008	,	,		15763	0.0		0.001	False		,,,				2504	0.001				p.T1142A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,4	MUC4	1505	4	0			c.A3424G						PASS	.						11.0	7.0	8.0					3																	195515027		676	1480	2156	SO:0001583	missense	4585	exon2			AGGAAGTGTCGGT	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.3424A>G	3.37:g.195515027T>C	ENSP00000417498:p.Thr1142Ala	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	441	28	0.0634921	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	.	.	.	.	.	.	.	.	.	.	-	2.896	-0.228667	0.06022	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34472	1.36;1.37	0.663	-1.33	0.09172	.	.	.	.	.	T	0.31009	0.0783	N	0.14661	0.345	0.09310	N	1	D	0.60160	0.987	D	0.63488	0.915	T	0.20107	-1.0285	8	.	.	.	.	3.2094	0.06677	0.0:0.3894:0.2364:0.3742	.	1142	E7ESK3	.	A	1142	ENSP00000417498:T1142A;ENSP00000420243:T1142A	.	T	-	1	0	MUC4	196999422	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-0.923000	0.04000	-1.925000	0.01063	-2.075000	0.00382	ACT	.	.	none		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HS3ST2	9956	hgsc.bcm.edu	37	16	22926511	22926511	+	Silent	SNP	A	A	G	rs35682499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:22926511A>G	ENST00000261374.3	+	2	1166	c.732A>G	c.(730-732)tcA>tcG	p.S244S		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	244					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|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 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)	p.S244S(1)		breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		TGGACGTGTCATGGAACGCCA	0.597													G|||	622	0.124201	0.2738	0.134	5008	,	,		18157	0.001		0.1252	False		,,,				2504	0.0409				p.S244S		Atlas-SNP	.											HS3ST2,NS,NS,0,1	HS3ST2	59	1	1	Substitution - coding silent(1)	pancreas(1)	c.A732G						PASS	.	G		1204,3190	706.4+/-407.4	160,884,1153	119.0	104.0	109.0		732	-10.4	0.4	16	dbSNP_126	109	1137,7463	766.5+/-407.6	75,987,3238	no	coding-synonymous	HS3ST2	NM_006043.1		235,1871,4391	GG,GA,AA		13.2209,27.401,18.016		244/368	22926511	2341,10653	2197	4300	6497	SO:0001819	synonymous_variant	9956	exon2			CGTGTCATGGAAC	AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.732A>G	16.37:g.22926511A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	134	68	0.507463	NM_006043	Q52LZ1	Silent	SNP	ENST00000261374.3	37	CCDS10606.1																																																																																			A|0.834;G|0.166	0.166	strong		0.597	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043	
MRPL53	116540	hgsc.bcm.edu	37	2	74699778	74699778	+	Missense_Mutation	SNP	C	C	A	rs1047911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74699778C>A	ENST00000258105.7	-	1	671	c.10G>T	c.(10-12)Gcc>Tcc	p.A4S	MRPL53_ENST00000409710.1_Missense_Mutation_p.A4S	NM_053050.4	NP_444278.1	Q96EL3	RM53_HUMAN	mitochondrial ribosomal protein L53	4			A -> S (in dbSNP:rs1047911).			mitochondrion (GO:0005739)|ribosome (GO:0005840)				central_nervous_system(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5						CGAGCCAAGGCAGCTGCCATG	0.602													C|||	2588	0.516773	0.8064	0.3098	5008	,	,		20314	0.8214		0.1581	False		,,,				2504	0.3272				p.A4S		Atlas-SNP	.											.	MRPL53	13	.	0			c.G10T						PASS	.	C	SER/ALA	3112,1294	679.3+/-403.7	1106,900,197	55.0	52.0	53.0		10	2.3	0.2	2	dbSNP_86	53	1187,7411	228.6+/-263.6	88,1011,3200	yes	missense	MRPL53	NM_053050.4	99	1194,1911,3397	AA,AC,CC		13.8055,29.369,33.0591	benign	4/113	74699778	4299,8705	2203	4299	6502	SO:0001583	missense	116540	exon1			CCAAGGCAGCTGC	BC012163	CCDS1944.1	2p13.1	2012-09-13			ENSG00000204822	ENSG00000204822		"""Mitochondrial ribosomal proteins / large subunits"""	16684	protein-coding gene	gene with protein product		611857				11551941	Standard	NM_053050		Approved		uc002sln.3	Q96EL3	OTTHUMG00000129961	ENST00000258105.7:c.10G>T	2.37:g.74699778C>A	ENSP00000258105:p.Ala4Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_053050		Missense_Mutation	SNP	ENST00000258105.7	37	CCDS1944.1	1092	0.5	396	0.8048780487804879	99	0.27348066298342544	474	0.8286713286713286	123	0.16226912928759896	C	5.013	0.188132	0.09547	0.70631	0.138055	ENSG00000204822	ENST00000258105;ENST00000409710	T;T	0.57595	0.76;0.39	5.09	2.26	0.28386	.	0.532852	0.21296	N	0.076882	T	0.00012	0.0000	N	0.14661	0.345	0.52099	P	5.900000000003125E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.38866	-0.9641	9	0.07482	T	0.82	-14.3176	3.6041	0.08035	0.1827:0.5686:0.1584:0.0903	rs1047911;rs3210341;rs11554618;rs56805532;rs1047911	4	Q96EL3	RM53_HUMAN	S	4	ENSP00000258105:A4S;ENSP00000386920:A4S	ENSP00000258105:A4S	A	-	1	0	MRPL53	74553286	0.793000	0.28825	0.169000	0.22859	0.002000	0.02628	0.255000	0.18333	0.280000	0.22209	-0.137000	0.14449	GCC	C|0.587;A|0.413	0.413	strong		0.602	MRPL53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252225.2	NM_053050	
RERE	473	hgsc.bcm.edu	37	1	8415621	8415621	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:8415621G>A	ENST00000337907.3	-	23	5159	c.4525C>T	c.(4525-4527)Ccc>Tcc	p.P1509S	RERE_ENST00000377464.1_Missense_Mutation_p.P1241S|RERE_ENST00000400907.2_Missense_Mutation_p.P527S|RERE_ENST00000476556.1_Missense_Mutation_p.P955S|RERE_ENST00000400908.2_Missense_Mutation_p.P1509S	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1509	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GACATGGGGGGTGGGATGGCC	0.652																																					p.P1509S		Atlas-SNP	.											.	RERE	129	.	0			c.C4525T						PASS	.						15.0	17.0	16.0					1																	8415621		2198	4291	6489	SO:0001583	missense	473	exon23			TGGGGGGTGGGAT	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.4525C>T	1.37:g.8415621G>A	ENSP00000338629:p.Pro1509Ser	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	58	36	0.62069	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.870072	0.91587	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000400907;ENST00000476556;ENST00000400908;ENST00000505225	T;T;T	0.47177	0.85;0.85;0.85	5.98	5.98	0.97165	.	.	.	.	.	T	0.64450	0.2599	L	0.60455	1.87	0.80722	D	1	D	0.54772	0.968	P	0.60117	0.869	T	0.61855	-0.6977	9	0.52906	T	0.07	-25.8584	19.4247	0.94737	0.0:0.0:1.0:0.0	.	1509	Q9P2R6	RERE_HUMAN	S	1509;1241;527;955;1509;165	ENSP00000338629:P1509S;ENSP00000366684:P1241S;ENSP00000383700:P1509S	ENSP00000338629:P1509S	P	-	1	0	RERE	8338208	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.807000	0.99171	2.843000	0.97960	0.585000	0.79938	CCC	.	.	none		0.652	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
NT5DC3	51559	hgsc.bcm.edu	37	12	104171742	104171742	+	Silent	SNP	C	C	T	rs17034524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	135	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	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	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634341	32634341	+	Missense_Mutation	SNP	A	A	G	rs3189152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32634341A>G	ENST00000399082.3	-	1	88	c.44T>C	c.(43-45)gTa>gCa	p.V15A	HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.V15A|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.V15A|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.V15A|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.V15A			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	15			A -> V (in allele DQB1*03:02, allele DQB1*03:03, allele DQB1*04:01, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*06:02 and allele DQB1*06:12; dbSNP:rs3189152). {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)"""	GACAGTTGCTACCCGAAGGTC	0.577									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				a|||	1916	0.382588	0.3646	0.3487	5008	,	,		10661	0.3661		0.3549	False		,,,				2504	0.4765				p.V15A	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,NS,carcinoma,0,1	HLA-DQB1	15	1	0			c.T44C						scavenged	.	G	ALA/VAL	1086,2800		255,576,1112	53.0	51.0	52.0		44	-0.2	0.0	6	dbSNP_105	52	2480,5732		644,1192,2270	yes	missense	HLA-DQB1	NM_002123.4	64	899,1768,3382	GG,GA,AA		30.1997,27.9465,29.4759	benign	15/262	32634341	3566,8532	1943	4106	6049	SO:0001583	missense	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GTTGCTACCCGAA		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.44T>C	6.37:g.32634341A>G	ENSP00000382032:p.Val15Ala	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	15	15	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		634	0.2902930402930403	133	0.2703252032520325	113	0.31215469613259667	187	0.3269230769230769	201	0.26517150395778366	.	0.440	-0.899235	0.02472	0.279465	0.301997	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.03496	3.91;8.45;8.45;8.45;8.45	4.07	-0.196	0.13232	.	536.546000	0.00447	N	0.000082	T	0.00906	0.0030	.	.	.	0.80722	P	0.0	B;B;B;B	0.14438	0.01;0.0;0.0;0.0	B;B;B;B	0.11329	0.006;0.0;0.0;0.0	T	0.47394	-0.9121	8	0.45353	T	0.12	.	2.9773	0.05942	0.1685:0.2496:0.4568:0.125	rs3189152;rs9274520	25;15;15;15	Q59F80;A2AAZ0;Q5Y7D6;Q5Y7A9	.;.;.;.	A	15	ENSP00000382032:V15A;ENSP00000382029:V15A;ENSP00000364080:V15A;ENSP00000407332:V15A;ENSP00000382034:V15A	ENSP00000364080:V15A	V	-	2	0	HLA-DQB1	32742319	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.331000	0.07914	-0.498000	0.06632	-3.953000	0.00015	GTA	A|0.710;G|0.290	0.290	strong		0.577	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
TIMELESS	8914	hgsc.bcm.edu	37	12	56822690	56822690	+	Silent	SNP	C	C	T	rs11832580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56822690C>T	ENST00000553532.1	-	11	1431	c.1281G>A	c.(1279-1281)aaG>aaA	p.K427K	TIMELESS_ENST00000554616.1_Intron|TIMELESS_ENST00000229201.4_Silent_p.K426K					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						AGGCAGCTTCCTTGCGGTCAG	0.532													C|||	256	0.0511182	0.1831	0.0187	5008	,	,		19438	0.0		0.001	False		,,,				2504	0.0				p.K427K		Atlas-SNP	.											.	TIMELESS	107	.	0			c.G1281A						PASS	.	C		702,3704	294.7+/-283.3	45,612,1546	109.0	95.0	100.0		1281	4.4	1.0	12	dbSNP_120	100	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	TIMELESS	NM_003920.3		45,616,5842	TT,TC,CC		0.0465,15.9328,5.4283		427/1209	56822690	706,12300	2203	4300	6503	SO:0001819	synonymous_variant	8914	exon11			AGCTTCCTTGCGG	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.1281G>A	12.37:g.56822690C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_003920		Silent	SNP	ENST00000553532.1	37	CCDS8918.1																																																																																			C|0.949;T|0.051	0.051	strong		0.532	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
ITIH1	3697	hgsc.bcm.edu	37	3	52823864	52823864	+	Missense_Mutation	SNP	A	A	T	rs61730358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52823864A>T	ENST00000273283.2	+	19	2339	c.2315A>T	c.(2314-2316)cAg>cTg	p.Q772L	ITIH1_ENST00000537050.1_Missense_Mutation_p.Q484L|ITIH1_ENST00000542827.1_3'UTR|ITIH1_ENST00000405128.3_Missense_Mutation_p.Q138L|ITIH1_ENST00000540715.1_Missense_Mutation_p.Q630L	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	772	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		GTGCTGCGGCAGGACGGGTAA	0.627													A|||	96	0.0191693	0.0681	0.0086	5008	,	,		20037	0.0		0.0	False		,,,				2504	0.0				p.Q772L		Atlas-SNP	.											.	ITIH1	108	.	0			c.A2315T						PASS	.	A	LEU/GLN,LEU/GLN,LEU/GLN,LEU/GLN	272,4134	152.9+/-186.6	11,250,1942	55.0	54.0	54.0		1889,1451,1451,2315	5.4	1.0	3	dbSNP_129	54	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	113,113,113,113	11,252,6240	TT,TA,AA		0.0233,6.1734,2.1067	benign,benign,benign,benign	630/770,484/624,484/624,772/912	52823864	274,12732	2203	4300	6503	SO:0001583	missense	3697	exon19			TGCGGCAGGACGG		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2315A>T	3.37:g.52823864A>T	ENSP00000273283:p.Gln772Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	A	15.98	2.991954	0.54041	0.061734	2.33E-4	ENSG00000055957	ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133;ENST00000405128	T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75	5.42	5.42	0.78866	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.203207	0.43919	D	0.000515	T	0.01254	0.0041	L	0.49350	1.555	0.33937	D	0.642752	B;P;B;P	0.42337	0.006;0.776;0.425;0.661	B;B;B;P	0.48982	0.015;0.41;0.182;0.597	T	0.06534	-1.0821	10	0.40728	T	0.16	-18.8137	12.9885	0.58606	1.0:0.0:0.0:0.0	rs61730358	630;138;373;772	F5H165;B5MCP1;Q9P1C5;P19827	.;.;.;ITIH1_HUMAN	L	772;630;484;325;138	ENSP00000273283:Q772L;ENSP00000443973:Q630L;ENSP00000443847:Q484L;ENSP00000395836:Q325L;ENSP00000384589:Q138L	ENSP00000273283:Q772L	Q	+	2	0	ITIH1	52798904	1.000000	0.71417	0.993000	0.49108	0.101000	0.19017	5.862000	0.69560	2.043000	0.60533	0.460000	0.39030	CAG	A|0.981;T|0.019	0.019	strong		0.627	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
PRR14L	253143	hgsc.bcm.edu	37	22	32110163	32110163	+	Missense_Mutation	SNP	G	G	A	rs140078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32110163G>A	ENST00000327423.6	-	4	3851	c.3662C>T	c.(3661-3663)tCg>tTg	p.S1221L	PRR14L_ENST00000461722.1_5'Flank|PRR14L_ENST00000434485.1_Missense_Mutation_p.S1221L|PRR14L_ENST00000397493.2_Missense_Mutation_p.S1221L	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1221			S -> L (in dbSNP:rs140078).							endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GCAAGACATCGACTCTTTTGA	0.373											OREG0003535	type=REGULATORY REGION|Gene=AK130944|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	A|||	1729	0.345248	0.5847	0.3055	5008	,	,		19890	0.1875		0.2048	False		,,,				2504	0.3569				p.S1221L		Atlas-SNP	.											.	PRR14L	198	.	0			c.C3662T						PASS	.	A	LEU/SER	729,655		195,339,158	210.0	155.0	172.0		3662	-0.9	0.0	22	dbSNP_78	172	680,2502		80,520,991	yes	missense	PRR14L	NM_173566.2	145	275,859,1149	AA,AG,GG		21.3702,47.3266,30.8585	benign	1221/2152	32110163	1409,3157	692	1591	2283	SO:0001583	missense	253143	exon4			GACATCGACTCTT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.3662C>T	22.37:g.32110163G>A	ENSP00000331845:p.Ser1221Leu	Somatic	125	0	0	829	WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	37	CCDS13900.2	649	0.29716117216117216	286	0.5813008130081301	104	0.287292817679558	105	0.18356643356643357	154	0.20316622691292877	A	0.005	-2.181697	0.00308	0.526734	0.213702	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.05649	3.41;3.42;3.42	5.53	-0.868	0.10652	.	0.739382	0.11730	N	0.535009	T	0.00012	0.0000	N	0.01297	-0.9	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	0.18555	-1.0333	8	.	.	.	0.8397	8.0433	0.30534	0.362:0.131:0.5069:0.0	rs140078;rs3804091;rs60386080;rs140078	1221;1221;1221	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	L	1221	ENSP00000380630:S1221L;ENSP00000331845:S1221L;ENSP00000388314:S1221L	.	S	-	2	0	PRR14L	30440163	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.533000	0.06157	-0.419000	0.07439	-1.242000	0.01536	TCG	G|0.689;A|0.311	0.311	strong		0.373	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
DUPD1	338599	hgsc.bcm.edu	37	10	76803567	76803567	+	Missense_Mutation	SNP	T	T	G	rs16931938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76803567T>G	ENST00000338487.5	-	2	408	c.409A>C	c.(409-411)Agc>Cgc	p.S137R		NM_001003892.1	NP_001003892.1	Q68J44	DUPD1_HUMAN	dual specificity phosphatase and pro isomerase domain containing 1	137	Tyrosine-protein phosphatase.		S -> R (in dbSNP:rs16931938).		protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(2)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					TGGTCGTCGCTTAGCGCTCTG	0.706													G|||	1507	0.300919	0.6543	0.2061	5008	,	,		6796	0.2738		0.0457	False		,,,				2504	0.181				p.S137R		Atlas-SNP	.											.	DUPD1	30	.	0			c.A409C						PASS	.	G	ARG/SER	2448,1958	550.5+/-378.0	702,1044,457	67.0	60.0	62.0		409	-1.6	0.0	10	dbSNP_123	62	425,8175	797.7+/-407.4	11,403,3886	yes	missense	DUPD1	NM_001003892.1	110	713,1447,4343	GG,GT,TT		4.9419,44.4394,22.0898	benign	137/221	76803567	2873,10133	2203	4300	6503	SO:0001583	missense	338599	exon2			CGTCGCTTAGCGC		CCDS31223.1	10q22.3	2011-06-09			ENSG00000188716	ENSG00000188716		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	23481	protein-coding gene	gene with protein product							Standard	NM_001003892		Approved	DUSP27	uc001jwq.1	Q68J44	OTTHUMG00000018512	ENST00000338487.5:c.409A>C	10.37:g.76803567T>G	ENSP00000340609:p.Ser137Arg	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_001003892	B2RP93	Missense_Mutation	SNP	ENST00000338487.5	37	CCDS31223.1	608	0.2783882783882784	335	0.6808943089430894	71	0.19613259668508287	171	0.29895104895104896	31	0.040897097625329816	G	10.15	1.270877	0.23221	0.555606	0.049419	ENSG00000188716	ENST00000338487	T	0.61392	0.11	4.63	-1.65	0.08291	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.810313	0.11263	N	0.582345	T	0.00012	0.0000	L	0.48260	1.515	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.44967	-0.9293	9	0.23891	T	0.37	-0.524	13.1202	0.59321	0.0:0.0959:0.2121:0.692	rs16931938;rs52825920;rs16931938	137	Q68J44	DUPD1_HUMAN	R	137	ENSP00000340609:S137R	ENSP00000340609:S137R	S	-	1	0	DUPD1	76473573	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.125000	0.15749	-0.950000	0.03659	-0.847000	0.03039	AGC	T|0.742;G|0.258	0.258	strong		0.706	DUPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048777.2	XM_291741	
MYOM2	9172	hgsc.bcm.edu	37	8	2092803	2092803	+	Silent	SNP	A	A	G	rs1063523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2092803A>G	ENST00000262113.4	+	37	4437	c.4296A>G	c.(4294-4296)acA>acG	p.T1432T	MYOM2_ENST00000523438.1_Silent_p.T857T|MYOM2_ENST00000520298.1_3'UTR	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	87	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	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	
TNFRSF19	55504	hgsc.bcm.edu	37	13	24242166	24242166	+	Missense_Mutation	SNP	C	C	T	rs35041805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:24242166C>T	ENST00000382258.4	+	8	988	c.784C>T	c.(784-786)Ccc>Tcc	p.P262S	TNFRSF19_ENST00000382263.3_Missense_Mutation_p.P262S|TNFRSF19_ENST00000403372.2_Missense_Mutation_p.P130S|TNFRSF19_ENST00000248484.4_Missense_Mutation_p.P262S	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	262					apoptotic process (GO:0006915)|hair follicle development (GO:0001942)|JNK cascade (GO:0007254)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)	tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	22		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		GGCCTGCAGCCCCAACCCGGC	0.562													C|||	88	0.0175719	0.0393	0.0216	5008	,	,		15996	0.0		0.0179	False		,,,				2504	0.0031				p.P262S		Atlas-SNP	.											.	TNFRSF19	52	.	0			c.C784T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	155,4251	103.0+/-141.5	5,145,2053	54.0	48.0	50.0		784,388,784,784	-11.2	0.0	13	dbSNP_126	50	132,8468	63.5+/-125.6	2,128,4170	yes	missense,missense,missense,missense	TNFRSF19	NM_001204458.1,NM_001204459.1,NM_018647.3,NM_148957.3	74,74,74,74	7,273,6223	TT,TC,CC		1.5349,3.5179,2.2067	benign,benign,benign,benign	262/418,130/286,262/424,262/418	24242166	287,12719	2203	4300	6503	SO:0001583	missense	55504	exon8			TGCAGCCCCAACC	AB040434	CCDS9301.1, CCDS9302.1, CCDS55893.1	13q12.11-q12.3	2008-07-18			ENSG00000127863	ENSG00000127863		"""Tumor necrosis factor receptor superfamily"""	11915	protein-coding gene	gene with protein product	"""toxicity and JNK inducer"""	606122				10764796, 10809768	Standard	NM_018647		Approved	TAJ-alpha, TROY, TAJ, TRADE	uc001uov.2	Q9NS68	OTTHUMG00000016568	ENST00000382258.4:c.784C>T	13.37:g.24242166C>T	ENSP00000371693:p.Pro262Ser	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	139	79	0.568345	NM_018647	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Missense_Mutation	SNP	ENST00000382258.4	37	CCDS9302.1	40	0.018315018315018316	27	0.054878048780487805	5	0.013812154696132596	0	0.0	8	0.010554089709762533	C	1.414	-0.574621	0.03882	0.035179	0.015349	ENSG00000127863	ENST00000248484;ENST00000403372;ENST00000382258;ENST00000382263	T;T;T;T	0.75477	-0.94;1.64;-0.94;-0.94	5.6	-11.2	0.00127	.	1.541490	0.03240	N	0.180303	T	0.07593	0.0191	N	0.02011	-0.69	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.10870	-1.0611	10	0.07482	T	0.82	1.7599	4.075	0.09899	0.1155:0.3711:0.3077:0.2057	rs35041805	130;262;262	B4E2I6;Q9NS68;Q9NS68-2	.;TNR19_HUMAN;.	S	262;130;262;262	ENSP00000248484:P262S;ENSP00000385408:P130S;ENSP00000371693:P262S;ENSP00000371698:P262S	ENSP00000248484:P262S	P	+	1	0	TNFRSF19	23140166	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-2.593000	0.00897	-4.787000	0.00032	-0.868000	0.02995	CCC	C|0.981;T|0.019	0.019	strong		0.562	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647	
TNC	3371	hgsc.bcm.edu	37	9	117803271	117803271	+	Missense_Mutation	SNP	C	C	T	rs2274750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117803271C>T	ENST00000350763.4	-	19	5752	c.5341G>A	c.(5341-5343)Gcc>Acc	p.A1781T	TNC_ENST00000340094.3_Missense_Mutation_p.A1417T|TNC_ENST00000537320.1_Missense_Mutation_p.A1144T|TNC_ENST00000346706.3_Missense_Mutation_p.A1235T|TNC_ENST00000542877.1_Missense_Mutation_p.A1418T|TNC_ENST00000345230.3_Missense_Mutation_p.A1144T|TNC_ENST00000535648.1_Missense_Mutation_p.A1326T|TNC_ENST00000341037.4_Missense_Mutation_p.A1599T|TNC_ENST00000423613.2_Missense_Mutation_p.A1508T	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1781	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.		A -> T (in dbSNP:rs2274750).		bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CCCTTCATGGCGATGATGCTG	0.507													C|||	411	0.0820687	0.0983	0.1527	5008	,	,		18369	0.1151		0.0318	False		,,,				2504	0.0276				p.A1781T		Atlas-SNP	.											TNC,NS,carcinoma,+2,1	TNC	282	1	0			c.G5341A	GRCh37	CM067722	TNC	M	rs2274750	PASS	.	C	THR/ALA	400,4006	200.4+/-223.7	14,372,1817	198.0	166.0	177.0		5341	4.1	0.9	9	dbSNP_100	177	266,8334	102.3+/-163.5	4,258,4038	yes	missense	TNC	NM_002160.3	58	18,630,5855	TT,TC,CC		3.093,9.0785,5.1207	possibly-damaging	1781/2202	117803271	666,12340	2203	4300	6503	SO:0001583	missense	3371	exon19			TCATGGCGATGAT		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5341G>A	9.37:g.117803271C>T	ENSP00000265131:p.Ala1781Thr	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	210	62	0.295238	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	174|174	0.07967032967032966|0.07967032967032966	48|48	0.0975609756097561|0.0975609756097561	44|44	0.12154696132596685|0.12154696132596685	56|56	0.0979020979020979|0.0979020979020979	26|26	0.03430079155672823|0.03430079155672823	C|C	22.7|22.7	4.323493|4.323493	0.81580|0.81580	0.090785|0.090785	0.03093|0.03093	ENSG00000041982|ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877|ENST00000544972	T;T;T;T;T;T;T;T;T|.	0.67523|.	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27|.	6.08|6.08	4.08|4.08	0.47627|0.47627	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	0.221485|.	0.47455|.	D|.	0.000227|.	T|T	0.04363|0.04363	0.0120|0.0120	M|M	0.89287|0.89287	3.02|3.02	0.53005|0.53005	P|P	3.399999999997849E-5|3.399999999997849E-5	D;P|.	0.61697|.	0.99;0.949|.	P;P|.	0.61132|.	0.884;0.743|.	T|T	0.58869|0.58869	-0.7560|-0.7560	9|4	0.72032|.	D|.	0.01|.	.|.	12.6089|12.6089	0.56540|0.56540	0.5553:0.4447:0.0:0.0|0.5553:0.4447:0.0:0.0	rs2274750;rs52811748;rs2274750|rs2274750;rs52811748;rs2274750	1508;1781|.	E9PC84;P24821|.	.;TENA_HUMAN|.	T|H	1417;1326;1235;1144;1781;1599;1508;1144;1418|343	ENSP00000344400:A1417T;ENSP00000438152:A1326T;ENSP00000344555:A1235T;ENSP00000345861:A1144T;ENSP00000265131:A1781T;ENSP00000339553:A1599T;ENSP00000411406:A1508T;ENSP00000443478:A1144T;ENSP00000442242:A1418T|.	ENSP00000344400:A1417T|.	A|R	-|-	1|2	0|0	TNC|TNC	116843092|116843092	0.997000|0.997000	0.39634|0.39634	0.929000|0.929000	0.37066|0.37066	0.752000|0.752000	0.42762|0.42762	2.473000|2.473000	0.45145|0.45145	1.556000|1.556000	0.49512|0.49512	0.655000|0.655000	0.94253|0.94253	GCC|CGC	C|0.937;T|0.063	0.063	strong		0.507	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
SLC39A11	201266	hgsc.bcm.edu	37	17	70645366	70645366	+	Missense_Mutation	SNP	C	C	G	rs115567758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:70645366C>G	ENST00000542342.2	-	8	822	c.734G>C	c.(733-735)gGc>gCc	p.G245A	SLC39A11_ENST00000579988.1_5'UTR|SLC39A11_ENST00000255559.3_Missense_Mutation_p.G238A	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	245					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			endometrium(1)|large_intestine(4)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						GACAGCCAGGCCCTCGGGGAA	0.557													C|||	3	0.000599042	0.0023	0.0	5008	,	,		21013	0.0		0.0	False		,,,				2504	0.0				p.G245A	NSCLC(95;736 1527 12296 39625 41839)	Atlas-SNP	.											.	SLC39A11	32	.	0			c.G734C						PASS	.	C	ALA/GLY,ALA/GLY	25,4381	29.9+/-59.1	0,25,2178	47.0	51.0	50.0		734,713	5.1	1.0	17	dbSNP_132	50	0,8600		0,0,4300	yes	missense,missense	SLC39A11	NM_001159770.1,NM_139177.3	60,60	0,25,6478	GG,GC,CC		0.0,0.5674,0.1922	probably-damaging,probably-damaging	245/343,238/336	70645366	25,12981	2203	4300	6503	SO:0001583	missense	201266	exon8			GCCAGGCCCTCGG	AF331643	CCDS11690.1, CCDS54160.1	17q24.3-q25.1	2014-08-12	2013-07-17	2003-10-24	ENSG00000133195	ENSG00000133195		"""Solute carriers"""	14463	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 26"""	C17orf26		11707075	Standard	NM_139177		Approved		uc002jjb.3	Q8N1S5	OTTHUMG00000178306	ENST00000542342.2:c.734G>C	17.37:g.70645366C>G	ENSP00000445829:p.Gly245Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_001159770	B2R8H7|Q8WZ81	Missense_Mutation	SNP	ENST00000542342.2	37	CCDS54160.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	15.55	2.865881	0.51588	0.005674	0.0	ENSG00000133195	ENST00000542342;ENST00000255559	T;T	0.48836	0.8;0.8	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.74642	0.3743	H	0.97051	3.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85832	0.1392	10	0.87932	D	0	.	18.3766	0.90437	0.0:1.0:0.0:0.0	.	245;238	Q8N1S5;Q8N1S5-2	S39AB_HUMAN;.	A	245;238	ENSP00000445829:G245A;ENSP00000255559:G238A	ENSP00000255559:G238A	G	-	2	0	SLC39A11	68156961	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.013000	0.76373	2.504000	0.84457	0.655000	0.94253	GGC	C|0.999;G|0.001	0.001	strong		0.557	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1		
LSG1	55341	hgsc.bcm.edu	37	3	194371925	194371925	+	Silent	SNP	A	A	G	rs35636619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:194371925A>G	ENST00000265245.5	-	9	1508	c.1194T>C	c.(1192-1194)ggT>ggC	p.G398G	AC046143.2_ENST00000582474.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	398	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				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)		TTGAACTCTTACCAACATTAG	0.418													A|||	13	0.00259585	0.0083	0.0014	5008	,	,		21914	0.0		0.001	False		,,,				2504	0.0				p.G398G		Atlas-SNP	.											.	LSG1	38	.	0			c.T1194C						PASS	.	A		13,4393	20.2+/-43.8	0,13,2190	162.0	146.0	151.0		1194	0.8	1.0	3	dbSNP_126	151	0,8600		0,0,4300	no	coding-synonymous	LSG1	NM_018385.2		0,13,6490	GG,GA,AA		0.0,0.2951,0.1		398/659	194371925	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	55341	exon9			ACTCTTACCAACA		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.1194T>C	3.37:g.194371925A>G		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	184	83	0.451087	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Silent	SNP	ENST00000265245.5	37	CCDS33922.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	10.82	1.457387	0.26161	0.002951	0.0	ENSG00000041802	ENST00000437613	.	.	.	6.06	0.824	0.18818	.	.	.	.	.	T	0.40322	0.1112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28073	-1.0055	4	.	.	.	.	0.5788	0.00708	0.4085:0.17:0.2244:0.1971	rs35636619	.	.	.	A	132	.	.	V	-	2	0	LSG1	195853214	0.841000	0.29509	1.000000	0.80357	0.996000	0.88848	-0.065000	0.11617	0.549000	0.28973	0.533000	0.62120	GTA	A|0.999;G|0.001	0.001	strong		0.418	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	
ARNT2	9915	hgsc.bcm.edu	37	15	80843578	80843578	+	Missense_Mutation	SNP	G	G	A	rs150765047	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80843578G>A	ENST00000303329.4	+	9	1081	c.916G>A	c.(916-918)Ggc>Agc	p.G306S	ARNT2_ENST00000533983.1_Missense_Mutation_p.G295S|ARNT2_ENST00000527771.1_Missense_Mutation_p.G295S	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	306					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)			TGTGGGACAAGGCAGTAAATA	0.413													G|||	10	0.00199681	0.0076	0.0	5008	,	,		22886	0.0		0.0	False		,,,				2504	0.0				p.G306S		Atlas-SNP	.											.	ARNT2	88	.	0			c.G916A						PASS	.	G	SER/GLY	23,4383	29.9+/-59.1	0,23,2180	128.0	117.0	121.0		916	4.0	1.0	15	dbSNP_134	121	0,8600		0,0,4300	yes	missense	ARNT2	NM_014862.3	56	0,23,6480	AA,AG,GG		0.0,0.522,0.1768	benign	306/718	80843578	23,12983	2203	4300	6503	SO:0001583	missense	9915	exon9			GGACAAGGCAGTA	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.916G>A	15.37:g.80843578G>A	ENSP00000307479:p.Gly306Ser	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	38	23	0.605263	NM_014862	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	37	CCDS32307.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	15.74	2.923805	0.52653	0.00522	0.0	ENSG00000172379	ENST00000360062;ENST00000303329;ENST00000540859	T	0.06142	3.34	4.9	3.98	0.46160	.	0.412872	0.25801	N	0.028211	T	0.03095	0.0091	N	0.16656	0.425	0.54753	D	0.999984	B	0.15719	0.014	B	0.17722	0.019	T	0.43163	-0.9408	10	0.18276	T	0.48	.	13.4258	0.61024	0.0763:0.0:0.9237:0.0	.	306	Q9HBZ2	ARNT2_HUMAN	S	295;306;306	ENSP00000307479:G306S	ENSP00000307479:G306S	G	+	1	0	ARNT2	78630633	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.471000	0.60182	1.060000	0.40578	0.655000	0.94253	GGC	G|0.999;A|0.001	0.001	strong		0.413	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2		
ACAN	176	hgsc.bcm.edu	37	15	89417238	89417238	+	Missense_Mutation	SNP	A	A	G	rs1126823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89417238A>G	ENST00000561243.1	+	16	7499	c.7499A>G	c.(7498-7500)cAg>cGg	p.Q2500R	ACAN_ENST00000439576.2_Missense_Mutation_p.Q2500R|ACAN_ENST00000559004.1_Missense_Mutation_p.Q2462R|ACAN_ENST00000352105.7_Intron			P16112	PGCA_HUMAN	aggrecan	2385					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GAGGAGCCTCAGATCACCTGC	0.642													G|||	2037	0.406749	0.7557	0.2939	5008	,	,		17716	0.2639		0.2366	False		,,,				2504	0.3374				p.Q2500R		Atlas-SNP	.											.	ACAN	220	.	0			c.A7499G						PASS	.	G	,ARG/GLN	2941,1391		1018,905,243	37.0	46.0	43.0		,7499	2.9	1.0	15	dbSNP_86	43	2138,6378		265,1608,2385	yes	intron,missense	ACAN	NM_001135.3,NM_013227.3	,43	1283,2513,2628	GG,GA,AA		25.1057,32.1099,39.5314	,benign	,2500/2531	89417238	5079,7769	2166	4258	6424	SO:0001583	missense	176	exon17			AGCCTCAGATCAC	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.7499A>G	15.37:g.89417238A>G	ENSP00000453342:p.Gln2500Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_013227	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	778	0.35622710622710624	355	0.7215447154471545	116	0.32044198895027626	142	0.24825174825174826	165	0.21767810026385223	G	3.690	-0.063804	0.07273	0.678901	0.251057	ENSG00000157766	ENST00000439576;ENST00000268134	T	0.65178	-0.14	5.17	2.92	0.33932	.	0.000000	0.29752	N	0.011285	T	0.00012	0.0000	.	.	.	0.49582	P	1.9299999999999873E-4	B	0.06786	0.001	B	0.04013	0.001	T	0.43621	-0.9380	8	0.02654	T	1	-7.0478	11.1267	0.48322	0.2384:0.0:0.7616:0.0	rs1126823;rs2280467;rs3182090;rs17415701;rs52823483;rs56687304;rs1126823	2500	E7EX88	.	R	2500;2386	ENSP00000387356:Q2500R	ENSP00000268134:Q2386R	Q	+	2	0	ACAN	87218242	1.000000	0.71417	0.993000	0.49108	0.969000	0.65631	1.990000	0.40717	0.591000	0.29711	-0.119000	0.15052	CAG	A|0.613;G|0.387	0.387	strong		0.642	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
BEST1	7439	hgsc.bcm.edu	37	11	61730234	61730234	+	Silent	SNP	T	T	C	rs1800009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61730234T>C	ENST00000378043.4	+	10	2251	c.1608T>C	c.(1606-1608)acT>acC	p.T536T	BEST1_ENST00000378042.3_Silent_p.T449T|BEST1_ENST00000449131.2_Silent_p.T476T|FTH1_ENST00000529191.1_Intron|FTH1_ENST00000529631.1_Intron|BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000301774.9_Silent_p.T164T	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	536					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						GGAGGAAAACTGTGGAGTTTA	0.463													C|||	2962	0.591454	0.5348	0.4899	5008	,	,		21553	0.8552		0.3539	False		,,,				2504	0.7127				p.T536T		Atlas-SNP	.											.	BEST1	85	.	0			c.T1608C						PASS	.	C	,	2166,2238	593.3+/-388.0	530,1106,566	109.0	111.0	110.0		1428,1608	-4.6	0.8	11	dbSNP_89	110	3026,5572	663.5+/-402.1	553,1920,1826	no	coding-synonymous,coding-synonymous	BEST1	NM_001139443.1,NM_004183.3	,	1083,3026,2392	CC,CT,TT		35.1942,49.1826,39.9323	,	476/605,536/586	61730234	5192,7810	2202	4299	6501	SO:0001819	synonymous_variant	7439	exon10			GAAAACTGTGGAG	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1608T>C	11.37:g.61730234T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	126	67	0.531746	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			C|0.406;N|0.000	0.406	strong		0.463	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
VNN1	8876	hgsc.bcm.edu	37	6	133015257	133015257	+	Missense_Mutation	SNP	C	C	G	rs45610032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133015257C>G	ENST00000367928.4	-	3	419	c.406G>C	c.(406-408)Gtg>Ctg	p.V136L		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	136	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		V -> L (in dbSNP:rs45610032). {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)		ATATTTGCCACAACATAGATA	0.438													C|||	38	0.00758786	0.0265	0.0043	5008	,	,		16984	0.0		0.0	False		,,,				2504	0.0				p.V136L		Atlas-SNP	.											.	VNN1	69	.	0			c.G406C						PASS	.	C	LEU/VAL	119,4287	90.2+/-128.9	3,113,2087	155.0	139.0	144.0		406	6.1	1.0	6	dbSNP_127	144	5,8595	3.7+/-12.6	0,5,4295	no	missense	VNN1	NM_004666.2	32	3,118,6382	GG,GC,CC		0.0581,2.7009,0.9534	benign	136/514	133015257	124,12882	2203	4300	6503	SO:0001583	missense	8876	exon3			TTGCCACAACATA	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.406G>C	6.37:g.133015257C>G	ENSP00000356905:p.Val136Leu	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	233	115	0.493562	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	25.6	4.658625	0.88154	0.027009	5.81E-4	ENSG00000112299	ENST00000367928	D	0.89485	-2.52	6.07	6.07	0.98685	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.000000	0.64402	D	0.000004	D	0.90140	0.6919	M	0.76002	2.32	0.58432	D	0.999998	P	0.37141	0.584	B	0.44044	0.439	D	0.89290	0.3618	10	0.52906	T	0.07	-8.8184	20.6439	0.99570	0.0:1.0:0.0:0.0	rs45610032	136	O95497	VNN1_HUMAN	L	136	ENSP00000356905:V136L	ENSP00000356905:V136L	V	-	1	0	VNN1	133056950	1.000000	0.71417	0.969000	0.41365	0.874000	0.50279	6.622000	0.74233	2.890000	0.99128	0.650000	0.86243	GTG	C|0.992;G|0.008	0.008	strong		0.438	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
MRPL32	64983	hgsc.bcm.edu	37	7	42971998	42971998	+	Missense_Mutation	SNP	A	A	G	rs111980169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:42971998A>G	ENST00000223324.2	+	1	200	c.13A>G	c.(13-15)Atg>Gtg	p.M5V	PSMA2_ENST00000538645.1_5'Flank|PSMA2_ENST00000445517.1_5'Flank|PSMA2_ENST00000223321.4_5'Flank|PSMA2_ENST00000442788.1_5'Flank	NM_031903.2	NP_114109.1	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32	5					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)	10						GGCGCTGGCCATGCTGGTCTT	0.637													A|||	23	0.00459265	0.0174	0.0	5008	,	,		15207	0.0		0.0	False		,,,				2504	0.0				p.M5V		Atlas-SNP	.											.	MRPL32	25	.	0			c.A13G						PASS	.	A	VAL/MET	44,4362	46.7+/-81.2	0,44,2159	57.0	60.0	59.0		13	-11.6	0.0	7	dbSNP_132	59	0,8600		0,0,4300	yes	missense	MRPL32	NM_031903.2	21	0,44,6459	GG,GA,AA		0.0,0.9986,0.3383	benign	5/189	42971998	44,12962	2203	4300	6503	SO:0001583	missense	64983	exon1			CTGGCCATGCTGG	AB051343	CCDS5468.1	7p14	2012-09-13			ENSG00000106591	ENSG00000106591		"""Mitochondrial ribosomal proteins / large subunits"""	14035	protein-coding gene	gene with protein product		611839				11543634	Standard	NM_031903		Approved	HSPC283, L32mt, MRP-L32, bMRP-59b	uc003tia.3	Q9BYC8	OTTHUMG00000155180	ENST00000223324.2:c.13A>G	7.37:g.42971998A>G	ENSP00000223324:p.Met5Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_031903	Q96Q68|Q9P098	Missense_Mutation	SNP	ENST00000223324.2	37	CCDS5468.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	11.56	1.675863	0.29783	0.009986	0.0	ENSG00000106591	ENST00000223324	.	.	.	5.97	-11.6	0.00059	.	1.135090	0.06109	N	0.666822	T	0.09730	0.0239	L	0.42245	1.32	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28427	-1.0044	9	0.02654	T	1	-2.6256	2.0049	0.03475	0.1081:0.2514:0.2373:0.4032	.	5	Q9BYC8	RM32_HUMAN	V	5	.	ENSP00000223324:M5V	M	+	1	0	MRPL32	42938523	0.000000	0.05858	0.005000	0.12908	0.224000	0.24922	-1.230000	0.02942	-1.610000	0.01583	0.477000	0.44152	ATG	A|0.995;G|0.005	0.005	strong		0.637	MRPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338669.1	NM_031903	
FCGBP	8857	hgsc.bcm.edu	37	19	40360928	40360928	+	Silent	SNP	G	G	A	rs1053686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	128	0	0		WXS	Illumina HiSeq	Phase_I	136	55	0.404412	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	
LY6H	4062	hgsc.bcm.edu	37	8	144240257	144240257	+	Silent	SNP	C	C	G	rs9694368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144240257C>G	ENST00000430474.2	-	3	315	c.150G>C	c.(148-150)acG>acC	p.T50T	LY6H_ENST00000342752.4_Silent_p.T71T|LY6H_ENST00000414417.2_Silent_p.T71T	NM_002347.4	NP_002338.3	O94772	LY6H_HUMAN	lymphocyte antigen 6 complex, locus H	50	UPAR/Ly6.				nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.T50T(1)		endometrium(1)|lung(1)|stomach(2)	4	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TGGCACACACCGTGTCGGACG	0.602													C|||	1610	0.321486	0.3101	0.2968	5008	,	,		16990	0.2768		0.3917	False		,,,				2504	0.3282				p.T71T		Atlas-SNP	.											LY6H,NS,carcinoma,0,1	LY6H	12	1	1	Substitution - coding silent(1)	stomach(1)	c.G213C						PASS	.	C	,,	1375,3031	453.2+/-350.3	209,957,1037	154.0	124.0	134.0		213,213,150	-6.5	0.8	8	dbSNP_119	134	3680,4920	527.3+/-381.1	774,2132,1394	no	coding-synonymous,coding-synonymous,coding-synonymous	LY6H	NM_001130478.1,NM_001135655.1,NM_002347.4	,,	983,3089,2431	GG,GC,CC		42.7907,31.2074,38.8667	,,	71/162,71/162,50/141	144240257	5055,7951	2203	4300	6503	SO:0001819	synonymous_variant	4062	exon3			ACACACCGTGTCG	AB012293	CCDS6396.1, CCDS47926.1	8q24.3	2008-08-01			ENSG00000176956	ENSG00000176956			6728	protein-coding gene	gene with protein product		603625				9799603	Standard	NM_001130478		Approved	NMLY6	uc011lkb.2	O94772	OTTHUMG00000154890	ENST00000430474.2:c.150G>C	8.37:g.144240257C>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	135	73	0.540741	NM_001135655	B2RAD2|J3KQI0|Q6IAX0	Silent	SNP	ENST00000430474.2	37	CCDS6396.1																																																																																			C|0.620;G|0.380	0.380	strong		0.602	LY6H-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337535.1		
TELO2	9894	hgsc.bcm.edu	37	16	1552107	1552107	+	Missense_Mutation	SNP	C	C	T	rs58099766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1552107C>T	ENST00000262319.6	+	12	1811	c.1532C>T	c.(1531-1533)gCt>gTt	p.A511V	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	511			A -> V (in dbSNP:rs58099766).		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)				AGCAGCAAGGCTCCTGCCTAC	0.632													C|||	115	0.0229633	0.0847	0.0043	5008	,	,		15233	0.0		0.0	False		,,,				2504	0.0				p.A511V		Atlas-SNP	.											.	TELO2	44	.	0			c.C1532T						PASS	.	C	VAL/ALA	328,4070	172.7+/-202.6	14,300,1885	67.0	64.0	65.0		1532	0.3	0.1	16	dbSNP_129	65	1,8599		0,1,4299	yes	missense	TELO2	NM_016111.3	64	14,301,6184	TT,TC,CC		0.0116,7.4579,2.5312	benign	511/838	1552107	329,12669	2199	4300	6499	SO:0001583	missense	9894	exon12			GCAAGGCTCCTGC	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.1532C>T	16.37:g.1552107C>T	ENSP00000262319:p.Ala511Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	48	0.02197802197802198	46	0.09349593495934959	2	0.0055248618784530384	0	0.0	0	0.0	C	10.54	1.379287	0.24944	0.074579	1.16E-4	ENSG00000100726	ENST00000437914;ENST00000262319	T	0.16743	2.32	5.67	0.301	0.15781	Telomere length regulation protein, conserved domain (1);	0.329093	0.36200	N	0.002734	T	0.00608	0.0020	M	0.76838	2.35	0.30705	N	0.749924	B	0.22800	0.075	B	0.24848	0.056	T	0.07309	-1.0779	10	0.29301	T	0.29	-4.6319	5.3866	0.16222	0.135:0.5696:0.0:0.2954	rs58099766	511	Q9Y4R8	TELO2_HUMAN	V	125;511	ENSP00000262319:A511V	ENSP00000262319:A511V	A	+	2	0	TELO2	1492108	0.983000	0.35010	0.139000	0.22197	0.033000	0.12548	2.614000	0.46359	0.055000	0.16094	0.655000	0.94253	GCT	C|0.972;T|0.028	0.028	strong		0.632	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
LRFN1	57622	hgsc.bcm.edu	37	19	39805188	39805188	+	Silent	SNP	C	C	T	rs115860908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39805188C>T	ENST00000248668.4	-	1	788	c.789G>A	c.(787-789)ctG>ctA	p.L263L	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	263	LRRCT.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			TCAGCCGCCGCAGCCAGAGCA	0.682													C|||	131	0.0261581	0.0908	0.0144	5008	,	,		14203	0.0		0.001	False		,,,				2504	0.0				p.L263L		Atlas-SNP	.											.	LRFN1	59	.	0			c.G789A						PASS	.	C		280,4082		10,260,1911	14.0	19.0	17.0		789	0.8	1.0	19	dbSNP_132	17	7,8559		0,7,4276	no	coding-synonymous	LRFN1	NM_020862.1		10,267,6187	TT,TC,CC		0.0817,6.4191,2.22		263/772	39805188	287,12641	2181	4283	6464	SO:0001819	synonymous_variant	57622	exon1			CCGCCGCAGCCAG	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.789G>A	19.37:g.39805188C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	34	0.666667	NM_020862	Q8TBS9	Silent	SNP	ENST00000248668.4	37	CCDS46071.1																																																																																			C|0.971;T|0.029	0.029	strong		0.682	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862	
PLEKHG4	25894	hgsc.bcm.edu	37	16	67320920	67320920	+	Silent	SNP	C	C	T	rs785029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67320920C>T	ENST00000360461.5	+	17	5478	c.2943C>T	c.(2941-2943)ctC>ctT	p.L981L	PLEKHG4_ENST00000379344.3_Silent_p.L981L|PLEKHG4_ENST00000450733.1_Silent_p.L900L|PLEKHG4_ENST00000427155.2_Silent_p.L981L	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	981	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		ACCTTGGTCTCACTGAGTGCT	0.632													C|||	121	0.0241613	0.0091	0.0432	5008	,	,		19662	0.0		0.0577	False		,,,				2504	0.0215				p.L981L		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.C2943T						PASS	.	C	,,,,	94,4302	77.3+/-115.6	0,94,2104	48.0	49.0	49.0		2943,2943,2943,2700,2943	1.9	1.0	16	dbSNP_86	49	598,8002	157.7+/-211.4	15,568,3717	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEKHG4	NM_001129727.1,NM_001129728.1,NM_001129729.1,NM_001129731.1,NM_015432.3	,,,,	15,662,5821	TT,TC,CC		6.9535,2.1383,5.3247	,,,,	981/1192,981/1192,981/1192,900/1111,981/1192	67320920	692,12304	2198	4300	6498	SO:0001819	synonymous_variant	25894	exon18			TGGTCTCACTGAG	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.2943C>T	16.37:g.67320920C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Silent	SNP	ENST00000360461.5	37	CCDS32466.1																																																																																			C|0.960;T|0.040	0.040	strong		0.632	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
MUC4	4585	hgsc.bcm.edu	37	3	195511822	195511822	+	Missense_Mutation	SNP	G	G	T	rs200327729		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511822G>T	ENST00000463781.3	-	2	7088	c.6629C>A	c.(6628-6630)cCt>cAt	p.P2210H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2210H	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.P2210H(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)		GCTGGTGACAGGAAGAGGGGT	0.597																																					p.P2210H		Atlas-SNP	.											MUC4_ENST00000463781,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,7	MUC4	1505	7	2	Substitution - Missense(2)	central_nervous_system(2)	c.C6629A						PASS	.						34.0	28.0	30.0					3																	195511822		689	1590	2279	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.6629C>A	3.37:g.195511822G>T	ENSP00000417498:p.Pro2210His	Somatic	424	1	0.00235849		WXS	Illumina HiSeq	Phase_I	308	99	0.321429	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	8.653	0.898651	0.17686	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.48;1.47	.	.	.	.	.	.	.	.	T	0.32010	0.0815	N	0.19112	0.55	0.22305	N	0.99921	D	0.64830	0.994	D	0.71656	0.974	T	0.18681	-1.0329	7	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	2210	E7ESK3	.	H	2210	ENSP00000417498:P2210H;ENSP00000420243:P2210H	.	P	-	2	0	MUC4	196996217	0.000000	0.05858	0.078000	0.20375	0.036000	0.12997	-1.771000	0.01789	0.064000	0.16427	0.064000	0.15345	CCT	G|0.998;T|0.002	0.002	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MYO1F	4542	hgsc.bcm.edu	37	19	8620636	8620636	+	Silent	SNP	C	C	T	rs73501540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8620636C>T	ENST00000338257.8	-	2	315	c.48G>A	c.(46-48)caG>caA	p.Q16Q		NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	16					defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						CCACGCCGCTCTGCTTCACGT	0.637													C|||	320	0.0638978	0.2322	0.0187	5008	,	,		13239	0.0		0.0	False		,,,				2504	0.0				p.Q16Q		Atlas-SNP	.											.	MYO1F	128	.	0			c.G48A						PASS	.	C		799,3379		64,671,1354	83.0	90.0	87.0		48	1.9	1.0	19	dbSNP_130	87	10,8402		0,10,4196	no	coding-synonymous	MYO1F	NM_012335.3		64,681,5550	TT,TC,CC		0.1189,19.124,6.4257		16/1099	8620636	809,11781	2089	4206	6295	SO:0001819	synonymous_variant	4542	exon2			GCCGCTCTGCTTC	X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"""Myosins / Myosin superfamily : Class I"""	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.48G>A	19.37:g.8620636C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_012335	Q8WWN7	Silent	SNP	ENST00000338257.8	37	CCDS42494.1																																																																																			C|0.966;T|0.034	0.034	strong		0.637	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2		
PIGN	23556	hgsc.bcm.edu	37	18	59814324	59814324	+	Missense_Mutation	SNP	G	G	C	rs9320001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	245	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	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	
CMYA5	202333	hgsc.bcm.edu	37	5	79027605	79027605	+	Missense_Mutation	SNP	T	T	C	rs6893869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79027605T>C	ENST00000446378.2	+	2	3048	c.3017T>C	c.(3016-3018)gTt>gCt	p.V1006A		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1006			V -> A (in dbSNP:rs6893869).		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)		p.V1006A(1)		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)		GCATCACAAGTTTCAATCCCT	0.403													T|||	1372	0.273962	0.5832	0.085	5008	,	,		21484	0.3621		0.0815	False		,,,				2504	0.0971				p.V1006A		Atlas-SNP	.											CMYA5,NS,carcinoma,0,1	CMYA5	643	1	1	Substitution - Missense(1)	stomach(1)	c.T3017C						PASS	.	T	ALA/VAL	1907,1939		472,963,488	73.0	69.0	70.0		3017	3.3	1.0	5	dbSNP_116	70	717,7529		39,639,3445	yes	missense	CMYA5	NM_153610.3	64	511,1602,3933	CC,CT,TT		8.6951,49.584,21.7003	benign	1006/4070	79027605	2624,9468	1923	4123	6046	SO:0001583	missense	202333	exon2			CACAAGTTTCAAT	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.3017T>C	5.37:g.79027605T>C	ENSP00000394770:p.Val1006Ala	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	172	172	1	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	625	0.28617216117216115	303	0.6158536585365854	31	0.0856353591160221	232	0.40559440559440557	59	0.07783641160949868	T	9.347	1.064534	0.20067	0.49584	0.086951	ENSG00000164309	ENST00000446378	T	0.60548	0.18	5.88	3.3	0.37823	.	0.864592	0.09833	N	0.749968	T	0.00012	0.0000	N	0.21583	0.68	0.80722	P	0.0	B	0.29188	0.236	B	0.20767	0.031	T	0.47114	-0.9142	9	0.02654	T	1	.	2.6076	0.04882	0.1434:0.0877:0.1488:0.6201	rs6893869;rs61614640;rs6893869	1006	Q8N3K9	CMYA5_HUMAN	A	1006	ENSP00000394770:V1006A	ENSP00000394770:V1006A	V	+	2	0	CMYA5	79063361	0.001000	0.12720	0.999000	0.59377	0.938000	0.57974	0.769000	0.26604	1.005000	0.39183	0.460000	0.39030	GTT	T|0.702;C|0.298	0.298	strong		0.403	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
NOL8	55035	hgsc.bcm.edu	37	9	95072907	95072907	+	Missense_Mutation	SNP	G	G	C	rs15717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95072907G>C	ENST00000535387.1	-	7	2408	c.2409C>G	c.(2407-2409)gaC>gaG	p.D803E	NOL8_ENST00000545558.1_Missense_Mutation_p.D841E|NOL8_ENST00000358855.4_Missense_Mutation_p.D773E|NOL8_ENST00000542053.1_Missense_Mutation_p.D773E|NOL8_ENST00000442668.2_Missense_Mutation_p.D841E					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						AATCAGATTCGTCATCATCAC	0.378													C|||	356	0.0710863	0.1188	0.0533	5008	,	,		22396	0.0446		0.0239	False		,,,				2504	0.0951				p.D841E		Atlas-SNP	.											.	NOL8	118	.	0			c.C2523G						PASS	.	C	GLU/ASP	398,3486		18,362,1562	151.0	140.0	144.0		2523	-2.0	0.1	9	dbSNP_52	144	350,7940		12,326,3807	yes	missense	NOL8	NM_017948.5	45	30,688,5369	CC,CG,GG		4.222,10.2472,6.1442	benign	841/1168	95072907	748,11426	1942	4145	6087	SO:0001583	missense	55035	exon9			AGATTCGTCATCA	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.2409C>G	9.37:g.95072907G>C	ENSP00000441300:p.Asp803Glu	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	161	91	0.565217	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	124	0.056776556776556776	67	0.13617886178861788	20	0.055248618784530384	20	0.03496503496503497	17	0.022427440633245383	C	0.796	-0.757244	0.03019	0.102472	0.04222	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8;1.8	5.9	-2.04	0.07343	.	0.142678	0.64402	N	0.000007	T	0.00039	0.0001	N	0.00450	-1.49	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17653	-1.0362	9	0.02654	T	1	-9.3841	2.5268	0.04693	0.0919:0.2999:0.2696:0.3386	rs15717;rs2236342;rs7025559;rs60708680;rs15717	773;841	Q76FK4-2;Q76FK4	.;NOL8_HUMAN	E	841;805;773;841;803;773;841	ENSP00000401177:D841E;ENSP00000351723:D773E;ENSP00000441140:D841E;ENSP00000441300:D803E;ENSP00000440709:D773E;ENSP00000414112:D841E	ENSP00000351723:D773E	D	-	3	2	NOL8	94112728	0.522000	0.26266	0.089000	0.20774	0.635000	0.38103	-0.115000	0.10741	-0.629000	0.05575	-0.752000	0.03492	GAC	G|0.940;C|0.060	0.060	strong		0.378	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68264867	68264867	+	Silent	SNP	A	A	G	rs12891164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	184	183	0.994565	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	
TG	7038	hgsc.bcm.edu	37	8	134125682	134125682	+	Missense_Mutation	SNP	G	G	A	rs1133076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134125682G>A	ENST00000220616.4	+	44	7629	c.7589G>A	c.(7588-7590)cGa>cAa	p.R2530Q	TG_ENST00000519543.1_Missense_Mutation_p.R663Q|TG_ENST00000542445.1_Missense_Mutation_p.R900Q|TG_ENST00000377869.1_Missense_Mutation_p.R2473Q	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2530			R -> Q (in dbSNP:rs1133076). {ECO:0000269|PubMed:10199792}.		hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GAGGAAAGTCGAGGCCGGACC	0.478													A|||	2691	0.53734	0.8041	0.3516	5008	,	,		18729	0.4028		0.492	False		,,,				2504	0.4939				p.R2530Q		Atlas-SNP	.											.	TG	416	.	0			c.G7589A						PASS	.	A	GLN/ARG	3390,1016	377.3+/-322.4	1301,788,114	67.0	74.0	72.0		7589	4.8	1.0	8	dbSNP_86	72	4078,4522	593.9+/-393.2	968,2142,1190	yes	missense	TG	NM_003235.4	43	2269,2930,1304	AA,AG,GG		47.4186,23.0595,42.5803	benign	2530/2769	134125682	7468,5538	2203	4300	6503	SO:0001583	missense	7038	exon44			AAAGTCGAGGCCG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.7589G>A	8.37:g.134125682G>A	ENSP00000220616:p.Arg2530Gln	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	1156	0.5293040293040293	406	0.8252032520325203	148	0.4088397790055249	223	0.38986013986013984	379	0.5	A	5.800	0.331826	0.10956	0.769405	0.474186	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	4.83	4.83	0.62350	Carboxylesterase, type B (1);	1.362880	0.04630	N	0.403510	T	0.00012	0.0000	N	0.00483	-1.445	0.49798	P	1.7999999999995797E-4	B;B;B	0.11235	0.001;0.0;0.004	B;B;B	0.04013	0.001;0.0;0.001	T	0.43327	-0.9398	9	0.02654	T	1	.	10.0443	0.42177	0.9198:0.0:0.0802:0.0	rs3194514	663;900;2530	E7EVM0;F5GWW5;P01266	.;.;THYG_HUMAN	Q	2473;1336;2530;900;663	ENSP00000367100:R2473Q;ENSP00000220616:R2530Q;ENSP00000441693:R900Q;ENSP00000430430:R663Q	ENSP00000220616:R2530Q	R	+	2	0	TG	134194864	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	5.139000	0.64801	0.797000	0.33971	-0.254000	0.11334	CGA	G|0.442;A|0.558	0.558	strong		0.478	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
TAS1R2	80834	hgsc.bcm.edu	37	1	19166894	19166894	+	Silent	SNP	G	G	A	rs11805253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19166894G>A	ENST00000375371.3	-	6	1740	c.1719C>T	c.(1717-1719)gcC>gcT	p.A573A		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	573					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)	AGCCCAGGGCGGCCAGCAGGG	0.612													G|||	262	0.0523163	0.1747	0.0303	5008	,	,		18191	0.001		0.003	False		,,,				2504	0.0061				p.A573A		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C1719T						PASS	.	G		529,3877	237.7+/-249.4	32,465,1706	49.0	51.0	50.0		1719	-7.5	0.0	1	dbSNP_120	50	61,8539	36.9+/-92.0	1,59,4240	no	coding-synonymous	TAS1R2	NM_152232.2		33,524,5946	AA,AG,GG		0.7093,12.0064,4.5364		573/840	19166894	590,12416	2203	4300	6503	SO:0001819	synonymous_variant	80834	exon6			CAGGGCGGCCAGC		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.1719C>T	1.37:g.19166894G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			G|0.959;A|0.041	0.041	strong		0.612	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
CARNS1	57571	hgsc.bcm.edu	37	11	67191449	67191449	+	Silent	SNP	T	T	C	rs1790747	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67191449T>C	ENST00000307823.3	+	9	2313	c.1861T>C	c.(1861-1863)Ttg>Ctg	p.L621L	CARNS1_ENST00000423745.2_Silent_p.L621L|CARNS1_ENST00000531040.1_Silent_p.L718L|CARNS1_ENST00000445895.2_Silent_p.L744L	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	621	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						TGGTGGGCGGTTGCTGGCTGC	0.652													C|||	1802	0.359824	0.8298	0.4063	5008	,	,		17757	0.2897		0.0835	False		,,,				2504	0.0481				p.L744L		Atlas-SNP	.											.	CARNS1	60	.	0			c.T2230C						PASS	.	C	,	2879,1419		993,893,263	119.0	143.0	135.0		2230,1861	3.9	0.8	11	dbSNP_89	135	653,7809		21,611,3599	no	coding-synonymous,coding-synonymous	CARNS1	NM_001166222.1,NM_020811.1	,	1014,1504,3862	CC,CT,TT		7.7169,33.0154,27.6803	,	744/951,621/828	67191449	3532,9228	2149	4231	6380	SO:0001819	synonymous_variant	57571	exon10			GGGCGGTTGCTGG		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"""ATP-grasp domain containing 1"""	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.1861T>C	11.37:g.67191449T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001166222	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Silent	SNP	ENST00000307823.3	37	CCDS44658.1																																																																																			T|0.648;C|0.352	0.352	strong		0.652	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811	
ZNF587	84914	hgsc.bcm.edu	37	19	58370744	58370744	+	Missense_Mutation	SNP	G	G	A	rs201869821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58370744G>A	ENST00000339656.5	+	3	1146	c.964G>A	c.(964-966)Ggg>Agg	p.G322R	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597652.1_5'Flank|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF587_ENST00000423137.1_Missense_Mutation_p.G321R|ZNF587_ENST00000419854.1_Missense_Mutation_p.G279R	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	322					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(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		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;0.0264)		CACTGGAGAAGGGCCTTATGA	0.473													.|||	671	0.133986	0.4274	0.0504	5008	,	,		18971	0.0526		0.0149	False		,,,				2504	0.0031				p.G322R	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.G964A						PASS	.	G	ARG/GLY,ARG/GLY	780,3588		221,338,1625	105.0	146.0	133.0		961,964	0.6	0.2	19	dbSNP_132	133	4,8596		0,4,4296	no	missense,missense	ZNF587	NM_001204817.1,NM_032828.3	125,125	221,342,5921	AA,AG,GG		0.0465,17.8571,6.0457	benign,benign	321/575,322/576	58370744	784,12184	2184	4300	6484	SO:0001583	missense	84914	exon3			GGAGAAGGGCCTT	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.964G>A	19.37:g.58370744G>A	ENSP00000345479:p.Gly322Arg	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	201	63	0.313433	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Missense_Mutation	SNP	ENST00000339656.5	37	CCDS12964.1	.	.	.	.	.	.	.	.	.	.	.	0.013	-1.627794	0.00813	0.178571	4.65E-4	ENSG00000198466	ENST00000376209;ENST00000423137;ENST00000339656;ENST00000540851;ENST00000419854	T;T;T	0.15603	2.41;2.41;2.41	1.76	0.637	0.17735	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00069	-2.28	0.27094	N	0.962789	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42103	-0.9471	8	0.10902	T	0.67	.	5.5186	0.16919	0.8297:0.0:0.1703:0.0	.	321;322	G3V0H5;Q96SQ5	.;ZN587_HUMAN	R	279;321;322;322;279	ENSP00000393865:G321R;ENSP00000345479:G322R;ENSP00000406999:G279R	ENSP00000345479:G322R	G	+	1	0	ZNF587	63062556	0.000000	0.05858	0.162000	0.22713	0.192000	0.23643	1.091000	0.30915	-0.047000	0.13423	0.195000	0.17529	GGG	G|0.999;A|0.001	0.001	weak		0.473	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
BEST1	7439	hgsc.bcm.edu	37	11	61730414	61730414	+	Intron	SNP	C	C	A	rs115379107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61730414C>A	ENST00000378043.4	+	10	2382				BEST1_ENST00000378042.3_Intron|BEST1_ENST00000449131.2_Silent_p.T536T|FTH1_ENST00000529191.1_Intron|FTH1_ENST00000529631.1_Intron|BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000301774.9_Silent_p.T224T	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						TGTGCCCCACCCCAGCTTCCC	0.557													C|||	141	0.028155	0.1014	0.0101	5008	,	,		20189	0.0		0.0	False		,,,				2504	0.0				p.T536T		Atlas-SNP	.											.	BEST1	85	.	0			c.C1608A						PASS	.	C	,	329,4041		12,305,1868	69.0	76.0	74.0		1608,	-0.5	0.0	11	dbSNP_132	74	0,8586		0,0,4293	no	coding-synonymous,intron	BEST1	NM_001139443.1,NM_004183.3	,	12,305,6161	AA,AC,CC		0.0,7.5286,2.5394	,	536/605,	61730414	329,12627	2185	4293	6478	SO:0001627	intron_variant	7439	exon9			CCCCACCCCAGCT	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1739+49C>A	11.37:g.61730414C>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	163	84	0.515337	NM_001139443	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			C|0.974;A|0.026	0.026	strong		0.557	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
SASH1	23328	hgsc.bcm.edu	37	6	148792617	148792617	+	Silent	SNP	A	A	G	rs1883625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	229	0	0		WXS	Illumina HiSeq	Phase_I	212	101	0.476415	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	
ADCY2	108	hgsc.bcm.edu	37	5	7706989	7706989	+	Silent	SNP	C	C	T	rs75986905	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:7706989C>T	ENST00000338316.4	+	8	1331	c.1242C>T	c.(1240-1242)aaC>aaT	p.N414N	ADCY2_ENST00000537121.1_Silent_p.N234N|RP11-711G10.1_ENST00000514105.2_RNA	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	414					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						CCTTGGCCAACCACATGGAAG	0.502													C|||	68	0.0135783	0.0484	0.0058	5008	,	,		20791	0.0		0.0	False		,,,				2504	0.0				p.N414N		Atlas-SNP	.											.	ADCY2	337	.	0			c.C1242T						PASS	.	C		199,4207	124.5+/-161.8	4,191,2008	176.0	155.0	162.0		1242	-3.5	1.0	5	dbSNP_132	162	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ADCY2	NM_020546.2		4,193,6306	TT,TC,CC		0.0233,4.5166,1.5454		414/1092	7706989	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	108	exon8			GGCCAACCACATG	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.1242C>T	5.37:g.7706989C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	248	123	0.495968	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																			C|0.985;T|0.015	0.015	strong		0.502	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
PAPLN	89932	hgsc.bcm.edu	37	14	73711394	73711394	+	Missense_Mutation	SNP	A	A	G	rs2280792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:73711394A>G	ENST00000554301.1	+	2	260	c.97A>G	c.(97-99)Agc>Ggc	p.S33G	PAPLN_ENST00000381166.3_Missense_Mutation_p.S33G|RP4-647C14.2_ENST00000554614.1_RNA|RNU6-419P_ENST00000517030.1_RNA|PAPLN_ENST00000555445.1_Missense_Mutation_p.S33G|PAPLN_ENST00000340738.5_Missense_Mutation_p.S33G|PAPLN_ENST00000427855.1_Missense_Mutation_p.S33G			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	33	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.		S -> G (in dbSNP:rs2280792).			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)		GGGACCCTGGAGCCAGTGGAG	0.642													G|||	1192	0.238019	0.1974	0.2824	5008	,	,		15588	0.4236		0.1243	False		,,,				2504	0.1871				p.S33G		Atlas-SNP	.											.	PAPLN	180	.	0			c.A97G						PASS	.	G	GLY/SER	874,3504		94,686,1409	16.0	15.0	15.0		97	5.1	1.0	14	dbSNP_100	15	1026,7564		72,882,3341	yes	missense	PAPLN	NM_173462.3	56	166,1568,4750	GG,GA,AA		11.9441,19.9635,14.6514	benign	33/1252	73711394	1900,11068	2189	4295	6484	SO:0001583	missense	89932	exon3			CCCTGGAGCCAGT	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.97A>G	14.37:g.73711394A>G	ENSP00000451803:p.Ser33Gly	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	147	71	0.482993	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		530	0.24267399267399267	104	0.21138211382113822	91	0.2513812154696133	231	0.40384615384615385	104	0.13720316622691292	G	15.61	2.883704	0.51908	0.199635	0.119441	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000394134;ENST00000554301;ENST00000555445	T;T;T;T;T	0.19105	2.17;2.17;2.17;2.17;2.17	5.1	5.1	0.69264	.	.	.	.	.	T	0.00012	0.0000	N	0.10707	0.03	0.40430	P	0.020066999999999946	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41448	-0.9508	8	0.07644	T	0.81	.	11.9223	0.52799	0.0811:0.0:0.9189:0.0	rs2280792;rs2280792	33;33;33	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	G	33	ENSP00000345395:S33G;ENSP00000403403:S33G;ENSP00000370558:S33G;ENSP00000451803:S33G;ENSP00000451729:S33G	ENSP00000216658:S33G	S	+	1	0	PAPLN	72781147	1.000000	0.71417	0.995000	0.50966	0.885000	0.51271	3.379000	0.52440	1.407000	0.46875	-0.215000	0.12644	AGC	A|0.795;G|0.205	0.205	strong		0.642	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
GAS8	2622	hgsc.bcm.edu	37	16	90095558	90095558	+	Intron	SNP	C	C	T	rs76646627		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:90095558C>T	ENST00000268699.4	+	2	212				GAS8_ENST00000536122.1_Intron|GAS8_ENST00000540721.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.G65S	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)		p.G65S(1)		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)		acggggcagcctacggggcag	0.672																																					p.G65S		Atlas-SNP	.											C16orf3,NS,carcinoma,0,2	C16orf3	14	2	1	Substitution - Missense(1)	lung(1)	c.G193A						scavenged	.						25.0	20.0	21.0					16																	90095558		2191	4298	6489	SO:0001627	intron_variant	750	exon1			GGCAGCCTACGGG	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1428C>T	16.37:g.90095558C>T		Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	247	13	0.0526316	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	C	9.046	0.990885	0.18966	.	.	ENSG00000221819	ENST00000408886	T	0.57595	0.39	1.2	-1.14	0.09741	.	.	.	.	.	T	0.23492	0.0568	N	0.08118	0	0.09310	N	1	B	0.22604	0.072	B	0.14578	0.011	T	0.14755	-1.0461	8	.	.	.	.	2.4936	0.04616	0.0:0.4385:0.3231:0.2384	.	73	O95177	CP003_HUMAN	S	65	ENSP00000386218:G65S	.	G	-	1	0	C16orf3	88623059	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.145000	0.10265	-0.326000	0.08564	0.407000	0.27541	GGC	C|0.500;T|0.500	0.500	weak		0.672	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
ZNF493	284443	hgsc.bcm.edu	37	19	21606429	21606429	+	Missense_Mutation	SNP	G	G	T	rs4621113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21606429G>T	ENST00000355504.4	+	2	850	c.584G>T	c.(583-585)tGt>tTt	p.C195F	ZNF493_ENST00000392288.2_Missense_Mutation_p.C323F|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	195			C -> F (in dbSNP:rs4621113). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.2}.		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(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						CCCTATAAATGTGAAGAATGT	0.333													.|||	2943	0.58766	0.6589	0.5476	5008	,	,		19736	0.6319		0.5	False		,,,				2504	0.5644				p.C323F		Atlas-SNP	.											.	ZNF493	178	.	0			c.G968T						PASS	.	G	PHE/CYS,PHE/CYS	2757,1641		867,1023,309	32.0	37.0	35.0		968,584	1.0	0.2	19	dbSNP_111	35	4437,4151		1205,2027,1062	no	missense,missense	ZNF493	NM_001076678.2,NM_175910.6	205,205	2072,3050,1371	TT,TG,GG		48.3349,37.3124,44.6019	probably-damaging,probably-damaging	323/775,195/647	21606429	7194,5792	2199	4294	6493	SO:0001583	missense	284443	exon4			ATAAATGTGAAGA	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.584G>T	19.37:g.21606429G>T	ENSP00000347691:p.Cys195Phe	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	35	0.614035	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	1284	0.5879120879120879	334	0.6788617886178862	202	0.5580110497237569	378	0.6608391608391608	370	0.48812664907651715	N	5.820	0.335504	0.11013	0.626876	0.516651	ENSG00000196268	ENST00000392288;ENST00000355504	D;D	0.85088	-1.94;-1.94	0.985	0.985	0.19779	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.94101	3.495	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.46992	-0.9151	8	0.87932	D	0	.	8.7583	0.34658	0.0:0.0:1.0:0.0	rs4621113;rs4621113	195;323	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	F	323;195	ENSP00000376110:C323F;ENSP00000347691:C195F	ENSP00000347691:C195F	C	+	2	0	ZNF493	21398269	1.000000	0.71417	0.194000	0.23346	0.190000	0.23558	6.598000	0.74122	0.399000	0.25367	0.404000	0.27445	TGT	G|0.458;T|0.542	0.542	strong		0.333	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
TRMT6	51605	hgsc.bcm.edu	37	20	5923203	5923203	+	Silent	SNP	T	T	C	rs394940|rs35671838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5923203T>C	ENST00000203001.2	-	7	1027	c.897A>G	c.(895-897)gaA>gaG	p.E299E	TRMT6_ENST00000473131.1_5'UTR|TRMT6_ENST00000453074.2_Silent_p.E129E	NM_015939.3	NP_057023.2	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6 homolog (S. cerevisiae)	299			E -> G (in dbSNP:rs451571). {ECO:0000269|PubMed:10810093, ECO:0000269|PubMed:14702039}.		regulation of translational initiation (GO:0006446)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	15						CATTCTCTTGTTCAGAAGCCT	0.448													T|||	1480	0.295527	0.5628	0.245	5008	,	,		20654	0.1994		0.1074	False		,,,				2504	0.2628				p.E299E		Atlas-SNP	.											.	TRMT6	28	.	0			c.A897G						PASS	.	T		2134,2272		531,1072,600	154.0	149.0	151.0		897	-12.3	0.0	20	dbSNP_80	151	900,7700		55,790,3455	no	coding-synonymous	TRMT6	NM_015939.3		586,1862,4055	CC,CT,TT		10.4651,48.434,23.3277		299/498	5923203	3034,9972	2203	4300	6503	SO:0001819	synonymous_variant	51605	exon7			CTCTTGTTCAGAA	AK000613	CCDS13093.1, CCDS63225.1	20p12.3	2009-01-12			ENSG00000089195	ENSG00000089195			20900	protein-coding gene	gene with protein product						16043508	Standard	NM_001281467		Approved	GCD10, MGC5029, Gcd10p, CGI-09	uc002wmh.1	Q9UJA5	OTTHUMG00000031816	ENST00000203001.2:c.897A>G	20.37:g.5923203T>C		Somatic	362	2	0.00552486		WXS	Illumina HiSeq	Phase_I	342	339	0.991228	NM_015939	B4DUV6|Q76P92|Q9BQV5|Q9ULR7|Q9Y2Z8	Silent	SNP	ENST00000203001.2	37	CCDS13093.1																																																																																			T|0.772;C|0.228	0.228	strong		0.448	TRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077889.2		
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642817	1642817	+	Silent	SNP	A	A	G	rs540908783|rs374921824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1642817A>G	ENST00000399682.1	-	1	551	c.507T>C	c.(505-507)ggT>ggC	p.G169G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ATGACCCACAACCTGAGGAGG	0.612													a|||	106	0.0211661	0.0393	0.0115	5008	,	,		14637	0.0119		0.0209	False		,,,				2504	0.0133				p.G169G		Atlas-SNP	.											KRTAP5-4,colon,carcinoma,0,3	KRTAP5-4	78	3	0			c.T507C						scavenged	.						24.0	35.0	32.0					11																	1642817		692	1591	2283	SO:0001819	synonymous_variant	387267	exon1			CCCACAACCTGAG	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.507T>C	11.37:g.1642817A>G		Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	186	8	0.0430108	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.612	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
TRMT11	60487	hgsc.bcm.edu	37	6	126319453	126319453	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:126319453C>T	ENST00000334379.5	+	5	500	c.379C>T	c.(379-381)Cga>Tga	p.R127*	TRMT11_ENST00000450358.1_Nonsense_Mutation_p.R127*|TRMT11_ENST00000368332.3_Nonsense_Mutation_p.R127*	NM_001031712.2	NP_001026882.2	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	127					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)|tRNA binding (GO:0000049)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(226;0.0356)		GAAAATCAAGCGAATAGATGT	0.303																																					p.R127X		Atlas-SNP	.											TRMT11,NS,carcinoma,-1,2	TRMT11	43	2	0			c.C379T						PASS	.						38.0	37.0	37.0					6																	126319453		2166	4290	6456	SO:0001587	stop_gained	60487	exon5			ATCAAGCGAATAG	AF182423	CCDS35496.1	6q11.1-q22.33	2009-06-15	2006-11-28	2006-11-28	ENSG00000066651	ENSG00000066651			21080	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 75"""	C6orf75			Standard	XM_006715546		Approved	MDS024, dJ187J11.2, TRM11, TRMT11-1	uc003qam.3	Q7Z4G4	OTTHUMG00000015515	ENST00000334379.5:c.379C>T	6.37:g.126319453C>T	ENSP00000333934:p.Arg127*	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	48	12	0.25	NM_001031712	E1P570|Q5JY11|Q6PGQ5|Q9HC13	Nonsense_Mutation	SNP	ENST00000334379.5	37	CCDS35496.1	.	.	.	.	.	.	.	.	.	.	C	36	5.666307	0.96745	.	.	ENSG00000066651	ENST00000334379;ENST00000450358;ENST00000368332;ENST00000444121;ENST00000446681	.	.	.	5.95	4.04	0.47022	.	0.174050	0.50627	D	0.000111	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-10.3198	12.802	0.57591	0.508:0.492:0.0:0.0	.	.	.	.	X	127;127;127;64;64	.	ENSP00000333934:R127X	R	+	1	2	TRMT11	126361146	1.000000	0.71417	0.963000	0.40424	0.939000	0.58152	5.384000	0.66225	1.483000	0.48342	0.655000	0.94253	CGA	.	.	none		0.303	TRMT11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_021820	
INSR	3643	hgsc.bcm.edu	37	19	7141775	7141775	+	Silent	SNP	G	G	A	rs2229431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7141775G>A	ENST00000302850.5	-	13	2737	c.2595C>T	c.(2593-2595)aaC>aaT	p.N865N	INSR_ENST00000341500.5_Silent_p.N853N	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	865	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)"""	AGTGGACGACGTTGTTCTCAA	0.502													G|||	435	0.086861	0.174	0.0519	5008	,	,		21956	0.0685		0.0686	False		,,,				2504	0.0317				p.N865N		Atlas-SNP	.											.	INSR	265	.	0			c.C2595T						PASS	.	G	,	671,3735	285.7+/-278.4	52,567,1584	178.0	131.0	147.0		2595,2559	-6.3	0.0	19	dbSNP_98	147	494,8106	142.6+/-198.8	15,464,3821	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	67,1031,5405	AA,AG,GG		5.7442,15.2292,8.9574	,	865/1383,853/1371	7141775	1165,11841	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon13			GACGACGTTGTTC	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.2595C>T	19.37:g.7141775G>A		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	260	134	0.515385	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			G|0.905;A|0.095	0.095	strong		0.502	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
SCP2	6342	hgsc.bcm.edu	37	1	53453714	53453714	+	Silent	SNP	G	G	T	rs7538935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53453714G>T	ENST00000528311.1	+	10	1040	c.744G>T	c.(742-744)acG>acT	p.T248T	SCP2_ENST00000371513.5_Silent_p.T285T|SCP2_ENST00000407246.2_Silent_p.T305T|SCP2_ENST00000473584.1_3'UTR|SCP2_ENST00000371514.3_Silent_p.T329T|SCP2_ENST00000371509.4_Silent_p.T285T	NM_001193617.1	NP_001180546.1	Q9BX26	SYCP2_HUMAN	sterol carrier protein 2	0					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	15						AAGGTGCAACGCTGGTTGATA	0.363													G|||	959	0.191494	0.553	0.1009	5008	,	,		16400	0.0407		0.0318	False		,,,				2504	0.0869				p.T329T		Atlas-SNP	.											SCP2,NS,carcinoma,0,1	SCP2	44	1	0			c.G987T						PASS	.	G	,,,,	1882,2524	539.1+/-375.2	421,1040,742	76.0	86.0	83.0		855,915,855,744,987	-4.8	0.2	1	dbSNP_116	83	386,8214	124.4+/-183.2	6,374,3920	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCP2	NM_001007098.2,NM_001193599.1,NM_001193600.1,NM_001193617.1,NM_002979.4	,,,,	427,1414,4662	TT,TG,GG		4.4884,42.7145,17.4381	,,,,	285/323,305/524,285/504,248/467,329/548	53453714	2268,10738	2203	4300	6503	SO:0001819	synonymous_variant	6342	exon11			TGCAACGCTGGTT	M75884	CCDS572.1, CCDS30719.1, CCDS41338.1, CCDS44149.1, CCDS44150.1, CCDS53317.1, CCDS53318.1, CCDS53319.1	1p32	2010-08-20			ENSG00000116171	ENSG00000116171			10606	protein-coding gene	gene with protein product		184755				1703300, 1718316	Standard	NM_001007098		Approved		uc001cur.2	P22307	OTTHUMG00000008936	ENST00000528311.1:c.744G>T	1.37:g.53453714G>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_002979	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Silent	SNP	ENST00000528311.1	37	CCDS53319.1																																																																																			G|0.815;T|0.185	0.185	strong		0.363	SCP2-010	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387558.1	NM_002979	
PCDH8	5100	hgsc.bcm.edu	37	13	53420886	53420886	+	Silent	SNP	G	G	A	rs5030684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:53420886G>A	ENST00000377942.3	-	1	1889	c.1686C>T	c.(1684-1686)taC>taT	p.Y562Y	PCDH8_ENST00000338862.4_Silent_p.Y562Y	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	562	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		TGCGCAGCGCGTAGATGGCTC	0.677													G|||	253	0.0505192	0.0643	0.0821	5008	,	,		15542	0.0109		0.0547	False		,,,				2504	0.046				p.Y562Y	GBM(36;25 841 9273 49207)	Atlas-SNP	.											.	PCDH8	95	.	0			c.C1686T						PASS	.	G	,	283,4063		13,257,1903	12.0	13.0	12.0		1686,1686	1.3	1.0	13	dbSNP_113	12	488,8036		15,458,3789	no	coding-synonymous,coding-synonymous	PCDH8	NM_002590.3,NM_032949.2	,	28,715,5692	AA,AG,GG		5.725,6.5117,5.9907	,	562/1071,562/974	53420886	771,12099	2173	4262	6435	SO:0001819	synonymous_variant	5100	exon1			CAGCGCGTAGATG	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"""Cadherins / Protocadherins : Non-clustered"""	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.1686C>T	13.37:g.53420886G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_002590	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Silent	SNP	ENST00000377942.3	37	CCDS9438.1																																																																																			G|0.951;A|0.049	0.049	strong		0.677	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590	
ZNF208	7757	hgsc.bcm.edu	37	19	22156470	22156470	+	Missense_Mutation	SNP	C	C	G	rs7255075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22156470C>G	ENST00000397126.4	-	4	1514	c.1366G>C	c.(1366-1368)Gaa>Caa	p.E456Q	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	456			E -> Q (in dbSNP:rs7255075).		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)				CCACATTCTTCACATTTGTAG	0.378													c|||	152	0.0303514	0.1089	0.0101	5008	,	,		21690	0.0		0.001	False		,,,				2504	0.0				p.E456Q		Atlas-SNP	.											ZNF208_ENST00000428290,NS,carcinoma,+2,3	ZNF208	817	3	0			c.G1366C						PASS	.	C	GLN/GLU	499,3789		22,455,1667	73.0	79.0	77.0		1366	0.6	0.0	19	dbSNP_116	77	3,8513		0,3,4255	no	missense	ZNF208	NM_007153.3	29	22,458,5922	GG,GC,CC		0.0352,11.6371,3.9206	possibly-damaging	456/1281	22156470	502,12302	2144	4258	6402	SO:0001583	missense	7757	exon4			ATTCTTCACATTT	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.1366G>C	19.37:g.22156470C>G	ENSP00000380315:p.Glu456Gln	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	63	0.028846153846153848	59	0.11991869918699187	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	12.09	1.832255	0.32421	0.116371	3.52E-4	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.18960	2.18	2.83	0.577	0.17385	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00328	0.0010	.	.	.	0.80722	P	0.0	P	0.44816	0.844	P	0.55667	0.781	T	0.13953	-1.0490	7	0.18710	T	0.47	.	3.6064	0.08043	0.0:0.2616:0.1947:0.5437	rs7255075;rs52824395;rs58613552;rs7255075	456	O43345	ZN208_HUMAN	Q	456	ENSP00000380315:E456Q	ENSP00000380315:E456Q	E	-	1	0	ZNF208	21948310	0.000000	0.05858	0.000000	0.03702	0.358000	0.29455	-4.155000	0.00284	-0.314000	0.08716	0.306000	0.20318	GAA	C|0.961;G|0.039	0.039	strong		0.378	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
NCAPD2	9918	hgsc.bcm.edu	37	12	6631169	6631169	+	Silent	SNP	C	C	A	rs917634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6631169C>A	ENST00000315579.5	+	15	2719	c.1920C>A	c.(1918-1920)atC>atA	p.I640I	NCAPD2_ENST00000545962.1_Silent_p.I595I	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	640					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						CCATTGGCATCATCAGCAAGA	0.423													C|||	2662	0.53155	0.5961	0.6225	5008	,	,		17799	0.5704		0.4742	False		,,,				2504	0.3988				p.I640I		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C1920A						PASS	.	C		2566,1840	635.7+/-396.4	758,1050,395	82.0	83.0	83.0		1920	5.0	1.0	12	dbSNP_86	83	3915,4685	547.1+/-385.1	903,2109,1288	no	coding-synonymous	NCAPD2	NM_014865.3		1661,3159,1683	AA,AC,CC		45.5233,41.7612,49.8308		640/1402	6631169	6481,6525	2203	4300	6503	SO:0001819	synonymous_variant	9918	exon15			TGGCATCATCAGC	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"""chromosome condensation related SMC associated protein 1"""	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.1920C>A	12.37:g.6631169C>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			C|0.475;A|0.524	0.524	strong		0.423	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
SHPK	23729	hgsc.bcm.edu	37	17	3526637	3526637	+	Missense_Mutation	SNP	C	C	T	rs150857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3526637C>T	ENST00000225519.3	-	4	745	c.643G>A	c.(643-645)Gag>Aag	p.E215K		NM_013276.2	NP_037408	Q9UHJ6	SHPK_HUMAN	sedoheptulokinase	215			E -> K (in dbSNP:rs150857). {ECO:0000269|PubMed:10673275}.		carbohydrate metabolic process (GO:0005975)|cellular response to interleukin-13 (GO:0035963)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|phosphorylation (GO:0016310)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|sedoheptulokinase activity (GO:0050277)			breast(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				COAD - Colon adenocarcinoma(5;0.0828)		ACTCACGTCTCTACGTTCCAG	0.562													C|||	1387	0.276957	0.4962	0.1744	5008	,	,		21811	0.2361		0.1113	False		,,,				2504	0.2658				p.E215K		Atlas-SNP	.											.	SHPK	34	.	0			c.G643A						PASS	.	C	LYS/GLU	1912,2494	547.3+/-377.3	430,1052,721	145.0	128.0	134.0		643	4.1	0.6	17	dbSNP_79	134	832,7768	191.4+/-237.6	54,724,3522	yes	missense	SHPK	NM_013276.2	56	484,1776,4243	TT,TC,CC		9.6744,43.3954,21.098	benign	215/479	3526637	2744,10262	2203	4300	6503	SO:0001583	missense	23729	exon4			ACGTCTCTACGTT	AF163573	CCDS11030.1	17p13	2008-02-08	2008-02-08	2008-02-08	ENSG00000197417	ENSG00000197417	2.7.1.14		1492	protein-coding gene	gene with protein product		605060	"""carbohydrate kinase-like"""	CARKL		10673275, 18186520	Standard	NM_013276		Approved	SHK	uc002fvz.1	Q9UHJ6	OTTHUMG00000090694	ENST00000225519.3:c.643G>A	17.37:g.3526637C>T	ENSP00000225519:p.Glu215Lys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	129	54	0.418605	NM_013276	B2R640|Q8WUH3	Missense_Mutation	SNP	ENST00000225519.3	37	CCDS11030.1	516	0.23626373626373626	253	0.5142276422764228	56	0.15469613259668508	121	0.21153846153846154	86	0.11345646437994723	C	12.44	1.937870	0.34189	0.433954	0.096744	ENSG00000197417	ENST00000225519	T	0.50277	0.75	5.15	4.12	0.48240	Carbohydrate kinase, FGGY, N-terminal (1);	0.397595	0.29093	N	0.013174	T	0.00012	0.0000	L	0.56280	1.765	0.35463	P	0.203353	B	0.30511	0.282	B	0.37198	0.243	T	0.51260	-0.8728	9	0.52906	T	0.07	.	15.4768	0.75489	0.0:0.8617:0.1383:0.0	rs150857;rs16953310;rs56508810;rs58041020;rs150857	215	Q9UHJ6	SHPK_HUMAN	K	215	ENSP00000225519:E215K	ENSP00000225519:E215K	E	-	1	0	SHPK	3473386	0.946000	0.32159	0.638000	0.29380	0.026000	0.11368	2.415000	0.44635	2.562000	0.86427	0.561000	0.74099	GAG	C|0.763;T|0.237	0.237	strong		0.562	SHPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207378.2		
LHB	3972	hgsc.bcm.edu	37	19	49519518	49519518	+	Missense_Mutation	SNP	G	G	T	rs116437960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49519518G>T	ENST00000221421.2	-	3	232	c.233C>A	c.(232-234)aCc>aAc	p.T78N	CTB-60B18.10_ENST00000600007.1_lincRNA	NM_000894.2	NP_000885.1	P01229	LSHB_HUMAN	luteinizing hormone beta polypeptide	78					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|male gonad development (GO:0008584)|peptide hormone processing (GO:0016486)|progesterone biosynthetic process (GO:0006701)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		ATCACGGTAGGTGCACACCAC	0.677													G|||	71	0.0141773	0.0507	0.0058	5008	,	,		17306	0.0		0.0	False		,,,				2504	0.0				p.T78N		Atlas-SNP	.											.	LHB	20	.	0			c.C233A						PASS	.	G	ASN/THR	181,4223	113.3+/-151.4	8,165,2029	89.0	80.0	83.0		233	1.4	1.0	19	dbSNP_132	83	3,8595	3.0+/-9.4	0,3,4296	no	missense	LHB	NM_000894.2	65	8,168,6325	TT,TG,GG		0.0349,4.1099,1.4152	benign	78/142	49519518	184,12818	2202	4299	6501	SO:0001583	missense	3972	exon3			CGGTAGGTGCACA		CCDS12748.1	19q13.3	2013-02-26				ENSG00000104826		"""Endogenous ligands"""	6584	protein-coding gene	gene with protein product	"""lutropin, beta chain"", ""interstitial cell stimulating hormone, beta chain"", ""luteinizing hormone beta subunit"""	152780				1191677	Standard	NM_000894		Approved	LSH-B, CGB4, hLHB	uc002plt.3	P01229		ENST00000221421.2:c.233C>A	19.37:g.49519518G>T	ENSP00000221421:p.Thr78Asn	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	119	48	0.403361	NM_000894	Q9UDI0	Missense_Mutation	SNP	ENST00000221421.2	37	CCDS12748.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	G	3.147	-0.175109	0.06421	0.041099	3.49E-4	ENSG00000104826	ENST00000221421;ENST00000391870	D	0.91792	-2.91	4.71	1.35	0.21983	Cystine knot (1);	0.000000	0.85682	D	0.000000	T	0.61185	0.2327	N	0.21448	0.665	0.45390	D	0.998374	B	0.10296	0.003	B	0.12156	0.007	T	0.66011	-0.6029	10	0.32370	T	0.25	-7.5582	11.6053	0.51029	0.0:0.0:0.6162:0.3838	.	78	P01229	LSHB_HUMAN	N	78;94	ENSP00000221421:T78N	ENSP00000221421:T78N	T	-	2	0	LHB	54211330	1.000000	0.71417	0.999000	0.59377	0.009000	0.06853	2.435000	0.44811	0.173000	0.19788	-3.593000	0.00028	ACC	G|0.988;T|0.012	0.012	strong		0.677	LHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466246.1	NM_000894	
RPP21	79897	hgsc.bcm.edu	37	6	30314567	30314567	+	Missense_Mutation	SNP	C	C	A	rs974963|rs35287137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30314567C>A	ENST00000442966.2	+	5	458	c.445C>A	c.(445-447)Cag>Aag	p.Q149K	TRIM39-RPP21_ENST00000513556.1_Missense_Mutation_p.Q410K|RPP21_ENST00000428040.2_Missense_Mutation_p.Q172K|RPP21_ENST00000436442.2_3'UTR|RPP21_ENST00000433076.2_Missense_Mutation_p.Q157K			Q9H633	RPP21_HUMAN	ribonuclease P/MRP 21kDa subunit	149			Q -> K (in dbSNP:rs974963). {ECO:0000269|PubMed:14574404}.		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						AATGCAGACTCAGGGTTCCAG	0.428													C|||	1866	0.372604	0.3018	0.4496	5008	,	,		21475	0.505		0.2435	False		,,,				2504	0.41				p.Q498K		Atlas-SNP	.											RPP21,NS,carcinoma,-1,1	.	.	1	0			c.C1492A						PASS	.	C	LYS/GLN,LYS/GLN,,LYS/GLN	839,2183		114,611,786	159.0	163.0	162.0		1492,469,,445	3.1	0.0	6	dbSNP_86	162	1309,4109		159,991,1559	yes	missense,missense,utr-3,missense	RPP21,TRIM39-RPP21	NM_001199119.1,NM_001199120.1,NM_001199121.1,NM_024839.2	53,53,,53	273,1602,2345	AA,AC,CC		24.1602,27.7631,25.4502	,,,	498/504,157/163,,149/155	30314567	2148,6292	1511	2709	4220	SO:0001583	missense	202658	exon10			CAGACTCAGGGTT	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.445C>A	6.37:g.30314567C>A	ENSP00000403833:p.Gln149Lys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	152	75	0.493421	NM_001199119	A2AAZ8|B0S834|B0S835|Q5JPL9|Q5JPM1|Q5STF8|Q5STF9|Q5STG2|Q5SU41|Q5SU42|Q86Y49|Q86Y50|Q86Y51|Q96F16	Missense_Mutation	SNP	ENST00000442966.2	37	CCDS4679.1	689	0.31547619047619047	141	0.2865853658536585	133	0.3674033149171271	256	0.44755244755244755	159	0.20976253298153033	C	9.914	1.210278	0.22289	0.277631	0.241602	ENSG00000204599;ENSG00000248167;ENSG00000241370;ENSG00000241370;ENSG00000241370	ENST00000412529;ENST00000513556;ENST00000433076;ENST00000442966;ENST00000428040	T;T;T;T	0.42131	0.98;1.52;1.52;1.52	4.94	3.1	0.35709	.	0.447252	0.19787	N	0.106087	T	0.14098	0.0341	N	0.19112	0.55	0.58432	P	1.0000000000287557E-6	B;B;B	0.10296	0.001;0.003;0.0	B;B;B	0.11329	0.006;0.004;0.0	T	0.06570	-1.0819	9	0.87932	D	0	-0.2296	11.6618	0.51352	0.0:0.6551:0.3449:0.0	rs974963;rs1060066;rs3173395;rs974963	412;149;172	F5H2V3;Q9H633;Q9H633-2	.;RPP21_HUMAN;.	K	412;410;157;149;172	ENSP00000424048:Q410K;ENSP00000409799:Q157K;ENSP00000403833:Q149K;ENSP00000394320:Q172K	ENSP00000394320:Q172K	Q	+	1	0	RPP21;TRIM39-RPP21;TRIM39	30422546	0.197000	0.23362	0.001000	0.08648	0.006000	0.05464	1.778000	0.38614	0.743000	0.32719	0.655000	0.94253	CAG	C|0.718;A|0.282	0.282	strong		0.428	RPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076451.2	NM_024839	
ALOX5	240	hgsc.bcm.edu	37	10	45878050	45878050	+	Silent	SNP	G	G	A	rs2228064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:45878050G>A	ENST00000374391.2	+	2	323	c.270G>A	c.(268-270)acG>acA	p.T90T	ALOX5_ENST00000542434.1_Silent_p.T90T	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	90	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	CGCTGAAGACGCCCCACGGGG	0.597													G|||	607	0.121206	0.3608	0.0519	5008	,	,		20104	0.0714		0.006	False		,,,				2504	0.0164				p.T90T		Atlas-SNP	.											ALOX5,right_lower_lobe,carcinoma,+1,1	ALOX5	88	1	0			c.G270A						PASS	.	G		1229,3177	423.8+/-340.2	151,927,1125	107.0	79.0	88.0		270	-6.7	0.8	10	dbSNP_98	88	40,8560	25.1+/-72.6	0,40,4260	yes	coding-synonymous	ALOX5	NM_000698.2		151,967,5385	AA,AG,GG		0.4651,27.8938,9.757		90/675	45878050	1269,11737	2203	4300	6503	SO:0001819	synonymous_variant	240	exon2			GAAGACGCCCCAC	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"""Arachidonate lipoxygenases"""	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.270G>A	10.37:g.45878050G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Silent	SNP	ENST00000374391.2	37	CCDS7212.1																																																																																			G|0.902;A|0.098	0.098	strong		0.597	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1		
SERPINI2	5276	hgsc.bcm.edu	37	3	167184878	167184878	+	Missense_Mutation	SNP	T	T	C	rs9841174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:167184878T>C	ENST00000476257.1	-	4	741	c.443A>G	c.(442-444)gAg>gGg	p.E148G	SERPINI2_ENST00000264677.4_Missense_Mutation_p.E148G|SERPINI2_ENST00000471111.1_Missense_Mutation_p.E148G|SERPINI2_ENST00000461846.1_Missense_Mutation_p.E148G|SERPINI2_ENST00000465031.1_5'Flank			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	148			E -> G (in dbSNP:rs9841174).		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						ACTTATCATCTCTGCACAAGC	0.338													t|||	2066	0.41254	0.3737	0.379	5008	,	,		14394	0.506		0.4006	False		,,,				2504	0.4049				p.E158G		Atlas-SNP	.											.	SERPINI2	85	.	0			c.A473G						PASS	.	C	GLY/GLU	1610,2796	496.5+/-363.6	307,996,900	93.0	93.0	93.0		443	3.3	1.0	3	dbSNP_119	93	3261,5339	488.2+/-372.3	638,1985,1677	yes	missense	SERPINI2	NM_006217.3	98	945,2981,2577	CC,CT,TT		37.9186,36.5411,37.4519	possibly-damaging	148/406	167184878	4871,8135	2203	4300	6503	SO:0001583	missense	5276	exon4			ATCATCTCTGCAC	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.443A>G	3.37:g.167184878T>C	ENSP00000420621:p.Glu148Gly	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_001012303		Missense_Mutation	SNP	ENST00000476257.1	37	CCDS3200.1	929	0.42536630036630035	202	0.4105691056910569	144	0.39779005524861877	282	0.493006993006993	301	0.3970976253298153	t	15.95	2.984489	0.53934	0.365411	0.379186	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111;ENST00000466903;ENST00000467583	D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.7	3.34	0.38264	Serpin domain (3);	0.464061	0.24613	N	0.037024	T	0.00012	0.0000	L	0.42632	1.34	0.43683	P	0.003878999999999966	P	0.40578	0.722	B	0.43990	0.438	T	0.30238	-0.9985	9	0.52906	T	0.07	.	10.0587	0.42261	0.0:0.1354:0.0:0.8646	rs9841174;rs52836184;rs61562449;rs9841174	148	O75830	SPI2_HUMAN	G	148;148;148;148;148;133	ENSP00000420621:E148G;ENSP00000417692:E148G;ENSP00000264677:E148G;ENSP00000419407:E148G;ENSP00000417752:E148G;ENSP00000419255:E133G	ENSP00000264677:E148G	E	-	2	0	SERPINI2	168667572	1.000000	0.71417	0.966000	0.40874	0.567000	0.35839	2.515000	0.45512	0.452000	0.26830	-0.253000	0.11424	GAG	C|0.395;N|0.001	0.395	strong		0.338	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
OR51Q1	390061	hgsc.bcm.edu	37	11	5443700	5443700	+	Silent	SNP	C	C	T	rs2736588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5443700C>T	ENST00000300778.4	+	1	360	c.270C>T	c.(268-270)aaC>aaT	p.N90N	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	90						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCTGGTTCAACGTTCGTAGAA	0.517													C|||	2272	0.453674	0.2799	0.3991	5008	,	,		23503	0.7024		0.3986	False		,,,				2504	0.5276				p.N90N		Atlas-SNP	.											.	OR51Q1	79	.	0			c.C270T						PASS	.	C		1332,3070	447.3+/-348.3	203,926,1072	158.0	141.0	147.0		270	-2.3	0.0	11	dbSNP_100	147	3373,5221	499.6+/-375.0	676,2021,1600	no	coding-synonymous	OR51Q1	NM_001004757.2		879,2947,2672	TT,TC,CC		39.2483,30.259,36.2034		90/318	5443700	4705,8291	2201	4297	6498	SO:0001819	synonymous_variant	390061	exon1			GTTCAACGTTCGT	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.270C>T	11.37:g.5443700C>T		Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	198	198	1	NM_001004757	B2RNN1	Silent	SNP	ENST00000300778.4	37	CCDS31381.1																																																																																			C|0.602;T|0.398	0.398	strong		0.517	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
OR10Q1	219960	hgsc.bcm.edu	37	11	57996289	57996289	+	Missense_Mutation	SNP	G	G	A	rs112800197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57996289G>A	ENST00000316770.2	-	1	101	c.59C>T	c.(58-60)gCg>gTg	p.A20V		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				TGTGGTGAACGCACGGAACAC	0.507													g|||	51	0.0101837	0.0378	0.0014	5008	,	,		17105	0.0		0.0	False		,,,				2504	0.0				p.A20V		Atlas-SNP	.											.	OR10Q1	79	.	0			c.C59T						PASS	.	G	VAL/ALA	114,4248		1,112,2068	126.0	133.0	130.0		59	-1.3	0.0	11	dbSNP_132	130	0,8558		0,0,4279	yes	missense	OR10Q1	NM_001004471.2	64	1,112,6347	AA,AG,GG		0.0,2.6135,0.8824	benign	20/320	57996289	114,12806	2181	4279	6460	SO:0001583	missense	219960	exon1			GTGAACGCACGGA	AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475		"""GPCR / Class A : Olfactory receptors"""	15134	protein-coding gene	gene with protein product							Standard	NM_001004471		Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.59C>T	11.37:g.57996289G>A	ENSP00000314324:p.Ala20Val	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	212	103	0.485849	NM_001004471	Q6IFG4	Missense_Mutation	SNP	ENST00000316770.2	37	CCDS31547.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	G	2.409	-0.335766	0.05278	0.026135	0.0	ENSG00000180475	ENST00000316770	T	0.00330	8.08	4.98	-1.34	0.09143	.	0.376700	0.19161	N	0.121185	T	0.00039	0.0001	N	0.10760	0.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33574	-0.9863	10	0.51188	T	0.08	.	7.7104	0.28673	0.3775:0.1422:0.4802:0.0	.	20	Q8NGQ4	O10Q1_HUMAN	V	20	ENSP00000314324:A20V	ENSP00000314324:A20V	A	-	2	0	OR10Q1	57752865	0.000000	0.05858	0.000000	0.03702	0.206000	0.24218	-0.355000	0.07671	-0.439000	0.07222	-0.295000	0.09555	GCG	G|0.991;A|0.009	0.009	strong		0.507	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471	
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346197	39346197	+	Missense_Mutation	SNP	G	G	A	rs139370444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39346197G>A	ENST00000398470.1	+	1	59	c.59G>A	c.(58-60)aGg>aAg	p.R20K	KRTAP9-1_ENST00000377723.3_Intron|KRTAP9-1_ENST00000318329.5_5'Flank	NM_001190460.1	NP_001177389.1	A8MXZ3	KRA91_HUMAN	keratin associated protein 9-1	20	30 X 5 AA repeats of C-C-[CGSVRQH]- [SQTNP]-[PTSI].					keratin filament (GO:0045095)				breast(1)|lung(3)	4						ACCTGCTGCAGGACAACCTGC	0.622													.|||	51	0.0101837	0.0371	0.0014	5008	,	,		18874	0.0		0.001	False		,,,				2504	0.0				p.R20K		Atlas-SNP	.											.	KRTAP9-1	34	.	0			c.G59A						PASS	.																																			SO:0001583	missense	728318	exon1			GCTGCAGGACAAC	AC006070	CCDS56029.1	17q21.2	2010-06-03			ENSG00000240542	ENSG00000240542		"""Keratin associated proteins"""	18912	protein-coding gene	gene with protein product			"""keratin associated protein 9-like 3"""	KRTAP9L3			Standard	NM_001190460		Approved	KAP9.1	uc021txf.1	A8MXZ3	OTTHUMG00000133636	ENST00000398470.1:c.59G>A	17.37:g.39346197G>A	ENSP00000381488:p.Arg20Lys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_001190460		Missense_Mutation	SNP	ENST00000398470.1	37	CCDS56029.1	22	0.010073260073260074	21	0.042682926829268296	1	0.0027624309392265192	0	0.0	0	0.0	G	2.812	-0.246655	0.05867	.	.	ENSG00000240542	ENST00000398470	T	0.00616	6.2	3.53	0.028	0.14157	.	.	.	.	.	T	0.00241	0.0007	L	0.56769	1.78	0.09310	N	1	.	.	.	.	.	.	T	0.40776	-0.9545	7	0.06099	T	0.92	.	6.7368	0.23413	0.4053:0.0:0.5947:0.0	.	.	.	.	K	20	ENSP00000381488:R20K	ENSP00000381488:R20K	R	+	2	0	KRTAP9-1	36599723	0.000000	0.05858	0.001000	0.08648	0.089000	0.18198	0.179000	0.16840	0.163000	0.19507	0.467000	0.42956	AGG	G|0.992;A|0.008	0.008	strong		0.622	KRTAP9-1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257781.1		
CNTD1	124817	hgsc.bcm.edu	37	17	40957849	40957849	+	Missense_Mutation	SNP	G	G	A	rs61995868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40957849G>A	ENST00000588408.1	+	4	803	c.527G>A	c.(526-528)cGa>cAa	p.R176Q	CNTD1_ENST00000588527.1_Missense_Mutation_p.R93Q|CNTD1_ENST00000315066.5_3'UTR	NM_173478.2	NP_775749.2	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1	176	Cyclin N-terminal.									central_nervous_system(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		TTGAACTTCCGAATTAATCTG	0.438													A|||	698	0.139377	0.3865	0.0346	5008	,	,		18180	0.0397		0.005	False		,,,				2504	0.1207				p.R176Q		Atlas-SNP	.											.	CNTD1	22	.	0			c.G527A						PASS	.	A	GLN/ARG	1454,2952	681.0+/-403.9	247,960,996	103.0	97.0	99.0		527	5.8	1.0	17	dbSNP_129	99	18,8582	818.5+/-406.9	0,18,4282	yes	missense	CNTD1	NM_173478.2	43	247,978,5278	AA,AG,GG		0.2093,33.0005,11.3179	benign	176/331	40957849	1472,11534	2203	4300	6503	SO:0001583	missense	124817	exon4			ACTTCCGAATTAA	AK097456	CCDS11440.1	17q21.31	2014-07-03	2006-03-31	2006-03-31	ENSG00000176563	ENSG00000176563			26847	protein-coding gene	gene with protein product			"""cyclin N-terminal domain containing"""	CNTD		24891606	Standard	NM_173478		Approved	FLJ40137	uc002ibm.4	Q8N815		ENST00000588408.1:c.527G>A	17.37:g.40957849G>A	ENSP00000465204:p.Arg176Gln	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	146	74	0.506849	NM_173478	Q658Q6|Q8NEP1	Missense_Mutation	SNP	ENST00000588408.1	37	CCDS11440.1	229	0.10485347985347986	193	0.39227642276422764	10	0.027624309392265192	22	0.038461538461538464	4	0.005277044854881266	A	8.649	0.897733	0.17686	0.330005	0.002093	ENSG00000176563	ENST00000315066	.	.	.	5.78	5.78	0.91487	Cyclin, N-terminal (1);Cyclin-like (2);	0.161867	0.56097	N	0.000032	T	0.00012	0.0000	N	0.01146	-0.985	0.54753	P	1.2000000000012001E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.34925	-0.9809	8	0.02654	T	1	-3.9094	11.9544	0.52973	0.9322:0.0:0.0678:0.0	rs61995868	176	Q8N815	CNTD1_HUMAN	Q	176	.	ENSP00000316647:R176Q	R	+	2	0	CNTD1	38211375	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.746000	0.47467	1.012000	0.39366	-0.269000	0.10298	CGA	G|0.891;A|0.109	0.109	strong		0.438	CNTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452398.1	NM_173478	
PRKACA	5566	hgsc.bcm.edu	37	19	14204527	14204527	+	Silent	SNP	G	G	C	rs3729858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14204527G>C	ENST00000308677.4	-	9	1039	c.843C>G	c.(841-843)cgC>cgG	p.R281R	PRKACA_ENST00000590853.1_Intron|PRKACA_ENST00000350356.3_5'UTR|SAMD1_ENST00000541938.1_5'Flank|PRKACA_ENST00000589994.1_Silent_p.R273R	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	281	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						GGTTCCCAAAGCGCTTGGTGA	0.547													G|||	29	0.00579073	0.0219	0.0	5008	,	,		20834	0.0		0.0	False		,,,				2504	0.0				p.R281R		Atlas-SNP	.											.	PRKACA	65	.	0			c.C843G						PASS	.	G	,	80,4326	69.2+/-107.0	1,78,2124	142.0	126.0	131.0		843,819	5.2	1.0	19	dbSNP_107	131	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PRKACA	NM_002730.3,NM_207518.1	,	1,78,6424	CC,CG,GG		0.0,1.8157,0.6151	,	281/352,273/344	14204527	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	5566	exon9			CCCAAAGCGCTTG		CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	2.7.11.1		9380	protein-coding gene	gene with protein product		601639				8884279	Standard	NM_002730		Approved	PKACa	uc002myc.3	P17612		ENST00000308677.4:c.843C>G	19.37:g.14204527G>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	165	85	0.515152	NM_002730	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Silent	SNP	ENST00000308677.4	37	CCDS12304.1																																																																																			G|0.995;C|0.005	0.005	strong		0.547	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730	
IFITM3	10410	hgsc.bcm.edu	37	11	320723	320723	+	Missense_Mutation	SNP	C	C	T	rs199582787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:320723C>T	ENST00000399808.4	-	1	327	c.91G>A	c.(91-93)Gtg>Atg	p.V31M	RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.V10M|IFITM3_ENST00000526811.1_Missense_Mutation_p.V10M|RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.14_ENST00000602809.1_lincRNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	31					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-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;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		GCCCCCAGCACAGCCACCTCG	0.612																																					p.V31M		Atlas-SNP	.											IFITM3,brain,glioma,0,1	IFITM3	132	1	0			c.G91A						scavenged	.						87.0	98.0	95.0					11																	320723		1967	4140	6107	SO:0001583	missense	10410	exon1			CCAGCACAGCCAC	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"""interferon induced transmembrane protein 3 (1-8U)"""			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.91G>A	11.37:g.320723C>T	ENSP00000382707:p.Val31Met	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	4	0.0412371	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	CCDS41585.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.526447	0.27299	.	.	ENSG00000142089	ENST00000399808;ENST00000270031;ENST00000526811	T;T	0.79454	-1.03;-1.27	4.61	-4.91	0.03085	.	11.488500	0.02440	N	0.084490	T	0.64516	0.2605	L	0.39147	1.195	0.09310	N	1	B	0.16802	0.019	B	0.15484	0.013	T	0.46400	-0.9194	10	0.13108	T	0.6	0.9022	6.4601	0.21952	0.1231:0.361:0.0:0.5159	.	31	Q01628	IFM3_HUMAN	M	31;15;10	ENSP00000382707:V31M;ENSP00000432108:V10M	ENSP00000372047:V15M	V	-	1	0	IFITM3	310723	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-1.638000	0.02013	-0.562000	0.06086	-1.790000	0.00627	GTG	.	.	weak		0.612	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034	
GBP4	115361	hgsc.bcm.edu	37	1	89655994	89655994	+	Silent	SNP	C	C	T	rs1410871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89655994C>T	ENST00000355754.6	-	7	1021	c.924G>A	c.(922-924)ggG>ggA	p.G308G		NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	308	GTPase domain (Globular). {ECO:0000250}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		CCACCAGAGTCCCCAGCCCTG	0.413													C|||	537	0.107228	0.3207	0.0403	5008	,	,		18431	0.0119		0.0298	False		,,,				2504	0.044				p.G308G		Atlas-SNP	.											.	GBP4	89	.	0			c.G924A						PASS	.	C		1199,3207	383.7+/-325.0	172,855,1176	56.0	58.0	57.0		924	-4.2	0.0	1	dbSNP_88	57	229,8371	89.4+/-151.6	1,227,4072	no	coding-synonymous	GBP4	NM_052941.4		173,1082,5248	TT,TC,CC		2.6628,27.2129,10.9795		308/641	89655994	1428,11578	2203	4300	6503	SO:0001819	synonymous_variant	115361	exon7			CAGAGTCCCCAGC	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.924G>A	1.37:g.89655994C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	156	84	0.538462	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Silent	SNP	ENST00000355754.6	37	CCDS721.1																																																																																			C|0.898;T|0.102	0.102	strong		0.413	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
TNS1	7145	hgsc.bcm.edu	37	2	218682474	218682474	+	Silent	SNP	A	A	G	rs12694422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218682474A>G	ENST00000171887.4	-	24	4721	c.4269T>C	c.(4267-4269)agT>agC	p.S1423S	TNS1_ENST00000419504.1_Silent_p.S1410S|TNS1_ENST00000430930.1_Silent_p.S1402S	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1423					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)		TGCTGCCCCCACTGGGACTGG	0.612													G|||	1887	0.376797	0.4009	0.428	5008	,	,		18286	0.246		0.4056	False		,,,				2504	0.4131				p.S1423S		Atlas-SNP	.											.	TNS1	251	.	0			c.T4269C						PASS	.	G		1721,2685	649.9+/-399.0	357,1007,839	77.0	70.0	73.0		4269	-5.5	0.7	2	dbSNP_121	73	3560,5040	628.6+/-398.1	744,2072,1484	no	coding-synonymous	TNS1	NM_022648.4		1101,3079,2323	GG,GA,AA		41.3953,39.0604,40.6043		1423/1736	218682474	5281,7725	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon24			GCCCCCACTGGGA	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.4269T>C	2.37:g.218682474A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			A|0.613;G|0.387	0.387	strong		0.612	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
CA6	765	hgsc.bcm.edu	37	1	9030964	9030964	+	Silent	SNP	C	C	T	rs3737665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9030964C>T	ENST00000377443.2	+	7	772	c.768C>T	c.(766-768)aaC>aaT	p.N256N	CA6_ENST00000377442.2_Silent_p.N196N|CA6_ENST00000476083.1_3'UTR|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	101	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	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		
MRPS9	64965	hgsc.bcm.edu	37	2	105705507	105705507	+	Silent	SNP	C	C	T	rs11538198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	34	0	0		WXS	Illumina HiSeq	Phase_I	48	17	0.354167	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	
GTDC1	79712	hgsc.bcm.edu	37	2	144966208	144966208	+	Silent	SNP	T	T	C	rs16823579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:144966208T>C	ENST00000392869.2	-	3	293	c.141A>G	c.(139-141)ttA>ttG	p.L47L	GTDC1_ENST00000241391.5_Silent_p.L47L|GTDC1_ENST00000463875.2_Intron|GTDC1_ENST00000344850.4_Silent_p.L47L|GTDC1_ENST00000542155.1_Silent_p.L47L|GTDC1_ENST00000392867.3_Silent_p.L47L|GTDC1_ENST00000409214.1_Silent_p.L47L|GTDC1_ENST00000467352.1_5'Flank|GTDC1_ENST00000409298.1_Silent_p.L47L	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	47					biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		GAGAGAAATATAAAGCAGATG	0.413													T|||	190	0.0379393	0.1384	0.0101	5008	,	,		16667	0.0		0.0	False		,,,				2504	0.0				p.L47L		Atlas-SNP	.											.	GTDC1	61	.	0			c.A141G						PASS	.	T	,,	568,3838	252.1+/-258.6	34,500,1669	81.0	82.0	82.0		141,141,141	-12.2	0.0	2	dbSNP_123	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	GTDC1	NM_001006636.3,NM_001164629.2,NM_024659.4	,,	34,502,5967	CC,CT,TT		0.0233,12.8915,4.3826	,,	47/459,47/459,47/374	144966208	570,12436	2203	4300	6503	SO:0001819	synonymous_variant	79712	exon4			GAAATATAAAGCA	AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			ENSG00000121964	ENSG00000121964		"""Glycosyltransferase group 1 domain containing"""	20887	protein-coding gene	gene with protein product	"""mannosyltransferase-like"""	610165				15068588, 21821951	Standard	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	Q4AE62	OTTHUMG00000131835	ENST00000392869.2:c.141A>G	2.37:g.144966208T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	64	41	0.640625	NM_001006636	A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Silent	SNP	ENST00000392869.2	37	CCDS33300.1																																																																																			T|0.957;C|0.043	0.043	strong		0.413	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2	NM_024659	
ELK1	2002	hgsc.bcm.edu	37	X	47498400	47498400	+	Missense_Mutation	SNP	C	C	T	rs1059579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47498400C>T	ENST00000247161.3	-	3	647	c.548G>A	c.(547-549)aGt>aAt	p.S183N	ELK1_ENST00000592066.1_Missense_Mutation_p.S129N|ELK1_ENST00000343894.4_Intron|ELK1_ENST00000376983.3_Missense_Mutation_p.S183N	NM_005229.4	NP_005220.2	P19419	ELK1_HUMAN	ELK1, member of ETS oncogene family	183			S -> N (in dbSNP:rs1059579). {ECO:0000269|PubMed:2539641}.		cell differentiation (GO:0030154)|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 transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|skin(2)	10						AGGAGCTGCACTGGGGAGCAC	0.672													T|||	537	0.142252	0.3366	0.0317	3775	,	,		12344	0.0625		0.005	False		,,,				2504	0.002				p.S183N		Atlas-SNP	.											.	ELK1	54	.	0			c.G548A						PASS	.	T	ASN/SER,ASN/SER	1349,2481		198,751,202,682,366	17.0	13.0	14.0		548,548	-0.9	0.3	X	dbSNP_86	14	28,6691		1,19,7,2407,1858	no	missense,missense	ELK1	NM_001114123.1,NM_005229.3	46,46	199,770,209,3089,2224	TT,TC,T,CC,C		0.4167,35.2219,13.0534	benign,benign	183/429,183/429	47498400	1377,9172	2199	4292	6491	SO:0001583	missense	2002	exon4			GCTGCACTGGGGA	M25269	CCDS14283.1, CCDS59165.1	Xp11.23	2010-07-20			ENSG00000126767	ENSG00000126767			3321	protein-coding gene	gene with protein product		311040				2539641	Standard	NM_001114123		Approved		uc010nhv.4	P19419	OTTHUMG00000021452	ENST00000247161.3:c.548G>A	X.37:g.47498400C>T	ENSP00000247161:p.Ser183Asn	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	180	59	0.327778	NM_001114123	B2R7H4|O75606|O95058|Q969X8|Q9UJM4	Missense_Mutation	SNP	ENST00000247161.3	37	CCDS14283.1	230	0.13863773357444242	123	0.33064516129032256	10	0.027932960893854747	26	0.046762589928057555	1	0.0013192612137203166	T	7.193	0.592017	0.13812	0.352219	0.004167	ENSG00000126767	ENST00000247161;ENST00000376983	T;T	0.21734	1.99;1.99	4.02	-0.858	0.10689	.	1.043230	0.07432	N	0.895821	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	0.9999999769773	B	0.02656	0.0	B	0.01281	0.0	T	0.49679	-0.8914	9	0.16420	T	0.52	.	10.7665	0.46297	0.0:0.6834:0.0:0.3166	rs1059579	183	P19419	ELK1_HUMAN	N	183	ENSP00000247161:S183N;ENSP00000366182:S183N	ENSP00000247161:S183N	S	-	2	0	ELK1	47383344	0.256000	0.24012	0.318000	0.25279	0.616000	0.37450	-0.277000	0.08502	-0.454000	0.07066	-0.407000	0.06327	AGT	C|0.847;T|0.153	0.153	strong		0.672	ELK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056436.1	NM_005229	
NFE2L3	9603	hgsc.bcm.edu	37	7	26224668	26224668	+	Silent	SNP	C	C	T	rs2074566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:26224668C>T	ENST00000056233.3	+	4	1609	c.1350C>T	c.(1348-1350)tgC>tgT	p.C450C		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	450					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						TAGGTTATTGCACTGACCATG	0.423													T|||	1783	0.35603	0.5325	0.2565	5008	,	,		22551	0.5466		0.1203	False		,,,				2504	0.2342				p.C450C		Atlas-SNP	.											.	NFE2L3	77	.	0			c.C1350T						PASS	.	T		2044,2362	609.9+/-391.4	468,1108,627	156.0	167.0	163.0		1350	-5.4	0.0	7	dbSNP_96	163	865,7735	779.5+/-407.7	52,761,3487	no	coding-synonymous	NFE2L3	NM_004289.6		520,1869,4114	TT,TC,CC		10.0581,46.3913,22.3666		450/695	26224668	2909,10097	2203	4300	6503	SO:0001819	synonymous_variant	9603	exon4			TTATTGCACTGAC	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"""basic leucine zipper proteins"""	7783	protein-coding gene	gene with protein product		604135	"""nuclear factor (erythroid-derived 2)-like 3"""			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1350C>T	7.37:g.26224668C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Silent	SNP	ENST00000056233.3	37	CCDS5396.1																																																																																			C|0.790;T|0.210	0.210	strong		0.423	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1		
MUC4	4585	hgsc.bcm.edu	37	3	195505839	195505839	+	Silent	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195505839A>T	ENST00000463781.3	-	2	13071	c.12612T>A	c.(12610-12612)ggT>ggA	p.G4204G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.G4204G	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.G4204G(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)		GGGTGGCGTGACCTGTGGATG	0.597																																					p.G4204G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,3	MUC4	1505	3	2	Substitution - coding silent(2)	kidney(2)	c.T12612A						scavenged	.						16.0	14.0	14.0					3																	195505839		689	1580	2269	SO:0001819	synonymous_variant	4585	exon2			GGCGTGACCTGTG	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.12612T>A	3.37:g.195505839A>T		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	281	6	0.0213523	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																																																																																			.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ARR3	407	hgsc.bcm.edu	37	X	69489530	69489530	+	Silent	SNP	C	C	T	rs3818862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:69489530C>T	ENST00000307959.8	+	3	78	c.27C>T	c.(25-27)agC>agT	p.S9S	ARR3_ENST00000374495.3_Silent_p.S9S	NM_004312.2	NP_004303.2	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	9					endocytosis (GO:0006897)|regulation of protein phosphorylation (GO:0001932)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)				endometrium(3)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	16						AGAAGACCAGCTCCAATGGGA	0.517													C|||	713	0.188874	0.1089	0.0778	3775	,	,		14008	0.3046		0.0437	False		,,,				2504	0.1677				p.S9S		Atlas-SNP	.											.	ARR3	41	.	0			c.C27T						PASS	.	C		448,3387		24,337,63,1271,508	53.0	51.0	52.0		27	2.7	1.0	X	dbSNP_107	52	395,6333		7,258,123,2163,1749	no	coding-synonymous	ARR3	NM_004312.2		31,595,186,3434,2257	TT,TC,T,CC,C		5.871,11.6819,7.9807		9/389	69489530	843,9720	2203	4300	6503	SO:0001819	synonymous_variant	407	exon3			GACCAGCTCCAAT		CCDS14399.1	Xq13.1	2013-10-11			ENSG00000120500	ENSG00000120500			710	protein-coding gene	gene with protein product	"""arrestin 4"""	301770				8224247	Standard	NM_004312		Approved	ARRX	uc004dyb.2	P36575	OTTHUMG00000021768	ENST00000307959.8:c.27C>T	X.37:g.69489530C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	141	67	0.475177	NM_004312	B5B0B9|Q5JT23|Q5JT24|Q6IBF5|Q96EN2	Silent	SNP	ENST00000307959.8	37	CCDS14399.1																																																																																			0|0.004;T|0.119	0.119	strong		0.517	ARR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057055.2	NM_004312	
SEMA6B	10501	hgsc.bcm.edu	37	19	4558422	4558422	+	Silent	SNP	C	C	A	rs115168835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4558422C>A	ENST00000586582.1	-	2	358	c.48G>T	c.(46-48)ctG>ctT	p.L16L	SEMA6B_ENST00000586965.1_Silent_p.L16L|SEMA6B_ENST00000301293.3_Silent_p.L16L	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	16					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)		GTAGCAGCAGCAGAAGCAGCA	0.736											OREG0025169	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	94	0.01877	0.0696	0.0029	5008	,	,		9644	0.0		0.0	False		,,,				2504	0.0				p.L16L		Atlas-SNP	.											.	SEMA6B	51	.	0			c.G48T						PASS	.	C		155,3605		0,155,1725	3.0	5.0	4.0		48	2.6	1.0	19	dbSNP_132	4	1,7703		0,1,3851	no	coding-synonymous	SEMA6B	NM_032108.3		0,156,5576	AA,AC,CC		0.013,4.1223,1.3608		16/889	4558422	156,11308	1880	3852	5732	SO:0001819	synonymous_variant	10501	exon2			CAGCAGCAGAAGC	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.48G>T	19.37:g.4558422C>A		Somatic	17	0	0	619	WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_032108	A5PKU4|F6IB19|Q9NRK9	Silent	SNP	ENST00000586582.1	37	CCDS12131.1																																																																																			C|0.985;A|0.015	0.015	strong		0.736	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
FLG	2312	hgsc.bcm.edu	37	1	152281136	152281136	+	Missense_Mutation	SNP	C	C	T	rs78125326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281136C>T	ENST00000368799.1	-	3	6261	c.6226G>A	c.(6226-6228)Gca>Aca	p.A2076T	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2076	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)			TGGCCACGTGCGGACTCTTTG	0.567									Ichthyosis				-|||	353	0.0704872	0.2496	0.0245	5008	,	,		29453	0.003		0.003	False		,,,				2504	0.0				p.A2076T		Atlas-SNP	.											.	FLG	900	.	0			c.G6226A						PASS	.	C	THR/ALA	898,3508		0,898,1305	315.0	259.0	278.0		6226	-4.7	0.0	1	dbSNP_131	278	11,8589		0,11,4289	no	missense	FLG	NM_002016.1	58	0,909,5594	TT,TC,CC		0.1279,20.3813,6.9891	benign	2076/4062	152281136	909,12097	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CACGTGCGGACTC	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.6226G>A	1.37:g.152281136C>T	ENSP00000357789:p.Ala2076Thr	Somatic	482	0	0		WXS	Illumina HiSeq	Phase_I	915	460	0.502732	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	125	0.05723443223443223	114	0.23170731707317074	9	0.024861878453038673	1	0.0017482517482517483	1	0.0013192612137203166	c	4.927	0.172270	0.09391	0.203813	0.001279	ENSG00000143631	ENST00000368799	T	0.01705	4.68	2.33	-4.66	0.03329	.	.	.	.	.	T	0.00241	0.0007	N	0.11064	0.09	0.09310	N	1	B	0.14438	0.01	B	0.12156	0.007	T	0.44360	-0.9333	9	0.13108	T	0.6	.	1.7607	0.02992	0.1438:0.1924:0.1433:0.5205	.	2076	P20930	FILA_HUMAN	T	2076	ENSP00000357789:A2076T	ENSP00000357789:A2076T	A	-	1	0	FLG	150547760	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.201000	0.01236	-2.043000	0.00913	-0.330000	0.08379	GCA	C|0.942;T|0.058	0.058	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CTNNA2	1496	hgsc.bcm.edu	37	2	80620370	80620370	+	Missense_Mutation	SNP	T	T	C	rs61754542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:80620370T>C	ENST00000402739.4	+	7	1096	c.1091T>C	c.(1090-1092)aTt>aCt	p.I364T	CTNNA2_ENST00000361291.4_Missense_Mutation_p.I398T|CTNNA2_ENST00000343114.3_Missense_Mutation_p.I43T|CTNNA2_ENST00000466387.1_Missense_Mutation_p.I364T|CTNNA2_ENST00000541047.1_Missense_Mutation_p.I364T|CTNNA2_ENST00000496558.1_Missense_Mutation_p.I364T|CTNNA2_ENST00000540488.1_Missense_Mutation_p.I364T	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	364					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CCTCTCAACATTGCGATTGAT	0.294													T|||	69	0.013778	0.0499	0.0014	5008	,	,		16684	0.0		0.001	False		,,,				2504	0.001				p.I364T		Atlas-SNP	.											.	CTNNA2	462	.	0			c.T1091C						PASS	.	T	THR/ILE,THR/ILE	161,3487		4,153,1667	99.0	93.0	95.0		1091,1091	5.9	1.0	2	dbSNP_129	95	4,8156		0,4,4076	yes	missense,missense	CTNNA2	NM_001164883.1,NM_004389.3	89,89	4,157,5743	CC,CT,TT		0.049,4.4134,1.3974	benign,benign	364/861,364/906	80620370	165,11643	1824	4080	5904	SO:0001583	missense	1496	exon8			TCAACATTGCGAT		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1091T>C	2.37:g.80620370T>C	ENSP00000384638:p.Ile364Thr	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	227	93	0.409692	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		24	0.01098901098901099	23	0.046747967479674794	0	0.0	0	0.0	1	0.0013192612137203166	T	8.517	0.867937	0.17250	0.044134	4.9E-4	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488;ENST00000343114;ENST00000409550	T;T;T;T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29;1.29;2.59;1.3	5.88	5.88	0.94601	.	0.135082	0.52532	D	0.000073	T	0.02342	0.0072	N	0.02142	-0.665	0.37091	D	0.89945	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.16808	-1.0390	9	.	.	.	.	15.9407	0.79750	0.0:0.0:0.0:1.0	rs61754542	364;364;364	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	T	364;364;398;364;364;364;43;29	ENSP00000418191:I364T;ENSP00000419295:I364T;ENSP00000355398:I398T;ENSP00000384638:I364T;ENSP00000444675:I364T;ENSP00000441705:I364T;ENSP00000341500:I43T;ENSP00000386587:I29T	.	I	+	2	0	CTNNA2	80473881	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.197000	0.42696	2.243000	0.73865	0.533000	0.62120	ATT	T|0.992;C|0.008	0.008	strong		0.294	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
ANKRD45	339416	hgsc.bcm.edu	37	1	173596273	173596273	+	Silent	SNP	A	A	G	rs12059068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173596273A>G	ENST00000333279.2	-	4	582	c.522T>C	c.(520-522)taT>taC	p.Y174Y		NM_198493.2	NP_940895.1	Q5TZF3	ANR45_HUMAN	ankyrin repeat domain 45	190										NS(2)|endometrium(2)|large_intestine(4)|lung(3)|skin(1)	12						CTTTTGCAATATATTTTTTCA	0.388													A|||	965	0.192692	0.6989	0.0504	5008	,	,		19880	0.0		0.005	False		,,,				2504	0.001				p.Y174Y		Atlas-SNP	.											.	ANKRD45	36	.	0			c.T522C						PASS	.	A		2539,1867	632.6+/-395.9	756,1027,420	124.0	128.0	127.0		522	-0.2	0.9	1	dbSNP_120	127	32,8568	19.2+/-60.6	0,32,4268	no	coding-synonymous	ANKRD45	NM_198493.2		756,1059,4688	GG,GA,AA		0.3721,42.374,19.7678		174/267	173596273	2571,10435	2203	4300	6503	SO:0001819	synonymous_variant	339416	exon4			TGCAATATATTTT		CCDS1309.1	1q25.1	2013-01-10			ENSG00000183831	ENSG00000183831		"""Ankyrin repeat domain containing"""	24786	protein-coding gene	gene with protein product	"""cancer/testis antigen 117"""						Standard	NM_198493		Approved	FLJ45235, CT117	uc001gja.1	Q5TZF3	OTTHUMG00000040546	ENST00000333279.2:c.522T>C	1.37:g.173596273A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_198493	A1A4G2|Q6ZST1	Silent	SNP	ENST00000333279.2	37	CCDS1309.1																																																																																			A|0.781;G|0.219	0.219	strong		0.388	ANKRD45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097580.2	NM_198493	
TCF4	6925	hgsc.bcm.edu	37	18	52901894	52901894	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:52901894A>G	ENST00000356073.4	-	16	1982	c.1371T>C	c.(1369-1371)gaT>gaC	p.D457D	TCF4_ENST00000564403.2_Silent_p.D463D|TCF4_ENST00000568673.1_Silent_p.D433D|TCF4_ENST00000457482.3_Silent_p.D297D|TCF4_ENST00000566279.1_Silent_p.D397D|TCF4_ENST00000566286.1_Silent_p.D454D|TCF4_ENST00000565018.2_Silent_p.D457D|TCF4_ENST00000567880.1_Silent_p.D397D|TCF4_ENST00000564999.1_Silent_p.D457D|TCF4_ENST00000543082.1_Silent_p.D415D|TCF4_ENST00000354452.3_Silent_p.D457D|TCF4_ENST00000540999.1_Silent_p.D433D|TCF4_ENST00000537856.3_Silent_p.D327D|TCF4_ENST00000570177.2_Silent_p.D327D|TCF4_ENST00000537578.1_Silent_p.D433D|TCF4_ENST00000568740.1_Silent_p.D432D|TCF4_ENST00000570287.2_Silent_p.D297D|TCF4_ENST00000398339.1_Silent_p.D559D|TCF4_ENST00000561992.1_Silent_p.D327D|TCF4_ENST00000564228.1_Silent_p.D386D|TCF4_ENST00000561831.3_Silent_p.D297D|TCF4_ENST00000544241.2_Silent_p.D386D	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	457					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GGGCCACGCCATCTTCACGAT	0.597											OREG0024990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D559D		Atlas-SNP	.											.	TCF4	178	.	0			c.T1677C						PASS	.						92.0	95.0	94.0					18																	52901894		2203	4300	6503	SO:0001819	synonymous_variant	6925	exon17			CACGCCATCTTCA	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"""Basic helix-loop-helix proteins"""	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1371T>C	18.37:g.52901894A>G		Somatic	70	0	0	988	WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Silent	SNP	ENST00000356073.4	37	CCDS11960.1																																																																																			.	.	none		0.597	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	
PRR12	57479	hgsc.bcm.edu	37	19	50100295	50100295	+	Silent	SNP	A	A	G	rs3745475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50100295A>G	ENST00000418929.2	+	4	2715	c.2703A>G	c.(2701-2703)ccA>ccG	p.P901P		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)		GCGTAGGCCCACCAAACTCGG	0.701													G|||	1877	0.3748	0.6263	0.3012	5008	,	,		9501	0.1915		0.2157	False		,,,				2504	0.4397				p.P901P		Atlas-SNP	.											.	PRR12	157	.	0			c.A2703G						PASS	.	G		1762,1864		429,904,480	4.0	6.0	6.0		2703	-9.3	0.0	19	dbSNP_107	6	1562,6316		152,1258,2529	no	coding-synonymous	PRR12	NM_020719.1		581,2162,3009	GG,GA,AA		19.8274,48.5935,28.8943		901/2037	50100295	3324,8180	1813	3939	5752	SO:0001819	synonymous_variant	57479	exon4			AGGCCCACCAAAC	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.2703A>G	19.37:g.50100295A>G		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_020719	E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	37	CCDS46143.1																																																																																			A|0.688;G|0.312	0.312	strong		0.701	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719	
OR52E6	390078	hgsc.bcm.edu	37	11	5862984	5862984	+	Missense_Mutation	SNP	G	G	C	rs10769272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5862984G>C	ENST00000329322.5	-	1	143	c.144C>G	c.(142-144)ttC>ttG	p.F48L	OR52E6_ENST00000379946.2_Missense_Mutation_p.F52L|TRIM5_ENST00000380027.1_Intron	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	143	0	0		WXS	Illumina HiSeq	Phase_I	146	77	0.527397	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	
PSG8	440533	hgsc.bcm.edu	37	19	43268235	43268235	+	Missense_Mutation	SNP	A	A	C	rs75257969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43268235A>C	ENST00000306511.4	-	2	360	c.263T>G	c.(262-264)aTa>aGa	p.I88R	PSG8_ENST00000406636.3_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.I88R|PSG8_ENST00000401467.2_Missense_Mutation_p.I88R	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	88	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)				ATATATAATTATTTGACCGTC	0.443													.|||	881	0.175919	0.444	0.134	5008	,	,		22187	0.0238		0.0726	False		,,,				2504	0.1063				p.I88R		Atlas-SNP	.											.	PSG8	101	.	0			c.T263G						PASS	.	C	ARG/ILE,,ARG/ILE	1670,2736	508.4+/-367.0	332,1006,865	260.0	277.0	271.0		263,,263	-2.7	0.0	19	dbSNP_131	271	593,8005	157.3+/-211.0	22,549,3728	no	missense,intron,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	97,,97	354,1555,4593	CC,CA,AA		6.897,37.9029,17.4023	benign,,benign	88/420,,88/427	43268235	2263,10741	2203	4299	6502	SO:0001583	missense	440533	exon2			ATAATTATTTGAC	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.263T>G	19.37:g.43268235A>C	ENSP00000305005:p.Ile88Arg	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	236	101	0.427966	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	340	0.15567765567765568	214	0.4349593495934959	56	0.15469613259668508	10	0.017482517482517484	60	0.079155672823219	a	0	-2.776694	0.00080	0.379029	0.06897	ENSG00000124467	ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.63580	-0.05;-0.05;-0.05	1.35	-2.7	0.06004	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.05554	-0.025	0.80722	P	0.0	B;B;B;B;B	0.06786	0.001;0.001;0.001;0.0;0.001	B;B;B;B;B	0.11329	0.005;0.002;0.006;0.003;0.005	T	0.17623	-1.0363	8	0.07030	T	0.85	.	1.0782	0.01637	0.3869:0.2945:0.1707:0.1479	.	88;88;88;88;88	B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.;.	R	88	ENSP00000385869:I88R;ENSP00000386090:I88R;ENSP00000305005:I88R	ENSP00000305005:I88R	I	-	2	0	PSG8	47960075	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.116000	0.00597	-5.032000	0.00023	-3.322000	0.00044	ATA	A|0.835;C|0.165	0.165	strong		0.443	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
CELA2B	51032	hgsc.bcm.edu	37	1	15808767	15808767	+	Missense_Mutation	SNP	G	G	A	rs3820071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:15808767G>A	ENST00000375910.3	+	4	260	c.235G>A	c.(235-237)Ggg>Agg	p.G79R	CELA2B_ENST00000494280.1_3'UTR	NM_015849.2	NP_056933	P08218	CEL2B_HUMAN	chymotrypsin-like elastase family, member 2B	79	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		G -> R (in dbSNP:rs3820071). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3646943}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8						CAGCTCCTCCGGGATCTACCG	0.567													G|||	1635	0.326478	0.2776	0.3473	5008	,	,		14119	0.5685		0.2416	False		,,,				2504	0.2157				p.G79R		Atlas-SNP	.											CELA2B_ENST00000422901,NS,carcinoma,-1,6	CELA2B	37	6	0			c.G235A						scavenged	.	G	ARG/GLY	1149,3257	407.5+/-334.3	143,863,1197	61.0	62.0	62.0		235	-6.2	0.2	1	dbSNP_107	62	2113,6487	363.2+/-333.1	270,1573,2457	yes	missense	CELA2B	NM_015849.2	125	413,2436,3654	AA,AG,GG		24.5698,26.0781,25.0807	benign	79/270	15808767	3262,9744	2203	4300	6503	SO:0001583	missense	51032	exon4			TCCTCCGGGATCT		CCDS30605.1	1p36.21	2009-07-09			ENSG00000215704	ENSG00000215704			29995	protein-coding gene	gene with protein product	"""pancreatic elastase IIB"""	609444				3646943, 16327289	Standard	NM_015849		Approved	RP11-265F14.2, ELA2B	uc001awl.3	P08218	OTTHUMG00000002259	ENST00000375910.3:c.235G>A	1.37:g.15808767G>A	ENSP00000365075:p.Gly79Arg	Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	114	72	0.631579	NM_015849	Q14D16|Q6ISM5|Q96QV5	Missense_Mutation	SNP	ENST00000375910.3	37	CCDS30605.1	741	0.3392857142857143	121	0.2459349593495935	112	0.30939226519337015	311	0.5437062937062938	197	0.2598944591029024	G	0	-2.798414	0.00076	0.260781	0.245698	ENSG00000215704	ENST00000375910;ENST00000375909;ENST00000422901	D;D	0.90261	-2.35;-2.64	3.08	-6.17	0.02091	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.574111	0.15655	N	0.251153	T	0.00012	0.0000	N	0.12887	0.27	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41484	-0.9506	9	0.02654	T	1	.	0.8149	0.01100	0.2489:0.3212:0.1134:0.3166	rs3820071;rs17214904;rs52801345;rs59821889;rs3820071	79	P08218	CEL2B_HUMAN	R	79;86;98	ENSP00000365075:G79R;ENSP00000399811:G98R	ENSP00000365074:G86R	G	+	1	0	CELA2B	15681354	0.000000	0.05858	0.173000	0.22940	0.003000	0.03518	-1.849000	0.01672	-0.954000	0.03640	-2.217000	0.00297	GGG	G|0.706;A|0.294	0.294	strong		0.567	CELA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006448.1	NM_015849	
TTBK2	146057	hgsc.bcm.edu	37	15	43170793	43170793	+	Missense_Mutation	SNP	A	A	G	rs6493068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43170793A>G	ENST00000267890.6	-	2	131	c.23T>C	c.(22-24)cTg>cCg	p.L8P	TTBK2_ENST00000567485.1_5'UTR|TTBK2_ENST00000567840.1_Missense_Mutation_p.L8P|TTBK2_ENST00000567274.1_Missense_Mutation_p.L8P	NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	8			L -> P (in dbSNP:rs6493068). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:19533200}.		cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		CAGGATATCCAGCTGCTCTCC	0.458													G|||	2578	0.514776	0.9592	0.2867	5008	,	,		15499	0.4157		0.2803	False		,,,				2504	0.4192				p.L8P		Atlas-SNP	.											.	TTBK2	82	.	0			c.T23C						PASS	.	G	PRO/LEU	3271,759		1343,585,87	159.0	179.0	173.0		23	5.3	0.9	15	dbSNP_116	173	2534,5802		356,1822,1990	yes	missense	TTBK2	NM_173500.3	98	1699,2407,2077	GG,GA,AA		30.3983,18.8337,46.9432	benign	8/1245	43170793	5805,6561	2015	4168	6183	SO:0001583	missense	146057	exon2			ATATCCAGCTGCT	AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"""spinocerebellar ataxia 11"""	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.23T>C	15.37:g.43170793A>G	ENSP00000267890:p.Leu8Pro	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	144	142	0.986111	NM_173500	O94932|Q6ZN52|Q8IVV1	Missense_Mutation	SNP	ENST00000267890.6	37	CCDS42029.1	1047	0.4793956043956044	465	0.9451219512195121	118	0.3259668508287293	242	0.4230769230769231	222	0.2928759894459103	G	14.23	2.474363	0.43942	0.811663	0.303983	ENSG00000128881	ENST00000267890	T	0.37235	1.21	5.29	5.29	0.74685	.	.	.	.	.	T	0.00012	0.0000	N	0.05124	-0.11	0.22330	P	0.999196997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27157	-1.0082	8	0.25106	T	0.35	.	14.2099	0.65756	0.0722:0.0:0.9278:0.0	rs6493068;rs52823398;rs6493068	8;8	Q6IQ55-3;Q6IQ55	.;TTBK2_HUMAN	P	8	ENSP00000267890:L8P	ENSP00000267890:L8P	L	-	2	0	TTBK2	40958085	1.000000	0.71417	0.892000	0.35008	0.883000	0.51084	5.237000	0.65360	1.242000	0.43836	-0.124000	0.14976	CTG	A|0.525;G|0.475	0.475	strong		0.458	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500	
RAD17	5884	hgsc.bcm.edu	37	5	68710032	68710032	+	Silent	SNP	G	G	A	rs145547419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68710032G>A	ENST00000509734.1	+	18	2637	c.1959G>A	c.(1957-1959)ctG>ctA	p.L653L	RAD17_ENST00000282891.6_Silent_p.L556L|RAD17_ENST00000504177.1_3'UTR|RAD17_ENST00000354312.3_Silent_p.L642L|RAD17_ENST00000380774.3_Silent_p.L653L|RAD17_ENST00000358030.2_Silent_p.L477L|RAD17_ENST00000521422.1_Silent_p.L477L|RAD17_ENST00000345306.6_Silent_p.L642L|MARVELD2_ENST00000325631.5_5'Flank|RAD17_ENST00000305138.4_Silent_p.L642L|RAD17_ENST00000361732.2_Silent_p.L642L|RAD17_ENST00000354868.5_Silent_p.L642L			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	653	Interaction with MCM7.				cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)						Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		CCAGTGAACTGCCTGCTAGCC	0.507								Other conserved DNA damage response genes																													p.L653L		Atlas-SNP	.											.	RAD17	49	.	0			c.G1959A						PASS	.	G	,,,,,,,	20,4386	28.1+/-56.4	0,20,2183	94.0	96.0	96.0		1926,1926,1959,1431,1668,1926,1926,1926	2.3	1.0	5	dbSNP_134	96	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAD17	NM_002873.1,NM_133338.1,NM_133339.1,NM_133340.1,NM_133341.1,NM_133342.1,NM_133343.1,NM_133344.1	,,,,,,,	0,20,6483	AA,AG,GG		0.0,0.4539,0.1538	,,,,,,,	642/671,642/671,653/682,477/506,556/585,642/671,642/671,642/671	68710032	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	5884	exon16			TGAACTGCCTGCT	AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"""RAD1 (S. pombe) homolog"""			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1959G>A	5.37:g.68710032G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_133339	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Silent	SNP	ENST00000509734.1	37	CCDS4003.1																																																																																			G|0.998;A|0.002	0.002	strong		0.507	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344	
PPFIBP2	8495	hgsc.bcm.edu	37	11	7673049	7673049	+	Missense_Mutation	SNP	C	C	G	rs77975665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7673049C>G	ENST00000299492.4	+	23	2798	c.2410C>G	c.(2410-2412)Cca>Gca	p.P804A	PPFIBP2_ENST00000533792.1_Missense_Mutation_p.P646A|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.P692A|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.P661A	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	804					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		AGCTTACACACCACTGACCAC	0.612													C|||	445	0.0888578	0.2542	0.0418	5008	,	,		19239	0.0149		0.004	False		,,,				2504	0.0624				p.P804A		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.C2410G						PASS	.	C	ALA/PRO	1038,3364	381.8+/-324.2	119,800,1282	117.0	116.0	117.0		2410	4.8	1.0	11	dbSNP_132	117	38,8554	26.3+/-74.7	0,38,4258	yes	missense	PPFIBP2	NM_003621.2	27	119,838,5540	GG,GC,CC		0.4423,23.5802,8.2807	probably-damaging	804/877	7673049	1076,11918	2201	4296	6497	SO:0001583	missense	8495	exon23			TACACACCACTGA	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.2410C>G	11.37:g.7673049C>G	ENSP00000299492:p.Pro804Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	46	13	0.282609	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	146|146	0.06684981684981685|0.06684981684981685	118|118	0.23983739837398374|0.23983739837398374	12|12	0.03314917127071823|0.03314917127071823	13|13	0.022727272727272728|0.022727272727272728	3|3	0.00395778364116095|0.00395778364116095	C|C	9.478|9.478	1.097421|1.097421	0.20552|0.20552	0.235802|0.235802	0.004423|0.004423	ENSG00000166387|ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181|ENST00000534552	T;T;T;T|.	0.36157|.	1.7;1.28;1.68;1.27|.	5.77|5.77	4.84|4.84	0.62591|0.62591	.|.	0.078622|.	0.53938|.	N|.	0.000047|.	T|T	0.00073|0.00073	0.0002|0.0002	M|M	0.76574|0.76574	2.34|2.34	0.09310|0.09310	P|P	0.99999648842|0.99999648842	B;B;P;B;B;B|.	0.36768|.	0.231;0.009;0.569;0.009;0.009;0.231|.	B;B;B;B;B;B|.	0.37480|.	0.128;0.016;0.251;0.01;0.016;0.08|.	T|T	0.00191|0.00191	-1.1936|-1.1936	9|5	0.15499|0.41790	T|T	0.54|0.15	-9.5207|-9.5207	15.0756|15.0756	0.72074|0.72074	0.0:0.846:0.154:0.0|0.0:0.846:0.154:0.0	.|.	692;692;727;646;661;804|.	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30|.	.;.;.;.;.;LIPB2_HUMAN|.	A|S	804;145;646;727;692;661|35	ENSP00000299492:P804A;ENSP00000436498:P646A;ENSP00000435469:P692A;ENSP00000437321:P661A|.	ENSP00000299492:P804A|ENSP00000436489:T35S	P|T	+|+	1|2	0|0	PPFIBP2|PPFIBP2	7629625|7629625	0.998000|0.998000	0.40836|0.40836	0.987000|0.987000	0.45799|0.45799	0.905000|0.905000	0.53344|0.53344	4.020000|4.020000	0.57189|0.57189	1.525000|1.525000	0.49052|0.49052	0.655000|0.655000	0.94253|0.94253	CCA|ACC	C|0.922;G|0.078	0.078	strong		0.612	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
PRRT4	401399	hgsc.bcm.edu	37	7	127999645	127999645	+	Missense_Mutation	SNP	C	C	T	rs56272205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:127999645C>T	ENST00000446477.2	-	3	714	c.401G>A	c.(400-402)cGg>cAg	p.R134Q	PRRT4_ENST00000535159.1_Missense_Mutation_p.R134Q|PRRT4_ENST00000435512.1_Missense_Mutation_p.R134Q|PRRT4_ENST00000489835.2_Missense_Mutation_p.R134Q	NM_001174164.1	NP_001167635.1	C9JH25	PRRT4_HUMAN	proline-rich transmembrane protein 4	134						integral component of membrane (GO:0016021)				endometrium(4)|prostate(1)	5						CCCAGAGCGCCGGGATGTGGA	0.647													C|||	612	0.122204	0.0847	0.0994	5008	,	,		14883	0.1131		0.162	False		,,,				2504	0.1575				p.R134Q		Atlas-SNP	.											PRRT4,caecum,carcinoma,0,1	PRRT4	31	1	0			c.G401A						PASS	.	C	GLN/ARG,GLN/ARG	102,1282		2,98,592	14.0	18.0	17.0		401,401	-0.4	0.0	7	dbSNP_129	17	507,2675		45,417,1129	yes	missense,missense	PRRT4	NM_001174164.1,NM_001114726.2	43,43	47,515,1721	TT,TC,CC		15.9334,7.3699,13.3377	benign,benign	134/900,134/430	127999645	609,3957	692	1591	2283	SO:0001583	missense	401399	exon3			GAGCGCCGGGATG	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.401G>A	7.37:g.127999645C>T	ENSP00000415026:p.Arg134Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	113	67	0.59292	NM_001174164	A4D0Z9|C9JVW7	Missense_Mutation	SNP	ENST00000446477.2	37	CCDS55160.1	273	0.125	45	0.09146341463414634	41	0.1132596685082873	82	0.14335664335664336	105	0.13852242744063326	C	5.695	0.312812	0.10789	0.073699	0.159334	ENSG00000224940	ENST00000489835;ENST00000446477;ENST00000535159;ENST00000435512;ENST00000489517;ENST00000464607;ENST00000495931	.	.	.	5.27	-0.37	0.12530	.	.	.	.	.	T	0.00109	0.0003	N	0.22421	0.69	0.80722	P	0.0	B;B	0.32128	0.357;0.307	B;B	0.26969	0.075;0.031	T	0.18023	-1.0350	7	0.25106	T	0.35	-0.5031	9.8115	0.40826	0.0916:0.5967:0.3116:0.0	rs56272205;rs61746550	134;134	C9JH25;C9JH25-2	PRRT4_HUMAN;.	Q	134	.	ENSP00000410779:R134Q	R	-	2	0	PRRT4	127786881	0.217000	0.23597	0.008000	0.14137	0.004000	0.04260	0.510000	0.22723	-0.060000	0.13132	-0.353000	0.07706	CGG	A|0.000;C|0.874;T|0.126	0.126	strong		0.647	PRRT4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001114726	
CDH23	64072	hgsc.bcm.edu	37	10	73553177	73553177	+	Silent	SNP	C	C	T	rs41281332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73553177C>T	ENST00000224721.6	+	47	6512	c.6507C>T	c.(6505-6507)atC>atT	p.I2169I	CDH23_ENST00000398788.3_5'Flank	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2164	Cadherin 20. {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						CCATTCTGATCGATGACATCA	0.597													C|||	131	0.0261581	0.0946	0.0072	5008	,	,		18788	0.0		0.001	False		,,,				2504	0.0				p.I2164I		Atlas-SNP	.											.	CDH23	365	.	0			c.C6492T						PASS	.	C		294,3964		11,272,1846	75.0	82.0	80.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6492	-2.9	1.0	10	dbSNP_127	80	4,8500		0,4,4248	no	coding-synonymous	CDH23	NM_022124.5		11,276,6094	TT,TC,CC		0.047,6.9047,2.3351		2164/3355	73553177	298,12464	2129	4252	6381	SO:0001819	synonymous_variant	64072	exon46			TCTGATCGATGAC	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.6507C>T	10.37:g.73553177C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	120	63	0.525	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				C|0.976;T|0.024	0.024	strong		0.597	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
TRDN	10345	hgsc.bcm.edu	37	6	123759243	123759243	+	Missense_Mutation	SNP	C	C	T	rs35766971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:123759243C>T	ENST00000398178.3	-	12	1037	c.1016G>A	c.(1015-1017)aGt>aAt	p.S339N	TRDN_ENST00000334268.4_Missense_Mutation_p.S339N|RP11-532N4.2_ENST00000427828.1_RNA|RP11-532N4.2_ENST00000587106.2_RNA|RP11-532N4.2_ENST00000589182.1_RNA|RP11-532N4.2_ENST00000434768.1_RNA|RP11-532N4.2_ENST00000587049.1_RNA|RP11-532N4.2_ENST00000418467.2_RNA	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	339			S -> N (in dbSNP:rs35766971).		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)		TTCCTTCTCACTTTTCTTTTT	0.353													C|||	66	0.0131789	0.0477	0.0043	5008	,	,		19093	0.0		0.0	False		,,,				2504	0.0				p.S340N		Atlas-SNP	.											TRDN,posterior_fossa,glioma,0,1	TRDN	88	1	0			c.G1019A						PASS	.	C	ASN/SER	123,3559		1,121,1719	124.0	119.0	121.0		1016	3.7	0.6	6	dbSNP_126	121	1,8137		0,1,4068	yes	missense	TRDN	NM_006073.2	46	1,122,5787	TT,TC,CC		0.0123,3.3406,1.0491	benign	339/730	123759243	124,11696	1841	4069	5910	SO:0001583	missense	10345	exon12			TTCTCACTTTTCT	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.1016G>A	6.37:g.123759243C>T	ENSP00000381240:p.Ser339Asn	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	37	CCDS55053.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	12.94	2.089922	0.36855	0.033406	1.23E-4	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.62788	-0.0;-0.0	5.49	3.72	0.42706	.	0.724189	0.13174	N	0.408030	T	0.25457	0.0619	L	0.27053	0.805	0.43499	D	0.995746	B;B;B	0.23650	0.089;0.089;0.089	B;B;B	0.22152	0.025;0.025;0.038	T	0.09122	-1.0689	10	0.19590	T	0.45	6.1703	6.726	0.23357	0.125:0.3677:0.5073:0.0	rs35766971	339;340;339	Q5SWK9;Q8IVK2;Q13061	.;.;TRDN_HUMAN	N	339	ENSP00000381240:S339N;ENSP00000333984:S339N	ENSP00000333984:S339N	S	-	2	0	TRDN	123800942	0.970000	0.33590	0.602000	0.28890	0.991000	0.79684	1.640000	0.37186	0.812000	0.34326	0.650000	0.86243	AGT	C|0.991;T|0.009	0.009	strong		0.353	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
DACT2	168002	hgsc.bcm.edu	37	6	168708816	168708816	+	Missense_Mutation	SNP	T	T	G	rs10945501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:168708816T>G	ENST00000366795.3	-	4	1709	c.1621A>C	c.(1621-1623)Aca>Cca	p.T541P	DACT2_ENST00000610183.1_Missense_Mutation_p.T371P|DACT2_ENST00000366796.3_Intron|DACT2_ENST00000607983.1_Missense_Mutation_p.T133P	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	541			T -> P (in dbSNP:rs10945501).		epithelial cell morphogenesis (GO:0003382)|hematopoietic progenitor cell differentiation (GO:0002244)|inner medullary collecting duct development (GO:0072061)|negative regulation of cell adhesion (GO:0007162)|negative regulation of nodal signaling pathway (GO:1900108)|skin development (GO:0043588)	mitochondrion (GO:0005739)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)|transcription factor binding (GO:0008134)			endometrium(1)	1		Breast(66;1.46e-05)|Ovarian(120;0.0728)		OV - Ovarian serous cystadenocarcinoma(33;5.33e-21)|BRCA - Breast invasive adenocarcinoma(81;1.18e-06)|GBM - Glioblastoma multiforme(31;0.000957)		CCCCTCCCTGTGGGCCAGTGG	0.701													G|||	2526	0.504393	0.7905	0.4107	5008	,	,		11834	0.3234		0.3688	False		,,,				2504	0.5102				p.T541P		Atlas-SNP	.											DACT2_ENST00000366795,rectum,carcinoma,0,2	DACT2	46	2	0			c.A1621C						PASS	.						8.0	12.0	11.0					6																	168708816		690	1585	2275	SO:0001583	missense	168002	exon4			TCCCTGTGGGCCA	AF318336	CCDS47519.1, CCDS69241.1, CCDS75554.1	6q27	2013-05-15	2013-05-15	2003-09-17	ENSG00000164488	ENSG00000164488			21231	protein-coding gene	gene with protein product		608966	"""chromosome 6 open reading frame 116"", ""dapper homolog 2, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 2 (Xenopus laevis)"""	C6orf116			Standard	NM_001286351		Approved	bA503C24.7, DAPPER2	uc003qwq.3	Q5SW24	OTTHUMG00000016046	ENST00000366795.3:c.1621A>C	6.37:g.168708816T>G	ENSP00000355760:p.Thr541Pro	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Missense_Mutation	SNP	ENST00000366795.3	37	CCDS47519.1	1004	0.4597069597069597	386	0.7845528455284553	152	0.4198895027624309	197	0.34440559440559443	269	0.3548812664907652	G	4.150	0.026308	0.08054	.	.	ENSG00000164488	ENST00000366795	T	0.41758	0.99	3.05	2.17	0.27698	.	1.930070	0.03734	N	0.253953	T	0.03871	0.0109	N	0.00729	-1.24	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.19160	-1.0314	9	0.18276	T	0.48	.	4.6907	0.12780	0.1176:0.0:0.6679:0.2145	rs10945501	541	Q5SW24	DACT2_HUMAN	P	541	ENSP00000355760:T541P	ENSP00000355760:T541P	T	-	1	0	DACT2	168451665	0.016000	0.18221	0.003000	0.11579	0.001000	0.01503	1.035000	0.30216	0.060000	0.16281	-0.225000	0.12378	ACA	T|0.545;G|0.455	0.455	strong		0.701	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
CPXM2	119587	hgsc.bcm.edu	37	10	125528048	125528048	+	Silent	SNP	G	G	A	rs1219725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:125528048G>A	ENST00000241305.3	-	9	1447	c.1293C>T	c.(1291-1293)taC>taT	p.Y431Y	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	431					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)		TTACCCCTTCGTAGGCCTTCT	0.612													G|||	1897	0.378794	0.1528	0.4784	5008	,	,		11886	0.5992		0.3738	False		,,,				2504	0.3916				p.Y431Y		Atlas-SNP	.											.	CPXM2	120	.	0			c.C1293T						PASS	.	G		844,3562	331.8+/-302.1	73,698,1432	68.0	56.0	60.0		1293	-4.3	0.4	10	dbSNP_87	60	3228,5372	485.9+/-371.8	614,2000,1686	no	coding-synonymous	CPXM2	NM_198148.2		687,2698,3118	AA,AG,GG		37.5349,19.1557,31.3086		431/757	125528048	4072,8934	2203	4300	6503	SO:0001819	synonymous_variant	119587	exon9			CCCTTCGTAGGCC	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.1293C>T	10.37:g.125528048G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_198148	B4E3Q2	Silent	SNP	ENST00000241305.3	37	CCDS7637.1																																																																																			G|0.654;A|0.346	0.346	strong		0.612	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148	
ZNF792	126375	hgsc.bcm.edu	37	19	35449760	35449760	+	Silent	SNP	G	G	C	rs2651080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:35449760G>C	ENST00000404801.1	-	4	1385	c.999C>G	c.(997-999)acC>acG	p.T333T	ZNF792_ENST00000605484.1_Silent_p.T266T	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	333					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(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GGCTTTCACCGGTGTGAACCC	0.478													G|||	1615	0.322484	0.4652	0.1844	5008	,	,		20270	0.2034		0.33	False		,,,				2504	0.3425				p.T333T	GBM(1;7 183 21053 22581 22847)	Atlas-SNP	.											ZNF792,NS,carcinoma,-1,2	ZNF792	46	2	0			c.C999G						PASS	.	G		1845,2561	530.8+/-373.0	370,1105,728	61.0	58.0	59.0		999	-4.1	0.3	19	dbSNP_100	59	2542,6058	407.7+/-349.2	384,1774,2142	no	coding-synonymous	ZNF792	NM_175872.4		754,2879,2870	CC,CG,GG		29.5581,41.8747,33.7306		333/633	35449760	4387,8619	2203	4300	6503	SO:0001819	synonymous_variant	126375	exon4			TTCACCGGTGTGA	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.999C>G	19.37:g.35449760G>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Silent	SNP	ENST00000404801.1	37	CCDS12440.2																																																																																			G|0.671;C|0.329	0.329	strong		0.478	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
NCAPD3	23310	hgsc.bcm.edu	37	11	134038949	134038949	+	Splice_Site	SNP	G	G	T	rs7927108	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134038949G>T	ENST00000534548.2	-	25	3166	c.3102C>A	c.(3100-3102)agC>agA	p.S1034R		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	1034			S -> R (in dbSNP:rs7927108).		mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		ACTCCCCGAAGCTGCAAAGGT	0.433													G|||	165	0.0329473	0.1195	0.0101	5008	,	,		20928	0.0		0.0	False		,,,				2504	0.0				p.S1034R		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C3102A						PASS	.	G	ARG/SER	400,4002	198.1+/-222.0	11,378,1812	54.0	53.0	53.0		3102	-4.5	0.4	11	dbSNP_116	53	2,8592	2.2+/-6.3	0,2,4295	yes	missense-near-splice	NCAPD3	NM_015261.2	110	11,380,6107	TT,TG,GG		0.0233,9.0868,3.0933	benign	1034/1499	134038949	402,12594	2201	4297	6498	SO:0001630	splice_region_variant	23310	exon25			CCCGAAGCTGCAA	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.3102-1C>A	11.37:g.134038949G>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	55	0.025183150183150184	53	0.10772357723577236	2	0.0055248618784530384	0	0.0	0	0.0	G	8.070	0.770068	0.15983	0.090868	2.33E-4	ENSG00000151503	ENST00000534548;ENST00000530396	T;T	0.46063	0.88;0.88	5.57	-4.49	0.03504	Armadillo-like helical (1);Armadillo-type fold (1);	0.288722	0.49305	N	0.000151	T	0.00384	0.0012	L	0.29908	0.895	0.80722	D	1	B	0.23937	0.094	B	0.28638	0.092	T	0.15292	-1.0442	10	0.13853	T	0.58	.	3.0773	0.06251	0.313:0.3092:0.2902:0.0876	rs7927108;rs52805171;rs7927108	1034	P42695	CNDD3_HUMAN	R	1034;70	ENSP00000433681:S1034R;ENSP00000435173:S70R	ENSP00000435173:S70R	S	-	3	2	NCAPD3	133544159	0.168000	0.22989	0.419000	0.26584	0.457000	0.32468	-0.280000	0.08468	-0.683000	0.05190	-0.258000	0.10820	AGC	G|0.966;T|0.034	0.034	strong		0.433	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	Missense_Mutation
MUC4	4585	hgsc.bcm.edu	37	3	195515026	195515026	+	Missense_Mutation	SNP	G	G	C	rs200763050		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515026G>C	ENST00000463781.3	-	2	3884	c.3425C>G	c.(3424-3426)aCt>aGt	p.T1142S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1142S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	616					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.T1142S(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)		TACTGAGGAAGTGTCGGTGAC	0.567																																					p.T1142S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	3	Substitution - Missense(3)	skin(2)|kidney(1)	c.C3425G						PASS	.						11.0	7.0	8.0					3																	195515026		675	1482	2157	SO:0001583	missense	4585	exon2			GAGGAAGTGTCGG	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.3425C>G	3.37:g.195515026G>C	ENSP00000417498:p.Thr1142Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	436	20	0.0458716	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	.	.	.	.	.	.	.	.	.	.	-	3.313	-0.140308	0.06669	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34667	1.35;1.35	0.545	-0.879	0.10613	.	.	.	.	.	T	0.31420	0.0796	N	0.14661	0.345	0.09310	N	1	D	0.60160	0.987	D	0.63488	0.915	T	0.16394	-1.0404	8	.	.	.	.	3.9497	0.09363	0.5686:0.0:0.4314:0.0	.	1142	E7ESK3	.	S	1142	ENSP00000417498:T1142S;ENSP00000420243:T1142S	.	T	-	2	0	MUC4	196999421	0.002000	0.14202	0.000000	0.03702	0.066000	0.16364	0.481000	0.22260	-0.332000	0.08489	0.064000	0.15345	ACT	G|0.998;C|0.002	0.002	weak		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PRRG4	79056	hgsc.bcm.edu	37	11	32874919	32874919	+	Missense_Mutation	SNP	C	C	A	rs34139105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:32874919C>A	ENST00000257836.3	+	6	780	c.527C>A	c.(526-528)cCa>cAa	p.P176Q		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	176			P -> Q (in dbSNP:rs34139105).			extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	7	Breast(20;0.206)					GCCTTGTCTCCATTGCCGCCT	0.517													C|||	271	0.0541134	0.0635	0.0346	5008	,	,		16129	0.0		0.0825	False		,,,				2504	0.0818				p.P176Q		Atlas-SNP	.											PRRG4,NS,carcinoma,+1,1	PRRG4	15	1	0			c.C527A						PASS	.	C	GLN/PRO	288,4116	159.2+/-191.8	8,272,1922	106.0	100.0	102.0		527	2.6	0.0	11	dbSNP_126	102	733,7865	176.6+/-226.4	26,681,3592	yes	missense	PRRG4	NM_024081.5	76	34,953,5514	AA,AC,CC		8.5252,6.5395,7.8526	possibly-damaging	176/227	32874919	1021,11981	2202	4299	6501	SO:0001583	missense	79056	exon6			TGTCTCCATTGCC	AF326351	CCDS7881.1	11p13	2008-02-05			ENSG00000135378	ENSG00000135378			30799	protein-coding gene	gene with protein product		611690				11171957	Standard	NM_024081		Approved	TMG4	uc001mtx.3	Q9BZD6	OTTHUMG00000166219	ENST00000257836.3:c.527C>A	11.37:g.32874919C>A	ENSP00000257836:p.Pro176Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_024081		Missense_Mutation	SNP	ENST00000257836.3	37	CCDS7881.1	115	0.052655677655677656	28	0.056910569105691054	14	0.03867403314917127	0	0.0	73	0.09630606860158311	C	6.598	0.478792	0.12521	0.065395	0.085252	ENSG00000135378	ENST00000257836	D	0.98012	-4.66	5.56	2.57	0.30868	.	0.152215	0.64402	D	0.000011	T	0.51568	0.1682	M	0.62723	1.935	0.09310	N	0.999997	P	0.50272	0.933	P	0.45577	0.486	T	0.71510	-0.4571	10	0.29301	T	0.29	-0.7029	6.8589	0.24056	0.0:0.6953:0.1443:0.1605	rs34139105	176	Q9BZD6	TMG4_HUMAN	Q	176	ENSP00000257836:P176Q	ENSP00000257836:P176Q	P	+	2	0	PRRG4	32831495	0.005000	0.15991	0.001000	0.08648	0.018000	0.09664	1.561000	0.36342	0.265000	0.21872	0.551000	0.68910	CCA	C|0.927;A|0.073	0.073	strong		0.517	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081	
CCDC153	283152	hgsc.bcm.edu	37	11	119063908	119063908	+	Missense_Mutation	SNP	C	C	T	rs2301574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	64	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	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	
BRICD5	283870	hgsc.bcm.edu	37	16	2259673	2259673	+	Missense_Mutation	SNP	T	T	C	rs144886139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2259673T>C	ENST00000562360.1	-	5	472	c.473A>G	c.(472-474)cAc>cGc	p.H158R	RP11-304L19.8_ENST00000561544.1_lincRNA|BRICD5_ENST00000328540.3_Missense_Mutation_p.H158R			Q6PL45	BRID5_HUMAN	BRICHOS domain containing 5	158	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.					integral component of membrane (GO:0016021)											CTGGGTGTGGTGGGTGTCCTG	0.687													T|||	42	0.00838658	0.031	0.0014	5008	,	,		14172	0.0		0.0	False		,,,				2504	0.0				p.H158R		Atlas-SNP	.											C16orf79,NS,carcinoma,+1,1	.	.	1	0			c.A473G						PASS	.	T	ARG/HIS	108,4288	77.3+/-115.6	1,106,2091	55.0	68.0	64.0		473	-1.1	0.0	16	dbSNP_134	64	2,8598	1.2+/-3.3	0,2,4298	yes	missense	C16orf79	NM_182563.3	29	1,108,6389	CC,CT,TT		0.0233,2.4568,0.8464	benign	158/229	2259673	110,12886	2198	4300	6498	SO:0001583	missense	283870	exon5			GTGTGGTGGGTGT	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.473A>G	16.37:g.2259673T>C	ENSP00000455052:p.His158Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_182563	C9J7K2|Q8IXU9	Missense_Mutation	SNP	ENST00000562360.1	37	CCDS10463.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	T	6.160	0.397772	0.11696	0.024568	2.33E-4	ENSG00000182685	ENST00000328540	T	0.77877	-1.13	5.82	-1.09	0.09904	BRICHOS (2);	0.980375	0.08392	N	0.952853	T	0.27765	0.0683	.	.	.	0.09310	N	0.999999	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.19614	-1.0300	9	0.07813	T	0.8	-22.7577	5.497	0.16807	0.0:0.3998:0.2833:0.3169	.	158;158	Q6PL45;Q6PL45-2	CP079_HUMAN;.	R	158	ENSP00000332389:H158R	ENSP00000332389:H158R	H	-	2	0	C16orf79	2199674	0.000000	0.05858	0.002000	0.10522	0.081000	0.17604	0.005000	0.13129	-0.143000	0.11334	0.459000	0.35465	CAC	T|0.993;C|0.007	0.007	strong		0.687	BRICD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435091.1	NM_182563	
GNL3L	54552	hgsc.bcm.edu	37	X	54578725	54578725	+	Splice_Site	SNP	C	C	T	rs147602603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54578725C>T	ENST00000336470.4	+	13	1321	c.1182C>T	c.(1180-1182)agC>agT	p.S394S	GNL3L_ENST00000360845.2_Splice_Site_p.S394S	NM_019067.5	NP_061940.1	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)-like	394					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	30						CCCAATGCAGCGGGAAGATCA	0.507													C|||	7	0.0018543	0.0053	0.0	3775	,	,		13898	0.0		0.0	False		,,,				2504	0.0				p.S394S		Atlas-SNP	.											.	GNL3L	73	.	0			c.C1182T						PASS	.	C	,	19,3816		0,17,2,1615,569	169.0	132.0	144.0		1182,1182	-7.2	0.4	X	dbSNP_134	144	0,6728		0,0,0,2428,1872	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	GNL3L	NM_001184819.1,NM_019067.5	,	0,17,2,4043,2441	TT,TC,T,CC,C		0.0,0.4954,0.1799	,	394/583,394/583	54578725	19,10544	2203	4300	6503	SO:0001630	splice_region_variant	54552	exon13			ATGCAGCGGGAAG	AK001475	CCDS14360.1	Xp11.22	2010-03-17			ENSG00000130119	ENSG00000130119			25553	protein-coding gene	gene with protein product		300873				12477932	Standard	NM_019067		Approved	FLJ10613	uc004dth.2	Q9NVN8	OTTHUMG00000021629	ENST00000336470.4:c.1182-1C>T	X.37:g.54578725C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	204	93	0.455882	NM_001184819		Silent	SNP	ENST00000336470.4	37	CCDS14360.1																																																																																			C|0.998;T|0.002	0.002	strong		0.507	GNL3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056805.1	NM_019067	Silent
FPR1	2357	hgsc.bcm.edu	37	19	52249900	52249900	+	Silent	SNP	G	G	A	rs5030879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52249900G>A	ENST00000595042.1	-	3	489	c.348C>T	c.(346-348)atC>atT	p.I116I	FPR1_ENST00000304748.4_Silent_p.I116I	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	116					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)	CAATGAGGGCGATCAGGAAGA	0.552													G|||	506	0.101038	0.3487	0.0403	5008	,	,		21499	0.002		0.003	False		,,,				2504	0.0123				p.I116I		Atlas-SNP	.											FPR1,colon,carcinoma,0,1	FPR1	64	1	0			c.C348T						PASS	.	G	,	1279,3127		191,897,1115	116.0	90.0	98.0		348,348	-3.7	0.3	19	dbSNP_113	98	38,8562		0,38,4262	no	coding-synonymous,coding-synonymous	FPR1	NM_001193306.1,NM_002029.3	,	191,935,5377	AA,AG,GG		0.4419,29.0286,10.1261	,	116/351,116/351	52249900	1317,11689	2203	4300	6503	SO:0001819	synonymous_variant	2357	exon3			GAGGGCGATCAGG	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.348C>T	19.37:g.52249900G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Silent	SNP	ENST00000595042.1	37	CCDS12839.1																																																																																			G|0.895;A|0.105	0.105	strong		0.552	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548556	32548556	+	Missense_Mutation	SNP	C	C	T	rs3830125		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32548556C>T	ENST00000360004.5	-	4	835	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	244					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						AACAGCCCGGCCCCAAGGAAG	0.552										Multiple Myeloma(14;0.17)																											p.A244T		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G730A						PASS	.						90.0	104.0	99.0					6																	32548556		1511	2709	4220	SO:0001583	missense	3123	exon4			GCCCGGCCCCAAG	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.730G>A	6.37:g.32548556C>T	ENSP00000353099:p.Ala244Thr	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	476	37	0.0777311	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	6.616	0.482155	0.12581	.	.	ENSG00000196126	ENST00000360004	T	0.00730	5.77	3.98	-0.294	0.12831	.	1.209560	0.05711	N	0.596048	T	0.00967	0.0032	L	0.54323	1.7	0.09310	N	1	B;B;D	0.76494	0.009;0.005;0.999	B;B;D	0.81914	0.03;0.014;0.995	T	0.46176	-0.9210	10	0.62326	D	0.03	.	4.2536	0.10707	0.1362:0.5351:0.2335:0.0951	rs3830125;rs17849963	244;244;244	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	T	244	ENSP00000353099:A244T	ENSP00000353099:A244T	A	-	1	0	HLA-DRB1	32656534	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	0.150000	0.16263	-0.354000	0.08212	-0.397000	0.06425	GCC	.	.	weak		0.552	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
OR5AU1	390445	hgsc.bcm.edu	37	14	21623489	21623489	+	Silent	SNP	C	C	T	rs45462402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21623489C>T	ENST00000304418.3	-	1	733	c.696G>A	c.(694-696)ggG>ggA	p.G232G		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(12)|pancreas(1)	21	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		GGATGGGTGGCCCATCACAGA	0.478													T|||	2547	0.508586	0.7262	0.389	5008	,	,		22675	0.6607		0.2087	False		,,,				2504	0.4509				p.G232G		Atlas-SNP	.											.	OR5AU1	46	.	0			c.G696A						PASS	.	T		2886,1520	479.2+/-358.4	951,984,268	83.0	73.0	77.0		696	1.7	1.0	14	dbSNP_127	77	1618,6982	742.1+/-407.2	145,1328,2827	no	coding-synonymous	OR5AU1	NM_001004731.1		1096,2312,3095	TT,TC,CC		18.814,34.4984,34.6302		232/363	21623489	4504,8502	2203	4300	6503	SO:0001819	synonymous_variant	390445	exon1			GGGTGGCCCATCA	AL157687	CCDS32042.1	14q11.2	2013-09-23			ENSG00000169327	ENSG00000169327		"""GPCR / Class A : Olfactory receptors"""	15362	protein-coding gene	gene with protein product							Standard	NM_001004731		Approved		uc010tlp.2	Q8NGC0	OTTHUMG00000170753	ENST00000304418.3:c.696G>A	14.37:g.21623489C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_001004731	B2RP78|Q6IEU2|Q96R10	Silent	SNP	ENST00000304418.3	37	CCDS32042.1																																																																																			C|0.637;T|0.363	0.363	strong		0.478	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1		
METTL4	64863	hgsc.bcm.edu	37	18	2555008	2555008	+	Missense_Mutation	SNP	T	T	G	rs12606220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2555008T>G	ENST00000574538.1	-	4	1264	c.489A>C	c.(487-489)ttA>ttC	p.L163F	METTL4_ENST00000319888.6_Missense_Mutation_p.L163F|snoU109_ENST00000459316.1_RNA	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	163			L -> F (in dbSNP:rs12606220).		nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						GGATCAACTGTAAAGATCCAT	0.363													T|||	614	0.122604	0.264	0.0994	5008	,	,		19543	0.1329		0.0467	False		,,,				2504	0.0153				p.L163F		Atlas-SNP	.											.	METTL4	40	.	0			c.A489C						PASS	.	T	PHE/LEU	999,3407	347.7+/-309.6	116,767,1320	110.0	130.0	123.0		489	-1.1	0.7	18	dbSNP_120	123	371,8229	117.7+/-177.3	9,353,3938	yes	missense	METTL4	NM_022840.3	22	125,1120,5258	GG,GT,TT		4.314,22.6736,10.5336	benign	163/473	2555008	1370,11636	2203	4300	6503	SO:0001583	missense	64863	exon4			CAACTGTAAAGAT		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.489A>C	18.37:g.2555008T>G	ENSP00000458290:p.Leu163Phe	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Missense_Mutation	SNP	ENST00000574538.1	37	CCDS11826.1	267	0.12225274725274725	144	0.2926829268292683	25	0.06906077348066299	68	0.11888111888111888	30	0.0395778364116095	T	12.78	2.040473	0.35989	0.226736	0.04314	ENSG00000101574	ENST00000319888	T	0.23754	1.89	5.85	-1.09	0.09904	.	0.825401	0.10955	N	0.615673	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P	0.38642	0.641	B	0.31614	0.133	T	0.36915	-0.9728	9	0.56958	D	0.05	-3.4072	0.7179	0.00935	0.258:0.3031:0.1325:0.3065	rs12606220;rs12606220	163	Q8N3J2	METL4_HUMAN	F	163	ENSP00000320349:L163F	ENSP00000320349:L163F	L	-	3	2	METTL4	2545008	0.000000	0.05858	0.734000	0.30879	0.810000	0.45777	0.176000	0.16782	-0.413000	0.07507	0.533000	0.62120	TTA	T|0.885;G|0.115	0.115	strong		0.363	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840	
AHRR	57491	hgsc.bcm.edu	37	5	376809	376809	+	Missense_Mutation	SNP	T	T	C	rs35008248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:376809T>C	ENST00000505113.1	+	4	385	c.341T>C	c.(340-342)cTg>cCg	p.L114P	AHRR_ENST00000316418.5_Missense_Mutation_p.L114P|AHRR_ENST00000512529.1_Intron	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	114	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.		L -> P (in dbSNP:rs35008248). {ECO:0000269|PubMed:11835227}.		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)			TCTGCCGTGCTGGAGGGAAGG	0.617													T|||	614	0.122604	0.444	0.0331	5008	,	,		18715	0.0		0.004	False		,,,				2504	0.0				p.L114P		Atlas-SNP	.											.	AHRR	67	.	0			c.T341C						PASS	.	T	PRO/LEU,PRO/LEU	1466,2816		247,972,922	34.0	40.0	38.0		341,341	-0.2	1.0	5	dbSNP_126	38	40,8474		0,40,4217	yes	missense,missense	AHRR	NM_001242412.1,NM_020731.4	98,98	247,1012,5139	CC,CT,TT		0.4698,34.2363,11.7693	benign,benign	114/702,114/720	376809	1506,11290	2141	4257	6398	SO:0001583	missense	57491	exon4			CCGTGCTGGAGGG	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.341T>C	5.37:g.376809T>C	ENSP00000424601:p.Leu114Pro	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_001242412	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	205	0.09386446886446886	194	0.3943089430894309	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	T	7.400	0.632654	0.14322	0.342363	0.004698	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000510400	T;T;T	0.47528	2.17;2.15;0.84	2.95	-0.189	0.13260	PAS (1);	0.720518	0.13147	N	0.410200	T	0.00012	0.0000	N	0.01352	-0.895	0.09310	P	0.99999999565809	B;B	0.17038	0.02;0.02	B;B	0.17098	0.017;0.012	T	0.46062	-0.9218	9	0.27785	T	0.31	.	5.7545	0.18164	0.5628:0.0:0.0:0.4372	rs35008248;rs57297657	114;114	A9YTQ3;A9YTQ3-2	AHRR_HUMAN;.	P	114;114;110	ENSP00000424601:L114P;ENSP00000323816:L114P;ENSP00000428893:L110P	ENSP00000323816:L114P	L	+	2	0	AHRR	429809	0.996000	0.38824	0.997000	0.53966	0.850000	0.48378	-0.134000	0.10436	-0.033000	0.13736	0.533000	0.62120	CTG	T|0.914;C|0.086	0.086	strong		0.617	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
HLA-G	3135	hgsc.bcm.edu	37	6	29797211	29797211	+	Silent	SNP	C	C	T	rs41562616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29797211C>T	ENST00000360323.6	+	4	660	c.636C>T	c.(634-636)caC>caT	p.H212H	HLA-G_ENST00000376828.2_Silent_p.H217H|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000428701.1_Silent_p.H212H|HLA-G_ENST00000376818.3_Silent_p.H120H			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	212	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)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CCAAGACACACGTGACCCACC	0.562													c|||	270	0.0539137	0.1127	0.0893	5008	,	,		19002	0.0079		0.0268	False		,,,				2504	0.0245				p.H212H		Atlas-SNP	.											.	HLA-G	90	.	0			c.C636T						PASS	.	C		402,4004		23,356,1824	100.0	105.0	103.0		636	-3.4	0.0	6	dbSNP_127	103	305,8295		8,289,4003	no	coding-synonymous	HLA-G	NM_002127.5		31,645,5827	TT,TC,CC		3.5465,9.1239,5.436		212/339	29797211	707,12299	2203	4300	6503	SO:0001819	synonymous_variant	3135	exon5			GACACACGTGACC		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.636C>T	6.37:g.29797211C>T		Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	237	123	0.518987	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			C|0.948;T|0.052	0.052	strong		0.562	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
DNM1L	10059	hgsc.bcm.edu	37	12	32854366	32854366	+	Silent	SNP	A	A	C	rs10844308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:32854366A>C	ENST00000549701.1	+	2	194	c.120A>C	c.(118-120)tcA>tcC	p.S40S	DNM1L_ENST00000548671.1_3'UTR|DNM1L_ENST00000553257.1_Silent_p.S40S|DNM1L_ENST00000266481.6_Silent_p.S40S|DNM1L_ENST00000381000.4_Silent_p.S40S|DNM1L_ENST00000547312.1_Silent_p.S40S|DNM1L_ENST00000358214.5_Silent_p.S40S|DNM1L_ENST00000452533.2_Silent_p.S40S|DNM1L_ENST00000414834.2_5'UTR			O00429	DNM1L_HUMAN	dynamin 1-like	40	Dynamin-type G.|GTPase domain.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GAAAGAGCTCAGTGCTAGAAA	0.423													a|||	634	0.126597	0.177	0.0937	5008	,	,		14408	0.0813		0.161	False		,,,				2504	0.093				p.S40S		Atlas-SNP	.											.	DNM1L	52	.	0			c.A120C						PASS	.		,,	721,3685	297.3+/-284.7	57,607,1539	66.0	72.0	70.0		120,120,120	0.2	1.0	12	dbSNP_120	70	1248,7352	250.1+/-277.1	105,1038,3157	no	coding-synonymous,coding-synonymous,coding-synonymous	DNM1L	NM_005690.3,NM_012062.3,NM_012063.2	,,	162,1645,4696	CC,CA,AA		14.5116,16.364,15.1392	,,	40/700,40/737,40/711	32854366	1969,11037	2203	4300	6503	SO:0001819	synonymous_variant	10059	exon2			GAGCTCAGTGCTA	AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.120A>C	12.37:g.32854366A>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	82	47	0.573171	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Silent	SNP	ENST00000549701.1	37	CCDS8729.1																																																																																			A|0.858;C|0.142	0.142	strong		0.423	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062	
XYLT1	64131	hgsc.bcm.edu	37	16	17211729	17211729	+	Silent	SNP	A	A	G	rs7201590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:17211729A>G	ENST00000261381.6	-	11	2415	c.2331T>C	c.(2329-2331)aaT>aaC	p.N777N		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	777					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TCACGGTCACATTAGGTCCCT	0.567													a|||	318	0.0634984	0.2322	0.0144	5008	,	,		18722	0.0		0.001	False		,,,				2504	0.0				p.N777N		Atlas-SNP	.											.	XYLT1	147	.	0			c.T2331C						PASS	.	A		846,3548	333.6+/-303.0	80,686,1431	179.0	146.0	157.0		2331	-3.3	1.0	16	dbSNP_116	157	19,8581	10.5+/-38.8	0,19,4281	no	coding-synonymous	XYLT1	NM_022166.3		80,705,5712	GG,GA,AA		0.2209,19.2535,6.6569		777/960	17211729	865,12129	2197	4300	6497	SO:0001819	synonymous_variant	64131	exon11			GGTCACATTAGGT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.2331T>C	16.37:g.17211729A>G		Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	275	160	0.581818	NM_022166	Q9H1B6	Silent	SNP	ENST00000261381.6	37	CCDS10569.1																																																																																			A|0.934;G|0.066	0.066	strong		0.567	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
PLEKHG4	25894	hgsc.bcm.edu	37	16	67320223	67320223	+	Missense_Mutation	SNP	G	G	A	rs3868142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67320223G>A	ENST00000360461.5	+	14	5024	c.2489G>A	c.(2488-2490)cGc>cAc	p.R830H	PLEKHG4_ENST00000379344.3_Missense_Mutation_p.R830H|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.R749H|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.R830H	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	830	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		R -> H (in dbSNP:rs3868142).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		AATAAGCCTCGCTCCGATGCC	0.562													G|||	1209	0.241414	0.6838	0.1023	5008	,	,		22224	0.003		0.0716	False		,,,				2504	0.1626				p.R830H		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.G2489A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	2418,1978	616.5+/-392.8	666,1086,446	161.0	122.0	135.0		2489,2489,2489,2246,2489	2.4	0.9	16	dbSNP_108	135	646,7954	165.2+/-217.4	24,598,3678	yes	missense,missense,missense,missense,missense	PLEKHG4	NM_001129727.1,NM_001129728.1,NM_001129729.1,NM_001129731.1,NM_015432.3	29,29,29,29,29	690,1684,4124	AA,AG,GG		7.5116,44.9955,23.5765	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	830/1192,830/1192,830/1192,749/1111,830/1192	67320223	3064,9932	2198	4300	6498	SO:0001583	missense	25894	exon15			AGCCTCGCTCCGA	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.2489G>A	16.37:g.67320223G>A	ENSP00000353646:p.Arg830His	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	37	CCDS32466.1	440	0.20146520146520147	340	0.6910569105691057	42	0.11602209944751381	2	0.0034965034965034965	56	0.07387862796833773	G	18.64	3.666874	0.67814	0.550045	0.075116	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.44	2.37	0.29283	Dbl homology (DH) domain (5);	0.000000	0.33834	N	0.004517	T	0.00012	0.0000	M	0.73962	2.25	0.80722	P	0.0	B;B	0.19706	0.03;0.038	B;B	0.15484	0.007;0.013	T	0.36016	-0.9765	9	0.72032	D	0.01	.	6.2219	0.20685	0.2146:0.0:0.6483:0.1372	rs3868142;rs61318038;rs3868142	749;830	Q58EX7-2;Q58EX7	.;PKHG4_HUMAN	H	830;830;830;749	ENSP00000353646:R830H;ENSP00000401118:R830H;ENSP00000368649:R830H;ENSP00000398030:R749H	ENSP00000353646:R830H	R	+	2	0	PLEKHG4	65877724	0.797000	0.28877	0.877000	0.34402	0.909000	0.53808	2.069000	0.41481	0.656000	0.30886	0.561000	0.74099	CGC	G|0.762;A|0.238	0.238	strong		0.562	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
ADAM21	8747	hgsc.bcm.edu	37	14	70924697	70924697	+	Missense_Mutation	SNP	A	A	G	rs386778613|rs45545935	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:70924697A>G	ENST00000603540.1	+	2	739	c.481A>G	c.(481-483)Ata>Gta	p.I161V	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.I161V	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	161				I -> V (in Ref. 1; AAD55255 and 3; AAI09025/AAI09026). {ECO:0000305}.	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)	p.I161V(1)		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)		GGTTTATAAGATAAACAGTAA	0.423													A|||	1254	0.250399	0.3026	0.1297	5008	,	,		19080	0.496		0.1173	False		,,,				2504	0.1493				p.I161V		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	1	Substitution - Missense(1)	stomach(1)	c.A481G						scavenged	.						39.0	48.0	45.0					14																	70924697		2156	4294	6450	SO:0001583	missense	8747	exon2			TATAAGATAAACA	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.481A>G	14.37:g.70924697A>G	ENSP00000474385:p.Ile161Val	Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	84	21	0.25	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	A	0.700	-0.791263	0.02884	.	.	ENSG00000139985	ENST00000267499	T	0.01119	5.31	3.76	-5.66	0.02451	.	0.559418	0.13492	U	0.383910	T	0.00815	0.0027	L	0.41236	1.265	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.48210	-0.9055	10	0.28530	T	0.3	.	0.3958	0.00418	0.2927:0.2858:0.1722:0.2492	rs45545935	161	Q9UKJ8	ADA21_HUMAN	V	161	ENSP00000267499:I161V	ENSP00000267499:I161V	I	+	1	0	ADAM21	69994450	0.000000	0.05858	0.025000	0.17156	0.459000	0.32528	-1.436000	0.02421	-0.597000	0.05813	0.455000	0.32223	ATA	A|0.947;G|0.053	0.053	strong		0.423	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
TNRC18	84629	hgsc.bcm.edu	37	7	5353252	5353252	+	Missense_Mutation	SNP	G	G	C	rs58819185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5353252G>C	ENST00000430969.1	-	27	7618	c.7270C>G	c.(7270-7272)Cca>Gca	p.P2424A	TNRC18_ENST00000399537.4_Missense_Mutation_p.P2424A	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2424	Pro-rich.						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)		AGGGGTGCTGGGGCCAGGGAG	0.726													G|||	321	0.0640974	0.2322	0.0144	5008	,	,		11967	0.0		0.004	False		,,,				2504	0.0				p.P2424A		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7270G						PASS	.	G	ALA/PRO	536,2586		36,464,1061	11.0	12.0	11.0		7270	0.1	0.1	7	dbSNP_129	11	1,7155		0,1,3577	no	missense	TNRC18	NM_001080495.2	27	36,465,4638	CC,CG,GG		0.014,17.1685,5.2248	benign	2424/2969	5353252	537,9741	1561	3578	5139	SO:0001583	missense	84629	exon27			GTGCTGGGGCCAG	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.7270C>G	7.37:g.5353252G>C	ENSP00000395538:p.Pro2424Ala	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	155	66	0.425806	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	109|109	0.04990842490842491|0.04990842490842491	101|101	0.20528455284552846|0.20528455284552846	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	g|g	0|0	-2.731061|-2.731061	0.00089|0.00089	0.171685|0.171685	1.4E-4|1.4E-4	ENSG00000182095|ENSG00000182095	ENST00000399537;ENST00000430969|ENST00000328270	T;T|.	0.12147|.	2.71;2.71|.	3.33|3.33	0.0546|0.0546	0.14311|0.14311	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	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	0.28004|0.28004	-1.0057|-1.0057	8|4	0.08381|.	T|.	0.77|.	.|.	8.9408|8.9408	0.35729|0.35729	0.0:0.4024:0.4584:0.1392|0.0:0.4024:0.4584:0.1392	rs58819185|rs58819185	2424|.	O15417|.	TNC18_HUMAN|.	A|R	2424|237	ENSP00000382452:P2424A;ENSP00000395538:P2424A|.	ENSP00000382452:P2424A|.	P|P	-|-	1|2	0|0	TNRC18|TNRC18	5319778|5319778	0.807000|0.807000	0.29009|0.29009	0.131000|0.131000	0.22000|0.22000	0.055000|0.055000	0.15305|0.15305	2.373000|2.373000	0.44266|0.44266	-0.063000|-0.063000	0.13065|0.13065	-3.803000|-3.803000	0.00020|0.00020	CCA|CCC	G|0.943;C|0.057	0.057	strong		0.726	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PAPPA	5069	hgsc.bcm.edu	37	9	118950208	118950208	+	Silent	SNP	G	G	T	rs80284365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:118950208G>T	ENST00000328252.3	+	2	1560	c.1191G>T	c.(1189-1191)gtG>gtT	p.V397V	PAPPA_ENST00000534838.1_5'Flank	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	397	Metalloprotease.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						AGCTGGACGTGCTGGAGGTGA	0.582													G|||	222	0.0443291	0.1581	0.0115	5008	,	,		19158	0.0		0.003	False		,,,				2504	0.002				p.V397V		Atlas-SNP	.											.	PAPPA	243	.	0			c.G1191T						PASS	.	G		626,3780	270.7+/-269.8	45,536,1622	71.0	61.0	64.0		1191	1.0	1.0	9	dbSNP_132	64	32,8568	20.4+/-63.3	1,30,4269	no	coding-synonymous	PAPPA	NM_002581.3		46,566,5891	TT,TG,GG		0.3721,14.2079,5.0592		397/1628	118950208	658,12348	2203	4300	6503	SO:0001819	synonymous_variant	5069	exon2			GGACGTGCTGGAG		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"""insulin-like growth factor-dependent IGF binding protein-4 protease"", ""aspecific BCL2 ARE-binding protein 2"", ""differentially placenta 1 expressed protein"""	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.1191G>T	9.37:g.118950208G>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	78	52	0.666667	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	37	CCDS6813.1																																																																																			G|0.955;T|0.045	0.045	strong		0.582	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
MUC17	140453	hgsc.bcm.edu	37	7	100677625	100677625	+	Silent	SNP	G	G	A	rs115078078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100677625G>A	ENST00000306151.4	+	3	2992	c.2928G>A	c.(2926-2928)tcG>tcA	p.S976S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	976	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)					TACCAACCTCGACTCCTAGTG	0.507																																					p.S976S		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.G2928A						scavenged	.	A		154,4252	793.6+/-415.2	0,154,2049	352.0	328.0	336.0		2928	-1.5	0.0	7	dbSNP_133	336	106,8494	808.3+/-407.2	0,106,4194	no	coding-synonymous	MUC17	NM_001040105.1		0,260,6243	AA,AG,GG		1.2326,3.4952,1.9991		976/4494	100677625	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACCTCGACTCCT	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.2928G>A	7.37:g.100677625G>A		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	257	48	0.18677	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.964;A|0.036	0.036	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CPNE1	8904	hgsc.bcm.edu	37	20	34214173	34214173	+	Missense_Mutation	SNP	G	G	A	rs11543239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34214173G>A	ENST00000317619.3	-	18	1998	c.1604C>T	c.(1603-1605)cCc>cTc	p.P535L	CPNE1_ENST00000397446.1_Missense_Mutation_p.P535L|CPNE1_ENST00000352393.4_Missense_Mutation_p.P535L|CPNE1_ENST00000397445.1_Missense_Mutation_p.P535L|CPNE1_ENST00000397442.1_Missense_Mutation_p.P479L|CPNE1_ENST00000317677.5_Missense_Mutation_p.P540L|CPNE1_ENST00000397443.1_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	66	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	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	
CEP192	55125	hgsc.bcm.edu	37	18	13056065	13056065	+	Missense_Mutation	SNP	C	C	G	rs61739695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13056065C>G	ENST00000325971.8	+	17	3281	c.1688C>G	c.(1687-1689)cCt>cGt	p.P563R	CEP192_ENST00000506447.1_Missense_Mutation_p.P1159R|CEP192_ENST00000430049.2_Missense_Mutation_p.P684R			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	563					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ACATCAAACCCTGAGGAATTG	0.512													C|||	61	0.0121805	0.0446	0.0029	5008	,	,		19222	0.0		0.0	False		,,,				2504	0.0				p.P1159R		Atlas-SNP	.											.	CEP192	340	.	0			c.C3476G						PASS	.	C	ARG/PRO	163,4243	108.2+/-146.6	2,159,2042	47.0	48.0	47.0		3476	0.8	0.0	18	dbSNP_129	47	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CEP192	NM_032142.3	103	2,160,6341	GG,GC,CC		0.0116,3.6995,1.261	benign	1159/2538	13056065	164,12842	2203	4300	6503	SO:0001583	missense	55125	exon19			CAAACCCTGAGGA	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.1688C>G	18.37:g.13056065C>G	ENSP00000317156:p.Pro563Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	5.196	0.221789	0.09863	0.036995	1.16E-4	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.05382	3.46;3.45;3.46	4.19	0.836	0.18891	.	1.225170	0.05804	N	0.612700	T	0.00580	0.0019	N	0.16478	0.41	0.09310	N	1	B;B;B	0.11235	0.002;0.003;0.004	B;B;B	0.08055	0.002;0.003;0.003	T	0.46775	-0.9167	10	0.19147	T	0.46	0.3765	0.6935	0.00895	0.3617:0.2925:0.1361:0.2097	rs61739695	684;1159;563	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	R	1159;563;563;684	ENSP00000427550:P1159R;ENSP00000317156:P563R;ENSP00000389190:P684R	ENSP00000317156:P563R	P	+	2	0	CEP192	13046065	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	0.012000	0.13287	0.270000	0.21984	0.563000	0.77884	CCT	C|0.986;G|0.014	0.014	strong		0.512	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
GPD1	2819	hgsc.bcm.edu	37	12	50498475	50498475	+	Missense_Mutation	SNP	A	A	G	rs2232202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50498475A>G	ENST00000301149.3	+	2	392	c.160A>G	c.(160-162)Atc>Gtc	p.I54V	GPD1_ENST00000547190.1_3'UTR|GPD1_ENST00000548814.1_Missense_Mutation_p.I54V	NM_001257199.1|NM_005276.3	NP_001244128.1|NP_005267.2	P21695	GPDA_HUMAN	glycerol-3-phosphate dehydrogenase 1 (soluble)	54			I -> V (in dbSNP:rs2232202). {ECO:0000269|PubMed:22226083}.		cellular lipid metabolic process (GO:0044255)|cellular response to cAMP (GO:0071320)|cellular response to tumor necrosis factor (GO:0071356)|gluconeogenesis (GO:0006094)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophosphate shuttle (GO:0006127)|glycerophospholipid biosynthetic process (GO:0046474)|NADH oxidation (GO:0006116)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrion (GO:0005739)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|NAD binding (GO:0051287)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						GACTGAGATCATCAACACGCA	0.542													A|||	56	0.0111821	0.0424	0.0	5008	,	,		20418	0.0		0.0	False		,,,				2504	0.0				p.I54V	NSCLC(141;1402 1905 9497 13391 44868)	Atlas-SNP	.											.	GPD1	23	.	0			c.A160G						PASS	.	A	VAL/ILE	177,4229	115.4+/-153.4	7,163,2033	126.0	112.0	117.0		160	5.7	1.0	12	dbSNP_98	117	1,8599		0,1,4299	yes	missense	GPD1	NM_005276.2	29	7,164,6332	GG,GA,AA		0.0116,4.0172,1.3686	probably-damaging	54/350	50498475	178,12828	2203	4300	6503	SO:0001583	missense	2819	exon2			GAGATCATCAACA		CCDS8799.1, CCDS58229.1	12q13.12	2013-09-20			ENSG00000167588	ENSG00000167588	1.1.1.8		4455	protein-coding gene	gene with protein product		138420					Standard	NM_005276		Approved		uc001rvz.4	P21695	OTTHUMG00000169813	ENST00000301149.3:c.160A>G	12.37:g.50498475A>G	ENSP00000301149:p.Ile54Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_005276	F8W1L5|Q8N1B0	Missense_Mutation	SNP	ENST00000301149.3	37	CCDS8799.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	A	26.3	4.724233	0.89298	0.040172	1.16E-4	ENSG00000167588	ENST00000301149;ENST00000547190;ENST00000548814	T;T	0.63913	-0.07;0.53	5.7	5.7	0.88788	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.57592	0.2064	M	0.89287	3.02	0.80722	D	1	D;D;D	0.76494	0.986;0.999;0.998	P;D;D	0.85130	0.908;0.99;0.997	T	0.78267	-0.2270	10	0.87932	D	0	-16.3048	16.2858	0.82720	1.0:0.0:0.0:0.0	rs2232202;rs52818556;rs2232202	54;54;54	B4DJ37;F8W1L5;P21695	.;.;GPDA_HUMAN	V	54	ENSP00000301149:I54V;ENSP00000446768:I54V	ENSP00000301149:I54V	I	+	1	0	GPD1	48784742	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.458000	0.80787	2.313000	0.78055	0.454000	0.30748	ATC	A|0.984;G|0.016	0.016	strong		0.542	GPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406018.1		
TG	7038	hgsc.bcm.edu	37	8	134128945	134128945	+	Missense_Mutation	SNP	A	A	G	rs10091530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134128945A>G	ENST00000220616.4	+	45	7887	c.7847A>G	c.(7846-7848)aAc>aGc	p.N2616S	TG_ENST00000519543.1_Missense_Mutation_p.N749S|TG_ENST00000542445.1_Missense_Mutation_p.N986S|TG_ENST00000377869.1_Missense_Mutation_p.N2559S	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2616			N -> S (in dbSNP:rs10091530).		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)		GCTCCTGAAAACTACGGCCAT	0.507													G|||	445	0.0888578	0.3222	0.0231	5008	,	,		19667	0.0		0.003	False		,,,				2504	0.0				p.N2616S		Atlas-SNP	.											.	TG	416	.	0			c.A7847G						PASS	.	G	SER/ASN	1189,3217	708.9+/-407.7	146,897,1160	99.0	79.0	86.0		7847	1.4	0.0	8	dbSNP_119	86	13,8587	818.8+/-406.8	0,13,4287	yes	missense	TG	NM_003235.4	46	146,910,5447	GG,GA,AA		0.1512,26.9859,9.2419	benign	2616/2769	134128945	1202,11804	2203	4300	6503	SO:0001583	missense	7038	exon45			CTGAAAACTACGG	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.7847A>G	8.37:g.134128945A>G	ENSP00000220616:p.Asn2616Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	168	0.07692307692307693	154	0.3130081300813008	13	0.03591160220994475	0	0.0	1	0.0013192612137203166	G	0.003	-2.513501	0.00153	0.269859	0.001512	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543;ENST00000521107	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;0.84	5.6	1.44	0.22558	Carboxylesterase, type B (1);	1.570080	0.03060	N	0.155775	T	0.00012	0.0000	N	0.01824	-0.7	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	0.16958	-1.0385	9	0.02654	T	1	.	7.3691	0.26792	0.2156:0.242:0.5423:0.0	rs10091530;rs52800587;rs10091530	749;986;2616	E7EVM0;F5GWW5;P01266	.;.;THYG_HUMAN	S	2559;1422;2616;986;749;65	ENSP00000367100:N2559S;ENSP00000220616:N2616S;ENSP00000441693:N986S;ENSP00000430430:N749S;ENSP00000430161:N65S	ENSP00000220616:N2616S	N	+	2	0	TG	134198127	0.953000	0.32496	0.010000	0.14722	0.036000	0.12997	0.683000	0.25349	0.064000	0.16427	-1.149000	0.01842	AAC	A|0.902;G|0.098;T|0.000	0.098	strong		0.507	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
GC	2638	hgsc.bcm.edu	37	4	72622566	72622566	+	Silent	SNP	A	A	G	rs4752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:72622566A>G	ENST00000273951.8	-	8	1240	c.897T>C	c.(895-897)tgT>tgC	p.C299C	GC_ENST00000513476.1_Silent_p.C299C|RNA5SP163_ENST00000410304.1_RNA|GC_ENST00000504199.1_Silent_p.C318C|GC_ENST00000503472.1_5'UTR	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	299	Albumin 2. {ECO:0000255|PROSITE- ProRule:PRU00769}.				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)			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)	TTTCTTGACAACAGTCTTCAA	0.418													A|||	529	0.105631	0.2965	0.0634	5008	,	,		16631	0.0794		0.0119	False		,,,				2504	0.001				p.C318C		Atlas-SNP	.											.	GC	132	.	0			c.T954C						PASS	.	A	,,	1038,3368	381.6+/-324.1	136,766,1301	74.0	74.0	74.0		897,897,954	0.4	1.0	4	dbSNP_52	74	31,8569	21.6+/-65.8	0,31,4269	no	coding-synonymous,coding-synonymous,coding-synonymous	GC	NM_000583.3,NM_001204306.1,NM_001204307.1	,,	136,797,5570	GG,GA,AA		0.3605,23.5588,8.2193	,,	299/475,299/475,318/494	72622566	1069,11937	2203	4300	6503	SO:0001819	synonymous_variant	2638	exon9			TTGACAACAGTCT	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.897T>C	4.37:g.72622566A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_001204307	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Silent	SNP	ENST00000273951.8	37	CCDS3550.1																																																																																			A|0.897;G|0.103	0.103	strong		0.418	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2		
ZNF543	125919	hgsc.bcm.edu	37	19	57840547	57840547	+	Missense_Mutation	SNP	A	A	G	rs10410649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	103	0	0		WXS	Illumina HiSeq	Phase_I	123	60	0.487805	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	
CCDC186	55088	hgsc.bcm.edu	37	10	115922774	115922774	+	Missense_Mutation	SNP	G	G	A	rs1061159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	173	0	0		WXS	Illumina HiSeq	Phase_I	176	87	0.494318	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		
TLR7	51284	hgsc.bcm.edu	37	X	12903659	12903659	+	Missense_Mutation	SNP	A	A	T	rs179008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:12903659A>T	ENST00000380659.3	+	3	171	c.32A>T	c.(31-33)cAa>cTa	p.Q11L		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	11			Q -> L (in dbSNP:rs179008). {ECO:0000269|PubMed:19924287}.		cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	CTGAAGAGACAAATTCTTATC	0.358													A|||	446	0.118146	0.0908	0.1599	3775	,	,		14565	0.0		0.1759	False		,,,				2504	0.0389				p.Q11L		Atlas-SNP	.											.	TLR7	125	.	0			c.A32T	GRCh37	CM084786	TLR7	M	rs179008	PASS	.	A	LEU/GLN	521,3314		25,397,74,1210,497	129.0	129.0	129.0		32	-5.4	0.0	X	dbSNP_79	129	1429,5299		98,792,441,1538,1431	yes	missense	TLR7	NM_016562.3	113	123,1189,515,2748,1928	TT,TA,T,AA,A		21.2396,13.5854,18.4607	benign	11/1050	12903659	1950,8613	2203	4300	6503	SO:0001583	missense	51284	exon3			AGAGACAAATTCT	AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.32A>T	X.37:g.12903659A>T	ENSP00000370034:p.Gln11Leu	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	173	81	0.468208	NM_016562	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	37	CCDS14151.1	253	0.1525015069318867	34	0.0735930735930736	38	0.1165644171779141	0	0.0	110	0.16224188790560473	A	8.200	0.797989	0.16327	0.135854	0.212396	ENSG00000196664	ENST00000380659	T	0.46819	0.86	5.72	-5.42	0.02640	.	0.888102	0.09632	N	0.776072	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	0.24657	-1.0154	9	0.37606	T	0.19	.	1.4567	0.02387	0.262:0.3564:0.1455:0.2361	rs179008;rs629938;rs17256060;rs179008	11	Q9NYK1	TLR7_HUMAN	L	11	ENSP00000370034:Q11L	ENSP00000370034:Q11L	Q	+	2	0	TLR7	12813580	0.000000	0.05858	0.000000	0.03702	0.519000	0.34347	0.053000	0.14184	-0.637000	0.05516	0.421000	0.28195	CAA	0|0.021;A|0.822;T|0.157	0.157	strong		0.358	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562	
HYDIN	54768	hgsc.bcm.edu	37	16	70954682	70954682	+	Missense_Mutation	SNP	G	G	A	rs143849088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70954682G>A	ENST00000393567.2	-	46	7747	c.7597C>T	c.(7597-7599)Cgg>Tgg	p.R2533W		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2533					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)				aggcgctcccgctccgccttc	0.697													G|||	17	0.00339457	0.0129	0.0	5008	,	,		19002	0.0		0.0	False		,,,				2504	0.0				p.R2533W		Atlas-SNP	.											.	HYDIN	788	.	0			c.C7597T						PASS	.	G	TRP/ARG	28,3858		0,28,1915	20.0	21.0	21.0		7594	-0.8	1.0	16	dbSNP_134	21	0,8242		0,0,4121	yes	missense	HYDIN	NM_032821.2	101	0,28,6036	AA,AG,GG		0.0,0.7205,0.2309	probably-damaging	2532/5121	70954682	28,12100	1943	4121	6064	SO:0001583	missense	54768	exon46			GCTCCCGCTCCGC	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.7597C>T	16.37:g.70954682G>A	ENSP00000377197:p.Arg2533Trp	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	18.32	3.597425	0.66332	0.007205	0.0	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01178	5.22	5.89	-0.796	0.10912	.	0.000000	0.33834	U	0.004514	T	0.01061	0.0035	N	0.14661	0.345	0.25478	N	0.987764	D	0.89917	1.0	D	0.72338	0.977	T	0.38134	-0.9675	10	0.72032	D	0.01	.	13.9873	0.64343	0.1005:0.0:0.6814:0.2181	.	2532	F8WD23	.	W	2533;2532	ENSP00000377197:R2533W	ENSP00000313052:R2532W	R	-	1	2	HYDIN	69512183	0.996000	0.38824	0.984000	0.44739	0.832000	0.47134	0.126000	0.15769	-0.426000	0.07360	-1.296000	0.01341	CGG	G|0.996;A|0.004	0.004	strong		0.697	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
ZNF479	90827	hgsc.bcm.edu	37	7	57187997	57187997	+	Missense_Mutation	SNP	A	A	T	rs146543279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:57187997A>T	ENST00000331162.4	-	5	1395	c.1125T>A	c.(1123-1125)caT>caA	p.H375Q		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	375					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			TCTCTCCAGTATGAATTCTCC	0.438													.|||	12	0.00239617	0.0091	0.0	5008	,	,		21893	0.0		0.0	False		,,,				2504	0.0				p.H375Q		Atlas-SNP	.											.	ZNF479	193	.	0			c.T1125A						PASS	.	A	GLN/HIS	39,4097		0,39,2029	42.0	43.0	43.0		1125	0.9	0.0	7	dbSNP_134	43	0,8454		0,0,4227	no	missense	ZNF479	NM_033273.1	24	0,39,6256	TT,TA,AA		0.0,0.9429,0.3098	probably-damaging	375/525	57187997	39,12551	2068	4227	6295	SO:0001583	missense	90827	exon5			TCCAGTATGAATT	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"""Zinc fingers, C2H2-type"", ""-"""	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.1125T>A	7.37:g.57187997A>T	ENSP00000333776:p.His375Gln	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	281	143	0.508897	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	37	CCDS43590.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	a	11.55	1.671267	0.29693	0.009429	0.0	ENSG00000185177	ENST00000331162	T	0.66995	-0.24	0.946	0.946	0.19549	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.71685	0.3369	M	0.86268	2.805	0.24579	N	0.993888	D	0.55385	0.971	D	0.65773	0.938	T	0.62501	-0.6841	9	0.87932	D	0	.	2.9462	0.05847	0.6852:0.0:0.3148:0.0	.	375	Q96JC4	ZN479_HUMAN	Q	375	ENSP00000333776:H375Q	ENSP00000333776:H375Q	H	-	3	2	ZNF479	57191939	0.998000	0.40836	0.011000	0.14972	0.010000	0.07245	0.567000	0.23608	0.339000	0.23719	0.329000	0.21502	CAT	A|0.998;T|0.002	0.002	strong		0.438	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202	
SFI1	9814	hgsc.bcm.edu	37	22	32014161	32014161	+	Silent	SNP	G	G	A	rs55735011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32014161G>A	ENST00000400288.2	+	32	3678	c.3573G>A	c.(3571-3573)ccG>ccA	p.P1191P	SFI1_ENST00000540643.1_Silent_p.P1136P|SFI1_ENST00000474741.1_Intron|PISD_ENST00000478893.1_5'Flank|SFI1_ENST00000432498.1_Silent_p.P1160P|SFI1_ENST00000443326.1_Silent_p.P1109P|SFI1_ENST00000400289.1_Silent_p.P1109P|SFI1_ENST00000443011.1_Silent_p.P1038P|SFI1_ENST00000414585.1_3'UTR	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	1191					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GAGAGGAGCCGGGGCCTGAGG	0.677													G|||	273	0.0545128	0.0915	0.0216	5008	,	,		17595	0.0069		0.0368	False		,,,				2504	0.0951				p.P1191P		Atlas-SNP	.											SFI1,NS,carcinoma,0,1	SFI1	78	1	0			c.G3573A						PASS	.	G	,	231,3733		7,217,1758	23.0	29.0	27.0		3573,3480	-4.4	0.0	22	dbSNP_129	27	232,8116		3,226,3945	no	coding-synonymous,coding-synonymous	SFI1	NM_001007467.1,NM_014775.2	,	10,443,5703	AA,AG,GG		2.7791,5.8274,3.7606	,	1191/1243,1160/1212	32014161	463,11849	1982	4174	6156	SO:0001819	synonymous_variant	9814	exon32			GGAGCCGGGGCCT	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.3573G>A	22.37:g.32014161G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	192	92	0.479167	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Silent	SNP	ENST00000400288.2	37	CCDS43004.1																																																																																			G|0.959;A|0.041	0.041	strong		0.677	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	
NEDD4	4734	hgsc.bcm.edu	37	15	56207811	56207811	+	Missense_Mutation	SNP	T	T	G	rs62043855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56207811T>G	ENST00000508342.1	-	1	1518	c.1219A>C	c.(1219-1221)Aat>Cat	p.N407H	NEDD4_ENST00000506154.1_Missense_Mutation_p.N407H|NEDD4_ENST00000338963.2_Missense_Mutation_p.N407H|NEDD4_ENST00000435532.3_Intron	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	407				N -> H (in Ref. 5; AL832063). {ECO:0000305}.	adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		GAATCAGAATTAAGCTTAATT	0.353													T|||	991	0.197883	0.1536	0.1455	5008	,	,		20956	0.3591		0.1541	False		,,,				2504	0.1738				p.N407H		Atlas-SNP	.											.	NEDD4	167	.	0			c.A1219C						PASS	.	T	,HIS/ASN	673,3713	281.6+/-276.1	53,567,1573	61.0	60.0	60.0		,1219	0.3	0.0	15	dbSNP_129	60	1064,7520	222.9+/-259.8	51,962,3279	yes	intron,missense	NEDD4	NM_006154.2,NM_198400.2	,68	104,1529,4852	GG,GT,TT		12.3952,15.3443,13.3924	,probably-damaging	,407/1248	56207811	1737,11233	2193	4292	6485	SO:0001583	missense	4734	exon1			CAGAATTAAGCTT	D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"""receptor-potentiating factor 1"""	602278	"""neural precursor cell expressed, developmentally down-regulated 4"""			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.1219A>C	15.37:g.56207811T>G	ENSP00000424827:p.Asn407His	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	209	94	0.449761	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	37		487|487	0.222985347985348|0.222985347985348	89|89	0.18089430894308944|0.18089430894308944	50|50	0.13812154696132597|0.13812154696132597	216|216	0.3776223776223776|0.3776223776223776	132|132	0.1741424802110818|0.1741424802110818	T|T	14.48|14.48	2.547116|2.547116	0.45383|0.45383	0.153443|0.153443	0.123952|0.123952	ENSG00000069869|ENSG00000069869	ENST00000508871|ENST00000508342;ENST00000338963;ENST00000506154	T|T;T;T	0.26373|0.23552	1.74|1.91;1.9;1.91	5.46|5.46	0.326|0.326	0.15908|0.15908	.|.	.|0.765588	.|0.10812	.|N	.|0.631469	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.14012	.|0.009;0.005;0.009	.|B;B;B	.|0.19946	.|0.016;0.007;0.027	T|T	0.38757|0.38757	-0.9646|-0.9646	6|9	0.87932|0.87932	D|D	0|0	.|.	5.6724|5.6724	0.17729|0.17729	0.0:0.1472:0.2813:0.5715|0.0:0.1472:0.2813:0.5715	rs62043855|rs62043855	.|407;407;407	.|P46934-2;P46934;P46934-3	.|.;NEDD4_HUMAN;.	F|H	14|407	ENSP00000422455:L14F|ENSP00000424827:N407H;ENSP00000345530:N407H;ENSP00000422705:N407H	ENSP00000422455:L14F|ENSP00000345530:N407H	L|N	-|-	3|1	2|0	NEDD4|NEDD4	53995103|53995103	0.092000|0.092000	0.21681|0.21681	0.000000|0.000000	0.03702|0.03702	0.971000|0.971000	0.66376|0.66376	0.561000|0.561000	0.23515|0.23515	-0.182000|-0.182000	0.10602|0.10602	0.377000|0.377000	0.23210|0.23210	TTA|AAT	T|0.841;G|0.159	0.159	strong		0.353	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400	
SLC12A4	6560	hgsc.bcm.edu	37	16	67980969	67980969	+	Silent	SNP	G	G	C	rs11860125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67980969G>C	ENST00000316341.3	-	17	2252	c.2112C>G	c.(2110-2112)ctC>ctG	p.L704L	SLC12A4_ENST00000537830.2_Silent_p.L698L|SLC12A4_ENST00000541864.2_Silent_p.L673L|CTC-479C5.17_ENST00000590594.1_lincRNA|SLC12A4_ENST00000572037.1_Silent_p.L656L|SLC12A4_ENST00000422611.2_Silent_p.L706L|SLC12A4_ENST00000338335.3_Silent_p.L704L|SLC12A4_ENST00000576616.1_Silent_p.L704L|LCAT_ENST00000264005.5_5'Flank	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	704					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	ACTTCACGTGGAGGTCCTCGT	0.657													C|||	741	0.147963	0.4297	0.0793	5008	,	,		16905	0.006		0.0467	False		,,,				2504	0.0665				p.L706L		Atlas-SNP	.											.	SLC12A4	81	.	0			c.C2118G						PASS	.	C	,,,,	1608,2782	627.4+/-394.9	300,1008,887	26.0	22.0	23.0		2112,2118,2094,2019,2112	-9.4	0.3	16	dbSNP_120	23	422,8176	771.7+/-407.7	12,398,3889	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC12A4	NM_001145961.1,NM_001145962.1,NM_001145963.1,NM_001145964.1,NM_005072.4	,,,,	312,1406,4776	CC,CG,GG		4.9081,36.6287,15.6298	,,,,	704/1080,706/1088,698/1080,673/1055,704/1086	67980969	2030,10958	2195	4299	6494	SO:0001819	synonymous_variant	6560	exon16			CACGTGGAGGTCC		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"""Solute carriers"""	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.2112C>G	16.37:g.67980969G>C		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Silent	SNP	ENST00000316341.3	37	CCDS10855.1																																																																																			G|0.849;C|0.151	0.151	strong		0.657	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072	
PLA2G4B	100137049	hgsc.bcm.edu	37	15	42137201	42137201	+	Missense_Mutation	SNP	G	G	A	rs34807597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42137201G>A	ENST00000452633.1	+	14	1524	c.1172G>A	c.(1171-1173)cGc>cAc	p.R391H	JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.R622H|PLA2G4B_ENST00000542534.2_Missense_Mutation_p.R622H|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.R622H|PLA2G4B_ENST00000458483.1_Missense_Mutation_p.R391H			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	391	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		R -> H (in dbSNP:rs34807597).		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)		GAGCGTGCCCGCTTGGGCTAC	0.672													G|||	77	0.0153754	0.0552	0.0043	5008	,	,		15685	0.0		0.001	False		,,,				2504	0.0				p.R622H		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.G1865A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	189,4209		7,175,2017	16.0	17.0	17.0		1172,1865,1865	-1.9	0.4	15	dbSNP_126	17	3,8581		0,3,4289	yes	missense,missense,missense	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	29,29,29	7,178,6306	AA,AG,GG		0.0349,4.2974,1.479	benign,benign,benign	391/782,622/894,622/1013	42137201	192,12790	2199	4292	6491	SO:0001583	missense	8681	exon18			GTGCCCGCTTGGG	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.1172G>A	15.37:g.42137201G>A	ENSP00000396045:p.Arg391His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	25	0.011446886446886446	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	.	10.30	1.310981	0.23821	0.042974	3.49E-4	ENSG00000168970;ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000382448;ENST00000342159;ENST00000458483;ENST00000452633	T;T;T;T	0.04603	3.59;3.59;3.59;3.59	5.51	-1.88	0.07713	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.492693	0.18810	N	0.130531	T	0.01156	0.0038	M	0.65498	2.005	0.09310	N	1	B;B;B;B	0.13594	0.008;0.0;0.003;0.003	B;B;B;B	0.12156	0.007;0.0;0.002;0.001	T	0.30001	-0.9993	10	0.62326	D	0.03	-2.658	5.6051	0.17374	0.6081:0.0:0.2403:0.1516	rs34807597	391;622;92;622	P0C869;P0C869-7;P0C869-4;P0C869-6	PA24B_HUMAN;.;.;.	H	622;622;391;391	ENSP00000371886:R622H;ENSP00000342785:R622H;ENSP00000416610:R391H;ENSP00000396045:R391H	ENSP00000342785:R622H	R	+	2	0	JMJD7-PLA2G4B;PLA2G4B	39924493	0.002000	0.14202	0.381000	0.26106	0.055000	0.15305	0.861000	0.27885	-0.138000	0.11434	0.561000	0.74099	CGC	G|0.984;A|0.016	0.016	strong		0.672	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633	
PLA1A	51365	hgsc.bcm.edu	37	3	119331892	119331892	+	Silent	SNP	C	C	G	rs2272269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119331892C>G	ENST00000273371.4	+	5	663	c.591C>G	c.(589-591)acC>acG	p.T197T	PLA1A_ENST00000495992.1_Silent_p.T181T|PLA1A_ENST00000494440.1_Silent_p.T181T|PLA1A_ENST00000488919.1_Silent_p.T24T	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	197					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CTGAGTACACCAGGGCCAGTG	0.582													C|||	1542	0.307907	0.4274	0.1484	5008	,	,		20410	0.4484		0.161	False		,,,				2504	0.2658				p.T197T		Atlas-SNP	.											.	PLA1A	65	.	0			c.C591G						PASS	.	C	,,	1842,2564	510.1+/-367.4	384,1074,745	58.0	44.0	49.0		543,72,591	4.1	1.0	3	dbSNP_100	49	1443,7157	258.7+/-282.2	112,1219,2969	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA1A	NM_001206960.1,NM_001206961.1,NM_015900.3	,,	496,2293,3714	GG,GC,CC		16.7791,41.8066,25.2576	,,	181/441,24/284,197/457	119331892	3285,9721	2203	4300	6503	SO:0001819	synonymous_variant	51365	exon5			GTACACCAGGGCC	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.591C>G	3.37:g.119331892C>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Silent	SNP	ENST00000273371.4	37	CCDS2991.1																																																																																			C|0.730;G|0.270	0.270	strong		0.582	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2		
SLC38A8	146167	hgsc.bcm.edu	37	16	84050218	84050218	+	Silent	SNP	G	G	A	rs13334006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84050218G>A	ENST00000299709.3	-	8	1067	c.1068C>T	c.(1066-1068)acC>acT	p.T356T		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	356					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						CGAGCGTCACGGTGACCCACA	0.627													G|||	295	0.0589058	0.2156	0.0144	5008	,	,		20259	0.0		0.0	False		,,,				2504	0.0				p.T356T		Atlas-SNP	.											.	SLC38A8	60	.	0			c.C1068T						PASS	.	G		822,3578	326.1+/-299.4	78,666,1456	74.0	67.0	69.0		1068	-7.5	0.0	16	dbSNP_121	69	12,8588	7.7+/-29.5	0,12,4288	no	coding-synonymous	SLC38A8	NM_001080442.1		78,678,5744	AA,AG,GG		0.1395,18.6818,6.4154		356/436	84050218	834,12166	2200	4300	6500	SO:0001819	synonymous_variant	146167	exon8			CGTCACGGTGACC		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.1068C>T	16.37:g.84050218G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_001080442		Silent	SNP	ENST00000299709.3	37	CCDS32495.1																																																																																			G|0.939;A|0.061	0.061	strong		0.627	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
ABCB11	8647	hgsc.bcm.edu	37	2	169836388	169836388	+	Silent	SNP	C	C	T	rs57509552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:169836388C>T	ENST00000263817.6	-	11	1309	c.1185G>A	c.(1183-1185)gaG>gaA	p.E395E		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	395					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)	TGTCTATTGTCTCAAAAATGC	0.463													C|||	104	0.0207668	0.0749	0.0072	5008	,	,		15538	0.0		0.0	False		,,,				2504	0.0				p.E395E		Atlas-SNP	.											.	ABCB11	136	.	0			c.G1185A						PASS	.	C		216,3524		4,208,1658	92.0	89.0	90.0		1185	-1.7	1.0	2	dbSNP_129	90	1,8207		0,1,4103	no	coding-synonymous	ABCB11	NM_003742.2		4,209,5761	TT,TC,CC		0.0122,5.7754,1.8162		395/1322	169836388	217,11731	1870	4104	5974	SO:0001819	synonymous_variant	8647	exon11			TATTGTCTCAAAA	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.1185G>A	2.37:g.169836388C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	37	CCDS46444.1																																																																																			C|0.980;T|0.020	0.020	strong		0.463	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138738204	138738204	+	Silent	SNP	G	G	A	rs11977775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:138738204G>A	ENST00000242351.5	-	12	2758	c.2442C>T	c.(2440-2442)taC>taT	p.Y814Y	ZC3HAV1_ENST00000464606.1_Silent_p.Y936Y	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	814	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						AACCTTTTCCGTATTTGTTTT	0.363													A|||	517	0.103235	0.2897	0.0504	5008	,	,		20828	0.0248		0.0338	False		,,,				2504	0.0409				p.Y814Y		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.C2442T						PASS	.	A		1173,3233	711.4+/-408.0	153,867,1183	119.0	123.0	121.0		2442	0.2	1.0	7	dbSNP_120	121	231,8369	808.7+/-407.2	1,229,4070	no	coding-synonymous	ZC3HAV1	NM_020119.3		154,1096,5253	AA,AG,GG		2.686,26.6228,10.795		814/903	138738204	1404,11602	2203	4300	6503	SO:0001819	synonymous_variant	56829	exon12			TTTTCCGTATTTG	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.2442C>T	7.37:g.138738204G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	102	32	0.313726	NM_020119	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Silent	SNP	ENST00000242351.5	37	CCDS5851.1																																																																																			G|0.898;A|0.102	0.102	strong		0.363	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
KBTBD6	89890	hgsc.bcm.edu	37	13	41706450	41706450	+	Silent	SNP	G	G	C	rs147388453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:41706450G>C	ENST00000379485.1	-	1	432	c.198C>G	c.(196-198)acC>acG	p.T66T	KBTBD6_ENST00000499385.2_Intron	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	66	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		CCACCTCGATGGTCACATCAC	0.607													G|||	43	0.00858626	0.031	0.0014	5008	,	,		18622	0.0		0.001	False		,,,				2504	0.0				p.T66T		Atlas-SNP	.											.	KBTBD6	83	.	0			c.C198G						PASS	.	G		152,4254	104.7+/-143.2	0,152,2051	89.0	89.0	89.0		198	3.7	1.0	13	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KBTBD6	NM_152903.4		0,153,6350	CC,CG,GG		0.0116,3.4498,1.1764		66/675	41706450	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	89890	exon1			CTCGATGGTCACA	AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"""BTB/POZ domain containing"""	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.198C>G	13.37:g.41706450G>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Silent	SNP	ENST00000379485.1	37	CCDS9376.1																																																																																			G|0.988;C|0.012	0.012	strong		0.607	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903	
CPNE3	8895	hgsc.bcm.edu	37	8	87558846	87558846	+	Missense_Mutation	SNP	G	G	C	rs41333046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87558846G>C	ENST00000521271.1	+	10	918	c.756G>C	c.(754-756)gaG>gaC	p.E252D	CPNE3_ENST00000198765.4_Missense_Mutation_p.E252D	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	252			E -> D (in dbSNP:rs41333046).		lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						GCATAAATGAGAAAAAAAGGC	0.308													G|||	571	0.114018	0.41	0.0303	5008	,	,		17040	0.004		0.003	False		,,,				2504	0.001				p.E252D		Atlas-SNP	.											CPNE3,NS,carcinoma,0,1	CPNE3	65	1	0			c.G756C						PASS	.	G	ASP/GLU	1372,3034	453.4+/-350.3	207,958,1038	90.0	103.0	98.0		756	1.6	1.0	8	dbSNP_127	98	14,8586	8.4+/-32.0	0,14,4286	yes	missense	CPNE3	NM_003909.3	45	207,972,5324	CC,CG,GG		0.1628,31.1394,10.6566	benign	252/538	87558846	1386,11620	2203	4300	6503	SO:0001583	missense	8895	exon10			AAATGAGAAAAAA	AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719			2316	protein-coding gene	gene with protein product		604207				9430674	Standard	NM_003909		Approved		uc003ydv.2	O75131		ENST00000521271.1:c.756G>C	8.37:g.87558846G>C	ENSP00000430934:p.Glu252Asp	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	270	141	0.522222	NM_003909	A8KA47|Q8IYA1	Missense_Mutation	SNP	ENST00000521271.1	37	CCDS6243.1	199|199	0.09111721611721611|0.09111721611721611	186|186	0.3780487804878049|0.3780487804878049	11|11	0.03038674033149171|0.03038674033149171	1|1	0.0017482517482517483|0.0017482517482517483	1|1	0.0013192612137203166|0.0013192612137203166	G|G	14.05|14.05	2.420410|2.420410	0.42918|0.42918	0.311394|0.311394	0.001628|0.001628	ENSG00000085719|ENSG00000085719	ENST00000198765;ENST00000521271|ENST00000517391	T;T|.	0.39787|.	1.06;1.06|.	5.52|5.52	1.62|1.62	0.23740|0.23740	C2 calcium/lipid-binding domain, CaLB (1);|.	0.106801|.	0.64402|.	D|.	0.000001|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.45352|0.45352	1.415|1.415	0.27719|0.27719	P|P	0.9451934|0.9451934	B|.	0.32051|.	0.354|.	B|.	0.26614|.	0.071|.	T|T	0.40739|0.40739	-0.9547|-0.9547	9|4	0.59425|.	D|.	0.04|.	-12.9148|-12.9148	9.7986|9.7986	0.40751|0.40751	0.5228:0.0:0.4772:0.0|0.5228:0.0:0.4772:0.0	rs41333046|rs41333046	252|.	O75131|.	CPNE3_HUMAN|.	D|T	252|141	ENSP00000198765:E252D;ENSP00000430934:E252D|.	ENSP00000198765:E252D|.	E|R	+|+	3|2	2|0	CPNE3|CPNE3	87627962|87627962	0.931000|0.931000	0.31567|0.31567	0.998000|0.998000	0.56505|0.56505	0.984000|0.984000	0.73092|0.73092	0.121000|0.121000	0.15667|0.15667	0.078000|0.078000	0.16900|0.16900	-0.355000|-0.355000	0.07637|0.07637	GAG|AGA	G|0.888;C|0.112	0.112	strong		0.308	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1		
TFRC	7037	hgsc.bcm.edu	37	3	195787102	195787102	+	Silent	SNP	C	C	T	rs111276121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195787102C>T	ENST00000360110.4	-	14	1654	c.1485G>A	c.(1483-1485)aaG>aaA	p.K495K	TFRC_ENST00000420415.1_Silent_p.K414K|TFRC_ENST00000465288.1_5'UTR|TFRC_ENST00000392396.3_Silent_p.K495K|TFRC_ENST00000535031.1_Silent_p.K213K|TFRC_ENST00000540528.1_3'UTR	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	495					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)	TGGCAGAAACCTTGAAGTTGC	0.338			T	BCL6	NHL								C|||	9	0.00179712	0.0068	0.0	5008	,	,		19006	0.0		0.0	False		,,,				2504	0.0				p.K495K		Atlas-SNP	.		Dom	yes		3	3q29	7037	"""transferrin receptor (p90, CD71)"""		L	.	TFRC	54	.	0			c.G1485A						PASS	.	C	,	27,4379	33.5+/-64.1	0,27,2176	158.0	144.0	148.0		1485,1485	-0.4	1.0	3	dbSNP_132	148	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TFRC	NM_001128148.1,NM_003234.2	,	0,27,6476	TT,TC,CC		0.0,0.6128,0.2076	,	495/761,495/761	195787102	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	7037	exon14			AGAAACCTTGAAG	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.1485G>A	3.37:g.195787102C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	164	86	0.52439	NM_001128148	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Silent	SNP	ENST00000360110.4	37	CCDS3312.1																																																																																			C|0.997;T|0.003	0.003	strong		0.338	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1		
ATP10A	57194	hgsc.bcm.edu	37	15	25962057	25962057	+	Silent	SNP	C	C	T	rs115618637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25962057C>T	ENST00000356865.6	-	9	1707	c.1596G>A	c.(1594-1596)acG>acA	p.T532T		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	532			T -> M (in dbSNP:rs2066703).		ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TTGGGTCGGGCGTGATATCCT	0.577													C|||	11	0.00219649	0.0083	0.0	5008	,	,		15659	0.0		0.0	False		,,,				2504	0.0				p.T532T		Atlas-SNP	.											.	ATP10A	270	.	0			c.G1596A						PASS	.	C		36,4370	40.0+/-72.8	0,36,2167	85.0	63.0	71.0		1596	-10.8	0.2	15	dbSNP_132	71	0,8600		0,0,4300	no	coding-synonymous	ATP10A	NM_024490.3		0,36,6467	TT,TC,CC		0.0,0.8171,0.2768		532/1500	25962057	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon9			GTCGGGCGTGATA	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1596G>A	15.37:g.25962057C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	113	47	0.415929	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			C|0.998;T|0.002	0.002	strong		0.577	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
PDE9A	5152	hgsc.bcm.edu	37	21	44189172	44189172	+	Silent	SNP	A	A	C	rs3087994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44189172A>C	ENST00000291539.6	+	17	1557	c.1497A>C	c.(1495-1497)gcA>gcC	p.A499A	PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000335512.4_Silent_p.A439A|PDE9A_ENST00000398224.3_Silent_p.A372A|PDE9A_ENST00000539837.1_Silent_p.A371A|PDE9A_ENST00000398227.3_Silent_p.A339A|PDE9A_ENST00000398232.3_Silent_p.A432A|PDE9A_ENST00000335440.6_Silent_p.A397A|PDE9A_ENST00000398234.3_Silent_p.A398A|PDE9A_ENST00000398225.3_Silent_p.A458A|PDE9A_ENST00000380328.2_Silent_p.A446A|PDE9A_ENST00000398229.3_Silent_p.A365A|PDE9A_ENST00000349112.3_Silent_p.A371A|PDE9A_ENST00000398236.3_Silent_p.A413A|PDE9A_ENST00000328862.6_Silent_p.A473A	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	499	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	TTCCTGTGGCACCGTTCATGG	0.507													C|||	2524	0.503994	0.6551	0.4308	5008	,	,		24250	0.4226		0.3708	False		,,,				2504	0.5726				p.A499A		Atlas-SNP	.											.	PDE9A	69	.	0			c.A1497C						PASS	.	C	,,,,,,,,,,,,,,,,,,,	2643,1763	522.5+/-370.8	784,1075,344	182.0	152.0	162.0		1317,1116,1113,1338,1194,876,876,1239,1017,846,1095,1191,876,846,1296,1374,1419,876,876,1497	1.4	1.0	21	dbSNP_102	162	3112,5488	658.7+/-401.6	587,1938,1775	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	,,,,,,,,,,,,,,,,,,,	1371,3013,2119	CC,CA,AA		36.186,40.0136,44.2488	,,,,,,,,,,,,,,,,,,,	439/534,372/467,371/466,446/541,398/493,292/387,292/387,413/508,339/434,282/377,365/460,397/492,292/387,282/377,432/527,458/553,473/568,292/387,292/387,499/594	44189172	5755,7251	2203	4300	6503	SO:0001819	synonymous_variant	5152	exon17			TGTGGCACCGTTC	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.1497A>C	21.37:g.44189172A>C		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Silent	SNP	ENST00000291539.6	37	CCDS13690.1																																																																																			T|0.000;G|0.000;C|0.437;A|0.562	0.437	strong		0.507	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
AREL1	9870	hgsc.bcm.edu	37	14	75142606	75142606	+	Silent	SNP	G	G	A	rs35864766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:75142606G>A	ENST00000356357.4	-	8	1391	c.876C>T	c.(874-876)ggC>ggT	p.G292G	AREL1_ENST00000557401.1_5'UTR	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	292					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										AAATGCTCACGCCTGAAGTGG	0.443													G|||	35	0.00698882	0.0008	0.0101	5008	,	,		20927	0.0		0.0129	False		,,,				2504	0.0143				p.G292G		Atlas-SNP	.											.	KIAA0317	68	.	0			c.C876T						PASS	.	G		21,3991		0,21,1985	139.0	140.0	140.0		876	-1.4	1.0	14	dbSNP_126	140	193,8157		6,181,3988	no	coding-synonymous	KIAA0317	NM_001039479.1		6,202,5973	AA,AG,GG		2.3114,0.5234,1.7311		292/824	75142606	214,12148	2006	4175	6181	SO:0001819	synonymous_variant	9870	exon8			GCTCACGCCTGAA	AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"""KIAA0317"""	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.876C>T	14.37:g.75142606G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	107	62	0.579439	NM_001039479	B4E2C7|Q7LDY1|Q8IYY9	Silent	SNP	ENST00000356357.4	37	CCDS41971.1	13	0.005952380952380952	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	8	0.010554089709762533	G	9.535	1.111930	0.20714	0.005234	0.023114	ENSG00000119682	ENST00000490805	.	.	.	5.87	-1.44	0.08856	.	.	.	.	.	T	0.22859	0.0552	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25847	-1.0120	4	.	.	.	.	0.1629	0.00105	0.3435:0.1631:0.1871:0.3063	rs35864766	.	.	.	V	40	.	.	A	-	2	0	KIAA0317	74212359	0.816000	0.29132	0.998000	0.56505	0.936000	0.57629	-0.124000	0.10595	-0.091000	0.12440	-0.383000	0.06682	GCG	G|0.985;A|0.015	0.015	strong		0.443	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821	
USP18	11274	hgsc.bcm.edu	37	22	18644597	18644597	+	Missense_Mutation	SNP	G	G	A	rs143481018		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:18644597G>A	ENST00000215794.7	+	4	725	c.295G>A	c.(295-297)Gtc>Atc	p.V99I		NM_017414.3	NP_059110.2	Q9UMW8	UBP18_HUMAN	ubiquitin specific peptidase 18	99	USP.				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)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|stomach(1)	10						GAGGAGAAGCGTCCCTTTCCA	0.577																																					p.V99I		Atlas-SNP	.											.	USP18	22	.	0			c.G295A						PASS	.						23.0	20.0	21.0					22																	18644597		2202	4295	6497	SO:0001583	missense	11274	exon4			AGAAGCGTCCCTT	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.295G>A	22.37:g.18644597G>A	ENSP00000215794:p.Val99Ile	Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	439	127	0.289294	NM_017414	Q53Y90|Q6IAD9|Q9NY71	Missense_Mutation	SNP	ENST00000215794.7	37	CCDS13752.1	.	.	.	.	.	.	.	.	.	.	.	16.12	3.034318	0.54896	.	.	ENSG00000184979	ENST00000215794	T	0.32023	1.47	5.57	2.19	0.27852	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.490245	0.22485	N	0.059456	T	0.24967	0.0606	N	0.26042	0.785	0.24638	N	0.993584	D	0.69078	0.997	P	0.57548	0.823	T	0.12863	-1.0531	10	0.08837	T	0.75	.	3.4873	0.07625	0.0914:0.1718:0.559:0.1778	.	99	Q9UMW8	UBP18_HUMAN	I	99	ENSP00000215794:V99I	ENSP00000215794:V99I	V	+	1	0	USP18	17024597	0.992000	0.36948	0.971000	0.41717	0.704000	0.40688	1.496000	0.35638	0.640000	0.30582	0.650000	0.86243	GTC	.	.	weak		0.577	USP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316368.1		
ZNF668	79759	hgsc.bcm.edu	37	16	31075439	31075439	+	Silent	SNP	G	G	A	rs34107331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31075439G>A	ENST00000538906.1	-	2	1126	c.342C>T	c.(340-342)tgC>tgT	p.C114C	ZNF668_ENST00000535577.1_Silent_p.C114C|ZNF668_ENST00000426488.2_Silent_p.C137C|ZNF668_ENST00000394983.2_Silent_p.C114C|AC135050.5_ENST00000568708.1_RNA|ZNF668_ENST00000539836.3_Silent_p.C137C|ZNF668_ENST00000300849.4_Silent_p.C114C|ZNF668_ENST00000564456.1_5'Flank	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	114					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						CGCACTCGGGGCACGGAAAGG	0.706													G|||	38	0.00758786	0.0257	0.0058	5008	,	,		14213	0.0		0.0	False		,,,				2504	0.0				p.C137C	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C411T						PASS	.	G	,,,	130,4260		2,126,2067	22.0	23.0	23.0		342,411,342,342	0.9	1.0	16	dbSNP_126	23	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	2,127,6364	AA,AG,GG		0.0116,2.9613,1.0088	,,,	114/620,137/643,114/620,114/620	31075439	131,12855	2195	4298	6493	SO:0001819	synonymous_variant	79759	exon3			CTCGGGGCACGGA		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.342C>T	16.37:g.31075439G>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1																																																																																			G|0.990;A|0.010	0.010	strong		0.706	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
WDR62	284403	hgsc.bcm.edu	37	19	36594404	36594404	+	Missense_Mutation	SNP	G	G	A	rs61743589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36594404G>A	ENST00000270301.7	+	30	3659	c.3659G>A	c.(3658-3660)cGt>cAt	p.R1220H	WDR62_ENST00000401500.2_Missense_Mutation_p.R1225H			O43379	WDR62_HUMAN	WD repeat domain 62	1220					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)			GCCAGCTCCCGTGCCAGGATA	0.652													G|||	112	0.0223642	0.0794	0.0101	5008	,	,		19415	0.0		0.0	False		,,,				2504	0.0				p.R1225H		Atlas-SNP	.											.	WDR62	102	.	0			c.G3674A						PASS	.	G	HIS/ARG,HIS/ARG	315,4091	168.7+/-199.5	11,293,1899	88.0	82.0	84.0		3674,3659	-9.4	0.0	19	dbSNP_129	84	5,8595	3.0+/-9.4	0,5,4295	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	29,29	11,298,6194	AA,AG,GG		0.0581,7.1493,2.4604	benign,benign	1225/1524,1220/1519	36594404	320,12686	2203	4300	6503	SO:0001583	missense	284403	exon30			GCTCCCGTGCCAG	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.3659G>A	19.37:g.36594404G>A	ENSP00000270301:p.Arg1220His	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	33	0.01510989010989011	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	0	0.0	G	1.107	-0.659223	0.03454	0.071493	5.81E-4	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.48201	0.91;0.82	4.93	-9.42	0.00610	.	1.133150	0.06589	N	0.751672	T	0.01558	0.0050	N	0.12182	0.205	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.13845	-1.0494	10	0.13853	T	0.58	1.1471	9.9297	0.41514	0.2448:0.0:0.6539:0.1013	rs61743589	1225;1220	O43379-4;O43379	.;WDR62_HUMAN	H	1225;1220	ENSP00000384792:R1225H;ENSP00000270301:R1220H	ENSP00000270301:R1220H	R	+	2	0	WDR62	41286244	0.000000	0.05858	0.026000	0.17262	0.275000	0.26752	-0.741000	0.04855	-2.003000	0.00962	-1.360000	0.01215	CGT	G|0.981;A|0.019	0.019	strong		0.652	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
LILRB2	10288	hgsc.bcm.edu	37	19	54782393	54782393	+	Missense_Mutation	SNP	T	T	G	rs116027944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782393T>G	ENST00000391749.4	-	7	1250	c.979A>C	c.(979-981)Atc>Ctc	p.I327L	LILRB2_ENST00000391748.1_Missense_Mutation_p.I327L|LILRB2_ENST00000391746.1_Missense_Mutation_p.I327L|LILRB2_ENST00000434421.1_Missense_Mutation_p.I211L|LILRB2_ENST00000314446.5_Missense_Mutation_p.I327L|LILRB2_ENST00000471216.1_5'Flank	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	327					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)		TGCACTGAGATGAAGGGTGTG	0.617													.|||	687	0.137181	0.4614	0.0447	5008	,	,		16248	0.0288		0.003	False		,,,				2504	0.0143				p.I327L		Atlas-SNP	.											.	LILRB2	94	.	0			c.A979C						PASS	.	G	LEU/ILE,LEU/ILE	180,4150		16,148,2001	45.0	62.0	56.0		979,979	1.4	0.0	19	dbSNP_132	56	0,8600		0,0,4300	no	missense,missense	LILRB2	NM_001080978.2,NM_005874.3	5,5	16,148,6301	GG,GT,TT		0.0,4.157,1.3921	benign,benign	327/598,327/599	54782393	180,12750	2165	4300	6465	SO:0001583	missense	10288	exon7			CTGAGATGAAGGG	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.979A>C	19.37:g.54782393T>G	ENSP00000375629:p.Ile327Leu	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	197	79	0.401015	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	127	0.05815018315018315	113	0.22967479674796748	7	0.019337016574585635	6	0.01048951048951049	1	0.0013192612137203166	N	0.020	-1.442400	0.01089	0.04157	0.0	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00616	6.2;6.2;6.2;6.2;6.2	2.54	1.41	0.22369	Immunoglobulin-like fold (1);	0.687149	0.11002	N	0.610383	T	0.00012	0.0000	N	0.00027	-2.645	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.002	T	0.31447	-0.9943	9	0.02654	T	1	.	7.4423	0.27190	0.0:0.0:0.5368:0.4632	.	327;344;327	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	L	327;327;327;327;211	ENSP00000375628:I327L;ENSP00000319960:I327L;ENSP00000375629:I327L;ENSP00000375626:I327L;ENSP00000410117:I211L	ENSP00000319960:I327L	I	-	1	0	LILRB2	59474205	0.000000	0.05858	0.041000	0.18516	0.004000	0.04260	0.145000	0.16157	-0.015000	0.14150	-0.401000	0.06369	ATC	T|0.962;G|0.038	0.038	strong		0.617	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
UGDH	7358	hgsc.bcm.edu	37	4	39515736	39515736	+	Silent	SNP	A	A	G	rs10019532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39515736A>G	ENST00000316423.6	-	3	573	c.231T>C	c.(229-231)gaT>gaC	p.D77D	UGDH_ENST00000515398.1_5'UTR|UGDH_ENST00000507089.1_5'UTR|UGDH_ENST00000501493.2_Silent_p.D77D|UGDH_ENST00000506179.1_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	187	0	0		WXS	Illumina HiSeq	Phase_I	155	86	0.554839	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	
SDF2	6388	hgsc.bcm.edu	37	17	26988852	26988852	+	Missense_Mutation	SNP	C	C	T	rs35404078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26988852C>T	ENST00000247020.4	-	1	341	c.43G>A	c.(43-45)Gct>Act	p.A15T	SDF2_ENST00000592250.1_Intron|SUPT6H_ENST00000314616.6_5'Flank|SUPT6H_ENST00000347486.4_5'Flank	NM_006923.3	NP_008854.2	Q99470	SDF2_HUMAN	stromal cell-derived factor 2	15			A -> T (in dbSNP:rs35404078).		protein glycosylation (GO:0006486)|protein O-linked mannosylation (GO:0035269)	extracellular space (GO:0005615)|membrane (GO:0016020)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Lung NSC(42;0.00431)					GCTCCCACAGCGCTCCACAAA	0.592													C|||	47	0.00938498	0.0325	0.0058	5008	,	,		17083	0.0		0.0	False		,,,				2504	0.0				p.A15T		Atlas-SNP	.											.	SDF2	17	.	0			c.G43A						PASS	.	C	THR/ALA	125,4281	92.5+/-131.2	1,123,2079	152.0	133.0	139.0		43	4.5	1.0	17	dbSNP_126	139	0,8600		0,0,4300	yes	missense	SDF2	NM_006923.2	58	1,123,6379	TT,TC,CC		0.0,2.837,0.9611	benign	15/212	26988852	125,12881	2203	4300	6503	SO:0001583	missense	6388	exon1			CCACAGCGCTCCA	BC001406	CCDS11238.1	17q11.2	2004-02-16			ENSG00000132581	ENSG00000132581			10675	protein-coding gene	gene with protein product		602934				8918255	Standard	NR_045585		Approved		uc002hbw.3	Q99470	OTTHUMG00000132681	ENST00000247020.4:c.43G>A	17.37:g.26988852C>T	ENSP00000247020:p.Ala15Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_006923	Q9BQ79	Missense_Mutation	SNP	ENST00000247020.4	37	CCDS11238.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	13.72	2.321744	0.41096	0.02837	0.0	ENSG00000132581	ENST00000247020	D	0.84516	-1.86	5.54	4.54	0.55810	.	0.694941	0.13447	N	0.387194	T	0.60064	0.2240	L	0.47716	1.5	0.24340	N	0.994965	B;B	0.26147	0.143;0.143	B;B	0.15484	0.013;0.013	T	0.57522	-0.7797	10	0.13853	T	0.58	-4.1998	15.2037	0.73159	0.0:0.8229:0.177:0.0	rs35404078	15;15	Q6IBU4;Q99470	.;SDF2_HUMAN	T	15	ENSP00000247020:A15T	ENSP00000247020:A15T	A	-	1	0	SDF2	24012979	0.517000	0.26226	0.998000	0.56505	0.367000	0.29736	1.004000	0.29822	2.598000	0.87819	0.561000	0.74099	GCT	C|0.990;T|0.010	0.010	strong		0.592	SDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255965.2	NM_006923	
GRID1	2894	hgsc.bcm.edu	37	10	88126072	88126072	+	Splice_Site	SNP	G	G	A	rs61856638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:88126072G>A	ENST00000327946.7	-	1	163	c.78C>T	c.(76-78)atC>atT	p.I26I		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	26					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CGCGCTTACCGATGTGGATGA	0.716										Multiple Myeloma(13;0.14)			G|||	1721	0.34365	0.5219	0.1398	5008	,	,		6767	0.5218		0.172	False		,,,				2504	0.2403				p.I26I		Atlas-SNP	.											.	GRID1	204	.	0			c.C78T						PASS	.	G		1885,2343		423,1039,652	10.0	9.0	10.0		78	2.2	1.0	10	dbSNP_129	10	1203,7105		112,979,3063	yes	coding-synonymous-near-splice	GRID1	NM_017551.2		535,2018,3715	AA,AG,GG		14.48,44.5837,24.6331		26/1010	88126072	3088,9448	2114	4154	6268	SO:0001630	splice_region_variant	2894	exon1			CTTACCGATGTGG	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.79+1C>T	10.37:g.88126072G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	25	16	0.64	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																			G|0.654;A|0.346	0.346	strong		0.716	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	Silent
CA6	765	hgsc.bcm.edu	37	1	9009452	9009452	+	Silent	SNP	C	C	T	rs61746465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9009452C>T	ENST00000377443.2	+	2	214	c.210C>T	c.(208-210)ggC>ggT	p.G70G	CA6_ENST00000377442.2_Intron|CA6_ENST00000480186.3_Silent_p.G70G|CA6_ENST00000476083.1_Intron|CA6_ENST00000377436.3_Silent_p.G70G	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	70			G -> A (in dbSNP:rs2274329).		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)	ATATGACAGGCTATGAGACCC	0.607													C|||	61	0.0121805	0.0439	0.0029	5008	,	,		20134	0.0		0.001	False		,,,				2504	0.0				p.G70G		Atlas-SNP	.											.	CA6	47	.	0			c.C210T						PASS	.	C		149,4257	102.1+/-140.7	5,139,2059	59.0	48.0	52.0		210	4.4	0.9	1	dbSNP_129	52	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	CA6	NM_001215.2		5,141,6357	TT,TC,CC		0.0233,3.3818,1.161		70/309	9009452	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	765	exon2			GACAGGCTATGAG	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.210C>T	1.37:g.9009452C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	111	64	0.576577	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Silent	SNP	ENST00000377443.2	37	CCDS30578.1																																																																																			C|0.988;T|0.012	0.012	strong		0.607	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
TMEM247	388946	hgsc.bcm.edu	37	2	46707851	46707851	+	Missense_Mutation	SNP	G	G	A	rs61995902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:46707851G>A	ENST00000434431.1	+	2	425	c.425G>A	c.(424-426)cGg>cAg	p.R142Q		NM_001145051.2	NP_001138523.1	A6NEH6	TM247_HUMAN	transmembrane protein 247	142						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											CAGCGGGAGCGGCAGCACGAG	0.667																																					p.R142Q		Atlas-SNP	.											ENSG00000187600_ENST00000434431,NS,carcinoma,0,2	.	.	2	0			c.G425A						scavenged	.						28.0	35.0	33.0					2																	46707851		692	1591	2283	SO:0001583	missense	388946	exon2			GGGAGCGGCAGCA		CCDS56117.1	2p21	2012-04-11			ENSG00000187600	ENSG00000187600			42967	protein-coding gene	gene with protein product							Standard	NM_001145051		Approved		uc010yod.3	A6NEH6	OTTHUMG00000153137	ENST00000434431.1:c.425G>A	2.37:g.46707851G>A	ENSP00000388684:p.Arg142Gln	Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	180	52	0.288889	NM_001145051		Missense_Mutation	SNP	ENST00000434431.1	37	CCDS56117.1	281	0.12866300366300365	44	0.08943089430894309	31	0.0856353591160221	177	0.3094405594405594	29	0.03825857519788918	G	8.581	0.882391	0.17467	.	.	ENSG00000187600	ENST00000434431	.	.	.	0.911	0.911	0.19343	.	1.824950	0.02980	N	0.145467	T	0.00012	0.0000	N	0.02539	-0.55	.	.	.	B	0.10296	0.003	B	0.06405	0.002	T	0.30880	-0.9963	8	0.11485	T	0.65	0.2519	7.3035	0.26434	0.0:0.0:1.0:0.0	rs61995902	142	A6NEH6	YB028_HUMAN	Q	142	.	ENSP00000388684:R142Q	R	+	2	0	AC018682.6	46561355	0.887000	0.30362	0.998000	0.56505	0.201000	0.24016	0.166000	0.16583	0.776000	0.33473	0.205000	0.17691	CGG	G|0.886;A|0.114	0.114	strong		0.667	TMEM247-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329726.1	NM_001145051	
DENND2D	79961	hgsc.bcm.edu	37	1	111738589	111738589	+	Silent	SNP	A	A	T	rs34558744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111738589A>T	ENST00000357640.4	-	6	823	c.594T>A	c.(592-594)gcT>gcA	p.A198A	DENND2D_ENST00000369752.5_Silent_p.A195A|DENND2D_ENST00000473682.1_5'UTR	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	198	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(1)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		TCTTCCCAGGAGCAGGGAAGG	0.557													A|||	56	0.0111821	0.0401	0.0043	5008	,	,		18465	0.0		0.0	False		,,,				2504	0.0				p.A198A		Atlas-SNP	.											.	DENND2D	50	.	0			c.T594A						PASS	.	A		190,4216	121.7+/-159.2	6,178,2019	106.0	100.0	102.0		594	-0.2	1.0	1	dbSNP_126	102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DENND2D	NM_024901.3		6,179,6318	TT,TA,AA		0.0116,4.3123,1.4686		198/472	111738589	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	79961	exon6			CCCAGGAGCAGGG		CCDS831.1, CCDS60219.1	1p13.3	2014-02-12	2005-08-17		ENSG00000162777	ENSG00000162777		"""DENN/MADD domain containing"""	26192	protein-coding gene	gene with protein product		615111				12477932	Standard	NM_024901		Approved	FLJ22457, RP5-1180E21.2	uc001eal.2	Q9H6A0	OTTHUMG00000012356	ENST00000357640.4:c.594T>A	1.37:g.111738589A>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_024901	Q5T5V6|Q9BSU0	Silent	SNP	ENST00000357640.4	37	CCDS831.1																																																																																			A|0.988;T|0.012	0.012	strong		0.557	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1	NM_024901	
FAM135A	57579	hgsc.bcm.edu	37	6	71245978	71245978	+	Silent	SNP	G	G	A	rs9446260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71245978G>A	ENST00000418814.2	+	19	4595	c.3981G>A	c.(3979-3981)tcG>tcA	p.S1327S	FAM135A_ENST00000457062.2_Silent_p.S1114S|FAM135A_ENST00000505769.1_Silent_p.S907S|FAM135A_ENST00000370479.3_Silent_p.S1114S|FAM135A_ENST00000361499.3_Silent_p.S1131S|FAM135A_ENST00000505868.1_Silent_p.S1327S	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1327										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						TTGGACATTCGTTGGGCAATT	0.333													G|||	128	0.0255591	0.0923	0.0058	5008	,	,		16102	0.0		0.002	False		,,,				2504	0.0				p.S1327S		Atlas-SNP	.											.	FAM135A	181	.	0			c.G3981A						PASS	.	G	,,	389,4015	196.4+/-220.7	12,365,1825	112.0	115.0	114.0		3393,3981,3342	-11.0	0.2	6	dbSNP_119	114	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	12,369,6120	AA,AG,GG		0.0465,8.8329,3.0226	,,	1131/1320,1327/1516,1114/1303	71245978	393,12609	2202	4299	6501	SO:0001819	synonymous_variant	57579	exon17			ACATTCGTTGGGC	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.3981G>A	6.37:g.71245978G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			G|0.972;A|0.028	0.028	strong		0.333	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
CDCA4	55038	hgsc.bcm.edu	37	14	105477613	105477613	+	Silent	SNP	T	T	C	rs7145565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105477613T>C	ENST00000336219.3	-	2	809	c.654A>G	c.(652-654)ccA>ccG	p.P218P	CDCA4_ENST00000392590.3_Silent_p.P218P	NM_017955.3	NP_060425.2	Q9BXL8	CDCA4_HUMAN	cell division cycle associated 4	218						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.142)		AGCTAGGGCCTGGGGTGGCCG	0.677													N|||	1424	0.284345	0.6059	0.2334	5008	,	,		14454	0.2282		0.1322	False		,,,				2504	0.1002				p.P218P		Atlas-SNP	.											.	CDCA4	18	.	0			c.A654G						PASS	.	C	,	2123,2281		537,1049,616	23.0	25.0	24.0		654,654	-9.3	0.0	14	dbSNP_116	24	915,7681		41,833,3424	no	coding-synonymous,coding-synonymous	CDCA4	NM_017955.3,NM_145701.2	,	578,1882,4040	CC,CT,TT		10.6445,48.2062,23.3692	,	218/242,218/242	105477613	3038,9962	2202	4298	6500	SO:0001819	synonymous_variant	55038	exon2			AGGGCCTGGGGTG	BG354577	CCDS9996.1	14q32.33	2014-02-14			ENSG00000170779	ENSG00000170779			14625	protein-coding gene	gene with protein product	"""hematopoietic progenitor protein"""	612270				12188893	Standard	NM_145701		Approved	FLJ20764, Hepp	uc001yqb.2	Q9BXL8	OTTHUMG00000170767	ENST00000336219.3:c.654A>G	14.37:g.105477613T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_017955	Q8TB18|Q9NWK7	Silent	SNP	ENST00000336219.3	37	CCDS9996.1																																																																																			T|0.770;C|0.230	0.230	strong		0.677	CDCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410311.1	NM_145701	
C21orf2	755	hgsc.bcm.edu	37	21	45759045	45759045	+	Silent	SNP	C	C	T	rs11870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45759045C>T	ENST00000339818.4	-	1	240	c.33G>A	c.(31-33)cgG>cgA	p.R11R	C21orf2_ENST00000325223.7_Silent_p.R11R|AP001062.9_ENST00000426029.1_RNA|C21orf2_ENST00000397956.3_Silent_p.R11R|C21orf2_ENST00000496321.1_5'Flank	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	11					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)		AGGCCTTGGCCCGGGTCAGAA	0.776													C|||	1633	0.326078	0.4493	0.3069	5008	,	,		8225	0.1528		0.2386	False		,,,				2504	0.4417				p.R11R		Atlas-SNP	.											.	C21orf2	10	.	0			c.G33A						PASS	.	C		1362,2514		240,882,816	5.0	4.0	5.0		33	0.5	1.0	21	dbSNP_52	5	1413,6169		169,1075,2547	no	coding-synonymous	C21orf2	NM_004928.2		409,1957,3363	TT,TC,CC		18.6362,35.1393,24.2189		11/257	45759045	2775,8683	1938	3791	5729	SO:0001819	synonymous_variant	755	exon1			CTTGGCCCGGGTC	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.33G>A	21.37:g.45759045C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Silent	SNP	ENST00000339818.4	37	CCDS13709.1																																																																																			C|0.721;T|0.279	0.279	strong		0.776	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
PZP	5858	hgsc.bcm.edu	37	12	9321501	9321501	+	Missense_Mutation	SNP	C	C	T	rs3213832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9321501C>T	ENST00000261336.2	-	17	2099	c.2071G>A	c.(2071-2073)Gtg>Atg	p.V691M	PZP_ENST00000539983.1_5'Flank|PZP_ENST00000381997.2_Missense_Mutation_p.V560M	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	691	Bait region.		V -> M (in dbSNP:rs3213832). {ECO:0000269|PubMed:1692292}.		female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CCTGCAGACACGGAAGGGATG	0.378													C|||	472	0.0942492	0.1785	0.036	5008	,	,		-128	0.0476		0.0636	False		,,,				2504	0.1012				p.V691M	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.G2071A						PASS	.	C	MET/VAL	663,3743	281.4+/-275.9	51,561,1591	126.0	126.0	126.0		2071	-2.9	0.0	12	dbSNP_106	126	525,8075	148.0+/-203.3	12,501,3787	yes	missense	PZP	NM_002864.2	21	63,1062,5378	TT,TC,CC		6.1047,15.0477,9.1342	benign	691/1483	9321501	1188,11818	2203	4300	6503	SO:0001583	missense	5858	exon17			CAGACACGGAAGG	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.2071G>A	12.37:g.9321501C>T	ENSP00000261336:p.Val691Met	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	75	44	0.586667	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	175	0.08012820512820513	86	0.17479674796747968	15	0.04143646408839779	26	0.045454545454545456	48	0.0633245382585752	C	1.030	-0.682213	0.03353	0.150477	0.061047	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.35048	1.53;1.33	1.69	-2.88	0.05682	.	45.459000	0.00357	U	0.000025	T	0.00073	0.0002	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.16396	0.0;0.017;0.0	B;B;B	0.08055	0.0;0.003;0.0	T	0.12760	-1.0535	9	0.33141	T	0.24	.	6.16	0.20358	0.0:0.5927:0.0:0.4073	rs3213832;rs52791055;rs3213832	691;560;691	B2R950;P20742-2;P20742	.;.;PZP_HUMAN	M	691;560	ENSP00000261336:V691M;ENSP00000371427:V560M	ENSP00000261336:V691M	V	-	1	0	PZP	9212768	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.232000	0.02936	-0.588000	0.05882	-1.458000	0.01028	GTG	C|0.907;T|0.093	0.093	strong		0.378	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
SLC6A5	9152	hgsc.bcm.edu	37	11	20652291	20652291	+	Silent	SNP	C	C	T	rs143680068		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:20652291C>T	ENST00000525748.1	+	10	1827	c.1554C>T	c.(1552-1554)ttC>ttT	p.F518F	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	518					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)	TTGCCGGCTTCGTCATCTTCT	0.493													C|||	1	0.000199681	0.0008	0.0	5008	,	,		23670	0.0		0.0	False		,,,				2504	0.0				p.F518F		Atlas-SNP	.											.	SLC6A5	151	.	0			c.C1554T						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	204.0	173.0	183.0		1554	-9.9	0.5	11	dbSNP_134	183	0,8600		0,0,4300	no	coding-synonymous	SLC6A5	NM_004211.3		0,9,6494	TT,TC,CC		0.0,0.2043,0.0692		518/798	20652291	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	9152	exon10			CGGCTTCGTCATC	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.1554C>T	11.37:g.20652291C>T		Somatic	316	1	0.00316456		WXS	Illumina HiSeq	Phase_I	298	138	0.463087	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	37	CCDS7854.1																																																																																			C|1.000;T|0.000	0.000	strong		0.493	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
KIAA1279	26128	hgsc.bcm.edu	37	10	70775329	70775329	+	Silent	SNP	G	G	A	rs16926021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70775329G>A	ENST00000361983.4	+	7	1125	c.1023G>A	c.(1021-1023)caG>caA	p.Q341Q		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	341					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						TTGATAAACAGTCTGAACTTA	0.373													G|||	306	0.0611022	0.2148	0.0303	5008	,	,		18364	0.0		0.001	False		,,,				2504	0.0				p.Q341Q		Atlas-SNP	.											.	KIAA1279	35	.	0			c.G1023A						PASS	.	G		817,3589	310.2+/-291.5	78,661,1464	78.0	82.0	80.0		1023	-2.0	0.9	10	dbSNP_123	80	11,8589	5.7+/-21.5	0,11,4289	no	coding-synonymous	KIAA1279	NM_015634.3		78,672,5753	AA,AG,GG		0.1279,18.5429,6.3663		341/622	70775329	828,12178	2203	4300	6503	SO:0001819	synonymous_variant	26128	exon7			TAAACAGTCTGAA	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.1023G>A	10.37:g.70775329G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Silent	SNP	ENST00000361983.4	37	CCDS7284.1																																																																																			G|0.946;A|0.054	0.054	strong		0.373	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634	
DNM1L	10059	hgsc.bcm.edu	37	12	32875406	32875406	+	Silent	SNP	A	A	G	rs10844318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:32875406A>G	ENST00000549701.1	+	9	992	c.918A>G	c.(916-918)acA>acG	p.T306T	DNM1L_ENST00000553257.1_Silent_p.T319T|DNM1L_ENST00000266481.6_Silent_p.T306T|DNM1L_ENST00000381000.4_Silent_p.T319T|DNM1L_ENST00000547312.1_Silent_p.T306T|DNM1L_ENST00000358214.5_Silent_p.T319T|DNM1L_ENST00000452533.2_Silent_p.T306T|DNM1L_ENST00000414834.2_Silent_p.T103T			O00429	DNM1L_HUMAN	dynamin 1-like	306	GTPase domain.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					AGTTGAAAACAAGAATAAATG	0.348													A|||	634	0.126597	0.177	0.0937	5008	,	,		16993	0.0813		0.161	False		,,,				2504	0.093				p.T306T		Atlas-SNP	.											.	DNM1L	52	.	0			c.A918G						PASS	.	A	,,	721,3685	294.1+/-283.0	57,607,1539	69.0	66.0	67.0		918,918,918	-2.5	1.0	12	dbSNP_120	67	1248,7352	249.0+/-276.5	105,1038,3157	no	coding-synonymous,coding-synonymous,coding-synonymous	DNM1L	NM_005690.3,NM_012062.3,NM_012063.2	,,	162,1645,4696	GG,GA,AA		14.5116,16.364,15.1392	,,	306/700,306/737,306/711	32875406	1969,11037	2203	4300	6503	SO:0001819	synonymous_variant	10059	exon9			GAAAACAAGAATA	AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.918A>G	12.37:g.32875406A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	126	56	0.444444	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Silent	SNP	ENST00000549701.1	37	CCDS8729.1																																																																																			A|0.859;G|0.141	0.141	strong		0.348	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062	
PLA2G4B	100137049	hgsc.bcm.edu	37	15	42139875	42139875	+	Silent	SNP	A	A	G	rs34424865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42139875A>G	ENST00000452633.1	+	21	2515	c.2163A>G	c.(2161-2163)gcA>gcG	p.A721A	JMJD7-PLA2G4B_ENST00000382448.4_Silent_p.A952A|PLA2G4B_ENST00000542534.2_Silent_p.A952A|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.Q890R|PLA2G4B_ENST00000458483.1_Silent_p.A721A			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	721	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)		AGGAGGCGGCAGCTGGGGAGG	0.617													a|||	78	0.0155751	0.0567	0.0029	5008	,	,		17421	0.0		0.001	False		,,,				2504	0.0				p.Q890R		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.A2669G						PASS	.	A	,ARG/GLN,	196,4210		8,180,2015	74.0	66.0	69.0		2163,2669,2856	-9.6	0.0	15	dbSNP_126	69	3,8597		0,3,4297	yes	coding-synonymous,missense,coding-synonymous	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	,43,	8,183,6312	GG,GA,AA		0.0349,4.4485,1.5301	,,	721/782,890/894,952/1013	42139875	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	8681	exon24			GGCGGCAGCTGGG	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.2163A>G	15.37:g.42139875A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_001198588	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	26	0.011904761904761904	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	5.025	0.190237	0.09547	0.044485	3.49E-4	ENSG00000168970	ENST00000342159	T	0.01484	4.84	4.77	-9.55	0.00569	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.47249	-0.9132	8	0.87932	D	0	-0.1604	2.4723	0.04567	0.2543:0.1668:0.4127:0.1662	rs34424865	890	P0C869-7	.	R	890	ENSP00000342785:Q890R	ENSP00000342785:Q890R	Q	+	2	0	JMJD7-PLA2G4B	39927167	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.099000	0.00295	-2.603000	0.00450	-2.852000	0.00102	CAG	A|0.984;G|0.016	0.016	strong		0.617	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633	
MYO5B	4645	hgsc.bcm.edu	37	18	47398549	47398549	+	Silent	SNP	G	G	A	rs3826579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47398549G>A	ENST00000285039.7	-	27	3890	c.3591C>T	c.(3589-3591)taC>taT	p.Y1197Y	MYO5B_ENST00000324581.6_Silent_p.Y338Y|MYO5B_ENST00000587895.1_5'UTR|Y_RNA_ENST00000364798.1_RNA	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1197					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TCAGACTATTGTAGGCCAGAT	0.512													G|||	1502	0.29992	0.2753	0.2291	5008	,	,		18058	0.4256		0.2177	False		,,,				2504	0.3384				p.Y1197Y		Atlas-SNP	.											.	MYO5B	178	.	0			c.C3591T						PASS	.	G		973,2901		123,727,1087	370.0	354.0	359.0		3591	2.5	1.0	18	dbSNP_107	359	1632,6638		163,1306,2666	no	coding-synonymous	MYO5B	NM_001080467.2		286,2033,3753	AA,AG,GG		19.734,25.1162,21.4509		1197/1849	47398549	2605,9539	1937	4135	6072	SO:0001819	synonymous_variant	4645	exon27			ACTATTGTAGGCC	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.3591C>T	18.37:g.47398549G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	210	94	0.447619	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			G|0.718;A|0.282	0.282	strong		0.512	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
SLC24A1	9187	hgsc.bcm.edu	37	15	65917355	65917355	+	Missense_Mutation	SNP	T	T	G	rs35571449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65917355T>G	ENST00000261892.6	+	2	1224	c.937T>G	c.(937-939)Ttg>Gtg	p.L313V	SLC24A1_ENST00000399033.4_Missense_Mutation_p.L313V|SLC24A1_ENST00000546330.1_Missense_Mutation_p.L313V|SLC24A1_ENST00000339868.6_Missense_Mutation_p.L313V|SLC24A1_ENST00000544319.2_Missense_Mutation_p.L313V|SLC24A1_ENST00000537259.1_Missense_Mutation_p.L313V	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	313			L -> V (in dbSNP:rs35571449).		calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						AACAGTCCTGTTGCATACCCC	0.567													G|||	283	0.0565096	0.0923	0.0331	5008	,	,		19803	0.0427		0.0457	False		,,,				2504	0.0501				p.L313V		Atlas-SNP	.											.	SLC24A1	58	.	0			c.T937G						PASS	.	G	VAL/LEU	346,3588		12,322,1633	68.0	73.0	71.0		937	1.3	0.0	15	dbSNP_126	71	468,7818		14,440,3689	yes	missense	SLC24A1	NM_004727.2	32	26,762,5322	GG,GT,TT		5.6481,8.7951,6.6612	benign	313/1100	65917355	814,11406	1967	4143	6110	SO:0001583	missense	9187	exon2			GTCCTGTTGCATA	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"""Solute carriers"""	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.937T>G	15.37:g.65917355T>G	ENSP00000261892:p.Leu313Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_004727	O43485|O75184|Q17RM9	Missense_Mutation	SNP	ENST00000261892.6	37	CCDS45284.1	103	0.04716117216117216	36	0.07317073170731707	14	0.03867403314917127	23	0.04020979020979021	30	0.0395778364116095	G	7.121	0.577890	0.13686	0.087951	0.056481	ENSG00000074621	ENST00000537259;ENST00000261892;ENST00000339868;ENST00000544319;ENST00000399033;ENST00000546330	T;T;T;T;T;T	0.63255	0.19;-0.03;-0.03;-0.03;-0.03;-0.03	5.47	1.33	0.21861	.	1.301030	0.04996	N	0.468147	T	0.01835	0.0058	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.12630	0.0;0.0;0.0;0.006;0.004	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.001;0.0	T	0.04333	-1.0959	10	0.37606	T	0.19	.	5.5269	0.16962	0.0793:0.2621:0.5314:0.1272	rs35571449;rs62013126;rs35571449	313;313;313;313;313	O60721-2;Q17RM9;O60721;F5H127;B4E1W0	.;.;NCKX1_HUMAN;.;.	V	313	ENSP00000439693:L313V;ENSP00000261892:L313V;ENSP00000341837:L313V;ENSP00000445163:L313V;ENSP00000381991:L313V;ENSP00000439190:L313V	ENSP00000261892:L313V	L	+	1	2	SLC24A1	63704408	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.132000	0.15891	-0.095000	0.12351	-1.913000	0.00520	TTG	T|0.948;G|0.052	0.052	strong		0.567	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727	
MRGPRF	116535	hgsc.bcm.edu	37	11	68773403	68773403	+	Silent	SNP	G	G	A	rs11544722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	47	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	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	
LCT	3938	hgsc.bcm.edu	37	2	136590746	136590746	+	Missense_Mutation	SNP	C	C	T	rs386833838|rs3754689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:136590746C>T	ENST00000264162.2	-	2	665	c.655G>A	c.(655-657)Gtt>Att	p.V219I		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	219	4 X approximate repeats.		V -> I (in dbSNP:rs3754689). {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)	CGCAGGACAACAGAGAGTTTT	0.532													C|||	1778	0.355032	0.5431	0.2637	5008	,	,		14970	0.372		0.2217	False		,,,				2504	0.2853				p.V219I		Atlas-SNP	.											LCT,colon,carcinoma,+1,2	LCT	309	2	0			c.G655A						PASS	.	C	ILE/VAL	1957,2449	553.3+/-378.7	416,1125,662	128.0	139.0	135.0		655	2.8	0.4	2	dbSNP_107	135	1558,7042	291.9+/-300.6	177,1204,2919	yes	missense	LCT	NM_002299.2	29	593,2329,3581	TT,TC,CC		18.1163,44.4167,27.026	benign	219/1928	136590746	3515,9491	2203	4300	6503	SO:0001583	missense	3938	exon2			GGACAACAGAGAG	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.655G>A	2.37:g.136590746C>T	ENSP00000264162:p.Val219Ile	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	740	0.33882783882783885	263	0.5345528455284553	105	0.2900552486187845	205	0.3583916083916084	167	0.22031662269129287	C	0.136	-1.108297	0.01813	0.444167	0.181163	ENSG00000115850	ENST00000264162	T	0.25579	1.79	5.57	2.81	0.32909	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.673132	0.14942	N	0.289431	T	0.00012	0.0000	N	0.02865	-0.47	0.46356	P	9.909999999999641E-4	B	0.14012	0.009	B	0.19666	0.026	T	0.47182	-0.9137	9	0.02654	T	1	-10.4532	7.644	0.28311	0.0:0.6662:0.0:0.3338	rs3754689;rs52836667;rs58590436;rs3754689	219	P09848	LPH_HUMAN	I	219	ENSP00000264162:V219I	ENSP00000264162:V219I	V	-	1	0	LCT	136307216	0.344000	0.24827	0.358000	0.25811	0.361000	0.29550	0.084000	0.14891	0.408000	0.25621	0.455000	0.32223	GTT	C|0.681;T|0.319	0.319	strong		0.532	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
FAT1	2195	hgsc.bcm.edu	37	4	187542356	187542356	+	Missense_Mutation	SNP	C	C	T	rs56790426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187542356C>T	ENST00000441802.2	-	10	5593	c.5384G>A	c.(5383-5385)cGa>cAa	p.R1795Q		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1795	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						ATCAGCTGCTCGAATCACCAG	0.423										HNSCC(5;0.00058)			C|||	44	0.00878594	0.0325	0.0014	5008	,	,		22564	0.0		0.0	False		,,,				2504	0.0				p.R1795Q	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G5384A						PASS	.	C	GLN/ARG	81,3883		1,79,1902	89.0	85.0	87.0		5384	4.7	1.0	4	dbSNP_129	87	1,8327		0,1,4163	yes	missense	FAT1	NM_005245.3	43	1,80,6065	TT,TC,CC		0.012,2.0434,0.6671	benign	1795/4589	187542356	82,12210	1982	4164	6146	SO:0001583	missense	2195	exon10			GCTGCTCGAATCA	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.5384G>A	4.37:g.187542356C>T	ENSP00000406229:p.Arg1795Gln	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	150	71	0.473333	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	8.328	0.825754	0.16749	0.020434	1.2E-4	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.01725	4.67	5.5	4.66	0.58398	Cadherin (4);Cadherin-like (1);	0.122272	0.56097	D	0.000036	T	0.00815	0.0027	N	0.25825	0.765	0.53005	D	0.999965	B	0.25007	0.116	B	0.23018	0.043	T	0.62586	-0.6823	10	0.21014	T	0.42	.	11.7859	0.52043	0.0:0.8082:0.1241:0.0676	rs56790426	1795	Q14517	FAT1_HUMAN	Q	1795;1797	ENSP00000406229:R1795Q	ENSP00000260147:R1797Q	R	-	2	0	FAT1	187779350	1.000000	0.71417	1.000000	0.80357	0.050000	0.14768	2.438000	0.44837	1.556000	0.49512	-0.150000	0.13652	CGA	C|0.993;T|0.007	0.007	strong		0.423	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
OR14I1	401994	hgsc.bcm.edu	37	1	248844695	248844695	+	Missense_Mutation	SNP	A	A	T	rs114135727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248844695A>T	ENST00000342623.3	-	1	934	c.911T>A	c.(910-912)gTg>gAg	p.V304E		NM_001004734.1	NP_001004734.1	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I, member 1	304						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(4)|large_intestine(2)|lung(24)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	35						ATATATCTTCACAAAGAGTCT	0.353													A|||	95	0.0189696	0.0703	0.0029	5008	,	,		17508	0.0		0.0	False		,,,				2504	0.0				p.V304E		Atlas-SNP	.											.	OR14I1	64	.	0			c.T911A						PASS	.	A	GLU/VAL	283,4123		10,263,1930	51.0	54.0	53.0		911	-2.2	0.0	1	dbSNP_132	53	0,8600		0,0,4300	yes	missense	OR14I1	NM_001004734.1	121	10,263,6230	TT,TA,AA		0.0,6.4231,2.1759	benign	304/312	248844695	283,12723	2203	4300	6503	SO:0001583	missense	401994	exon1			ATCTTCACAAAGA		CCDS31125.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000189181	ENSG00000189181		"""GPCR / Class A : Olfactory receptors"""	19575	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BU, member 1"""	OR5BU1P, OR5BU1			Standard	NM_001004734		Approved		uc001ieu.1	A6ND48	OTTHUMG00000040378	ENST00000342623.3:c.911T>A	1.37:g.248844695A>T	ENSP00000339726:p.Val304Glu	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_001004734		Missense_Mutation	SNP	ENST00000342623.3	37	CCDS31125.1	39	0.017857142857142856	39	0.07926829268292683	0	0.0	0	0.0	0	0.0	.	0.008	-1.879400	0.00537	0.064231	0.0	ENSG00000189181	ENST00000342623	T	0.37235	1.21	2.84	-2.22	0.06952	.	2.383690	0.01770	N	0.031135	T	0.00637	0.0021	N	0.04373	-0.215	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11084	-1.0602	10	0.06236	T	0.91	.	0.9342	0.01341	0.3966:0.2734:0.1869:0.1431	.	304	A6ND48	O14I1_HUMAN	E	304	ENSP00000339726:V304E	ENSP00000339726:V304E	V	-	2	0	OR14I1	246911318	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.457000	0.02374	-0.041000	0.13558	-0.505000	0.04504	GTG	A|0.982;T|0.018	0.018	strong		0.353	OR14I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097128.1	NM_001004734	
EVC2	132884	hgsc.bcm.edu	37	4	5570221	5570221	+	Silent	SNP	G	G	A	rs12511039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:5570221G>A	ENST00000344408.5	-	20	3560	c.3507C>T	c.(3505-3507)caC>caT	p.H1169H	EVC2_ENST00000310917.2_Silent_p.H1089H|EVC2_ENST00000344938.1_Silent_p.H1169H	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	1169					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.H1169H(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						TCTCAGCTGCGTGGTCCACAT	0.697													G|||	2208	0.440895	0.1566	0.3703	5008	,	,		13114	0.876		0.3111	False		,,,				2504	0.5603				p.H1169H		Atlas-SNP	.											EVC2,NS,lymphoid_neoplasm,0,1	EVC2	202	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C3507T						PASS	.	G	,	749,3653		74,601,1526	24.0	24.0	24.0		3267,3507	3.5	0.0	4	dbSNP_120	24	2584,6014		374,1836,2089	no	coding-synonymous,coding-synonymous	EVC2	NM_001166136.1,NM_147127.4	,	448,2437,3615	AA,AG,GG		30.0535,17.015,25.6385	,	1089/1229,1169/1309	5570221	3333,9667	2201	4299	6500	SO:0001819	synonymous_variant	132884	exon20			AGCTGCGTGGTCC	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.3507C>T	4.37:g.5570221G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_147127	Q86YT3|Q86YT4|Q8NG49	Silent	SNP	ENST00000344408.5	37	CCDS3382.2																																																																																			G|0.656;A|0.344	0.344	strong		0.697	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
ALPK1	80216	hgsc.bcm.edu	37	4	113352397	113352397	+	Missense_Mutation	SNP	G	G	A	rs2074388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:113352397G>A	ENST00000458497.1	+	11	1973	c.1694G>A	c.(1693-1695)gGt>gAt	p.G565D	ALPK1_ENST00000177648.9_Missense_Mutation_p.G565D|ALPK1_ENST00000504176.2_Missense_Mutation_p.G487D	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	565			G -> D (in dbSNP:rs2074388). {ECO:0000269|PubMed:10021370, ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.5}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		TACAGCAATGGTGAGGGAGCT	0.507													G|||	3142	0.627396	0.7239	0.5576	5008	,	,		21715	0.6369		0.6173	False		,,,				2504	0.547				p.G565D		Atlas-SNP	.											.	ALPK1	125	.	0			c.G1694A						PASS	.	G	ASP/GLY,ASP/GLY	3084,1322	696.4+/-406.1	1076,932,195	99.0	99.0	99.0		1694,1694	1.8	0.0	4	dbSNP_96	99	5420,3180	654.2+/-401.1	1706,2008,586	yes	missense,missense	ALPK1	NM_001102406.1,NM_025144.3	94,94	2782,2940,781	AA,AG,GG		36.9767,30.0045,34.6148	benign,benign	565/1245,565/1245	113352397	8504,4502	2203	4300	6503	SO:0001583	missense	80216	exon11			GCAATGGTGAGGG	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.1694G>A	4.37:g.113352397G>A	ENSP00000398048:p.Gly565Asp	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	1393	0.6378205128205128	343	0.6971544715447154	200	0.5524861878453039	375	0.6555944055944056	475	0.6266490765171504	G	13.58	2.279331	0.40294	0.699955	0.630233	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.02395	4.38;4.38;4.31	4.61	1.76	0.24704	.	0.718387	0.12973	N	0.423936	T	0.00012	0.0000	M	0.64997	1.995	0.80722	P	0.0	D;D	0.67145	0.996;0.987	P;P	0.56563	0.801;0.638	T	0.04165	-1.0972	9	0.29301	T	0.29	-4.1767	7.7266	0.28763	0.0:0.2951:0.4022:0.3027	rs2074388;rs17628348;rs56802581;rs2074388	487;565	F5H138;Q96QP1	.;ALPK1_HUMAN	D	565;565;487	ENSP00000398048:G565D;ENSP00000177648:G565D;ENSP00000426044:G487D	ENSP00000177648:G565D	G	+	2	0	ALPK1	113571846	0.004000	0.15560	0.001000	0.08648	0.017000	0.09413	0.724000	0.25954	0.195000	0.20347	0.655000	0.94253	GGT	G|0.353;A|0.647	0.647	strong		0.507	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
BLOC1S2	282991	hgsc.bcm.edu	37	10	102046402	102046402	+	Silent	SNP	G	G	C	rs12250221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102046402G>C	ENST00000370372.2	-	1	67	c.15C>G	c.(13-15)gcC>gcG	p.A5A	BLOC1S2_ENST00000361832.2_5'UTR|BLOC1S2_ENST00000441611.1_5'Flank	NM_173809.4	NP_776170.2	Q6QNY1	BL1S2_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 2	5					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|melanosome organization (GO:0032438)|microtubule nucleation (GO:0007020)|mitochondrial outer membrane permeabilization (GO:0097345)|neuron projection development (GO:0031175)|platelet dense granule organization (GO:0060155)|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)	BLOC-1 complex (GO:0031083)|centrosome (GO:0005813)|gamma-tubulin complex (GO:0000930)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	gamma-tubulin binding (GO:0043015)|protein C-terminus binding (GO:0008022)			large_intestine(1)|lung(2)|ovary(1)	4		Colorectal(252;0.117)		Epithelial(162;2.44e-10)|all cancers(201;1.97e-08)		GTACGCCCTCGGCTGCCGCCG	0.751													-|||	293	0.0585064	0.2148	0.0115	5008	,	,		12869	0.0		0.001	False		,,,				2504	0.0				p.A5A		Atlas-SNP	.											.	BLOC1S2	10	.	0			c.C15G						PASS	.			564,3608		30,504,1552	8.0	12.0	11.0		15	-6.3	0.1	10	dbSNP_120	11	10,8242		0,10,4116	no	coding-synonymous	BLOC1S2	NM_173809.2		30,514,5668	CC,CG,GG		0.1212,13.5187,4.6201		5/143	102046402	574,11850	2086	4126	6212	SO:0001819	synonymous_variant	282991	exon1			GCCCTCGGCTGCC	AK054697	CCDS7490.1, CCDS73179.1	10q24.31	2012-08-01	2008-08-11		ENSG00000196072	ENSG00000196072		"""Biogenesis of lysosomal organelles complex-1 subunits"""	20984	protein-coding gene	gene with protein product	"""centrosome protein oncogene"", ""Biogenesis of Lysosome-related Organelles complex-1 Subunit 2"", ""BLOC-1 subunit 2"""	609768				11483580, 15102850	Standard	NM_173809		Approved	MGC10120, FLJ30135, BLOS2	uc001kqw.2	Q6QNY1	OTTHUMG00000018908	ENST00000370372.2:c.15C>G	10.37:g.102046402G>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_173809	B4DQV2|Q5W040|Q8WUI8	Silent	SNP	ENST00000370372.2	37	CCDS7490.1																																																																																			G|0.949;C|0.051	0.051	strong		0.751	BLOC1S2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049861.2	NM_173809	
ADCK2	90956	hgsc.bcm.edu	37	7	140373326	140373326	+	Missense_Mutation	SNP	A	A	G	rs2968558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140373326A>G	ENST00000072869.4	+	1	374	c.196A>G	c.(196-198)Agt>Ggt	p.S66G	ADCK2_ENST00000476491.1_Missense_Mutation_p.S66G	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	66			S -> G (in dbSNP:rs2968558).			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)					TGACGTTCTGAGTCGGCGAAG	0.726													G|||	1586	0.316693	0.7163	0.219	5008	,	,		11219	0.1071		0.1133	False		,,,				2504	0.271				p.S66G		Atlas-SNP	.											.	ADCK2	37	.	0			c.A196G						PASS	.	G	GLY/SER	2627,1749		811,1005,372	14.0	16.0	15.0		196	-4.9	0.0	7	dbSNP_101	15	857,7691		55,747,3472	yes	missense	ADCK2	NM_052853.3	56	866,1752,3844	GG,GA,AA		10.0257,39.968,26.9576	benign	66/627	140373326	3484,9440	2188	4274	6462	SO:0001583	missense	90956	exon1			GTTCTGAGTCGGC	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.196A>G	7.37:g.140373326A>G	ENSP00000072869:p.Ser66Gly	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_052853	Q96CN6|Q9Y6T5	Missense_Mutation	SNP	ENST00000072869.4	37	CCDS5861.1	546	0.25	341	0.693089430894309	64	0.17679558011049723	57	0.09965034965034965	84	0.11081794195250659	G	6.626	0.483865	0.12581	0.60032	0.100257	ENSG00000133597	ENST00000072869;ENST00000476491	T;T	0.45276	0.9;0.9	4.11	-4.94	0.03057	.	0.667670	0.13198	N	0.406203	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	0.37126	-0.9719	9	0.13108	T	0.6	-22.6628	3.311	0.07016	0.0947:0.2375:0.4012:0.2666	rs2968558;rs11540283;rs60835851	66;66	C9JE15;Q7Z695	.;ADCK2_HUMAN	G	66	ENSP00000072869:S66G;ENSP00000420512:S66G	ENSP00000072869:S66G	S	+	1	0	ADCK2	140019795	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.288000	0.08377	-0.902000	0.03886	-1.464000	0.01018	AGT	A|0.744;G|0.256	0.256	strong		0.726	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853	
HSD17B4	3295	hgsc.bcm.edu	37	5	118877677	118877677	+	Silent	SNP	C	C	T	rs12714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118877677C>T	ENST00000256216.6	+	24	2332	c.2199C>T	c.(2197-2199)taC>taT	p.Y733Y	HSD17B4_ENST00000515320.1_Silent_p.Y715Y|HSD17B4_ENST00000522415.1_3'UTR|HSD17B4_ENST00000504811.1_Silent_p.Y758Y|HSD17B4_ENST00000414835.2_Silent_p.Y593Y|HSD17B4_ENST00000510025.1_Silent_p.Y709Y|HSD17B4_ENST00000509514.1_Silent_p.Y471Y|HSD17B4_ENST00000513628.1_Silent_p.Y596Y	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	733	SCP2.				alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		TTAAAGACTACGCCAAGCTCT	0.408													T|||	249	0.0497204	0.146	0.0072	5008	,	,		15192	0.001		0.001	False		,,,				2504	0.0501				p.Y758Y	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.C2274T						PASS	.	T	,,	492,3912	780.4+/-414.4	32,428,1742	58.0	58.0	58.0		2199,2274,2145	-10.0	0.2	5	dbSNP_52	58	16,8584	818.4+/-406.9	0,16,4284	no	coding-synonymous,coding-synonymous,coding-synonymous	HSD17B4	NM_000414.3,NM_001199291.1,NM_001199292.1	,,	32,444,6026	TT,TC,CC		0.186,11.1717,3.9065	,,	733/737,758/762,715/719	118877677	508,12496	2202	4300	6502	SO:0001819	synonymous_variant	3295	exon25			AGACTACGCCAAG		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.2199C>T	5.37:g.118877677C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	154	79	0.512987	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Silent	SNP	ENST00000256216.6	37	CCDS4126.1																																																																																			C|0.960;T|0.040	0.040	strong		0.408	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	
VAV2	7410	hgsc.bcm.edu	37	9	136662928	136662928	+	Silent	SNP	A	A	G	rs7865299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136662928A>G	ENST00000371850.3	-	10	871	c.840T>C	c.(838-840)ctT>ctC	p.L280L	VAV2_ENST00000371851.1_Silent_p.L275L|VAV2_ENST00000406606.3_Silent_p.L275L	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	280	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		CGTAGATCAGAAGCCTGGACG	0.587													G|||	1306	0.260783	0.5129	0.2507	5008	,	,		16522	0.0863		0.169	False		,,,				2504	0.2014				p.L280L		Atlas-SNP	.											.	VAV2	165	.	0			c.T840C						PASS	.	G	,	2022,2384	608.6+/-391.2	484,1054,665	100.0	85.0	90.0		840,825	-1.0	1.0	9	dbSNP_116	90	1748,6852	733.1+/-406.9	180,1388,2732	no	coding-synonymous,coding-synonymous	VAV2	NM_001134398.1,NM_003371.3	,	664,2442,3397	GG,GA,AA		20.3256,45.892,28.9866	,	280/879,275/840	136662928	3770,9236	2203	4300	6503	SO:0001819	synonymous_variant	7410	exon10			GATCAGAAGCCTG		CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12658	protein-coding gene	gene with protein product		600428	"""vav 2 oncogene"""			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.840T>C	9.37:g.136662928A>G		Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_001134398	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Silent	SNP	ENST00000371850.3	37	CCDS48053.1																																																																																			A|0.741;G|0.259	0.259	strong		0.587	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1		
PRR27	401137	hgsc.bcm.edu	37	4	71024268	71024268	+	Missense_Mutation	SNP	A	A	G	rs116632053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71024268A>G	ENST00000344526.5	+	3	488	c.299A>G	c.(298-300)aAt>aGt	p.N100S	C4orf40_ENST00000502441.2_Intron|C4orf40_ENST00000502294.1_Missense_Mutation_p.N100S	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		100	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						ACTCAGTTGAATGTTCCTCCT	0.512													A|||	48	0.00958466	0.0348	0.0029	5008	,	,		20664	0.0		0.0	False		,,,				2504	0.0				p.N100S		Atlas-SNP	.											.	C4orf40	19	.	0			c.A299G						PASS	.	A	SER/ASN	178,4228	115.4+/-153.4	1,176,2026	264.0	254.0	257.0		299	-7.7	0.0	4	dbSNP_132	257	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C4orf40	NM_214711.3	46	1,177,6325	GG,GA,AA		0.0116,4.0399,1.3763	benign	100/220	71024268	179,12827	2203	4300	6503	SO:0001583	missense	401137	exon3			AGTTGAATGTTCC																												ENST00000344526.5:c.299A>G	4.37:g.71024268A>G	ENSP00000343172:p.Asn100Ser	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	213	100	0.469484	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	A	10.53	1.375740	0.24857	0.040399	1.16E-4	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.34859	1.34;1.34	3.84	-7.67	0.01272	.	.	.	.	.	T	0.02767	0.0083	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.13407	0.009	T	0.17992	-1.0351	9	0.13853	T	0.58	0.3329	1.6043	0.02681	0.3253:0.1509:0.0919:0.4319	.	100	Q6MZM9	CD040_HUMAN	S	100	ENSP00000426249:N100S;ENSP00000343172:N100S	ENSP00000343172:N100S	N	+	2	0	C4orf40	71058857	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.709000	0.00819	-2.592000	0.00456	-0.842000	0.03052	AAT	A|0.986;G|0.014	0.014	strong		0.512	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
DNHD1	144132	hgsc.bcm.edu	37	11	6530138	6530138	+	Missense_Mutation	SNP	G	G	A	rs2555152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6530138G>A	ENST00000527990.2	+	3	949	c.949G>A	c.(949-951)Gac>Aac	p.D317N	DNHD1_ENST00000254579.6_Missense_Mutation_p.D317N|DNHD1_ENST00000354685.3_Missense_Mutation_p.D317N			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	317			D -> N (in dbSNP:rs2555152).		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)		GGTGCCACCCGACAAGGTGAA	0.512													G|||	199	0.0397364	0.1452	0.0086	5008	,	,		19143	0.001		0.0	False		,,,				2504	0.0				p.D317N		Atlas-SNP	.											.	DNHD1	198	.	0			c.G949A						PASS	.	G	ASN/ASP,ASN/ASP	526,3876	241.2+/-251.7	39,448,1714	126.0	110.0	115.0		949,949	-1.4	0.3	11	dbSNP_100	115	6,8586	4.3+/-15.6	0,6,4290	yes	missense,missense	DNHD1	NM_144666.2,NM_173589.3	23,23	39,454,6004	AA,AG,GG		0.0698,11.9491,4.0942	benign,benign	317/4754,317/598	6530138	532,12462	2201	4296	6497	SO:0001583	missense	144132	exon4			CCACCCGACAAGG	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.949G>A	11.37:g.6530138G>A	ENSP00000436180:p.Asp317Asn	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	63	0.028846153846153848	60	0.12195121951219512	3	0.008287292817679558	0	0.0	0	0.0	G	3.791	-0.043754	0.07452	0.119491	6.98E-4	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.13307	2.6;2.6;2.6	5.83	-1.38	0.09027	.	1.055320	0.07371	N	0.885883	T	0.00073	0.0002	N	0.04043	-0.29	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44205	-0.9343	10	0.15499	T	0.54	.	1.9717	0.03407	0.4587:0.1254:0.2943:0.1216	rs2555152;rs56854107;rs2555152	317;317	Q96M86;Q96M86-4	DNHD1_HUMAN;.	N	317	ENSP00000254579:D317N;ENSP00000346716:D317N;ENSP00000436180:D317N	ENSP00000254579:D317N	D	+	1	0	DNHD1	6486714	0.000000	0.05858	0.341000	0.25589	0.889000	0.51656	-0.054000	0.11826	-0.108000	0.12066	-0.300000	0.09419	GAC	G|0.962;A|0.038	0.038	strong		0.512	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
DZANK1	55184	hgsc.bcm.edu	37	20	18445963	18445963	+	Silent	SNP	A	A	G	rs6035051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:18445963A>G	ENST00000358866.6	-	1	62	c.40T>C	c.(40-42)Tta>Cta	p.L14L	DZANK1_ENST00000262547.5_Silent_p.L14L|DZANK1_ENST00000357236.4_5'UTR|POLR3F_ENST00000377603.4_5'Flank|DZANK1_ENST00000329494.5_Silent_p.L14L			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	14							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						GGCACTCGTAATGGTATGATC	0.353													G|||	2893	0.577676	0.6157	0.572	5008	,	,		15653	0.6101		0.5567	False		,,,				2504	0.5184				p.L14L		Atlas-SNP	.											DZANK1,caecum,carcinoma,+1,1	DZANK1	65	1	0			c.T40C						PASS	.	G		2283,1531		693,897,317	97.0	89.0	92.0		40	2.1	1.0	20	dbSNP_114	92	4686,3560		1323,2040,760	no	coding-synonymous	DZANK1	NM_001099407.1		2016,2937,1077	GG,GA,AA		43.1724,40.1416,42.2139		14/753	18445963	6969,5091	1907	4123	6030	SO:0001819	synonymous_variant	55184	exon2			CTCGTAATGGTAT	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"""Ankyrin repeat domain containing"""	15858	protein-coding gene	gene with protein product	"""ankyrin repeat domain 64"""		"""chromosome 20 open reading frame 12"""	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.40T>C	20.37:g.18445963A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Silent	SNP	ENST00000358866.6	37	CCDS46582.1																																																																																			A|0.419;G|0.581	0.581	strong		0.353	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407	
PNPLA3	80339	hgsc.bcm.edu	37	22	44324730	44324730	+	Silent	SNP	C	C	T	rs738408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44324730C>T	ENST00000216180.3	+	3	620	c.447C>T	c.(445-447)ccC>ccT	p.P149P	PNPLA3_ENST00000423180.2_Silent_p.P145P|PNPLA3_ENST00000478713.1_3'UTR	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	149	Patatin.				acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)	p.P149P(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				GCTTCATCCCCTTCTACAGTG	0.502													T|||	1313	0.262181	0.118	0.4841	5008	,	,		20434	0.3502		0.2256	False		,,,				2504	0.2464				p.P149P		Atlas-SNP	.											PNPLA3,NS,carcinoma,0,1	PNPLA3	53	1	1	Substitution - coding silent(1)	stomach(1)	c.C447T						PASS	.	T		637,3769	764.4+/-413.3	57,523,1623	303.0	254.0	271.0		447	-4.8	0.0	22	dbSNP_86	271	1890,6710	723.2+/-406.4	208,1474,2618	no	coding-synonymous	PNPLA3	NM_025225.2		265,1997,4241	TT,TC,CC		21.9767,14.4576,19.4295		149/482	44324730	2527,10479	2203	4300	6503	SO:0001819	synonymous_variant	80339	exon3			CATCCCCTTCTAC		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"""Patatin-like phospholipase domain containing"""	18590	protein-coding gene	gene with protein product		609567	"""chromosome 22 open reading frame 20"", ""adiponutrin"""	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.447C>T	22.37:g.44324730C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	171	77	0.450292	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Silent	SNP	ENST00000216180.3	37	CCDS14054.1																																																																																			C|0.802;T|0.198	0.198	strong		0.502	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225	
RBM33	155435	hgsc.bcm.edu	37	7	155531080	155531080	+	Missense_Mutation	SNP	A	A	G	rs3735576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	76	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	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	
FHL5	9457	hgsc.bcm.edu	37	6	97058567	97058567	+	Silent	SNP	A	A	G	rs2273622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:97058567A>G	ENST00000326771.2	+	6	1004	c.624A>G	c.(622-624)ccA>ccG	p.P208P	FHL5_ENST00000541107.1_Silent_p.P208P	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	208	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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)		ACGACTATCCATTCTGCGTGG	0.428													A|||	689	0.13758	0.115	0.183	5008	,	,		18288	0.0357		0.2117	False		,,,				2504	0.1646				p.P208P		Atlas-SNP	.											FHL5,NS,malignant_melanoma,+2,1	FHL5	73	1	0			c.A624G						scavenged	.	A	,	492,3914	228.1+/-243.1	25,442,1736	245.0	225.0	232.0		624,624	-3.3	1.0	6	dbSNP_100	232	1673,6927	307.0+/-308.2	175,1323,2802	no	coding-synonymous,coding-synonymous	FHL5	NM_001170807.1,NM_020482.4	,	200,1765,4538	GG,GA,AA		19.4535,11.1666,16.6462	,	208/285,208/285	97058567	2165,10841	2203	4300	6503	SO:0001819	synonymous_variant	9457	exon6			CTATCCATTCTGC	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.624A>G	6.37:g.97058567A>G		Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	211	107	0.507109	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Silent	SNP	ENST00000326771.2	37	CCDS5035.1																																																																																			A|0.841;G|0.159	0.159	strong		0.428	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
SLC8A3	6547	hgsc.bcm.edu	37	14	70512964	70512964	+	Silent	SNP	G	G	A	rs144234198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:70512964G>A	ENST00000381269.2	-	8	3237	c.2484C>T	c.(2482-2484)aaC>aaT	p.N828N	SLC8A3_ENST00000357887.3_Silent_p.N826N|SLC8A3_ENST00000356921.2_Silent_p.N822N|SLC8A3_ENST00000394330.2_Silent_p.N185N|SLC8A3_ENST00000528359.1_Silent_p.N826N|SLC8A3_ENST00000533541.1_3'UTR|SLC8A3_ENST00000216568.7_Silent_p.N199N|SLC8A3_ENST00000534137.1_Silent_p.N825N	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	828					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)		CATTGACGGCGTTGCTGCCCG	0.602											OREG0022773	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N828N		Atlas-SNP	.											SLC8A3_ENST00000357887,colon,carcinoma,0,2	SLC8A3	234	2	0			c.C2484T						PASS	.	G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	49.0	43.0	45.0		597,2478,2475,2466,555,2484	-3.9	0.9	14	dbSNP_134	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC8A3	NM_001130417.1,NM_033262.3,NM_058240.2,NM_182932.1,NM_182936.1,NM_183002.1	,,,,,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,,,,,	199/299,826/926,825/925,822/922,185/285,828/928	70512964	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	6547	exon8			GACGGCGTTGCTG	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.2484C>T	14.37:g.70512964G>A		Somatic	94	0	0	1122	WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	37	CCDS35498.1																																																																																			G|1.000;A|0.000	0.000	strong		0.602	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1		
TTN	7273	hgsc.bcm.edu	37	2	179552895	179552895	+	Missense_Mutation	SNP	C	C	T	rs72650028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179552895C>T	ENST00000591111.1	-	125	31527	c.31303G>A	c.(31303-31305)Gtt>Att	p.V10435I	TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V10752I|TTN_ENST00000342992.6_Missense_Mutation_p.V9508I|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTCTATAAACTGAAATGGAC	0.393													C|||	66	0.0131789	0.0477	0.0043	5008	,	,		19860	0.0		0.0	False		,,,				2504	0.0				p.V10752I		Atlas-SNP	.											.	TTN	18412	.	0			c.G32254A						PASS	.	C	ILE/VAL,,,	126,3626		1,124,1751	168.0	169.0	168.0		28522,,,	4.9	1.0	2	dbSNP_130	168	2,8194		0,2,4096	yes	missense,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	29,,,	1,126,5847	TT,TC,CC		0.0244,3.3582,1.0713	possibly-damaging,,,	9508/33424,,,	179552895	128,11820	1876	4098	5974	SO:0001583	missense	7273	exon127			TATAAACTGAAAT	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.31303G>A	2.37:g.179552895C>T	ENSP00000465570:p.Val10435Ile	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	147	78	0.530612	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		22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	14.87	2.665728	0.47677	0.033582	2.44E-4	ENSG00000155657	ENST00000342992	T	0.71222	-0.55	4.94	4.94	0.65067	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.47985	0.1475	L	0.49778	1.585	0.80722	D	1	P	0.44690	0.841	P	0.55824	0.785	T	0.69355	-0.5167	9	0.87932	D	0	.	14.0185	0.64539	0.0:1.0:0.0:0.0	.	10435	Q8WZ42	TITIN_HUMAN	I	9508	ENSP00000343764:V9508I	ENSP00000343764:V9508I	V	-	1	0	TTN	179261140	0.996000	0.38824	1.000000	0.80357	0.951000	0.60555	2.506000	0.45433	2.460000	0.83146	0.467000	0.42956	GTT	C|0.991;T|0.009	0.009	strong		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
EPS15	2060	hgsc.bcm.edu	37	1	51912760	51912760	+	Silent	SNP	T	T	G	rs34704431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:51912760T>G	ENST00000371733.3	-	10	765	c.669A>C	c.(667-669)gcA>gcC	p.A223A	EPS15_ENST00000371730.2_Silent_p.A223A	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	223	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.|Interaction with DAB2. {ECO:0000250}.				cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						TAGCTTTTTCTGCAGGGGATA	0.363			T	MLL	ALL								T|||	235	0.0469249	0.0983	0.0274	5008	,	,		17178	0.0109		0.0328	False		,,,				2504	0.0429				p.A223A		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	EPS15,NS,carcinoma,-2,1	EPS15	72	1	1	Whole gene deletion(1)	central_nervous_system(1)	c.A669C						PASS	.	T		349,4057	178.3+/-207.1	14,321,1868	94.0	97.0	96.0		669	2.1	1.0	1	dbSNP_126	96	273,8327	103.1+/-164.3	4,265,4031	no	coding-synonymous	EPS15	NM_001981.2		18,586,5899	GG,GT,TT		3.1744,7.921,4.7824		223/897	51912760	622,12384	2203	4300	6503	SO:0001819	synonymous_variant	2060	exon10			TTTTTCTGCAGGG	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"""EF-hand domain containing"""	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.669A>C	1.37:g.51912760T>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Silent	SNP	ENST00000371733.3	37	CCDS557.1																																																																																			T|0.955;G|0.045	0.045	strong		0.363	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	
SHCBP1L	81626	hgsc.bcm.edu	37	1	182922003	182922003	+	Missense_Mutation	SNP	G	G	T	rs13373887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182922003G>T	ENST00000367547.3	-	1	502	c.266C>A	c.(265-267)gCg>gAg	p.A89E	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_5'Flank	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	161										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						GGGCTCCTccgccgccgccgc	0.741													T|||	190	0.0379393	0.1293	0.0159	5008	,	,		11211	0.0		0.005	False		,,,				2504	0.0031				p.A89E		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.C266A						PASS	.	T	GLU/ALA	443,3869		18,407,1731	6.0	7.0	7.0		266	0.0	0.0	1	dbSNP_121	7	23,8443		0,23,4210	yes	missense	SHCBP1L	NM_030933.2	107	18,430,5941	TT,TG,GG		0.2717,10.2737,3.6469	benign	89/654	182922003	466,12312	2156	4233	6389	SO:0001583	missense	81626	exon1			TCCTCCGCCGCCG	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 14"""	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.266C>A	1.37:g.182922003G>T	ENSP00000356518:p.Ala89Glu	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	37	28	0.756757	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	37	CCDS30955.1	66	0.03021978021978022	60	0.12195121951219512	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	0.005	-2.169349	0.00315	0.102737	0.002717	ENSG00000157060	ENST00000367547;ENST00000287709	T	0.39229	1.09	3.96	0.04	0.14207	.	1.066270	0.07492	N	0.905864	T	0.00178	0.0005	N	0.01874	-0.695	0.21499	N	0.999663	B	0.02656	0.0	B	0.04013	0.001	T	0.09930	-1.0652	10	0.02654	T	1	.	4.0773	0.09911	0.0:0.2058:0.3591:0.4351	rs13373887	89	Q9BZQ2-3	.	E	89;158	ENSP00000356518:A89E	ENSP00000287709:A158E	A	-	2	0	SHCBP1L	181188626	.	.	0.003000	0.11579	0.009000	0.06853	.	.	-0.560000	0.06102	-0.865000	0.03005	GCG	G|0.965;T|0.035	0.035	strong		0.741	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933	
FAM21A	387680	hgsc.bcm.edu	37	10	51827934	51827934	+	Missense_Mutation	SNP	G	G	A	rs55875820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:51827934G>A	ENST00000282633.5	+	2	118	c.73G>A	c.(73-75)Gtg>Atg	p.V25M	RP11-324H6.5_ENST00000456967.1_RNA|FAM21A_ENST00000314664.7_Missense_Mutation_p.V25M|FAM21A_ENST00000351071.6_Missense_Mutation_p.V25M	NM_001005751.1	NP_001005751.1	Q641Q2	FA21A_HUMAN	family with sequence similarity 21, member A	25					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)				breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	15						GCCGTGGTCGGTGGAGGAGAT	0.701													.|||	1540	0.307508	0.0681	0.3213	5008	,	,		12321	0.3304		0.5189	False		,,,				2504	0.3804				p.V25M		Atlas-SNP	.											FAM21A,NS,carcinoma,0,1	FAM21A	32	1	0			c.G73A						PASS	.	G	MET/VAL	488,3032		88,312,1360	8.0	12.0	11.0		73	1.6	1.0	10	dbSNP_129	11	3767,4229		1086,1595,1317	no	missense	FAM21A	NM_001005751.1	21	1174,1907,2677	AA,AG,GG		47.1111,13.8636,36.9486	benign	25/1342	51827934	4255,7261	1760	3998	5758	SO:0001583	missense	387680	exon2			TGGTCGGTGGAGG	BC082258	CCDS41527.1	10q11.23	2014-06-19			ENSG00000099290	ENSG00000099290			23416	protein-coding gene	gene with protein product			"""family with sequence similarity 21, member B"""	FAM21B			Standard	XM_005269805		Approved	bA56A21.1, bA98I6.1, FLJ10824	uc001jjb.3	Q641Q2	OTTHUMG00000018225	ENST00000282633.5:c.73G>A	10.37:g.51827934G>A	ENSP00000282633:p.Val25Met	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_001005751	A2A3S2|A2A3U6|Q6DHY0	Missense_Mutation	SNP	ENST00000282633.5	37	CCDS41527.1	677	0.309981684981685	36	0.07317073170731707	112	0.30939226519337015	189	0.3304195804195804	340	0.44854881266490765	G	13.62	2.291169	0.40494	0.138636	0.471111	ENSG00000099290	ENST00000351071;ENST00000314664;ENST00000434114;ENST00000282633	.	.	.	2.71	1.65	0.23941	.	0.156736	0.42821	D	0.000653	T	0.00012	0.0000	L	0.59912	1.85	0.09310	P	0.9999999999999996	B;B;B	0.30634	0.181;0.288;0.181	B;B;B	0.34722	0.136;0.136;0.188	T	0.46803	-0.9165	8	0.72032	D	0.01	-9.0815	6.6531	0.22973	0.0:0.0:0.5652:0.4347	rs55875820	25;25;25	E7ESD2;Q641Q2-2;Q641Q2	.;.;FA21A_HUMAN	M	25;25;24;25	.	ENSP00000282633:V25M	V	+	1	0	FAM21A	51497940	1.000000	0.71417	1.000000	0.80357	0.689000	0.40095	2.625000	0.46452	1.523000	0.49018	0.194000	0.17425	GTG	G|0.689;A|0.311	0.311	strong		0.701	FAM21A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276917.2	NM_001005751	
GMFG	9535	hgsc.bcm.edu	37	19	39826131	39826131	+	Missense_Mutation	SNP	G	G	T	rs1801733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39826131G>T	ENST00000597595.1	-	2	252	c.44C>A	c.(43-45)aCa>aAa	p.T15K	GMFG_ENST00000601387.1_Intron|GMFG_ENST00000600322.1_5'UTR|GMFG_ENST00000594700.1_Missense_Mutation_p.T15K|GMFG_ENST00000602185.1_Intron|GMFG_ENST00000595636.1_Missense_Mutation_p.T15K|GMFG_ENST00000253054.8_5'UTR|GMFG_ENST00000598034.1_Missense_Mutation_p.T15K	NM_004877.2	NP_004868.1	O60234	GMFG_HUMAN	glia maturation factor, gamma	15	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				negative regulation of protein kinase activity (GO:0006469)|positive regulation of catalytic activity (GO:0043085)|protein phosphorylation (GO:0006468)	intracellular (GO:0005622)	enzyme activator activity (GO:0008047)|protein kinase inhibitor activity (GO:0004860)			breast(1)|large_intestine(2)|liver(2)|lung(3)|skin(1)|stomach(1)	10	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.15e-27)|all cancers(26;1.3e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			CAGCTTTTCTGTTAGCTCTGG	0.572													G|||	79	0.0157748	0.056	0.0072	5008	,	,		17456	0.0		0.0	False		,,,				2504	0.0				p.T15K		Atlas-SNP	.											.	GMFG	16	.	0			c.C44A						PASS	.	G	LYS/THR	212,4194	127.0+/-164.0	8,196,1999	149.0	116.0	127.0		44	2.1	1.0	19	dbSNP_89	127	13,8587	9.8+/-36.6	0,13,4287	yes	missense	GMFG	NM_004877.2	78	8,209,6286	TT,TG,GG		0.1512,4.8116,1.73	benign	15/143	39826131	225,12781	2203	4300	6503	SO:0001583	missense	9535	exon2			TTTTCTGTTAGCT	AB001993	CCDS12532.1, CCDS74364.1	19q13.2	2014-08-12			ENSG00000130755	ENSG00000130755			4374	protein-coding gene	gene with protein product		604104				9545571, 9653160, 17127212	Standard	XM_005259440		Approved		uc002okz.4	O60234	OTTHUMG00000182811	ENST00000597595.1:c.44C>A	19.37:g.39826131G>T	ENSP00000472249:p.Thr15Lys	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	179	74	0.413408	NM_004877	Q6IB37	Missense_Mutation	SNP	ENST00000597595.1	37	CCDS12532.1	41	0.018772893772893772	37	0.07520325203252033	4	0.011049723756906077	0	0.0	0	0.0	G	0.825	-0.747109	0.03065	0.048116	0.001512	ENSG00000130755	ENST00000253054	.	.	.	4.18	2.07	0.26955	Actin-binding, cofilin/tropomyosin type (3);	0.077251	0.46442	N	0.000283	T	0.00241	0.0007	N	0.00265	-1.74	0.28216	N	0.926737	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29640	-1.0005	9	0.02654	T	1	-19.027	1.2964	0.02070	0.1769:0.1034:0.1922:0.5276	rs1801733;rs52801314	15;15	O60234;Q6IB37	GMFG_HUMAN;.	K	15	.	ENSP00000253054:T15K	T	-	2	0	GMFG	44517971	0.864000	0.29904	0.990000	0.47175	0.765000	0.43378	0.310000	0.19356	0.188000	0.20168	-1.238000	0.01547	ACA	G|0.980;T|0.020	0.020	strong		0.572	GMFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463839.1		
KDM1A	23028	hgsc.bcm.edu	37	1	23409803	23409803	+	Silent	SNP	G	G	A	rs150794224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23409803G>A	ENST00000356634.3	+	19	2654	c.2505G>A	c.(2503-2505)acG>acA	p.T835T	KDM1A_ENST00000542151.1_Silent_p.T859T|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.T859T	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	835	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|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)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CCATGTATACGCTGCCTCGCC	0.562													G|||	23	0.00459265	0.0159	0.0029	5008	,	,		18489	0.0		0.0	False		,,,				2504	0.0				p.T859T		Atlas-SNP	.											.	KDM1A	49	.	0			c.G2577A						PASS	.	G	,	43,4363	46.7+/-81.2	0,43,2160	84.0	70.0	75.0		2577,2505	-6.8	0.0	1	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KDM1A	NM_001009999.2,NM_015013.3	,	0,44,6459	AA,AG,GG		0.0116,0.9759,0.3383	,	859/877,835/853	23409803	44,12962	2203	4300	6503	SO:0001819	synonymous_variant	23028	exon21			GTATACGCTGCCT	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"""Chromatin-modifying enzymes / K-demethylases"""	29079	protein-coding gene	gene with protein product		609132	"""amine oxidase (flavin containing) domain 2"", ""lysine (K)-specific demethylase 1"""	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.2505G>A	1.37:g.23409803G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	69	43	0.623188	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																			G|0.997;A|0.003	0.003	strong		0.562	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013	
FAM129C	199786	hgsc.bcm.edu	37	19	17643125	17643125	+	Silent	SNP	C	C	T	rs73504248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17643125C>T	ENST00000335393.4	+	4	471	c.333C>T	c.(331-333)caC>caT	p.H111H	FAM129C_ENST00000599124.1_Silent_p.H80H|FAM129C_ENST00000601861.1_Silent_p.H80H|FAM129C_ENST00000597887.1_3'UTR|FAM129C_ENST00000300971.2_Silent_p.H111H|FAM129C_ENST00000599164.1_Silent_p.H80H|FAM129C_ENST00000595684.1_Silent_p.H111H|FAM129C_ENST00000600871.1_Silent_p.H57H|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000332386.5_Silent_p.H111H|FAM129C_ENST00000352727.3_Silent_p.H111H	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	111										autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						TTCGGGGCCACCCACCCCGGT	0.647													C|||	105	0.0209665	0.0764	0.0058	5008	,	,		16326	0.0		0.0	False		,,,				2504	0.0				p.H111H		Atlas-SNP	.											.	FAM129C	110	.	0			c.C333T						PASS	.	C	,	316,4090	168.3+/-199.2	13,290,1900	67.0	66.0	66.0		333,333	-2.6	0.0	19	dbSNP_130	66	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	FAM129C	NM_001098524.1,NM_173544.4	,	13,292,6198	TT,TC,CC		0.0233,7.172,2.445	,	111/652,111/698	17643125	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	199786	exon4			GGGCCACCCACCC	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.333C>T	19.37:g.17643125C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	219	219	1	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Silent	SNP	ENST00000335393.4	37	CCDS12362.1																																																																																			C|0.976;T|0.024	0.024	strong		0.647	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
CCDC65	85478	hgsc.bcm.edu	37	12	49308261	49308261	+	Silent	SNP	C	C	T	rs143088014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49308261C>T	ENST00000320516.4	+	3	563	c.375C>T	c.(373-375)gaC>gaT	p.D125D	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Silent_p.D125D	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	125										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						ACAATGTTGACCAGCTCTTGG	0.537													C|||	8	0.00159744	0.0053	0.0014	5008	,	,		17358	0.0		0.0	False		,,,				2504	0.0				p.D125D		Atlas-SNP	.											.	CCDC65	41	.	0			c.C375T						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	85.0	74.0	78.0		375	1.2	1.0	12	dbSNP_134	78	1,8599		0,1,4299	no	coding-synonymous	CCDC65	NM_033124.4		0,16,6487	TT,TC,CC		0.0116,0.3404,0.123		125/485	49308261	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	85478	exon3			TGTTGACCAGCTC		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.375C>T	12.37:g.49308261C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	67	25	0.373134	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Silent	SNP	ENST00000320516.4	37	CCDS8772.1																																																																																			C|0.999;T|0.001	0.001	strong		0.537	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
ZNF862	643641	hgsc.bcm.edu	37	7	149547273	149547273	+	Silent	SNP	G	G	A	rs112719493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149547273G>A	ENST00000223210.4	+	5	1208	c.963G>A	c.(961-963)tcG>tcA	p.S321S		NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	321					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)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						AGGGGCTGTCGGAGGAGGTTC	0.612													G|||	225	0.0449281	0.1581	0.0101	5008	,	,		15716	0.0		0.0	False		,,,				2504	0.0092				p.S321S		Atlas-SNP	.											.	ZNF862	97	.	0			c.G963A						PASS	.	G		531,3645		31,469,1588	71.0	78.0	75.0		963	-0.2	0.2	7	dbSNP_132	75	17,8453		0,17,4218	no	coding-synonymous	ZNF862	NM_001099220.1		31,486,5806	AA,AG,GG		0.2007,12.7155,4.3334		321/1170	149547273	548,12098	2088	4235	6323	SO:0001819	synonymous_variant	643641	exon5			GCTGTCGGAGGAG	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.963G>A	7.37:g.149547273G>A		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	228	227	0.995614	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	37	CCDS47741.1																																																																																			G|0.960;A|0.040	0.040	strong		0.612	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
MORC1	27136	hgsc.bcm.edu	37	3	108754214	108754214	+	Missense_Mutation	SNP	T	T	C	rs3762697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	122	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	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		
ASAH1	427	hgsc.bcm.edu	37	8	17930772	17930772	+	Intron	SNP	C	C	T	rs3753115	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17930772C>T	ENST00000262097.6	-	3	437				ASAH1_ENST00000417108.2_Intron|ASAH1_ENST00000381733.4_Intron|ASAH1_ENST00000520781.1_Intron|ASAH1_ENST00000314146.10_Missense_Mutation_p.V63I|ASAH1_ENST00000520051.1_Intron	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)		CACCTTATAACAGCAGGGAAG	0.328													T|||	2071	0.413538	0.2504	0.5735	5008	,	,		19990	0.3532		0.4771	False		,,,				2504	0.5174				p.V63I		Atlas-SNP	.											.	ASAH1	71	.	0			c.G187A						PASS	.	T	ILE/VAL,,	880,2254		138,604,825	60.0	44.0	49.0		187,,	-1.6	0.0	8	dbSNP_107	49	3484,3676		840,1804,936	yes	missense,intron,intron	ASAH1	NM_001127505.1,NM_004315.4,NM_177924.3	29,,	978,2408,1761	TT,TC,CC		48.6592,28.0791,42.3936	,,	63/390,,	17930772	4364,5930	1567	3580	5147	SO:0001627	intron_variant	427	exon3			TTATAACAGCAGG	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	ENST00000262097.6:c.126-1873G>A	8.37:g.17930772C>T		Somatic	463	0	0		WXS	Illumina HiSeq	Phase_I	327	107	0.327217	NM_001127505	E9PDS0|Q6W898|Q96AS2	Missense_Mutation	SNP	ENST00000262097.6	37	CCDS6006.1	920	0.42124542124542125	148	0.3008130081300813	219	0.6049723756906077	200	0.34965034965034963	353	0.4656992084432718	T	2.153	-0.394073	0.04899	0.280791	0.486592	ENSG00000104763	ENST00000314146	T	0.70869	-0.52	3.6	-1.63	0.08345	.	.	.	.	.	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	0.44877	-0.9299	8	0.19590	T	0.45	.	2.3428	0.04264	0.1861:0.4184:0.2471:0.1484	rs3753115;rs58952721;rs3753115	63	E9PDS0	.	I	63	ENSP00000326970:V63I	ENSP00000326970:V63I	V	-	1	0	ASAH1	17975052	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.047000	0.03521	-0.675000	0.05246	-2.597000	0.00163	GTT	C|0.584;T|0.416	0.416	strong		0.328	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	
NTRK3	4916	hgsc.bcm.edu	37	15	88680684	88680684	+	Silent	SNP	G	G	A	rs1128994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:88680684G>A	ENST00000360948.2	-	6	734	c.573C>T	c.(571-573)aaC>aaT	p.N191N	NTRK3_ENST00000558676.1_Silent_p.N191N|NTRK3_ENST00000540489.2_Silent_p.N191N|NTRK3_ENST00000394480.2_Silent_p.N191N|NTRK3_ENST00000357724.2_Silent_p.N191N|NTRK3_ENST00000542733.2_Silent_p.N93N|NTRK3_ENST00000557856.1_Silent_p.N191N|NTRK3_ENST00000317501.3_Silent_p.N191N|NTRK3_ENST00000355254.2_Silent_p.N191N	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	191	LRRCT.				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)		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)			AGCCATCAGCGTTGATGCAGT	0.587			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)			G|||	1356	0.270767	0.3555	0.2046	5008	,	,		19398	0.2222		0.2624	False		,,,				2504	0.2618				p.N191N		Atlas-SNP	.		Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	.	NTRK3	587	.	0			c.C573T						PASS	.	G	,,	1624,2778	498.8+/-364.2	300,1024,877	141.0	105.0	117.0		573,573,573	-2.5	0.0	15	dbSNP_86	117	2317,6281	390.4+/-343.3	295,1727,2277	no	coding-synonymous,coding-synonymous,coding-synonymous	NTRK3	NM_001007156.2,NM_001012338.2,NM_002530.3	,,	595,2751,3154	AA,AG,GG		26.9481,36.8923,30.3154	,,	191/613,191/840,191/826	88680684	3941,9059	2201	4299	6500	SO:0001819	synonymous_variant	4916	exon7			ATCAGCGTTGATG	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.573C>T	15.37:g.88680684G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	ENST00000360948.2	37	CCDS32322.1																																																																																			G|0.705;A|0.295	0.295	strong		0.587	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
GEMIN5	25929	hgsc.bcm.edu	37	5	154282235	154282235	+	Splice_Site	SNP	T	T	C	rs1421813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:154282235T>C	ENST00000285873.7	-	20	2805	c.2730A>G	c.(2728-2730)ggA>ggG	p.G910G		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	910					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AGTGACCTTTTCCTGTTTGAA	0.418													T|||	634	0.126597	0.2012	0.1988	5008	,	,		22243	0.0536		0.0895	False		,,,				2504	0.0879				p.G910G		Atlas-SNP	.											.	GEMIN5	120	.	0			c.A2730G						PASS	.	T		810,3596	306.0+/-289.3	82,646,1475	150.0	146.0	147.0		2730	-3.4	1.0	5	dbSNP_88	147	627,7973	153.9+/-208.2	18,591,3691	yes	coding-synonymous-near-splice	GEMIN5	NM_015465.3		100,1237,5166	CC,CT,TT		7.2907,18.384,11.0487		910/1509	154282235	1437,11569	2203	4300	6503	SO:0001630	splice_region_variant	25929	exon20			ACCTTTTCCTGTT	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"""WD repeat domain containing"""	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.2729-1A>G	5.37:g.154282235T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Silent	SNP	ENST00000285873.7	37	CCDS4330.1																																																																																			T|0.893;C|0.107	0.107	strong		0.418	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1		Silent
RFPL3	10738	hgsc.bcm.edu	37	22	32754386	32754386	+	Missense_Mutation	SNP	C	C	A	rs9621427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32754386C>A	ENST00000249007.4	+	1	533	c.328C>A	c.(328-330)Ctg>Atg	p.L110M	RFPL3_ENST00000397468.1_Missense_Mutation_p.L81M|RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000382088.3_Missense_Mutation_p.L81M	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	110	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		L -> M (in dbSNP:rs9621427). {ECO:0000269|PubMed:15489334}.				zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GGAGCCCAAGCTGAAGAAGAT	0.502													c|||	523	0.104433	0.1846	0.1138	5008	,	,		18313	0.0456		0.0557	False		,,,				2504	0.1002				p.L110M		Atlas-SNP	.											.	RFPL3	91	.	0			c.C328A						PASS	.	C	MET/LEU,MET/LEU	803,3603	321.3+/-297.0	68,667,1468	109.0	109.0	109.0		328,241	0.7	0.0	22	dbSNP_119	109	499,8101	144.3+/-200.2	15,469,3816	no	missense,missense	RFPL3	NM_001098535.1,NM_006604.2	15,15	83,1136,5284	AA,AC,CC		5.8023,18.2251,10.0108	probably-damaging,probably-damaging	110/318,81/289	32754386	1302,11704	2203	4300	6503	SO:0001583	missense	10738	exon1			CCCAAGCTGAAGA	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.328C>A	22.37:g.32754386C>A	ENSP00000249007:p.Leu110Met	Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	249	117	0.46988	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	37	CCDS43011.1	192	0.08791208791208792	95	0.19308943089430894	36	0.09944751381215469	25	0.043706293706293704	36	0.047493403693931395	C	11.53	1.666884	0.29604	0.182251	0.058023	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	T;T;T	0.61392	0.11;0.11;0.11	0.664	0.664	0.17890	RDM domain, Ret finger protein-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.00178	0.0005	L	0.54323	1.7	0.80722	P	0.0	D	0.56287	0.975	P	0.61328	0.887	T	0.18903	-1.0322	7	0.72032	D	0.01	.	.	.	.	rs9621427;rs17852987;rs52805018;rs9621427	110	O75679	RFPL3_HUMAN	M	81;110;81	ENSP00000380609:L81M;ENSP00000249007:L110M;ENSP00000371520:L81M	ENSP00000249007:L110M	L	+	1	2	RFPL3	31084386	0.027000	0.19231	0.021000	0.16686	0.462000	0.32619	-0.912000	0.04046	0.624000	0.30286	0.194000	0.17425	CTG	C|0.903;A|0.097	0.097	strong		0.502	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
FBXL5	26234	hgsc.bcm.edu	37	4	15627092	15627092	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:15627092A>G	ENST00000341285.3	-	9	1757	c.1633T>C	c.(1633-1635)Tat>Cat	p.Y545H	FBXL5_ENST00000412094.2_Missense_Mutation_p.Y528H|FBXL5_ENST00000382358.4_Missense_Mutation_p.Y419H	NM_001193534.1|NM_001193535.1|NM_012161.3	NP_001180463.1|NP_001180464.1|NP_036293.1	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5	545					iron ion homeostasis (GO:0055072)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	iron ion binding (GO:0005506)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13						TGACCACAATACGCAAAGGCT	0.423																																					p.Y545H		Atlas-SNP	.											.	FBXL5	52	.	0			c.T1633C						PASS	.						71.0	58.0	62.0					4																	15627092		2203	4300	6503	SO:0001583	missense	26234	exon9			CACAATACGCAAA	AF174591	CCDS3415.1, CCDS54745.1	4p15.33	2011-06-09			ENSG00000118564	ENSG00000118564		"""F-boxes / Leucine-rich repeats"""	13602	protein-coding gene	gene with protein product		605655				10531035	Standard	NM_012161		Approved	FBL4, FBL5, FLR1	uc003goc.2	Q9UKA1	OTTHUMG00000097097	ENST00000341285.3:c.1633T>C	4.37:g.15627092A>G	ENSP00000344866:p.Tyr545His	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	134	6	0.0447761	NM_012161	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Missense_Mutation	SNP	ENST00000341285.3	37	CCDS3415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.187808|4.187808	0.78789|0.78789	.|.	.|.	ENSG00000118564|ENSG00000118564	ENST00000513163|ENST00000341285;ENST00000412094;ENST00000382358	.|T;T;T	.|0.38401	.|1.17;1.19;1.14	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	.|0.108992	.|0.64402	.|D	.|0.000005	T|T	0.48095|0.48095	0.1481|0.1481	L|L	0.29908|0.29908	0.895|0.895	0.50467|0.50467	D|D	0.999876|0.999876	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.85130	.|0.997;0.994	T|T	0.36601|0.36601	-0.9741|-0.9741	5|10	.|0.30078	.|T	.|0.28	-20.3568|-20.3568	16.0006|16.0006	0.80290|0.80290	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|528;545	.|Q9UKA1-2;Q9UKA1	.|.;FBXL5_HUMAN	A|H	465|545;528;419	.|ENSP00000344866:Y545H;ENSP00000408679:Y528H;ENSP00000371795:Y419H	.|ENSP00000344866:Y545H	V|Y	-|-	2|1	0|0	FBXL5|FBXL5	15236190|15236190	0.997000|0.997000	0.39634|0.39634	0.864000|0.864000	0.33941|0.33941	0.943000|0.943000	0.58893|0.58893	3.468000|3.468000	0.53086|0.53086	2.180000|2.180000	0.69256|0.69256	0.460000|0.460000	0.39030|0.39030	GTA|TAT	.	.	none		0.423	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2		
FBXO22	26263	hgsc.bcm.edu	37	15	76205550	76205550	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:76205550C>T	ENST00000308275.3	+	3	391	c.286C>T	c.(286-288)Cgc>Tgc	p.R96C	FBXO22_ENST00000453211.2_Missense_Mutation_p.R96C|FBXO22_ENST00000540507.1_5'UTR	NM_147188.2	NP_671717.1	Q8NEZ5	FBX22_HUMAN	F-box protein 22	96					cellular protein modification process (GO:0006464)|cellular response to starvation (GO:0009267)|nucleocytoplasmic transport (GO:0006913)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein polyubiquitination (GO:0000209)|regulation of skeletal muscle fiber development (GO:0048742)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GCAGAATGTTCGCATCTTACC	0.383																																					p.R96C		Atlas-SNP	.											FBXO22_ENST00000453211,NS,carcinoma,0,3	FBXO22	60	3	0			c.C286T						PASS	.						65.0	69.0	68.0					15																	76205550		2197	4294	6491	SO:0001583	missense	26263	exon3			AATGTTCGCATCT	AF174602	CCDS10287.1, CCDS45310.1	15q23	2008-10-03	2004-06-15		ENSG00000167196	ENSG00000167196		"""F-boxes /  ""other"""""	13593	protein-coding gene	gene with protein product	"""FIST domain containing 1"""	609096	"""F-box only protein 22"""			10531035, 10531037, 17855421	Standard	NM_147188		Approved	FBX22, FISTC1	uc002bbk.3	Q8NEZ5	OTTHUMG00000142841	ENST00000308275.3:c.286C>T	15.37:g.76205550C>T	ENSP00000307833:p.Arg96Cys	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	20	11	0.55	NM_012170	Q0D2P8|Q6PIL5|Q8IXW3|Q9H824|Q9UKC0	Missense_Mutation	SNP	ENST00000308275.3	37	CCDS10287.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.729883	0.48833	.	.	ENSG00000167196	ENST00000308275;ENST00000453211	.	.	.	5.95	5.95	0.96441	.	0.409490	0.29676	N	0.011486	T	0.39937	0.1097	N	0.08118	0	0.80722	D	1	P;D	0.57571	0.916;0.98	B;P	0.46049	0.23;0.502	T	0.37663	-0.9696	9	0.39692	T	0.17	-3.1292	17.1124	0.86679	0.0:1.0:0.0:0.0	.	96;96	Q8NEZ5;Q8NEZ5-3	FBX22_HUMAN;.	C	96	.	ENSP00000307833:R96C	R	+	1	0	FBXO22	73992605	0.995000	0.38212	0.523000	0.27875	0.842000	0.47809	2.942000	0.49018	2.824000	0.97209	0.655000	0.94253	CGC	.	.	none		0.383	FBXO22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286477.2	NM_147188	
MUC4	4585	hgsc.bcm.edu	37	3	195512734	195512734	+	Missense_Mutation	SNP	T	T	G	rs529505943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512734T>G	ENST00000463781.3	-	2	6176	c.5717A>C	c.(5716-5718)cAt>cCt	p.H1906P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H1906P	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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.H1906R(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)		GTCGGTGACATGAAGAGGGGT	0.567													.|||	5	0.000998403	0.0015	0.0	5008	,	,		42586	0.0		0.001	False		,,,				2504	0.002				p.H1906P		Atlas-SNP	.											MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	NS(2)	c.A5717C						scavenged	.						43.0	38.0	40.0					3																	195512734		690	1591	2281	SO:0001583	missense	4585	exon2			GTGACATGAAGAG	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.5717A>C	3.37:g.195512734T>G	ENSP00000417498:p.His1906Pro	Somatic	399	2	0.00501253		WXS	Illumina HiSeq	Phase_I	327	27	0.0825688	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	.	.	.	.	.	.	.	.	.	.	-	5.462	0.270280	0.10349	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.53;1.52	0.844	-1.69	0.08186	.	.	.	.	.	T	0.09069	0.0224	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21042	-1.0257	8	.	.	.	.	2.2178	0.03964	0.0:0.333:0.3361:0.331	.	1906	E7ESK3	.	P	1906	ENSP00000417498:H1906P;ENSP00000420243:H1906P	.	H	-	2	0	MUC4	196997129	0.002000	0.14202	0.005000	0.12908	0.007000	0.05969	-0.537000	0.06128	-1.928000	0.01059	-1.950000	0.00486	CAT	.	.	none		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MTTP	4547	hgsc.bcm.edu	37	4	100510903	100510903	+	Missense_Mutation	SNP	A	A	G	rs3792683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100510903A>G	ENST00000265517.5	+	4	700	c.497A>G	c.(496-498)aAt>aGt	p.N166S	MTTP_ENST00000511045.1_Missense_Mutation_p.N193S|MTTP_ENST00000457717.1_Missense_Mutation_p.N166S			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	166	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		N -> S (in dbSNP:rs3792683).		cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	GGAACCACCAATGAGGTACTT	0.348													A|||	573	0.114417	0.1929	0.0692	5008	,	,		17528	0.2143		0.0159	False		,,,				2504	0.0389				p.N166S		Atlas-SNP	.											MTTP,NS,carcinoma,-1,1	MTTP	127	1	0			c.A497G						PASS	.	A	SER/ASN	763,3643	309.1+/-290.9	69,625,1509	76.0	78.0	77.0		497	4.1	0.9	4	dbSNP_107	77	351,8249	118.1+/-177.6	5,341,3954	yes	missense	MTTP	NM_000253.2	46	74,966,5463	GG,GA,AA		4.0814,17.3173,8.5653	benign	166/895	100510903	1114,11892	2203	4300	6503	SO:0001583	missense	4547	exon5			CCACCAATGAGGT		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.497A>G	4.37:g.100510903A>G	ENSP00000265517:p.Asn166Ser	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	17	0.333333	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	268	0.1227106227106227	91	0.18495934959349594	20	0.055248618784530384	142	0.24825174825174826	15	0.01978891820580475	A	2.852	-0.238086	0.05944	0.173173	0.040814	ENSG00000138823	ENST00000506883;ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T;T	0.14022	2.54;3.56;3.56;3.56	5.35	4.13	0.48395	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.639345	0.17178	N	0.183997	T	0.00012	0.0000	L	0.29908	0.895	0.45194	P	0.0017930000000000446	B;B	0.33777	0.013;0.425	B;B	0.31946	0.03;0.138	T	0.37820	-0.9689	9	0.09338	T	0.73	-25.0927	3.6587	0.08230	0.607:0.2013:0.1916:0.0	rs3792683;rs52834225;rs3792683	193;166	E9PBP6;P55157	.;MTP_HUMAN	S	176;193;166;166;166	ENSP00000426755:N176S;ENSP00000427679:N193S;ENSP00000400821:N166S;ENSP00000265517:N166S	ENSP00000265517:N166S	N	+	2	0	MTTP	100729926	0.014000	0.17966	0.944000	0.38274	0.988000	0.76386	0.371000	0.20450	0.833000	0.34828	0.533000	0.62120	AAT	A|0.901;G|0.099	0.099	strong		0.348	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
PAPSS1	9061	hgsc.bcm.edu	37	4	108552787	108552787	+	Splice_Site	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:108552787T>C	ENST00000265174.4	-	11	2008	c.1736A>G	c.(1735-1737)cAc>cGc	p.H579R		NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	579					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)		TAAGACTTACTGTTCAGAGTC	0.403																																					p.H579R		Atlas-SNP	.											.	PAPSS1	57	.	0			c.A1736G						PASS	.						113.0	111.0	112.0					4																	108552787		2203	4300	6503	SO:0001630	splice_region_variant	9061	exon11			ACTTACTGTTCAG	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.1736+1A>G	4.37:g.108552787T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	45	0.401786	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Missense_Mutation	SNP	ENST00000265174.4	37	CCDS3676.1	.	.	.	.	.	.	.	.	.	.	T	4.243	0.044005	0.08196	.	.	ENSG00000138801	ENST00000265174	T	0.26957	1.7	5.62	5.62	0.85841	Sulphate adenylyltransferase (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.188956	0.56097	D	0.000029	T	0.06096	0.0158	N	0.00125	-2.05	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37267	-0.9713	9	.	.	.	-22.1456	15.8538	0.78960	0.0:0.0:0.0:1.0	.	579	O43252	PAPS1_HUMAN	R	579	ENSP00000265174:H579R	.	H	-	2	0	PAPSS1	108772236	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.979000	0.40608	2.141000	0.66446	0.528000	0.53228	CAC	.	.	none		0.403	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2		Missense_Mutation
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464046	39464046	+	Missense_Mutation	SNP	G	G	C	rs2074286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	127	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	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	
TEP1	7011	hgsc.bcm.edu	37	14	20846950	20846950	+	Missense_Mutation	SNP	C	C	T	rs8022805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20846950C>T	ENST00000262715.5	-	37	5355	c.5315G>A	c.(5314-5316)cGg>cAg	p.R1772Q	TEP1_ENST00000545983.1_Missense_Mutation_p.R110Q|TEP1_ENST00000556935.1_Missense_Mutation_p.R1664Q	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1772			R -> Q (in dbSNP:rs8022805).		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)		GGCTAGCAGCCGGCAGTCTGG	0.577													C|||	154	0.0307508	0.003	0.0303	5008	,	,		19563	0.0		0.0586	False		,,,				2504	0.0716				p.R1772Q		Atlas-SNP	.											.	TEP1	224	.	0			c.G5315A						PASS	.	C	GLN/ARG	48,4358	50.9+/-86.3	0,48,2155	83.0	80.0	81.0		5315	4.9	1.0	14	dbSNP_116	81	497,8103	143.3+/-199.3	21,455,3824	yes	missense	TEP1	NM_007110.4	43	21,503,5979	TT,TC,CC		5.7791,1.0894,4.1904	probably-damaging	1772/2628	20846950	545,12461	2203	4300	6503	SO:0001583	missense	7011	exon37			AGCAGCCGGCAGT		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.5315G>A	14.37:g.20846950C>T	ENSP00000262715:p.Arg1772Gln	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	142	73	0.514085	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	62	0.028388278388278388	0	0.0	12	0.03314917127071823	0	0.0	50	0.06596306068601583	C	22.4	4.290462	0.80914	0.010894	0.057791	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	T;T;T	0.59083	0.29;0.29;0.29	5.76	4.87	0.63330	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.118143	0.53938	D	0.000055	T	0.11324	0.0276	L	0.37800	1.135	0.41831	D	0.990077	D;D;D;D	0.89917	0.992;1.0;0.999;1.0	P;D;D;D	0.68765	0.838;0.933;0.928;0.96	T	0.16335	-1.0406	10	0.31617	T	0.26	-32.352	9.7346	0.40379	0.0:0.9085:0.0:0.0915	rs8022805;rs8022805	110;1664;1115;1772	B4E0B6;G3V5X7;G3V2A4;Q99973	.;.;.;TEP1_HUMAN	Q	1772;1772;1664;110	ENSP00000262715:R1772Q;ENSP00000452574:R1664Q;ENSP00000438849:R110Q	ENSP00000262715:R1772Q	R	-	2	0	TEP1	19916790	0.208000	0.23494	1.000000	0.80357	0.798000	0.45092	0.601000	0.24119	2.724000	0.93272	0.563000	0.77884	CGG	C|0.963;T|0.037	0.037	strong		0.577	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416775	105416775	+	Silent	SNP	C	C	A	rs60880494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416775C>A	ENST00000333244.5	-	7	5132	c.5013G>T	c.(5011-5013)tcG>tcT	p.S1671S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1671						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)			TGCCTGGGGCCGACACCCCAA	0.602													.|||	107	0.0213658	0.0613	0.0058	5008	,	,		17088	0.005		0.001	False		,,,				2504	0.0164				p.S1671S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G5013T						PASS	.	T		136,3744		13,110,1817	190.0	222.0	212.0		5013	-5.7	0.0	14	dbSNP_129	212	15,8193		2,11,4091	no	coding-synonymous	AHNAK2	NM_138420.2		15,121,5908	AA,AC,CC		0.1827,3.5052,1.2492		1671/5796	105416775	151,11937	1940	4104	6044	SO:0001819	synonymous_variant	113146	exon7			TGGGGCCGACACC	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.5013G>T	14.37:g.105416775C>A		Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	213	82	0.384977	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.015;C|0.985	0.015	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
LINC00283	100874057	hgsc.bcm.edu	37	13	103398453	103398453	+	RNA	SNP	C	C	A	rs141118373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103398453C>A	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		TCTAAAGGACCCATTTGGAGA	0.408													C|||	57	0.0113818	0.0408	0.0043	5008	,	,		20326	0.0		0.0	False		,,,				2504	0.0				p.G1532C		Atlas-SNP	.											.	.	.	.	0			c.G4594T						PASS	.	C	CYS/GLY	29,1355		0,29,663	111.0	96.0	101.0		4594	-0.2	0.0	13	dbSNP_134	101	0,3180		0,0,1590	yes	missense	CCDC168	NM_001146197.1	159	0,29,2253	AA,AC,CC		0.0,2.0954,0.6354		1532/7082	103398453	29,4535	692	1590	2282			643677	exon4			AAGGACCCATTTG			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103398453C>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	206	108	0.524272	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				C|0.991;A|0.009	0.009	strong		0.408	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
MUC4	4585	hgsc.bcm.edu	37	3	195509122	195509122	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509122G>A	ENST00000463781.3	-	2	9788	c.9329C>T	c.(9328-9330)cCt>cTt	p.P3110L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P3110L	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.P3110L(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)		TGCTGAGGAAGGGCTAGTGAC	0.587																																					p.P3110L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.C9329T						PASS	.						20.0	11.0	14.0					3																	195509122		672	1557	2229	SO:0001583	missense	4585	exon2			GAGGAAGGGCTAG	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.9329C>T	3.37:g.195509122G>A	ENSP00000417498:p.Pro3110Leu	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	307	59	0.192182	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	1.472	-0.559628	0.03967	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.54;1.61	.	.	.	.	.	.	.	.	T	0.13798	0.0334	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.30119	-0.9989	7	.	.	.	.	4.4512	0.11621	0.7405:0.0:0.2595:0.0	.	2982	E7ESK3	.	L	3110	ENSP00000417498:P3110L;ENSP00000420243:P3110L	.	P	-	2	0	MUC4	196993901	0.001000	0.12720	0.025000	0.17156	0.000000	0.00434	0.608000	0.24223	-0.414000	0.07495	0.000000	0.15137	CCT	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PEX19	5824	hgsc.bcm.edu	37	1	160253413	160253413	+	Silent	SNP	G	G	A	rs141911166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160253413G>A	ENST00000368072.5	-	2	108	c.87C>T	c.(85-87)ttC>ttT	p.F29F	DCAF8_ENST00000608310.1_Intron|DCAF8_ENST00000556710.1_Intron|PEX19_ENST00000440949.3_5'UTR|PEX19_ENST00000532508.1_5'UTR	NM_001193644.1|NM_002857.3	NP_001180573.1|NP_002848.1	P40855	PEX19_HUMAN	peroxisomal biogenesis factor 19	29	Docking to the peroxisome membrane and binding to PEX3.|Necessary for PEX19 function on peroxisome biogenesis.				chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|establishment of protein localization to peroxisome (GO:0072663)|negative regulation of lipid binding (GO:1900131)|peroxisome fission (GO:0016559)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	ATPase binding (GO:0051117)|peroxisome membrane class-1 targeting sequence binding (GO:0036105)|protein N-terminus binding (GO:0047485)			cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)	11	all_cancers(52;1.27e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGGCTTTATCGAAATCATCAA	0.532													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18595	0.0		0.0	False		,,,				2504	0.0				p.F29F		Atlas-SNP	.											PEX19,NS,carcinoma,0,3	PEX19	34	3	0			c.C87T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	81.0	75.0	77.0		87,87	1.1	1.0	1	dbSNP_134	77	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PEX19	NM_001193644.1,NM_002857.3	,	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	,	29/280,29/300	160253413	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5824	exon2			TTTATCGAAATCA	Y09048	CCDS1201.1	1q22	2008-07-18	2004-03-17	2004-03-19	ENSG00000162735	ENSG00000162735			9713	protein-coding gene	gene with protein product	"""housekeeping gene, 33kD"""	600279	"""peroxisomal farnesylated protein"""	PXF		9339377, 10051604	Standard	NM_002857		Approved	HK33, D1S2223E, PMP1, PMPI, PXMP1		P40855	OTTHUMG00000033112	ENST00000368072.5:c.87C>T	1.37:g.160253413G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_002857	D3DVE7|Q5QNY4|Q8NI97	Silent	SNP	ENST00000368072.5	37	CCDS1201.1																																																																																			G|1.000;A|0.000	0.000	strong		0.532	PEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080642.2	NM_002857	
HPS5	11234	hgsc.bcm.edu	37	11	18327684	18327684	+	Silent	SNP	G	G	T	rs1140047	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18327684G>T	ENST00000349215.3	-	7	1099	c.822C>A	c.(820-822)ctC>ctA	p.L274L	HPS5_ENST00000396253.3_Silent_p.L160L|HPS5_ENST00000531848.1_Silent_p.L160L|HPS5_ENST00000438420.2_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	137	0	0		WXS	Illumina HiSeq	Phase_I	169	71	0.420118	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	
DSCAML1	57453	hgsc.bcm.edu	37	11	117303858	117303858	+	Silent	SNP	T	T	C	rs11216382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117303858T>C	ENST00000321322.6	-	29	5203	c.5202A>G	c.(5200-5202)caA>caG	p.Q1734Q	DSCAML1_ENST00000527706.1_Silent_p.Q1464Q	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1674					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)		ACTCACCCAGTTGCTTGATGC	0.587													C|||	706	0.140974	0.2557	0.1758	5008	,	,		18607	0.0565		0.1551	False		,,,				2504	0.0337				p.Q1734Q		Atlas-SNP	.											DSCAML1,NS,carcinoma,-2,1	DSCAML1	286	1	0			c.A5202G						PASS	.	C		1077,3325	719.8+/-409.0	131,815,1255	111.0	94.0	100.0		5202	2.6	1.0	11	dbSNP_120	100	1439,7153	749.8+/-407.4	118,1203,2975	yes	coding-synonymous	DSCAML1	NM_020693.2		249,2018,4230	CC,CT,TT		16.7481,24.4662,19.3628		1734/2114	117303858	2516,10478	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon29			ACCCAGTTGCTTG		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.5202A>G	11.37:g.117303858T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			T|0.826;C|0.174	0.174	strong		0.587	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
KRT16	3868	hgsc.bcm.edu	37	17	39767947	39767947	+	Silent	SNP	C	C	T	rs144914208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39767947C>T	ENST00000301653.4	-	2	622	c.558G>A	c.(556-558)gcG>gcA	p.A186A		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	186	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)				AAATGGGCTGCGCATTCTCAA	0.577													c|||	105	0.0209665	0.0749	0.0072	5008	,	,		20382	0.0		0.001	False		,,,				2504	0.0				p.A186A		Atlas-SNP	.											KRT16,colon,carcinoma,-1,1	KRT16	45	1	0			c.G558A						PASS	.	T		282,4124	146.5+/-181.1	7,268,1928	29.0	27.0	28.0		558	-7.1	0.3	17	dbSNP_134	28	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	KRT16	NM_005557.3		7,269,6224	TT,TC,CC		0.0116,6.4004,2.1769		186/474	39767947	283,12717	2203	4297	6500	SO:0001819	synonymous_variant	3868	exon2			GGGCTGCGCATTC	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.558G>A	17.37:g.39767947C>T		Somatic	390	0	0		WXS	Illumina HiSeq	Phase_I	379	169	0.44591	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Silent	SNP	ENST00000301653.4	37	CCDS11401.1																																																																																			C|0.978;T|0.022	0.022	strong		0.577	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557	
PUS7L	83448	hgsc.bcm.edu	37	12	44130205	44130205	+	Silent	SNP	G	G	A	rs12309260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:44130205G>A	ENST00000416848.2	-	7	2192	c.1704C>T	c.(1702-1704)gaC>gaT	p.D568D	PUS7L_ENST00000551923.1_Silent_p.D568D|PUS7L_ENST00000344862.5_Silent_p.D568D|PUS7L_ENST00000431332.3_Silent_p.D255D	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	568	TRUD. {ECO:0000255|PROSITE- ProRule:PRU00342}.				pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		GGAAATTCTCGTCATCAATGT	0.373													G|||	61	0.0121805	0.0431	0.0043	5008	,	,		18654	0.0		0.001	False		,,,				2504	0.0				p.D568D		Atlas-SNP	.											.	PUS7L	73	.	0			c.C1704T						PASS	.	G	,,	178,4228	115.4+/-153.4	2,174,2027	158.0	146.0	150.0		1704,1704,1704	-5.5	0.0	12	dbSNP_120	150	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	PUS7L	NM_001098614.1,NM_001098615.1,NM_031292.3	,,	2,176,6325	AA,AG,GG		0.0233,4.0399,1.384	,,	568/702,568/702,568/702	44130205	180,12826	2203	4300	6503	SO:0001819	synonymous_variant	83448	exon7			ATTCTCGTCATCA	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.1704C>T	12.37:g.44130205G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Silent	SNP	ENST00000416848.2	37	CCDS8743.1																																																																																			G|0.988;A|0.012	0.012	strong		0.373	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292	
PTK6	5753	hgsc.bcm.edu	37	20	62166313	62166313	+	Silent	SNP	C	C	T	rs310640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62166313C>T	ENST00000217185.2	-	2	357	c.330G>A	c.(328-330)ccG>ccA	p.P110P	PTK6_ENST00000542869.1_Intron	NM_005975.3	NP_005966.1	Q13882	PTK6_HUMAN	protein tyrosine kinase 6	110	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|intestinal epithelial cell differentiation (GO:0060575)|negative regulation of growth (GO:0045926)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(1)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	15	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)		Vandetanib(DB05294)	AGTCGGCACTCGGCTTCTCGC	0.692													c|||	583	0.116414	0.3638	0.0562	5008	,	,		15105	0.0139		0.0268	False		,,,				2504	0.0225				p.P110P		Atlas-SNP	.											.	PTK6	33	.	0			c.G330A						PASS	.			1378,2998		220,938,1030	15.0	18.0	17.0		330	-6.0	0.0	20	dbSNP_79	17	166,8408		2,162,4123	no	coding-synonymous	PTK6	NM_005975.2		222,1100,5153	TT,TC,CC		1.9361,31.4899,11.9228		110/452	62166313	1544,11406	2188	4287	6475	SO:0001819	synonymous_variant	5753	exon2			GGCACTCGGCTTC	U61412	CCDS13524.1, CCDS74750.1	20q13.3	2013-02-18	2013-02-18		ENSG00000101213	ENSG00000101213	2.7.10.1	"""SH2 domain containing"""	9617	protein-coding gene	gene with protein product		602004	"""PTK6 protein tyrosine kinase 6"""			8247543, 9284935	Standard	NM_005975		Approved	BRK	uc002yfg.4	Q13882	OTTHUMG00000033039	ENST00000217185.2:c.330G>A	20.37:g.62166313C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_005975	B2RCR3|B4DW46|Q58F01	Silent	SNP	ENST00000217185.2	37	CCDS13524.1																																																																																			C|0.869;T|0.131	0.131	strong		0.692	PTK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080313.1		
ST3GAL4	6484	hgsc.bcm.edu	37	11	126278075	126278075	+	Silent	SNP	C	C	T	rs2230279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:126278075C>T	ENST00000526727.1	+	6	797	c.423C>T	c.(421-423)taC>taT	p.Y141Y	ST3GAL4_ENST00000444328.2_Silent_p.Y141Y|ST3GAL4_ENST00000392669.2_Silent_p.Y141Y|ST3GAL4_ENST00000526756.1_3'UTR|ST3GAL4_ENST00000356132.4_Silent_p.Y147Y|ST3GAL4_ENST00000534083.1_Silent_p.Y141Y|ST3GAL4_ENST00000449406.2_Silent_p.Y130Y|ST3GAL4_ENST00000227495.6_Silent_p.Y137Y|ST3GAL4_ENST00000534457.1_Silent_p.Y136Y|ST3GAL4_ENST00000530591.1_Silent_p.Y137Y|ST3GAL4_ENST00000532243.1_Silent_p.Y140Y			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	141					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)			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)		TCAACAAGTACGATGTGGTCA	0.582													C|||	1727	0.344848	0.3623	0.3256	5008	,	,		19286	0.5079		0.3101	False		,,,				2504	0.2025				p.Y141Y		Atlas-SNP	.											.	ST3GAL4	25	.	0			c.C423T						PASS	.	C		1546,2856	485.5+/-360.3	270,1006,925	166.0	169.0	168.0		411	2.3	1.0	11	dbSNP_98	168	2582,6014	419.5+/-353.1	365,1852,2081	no	coding-synonymous	ST3GAL4	NM_006278.1		635,2858,3006	TT,TC,CC		30.0372,35.1204,31.7587		137/330	126278075	4128,8870	2201	4298	6499	SO:0001819	synonymous_variant	6484	exon7			CAAGTACGATGTG	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.423C>T	11.37:g.126278075C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	213	100	0.469484	NM_001254757	A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	Silent	SNP	ENST00000526727.1	37	CCDS58193.1																																																																																			C|0.657;T|0.343	0.343	strong		0.582	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278	
ATAD3C	219293	hgsc.bcm.edu	37	1	1403894	1403894	+	Missense_Mutation	SNP	A	A	G	rs145079480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1403894A>G	ENST00000378785.2	+	12	2215	c.1220A>G	c.(1219-1221)gAg>gGg	p.E407G		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	407							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)		CCCGAGGACGAGCAACCCTCA	0.642													N|||	127	0.0253594	0.0923	0.0072	5008	,	,		14787	0.0		0.0	False		,,,				2504	0.0				p.E407G		Atlas-SNP	.											.	ATAD3C	23	.	0			c.A1220G						PASS	.	A	GLY/GLU	425,3979		20,385,1797	22.0	25.0	24.0		1220	-0.4	0.0	1	dbSNP_134	24	0,8590		0,0,4295	no	missense	ATAD3C	NM_001039211.2	98	20,385,6092	GG,GA,AA		0.0,9.6503,3.2707	benign	407/412	1403894	425,12569	2202	4295	6497	SO:0001583	missense	219293	exon12			AGGACGAGCAACC	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.1220A>G	1.37:g.1403894A>G	ENSP00000368062:p.Glu407Gly	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	276	108	0.391304	NM_001039211	Q8N1Z5	Missense_Mutation	SNP	ENST00000378785.2	37	CCDS44039.1	60	0.027472527472527472	56	0.11382113821138211	4	0.011049723756906077	0	0.0	0	0.0	.	5.440	0.266325	0.10294	0.096503	0.0	ENSG00000215915	ENST00000378785	D	0.94184	-3.37	1.1	-0.358	0.12575	.	.	.	.	.	T	0.13329	0.0323	L	0.36672	1.1	0.80722	P	0.0	B	0.22480	0.07	B	0.19148	0.024	T	0.57980	-0.7717	8	0.34782	T	0.22	.	4.8484	0.13524	0.6826:0.3174:0.0:0.0	.	407	Q5T2N8	ATD3C_HUMAN	G	407	ENSP00000368062:E407G	ENSP00000368062:E407G	E	+	2	0	ATAD3C	1393757	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.745000	0.26259	-0.095000	0.12351	0.163000	0.16589	GAG	A|0.972;G|0.028	0.028	strong		0.642	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
ABCB5	340273	hgsc.bcm.edu	37	7	20698270	20698270	+	Missense_Mutation	SNP	A	A	G	rs2301641	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20698270A>G	ENST00000404938.2	+	14	2330	c.1678A>G	c.(1678-1680)Aag>Gag	p.K560E	ABCB5_ENST00000406935.1_Missense_Mutation_p.K115E|ABCB5_ENST00000443026.2_Missense_Mutation_p.K115E|ABCB5_ENST00000258738.6_Missense_Mutation_p.K115E	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	560	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		K -> E (in dbSNP:rs2301641). {ECO:0000269|PubMed:15760339}.		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						TTCAGAAAGCAAGTCAGCTGT	0.433													G|||	1822	0.363818	0.584	0.3127	5008	,	,		19820	0.2024		0.328	False		,,,				2504	0.3057				p.K560E		Atlas-SNP	.											.	ABCB5	357	.	0			c.A1678G						PASS	.	G	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	2460,1946	552.4+/-378.5	699,1062,442	98.0	86.0	90.0		1678,343,343,343	4.7	0.6	7	dbSNP_100	90	2742,5858	680.3+/-403.6	438,1866,1996	yes	missense,missense,missense,missense	ABCB5	NM_001163941.1,NM_001163942.1,NM_001163993.1,NM_178559.5	56,56,56,56	1137,2928,2438	GG,GA,AA		31.8837,44.167,39.9969	benign,benign,benign,benign	560/1258,115/132,115/127,115/813	20698270	5202,7804	2203	4300	6503	SO:0001583	missense	340273	exon14			GAAAGCAAGTCAG	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.1678A>G	7.37:g.20698270A>G	ENSP00000384881:p.Lys560Glu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	57	0.678571	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	739	0.3383699633699634	256	0.5203252032520326	114	0.3149171270718232	117	0.20454545454545456	252	0.3324538258575198	G	1.621	-0.521441	0.04171	0.55833	0.318837	ENSG00000004846	ENST00000404938;ENST00000443026;ENST00000406935;ENST00000258738	T;D;D;T	0.86956	-0.33;-2.19;-2.19;-0.33	5.58	4.69	0.59074	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.64402	N	0.000011	T	0.00012	0.0000	N	0.00028	-2.635	0.43994	P	0.003306999999999949	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	0.42799	-0.9430	9	0.02654	T	1	.	12.5024	0.55962	0.143:0.0:0.857:0.0	rs2301641;rs52809626;rs61332247;rs2301641	115;560;115;115	B5MD19;A7BKA4;Q2M3G0;Q2M3G0-2	.;.;ABCB5_HUMAN;.	E	560;115;115;115	ENSP00000384881:K560E;ENSP00000406730:K115E;ENSP00000383899:K115E;ENSP00000258738:K115E	ENSP00000258738:K115E	K	+	1	0	ABCB5	20664795	1.000000	0.71417	0.610000	0.28997	0.006000	0.05464	6.508000	0.73721	1.511000	0.48818	-0.128000	0.14901	AAG	A|0.625;G|0.375	0.375	strong		0.433	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
ITGB3	3690	hgsc.bcm.edu	37	17	45369777	45369777	+	Silent	SNP	A	A	G	rs4642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45369777A>G	ENST00000559488.1	+	10	1549	c.1533A>G	c.(1531-1533)gaA>gaG	p.E511E	ITGB3_ENST00000435993.2_Silent_p.E464E|ITGB3_ENST00000560629.1_Missense_Mutation_p.M500V	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	511	Cysteine-rich tandem repeats.				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)	AGCAGGACGAATGCAGCCCCC	0.627													G|||	1439	0.28734	0.2564	0.268	5008	,	,		17283	0.3313		0.2903	False		,,,				2504	0.2945				p.E511E		Atlas-SNP	.											ITGB3_ENST00000435993,colon,carcinoma,0,2	ITGB3	157	2	0			c.A1533G						PASS	.	G		1187,3219	710.8+/-407.9	156,875,1172	87.0	77.0	81.0		1533	5.4	1.0	17	dbSNP_52	81	2506,6094	694.2+/-404.7	356,1794,2150	no	coding-synonymous	ITGB3	NM_000212.2		512,2669,3322	GG,GA,AA		29.1395,26.9405,28.3946		511/789	45369777	3693,9313	2203	4300	6503	SO:0001819	synonymous_variant	3690	exon10			GGACGAATGCAGC		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.1533A>G	17.37:g.45369777A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	37	CCDS11511.1																																																																																			A|0.710;G|0.290	0.290	strong		0.627	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1606150	1606150	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1606150G>A	ENST00000382171.2	-	1	363	c.330C>T	c.(328-330)ggC>ggT	p.G110G	KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	110	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCACAAGAGCCACAGCCCC	0.667																																					p.G110G		Atlas-SNP	.											.	KRTAP5-1	74	.	0			c.C330T						PASS	.						28.0	40.0	36.0					11																	1606150		2036	4035	6071	SO:0001819	synonymous_variant	387264	exon1			ACAAGAGCCACAG	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.330C>T	11.37:g.1606150G>A		Somatic	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	102	42	0.411765	NM_001005922		Silent	SNP	ENST00000382171.2	37	CCDS31330.1																																																																																			.	.	none		0.667	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
RGPD8	727851	hgsc.bcm.edu	37	2	113147751	113147751	+	Missense_Mutation	SNP	A	A	C	rs561418400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113147751A>C	ENST00000302558.3	-	20	2962	c.2771T>G	c.(2770-2772)tTt>tGt	p.F924C	RGPD8_ENST00000409750.1_Missense_Mutation_p.F784C	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	924					protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)			endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						CGAAATGCCAAATTTAAATCC	0.398													.|||	287	0.0573083	0.2126	0.0086	5008	,	,		19416	0.0		0.0	False		,,,				2504	0.0				p.F924C		Atlas-SNP	.											.	RGPD8	81	.	0			c.T2771G						PASS	.						6.0	9.0	8.0					2																	113147751		655	1498	2153	SO:0001583	missense	727851	exon20			ATGCCAAATTTAA	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"""Tetratricopeptide (TTC) repeat domain containing"""	9849	protein-coding gene	gene with protein product		602752	"""RAN binding protein 2-like 1"""	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.2771T>G	2.37:g.113147751A>C	ENSP00000306637:p.Phe924Cys	Somatic	627	0	0		WXS	Illumina HiSeq	Phase_I	720	230	0.319444	NM_001164463	Q5CZA8	Missense_Mutation	SNP	ENST00000302558.3	37	CCDS46394.1	.	.	.	.	.	.	.	.	.	.	-	11.55	1.670972	0.29693	.	.	ENSG00000169629	ENST00000302558;ENST00000409750	T;T	0.52983	0.65;0.64	2.33	2.33	0.28932	.	.	.	.	.	T	0.61223	0.2330	M	0.73598	2.24	0.80722	D	1	D	0.76494	0.999	D	0.66979	0.948	T	0.59359	-0.7469	9	0.37606	T	0.19	-28.0606	8.2389	0.31645	1.0:0.0:0.0:0.0	.	924	O14715	RGPD8_HUMAN	C	924;784	ENSP00000306637:F924C;ENSP00000386511:F784C	ENSP00000306637:F924C	F	-	2	0	RGPD8	112864222	1.000000	0.71417	0.998000	0.56505	0.288000	0.27193	8.054000	0.89451	1.076000	0.40961	0.147000	0.16070	TTT	.	.	none		0.398	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279	
LRRN4	164312	hgsc.bcm.edu	37	20	6021703	6021703	+	Missense_Mutation	SNP	C	C	T	rs116777692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:6021703C>T	ENST00000378858.4	-	5	2412	c.2188G>A	c.(2188-2190)Gat>Aat	p.D730N		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	730					long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	27						GGGTAATCATCAAAGGCCGGG	0.612													C|||	25	0.00499201	0.0189	0.0	5008	,	,		17219	0.0		0.0	False		,,,				2504	0.0				p.D730N		Atlas-SNP	.											.	LRRN4	54	.	0			c.G2188A						PASS	.	C	ASN/ASP	144,4262	91.6+/-130.3	3,138,2062	37.0	36.0	36.0		2188	2.0	0.0	20	dbSNP_132	36	1,8599		0,1,4299	yes	missense	LRRN4	NM_152611.3	23	3,139,6361	TT,TC,CC		0.0116,3.2683,1.1149	benign	730/741	6021703	145,12861	2203	4300	6503	SO:0001583	missense	164312	exon5			AATCATCAAAGGC	AL118505	CCDS13097.1	20p12.3	2013-02-11	2008-05-20	2008-05-20	ENSG00000125872	ENSG00000125872		"""Fibronectin type III domain containing"""	16208	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 75"""	C20orf75		15870286	Standard	NM_152611		Approved	dJ1056H1.1, NLRR4	uc002wmo.3	Q8WUT4	OTTHUMG00000031825	ENST00000378858.4:c.2188G>A	20.37:g.6021703C>T	ENSP00000368135:p.Asp730Asn	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	198	78	0.393939	NM_152611	A8K258|Q5JWV6|Q9H419	Missense_Mutation	SNP	ENST00000378858.4	37	CCDS13097.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	13.49	2.252207	0.39797	0.032683	1.16E-4	ENSG00000125872	ENST00000378858	T	0.61392	0.11	3.97	2.01	0.26516	.	0.648332	0.14770	N	0.299431	T	0.16514	0.0397	N	0.19112	0.55	0.09310	N	1	P	0.44877	0.845	B	0.43478	0.421	T	0.07366	-1.0776	10	0.09590	T	0.72	.	8.1533	0.31154	0.0:0.7545:0.1586:0.0869	.	730	Q8WUT4	LRRN4_HUMAN	N	730	ENSP00000368135:D730N	ENSP00000368135:D730N	D	-	1	0	LRRN4	5969703	0.075000	0.21258	0.001000	0.08648	0.305000	0.27757	1.403000	0.34612	0.618000	0.30179	0.655000	0.94253	GAT	C|0.990;T|0.010	0.010	strong		0.612	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611	
MYO19	80179	hgsc.bcm.edu	37	17	34859831	34859831	+	Silent	SNP	G	G	A	rs73276768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34859831G>A	ENST00000431794.3	-	20	2457	c.1935C>T	c.(1933-1935)ctC>ctT	p.L645L	MYO19_ENST00000268852.9_Silent_p.L445L	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	645	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TGGTCTCCACGAGGCCACAGG	0.632													G|||	22	0.00439297	0.0166	0.0	5008	,	,		18572	0.0		0.0	False		,,,				2504	0.0				p.L645L		Atlas-SNP	.											.	MYO19	130	.	0			c.C1935T						PASS	.	G	,	68,4038		3,62,1988	17.0	21.0	19.0		1935,1335	-11.3	0.9	17	dbSNP_130	19	1,8385		0,1,4192	no	coding-synonymous,coding-synonymous	MYO19	NM_001163735.1,NM_025109.5	,	3,63,6180	AA,AG,GG		0.0119,1.6561,0.5524	,	645/971,445/771	34859831	69,12423	2053	4193	6246	SO:0001819	synonymous_variant	80179	exon21			CTCCACGAGGCCA	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.1935C>T	17.37:g.34859831G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_001163735	Q59GS4|Q9H5X2	Silent	SNP	ENST00000431794.3	37	CCDS54112.1																																																																																			G|0.996;A|0.004	0.004	strong		0.632	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
TMEM140	55281	hgsc.bcm.edu	37	7	134849690	134849690	+	Missense_Mutation	SNP	T	T	C	rs76023601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:134849690T>C	ENST00000275767.3	+	2	720	c.497T>C	c.(496-498)aTa>aCa	p.I166T	C7orf49_ENST00000459937.1_Intron	NM_018295.3	NP_060765.4	Q9NV12	TM140_HUMAN	transmembrane protein 140	166						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)	5						CTCTTGCTTATAGCCATGGCT	0.567													T|||	9	0.00179712	0.0061	0.0	5008	,	,		20525	0.001		0.0	False		,,,				2504	0.0				p.I166T		Atlas-SNP	.											.	TMEM140	18	.	0			c.T497C						PASS	.	T	THR/ILE	27,4379	30.8+/-60.4	0,27,2176	48.0	48.0	48.0		497	0.2	0.0	7	dbSNP_131	48	0,8600		0,0,4300	yes	missense	TMEM140	NM_018295.3	89	0,27,6476	CC,CT,TT		0.0,0.6128,0.2076	benign	166/186	134849690	27,12979	2203	4300	6503	SO:0001583	missense	55281	exon2			TGCTTATAGCCAT	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.497T>C	7.37:g.134849690T>C	ENSP00000275767:p.Ile166Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	214	98	0.457944	NM_018295	A4D1P9|Q8WUC3	Missense_Mutation	SNP	ENST00000275767.3	37	CCDS5837.1	4	0.0018315018315018315	3	0.006097560975609756	0	0.0	1	0.0017482517482517483	0	0.0	T	11.24	1.579014	0.28180	0.006128	0.0	ENSG00000146859	ENST00000275767;ENST00000456488	T	0.20069	2.1	5.28	0.166	0.14999	.	1.753430	0.02512	N	0.091627	T	0.08358	0.0208	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.28618	-1.0038	10	0.62326	D	0.03	-1.1492	5.0072	0.14293	0.0:0.1578:0.2972:0.545	.	166	Q9NV12	TM140_HUMAN	T	166;129	ENSP00000275767:I166T	ENSP00000275767:I166T	I	+	2	0	TMEM140	134500230	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.605000	0.24179	-0.098000	0.12285	-0.258000	0.10820	ATA	T|0.998;C|0.002	0.002	strong		0.567	TMEM140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340017.2	NM_018295	
FAM196A	642938	hgsc.bcm.edu	37	10	128974220	128974220	+	Missense_Mutation	SNP	G	G	A	rs11594560	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:128974220G>A	ENST00000522781.1	-	4	995	c.440C>T	c.(439-441)gCg>gTg	p.A147V	DOCK1_ENST00000280333.6_Intron|FAM196A_ENST00000424811.2_Missense_Mutation_p.A147V	NM_001039762.2	NP_001034851.1	Q6ZSG2	F196A_HUMAN	family with sequence similarity 196, member A	147			A -> V (in dbSNP:rs11594560).							breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CTTCTCTTTCGCATCTGTTAG	0.547													G|||	830	0.165735	0.0446	0.2133	5008	,	,		17929	0.0347		0.2793	False		,,,				2504	0.3139				p.A147V		Atlas-SNP	.											.	FAM196A	55	.	0			c.C440T						PASS	.	G	VAL/ALA,	341,4065	178.0+/-206.8	14,313,1876	90.0	85.0	87.0		440,	2.6	0.0	10	dbSNP_120	87	2355,6245	393.7+/-344.5	324,1707,2269	yes	missense,intron	DOCK1,FAM196A	NM_001039762.2,NM_001380.3	64,	338,2020,4145	AA,AG,GG		27.3837,7.7394,20.7289	benign,	147/480,	128974220	2696,10310	2203	4300	6503	SO:0001583	missense	642938	exon4			TCTTTCGCATCTG		CCDS31312.1	10q26.2	2009-09-11	2009-09-11	2009-09-11		ENSG00000188916			33859	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 141"""	C10orf141			Standard	NM_001039762		Approved	FLJ45557	uc001ljv.1	Q6ZSG2		ENST00000522781.1:c.440C>T	10.37:g.128974220G>A	ENSP00000429763:p.Ala147Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	158	83	0.525316	NM_001039762	B2RNT4|B7ZME7	Missense_Mutation	SNP	ENST00000522781.1	37	CCDS31312.1	346	0.15842490842490842	27	0.054878048780487805	92	0.2541436464088398	12	0.02097902097902098	215	0.2836411609498681	G	0.008	-1.931052	0.00488	0.077394	0.273837	ENSG00000188916	ENST00000522781;ENST00000424811	T;T	0.42513	0.97;0.97	4.46	2.58	0.30949	.	1.061370	0.07259	N	0.867102	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B	0.13145	0.007;0.003	B;B	0.09377	0.001;0.004	T	0.35375	-0.9791	9	0.02654	T	1	.	6.43	0.21790	0.3258:0.0:0.6742:0.0	rs11594560;rs56480626;rs60757760;rs11594560	147;147	B7ZME7;Q6ZSG2	.;F196A_HUMAN	V	147	ENSP00000429763:A147V;ENSP00000428730:A147V	ENSP00000428730:A147V	A	-	2	0	FAM196A	128864210	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	0.577000	0.23758	1.180000	0.42898	0.563000	0.77884	GCG	G|0.829;A|0.171	0.171	strong		0.547	FAM196A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050978.2	NM_001039762	
OVCH2	341277	hgsc.bcm.edu	37	11	7727886	7727886	+	lincRNA	SNP	C	C	T	rs7927138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7727886C>T	ENST00000527565.1	-	0	542				OVCH2_ENST00000534193.2_RNA|RP11-35J10.4_ENST00000527443.1_RNA|OVCH2_ENST00000454689.1_RNA																							AGATTTACCTCGTTCAAAAAA	0.378													C|||	2019	0.403155	0.205	0.5144	5008	,	,		19440	0.4157		0.3728	False		,,,				2504	0.6104				p.R19Q		Atlas-SNP	.											OVCH2,NS,carcinoma,0,2	OVCH2	47	2	0			c.G56A						PASS	.	C	GLN/ARG	892,2764		108,676,1044	96.0	90.0	92.0		56	0.0	0.2	11	dbSNP_116	92	2993,5169		562,1869,1650	yes	missense	OVCH2	NM_198185.2	43	670,2545,2694	TT,TC,CC		36.6699,24.3982,32.8736	benign	19/565	7727886	3885,7933	1828	4081	5909			341277	exon1			TTACCTCGTTCAA																													11.37:g.7727886C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	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		
YTHDC2	64848	hgsc.bcm.edu	37	5	112899702	112899702	+	Silent	SNP	A	A	G	rs6886628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	241	0	0		WXS	Illumina HiSeq	Phase_I	255	132	0.517647	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	
FAT3	120114	hgsc.bcm.edu	37	11	92623877	92623877	+	Silent	SNP	G	G	A	rs12277422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	100	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	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	
C16orf71	146562	hgsc.bcm.edu	37	16	4790304	4790304	+	Missense_Mutation	SNP	C	C	T	rs527269249|rs17137230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4790304C>T	ENST00000299320.5	+	4	905	c.427C>T	c.(427-429)Ccc>Tcc	p.P143S	RP11-127I20.7_ENST00000588099.1_RNA|C16orf71_ENST00000590191.1_Missense_Mutation_p.P157S	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	143			P -> S (in dbSNP:rs17137230).							breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						GGCCGAGGAGCCCCCCAGGTG	0.597													A|||	66	0.0131789	0.0469	0.0058	5008	,	,		15525	0.0		0.0	False		,,,				2504	0.0				p.P143S		Atlas-SNP	.											.	C16orf71	46	.	0			c.C427T						PASS	.	A	SER/PRO	250,4144		11,228,1958	67.0	74.0	72.0		427	3.0	0.2	16	dbSNP_123	72	3,8597		0,3,4297	yes	missense	C16orf71	NM_139170.2	74	11,231,6255	TT,TC,CC		0.0349,5.6896,1.9471	benign	143/521	4790304	253,12741	2197	4300	6497	SO:0001583	missense	146562	exon4			GAGGAGCCCCCCA	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.427C>T	16.37:g.4790304C>T	ENSP00000299320:p.Pro143Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	192	103	0.536458	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	14.78	2.636363	0.47049	0.056896	3.49E-4	ENSG00000166246	ENST00000299320	T	0.08807	3.05	4.05	2.95	0.34219	.	0.488693	0.16973	N	0.192010	T	0.00412	0.0013	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46470	-0.9189	10	0.23891	T	0.37	-3.9933	3.8797	0.09072	0.6631:0.2192:0.1178:0.0	rs17137230;rs52805275;rs17137230	143	Q8IYS4	CP071_HUMAN	S	143	ENSP00000299320:P143S	ENSP00000299320:P143S	P	+	1	0	C16orf71	4730305	0.001000	0.12720	0.189000	0.23252	0.035000	0.12851	0.195000	0.17155	0.253000	0.21552	-0.559000	0.04183	CCC	C|0.980;T|0.020	0.020	strong		0.597	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
PELP1	27043	hgsc.bcm.edu	37	17	4576623	4576623	+	Silent	SNP	G	G	A	rs191748391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4576623G>A	ENST00000574876.1	-	15	1784	c.1767C>T	c.(1765-1767)gcC>gcT	p.A589A	AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000301396.4_Silent_p.A733A|PELP1_ENST00000269230.7_Intron|PELP1_ENST00000572293.1_Silent_p.A639A|PELP1_ENST00000436683.2_Silent_p.A442A			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	589					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						GAGGAGACGGGGCCAGCAGCA	0.647													G|||	4	0.000798722	0.003	0.0	5008	,	,		16322	0.0		0.0	False		,,,				2504	0.0				p.A589A		Atlas-SNP	.											.	PELP1	102	.	0			c.C1767T						PASS	.	G		8,4302		0,8,2147	18.0	30.0	26.0		1767	-11.1	0.0	17		26	0,8548		0,0,4274	no	coding-synonymous	PELP1	NM_014389.2		0,8,6421	AA,AG,GG		0.0,0.1856,0.0622		589/1131	4576623	8,12850	2155	4274	6429	SO:0001819	synonymous_variant	27043	exon15			AGACGGGGCCAGC		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.1767C>T	17.37:g.4576623G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	194	97	0.5	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			G|0.999;A|0.001	0.001	strong		0.647	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
PAQR8	85315	hgsc.bcm.edu	37	6	52269046	52269046	+	Silent	SNP	C	C	G	rs3799274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:52269046C>G	ENST00000442253.2	+	2	1209	c.1035C>G	c.(1033-1035)gtC>gtG	p.V345V	PAQR8_ENST00000360726.3_Silent_p.V345V	NM_133367.4	NP_588608.1	Q8TEZ7	MPRB_HUMAN	progestin and adipoQ receptor family member VIII	345					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)			endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(2)	17	Lung NSC(77;0.0875)					GGCACAAAGTCAAGGCCAGAC	0.547													C|||	592	0.118211	0.2133	0.1009	5008	,	,		19598	0.0327		0.1402	False		,,,				2504	0.0675				p.V345V		Atlas-SNP	.											PAQR8,NS,carcinoma,0,1	PAQR8	31	1	0			c.C1035G						PASS	.	C		819,3587		78,663,1462	20.0	19.0	19.0		1035	4.6	1.0	6	dbSNP_107	19	1123,7477		81,961,3258	no	coding-synonymous	PAQR8	NM_133367.4		159,1624,4720	GG,GC,CC		13.0581,18.5883,14.9316		345/355	52269046	1942,11064	2203	4300	6503	SO:0001819	synonymous_variant	85315	exon2			CAAAGTCAAGGCC	AF347029	CCDS4941.1	6p12	2012-08-10	2005-05-20	2005-05-20	ENSG00000170915	ENSG00000170915			15708	protein-coding gene	gene with protein product		607780	"""chromosome 6 open reading frame 33"""	C6orf33		11676489, 12574519	Standard	NM_133367		Approved	LMPB1, MPRB	uc003pao.4	Q8TEZ7	OTTHUMG00000014846	ENST00000442253.2:c.1035C>G	6.37:g.52269046C>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_133367	B2RCF6|Q86WL0|Q8N6D3|Q9HD02	Silent	SNP	ENST00000442253.2	37	CCDS4941.1																																																																																			T|0.000;G|0.131;C|0.869	0.131	strong		0.547	PAQR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040903.2	NM_133367	
TRIM56	81844	hgsc.bcm.edu	37	7	100731748	100731748	+	Silent	SNP	T	T	G	rs61730718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100731748T>G	ENST00000306085.6	+	3	1452	c.1155T>G	c.(1153-1155)ggT>ggG	p.G385G		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	385					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)					ACGGAGCTGGTACCCAGGGAG	0.627													T|||	347	0.0692891	0.177	0.0605	5008	,	,		15776	0.001		0.0567	False		,,,				2504	0.0133				p.G385G	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.T1155G						PASS	.	T		578,3604		36,506,1549	41.0	54.0	49.0		1155	-4.7	0.0	7	dbSNP_129	49	637,7817		29,579,3619	no	coding-synonymous	TRIM56	NM_030961.1		65,1085,5168	GG,GT,TT		7.5349,13.8211,9.6154		385/756	100731748	1215,11421	2091	4227	6318	SO:0001819	synonymous_variant	81844	exon3			AGCTGGTACCCAG	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.1155T>G	7.37:g.100731748T>G		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																			T|0.931;G|0.069	0.069	strong		0.627	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961	
MET	4233	hgsc.bcm.edu	37	7	116340269	116340269	+	Silent	SNP	C	C	T	rs28444388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:116340269C>T	ENST00000318493.6	+	2	1318	c.1131C>T	c.(1129-1131)atC>atT	p.I377I	MET_ENST00000397752.3_Silent_p.I377I|MET_ENST00000436117.2_Silent_p.I377I			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)			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)			TCAACAAGATCGTCAACAAAA	0.433			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				C|||	311	0.0621006	0.2262	0.013	5008	,	,		19263	0.0		0.002	False		,,,				2504	0.001				p.I377I		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.C1131T						PASS	.	C	,	744,3114		78,588,1263	105.0	97.0	100.0		1131,1131	-7.2	0.7	7	dbSNP_125	100	9,8271		0,9,4131	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	78,597,5394	TT,TC,CC		0.1087,19.2846,6.2037	,	377/1391,377/1409	116340269	753,11385	1929	4140	6069	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CAAGATCGTCAAC	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.1131C>T	7.37:g.116340269C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.967;T|0.033	0.033	strong		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
OR5L2	26338	hgsc.bcm.edu	37	11	55595017	55595017	+	Missense_Mutation	SNP	G	G	T	rs117277709|rs34954823|rs386753700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55595017G>T	ENST00000378397.1	+	1	323	c.323G>T	c.(322-324)gGa>gTa	p.G108V		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	108						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G108V(1)		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)				TGCACATGTGGAGTCACTGAG	0.483										HNSCC(27;0.073)			N|||	342	0.0682907	0.0938	0.036	5008	,	,		22494	0.0704		0.0736	False		,,,				2504	0.0491				p.G108V		Atlas-SNP	.											OR5L2,NS,carcinoma,-1,2	OR5L2	135	2	1	Substitution - Missense(1)	stomach(1)	c.G323T						PASS	.						184.0	173.0	177.0					11																	55595017		2190	4290	6480	SO:0001583	missense	26338	exon1			CATGTGGAGTCAC	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.323G>T	11.37:g.55595017G>T	ENSP00000367650:p.Gly108Val	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	134	49	0.365672	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.868356	0.00063	.	.	ENSG00000205030	ENST00000378397	T	0.01359	4.98	5.18	-5.23	0.02798	GPCR, rhodopsin-like superfamily (1);	0.868328	0.09720	N	0.764589	T	0.00815	0.0027	N	0.13272	0.32	0.09310	N	0.999996	B	0.02656	0.0	B	0.04013	0.001	T	0.48019	-0.9071	10	0.02654	T	1	3.6392	9.8956	0.41316	0.0:0.2622:0.5569:0.1809	.	108	Q8NGL0	OR5L2_HUMAN	V	108	ENSP00000367650:G108V	ENSP00000367650:G108V	G	+	2	0	OR5L2	55351593	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-6.226000	0.00075	-0.884000	0.03976	-1.313000	0.01306	GGA	.	.	weak		0.483	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
UBR4	23352	hgsc.bcm.edu	37	1	19467322	19467322	+	Silent	SNP	G	G	A	rs139618268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19467322G>A	ENST00000375254.3	-	58	8580	c.8553C>T	c.(8551-8553)tcC>tcT	p.S2851S	UBR4_ENST00000375226.2_Intron|UBR4_ENST00000375267.2_Silent_p.S2851S|UBR4_ENST00000375217.2_Intron	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2851					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)			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)		CGTCCAGAGAGGAAGAGCTGG	0.622													G|||	3	0.000599042	0.0023	0.0	5008	,	,		19916	0.0		0.0	False		,,,				2504	0.0				p.S2851S		Atlas-SNP	.											.	UBR4	415	.	0			c.C8553T						PASS	.	G		17,4389	22.3+/-47.3	0,17,2186	66.0	60.0	62.0		8553	4.8	1.0	1	dbSNP_134	62	0,8600		0,0,4300	no	coding-synonymous	UBR4	NM_020765.2		0,17,6486	AA,AG,GG		0.0,0.3858,0.1307		2851/5184	19467322	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon58			CAGAGAGGAAGAG	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.8553C>T	1.37:g.19467322G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			G|0.999;A|0.001	0.001	strong		0.622	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
MTERF4	130916	hgsc.bcm.edu	37	2	242039198	242039198	+	Missense_Mutation	SNP	T	T	C	rs3796093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242039198T>C	ENST00000391980.2	-	2	191	c.133A>G	c.(133-135)Aca>Gca	p.T45A	MTERFD2_ENST00000406593.1_Intron|MTERFD2_ENST00000407095.3_Missense_Mutation_p.T45A|MTERFD2_ENST00000464344.2_Intron|MTERFD2_ENST00000495694.1_Missense_Mutation_p.T45A	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		45			T -> A (in dbSNP:rs3796093).		rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		TTGGAGGCTGTAGTCAGTTTG	0.517													T|||	471	0.0940495	0.1369	0.0951	5008	,	,		20220	0.124		0.0626	False		,,,				2504	0.0368				p.T45A		Atlas-SNP	.											.	MTERFD2	33	.	0			c.A133G						PASS	.	T	ALA/THR	625,3781	271.6+/-270.3	51,523,1629	69.0	69.0	69.0		133	0.6	0.0	2	dbSNP_107	69	585,8015	156.4+/-210.3	21,543,3736	yes	missense	MTERFD2	NM_182501.3	58	72,1066,5365	CC,CT,TT		6.8023,14.1852,9.3034	benign	45/382	242039198	1210,11796	2203	4300	6503	SO:0001583	missense	130916	exon2			AGGCTGTAGTCAG																												ENST00000391980.2:c.133A>G	2.37:g.242039198T>C	ENSP00000375840:p.Thr45Ala	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	130	51	0.392308	NM_182501	A8K6K0|Q9P0E0	Missense_Mutation	SNP	ENST00000391980.2	37	CCDS2544.1	227	0.10393772893772894	75	0.1524390243902439	35	0.09668508287292818	70	0.12237762237762238	47	0.06200527704485488	T	20.3	3.965965	0.74131	0.141852	0.068023	ENSG00000122085	ENST00000495694;ENST00000401626;ENST00000391980;ENST00000424798;ENST00000407095;ENST00000434791	T;T;T;T;T;T	0.60797	0.16;0.21;1.94;0.91;0.93;0.32	4.57	0.636	0.17729	.	0.480627	0.17001	N	0.190890	T	0.00241	0.0007	L	0.36672	1.1	0.80722	P	0.0	B;B	0.21452	0.036;0.056	B;B	0.15870	0.012;0.014	T	0.03483	-1.1032	9	0.46703	T	0.11	-22.0028	4.1038	0.10026	0.0:0.2002:0.1768:0.623	rs3796093;rs52805218;rs60253284;rs3796093	45;45	B4DKD5;Q7Z6M4	.;MTER2_HUMAN	A	45;45;45;38;45;24	ENSP00000419315:T45A;ENSP00000385183:T45A;ENSP00000375840:T45A;ENSP00000409023:T38A;ENSP00000385630:T45A;ENSP00000393063:T24A	ENSP00000241527:T45A	T	-	1	0	MTERFD2	241687871	0.001000	0.12720	0.002000	0.10522	0.721000	0.41392	0.055000	0.14229	0.142000	0.18901	0.482000	0.46254	ACA	T|0.899;C|0.101	0.101	strong		0.517	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4		
IRAK1	3654	hgsc.bcm.edu	37	X	153284746	153284746	+	Missense_Mutation	SNP	G	G	A	rs11465829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153284746G>A	ENST00000369980.3	-	3	505	c.338C>T	c.(337-339)aCc>aTc	p.T113I	MIR718_ENST00000390190.2_RNA|IRAK1_ENST00000477274.1_5'Flank|IRAK1_ENST00000369974.2_Missense_Mutation_p.T113I|IRAK1_ENST00000393682.1_Missense_Mutation_p.T139I|IRAK1_ENST00000429936.2_Missense_Mutation_p.T139I|IRAK1_ENST00000393687.2_Missense_Mutation_p.T113I	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	113	ProST region.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CGGGGCAGTGGTGCCTGGGGA	0.736													G|||	9	0.00238411	0.0053	0.0029	3775	,	,		7576	0.0		0.0	False		,,,				2504	0.0				p.T113I		Atlas-SNP	.											.	IRAK1	107	.	0			c.C338T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR	31,3695		0,23,8,1557,558	13.0	17.0	16.0		338,338,338	3.9	0.0	X	dbSNP_120	16	3,6649		0,0,3,2406,1837	no	missense,missense,missense	IRAK1	NM_001025242.1,NM_001025243.1,NM_001569.3	89,89,89	0,23,11,3963,2395	AA,AG,A,GG,G		0.0451,0.832,0.3276	possibly-damaging,possibly-damaging,possibly-damaging	113/683,113/634,113/713	153284746	34,10344	2146	4246	6392	SO:0001583	missense	3654	exon3			GCAGTGGTGCCTG	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.338C>T	X.37:g.153284746G>A	ENSP00000358997:p.Thr113Ile	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	113	47	0.415929	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Missense_Mutation	SNP	ENST00000369980.3	37	CCDS14740.1	2	0.0012055455093429777	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	.	24.3	4.518780	0.85495	0.00832	4.51E-4	ENSG00000184216	ENST00000369980;ENST00000369974;ENST00000393682;ENST00000444230;ENST00000393687;ENST00000429936	T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24	4.82	3.92	0.45320	DEATH-like (1);	0.135643	0.33401	N	0.004960	T	0.45478	0.1344	M	0.63428	1.95	0.09310	N	0.999997	P;P;P;P	0.45827	0.651;0.867;0.501;0.634	B;B;B;B	0.41619	0.153;0.361;0.109;0.219	T	0.46610	-0.9179	10	0.52906	T	0.07	-5.7048	9.8845	0.41253	0.0:0.2038:0.7962:0.0	rs11465829	139;113;113;113	D3YTB5;P51617-4;P51617;P51617-2	.;.;IRAK1_HUMAN;.	I	113;113;139;109;113;139	ENSP00000358997:T113I;ENSP00000358991:T113I;ENSP00000377287:T139I;ENSP00000399974:T109I;ENSP00000377291:T113I;ENSP00000392662:T139I	ENSP00000358990:T139I	T	-	2	0	IRAK1	152937940	0.019000	0.18553	0.046000	0.18839	0.721000	0.41392	1.183000	0.32041	0.767000	0.33267	0.436000	0.28706	ACC	G|0.984;0|0.014	.	strong		0.736	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3		
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037579	33037579	+	Missense_Mutation	SNP	A	A	T	rs2308912|rs36013091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33037579A>T	ENST00000419277.1	-	3	314	c.185T>A	c.(184-186)aTg>aAg	p.M62K	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.M62K|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	62	Alpha-1.		M -> K (in dbSNP:rs2308912).|M -> L (in dbSNP:rs2308911).|M -> Q (in allele DPA1*01:06, allele DPA1*02:01, allele DPA1*02:02 and allele DPA1*02:04; requires 2 nucleotide substitutions; dbSNP:rs36013091).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CACATAGAACATCTCATCTTC	0.483													.|||	2159	0.43111	0.5794	0.2795	5008	,	,		19351	0.6508		0.1869	False		,,,				2504	0.363				p.M62K		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.T185A						PASS	.	A	LYS/MET,LYS/MET,LYS/MET	53,2967		2,49,1459	62.0	87.0	78.0		185,185,185	-6.0	0.0	6	dbSNP_126	78	9,5409		0,9,2700	yes	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	95,95,95	2,58,4159	TT,TA,AA		0.1661,1.755,0.7348	possibly-damaging,possibly-damaging,possibly-damaging	62/261,62/261,62/261	33037579	62,8376	1510	2709	4219	SO:0001583	missense	3113	exon2			TAGAACATCTCAT	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.185T>A	6.37:g.33037579A>T	ENSP00000393566:p.Met62Lys	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	762	0.3489010989010989	239	0.48577235772357724	78	0.2154696132596685	331	0.5786713286713286	114	0.1503957783641161	A	0.028	-1.354560	0.01256	0.01755	0.001661	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.00737	5.76;5.76;5.76	3.0	-5.99	0.02213	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	2.490280	0.02659	U	0.107291	T	0.00440	0.0014	L	0.41415	1.275	0.80722	P	0.0	B	0.26602	0.154	B	0.42995	0.404	T	0.32719	-0.9896	9	0.30854	T	0.27	.	10.1803	0.42963	0.4129:0.0:0.0:0.5871	rs2308912;rs12722002	62	P20036	DPA1_HUMAN	K	62	ENSP00000393566:M62K;ENSP00000402872:M62K;ENSP00000390929:M62K	ENSP00000393566:M62K	M	-	2	0	HLA-DPA1	33145557	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.558000	0.05978	-3.072000	0.00253	-1.638000	0.00776	ATG	.	.	alt		0.483	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
FLG	2312	hgsc.bcm.edu	37	1	152280691	152280691	+	Missense_Mutation	SNP	A	A	T	rs117945779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152280691A>T	ENST00000368799.1	-	3	6706	c.6671T>A	c.(6670-6672)cTg>cAg	p.L2224Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	479	0	0		WXS	Illumina HiSeq	Phase_I	568	91	0.160211	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	
SLC4A7	9497	hgsc.bcm.edu	37	3	27436247	27436247	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:27436247T>C	ENST00000295736.5	-	20	2922	c.2852A>G	c.(2851-2853)tAt>tGt	p.Y951C	SLC4A7_ENST00000455077.1_Missense_Mutation_p.Y832C|SLC4A7_ENST00000388777.4_Missense_Mutation_p.Y501C|SLC4A7_ENST00000437179.1_Missense_Mutation_p.Y832C|SLC4A7_ENST00000440156.1_Missense_Mutation_p.Y947C|SLC4A7_ENST00000446700.1_Missense_Mutation_p.Y943C|SLC4A7_ENST00000428386.1_Missense_Mutation_p.Y827C|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000435667.2_Missense_Mutation_p.Y836C|SLC4A7_ENST00000445684.1_Missense_Mutation_p.Y947C|SLC4A7_ENST00000454389.1_Missense_Mutation_p.Y960C	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	951					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)	ATCAAGGTGATAGCCAGCTCC	0.393																																					p.Y951C		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A2852G						PASS	.						101.0	93.0	96.0					3																	27436247		2203	4300	6503	SO:0001583	missense	9497	exon20			AGGTGATAGCCAG	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.2852A>G	3.37:g.27436247T>C	ENSP00000295736:p.Tyr951Cys	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.526853	0.85706	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000428179	D;D;D;D;D;D;D;D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58	5.84	5.84	0.93424	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94095	0.8107	H	0.96365	3.81	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.95792	0.8825	10	0.87932	D	0	.	16.2194	0.82247	0.0:0.0:0.0:1.0	.	947;832;943;947;960;501;827;951;832	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	C	502;951;827;960;947;832;943;832;947;836;501;847	ENSP00000411031:Y502C;ENSP00000295736:Y951C;ENSP00000416368:Y827C;ENSP00000390394:Y960C;ENSP00000414797:Y947C;ENSP00000394252:Y832C;ENSP00000406605:Y943C;ENSP00000407382:Y832C;ENSP00000406804:Y947C;ENSP00000395336:Y836C;ENSP00000373429:Y501C;ENSP00000388703:Y847C	ENSP00000295736:Y951C	Y	-	2	0	SLC4A7	27411251	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.234000	0.73211	0.528000	0.53228	TAT	.	.	none		0.393	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
KIF26A	26153	hgsc.bcm.edu	37	14	104638926	104638926	+	Silent	SNP	G	G	A	rs2275595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:104638926G>A	ENST00000423312.2	+	7	1341	c.1341G>A	c.(1339-1341)tcG>tcA	p.S447S	KIF26A_ENST00000315264.7_Silent_p.S308S	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	447	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)		AAGTCTGCTCGGGGACCGTGG	0.642													G|||	354	0.0706869	0.2163	0.0231	5008	,	,		17254	0.0228		0.004	False		,,,				2504	0.0256				p.S447S		Atlas-SNP	.											.	KIF26A	84	.	0			c.G1341A						PASS	.	G		715,3455		52,611,1422	63.0	67.0	66.0		1341	-3.5	1.0	14	dbSNP_100	66	14,8402		0,14,4194	no	coding-synonymous	KIF26A	NM_015656.1		52,625,5616	AA,AG,GG		0.1663,17.1463,5.7922		447/1883	104638926	729,11857	2085	4208	6293	SO:0001819	synonymous_variant	26153	exon7			CTGCTCGGGGACC	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.1341G>A	14.37:g.104638926G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			G|0.932;A|0.068	0.068	strong		0.642	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
CELSR1	9620	hgsc.bcm.edu	37	22	46760102	46760102	+	Silent	SNP	C	C	T	rs6008778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46760102C>T	ENST00000262738.3	-	34	8825	c.8826G>A	c.(8824-8826)acG>acA	p.T2942T		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2942					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)		GCGTCTGCTCCGTCAGCGTCA	0.662													C|||	272	0.0543131	0.1974	0.013	5008	,	,		15944	0.0		0.001	False		,,,				2504	0.001				p.T2942T		Atlas-SNP	.											.	CELSR1	242	.	0			c.G8826A						PASS	.	C		761,3639		66,629,1505	38.0	47.0	44.0		8826	-1.3	0.3	22	dbSNP_114	44	18,8570		0,18,4276	no	coding-synonymous	CELSR1	NM_014246.1		66,647,5781	TT,TC,CC		0.2096,17.2955,5.9978		2942/3015	46760102	779,12209	2200	4294	6494	SO:0001819	synonymous_variant	9620	exon34			CTGCTCCGTCAGC	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.8826G>A	22.37:g.46760102C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			C|0.948;T|0.052	0.052	strong		0.662	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
CARKD	55739	hgsc.bcm.edu	37	13	111279817	111279817	+	Missense_Mutation	SNP	A	A	G	rs3742191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:111279817A>G	ENST00000309957.2	+	5	432	c.418A>G	c.(418-420)Aag>Gag	p.K140E	CARKD_ENST00000397191.4_Missense_Mutation_p.K77E|CARKD_ENST00000470164.2_3'UTR|CARKD_ENST00000424185.2_Missense_Mutation_p.K30E|CARKD_ENST00000458711.2_Intron	NM_001242881.1|NM_018210.3	NP_001229810.1|NP_060680.2			carbohydrate kinase domain containing											NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	15						TGAGGTGGAGAAGTGGCTGCC	0.478													A|||	311	0.0621006	0.0204	0.0922	5008	,	,		16742	0.1091		0.0358	False		,,,				2504	0.0757				p.K140E		Atlas-SNP	.											.	CARKD	36	.	0			c.A418G						PASS	.	A	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	121,4285	91.1+/-129.8	2,117,2084	117.0	98.0	104.0		418,364,88,418	-0.2	0.0	13	dbSNP_107	104	315,8285	112.0+/-172.2	5,305,3990	no	missense,missense,missense,missense	CARKD	NM_001242881.1,NM_001242882.1,NM_001242883.1,NM_018210.3	56,56,56,56	7,422,6074	GG,GA,AA		3.6628,2.7463,3.3523	benign,benign,benign,benign	140/348,122/330,30/238,140/391	111279817	436,12570	2203	4300	6503	SO:0001583	missense	55739	exon5			GTGGAGAAGTGGC	AF151071	CCDS9513.1, CCDS55903.1	13q34	2008-12-19			ENSG00000213995	ENSG00000213995			25576	protein-coding gene	gene with protein product		615910					Standard	NM_018210		Approved	LP3298, FLJ10769	uc001vrc.3	Q8IW45	OTTHUMG00000017345	ENST00000309957.2:c.418A>G	13.37:g.111279817A>G	ENSP00000311984:p.Lys140Glu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	160	82	0.5125	NM_018210		Missense_Mutation	SNP	ENST00000309957.2	37	CCDS9513.1	115	0.052655677655677656	11	0.022357723577235773	28	0.07734806629834254	45	0.07867132867132867	31	0.040897097625329816	A	4.322	0.059086	0.08339	0.027463	0.036628	ENSG00000213995	ENST00000424185;ENST00000439607;ENST00000397191;ENST00000309957	T;T;T	0.20200	2.15;2.09;2.15	5.13	-0.227	0.13102	Uncharacterised domain, carbohydrate kinase-related (3);	0.276420	0.39274	N	0.001406	T	0.00356	0.0011	N	0.05259	-0.085	0.09310	N	0.999997	B;B;B;B;B	0.19445	0.002;0.001;0.034;0.036;0.001	B;B;B;B;B	0.21360	0.011;0.006;0.034;0.021;0.006	T	0.32851	-0.9891	10	0.06494	T	0.89	-0.249	5.5108	0.16880	0.6381:0.1353:0.2266:0.0	rs3742191;rs3742191	30;122;77;140;140	Q8IW45-4;B4DKX7;B7Z3Q0;Q8IW45-2;Q8IW45	.;.;.;.;CARKD_HUMAN	E	30;122;77;140	ENSP00000413191:K30E;ENSP00000380375:K77E;ENSP00000311984:K140E	ENSP00000311984:K140E	K	+	1	0	CARKD	110077818	0.887000	0.30362	0.000000	0.03702	0.324000	0.28378	1.784000	0.38674	-0.259000	0.09432	0.459000	0.35465	AAG	A|0.955;G|0.045	0.045	strong		0.478	CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210	
PELP1	27043	hgsc.bcm.edu	37	17	4574751	4574751	+	Missense_Mutation	SNP	T	T	A	rs9436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	80	0	0		WXS	Illumina HiSeq	Phase_I	104	41	0.394231	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	
APC	324	hgsc.bcm.edu	37	5	112176556	112176556	+	Silent	SNP	G	G	A	rs34506289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112176556G>A	ENST00000457016.1	+	16	5645	c.5265G>A	c.(5263-5265)gcG>gcA	p.A1755A	APC_ENST00000257430.4_Silent_p.A1755A|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Silent_p.A1755A			P25054	APC_HUMAN	adenomatous polyposis coli	1755	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)		AAGCATCTGCGTCTTCTTCTG	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)			G|||	21	0.00419329	0.0068	0.0029	5008	,	,		19623	0.001		0.006	False		,,,				2504	0.0031				p.A1755A	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.G5265A						PASS	.	G	,,	43,4361	44.6+/-78.6	0,43,2159	56.0	55.0	56.0		5265,5265,5211	1.6	0.0	5	dbSNP_126	56	79,8517	43.6+/-101.6	1,77,4220	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	1,120,6379	AA,AG,GG		0.919,0.9764,0.9385	,,	1755/2844,1755/2844,1737/2826	112176556	122,12878	2202	4298	6500	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,	ATCTGCGTCTTCT	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.5265G>A	5.37:g.112176556G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	109	41	0.376147	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.992;A|0.008	0.008	strong		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
CRISP3	10321	hgsc.bcm.edu	37	6	49701439	49701439	+	Missense_Mutation	SNP	C	C	A	rs1864312	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49701439C>A	ENST00000393666.1	-	4	406	c.400G>T	c.(400-402)Gca>Tca	p.A134S	CRISP3_ENST00000423399.2_Missense_Mutation_p.A44S|CRISP3_ENST00000371159.4_Missense_Mutation_p.A165S|CRISP3_ENST00000263045.4_Missense_Mutation_p.A147S|CRISP3_ENST00000433368.2_Missense_Mutation_p.A157S			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	134	SCP.		A -> S (in dbSNP:rs1864312). {ECO:0000269|PubMed:14702039}.		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)			CCAACCACTGCGTTGGGAGTC	0.403													C|||	1831	0.365615	0.2579	0.5821	5008	,	,		18832	0.3105		0.4682	False		,,,				2504	0.3088				p.A157S		Atlas-SNP	.											.	CRISP3	67	.	0			c.G469T						PASS	.	C	SER/ALA,SER/ALA	1322,3084	443.9+/-347.2	198,926,1079	121.0	114.0	117.0		469,439	3.2	0.0	6	dbSNP_92	117	3754,4846	534.0+/-382.5	806,2142,1352	yes	missense,missense	CRISP3	NM_001190986.1,NM_006061.2	99,99	1004,3068,2431	AA,AC,CC		43.6512,30.0045,39.0281	benign,benign	157/269,147/259	49701439	5076,7930	2203	4300	6503	SO:0001583	missense	10321	exon5			CCACTGCGTTGGG	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.400G>T	6.37:g.49701439C>A	ENSP00000377274:p.Ala134Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_001190986	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Missense_Mutation	SNP	ENST00000393666.1	37		877	0.4015567765567766	130	0.26422764227642276	207	0.5718232044198895	184	0.32167832167832167	356	0.46965699208443273	C	7.197	0.592611	0.13875	0.300045	0.436512	ENSG00000096006	ENST00000263045;ENST00000433368;ENST00000393666;ENST00000423399;ENST00000371159;ENST00000354620	T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23	5.1	3.18	0.36537	CAP domain (3);	1.214940	0.06207	U	0.684266	T	0.01189	0.0039	N	0.04387	-0.21	0.80722	P	0.0	B	0.27380	0.177	B	0.31751	0.135	T	0.39860	-0.9593	9	0.07813	T	0.8	.	7.8096	0.29223	0.0:0.7193:0.1797:0.1009	rs1864312;rs13192472;rs52804712;rs59808203;rs1864312	134	P54108	CRIS3_HUMAN	S	147;157;134;44;165;157	ENSP00000263045:A147S;ENSP00000389026:A157S;ENSP00000377274:A134S;ENSP00000410469:A44S;ENSP00000360201:A165S;ENSP00000346636:A157S	ENSP00000263045:A147S	A	-	1	0	CRISP3	49809398	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	0.738000	0.26158	1.146000	0.42352	0.585000	0.79938	GCA	C|0.618;A|0.382	0.382	strong		0.403	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061	
WDR25	79446	hgsc.bcm.edu	37	14	100996312	100996312	+	Silent	SNP	T	T	C	rs13065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:100996312T>C	ENST00000335290.6	+	7	1795	c.1569T>C	c.(1567-1569)taT>taC	p.Y523Y	WDR25_ENST00000542471.2_Silent_p.Y266Y|WDR25_ENST00000402312.3_Silent_p.Y523Y|WDR25_ENST00000554998.1_Silent_p.Y523Y|WDR25_ENST00000557502.1_3'UTR	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	523										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				GCACCACCTATCACCCCGTGC	0.642													C|||	3212	0.641374	0.9705	0.611	5008	,	,		19149	0.6974		0.4155	False		,,,				2504	0.3926				p.Y523Y		Atlas-SNP	.											WDR25,NS,carcinoma,0,1	WDR25	37	1	0			c.T1569C						PASS	.	C	,	3873,533	242.1+/-252.3	1710,453,40	82.0	75.0	77.0		1569,1569	0.8	1.0	14	dbSNP_52	77	3368,5232	640.7+/-399.6	670,2028,1602	no	coding-synonymous,coding-synonymous	WDR25	NM_001161476.1,NM_024515.4	,	2380,2481,1642	CC,CT,TT		39.1628,12.0971,44.3257	,	523/545,523/545	100996312	7241,5765	2203	4300	6503	SO:0001819	synonymous_variant	79446	exon7			CACCTATCACCCC	BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"""WD repeat domain containing"""	21064	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 67"""	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.1569T>C	14.37:g.100996312T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Silent	SNP	ENST00000335290.6	37	CCDS32157.1																																																																																			T|0.409;C|0.591	0.591	strong		0.642	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515	
RNFT2	84900	hgsc.bcm.edu	37	12	117187907	117187907	+	Silent	SNP	T	T	C	rs111256849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117187907T>C	ENST00000257575.4	+	4	578	c.345T>C	c.(343-345)caT>caC	p.H115H	RNFT2_ENST00000407967.3_Silent_p.H115H|RNFT2_ENST00000392549.2_Silent_p.H115H|RNFT2_ENST00000319176.7_Silent_p.H115H			Q96EX2	RNFT2_HUMAN	ring finger protein, transmembrane 2	115	His-rich.					integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	6	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		CCCACCACCATTTCCACCATG	0.746													C|||	1284	0.25639	0.4826	0.1326	5008	,	,		12011	0.1786		0.166	False		,,,				2504	0.2117				p.H115H		Atlas-SNP	.											RNFT2,NS,carcinoma,0,4	RNFT2	28	4	0			c.T345C						PASS	.	C	,	1295,2539		234,827,856	3.0	4.0	4.0		345,345	3.2	1.0	12	dbSNP_132	4	888,6786		67,754,3016	no	coding-synonymous,coding-synonymous	RNFT2	NM_001109903.1,NM_032814.3	,	301,1581,3872	CC,CT,TT		11.5715,33.7767,18.9694	,	115/445,115/421	117187907	2183,9325	1917	3837	5754	SO:0001819	synonymous_variant	84900	exon4			CCACCATTTCCAC	AK027533	CCDS9180.2, CCDS44987.1	12q24.22	2013-01-09	2008-02-26	2008-02-26	ENSG00000135119	ENSG00000135119		"""RING-type (C3HC4) zinc fingers"""	25905	protein-coding gene	gene with protein product			"""transmembrane protein 118"""	TMEM118		12477932	Standard	NM_032814		Approved	FLJ14627	uc009zwn.3	Q96EX2	OTTHUMG00000150882	ENST00000257575.4:c.345T>C	12.37:g.117187907T>C		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_001109903	E9PAM7|Q96SU5	Silent	SNP	ENST00000257575.4	37	CCDS44987.1																																																																																			T|0.767;C|0.233	0.233	strong		0.746	RNFT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320417.1	NM_032814	
RAB40AL	282808	hgsc.bcm.edu	37	X	102192315	102192315	+	Missense_Mutation	SNP	G	G	C	rs61745030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192315G>C	ENST00000218249.5	+	1	116	c.69G>C	c.(67-69)agG>agC	p.R23S	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	23					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						TGGGCGACAGGGACGTAGGCA	0.677													.|||	989	0.261987	0.4085	0.0677	3775	,	,		9895	0.1171		0.005	False		,,,				2504	0.2853				p.R23S		Atlas-SNP	.											.	RAB40AL	33	.	0			c.G69C						PASS	.	C	SER/ARG	1646,2189		331,710,274,591,297	48.0	64.0	59.0		69	-0.0	0.5	X	dbSNP_129	59	31,6697		0,24,7,2404,1865	yes	missense	RAB40AL	NM_001031834.1	110	331,734,281,2995,2162	CC,CG,C,GG,G		0.4608,42.9205,15.8762	benign	23/279	102192315	1677,8886	2203	4300	6503	SO:0001583	missense	282808	exon1			CGACAGGGACGTA	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"""Ras like GTPase"""	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.69G>C	X.37:g.102192315G>C	ENSP00000218249:p.Arg23Ser	Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	256	254	0.992188	NM_001031834	Q495H3	Missense_Mutation	SNP	ENST00000218249.5	37	CCDS35353.1	286	0.1723930078360458	142	0.3837837837837838	11	0.03142857142857143	47	0.08801498127340825	3	0.00395778364116095	.	0.050	-1.253647	0.01457	0.429205	0.004608	ENSG00000102128	ENST00000218249	T	0.74737	-0.87	0.99	-0.00522	0.14018	Small GTP-binding protein domain (1);	0.000000	0.56097	N	0.000031	T	0.00012	0.0000	N	0.00037	-2.53	0.51233	P	8.399999999997299E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.30297	-0.9983	9	0.02654	T	1	.	2.6358	0.04957	0.0:0.3265:0.2617:0.4118	rs61745030	23	P0C0E4	RB40L_HUMAN	S	23	ENSP00000218249:R23S	ENSP00000218249:R23S	R	+	3	2	RAB40AL	102078971	0.997000	0.39634	0.473000	0.27253	0.038000	0.13279	0.197000	0.17197	-0.599000	0.05798	-0.355000	0.07637	AGG	G|0.821;C|0.179	0.179	strong		0.677	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834	
RFX6	222546	hgsc.bcm.edu	37	6	117244374	117244374	+	Silent	SNP	T	T	C	rs7770158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117244374T>C	ENST00000332958.2	+	14	1558	c.1542T>C	c.(1540-1542)aaT>aaC	p.N514N		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	514					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						CCTTGAACAATGCATCCAGTT	0.338													T|||	1702	0.339856	0.2927	0.2896	5008	,	,		20919	0.4236		0.2286	False		,,,				2504	0.4673				p.N514N		Atlas-SNP	.											.	RFX6	141	.	0			c.T1542C						PASS	.	T		1232,3174	424.2+/-340.4	180,872,1151	148.0	136.0	140.0		1542	0.7	1.0	6	dbSNP_116	140	1528,7072	288.1+/-298.6	143,1242,2915	no	coding-synonymous	RFX6	NM_173560.3		323,2114,4066	CC,CT,TT		17.7674,27.9619,21.221		514/929	117244374	2760,10246	2203	4300	6503	SO:0001819	synonymous_variant	222546	exon14			GAACAATGCATCC	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1542T>C	6.37:g.117244374T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	154	82	0.532468	NM_173560	Q5T6B3	Silent	SNP	ENST00000332958.2	37	CCDS5113.1																																																																																			T|0.747;C|0.253	0.253	strong		0.338	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560	
ACTRT2	140625	hgsc.bcm.edu	37	1	2938697	2938697	+	Silent	SNP	T	T	G	rs3795262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:2938697T>G	ENST00000378404.2	+	1	652	c.447T>G	c.(445-447)tcT>tcG	p.S149S		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	149						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		TCTACGCCTCTGCCTGTGTCA	0.622													G|||	1047	0.209065	0.1657	0.2435	5008	,	,		18354	0.3958		0.163	False		,,,				2504	0.0982				p.S149S		Atlas-SNP	.											.	ACTRT2	69	.	0			c.T447G						PASS	.	G		736,3670	756.4+/-412.6	65,606,1532	63.0	58.0	59.0		447	-9.7	0.4	1	dbSNP_107	59	1542,7058	744.7+/-407.2	125,1292,2883	no	coding-synonymous	ACTRT2	NM_080431.4		190,1898,4415	GG,GT,TT		17.9302,16.7045,17.515		149/378	2938697	2278,10728	2203	4300	6503	SO:0001819	synonymous_variant	140625	exon1			CGCCTCTGCCTGT	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.447T>G	1.37:g.2938697T>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	161	83	0.515528	NM_080431	B1AN52|Q8NHS6|Q8TDG1	Silent	SNP	ENST00000378404.2	37	CCDS45.1																																																																																			T|0.796;G|0.204	0.204	strong		0.622	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431	
TTC31	64427	hgsc.bcm.edu	37	2	74710491	74710491	+	Missense_Mutation	SNP	C	C	T	rs6707475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74710491C>T	ENST00000233623.5	+	2	90	c.83C>T	c.(82-84)gCa>gTa	p.A28V	CCDC142_ENST00000471713.1_5'Flank|TTC31_ENST00000410003.1_Missense_Mutation_p.A28V|TTC31_ENST00000463189.1_3'UTR|TTC31_ENST00000442235.2_5'UTR|CCDC142_ENST00000290418.4_5'Flank|CCDC142_ENST00000393965.3_5'Flank	NM_022492.4	NP_071937.4	Q49AM3	TTC31_HUMAN	tetratricopeptide repeat domain 31	28			A -> V (in dbSNP:rs6707475). {ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						GTCGCTGCTGCACCCAAACTT	0.582											OREG0014719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2741	0.547324	0.907	0.3256	5008	,	,		17254	0.8224		0.159	False		,,,				2504	0.3344				p.A28V		Atlas-SNP	.											.	TTC31	23	.	0			c.C83T						PASS	.	T	VAL/ALA	2987,943		1146,695,124	63.0	71.0	68.0		83	0.3	0.8	2	dbSNP_116	68	1204,7124		95,1014,3055	yes	missense	TTC31	NM_022492.4	64	1241,1709,3179	TT,TC,CC		14.4573,23.9949,34.1899	benign	28/520	74710491	4191,8067	1965	4164	6129	SO:0001583	missense	64427	exon2			CTGCTGCACCCAA	AK026819	CCDS42701.1	2p13.1	2013-01-11			ENSG00000115282	ENSG00000115282		"""Tetratricopeptide (TTC) repeat domain containing"""	25759	protein-coding gene	gene with protein product						12477932	Standard	NM_022492		Approved	FLJ12788	uc002slt.2	Q49AM3	OTTHUMG00000152887	ENST00000233623.5:c.83C>T	2.37:g.74710491C>T	ENSP00000233623:p.Ala28Val	Somatic	75	0	0	1154	WXS	Illumina HiSeq	Phase_I	71	71	1	NM_022492	Q4KN40|Q53FD4|Q9H9F7	Missense_Mutation	SNP	ENST00000233623.5	37	CCDS42701.1	1119	0.5123626373626373	436	0.8861788617886179	98	0.27071823204419887	470	0.8216783216783217	115	0.1517150395778364	T	14.44	2.534928	0.45073	0.760051	0.144573	ENSG00000115282	ENST00000410003;ENST00000435361;ENST00000441635;ENST00000233623	T;T	0.38077	1.16;1.16	4.27	0.28	0.15682	.	0.280031	0.23373	N	0.048891	T	0.00012	0.0000	N	0.00347	-1.61	0.09310	P	0.9999999999531156	B	0.02656	0.0	B	0.01281	0.0	T	0.29579	-1.0007	9	0.02654	T	1	-1.4487	3.1691	0.06546	0.1962:0.3671:0.0:0.4367	rs6707475;rs52813769;rs59381657;rs6707475	28	Q49AM3	TTC31_HUMAN	V	28	ENSP00000387213:A28V;ENSP00000233623:A28V	ENSP00000233623:A28V	A	+	2	0	TTC31	74563999	0.061000	0.20836	0.771000	0.31576	0.900000	0.52787	-0.054000	0.11826	-0.006000	0.14370	-0.254000	0.11334	GCA	C|0.514;T|0.486	0.486	strong		0.582	TTC31-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328422.1	NM_022492	
CREB3L3	84699	hgsc.bcm.edu	37	19	4171825	4171825	+	Silent	SNP	G	G	A	rs115268777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4171825G>A	ENST00000078445.2	+	10	1392	c.1245G>A	c.(1243-1245)acG>acA	p.T415T	CREB3L3_ENST00000602257.1_Silent_p.T413T|CREB3L3_ENST00000595923.1_Silent_p.T414T|CREB3L3_ENST00000602147.1_3'UTR|CREB3L3_ENST00000252587.3_3'UTR	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	415					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAATTCGACGGAGGAGCTGG	0.672													G|||	52	0.0103834	0.0393	0.0	5008	,	,		16107	0.0		0.0	False		,,,				2504	0.0				p.T415T		Atlas-SNP	.											.	CREB3L3	53	.	0			c.G1245A						PASS	.	G		158,4248	104.3+/-142.8	3,152,2048	37.0	41.0	40.0		1245	-4.7	0.0	19	dbSNP_132	40	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	CREB3L3	NM_032607.1		3,153,6342	AA,AG,GG		0.0116,3.586,1.2235		415/462	4171825	159,12837	2203	4295	6498	SO:0001819	synonymous_variant	84699	exon10			TTCGACGGAGGAG		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"""basic leucine zipper proteins"""	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.1245G>A	19.37:g.4171825G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	125	68	0.544	NM_032607	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	37	CCDS12121.1																																																																																			G|0.988;A|0.012	0.012	strong		0.672	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	
PSG1	5669	hgsc.bcm.edu	37	19	43382402	43382402	+	Silent	SNP	G	G	A	rs17423717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43382402G>A	ENST00000436291.2	-	2	209	c.93C>T	c.(91-93)ccC>ccT	p.P31P	PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000595356.1_Silent_p.P31P|PSG1_ENST00000595124.1_Silent_p.P31P|PSG1_ENST00000403380.3_Silent_p.P31P|PSG1_ENST00000312439.6_Silent_p.P31P|PSG1_ENST00000244296.2_Silent_p.P31P	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	31					female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				GGGCAGTGGTGGGCAGGTTCC	0.493													.|||	52	0.0103834	0.0212	0.0072	5008	,	,		19198	0.005		0.002	False		,,,				2504	0.0123				p.P31P		Atlas-SNP	.											PSG1_ENST00000312439,NS,carcinoma,-1,4	PSG1	196	4	0			c.C93T						scavenged	.						142.0	154.0	150.0					19																	43382402		2203	4299	6502	SO:0001819	synonymous_variant	5669	exon2			AGTGGTGGGCAGG		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.93C>T	19.37:g.43382402G>A		Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	333	27	0.0810811	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Silent	SNP	ENST00000436291.2	37	CCDS54275.1																																																																																			G|0.996;A|0.004	0.004	strong		0.493	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
ZNF577	84765	hgsc.bcm.edu	37	19	52376172	52376172	+	Missense_Mutation	SNP	T	T	A	rs9807853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52376172T>A	ENST00000301399.5	-	7	1436	c.1071A>T	c.(1069-1071)agA>agT	p.R357S	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.R298S|ZNF577_ENST00000451628.2_Missense_Mutation_p.R298S	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	357			R -> S (in dbSNP:rs9807853).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TGCCACATTCTCTGCATGAAT	0.428													g|||	853	0.170327	0.2943	0.1427	5008	,	,		21581	0.0427		0.0358	False		,,,				2504	0.2924				p.R357S		Atlas-SNP	.											ZNF577,bladder,carcinoma,-1,1	ZNF577	63	1	0			c.A1071T						PASS	.	A	SER/ARG,SER/ARG	1178,3228		167,844,1192	77.0	75.0	76.0		894,1071	-2.1	0.1	19	dbSNP_119	76	165,8435		1,163,4136	yes	missense,missense	ZNF577	NM_001135590.1,NM_032679.2	110,110	168,1007,5328	AA,AT,TT		1.9186,26.7363,10.326	benign,benign	298/427,357/486	52376172	1343,11663	2203	4300	6503	SO:0001583	missense	84765	exon7			ACATTCTCTGCAT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1071A>T	19.37:g.52376172T>A	ENSP00000301399:p.Arg357Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	37	CCDS12842.2	219	0.10027472527472528	117	0.23780487804878048	50	0.13812154696132597	25	0.043706293706293704	27	0.03562005277044855	.	0.001	-3.245965	0.00022	0.267363	0.019186	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.14516	2.5;2.5;2.5;2.5	2.95	-2.07	0.07276	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.01277	-0.915	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41787	-0.9489	8	0.09338	T	0.73	.	2.018	0.03502	0.4662:0.1274:0.2809:0.1255	rs9807853;rs52829822;rs9807853	357;298	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	S	357;298;298;357	ENSP00000301399:R357S;ENSP00000413476:R298S;ENSP00000389652:R298S;ENSP00000404509:R357S	ENSP00000301399:R357S	R	-	3	2	ZNF577	57067984	0.000000	0.05858	0.097000	0.21041	0.396000	0.30629	-3.994000	0.00318	-0.801000	0.04427	-2.196000	0.00310	AGA	T|0.898;A|0.102	0.102	strong		0.428	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
GAB4	128954	hgsc.bcm.edu	37	22	17472785	17472785	+	Silent	SNP	G	G	A	rs116325774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17472785G>A	ENST00000400588.1	-	2	563	c.456C>T	c.(454-456)ggC>ggT	p.G152G	GAB4_ENST00000523144.1_5'UTR	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	152	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									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)				CCTGCCTGAAGCCACAGATCT	0.547													G|||	30	0.00599042	0.0227	0.0	5008	,	,		21341	0.0		0.0	False		,,,				2504	0.0				p.G152G		Atlas-SNP	.											GAB4,NS,carcinoma,-1,1	GAB4	95	1	0			c.C456T						scavenged	.	G		60,4346	55.5+/-91.7	1,58,2144	241.0	243.0	242.0		456	1.8	1.0	22	dbSNP_132	242	0,8600		0,0,4300	no	coding-synonymous	GAB4	NM_001037814.1		1,58,6444	AA,AG,GG		0.0,1.3618,0.4613		152/575	17472785	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	128954	exon2			CCTGAAGCCACAG	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.456C>T	22.37:g.17472785G>A		Somatic	272	2	0.00735294		WXS	Illumina HiSeq	Phase_I	284	136	0.478873	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			G|0.994;A|0.006	0.006	strong		0.547	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
LRRC23	10233	hgsc.bcm.edu	37	12	7015075	7015075	+	Missense_Mutation	SNP	A	A	C	rs2071072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7015075A>C	ENST00000007969.8	+	3	413	c.193A>C	c.(193-195)Aat>Cat	p.N65H	LRRC23_ENST00000436789.1_Missense_Mutation_p.N65H|LRRC23_ENST00000429740.1_Missense_Mutation_p.N65H|LRRC23_ENST00000323702.5_Missense_Mutation_p.N65H|LRRC23_ENST00000433346.1_Missense_Mutation_p.N65H|LRRC23_ENST00000443597.2_Missense_Mutation_p.N65H|LRRC23_ENST00000449039.1_Intron	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	65			N -> H (in dbSNP:rs2071072).							NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						TAAGACAGGCAATGGGCTGGC	0.552													A|||	239	0.0477236	0.0	0.0	5008	,	,		-128	0.2183		0.0	False		,,,				2504	0.0194				p.N65H		Atlas-SNP	.											.	LRRC23	46	.	0			c.A193C						PASS	.	A	HIS/ASN,HIS/ASN,HIS/ASN	4,4402	8.1+/-20.4	0,4,2199	111.0	100.0	104.0		193,193,193	4.3	0.1	12	dbSNP_96	104	0,8600		0,0,4300	yes	missense,missense,missense	LRRC23	NM_001135217.1,NM_006992.3,NM_201650.2	68,68,68	0,4,6499	CC,CA,AA		0.0,0.0908,0.0308	possibly-damaging,possibly-damaging,possibly-damaging	65/344,65/313,65/344	7015075	4,13002	2203	4300	6503	SO:0001583	missense	10233	exon3			ACAGGCAATGGGC	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.193A>C	12.37:g.7015075A>C	ENSP00000007969:p.Asn65His	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_001135217	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Missense_Mutation	SNP	ENST00000007969.8	37	CCDS8569.1	113	0.051739926739926737	0	0.0	0	0.0	113	0.19755244755244755	0	0.0	A	19.41	3.821461	0.71028	9.08E-4	0.0	ENSG00000010626	ENST00000433346;ENST00000007969;ENST00000323702;ENST00000443597;ENST00000415834;ENST00000436789;ENST00000429740	T;T;T;T;T;T;T	0.68331	1.77;-0.02;-0.32;-0.02;0.64;1.79;1.34	5.51	4.33	0.51752	.	.	.	.	.	T	0.00241	0.0007	M	0.64404	1.975	0.41971	P	0.009241999999999972	D;D;D;D	0.76494	0.987;0.999;0.992;0.991	D;P;P;P	0.65573	0.936;0.907;0.778;0.847	T	0.07501	-1.0769	8	0.45353	T	0.12	-0.5611	11.3578	0.49625	0.8638:0.0:0.0:0.1362	rs2071072;rs17790798;rs52809345;rs2071072	65;65;65;65	E9PDZ4;Q53EV4-2;Q53EV4;C9JKE8	.;.;LRC23_HUMAN;.	H	65	ENSP00000402554:N65H;ENSP00000007969:N65H;ENSP00000317464:N65H;ENSP00000390932:N65H;ENSP00000408066:N65H;ENSP00000396049:N65H;ENSP00000397192:N65H	ENSP00000007969:N65H	N	+	1	0	LRRC23	6885336	0.998000	0.40836	0.059000	0.19551	0.909000	0.53808	5.004000	0.63966	0.869000	0.35703	0.459000	0.35465	AAT	A|0.951;C|0.049	0.049	strong		0.552	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992	
PCF11	51585	hgsc.bcm.edu	37	11	82880341	82880341	+	Silent	SNP	G	G	A	rs12284052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:82880341G>A	ENST00000298281.4	+	8	3416	c.2964G>A	c.(2962-2964)caG>caA	p.Q988Q		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	988	Gly-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|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 factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						CACATGGTCAGCCAGGGGTTG	0.517													A|||	1226	0.244808	0.6657	0.1167	5008	,	,		20858	0.0496		0.0835	False		,,,				2504	0.1339				p.Q988Q		Atlas-SNP	.											.	PCF11	220	.	0			c.G2964A						PASS	.	A		2068,1764		558,952,406	90.0	92.0	91.0		2964	-1.0	1.0	11	dbSNP_120	91	727,7533		29,669,3432	no	coding-synonymous	PCF11	NM_015885.3		587,1621,3838	AA,AG,GG		8.8015,46.0334,23.1145		988/1556	82880341	2795,9297	1916	4130	6046	SO:0001819	synonymous_variant	51585	exon8			TGGTCAGCCAGGG	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.2964G>A	11.37:g.82880341G>A		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	206	206	1	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	37	CCDS44689.1																																																																																			G|0.783;A|0.217	0.217	strong		0.517	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
IVL	3713	hgsc.bcm.edu	37	1	152882811	152882811	+	Missense_Mutation	SNP	G	G	A	rs75111974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152882811G>A	ENST00000368764.3	+	2	602	c.538G>A	c.(538-540)Gag>Aag	p.E180K	IVL_ENST00000392667.2_Missense_Mutation_p.E34K			P07476	INVO_HUMAN	involucrin	180	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ggagcagcaggaggggcagct	0.647													G|||	107	0.0213658	0.0779	0.0058	5008	,	,		15888	0.0		0.0	False		,,,				2504	0.0				p.E180K		Atlas-SNP	.											.	IVL	100	.	0			c.G538A						PASS	.	G	LYS/GLU	255,4147		3,249,1949	13.0	15.0	14.0		538	0.1	0.0	1	dbSNP_131	14	2,8584		0,2,4291	no	missense	IVL	NM_005547.2	56	3,251,6240	AA,AG,GG		0.0233,5.7928,1.9787	possibly-damaging	180/586	152882811	257,12731	2201	4293	6494	SO:0001583	missense	3713	exon2			CAGCAGGAGGGGC	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.538G>A	1.37:g.152882811G>A	ENSP00000357753:p.Glu180Lys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	205	112	0.546341	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	G	9.931	1.214712	0.22289	0.057928	2.33E-4	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.11495	3.0;2.77	3.55	0.138	0.14793	.	.	.	.	.	T	0.03520	0.0101	L	0.38531	1.155	0.09310	N	1	P	0.38280	0.625	B	0.39738	0.308	T	0.39761	-0.9598	9	0.25106	T	0.35	.	12.3464	0.55124	0.0:0.5062:0.4938:0.0	rs62641593	180	P07476	INVO_HUMAN	K	180;34	ENSP00000357753:E180K;ENSP00000376435:E34K	ENSP00000357753:E180K	E	+	1	0	IVL	151149435	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.353000	0.20130	0.285000	0.22329	-0.662000	0.03851	GAG	G|0.980;A|0.020	0.020	strong		0.647	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
RDH8	50700	hgsc.bcm.edu	37	19	10131401	10131401	+	Silent	SNP	T	T	C	rs2233796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10131401T>C	ENST00000171214.1	+	4	708	c.459T>C	c.(457-459)gaT>gaC	p.D153D	RDH8_ENST00000591589.1_Silent_p.D173D	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	153					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)	TCTTCAACGATGTCTATGCAG	0.567													T|||	93	0.0185703	0.0514	0.013	5008	,	,		16799	0.0		0.0129	False		,,,				2504	0.0031				p.D173D		Atlas-SNP	.											.	RDH8	51	.	0			c.T519C						PASS	.	T		233,4173	136.9+/-172.8	4,225,1974	84.0	71.0	76.0		459	-7.0	0.3	19	dbSNP_98	76	127,8473	63.5+/-125.6	1,125,4174	no	coding-synonymous	RDH8	NM_015725.2		5,350,6148	CC,CT,TT		1.4767,5.2882,2.768		153/312	10131401	360,12646	2203	4300	6503	SO:0001819	synonymous_variant	50700	exon4			CAACGATGTCTAT	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.459T>C	19.37:g.10131401T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_015725	Q9H838	Silent	SNP	ENST00000171214.1	37																																																																																				T|0.974;C|0.026	0.026	strong		0.567	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
TRIM49	57093	hgsc.bcm.edu	37	11	89531619	89531619	+	Silent	SNP	A	A	G	rs11824402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:89531619A>G	ENST00000329758.1	-	8	1366	c.1038T>C	c.(1036-1038)caT>caC	p.H346H	TRIM49_ENST00000532501.2_Silent_p.H269H	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	346	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			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)				AGTCCCCTACATGGACCTCCC	0.448																																					p.H346H		Atlas-SNP	.											.	TRIM49	45	.	0			c.T1038C						PASS	.						31.0	36.0	35.0					11																	89531619		2139	4257	6396	SO:0001819	synonymous_variant	57093	exon8			CCCTACATGGACC	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.1038T>C	11.37:g.89531619A>G		Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	180	84	0.466667	NM_020358	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Silent	SNP	ENST00000329758.1	37	CCDS8287.1																																																																																			.	.	weak		0.448	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358	
NOS1	4842	hgsc.bcm.edu	37	12	117685255	117685255	+	Silent	SNP	G	G	A	rs41410247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117685255G>A	ENST00000338101.4	-	18	2827	c.2823C>T	c.(2821-2823)ctC>ctT	p.L941L	NOS1_ENST00000317775.6_Silent_p.L907L|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GTTCTTCCAGGAGGGTGTCCA	0.552													G|||	37	0.00738818	0.0272	0.0014	5008	,	,		16371	0.0		0.0	False		,,,				2504	0.0				p.L941L	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C2823T						PASS	.	G	,,,	95,3833		0,95,1869	91.0	91.0	91.0		2721,1713,1713,2823	2.7	1.0	12	dbSNP_127	91	5,8315		0,5,4155	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	0,100,6024	AA,AG,GG		0.0601,2.4185,0.8165	,,,	907/1435,571/1099,571/1099,941/1469	117685255	100,12148	1964	4160	6124	SO:0001819	synonymous_variant	4842	exon19			TTCCAGGAGGGTG		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2823C>T	12.37:g.117685255G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	157	72	0.458599	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.995;A|0.005	0.005	strong		0.552	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
GSTM5	2949	hgsc.bcm.edu	37	1	110257835	110257835	+	Silent	SNP	C	C	T	rs386634508|rs67757008|rs78183574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110257835C>T	ENST00000256593.3	+	7	598	c.540C>T	c.(538-540)aaC>aaT	p.N180N	GSTM5_ENST00000369813.1_Silent_p.N139N|GSTM5_ENST00000492718.1_3'UTR|GSTM5_ENST00000369812.5_Silent_p.N199N	NM_000851.3	NP_000842.2	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5	180	GST C-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)			NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	CCTTCCTAAACTTGAAGGACT	0.478													C|||	703	0.140375	0.3941	0.0663	5008	,	,		19824	0.001		0.0845	False		,,,				2504	0.0511				p.N180N		Atlas-SNP	.											GSTM5,brain,glioma,0,2	GSTM5	89	2	0			c.C540T						PASS	.																																			SO:0001819	synonymous_variant	2949	exon7			CCTAAACTTGAAG	L02321	CCDS811.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134201	ENSG00000134201	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4637	protein-coding gene	gene with protein product		138385	"""glutathione S-transferase M5"""			8473333	Standard	NM_000851		Approved		uc001dyn.3	P46439	OTTHUMG00000011644	ENST00000256593.3:c.540C>T	1.37:g.110257835C>T		Somatic	537	2	0.00372439		WXS	Illumina HiSeq	Phase_I	578	286	0.49481	NM_000851	A8K0V8|Q6PD78	Silent	SNP	ENST00000256593.3	37	CCDS811.1																																																																																			C|0.907;T|0.093	0.093	strong		0.478	GSTM5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032200.1	NM_000851	
PLD1	5337	hgsc.bcm.edu	37	3	171395468	171395468	+	Silent	SNP	A	A	G	rs2124147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:171395468A>G	ENST00000351298.4	-	17	2010	c.1884T>C	c.(1882-1884)cgT>cgC	p.R628R	PLD1_ENST00000356327.5_Silent_p.R590R|PLD1_ENST00000342215.6_Missense_Mutation_p.V519A|PLD1_ENST00000340989.4_Silent_p.R628R	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	628	Catalytic.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	TCTGTAAACTACGGATGGACC	0.488													G|||	2327	0.464657	0.7269	0.4597	5008	,	,		17426	0.3234		0.3926	False		,,,				2504	0.3333				p.R628R	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.T1884C						PASS	.	G	,	2940,1466	472.4+/-356.4	961,1018,224	121.0	114.0	117.0		1770,1884	0.5	1.0	3	dbSNP_96	117	3690,4910	621.3+/-397.2	798,2094,1408	no	coding-synonymous,coding-synonymous	PLD1	NM_001130081.2,NM_002662.4	,	1759,3112,1632	GG,GA,AA		42.907,33.2728,49.0235	,	590/1037,628/1075	171395468	6630,6376	2203	4300	6503	SO:0001819	synonymous_variant	5337	exon17			TAAACTACGGATG	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.1884T>C	3.37:g.171395468A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_002662		Silent	SNP	ENST00000351298.4	37	CCDS3216.1	1006	0.4606227106227106	383	0.7784552845528455	152	0.4198895027624309	169	0.29545454545454547	302	0.39841688654353563	G	9.936	1.216235	0.22373	0.667272	0.42907	ENSG00000075651	ENST00000342215	T	0.30448	1.53	6.05	0.511	0.16989	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47276	P	6.220000000000114E-4	.	.	.	.	.	.	T	0.37009	-0.9724	5	0.06099	T	0.92	-10.5471	3.7192	0.08449	0.222:0.0868:0.5051:0.1861	rs2124147;rs52831340;rs60164524;rs2124147	.	.	.	A	519	ENSP00000339936:V519A	ENSP00000339936:V519A	V	-	2	0	PLD1	172878162	1.000000	0.71417	0.965000	0.40720	0.826000	0.46750	0.739000	0.26173	-0.056000	0.13221	-0.755000	0.03482	GTA	A|0.510;G|0.490	0.490	strong		0.488	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
UTP20	27340	hgsc.bcm.edu	37	12	101776996	101776996	+	Missense_Mutation	SNP	G	G	C	rs1061436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101776996G>C	ENST00000261637.4	+	59	8008	c.7834G>C	c.(7834-7836)Gag>Cag	p.E2612Q		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2612			E -> Q (in dbSNP:rs1061436).		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						GGTGAAGGAAGAGCTCGGCAG	0.532													G|||	435	0.086861	0.0182	0.1153	5008	,	,		14588	0.0278		0.165	False		,,,				2504	0.1401				p.E2612Q		Atlas-SNP	.											.	UTP20	222	.	0			c.G7834C						PASS	.	G	GLN/GLU	169,4237	111.2+/-149.4	4,161,2038	62.0	70.0	67.0		7834	2.4	0.0	12	dbSNP_86	67	1432,7168	275.4+/-291.8	119,1194,2987	yes	missense	UTP20	NM_014503.2	29	123,1355,5025	CC,CG,GG		16.6512,3.8357,12.3097	benign	2612/2786	101776996	1601,11405	2203	4300	6503	SO:0001583	missense	27340	exon59			AAGGAAGAGCTCG	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.7834G>C	12.37:g.101776996G>C	ENSP00000261637:p.Glu2612Gln	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	203	0.09294871794871795	11	0.022357723577235773	46	0.1270718232044199	16	0.027972027972027972	130	0.17150395778364116	G	12.10	1.836371	0.32421	0.038357	0.166512	ENSG00000120800	ENST00000261637	T	0.04970	3.52	5.46	2.43	0.29744	.	0.501020	0.18522	N	0.138727	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P	0.35656	0.514	B	0.25291	0.059	T	0.43734	-0.9373	9	0.15499	T	0.54	-4.2624	10.1662	0.42882	0.0699:0.2572:0.6729:0.0	rs1061436;rs3202548;rs3816569;rs17415284;rs1061436	2612	O75691	UTP20_HUMAN	Q	2612	ENSP00000261637:E2612Q	ENSP00000261637:E2612Q	E	+	1	0	UTP20	100301127	0.416000	0.25424	0.002000	0.10522	0.001000	0.01503	2.618000	0.46393	0.657000	0.30906	0.643000	0.83706	GAG	G|0.878;C|0.122	0.122	strong		0.532	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
DBX1	120237	hgsc.bcm.edu	37	11	20178717	20178717	+	Silent	SNP	G	G	T	rs831464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:20178717G>T	ENST00000524983.2	-	3	826	c.538C>A	c.(538-540)Cgg>Agg	p.R180R	DBX1_ENST00000227256.3_Silent_p.R180R			A6NMT0	DBX1_HUMAN	developing brain homeobox 1	180					regulation of transcription from RNA polymerase II promoter (GO:0006357)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)	21						AGCATGCCCCGCCGAGGCTTC	0.667													G|||	494	0.0986422	0.2405	0.0836	5008	,	,		11232	0.0198		0.0805	False		,,,				2504	0.0174				p.R180R		Atlas-SNP	.											DBX1,NS,carcinoma,0,1	DBX1	39	1	0			c.C538A						PASS	.	G		936,3464		105,726,1369	13.0	13.0	13.0		538	1.4	1.0	11	dbSNP_86	13	617,7969		26,565,3702	no	coding-synonymous	DBX1	NM_001029865.2		131,1291,5071	TT,TG,GG		7.1861,21.2727,11.959		180/344	20178717	1553,11433	2200	4293	6493	SO:0001819	synonymous_variant	120237	exon3			TGCCCCGCCGAGG			11p15.1	2011-06-20				ENSG00000109851		"""Homeoboxes / ANTP class : NKL subclass"""	33185	protein-coding gene	gene with protein product						11239429	Standard	NM_001029865		Approved		uc021qey.1	A6NMT0		ENST00000524983.2:c.538C>A	11.37:g.20178717G>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_001029865		Silent	SNP	ENST00000524983.2	37																																																																																				G|0.881;T|0.119	0.119	strong		0.667	DBX1-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387585.2	NM_001029865	
MUC4	4585	hgsc.bcm.edu	37	3	195511608	195511608	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511608T>C	ENST00000463781.3	-	2	7302	c.6843A>G	c.(6841-6843)gtA>gtG	p.V2281V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V2281V	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)		CACCTGTGGATACTGAGGAAA	0.582																																					p.V2281V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.A6843G						scavenged	.																																			SO:0001819	synonymous_variant	4585	exon2			TGTGGATACTGAG	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.6843A>G	3.37:g.195511608T>C		Somatic	505	1	0.0019802		WXS	Illumina HiSeq	Phase_I	167	18	0.107784	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																																																																																			.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZDHHC7	55625	hgsc.bcm.edu	37	16	85011548	85011548	+	Missense_Mutation	SNP	C	C	T	rs13334011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:85011548C>T	ENST00000313732.4	-	6	953	c.601G>A	c.(601-603)Gtc>Atc	p.V201I	ZDHHC7_ENST00000564466.1_Missense_Mutation_p.V238I|ZDHHC7_ENST00000569488.1_5'UTR	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	201			V -> I (in dbSNP:rs13334011).		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						TGCCCTCGGACACAGGAGATG	0.443													C|||	134	0.0267572	0.0968	0.0086	5008	,	,		19553	0.0		0.0	False		,,,				2504	0.0				p.V238I		Atlas-SNP	.											.	ZDHHC7	55	.	0			c.G712A						PASS	.	C	ILE/VAL,ILE/VAL	332,4066	175.1+/-204.6	13,306,1880	138.0	130.0	133.0		712,601	5.2	1.0	16	dbSNP_121	133	7,8593	5.0+/-18.6	0,7,4293	yes	missense,missense	ZDHHC7	NM_001145548.1,NM_017740.2	29,29	13,313,6173	TT,TC,CC		0.0814,7.5489,2.6081	benign,benign	238/346,201/309	85011548	339,12659	2199	4300	6499	SO:0001583	missense	55625	exon7			CTCGGACACAGGA	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.601G>A	16.37:g.85011548C>T	ENSP00000315604:p.Val201Ile	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	187	91	0.486631	NM_001145548	D3DUM1|Q8WV42|Q9NVD8	Missense_Mutation	SNP	ENST00000313732.4	37	CCDS10950.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	C	11.97	1.796547	0.31777	0.075489	8.14E-4	ENSG00000153786	ENST00000313732;ENST00000344861	T;T	0.39229	1.09;1.09	5.21	5.21	0.72293	.	0.056982	0.64402	D	0.000001	T	0.00845	0.0028	N	0.17631	0.505	0.58432	D	0.999999	B;B	0.12630	0.006;0.004	B;B	0.17979	0.02;0.02	T	0.01652	-1.1303	10	0.26408	T	0.33	-23.2644	17.7601	0.88462	0.0:1.0:0.0:0.0	rs13334011;rs56605352;rs13334011	238;201	Q9NXF8-2;Q9NXF8	.;ZDHC7_HUMAN	I	201;238	ENSP00000315604:V201I;ENSP00000341681:V238I	ENSP00000315604:V201I	V	-	1	0	ZDHHC7	83569049	1.000000	0.71417	0.995000	0.50966	0.805000	0.45488	3.515000	0.53429	2.428000	0.82296	0.561000	0.74099	GTC	C|0.962;T|0.038	0.038	strong		0.443	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740	
PCBP3	54039	hgsc.bcm.edu	37	21	47329352	47329352	+	Silent	SNP	T	T	C	rs2277812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47329352T>C	ENST00000400314.1	+	8	761	c.423T>C	c.(421-423)tgT>tgC	p.C141C	PCBP3_ENST00000400310.1_Silent_p.C141C|PCBP3_ENST00000400309.1_Silent_p.C141C|PCBP3_ENST00000449640.1_Silent_p.C141C|PCBP3_ENST00000400308.1_Silent_p.C141C|PCBP3_ENST00000400304.1_Silent_p.C109C			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	141	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		CCAGCCAGTGTGGGTCCCTGA	0.627													C|||	4414	0.88139	0.9531	0.8098	5008	,	,		14211	0.997		0.7068	False		,,,				2504	0.8957				p.C141C		Atlas-SNP	.											.	PCBP3	82	.	0			c.T423C						PASS	.	C	,	3831,301		1777,277,12	47.0	55.0	53.0		423,423	-8.4	0.1	21	dbSNP_100	53	5860,2590		2044,1772,409	no	coding-synonymous,coding-synonymous	PCBP3	NM_001130141.1,NM_020528.2	,	3821,2049,421	CC,CT,TT		30.6509,7.2846,22.9773	,	141/346,141/372	47329352	9691,2891	2066	4225	6291	SO:0001819	synonymous_variant	54039	exon6			CCAGTGTGGGTCC	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"""poly(rC)-binding protein 3"""			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.423T>C	21.37:g.47329352T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_001130141	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Silent	SNP	ENST00000400314.1	37	CCDS42974.2																																																																																			T|0.204;C|0.796	0.796	strong		0.627	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2		
CYP4F12	66002	hgsc.bcm.edu	37	19	15791081	15791081	+	Missense_Mutation	SNP	T	T	C	rs146740964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791081T>C	ENST00000550308.1	+	4	751	c.371T>C	c.(370-372)tTc>tCc	p.F124S	CYP4F12_ENST00000324632.10_Missense_Mutation_p.F124S	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	124					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GATAATCTCTTCATCAGGTTC	0.572													.|||	103	0.0205671	0.0734	0.0072	5008	,	,		20653	0.0		0.001	False		,,,				2504	0.0				p.F124S		Atlas-SNP	.											.	CYP4F12	89	.	0			c.T371C						PASS	.	C	SER/PHE	125,4253		1,123,2065	133.0	138.0	136.0		371	-1.0	0.0	19	dbSNP_134	136	2,8586		0,2,4292	yes	missense	CYP4F12	NM_023944.3	155	1,125,6357	CC,CT,TT		0.0233,2.8552,0.9795	benign	124/525	15791081	127,12839	2189	4294	6483	SO:0001583	missense	66002	exon4			ATCTCTTCATCAG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.371T>C	19.37:g.15791081T>C	ENSP00000448998:p.Phe124Ser	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	374	93	0.248663	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	37	0.01694139194139194	34	0.06910569105691057	3	0.008287292817679558	0	0.0	0	0.0	.	3.728	-0.056179	0.07362	0.028552	2.33E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.70516	-0.49;-0.49	2.92	-1.0	0.10196	.	0.280349	0.26467	N	0.024209	T	0.08133	0.0203	N	0.17872	0.535	0.09310	N	1	B;P;B	0.34522	0.432;0.455;0.004	B;P;B	0.44811	0.344;0.461;0.091	T	0.20140	-1.0284	10	0.30078	T	0.28	.	4.0942	0.09983	0.1789:0.1265:0.0:0.6945	.	124;124;124	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	S	124	ENSP00000448998:F124S;ENSP00000321821:F124S	ENSP00000321821:F124S	F	+	2	0	CYP4F12	15652081	0.049000	0.20398	0.004000	0.12327	0.000000	0.00434	0.065000	0.14466	-0.503000	0.06586	-3.688000	0.00024	TTC	T|0.989;C|0.011	0.011	strong		0.572	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
EHHADH	1962	hgsc.bcm.edu	37	3	184910042	184910042	+	Missense_Mutation	SNP	A	A	G	rs11927618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184910042A>G	ENST00000231887.3	-	7	2219	c.2144T>C	c.(2143-2145)tTg>tCg	p.L715S	EHHADH-AS1_ENST00000417720.1_RNA|EHHADH_ENST00000456310.1_Missense_Mutation_p.L619S	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	715			L -> S (in dbSNP:rs11927618).		fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			GGAGCCTGCCAAGCTTTGCCA	0.438													A|||	136	0.0271565	0.0976	0.0086	5008	,	,		19259	0.0		0.001	False		,,,				2504	0.0				p.L715S		Atlas-SNP	.											.	EHHADH	73	.	0			c.T2144C						PASS	.	A	SER/LEU,SER/LEU	328,4078	169.1+/-199.8	18,292,1893	71.0	77.0	75.0		1856,2144	5.9	1.0	3	dbSNP_120	75	2,8598		0,2,4298	yes	missense,missense	EHHADH	NM_001166415.1,NM_001966.3	145,145	18,294,6191	GG,GA,AA		0.0233,7.4444,2.5373	possibly-damaging,possibly-damaging	619/628,715/724	184910042	330,12676	2203	4300	6503	SO:0001583	missense	1962	exon7			CCTGCCAAGCTTT	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"""enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"""	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.2144T>C	3.37:g.184910042A>G	ENSP00000231887:p.Leu715Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	42	0.019230769230769232	38	0.07723577235772358	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	14.60	2.584965	0.46110	0.074444	2.33E-4	ENSG00000113790	ENST00000231887;ENST00000456310	T;T	0.75050	-0.49;-0.9	5.91	5.91	0.95273	.	0.563402	0.17628	N	0.167493	T	0.06690	0.0171	N	0.14661	0.345	0.80722	D	1	P	0.48834	0.916	B	0.41988	0.372	T	0.16571	-1.0398	10	0.33940	T	0.23	-11.2071	11.1978	0.48724	0.8307:0.0:0.0:0.1693	rs11927618;rs11927618	715	Q08426	ECHP_HUMAN	S	715;619	ENSP00000231887:L715S;ENSP00000387746:L619S	ENSP00000231887:L715S	L	-	2	0	EHHADH	186392736	0.991000	0.36638	0.998000	0.56505	0.771000	0.43674	2.683000	0.46943	2.254000	0.74563	0.533000	0.62120	TTG	A|0.975;G|0.025	0.025	strong		0.438	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1		
FAM13A	10144	hgsc.bcm.edu	37	4	89653257	89653257	+	Silent	SNP	G	G	A	rs1801915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:89653257G>A	ENST00000264344.5	-	22	2946	c.2739C>T	c.(2737-2739)gaC>gaT	p.D913D	FAM13A_ENST00000508369.1_Silent_p.D587D|FAM13A-AS1_ENST00000500765.1_RNA|FAM13A_ENST00000395002.2_Silent_p.D559D|FAM13A_ENST00000511976.1_Silent_p.D499D|FAM13A_ENST00000503556.1_Silent_p.D573D|FAM13A_ENST00000513837.1_Silent_p.D559D	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	913					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(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						CTTCGAATTGGTCCAGAAAGC	0.458													G|||	987	0.197085	0.2042	0.1931	5008	,	,		1847	0.2321		0.1561	False		,,,				2504	0.1963				p.D913D		Atlas-SNP	.											.	FAM13A	181	.	0			c.C2739T						PASS	.	G	,	833,3573	329.3+/-301.0	77,679,1447	166.0	141.0	149.0		1761,2739	4.5	1.0	4	dbSNP_89	149	1261,7339	251.8+/-278.1	96,1069,3135	no	coding-synonymous,coding-synonymous	FAM13A	NM_001015045.1,NM_014883.2	,	173,1748,4582	AA,AG,GG		14.6628,18.906,16.1003	,	587/698,913/1024	89653257	2094,10912	2203	4300	6503	SO:0001819	synonymous_variant	10144	exon22			GAATTGGTCCAGA	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"""Rho GTPase activating proteins"""	19367	protein-coding gene	gene with protein product		613299	"""family with sequence similarity 13, member A1"""	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.2739C>T	4.37:g.89653257G>A		Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	254	116	0.456693	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Silent	SNP	ENST00000264344.5	37	CCDS34029.1																																																																																			G|0.831;A|0.169	0.169	strong		0.458	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
PTPN12	5782	hgsc.bcm.edu	37	7	77247821	77247821	+	Missense_Mutation	SNP	G	G	A	rs9640663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.	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	41	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	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		
PCSK9	255738	hgsc.bcm.edu	37	1	55523855	55523855	+	Missense_Mutation	SNP	G	G	A	rs28362263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55523855G>A	ENST00000302118.5	+	8	1617	c.1327G>A	c.(1327-1329)Gcc>Acc	p.A443T	PCSK9_ENST00000490692.1_3'UTR|PCSK9_ENST00000543384.1_Intron	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	443			A -> T (polymorphism associated with lower plasma levels of low-density lipoprotein cholesterol; more extensive cleavage by furin and PCSK5; dbSNP:rs28362263). {ECO:0000269|PubMed:16465619, ECO:0000269|Ref.4}.		apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						CCTGGTGGCCGCCCTGCCCCC	0.622													G|||	133	0.0265575	0.0961	0.0086	5008	,	,		17784	0.0		0.0	False		,,,				2504	0.0				p.A443T	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.G1327A						PASS	.	G	THR/ALA	369,4037	177.6+/-206.5	17,335,1851	37.0	37.0	37.0		1327	-6.2	0.1	1	dbSNP_125	37	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PCSK9	NM_174936.3	58	17,336,6150	AA,AG,GG		0.0116,8.3749,2.8448	benign	443/693	55523855	370,12636	2203	4300	6503	SO:0001583	missense	255738	exon8			GTGGCCGCCCTGC	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1327G>A	1.37:g.55523855G>A	ENSP00000303208:p.Ala443Thr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	168	91	0.541667	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	37	CCDS603.1	47	0.02152014652014652	45	0.09146341463414634	2	0.0055248618784530384	0	0.0	0	0.0	G	13.27	2.187335	0.38609	0.083749	1.16E-4	ENSG00000169174	ENST00000302118	T	0.70631	-0.5	4.72	-6.25	0.02039	Peptidase S8/S53, subtilisin/kexin/sedolisin (1);	0.470801	0.19105	N	0.122587	T	0.01730	0.0055	N	0.14661	0.345	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.03922	-1.0992	9	0.21540	T	0.41	-0.8697	4.4821	0.11773	0.2381:0.1019:0.5586:0.1015	rs28362263	443	Q8NBP7	PCSK9_HUMAN	T	443	ENSP00000303208:A443T	ENSP00000303208:A443T	A	+	1	0	PCSK9	55296443	0.001000	0.12720	0.065000	0.19835	0.846000	0.48090	0.968000	0.29357	-0.694000	0.05113	-0.311000	0.09066	GCC	G|0.975;A|0.025	0.025	strong		0.622	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
CAND2	23066	hgsc.bcm.edu	37	3	12848822	12848822	+	Missense_Mutation	SNP	T	T	C	rs11718898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:12848822T>C	ENST00000456430.2	+	3	271	c.230T>C	c.(229-231)gTc>gCc	p.V77A	CAND2_ENST00000466558.1_3'UTR|CAND2_ENST00000295989.5_Intron	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	77					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CCTCTGGTGGTCAAAGTGAAG	0.582													C|||	3002	0.599441	0.9735	0.5115	5008	,	,		19788	0.2907		0.7008	False		,,,				2504	0.3701				p.V77A	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.T230C						PASS	.	C	ALA/VAL,	1281,103		591,99,2	89.0	89.0	89.0		230,	3.8	1.0	3	dbSNP_120	89	2100,1082		695,710,186	yes	missense,intron	CAND2	NM_001162499.1,NM_012298.2	64,	1286,809,188	CC,CT,TT		34.0038,7.4422,25.9527	benign,	77/1237,	12848822	3381,1185	692	1591	2283	SO:0001583	missense	23066	exon3			TGGTGGTCAAAGT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.230T>C	3.37:g.12848822T>C	ENSP00000387641:p.Val77Ala	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	193	193	1	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1330	0.6089743589743589	471	0.9573170731707317	185	0.511049723756906	150	0.26223776223776224	524	0.6912928759894459	C	13.80	2.345690	0.41498	0.925578	0.659962	ENSG00000144712	ENST00000456430	T	0.64438	-0.1	5.63	3.85	0.44370	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999999998	B	0.02656	0.0	B	0.01281	0.0	T	0.34875	-0.9811	8	0.09843	T	0.71	-6.7597	5.7286	0.18026	0.0764:0.1413:0.6371:0.1452	rs11718898;rs17773733;rs56779280;rs11718898	77	O75155	CAND2_HUMAN	A	77	ENSP00000387641:V77A	ENSP00000387641:V77A	V	+	2	0	CAND2	12823822	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	5.661000	0.68025	0.763000	0.33175	-0.936000	0.02699	GTC	C|0.622;N|0.000	0.622	strong		0.582	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
PRSS38	339501	hgsc.bcm.edu	37	1	228003843	228003843	+	Silent	SNP	C	C	T	rs113353225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228003843C>T	ENST00000366757.3	+	2	225	c.201C>T	c.(199-201)ccC>ccT	p.P67P		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	67	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						TCCCTGCGCCCGAGAGGAAGT	0.672													C|||	73	0.0145767	0.0537	0.0029	5008	,	,		14096	0.0		0.0	False		,,,				2504	0.0				p.P67P		Atlas-SNP	.											.	PRSS38	55	.	0			c.C201T						PASS	.	C		279,4127	151.8+/-185.6	4,271,1928	67.0	75.0	73.0		201	-8.3	0.0	1	dbSNP_132	73	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PRSS38	NM_183062.2		4,272,6226	TT,TC,CC		0.0116,6.3323,2.1532		67/327	228003843	280,12724	2203	4299	6502	SO:0001819	synonymous_variant	339501	exon2			TGCGCCCGAGAGG		CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"""Serine peptidases / Serine peptidases"""	29625	protein-coding gene	gene with protein product	"""marapsin 2"""					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.201C>T	1.37:g.228003843C>T		Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	246	139	0.565041	NM_183062	Q7RTY6	Silent	SNP	ENST00000366757.3	37	CCDS1563.1																																																																																			C|0.982;T|0.018	0.018	strong		0.672	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062	
AHCTF1	25909	hgsc.bcm.edu	37	1	247013203	247013203	+	Silent	SNP	G	G	A	rs41308156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247013203G>A	ENST00000391829.2	-	33	6228	c.6105C>T	c.(6103-6105)aaC>aaT	p.N2035N	AHCTF1_ENST00000366508.1_Silent_p.N2070N|AHCTF1_ENST00000326225.3_Silent_p.N2044N|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	2035	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				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)			AAAGTTCCTCGTTTGGCACTA	0.383													G|||	221	0.0441294	0.1641	0.0058	5008	,	,		19777	0.0		0.0	False		,,,				2504	0.0				p.N2044N	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.C6132T						PASS	.	G		555,3851	241.8+/-252.1	29,497,1677	59.0	60.0	60.0		6132	0.8	0.9	1	dbSNP_127	60	5,8589	4.3+/-15.6	0,5,4292	no	coding-synonymous	AHCTF1	NM_015446.4		29,502,5969	AA,AG,GG		0.0582,12.5965,4.3077		2044/2276	247013203	560,12440	2203	4297	6500	SO:0001819	synonymous_variant	25909	exon33			TTCCTCGTTTGGC		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.6105C>T	1.37:g.247013203G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	231	101	0.437229	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	37																																																																																				.	.	weak		0.383	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
ECT2L	345930	hgsc.bcm.edu	37	6	139170412	139170412	+	Missense_Mutation	SNP	A	A	G	rs75962473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139170412A>G	ENST00000423192.1	+	8	1071	c.910A>G	c.(910-912)Atg>Gtg	p.M304V	ECT2L_ENST00000541398.1_Missense_Mutation_p.M235V|ECT2L_ENST00000367682.2_Missense_Mutation_p.M304V			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	304							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						CCAGATGGTGATGGAGAGTGT	0.398			"""N, Splice, Mis"""		ETP ALL								G|||	67	0.0133786	0.0477	0.0058	5008	,	,		15878	0.0		0.0	False		,,,				2504	0.0				p.M304V		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A910G						PASS	.	G	VAL/MET,VAL/MET	132,3612		4,124,1744	213.0	193.0	199.0		910,910	3.8	0.7	6	dbSNP_131	199	4,8222		0,4,4109	yes	missense,missense	ECT2L	NM_001077706.2,NM_001195037.2	21,21	4,128,5853	GG,GA,AA		0.0486,3.5256,1.1362	benign,benign	304/905,304/905	139170412	136,11834	1872	4113	5985	SO:0001583	missense	345930	exon8			ATGGTGATGGAGA		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"""Rho guanine nucleotide exchange factors"", ""F-boxes /  ""other"""""	21118	protein-coding gene	gene with protein product	"""lung specific F-box and DH domain containing protein"", ""F-box protein 49"""		"""chromosome 6 open reading frame 91"", ""epithelial cell transforming sequence 2 oncogene-like"""	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.910A>G	6.37:g.139170412A>G	ENSP00000387388:p.Met304Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	37	CCDS43508.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	G	0.004	-2.271576	0.00257	0.035256	4.86E-4	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	T;T;T	0.72942	0.41;0.41;-0.7	5.6	3.8	0.43715	.	1.849090	0.04925	N	0.455693	T	0.14056	0.0340	N	0.01109	-1.01	0.19300	N	0.999979	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34950	-0.9808	10	0.02654	T	1	-0.0057	7.1142	0.25407	0.1538:0.1408:0.7055:0.0	.	235;304	F5H7S9;Q008S8	.;ECT2L_HUMAN	V	304;304;235	ENSP00000387388:M304V;ENSP00000356655:M304V;ENSP00000442307:M235V	ENSP00000356655:M304V	M	+	1	0	ECT2L	139212105	1.000000	0.71417	0.718000	0.30602	0.010000	0.07245	0.951000	0.29135	0.406000	0.25560	-0.186000	0.12905	ATG	A|0.992;G|0.008	0.008	strong		0.398	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	
IVL	3713	hgsc.bcm.edu	37	1	152882610	152882610	+	Missense_Mutation	SNP	A	A	G	rs2229496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152882610A>G	ENST00000368764.3	+	2	401	c.337A>G	c.(337-339)Aca>Gca	p.T113A	IVL_ENST00000392667.2_5'UTR			P07476	INVO_HUMAN	involucrin	113			T -> A (in dbSNP:rs2229496).		isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCAGGAGAAAACACAAAGGGA	0.493													G|||	2072	0.413738	0.6808	0.2997	5008	,	,		21641	0.5615		0.1083	False		,,,				2504	0.2955				p.T113A		Atlas-SNP	.											.	IVL	100	.	0			c.A337G						PASS	.	G	ALA/THR	2534,1872	542.0+/-375.9	740,1054,409	57.0	60.0	59.0		337	-0.6	0.0	1	dbSNP_98	59	789,7811	783.7+/-407.6	38,713,3549	yes	missense	IVL	NM_005547.2	58	778,1767,3958	GG,GA,AA		9.1744,42.4875,25.5497	benign	113/586	152882610	3323,9683	2203	4300	6503	SO:0001583	missense	3713	exon2			GAGAAAACACAAA	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.337A>G	1.37:g.152882610A>G	ENSP00000357753:p.Thr113Ala	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	856	0.39194139194139194	342	0.6951219512195121	101	0.27900552486187846	333	0.5821678321678322	80	0.10554089709762533	G	0.819	-0.749185	0.03065	0.575125	0.091744	ENSG00000163207	ENST00000368764	T	0.06849	3.25	3.65	-0.585	0.11698	.	.	.	.	.	T	0.00637	0.0021	N	0.02539	-0.55	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44982	-0.9292	8	0.08381	T	0.77	.	4.9328	0.13926	0.51:0.164:0.326:0.0	rs2229496;rs2339485;rs59054145;rs2229496	113	P07476	INVO_HUMAN	A	113	ENSP00000357753:T113A	ENSP00000357753:T113A	T	+	1	0	IVL	151149234	0.000000	0.05858	0.000000	0.03702	0.189000	0.23516	-0.796000	0.04575	-0.530000	0.06349	-0.441000	0.05720	ACA	A|0.668;G|0.332	0.332	strong		0.493	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
KRTAP24-1	643803	hgsc.bcm.edu	37	21	31654809	31654809	+	Missense_Mutation	SNP	C	C	T	rs77638540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31654809C>T	ENST00000340345.4	-	1	467	c.442G>A	c.(442-444)Ggt>Agt	p.G148S		NM_001085455.1	NP_001078924.1	Q3LI83	KR241_HUMAN	keratin associated protein 24-1	148						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|large_intestine(3)|lung(7)|urinary_tract(3)	14						CAGTTGGAACCGTTGCGGAGG	0.483													C|||	358	0.0714856	0.1513	0.0389	5008	,	,		20814	0.0069		0.0368	False		,,,				2504	0.089				p.G148S		Atlas-SNP	.											.	KRTAP24-1	44	.	0			c.G442A						PASS	.	C	SER/GLY	450,3458		23,404,1527	126.0	127.0	127.0		442	0.9	0.0	21	dbSNP_131	127	331,7989		9,313,3838	yes	missense	KRTAP24-1	NM_001085455.1	56	32,717,5365	TT,TC,CC		3.9784,11.5148,6.387	benign	148/255	31654809	781,11447	1954	4160	6114	SO:0001583	missense	643803	exon1			TGGAACCGTTGCG	AB096935	CCDS42915.1	21q22.11	2007-11-23			ENSG00000188694	ENSG00000188694		"""Keratin associated proteins"""	33902	protein-coding gene	gene with protein product							Standard	NM_001085455		Approved	KAP24.1	uc002ynv.3	Q3LI83	OTTHUMG00000125483	ENST00000340345.4:c.442G>A	21.37:g.31654809C>T	ENSP00000339238:p.Gly148Ser	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	172	86	0.5	NM_001085455	Q1XDX0	Missense_Mutation	SNP	ENST00000340345.4	37	CCDS42915.1	114	0.0521978021978022	68	0.13821138211382114	17	0.04696132596685083	3	0.005244755244755245	26	0.03430079155672823	C	11.26	1.587728	0.28268	0.115148	0.039784	ENSG00000188694	ENST00000340345	T	0.03607	3.87	4.96	0.877	0.19145	.	0.655352	0.12549	N	0.459217	T	0.00039	0.0001	L	0.57536	1.79	0.09310	N	1	P	0.52316	0.952	B	0.43225	0.412	T	0.34403	-0.9830	10	0.11794	T	0.64	-0.8583	2.2788	0.04109	0.1556:0.5163:0.1511:0.1771	.	148	Q3LI83	KR241_HUMAN	S	148	ENSP00000339238:G148S	ENSP00000339238:G148S	G	-	1	0	KRTAP24-1	30576680	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.057000	0.14279	0.034000	0.15491	-0.218000	0.12543	GGT	C|0.951;T|0.049	0.049	strong		0.483	KRTAP24-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246806.2	NM_001085455	
NOL8	55035	hgsc.bcm.edu	37	9	95081569	95081569	+	Silent	SNP	T	T	C	rs16908298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95081569T>C	ENST00000535387.1	-	4	350	c.351A>G	c.(349-351)ttA>ttG	p.L117L	NOL8_ENST00000545558.1_Silent_p.L117L|NOL8_ENST00000543985.1_5'Flank|NOL8_ENST00000358855.4_Silent_p.L49L|NOL8_ENST00000542053.1_Silent_p.L49L|NOL8_ENST00000442668.2_Silent_p.L117L					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						CTGTCTTTTCTAACAAGTTGG	0.428													T|||	166	0.033147	0.1172	0.0159	5008	,	,		20037	0.0		0.0	False		,,,				2504	0.0				p.L117L		Atlas-SNP	.											.	NOL8	118	.	0			c.A351G						PASS	.	T		382,3474		15,352,1561	183.0	167.0	172.0		351	-3.3	0.0	9	dbSNP_123	172	9,8229		0,9,4110	no	coding-synonymous	NOL8	NM_017948.5		15,361,5671	CC,CT,TT		0.1092,9.9066,3.233		117/1168	95081569	391,11703	1928	4119	6047	SO:0001819	synonymous_variant	55035	exon5			CTTTTCTAACAAG	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.351A>G	9.37:g.95081569T>C		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	241	156	0.647303	NM_017948		Silent	SNP	ENST00000535387.1	37	CCDS47993.1																																																																																			T|0.969;C|0.031	0.031	strong		0.428	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144856852	144856852	+	Silent	SNP	C	C	T	rs377520030		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144856852C>T	ENST00000369354.3	-	40	6822	c.6633G>A	c.(6631-6633)gcG>gcA	p.A2211A	PDE4DIP_ENST00000369356.4_Silent_p.A2211A|PDE4DIP_ENST00000313382.9_Silent_p.A2105A|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000530740.1_Silent_p.A2296A|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369359.4_Silent_p.A2347A			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2211					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)	p.A2211A(1)		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)		GGAAGCTGCACGCTGATCTCA	0.502			T	PDGFRB	MPD																																p.A2211A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,NS,carcinoma,-1,3	PDE4DIP	817	3	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G6633A						PASS	.						39.0	31.0	34.0					1																	144856852		2199	4286	6485	SO:0001819	synonymous_variant	9659	exon40			GCTGCACGCTGAT	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.6633G>A	1.37:g.144856852C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	222	51	0.22973	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	.	5.637	0.302253	0.10678	.	.	ENSG00000178104	ENST00000530130	.	.	.	4.52	-1.01	0.10169	.	.	.	.	.	T	0.12263	0.0298	.	.	.	0.32646	N	0.519982	.	.	.	.	.	.	T	0.19745	-1.0296	4	.	.	.	.	1.5392	0.02551	0.1278:0.2204:0.3685:0.2833	.	.	.	.	H	288	.	.	R	-	2	0	PDE4DIP	143568209	0.000000	0.05858	0.052000	0.19188	0.068000	0.16541	-1.120000	0.03273	0.239000	0.21243	-0.693000	0.03709	CGT	.	.	none		0.502	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
VWDE	221806	hgsc.bcm.edu	37	7	12401021	12401021	+	Missense_Mutation	SNP	C	C	T	rs80272295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12401021C>T	ENST00000275358.3	-	14	3213	c.3025G>A	c.(3025-3027)Ggg>Agg	p.G1009R		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1009						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						GTTGGTTTCCCACCCACCAGA	0.368													C|||	539	0.107628	0.0408	0.0764	5008	,	,		15191	0.1925		0.1044	False		,,,				2504	0.136				p.G1009R		Atlas-SNP	.											.	VWDE	123	.	0			c.G3025A						PASS	.	C	ARG/GLY	66,1318		1,64,627	66.0	58.0	60.0		3025	0.8	0.0	7	dbSNP_131	60	363,2819		21,321,1249	yes	missense	VWDE	NM_001135924.1	125	22,385,1876	TT,TC,CC		11.4079,4.7688,9.3955	benign	1009/1591	12401021	429,4137	692	1591	2283	SO:0001583	missense	221806	exon14			GTTTCCCACCCAC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.3025G>A	7.37:g.12401021C>T	ENSP00000275358:p.Gly1009Arg	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	128	55	0.429688	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	268	0.1227106227106227	20	0.04065040650406504	28	0.07734806629834254	133	0.23251748251748253	87	0.11477572559366754	C	5.212	0.224656	0.09916	0.047688	0.114079	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.82711	-1.64	3.95	0.825	0.18824	.	0.679487	0.14045	N	0.345153	T	0.00073	0.0002	L	0.39898	1.24	0.52099	P	5.500000000002725E-5	B	0.23735	0.09	B	0.21360	0.034	T	0.07849	-1.0751	9	0.49607	T	0.09	.	9.2882	0.37771	0.0:0.6482:0.2713:0.0805	.	1009	Q8N2E2	VWDE_HUMAN	R	1009;463	ENSP00000275358:G1009R	ENSP00000275358:G1009R	G	-	1	0	VWDE	12367546	0.871000	0.30034	0.028000	0.17463	0.052000	0.14988	4.286000	0.58995	0.426000	0.26116	0.655000	0.94253	GGG	C|0.885;T|0.115	0.115	strong		0.368	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414316	105414316	+	Missense_Mutation	SNP	G	G	A	rs145541349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105414316G>A	ENST00000333244.5	-	7	7591	c.7472C>T	c.(7471-7473)cCg>cTg	p.P2491L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2491						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)			CCCGAATGACGGCATCTTGAA	0.612													.|||	100	0.0199681	0.0741	0.0029	5008	,	,		18046	0.0		0.0	False		,,,				2504	0.0				p.P2491L		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,+1,2	AHNAK2	719	2	0			c.C7472T						scavenged	.	G	LEU/PRO	217,3819		11,195,1812	175.0	202.0	193.0		7472	3.7	0.8	14	dbSNP_134	193	0,8354		0,0,4177	no	missense	AHNAK2	NM_138420.2	98	11,195,5989	AA,AG,GG		0.0,5.3766,1.7514	probably-damaging	2491/5796	105414316	217,12173	2018	4177	6195	SO:0001583	missense	113146	exon7			AATGACGGCATCT	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.7472C>T	14.37:g.105414316G>A	ENSP00000353114:p.Pro2491Leu	Somatic	303	2	0.00660066		WXS	Illumina HiSeq	Phase_I	259	128	0.494208	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	31	0.014194139194139194	31	0.06300813008130081	0	0.0	0	0.0	0	0.0	g	16.25	3.069305	0.55539	0.053766	0.0	ENSG00000185567	ENST00000333244	T	0.03212	4.01	3.74	3.74	0.42951	.	.	.	.	.	T	0.03011	0.0089	H	0.95328	3.655	0.48632	D	0.999681	D	0.89917	1.0	D	0.97110	1.0	T	0.13469	-1.0508	9	0.42905	T	0.14	.	15.5871	0.76491	0.0:0.0:1.0:0.0	.	2491	Q8IVF2	AHNK2_HUMAN	L	2491	ENSP00000353114:P2491L	ENSP00000353114:P2491L	P	-	2	0	AHNAK2	104485361	0.998000	0.40836	0.839000	0.33178	0.181000	0.23173	3.089000	0.50183	1.642000	0.50584	0.485000	0.47835	CCG	G|0.988;A|0.012	0.012	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
RFX7	64864	hgsc.bcm.edu	37	15	56388033	56388033	+	Silent	SNP	T	T	C	rs12439907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56388033T>C	ENST00000559447.2	-	9	1873	c.1602A>G	c.(1600-1602)ttA>ttG	p.L534L	RFX7_ENST00000317318.6_Silent_p.L631L|RFX7_ENST00000422057.1_Silent_p.L534L|RFX7_ENST00000423270.1_Silent_p.L631L			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	534					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TGGTGAAAGTTAAGTTCTGAG	0.418													T|||	1364	0.272364	0.0794	0.2767	5008	,	,		23220	0.5		0.1968	False		,,,				2504	0.3732				p.L631L		Atlas-SNP	.											.	RFX7	170	.	0			c.A1893G						PASS	.	T		459,3521		27,405,1558	81.0	79.0	79.0		1893	0.1	1.0	15	dbSNP_120	79	1733,6607		179,1375,2616	no	coding-synonymous	RFX7	NM_022841.5		206,1780,4174	CC,CT,TT		20.7794,11.5327,17.7922		631/1461	56388033	2192,10128	1990	4170	6160	SO:0001819	synonymous_variant	64864	exon9			GAAAGTTAAGTTC			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.1602A>G	15.37:g.56388033T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																				T|0.747;C|0.253	0.253	strong		0.418	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
NEURL4	84461	hgsc.bcm.edu	37	17	7221454	7221454	+	Silent	SNP	G	G	A	rs73239601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7221454G>A	ENST00000399464.2	-	25	4005	c.3990C>T	c.(3988-3990)gcC>gcT	p.A1330A	NEURL4_ENST00000570460.1_Silent_p.A1306A|NEURL4_ENST00000574120.1_5'UTR|GPS2_ENST00000391950.3_5'Flank|NEURL4_ENST00000315614.7_Silent_p.A1328A|GPS2_ENST00000380728.2_5'Flank|RP11-542C16.2_ENST00000575474.1_Missense_Mutation_p.P144L|GPS2_ENST00000389167.5_5'Flank	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1330						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						GAGGACTAGCGGCAGGTGGTG	0.592													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18299	0.0		0.0	False		,,,				2504	0.0				p.A1330A		Atlas-SNP	.											.	NEURL4	192	.	0			c.C3990T						PASS	.	G	,	22,4102		0,22,2040	82.0	93.0	89.0		3984,3990	1.4	0.1	17	dbSNP_130	89	1,8389		0,1,4194	no	coding-synonymous,coding-synonymous	NEURL4	NM_001005408.1,NM_032442.2	,	0,23,6234	AA,AG,GG		0.0119,0.5335,0.1838	,	1328/1561,1330/1563	7221454	23,12491	2062	4195	6257	SO:0001819	synonymous_variant	84461	exon25			ACTAGCGGCAGGT		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.3990C>T	17.37:g.7221454G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Silent	SNP	ENST00000399464.2	37	CCDS42251.1																																																																																			G|0.999;A|0.001	0.001	strong		0.592	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	
FSTL4	23105	hgsc.bcm.edu	37	5	132535225	132535225	+	Silent	SNP	G	G	A	rs61740558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132535225G>A	ENST00000265342.7	-	16	2340	c.2091C>T	c.(2089-2091)gaC>gaT	p.D697D	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	697						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.D697D(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGAAGCGCCCGTCGGGGGATG	0.607													G|||	110	0.0219649	0.0772	0.0115	5008	,	,		18282	0.0		0.0	False		,,,				2504	0.0				p.D697D		Atlas-SNP	.											FSTL4,colon,carcinoma,0,2	FSTL4	74	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C2091T						PASS	.	G		270,4136	151.8+/-185.6	9,252,1942	49.0	52.0	51.0		2091	-4.1	0.6	5	dbSNP_129	51	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	FSTL4	NM_015082.1		9,258,6236	AA,AG,GG		0.0698,6.128,2.1221		697/843	132535225	276,12730	2203	4300	6503	SO:0001819	synonymous_variant	23105	exon16			GCGCCCGTCGGGG	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.2091C>T	5.37:g.132535225G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	68	0.576271	NM_015082	Q8TBU0|Q9UPU1	Silent	SNP	ENST00000265342.7	37	CCDS34238.1																																																																																			G|0.980;A|0.020	0.020	strong		0.607	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
FLG	2312	hgsc.bcm.edu	37	1	152280907	152280907	+	Missense_Mutation	SNP	G	G	T	rs77249082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152280907G>T	ENST00000368799.1	-	3	6490	c.6455C>A	c.(6454-6456)tCc>tAc	p.S2152Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2152	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)			CTCTTGGTGGGACCCCTGTCT	0.587									Ichthyosis																												p.S2152Y		Atlas-SNP	.											.	FLG	900	.	0			c.C6455A						PASS	.	G	TYR/SER	1189,3217		0,1189,1014	385.0	319.0	341.0		6455	1.0	0.0	1	dbSNP_131	341	14,8586		0,14,4286	no	missense	FLG	NM_002016.1	144	0,1203,5300	TT,TG,GG		0.1628,26.9859,9.2496	probably-damaging	2152/4062	152280907	1203,11803	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGTGGGACCCCT	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.6455C>A	1.37:g.152280907G>T	ENSP00000357789:p.Ser2152Tyr	Somatic	462	2	0.004329		WXS	Illumina HiSeq	Phase_I	820	371	0.452439	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	4.230	0.041569	0.08196	0.269859	0.001628	ENSG00000143631	ENST00000368799	T	0.03801	3.8	3.02	1.01	0.19927	.	.	.	.	.	T	0.03651	0.0104	L	0.55103	1.725	0.09310	N	1	D	0.59357	0.985	P	0.56278	0.795	T	0.36040	-0.9764	9	0.39692	T	0.17	.	4.3236	0.11029	0.1405:0.2356:0.6239:0.0	.	2152	P20930	FILA_HUMAN	Y	2152	ENSP00000357789:S2152Y	ENSP00000357789:S2152Y	S	-	2	0	FLG	150547531	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.014000	0.03641	0.122000	0.18314	0.485000	0.47835	TCC	G|0.500;T|0.500	0.500	strong		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SCN4A	6329	hgsc.bcm.edu	37	17	62018239	62018239	+	Silent	SNP	G	G	A	rs2227907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62018239G>A	ENST00000435607.1	-	24	5479	c.5403C>T	c.(5401-5403)gcC>gcT	p.A1801A	SCN4A_ENST00000578147.1_Silent_p.A1801A	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1801					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)	TAGTGGGTCCGGCGTCCCCTG	0.657													G|||	686	0.136981	0.497	0.0317	5008	,	,		17192	0.002		0.002	False		,,,				2504	0.0031				p.A1801A		Atlas-SNP	.											.	SCN4A	205	.	0			c.C5403T						PASS	.	G		1555,2615		295,965,825	34.0	41.0	39.0		5403	-9.2	0.0	17	dbSNP_98	39	14,8368		0,14,4177	no	coding-synonymous	SCN4A	NM_000334.4		295,979,5002	AA,AG,GG		0.167,37.2902,12.5		1801/1837	62018239	1569,10983	2085	4191	6276	SO:0001819	synonymous_variant	6329	exon24			GGGTCCGGCGTCC	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.5403C>T	17.37:g.62018239G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	112	110	0.982143	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			G|0.844;A|0.156	0.156	strong		0.657	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
RAB17	64284	hgsc.bcm.edu	37	2	238494681	238494681	+	Silent	SNP	G	G	A	rs34052613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	209	0	0		WXS	Illumina HiSeq	Phase_I	222	122	0.54955	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		
WDR90	197335	hgsc.bcm.edu	37	16	716287	716287	+	Silent	SNP	C	C	A	rs9934288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:716287C>A	ENST00000293879.4	+	37	4677	c.4677C>A	c.(4675-4677)acC>acA	p.T1559T	WDR90_ENST00000315764.4_Silent_p.T158T|WDR90_ENST00000549091.1_Silent_p.T1561T|WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000547944.1_Silent_p.T158T|RHOT2_ENST00000315082.4_5'Flank			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1559										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CAGGGACAACCTTCCGTGTGC	0.627													C|||	834	0.166534	0.1815	0.1412	5008	,	,		18634	0.3065		0.0765	False		,,,				2504	0.1125				p.T1559T		Atlas-SNP	.											.	WDR90	107	.	0			c.C4677A						PASS	.	C		611,3449		42,527,1461	46.0	55.0	52.0		4677	-1.2	0.3	16	dbSNP_119	52	741,7613		27,687,3463	no	coding-synonymous	WDR90	NM_145294.4		69,1214,4924	AA,AC,CC		8.87,15.0493,10.8909		1559/1749	716287	1352,11062	2030	4177	6207	SO:0001819	synonymous_variant	197335	exon37			GACAACCTTCCGT	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.4677C>A	16.37:g.716287C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			C|0.854;A|0.146	0.146	strong		0.627	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
BCL2A1	597	hgsc.bcm.edu	37	15	80263406	80263406	+	Missense_Mutation	SNP	C	C	T	rs1138357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80263406C>T	ENST00000267953.3	-	1	382	c.56G>A	c.(55-57)tGc>tAc	p.C19Y	BCL2A1_ENST00000335661.6_Missense_Mutation_p.C19Y	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	19			C -> Y (in dbSNP:rs1138357). {ECO:0000269|Ref.6}.		extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						CTGTAGGACGCACTGCAGATA	0.463													T|||	1763	0.352037	0.2572	0.2767	5008	,	,		20116	0.5367		0.2565	False		,,,				2504	0.4417				p.C19Y		Atlas-SNP	.											.	BCL2A1	28	.	0			c.G56A						PASS	.	T	TYR/CYS,TYR/CYS	1063,3343	723.6+/-409.4	115,833,1255	93.0	85.0	88.0		56,56	1.9	0.0	15	dbSNP_86	88	2210,6390	710.7+/-405.8	263,1684,2353	yes	missense,missense	BCL2A1	NM_001114735.1,NM_004049.3	194,194	378,2517,3608	TT,TC,CC		25.6977,24.1262,25.1653	benign,benign	19/164,19/176	80263406	3273,9733	2203	4300	6503	SO:0001583	missense	597	exon1			AGGACGCACTGCA		CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.56G>A	15.37:g.80263406C>T	ENSP00000267953:p.Cys19Tyr	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	171	75	0.438596	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	733	0.3356227106227106	114	0.23170731707317074	117	0.32320441988950277	311	0.5437062937062938	191	0.2519788918205805	T	0.042	-1.282248	0.01398	0.241262	0.256977	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.16597	2.33;2.33	5.63	1.93	0.25924	.	1.078550	0.07069	N	0.835026	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46456	-0.9190	9	0.02654	T	1	-10.7493	4.1144	0.10074	0.2557:0.1385:0.0:0.6058	rs1138357;rs2070264;rs3202145;rs3743425;rs16971625;rs52797061;rs61411122;rs1138357	19;19	Q86W13;Q16548	.;B2LA1_HUMAN	Y	19	ENSP00000267953:C19Y;ENSP00000335250:C19Y	ENSP00000267953:C19Y	C	-	2	0	BCL2A1	78050461	0.007000	0.16637	0.000000	0.03702	0.002000	0.02628	1.334000	0.33827	-0.156000	0.11079	-1.170000	0.01741	TGC	C|0.708;T|0.292	0.292	strong		0.463	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049	
CHST5	23563	hgsc.bcm.edu	37	16	75564172	75564172	+	Silent	SNP	C	C	G	rs74355367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75564172C>G	ENST00000336257.3	-	3	1505	c.111G>C	c.(109-111)ctG>ctC	p.L37L	CHST5_ENST00000541075.1_Silent_p.L43L|RP11-77K12.7_ENST00000460606.1_3'UTR	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	37					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)	24						TGGTCTGTGCCAGGAGGAGCA	0.672													C|||	193	0.0385383	0.1422	0.0072	5008	,	,		17477	0.0		0.0	False		,,,				2504	0.0				p.L37L		Atlas-SNP	.											.	CHST5	47	.	0			c.G111C						PASS	.	C		537,3859	225.9+/-241.6	27,483,1688	32.0	28.0	29.0		111	1.1	1.0	16	dbSNP_131	29	16,8582	9.1+/-34.3	0,16,4283	no	coding-synonymous	CHST5	NM_024533.4		27,499,5971	GG,GC,CC		0.1861,12.2157,4.2558		37/412	75564172	553,12441	2198	4299	6497	SO:0001819	synonymous_variant	23563	exon3			CTGTGCCAGGAGG	AF176839	CCDS10919.1	16q23.1	2008-02-05			ENSG00000135702	ENSG00000135702		"""Sulfotransferases, membrane-bound"""	1973	protein-coding gene	gene with protein product		604817				10491328, 11017086	Standard	NM_024533		Approved	I-GLCNAC-6-ST, FLJ22167	uc002fei.3	Q9GZS9	OTTHUMG00000137610	ENST00000336257.3:c.111G>C	16.37:g.75564172C>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Silent	SNP	ENST00000336257.3	37	CCDS10919.1																																																																																			C|0.955;G|0.045	0.045	strong		0.672	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126	
ZNF554	115196	hgsc.bcm.edu	37	19	2823100	2823100	+	Missense_Mutation	SNP	G	G	A	rs181024964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2823100G>A	ENST00000317243.5	+	2	314	c.116G>A	c.(115-117)cGc>cAc	p.R39H	ZNF554_ENST00000591265.1_Missense_Mutation_p.R39H	NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	39					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TACCTGCCCCGCTGGTCCCAG	0.567													G|||	7	0.00139776	0.0045	0.0	5008	,	,		18086	0.001		0.0	False		,,,				2504	0.0				p.R39H		Atlas-SNP	.											.	ZNF554	47	.	0			c.G116A						PASS	.	G	HIS/ARG	7,3795		0,7,1894	51.0	55.0	54.0		116	0.6	0.0	19		54	0,8248		0,0,4124	yes	missense	ZNF554	NM_001102651.1	29	0,7,6018	AA,AG,GG		0.0,0.1841,0.0581	possibly-damaging	39/539	2823100	7,12043	1901	4124	6025	SO:0001583	missense	115196	exon2			TGCCCCGCTGGTC	AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"""Zinc fingers, C2H2-type"", ""-"""	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.116G>A	19.37:g.2823100G>A	ENSP00000321132:p.Arg39His	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_001102651	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	5	0.0022893772893772895	3	0.006097560975609756	0	0.0	2	0.0034965034965034965	0	0.0	G	6.811	0.518786	0.13005	0.001841	0.0	ENSG00000172006	ENST00000317243	T	0.07021	3.23	1.71	0.624	0.17659	Krueppel-associated box (1);	.	.	.	.	T	0.02267	0.0070	N	0.08118	0	0.09310	N	1	P	0.35050	0.482	B	0.24974	0.057	T	0.40813	-0.9543	9	0.56958	D	0.05	.	5.8806	0.18854	0.0:0.6302:0.3698:0.0	.	39	Q86TJ5	ZN554_HUMAN	H	39	ENSP00000321132:R39H	ENSP00000321132:R39H	R	+	2	0	ZNF554	2774100	0.000000	0.05858	0.041000	0.18516	0.029000	0.11900	-0.244000	0.08903	0.276000	0.22118	-0.502000	0.04539	CGC	G|0.998;A|0.002	0.002	strong		0.567	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303	
PALLD	23022	hgsc.bcm.edu	37	4	169611765	169611765	+	Silent	SNP	C	C	T	rs17054482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169611765C>T	ENST00000505667.1	+	7	1520	c.1347C>T	c.(1345-1347)aaC>aaT	p.N449N	PALLD_ENST00000335742.7_Silent_p.N67N|PALLD_ENST00000333488.4_Silent_p.N326N|PALLD_ENST00000261509.6_Silent_p.N449N|PALLD_ENST00000512127.1_Silent_p.N67N			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	449	Ig-like C2-type 2.				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)		AACTGCAAAACACAGCCGTGG	0.498									Pancreatic Cancer, Familial Clustering of				c|||	210	0.0419329	0.1498	0.0159	5008	,	,		17440	0.0		0.001	False		,,,				2504	0.0				p.N449N	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C1347T						PASS	.	T	,,	570,3836	251.8+/-258.4	41,488,1674	80.0	94.0	90.0		1347,201,1347	3.2	0.9	4	dbSNP_123	90	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_001166109.1,NM_016081.3	,,	41,496,5966	TT,TC,CC		0.093,12.9369,4.4441	,,	449/1124,67/778,449/1107	169611765	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon7	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GCAAAACACAGCC	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.1347C>T	4.37:g.169611765C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			C|0.962;T|0.038	0.038	strong		0.498	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
ABCA7	10347	hgsc.bcm.edu	37	19	1058635	1058635	+	Missense_Mutation	SNP	C	C	T	rs73505232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1058635C>T	ENST00000263094.6	+	38	5399	c.5168C>T	c.(5167-5169)tCa>tTa	p.S1723L	ABCA7_ENST00000433129.1_Missense_Mutation_p.S1723L|ABCA7_ENST00000435683.2_Missense_Mutation_p.S1585L	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1723					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)		CAGTTCCAGTCACCCCTGCGC	0.552													C|||	196	0.0391374	0.143	0.0101	5008	,	,		17265	0.0		0.0	False		,,,				2504	0.0				p.S1723L		Atlas-SNP	.											.	ABCA7	174	.	0			c.C5168T						PASS	.	C	LEU/SER	578,3828	256.1+/-261.0	45,488,1670	60.0	62.0	61.0		5168	4.2	1.0	19	dbSNP_130	61	0,8600		0,0,4300	yes	missense	ABCA7	NM_019112.3	145	45,488,5970	TT,TC,CC		0.0,13.1185,4.4441	probably-damaging	1723/2147	1058635	578,12428	2203	4300	6503	SO:0001583	missense	10347	exon38			TCCAGTCACCCCT	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.5168C>T	19.37:g.1058635C>T	ENSP00000263094:p.Ser1723Leu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	79	0.036172161172161175	74	0.15040650406504066	5	0.013812154696132596	0	0.0	0	0.0	C	20.3	3.973946	0.74246	0.131185	0.0	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.87650	-2.28;-2.28	4.23	4.23	0.50019	.	.	.	.	.	T	0.09730	0.0239	M	0.88450	2.955	0.28999	N	0.887598	P;D	0.61697	0.899;0.99	P;D	0.67103	0.735;0.949	T	0.35599	-0.9782	9	0.87932	D	0	.	15.318	0.74095	0.0:1.0:0.0:0.0	.	848;1723	D6W5Y0;Q8IZY2	.;ABCA7_HUMAN	L	1723	ENSP00000263094:S1723L;ENSP00000414062:S1723L	ENSP00000263094:S1723L	S	+	2	0	ABCA7	1009635	0.985000	0.35326	0.982000	0.44146	0.997000	0.91878	2.532000	0.45659	2.180000	0.69256	0.561000	0.74099	TCA	C|0.952;T|0.048	0.048	strong		0.552	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
ARPC1B	10095	hgsc.bcm.edu	37	7	98984354	98984354	+	Missense_Mutation	SNP	G	G	C	rs1045012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:98984354G>C	ENST00000451682.1	+	5	420	c.111G>C	c.(109-111)aaG>aaC	p.K37N	ARPC1B_ENST00000474880.1_3'UTR|ARPC1A_ENST00000432884.2_3'UTR|ARPC1B_ENST00000252725.5_Missense_Mutation_p.K37N			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	37			K -> N (in dbSNP:rs1045012).		Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			TCTATGAAAAGAGCGGTGCCA	0.577													G|||	391	0.0780751	0.1778	0.0634	5008	,	,		21294	0.0327		0.0338	False		,,,				2504	0.046				p.K37N		Atlas-SNP	.											.	ARPC1B	41	.	0			c.G111C						PASS	.	G	ASN/LYS	688,3718	289.8+/-280.6	46,596,1561	186.0	161.0	169.0		111	5.2	1.0	7	dbSNP_86	169	359,8241	119.9+/-179.2	11,337,3952	yes	missense	ARPC1B	NM_005720.3	94	57,933,5513	CC,CG,GG		4.1744,15.6151,8.0501	benign	37/373	98984354	1047,11959	2203	4300	6503	SO:0001583	missense	10095	exon3			TGAAAAGAGCGGT	AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"""Actin related protein 2/3 complex subunits"", ""WD repeat domain containing"""	704	protein-coding gene	gene with protein product	"""ARP2/3 protein complex subunit p41"", ""actin related protein 2/3 complex, subunit 1A (41 kD)"""	604223	"""actin related protein 2/3 complex, subunit 1B (41 kD)"""			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.111G>C	7.37:g.98984354G>C	ENSP00000389631:p.Lys37Asn	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_005720	Q9BU00	Missense_Mutation	SNP	ENST00000451682.1	37	CCDS5661.1	145	0.06639194139194139	70	0.14227642276422764	30	0.08287292817679558	18	0.03146853146853147	27	0.03562005277044855	G	12.54	1.969222	0.34754	0.156151	0.041744	ENSG00000130429	ENST00000443222;ENST00000414376;ENST00000252725;ENST00000455009;ENST00000418347;ENST00000417330;ENST00000431816;ENST00000427217;ENST00000458033;ENST00000451682	T;T;T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.17	5.17	0.71159	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.049416	0.85682	D	0.000000	T	0.00784	0.0026	M	0.81239	2.535	0.20403	P	0.9999050461	D;D	0.64830	0.994;0.994	D;D	0.64776	0.929;0.929	T	0.33163	-0.9879	9	0.24483	T	0.36	-37.4929	12.4073	0.55447	0.0777:0.0:0.9223:0.0	rs1045012;rs3174603;rs10341021;rs11556756;rs1045012	37;37	A4D275;O15143	.;ARC1B_HUMAN	N	37	ENSP00000413173:K37N;ENSP00000398620:K37N;ENSP00000252725:K37N;ENSP00000410238:K37N;ENSP00000413067:K37N;ENSP00000403324:K37N;ENSP00000398110:K37N;ENSP00000403211:K37N;ENSP00000388802:K37N;ENSP00000389631:K37N	ENSP00000252725:K37N	K	+	3	2	ARPC1B	98822290	1.000000	0.71417	0.996000	0.52242	0.069000	0.16628	1.437000	0.34991	2.577000	0.86979	0.561000	0.74099	AAG	G|0.926;C|0.074	0.074	strong		0.577	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720	
MMP25	64386	hgsc.bcm.edu	37	16	3109032	3109032	+	Missense_Mutation	SNP	G	G	A	rs7188234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3109032G>A	ENST00000336577.4	+	10	1859	c.1622G>A	c.(1621-1623)gGa>gAa	p.G541E	RP11-473M20.7_ENST00000573878.1_RNA|RP11-473M20.7_ENST00000572574.1_RNA|RP11-473M20.7_ENST00000573130.1_RNA|RP11-473M20.7_ENST00000572222.1_RNA|RP11-473M20.7_ENST00000576250.1_RNA|RP11-473M20.7_ENST00000573953.1_RNA|RP11-473M20.7_ENST00000570949.1_RNA|RP11-473M20.7_ENST00000572427.1_RNA	NM_022468.4	NP_071913.1	Q9H239	MMP28_HUMAN	matrix metallopeptidase 25	0					negative regulation of macrophage chemotaxis (GO:0010760)	cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	14					Marimastat(DB00786)	CAGGCCGCAGGACGTTGGCCT	0.706													G|||	454	0.090655	0.1929	0.0793	5008	,	,		9637	0.0		0.0895	False		,,,				2504	0.0552				p.G541E	NSCLC(147;665 1067 3888 6863 19894 30469 40247 45633 51336)	Atlas-SNP	.											.	MMP25	35	.	0			c.G1622A						PASS	.	G	GLU/GLY	716,3544		62,592,1476	12.0	10.0	10.0		1622	0.6	0.0	16	dbSNP_116	10	695,7687		33,629,3529	yes	missense	MMP25	NM_022468.4	98	95,1221,5005	AA,AG,GG		8.2916,16.8075,11.1612	probably-damaging	541/563	3109032	1411,11231	2130	4191	6321	SO:0001583	missense	64386	exon10			CCGCAGGACGTTG	AF145442	CCDS10492.1	16p13.3	2008-02-05	2005-08-08			ENSG00000008516			14246	protein-coding gene	gene with protein product		608482	"""matrix metalloproteinase 25"", ""matrix metallopeptidase-like 1"""	MMPL1, MMP20		10628838, 10706098	Standard	NM_022468		Approved	MT6-MMP	uc002cth.3	Q9NPA2		ENST00000336577.4:c.1622G>A	16.37:g.3109032G>A	ENSP00000337816:p.Gly541Glu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_022468	Q96F04|Q96TE2	Missense_Mutation	SNP	ENST00000336577.4	37	CCDS10492.1	194	0.08882783882783883	99	0.20121951219512196	32	0.08839779005524862	0	0.0	63	0.08311345646437995	g	15.99	2.994496	0.54041	0.168075	0.082916	ENSG00000008516	ENST00000336577	T	0.15603	2.41	4.14	0.638	0.17742	.	1.216660	0.06187	N	0.680715	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.32798	-0.9893	9	0.02654	T	1	.	1.7657	0.03001	0.1251:0.2068:0.4564:0.2117	rs7188234;rs7188234	541	Q9NPA2	MMP25_HUMAN	E	541	ENSP00000337816:G541E	ENSP00000337816:G541E	G	+	2	0	MMP25	3049033	0.003000	0.15002	0.002000	0.10522	0.010000	0.07245	0.432000	0.21461	0.194000	0.20326	-0.550000	0.04213	GGA	G|0.889;A|0.111	0.111	strong		0.706	MMP25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437116.1	NM_022468	
GPAM	57678	hgsc.bcm.edu	37	10	113920465	113920465	+	Silent	SNP	G	G	A	rs2277207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	237	0	0		WXS	Illumina HiSeq	Phase_I	229	229	1	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	
ANKFN1	162282	hgsc.bcm.edu	37	17	54450073	54450073	+	Missense_Mutation	SNP	G	G	A	rs115263675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:54450073G>A	ENST00000318698.2	+	6	712	c.677G>A	c.(676-678)aGt>aAt	p.S226N	ANKFN1_ENST00000566473.2_Missense_Mutation_p.S226N	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	226										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						GAGAGGGTGAGTGAACTGTCT	0.502													G|||	77	0.0153754	0.056	0.0043	5008	,	,		17983	0.0		0.0	False		,,,				2504	0.0				p.S226N		Atlas-SNP	.											.	ANKFN1	115	.	0			c.G677A						PASS	.	G	ASN/SER	210,4196	128.2+/-165.1	3,204,1996	157.0	148.0	151.0		677	2.1	1.0	17	dbSNP_132	151	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ANKFN1	NM_153228.2	46	3,205,6295	AA,AG,GG		0.0116,4.7662,1.6223	benign	226/764	54450073	211,12795	2203	4300	6503	SO:0001583	missense	162282	exon6			GGGTGAGTGAACT	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.677G>A	17.37:g.54450073G>A	ENSP00000321627:p.Ser226Asn	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_153228		Missense_Mutation	SNP	ENST00000318698.2	37	CCDS32686.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	G	6.241	0.412619	0.11812	0.047662	1.16E-4	ENSG00000153930	ENST00000318698	T	0.22539	1.95	5.64	2.14	0.27477	.	0.409722	0.29799	N	0.011164	T	0.00784	0.0026	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	10	0.16896	T	0.51	-6.438	4.4468	0.11602	0.1486:0.2008:0.5381:0.1125	.	226	Q8N957	ANKF1_HUMAN	N	226	ENSP00000321627:S226N	ENSP00000321627:S226N	S	+	2	0	ANKFN1	51805072	0.802000	0.28943	0.995000	0.50966	0.985000	0.73830	0.633000	0.24598	1.317000	0.45149	0.462000	0.41574	AGT	G|0.982;A|0.018	0.018	strong		0.502	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228	
MGAM	8972	hgsc.bcm.edu	37	7	141719078	141719078	+	Missense_Mutation	SNP	A	A	G	rs114936410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141719078A>G	ENST00000549489.2	+	4	502	c.407A>G	c.(406-408)cAt>cGt	p.H136R	MGAM_ENST00000475668.2_Missense_Mutation_p.H136R	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	136					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)	TCCAAGAATCATAGCTACCAT	0.502													A|||	33	0.00658946	0.0234	0.0029	5008	,	,		18070	0.0		0.0	False		,,,				2504	0.0				p.H136R		Atlas-SNP	.											.	MGAM	767	.	0			c.A407G						PASS	.	A	ARG/HIS	70,4000		2,66,1967	86.0	90.0	89.0		407	3.7	1.0	7	dbSNP_132	89	0,8392		0,0,4196	yes	missense	MGAM	NM_004668.2	29	2,66,6163	GG,GA,AA		0.0,1.7199,0.5617	possibly-damaging	136/1858	141719078	70,12392	2035	4196	6231	SO:0001583	missense	8972	exon4			AGAATCATAGCTA	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.407A>G	7.37:g.141719078A>G	ENSP00000447378:p.His136Arg	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	A	11.07	1.531130	0.27387	0.017199	0.0	ENSG00000257335	ENST00000465654;ENST00000549489;ENST00000497673;ENST00000475668;ENST00000548812	T;D;T	0.85339	-0.82;-1.97;0.55	4.85	3.7	0.42460	Glycoside hydrolase-type carbohydrate-binding (1);P-type trefoil (2);	0.276318	0.26251	N	0.025446	T	0.50752	0.1634	M	0.63843	1.955	0.32573	N	0.529585	P	0.44195	0.828	B	0.34385	0.181	T	0.74287	-0.3714	10	0.51188	T	0.08	.	8.8349	0.35107	0.9101:0.0:0.0899:0.0	.	136	O43451	MGA_HUMAN	R	136;136;136;136;13	ENSP00000419372:H136R;ENSP00000447378:H136R;ENSP00000417103:H136R	ENSP00000316431:H13R	H	+	2	0	MGAM	141365547	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	6.413000	0.73308	0.992000	0.38840	-0.476000	0.04901	CAT	A|0.990;G|0.010	0.010	strong		0.502	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
LGSN	51557	hgsc.bcm.edu	37	6	64004905	64004905	+	Missense_Mutation	SNP	T	T	A	rs2459568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:64004905T>A	ENST00000370657.4	-	2	109	c.76A>T	c.(76-78)Aac>Tac	p.N26Y	LGSN_ENST00000370658.5_Missense_Mutation_p.N26Y			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	26			N -> Y (in dbSNP:rs2459568).		glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)			NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CTTAATGTGTTCATGCTGTTG	0.343													T|||	68	0.0135783	0.0499	0.0029	5008	,	,		18219	0.0		0.0	False		,,,				2504	0.0				p.N26Y		Atlas-SNP	.											.	LGSN	82	.	0			c.A76T						PASS	.	T	TYR/ASN,TYR/ASN	174,4232	114.2+/-152.2	4,166,2033	267.0	240.0	249.0		76,76	1.8	0.0	6	dbSNP_100	249	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	LGSN	NM_001143940.1,NM_016571.2	143,143	4,169,6330	AA,AT,TT		0.0349,3.9492,1.3609	benign,benign	26/209,26/510	64004905	177,12829	2203	4300	6503	SO:0001583	missense	51557	exon2			ATGTGTTCATGCT	AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"""glutamate-ammonia ligase (glutamine synthetase) domain containing 1"""	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.76A>T	6.37:g.64004905T>A	ENSP00000359691:p.Asn26Tyr	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	362	163	0.450276	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	37	CCDS4964.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	T	2.447	-0.327180	0.05350	0.039492	3.49E-4	ENSG00000146166	ENST00000370658;ENST00000370657	T;T	0.26660	1.72;1.83	4.71	1.8	0.24995	.	0.346161	0.36409	N	0.002618	T	0.02848	0.0085	N	0.02011	-0.69	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.10450	0.005;0.001;0.0	T	0.41142	-0.9525	10	0.46703	T	0.11	-6.0146	7.4053	0.26987	0.498:0.0:0.0:0.502	rs2459568;rs52826076;rs2459568	26;26;26	Q5TDP6-3;Q5TDP6-2;Q5TDP6	.;.;LGSN_HUMAN	Y	26	ENSP00000359692:N26Y;ENSP00000359691:N26Y	ENSP00000359691:N26Y	N	-	1	0	LGSN	64062864	0.001000	0.12720	0.003000	0.11579	0.007000	0.05969	0.975000	0.29449	0.746000	0.32786	-0.403000	0.06358	AAC	T|0.988;A|0.012	0.012	strong		0.343	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571	
SERPINA10	51156	hgsc.bcm.edu	37	14	94756750	94756750	+	Missense_Mutation	SNP	T	T	C	rs941591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94756750T>C	ENST00000393096.1	-	2	646	c.181A>G	c.(181-183)Agt>Ggt	p.S61G	SERPINA10_ENST00000261994.4_Missense_Mutation_p.S61G|SERPINA10_ENST00000554173.1_Missense_Mutation_p.S61G|SERPINA10_ENST00000554723.1_Missense_Mutation_p.S101G	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	80	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	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	
PIGN	23556	hgsc.bcm.edu	37	18	59814268	59814268	+	Silent	SNP	G	G	A	rs9320000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	260	0	0		WXS	Illumina HiSeq	Phase_I	167	166	0.994012	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	
CCDC28A	25901	hgsc.bcm.edu	37	6	139094936	139094936	+	Missense_Mutation	SNP	C	C	A	rs34538642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139094936C>A	ENST00000332797.6	+	1	280	c.125C>A	c.(124-126)tCc>tAc	p.S42Y		NM_015439.2	NP_056254.1	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A	42			S -> Y (in dbSNP:rs34538642).							autonomic_ganglia(1)|large_intestine(3)|lung(8)|ovary(1)	13				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		AGGAGCGGGTCCCGGGATGTG	0.632													C|||	298	0.0595048	0.2148	0.0187	5008	,	,		16083	0.0		0.001	False		,,,				2504	0.0				p.S42Y		Atlas-SNP	.											.	CCDC28A	34	.	0			c.C125A						PASS	.	C	TYR/SER	746,3660	301.3+/-286.8	70,606,1527	83.0	103.0	96.0		125	-9.6	0.0	6	dbSNP_126	96	10,8590	7.7+/-29.5	0,10,4290	yes	missense	CCDC28A	NM_015439.2	144	70,616,5817	AA,AC,CC		0.1163,16.9315,5.8127	benign	42/275	139094936	756,12250	2203	4300	6503	SO:0001583	missense	25901	exon1			GCGGGTCCCGGGA	AY167571	CCDS5192.1	6q23.1-q24.1	2008-02-05	2005-09-12	2005-09-12	ENSG00000024862	ENSG00000024862			21098	protein-coding gene	gene with protein product		615353	"""chromosome 6 open reading frame 80"""	C6orf80			Standard	NM_015439		Approved	CCRL1AP, DKFZp586D0623	uc003qie.3	Q8IWP9	OTTHUMG00000015683	ENST00000332797.6:c.125C>A	6.37:g.139094936C>A	ENSP00000332716:p.Ser42Tyr	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	270	126	0.466667	NM_015439	E1P591|Q32NC7|Q66K67|Q96E23|Q9Y430	Missense_Mutation	SNP	ENST00000332797.6	37	CCDS5192.1	98	0.04487179487179487	95	0.19308943089430894	3	0.008287292817679558	0	0.0	0	0.0	C	4.671	0.124775	0.08931	0.169315	0.001163	ENSG00000024862	ENST00000332797	T	0.26067	1.76	4.79	-9.58	0.00559	.	5.212620	0.00597	N	0.000373	T	0.01730	0.0055	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22382	-1.0218	9	0.07175	T	0.84	6.5122	2.2197	0.03969	0.342:0.154:0.3568:0.1471	rs34538642	42	Q8IWP9	CC28A_HUMAN	Y	42	ENSP00000332716:S42Y	ENSP00000332716:S42Y	S	+	2	0	CCDC28A	139136629	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.827000	0.04424	-2.758000	0.00371	-0.268000	0.10319	TCC	C|0.946;A|0.054	0.054	strong		0.632	CCDC28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042444.1	NM_015439	
APOB	338	hgsc.bcm.edu	37	2	21258523	21258523	+	Missense_Mutation	SNP	C	C	T	rs61741625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:21258523C>T	ENST00000233242.1	-	7	878	c.751G>A	c.(751-753)Gct>Act	p.A251T	APOB_ENST00000399256.4_Missense_Mutation_p.A251T	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	251	Heparin-binding.|Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				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)					TTCCTCTTAGCGTCCAGTGTG	0.502													C|||	13	0.00259585	0.0098	0.0	5008	,	,		21477	0.0		0.0	False		,,,				2504	0.0				p.A251T		Atlas-SNP	.											.	APOB	761	.	0			c.G751A						PASS	.	C	THR/ALA	34,4372	38.4+/-70.7	0,34,2169	130.0	105.0	114.0		751	-8.5	0.0	2	dbSNP_129	114	0,8600		0,0,4300	yes	missense	APOB	NM_000384.2	58	0,34,6469	TT,TC,CC		0.0,0.7717,0.2614	benign	251/4564	21258523	34,12972	2203	4300	6503	SO:0001583	missense	338	exon7			TCTTAGCGTCCAG	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.751G>A	2.37:g.21258523C>T	ENSP00000233242:p.Ala251Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	106	58	0.54717	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	C	13.65	2.299459	0.40694	0.007717	0.0	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.04809	3.55;3.55	5.73	-8.49	0.00931	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	1.266020	0.05424	N	0.544746	T	0.01029	0.0034	N	0.22421	0.69	0.09310	N	1	P	0.39520	0.676	B	0.32289	0.143	T	0.38628	-0.9652	10	0.21014	T	0.42	.	4.2167	0.10539	0.3063:0.3153:0.3062:0.0722	.	251	P04114	APOB_HUMAN	T	251	ENSP00000233242:A251T;ENSP00000382200:A251T	ENSP00000233242:A251T	A	-	1	0	APOB	21112028	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.261000	0.02855	-1.679000	0.01452	-1.193000	0.01689	GCT	C|0.997;T|0.003	0.003	strong		0.502	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
SLC27A5	10998	hgsc.bcm.edu	37	19	59023174	59023174	+	Missense_Mutation	SNP	A	A	G	rs35350976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:59023174A>G	ENST00000263093.2	-	1	258	c.149T>C	c.(148-150)aTg>aCg	p.M50T	SLC27A5_ENST00000601355.1_Missense_Mutation_p.M50T	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	50			M -> T (in dbSNP:rs35350976).		bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		CCGTGCTAACATGGCCAGCCC	0.701													A|||	809	0.161542	0.1823	0.1715	5008	,	,		17235	0.0556		0.2187	False		,,,				2504	0.1769				p.M50T		Atlas-SNP	.											.	SLC27A5	58	.	0			c.T149C						PASS	.	A	THR/MET	749,3597		75,599,1499	9.0	11.0	10.0		149	-0.9	0.0	19	dbSNP_126	10	1449,7049		128,1193,2928	yes	missense	SLC27A5	NM_012254.2	81	203,1792,4427	GG,GA,AA		17.0511,17.2342,17.113	benign	50/691	59023174	2198,10646	2173	4249	6422	SO:0001583	missense	10998	exon1			GCTAACATGGCCA	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.149T>C	19.37:g.59023174A>G	ENSP00000263093:p.Met50Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	349	0.15979853479853479	100	0.2032520325203252	62	0.1712707182320442	34	0.05944055944055944	153	0.20184696569920843	a	8.140	0.784999	0.16189	0.172342	0.170511	ENSG00000083807	ENST00000263093	T	0.51574	0.7	4.31	-0.944	0.10392	.	2.348050	0.01898	N	0.038985	T	0.00039	0.0001	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09818	-1.0657	9	0.34782	T	0.22	-0.0265	0.6905	0.00890	0.3719:0.1775:0.1056:0.345	rs35350976	50	Q9Y2P5	S27A5_HUMAN	T	50	ENSP00000263093:M50T	ENSP00000263093:M50T	M	-	2	0	SLC27A5	63714986	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.040000	0.13905	-0.051000	0.13334	0.374000	0.22700	ATG	A|0.840;G|0.160	0.160	strong		0.701	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
OXTR	5021	hgsc.bcm.edu	37	3	8809184	8809184	+	Silent	SNP	G	G	A	rs237902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:8809184G>A	ENST00000316793.3	-	3	1314	c.690C>T	c.(688-690)aaC>aaT	p.N230N	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	230					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	TGAGCCGCAAGTTCTGCCAGA	0.667													G|||	1240	0.247604	0.3124	0.2305	5008	,	,		14583	0.0546		0.327	False		,,,				2504	0.2894				p.N230N		Atlas-SNP	.											OXTR,NS,carcinoma,0,1	OXTR	31	1	0			c.C690T						PASS	.	G		1325,3073		208,909,1082	21.0	20.0	21.0		690	-1.7	0.0	3	dbSNP_79	21	2954,5642		522,1910,1866	no	coding-synonymous	OXTR	NM_000916.3		730,2819,2948	AA,AG,GG		34.3648,30.1273,32.9306		230/390	8809184	4279,8715	2199	4298	6497	SO:0001819	synonymous_variant	5021	exon3			CCGCAAGTTCTGC		CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.690C>T	3.37:g.8809184G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_000916	Q15071	Silent	SNP	ENST00000316793.3	37	CCDS2570.1																																																																																			G|0.714;A|0.286	0.286	strong		0.667	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2		
NUP155	9631	hgsc.bcm.edu	37	5	37294473	37294473	+	Silent	SNP	T	T	C	rs1045908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37294473T>C	ENST00000231498.3	-	33	4091	c.3888A>G	c.(3886-3888)ttA>ttG	p.L1296L	NUP155_ENST00000513532.1_Silent_p.L1232L|NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000381843.2_Silent_p.L1237L	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	146	0	0		WXS	Illumina HiSeq	Phase_I	158	78	0.493671	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	
OBSL1	23363	hgsc.bcm.edu	37	2	220417266	220417266	+	Missense_Mutation	SNP	C	C	T	rs59332477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220417266C>T	ENST00000404537.1	-	18	5356	c.5300G>A	c.(5299-5301)cGa>cAa	p.R1767Q	OBSL1_ENST00000265318.4_3'UTR|OBSL1_ENST00000373876.1_Missense_Mutation_p.R1675Q	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1767					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)		ACCTTCCTGTCGGATGCGGAC	0.731													C|||	1886	0.376597	0.3495	0.5202	5008	,	,		10361	0.3819		0.4583	False		,,,				2504	0.2219				p.R1767Q		Atlas-SNP	.											.	OBSL1	120	.	0			c.G5300A						PASS	.	C	GLN/ARG	1409,2443		283,843,800	9.0	13.0	12.0		5300	4.6	1.0	2	dbSNP_129	12	3644,4534		865,1914,1310	yes	missense	OBSL1	NM_015311.2	43	1148,2757,2110	TT,TC,CC		44.5586,36.5784,42.0033	probably-damaging	1767/1897	220417266	5053,6977	1926	4089	6015	SO:0001583	missense	23363	exon18			TCCTGTCGGATGC	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.5300G>A	2.37:g.220417266C>T	ENSP00000385636:p.Arg1767Gln	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_015311	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	37	CCDS46520.1	913	0.41804029304029305	163	0.3313008130081301	168	0.46408839779005523	228	0.3986013986013986	354	0.46701846965699206	C	22.2	4.252406	0.80135	0.365784	0.445586	ENSG00000124006	ENST00000404537;ENST00000373876	T;T	0.66995	-0.24;-0.24	4.61	4.61	0.57282	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.41356	1.27	0.09310	P	1.0	D	0.89917	1.0	D	0.85130	0.997	T	0.44997	-0.9291	8	0.20519	T	0.43	.	14.2902	0.66273	0.0:1.0:0.0:0.0	rs59332477;rs62191611	1767	O75147	OBSL1_HUMAN	Q	1767;1675	ENSP00000385636:R1767Q;ENSP00000362983:R1675Q	ENSP00000362983:R1675Q	R	-	2	0	OBSL1	220125510	0.997000	0.39634	1.000000	0.80357	0.840000	0.47671	3.585000	0.53943	2.390000	0.81377	0.655000	0.94253	CGA	C|0.582;T|0.418	0.418	strong		0.731	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
MST1L	11223	hgsc.bcm.edu	37	1	17084269	17084269	+	RNA	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17084269G>A	ENST00000455405.2	-	0	539							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.A583V(1)									ACCCCAGCCTGCAATCTCACA	0.582																																					p.A583V		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	lung(1)	c.C1748T						PASS	.																																					11223	exon13			CAGCCTGCAATCT	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.17084269G>A		Somatic	693	0	0		WXS	Illumina HiSeq	Phase_I	799	59	0.0738423	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	12.34	1.908191	0.33721	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.169554	0.27981	N	0.017080	T	0.62829	0.2460	.	.	.	.	.	.	D;D	0.71674	0.979;0.998	P;D	0.63033	0.801;0.91	T	0.69881	-0.5025	5	0.40728	T	0.16	.	.	.	.	.	583;609	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	V	583;609	.	ENSP00000439273:A583V	A	-	2	0	MST1P9	16956856	1.000000	0.71417	0.995000	0.50966	0.000000	0.00434	5.747000	0.68689	0.502000	0.28037	0.000000	0.15137	GCA	.	.	none		0.582	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10524957	10524957	+	Silent	SNP	G	G	T	rs34430103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:10524957G>T	ENST00000396560.2	+	3	707	c.480G>T	c.(478-480)ggG>ggT	p.G160G	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Silent_p.G160G|ATF7IP2_ENST00000324570.5_Silent_p.G160G|ATF7IP2_ENST00000356427.2_Silent_p.G160G	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	160					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AGCATGAGGGGGCTTGTAGTC	0.448													G|||	899	0.179513	0.2436	0.2061	5008	,	,		20164	0.1577		0.1004	False		,,,				2504	0.1779				p.G160G		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.G480T						PASS	.	G		948,3446	360.6+/-315.3	98,752,1347	106.0	96.0	99.0		480	-1.1	0.0	16	dbSNP_126	99	1002,7598	216.3+/-255.4	56,890,3354	no	coding-synonymous	ATF7IP2	NM_024997.2		154,1642,4701	TT,TG,GG		11.6512,21.5749,15.0069		160/683	10524957	1950,11044	2197	4300	6497	SO:0001819	synonymous_variant	80063	exon3			TGAGGGGGCTTGT	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.480G>T	16.37:g.10524957G>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	213	210	0.985915	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Silent	SNP	ENST00000396560.2	37	CCDS10540.1																																																																																			G|0.848;T|0.152	0.152	strong		0.448	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
MATK	4145	hgsc.bcm.edu	37	19	3789321	3789321	+	5'Flank	SNP	G	G	A	rs74830030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3789321G>A	ENST00000310132.6	-	0	0				MATK_ENST00000395040.2_5'Flank|MATK_ENST00000590821.1_5'UTR|MATK_ENST00000395045.2_Nonsense_Mutation_p.R9*	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase						cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		ccttctcttcgttcagcaggg	0.493													G|||	104	0.0207668	0.0726	0.0115	5008	,	,		19422	0.0		0.0	False		,,,				2504	0.0				p.R9X		Atlas-SNP	.											.	MATK	108	.	0			c.C25T						PASS	.	G	stop/ARG	253,4153	146.5+/-181.1	8,237,1958	46.0	44.0	45.0		25	-2.8	0.0	19	dbSNP_131	45	1,8599		0,1,4299	yes	stop-gained	MATK	NM_002378.3		8,238,6257	AA,AG,GG		0.0116,5.7422,1.9529		9/509	3789321	254,12752	2203	4300	6503	SO:0001631	upstream_gene_variant	4145	exon2			CTCTTCGTTCAGC	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"""SH2 domain containing"""	6906	protein-coding gene	gene with protein product	"""Csk-homologous kinase"", ""tyrosine-protein kinase CTK"", ""protein kinase HYL"", ""hematopoietic consensus tyrosine-lacking kinase"", ""tyrosylprotein kinase"", ""hydroxyaryl-protein kinase"", ""Csk-type protein tyrosine kinase"", ""HYL tyrosine kinase"", ""tyrosine kinase MATK"", ""leukocyte carboxyl-terminal src kinase related"""	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679			19.37:g.3789321G>A	Exception_encountered	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	68	0.557377	NM_002378	B3KNZ9|Q9NST8	Nonsense_Mutation	SNP	ENST00000310132.6	37	CCDS12114.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	G	19.36	3.813366	0.70912	0.057422	1.16E-4	ENSG00000007264	ENST00000395045	.	.	.	1.4	-2.8	0.05823	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	2.4484	4.5873	0.12289	0.0:0.4596:0.3083:0.2321	.	.	.	.	X	9	.	ENSP00000378485:R9X	R	-	1	2	MATK	3740321	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.190000	0.09615	-0.756000	0.04703	0.455000	0.32223	CGA	G|0.980;A|0.020	0.020	strong		0.493	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355	
PKN3	29941	hgsc.bcm.edu	37	9	131467782	131467782	+	Silent	SNP	C	C	T	rs55665019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131467782C>T	ENST00000291906.4	+	2	618	c.225C>T	c.(223-225)caC>caT	p.H75H		NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	75					epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						GGGAGCTGCACGCCCGAATCC	0.706													C|||	530	0.105831	0.3767	0.0317	5008	,	,		15403	0.0069		0.003	False		,,,				2504	0.0				p.H75H		Atlas-SNP	.											.	PKN3	62	.	0			c.C225T						PASS	.	C		1131,3035		106,919,1058	4.0	4.0	4.0		225	-10.4	0.1	9	dbSNP_129	4	36,8126		0,36,4045	no	coding-synonymous	PKN3	NM_013355.3		106,955,5103	TT,TC,CC		0.4411,27.1483,9.4663		75/890	131467782	1167,11161	2083	4081	6164	SO:0001819	synonymous_variant	29941	exon2			GCTGCACGCCCGA	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.225C>T	9.37:g.131467782C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	15	11	0.733333	NM_013355	Q9UM03	Silent	SNP	ENST00000291906.4	37	CCDS6908.1																																																																																			C|0.909;T|0.091	0.091	strong		0.706	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355	
DNAH5	1767	hgsc.bcm.edu	37	5	13913885	13913885	+	Silent	SNP	A	A	G	rs3213936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	106	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	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	
PCDHGA12	26025	hgsc.bcm.edu	37	5	140890573	140890573	+	Missense_Mutation	SNP	C	C	T	rs148119281		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140890573C>T	ENST00000252085.3	+	4	2774	c.2632C>T	c.(2632-2634)Cgc>Tgc	p.R878C	PCDHGA8_ENST00000398604.2_Missense_Mutation_p.R878C|PCDHGC4_ENST00000306593.1_Missense_Mutation_p.R884C|PCDHGA11_ENST00000518882.1_Missense_Mutation_p.R696C|PCDHGA10_ENST00000398610.2_Missense_Mutation_p.R882C|PCDHGC5_ENST00000252087.1_Missense_Mutation_p.R890C|PCDHGC3_ENST00000308177.3_Missense_Mutation_p.R880C|PCDHGA9_ENST00000573521.1_Missense_Mutation_p.R878C|PCDHGB1_ENST00000523390.1_Missense_Mutation_p.R873C|PCDHGB2_ENST00000522605.1_Missense_Mutation_p.R877C|PCDHGB7_ENST00000398594.2_Missense_Mutation_p.R875C|PCDHGA3_ENST00000253812.6_Missense_Mutation_p.R878C|PCDHGA1_ENST00000517417.1_Missense_Mutation_p.R877C|PCDHGB4_ENST00000519479.1_Missense_Mutation_p.R869C|PCDHGA4_ENST00000571252.1_Missense_Mutation_p.R877C|PCDHGA5_ENST00000518069.1_Missense_Mutation_p.R877C|PCDHGB3_ENST00000576222.1_Missense_Mutation_p.R875C|PCDHGA6_ENST00000517434.1_Missense_Mutation_p.R878C|PCDHGA2_ENST00000394576.2_Missense_Mutation_p.R878C|PCDHGA7_ENST00000518325.1_Missense_Mutation_p.R878C|PCDHGA11_ENST00000398587.2_Missense_Mutation_p.R881C|PCDHGB6_ENST00000520790.1_Missense_Mutation_p.R876C	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	878					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATTGAGCGCCCGCTACGGACC	0.617																																					p.R890C		Atlas-SNP	.											PCDHG_cluster,NS,carcinoma,-1,24	PCDHGC5	199	24	0			c.C2668T						scavenged	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	93.0	98.0	96.0		2638,2632,2605,2629,2644,2641,2632,2632,2629,2629,2632,2632,2632,2617,2629,2623,2605,2626,2623,2650,2668,2632,2086,238	4.0	1.0	5	dbSNP_134	96	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGC5,PCDHGC4,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_018928.2,NM_018929.2,NM_032088.1,NM_032092.1,NM_032403.1	180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	880/935,878/933,869/924,877/932,882/937,881/936,878/933,878/933,877/932,877/932,878/933,878/933,878/933,873/928,877/932,875/930,869/924,876/931,875/930,884/939,890/945,878/933,696/751,80/135	140890573	1,13005	2203	4300	6503	SO:0001583	missense	56097	exon4			AGCGCCCGCTACG	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"""Cadherins / Protocadherins : Clustered"""	8699	other	protocadherin	"""fibroblast cadherin FIB3"""	603059	"""cadherin 21"""	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.2632C>T	5.37:g.140890573C>T	ENSP00000252085:p.Arg878Cys	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	233	3	0.0128755	NM_018929	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	37	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731040	0.69074	2.27E-4	0.0	ENSG00000204956;ENSG00000081853;ENSG00000254245;ENSG00000254221;ENSG00000253910;ENSG00000253485;ENSG00000253731;ENSG00000253537;ENSG00000253953;ENSG00000253767;ENSG00000253305;ENSG00000253846;ENSG00000254122;ENSG00000253873;ENSG00000253873;ENSG00000253159;ENSG00000240184;ENSG00000242419;ENSG00000240764	ENST00000517417;ENST00000394576;ENST00000253812;ENST00000523390;ENST00000522605;ENST00000518069;ENST00000517434;ENST00000518325;ENST00000519479;ENST00000398604;ENST00000520790;ENST00000398610;ENST00000398594;ENST00000398587;ENST00000518882;ENST00000252085;ENST00000308177;ENST00000306593;ENST00000252087	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96200	-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94;-3.94	4.9	4.04	0.47022	.	0.000000	0.46442	D	0.000281	D	0.95648	0.8585	L	0.41236	1.265	0.54753	D	0.999988	D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;P;D;D	0.89917	0.97;0.599;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;0.901;1.0;1.0	B;B;D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;P;D;D	0.97110	0.318;0.064;0.999;0.996;0.991;0.999;1.0;0.999;0.991;0.926;1.0;0.84;1.0;0.999;1.0;0.999;0.999;1.0;0.999;1.0;0.926;0.548;1.0;0.993	D	0.95192	0.8309	10	0.87932	D	0	.	9.1172	0.36764	0.1458:0.7772:0.0:0.0769	.	890;884;80;880;878;881;696;875;882;876;878;869;878;869;878;878;875;877;877;877;873;878;878;877	Q9Y5F6;Q9Y5F7;Q9BR81;Q9UN70;O60330;Q9Y5H2;Q9Y5H2-3;Q9Y5F8;Q9Y5H3;Q9Y5F9;Q9Y5G4;Q9Y5G0;Q9Y5G5;Q9UN71;Q9Y5G6;Q9Y5G7;Q9Y5G1;Q9Y5G8;Q9Y5G2;Q9Y5G9;Q9Y5G3;Q9Y5H0;Q9Y5H1;Q9Y5H4	PCDGM_HUMAN;PCDGL_HUMAN;.;PCDGK_HUMAN;PCDGC_HUMAN;PCDGB_HUMAN;.;PCDGJ_HUMAN;PCDGA_HUMAN;PCDGI_HUMAN;PCDG9_HUMAN;PCDGH_HUMAN;PCDG8_HUMAN;PCDGG_HUMAN;PCDG7_HUMAN;PCDG6_HUMAN;PCDGF_HUMAN;PCDG5_HUMAN;PCDGE_HUMAN;PCDG4_HUMAN;PCDGD_HUMAN;PCDG3_HUMAN;PCDG2_HUMAN;PCDG1_HUMAN	C	877;878;878;873;877;877;878;878;869;878;876;882;875;881;696;878;880;884;890	ENSP00000431083:R877C;ENSP00000378077:R878C;ENSP00000253812:R878C;ENSP00000429273:R873C;ENSP00000429018:R877C;ENSP00000429834:R877C;ENSP00000429601:R878C;ENSP00000430024:R878C;ENSP00000428288:R869C;ENSP00000381605:R878C;ENSP00000428603:R876C;ENSP00000381611:R882C;ENSP00000381594:R875C;ENSP00000381589:R881C;ENSP00000428333:R696C;ENSP00000252085:R878C;ENSP00000312070:R880C;ENSP00000306918:R884C;ENSP00000252087:R890C	ENSP00000381611:R882C	R	+	1	0	PCDHGA12;PCDHGA10;PCDHGA11;PCDHGB7;PCDHGA8;PCDHGC5;PCDHGA7;PCDHGB6;PCDHGC4;PCDHGA6;PCDHGC3;PCDHGA5;PCDHGA3;PCDHGB2;PCDHGA2;PCDHGA1;PCDHGB4;PCDHGB1	140870757	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	3.317000	0.51968	1.290000	0.44636	0.511000	0.50034	CGC	C|1.000;T|0.000	0.000	weak		0.617	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735	
CDYL	9425	hgsc.bcm.edu	37	6	4943846	4943846	+	Silent	SNP	T	T	C	rs11963443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4943846T>C	ENST00000328908.5	+	7	1481	c.1350T>C	c.(1348-1350)atT>atC	p.I450I	CDYL_ENST00000343762.5_Silent_p.I264I|CDYL_ENST00000397588.3_Silent_p.I396I|CDYL_ENST00000449732.2_Silent_p.I264I|CDYL_ENST00000472453.1_3'UTR			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	450					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		GCCCAGCCATTGGTCTAGGAG	0.398													T|||	508	0.101438	0.3616	0.0288	5008	,	,		18292	0.0		0.0089	False		,,,				2504	0.001				p.I396I		Atlas-SNP	.											.	CDYL	74	.	0			c.T1188C						PASS	.	T	,,	1382,3024	456.1+/-351.2	234,914,1055	125.0	125.0	125.0		792,792,1188	-1.1	0.9	6	dbSNP_120	125	36,8564	23.4+/-69.3	0,36,4264	no	coding-synonymous,coding-synonymous,coding-synonymous	CDYL	NM_001143970.1,NM_001143971.1,NM_004824.3	,,	234,950,5319	CC,CT,TT		0.4186,31.3663,10.9027	,,	264/413,264/413,396/545	4943846	1418,11588	2203	4300	6503	SO:0001819	synonymous_variant	9425	exon5			AGCCATTGGTCTA	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.1350T>C	6.37:g.4943846T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Silent	SNP	ENST00000328908.5	37																																																																																				T|0.895;C|0.105	0.105	strong		0.398	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824	
CPA1	1357	hgsc.bcm.edu	37	7	130021488	130021488	+	Silent	SNP	G	G	C	rs1126899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:130021488G>C	ENST00000011292.3	+	3	315	c.165G>C	c.(163-165)ggG>ggC	p.G55G	CPA1_ENST00000484324.1_5'UTR	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	55					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)					TCTGGCGGGGGCCTGCCCACC	0.677													C|||	2916	0.582268	0.6611	0.5504	5008	,	,		14677	0.621		0.5467	False		,,,				2504	0.4949				p.G55G		Atlas-SNP	.											.	CPA1	73	.	0			c.G165C						PASS	.	C		2828,1578		921,986,296	34.0	30.0	32.0		165	-0.2	0.0	7	dbSNP_86	32	4333,4265		1131,2071,1097	no	coding-synonymous	CPA1	NM_001868.2		2052,3057,1393	CC,CG,GG		49.6046,35.8148,44.9323		55/420	130021488	7161,5843	2203	4299	6502	SO:0001819	synonymous_variant	1357	exon3			GCGGGGGCCTGCC		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.165G>C	7.37:g.130021488G>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	117	115	0.982906	NM_001868	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	Silent	SNP	ENST00000011292.3	37	CCDS5820.1																																																																																			C|0.552;G|0.448	0.552	strong		0.677	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868	
CIRH1A	84916	hgsc.bcm.edu	37	16	69191012	69191012	+	Missense_Mutation	SNP	G	G	A	rs8056684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69191012G>A	ENST00000314423.7	+	12	1490	c.1313G>A	c.(1312-1314)cGc>cAc	p.R438H	CIRH1A_ENST00000563094.1_Missense_Mutation_p.R438H|CIRH1A_ENST00000352319.4_Intron			Q969X6	CIR1A_HUMAN	cirrhosis, autosomal recessive 1A (cirhin)	438			R -> H (in dbSNP:rs8056684).		maturation of SSU-rRNA (GO:0030490)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(108;0.125)		GCATTCCTTCGCTCTGCCCTT	0.443													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		19933	0.0		0.0	False		,,,				2504	0.0				p.R438H	Melanoma(69;1156 1278 4951 8715 52012)	Atlas-SNP	.											.	CIRH1A	48	.	0			c.G1313A						PASS	.	G	HIS/ARG	91,4305	75.2+/-113.4	1,89,2108	97.0	89.0	92.0		1313	0.4	1.0	16	dbSNP_116	92	0,8600		0,0,4300	yes	missense	CIRH1A	NM_032830.2	29	1,89,6408	AA,AG,GG		0.0,2.0701,0.7002	benign	438/687	69191012	91,12905	2198	4300	6498	SO:0001583	missense	84916	exon12			TCCTTCGCTCTGC	AB075868	CCDS10872.1	16q22	2014-04-07			ENSG00000141076	ENSG00000141076		"""WD repeat domain containing"""	1983	protein-coding gene	gene with protein product	"""UTP4, small subunit (SSU) processome component, homolog (yeast)"""	607456				10820129, 20385600	Standard	NM_032830		Approved	NAIC, FLJ14728, KIAA1988, TEX292, CIRHIN, UTP4	uc002ews.4	Q969X6	OTTHUMG00000137570	ENST00000314423.7:c.1313G>A	16.37:g.69191012G>A	ENSP00000327179:p.Arg438His	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	155	69	0.445161	NM_032830	Q8NCD9|Q8TF14|Q96SP0|Q96SR9|Q96SZ9|Q96T13|Q9BWK6	Missense_Mutation	SNP	ENST00000314423.7	37	CCDS10872.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	G	11.42	1.632635	0.29068	0.020701	0.0	ENSG00000141076	ENST00000314423	T	0.29917	1.55	5.63	0.418	0.16429	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.577687	0.20003	N	0.101285	T	0.04092	0.0114	N	0.04959	-0.14	0.22389	N	0.999142	B;B	0.10296	0.0;0.003	B;B	0.01281	0.0;0.0	T	0.18903	-1.0322	10	0.38643	T	0.18	.	7.8446	0.29419	0.5019:0.0:0.4981:0.0	rs8056684;rs52807145;rs8056684	438;438	Q969X6;Q969X6-3	CIR1A_HUMAN;.	H	438	ENSP00000327179:R438H	ENSP00000327179:R438H	R	+	2	0	CIRH1A	67748513	0.806000	0.28996	0.991000	0.47740	0.870000	0.49936	0.011000	0.13264	0.341000	0.23771	0.455000	0.32223	CGC	G|0.990;A|0.010	0.010	strong		0.443	CIRH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268950.2	NM_032830	
S100A3	6274	hgsc.bcm.edu	37	1	153520898	153520898	+	Missense_Mutation	SNP	G	G	A	rs61731550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153520898G>A	ENST00000368713.3	-	2	260	c.64C>T	c.(64-66)Cgc>Tgc	p.R22C	S100A3_ENST00000368712.1_Missense_Mutation_p.R22C|S100A4_ENST00000368714.1_Intron|S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000368716.4_5'Flank	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	22	EF-hand 1.					cytoplasm (GO:0005737)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|liver(1)|lung(1)	3	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)			TCCCCACAGCGCCCTGCGTAT	0.622													G|||	51	0.0101837	0.0363	0.0043	5008	,	,		17589	0.0		0.0	False		,,,				2504	0.0				p.R22C		Atlas-SNP	.											.	S100A3	7	.	0			c.C64T						PASS	.	G	CYS/ARG	128,4278	94.4+/-133.1	2,124,2077	153.0	147.0	149.0		64	3.4	0.0	1	dbSNP_129	149	0,8600		0,0,4300	yes	missense	S100A3	NM_002960.1	180	2,124,6377	AA,AG,GG		0.0,2.9051,0.9842	probably-damaging	22/102	153520898	128,12878	2203	4300	6503	SO:0001583	missense	6274	exon2			CACAGCGCCCTGC	BC012893	CCDS1043.1	1q21	2008-02-05	2001-11-28		ENSG00000188015	ENSG00000188015		"""S100 calcium binding proteins"""	10493	protein-coding gene	gene with protein product		176992	"""S100 calcium-binding protein A3"""	S100E		8341667	Standard	NM_002960		Approved		uc001fca.1	P33764	OTTHUMG00000013550	ENST00000368713.3:c.64C>T	1.37:g.153520898G>A	ENSP00000357702:p.Arg22Cys	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_002960	D3DV51|Q6FGE4	Missense_Mutation	SNP	ENST00000368713.3	37	CCDS1043.1	17	0.007783882783882784	14	0.028455284552845527	3	0.008287292817679558	0	0.0	0	0.0	G	12.38	1.921365	0.33908	0.029051	0.0	ENSG00000188015	ENST00000368713;ENST00000368712	T;T	0.12039	2.72;2.72	5.42	3.43	0.39272	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.495237	0.19790	N	0.106001	T	0.09512	0.0234	M	0.67569	2.06	0.18873	N	0.999985	D	0.64830	0.994	P	0.48770	0.589	T	0.09751	-1.0660	10	0.87932	D	0	.	6.1806	0.20470	0.094:0.0:0.7225:0.1835	.	22	P33764	S10A3_HUMAN	C	22	ENSP00000357702:R22C;ENSP00000357701:R22C	ENSP00000357701:R22C	R	-	1	0	S100A3	151787522	0.002000	0.14202	0.002000	0.10522	0.003000	0.03518	1.236000	0.32683	1.295000	0.44724	0.643000	0.83706	CGC	G|0.991;A|0.009	0.009	strong		0.622	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960	
H2BFWT	158983	hgsc.bcm.edu	37	X	103267865	103267865	+	Missense_Mutation	SNP	C	C	T	rs553509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:103267865C>T	ENST00000217926.5	-	1	394	c.368G>A	c.(367-369)cGc>cAc	p.R123H	H2BFM_ENST00000243297.5_5'Flank	NM_001002916.3	NP_001002916.3	Q7Z2G1	H2BWT_HUMAN	H2B histone family, member W, testis-specific	123			R -> H (in dbSNP:rs553509). {ECO:0000269|PubMed:15475252, ECO:0000269|PubMed:15489334}.			membrane (GO:0016020)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	16						GCGGGCCAGGCGACCAGCCTC	0.647													.|||	2193	0.580927	0.438	0.3098	3775	,	,		13169	0.4603		0.5089	False		,,,				2504	0.4325				p.R123H		Atlas-SNP	.											.	H2BFWT	33	.	0			c.G368A						PASS	.	C	HIS/ARG	2258,1577		574,775,335,283,236	36.0	33.0	34.0		368	-2.7	0.0	X	dbSNP_83	34	4476,2251		1080,1091,1225,257,646	yes	missense	H2BFWT	NM_001002916.3	29	1654,1866,1560,540,882	TT,TC,T,CC,C		33.4622,41.1213,36.2431	benign	123/176	103267865	6734,3828	2203	4299	6502	SO:0001583	missense	158983	exon1			GCCAGGCGACCAG	BC038109	CCDS35362.1	Xq22.2	2011-01-27			ENSG00000123569	ENSG00000123569		"""Histones / Replication-independent"""	27252	protein-coding gene	gene with protein product		300507				12477932	Standard	NM_001002916		Approved		uc004elr.3	Q7Z2G1	OTTHUMG00000022120	ENST00000217926.5:c.368G>A	X.37:g.103267865C>T	ENSP00000354723:p.Arg123His	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	242	89	0.367769	NM_001002916	B1AK72|Q147W3	Missense_Mutation	SNP	ENST00000217926.5	37	CCDS35362.1	968	0.5834840265220012	141	0.375	88	0.32116788321167883	170	0.4146341463414634	271	0.5132575757575758	.	9.810	1.182830	0.21870	0.588787	0.665378	ENSG00000123569	ENST00000217926	T	0.27890	1.64	2.84	-2.67	0.06059	Histone-fold (2);Histone core (1);	1.333640	0.06752	U	0.780175	T	0.00012	0.0000	L	0.43598	1.365	0.80722	P	0.0	B	0.16166	0.016	B	0.17098	0.017	T	0.44143	-0.9347	9	0.62326	D	0.03	.	3.36	0.07182	0.3156:0.366:0.0:0.3184	rs553509;rs17340491;rs58833763	123	Q7Z2G1	H2BWT_HUMAN	H	123	ENSP00000354723:R123H	ENSP00000354723:R123H	R	-	2	0	H2BFWT	103154521	0.994000	0.37717	0.000000	0.03702	0.000000	0.00434	0.783000	0.26802	-0.944000	0.03686	-0.849000	0.03036	CGC	C|0.378;0|0.003	.	strong		0.647	H2BFWT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057756.2	NM_001002916	
AKR1C3	8644	hgsc.bcm.edu	37	10	5138607	5138607	+	Silent	SNP	G	G	A	rs7741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5138607G>A	ENST00000380554.3	+	2	742	c.90G>A	c.(88-90)ccG>ccA	p.P30P	AKR1C3_ENST00000439082.2_5'UTR|U8_ENST00000459536.1_RNA|AKR1C3_ENST00000605149.1_Silent_p.P7P|AKR1C3_ENST00000470862.2_3'UTR	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	30					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	TCCAGGTTCCGAGAAGTAAAG	0.438													G|||	1083	0.216254	0.3381	0.196	5008	,	,		20326	0.0		0.3648	False		,,,				2504	0.136				p.P30P		Atlas-SNP	.											.	AKR1C3	21	.	0			c.G90A						PASS	.	G		1485,2921	475.7+/-357.4	246,993,964	72.0	68.0	69.0		90	-3.2	0.0	10	dbSNP_52	69	3041,5557	468.9+/-367.4	544,1953,1802	no	coding-synonymous	AKR1C3	NM_003739.4		790,2946,2766	AA,AG,GG		35.3687,33.704,34.8047		30/324	5138607	4526,8478	2203	4299	6502	SO:0001819	synonymous_variant	8644	exon2			GGTTCCGAGAAGT	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"""Aldo-keto reductases"""	386	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase X"", ""prostaglandin F synthase"", ""3-alpha hydroxysteroid dehydrogenase, type II"""	603966	"""hydroxysteroid (17-beta) dehydrogenase 5"", ""aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"""	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.90G>A	10.37:g.5138607G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	173	73	0.421965	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Silent	SNP	ENST00000380554.3	37	CCDS7063.1																																																																																			G|0.710;A|0.290	0.290	strong		0.438	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
MYH7B	57644	hgsc.bcm.edu	37	20	33568455	33568455	+	Silent	SNP	T	T	C	rs61746163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33568455T>C	ENST00000262873.7	+	6	635	c.543T>C	c.(541-543)gcT>gcC	p.A181A	MYH7B_ENST00000481922.1_3'UTR	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	139	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CCGTAGTGGCTGCTTACAAGG	0.557													C|||	16	0.00319489	0.0121	0.0	5008	,	,		17350	0.0		0.0	False		,,,				2504	0.0				p.A181A		Atlas-SNP	.											.	MYH7B	145	.	0			c.T543C						PASS	.	C		58,4302	745.2+/-411.6	0,58,2122	100.0	111.0	107.0		543	-8.9	0.1	20	dbSNP_129	107	1,8587	799.2+/-407.4	0,1,4293	no	coding-synonymous	MYH7B	NM_020884.3		0,59,6415	CC,CT,TT		0.0116,1.3303,0.4557		181/1984	33568455	59,12889	2180	4294	6474	SO:0001819	synonymous_variant	57644	exon8			AGTGGCTGCTTAC	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.543T>C	20.37:g.33568455T>C		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	171	89	0.520468	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			T|0.994;C|0.006	0.006	strong		0.557	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
MEIOB	254528	hgsc.bcm.edu	37	16	1894961	1894961	+	Missense_Mutation	SNP	A	A	G	rs9806945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1894961A>G	ENST00000397344.3	-	10	976	c.782T>C	c.(781-783)aTa>aCa	p.I261T	LA16c-429E7.1_ENST00000570247.1_RNA|MEIOB_ENST00000412554.2_Missense_Mutation_p.I261T|MEIOB_ENST00000470044.1_Missense_Mutation_p.I54T|MEIOB_ENST00000452149.2_Missense_Mutation_p.I261T|MEIOB_ENST00000325962.3_Missense_Mutation_p.I261T	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	261			I -> T (in dbSNP:rs9806945).		double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										AGCTTCTGGTATATCTTAAAT	0.249													G|||	1010	0.201677	0.1831	0.2262	5008	,	,		16259	0.1736		0.1819	False		,,,				2504	0.2587				p.I261T		Atlas-SNP	.											.	.	.	.	0			c.T782C						PASS	.	G	THR/ILE,THR/ILE	789,3597	726.1+/-409.7	80,629,1484	38.0	38.0	38.0		782,782	4.9	1.0	16	dbSNP_119	38	1319,7251	738.4+/-407.1	109,1101,3075	yes	missense,missense	C16orf73	NM_001163560.2,NM_152764.2	89,89	189,1730,4559	GG,GA,AA		15.3909,17.9891,16.2705	benign,benign	261/472,261/443	1894961	2108,10848	2193	4285	6478	SO:0001583	missense	254528	exon10			TCTGGTATATCTT	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 73"""	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.782T>C	16.37:g.1894961A>G	ENSP00000380504:p.Ile261Thr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	139	60	0.431655	NM_001163560	B1AK39|C9J0S1|Q96RY0	Missense_Mutation	SNP	ENST00000397344.3	37	CCDS10449.2	396	0.1813186813186813	91	0.18495934959349594	62	0.1712707182320442	101	0.17657342657342656	142	0.18733509234828497	G	0.037	-1.303042	0.01353	0.179891	0.153909	ENSG00000162039	ENST00000412554;ENST00000452149;ENST00000325962;ENST00000397344	T;T;T;T	0.04502	3.61;3.61;3.61;3.61	5.98	4.91	0.64330	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.166727	0.53938	N	0.000054	T	0.00012	0.0000	N	0.00069	-2.28	0.53005	P	3.2999999999949736E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34527	-0.9825	9	0.10377	T	0.69	.	10.2088	0.43128	0.1842:0.0:0.8158:0.0	rs9806945;rs52797208;rs59366262;rs9806945	261;261	C9J0S1;Q8N635	.;CP073_HUMAN	T	261	ENSP00000390778:I261T;ENSP00000391033:I261T;ENSP00000314484:I261T;ENSP00000380504:I261T	ENSP00000314484:I261T	I	-	2	0	C16orf73	1834962	1.000000	0.71417	0.972000	0.41901	0.134000	0.20937	2.440000	0.44855	0.686000	0.31488	-0.186000	0.12905	ATA	A|0.839;G|0.161	0.161	strong		0.249	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764	
C9orf78	51759	hgsc.bcm.edu	37	9	132597021	132597021	+	Silent	SNP	C	C	T	rs3814547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132597021C>T	ENST00000372447.3	-	2	161	c.108G>A	c.(106-108)gaG>gaA	p.E36E	C9orf78_ENST00000461762.1_5'Flank|USP20_ENST00000315480.4_5'Flank|USP20_ENST00000358355.1_5'Flank|USP20_ENST00000372429.3_5'Flank	NM_016520.2	NP_057604.1	Q9NZ63	CI078_HUMAN	chromosome 9 open reading frame 78	36						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E36E(1)		kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)	13		Ovarian(14;0.00556)				AGTTCTGTACCTCTCTGGTCT	0.547													C|||	1166	0.232827	0.1997	0.2133	5008	,	,		17649	0.2143		0.2753	False		,,,				2504	0.2669				p.E36E		Atlas-SNP	.											C9orf78,NS,carcinoma,0,1	C9orf78	26	1	1	Substitution - coding silent(1)	stomach(1)	c.G108A						PASS	.	C		912,3494	348.0+/-309.7	91,730,1382	148.0	137.0	141.0		108	-1.2	1.0	9	dbSNP_107	141	2151,6449	368.4+/-335.1	278,1595,2427	no	coding-synonymous	C9orf78	NM_016520.2		369,2325,3809	TT,TC,CC		25.0116,20.699,23.5507		36/290	132597021	3063,9943	2203	4300	6503	SO:0001819	synonymous_variant	51759	exon2			CTGTACCTCTCTG	BC017570	CCDS6931.1	9q34.2	2012-03-16			ENSG00000136819	ENSG00000136819			24932	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 59"""					11042152, 12097419	Standard	NM_016520		Approved	HSPC220, HCA59	uc004byp.3	Q9NZ63	OTTHUMG00000020796	ENST00000372447.3:c.108G>A	9.37:g.132597021C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	150	51	0.34	NM_016520	B3KPX8|Q8WVU6|Q9NT39	Silent	SNP	ENST00000372447.3	37	CCDS6931.1																																																																																			C|0.765;T|0.235	0.235	strong		0.547	C9orf78-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054625.1	NM_016520	
SLC7A14	57709	hgsc.bcm.edu	37	3	170184949	170184949	+	Missense_Mutation	SNP	G	G	A	rs73040363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:170184949G>A	ENST00000231706.5	-	8	2525	c.2210C>T	c.(2209-2211)gCg>gTg	p.A737V	CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	737					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			GTTTGCCTTCGCATCTGACAT	0.522													G|||	254	0.0507188	0.1853	0.013	5008	,	,		15259	0.0		0.0	False		,,,				2504	0.0				p.A737V		Atlas-SNP	.											.	SLC7A14	110	.	0			c.C2210T						PASS	.	G	VAL/ALA	720,3686	299.3+/-285.7	65,590,1548	127.0	112.0	117.0		2210	3.1	0.6	3	dbSNP_130	117	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC7A14	NM_020949.2	64	65,591,5847	AA,AG,GG		0.0116,16.3414,5.5436	benign	737/772	170184949	721,12285	2203	4300	6503	SO:0001583	missense	57709	exon8			GCCTTCGCATCTG	BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"""Solute carriers"""	29326	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 142"""	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.2210C>T	3.37:g.170184949G>A	ENSP00000231706:p.Ala737Val	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	183	91	0.497268	NM_020949	B3KV33|Q9HCF9	Missense_Mutation	SNP	ENST00000231706.5	37	CCDS33892.1	91	0.041666666666666664	88	0.17886178861788618	3	0.008287292817679558	0	0.0	0	0.0	G	9.365	1.068998	0.20147	0.163414	1.16E-4	ENSG00000013293	ENST00000231706	D	0.87491	-2.26	5.9	3.12	0.35913	.	0.505258	0.19518	N	0.112357	T	0.00356	0.0011	N	0.08118	0	0.35570	P	0.19459400000000004	B	0.27971	0.196	B	0.21917	0.037	T	0.10613	-1.0622	9	0.32370	T	0.25	.	12.8923	0.58078	0.0:0.2338:0.6445:0.1217	.	737	Q8TBB6	S7A14_HUMAN	V	737	ENSP00000231706:A737V	ENSP00000231706:A737V	A	-	2	0	SLC7A14	171667643	0.250000	0.23951	0.578000	0.28575	0.219000	0.24729	1.457000	0.35212	0.393000	0.25203	-0.932000	0.02703	GCG	G|0.942;A|0.058	0.058	strong		0.522	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949	
TAF1A	9015	hgsc.bcm.edu	37	1	222734803	222734803	+	Silent	SNP	G	G	C	rs1134898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:222734803G>C	ENST00000352967.4	-	10	1331	c.1143C>G	c.(1141-1143)ggC>ggG	p.G381G	TAF1A_ENST00000391882.1_Silent_p.G267G|TAF1A_ENST00000350027.4_Silent_p.G381G|TAF1A_ENST00000366890.1_Silent_p.G267G	NM_005681.3	NP_005672.1	Q15573	TAF1A_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa	381					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)		TGAAATGAAAGCCTGGCCACC	0.433													G|||	1565	0.3125	0.0234	0.353	5008	,	,		19439	0.3671		0.5119	False		,,,				2504	0.4131				p.G381G		Atlas-SNP	.											.	TAF1A	35	.	0			c.C1143G						PASS	.	G	,,	458,3948	216.1+/-234.9	29,400,1774	84.0	85.0	85.0		1143,1143,801	1.5	0.5	1	dbSNP_86	85	4170,4430	566.0+/-388.6	1027,2116,1157	no	coding-synonymous,coding-synonymous,coding-synonymous	TAF1A	NM_001201536.1,NM_005681.3,NM_139352.2	,,	1056,2516,2931	CC,CG,GG		48.4884,10.3949,35.5836	,,	381/451,381/451,267/337	222734803	4628,8378	2203	4300	6503	SO:0001819	synonymous_variant	9015	exon10			ATGAAAGCCTGGC	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.1143C>G	1.37:g.222734803G>C		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	200	94	0.47	NM_001201536	B2RDZ8|D3DTB7|Q9NWA1	Silent	SNP	ENST00000352967.4	37	CCDS1531.1																																																																																			G|0.637;C|0.363	0.363	strong		0.433	TAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091493.2	NM_005681	
PTP4A1	7803	hgsc.bcm.edu	37	6	64289968	64289968	+	Silent	SNP	G	G	T	rs1618240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:64289968G>T	ENST00000370651.3	+	6	1564	c.411G>T	c.(409-411)cgG>cgT	p.R137R	PTP4A1_ENST00000370650.2_Silent_p.R112R	NM_003463.3	NP_003454.1	Q93096	TP4A1_HUMAN	protein tyrosine phosphatase type IVA, member 1	137	Tyrosine-protein phosphatase.				cell cycle (GO:0007049)|multicellular organismal development (GO:0007275)|positive regulation of cell migration (GO:0030335)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			large_intestine(3)|lung(4)|skin(1)	8	all_cancers(3;0.071)|all_epithelial(2;0.0146)|Lung NSC(77;0.175)		Epithelial(2;0.0365)|LUSC - Lung squamous cell carcinoma(74;0.0644)|all cancers(2;0.112)|Lung(124;0.13)			CCAGAAAGCGGCGTGGAGCTT	0.403													G|||	100	0.0199681	0.0741	0.0029	5008	,	,		16055	0.0		0.0	False		,,,				2504	0.0				p.R137R	Pancreas(91;1019 1502 28028 38110 51645)	Atlas-SNP	.											.	PTP4A1	13	.	0			c.G411T						PASS	.	G		253,4153	143.5+/-178.5	12,229,1962	85.0	87.0	87.0		411	4.0	1.0	6	dbSNP_89	87	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PTP4A1	NM_003463.3		12,232,6259	TT,TG,GG		0.0349,5.7422,1.9683		137/174	64289968	256,12750	2203	4300	6503	SO:0001819	synonymous_variant	7803	exon6			AAAGCGGCGTGGA	U48296	CCDS4965.1	6q12	2011-06-09			ENSG00000112245	ENSG00000112245		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"""	9634	protein-coding gene	gene with protein product		601585				9642300	Standard	NM_003463		Approved	PTPCAAX1, PRL-1	uc003pel.3	Q93096	OTTHUMG00000014949	ENST00000370651.3:c.411G>T	6.37:g.64289968G>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	29	16	0.551724	NM_003463	B2R6C8|O00648|Q49A54	Silent	SNP	ENST00000370651.3	37	CCDS4965.1																																																																																			G|0.980;T|0.020	0.020	strong		0.403	PTP4A1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041083.2		
TMPRSS15	5651	hgsc.bcm.edu	37	21	19651307	19651307	+	Missense_Mutation	SNP	G	G	A	rs73320125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:19651307G>A	ENST00000284885.3	-	23	2771	c.2738C>T	c.(2737-2739)gCt>gTt	p.A913V		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	913	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CCCCCAACCAGCAATAGAACA	0.328													G|||	247	0.0493211	0.1657	0.0202	5008	,	,		10352	0.006		0.008	False		,,,				2504	0.0				p.A913V		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.C2738T						PASS	.	G	VAL/ALA	691,3715	276.6+/-273.2	44,603,1556	49.0	50.0	50.0		2738	4.9	1.0	21	dbSNP_130	50	60,8534	34.8+/-89.0	0,60,4237	yes	missense	TMPRSS15	NM_002772.2	64	44,663,5793	AA,AG,GG		0.6982,15.6832,5.7769	probably-damaging	913/1020	19651307	751,12249	2203	4297	6500	SO:0001583	missense	5651	exon23			CAACCAGCAATAG		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.2738C>T	21.37:g.19651307G>A	ENSP00000284885:p.Ala913Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	109	39	0.357798	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	76	0.0347985347985348	60	0.12195121951219512	8	0.022099447513812154	2	0.0034965034965034965	6	0.0079155672823219	G	15.55	2.867744	0.51588	0.156832	0.006982	ENSG00000154646	ENST00000284885	D	0.93076	-3.16	5.76	4.88	0.63580	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	T	0.08268	0.0206	L	0.46947	1.48	0.51012	D	0.9999	D	0.89917	1.0	D	0.75020	0.985	T	0.42682	-0.9437	9	.	.	.	.	15.5022	0.75709	0.0:0.0:0.8607:0.1393	.	913	P98073	ENTK_HUMAN	V	913	ENSP00000284885:A913V	.	A	-	2	0	TMPRSS15	18573178	1.000000	0.71417	1.000000	0.80357	0.009000	0.06853	6.057000	0.71119	1.448000	0.47680	-0.133000	0.14855	GCT	G|0.953;A|0.047	0.047	strong		0.328	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
GOLM1	51280	hgsc.bcm.edu	37	9	88651370	88651370	+	Missense_Mutation	SNP	T	T	C	rs2297002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:88651370T>C	ENST00000388712.3	-	7	818	c.650A>G	c.(649-651)cAc>cGc	p.H217R	GOLM1_ENST00000257504.6_5'UTR|GOLM1_ENST00000388711.3_Missense_Mutation_p.H217R	NM_016548.3	NP_057632.2	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	217			H -> R (in dbSNP:rs2297002).		nucleus organization (GO:0006997)|regulation of lipid metabolic process (GO:0019216)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)		p.H217R(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17						CACCTCTGTGTGTGGCAGGCC	0.577													C|||	1148	0.229233	0.4546	0.0879	5008	,	,		18134	0.3492		0.005	False		,,,				2504	0.1319				p.H217R		Atlas-SNP	.											GOLM1,NS,carcinoma,0,1	GOLM1	36	1	1	Substitution - Missense(1)	stomach(1)	c.A650G						PASS	.	C	ARG/HIS,ARG/HIS	1736,2670	647.9+/-398.6	351,1034,818	105.0	90.0	95.0		650,650	-3.2	0.0	9	dbSNP_100	95	49,8551	817.1+/-406.9	0,49,4251	yes	missense,missense	GOLM1	NM_016548.3,NM_177937.2	29,29	351,1083,5069	CC,CT,TT		0.5698,39.4008,13.7244	benign,benign	217/402,217/402	88651370	1785,11221	2203	4300	6503	SO:0001583	missense	51280	exon7			TCTGTGTGTGGCA	AF236056	CCDS35054.1	9q21.33	2012-12-13	2007-07-30	2007-07-30	ENSG00000135052	ENSG00000135052			15451	protein-coding gene	gene with protein product		606804	"""golgi phosphoprotein 2"", ""chromosome 9 open reading frame 155"""	GOLPH2, C9orf155		10831838, 18953438, 22542941	Standard	NM_016548		Approved	GP73, FLJ23608, bA379P1.3	uc004aol.3	Q8NBJ4	OTTHUMG00000020130	ENST00000388712.3:c.650A>G	9.37:g.88651370T>C	ENSP00000373364:p.His217Arg	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	112	73	0.651786	NM_016548	Q6IAF4|Q9NRB9	Missense_Mutation	SNP	ENST00000388712.3	37	CCDS35054.1	476	0.21794871794871795	203	0.41260162601626016	31	0.0856353591160221	237	0.4143356643356643	5	0.006596306068601583	C	3.673	-0.067038	0.07273	0.394008	0.005698	ENSG00000135052	ENST00000388712;ENST00000388711	T;T	0.40476	1.03;1.03	3.93	-3.2	0.05156	.	1.770890	0.02390	N	0.079638	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	0.36311	-0.9753	9	0.25106	T	0.35	-0.044	8.6564	0.34066	0.0:0.0925:0.5461:0.3614	rs2297002;rs52804982;rs57362226;rs2297002	217	Q8NBJ4	GOLM1_HUMAN	R	217	ENSP00000373364:H217R;ENSP00000373363:H217R	ENSP00000373363:H217R	H	-	2	0	GOLM1	87841190	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.416000	0.07097	-1.017000	0.03367	-1.163000	0.01768	CAC	T|0.830;C|0.170	0.170	strong		0.577	GOLM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052904.2	NM_177937	
DNAH10	196385	hgsc.bcm.edu	37	12	124417889	124417889	+	Silent	SNP	C	C	T	rs4930721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124417889C>T	ENST00000409039.3	+	76	12979	c.12954C>T	c.(12952-12954)agC>agT	p.S4318S	DNAH10_ENST00000538983.1_3'UTR|CCDC92_ENST00000544798.1_Intron|RP11-380L11.3_ENST00000602292.1_RNA|DNAH10OS_ENST00000514254.2_Intron	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4318					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)		TGACCGAGAGCGAGCCCAGCG	0.607													C|||	1305	0.260583	0.3109	0.3228	5008	,	,		16949	0.123		0.3479	False		,,,				2504	0.2004				p.S4318S		Atlas-SNP	.											.	DNAH10	888	.	0			c.C12954T						PASS	.	C		1200,2700		172,856,922	16.0	18.0	17.0		12954	-9.1	0.0	12	dbSNP_111	17	2550,5748		381,1788,1980	no	coding-synonymous	DNAH10	NM_207437.3		553,2644,2902	TT,TC,CC		30.7303,30.7692,30.7427		4318/4472	124417889	3750,8448	1950	4149	6099	SO:0001819	synonymous_variant	196385	exon76			CGAGAGCGAGCCC	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.12954C>T	12.37:g.124417889C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.719;T|0.281	0.281	strong		0.607	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
CACNA1A	773	hgsc.bcm.edu	37	19	13409390	13409390	+	Silent	SNP	C	C	T	rs16025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13409390C>T	ENST00000360228.5	-	19	3056	c.3057G>A	c.(3055-3057)agG>agA	p.R1019R	CACNA1A_ENST00000573710.2_Silent_p.R1020R	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1020					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CCTTGTCCTCCCTCCGCGCGT	0.652													C|||	620	0.123802	0.1203	0.1369	5008	,	,		9654	0.1171		0.1501	False		,,,				2504	0.0992				p.R1020R		Atlas-SNP	.											CACNA1A_ENST00000360228,NS,carcinoma,0,4	CACNA1A	715	4	0			c.G3060A						scavenged	.	C	,,,,	371,2877		22,327,1275	22.0	23.0	23.0		3069,3060,3057,3060,3069	2.0	1.0	19	dbSNP_54	23	798,5418		47,704,2357	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	69,1031,3632	TT,TC,CC		12.8378,11.4224,12.3521	,,,,	1023/2267,1020/2262,1019/2507,1020/2264,1023/2513	13409390	1169,8295	1624	3108	4732	SO:0001819	synonymous_variant	773	exon19			GTCCTCCCTCCGC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3057G>A	19.37:g.13409390C>T		Somatic	168	2	0.0119048		WXS	Illumina HiSeq	Phase_I	150	148	0.986667	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			C|0.871;T|0.129	0.129	strong		0.652	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
GYPC	2995	hgsc.bcm.edu	37	2	127453664	127453664	+	Silent	SNP	A	A	C	rs1050967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:127453664A>C	ENST00000259254.4	+	4	664	c.333A>C	c.(331-333)ggA>ggC	p.G111G	GYPC_ENST00000409836.3_Silent_p.G92G|GYPC_ENST00000464053.1_3'UTR|GYPC_ENST00000356887.7_Silent_p.G90G	NM_002101.4	NP_002092.1	P04921	GLPC_HUMAN	glycophorin C (Gerbich blood group)	111						cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|prostate(2)|urinary_tract(1)	13	Colorectal(110;0.0533)			BRCA - Breast invasive adenocarcinoma(221;0.075)		CCCTGCAGGGAGACCCTGCCC	0.552													C|||	3080	0.615016	0.7474	0.572	5008	,	,		20823	0.6806		0.5497	False		,,,				2504	0.4663				p.G111G	Melanoma(110;806 1600 6704 9981 33404)	Atlas-SNP	.											.	GYPC	27	.	0			c.A333C						PASS	.	C	,	3045,1361	452.2+/-349.9	1058,929,216	126.0	102.0	110.0		333,276	-9.6	0.0	2	dbSNP_86	110	4748,3852	542.4+/-384.2	1325,2098,877	no	coding-synonymous,coding-synonymous	GYPC	NM_002101.3,NM_016815.2	,	2383,3027,1093	CC,CA,AA		44.7907,30.8897,40.0815	,	111/129,92/110	127453664	7793,5213	2203	4300	6503	SO:0001819	synonymous_variant	2995	exon4			GCAGGGAGACCCT		CCDS2136.1, CCDS46402.1, CCDS58724.1	2q14-q21	2014-07-19			ENSG00000136732	ENSG00000136732		"""CD molecules"", ""Blood group antigens"""	4704	protein-coding gene	gene with protein product		110750					Standard	NM_016815		Approved	GPC, GYPD, Ge, CD236, CD236R	uc002tnq.4	P04921	OTTHUMG00000131464	ENST00000259254.4:c.333A>C	2.37:g.127453664A>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_002101	B2R522|Q53SV9|Q92642	Silent	SNP	ENST00000259254.4	37	CCDS2136.1																																																																																			A|0.405;C|0.595	0.595	strong		0.552	GYPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254297.1	NM_002101	
GARS	2617	hgsc.bcm.edu	37	7	30673401	30673401	+	Silent	SNP	A	A	G	rs4593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30673401A>G	ENST00000389266.3	+	17	2386	c.2145A>G	c.(2143-2145)acA>acG	p.T715T		NM_002047.2	NP_002038.2	P41250	SYG_HUMAN	glycyl-tRNA synthetase	715					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|glycyl-tRNA aminoacylation (GO:0006426)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|glycine-tRNA ligase activity (GO:0004820)|protein dimerization activity (GO:0046983)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	24					Glycine(DB00145)	GCAACATCACATGGGCTGATG	0.448													A|||	383	0.0764776	0.2474	0.0403	5008	,	,		18938	0.0		0.0278	False		,,,				2504	0.0				p.T715T		Atlas-SNP	.											.	GARS	52	.	0			c.A2145G						PASS	.	A		839,2989		84,671,1159	105.0	98.0	100.0		2145	-2.8	1.0	7	dbSNP_52	100	278,7986		4,270,3858	no	coding-synonymous	GARS	NM_002047.2		88,941,5017	GG,GA,AA		3.364,21.9175,9.2375		715/740	30673401	1117,10975	1914	4132	6046	SO:0001819	synonymous_variant	2617	exon17			CATCACATGGGCT	AK074524	CCDS43564.1	7p15	2014-09-17	2004-02-13		ENSG00000106105	ENSG00000106105	6.1.1.14	"""Aminoacyl tRNA synthetases / Class II"""	4162	protein-coding gene	gene with protein product	"""glycine tRNA ligase"""	600287	"""Charcot-Marie-Tooth neuropathy 2D"""	CMT2D		8595897, 8872480	Standard	NM_002047		Approved	GlyRS, DSMAV, SMAD1	uc003tbm.3	P41250	OTTHUMG00000152769	ENST00000389266.3:c.2145A>G	7.37:g.30673401A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	48	28	0.583333	NM_002047	B3KQA2|B4DIA0|Q969Y1	Silent	SNP	ENST00000389266.3	37	CCDS43564.1																																																																																			A|0.940;G|0.060	0.060	strong		0.448	GARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327735.1	NM_002047	
CTTN	2017	hgsc.bcm.edu	37	11	70279766	70279766	+	Silent	SNP	C	C	T	rs643301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:70279766C>T	ENST00000301843.8	+	17	1664	c.1458C>T	c.(1456-1458)taC>taT	p.Y486Y	CTTN_ENST00000376561.3_Silent_p.Y449Y|CTTN_ENST00000538675.1_Silent_p.Y170Y|CTTN_ENST00000346329.3_Silent_p.Y449Y	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	486					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)		ACAGCACCTACGATGAGTACG	0.532													C|||	917	0.183107	0.2413	0.134	5008	,	,		16466	0.0119		0.1988	False		,,,				2504	0.2996				p.Y486Y		Atlas-SNP	.											.	CTTN	162	.	0			c.C1458T						PASS	.		,,	973,3427	366.4+/-317.8	105,763,1332	156.0	150.0	152.0		1347,1458,1347	-2.7	0.0	11	dbSNP_83	152	1801,6787	325.0+/-316.7	195,1411,2688	no	coding-synonymous,coding-synonymous,coding-synonymous	CTTN	NM_001184740.1,NM_005231.3,NM_138565.2	,,	300,2174,4020	TT,TC,CC		20.9711,22.1136,21.3582	,,	449/635,486/551,449/514	70279766	2774,10214	2200	4294	6494	SO:0001819	synonymous_variant	2017	exon17			CACCTACGATGAG	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.1458C>T	11.37:g.70279766C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_005231	Q8N707|Q96H99	Silent	SNP	ENST00000301843.8	37	CCDS41680.1																																																																																			C|0.811;T|0.189	0.189	strong		0.532	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565	
ZNF135	7694	hgsc.bcm.edu	37	19	58572959	58572959	+	Silent	SNP	G	G	A	rs2288274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58572959G>A	ENST00000313434.5	+	3	146	c.45G>A	c.(43-45)acG>acA	p.T15T	ZNF135_ENST00000506786.1_5'UTR|ZNF135_ENST00000359978.6_Silent_p.T27T|ZNF135_ENST00000439855.2_Silent_p.T15T|ZNF135_ENST00000511556.1_Silent_p.T15T|ZNF135_ENST00000401053.4_Silent_p.T27T	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	15	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		AGCAAGTGACGTTTGAGGACG	0.602													G|||	1351	0.269768	0.2859	0.2277	5008	,	,		18117	0.2649		0.2992	False		,,,				2504	0.2526				p.T27T		Atlas-SNP	.											ZNF135_ENST00000401053,colon,carcinoma,+1,3	ZNF135	159	3	0			c.G81A						scavenged	.	G	,,,,	1289,3117	438.0+/-345.2	185,919,1099	133.0	117.0	122.0		81,81,81,45,81	-1.0	0.9	19	dbSNP_100	122	2345,6255	392.4+/-344.0	308,1729,2263	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF135	NM_001164527.1,NM_001164529.1,NM_001164530.1,NM_003436.3,NM_007134.1	,,,,	493,2648,3362	AA,AG,GG		27.2674,29.2556,27.941	,,,,	27/124,27/116,27/391,15/671,27/683	58572959	3634,9372	2203	4300	6503	SO:0001819	synonymous_variant	7694	exon2			AGTGACGTTTGAG	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"""Zinc fingers, C2H2-type"", ""-"""	12919	protein-coding gene	gene with protein product		604077	"""zinc finger protein 61"", ""zinc finger protein 135 (clone pHZ-17)"""	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.45G>A	19.37:g.58572959G>A		Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	229	102	0.445415	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Silent	SNP	ENST00000313434.5	37		625	0.28617216117216115	158	0.32113821138211385	80	0.22099447513812154	158	0.2762237762237762	229	0.3021108179419525	G	7.475	0.647440	0.14516	0.292556	0.272674	ENSG00000176293	ENST00000391699	.	.	.	2.52	-1.02	0.10135	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999899716	.	.	.	.	.	.	T	0.42207	-0.9465	3	.	.	.	.	1.8703	0.03207	0.1896:0.2962:0.3818:0.1323	rs2288274;rs56480989;rs57809788;rs2288274	.	.	.	H	21	.	.	R	+	2	0	ZNF135	63264771	0.000000	0.05858	0.950000	0.38849	0.869000	0.49853	-2.496000	0.00970	-0.105000	0.12132	-1.339000	0.01253	CGT	G|0.716;A|0.284	0.284	strong		0.602	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436	
OBSCN	84033	hgsc.bcm.edu	37	1	228407260	228407260	+	Intron	SNP	G	G	A	rs1771484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228407260G>A	ENST00000422127.1	+	8	2697				OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000570156.2_Silent_p.E963E|OBSCN_ENST00000284548.11_Intron|OBSCN_ENST00000366709.4_Intron	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)				ACAGCTGTGAGGCCAGGGGAC	0.642													G|||	1388	0.277157	0.3147	0.3487	5008	,	,		19787	0.1746		0.3588	False		,,,				2504	0.1973				p.E963E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G2889A						PASS	.																																			SO:0001627	intron_variant	84033	exon9			CTGTGAGGCCAGG	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.2653+2271G>A	1.37:g.228407260G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	128	68	0.53125	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																																																																																			G|0.718;A|0.282	0.282	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
KMT2A	4297	hgsc.bcm.edu	37	11	118373861	118373861	+	Silent	SNP	C	C	T	rs2071702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118373861C>T	ENST00000389506.5	+	27	7245	c.7245C>T	c.(7243-7245)aaC>aaT	p.N2415N	KMT2A_ENST00000354520.4_Silent_p.N2377N|KMT2A_ENST00000534358.1_Silent_p.N2418N			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2415					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CCATTATCAACGAACATATGG	0.378													T|||	334	0.0666933	0.115	0.0476	5008	,	,		22088	0.0258		0.0626	False		,,,				2504	0.0613				p.N2418N		Atlas-SNP	.											.	MLL	548	.	0			c.C7254T						PASS	.	T	,	505,3895	766.1+/-413.4	32,441,1727	63.0	61.0	61.0		7254,7245	-4.9	0.0	11	dbSNP_96	61	526,8066	793.8+/-407.5	21,484,3791	no	coding-synonymous,coding-synonymous	MLL	NM_001197104.1,NM_005933.3	,	53,925,5518	TT,TC,CC		6.122,11.4773,7.9357	,	2418/3973,2415/3970	118373861	1031,11961	2200	4296	6496	SO:0001819	synonymous_variant	4297	exon27			TATCAACGAACAT	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.7245C>T	11.37:g.118373861C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	37	CCDS31686.1																																																																																			C|0.930;T|0.070	0.070	strong		0.378	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
CLDN23	137075	hgsc.bcm.edu	37	8	8560151	8560151	+	Silent	SNP	G	G	A	rs61754959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8560151G>A	ENST00000519106.1	+	1	704	c.243G>A	c.(241-243)cgG>cgA	p.R81R		NM_194284.2	NP_919260.2	Q96B33	CLD23_HUMAN	claudin 23	81					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	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(2)	2		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.071)|READ - Rectum adenocarcinoma(644;0.238)		TGGTGGCGCGGGCACTCATGG	0.711													G|||	170	0.0339457	0.087	0.0159	5008	,	,		14724	0.0		0.0358	False		,,,				2504	0.0082				p.R81R		Atlas-SNP	.											.	CLDN23	5	.	0			c.G243A						PASS	.	G		285,4007		7,271,1868	12.0	17.0	15.0		243	1.8	0.9	8	dbSNP_129	15	318,8120		6,306,3907	no	coding-synonymous	CLDN23	NM_194284.2		13,577,5775	AA,AG,GG		3.7687,6.6403,4.7368		81/293	8560151	603,12127	2146	4219	6365	SO:0001819	synonymous_variant	137075	exon1			GGCGCGGGCACTC	AK123547	CCDS55195.1	8p23.1	2006-04-12				ENSG00000253958		"""Claudins"""	17591	protein-coding gene	gene with protein product		609203				12736707	Standard	NM_194284		Approved	CLDNL	uc003wsi.3	Q96B33		ENST00000519106.1:c.243G>A	8.37:g.8560151G>A		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	22	18	0.818182	NM_194284	Q08AJ3	Silent	SNP	ENST00000519106.1	37	CCDS55195.1																																																																																			G|0.968;A|0.032	0.032	strong		0.711	CLDN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374721.1	NM_194284	
SSPO	23145	hgsc.bcm.edu	37	7	149493519	149493519	+	RNA	SNP	C	C	T	rs57595625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149493519C>T	ENST00000378016.2	+	0	6595							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)			CCGCATGGTGCAGGCGAGGTT	0.617													C|||	145	0.0289537	0.1059	0.0072	5008	,	,		18965	0.0		0.0	False		,,,				2504	0.0				p.Q2199X		Atlas-SNP	.											.	.	.	.	0			c.C6595T						PASS	.	C		345,3947		8,329,1809	100.0	114.0	110.0		6599	3.6	1.0	7	dbSNP_129	110	3,8491		0,3,4244	yes	coding-notMod3	SSPO	NM_198455.2		8,332,6053	TT,TC,CC		0.0353,8.0382,2.7217			149493519	348,12438	2146	4247	6393			23145	exon44			ATGGTGCAGGCGA	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.149493519C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	139	73	0.52518	NM_198455	Q76B61	Nonsense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.972;T|0.028	0.028	strong		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
SMIM5	643008	hgsc.bcm.edu	37	17	73636368	73636368	+	Silent	SNP	C	C	T	rs117954398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73636368C>T	ENST00000537494.1	+	1	3694	c.87C>T	c.(85-87)ccC>ccT	p.P29P	RECQL5_ENST00000423245.2_Intron|RECQL5_ENST00000317905.5_Intron|SMIM5_ENST00000375215.3_Silent_p.P29P			Q71RC9	SMIM5_HUMAN	small integral membrane protein 5	29						integral component of membrane (GO:0016021)											AGGCTGAGCCCGTGGAGATCG	0.627													C|||	19	0.00379393	0.0	0.0	5008	,	,		18017	0.0		0.0189	False		,,,				2504	0.0				p.P29P		Atlas-SNP	.											.	.	.	.	0			c.C87T						PASS	.	C	,	9,1375		0,9,683	104.0	108.0	107.0		87,	-7.9	0.9	17	dbSNP_132	107	43,3139		0,43,1548	no	coding-synonymous,intron	RECQL5,C17orf109	NM_001162995.2,NM_004259.6	,	0,52,2231	TT,TC,CC		1.3514,0.6503,1.1389	,	29/78,	73636368	52,4514	692	1591	2283	SO:0001819	synonymous_variant	643008	exon2			TGAGCCCGTGGAG		CCDS54165.1	17q25.1	2014-01-02	2012-10-23	2012-10-23	ENSG00000204323	ENSG00000204323			40030	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 109"""	C17orf109		24318988	Standard	NM_001162995		Approved		uc002jow.2	Q71RC9	OTTHUMG00000167882	ENST00000537494.1:c.87C>T	17.37:g.73636368C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	141	62	0.439716	NM_001162995		Silent	SNP	ENST00000537494.1	37	CCDS54165.1																																																																																			C|0.994;T|0.006	0.006	strong		0.627	SMIM5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396808.2	NM_001162995	
OR7A10	390892	hgsc.bcm.edu	37	19	14952560	14952560	+	Missense_Mutation	SNP	G	G	T	rs12985894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14952560G>T	ENST00000248058.1	-	1	129	c.130C>A	c.(130-132)Ctc>Atc	p.L44I		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					AGGATGATGAGCAGGTTCCCG	0.512													.|||	618	0.123403	0.143	0.1196	5008	,	,		18213	0.0903		0.1541	False		,,,				2504	0.1022				p.L44I		Atlas-SNP	.											.	OR7A10	33	.	0			c.C130A						PASS	.	G	ILE/LEU	675,3731	285.7+/-278.4	58,559,1586	70.0	66.0	67.0		130	2.8	1.0	19	dbSNP_121	67	1455,7139	277.4+/-292.8	140,1175,2982	no	missense	OR7A10	NM_001005190.1	5	198,1734,4568	TT,TG,GG		16.9304,15.32,16.3846	possibly-damaging	44/310	14952560	2130,10870	2203	4297	6500	SO:0001583	missense	390892	exon1			TGATGAGCAGGTT		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.130C>A	19.37:g.14952560G>T	ENSP00000248058:p.Leu44Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	109	61	0.559633	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	260	0.11904761904761904	69	0.1402439024390244	48	0.13259668508287292	27	0.0472027972027972	116	0.15303430079155672	g	9.293	1.051138	0.19827	0.1532	0.169304	ENSG00000127515	ENST00000248058	T	0.02606	4.23	2.79	2.79	0.32731	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34133	U	0.004236	T	0.00039	0.0001	L	0.60904	1.88	0.48452	P	3.4199999999995345E-4	P	0.46327	0.876	P	0.54238	0.746	T	0.25293	-1.0136	9	0.72032	D	0.01	.	7.1625	0.25672	0.0:0.0:0.7333:0.2667	rs12985894	44	O76100	OR7AA_HUMAN	I	44	ENSP00000248058:L44I	ENSP00000248058:L44I	L	-	1	0	OR7A10	14813560	0.000000	0.05858	1.000000	0.80357	0.286000	0.27126	-0.617000	0.05584	1.572000	0.49736	0.430000	0.28490	CTC	G|0.856;T|0.144	0.144	strong		0.512	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
C9orf3	84909	hgsc.bcm.edu	37	9	97563076	97563076	+	Missense_Mutation	SNP	C	C	T	rs34557833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:97563076C>T	ENST00000375315.2	+	4	1156	c.1156C>T	c.(1156-1158)Cgc>Tgc	p.R386C	C9orf3_ENST00000277198.2_Missense_Mutation_p.R386C|C9orf3_ENST00000297979.5_Missense_Mutation_p.R386C|C9orf3_ENST00000395357.2_Missense_Mutation_p.R6C	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	386			R -> C (in dbSNP:rs34557833).		leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		ATACCCCTGCCGCTTCCAGAA	0.507													C|||	30	0.00599042	0.0227	0.0	5008	,	,		20701	0.0		0.0	False		,,,				2504	0.0				p.R386C		Atlas-SNP	.											.	C9orf3	100	.	0			c.C1156T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	58,4348	56.2+/-92.4	0,58,2145	102.0	94.0	97.0		1156,1156,1156	4.4	1.0	9	dbSNP_126	97	0,8600		0,0,4300	yes	missense,missense,missense	C9orf3	NM_001193329.1,NM_001193331.2,NM_032823.5	180,180,180	0,58,6445	TT,TC,CC		0.0,1.3164,0.4459	possibly-damaging,possibly-damaging,possibly-damaging	386/820,386/567,386/721	97563076	58,12948	2203	4300	6503	SO:0001583	missense	84909	exon5			CCCTGCCGCTTCC	AF043896	CCDS6713.1, CCDS55327.1, CCDS55328.1	9q22	2013-06-27			ENSG00000148120	ENSG00000148120			1361	protein-coding gene	gene with protein product	aminopeptidase O					15687497	Standard	NM_001193329		Approved	C90RF3, FLJ14675, APO, AOPEP, AP-O	uc004ava.3	Q8N6M6	OTTHUMG00000020276	ENST00000375315.2:c.1156C>T	9.37:g.97563076C>T	ENSP00000364464:p.Arg386Cys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	141	88	0.624114	NM_001193331	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	37	CCDS55328.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	23.3	4.397577	0.83120	0.013164	0.0	ENSG00000148120	ENST00000277198;ENST00000297979;ENST00000375315;ENST00000424143;ENST00000428313;ENST00000395357	T;T;T;T;T;T	0.15952	4.18;2.39;2.74;2.43;2.38;4.18	5.28	4.38	0.52667	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.24084	0.0583	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.995;0.998	T	0.13710	-1.0499	10	0.72032	D	0.01	-13.0857	15.6642	0.77213	0.1375:0.8625:0.0:0.0	rs34557833	386;386;386;386	Q8N6M6;Q8N6M6-4;Q8N6M6-2;Q8N6M6-3	AMPO_HUMAN;.;.;.	C	386;386;386;209;168;6	ENSP00000277198:R386C;ENSP00000297979:R386C;ENSP00000364464:R386C;ENSP00000402171:R209C;ENSP00000401854:R168C;ENSP00000378763:R6C	ENSP00000277198:R386C	R	+	1	0	C9orf3	96602897	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.291000	0.59025	1.432000	0.47375	0.650000	0.86243	CGC	C|0.995;T|0.005	0.005	strong		0.507	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823	
KCNU1	157855	hgsc.bcm.edu	37	8	36767024	36767024	+	Missense_Mutation	SNP	T	T	C	rs28608091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:36767024T>C	ENST00000399881.3	+	21	2339	c.2302T>C	c.(2302-2304)Tgg>Cgg	p.W768R		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	768			W -> R (in dbSNP:rs28608091).		multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		GCGATTTCTCTGGAATTTTCC	0.363													C|||	1902	0.379792	0.3268	0.4827	5008	,	,		16997	0.376		0.4006	False		,,,				2504	0.3609				p.W768R		Atlas-SNP	.											.	KCNU1	359	.	0			c.T2302C						PASS	.	C	ARG/TRP	1230,2436		205,820,808	115.0	114.0	114.0		2302	2.6	1.0	8	dbSNP_125	114	3255,4909		659,1937,1486	yes	missense	KCNU1	NM_001031836.2	101	864,2757,2294	CC,CT,TT		39.8702,33.5516,37.9121	benign	768/1150	36767024	4485,7345	1833	4082	5915	SO:0001583	missense	157855	exon21			TTTCTCTGGAATT	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2302T>C	8.37:g.36767024T>C	ENSP00000382770:p.Trp768Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	108	57	0.527778	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	811	0.37133699633699635	144	0.2926829268292683	169	0.46685082872928174	203	0.3548951048951049	295	0.3891820580474934	C	0.875	-0.730645	0.03135	0.335516	0.398702	ENSG00000215262	ENST00000399881	T	0.39787	1.06	5.8	2.64	0.31445	.	0.229234	0.21687	N	0.070624	T	0.00012	0.0000	N	0.01267	-0.92	0.09310	P	0.99999999579857	B	0.02656	0.0	B	0.01281	0.0	T	0.46484	-0.9188	9	0.06494	T	0.89	-4.8224	8.6358	0.33948	0.2308:0.6384:0.0:0.1308	rs28608091	768	A8MYU2	KCNU1_HUMAN	R	768	ENSP00000382770:W768R	ENSP00000382770:W768R	W	+	1	0	KCNU1	36886182	0.670000	0.27512	0.979000	0.43373	0.017000	0.09413	1.370000	0.34238	0.356000	0.24157	-0.119000	0.15052	TGG	T|0.627;C|0.373	0.373	strong		0.363	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
LHFPL1	340596	hgsc.bcm.edu	37	X	111914244	111914244	+	Silent	SNP	A	A	G	rs7064462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:111914244A>G	ENST00000371968.3	-	2	614	c.375T>C	c.(373-375)ttT>ttC	p.F125F	LHFPL1_ENST00000478229.1_Intron|LHFPL1_ENST00000536453.1_Silent_p.F125F	NM_178175.3	NP_835469.1	Q86WI0	LHPL1_HUMAN	lipoma HMGIC fusion partner-like 1	125						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)	13						TACCTCCAACAAACTGCGCTG	0.572													G|||	871	0.230728	0.5477	0.0893	3775	,	,		14285	0.0		0.0716	False		,,,				2504	0.0133				p.F125F		Atlas-SNP	.											.	LHFPL1	28	.	0			c.T375C						PASS	.	G		2395,1440		655,732,353,245,218	82.0	62.0	68.0		375	-8.0	0.2	X	dbSNP_116	68	522,6206		11,348,152,2069,1720	no	coding-synonymous	LHFPL1	NM_178175.3		666,1080,505,2314,1938	GG,GA,G,AA,A		7.7586,37.5489,27.6153		125/221	111914244	2917,7646	2203	4300	6503	SO:0001819	synonymous_variant	340596	exon2			TCCAACAAACTGC	AY217350	CCDS14562.1	Xq23	2008-02-05			ENSG00000182508	ENSG00000182508			6587	protein-coding gene	gene with protein product		300566				10329012	Standard	NM_178175		Approved		uc004epq.3	Q86WI0	OTTHUMG00000022214	ENST00000371968.3:c.375T>C	X.37:g.111914244A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	100	62	0.62	NM_178175	A8K1N1|Q496M9|Q496N0|Q6UXU2	Silent	SNP	ENST00000371968.3	37	CCDS14562.1																																																																																			A|0.714;0|0.003	.	strong		0.572	LHFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057947.1	NM_178175	
OGFOD3	79701	hgsc.bcm.edu	37	17	80373453	80373453	+	Missense_Mutation	SNP	G	G	A	rs61742456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80373453G>A	ENST00000313056.5	-	2	276	c.125C>T	c.(124-126)cCg>cTg	p.P42L	Y_RNA_ENST00000364369.1_RNA|OGFOD3_ENST00000329197.5_Missense_Mutation_p.P42L|HEXDC_ENST00000337014.6_5'Flank	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	42						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)										CCTTAGCCACGGCCTCTGCCA	0.672													G|||	13	0.00259585	0.0038	0.0072	5008	,	,		15837	0.0		0.002	False		,,,				2504	0.001				p.P42L		Atlas-SNP	.											.	.	.	.	0			c.C125T						PASS	.	G	LEU/PRO,LEU/PRO	11,4395	15.5+/-35.6	0,11,2192	28.0	32.0	30.0		125,125	-6.8	0.0	17	dbSNP_129	30	32,8568	20.4+/-63.3	0,32,4268	yes	missense,missense	C17orf101	NM_024648.2,NM_175902.4	98,98	0,43,6460	AA,AG,GG		0.3721,0.2497,0.3306	benign,benign	42/320,42/332	80373453	43,12963	2203	4300	6503	SO:0001583	missense	79701	exon2			AGCCACGGCCTCT	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.125C>T	17.37:g.80373453G>A	ENSP00000320116:p.Pro42Leu	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	54	32	0.592593	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Missense_Mutation	SNP	ENST00000313056.5	37	CCDS11811.1	5	0.0022893772893772895	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	10.25	1.299021	0.23650	0.002497	0.003721	ENSG00000181396	ENST00000313056;ENST00000329197	T;T	0.28895	2.05;1.59	5.0	-6.77	0.01727	.	0.937389	0.08845	N	0.885310	T	0.10078	0.0247	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.21280	-1.0250	10	0.27082	T	0.32	-1.2083	0.9917	0.01458	0.2458:0.3165:0.1245:0.3132	.	42;42	Q6PK18;Q6PK18-2	CQ101_HUMAN;.	L	42	ENSP00000320116:P42L;ENSP00000330075:P42L	ENSP00000320116:P42L	P	-	2	0	C17orf101	77966742	0.044000	0.20184	0.000000	0.03702	0.021000	0.10359	0.283000	0.18846	-1.664000	0.01479	-0.857000	0.03018	CCG	G|0.997;A|0.003	0.003	strong		0.672	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	
PTPRJ	5795	hgsc.bcm.edu	37	11	48149352	48149352	+	Missense_Mutation	SNP	G	G	A	rs2229703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48149352G>A	ENST00000418331.2	+	7	1466	c.1114G>A	c.(1114-1116)Gtc>Atc	p.V372I	PTPRJ_ENST00000440289.2_Missense_Mutation_p.V372I	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	372	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs2229703).		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.V372L(1)		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						GGTTTTTGACGTCACCGCTGT	0.498													G|||	156	0.0311502	0.1112	0.0115	5008	,	,		23784	0.0		0.0	False		,,,				2504	0.001				p.V372I		Atlas-SNP	.											PTPRJ_ENST00000418331,rectum,carcinoma,-1,5	PTPRJ	225	5	1	Substitution - Missense(1)	kidney(1)	c.G1114A						PASS	.	G	ILE/VAL,ILE/VAL	397,4005	197.7+/-221.8	9,379,1813	108.0	95.0	99.0		1114,1114	-11.5	0.0	11	dbSNP_98	99	4,8592	1.2+/-3.3	0,4,4294	yes	missense,missense	PTPRJ	NM_001098503.1,NM_002843.3	29,29	9,383,6107	AA,AG,GG		0.0465,9.0186,3.0851	benign,benign	372/540,372/1338	48149352	401,12597	2201	4298	6499	SO:0001583	missense	5795	exon7			TTTGACGTCACCG	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.1114G>A	11.37:g.48149352G>A	ENSP00000400010:p.Val372Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	96	38	0.395833	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	G	4.166	0.029336	0.08054	0.090186	4.65E-4	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289	T;T	0.59906	0.23;0.23	5.75	-11.5	0.00074	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00637	0.0021	N	0.04297	-0.235	0.09310	N	1	B;P	0.36027	0.035;0.533	B;B	0.34652	0.024;0.187	T	0.28713	-1.0035	9	0.23302	T	0.38	.	9.7949	0.40728	0.1072:0.3001:0.5182:0.0745	rs2229703;rs16905649;rs56484607;rs16905649	372;372	Q12913;Q6P4H4	PTPRJ_HUMAN;.	I	372	ENSP00000400010:V372I;ENSP00000409733:V372I	ENSP00000278456:V372I	V	+	1	0	PTPRJ	48105928	0.000000	0.05858	0.000000	0.03702	0.188000	0.23474	-1.405000	0.02492	-3.757000	0.00111	-0.136000	0.14681	GTC	G|0.964;A|0.036	0.036	strong		0.498	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
CENPE	1062	hgsc.bcm.edu	37	4	104070041	104070041	+	Missense_Mutation	SNP	G	G	A	rs79431579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:104070041G>A	ENST00000265148.3	-	28	3892	c.3803C>T	c.(3802-3804)aCt>aTt	p.T1268I	CENPE_ENST00000380026.3_Missense_Mutation_p.T1243I	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1268					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TAAGTCCTGAGTATTTATTAT	0.338													G|||	53	0.0105831	0.0318	0.0101	5008	,	,		19012	0.0		0.001	False		,,,				2504	0.0031				p.T1268I		Atlas-SNP	.											.	CENPE	253	.	0			c.C3803T						PASS	.	G	ILE/THR	160,4246	106.9+/-145.3	4,152,2047	138.0	143.0	141.0		3803	-6.5	0.0	4	dbSNP_131	141	15,8585	10.5+/-38.8	0,15,4285	yes	missense	CENPE	NM_001813.2	89	4,167,6332	AA,AG,GG		0.1744,3.6314,1.3455	benign	1268/2702	104070041	175,12831	2203	4300	6503	SO:0001583	missense	1062	exon28			TCCTGAGTATTTA	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.3803C>T	4.37:g.104070041G>A	ENSP00000265148:p.Thr1268Ile	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	185	92	0.497297	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	24	0.01098901098901099	20	0.04065040650406504	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	11.01	1.512446	0.27123	0.036314	0.001744	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.71341	-0.56;-0.56	4.06	-6.52	0.01872	.	.	.	.	.	T	0.11239	0.0274	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	0.14364	-1.0475	9	0.16896	T	0.51	.	6.5259	0.22301	0.2333:0.0:0.5348:0.232	.	1243;1268	Q02224-3;Q02224	.;CENPE_HUMAN	I	1268;1268;1243	ENSP00000265148:T1268I;ENSP00000369365:T1243I	ENSP00000265148:T1268I	T	-	2	0	CENPE	104289490	0.000000	0.05858	0.000000	0.03702	0.537000	0.34900	-1.463000	0.02361	-1.120000	0.02953	-1.155000	0.01812	ACT	G|0.985;A|0.015	0.015	strong		0.338	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FPR1	2357	hgsc.bcm.edu	37	19	52249672	52249672	+	Missense_Mutation	SNP	A	A	C	rs1042229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52249672A>C	ENST00000595042.1	-	3	717	c.576T>G	c.(574-576)aaT>aaG	p.N192K	FPR1_ENST00000304748.4_Missense_Mutation_p.N192K	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	192			N -> K (in dbSNP:rs1042229). {ECO:0000269|PubMed:1612600, ECO:0000269|Ref.7}.		activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)	p.N192N(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	CAACGGCCACATTTATCCTCT	0.498													C|||	1831	0.365615	0.4879	0.2882	5008	,	,		21616	0.2917		0.3588	False		,,,				2504	0.3384				p.N192K		Atlas-SNP	.											FPR1,NS,carcinoma,0,1	FPR1	64	1	1	Substitution - coding silent(1)	stomach(1)	c.T576G						PASS	.	C	LYS/ASN,LYS/ASN	2231,2175		528,1175,500	118.0	109.0	112.0		576,576	1.5	0.0	19	dbSNP_86	112	3403,5197		522,2359,1419	yes	missense,missense	FPR1	NM_001193306.1,NM_002029.3	94,94	1050,3534,1919	CC,CA,AA		39.5698,49.3645,43.3185	benign,benign	192/351,192/351	52249672	5634,7372	2203	4300	6503	SO:0001583	missense	2357	exon3			GGCCACATTTATC	M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"""GPCR / Class A : Formyl peptide receptors"""	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.576T>G	19.37:g.52249672A>C	ENSP00000471493:p.Asn192Lys	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	37	CCDS12839.1	879	0.4024725274725275	240	0.4878048780487805	139	0.3839779005524862	203	0.3548951048951049	297	0.391820580474934	.	0.033	-1.321458	0.01320	0.506355	0.395698	ENSG00000171051	ENST00000304748	T	0.61040	0.14	3.66	1.46	0.22682	GPCR, rhodopsin-like superfamily (1);	0.550741	0.14764	N	0.299814	T	0.00012	0.0000	N	0.01482	-0.84	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.43426	-0.9392	9	0.02654	T	1	.	3.6023	0.08030	0.1799:0.5269:0.0:0.2932	rs1042229;rs52821418;rs1042229	192	P21462	FPR1_HUMAN	K	192	ENSP00000302707:N192K	ENSP00000302707:N192K	N	-	3	2	FPR1	56941484	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.000000	0.12993	0.009000	0.14813	-0.121000	0.15023	AAT	G|0.018;C|0.428;A|0.554	0.428	strong		0.498	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029	
ACCSL	390110	hgsc.bcm.edu	37	11	44069589	44069589	+	Start_Codon_SNP	SNP	G	G	A	rs3094398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44069589G>A	ENST00000378832.1	+	1	59	c.3G>A	c.(1-3)atG>atA	p.M1I		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	1					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						CCCGGAGTATGAGTCATCGGT	0.562													G|||	72	0.014377	0.053	0.0029	5008	,	,		20512	0.0		0.0	False		,,,				2504	0.0				p.M1I		Atlas-SNP	.											.	ACCSL	57	.	0			c.G3A						PASS	.	G	ILE/MET	158,3748		1,156,1796	58.0	60.0	59.0		3	0.3	0.0	11	dbSNP_103	59	0,8304		0,0,4152	yes	missense	ACCSL	NM_001031854.2	10	1,156,5948	AA,AG,GG		0.0,4.0451,1.294	benign	1/569	44069589	158,12052	1953	4152	6105	SO:0001582	initiator_codon_variant	390110	exon1			GAGTATGAGTCAT		CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.3G>A	11.37:g.44069589G>A	ENSP00000368109:p.Met1Ile	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_001031854		Missense_Mutation	SNP	ENST00000378832.1	37	CCDS41636.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	G	8.750	0.921130	0.17982	0.040451	0.0	ENSG00000205126	ENST00000378832	T	0.69040	-0.37	3.28	0.309	0.15820	.	0.437153	0.18726	N	0.132862	T	0.06554	0.0168	.	.	.	0.49299	D	0.999777	B	0.22003	0.063	B	0.14023	0.01	T	0.05666	-1.0871	9	0.46703	T	0.11	-1.1221	4.9599	0.14061	0.4511:0.0:0.5489:0.0	rs3094398;rs52832585;rs56504395;rs3094398	1	Q4AC99	1A1L2_HUMAN	I	1	ENSP00000368109:M1I	ENSP00000368109:M1I	M	+	3	0	ACCSL	44026165	0.115000	0.22152	0.024000	0.17045	0.018000	0.09664	0.130000	0.15850	0.065000	0.16485	0.563000	0.77884	ATG	G|0.977;A|0.023	0.023	strong		0.562	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854	Missense_Mutation
SERPINE2	5270	hgsc.bcm.edu	37	2	224862842	224862842	+	Silent	SNP	A	A	G	rs12457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:224862842A>G	ENST00000258405.4	-	3	719	c.477T>C	c.(475-477)aaT>aaC	p.N159N	SERPINE2_ENST00000447280.2_Silent_p.N171N|SERPINE2_ENST00000409840.3_Silent_p.N159N|SERPINE2_ENST00000409304.1_Silent_p.N159N	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	159				N -> D (in Ref. 4; BAG35401). {ECO:0000305}.	blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CCCTGGTTTCATTTTTAACCC	0.453													G|||	1272	0.253994	0.4826	0.2161	5008	,	,		20707	0.129		0.1909	False		,,,				2504	0.1656				p.N171N		Atlas-SNP	.											.	SERPINE2	103	.	0			c.T513C						PASS	.	G	,,	1957,2449	621.9+/-393.8	440,1077,686	71.0	66.0	68.0		477,513,477	-1.8	0.5	2	dbSNP_116	68	1679,6921	739.8+/-407.1	161,1357,2782	no	coding-synonymous,coding-synonymous,coding-synonymous	SERPINE2	NM_001136528.1,NM_001136530.1,NM_006216.3	,,	601,2434,3468	GG,GA,AA		19.5233,44.4167,27.9563	,,	159/398,171/410,159/399	224862842	3636,9370	2203	4300	6503	SO:0001819	synonymous_variant	5270	exon3			GGTTTCATTTTTA	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"""Serine (or cysteine) peptidase inhibitors"""	8951	protein-coding gene	gene with protein product	"""glial-derived nexin 1"""	177010	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"""	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.477T>C	2.37:g.224862842A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	45	0.428571	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Silent	SNP	ENST00000258405.4	37	CCDS2460.1																																																																																			A|0.718;G|0.282	0.282	strong		0.453	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216	
CCDC116	164592	hgsc.bcm.edu	37	22	21989230	21989230	+	Missense_Mutation	SNP	C	C	T	rs41279987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21989230C>T	ENST00000292779.3	+	4	1039	c.878C>T	c.(877-879)cCg>cTg	p.P293L	CCDC116_ENST00000607942.1_Missense_Mutation_p.P293L	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	293			P -> L (in dbSNP:rs41279987).							endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					GGCTACTGTCCGCTCCGTGAG	0.597													C|||	124	0.0247604	0.0893	0.0086	5008	,	,		19728	0.0		0.0	False		,,,				2504	0.0				p.P293L		Atlas-SNP	.											CCDC116,NS,carcinoma,-1,1	CCDC116	56	1	0			c.C878T						PASS	.	C	LEU/PRO	278,4128	155.5+/-188.7	7,264,1932	78.0	80.0	79.0		878	2.1	0.0	22	dbSNP_127	79	3,8597	3.0+/-9.4	0,3,4297	yes	missense	CCDC116	NM_152612.2	98	7,267,6229	TT,TC,CC		0.0349,6.3096,2.1605	benign	293/614	21989230	281,12725	2203	4300	6503	SO:0001583	missense	164592	exon4			ACTGTCCGCTCCG	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.878C>T	22.37:g.21989230C>T	ENSP00000292779:p.Pro293Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	C	11.67	1.706989	0.30232	0.063096	3.49E-4	ENSG00000161180	ENST00000292779	T	0.12465	2.68	4.39	2.13	0.27403	.	0.960630	0.08582	N	0.924354	T	0.00328	0.0010	L	0.34521	1.04	0.09310	N	1	P;P	0.38863	0.65;0.65	B;B	0.29524	0.103;0.064	T	0.33624	-0.9861	10	0.72032	D	0.01	-14.4612	4.7066	0.12853	0.2143:0.6741:0.0:0.1116	rs41279987	293;293	B7Z7H5;Q8IYX3-2	.;.	L	293	ENSP00000292779:P293L	ENSP00000292779:P293L	P	+	2	0	CCDC116	20319230	0.000000	0.05858	0.003000	0.11579	0.260000	0.26232	0.439000	0.21575	1.216000	0.43427	0.561000	0.74099	CCG	C|0.974;T|0.026	0.026	strong		0.597	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
CALCRL	10203	hgsc.bcm.edu	37	2	188250275	188250275	+	Missense_Mutation	SNP	A	A	T	rs13391909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:188250275A>T	ENST00000409998.1	-	5	829	c.48T>A	c.(46-48)ttT>ttA	p.F16L	CALCRL_ENST00000410068.1_Missense_Mutation_p.F16L|AC007319.1_ENST00000453517.1_RNA|CALCRL_ENST00000392370.3_Missense_Mutation_p.F16L|AC007319.1_ENST00000412276.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	16			F -> L (in dbSNP:rs13391909).		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)			endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			TGCTTACCATAAAAAAAGGCA	0.274													A|||	207	0.0413339	0.1483	0.0159	5008	,	,		15603	0.0		0.0	False		,,,				2504	0.0				p.F16L		Atlas-SNP	.											.	CALCRL	73	.	0			c.T48A						PASS	.	A	LEU/PHE	527,3865		26,475,1695	30.0	33.0	32.0		48	-3.4	0.0	2	dbSNP_121	32	8,8520		0,8,4256	yes	missense	CALCRL	NM_005795.4	22	26,483,5951	TT,TA,AA		0.0938,11.9991,4.1409	benign	16/462	188250275	535,12385	2196	4264	6460	SO:0001583	missense	10203	exon3			TACCATAAAAAAA	U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"""GPCR / Class B : Calcitonin receptors"""	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.48T>A	2.37:g.188250275A>T	ENSP00000386972:p.Phe16Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_001271751	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	37	CCDS2293.1	96	0.04395604395604396	92	0.18699186991869918	4	0.011049723756906077	0	0.0	0	0.0	A	0.734	-0.779016	0.02929	0.119991	9.38E-4	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068;ENST00000447403;ENST00000410102	T;T;T;T;T	0.59906	1.04;1.04;1.04;1.57;0.23	5.81	-3.39	0.04868	.	1.007640	0.07990	N	0.986908	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07501	-1.0769	9	0.09843	T	0.71	.	4.5787	0.12248	0.3334:0.0:0.1511:0.5155	rs13391909;rs52830213;rs13391909	16	Q16602	CALRL_HUMAN	L	16	ENSP00000376177:F16L;ENSP00000386972:F16L;ENSP00000387190:F16L;ENSP00000415626:F16L;ENSP00000386599:F16L	ENSP00000376177:F16L	F	-	3	2	CALCRL	187958520	0.102000	0.21896	0.017000	0.16124	0.202000	0.24057	0.018000	0.13422	-0.859000	0.04105	-0.468000	0.05107	TTT	A|0.954;T|0.046	0.046	strong		0.274	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795	
UBR4	23352	hgsc.bcm.edu	37	1	19482788	19482788	+	Missense_Mutation	SNP	T	T	C	rs145733997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19482788T>C	ENST00000375254.3	-	42	6076	c.6049A>G	c.(6049-6051)Att>Gtt	p.I2017V	UBR4_ENST00000375226.2_Missense_Mutation_p.I2017V|UBR4_ENST00000375267.2_Missense_Mutation_p.I2017V|UBR4_ENST00000375217.2_Missense_Mutation_p.I2017V	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2017					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)			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)		GCGGTGACAATTGCTAACTCG	0.433													T|||	15	0.00299521	0.0106	0.0	5008	,	,		21210	0.0		0.0	False		,,,				2504	0.001				p.I2017V		Atlas-SNP	.											.	UBR4	415	.	0			c.A6049G						PASS	.	T	VAL/ILE	11,4395	19.1+/-41.9	0,11,2192	132.0	119.0	123.0		6049	5.4	1.0	1	dbSNP_134	123	0,8600		0,0,4300	yes	missense	UBR4	NM_020765.2	29	0,11,6492	CC,CT,TT		0.0,0.2497,0.0846	benign	2017/5184	19482788	11,12995	2203	4300	6503	SO:0001583	missense	23352	exon42			TGACAATTGCTAA	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.6049A>G	1.37:g.19482788T>C	ENSP00000364403:p.Ile2017Val	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	192	95	0.494792	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	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	11.40	1.626757	0.28978	0.002497	0.0	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;3.45	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.08980	0.0222	N	0.01482	-0.84	0.80722	D	1	P	0.35745	0.518	P	0.47827	0.558	T	0.47636	-0.9102	10	0.09590	T	0.72	.	15.6048	0.76658	0.0:0.0:0.0:1.0	.	2017	Q5T4S7	UBR4_HUMAN	V	2017;2017;2017;2017;727;1233	ENSP00000364403:I2017V;ENSP00000364416:I2017V;ENSP00000364365:I2017V;ENSP00000364374:I2017V;ENSP00000404897:I727V	ENSP00000364365:I2017V	I	-	1	0	UBR4	19355375	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	5.563000	0.67352	2.270000	0.75569	0.482000	0.46254	ATT	T|0.999;C|0.001	0.001	strong		0.433	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
RAD51D	5892	hgsc.bcm.edu	37	17	33445549	33445549	+	Silent	SNP	G	G	A	rs9901455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33445549G>A	ENST00000345365.6	-	3	489	c.234C>T	c.(232-234)tcC>tcT	p.S78S	RAD51D_ENST00000394589.4_Silent_p.S78S|RAD51D_ENST00000460118.2_5'UTR|RAD51D_ENST00000335858.7_Intron|RAD51D_ENST00000360276.3_Silent_p.S78S|RAD51D_ENST00000357906.3_Silent_p.S78S|RAD51D_ENST00000590380.1_Intron|RAD51L3-RFFL_ENST00000593039.1_Intron|RAD51D_ENST00000590016.1_Intron	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D	78	Preferencially binds ssDNA.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|reciprocal meiotic recombination (GO:0007131)|strand invasion (GO:0042148)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|gamma-tubulin binding (GO:0043015)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						GGATGGCAGTGGAGGTCTTCA	0.587								Direct reversal of damage					G|||	939	0.1875	0.3517	0.1153	5008	,	,		16450	0.2262		0.0755	False		,,,				2504	0.092				p.S78S		Atlas-SNP	.											.	RAD51D	53	.	0			c.C234T						PASS	.	G	,,	1357,3049	451.0+/-349.5	209,939,1055	90.0	92.0	92.0		,234,	3.8	1.0	17	dbSNP_119	92	705,7895	173.6+/-224.1	25,655,3620	no	intron,coding-synonymous,intron	RAD51D	NM_001142571.1,NM_002878.3,NM_133629.2	,,	234,1594,4675	AA,AG,GG		8.1977,30.7989,15.8542	,,	,78/329,	33445549	2062,10944	2203	4300	6503	SO:0001819	synonymous_variant	5892	exon3			GGCAGTGGAGGTC	AF034956	CCDS11287.1, CCDS11288.1, CCDS45646.1	17q11	2014-09-17	2013-07-02	2011-07-01	ENSG00000185379	ENSG00000185379			9823	protein-coding gene	gene with protein product	"""recombination repair protein"", ""DNA repair protein RAD51 homolog 4"""	602954	"""RAD51 (S. cerevisiae)-like 3"", ""RAD51-like 3 (S. cerevisiae)"", ""RAD51 homolog D (S. cerevisiae)"""	RAD51L3		9570954	Standard	NM_001142571		Approved	R51H3, Trad, HsTRAD	uc010ctj.2	O75771	OTTHUMG00000132930	ENST00000345365.6:c.234C>T	17.37:g.33445549G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_002878	B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Silent	SNP	ENST00000345365.6	37	CCDS11287.1																																																																																			G|0.828;A|0.172	0.172	strong		0.587	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878	
TGM6	343641	hgsc.bcm.edu	37	20	2398017	2398017	+	Silent	SNP	G	G	A	rs2295077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2398017G>A	ENST00000202625.2	+	10	1537	c.1476G>A	c.(1474-1476)aaG>aaA	p.K492K	TGM6_ENST00000381423.1_Silent_p.K492K	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	492					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	CTGCCACCAAGCCCAGCATCG	0.652													G|||	1625	0.324481	0.5121	0.1931	5008	,	,		18063	0.3333		0.1561	False		,,,				2504	0.3282				p.K492K		Atlas-SNP	.											.	TGM6	126	.	0			c.G1476A						PASS	.	G		2056,2350	552.3+/-378.5	483,1090,630	43.0	38.0	40.0		1476	3.6	1.0	20	dbSNP_100	40	1476,7124	274.3+/-291.2	120,1236,2944	no	coding-synonymous	TGM6	NM_198994.2		603,2326,3574	AA,AG,GG		17.1628,46.6636,27.1567		492/707	2398017	3532,9474	2203	4300	6503	SO:0001819	synonymous_variant	343641	exon10			CACCAAGCCCAGC	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1476G>A	20.37:g.2398017G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	37	CCDS13025.1																																																																																			G|0.719;A|0.281	0.281	strong		0.652	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
ABCC11	85320	hgsc.bcm.edu	37	16	48250031	48250031	+	Silent	SNP	T	T	C	rs11860868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48250031T>C	ENST00000394747.1	-	6	1294	c.945A>G	c.(943-945)ccA>ccG	p.P315P	ABCC11_ENST00000356608.2_Silent_p.P315P|ABCC11_ENST00000353782.5_Silent_p.P315P|ABCC11_ENST00000394748.1_Silent_p.P315P|ABCC11_ENST00000537808.1_Silent_p.P315P	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	315	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|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)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	TTACCGCCAGTGGGAAAACCA	0.473													C|||	295	0.0589058	0.2156	0.013	5008	,	,		21846	0.0		0.001	False		,,,				2504	0.0				p.P315P		Atlas-SNP	.											.	ABCC11	177	.	0			c.A945G						PASS	.	C	,,	768,3634	752.7+/-412.3	65,638,1498	128.0	132.0	130.0		945,945,945	-6.8	0.0	16	dbSNP_120	130	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	65,642,5794	CC,CT,TT		0.0465,17.4466,5.9375	,,	315/1383,315/1383,315/1345	48250031	772,12230	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon6			CGCCAGTGGGAAA	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.945A>G	16.37:g.48250031T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			T|0.927;C|0.073	0.073	strong		0.473	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
MT-ND4	4538	hgsc.bcm.edu	37	M	11719	11719	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11719G>A	ENST00000361381.2	+	1	960	c.960G>A	c.(958-960)ggG>ggA	p.G320G	MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TE_ENST00000387459.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	320					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						ATCGCCCACGGACTCACATCC	0.483																																					p.G320G		Atlas-SNP	.											.	.	.	.	0			c.G960A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CCACGGGCTTACA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.960G>A	M.37:g.11719G>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.483	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
NWD1	284434	hgsc.bcm.edu	37	19	16899865	16899865	+	Missense_Mutation	SNP	A	A	G	rs2608738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16899865A>G	ENST00000552788.1	+	11	2804	c.2804A>G	c.(2803-2805)cAc>cGc	p.H935R	NWD1_ENST00000523826.1_Missense_Mutation_p.H729R|NWD1_ENST00000339803.6_Missense_Mutation_p.H800R|NWD1_ENST00000549814.1_Missense_Mutation_p.H935R|NWD1_ENST00000379808.3_Missense_Mutation_p.H935R|NWD1_ENST00000524140.2_Missense_Mutation_p.H935R			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	935			H -> R (in dbSNP:rs2608738).				ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TACACGCTGCACTTGTGGAAC	0.502													G|||	1014	0.202476	0.6195	0.0749	5008	,	,		18661	0.0		0.0457	False		,,,				2504	0.0992				p.H935R		Atlas-SNP	.											NWD1_ENST00000524140,colon,carcinoma,0,2	NWD1	303	2	0			c.A2804G						PASS	.	G	ARG/HIS	2185,2221	591.2+/-387.5	563,1059,581	113.0	110.0	111.0		2804	5.7	0.8	19	dbSNP_100	111	411,8189	801.2+/-407.4	9,393,3898	yes	missense	NWD1	NM_001007525.3	29	572,1452,4479	GG,GA,AA		4.7791,49.5915,19.96	benign	935/1433	16899865	2596,10410	2203	4300	6503	SO:0001583	missense	284434	exon13			CGCTGCACTTGTG	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.2804A>G	19.37:g.16899865A>G	ENSP00000447224:p.His935Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		350	0.16025641025641027	290	0.5894308943089431	24	0.06629834254143646	0	0.0	36	0.047493403693931395	G	0.025	-1.384694	0.01194	0.495915	0.047791	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74	5.65	5.65	0.86999	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.060649	0.64402	N	0.000006	T	0.00012	0.0000	N	0.00599	-1.345	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	0.40040	-0.9584	9	0.07482	T	0.82	-12.7912	10.8097	0.46540	0.0877:0.0:0.9123:0.0	rs2608738;rs57504421;rs2608738	935;935;800	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	R	800;935;935;935;729;935;800	ENSP00000428579:H935R;ENSP00000447548:H935R;ENSP00000369136:H935R;ENSP00000428955:H729R;ENSP00000447224:H935R;ENSP00000340159:H800R	ENSP00000340159:H800R	H	+	2	0	NWD1	16760865	0.991000	0.36638	0.815000	0.32552	0.011000	0.07611	2.810000	0.47979	1.403000	0.46800	-0.186000	0.12905	CAC	A|0.798;G|0.202	0.202	strong		0.502	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
RNF157	114804	hgsc.bcm.edu	37	17	74163821	74163821	+	Silent	SNP	G	G	A	rs2289603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74163821G>A	ENST00000269391.6	-	4	486	c.354C>T	c.(352-354)taC>taT	p.Y118Y	RNF157_ENST00000319945.6_Silent_p.Y118Y	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	118							zinc ion binding (GO:0008270)			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)			ACTCAACATTGTAGTGGACTT	0.468													G|||	984	0.196486	0.1959	0.2334	5008	,	,		18539	0.1399		0.1819	False		,,,				2504	0.2444				p.Y118Y	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.C354T						PASS	.	G		876,3530	341.8+/-306.9	99,678,1426	193.0	172.0	179.0		354	5.0	1.0	17	dbSNP_100	179	1609,6991	299.4+/-304.4	142,1325,2833	no	coding-synonymous	RNF157	NM_052916.2		241,2003,4259	AA,AG,GG		18.7093,19.882,19.1066		118/680	74163821	2485,10521	2203	4300	6503	SO:0001819	synonymous_variant	114804	exon4			AACATTGTAGTGG	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.354C>T	17.37:g.74163821G>A		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	229	229	1	NM_052916	Q8NB72|Q96N56	Silent	SNP	ENST00000269391.6	37	CCDS32740.1																																																																																			G|0.818;A|0.182	0.182	strong		0.468	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732	
GRID2IP	392862	hgsc.bcm.edu	37	7	6554126	6554126	+	Missense_Mutation	SNP	C	C	A	rs115745154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6554126C>A	ENST00000457091.2	-	8	1302	c.1303G>T	c.(1303-1305)Gtg>Ttg	p.V435L	GRID2IP_ENST00000435185.1_Missense_Mutation_p.V252L|GRID2IP_ENST00000452113.1_Missense_Mutation_p.V245L	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	435					long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						GTGTCCAGCACAGGGTAGACG	0.562													C|||	76	0.0151757	0.0537	0.0029	5008	,	,		21578	0.0		0.003	False		,,,				2504	0.0				p.V435L		Atlas-SNP	.											.	GRID2IP	82	.	0			c.G1303T						PASS	.	C	LEU/VAL	54,1330		0,54,638	105.0	112.0	110.0		1303	4.6	1.0	7	dbSNP_132	110	4,3178		0,4,1587	yes	missense	GRID2IP	NM_001145118.1	32	0,58,2225	AA,AC,CC		0.1257,3.9017,1.2703	benign	435/1212	6554126	58,4508	692	1591	2283	SO:0001583	missense	392862	exon8			CCAGCACAGGGTA		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.1303G>T	7.37:g.6554126C>A	ENSP00000397351:p.Val435Leu	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001145118		Missense_Mutation	SNP	ENST00000457091.2	37	CCDS47537.1	32	0.014652014652014652	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	28.6	4.930134	0.92389	0.039017	0.001257	ENSG00000215045	ENST00000452113;ENST00000435185;ENST00000457091	T;T;T	0.55588	0.51;0.51;0.53	4.61	4.61	0.57282	.	0.000000	0.64402	U	0.000001	T	0.22244	0.0536	M	0.63843	1.955	0.80722	D	1	D	0.64830	0.994	D	0.72625	0.978	T	0.56974	-0.7890	10	0.87932	D	0	.	15.3026	0.73966	0.0:1.0:0.0:0.0	.	435	A4D2P6	GRD2I_HUMAN	L	245;252;435	ENSP00000397887:V245L;ENSP00000408364:V252L;ENSP00000397351:V435L	ENSP00000408364:V252L	V	-	1	0	GRID2IP	6520651	1.000000	0.71417	0.988000	0.46212	0.970000	0.65996	5.714000	0.68422	2.263000	0.75096	0.563000	0.77884	GTG	C|0.986;A|0.014	0.014	strong		0.562	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
GPR98	84059	hgsc.bcm.edu	37	5	90046508	90046508	+	Silent	SNP	A	A	T	rs138029547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:90046508A>T	ENST00000405460.2	+	53	11211	c.11115A>T	c.(11113-11115)tcA>tcT	p.S3705S		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3705	Calx-beta 24. {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)		TTCCTACCTCAGGAGTGGTAT	0.378													A|||	6	0.00119808	0.0045	0.0	5008	,	,		8333	0.0		0.0	False		,,,				2504	0.0				p.S3705S		Atlas-SNP	.											.	GPR98	605	.	0			c.A11115T						PASS	.	A		20,3702		1,18,1842	161.0	160.0	161.0		11115	-0.2	1.0	5	dbSNP_134	161	0,8178		0,0,4089	no	coding-synonymous	GPR98	NM_032119.3		1,18,5931	TT,TA,AA		0.0,0.5373,0.1681		3705/6307	90046508	20,11880	1861	4089	5950	SO:0001819	synonymous_variant	84059	exon53			TACCTCAGGAGTG	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.11115A>T	5.37:g.90046508A>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	45	0.5625	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	10.33	1.319299	0.23994	0.005373	0.0	ENSG00000164199	ENST00000509621	.	.	.	5.22	-0.155	0.13395	.	.	.	.	.	T	0.36635	0.0974	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17899	-1.0354	4	.	.	.	.	4.082	0.09931	0.4998:0.0:0.2692:0.231	.	.	.	.	L	1271	.	.	Q	+	2	0	GPR98	90082264	0.932000	0.31603	0.997000	0.53966	0.994000	0.84299	0.065000	0.14466	-0.183000	0.10585	-0.250000	0.11733	CAG	A|0.999;G|0.001	.	strong		0.378	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
PTPRQ	374462	hgsc.bcm.edu	37	12	80935345	80935345	+	Missense_Mutation	SNP	T	T	C	rs6539524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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	61	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	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	
WWP1	11059	hgsc.bcm.edu	37	8	87439926	87439926	+	Silent	SNP	C	C	T	rs60177164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87439926C>T	ENST00000517970.1	+	11	1519	c.1212C>T	c.(1210-1212)acC>acT	p.T404T	WWP1_ENST00000349423.2_Silent_p.T186T|WWP1_ENST00000341922.2_Silent_p.T274T|WWP1_ENST00000265428.4_Silent_p.T404T	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	404	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						ATCATAACACCAGAACAACAA	0.393													C|||	793	0.158347	0.5265	0.0749	5008	,	,		15248	0.002		0.0278	False		,,,				2504	0.0153				p.T404T		Atlas-SNP	.											.	WWP1	97	.	0			c.C1212T						PASS	.	C		1754,2652	522.7+/-370.9	352,1050,801	154.0	149.0	151.0		1212	2.7	1.0	8	dbSNP_129	151	195,8405	84.5+/-147.0	1,193,4106	no	coding-synonymous	WWP1	NM_007013.3		353,1243,4907	TT,TC,CC		2.2674,39.8094,14.9854		404/923	87439926	1949,11057	2203	4300	6503	SO:0001819	synonymous_variant	11059	exon11			TAACACCAGAACA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1212C>T	8.37:g.87439926C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_007013	O00307|Q5YLC1|Q96BP4	Silent	SNP	ENST00000517970.1	37	CCDS6242.1																																																																																			C|0.862;T|0.138	0.138	strong		0.393	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013	
ALOX15B	247	hgsc.bcm.edu	37	17	7951819	7951819	+	Missense_Mutation	SNP	A	A	G	rs4792147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7951819A>G	ENST00000380183.4	+	14	2106	c.1967A>G	c.(1966-1968)cAg>cGg	p.Q656R	ALOX15B_ENST00000573359.1_Missense_Mutation_p.Q582R|ALOX15B_ENST00000572022.1_Missense_Mutation_p.Q644R|ALOX15B_ENST00000380173.2_Missense_Mutation_p.Q627R	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	656	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		Q -> R (in dbSNP:rs4792147). {ECO:0000269|PubMed:11350124, ECO:0000269|PubMed:11839751, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9177185}.		apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						GAGCGGAACCAGGGCCTGGTG	0.617													G|||	3257	0.650359	0.8775	0.5778	5008	,	,		16415	0.5506		0.5119	False		,,,				2504	0.6401				p.Q656R		Atlas-SNP	.											.	ALOX15B	66	.	0			c.A1967G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN	3558,848	334.1+/-303.3	1444,670,89	87.0	90.0	89.0		1880,1745,1967	-1.7	0.0	17	dbSNP_111	89	4308,4292	577.2+/-390.5	1079,2150,1071	yes	missense,missense,missense	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	43,43,43	2523,2820,1160	GG,GA,AA		49.907,19.2465,39.5202	benign,benign,benign	627/648,582/603,656/677	7951819	7866,5140	2203	4300	6503	SO:0001583	missense	247	exon14			GGAACCAGGGCCT	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1967A>G	17.37:g.7951819A>G	ENSP00000369530:p.Gln656Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	1303	0.5966117216117216	413	0.8394308943089431	195	0.5386740331491713	321	0.5611888111888111	374	0.49340369393139843	G	7.178	0.589071	0.13812	0.807535	0.50093	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	T;T	0.76316	-1.01;-1.01	3.74	-1.69	0.08186	Lipoxygenase, C-terminal (3);	1.304660	0.04587	N	0.396096	T	0.00012	0.0000	N	0.12961	0.28	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.10450	0.005;0.001;0.001	T	0.40961	-0.9535	9	0.25751	T	0.34	-5.7717	10.5555	0.45114	0.7064:0.0:0.2936:0.0	rs4792147;rs17855861;rs17857053;rs52802887;rs60011980;rs4792147	582;627;656	O15296-2;O15296-4;O15296	.;.;LX15B_HUMAN	R	627;582;656	ENSP00000369520:Q627R;ENSP00000369530:Q656R	ENSP00000344337:Q582R	Q	+	2	0	ALOX15B	7892544	0.000000	0.05858	0.017000	0.16124	0.445000	0.32107	0.081000	0.14823	-0.947000	0.03673	-0.974000	0.02594	CAG	A|0.391;C|0.000;G|0.609	0.609	strong		0.617	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
APRT	353	hgsc.bcm.edu	37	16	88874632	88874632	+	IGR	SNP	C	C	G	rs572275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88874632C>G	ENST00000378364.3	-	0	947				CDT1_ENST00000301019.4_Silent_p.L529L	NM_000485.2	NP_000476.1	P07741	APT_HUMAN	adenine phosphoribosyltransferase						adenine salvage (GO:0006168)|AMP salvage (GO:0044209)|cellular response to insulin stimulus (GO:0032869)|grooming behavior (GO:0007625)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	adenine binding (GO:0002055)|adenine phosphoribosyltransferase activity (GO:0003999)|AMP binding (GO:0016208)			cervix(1)|endometrium(1)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)	CCGCGGACCTCGCCCACATCA	0.667													G|||	2768	0.552716	0.7489	0.4942	5008	,	,		17709	0.6637		0.3767	False		,,,				2504	0.3957				p.L529L		Atlas-SNP	.											.	CDT1	30	.	0			c.C1587G						PASS	.	G		3098,1278	405.1+/-333.4	1101,896,191	46.0	36.0	40.0		1587	1.0	0.0	16	dbSNP_83	40	3170,5426	623.9+/-397.5	577,2016,1705	no	coding-synonymous	CDT1	NM_030928.3		1678,2912,1896	GG,GC,CC		36.8776,29.2048,48.3195		529/547	88874632	6268,6704	2188	4298	6486	SO:0001628	intergenic_variant	81620	exon10			GGACCTCGCCCAC		CCDS32511.1, CCDS45546.1	16q24	2012-10-02				ENSG00000198931	2.4.2.7		626	protein-coding gene	gene with protein product		102600					Standard	NM_000485		Approved		uc002flv.3	P07741			16.37:g.88874632C>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_030928	G5E9J2|Q3KP55|Q68DF9	Silent	SNP	ENST00000378364.3	37	CCDS32511.1																																																																																			C|0.482;G|0.518	0.518	strong		0.667	APRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430000.2	NM_000485	
ZAR1L	646799	hgsc.bcm.edu	37	13	32885658	32885658	+	Silent	SNP	G	G	A	rs371193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:32885658G>A	ENST00000533490.2	-	3	823	c.405C>T	c.(403-405)ccC>ccT	p.P135P	ZAR1L_ENST00000345108.6_Silent_p.P135P			A6NP61	ZAR1L_HUMAN	zygote arrest 1-like	135						cytoplasm (GO:0005737)				NS(1)|kidney(1)	2						GGCCGGTGGCGGGCGAAGTGA	0.731													g|||	803	0.160343	0.1785	0.1412	5008	,	,		13103	0.1528		0.1938	False		,,,				2504	0.1227				p.P135P		Atlas-SNP	.											.	ZAR1L	17	.	0			c.C405T						PASS	.						2.0	3.0	3.0					13																	32885658		495	1316	1811	SO:0001819	synonymous_variant	646799	exon1			GGTGGCGGGCGAA		CCDS45023.1	13q13.1	2014-02-20			ENSG00000189167	ENSG00000189167			37116	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 7"""					18442940	Standard	NM_001136571		Approved	Z3CXXC7	uc010abc.1	A6NP61	OTTHUMG00000016694	ENST00000533490.2:c.405C>T	13.37:g.32885658G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	NM_001136571	B2RV03|B7ZBU2	Silent	SNP	ENST00000533490.2	37	CCDS45023.1																																																																																			A|0.173;C|0.006	0.173	strong		0.731	ZAR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044403.5		
IFIH1	64135	hgsc.bcm.edu	37	2	163137983	163137983	+	Missense_Mutation	SNP	T	T	C	rs10930046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:163137983T>C	ENST00000263642.2	-	7	1774	c.1379A>G	c.(1378-1380)cAt>cGt	p.H460R		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	460	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		H -> R (in dbSNP:rs10930046).		cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						CATCAAATAATGCCTCATGAT	0.353													C|||	970	0.19369	0.447	0.3184	5008	,	,		18999	0.125		0.0119	False		,,,				2504	0.0204				p.H460R		Atlas-SNP	.											.	IFIH1	102	.	0			c.A1379G						PASS	.	C	ARG/HIS	1828,2578	636.9+/-396.7	381,1066,756	124.0	111.0	116.0		1379	5.9	1.0	2	dbSNP_120	116	122,8476	813.4+/-407.0	0,122,4177	yes	missense	IFIH1	NM_022168.2	29	381,1188,4933	CC,CT,TT		1.4189,41.4889,14.9954	benign	460/1026	163137983	1950,11054	2203	4299	6502	SO:0001583	missense	64135	exon7			AAATAATGCCTCA	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.1379A>G	2.37:g.163137983T>C	ENSP00000263642:p.His460Arg	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	119	72	0.605042	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	406	0.1858974358974359	235	0.47764227642276424	88	0.2430939226519337	73	0.12762237762237763	10	0.013192612137203167	C	7.969	0.748690	0.15710	0.414889	0.014189	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.49432	0.78	5.91	5.91	0.95273	DEAD-like helicase (2);Helicase/UvrB domain (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00771	-1.2	0.33312	P	0.433782	B	0.02656	0.0	B	0.01281	0.0	T	0.38329	-0.9666	9	0.02654	T	1	-9.0386	15.3485	0.74363	0.0:0.9333:0.0:0.0667	rs10930046;rs35105566;rs59144542;rs10930046	460	Q9BYX4	IFIH1_HUMAN	R	460	ENSP00000263642:H460R	ENSP00000263642:H460R	H	-	2	0	IFIH1	162846229	1.000000	0.71417	0.987000	0.45799	0.751000	0.42716	4.974000	0.63771	1.525000	0.49052	-0.119000	0.15052	CAT	T|0.838;C|0.162	0.162	strong		0.353	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168	
NLRP8	126205	hgsc.bcm.edu	37	19	56459342	56459342	+	Missense_Mutation	SNP	C	C	T	rs306507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56459342C>T	ENST00000291971.3	+	1	145	c.74C>T	c.(73-75)cCg>cTg	p.P25L	NLRP8_ENST00000590542.1_Missense_Mutation_p.P25L	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	25			P -> L (in dbSNP:rs306507).		neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		TCTCATATTCCGCCCTGGACA	0.517													C|||	3612	0.721246	0.7307	0.7565	5008	,	,		15783	0.8115		0.5984	False		,,,				2504	0.7168				p.P25L		Atlas-SNP	.											.	NLRP8	225	.	0			c.C74T						PASS	.	C	LEU/PRO	3141,1265	702.5+/-406.9	1125,891,187	203.0	159.0	174.0		74	0.8	0.0	19	dbSNP_79	174	5025,3575	628.9+/-398.2	1474,2077,749	yes	missense	NLRP8	NM_176811.2	98	2599,2968,936	TT,TC,CC		41.5698,28.7108,37.2136	possibly-damaging	25/1049	56459342	8166,4840	2203	4300	6503	SO:0001583	missense	126205	exon1			ATATTCCGCCCTG	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.74C>T	19.37:g.56459342C>T	ENSP00000291971:p.Pro25Leu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	1561	0.7147435897435898	359	0.7296747967479674	261	0.7209944751381215	475	0.8304195804195804	466	0.6147757255936676	C	6.905	0.536617	0.13188	0.712892	0.584302	ENSG00000179709	ENST00000291971	T	0.73681	-0.77	1.85	0.802	0.18686	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;B	0.42961	0.795;0.026	B;B	0.31245	0.126;0.002	T	0.48456	-0.9034	8	0.07990	T	0.79	.	4.3068	0.10951	0.0:0.7926:0.0:0.2074	rs306507;rs17712414;rs52789350;rs60413112;rs306507	25;25	Q86W28-2;Q86W28	.;NALP8_HUMAN	L	25	ENSP00000291971:P25L	ENSP00000291971:P25L	P	+	2	0	NLRP8	61151154	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-0.441000	0.06879	0.358000	0.24211	-0.351000	0.07748	CCG	C|0.326;T|0.674	0.674	strong		0.517	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
N4BP2L2	10443	hgsc.bcm.edu	37	13	33110539	33110539	+	Missense_Mutation	SNP	C	C	A	rs144941975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33110539C>A	ENST00000267068.3	-	2	790	c.626G>T	c.(625-627)gGt>gTt	p.G209V	N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000399396.3_Intron|N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.G209V	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	209					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		ATTATTATGACCCTCATAAAA	0.338													C|||	8	0.00159744	0.0053	0.0014	5008	,	,		19947	0.0		0.0	False		,,,				2504	0.0				p.G209V		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.G626T						PASS	.	C	VAL/GLY,	34,4372	37.6+/-69.7	0,34,2169	68.0	69.0	68.0		626,	-3.3	0.0	13	dbSNP_134	68	0,8600		0,0,4300	yes	missense,intron	N4BP2L2	NM_014887.2,NM_033111.3	109,	0,34,6469	AA,AC,CC		0.0,0.7717,0.2614	,	209/584,	33110539	34,12972	2203	4300	6503	SO:0001583	missense	10443	exon2			TTATGACCCTCAT	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"""phosphonoformate immuno-associated protein 5"""	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.626G>T	13.37:g.33110539C>A	ENSP00000267068:p.Gly209Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	100	40	0.4	NM_014887	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	37	CCDS9346.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	5.665	0.307323	0.10733	0.007717	0.0	ENSG00000244754	ENST00000446957;ENST00000505213;ENST00000267068	T;T;T	0.42513	0.97;0.97;0.97	5.58	-3.31	0.04988	.	.	.	.	.	T	0.21347	0.0514	L	0.47716	1.5	0.09310	N	1	P;P	0.45902	0.868;0.454	B;B	0.34038	0.174;0.08	T	0.13150	-1.0520	9	0.62326	D	0.03	-15.1664	10.2296	0.43247	0.0:0.2989:0.0999:0.6013	.	209;209	D6R968;Q92802	.;N42L2_HUMAN	V	209	ENSP00000394239:G209V;ENSP00000423362:G209V;ENSP00000267068:G209V	ENSP00000267068:G209V	G	-	2	0	N4BP2L2	32008539	0.000000	0.05858	0.000000	0.03702	0.109000	0.19521	-0.411000	0.07142	-0.881000	0.03992	0.563000	0.77884	GGT	C|0.998;A|0.002	0.002	strong		0.338	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887	
ICA1	3382	hgsc.bcm.edu	37	7	8198226	8198226	+	Silent	SNP	A	A	C	rs7798010	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:8198226A>C	ENST00000402384.3	-	7	902	c.636T>G	c.(634-636)gtT>gtG	p.V212V	ICA1_ENST00000396675.3_Silent_p.V212V|ICA1_ENST00000406470.2_Silent_p.V212V|ICA1_ENST00000422063.2_Silent_p.V212V|ICA1_ENST00000401396.1_Silent_p.V200V|ICA1_ENST00000407906.1_Silent_p.V212V|ICA1_ENST00000265577.7_Silent_p.V211V			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa	212	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		CTTTTTGACAAACATCCATCT	0.373													C|||	640	0.127796	0.4221	0.0447	5008	,	,		20615	0.0		0.0169	False		,,,				2504	0.0348				p.F212L		Atlas-SNP	.											.	ICA1	65	.	0			c.T636G						PASS	.	C	,,	1638,2768	659.2+/-400.5	304,1030,869	154.0	135.0	141.0		636,636,636	3.2	1.0	7	dbSNP_116	141	109,8491	814.3+/-407.0	0,109,4191	no	coding-synonymous,coding-synonymous,coding-synonymous	ICA1	NM_001136020.1,NM_004968.2,NM_022307.2	,,	304,1139,5060	CC,CA,AA		1.2674,37.1766,13.4323	,,	212/484,212/484,212/484	8198226	1747,11259	2203	4300	6503	SO:0001819	synonymous_variant	3382	exon7			TTGACAAACATCC		CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"""islet cell autoantigen 1 (69kD)"""			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.636T>G	7.37:g.8198226A>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_001136020	A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Missense_Mutation	SNP	ENST00000402384.3	37	CCDS34602.1																																																																																			A|0.880;C|0.120	0.120	strong		0.373	ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324793.1	NM_004968	
AOAH	313	hgsc.bcm.edu	37	7	36657940	36657940	+	Silent	SNP	T	T	A	rs3735385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:36657940T>A	ENST00000258749.5	-	10	1113	c.714A>T	c.(712-714)ccA>ccT	p.P238P	AOAH_ENST00000535891.1_Silent_p.P206P|AOAH_ENST00000431169.1_Silent_p.P238P	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	238					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						CTCCATCTTTTGGATCGACAC	0.318													T|||	275	0.0549121	0.0076	0.1124	5008	,	,		19720	0.123		0.007	False		,,,				2504	0.0573				p.P238P		Atlas-SNP	.											.	AOAH	79	.	0			c.A714T						PASS	.	T	,,	74,4332	66.4+/-103.9	0,74,2129	108.0	104.0	105.0		714,618,714	-1.5	1.0	7	dbSNP_107	105	29,8571	19.8+/-62.0	0,29,4271	no	coding-synonymous,coding-synonymous,coding-synonymous	AOAH	NM_001177506.1,NM_001177507.1,NM_001637.3	,,	0,103,6400	AA,AT,TT		0.3372,1.6795,0.7919	,,	238/689,206/544,238/576	36657940	103,12903	2203	4300	6503	SO:0001819	synonymous_variant	313	exon10			ATCTTTTGGATCG	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.714A>T	7.37:g.36657940T>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	88	33	0.375	NM_001637	A4D1Y5|B7Z490|Q53F13	Silent	SNP	ENST00000258749.5	37	CCDS5448.1																																																																																			T|0.975;A|0.025	0.025	strong		0.318	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	
FLG	2312	hgsc.bcm.edu	37	1	152283862	152283862	+	Missense_Mutation	SNP	G	G	C	rs58001094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_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	383	0	0		WXS	Illumina HiSeq	Phase_I	430	402	0.934884	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	
LRRC14	9684	hgsc.bcm.edu	37	8	145745268	145745268	+	Silent	SNP	G	G	A	rs116791876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145745268G>A	ENST00000292524.1	+	2	305	c.159G>A	c.(157-159)acG>acA	p.T53T	RECQL4_ENST00000428558.2_5'Flank|LRRC14_ENST00000529022.1_Silent_p.T53T|RECQL4_ENST00000532237.1_5'Flank	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	53										endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-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;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TGGTACACACGTGGCCCTTCC	0.627													G|||	31	0.0061901	0.0212	0.0043	5008	,	,		21870	0.0		0.0	False		,,,				2504	0.0				p.T53T		Atlas-SNP	.											.	LRRC14	25	.	0			c.G159A						PASS	.	G		61,4345	58.1+/-94.6	0,61,2142	98.0	95.0	96.0		159	-8.8	0.0	8	dbSNP_132	96	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	LRRC14	NM_014665.2		0,62,6441	AA,AG,GG		0.0116,1.3845,0.4767		53/494	145745268	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	9684	exon3			ACACACGTGGCCC	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179	ENST00000292524.1:c.159G>A	8.37:g.145745268G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	144	85	0.590278	NM_001272036	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			G|0.994;A|0.006	0.006	strong		0.627	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
ACBD5	91452	hgsc.bcm.edu	37	10	27508758	27508758	+	Silent	SNP	T	T	C	rs10764690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:27508758T>C	ENST00000375888.1	-	6	610	c.546A>G	c.(544-546)ccA>ccG	p.P182P	ACBD5_ENST00000396271.3_Silent_p.P173P|ACBD5_ENST00000375897.3_Silent_p.P64P|ACBD5_ENST00000375905.4_Silent_p.P138P|ACBD5_ENST00000476758.1_5'UTR|ACBD5_ENST00000375901.1_Silent_p.P64P			Q5T8D3	ACBD5_HUMAN	acyl-CoA binding domain containing 5	182					peroxisome degradation (GO:0030242)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisome (GO:0005777)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						TTTTGGCGTTTGGAGTAGAAG	0.388													T|||	1592	0.317891	0.0696	0.3905	5008	,	,		4066	0.4147		0.4652	False		,,,				2504	0.3507				p.P173P		Atlas-SNP	.											ACBD5_ENST00000396271,NS,adenoma,0,2	ACBD5	75	2	0			c.A519G						PASS	.	T	,	714,3692	297.3+/-284.7	54,606,1543	131.0	114.0	119.0		414,519	2.0	1.0	10	dbSNP_120	119	4408,4192	584.9+/-391.8	1149,2110,1041	no	coding-synonymous,coding-synonymous	ACBD5	NM_001042473.2,NM_145698.3	,	1203,2716,2584	CC,CT,TT		48.7442,16.2052,39.3818	,	138/491,173/526	27508758	5122,7884	2203	4300	6503	SO:0001819	synonymous_variant	91452	exon6			GGCGTTTGGAGTA	AF505653	CCDS7154.1, CCDS44368.1, CCDS73079.1	10p12.1	2010-04-30	2010-04-30		ENSG00000107897	ENSG00000107897			23338	protein-coding gene	gene with protein product			"""acyl-Coenzyme A binding domain containing 5"""			12056414	Standard	NR_024150		Approved	DKFZp434A2417, KIAA1996	uc010qdp.2	Q5T8D3	OTTHUMG00000017854	ENST00000375888.1:c.546A>G	10.37:g.27508758T>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	199	98	0.492462	NM_145698	B3KQ56|D3DRW0|Q5T8D4|Q5T8E1|Q5T8E2|Q86UV1|Q8N6E3|Q9UFB5	Silent	SNP	ENST00000375888.1	37																																																																																				T|0.634;C|0.366	0.366	strong		0.388	ACBD5-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000047314.1	NM_145698	
KIF23	9493	hgsc.bcm.edu	37	15	69714347	69714347	+	Silent	SNP	T	T	C	rs34969957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:69714347T>C	ENST00000260363.4	+	5	450	c.333T>C	c.(331-333)taT>taC	p.Y111Y	KIF23_ENST00000352331.4_Silent_p.Y111Y|KIF23_ENST00000559279.1_Silent_p.Y111Y|KIF23_ENST00000558585.1_5'Flank|KIF23_ENST00000537891.1_5'Flank|KIF23_ENST00000395392.2_Silent_p.Y111Y	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	111	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)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						TTTTTACATATGGTGTGACGG	0.408													T|||	60	0.0119808	0.0401	0.0043	5008	,	,		17202	0.0		0.003	False		,,,				2504	0.001				p.Y111Y		Atlas-SNP	.											.	KIF23	57	.	0			c.T333C						PASS	.	T	,	162,4236	110.8+/-149.0	4,154,2041	110.0	88.0	96.0		333,333	-0.3	1.0	15	dbSNP_126	96	6,8590	5.0+/-18.6	0,6,4292	no	coding-synonymous,coding-synonymous	KIF23	NM_004856.5,NM_138555.2	,	4,160,6333	CC,CT,TT		0.0698,3.6835,1.2929	,	111/857,111/961	69714347	168,12826	2199	4298	6497	SO:0001819	synonymous_variant	9493	exon5			TACATATGGTGTG	X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"""Kinesins"""	6392	protein-coding gene	gene with protein product		605064	"""kinesin-like 5 (mitotic kinesin-like protein 1)"""	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.333T>C	15.37:g.69714347T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	180	90	0.5	NM_138555	Q8WVP0	Silent	SNP	ENST00000260363.4	37	CCDS32278.1																																																																																			T|0.985;C|0.015	0.015	strong		0.408	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
UBXN11	91544	hgsc.bcm.edu	37	1	26608873	26608873	+	Missense_Mutation	SNP	T	T	A	rs1134583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26608873T>A	ENST00000374222.1	-	16	1944	c.1480A>T	c.(1480-1482)Agt>Tgt	p.S494C	UBXN11_ENST00000314675.7_Missense_Mutation_p.S374C|UBXN11_ENST00000374217.2_Missense_Mutation_p.S461C|UBXN11_ENST00000374221.3_Missense_Mutation_p.S494C|UBXN11_ENST00000357089.4_Missense_Mutation_p.S461C|UBXN11_ENST00000374223.1_Missense_Mutation_p.S251C			Q5T124	UBX11_HUMAN	UBX domain protein 11	494	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggaccgggactggggccggga	0.711																																					p.S494C		Atlas-SNP	.											UBXN11,NS,carcinoma,0,1	UBXN11	54	1	1	Deletion - In frame(1)	ovary(1)	c.A1480T						scavenged	.						28.0	33.0	32.0					1																	26608873		1776	4034	5810	SO:0001583	missense	91544	exon16			CGGGACTGGGGCC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1480A>T	1.37:g.26608873T>A	ENSP00000363339:p.Ser494Cys	Somatic	40	6	0.15		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	T	10.17	1.275650	0.23307	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.19250	2.16;2.17;2.43;2.41;2.41;2.43	1.27	-0.135	0.13477	.	.	.	.	.	T	0.08268	0.0206	N	0.08118	0	0.09310	N	0.999997	P;P;P;P	0.50819	0.939;0.893;0.939;0.9	B;B;B;B	0.37601	0.187;0.187;0.254;0.129	T	0.21895	-1.0232	9	0.66056	D	0.02	.	5.0204	0.14358	0.0:0.3611:0.0:0.6389	rs1134583;rs17838089	461;456;374;494	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	C	374;251;461;494;494;461	ENSP00000324721:S374C;ENSP00000363340:S251C;ENSP00000349601:S461C;ENSP00000363338:S494C;ENSP00000363339:S494C;ENSP00000363334:S461C	ENSP00000324721:S374C	S	-	1	0	UBXN11	26481460	0.000000	0.05858	0.011000	0.14972	0.011000	0.07611	-1.315000	0.02713	-0.170000	0.10816	-0.582000	0.04134	AGT	T|0.870;A|0.130	0.130	strong		0.711	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
BACE1	23621	hgsc.bcm.edu	37	11	117186285	117186285	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117186285T>C	ENST00000313005.6	-	1	687	c.227A>G	c.(226-228)tAc>tGc	p.Y76C	BACE1_ENST00000513780.1_Missense_Mutation_p.Y76C|BACE1_ENST00000428381.2_Missense_Mutation_p.Y76C|BACE1_ENST00000528053.1_Missense_Mutation_p.Y76C|BACE1_ENST00000514464.1_5'UTR|AP000892.4_ENST00000504906.1_RNA|BACE1_ENST00000445823.2_Missense_Mutation_p.Y76C	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	76					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)		CATCTCCACGTAGTAGCCCTG	0.677																																					p.Y76C		Atlas-SNP	.											.	BACE1	33	.	0			c.A227G						PASS	.						45.0	44.0	44.0					11																	117186285		2201	4296	6497	SO:0001583	missense	23621	exon1			TCCACGTAGTAGC	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.227A>G	11.37:g.117186285T>C	ENSP00000318585:p.Tyr76Cys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	87	4	0.045977	NM_138972	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Missense_Mutation	SNP	ENST00000313005.6	37	CCDS8383.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420349	0.83559	.	.	ENSG00000186318	ENST00000313005;ENST00000528053;ENST00000428381;ENST00000513780;ENST00000445823	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	4.99	4.99	0.66335	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.061196	0.64402	D	0.000002	T	0.72179	0.3428	M	0.89414	3.03	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0	D;D;D;D;D	0.91635	0.999;0.998;0.982;0.964;0.999	T	0.78186	-0.2302	10	0.87932	D	0	.	12.6208	0.56601	0.0:0.0:0.0:1.0	.	76;76;76;76;76	Q76KP0;P56817;P56817-3;P56817-4;P56817-2	.;BACE1_HUMAN;.;.;.	C	76	ENSP00000318585:Y76C;ENSP00000431848:Y76C;ENSP00000402228:Y76C;ENSP00000424536:Y76C;ENSP00000403685:Y76C	ENSP00000318585:Y76C	Y	-	2	0	BACE1	116691495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.012000	0.76366	1.866000	0.54105	0.533000	0.62120	TAC	.	.	none		0.677	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1		
